
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m1_run2.nuc.txt

#NT
GCUGG	chr19:39874440-39874665(+)$1	225	191	196	15.0000
GCUGG	chr1:160968203-160968423(-)$1	220	112	117	15.0000
GCUGG	chr12:122717254-122717472(-)$1	218	10	15	15.0000
GCUGG	chr17:37617934-37618152(+)$1	218	26	31	15.0000
GCUGG	chr19:868293-868517(-)$1	224	83	88	15.0000
GCUGG	chr22:18036636-18036850(+)$1	214	78	83	15.0000
GCUGG	chr6:31237953-31238168(-)$1	215	176	181	15.0000
gcugg	chr22:41322991-41323216(+)$1	225	206	211	15.0000
GCUGG	chr17:79879778-79879996(-)$1	218	63	68	15.0000
GCUGG	chr17:54967083-54967303(-)$1	220	193	198	15.0000
GCUGG	chr8:23147383-23147630(+)$1	247	116	121	15.0000
GCUGG	chr19:41250948-41251197(-)$1	249	57	62	15.0000
gcugg	chr7:87538172-87538393(+)$1	221	75	80	15.0000
GCUGG	chr17:34070053-34070277(+)$1	224	98	103	15.0000
GCUGG	chr1:33282743-33282994(-)$1	251	50	55	15.0000
GCUGG	chr10:72326434-72326651(+)$1	217	123	128	15.0000
GCUGG	chr19:41784895-41785178(+)$1	283	153	158	15.0000
GCUGG	chr2:239356825-239357056(+)$1	231	22	27	15.0000
GCUGG	chr8:145583214-145583434(+)$1	220	123	128	15.0000
GCUGG	chr10:101089773-101089998(+)$1	225	114	119	15.0000
GCUGG	chr19:39669630-39669880(+)$1	250	133	138	15.0000
GCUGG	chr6:33171618-33171849(+)$1	231	121	126	15.0000
GCUGG	chr5:65374847-65375068(+)$1	221	33	38	15.0000
GCUGG	chr11:60690354-60690569(+)$1	215	89	94	15.0000
GCUGG	chr20:60776774-60776993(+)$1	219	103	108	15.0000
GCUGG	chr12:6438438-6438660(-)$1	222	23	28	15.0000
GCUGG	chr1:228363246-228363465(+)$1	219	2	7	15.0000
GCUGG	chr9:131572309-131572542(+)$1	233	25	30	15.0000
GCUGG	chr17:5353554-5353774(-)$1	220	13	18	15.0000
GCUGG	chr19:18576253-18576474(-)$1	221	11	16	15.0000
GCUGG	chr1:167391770-167391980(+)$1	210	63	68	15.0000
GCUGG	chr14:20760153-20760380(-)$1	227	159	164	15.0000
GCUGG	chr7:97501572-97501817(-)$1	245	8	13	15.0000
GCUGG	chr22:43267058-43267314(-)$1	256	93	98	15.0000
GCUGG	chr19:40901572-40901839(-)$1	267	70	75	15.0000
gcugg	chr12:113596461-113596752(-)$1	291	160	165	15.0000
gcugg	chr20:57024801-57025035(+)$1	234	57	62	15.0000
GCUGG	chr9:134340270-134340493(+)$1	223	37	42	15.0000
GCUGG	chr19:1010484-1010717(-)$1	233	212	217	15.0000
GCUGG	chr19:34941137-34941354(+)$1	217	165	170	15.0000
GCUGG	chr14:102430853-102431107(+)$1	254	110	115	15.0000
GCUGG	chr17:80758724-80758940(+)$1	216	82	87	15.0000
GCUGG	chrX:53221555-53221766(-)$1	211	152	157	15.0000
GCUGG	chr2:182794270-182794495(+)$1	225	113	118	15.0000
GCUGG	chr1:29508190-29508411(-)$1	221	110	115	15.0000
GCUGG	chr5:7877982-7878193(+)$1	211	102	107	15.0000
GCUGG	chr15:68581909-68582151(+)$1	242	72	77	15.0000
GCUGG	chr14:24899966-24900204(+)$1	238	134	139	15.0000

#otherMatches

#Struct PSSM
bb:CC	chr7:150910237-150910456(-)$1	219	197	202	15.0000
BB}DD	chr19:39874440-39874665(+)$1	225	191	196	15.0000
ddd!!	chr1:160968203-160968423(-)$1	220	112	117	15.0000
ggggl	chr12:122717254-122717472(-)$1	218	10	15	15.0000
C{BBg	chr17:37617934-37618152(+)$1	218	26	31	15.0000
EEEEE	chr19:868293-868517(-)$1	224	83	88	15.0000
ccc[b	chr22:18036636-18036850(+)$1	214	78	83	15.0000
"bboo	chr6:31237953-31238168(-)$1	215	176	181	15.0000
ddddm	chr22:41322991-41323216(+)$1	225	206	211	15.0000
ddppp	chr17:79879778-79879996(-)$1	218	63	68	15.0000
ca]ff	chr17:54967083-54967303(-)$1	220	193	198	15.0000
eeeeE	chr8:23147383-23147630(+)$1	247	116	121	15.0000
eeeee	chr19:41250948-41251197(-)$1	249	57	62	15.0000
hhhhh	chr7:87538172-87538393(+)$1	221	75	80	15.0000
d22gg	chr17:34070053-34070277(+)$1	224	98	103	15.0000
ggggg	chr1:33282743-33282994(-)$1	251	50	55	15.0000
eeee2	chr10:72326434-72326651(+)$1	217	123	128	15.0000
fffff	chr19:41784895-41785178(+)$1	283	153	158	15.0000
hhhhh	chr2:239356825-239357056(+)$1	231	22	27	15.0000
bb]cc	chr8:145583214-145583434(+)$1	220	123	128	15.0000
cc[a[	chr10:101089773-101089998(+)$1	225	114	119	15.0000
fff]a	chr19:39669630-39669880(+)$1	250	133	138	15.0000
ccc!!	chr6:33171618-33171849(+)$1	231	121	126	15.0000
!!ccc	chr5:65374847-65375068(+)$1	221	33	38	15.0000
bb[ff	chr11:60690354-60690569(+)$1	215	89	94	15.0000
!dddd	chr20:60776774-60776993(+)$1	219	103	108	15.0000
cccdd	chr12:6438438-6438660(-)$1	222	23	28	15.0000
:HHHH	chr1:228363246-228363465(+)$1	219	2	7	15.0000
nnnhh	chr9:131572309-131572542(+)$1	233	25	30	15.0000
ee[gg	chr17:5353554-5353774(-)$1	220	13	18	15.0000
]dddd	chr19:18576253-18576474(-)$1	221	11	16	15.0000
:::ee	chr1:167391770-167391980(+)$1	210	63	68	15.0000
dddd[	chr14:20760153-20760380(-)$1	227	159	164	15.0000
CKKFF	chr7:97501572-97501817(-)$1	245	8	13	15.0000
nnnnn	chr22:43267058-43267314(-)$1	256	93	98	15.0000
ccccc	chr19:40901572-40901839(-)$1	267	70	75	15.0000
iiiii	chr12:113596461-113596752(-)$1	291	160	165	15.0000
ff[dd	chr20:57024801-57025035(+)$1	234	57	62	15.0000
dddcc	chr9:134340270-134340493(+)$1	223	37	42	15.0000
EYYDD	chr19:1010484-1010717(-)$1	233	212	217	15.0000
effff	chr19:34941137-34941354(+)$1	217	165	170	15.0000
bb[bb	chr14:102430853-102431107(+)$1	254	110	115	15.0000
eeeqq	chr17:80758724-80758940(+)$1	216	82	87	15.0000
BYYFF	chrX:53221555-53221766(-)$1	211	152	157	15.0000
ccccc	chr2:182794270-182794495(+)$1	225	113	118	15.0000
ddbbd	chr1:29508190-29508411(-)$1	221	110	115	15.0000
ddd##	chr5:7877982-7878193(+)$1	211	102	107	15.0000
cccgg	chr15:68581909-68582151(+)$1	242	72	77	15.0000
eeeee	chr14:24899966-24900204(+)$1	238	134	139	15.0000

#DB
)).))	chr7:150910237-150910456(-)$1	1	197	202	15.0000
)).))	chr19:39874440-39874665(+)$1	1	191	196	15.0000
(((..	chr1:160968203-160968423(-)$1	1	112	117	15.0000
((((.	chr12:122717254-122717472(-)$1	1	10	15	15.0000
(.(((	chr17:37617934-37618152(+)$1	1	26	31	15.0000
(((((	chr19:868293-868517(-)$1	1	83	88	15.0000
(((.(	chr22:18036636-18036850(+)$1	1	78	83	15.0000
.((..	chr6:31237953-31238168(-)$1	1	176	181	15.0000
((((.	chr22:41322991-41323216(+)$1	1	206	211	15.0000
((...	chr17:79879778-79879996(-)$1	1	63	68	15.0000
)).))	chr17:54967083-54967303(-)$1	1	193	198	15.0000
)))))	chr8:23147383-23147630(+)$1	1	116	121	15.0000
(((((	chr19:41250948-41251197(-)$1	1	57	62	15.0000
(((((	chr7:87538172-87538393(+)$1	1	75	80	15.0000
)..))	chr17:34070053-34070277(+)$1	1	98	103	15.0000
)))))	chr1:33282743-33282994(-)$1	1	50	55	15.0000
)))).	chr10:72326434-72326651(+)$1	1	123	128	15.0000
(((((	chr19:41784895-41785178(+)$1	1	153	158	15.0000
(((((	chr2:239356825-239357056(+)$1	1	22	27	15.0000
)).))	chr8:145583214-145583434(+)$1	1	123	128	15.0000
((.(.	chr10:101089773-101089998(+)$1	1	114	119	15.0000
))).)	chr19:39669630-39669880(+)$1	1	133	138	15.0000
(((..	chr6:33171618-33171849(+)$1	1	121	126	15.0000
..(((	chr5:65374847-65375068(+)$1	1	33	38	15.0000
((.((	chr11:60690354-60690569(+)$1	1	89	94	15.0000
.((((	chr20:60776774-60776993(+)$1	1	103	108	15.0000
(((((	chr12:6438438-6438660(-)$1	1	23	28	15.0000
.((((	chr1:228363246-228363465(+)$1	1	2	7	15.0000
...))	chr9:131572309-131572542(+)$1	1	25	30	15.0000
((.((	chr17:5353554-5353774(-)$1	1	13	18	15.0000
.))))	chr19:18576253-18576474(-)$1	1	11	16	15.0000
...((	chr1:167391770-167391980(+)$1	1	63	68	15.0000
((((.	chr14:20760153-20760380(-)$1	1	159	164	15.0000
(..((	chr7:97501572-97501817(-)$1	1	8	13	15.0000
.....	chr22:43267058-43267314(-)$1	1	93	98	15.0000
)))))	chr19:40901572-40901839(-)$1	1	70	75	15.0000
)))))	chr12:113596461-113596752(-)$1	1	160	165	15.0000
((.((	chr20:57024801-57025035(+)$1	1	57	62	15.0000
)))))	chr9:134340270-134340493(+)$1	1	37	42	15.0000
)..))	chr19:1010484-1010717(-)$1	1	212	217	15.0000
)))))	chr19:34941137-34941354(+)$1	1	165	170	15.0000
((.((	chr14:102430853-102431107(+)$1	1	110	115	15.0000
(((..	chr17:80758724-80758940(+)$1	1	82	87	15.0000
)..))	chrX:53221555-53221766(-)$1	1	152	157	15.0000
))(((	chr2:182794270-182794495(+)$1	1	113	118	15.0000
)))))	chr1:29508190-29508411(-)$1	1	110	115	15.0000
(((..	chr5:7877982-7878193(+)$1	1	102	107	15.0000
)))))	chr15:68581909-68582151(+)$1	1	72	77	15.0000
(((((	chr14:24899966-24900204(+)$1	1	134	139	15.0000

#PSSM
G : 0.89	g : 0.10	
C : 0.89	c : 0.10	
U : 0.89	u : 0.10	
G : 0.89	g : 0.10	
G : 0.89	g : 0.10	

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m2_run2.nuc.txt

#NT
UUAUUUUU	chr21:31851995-31852222(-)$1	227	102	110	19.6944
UUCUUUUU	chr14:55512290-55512510(+)$1	220	108	116	16.2916
AUAUUUUU	chr6:91224892-91225117(-)$1	225	114	122	16.5694
UUAUUUUA	chrX:123043404-123043631(+)$1	227	211	219	15.4583
AUAUUUUU	chr19:30498303-30498524(+)$1	221	121	129	16.5694
UUUUUUUU	chr1:193057344-193057568(+)$1	224	169	177	16.2222
GUAUUUUU	chr5:56217003-56217228(-)$1	225	44	52	16.1527
UUAUGUUU	chr12:53807151-53807373(+)$1	222	156	164	15.1111
UUAUUAUU	chrX:119571979-119572202(-)$1	223	102	110	15.4583
AUAUUUUU	chr10:114926396-114926620(+)$1	224	161	169	16.5694
UUAUUUUU	chr2:234203845-234204075(+)$1	230	191	199	19.6944
AUAUUUUU	chr18:11852643-11852866(+)$1	223	72	80	16.5694
UUUUUUUU	chr5:151183926-151184145(+)$1	219	20	28	16.2222
UUGUUUUU	chr1:85731833-85732057(-)$1	224	4	12	16.0138
UUAGUUUU	chr3:69154147-69154373(+)$1	226	95	103	15.0416
AUAUUUUU	chr14:31087062-31087291(+)$1	229	107	115	16.5694
CUAUUUUU	chr11:110333121-110333356(+)$1	235	107	115	16.0833
UUCUUUUU	chr12:98928492-98928715(+)$1	223	39	47	16.2916
UUAUUUUA	chr2:70451496-70451726(-)$1	230	132	140	15.4583
UUAUUGUU	chr1:161070314-161070557(-)$1	243	138	146	15.3194
UUAUUUGU	chr2:182794368-182794599(+)$1	231	151	159	15.1805
UCAUUUUU	chr13:53050354-53050577(+)$1	223	10	18	14.8333
UUAUUAUU	chr3:137892244-137892464(-)$1	220	110	118	15.4583
UUAUGUUU	chrX:123045805-123046026(+)$1	221	94	102	15.1111
UUAUUUUU	chr8:30643224-30643457(-)$1	233	73	81	19.6944
UUAUUUCU	chr1:35484494-35484720(-)$1	226	187	195	15.1805
UUAUAUUU	chr12:21670623-21670845(+)$1	222	105	113	15.0416
UUAUUUGU	chr6:149979232-149979453(-)$1	221	91	99	15.1805
UUUUUUUU	chr21:43409477-43409696(-)$1	219	171	179	16.2222
CUAUUUUU	chr5:175773832-175774059(-)$1	227	15	23	16.0833
UUAUUAUU	chr18:44398072-44398295(-)$1	223	28	36	15.4583
auauuuuu	chr3:53919171-53919390(-)$1	219	76	84	16.5694
UUAUCUUU	chr4:145916243-145916467(-)$1	224	102	110	15.0416
GUAUUUUU	chr20:61509402-61509633(-)$1	231	30	38	16.1527
UUACUUUU	chr6:127610589-127610810(-)$1	221	125	133	15.0416
UUAUUUUU	chr12:120899732-120899957(-)$1	225	159	167	19.6944
AUAUUUUU	chr4:52781344-52781569(+)$1	225	10	18	16.5694
UUAUUUUC	chr13:103418409-103418633(-)$1	224	112	120	15.4583
UUCUUUUU	chr4:170641954-170642184(+)$1	230	47	55	16.2916
AUAUUUUU	chr11:102268829-102269051(-)$1	222	101	109	16.5694
UUAUUUUU	chr11:108344360-108344582(-)$1	222	163	171	19.6944
UUGUUUUU	chr10:46159139-46159367(-)$1	228	65	73	16.0138
UUAUUUUG	chr1:210416859-210417089(+)$1	230	50	58	15.3888
UUUUUUUU	chr12:51213782-51214012(+)$1	230	101	109	16.2222
AUAUUUUU	chr1:16786340-16786567(+)$1	227	215	223	16.5694
uuaauuuu	chr10:75001795-75002018(-)$1	223	96	104	15.1111
UUCUUUUU	chr20:17948600-17948820(-)$1	220	100	108	16.2916
UUAUUUUC	chr6:11134905-11135128(+)$1	223	179	187	15.4583
UUAUUUCU	chr10:17757490-17757717(+)$1	227	109	117	15.1805
UUAUUUUU	chr3:140683354-140683578(+)$1	224	5	13	19.6944
UUCUUUUU	chrX:135044666-135044896(-)$1	230	110	118	16.2916
GUAUUUUU	chr1:157094483-157094709(-)$1	226	200	208	16.1527
UUAUUUUU	chr11:67924322-67924547(-)$1	225	158	166	19.6944
uuAUUGUU	chr6:117055738-117055962(+)$1	224	16	24	15.3194
UUAUUCUU	chr7:90016567-90016791(+)$1	224	111	119	15.2499
uucuuuuu	chr17:48771438-48771663(-)$1	225	159	167	16.2916
UUAUUUUU	chr9:125617996-125618213(-)$1	217	38	46	19.6944
UUAUUUAU	chr2:135714502-135714724(+)$1	222	51	59	15.1111
UUAUUUUG	chr2:32248957-32249187(-)$1	230	91	99	15.3888
CUAUUUUU	chr1:207967475-207967702(+)$1	227	39	47	16.0833
UUCUUUUU	chr10:13252639-13252866(+)$1	227	102	110	16.2916
uuauuuuu	chr18:48701716-48701951(-)$1	235	118	126	19.6944
uuauuuuu	chr1:75230688-75230917(+)$1	229	104	112	19.6944
UUAUUUUA	chr5:151188046-151188271(+)$1	225	56	64	15.4583
uuuuuuuu	chr1:150281284-150281508(+)$1	224	146	154	16.2222
UUAUUAUU	chr5:60455144-60455370(-)$1	226	64	72	15.4583
UUAAUUUU	chr2:242291490-242291720(+)$1	230	3	11	15.1111
UUUUUUUU	chr1:203770574-203770802(+)$1	228	201	209	16.2222
guauuuuu	chrX:53404948-53405190(-)$1	242	144	152	16.1527
UUGUUUUU	chr21:15744341-15744571(-)$1	230	12	20	16.0138
AUAUUUUU	chrX:103435634-103435857(+)$1	223	173	181	16.5694

#otherMatches

#Struct PSSM
ppppppee	chr4:2242616-2242835(-)$1	219	97	105	15.4583
JJJJJJ::	chr21:31851995-31852222(-)$1	227	102	110	19.6944
ffffffmm	chr14:55512290-55512510(+)$1	220	108	116	16.2916
ee4444gg	chr6:91224892-91225117(-)$1	225	114	122	16.5694
YYCCC~~~	chrX:123043404-123043631(+)$1	227	211	219	15.4583
gmmmmggg	chr19:30498303-30498524(+)$1	221	121	129	16.5694
qqqqqqqq	chr1:193057344-193057568(+)$1	224	169	177	16.2222
ccc66666	chr5:56217003-56217228(-)$1	225	44	52	16.1527
:dddd[dd	chr12:53807151-53807373(+)$1	222	156	164	15.1111
gggggggf	chrX:119571979-119572202(-)$1	223	102	110	15.4583
hhh22ddd	chr10:114926396-114926620(+)$1	224	161	169	16.5694
::::::::	chr2:234203845-234204075(+)$1	230	191	199	19.6944
ff::::::	chr18:11852643-11852866(+)$1	223	72	80	16.5694
^^^^^^^^	chr5:151183926-151184145(+)$1	219	20	28	16.2222
!!ddddoo	chr1:85731833-85732057(-)$1	224	4	12	16.0138
:::ggggg	chr3:69154147-69154373(+)$1	226	95	103	15.0416
ff======	chr14:31087062-31087291(+)$1	229	107	115	16.5694
gggggg::	chr11:110333121-110333356(+)$1	235	107	115	16.0833
H:::::::	chr12:98928492-98928715(+)$1	223	39	47	16.2916
========	chr2:70451496-70451726(-)$1	230	132	140	15.4583
((((ffff	chr1:161070314-161070557(-)$1	243	138	146	15.3194
cc333hhh	chr2:182794368-182794599(+)$1	231	151	159	15.1805
CRRRRRRR	chr13:53050354-53050577(+)$1	223	10	18	14.8333
!!eeeeeq	chr3:137892244-137892464(-)$1	220	110	118	15.4583
ZEEEEE}C	chrX:123045805-123046026(+)$1	221	94	102	15.1111
%%ffffff	chr8:30643224-30643457(-)$1	233	73	81	19.6944
meeeee44	chr1:35484494-35484720(-)$1	226	187	195	15.1805
fff::::g	chr12:21670623-21670845(+)$1	222	105	113	15.0416
========	chr6:149979232-149979453(-)$1	221	91	99	15.1805
eehhhhhh	chr21:43409477-43409696(-)$1	219	171	179	16.2222
ggg^^^^^	chr5:175773832-175774059(-)$1	227	15	23	16.0833
::::::::	chr18:44398072-44398295(-)$1	223	28	36	15.4583
dddd4444	chr3:53919171-53919390(-)$1	219	76	84	16.5694
]bb4444f	chr4:145916243-145916467(-)$1	224	102	110	15.0416
uuuuuuuu	chr20:61509402-61509633(-)$1	231	30	38	16.1527
LHHHHHHH	chr6:127610589-127610810(-)$1	221	125	133	15.0416
dd:IIIII	chr12:120899732-120899957(-)$1	225	159	167	19.6944
::::::::	chr4:52781344-52781569(+)$1	225	10	18	16.5694
iiiiiiii	chr13:103418409-103418633(-)$1	224	112	120	15.4583
i^^^^^^^	chr4:170641954-170642184(+)$1	230	47	55	16.2916
cccmmmmc	chr11:102268829-102269051(-)$1	222	101	109	16.5694
###fffff	chr11:108344360-108344582(-)$1	222	163	171	19.6944
mmiiiiii	chr10:46159139-46159367(-)$1	228	65	73	16.0138
gggggg[f	chr1:210416859-210417089(+)$1	230	50	58	15.3888
]ccc]ccc	chr12:51213782-51214012(+)$1	230	101	109	16.2222
ppppeeee	chr1:16786340-16786567(+)$1	227	215	223	16.5694
iiiiiii:	chr10:75001795-75002018(-)$1	223	96	104	15.1111
2iiiiiii	chr20:17948600-17948820(-)$1	220	100	108	16.2916
d>>>>>>>	chr6:11134905-11135128(+)$1	223	179	187	15.4583
##ffffff	chr10:17757490-17757717(+)$1	227	109	117	15.1805
::::::::	chr3:140683354-140683578(+)$1	224	5	13	19.6944
g[eeeee(	chrX:135044666-135044896(-)$1	230	110	118	16.2916
FFFFFFFY	chr1:157094483-157094709(-)$1	226	200	208	16.1527
::::::::	chr11:67924322-67924547(-)$1	225	158	166	19.6944
D{DDDDKK	chr6:117055738-117055962(+)$1	224	16	24	15.3194
:::FFFFF	chr7:90016567-90016791(+)$1	224	111	119	15.2499
2eeeee55	chr17:48771438-48771663(-)$1	225	159	167	16.2916
^^^^^^^^	chr9:125617996-125618213(-)$1	217	38	46	19.6944
eeennnnn	chr2:135714502-135714724(+)$1	222	51	59	15.1111
dddd!!dd	chr2:32248957-32249187(-)$1	230	91	99	15.3888
gggggFFF	chr1:207967475-207967702(+)$1	227	39	47	16.0833
iiiiiicc	chr10:13252639-13252866(+)$1	227	102	110	16.2916
oeeeee44	chr18:48701716-48701951(-)$1	235	118	126	19.6944
HHHFFFFF	chr1:75230688-75230917(+)$1	229	104	112	19.6944
::::::::	chr5:151188046-151188271(+)$1	225	56	64	15.4583
mmmmffff	chr1:150281284-150281508(+)$1	224	146	154	16.2222
ccc]bb]f	chr5:60455144-60455370(-)$1	226	64	72	15.4583
::::::::	chr2:242291490-242291720(+)$1	230	3	11	15.1111
DDYYEEEE	chr1:203770574-203770802(+)$1	228	201	209	16.2222
[eeeee##	chrX:53404948-53405190(-)$1	242	144	152	16.1527
EEEE{EEE	chr21:15744341-15744571(-)$1	230	12	20	16.0138
::::::::	chrX:103435634-103435857(+)$1	223	173	181	16.5694

#DB
......))	chr4:2242616-2242835(-)$1	1	97	105	15.4583
((((((..	chr21:31851995-31852222(-)$1	1	102	110	19.6944
((((((..	chr14:55512290-55512510(+)$1	1	108	116	16.2916
))....))	chr6:91224892-91225117(-)$1	1	114	122	16.5694
..)))...	chrX:123043404-123043631(+)$1	1	211	219	15.4583
(....)))	chr19:30498303-30498524(+)$1	1	121	129	16.5694
........	chr1:193057344-193057568(+)$1	1	169	177	16.2222
))).....	chr5:56217003-56217228(-)$1	1	44	52	16.1527
.((((.((	chr12:53807151-53807373(+)$1	1	156	164	15.1111
)))))))(	chrX:119571979-119572202(-)$1	1	102	110	15.4583
)))..)))	chr10:114926396-114926620(+)$1	1	161	169	16.5694
........	chr2:234203845-234204075(+)$1	1	191	199	19.6944
))......	chr18:11852643-11852866(+)$1	1	72	80	16.5694
........	chr5:151183926-151184145(+)$1	1	20	28	16.2222
..((((..	chr1:85731833-85732057(-)$1	1	4	12	16.0138
...(((((	chr3:69154147-69154373(+)$1	1	95	103	15.0416
))((((((	chr14:31087062-31087291(+)$1	1	107	115	16.5694
))))))..	chr11:110333121-110333356(+)$1	1	107	115	16.0833
(.......	chr12:98928492-98928715(+)$1	1	39	47	16.2916
((((((((	chr2:70451496-70451726(-)$1	1	132	140	15.4583
....((((	chr1:161070314-161070557(-)$1	1	138	146	15.3194
))...)))	chr2:182794368-182794599(+)$1	1	151	159	15.1805
(.......	chr13:53050354-53050577(+)$1	1	10	18	14.8333
..(((((.	chr3:137892244-137892464(-)$1	1	110	118	15.4583
.))))).)	chrX:123045805-123046026(+)$1	1	94	102	15.1111
..((((((	chr8:30643224-30643457(-)$1	1	73	81	19.6944
.)))))..	chr1:35484494-35484720(-)$1	1	187	195	15.1805
)))....(	chr12:21670623-21670845(+)$1	1	105	113	15.0416
))))))))	chr6:149979232-149979453(-)$1	1	91	99	15.1805
((((((((	chr21:43409477-43409696(-)$1	1	171	179	16.2222
(((.....	chr5:175773832-175774059(-)$1	1	15	23	16.0833
........	chr18:44398072-44398295(-)$1	1	28	36	15.4583
))))....	chr3:53919171-53919390(-)$1	1	76	84	16.5694
.))....)	chr4:145916243-145916467(-)$1	1	102	110	15.0416
........	chr20:61509402-61509633(-)$1	1	30	38	16.1527
.(((((((	chr6:127610589-127610810(-)$1	1	125	133	15.0416
)).)))))	chr12:120899732-120899957(-)$1	1	159	167	19.6944
........	chr4:52781344-52781569(+)$1	1	10	18	16.5694
))))))))	chr13:103418409-103418633(-)$1	1	112	120	15.4583
(.......	chr4:170641954-170642184(+)$1	1	47	55	16.2916
(((....)	chr11:102268829-102269051(-)$1	1	101	109	16.5694
...(((((	chr11:108344360-108344582(-)$1	1	163	171	19.6944
..))))))	chr10:46159139-46159367(-)$1	1	65	73	16.0138
((((((.(	chr1:210416859-210417089(+)$1	1	50	58	15.3888
.))).)))	chr12:51213782-51214012(+)$1	1	101	109	16.2222
....))))	chr1:16786340-16786567(+)$1	1	215	223	16.5694
))))))).	chr10:75001795-75002018(-)$1	1	96	104	15.1111
.)))))))	chr20:17948600-17948820(-)$1	1	100	108	16.2916
).......	chr6:11134905-11135128(+)$1	1	179	187	15.4583
..((((((	chr10:17757490-17757717(+)$1	1	109	117	15.1805
........	chr3:140683354-140683578(+)$1	1	5	13	19.6944
(.(((((.	chrX:135044666-135044896(-)$1	1	110	118	16.2916
))))))).	chr1:157094483-157094709(-)$1	1	200	208	16.1527
........	chr11:67924322-67924547(-)$1	1	158	166	19.6944
(.((((..	chr6:117055738-117055962(+)$1	1	16	24	15.3194
...)))))	chr7:90016567-90016791(+)$1	1	111	119	15.2499
.)))))..	chr17:48771438-48771663(-)$1	1	159	167	16.2916
........	chr9:125617996-125618213(-)$1	1	38	46	19.6944
(((.....	chr2:135714502-135714724(+)$1	1	51	59	15.1111
((((..((	chr2:32248957-32249187(-)$1	1	91	99	15.3888
)))))(((	chr1:207967475-207967702(+)$1	1	39	47	16.0833
((((((((	chr10:13252639-13252866(+)$1	1	102	110	16.2916
.)))))..	chr18:48701716-48701951(-)$1	1	118	126	19.6944
((((((((	chr1:75230688-75230917(+)$1	1	104	112	19.6944
........	chr5:151188046-151188271(+)$1	1	56	64	15.4583
....))))	chr1:150281284-150281508(+)$1	1	146	154	16.2222
))).)).)	chr5:60455144-60455370(-)$1	1	64	72	15.4583
........	chr2:242291490-242291720(+)$1	1	3	11	15.1111
))..))))	chr1:203770574-203770802(+)$1	1	201	209	16.2222
.(((((..	chrX:53404948-53405190(-)$1	1	144	152	16.1527
((((.(((	chr21:15744341-15744571(-)$1	1	12	20	16.0138
........	chrX:103435634-103435857(+)$1	1	173	181	16.5694

#PSSM
U : 0.68	A : 0.12	u : 0.08	G : 0.04	C : 0.04	a : 0.01	g : 0.01	
U : 0.87	u : 0.11	C : 0.01	
A : 0.70	C : 0.08	U : 0.06	a : 0.06	G : 0.04	c : 0.01	u : 0.01	
U : 0.86	u : 0.08	G : 0.01	C : 0.01	a : 0.01	A : 0.01	
U : 0.84	u : 0.09	G : 0.02	A : 0.01	C : 0.01	
U : 0.80	u : 0.09	A : 0.05	G : 0.02	C : 0.01	
U : 0.83	u : 0.09	G : 0.02	C : 0.02	A : 0.01	
U : 0.79	u : 0.09	C : 0.04	A : 0.04	G : 0.02	

#score	1177.4444444444425
#seq	72
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m3_run2.nuc.txt

#NT
UUAUUCUU	chr1:150785685-150785886(-)$1	201	47	55	13.9074
UUUUUCUU	chr15:89801862-89802063(+)$1	201	55	63	18.3518
UUUUUAUU	chr3:25656638-25656839(-)$1	201	48	56	15.2037
GUUUUCUU	chr13:42752213-42752414(+)$1	201	41	49	17.6111
AUUUUCUU	chr11:74500607-74500808(+)$1	201	40	48	16.3148
UUUUUCUU	chr11:47827695-47827896(-)$1	201	18	26	18.3518
UUUUUGUU	chr10:103921278-103921479(+)$1	201	20	28	15.2962
CUUUUUUU	chr3:132175046-132175247(+)$1	201	6	14	13.2592
GUUUUCAU	chr12:122966096-122966297(-)$1	201	32	40	13.1666
UUUUUCUU	chr12:96986254-96986455(+)$1	201	60	68	18.3518
CUUUUCUU	chr12:56571714-56571915(-)$1	201	26	34	16.4999
UUAUUCUU	chr18:13100379-13100580(+)$1	201	190	198	13.9074
UUUUUCUU	chr1:182845898-182846099(+)$1	201	49	57	18.3518
uuuuuCUC	chr6:121427187-121427388(-)$1	201	61	69	13.9074
UUUUUCAU	chr5:43494577-43494778(-)$1	201	51	59	13.9074
CUUUUUUU	chr8:17067428-17067629(+)$1	201	2	10	13.2592
UUUAUCUU	chr2:58387191-58387392(-)$1	201	57	65	13.7222
UUUUUCUU	chr9:123232347-123232548(-)$1	201	32	40	18.3518
AUUUUGUU	chr12:124071219-124071420(+)$1	201	166	174	13.2592
UUUGUCUU	chr19:48626384-48626585(-)$1	201	82	90	13.7222
GUUUUAUU	chr13:47324626-47324827(+)$1	201	26	34	14.4629
UUUUUGUU	chr2:238668674-238668875(+)$1	201	19	27	15.2962
UUUUUCUC	chr16:24567574-24567775(+)$1	201	14	22	13.9074
GUUUUCAU	chr2:48045874-48046075(-)$1	201	164	172	13.1666
CUUUUCUU	chr8:107719358-107719559(+)$1	201	184	192	16.4999
GUUUUGUU	chr3:52692148-52692349(-)$1	201	170	178	14.5555
GUGUUCUU	chr17:79634711-79634912(+)$1	201	31	39	13.0740
GUUUUCUU	chr2:128252385-128252586(-)$1	201	150	158	17.6111
GUUUUAUU	chr2:136396435-136396636(+)$1	201	10	18	14.4629
UUUUUCUU	chr10:118671228-118671429(-)$1	201	50	58	18.3518
GUUUUGUU	chr14:90756835-90757036(-)$1	201	40	48	14.5555
UUUUUCUU	chr1:182357747-182357948(-)$1	201	49	57	18.3518
UUUUUCUU	chr11:34093219-34093420(+)$1	201	36	44	18.3518
AUUUucuu	chr10:18874824-18875025(-)$1	201	161	169	16.3148
UAUUUCUU	chr5:68737314-68737515(+)$1	201	30	38	13.6296
GUUUUUUU	chr9:98238295-98238496(-)$1	201	39	47	14.3703
GUUUACUU	chr6:90399512-90399713(-)$1	201	133	141	13.0740
UUUUUCUU	chr5:10429947-10430148(+)$1	201	35	43	18.3518
GUUUUCUC	chr5:137909726-137909927(-)$1	201	48	56	13.1666
CUUUUAUU	chr2:47378544-47378745(-)$1	201	125	133	13.3518
GUUCUCUU	chr11:77823681-77823882(-)$1	201	1	9	12.9814
UUUUUCUU	chr21:34110496-34110697(-)$1	201	51	59	18.3518
uuuUACUU	chrX:122799508-122799709(-)$1	201	3	11	13.8148
GUUUGCUU	chr8:48887216-48887417(+)$1	201	42	50	12.9814
GUUUUCUU	chr10:94269779-94269980(-)$1	201	49	57	17.6111
UUUUUCUU	chr7:135047795-135047996(-)$1	201	38	46	18.3518
UUUUUCUU	chr6:97679338-97679539(-)$1	201	156	164	18.3518
AUUUUCUU	chr10:70105705-70105906(-)$1	201	49	57	16.3148
UUUUUCUU	chr12:72164324-72164525(+)$1	201	7	15	18.3518
GUCUUCUU	chr3:47727501-47727702(-)$1	201	26	34	13.0740
UUUUUGUU	chr2:153003685-153003886(-)$1	201	30	38	15.2962
GUUUUAUU	chr11:125523604-125523805(+)$1	201	148	156	14.4629
GCUUUCUU	chr1:154317103-154317304(+)$1	201	79	87	12.8888

#otherMatches

#Struct PSSM
::::::::	chr8:48731958-48732159(-)$1	201	63	71	13.2592
((((((((	chr1:150785685-150785886(-)$1	201	47	55	13.9074
========	chr15:89801862-89802063(+)$1	201	55	63	18.3518
IIIIIIKK	chr3:25656638-25656839(-)$1	201	48	56	15.2037
hhhhhh""	chr13:42752213-42752414(+)$1	201	41	49	17.6111
oooooeee	chr11:74500607-74500808(+)$1	201	40	48	16.3148
ddrrrrrr	chr11:47827695-47827896(-)$1	201	18	26	18.3518
gggggg##	chr10:103921278-103921479(+)$1	201	20	28	15.2962
::::::::	chr3:132175046-132175247(+)$1	201	6	14	13.2592
ggggg333	chr12:122966096-122966297(-)$1	201	32	40	13.1666
cc####cc	chr12:96986254-96986455(+)$1	201	60	68	18.3518
####eeee	chr12:56571714-56571915(-)$1	201	26	34	16.4999
II}FFFFF	chr18:13100379-13100580(+)$1	201	190	198	13.9074
::::::::	chr1:182845898-182846099(+)$1	201	49	57	18.3518
hhhh5555	chr6:121427187-121427388(-)$1	201	61	69	13.9074
ffffff::	chr5:43494577-43494778(-)$1	201	51	59	13.9074
GGGGG:::	chr8:17067428-17067629(+)$1	201	2	10	13.2592
fff+++++	chr2:58387191-58387392(-)$1	201	57	65	13.7222
!hhhhhhh	chr9:123232347-123232548(-)$1	201	32	40	18.3518
^^^^^^^^	chr12:124071219-124071420(+)$1	201	166	174	13.2592
ooooooff	chr19:48626384-48626585(-)$1	201	82	90	13.7222
d:::::::	chr13:47324626-47324827(+)$1	201	26	34	14.4629
:::ggggg	chr2:238668674-238668875(+)$1	201	19	27	15.2962
hhhhh###	chr16:24567574-24567775(+)$1	201	14	22	13.9074
ggmmmmgg	chr2:48045874-48046075(-)$1	201	164	172	13.1666
vvvvvvvv	chr8:107719358-107719559(+)$1	201	184	192	16.4999
dd======	chr3:52692148-52692349(-)$1	201	170	178	14.5555
BB{IIIII	chr17:79634711-79634912(+)$1	201	31	39	13.0740
E?????EE	chr2:128252385-128252586(-)$1	201	150	158	17.6111
DDDccc[d	chr2:136396435-136396636(+)$1	201	10	18	14.4629
=====:JJ	chr10:118671228-118671429(-)$1	201	50	58	18.3518
dooooood	chr14:90756835-90757036(-)$1	201	40	48	14.5555
:::JJJJJ	chr1:182357747-182357948(-)$1	201	49	57	18.3518
hh[ccc[c	chr11:34093219-34093420(+)$1	201	36	44	18.3518
IIIII}GG	chr10:18874824-18875025(-)$1	201	161	169	16.3148
:::fffff	chr5:68737314-68737515(+)$1	201	30	38	13.6296
++++++++	chr9:98238295-98238496(-)$1	201	39	47	14.3703
bbdddd44	chr6:90399512-90399713(-)$1	201	133	141	13.0740
nnnnneee	chr5:10429947-10430148(+)$1	201	35	43	18.3518
GGGG:ccc	chr5:137909726-137909927(-)$1	201	48	56	13.1666
)))))ddd	chr2:47378544-47378745(-)$1	201	125	133	13.3518
DDDD:::e	chr11:77823681-77823882(-)$1	201	1	9	12.9814
^^^^^^^^	chr21:34110496-34110697(-)$1	201	51	59	18.3518
::HHHHHH	chrX:122799508-122799709(-)$1	201	3	11	13.8148
cc::ccc[	chr8:48887216-48887417(+)$1	201	42	50	12.9814
e!!ddddl	chr10:94269779-94269980(-)$1	201	49	57	17.6111
::::::::	chr7:135047795-135047996(-)$1	201	38	46	18.3518
GGGccc[d	chr6:97679338-97679539(-)$1	201	156	164	18.3518
::::gggg	chr10:70105705-70105906(-)$1	201	49	57	16.3148
DD{IIIII	chr12:72164324-72164525(+)$1	201	7	15	18.3518
========	chr3:47727501-47727702(-)$1	201	26	34	13.0740
IIIDDDD:	chr2:153003685-153003886(-)$1	201	30	38	15.2962
c]hhhhhh	chr11:125523604-125523805(+)$1	201	148	156	14.4629
eeeerrrr	chr1:154317103-154317304(+)$1	201	79	87	12.8888

#DB
........	chr8:48731958-48732159(-)$1	1	63	71	13.2592
........	chr1:150785685-150785886(-)$1	1	47	55	13.9074
((((((((	chr15:89801862-89802063(+)$1	1	55	63	18.3518
((((((..	chr3:25656638-25656839(-)$1	1	48	56	15.2037
((((((..	chr13:42752213-42752414(+)$1	1	41	49	17.6111
.....)))	chr11:74500607-74500808(+)$1	1	40	48	16.3148
((......	chr11:47827695-47827896(-)$1	1	18	26	18.3518
((((((..	chr10:103921278-103921479(+)$1	1	20	28	15.2962
........	chr3:132175046-132175247(+)$1	1	6	14	13.2592
)))))...	chr12:122966096-122966297(-)$1	1	32	40	13.1666
((....((	chr12:96986254-96986455(+)$1	1	60	68	18.3518
....((((	chr12:56571714-56571915(-)$1	1	26	34	16.4999
)).)))))	chr18:13100379-13100580(+)$1	1	190	198	13.9074
........	chr1:182845898-182846099(+)$1	1	49	57	18.3518
))))....	chr6:121427187-121427388(-)$1	1	61	69	13.9074
))))))..	chr5:43494577-43494778(-)$1	1	51	59	13.9074
(((((...	chr8:17067428-17067629(+)$1	1	2	10	13.2592
(((.....	chr2:58387191-58387392(-)$1	1	57	65	13.7222
.(((((((	chr9:123232347-123232548(-)$1	1	32	40	18.3518
........	chr12:124071219-124071420(+)$1	1	166	174	13.2592
......))	chr19:48626384-48626585(-)$1	1	82	90	13.7222
).......	chr13:47324626-47324827(+)$1	1	26	34	14.4629
...(((((	chr2:238668674-238668875(+)$1	1	19	27	15.2962
(((((...	chr16:24567574-24567775(+)$1	1	14	22	13.9074
((....))	chr2:48045874-48046075(-)$1	1	164	172	13.1666
........	chr8:107719358-107719559(+)$1	1	184	192	16.4999
))))))))	chr3:52692148-52692349(-)$1	1	170	178	14.5555
((.(((((	chr17:79634711-79634912(+)$1	1	31	39	13.0740
).....))	chr2:128252385-128252586(-)$1	1	150	158	17.6111
((((((.(	chr2:136396435-136396636(+)$1	1	10	18	14.4629
))))).((	chr10:118671228-118671429(-)$1	1	50	58	18.3518
(......)	chr14:90756835-90757036(-)$1	1	40	48	14.5555
...(((((	chr1:182357747-182357948(-)$1	1	49	57	18.3518
((.(((.(	chr11:34093219-34093420(+)$1	1	36	44	18.3518
))))).))	chr10:18874824-18875025(-)$1	1	161	169	16.3148
...(((((	chr5:68737314-68737515(+)$1	1	30	38	13.6296
........	chr9:98238295-98238496(-)$1	1	39	47	14.3703
))))))..	chr6:90399512-90399713(-)$1	1	133	141	13.0740
.....)))	chr5:10429947-10430148(+)$1	1	35	43	18.3518
((((.(((	chr5:137909726-137909927(-)$1	1	48	56	13.1666
.....(((	chr2:47378544-47378745(-)$1	1	125	133	13.3518
((((...(	chr11:77823681-77823882(-)$1	1	1	9	12.9814
........	chr21:34110496-34110697(-)$1	1	51	59	18.3518
..((((((	chrX:122799508-122799709(-)$1	1	3	11	13.8148
))..(((.	chr8:48887216-48887417(+)$1	1	42	50	12.9814
(..((((.	chr10:94269779-94269980(-)$1	1	49	57	17.6111
........	chr7:135047795-135047996(-)$1	1	38	46	18.3518
)))(((.(	chr6:97679338-97679539(-)$1	1	156	164	18.3518
....((((	chr10:70105705-70105906(-)$1	1	49	57	16.3148
((.(((((	chr12:72164324-72164525(+)$1	1	7	15	18.3518
((((((((	chr3:47727501-47727702(-)$1	1	26	34	13.0740
(((((((.	chr2:153003685-153003886(-)$1	1	30	38	15.2962
).))))))	chr11:125523604-125523805(+)$1	1	148	156	14.4629
((((....	chr1:154317103-154317304(+)$1	1	79	87	12.8888

#PSSM
U : 0.44	G : 0.33	C : 0.11	A : 0.07	u : 0.03	
U : 0.90	u : 0.05	A : 0.01	C : 0.01	
U : 0.87	u : 0.05	A : 0.03	G : 0.01	C : 0.01	
U : 0.90	u : 0.03	A : 0.01	G : 0.01	C : 0.01	
U : 0.88	u : 0.05	A : 0.03	G : 0.01	
C : 0.70	G : 0.11	A : 0.09	U : 0.05	u : 0.01	c : 0.01	
U : 0.90	A : 0.05	u : 0.03	
U : 0.90	C : 0.05	u : 0.03	

#score	829.7037037037027
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m1_run1.nuc.txt

#NT
CUGUAAAUA	chr5:102508861-102509085(+)$1	224	103	112	19.1818
UUGUAUAUA	chr4:26422085-26422317(+)$1	232	108	117	17.5454
UUUUAAAUA	chr17:65074257-65074489(-)$1	232	112	121	16.0909
UUGUAAAUU	chr4:41941263-41941495(+)$1	232	113	122	17.5454
UUGUAAAGA	chr19:37210742-37210962(+)$1	220	65	74	16.1818
AUGUAAAUA	chr1:94654784-94655008(-)$1	224	102	111	19.9090
UUGUAUAUA	chr10:70513541-70513765(+)$1	224	110	119	17.5454
AGGUAAAUA	chr6:18226306-18226530(-)$1	224	124	133	15.2727
AUGUAUAUA	chr14:45571682-45571914(+)$1	232	110	119	16.8181
AUGUACAUA	chr2:61719416-61719661(-)$1	245	111	120	16.6363
AUGUAUAUA	chr9:98229448-98229680(-)$1	232	129	138	16.8181
UUGUAAAUU	chr20:47705691-47705916(+)$1	225	180	189	17.5454
UUGUAAAAA	chr21:28210676-28210899(-)$1	223	106	115	16.4545
AUGUAUAUA	chr17:15133914-15134187(-)$1	273	110	119	16.8181
AUGUAAAUA	chr15:32929903-32930156(+)$1	253	168	177	19.9090
UUGUAAAUU	chr5:95234166-95234398(-)$1	232	101	110	17.5454
AUGUAAAUA	chr19:12127125-12127364(-)$1	239	111	120	19.9090
AUGUAAAUU	chr7:35006411-35006643(-)$1	232	104	113	16.8181
UUGUAGAUA	chr22:46725152-46725378(+)$1	226	109	118	17.4545
UUGUAAAUA	chr6:56919214-56919447(+)$1	233	103	112	20.6363
AUGUAAAUA	chr2:71377016-71377275(+)$1	259	144	153	19.9090
UUGUAAAUA	chr13:31232110-31232361(+)$1	251	76	85	20.6363
CUGUAAAUA	chr8:67577088-67577309(-)$1	221	109	118	19.1818
UUGUAUAUA	chr14:20825756-20826008(+)$1	252	126	135	17.5454
CUGUAAAUC	chr3:41280725-41280946(+)$1	221	102	111	15.2727
UUGUAGAUA	chr10:119044242-119044474(-)$1	232	110	119	17.4545
GUGUACAUA	chr2:176973605-176973833(+)$1	228	112	121	15.0909
CUGUAAAUA	chr2:24483951-24484184(-)$1	233	130	139	19.1818
UUGUAAAUU	chr1:25549742-25549963(-)$1	221	17	26	17.5454
AUGUAAAAA	chr10:60128417-60128653(+)$1	236	102	111	15.7272
UGGUAAAUA	chr3:122133611-122133838(-)$1	227	125	134	16.0000
AUGUAAAUU	chrX:75397711-75397951(+)$1	240	119	128	16.8181
UUGUAAAUU	chr7:5104538-5104760(+)$1	222	110	119	17.5454
CUGUAAAUA	chr18:77893409-77893655(+)$1	246	117	126	19.1818
UUGUUAAUA	chr13:108881591-108881824(+)$1	233	113	122	15.9090
CUGUAAAAA	chr1:40705480-40705707(+)$1	227	106	115	15.0000
AUGUACAUA	chr3:73432403-73432627(-)$1	224	128	137	16.6363
CUGUAAAUU	chr14:61442493-61442728(-)$1	235	108	117	16.0909
AUGUAGAUA	chr3:124456847-124457069(+)$1	222	104	113	16.7272
CUGUAGAUA	chr16:24583031-24583270(+)$1	239	34	43	16.0000
AUGUAAAAA	chr19:38125771-38126000(-)$1	229	52	61	15.7272
UUGUAAAUA	chr2:219447594-219447835(+)$1	241	103	112	20.6363
AUUUAAAUA	chr10:91178292-91178518(+)$1	226	107	116	15.3636
UUGUACAUA	chr10:133769322-133769552(+)$1	230	115	124	17.3636
UUGUAAAUA	chr3:56707578-56707805(-)$1	227	97	106	20.6363
UUGUGAAUA	chr14:32560333-32560568(+)$1	235	77	86	15.9090
AUGUAGAUA	chr2:211018680-211018910(-)$1	230	88	97	16.7272
CUAUAAAUA	chr2:37428668-37428896(-)$1	228	112	121	14.5454
CUGUAAAUU	chr3:56660975-56661204(-)$1	229	104	113	16.0909
UUGGAAAUA	chr15:68582921-68583147(+)$1	226	20	29	16.0000
UUGUAAAUU	chr5:114860230-114860454(-)$1	224	101	110	17.5454
UUGUAAAUA	chr15:34395323-34395566(+)$1	243	106	115	20.6363
UUGGAAAUA	chr1:244218566-244218814(+)$1	248	96	105	16.0000
AUGUAAGUA	chr20:47686683-47686915(+)$1	232	149	158	15.0909

#otherMatches

#Struct PSSM
2========	chr1:243827980-243828203(-)$1	223	207	216	20.6363
^^^^^^^^^	chr5:102508861-102509085(+)$1	224	103	112	19.1818
dddd::fff	chr4:26422085-26422317(+)$1	232	108	117	17.5454
:::::::::	chr17:65074257-65074489(-)$1	232	112	121	16.0909
qqbb:::::	chr4:41941263-41941495(+)$1	232	113	122	17.5454
iinnnnnii	chr19:37210742-37210962(+)$1	220	65	74	16.1818
ffffooooo	chr1:94654784-94655008(-)$1	224	102	111	19.9090
###cccppp	chr10:70513541-70513765(+)$1	224	110	119	17.5454
2eeeeeggg	chr6:18226306-18226530(-)$1	224	124	133	15.2727
::ggggggg	chr14:45571682-45571914(+)$1	232	110	119	16.8181
eeeee]ggg	chr2:61719416-61719661(-)$1	245	111	120	16.6363
77eeeee22	chr9:98229448-98229680(-)$1	232	129	138	16.8181
mmbb:::::	chr20:47705691-47705916(+)$1	225	180	189	17.5454
gggggg:::	chr21:28210676-28210899(-)$1	223	106	115	16.4545
ffffnnnnn	chr17:15133914-15134187(-)$1	273	110	119	16.8181
ttttttttt	chr15:32929903-32930156(+)$1	253	168	177	19.9090
e]bb:::::	chr5:95234166-95234398(-)$1	232	101	110	17.5454
:::::::ff	chr19:12127125-12127364(-)$1	239	111	120	19.9090
iiiiiiiit	chr7:35006411-35006643(-)$1	232	104	113	16.8181
88eeeeedd	chr22:46725152-46725378(+)$1	226	109	118	17.4545
fffffqqqq	chr6:56919214-56919447(+)$1	233	103	112	20.6363
ppppppeee	chr2:71377016-71377275(+)$1	259	144	153	19.9090
eee333ddd	chr13:31232110-31232361(+)$1	251	76	85	20.6363
mmcccGGGG	chr8:67577088-67577309(-)$1	221	109	118	19.1818
ggggggggg	chr14:20825756-20826008(+)$1	252	126	135	17.5454
eeeuuuuuu	chr3:41280725-41280946(+)$1	221	102	111	15.2727
d]bb:::::	chr10:119044242-119044474(-)$1	232	110	119	17.4545
bbqqqqqqq	chr2:176973605-176973833(+)$1	228	112	121	15.0909
#cccmmmmc	chr2:24483951-24484184(-)$1	233	130	139	19.1818
DDDDOOOOO	chr1:25549742-25549963(-)$1	221	17	26	17.5454
::JJJJJJJ	chr10:60128417-60128653(+)$1	236	102	111	15.7272
!!cccvvvv	chr3:122133611-122133838(-)$1	227	125	134	16.0000
:::::::::	chrX:75397711-75397951(+)$1	240	119	128	16.8181
e55555eee	chr7:5104538-5104760(+)$1	222	110	119	17.5454
ffff:DDDD	chr18:77893409-77893655(+)$1	246	117	126	19.1818
qqa]dddd:	chr13:108881591-108881824(+)$1	233	113	122	15.9090
xxxxxxxxx	chr1:40705480-40705707(+)$1	227	106	115	15.0000
iiiiiii[c	chr3:73432403-73432627(-)$1	224	128	137	16.6363
2dddd::::	chr14:61442493-61442728(-)$1	235	108	117	16.0909
dd[ddddll	chr3:124456847-124457069(+)$1	222	104	113	16.7272
nccc:::::	chr16:24583031-24583270(+)$1	239	34	43	16.0000
ffffooooo	chr19:38125771-38126000(-)$1	229	52	61	15.7272
ggGGGGGGG	chr2:219447594-219447835(+)$1	241	103	112	20.6363
:::::::::	chr10:91178292-91178518(+)$1	226	107	116	15.3636
dddd[aqqq	chr10:133769322-133769552(+)$1	230	115	124	17.3636
!!aqqqqqq	chr3:56707578-56707805(-)$1	227	97	106	20.6363
""bbnnnnn	chr14:32560333-32560568(+)$1	235	77	86	15.9090
cc]cccddd	chr2:211018680-211018910(-)$1	230	88	97	16.7272
ddddqqqqq	chr2:37428668-37428896(-)$1	228	112	121	14.5454
]ccc:::::	chr3:56660975-56661204(-)$1	229	104	113	16.0909
IIIILLLDD	chr15:68582921-68583147(+)$1	226	20	29	16.0000
E{BBNNNNN	chr5:114860230-114860454(-)$1	224	101	110	17.5454
]eeeee22f	chr15:34395323-34395566(+)$1	243	106	115	20.6363
cccbb::::	chr1:244218566-244218814(+)$1	248	96	105	16.0000
DDYYGGGGG	chr20:47686683-47686915(+)$1	232	149	158	15.0909

#DB
.))))))))	chr1:243827980-243828203(-)$1	1	207	216	20.6363
.........	chr5:102508861-102509085(+)$1	1	103	112	19.1818
))))..(((	chr4:26422085-26422317(+)$1	1	108	117	17.5454
.........	chr17:65074257-65074489(-)$1	1	112	121	16.0909
..)).....	chr4:41941263-41941495(+)$1	1	113	122	17.5454
((.....))	chr19:37210742-37210962(+)$1	1	65	74	16.1818
((((.....	chr1:94654784-94655008(-)$1	1	102	111	19.9090
...(((...	chr10:70513541-70513765(+)$1	1	110	119	17.5454
.)))))(((	chr6:18226306-18226530(-)$1	1	124	133	15.2727
..(((((((	chr14:45571682-45571914(+)$1	1	110	119	16.8181
))))).)))	chr2:61719416-61719661(-)$1	1	111	120	16.6363
..)))))..	chr9:98229448-98229680(-)$1	1	129	138	16.8181
..)).....	chr20:47705691-47705916(+)$1	1	180	189	17.5454
))))))...	chr21:28210676-28210899(-)$1	1	106	115	16.4545
((((.....	chr17:15133914-15134187(-)$1	1	110	119	16.8181
.........	chr15:32929903-32930156(+)$1	1	168	177	19.9090
).)).....	chr5:95234166-95234398(-)$1	1	101	110	17.5454
.......((	chr19:12127125-12127364(-)$1	1	111	120	19.9090
((((((((.	chr7:35006411-35006643(-)$1	1	104	113	16.8181
..)))))))	chr22:46725152-46725378(+)$1	1	109	118	17.4545
(((((....	chr6:56919214-56919447(+)$1	1	103	112	20.6363
......)))	chr2:71377016-71377275(+)$1	1	144	153	19.9090
)))...)))	chr13:31232110-31232361(+)$1	1	76	85	20.6363
..)))))))	chr8:67577088-67577309(-)$1	1	109	118	19.1818
)))))))))	chr14:20825756-20826008(+)$1	1	126	135	17.5454
(((......	chr3:41280725-41280946(+)$1	1	102	111	15.2727
).)).....	chr10:119044242-119044474(-)$1	1	110	119	17.4545
((.......	chr2:176973605-176973833(+)$1	1	112	121	15.0909
.(((....)	chr2:24483951-24484184(-)$1	1	130	139	19.1818
((((.....	chr1:25549742-25549963(-)$1	1	17	26	17.5454
..(((((((	chr10:60128417-60128653(+)$1	1	102	111	15.7272
..(((....	chr3:122133611-122133838(-)$1	1	125	134	16.0000
.........	chrX:75397711-75397951(+)$1	1	119	128	16.8181
).....)))	chr7:5104538-5104760(+)$1	1	110	119	17.5454
)))).))))	chr18:77893409-77893655(+)$1	1	117	126	19.1818
..).)))).	chr13:108881591-108881824(+)$1	1	113	122	15.9090
.........	chr1:40705480-40705707(+)$1	1	106	115	15.0000
(((((((.(	chr3:73432403-73432627(-)$1	1	128	137	16.6363
.))))....	chr14:61442493-61442728(-)$1	1	108	117	16.0909
((.((((..	chr3:124456847-124457069(+)$1	1	104	113	16.7272
.))).....	chr16:24583031-24583270(+)$1	1	34	43	16.0000
((((.....	chr19:38125771-38126000(-)$1	1	52	61	15.7272
)))))))))	chr2:219447594-219447835(+)$1	1	103	112	20.6363
.........	chr10:91178292-91178518(+)$1	1	107	116	15.3636
((((.(...	chr10:133769322-133769552(+)$1	1	115	124	17.3636
..(......	chr3:56707578-56707805(-)$1	1	97	106	20.6363
..((.....	chr14:32560333-32560568(+)$1	1	77	86	15.9090
)).))))))	chr2:211018680-211018910(-)$1	1	88	97	16.7272
((((.....	chr2:37428668-37428896(-)$1	1	112	121	14.5454
.))).....	chr3:56660975-56661204(-)$1	1	104	113	16.0909
((((...((	chr15:68582921-68583147(+)$1	1	20	29	16.0000
(.((.....	chr5:114860230-114860454(-)$1	1	101	110	17.5454
.)))))..)	chr15:34395323-34395566(+)$1	1	106	115	20.6363
)))))....	chr1:244218566-244218814(+)$1	1	96	105	16.0000
))..)))))	chr20:47686683-47686915(+)$1	1	149	158	15.0909

#PSSM
U : 0.45	A : 0.32	C : 0.18	u : 0.01	G : 0.01	
U : 0.94	G : 0.03	u : 0.01	
G : 0.92	U : 0.03	g : 0.01	A : 0.01	
U : 0.94	G : 0.03	u : 0.01	
A : 0.94	a : 0.01	U : 0.01	G : 0.01	
A : 0.70	U : 0.10	G : 0.09	C : 0.07	a : 0.01	
A : 0.96	a : 0.01	G : 0.01	
U : 0.89	A : 0.07	u : 0.01	G : 0.01	
A : 0.78	U : 0.18	a : 0.01	C : 0.01	

#score	955.0000000000002
#seq	55
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m3_run2.nuc.txt

#NT
UAAAUAUAUAA	chr22:30423597-30423835(+)$1	238	206	217	19.2727
uauaucuacau	chr1:227847347-227847581(+)$1	234	109	120	15.0000
caaauauguau	chr4:156264185-156264422(-)$1	237	36	47	15.9090
UAAAUGUAUAU	chr10:89513918-89514142(-)$1	224	94	105	22.0909
UAAAAAUAUAU	chr5:66464725-66464952(+)$1	227	100	111	19.1818
UAAAUCCAUGU	chr17:65067194-65067417(-)$1	223	107	118	14.0909
UAUAUAUAUAU	chr4:38701319-38701563(+)$1	244	118	129	21.1818
GAAAUGUAUAG	chr9:89559383-89559610(-)$1	227	25	36	14.2727
uacauguauau	chr6:99321042-99321305(-)$1	263	125	136	19.3636
UACAUAUAUAU	chr20:62588128-62588376(-)$1	248	124	135	20.9090
AAAAUCUAAAU	chr3:124949659-124949893(-)$1	234	4	15	14.2727
UAAAUAUAUUU	chr1:112255905-112256139(+)$1	234	5	16	20.0909
uuuauauauau	chr9:125611715-125611964(-)$1	249	115	126	17.0000
UAAUUGUAUAU	chr14:103809678-103809906(+)$1	228	109	120	17.4545
UUAAUAAAUAU	chr12:89981775-89982002(-)$1	227	146	157	14.9999
UACAUAUAUAG	chr7:116146481-116146713(+)$1	232	120	131	16.6363
UAAAAAUAUAU	chr3:126061509-126061741(-)$1	232	220	231	19.1818
uaaauauauau	chr17:36891189-36891420(-)$1	231	74	85	23.6363
AAAAUCUAUAG	chr2:152656606-152656850(-)$1	244	153	164	14.0000
UAAAUAUGCAU	chr18:8638274-8638505(+)$1	231	115	126	15.6363
AAAAUACAUAU	chr5:74668288-74668523(-)$1	235	51	62	16.1818
UAAAUUUAAAU	chr16:46990486-46990729(-)$1	243	118	129	17.3636
UAUAUGUAUAU	chr19:37640167-37640413(-)$1	246	146	157	19.6363
GAAAUGUAUAU	chr14:74666142-74666367(+)$1	225	84	95	18.5454
GAAAUUUAUUU	chr7:140419104-140419331(-)$1	227	79	90	14.2727
UAUAUGUUUAU	chr1:116236457-116236681(+)$1	224	87	98	15.9090
UAAAUGUUUAA	chr1:85112676-85112915(-)$1	239	123	134	14.0000
UCAAUAUUUAU	chr12:46752367-46752699(-)$1	332	157	168	15.4545
UUCauauauau	chr12:99128945-99129179(+)$1	234	102	113	16.7272
uacauauauau	chr3:73115286-73115531(+)$1	245	101	112	20.9090
UAGAUCUACAU	chr13:45007893-45008115(-)$1	222	119	130	14.1818
UAUAUAUAUGU	chr5:175953754-175953976(-)$1	222	103	114	17.9090
AAAAUUUAAAU	chr13:25909759-25910009(+)$1	250	177	188	14.0909
aaaaucuauuu	chr18:42647854-42648093(+)$1	239	71	82	14.7272
UAAAUCUAUAU	chr1:155851771-155852003(+)$1	232	107	118	21.5454
uauauauaaau	chr1:56960682-56960935(-)$1	253	110	121	17.1818
UAAAAGUAUAU	chr17:57685063-57685291(+)$1	228	122	133	17.6363
aaaauauauau	chr20:13695019-13695249(-)$1	230	101	112	20.3636
UAAAUGUUUAU	chr12:125515510-125515741(+)$1	231	204	215	18.3636
UAAAUAUAUAU	chr1:100548471-100548711(+)$1	240	116	127	23.6363
UAAAUAUAUGU	chr1:113667213-113667445(+)$1	232	106	117	20.3636
uaaauauuuau	chr8:440180-440412(-)$1	232	191	202	19.9090
UAAUUGUAUAU	chr2:230899673-230899908(-)$1	235	114	125	17.4545
UUAAUGUAUAU	chr2:111924321-111924553(+)$1	232	110	121	17.9090
uaaauauauau	chr17:7560955-7561187(+)$1	232	112	123	23.6363
UACAUGUAUGU	chrX:118151987-118152220(+)$1	233	173	184	16.0909
uauauuuauau	chr1:231471144-231471372(-)$1	228	113	124	18.9090
UAAAUACAUUU	chr12:121201584-121201829(-)$1	245	109	120	15.9090
uacauauauau	chr12:121201985-121202264(-)$1	279	127	138	20.9090
UAAAUAUCUGU	chr3:28365058-28365298(-)$1	240	119	130	16.2727
AAAAUAUAUGU	chr20:49370026-49370251(+)$1	225	24	35	17.0909
UAUAUAUAUCU	chr3:38533592-38533818(+)$1	226	75	86	17.3636
GAUAUUUAUAU	chr4:71850720-71850950(+)$1	230	99	110	15.3636
UAAAUACAUAU	chr1:165877201-165877487(+)$1	286	119	130	19.4545

#otherMatches

#Struct PSSM
=======dddd	chr2:37324993-37325229(+)$1	236	104	115	16.4545
ewwwwwwwwww	chr22:30423597-30423835(+)$1	238	206	217	19.2727
eeeeeoooooo	chr1:227847347-227847581(+)$1	234	109	120	15.0000
)))))))hhhh	chr4:156264185-156264422(-)$1	237	36	47	15.9090
===========	chr10:89513918-89514142(-)$1	224	94	105	22.0909
dduuuuuuuuu	chr5:66464725-66464952(+)$1	227	100	111	19.1818
:::::::dddd	chr17:65067194-65067417(-)$1	223	107	118	14.0909
::::::::fff	chr4:38701319-38701563(+)$1	244	118	129	21.1818
ee!!bb[eeee	chr9:89559383-89559610(-)$1	227	25	36	14.2727
===========	chr6:99321042-99321305(-)$1	263	125	136	19.3636
mmmhhhhhhhh	chr20:62588128-62588376(-)$1	248	124	135	20.9090
HHHHBB{DDDD	chr3:124949659-124949893(-)$1	234	4	15	14.2727
::ggggggg))	chr1:112255905-112256139(+)$1	234	5	16	20.0909
ff::::hhhhh	chr9:125611715-125611964(-)$1	249	115	126	17.0000
cc]ffffff::	chr14:103809678-103809906(+)$1	228	109	120	17.4545
hhhgggggggl	chr12:89981775-89982002(-)$1	227	146	157	14.9999
::::eeeee!!	chr7:116146481-116146713(+)$1	232	120	131	16.6363
22iiiiiiiii	chr3:126061509-126061741(-)$1	232	220	231	19.1818
:::JJJJJJJJ	chr17:36891189-36891420(-)$1	231	74	85	23.6363
:::::::::cc	chr2:152656606-152656850(-)$1	244	153	164	14.0000
dd::::ddddm	chr18:8638274-8638505(+)$1	231	115	126	15.6363
::::::eeeee	chr5:74668288-74668523(-)$1	235	51	62	16.1818
+++++++++++	chr16:46990486-46990729(-)$1	243	118	129	17.3636
hhhhhhhmmmm	chr19:37640167-37640413(-)$1	246	146	157	19.6363
:::::eeeee"	chr14:74666142-74666367(+)$1	225	84	95	18.5454
mmmmdddd22d	chr7:140419104-140419331(-)$1	227	79	90	14.2727
e::::::::GG	chr1:116236457-116236681(+)$1	224	87	98	15.9090
hhhhhhh!!ee	chr1:85112676-85112915(-)$1	239	123	134	14.0000
""eeeee[ddd	chr12:46752367-46752699(-)$1	332	157	168	15.4545
dddd[hhhhhh	chr12:99128945-99129179(+)$1	234	102	113	16.7272
::::iiiiiii	chr3:73115286-73115531(+)$1	245	101	112	20.9090
cccyyyyyyyy	chr13:45007893-45008115(-)$1	222	119	130	14.1818
qqqffffff22	chr5:175953754-175953976(-)$1	222	103	114	17.9090
g22ffffff55	chr13:25909759-25910009(+)$1	250	177	188	14.0909
::::::ddddq	chr18:42647854-42648093(+)$1	239	71	82	14.7272
::::::eeeee	chr1:155851771-155852003(+)$1	232	107	118	21.5454
hhhhhhppppp	chr1:56960682-56960935(-)$1	253	110	121	17.1818
neeeee::ggg	chr17:57685063-57685291(+)$1	228	122	133	17.6363
:::::::::::	chr20:13695019-13695249(-)$1	230	101	112	20.3636
>>>>>>>>ddd	chr12:125515510-125515741(+)$1	231	204	215	18.3636
dd]dddd]ddd	chr1:100548471-100548711(+)$1	240	116	127	23.6363
ddqqqqqqqqd	chr1:113667213-113667445(+)$1	232	106	117	20.3636
dd333ddddee	chr8:440180-440412(-)$1	232	191	202	19.9090
!bb!!ffffff	chr2:230899673-230899908(-)$1	235	114	125	17.4545
ffffff[dddd	chr2:111924321-111924553(+)$1	232	110	121	17.9090
mmmggggggg:	chr17:7560955-7561187(+)$1	232	112	123	23.6363
!!bb=======	chrX:118151987-118152220(+)$1	233	173	184	16.0909
eeeee:::::i	chr1:231471144-231471372(-)$1	228	113	124	18.9090
gggggggg^^^	chr12:121201584-121201829(-)$1	245	109	120	15.9090
cciiiiiiiii	chr12:121201985-121202264(-)$1	279	127	138	20.9090
IIIIIIIII::	chr3:28365058-28365298(-)$1	240	119	130	16.2727
ffffrrrrrrr	chr20:49370026-49370251(+)$1	225	24	35	17.0909
DDMMMMHHHHH	chr3:38533592-38533818(+)$1	226	75	86	17.3636
eeeeemmmmee	chr4:71850720-71850950(+)$1	230	99	110	15.3636
bb::eeeee""	chr1:165877201-165877487(+)$1	286	119	130	19.4545

#DB
(((((((((((	chr2:37324993-37325229(+)$1	1	104	115	16.4545
(..........	chr22:30423597-30423835(+)$1	1	206	217	19.2727
(((((......	chr1:227847347-227847581(+)$1	1	109	120	15.0000
.......((((	chr4:156264185-156264422(-)$1	1	36	47	15.9090
)))))))))))	chr10:89513918-89514142(-)$1	1	94	105	22.0909
((.........	chr5:66464725-66464952(+)$1	1	100	111	19.1818
.......((((	chr17:65067194-65067417(-)$1	1	107	118	14.0909
........(((	chr4:38701319-38701563(+)$1	1	118	129	21.1818
((..((.((((	chr9:89559383-89559610(-)$1	1	25	36	14.2727
(((((((((((	chr6:99321042-99321305(-)$1	1	125	136	19.3636
...))))))))	chr20:62588128-62588376(-)$1	1	124	135	20.9090
((((((.((((	chr3:124949659-124949893(-)$1	1	4	15	14.2727
..(((((((..	chr1:112255905-112256139(+)$1	1	5	16	20.0909
))....(((((	chr9:125611715-125611964(-)$1	1	115	126	17.0000
)).))))))..	chr14:103809678-103809906(+)$1	1	109	120	17.4545
((((((((((.	chr12:89981775-89982002(-)$1	1	146	157	14.9999
....(((((..	chr7:116146481-116146713(+)$1	1	120	131	16.6363
..)))))))))	chr3:126061509-126061741(-)$1	1	220	231	19.1818
...((((((((	chr17:36891189-36891420(-)$1	1	74	85	23.6363
.........((	chr2:152656606-152656850(-)$1	1	153	164	14.0000
))....((((.	chr18:8638274-8638505(+)$1	1	115	126	15.6363
......(((((	chr5:74668288-74668523(-)$1	1	51	62	16.1818
...........	chr16:46990486-46990729(-)$1	1	118	129	17.3636
(((((((....	chr19:37640167-37640413(-)$1	1	146	157	19.6363
.....(((((.	chr14:74666142-74666367(+)$1	1	84	95	18.5454
....))))..)	chr7:140419104-140419331(-)$1	1	79	90	14.2727
)........((	chr1:116236457-116236681(+)$1	1	87	98	15.9090
(((((((..((	chr1:85112676-85112915(-)$1	1	123	134	14.0000
..(((((.(((	chr12:46752367-46752699(-)$1	1	157	168	15.4545
((((.((((((	chr12:99128945-99129179(+)$1	1	102	113	16.7272
....(((((((	chr3:73115286-73115531(+)$1	1	101	112	20.9090
(((........	chr13:45007893-45008115(-)$1	1	119	130	14.1818
...))))))..	chr5:175953754-175953976(-)$1	1	103	114	17.9090
)..))))))..	chr13:25909759-25910009(+)$1	1	177	188	14.0909
......((((.	chr18:42647854-42648093(+)$1	1	71	82	14.7272
......(((((	chr1:155851771-155852003(+)$1	1	107	118	21.5454
((((((.....	chr1:56960682-56960935(-)$1	1	110	121	17.1818
.)))))..(((	chr17:57685063-57685291(+)$1	1	122	133	17.6363
...........	chr20:13695019-13695249(-)$1	1	101	112	20.3636
........)))	chr12:125515510-125515741(+)$1	1	204	215	18.3636
)).)))).)))	chr1:100548471-100548711(+)$1	1	116	127	23.6363
((........)	chr1:113667213-113667445(+)$1	1	106	117	20.3636
))...))))))	chr8:440180-440412(-)$1	1	191	202	19.9090
.((..((((((	chr2:230899673-230899908(-)$1	1	114	125	17.4545
((((((.((((	chr2:111924321-111924553(+)$1	1	110	121	17.9090
...))))))).	chr17:7560955-7561187(+)$1	1	112	123	23.6363
..(((((((((	chrX:118151987-118152220(+)$1	1	173	184	16.0909
))))).....(	chr1:231471144-231471372(-)$1	1	113	124	18.9090
)(((((((...	chr12:121201584-121201829(-)$1	1	109	120	15.9090
))(((((((((	chr12:121201985-121202264(-)$1	1	127	138	20.9090
)))))))))..	chr3:28365058-28365298(-)$1	1	119	130	16.2727
((((.......	chr20:49370026-49370251(+)$1	1	24	35	17.0909
((....(((((	chr3:38533592-38533818(+)$1	1	75	86	17.3636
(((((....))	chr4:71850720-71850950(+)$1	1	99	110	15.3636
))..(((((..	chr1:165877201-165877487(+)$1	1	119	130	19.4545

#PSSM
U : 0.60	u : 0.18	A : 0.09	G : 0.07	a : 0.03	c : 0.01	
A : 0.69	a : 0.21	U : 0.05	u : 0.01	C : 0.01	
A : 0.56	a : 0.10	U : 0.10	u : 0.07	C : 0.07	c : 0.05	G : 0.01	
A : 0.70	a : 0.25	U : 0.03	
U : 0.69	u : 0.25	A : 0.05	
A : 0.36	G : 0.21	a : 0.18	C : 0.09	U : 0.07	c : 0.03	g : 0.01	u : 0.01	
U : 0.65	u : 0.25	C : 0.07	A : 0.01	
A : 0.61	a : 0.21	U : 0.07	G : 0.03	g : 0.01	u : 0.01	C : 0.01	
U : 0.65	u : 0.21	A : 0.05	C : 0.03	c : 0.01	a : 0.01	
A : 0.54	a : 0.23	G : 0.12	U : 0.05	u : 0.01	C : 0.01	
U : 0.65	u : 0.25	G : 0.05	A : 0.03	

#score	975.9090909090911
#seq	55
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m2_run1.nuc.txt

#NT
AAGAAAA	chr19:5691229-5691564(+)$1	335	226	233	12.7187
CAGAAGA	chr10:70661038-70661301(+)$1	263	168	175	13.5000
CAGAAGA	chr11:122931239-122931606(-)$1	367	52	59	13.5000
AAGAAGA	chr19:50000350-50000682(+)$1	332	142	149	17.1718
AAGAAUA	chr3:9477324-9477613(+)$1	289	18	25	12.6406
AAGAAGA	chr1:150429743-150430034(+)$1	291	56	63	17.1718
AAAAAGA	chr12:111157704-111158166(-)$1	462	370	377	13.1093
AAGAAGG	chr19:40741803-40742111(-)$1	308	295	302	13.2656
AAGAGGA	chr6:116600818-116601080(-)$1	262	108	115	12.7968
AAGAAGC	chr15:66791814-66792090(-)$1	276	181	188	13.2656
AAGAAGA	chr15:66792293-66792574(-)$1	281	61	68	17.1718
AAGAAGA	chr6:31807229-31807634(+)$1	405	307	314	17.1718
CAGAAGA	chr1:93307222-93307575(+)$1	353	128	135	13.5000
AAGAAGU	chr2:242289387-242289690(+)$1	303	219	226	13.1093
AAGAAGA	chr10:38241044-38241298(-)$1	254	220	227	17.1718
AAGAACA	chr10:102116340-102116583(+)$1	243	132	139	12.7187
AAGAAGA	chr6:44219635-44220002(+)$1	367	285	292	17.1718
AUGAAGA	chr10:95660957-95661222(+)$1	265	140	147	12.7187
AAAAAGA	chrX:77381217-77381636(+)$1	419	380	387	13.1093
AGGAAGA	chr10:43882823-43883093(-)$1	270	131	138	12.7968
AACAAGA	chr5:149823704-149823970(-)$1	266	121	128	12.7968
AUGAAGA	chr15:52843940-52844317(-)$1	377	61	68	12.7187
AAGGAGA	chr17:30795971-30796286(+)$1	315	19	26	12.7968
AAGAUGA	chr6:38650483-38650751(-)$1	268	114	121	12.9531
AAGGAGA	chr10:85910364-85910736(+)$1	372	8	15	12.7968
AAGAUGA	chr15:66793186-66793543(-)$1	357	38	45	12.9531
AAAAAGA	chr10:129907185-129907508(-)$1	323	119	126	13.1093
AAGAAGA	chrX:153297841-153298077(-)$1	236	149	156	17.1718
AAGAAGA	chr6:32945818-32946062(+)$1	244	168	175	17.1718
AAGUAGA	chr12:76741082-76741320(-)$1	238	2	9	12.8750
UAGAAGA	chr5:114956098-114956399(-)$1	301	59	66	13.1875
AAGAAAA	chr8:74204373-74204740(-)$1	367	201	208	12.7187
AAGAUGA	chrX:117032982-117033266(-)$1	284	265	272	12.9531
CAGAAGA	chr22:39711273-39711552(-)$1	279	13	20	13.5000
UAGAAGA	chr22:29191097-29191377(-)$1	280	0	7	13.1875
AGGAAGA	chr12:104340518-104340770(+)$1	252	43	50	12.7968
AAGAAGG	chr19:3984033-3984349(-)$1	316	40	47	13.2656
AAGAUGA	chr8:55060077-55060477(+)$1	400	56	63	12.9531
AAGAAGC	chr5:137089062-137089495(-)$1	433	31	38	13.2656
AAGAAGG	chr22:38620722-38621058(-)$1	336	12	19	13.2656
AAGAAGA	chr1:93825988-93826362(+)$1	374	185	192	17.1718
AAUAAGA	chr16:2813690-2813942(+)$1	252	177	184	12.7968
AAGAAGA	chr13:53216807-53217178(+)$1	371	157	164	17.1718
AAGAAGG	chr7:155255198-155255562(+)$1	364	79	86	13.2656
CAGAAGA	chr12:6646649-6647025(+)$1	376	127	134	13.5000
CAGAAGA	chr19:40486156-40486430(+)$1	274	135	142	13.5000
AAGAACA	chr17:39846256-39846541(+)$1	285	158	165	12.7187
AAGAAGC	chr2:101620519-101620845(+)$1	326	107	114	13.2656
AAGAAGU	chrX:100646347-100646652(+)$1	305	132	139	13.1093
AAGAAGA	chr10:7840888-7841124(+)$1	236	102	109	17.1718
UAGAAGA	chr8:41472381-41472622(+)$1	241	1	8	13.1875
AAAAAGA	chr3:185639698-185639973(-)$1	275	124	131	13.1093
AAGUAGA	chr19:3982143-3982522(-)$1	379	242	249	12.8750
CAGAAGA	chr17:7477797-7478096(+)$1	299	216	223	13.5000
AAAAAGA	chr3:169700852-169701129(+)$1	277	117	124	13.1093
AAGCAGA	chr20:2446253-2446512(-)$1	259	64	71	12.7187
AGGAAGA	chr19:49376910-49377173(+)$1	263	70	77	12.7968
AAGAAGA	chr1:173456773-173457010(+)$1	237	137	144	17.1718
AAGAAGA	chr1:27745402-27745689(-)$1	287	226	233	17.1718
AAGUAGA	chr12:57038902-57039237(-)$1	335	285	292	12.8750
AAGAAGA	chr12:56511182-56511484(+)$1	302	95	102	17.1718
AAGAAGA	chr4:108871441-108871755(+)$1	314	149	156	17.1718
AAGAAGC	chr6:137524698-137524922(-)$1	224	60	67	13.2656

#otherMatches

#Struct PSSM
d!!cccs	chr17:58725247-58725540(+)$1	293	173	180	12.7968
yyyyyye	chr19:5691229-5691564(+)$1	335	226	233	12.7187
ffffff[	chr10:70661038-70661301(+)$1	263	168	175	13.5000
cc4444b	chr11:122931239-122931606(-)$1	367	52	59	13.5000
qqeeeee	chr19:50000350-50000682(+)$1	332	142	149	17.1718
fffrrrr	chr3:9477324-9477613(+)$1	289	18	25	12.6406
:HHHHHH	chr1:150429743-150430034(+)$1	291	56	63	17.1718
iiiiii:	chr12:111157704-111158166(-)$1	462	370	377	13.1093
??DDDD}	chr19:40741803-40742111(-)$1	308	295	302	13.2656
wwwwwww	chr6:116600818-116601080(-)$1	262	108	115	12.7968
nnnnnff	chr15:66791814-66792090(-)$1	276	181	188	13.2656
]ccc:::	chr15:66792293-66792574(-)$1	281	61	68	17.1718
333ffff	chr6:31807229-31807634(+)$1	405	307	314	17.1718
2ffffff	chr1:93307222-93307575(+)$1	353	128	135	13.5000
:::::CC	chr2:242289387-242289690(+)$1	303	219	226	13.1093
/IIIIII	chr10:38241044-38241298(-)$1	254	220	227	17.1718
:::::::	chr10:102116340-102116583(+)$1	243	132	139	12.7187
+++++++	chr6:44219635-44220002(+)$1	367	285	292	17.1718
vvvvvvv	chr10:95660957-95661222(+)$1	265	140	147	12.7187
:ffffff	chrX:77381217-77381636(+)$1	419	380	387	13.1093
44dddd2	chr10:43882823-43883093(-)$1	270	131	138	12.7968
dddd[bb	chr5:149823704-149823970(-)$1	266	121	128	12.7968
EEEE{BB	chr15:52843940-52844317(-)$1	377	61	68	12.7187
iiiiiii	chr17:30795971-30796286(+)$1	315	19	26	12.7968
ff!!a!!	chr6:38650483-38650751(-)$1	268	114	121	12.9531
{GGGGGG	chr10:85910364-85910736(+)$1	372	8	15	12.7968
GGGGGGF	chr15:66793186-66793543(-)$1	357	38	45	12.9531
wwwwwww	chr10:129907185-129907508(-)$1	323	119	126	13.1093
????FFF	chrX:153297841-153298077(-)$1	236	149	156	17.1718
EEEE}DD	chr6:32945818-32946062(+)$1	244	168	175	17.1718
:CCC{FF	chr12:76741082-76741320(-)$1	238	2	9	12.8750
nnbb]dd	chr5:114956098-114956399(-)$1	301	59	66	13.1875
]bb5555	chr8:74204373-74204740(-)$1	367	201	208	12.7187
:::BB}I	chrX:117032982-117033266(-)$1	284	265	272	12.9531
C::::::	chr22:39711273-39711552(-)$1	279	13	20	13.5000
::::eee	chr22:29191097-29191377(-)$1	280	0	7	13.1875
=======	chr12:104340518-104340770(+)$1	252	43	50	12.7968
qqbb]cc	chr19:3984033-3984349(-)$1	316	40	47	13.2656
:::::::	chr8:55060077-55060477(+)$1	400	56	63	12.9531
!eeeee!	chr5:137089062-137089495(-)$1	433	31	38	13.2656
ENNNNNE	chr22:38620722-38621058(-)$1	336	12	19	13.2656
]gggggg	chr1:93825988-93826362(+)$1	374	185	192	17.1718
>>>>>>>	chr16:2813690-2813942(+)$1	252	177	184	12.7968
%bboooo	chr13:53216807-53217178(+)$1	371	157	164	17.1718
&&&&&ee	chr7:155255198-155255562(+)$1	364	79	86	13.2656
cccmmmm	chr12:6646649-6647025(+)$1	376	127	134	13.5000
:ffffff	chr19:40486156-40486430(+)$1	274	135	142	13.5000
cqqqqqq	chr17:39846256-39846541(+)$1	285	158	165	12.7187
mmmdddd	chr2:101620519-101620845(+)$1	326	107	114	13.2656
ooeeeee	chrX:100646347-100646652(+)$1	305	132	139	13.1093
===]ddd	chr10:7840888-7841124(+)$1	236	102	109	17.1718
:::::::	chr8:41472381-41472622(+)$1	241	1	8	13.1875
00000bb	chr3:185639698-185639973(-)$1	275	124	131	13.1093
DDDD}EE	chr19:3982143-3982522(-)$1	379	242	249	12.8750
bbqqqqq	chr17:7477797-7478096(+)$1	299	216	223	13.5000
:::::::	chr3:169700852-169701129(+)$1	277	117	124	13.1093
ee22fff	chr20:2446253-2446512(-)$1	259	64	71	12.7187
ddd[eee	chr19:49376910-49377173(+)$1	263	70	77	12.7968
22dddd2	chr1:173456773-173457010(+)$1	237	137	144	17.1718
A::::::	chr1:27745402-27745689(-)$1	287	226	233	17.1718
$$$$$cc	chr12:57038902-57039237(-)$1	335	285	292	12.8750
+++++++	chr12:56511182-56511484(+)$1	302	95	102	17.1718
55555hh	chr4:108871441-108871755(+)$1	314	149	156	17.1718
ffff]ff	chr6:137524698-137524922(-)$1	224	60	67	13.2656

#DB
(..(((.	chr17:58725247-58725540(+)$1	1	173	180	12.7968
......)	chr19:5691229-5691564(+)$1	1	226	233	12.7187
((((((.	chr10:70661038-70661301(+)$1	1	168	175	13.5000
))....)	chr11:122931239-122931606(-)$1	1	52	59	13.5000
..)))))	chr19:50000350-50000682(+)$1	1	142	149	17.1718
(((....	chr3:9477324-9477613(+)$1	1	18	25	12.6406
.))))))	chr1:150429743-150430034(+)$1	1	56	63	17.1718
)))))).	chr12:111157704-111158166(-)$1	1	370	377	13.1093
..)))).	chr19:40741803-40742111(-)$1	1	295	302	13.2656
.......	chr6:116600818-116601080(-)$1	1	108	115	12.7968
.....))	chr15:66791814-66792090(-)$1	1	181	188	13.2656
.)))...	chr15:66792293-66792574(-)$1	1	61	68	17.1718
...))))	chr6:31807229-31807634(+)$1	1	307	314	17.1718
.))))))	chr1:93307222-93307575(+)$1	1	128	135	13.5000
.....))	chr2:242289387-242289690(+)$1	1	219	226	13.1093
.))))))	chr10:38241044-38241298(-)$1	1	220	227	17.1718
.......	chr10:102116340-102116583(+)$1	1	132	139	12.7187
.......	chr6:44219635-44220002(+)$1	1	285	292	17.1718
.......	chr10:95660957-95661222(+)$1	1	140	147	12.7187
.((((((	chrX:77381217-77381636(+)$1	1	380	387	13.1093
..)))).	chr10:43882823-43883093(-)$1	1	131	138	12.7968
((((.((	chr5:149823704-149823970(-)$1	1	121	128	12.7968
((((.((	chr15:52843940-52844317(-)$1	1	61	68	12.7187
(((((((	chr17:30795971-30796286(+)$1	1	19	26	12.7968
((..(..	chr6:38650483-38650751(-)$1	1	114	121	12.9531
.((((((	chr10:85910364-85910736(+)$1	1	8	15	12.7968
(((((((	chr15:66793186-66793543(-)$1	1	38	45	12.9531
.......	chr10:129907185-129907508(-)$1	1	119	126	13.1093
....)))	chrX:153297841-153298077(-)$1	1	149	156	17.1718
)))).))	chr6:32945818-32946062(+)$1	1	168	175	17.1718
.(((.((	chr12:76741082-76741320(-)$1	1	2	9	12.8750
..)).))	chr5:114956098-114956399(-)$1	1	59	66	13.1875
.))....	chr8:74204373-74204740(-)$1	1	201	208	12.7187
...)).)	chrX:117032982-117033266(-)$1	1	265	272	12.9531
(......	chr22:39711273-39711552(-)$1	1	13	20	13.5000
....(((	chr22:29191097-29191377(-)$1	1	0	7	13.1875
)))))))	chr12:104340518-104340770(+)$1	1	43	50	12.7968
..)).))	chr19:3984033-3984349(-)$1	1	40	47	13.2656
.......	chr8:55060077-55060477(+)$1	1	56	63	12.9531
.(((((.	chr5:137089062-137089495(-)$1	1	31	38	13.2656
(.....(	chr22:38620722-38621058(-)$1	1	12	19	13.2656
.))))))	chr1:93825988-93826362(+)$1	1	185	192	17.1718
.......	chr16:2813690-2813942(+)$1	1	177	184	12.7968
.((....	chr13:53216807-53217178(+)$1	1	157	164	17.1718
.....((	chr7:155255198-155255562(+)$1	1	79	86	13.2656
(((....	chr12:6646649-6647025(+)$1	1	127	134	13.5000
.((((((	chr19:40486156-40486430(+)$1	1	135	142	13.5000
(......	chr17:39846256-39846541(+)$1	1	158	165	12.7187
...))))	chr2:101620519-101620845(+)$1	1	107	114	13.2656
..)))))	chrX:100646347-100646652(+)$1	1	132	139	13.1093
))).)))	chr10:7840888-7841124(+)$1	1	102	109	17.1718
.......	chr8:41472381-41472622(+)$1	1	1	8	13.1875
.....))	chr3:185639698-185639973(-)$1	1	124	131	13.1093
)))).))	chr19:3982143-3982522(-)$1	1	242	249	12.8750
((.....	chr17:7477797-7478096(+)$1	1	216	223	13.5000
.......	chr3:169700852-169701129(+)$1	1	117	124	13.1093
))..)))	chr20:2446253-2446512(-)$1	1	64	71	12.7187
(((.(((	chr19:49376910-49377173(+)$1	1	70	77	12.7968
..)))).	chr1:173456773-173457010(+)$1	1	137	144	17.1718
)......	chr1:27745402-27745689(-)$1	1	226	233	17.1718
.....((	chr12:57038902-57039237(-)$1	1	285	292	12.8750
.......	chr12:56511182-56511484(+)$1	1	95	102	17.1718
.....))	chr4:108871441-108871755(+)$1	1	149	156	17.1718
)))).))	chr6:137524698-137524922(-)$1	1	60	67	13.2656

#PSSM
A : 0.84	C : 0.10	U : 0.04	
A : 0.92	G : 0.04	U : 0.03	
G : 0.89	A : 0.07	C : 0.01	U : 0.01	
A : 0.90	U : 0.04	G : 0.03	C : 0.01	
A : 0.90	U : 0.06	G : 0.03	
G : 0.92	A : 0.03	C : 0.03	U : 0.01	
A : 0.84	G : 0.06	C : 0.06	U : 0.03	

#score	896.8125
#seq	64
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m3_run1.nuc.txt

#NT
UUUUCU	chr2:152659270-152659497(-)$1	227	55	61	18.0000
UUUUCU	chr17:79536017-79536237(-)$1	220	87	93	18.0000
UUUUCU	chr2:48027155-48027384(+)$1	229	201	207	18.0000
UUUUCU	chr8:101270471-101270692(-)$1	221	34	40	18.0000
UUUUCU	chr14:53239201-53239424(+)$1	223	75	81	18.0000
UUUUCU	chr10:60157372-60157596(+)$1	224	78	84	18.0000
UUUUCU	chr17:28795304-28795528(+)$1	224	57	63	18.0000
UUUUCU	chr21:19162615-19162843(-)$1	228	137	143	18.0000
UUUUCU	chr13:31710887-31711111(-)$1	224	19	25	18.0000
UUUUCU	chr10:95347387-95347605(-)$1	218	136	142	18.0000
UUUUCU	chr6:83878748-83878972(-)$1	224	153	159	18.0000
uuuucu	chr16:25248212-25248442(-)$1	230	114	120	18.0000
UUUUCU	chr1:205580925-205581141(-)$1	216	59	65	18.0000
UUUUCU	chr17:49254718-49254948(-)$1	230	209	215	18.0000
UUUUCU	chr7:6442753-6442973(+)$1	220	178	184	18.0000
UUUUCU	chr6:159057664-159057884(-)$1	220	104	110	18.0000
UUUUCU	chr12:4598708-4598931(-)$1	223	184	190	18.0000
UUUUCU	chr16:46833342-46833571(-)$1	229	187	193	18.0000
UUUUCU	chr18:22032504-22032725(+)$1	221	212	218	18.0000
UUUUCU	chr7:6729670-6729972(-)$1	302	181	187	18.0000
UUUUCU	chr1:203277071-203277302(+)$1	231	80	86	18.0000
UUUUCU	chr1:36528360-36528590(+)$1	230	179	185	18.0000
UUUUCU	chr3:101486124-101486354(+)$1	230	78	84	18.0000
UUUUCU	chr9:37439840-37440103(-)$1	263	252	258	18.0000
UUUUCU	chr17:57771273-57771503(+)$1	230	183	189	18.0000
UUUUCU	chr10:43881880-43882106(-)$1	226	168	174	18.0000
UUUUCU	chr2:176041993-176042211(-)$1	218	168	174	18.0000
UUUUCU	chr7:138987717-138987948(+)$1	231	78	84	18.0000
UUUUCU	chr21:40562134-40562354(-)$1	220	25	31	18.0000
UUUUCU	chr15:42503169-42503397(-)$1	228	145	151	18.0000
UUUUCU	chr8:87571515-87571736(+)$1	221	134	140	18.0000
UUUUCU	chr3:186504865-186505091(+)$1	226	112	118	18.0000
UUUUCU	chr4:71895819-71896062(+)$1	243	195	201	18.0000
UUUUCU	chr3:125248535-125248778(-)$1	243	88	94	18.0000
UUUUCU	chr12:22601635-22601857(-)$1	222	130	136	18.0000
UUUUCU	chrX:150575579-150575793(+)$1	214	84	90	18.0000
UUUUCU	chr14:59971216-59971441(+)$1	225	126	132	18.0000
UUUUCU	chrX:134185029-134185253(-)$1	224	108	114	18.0000
UUUUCU	chr3:15112687-15112917(-)$1	230	123	129	18.0000
UUUUCU	chr14:81940370-81940579(-)$1	209	21	27	18.0000

#otherMatches

#Struct PSSM
^^^^^^	chr1:9989242-9989495(-)$1	253	114	120	18.0000
99999f	chr2:152659270-152659497(-)$1	227	55	61	18.0000
cccqqq	chr17:79536017-79536237(-)$1	220	87	93	18.0000
::::::	chr2:48027155-48027384(+)$1	229	201	207	18.0000
pppggg	chr8:101270471-101270692(-)$1	221	34	40	18.0000
::::ee	chr14:53239201-53239424(+)$1	223	75	81	18.0000
GGGG:f	chr10:60157372-60157596(+)$1	224	78	84	18.0000
EE::gg	chr17:28795304-28795528(+)$1	224	57	63	18.0000
::::::	chr21:19162615-19162843(-)$1	228	137	143	18.0000
oooeee	chr13:31710887-31711111(-)$1	224	19	25	18.0000
=====(	chr10:95347387-95347605(-)$1	218	136	142	18.0000
fvvvvv	chr6:83878748-83878972(-)$1	224	153	159	18.0000
####ap	chr16:25248212-25248442(-)$1	230	114	120	18.0000
:::::f	chr1:205580925-205581141(-)$1	216	59	65	18.0000
rrrrrr	chr17:49254718-49254948(-)$1	230	209	215	18.0000
dddmmm	chr7:6442753-6442973(+)$1	220	178	184	18.0000
[ccc##	chr6:159057664-159057884(-)$1	220	104	110	18.0000
9999cc	chr12:4598708-4598931(-)$1	223	184	190	18.0000
::::DD	chr16:46833342-46833571(-)$1	229	187	193	18.0000
::::::	chr18:22032504-22032725(+)$1	221	212	218	18.0000
::::::	chr7:6729670-6729972(-)$1	302	181	187	18.0000
HHHHHH	chr1:203277071-203277302(+)$1	231	80	86	18.0000
GGG}GG	chr1:36528360-36528590(+)$1	230	179	185	18.0000
FFFFFF	chr3:101486124-101486354(+)$1	230	78	84	18.0000
:::::E	chr9:37439840-37440103(-)$1	263	252	258	18.0000
BBZZZG	chr17:57771273-57771503(+)$1	230	183	189	18.0000
eeeee]	chr10:43881880-43882106(-)$1	226	168	174	18.0000
======	chr2:176041993-176042211(-)$1	218	168	174	18.0000
eeeeem	chr7:138987717-138987948(+)$1	231	78	84	18.0000
qqqccc	chr21:40562134-40562354(-)$1	220	25	31	18.0000
mmmccc	chr15:42503169-42503397(-)$1	228	145	151	18.0000
++++++	chr8:87571515-87571736(+)$1	221	134	140	18.0000
444ddd	chr3:186504865-186505091(+)$1	226	112	118	18.0000
444bb4	chr4:71895819-71896062(+)$1	243	195	201	18.0000
mmffff	chr3:125248535-125248778(-)$1	243	88	94	18.0000
eeeee2	chr12:22601635-22601857(-)$1	222	130	136	18.0000
qqqqqa	chrX:150575579-150575793(+)$1	214	84	90	18.0000
nnnnee	chr14:59971216-59971441(+)$1	225	126	132	18.0000
rrccc5	chrX:134185029-134185253(-)$1	224	108	114	18.0000
::::::	chr3:15112687-15112917(-)$1	230	123	129	18.0000
%%%%%%	chr14:81940370-81940579(-)$1	209	21	27	18.0000

#DB
......	chr1:9989242-9989495(-)$1	1	114	120	18.0000
.....)	chr2:152659270-152659497(-)$1	1	55	61	18.0000
(((...	chr17:79536017-79536237(-)$1	1	87	93	18.0000
......	chr2:48027155-48027384(+)$1	1	201	207	18.0000
...)))	chr8:101270471-101270692(-)$1	1	34	40	18.0000
....((	chr14:53239201-53239424(+)$1	1	75	81	18.0000
((((.(	chr10:60157372-60157596(+)$1	1	78	84	18.0000
((..((	chr17:28795304-28795528(+)$1	1	57	63	18.0000
......	chr21:19162615-19162843(-)$1	1	137	143	18.0000
...)))	chr13:31710887-31711111(-)$1	1	19	25	18.0000
(((((.	chr10:95347387-95347605(-)$1	1	136	142	18.0000
(.....	chr6:83878748-83878972(-)$1	1	153	159	18.0000
....(.	chr16:25248212-25248442(-)$1	1	114	120	18.0000
.....(	chr1:205580925-205581141(-)$1	1	59	65	18.0000
......	chr17:49254718-49254948(-)$1	1	209	215	18.0000
(((...	chr7:6442753-6442973(+)$1	1	178	184	18.0000
.(((..	chr6:159057664-159057884(-)$1	1	104	110	18.0000
....))	chr12:4598708-4598931(-)$1	1	184	190	18.0000
....))	chr16:46833342-46833571(-)$1	1	187	193	18.0000
......	chr18:22032504-22032725(+)$1	1	212	218	18.0000
......	chr7:6729670-6729972(-)$1	1	181	187	18.0000
((((((	chr1:203277071-203277302(+)$1	1	80	86	18.0000
))).))	chr1:36528360-36528590(+)$1	1	179	185	18.0000
((((((	chr3:101486124-101486354(+)$1	1	78	84	18.0000
.....)	chr9:37439840-37440103(-)$1	1	252	258	18.0000
))...)	chr17:57771273-57771503(+)$1	1	183	189	18.0000
))))).	chr10:43881880-43882106(-)$1	1	168	174	18.0000
))))))	chr2:176041993-176042211(-)$1	1	168	174	18.0000
(((((.	chr7:138987717-138987948(+)$1	1	78	84	18.0000
...)))	chr21:40562134-40562354(-)$1	1	25	31	18.0000
...)))	chr15:42503169-42503397(-)$1	1	145	151	18.0000
......	chr8:87571515-87571736(+)$1	1	134	140	18.0000
...)))	chr3:186504865-186505091(+)$1	1	112	118	18.0000
...)).	chr4:71895819-71896062(+)$1	1	195	201	18.0000
..))))	chr3:125248535-125248778(-)$1	1	88	94	18.0000
))))).	chr12:22601635-22601857(-)$1	1	130	136	18.0000
.....)	chrX:150575579-150575793(+)$1	1	84	90	18.0000
....))	chr14:59971216-59971441(+)$1	1	126	132	18.0000
..))).	chrX:134185029-134185253(-)$1	1	108	114	18.0000
......	chr3:15112687-15112917(-)$1	1	123	129	18.0000
......	chr14:81940370-81940579(-)$1	1	21	27	18.0000

#PSSM
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
C : 0.97	c : 0.02	
U : 0.97	u : 0.02	

#score	738.0000000000001
#seq	41
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m3_run2.nuc.txt

#NT
CACAGA	chr3:9876609-9876810(+)$1	201	121	127	14.5686
AACAGA	chr15:66633518-66633719(-)$1	201	134	140	11.8235
CCCAGA	chr8:20068639-20068840(+)$1	201	79	85	12.0196
CUCAGA	chr10:102304649-102304850(+)$1	201	103	109	12.3137
CACAGA	chr2:39476778-39476979(-)$1	201	23	29	14.5686
CUCAGA	chr20:44576338-44576539(+)$1	201	124	130	12.3137
CACAGA	chr12:25297445-25297646(-)$1	201	36	42	14.5686
AACAGA	chr7:30668107-30668308(+)$1	201	167	173	11.8235
GACAGA	chr22:51050005-51050206(+)$1	201	39	45	11.6274
UACAGA	chr4:103723645-103723846(-)$1	201	46	52	11.9215
CCCAGA	chr5:112227657-112227858(+)$1	201	158	164	12.0196
AACAGA	chr12:110777283-110777484(+)$1	201	103	109	11.8235
AACAGA	chr17:49362530-49362731(+)$1	201	122	128	11.8235
CUCAGA	chr3:169498410-169498611(+)$1	201	9	15	12.3137
CUCAGA	chr3:196081388-196081589(-)$1	201	139	145	12.3137
CACAGA	chr10:28884789-28884990(+)$1	201	160	166	14.5686
CCCAGA	chr2:25043506-25043707(+)$1	201	145	151	12.0196
CCCAGA	chr17:79988578-79988779(+)$1	201	20	26	12.0196
UACAGA	chr5:112175795-112175996(+)$1	201	42	48	11.9215
UACAGA	chr6:17507327-17507528(+)$1	201	67	73	11.9215
CACAGA	chr5:6607342-6607543(-)$1	201	102	108	14.5686
CUCAGA	chr16:18820342-18820543(-)$1	201	51	57	12.3137
UACAGA	chr6:44267459-44267660(-)$1	201	149	155	11.9215
GACAGA	chr5:138266157-138266358(+)$1	201	171	177	11.6274
GACAGA	chr9:140007570-140007771(-)$1	201	84	90	11.6274
CACAGA	chr1:21268403-21268604(-)$1	201	82	88	14.5686
CACAGA	chr1:85598483-85598684(+)$1	201	164	170	14.5686
CACAGA	chr5:134223670-134223871(+)$1	201	54	60	14.5686
CACAGA	chr10:70513654-70513855(+)$1	201	102	108	14.5686
CUCAGA	chr12:102590591-102590792(+)$1	201	99	105	12.3137
CUCAGA	chr11:118622681-118622882(-)$1	201	192	198	12.3137
CACAGA	chr19:58978712-58978913(+)$1	201	194	200	14.5686
AACAGA	chr5:122685609-122685810(-)$1	201	79	85	11.8235
GACAGA	chr2:61607392-61607593(-)$1	201	129	135	11.6274
UACAGA	chr19:35175244-35175445(+)$1	201	51	57	11.9215
CUCAGA	chr4:15640062-15640263(-)$1	201	28	34	12.3137
CCCAGA	chr1:224592095-224592296(-)$1	201	125	131	12.0196
CACAGA	chr3:23932015-23932216(+)$1	201	117	123	14.5686
CACAGA	chr3:48491424-48491625(+)$1	201	32	38	14.5686
CACAGA	chr5:137506672-137506873(-)$1	201	19	25	14.5686
CGCAGA	chr17:35870586-35870787(+)$1	201	187	193	11.4313
CUCAGA	chr11:4156225-4156426(+)$1	201	144	150	12.3137
UACAGA	chr12:94703700-94703901(-)$1	201	71	77	11.9215
CCCAGA	chrX:152037997-152038198(+)$1	201	110	116	12.0196
CACAGA	chr17:33951400-33951601(+)$1	201	91	97	14.5686
CACAGA	chr16:277261-277462(-)$1	201	20	26	14.5686
CUCAGA	chr14:74387599-74387800(+)$1	201	125	131	12.3137
CCCAGA	chr1:154935727-154935928(-)$1	201	36	42	12.0196
UACAGA	chr6:149731390-149731591(+)$1	201	102	108	11.9215
aacaga	chr9:100777672-100777873(+)$1	201	13	19	11.8235

#otherMatches

#Struct PSSM
ccclll	chr10:70666431-70666632(+)$1	201	30	36	14.5686
qqqbb]	chr3:9876609-9876810(+)$1	201	121	127	14.5686
ccc:::	chr15:66633518-66633719(-)$1	201	134	140	11.8235
bbmmmm	chr8:20068639-20068840(+)$1	201	79	85	12.0196
333ccc	chr10:102304649-102304850(+)$1	201	103	109	12.3137
fffff#	chr2:39476778-39476979(-)$1	201	23	29	14.5686
ccmmmm	chr20:44576338-44576539(+)$1	201	124	130	12.3137
::iiii	chr12:25297445-25297646(-)$1	201	36	42	14.5686
444eee	chr7:30668107-30668308(+)$1	201	167	173	11.8235
dd[eee	chr22:51050005-51050206(+)$1	201	39	45	11.6274
:::fff	chr4:103723645-103723846(-)$1	201	46	52	11.9215
uuuuuu	chr5:112227657-112227858(+)$1	201	158	164	12.0196
"eeeee	chr12:110777283-110777484(+)$1	201	103	109	11.8235
eeeemm	chr17:49362530-49362731(+)$1	201	122	128	11.8235
dd[ddd	chr3:169498410-169498611(+)$1	201	9	15	12.3137
eee:::	chr3:196081388-196081589(-)$1	201	139	145	12.3137
offfff	chr10:28884789-28884990(+)$1	201	160	166	14.5686
qqccc:	chr2:25043506-25043707(+)$1	201	145	151	12.0196
ILLLA{	chr17:79988578-79988779(+)$1	201	20	26	12.0196
:cccoo	chr5:112175795-112175996(+)$1	201	42	48	11.9215
2eeeee	chr6:17507327-17507528(+)$1	201	67	73	11.9215
::::::	chr5:6607342-6607543(-)$1	201	102	108	14.5686
cccppp	chr16:18820342-18820543(-)$1	201	51	57	12.3137
eeeeep	chr6:44267459-44267660(-)$1	201	149	155	11.9215
qqqqqq	chr5:138266157-138266358(+)$1	201	171	177	11.6274
A{DDDD	chr9:140007570-140007771(-)$1	201	84	90	11.6274
gg%%%%	chr1:21268403-21268604(-)$1	201	82	88	14.5686
rrrrbb	chr1:85598483-85598684(+)$1	201	164	170	14.5686
66ccc]	chr5:134223670-134223871(+)$1	201	54	60	14.5686
cc]eee	chr10:70513654-70513855(+)$1	201	102	108	14.5686
%%cccm	chr12:102590591-102590792(+)$1	201	99	105	12.3137
EE::::	chr11:118622681-118622882(-)$1	201	192	198	12.3137
a]a]cc	chr19:58978712-58978913(+)$1	201	194	200	14.5686
444ggg	chr5:122685609-122685810(-)$1	201	79	85	11.8235
::::dd	chr2:61607392-61607593(-)$1	201	129	135	11.6274
44bb33	chr19:35175244-35175445(+)$1	201	51	57	11.9215
ccc!!e	chr4:15640062-15640263(-)$1	201	28	34	12.3137
>>>>>>	chr1:224592095-224592296(-)$1	201	125	131	12.0196
booooo	chr3:23932015-23932216(+)$1	201	117	123	14.5686
mmmmcc	chr3:48491424-48491625(+)$1	201	32	38	14.5686
eooooo	chr5:137506672-137506873(-)$1	201	19	25	14.5686
00ccc]	chr17:35870586-35870787(+)$1	201	187	193	11.4313
hhhhh#	chr11:4156225-4156426(+)$1	201	144	150	12.3137
>>>hhh	chr12:94703700-94703901(-)$1	201	71	77	11.9215
ttttee	chrX:152037997-152038198(+)$1	201	110	116	12.0196
ddccc!	chr17:33951400-33951601(+)$1	201	91	97	14.5686
bb[iii	chr16:277261-277462(-)$1	201	20	26	14.5686
e]dddd	chr14:74387599-74387800(+)$1	201	125	131	12.3137
$$$ccc	chr1:154935727-154935928(-)$1	201	36	42	12.0196
iiiiii	chr6:149731390-149731591(+)$1	201	102	108	11.9215
KDDDD:	chr9:100777672-100777873(+)$1	201	13	19	11.8235

#DB
(((...	chr10:70666431-70666632(+)$1	1	30	36	14.5686
...)).	chr3:9876609-9876810(+)$1	1	121	127	14.5686
)))...	chr15:66633518-66633719(-)$1	1	134	140	11.8235
((....	chr8:20068639-20068840(+)$1	1	79	85	12.0196
...)))	chr10:102304649-102304850(+)$1	1	103	109	12.3137
(((((.	chr2:39476778-39476979(-)$1	1	23	29	14.5686
((....	chr20:44576338-44576539(+)$1	1	124	130	12.3137
..((((	chr12:25297445-25297646(-)$1	1	36	42	14.5686
...)))	chr7:30668107-30668308(+)$1	1	167	173	11.8235
((.(((	chr22:51050005-51050206(+)$1	1	39	45	11.6274
...(((	chr4:103723645-103723846(-)$1	1	46	52	11.9215
......	chr5:112227657-112227858(+)$1	1	158	164	12.0196
.(((((	chr12:110777283-110777484(+)$1	1	103	109	11.8235
((((..	chr17:49362530-49362731(+)$1	1	122	128	11.8235
((.(((	chr3:169498410-169498611(+)$1	1	9	15	12.3137
)))...	chr3:196081388-196081589(-)$1	1	139	145	12.3137
.)))))	chr10:28884789-28884990(+)$1	1	160	166	14.5686
..))).	chr2:25043506-25043707(+)$1	1	145	151	12.0196
(...(.	chr17:79988578-79988779(+)$1	1	20	26	12.0196
.(((..	chr5:112175795-112175996(+)$1	1	42	48	11.9215
.)))))	chr6:17507327-17507528(+)$1	1	67	73	11.9215
......	chr5:6607342-6607543(-)$1	1	102	108	14.5686
(((...	chr16:18820342-18820543(-)$1	1	51	57	12.3137
(((((.	chr6:44267459-44267660(-)$1	1	149	155	11.9215
......	chr5:138266157-138266358(+)$1	1	171	177	11.6274
(.((((	chr9:140007570-140007771(-)$1	1	84	90	11.6274
((....	chr1:21268403-21268604(-)$1	1	82	88	14.5686
....))	chr1:85598483-85598684(+)$1	1	164	170	14.5686
..))).	chr5:134223670-134223871(+)$1	1	54	60	14.5686
)).)))	chr10:70513654-70513855(+)$1	1	102	108	14.5686
..(((.	chr12:102590591-102590792(+)$1	1	99	105	12.3137
))....	chr11:118622681-118622882(-)$1	1	192	198	12.3137
).).))	chr19:58978712-58978913(+)$1	1	194	200	14.5686
...)))	chr5:122685609-122685810(-)$1	1	79	85	11.8235
....((	chr2:61607392-61607593(-)$1	1	129	135	11.6274
..))..	chr19:35175244-35175445(+)$1	1	51	57	11.9215
(((..(	chr4:15640062-15640263(-)$1	1	28	34	12.3137
......	chr1:224592095-224592296(-)$1	1	125	131	12.0196
(.....	chr3:23932015-23932216(+)$1	1	117	123	14.5686
....))	chr3:48491424-48491625(+)$1	1	32	38	14.5686
(.....	chr5:137506672-137506873(-)$1	1	19	25	14.5686
..))).	chr17:35870586-35870787(+)$1	1	187	193	11.4313
(((((.	chr11:4156225-4156426(+)$1	1	144	150	12.3137
...)))	chr12:94703700-94703901(-)$1	1	71	77	11.9215
....))	chrX:152037997-152038198(+)$1	1	110	116	12.0196
(((((.	chr17:33951400-33951601(+)$1	1	91	97	14.5686
((.(((	chr16:277261-277462(-)$1	1	20	26	14.5686
).))))	chr14:74387599-74387800(+)$1	1	125	131	12.3137
...(((	chr1:154935727-154935928(-)$1	1	36	42	12.0196
))))))	chr6:149731390-149731591(+)$1	1	102	108	11.9215
.((((.	chr9:100777672-100777873(+)$1	1	13	19	11.8235

#PSSM
C : 0.66	U : 0.13	A : 0.09	G : 0.07	a : 0.01	
A : 0.62	U : 0.19	C : 0.13	G : 0.01	a : 0.01	
C : 0.98	c : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	

#score	652.7058823529416
#seq	51
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m3_run1.nuc.txt

#NT
AUUUUCAA	chr14:74429638-74429878(+)$1	240	131	139	16.0000
AUAUUUAA	chr7:73096986-73097226(-)$1	240	146	154	15.5000
UUUUUUCA	chr5:54948256-54948496(-)$1	240	116	124	13.2000
AUUUUCAA	chr12:46758071-46758311(-)$1	240	125	133	16.0000
AUUUCUAA	chr2:55252584-55252824(-)$1	240	128	136	15.3000
UUUUUUAA	chr9:34398153-34398393(-)$1	240	121	129	16.8000
uuuuuuaa	chr5:72354210-72354450(+)$1	240	167	175	16.8000
ACUUUUAA	chr13:39585374-39585614(-)$1	240	115	123	15.4000
AUUUUUCA	chr15:26792865-26793105(-)$1	240	179	187	16.3000
AUUUUUAA	chr3:57647129-57647369(-)$1	240	58	66	19.9000
AUUUUAAA	chr5:79770395-79770635(+)$1	240	34	42	15.7000
AUUUUCAA	chr7:63981671-63981911(-)$1	240	114	122	16.0000
UUUUUUAA	chr17:5386062-5386302(-)$1	240	89	97	16.8000
AUUUUUAA	chr3:15288160-15288400(+)$1	240	183	191	19.9000
AUUUUUAG	chr19:14203260-14203500(-)$1	240	66	74	15.7000
AUUUUUAA	chr5:74893735-74893975(+)$1	240	129	137	19.9000
UUUUUUAA	chr2:32530534-32530776(+)$1	242	13	21	16.8000
AUUUUUAA	chr11:47774427-47774667(-)$1	240	217	225	19.9000
auuuuuaa	chr2:175664731-175664971(-)$1	240	128	136	19.9000
AUUUUUAG	chr8:66651693-66651933(-)$1	240	189	197	15.7000
AUUUCUAA	chr19:38055997-38056237(-)$1	240	108	116	15.3000
AAUUUUAA	chr3:169802047-169802287(+)$1	240	141	149	15.3000
AUUUUUAU	chr3:132153307-132153547(+)$1	240	59	67	15.8000
AUUUUUAU	chr1:64038061-64038301(+)$1	240	37	45	15.8000
UUUUUUAA	chr12:42503354-42503594(-)$1	240	83	91	16.8000
GUUUUUAA	chr9:36356247-36356487(-)$1	240	221	229	16.2000
AUUUUUUA	chr3:100013892-100014143(+)$1	251	118	126	15.9000
AUUUUUAA	chr15:48434387-48434667(-)$1	280	29	37	19.9000
AUUUUUAA	chr15:26812706-26812946(-)$1	240	228	236	19.9000
AUAUUUAA	chr14:55618385-55618625(-)$1	240	218	226	15.5000
AUUUUUAA	chr4:164049948-164050188(-)$1	240	224	232	19.9000
UUUUUUCA	chr21:34931511-34931751(+)$1	240	155	163	13.2000
CUUUUUAA	chr11:82959025-82959265(+)$1	240	113	121	16.1000
AUUUUUAU	chr11:19191975-19192215(+)$1	240	112	120	15.8000
AUUUUUCA	chrX:135080182-135080424(+)$1	242	104	112	16.3000
AUUUUUAA	chr7:91503266-91503506(-)$1	240	110	118	19.9000
UUUUUUAA	chr19:34945250-34945490(+)$1	240	53	61	16.8000
AUUUUGAA	chr14:69695545-69695785(+)$1	240	134	142	15.8000
GUUUUUAA	chr4:102001621-102001861(-)$1	240	179	187	16.2000
ACUUUUAA	chr8:56675194-56675440(-)$1	246	77	85	15.4000
AUUUUCAA	chr13:41507448-41507688(-)$1	240	170	178	16.0000
AUUUUUCA	chr19:30500106-30500346(+)$1	240	125	133	16.3000
AUUUUUAA	chr12:27067246-27067486(-)$1	240	128	136	19.9000
auuuuuua	chr19:42411460-42411700(+)$1	240	116	124	15.9000
AUCUUUAA	chr20:10389237-10389477(-)$1	240	11	19	15.4000
AUUUUUCA	chr13:79189940-79190180(-)$1	240	158	166	16.3000
AUUUUUAC	chr2:86344115-86344355(+)$1	240	67	75	15.6000
AUUUUGAA	chr5:90106226-90106466(+)$1	240	68	76	15.8000
AUUUUUAA	chr4:56819295-56819535(+)$1	240	164	172	19.9000

#otherMatches

#Struct PSSM
eeeeeqqq	chr2:223339207-223339447(+)$1	240	20	28	15.4000
&&&&&&dd	chr14:74429638-74429878(+)$1	240	131	139	16.0000
^^^^^^^^	chr7:73096986-73097226(-)$1	240	146	154	15.5000
++++++++	chr5:54948256-54948496(-)$1	240	116	124	13.2000
iiiiiii:	chr12:46758071-46758311(-)$1	240	125	133	16.0000
[ddddmmm	chr2:55252584-55252824(-)$1	240	128	136	15.3000
qqqqcccd	chr9:34398153-34398393(-)$1	240	121	129	16.8000
iiiiinnn	chr5:72354210-72354450(+)$1	240	167	175	16.8000
:::::::J	chr13:39585374-39585614(-)$1	240	115	123	15.4000
dmmmmddd	chr15:26792865-26793105(-)$1	240	179	187	16.3000
gzzzzzzz	chr3:57647129-57647369(-)$1	240	58	66	19.9000
::::::ff	chr5:79770395-79770635(+)$1	240	34	42	15.7000
ii^^^^^^	chr7:63981671-63981911(-)$1	240	114	122	16.0000
JJJ:::::	chr17:5386062-5386302(-)$1	240	89	97	16.8000
eeemmmme	chr3:15288160-15288400(+)$1	240	183	191	19.9000
B:::::a[	chr19:14203260-14203500(-)$1	240	66	74	15.7000
[ddddnnn	chr5:74893735-74893975(+)$1	240	129	137	19.9000
KEEEEEKK	chr2:32530534-32530776(+)$1	242	13	21	16.8000
flllffff	chr11:47774427-47774667(-)$1	240	217	225	19.9000
JJJJJJJJ	chr2:175664731-175664971(-)$1	240	128	136	19.9000
ff4444cc	chr8:66651693-66651933(-)$1	240	189	197	15.7000
qffffffe	chr19:38055997-38056237(-)$1	240	108	116	15.3000
iiiiii::	chr3:169802047-169802287(+)$1	240	141	149	15.3000
hhhhhhhh	chr3:132153307-132153547(+)$1	240	59	67	15.8000
22iiiiii	chr1:64038061-64038301(+)$1	240	37	45	15.8000
ooooooff	chr12:42503354-42503594(-)$1	240	83	91	16.8000
BB~~~~EE	chr9:36356247-36356487(-)$1	240	221	229	16.2000
((((((ii	chr3:100013892-100014143(+)$1	251	118	126	15.9000
c22=====	chr15:48434387-48434667(-)$1	280	29	37	19.9000
::::::::	chr15:26812706-26812946(-)$1	240	228	236	19.9000
ffffpppp	chr14:55618385-55618625(-)$1	240	218	226	15.5000
::::::::	chr4:164049948-164050188(-)$1	240	224	232	19.9000
ddd!!ggg	chr21:34931511-34931751(+)$1	240	155	163	13.2000
EEEEE~~~	chr11:82959025-82959265(+)$1	240	113	121	16.1000
++++++++	chr11:19191975-19192215(+)$1	240	112	120	15.8000
fvvvvvvv	chrX:135080182-135080424(+)$1	242	104	112	16.3000
gxxxxxxx	chr7:91503266-91503506(-)$1	240	110	118	19.9000
eeee6666	chr19:34945250-34945490(+)$1	240	53	61	16.8000
iiiiiiil	chr14:69695545-69695785(+)$1	240	134	142	15.8000
eee:::::	chr4:102001621-102001861(-)$1	240	179	187	16.2000
::::::::	chr8:56675194-56675440(-)$1	246	77	85	15.4000
mmmhhhhh	chr13:41507448-41507688(-)$1	240	170	178	16.0000
^^^dddd]	chr19:30500106-30500346(+)$1	240	125	133	16.3000
:::hhhhh	chr12:27067246-27067486(-)$1	240	128	136	19.9000
[eeeee!!	chr19:42411460-42411700(+)$1	240	116	124	15.9000
uuuuuuuu	chr20:10389237-10389477(-)$1	240	11	19	15.4000
::::EEEE	chr13:79189940-79190180(-)$1	240	158	166	16.3000
eeeeee[d	chr2:86344115-86344355(+)$1	240	67	75	15.6000
===####e	chr5:90106226-90106466(+)$1	240	68	76	15.8000
!!iiiiii	chr4:56819295-56819535(+)$1	240	164	172	19.9000

#DB
(((((...	chr2:223339207-223339447(+)$1	1	20	28	15.4000
......((	chr14:74429638-74429878(+)$1	1	131	139	16.0000
........	chr7:73096986-73097226(-)$1	1	146	154	15.5000
........	chr5:54948256-54948496(-)$1	1	116	124	13.2000
))))))).	chr12:46758071-46758311(-)$1	1	125	133	16.0000
.((((...	chr2:55252584-55252824(-)$1	1	128	136	15.3000
....))))	chr9:34398153-34398393(-)$1	1	121	129	16.8000
(((((...	chr5:72354210-72354450(+)$1	1	167	175	16.8000
.......(	chr13:39585374-39585614(-)$1	1	115	123	15.4000
(....)))	chr15:26792865-26793105(-)$1	1	179	187	16.3000
(.......	chr3:57647129-57647369(-)$1	1	58	66	19.9000
......((	chr5:79770395-79770635(+)$1	1	34	42	15.7000
((......	chr7:63981671-63981911(-)$1	1	114	122	16.0000
(((.....	chr17:5386062-5386302(-)$1	1	89	97	16.8000
(((....)	chr3:15288160-15288400(+)$1	1	183	191	19.9000
(.....(.	chr19:14203260-14203500(-)$1	1	66	74	15.7000
.((((...	chr5:74893735-74893975(+)$1	1	129	137	19.9000
.(((((..	chr2:32530534-32530776(+)$1	1	13	21	16.8000
(...))))	chr11:47774427-47774667(-)$1	1	217	225	19.9000
((((((((	chr2:175664731-175664971(-)$1	1	128	136	19.9000
))....))	chr8:66651693-66651933(-)$1	1	189	197	15.7000
.)))))))	chr19:38055997-38056237(-)$1	1	108	116	15.3000
))))))..	chr3:169802047-169802287(+)$1	1	141	149	15.3000
((((((((	chr3:132153307-132153547(+)$1	1	59	67	15.8000
..))))))	chr1:64038061-64038301(+)$1	1	37	45	15.8000
......))	chr12:42503354-42503594(-)$1	1	83	91	16.8000
))....))	chr9:36356247-36356487(-)$1	1	221	229	16.2000
......((	chr3:100013892-100014143(+)$1	1	118	126	15.9000
)..)))))	chr15:48434387-48434667(-)$1	1	29	37	19.9000
........	chr15:26812706-26812946(-)$1	1	228	236	19.9000
((((....	chr14:55618385-55618625(-)$1	1	218	226	15.5000
........	chr4:164049948-164050188(-)$1	1	224	232	19.9000
(((..(((	chr21:34931511-34931751(+)$1	1	155	163	13.2000
)))))...	chr11:82959025-82959265(+)$1	1	113	121	16.1000
........	chr11:19191975-19192215(+)$1	1	112	120	15.8000
(.......	chrX:135080182-135080424(+)$1	1	104	112	16.3000
(.......	chr7:91503266-91503506(-)$1	1	110	118	19.9000
))))....	chr19:34945250-34945490(+)$1	1	53	61	16.8000
(((((((.	chr14:69695545-69695785(+)$1	1	134	142	15.8000
))).....	chr4:102001621-102001861(-)$1	1	179	187	16.2000
........	chr8:56675194-56675440(-)$1	1	77	85	15.4000
...)))))	chr13:41507448-41507688(-)$1	1	170	178	16.0000
...)))).	chr19:30500106-30500346(+)$1	1	125	133	16.3000
...(((((	chr12:27067246-27067486(-)$1	1	128	136	19.9000
.(((((..	chr19:42411460-42411700(+)$1	1	116	124	15.9000
........	chr20:10389237-10389477(-)$1	1	11	19	15.4000
....))))	chr13:79189940-79190180(-)$1	1	158	166	16.3000
((((((.(	chr2:86344115-86344355(+)$1	1	67	75	15.6000
(((....(	chr5:90106226-90106466(+)$1	1	68	76	15.8000
..((((((	chr4:56819295-56819535(+)$1	1	164	172	19.9000

#PSSM
A : 0.74	U : 0.14	a : 0.04	G : 0.04	u : 0.02	C : 0.02	
U : 0.88	u : 0.06	C : 0.04	A : 0.02	
U : 0.86	u : 0.06	A : 0.04	G : 0.02	C : 0.02	
U : 0.94	u : 0.06	
U : 0.90	u : 0.06	C : 0.04	
U : 0.80	C : 0.08	u : 0.06	G : 0.04	A : 0.02	
A : 0.80	C : 0.12	a : 0.04	U : 0.02	u : 0.02	
A : 0.82	a : 0.06	U : 0.06	G : 0.04	C : 0.02	

#score	835.8000000000001
#seq	50
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m2_run2.nuc.txt

#NT
CCCUGCCU	chr7:74072143-74072377(+)$1	234	50	58	11.6851
UCCUGUCU	chr22:22319586-22319820(-)$1	234	60	68	11.5925
UCCUUGCU	chr19:44242184-44242406(-)$1	222	25	33	10.3888
CCCUGUCU	chr2:178479447-178479671(-)$1	224	95	103	11.4074
GCCUGGGU	chr19:2272996-2273223(+)$1	227	193	201	11.5925
GGCUGGCU	chr11:118885991-118886212(+)$1	221	102	110	11.4999
UCCUGGCC	chr9:103109443-103109664(-)$1	221	166	174	12.4259
GCCGGGCA	chr16:31201314-31201551(+)$1	237	91	99	9.8333
CCCUGCCU	chr19:56179813-56180040(+)$1	227	146	154	11.6851
GCCUGACU	chr11:93474505-93474726(-)$1	221	30	38	12.7037
GCCUGCCC	chr17:27416991-27417216(-)$1	225	29	37	10.5740
GCCUGACU	chr2:158593760-158593990(-)$1	230	14	22	12.7037
CCCUGGCU	chr17:80369246-80369467(-)$1	221	41	49	14.7407
gccgggcc	chr14:50998734-50998957(-)$1	223	5	13	10.2962
CCCUGGGU	chr11:60670835-60671059(-)$1	224	11	19	10.2037
CCCCGGCU	chr9:140008884-140009106(-)$1	222	94	102	11.7777
GCCUGUCU	chr2:96949590-96949816(-)$1	226	73	81	12.7962
GCAUGGCU	chr19:54634662-54634883(+)$1	221	145	153	11.4074
UCCUGGCC	chr20:34843588-34843815(+)$1	227	128	136	12.4259
UCCAGGCU	chr19:49993159-49993404(+)$1	245	174	182	11.7777
GCCUGGCU	chr3:47888253-47888490(+)$1	237	141	149	16.1296
GCCUGGCC	chr17:7124007-7124232(+)$1	225	41	49	13.6296
CCCUGGCA	chr3:49759571-49759802(-)$1	231	111	119	11.7777
CCCUGGCA	chr16:67906888-67907111(+)$1	223	49	57	11.7777
UCCCGGCU	chr5:65440085-65440317(+)$1	232	53	61	11.9629
GCCUUGCU	chr3:41281234-41281464(+)$1	230	163	171	11.5925
CCCGGGCU	chr3:131221645-131221874(-)$1	229	196	204	11.4074
UCCAGGCU	chr11:62460044-62460276(-)$1	232	215	223	11.7777
GCCAGCCU	chr6:36514883-36515108(-)$1	225	59	67	9.9259
UCCUGGCU	chr19:36113446-36113667(+)$1	221	35	43	14.9259
GCCUCGCU	chr8:124054365-124054589(-)$1	224	55	63	11.4999
CCGUGGCU	chr9:131183095-131183316(+)$1	221	112	120	10.0185
UCCUGGUU	chr19:12814457-12814681(-)$1	224	13	21	10.2962
GCCCGGCC	chr12:105501436-105501670(+)$1	234	14	22	10.6666
GCCCGGCA	chr12:62965153-62965375(+)$1	222	123	131	10.2037
GCCUGCCC	chr19:56915618-56915843(+)$1	225	73	81	10.5740
GCCUGGCG	chr21:44299502-44299724(-)$1	222	41	49	13.2592
gccugccu	chr12:64798342-64798577(+)$1	235	5	13	13.0740
UCCUGGCG	chr5:33460917-33461139(+)$1	222	114	122	12.0555
GCCUGGCG	chr15:28520008-28520251(-)$1	243	188	196	13.2592
UCCUGGCU	chr12:57883996-57884220(+)$1	224	86	94	14.9259
GCCAGGCC	chr19:1301201-1301439(+)$1	238	133	141	10.4814
GCCCGCCU	chr16:721002-721227(+)$1	225	10	18	10.1111
GCCCGGCU	chr21:33104063-33104287(-)$1	224	195	203	13.1666
GCCUGGCC	chr14:31676225-31676445(-)$1	220	147	155	13.6296
UUCUGGCU	chr16:67262651-67262877(+)$1	226	121	129	10.2962
UCCUGGCU	chr16:19729119-19729342(-)$1	223	132	140	14.9259
CCCUGGCU	chr15:72491480-72491705(-)$1	225	66	74	14.7407
CCCUGUCU	chr10:58117809-58118039(-)$1	230	75	83	11.4074
GCCUGGCG	chr13:74708114-74708348(-)$1	234	147	155	13.2592
acccggcU	chr3:49155298-49155524(-)$1	226	78	86	10.7592
UCCUGGCG	chrX:119763735-119763958(-)$1	223	35	43	12.0555
GCCAGACU	chr15:70341630-70341849(-)$1	219	165	173	9.5555

#otherMatches

#Struct PSSM
cc]bb]cc	chr11:75111457-75111682(+)$1	225	213	221	11.4999
E:::ccc[	chr7:74072143-74072377(+)$1	234	50	58	11.6851
c:cccnnn	chr22:22319586-22319820(-)$1	234	60	68	11.5925
:::::ccc	chr19:44242184-44242406(-)$1	222	25	33	10.3888
ddddqqqq	chr2:178479447-178479671(-)$1	224	95	103	11.4074
DDDDbboo	chr19:2272996-2273223(+)$1	227	193	201	11.5925
meeeeeee	chr11:118885991-118886212(+)$1	221	102	110	11.4999
:::GGGGG	chr9:103109443-103109664(-)$1	221	166	174	12.4259
[ddddttt	chr16:31201314-31201551(+)$1	237	91	99	9.8333
::::::::	chr19:56179813-56180040(+)$1	227	146	154	11.6851
iiii[abb	chr11:93474505-93474726(-)$1	221	30	38	12.7037
::::BB{D	chr17:27416991-27417216(-)$1	225	29	37	10.5740
eeennnnn	chr2:158593760-158593990(-)$1	230	14	22	12.7037
GGGGGGG:	chr17:80369246-80369467(-)$1	221	41	49	14.7407
CC{GGGGG	chr14:50998734-50998957(-)$1	223	5	13	10.2962
####dddd	chr11:60670835-60671059(-)$1	224	11	19	10.2037
affffff!	chr9:140008884-140009106(-)$1	222	94	102	11.7777
eeeee:::	chr2:96949590-96949816(-)$1	226	73	81	12.7962
"a[eeeee	chr19:54634662-54634883(+)$1	221	145	153	11.4074
g:EEEEEL	chr20:34843588-34843815(+)$1	227	128	136	12.4259
5555dddd	chr19:49993159-49993404(+)$1	245	174	182	11.7777
=:CCCYYG	chr3:47888253-47888490(+)$1	237	141	149	16.1296
]hhhhhhh	chr17:7124007-7124232(+)$1	225	41	49	13.6296
iddddooo	chr3:49759571-49759802(-)$1	231	111	119	11.7777
""ffffff	chr16:67906888-67907111(+)$1	223	49	57	11.7777
[ffffffb	chr5:65440085-65440317(+)$1	232	53	61	11.9629
9bb333ee	chr3:41281234-41281464(+)$1	230	163	171	11.5925
]ffffff:	chr3:131221645-131221874(-)$1	229	196	204	11.4074
mmmmccce	chr11:62460044-62460276(-)$1	232	215	223	11.7777
a]eeeee2	chr6:36514883-36515108(-)$1	225	59	67	9.9259
c]gggggg	chr19:36113446-36113667(+)$1	221	35	43	14.9259
ccc[ccc[	chr8:124054365-124054589(-)$1	224	55	63	11.4999
e]iiiiii	chr9:131183095-131183316(+)$1	221	112	120	10.0185
ffffff""	chr19:12814457-12814681(-)$1	224	13	21	10.2962
!=======	chr12:105501436-105501670(+)$1	234	14	22	10.6666
ddddEEEE	chr12:62965153-62965375(+)$1	222	123	131	10.2037
bmmmmbba	chr19:56915618-56915843(+)$1	225	73	81	10.5740
ffccc[bb	chr21:44299502-44299724(-)$1	222	41	49	13.2592
{GGGGGGG	chr12:64798342-64798577(+)$1	235	5	13	13.0740
gggcccbb	chr5:33460917-33461139(+)$1	222	114	122	12.0555
ee22dddd	chr15:28520008-28520251(-)$1	243	188	196	13.2592
ffffff:E	chr12:57883996-57884220(+)$1	224	86	94	14.9259
hhhhhqqq	chr19:1301201-1301439(+)$1	238	133	141	10.4814
ccc[ccc[	chr16:721002-721227(+)$1	225	10	18	10.1111
gggggHHH	chr21:33104063-33104287(-)$1	224	195	203	13.1666
hhh22a]e	chr14:31676225-31676445(-)$1	220	147	155	13.6296
7777ccc2	chr16:67262651-67262877(+)$1	226	121	129	10.2962
ggg]hhhh	chr16:19729119-19729342(-)$1	223	132	140	14.9259
!!dddd""	chr15:72491480-72491705(-)$1	225	66	74	14.7407
:ddddsss	chr10:58117809-58118039(-)$1	230	75	83	11.4074
eeeccc[f	chr13:74708114-74708348(-)$1	234	147	155	13.2592
6iiiiiii	chr3:49155298-49155524(-)$1	226	78	86	10.7592
!!bb[bbw	chrX:119763735-119763958(-)$1	223	35	43	12.0555
dggggggg	chr15:70341630-70341849(-)$1	219	165	173	9.5555

#DB
)).)).))	chr11:75111457-75111682(+)$1	1	213	221	11.4999
(...(((.	chr7:74072143-74072377(+)$1	1	50	58	11.6851
).(((...	chr22:22319586-22319820(-)$1	1	60	68	11.5925
.....(((	chr19:44242184-44242406(-)$1	1	25	33	10.3888
((((....	chr2:178479447-178479671(-)$1	1	95	103	11.4074
))))((..	chr19:2272996-2273223(+)$1	1	193	201	11.5925
.)))))((	chr11:118885991-118886212(+)$1	1	102	110	11.4999
...)))))	chr9:103109443-103109664(-)$1	1	166	174	12.4259
.((((...	chr16:31201314-31201551(+)$1	1	91	99	9.8333
........	chr19:56179813-56180040(+)$1	1	146	154	11.6851
((((.(((	chr11:93474505-93474726(-)$1	1	30	38	12.7037
....((.(	chr17:27416991-27417216(-)$1	1	29	37	10.5740
(((.....	chr2:158593760-158593990(-)$1	1	14	22	12.7037
(((((((.	chr17:80369246-80369467(-)$1	1	41	49	14.7407
((.(((((	chr14:50998734-50998957(-)$1	1	5	13	10.2962
....((((	chr11:60670835-60671059(-)$1	1	11	19	10.2037
(((((((.	chr9:140008884-140009106(-)$1	1	94	102	11.7777
)))))...	chr2:96949590-96949816(-)$1	1	73	81	12.7962
.(.(((((	chr19:54634662-54634883(+)$1	1	145	153	11.4074
).(((((.	chr20:34843588-34843815(+)$1	1	128	136	12.4259
....))))	chr19:49993159-49993404(+)$1	1	174	182	11.7777
).)))..)	chr3:47888253-47888490(+)$1	1	141	149	16.1296
.)))))))	chr17:7124007-7124232(+)$1	1	41	49	13.6296
)((((...	chr3:49759571-49759802(-)$1	1	111	119	11.7777
..((((((	chr16:67906888-67907111(+)$1	1	49	57	11.7777
.(((((((	chr5:65440085-65440317(+)$1	1	53	61	11.9629
.))...))	chr3:41281234-41281464(+)$1	1	163	171	11.5925
.)))))).	chr3:131221645-131221874(-)$1	1	196	204	11.4074
....))))	chr11:62460044-62460276(-)$1	1	215	223	11.7777
).))))).	chr6:36514883-36515108(-)$1	1	59	67	9.9259
).))))))	chr19:36113446-36113667(+)$1	1	35	43	14.9259
(((.(((.	chr8:124054365-124054589(-)$1	1	55	63	11.4999
).))))))	chr9:131183095-131183316(+)$1	1	112	120	10.0185
((((((..	chr19:12814457-12814681(-)$1	1	13	21	10.2962
.(((((((	chr12:105501436-105501670(+)$1	1	14	22	10.6666
))))))))	chr12:62965153-62965375(+)$1	1	123	131	10.2037
(....)))	chr19:56915618-56915843(+)$1	1	73	81	10.5740
))(((.((	chr21:44299502-44299724(-)$1	1	41	49	13.2592
.(((((((	chr12:64798342-64798577(+)$1	1	5	13	13.0740
))))))))	chr5:33460917-33461139(+)$1	1	114	122	12.0555
))..))))	chr15:28520008-28520251(-)$1	1	188	196	13.2592
)))))).(	chr12:57883996-57884220(+)$1	1	86	94	14.9259
(((((...	chr19:1301201-1301439(+)$1	1	133	141	10.4814
(((.(((.	chr16:721002-721227(+)$1	1	10	18	10.1111
))))))))	chr21:33104063-33104287(-)$1	1	195	203	13.1666
)))..).)	chr14:31676225-31676445(-)$1	1	147	155	13.6296
....))).	chr16:67262651-67262877(+)$1	1	121	129	10.2962
))).))))	chr16:19729119-19729342(-)$1	1	132	140	14.9259
..((((..	chr15:72491480-72491705(-)$1	1	66	74	14.7407
.((((...	chr10:58117809-58118039(-)$1	1	75	83	11.4074
((((((.(	chr13:74708114-74708348(-)$1	1	147	155	13.2592
.)))))))	chr3:49155298-49155524(-)$1	1	78	86	10.7592
..((.((.	chrX:119763735-119763958(-)$1	1	35	43	12.0555
))))))))	chr15:70341630-70341849(-)$1	1	165	173	9.5555

#PSSM
G : 0.46	U : 0.25	C : 0.22	g : 0.03	a : 0.01	
C : 0.88	c : 0.05	A : 0.01	G : 0.01	U : 0.01	
C : 0.90	c : 0.05	A : 0.01	G : 0.01	
U : 0.70	C : 0.11	A : 0.09	G : 0.03	g : 0.01	u : 0.01	c : 0.01	
G : 0.88	g : 0.05	U : 0.03	C : 0.01	
G : 0.70	C : 0.11	U : 0.07	A : 0.05	g : 0.03	c : 0.01	
C : 0.88	c : 0.05	G : 0.03	U : 0.01	
U : 0.64	C : 0.14	G : 0.09	A : 0.07	c : 0.01	u : 0.01	

#score	644.1481481481474
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m2_run1.nuc.txt

#NT
CUUU	chr20:52183688-52183968(-)$1	280	15	19	12.0000
CUUU	chr6:109484856-109485096(+)$1	240	1	5	12.0000
CUUU	chr12:133345629-133345869(-)$1	240	182	186	12.0000
CUUU	chr3:53320024-53320344(-)$1	320	30	34	12.0000
CUUU	chr2:29023331-29023571(+)$1	240	56	60	12.0000
CUUU	chr5:159504321-159504561(-)$1	240	0	4	12.0000
CUUU	chr21:16335756-16335996(-)$1	240	69	73	12.0000
CUUU	chr4:69179250-69179490(-)$1	240	2	6	12.0000
CUUU	chr5:137842174-137842414(-)$1	240	147	151	12.0000
CUUU	chr6:52363446-52363686(-)$1	240	15	19	12.0000
CUUU	chr12:76440070-76440310(-)$1	240	5	9	12.0000
CUUU	chr1:155258923-155259163(+)$1	240	194	198	12.0000
CUUU	chr8:64124917-64125157(+)$1	240	2	6	12.0000
CUUU	chr17:61771820-61772060(+)$1	240	118	122	12.0000
CUUU	chr1:47098867-47099107(-)$1	240	108	112	12.0000
CUUU	chr2:160624027-160624267(+)$1	240	17	21	12.0000
CUUU	chr15:43317005-43317245(-)$1	240	34	38	12.0000
CUUU	chr14:55511732-55512012(+)$1	280	87	91	12.0000
CUUU	chr1:249142889-249143129(+)$1	240	63	67	12.0000
CUUU	chr15:69739141-69739381(+)$1	240	40	44	12.0000
CUUU	chr3:49050494-49050734(+)$1	240	130	134	12.0000
CUUU	chr22:32353319-32353559(+)$1	240	4	8	12.0000
CUUU	chr16:66544054-66544304(-)$1	250	51	55	12.0000
CUUU	chr16:23076047-23076287(-)$1	240	112	116	12.0000
CUUU	chr14:61179720-61179960(-)$1	240	26	30	12.0000
CUUU	chr11:134031625-134031865(-)$1	240	31	35	12.0000
CUUU	chr10:124190356-124190677(+)$1	321	239	243	12.0000
CUUU	chr3:57913131-57913371(+)$1	240	70	74	12.0000
CUUU	chr1:110038290-110038530(+)$1	240	1	5	12.0000
CUUU	chr1:31345377-31345617(-)$1	240	164	168	12.0000
CUUU	chr3:10191901-10192141(+)$1	240	103	107	12.0000
CUUU	chr11:8968904-8969144(-)$1	240	34	38	12.0000
CUUU	chr10:69676689-69676929(+)$1	240	84	88	12.0000
CUUU	chr7:101892818-101893058(+)$1	240	28	32	12.0000
CUUU	chr11:130100288-130100528(-)$1	240	1	5	12.0000
CUUU	chr19:58051227-58051467(+)$1	240	128	132	12.0000
CUUU	chr3:172348618-172348858(-)$1	240	61	65	12.0000
CUUU	chr6:33424759-33425006(+)$1	247	36	40	12.0000
CUUU	chr17:12044887-12045127(+)$1	240	184	188	12.0000
CUUU	chr8:21961673-21961913(+)$1	240	156	160	12.0000
CUUU	chr5:179032784-179033024(-)$1	240	119	123	12.0000
CUUU	chr5:137804809-137805089(+)$1	280	61	65	12.0000
CUUU	chr11:3381272-3381512(-)$1	240	2	6	12.0000
CUUU	chr1:6245438-6245678(-)$1	240	164	168	12.0000
CUUU	chr18:9546761-9547001(-)$1	240	20	24	12.0000
CUUU	chr7:90044105-90044425(+)$1	320	119	123	12.0000
CUUU	chr5:114950854-114951100(-)$1	246	53	57	12.0000
CUUU	chr1:26158999-26159239(+)$1	240	199	203	12.0000
CUUU	chr12:50156572-50156892(+)$1	320	121	125	12.0000
CUUU	chrX:70795534-70795774(+)$1	240	5	9	12.0000
CUUU	chr1:24088119-24088439(+)$1	320	122	126	12.0000
CUUU	chr15:66628986-66629226(-)$1	240	93	97	12.0000
CUUU	chr13:23929171-23929411(-)$1	240	6	10	12.0000
cUUU	chr17:56422457-56422697(-)$1	240	148	152	12.0000
CUUU	chr1:53290815-53291055(+)$1	240	59	63	12.0000
CUUU	chr1:229577535-229577775(-)$1	240	125	129	12.0000
CUUU	chr10:112045967-112046207(+)$1	240	136	140	12.0000
CUUU	chr4:40425276-40425516(-)$1	240	27	31	12.0000
CUUU	chr22:29183419-29183659(+)$1	240	212	216	12.0000
CUUU	chr3:39183519-39183760(-)$1	241	8	12	12.0000
CUUU	chr20:48521140-48521380(-)$1	240	76	80	12.0000
CUUU	chr3:53276088-53276328(-)$1	240	115	119	12.0000
CUUU	chr16:11962706-11962946(-)$1	240	18	22	12.0000
CUUU	chr6:138412338-138412578(-)$1	240	49	53	12.0000
CUUU	chr22:29450809-29451049(+)$1	240	15	19	12.0000
CUUU	chr9:124103305-124103545(-)$1	240	117	121	12.0000
CUUU	chr5:148731457-148731709(+)$1	252	48	52	12.0000
CUUU	chr1:89426968-89427208(-)$1	240	218	222	12.0000
CUUU	chr3:129273984-129274224(-)$1	240	137	141	12.0000
CUUU	chr2:63273461-63273701(+)$1	240	55	59	12.0000
cuuu	chr9:101979242-101979482(-)$1	240	122	126	12.0000
CUUU	chr19:16685804-16686044(-)$1	240	12	16	12.0000
CUUU	chr2:55199657-55199897(-)$1	240	79	83	12.0000
CUUU	chr6:28871827-28872067(-)$1	240	57	61	12.0000
CUUU	chr3:179110658-179110898(+)$1	240	26	30	12.0000
CUUU	chr1:231696785-231697025(+)$1	240	71	75	12.0000
CUUU	chr5:41917634-41917882(+)$1	248	43	47	12.0000
CUUU	chr6:79650273-79650513(-)$1	240	24	28	12.0000
CUUU	chr11:20405003-20405243(+)$1	240	24	28	12.0000
CUUU	chr9:82339889-82340129(+)$1	240	20	24	12.0000
CUUU	chr12:69971137-69971377(+)$1	240	16	20	12.0000
CUUU	chr5:38475353-38475593(-)$1	240	13	17	12.0000
CUUU	chr11:6703078-6703325(-)$1	247	26	30	12.0000
CUUU	chr11:6504532-6504772(+)$1	240	32	36	12.0000
CUUU	chr6:2785505-2785745(+)$1	240	42	46	12.0000

#otherMatches

#Struct PSSM
::::	chr19:14071722-14071962(+)$1	240	5	9	12.0000
EEff	chr20:52183688-52183968(-)$1	280	15	19	12.0000
::FF	chr6:109484856-109485096(+)$1	240	1	5	12.0000
5555	chr12:133345629-133345869(-)$1	240	182	186	12.0000
oooo	chr3:53320024-53320344(-)$1	320	30	34	12.0000
ccmm	chr2:29023331-29023571(+)$1	240	56	60	12.0000
:FFF	chr5:159504321-159504561(-)$1	240	0	4	12.0000
QEEE	chr21:16335756-16335996(-)$1	240	69	73	12.0000
cnnn	chr4:69179250-69179490(-)$1	240	2	6	12.0000
cooo	chr5:137842174-137842414(-)$1	240	147	151	12.0000
cc[d	chr6:52363446-52363686(-)$1	240	15	19	12.0000
JJJJ	chr12:76440070-76440310(-)$1	240	5	9	12.0000
>>>>	chr1:155258923-155259163(+)$1	240	194	198	12.0000
HHHH	chr8:64124917-64125157(+)$1	240	2	6	12.0000
oooo	chr17:61771820-61772060(+)$1	240	118	122	12.0000
^^^^	chr1:47098867-47099107(-)$1	240	108	112	12.0000
22ff	chr2:160624027-160624267(+)$1	240	17	21	12.0000
666c	chr15:43317005-43317245(-)$1	240	34	38	12.0000
[a!!	chr14:55511732-55512012(+)$1	280	87	91	12.0000
vvvv	chr1:249142889-249143129(+)$1	240	63	67	12.0000
uuuu	chr15:69739141-69739381(+)$1	240	40	44	12.0000
''''	chr3:49050494-49050734(+)$1	240	130	134	12.0000
::::	chr22:32353319-32353559(+)$1	240	4	8	12.0000
iiii	chr16:66544054-66544304(-)$1	250	51	55	12.0000
b999	chr16:23076047-23076287(-)$1	240	112	116	12.0000
::::	chr14:61179720-61179960(-)$1	240	26	30	12.0000
[ccc	chr11:134031625-134031865(-)$1	240	31	35	12.0000
cc[f	chr10:124190356-124190677(+)$1	321	239	243	12.0000
>>>>	chr3:57913131-57913371(+)$1	240	70	74	12.0000
::::	chr1:110038290-110038530(+)$1	240	1	5	12.0000
tttd	chr1:31345377-31345617(-)$1	240	164	168	12.0000
ee##	chr3:10191901-10192141(+)$1	240	103	107	12.0000
FFFF	chr11:8968904-8969144(-)$1	240	34	38	12.0000
dddd	chr10:69676689-69676929(+)$1	240	84	88	12.0000
^^^^	chr7:101892818-101893058(+)$1	240	28	32	12.0000
::::	chr11:130100288-130100528(-)$1	240	1	5	12.0000
i22c	chr19:58051227-58051467(+)$1	240	128	132	12.0000
!ddd	chr3:172348618-172348858(-)$1	240	61	65	12.0000
aooo	chr6:33424759-33425006(+)$1	247	36	40	12.0000
ooff	chr17:12044887-12045127(+)$1	240	184	188	12.0000
HHHY	chr8:21961673-21961913(+)$1	240	156	160	12.0000
====	chr5:179032784-179033024(-)$1	240	119	123	12.0000
GGGG	chr5:137804809-137805089(+)$1	280	61	65	12.0000
::::	chr11:3381272-3381512(-)$1	240	2	6	12.0000
dddd	chr1:6245438-6245678(-)$1	240	164	168	12.0000
!eee	chr18:9546761-9547001(-)$1	240	20	24	12.0000
]eee	chr7:90044105-90044425(+)$1	320	119	123	12.0000
cooo	chr5:114950854-114951100(-)$1	246	53	57	12.0000
ffff	chr1:26158999-26159239(+)$1	240	199	203	12.0000
^^^^	chr12:50156572-50156892(+)$1	320	121	125	12.0000
dlll	chrX:70795534-70795774(+)$1	240	5	9	12.0000
blll	chr1:24088119-24088439(+)$1	320	122	126	12.0000
dd!!	chr15:66628986-66629226(-)$1	240	93	97	12.0000
fff[	chr13:23929171-23929411(-)$1	240	6	10	12.0000
ggg:	chr17:56422457-56422697(-)$1	240	148	152	12.0000
ssss	chr1:53290815-53291055(+)$1	240	59	63	12.0000
::::	chr1:229577535-229577775(-)$1	240	125	129	12.0000
h22b	chr10:112045967-112046207(+)$1	240	136	140	12.0000
gggg	chr4:40425276-40425516(-)$1	240	27	31	12.0000
eell	chr22:29183419-29183659(+)$1	240	212	216	12.0000
EEEE	chr3:39183519-39183760(-)$1	241	8	12	12.0000
JJJJ	chr20:48521140-48521380(-)$1	240	76	80	12.0000
c:::	chr3:53276088-53276328(-)$1	240	115	119	12.0000
rrrr	chr16:11962706-11962946(-)$1	240	18	22	12.0000
hhhh	chr6:138412338-138412578(-)$1	240	49	53	12.0000
MMMM	chr22:29450809-29451049(+)$1	240	15	19	12.0000
eeee	chr9:124103305-124103545(-)$1	240	117	121	12.0000
&&&&	chr5:148731457-148731709(+)$1	252	48	52	12.0000
22bb	chr1:89426968-89427208(-)$1	240	218	222	12.0000
++++	chr3:129273984-129274224(-)$1	240	137	141	12.0000
::::	chr2:63273461-63273701(+)$1	240	55	59	12.0000
HH??	chr9:101979242-101979482(-)$1	240	122	126	12.0000
::::	chr19:16685804-16686044(-)$1	240	12	16	12.0000
hhhh	chr2:55199657-55199897(-)$1	240	79	83	12.0000
FFFF	chr6:28871827-28872067(-)$1	240	57	61	12.0000
====	chr3:179110658-179110898(+)$1	240	26	30	12.0000
IIII	chr1:231696785-231697025(+)$1	240	71	75	12.0000
ssss	chr5:41917634-41917882(+)$1	248	43	47	12.0000
b[==	chr6:79650273-79650513(-)$1	240	24	28	12.0000
WJJJ	chr11:20405003-20405243(+)$1	240	24	28	12.0000
::::	chr9:82339889-82340129(+)$1	240	20	24	12.0000
nnnn	chr12:69971137-69971377(+)$1	240	16	20	12.0000
KKBB	chr5:38475353-38475593(-)$1	240	13	17	12.0000
NNNN	chr11:6703078-6703325(-)$1	247	26	30	12.0000
++++	chr11:6504532-6504772(+)$1	240	32	36	12.0000
BKKH	chr6:2785505-2785745(+)$1	240	42	46	12.0000

#DB
....	chr19:14071722-14071962(+)$1	1	5	9	12.0000
((((	chr20:52183688-52183968(-)$1	1	15	19	12.0000
..((	chr6:109484856-109485096(+)$1	1	1	5	12.0000
....	chr12:133345629-133345869(-)$1	1	182	186	12.0000
....	chr3:53320024-53320344(-)$1	1	30	34	12.0000
((..	chr2:29023331-29023571(+)$1	1	56	60	12.0000
.(((	chr5:159504321-159504561(-)$1	1	0	4	12.0000
.(((	chr21:16335756-16335996(-)$1	1	69	73	12.0000
(...	chr4:69179250-69179490(-)$1	1	2	6	12.0000
(...	chr5:137842174-137842414(-)$1	1	147	151	12.0000
((.(	chr6:52363446-52363686(-)$1	1	15	19	12.0000
((((	chr12:76440070-76440310(-)$1	1	5	9	12.0000
....	chr1:155258923-155259163(+)$1	1	194	198	12.0000
((((	chr8:64124917-64125157(+)$1	1	2	6	12.0000
....	chr17:61771820-61772060(+)$1	1	118	122	12.0000
....	chr1:47098867-47099107(-)$1	1	108	112	12.0000
..))	chr2:160624027-160624267(+)$1	1	17	21	12.0000
...)	chr15:43317005-43317245(-)$1	1	34	38	12.0000
.(..	chr14:55511732-55512012(+)$1	1	87	91	12.0000
....	chr1:249142889-249143129(+)$1	1	63	67	12.0000
....	chr15:69739141-69739381(+)$1	1	40	44	12.0000
....	chr3:49050494-49050734(+)$1	1	130	134	12.0000
....	chr22:32353319-32353559(+)$1	1	4	8	12.0000
))))	chr16:66544054-66544304(-)$1	1	51	55	12.0000
)...	chr16:23076047-23076287(-)$1	1	112	116	12.0000
....	chr14:61179720-61179960(-)$1	1	26	30	12.0000
.(((	chr11:134031625-134031865(-)$1	1	31	35	12.0000
((.(	chr10:124190356-124190677(+)$1	1	239	243	12.0000
....	chr3:57913131-57913371(+)$1	1	70	74	12.0000
....	chr1:110038290-110038530(+)$1	1	1	5	12.0000
...)	chr1:31345377-31345617(-)$1	1	164	168	12.0000
((..	chr3:10191901-10192141(+)$1	1	103	107	12.0000
((((	chr11:8968904-8969144(-)$1	1	34	38	12.0000
))))	chr10:69676689-69676929(+)$1	1	84	88	12.0000
....	chr7:101892818-101893058(+)$1	1	28	32	12.0000
....	chr11:130100288-130100528(-)$1	1	1	5	12.0000
)..)	chr19:58051227-58051467(+)$1	1	128	132	12.0000
.(((	chr3:172348618-172348858(-)$1	1	61	65	12.0000
(...	chr6:33424759-33425006(+)$1	1	36	40	12.0000
..))	chr17:12044887-12045127(+)$1	1	184	188	12.0000
))).	chr8:21961673-21961913(+)$1	1	156	160	12.0000
))))	chr5:179032784-179033024(-)$1	1	119	123	12.0000
((((	chr5:137804809-137805089(+)$1	1	61	65	12.0000
....	chr11:3381272-3381512(-)$1	1	2	6	12.0000
((((	chr1:6245438-6245678(-)$1	1	164	168	12.0000
.(((	chr18:9546761-9547001(-)$1	1	20	24	12.0000
.)))	chr7:90044105-90044425(+)$1	1	119	123	12.0000
(...	chr5:114950854-114951100(-)$1	1	53	57	12.0000
((((	chr1:26158999-26159239(+)$1	1	199	203	12.0000
....	chr12:50156572-50156892(+)$1	1	121	125	12.0000
(...	chrX:70795534-70795774(+)$1	1	5	9	12.0000
(...	chr1:24088119-24088439(+)$1	1	122	126	12.0000
((..	chr15:66628986-66629226(-)$1	1	93	97	12.0000
(((.	chr13:23929171-23929411(-)$1	1	6	10	12.0000
))).	chr17:56422457-56422697(-)$1	1	148	152	12.0000
....	chr1:53290815-53291055(+)$1	1	59	63	12.0000
....	chr1:229577535-229577775(-)$1	1	125	129	12.0000
)..)	chr10:112045967-112046207(+)$1	1	136	140	12.0000
((((	chr4:40425276-40425516(-)$1	1	27	31	12.0000
((..	chr22:29183419-29183659(+)$1	1	212	216	12.0000
((((	chr3:39183519-39183760(-)$1	1	8	12	12.0000
((((	chr20:48521140-48521380(-)$1	1	76	80	12.0000
)...	chr3:53276088-53276328(-)$1	1	115	119	12.0000
....	chr16:11962706-11962946(-)$1	1	18	22	12.0000
))))	chr6:138412338-138412578(-)$1	1	49	53	12.0000
....	chr22:29450809-29451049(+)$1	1	15	19	12.0000
((((	chr9:124103305-124103545(-)$1	1	117	121	12.0000
....	chr5:148731457-148731709(+)$1	1	48	52	12.0000
..))	chr1:89426968-89427208(-)$1	1	218	222	12.0000
....	chr3:129273984-129274224(-)$1	1	137	141	12.0000
....	chr2:63273461-63273701(+)$1	1	55	59	12.0000
))..	chr9:101979242-101979482(-)$1	1	122	126	12.0000
....	chr19:16685804-16686044(-)$1	1	12	16	12.0000
))))	chr2:55199657-55199897(-)$1	1	79	83	12.0000
((((	chr6:28871827-28872067(-)$1	1	57	61	12.0000
((((	chr3:179110658-179110898(+)$1	1	26	30	12.0000
((((	chr1:231696785-231697025(+)$1	1	71	75	12.0000
....	chr5:41917634-41917882(+)$1	1	43	47	12.0000
(.((	chr6:79650273-79650513(-)$1	1	24	28	12.0000
.(((	chr11:20405003-20405243(+)$1	1	24	28	12.0000
....	chr9:82339889-82340129(+)$1	1	20	24	12.0000
....	chr12:69971137-69971377(+)$1	1	16	20	12.0000
..((	chr5:38475353-38475593(-)$1	1	13	17	12.0000
....	chr11:6703078-6703325(-)$1	1	26	30	12.0000
....	chr11:6504532-6504772(+)$1	1	32	36	12.0000
(..(	chr6:2785505-2785745(+)$1	1	42	46	12.0000

#PSSM
C : 0.97	c : 0.02	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_UTR_m3_run1.nuc.txt

#NT
UCCU	chr1:45212303-45212528(+)$1	225	55	59	11.9999
UCCU	chr16:75611314-75611543(+)$1	229	102	106	11.9999
UCCU	chr19:37035495-37035735(-)$1	240	129	133	11.9999
UCCU	chr1:85784667-85784896(-)$1	229	135	139	11.9999
UCCU	chr16:31925826-31926050(+)$1	224	167	171	11.9999
UCCU	chrX:46920047-46920277(+)$1	230	45	49	11.9999
UCCU	chr1:229643931-229644166(-)$1	235	146	150	11.9999
uCCU	chr19:15348209-15348467(-)$1	258	82	86	11.9999
UCCU	chr17:43002195-43002429(-)$1	234	44	48	11.9999
UCCU	chr19:46273209-46273452(-)$1	243	94	98	11.9999
UCCU	chr17:8108565-8108801(-)$1	236	48	52	11.9999
UCCU	chr14:104025482-104025713(-)$1	231	42	46	11.9999
UCCU	chr7:48015827-48016061(-)$1	234	55	59	11.9999
UCCU	chr20:61920242-61920465(+)$1	223	17	21	11.9999
UCCU	chr7:99217099-99217329(+)$1	230	22	26	11.9999
UCCU	chr18:657750-657979(+)$1	229	110	114	11.9999
UCCU	chr7:75956031-75956257(-)$1	226	65	69	11.9999
UCCU	chr1:67878690-67878937(-)$1	247	5	9	11.9999
UCCU	chr19:12826400-12826631(-)$1	231	58	62	11.9999
UCCU	chr19:39979153-39979383(+)$1	230	174	178	11.9999
UCCU	chr19:1434978-1435206(+)$1	228	214	218	11.9999
UCCU	chr15:66180302-66180553(+)$1	251	0	4	11.9999
UCCU	chr14:102547510-102547748(-)$1	238	143	147	11.9999
UCCU	chr17:73775688-73775941(-)$1	253	145	149	11.9999
UCCU	chr13:111291420-111291657(+)$1	237	144	148	11.9999
UCCU	chr22:29191097-29191324(-)$1	227	18	22	11.9999
UCCU	chr3:160969785-160970008(+)$1	223	75	79	11.9999
UCCU	chr1:32798763-32798990(+)$1	227	160	164	11.9999
UCCU	chr19:13250020-13250271(+)$1	251	104	108	11.9999
UCCU	chr12:110972589-110972808(-)$1	219	97	101	11.9999
UCCU	chr3:50362941-50363172(-)$1	231	54	58	11.9999
UCCU	chr17:26687713-26687942(+)$1	229	32	36	11.9999
UCCU	chr19:3976034-3976280(-)$1	246	153	157	11.9999
UCCU	chr19:12242400-12242629(-)$1	229	212	216	11.9999
UCCU	chr12:111158395-111158670(-)$1	275	10	14	11.9999
UCCU	chr19:54963178-54963409(+)$1	231	75	79	11.9999
UCCU	chr3:184043173-184043406(+)$1	233	1	5	11.9999
UCCU	chr20:62612455-62612701(+)$1	246	108	112	11.9999
UCCU	chr17:2227895-2228124(-)$1	229	86	90	11.9999
UCCU	chr15:75144321-75144557(-)$1	236	199	203	11.9999
UCCU	chr5:38942214-38942443(-)$1	229	32	36	11.9999
UCCU	chr19:33872241-33872464(+)$1	223	49	53	11.9999
UCCU	chr2:174228470-174228712(+)$1	242	61	65	11.9999
UCCU	chr19:18120521-18120742(+)$1	221	58	62	11.9999
UCCU	chr14:54944505-54944754(-)$1	249	56	60	11.9999
UCCU	chr17:79477108-79477337(-)$1	229	97	101	11.9999
UCCU	chr6:76344392-76344627(+)$1	235	214	218	11.9999
UCCU	chr6:52149324-52149554(-)$1	230	31	35	11.9999
UCCU	chr5:154255766-154255996(+)$1	230	13	17	11.9999
UCCU	chr19:50000449-50000685(+)$1	236	53	57	11.9999
UCCU	chr17:4083019-4083247(-)$1	228	66	70	11.9999
UCCU	chr22:35660668-35660897(+)$1	229	112	116	11.9999
UCCU	chr14:20926027-20926257(-)$1	230	8	12	11.9999
UCCU	chr7:42956900-42957143(-)$1	243	111	115	11.9999
UCCU	chr5:68473421-68473652(+)$1	231	182	186	11.9999
UCCU	chr5:157187297-157187524(+)$1	227	50	54	11.9999
UCCU	chr17:40925407-40925647(+)$1	240	47	51	11.9999
UCCU	chr5:172742574-172742803(-)$1	229	71	75	11.9999
UCCU	chr19:9546063-9546308(-)$1	245	13	17	11.9999
UCCU	chr17:47131580-47131810(+)$1	230	85	89	11.9999
UCCU	chr1:212619294-212619521(+)$1	227	116	120	11.9999
UCCU	chr19:1576747-1576972(-)$1	225	73	77	11.9999
UCCU	chr9:80333120-80333347(-)$1	227	204	208	11.9999
UCCU	chr7:97481546-97481789(-)$1	243	59	63	11.9999
UCCU	chr12:89983904-89984140(-)$1	236	130	134	11.9999
UCCU	chr2:190339334-190339562(+)$1	228	130	134	11.9999
UCCU	chr14:64855015-64855248(+)$1	233	56	60	11.9999
UCCU	chr22:41924464-41924695(+)$1	231	9	13	11.9999
UCCU	chr4:39784149-39784373(+)$1	224	43	47	11.9999
UCCU	chr12:50821565-50821789(+)$1	224	8	12	11.9999
UCCU	chr3:156874689-156874922(-)$1	233	228	232	11.9999
UCCU	chr3:195776360-195776595(-)$1	235	125	129	11.9999
UCCU	chr16:87864761-87864984(-)$1	223	144	148	11.9999

#otherMatches

#Struct PSSM
CCDD	chr19:49119242-49119471(-)$1	229	52	56	11.9999
9999	chr1:45212303-45212528(+)$1	225	55	59	11.9999
GGGG	chr16:75611314-75611543(+)$1	229	102	106	11.9999
gggg	chr19:37035495-37035735(-)$1	240	129	133	11.9999
ffff	chr1:85784667-85784896(-)$1	229	135	139	11.9999
cc55	chr16:31925826-31926050(+)$1	224	167	171	11.9999
dddd	chrX:46920047-46920277(+)$1	230	45	49	11.9999
ff33	chr1:229643931-229644166(-)$1	235	146	150	11.9999
::::	chr19:15348209-15348467(-)$1	258	82	86	11.9999
nbb]	chr17:43002195-43002429(-)$1	234	44	48	11.9999
ssss	chr19:46273209-46273452(-)$1	243	94	98	11.9999
dddd	chr17:8108565-8108801(-)$1	236	48	52	11.9999
Eggg	chr14:104025482-104025713(-)$1	231	42	46	11.9999
TTTT	chr7:48015827-48016061(-)$1	234	55	59	11.9999
oddd	chr20:61920242-61920465(+)$1	223	17	21	11.9999
II{C	chr7:99217099-99217329(+)$1	230	22	26	11.9999
ccc]	chr18:657750-657979(+)$1	229	110	114	11.9999
d[gg	chr7:75956031-75956257(-)$1	226	65	69	11.9999
BBBB	chr1:67878690-67878937(-)$1	247	5	9	11.9999
ccc:	chr19:12826400-12826631(-)$1	231	58	62	11.9999
hhhh	chr19:39979153-39979383(+)$1	230	174	178	11.9999
JJJJ	chr19:1434978-1435206(+)$1	228	214	218	11.9999
:::e	chr15:66180302-66180553(+)$1	251	0	4	11.9999
mmmm	chr14:102547510-102547748(-)$1	238	143	147	11.9999
eee[	chr17:73775688-73775941(-)$1	253	145	149	11.9999
eeee	chr13:111291420-111291657(+)$1	237	144	148	11.9999
DDDD	chr22:29191097-29191324(-)$1	227	18	22	11.9999
b]cc	chr3:160969785-160970008(+)$1	223	75	79	11.9999
ccc[	chr1:32798763-32798990(+)$1	227	160	164	11.9999
CCC{	chr19:13250020-13250271(+)$1	251	104	108	11.9999
::::	chr12:110972589-110972808(-)$1	219	97	101	11.9999
oooo	chr3:50362941-50363172(-)$1	231	54	58	11.9999
{EEE	chr17:26687713-26687942(+)$1	229	32	36	11.9999
meee	chr19:3976034-3976280(-)$1	246	153	157	11.9999
ccc]	chr19:12242400-12242629(-)$1	229	212	216	11.9999
HHHH	chr12:111158395-111158670(-)$1	275	10	14	11.9999
[bb!	chr19:54963178-54963409(+)$1	231	75	79	11.9999
::::	chr3:184043173-184043406(+)$1	233	1	5	11.9999
KDDD	chr20:62612455-62612701(+)$1	246	108	112	11.9999
h]bb	chr17:2227895-2228124(-)$1	229	86	90	11.9999
qqqq	chr15:75144321-75144557(-)$1	236	199	203	11.9999
NNCC	chr5:38942214-38942443(-)$1	229	32	36	11.9999
cccy	chr19:33872241-33872464(+)$1	223	49	53	11.9999
%%bb	chr2:174228470-174228712(+)$1	242	61	65	11.9999
qqqq	chr19:18120521-18120742(+)$1	221	58	62	11.9999
FFFF	chr14:54944505-54944754(-)$1	249	56	60	11.9999
rrrr	chr17:79477108-79477337(-)$1	229	97	101	11.9999
:::F	chr6:76344392-76344627(+)$1	235	214	218	11.9999
BBEE	chr6:52149324-52149554(-)$1	230	31	35	11.9999
ddd[	chr5:154255766-154255996(+)$1	230	13	17	11.9999
ddee	chr19:50000449-50000685(+)$1	236	53	57	11.9999
GGGG	chr17:4083019-4083247(-)$1	228	66	70	11.9999
HHHH	chr22:35660668-35660897(+)$1	229	112	116	11.9999
hhhh	chr14:20926027-20926257(-)$1	230	8	12	11.9999
++++	chr7:42956900-42957143(-)$1	243	111	115	11.9999
ccee	chr5:68473421-68473652(+)$1	231	182	186	11.9999
b333	chr5:157187297-157187524(+)$1	227	50	54	11.9999
hbbo	chr17:40925407-40925647(+)$1	240	47	51	11.9999
e[dd	chr5:172742574-172742803(-)$1	229	71	75	11.9999
[ggg	chr19:9546063-9546308(-)$1	245	13	17	11.9999
eeel	chr17:47131580-47131810(+)$1	230	85	89	11.9999
ffff	chr1:212619294-212619521(+)$1	227	116	120	11.9999
gggg	chr19:1576747-1576972(-)$1	225	73	77	11.9999
}CCC	chr9:80333120-80333347(-)$1	227	204	208	11.9999
^^^^	chr7:97481546-97481789(-)$1	243	59	63	11.9999
cc]e	chr12:89983904-89984140(-)$1	236	130	134	11.9999
DDRR	chr2:190339334-190339562(+)$1	228	130	134	11.9999
mddd	chr14:64855015-64855248(+)$1	233	56	60	11.9999
ffff	chr22:41924464-41924695(+)$1	231	9	13	11.9999
eeee	chr4:39784149-39784373(+)$1	224	43	47	11.9999
uuuu	chr12:50821565-50821789(+)$1	224	8	12	11.9999
::::	chr3:156874689-156874922(-)$1	233	228	232	11.9999
::::	chr3:195776360-195776595(-)$1	235	125	129	11.9999
dddd	chr16:87864761-87864984(-)$1	223	144	148	11.9999

#DB
((((	chr19:49119242-49119471(-)$1	1	52	56	11.9999
....	chr1:45212303-45212528(+)$1	1	55	59	11.9999
((((	chr16:75611314-75611543(+)$1	1	102	106	11.9999
((((	chr19:37035495-37035735(-)$1	1	129	133	11.9999
))))	chr1:85784667-85784896(-)$1	1	135	139	11.9999
))..	chr16:31925826-31926050(+)$1	1	167	171	11.9999
((((	chrX:46920047-46920277(+)$1	1	45	49	11.9999
))..	chr1:229643931-229644166(-)$1	1	146	150	11.9999
....	chr19:15348209-15348467(-)$1	1	82	86	11.9999
.)).	chr17:43002195-43002429(-)$1	1	44	48	11.9999
....	chr19:46273209-46273452(-)$1	1	94	98	11.9999
))))	chr17:8108565-8108801(-)$1	1	48	52	11.9999
((((	chr14:104025482-104025713(-)$1	1	42	46	11.9999
....	chr7:48015827-48016061(-)$1	1	55	59	11.9999
.)))	chr20:61920242-61920465(+)$1	1	17	21	11.9999
((.(	chr7:99217099-99217329(+)$1	1	22	26	11.9999
))).	chr18:657750-657979(+)$1	1	110	114	11.9999
(.((	chr7:75956031-75956257(-)$1	1	65	69	11.9999
((((	chr1:67878690-67878937(-)$1	1	5	9	11.9999
))).	chr19:12826400-12826631(-)$1	1	58	62	11.9999
((((	chr19:39979153-39979383(+)$1	1	174	178	11.9999
))))	chr19:1434978-1435206(+)$1	1	214	218	11.9999
...(	chr15:66180302-66180553(+)$1	1	0	4	11.9999
....	chr14:102547510-102547748(-)$1	1	143	147	11.9999
(((.	chr17:73775688-73775941(-)$1	1	145	149	11.9999
))))	chr13:111291420-111291657(+)$1	1	144	148	11.9999
((((	chr22:29191097-29191324(-)$1	1	18	22	11.9999
).))	chr3:160969785-160970008(+)$1	1	75	79	11.9999
(((.	chr1:32798763-32798990(+)$1	1	160	164	11.9999
(((.	chr19:13250020-13250271(+)$1	1	104	108	11.9999
....	chr12:110972589-110972808(-)$1	1	97	101	11.9999
....	chr3:50362941-50363172(-)$1	1	54	58	11.9999
.(((	chr17:26687713-26687942(+)$1	1	32	36	11.9999
.)))	chr19:3976034-3976280(-)$1	1	153	157	11.9999
))).	chr19:12242400-12242629(-)$1	1	212	216	11.9999
((((	chr12:111158395-111158670(-)$1	1	10	14	11.9999
.((.	chr19:54963178-54963409(+)$1	1	75	79	11.9999
....	chr3:184043173-184043406(+)$1	1	1	5	11.9999
.(((	chr20:62612455-62612701(+)$1	1	108	112	11.9999
).))	chr17:2227895-2228124(-)$1	1	86	90	11.9999
....	chr15:75144321-75144557(-)$1	1	199	203	11.9999
..((	chr5:38942214-38942443(-)$1	1	32	36	11.9999
(((.	chr19:33872241-33872464(+)$1	1	49	53	11.9999
..((	chr2:174228470-174228712(+)$1	1	61	65	11.9999
....	chr19:18120521-18120742(+)$1	1	58	62	11.9999
((((	chr14:54944505-54944754(-)$1	1	56	60	11.9999
....	chr17:79477108-79477337(-)$1	1	97	101	11.9999
...)	chr6:76344392-76344627(+)$1	1	214	218	11.9999
((((	chr6:52149324-52149554(-)$1	1	31	35	11.9999
(((.	chr5:154255766-154255996(+)$1	1	13	17	11.9999
))))	chr19:50000449-50000685(+)$1	1	53	57	11.9999
((((	chr17:4083019-4083247(-)$1	1	66	70	11.9999
((((	chr22:35660668-35660897(+)$1	1	112	116	11.9999
((((	chr14:20926027-20926257(-)$1	1	8	12	11.9999
....	chr7:42956900-42957143(-)$1	1	111	115	11.9999
((((	chr5:68473421-68473652(+)$1	1	182	186	11.9999
)...	chr5:157187297-157187524(+)$1	1	50	54	11.9999
(((.	chr17:40925407-40925647(+)$1	1	47	51	11.9999
(.((	chr5:172742574-172742803(-)$1	1	71	75	11.9999
.(((	chr19:9546063-9546308(-)$1	1	13	17	11.9999
(((.	chr17:47131580-47131810(+)$1	1	85	89	11.9999
))))	chr1:212619294-212619521(+)$1	1	116	120	11.9999
))))	chr19:1576747-1576972(-)$1	1	73	77	11.9999
.)))	chr9:80333120-80333347(-)$1	1	204	208	11.9999
....	chr7:97481546-97481789(-)$1	1	59	63	11.9999
)).)	chr12:89983904-89984140(-)$1	1	130	134	11.9999
((..	chr2:190339334-190339562(+)$1	1	130	134	11.9999
.)))	chr14:64855015-64855248(+)$1	1	56	60	11.9999
((((	chr22:41924464-41924695(+)$1	1	9	13	11.9999
((((	chr4:39784149-39784373(+)$1	1	43	47	11.9999
....	chr12:50821565-50821789(+)$1	1	8	12	11.9999
....	chr3:156874689-156874922(-)$1	1	228	232	11.9999
....	chr3:195776360-195776595(-)$1	1	125	129	11.9999
))))	chr16:87864761-87864984(-)$1	1	144	148	11.9999

#PSSM
U : 0.98	u : 0.01	
C : 0.99	
C : 0.99	
U : 0.99	

#score	887.9999999999995
#seq	74
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m1_run2.nuc.txt

#NT
UUUCU	chr1:222818837-222819053(+)$1	216	22	27	15.0000
UUUCU	chr3:15064667-15064874(+)$1	207	3	8	15.0000
UUUCU	chrX:106890785-106891008(+)$1	223	118	123	15.0000
UUUCU	chrM:9835-10051(+)$1	216	122	127	15.0000
UUUCU	chr1:163043180-163043403(-)$1	223	69	74	15.0000
UUUCU	chr20:30784512-30784735(-)$1	223	73	78	15.0000
UUUCU	chr2:170663201-170663431(+)$1	230	73	78	15.0000
UUUCU	chr1:150413310-150413540(+)$1	230	26	31	15.0000
UUUCU	chr1:150550706-150550960(-)$1	254	107	112	15.0000
UUUCU	chr16:11940576-11940800(-)$1	224	41	46	15.0000
UUUCU	chr17:40483403-40483615(-)$1	212	51	56	15.0000
UUUCU	chr14:24632143-24632364(+)$1	221	19	24	15.0000
UUUCU	chr18:21046067-21046288(+)$1	221	196	201	15.0000
UUUCU	chr1:54675676-54675898(+)$1	222	181	186	15.0000
UUUCU	chr21:15884696-15884919(-)$1	223	16	21	15.0000
uuucu	chr18:12986746-12986978(+)$1	232	5	10	15.0000
UUUCU	chr4:48371873-48372099(+)$1	226	179	184	15.0000
UUUCU	chr6:28195611-28195834(+)$1	223	207	212	15.0000
UUUCU	chr15:63419459-63419686(+)$1	227	39	44	15.0000
UUUCU	chr10:70765475-70765692(+)$1	217	1	6	15.0000
UUUCU	chr5:118183788-118184010(-)$1	222	116	121	15.0000
UUUCU	chr22:41574807-41575039(+)$1	232	25	30	15.0000
UUUCU	chr11:7614270-7614491(+)$1	221	76	81	15.0000
UUUCU	chr12:6700814-6701039(-)$1	225	11	16	15.0000
UUUCU	chr17:57682423-57682643(+)$1	220	39	44	15.0000
UUUCU	chr9:115232614-115232840(+)$1	226	84	89	15.0000
UUUCU	chr1:201843292-201843515(+)$1	223	70	75	15.0000
UUUCU	chr3:69113121-69113342(-)$1	221	113	118	15.0000
UUUCU	chr2:190682645-190682864(+)$1	219	77	82	15.0000
UUUCU	chrX:79999526-79999746(-)$1	220	76	81	15.0000
UUUCU	chr8:15516932-15517162(+)$1	230	4	9	15.0000
UUUCU	chr2:100055245-100055479(-)$1	234	94	99	15.0000
UUUCU	chrX:16870603-16870828(-)$1	225	68	73	15.0000
UUUCU	chr8:86021768-86021993(+)$1	225	49	54	15.0000
UUUCU	chr16:69368519-69368742(-)$1	223	217	222	15.0000
UUUCU	chr7:135287492-135287711(+)$1	219	34	39	15.0000
UUUCU	chrX:75396660-75396878(+)$1	218	172	177	15.0000
UUUCU	chr9:15486803-15487017(-)$1	214	203	208	15.0000
UUUCU	chr16:14327928-14328152(+)$1	224	16	21	15.0000
UUUCU	chr12:57036357-57036601(-)$1	244	184	189	15.0000
UUUCU	chr2:183860435-183860666(-)$1	231	119	124	15.0000
UUUCU	chr7:77402375-77402598(+)$1	223	68	73	15.0000
UUUCU	chr3:32576012-32576229(-)$1	217	69	74	15.0000
UUUCU	chr8:71126068-71126324(-)$1	256	0	5	15.0000
UUUCU	chr20:49510883-49511114(-)$1	231	82	87	15.0000
UUUCU	chr1:70736491-70736713(-)$1	222	54	59	15.0000
UUUCU	chr12:121157680-121157904(+)$1	224	15	20	15.0000
UUUCU	chr17:17965093-17965310(+)$1	217	71	76	15.0000
UUUCU	chr3:25671825-25672055(-)$1	230	22	27	15.0000
UUUCU	chr11:57505334-57505552(+)$1	218	111	116	15.0000
UUUCU	chr5:145539893-145540114(-)$1	221	27	32	15.0000
UUUCU	chr1:16055100-16055323(+)$1	223	99	104	15.0000
UUUCU	chr14:96986297-96986569(+)$1	272	22	27	15.0000
uuucu	chr1:14068530-14068752(+)$1	222	174	179	15.0000
UUUCU	chr11:118453902-118454125(+)$1	223	210	215	15.0000
UUUCU	chr12:106729432-106729667(+)$1	235	38	43	15.0000
UUUCU	chr9:21334345-21334569(-)$1	224	54	59	15.0000

#otherMatches

#Struct PSSM
ggggg	chr9:77632106-77632331(-)$1	225	49	54	15.0000
EEEDD	chr1:222818837-222819053(+)$1	216	22	27	15.0000
GGGGG	chr3:15064667-15064874(+)$1	207	3	8	15.0000
hhddd	chrX:106890785-106891008(+)$1	223	118	123	15.0000
$$$$$	chrM:9835-10051(+)$1	216	122	127	15.0000
^^^^^	chr1:163043180-163043403(-)$1	223	69	74	15.0000
::::f	chr20:30784512-30784735(-)$1	223	73	78	15.0000
""eee	chr2:170663201-170663431(+)$1	230	73	78	15.0000
hhhhh	chr1:150413310-150413540(+)$1	230	26	31	15.0000
cccbb	chr1:150550706-150550960(-)$1	254	107	112	15.0000
=====	chr16:11940576-11940800(-)$1	224	41	46	15.0000
=====	chr17:40483403-40483615(-)$1	212	51	56	15.0000
cc[gg	chr14:24632143-24632364(+)$1	221	19	24	15.0000
ggggg	chr18:21046067-21046288(+)$1	221	196	201	15.0000
JJJJJ	chr1:54675676-54675898(+)$1	222	181	186	15.0000
fffff	chr21:15884696-15884919(-)$1	223	16	21	15.0000
:::::	chr18:12986746-12986978(+)$1	232	5	10	15.0000
boooo	chr4:48371873-48372099(+)$1	226	179	184	15.0000
33ddd	chr6:28195611-28195834(+)$1	223	207	212	15.0000
FFFFF	chr15:63419459-63419686(+)$1	227	39	44	15.0000
:::::	chr10:70765475-70765692(+)$1	217	1	6	15.0000
333bb	chr5:118183788-118184010(-)$1	222	116	121	15.0000
cnnnn	chr22:41574807-41575039(+)$1	232	25	30	15.0000
:::::	chr11:7614270-7614491(+)$1	221	76	81	15.0000
:::::	chr12:6700814-6701039(-)$1	225	11	16	15.0000
=====	chr17:57682423-57682643(+)$1	220	39	44	15.0000
^^^^^	chr9:115232614-115232840(+)$1	226	84	89	15.0000
f]eee	chr1:201843292-201843515(+)$1	223	70	75	15.0000
&&&&&	chr3:69113121-69113342(-)$1	221	113	118	15.0000
33fff	chr2:190682645-190682864(+)$1	219	77	82	15.0000
mmbb]	chrX:79999526-79999746(-)$1	220	76	81	15.0000
::EEE	chr8:15516932-15517162(+)$1	230	4	9	15.0000
qdddd	chr2:100055245-100055479(-)$1	234	94	99	15.0000
:::::	chrX:16870603-16870828(-)$1	225	68	73	15.0000
:dddd	chr8:86021768-86021993(+)$1	225	49	54	15.0000
HHHHH	chr16:69368519-69368742(-)$1	223	217	222	15.0000
mmeee	chr7:135287492-135287711(+)$1	219	34	39	15.0000
ggggg	chrX:75396660-75396878(+)$1	218	172	177	15.0000
::::F	chr9:15486803-15487017(-)$1	214	203	208	15.0000
::eee	chr16:14327928-14328152(+)$1	224	16	21	15.0000
=====	chr12:57036357-57036601(-)$1	244	184	189	15.0000
hhhhh	chr2:183860435-183860666(-)$1	231	119	124	15.0000
ddd[e	chr7:77402375-77402598(+)$1	223	68	73	15.0000
ldddd	chr3:32576012-32576229(-)$1	217	69	74	15.0000
:::FF	chr8:71126068-71126324(-)$1	256	0	5	15.0000
ddd$$	chr20:49510883-49511114(-)$1	231	82	87	15.0000
%%%%%	chr1:70736491-70736713(-)$1	222	54	59	15.0000
:::GG	chr12:121157680-121157904(+)$1	224	15	20	15.0000
lllcc	chr17:17965093-17965310(+)$1	217	71	76	15.0000
C{EEE	chr3:25671825-25672055(-)$1	230	22	27	15.0000
+++++	chr11:57505334-57505552(+)$1	218	111	116	15.0000
FFFFF	chr5:145539893-145540114(-)$1	221	27	32	15.0000
ddooo	chr1:16055100-16055323(+)$1	223	99	104	15.0000
JJJJJ	chr14:96986297-96986569(+)$1	272	22	27	15.0000
JJ:::	chr1:14068530-14068752(+)$1	222	174	179	15.0000
dGGGG	chr11:118453902-118454125(+)$1	223	210	215	15.0000
gggg"	chr12:106729432-106729667(+)$1	235	38	43	15.0000
::::c	chr9:21334345-21334569(-)$1	224	54	59	15.0000

#DB
)))))	chr9:77632106-77632331(-)$1	1	49	54	15.0000
(((((	chr1:222818837-222819053(+)$1	1	22	27	15.0000
(((((	chr3:15064667-15064874(+)$1	1	3	8	15.0000
(((((	chrX:106890785-106891008(+)$1	1	118	123	15.0000
.....	chrM:9835-10051(+)$1	1	122	127	15.0000
.....	chr1:163043180-163043403(-)$1	1	69	74	15.0000
....(	chr20:30784512-30784735(-)$1	1	73	78	15.0000
..(((	chr2:170663201-170663431(+)$1	1	73	78	15.0000
(((((	chr1:150413310-150413540(+)$1	1	26	31	15.0000
(((((	chr1:150550706-150550960(-)$1	1	107	112	15.0000
(((((	chr16:11940576-11940800(-)$1	1	41	46	15.0000
)))))	chr17:40483403-40483615(-)$1	1	51	56	15.0000
((.((	chr14:24632143-24632364(+)$1	1	19	24	15.0000
(((((	chr18:21046067-21046288(+)$1	1	196	201	15.0000
)))))	chr1:54675676-54675898(+)$1	1	181	186	15.0000
(((((	chr21:15884696-15884919(-)$1	1	16	21	15.0000
.....	chr18:12986746-12986978(+)$1	1	5	10	15.0000
(....	chr4:48371873-48372099(+)$1	1	179	184	15.0000
..)))	chr6:28195611-28195834(+)$1	1	207	212	15.0000
(((((	chr15:63419459-63419686(+)$1	1	39	44	15.0000
.....	chr10:70765475-70765692(+)$1	1	1	6	15.0000
...))	chr5:118183788-118184010(-)$1	1	116	121	15.0000
(....	chr22:41574807-41575039(+)$1	1	25	30	15.0000
.....	chr11:7614270-7614491(+)$1	1	76	81	15.0000
.....	chr12:6700814-6701039(-)$1	1	11	16	15.0000
(((((	chr17:57682423-57682643(+)$1	1	39	44	15.0000
.....	chr9:115232614-115232840(+)$1	1	84	89	15.0000
).)))	chr1:201843292-201843515(+)$1	1	70	75	15.0000
.....	chr3:69113121-69113342(-)$1	1	113	118	15.0000
..)))	chr2:190682645-190682864(+)$1	1	77	82	15.0000
..)).	chrX:79999526-79999746(-)$1	1	76	81	15.0000
..(((	chr8:15516932-15517162(+)$1	1	4	9	15.0000
.))))	chr2:100055245-100055479(-)$1	1	94	99	15.0000
.....	chrX:16870603-16870828(-)$1	1	68	73	15.0000
.((((	chr8:86021768-86021993(+)$1	1	49	54	15.0000
)))))	chr16:69368519-69368742(-)$1	1	217	222	15.0000
..)))	chr7:135287492-135287711(+)$1	1	34	39	15.0000
)))))	chrX:75396660-75396878(+)$1	1	172	177	15.0000
....)	chr9:15486803-15487017(-)$1	1	203	208	15.0000
..(((	chr16:14327928-14328152(+)$1	1	16	21	15.0000
)))))	chr12:57036357-57036601(-)$1	1	184	189	15.0000
(((((	chr2:183860435-183860666(-)$1	1	119	124	15.0000
(((.(	chr7:77402375-77402598(+)$1	1	68	73	15.0000
.))))	chr3:32576012-32576229(-)$1	1	69	74	15.0000
...((	chr8:71126068-71126324(-)$1	1	0	5	15.0000
(((..	chr20:49510883-49511114(-)$1	1	82	87	15.0000
.....	chr1:70736491-70736713(-)$1	1	54	59	15.0000
...((	chr12:121157680-121157904(+)$1	1	15	20	15.0000
...))	chr17:17965093-17965310(+)$1	1	71	76	15.0000
(.(((	chr3:25671825-25672055(-)$1	1	22	27	15.0000
.....	chr11:57505334-57505552(+)$1	1	111	116	15.0000
(((((	chr5:145539893-145540114(-)$1	1	27	32	15.0000
((...	chr1:16055100-16055323(+)$1	1	99	104	15.0000
(((((	chr14:96986297-96986569(+)$1	1	22	27	15.0000
))...	chr1:14068530-14068752(+)$1	1	174	179	15.0000
)))))	chr11:118453902-118454125(+)$1	1	210	215	15.0000
((((.	chr12:106729432-106729667(+)$1	1	38	43	15.0000
....(	chr9:21334345-21334569(-)$1	1	54	59	15.0000

#PSSM
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
C : 0.96	c : 0.03	
U : 0.96	u : 0.03	

#score	870.0000000000005
#seq	58
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m2_run1.nuc.txt

#NT
AAGA	chr16:339452-339674(-)$1	222	70	74	12.0000
AAGA	chr6:30577575-30577793(-)$1	218	97	101	12.0000
AAGA	chrX:24024131-24024357(-)$1	226	173	177	12.0000
AAGA	chr19:9676767-9676981(-)$1	214	6	10	12.0000
AAGA	chr2:232322303-232322530(-)$1	227	38	42	12.0000
AAGA	chr6:110428255-110428472(-)$1	217	86	90	12.0000
AAGA	chr2:230666902-230667121(-)$1	219	160	164	12.0000
AAGA	chr12:57037617-57037837(-)$1	220	35	39	12.0000
AAGA	chr11:17112852-17113072(-)$1	220	73	77	12.0000
AAGA	chr10:129903752-129903980(-)$1	228	65	69	12.0000
AAGA	chr3:15726750-15726968(-)$1	218	32	36	12.0000
AAGA	chr13:111114372-111114588(+)$1	216	53	57	12.0000
AAGA	chr1:229771008-229771224(+)$1	216	150	154	12.0000
AAGA	chr1:182850369-182850588(+)$1	219	199	203	12.0000
AAGA	chr5:139884668-139884885(+)$1	217	90	94	12.0000
AAGA	chr1:86167783-86168008(-)$1	225	134	138	12.0000
AAGA	chr1:39853671-39853890(+)$1	219	75	79	12.0000
AAGA	chr14:64473735-64473957(+)$1	222	69	73	12.0000
AAGA	chr6:26156630-26156866(+)$1	236	36	40	12.0000
AAGA	chr9:32543096-32543317(-)$1	221	134	138	12.0000
AAGA	chr15:35274504-35274729(-)$1	225	74	78	12.0000
AAGA	chr17:1563716-1563938(-)$1	222	120	124	12.0000
AAGA	chr1:23418614-23418834(-)$1	220	205	209	12.0000
AAGA	chr4:187628479-187628695(-)$1	216	211	215	12.0000
AAGA	chr12:6632033-6632257(+)$1	224	210	214	12.0000
AAGA	chr16:2813163-2813384(+)$1	221	140	144	12.0000
AAGA	chr14:95560188-95560407(-)$1	219	153	157	12.0000
AAGA	chr1:1696688-1696901(-)$1	213	69	73	12.0000
AAGA	chr5:162868812-162869031(+)$1	219	100	104	12.0000
AAGA	chr15:75684672-75684888(-)$1	216	8	12	12.0000
AAGA	chr2:128479313-128479544(-)$1	231	40	44	12.0000
AAGA	chr6:149699167-149699390(+)$1	223	36	40	12.0000
AAGA	chr5:74869463-74869681(+)$1	218	162	166	12.0000
AAGA	chr21:18970906-18971132(-)$1	226	37	41	12.0000
aaga	chr6:30550135-30550352(+)$1	217	45	49	12.0000
AAGA	chr2:69581526-69581747(-)$1	221	164	168	12.0000
AAGA	chr3:37365782-37366000(+)$1	218	96	100	12.0000
AAGA	chr16:70562749-70562971(+)$1	222	38	42	12.0000
AAGA	chr2:37455197-37455416(-)$1	219	55	59	12.0000
aaga	chr19:41781997-41782239(+)$1	242	11	15	12.0000
AAGA	chr5:176719027-176719243(+)$1	216	21	25	12.0000
AAGA	chr2:74057921-74058142(+)$1	221	96	100	12.0000
AAGA	chr16:85699688-85699906(+)$1	218	84	88	12.0000
AAGA	chr13:42876078-42876301(+)$1	223	60	64	12.0000
AAGA	chr1:171548424-171548646(+)$1	222	190	194	12.0000
AAGA	chr12:22622592-22622811(-)$1	219	97	101	12.0000
AAGA	chr14:95562062-95562287(-)$1	225	41	45	12.0000
AAGA	chr6:31631660-31631876(-)$1	216	174	178	12.0000
AAGA	chr18:32917225-32917448(-)$1	223	210	214	12.0000
AAGA	chr11:32955944-32956163(+)$1	219	178	182	12.0000
AAGA	chr20:30386095-30386315(+)$1	220	122	126	12.0000
AAGA	chr10:27406506-27406729(-)$1	223	5	9	12.0000
AAGA	chr13:31231968-31232189(+)$1	221	11	15	12.0000
AAGA	chr12:76446897-76447117(-)$1	220	12	16	12.0000
AAGA	chr22:32111595-32111817(-)$1	222	19	23	12.0000
AAGA	chr5:64959997-64960217(+)$1	220	31	35	12.0000
AAGA	chr1:120462120-120462336(-)$1	216	8	12	12.0000
AAGA	chr1:197061044-197061260(-)$1	216	154	158	12.0000
AAGA	chr21:34925159-34925396(+)$1	237	189	193	12.0000
AAGA	chr16:23690524-23690760(+)$1	236	17	21	12.0000
AAGA	chr1:62910690-62910911(+)$1	221	1	5	12.0000
AAGA	chr1:36213526-36213753(-)$1	227	166	170	12.0000
AAGA	chr9:96261044-96261268(+)$1	224	57	61	12.0000
AAGA	chr15:66794887-66795108(-)$1	221	177	181	12.0000
AAGA	chr9:135150596-135150814(-)$1	218	24	28	12.0000
AAGA	chr6:100988061-100988281(-)$1	220	25	29	12.0000
AAGA	chr17:57289044-57289271(+)$1	227	190	194	12.0000
AAGA	chr12:110760726-110760953(+)$1	227	125	129	12.0000
AAGA	chr1:214818230-214818458(+)$1	228	12	16	12.0000
AAGA	chr10:129904470-129904683(-)$1	213	68	72	12.0000
AAGA	chr1:6586736-6586954(-)$1	218	128	132	12.0000
AAGA	chr8:77617741-77617961(+)$1	220	2	6	12.0000
AAGA	chr6:143091269-143091489(-)$1	220	3	7	12.0000
AAGA	chr17:1782754-1782972(+)$1	218	116	120	12.0000
AAGA	chr14:103805954-103806180(+)$1	226	108	112	12.0000
AAGA	chr17:38569683-38569900(-)$1	217	90	94	12.0000
AAGA	chr17:1558618-1558843(-)$1	225	84	88	12.0000
AAGA	chr13:110434940-110435158(-)$1	218	73	77	12.0000
AAGA	chr1:24113749-24113963(+)$1	214	155	159	12.0000
AAGA	chr3:107881300-107881521(-)$1	221	30	34	12.0000
AAGA	chr20:35661087-35661310(-)$1	223	102	106	12.0000

#otherMatches

#Struct PSSM
:bb[	chr20:40033696-40033914(-)$1	218	59	63	12.0000
2ddd	chr16:339452-339674(-)$1	222	70	74	12.0000
uuuu	chr6:30577575-30577793(-)$1	218	97	101	12.0000
YYDD	chrX:24024131-24024357(-)$1	226	173	177	12.0000
e+++	chr19:9676767-9676981(-)$1	214	6	10	12.0000
ddd]	chr2:232322303-232322530(-)$1	227	38	42	12.0000
!!ee	chr6:110428255-110428472(-)$1	217	86	90	12.0000
====	chr2:230666902-230667121(-)$1	219	160	164	12.0000
qqqq	chr12:57037617-57037837(-)$1	220	35	39	12.0000
gggg	chr11:17112852-17113072(-)$1	220	73	77	12.0000
qqqq	chr10:129903752-129903980(-)$1	228	65	69	12.0000
eeee	chr3:15726750-15726968(-)$1	218	32	36	12.0000
iiii	chr13:111114372-111114588(+)$1	216	53	57	12.0000
%%%%	chr1:229771008-229771224(+)$1	216	150	154	12.0000
}HHH	chr1:182850369-182850588(+)$1	219	199	203	12.0000
g:::	chr5:139884668-139884885(+)$1	217	90	94	12.0000
fff]	chr1:86167783-86168008(-)$1	225	134	138	12.0000
:ccc	chr1:39853671-39853890(+)$1	219	75	79	12.0000
d:hh	chr14:64473735-64473957(+)$1	222	69	73	12.0000
beee	chr6:26156630-26156866(+)$1	236	36	40	12.0000
ppdd	chr9:32543096-32543317(-)$1	221	134	138	12.0000
HHHH	chr15:35274504-35274729(-)$1	225	74	78	12.0000
G}DD	chr17:1563716-1563938(-)$1	222	120	124	12.0000
pppb	chr1:23418614-23418834(-)$1	220	205	209	12.0000
FFFF	chr4:187628479-187628695(-)$1	216	211	215	12.0000
cFFF	chr12:6632033-6632257(+)$1	224	210	214	12.0000
::::	chr16:2813163-2813384(+)$1	221	140	144	12.0000
dd!!	chr14:95560188-95560407(-)$1	219	153	157	12.0000
::::	chr1:1696688-1696901(-)$1	213	69	73	12.0000
::::	chr5:162868812-162869031(+)$1	219	100	104	12.0000
::::	chr15:75684672-75684888(-)$1	216	8	12	12.0000
^^^^	chr2:128479313-128479544(-)$1	231	40	44	12.0000
cccc	chr6:149699167-149699390(+)$1	223	36	40	12.0000
22a]	chr5:74869463-74869681(+)$1	218	162	166	12.0000
eee:	chr21:18970906-18971132(-)$1	226	37	41	12.0000
cc44	chr6:30550135-30550352(+)$1	217	45	49	12.0000
eeee	chr2:69581526-69581747(-)$1	221	164	168	12.0000
eeee	chr3:37365782-37366000(+)$1	218	96	100	12.0000
hhmm	chr16:70562749-70562971(+)$1	222	38	42	12.0000
::::	chr2:37455197-37455416(-)$1	219	55	59	12.0000
::::	chr19:41781997-41782239(+)$1	242	11	15	12.0000
:ddd	chr5:176719027-176719243(+)$1	216	21	25	12.0000
nnnn	chr2:74057921-74058142(+)$1	221	96	100	12.0000
0000	chr16:85699688-85699906(+)$1	218	84	88	12.0000
c[cc	chr13:42876078-42876301(+)$1	223	60	64	12.0000
^^^^	chr1:171548424-171548646(+)$1	222	190	194	12.0000
eeee	chr12:22622592-22622811(-)$1	219	97	101	12.0000
qqqq	chr14:95562062-95562287(-)$1	225	41	45	12.0000
nnnn	chr6:31631660-31631876(-)$1	216	174	178	12.0000
gggg	chr18:32917225-32917448(-)$1	223	210	214	12.0000
hhhh	chr11:32955944-32956163(+)$1	219	178	182	12.0000
ooob	chr20:30386095-30386315(+)$1	220	122	126	12.0000
::BB	chr10:27406506-27406729(-)$1	223	5	9	12.0000
FFFF	chr13:31231968-31232189(+)$1	221	11	15	12.0000
IIII	chr12:76446897-76447117(-)$1	220	12	16	12.0000
qqqf	chr22:32111595-32111817(-)$1	222	19	23	12.0000
[hhh	chr5:64959997-64960217(+)$1	220	31	35	12.0000
eeeo	chr1:120462120-120462336(-)$1	216	8	12	12.0000
!a[d	chr1:197061044-197061260(-)$1	216	154	158	12.0000
::ee	chr21:34925159-34925396(+)$1	237	189	193	12.0000
pppp	chr16:23690524-23690760(+)$1	236	17	21	12.0000
FFFF	chr1:62910690-62910911(+)$1	221	1	5	12.0000
ffff	chr1:36213526-36213753(-)$1	227	166	170	12.0000
rrrr	chr9:96261044-96261268(+)$1	224	57	61	12.0000
::::	chr15:66794887-66795108(-)$1	221	177	181	12.0000
GG::	chr9:135150596-135150814(-)$1	218	24	28	12.0000
d[dd	chr6:100988061-100988281(-)$1	220	25	29	12.0000
JJJJ	chr17:57289044-57289271(+)$1	227	190	194	12.0000
%hhh	chr12:110760726-110760953(+)$1	227	125	129	12.0000
::::	chr1:214818230-214818458(+)$1	228	12	16	12.0000
eeee	chr10:129904470-129904683(-)$1	213	68	72	12.0000
eee[	chr1:6586736-6586954(-)$1	218	128	132	12.0000
C{BB	chr8:77617741-77617961(+)$1	220	2	6	12.0000
FFFF	chr6:143091269-143091489(-)$1	220	3	7	12.0000
mmmm	chr17:1782754-1782972(+)$1	218	116	120	12.0000
eeee	chr14:103805954-103806180(+)$1	226	108	112	12.0000
##cc	chr17:38569683-38569900(-)$1	217	90	94	12.0000
^^^^	chr17:1558618-1558843(-)$1	225	84	88	12.0000
::::	chr13:110434940-110435158(-)$1	218	73	77	12.0000
::::	chr1:24113749-24113963(+)$1	214	155	159	12.0000
mmmf	chr3:107881300-107881521(-)$1	221	30	34	12.0000
rrbb	chr20:35661087-35661310(-)$1	223	102	106	12.0000

#DB
.((.	chr20:40033696-40033914(-)$1	1	59	63	12.0000
.)))	chr16:339452-339674(-)$1	1	70	74	12.0000
....	chr6:30577575-30577793(-)$1	1	97	101	12.0000
..))	chrX:24024131-24024357(-)$1	1	173	177	12.0000
(...	chr19:9676767-9676981(-)$1	1	6	10	12.0000
))).	chr2:232322303-232322530(-)$1	1	38	42	12.0000
..((	chr6:110428255-110428472(-)$1	1	86	90	12.0000
((((	chr2:230666902-230667121(-)$1	1	160	164	12.0000
....	chr12:57037617-57037837(-)$1	1	35	39	12.0000
))))	chr11:17112852-17113072(-)$1	1	73	77	12.0000
....	chr10:129903752-129903980(-)$1	1	65	69	12.0000
((((	chr3:15726750-15726968(-)$1	1	32	36	12.0000
((((	chr13:111114372-111114588(+)$1	1	53	57	12.0000
....	chr1:229771008-229771224(+)$1	1	150	154	12.0000
.)))	chr1:182850369-182850588(+)$1	1	199	203	12.0000
)...	chr5:139884668-139884885(+)$1	1	90	94	12.0000
))).	chr1:86167783-86168008(-)$1	1	134	138	12.0000
.(((	chr1:39853671-39853890(+)$1	1	75	79	12.0000
).((	chr14:64473735-64473957(+)$1	1	69	73	12.0000
)(((	chr6:26156630-26156866(+)$1	1	36	40	12.0000
..))	chr9:32543096-32543317(-)$1	1	134	138	12.0000
((((	chr15:35274504-35274729(-)$1	1	74	78	12.0000
).))	chr17:1563716-1563938(-)$1	1	120	124	12.0000
...)	chr1:23418614-23418834(-)$1	1	205	209	12.0000
))))	chr4:187628479-187628695(-)$1	1	211	215	12.0000
))))	chr12:6632033-6632257(+)$1	1	210	214	12.0000
....	chr16:2813163-2813384(+)$1	1	140	144	12.0000
((..	chr14:95560188-95560407(-)$1	1	153	157	12.0000
....	chr1:1696688-1696901(-)$1	1	69	73	12.0000
....	chr5:162868812-162869031(+)$1	1	100	104	12.0000
....	chr15:75684672-75684888(-)$1	1	8	12	12.0000
....	chr2:128479313-128479544(-)$1	1	40	44	12.0000
)(((	chr6:149699167-149699390(+)$1	1	36	40	12.0000
..).	chr5:74869463-74869681(+)$1	1	162	166	12.0000
))).	chr21:18970906-18971132(-)$1	1	37	41	12.0000
))..	chr6:30550135-30550352(+)$1	1	45	49	12.0000
((((	chr2:69581526-69581747(-)$1	1	164	168	12.0000
((((	chr3:37365782-37366000(+)$1	1	96	100	12.0000
((..	chr16:70562749-70562971(+)$1	1	38	42	12.0000
....	chr2:37455197-37455416(-)$1	1	55	59	12.0000
....	chr19:41781997-41782239(+)$1	1	11	15	12.0000
.(((	chr5:176719027-176719243(+)$1	1	21	25	12.0000
....	chr2:74057921-74058142(+)$1	1	96	100	12.0000
....	chr16:85699688-85699906(+)$1	1	84	88	12.0000
(.((	chr13:42876078-42876301(+)$1	1	60	64	12.0000
....	chr1:171548424-171548646(+)$1	1	190	194	12.0000
))))	chr12:22622592-22622811(-)$1	1	97	101	12.0000
....	chr14:95562062-95562287(-)$1	1	41	45	12.0000
....	chr6:31631660-31631876(-)$1	1	174	178	12.0000
))))	chr18:32917225-32917448(-)$1	1	210	214	12.0000
((((	chr11:32955944-32956163(+)$1	1	178	182	12.0000
...)	chr20:30386095-30386315(+)$1	1	122	126	12.0000
..((	chr10:27406506-27406729(-)$1	1	5	9	12.0000
((((	chr13:31231968-31232189(+)$1	1	11	15	12.0000
((((	chr12:76446897-76447117(-)$1	1	12	16	12.0000
...)	chr22:32111595-32111817(-)$1	1	19	23	12.0000
.(((	chr5:64959997-64960217(+)$1	1	31	35	12.0000
(((.	chr1:120462120-120462336(-)$1	1	8	12	12.0000
.(.(	chr1:197061044-197061260(-)$1	1	154	158	12.0000
..((	chr21:34925159-34925396(+)$1	1	189	193	12.0000
....	chr16:23690524-23690760(+)$1	1	17	21	12.0000
((((	chr1:62910690-62910911(+)$1	1	1	5	12.0000
))))	chr1:36213526-36213753(-)$1	1	166	170	12.0000
....	chr9:96261044-96261268(+)$1	1	57	61	12.0000
....	chr15:66794887-66795108(-)$1	1	177	181	12.0000
((..	chr9:135150596-135150814(-)$1	1	24	28	12.0000
(.((	chr6:100988061-100988281(-)$1	1	25	29	12.0000
))))	chr17:57289044-57289271(+)$1	1	190	194	12.0000
.(((	chr12:110760726-110760953(+)$1	1	125	129	12.0000
....	chr1:214818230-214818458(+)$1	1	12	16	12.0000
((((	chr10:129904470-129904683(-)$1	1	68	72	12.0000
(((.	chr1:6586736-6586954(-)$1	1	128	132	12.0000
(.((	chr8:77617741-77617961(+)$1	1	2	6	12.0000
((((	chr6:143091269-143091489(-)$1	1	3	7	12.0000
....	chr17:1782754-1782972(+)$1	1	116	120	12.0000
((((	chr14:103805954-103806180(+)$1	1	108	112	12.0000
..((	chr17:38569683-38569900(-)$1	1	90	94	12.0000
....	chr17:1558618-1558843(-)$1	1	84	88	12.0000
....	chr13:110434940-110435158(-)$1	1	73	77	12.0000
....	chr1:24113749-24113963(+)$1	1	155	159	12.0000
...)	chr3:107881300-107881521(-)$1	1	30	34	12.0000
..))	chr20:35661087-35661310(-)$1	1	102	106	12.0000

#PSSM
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	
A : 0.97	a : 0.02	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m1_run2.nuc.txt

#NT
AAAAA	chr6:119135946-119136166(-)$1	220	167	172	15.0000
AAAAA	chr7:79841993-79842220(+)$1	227	144	149	15.0000
AAAAA	chr11:18031558-18031783(-)$1	225	105	110	15.0000
AAAAA	chr13:33017486-33017708(-)$1	222	19	24	15.0000
AAAAA	chr12:72176270-72176489(+)$1	219	11	16	15.0000
AAAAA	chr1:235938204-235938437(-)$1	233	193	198	15.0000
AAAAA	chr5:82876055-82876279(+)$1	224	108	113	15.0000
AAAAA	chr7:138268502-138268730(+)$1	228	116	121	15.0000
AAAAA	chr9:116812156-116812376(+)$1	220	36	41	15.0000
AAAAA	chr5:177632787-177633022(+)$1	235	55	60	15.0000
AAAAA	chr19:38229654-38229874(-)$1	220	79	84	15.0000
AAAAA	chr19:38126378-38126612(-)$1	234	138	143	15.0000
AAAAA	chr17:29676081-29676305(+)$1	224	6	11	15.0000
AAAAA	chr9:98774685-98774908(+)$1	223	133	138	15.0000
AAAAA	chr1:14107633-14107859(+)$1	226	50	55	15.0000
AAAAA	chr13:23909318-23909547(-)$1	229	116	121	15.0000
AAAAA	chr9:39086564-39086791(-)$1	227	10	15	15.0000
AAAAA	chr5:5463960-5464186(+)$1	226	137	142	15.0000
AAAAA	chr2:183790311-183790534(-)$1	223	191	196	15.0000
AAAAA	chr14:92609441-92609671(+)$1	230	104	109	15.0000
AAAAA	chr3:156645155-156645383(+)$1	228	144	149	15.0000
AAAAA	chrM:9958-10199(+)$1	241	90	95	15.0000
AAAAA	chr13:48942616-48942836(+)$1	220	70	75	15.0000
AAAAA	chr9:114476610-114476832(+)$1	222	46	51	15.0000
AAAAA	chr10:32328182-32328411(-)$1	229	210	215	15.0000
AAAAA	chr8:71486424-71486649(-)$1	225	61	66	15.0000
AAAAA	chr3:150281225-150281446(+)$1	221	15	20	15.0000
AAAAA	chr2:169626068-169626289(+)$1	221	207	212	15.0000
AAAAA	chr10:92635692-92635912(+)$1	220	28	33	15.0000
aaaaa	chr1:92515814-92516040(+)$1	226	211	216	15.0000
AAAAA	chr4:166254629-166254856(+)$1	227	127	132	15.0000
AAAAA	chr12:123006623-123006849(-)$1	226	63	68	15.0000
AAAAA	chr5:130980230-130980494(-)$1	264	124	129	15.0000
AAAAA	chr13:32893270-32893504(+)$1	234	32	37	15.0000
AAAAA	chr4:159640296-159640521(-)$1	225	158	163	15.0000
AAAAA	chr5:135489711-135489935(+)$1	224	90	95	15.0000
AAAAA	chr6:56418228-56418452(-)$1	224	206	211	15.0000
AAAAA	chr1:145508462-145508688(+)$1	226	104	109	15.0000
AAAAA	chr21:34948615-34948840(-)$1	225	126	131	15.0000
AAAAA	chr5:38530533-38530762(-)$1	229	148	153	15.0000
AAAAA	chr11:86519021-86519245(+)$1	224	203	208	15.0000
AAAAA	chr1:86167783-86168008(-)$1	225	30	35	15.0000
AAAAA	chr13:42875496-42875718(+)$1	222	76	81	15.0000
aaaaa	chr7:106964795-106965017(-)$1	222	25	30	15.0000
AAAAA	chr17:27614347-27614567(-)$1	220	24	29	15.0000
AAAAA	chrM:11028-11250(+)$1	222	4	9	15.0000
AAAAA	chr4:95147216-95147439(+)$1	223	112	117	15.0000
AAAAA	chr5:162910245-162910473(+)$1	228	36	41	15.0000
AAAAA	chr15:78834866-78835086(+)$1	220	99	104	15.0000

#otherMatches

#Struct PSSM
::::E	chr20:34241484-34241708(-)$1	224	17	22	15.0000
qqqqq	chr6:119135946-119136166(-)$1	220	167	172	15.0000
qqqqq	chr7:79841993-79842220(+)$1	227	144	149	15.0000
:::::	chr11:18031558-18031783(-)$1	225	105	110	15.0000
xxxxx	chr13:33017486-33017708(-)$1	222	19	24	15.0000
sssss	chr12:72176270-72176489(+)$1	219	11	16	15.0000
d::::	chr1:235938204-235938437(-)$1	233	193	198	15.0000
:::::	chr5:82876055-82876279(+)$1	224	108	113	15.0000
h:fff	chr7:138268502-138268730(+)$1	228	116	121	15.0000
crrrr	chr9:116812156-116812376(+)$1	220	36	41	15.0000
ooooo	chr5:177632787-177633022(+)$1	235	55	60	15.0000
hhhrr	chr19:38229654-38229874(-)$1	220	79	84	15.0000
qqqqq	chr19:38126378-38126612(-)$1	234	138	143	15.0000
:::::	chr17:29676081-29676305(+)$1	224	6	11	15.0000
:::::	chr9:98774685-98774908(+)$1	223	133	138	15.0000
fffff	chr1:14107633-14107859(+)$1	226	50	55	15.0000
:::::	chr13:23909318-23909547(-)$1	229	116	121	15.0000
:::::	chr9:39086564-39086791(-)$1	227	10	15	15.0000
:::::	chr5:5463960-5464186(+)$1	226	137	142	15.0000
C@@@@	chr2:183790311-183790534(-)$1	223	191	196	15.0000
^^^^^	chr14:92609441-92609671(+)$1	230	104	109	15.0000
:::hh	chr3:156645155-156645383(+)$1	228	144	149	15.0000
ddJJJ	chrM:9958-10199(+)$1	241	90	95	15.0000
fff!!	chr13:48942616-48942836(+)$1	220	70	75	15.0000
EEE:e	chr9:114476610-114476832(+)$1	222	46	51	15.0000
C::::	chr10:32328182-32328411(-)$1	229	210	215	15.0000
)))cc	chr8:71486424-71486649(-)$1	225	61	66	15.0000
:::::	chr3:150281225-150281446(+)$1	221	15	20	15.0000
:::::	chr2:169626068-169626289(+)$1	221	207	212	15.0000
{GGGG	chr10:92635692-92635912(+)$1	220	28	33	15.0000
f22ee	chr1:92515814-92516040(+)$1	226	211	216	15.0000
ff]ee	chr4:166254629-166254856(+)$1	227	127	132	15.0000
:::::	chr12:123006623-123006849(-)$1	226	63	68	15.0000
f####	chr5:130980230-130980494(-)$1	264	124	129	15.0000
:::::	chr13:32893270-32893504(+)$1	234	32	37	15.0000
##fff	chr4:159640296-159640521(-)$1	225	158	163	15.0000
eeee]	chr5:135489711-135489935(+)$1	224	90	95	15.0000
d::::	chr6:56418228-56418452(-)$1	224	206	211	15.0000
xxxxx	chr1:145508462-145508688(+)$1	226	104	109	15.0000
\\\\\	chr21:34948615-34948840(-)$1	225	126	131	15.0000
ddd::	chr5:38530533-38530762(-)$1	229	148	153	15.0000
ooooo	chr11:86519021-86519245(+)$1	224	203	208	15.0000
=====	chr1:86167783-86168008(-)$1	225	30	35	15.0000
b::::	chr13:42875496-42875718(+)$1	222	76	81	15.0000
::===	chr7:106964795-106965017(-)$1	222	25	30	15.0000
f&&&&	chr17:27614347-27614567(-)$1	220	24	29	15.0000
C::::	chrM:11028-11250(+)$1	222	4	9	15.0000
uuuuu	chr4:95147216-95147439(+)$1	223	112	117	15.0000
D::::	chr5:162910245-162910473(+)$1	228	36	41	15.0000
===""	chr15:78834866-78835086(+)$1	220	99	104	15.0000

#DB
....(	chr20:34241484-34241708(-)$1	1	17	22	15.0000
.....	chr6:119135946-119136166(-)$1	1	167	172	15.0000
.....	chr7:79841993-79842220(+)$1	1	144	149	15.0000
.....	chr11:18031558-18031783(-)$1	1	105	110	15.0000
.....	chr13:33017486-33017708(-)$1	1	19	24	15.0000
.....	chr12:72176270-72176489(+)$1	1	11	16	15.0000
)....	chr1:235938204-235938437(-)$1	1	193	198	15.0000
.....	chr5:82876055-82876279(+)$1	1	108	113	15.0000
).(((	chr7:138268502-138268730(+)$1	1	116	121	15.0000
(....	chr9:116812156-116812376(+)$1	1	36	41	15.0000
.....	chr5:177632787-177633022(+)$1	1	55	60	15.0000
(((..	chr19:38229654-38229874(-)$1	1	79	84	15.0000
.....	chr19:38126378-38126612(-)$1	1	138	143	15.0000
.....	chr17:29676081-29676305(+)$1	1	6	11	15.0000
.....	chr9:98774685-98774908(+)$1	1	133	138	15.0000
(((((	chr1:14107633-14107859(+)$1	1	50	55	15.0000
.....	chr13:23909318-23909547(-)$1	1	116	121	15.0000
.....	chr9:39086564-39086791(-)$1	1	10	15	15.0000
.....	chr5:5463960-5464186(+)$1	1	137	142	15.0000
)....	chr2:183790311-183790534(-)$1	1	191	196	15.0000
.....	chr14:92609441-92609671(+)$1	1	104	109	15.0000
...((	chr3:156645155-156645383(+)$1	1	144	149	15.0000
)))))	chrM:9958-10199(+)$1	1	90	95	15.0000
(((..	chr13:48942616-48942836(+)$1	1	70	75	15.0000
(((.(	chr9:114476610-114476832(+)$1	1	46	51	15.0000
)....	chr10:32328182-32328411(-)$1	1	210	215	15.0000
...((	chr8:71486424-71486649(-)$1	1	61	66	15.0000
.....	chr3:150281225-150281446(+)$1	1	15	20	15.0000
.....	chr2:169626068-169626289(+)$1	1	207	212	15.0000
.((((	chr10:92635692-92635912(+)$1	1	28	33	15.0000
)..))	chr1:92515814-92516040(+)$1	1	211	216	15.0000
)).))	chr4:166254629-166254856(+)$1	1	127	132	15.0000
.....	chr12:123006623-123006849(-)$1	1	63	68	15.0000
(....	chr5:130980230-130980494(-)$1	1	124	129	15.0000
.....	chr13:32893270-32893504(+)$1	1	32	37	15.0000
..(((	chr4:159640296-159640521(-)$1	1	158	163	15.0000
)))).	chr5:135489711-135489935(+)$1	1	90	95	15.0000
)....	chr6:56418228-56418452(-)$1	1	206	211	15.0000
.....	chr1:145508462-145508688(+)$1	1	104	109	15.0000
.....	chr21:34948615-34948840(-)$1	1	126	131	15.0000
)))..	chr5:38530533-38530762(-)$1	1	148	153	15.0000
.....	chr11:86519021-86519245(+)$1	1	203	208	15.0000
)))))	chr1:86167783-86168008(-)$1	1	30	35	15.0000
)....	chr13:42875496-42875718(+)$1	1	76	81	15.0000
..(((	chr7:106964795-106965017(-)$1	1	25	30	15.0000
(....	chr17:27614347-27614567(-)$1	1	24	29	15.0000
(....	chrM:11028-11250(+)$1	1	4	9	15.0000
.....	chr4:95147216-95147439(+)$1	1	112	117	15.0000
(....	chr5:162910245-162910473(+)$1	1	36	41	15.0000
(((..	chr15:78834866-78835086(+)$1	1	99	104	15.0000

#PSSM
A : 0.96	a : 0.04	
A : 0.96	a : 0.04	
A : 0.96	a : 0.04	
A : 0.96	a : 0.04	
A : 0.96	a : 0.04	

#score	750.0000000000001
#seq	50
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m3_run1.nuc.txt

#NT
UUUCU	chr2:233655672-233655914(+)$1	242	36	41	15.0000
UUUCU	chr10:96333620-96333845(+)$1	225	27	32	15.0000
uuucu	chr9:95009706-95009933(-)$1	227	1	6	15.0000
UUUCU	chr9:95033773-95033998(-)$1	225	53	58	15.0000
UUUCU	chr13:74708114-74708348(-)$1	234	2	7	15.0000
UUUCU	chr3:10302225-10302454(+)$1	229	190	195	15.0000
UUUCU	chr5:85916253-85916483(+)$1	230	121	126	15.0000
UUUCU	chr15:72766611-72766841(+)$1	230	101	106	15.0000
UUUCU	chr10:116622008-116622231(+)$1	223	161	166	15.0000
UUUCU	chr3:24019515-24019738(+)$1	223	29	34	15.0000
UUUCU	chr6:97681646-97681871(-)$1	225	74	79	15.0000
UUUCU	chr7:102950693-102950913(+)$1	220	6	11	15.0000
UUUCU	chr17:62499840-62500073(-)$1	233	55	60	15.0000
UUUCU	chr14:103801888-103802115(+)$1	227	91	96	15.0000
UUUCU	chr10:58117809-58118039(-)$1	230	161	166	15.0000
UUUCU	chr18:57571035-57571257(+)$1	222	200	205	15.0000
UUUCU	chr18:67755252-67755478(-)$1	226	75	80	15.0000
UUUCU	chr7:97481400-97481624(-)$1	224	86	91	15.0000
UUUCU	chr10:135111436-135111660(-)$1	224	11	16	15.0000
UUUCU	chr16:56548379-56548600(-)$1	221	87	92	15.0000
UUUCU	chr12:123705818-123706049(-)$1	231	55	60	15.0000
UUUCU	chr17:27050620-27050866(+)$1	246	192	197	15.0000
UUUCU	chr15:64423932-64424160(+)$1	228	176	181	15.0000
UUUCU	chr17:78369479-78369708(-)$1	229	93	98	15.0000
UUUCU	chr12:96252706-96252945(+)$1	239	37	42	15.0000
UUUCU	chr16:24826484-24826711(+)$1	227	151	156	15.0000
UUUCU	chr17:3717585-3717811(-)$1	226	19	24	15.0000
UUUCU	chr9:95050043-95050274(-)$1	231	12	17	15.0000
UUUCU	chr18:32446729-32446954(+)$1	225	119	124	15.0000
UUUCU	chr6:82933134-82933354(-)$1	220	207	212	15.0000
UUUCU	chr17:8131736-8131966(-)$1	230	12	17	15.0000
UUUCU	chr22:47188341-47188569(+)$1	228	60	65	15.0000
UUUCU	chr19:2430493-2430721(-)$1	228	216	221	15.0000
UUUCU	chr5:179048264-179048494(-)$1	230	85	90	15.0000
UUUCU	chr5:74807217-74807444(-)$1	227	62	67	15.0000
UUUCU	chr16:58557186-58557413(-)$1	227	0	5	15.0000
UUUCU	chr16:89165033-89165261(+)$1	228	165	170	15.0000
UUUCU	chr17:46051242-46051488(+)$1	246	47	52	15.0000
UUUCU	chr4:763277-763502(+)$1	225	12	17	15.0000
UUUCU	chr20:34309567-34309822(-)$1	255	221	226	15.0000
UUUCU	chr14:74756966-74757190(-)$1	224	28	33	15.0000
UUUCU	chr2:228419150-228419373(+)$1	223	51	56	15.0000
UUUCU	chr1:97189024-97189246(+)$1	222	84	89	15.0000
UUUCU	chr11:65820443-65820672(+)$1	229	40	45	15.0000
UUUCU	chr5:179044716-179044984(-)$1	268	12	17	15.0000
UUUCU	chr19:59055770-59056007(+)$1	237	25	30	15.0000
UUUCU	chr14:102549897-102550125(-)$1	228	180	185	15.0000
UUUCU	chr7:148514263-148514486(-)$1	223	127	132	15.0000
UUUCU	chr19:2236761-2237000(+)$1	239	62	67	15.0000
UUUCU	chr17:62502102-62502351(-)$1	249	71	76	15.0000
UUUCU	chr12:56578536-56578772(-)$1	236	36	41	15.0000
UUUCU	chr9:95036612-95036833(-)$1	221	19	24	15.0000
UUUCU	chr5:180669158-180669382(-)$1	224	13	18	15.0000
UUUCU	chr7:142991265-142991494(+)$1	229	39	44	15.0000
UUUCU	chr2:97372414-97372636(-)$1	222	53	58	15.0000

#otherMatches

#Struct PSSM
eee]c	chr3:122943932-122944168(+)$1	236	83	88	15.0000
hhhhh	chr2:233655672-233655914(+)$1	242	36	41	15.0000
CCCCf	chr10:96333620-96333845(+)$1	225	27	32	15.0000
:::::	chr9:95009706-95009933(-)$1	227	1	6	15.0000
^^^^^	chr9:95033773-95033998(-)$1	225	53	58	15.0000
c"""d	chr13:74708114-74708348(-)$1	234	2	7	15.0000
sssa2	chr3:10302225-10302454(+)$1	229	190	195	15.0000
ddbb2	chr5:85916253-85916483(+)$1	230	121	126	15.0000
&&&&&	chr15:72766611-72766841(+)$1	230	101	106	15.0000
iiiii	chr10:116622008-116622231(+)$1	223	161	166	15.0000
((((h	chr3:24019515-24019738(+)$1	223	29	34	15.0000
c22cc	chr6:97681646-97681871(-)$1	225	74	79	15.0000
KDDDD	chr7:102950693-102950913(+)$1	220	6	11	15.0000
####b	chr17:62499840-62500073(-)$1	233	55	60	15.0000
&&&&&	chr14:103801888-103802115(+)$1	227	91	96	15.0000
eee[c	chr10:58117809-58118039(-)$1	230	161	166	15.0000
ppphh	chr18:57571035-57571257(+)$1	222	200	205	15.0000
yyyyy	chr18:67755252-67755478(-)$1	226	75	80	15.0000
dddd2	chr7:97481400-97481624(-)$1	224	86	91	15.0000
:::dd	chr10:135111436-135111660(-)$1	224	11	16	15.0000
ggrrr	chr16:56548379-56548600(-)$1	221	87	92	15.0000
fffff	chr12:123705818-123706049(-)$1	231	55	60	15.0000
e%%%%	chr17:27050620-27050866(+)$1	246	192	197	15.0000
:::::	chr15:64423932-64424160(+)$1	228	176	181	15.0000
fff[b	chr17:78369479-78369708(-)$1	229	93	98	15.0000
::ggg	chr12:96252706-96252945(+)$1	239	37	42	15.0000
h####	chr16:24826484-24826711(+)$1	227	151	156	15.0000
ggggi	chr17:3717585-3717811(-)$1	226	19	24	15.0000
GGGGG	chr9:95050043-95050274(-)$1	231	12	17	15.0000
ooooo	chr18:32446729-32446954(+)$1	225	119	124	15.0000
//DDD	chr6:82933134-82933354(-)$1	220	207	212	15.0000
HHHHH	chr17:8131736-8131966(-)$1	230	12	17	15.0000
5555=	chr22:47188341-47188569(+)$1	228	60	65	15.0000
wweee	chr19:2430493-2430721(-)$1	228	216	221	15.0000
dd555	chr5:179048264-179048494(-)$1	230	85	90	15.0000
qqqqq	chr5:74807217-74807444(-)$1	227	62	67	15.0000
:::::	chr16:58557186-58557413(-)$1	227	0	5	15.0000
"ccc[	chr16:89165033-89165261(+)$1	228	165	170	15.0000
sssss	chr17:46051242-46051488(+)$1	246	47	52	15.0000
hhh""	chr4:763277-763502(+)$1	225	12	17	15.0000
22ccc	chr20:34309567-34309822(-)$1	255	221	226	15.0000
:::::	chr14:74756966-74757190(-)$1	224	28	33	15.0000
::::e	chr2:228419150-228419373(+)$1	223	51	56	15.0000
]ffff	chr1:97189024-97189246(+)$1	222	84	89	15.0000
=====	chr11:65820443-65820672(+)$1	229	40	45	15.0000
nnnnf	chr5:179044716-179044984(-)$1	268	12	17	15.0000
OEEEE	chr19:59055770-59056007(+)$1	237	25	30	15.0000
fffpp	chr14:102549897-102550125(-)$1	228	180	185	15.0000
dddd]	chr7:148514263-148514486(-)$1	223	127	132	15.0000
FFFFF	chr19:2236761-2237000(+)$1	239	62	67	15.0000
JJJJJ	chr17:62502102-62502351(-)$1	249	71	76	15.0000
::GGG	chr12:56578536-56578772(-)$1	236	36	41	15.0000
hhhhh	chr9:95036612-95036833(-)$1	221	19	24	15.0000
:::::	chr5:180669158-180669382(-)$1	224	13	18	15.0000
::::F	chr7:142991265-142991494(+)$1	229	39	44	15.0000
:::::	chr2:97372414-97372636(-)$1	222	53	58	15.0000

#DB
))).)	chr3:122943932-122944168(+)$1	1	83	88	15.0000
(((((	chr2:233655672-233655914(+)$1	1	36	41	15.0000
(((((	chr10:96333620-96333845(+)$1	1	27	32	15.0000
.....	chr9:95009706-95009933(-)$1	1	1	6	15.0000
.....	chr9:95033773-95033998(-)$1	1	53	58	15.0000
(...(	chr13:74708114-74708348(-)$1	1	2	7	15.0000
...).	chr3:10302225-10302454(+)$1	1	190	195	15.0000
)))).	chr5:85916253-85916483(+)$1	1	121	126	15.0000
.....	chr15:72766611-72766841(+)$1	1	101	106	15.0000
)))))	chr10:116622008-116622231(+)$1	1	161	166	15.0000
....(	chr3:24019515-24019738(+)$1	1	29	34	15.0000
)..))	chr6:97681646-97681871(-)$1	1	74	79	15.0000
.((((	chr7:102950693-102950913(+)$1	1	6	11	15.0000
....(	chr17:62499840-62500073(-)$1	1	55	60	15.0000
.....	chr14:103801888-103802115(+)$1	1	91	96	15.0000
(((.(	chr10:58117809-58118039(-)$1	1	161	166	15.0000
...))	chr18:57571035-57571257(+)$1	1	200	205	15.0000
.....	chr18:67755252-67755478(-)$1	1	75	80	15.0000
)))).	chr7:97481400-97481624(-)$1	1	86	91	15.0000
...((	chr10:135111436-135111660(-)$1	1	11	16	15.0000
((...	chr16:56548379-56548600(-)$1	1	87	92	15.0000
(((((	chr12:123705818-123706049(-)$1	1	55	60	15.0000
(....	chr17:27050620-27050866(+)$1	1	192	197	15.0000
.....	chr15:64423932-64424160(+)$1	1	176	181	15.0000
(((.(	chr17:78369479-78369708(-)$1	1	93	98	15.0000
..(((	chr12:96252706-96252945(+)$1	1	37	42	15.0000
(....	chr16:24826484-24826711(+)$1	1	151	156	15.0000
(((((	chr17:3717585-3717811(-)$1	1	19	24	15.0000
(((((	chr9:95050043-95050274(-)$1	1	12	17	15.0000
.....	chr18:32446729-32446954(+)$1	1	119	124	15.0000
..)))	chr6:82933134-82933354(-)$1	1	207	212	15.0000
(((((	chr17:8131736-8131966(-)$1	1	12	17	15.0000
....)	chr22:47188341-47188569(+)$1	1	60	65	15.0000
..)))	chr19:2430493-2430721(-)$1	1	216	221	15.0000
))...	chr5:179048264-179048494(-)$1	1	85	90	15.0000
.....	chr5:74807217-74807444(-)$1	1	62	67	15.0000
.....	chr16:58557186-58557413(-)$1	1	0	5	15.0000
.(((.	chr16:89165033-89165261(+)$1	1	165	170	15.0000
.....	chr17:46051242-46051488(+)$1	1	47	52	15.0000
(((..	chr4:763277-763502(+)$1	1	12	17	15.0000
..)))	chr20:34309567-34309822(-)$1	1	221	226	15.0000
.....	chr14:74756966-74757190(-)$1	1	28	33	15.0000
....(	chr2:228419150-228419373(+)$1	1	51	56	15.0000
.))))	chr1:97189024-97189246(+)$1	1	84	89	15.0000
(((((	chr11:65820443-65820672(+)$1	1	40	45	15.0000
....)	chr5:179044716-179044984(-)$1	1	12	17	15.0000
.((((	chr19:59055770-59056007(+)$1	1	25	30	15.0000
(((..	chr14:102549897-102550125(-)$1	1	180	185	15.0000
)))).	chr7:148514263-148514486(-)$1	1	127	132	15.0000
(((((	chr19:2236761-2237000(+)$1	1	62	67	15.0000
(((((	chr17:62502102-62502351(-)$1	1	71	76	15.0000
..(((	chr12:56578536-56578772(-)$1	1	36	41	15.0000
(((((	chr9:95036612-95036833(-)$1	1	19	24	15.0000
.....	chr5:180669158-180669382(-)$1	1	13	18	15.0000
....(	chr7:142991265-142991494(+)$1	1	39	44	15.0000
.....	chr2:97372414-97372636(-)$1	1	53	58	15.0000

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	

#score	840.0000000000005
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m2_run1.nuc.txt

#NT
AGAA	chr1:115280525-115280752(-)$1	227	135	139	11.9999
AGAA	chr22:39910176-39910398(+)$1	222	82	86	11.9999
AGAA	chr1:115263202-115263430(-)$1	228	158	162	11.9999
AGAA	chr10:127530310-127530531(+)$1	221	119	123	11.9999
AGAA	chr1:113240535-113240762(+)$1	227	161	165	11.9999
AGAA	chr19:3976159-3976393(-)$1	234	217	221	11.9999
AGAA	chr1:113239260-113239476(+)$1	216	90	94	11.9999
AGAA	chr17:37006577-37006800(-)$1	223	113	117	11.9999
AGAA	chr6:30691304-30691552(+)$1	248	2	6	11.9999
AGAA	chr1:33149750-33149988(+)$1	238	98	102	11.9999
AGAA	chr12:98926905-98927139(+)$1	234	74	78	11.9999
AGAA	chr1:200377234-200377457(-)$1	223	26	30	11.9999
AGAA	chr13:42891677-42891912(+)$1	235	104	108	11.9999
AGAA	chr20:17930869-17931115(-)$1	246	100	104	11.9999
AGAA	chr19:37238531-37238796(-)$1	265	39	43	11.9999
AGAA	chr2:48027236-48027467(+)$1	231	6	10	11.9999
AGAA	chr8:101721636-101721872(-)$1	236	6	10	11.9999
AGAA	chr11:122929293-122929520(-)$1	227	151	155	11.9999
AGAA	chr1:16254524-16254753(+)$1	229	31	35	11.9999
AGAA	chr20:2637633-2637865(+)$1	232	32	36	11.9999
AGAA	chr13:25671962-25672203(+)$1	241	131	135	11.9999
AGAA	chr17:44159743-44159972(-)$1	229	181	185	11.9999
AGAA	chr1:16255782-16256028(+)$1	246	61	65	11.9999
AGAA	chr3:9517642-9517875(+)$1	233	154	158	11.9999
AGAA	chrX:13790896-13791129(-)$1	233	69	73	11.9999
AGAA	chr7:128412479-128412737(+)$1	258	53	57	11.9999
AGAA	chr12:112845943-112846233(-)$1	290	98	102	11.9999
AGAA	chr17:7474115-7474351(+)$1	236	14	18	11.9999
AGAA	chr1:203821341-203821552(+)$1	211	73	77	11.9999
AGAA	chr12:49420945-49421156(-)$1	211	143	147	11.9999
AGAA	chr1:46654253-46654494(-)$1	241	126	130	11.9999
AGAA	chr11:17096985-17097223(-)$1	238	118	122	11.9999
AGAA	chr1:62914072-62914305(+)$1	233	29	33	11.9999
AGAA	chr7:6189372-6189590(-)$1	218	38	42	11.9999
AGAA	chr12:56507550-56507793(+)$1	243	14	18	11.9999
AGAA	chr2:44547253-44547476(-)$1	223	180	184	11.9999
AGAA	chr1:93307301-93307550(+)$1	249	50	54	11.9999
AGAA	chr1:16257031-16257270(+)$1	239	80	84	11.9999
AGAA	chr19:37036666-37036906(-)$1	240	98	102	11.9999
AGAA	chr3:186506936-186507164(+)$1	228	34	38	11.9999
AGAA	chrX:84525986-84526211(+)$1	225	19	23	11.9999
AGAA	chr21:34931844-34932086(+)$1	242	28	32	11.9999
AGAA	chr1:62905381-62905641(+)$1	260	149	153	11.9999
AGAA	chr21:34947836-34948078(+)$1	242	81	85	11.9999
AGAA	chr10:103546121-103546347(-)$1	226	44	48	11.9999
AGAA	chr1:40705366-40705618(+)$1	252	56	60	11.9999
AGAA	chr7:24681265-24681501(+)$1	236	83	87	11.9999
AGAA	chr10:15863564-15863823(-)$1	259	96	100	11.9999
AGAA	chr1:16256575-16256838(+)$1	263	110	114	11.9999
AGAA	chr1:28564259-28564470(+)$1	211	100	104	11.9999
AGAA	chr21:33040649-33040896(-)$1	247	128	132	11.9999
AGAA	chr8:101721319-101721551(-)$1	232	104	108	11.9999
AGAA	chr1:204375180-204375417(-)$1	237	44	48	11.9999
AGAA	chr19:3976124-3976356(-)$1	232	180	184	11.9999
AGAA	chr10:129902295-129902522(-)$1	227	57	61	11.9999
AGAA	chr17:41151984-41152219(+)$1	235	59	63	11.9999
AGAA	chr12:57106198-57106435(-)$1	237	68	72	11.9999
AGAA	chrX:84525776-84525991(+)$1	215	2	6	11.9999
AGAA	chr17:1257453-1257688(-)$1	235	80	84	11.9999
AGAA	chr6:32944448-32944671(+)$1	223	89	93	11.9999
AGAA	chr5:37303309-37303529(-)$1	220	107	111	11.9999
AGAA	chr15:30926490-30926733(+)$1	243	39	43	11.9999
AGAA	chrX:84525659-84525878(+)$1	219	96	100	11.9999
AGAA	chr7:44869631-44869886(-)$1	255	124	128	11.9999
AGAA	chr5:162866393-162866622(+)$1	229	4	8	11.9999
AGAA	chrX:53575917-53576177(-)$1	260	16	20	11.9999
AGAA	chr1:40034394-40034629(-)$1	235	41	45	11.9999
AGAA	chr2:44547605-44547830(-)$1	225	191	195	11.9999
AGAA	chr5:40832475-40832722(-)$1	247	116	120	11.9999
AGAA	chr5:140501706-140501925(-)$1	219	91	95	11.9999
AGAA	chr7:6502517-6502785(-)$1	268	59	63	11.9999
AGAA	chr15:66625406-66625651(-)$1	245	56	60	11.9999
AGAA	chr5:61686703-61686936(+)$1	233	123	127	11.9999
AGAA	chr12:67700136-67700367(+)$1	231	2	6	11.9999
AGAA	chr1:115272883-115273142(-)$1	259	28	32	11.9999
agaa	chr1:24294040-24294285(-)$1	245	24	28	11.9999
AGAA	chrX:135954347-135954603(-)$1	256	49	53	11.9999
AGAA	chr10:28884795-28885049(+)$1	254	85	89	11.9999
AGAA	chr8:29921239-29921462(-)$1	223	62	66	11.9999
AGAA	chr1:16260532-16260752(+)$1	220	106	110	11.9999
AGAA	chr1:113456670-113456906(-)$1	236	85	89	11.9999
AGAA	chr17:56082183-56082413(-)$1	230	33	37	11.9999
AGAA	chr2:152298328-152298558(+)$1	230	124	128	11.9999
AGAA	chr1:220151786-220152011(-)$1	225	0	4	11.9999
AGAA	chr2:61712811-61713088(-)$1	277	45	49	11.9999
AGAA	chr1:16264261-16264504(+)$1	243	43	47	11.9999
AGAA	chr21:30319714-30319935(-)$1	221	70	74	11.9999

#otherMatches

#Struct PSSM
ffff	chr20:61490734-61490970(-)$1	236	178	182	11.9999
dd&&	chr1:115280525-115280752(-)$1	227	135	139	11.9999
%%%%	chr22:39910176-39910398(+)$1	222	82	86	11.9999
2ddd	chr1:115263202-115263430(-)$1	228	158	162	11.9999
oooo	chr10:127530310-127530531(+)$1	221	119	123	11.9999
ee""	chr1:113240535-113240762(+)$1	227	161	165	11.9999
nnnn	chr19:3976159-3976393(-)$1	234	217	221	11.9999
cc::	chr1:113239260-113239476(+)$1	216	90	94	11.9999
pppp	chr17:37006577-37006800(-)$1	223	113	117	11.9999
c!!b	chr6:30691304-30691552(+)$1	248	2	6	11.9999
====	chr1:33149750-33149988(+)$1	238	98	102	11.9999
bb[e	chr12:98926905-98927139(+)$1	234	74	78	11.9999
::::	chr1:200377234-200377457(-)$1	223	26	30	11.9999
mmee	chr13:42891677-42891912(+)$1	235	104	108	11.9999
====	chr20:17930869-17931115(-)$1	246	100	104	11.9999
cc::	chr19:37238531-37238796(-)$1	265	39	43	11.9999
GGGG	chr2:48027236-48027467(+)$1	231	6	10	11.9999
EE::	chr8:101721636-101721872(-)$1	236	6	10	11.9999
::::	chr11:122929293-122929520(-)$1	227	151	155	11.9999
::::	chr1:16254524-16254753(+)$1	229	31	35	11.9999
wwww	chr20:2637633-2637865(+)$1	232	32	36	11.9999
dd22	chr13:25671962-25672203(+)$1	241	131	135	11.9999
FFF}	chr17:44159743-44159972(-)$1	229	181	185	11.9999
CCCK	chr1:16255782-16256028(+)$1	246	61	65	11.9999
bqqq	chr3:9517642-9517875(+)$1	233	154	158	11.9999
yyyy	chrX:13790896-13791129(-)$1	233	69	73	11.9999
GGGG	chr7:128412479-128412737(+)$1	258	53	57	11.9999
2a22	chr12:112845943-112846233(-)$1	290	98	102	11.9999
iiii	chr17:7474115-7474351(+)$1	236	14	18	11.9999
:ddd	chr1:203821341-203821552(+)$1	211	73	77	11.9999
bb77	chr12:49420945-49421156(-)$1	211	143	147	11.9999
hhhh	chr1:46654253-46654494(-)$1	241	126	130	11.9999
eemm	chr11:17096985-17097223(-)$1	238	118	122	11.9999
ffff	chr1:62914072-62914305(+)$1	233	29	33	11.9999
g"""	chr7:6189372-6189590(-)$1	218	38	42	11.9999
FFLL	chr12:56507550-56507793(+)$1	243	14	18	11.9999
qddd	chr2:44547253-44547476(-)$1	223	180	184	11.9999
ffff	chr1:93307301-93307550(+)$1	249	50	54	11.9999
ggg:	chr1:16257031-16257270(+)$1	239	80	84	11.9999
eemm	chr19:37036666-37036906(-)$1	240	98	102	11.9999
ffff	chr3:186506936-186507164(+)$1	228	34	38	11.9999
!!ff	chrX:84525986-84526211(+)$1	225	19	23	11.9999
::::	chr21:34931844-34932086(+)$1	242	28	32	11.9999
qqqq	chr1:62905381-62905641(+)$1	260	149	153	11.9999
dddd	chr21:34947836-34948078(+)$1	242	81	85	11.9999
uuuu	chr10:103546121-103546347(-)$1	226	44	48	11.9999
{DDD	chr1:40705366-40705618(+)$1	252	56	60	11.9999
]ccc	chr7:24681265-24681501(+)$1	236	83	87	11.9999
###c	chr10:15863564-15863823(-)$1	259	96	100	11.9999
F|||	chr1:16256575-16256838(+)$1	263	110	114	11.9999
qqqq	chr1:28564259-28564470(+)$1	211	100	104	11.9999
cc]d	chr21:33040649-33040896(-)$1	247	128	132	11.9999
qqqq	chr8:101721319-101721551(-)$1	232	104	108	11.9999
:ggg	chr1:204375180-204375417(-)$1	237	44	48	11.9999
nnnn	chr19:3976124-3976356(-)$1	232	180	184	11.9999
DDDM	chr10:129902295-129902522(-)$1	227	57	61	11.9999
GGGG	chr17:41151984-41152219(+)$1	235	59	63	11.9999
dddt	chr12:57106198-57106435(-)$1	237	68	72	11.9999
::::	chrX:84525776-84525991(+)$1	215	2	6	11.9999
c:ee	chr17:1257453-1257688(-)$1	235	80	84	11.9999
ccc[	chr6:32944448-32944671(+)$1	223	89	93	11.9999
!ddd	chr5:37303309-37303529(-)$1	220	107	111	11.9999
"bb#	chr15:30926490-30926733(+)$1	243	39	43	11.9999
gggg	chrX:84525659-84525878(+)$1	219	96	100	11.9999
gggg	chr7:44869631-44869886(-)$1	255	124	128	11.9999
eee!	chr5:162866393-162866622(+)$1	229	4	8	11.9999
EE::	chrX:53575917-53576177(-)$1	260	16	20	11.9999
::::	chr1:40034394-40034629(-)$1	235	41	45	11.9999
9999	chr2:44547605-44547830(-)$1	225	191	195	11.9999
::::	chr5:40832475-40832722(-)$1	247	116	120	11.9999
ffff	chr5:140501706-140501925(-)$1	219	91	95	11.9999
3bb2	chr7:6502517-6502785(-)$1	268	59	63	11.9999
#ddd	chr15:66625406-66625651(-)$1	245	56	60	11.9999
ee]c	chr5:61686703-61686936(+)$1	233	123	127	11.9999
::::	chr12:67700136-67700367(+)$1	231	2	6	11.9999
IIII	chr1:115272883-115273142(-)$1	259	28	32	11.9999
]bb:	chr1:24294040-24294285(-)$1	245	24	28	11.9999
ff''	chrX:135954347-135954603(-)$1	256	49	53	11.9999
dppp	chr10:28884795-28885049(+)$1	254	85	89	11.9999
gggg	chr8:29921239-29921462(-)$1	223	62	66	11.9999
eee:	chr1:16260532-16260752(+)$1	220	106	110	11.9999
:hhh	chr1:113456670-113456906(-)$1	236	85	89	11.9999
&&&&	chr17:56082183-56082413(-)$1	230	33	37	11.9999
ccc2	chr2:152298328-152298558(+)$1	230	124	128	11.9999
FFFF	chr1:220151786-220152011(-)$1	225	0	4	11.9999
eeee	chr2:61712811-61713088(-)$1	277	45	49	11.9999
7777	chr1:16264261-16264504(+)$1	243	43	47	11.9999
mbb]	chr21:30319714-30319935(-)$1	221	70	74	11.9999

#DB
))))	chr20:61490734-61490970(-)$1	1	178	182	11.9999
((..	chr1:115280525-115280752(-)$1	1	135	139	11.9999
....	chr22:39910176-39910398(+)$1	1	82	86	11.9999
.)))	chr1:115263202-115263430(-)$1	1	158	162	11.9999
....	chr10:127530310-127530531(+)$1	1	119	123	11.9999
((..	chr1:113240535-113240762(+)$1	1	161	165	11.9999
....	chr19:3976159-3976393(-)$1	1	217	221	11.9999
))..	chr1:113239260-113239476(+)$1	1	90	94	11.9999
....	chr17:37006577-37006800(-)$1	1	113	117	11.9999
(..(	chr6:30691304-30691552(+)$1	1	2	6	11.9999
((((	chr1:33149750-33149988(+)$1	1	98	102	11.9999
((.(	chr12:98926905-98927139(+)$1	1	74	78	11.9999
....	chr1:200377234-200377457(-)$1	1	26	30	11.9999
..))	chr13:42891677-42891912(+)$1	1	104	108	11.9999
))))	chr20:17930869-17931115(-)$1	1	100	104	11.9999
))..	chr19:37238531-37238796(-)$1	1	39	43	11.9999
((((	chr2:48027236-48027467(+)$1	1	6	10	11.9999
((..	chr8:101721636-101721872(-)$1	1	6	10	11.9999
....	chr11:122929293-122929520(-)$1	1	151	155	11.9999
....	chr1:16254524-16254753(+)$1	1	31	35	11.9999
....	chr20:2637633-2637865(+)$1	1	32	36	11.9999
))..	chr13:25671962-25672203(+)$1	1	131	135	11.9999
))).	chr17:44159743-44159972(-)$1	1	181	185	11.9999
(((.	chr1:16255782-16256028(+)$1	1	61	65	11.9999
(...	chr3:9517642-9517875(+)$1	1	154	158	11.9999
....	chrX:13790896-13791129(-)$1	1	69	73	11.9999
((((	chr7:128412479-128412737(+)$1	1	53	57	11.9999
.)..	chr12:112845943-112846233(-)$1	1	98	102	11.9999
((((	chr17:7474115-7474351(+)$1	1	14	18	11.9999
.(((	chr1:203821341-203821552(+)$1	1	73	77	11.9999
))..	chr12:49420945-49421156(-)$1	1	143	147	11.9999
))))	chr1:46654253-46654494(-)$1	1	126	130	11.9999
((..	chr11:17096985-17097223(-)$1	1	118	122	11.9999
((((	chr1:62914072-62914305(+)$1	1	29	33	11.9999
(...	chr7:6189372-6189590(-)$1	1	38	42	11.9999
((..	chr12:56507550-56507793(+)$1	1	14	18	11.9999
.)))	chr2:44547253-44547476(-)$1	1	180	184	11.9999
))))	chr1:93307301-93307550(+)$1	1	50	54	11.9999
))).	chr1:16257031-16257270(+)$1	1	80	84	11.9999
((..	chr19:37036666-37036906(-)$1	1	98	102	11.9999
((((	chr3:186506936-186507164(+)$1	1	34	38	11.9999
..((	chrX:84525986-84526211(+)$1	1	19	23	11.9999
....	chr21:34931844-34932086(+)$1	1	28	32	11.9999
....	chr1:62905381-62905641(+)$1	1	149	153	11.9999
((((	chr21:34947836-34948078(+)$1	1	81	85	11.9999
....	chr10:103546121-103546347(-)$1	1	44	48	11.9999
.(((	chr1:40705366-40705618(+)$1	1	56	60	11.9999
.)))	chr7:24681265-24681501(+)$1	1	83	87	11.9999
...(	chr10:15863564-15863823(-)$1	1	96	100	11.9999
)...	chr1:16256575-16256838(+)$1	1	110	114	11.9999
....	chr1:28564259-28564470(+)$1	1	100	104	11.9999
)).)	chr21:33040649-33040896(-)$1	1	128	132	11.9999
....	chr8:101721319-101721551(-)$1	1	104	108	11.9999
.(((	chr1:204375180-204375417(-)$1	1	44	48	11.9999
....	chr19:3976124-3976356(-)$1	1	180	184	11.9999
(((.	chr10:129902295-129902522(-)$1	1	57	61	11.9999
((((	chr17:41151984-41152219(+)$1	1	59	63	11.9999
(((.	chr12:57106198-57106435(-)$1	1	68	72	11.9999
....	chrX:84525776-84525991(+)$1	1	2	6	11.9999
).((	chr17:1257453-1257688(-)$1	1	80	84	11.9999
(((.	chr6:32944448-32944671(+)$1	1	89	93	11.9999
.(((	chr5:37303309-37303529(-)$1	1	107	111	11.9999
.((.	chr15:30926490-30926733(+)$1	1	39	43	11.9999
))))	chrX:84525659-84525878(+)$1	1	96	100	11.9999
))))	chr7:44869631-44869886(-)$1	1	124	128	11.9999
(((.	chr5:162866393-162866622(+)$1	1	4	8	11.9999
((..	chrX:53575917-53576177(-)$1	1	16	20	11.9999
....	chr1:40034394-40034629(-)$1	1	41	45	11.9999
....	chr2:44547605-44547830(-)$1	1	191	195	11.9999
....	chr5:40832475-40832722(-)$1	1	116	120	11.9999
))))	chr5:140501706-140501925(-)$1	1	91	95	11.9999
.)).	chr7:6502517-6502785(-)$1	1	59	63	11.9999
.(((	chr15:66625406-66625651(-)$1	1	56	60	11.9999
)).)	chr5:61686703-61686936(+)$1	1	123	127	11.9999
....	chr12:67700136-67700367(+)$1	1	2	6	11.9999
((((	chr1:115272883-115273142(-)$1	1	28	32	11.9999
.)).	chr1:24294040-24294285(-)$1	1	24	28	11.9999
((..	chrX:135954347-135954603(-)$1	1	49	53	11.9999
(...	chr10:28884795-28885049(+)$1	1	85	89	11.9999
((((	chr8:29921239-29921462(-)$1	1	62	66	11.9999
))).	chr1:16260532-16260752(+)$1	1	106	110	11.9999
.(((	chr1:113456670-113456906(-)$1	1	85	89	11.9999
....	chr17:56082183-56082413(-)$1	1	33	37	11.9999
))).	chr2:152298328-152298558(+)$1	1	124	128	11.9999
((((	chr1:220151786-220152011(-)$1	1	0	4	11.9999
))))	chr2:61712811-61713088(-)$1	1	45	49	11.9999
....	chr1:16264261-16264504(+)$1	1	43	47	11.9999
.)).	chr21:30319714-30319935(-)$1	1	70	74	11.9999

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	

#score	1055.9999999999998
#seq	88
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUUUUUUU	chr5:112204475-112204719(+)$1	244	116	126	18.4482
AGUUUUUUUU	chr6:24423877-24424104(+)$1	227	66	76	18.3620
uguuuuuuuu	chr18:12986675-12986900(+)$1	225	125	135	21.9827
UGCCUUUUUU	chr10:85912208-85912430(+)$1	222	52	62	15.4310
uguauuucuu	chr12:66737290-66737514(+)$1	224	97	107	15.5172
UGUAUUUUCU	chr3:119540322-119540549(-)$1	227	98	108	15.1724
UAUGUUUUUU	chr8:95805915-95806147(+)$1	232	5	15	15.6034
UGUAUUUUGU	chr19:18545095-18545322(+)$1	227	174	184	15.0862
UGUAUUCUUU	chr22:29183990-29184214(+)$1	224	188	198	15.1724
AGUUUUUUUU	chr1:226548484-226548704(-)$1	220	43	53	18.3620
UAUUUUAUUU	chr5:65478967-65479194(+)$1	227	7	17	15.0000
UGUUUUCCUU	chr3:170111100-170111333(+)$1	233	4	14	14.0517
UUUUUUUUUU	chr21:35470188-35470417(+)$1	229	103	113	18.4482
UGUUUGUUUU	chr5:114859168-114859394(-)$1	226	94	104	17.9310
UGCUAUUUUU	chr7:107399984-107400205(+)$1	221	45	55	14.3103
UGCUGUUUUU	chr1:245006658-245006905(-)$1	247	49	59	14.1379
UGUAUUGUUU	chr10:82191847-82192071(+)$1	224	65	75	15.0000
UGGUUUUUUU	chr2:210884894-210885127(+)$1	233	29	39	18.4482
UGUAUAUUUU	chr8:31031114-31031345(+)$1	231	88	98	15.5172
UGUAUUUUUC	chr2:160624856-160625084(+)$1	228	34	44	14.7413
AGUCUUUUUU	chr12:77244799-77245028(+)$1	229	97	107	15.0862
UGUUUUUCUU	chr6:116956761-116956989(-)$1	228	214	224	18.1896
UGUUUUUUUU	chr6:159054770-159054996(+)$1	226	62	72	21.9827
AGUUUUUUUU	chr18:57571361-57571583(+)$1	222	48	58	18.3620
UGAUUUUUUA	chr15:40954721-40954947(+)$1	226	39	49	14.2241
UACUUUUUUU	chr10:120441807-120442032(-)$1	225	112	122	15.8620
UCUUUUUUUU	chrX:118718189-118718415(+)$1	226	208	218	18.5344
UGUUUAUAUU	chr9:80944466-80944719(+)$1	253	78	88	14.0517
UGUAUUUGUU	chr1:51737253-51737485(+)$1	232	35	45	15.3448
UGUUUCCUUU	chr2:135713146-135713376(+)$1	230	24	34	13.7931
UGUUUUUUUU	chr15:52841346-52841567(-)$1	221	0	10	21.9827
UGUUUUUCCU	chr4:71896023-71896259(+)$1	236	25	35	14.0517
UGAUUUUUUU	chr19:34891070-34891291(+)$1	221	181	191	18.6206
UAUAUUUUUU	chr1:59247106-59247329(-)$1	223	108	118	16.4655
UAUUAUUUUU	chr16:24583889-24584116(+)$1	227	101	111	14.7413
UGUUUCUGUU	chr14:77253507-77253732(-)$1	225	62	72	13.9655
UGUUUUUUUA	chr1:117117106-117117329(-)$1	223	210	220	17.5862
UGCUAUUUUU	chr4:22389068-22389291(-)$1	223	125	135	14.3103
AGAUUUUUUU	chr19:35176474-35176695(+)$1	221	186	196	15.0000
uauuuuuugu	chr1:77557619-77557839(-)$1	220	138	148	14.9137
UAUUUUUUUA	chr6:117881348-117881574(-)$1	226	44	54	14.7413
UGUUUUUUUU	chr17:1553825-1554057(-)$1	232	150	160	21.9827
UGUAUUUUAU	chr4:95585308-95585529(+)$1	221	119	129	15.0862
UCUUUUUUUU	chr1:202861082-202861306(-)$1	224	80	90	18.5344
UGUUUUUUUU	chr14:21731645-21731864(-)$1	219	40	50	21.9827
UGUCUGUUUU	chr2:238008545-238008767(+)$1	222	39	49	14.6551
UGGUUUAUUU	chr5:79923559-79923781(-)$1	222	84	94	14.3103
UAUUUUUCUU	chr6:151779388-151779612(+)$1	224	52	62	15.3448
UAUUUUUUCU	chr8:26362265-26362499(-)$1	234	17	27	15.0000
AGUCUUUUUU	chr7:134654266-134654495(+)$1	229	211	221	15.0862
UAAUUUUUUU	chr7:105731885-105732106(-)$1	221	105	115	15.7758
UGGUUUUUAU	chr21:30426675-30426896(+)$1	221	18	28	14.2241
ACUUUUUUUU	chr14:50081255-50081485(+)$1	230	146	156	14.9137
UGUUUAUGUU	chr1:109181436-109181659(+)$1	223	140	150	14.2241
UGUUUUAUUU	chr20:7967915-7968136(-)$1	221	72	82	17.8448
ugcauuuuuu	chr11:30359295-30359523(+)$1	228	167	177	16.0344
AGUUUAUUUU	chr4:39781989-39782215(+)$1	226	9	19	14.5689

#otherMatches

#Struct PSSM
:CCCFFFFFF	chr7:89865195-89865419(+)$1	224	1	11	14.8275
::::::::::	chr5:112204475-112204719(+)$1	244	116	126	18.4482
==========	chr6:24423877-24424104(+)$1	227	66	76	18.3620
::::::::::	chr18:12986675-12986900(+)$1	225	125	135	21.9827
c::ccc"""d	chr10:85912208-85912430(+)$1	222	52	62	15.4310
:HHHHHHHH:	chr12:66737290-66737514(+)$1	224	97	107	15.5172
hhhhhhhh%%	chr3:119540322-119540549(-)$1	227	98	108	15.1724
FFFFFFffff	chr8:95805915-95806147(+)$1	232	5	15	15.6034
:::::::::=	chr19:18545095-18545322(+)$1	227	174	184	15.0862
ppeeeeeiii	chr22:29183990-29184214(+)$1	224	188	198	15.1724
++++++++++	chr1:226548484-226548704(-)$1	220	43	53	18.3620
====!!eeee	chr5:65478967-65479194(+)$1	227	7	17	15.0000
::::HHHHHH	chr3:170111100-170111333(+)$1	233	4	14	14.0517
DDD{IIIIII	chr21:35470188-35470417(+)$1	229	103	113	18.4482
oeeeee::::	chr5:114859168-114859394(-)$1	226	94	104	17.9310
f''''''''f	chr7:107399984-107400205(+)$1	221	45	55	14.3103
fffff22ddd	chr1:245006658-245006905(-)$1	247	49	59	14.1379
::::::eeee	chr10:82191847-82192071(+)$1	224	65	75	15.0000
niiiiiiiii	chr2:210884894-210885127(+)$1	233	29	39	18.4482
ffff333ccc	chr8:31031114-31031345(+)$1	231	88	98	15.5172
++++++++++	chr2:160624856-160625084(+)$1	228	34	44	14.7413
ffffff::::	chr12:77244799-77245028(+)$1	229	97	107	15.0862
hhhh::::::	chr6:116956761-116956989(-)$1	228	214	224	18.1896
[=========	chr6:159054770-159054996(+)$1	226	62	72	21.9827
eeooooooee	chr18:57571361-57571583(+)$1	222	48	58	18.3620
qqqqqqqqcc	chr15:40954721-40954947(+)$1	226	39	49	14.2241
::::::::::	chr10:120441807-120442032(-)$1	225	112	122	15.8620
::::::::::	chrX:118718189-118718415(+)$1	226	208	218	18.5344
EEEE{CCCLL	chr9:80944466-80944719(+)$1	253	78	88	14.0517
h+++++++++	chr1:51737253-51737485(+)$1	232	35	45	15.3448
eeeee[bb##	chr2:135713146-135713376(+)$1	230	24	34	13.7931
:FFFFFFNNN	chr15:52841346-52841567(-)$1	221	0	10	21.9827
cdddd$$$$$	chr4:71896023-71896259(+)$1	236	25	35	14.0517
ddd:::::::	chr19:34891070-34891291(+)$1	221	181	191	18.6206
hhhhh:::::	chr1:59247106-59247329(-)$1	223	108	118	16.4655
::::::::::	chr16:24583889-24584116(+)$1	227	101	111	14.7413
ccccccoooo	chr14:77253507-77253732(-)$1	225	62	72	13.9655
:GGGGGGGDD	chr1:117117106-117117329(-)$1	223	210	220	17.5862
d+++++++++	chr4:22389068-22389291(-)$1	223	125	135	14.3103
::========	chr19:35176474-35176695(+)$1	221	186	196	15.0000
:::::::fff	chr1:77557619-77557839(-)$1	220	138	148	14.9137
UUUUUUUGGG	chr6:117881348-117881574(-)$1	226	44	54	14.7413
wwwwwwwwww	chr17:1553825-1554057(-)$1	232	150	160	21.9827
qccc4444ee	chr4:95585308-95585529(+)$1	221	119	129	15.0862
JJJJJJJJJJ	chr1:202861082-202861306(-)$1	224	80	90	18.5344
e[bb!!dddd	chr14:21731645-21731864(-)$1	219	40	50	21.9827
cc"""ccc[d	chr2:238008545-238008767(+)$1	222	39	49	14.6551
ffffff:::E	chr5:79923559-79923781(-)$1	222	84	94	14.3103
=====####d	chr6:151779388-151779612(+)$1	224	52	62	15.3448
eee!!dddd[	chr8:26362265-26362499(-)$1	234	17	27	15.0000
DDDD::::::	chr7:134654266-134654495(+)$1	229	211	221	15.0862
::::::::::	chr7:105731885-105732106(-)$1	221	105	115	15.7758
hhhhhh"""e	chr21:30426675-30426896(+)$1	221	18	28	14.2241
zzzzzzzzzz	chr14:50081255-50081485(+)$1	230	146	156	14.9137
eee]======	chr1:109181436-109181659(+)$1	223	140	150	14.2241
iiiiiii]==	chr20:7967915-7968136(-)$1	221	72	82	17.8448
:IIIIIIIII	chr11:30359295-30359523(+)$1	228	167	177	16.0344
eeee((((((	chr4:39781989-39782215(+)$1	226	9	19	14.5689

#DB
.(((((((((	chr7:89865195-89865419(+)$1	1	1	11	14.8275
..........	chr5:112204475-112204719(+)$1	1	116	126	18.4482
((((((((((	chr6:24423877-24424104(+)$1	1	66	76	18.3620
..........	chr18:12986675-12986900(+)$1	1	125	135	21.9827
)..(((...(	chr10:85912208-85912430(+)$1	1	52	62	15.4310
.((((((((.	chr12:66737290-66737514(+)$1	1	97	107	15.5172
((((((((..	chr3:119540322-119540549(-)$1	1	98	108	15.1724
((((((((((	chr8:95805915-95806147(+)$1	1	5	15	15.6034
.........(	chr19:18545095-18545322(+)$1	1	174	184	15.0862
..))))))))	chr22:29183990-29184214(+)$1	1	188	198	15.1724
..........	chr1:226548484-226548704(-)$1	1	43	53	18.3620
((((..((((	chr5:65478967-65479194(+)$1	1	7	17	15.0000
....((((((	chr3:170111100-170111333(+)$1	1	4	14	14.0517
(((.((((((	chr21:35470188-35470417(+)$1	1	103	113	18.4482
.)))))....	chr5:114859168-114859394(-)$1	1	94	104	17.9310
(........(	chr7:107399984-107400205(+)$1	1	45	55	14.3103
)))))..)))	chr1:245006658-245006905(-)$1	1	49	59	14.1379
......((((	chr10:82191847-82192071(+)$1	1	65	75	15.0000
.)))))))))	chr2:210884894-210885127(+)$1	1	29	39	18.4482
))))...)))	chr8:31031114-31031345(+)$1	1	88	98	15.5172
..........	chr2:160624856-160625084(+)$1	1	34	44	14.7413
))))))....	chr12:77244799-77245028(+)$1	1	97	107	15.0862
))))......	chr6:116956761-116956989(-)$1	1	214	224	18.1896
.(((((((((	chr6:159054770-159054996(+)$1	1	62	72	21.9827
((......))	chr18:57571361-57571583(+)$1	1	48	58	18.3620
........))	chr15:40954721-40954947(+)$1	1	39	49	14.2241
..........	chr10:120441807-120442032(-)$1	1	112	122	15.8620
..........	chrX:118718189-118718415(+)$1	1	208	218	18.5344
((((.(((..	chr9:80944466-80944719(+)$1	1	78	88	14.0517
(.........	chr1:51737253-51737485(+)$1	1	35	45	15.3448
(((((.((..	chr2:135713146-135713376(+)$1	1	24	34	13.7931
.((((((...	chr15:52841346-52841567(-)$1	1	0	10	21.9827
(((((.....	chr4:71896023-71896259(+)$1	1	25	35	14.0517
))).......	chr19:34891070-34891291(+)$1	1	181	191	18.6206
))))).....	chr1:59247106-59247329(-)$1	1	108	118	16.4655
..........	chr16:24583889-24584116(+)$1	1	101	111	14.7413
)))(((....	chr14:77253507-77253732(-)$1	1	62	72	13.9655
.)))))))))	chr1:117117106-117117329(-)$1	1	210	220	17.5862
(.........	chr4:22389068-22389291(-)$1	1	125	135	14.3103
..((((((((	chr19:35176474-35176695(+)$1	1	186	196	15.0000
.......(((	chr1:77557619-77557839(-)$1	1	138	148	14.9137
.......(((	chr6:117881348-117881574(-)$1	1	44	54	14.7413
..........	chr17:1553825-1554057(-)$1	1	150	160	21.9827
.)))....))	chr4:95585308-95585529(+)$1	1	119	129	15.0862
((((((((((	chr1:202861082-202861306(-)$1	1	80	90	18.5344
(.((..((((	chr14:21731645-21731864(-)$1	1	40	50	21.9827
((...(((.(	chr2:238008545-238008767(+)$1	1	39	49	14.6551
))))))...)	chr5:79923559-79923781(-)$1	1	84	94	14.3103
(((((....(	chr6:151779388-151779612(+)$1	1	52	62	15.3448
(((..((((.	chr8:26362265-26362499(-)$1	1	17	27	15.0000
))))......	chr7:134654266-134654495(+)$1	1	211	221	15.0862
..........	chr7:105731885-105732106(-)$1	1	105	115	15.7758
((((((...(	chr21:30426675-30426896(+)$1	1	18	28	14.2241
..........	chr14:50081255-50081485(+)$1	1	146	156	14.9137
))).))))))	chr1:109181436-109181659(+)$1	1	140	150	14.2241
))))))).))	chr20:7967915-7968136(-)$1	1	72	82	17.8448
.)))))))))	chr11:30359295-30359523(+)$1	1	167	177	16.0344
((((......	chr4:39781989-39782215(+)$1	1	9	19	14.5689

#PSSM
U : 0.79	A : 0.13	u : 0.06	
G : 0.68	A : 0.15	g : 0.05	C : 0.05	U : 0.03	a : 0.01	
U : 0.70	A : 0.08	C : 0.08	u : 0.05	G : 0.05	c : 0.01	
U : 0.68	A : 0.15	C : 0.06	u : 0.03	a : 0.03	G : 0.01	
U : 0.86	u : 0.06	A : 0.05	G : 0.01	
U : 0.77	A : 0.08	u : 0.06	G : 0.03	C : 0.03	
U : 0.81	u : 0.06	C : 0.05	A : 0.05	G : 0.01	
U : 0.79	C : 0.06	u : 0.05	G : 0.05	c : 0.01	A : 0.01	
U : 0.82	u : 0.05	C : 0.05	A : 0.03	G : 0.01	g : 0.01	
U : 0.86	u : 0.06	A : 0.05	C : 0.01	

#score	942.9310344827588
#seq	58
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m1_run1.nuc.txt

#NT
UUUUUG	chr3:10188168-10188416(+)$1	248	128	134	16.7878
UUUUUA	chr1:31425015-31425270(-)$1	255	41	47	14.2121
UUUUUG	chr17:65944100-65944349(+)$1	249	2	8	16.7878
UUUUUG	chr10:28908366-28908600(+)$1	234	106	112	16.7878
UUUUUG	chr6:111621215-111621445(-)$1	230	60	66	16.7878
UUUUUA	chr1:154186292-154186518(-)$1	226	56	62	14.2121
UUUUUA	chr1:115280525-115280752(-)$1	227	52	58	14.2121
UUUUUG	chr5:134192926-134193154(+)$1	228	51	57	16.7878
UUUUUG	chr22:50637408-50637656(+)$1	248	82	88	16.7878
UUUUUG	chr7:105733368-105733598(-)$1	230	3	9	16.7878
UUUUUG	chr5:36183943-36184196(+)$1	253	123	129	16.7878
UUUUUA	chr4:122737900-122738140(-)$1	240	12	18	14.2121
UUUUUG	chr12:112845943-112846233(-)$1	290	248	254	16.7878
UUUUUG	chr5:176696585-176696826(+)$1	241	106	112	16.7878
UUUUUG	chr1:205683540-205683787(-)$1	247	122	128	16.7878
UUUUUG	chr12:50152946-50153194(+)$1	248	100	106	16.7878
UUUUUG	chr6:75965705-75965942(-)$1	237	8	14	16.7878
UUUUUG	chr1:31465130-31465364(-)$1	234	102	108	16.7878
UUUUUG	chr16:18852981-18853215(-)$1	234	5	11	16.7878
UUUUUG	chr7:128412479-128412737(+)$1	258	13	19	16.7878
UUUUUG	chr20:34302165-34302377(-)$1	212	186	192	16.7878
UUUUUG	chr5:162866393-162866622(+)$1	229	150	156	16.7878
UUUUUG	chr1:243800826-243801068(-)$1	242	186	192	16.7878
UUUUUA	chr5:68473060-68473290(+)$1	230	193	199	14.2121
UUUUUA	chr19:34935879-34936126(+)$1	247	136	142	14.2121
UUUUUG	chr1:33149750-33149988(+)$1	238	12	18	16.7878
UUUUUA	chr5:180664579-180664818(-)$1	239	13	19	14.2121
UUUUUG	chr10:126630965-126631204(+)$1	239	7	13	16.7878
UUUUUG	chr1:229440881-229441115(+)$1	234	185	191	16.7878
UUUUUG	chr10:7844165-7844424(+)$1	259	5	11	16.7878
UUUUUG	chr1:115266481-115266723(-)$1	242	27	33	16.7878
UUUUUA	chr17:38545606-38545890(-)$1	284	228	234	14.2121

#otherMatches

#Struct PSSM
GGGGG:	chr1:214819501-214819730(+)$1	229	10	16	16.7878
hh::dd	chr3:10188168-10188416(+)$1	248	128	134	16.7878
NNNNCC	chr1:31425015-31425270(-)$1	255	41	47	14.2121
FFFFFe	chr17:65944100-65944349(+)$1	249	2	8	16.7878
""dddd	chr10:28908366-28908600(+)$1	234	106	112	16.7878
hhhhhh	chr6:111621215-111621445(-)$1	230	60	66	16.7878
:::eee	chr1:154186292-154186518(-)$1	226	56	62	14.2121
mmmm==	chr1:115280525-115280752(-)$1	227	52	58	14.2121
f::::I	chr5:134192926-134193154(+)$1	228	51	57	16.7878
GGGGGC	chr22:50637408-50637656(+)$1	248	82	88	16.7878
:::::g	chr7:105733368-105733598(-)$1	230	3	9	16.7878
seeeee	chr5:36183943-36184196(+)$1	253	123	129	16.7878
ee!!gg	chr4:122737900-122738140(-)$1	240	12	18	14.2121
eee!!a	chr12:112845943-112846233(-)$1	290	248	254	16.7878
hhhhhh	chr5:176696585-176696826(+)$1	241	106	112	16.7878
nnnnne	chr1:205683540-205683787(-)$1	247	122	128	16.7878
!a!!cc	chr12:50152946-50153194(+)$1	248	100	106	16.7878
mmmmcc	chr6:75965705-75965942(-)$1	237	8	14	16.7878
ssssss	chr1:31465130-31465364(-)$1	234	102	108	16.7878
nnnndd	chr16:18852981-18853215(-)$1	234	5	11	16.7878
GGGGLL	chr7:128412479-128412737(+)$1	258	13	19	16.7878
YYCCCH	chr20:34302165-34302377(-)$1	212	186	192	16.7878
ee"""c	chr5:162866393-162866622(+)$1	229	150	156	16.7878
::::::	chr1:243800826-243801068(-)$1	242	186	192	16.7878
::::::	chr5:68473060-68473290(+)$1	230	193	199	14.2121
fffnnn	chr19:34935879-34936126(+)$1	247	136	142	14.2121
pppppa	chr1:33149750-33149988(+)$1	238	12	18	16.7878
::::::	chr5:180664579-180664818(-)$1	239	13	19	14.2121
F::::c	chr10:126630965-126631204(+)$1	239	7	13	16.7878
mmmmcc	chr1:229440881-229441115(+)$1	234	185	191	16.7878
FF::ff	chr10:7844165-7844424(+)$1	259	5	11	16.7878
JJJJJJ	chr1:115266481-115266723(-)$1	242	27	33	16.7878
hhhhoo	chr17:38545606-38545890(-)$1	284	228	234	14.2121

#DB
(((((.	chr1:214819501-214819730(+)$1	1	10	16	16.7878
))..((	chr3:10188168-10188416(+)$1	1	128	134	16.7878
....((	chr1:31425015-31425270(-)$1	1	41	47	14.2121
((((((	chr17:65944100-65944349(+)$1	1	2	8	16.7878
..((((	chr10:28908366-28908600(+)$1	1	106	112	16.7878
))))))	chr6:111621215-111621445(-)$1	1	60	66	16.7878
...(((	chr1:154186292-154186518(-)$1	1	56	62	14.2121
....))	chr1:115280525-115280752(-)$1	1	52	58	14.2121
)....(	chr5:134192926-134193154(+)$1	1	51	57	16.7878
((((((	chr22:50637408-50637656(+)$1	1	82	88	16.7878
.....(	chr7:105733368-105733598(-)$1	1	3	9	16.7878
.)))))	chr5:36183943-36184196(+)$1	1	123	129	16.7878
((..((	chr4:122737900-122738140(-)$1	1	12	18	14.2121
(((..(	chr12:112845943-112846233(-)$1	1	248	254	16.7878
((((((	chr5:176696585-176696826(+)$1	1	106	112	16.7878
.....)	chr1:205683540-205683787(-)$1	1	122	128	16.7878
.(..((	chr12:50152946-50153194(+)$1	1	100	106	16.7878
....))	chr6:75965705-75965942(-)$1	1	8	14	16.7878
......	chr1:31465130-31465364(-)$1	1	102	108	16.7878
....))	chr16:18852981-18853215(-)$1	1	5	11	16.7878
((((..	chr7:128412479-128412737(+)$1	1	13	19	16.7878
..))))	chr20:34302165-34302377(-)$1	1	186	192	16.7878
((...(	chr5:162866393-162866622(+)$1	1	150	156	16.7878
......	chr1:243800826-243801068(-)$1	1	186	192	16.7878
......	chr5:68473060-68473290(+)$1	1	193	199	14.2121
(((...	chr19:34935879-34936126(+)$1	1	136	142	14.2121
.....)	chr1:33149750-33149988(+)$1	1	12	18	16.7878
......	chr5:180664579-180664818(-)$1	1	13	19	14.2121
(....(	chr10:126630965-126631204(+)$1	1	7	13	16.7878
....))	chr1:229440881-229441115(+)$1	1	185	191	16.7878
((..((	chr10:7844165-7844424(+)$1	1	5	11	16.7878
((((((	chr1:115266481-115266723(-)$1	1	27	33	16.7878
((((..	chr17:38545606-38545890(-)$1	1	228	234	14.2121

#PSSM
U : 0.99	
U : 0.99	
U : 0.99	
U : 0.99	
U : 0.99	
G : 0.75	A : 0.24	

#score	533.3939393939388
#seq	33
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m2_run2.nuc.txt

#NT
UCA	chr1:211746501-211746726(-)$1	225	62	65	9.0000
UCA	chr11:10825617-10825839(-)$1	222	93	96	9.0000
UCA	chr6:11581385-11581620(+)$1	235	24	27	9.0000
UCA	chr1:179887409-179887642(+)$1	233	10	13	9.0000
UCA	chr5:122951856-122952079(+)$1	223	6	9	9.0000
UCA	chr18:29205174-29205401(-)$1	227	123	126	9.0000
UCA	chr1:203768687-203768919(+)$1	232	2	5	9.0000
UCA	chr10:63168823-63169057(-)$1	234	41	44	9.0000
UCA	chr22:32077777-32077997(-)$1	220	89	92	9.0000
UCA	chr7:138985760-138985984(+)$1	224	12	15	9.0000
UCA	chr9:95077999-95078228(-)$1	229	120	123	9.0000
UCA	chr13:77455720-77455944(-)$1	224	46	49	9.0000
UCA	chr6:86322047-86322281(-)$1	234	136	139	9.0000
UCA	chr7:44916215-44916437(-)$1	222	31	34	9.0000
UCA	chr8:28425494-28425717(+)$1	223	33	36	9.0000
UCA	chr2:198256355-198256573(-)$1	218	29	32	9.0000
UCA	chr11:130100457-130100683(-)$1	226	8	11	9.0000
UCA	chr1:245016793-245017030(-)$1	237	199	202	9.0000
UCA	chr11:108029515-108029739(-)$1	224	11	14	9.0000
UCA	chr13:46626692-46626916(-)$1	224	193	196	9.0000
UCA	chrX:103436428-103436651(+)$1	223	23	26	9.0000
uca	chr11:8019431-8019661(+)$1	230	114	117	9.0000
UCA	chr11:47490778-47491015(-)$1	237	39	42	9.0000
UCA	chr15:45899367-45899592(+)$1	225	75	78	9.0000
UCA	chr10:98722348-98722571(+)$1	223	13	16	9.0000
UCA	chr12:118471001-118471232(+)$1	231	89	92	9.0000
UCA	chr2:201844595-201844815(-)$1	220	110	113	9.0000
UCA	chr11:32126167-32126410(+)$1	243	20	23	9.0000
UCA	chr12:53807544-53807779(+)$1	235	118	121	9.0000
UCA	chr18:19445691-19445917(+)$1	226	99	102	9.0000
UCA	chr10:115670260-115670485(+)$1	225	22	25	9.0000
UCA	chr7:138983990-138984217(+)$1	227	31	34	9.0000
UCA	chr1:229576960-229577191(-)$1	231	10	13	9.0000
UCA	chr5:135513725-135513955(+)$1	230	64	67	9.0000
UCA	chrX:46740627-46740851(+)$1	224	5	8	9.0000
UCA	chr1:100661618-100661839(-)$1	221	101	104	9.0000
UCA	chr16:48395202-48395426(-)$1	224	125	128	9.0000
UCA	chr2:231683315-231683538(+)$1	223	4	7	9.0000
uca	chr17:54965809-54966032(-)$1	223	46	49	9.0000
UCA	chr6:114261914-114262136(-)$1	222	35	38	9.0000
UCA	chr1:235506388-235506614(+)$1	226	143	146	9.0000
UCA	chr10:115676351-115676576(+)$1	225	7	10	9.0000
UCA	chr12:9092879-9093116(-)$1	237	111	114	9.0000
UCA	chr1:204374455-204374697(-)$1	242	29	32	9.0000
UCA	chr16:69341249-69341473(+)$1	224	19	22	9.0000
UCA	chr1:156691608-156691834(-)$1	226	14	17	9.0000
UCA	chr11:106549525-106549749(-)$1	224	8	11	9.0000
UCA	chr11:13752462-13752695(+)$1	233	35	38	9.0000
UCA	chr16:19553251-19553481(+)$1	230	94	97	9.0000
UCA	chr9:114985013-114985239(-)$1	226	8	11	9.0000
UCA	chr3:196555188-196555420(+)$1	232	50	53	9.0000
UCA	chr8:29964727-29964961(+)$1	234	16	19	9.0000
UCA	chr11:58921820-58922043(+)$1	223	18	21	9.0000
UCA	chr17:40767092-40767317(+)$1	225	35	38	9.0000
UCA	chr12:109179283-109179504(-)$1	221	113	116	9.0000
UCA	chr12:111157937-111158165(-)$1	228	29	32	9.0000
UCA	chr1:227968750-227968971(+)$1	221	6	9	9.0000
UCA	chr20:30389013-30389246(+)$1	233	82	85	9.0000
UCA	chr3:188592329-188592569(+)$1	240	13	16	9.0000
UCA	chr5:151185230-151185463(+)$1	233	38	41	9.0000
UCA	chr9:123941669-123941906(-)$1	237	56	59	9.0000
UCA	chr18:319354-319579(-)$1	225	68	71	9.0000
UCA	chr11:32998414-32998642(+)$1	228	24	27	9.0000
UCA	chr12:125515456-125515677(+)$1	221	132	135	9.0000
UCA	chr5:112173966-112174208(+)$1	242	7	10	9.0000
UCA	chr5:133938136-133938371(-)$1	235	110	113	9.0000
UCA	chr12:100734003-100734227(+)$1	224	75	78	9.0000
UCA	chr9:72332012-72332241(-)$1	229	14	17	9.0000
UCA	chr3:73118120-73118353(+)$1	233	29	32	9.0000
uca	chr11:17394127-17394350(+)$1	223	62	65	9.0000
UCA	chr5:137843300-137843523(-)$1	223	1	4	9.0000
UCA	chr5:78622450-78622672(+)$1	222	104	107	9.0000
UCA	chr3:58304764-58305009(+)$1	245	52	55	9.0000
uca	chr5:81569754-81569985(-)$1	231	37	40	9.0000
UCA	chr6:163994187-163994409(+)$1	222	30	33	9.0000
UCA	chr1:87571711-87571937(+)$1	226	101	104	9.0000
UCA	chr2:128057562-128057786(-)$1	224	43	46	9.0000
UCA	chr17:44249062-44249290(-)$1	228	54	57	9.0000
UCA	chr8:105502082-105502304(-)$1	222	97	100	9.0000
UCA	chr18:43845181-43845417(+)$1	236	48	51	9.0000
UCA	chr20:33097677-33097909(+)$1	232	64	67	9.0000
UCA	chr2:87002693-87002917(+)$1	224	27	30	9.0000
UCA	chr10:69677427-69677653(+)$1	226	150	153	9.0000
UCA	chr6:144147811-144148036(+)$1	225	25	28	9.0000
UCA	chr12:42481298-42481521(-)$1	223	14	17	9.0000
uca	chr1:97285485-97285712(+)$1	227	176	179	9.0000
UCA	chr15:52357675-52357904(+)$1	229	13	16	9.0000
UCA	chr8:22879250-22879503(-)$1	253	171	174	9.0000
UCA	chr16:15705396-15705621(-)$1	225	95	98	9.0000
UCA	chr6:111545879-111546104(+)$1	225	99	102	9.0000
UCA	chr13:108885562-108885794(+)$1	232	11	14	9.0000
UCA	chrX:133561303-133561534(+)$1	231	2	5	9.0000
UCA	chrX:24231971-24232221(+)$1	250	42	45	9.0000
UCA	chr13:42893443-42893686(+)$1	243	24	27	9.0000
UCA	chr3:38530525-38530756(+)$1	231	22	25	9.0000
UCA	chr18:28647816-28648041(-)$1	225	168	171	9.0000
UCA	chr3:196311927-196312156(+)$1	229	47	50	9.0000
UCA	chr14:103807317-103807547(+)$1	230	30	33	9.0000
UCA	chrX:129537796-129538025(+)$1	229	12	15	9.0000

#otherMatches

#Struct PSSM
:::	chr5:98129623-98129851(+)$1	228	0	3	9.0000
hhh	chr1:211746501-211746726(-)$1	225	62	65	9.0000
JJJ	chr11:10825617-10825839(-)$1	222	93	96	9.0000
mbb	chr6:11581385-11581620(+)$1	235	24	27	9.0000
WWW	chr1:179887409-179887642(+)$1	233	10	13	9.0000
::F	chr5:122951856-122952079(+)$1	223	6	9	9.0000
cc2	chr18:29205174-29205401(-)$1	227	123	126	9.0000
C{E	chr1:203768687-203768919(+)$1	232	2	5	9.0000
::d	chr10:63168823-63169057(-)$1	234	41	44	9.0000
mbb	chr22:32077777-32077997(-)$1	220	89	92	9.0000
EEE	chr7:138985760-138985984(+)$1	224	12	15	9.0000
FFF	chr9:95077999-95078228(-)$1	229	120	123	9.0000
eee	chr13:77455720-77455944(-)$1	224	46	49	9.0000
!cc	chr6:86322047-86322281(-)$1	234	136	139	9.0000
DLL	chr7:44916215-44916437(-)$1	222	31	34	9.0000
lee	chr8:28425494-28425717(+)$1	223	33	36	9.0000
eee	chr2:198256355-198256573(-)$1	218	29	32	9.0000
{DD	chr11:130100457-130100683(-)$1	226	8	11	9.0000
gnn	chr1:245016793-245017030(-)$1	237	199	202	9.0000
DDD	chr11:108029515-108029739(-)$1	224	11	14	9.0000
rre	chr13:46626692-46626916(-)$1	224	193	196	9.0000
ttt	chrX:103436428-103436651(+)$1	223	23	26	9.0000
FYY	chr11:8019431-8019661(+)$1	230	114	117	9.0000
ddd	chr11:47490778-47491015(-)$1	237	39	42	9.0000
ddm	chr15:45899367-45899592(+)$1	225	75	78	9.0000
fmm	chr10:98722348-98722571(+)$1	223	13	16	9.0000
GGG	chr12:118471001-118471232(+)$1	231	89	92	9.0000
:::	chr2:201844595-201844815(-)$1	220	110	113	9.0000
MMM	chr11:32126167-32126410(+)$1	243	20	23	9.0000
ppd	chr12:53807544-53807779(+)$1	235	118	121	9.0000
fff	chr18:19445691-19445917(+)$1	226	99	102	9.0000
vvv	chr10:115670260-115670485(+)$1	225	22	25	9.0000
uuu	chr7:138983990-138984217(+)$1	227	31	34	9.0000
JJJ	chr1:229576960-229577191(-)$1	231	10	13	9.0000
:::	chr5:135513725-135513955(+)$1	230	64	67	9.0000
{GG	chrX:46740627-46740851(+)$1	224	5	8	9.0000
:::	chr1:100661618-100661839(-)$1	221	101	104	9.0000
CCZ	chr16:48395202-48395426(-)$1	224	125	128	9.0000
:::	chr2:231683315-231683538(+)$1	223	4	7	9.0000
>>>	chr17:54965809-54966032(-)$1	223	46	49	9.0000
::f	chr6:114261914-114262136(-)$1	222	35	38	9.0000
:::	chr1:235506388-235506614(+)$1	226	143	146	9.0000
DDD	chr10:115676351-115676576(+)$1	225	7	10	9.0000
^dd	chr12:9092879-9093116(-)$1	237	111	114	9.0000
]ee	chr1:204374455-204374697(-)$1	242	29	32	9.0000
(((	chr16:69341249-69341473(+)$1	224	19	22	9.0000
ppp	chr1:156691608-156691834(-)$1	226	14	17	9.0000
ccc	chr11:106549525-106549749(-)$1	224	8	11	9.0000
eeb	chr11:13752462-13752695(+)$1	233	35	38	9.0000
bb]	chr16:19553251-19553481(+)$1	230	94	97	9.0000
::f	chr9:114985013-114985239(-)$1	226	8	11	9.0000
ccc	chr3:196555188-196555420(+)$1	232	50	53	9.0000
ee[	chr8:29964727-29964961(+)$1	234	16	19	9.0000
ccc	chr11:58921820-58922043(+)$1	223	18	21	9.0000
ddd	chr17:40767092-40767317(+)$1	225	35	38	9.0000
ddd	chr12:109179283-109179504(-)$1	221	113	116	9.0000
hhh	chr12:111157937-111158165(-)$1	228	29	32	9.0000
CCM	chr1:227968750-227968971(+)$1	221	6	9	9.0000
fdd	chr20:30389013-30389246(+)$1	233	82	85	9.0000
EEE	chr3:188592329-188592569(+)$1	240	13	16	9.0000
fff	chr5:151185230-151185463(+)$1	233	38	41	9.0000
[dd	chr9:123941669-123941906(-)$1	237	56	59	9.0000
ddq	chr18:319354-319579(-)$1	225	68	71	9.0000
qqd	chr11:32998414-32998642(+)$1	228	24	27	9.0000
g""	chr12:125515456-125515677(+)$1	221	132	135	9.0000
::G	chr5:112173966-112174208(+)$1	242	7	10	9.0000
JJJ	chr5:133938136-133938371(-)$1	235	110	113	9.0000
qqq	chr12:100734003-100734227(+)$1	224	75	78	9.0000
FFF	chr9:72332012-72332241(-)$1	229	14	17	9.0000
==m	chr3:73118120-73118353(+)$1	233	29	32	9.0000
hhh	chr11:17394127-17394350(+)$1	223	62	65	9.0000
eee	chr5:137843300-137843523(-)$1	223	1	4	9.0000
eee	chr5:78622450-78622672(+)$1	222	104	107	9.0000
ppp	chr3:58304764-58305009(+)$1	245	52	55	9.0000
f%%	chr5:81569754-81569985(-)$1	231	37	40	9.0000
hhh	chr6:163994187-163994409(+)$1	222	30	33	9.0000
eee	chr1:87571711-87571937(+)$1	226	101	104	9.0000
^^i	chr2:128057562-128057786(-)$1	224	43	46	9.0000
b""	chr17:44249062-44249290(-)$1	228	54	57	9.0000
fff	chr8:105502082-105502304(-)$1	222	97	100	9.0000
ddd	chr18:43845181-43845417(+)$1	236	48	51	9.0000
ggg	chr20:33097677-33097909(+)$1	232	64	67	9.0000
eee	chr2:87002693-87002917(+)$1	224	27	30	9.0000
ppp	chr10:69677427-69677653(+)$1	226	150	153	9.0000
NCC	chr6:144147811-144148036(+)$1	225	25	28	9.0000
cco	chr12:42481298-42481521(-)$1	223	14	17	9.0000
ee[	chr1:97285485-97285712(+)$1	227	176	179	9.0000
ooo	chr15:52357675-52357904(+)$1	229	13	16	9.0000
ee:	chr8:22879250-22879503(-)$1	253	171	174	9.0000
f::	chr16:15705396-15705621(-)$1	225	95	98	9.0000
dll	chr6:111545879-111546104(+)$1	225	99	102	9.0000
hhh	chr13:108885562-108885794(+)$1	232	11	14	9.0000
:::	chrX:133561303-133561534(+)$1	231	2	5	9.0000
hhh	chrX:24231971-24232221(+)$1	250	42	45	9.0000
LLL	chr13:42893443-42893686(+)$1	243	24	27	9.0000
fff	chr3:38530525-38530756(+)$1	231	22	25	9.0000
ggg	chr18:28647816-28648041(-)$1	225	168	171	9.0000
ttt	chr3:196311927-196312156(+)$1	229	47	50	9.0000
dd3	chr14:103807317-103807547(+)$1	230	30	33	9.0000
d""	chrX:129537796-129538025(+)$1	229	12	15	9.0000

#DB
...	chr5:98129623-98129851(+)$1	1	0	3	9.0000
(((	chr1:211746501-211746726(-)$1	1	62	65	9.0000
(((	chr11:10825617-10825839(-)$1	1	93	96	9.0000
.))	chr6:11581385-11581620(+)$1	1	24	27	9.0000
...	chr1:179887409-179887642(+)$1	1	10	13	9.0000
..(	chr5:122951856-122952079(+)$1	1	6	9	9.0000
)).	chr18:29205174-29205401(-)$1	1	123	126	9.0000
(.(	chr1:203768687-203768919(+)$1	1	2	5	9.0000
..(	chr10:63168823-63169057(-)$1	1	41	44	9.0000
.))	chr22:32077777-32077997(-)$1	1	89	92	9.0000
(((	chr7:138985760-138985984(+)$1	1	12	15	9.0000
(((	chr9:95077999-95078228(-)$1	1	120	123	9.0000
(((	chr13:77455720-77455944(-)$1	1	46	49	9.0000
.((	chr6:86322047-86322281(-)$1	1	136	139	9.0000
(..	chr7:44916215-44916437(-)$1	1	31	34	9.0000
.))	chr8:28425494-28425717(+)$1	1	33	36	9.0000
)))	chr2:198256355-198256573(-)$1	1	29	32	9.0000
.((	chr11:130100457-130100683(-)$1	1	8	11	9.0000
(..	chr1:245016793-245017030(-)$1	1	199	202	9.0000
(((	chr11:108029515-108029739(-)$1	1	11	14	9.0000
..)	chr13:46626692-46626916(-)$1	1	193	196	9.0000
...	chrX:103436428-103436651(+)$1	1	23	26	9.0000
)..	chr11:8019431-8019661(+)$1	1	114	117	9.0000
(((	chr11:47490778-47491015(-)$1	1	39	42	9.0000
((.	chr15:45899367-45899592(+)$1	1	75	78	9.0000
(..	chr10:98722348-98722571(+)$1	1	13	16	9.0000
)))	chr12:118471001-118471232(+)$1	1	89	92	9.0000
...	chr2:201844595-201844815(-)$1	1	110	113	9.0000
...	chr11:32126167-32126410(+)$1	1	20	23	9.0000
..)	chr12:53807544-53807779(+)$1	1	118	121	9.0000
(((	chr18:19445691-19445917(+)$1	1	99	102	9.0000
...	chr10:115670260-115670485(+)$1	1	22	25	9.0000
...	chr7:138983990-138984217(+)$1	1	31	34	9.0000
(((	chr1:229576960-229577191(-)$1	1	10	13	9.0000
...	chr5:135513725-135513955(+)$1	1	64	67	9.0000
.((	chrX:46740627-46740851(+)$1	1	5	8	9.0000
...	chr1:100661618-100661839(-)$1	1	101	104	9.0000
)).	chr16:48395202-48395426(-)$1	1	125	128	9.0000
...	chr2:231683315-231683538(+)$1	1	4	7	9.0000
...	chr17:54965809-54966032(-)$1	1	46	49	9.0000
..(	chr6:114261914-114262136(-)$1	1	35	38	9.0000
...	chr1:235506388-235506614(+)$1	1	143	146	9.0000
(((	chr10:115676351-115676576(+)$1	1	7	10	9.0000
.))	chr12:9092879-9093116(-)$1	1	111	114	9.0000
.))	chr1:204374455-204374697(-)$1	1	29	32	9.0000
...	chr16:69341249-69341473(+)$1	1	19	22	9.0000
...	chr1:156691608-156691834(-)$1	1	14	17	9.0000
(((	chr11:106549525-106549749(-)$1	1	8	11	9.0000
)))	chr11:13752462-13752695(+)$1	1	35	38	9.0000
)).	chr16:19553251-19553481(+)$1	1	94	97	9.0000
..(	chr9:114985013-114985239(-)$1	1	8	11	9.0000
)))	chr3:196555188-196555420(+)$1	1	50	53	9.0000
((.	chr8:29964727-29964961(+)$1	1	16	19	9.0000
(((	chr11:58921820-58922043(+)$1	1	18	21	9.0000
)))	chr17:40767092-40767317(+)$1	1	35	38	9.0000
)))	chr12:109179283-109179504(-)$1	1	113	116	9.0000
(((	chr12:111157937-111158165(-)$1	1	29	32	9.0000
((.	chr1:227968750-227968971(+)$1	1	6	9	9.0000
(((	chr20:30389013-30389246(+)$1	1	82	85	9.0000
(((	chr3:188592329-188592569(+)$1	1	13	16	9.0000
(((	chr5:151185230-151185463(+)$1	1	38	41	9.0000
.((	chr9:123941669-123941906(-)$1	1	56	59	9.0000
((.	chr18:319354-319579(-)$1	1	68	71	9.0000
..)	chr11:32998414-32998642(+)$1	1	24	27	9.0000
(..	chr12:125515456-125515677(+)$1	1	132	135	9.0000
..(	chr5:112173966-112174208(+)$1	1	7	10	9.0000
(((	chr5:133938136-133938371(-)$1	1	110	113	9.0000
...	chr12:100734003-100734227(+)$1	1	75	78	9.0000
(((	chr9:72332012-72332241(-)$1	1	14	17	9.0000
((.	chr3:73118120-73118353(+)$1	1	29	32	9.0000
(((	chr11:17394127-17394350(+)$1	1	62	65	9.0000
(((	chr5:137843300-137843523(-)$1	1	1	4	9.0000
)))	chr5:78622450-78622672(+)$1	1	104	107	9.0000
...	chr3:58304764-58305009(+)$1	1	52	55	9.0000
(..	chr5:81569754-81569985(-)$1	1	37	40	9.0000
)))	chr6:163994187-163994409(+)$1	1	30	33	9.0000
)))	chr1:87571711-87571937(+)$1	1	101	104	9.0000
..)	chr2:128057562-128057786(-)$1	1	43	46	9.0000
(..	chr17:44249062-44249290(-)$1	1	54	57	9.0000
)))	chr8:105502082-105502304(-)$1	1	97	100	9.0000
(((	chr18:43845181-43845417(+)$1	1	48	51	9.0000
)))	chr20:33097677-33097909(+)$1	1	64	67	9.0000
(((	chr2:87002693-87002917(+)$1	1	27	30	9.0000
...	chr10:69677427-69677653(+)$1	1	150	153	9.0000
.((	chr6:144147811-144148036(+)$1	1	25	28	9.0000
((.	chr12:42481298-42481521(-)$1	1	14	17	9.0000
((.	chr1:97285485-97285712(+)$1	1	176	179	9.0000
...	chr15:52357675-52357904(+)$1	1	13	16	9.0000
)).	chr8:22879250-22879503(-)$1	1	171	174	9.0000
)..	chr16:15705396-15705621(-)$1	1	95	98	9.0000
(..	chr6:111545879-111546104(+)$1	1	99	102	9.0000
(((	chr13:108885562-108885794(+)$1	1	11	14	9.0000
...	chrX:133561303-133561534(+)$1	1	2	5	9.0000
)))	chrX:24231971-24232221(+)$1	1	42	45	9.0000
...	chr13:42893443-42893686(+)$1	1	24	27	9.0000
(((	chr3:38530525-38530756(+)$1	1	22	25	9.0000
)))	chr18:28647816-28648041(-)$1	1	168	171	9.0000
...	chr3:196311927-196312156(+)$1	1	47	50	9.0000
)).	chr14:103807317-103807547(+)$1	1	30	33	9.0000
(..	chrX:129537796-129538025(+)$1	1	12	15	9.0000

#PSSM
U : 0.95	u : 0.05	
C : 0.95	c : 0.05	
A : 0.95	a : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m1_run2.nuc.txt

#NT
CAG	chr1:115280549-115280778(-)$1	229	50	53	9.0000
CAG	chr7:128843299-128843530(+)$1	231	19	22	9.0000
CAG	chr7:148987034-148987255(+)$1	221	12	15	9.0000
CAG	chr10:930309-930538(-)$1	229	89	92	9.0000
CAG	chr12:123099944-123100169(+)$1	225	69	72	9.0000
CAG	chr13:99947422-99947650(+)$1	228	8	11	9.0000
CAG	chr21:33750659-33750895(-)$1	236	63	66	9.0000
CAG	chrM:11700-11953(+)$1	253	73	76	9.0000
CAG	chr1:145439746-145439985(+)$1	239	28	31	9.0000
CAG	chr12:46600837-46601095(-)$1	258	73	76	9.0000
CAG	chr16:58619239-58619459(-)$1	220	23	26	9.0000
CAG	chrX:122745204-122745428(-)$1	224	36	39	9.0000
CAG	chr16:31195170-31195396(+)$1	226	8	11	9.0000
CAG	chr19:12825808-12826032(-)$1	224	0	3	9.0000
CAG	chr4:57886979-57887212(+)$1	233	30	33	9.0000
CAG	chr1:41457381-41457603(+)$1	222	63	66	9.0000
CAG	chr1:90179636-90179856(+)$1	220	82	85	9.0000
CAG	chr4:56262312-56262575(+)$1	263	36	39	9.0000
CAG	chr1:220213433-220213657(-)$1	224	58	61	9.0000
CAG	chr1:39951315-39951544(+)$1	229	4	7	9.0000
CAG	chr1:17749110-17749340(-)$1	230	5	8	9.0000
CAG	chr19:18546873-18547096(-)$1	223	0	3	9.0000
cag	chr19:49589683-49589908(+)$1	225	149	152	9.0000
CAG	chrX:122820306-122820531(-)$1	225	25	28	9.0000
CAG	chr17:80053176-80053404(-)$1	228	16	19	9.0000
CAG	chr13:25486796-25487049(-)$1	253	4	7	9.0000
CAG	chr5:137495672-137495903(-)$1	231	3	6	9.0000
CAG	chr19:1986839-1987058(-)$1	219	8	11	9.0000
CAG	chr16:2282436-2282676(+)$1	240	17	20	9.0000
CAG	chr1:37967353-37967578(-)$1	225	17	20	9.0000
CAG	chr11:130003460-130003687(+)$1	227	26	29	9.0000
CAG	chr19:54634662-54634883(+)$1	221	20	23	9.0000
CAG	chr10:1062939-1063167(+)$1	228	2	5	9.0000
CAG	chr4:8442688-8442917(+)$1	229	48	51	9.0000
CAG	chr19:19638418-19638659(+)$1	241	35	38	9.0000
CAG	chr7:72395938-72396161(+)$1	223	61	64	9.0000
CAG	chr20:2446301-2446524(-)$1	223	2	5	9.0000
CAG	chr10:129906723-129906959(-)$1	236	20	23	9.0000
CAG	chr9:139793134-139793377(+)$1	243	50	53	9.0000
CAG	chr19:44676968-44677197(+)$1	229	41	44	9.0000
CAG	chrX:70753028-70753271(+)$1	243	7	10	9.0000
CAG	chr6:131916989-131917216(-)$1	227	28	31	9.0000
CAG	chr11:63953614-63953836(+)$1	222	44	47	9.0000
CAG	chr8:141595276-141595504(-)$1	228	45	48	9.0000
cag	chr17:36878243-36878470(+)$1	227	25	28	9.0000
CAG	chr19:4491511-4491743(+)$1	232	1	4	9.0000
CAG	chr11:69587578-69587800(-)$1	222	128	131	9.0000
CAG	chr1:47133851-47134075(-)$1	224	132	135	9.0000
CAG	chr1:31465136-31465364(-)$1	228	44	47	9.0000
CAG	chr10:70482165-70482404(+)$1	239	114	117	9.0000
CAG	chr19:36106156-36106383(+)$1	227	13	16	9.0000
CAG	chr15:91454618-91454840(+)$1	222	24	27	9.0000
CAG	chr7:5269182-5269411(+)$1	229	5	8	9.0000
CAG	chr12:112485372-112485596(-)$1	224	8	11	9.0000
CAG	chr19:7593953-7594182(+)$1	229	3	6	9.0000
CAG	chr7:134882720-134882966(-)$1	246	22	25	9.0000
CAG	chr5:176939423-176939647(-)$1	224	3	6	9.0000
CAG	chr19:10221335-10221605(+)$1	270	34	37	9.0000
CAG	chr2:232326444-232326698(-)$1	254	13	16	9.0000
CAG	chr19:4659787-4660012(-)$1	225	64	67	9.0000
CAG	chr19:46289078-46289297(-)$1	219	25	28	9.0000
CAG	chr10:75883440-75883676(-)$1	236	5	8	9.0000
CAG	chr11:11924167-11924410(+)$1	243	123	126	9.0000
CAG	chr20:34542058-34542288(-)$1	230	24	27	9.0000
CAG	chr16:31198030-31198254(+)$1	224	89	92	9.0000
CAG	chr1:29485834-29486058(-)$1	224	114	117	9.0000
CAG	chr11:60670835-60671059(-)$1	224	49	52	9.0000
CAG	chr19:3980413-3980643(-)$1	230	66	69	9.0000
CAG	chr14:105886270-105886498(+)$1	228	119	122	9.0000
CAG	chr11:65826665-65826892(+)$1	227	43	46	9.0000
CAG	chr3:131221645-131221874(-)$1	229	60	63	9.0000
CAG	chr12:53856194-53856423(+)$1	229	20	23	9.0000
CAG	chr4:37687801-37688064(-)$1	263	56	59	9.0000
CAG	chr1:24020263-24020496(+)$1	233	30	33	9.0000
CAG	chr13:113210325-113210547(-)$1	222	10	13	9.0000
CAG	chr5:137909657-137909882(-)$1	225	21	24	9.0000
CAG	chr18:74639941-74640162(+)$1	221	32	35	9.0000
CAG	chr19:45898779-45899006(-)$1	227	5	8	9.0000
CAG	chr17:80019424-80019644(-)$1	220	26	29	9.0000
CAG	chr19:3984121-3984373(-)$1	252	22	25	9.0000
CAG	chr2:86333330-86333560(+)$1	230	26	29	9.0000
CAG	chr12:520917-521142(+)$1	225	0	3	9.0000
CAG	chr22:21272164-21272387(+)$1	223	1	4	9.0000
CAG	chr1:36291495-36291724(+)$1	229	57	60	9.0000
CAG	chr16:84125248-84125473(-)$1	225	91	94	9.0000
CAG	chr17:1303301-1303545(-)$1	244	15	18	9.0000
CAG	chrM:10500-10729(+)$1	229	181	184	9.0000
CAG	chr18:34408618-34408847(-)$1	229	8	11	9.0000
CAG	chr20:32273877-32274113(-)$1	236	136	139	9.0000
CAG	chr5:162896569-162896813(+)$1	244	41	44	9.0000
CAG	chr2:224822189-224822433(+)$1	244	27	30	9.0000
CAG	chr9:139815446-139815680(+)$1	234	40	43	9.0000
CAG	chrX:53222638-53222867(-)$1	229	13	16	9.0000
CAG	chr12:62965153-62965375(+)$1	222	15	18	9.0000
CAG	chr6:158910596-158910817(+)$1	221	20	23	9.0000
CAG	chr17:79634729-79634953(+)$1	224	26	29	9.0000
CAG	chr12:39763432-39763653(-)$1	221	91	94	9.0000
CAG	chr3:10130411-10130631(+)$1	220	18	21	9.0000
CAG	chr12:112585799-112586024(+)$1	225	75	78	9.0000

#otherMatches

#Struct PSSM
:::	chr1:78429656-78429878(-)$1	222	67	70	9.0000
ddd	chr1:115280549-115280778(-)$1	229	50	53	9.0000
C{B	chr7:128843299-128843530(+)$1	231	19	22	9.0000
CLL	chr7:148987034-148987255(+)$1	221	12	15	9.0000
eee	chr10:930309-930538(-)$1	229	89	92	9.0000
+dd	chr12:123099944-123100169(+)$1	225	69	72	9.0000
FF{	chr13:99947422-99947650(+)$1	228	8	11	9.0000
]==	chr21:33750659-33750895(-)$1	236	63	66	9.0000
BBB	chrM:11700-11953(+)$1	253	73	76	9.0000
DDD	chr1:145439746-145439985(+)$1	239	28	31	9.0000
fff	chr12:46600837-46601095(-)$1	258	73	76	9.0000
{GG	chr16:58619239-58619459(-)$1	220	23	26	9.0000
"""	chrX:122745204-122745428(-)$1	224	36	39	9.0000
WWW	chr16:31195170-31195396(+)$1	226	8	11	9.0000
::d	chr19:12825808-12826032(-)$1	224	0	3	9.0000
{JJ	chr4:57886979-57887212(+)$1	233	30	33	9.0000
fff	chr1:41457381-41457603(+)$1	222	63	66	9.0000
mmm	chr1:90179636-90179856(+)$1	220	82	85	9.0000
c!!	chr4:56262312-56262575(+)$1	263	36	39	9.0000
EEE	chr1:220213433-220213657(-)$1	224	58	61	9.0000
eee	chr1:39951315-39951544(+)$1	229	4	7	9.0000
:::	chr1:17749110-17749340(-)$1	230	5	8	9.0000
ccc	chr19:18546873-18547096(-)$1	223	0	3	9.0000
ddd	chr19:49589683-49589908(+)$1	225	149	152	9.0000
eee	chrX:122820306-122820531(-)$1	225	25	28	9.0000
eee	chr17:80053176-80053404(-)$1	228	16	19	9.0000
:::	chr13:25486796-25487049(-)$1	253	4	7	9.0000
:ee	chr5:137495672-137495903(-)$1	231	3	6	9.0000
[ff	chr19:1986839-1987058(-)$1	219	8	11	9.0000
===	chr16:2282436-2282676(+)$1	240	17	20	9.0000
c:g	chr1:37967353-37967578(-)$1	225	17	20	9.0000
qqq	chr11:130003460-130003687(+)$1	227	26	29	9.0000
"bb	chr19:54634662-54634883(+)$1	221	20	23	9.0000
EEE	chr10:1062939-1063167(+)$1	228	2	5	9.0000
fff	chr4:8442688-8442917(+)$1	229	48	51	9.0000
nni	chr19:19638418-19638659(+)$1	241	35	38	9.0000
eee	chr7:72395938-72396161(+)$1	223	61	64	9.0000
Cee	chr20:2446301-2446524(-)$1	223	2	5	9.0000
ccc	chr10:129906723-129906959(-)$1	236	20	23	9.0000
i[c	chr9:139793134-139793377(+)$1	243	50	53	9.0000
"dd	chr19:44676968-44677197(+)$1	229	41	44	9.0000
:dd	chrX:70753028-70753271(+)$1	243	7	10	9.0000
occ	chr6:131916989-131917216(-)$1	227	28	31	9.0000
ff"	chr11:63953614-63953836(+)$1	222	44	47	9.0000
B:e	chr8:141595276-141595504(-)$1	228	45	48	9.0000
ggg	chr17:36878243-36878470(+)$1	227	25	28	9.0000
::B	chr19:4491511-4491743(+)$1	232	1	4	9.0000
d22	chr11:69587578-69587800(-)$1	222	128	131	9.0000
mmb	chr1:47133851-47134075(-)$1	224	132	135	9.0000
bbd	chr1:31465136-31465364(-)$1	228	44	47	9.0000
22d	chr10:70482165-70482404(+)$1	239	114	117	9.0000
HHH	chr19:36106156-36106383(+)$1	227	13	16	9.0000
##d	chr15:91454618-91454840(+)$1	222	24	27	9.0000
ggg	chr7:5269182-5269411(+)$1	229	5	8	9.0000
::D	chr12:112485372-112485596(-)$1	224	8	11	9.0000
D:c	chr19:7593953-7594182(+)$1	229	3	6	9.0000
{BB	chr7:134882720-134882966(-)$1	246	22	25	9.0000
b[e	chr5:176939423-176939647(-)$1	224	3	6	9.0000
fff	chr19:10221335-10221605(+)$1	270	34	37	9.0000
)))	chr2:232326444-232326698(-)$1	254	13	16	9.0000
a22	chr19:4659787-4660012(-)$1	225	64	67	9.0000
::h	chr19:46289078-46289297(-)$1	219	25	28	9.0000
GGG	chr10:75883440-75883676(-)$1	236	5	8	9.0000
ccc	chr11:11924167-11924410(+)$1	243	123	126	9.0000
mmm	chr20:34542058-34542288(-)$1	230	24	27	9.0000
hhh	chr16:31198030-31198254(+)$1	224	89	92	9.0000
nnd	chr1:29485834-29486058(-)$1	224	114	117	9.0000
b::	chr11:60670835-60671059(-)$1	224	49	52	9.0000
eee	chr19:3980413-3980643(-)$1	230	66	69	9.0000
::g	chr14:105886270-105886498(+)$1	228	119	122	9.0000
DDO	chr11:65826665-65826892(+)$1	227	43	46	9.0000
CCK	chr3:131221645-131221874(-)$1	229	60	63	9.0000
ffD	chr12:53856194-53856423(+)$1	229	20	23	9.0000
d]d	chr4:37687801-37688064(-)$1	263	56	59	9.0000
obb	chr1:24020263-24020496(+)$1	233	30	33	9.0000
::c	chr13:113210325-113210547(-)$1	222	10	13	9.0000
ddd	chr5:137909657-137909882(-)$1	225	21	24	9.0000
::e	chr18:74639941-74640162(+)$1	221	32	35	9.0000
::B	chr19:45898779-45899006(-)$1	227	5	8	9.0000
ddd	chr17:80019424-80019644(-)$1	220	26	29	9.0000
%%d	chr19:3984121-3984373(-)$1	252	22	25	9.0000
FFF	chr2:86333330-86333560(+)$1	230	26	29	9.0000
DDD	chr12:520917-521142(+)$1	225	0	3	9.0000
B{D	chr22:21272164-21272387(+)$1	223	1	4	9.0000
lld	chr1:36291495-36291724(+)$1	229	57	60	9.0000
fff	chr16:84125248-84125473(-)$1	225	91	94	9.0000
qqq	chr17:1303301-1303545(-)$1	244	15	18	9.0000
cce	chrM:10500-10729(+)$1	229	181	184	9.0000
KKI	chr18:34408618-34408847(-)$1	229	8	11	9.0000
DDD	chr20:32273877-32274113(-)$1	236	136	139	9.0000
iii	chr5:162896569-162896813(+)$1	244	41	44	9.0000
HHH	chr2:224822189-224822433(+)$1	244	27	30	9.0000
DBB	chr9:139815446-139815680(+)$1	234	40	43	9.0000
ddq	chrX:53222638-53222867(-)$1	229	13	16	9.0000
HHH	chr12:62965153-62965375(+)$1	222	15	18	9.0000
eee	chr6:158910596-158910817(+)$1	221	20	23	9.0000
:::	chr17:79634729-79634953(+)$1	224	26	29	9.0000
cc2	chr12:39763432-39763653(-)$1	221	91	94	9.0000
DDD	chr3:10130411-10130631(+)$1	220	18	21	9.0000
ddd	chr12:112585799-112586024(+)$1	225	75	78	9.0000

#DB
...	chr1:78429656-78429878(-)$1	1	67	70	9.0000
(((	chr1:115280549-115280778(-)$1	1	50	53	9.0000
(.(	chr7:128843299-128843530(+)$1	1	19	22	9.0000
(..	chr7:148987034-148987255(+)$1	1	12	15	9.0000
)))	chr10:930309-930538(-)$1	1	89	92	9.0000
.((	chr12:123099944-123100169(+)$1	1	69	72	9.0000
((.	chr13:99947422-99947650(+)$1	1	8	11	9.0000
.))	chr21:33750659-33750895(-)$1	1	63	66	9.0000
(((	chrM:11700-11953(+)$1	1	73	76	9.0000
(((	chr1:145439746-145439985(+)$1	1	28	31	9.0000
(((	chr12:46600837-46601095(-)$1	1	73	76	9.0000
.((	chr16:58619239-58619459(-)$1	1	23	26	9.0000
...	chrX:122745204-122745428(-)$1	1	36	39	9.0000
...	chr16:31195170-31195396(+)$1	1	8	11	9.0000
..(	chr19:12825808-12826032(-)$1	1	0	3	9.0000
.((	chr4:57886979-57887212(+)$1	1	30	33	9.0000
(((	chr1:41457381-41457603(+)$1	1	63	66	9.0000
...	chr1:90179636-90179856(+)$1	1	82	85	9.0000
(..	chr4:56262312-56262575(+)$1	1	36	39	9.0000
(((	chr1:220213433-220213657(-)$1	1	58	61	9.0000
(((	chr1:39951315-39951544(+)$1	1	4	7	9.0000
...	chr1:17749110-17749340(-)$1	1	5	8	9.0000
(((	chr19:18546873-18547096(-)$1	1	0	3	9.0000
)))	chr19:49589683-49589908(+)$1	1	149	152	9.0000
)))	chrX:122820306-122820531(-)$1	1	25	28	9.0000
(((	chr17:80053176-80053404(-)$1	1	16	19	9.0000
...	chr13:25486796-25487049(-)$1	1	4	7	9.0000
.((	chr5:137495672-137495903(-)$1	1	3	6	9.0000
.((	chr19:1986839-1987058(-)$1	1	8	11	9.0000
(((	chr16:2282436-2282676(+)$1	1	17	20	9.0000
).(	chr1:37967353-37967578(-)$1	1	17	20	9.0000
...	chr11:130003460-130003687(+)$1	1	26	29	9.0000
.((	chr19:54634662-54634883(+)$1	1	20	23	9.0000
(((	chr10:1062939-1063167(+)$1	1	2	5	9.0000
)))	chr4:8442688-8442917(+)$1	1	48	51	9.0000
..)	chr19:19638418-19638659(+)$1	1	35	38	9.0000
)))	chr7:72395938-72396161(+)$1	1	61	64	9.0000
(((	chr20:2446301-2446524(-)$1	1	2	5	9.0000
(((	chr10:129906723-129906959(-)$1	1	20	23	9.0000
(.(	chr9:139793134-139793377(+)$1	1	50	53	9.0000
.((	chr19:44676968-44677197(+)$1	1	41	44	9.0000
.((	chrX:70753028-70753271(+)$1	1	7	10	9.0000
.))	chr6:131916989-131917216(-)$1	1	28	31	9.0000
((.	chr11:63953614-63953836(+)$1	1	44	47	9.0000
(.(	chr8:141595276-141595504(-)$1	1	45	48	9.0000
(((	chr17:36878243-36878470(+)$1	1	25	28	9.0000
..(	chr19:4491511-4491743(+)$1	1	1	4	9.0000
)..	chr11:69587578-69587800(-)$1	1	128	131	9.0000
..)	chr1:47133851-47134075(-)$1	1	132	135	9.0000
)))	chr1:31465136-31465364(-)$1	1	44	47	9.0000
..)	chr10:70482165-70482404(+)$1	1	114	117	9.0000
(((	chr19:36106156-36106383(+)$1	1	13	16	9.0000
..(	chr15:91454618-91454840(+)$1	1	24	27	9.0000
(((	chr7:5269182-5269411(+)$1	1	5	8	9.0000
..(	chr12:112485372-112485596(-)$1	1	8	11	9.0000
(.(	chr19:7593953-7594182(+)$1	1	3	6	9.0000
.((	chr7:134882720-134882966(-)$1	1	22	25	9.0000
(.(	chr5:176939423-176939647(-)$1	1	3	6	9.0000
(((	chr19:10221335-10221605(+)$1	1	34	37	9.0000
...	chr2:232326444-232326698(-)$1	1	13	16	9.0000
)..	chr19:4659787-4660012(-)$1	1	64	67	9.0000
..(	chr19:46289078-46289297(-)$1	1	25	28	9.0000
(((	chr10:75883440-75883676(-)$1	1	5	8	9.0000
)))	chr11:11924167-11924410(+)$1	1	123	126	9.0000
...	chr20:34542058-34542288(-)$1	1	24	27	9.0000
)))	chr16:31198030-31198254(+)$1	1	89	92	9.0000
..)	chr1:29485834-29486058(-)$1	1	114	117	9.0000
)..	chr11:60670835-60671059(-)$1	1	49	52	9.0000
)))	chr19:3980413-3980643(-)$1	1	66	69	9.0000
..(	chr14:105886270-105886498(+)$1	1	119	122	9.0000
((.	chr11:65826665-65826892(+)$1	1	43	46	9.0000
((.	chr3:131221645-131221874(-)$1	1	60	63	9.0000
))(	chr12:53856194-53856423(+)$1	1	20	23	9.0000
).)	chr4:37687801-37688064(-)$1	1	56	59	9.0000
.))	chr1:24020263-24020496(+)$1	1	30	33	9.0000
..(	chr13:113210325-113210547(-)$1	1	10	13	9.0000
(((	chr5:137909657-137909882(-)$1	1	21	24	9.0000
..(	chr18:74639941-74640162(+)$1	1	32	35	9.0000
..(	chr19:45898779-45899006(-)$1	1	5	8	9.0000
(((	chr17:80019424-80019644(-)$1	1	26	29	9.0000
..(	chr19:3984121-3984373(-)$1	1	22	25	9.0000
(((	chr2:86333330-86333560(+)$1	1	26	29	9.0000
(((	chr12:520917-521142(+)$1	1	0	3	9.0000
(.(	chr22:21272164-21272387(+)$1	1	1	4	9.0000
..)	chr1:36291495-36291724(+)$1	1	57	60	9.0000
(((	chr16:84125248-84125473(-)$1	1	91	94	9.0000
...	chr17:1303301-1303545(-)$1	1	15	18	9.0000
)))	chrM:10500-10729(+)$1	1	181	184	9.0000
..(	chr18:34408618-34408847(-)$1	1	8	11	9.0000
(((	chr20:32273877-32274113(-)$1	1	136	139	9.0000
)))	chr5:162896569-162896813(+)$1	1	41	44	9.0000
(((	chr2:224822189-224822433(+)$1	1	27	30	9.0000
(((	chr9:139815446-139815680(+)$1	1	40	43	9.0000
((.	chrX:53222638-53222867(-)$1	1	13	16	9.0000
(((	chr12:62965153-62965375(+)$1	1	15	18	9.0000
)))	chr6:158910596-158910817(+)$1	1	20	23	9.0000
...	chr17:79634729-79634953(+)$1	1	26	29	9.0000
)).	chr12:39763432-39763653(-)$1	1	91	94	9.0000
(((	chr3:10130411-10130631(+)$1	1	18	21	9.0000
(((	chr12:112585799-112586024(+)$1	1	75	78	9.0000

#PSSM
C : 0.98	c : 0.02	
A : 0.98	a : 0.02	
G : 0.98	g : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m3_run1.nuc.txt

#NT
CAAUGGGCGAGCCGGGCUGGAGGCGAUGGGCGUGGCCGCAGCGCCGGGGCCCUCAGAUCGAGGCUGCCUCCCCCUCUCAGCCGGCAGCACAUUCCGUCGCCUUGCCGCCGCCCGGCCCCACAGUUGUCUUUGCCGGAGCUGCAGUCGCGCUGGGGUUAGGGCGGGGGGGCGGGCGGGGAGAGGAGAAGGCCGCGGCGGAGGCAGGUGAGAGGAGGAAG	chr3:160283195-160283423(-)$1	228	10	228	329.0000

#otherMatches

#Struct PSSM
fff$$$$$gggggggmmmmggggggg666666ffffffDDDD{CCCddddnnnnnddddIIIIIIIII::ddddmmmmddddhhhhhhhhccceeeee!!dddd!!ggggggglllggggggg22dddd22eeeee22ccc333hhhhhhhh:::ggggggg!!ccc[bb[cccooooooccc]bb22ccc22gggggggIIIIIIIII~~~~CCC}D	chr1:36614964-36615189(-)$1	225	4	222	329.0000
cmmmmccc]ggggggg:::::dddd[bbccclllccc]bb]ddddeeeeeddddnnnnndddd22eeeeebbggggggg[bb[bb%%%%%%iiiiiiiiiccc[bb[ggggggg[dddd####ggggggg[ccc!!ccc[bbmmmmbbccc22ccc]gggggggdddd]gggggggbb]ccc999999999iiiiiiiiibb]bbggggggg]bb:::	chr3:160283195-160283423(-)$1	228	10	228	329.0000

#DB
(((.....(((((((....)))))))......))))))((((.(((((((.....))))(((((((((..((((....))))((((((((((((((((..((((..(((((((...)))))))..))))..)))))..)))...))))))))...(((((((..(((.((.(((......))).))..)))..))))))))))))))))....))).)	chr1:36614964-36615189(-)$1	1	4	222	329.0000
(....))).))))))).....((((.(((((...))).)).))))(((((((((.....))))..)))))(((((((((.((.((......((((((((((((.((.(((((((.((((....(((((((.(((..(((.((....)))))..))).))))))))))).))))))))).))).........))))))))))).))))))))).))...	chr3:160283195-160283423(-)$1	1	10	228	329.0000

#PSSM
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
C : 1.00	
C : 1.00	
A : 0.50	G : 0.50	
C : 1.00	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
C : 1.00	
C : 1.00	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
C : 0.50	G : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
U : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
C : 1.00	
G : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
G : 1.00	
U : 1.00	
C : 1.00	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
G : 1.00	
U : 0.50	C : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
C : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 1.00	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
G : 1.00	

#score	658.0
#seq	2
#width	218
#escape	false
#onStep	13385
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m1_run1.nuc.txt

#NT
UACUUUUUUAU	chr13:79888497-79888718(-)$1	221	99	110	16.5555
UCUUUUCUUUU	chr15:45009734-45009951(+)$1	217	56	67	17.4444
GAuuuuuuuuu	chr4:140310340-140310563(+)$1	223	6	17	22.0000
UCUUUUAUUUU	chr3:107525020-107525255(+)$1	235	117	128	17.3333
AAUUUUUUUUU	chr19:34687439-34687669(+)$1	230	33	44	22.1111
UAUCUUUUAUU	chr6:138412803-138413033(-)$1	230	32	43	16.8888
UAUUUAUUUGU	chr12:1895379-1895598(+)$1	219	168	179	17.2222
UGUUUGUUUUU	chr12:4412521-4412751(+)$1	230	160	171	17.2222
UAUUUUCUUCU	chr14:31171446-31171676(+)$1	230	143	154	17.4444
UAUUUUUUGUA	chr5:141000398-141000617(-)$1	219	159	170	16.2222
uuuuuuuuuuu	chr14:45397750-45397973(-)$1	223	65	76	21.3333
GAUUUUUUUUU	chr16:18803064-18803286(-)$1	222	99	110	22.0000
UAAUUUUGUUU	chr1:200375950-200376189(-)$1	239	80	91	16.2222
UAUAGUUUUUU	chr5:139916844-139917073(+)$1	229	29	40	16.6666
GAUUUUUUUUU	chr14:99978557-99978784(-)$1	227	5	16	22.0000
GAUUUCUUUUU	chr8:42396030-42396260(-)$1	230	30	41	18.0000
UAUGUAUUUUU	chr17:74730564-74730794(-)$1	230	130	141	17.0000
UAUGUUUUUAU	chr7:105246099-105246330(-)$1	231	61	72	17.0000
UAUUUUUUAGU	chr2:161129235-161129465(-)$1	230	49	60	17.2222
uauuuuuuuug	chr1:90496259-90496489(+)$1	230	132	143	20.3333
AAUUUUUUUGU	chr4:123283537-123283770(+)$1	233	162	173	18.3333
AAUUUUCUUUU	chr11:63394826-63395051(-)$1	225	100	111	18.4444
UGUUUUAUUUU	chr5:172561518-172561738(+)$1	220	124	135	17.4444
UAAUUUUUUCU	chr7:87840107-87840325(-)$1	218	158	169	16.8888
UAUUUGCUUUU	chr9:86276301-86276526(-)$1	225	120	131	17.2222
UAUUUUUUUUU	chr7:86823967-86824192(+)$1	225	8	19	24.8888
UAUUUUUUUUU	chr4:17625567-17625797(+)$1	230	69	80	24.8888
GAUUUUUUUUU	chr6:64290471-64290714(+)$1	243	160	171	22.0000
AAUUUUUCUUU	chr5:126887705-126887925(+)$1	220	31	42	17.5555
uuuuuuuuuuu	chr16:2508069-2508299(+)$1	230	185	196	21.3333
aauuuuuuauu	chr1:145512212-145512444(+)$1	232	169	180	18.2222
UAUUUUUUUCU	chrX:11139876-11140096(+)$1	220	83	94	21.1111
UAUUAUUUUUU	chr6:79648883-79649108(-)$1	225	105	116	20.8888
UAUUUUUUAUU	chr1:244220632-244220855(+)$1	223	157	168	21.0000
UAUUAUAUUUU	chr6:89793933-89794155(+)$1	222	126	137	17.1111
UAAUUUUUGUU	chr2:38523255-38523485(-)$1	230	44	55	16.5555
UAUUGAUUUUU	chr12:50569670-50569890(-)$1	220	17	28	17.0000
AAUUUUUUUUU	chr4:89647539-89647765(-)$1	226	100	111	22.1111
uuuuuuuuuuu	chr3:63988722-63988946(+)$1	224	159	170	21.3333
UUUUAUUUUUU	chr1:202550157-202550383(+)$1	226	101	112	17.3333
UAUUUCUGUUU	chr4:146055328-146055545(-)$1	217	105	116	16.4444
UAUUUUGUUUC	chr7:135122990-135123228(-)$1	238	35	46	16.3333
AAUCUUUUUUU	chr1:32830771-32831001(-)$1	230	25	36	18.0000
GAUUGUUUUUU	chr10:70105057-70105277(-)$1	220	47	58	18.0000

#otherMatches

#Struct PSSM
[cccooooooc	chr11:10826374-10826592(-)$1	218	193	204	17.2222
eeeqqqqqqqq	chr13:79888497-79888718(-)$1	221	99	110	16.5555
xxxxxxxxxxx	chr15:45009734-45009951(+)$1	217	56	67	17.4444
ee^^^^^^^^^	chr4:140310340-140310563(+)$1	223	6	17	22.0000
IIIIII~~~~D	chr3:107525020-107525255(+)$1	235	117	128	17.3333
ggg''''''''	chr19:34687439-34687669(+)$1	230	33	44	22.1111
bbhhhhhhhh[	chr6:138412803-138413033(-)$1	230	32	43	16.8888
ccooooooccc	chr12:1895379-1895598(+)$1	219	168	179	17.2222
3eeeee77777	chr12:4412521-4412751(+)$1	230	160	171	17.2222
JJJJJJJ::hh	chr14:31171446-31171676(+)$1	230	143	154	17.4444
eeennnnneee	chr5:141000398-141000617(-)$1	219	159	170	16.2222
:::::::::::	chr14:45397750-45397973(-)$1	223	65	76	21.3333
dddqqqqqqqq	chr16:18803064-18803286(-)$1	222	99	110	22.0000
%%%%%%fffff	chr1:200375950-200376189(-)$1	239	80	91	16.2222
%%%%eeeeett	chr5:139916844-139917073(+)$1	229	29	40	16.6666
:::::::::::	chr14:99978557-99978784(-)$1	227	5	16	22.0000
ggmmmmggggg	chr8:42396030-42396260(-)$1	230	30	41	18.0000
!!eeeeemmmm	chr17:74730564-74730794(-)$1	230	130	141	17.0000
B{JJJJJJJJJ	chr7:105246099-105246330(-)$1	231	61	72	17.0000
ggg!!ddddnn	chr2:161129235-161129465(-)$1	230	49	60	17.2222
:::::::::::	chr1:90496259-90496489(+)$1	230	132	143	20.3333
ddd::::::ee	chr4:123283537-123283770(+)$1	233	162	173	18.3333
cc4444eeeee	chr11:63394826-63395051(-)$1	225	100	111	18.4444
GGGGGG}JJJJ	chr5:172561518-172561738(+)$1	220	124	135	17.4444
""ccc!!ffff	chr7:87840107-87840325(-)$1	218	158	169	16.8888
dd!!ggggggg	chr9:86276301-86276526(-)$1	225	120	131	17.2222
ffffqqqqqqq	chr7:86823967-86824192(+)$1	225	8	19	24.8888
hhhhh::::dd	chr4:17625567-17625797(+)$1	230	69	80	24.8888
ddd::::gggg	chr6:64290471-64290714(+)$1	243	160	171	22.0000
c$$$$$fffff	chr5:126887705-126887925(+)$1	220	31	42	17.5555
JJJJJJJJJ::	chr16:2508069-2508299(+)$1	230	185	196	21.3333
ddqqqqqqqqd	chr1:145512212-145512444(+)$1	232	169	180	18.2222
hhhhhhhheee	chrX:11139876-11140096(+)$1	220	83	94	21.1111
oooccc55555	chr6:79648883-79649108(-)$1	225	105	116	20.8888
ddd22hhhhhh	chr1:244220632-244220855(+)$1	223	157	168	21.0000
fffCCC}HHHH	chr6:89793933-89794155(+)$1	222	126	137	17.1111
''''''''ggg	chr2:38523255-38523485(-)$1	230	44	55	16.5555
e!!ddddmmmm	chr12:50569670-50569890(-)$1	220	17	28	17.0000
]hhhhhhhh22	chr4:89647539-89647765(-)$1	226	100	111	22.1111
gggg:::::::	chr3:63988722-63988946(+)$1	224	159	170	21.3333
:::::::::::	chr1:202550157-202550383(+)$1	226	101	112	17.3333
==>>>>>>>>>	chr4:146055328-146055545(-)$1	217	105	116	16.4444
oooodddd:::	chr7:135122990-135123228(-)$1	238	35	46	16.3333
JJJJJJJJJJJ	chr1:32830771-32831001(-)$1	230	25	36	18.0000
ffuuuuuuuuu	chr10:70105057-70105277(-)$1	220	47	58	18.0000

#DB
.(((......)	chr11:10826374-10826592(-)$1	1	193	204	17.2222
(((........	chr13:79888497-79888718(-)$1	1	99	110	16.5555
...........	chr15:45009734-45009951(+)$1	1	56	67	17.4444
((.........	chr4:140310340-140310563(+)$1	1	6	17	22.0000
))))))....)	chr3:107525020-107525255(+)$1	1	117	128	17.3333
(((........	chr19:34687439-34687669(+)$1	1	33	44	22.1111
((((((((((.	chr6:138412803-138413033(-)$1	1	32	43	16.8888
((......)))	chr12:1895379-1895598(+)$1	1	168	179	17.2222
.))))).....	chr12:4412521-4412751(+)$1	1	160	171	17.2222
)))))))..((	chr14:31171446-31171676(+)$1	1	143	154	17.4444
(((.....)))	chr5:141000398-141000617(-)$1	1	159	170	16.2222
...........	chr14:45397750-45397973(-)$1	1	65	76	21.3333
(((........	chr16:18803064-18803286(-)$1	1	99	110	22.0000
......(((((	chr1:200375950-200376189(-)$1	1	80	91	16.2222
....(((((..	chr5:139916844-139917073(+)$1	1	29	40	16.6666
...........	chr14:99978557-99978784(-)$1	1	5	16	22.0000
((....)))))	chr8:42396030-42396260(-)$1	1	30	41	18.0000
..(((((....	chr17:74730564-74730794(-)$1	1	130	141	17.0000
(.(((((((((	chr7:105246099-105246330(-)$1	1	61	72	17.0000
(((..((((..	chr2:161129235-161129465(-)$1	1	49	60	17.2222
...........	chr1:90496259-90496489(+)$1	1	132	143	20.3333
)))......((	chr4:123283537-123283770(+)$1	1	162	173	18.3333
))....)))))	chr11:63394826-63395051(-)$1	1	100	111	18.4444
)))))).))))	chr5:172561518-172561738(+)$1	1	124	135	17.4444
..(((..((((	chr7:87840107-87840325(-)$1	1	158	169	16.8888
((..(((((((	chr9:86276301-86276526(-)$1	1	120	131	17.2222
((((.......	chr7:86823967-86824192(+)$1	1	8	19	24.8888
)))))....((	chr4:17625567-17625797(+)$1	1	69	80	24.8888
)))....((((	chr6:64290471-64290714(+)$1	1	160	171	22.0000
(.....(((((	chr5:126887705-126887925(+)$1	1	31	42	17.5555
)))))))))..	chr16:2508069-2508299(+)$1	1	185	196	21.3333
((........)	chr1:145512212-145512444(+)$1	1	169	180	18.2222
)))))))))))	chrX:11139876-11140096(+)$1	1	83	94	21.1111
...))).....	chr6:79648883-79649108(-)$1	1	105	116	20.8888
)))..))))))	chr1:244220632-244220855(+)$1	1	157	168	21.0000
)))))).))))	chr6:89793933-89794155(+)$1	1	126	137	17.1111
........(((	chr2:38523255-38523485(-)$1	1	44	55	16.5555
(..((((....	chr12:50569670-50569890(-)$1	1	17	28	17.0000
.))))))))..	chr4:89647539-89647765(-)$1	1	100	111	22.1111
)))).......	chr3:63988722-63988946(+)$1	1	159	170	21.3333
...........	chr1:202550157-202550383(+)$1	1	101	112	17.3333
)).........	chr4:146055328-146055545(-)$1	1	105	116	16.4444
....))))...	chr7:135122990-135123228(-)$1	1	35	46	16.3333
(((((((((((	chr1:32830771-32831001(-)$1	1	25	36	18.0000
((.........	chr10:70105057-70105277(-)$1	1	47	58	18.0000

#PSSM
U : 0.62	G : 0.13	A : 0.13	u : 0.08	a : 0.02	
A : 0.75	G : 0.06	u : 0.06	C : 0.04	a : 0.04	U : 0.02	
U : 0.77	u : 0.13	A : 0.06	C : 0.02	
U : 0.73	u : 0.13	G : 0.06	C : 0.04	A : 0.02	
U : 0.73	u : 0.13	G : 0.06	A : 0.06	
U : 0.71	u : 0.13	A : 0.06	G : 0.04	C : 0.04	
U : 0.68	u : 0.13	C : 0.08	A : 0.06	G : 0.02	
U : 0.80	u : 0.13	G : 0.04	C : 0.02	
U : 0.75	u : 0.11	A : 0.06	G : 0.04	a : 0.02	
U : 0.68	u : 0.13	G : 0.06	C : 0.06	A : 0.04	
U : 0.82	u : 0.11	A : 0.02	g : 0.02	C : 0.02	

#score	845.8888888888891
#seq	45
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_UTR_m3_run2.nuc.txt

#NT
UUC	chr4:52888793-52889015(-)$1	222	25	28	9.0000
uuc	chr12:117295299-117295521(-)$1	222	39	42	9.0000
UUC	chr10:101464566-101464785(+)$1	219	7	10	9.0000
UUC	chr2:128059485-128059712(-)$1	227	2	5	9.0000
UUC	chr6:31506476-31506734(-)$1	258	39	42	9.0000
UUC	chr17:42476106-42476323(-)$1	217	70	73	9.0000
UUC	chr7:155101579-155101802(+)$1	223	1	4	9.0000
UUC	chr14:99979177-99979402(-)$1	225	89	92	9.0000
UUC	chr2:74334739-74334962(+)$1	223	70	73	9.0000
UUC	chr4:122831358-122831572(-)$1	214	128	131	9.0000
UUC	chr3:53262964-53263178(-)$1	214	9	12	9.0000
UUC	chr8:95507014-95507237(-)$1	223	19	22	9.0000
UUC	chr11:61495601-61495818(+)$1	217	7	10	9.0000
UUC	chr17:74386160-74386395(-)$1	235	14	17	9.0000
UUC	chr20:23351003-23351230(+)$1	227	49	52	9.0000
UUC	chr1:52242463-52242682(+)$1	219	12	15	9.0000
UUC	chr8:38127572-38127796(-)$1	224	82	85	9.0000
UUC	chr12:56811216-56811438(-)$1	222	65	68	9.0000
UUC	chr1:33961089-33961307(+)$1	218	63	66	9.0000
UUC	chr7:17833785-17834005(-)$1	220	47	50	9.0000
UUC	chr2:242166830-242167054(-)$1	224	36	39	9.0000
UUC	chr5:154193709-154193935(+)$1	226	142	145	9.0000
UUC	chr18:12308214-12308426(+)$1	212	52	55	9.0000
UUC	chr2:196581606-196581824(+)$1	218	7	10	9.0000
UUC	chr1:40042116-40042364(-)$1	248	64	67	9.0000
UUC	chr8:66546233-66546451(-)$1	218	61	64	9.0000
UUC	chr12:109547932-109548165(+)$1	233	45	48	9.0000
UUC	chr16:30959389-30959618(+)$1	229	85	88	9.0000
UUC	chr4:187510053-187510312(-)$1	259	103	106	9.0000
UUC	chr21:35476882-35477109(+)$1	227	41	44	9.0000
UUC	chr12:117155337-117155569(-)$1	232	25	28	9.0000
UUC	chr7:101900115-101900329(+)$1	214	44	47	9.0000
UUC	chr1:38280230-38280450(-)$1	220	36	39	9.0000
UUC	chr19:34935868-34936088(+)$1	220	100	103	9.0000
UUC	chr8:104330877-104331104(+)$1	227	28	31	9.0000
UUC	chr5:179321299-179321527(-)$1	228	114	117	9.0000
UUC	chr8:144406129-144406352(-)$1	223	13	16	9.0000
UUC	chr17:45901687-45901909(-)$1	222	31	34	9.0000
UUC	chr17:65362517-65362738(-)$1	221	38	41	9.0000
uuc	chr12:12270959-12271190(-)$1	231	28	31	9.0000
UUC	chr20:48330128-48330353(-)$1	225	183	186	9.0000
UUC	chr8:146279537-146279772(+)$1	235	76	79	9.0000
UUC	chr17:28791782-28792002(+)$1	220	34	37	9.0000
UUC	chr10:75530671-75530926(+)$1	255	29	32	9.0000
UUC	chr7:6388262-6388488(-)$1	226	5	8	9.0000
UUC	chr22:35689833-35690068(+)$1	235	57	60	9.0000
UUC	chr12:52388004-52388250(+)$1	246	77	80	9.0000
UUC	chr1:19233636-19233871(-)$1	235	9	12	9.0000
UUC	chr3:49154805-49155027(-)$1	222	47	50	9.0000
UUC	chr2:86308627-86308848(-)$1	221	4	7	9.0000
UUC	chr2:27439770-27439990(+)$1	220	2	5	9.0000
UUC	chr5:149231940-149232159(+)$1	219	25	28	9.0000
UUC	chr20:1147111-1147330(+)$1	219	5	8	9.0000
UUC	chr5:10250334-10250633(+)$1	299	60	63	9.0000
UUC	chr15:72491572-72491858(-)$1	286	155	158	9.0000
UUC	chr3:141166005-141166230(+)$1	225	67	70	9.0000
UUC	chr19:15483010-15483235(-)$1	225	11	14	9.0000
UUC	chr20:34330017-34330231(-)$1	214	93	96	9.0000
UUC	chr15:63558523-63558741(+)$1	218	23	26	9.0000
UUC	chr16:23478481-23478698(-)$1	217	50	53	9.0000
UUC	chr16:58197585-58197813(-)$1	228	65	68	9.0000
UUC	chr6:116599389-116599600(-)$1	211	5	8	9.0000
UUC	chr22:50357028-50357263(+)$1	235	29	32	9.0000
UUC	chr12:56676116-56676351(-)$1	235	3	6	9.0000
UUC	chr1:32663105-32663328(+)$1	223	28	31	9.0000
UUC	chr10:74646258-74646480(+)$1	222	58	61	9.0000
UUC	chr4:186066882-186067105(+)$1	223	5	8	9.0000
UUC	chr22:19119537-19119762(-)$1	225	131	134	9.0000
UUC	chr3:12875662-12875877(-)$1	215	50	53	9.0000
UUC	chr11:33730700-33730917(-)$1	217	71	74	9.0000
UUC	chr12:46755991-46756241(-)$1	250	38	41	9.0000
UUC	chr3:185208624-185208842(-)$1	218	105	108	9.0000
UUC	chr1:9663828-9664062(+)$1	234	38	41	9.0000
UUC	chr10:133769312-133769540(+)$1	228	53	56	9.0000
UUC	chr12:57057359-57057580(-)$1	221	88	91	9.0000
UUC	chr1:51439843-51440064(+)$1	221	91	94	9.0000
UUC	chr10:51589186-51589401(+)$1	215	70	73	9.0000
UUC	chr2:130910061-130910275(-)$1	214	22	25	9.0000
UUC	chr3:113438525-113438749(-)$1	224	26	29	9.0000
UUC	chr16:24551802-24552028(+)$1	226	32	35	9.0000
UUC	chr19:4690793-4691048(-)$1	255	51	54	9.0000
UUC	chr22:51039148-51039365(+)$1	217	122	125	9.0000
UUC	chr17:28792160-28792391(+)$1	231	20	23	9.0000
UUC	chr9:139916801-139917028(-)$1	227	83	86	9.0000
UUC	chrX:47006756-47006986(+)$1	230	153	156	9.0000
UUC	chr11:94608480-94608691(+)$1	211	6	9	9.0000
UUC	chrX:129190943-129191156(+)$1	213	49	52	9.0000
UUC	chr2:96936979-96937225(+)$1	246	77	80	9.0000
UUc	chr2:238673931-238674153(+)$1	222	15	18	9.0000
UUC	chr11:107879917-107880135(+)$1	218	120	123	9.0000
UUC	chr19:1986105-1986346(-)$1	241	25	28	9.0000

#otherMatches

#Struct PSSM
fff	chr8:90996675-90996900(-)$1	225	180	183	9.0000
ddd	chr4:52888793-52889015(-)$1	222	25	28	9.0000
:::	chr12:117295299-117295521(-)$1	222	39	42	9.0000
:cc	chr10:101464566-101464785(+)$1	219	7	10	9.0000
eee	chr2:128059485-128059712(-)$1	227	2	5	9.0000
:ee	chr6:31506476-31506734(-)$1	258	39	42	9.0000
hhh	chr17:42476106-42476323(-)$1	217	70	73	9.0000
:::	chr7:155101579-155101802(+)$1	223	1	4	9.0000
!bb	chr14:99979177-99979402(-)$1	225	89	92	9.0000
:::	chr2:74334739-74334962(+)$1	223	70	73	9.0000
3cc	chr4:122831358-122831572(-)$1	214	128	131	9.0000
FF:	chr3:53262964-53263178(-)$1	214	9	12	9.0000
ccc	chr8:95507014-95507237(-)$1	223	19	22	9.0000
DGG	chr11:61495601-61495818(+)$1	217	7	10	9.0000
fff	chr17:74386160-74386395(-)$1	235	14	17	9.0000
ddq	chr20:23351003-23351230(+)$1	227	49	52	9.0000
imm	chr1:52242463-52242682(+)$1	219	12	15	9.0000
:::	chr8:38127572-38127796(-)$1	224	82	85	9.0000
"""	chr12:56811216-56811438(-)$1	222	65	68	9.0000
8cc	chr1:33961089-33961307(+)$1	218	63	66	9.0000
FFF	chr7:17833785-17834005(-)$1	220	47	50	9.0000
:::	chr2:242166830-242167054(-)$1	224	36	39	9.0000
gg!	chr5:154193709-154193935(+)$1	226	142	145	9.0000
fff	chr18:12308214-12308426(+)$1	212	52	55	9.0000
:::	chr2:196581606-196581824(+)$1	218	7	10	9.0000
mmm	chr1:40042116-40042364(-)$1	248	64	67	9.0000
fee	chr8:66546233-66546451(-)$1	218	61	64	9.0000
[cc	chr12:109547932-109548165(+)$1	233	45	48	9.0000
]dd	chr16:30959389-30959618(+)$1	229	85	88	9.0000
bbf	chr4:187510053-187510312(-)$1	259	103	106	9.0000
iii	chr21:35476882-35477109(+)$1	227	41	44	9.0000
EEE	chr12:117155337-117155569(-)$1	232	25	28	9.0000
FFF	chr7:101900115-101900329(+)$1	214	44	47	9.0000
""b	chr1:38280230-38280450(-)$1	220	36	39	9.0000
ggg	chr19:34935868-34936088(+)$1	220	100	103	9.0000
EEE	chr8:104330877-104331104(+)$1	227	28	31	9.0000
)))	chr5:179321299-179321527(-)$1	228	114	117	9.0000
[hh	chr8:144406129-144406352(-)$1	223	13	16	9.0000
eee	chr17:45901687-45901909(-)$1	222	31	34	9.0000
eee	chr17:65362517-65362738(-)$1	221	38	41	9.0000
ddd	chr12:12270959-12271190(-)$1	231	28	31	9.0000
DDD	chr20:48330128-48330353(-)$1	225	183	186	9.0000
ggg	chr8:146279537-146279772(+)$1	235	76	79	9.0000
:::	chr17:28791782-28792002(+)$1	220	34	37	9.0000
PPP	chr10:75530671-75530926(+)$1	255	29	32	9.0000
:::	chr7:6388262-6388488(-)$1	226	5	8	9.0000
ooo	chr22:35689833-35690068(+)$1	235	57	60	9.0000
ggg	chr12:52388004-52388250(+)$1	246	77	80	9.0000
:::	chr1:19233636-19233871(-)$1	235	9	12	9.0000
KKH	chr3:49154805-49155027(-)$1	222	47	50	9.0000
:::	chr2:86308627-86308848(-)$1	221	4	7	9.0000
:::	chr2:27439770-27439990(+)$1	220	2	5	9.0000
%%%	chr5:149231940-149232159(+)$1	219	25	28	9.0000
hhh	chr20:1147111-1147330(+)$1	219	5	8	9.0000
eee	chr5:10250334-10250633(+)$1	299	60	63	9.0000
fff	chr15:72491572-72491858(-)$1	286	155	158	9.0000
ddd	chr3:141166005-141166230(+)$1	225	67	70	9.0000
fff	chr19:15483010-15483235(-)$1	225	11	14	9.0000
ccc	chr20:34330017-34330231(-)$1	214	93	96	9.0000
eee	chr15:63558523-63558741(+)$1	218	23	26	9.0000
===	chr16:23478481-23478698(-)$1	217	50	53	9.0000
{CC	chr16:58197585-58197813(-)$1	228	65	68	9.0000
KEE	chr6:116599389-116599600(-)$1	211	5	8	9.0000
cc'	chr22:50357028-50357263(+)$1	235	29	32	9.0000
GGG	chr12:56676116-56676351(-)$1	235	3	6	9.0000
EEE	chr1:32663105-32663328(+)$1	223	28	31	9.0000
GGG	chr10:74646258-74646480(+)$1	222	58	61	9.0000
GGG	chr4:186066882-186067105(+)$1	223	5	8	9.0000
GGG	chr22:19119537-19119762(-)$1	225	131	134	9.0000
:::	chr3:12875662-12875877(-)$1	215	50	53	9.0000
eee	chr11:33730700-33730917(-)$1	217	71	74	9.0000
eee	chr12:46755991-46756241(-)$1	250	38	41	9.0000
hhh	chr3:185208624-185208842(-)$1	218	105	108	9.0000
hnn	chr1:9663828-9664062(+)$1	234	38	41	9.0000
ddd	chr10:133769312-133769540(+)$1	228	53	56	9.0000
ii:	chr12:57057359-57057580(-)$1	221	88	91	9.0000
fff	chr1:51439843-51440064(+)$1	221	91	94	9.0000
ccc	chr10:51589186-51589401(+)$1	215	70	73	9.0000
:::	chr2:130910061-130910275(-)$1	214	22	25	9.0000
e%%	chr3:113438525-113438749(-)$1	224	26	29	9.0000
MMG	chr16:24551802-24552028(+)$1	226	32	35	9.0000
FFF	chr19:4690793-4691048(-)$1	255	51	54	9.0000
ooo	chr22:51039148-51039365(+)$1	217	122	125	9.0000
:==	chr17:28792160-28792391(+)$1	231	20	23	9.0000
b!!	chr9:139916801-139917028(-)$1	227	83	86	9.0000
FF}	chrX:47006756-47006986(+)$1	230	153	156	9.0000
:::	chr11:94608480-94608691(+)$1	211	6	9	9.0000
:::	chrX:129190943-129191156(+)$1	213	49	52	9.0000
HHH	chr2:96936979-96937225(+)$1	246	77	80	9.0000
:::	chr2:238673931-238674153(+)$1	222	15	18	9.0000
iii	chr11:107879917-107880135(+)$1	218	120	123	9.0000
eee	chr19:1986105-1986346(-)$1	241	25	28	9.0000

#DB
(((	chr8:90996675-90996900(-)$1	1	180	183	9.0000
)))	chr4:52888793-52889015(-)$1	1	25	28	9.0000
...	chr12:117295299-117295521(-)$1	1	39	42	9.0000
.((	chr10:101464566-101464785(+)$1	1	7	10	9.0000
(((	chr2:128059485-128059712(-)$1	1	2	5	9.0000
.((	chr6:31506476-31506734(-)$1	1	39	42	9.0000
)))	chr17:42476106-42476323(-)$1	1	70	73	9.0000
...	chr7:155101579-155101802(+)$1	1	1	4	9.0000
.((	chr14:99979177-99979402(-)$1	1	89	92	9.0000
...	chr2:74334739-74334962(+)$1	1	70	73	9.0000
.))	chr4:122831358-122831572(-)$1	1	128	131	9.0000
((.	chr3:53262964-53263178(-)$1	1	9	12	9.0000
(((	chr8:95507014-95507237(-)$1	1	19	22	9.0000
(((	chr11:61495601-61495818(+)$1	1	7	10	9.0000
)))	chr17:74386160-74386395(-)$1	1	14	17	9.0000
((.	chr20:23351003-23351230(+)$1	1	49	52	9.0000
(..	chr1:52242463-52242682(+)$1	1	12	15	9.0000
...	chr8:38127572-38127796(-)$1	1	82	85	9.0000
...	chr12:56811216-56811438(-)$1	1	65	68	9.0000
.))	chr1:33961089-33961307(+)$1	1	63	66	9.0000
(((	chr7:17833785-17834005(-)$1	1	47	50	9.0000
...	chr2:242166830-242167054(-)$1	1	36	39	9.0000
((.	chr5:154193709-154193935(+)$1	1	142	145	9.0000
(((	chr18:12308214-12308426(+)$1	1	52	55	9.0000
...	chr2:196581606-196581824(+)$1	1	7	10	9.0000
...	chr1:40042116-40042364(-)$1	1	64	67	9.0000
)))	chr8:66546233-66546451(-)$1	1	61	64	9.0000
.((	chr12:109547932-109548165(+)$1	1	45	48	9.0000
.))	chr16:30959389-30959618(+)$1	1	85	88	9.0000
)))	chr4:187510053-187510312(-)$1	1	103	106	9.0000
(((	chr21:35476882-35477109(+)$1	1	41	44	9.0000
(((	chr12:117155337-117155569(-)$1	1	25	28	9.0000
(((	chr7:101900115-101900329(+)$1	1	44	47	9.0000
..(	chr1:38280230-38280450(-)$1	1	36	39	9.0000
(((	chr19:34935868-34936088(+)$1	1	100	103	9.0000
(((	chr8:104330877-104331104(+)$1	1	28	31	9.0000
...	chr5:179321299-179321527(-)$1	1	114	117	9.0000
.((	chr8:144406129-144406352(-)$1	1	13	16	9.0000
(((	chr17:45901687-45901909(-)$1	1	31	34	9.0000
(((	chr17:65362517-65362738(-)$1	1	38	41	9.0000
(((	chr12:12270959-12271190(-)$1	1	28	31	9.0000
)))	chr20:48330128-48330353(-)$1	1	183	186	9.0000
(((	chr8:146279537-146279772(+)$1	1	76	79	9.0000
...	chr17:28791782-28792002(+)$1	1	34	37	9.0000
...	chr10:75530671-75530926(+)$1	1	29	32	9.0000
...	chr7:6388262-6388488(-)$1	1	5	8	9.0000
...	chr22:35689833-35690068(+)$1	1	57	60	9.0000
)))	chr12:52388004-52388250(+)$1	1	77	80	9.0000
...	chr1:19233636-19233871(-)$1	1	9	12	9.0000
..(	chr3:49154805-49155027(-)$1	1	47	50	9.0000
...	chr2:86308627-86308848(-)$1	1	4	7	9.0000
...	chr2:27439770-27439990(+)$1	1	2	5	9.0000
...	chr5:149231940-149232159(+)$1	1	25	28	9.0000
(((	chr20:1147111-1147330(+)$1	1	5	8	9.0000
)))	chr5:10250334-10250633(+)$1	1	60	63	9.0000
)))	chr15:72491572-72491858(-)$1	1	155	158	9.0000
)))	chr3:141166005-141166230(+)$1	1	67	70	9.0000
(((	chr19:15483010-15483235(-)$1	1	11	14	9.0000
(((	chr20:34330017-34330231(-)$1	1	93	96	9.0000
(((	chr15:63558523-63558741(+)$1	1	23	26	9.0000
)))	chr16:23478481-23478698(-)$1	1	50	53	9.0000
.((	chr16:58197585-58197813(-)$1	1	65	68	9.0000
.((	chr6:116599389-116599600(-)$1	1	5	8	9.0000
((.	chr22:50357028-50357263(+)$1	1	29	32	9.0000
(((	chr12:56676116-56676351(-)$1	1	3	6	9.0000
(((	chr1:32663105-32663328(+)$1	1	28	31	9.0000
(((	chr10:74646258-74646480(+)$1	1	58	61	9.0000
(((	chr4:186066882-186067105(+)$1	1	5	8	9.0000
)))	chr22:19119537-19119762(-)$1	1	131	134	9.0000
...	chr3:12875662-12875877(-)$1	1	50	53	9.0000
(((	chr11:33730700-33730917(-)$1	1	71	74	9.0000
(((	chr12:46755991-46756241(-)$1	1	38	41	9.0000
(((	chr3:185208624-185208842(-)$1	1	105	108	9.0000
(..	chr1:9663828-9664062(+)$1	1	38	41	9.0000
(((	chr10:133769312-133769540(+)$1	1	53	56	9.0000
)).	chr12:57057359-57057580(-)$1	1	88	91	9.0000
(((	chr1:51439843-51440064(+)$1	1	91	94	9.0000
(((	chr10:51589186-51589401(+)$1	1	70	73	9.0000
...	chr2:130910061-130910275(-)$1	1	22	25	9.0000
(..	chr3:113438525-113438749(-)$1	1	26	29	9.0000
..(	chr16:24551802-24552028(+)$1	1	32	35	9.0000
(((	chr19:4690793-4691048(-)$1	1	51	54	9.0000
...	chr22:51039148-51039365(+)$1	1	122	125	9.0000
.((	chr17:28792160-28792391(+)$1	1	20	23	9.0000
(..	chr9:139916801-139917028(-)$1	1	83	86	9.0000
)).	chrX:47006756-47006986(+)$1	1	153	156	9.0000
...	chr11:94608480-94608691(+)$1	1	6	9	9.0000
...	chrX:129190943-129191156(+)$1	1	49	52	9.0000
(((	chr2:96936979-96937225(+)$1	1	77	80	9.0000
...	chr2:238673931-238674153(+)$1	1	15	18	9.0000
(((	chr11:107879917-107880135(+)$1	1	120	123	9.0000
(((	chr19:1986105-1986346(-)$1	1	25	28	9.0000

#PSSM
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
C : 0.96	c : 0.03	

#score	828.0000000000007
#seq	92
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_UTR_m3_run1.nuc.txt

#NT
UCAUGU	chr12:88591169-88591463(+)$1	294	28	34	11.0172
UCAUAU	chr1:161088512-161088771(+)$1	259	43	49	11.0172
UAAUUU	chr13:50275071-50275412(-)$1	341	180	186	11.9655
UCAGUU	chr11:111933156-111933424(+)$1	268	5	11	11.0172
UCAUUU	chr5:74894384-74894706(+)$1	322	198	204	15.4137
UCAUUU	chr12:101021382-101021624(+)$1	242	62	68	15.4137
UCAUUU	chr14:55535305-55535600(+)$1	295	210	216	15.4137
UCUUUU	chr2:216983687-216983987(+)$1	300	70	76	11.7068
UGAUUU	chr4:159590511-159590837(-)$1	326	70	76	11.7068
UCAGUU	chr10:93623833-93624212(+)$1	379	192	198	11.0172
UCAUUU	chr1:185069729-185070096(+)$1	367	254	260	15.4137
UCAUUU	chr1:53287872-53288233(+)$1	361	326	332	15.4137
UAAUUU	chr8:124261365-124261667(-)$1	302	157	163	11.9655
ucaauu	chr19:37237046-37237283(-)$1	237	33	39	10.8448
UCUUUU	chr7:32908191-32908591(-)$1	400	220	226	11.7068
UCAUUU	chr11:16776917-16777188(+)$1	271	48	54	15.4137
ucauuu	chr10:43085676-43085922(-)$1	246	223	229	15.4137
UCAUUU	chrX:20142495-20142982(-)$1	487	52	58	15.4137
UCUUUU	chr8:107764156-107764441(+)$1	285	126	132	11.7068
UCAUGU	chr16:21666515-21666892(+)$1	377	352	358	11.0172
UCCUUU	chr11:117040394-117040715(+)$1	321	273	279	11.4482
UCAUUU	chr21:27252768-27253084(-)$1	316	76	82	15.4137
UGAUUU	chr13:79173210-79173552(-)$1	342	252	258	11.7068
UUAUUU	chr20:45838451-45838773(-)$1	322	305	311	11.7068
UUAUUU	chr16:24831371-24831696(+)$1	325	22	28	11.7068
UAAUUU	chr2:29022874-29023169(+)$1	295	18	24	11.9655
UCAUUU	chr7:127011185-127011474(-)$1	289	235	241	15.4137
UGAUUU	chr16:14042114-14042445(+)$1	331	32	38	11.7068
UCUUUU	chr22:39257368-39257663(-)$1	295	156	162	11.7068
UCAUUU	chr19:40575864-40576207(-)$1	343	147	153	15.4137
UCAUUU	chr3:149459258-149459591(-)$1	333	71	77	15.4137
UCAUUU	chr8:61778812-61779047(+)$1	235	129	135	15.4137
UAAUUU	chr5:98131405-98131660(+)$1	255	27	33	11.9655
UCAUUU	chr12:123776781-123777048(-)$1	267	68	74	15.4137
ucauuu	chr2:176791624-176791990(-)$1	366	197	203	15.4137
UCUUUU	chr21:34117032-34117318(-)$1	286	227	233	11.7068
UCAUUU	chr3:15480646-15481029(+)$1	383	198	204	15.4137
UCAUUU	chr22:40725826-40726152(+)$1	326	268	274	15.4137
UCAUUU	chr10:28909529-28909977(+)$1	448	157	163	15.4137
UCAUUU	chr10:49643715-49644152(+)$1	437	376	382	15.4137
UCAUCU	chr2:42577722-42578066(-)$1	344	227	233	10.9310
UCAUUU	chr5:64019917-64020221(-)$1	304	259	265	15.4137
UCAUUU	chr17:8272942-8273199(-)$1	257	107	113	15.4137
UCAUUU	chr3:47087944-47088209(-)$1	265	82	88	15.4137
UCCUUU	chr17:27871009-27871419(+)$1	410	162	168	11.4482
UCAUUU	chr15:59951382-59951653(-)$1	271	44	50	15.4137
UCAUUU	chr10:103922279-103922649(+)$1	370	306	312	15.4137
ucauuu	chr10:38347788-38348114(+)$1	326	54	60	15.4137
UCAUUU	chr8:103219789-103220079(-)$1	290	215	221	15.4137
UCAUUU	chr1:53291079-53291370(+)$1	291	107	113	15.4137
UAAUUU	chr16:15153874-15154160(-)$1	286	166	172	11.9655
UCAUUU	chr6:52867035-52867303(-)$1	268	134	140	15.4137
UCCUUU	chr8:81550829-81551305(-)$1	476	182	188	11.4482
UUAUUU	chr17:64806517-64806897(+)$1	380	360	366	11.7068
UCAUAU	chr2:176042400-176042694(-)$1	294	14	20	11.0172
UCAGUU	chr1:110135568-110135949(+)$1	381	277	283	11.0172
UCUUUU	chr10:101474025-101474466(-)$1	441	254	260	11.7068

#otherMatches

#Struct PSSM
bb[ddd	chr1:205579363-205579605(-)$1	242	118	124	11.9655
::::::	chr12:88591169-88591463(+)$1	294	28	34	11.0172
mmeeee	chr1:161088512-161088771(+)$1	259	43	49	11.0172
qqqqa2	chr13:50275071-50275412(-)$1	341	180	186	11.9655
GGGGG{	chr11:111933156-111933424(+)$1	268	5	11	11.0172
]ccc::	chr5:74894384-74894706(+)$1	322	198	204	15.4137
^^^^^^	chr12:101021382-101021624(+)$1	242	62	68	15.4137
fnnnnn	chr14:55535305-55535600(+)$1	295	210	216	15.4137
ffffff	chr2:216983687-216983987(+)$1	300	70	76	11.7068
::::::	chr4:159590511-159590837(-)$1	326	70	76	11.7068
]ccc]h	chr10:93623833-93624212(+)$1	379	192	198	11.0172
::::::	chr1:185069729-185070096(+)$1	367	254	260	15.4137
#bbmmm	chr1:53287872-53288233(+)$1	361	326	332	15.4137
c:::::	chr8:124261365-124261667(-)$1	302	157	163	11.9655
::::::	chr19:37237046-37237283(-)$1	237	33	39	10.8448
h%%%%%	chr7:32908191-32908591(-)$1	400	220	226	11.7068
8=====	chr11:16776917-16777188(+)$1	271	48	54	15.4137
55eeee	chr10:43085676-43085922(-)$1	246	223	229	15.4137
ccc22b	chrX:20142495-20142982(-)$1	487	52	58	15.4137
bbeeee	chr8:107764156-107764441(+)$1	285	126	132	11.7068
}BB}HH	chr16:21666515-21666892(+)$1	377	352	358	11.0172
ff:FFF	chr11:117040394-117040715(+)$1	321	273	279	11.4482
::::::	chr21:27252768-27253084(-)$1	316	76	82	15.4137
DD~~~~	chr13:79173210-79173552(-)$1	342	252	258	11.7068
HHHHHH	chr20:45838451-45838773(-)$1	322	305	311	11.7068
ccnnnn	chr16:24831371-24831696(+)$1	325	22	28	11.7068
::::::	chr2:29022874-29023169(+)$1	295	18	24	11.9655
::::::	chr7:127011185-127011474(-)$1	289	235	241	15.4137
iiiiii	chr16:14042114-14042445(+)$1	331	32	38	11.7068
oo====	chr22:39257368-39257663(-)$1	295	156	162	11.7068
::::::	chr19:40575864-40576207(-)$1	343	147	153	15.4137
eedddd	chr3:149459258-149459591(-)$1	333	71	77	15.4137
B:::::	chr8:61778812-61779047(+)$1	235	129	135	15.4137
&&&&dd	chr5:98131405-98131660(+)$1	255	27	33	11.9655
hhhh""	chr12:123776781-123777048(-)$1	267	68	74	15.4137
^^^^^^	chr2:176791624-176791990(-)$1	366	197	203	15.4137
ooooee	chr21:34117032-34117318(-)$1	286	227	233	11.7068
cccmmm	chr3:15480646-15481029(+)$1	383	198	204	15.4137
bb::::	chr22:40725826-40726152(+)$1	326	268	274	15.4137
ffff++	chr10:28909529-28909977(+)$1	448	157	163	15.4137
ddd]ee	chr10:49643715-49644152(+)$1	437	376	382	15.4137
DDD}EE	chr2:42577722-42578066(-)$1	344	227	233	10.9310
gccctt	chr5:64019917-64020221(-)$1	304	259	265	15.4137
ddwwww	chr17:8272942-8273199(-)$1	257	107	113	15.4137
000000	chr3:47087944-47088209(-)$1	265	82	88	15.4137
:::::h	chr17:27871009-27871419(+)$1	410	162	168	11.4482
!!dddd	chr15:59951382-59951653(-)$1	271	44	50	15.4137
[bbttt	chr10:103922279-103922649(+)$1	370	306	312	15.4137
eeeell	chr10:38347788-38348114(+)$1	326	54	60	15.4137
JJJJJJ	chr8:103219789-103220079(-)$1	290	215	221	15.4137
dddd22	chr1:53291079-53291370(+)$1	291	107	113	15.4137
e!!eee	chr16:15153874-15154160(-)$1	286	166	172	11.9655
ceeeee	chr6:52867035-52867303(-)$1	268	134	140	15.4137
dddd55	chr8:81550829-81551305(-)$1	476	182	188	11.4482
EEEE@@	chr17:64806517-64806897(+)$1	380	360	366	11.7068
iipppp	chr2:176042400-176042694(-)$1	294	14	20	11.0172
ffffff	chr1:110135568-110135949(+)$1	381	277	283	11.0172
dddd[c	chr10:101474025-101474466(-)$1	441	254	260	11.7068

#DB
((.(((	chr1:205579363-205579605(-)$1	1	118	124	11.9655
......	chr12:88591169-88591463(+)$1	1	28	34	11.0172
..))))	chr1:161088512-161088771(+)$1	1	43	49	11.0172
....).	chr13:50275071-50275412(-)$1	1	180	186	11.9655
(((((.	chr11:111933156-111933424(+)$1	1	5	11	11.0172
.)))..	chr5:74894384-74894706(+)$1	1	198	204	15.4137
......	chr12:101021382-101021624(+)$1	1	62	68	15.4137
(.....	chr14:55535305-55535600(+)$1	1	210	216	15.4137
((((((	chr2:216983687-216983987(+)$1	1	70	76	11.7068
......	chr4:159590511-159590837(-)$1	1	70	76	11.7068
.))).)	chr10:93623833-93624212(+)$1	1	192	198	11.0172
......	chr1:185069729-185070096(+)$1	1	254	260	15.4137
.((...	chr1:53287872-53288233(+)$1	1	326	332	15.4137
).....	chr8:124261365-124261667(-)$1	1	157	163	11.9655
......	chr19:37237046-37237283(-)$1	1	33	39	10.8448
(.....	chr7:32908191-32908591(-)$1	1	220	226	11.7068
.)))))	chr11:16776917-16777188(+)$1	1	48	54	15.4137
..))))	chr10:43085676-43085922(-)$1	1	223	229	15.4137
)))..)	chrX:20142495-20142982(-)$1	1	52	58	15.4137
))))))	chr8:107764156-107764441(+)$1	1	126	132	11.7068
.)).))	chr16:21666515-21666892(+)$1	1	352	358	11.0172
)).)))	chr11:117040394-117040715(+)$1	1	273	279	11.4482
......	chr21:27252768-27253084(-)$1	1	76	82	15.4137
))....	chr13:79173210-79173552(-)$1	1	252	258	11.7068
))))))	chr20:45838451-45838773(-)$1	1	305	311	11.7068
((....	chr16:24831371-24831696(+)$1	1	22	28	11.7068
......	chr2:29022874-29023169(+)$1	1	18	24	11.9655
......	chr7:127011185-127011474(-)$1	1	235	241	15.4137
((((((	chr16:14042114-14042445(+)$1	1	32	38	11.7068
..))))	chr22:39257368-39257663(-)$1	1	156	162	11.7068
......	chr19:40575864-40576207(-)$1	1	147	153	15.4137
((((((	chr3:149459258-149459591(-)$1	1	71	77	15.4137
).....	chr8:61778812-61779047(+)$1	1	129	135	15.4137
....((	chr5:98131405-98131660(+)$1	1	27	33	11.9655
((((..	chr12:123776781-123777048(-)$1	1	68	74	15.4137
......	chr2:176791624-176791990(-)$1	1	197	203	15.4137
....))	chr21:34117032-34117318(-)$1	1	227	233	11.7068
(((...	chr3:15480646-15481029(+)$1	1	198	204	15.4137
))....	chr22:40725826-40726152(+)$1	1	268	274	15.4137
((((..	chr10:28909529-28909977(+)$1	1	157	163	15.4137
))).))	chr10:49643715-49644152(+)$1	1	376	382	15.4137
))).))	chr2:42577722-42578066(-)$1	1	227	233	10.9310
((((..	chr5:64019917-64020221(-)$1	1	259	265	15.4137
((....	chr17:8272942-8273199(-)$1	1	107	113	15.4137
......	chr3:47087944-47088209(-)$1	1	82	88	15.4137
.....(	chr17:27871009-27871419(+)$1	1	162	168	11.4482
..((((	chr15:59951382-59951653(-)$1	1	44	50	15.4137
.((...	chr10:103922279-103922649(+)$1	1	306	312	15.4137
((((..	chr10:38347788-38348114(+)$1	1	54	60	15.4137
))))))	chr8:103219789-103220079(-)$1	1	215	221	15.4137
))))..	chr1:53291079-53291370(+)$1	1	107	113	15.4137
(..(((	chr16:15153874-15154160(-)$1	1	166	172	11.9655
((((((	chr6:52867035-52867303(-)$1	1	134	140	15.4137
))))..	chr8:81550829-81551305(-)$1	1	182	188	11.4482
))))..	chr17:64806517-64806897(+)$1	1	360	366	11.7068
((....	chr2:176042400-176042694(-)$1	1	14	20	11.0172
))))))	chr1:110135568-110135949(+)$1	1	277	283	11.0172
((((.(	chr10:101474025-101474466(-)$1	1	254	260	11.7068

#PSSM
U : 0.93	u : 0.06	
C : 0.72	A : 0.10	c : 0.06	G : 0.05	U : 0.05	
A : 0.77	U : 0.10	a : 0.06	C : 0.05	
U : 0.87	G : 0.05	u : 0.05	a : 0.01	
U : 0.84	u : 0.06	G : 0.03	A : 0.03	C : 0.01	
U : 0.93	u : 0.06	

#score	777.103448275862
#seq	58
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m1_run1.nuc.txt

#NT
AGA	chrM:12523-12755(+)$1	232	59	62	8.9999
AGA	chrM:11700-11927(+)$1	227	190	193	8.9999
AGA	chr19:21300580-21300812(+)$1	232	2	5	8.9999
AGA	chr10:27422867-27423093(-)$1	226	40	43	8.9999
AGA	chr2:152314250-152314480(+)$1	230	26	29	8.9999
AGA	chr11:46742269-46742492(+)$1	223	76	79	8.9999
AGA	chr8:67955363-67955591(-)$1	228	54	57	8.9999
AGA	chr2:145156339-145156576(-)$1	237	57	60	8.9999
AGA	chr7:64388425-64388657(+)$1	232	38	41	8.9999
AGA	chr2:187618595-187618817(+)$1	222	24	27	8.9999
AGA	chrM:6150-6393(+)$1	243	182	185	8.9999
AGA	chr19:10870331-10870561(+)$1	230	49	52	8.9999
AGA	chr19:36728103-36728331(+)$1	228	16	19	8.9999
AGA	chr20:376844-377084(+)$1	240	14	17	8.9999
AGA	chr6:56505096-56505323(-)$1	227	1	4	8.9999
AGA	chr19:56179813-56180040(+)$1	227	12	15	8.9999
AGA	chr17:29219572-29219804(+)$1	232	24	27	8.9999
AGA	chr1:151380539-151380766(-)$1	227	23	26	8.9999
AGA	chr17:26653630-26653862(+)$1	232	54	57	8.9999
AGA	chr20:3845224-3845456(+)$1	232	202	205	8.9999
AGA	chr21:37415924-37416163(-)$1	239	80	83	8.9999
AGA	chr5:180666397-180666647(-)$1	250	69	72	8.9999
AGA	chr9:125797133-125797365(+)$1	232	19	22	8.9999
AGA	chr17:26959087-26959314(-)$1	227	186	189	8.9999
AGA	chr12:54448883-54449108(+)$1	225	42	45	8.9999
AGA	chr7:64292463-64292690(+)$1	227	49	52	8.9999
AGA	chr17:76045574-76045806(+)$1	232	39	42	8.9999
AGA	chr3:152554421-152554653(+)$1	232	21	24	8.9999
AGA	chrM:6442-6670(+)$1	228	94	97	8.9999
AGA	chr19:41257233-41257465(+)$1	232	19	22	8.9999
AGA	chr6:111694185-111694417(-)$1	232	14	17	8.9999
AGA	chrX:107976466-107976689(-)$1	223	42	45	8.9999
AGA	chr20:42333773-42334025(+)$1	252	125	128	8.9999
AGA	chr1:39913019-39913245(+)$1	226	95	98	8.9999
AGA	chr17:7414663-7414894(+)$1	231	80	83	8.9999
AGA	chrX:71493625-71493855(-)$1	230	51	54	8.9999
AGA	chr12:123022872-123023102(+)$1	230	11	14	8.9999
AGA	chr21:26957898-26958130(-)$1	232	72	75	8.9999
AGA	chr7:150935434-150935657(+)$1	223	0	3	8.9999
AGA	chr19:9065466-9065698(-)$1	232	1	4	8.9999
AGA	chr7:12269209-12269441(+)$1	232	93	96	8.9999
AGA	chr5:139908405-139908637(+)$1	232	0	3	8.9999
AGA	chr2:111395503-111395729(-)$1	226	47	50	8.9999
AGA	chrM:8288-8520(+)$1	232	1	4	8.9999
AGA	chr5:36170375-36170605(+)$1	230	144	147	8.9999
AGA	chr10:133757443-133757665(+)$1	222	60	63	8.9999
aga	chr2:203623888-203624113(+)$1	225	4	7	8.9999
AGA	chr1:161009666-161009898(-)$1	232	104	107	8.9999
AGA	chr1:97250617-97250844(+)$1	227	2	5	8.9999
AGA	chr8:8875790-8876012(+)$1	222	24	27	8.9999
AGA	chr12:11174233-11174459(-)$1	226	55	58	8.9999
AGA	chr12:46758155-46758381(-)$1	226	52	55	8.9999
AGA	chr10:70719633-70719865(+)$1	232	19	22	8.9999
AGA	chr22:31884515-31884747(-)$1	232	20	23	8.9999
AGA	chr5:32380094-32380318(-)$1	224	38	41	8.9999
AGA	chrX:119580137-119580372(-)$1	235	21	24	8.9999
AGA	chr7:64167756-64167988(+)$1	232	2	5	8.9999
AGA	chr10:71977550-71977774(-)$1	224	23	26	8.9999
AGA	chr7:150935471-150935694(+)$1	223	58	61	8.9999
AGA	chr19:38871482-38871725(+)$1	243	114	117	8.9999
AGA	chr16:419051-419273(-)$1	222	10	13	8.9999
AGA	chr16:24815482-24815714(+)$1	232	25	28	8.9999
AGA	chr17:46937673-46937905(+)$1	232	9	12	8.9999
AGA	chr13:99098260-99098492(+)$1	232	22	25	8.9999
AGA	chr4:77979634-77979860(-)$1	226	1	4	8.9999
AGA	chr10:38344712-38344944(+)$1	232	56	59	8.9999
AGA	chr4:184367627-184367855(+)$1	228	21	24	8.9999
AGA	chr10:75532479-75532711(+)$1	232	30	33	8.9999
AGA	chr15:70350480-70350706(-)$1	226	28	31	8.9999
AGA	chr2:120734514-120734746(+)$1	232	43	46	8.9999
AGA	chr5:37351250-37351483(-)$1	233	74	77	8.9999
AGA	chr15:66030049-66030275(-)$1	226	35	38	8.9999
AGA	chr14:103958226-103958468(+)$1	242	84	87	8.9999
AGA	chr3:48678753-48678975(-)$1	222	16	19	8.9999
AGA	chr5:145826844-145827071(+)$1	227	28	31	8.9999
AGA	chr21:47545669-47545890(+)$1	221	134	137	8.9999
AGA	chr6:43527829-43528061(-)$1	232	40	43	8.9999
AGA	chr19:35769550-35769782(+)$1	232	71	74	8.9999
AGA	chr14:100820682-100820910(-)$1	228	5	8	8.9999
AGA	chr12:994135-994367(+)$1	232	150	153	8.9999
AGA	chr19:58452293-58452515(-)$1	222	38	41	8.9999
AGA	chrM:11884-12135(-)$1	251	41	44	8.9999
AGA	chr6:80749842-80750074(+)$1	232	95	98	8.9999
AGA	chr4:83276373-83276602(-)$1	229	46	49	8.9999
AGA	chr10:8006713-8006936(+)$1	223	10	13	8.9999
AGA	chr16:85695122-85695354(+)$1	232	24	27	8.9999
AGA	chrM:13039-13295(+)$1	256	8	11	8.9999
AGA	chrM:11213-11447(+)$1	234	98	101	8.9999
AGA	chrM:8090-8312(-)$1	222	23	26	8.9999
AGA	chr12:49087315-49087563(-)$1	248	2	5	8.9999
AGA	chr19:49118500-49118722(-)$1	222	16	19	8.9999
AGA	chr8:109488050-109488276(+)$1	226	7	10	8.9999
AGA	chr7:127017170-127017401(-)$1	231	49	52	8.9999
AGA	chrM:11146-11408(+)$1	262	33	36	8.9999
AGA	chrM:5256-5501(+)$1	245	17	20	8.9999
AGA	chrM:6115-6340(-)$1	225	51	54	8.9999

#otherMatches

#Struct PSSM
ddt	chrM:13982-14258(+)$1	276	13	16	8.9999
:::	chrM:12523-12755(+)$1	232	59	62	8.9999
hhh	chrM:11700-11927(+)$1	227	190	193	8.9999
:::	chr19:21300580-21300812(+)$1	232	2	5	8.9999
FFF	chr10:27422867-27423093(-)$1	226	40	43	8.9999
bbn	chr2:152314250-152314480(+)$1	230	26	29	8.9999
ooo	chr11:46742269-46742492(+)$1	223	76	79	8.9999
[bb	chr8:67955363-67955591(-)$1	228	54	57	8.9999
:EE	chr2:145156339-145156576(-)$1	237	57	60	8.9999
fff	chr7:64388425-64388657(+)$1	232	38	41	8.9999
ooo	chr2:187618595-187618817(+)$1	222	24	27	8.9999
FFF	chrM:6150-6393(+)$1	243	182	185	8.9999
ddd	chr19:10870331-10870561(+)$1	230	49	52	8.9999
yyy	chr19:36728103-36728331(+)$1	228	16	19	8.9999
III	chr20:376844-377084(+)$1	240	14	17	8.9999
:DD	chr6:56505096-56505323(-)$1	227	1	4	8.9999
{CC	chr19:56179813-56180040(+)$1	227	12	15	8.9999
fff	chr17:29219572-29219804(+)$1	232	24	27	8.9999
eee	chr1:151380539-151380766(-)$1	227	23	26	8.9999
ddd	chr17:26653630-26653862(+)$1	232	54	57	8.9999
cc[	chr20:3845224-3845456(+)$1	232	202	205	8.9999
$gg	chr21:37415924-37416163(-)$1	239	80	83	8.9999
:dd	chr5:180666397-180666647(-)$1	250	69	72	8.9999
GGG	chr9:125797133-125797365(+)$1	232	19	22	8.9999
3ee	chr17:26959087-26959314(-)$1	227	186	189	8.9999
ff:	chr12:54448883-54449108(+)$1	225	42	45	8.9999
ddc	chr7:64292463-64292690(+)$1	227	49	52	8.9999
ma2	chr17:76045574-76045806(+)$1	232	39	42	8.9999
fff	chr3:152554421-152554653(+)$1	232	21	24	8.9999
:EE	chrM:6442-6670(+)$1	228	94	97	8.9999
hhh	chr19:41257233-41257465(+)$1	232	19	22	8.9999
GGG	chr6:111694185-111694417(-)$1	232	14	17	8.9999
ccc	chrX:107976466-107976689(-)$1	223	42	45	8.9999
dac	chr20:42333773-42334025(+)$1	252	125	128	8.9999
iii	chr1:39913019-39913245(+)$1	226	95	98	8.9999
fff	chr17:7414663-7414894(+)$1	231	80	83	8.9999
FFF	chrX:71493625-71493855(-)$1	230	51	54	8.9999
ee:	chr12:123022872-123023102(+)$1	230	11	14	8.9999
ddd	chr21:26957898-26958130(-)$1	232	72	75	8.9999
:::	chr7:150935434-150935657(+)$1	223	0	3	8.9999
ccc	chr19:9065466-9065698(-)$1	232	1	4	8.9999
bb]	chr7:12269209-12269441(+)$1	232	93	96	8.9999
:::	chr5:139908405-139908637(+)$1	232	0	3	8.9999
:GG	chr2:111395503-111395729(-)$1	226	47	50	8.9999
:CC	chrM:8288-8520(+)$1	232	1	4	8.9999
cnn	chr5:36170375-36170605(+)$1	230	144	147	8.9999
g""	chr10:133757443-133757665(+)$1	222	60	63	8.9999
fff	chr2:203623888-203624113(+)$1	225	4	7	8.9999
ddd	chr1:161009666-161009898(-)$1	232	104	107	8.9999
HHH	chr1:97250617-97250844(+)$1	227	2	5	8.9999
FFF	chr8:8875790-8876012(+)$1	222	24	27	8.9999
hhh	chr12:11174233-11174459(-)$1	226	55	58	8.9999
GGG	chr12:46758155-46758381(-)$1	226	52	55	8.9999
ddd	chr10:70719633-70719865(+)$1	232	19	22	8.9999
coo	chr22:31884515-31884747(-)$1	232	20	23	8.9999
fff	chr5:32380094-32380318(-)$1	224	38	41	8.9999
GGG	chrX:119580137-119580372(-)$1	235	21	24	8.9999
:bb	chr7:64167756-64167988(+)$1	232	2	5	8.9999
fff	chr10:71977550-71977774(-)$1	224	23	26	8.9999
hhh	chr7:150935471-150935694(+)$1	223	58	61	8.9999
]dd	chr19:38871482-38871725(+)$1	243	114	117	8.9999
III	chr16:419051-419273(-)$1	222	10	13	8.9999
mdd	chr16:24815482-24815714(+)$1	232	25	28	8.9999
GGG	chr17:46937673-46937905(+)$1	232	9	12	8.9999
==n	chr13:99098260-99098492(+)$1	232	22	25	8.9999
fff	chr4:77979634-77979860(-)$1	226	1	4	8.9999
b!!	chr10:38344712-38344944(+)$1	232	56	59	8.9999
:cc	chr4:184367627-184367855(+)$1	228	21	24	8.9999
dd:	chr10:75532479-75532711(+)$1	232	30	33	8.9999
ooo	chr15:70350480-70350706(-)$1	226	28	31	8.9999
eee	chr2:120734514-120734746(+)$1	232	43	46	8.9999
FFF	chr5:37351250-37351483(-)$1	233	74	77	8.9999
ddc	chr15:66030049-66030275(-)$1	226	35	38	8.9999
bb[	chr14:103958226-103958468(+)$1	242	84	87	8.9999
mmm	chr3:48678753-48678975(-)$1	222	16	19	8.9999
ggg	chr5:145826844-145827071(+)$1	227	28	31	8.9999
]a6	chr21:47545669-47545890(+)$1	221	134	137	8.9999
mmm	chr6:43527829-43528061(-)$1	232	40	43	8.9999
!dd	chr19:35769550-35769782(+)$1	232	71	74	8.9999
::G	chr14:100820682-100820910(-)$1	228	5	8	8.9999
ggg	chr12:994135-994367(+)$1	232	150	153	8.9999
eee	chr19:58452293-58452515(-)$1	222	38	41	8.9999
a[g	chrM:11884-12135(-)$1	251	41	44	8.9999
ccd	chr6:80749842-80750074(+)$1	232	95	98	8.9999
dde	chr4:83276373-83276602(-)$1	229	46	49	8.9999
:bb	chr10:8006713-8006936(+)$1	223	10	13	8.9999
[bb	chr16:85695122-85695354(+)$1	232	24	27	8.9999
GGG	chrM:13039-13295(+)$1	256	8	11	8.9999
^^^	chrM:11213-11447(+)$1	234	98	101	8.9999
:::	chrM:8090-8312(-)$1	222	23	26	8.9999
:::	chr12:49087315-49087563(-)$1	248	2	5	8.9999
KDD	chr19:49118500-49118722(-)$1	222	16	19	8.9999
JJJ	chr8:109488050-109488276(+)$1	226	7	10	8.9999
ggg	chr7:127017170-127017401(-)$1	231	49	52	8.9999
:::	chrM:11146-11408(+)$1	262	33	36	8.9999
dd^	chrM:5256-5501(+)$1	245	17	20	8.9999
GGG	chrM:6115-6340(-)$1	225	51	54	8.9999

#DB
((.	chrM:13982-14258(+)$1	1	13	16	8.9999
...	chrM:12523-12755(+)$1	1	59	62	8.9999
(((	chrM:11700-11927(+)$1	1	190	193	8.9999
...	chr19:21300580-21300812(+)$1	1	2	5	8.9999
(((	chr10:27422867-27423093(-)$1	1	40	43	8.9999
((.	chr2:152314250-152314480(+)$1	1	26	29	8.9999
...	chr11:46742269-46742492(+)$1	1	76	79	8.9999
.((	chr8:67955363-67955591(-)$1	1	54	57	8.9999
.((	chr2:145156339-145156576(-)$1	1	57	60	8.9999
)))	chr7:64388425-64388657(+)$1	1	38	41	8.9999
...	chr2:187618595-187618817(+)$1	1	24	27	8.9999
)))	chrM:6150-6393(+)$1	1	182	185	8.9999
(((	chr19:10870331-10870561(+)$1	1	49	52	8.9999
...	chr19:36728103-36728331(+)$1	1	16	19	8.9999
(((	chr20:376844-377084(+)$1	1	14	17	8.9999
.((	chr6:56505096-56505323(-)$1	1	1	4	8.9999
.((	chr19:56179813-56180040(+)$1	1	12	15	8.9999
(((	chr17:29219572-29219804(+)$1	1	24	27	8.9999
(((	chr1:151380539-151380766(-)$1	1	23	26	8.9999
(((	chr17:26653630-26653862(+)$1	1	54	57	8.9999
((.	chr20:3845224-3845456(+)$1	1	202	205	8.9999
.((	chr21:37415924-37416163(-)$1	1	80	83	8.9999
.((	chr5:180666397-180666647(-)$1	1	69	72	8.9999
(((	chr9:125797133-125797365(+)$1	1	19	22	8.9999
.))	chr17:26959087-26959314(-)$1	1	186	189	8.9999
)).	chr12:54448883-54449108(+)$1	1	42	45	8.9999
(((	chr7:64292463-64292690(+)$1	1	49	52	8.9999
.).	chr17:76045574-76045806(+)$1	1	39	42	8.9999
(((	chr3:152554421-152554653(+)$1	1	21	24	8.9999
.((	chrM:6442-6670(+)$1	1	94	97	8.9999
(((	chr19:41257233-41257465(+)$1	1	19	22	8.9999
(((	chr6:111694185-111694417(-)$1	1	14	17	8.9999
(((	chrX:107976466-107976689(-)$1	1	42	45	8.9999
(((	chr20:42333773-42334025(+)$1	1	125	128	8.9999
)))	chr1:39913019-39913245(+)$1	1	95	98	8.9999
)))	chr17:7414663-7414894(+)$1	1	80	83	8.9999
(((	chrX:71493625-71493855(-)$1	1	51	54	8.9999
)).	chr12:123022872-123023102(+)$1	1	11	14	8.9999
)))	chr21:26957898-26958130(-)$1	1	72	75	8.9999
...	chr7:150935434-150935657(+)$1	1	0	3	8.9999
(((	chr19:9065466-9065698(-)$1	1	1	4	8.9999
)).	chr7:12269209-12269441(+)$1	1	93	96	8.9999
...	chr5:139908405-139908637(+)$1	1	0	3	8.9999
.((	chr2:111395503-111395729(-)$1	1	47	50	8.9999
.((	chrM:8288-8520(+)$1	1	1	4	8.9999
(..	chr5:36170375-36170605(+)$1	1	144	147	8.9999
(..	chr10:133757443-133757665(+)$1	1	60	63	8.9999
(((	chr2:203623888-203624113(+)$1	1	4	7	8.9999
(((	chr1:161009666-161009898(-)$1	1	104	107	8.9999
(((	chr1:97250617-97250844(+)$1	1	2	5	8.9999
(((	chr8:8875790-8876012(+)$1	1	24	27	8.9999
(((	chr12:11174233-11174459(-)$1	1	55	58	8.9999
(((	chr12:46758155-46758381(-)$1	1	52	55	8.9999
(((	chr10:70719633-70719865(+)$1	1	19	22	8.9999
(..	chr22:31884515-31884747(-)$1	1	20	23	8.9999
(((	chr5:32380094-32380318(-)$1	1	38	41	8.9999
(((	chrX:119580137-119580372(-)$1	1	21	24	8.9999
.((	chr7:64167756-64167988(+)$1	1	2	5	8.9999
(((	chr10:71977550-71977774(-)$1	1	23	26	8.9999
(((	chr7:150935471-150935694(+)$1	1	58	61	8.9999
.))	chr19:38871482-38871725(+)$1	1	114	117	8.9999
(((	chr16:419051-419273(-)$1	1	10	13	8.9999
.))	chr16:24815482-24815714(+)$1	1	25	28	8.9999
(((	chr17:46937673-46937905(+)$1	1	9	12	8.9999
((.	chr13:99098260-99098492(+)$1	1	22	25	8.9999
(((	chr4:77979634-77979860(-)$1	1	1	4	8.9999
(..	chr10:38344712-38344944(+)$1	1	56	59	8.9999
.((	chr4:184367627-184367855(+)$1	1	21	24	8.9999
)).	chr10:75532479-75532711(+)$1	1	30	33	8.9999
...	chr15:70350480-70350706(-)$1	1	28	31	8.9999
)))	chr2:120734514-120734746(+)$1	1	43	46	8.9999
)))	chr5:37351250-37351483(-)$1	1	74	77	8.9999
(((	chr15:66030049-66030275(-)$1	1	35	38	8.9999
((.	chr14:103958226-103958468(+)$1	1	84	87	8.9999
...	chr3:48678753-48678975(-)$1	1	16	19	8.9999
)))	chr5:145826844-145827071(+)$1	1	28	31	8.9999
.).	chr21:47545669-47545890(+)$1	1	134	137	8.9999
...	chr6:43527829-43528061(-)$1	1	40	43	8.9999
.((	chr19:35769550-35769782(+)$1	1	71	74	8.9999
..(	chr14:100820682-100820910(-)$1	1	5	8	8.9999
(((	chr12:994135-994367(+)$1	1	150	153	8.9999
)))	chr19:58452293-58452515(-)$1	1	38	41	8.9999
(.(	chrM:11884-12135(-)$1	1	41	44	8.9999
))(	chr6:80749842-80750074(+)$1	1	95	98	8.9999
)))	chr4:83276373-83276602(-)$1	1	46	49	8.9999
.((	chr10:8006713-8006936(+)$1	1	10	13	8.9999
.((	chr16:85695122-85695354(+)$1	1	24	27	8.9999
(((	chrM:13039-13295(+)$1	1	8	11	8.9999
...	chrM:11213-11447(+)$1	1	98	101	8.9999
...	chrM:8090-8312(-)$1	1	23	26	8.9999
...	chr12:49087315-49087563(-)$1	1	2	5	8.9999
.((	chr19:49118500-49118722(-)$1	1	16	19	8.9999
(((	chr8:109488050-109488276(+)$1	1	7	10	8.9999
(((	chr7:127017170-127017401(-)$1	1	49	52	8.9999
...	chrM:11146-11408(+)$1	1	33	36	8.9999
((.	chrM:5256-5501(+)$1	1	17	20	8.9999
)))	chrM:6115-6340(-)$1	1	51	54	8.9999

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m3_run1.nuc.txt

#NT
AUG	chr4:77080952-77081192(-)$1	240	7	10	8.9999
AUG	chr4:144135075-144135315(+)$1	240	74	77	8.9999
AUG	chr17:5393057-5393297(+)$1	240	2	5	8.9999
AUG	chr11:86662431-86662671(-)$1	240	6	9	8.9999
AUG	chr1:16724044-16724284(+)$1	240	57	60	8.9999
AUG	chr10:104574910-104575190(+)$1	280	18	21	8.9999
AUG	chr17:47905486-47905726(+)$1	240	19	22	8.9999
AUG	chr11:205090-205330(-)$1	240	130	133	8.9999
AUG	chr9:135768134-135768374(-)$1	240	116	119	8.9999
AUG	chr11:44954398-44954638(-)$1	240	78	81	8.9999
AUG	chr13:49782786-49783026(+)$1	240	18	21	8.9999
AUG	chr2:3501750-3501990(-)$1	240	3	6	8.9999
AUG	chr7:86825179-86825459(+)$1	280	10	13	8.9999
AUG	chr20:62521754-62521994(+)$1	240	11	14	8.9999
AUG	chr7:32908401-32908641(-)$1	240	21	24	8.9999
AUG	chr3:134197112-134197352(-)$1	240	28	31	8.9999
AUG	chr20:56935454-56935694(+)$1	240	5	8	8.9999
AUG	chr22:40727545-40727785(+)$1	240	2	5	8.9999
AUG	chr4:129191356-129191600(-)$1	244	26	29	8.9999
AUG	chr4:183723093-183723364(+)$1	271	50	53	8.9999
AUG	chr2:122523188-122523428(+)$1	240	14	17	8.9999
AUG	chr19:582909-583149(+)$1	240	104	107	8.9999
AUG	chr5:6668416-6668656(+)$1	240	6	9	8.9999
AUG	chr1:156436461-156436701(-)$1	240	36	39	8.9999
AUG	chr22:22117388-22117628(-)$1	240	5	8	8.9999
AUG	chr2:113321855-113322095(+)$1	240	36	39	8.9999
AUG	chr15:75759409-75759649(-)$1	240	34	37	8.9999
AUG	chrX:129272522-129272762(-)$1	240	40	43	8.9999
AUG	chr16:24583752-24584037(+)$1	285	73	76	8.9999
AUG	chr1:231470334-231470574(-)$1	240	137	140	8.9999
AUG	chr16:71962516-71962764(+)$1	248	104	107	8.9999
AUG	chr21:43410281-43410521(-)$1	240	69	72	8.9999
AUG	chr7:6369375-6369615(-)$1	240	56	59	8.9999
AUG	chr10:101152197-101152437(+)$1	240	18	21	8.9999
AUG	chr11:118527937-118528217(+)$1	280	135	138	8.9999
AUG	chr3:88103743-88103983(-)$1	240	20	23	8.9999
AUG	chr4:169848918-169849158(+)$1	240	9	12	8.9999
AUG	chr1:26451584-26451824(+)$1	240	23	26	8.9999
AUG	chr22:32081112-32081352(-)$1	240	71	74	8.9999
AUG	chr4:99983600-99983840(+)$1	240	180	183	8.9999
aug	chr17:42876012-42876292(-)$1	280	22	25	8.9999
AUG	chr5:74669358-74669598(-)$1	240	2	5	8.9999
AUG	chr7:129068387-129068627(+)$1	240	16	19	8.9999
AUG	chr2:43799985-43800225(-)$1	240	6	9	8.9999
AUG	chr2:128462616-128462856(-)$1	240	36	39	8.9999
AUG	chr14:75128854-75129094(-)$1	240	10	13	8.9999
AUG	chr14:61112043-61112283(-)$1	240	51	54	8.9999
aug	chr11:129992184-129992424(+)$1	240	65	68	8.9999
AUG	chrX:71492354-71492594(-)$1	240	75	78	8.9999
AUG	chr19:56103151-56103391(-)$1	240	19	22	8.9999
AUG	chr10:112658648-112658888(+)$1	240	41	44	8.9999
AUG	chr3:120049783-120050023(-)$1	240	21	24	8.9999
AUG	chr7:115898081-115898331(+)$1	250	53	56	8.9999
AUG	chr17:46673026-46673266(-)$1	240	25	28	8.9999
AUG	chr3:137880105-137880345(-)$1	240	37	40	8.9999
aug	chr14:45496455-45496695(+)$1	240	17	20	8.9999
AUG	chr2:211340989-211341229(-)$1	240	109	112	8.9999
AUG	chr6:122764600-122764840(-)$1	240	5	8	8.9999
AUG	chr3:14530309-14530552(+)$1	243	37	40	8.9999
AUG	chr4:89647833-89648073(-)$1	240	11	14	8.9999
AUG	chr4:53462698-53462946(-)$1	248	3	6	8.9999
AUG	chr3:142778562-142778802(+)$1	240	159	162	8.9999
AUG	chr4:103717056-103717298(-)$1	242	15	18	8.9999
AUG	chr1:145688214-145688454(+)$1	240	87	90	8.9999
AUG	chr10:11375970-11376210(+)$1	240	203	206	8.9999
AUG	chr20:5527866-5528106(-)$1	240	63	66	8.9999
AUG	chr15:40760205-40760445(+)$1	240	5	8	8.9999
AUG	chr2:100024449-100024689(-)$1	240	56	59	8.9999
AUG	chr5:139062530-139062770(+)$1	240	47	50	8.9999
aug	chr14:61441446-61441686(-)$1	240	103	106	8.9999
AUG	chr2:128030340-128030580(-)$1	240	80	83	8.9999
AUG	chr1:109472556-109472796(-)$1	240	25	28	8.9999
AUG	chr16:23652394-23652634(-)$1	240	156	159	8.9999
AUG	chr4:762201-762441(+)$1	240	23	26	8.9999
AUG	chr6:43129004-43129244(+)$1	240	44	47	8.9999
AUG	chr1:92146376-92146616(-)$1	240	28	31	8.9999
AUG	chr1:211487532-211487772(+)$1	240	38	41	8.9999
AUG	chr3:134196447-134196687(-)$1	240	35	38	8.9999
AUG	chr1:52497835-52498075(-)$1	240	52	55	8.9999
AUG	chr15:77776996-77777236(+)$1	240	171	174	8.9999
AUG	chr5:1462977-1463301(-)$1	324	45	48	8.9999
AUG	chr3:49067554-49067794(-)$1	240	112	115	8.9999
AUG	chr2:73453144-73453384(+)$1	240	108	111	8.9999
AUG	chr9:95077468-95077708(-)$1	240	8	11	8.9999
AUG	chr13:30338548-30338788(-)$1	240	16	19	8.9999
AUG	chr1:57177214-57177494(+)$1	280	94	97	8.9999
AUG	chr17:2287267-2287547(-)$1	280	79	82	8.9999
AUG	chr17:56430945-56431185(-)$1	240	61	64	8.9999
AUG	chr5:89808140-89808380(+)$1	240	41	44	8.9999
AUG	chr9:132997295-132997535(+)$1	240	134	137	8.9999
AUG	chrX:147030415-147030655(+)$1	240	45	48	8.9999
AUG	chr4:38699977-38700217(+)$1	240	67	70	8.9999
aug	chr9:100777684-100777924(+)$1	240	6	9	8.9999
AUG	chr3:14713155-14713395(+)$1	240	1	4	8.9999
AUG	chr17:4871587-4871827(-)$1	240	131	134	8.9999

#otherMatches

#Struct PSSM
::e	chr11:67165123-67165408(+)$1	285	249	252	8.9999
:::	chr4:77080952-77081192(-)$1	240	7	10	8.9999
>>>	chr4:144135075-144135315(+)$1	240	74	77	8.9999
:::	chr17:5393057-5393297(+)$1	240	2	5	8.9999
:::	chr11:86662431-86662671(-)$1	240	6	9	8.9999
NEE	chr1:16724044-16724284(+)$1	240	57	60	8.9999
ddd	chr10:104574910-104575190(+)$1	280	18	21	8.9999
nnn	chr17:47905486-47905726(+)$1	240	19	22	8.9999
^^^	chr11:205090-205330(-)$1	240	130	133	8.9999
!bb	chr9:135768134-135768374(-)$1	240	116	119	8.9999
2hh	chr11:44954398-44954638(-)$1	240	78	81	8.9999
fff	chr13:49782786-49783026(+)$1	240	18	21	8.9999
CKK	chr2:3501750-3501990(-)$1	240	3	6	8.9999
:::	chr7:86825179-86825459(+)$1	280	10	13	8.9999
:::	chr20:62521754-62521994(+)$1	240	11	14	8.9999
HHH	chr7:32908401-32908641(-)$1	240	21	24	8.9999
:::	chr3:134197112-134197352(-)$1	240	28	31	8.9999
DLL	chr20:56935454-56935694(+)$1	240	5	8	8.9999
:::	chr22:40727545-40727785(+)$1	240	2	5	8.9999
&dd	chr4:129191356-129191600(-)$1	244	26	29	8.9999
nna	chr4:183723093-183723364(+)$1	271	50	53	8.9999
JMM	chr2:122523188-122523428(+)$1	240	14	17	8.9999
qqd	chr19:582909-583149(+)$1	240	104	107	8.9999
::B	chr5:6668416-6668656(+)$1	240	6	9	8.9999
sss	chr1:156436461-156436701(-)$1	240	36	39	8.9999
ccc	chr22:22117388-22117628(-)$1	240	5	8	8.9999
EEE	chr2:113321855-113322095(+)$1	240	36	39	8.9999
iii	chr15:75759409-75759649(-)$1	240	34	37	8.9999
{DD	chrX:129272522-129272762(-)$1	240	40	43	8.9999
H{B	chr16:24583752-24584037(+)$1	285	73	76	8.9999
ff:	chr1:231470334-231470574(-)$1	240	137	140	8.9999
#cc	chr16:71962516-71962764(+)$1	248	104	107	8.9999
===	chr21:43410281-43410521(-)$1	240	69	72	8.9999
hhh	chr7:6369375-6369615(-)$1	240	56	59	8.9999
:EE	chr10:101152197-101152437(+)$1	240	18	21	8.9999
hhh	chr11:118527937-118528217(+)$1	280	135	138	8.9999
[cc	chr3:88103743-88103983(-)$1	240	20	23	8.9999
gnn	chr4:169848918-169849158(+)$1	240	9	12	8.9999
$ee	chr1:26451584-26451824(+)$1	240	23	26	8.9999
!dd	chr22:32081112-32081352(-)$1	240	71	74	8.9999
eee	chr4:99983600-99983840(+)$1	240	180	183	8.9999
]gg	chr17:42876012-42876292(-)$1	280	22	25	8.9999
GGG	chr5:74669358-74669598(-)$1	240	2	5	8.9999
eee	chr7:129068387-129068627(+)$1	240	16	19	8.9999
:hh	chr2:43799985-43800225(-)$1	240	6	9	8.9999
fff	chr2:128462616-128462856(-)$1	240	36	39	8.9999
D{G	chr14:75128854-75129094(-)$1	240	10	13	8.9999
^^^	chr14:61112043-61112283(-)$1	240	51	54	8.9999
33c	chr11:129992184-129992424(+)$1	240	65	68	8.9999
oa]	chrX:71492354-71492594(-)$1	240	75	78	8.9999
gg#	chr19:56103151-56103391(-)$1	240	19	22	8.9999
:::	chr10:112658648-112658888(+)$1	240	41	44	8.9999
EE{	chr3:120049783-120050023(-)$1	240	21	24	8.9999
fff	chr7:115898081-115898331(+)$1	250	53	56	8.9999
SSS	chr17:46673026-46673266(-)$1	240	25	28	8.9999
eee	chr3:137880105-137880345(-)$1	240	37	40	8.9999
GGG	chr14:45496455-45496695(+)$1	240	17	20	8.9999
$$c	chr2:211340989-211341229(-)$1	240	109	112	8.9999
FBB	chr6:122764600-122764840(-)$1	240	5	8	8.9999
JJJ	chr3:14530309-14530552(+)$1	243	37	40	8.9999
GG{	chr4:89647833-89648073(-)$1	240	11	14	8.9999
fff	chr4:53462698-53462946(-)$1	248	3	6	8.9999
dd4	chr3:142778562-142778802(+)$1	240	159	162	8.9999
D{A	chr4:103717056-103717298(-)$1	242	15	18	8.9999
ggg	chr1:145688214-145688454(+)$1	240	87	90	8.9999
:A}	chr10:11375970-11376210(+)$1	240	203	206	8.9999
dd>	chr20:5527866-5528106(-)$1	240	63	66	8.9999
:::	chr15:40760205-40760445(+)$1	240	5	8	8.9999
&ff	chr2:100024449-100024689(-)$1	240	56	59	8.9999
{CC	chr5:139062530-139062770(+)$1	240	47	50	8.9999
:::	chr14:61441446-61441686(-)$1	240	103	106	8.9999
!bb	chr2:128030340-128030580(-)$1	240	80	83	8.9999
cc3	chr1:109472556-109472796(-)$1	240	25	28	8.9999
%%%	chr16:23652394-23652634(-)$1	240	156	159	8.9999
JJJ	chr4:762201-762441(+)$1	240	23	26	8.9999
gqq	chr6:43129004-43129244(+)$1	240	44	47	8.9999
FFF	chr1:92146376-92146616(-)$1	240	28	31	8.9999
fll	chr1:211487532-211487772(+)$1	240	38	41	8.9999
E{C	chr3:134196447-134196687(-)$1	240	35	38	8.9999
fff	chr1:52497835-52498075(-)$1	240	52	55	8.9999
:==	chr15:77776996-77777236(+)$1	240	171	174	8.9999
{EE	chr5:1462977-1463301(-)$1	324	45	48	8.9999
""f	chr3:49067554-49067794(-)$1	240	112	115	8.9999
E{H	chr2:73453144-73453384(+)$1	240	108	111	8.9999
DDD	chr9:95077468-95077708(-)$1	240	8	11	8.9999
""c	chr13:30338548-30338788(-)$1	240	16	19	8.9999
dd:	chr1:57177214-57177494(+)$1	280	94	97	8.9999
hhh	chr17:2287267-2287547(-)$1	280	79	82	8.9999
mmi	chr17:56430945-56431185(-)$1	240	61	64	8.9999
fff	chr5:89808140-89808380(+)$1	240	41	44	8.9999
d]d	chr9:132997295-132997535(+)$1	240	134	137	8.9999
ee&	chrX:147030415-147030655(+)$1	240	45	48	8.9999
$cc	chr4:38699977-38700217(+)$1	240	67	70	8.9999
LLB	chr9:100777684-100777924(+)$1	240	6	9	8.9999
CC{	chr3:14713155-14713395(+)$1	240	1	4	8.9999
666	chr17:4871587-4871827(-)$1	240	131	134	8.9999

#DB
..(	chr11:67165123-67165408(+)$1	1	249	252	8.9999
...	chr4:77080952-77081192(-)$1	1	7	10	8.9999
...	chr4:144135075-144135315(+)$1	1	74	77	8.9999
...	chr17:5393057-5393297(+)$1	1	2	5	8.9999
...	chr11:86662431-86662671(-)$1	1	6	9	8.9999
.((	chr1:16724044-16724284(+)$1	1	57	60	8.9999
(((	chr10:104574910-104575190(+)$1	1	18	21	8.9999
...	chr17:47905486-47905726(+)$1	1	19	22	8.9999
...	chr11:205090-205330(-)$1	1	130	133	8.9999
.((	chr9:135768134-135768374(-)$1	1	116	119	8.9999
.))	chr11:44954398-44954638(-)$1	1	78	81	8.9999
)))	chr13:49782786-49783026(+)$1	1	18	21	8.9999
(..	chr2:3501750-3501990(-)$1	1	3	6	8.9999
...	chr7:86825179-86825459(+)$1	1	10	13	8.9999
...	chr20:62521754-62521994(+)$1	1	11	14	8.9999
(((	chr7:32908401-32908641(-)$1	1	21	24	8.9999
...	chr3:134197112-134197352(-)$1	1	28	31	8.9999
(..	chr20:56935454-56935694(+)$1	1	5	8	8.9999
...	chr22:40727545-40727785(+)$1	1	2	5	8.9999
.((	chr4:129191356-129191600(-)$1	1	26	29	8.9999
..)	chr4:183723093-183723364(+)$1	1	50	53	8.9999
(..	chr2:122523188-122523428(+)$1	1	14	17	8.9999
..)	chr19:582909-583149(+)$1	1	104	107	8.9999
..(	chr5:6668416-6668656(+)$1	1	6	9	8.9999
...	chr1:156436461-156436701(-)$1	1	36	39	8.9999
(((	chr22:22117388-22117628(-)$1	1	5	8	8.9999
(((	chr2:113321855-113322095(+)$1	1	36	39	8.9999
(((	chr15:75759409-75759649(-)$1	1	34	37	8.9999
.((	chrX:129272522-129272762(-)$1	1	40	43	8.9999
(.(	chr16:24583752-24584037(+)$1	1	73	76	8.9999
)).	chr1:231470334-231470574(-)$1	1	137	140	8.9999
.((	chr16:71962516-71962764(+)$1	1	104	107	8.9999
(((	chr21:43410281-43410521(-)$1	1	69	72	8.9999
)))	chr7:6369375-6369615(-)$1	1	56	59	8.9999
.((	chr10:101152197-101152437(+)$1	1	18	21	8.9999
(((	chr11:118527937-118528217(+)$1	1	135	138	8.9999
.((	chr3:88103743-88103983(-)$1	1	20	23	8.9999
(..	chr4:169848918-169849158(+)$1	1	9	12	8.9999
.((	chr1:26451584-26451824(+)$1	1	23	26	8.9999
.((	chr22:32081112-32081352(-)$1	1	71	74	8.9999
(((	chr4:99983600-99983840(+)$1	1	180	183	8.9999
.))	chr17:42876012-42876292(-)$1	1	22	25	8.9999
(((	chr5:74669358-74669598(-)$1	1	2	5	8.9999
(((	chr7:129068387-129068627(+)$1	1	16	19	8.9999
.((	chr2:43799985-43800225(-)$1	1	6	9	8.9999
)))	chr2:128462616-128462856(-)$1	1	36	39	8.9999
(.(	chr14:75128854-75129094(-)$1	1	10	13	8.9999
...	chr14:61112043-61112283(-)$1	1	51	54	8.9999
..)	chr11:129992184-129992424(+)$1	1	65	68	8.9999
.).	chrX:71492354-71492594(-)$1	1	75	78	8.9999
((.	chr19:56103151-56103391(-)$1	1	19	22	8.9999
...	chr10:112658648-112658888(+)$1	1	41	44	8.9999
((.	chr3:120049783-120050023(-)$1	1	21	24	8.9999
)))	chr7:115898081-115898331(+)$1	1	53	56	8.9999
...	chr17:46673026-46673266(-)$1	1	25	28	8.9999
(((	chr3:137880105-137880345(-)$1	1	37	40	8.9999
(((	chr14:45496455-45496695(+)$1	1	17	20	8.9999
..(	chr2:211340989-211341229(-)$1	1	109	112	8.9999
(((	chr6:122764600-122764840(-)$1	1	5	8	8.9999
(((	chr3:14530309-14530552(+)$1	1	37	40	8.9999
((.	chr4:89647833-89648073(-)$1	1	11	14	8.9999
(((	chr4:53462698-53462946(-)$1	1	3	6	8.9999
)).	chr3:142778562-142778802(+)$1	1	159	162	8.9999
(.(	chr4:103717056-103717298(-)$1	1	15	18	8.9999
(((	chr1:145688214-145688454(+)$1	1	87	90	8.9999
.).	chr10:11375970-11376210(+)$1	1	203	206	8.9999
)).	chr20:5527866-5528106(-)$1	1	63	66	8.9999
...	chr15:40760205-40760445(+)$1	1	5	8	8.9999
.((	chr2:100024449-100024689(-)$1	1	56	59	8.9999
.((	chr5:139062530-139062770(+)$1	1	47	50	8.9999
...	chr14:61441446-61441686(-)$1	1	103	106	8.9999
.((	chr2:128030340-128030580(-)$1	1	80	83	8.9999
)).	chr1:109472556-109472796(-)$1	1	25	28	8.9999
...	chr16:23652394-23652634(-)$1	1	156	159	8.9999
(((	chr4:762201-762441(+)$1	1	23	26	8.9999
(..	chr6:43129004-43129244(+)$1	1	44	47	8.9999
(((	chr1:92146376-92146616(-)$1	1	28	31	8.9999
(..	chr1:211487532-211487772(+)$1	1	38	41	8.9999
(.(	chr3:134196447-134196687(-)$1	1	35	38	8.9999
(((	chr1:52497835-52498075(-)$1	1	52	55	8.9999
.((	chr15:77776996-77777236(+)$1	1	171	174	8.9999
.((	chr5:1462977-1463301(-)$1	1	45	48	8.9999
..(	chr3:49067554-49067794(-)$1	1	112	115	8.9999
(.(	chr2:73453144-73453384(+)$1	1	108	111	8.9999
(((	chr9:95077468-95077708(-)$1	1	8	11	8.9999
..(	chr13:30338548-30338788(-)$1	1	16	19	8.9999
)).	chr1:57177214-57177494(+)$1	1	94	97	8.9999
(((	chr17:2287267-2287547(-)$1	1	79	82	8.9999
..)	chr17:56430945-56431185(-)$1	1	61	64	8.9999
(((	chr5:89808140-89808380(+)$1	1	41	44	8.9999
).)	chr9:132997295-132997535(+)$1	1	134	137	8.9999
((.	chrX:147030415-147030655(+)$1	1	45	48	8.9999
.((	chr4:38699977-38700217(+)$1	1	67	70	8.9999
..(	chr9:100777684-100777924(+)$1	1	6	9	8.9999
((.	chr3:14713155-14713395(+)$1	1	1	4	8.9999
...	chr17:4871587-4871827(-)$1	1	131	134	8.9999

#PSSM
A : 0.94	a : 0.05	
U : 0.94	u : 0.05	
G : 0.94	g : 0.05	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_UTR_m1_run2.nuc.txt

#NT
cuuauuuuuauuuuu	chr6:34845760-34846000(-)$1	240	121	136	27.4038
CUUUUCUUUGCUUUU	chr14:69926351-69926595(+)$1	244	105	120	23.2692
Cuuuuuuuuuuuuuu	chr8:77894943-77895183(-)$1	240	122	137	34.9999
CUCUUGAUUUUUUUU	chr17:5386062-5386302(-)$1	240	79	94	23.2692
AUUUUUUUUGUUUUU	chr4:100469832-100470074(-)$1	242	46	61	28.6538
CUGAUUUUUUUUGUU	chr6:33171913-33172153(+)$1	240	205	220	22.8846
CGUUUUUUUUUCUUU	chr11:118622149-118622389(-)$1	240	110	125	26.8269
auuuauuuuauuuuu	chr6:96055700-96055940(+)$1	240	111	126	24.8076
cuuuuuuuuuuuuuu	chr6:33269267-33269507(-)$1	240	140	155	34.9999
Guuuuuuguauuuuu	chr4:115597930-115598170(+)$1	240	110	125	23.7499
CUUCUGAUUUUUUUU	chr20:34237592-34237832(-)$1	240	134	149	22.9807
CUUUUUCUCUUUUCU	chr17:61670148-61670394(+)$1	246	120	135	22.4038
Cauuuaauuuuuuuu	chr2:64819437-64819677(+)$1	240	181	196	22.7884
Auuuuuuuuuuuuuu	chr3:9519193-9519433(+)$1	240	169	184	32.3076
cuuucucuuuuucuu	chr11:62566436-62566676(-)$1	240	15	30	23.3653
cguuuuguuuucuuu	chr19:41813332-41813573(+)$1	241	204	219	23.1730
CUUUUUUUUUUUUUU	chrX:15844721-15844961(-)$1	240	46	61	34.9999
CUUUUUUUAUUUUUU	chr10:104575289-104575529(+)$1	240	122	137	30.3846
CUUUUUGUUGUUUAU	chr21:38886808-38887048(+)$1	240	133	148	23.3653
CUUUUUUUUUUUUUU	chr2:200792281-200792521(+)$1	240	6	21	34.9999
CUGUUUUUUUUUUUA	chr18:77897170-77897410(+)$1	240	111	126	26.3461
guuuuuguuuuuguu	chr2:96851060-96851300(-)$1	240	157	172	24.0384
CUUUUUCUUUUUUUU	chr5:122950138-122950378(+)$1	240	109	124	31.2499
AUUUUUUUUUUCUUU	chr1:225683418-225683667(-)$1	249	27	42	28.4615
GUUGUUUUUUUUUUU	chr6:114181876-114182156(+)$1	280	34	49	27.6923
CUUUUUUUUUCUUCU	chr21:27143642-27143886(+)$1	244	111	126	27.0192
CUUUUUGUUUUUAUU	chr2:170487201-170487441(+)$1	240	63	78	27.2115
Cuuuuuuuuuuuuuu	chr22:36623260-36623500(-)$1	240	112	127	34.9999
AUAUUUUUUUCUUUU	chr2:48605399-48605639(+)$1	240	123	138	24.4230
CUUUAAUUUUUUUUU	chr7:99752002-99752259(-)$1	257	119	134	26.7307
Cuuuuuuuucuuuuu	chr2:30864606-30864886(+)$1	280	146	161	31.3461
CUUUUUUUUUUUUUU	chr12:72097613-72097853(+)$1	240	47	62	34.9999
CUCUCUUUUUUUUUU	chr11:33094689-33095007(+)$1	318	105	120	27.0192
CAUUUUUUUCUUUCU	chr5:32229254-32229494(-)$1	240	120	135	22.8846
Cuuuuuuuuuuuuuu	chr5:71503647-71503927(+)$1	280	141	156	34.9999
CUUUUUUUGUUUCUU	chr19:21304546-21304786(+)$1	240	100	115	26.6346
cuuuuuuuuuuuuuu	chr16:46990242-46990482(-)$1	240	117	132	34.9999
CUUUGUUUUUUCUUU	chr7:111367013-111367253(-)$1	240	120	135	27.0192
auuuuuuuuuauuuu	chr14:81940080-81940320(-)$1	240	91	106	28.0769
CUCUUUUUUUCUUUG	chr1:38002422-38002662(-)$1	240	125	140	22.6923
guuuuuuuuuuuuuu	chr10:121334066-121334309(-)$1	243	189	204	31.7307
AUUUGUUUUUUGUUU	chr1:173904733-173904973(-)$1	240	96	111	23.9423
CUUGUGUUUUUUUUU	chr1:185069523-185069763(+)$1	240	146	161	26.8269
AUCCUUUUUUUUUUU	chr16:2652971-2653211(+)$1	240	114	129	24.3269
CAUUUUUCUUUUCUU	chr16:19711776-19712023(+)$1	247	115	130	22.4999
CUUGUUUAUAUUUUU	chr3:176742613-176742853(-)$1	240	96	111	23.0769
AUUUUUUUUCCUUUU	chr1:160398126-160398366(+)$1	240	112	127	24.9038
CUGUUUUUUUUUCAU	chr2:111395358-111395598(-)$1	240	119	134	22.9807
AUUUUUUUUUUCCUU	chr6:64290869-64291109(+)$1	240	177	192	24.7115
CUUUAUUAUUUAUUU	chr1:879830-880070(-)$1	240	120	135	22.3076
CUUUUUUUUACUUUU	chr2:203426146-203426386(+)$1	240	119	134	27.7884

#otherMatches

#Struct PSSM
:::::::::::::::	chr4:99799630-99799870(-)$1	240	117	132	34.9999
eeee>>>>>>>>>>>	chr6:34845760-34846000(-)$1	240	121	136	27.4038
22dddd333eeeee3	chr14:69926351-69926595(+)$1	244	105	120	23.2692
DDDD}EEEEE:::::	chr8:77894943-77895183(-)$1	240	122	137	34.9999
D{JJJJJJJJJJJ::	chr17:5386062-5386302(-)$1	240	79	94	23.2692
HHH::::::eeeeep	chr4:100469832-100470074(-)$1	242	46	61	28.6538
============333	chr6:33171913-33172153(+)$1	240	205	220	22.8846
4ccc22ffffff777	chr11:118622149-118622389(-)$1	240	110	125	26.8269
hhhh(((((((((gg	chr6:96055700-96055940(+)$1	240	111	126	24.8076
:::::::::::::::	chr6:33269267-33269507(-)$1	240	140	155	34.9999
qqqqqqbb=======	chr4:115597930-115598170(+)$1	240	110	125	23.7499
:============!!	chr20:34237592-34237832(-)$1	240	134	149	22.9807
333hhhhhhhh22dd	chr17:61670148-61670394(+)$1	246	120	135	22.4038
yyyyyyyyyyydddd	chr2:64819437-64819677(+)$1	240	181	196	22.7884
:::::::::::::::	chr3:9519193-9519433(+)$1	240	169	184	32.3076
:::::::::::::::	chr11:62566436-62566676(-)$1	240	15	30	23.3653
fffff[ddddnnnnn	chr19:41813332-41813573(+)$1	241	204	219	23.1730
eeeevvvvvvvvvvv	chrX:15844721-15844961(-)$1	240	46	61	34.9999
:::ffffffnnnnnf	chr10:104575289-104575529(+)$1	240	122	137	30.3846
llffffff]dddd::	chr21:38886808-38887048(+)$1	240	133	148	23.3653
eeee[eeeeeooooo	chr2:200792281-200792521(+)$1	240	6	21	34.9999
:::::::::::::::	chr18:77897170-77897410(+)$1	240	111	126	26.3461
c]ccc]iiiiiiiii	chr2:96851060-96851300(-)$1	240	157	172	24.0384
:::::::::::::::	chr5:122950138-122950378(+)$1	240	109	124	31.2499
iqqqqqqqqiiiiii	chr1:225683418-225683667(-)$1	249	27	42	28.4615
c]eeeeeIIIIIIII	chr6:114181876-114182156(+)$1	280	34	49	27.6923
^^^^^^^^^^^^^^^	chr21:27143642-27143886(+)$1	244	111	126	27.0192
gggggg[eeeeezzz	chr2:170487201-170487441(+)$1	240	63	78	27.2115
:::::::::::::::	chr22:36623260-36623500(-)$1	240	112	127	34.9999
h::::::::::::::	chr2:48605399-48605639(+)$1	240	123	138	24.4230
:::::ffffff[ggg	chr7:99752002-99752259(-)$1	257	119	134	26.7307
iiiiii>>>>>>>>>	chr2:30864606-30864886(+)$1	280	146	161	31.3461
ggg22eeeee]ffff	chr12:72097613-72097853(+)$1	240	47	62	34.9999
e]ddddJJJJJJJJJ	chr11:33094689-33095007(+)$1	318	105	120	27.0192
hhhhhh22a]fffff	chr5:32229254-32229494(-)$1	240	120	135	22.8846
:::::::::::::::	chr5:71503647-71503927(+)$1	280	141	156	34.9999
iiiiii(((((((((	chr19:21304546-21304786(+)$1	240	100	115	26.6346
::::::::::::fff	chr16:46990242-46990482(-)$1	240	117	132	34.9999
iieeeee++++++++	chr7:111367013-111367253(-)$1	240	120	135	27.0192
eee[==========%	chr14:81940080-81940320(-)$1	240	91	106	28.0769
dddtttttttttttd	chr1:38002422-38002662(-)$1	240	125	140	22.6923
E::::::::::::::	chr10:121334066-121334309(-)$1	243	189	204	31.7307
eooooooeeeee:::	chr1:173904733-173904973(-)$1	240	96	111	23.9423
GGGGGG:::::::::	chr1:185069523-185069763(+)$1	240	146	161	26.8269
:::::::::::::::	chr16:2652971-2653211(+)$1	240	114	129	24.3269
:::::::::::::::	chr16:19711776-19712023(+)$1	247	115	130	22.4999
[gggggggyyyyyyy	chr3:176742613-176742853(-)$1	240	96	111	23.0769
dddd22ddddccc::	chr1:160398126-160398366(+)$1	240	112	127	24.9038
4ccc22eeeee6666	chr2:111395358-111395598(-)$1	240	119	134	22.9807
:::::::::::::::	chr6:64290869-64291109(+)$1	240	177	192	24.7115
bb+++++++++++++	chr1:879830-880070(-)$1	240	120	135	22.3076
^^^^^^^^^^^^^^^	chr2:203426146-203426386(+)$1	240	119	134	27.7884

#DB
...............	chr4:99799630-99799870(-)$1	1	117	132	34.9999
))))...........	chr6:34845760-34846000(-)$1	1	121	136	27.4038
..))))...))))).	chr14:69926351-69926595(+)$1	1	105	120	23.2692
)))).))))).....	chr8:77894943-77895183(-)$1	1	122	137	34.9999
(.(((((((((((..	chr17:5386062-5386302(-)$1	1	79	94	23.2692
(((......(((((.	chr4:100469832-100470074(-)$1	1	46	61	28.6538
))))))))))))...	chr6:33171913-33172153(+)$1	1	205	220	22.8846
.)))..))))))...	chr11:118622149-118622389(-)$1	1	110	125	26.8269
((((.........((	chr6:96055700-96055940(+)$1	1	111	126	24.8076
...............	chr6:33269267-33269507(-)$1	1	140	155	34.9999
......)))))))))	chr4:115597930-115598170(+)$1	1	110	125	23.7499
.((((((((((((..	chr20:34237592-34237832(-)$1	1	134	149	22.9807
...))))))))..))	chr17:61670148-61670394(+)$1	1	120	135	22.4038
...........))))	chr2:64819437-64819677(+)$1	1	181	196	22.7884
...............	chr3:9519193-9519433(+)$1	1	169	184	32.3076
...............	chr11:62566436-62566676(-)$1	1	15	30	23.3653
(((((.((((.....	chr19:41813332-41813573(+)$1	1	204	219	23.1730
((((...........	chrX:15844721-15844961(-)$1	1	46	61	34.9999
...((((((.....)	chr10:104575289-104575529(+)$1	1	122	137	30.3846
..)))))).))))..	chr21:38886808-38887048(+)$1	1	133	148	23.3653
((((.(((((.....	chr2:200792281-200792521(+)$1	1	6	21	34.9999
...............	chr18:77897170-77897410(+)$1	1	111	126	26.3461
).))).)))))))))	chr2:96851060-96851300(-)$1	1	157	172	24.0384
...............	chr5:122950138-122950378(+)$1	1	109	124	31.2499
(........))))))	chr1:225683418-225683667(-)$1	1	27	42	28.4615
).)))))((((((((	chr6:114181876-114182156(+)$1	1	34	49	27.6923
...............	chr21:27143642-27143886(+)$1	1	111	126	27.0192
((((((.(((((...	chr2:170487201-170487441(+)$1	1	63	78	27.2115
...............	chr22:36623260-36623500(-)$1	1	112	127	34.9999
)..............	chr2:48605399-48605639(+)$1	1	123	138	24.4230
.....((((((.(((	chr7:99752002-99752259(-)$1	1	119	134	26.7307
)))))).........	chr2:30864606-30864886(+)$1	1	146	161	31.3461
)))..))))).))))	chr12:72097613-72097853(+)$1	1	47	62	34.9999
).))))(((((((((	chr11:33094689-33095007(+)$1	1	105	120	27.0192
))))))..).)))))	chr5:32229254-32229494(-)$1	1	120	135	22.8846
...............	chr5:71503647-71503927(+)$1	1	141	156	34.9999
((((((.........	chr19:21304546-21304786(+)$1	1	100	115	26.6346
............(((	chr16:46990242-46990482(-)$1	1	117	132	34.9999
(((((((........	chr7:111367013-111367253(-)$1	1	120	135	27.0192
(((.((((((((((.	chr14:81940080-81940320(-)$1	1	91	106	28.0769
(((...........)	chr1:38002422-38002662(-)$1	1	125	140	22.6923
)..............	chr10:121334066-121334309(-)$1	1	189	204	31.7307
(......)))))...	chr1:173904733-173904973(-)$1	1	96	111	23.9423
((((((.........	chr1:185069523-185069763(+)$1	1	146	161	26.8269
...............	chr16:2652971-2653211(+)$1	1	114	129	24.3269
...............	chr16:19711776-19712023(+)$1	1	115	130	22.4999
.(((((((.......	chr3:176742613-176742853(-)$1	1	96	111	23.0769
))))..)))))))..	chr1:160398126-160398366(+)$1	1	112	127	24.9038
.)))..)))))....	chr2:111395358-111395598(-)$1	1	119	134	22.9807
...............	chr6:64290869-64291109(+)$1	1	177	192	24.7115
((.............	chr1:879830-880070(-)$1	1	120	135	22.3076
...............	chr2:203426146-203426386(+)$1	1	119	134	27.7884

#PSSM
C : 0.63	A : 0.15	c : 0.09	a : 0.03	G : 0.03	g : 0.03	
U : 0.61	u : 0.28	A : 0.03	G : 0.01	a : 0.01	g : 0.01	
U : 0.51	u : 0.32	C : 0.07	G : 0.05	A : 0.01	
U : 0.55	u : 0.30	G : 0.05	C : 0.03	a : 0.01	A : 0.01	
U : 0.57	u : 0.28	A : 0.03	G : 0.03	a : 0.01	c : 0.01	C : 0.01	
U : 0.57	u : 0.30	G : 0.05	C : 0.01	a : 0.01	A : 0.01	
U : 0.55	u : 0.24	A : 0.03	C : 0.03	g : 0.03	G : 0.03	a : 0.01	c : 0.01	
U : 0.61	u : 0.30	A : 0.03	g : 0.01	C : 0.01	
U : 0.61	u : 0.32	C : 0.01	A : 0.01	G : 0.01	
U : 0.53	u : 0.24	a : 0.05	G : 0.05	C : 0.03	A : 0.03	c : 0.01	
U : 0.55	u : 0.30	C : 0.11	a : 0.01	
U : 0.55	u : 0.30	C : 0.07	c : 0.01	G : 0.01	A : 0.01	
U : 0.55	u : 0.28	C : 0.07	G : 0.01	c : 0.01	g : 0.01	A : 0.01	
U : 0.57	u : 0.32	C : 0.05	A : 0.03	
U : 0.63	u : 0.32	A : 0.01	G : 0.01	

#score	1420.5769230769224
#seq	52
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_CDS_m1_run1.nuc.txt

#NT
UGUCCU	chr1:23885348-23885572(-)$1	224	130	136	10.1014
UGUGCU	chr19:23544962-23545192(-)$1	230	189	195	10.1014
UGUUCU	chr2:32836416-32836641(+)$1	225	72	78	13.7971
UUUUCU	chr6:160109097-160109319(-)$1	222	117	123	11.1884
ugUACU	chr7:107546646-107546872(+)$1	226	13	19	9.9565
UUUUCU	chr20:31022180-31022399(+)$1	219	32	38	11.1884
UGUUUU	chr17:53485017-53485243(-)$1	226	75	81	10.6086
UAUUCU	chr7:5569082-5569315(-)$1	233	10	16	10.6811
UGUUUU	chr11:125513639-125513864(+)$1	225	32	38	10.6086
UAUUCU	chr15:54860016-54860238(-)$1	222	66	72	10.6811
UUUUCU	chr10:90768598-90768828(+)$1	230	39	45	11.1884
UUUUCU	chr5:134010316-134010536(+)$1	220	164	170	11.1884
UGUGCU	chr12:54769533-54769758(-)$1	225	40	46	10.1014
UGUGCU	chr16:71823117-71823342(-)$1	225	50	56	10.1014
UGAUCU	chr14:32561730-32561952(+)$1	222	40	46	9.3043
UGUCCU	chr17:3386721-3386942(+)$1	221	203	209	10.1014
UGUUUU	chr5:96332031-96332253(+)$1	222	44	50	10.6086
UAUUCU	chr6:35587833-35588055(+)$1	222	136	142	10.6811
UGUUUU	chr10:3823580-3823803(-)$1	223	98	104	10.6086
UGUUAU	chr2:32445257-32445480(+)$1	223	1	7	10.1014
UGUUCU	chr1:33295464-33295684(-)$1	220	81	87	13.7971
UGUGCU	chr2:27259469-27259695(+)$1	226	125	131	10.1014
AGUUCU	chr5:140952998-140953219(-)$1	221	85	91	9.2318
UUUUCU	chr10:115377113-115377331(-)$1	218	4	10	11.1884
UUUUCU	chr4:144469016-144469234(+)$1	218	150	156	11.1884
UUUUCU	chr20:33732703-33732921(-)$1	218	61	67	11.1884
UAUUCU	chr12:57704090-57704308(-)$1	218	81	87	10.6811
UGUUUU	chr6:108544126-108544349(-)$1	223	20	26	10.6086
UUUUCU	chr2:55518728-55518953(-)$1	225	29	35	11.1884
UGUUCU	chr2:74392308-74392538(-)$1	230	109	115	13.7971
UGUCCU	chr1:161022969-161023196(-)$1	227	154	160	10.1014
UGUUUU	chr7:148427227-148427457(+)$1	230	210	216	10.6086
UGUUCU	chr11:82984784-82985003(-)$1	219	172	178	13.7971
UGCUCU	chr1:19410906-19411132(-)$1	226	14	20	9.5217
UGUUCU	chr8:23301895-23302118(-)$1	223	205	211	13.7971
UGCUCU	chr12:49427350-49427571(-)$1	221	195	201	9.5217
UGUUCU	chr19:47424342-47424572(+)$1	230	97	103	13.7971
UGUUGU	chrX:135092527-135092751(-)$1	224	116	122	10.0289
UGUACU	chr2:203974805-203975027(+)$1	222	0	6	9.9565
UUUUCU	chr3:112068516-112068739(+)$1	223	19	25	11.1884
UGUUCU	chr17:650842-651072(-)$1	230	76	82	13.7971
UCUUCU	chr1:155451860-155452080(-)$1	220	4	10	10.6086
UUUUCU	chr12:22811903-22812119(+)$1	216	13	19	11.1884
UGUCCU	chr1:26189562-26189781(-)$1	219	130	136	10.1014
UAUUCU	chr10:11997184-11997401(-)$1	217	0	6	10.6811
AGUUCU	chr19:50831823-50832043(-)$1	220	104	110	9.2318
UGUCCU	chr9:36217262-36217487(-)$1	225	19	25	10.1014
UCUUCU	chr4:39506772-39506992(-)$1	220	6	12	10.6086
UCUUCU	chrX:114244036-114244259(+)$1	223	63	69	10.6086
UGCUCU	chr12:94648935-94649154(+)$1	219	9	15	9.5217
AGUUCU	chr16:9009210-9009435(-)$1	225	147	153	9.2318
UGUGCU	chr3:33087604-33087828(+)$1	224	95	101	10.1014
UGUUUU	chr12:96354130-96354346(+)$1	216	2	8	10.6086
UGGUCU	chr2:33811581-33811802(-)$1	221	156	162	9.3043
UGUUGU	chr12:72013907-72014137(-)$1	230	18	24	10.0289
UGUUAU	chr2:231333677-231333897(+)$1	220	204	210	10.1014
UUUUCU	chr11:17143736-17143955(-)$1	219	0	6	11.1884
UGUUCU	chr15:59377813-59378034(+)$1	221	24	30	13.7971
UGUUCU	chr1:220232201-220232422(-)$1	221	113	119	13.7971
UGUUCU	chr9:5763323-5763542(+)$1	219	43	49	13.7971
UCUUCU	chr1:211960900-211961127(-)$1	227	18	24	10.6086
UGUUUU	chrX:41076419-41076636(+)$1	217	25	31	10.6086
UUUUCU	chr2:225658043-225658263(-)$1	220	71	77	11.1884
UGUUUU	chr16:74496364-74496586(-)$1	222	24	30	10.6086
UGUACU	chrX:53652804-53653023(-)$1	219	24	30	9.9565
UGUUAU	chr16:11348607-11348831(-)$1	224	174	180	10.1014
UGUUUU	chr12:30792437-30792667(-)$1	230	21	27	10.6086
UGCUCU	chr2:197990053-197990273(-)$1	220	143	149	9.5217

#otherMatches

#Struct PSSM
[bbqqq	chr2:215645468-215645687(-)$1	219	173	179	13.7971
ccc]dd	chr1:23885348-23885572(-)$1	224	130	136	10.1014
c[annn	chr19:23544962-23545192(-)$1	230	189	195	10.1014
cccc!!	chr2:32836416-32836641(+)$1	225	72	78	13.7971
======	chr6:160109097-160109319(-)$1	222	117	123	11.1884
IIIIII	chr7:107546646-107546872(+)$1	226	13	19	9.9565
++++++	chr20:31022180-31022399(+)$1	219	32	38	11.1884
%%%%%%	chr17:53485017-53485243(-)$1	226	75	81	10.6086
CKKFFF	chr7:5569082-5569315(-)$1	233	10	16	10.6811
gggggg	chr11:125513639-125513864(+)$1	225	32	38	10.6086
ddd555	chr15:54860016-54860238(-)$1	222	66	72	10.6811
IIIIII	chr10:90768598-90768828(+)$1	230	39	45	11.1884
JJJJYY	chr5:134010316-134010536(+)$1	220	164	170	11.1884
:::::g	chr12:54769533-54769758(-)$1	225	40	46	10.1014
NNGGGG	chr16:71823117-71823342(-)$1	225	50	56	10.1014
b]dddd	chr14:32561730-32561952(+)$1	222	40	46	9.3043
dd]a::	chr17:3386721-3386942(+)$1	221	203	209	10.1014
zzzzzz	chr5:96332031-96332253(+)$1	222	44	50	10.6086
$$$$cc	chr6:35587833-35588055(+)$1	222	136	142	10.6811
fffffd	chr10:3823580-3823803(-)$1	223	98	104	10.6086
ccc!!f	chr2:32445257-32445480(+)$1	223	1	7	10.1014
EEEECC	chr1:33295464-33295684(-)$1	220	81	87	13.7971
ennnnn	chr2:27259469-27259695(+)$1	226	125	131	10.1014
d]eeee	chr5:140952998-140953219(-)$1	221	85	91	9.2318
iiiiii	chr10:115377113-115377331(-)$1	218	4	10	11.1884
hhhhhh	chr4:144469016-144469234(+)$1	218	150	156	11.1884
hh::::	chr20:33732703-33732921(-)$1	218	61	67	11.1884
c[cccm	chr12:57704090-57704308(-)$1	218	81	87	10.6811
JJJJJJ	chr6:108544126-108544349(-)$1	223	20	26	10.6086
rrrrrr	chr2:55518728-55518953(-)$1	225	29	35	11.1884
999eee	chr2:74392308-74392538(-)$1	230	109	115	13.7971
iiiiii	chr1:161022969-161023196(-)$1	227	154	160	10.1014
:EEEEE	chr7:148427227-148427457(+)$1	230	210	216	10.6086
ddddoo	chr11:82984784-82985003(-)$1	219	172	178	13.7971
hhhhhh	chr1:19410906-19411132(-)$1	226	14	20	9.5217
[annnn	chr8:23301895-23302118(-)$1	223	205	211	13.7971
dddd44	chr12:49427350-49427571(-)$1	221	195	201	9.5217
eeeeee	chr19:47424342-47424572(+)$1	230	97	103	13.7971
b22ddd	chrX:135092527-135092751(-)$1	224	116	122	10.0289
ccceee	chr2:203974805-203975027(+)$1	222	0	6	9.9565
::::::	chr3:112068516-112068739(+)$1	223	19	25	11.1884
nnnfff	chr17:650842-651072(-)$1	230	76	82	13.7971
::FFFF	chr1:155451860-155452080(-)$1	220	4	10	10.6086
::::DD	chr12:22811903-22812119(+)$1	216	13	19	11.1884
xxxxxx	chr1:26189562-26189781(-)$1	219	130	136	10.1014
::::::	chr10:11997184-11997401(-)$1	217	0	6	10.6811
ddoooo	chr19:50831823-50832043(-)$1	220	104	110	9.2318
ffffff	chr9:36217262-36217487(-)$1	225	19	25	10.1014
EEE:ff	chr4:39506772-39506992(-)$1	220	6	12	10.6086
eeee##	chrX:114244036-114244259(+)$1	223	63	69	10.6086
EELLLI	chr12:94648935-94649154(+)$1	219	9	15	9.5217
g:::::	chr16:9009210-9009435(-)$1	225	147	153	9.2318
!!bbbb	chr3:33087604-33087828(+)$1	224	95	101	10.1014
FFFFFM	chr12:96354130-96354346(+)$1	216	2	8	10.6086
dddd::	chr2:33811581-33811802(-)$1	221	156	162	9.3043
GGGGKK	chr12:72013907-72014137(-)$1	230	18	24	10.0289
::::::	chr2:231333677-231333897(+)$1	220	204	210	10.1014
::::::	chr11:17143736-17143955(-)$1	219	0	6	11.1884
uuuuuu	chr15:59377813-59378034(+)$1	221	24	30	13.7971
:=====	chr1:220232201-220232422(-)$1	221	113	119	13.7971
gggggg	chr9:5763323-5763542(+)$1	219	43	49	13.7971
BBOOOO	chr1:211960900-211961127(-)$1	227	18	24	10.6086
cc[ddd	chrX:41076419-41076636(+)$1	217	25	31	10.6086
ffff:e	chr2:225658043-225658263(-)$1	220	71	77	11.1884
[bb!!b	chr16:74496364-74496586(-)$1	222	24	30	10.6086
ff::bb	chrX:53652804-53653023(-)$1	219	24	30	9.9565
ddd:::	chr16:11348607-11348831(-)$1	224	174	180	10.1014
::::::	chr12:30792437-30792667(-)$1	230	21	27	10.6086
:ddddo	chr2:197990053-197990273(-)$1	220	143	149	9.5217

#DB
.((...	chr2:215645468-215645687(-)$1	1	173	179	13.7971
))).))	chr1:23885348-23885572(-)$1	1	130	136	10.1014
(.(...	chr19:23544962-23545192(-)$1	1	189	195	10.1014
((((..	chr2:32836416-32836641(+)$1	1	72	78	13.7971
))))))	chr6:160109097-160109319(-)$1	1	117	123	11.1884
((((((	chr7:107546646-107546872(+)$1	1	13	19	9.9565
......	chr20:31022180-31022399(+)$1	1	32	38	11.1884
......	chr17:53485017-53485243(-)$1	1	75	81	10.6086
(..(((	chr7:5569082-5569315(-)$1	1	10	16	10.6811
))))))	chr11:125513639-125513864(+)$1	1	32	38	10.6086
)))...	chr15:54860016-54860238(-)$1	1	66	72	10.6811
((((((	chr10:90768598-90768828(+)$1	1	39	45	11.1884
))))..	chr5:134010316-134010536(+)$1	1	164	170	11.1884
.....(	chr12:54769533-54769758(-)$1	1	40	46	10.1014
..((((	chr16:71823117-71823342(-)$1	1	50	56	10.1014
).))))	chr14:32561730-32561952(+)$1	1	40	46	9.3043
)).)..	chr17:3386721-3386942(+)$1	1	203	209	10.1014
......	chr5:96332031-96332253(+)$1	1	44	50	10.6086
....((	chr6:35587833-35588055(+)$1	1	136	142	10.6811
((((((	chr10:3823580-3823803(-)$1	1	98	104	10.6086
(((..(	chr2:32445257-32445480(+)$1	1	1	7	10.1014
((((((	chr1:33295464-33295684(-)$1	1	81	87	13.7971
(.....	chr2:27259469-27259695(+)$1	1	125	131	10.1014
).))))	chr5:140952998-140953219(-)$1	1	85	91	9.2318
((((((	chr10:115377113-115377331(-)$1	1	4	10	11.1884
((((((	chr4:144469016-144469234(+)$1	1	150	156	11.1884
))....	chr20:33732703-33732921(-)$1	1	61	67	11.1884
(.(((.	chr12:57704090-57704308(-)$1	1	81	87	10.6811
((((((	chr6:108544126-108544349(-)$1	1	20	26	10.6086
......	chr2:55518728-55518953(-)$1	1	29	35	11.1884
...)))	chr2:74392308-74392538(-)$1	1	109	115	13.7971
))))))	chr1:161022969-161023196(-)$1	1	154	160	10.1014
.)))))	chr7:148427227-148427457(+)$1	1	210	216	10.6086
((((..	chr11:82984784-82985003(-)$1	1	172	178	13.7971
((((((	chr1:19410906-19411132(-)$1	1	14	20	9.5217
.(....	chr8:23301895-23302118(-)$1	1	205	211	13.7971
))))..	chr12:49427350-49427571(-)$1	1	195	201	9.5217
))))))	chr19:47424342-47424572(+)$1	1	97	103	13.7971
)..)))	chrX:135092527-135092751(-)$1	1	116	122	10.0289
((((((	chr2:203974805-203975027(+)$1	1	0	6	9.9565
......	chr3:112068516-112068739(+)$1	1	19	25	11.1884
...)))	chr17:650842-651072(-)$1	1	76	82	13.7971
..((((	chr1:155451860-155452080(-)$1	1	4	10	10.6086
....((	chr12:22811903-22812119(+)$1	1	13	19	11.1884
......	chr1:26189562-26189781(-)$1	1	130	136	10.1014
......	chr10:11997184-11997401(-)$1	1	0	6	10.6811
((....	chr19:50831823-50832043(-)$1	1	104	110	9.2318
((((((	chr9:36217262-36217487(-)$1	1	19	25	10.1014
(((.((	chr4:39506772-39506992(-)$1	1	6	12	10.6086
((((..	chrX:114244036-114244259(+)$1	1	63	69	10.6086
((...(	chr12:94648935-94649154(+)$1	1	9	15	9.5217
).....	chr16:9009210-9009435(-)$1	1	147	153	9.2318
..((((	chr3:33087604-33087828(+)$1	1	95	101	10.1014
(((((.	chr12:96354130-96354346(+)$1	1	2	8	10.6086
))))..	chr2:33811581-33811802(-)$1	1	156	162	9.3043
((((..	chr12:72013907-72014137(-)$1	1	18	24	10.0289
......	chr2:231333677-231333897(+)$1	1	204	210	10.1014
......	chr11:17143736-17143955(-)$1	1	0	6	11.1884
......	chr15:59377813-59378034(+)$1	1	24	30	13.7971
.(((((	chr1:220232201-220232422(-)$1	1	113	119	13.7971
((((((	chr9:5763323-5763542(+)$1	1	43	49	13.7971
((....	chr1:211960900-211961127(-)$1	1	18	24	10.6086
((.(((	chrX:41076419-41076636(+)$1	1	25	31	10.6086
)))).(	chr2:225658043-225658263(-)$1	1	71	77	11.1884
.((..(	chr16:74496364-74496586(-)$1	1	24	30	10.6086
))..((	chrX:53652804-53653023(-)$1	1	24	30	9.9565
)))...	chr16:11348607-11348831(-)$1	1	174	180	10.1014
......	chr12:30792437-30792667(-)$1	1	21	27	10.6086
.((((.	chr2:197990053-197990273(-)$1	1	143	149	9.5217

#PSSM
U : 0.94	A : 0.04	u : 0.01	
G : 0.68	U : 0.17	A : 0.07	C : 0.05	g : 0.01	
U : 0.91	C : 0.05	A : 0.01	G : 0.01	
U : 0.81	C : 0.07	G : 0.07	A : 0.04	
C : 0.78	U : 0.14	A : 0.04	G : 0.02	
U : 0.99	

#score	753.5942028985494
#seq	69
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m3_run2.nuc.txt

#NT
AAGA	chr1:7527818-7528040(-)$1	222	52	56	12.0000
AAGA	chr9:103108962-103109192(-)$1	230	87	91	12.0000
AAGA	chr1:197059274-197059499(-)$1	225	8	12	12.0000
AAGA	chr15:32929798-32930023(+)$1	225	26	30	12.0000
AAGA	chr3:130685951-130686181(+)$1	230	151	155	12.0000
AAGA	chr1:245019263-245019488(-)$1	225	94	98	12.0000
AAGA	chr17:53485013-53485243(-)$1	230	139	143	12.0000
AAGA	chr8:71569987-71570217(-)$1	230	145	149	12.0000
AAGA	chr1:37947965-37948192(+)$1	227	130	134	12.0000
AAGA	chr15:66832414-66832644(+)$1	230	64	68	12.0000
AAGA	chr8:98289040-98289265(-)$1	225	4	8	12.0000
AAGA	chr5:95234164-95234394(-)$1	230	148	152	12.0000
AAGA	chr8:37595390-37595615(+)$1	225	122	126	12.0000
AAGA	chr9:86300816-86301046(-)$1	230	52	56	12.0000
AAGA	chr2:183866833-183867063(-)$1	230	24	28	12.0000
AAGA	chr17:66267423-66267646(-)$1	223	4	8	12.0000
AAGA	chr3:130653366-130653596(+)$1	230	191	195	12.0000
AAGA	chr15:59502627-59502857(-)$1	230	59	63	12.0000
AAGA	chr18:32826147-32826371(+)$1	224	105	109	12.0000
AAGA	chr3:4716688-4716913(+)$1	225	132	136	12.0000
AAGA	chrX:104464927-104465147(+)$1	220	46	50	12.0000
AAGA	chr6:170852608-170852838(-)$1	230	144	148	12.0000
AAGA	chr4:114378569-114378796(-)$1	227	205	209	12.0000
AAGA	chr16:47462599-47462826(-)$1	227	97	101	12.0000
AAGA	chr19:49118501-49118726(-)$1	225	123	127	12.0000
AAGA	chr17:76045575-76045808(+)$1	233	37	41	12.0000
AAGA	chr1:28148707-28148934(+)$1	227	46	50	12.0000
AAGA	chr5:14508370-14508603(+)$1	233	223	227	12.0000
AAGA	chr17:29161297-29161521(+)$1	224	132	136	12.0000
AAGA	chr17:65214696-65214926(-)$1	230	10	14	12.0000
AAGA	chr17:73144577-73144807(-)$1	230	114	118	12.0000
AAGA	chr4:175158596-175158821(-)$1	225	136	140	12.0000
AAGA	chr6:13486809-13487039(-)$1	230	26	30	12.0000
AAGA	chr21:34721637-34721867(+)$1	230	217	221	12.0000
AAGA	chr5:43628360-43628590(+)$1	230	33	37	12.0000
AAGA	chr5:64867610-64867833(+)$1	223	125	129	12.0000
AAGA	chr19:16259491-16259721(+)$1	230	151	155	12.0000
AAGA	chr20:49509816-49510042(-)$1	226	191	195	12.0000
AAGA	chr1:231471278-231471508(-)$1	230	24	28	12.0000
AAGA	chr6:18249937-18250161(-)$1	224	5	9	12.0000
AAGA	chr3:121410385-121410615(-)$1	230	32	36	12.0000
AAGA	chr6:149833273-149833500(-)$1	227	97	101	12.0000
AAGA	chr17:65907535-65907760(+)$1	225	33	37	12.0000
AAGA	chr9:5763238-5763465(+)$1	227	139	143	12.0000
AAGA	chr5:31552794-31553024(+)$1	230	132	136	12.0000
AAGA	chr19:34818281-34818505(+)$1	224	58	62	12.0000
AAGA	chr11:18373380-18373605(+)$1	225	0	4	12.0000
AAGA	chr7:98984214-98984444(+)$1	230	137	141	12.0000
AAGA	chr5:36143284-36143509(-)$1	225	139	143	12.0000
AAGA	chr2:61749698-61749921(-)$1	223	148	152	12.0000
AAGA	chr12:56574764-56574985(-)$1	221	141	145	12.0000
AAGA	chr21:34715767-34715992(+)$1	225	46	50	12.0000
AAGA	chr19:20989811-20990041(+)$1	230	8	12	12.0000
AAGA	chr16:50257008-50257233(+)$1	225	89	93	12.0000
AAGA	chr11:122930362-122930592(-)$1	230	39	43	12.0000
AAGA	chr5:37026264-37026494(+)$1	230	124	128	12.0000
AAGA	chr2:105959432-105959656(+)$1	224	212	216	12.0000
AAGA	chr10:88213321-88213551(-)$1	230	141	145	12.0000
AAGA	chr12:51207980-51208210(+)$1	230	192	196	12.0000
AAGA	chr2:215880122-215880353(-)$1	231	27	31	12.0000
AAGA	chr22:31330749-31330975(-)$1	226	61	65	12.0000
AAGA	chr12:80014804-80015029(-)$1	225	58	62	12.0000
AAGA	chr14:64457135-64457360(+)$1	225	34	38	12.0000
AAGA	chr9:5763482-5763705(+)$1	223	153	157	12.0000
AAGA	chr9:26919257-26919482(-)$1	225	63	67	12.0000
AAGA	chr11:58317377-58317600(-)$1	223	39	43	12.0000
AAGA	chr6:122774888-122775118(-)$1	230	174	178	12.0000
AAGA	chr2:158272428-158272652(-)$1	224	122	126	12.0000
AAGA	chr2:203765649-203765879(-)$1	230	4	8	12.0000
AAGA	chr14:50295683-50295913(-)$1	230	57	61	12.0000
AAGA	chr14:55467209-55467432(-)$1	223	8	12	12.0000
aaga	chr11:10874974-10875217(-)$1	243	50	54	12.0000
AAGA	chr15:45007684-45007933(+)$1	249	49	53	12.0000
AAGA	chr7:135078861-135079094(-)$1	233	74	78	12.0000
AAGA	chr1:112308681-112308911(+)$1	230	3	7	12.0000
AAGA	chr6:119226754-119226984(+)$1	230	147	151	12.0000
AAGA	chr6:18258096-18258320(-)$1	224	77	81	12.0000
AAGA	chr11:6569505-6569732(+)$1	227	41	45	12.0000
AAGA	chr14:103341946-103342171(+)$1	225	35	39	12.0000
AAGA	chr8:48842345-48842570(-)$1	225	127	131	12.0000
AAGA	chr3:71015051-71015281(-)$1	230	162	166	12.0000

#otherMatches

#Struct PSSM
d[ee	chr4:48381704-48381924(+)$1	220	86	90	12.0000
::::	chr1:7527818-7528040(-)$1	222	52	56	12.0000
uuuu	chr9:103108962-103109192(-)$1	230	87	91	12.0000
FFFR	chr1:197059274-197059499(-)$1	225	8	12	12.0000
::::	chr15:32929798-32930023(+)$1	225	26	30	12.0000
JJJ}	chr3:130685951-130686181(+)$1	230	151	155	12.0000
NNNN	chr1:245019263-245019488(-)$1	225	94	98	12.0000
eeee	chr17:53485013-53485243(-)$1	230	139	143	12.0000
rrrr	chr8:71569987-71570217(-)$1	230	145	149	12.0000
!!dd	chr1:37947965-37948192(+)$1	227	130	134	12.0000
$$gg	chr15:66832414-66832644(+)$1	230	64	68	12.0000
::::	chr8:98289040-98289265(-)$1	225	4	8	12.0000
dccc	chr5:95234164-95234394(-)$1	230	148	152	12.0000
pbb2	chr8:37595390-37595615(+)$1	225	122	126	12.0000
cc]e	chr9:86300816-86301046(-)$1	230	52	56	12.0000
::::	chr2:183866833-183867063(-)$1	230	24	28	12.0000
KKDD	chr17:66267423-66267646(-)$1	223	4	8	12.0000
ddqq	chr3:130653366-130653596(+)$1	230	191	195	12.0000
##bb	chr15:59502627-59502857(-)$1	230	59	63	12.0000
gggg	chr18:32826147-32826371(+)$1	224	105	109	12.0000
!bb[	chr3:4716688-4716913(+)$1	225	132	136	12.0000
oooo	chrX:104464927-104465147(+)$1	220	46	50	12.0000
iii:	chr6:170852608-170852838(-)$1	230	144	148	12.0000
::cc	chr4:114378569-114378796(-)$1	227	205	209	12.0000
rrrr	chr16:47462599-47462826(-)$1	227	97	101	12.0000
dddd	chr19:49118501-49118726(-)$1	225	123	127	12.0000
mma2	chr17:76045575-76045808(+)$1	233	37	41	12.0000
ccc]	chr1:28148707-28148934(+)$1	227	46	50	12.0000
mmmm	chr5:14508370-14508603(+)$1	233	223	227	12.0000
]ddd	chr17:29161297-29161521(+)$1	224	132	136	12.0000
HKKB	chr17:65214696-65214926(-)$1	230	10	14	12.0000
YYAY	chr17:73144577-73144807(-)$1	230	114	118	12.0000
d000	chr4:175158596-175158821(-)$1	225	136	140	12.0000
C{BB	chr6:13486809-13487039(-)$1	230	26	30	12.0000
HHHH	chr21:34721637-34721867(+)$1	230	217	221	12.0000
rrrr	chr5:43628360-43628590(+)$1	230	33	37	12.0000
GGGG	chr5:64867610-64867833(+)$1	223	125	129	12.0000
9999	chr19:16259491-16259721(+)$1	230	151	155	12.0000
oocc	chr20:49509816-49510042(-)$1	226	191	195	12.0000
fff"	chr1:231471278-231471508(-)$1	230	24	28	12.0000
::::	chr6:18249937-18250161(-)$1	224	5	9	12.0000
2bb2	chr3:121410385-121410615(-)$1	230	32	36	12.0000
::dd	chr6:149833273-149833500(-)$1	227	97	101	12.0000
::::	chr17:65907535-65907760(+)$1	225	33	37	12.0000
ffff	chr9:5763238-5763465(+)$1	227	139	143	12.0000
gggg	chr5:31552794-31553024(+)$1	230	132	136	12.0000
ssss	chr19:34818281-34818505(+)$1	224	58	62	12.0000
::BB	chr11:18373380-18373605(+)$1	225	0	4	12.0000
occc	chr7:98984214-98984444(+)$1	230	137	141	12.0000
FFFF	chr5:36143284-36143509(-)$1	225	139	143	12.0000
eeel	chr2:61749698-61749921(-)$1	223	148	152	12.0000
::DD	chr12:56574764-56574985(-)$1	221	141	145	12.0000
::::	chr21:34715767-34715992(+)$1	225	46	50	12.0000
::::	chr19:20989811-20990041(+)$1	230	8	12	12.0000
::::	chr16:50257008-50257233(+)$1	225	89	93	12.0000
ffff	chr11:122930362-122930592(-)$1	230	39	43	12.0000
DD::	chr5:37026264-37026494(+)$1	230	124	128	12.0000
::::	chr2:105959432-105959656(+)$1	224	212	216	12.0000
dddd	chr10:88213321-88213551(-)$1	230	141	145	12.0000
::EE	chr12:51207980-51208210(+)$1	230	192	196	12.0000
{BB{	chr2:215880122-215880353(-)$1	231	27	31	12.0000
:ccc	chr22:31330749-31330975(-)$1	226	61	65	12.0000
eeee	chr12:80014804-80015029(-)$1	225	58	62	12.0000
ff::	chr14:64457135-64457360(+)$1	225	34	38	12.0000
eee:	chr9:5763482-5763705(+)$1	223	153	157	12.0000
MMEE	chr9:26919257-26919482(-)$1	225	63	67	12.0000
gggg	chr11:58317377-58317600(-)$1	223	39	43	12.0000
IIII	chr6:122774888-122775118(-)$1	230	174	178	12.0000
nnne	chr2:158272428-158272652(-)$1	224	122	126	12.0000
EEBB	chr2:203765649-203765879(-)$1	230	4	8	12.0000
bb22	chr14:50295683-50295913(-)$1	230	57	61	12.0000
:iii	chr14:55467209-55467432(-)$1	223	8	12	12.0000
ffff	chr11:10874974-10875217(-)$1	243	50	54	12.0000
HHHH	chr15:45007684-45007933(+)$1	249	49	53	12.0000
ccco	chr7:135078861-135079094(-)$1	233	74	78	12.0000
ddqq	chr1:112308681-112308911(+)$1	230	3	7	12.0000
eeed	chr6:119226754-119226984(+)$1	230	147	151	12.0000
niii	chr6:18258096-18258320(-)$1	224	77	81	12.0000
EEEE	chr11:6569505-6569732(+)$1	227	41	45	12.0000
::::	chr14:103341946-103342171(+)$1	225	35	39	12.0000
dddd	chr8:48842345-48842570(-)$1	225	127	131	12.0000
oooo	chr3:71015051-71015281(-)$1	230	162	166	12.0000

#DB
(.((	chr4:48381704-48381924(+)$1	1	86	90	12.0000
....	chr1:7527818-7528040(-)$1	1	52	56	12.0000
....	chr9:103108962-103109192(-)$1	1	87	91	12.0000
(((.	chr1:197059274-197059499(-)$1	1	8	12	12.0000
....	chr15:32929798-32930023(+)$1	1	26	30	12.0000
))).	chr3:130685951-130686181(+)$1	1	151	155	12.0000
....	chr1:245019263-245019488(-)$1	1	94	98	12.0000
((((	chr17:53485013-53485243(-)$1	1	139	143	12.0000
....	chr8:71569987-71570217(-)$1	1	145	149	12.0000
..((	chr1:37947965-37948192(+)$1	1	130	134	12.0000
..((	chr15:66832414-66832644(+)$1	1	64	68	12.0000
....	chr8:98289040-98289265(-)$1	1	4	8	12.0000
((((	chr5:95234164-95234394(-)$1	1	148	152	12.0000
.)).	chr8:37595390-37595615(+)$1	1	122	126	12.0000
)).)	chr9:86300816-86301046(-)$1	1	52	56	12.0000
....	chr2:183866833-183867063(-)$1	1	24	28	12.0000
..((	chr17:66267423-66267646(-)$1	1	4	8	12.0000
((..	chr3:130653366-130653596(+)$1	1	191	195	12.0000
..((	chr15:59502627-59502857(-)$1	1	59	63	12.0000
((((	chr18:32826147-32826371(+)$1	1	105	109	12.0000
.((.	chr3:4716688-4716913(+)$1	1	132	136	12.0000
....	chrX:104464927-104465147(+)$1	1	46	50	12.0000
))).	chr6:170852608-170852838(-)$1	1	144	148	12.0000
..((	chr4:114378569-114378796(-)$1	1	205	209	12.0000
....	chr16:47462599-47462826(-)$1	1	97	101	12.0000
))))	chr19:49118501-49118726(-)$1	1	123	127	12.0000
..).	chr17:76045575-76045808(+)$1	1	37	41	12.0000
))).	chr1:28148707-28148934(+)$1	1	46	50	12.0000
....	chr5:14508370-14508603(+)$1	1	223	227	12.0000
.)))	chr17:29161297-29161521(+)$1	1	132	136	12.0000
(..(	chr17:65214696-65214926(-)$1	1	10	14	12.0000
..).	chr17:73144577-73144807(-)$1	1	114	118	12.0000
)...	chr4:175158596-175158821(-)$1	1	136	140	12.0000
(.((	chr6:13486809-13487039(-)$1	1	26	30	12.0000
))))	chr21:34721637-34721867(+)$1	1	217	221	12.0000
....	chr5:43628360-43628590(+)$1	1	33	37	12.0000
))))	chr5:64867610-64867833(+)$1	1	125	129	12.0000
....	chr19:16259491-16259721(+)$1	1	151	155	12.0000
..))	chr20:49509816-49510042(-)$1	1	191	195	12.0000
(((.	chr1:231471278-231471508(-)$1	1	24	28	12.0000
....	chr6:18249937-18250161(-)$1	1	5	9	12.0000
.)).	chr3:121410385-121410615(-)$1	1	32	36	12.0000
..((	chr6:149833273-149833500(-)$1	1	97	101	12.0000
....	chr17:65907535-65907760(+)$1	1	33	37	12.0000
((((	chr9:5763238-5763465(+)$1	1	139	143	12.0000
((((	chr5:31552794-31553024(+)$1	1	132	136	12.0000
....	chr19:34818281-34818505(+)$1	1	58	62	12.0000
..((	chr11:18373380-18373605(+)$1	1	0	4	12.0000
.)))	chr7:98984214-98984444(+)$1	1	137	141	12.0000
((((	chr5:36143284-36143509(-)$1	1	139	143	12.0000
(((.	chr2:61749698-61749921(-)$1	1	148	152	12.0000
..))	chr12:56574764-56574985(-)$1	1	141	145	12.0000
....	chr21:34715767-34715992(+)$1	1	46	50	12.0000
....	chr19:20989811-20990041(+)$1	1	8	12	12.0000
....	chr16:50257008-50257233(+)$1	1	89	93	12.0000
))))	chr11:122930362-122930592(-)$1	1	39	43	12.0000
))..	chr5:37026264-37026494(+)$1	1	124	128	12.0000
....	chr2:105959432-105959656(+)$1	1	212	216	12.0000
((((	chr10:88213321-88213551(-)$1	1	141	145	12.0000
..))	chr12:51207980-51208210(+)$1	1	192	196	12.0000
.((.	chr2:215880122-215880353(-)$1	1	27	31	12.0000
.(((	chr22:31330749-31330975(-)$1	1	61	65	12.0000
))))	chr12:80014804-80015029(-)$1	1	58	62	12.0000
))..	chr14:64457135-64457360(+)$1	1	34	38	12.0000
))).	chr9:5763482-5763705(+)$1	1	153	157	12.0000
..((	chr9:26919257-26919482(-)$1	1	63	67	12.0000
((((	chr11:58317377-58317600(-)$1	1	39	43	12.0000
))))	chr6:122774888-122775118(-)$1	1	174	178	12.0000
...)	chr2:158272428-158272652(-)$1	1	122	126	12.0000
((((	chr2:203765649-203765879(-)$1	1	4	8	12.0000
))..	chr14:50295683-50295913(-)$1	1	57	61	12.0000
.(((	chr14:55467209-55467432(-)$1	1	8	12	12.0000
((((	chr11:10874974-10875217(-)$1	1	50	54	12.0000
((((	chr15:45007684-45007933(+)$1	1	49	53	12.0000
(((.	chr7:135078861-135079094(-)$1	1	74	78	12.0000
((..	chr1:112308681-112308911(+)$1	1	3	7	12.0000
))))	chr6:119226754-119226984(+)$1	1	147	151	12.0000
.)))	chr6:18258096-18258320(-)$1	1	77	81	12.0000
((((	chr11:6569505-6569732(+)$1	1	41	45	12.0000
....	chr14:103341946-103342171(+)$1	1	35	39	12.0000
((((	chr8:48842345-48842570(-)$1	1	127	131	12.0000
....	chr3:71015051-71015281(-)$1	1	162	166	12.0000

#PSSM
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m3_run1.nuc.txt

#NT
CUUUUUUU	chr10:98718469-98718690(+)$1	221	45	53	16.0535
auuuuauu	chr17:53469928-53470152(-)$1	224	47	55	16.3214
AUUGUUUU	chr14:91337830-91338060(-)$1	230	148	156	16.3214
AUUUUUUU	chr12:69970847-69971070(+)$1	223	88	96	20.5178
guuuuuuu	chr3:176742325-176742550(-)$1	225	17	25	16.0535
AUUUUUUU	chr13:41132348-41132593(-)$1	245	80	88	20.5178
AUUUUUUU	chr5:112350981-112351211(+)$1	230	61	69	20.5178
AUUUUGUU	chr13:33678598-33678828(-)$1	230	198	206	16.2321
AUUUUUUU	chr16:15689803-15690022(-)$1	219	111	119	20.5178
AUAUUUUU	chr5:137273894-137274124(-)$1	230	149	157	16.7678
AUAUUUUU	chr6:17615258-17615477(-)$1	219	72	80	16.7678
AUUGUUUU	chr2:201775048-201775278(-)$1	230	30	38	16.3214
AUGUUUUU	chr14:97003273-97003492(+)$1	219	24	32	16.6785
AUGUUUUU	chrX:147032334-147032554(+)$1	220	191	199	16.6785
guuuuuuu	chr5:38940077-38940292(-)$1	215	35	43	16.0535
AUUUAUUU	chr14:103377530-103377753(+)$1	223	168	176	16.7678
Auuuuuuu	chr12:69233721-69233951(+)$1	230	212	220	20.5178
AUUUUUUU	chr12:77417181-77417402(-)$1	221	145	153	20.5178
auuuuuuu	chr16:11020246-11020468(+)$1	222	159	167	20.5178
auuguuUU	chr1:160397282-160397501(+)$1	219	95	103	16.3214
AUUUUAUU	chr1:213164412-213164633(+)$1	221	162	170	16.3214
AUGUUUUU	chr12:21670878-21671105(+)$1	227	72	80	16.6785
AUUUUUUU	chr11:67025115-67025340(+)$1	225	76	84	20.5178
AUUUGUUU	chr9:5775318-5775548(+)$1	230	30	38	16.5892
AUUUAUUU	chr6:149980639-149980869(-)$1	230	75	83	16.7678
CUUUUUUU	chr19:2428114-2428344(-)$1	230	97	105	16.0535
AUUUUUUU	chr7:104746306-104746531(+)$1	225	149	157	20.5178
AUUAUUUU	chr8:22879366-22879591(-)$1	225	133	141	16.3214
AUUUUCUU	chr3:150342500-150342730(+)$1	230	86	94	16.1428
AUUUUUUU	chr2:87000607-87000834(+)$1	227	204	212	20.5178
AUUUUGUU	chr3:107528521-107528744(+)$1	223	189	197	16.2321
AUUUUUAU	chr14:95883894-95884112(-)$1	218	180	188	15.7857
AUUUCUUU	chr8:103660926-103661151(-)$1	225	87	95	16.7678
AUUAUUUU	chr4:103183605-103183829(-)$1	224	202	210	16.3214
AUUUCUUU	chr8:81545287-81545508(-)$1	221	177	185	16.7678
AUUUUAUU	chr5:126888179-126888409(+)$1	230	115	123	16.3214
AUUUCUUU	chr4:17627048-17627274(+)$1	226	165	173	16.7678
AUUUUUUU	chr16:69732137-69732360(+)$1	223	61	69	20.5178
AUUUAUUU	chr14:77491271-77491489(-)$1	218	21	29	16.7678
AGUUUUUU	chr7:87464753-87464974(-)$1	221	110	118	15.8750
AUUUCUUU	chr5:76723864-76724091(-)$1	227	211	219	16.7678
AUUUUUCU	chr7:12273673-12273897(+)$1	224	139	147	15.7857
AUUUUUUU	chr4:17882496-17882720(-)$1	224	62	70	20.5178
AUAUUUUU	chr6:111549592-111549817(+)$1	225	189	197	16.7678
AUAUUUUU	chr5:96369378-96369602(+)$1	224	102	110	16.7678
AUUUUUUU	chr2:29023726-29023948(+)$1	222	192	200	20.5178
AUUAUUUU	chr6:32546464-32546705(-)$1	241	213	221	16.3214
AUUUUUUU	chr1:31732442-31732672(-)$1	230	53	61	20.5178
AUGUUUUU	chr7:64865579-64865804(+)$1	225	96	104	16.6785
AUUUUUUU	chr7:131179295-131179525(+)$1	230	48	56	20.5178
AUUUAUUU	chr14:78182074-78182293(+)$1	219	152	160	16.7678
AUUUUUUU	chr10:43881456-43881686(-)$1	230	185	193	20.5178
AUAUUUUU	chr17:27872947-27873168(+)$1	221	116	124	16.7678
AGUUUUUU	chr14:62213835-62214065(+)$1	230	179	187	15.8750
AUUUGUUU	chr15:78790726-78790948(+)$1	222	94	102	16.5892

#otherMatches

#Struct PSSM
JJ::::::	chr17:54942964-54943185(+)$1	221	38	46	20.5178
HHHHHHH{	chr10:98718469-98718690(+)$1	221	45	53	16.0535
eeeqqqqq	chr17:53469928-53470152(-)$1	224	47	55	16.3214
nnnccc33	chr14:91337830-91338060(-)$1	230	148	156	16.3214
qqqbb22e	chr12:69970847-69971070(+)$1	223	88	96	20.5178
c&&&&&&&	chr3:176742325-176742550(-)$1	225	17	25	16.0535
ffff"""e	chr13:41132348-41132593(-)$1	245	80	88	20.5178
::::::::	chr5:112350981-112351211(+)$1	230	61	69	20.5178
hhhhhh##	chr13:33678598-33678828(-)$1	230	198	206	16.2321
::::::::	chr16:15689803-15690022(-)$1	219	111	119	20.5178
d+++++++	chr5:137273894-137274124(-)$1	230	149	157	16.7678
DKKGGGGG	chr6:17615258-17615477(-)$1	219	72	80	16.7678
fffcccgg	chr2:201775048-201775278(-)$1	230	30	38	16.3214
ffffff44	chr14:97003273-97003492(+)$1	219	24	32	16.6785
JJJJJJJ:	chrX:147032334-147032554(+)$1	220	191	199	16.6785
DDLLLGGG	chr5:38940077-38940292(-)$1	215	35	43	16.0535
ff::::::	chr14:103377530-103377753(+)$1	223	168	176	16.7678
99999999	chr12:69233721-69233951(+)$1	230	212	220	20.5178
::::::::	chr12:77417181-77417402(-)$1	221	145	153	20.5178
^^^^^^^^	chr16:11020246-11020468(+)$1	222	159	167	20.5178
ff]eeeee	chr1:160397282-160397501(+)$1	219	95	103	16.3214
::iiiiii	chr1:213164412-213164633(+)$1	221	162	170	16.3214
::::::::	chr12:21670878-21671105(+)$1	227	72	80	16.6785
========	chr11:67025115-67025340(+)$1	225	76	84	20.5178
::======	chr9:5775318-5775548(+)$1	230	30	38	16.5892
g'''''''	chr6:149980639-149980869(-)$1	230	75	83	16.7678
gggggg::	chr19:2428114-2428344(-)$1	230	97	105	16.0535
GGJJJJJJ	chr7:104746306-104746531(+)$1	225	149	157	20.5178
[ccc[eee	chr8:22879366-22879591(-)$1	225	133	141	16.3214
uuuuuuuu	chr3:150342500-150342730(+)$1	230	86	94	16.1428
ennnnnee	chr2:87000607-87000834(+)$1	227	204	212	20.5178
4444eeee	chr3:107528521-107528744(+)$1	223	189	197	16.2321
5555gggg	chr14:95883894-95884112(-)$1	218	180	188	15.7857
::ffffff	chr8:103660926-103661151(-)$1	225	87	95	16.7678
:::::DDD	chr4:103183605-103183829(-)$1	224	202	210	16.3214
%%%bb[dd	chr8:81545287-81545508(-)$1	221	177	185	16.7678
oooggggg	chr5:126888179-126888409(+)$1	230	115	123	16.3214
>>>>>>>>	chr4:17627048-17627274(+)$1	226	165	173	16.7678
dooooood	chr16:69732137-69732360(+)$1	223	61	69	20.5178
cCCC{DDD	chr14:77491271-77491489(-)$1	218	21	29	16.7678
fffff"""	chr7:87464753-87464974(-)$1	221	110	118	15.8750
77777eee	chr5:76723864-76724091(-)$1	227	211	219	16.7678
gggqqqqq	chr7:12273673-12273897(+)$1	224	139	147	15.7857
fnnnnnff	chr4:17882496-17882720(-)$1	224	62	70	20.5178
fffffmmm	chr6:111549592-111549817(+)$1	225	189	197	16.7678
dddd[eee	chr5:96369378-96369602(+)$1	224	102	110	16.7678
D\\\\\\\	chr2:29023726-29023948(+)$1	222	192	200	20.5178
iiiiiicc	chr6:32546464-32546705(-)$1	241	213	221	16.3214
::::::::	chr1:31732442-31732672(-)$1	230	53	61	20.5178
========	chr7:64865579-64865804(+)$1	225	96	104	16.6785
duuuuuuu	chr7:131179295-131179525(+)$1	230	48	56	20.5178
ohhhhhhh	chr14:78182074-78182293(+)$1	219	152	160	16.7678
^^^^^^^^	chr10:43881456-43881686(-)$1	230	185	193	20.5178
^^^^^^^^	chr17:27872947-27873168(+)$1	221	116	124	16.7678
dddd]ddd	chr14:62213835-62214065(+)$1	230	179	187	15.8750
hhhhhhh[	chr15:78790726-78790948(+)$1	222	94	102	16.5892

#DB
((......	chr17:54942964-54943185(+)$1	1	38	46	20.5178
(((((((.	chr10:98718469-98718690(+)$1	1	45	53	16.0535
(((.....	chr17:53469928-53470152(-)$1	1	47	55	16.3214
...)))..	chr14:91337830-91338060(-)$1	1	148	156	16.3214
...))..)	chr12:69970847-69971070(+)$1	1	88	96	20.5178
(.......	chr3:176742325-176742550(-)$1	1	17	25	16.0535
((((...(	chr13:41132348-41132593(-)$1	1	80	88	20.5178
........	chr5:112350981-112351211(+)$1	1	61	69	20.5178
((((((..	chr13:33678598-33678828(-)$1	1	198	206	16.2321
........	chr16:15689803-15690022(-)$1	1	111	119	20.5178
(.......	chr5:137273894-137274124(-)$1	1	149	157	16.7678
(..(((((	chr6:17615258-17615477(-)$1	1	72	80	16.7678
)))(((((	chr2:201775048-201775278(-)$1	1	30	38	16.3214
))))))..	chr14:97003273-97003492(+)$1	1	24	32	16.6785
))))))).	chrX:147032334-147032554(+)$1	1	191	199	16.6785
((...(((	chr5:38940077-38940292(-)$1	1	35	43	16.0535
))......	chr14:103377530-103377753(+)$1	1	168	176	16.7678
........	chr12:69233721-69233951(+)$1	1	212	220	20.5178
........	chr12:77417181-77417402(-)$1	1	145	153	20.5178
........	chr16:11020246-11020468(+)$1	1	159	167	20.5178
)).)))))	chr1:160397282-160397501(+)$1	1	95	103	16.3214
..((((((	chr1:213164412-213164633(+)$1	1	162	170	16.3214
........	chr12:21670878-21671105(+)$1	1	72	80	16.6785
))))))))	chr11:67025115-67025340(+)$1	1	76	84	20.5178
..((((((	chr9:5775318-5775548(+)$1	1	30	38	16.5892
(.......	chr6:149980639-149980869(-)$1	1	75	83	16.7678
))))))..	chr19:2428114-2428344(-)$1	1	97	105	16.0535
))))))))	chr7:104746306-104746531(+)$1	1	149	157	20.5178
.(((.(((	chr8:22879366-22879591(-)$1	1	133	141	16.3214
........	chr3:150342500-150342730(+)$1	1	86	94	16.1428
(.....))	chr2:87000607-87000834(+)$1	1	204	212	20.5178
....))))	chr3:107528521-107528744(+)$1	1	189	197	16.2321
....))))	chr14:95883894-95884112(-)$1	1	180	188	15.7857
..((((((	chr8:103660926-103661151(-)$1	1	87	95	16.7678
.....)))	chr4:103183605-103183829(-)$1	1	202	210	16.3214
...((.((	chr8:81545287-81545508(-)$1	1	177	185	16.7678
...)))))	chr5:126888179-126888409(+)$1	1	115	123	16.3214
........	chr4:17627048-17627274(+)$1	1	165	173	16.7678
(......)	chr16:69732137-69732360(+)$1	1	61	69	20.5178
)(((.(((	chr14:77491271-77491489(-)$1	1	21	29	16.7678
(((((...	chr7:87464753-87464974(-)$1	1	110	118	15.8750
.....)))	chr5:76723864-76724091(-)$1	1	211	219	16.7678
(((.....	chr7:12273673-12273897(+)$1	1	139	147	15.7857
(.....))	chr4:17882496-17882720(-)$1	1	62	70	20.5178
(((((...	chr6:111549592-111549817(+)$1	1	189	197	16.7678
((((.(((	chr5:96369378-96369602(+)$1	1	102	110	16.7678
).......	chr2:29023726-29023948(+)$1	1	192	200	20.5178
((((((((	chr6:32546464-32546705(-)$1	1	213	221	16.3214
........	chr1:31732442-31732672(-)$1	1	53	61	20.5178
((((((((	chr7:64865579-64865804(+)$1	1	96	104	16.6785
(.......	chr7:131179295-131179525(+)$1	1	48	56	20.5178
.)))))))	chr14:78182074-78182293(+)$1	1	152	160	16.7678
........	chr10:43881456-43881686(-)$1	1	185	193	20.5178
........	chr17:27872947-27873168(+)$1	1	116	124	16.7678
)))).)))	chr14:62213835-62214065(+)$1	1	179	187	15.8750
(((((((.	chr15:78790726-78790948(+)$1	1	94	102	16.5892

#PSSM
A : 0.85	a : 0.07	C : 0.03	g : 0.03	
U : 0.83	u : 0.12	G : 0.03	
U : 0.71	u : 0.12	A : 0.08	G : 0.07	
U : 0.78	u : 0.10	A : 0.05	G : 0.03	g : 0.01	
U : 0.69	u : 0.12	A : 0.07	C : 0.07	G : 0.03	
U : 0.78	u : 0.10	G : 0.03	A : 0.03	a : 0.01	C : 0.01	
U : 0.85	u : 0.10	A : 0.01	C : 0.01	
U : 0.89	u : 0.10	

#score	989.7142857142858
#seq	56
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m3_run1.nuc.txt

#NT
CAAAAAAAUAAUAAUAAGUUAGCUCUGAAGGGCAGAGGGAAUACCCAAGCCCCUGAUGCCUAUGAGAAGUCCCUGGACUUCAACCCUCCUGUUGUUUGGCCUUAGCCCAGAGGGAGCUGCUCACCUGAGCACCCUUGGGGGUGGGCAGAGAGGCAGGGUGGGAUUUUAGAGUUAGUGUCUGUGCGGGGGCAGCCCUGAGCCUGGAGUUGAGACUUUGGGGUCUCUUAGUUUGGAGGUGUUGAGUGCAUUUGUGCCCCUGCCUGGUUGAGAGCUUCUUGGUACCUCUUGCCACCCCUUCUCACUGCCCUGACCCAACCCCACUGGACCUUGAUGCUGCGAGGAGUGGUGUCCUGACGGACUCAGCAC	chr22:41830859-41831243(-)$1	384	14	380	495.5000

#otherMatches

#Struct PSSM
444ffffff55555iiiiiiiii::bb!!ddddmmmmdddd22bb:::::JJJJJJJJJJMMMMCCCCCC:::ffffffdddd[bb[eeeee$$$$$ddddmmmmdddd666666eeeeebb]dddd]ffffff:A{DDDDDDDDeeeee[a[eeeeemmmmeeeee]aeeeee:BB{HHHHHHHH{DDDD::::eeeee[dddd[eeeeepppppppeeeeeddddeeeeeffffffddddccclllccc]dddd]ffffff:DDDD}HHHHHHHHBB::::gggggggeeeee!!eeeeeeeeeemmmmeeeee22eeeee22eeeee]ggggggg:DDDD}DDDD}A:::::::ccc[cccoo	chr16:30087290-30087750(+)$1	460	65	431	495.5000
ooohhhhhhhh::::::::JJJJJJJJJJeeeee[ddddtttttttttttdddd22eeeee::::ffffffmmmmffffff::cccggggggg[ccc[dddd[a[ccc[eeeee"""eeeeemmmmeeeeeeeeee]ccc]adddd]ccc]ggggggg]ccc::JJJJJJJJJJCCC{CCC:iiiiiiiiibb[bb[ccceeeee[a[ffffffmmmmffffff22a]eeeee4444ccc]bb]bb55555iiiiiiiii::cccffffff$$$$$eeeeennnnneeeee4444ffffff22ccc:::::::::::eeeee"""eeeeeooooooeeeeeeeeee:ddddmmmmdddd:CCCCCC	chr22:41830859-41831243(-)$1	384	14	380	495.5000

#DB
...)))))).....)))))))))..((..((((....))))..)).....((((((((((....((((((...((((((((((.((.(((((.....((((....))))......))))))).)))).)))))).(.(((((((((((((.(.(((((....))))).)))))).((.((((((((.((((....(((((.((((.(((((.......))))))))))))))(((((((((((((...))).)))).)))))).)))).))))))))))....((((((((((((..((((((((((....)))))..)))))..))))).))))))).)))).)))).).......(((.(((..	chr16:30087290-30087750(+)$1	1	65	431	495.5000
...))))))))........(((((((((((((((.((((...........))))..)))))....((((((....))))))..((((((((((.(((.((((.(.(((.(((((...(((((....)))))))))).))).))))).))).))))))).)))..))))))))))(((.(((.(((((((((((.((.((((((((.(.((((((....))))))..).)))))....))).)).)).....)))))))))..(((((((((.....(((((.....)))))....))))))..)))...........(((((...(((((......)))))))))).((((....)))).))))))	chr22:41830859-41831243(-)$1	1	14	380	495.5000

#PSSM
A : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	U : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
C : 1.00	
C : 1.00	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
C : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
C : 0.50	U : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	C : 0.50	
U : 0.50	C : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
C : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
C : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
C : 0.50	G : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
U : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
G : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
C : 0.50	U : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
C : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
C : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
U : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
G : 0.50	C : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
C : 1.00	
U : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 0.50	G : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	

#score	991.0
#seq	2
#width	366
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m3_run2.nuc.txt

#NT
CUCAUUAAACAUCAAAGAAUACACACAGGUGAAAAACCUUAUGAAUGUAAUGAAUGUGGGAAGUCAUUCUCUGAGAAGUCAACCCUUACUAAACAUCUAAGAACUCACACAGGUGAGAAACCUUAUGAAUGUAUUCAGUGUGGAAAAUUUUUCUGCUACUACUCCGGUUUCACAGAACAUCUGAGAAGACACACAGGGGAGAAACCUUUUGGAUGUAAUGAAUGUGGGAAAACCU	chr10:38407264-38407505(+)$1	241	6	241	532.5000

#otherMatches

#Struct PSSM
eee333ccc55555bb333ggggggg::::::::::::ffffff[ffffff[ccc[eeeee!!cccpppppppccc22eeeeeccc]ffffff22ffffffEEEEELLLFFFFFF{BBKKBBffffff$$$$$dddd[eeeeeuuuuuuuuuuuueeeee4444dddd4444ffffff:::::::::::hhhhhhhh^^^^^^^^^^^^^^^^^^^^^hhhhhhhhBBZZZBBFF	chr19:44980925-44981264(-)$1	339	88	323	532.5000
B{DDDDKKEEEEE:::GGGGGGG:::ddddnnnnndddd::::::::::::eeeeeqqqqqqqqeeeeeccc[ccc[bbvvvvvvvvvvvvvbb]ccc]ccc:eeeeemmmmeeeee::::::::::::GGGGGGGcccggggggglllggggggg]ccc:::::a!!ccc[ddddllldddd]ccc22a:bb[ddddoooooodddd]bbEEEEE~~~~DDDD}BB::::::::	chr10:38407264-38407505(+)$1	241	6	241	532.5000

#DB
)))...))).....))...)))))))............((((((.((((((.(((.(((((..(((.......)))..)))))))).))))))..))))))(((((...((((((.((..((((((((.....((((.(((((............)))))....))))....))))))...........((((((((.....................))))))))))...))))	chr19:44980925-44981264(-)$1	1	88	323	532.5000
(.((((..(((((...(((((((...((((.....))))............(((((........)))))(((.(((.((.............)).))).))).(((((....)))))............)))))))((((((((((...))))))).))).....(..(((.((((...)))).)))..).((.((((......)))).)))))))....)))).))........	chr10:38407264-38407505(+)$1	1	6	241	532.5000

#PSSM
C : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
U : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
U : 1.00	
U : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
G : 0.50	A : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
C : 1.00	
U : 0.50	C : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
C : 1.00	
C : 1.00	
U : 1.00	

#score	1065.0
#seq	2
#width	235
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m1_run2.nuc.txt

#NT
AGCU	chr14:21971816-21972039(+)$1	223	89	93	11.9999
AGCU	chr14:77935383-77935612(+)$1	229	87	91	11.9999
AGCU	chr18:19203649-19203893(+)$1	244	90	94	11.9999
AGCU	chr11:66372897-66373117(+)$1	220	41	45	11.9999
AGCU	chr15:40998302-40998551(-)$1	249	12	16	11.9999
AGCU	chr11:11394003-11394232(-)$1	229	14	18	11.9999
AGCU	chr6:43604032-43604262(+)$1	230	147	151	11.9999
AGCU	chr14:21971351-21971616(+)$1	265	123	127	11.9999
AGCU	chr16:54145650-54145919(+)$1	269	154	158	11.9999
AGCU	chr2:100938421-100938642(+)$1	221	0	4	11.9999
AGCU	chr22:22893289-22893520(-)$1	231	70	74	11.9999
AGCU	chr4:174253128-174253386(-)$1	258	236	240	11.9999
AGCU	chr9:131565432-131565653(+)$1	221	99	103	11.9999
AGCU	chr3:183882576-183882806(+)$1	230	66	70	11.9999
AGCU	chr15:41010944-41011183(+)$1	239	5	9	11.9999
AGCU	chr4:2252835-2253070(-)$1	235	72	76	11.9999
AGCU	chr17:79846989-79847219(-)$1	230	77	81	11.9999
AGCU	chr12:110781022-110781252(+)$1	230	64	68	11.9999
AGCU	chr7:99998646-99998874(+)$1	228	45	49	11.9999
AGCU	chr5:37379495-37379715(+)$1	220	45	49	11.9999
AGCU	chr1:179989406-179989638(+)$1	232	40	44	11.9999
AGCU	chr19:47570473-47570704(-)$1	231	43	47	11.9999
AGCU	chr19:50534226-50534446(+)$1	220	22	26	11.9999
AGCU	chr1:155110377-155110597(-)$1	220	188	192	11.9999
AGCU	chr4:119631278-119631509(-)$1	231	187	191	11.9999
AGCU	chr1:1007839-1008065(+)$1	226	19	23	11.9999
AGCU	chr17:38554768-38554992(-)$1	224	106	110	11.9999
AGCU	chr2:232326151-232326395(-)$1	244	65	69	11.9999
AGCU	chr19:42373010-42373234(+)$1	224	13	17	11.9999
AGCU	chr3:14154363-14154588(-)$1	225	153	157	11.9999
AGCU	chr16:53843950-53844207(+)$1	257	120	124	11.9999
AGCU	chr19:13029956-13030180(-)$1	224	44	48	11.9999
AGCU	chr11:17096907-17097132(-)$1	225	135	139	11.9999
AGCU	chr14:23240160-23240382(+)$1	222	16	20	11.9999
AGCU	chr16:30664153-30664376(+)$1	223	45	49	11.9999
AGCU	chr9:96289357-96289578(+)$1	221	3	7	11.9999
AGCU	chr15:40990896-40991120(+)$1	224	76	80	11.9999
AGCU	chr19:45648706-45648930(+)$1	224	13	17	11.9999
AGCU	chr16:70713600-70713845(-)$1	245	133	137	11.9999
AGCU	chr12:34179668-34179896(+)$1	228	83	87	11.9999
AGCU	chr1:85725193-85725418(-)$1	225	129	133	11.9999
AGCU	chr16:69362891-69363115(-)$1	224	191	195	11.9999
AGCU	chrX:48761886-48762106(-)$1	220	35	39	11.9999
AGCU	chr6:170112404-170112626(-)$1	222	5	9	11.9999
AGCU	chr12:10856624-10856849(-)$1	225	35	39	11.9999
AGCU	chrX:129139083-129139310(+)$1	227	33	37	11.9999
AGCU	chr21:47676701-47676920(-)$1	219	29	33	11.9999
AGCU	chr6:26217280-26217505(+)$1	225	115	119	11.9999
AGCU	chr14:21971870-21972125(+)$1	255	35	39	11.9999
AGCU	chr20:3765449-3765681(-)$1	232	6	10	11.9999
AGCU	chr12:112696849-112697068(-)$1	219	121	125	11.9999
AGCU	chr17:17067875-17068105(+)$1	230	79	83	11.9999
AGCU	chr2:201334554-201334779(+)$1	225	113	117	11.9999
AGCU	chr16:53859836-53860170(+)$1	334	237	241	11.9999
AGCU	chr20:17608061-17608284(-)$1	223	11	15	11.9999
AGCU	chr17:8159477-8159702(+)$1	225	139	143	11.9999
AGCU	chr17:42284588-42284826(-)$1	238	166	170	11.9999
AGCU	chr12:109530294-109530521(-)$1	227	10	14	11.9999
AGCU	chr12:112641390-112641618(-)$1	228	206	210	11.9999
AGCU	chr22:39714957-39715218(-)$1	261	14	18	11.9999
AGCU	chr10:75832457-75832686(+)$1	229	72	76	11.9999
AGCU	chr8:101724891-101725116(-)$1	225	0	4	11.9999
AGCU	chr19:15366079-15366331(-)$1	252	26	30	11.9999
AGCU	chr3:170858103-170858323(+)$1	220	76	80	11.9999
AGCU	chr19:13067641-13067870(-)$1	229	85	89	11.9999
AGCU	chr7:151329101-151329320(-)$1	219	59	63	11.9999
AGCU	chr10:76980463-76980684(+)$1	221	136	140	11.9999
AGCU	chr6:160169228-160169488(+)$1	260	227	231	11.9999
AGCU	chr13:77825325-77825551(-)$1	226	169	173	11.9999
AGCU	chr5:98129055-98129285(+)$1	230	16	20	11.9999
AGCU	chr1:202302313-202302552(-)$1	239	138	142	11.9999
AGCU	chr4:184367370-184367590(-)$1	220	48	52	11.9999
AGCU	chr19:36633512-36633732(+)$1	220	22	26	11.9999

#otherMatches

#Struct PSSM
ffff	chr10:75186286-75186513(-)$1	227	98	102	11.9999
2ccc	chr14:21971816-21972039(+)$1	223	89	93	11.9999
22ac	chr14:77935383-77935612(+)$1	229	87	91	11.9999
ee22	chr18:19203649-19203893(+)$1	244	90	94	11.9999
MCCC	chr11:66372897-66373117(+)$1	220	41	45	11.9999
ffff	chr15:40998302-40998551(-)$1	249	12	16	11.9999
!ddd	chr11:11394003-11394232(-)$1	229	14	18	11.9999
ffdd	chr6:43604032-43604262(+)$1	230	147	151	11.9999
ffff	chr14:21971351-21971616(+)$1	265	123	127	11.9999
hhgg	chr16:54145650-54145919(+)$1	269	154	158	11.9999
:DDD	chr2:100938421-100938642(+)$1	221	0	4	11.9999
DD::	chr22:22893289-22893520(-)$1	231	70	74	11.9999
GGG:	chr4:174253128-174253386(-)$1	258	236	240	11.9999
cc33	chr9:131565432-131565653(+)$1	221	99	103	11.9999
FFFF	chr3:183882576-183882806(+)$1	230	66	70	11.9999
ee[d	chr15:41010944-41011183(+)$1	239	5	9	11.9999
mmmm	chr4:2252835-2253070(-)$1	235	72	76	11.9999
fff:	chr17:79846989-79847219(-)$1	230	77	81	11.9999
gg&&	chr12:110781022-110781252(+)$1	230	64	68	11.9999
eee:	chr7:99998646-99998874(+)$1	228	45	49	11.9999
eee[	chr5:37379495-37379715(+)$1	220	45	49	11.9999
:ddd	chr1:179989406-179989638(+)$1	232	40	44	11.9999
eeee	chr19:47570473-47570704(-)$1	231	43	47	11.9999
ffff	chr19:50534226-50534446(+)$1	220	22	26	11.9999
ZDDD	chr1:155110377-155110597(-)$1	220	188	192	11.9999
ZZBB	chr4:119631278-119631509(-)$1	231	187	191	11.9999
DDKK	chr1:1007839-1008065(+)$1	226	19	23	11.9999
i::e	chr17:38554768-38554992(-)$1	224	106	110	11.9999
3fff	chr2:232326151-232326395(-)$1	244	65	69	11.9999
dd!!	chr19:42373010-42373234(+)$1	224	13	17	11.9999
sccc	chr3:14154363-14154588(-)$1	225	153	157	11.9999
eeee	chr16:53843950-53844207(+)$1	257	120	124	11.9999
!!bb	chr19:13029956-13030180(-)$1	224	44	48	11.9999
ffbb	chr11:17096907-17097132(-)$1	225	135	139	11.9999
EEEE	chr14:23240160-23240382(+)$1	222	16	20	11.9999
cc!!	chr16:30664153-30664376(+)$1	223	45	49	11.9999
::GG	chr9:96289357-96289578(+)$1	221	3	7	11.9999
::::	chr15:40990896-40991120(+)$1	224	76	80	11.9999
mmmm	chr19:45648706-45648930(+)$1	224	13	17	11.9999
mmmm	chr16:70713600-70713845(-)$1	245	133	137	11.9999
Eeee	chr12:34179668-34179896(+)$1	228	83	87	11.9999
]eee	chr1:85725193-85725418(-)$1	225	129	133	11.9999
GGGG	chr16:69362891-69363115(-)$1	224	191	195	11.9999
LA{J	chrX:48761886-48762106(-)$1	220	35	39	11.9999
::::	chr6:170112404-170112626(-)$1	222	5	9	11.9999
E{CC	chr12:10856624-10856849(-)$1	225	35	39	11.9999
ooa]	chrX:129139083-129139310(+)$1	227	33	37	11.9999
{CCC	chr21:47676701-47676920(-)$1	219	29	33	11.9999
:hhh	chr6:26217280-26217505(+)$1	225	115	119	11.9999
dddd	chr14:21971870-21972125(+)$1	255	35	39	11.9999
!!dd	chr20:3765449-3765681(-)$1	232	6	10	11.9999
:bbm	chr12:112696849-112697068(-)$1	219	121	125	11.9999
^^^^	chr17:17067875-17068105(+)$1	230	79	83	11.9999
]ccc	chr2:201334554-201334779(+)$1	225	113	117	11.9999
eee:	chr16:53859836-53860170(+)$1	334	237	241	11.9999
FFFF	chr20:17608061-17608284(-)$1	223	11	15	11.9999
"ddd	chr17:8159477-8159702(+)$1	225	139	143	11.9999
pppp	chr17:42284588-42284826(-)$1	238	166	170	11.9999
GGGG	chr12:109530294-109530521(-)$1	227	10	14	11.9999
:FFF	chr12:112641390-112641618(-)$1	228	206	210	11.9999
:ddd	chr22:39714957-39715218(-)$1	261	14	18	11.9999
eeee	chr10:75832457-75832686(+)$1	229	72	76	11.9999
::::	chr8:101724891-101725116(-)$1	225	0	4	11.9999
mccc	chr19:15366079-15366331(-)$1	252	26	30	11.9999
ggg3	chr3:170858103-170858323(+)$1	220	76	80	11.9999
eeee	chr19:13067641-13067870(-)$1	229	85	89	11.9999
eeec	chr7:151329101-151329320(-)$1	219	59	63	11.9999
:fff	chr10:76980463-76980684(+)$1	221	136	140	11.9999
mmbb	chr6:160169228-160169488(+)$1	260	227	231	11.9999
]aff	chr13:77825325-77825551(-)$1	226	169	173	11.9999
hhhh	chr5:98129055-98129285(+)$1	230	16	20	11.9999
FF:d	chr1:202302313-202302552(-)$1	239	138	142	11.9999
hhhh	chr4:184367370-184367590(-)$1	220	48	52	11.9999
ccnn	chr19:36633512-36633732(+)$1	220	22	26	11.9999

#DB
))))	chr10:75186286-75186513(-)$1	1	98	102	11.9999
.)))	chr14:21971816-21972039(+)$1	1	89	93	11.9999
..))	chr14:77935383-77935612(+)$1	1	87	91	11.9999
))..	chr18:19203649-19203893(+)$1	1	90	94	11.9999
.(((	chr11:66372897-66373117(+)$1	1	41	45	11.9999
((((	chr15:40998302-40998551(-)$1	1	12	16	11.9999
.(((	chr11:11394003-11394232(-)$1	1	14	18	11.9999
))((	chr6:43604032-43604262(+)$1	1	147	151	11.9999
))))	chr14:21971351-21971616(+)$1	1	123	127	11.9999
))((	chr16:54145650-54145919(+)$1	1	154	158	11.9999
.(((	chr2:100938421-100938642(+)$1	1	0	4	11.9999
))..	chr22:22893289-22893520(-)$1	1	70	74	11.9999
))).	chr4:174253128-174253386(-)$1	1	236	240	11.9999
))..	chr9:131565432-131565653(+)$1	1	99	103	11.9999
((((	chr3:183882576-183882806(+)$1	1	66	70	11.9999
((.(	chr15:41010944-41011183(+)$1	1	5	9	11.9999
....	chr4:2252835-2253070(-)$1	1	72	76	11.9999
))).	chr17:79846989-79847219(-)$1	1	77	81	11.9999
((..	chr12:110781022-110781252(+)$1	1	64	68	11.9999
))).	chr7:99998646-99998874(+)$1	1	45	49	11.9999
(((.	chr5:37379495-37379715(+)$1	1	45	49	11.9999
.(((	chr1:179989406-179989638(+)$1	1	40	44	11.9999
((((	chr19:47570473-47570704(-)$1	1	43	47	11.9999
((((	chr19:50534226-50534446(+)$1	1	22	26	11.9999
.)))	chr1:155110377-155110597(-)$1	1	188	192	11.9999
..))	chr4:119631278-119631509(-)$1	1	187	191	11.9999
((..	chr1:1007839-1008065(+)$1	1	19	23	11.9999
)..(	chr17:38554768-38554992(-)$1	1	106	110	11.9999
.)))	chr2:232326151-232326395(-)$1	1	65	69	11.9999
((..	chr19:42373010-42373234(+)$1	1	13	17	11.9999
.)))	chr3:14154363-14154588(-)$1	1	153	157	11.9999
((((	chr16:53843950-53844207(+)$1	1	120	124	11.9999
..((	chr19:13029956-13030180(-)$1	1	44	48	11.9999
))))	chr11:17096907-17097132(-)$1	1	135	139	11.9999
((((	chr14:23240160-23240382(+)$1	1	16	20	11.9999
((..	chr16:30664153-30664376(+)$1	1	45	49	11.9999
..((	chr9:96289357-96289578(+)$1	1	3	7	11.9999
....	chr15:40990896-40991120(+)$1	1	76	80	11.9999
....	chr19:45648706-45648930(+)$1	1	13	17	11.9999
....	chr16:70713600-70713845(-)$1	1	133	137	11.9999
((((	chr12:34179668-34179896(+)$1	1	83	87	11.9999
.)))	chr1:85725193-85725418(-)$1	1	129	133	11.9999
))))	chr16:69362891-69363115(-)$1	1	191	195	11.9999
.(.(	chrX:48761886-48762106(-)$1	1	35	39	11.9999
....	chr6:170112404-170112626(-)$1	1	5	9	11.9999
(.((	chr12:10856624-10856849(-)$1	1	35	39	11.9999
..).	chrX:129139083-129139310(+)$1	1	33	37	11.9999
.(((	chr21:47676701-47676920(-)$1	1	29	33	11.9999
.(((	chr6:26217280-26217505(+)$1	1	115	119	11.9999
((((	chr14:21971870-21972125(+)$1	1	35	39	11.9999
..((	chr20:3765449-3765681(-)$1	1	6	10	11.9999
.((.	chr12:112696849-112697068(-)$1	1	121	125	11.9999
....	chr17:17067875-17068105(+)$1	1	79	83	11.9999
.)))	chr2:201334554-201334779(+)$1	1	113	117	11.9999
))).	chr16:53859836-53860170(+)$1	1	237	241	11.9999
((((	chr20:17608061-17608284(-)$1	1	11	15	11.9999
.(((	chr17:8159477-8159702(+)$1	1	139	143	11.9999
....	chr17:42284588-42284826(-)$1	1	166	170	11.9999
((((	chr12:109530294-109530521(-)$1	1	10	14	11.9999
.)))	chr12:112641390-112641618(-)$1	1	206	210	11.9999
.(((	chr22:39714957-39715218(-)$1	1	14	18	11.9999
((((	chr10:75832457-75832686(+)$1	1	72	76	11.9999
....	chr8:101724891-101725116(-)$1	1	0	4	11.9999
.)))	chr19:15366079-15366331(-)$1	1	26	30	11.9999
))).	chr3:170858103-170858323(+)$1	1	76	80	11.9999
((((	chr19:13067641-13067870(-)$1	1	85	89	11.9999
((((	chr7:151329101-151329320(-)$1	1	59	63	11.9999
.(((	chr10:76980463-76980684(+)$1	1	136	140	11.9999
..))	chr6:160169228-160169488(+)$1	1	227	231	11.9999
.)))	chr13:77825325-77825551(-)$1	1	169	173	11.9999
((((	chr5:98129055-98129285(+)$1	1	16	20	11.9999
)).(	chr1:202302313-202302552(-)$1	1	138	142	11.9999
((((	chr4:184367370-184367590(-)$1	1	48	52	11.9999
((..	chr19:36633512-36633732(+)$1	1	22	26	11.9999

#PSSM
A : 0.99	
G : 0.99	
C : 0.99	
U : 0.99	

#score	887.9999999999995
#seq	74
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m1_run1.nuc.txt

#NT
UCU	chr1:76254774-76254994(+)$1	220	9	12	8.9999
UCU	chr11:61895558-61895777(+)$1	219	43	46	8.9999
UCU	chrX:17744153-17744379(+)$1	226	32	35	8.9999
UCU	chr2:224822216-224822447(+)$1	231	122	125	8.9999
UCU	chr19:39218527-39218764(+)$1	237	10	13	8.9999
UCU	chr16:2569564-2569823(+)$1	259	115	118	8.9999
UCU	chr1:156915812-156916031(-)$1	219	3	6	8.9999
UCU	chr1:153638070-153638301(-)$1	231	49	52	8.9999
UCU	chr12:22199138-22199350(+)$1	212	133	136	8.9999
UCU	chr1:24078268-24078494(+)$1	226	42	45	8.9999
UCU	chr1:171544060-171544278(+)$1	218	11	14	8.9999
UCU	chr20:35219325-35219546(+)$1	221	22	25	8.9999
UCU	chr15:83698794-83699015(-)$1	221	44	47	8.9999
UCU	chr16:30364857-30365089(-)$1	232	62	65	8.9999
ucu	chr11:65830382-65830680(+)$1	298	9	12	8.9999
UCU	chr10:76936186-76936415(+)$1	229	2	5	8.9999
UCU	chr1:184868281-184868503(-)$1	222	0	3	8.9999
UCU	chr14:95569603-95569829(-)$1	226	2	5	8.9999
UCU	chr13:23906055-23906284(-)$1	229	31	34	8.9999
UCU	chr20:17970520-17970731(+)$1	211	13	16	8.9999
UCU	chr4:103498025-103498256(+)$1	231	0	3	8.9999
UCU	chr1:57173158-57173392(+)$1	234	9	12	8.9999
UCU	chr20:50721089-50721313(-)$1	224	17	20	8.9999
UCU	chr14:90778714-90778957(-)$1	243	39	42	8.9999
UCU	chr5:82843752-82843991(+)$1	239	54	57	8.9999
UCU	chr13:50050990-50051206(+)$1	216	3	6	8.9999
UCU	chr1:215777388-215777628(+)$1	240	69	72	8.9999
UCU	chr8:145625530-145625755(-)$1	225	155	158	8.9999
UCU	chr1:12065755-12065990(+)$1	235	0	3	8.9999
UCU	chr20:62195430-62195678(-)$1	248	20	23	8.9999
UCU	chr8:141551241-141551466(-)$1	225	127	130	8.9999
UCU	chr12:56992926-56993159(-)$1	233	96	99	8.9999
UCU	chr19:14066642-14066881(+)$1	239	115	118	8.9999
UCU	chr9:131764073-131764298(+)$1	225	11	14	8.9999
UCU	chr5:56177937-56178165(+)$1	228	6	9	8.9999
UCU	chr10:32576017-32576243(-)$1	226	7	10	8.9999
UCU	chr2:54035411-54035631(+)$1	220	87	90	8.9999
UCU	chr19:806428-806652(+)$1	224	95	98	8.9999
UCU	chr17:20149175-20149401(+)$1	226	2	5	8.9999
UCU	chr19:16963823-16964049(+)$1	226	45	48	8.9999
UCU	chr19:19231809-19232025(-)$1	216	16	19	8.9999
UCU	chr11:63970569-63970800(+)$1	231	142	145	8.9999
UCU	chr11:62362405-62362626(-)$1	221	22	25	8.9999
UCU	chrX:54334304-54334524(-)$1	220	125	128	8.9999
UCU	chrX:47040901-47041122(+)$1	221	36	39	8.9999
UCU	chr21:30701784-30702013(+)$1	229	18	21	8.9999
UCU	chr20:35399184-35399418(-)$1	234	28	31	8.9999
UCU	chr5:140958558-140958801(-)$1	243	11	14	8.9999
UCU	chr17:41345136-41345364(+)$1	228	205	208	8.9999
UCU	chr19:5207941-5208162(-)$1	221	0	3	8.9999
UCU	chr4:87556314-87556564(+)$1	250	4	7	8.9999
UCU	chr19:36213404-36213641(+)$1	237	55	58	8.9999
UCU	chr12:56996418-56996663(-)$1	245	13	16	8.9999
UCU	chr1:19582407-19582633(+)$1	226	71	74	8.9999
UCU	chr1:16200656-16200877(+)$1	221	25	28	8.9999
UCU	chr15:75130957-75131176(-)$1	219	35	38	8.9999
UCU	chr6:28402737-28402955(-)$1	218	10	13	8.9999
UCU	chr1:2235675-2235962(+)$1	287	34	37	8.9999
UCU	chr2:73490280-73490502(-)$1	222	55	58	8.9999
UCU	chr11:46680842-46681064(+)$1	222	16	19	8.9999
UCU	chr22:36886187-36886400(-)$1	213	26	29	8.9999
UCU	chr6:26020633-26020857(+)$1	224	114	117	8.9999
UCU	chr2:235951465-235951684(+)$1	219	208	211	8.9999
UCU	chr7:129832469-129832689(-)$1	220	9	12	8.9999
UCU	chr7:1533402-1533613(-)$1	211	15	18	8.9999
UCU	chr22:21800785-21801003(+)$1	218	8	11	8.9999
UCU	chr10:124915083-124915304(+)$1	221	56	59	8.9999
UCU	chr17:4925287-4925528(+)$1	241	52	55	8.9999
UCU	chr1:24104988-24105211(+)$1	223	177	180	8.9999
UCU	chr15:65758994-65759211(-)$1	217	16	19	8.9999
UCU	chr5:141357964-141358190(+)$1	226	18	21	8.9999
UCU	chr18:47810708-47810950(-)$1	242	5	8	8.9999
UCU	chr17:79681922-79682136(+)$1	214	37	40	8.9999
UCU	chr12:57892270-57892504(+)$1	234	10	13	8.9999
UCU	chr11:57428689-57428917(+)$1	228	143	146	8.9999
UCU	chr9:138395421-138395650(+)$1	229	91	94	8.9999
UCU	chr5:132227886-132228113(-)$1	227	21	24	8.9999
UCU	chr11:77377897-77378115(-)$1	218	131	134	8.9999
UCU	chr6:30856969-30857187(+)$1	218	90	93	8.9999
UCU	chr19:56125680-56125904(+)$1	224	70	73	8.9999
UCU	chr14:59112374-59112599(+)$1	225	76	79	8.9999
UCU	chr2:232653278-232653496(+)$1	218	31	34	8.9999
UCU	chr11:62299317-62299548(-)$1	231	112	115	8.9999
UCU	chr17:78341797-78342007(+)$1	210	13	16	8.9999
UCU	chr19:11303992-11304222(-)$1	230	113	116	8.9999
UCU	chr9:72914933-72915145(+)$1	212	59	62	8.9999
UCU	chr1:16254712-16254939(+)$1	227	153	156	8.9999
UCU	chrX:123200141-123200358(+)$1	217	1	4	8.9999
UCU	chr17:63010602-63010837(-)$1	235	130	133	8.9999
UCU	chr7:129841605-129841833(-)$1	228	3	6	8.9999
UCU	chr10:64952647-64952863(-)$1	216	6	9	8.9999
UCU	chr12:49433871-49434102(-)$1	231	143	146	8.9999
UCU	chr2:27257966-27258198(+)$1	232	85	88	8.9999
UCU	chr21:34926883-34927138(+)$1	255	0	3	8.9999
UCU	chr6:90399724-90399947(-)$1	223	11	14	8.9999
UCU	chr2:39347388-39347609(-)$1	221	15	18	8.9999
UCU	chrX:63412079-63412299(-)$1	220	64	67	8.9999
UCU	chr6:26285291-26285589(-)$1	298	3	6	8.9999

#otherMatches

#Struct PSSM
nnn	chr18:67992521-67992749(+)$1	228	105	108	8.9999
III	chr1:76254774-76254994(+)$1	220	9	12	8.9999
ddd	chr11:61895558-61895777(+)$1	219	43	46	8.9999
:::	chrX:17744153-17744379(+)$1	226	32	35	8.9999
fff	chr2:224822216-224822447(+)$1	231	122	125	8.9999
doo	chr19:39218527-39218764(+)$1	237	10	13	8.9999
!bb	chr16:2569564-2569823(+)$1	259	115	118	8.9999
:::	chr1:156915812-156916031(-)$1	219	3	6	8.9999
ggg	chr1:153638070-153638301(-)$1	231	49	52	8.9999
ffc	chr12:22199138-22199350(+)$1	212	133	136	8.9999
gg3	chr1:24078268-24078494(+)$1	226	42	45	8.9999
HHH	chr1:171544060-171544278(+)$1	218	11	14	8.9999
NNN	chr20:35219325-35219546(+)$1	221	22	25	8.9999
fee	chr15:83698794-83699015(-)$1	221	44	47	8.9999
eee	chr16:30364857-30365089(-)$1	232	62	65	8.9999
===	chr11:65830382-65830680(+)$1	298	9	12	8.9999
dd[	chr10:76936186-76936415(+)$1	229	2	5	8.9999
::E	chr1:184868281-184868503(-)$1	222	0	3	8.9999
::D	chr14:95569603-95569829(-)$1	226	2	5	8.9999
imm	chr13:23906055-23906284(-)$1	229	31	34	8.9999
EEE	chr20:17970520-17970731(+)$1	211	13	16	8.9999
FFF	chr4:103498025-103498256(+)$1	231	0	3	8.9999
eee	chr1:57173158-57173392(+)$1	234	9	12	8.9999
HHH	chr20:50721089-50721313(-)$1	224	17	20	8.9999
fff	chr14:90778714-90778957(-)$1	243	39	42	8.9999
:::	chr5:82843752-82843991(+)$1	239	54	57	8.9999
DBB	chr13:50050990-50051206(+)$1	216	3	6	8.9999
lle	chr1:215777388-215777628(+)$1	240	69	72	8.9999
doo	chr8:145625530-145625755(-)$1	225	155	158	8.9999
HHH	chr1:12065755-12065990(+)$1	235	0	3	8.9999
fmm	chr20:62195430-62195678(-)$1	248	20	23	8.9999
ee:	chr8:141551241-141551466(-)$1	225	127	130	8.9999
SSS	chr12:56992926-56993159(-)$1	233	96	99	8.9999
""e	chr19:14066642-14066881(+)$1	239	115	118	8.9999
BB{	chr9:131764073-131764298(+)$1	225	11	14	8.9999
:::	chr5:56177937-56178165(+)$1	228	6	9	8.9999
ggg	chr10:32576017-32576243(-)$1	226	7	10	8.9999
gll	chr2:54035411-54035631(+)$1	220	87	90	8.9999
eee	chr19:806428-806652(+)$1	224	95	98	8.9999
:::	chr17:20149175-20149401(+)$1	226	2	5	8.9999
::F	chr19:16963823-16964049(+)$1	226	45	48	8.9999
vvv	chr19:19231809-19232025(-)$1	216	16	19	8.9999
hhh	chr11:63970569-63970800(+)$1	231	142	145	8.9999
###	chr11:62362405-62362626(-)$1	221	22	25	8.9999
hhh	chrX:54334304-54334524(-)$1	220	125	128	8.9999
CC{	chrX:47040901-47041122(+)$1	221	36	39	8.9999
DDD	chr21:30701784-30702013(+)$1	229	18	21	8.9999
FF{	chr20:35399184-35399418(-)$1	234	28	31	8.9999
c[f	chr5:140958558-140958801(-)$1	243	11	14	8.9999
ddd	chr17:41345136-41345364(+)$1	228	205	208	8.9999
:::	chr19:5207941-5208162(-)$1	221	0	3	8.9999
fff	chr4:87556314-87556564(+)$1	250	4	7	8.9999
iii	chr19:36213404-36213641(+)$1	237	55	58	8.9999
{DD	chr12:56996418-56996663(-)$1	245	13	16	8.9999
::e	chr1:19582407-19582633(+)$1	226	71	74	8.9999
ncc	chr1:16200656-16200877(+)$1	221	25	28	8.9999
[dd	chr15:75130957-75131176(-)$1	219	35	38	8.9999
LLH	chr6:28402737-28402955(-)$1	218	10	13	8.9999
DDC	chr1:2235675-2235962(+)$1	287	34	37	8.9999
ddd	chr2:73490280-73490502(-)$1	222	55	58	8.9999
+++	chr11:46680842-46681064(+)$1	222	16	19	8.9999
rdd	chr22:36886187-36886400(-)$1	213	26	29	8.9999
cc[	chr6:26020633-26020857(+)$1	224	114	117	8.9999
CCC	chr2:235951465-235951684(+)$1	219	208	211	8.9999
::F	chr7:129832469-129832689(-)$1	220	9	12	8.9999
d[d	chr7:1533402-1533613(-)$1	211	15	18	8.9999
mmm	chr22:21800785-21801003(+)$1	218	8	11	8.9999
eee	chr10:124915083-124915304(+)$1	221	56	59	8.9999
e!!	chr17:4925287-4925528(+)$1	241	52	55	8.9999
qqq	chr1:24104988-24105211(+)$1	223	177	180	8.9999
ccc	chr15:65758994-65759211(-)$1	217	16	19	8.9999
fff	chr5:141357964-141358190(+)$1	226	18	21	8.9999
e[f	chr18:47810708-47810950(-)$1	242	5	8	8.9999
dCC	chr17:79681922-79682136(+)$1	214	37	40	8.9999
ccc	chr12:57892270-57892504(+)$1	234	10	13	8.9999
33b	chr11:57428689-57428917(+)$1	228	143	146	8.9999
888	chr9:138395421-138395650(+)$1	229	91	94	8.9999
ddd	chr5:132227886-132228113(-)$1	227	21	24	8.9999
ddd	chr11:77377897-77378115(-)$1	218	131	134	8.9999
bbo	chr6:30856969-30857187(+)$1	218	90	93	8.9999
::h	chr19:56125680-56125904(+)$1	224	70	73	8.9999
[dd	chr14:59112374-59112599(+)$1	225	76	79	8.9999
HHH	chr2:232653278-232653496(+)$1	218	31	34	8.9999
ccr	chr11:62299317-62299548(-)$1	231	112	115	8.9999
ppp	chr17:78341797-78342007(+)$1	210	13	16	8.9999
c""	chr19:11303992-11304222(-)$1	230	113	116	8.9999
bbm	chr9:72914933-72915145(+)$1	212	59	62	8.9999
EEE	chr1:16254712-16254939(+)$1	227	153	156	8.9999
:::	chrX:123200141-123200358(+)$1	217	1	4	8.9999
f##	chr17:63010602-63010837(-)$1	235	130	133	8.9999
GGG	chr7:129841605-129841833(-)$1	228	3	6	8.9999
lld	chr10:64952647-64952863(-)$1	216	6	9	8.9999
fff	chr12:49433871-49434102(-)$1	231	143	146	8.9999
:::	chr2:27257966-27258198(+)$1	232	85	88	8.9999
::I	chr21:34926883-34927138(+)$1	255	0	3	8.9999
:::	chr6:90399724-90399947(-)$1	223	11	14	8.9999
GGG	chr2:39347388-39347609(-)$1	221	15	18	8.9999
HHH	chrX:63412079-63412299(-)$1	220	64	67	8.9999
EEE	chr6:26285291-26285589(-)$1	298	3	6	8.9999

#DB
...	chr18:67992521-67992749(+)$1	1	105	108	8.9999
(((	chr1:76254774-76254994(+)$1	1	9	12	8.9999
(((	chr11:61895558-61895777(+)$1	1	43	46	8.9999
...	chrX:17744153-17744379(+)$1	1	32	35	8.9999
)))	chr2:224822216-224822447(+)$1	1	122	125	8.9999
(..	chr19:39218527-39218764(+)$1	1	10	13	8.9999
.((	chr16:2569564-2569823(+)$1	1	115	118	8.9999
...	chr1:156915812-156916031(-)$1	1	3	6	8.9999
)))	chr1:153638070-153638301(-)$1	1	49	52	8.9999
)))	chr12:22199138-22199350(+)$1	1	133	136	8.9999
)).	chr1:24078268-24078494(+)$1	1	42	45	8.9999
(((	chr1:171544060-171544278(+)$1	1	11	14	8.9999
...	chr20:35219325-35219546(+)$1	1	22	25	8.9999
(((	chr15:83698794-83699015(-)$1	1	44	47	8.9999
(((	chr16:30364857-30365089(-)$1	1	62	65	8.9999
(((	chr11:65830382-65830680(+)$1	1	9	12	8.9999
((.	chr10:76936186-76936415(+)$1	1	2	5	8.9999
..(	chr1:184868281-184868503(-)$1	1	0	3	8.9999
..(	chr14:95569603-95569829(-)$1	1	2	5	8.9999
(..	chr13:23906055-23906284(-)$1	1	31	34	8.9999
(((	chr20:17970520-17970731(+)$1	1	13	16	8.9999
(((	chr4:103498025-103498256(+)$1	1	0	3	8.9999
(((	chr1:57173158-57173392(+)$1	1	9	12	8.9999
(((	chr20:50721089-50721313(-)$1	1	17	20	8.9999
(((	chr14:90778714-90778957(-)$1	1	39	42	8.9999
...	chr5:82843752-82843991(+)$1	1	54	57	8.9999
(((	chr13:50050990-50051206(+)$1	1	3	6	8.9999
..)	chr1:215777388-215777628(+)$1	1	69	72	8.9999
(..	chr8:145625530-145625755(-)$1	1	155	158	8.9999
(((	chr1:12065755-12065990(+)$1	1	0	3	8.9999
(..	chr20:62195430-62195678(-)$1	1	20	23	8.9999
)).	chr8:141551241-141551466(-)$1	1	127	130	8.9999
...	chr12:56992926-56993159(-)$1	1	96	99	8.9999
..(	chr19:14066642-14066881(+)$1	1	115	118	8.9999
((.	chr9:131764073-131764298(+)$1	1	11	14	8.9999
...	chr5:56177937-56178165(+)$1	1	6	9	8.9999
(((	chr10:32576017-32576243(-)$1	1	7	10	8.9999
(..	chr2:54035411-54035631(+)$1	1	87	90	8.9999
)))	chr19:806428-806652(+)$1	1	95	98	8.9999
...	chr17:20149175-20149401(+)$1	1	2	5	8.9999
..(	chr19:16963823-16964049(+)$1	1	45	48	8.9999
...	chr19:19231809-19232025(-)$1	1	16	19	8.9999
(((	chr11:63970569-63970800(+)$1	1	142	145	8.9999
...	chr11:62362405-62362626(-)$1	1	22	25	8.9999
)))	chrX:54334304-54334524(-)$1	1	125	128	8.9999
((.	chrX:47040901-47041122(+)$1	1	36	39	8.9999
(((	chr21:30701784-30702013(+)$1	1	18	21	8.9999
((.	chr20:35399184-35399418(-)$1	1	28	31	8.9999
(.(	chr5:140958558-140958801(-)$1	1	11	14	8.9999
)))	chr17:41345136-41345364(+)$1	1	205	208	8.9999
...	chr19:5207941-5208162(-)$1	1	0	3	8.9999
(((	chr4:87556314-87556564(+)$1	1	4	7	8.9999
)))	chr19:36213404-36213641(+)$1	1	55	58	8.9999
.((	chr12:56996418-56996663(-)$1	1	13	16	8.9999
..(	chr1:19582407-19582633(+)$1	1	71	74	8.9999
.))	chr1:16200656-16200877(+)$1	1	25	28	8.9999
.((	chr15:75130957-75131176(-)$1	1	35	38	8.9999
..(	chr6:28402737-28402955(-)$1	1	10	13	8.9999
(((	chr1:2235675-2235962(+)$1	1	34	37	8.9999
(((	chr2:73490280-73490502(-)$1	1	55	58	8.9999
...	chr11:46680842-46681064(+)$1	1	16	19	8.9999
.))	chr22:36886187-36886400(-)$1	1	26	29	8.9999
((.	chr6:26020633-26020857(+)$1	1	114	117	8.9999
)))	chr2:235951465-235951684(+)$1	1	208	211	8.9999
..(	chr7:129832469-129832689(-)$1	1	9	12	8.9999
(.(	chr7:1533402-1533613(-)$1	1	15	18	8.9999
...	chr22:21800785-21801003(+)$1	1	8	11	8.9999
)))	chr10:124915083-124915304(+)$1	1	56	59	8.9999
(..	chr17:4925287-4925528(+)$1	1	52	55	8.9999
...	chr1:24104988-24105211(+)$1	1	177	180	8.9999
)))	chr15:65758994-65759211(-)$1	1	16	19	8.9999
(((	chr5:141357964-141358190(+)$1	1	18	21	8.9999
(.(	chr18:47810708-47810950(-)$1	1	5	8	8.9999
)((	chr17:79681922-79682136(+)$1	1	37	40	8.9999
(((	chr12:57892270-57892504(+)$1	1	10	13	8.9999
..)	chr11:57428689-57428917(+)$1	1	143	146	8.9999
...	chr9:138395421-138395650(+)$1	1	91	94	8.9999
(((	chr5:132227886-132228113(-)$1	1	21	24	8.9999
(((	chr11:77377897-77378115(-)$1	1	131	134	8.9999
((.	chr6:30856969-30857187(+)$1	1	90	93	8.9999
..(	chr19:56125680-56125904(+)$1	1	70	73	8.9999
.((	chr14:59112374-59112599(+)$1	1	76	79	8.9999
(((	chr2:232653278-232653496(+)$1	1	31	34	8.9999
((.	chr11:62299317-62299548(-)$1	1	112	115	8.9999
...	chr17:78341797-78342007(+)$1	1	13	16	8.9999
(..	chr19:11303992-11304222(-)$1	1	113	116	8.9999
((.	chr9:72914933-72915145(+)$1	1	59	62	8.9999
)))	chr1:16254712-16254939(+)$1	1	153	156	8.9999
...	chrX:123200141-123200358(+)$1	1	1	4	8.9999
(..	chr17:63010602-63010837(-)$1	1	130	133	8.9999
(((	chr7:129841605-129841833(-)$1	1	3	6	8.9999
..)	chr10:64952647-64952863(-)$1	1	6	9	8.9999
(((	chr12:49433871-49434102(-)$1	1	143	146	8.9999
...	chr2:27257966-27258198(+)$1	1	85	88	8.9999
..(	chr21:34926883-34927138(+)$1	1	0	3	8.9999
...	chr6:90399724-90399947(-)$1	1	11	14	8.9999
(((	chr2:39347388-39347609(-)$1	1	15	18	8.9999
(((	chrX:63412079-63412299(-)$1	1	64	67	8.9999
(((	chr6:26285291-26285589(-)$1	1	3	6	8.9999

#PSSM
U : 0.98	u : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m1_run2.nuc.txt

#NT
UUUUUUUUU	chr1:210186937-210187160(+)$1	223	25	34	18.2931
UUUCUUUUC	chr14:51098938-51099159(-)$1	221	111	120	17.0000
uuuauuuuu	chr1:193094183-193094409(+)$1	226	204	213	21.3103
UUUAUUUCU	chr19:38055999-38056234(-)$1	235	102	111	17.0862
UUUAUUUUU	chr5:118844701-118844936(+)$1	235	106	115	21.3103
UUUGUUUUU	chr12:88542119-88542354(+)$1	235	54	63	17.9482
UUUAUUUUA	chr11:108153444-108153679(+)$1	235	121	130	19.0689
UCUAUUUUU	chr4:185550324-185550545(-)$1	221	103	112	16.6551
CUUAUUUUU	chr1:165621126-165621347(+)$1	221	109	118	16.8275
uuuauuuua	chr2:175664732-175664957(-)$1	225	104	113	19.0689
UUUGUUUUC	chr2:44566374-44566594(-)$1	220	96	105	16.3965
UUUAUUUUG	chr14:36339430-36339666(+)$1	236	47	56	18.7241
UUUAUGUUU	chr1:220275801-220276018(+)$1	217	8	17	16.5689
UUUAUUUUA	chr5:145863060-145863281(+)$1	221	30	39	19.0689
UUUAUUUCU	chr14:31107253-31107479(+)$1	226	116	125	17.0862
UUUAUUUUU	chr2:120734438-120734659(+)$1	221	109	118	21.3103
UUUUUUUUA	chr11:61133406-61133624(+)$1	218	92	101	16.0517
UUUAUUUAU	chr13:96579240-96579460(-)$1	220	43	52	17.0862
UUUAAUUUA	chr16:67174366-67174592(+)$1	226	18	27	14.6724
UUUCUUUUC	chr11:121177017-121177242(+)$1	225	65	74	17.0000
UUUAUUUUU	chr2:32530539-32530778(+)$1	239	124	133	21.3103
UUUUUUUUU	chr22:19954815-19955036(+)$1	221	101	110	18.2931
UUUAUUUUC	chr7:63981671-63981906(-)$1	235	106	115	19.7586
UUUAUUUUG	chr2:198256919-198257140(-)$1	221	122	131	18.7241
UUUUUUUUA	chr5:37226671-37226891(-)$1	220	6	15	16.0517
UUUCUUUUC	chr10:98303777-98303997(-)$1	220	23	32	17.0000
UUUCUUUUC	chr12:76446897-76447117(-)$1	220	206	215	17.0000
UGUAUUUUC	chr4:83368974-83369194(+)$1	220	71	80	15.1896
uuuacuuuu	chr10:101473102-101473329(-)$1	227	111	120	16.7413
UUUCUUUUU	chr3:196666125-196666346(-)$1	221	104	113	18.5517
UUUAUUCUU	chr16:11940577-11940800(-)$1	223	76	85	16.8275
UUUAUUUCU	chr1:115272793-115273028(-)$1	235	186	195	17.0862
UUUCUUUUU	chr7:135612282-135612493(-)$1	211	82	91	18.5517
UUUAUUUUU	chr2:196544712-196544931(+)$1	219	102	111	21.3103
UUUAUUUAU	chr4:85730962-85731185(-)$1	223	105	114	17.0862
uuuauuuuu	chr5:72351769-72351991(+)$1	222	201	210	21.3103
UUUAAUUUU	chrX:14883192-14883415(-)$1	223	202	211	16.9137
UUUAUUUUC	chr12:102313841-102314071(+)$1	230	99	108	19.7586
UUUUUUUUA	chr8:71550711-71550933(-)$1	222	21	30	16.0517
UUUCUUUUG	chr8:38184206-38184428(-)$1	222	32	41	15.9655
CUUAUUUUU	chr5:68398835-68399053(+)$1	218	183	192	16.8275
UUUAUUCUU	chr10:95266663-95266890(+)$1	227	195	204	16.8275
UUUCUUUUU	chr5:70860608-70860846(+)$1	238	120	129	18.5517
UUUAUAUUC	chr5:37351284-37351507(-)$1	223	104	113	15.0172
UUUAUUUUU	chr15:42858861-42859085(+)$1	224	161	170	21.3103
UUUAAUUUU	chr4:48036800-48037025(+)$1	225	74	83	16.9137
UUUCUUUUU	chr5:34918334-34918569(+)$1	235	119	128	18.5517
UUUAUUGUU	chr5:138208829-138209050(-)$1	221	87	96	16.7413
UUGAUUUUU	chr15:26792866-26793096(-)$1	230	167	176	16.4827
UUUAUUUAU	chr12:77235668-77235894(+)$1	226	103	112	17.0862
AUUAUUUUU	chr14:95590483-95590715(-)$1	232	139	148	16.8275
AUUAUUUUC	chr6:74201963-74202193(-)$1	230	106	115	15.2758
UUUAUUUUC	chr1:247264178-247264398(-)$1	220	103	112	19.7586
UGUAUUUUC	chr5:134235172-134235407(+)$1	235	97	106	15.1896
UUUAUUUUC	chr22:31851098-31851326(+)$1	228	117	126	19.7586
UUUUUUUUC	chr12:75893495-75893720(+)$1	225	97	106	16.7413
UUUAUUUUC	chr3:125725175-125725394(-)$1	219	104	113	19.7586

#otherMatches

#Struct PSSM
ooooodddd	chr5:134231990-134232210(+)$1	220	32	41	16.7413
IIIIIIIII	chr1:210186937-210187160(+)$1	223	25	34	18.2931
b]bb55555	chr14:51098938-51099159(-)$1	221	111	120	17.0000
:::::eeee	chr1:193094183-193094409(+)$1	226	204	213	21.3103
qqqqfffff	chr19:38055999-38056234(-)$1	235	102	111	17.0862
:::::::::	chr5:118844701-118844936(+)$1	235	106	115	21.3103
22eeeee::	chr12:88542119-88542354(+)$1	235	54	63	17.9482
e[eeeeevv	chr11:108153444-108153679(+)$1	235	121	130	19.0689
!eeeee"""	chr4:185550324-185550545(-)$1	221	103	112	16.6551
:::::::::	chr1:165621126-165621347(+)$1	221	109	118	16.8275
===[dddd"	chr2:175664732-175664957(-)$1	225	104	113	19.0689
======>>>	chr2:44566374-44566594(-)$1	220	96	105	16.3965
=========	chr14:36339430-36339666(+)$1	236	47	56	18.7241
KKFFFFFF:	chr1:220275801-220276018(+)$1	217	8	17	16.5689
cpppppppc	chr5:145863060-145863281(+)$1	221	30	39	19.0689
:hhhhhhhh	chr14:31107253-31107479(+)$1	226	116	125	17.0862
%%%%%iiii	chr2:120734438-120734659(+)$1	221	109	118	21.3103
wwwwwwwww	chr11:61133406-61133624(+)$1	218	92	101	16.0517
nnnffffff	chr13:96579240-96579460(-)$1	220	43	52	17.0862
iii[dddd[	chr16:67174366-67174592(+)$1	226	18	27	14.6724
dd]ffffff	chr11:121177017-121177242(+)$1	225	65	74	17.0000
c[ccc!!dd	chr2:32530539-32530778(+)$1	239	124	133	21.3103
:::::::::	chr22:19954815-19955036(+)$1	221	101	110	18.2931
iiiii^^^^	chr7:63981671-63981906(-)$1	235	106	115	19.7586
fffff:fff	chr2:198256919-198257140(-)$1	221	122	131	18.7241
::::GGGGG	chr5:37226671-37226891(-)$1	220	6	15	16.0517
=====mmmm	chr10:98303777-98303997(-)$1	220	23	32	17.0000
ZIIIIIIII	chr12:76446897-76447117(-)$1	220	206	215	17.0000
(cccqqqqq	chr4:83368974-83369194(+)$1	220	71	80	15.1896
!eeeeerrr	chr10:101473102-101473329(-)$1	227	111	120	16.7413
EEEKKEEEE	chr3:196666125-196666346(-)$1	221	104	113	18.5517
%%cccqqqq	chr16:11940577-11940800(-)$1	223	76	85	16.8275
5555hhhhh	chr1:115272793-115273028(-)$1	235	186	195	17.0862
+++++++++	chr7:135612282-135612493(-)$1	211	82	91	18.5517
DDDD{DDDD	chr2:196544712-196544931(+)$1	219	102	111	21.3103
vvvvvvvvv	chr4:85730962-85731185(-)$1	223	105	114	17.0862
FFFFFZZZB	chr5:72351769-72351991(+)$1	222	201	210	21.3103
f::::::::	chrX:14883192-14883415(-)$1	223	202	211	16.9137
:::::::::	chr12:102313841-102314071(+)$1	230	99	108	19.7586
=======mm	chr8:71550711-71550933(-)$1	222	21	30	16.0517
iiiiiiiii	chr8:38184206-38184428(-)$1	222	32	41	15.9655
hhhhhhooo	chr5:68398835-68399053(+)$1	218	183	192	16.8275
FFEEEEECC	chr10:95266663-95266890(+)$1	227	195	204	16.8275
dddd:::::	chr5:70860608-70860846(+)$1	238	120	129	18.5517
:::::::::	chr5:37351284-37351507(-)$1	223	104	113	15.0172
gggg:::::	chr15:42858861-42859085(+)$1	224	161	170	21.3103
7777ggggg	chr4:48036800-48037025(+)$1	225	74	83	16.9137
=======oo	chr5:34918334-34918569(+)$1	235	119	128	18.5517
mm=======	chr5:138208829-138209050(-)$1	221	87	96	16.7413
ddddmmmmd	chr15:26792866-26793096(-)$1	230	167	176	16.4827
:::::::::	chr12:77235668-77235894(+)$1	226	103	112	17.0862
hhhh]gggg	chr14:95590483-95590715(-)$1	232	139	148	16.8275
:::::::::	chr6:74201963-74202193(-)$1	230	106	115	15.2758
pppphhhhh	chr1:247264178-247264398(-)$1	220	103	112	19.7586
f[ccc[eee	chr5:134235172-134235407(+)$1	235	97	106	15.1896
ppffffff:	chr22:31851098-31851326(+)$1	228	117	126	19.7586
::::FFFFF	chr12:75893495-75893720(+)$1	225	97	106	16.7413
I::::::::	chr3:125725175-125725394(-)$1	219	104	113	19.7586

#DB
.....))))	chr5:134231990-134232210(+)$1	1	32	41	16.7413
(((((((((	chr1:210186937-210187160(+)$1	1	25	34	18.2931
).)).....	chr14:51098938-51099159(-)$1	1	111	120	17.0000
.....((((	chr1:193094183-193094409(+)$1	1	204	213	21.3103
....)))))	chr19:38055999-38056234(-)$1	1	102	111	17.0862
.........	chr5:118844701-118844936(+)$1	1	106	115	21.3103
..)))))..	chr12:88542119-88542354(+)$1	1	54	63	17.9482
(.(((((..	chr11:108153444-108153679(+)$1	1	121	130	19.0689
.(((((...	chr4:185550324-185550545(-)$1	1	103	112	16.6551
.........	chr1:165621126-165621347(+)$1	1	109	118	16.8275
(((.((((.	chr2:175664732-175664957(-)$1	1	104	113	19.0689
))))))...	chr2:44566374-44566594(-)$1	1	96	105	16.3965
(((((((((	chr14:36339430-36339666(+)$1	1	47	56	18.7241
..((((((.	chr1:220275801-220276018(+)$1	1	8	17	16.5689
(.......)	chr5:145863060-145863281(+)$1	1	30	39	19.0689
.((((((((	chr14:31107253-31107479(+)$1	1	116	125	17.0862
.....((((	chr2:120734438-120734659(+)$1	1	109	118	21.3103
.........	chr11:61133406-61133624(+)$1	1	92	101	16.0517
...))))))	chr13:96579240-96579460(-)$1	1	43	52	17.0862
(((.((((.	chr16:67174366-67174592(+)$1	1	18	27	14.6724
)).))))))	chr11:121177017-121177242(+)$1	1	65	74	17.0000
(.(((..((	chr2:32530539-32530778(+)$1	1	124	133	21.3103
.........	chr22:19954815-19955036(+)$1	1	101	110	18.2931
(((((....	chr7:63981671-63981906(-)$1	1	106	115	19.7586
))))).(((	chr2:198256919-198257140(-)$1	1	122	131	18.7241
....(((((	chr5:37226671-37226891(-)$1	1	6	15	16.0517
(((((....	chr10:98303777-98303997(-)$1	1	23	32	17.0000
.))))))))	chr12:76446897-76447117(-)$1	1	206	215	17.0000
.(((.....	chr4:83368974-83369194(+)$1	1	71	80	15.1896
.(((((...	chr10:101473102-101473329(-)$1	1	111	120	16.7413
(((..((((	chr3:196666125-196666346(-)$1	1	104	113	18.5517
..(((....	chr16:11940577-11940800(-)$1	1	76	85	16.8275
....)))))	chr1:115272793-115273028(-)$1	1	186	195	17.0862
.........	chr7:135612282-135612493(-)$1	1	82	91	18.5517
((((.((((	chr2:196544712-196544931(+)$1	1	102	111	21.3103
.........	chr4:85730962-85731185(-)$1	1	105	114	17.0862
)))))...)	chr5:72351769-72351991(+)$1	1	201	210	21.3103
)........	chrX:14883192-14883415(-)$1	1	202	211	16.9137
.........	chr12:102313841-102314071(+)$1	1	99	108	19.7586
(((((((..	chr8:71550711-71550933(-)$1	1	21	30	16.0517
(((((((((	chr8:38184206-38184428(-)$1	1	32	41	15.9655
((((((...	chr5:68398835-68399053(+)$1	1	183	192	16.8275
)))))))))	chr10:95266663-95266890(+)$1	1	195	204	16.8275
)))).....	chr5:70860608-70860846(+)$1	1	120	129	18.5517
.........	chr5:37351284-37351507(-)$1	1	104	113	15.0172
)))).....	chr15:42858861-42859085(+)$1	1	161	170	21.3103
....)))))	chr4:48036800-48037025(+)$1	1	74	83	16.9137
(((((((..	chr5:34918334-34918569(+)$1	1	119	128	18.5517
..)))))))	chr5:138208829-138209050(-)$1	1	87	96	16.7413
((((....)	chr15:26792866-26793096(-)$1	1	167	176	16.4827
.........	chr12:77235668-77235894(+)$1	1	103	112	17.0862
)))).))))	chr14:95590483-95590715(-)$1	1	139	148	16.8275
.........	chr6:74201963-74202193(-)$1	1	106	115	15.2758
....)))))	chr1:247264178-247264398(-)$1	1	103	112	19.7586
(.(((.(((	chr5:134235172-134235407(+)$1	1	97	106	15.1896
..)))))).	chr22:31851098-31851326(+)$1	1	117	126	19.7586
....)))))	chr12:75893495-75893720(+)$1	1	97	106	16.7413
(........	chr3:125725175-125725394(-)$1	1	104	113	19.7586

#PSSM
U : 0.86	u : 0.06	C : 0.03	A : 0.03	
U : 0.87	u : 0.06	G : 0.03	C : 0.01	
U : 0.91	u : 0.06	G : 0.01	
A : 0.63	C : 0.15	U : 0.10	a : 0.06	G : 0.03	
U : 0.87	u : 0.05	A : 0.05	c : 0.01	
U : 0.89	u : 0.06	G : 0.01	A : 0.01	
U : 0.86	u : 0.06	C : 0.03	A : 0.01	G : 0.01	
U : 0.82	u : 0.06	C : 0.05	A : 0.05	
U : 0.51	C : 0.25	A : 0.10	u : 0.05	G : 0.05	a : 0.01	

#score	1032.3793103448281
#seq	58
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m3_run1.nuc.txt

#NT
GAAGGUG	chr19:10260459-10260686(-)$1	227	68	75	13.4590
GGAGGUG	chr19:48630438-48630662(-)$1	224	56	63	17.1475
GGAGGUG	chr10:119134147-119134364(-)$1	217	207	214	17.1475
GGAGGUG	chr1:19432966-19433197(-)$1	231	49	56	17.1475
ggaggug	chr16:31195537-31195760(+)$1	223	158	165	17.1475
GGAGGUU	chr6:111196206-111196430(+)$1	224	143	150	12.7213
GGAGAUG	chr1:162467696-162467920(+)$1	224	16	23	13.0491
GGAGCUG	chr9:5742843-5743074(+)$1	231	42	49	13.4590
GGAGGUA	chr1:19426786-19427007(-)$1	221	134	141	12.7213
GGAGGUU	chr16:30998184-30998420(+)$1	236	81	88	12.7213
GGAGGAG	chr21:45139130-45139359(+)$1	229	47	54	13.3770
GGUGGUG	chr9:110249867-110250094(-)$1	227	199	206	12.6393
GGGGGUG	chr16:5122895-5123118(+)$1	223	183	190	12.5573
GUAGGUG	chr19:3981247-3981496(-)$1	249	42	49	13.1311
GCAGGUG	chr12:51102217-51102442(+)$1	225	124	131	13.1311
GAAGGUG	chr14:103357621-103357846(+)$1	225	129	136	13.4590
GGAGGUG	chr19:3983121-3983358(-)$1	237	189	196	17.1475
GGAGGUA	chr9:134311906-134312140(+)$1	234	199	206	12.7213
GAAGGUG	chr1:149949263-149949488(-)$1	225	124	131	13.4590
GGAGGUG	chr2:9658209-9658430(-)$1	221	180	187	17.1475
GGAGCUG	chr3:64007988-64008209(-)$1	221	122	129	13.4590
GGAGGUG	chr16:31201266-31201489(+)$1	223	192	199	17.1475
GGUGGUG	chr17:40367945-40368172(-)$1	227	65	72	12.6393
GGAGCUG	chr15:72502648-72502875(-)$1	227	2	9	13.4590
GGACGUG	chr21:34926704-34926955(+)$1	251	116	123	12.8032
GGAGAUG	chr19:39879313-39879550(-)$1	237	122	129	13.0491
GGAGGUG	chr22:42987922-42988158(-)$1	236	127	134	17.1475
GGAGCUG	chr7:128843299-128843530(+)$1	231	10	17	13.4590
GGAGGAG	chr19:2272996-2273223(+)$1	227	98	105	13.3770
GGAGGUG	chr8:144658565-144658791(-)$1	226	206	213	17.1475
UGAGGUG	chr17:44248134-44248375(-)$1	241	37	44	12.8852
AGAGGUG	chr5:140022070-140022295(+)$1	225	216	223	12.8032
CGAGGUG	chr19:6416414-6416652(-)$1	238	148	155	12.7213
GGAGGAG	chr1:150938626-150938857(-)$1	231	143	150	13.3770
GGAGGAG	chr3:56716688-56716918(-)$1	230	173	180	13.3770
GGAGGUG	chr17:36868028-36868268(+)$1	240	119	126	17.1475
GGCGGUG	chr7:26235944-26236176(-)$1	232	104	111	12.5573
AGAGGUG	chr12:58144912-58145140(-)$1	228	174	181	12.8032
GGAGCUG	chr12:49424330-49424556(-)$1	226	4	11	13.4590
UGAGGUG	chr12:53681988-53682210(+)$1	222	152	159	12.8852
GAAGGUG	chr20:62373459-62373688(+)$1	229	67	74	13.4590
GGAGGAG	chr19:19638418-19638659(+)$1	241	118	125	13.3770
GGACGUG	chr14:53417162-53417391(-)$1	229	151	158	12.8032
GUAGGUG	chr3:69126937-69127158(-)$1	221	31	38	13.1311
GAAGGUG	chr20:21327008-21327235(+)$1	227	0	7	13.4590
GGAGCUG	chr7:44605482-44605709(-)$1	227	126	133	13.4590
GGAAGUG	chr1:212208598-212208838(-)$1	240	195	202	12.7213
GGAGGAG	chr1:204379521-204379765(-)$1	244	200	207	13.3770
GGAGGUG	chr16:30775515-30775738(+)$1	223	66	73	17.1475
GGAGCUG	chrX:53222638-53222867(-)$1	229	53	60	13.4590
GGAGGGG	chr1:109756600-109756834(+)$1	234	50	57	12.8852
GGAGGUG	chr15:41961562-41961783(+)$1	221	168	175	17.1475
GGACGUG	chr8:106814726-106814957(+)$1	231	61	68	12.8032
ggaggag	chr5:149212940-149213162(+)$1	222	6	13	13.3770
GGAGGUC	chr1:155903450-155903672(-)$1	222	101	108	12.6393
GAAGGUG	chr16:30721261-30721505(+)$1	244	152	159	13.4590
GCAGGUG	chr1:151206718-151206946(+)$1	228	14	21	13.1311
UGAGGUG	chr5:71493077-71493306(+)$1	229	1	8	12.8852
GGAGGUG	chr20:21336629-21336855(+)$1	226	105	112	17.1475
GGAGGUG	chr1:117639921-117640144(+)$1	223	75	82	17.1475

#otherMatches

#Struct PSSM
ddd22gg	chr8:61655054-61655277(+)$1	223	182	189	12.7213
IIIIIII	chr19:10260459-10260686(-)$1	227	68	75	13.4590
GGGGGDD	chr19:48630438-48630662(-)$1	224	56	63	17.1475
DDDCCC:	chr10:119134147-119134364(-)$1	217	207	214	17.1475
BB{JJJJ	chr1:19432966-19433197(-)$1	231	49	56	17.1475
hhhhhhh	chr16:31195537-31195760(+)$1	223	158	165	17.1475
hhcccoo	chr6:111196206-111196430(+)$1	224	143	150	12.7213
ddqqqqq	chr1:162467696-162467920(+)$1	224	16	23	13.0491
ffffeee	chr9:5742843-5743074(+)$1	231	42	49	13.4590
dddccc"	chr1:19426786-19427007(-)$1	221	134	141	12.7213
""bbbb[	chr16:30998184-30998420(+)$1	236	81	88	12.7213
rrrrrrr	chr21:45139130-45139359(+)$1	229	47	54	13.3770
ffffff]	chr9:110249867-110250094(-)$1	227	199	206	12.6393
:EEEEE~	chr16:5122895-5123118(+)$1	223	183	190	12.5573
c"""ddd	chr19:3981247-3981496(-)$1	249	42	49	13.1311
ppppppp	chr12:51102217-51102442(+)$1	225	124	131	13.1311
ggggggg	chr14:103357621-103357846(+)$1	225	129	136	13.4590
ffffffc	chr19:3983121-3983358(-)$1	237	189	196	17.1475
GGGGG::	chr9:134311906-134312140(+)$1	234	199	206	12.7213
qqqqqqq	chr1:149949263-149949488(-)$1	225	124	131	13.4590
ggggg[h	chr2:9658209-9658430(-)$1	221	180	187	17.1475
d::bbqq	chr3:64007988-64008209(-)$1	221	122	129	13.4590
BBCCC}G	chr16:31201266-31201489(+)$1	223	192	199	17.1475
ggg[bb#	chr17:40367945-40368172(-)$1	227	65	72	12.6393
:EEEEE:	chr15:72502648-72502875(-)$1	227	2	9	13.4590
ee!!bbb	chr21:34926704-34926955(+)$1	251	116	123	12.8032
dddd(((	chr19:39879313-39879550(-)$1	237	122	129	13.0491
dd[iiii	chr22:42987922-42988158(-)$1	236	127	134	17.1475
BB{CCC{	chr7:128843299-128843530(+)$1	231	10	17	13.4590
bb]ccc]	chr19:2272996-2273223(+)$1	227	98	105	13.3770
ZZCCC}C	chr8:144658565-144658791(-)$1	226	206	213	17.1475
ffff[cc	chr17:44248134-44248375(-)$1	241	37	44	12.8852
GGGGGG:	chr5:140022070-140022295(+)$1	225	216	223	12.8032
iiiiiii	chr19:6416414-6416652(-)$1	238	148	155	12.7213
bb[bb[d	chr1:150938626-150938857(-)$1	231	143	150	13.3770
bb[cccr	chr3:56716688-56716918(-)$1	230	173	180	13.3770
bb[dddd	chr17:36868028-36868268(+)$1	240	119	126	17.1475
ccc####	chr7:26235944-26236176(-)$1	232	104	111	12.5573
777eeee	chr12:58144912-58145140(-)$1	228	174	181	12.8032
ee!!ddd	chr12:49424330-49424556(-)$1	226	4	11	13.4590
dddd:::	chr12:53681988-53682210(+)$1	222	152	159	12.8852
HH::ddd	chr20:62373459-62373688(+)$1	229	67	74	13.4590
d22bb]c	chr19:19638418-19638659(+)$1	241	118	125	13.3770
ddggggg	chr14:53417162-53417391(-)$1	229	151	158	12.8032
II:gggg	chr3:69126937-69127158(-)$1	221	31	38	13.1311
::EEEEE	chr20:21327008-21327235(+)$1	227	0	7	13.4590
hhhhhhh	chr7:44605482-44605709(-)$1	227	126	133	13.4590
h]abbdd	chr1:212208598-212208838(-)$1	240	195	202	12.7213
FYYGGGG	chr1:204379521-204379765(-)$1	244	200	207	13.3770
##bbooo	chr16:30775515-30775738(+)$1	223	66	73	17.1475
EE{AKKG	chrX:53222638-53222867(-)$1	229	53	60	13.4590
GGGGGKK	chr1:109756600-109756834(+)$1	234	50	57	12.8852
fffccc[	chr15:41961562-41961783(+)$1	221	168	175	17.1475
[bba[cc	chr8:106814726-106814957(+)$1	231	61	68	12.8032
:::::::	chr5:149212940-149213162(+)$1	222	6	13	13.3770
fffff55	chr1:155903450-155903672(-)$1	222	101	108	12.6393
$$bblll	chr16:30721261-30721505(+)$1	244	152	159	13.4590
KCCCDDD	chr1:151206718-151206946(+)$1	228	14	21	13.1311
DDDFFFF	chr5:71493077-71493306(+)$1	229	1	8	12.8852
!gggggg	chr20:21336629-21336855(+)$1	226	105	112	17.1475
eeeee]f	chr1:117639921-117640144(+)$1	223	75	82	17.1475

#DB
)))..))	chr8:61655054-61655277(+)$1	1	182	189	12.7213
(((((((	chr19:10260459-10260686(-)$1	1	68	75	13.4590
(((((((	chr19:48630438-48630662(-)$1	1	56	63	17.1475
)))))).	chr10:119134147-119134364(-)$1	1	207	214	17.1475
((.((((	chr1:19432966-19433197(-)$1	1	49	56	17.1475
(((((((	chr16:31195537-31195760(+)$1	1	158	165	17.1475
(((((..	chr6:111196206-111196430(+)$1	1	143	150	12.7213
((.....	chr1:162467696-162467920(+)$1	1	16	23	13.0491
(((((((	chr9:5742843-5743074(+)$1	1	42	49	13.4590
((((((.	chr1:19426786-19427007(-)$1	1	134	141	12.7213
..((((.	chr16:30998184-30998420(+)$1	1	81	88	12.7213
.......	chr21:45139130-45139359(+)$1	1	47	54	13.3770
)))))).	chr9:110249867-110250094(-)$1	1	199	206	12.6393
.))))).	chr16:5122895-5123118(+)$1	1	183	190	12.5573
(...(((	chr19:3981247-3981496(-)$1	1	42	49	13.1311
.......	chr12:51102217-51102442(+)$1	1	124	131	13.1311
(((((((	chr14:103357621-103357846(+)$1	1	129	136	13.4590
)))))))	chr19:3983121-3983358(-)$1	1	189	196	17.1475
)))))..	chr9:134311906-134312140(+)$1	1	199	206	12.7213
.......	chr1:149949263-149949488(-)$1	1	124	131	13.4590
(((((.(	chr2:9658209-9658430(-)$1	1	180	187	17.1475
)..((..	chr3:64007988-64008209(-)$1	1	122	129	13.4590
))))).)	chr16:31201266-31201489(+)$1	1	192	199	17.1475
(((.((.	chr17:40367945-40368172(-)$1	1	65	72	12.6393
.(((((.	chr15:72502648-72502875(-)$1	1	2	9	13.4590
((..(((	chr21:34926704-34926955(+)$1	1	116	123	12.8032
((((...	chr19:39879313-39879550(-)$1	1	122	129	13.0491
((.((((	chr22:42987922-42988158(-)$1	1	127	134	17.1475
((.(((.	chr7:128843299-128843530(+)$1	1	10	17	13.4590
)).))).	chr19:2272996-2273223(+)$1	1	98	105	13.3770
..))).)	chr8:144658565-144658791(-)$1	1	206	213	17.1475
((((.((	chr17:44248134-44248375(-)$1	1	37	44	12.8852
)))))).	chr5:140022070-140022295(+)$1	1	216	223	12.8032
(((((((	chr19:6416414-6416652(-)$1	1	148	155	12.7213
((.((.(	chr1:150938626-150938857(-)$1	1	143	150	13.3770
((.(((.	chr3:56716688-56716918(-)$1	1	173	180	13.3770
((.((((	chr17:36868028-36868268(+)$1	1	119	126	17.1475
(((....	chr7:26235944-26236176(-)$1	1	104	111	12.5573
...))))	chr12:58144912-58145140(-)$1	1	174	181	12.8032
((..(((	chr12:49424330-49424556(-)$1	1	4	11	13.4590
))))...	chr12:53681988-53682210(+)$1	1	152	159	12.8852
((..(((	chr20:62373459-62373688(+)$1	1	67	74	13.4590
)..)).)	chr19:19638418-19638659(+)$1	1	118	125	13.3770
(((((((	chr14:53417162-53417391(-)$1	1	151	158	12.8032
((.((((	chr3:69126937-69127158(-)$1	1	31	38	13.1311
..(((((	chr20:21327008-21327235(+)$1	1	0	7	13.4590
)))))))	chr7:44605482-44605709(-)$1	1	126	133	13.4590
).)))))	chr1:212208598-212208838(-)$1	1	195	202	12.7213
)..))))	chr1:204379521-204379765(-)$1	1	200	207	13.3770
..((...	chr16:30775515-30775738(+)$1	1	66	73	17.1475
((.(..(	chrX:53222638-53222867(-)$1	1	53	60	13.4590
(((((..	chr1:109756600-109756834(+)$1	1	50	57	12.8852
((((((.	chr15:41961562-41961783(+)$1	1	168	175	17.1475
.(((.((	chr8:106814726-106814957(+)$1	1	61	68	12.8032
.......	chr5:149212940-149213162(+)$1	1	6	13	13.3770
)))))..	chr1:155903450-155903672(-)$1	1	101	108	12.6393
..((...	chr16:30721261-30721505(+)$1	1	152	159	13.4590
.((((((	chr1:151206718-151206946(+)$1	1	14	21	13.1311
(((((((	chr5:71493077-71493306(+)$1	1	1	8	12.8852
.((((((	chr20:21336629-21336855(+)$1	1	105	112	17.1475
))))).)	chr1:117639921-117640144(+)$1	1	75	82	17.1475

#PSSM
G : 0.86	U : 0.04	g : 0.03	A : 0.03	C : 0.01	
G : 0.80	A : 0.09	g : 0.03	U : 0.03	C : 0.03	
A : 0.90	a : 0.03	U : 0.03	G : 0.01	C : 0.01	
G : 0.88	C : 0.04	A : 0.03	g : 0.03	
G : 0.81	C : 0.11	g : 0.03	A : 0.03	
U : 0.85	A : 0.09	u : 0.01	G : 0.01	a : 0.01	
G : 0.88	g : 0.03	U : 0.03	A : 0.03	C : 0.01	

#score	854.9344262295089
#seq	61
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m2_run1.nuc.txt

#NT
auaaaaau	chr8:120843832-120844053(-)$1	221	35	43	12.2089
AGAAAACU	chr7:44874033-44874256(-)$1	223	143	151	12.3582
AGAAAAGC	chr8:87563332-87563557(+)$1	225	32	40	12.0597
AGAGAAAA	chr11:13721882-13722106(+)$1	224	19	27	12.5074
AGAAAAUA	chr1:197112528-197112753(-)$1	225	16	24	13.0298
AGACAAAA	chr3:98239905-98240126(-)$1	221	196	204	12.3582
AGAAAUAA	chr7:152346070-152346300(-)$1	230	45	53	12.5074
CGAAAAAU	chrM:3148-3453(+)$1	305	231	239	12.4328
AGCAAAAA	chr1:197111637-197111863(-)$1	226	29	37	12.5820
AGAAAAAC	chr19:44611689-44611922(+)$1	233	63	71	16.3134
AGAAAAAC	chr22:28254366-28254583(-)$1	217	88	96	16.3134
AGGAAAAA	chr7:104715055-104715282(+)$1	227	159	167	12.7313
AUAAAAAU	chr1:20981025-20981252(-)$1	227	176	184	12.2089
AGAAGAAA	chr11:94917484-94917710(-)$1	226	8	16	13.1791
AGAAGAAU	chr14:58674612-58674836(+)$1	224	73	81	12.8059
AGAAAGAC	chr6:116987946-116988166(-)$1	220	37	45	12.1343
AGAAAAAA	chr20:17950482-17950706(+)$1	224	132	140	16.9104
AGGAAAAA	chr8:33354050-33354273(+)$1	223	4	12	12.7313
AGAAGAAU	chr10:112655698-112655927(+)$1	229	87	95	12.8059
AGAACAAA	chr11:27520882-27521109(-)$1	227	98	106	12.7313
AGAAAAAU	chr2:32249177-32249399(-)$1	222	162	170	16.5373
ACAAAAAC	chr20:34242750-34242977(-)$1	227	163	171	11.8358
AGAAAAAC	chr19:9676517-9676752(-)$1	235	137	145	16.3134
AGAAAGAG	chr15:32929904-32930127(+)$1	223	51	59	11.2388
UGAAAAAU	chr17:34147070-34147342(+)$1	272	218	226	12.5820
AGAAUAAA	chr5:102886487-102886708(-)$1	221	126	134	12.8059
AGAAGAAC	chr21:34931515-34931747(+)$1	232	97	105	12.5820
AGCAAAAU	chr19:32844030-32844251(+)$1	221	151	159	12.2089
AGAAAAAU	chr20:43615692-43615917(+)$1	225	149	157	16.5373
AGAAAAUU	chr19:44352318-44352539(+)$1	221	119	127	12.6567
AGAGAAAC	chr19:38230830-38231053(-)$1	223	52	60	11.9104
agaaaaaC	chr14:23794381-23794601(+)$1	220	190	198	16.3134
AGAUAAAC	chr6:151779388-151779612(+)$1	224	139	147	11.7611
AGAAAAAA	chr2:170487207-170487441(+)$1	234	216	224	16.9104
AGAAAAAU	chrM:9970-10199(+)$1	229	181	189	16.5373
AGAAGAAA	chr15:43324699-43324923(-)$1	224	123	131	13.1791
AGAAAAUA	chr17:34893439-34893659(+)$1	220	72	80	13.0298
AGAAAAAG	chr10:119043756-119043979(-)$1	223	162	170	15.4179
AGAAGAAA	chr11:812705-812943(+)$1	238	60	68	13.1791
UGAAAAAC	chr1:70761752-70761995(-)$1	243	7	15	12.3582
AGAAUAAC	chr1:54433435-54433658(+)$1	223	97	105	12.2089
CGAAAAAA	chr1:220197639-220197858(-)$1	219	10	18	12.8059
UGAAAAAU	chr10:27415543-27415769(-)$1	226	97	105	12.5820
AGAAAAAA	chr5:110081888-110082111(+)$1	223	50	58	16.9104
AGAAACAC	chr8:26227565-26227785(+)$1	220	130	138	11.9850
auaaaaau	chr1:54509051-54509274(-)$1	223	36	44	12.2089
AGAAGAAG	chr2:61710094-61710317(-)$1	223	131	139	11.6865
AGAAAAUU	chr2:176959203-176959435(+)$1	232	217	225	12.6567
GGAAAAAA	chr7:112424520-112424743(-)$1	223	30	38	12.6567
AGAAAGAU	chr11:20529827-20530048(+)$1	221	61	69	12.3582
AGAAAAAC	chr19:44591099-44591323(+)$1	224	136	144	16.3134
CGAAAAAG	chr20:34241484-34241708(-)$1	224	15	23	11.3134
aggaaaaa	chr10:70765399-70765625(+)$1	226	29	37	12.7313
AAAAAAAU	chr14:29237803-29238025(+)$1	222	213	221	12.1343
AGGAAAAC	chr17:27613750-27613986(-)$1	236	62	70	12.1343
AGAAACAU	chr1:165860378-165860601(+)$1	223	53	61	12.2089
AGUAAAAA	chrX:123220459-123220681(+)$1	222	97	105	12.5074
AGAAAAAU	chr11:93471181-93471403(-)$1	222	108	116	16.5373
AGAAAGAC	chr7:112101984-112102213(+)$1	229	129	137	12.1343
UGAAAAAG	chr6:75969056-75969273(-)$1	217	121	129	11.4626
AGAAAAAC	chr4:52765395-52765622(+)$1	227	52	60	16.3134
AGAAAAUA	chr1:231696798-231697025(+)$1	227	190	198	13.0298
AGAGAAAA	chr11:32996736-32996959(+)$1	223	74	82	12.5074
aaaaaaaa	chr4:122737442-122737663(-)$1	221	160	168	12.5074
AGAAAAUA	chr11:31392272-31392506(+)$1	234	212	220	13.0298
UGAAAAAA	chr4:166254629-166254856(+)$1	227	125	133	12.9552

#otherMatches

#Struct PSSM
c55555ee	chr19:40580689-40580916(-)$1	227	126	134	12.3582
e!!ddddn	chr8:120843832-120844053(-)$1	221	35	43	12.2089
eemmmmee	chr7:44874033-44874256(-)$1	223	143	151	12.3582
ssseeeee	chr8:87563332-87563557(+)$1	225	32	40	12.0597
CDDDD:::	chr11:13721882-13722106(+)$1	224	19	27	12.5074
hhhh::::	chr1:197112528-197112753(-)$1	225	16	24	13.0298
>>>>>>>>	chr3:98239905-98240126(-)$1	221	196	204	12.3582
eeee0000	chr7:152346070-152346300(-)$1	230	45	53	12.5074
::::::::	chrM:3148-3453(+)$1	305	231	239	12.4328
^^^^^^^^	chr1:197111637-197111863(-)$1	226	29	37	12.5820
ee::::::	chr19:44611689-44611922(+)$1	233	63	71	16.3134
e]eeeee]	chr22:28254366-28254583(-)$1	217	88	96	16.3134
^eeeee22	chr7:104715055-104715282(+)$1	227	159	167	12.7313
::::eeee	chr1:20981025-20981252(-)$1	227	176	184	12.2089
:CCCLLLF	chr11:94917484-94917710(-)$1	226	8	16	13.1791
]ccc]ddd	chr14:58674612-58674836(+)$1	224	73	81	12.8059
::::::::	chr6:116987946-116988166(-)$1	220	37	45	12.1343
tttttttt	chr20:17950482-17950706(+)$1	224	132	140	16.9104
hhhh&&&&	chr8:33354050-33354273(+)$1	223	4	12	12.7313
:eeeeell	chr10:112655698-112655927(+)$1	229	87	95	12.8059
++++++++	chr11:27520882-27521109(-)$1	227	98	106	12.7313
::::::::	chr2:32249177-32249399(-)$1	222	162	170	16.5373
vvvvvvvc	chr20:34242750-34242977(-)$1	227	163	171	11.8358
^^^^^^^^	chr19:9676517-9676752(-)$1	235	137	145	16.3134
:::::::c	chr15:32929904-32930127(+)$1	223	51	59	11.2388
dmmmmddd	chr17:34147070-34147342(+)$1	272	218	226	12.5820
ggqqqqqq	chr5:102886487-102886708(-)$1	221	126	134	12.8059
[aoooooo	chr21:34931515-34931747(+)$1	232	97	105	12.5820
dddd4444	chr19:32844030-32844251(+)$1	221	151	159	12.2089
HHHHHHHY	chr20:43615692-43615917(+)$1	225	149	157	16.5373
55555fff	chr19:44352318-44352539(+)$1	221	119	127	12.6567
ddnnnnnd	chr19:38230830-38231053(-)$1	223	52	60	11.9104
@@@@@@@@	chr14:23794381-23794601(+)$1	220	190	198	16.3134
:ffffffl	chr6:151779388-151779612(+)$1	224	139	147	11.7611
:::::::A	chr2:170487207-170487441(+)$1	234	216	224	16.9104
eeee>>>>	chrM:9970-10199(+)$1	229	181	189	16.5373
+ddddnnn	chr15:43324699-43324923(-)$1	224	123	131	13.1791
ccc22bb]	chr17:34893439-34893659(+)$1	220	72	80	13.0298
ffff9999	chr10:119043756-119043979(-)$1	223	162	170	15.4179
===:BB{E	chr11:812705-812943(+)$1	238	60	68	13.1791
HHHHHHKK	chr1:70761752-70761995(-)$1	243	7	15	12.3582
eeee333f	chr1:54433435-54433658(+)$1	223	97	105	12.2089
qqqqqqqq	chr1:220197639-220197858(-)$1	219	10	18	12.8059
hh::::::	chr10:27415543-27415769(-)$1	226	97	105	12.5820
ggg:::::	chr5:110081888-110082111(+)$1	223	50	58	16.9104
EEYYDDDD	chr8:26227565-26227785(+)$1	220	130	138	11.9850
!iiiiiii	chr1:54509051-54509274(-)$1	223	36	44	12.2089
qqqqqqqa	chr2:61710094-61710317(-)$1	223	131	139	11.6865
>>>>>>gg	chr2:176959203-176959435(+)$1	232	217	225	12.6567
ddd!!ddd	chr7:112424520-112424743(-)$1	223	30	38	12.6567
EEENNNNN	chr11:20529827-20530048(+)$1	221	61	69	12.3582
::::::::	chr19:44591099-44591323(+)$1	224	136	144	16.3134
::::::EE	chr20:34241484-34241708(-)$1	224	15	23	11.3134
fff:::::	chr10:70765399-70765625(+)$1	226	29	37	12.7313
::::::::	chr14:29237803-29238025(+)$1	222	213	221	12.1343
cccmmmmc	chr17:27613750-27613986(-)$1	236	62	70	12.1343
qqqqqqgg	chr1:165860378-165860601(+)$1	223	53	61	12.2089
{EEEEE::	chrX:123220459-123220681(+)$1	222	97	105	12.5074
iwwwwwww	chr11:93471181-93471403(-)$1	222	108	116	16.5373
ddd]bb::	chr7:112101984-112102213(+)$1	229	129	137	12.1343
hhhhhh55	chr6:75969056-75969273(-)$1	217	121	129	11.4626
hhhhhhhh	chr4:52765395-52765622(+)$1	227	52	60	16.3134
IIIIIII_	chr1:231696798-231697025(+)$1	227	190	198	13.0298
fffff!!d	chr11:32996736-32996959(+)$1	223	74	82	12.5074
vvvvvggg	chr4:122737442-122737663(-)$1	221	160	168	12.5074
qqqqqqqq	chr11:31392272-31392506(+)$1	234	212	220	13.0298
ffff]eee	chr4:166254629-166254856(+)$1	227	125	133	12.9552

#DB
).....))	chr19:40580689-40580916(-)$1	1	126	134	12.3582
(..((((.	chr8:120843832-120844053(-)$1	1	35	43	12.2089
((....))	chr7:44874033-44874256(-)$1	1	143	151	12.3582
...)))))	chr8:87563332-87563557(+)$1	1	32	40	12.0597
(((((...	chr11:13721882-13722106(+)$1	1	19	27	12.5074
))))....	chr1:197112528-197112753(-)$1	1	16	24	13.0298
........	chr3:98239905-98240126(-)$1	1	196	204	12.3582
))))....	chr7:152346070-152346300(-)$1	1	45	53	12.5074
........	chrM:3148-3453(+)$1	1	231	239	12.4328
........	chr1:197111637-197111863(-)$1	1	29	37	12.5820
))......	chr19:44611689-44611922(+)$1	1	63	71	16.3134
).))))).	chr22:28254366-28254583(-)$1	1	88	96	16.3134
.)))))..	chr7:104715055-104715282(+)$1	1	159	167	12.7313
....((((	chr1:20981025-20981252(-)$1	1	176	184	12.2089
.(((...(	chr11:94917484-94917710(-)$1	1	8	16	13.1791
.))).)))	chr14:58674612-58674836(+)$1	1	73	81	12.8059
........	chr6:116987946-116988166(-)$1	1	37	45	12.1343
........	chr20:17950482-17950706(+)$1	1	132	140	16.9104
((((....	chr8:33354050-33354273(+)$1	1	4	12	12.7313
.(((((..	chr10:112655698-112655927(+)$1	1	87	95	12.8059
........	chr11:27520882-27521109(-)$1	1	98	106	12.7313
........	chr2:32249177-32249399(-)$1	1	162	170	16.5373
.......)	chr20:34242750-34242977(-)$1	1	163	171	11.8358
........	chr19:9676517-9676752(-)$1	1	137	145	16.3134
.......(	chr15:32929904-32930127(+)$1	1	51	59	11.2388
(....)))	chr17:34147070-34147342(+)$1	1	218	226	12.5820
((......	chr5:102886487-102886708(-)$1	1	126	134	12.8059
.(......	chr21:34931515-34931747(+)$1	1	97	105	12.5820
))))....	chr19:32844030-32844251(+)$1	1	151	159	12.2089
))))))).	chr20:43615692-43615917(+)$1	1	149	157	16.5373
.....)))	chr19:44352318-44352539(+)$1	1	119	127	12.6567
((.....)	chr19:38230830-38231053(-)$1	1	52	60	11.9104
........	chr14:23794381-23794601(+)$1	1	190	198	16.3134
.((((((.	chr6:151779388-151779612(+)$1	1	139	147	11.7611
.......)	chr2:170487207-170487441(+)$1	1	216	224	16.9104
))))....	chrM:9970-10199(+)$1	1	181	189	16.5373
.((((...	chr15:43324699-43324923(-)$1	1	123	131	13.1791
)))..)).	chr17:34893439-34893659(+)$1	1	72	80	13.0298
))))....	chr10:119043756-119043979(-)$1	1	162	170	15.4179
))).((.(	chr11:812705-812943(+)$1	1	60	68	13.1791
((((((..	chr1:70761752-70761995(-)$1	1	7	15	12.3582
))))...)	chr1:54433435-54433658(+)$1	1	97	105	12.2089
........	chr1:220197639-220197858(-)$1	1	10	18	12.8059
))......	chr10:27415543-27415769(-)$1	1	97	105	12.5820
))).....	chr5:110081888-110082111(+)$1	1	50	58	16.9104
))..))))	chr8:26227565-26227785(+)$1	1	130	138	11.9850
.(((((((	chr1:54509051-54509274(-)$1	1	36	44	12.2089
.......)	chr2:61710094-61710317(-)$1	1	131	139	11.6865
......))	chr2:176959203-176959435(+)$1	1	217	225	12.6567
(((..(((	chr7:112424520-112424743(-)$1	1	30	38	12.6567
(((.....	chr11:20529827-20530048(+)$1	1	61	69	12.3582
........	chr19:44591099-44591323(+)$1	1	136	144	16.3134
......((	chr20:34241484-34241708(-)$1	1	15	23	11.3134
))).....	chr10:70765399-70765625(+)$1	1	29	37	12.7313
........	chr14:29237803-29238025(+)$1	1	213	221	12.1343
(((....)	chr17:27613750-27613986(-)$1	1	62	70	12.1343
......))	chr1:165860378-165860601(+)$1	1	53	61	12.2089
.(((((..	chrX:123220459-123220681(+)$1	1	97	105	12.5074
(.......	chr11:93471181-93471403(-)$1	1	108	116	16.5373
))).))..	chr7:112101984-112102213(+)$1	1	129	137	12.1343
))))))..	chr6:75969056-75969273(-)$1	1	121	129	11.4626
))))))))	chr4:52765395-52765622(+)$1	1	52	60	16.3134
))))))).	chr1:231696798-231697025(+)$1	1	190	198	13.0298
(((((..(	chr11:32996736-32996959(+)$1	1	74	82	12.5074
.....)))	chr4:122737442-122737663(-)$1	1	160	168	12.5074
........	chr11:31392272-31392506(+)$1	1	212	220	13.0298
)))).)))	chr4:166254629-166254856(+)$1	1	125	133	12.9552

#PSSM
A : 0.79	a : 0.07	U : 0.07	C : 0.04	G : 0.01	
G : 0.88	u : 0.02	g : 0.02	U : 0.01	C : 0.01	A : 0.01	a : 0.01	
A : 0.83	a : 0.05	G : 0.04	C : 0.02	g : 0.01	U : 0.01	
A : 0.85	a : 0.07	G : 0.04	C : 0.01	U : 0.01	
A : 0.77	G : 0.10	a : 0.07	U : 0.02	C : 0.01	
A : 0.82	a : 0.07	G : 0.05	C : 0.02	U : 0.01	
A : 0.79	U : 0.08	a : 0.07	C : 0.02	G : 0.01	
A : 0.34	U : 0.26	C : 0.25	G : 0.07	u : 0.02	a : 0.02	

#score	889.0447761194038
#seq	67
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m2_run2.nuc.txt

#NT
AAUAA	chr6:71245921-71246151(+)$1	230	68	73	15.0000
AAUAA	chr2:203431796-203432026(+)$1	230	73	78	15.0000
AAUAA	chr13:39622910-39623142(+)$1	232	36	41	15.0000
AAUAA	chr10:98719129-98719359(+)$1	230	37	42	15.0000
AAUAA	chr12:49921025-49921264(+)$1	239	151	156	15.0000
AAUAA	chr16:20808163-20808393(-)$1	230	174	179	15.0000
AAUAA	chr12:111086537-111086767(-)$1	230	139	144	15.0000
AAUAA	chr18:723134-723363(-)$1	229	149	154	15.0000
aauaa	chr1:14113950-14114162(+)$1	212	183	188	15.0000
AAUAA	chr10:105359315-105359545(-)$1	230	80	85	15.0000
AAUAA	chr18:66341079-66341303(-)$1	224	129	134	15.0000
AAUAA	chr6:107016519-107016743(+)$1	224	115	120	15.0000
AAUAA	chr17:27584452-27584682(-)$1	230	106	111	15.0000
AAUAA	chr2:106510063-106510293(+)$1	230	125	130	15.0000
AAUAA	chr1:1716652-1716882(-)$1	230	134	139	15.0000
AAUAA	chr1:203277710-203277940(+)$1	230	121	126	15.0000
AAUAA	chr17:29110853-29111086(-)$1	233	112	117	15.0000
AAUAA	chr14:51187089-51187319(-)$1	230	106	111	15.0000
AAUAA	chr19:55602261-55602491(-)$1	230	184	189	15.0000
AAUAA	chr9:123665222-123665448(-)$1	226	101	106	15.0000
AAUAA	chr7:86541303-86541533(-)$1	230	223	228	15.0000
aauaa	chr9:79002023-79002246(-)$1	223	136	141	15.0000
AAUAA	chr2:208466658-208466884(+)$1	226	110	115	15.0000
AAUAA	chr14:39501228-39501454(-)$1	226	123	128	15.0000
AAUAA	chr5:171638455-171638685(-)$1	230	23	28	15.0000
AAUAA	chr19:21242496-21242726(+)$1	230	217	222	15.0000
AAUAA	chr8:66514757-66514987(-)$1	230	13	18	15.0000
AAUAA	chr11:111611656-111611883(-)$1	227	0	5	15.0000
AAUAA	chr4:128754882-128755105(+)$1	223	21	26	15.0000
AAUAA	chr6:159056311-159056532(+)$1	221	131	136	15.0000
AAUAA	chr8:131064961-131065191(-)$1	230	176	181	15.0000
aauaa	chr2:74381369-74381596(-)$1	227	59	64	15.0000
AAUAA	chr13:114110314-114110554(-)$1	240	107	112	15.0000
AAUAA	chr11:244624-244862(+)$1	238	199	204	15.0000
AAUAA	chr7:6729504-6729731(-)$1	227	109	114	15.0000
AAUAA	chr5:32601607-32601837(+)$1	230	74	79	15.0000
AAUAA	chr18:72913065-72913294(-)$1	229	115	120	15.0000
AAUAA	chr11:67131642-67131864(-)$1	222	205	210	15.0000
aauaa	chrX:96858568-96858798(+)$1	230	198	203	15.0000
AAUAA	chr20:35240713-35240940(+)$1	227	184	189	15.0000
AAUAA	chr5:100146140-100146370(-)$1	230	124	129	15.0000
AAUAA	chr12:69136211-69136436(+)$1	225	77	82	15.0000
AAUAA	chr11:118396661-118396884(+)$1	223	24	29	15.0000
AAUAA	chr4:153243420-153243642(-)$1	222	19	24	15.0000
AAUAA	chr18:43846332-43846562(+)$1	230	68	73	15.0000
AAUAA	chr11:19197614-19197844(+)$1	230	38	43	15.0000
AAUAA	chr8:96167535-96167765(+)$1	230	2	7	15.0000
AAUAA	chr2:211298020-211298250(-)$1	230	102	107	15.0000

#otherMatches

#Struct PSSM
:::::	chr9:5920507-5920734(-)$1	227	9	14	15.0000
:::::	chr6:71245921-71246151(+)$1	230	68	73	15.0000
uuuuu	chr2:203431796-203432026(+)$1	230	73	78	15.0000
fff$$	chr13:39622910-39623142(+)$1	232	36	41	15.0000
hhh[b	chr10:98719129-98719359(+)$1	230	37	42	15.0000
uuuuu	chr12:49921025-49921264(+)$1	239	151	156	15.0000
ccmmm	chr16:20808163-20808393(-)$1	230	174	179	15.0000
:::::	chr12:111086537-111086767(-)$1	230	139	144	15.0000
ooooo	chr18:723134-723363(-)$1	229	149	154	15.0000
^^^^^	chr1:14113950-14114162(+)$1	212	183	188	15.0000
###ee	chr10:105359315-105359545(-)$1	230	80	85	15.0000
EEEEY	chr18:66341079-66341303(-)$1	224	129	134	15.0000
:::::	chr6:107016519-107016743(+)$1	224	115	120	15.0000
RRRRR	chr17:27584452-27584682(-)$1	230	106	111	15.0000
:::::	chr2:106510063-106510293(+)$1	230	125	130	15.0000
ooooo	chr1:1716652-1716882(-)$1	230	134	139	15.0000
xxxxx	chr1:203277710-203277940(+)$1	230	121	126	15.0000
66ggg	chr17:29110853-29111086(-)$1	233	112	117	15.0000
nnnee	chr14:51187089-51187319(-)$1	230	106	111	15.0000
qqqqq	chr19:55602261-55602491(-)$1	230	184	189	15.0000
:::::	chr9:123665222-123665448(-)$1	226	101	106	15.0000
:::::	chr7:86541303-86541533(-)$1	230	223	228	15.0000
qqqqq	chr9:79002023-79002246(-)$1	223	136	141	15.0000
wwwww	chr2:208466658-208466884(+)$1	226	110	115	15.0000
rrrrr	chr14:39501228-39501454(-)$1	226	123	128	15.0000
:::::	chr5:171638455-171638685(-)$1	230	23	28	15.0000
FFFYY	chr19:21242496-21242726(+)$1	230	217	222	15.0000
uuuuu	chr8:66514757-66514987(-)$1	230	13	18	15.0000
:::::	chr11:111611656-111611883(-)$1	227	0	5	15.0000
ffppp	chr4:128754882-128755105(+)$1	223	21	26	15.0000
eFFFF	chr6:159056311-159056532(+)$1	221	131	136	15.0000
:::::	chr8:131064961-131065191(-)$1	230	176	181	15.0000
====2	chr2:74381369-74381596(-)$1	227	59	64	15.0000
:::::	chr13:114110314-114110554(-)$1	240	107	112	15.0000
ggggl	chr11:244624-244862(+)$1	238	199	204	15.0000
xxxxx	chr7:6729504-6729731(-)$1	227	109	114	15.0000
cc[dd	chr5:32601607-32601837(+)$1	230	74	79	15.0000
:::::	chr18:72913065-72913294(-)$1	229	115	120	15.0000
:::::	chr11:67131642-67131864(-)$1	222	205	210	15.0000
:::::	chrX:96858568-96858798(+)$1	230	198	203	15.0000
d[ccc	chr20:35240713-35240940(+)$1	227	184	189	15.0000
fffff	chr5:100146140-100146370(-)$1	230	124	129	15.0000
ggggg	chr12:69136211-69136436(+)$1	225	77	82	15.0000
!ccc[	chr11:118396661-118396884(+)$1	223	24	29	15.0000
:::::	chr4:153243420-153243642(-)$1	222	19	24	15.0000
eeeee	chr18:43846332-43846562(+)$1	230	68	73	15.0000
^^ccc	chr11:19197614-19197844(+)$1	230	38	43	15.0000
hhhhh	chr8:96167535-96167765(+)$1	230	2	7	15.0000
ccmmm	chr2:211298020-211298250(-)$1	230	102	107	15.0000

#DB
.....	chr9:5920507-5920734(-)$1	1	9	14	15.0000
.....	chr6:71245921-71246151(+)$1	1	68	73	15.0000
.....	chr2:203431796-203432026(+)$1	1	73	78	15.0000
(((..	chr13:39622910-39623142(+)$1	1	36	41	15.0000
(((.(	chr10:98719129-98719359(+)$1	1	37	42	15.0000
.....	chr12:49921025-49921264(+)$1	1	151	156	15.0000
((...	chr16:20808163-20808393(-)$1	1	174	179	15.0000
.....	chr12:111086537-111086767(-)$1	1	139	144	15.0000
.....	chr18:723134-723363(-)$1	1	149	154	15.0000
.....	chr1:14113950-14114162(+)$1	1	183	188	15.0000
...((	chr10:105359315-105359545(-)$1	1	80	85	15.0000
)))).	chr18:66341079-66341303(-)$1	1	129	134	15.0000
.....	chr6:107016519-107016743(+)$1	1	115	120	15.0000
.....	chr17:27584452-27584682(-)$1	1	106	111	15.0000
.....	chr2:106510063-106510293(+)$1	1	125	130	15.0000
.....	chr1:1716652-1716882(-)$1	1	134	139	15.0000
.....	chr1:203277710-203277940(+)$1	1	121	126	15.0000
..)))	chr17:29110853-29111086(-)$1	1	112	117	15.0000
...))	chr14:51187089-51187319(-)$1	1	106	111	15.0000
.....	chr19:55602261-55602491(-)$1	1	184	189	15.0000
.....	chr9:123665222-123665448(-)$1	1	101	106	15.0000
.....	chr7:86541303-86541533(-)$1	1	223	228	15.0000
.....	chr9:79002023-79002246(-)$1	1	136	141	15.0000
.....	chr2:208466658-208466884(+)$1	1	110	115	15.0000
.....	chr14:39501228-39501454(-)$1	1	123	128	15.0000
.....	chr5:171638455-171638685(-)$1	1	23	28	15.0000
)))..	chr19:21242496-21242726(+)$1	1	217	222	15.0000
.....	chr8:66514757-66514987(-)$1	1	13	18	15.0000
.....	chr11:111611656-111611883(-)$1	1	0	5	15.0000
((...	chr4:128754882-128755105(+)$1	1	21	26	15.0000
)))))	chr6:159056311-159056532(+)$1	1	131	136	15.0000
.....	chr8:131064961-131065191(-)$1	1	176	181	15.0000
)))).	chr2:74381369-74381596(-)$1	1	59	64	15.0000
.....	chr13:114110314-114110554(-)$1	1	107	112	15.0000
((((.	chr11:244624-244862(+)$1	1	199	204	15.0000
.....	chr7:6729504-6729731(-)$1	1	109	114	15.0000
((.((	chr5:32601607-32601837(+)$1	1	74	79	15.0000
.....	chr18:72913065-72913294(-)$1	1	115	120	15.0000
.....	chr11:67131642-67131864(-)$1	1	205	210	15.0000
.....	chrX:96858568-96858798(+)$1	1	198	203	15.0000
(.(((	chr20:35240713-35240940(+)$1	1	184	189	15.0000
)))))	chr5:100146140-100146370(-)$1	1	124	129	15.0000
(((((	chr12:69136211-69136436(+)$1	1	77	82	15.0000
.(((.	chr11:118396661-118396884(+)$1	1	24	29	15.0000
.....	chr4:153243420-153243642(-)$1	1	19	24	15.0000
)))))	chr18:43846332-43846562(+)$1	1	68	73	15.0000
..)))	chr11:19197614-19197844(+)$1	1	38	43	15.0000
(((((	chr8:96167535-96167765(+)$1	1	2	7	15.0000
((...	chr2:211298020-211298250(-)$1	1	102	107	15.0000

#PSSM
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	
U : 0.91	u : 0.08	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m2_run2.nuc.txt

#NT
AGAG	chr22:39261007-39261230(-)$1	223	58	62	11.9999
AGAG	chr7:97481460-97481675(-)$1	215	182	186	11.9999
AGAG	chr17:27957395-27957612(-)$1	217	8	12	11.9999
agag	chr8:26364262-26364486(-)$1	224	209	213	11.9999
agag	chr19:48956757-48956977(+)$1	220	20	24	11.9999
AGAG	chr16:4659039-4659256(-)$1	217	26	30	11.9999
AGAG	chr12:25359824-25360054(-)$1	230	25	29	11.9999
AGAG	chr2:220085884-220086111(-)$1	227	142	146	11.9999
AGAG	chr10:93811563-93811783(-)$1	220	14	18	11.9999
AGAG	chr22:38668792-38669016(-)$1	224	71	75	11.9999
AGAG	chr10:73060021-73060245(+)$1	224	99	103	11.9999
AGAG	chr7:148981411-148981636(+)$1	225	36	40	11.9999
AGAG	chr9:132572435-132572688(+)$1	253	68	72	11.9999
AGAG	chr4:2069402-2069627(+)$1	225	218	222	11.9999
AGAG	chr1:46125845-46126132(-)$1	287	120	124	11.9999
AGAG	chr12:57926423-57926642(-)$1	219	57	61	11.9999
AGAG	chr7:120496750-120496975(-)$1	225	164	168	11.9999
AGAG	chr19:13873792-13874016(+)$1	224	79	83	11.9999
AGAG	chr12:117298301-117298534(-)$1	233	47	51	11.9999
AGAG	chr2:48031976-48032216(+)$1	240	147	151	11.9999
AGAG	chr19:16629195-16629424(-)$1	229	69	73	11.9999
AGAG	chr7:97836032-97836269(+)$1	237	142	146	11.9999
AGAG	chr14:55534776-55534994(+)$1	218	150	154	11.9999
AGAG	chr7:100031104-100031345(+)$1	241	98	102	11.9999
AGAG	chr8:1729963-1730177(+)$1	214	25	29	11.9999
AGAG	chr1:11847915-11848174(-)$1	259	206	210	11.9999
AGAG	chr13:30084773-30085001(-)$1	228	190	194	11.9999
AGAG	chr13:30084083-30084314(-)$1	231	73	77	11.9999
AGAG	chr9:123525955-123526188(-)$1	233	82	86	11.9999
AGAG	chr21:45175848-45176085(+)$1	237	40	44	11.9999
AGAG	chr3:100428272-100428492(+)$1	220	89	93	11.9999
AGAG	chr1:44088865-44089084(+)$1	219	0	4	11.9999
AGAG	chr20:2125532-2125767(+)$1	235	97	101	11.9999
AGAG	chr1:173991205-173991436(-)$1	231	104	108	11.9999
AGAG	chr9:123525804-123526032(-)$1	228	157	161	11.9999
AGAG	chr6:27806325-27806538(+)$1	213	59	63	11.9999
AGAG	chr22:39912852-39913067(+)$1	215	189	193	11.9999
AGAG	chr6:31936130-31936354(+)$1	224	103	107	11.9999
AGAG	chrX:53406418-53406662(-)$1	244	73	77	11.9999
AGAG	chr8:124286293-124286516(-)$1	223	38	42	11.9999
AGAG	chr9:132997030-132997256(+)$1	226	145	149	11.9999
AGAG	chr14:24586807-24587022(+)$1	215	67	71	11.9999
AGAG	chrX:153580158-153580485(-)$1	327	5	9	11.9999
AGAG	chr3:15481053-15481283(+)$1	230	21	25	11.9999
AGAG	chr20:60709865-60710137(+)$1	272	32	36	11.9999
AGAG	chr2:220084040-220084307(-)$1	267	112	116	11.9999
AGAG	chr17:42476733-42476964(-)$1	231	42	46	11.9999
AGAG	chr12:54626590-54626826(-)$1	236	0	4	11.9999
AGAG	chr4:15683405-15683621(+)$1	216	39	43	11.9999
AGAG	chr3:47098771-47098991(-)$1	220	71	75	11.9999
AGAG	chr21:33687108-33687336(-)$1	228	50	54	11.9999
AGAG	chr11:94607015-94607240(+)$1	225	109	113	11.9999
AGAG	chr14:100835370-100835614(-)$1	244	79	83	11.9999
AGAG	chr15:75094999-75095227(+)$1	228	134	138	11.9999
AGAG	chr16:28856190-28856418(-)$1	228	122	126	11.9999
AGAG	chr7:133977142-133977366(-)$1	224	128	132	11.9999
AGAG	chr1:23413140-23413375(-)$1	235	11	15	11.9999
AGAG	chr17:40352734-40352956(-)$1	222	24	28	11.9999
AGAG	chr12:49161491-49161725(-)$1	234	90	94	11.9999
AGAG	chr22:29191214-29191427(-)$1	213	3	7	11.9999
AGAG	chr9:112542603-112542819(+)$1	216	170	174	11.9999
AGAG	chr15:42706718-42706956(-)$1	238	7	11	11.9999
AGAG	chr17:75084801-75085019(+)$1	218	125	129	11.9999
AGAG	chr11:47491442-47491679(-)$1	237	118	122	11.9999
AGAG	chr19:18679874-18680089(+)$1	215	152	156	11.9999
AGAG	chrX:153671169-153671390(+)$1	221	46	50	11.9999
AGAG	chr17:5012756-5012975(-)$1	219	13	17	11.9999
AGAG	chr17:25950912-25951131(+)$1	219	55	59	11.9999
AGAG	chr17:76967829-76968052(-)$1	223	57	61	11.9999
AGAG	chr15:64463171-64463389(-)$1	218	127	131	11.9999
AGAG	chr6:159187585-159187817(-)$1	232	197	201	11.9999
AGAG	chr1:182352598-182352811(-)$1	213	74	78	11.9999
AGAG	chr11:6498303-6498525(-)$1	222	170	174	11.9999
AGAG	chr12:122631552-122631778(+)$1	226	127	131	11.9999
AGAG	chr4:39776418-39776642(+)$1	224	95	99	11.9999
AGAG	chr2:235963307-235963569(+)$1	262	52	56	11.9999
AGAG	chrX:153582658-153582884(-)$1	226	40	44	11.9999
AGAG	chr12:53682230-53682495(+)$1	265	39	43	11.9999
AGAG	chr1:27107724-27107944(+)$1	220	67	71	11.9999

#otherMatches

#Struct PSSM
cc[c	chr19:41248373-41248616(-)$1	243	53	57	11.9999
"iii	chr22:39261007-39261230(-)$1	223	58	62	11.9999
ddoo	chr7:97481460-97481675(-)$1	215	182	186	11.9999
IIMM	chr17:27957395-27957612(-)$1	217	8	12	11.9999
JJJJ	chr8:26364262-26364486(-)$1	224	209	213	11.9999
:eee	chr19:48956757-48956977(+)$1	220	20	24	11.9999
eeee	chr16:4659039-4659256(-)$1	217	26	30	11.9999
ffff	chr12:25359824-25360054(-)$1	230	25	29	11.9999
GGGG	chr2:220085884-220086111(-)$1	227	142	146	11.9999
JJJK	chr10:93811563-93811783(-)$1	220	14	18	11.9999
ccee	chr22:38668792-38669016(-)$1	224	71	75	11.9999
55ee	chr10:73060021-73060245(+)$1	224	99	103	11.9999
CMMM	chr7:148981411-148981636(+)$1	225	36	40	11.9999
[ddd	chr9:132572435-132572688(+)$1	253	68	72	11.9999
ddcc	chr4:2069402-2069627(+)$1	225	218	222	11.9999
ffff	chr1:46125845-46126132(-)$1	287	120	124	11.9999
==[a	chr12:57926423-57926642(-)$1	219	57	61	11.9999
ddd$	chr7:120496750-120496975(-)$1	225	164	168	11.9999
cc]a	chr19:13873792-13874016(+)$1	224	79	83	11.9999
444g	chr12:117298301-117298534(-)$1	233	47	51	11.9999
ccqq	chr2:48031976-48032216(+)$1	240	147	151	11.9999
gfff	chr19:16629195-16629424(-)$1	229	69	73	11.9999
"""b	chr7:97836032-97836269(+)$1	237	142	146	11.9999
ggg:	chr14:55534776-55534994(+)$1	218	150	154	11.9999
C}CC	chr7:100031104-100031345(+)$1	241	98	102	11.9999
ee33	chr8:1729963-1730177(+)$1	214	25	29	11.9999
bbff	chr1:11847915-11848174(-)$1	259	206	210	11.9999
J:ff	chr13:30084773-30085001(-)$1	228	190	194	11.9999
:eee	chr13:30084083-30084314(-)$1	231	73	77	11.9999
cccc	chr9:123525955-123526188(-)$1	233	82	86	11.9999
CLLL	chr21:45175848-45176085(+)$1	237	40	44	11.9999
:ddd	chr3:100428272-100428492(+)$1	220	89	93	11.9999
eeee	chr1:44088865-44089084(+)$1	219	0	4	11.9999
nnne	chr20:2125532-2125767(+)$1	235	97	101	11.9999
rrrc	chr1:173991205-173991436(-)$1	231	104	108	11.9999
e]a:	chr9:123525804-123526032(-)$1	228	157	161	11.9999
mbb]	chr6:27806325-27806538(+)$1	213	59	63	11.9999
FFFF	chr22:39912852-39913067(+)$1	215	189	193	11.9999
gIII	chr6:31936130-31936354(+)$1	224	103	107	11.9999
dd22	chrX:53406418-53406662(-)$1	244	73	77	11.9999
mmme	chr8:124286293-124286516(-)$1	223	38	42	11.9999
oooo	chr9:132997030-132997256(+)$1	226	145	149	11.9999
EE{D	chr14:24586807-24587022(+)$1	215	67	71	11.9999
::::	chrX:153580158-153580485(-)$1	327	5	9	11.9999
::::	chr3:15481053-15481283(+)$1	230	21	25	11.9999
EEEE	chr20:60709865-60710137(+)$1	272	32	36	11.9999
!!dd	chr2:220084040-220084307(-)$1	267	112	116	11.9999
:fff	chr17:42476733-42476964(-)$1	231	42	46	11.9999
:CCC	chr12:54626590-54626826(-)$1	236	0	4	11.9999
{Agg	chr4:15683405-15683621(+)$1	216	39	43	11.9999
qqqq	chr3:47098771-47098991(-)$1	220	71	75	11.9999
$ddd	chr21:33687108-33687336(-)$1	228	50	54	11.9999
ffff	chr11:94607015-94607240(+)$1	225	109	113	11.9999
ffff	chr14:100835370-100835614(-)$1	244	79	83	11.9999
rddd	chr15:75094999-75095227(+)$1	228	134	138	11.9999
bb[b	chr16:28856190-28856418(-)$1	228	122	126	11.9999
::::	chr7:133977142-133977366(-)$1	224	128	132	11.9999
EEEE	chr1:23413140-23413375(-)$1	235	11	15	11.9999
EEEE	chr17:40352734-40352956(-)$1	222	24	28	11.9999
llle	chr12:49161491-49161725(-)$1	234	90	94	11.9999
FFFF	chr22:29191214-29191427(-)$1	213	3	7	11.9999
c]ff	chr9:112542603-112542819(+)$1	216	170	174	11.9999
eeee	chr15:42706718-42706956(-)$1	238	7	11	11.9999
rrrr	chr17:75084801-75085019(+)$1	218	125	129	11.9999
gggg	chr11:47491442-47491679(-)$1	237	118	122	11.9999
dddd	chr19:18679874-18680089(+)$1	215	152	156	11.9999
iiii	chrX:153671169-153671390(+)$1	221	46	50	11.9999
dddd	chr17:5012756-5012975(-)$1	219	13	17	11.9999
qfff	chr17:25950912-25951131(+)$1	219	55	59	11.9999
555f	chr17:76967829-76968052(-)$1	223	57	61	11.9999
fffe	chr15:64463171-64463389(-)$1	218	127	131	11.9999
bb]h	chr6:159187585-159187817(-)$1	232	197	201	11.9999
sddd	chr1:182352598-182352811(-)$1	213	74	78	11.9999
[a[g	chr11:6498303-6498525(-)$1	222	170	174	11.9999
::::	chr12:122631552-122631778(+)$1	226	127	131	11.9999
gg[a	chr4:39776418-39776642(+)$1	224	95	99	11.9999
FF{F	chr2:235963307-235963569(+)$1	262	52	56	11.9999
nnnb	chrX:153582658-153582884(-)$1	226	40	44	11.9999
::::	chr12:53682230-53682495(+)$1	265	39	43	11.9999
KEEE	chr1:27107724-27107944(+)$1	220	67	71	11.9999

#DB
((.(	chr19:41248373-41248616(-)$1	1	53	57	11.9999
.(((	chr22:39261007-39261230(-)$1	1	58	62	11.9999
((..	chr7:97481460-97481675(-)$1	1	182	186	11.9999
((..	chr17:27957395-27957612(-)$1	1	8	12	11.9999
))))	chr8:26364262-26364486(-)$1	1	209	213	11.9999
.(((	chr19:48956757-48956977(+)$1	1	20	24	11.9999
((((	chr16:4659039-4659256(-)$1	1	26	30	11.9999
))))	chr12:25359824-25360054(-)$1	1	25	29	11.9999
((((	chr2:220085884-220086111(-)$1	1	142	146	11.9999
(((.	chr10:93811563-93811783(-)$1	1	14	18	11.9999
((((	chr22:38668792-38669016(-)$1	1	71	75	11.9999
..))	chr10:73060021-73060245(+)$1	1	99	103	11.9999
(...	chr7:148981411-148981636(+)$1	1	36	40	11.9999
.(((	chr9:132572435-132572688(+)$1	1	68	72	11.9999
))))	chr4:2069402-2069627(+)$1	1	218	222	11.9999
((((	chr1:46125845-46126132(-)$1	1	120	124	11.9999
((.(	chr12:57926423-57926642(-)$1	1	57	61	11.9999
(((.	chr7:120496750-120496975(-)$1	1	164	168	11.9999
)).)	chr19:13873792-13874016(+)$1	1	79	83	11.9999
...)	chr12:117298301-117298534(-)$1	1	47	51	11.9999
((..	chr2:48031976-48032216(+)$1	1	147	151	11.9999
))))	chr19:16629195-16629424(-)$1	1	69	73	11.9999
...(	chr7:97836032-97836269(+)$1	1	142	146	11.9999
))).	chr14:55534776-55534994(+)$1	1	150	154	11.9999
).))	chr7:100031104-100031345(+)$1	1	98	102	11.9999
))..	chr8:1729963-1730177(+)$1	1	25	29	11.9999
))))	chr1:11847915-11848174(-)$1	1	206	210	11.9999
).((	chr13:30084773-30085001(-)$1	1	190	194	11.9999
.(((	chr13:30084083-30084314(-)$1	1	73	77	11.9999
((((	chr9:123525955-123526188(-)$1	1	82	86	11.9999
(...	chr21:45175848-45176085(+)$1	1	40	44	11.9999
.(((	chr3:100428272-100428492(+)$1	1	89	93	11.9999
((((	chr1:44088865-44089084(+)$1	1	0	4	11.9999
...)	chr20:2125532-2125767(+)$1	1	97	101	11.9999
...)	chr1:173991205-173991436(-)$1	1	104	108	11.9999
).).	chr9:123525804-123526032(-)$1	1	157	161	11.9999
.)).	chr6:27806325-27806538(+)$1	1	59	63	11.9999
))))	chr22:39912852-39913067(+)$1	1	189	193	11.9999
))))	chr6:31936130-31936354(+)$1	1	103	107	11.9999
))..	chrX:53406418-53406662(-)$1	1	73	77	11.9999
...)	chr8:124286293-124286516(-)$1	1	38	42	11.9999
....	chr9:132997030-132997256(+)$1	1	145	149	11.9999
((.(	chr14:24586807-24587022(+)$1	1	67	71	11.9999
....	chrX:153580158-153580485(-)$1	1	5	9	11.9999
....	chr3:15481053-15481283(+)$1	1	21	25	11.9999
((((	chr20:60709865-60710137(+)$1	1	32	36	11.9999
..((	chr2:220084040-220084307(-)$1	1	112	116	11.9999
.(((	chr17:42476733-42476964(-)$1	1	42	46	11.9999
.(((	chr12:54626590-54626826(-)$1	1	0	4	11.9999
.(((	chr4:15683405-15683621(+)$1	1	39	43	11.9999
....	chr3:47098771-47098991(-)$1	1	71	75	11.9999
.(((	chr21:33687108-33687336(-)$1	1	50	54	11.9999
))))	chr11:94607015-94607240(+)$1	1	109	113	11.9999
((((	chr14:100835370-100835614(-)$1	1	79	83	11.9999
.)))	chr15:75094999-75095227(+)$1	1	134	138	11.9999
((.(	chr16:28856190-28856418(-)$1	1	122	126	11.9999
....	chr7:133977142-133977366(-)$1	1	128	132	11.9999
((((	chr1:23413140-23413375(-)$1	1	11	15	11.9999
((((	chr17:40352734-40352956(-)$1	1	24	28	11.9999
...)	chr12:49161491-49161725(-)$1	1	90	94	11.9999
((((	chr22:29191214-29191427(-)$1	1	3	7	11.9999
).))	chr9:112542603-112542819(+)$1	1	170	174	11.9999
((((	chr15:42706718-42706956(-)$1	1	7	11	11.9999
....	chr17:75084801-75085019(+)$1	1	125	129	11.9999
((((	chr11:47491442-47491679(-)$1	1	118	122	11.9999
))((	chr19:18679874-18680089(+)$1	1	152	156	11.9999
))))	chrX:153671169-153671390(+)$1	1	46	50	11.9999
))))	chr17:5012756-5012975(-)$1	1	13	17	11.9999
.)))	chr17:25950912-25951131(+)$1	1	55	59	11.9999
...)	chr17:76967829-76968052(-)$1	1	57	61	11.9999
)))(	chr15:64463171-64463389(-)$1	1	127	131	11.9999
)).)	chr6:159187585-159187817(-)$1	1	197	201	11.9999
.)))	chr1:182352598-182352811(-)$1	1	74	78	11.9999
.(.(	chr11:6498303-6498525(-)$1	1	170	174	11.9999
....	chr12:122631552-122631778(+)$1	1	127	131	11.9999
((.(	chr4:39776418-39776642(+)$1	1	95	99	11.9999
((.(	chr2:235963307-235963569(+)$1	1	52	56	11.9999
...)	chrX:153582658-153582884(-)$1	1	40	44	11.9999
....	chr12:53682230-53682495(+)$1	1	39	43	11.9999
.(((	chr1:27107724-27107944(+)$1	1	67	71	11.9999

#PSSM
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	

#score	959.9999999999994
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m1_run1.nuc.txt

#NT
AUUUUGUUUU	chrX:11139970-11140191(+)$1	221	155	165	19.6551
AUUUUCUUUU	chr15:62145635-62145865(-)$1	230	59	69	19.0517
AUUUUCUUUU	chr6:158932255-158932473(+)$1	218	153	163	19.0517
AGUUUAUAUU	chr5:90665540-90665763(-)$1	223	71	81	13.4482
UUUUUAUUUU	chr20:4762850-4763075(-)$1	225	103	113	18.7931
UUUUUUUUUU	chr5:137274906-137275130(-)$1	224	205	215	17.5000
AUUAUAUCUU	chr3:113442202-113442421(-)$1	219	6	16	12.4137
AAUUUAUUUU	chr6:32948749-32948973(+)$1	224	103	113	17.3275
AAUUAAUUUU	chr1:78482726-78482951(+)$1	225	16	26	13.3620
AUUAUUUUUU	chr17:42269930-42270160(-)$1	230	128	138	15.3448
AUUUUCUUUU	chr8:81433737-81433957(+)$1	220	174	184	19.0517
AUUUUUGUUU	chr15:73044463-73044681(-)$1	218	187	197	15.7758
AUUUUCUUUC	chr8:38708674-38708904(+)$1	230	100	110	15.2586
AUUUAUUUUU	chr2:74381989-74382214(-)$1	225	52	62	15.9482
auguaAUUUU	chr5:175953906-175954136(-)$1	230	80	90	12.6724
GUUUUUUUUU	chr12:25362550-25362776(-)$1	226	210	220	17.2413
UUUUUAUAUU	chr7:20176578-20176799(-)$1	221	20	30	14.9137
CUUUUUUUUU	chr17:56050627-56050857(-)$1	230	175	185	17.2413
AUUUCAUUUC	chr6:159057471-159057682(-)$1	211	49	59	13.3620
AUUUUAUGUA	chr9:5775118-5775336(+)$1	218	202	212	13.1034
GUUCUAUUUU	chr13:51939403-51939623(-)$1	220	27	37	13.8793
UUUUGAUUUU	chr1:204522258-204522479(+)$1	221	63	73	14.9137
CUUUUGUUUU	chr9:123943132-123943351(-)$1	219	150	160	16.9827
AGUUCAUUUU	chr6:99847726-99847944(-)$1	218	88	98	13.2758
AUUUUGAUUU	chr20:17922715-17922940(-)$1	225	61	71	15.6896
AUUUUAAAUU	chr15:65953615-65953845(-)$1	230	87	97	13.3620
UUUUUGUUUU	chrX:106956679-106956909(-)$1	230	186	196	17.2413
AAUUUAUUUA	chr5:38940705-38940932(-)$1	227	60	70	13.3620
AUUUGUUUUU	chr3:182637081-182637305(+)$1	224	165	175	16.0344
AUUUUUUUCU	chr11:64532656-64532882(-)$1	226	79	89	15.1724
GUUUUAUUUC	chr22:38881217-38881438(-)$1	221	99	109	14.7413
UUUUUUUUUU	chr21:34809380-34809621(+)$1	241	56	66	17.5000
AUUUUUUUUU	chr6:32610874-32611100(+)$1	226	39	49	19.9137
CUUUUUUUUU	chr19:48714452-48714673(-)$1	221	181	191	17.2413
UUUUUUUUUU	chr7:100163449-100163679(+)$1	230	72	82	17.5000
AUUUUUUGUU	chr8:98735116-98735346(+)$1	230	160	170	15.7758
AUAUUACUUU	chr4:140309547-140309766(+)$1	219	29	39	12.6724
GUUUUGUUUU	chr7:20450230-20450477(+)$1	247	48	58	16.9827
AUUUUAUUGU	chr15:55648717-55648936(-)$1	219	59	69	16.4655
auuuuaauuu	chr3:183399464-183399694(+)$1	230	9	19	17.2413
CUUUUGUUUU	chr4:48138834-48139054(-)$1	220	116	126	16.9827
AGUUUGUUUU	chr7:93623149-93623374(-)$1	225	78	88	15.7758
AUUUUGUUUU	chr2:20449809-20450049(-)$1	240	53	63	19.6551
UAUUUAUUUU	chr15:52015679-52015900(-)$1	221	37	47	14.9137
CUUUUAUUUC	chr1:150548231-150548461(-)$1	230	107	117	14.7413
AUUUGAUUUC	chr8:37611786-37612008(+)$1	222	191	201	13.5344
GUUUUAUUUG	chr15:52100655-52100874(+)$1	219	181	191	14.3965
AUAUUAAUUU	chr10:49644871-49645101(+)$1	230	102	112	12.8448
AUUUGAUAUU	chr15:38644437-38644667(+)$1	230	94	104	13.4482
UUUUUAUUUA	chr5:32601554-32601784(+)$1	230	103	113	14.8275
AUUUUAUUUU	chr16:85955018-85955242(+)$1	224	105	115	21.2068
AUAUUAUUUU	chr12:83527777-83527994(+)$1	217	140	150	16.8103
GGUUUAUUUU	chr18:67993568-67993798(+)$1	230	115	125	14.6551
AUUUUGGUUU	chr17:38291084-38291306(-)$1	222	4	14	15.5172
AUUUUAUAUU	chr12:76747785-76748010(-)$1	225	60	70	17.3275
AUUUUGCUUU	chr2:215591852-215592075(-)$1	223	107	117	15.5172
ACUUUGUUUU	chr12:31535081-31535304(-)$1	223	144	154	15.5172

#otherMatches

#Struct PSSM
ccxxxxxxxx	chr20:5170910-5171132(+)$1	222	76	86	17.2413
mmdddd::::	chrX:11139970-11140191(+)$1	221	155	165	19.6551
wwwwwwwwww	chr15:62145635-62145865(-)$1	230	59	69	19.0517
CZZZHHHHHH	chr6:158932255-158932473(+)$1	218	153	163	19.0517
!!ddddllld	chr5:90665540-90665763(-)$1	223	71	81	13.4482
dddppppppp	chr20:4762850-4763075(-)$1	225	103	113	18.7931
::::::::::	chr5:137274906-137275130(-)$1	224	205	215	17.5000
:::::::::I	chr3:113442202-113442421(-)$1	219	6	16	12.4137
ccc22hhhhh	chr6:32948749-32948973(+)$1	224	103	113	17.3275
ffooooooff	chr1:78482726-78482951(+)$1	225	16	26	13.3620
iiii::::::	chr17:42269930-42270160(-)$1	230	128	138	15.3448
dooooooddd	chr8:81433737-81433957(+)$1	220	174	184	19.0517
e:JJJJJJJJ	chr15:73044463-73044681(-)$1	218	187	197	15.7758
boooooobb]	chr8:38708674-38708904(+)$1	230	100	110	15.2586
cqqqqqqqqc	chr2:74381989-74382214(-)$1	225	52	62	15.9482
==========	chr5:175953906-175954136(-)$1	230	80	90	12.6724
eooooooeee	chr12:25362550-25362776(-)$1	226	210	220	17.2413
hhhhhh:fff	chr7:20176578-20176799(-)$1	221	20	30	14.9137
ddd>>>>>>>	chr17:56050627-56050857(-)$1	230	175	185	17.2413
MMMHHHHHHH	chr6:159057471-159057682(-)$1	211	49	59	13.3620
IIIIIIII}C	chr9:5775118-5775336(+)$1	218	202	212	13.1034
ddd[bboooo	chr13:51939403-51939623(-)$1	220	27	37	13.8793
d####dddd$	chr1:204522258-204522479(+)$1	221	63	73	14.9137
eeeee:::::	chr9:123943132-123943351(-)$1	219	150	160	16.9827
ddd]eeeee:	chr6:99847726-99847944(-)$1	218	88	98	13.2758
[bb!!eeeee	chr20:17922715-17922940(-)$1	225	61	71	15.6896
JJJJJJJJJ{	chr15:65953615-65953845(-)$1	230	87	97	13.3620
ggggg$$$$$	chrX:106956679-106956909(-)$1	230	186	196	17.2413
:::::::::i	chr5:38940705-38940932(-)$1	227	60	70	13.3620
gggg[a####	chr3:182637081-182637305(+)$1	224	165	175	16.0344
eeee::::::	chr11:64532656-64532882(-)$1	226	79	89	15.1724
gggggdddd$	chr22:38881217-38881438(-)$1	221	99	109	14.7413
$$$$$ggggg	chr21:34809380-34809621(+)$1	241	56	66	17.5000
::::::::::	chr6:32610874-32611100(+)$1	226	39	49	19.9137
^^^^^^^^^^	chr19:48714452-48714673(-)$1	221	181	191	17.2413
==========	chr7:100163449-100163679(+)$1	230	72	82	17.5000
dddggggggg	chr8:98735116-98735346(+)$1	230	160	170	15.7758
ddd!!dddd#	chr4:140309547-140309766(+)$1	219	29	39	12.6724
FFFFFFPPPP	chr7:20450230-20450477(+)$1	247	48	58	16.9827
ggg>>>>>>>	chr15:55648717-55648936(-)$1	219	59	69	16.4655
::::::::::	chr3:183399464-183399694(+)$1	230	9	19	17.2413
:::::=====	chr4:48138834-48139054(-)$1	220	116	126	16.9827
EEFFFFFF{D	chr7:93623149-93623374(-)$1	225	78	88	15.7758
ii:::::fff	chr2:20449809-20450049(-)$1	240	53	63	19.6551
eee!!hhhhh	chr15:52015679-52015900(-)$1	221	37	47	14.9137
:::::eeeee	chr1:150548231-150548461(-)$1	230	107	117	14.7413
]ffffffeee	chr8:37611786-37612008(+)$1	222	191	201	13.5344
eee$$$$$dd	chr15:52100655-52100874(+)$1	219	181	191	14.3965
::::eeeeem	chr10:49644871-49645101(+)$1	230	102	112	12.8448
333dddd:::	chr15:38644437-38644667(+)$1	230	94	104	13.4482
::::::ffff	chr5:32601554-32601784(+)$1	230	103	113	14.8275
999dddd444	chr16:85955018-85955242(+)$1	224	105	115	21.2068
mffffff:::	chr12:83527777-83527994(+)$1	217	140	150	16.8103
4444dddd::	chr18:67993568-67993798(+)$1	230	115	125	14.6551
:::::FFFFF	chr17:38291084-38291306(-)$1	222	4	14	15.5172
++++++++++	chr12:76747785-76748010(-)$1	225	60	70	17.3275
:::::CCCKK	chr2:215591852-215592075(-)$1	223	107	117	15.5172
(((((ggggg	chr12:31535081-31535304(-)$1	223	144	154	15.5172

#DB
((........	chr20:5170910-5171132(+)$1	1	76	86	17.2413
..))))....	chrX:11139970-11140191(+)$1	1	155	165	19.6551
..........	chr15:62145635-62145865(-)$1	1	59	69	19.0517
)...))))))	chr6:158932255-158932473(+)$1	1	153	163	19.0517
..((((...)	chr5:90665540-90665763(-)$1	1	71	81	13.4482
(((.......	chr20:4762850-4763075(-)$1	1	103	113	18.7931
..........	chr5:137274906-137275130(-)$1	1	205	215	17.5000
.........(	chr3:113442202-113442421(-)$1	1	6	16	12.4137
)))..)))))	chr6:32948749-32948973(+)$1	1	103	113	17.3275
((......))	chr1:78482726-78482951(+)$1	1	16	26	13.3620
))))......	chr17:42269930-42270160(-)$1	1	128	138	15.3448
(......)))	chr8:81433737-81433957(+)$1	1	174	184	19.0517
).))))))))	chr15:73044463-73044681(-)$1	1	187	197	15.7758
(......)).	chr8:38708674-38708904(+)$1	1	100	110	15.2586
(........)	chr2:74381989-74382214(-)$1	1	52	62	15.9482
))))))))))	chr5:175953906-175954136(-)$1	1	80	90	12.6724
(......)))	chr12:25362550-25362776(-)$1	1	210	220	17.2413
)))))).(((	chr7:20176578-20176799(-)$1	1	20	30	14.9137
))).......	chr17:56050627-56050857(-)$1	1	175	185	17.2413
...(((((((	chr6:159057471-159057682(-)$1	1	49	59	13.3620
)))))))).)	chr9:5775118-5775336(+)$1	1	202	212	13.1034
(((.((....	chr13:51939403-51939623(-)$1	1	27	37	13.8793
(....((((.	chr1:204522258-204522479(+)$1	1	63	73	14.9137
))))).....	chr9:123943132-123943351(-)$1	1	150	160	16.9827
))).))))).	chr6:99847726-99847944(-)$1	1	88	98	13.2758
.((..(((((	chr20:17922715-17922940(-)$1	1	61	71	15.6896
(((((((((.	chr15:65953615-65953845(-)$1	1	87	97	13.3620
(((((.....	chrX:106956679-106956909(-)$1	1	186	196	17.2413
.........(	chr5:38940705-38940932(-)$1	1	60	70	13.3620
((((.(....	chr3:182637081-182637305(+)$1	1	165	175	16.0344
))))......	chr11:64532656-64532882(-)$1	1	79	89	15.1724
(((((((((.	chr22:38881217-38881438(-)$1	1	99	109	14.7413
.....(((((	chr21:34809380-34809621(+)$1	1	56	66	17.5000
..........	chr6:32610874-32611100(+)$1	1	39	49	19.9137
..........	chr19:48714452-48714673(-)$1	1	181	191	17.2413
((((((((((	chr7:100163449-100163679(+)$1	1	72	82	17.5000
))))))))))	chr8:98735116-98735346(+)$1	1	160	170	15.7758
(((..((((.	chr4:140309547-140309766(+)$1	1	29	39	12.6724
((((((....	chr7:20450230-20450477(+)$1	1	48	58	16.9827
))).......	chr15:55648717-55648936(-)$1	1	59	69	16.4655
..........	chr3:183399464-183399694(+)$1	1	9	19	17.2413
.....(((((	chr4:48138834-48139054(-)$1	1	116	126	16.9827
((((((((.(	chr7:93623149-93623374(-)$1	1	78	88	15.7758
)).....(((	chr2:20449809-20450049(-)$1	1	53	63	19.6551
(((..(((((	chr15:52015679-52015900(-)$1	1	37	47	14.9137
.....(((((	chr1:150548231-150548461(-)$1	1	107	117	14.7413
.))))))(((	chr8:37611786-37612008(+)$1	1	191	201	13.5344
(((.....((	chr15:52100655-52100874(+)$1	1	181	191	14.3965
....(((((.	chr10:49644871-49645101(+)$1	1	102	112	12.8448
...))))...	chr15:38644437-38644667(+)$1	1	94	104	13.4482
......((((	chr5:32601554-32601784(+)$1	1	103	113	14.8275
...))))...	chr16:85955018-85955242(+)$1	1	105	115	21.2068
.))))))...	chr12:83527777-83527994(+)$1	1	140	150	16.8103
....))))..	chr18:67993568-67993798(+)$1	1	115	125	14.6551
.....(((((	chr17:38291084-38291306(-)$1	1	4	14	15.5172
..........	chr12:76747785-76748010(-)$1	1	60	70	17.3275
.....(((..	chr2:215591852-215592075(-)$1	1	107	117	15.5172
.....(((((	chr12:31535081-31535304(-)$1	1	144	154	15.5172

#PSSM
A : 0.60	U : 0.15	C : 0.10	G : 0.10	a : 0.03	
U : 0.81	G : 0.06	A : 0.06	u : 0.03	C : 0.01	
U : 0.91	A : 0.05	g : 0.01	u : 0.01	
U : 0.91	A : 0.03	u : 0.03	C : 0.01	
U : 0.82	G : 0.06	A : 0.03	C : 0.03	a : 0.01	u : 0.01	
A : 0.48	U : 0.24	G : 0.18	C : 0.06	a : 0.01	
U : 0.86	A : 0.05	G : 0.03	C : 0.03	a : 0.01	
U : 0.84	A : 0.08	G : 0.03	C : 0.01	u : 0.01	
U : 0.94	C : 0.01	G : 0.01	u : 0.01	
U : 0.82	C : 0.08	A : 0.05	u : 0.01	G : 0.01	

#score	921.379310344828
#seq	58
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUAUUUUA	chr1:19232920-19233149(-)$1	229	49	59	18.9814
UUUUCUUUUU	chr2:164461054-164461281(-)$1	227	65	75	19.8148
UUUUGUUUUC	chr10:32298561-32298785(-)$1	224	133	143	21.2962
uuuuguuuug	chr15:85348824-85349058(+)$1	234	152	162	21.3888
uuuuuuauuu	chr12:75895417-75895655(-)$1	238	39	49	16.1111
UUUUGUUAUG	chr5:151184806-151185050(+)$1	244	16	26	16.8518
GUUUGUUUUG	chr17:26655050-26655280(+)$1	230	208	218	17.2222
UUUUGUCUUA	chr21:40567978-40568204(-)$1	226	95	105	17.4999
uuuuguauuu	chr2:179374358-179374583(+)$1	225	14	24	18.3333
UUUAGUUUUG	chr1:226548571-226548798(-)$1	227	26	36	16.5740
uuuuuuuuuu	chr19:1554862-1555085(-)$1	223	158	168	20.0925
UUUUUUUUUC	chr9:104152469-104152705(-)$1	236	101	111	19.0740
UUUUUUAUUU	chr14:67850052-67850292(+)$1	240	210	220	16.1111
UUUUAUUUUA	chr17:18785819-18786045(+)$1	226	195	205	18.9814
UUUUGUUUUG	chr1:154556873-154557140(-)$1	267	167	177	21.3888
UUAUGUUUUC	chr22:45583118-45583350(+)$1	232	68	78	16.8518
UUUUAUUUUG	chr16:12758592-12758824(-)$1	232	123	133	18.8888
guuuguuuuc	chr17:65979443-65979664(+)$1	221	185	195	17.1296
UUUUGUUUUG	chr1:198289080-198289306(+)$1	226	207	217	21.3888
UUUUUUUUUU	chr1:225683454-225683685(-)$1	231	46	56	20.0925
UCUUGUUUUU	chr17:62522191-62522413(+)$1	222	132	142	17.7777
UUCUGUUUUA	chr2:37208332-37208558(-)$1	226	11	21	17.0370
UUUUGUCUUC	chr15:44086495-44086717(+)$1	222	191	201	17.3148
UUCUGUUUUA	chr5:180669161-180669445(-)$1	284	80	90	17.0370
UUUUCUUUUU	chr3:100295951-100296172(+)$1	221	68	78	19.8148
UUUUGUUAUU	chr14:51101573-51101800(-)$1	227	32	42	17.7777
UUAUGUUUUA	chr11:85372329-85372550(-)$1	221	130	140	17.0370
UUUUGUUUUA	chr3:127788686-127788913(+)$1	227	95	105	21.4814
CUUUGUUUUC	chr2:109501726-109501959(+)$1	233	4	14	16.9444
UUUUCUUUUG	chr2:74185899-74186125(+)$1	226	126	136	18.8888
UUUUCUUUUU	chr17:42884694-42884918(-)$1	224	62	72	19.8148
UUUUUUUUUA	chr19:10427710-10427937(-)$1	227	200	210	19.2592
UUUUAUUUUA	chr13:39623928-39624167(+)$1	239	72	82	18.9814
UUUUGGUUUA	chr11:102269328-102269551(-)$1	223	7	17	16.7592
UUUUGUUUUU	chr11:108342785-108343008(-)$1	223	181	191	22.3148
UUUUGUGUUU	chr2:87001389-87001613(+)$1	224	169	179	18.2407
UUUUGUUUGU	chr11:14300030-14300255(-)$1	225	165	175	17.4999
uuuuauuuuC	chr11:118394345-118394573(+)$1	228	59	69	18.7962
uauuguuuuu	chr3:120114981-120115215(-)$1	234	129	139	17.9629
UUUUGUUCUA	chr6:70500139-70500385(-)$1	246	5	15	16.8518
GUUUGUUUUU	chr11:65763927-65764154(-)$1	227	174	184	18.1481
UUUUUUUUUU	chr11:63971743-63971971(+)$1	228	137	147	20.0925
AUUUGUUUUC	chr1:38002923-38003170(-)$1	247	46	56	17.0370
UUUUUUUUUU	chr6:135285912-135286181(-)$1	269	202	212	20.0925
uuuugucuuc	chrX:152613415-152613639(+)$1	224	108	118	17.3148
uauuguuuua	chr14:53106752-53106980(-)$1	228	69	79	17.1296
UUUUCUUUUU	chr11:1296101-1296333(-)$1	232	29	39	19.8148
UUUUCUUUUU	chr17:34069065-34069292(+)$1	227	47	57	19.8148
UUUUGAUUUG	chr2:105476190-105476434(+)$1	244	2	12	16.6666
UUUUGUGUUU	chr10:60154833-60155072(+)$1	239	199	209	18.2407
UUUUGUUUUG	chr1:156046000-156046232(-)$1	232	154	164	21.3888
UUUUUUUUUC	chr22:29696274-29696497(+)$1	223	62	72	19.0740
UAUUGUUUUG	chr13:98120072-98120297(+)$1	225	38	48	17.0370

#otherMatches

#Struct PSSM
a]ggggggg:	chr5:7900629-7900872(+)$1	243	118	128	15.5555
ppppppffff	chr1:19232920-19233149(-)$1	229	49	59	18.9814
^^^^^^^^^^	chr2:164461054-164461281(-)$1	227	65	75	19.8148
ddd:ffffff	chr10:32298561-32298785(-)$1	224	133	143	21.2962
gggoooooog	chr15:85348824-85349058(+)$1	234	152	162	21.3888
pppppdddd4	chr12:75895417-75895655(-)$1	238	39	49	16.1111
d:::::::EE	chr5:151184806-151185050(+)$1	244	16	26	16.8518
hhhhhh333e	chr17:26655050-26655280(+)$1	230	208	218	17.2222
dd22ccc:::	chr21:40567978-40568204(-)$1	226	95	105	17.4999
::::::::::	chr2:179374358-179374583(+)$1	225	14	24	18.3333
dddd[hhhhh	chr1:226548571-226548798(-)$1	227	26	36	16.5740
hhhhhhh!!h	chr19:1554862-1555085(-)$1	223	158	168	20.0925
xxxxxxffff	chr9:104152469-104152705(-)$1	236	101	111	19.0740
::::IIIIII	chr14:67850052-67850292(+)$1	240	210	220	16.1111
FFFF}FFFFF	chr17:18785819-18786045(+)$1	226	195	205	18.9814
ooooofffff	chr1:154556873-154557140(-)$1	267	167	177	21.3888
333bb4444e	chr22:45583118-45583350(+)$1	232	68	78	16.8518
hh[ffffffb	chr16:12758592-12758824(-)$1	232	123	133	18.8888
ffffff333c	chr17:65979443-65979664(+)$1	221	185	195	17.1296
iiiiiiiii:	chr1:198289080-198289306(+)$1	226	207	217	21.3888
qqqqqqqqii	chr1:225683454-225683685(-)$1	231	46	56	20.0925
iiiiiiiiib	chr17:62522191-62522413(+)$1	222	132	142	17.7777
b[dddd!!dd	chr2:37208332-37208558(-)$1	226	11	21	17.0370
>>>>>>>>>>	chr15:44086495-44086717(+)$1	222	191	201	17.3148
:ccc!!dddd	chr5:180669161-180669445(-)$1	284	80	90	17.0370
=====ttttt	chr3:100295951-100296172(+)$1	221	68	78	19.8148
FFFDDDD::d	chr14:51101573-51101800(-)$1	227	32	42	17.7777
::::::::::	chr11:85372329-85372550(-)$1	221	130	140	17.0370
mmmmccc333	chr3:127788686-127788913(+)$1	227	95	105	21.4814
DDDKKEEEEE	chr2:109501726-109501959(+)$1	233	4	14	16.9444
hhhhh"""cc	chr2:74185899-74186125(+)$1	226	126	136	18.8888
ffffff!!gg	chr17:42884694-42884918(-)$1	224	62	72	19.8148
^^^^^^^^^^	chr19:10427710-10427937(-)$1	227	200	210	19.2592
gggggg"""f	chr13:39623928-39624167(+)$1	239	72	82	18.9814
:::ffffff&	chr11:102269328-102269551(-)$1	223	7	17	16.7592
::EEEEEGGG	chr11:108342785-108343008(-)$1	223	181	191	22.3148
====]a4444	chr2:87001389-87001613(+)$1	224	169	179	18.2407
ffffddddqq	chr11:14300030-14300255(-)$1	225	165	175	17.4999
gggg]bb444	chr11:118394345-118394573(+)$1	228	59	69	18.7962
ffqqqqqqqq	chr3:120114981-120115215(-)$1	234	129	139	17.9629
:::::ccc!!	chr6:70500139-70500385(-)$1	246	5	15	16.8518
==========	chr11:65763927-65764154(-)$1	227	174	184	18.1481
::::::::::	chr11:63971743-63971971(+)$1	228	137	147	20.0925
ee::ffffff	chr1:38002923-38003170(-)$1	247	46	56	17.0370
======="""	chr6:135285912-135286181(-)$1	269	202	212	20.0925
::::eeeeeb	chrX:152613415-152613639(+)$1	224	108	118	17.3148
::::::::::	chr14:53106752-53106980(-)$1	228	69	79	17.1296
^^^^^^^^^^	chr11:1296101-1296333(-)$1	232	29	39	19.8148
"""ccctttt	chr17:34069065-34069292(+)$1	227	47	57	19.8148
:GGGGGGGdd	chr2:105476190-105476434(+)$1	244	2	12	16.6666
hhhhha[eee	chr10:60154833-60155072(+)$1	239	199	209	18.2407
mmmmeeeeeb	chr1:156046000-156046232(-)$1	232	154	164	21.3888
hhhh$$$$$a	chr22:29696274-29696497(+)$1	223	62	72	19.0740
nnffffff66	chr13:98120072-98120297(+)$1	225	38	48	17.0370

#DB
).))))))).	chr5:7900629-7900872(+)$1	1	118	128	15.5555
......))))	chr1:19232920-19233149(-)$1	1	49	59	18.9814
..........	chr2:164461054-164461281(-)$1	1	65	75	19.8148
))).((((((	chr10:32298561-32298785(-)$1	1	133	143	21.2962
(((......)	chr15:85348824-85349058(+)$1	1	152	162	21.3888
.....)))).	chr12:75895417-75895655(-)$1	1	39	49	16.1111
).......((	chr5:151184806-151185050(+)$1	1	16	26	16.8518
))))))...)	chr17:26655050-26655280(+)$1	1	208	218	17.2222
))..)))...	chr21:40567978-40568204(-)$1	1	95	105	17.4999
..........	chr2:179374358-179374583(+)$1	1	14	24	18.3333
((((.(((((	chr1:226548571-226548798(-)$1	1	26	36	16.5740
(((((((..(	chr19:1554862-1555085(-)$1	1	158	168	20.0925
......))))	chr9:104152469-104152705(-)$1	1	101	111	19.0740
....))))))	chr14:67850052-67850292(+)$1	1	210	220	16.1111
)))).)))))	chr17:18785819-18786045(+)$1	1	195	205	18.9814
.....)))))	chr1:154556873-154557140(-)$1	1	167	177	21.3888
...))....)	chr22:45583118-45583350(+)$1	1	68	78	16.8518
((.(((((((	chr16:12758592-12758824(-)$1	1	123	133	18.8888
))))))...)	chr17:65979443-65979664(+)$1	1	185	195	17.1296
))))))))).	chr1:198289080-198289306(+)$1	1	207	217	21.3888
........))	chr1:225683454-225683685(-)$1	1	46	56	20.0925
))))))))))	chr17:62522191-62522413(+)$1	1	132	142	17.7777
(.((((..((	chr2:37208332-37208558(-)$1	1	11	21	17.0370
..........	chr15:44086495-44086717(+)$1	1	191	201	17.3148
.(((..((((	chr5:180669161-180669445(-)$1	1	80	90	17.0370
(((((.....	chr3:100295951-100296172(+)$1	1	68	78	19.8148
(((((((..(	chr14:51101573-51101800(-)$1	1	32	42	17.7777
..........	chr11:85372329-85372550(-)$1	1	130	140	17.0370
....)))...	chr3:127788686-127788913(+)$1	1	95	105	21.4814
(((..(((((	chr2:109501726-109501959(+)$1	1	4	14	16.9444
(((((...((	chr2:74185899-74186125(+)$1	1	126	136	18.8888
((((((..((	chr17:42884694-42884918(-)$1	1	62	72	19.8148
..........	chr19:10427710-10427937(-)$1	1	200	210	19.2592
((((((...(	chr13:39623928-39624167(+)$1	1	72	82	18.9814
...((((((.	chr11:102269328-102269551(-)$1	1	7	17	16.7592
..))))))))	chr11:108342785-108343008(-)$1	1	181	191	22.3148
)))).)....	chr2:87001389-87001613(+)$1	1	169	179	18.2407
))))((((..	chr11:14300030-14300255(-)$1	1	165	175	17.4999
)))).))...	chr11:118394345-118394573(+)$1	1	59	69	18.7962
((........	chr3:120114981-120115215(-)$1	1	129	139	17.9629
.....(((..	chr6:70500139-70500385(-)$1	1	5	15	16.8518
))))))))))	chr11:65763927-65764154(-)$1	1	174	184	18.1481
..........	chr11:63971743-63971971(+)$1	1	137	147	20.0925
))..((((((	chr1:38002923-38003170(-)$1	1	46	56	17.0370
(((((((...	chr6:135285912-135286181(-)$1	1	202	212	20.0925
....((((((	chrX:152613415-152613639(+)$1	1	108	118	17.3148
..........	chr14:53106752-53106980(-)$1	1	69	79	17.1296
..........	chr11:1296101-1296333(-)$1	1	29	39	19.8148
...(((....	chr17:34069065-34069292(+)$1	1	47	57	19.8148
.(((((((((	chr2:105476190-105476434(+)$1	1	2	12	16.6666
((((((.(((	chr10:60154833-60155072(+)$1	1	199	209	18.2407
....)))))(	chr1:156046000-156046232(-)$1	1	154	164	21.3888
((((.....(	chr22:29696274-29696497(+)$1	1	62	72	19.0740
..))))))..	chr13:98120072-98120297(+)$1	1	38	48	17.0370

#PSSM
U : 0.74	u : 0.14	A : 0.03	G : 0.03	g : 0.01	C : 0.01	
U : 0.79	u : 0.12	a : 0.03	C : 0.01	A : 0.01	
U : 0.75	u : 0.16	A : 0.03	C : 0.03	
U : 0.81	u : 0.16	A : 0.01	
G : 0.49	U : 0.12	C : 0.11	g : 0.11	A : 0.09	u : 0.03	a : 0.01	
U : 0.79	u : 0.16	G : 0.01	A : 0.01	
U : 0.74	u : 0.11	a : 0.03	C : 0.03	G : 0.03	A : 0.01	c : 0.01	
U : 0.77	u : 0.16	A : 0.03	C : 0.01	
U : 0.81	u : 0.16	G : 0.01	
U : 0.31	A : 0.20	G : 0.18	C : 0.14	u : 0.07	c : 0.03	g : 0.01	a : 0.01	

#score	999.0740740740735
#seq	54
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m1_run1.nuc.txt

#NT
UUC	chr5:71403228-71403447(+)$1	219	48	51	9.0000
UUC	chr6:38644120-38644370(-)$1	250	4	7	9.0000
UUC	chr5:137087246-137087497(-)$1	251	68	71	9.0000
UUC	chr16:3724239-3724483(-)$1	244	39	42	9.0000
UUC	chr9:95060492-95060718(-)$1	226	12	15	9.0000
UUC	chr3:51431512-51431738(+)$1	226	4	7	9.0000
UUC	chr8:23146430-23146689(+)$1	259	78	81	9.0000
UUC	chr19:10791661-10791905(+)$1	244	19	22	9.0000
UUC	chr12:96252652-96252872(+)$1	220	92	95	9.0000
UUC	chr17:76219859-76220098(+)$1	239	42	45	9.0000
UUC	chr16:2551226-2551467(+)$1	241	0	3	9.0000
UUC	chr5:31554638-31554887(+)$1	249	2	5	9.0000
UUC	chr5:10250333-10250612(+)$1	279	61	64	9.0000
UUC	chr5:133291189-133291417(-)$1	228	83	86	9.0000
UUC	chr19:2426464-2426729(-)$1	265	18	21	9.0000
UUC	chr19:19638006-19638259(+)$1	253	68	71	9.0000
UUC	chr19:49999583-49999827(+)$1	244	37	40	9.0000
UUC	chr11:763692-763925(+)$1	233	25	28	9.0000
UUC	chr12:57625490-57625743(+)$1	253	154	157	9.0000
UUC	chr20:2443640-2443914(-)$1	274	11	14	9.0000
UUC	chr1:159888345-159888577(-)$1	232	62	65	9.0000
UUC	chr16:67473111-67473337(-)$1	226	44	47	9.0000
UUC	chr14:76117336-76117573(-)$1	237	8	11	9.0000
UUC	chr19:2430742-2430971(-)$1	229	0	3	9.0000
UUC	chr3:23961435-23961738(+)$1	303	47	50	9.0000
UUC	chr14:23495218-23495471(-)$1	253	200	203	9.0000
UUC	chr19:34960554-34960805(+)$1	251	96	99	9.0000
UUC	chr1:245006893-245007128(-)$1	235	33	36	9.0000
UUC	chr19:33204537-33204767(+)$1	230	37	40	9.0000
UUC	chr1:41157339-41157569(+)$1	230	73	76	9.0000
UUC	chr1:235506137-235506379(+)$1	242	40	43	9.0000
UUC	chr12:112845999-112846239(-)$1	240	63	66	9.0000
UUC	chrX:153580671-153580898(-)$1	227	188	191	9.0000
UUC	chr1:245017554-245017778(-)$1	224	56	59	9.0000
UUC	chr17:6920143-6920406(+)$1	263	78	81	9.0000
UUC	chr8:37556990-37557227(+)$1	237	34	37	9.0000
UUC	chr5:79277869-79278109(-)$1	240	20	23	9.0000
UUC	chr19:16630860-16631103(-)$1	243	17	20	9.0000
UUC	chr5:162871409-162871639(+)$1	230	16	19	9.0000
UUC	chr3:128889143-128889390(-)$1	247	100	103	9.0000
UUC	chr7:102097669-102097915(-)$1	246	54	57	9.0000
UUC	chr15:72491928-72492164(-)$1	236	53	56	9.0000
UUC	chr19:47112361-47112591(+)$1	230	8	11	9.0000
UUC	chr19:8468575-8468806(+)$1	231	174	177	9.0000
UUC	chr7:100875422-100875648(-)$1	226	25	28	9.0000
UUC	chr4:122744775-122745009(-)$1	234	38	41	9.0000
UUC	chr17:76166823-76167055(+)$1	232	77	80	9.0000
UUC	chr6:80982760-80982988(+)$1	228	55	58	9.0000
UUC	chr3:124456670-124456896(+)$1	226	35	38	9.0000
UUC	chrX:47088792-47089044(+)$1	252	9	12	9.0000
UUC	chr21:44520481-44520703(-)$1	222	38	41	9.0000
UUC	chr9:116170651-116170891(-)$1	240	2	5	9.0000
UUC	chr10:7830073-7830318(+)$1	245	40	43	9.0000
UUC	chr1:205683571-205683851(-)$1	280	43	46	9.0000
UUC	chr17:73389569-73389823(-)$1	254	53	56	9.0000
UUC	chr20:44445347-44445625(+)$1	278	100	103	9.0000
UUC	chr10:129897182-129897428(-)$1	246	24	27	9.0000
UUC	chr19:33790743-33790973(-)$1	230	52	55	9.0000
UUC	chr20:2446304-2446542(-)$1	238	55	58	9.0000
UUC	chr19:17449667-17449901(+)$1	234	4	7	9.0000
UUC	chr17:41154617-41154851(+)$1	234	121	124	9.0000
UUC	chr19:42365141-42365381(+)$1	240	18	21	9.0000
UUC	chr15:75122573-75122799(+)$1	226	30	33	9.0000
UUC	chr12:74934568-74934798(+)$1	230	10	13	9.0000
UUC	chr3:197680774-197681006(+)$1	232	71	74	9.0000
UUC	chr17:46147889-46148117(-)$1	228	5	8	9.0000
UUC	chr17:41154653-41154894(+)$1	241	85	88	9.0000
UUC	chr6:43752782-43753018(+)$1	236	29	32	9.0000
UUC	chr3:169712040-169712271(+)$1	231	37	40	9.0000
UUC	chrX:23801219-23801524(+)$1	305	30	33	9.0000
UUC	chr10:95288313-95288551(+)$1	238	76	79	9.0000
UUC	chr12:6977932-6978160(+)$1	228	54	57	9.0000
UUC	chr1:20978671-20978899(-)$1	228	209	212	9.0000
UUC	chr5:130762207-130762433(-)$1	226	184	187	9.0000
UUC	chr1:183522164-183522385(+)$1	221	73	76	9.0000
UUC	chr5:180665108-180665338(-)$1	230	20	23	9.0000
UUC	chr17:38153709-38153958(+)$1	249	116	119	9.0000
UUC	chr10:75010432-75010671(-)$1	239	10	13	9.0000
UUC	chr20:48506982-48507207(+)$1	225	26	29	9.0000
UUC	chr11:10826364-10826592(-)$1	228	15	18	9.0000
UUC	chr1:46073313-46073544(+)$1	231	4	7	9.0000
uuc	chr5:167976618-167976849(-)$1	231	31	34	9.0000
uuc	chr19:39395586-39395810(+)$1	224	7	10	9.0000
UUC	chr20:48569630-48569857(+)$1	227	13	16	9.0000
uuc	chr10:75003138-75003368(-)$1	230	4	7	9.0000
UUC	chr5:140699946-140700183(-)$1	237	49	52	9.0000
UUC	chr13:25910138-25910362(+)$1	224	24	27	9.0000
UUC	chr7:44253281-44253508(+)$1	227	93	96	9.0000
UUC	chr16:29822010-29822298(+)$1	288	91	94	9.0000
UUC	chr6:26199353-26199579(-)$1	226	14	17	9.0000
UUC	chr16:28846570-28846810(+)$1	240	6	9	9.0000
UUC	chr6:109689389-109689633(-)$1	244	10	13	9.0000
UUC	chr11:64536437-64536673(-)$1	236	39	42	9.0000
UUC	chr11:75115778-75116008(+)$1	230	178	181	9.0000
UUC	chr16:2012782-2013009(-)$1	227	14	17	9.0000
uuc	chr8:37917327-37917551(+)$1	224	11	14	9.0000
UUC	chr8:17094641-17094870(-)$1	229	92	95	9.0000
UUC	chr22:39900396-39900620(+)$1	224	20	23	9.0000
UUC	chr12:50383230-50383460(-)$1	230	109	112	9.0000

#otherMatches

#Struct PSSM
JJJ	chr16:417450-417685(-)$1	235	49	52	9.0000
:dd	chr5:71403228-71403447(+)$1	219	48	51	9.0000
eee	chr6:38644120-38644370(-)$1	250	4	7	9.0000
f33	chr5:137087246-137087497(-)$1	251	68	71	9.0000
ccd	chr16:3724239-3724483(-)$1	244	39	42	9.0000
fdd	chr9:95060492-95060718(-)$1	226	12	15	9.0000
:::	chr3:51431512-51431738(+)$1	226	4	7	9.0000
HHH	chr8:23146430-23146689(+)$1	259	78	81	9.0000
GGG	chr19:10791661-10791905(+)$1	244	19	22	9.0000
:gg	chr12:96252652-96252872(+)$1	220	92	95	9.0000
^^^	chr17:76219859-76220098(+)$1	239	42	45	9.0000
::e	chr16:2551226-2551467(+)$1	241	0	3	9.0000
:::	chr5:31554638-31554887(+)$1	249	2	5	9.0000
eee	chr5:10250333-10250612(+)$1	279	61	64	9.0000
ggg	chr5:133291189-133291417(-)$1	228	83	86	9.0000
{DD	chr19:2426464-2426729(-)$1	265	18	21	9.0000
2ee	chr19:19638006-19638259(+)$1	253	68	71	9.0000
qqq	chr19:49999583-49999827(+)$1	244	37	40	9.0000
]dd	chr11:763692-763925(+)$1	233	25	28	9.0000
[dd	chr12:57625490-57625743(+)$1	253	154	157	9.0000
GGG	chr20:2443640-2443914(-)$1	274	11	14	9.0000
eee	chr1:159888345-159888577(-)$1	232	62	65	9.0000
hhh	chr16:67473111-67473337(-)$1	226	44	47	9.0000
:::	chr14:76117336-76117573(-)$1	237	8	11	9.0000
:::	chr19:2430742-2430971(-)$1	229	0	3	9.0000
eee	chr3:23961435-23961738(+)$1	303	47	50	9.0000
777	chr14:23495218-23495471(-)$1	253	200	203	9.0000
::c	chr19:34960554-34960805(+)$1	251	96	99	9.0000
DDD	chr1:245006893-245007128(-)$1	235	33	36	9.0000
ccc	chr19:33204537-33204767(+)$1	230	37	40	9.0000
ccc	chr1:41157339-41157569(+)$1	230	73	76	9.0000
qqq	chr1:235506137-235506379(+)$1	242	40	43	9.0000
ccc	chr12:112845999-112846239(-)$1	240	63	66	9.0000
Cbb	chrX:153580671-153580898(-)$1	227	188	191	9.0000
qbb	chr1:245017554-245017778(-)$1	224	56	59	9.0000
iii	chr17:6920143-6920406(+)$1	263	78	81	9.0000
qqq	chr8:37556990-37557227(+)$1	237	34	37	9.0000
ee[	chr5:79277869-79278109(-)$1	240	20	23	9.0000
ddd	chr19:16630860-16631103(-)$1	243	17	20	9.0000
HHH	chr5:162871409-162871639(+)$1	230	16	19	9.0000
eee	chr3:128889143-128889390(-)$1	247	100	103	9.0000
JJJ	chr7:102097669-102097915(-)$1	246	54	57	9.0000
iii	chr15:72491928-72492164(-)$1	236	53	56	9.0000
###	chr19:47112361-47112591(+)$1	230	8	11	9.0000
ggg	chr19:8468575-8468806(+)$1	231	174	177	9.0000
::e	chr7:100875422-100875648(-)$1	226	25	28	9.0000
eee	chr4:122744775-122745009(-)$1	234	38	41	9.0000
===	chr17:76166823-76167055(+)$1	232	77	80	9.0000
555	chr6:80982760-80982988(+)$1	228	55	58	9.0000
ggg	chr3:124456670-124456896(+)$1	226	35	38	9.0000
ggg	chrX:47088792-47089044(+)$1	252	9	12	9.0000
!bb	chr21:44520481-44520703(-)$1	222	38	41	9.0000
:::	chr9:116170651-116170891(-)$1	240	2	5	9.0000
===	chr10:7830073-7830318(+)$1	245	40	43	9.0000
2dd	chr1:205683571-205683851(-)$1	280	43	46	9.0000
C{E	chr17:73389569-73389823(-)$1	254	53	56	9.0000
:::	chr20:44445347-44445625(+)$1	278	100	103	9.0000
!!b	chr10:129897182-129897428(-)$1	246	24	27	9.0000
iii	chr19:33790743-33790973(-)$1	230	52	55	9.0000
:hh	chr20:2446304-2446542(-)$1	238	55	58	9.0000
ddd	chr19:17449667-17449901(+)$1	234	4	7	9.0000
h]e	chr17:41154617-41154851(+)$1	234	121	124	9.0000
ppp	chr19:42365141-42365381(+)$1	240	18	21	9.0000
nnn	chr15:75122573-75122799(+)$1	226	30	33	9.0000
RRR	chr12:74934568-74934798(+)$1	230	10	13	9.0000
BB{	chr3:197680774-197681006(+)$1	232	71	74	9.0000
!cc	chr17:46147889-46148117(-)$1	228	5	8	9.0000
h]e	chr17:41154653-41154894(+)$1	241	85	88	9.0000
ddd	chr6:43752782-43753018(+)$1	236	29	32	9.0000
ddd	chr3:169712040-169712271(+)$1	231	37	40	9.0000
f$$	chrX:23801219-23801524(+)$1	305	30	33	9.0000
+++	chr10:95288313-95288551(+)$1	238	76	79	9.0000
ooo	chr12:6977932-6978160(+)$1	228	54	57	9.0000
2cc	chr1:20978671-20978899(-)$1	228	209	212	9.0000
JJJ	chr5:130762207-130762433(-)$1	226	184	187	9.0000
EEE	chr1:183522164-183522385(+)$1	221	73	76	9.0000
c[c	chr5:180665108-180665338(-)$1	230	20	23	9.0000
iii	chr17:38153709-38153958(+)$1	249	116	119	9.0000
ggg	chr10:75010432-75010671(-)$1	239	10	13	9.0000
BKK	chr20:48506982-48507207(+)$1	225	26	29	9.0000
JJJ	chr11:10826364-10826592(-)$1	228	15	18	9.0000
fff	chr1:46073313-46073544(+)$1	231	4	7	9.0000
GGG	chr5:167976618-167976849(-)$1	231	31	34	9.0000
:::	chr19:39395586-39395810(+)$1	224	7	10	9.0000
{CC	chr20:48569630-48569857(+)$1	227	13	16	9.0000
FFF	chr10:75003138-75003368(-)$1	230	4	7	9.0000
EEE	chr5:140699946-140700183(-)$1	237	49	52	9.0000
ppp	chr13:25910138-25910362(+)$1	224	24	27	9.0000
ooc	chr7:44253281-44253508(+)$1	227	93	96	9.0000
hhh	chr16:29822010-29822298(+)$1	288	91	94	9.0000
:::	chr6:26199353-26199579(-)$1	226	14	17	9.0000
HHH	chr16:28846570-28846810(+)$1	240	6	9	9.0000
fff	chr6:109689389-109689633(-)$1	244	10	13	9.0000
coo	chr11:64536437-64536673(-)$1	236	39	42	9.0000
e::	chr11:75115778-75116008(+)$1	230	178	181	9.0000
ppp	chr16:2012782-2013009(-)$1	227	14	17	9.0000
:::	chr8:37917327-37917551(+)$1	224	11	14	9.0000
c[c	chr8:17094641-17094870(-)$1	229	92	95	9.0000
iii	chr22:39900396-39900620(+)$1	224	20	23	9.0000
&&&	chr12:50383230-50383460(-)$1	230	109	112	9.0000

#DB
(((	chr16:417450-417685(-)$1	1	49	52	9.0000
.((	chr5:71403228-71403447(+)$1	1	48	51	9.0000
(((	chr6:38644120-38644370(-)$1	1	4	7	9.0000
)..	chr5:137087246-137087497(-)$1	1	68	71	9.0000
)))	chr16:3724239-3724483(-)$1	1	39	42	9.0000
(((	chr9:95060492-95060718(-)$1	1	12	15	9.0000
...	chr3:51431512-51431738(+)$1	1	4	7	9.0000
(((	chr8:23146430-23146689(+)$1	1	78	81	9.0000
(((	chr19:10791661-10791905(+)$1	1	19	22	9.0000
.((	chr12:96252652-96252872(+)$1	1	92	95	9.0000
...	chr17:76219859-76220098(+)$1	1	42	45	9.0000
..(	chr16:2551226-2551467(+)$1	1	0	3	9.0000
...	chr5:31554638-31554887(+)$1	1	2	5	9.0000
(((	chr5:10250333-10250612(+)$1	1	61	64	9.0000
(((	chr5:133291189-133291417(-)$1	1	83	86	9.0000
.((	chr19:2426464-2426729(-)$1	1	18	21	9.0000
.))	chr19:19638006-19638259(+)$1	1	68	71	9.0000
...	chr19:49999583-49999827(+)$1	1	37	40	9.0000
.))	chr11:763692-763925(+)$1	1	25	28	9.0000
.((	chr12:57625490-57625743(+)$1	1	154	157	9.0000
(((	chr20:2443640-2443914(-)$1	1	11	14	9.0000
)))	chr1:159888345-159888577(-)$1	1	62	65	9.0000
)))	chr16:67473111-67473337(-)$1	1	44	47	9.0000
...	chr14:76117336-76117573(-)$1	1	8	11	9.0000
...	chr19:2430742-2430971(-)$1	1	0	3	9.0000
(((	chr3:23961435-23961738(+)$1	1	47	50	9.0000
...	chr14:23495218-23495471(-)$1	1	200	203	9.0000
..(	chr19:34960554-34960805(+)$1	1	96	99	9.0000
(((	chr1:245006893-245007128(-)$1	1	33	36	9.0000
)))	chr19:33204537-33204767(+)$1	1	37	40	9.0000
)))	chr1:41157339-41157569(+)$1	1	73	76	9.0000
...	chr1:235506137-235506379(+)$1	1	40	43	9.0000
(((	chr12:112845999-112846239(-)$1	1	63	66	9.0000
)((	chrX:153580671-153580898(-)$1	1	188	191	9.0000
.))	chr1:245017554-245017778(-)$1	1	56	59	9.0000
)))	chr17:6920143-6920406(+)$1	1	78	81	9.0000
...	chr8:37556990-37557227(+)$1	1	34	37	9.0000
((.	chr5:79277869-79278109(-)$1	1	20	23	9.0000
(((	chr19:16630860-16631103(-)$1	1	17	20	9.0000
(((	chr5:162871409-162871639(+)$1	1	16	19	9.0000
)))	chr3:128889143-128889390(-)$1	1	100	103	9.0000
)))	chr7:102097669-102097915(-)$1	1	54	57	9.0000
(((	chr15:72491928-72492164(-)$1	1	53	56	9.0000
...	chr19:47112361-47112591(+)$1	1	8	11	9.0000
)))	chr19:8468575-8468806(+)$1	1	174	177	9.0000
..(	chr7:100875422-100875648(-)$1	1	25	28	9.0000
(((	chr4:122744775-122745009(-)$1	1	38	41	9.0000
(((	chr17:76166823-76167055(+)$1	1	77	80	9.0000
...	chr6:80982760-80982988(+)$1	1	55	58	9.0000
)))	chr3:124456670-124456896(+)$1	1	35	38	9.0000
(((	chrX:47088792-47089044(+)$1	1	9	12	9.0000
.((	chr21:44520481-44520703(-)$1	1	38	41	9.0000
...	chr9:116170651-116170891(-)$1	1	2	5	9.0000
(((	chr10:7830073-7830318(+)$1	1	40	43	9.0000
.))	chr1:205683571-205683851(-)$1	1	43	46	9.0000
(.(	chr17:73389569-73389823(-)$1	1	53	56	9.0000
...	chr20:44445347-44445625(+)$1	1	100	103	9.0000
..(	chr10:129897182-129897428(-)$1	1	24	27	9.0000
(((	chr19:33790743-33790973(-)$1	1	52	55	9.0000
.((	chr20:2446304-2446542(-)$1	1	55	58	9.0000
(((	chr19:17449667-17449901(+)$1	1	4	7	9.0000
).)	chr17:41154617-41154851(+)$1	1	121	124	9.0000
...	chr19:42365141-42365381(+)$1	1	18	21	9.0000
...	chr15:75122573-75122799(+)$1	1	30	33	9.0000
...	chr12:74934568-74934798(+)$1	1	10	13	9.0000
((.	chr3:197680774-197681006(+)$1	1	71	74	9.0000
.((	chr17:46147889-46148117(-)$1	1	5	8	9.0000
).)	chr17:41154653-41154894(+)$1	1	85	88	9.0000
(((	chr6:43752782-43753018(+)$1	1	29	32	9.0000
(((	chr3:169712040-169712271(+)$1	1	37	40	9.0000
(..	chrX:23801219-23801524(+)$1	1	30	33	9.0000
...	chr10:95288313-95288551(+)$1	1	76	79	9.0000
...	chr12:6977932-6978160(+)$1	1	54	57	9.0000
.))	chr1:20978671-20978899(-)$1	1	209	212	9.0000
)))	chr5:130762207-130762433(-)$1	1	184	187	9.0000
(((	chr1:183522164-183522385(+)$1	1	73	76	9.0000
(.(	chr5:180665108-180665338(-)$1	1	20	23	9.0000
(((	chr17:38153709-38153958(+)$1	1	116	119	9.0000
(((	chr10:75010432-75010671(-)$1	1	10	13	9.0000
(..	chr20:48506982-48507207(+)$1	1	26	29	9.0000
(((	chr11:10826364-10826592(-)$1	1	15	18	9.0000
(((	chr1:46073313-46073544(+)$1	1	4	7	9.0000
(((	chr5:167976618-167976849(-)$1	1	31	34	9.0000
...	chr19:39395586-39395810(+)$1	1	7	10	9.0000
.((	chr20:48569630-48569857(+)$1	1	13	16	9.0000
(((	chr10:75003138-75003368(-)$1	1	4	7	9.0000
(((	chr5:140699946-140700183(-)$1	1	49	52	9.0000
...	chr13:25910138-25910362(+)$1	1	24	27	9.0000
..)	chr7:44253281-44253508(+)$1	1	93	96	9.0000
(((	chr16:29822010-29822298(+)$1	1	91	94	9.0000
...	chr6:26199353-26199579(-)$1	1	14	17	9.0000
(((	chr16:28846570-28846810(+)$1	1	6	9	9.0000
(((	chr6:109689389-109689633(-)$1	1	10	13	9.0000
(..	chr11:64536437-64536673(-)$1	1	39	42	9.0000
)..	chr11:75115778-75116008(+)$1	1	178	181	9.0000
...	chr16:2012782-2013009(-)$1	1	14	17	9.0000
...	chr8:37917327-37917551(+)$1	1	11	14	9.0000
(.(	chr8:17094641-17094870(-)$1	1	92	95	9.0000
)))	chr22:39900396-39900620(+)$1	1	20	23	9.0000
...	chr12:50383230-50383460(-)$1	1	109	112	9.0000

#PSSM
U : 0.96	u : 0.04	
U : 0.96	u : 0.04	
C : 0.96	c : 0.04	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m2_run2.nuc.txt

#NT
CUUU	chr5:176370333-176370555(-)$1	222	155	159	11.9999
CUUU	chr12:69652653-69652878(+)$1	225	100	104	11.9999
CUUU	chrX:40993924-40994155(+)$1	231	42	46	11.9999
CUUU	chr19:21719463-21719697(+)$1	234	18	22	11.9999
CUUU	chr21:33066482-33066704(-)$1	222	28	32	11.9999
CUUU	chr2:153591415-153591640(+)$1	225	65	69	11.9999
CUUU	chr10:24834786-24835018(+)$1	232	1	5	11.9999
CUUU	chr14:101350949-101351175(+)$1	226	11	15	11.9999
CUUU	chr12:54448883-54449108(+)$1	225	13	17	11.9999
CUUU	chr2:65300059-65300291(+)$1	232	79	83	11.9999
CUUU	chr12:63954167-63954399(-)$1	232	163	167	11.9999
CUUU	chr16:29821402-29821660(+)$1	258	220	224	11.9999
CUUU	chr19:3976160-3976400(-)$1	240	19	23	11.9999
CUUU	chr1:46532550-46532772(-)$1	222	63	67	11.9999
CUUU	chr3:42916535-42916767(-)$1	232	92	96	11.9999
CUUU	chr12:29493994-29494226(-)$1	232	42	46	11.9999
CUUU	chrM:14239-14517(+)$1	278	113	117	11.9999
CUUU	chr3:148788994-148789227(-)$1	233	203	207	11.9999
CUUU	chr1:39913019-39913245(+)$1	226	9	13	11.9999
CUUU	chr14:73743219-73743452(-)$1	233	54	58	11.9999
CUUU	chr1:150266711-150266954(+)$1	243	5	9	11.9999
CUUU	chr8:8875790-8876012(+)$1	222	1	5	11.9999
CUUU	chr12:57114726-57114959(-)$1	233	100	104	11.9999
CUUU	chr1:16632214-16632444(-)$1	230	17	21	11.9999
CUUU	chr11:62655880-62656116(+)$1	236	95	99	11.9999
CUUU	chr12:53897425-53897659(+)$1	234	73	77	11.9999
CUUU	chrM:11213-11447(+)$1	234	151	155	11.9999
CUUU	chr22:39714954-39715218(-)$1	264	177	181	11.9999
CUUU	chr16:11643218-11643445(-)$1	227	80	84	11.9999
CUUU	chrX:153281935-153282167(-)$1	232	117	121	11.9999
CUUU	chrM:9959-10231(+)$1	272	35	39	11.9999
CUUU	chrM:3680-3913(+)$1	233	103	107	11.9999
CUUU	chr11:130108359-130108591(-)$1	232	2	6	11.9999
CUUU	chr12:46758155-46758381(-)$1	226	85	89	11.9999
CUUU	chr19:38125968-38126194(-)$1	226	63	67	11.9999
CUUU	chr1:54704657-54704889(-)$1	232	97	101	11.9999
CUUU	chr17:5336526-5336750(-)$1	224	68	72	11.9999
CUUU	chr5:32380094-32380318(-)$1	224	156	160	11.9999
CUUU	chr12:123022872-123023102(+)$1	230	36	40	11.9999
CUUU	chr19:58452293-58452515(-)$1	222	4	8	11.9999
CUUU	chr4:125592932-125593160(-)$1	228	184	188	11.9999
CUUU	chr12:123086048-123086272(+)$1	224	157	161	11.9999
CUUU	chr2:190331053-190331278(+)$1	225	52	56	11.9999
CUUU	chr18:67993081-67993313(+)$1	232	36	40	11.9999
CUUU	chr1:116224928-116225160(+)$1	232	25	29	11.9999
CUUU	chr5:36170375-36170605(+)$1	230	38	42	11.9999
CUUU	chr7:64388425-64388657(+)$1	232	6	10	11.9999
CUUU	chrM:7760-7997(+)$1	237	75	79	11.9999
CUUU	chr7:102952520-102952753(+)$1	233	71	75	11.9999
CUUU	chr21:37415924-37416163(-)$1	239	95	99	11.9999
CUUU	chr19:35769550-35769782(+)$1	232	94	98	11.9999
CUUU	chr8:61136995-61137221(-)$1	226	68	72	11.9999
CUUU	chrM:11753-12065(+)$1	312	73	77	11.9999
CUUU	chr17:46937673-46937905(+)$1	232	2	6	11.9999
CUUU	chr1:154199667-154199896(+)$1	229	63	67	11.9999
CUUU	chrM:6817-7059(-)$1	242	197	201	11.9999
CUUU	chrX:71493625-71493855(-)$1	230	59	63	11.9999
CUUU	chrM:15712-15965(+)$1	253	4	8	11.9999
CUUU	chr17:29170922-29171151(+)$1	229	42	46	11.9999
CUUU	chr19:6420014-6420237(-)$1	223	52	56	11.9999
CUUU	chrM:12434-12711(+)$1	277	31	35	11.9999
CUUU	chr10:71977550-71977774(-)$1	224	103	107	11.9999
CUUU	chr3:18390626-18390853(-)$1	227	117	121	11.9999
CUUU	chrX:119580137-119580372(-)$1	235	32	36	11.9999
CUUU	chrM:4610-4868(+)$1	258	189	193	11.9999
CUUU	chr8:117869511-117869739(-)$1	228	72	76	11.9999
CUUU	chr4:83763430-83763662(-)$1	232	226	230	11.9999
CUUU	chr1:97250617-97250844(+)$1	227	217	221	11.9999
CUUU	chr4:104057269-104057501(-)$1	232	81	85	11.9999
CUUU	chr6:43527829-43528061(-)$1	232	2	6	11.9999
CUUU	chr3:15288787-15289019(+)$1	232	30	34	11.9999
CUUU	chr8:81411855-81412087(+)$1	232	64	68	11.9999
CUUU	chr12:46321364-46321593(-)$1	229	61	65	11.9999
CUUU	chr2:96852910-96853134(-)$1	224	86	90	11.9999
CUUU	chr11:22257680-22257905(+)$1	225	9	13	11.9999
CUUU	chr1:36068776-36068999(-)$1	223	163	167	11.9999
CUUU	chr6:26031909-26032148(-)$1	239	171	175	11.9999
CUUU	chr14:101349237-101349494(+)$1	257	11	15	11.9999

#otherMatches

#Struct PSSM
::::	chr8:66639319-66639557(-)$1	238	4	8	11.9999
c(((	chr5:176370333-176370555(-)$1	222	155	159	11.9999
cc[c	chr12:69652653-69652878(+)$1	225	100	104	11.9999
CLLL	chrX:40993924-40994155(+)$1	231	42	46	11.9999
c:::	chr19:21719463-21719697(+)$1	234	18	22	11.9999
pppp	chr21:33066482-33066704(-)$1	222	28	32	11.9999
$$$$	chr2:153591415-153591640(+)$1	225	65	69	11.9999
::::	chr10:24834786-24835018(+)$1	232	1	5	11.9999
++++	chr14:101350949-101351175(+)$1	226	11	15	11.9999
:fff	chr12:54448883-54449108(+)$1	225	13	17	11.9999
b444	chr2:65300059-65300291(+)$1	232	79	83	11.9999
ppcc	chr12:63954167-63954399(-)$1	232	163	167	11.9999
====	chr16:29821402-29821660(+)$1	258	220	224	11.9999
IIII	chr19:3976160-3976400(-)$1	240	19	23	11.9999
fff7	chr1:46532550-46532772(-)$1	222	63	67	11.9999
JJJJ	chr3:42916535-42916767(-)$1	232	92	96	11.9999
mmee	chr12:29493994-29494226(-)$1	232	42	46	11.9999
::::	chrM:14239-14517(+)$1	278	113	117	11.9999
sssf	chr3:148788994-148789227(-)$1	233	203	207	11.9999
{EEE	chr1:39913019-39913245(+)$1	226	9	13	11.9999
eeee	chr14:73743219-73743452(-)$1	233	54	58	11.9999
::::	chr1:150266711-150266954(+)$1	243	5	9	11.9999
::::	chr8:8875790-8876012(+)$1	222	1	5	11.9999
gggg	chr12:57114726-57114959(-)$1	233	100	104	11.9999
cccq	chr1:16632214-16632444(-)$1	230	17	21	11.9999
9999	chr11:62655880-62656116(+)$1	236	95	99	11.9999
%%%%	chr12:53897425-53897659(+)$1	234	73	77	11.9999
dd]e	chrM:11213-11447(+)$1	234	151	155	11.9999
gg22	chr22:39714954-39715218(-)$1	264	177	181	11.9999
NNNN	chr16:11643218-11643445(-)$1	227	80	84	11.9999
GYYD	chrX:153281935-153282167(-)$1	232	117	121	11.9999
JJJJ	chrM:9959-10231(+)$1	272	35	39	11.9999
6666	chrM:3680-3913(+)$1	233	103	107	11.9999
::::	chr11:130108359-130108591(-)$1	232	2	6	11.9999
!!dd	chr12:46758155-46758381(-)$1	226	85	89	11.9999
::::	chr19:38125968-38126194(-)$1	226	63	67	11.9999
$$$$	chr1:54704657-54704889(-)$1	232	97	101	11.9999
====	chr17:5336526-5336750(-)$1	224	68	72	11.9999
:::=	chr5:32380094-32380318(-)$1	224	156	160	11.9999
chhh	chr12:123022872-123023102(+)$1	230	36	40	11.9999
GGGG	chr19:58452293-58452515(-)$1	222	4	8	11.9999
bb]c	chr4:125592932-125593160(-)$1	228	184	188	11.9999
gggg	chr12:123086048-123086272(+)$1	224	157	161	11.9999
ffff	chr2:190331053-190331278(+)$1	225	52	56	11.9999
DKKD	chr18:67993081-67993313(+)$1	232	36	40	11.9999
d:::	chr1:116224928-116225160(+)$1	232	25	29	11.9999
EELL	chr5:36170375-36170605(+)$1	230	38	42	11.9999
DDDD	chr7:64388425-64388657(+)$1	232	6	10	11.9999
::::	chrM:7760-7997(+)$1	237	75	79	11.9999
ee88	chr7:102952520-102952753(+)$1	233	71	75	11.9999
gggg	chr21:37415924-37416163(-)$1	239	95	99	11.9999
FFFF	chr19:35769550-35769782(+)$1	232	94	98	11.9999
::::	chr8:61136995-61137221(-)$1	226	68	72	11.9999
22bb	chrM:11753-12065(+)$1	312	73	77	11.9999
C:::	chr17:46937673-46937905(+)$1	232	2	6	11.9999
====	chr1:154199667-154199896(+)$1	229	63	67	11.9999
fff3	chrM:6817-7059(-)$1	242	197	201	11.9999
EEEh	chrX:71493625-71493855(-)$1	230	59	63	11.9999
::::	chrM:15712-15965(+)$1	253	4	8	11.9999
GGGG	chr17:29170922-29171151(+)$1	229	42	46	11.9999
GGGG	chr19:6420014-6420237(-)$1	223	52	56	11.9999
QQQF	chrM:12434-12711(+)$1	277	31	35	11.9999
tttt	chr10:71977550-71977774(-)$1	224	103	107	11.9999
b]ii	chr3:18390626-18390853(-)$1	227	117	121	11.9999
ddnn	chrX:119580137-119580372(-)$1	235	32	36	11.9999
::::	chrM:4610-4868(+)$1	258	189	193	11.9999
ggg"	chr8:117869511-117869739(-)$1	228	72	76	11.9999
::::	chr4:83763430-83763662(-)$1	232	226	230	11.9999
::::	chr1:97250617-97250844(+)$1	227	217	221	11.9999
DDDD	chr4:104057269-104057501(-)$1	232	81	85	11.9999
::::	chr6:43527829-43528061(-)$1	232	2	6	11.9999
]===	chr3:15288787-15289019(+)$1	232	30	34	11.9999
nnnn	chr8:81411855-81412087(+)$1	232	64	68	11.9999
2eee	chr12:46321364-46321593(-)$1	229	61	65	11.9999
ccc!	chr2:96852910-96853134(-)$1	224	86	90	11.9999
:::i	chr11:22257680-22257905(+)$1	225	9	13	11.9999
9999	chr1:36068776-36068999(-)$1	223	163	167	11.9999
ffff	chr6:26031909-26032148(-)$1	239	171	175	11.9999
DLLL	chr14:101349237-101349494(+)$1	257	11	15	11.9999

#DB
....	chr8:66639319-66639557(-)$1	1	4	8	11.9999
(...	chr5:176370333-176370555(-)$1	1	155	159	11.9999
((.(	chr12:69652653-69652878(+)$1	1	100	104	11.9999
(...	chrX:40993924-40994155(+)$1	1	42	46	11.9999
)...	chr19:21719463-21719697(+)$1	1	18	22	11.9999
....	chr21:33066482-33066704(-)$1	1	28	32	11.9999
....	chr2:153591415-153591640(+)$1	1	65	69	11.9999
....	chr10:24834786-24835018(+)$1	1	1	5	11.9999
....	chr14:101350949-101351175(+)$1	1	11	15	11.9999
.(((	chr12:54448883-54449108(+)$1	1	13	17	11.9999
)...	chr2:65300059-65300291(+)$1	1	79	83	11.9999
..))	chr12:63954167-63954399(-)$1	1	163	167	11.9999
))))	chr16:29821402-29821660(+)$1	1	220	224	11.9999
((((	chr19:3976160-3976400(-)$1	1	19	23	11.9999
))).	chr1:46532550-46532772(-)$1	1	63	67	11.9999
((((	chr3:42916535-42916767(-)$1	1	92	96	11.9999
..))	chr12:29493994-29494226(-)$1	1	42	46	11.9999
....	chrM:14239-14517(+)$1	1	113	117	11.9999
...)	chr3:148788994-148789227(-)$1	1	203	207	11.9999
.(((	chr1:39913019-39913245(+)$1	1	9	13	11.9999
))))	chr14:73743219-73743452(-)$1	1	54	58	11.9999
....	chr1:150266711-150266954(+)$1	1	5	9	11.9999
....	chr8:8875790-8876012(+)$1	1	1	5	11.9999
))))	chr12:57114726-57114959(-)$1	1	100	104	11.9999
(((.	chr1:16632214-16632444(-)$1	1	17	21	11.9999
....	chr11:62655880-62656116(+)$1	1	95	99	11.9999
....	chr12:53897425-53897659(+)$1	1	73	77	11.9999
)).)	chrM:11213-11447(+)$1	1	151	155	11.9999
))..	chr22:39714954-39715218(-)$1	1	177	181	11.9999
....	chr16:11643218-11643445(-)$1	1	80	84	11.9999
)..)	chrX:153281935-153282167(-)$1	1	117	121	11.9999
((((	chrM:9959-10231(+)$1	1	35	39	11.9999
....	chrM:3680-3913(+)$1	1	103	107	11.9999
....	chr11:130108359-130108591(-)$1	1	2	6	11.9999
..((	chr12:46758155-46758381(-)$1	1	85	89	11.9999
....	chr19:38125968-38126194(-)$1	1	63	67	11.9999
....	chr1:54704657-54704889(-)$1	1	97	101	11.9999
))))	chr17:5336526-5336750(-)$1	1	68	72	11.9999
...(	chr5:32380094-32380318(-)$1	1	156	160	11.9999
((((	chr12:123022872-123023102(+)$1	1	36	40	11.9999
((((	chr19:58452293-58452515(-)$1	1	4	8	11.9999
)).)	chr4:125592932-125593160(-)$1	1	184	188	11.9999
))))	chr12:123086048-123086272(+)$1	1	157	161	11.9999
((((	chr2:190331053-190331278(+)$1	1	52	56	11.9999
(..(	chr18:67993081-67993313(+)$1	1	36	40	11.9999
)...	chr1:116224928-116225160(+)$1	1	25	29	11.9999
((..	chr5:36170375-36170605(+)$1	1	38	42	11.9999
((((	chr7:64388425-64388657(+)$1	1	6	10	11.9999
....	chrM:7760-7997(+)$1	1	75	79	11.9999
))..	chr7:102952520-102952753(+)$1	1	71	75	11.9999
))))	chr21:37415924-37416163(-)$1	1	95	99	11.9999
((((	chr19:35769550-35769782(+)$1	1	94	98	11.9999
....	chr8:61136995-61137221(-)$1	1	68	72	11.9999
..))	chrM:11753-12065(+)$1	1	73	77	11.9999
(...	chr17:46937673-46937905(+)$1	1	2	6	11.9999
((((	chr1:154199667-154199896(+)$1	1	63	67	11.9999
))).	chrM:6817-7059(-)$1	1	197	201	11.9999
((((	chrX:71493625-71493855(-)$1	1	59	63	11.9999
....	chrM:15712-15965(+)$1	1	4	8	11.9999
((((	chr17:29170922-29171151(+)$1	1	42	46	11.9999
((((	chr19:6420014-6420237(-)$1	1	52	56	11.9999
...(	chrM:12434-12711(+)$1	1	31	35	11.9999
....	chr10:71977550-71977774(-)$1	1	103	107	11.9999
).))	chr3:18390626-18390853(-)$1	1	117	121	11.9999
((..	chrX:119580137-119580372(-)$1	1	32	36	11.9999
....	chrM:4610-4868(+)$1	1	189	193	11.9999
(((.	chr8:117869511-117869739(-)$1	1	72	76	11.9999
....	chr4:83763430-83763662(-)$1	1	226	230	11.9999
....	chr1:97250617-97250844(+)$1	1	217	221	11.9999
((((	chr4:104057269-104057501(-)$1	1	81	85	11.9999
....	chr6:43527829-43528061(-)$1	1	2	6	11.9999
.)))	chr3:15288787-15289019(+)$1	1	30	34	11.9999
....	chr8:81411855-81412087(+)$1	1	64	68	11.9999
.)))	chr12:46321364-46321593(-)$1	1	61	65	11.9999
(((.	chr2:96852910-96853134(-)$1	1	86	90	11.9999
...(	chr11:22257680-22257905(+)$1	1	9	13	11.9999
....	chr1:36068776-36068999(-)$1	1	163	167	11.9999
((((	chr6:26031909-26032148(-)$1	1	171	175	11.9999
(...	chr14:101349237-101349494(+)$1	1	11	15	11.9999

#PSSM
C : 0.99	
U : 0.99	
U : 0.99	
U : 0.99	

#score	947.9999999999995
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_CDS_m3_run2.nuc.txt

#NT
AGG	chr3:11606276-11606502(-)$1	226	7	10	9.0000
AGG	chr11:314194-314414(+)$1	220	36	39	9.0000
AGG	chr1:156290653-156290879(-)$1	226	1	4	9.0000
AGG	chr15:40756586-40756803(+)$1	217	2	5	9.0000
AGG	chr4:2933503-2933733(-)$1	230	68	71	9.0000
AGG	chr4:2933241-2933471(-)$1	230	89	92	9.0000
AGG	chr2:68620243-68620465(+)$1	222	48	51	9.0000
AGG	chr11:34161958-34162176(+)$1	218	0	3	9.0000
AGG	chr12:76780307-76780526(-)$1	219	84	87	9.0000
AGG	chr1:202700881-202701111(-)$1	230	42	45	9.0000
AGG	chr2:242275374-242275599(+)$1	225	42	45	9.0000
AGG	chr1:182354819-182355041(-)$1	222	17	20	9.0000
AGG	chr3:141164139-141164360(+)$1	221	5	8	9.0000
AGG	chr3:15115756-15115982(-)$1	226	63	66	9.0000
AGG	chrX:48891594-48891817(-)$1	223	62	65	9.0000
AGG	chr15:86118378-86118596(+)$1	218	53	56	9.0000
AGG	chr11:68552301-68552523(-)$1	222	94	97	9.0000
AGG	chr9:136232766-136232990(-)$1	224	47	50	9.0000
AGG	chr8:92083374-92083594(+)$1	220	0	3	9.0000
AGG	chr8:103663502-103663724(-)$1	222	106	109	9.0000
AGG	chr9:139744377-139744595(+)$1	218	45	48	9.0000
AGG	chr17:5264543-5264764(+)$1	221	3	6	9.0000
AGG	chr16:53358388-53358619(+)$1	231	136	139	9.0000
AGG	chr1:151288402-151288627(-)$1	225	11	14	9.0000
AGG	chr11:46686940-46687162(+)$1	222	8	11	9.0000
AGG	chr12:31440479-31440701(-)$1	222	132	135	9.0000
AGG	chr22:39262225-39262444(-)$1	219	52	55	9.0000
AGG	chr4:184367391-184367605(+)$1	214	107	110	9.0000
AGG	chr6:160105808-160106038(-)$1	230	24	27	9.0000
AGG	chr11:57321888-57322118(-)$1	230	20	23	9.0000
AGG	chr1:25775235-25775455(+)$1	220	18	21	9.0000
AGG	chr5:43277190-43277410(+)$1	220	21	24	9.0000
AGG	chr15:49431639-49431871(-)$1	232	145	148	9.0000
AGG	chr2:27259527-27259753(+)$1	226	2	5	9.0000
AGG	chr7:6054766-6054985(+)$1	219	8	11	9.0000
AGG	chr5:32407002-32407221(-)$1	219	9	12	9.0000
AGG	chr3:42827500-42827720(-)$1	220	64	67	9.0000
AGG	chr16:2024837-2025056(+)$1	219	21	24	9.0000
AGG	chr14:73750743-73750962(-)$1	219	46	49	9.0000
AGG	chr9:80854898-80855121(+)$1	223	38	41	9.0000
AGG	chr14:20813067-20813287(-)$1	220	90	93	9.0000
AGG	chr4:122782641-122782859(-)$1	218	23	26	9.0000
AGG	chr21:33747633-33747863(-)$1	230	96	99	9.0000
AGG	chr3:194168486-194168716(-)$1	230	134	137	9.0000
AGG	chr1:173809945-173810165(+)$1	220	159	162	9.0000
AGG	chr21:34924482-34924701(+)$1	219	7	10	9.0000
AGG	chr8:27382795-27383016(+)$1	221	49	52	9.0000
AGG	chr5:126860485-126860703(+)$1	218	26	29	9.0000
AGG	chr12:109520679-109520900(+)$1	221	141	144	9.0000
AGG	chr19:9269410-9269640(+)$1	230	2	5	9.0000
AGG	chr7:133979618-133979841(-)$1	223	8	11	9.0000
AGG	chr2:237489832-237490058(+)$1	226	9	12	9.0000
AGG	chr2:211018731-211018961(-)$1	230	58	61	9.0000
AGG	chr11:10015381-10015611(-)$1	230	201	204	9.0000
AGG	chr10:4875507-4875727(+)$1	220	92	95	9.0000
AGG	chr8:28908948-28909172(+)$1	224	15	18	9.0000
AGG	chr1:101705066-101705290(+)$1	224	158	161	9.0000
agg	chr22:37705211-37705435(+)$1	224	12	15	9.0000
AGG	chr19:49386898-49387120(+)$1	222	51	54	9.0000
AGG	chr14:60752364-60752594(+)$1	230	53	56	9.0000
AGG	chr9:2081822-2082041(+)$1	219	13	16	9.0000
AGG	chr17:7162049-7162272(+)$1	223	30	33	9.0000
AGG	chr13:98645351-98645572(+)$1	221	191	194	9.0000
AGG	chr11:66039170-66039390(+)$1	220	38	41	9.0000
AGG	chr2:20234694-20234919(-)$1	225	34	37	9.0000
AGG	chr5:40730267-40730505(-)$1	238	68	71	9.0000
AGG	chr19:46137581-46137800(-)$1	219	172	175	9.0000
AGG	chr19:13919809-13920039(+)$1	230	23	26	9.0000
AGG	chr6:90051939-90052169(-)$1	230	27	30	9.0000
AGG	chr16:83842897-83843116(+)$1	219	72	75	9.0000
AGG	chr4:99358032-99358250(+)$1	218	11	14	9.0000
AGG	chr11:57099801-57100031(-)$1	230	97	100	9.0000
AGG	chr15:74748849-74749067(-)$1	218	20	23	9.0000
AGG	chr16:16101607-16101825(+)$1	218	3	6	9.0000
AGG	chr9:2648177-2648396(-)$1	219	17	20	9.0000
AGG	chr12:130831404-130831624(-)$1	220	61	64	9.0000
AGG	chr1:154090141-154090363(-)$1	222	5	8	9.0000
agg	chr14:24769865-24770095(+)$1	230	0	3	9.0000
AGG	chr14:20857325-20857543(-)$1	218	43	46	9.0000
AGG	chr16:48295261-48295482(+)$1	221	71	74	9.0000
AGG	chr20:52194787-52195013(-)$1	226	40	43	9.0000
AGG	chr10:124806649-124806871(+)$1	222	1	4	9.0000
AGG	chrX:128962965-128963183(-)$1	218	24	27	9.0000
AGG	chr15:72767228-72767453(+)$1	225	35	38	9.0000
AGG	chr1:35656903-35657124(-)$1	221	21	24	9.0000
AGG	chr2:223423342-223423572(+)$1	230	138	141	9.0000
AGG	chr1:179886624-179886847(+)$1	223	0	3	9.0000
AGG	chr16:2570402-2570621(+)$1	219	70	73	9.0000
AGG	chr6:111631023-111631253(-)$1	230	54	57	9.0000
AGG	chr3:196613371-196613593(+)$1	222	8	11	9.0000
AGG	chr11:92881734-92881964(-)$1	230	71	74	9.0000
AGG	chr1:28337445-28337665(-)$1	220	66	69	9.0000
AGG	chr16:30732564-30732794(+)$1	230	57	60	9.0000
AGG	chr3:23996030-23996256(+)$1	226	60	63	9.0000
AGG	chr12:130831403-130831633(+)$1	230	43	46	9.0000
AGG	chr1:110116494-110116711(+)$1	217	34	37	9.0000
AGG	chr2:74755826-74756051(-)$1	225	97	100	9.0000

#otherMatches

#Struct PSSM
2cc	chr6:26189029-26189259(-)$1	230	16	19	9.0000
ggg	chr3:11606276-11606502(-)$1	226	7	10	9.0000
eee	chr11:314194-314414(+)$1	220	36	39	9.0000
fff	chr1:156290653-156290879(-)$1	226	1	4	9.0000
::c	chr15:40756586-40756803(+)$1	217	2	5	9.0000
EEE	chr4:2933503-2933733(-)$1	230	68	71	9.0000
22d	chr4:2933241-2933471(-)$1	230	89	92	9.0000
eee	chr2:68620243-68620465(+)$1	222	48	51	9.0000
ccc	chr11:34161958-34162176(+)$1	218	0	3	9.0000
ggg	chr12:76780307-76780526(-)$1	219	84	87	9.0000
iii	chr1:202700881-202701111(-)$1	230	42	45	9.0000
[ee	chr2:242275374-242275599(+)$1	225	42	45	9.0000
!!b	chr1:182354819-182355041(-)$1	222	17	20	9.0000
FF:	chr3:141164139-141164360(+)$1	221	5	8	9.0000
hhh	chr3:15115756-15115982(-)$1	226	63	66	9.0000
FFF	chrX:48891594-48891817(-)$1	223	62	65	9.0000
ccD	chr15:86118378-86118596(+)$1	218	53	56	9.0000
nbb	chr11:68552301-68552523(-)$1	222	94	97	9.0000
eee	chr9:136232766-136232990(-)$1	224	47	50	9.0000
::e	chr8:92083374-92083594(+)$1	220	0	3	9.0000
:bb	chr8:103663502-103663724(-)$1	222	106	109	9.0000
iii	chr9:139744377-139744595(+)$1	218	45	48	9.0000
EEE	chr17:5264543-5264764(+)$1	221	3	6	9.0000
:ee	chr16:53358388-53358619(+)$1	231	136	139	9.0000
:FF	chr1:151288402-151288627(-)$1	225	11	14	9.0000
[a[	chr11:46686940-46687162(+)$1	222	8	11	9.0000
ggg	chr12:31440479-31440701(-)$1	222	132	135	9.0000
ldd	chr22:39262225-39262444(-)$1	219	52	55	9.0000
ccc	chr4:184367391-184367605(+)$1	214	107	110	9.0000
BBK	chr6:160105808-160106038(-)$1	230	24	27	9.0000
:cc	chr11:57321888-57322118(-)$1	230	20	23	9.0000
eee	chr1:25775235-25775455(+)$1	220	18	21	9.0000
BBD	chr5:43277190-43277410(+)$1	220	21	24	9.0000
ddd	chr15:49431639-49431871(-)$1	232	145	148	9.0000
:BB	chr2:27259527-27259753(+)$1	226	2	5	9.0000
:::	chr7:6054766-6054985(+)$1	219	8	11	9.0000
EE:	chr5:32407002-32407221(-)$1	219	9	12	9.0000
eee	chr3:42827500-42827720(-)$1	220	64	67	9.0000
:CC	chr16:2024837-2025056(+)$1	219	21	24	9.0000
:cc	chr14:73750743-73750962(-)$1	219	46	49	9.0000
ddd	chr9:80854898-80855121(+)$1	223	38	41	9.0000
eee	chr14:20813067-20813287(-)$1	220	90	93	9.0000
cbb	chr4:122782641-122782859(-)$1	218	23	26	9.0000
iii	chr21:33747633-33747863(-)$1	230	96	99	9.0000
iii	chr3:194168486-194168716(-)$1	230	134	137	9.0000
ncc	chr1:173809945-173810165(+)$1	220	159	162	9.0000
ddd	chr21:34924482-34924701(+)$1	219	7	10	9.0000
===	chr8:27382795-27383016(+)$1	221	49	52	9.0000
:::	chr5:126860485-126860703(+)$1	218	26	29	9.0000
ccf	chr12:109520679-109520900(+)$1	221	141	144	9.0000
DDD	chr19:9269410-9269640(+)$1	230	2	5	9.0000
EEE	chr7:133979618-133979841(-)$1	223	8	11	9.0000
CC{	chr2:237489832-237490058(+)$1	226	9	12	9.0000
rrc	chr2:211018731-211018961(-)$1	230	58	61	9.0000
:CC	chr11:10015381-10015611(-)$1	230	201	204	9.0000
::=	chr10:4875507-4875727(+)$1	220	92	95	9.0000
:gg	chr8:28908948-28909172(+)$1	224	15	18	9.0000
DDD	chr1:101705066-101705290(+)$1	224	158	161	9.0000
:HH	chr22:37705211-37705435(+)$1	224	12	15	9.0000
!ff	chr19:49386898-49387120(+)$1	222	51	54	9.0000
4bb	chr14:60752364-60752594(+)$1	230	53	56	9.0000
FFF	chr9:2081822-2082041(+)$1	219	13	16	9.0000
ndd	chr17:7162049-7162272(+)$1	223	30	33	9.0000
ggg	chr13:98645351-98645572(+)$1	221	191	194	9.0000
III	chr11:66039170-66039390(+)$1	220	38	41	9.0000
III	chr2:20234694-20234919(-)$1	225	34	37	9.0000
[dd	chr5:40730267-40730505(-)$1	238	68	71	9.0000
444	chr19:46137581-46137800(-)$1	219	172	175	9.0000
ppf	chr19:13919809-13920039(+)$1	230	23	26	9.0000
ddd	chr6:90051939-90052169(-)$1	230	27	30	9.0000
bbh	chr16:83842897-83843116(+)$1	219	72	75	9.0000
DDD	chr4:99358032-99358250(+)$1	218	11	14	9.0000
bbo	chr11:57099801-57100031(-)$1	230	97	100	9.0000
{FF	chr15:74748849-74749067(-)$1	218	20	23	9.0000
C{E	chr16:16101607-16101825(+)$1	218	3	6	9.0000
bb]	chr9:2648177-2648396(-)$1	219	17	20	9.0000
"dd	chr12:130831404-130831624(-)$1	220	61	64	9.0000
iii	chr1:154090141-154090363(-)$1	222	5	8	9.0000
:bb	chr14:24769865-24770095(+)$1	230	0	3	9.0000
cc2	chr14:20857325-20857543(-)$1	218	43	46	9.0000
iii	chr16:48295261-48295482(+)$1	221	71	74	9.0000
===	chr20:52194787-52195013(-)$1	226	40	43	9.0000
:::	chr10:124806649-124806871(+)$1	222	1	4	9.0000
iii	chrX:128962965-128963183(-)$1	218	24	27	9.0000
444	chr15:72767228-72767453(+)$1	225	35	38	9.0000
ccc	chr1:35656903-35657124(-)$1	221	21	24	9.0000
!cc	chr2:223423342-223423572(+)$1	230	138	141	9.0000
eee	chr1:179886624-179886847(+)$1	223	0	3	9.0000
]dd	chr16:2570402-2570621(+)$1	219	70	73	9.0000
EEK	chr6:111631023-111631253(-)$1	230	54	57	9.0000
JJJ	chr3:196613371-196613593(+)$1	222	8	11	9.0000
ggg	chr11:92881734-92881964(-)$1	230	71	74	9.0000
bbe	chr1:28337445-28337665(-)$1	220	66	69	9.0000
EEE	chr16:30732564-30732794(+)$1	230	57	60	9.0000
fff	chr3:23996030-23996256(+)$1	226	60	63	9.0000
eee	chr12:130831403-130831633(+)$1	230	43	46	9.0000
ddq	chr1:110116494-110116711(+)$1	217	34	37	9.0000
2==	chr2:74755826-74756051(-)$1	225	97	100	9.0000

#DB
.))	chr6:26189029-26189259(-)$1	1	16	19	9.0000
(((	chr3:11606276-11606502(-)$1	1	7	10	9.0000
(((	chr11:314194-314414(+)$1	1	36	39	9.0000
(((	chr1:156290653-156290879(-)$1	1	1	4	9.0000
..(	chr15:40756586-40756803(+)$1	1	2	5	9.0000
(((	chr4:2933503-2933733(-)$1	1	68	71	9.0000
..)	chr4:2933241-2933471(-)$1	1	89	92	9.0000
)))	chr2:68620243-68620465(+)$1	1	48	51	9.0000
(((	chr11:34161958-34162176(+)$1	1	0	3	9.0000
(((	chr12:76780307-76780526(-)$1	1	84	87	9.0000
(((	chr1:202700881-202701111(-)$1	1	42	45	9.0000
.((	chr2:242275374-242275599(+)$1	1	42	45	9.0000
..(	chr1:182354819-182355041(-)$1	1	17	20	9.0000
((.	chr3:141164139-141164360(+)$1	1	5	8	9.0000
)))	chr3:15115756-15115982(-)$1	1	63	66	9.0000
(((	chrX:48891594-48891817(-)$1	1	62	65	9.0000
))(	chr15:86118378-86118596(+)$1	1	53	56	9.0000
.))	chr11:68552301-68552523(-)$1	1	94	97	9.0000
)))	chr9:136232766-136232990(-)$1	1	47	50	9.0000
..(	chr8:92083374-92083594(+)$1	1	0	3	9.0000
.((	chr8:103663502-103663724(-)$1	1	106	109	9.0000
(((	chr9:139744377-139744595(+)$1	1	45	48	9.0000
(((	chr17:5264543-5264764(+)$1	1	3	6	9.0000
.((	chr16:53358388-53358619(+)$1	1	136	139	9.0000
.((	chr1:151288402-151288627(-)$1	1	11	14	9.0000
.(.	chr11:46686940-46687162(+)$1	1	8	11	9.0000
)))	chr12:31440479-31440701(-)$1	1	132	135	9.0000
.))	chr22:39262225-39262444(-)$1	1	52	55	9.0000
)))	chr4:184367391-184367605(+)$1	1	107	110	9.0000
((.	chr6:160105808-160106038(-)$1	1	24	27	9.0000
.((	chr11:57321888-57322118(-)$1	1	20	23	9.0000
(((	chr1:25775235-25775455(+)$1	1	18	21	9.0000
(((	chr5:43277190-43277410(+)$1	1	21	24	9.0000
)))	chr15:49431639-49431871(-)$1	1	145	148	9.0000
.((	chr2:27259527-27259753(+)$1	1	2	5	9.0000
...	chr7:6054766-6054985(+)$1	1	8	11	9.0000
((.	chr5:32407002-32407221(-)$1	1	9	12	9.0000
)))	chr3:42827500-42827720(-)$1	1	64	67	9.0000
.((	chr16:2024837-2025056(+)$1	1	21	24	9.0000
.((	chr14:73750743-73750962(-)$1	1	46	49	9.0000
(((	chr9:80854898-80855121(+)$1	1	38	41	9.0000
(((	chr14:20813067-20813287(-)$1	1	90	93	9.0000
)((	chr4:122782641-122782859(-)$1	1	23	26	9.0000
)))	chr21:33747633-33747863(-)$1	1	96	99	9.0000
)))	chr3:194168486-194168716(-)$1	1	134	137	9.0000
.))	chr1:173809945-173810165(+)$1	1	159	162	9.0000
(((	chr21:34924482-34924701(+)$1	1	7	10	9.0000
)))	chr8:27382795-27383016(+)$1	1	49	52	9.0000
...	chr5:126860485-126860703(+)$1	1	26	29	9.0000
))(	chr12:109520679-109520900(+)$1	1	141	144	9.0000
(((	chr19:9269410-9269640(+)$1	1	2	5	9.0000
(((	chr7:133979618-133979841(-)$1	1	8	11	9.0000
((.	chr2:237489832-237490058(+)$1	1	9	12	9.0000
..)	chr2:211018731-211018961(-)$1	1	58	61	9.0000
.))	chr11:10015381-10015611(-)$1	1	201	204	9.0000
..(	chr10:4875507-4875727(+)$1	1	92	95	9.0000
.((	chr8:28908948-28909172(+)$1	1	15	18	9.0000
)))	chr1:101705066-101705290(+)$1	1	158	161	9.0000
.((	chr22:37705211-37705435(+)$1	1	12	15	9.0000
.((	chr19:49386898-49387120(+)$1	1	51	54	9.0000
.))	chr14:60752364-60752594(+)$1	1	53	56	9.0000
(((	chr9:2081822-2082041(+)$1	1	13	16	9.0000
.))	chr17:7162049-7162272(+)$1	1	30	33	9.0000
(((	chr13:98645351-98645572(+)$1	1	191	194	9.0000
(((	chr11:66039170-66039390(+)$1	1	38	41	9.0000
(((	chr2:20234694-20234919(-)$1	1	34	37	9.0000
.((	chr5:40730267-40730505(-)$1	1	68	71	9.0000
...	chr19:46137581-46137800(-)$1	1	172	175	9.0000
..)	chr19:13919809-13920039(+)$1	1	23	26	9.0000
)))	chr6:90051939-90052169(-)$1	1	27	30	9.0000
)))	chr16:83842897-83843116(+)$1	1	72	75	9.0000
(((	chr4:99358032-99358250(+)$1	1	11	14	9.0000
((.	chr11:57099801-57100031(-)$1	1	97	100	9.0000
.((	chr15:74748849-74749067(-)$1	1	20	23	9.0000
(.(	chr16:16101607-16101825(+)$1	1	3	6	9.0000
)).	chr9:2648177-2648396(-)$1	1	17	20	9.0000
.((	chr12:130831404-130831624(-)$1	1	61	64	9.0000
(((	chr1:154090141-154090363(-)$1	1	5	8	9.0000
.((	chr14:24769865-24770095(+)$1	1	0	3	9.0000
)).	chr14:20857325-20857543(-)$1	1	43	46	9.0000
)))	chr16:48295261-48295482(+)$1	1	71	74	9.0000
)))	chr20:52194787-52195013(-)$1	1	40	43	9.0000
...	chr10:124806649-124806871(+)$1	1	1	4	9.0000
(((	chrX:128962965-128963183(-)$1	1	24	27	9.0000
...	chr15:72767228-72767453(+)$1	1	35	38	9.0000
(((	chr1:35656903-35657124(-)$1	1	21	24	9.0000
.((	chr2:223423342-223423572(+)$1	1	138	141	9.0000
(((	chr1:179886624-179886847(+)$1	1	0	3	9.0000
.))	chr16:2570402-2570621(+)$1	1	70	73	9.0000
((.	chr6:111631023-111631253(-)$1	1	54	57	9.0000
(((	chr3:196613371-196613593(+)$1	1	8	11	9.0000
)))	chr11:92881734-92881964(-)$1	1	71	74	9.0000
)))	chr1:28337445-28337665(-)$1	1	66	69	9.0000
(((	chr16:30732564-30732794(+)$1	1	57	60	9.0000
)))	chr3:23996030-23996256(+)$1	1	60	63	9.0000
)))	chr12:130831403-130831633(+)$1	1	43	46	9.0000
((.	chr1:110116494-110116711(+)$1	1	34	37	9.0000
.))	chr2:74755826-74756051(-)$1	1	97	100	9.0000

#PSSM
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	
G : 0.97	g : 0.02	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m1_run2.nuc.txt

#NT
uuuuuuuAGUUUUUAUUU	chr3:160218902-160219172(-)$1	270	98	116	32.4782
UUUAUUGAUUUUUUUUUU	chr1:32384562-32384836(-)$1	274	101	119	27.4782
UUGUUUUUGUUUUAAUUU	chr2:101612393-101612619(+)$1	226	127	145	29.9782
UUGUUUUGAGuauuuuuu	chr5:55235784-55236045(-)$1	261	168	186	26.2826
UUUUUUUUUUUUUUUUUU	chr2:36777276-36777540(+)$1	264	101	119	36.6086
uuuuuuuuuuuuuuuuuu	chr17:4442513-4442764(-)$1	251	107	125	36.6086
UUGUUUUAGUCAUUUUCU	chr9:79001578-79001826(-)$1	248	162	180	23.8913
uucuuuuuuuuuuuuuuu	chr11:63396237-63396467(-)$1	230	135	153	35.8478
UUGUUUUGUUUGUUUGUU	chr1:65880193-65880431(+)$1	238	80	98	27.3695
uuguuuugguuuuuuuuu	chr7:5567171-5567409(-)$1	238	130	148	35.7391
CUGUUUUAAUUUUGUUUU	chr5:58267231-58267529(-)$1	298	18	36	28.3478
uauuuuuaauuuuuGUUU	chr1:151264528-151264759(-)$1	231	112	130	27.4782
UAGUUUUUUUUUUUCUUC	chr1:68168019-68168338(-)$1	319	32	50	25.8478
UUGUUUUGCUAUUUUUUU	chr1:84702218-84702504(+)$1	286	221	239	30.9565
UUUUUGUUGUUUUUUUUU	chr5:148731873-148732147(+)$1	274	125	143	31.8260
UUCUUUUUGUUUCUUUUA	chr19:57804699-57804998(+)$1	299	146	164	27.3695
UUUUAGUAAUUUCUUUUU	chr1:85732936-85733168(-)$1	232	61	79	22.5869
uuguuuuuguuuuuuuuu	chr9:73002270-73002498(-)$1	228	91	109	37.1521
UUAUUUUACUUUUUUUUA	chr6:114181769-114182003(+)$1	234	110	128	30.6304
UUGUUUUCUUUUUUCUGU	chr13:98045386-98045697(+)$1	311	126	144	28.0217
AUCUUUUUUUUUCUUUUU	chr9:123579210-123579512(-)$1	302	4	22	28.1304
UUUUUUUCCAUUCUUUUU	chr1:185069929-185070162(+)$1	233	109	127	25.6304
UUUUUUUUUUUUUUUUUU	chr3:167727040-167727267(-)$1	227	31	49	36.6086
uuauuuuacuuguuuuua	chr19:16965544-16965772(+)$1	228	93	111	26.6086
UUCUUUUUAUUUUCUUUU	chr11:35252605-35252844(+)$1	239	110	128	30.8478
UUUUUGUUGUUUUUUUUU	chr5:148731955-148732254(+)$1	299	43	61	31.8260
uucuuuuuuuuuuuuuuu	chr4:140394877-140395135(+)$1	258	176	194	35.8478
uuguuuuuguuuuuuuuu	chr2:232319507-232319739(-)$1	232	159	177	37.1521
UAGUUUUAGUUUUUAUUU	chr15:35272103-35272333(-)$1	230	45	63	29.4347
GUUUUUUACUUUUCCUUU	chr3:45052757-45052985(+)$1	228	103	121	24.4347
GUAUUUUAAUUAUAUUUU	chr9:101979837-101980063(-)$1	226	104	122	22.6956
CUGAUUUUUUUUUUUUUU	chr5:65375089-65375408(+)$1	319	107	125	29.4347
ACGUUUUUUUUUUUUUUU	chr5:137087685-137087968(-)$1	283	148	166	29.4347
UUGUUUUAUUUUUACUAU	chr5:10436572-10436809(+)$1	237	106	124	25.8478
UAAUUUUAUUUUCAUUUU	chr8:116423218-116423498(-)$1	280	132	150	23.8913
UUGUUUUGCUUUUUGUUU	chr9:34087964-34088247(-)$1	283	72	90	31.7173
UUAUUUUCCUAUUUUUAU	chr3:23631361-23631642(+)$1	281	50	68	24.5434
CUUUUUUAGUUGUUUUUC	chr8:48974455-48974705(+)$1	250	2	20	23.8913
uuguuuuuguuuuuuuuu	chr14:89627016-89627248(-)$1	232	4	22	37.1521
uuggcuuucuuuuuuuuu	chr1:115315837-115316094(-)$1	257	126	144	28.2391
AUUUGUUACUUUUCUUUU	chr1:52552731-52552955(+)$1	224	95	113	23.6739
uugucuuuuuuuuuuuuu	chr3:9848150-9848440(+)$1	290	45	63	33.4565
UUGUUUUAGUUUUUUUUU	chr17:60021999-60022222(-)$1	223	162	180	36.9347
UUGCUUGAUUUUUUUUUU	chr7:131185808-131186059(-)$1	251	97	115	28.3478
UUCUUUUCCUUUUUUUUU	chr16:29821793-29822137(+)$1	344	181	199	33.4565

#otherMatches

#Struct PSSM
gggg[eeeee[ggggggg	chr2:20648949-20649204(+)$1	255	117	135	28.5652
:::::::::::::::::d	chr3:160218902-160219172(-)$1	270	98	116	32.4782
e:::::::HHHHHHHH}C	chr1:32384562-32384836(-)$1	274	101	119	27.4782
hh]==========:::::	chr2:101612393-101612619(+)$1	226	127	145	29.9782
hhhhhh[eeeeepppppp	chr5:55235784-55236045(-)$1	261	168	186	26.2826
:::::::::::::::hhh	chr2:36777276-36777540(+)$1	264	101	119	36.6086
dd^^^^^^^^^^^^^^^^	chr17:4442513-4442764(-)$1	251	107	125	36.6086
5ccc]eeeeeccc:::::	chr9:79001578-79001826(-)$1	248	162	180	23.8913
wwwwwwwwwwwwwwhhhh	chr11:63396237-63396467(-)$1	230	135	153	35.8478
:HHHHHHHH::::::hhh	chr1:65880193-65880431(+)$1	238	80	98	27.3695
=======ffffffeeeee	chr7:5567171-5567409(-)$1	238	130	148	35.7391
{IIIIIIIII========	chr5:58267231-58267529(-)$1	298	18	36	28.3478
iiiiii[cccmmmmccc]	chr1:151264528-151264759(-)$1	231	112	130	27.4782
dFFFFFFJJJJJJJJJJ:	chr1:68168019-68168338(-)$1	319	32	50	25.8478
ooccc22eeeee4444ee	chr1:84702218-84702504(+)$1	286	221	239	30.9565
nneeeee:::::::::::	chr5:148731873-148732147(+)$1	274	125	143	31.8260
hhhh::::::::::::gg	chr19:57804699-57804998(+)$1	299	146	164	27.3695
mmmmdddd:::::::HHH	chr1:85732936-85733168(-)$1	232	61	79	22.5869
gggggg>>>>>>>>>>>>	chr9:73002270-73002498(-)$1	228	91	109	37.1521
fff::::::::::::::e	chr6:114181769-114182003(+)$1	234	110	128	30.6304
qffffff::::::::ggg	chr13:98045386-98045697(+)$1	311	126	144	28.0217
:::::::::::JJJJJJJ	chr9:123579210-123579512(-)$1	302	4	22	28.1304
:::::::::::GGGGGGG	chr1:185069929-185070162(+)$1	233	109	127	25.6304
::::::::::::::::::	chr3:167727040-167727267(-)$1	227	31	49	36.6086
boooooobb55555hhhh	chr19:16965544-16965772(+)$1	228	93	111	26.6086
::::::::::hhhhhhhh	chr11:35252605-35252844(+)$1	239	110	128	30.8478
nneeeee:::::::::::	chr5:148731955-148732254(+)$1	299	43	61	31.8260
d^^^^^^^^^^^^^^^^^	chr4:140394877-140395135(+)$1	258	176	194	35.8478
::::==============	chr2:232319507-232319739(-)$1	232	159	177	37.1521
ooooggggggg:::::::	chr15:35272103-35272333(-)$1	230	45	63	29.4347
WWWWWWWWWWWWWWWWWG	chr3:45052757-45052985(+)$1	228	103	121	24.4347
fff"""eeeeeuuuuuuu	chr9:101979837-101980063(-)$1	226	104	122	22.6956
EEEE::::::::::::::	chr5:65375089-65375408(+)$1	319	107	125	29.4347
::::::::::::::::::	chr5:137087685-137087968(-)$1	283	148	166	29.4347
===:::::::::::dddd	chr5:10436572-10436809(+)$1	237	106	124	25.8478
ee4444ggggggg66666	chr8:116423218-116423498(-)$1	280	132	150	23.8913
fooooooffffff]a]dd	chr9:34087964-34088247(-)$1	283	72	90	31.7173
f"""ccc!!bbmmmmbb2	chr3:23631361-23631642(+)$1	281	50	68	24.5434
:::::::::::::EEEEE	chr8:48974455-48974705(+)$1	250	2	20	23.8913
:IIIIIIIII::::::::	chr14:89627016-89627248(-)$1	232	4	22	37.1521
"""hhhhhhhh[ffffff	chr1:115315837-115316094(-)$1	257	126	144	28.2391
:eeeee!!cccxxxxxxx	chr1:52552731-52552955(+)$1	224	95	113	23.6739
::::::::::::::::::	chr3:9848150-9848440(+)$1	290	45	63	33.4565
^^^^^^^^^^^^^^^^^^	chr17:60021999-60022222(-)$1	223	162	180	36.9347
mmeeeeeeeeee[fffff	chr7:131185808-131186059(-)$1	251	97	115	28.3478
==================	chr16:29821793-29822137(+)$1	344	181	199	33.4565

#DB
((((.(((((.(((((((	chr2:20648949-20649204(+)$1	1	117	135	28.5652
.................(	chr3:160218902-160219172(-)$1	1	98	116	32.4782
).......)))))))).)	chr1:32384562-32384836(-)$1	1	101	119	27.4782
)).)))))))))).....	chr2:101612393-101612619(+)$1	1	127	145	29.9782
((((((.(((((......	chr5:55235784-55236045(-)$1	1	168	186	26.2826
...............(((	chr2:36777276-36777540(+)$1	1	101	119	36.6086
((................	chr17:4442513-4442764(-)$1	1	107	125	36.6086
.))).)))))))).....	chr9:79001578-79001826(-)$1	1	162	180	23.8913
..............))))	chr11:63396237-63396467(-)$1	1	135	153	35.8478
.((((((((......(((	chr1:65880193-65880431(+)$1	1	80	98	27.3695
)))))))))))))(((((	chr7:5567171-5567409(-)$1	1	130	148	35.7391
.(((((((((((((((((	chr5:58267231-58267529(-)$1	1	18	36	28.3478
((((((.(((....))).	chr1:151264528-151264759(-)$1	1	112	130	27.4782
)((((((((((((((((.	chr1:68168019-68168338(-)$1	1	32	50	25.8478
..)))..)))))....))	chr1:84702218-84702504(+)$1	1	221	239	30.9565
..)))))...........	chr5:148731873-148732147(+)$1	1	125	143	31.8260
))))............((	chr19:57804699-57804998(+)$1	1	146	164	27.3695
....)))).......(((	chr1:85732936-85733168(-)$1	1	61	79	22.5869
))))))............	chr9:73002270-73002498(-)$1	1	91	109	37.1521
)))..............(	chr6:114181769-114182003(+)$1	1	110	128	30.6304
.))))))........(((	chr13:98045386-98045697(+)$1	1	126	144	28.0217
...........(((((((	chr9:123579210-123579512(-)$1	1	4	22	28.1304
...........)))))))	chr1:185069929-185070162(+)$1	1	109	127	25.6304
..................	chr3:167727040-167727267(-)$1	1	31	49	36.6086
(......)).....))))	chr19:16965544-16965772(+)$1	1	93	111	26.6086
..........((((((((	chr11:35252605-35252844(+)$1	1	110	128	30.8478
..)))))...........	chr5:148731955-148732254(+)$1	1	43	61	31.8260
(.................	chr4:140394877-140395135(+)$1	1	176	194	35.8478
....((((((((((((((	chr2:232319507-232319739(-)$1	1	159	177	37.1521
....))))))).......	chr15:35272103-35272333(-)$1	1	45	63	29.4347
.................(	chr3:45052757-45052985(+)$1	1	103	121	24.4347
(((...(((((.......	chr9:101979837-101980063(-)$1	1	104	122	22.6956
))))..............	chr5:65375089-65375408(+)$1	1	107	125	29.4347
..................	chr5:137087685-137087968(-)$1	1	148	166	29.4347
)))...........((((	chr5:10436572-10436809(+)$1	1	106	124	25.8478
))....))))))).....	chr8:116423218-116423498(-)$1	1	132	150	23.8913
(......)))))).).))	chr9:34087964-34088247(-)$1	1	72	90	31.7173
(...(((..((....)).	chr3:23631361-23631642(+)$1	1	50	68	24.5434
.............(((((	chr8:48974455-48974705(+)$1	1	2	20	23.8913
.(((((((((........	chr14:89627016-89627248(-)$1	1	4	22	37.1521
...((((((((.((((((	chr1:115315837-115316094(-)$1	1	126	144	28.2391
.(((((..(((.......	chr1:52552731-52552955(+)$1	1	95	113	23.6739
..................	chr3:9848150-9848440(+)$1	1	45	63	33.4565
..................	chr17:60021999-60022222(-)$1	1	162	180	36.9347
..)))))(((((.(((((	chr7:131185808-131186059(-)$1	1	97	115	28.3478
((((((((((((((((((	chr16:29821793-29822137(+)$1	1	181	199	33.4565

#PSSM
U : 0.56	u : 0.26	C : 0.06	A : 0.06	G : 0.04	
U : 0.65	u : 0.23	A : 0.06	a : 0.02	C : 0.02	
G : 0.34	U : 0.21	g : 0.13	C : 0.08	A : 0.08	u : 0.06	c : 0.04	a : 0.02	
U : 0.67	u : 0.23	A : 0.04	g : 0.02	C : 0.02	
U : 0.67	u : 0.21	c : 0.04	C : 0.02	A : 0.02	G : 0.02	
U : 0.67	u : 0.26	G : 0.06	
U : 0.69	u : 0.26	G : 0.04	
A : 0.32	U : 0.23	u : 0.17	G : 0.10	C : 0.08	a : 0.04	g : 0.02	
U : 0.28	G : 0.19	C : 0.17	A : 0.10	u : 0.08	g : 0.08	c : 0.04	a : 0.02	
U : 0.71	u : 0.23	G : 0.02	A : 0.02	
U : 0.67	u : 0.26	A : 0.04	C : 0.02	
U : 0.65	u : 0.21	A : 0.04	G : 0.04	a : 0.02	g : 0.02	
U : 0.63	u : 0.26	C : 0.10	
U : 0.56	u : 0.26	A : 0.08	C : 0.06	G : 0.02	
U : 0.54	u : 0.23	A : 0.08	C : 0.08	G : 0.04	
U : 0.73	u : 0.23	G : 0.02	
U : 0.67	u : 0.23	A : 0.04	C : 0.02	G : 0.02	
U : 0.67	u : 0.21	C : 0.04	A : 0.04	a : 0.02	

#score	1370.3043478260854
#seq	46
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m1_run1.nuc.txt

#NT
UUUAUUUU	chr2:198256909-198257149(-)$1	240	131	139	19.9848
AUUAUUUU	chr8:125498221-125498461(+)$1	240	131	139	15.6666
UUUAUUUC	chr1:225591018-225591258(-)$1	240	126	134	16.2727
UUUAUCUU	chr3:132153307-132153547(+)$1	240	62	70	15.5151
UUUGUUUU	chr2:170487201-170487441(+)$1	240	66	74	16.6515
UUUCUUUU	chr9:19096605-19096845(-)$1	240	41	49	16.3484
UUCAUUUU	chr10:91178278-91178518(+)$1	240	163	171	15.5151
UUUAUUCU	chr14:74363092-74363332(+)$1	240	117	125	15.4393
UUUAUUUA	chr2:39519823-39520063(-)$1	240	87	95	16.0454
UUUCUUUU	chr10:122619627-122619867(+)$1	240	125	133	16.3484
UUUAUUUC	chr20:47768143-47768383(-)$1	240	88	96	16.2727
UUUAUUUU	chrX:138901401-138901641(-)$1	240	116	124	19.9848
UUUACUUU	chr3:169801936-169802176(+)$1	240	24	32	15.4393
UUUCUUUU	chr5:70860605-70860845(+)$1	240	123	131	16.3484
UUUAUUUA	chr19:9676516-9676756(-)$1	240	106	114	16.0454
UUUGUUUU	chr21:34931511-34931751(+)$1	240	5	13	16.6515
UUUCUUUU	chr10:75299143-75299383(-)$1	240	7	15	16.3484
UUGAUUUU	chr15:26792865-26793105(-)$1	240	176	184	15.5151
UUUAUUUU	chr6:70410619-70410859(-)$1	240	143	151	19.9848
UCUAUUUU	chr1:64038061-64038301(+)$1	240	34	42	15.4393
UUUAUUUU	chr2:55825477-55825717(-)$1	240	124	132	19.9848
UUUAUUUU	chr6:96034241-96034481(+)$1	240	125	133	19.9848
UAUAUUUU	chr5:102440194-102440434(-)$1	240	123	131	15.5151
UUUAUCUU	chr11:121177751-121177991(+)$1	240	122	130	15.5151
UUUAUUUU	chr6:5260852-5261103(-)$1	251	115	123	19.9848
UUUGUUUU	chr9:123955541-123955783(-)$1	242	75	83	16.6515
UUUAUUUU	chr11:82959025-82959265(+)$1	240	125	133	19.9848
UUUGUUUU	chr11:27371701-27371941(-)$1	240	184	192	16.6515
UUCAUUUU	chr13:67800731-67800971(-)$1	240	10	18	15.5151
UUUGUUUU	chr15:64423901-64424141(+)$1	240	231	239	16.6515
UUUAUUUU	chr2:191300868-191301108(+)$1	240	107	115	19.9848
UUUAGUUU	chr9:36356247-36356487(-)$1	240	217	225	15.4393
CUUAUUUU	chr4:17825195-17825435(+)$1	240	105	113	15.6666
UUAAUUUU	chr15:78337164-78337404(-)$1	240	123	131	15.4393
UUUAUUUG	chr3:169802312-169802552(+)$1	240	23	31	15.9696
UUUAUUUC	chr11:18330416-18330656(-)$1	240	3	11	16.2727
CUUAUUUU	chr14:31364018-31364258(-)$1	240	131	139	15.6666
uuuauuuu	chr5:61778838-61779078(+)$1	240	74	82	19.9848
UUUUUUUU	chr7:152346068-152346309(-)$1	241	82	90	16.1969
AUUAUUUU	chr2:160032846-160033086(+)$1	240	42	50	15.6666
AUUAUUUU	chr1:47716692-47716932(-)$1	240	115	123	15.6666
UUUAUUAU	chr11:19191975-19192215(+)$1	240	115	123	15.3636
UUUAUUUU	chr10:1038365-1038605(+)$1	240	43	51	19.9848
UAUAUUUU	chr1:54262328-54262568(-)$1	240	7	15	15.5151
UGUAUUUU	chr16:66651141-66651381(-)$1	240	33	41	15.5151
UUUAUUUC	chr19:38055997-38056237(-)$1	240	105	113	16.2727
CUUAUUUU	chr18:28667554-28667797(-)$1	243	0	8	15.6666
UUUGUUUU	chr12:12814039-12814279(-)$1	240	218	226	16.6515
UGUAUUUU	chr6:107361017-107361258(+)$1	241	74	82	15.5151
UUGAUUUU	chr18:29218560-29218800(-)$1	240	6	14	15.5151
UUUAGUUU	chr20:5155763-5156003(+)$1	240	183	191	15.4393
UUUAUUUG	chr11:9812011-9812251(-)$1	240	25	33	15.9696
uuuauuua	chr19:7184453-7184693(-)$1	240	0	8	16.0454
UUUAUUUC	chr5:115822415-115822655(-)$1	240	120	128	16.2727
UUUAUUUU	chr2:54150410-54150650(-)$1	240	198	206	19.9848
UUUAUUCU	chr13:39585374-39585614(-)$1	240	125	133	15.4393
UUUAUUUU	chr1:165697120-165697363(-)$1	243	116	124	19.9848
UUUAUUUC	chrX:41055464-41055704(+)$1	240	29	37	16.2727
UUUAUUGU	chr8:27680565-27680805(-)$1	240	42	50	15.3636
UUUGUUUU	chr4:102001621-102001861(-)$1	240	49	57	16.6515
UUUAUUUU	chr5:43644758-43644998(+)$1	240	72	80	19.9848
UUUAUCUU	chr5:54948256-54948496(-)$1	240	65	73	15.5151
UUUACUUU	chr3:194140543-194140783(-)$1	240	64	72	15.4393
UUUAUAUU	chr14:62213692-62213942(+)$1	250	172	180	15.3636
UUUGUUUU	chr20:18526506-18526746(+)$1	240	65	73	16.6515

#otherMatches

#Struct PSSM
::::::::	chr11:9459608-9459848(+)$1	240	0	8	16.1969
eeee"""d	chr2:198256909-198257149(-)$1	240	131	139	19.9848
::::::::	chr8:125498221-125498461(+)$1	240	131	139	15.6666
))))ccc[	chr1:225591018-225591258(-)$1	240	126	134	16.2727
hhhhh[dd	chr3:132153307-132153547(+)$1	240	62	70	15.5151
ggg[eeee	chr2:170487201-170487441(+)$1	240	66	74	16.6515
"eeeee^^	chr9:19096605-19096845(-)$1	240	41	49	16.3484
EEE}BB}C	chr10:91178278-91178518(+)$1	240	163	171	15.5151
00000000	chr14:74363092-74363332(+)$1	240	117	125	15.4393
foooooof	chr2:39519823-39520063(-)$1	240	87	95	16.0454
c=======	chr10:122619627-122619867(+)$1	240	125	133	16.3484
ffdddd$$	chr20:47768143-47768383(-)$1	240	88	96	16.2727
eeee::::	chrX:138901401-138901641(-)$1	240	116	124	19.9848
ffffffll	chr3:169801936-169802176(+)$1	240	24	32	15.4393
dddd::::	chr5:70860605-70860845(+)$1	240	123	131	16.3484
ggg"""cc	chr19:9676516-9676756(-)$1	240	106	114	16.0454
hhhh!!cc	chr21:34931511-34931751(+)$1	240	5	13	16.6515
:GGGGGGG	chr10:75299143-75299383(-)$1	240	7	15	16.3484
ddddmmmm	chr15:26792865-26793105(-)$1	240	176	184	15.5151
ii"""eee	chr6:70410619-70410859(-)$1	240	143	151	19.9848
ggg22iii	chr1:64038061-64038301(+)$1	240	34	42	15.4393
ggggggg[	chr2:55825477-55825717(-)$1	240	124	132	19.9848
!eeeeeqq	chr6:96034241-96034481(+)$1	240	125	133	19.9848
::::::ff	chr5:102440194-102440434(-)$1	240	123	131	15.5151
>>>ccc]e	chr11:121177751-121177991(+)$1	240	122	130	15.5151
::::::::	chr6:5260852-5261103(-)$1	251	115	123	19.9848
gggggg::	chr9:123955541-123955783(-)$1	242	75	83	16.6515
FFFIIIII	chr11:82959025-82959265(+)$1	240	125	133	19.9848
""eeeee[	chr11:27371701-27371941(-)$1	240	184	192	16.6515
:FFFFFF:	chr13:67800731-67800971(-)$1	240	10	18	15.5151
EEEEE:::	chr15:64423901-64424141(+)$1	240	231	239	16.6515
::::::::	chr2:191300868-191301108(+)$1	240	107	115	19.9848
EEE}BB~~	chr9:36356247-36356487(-)$1	240	217	225	15.4393
^^^^^^^^	chr4:17825195-17825435(+)$1	240	105	113	15.6666
gg"""eee	chr15:78337164-78337404(-)$1	240	123	131	15.4393
:::::::h	chr3:169802312-169802552(+)$1	240	23	31	15.9696
::::::::	chr11:18330416-18330656(-)$1	240	3	11	16.2727
appppppp	chr14:31364018-31364258(-)$1	240	131	139	15.6666
ff::::::	chr5:61778838-61779078(+)$1	240	74	82	19.9848
:::::::c	chr7:152346068-152346309(-)$1	241	82	90	16.1969
llffffff	chr2:160032846-160033086(+)$1	240	42	50	15.6666
::::::::	chr1:47716692-47716932(-)$1	240	115	123	15.6666
++++++++	chr11:19191975-19192215(+)$1	240	115	123	15.3636
wwwwwwww	chr10:1038365-1038605(+)$1	240	43	51	19.9848
EEEEKKEE	chr1:54262328-54262568(-)$1	240	7	15	15.5151
&dddd[dd	chr16:66651141-66651381(-)$1	240	33	41	15.5151
qqqqffff	chr19:38055997-38056237(-)$1	240	105	113	16.2727
:::::::E	chr18:28667554-28667797(-)$1	243	0	8	15.6666
:::EEEEE	chr12:12814039-12814279(-)$1	240	218	226	16.6515
eeddddnn	chr6:107361017-107361258(+)$1	241	74	82	15.5151
fqqqqqqq	chr18:29218560-29218800(-)$1	240	6	14	15.5151
++++++++	chr20:5155763-5156003(+)$1	240	183	191	15.4393
ggggggmm	chr11:9812011-9812251(-)$1	240	25	33	15.9696
::::::::	chr19:7184453-7184693(-)$1	240	0	8	16.0454
^^^^^^^^	chr5:115822415-115822655(-)$1	240	120	128	16.2727
ffffoooo	chr2:54150410-54150650(-)$1	240	198	206	19.9848
JJJJJJJJ	chr13:39585374-39585614(-)$1	240	125	133	15.4393
>>>>>>>>	chr1:165697120-165697363(-)$1	243	116	124	19.9848
44ffffff	chrX:41055464-41055704(+)$1	240	29	37	16.2727
uuuuuuuu	chr8:27680565-27680805(-)$1	240	42	50	15.3636
NNCCCLLL	chr4:102001621-102001861(-)$1	240	49	57	16.6515
gggggooo	chr5:43644758-43644998(+)$1	240	72	80	19.9848
dddd22dd	chr5:54948256-54948496(-)$1	240	65	73	15.5151
iiiiiii!	chr3:194140543-194140783(-)$1	240	64	72	15.4393
)))))))f	chr14:62213692-62213942(+)$1	250	172	180	15.3636
GG{DDDD:	chr20:18526506-18526746(+)$1	240	65	73	16.6515

#DB
........	chr11:9459608-9459848(+)$1	1	0	8	16.1969
((((...(	chr2:198256909-198257149(-)$1	1	131	139	19.9848
........	chr8:125498221-125498461(+)$1	1	131	139	15.6666
....(((.	chr1:225591018-225591258(-)$1	1	126	134	16.2727
(((((.((	chr3:132153307-132153547(+)$1	1	62	70	15.5151
(((.((((	chr2:170487201-170487441(+)$1	1	66	74	16.6515
.(((((..	chr9:19096605-19096845(-)$1	1	41	49	16.3484
))).)).)	chr10:91178278-91178518(+)$1	1	163	171	15.5151
........	chr14:74363092-74363332(+)$1	1	117	125	15.4393
(......)	chr2:39519823-39520063(-)$1	1	87	95	16.0454
))))))))	chr10:122619627-122619867(+)$1	1	125	133	16.3484
((((((..	chr20:47768143-47768383(-)$1	1	88	96	16.2727
))))....	chrX:138901401-138901641(-)$1	1	116	124	19.9848
((((((..	chr3:169801936-169802176(+)$1	1	24	32	15.4393
))))....	chr5:70860605-70860845(+)$1	1	123	131	16.3484
(((...((	chr19:9676516-9676756(-)$1	1	106	114	16.0454
((((..((	chr21:34931511-34931751(+)$1	1	5	13	16.6515
.(((((((	chr10:75299143-75299383(-)$1	1	7	15	16.3484
((((....	chr15:26792865-26793105(-)$1	1	176	184	15.5151
((...(((	chr6:70410619-70410859(-)$1	1	143	151	19.9848
)))..)))	chr1:64038061-64038301(+)$1	1	34	42	15.4393
(((((((.	chr2:55825477-55825717(-)$1	1	124	132	19.9848
.(((((..	chr6:96034241-96034481(+)$1	1	125	133	19.9848
......((	chr5:102440194-102440434(-)$1	1	123	131	15.5151
...))).)	chr11:121177751-121177991(+)$1	1	122	130	15.5151
........	chr6:5260852-5261103(-)$1	1	115	123	19.9848
))))))..	chr9:123955541-123955783(-)$1	1	75	83	16.6515
))))))))	chr11:82959025-82959265(+)$1	1	125	133	19.9848
..(((((.	chr11:27371701-27371941(-)$1	1	184	192	16.6515
.((((((.	chr13:67800731-67800971(-)$1	1	10	18	15.5151
)))))...	chr15:64423901-64424141(+)$1	1	231	239	16.6515
........	chr2:191300868-191301108(+)$1	1	107	115	19.9848
))).))..	chr9:36356247-36356487(-)$1	1	217	225	15.4393
........	chr4:17825195-17825435(+)$1	1	105	113	15.6666
((...(((	chr15:78337164-78337404(-)$1	1	123	131	15.4393
.......(	chr3:169802312-169802552(+)$1	1	23	31	15.9696
........	chr11:18330416-18330656(-)$1	1	3	11	16.2727
(.......	chr14:31364018-31364258(-)$1	1	131	139	15.6666
))......	chr5:61778838-61779078(+)$1	1	74	82	19.9848
.......(	chr7:152346068-152346309(-)$1	1	82	90	16.1969
..))))))	chr2:160032846-160033086(+)$1	1	42	50	15.6666
........	chr1:47716692-47716932(-)$1	1	115	123	15.6666
........	chr11:19191975-19192215(+)$1	1	115	123	15.3636
........	chr10:1038365-1038605(+)$1	1	43	51	19.9848
((((..((	chr1:54262328-54262568(-)$1	1	7	15	15.5151
.((((.((	chr16:66651141-66651381(-)$1	1	33	41	15.5151
....))))	chr19:38055997-38056237(-)$1	1	105	113	16.2727
.......(	chr18:28667554-28667797(-)$1	1	0	8	15.6666
...)))))	chr12:12814039-12814279(-)$1	1	218	226	16.6515
((((((..	chr6:107361017-107361258(+)$1	1	74	82	15.5151
(.......	chr18:29218560-29218800(-)$1	1	6	14	15.5151
........	chr20:5155763-5156003(+)$1	1	183	191	15.4393
((((((..	chr11:9812011-9812251(-)$1	1	25	33	15.9696
........	chr19:7184453-7184693(-)$1	1	0	8	16.0454
........	chr5:115822415-115822655(-)$1	1	120	128	16.2727
((((....	chr2:54150410-54150650(-)$1	1	198	206	19.9848
((((((((	chr13:39585374-39585614(-)$1	1	125	133	15.4393
........	chr1:165697120-165697363(-)$1	1	116	124	19.9848
..))))))	chrX:41055464-41055704(+)$1	1	29	37	16.2727
........	chr8:27680565-27680805(-)$1	1	42	50	15.3636
..(((...	chr4:102001621-102001861(-)$1	1	49	57	16.6515
(((((...	chr5:43644758-43644998(+)$1	1	72	80	19.9848
))))..))	chr5:54948256-54948496(-)$1	1	65	73	15.5151
(((((((.	chr3:194140543-194140783(-)$1	1	64	72	15.4393
.......(	chr14:62213692-62213942(+)$1	1	172	180	15.3636
((.((((.	chr20:18526506-18526746(+)$1	1	65	73	16.6515

#PSSM
U : 0.86	u : 0.04	A : 0.04	C : 0.04	
U : 0.87	u : 0.04	A : 0.03	G : 0.03	C : 0.01	
U : 0.87	u : 0.04	C : 0.03	G : 0.03	A : 0.01	
A : 0.75	G : 0.12	C : 0.06	a : 0.03	u : 0.01	U : 0.01	
U : 0.89	u : 0.04	C : 0.03	G : 0.03	
U : 0.89	u : 0.04	C : 0.04	A : 0.01	
U : 0.89	u : 0.04	C : 0.03	A : 0.01	G : 0.01	
U : 0.80	C : 0.09	u : 0.03	A : 0.03	G : 0.03	a : 0.01	

#score	1102.7878787878776
#seq	66
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_UTR_m1_run2.nuc.txt

#NT
AGCUGG	chr10:75006861-75007088(-)$1	227	97	103	10.9365
AGGAGG	chr20:47860257-47860487(+)$1	230	102	108	11.4126
AGGUGG	chr19:49256630-49256849(-)$1	219	107	113	14.1111
AGCUGG	chr14:55615047-55615274(-)$1	227	114	120	10.9365
AGGUGG	chr19:19638418-19638659(+)$1	241	159	165	14.1111
AGUUGG	chr13:20633546-20633796(+)$1	250	203	209	10.6190
AGGCGG	chr17:7387602-7387825(+)$1	223	124	130	10.9365
AGGCGG	chr16:2802618-2802838(+)$1	220	42	48	10.9365
AGGCGG	chr18:34408618-34408847(-)$1	229	61	67	10.9365
AGGAGG	chr19:1269277-1269501(+)$1	224	67	73	11.4126
AGGAGG	chr12:57893998-57894234(+)$1	236	42	48	11.4126
UGGUGG	chr4:6374205-6374426(-)$1	221	27	33	9.9047
ACGUGG	chr16:87788709-87788935(-)$1	226	176	182	9.9047
AAGUGG	chr19:10789245-10789471(+)$1	226	123	129	9.9841
AGGGGG	chr11:67379610-67379833(+)$1	223	18	24	11.0158
AGGUGG	chr1:29485834-29486058(-)$1	224	58	64	14.1111
AGAUGG	chr5:74807217-74807444(-)$1	227	10	16	11.1746
AGCUGG	chr5:65222175-65222413(+)$1	238	105	111	10.9365
AUGUGG	chr11:62396637-62396867(-)$1	230	26	32	9.9841
UGGUGG	chr19:41302493-41302717(+)$1	224	99	105	9.9047
AGGAGG	chr17:7842802-7843031(+)$1	229	26	32	11.4126
AGGUGG	chr4:13485771-13485991(-)$1	220	40	46	14.1111
AGAUGG	chr17:35985956-35986179(-)$1	223	77	83	11.1746
AGGAGG	chr10:73993042-73993270(+)$1	228	80	86	11.4126
AGGAGG	chr12:12630356-12630582(-)$1	226	202	208	11.4126
AGGGGG	chr19:36104554-36104777(+)$1	223	91	97	11.0158
UGGUGG	chr19:14520010-14520241(-)$1	231	26	32	9.9047
AGAUGG	chr17:1326647-1326875(-)$1	228	93	99	11.1746
AGGUGG	chr1:225840501-225840729(-)$1	228	64	70	14.1111
AGGGGG	chr15:93443595-93443814(+)$1	219	66	72	11.0158
AGGUGG	chr1:193028301-193028523(-)$1	222	102	108	14.1111
AGGUGG	chr9:95027704-95027927(-)$1	223	90	96	14.1111
AGAUGG	chr1:214549499-214549729(-)$1	230	201	207	11.1746
AGAUGG	chr15:40491728-40491949(+)$1	221	141	147	11.1746
UGGUGG	chr17:55193490-55193711(+)$1	221	19	25	9.9047
AAGUGG	chr19:16653111-16653340(-)$1	229	21	27	9.9841
AGGUGG	chr9:115633496-115633720(+)$1	224	135	141	14.1111
AUGUGG	chr19:36579848-36580070(+)$1	222	47	53	9.9841
AGAUGG	chr3:48960100-48960319(+)$1	219	78	84	11.1746
AGGUGG	chr7:97481400-97481624(-)$1	224	52	58	14.1111
AGGAGG	chr3:119813024-119813255(-)$1	231	55	61	11.4126
AGGUGG	chr12:6660509-6660735(-)$1	226	170	176	14.1111
AGAUGG	chr8:17780416-17780637(+)$1	221	94	100	11.1746
AGGUGG	chr6:38670741-38670969(-)$1	228	221	227	14.1111
AGCUGG	chr22:47188341-47188569(+)$1	228	9	15	10.9365
AGCUGG	chr9:95032139-95032360(-)$1	221	129	135	10.9365
ACGUGG	chr17:30677162-30677392(+)$1	230	43	49	9.9047
AGGAGG	chr1:235491198-235491437(-)$1	239	207	213	11.4126
AGUUGG	chr1:52227511-52227738(+)$1	227	73	79	10.6190
AGGAGG	chr17:41244486-41244711(-)$1	225	4	10	11.4126
AAGUGG	chr1:93544809-93545031(+)$1	222	67	73	9.9841
AUGUGG	chr19:58319030-58319253(-)$1	223	133	139	9.9841
AGGUGG	chr3:153839673-153839893(+)$1	220	124	130	14.1111
AGGGGG	chr20:33981861-33982085(-)$1	224	159	165	11.0158
AGAUGG	chr19:46119961-46120189(-)$1	228	76	82	11.1746
AGGAGG	chr8:37636586-37636829(+)$1	243	67	73	11.4126
AGAUGG	chr2:233655672-233655914(+)$1	242	79	85	11.1746
AGCUGG	chr3:12881726-12881948(-)$1	222	106	112	10.9365
AGGUGG	chr2:99225028-99225253(+)$1	225	112	118	14.1111
AGGCGG	chr1:167905027-167905253(-)$1	226	62	68	10.9365
uggugg	chr14:100259750-100259975(+)$1	225	168	174	9.9047
AGGGGG	chr15:70389575-70389804(-)$1	229	51	57	11.0158

#otherMatches

#Struct PSSM
fdddde	chr11:11924167-11924410(+)$1	243	92	98	14.1111
gggggm	chr10:75006861-75007088(-)$1	227	97	103	10.9365
eeeeff	chr20:47860257-47860487(+)$1	230	102	108	11.4126
KFFFFF	chr19:49256630-49256849(-)$1	219	107	113	14.1111
cc::BB	chr14:55615047-55615274(-)$1	227	114	120	10.9365
]eeeee	chr19:19638418-19638659(+)$1	241	159	165	14.1111
HHYYDD	chr13:20633546-20633796(+)$1	250	203	209	10.6190
$eeeee	chr17:7387602-7387825(+)$1	223	124	130	10.9365
:fffff	chr16:2802618-2802838(+)$1	220	42	48	10.9365
FFFFF}	chr18:34408618-34408847(-)$1	229	61	67	10.9365
qqqqqb	chr19:1269277-1269501(+)$1	224	67	73	11.4126
ee!!ff	chr12:57893998-57894234(+)$1	236	42	48	11.4126
ee[ccc	chr4:6374205-6374426(-)$1	221	27	33	9.9047
ttttee	chr16:87788709-87788935(-)$1	226	176	182	9.9047
ggeeee	chr19:10789245-10789471(+)$1	226	123	129	9.9841
:HHHHH	chr11:67379610-67379833(+)$1	223	18	24	11.0158
iiiiii	chr1:29485834-29486058(-)$1	224	58	64	14.1111
FFKKBB	chr5:74807217-74807444(-)$1	227	10	16	11.1746
ee22bb	chr5:65222175-65222413(+)$1	238	105	111	10.9365
[bb[ee	chr11:62396637-62396867(-)$1	230	26	32	9.9841
GGG:dd	chr19:41302493-41302717(+)$1	224	99	105	9.9047
qqa]ii	chr17:7842802-7843031(+)$1	229	26	32	11.4126
JJJJJJ	chr4:13485771-13485991(-)$1	220	40	46	14.1111
:DDDDC	chr17:35985956-35986179(-)$1	223	77	83	11.1746
:hhhhh	chr10:73993042-73993270(+)$1	228	80	86	11.4126
ccc]cc	chr12:12630356-12630582(-)$1	226	202	208	11.4126
cc]a]b	chr19:36104554-36104777(+)$1	223	91	97	11.0158
ddddmm	chr19:14520010-14520241(-)$1	231	26	32	9.9047
:HHHHH	chr17:1326647-1326875(-)$1	228	93	99	11.1746
[eeeee	chr1:225840501-225840729(-)$1	228	64	70	14.1111
hhhhhh	chr15:93443595-93443814(+)$1	219	66	72	11.0158
!!dddd	chr1:193028301-193028523(-)$1	222	102	108	14.1111
eeJJJJ	chr9:95027704-95027927(-)$1	223	90	96	14.1111
::::EE	chr1:214549499-214549729(-)$1	230	201	207	11.1746
bb[ddd	chr15:40491728-40491949(+)$1	221	141	147	11.1746
{CCC{B	chr17:55193490-55193711(+)$1	221	19	25	9.9047
HHHHHH	chr19:16653111-16653340(-)$1	229	21	27	9.9841
!!bboo	chr9:115633496-115633720(+)$1	224	135	141	14.1111
:::::C	chr19:36579848-36580070(+)$1	222	47	53	9.9841
lhhhhh	chr3:48960100-48960319(+)$1	219	78	84	11.1746
::::ii	chr7:97481400-97481624(-)$1	224	52	58	14.1111
$$$$$a	chr3:119813024-119813255(-)$1	231	55	61	11.4126
44dddd	chr12:6660509-6660735(-)$1	226	170	176	14.1111
ccc]ee	chr8:17780416-17780637(+)$1	221	94	100	11.1746
_BB}BB	chr6:38670741-38670969(-)$1	228	221	227	14.1111
F=====	chr22:47188341-47188569(+)$1	228	9	15	10.9365
ndddd]	chr9:95032139-95032360(-)$1	221	129	135	10.9365
ccc]ff	chr17:30677162-30677392(+)$1	230	43	49	9.9047
YA}DDD	chr1:235491198-235491437(-)$1	239	207	213	11.4126
bb]eee	chr1:52227511-52227738(+)$1	227	73	79	10.6190
:DDDDA	chr17:41244486-41244711(-)$1	225	4	10	11.4126
::GGGG	chr1:93544809-93545031(+)$1	222	67	73	9.9841
hhhhhh	chr19:58319030-58319253(-)$1	223	133	139	9.9841
dd:ddd	chr3:153839673-153839893(+)$1	220	124	130	14.1111
!a[ggg	chr20:33981861-33982085(-)$1	224	159	165	11.0158
qqqqbb	chr19:46119961-46120189(-)$1	228	76	82	11.1746
ffffff	chr8:37636586-37636829(+)$1	243	67	73	11.4126
ddddbb	chr2:233655672-233655914(+)$1	242	79	85	11.1746
ffffff	chr3:12881726-12881948(-)$1	222	106	112	10.9365
bbeeee	chr2:99225028-99225253(+)$1	225	112	118	14.1111
{CCCcc	chr1:167905027-167905253(-)$1	226	62	68	10.9365
bb333f	chr14:100259750-100259975(+)$1	225	168	174	9.9047
EEEBBf	chr15:70389575-70389804(-)$1	229	51	57	11.0158

#DB
)(((((	chr11:11924167-11924410(+)$1	1	92	98	14.1111
(((((.	chr10:75006861-75007088(-)$1	1	97	103	10.9365
))))))	chr20:47860257-47860487(+)$1	1	102	108	11.4126
.(((((	chr19:49256630-49256849(-)$1	1	107	113	14.1111
))..))	chr14:55615047-55615274(-)$1	1	114	120	10.9365
.)))))	chr19:19638418-19638659(+)$1	1	159	165	14.1111
))..))	chr13:20633546-20633796(+)$1	1	203	209	10.6190
.(((((	chr17:7387602-7387825(+)$1	1	124	130	10.9365
.(((((	chr16:2802618-2802838(+)$1	1	42	48	10.9365
))))).	chr18:34408618-34408847(-)$1	1	61	67	10.9365
.....)	chr19:1269277-1269501(+)$1	1	67	73	11.4126
((..((	chr12:57893998-57894234(+)$1	1	42	48	11.4126
((.(((	chr4:6374205-6374426(-)$1	1	27	33	9.9047
....))	chr16:87788709-87788935(-)$1	1	176	182	9.9047
))))))	chr19:10789245-10789471(+)$1	1	123	129	9.9841
.(((((	chr11:67379610-67379833(+)$1	1	18	24	11.0158
))))))	chr1:29485834-29486058(-)$1	1	58	64	14.1111
((..((	chr5:74807217-74807444(-)$1	1	10	16	11.1746
))..))	chr5:65222175-65222413(+)$1	1	105	111	10.9365
.((.((	chr11:62396637-62396867(-)$1	1	26	32	9.9841
))).((	chr19:41302493-41302717(+)$1	1	99	105	9.9047
..).))	chr17:7842802-7843031(+)$1	1	26	32	11.4126
((((((	chr4:13485771-13485991(-)$1	1	40	46	14.1111
.(((((	chr17:35985956-35986179(-)$1	1	77	83	11.1746
.(((((	chr10:73993042-73993270(+)$1	1	80	86	11.4126
))).))	chr12:12630356-12630582(-)$1	1	202	208	11.4126
)).).)	chr19:36104554-36104777(+)$1	1	91	97	11.0158
((((..	chr19:14520010-14520241(-)$1	1	26	32	9.9047
.)))))	chr17:1326647-1326875(-)$1	1	93	99	11.1746
.(((((	chr1:225840501-225840729(-)$1	1	64	70	14.1111
))))))	chr15:93443595-93443814(+)$1	1	66	72	11.0158
..((((	chr1:193028301-193028523(-)$1	1	102	108	14.1111
))))))	chr9:95027704-95027927(-)$1	1	90	96	14.1111
....))	chr1:214549499-214549729(-)$1	1	201	207	11.1746
((.(((	chr15:40491728-40491949(+)$1	1	141	147	11.1746
.(((.(	chr17:55193490-55193711(+)$1	1	19	25	9.9047
((((((	chr19:16653111-16653340(-)$1	1	21	27	9.9841
..((..	chr9:115633496-115633720(+)$1	1	135	141	14.1111
.....(	chr19:36579848-36580070(+)$1	1	47	53	9.9841
.)))))	chr3:48960100-48960319(+)$1	1	78	84	11.1746
....((	chr7:97481400-97481624(-)$1	1	52	58	14.1111
.....(	chr3:119813024-119813255(-)$1	1	55	61	11.4126
..))))	chr12:6660509-6660735(-)$1	1	170	176	14.1111
))).))	chr8:17780416-17780637(+)$1	1	94	100	11.1746
.)).))	chr6:38670741-38670969(-)$1	1	221	227	14.1111
((((((	chr22:47188341-47188569(+)$1	1	9	15	10.9365
.)))).	chr9:95032139-95032360(-)$1	1	129	135	10.9365
))).))	chr17:30677162-30677392(+)$1	1	43	49	9.9047
.).)))	chr1:235491198-235491437(-)$1	1	207	213	11.4126
)).)))	chr1:52227511-52227738(+)$1	1	73	79	10.6190
.(((((	chr17:41244486-41244711(-)$1	1	4	10	11.4126
..))))	chr1:93544809-93545031(+)$1	1	67	73	9.9841
((((((	chr19:58319030-58319253(-)$1	1	133	139	9.9841
)).(((	chr3:153839673-153839893(+)$1	1	124	130	14.1111
.(.(((	chr20:33981861-33982085(-)$1	1	159	165	11.0158
....))	chr19:46119961-46120189(-)$1	1	76	82	11.1746
((((((	chr8:37636586-37636829(+)$1	1	67	73	11.4126
))))((	chr2:233655672-233655914(+)$1	1	79	85	11.1746
))))))	chr3:12881726-12881948(-)$1	1	106	112	10.9365
((((((	chr2:99225028-99225253(+)$1	1	112	118	14.1111
.(((((	chr1:167905027-167905253(-)$1	1	62	68	10.9365
))...)	chr14:100259750-100259975(+)$1	1	168	174	9.9047
((((((	chr15:70389575-70389804(-)$1	1	51	57	11.0158

#PSSM
A : 0.90	U : 0.06	a : 0.01	u : 0.01	
G : 0.85	A : 0.04	U : 0.04	C : 0.03	g : 0.01	
G : 0.71	A : 0.14	C : 0.09	U : 0.03	g : 0.01	
U : 0.68	A : 0.15	G : 0.07	C : 0.06	u : 0.01	
G : 0.98	g : 0.01	
G : 0.98	g : 0.01	

#score	727.1746031746022
#seq	63
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m2_run2.nuc.txt

#NT
AUUUUCAAU	chr4:126370793-126371017(+)$1	224	156	165	11.9206
UUGUUCUUU	chr1:36767083-36767318(+)$1	235	40	49	12.1587
UUUUUUUAC	chrX:153994106-153994327(+)$1	221	16	25	12.7142
UUUUUCCAG	chr13:49833470-49833695(+)$1	225	142	151	11.7619
UUUUUCAAG	chr19:35174922-35175153(+)$1	231	141	150	11.9999
UUUUUUCAU	chr10:129910131-129910373(-)$1	242	13	22	12.5555
UUUUCAUAU	chr4:144135417-144135638(+)$1	221	13	22	11.1269
UUUUUCUUU	chr4:166215492-166215712(+)$1	220	137	146	16.0476
UUUCUCUAC	chrM:14905-15156(+)$1	251	160	169	11.0476
UUUAUCUAA	chr3:121410388-121410615(-)$1	227	216	225	10.3333
UAUUUCUAU	chr1:203818983-203819211(+)$1	228	176	185	14.5396
CUUUUCUUU	chr1:62915848-62916087(+)$1	239	45	54	12.3968
UUGUUCCAU	chr6:86346669-86346901(-)$1	232	83	92	11.4444
UUGUUCUGU	chr16:53190706-53190934(+)$1	228	77	86	11.3650
UUGUUCUAU	chr16:46652057-46652282(-)$1	225	123	132	14.6190
UUUGUUUAU	chr6:87966672-87966898(+)$1	226	131	140	11.2857
UUUUUUUAC	chrX:96212963-96213185(+)$1	222	202	211	12.7142
UUUUUCAAC	chr14:95562731-95562961(-)$1	230	117	126	12.5555
UAUUUUUAU	chr12:80190562-80190795(-)$1	233	3	12	11.7619
UUUUUCUAU	chr7:135635298-135635523(-)$1	225	203	212	18.5079
UUUUUCCUU	chr1:173772063-173772306(-)$1	243	233	242	12.8730
AUUUUCUAC	chr9:138847104-138847329(-)$1	225	35	44	11.8412
AUUUUCGAU	chr7:32908914-32909149(-)$1	235	53	62	11.3650
UAUUUAUAU	chr19:41257192-41257416(+)$1	224	153	162	11.5238
UCGUUCUAU	chr19:44376892-44377119(-)$1	227	181	190	10.5714
UUUUUCUUU	chr21:33057622-33057855(-)$1	233	156	165	16.0476
CUUUUCUUU	chr9:104170934-104171168(+)$1	234	143	152	12.3968
UUGUUCUAC	chr2:74399746-74399968(-)$1	222	27	36	11.6031
UUUUUUUAU	chr5:32364170-32364399(-)$1	229	192	201	15.7301
GUUUUCGAU	chr8:95550446-95550670(-)$1	224	163	172	11.1269
UUUUUCAAG	chr15:56208145-56208367(-)$1	222	15	24	11.9999
UUUUUGUGU	chrX:123181150-123181373(+)$1	223	2	11	11.7619
UUUUUCUGC	chr17:26686293-26686511(+)$1	218	30	39	12.2380
UUUUUCUUU	chr4:39891830-39892051(-)$1	221	5	14	16.0476
UUUCUCAAU	chr1:54269533-54269754(-)$1	221	100	109	11.1269
UUUUUCAAU	chr11:10826404-10826625(-)$1	221	3	12	15.5714
UCUUUCUAU	chr6:64356370-64356596(+)$1	226	50	59	14.4603
UUUUUAUAU	chr16:24576033-24576276(+)$1	243	191	200	15.4920
AUUUCCUAU	chrM:15519-15751(+)$1	232	45	54	10.4920
GUUUUCUCU	chr17:1580786-1581048(-)$1	262	197	206	11.3650
UUAUUCUUU	chr6:109311825-109312042(-)$1	217	27	36	11.7619
CUUUUCUAA	chr3:156422552-156422777(+)$1	225	115	124	11.2063
UGUUUAUAU	chr2:128093348-128093567(-)$1	219	11	20	11.3650
UUUUUCUCU	chr1:220152816-220153055(-)$1	239	78	87	15.2539
AGUUUCUAU	chr1:155448555-155448783(-)$1	228	98	107	10.7301
UUUGUUUAU	chr15:35271855-35272090(-)$1	235	21	30	11.2857
UUUUUUUUU	chr6:49459809-49460031(+)$1	222	185	194	13.2698
UUUUCCAAU	chr12:100720370-100720604(+)$1	234	211	220	11.2063
UUUUUCUAU	chrM:10063-10340(-)$1	277	182	191	18.5079
UUUUCCUAC	chr5:58285580-58285809(-)$1	229	52	61	11.1269
UUCUUCUAU	chr2:201434388-201434615(+)$1	227	198	207	14.2222
UUUUUAAAU	chr1:76260099-76260319(+)$1	220	84	93	12.5555
UCUUUCUAU	chr2:73678805-73679041(+)$1	236	117	126	14.4603
CUUUUCUAC	chr8:77616794-77617015(+)$1	221	8	17	11.8412
CUUUUCUUU	chr1:91405644-91405871(-)$1	227	102	111	12.3968
UAUUUCUUU	chr11:34118656-34118882(+)$1	226	59	68	12.0793
UUUUUAUAU	chr17:38557111-38557345(-)$1	234	61	70	15.4920
UUUUUCUUU	chr4:87685682-87685914(+)$1	232	48	57	16.0476
UUUUUAUCU	chr4:110441470-110441694(+)$1	224	38	47	12.2380
UUUUUCCUU	chr6:83891442-83891668(-)$1	226	4	13	12.8730
UUUUUCUAC	chr14:32562691-32562913(+)$1	222	74	83	15.4920
UUUUUUCAU	chr2:55785835-55786072(-)$1	237	211	220	12.5555

#otherMatches

#Struct PSSM
)))))))))	chr13:23908523-23908744(-)$1	221	29	38	12.7936
ggggrrrrr	chr4:126370793-126371017(+)$1	224	156	165	11.9206
LLLJJJJJJ	chr1:36767083-36767318(+)$1	235	40	49	12.1587
zzzzzzzzz	chrX:153994106-153994327(+)$1	221	16	25	12.7142
:::ffffff	chr13:49833470-49833695(+)$1	225	142	151	11.7619
::::ggggg	chr19:35174922-35175153(+)$1	231	141	150	11.9999
[ggggggg[	chr10:129910131-129910373(-)$1	242	13	22	12.5555
:::iiiiii	chr4:144135417-144135638(+)$1	221	13	22	11.1269
99999ccc5	chr4:166215492-166215712(+)$1	220	137	146	16.0476
:::::::::	chrM:14905-15156(+)$1	251	160	169	11.0476
@@FFFFFF:	chr3:121410388-121410615(-)$1	227	216	225	10.3333
eeemmmmee	chr1:203818983-203819211(+)$1	228	176	185	14.5396
ttttttttt	chr1:62915848-62916087(+)$1	239	45	54	12.3968
""ggggggg	chr6:86346669-86346901(-)$1	232	83	92	11.4444
sssssssdd	chr16:53190706-53190934(+)$1	228	77	86	11.3650
fffff::::	chr16:46652057-46652282(-)$1	225	123	132	14.6190
eeee:::::	chr6:87966672-87966898(+)$1	226	131	140	11.2857
eeeebb22e	chrX:96212963-96213185(+)$1	222	202	211	12.7142
]bb22bb44	chr14:95562731-95562961(-)$1	230	117	126	12.5555
:::::::::	chr12:80190562-80190795(-)$1	233	3	12	11.7619
JJJJJJJJE	chr7:135635298-135635523(-)$1	225	203	212	18.5079
:::::::::	chr1:173772063-173772306(-)$1	243	233	242	12.8730
yyyeeeee:	chr9:138847104-138847329(-)$1	225	35	44	11.8412
!ggggggg[	chr7:32908914-32909149(-)$1	235	53	62	11.3650
+++++++++	chr19:41257192-41257416(+)$1	224	153	162	11.5238
dd::::::C	chr19:44376892-44377119(-)$1	227	181	190	10.5714
^^^^^^^^^	chr21:33057622-33057855(-)$1	233	156	165	16.0476
c::gggggg	chr9:104170934-104171168(+)$1	234	143	152	12.3968
CCKKCCCNN	chr2:74399746-74399968(-)$1	222	27	36	11.6031
JJJJJJJJJ	chr5:32364170-32364399(-)$1	229	192	201	15.7301
ffflllfff	chr8:95550446-95550670(-)$1	224	163	172	11.1269
lccc]dddd	chr15:56208145-56208367(-)$1	222	15	24	11.9999
iiiiiiiii	chrX:123181150-123181373(+)$1	223	2	11	11.7619
JJJJJJJJJ	chr17:26686293-26686511(+)$1	218	30	39	12.2380
d[cccqqqq	chr4:39891830-39892051(-)$1	221	5	14	16.0476
JJJJJKKDD	chr1:54269533-54269754(-)$1	221	100	109	11.1269
:::::::::	chr11:10826404-10826625(-)$1	221	3	12	15.5714
hhhhhhrrr	chr6:64356370-64356596(+)$1	226	50	59	14.4603
======:::	chr16:24576033-24576276(+)$1	243	191	200	15.4920
:::::::::	chrM:15519-15751(+)$1	232	45	54	10.4920
buuuuuuuu	chr17:1580786-1581048(-)$1	262	197	206	11.3650
sssseeeee	chr6:109311825-109312042(-)$1	217	27	36	11.7619
ff:::::::	chr3:156422552-156422777(+)$1	225	115	124	11.2063
cccmmmmcc	chr2:128093348-128093567(-)$1	219	11	20	11.3650
:::ccc[gg	chr1:220152816-220153055(-)$1	239	78	87	15.2539
bb!!dddd^	chr1:155448555-155448783(-)$1	228	98	107	10.7301
GGGGG::::	chr15:35271855-35272090(-)$1	235	21	30	11.2857
oooohhhhh	chr6:49459809-49460031(+)$1	222	185	194	13.2698
BB}EEEEED	chr12:100720370-100720604(+)$1	234	211	220	11.2063
ccchhhhhh	chrM:10063-10340(-)$1	277	182	191	18.5079
gggggg::D	chr5:58285580-58285809(-)$1	229	52	61	11.1269
fffff::::	chr2:201434388-201434615(+)$1	227	198	207	14.2222
:iiiiiiii	chr1:76260099-76260319(+)$1	220	84	93	12.5555
^^^^^^^^^	chr2:73678805-73679041(+)$1	236	117	126	14.4603
=======[d	chr8:77616794-77617015(+)$1	221	8	17	11.8412
c[ggggggg	chr1:91405644-91405871(-)$1	227	102	111	12.3968
ppppppggg	chr11:34118656-34118882(+)$1	226	59	68	12.0793
cc[ddddll	chr17:38557111-38557345(-)$1	234	61	70	15.4920
c!!ccc[cc	chr4:87685682-87685914(+)$1	232	48	57	16.0476
&&&&&iiii	chr4:110441470-110441694(+)$1	224	38	47	12.2380
B{HHHHHHH	chr6:83891442-83891668(-)$1	226	4	13	12.8730
:::::::::	chr14:32562691-32562913(+)$1	222	74	83	15.4920
hhhhhhhhp	chr2:55785835-55786072(-)$1	237	211	220	12.5555

#DB
.........	chr13:23908523-23908744(-)$1	1	29	38	12.7936
((((.....	chr4:126370793-126371017(+)$1	1	156	165	11.9206
...((((((	chr1:36767083-36767318(+)$1	1	40	49	12.1587
.........	chrX:153994106-153994327(+)$1	1	16	25	12.7142
...((((((	chr13:49833470-49833695(+)$1	1	142	151	11.7619
....(((((	chr19:35174922-35175153(+)$1	1	141	150	11.9999
.(((((((.	chr10:129910131-129910373(-)$1	1	13	22	12.5555
...((((((	chr4:144135417-144135638(+)$1	1	13	22	11.1269
.....))).	chr4:166215492-166215712(+)$1	1	137	146	16.0476
.........	chrM:14905-15156(+)$1	1	160	169	11.0476
..)))))).	chr3:121410388-121410615(-)$1	1	216	225	10.3333
(((....))	chr1:203818983-203819211(+)$1	1	176	185	14.5396
.........	chr1:62915848-62916087(+)$1	1	45	54	12.3968
..(((((((	chr6:86346669-86346901(-)$1	1	83	92	11.4444
.......))	chr16:53190706-53190934(+)$1	1	77	86	11.3650
)))))....	chr16:46652057-46652282(-)$1	1	123	132	14.6190
)))).....	chr6:87966672-87966898(+)$1	1	131	140	11.2857
))))))..)	chrX:96212963-96213185(+)$1	1	202	211	12.7142
.))..))..	chr14:95562731-95562961(-)$1	1	117	126	12.5555
.........	chr12:80190562-80190795(-)$1	1	3	12	11.7619
)))))))))	chr7:135635298-135635523(-)$1	1	203	212	18.5079
.........	chr1:173772063-173772306(-)$1	1	233	242	12.8730
...))))).	chr9:138847104-138847329(-)$1	1	35	44	11.8412
.(((((((.	chr7:32908914-32909149(-)$1	1	53	62	11.3650
.........	chr19:41257192-41257416(+)$1	1	153	162	11.5238
))......)	chr19:44376892-44377119(-)$1	1	181	190	10.5714
.........	chr21:33057622-33057855(-)$1	1	156	165	16.0476
)..((((((	chr9:104170934-104171168(+)$1	1	143	152	12.3968
((..(((..	chr2:74399746-74399968(-)$1	1	27	36	11.6031
)))))))))	chr5:32364170-32364399(-)$1	1	192	201	15.7301
(((...)))	chr8:95550446-95550670(-)$1	1	163	172	11.1269
.))).))))	chr15:56208145-56208367(-)$1	1	15	24	11.9999
(((((((((	chrX:123181150-123181373(+)$1	1	2	11	11.7619
(((((((((	chr17:26686293-26686511(+)$1	1	30	39	12.2380
(.(((....	chr4:39891830-39892051(-)$1	1	5	14	16.0476
(((((..((	chr1:54269533-54269754(-)$1	1	100	109	11.1269
.........	chr11:10826404-10826625(-)$1	1	3	12	15.5714
((((((...	chr6:64356370-64356596(+)$1	1	50	59	14.4603
))))))...	chr16:24576033-24576276(+)$1	1	191	200	15.4920
.........	chrM:15519-15751(+)$1	1	45	54	10.4920
(........	chr17:1580786-1581048(-)$1	1	197	206	11.3650
....)))))	chr6:109311825-109312042(-)$1	1	27	36	11.7619
)).......	chr3:156422552-156422777(+)$1	1	115	124	11.2063
(((....))	chr2:128093348-128093567(-)$1	1	11	20	11.3650
...(((.((	chr1:220152816-220153055(-)$1	1	78	87	15.2539
((..((((.	chr1:155448555-155448783(-)$1	1	98	107	10.7301
(((((....	chr15:35271855-35272090(-)$1	1	21	30	11.2857
....)))))	chr6:49459809-49460031(+)$1	1	185	194	13.2698
)).))))))	chr12:100720370-100720604(+)$1	1	211	220	11.2063
)))))))))	chrM:10063-10340(-)$1	1	182	191	18.5079
))))))..(	chr5:58285580-58285809(-)$1	1	52	61	11.1269
)))))....	chr2:201434388-201434615(+)$1	1	198	207	14.2222
.((((((((	chr1:76260099-76260319(+)$1	1	84	93	12.5555
.........	chr2:73678805-73679041(+)$1	1	117	126	14.4603
(((((((.(	chr8:77616794-77617015(+)$1	1	8	17	11.8412
(.(((((((	chr1:91405644-91405871(-)$1	1	102	111	12.3968
......)))	chr11:34118656-34118882(+)$1	1	59	68	12.0793
((.((((..	chr17:38557111-38557345(-)$1	1	61	70	15.4920
(..(((.((	chr4:87685682-87685914(+)$1	1	48	57	16.0476
.....((((	chr4:110441470-110441694(+)$1	1	38	47	12.2380
(.(((((((	chr6:83891442-83891668(-)$1	1	4	13	12.8730
.........	chr14:32562691-32562913(+)$1	1	74	83	15.4920
((((((((.	chr2:55785835-55786072(-)$1	1	211	220	12.5555

#PSSM
U : 0.80	A : 0.07	C : 0.07	G : 0.03	
U : 0.85	A : 0.06	C : 0.04	G : 0.03	
U : 0.87	G : 0.09	A : 0.01	C : 0.01	
U : 0.92	C : 0.03	G : 0.03	A : 0.01	
U : 0.93	C : 0.06	
C : 0.71	U : 0.15	A : 0.11	G : 0.01	
U : 0.73	A : 0.14	C : 0.09	G : 0.03	
A : 0.69	U : 0.20	G : 0.04	C : 0.04	
U : 0.76	C : 0.15	G : 0.04	A : 0.03	

#score	809.2539682539672
#seq	63
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m1_run2.nuc.txt

#NT
GAA	chr22:36913309-36913529(-)$1	220	95	98	8.9999
GAA	chr4:10446328-10446551(-)$1	223	16	19	8.9999
GAA	chr10:96112584-96112806(-)$1	222	3	6	8.9999
GAA	chr5:138266428-138266646(+)$1	218	138	141	8.9999
GAA	chr9:125004088-125004304(-)$1	216	7	10	8.9999
GAA	chr6:87970709-87970930(+)$1	221	25	28	8.9999
GAA	chr11:64543893-64544112(-)$1	219	27	30	8.9999
GAA	chr17:7415708-7415926(+)$1	218	129	132	8.9999
gaa	chr6:97702471-97702690(-)$1	219	14	17	8.9999
GAA	chr5:141364350-141364573(+)$1	223	16	19	8.9999
GAA	chr22:32110645-32110862(-)$1	217	130	133	8.9999
GAA	chr1:205683511-205683729(-)$1	218	69	72	8.9999
GAA	chr11:32955944-32956163(+)$1	219	14	17	8.9999
GAA	chr11:32956428-32956646(+)$1	218	15	18	8.9999
GAA	chr1:52940723-52940944(-)$1	221	15	18	8.9999
GAA	chr12:98926915-98927132(+)$1	217	14	17	8.9999
GAA	chr1:54291371-54291597(-)$1	226	22	25	8.9999
GAA	chr1:213186511-213186729(-)$1	218	29	32	8.9999
GAA	chr19:44660717-44660938(+)$1	221	54	57	8.9999
GAA	chr19:32954240-32954465(+)$1	225	65	68	8.9999
GAA	chr1:226564754-226564971(-)$1	217	25	28	8.9999
GAA	chr17:62496281-62496498(-)$1	217	79	82	8.9999
GAA	chr22:38890573-38890792(-)$1	219	27	30	8.9999
GAA	chr8:48792007-48792228(-)$1	221	66	69	8.9999
GAA	chr17:62499020-62499240(-)$1	220	66	69	8.9999
GAA	chr12:69987191-69987412(+)$1	221	120	123	8.9999
GAA	chr6:28542898-28543119(-)$1	221	3	6	8.9999
GAA	chr7:135298900-135299121(+)$1	221	64	67	8.9999
GAA	chr17:40010339-40010558(-)$1	219	51	54	8.9999
GAA	chr1:220197639-220197858(-)$1	219	1	4	8.9999
GAA	chr9:135140021-135140243(-)$1	222	132	135	8.9999
gaa	chr15:45713198-45713418(+)$1	220	10	13	8.9999
GAA	chr14:102550168-102550390(-)$1	222	34	37	8.9999
GAA	chr1:213181562-213181783(-)$1	221	19	22	8.9999
GAA	chr3:178947020-178947238(+)$1	218	38	41	8.9999
GAA	chrX:13790897-13791122(-)$1	225	60	63	8.9999
GAA	chr5:56546688-56546909(+)$1	221	3	6	8.9999
GAA	chr16:72991730-72991952(-)$1	222	172	175	8.9999
GAA	chr10:62551659-62551883(+)$1	224	15	18	8.9999
GAA	chr17:60042440-60042661(-)$1	221	88	91	8.9999
GAA	chr19:37618918-37619139(+)$1	221	52	55	8.9999
GAA	chr6:44387216-44387434(+)$1	218	13	16	8.9999
GAA	chr2:145157561-145157784(-)$1	223	26	29	8.9999
gaa	chr14:93649711-93649933(-)$1	222	39	42	8.9999
GAA	chr7:97822453-97822670(+)$1	217	15	18	8.9999
GAA	chr5:70793124-70793345(+)$1	221	53	56	8.9999
GAA	chr17:15968784-15969003(-)$1	219	74	77	8.9999
GAA	chr5:145857985-145858209(+)$1	224	3	6	8.9999
GAA	chr9:138703319-138703538(-)$1	219	43	46	8.9999
GAA	chr9:37440842-37441059(-)$1	217	8	11	8.9999
GAA	chr5:135510104-135510325(+)$1	221	36	39	8.9999
GAA	chr9:32541771-32541992(-)$1	221	42	45	8.9999
GAA	chr16:31926562-31926780(+)$1	218	43	46	8.9999
GAA	chr4:57796141-57796357(+)$1	216	0	3	8.9999
GAA	chr7:127014464-127014684(-)$1	220	1	4	8.9999
GAA	chr10:27422868-27423093(-)$1	225	54	57	8.9999
GAA	chr6:7572162-7572381(+)$1	219	1	4	8.9999
GAA	chrX:84525834-84526054(+)$1	220	13	16	8.9999
GAA	chr19:52519413-52519631(-)$1	218	36	39	8.9999
GAA	chrX:39914605-39914821(-)$1	216	76	79	8.9999
GAA	chr15:35274041-35274260(-)$1	219	20	23	8.9999
GAA	chr19:38056336-38056557(-)$1	221	39	42	8.9999
GAA	chr3:52643437-52643655(-)$1	218	31	34	8.9999
GAA	chr1:78031236-78031453(-)$1	217	9	12	8.9999
GAA	chr19:9676935-9677154(-)$1	219	24	27	8.9999
GAA	chr4:36126408-36126622(+)$1	214	13	16	8.9999
GAA	chr10:129905891-129906113(-)$1	222	21	24	8.9999
GAA	chr11:105881421-105881639(-)$1	218	6	9	8.9999
GAA	chr9:37357026-37357242(+)$1	216	8	11	8.9999
GAA	chr2:183860434-183860653(-)$1	219	4	7	8.9999
GAA	chr1:214794002-214794225(+)$1	223	27	30	8.9999
GAA	chr5:112176300-112176524(+)$1	224	7	10	8.9999
GAA	chr1:55608562-55608782(-)$1	220	5	8	8.9999
GAA	chr15:25615891-25616110(-)$1	219	11	14	8.9999
GAA	chr2:37501677-37501897(-)$1	220	57	60	8.9999
GAA	chr12:67703698-67703918(+)$1	220	2	5	8.9999
GAA	chr16:20814050-20814267(-)$1	217	44	47	8.9999
GAA	chr1:62916411-62916632(+)$1	221	13	16	8.9999
GAA	chr8:28413217-28413438(+)$1	221	43	46	8.9999
GAA	chr11:34118662-34118888(+)$1	226	39	42	8.9999
GAA	chr2:55825475-55825696(-)$1	221	73	76	8.9999
GAA	chr1:203767054-203767271(+)$1	217	60	63	8.9999
gaa	chr5:71491303-71491520(+)$1	217	0	3	8.9999
GAA	chrX:123185117-123185334(+)$1	217	51	54	8.9999
GAA	chr11:9597458-9597678(+)$1	220	51	54	8.9999
GAA	chr9:6012589-6012811(-)$1	222	63	66	8.9999
GAA	chr5:68737304-68737523(+)$1	219	14	17	8.9999
GAA	chr19:37618160-37618385(+)$1	225	3	6	8.9999
GAA	chr19:21300581-21300814(+)$1	233	2	5	8.9999
GAA	chr2:37520265-37520482(-)$1	217	5	8	8.9999
GAA	chr20:34241484-34241708(-)$1	224	16	19	8.9999
GAA	chr10:27458891-27459112(+)$1	221	19	22	8.9999
GAA	chr19:41800424-41800642(+)$1	218	61	64	8.9999
GAA	chr12:76739883-76740101(-)$1	218	2	5	8.9999
GAA	chr3:97595932-97596148(+)$1	216	82	85	8.9999
GAA	chr22:22160104-22160322(-)$1	218	16	19	8.9999
GAA	chr2:230670455-230670672(-)$1	217	173	176	8.9999
GAA	chr9:80932564-80932789(+)$1	225	90	93	8.9999

#otherMatches

#Struct PSSM
ccc	chr2:231682395-231682613(+)$1	218	82	85	8.9999
d[d	chr22:36913309-36913529(-)$1	220	95	98	8.9999
RGG	chr4:10446328-10446551(-)$1	223	16	19	8.9999
EEE	chr10:96112584-96112806(-)$1	222	3	6	8.9999
bpp	chr5:138266428-138266646(+)$1	218	138	141	8.9999
g""	chr9:125004088-125004304(-)$1	216	7	10	8.9999
:::	chr6:87970709-87970930(+)$1	221	25	28	8.9999
ddd	chr11:64543893-64544112(-)$1	219	27	30	8.9999
ccn	chr17:7415708-7415926(+)$1	218	129	132	8.9999
H::	chr6:97702471-97702690(-)$1	219	14	17	8.9999
JJJ	chr5:141364350-141364573(+)$1	223	16	19	8.9999
:::	chr22:32110645-32110862(-)$1	217	130	133	8.9999
eee	chr1:205683511-205683729(-)$1	218	69	72	8.9999
ddd	chr11:32955944-32956163(+)$1	219	14	17	8.9999
:::	chr11:32956428-32956646(+)$1	218	15	18	8.9999
fff	chr1:52940723-52940944(-)$1	221	15	18	8.9999
OOO	chr12:98926915-98927132(+)$1	217	14	17	8.9999
JJ:	chr1:54291371-54291597(-)$1	226	22	25	8.9999
bll	chr1:213186511-213186729(-)$1	218	29	32	8.9999
dd:	chr19:44660717-44660938(+)$1	221	54	57	8.9999
c##	chr19:32954240-32954465(+)$1	225	65	68	8.9999
C::	chr1:226564754-226564971(-)$1	217	25	28	8.9999
555	chr17:62496281-62496498(-)$1	217	79	82	8.9999
yyy	chr22:38890573-38890792(-)$1	219	27	30	8.9999
hhh	chr8:48792007-48792228(-)$1	221	66	69	8.9999
CCK	chr17:62499020-62499240(-)$1	220	66	69	8.9999
d::	chr12:69987191-69987412(+)$1	221	120	123	8.9999
d##	chr6:28542898-28543119(-)$1	221	3	6	8.9999
GGG	chr7:135298900-135299121(+)$1	221	64	67	8.9999
nnc	chr17:40010339-40010558(-)$1	219	51	54	8.9999
:::	chr1:220197639-220197858(-)$1	219	1	4	8.9999
ccc	chr9:135140021-135140243(-)$1	222	132	135	8.9999
eee	chr15:45713198-45713418(+)$1	220	10	13	8.9999
bnn	chr14:102550168-102550390(-)$1	222	34	37	8.9999
:::	chr1:213181562-213181783(-)$1	221	19	22	8.9999
[a!	chr3:178947020-178947238(+)$1	218	38	41	8.9999
yyy	chrX:13790897-13791122(-)$1	225	60	63	8.9999
DDD	chr5:56546688-56546909(+)$1	221	3	6	8.9999
dd2	chr16:72991730-72991952(-)$1	222	172	175	8.9999
gg[	chr10:62551659-62551883(+)$1	224	15	18	8.9999
ddd	chr17:60042440-60042661(-)$1	221	88	91	8.9999
F::	chr19:37618918-37619139(+)$1	221	52	55	8.9999
:::	chr6:44387216-44387434(+)$1	218	13	16	8.9999
CCC	chr2:145157561-145157784(-)$1	223	26	29	8.9999
d!!	chr14:93649711-93649933(-)$1	222	39	42	8.9999
ccc	chr7:97822453-97822670(+)$1	217	15	18	8.9999
ppp	chr5:70793124-70793345(+)$1	221	53	56	8.9999
e::	chr17:15968784-15969003(-)$1	219	74	77	8.9999
III	chr5:145857985-145858209(+)$1	224	3	6	8.9999
GGG	chr9:138703319-138703538(-)$1	219	43	46	8.9999
DNN	chr9:37440842-37441059(-)$1	217	8	11	8.9999
ccc	chr5:135510104-135510325(+)$1	221	36	39	8.9999
:::	chr9:32541771-32541992(-)$1	221	42	45	8.9999
%%b	chr16:31926562-31926780(+)$1	218	43	46	8.9999
:::	chr4:57796141-57796357(+)$1	216	0	3	8.9999
:::	chr7:127014464-127014684(-)$1	220	1	4	8.9999
ddd	chr10:27422868-27423093(-)$1	225	54	57	8.9999
:DD	chr6:7572162-7572381(+)$1	219	1	4	8.9999
:::	chrX:84525834-84526054(+)$1	220	13	16	8.9999
:::	chr19:52519413-52519631(-)$1	218	36	39	8.9999
JJJ	chrX:39914605-39914821(-)$1	216	76	79	8.9999
ggg	chr15:35274041-35274260(-)$1	219	20	23	8.9999
d::	chr19:38056336-38056557(-)$1	221	39	42	8.9999
bll	chr3:52643437-52643655(-)$1	218	31	34	8.9999
E::	chr1:78031236-78031453(-)$1	217	9	12	8.9999
qqq	chr19:9676935-9677154(-)$1	219	24	27	8.9999
""e	chr4:36126408-36126622(+)$1	214	13	16	8.9999
D::	chr10:129905891-129906113(-)$1	222	21	24	8.9999
:::	chr11:105881421-105881639(-)$1	218	6	9	8.9999
qqq	chr9:37357026-37357242(+)$1	216	8	11	8.9999
CC{	chr2:183860434-183860653(-)$1	219	4	7	8.9999
+++	chr1:214794002-214794225(+)$1	223	27	30	8.9999
qqq	chr5:112176300-112176524(+)$1	224	7	10	8.9999
ggg	chr1:55608562-55608782(-)$1	220	5	8	8.9999
F::	chr15:25615891-25616110(-)$1	219	11	14	8.9999
ddd	chr2:37501677-37501897(-)$1	220	57	60	8.9999
GGG	chr12:67703698-67703918(+)$1	220	2	5	8.9999
e33	chr16:20814050-20814267(-)$1	217	44	47	8.9999
b!!	chr1:62916411-62916632(+)$1	221	13	16	8.9999
==:	chr8:28413217-28413438(+)$1	221	43	46	8.9999
Edd	chr11:34118662-34118888(+)$1	226	39	42	8.9999
ggg	chr2:55825475-55825696(-)$1	221	73	76	8.9999
qqq	chr1:203767054-203767271(+)$1	217	60	63	8.9999
:::	chr5:71491303-71491520(+)$1	217	0	3	8.9999
eeo	chrX:123185117-123185334(+)$1	217	51	54	8.9999
bbm	chr11:9597458-9597678(+)$1	220	51	54	8.9999
fff	chr9:6012589-6012811(-)$1	222	63	66	8.9999
HHH	chr5:68737304-68737523(+)$1	219	14	17	8.9999
:::	chr19:37618160-37618385(+)$1	225	3	6	8.9999
:::	chr19:21300581-21300814(+)$1	233	2	5	8.9999
:::	chr2:37520265-37520482(-)$1	217	5	8	8.9999
:::	chr20:34241484-34241708(-)$1	224	16	19	8.9999
e:B	chr10:27458891-27459112(+)$1	221	19	22	8.9999
h##	chr19:41800424-41800642(+)$1	218	61	64	8.9999
:::	chr12:76739883-76740101(-)$1	218	2	5	8.9999
hhh	chr3:97595932-97596148(+)$1	216	82	85	8.9999
EE:	chr22:22160104-22160322(-)$1	218	16	19	8.9999
ccc	chr2:230670455-230670672(-)$1	217	173	176	8.9999
fqq	chr9:80932564-80932789(+)$1	225	90	93	8.9999

#DB
)))	chr2:231682395-231682613(+)$1	1	82	85	8.9999
(.(	chr22:36913309-36913529(-)$1	1	95	98	8.9999
.((	chr4:10446328-10446551(-)$1	1	16	19	8.9999
(((	chr10:96112584-96112806(-)$1	1	3	6	8.9999
(..	chr5:138266428-138266646(+)$1	1	138	141	8.9999
(..	chr9:125004088-125004304(-)$1	1	7	10	8.9999
...	chr6:87970709-87970930(+)$1	1	25	28	8.9999
)))	chr11:64543893-64544112(-)$1	1	27	30	8.9999
((.	chr17:7415708-7415926(+)$1	1	129	132	8.9999
(..	chr6:97702471-97702690(-)$1	1	14	17	8.9999
(((	chr5:141364350-141364573(+)$1	1	16	19	8.9999
...	chr22:32110645-32110862(-)$1	1	130	133	8.9999
)))	chr1:205683511-205683729(-)$1	1	69	72	8.9999
)))	chr11:32955944-32956163(+)$1	1	14	17	8.9999
...	chr11:32956428-32956646(+)$1	1	15	18	8.9999
(((	chr1:52940723-52940944(-)$1	1	15	18	8.9999
...	chr12:98926915-98927132(+)$1	1	14	17	8.9999
((.	chr1:54291371-54291597(-)$1	1	22	25	8.9999
(..	chr1:213186511-213186729(-)$1	1	29	32	8.9999
)).	chr19:44660717-44660938(+)$1	1	54	57	8.9999
(..	chr19:32954240-32954465(+)$1	1	65	68	8.9999
(..	chr1:226564754-226564971(-)$1	1	25	28	8.9999
...	chr17:62496281-62496498(-)$1	1	79	82	8.9999
...	chr22:38890573-38890792(-)$1	1	27	30	8.9999
)))	chr8:48792007-48792228(-)$1	1	66	69	8.9999
((.	chr17:62499020-62499240(-)$1	1	66	69	8.9999
)..	chr12:69987191-69987412(+)$1	1	120	123	8.9999
(..	chr6:28542898-28543119(-)$1	1	3	6	8.9999
(((	chr7:135298900-135299121(+)$1	1	64	67	8.9999
..)	chr17:40010339-40010558(-)$1	1	51	54	8.9999
...	chr1:220197639-220197858(-)$1	1	1	4	8.9999
(((	chr9:135140021-135140243(-)$1	1	132	135	8.9999
(((	chr15:45713198-45713418(+)$1	1	10	13	8.9999
(..	chr14:102550168-102550390(-)$1	1	34	37	8.9999
...	chr1:213181562-213181783(-)$1	1	19	22	8.9999
.(.	chr3:178947020-178947238(+)$1	1	38	41	8.9999
...	chrX:13790897-13791122(-)$1	1	60	63	8.9999
(((	chr5:56546688-56546909(+)$1	1	3	6	8.9999
)).	chr16:72991730-72991952(-)$1	1	172	175	8.9999
((.	chr10:62551659-62551883(+)$1	1	15	18	8.9999
)))	chr17:60042440-60042661(-)$1	1	88	91	8.9999
(..	chr19:37618918-37619139(+)$1	1	52	55	8.9999
...	chr6:44387216-44387434(+)$1	1	13	16	8.9999
(((	chr2:145157561-145157784(-)$1	1	26	29	8.9999
(..	chr14:93649711-93649933(-)$1	1	39	42	8.9999
(((	chr7:97822453-97822670(+)$1	1	15	18	8.9999
...	chr5:70793124-70793345(+)$1	1	53	56	8.9999
)..	chr17:15968784-15969003(-)$1	1	74	77	8.9999
(((	chr5:145857985-145858209(+)$1	1	3	6	8.9999
(((	chr9:138703319-138703538(-)$1	1	43	46	8.9999
(..	chr9:37440842-37441059(-)$1	1	8	11	8.9999
)))	chr5:135510104-135510325(+)$1	1	36	39	8.9999
...	chr9:32541771-32541992(-)$1	1	42	45	8.9999
..(	chr16:31926562-31926780(+)$1	1	43	46	8.9999
...	chr4:57796141-57796357(+)$1	1	0	3	8.9999
...	chr7:127014464-127014684(-)$1	1	1	4	8.9999
(((	chr10:27422868-27423093(-)$1	1	54	57	8.9999
.((	chr6:7572162-7572381(+)$1	1	1	4	8.9999
...	chrX:84525834-84526054(+)$1	1	13	16	8.9999
...	chr19:52519413-52519631(-)$1	1	36	39	8.9999
(((	chrX:39914605-39914821(-)$1	1	76	79	8.9999
)))	chr15:35274041-35274260(-)$1	1	20	23	8.9999
)..	chr19:38056336-38056557(-)$1	1	39	42	8.9999
(..	chr3:52643437-52643655(-)$1	1	31	34	8.9999
(..	chr1:78031236-78031453(-)$1	1	9	12	8.9999
...	chr19:9676935-9677154(-)$1	1	24	27	8.9999
..(	chr4:36126408-36126622(+)$1	1	13	16	8.9999
(..	chr10:129905891-129906113(-)$1	1	21	24	8.9999
...	chr11:105881421-105881639(-)$1	1	6	9	8.9999
...	chr9:37357026-37357242(+)$1	1	8	11	8.9999
((.	chr2:183860434-183860653(-)$1	1	4	7	8.9999
...	chr1:214794002-214794225(+)$1	1	27	30	8.9999
...	chr5:112176300-112176524(+)$1	1	7	10	8.9999
(((	chr1:55608562-55608782(-)$1	1	5	8	8.9999
(..	chr15:25615891-25616110(-)$1	1	11	14	8.9999
(((	chr2:37501677-37501897(-)$1	1	57	60	8.9999
(((	chr12:67703698-67703918(+)$1	1	2	5	8.9999
)..	chr16:20814050-20814267(-)$1	1	44	47	8.9999
(..	chr1:62916411-62916632(+)$1	1	13	16	8.9999
)).	chr8:28413217-28413438(+)$1	1	43	46	8.9999
(((	chr11:34118662-34118888(+)$1	1	39	42	8.9999
(((	chr2:55825475-55825696(-)$1	1	73	76	8.9999
...	chr1:203767054-203767271(+)$1	1	60	63	8.9999
...	chr5:71491303-71491520(+)$1	1	0	3	8.9999
((.	chrX:123185117-123185334(+)$1	1	51	54	8.9999
((.	chr11:9597458-9597678(+)$1	1	51	54	8.9999
(((	chr9:6012589-6012811(-)$1	1	63	66	8.9999
(((	chr5:68737304-68737523(+)$1	1	14	17	8.9999
...	chr19:37618160-37618385(+)$1	1	3	6	8.9999
...	chr19:21300581-21300814(+)$1	1	2	5	8.9999
...	chr2:37520265-37520482(-)$1	1	5	8	8.9999
...	chr20:34241484-34241708(-)$1	1	16	19	8.9999
).(	chr10:27458891-27459112(+)$1	1	19	22	8.9999
(..	chr19:41800424-41800642(+)$1	1	61	64	8.9999
...	chr12:76739883-76740101(-)$1	1	2	5	8.9999
)))	chr3:97595932-97596148(+)$1	1	82	85	8.9999
((.	chr22:22160104-22160322(-)$1	1	16	19	8.9999
(((	chr2:230670455-230670672(-)$1	1	173	176	8.9999
(..	chr9:80932564-80932789(+)$1	1	90	93	8.9999

#PSSM
G : 0.95	g : 0.04	
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m3_run1.nuc.txt

#NT
UGG	chr2:130948134-130948397(+)$1	263	34	37	9.0000
UGG	chr17:8108506-8108790(-)$1	284	1	4	9.0000
UGG	chr10:43882688-43882934(-)$1	246	2	5	9.0000
UGG	chr20:60963264-60963520(+)$1	256	16	19	9.0000
UGG	chr5:14758560-14758798(-)$1	238	136	139	9.0000
UGG	chr17:79826165-79826559(-)$1	394	47	50	9.0000
UGG	chr16:449526-449839(+)$1	313	1	4	9.0000
UGG	chrX:100646347-100646652(+)$1	305	10	13	9.0000
UGG	chr8:38034343-38034728(+)$1	385	4	7	9.0000
UGG	chr16:30747479-30747807(+)$1	328	35	38	9.0000
UGG	chr2:232324817-232325098(-)$1	281	37	40	9.0000
UGG	chr19:49993633-49993933(+)$1	300	0	3	9.0000
UGG	chr17:47126661-47127101(+)$1	440	11	14	9.0000
UGG	chr12:124114860-124115172(-)$1	312	49	52	9.0000
UGG	chr6:33243641-33243943(+)$1	302	39	42	9.0000
UGG	chr19:39924061-39924309(-)$1	248	3	6	9.0000
UGG	chr12:21794895-21795159(-)$1	264	3	6	9.0000
UGG	chr1:116932009-116932356(+)$1	347	61	64	9.0000
UGG	chr4:109543014-109543280(+)$1	266	57	60	9.0000
UGG	chr3:128888977-128889409(-)$1	432	8	11	9.0000
UGG	chr13:27829305-27829563(+)$1	258	45	48	9.0000
UGG	chr6:31498730-31499074(-)$1	344	14	17	9.0000
UGG	chr19:59058863-59059157(+)$1	294	33	36	9.0000
UGG	chr6:44217311-44217665(+)$1	354	50	53	9.0000
UGG	chr12:98991533-98991826(+)$1	293	12	15	9.0000
UGG	chr1:213181549-213181797(-)$1	248	6	9	9.0000
UGG	chr8:26227720-26228068(+)$1	348	64	67	9.0000
UGG	chr3:47162342-47162697(-)$1	355	69	72	9.0000
ugg	chr10:62539798-62540047(+)$1	249	10	13	9.0000
UGG	chr16:47487823-47488104(-)$1	281	68	71	9.0000
UGG	chr6:26158438-26158929(+)$1	491	137	140	9.0000
UGG	chr3:113442793-113443024(-)$1	231	6	9	9.0000
UGG	chr11:94231566-94231932(+)$1	366	34	37	9.0000
UGG	chr19:39923755-39924158(-)$1	403	8	11	9.0000
UGG	chr6:160206317-160206565(-)$1	248	87	90	9.0000
UGG	chr7:25163010-25163466(-)$1	456	6	9	9.0000
UGG	chr1:23637120-23637390(-)$1	270	26	29	9.0000
UGG	chr9:86585711-86585927(-)$1	216	102	105	9.0000
UGG	chr22:41320323-41320586(+)$1	263	71	74	9.0000
UGG	chr12:95365016-95365389(-)$1	373	0	3	9.0000
UGG	chr20:34542012-34542321(-)$1	309	108	111	9.0000
UGG	chr5:180663829-180664084(-)$1	255	53	56	9.0000
UGG	chr17:75199590-75199840(+)$1	250	20	23	9.0000
UGG	chr3:49166115-49166352(-)$1	237	12	15	9.0000
UGG	chr9:91929985-91930312(+)$1	327	68	71	9.0000
UGG	chr21:34923442-34923861(+)$1	419	2	5	9.0000
UGG	chr2:32639932-32640194(+)$1	262	40	43	9.0000
UGG	chr14:102548506-102548801(-)$1	295	21	24	9.0000
UGG	chr7:97481352-97481850(-)$1	498	86	89	9.0000
UGG	chr11:66393965-66394385(+)$1	420	61	64	9.0000
UGG	chr4:99993410-99993675(-)$1	265	8	11	9.0000
UGG	chr12:6646166-6646482(+)$1	316	6	9	9.0000
UGG	chr16:2011961-2012371(-)$1	410	6	9	9.0000
UGG	chr16:74670143-74670390(-)$1	247	78	81	9.0000
UGG	chr15:66792293-66792574(-)$1	281	186	189	9.0000
UGG	chr18:47016756-47017022(-)$1	266	42	45	9.0000
UGG	chr9:135554035-135554290(+)$1	255	57	60	9.0000
UGG	chr10:70100830-70101166(+)$1	336	0	3	9.0000
UGG	chr22:21272240-21272633(+)$1	393	21	24	9.0000
UGG	chr1:1509789-1510170(-)$1	381	71	74	9.0000
UGG	chr6:31593752-31594039(+)$1	287	0	3	9.0000
UGG	chr6:116600049-116600308(-)$1	259	0	3	9.0000
UGG	chr19:55915657-55915946(-)$1	289	22	25	9.0000
UGG	chr6:27419224-27419476(-)$1	252	133	136	9.0000
UGG	chr8:42977726-42977970(+)$1	244	1	4	9.0000
UGG	chrX:24024484-24024917(-)$1	433	61	64	9.0000
UGG	chr7:157177460-157177780(+)$1	320	113	116	9.0000
UGG	chr1:161070313-161070649(-)$1	336	91	94	9.0000
UGG	chr16:1828045-1828307(-)$1	262	66	69	9.0000
UGG	chr19:47278632-47279104(-)$1	472	34	37	9.0000
UGG	chr1:44441873-44442146(+)$1	273	14	17	9.0000
UGG	chr6:137524698-137524922(-)$1	224	32	35	9.0000
UGG	chr1:35652560-35652823(-)$1	263	14	17	9.0000
UGG	chr16:75675361-75675632(-)$1	271	134	137	9.0000
UGG	chr1:228284678-228285029(+)$1	351	5	8	9.0000
UGG	chr2:74438225-74438518(+)$1	293	211	214	9.0000
UGG	chr16:89627247-89627571(+)$1	324	21	24	9.0000
UGG	chr11:75115615-75116012(+)$1	397	36	39	9.0000
UGG	chr17:7481044-7481334(+)$1	290	7	10	9.0000
UGG	chr17:65336841-65337197(-)$1	356	149	152	9.0000
UGG	chr3:12626527-12626828(-)$1	301	5	8	9.0000
UGG	chr19:3982143-3982522(-)$1	379	122	125	9.0000
UGG	chr11:118472240-118472511(+)$1	271	17	20	9.0000
UGG	chr16:87867919-87868242(-)$1	323	3	6	9.0000
UGG	chr19:51301287-51301671(-)$1	384	7	10	9.0000
UGG	chr1:228295281-228295518(-)$1	237	12	15	9.0000
UGG	chr22:19035913-19036171(-)$1	258	45	48	9.0000
UGG	chr19:39924204-39924501(-)$1	297	7	10	9.0000
UGG	chr20:377050-377459(+)$1	409	78	81	9.0000
UGG	chr9:131455816-131456187(+)$1	371	16	19	9.0000
UGG	chr16:29827840-29828101(+)$1	261	0	3	9.0000
UGG	chr6:74229505-74229878(-)$1	373	16	19	9.0000
UGG	chr5:149825071-149825347(-)$1	276	27	30	9.0000
UGG	chr12:56511182-56511484(+)$1	302	7	10	9.0000
UGG	chrX:71494802-71495100(-)$1	298	3	6	9.0000
UGG	chr15:68582611-68582859(+)$1	248	25	28	9.0000
UGG	chr22:29191097-29191377(-)$1	280	24	27	9.0000
UGG	chr14:103986705-103987029(-)$1	324	1	4	9.0000
UGG	chr1:32505015-32505274(+)$1	259	29	32	9.0000

#otherMatches

#Struct PSSM
2dd	chr5:176764620-176764886(-)$1	266	22	25	9.0000
ggg	chr2:130948134-130948397(+)$1	263	34	37	9.0000
:CC	chr17:8108506-8108790(-)$1	284	1	4	9.0000
DD{	chr10:43882688-43882934(-)$1	246	2	5	9.0000
b[e	chr20:60963264-60963520(+)$1	256	16	19	9.0000
c]b	chr5:14758560-14758798(-)$1	238	136	139	9.0000
eee	chr17:79826165-79826559(-)$1	394	47	50	9.0000
B{I	chr16:449526-449839(+)$1	313	1	4	9.0000
mcc	chrX:100646347-100646652(+)$1	305	10	13	9.0000
GGG	chr8:38034343-38034728(+)$1	385	4	7	9.0000
cll	chr16:30747479-30747807(+)$1	328	35	38	9.0000
'''	chr2:232324817-232325098(-)$1	281	37	40	9.0000
III	chr19:49993633-49993933(+)$1	300	0	3	9.0000
LCC	chr17:47126661-47127101(+)$1	440	11	14	9.0000
mme	chr12:124114860-124115172(-)$1	312	49	52	9.0000
{GG	chr6:33243641-33243943(+)$1	302	39	42	9.0000
fff	chr19:39924061-39924309(-)$1	248	3	6	9.0000
DDD	chr12:21794895-21795159(-)$1	264	3	6	9.0000
qqq	chr1:116932009-116932356(+)$1	347	61	64	9.0000
fff	chr4:109543014-109543280(+)$1	266	57	60	9.0000
ddd	chr3:128888977-128889409(-)$1	432	8	11	9.0000
GGG	chr13:27829305-27829563(+)$1	258	45	48	9.0000
hhh	chr6:31498730-31499074(-)$1	344	14	17	9.0000
HGG	chr19:59058863-59059157(+)$1	294	33	36	9.0000
:dd	chr6:44217311-44217665(+)$1	354	50	53	9.0000
cc[	chr12:98991533-98991826(+)$1	293	12	15	9.0000
HHH	chr1:213181549-213181797(-)$1	248	6	9	9.0000
cc[	chr8:26227720-26228068(+)$1	348	64	67	9.0000
eee	chr3:47162342-47162697(-)$1	355	69	72	9.0000
eee	chr10:62539798-62540047(+)$1	249	10	13	9.0000
fff	chr16:47487823-47488104(-)$1	281	68	71	9.0000
DDD	chr6:26158438-26158929(+)$1	491	137	140	9.0000
ddd	chr3:113442793-113443024(-)$1	231	6	9	9.0000
JJJ	chr11:94231566-94231932(+)$1	366	34	37	9.0000
GGG	chr19:39923755-39924158(-)$1	403	8	11	9.0000
ddd	chr6:160206317-160206565(-)$1	248	87	90	9.0000
GGG	chr7:25163010-25163466(-)$1	456	6	9	9.0000
hhh	chr1:23637120-23637390(-)$1	270	26	29	9.0000
c]c	chr9:86585711-86585927(-)$1	216	102	105	9.0000
2cc	chr22:41320323-41320586(+)$1	263	71	74	9.0000
ccc	chr12:95365016-95365389(-)$1	373	0	3	9.0000
f]a	chr20:34542012-34542321(-)$1	309	108	111	9.0000
]bb	chr5:180663829-180664084(-)$1	255	53	56	9.0000
dde	chr17:75199590-75199840(+)$1	250	20	23	9.0000
GDD	chr3:49166115-49166352(-)$1	237	12	15	9.0000
c::	chr9:91929985-91930312(+)$1	327	68	71	9.0000
GGG	chr21:34923442-34923861(+)$1	419	2	5	9.0000
eee	chr2:32639932-32640194(+)$1	262	40	43	9.0000
FF{	chr14:102548506-102548801(-)$1	295	21	24	9.0000
fff	chr7:97481352-97481850(-)$1	498	86	89	9.0000
nee	chr11:66393965-66394385(+)$1	420	61	64	9.0000
HHH	chr4:99993410-99993675(-)$1	265	8	11	9.0000
KDD	chr12:6646166-6646482(+)$1	316	6	9	9.0000
qqq	chr16:2011961-2012371(-)$1	410	6	9	9.0000
ccc	chr16:74670143-74670390(-)$1	247	78	81	9.0000
EEE	chr15:66792293-66792574(-)$1	281	186	189	9.0000
ggg	chr18:47016756-47017022(-)$1	266	42	45	9.0000
{DD	chr9:135554035-135554290(+)$1	255	57	60	9.0000
:::	chr10:70100830-70101166(+)$1	336	0	3	9.0000
JDD	chr22:21272240-21272633(+)$1	393	21	24	9.0000
{CC	chr1:1509789-1510170(-)$1	381	71	74	9.0000
:::	chr6:31593752-31594039(+)$1	287	0	3	9.0000
:::	chr6:116600049-116600308(-)$1	259	0	3	9.0000
Ddd	chr19:55915657-55915946(-)$1	289	22	25	9.0000
ddd	chr6:27419224-27419476(-)$1	252	133	136	9.0000
:BB	chr8:42977726-42977970(+)$1	244	1	4	9.0000
ugg	chrX:24024484-24024917(-)$1	433	61	64	9.0000
bbd	chr7:157177460-157177780(+)$1	320	113	116	9.0000
JJJ	chr1:161070313-161070649(-)$1	336	91	94	9.0000
ddd	chr16:1828045-1828307(-)$1	262	66	69	9.0000
e]c	chr19:47278632-47279104(-)$1	472	34	37	9.0000
{EE	chr1:44441873-44442146(+)$1	273	14	17	9.0000
fff	chr6:137524698-137524922(-)$1	224	32	35	9.0000
EEE	chr1:35652560-35652823(-)$1	263	14	17	9.0000
hhh	chr16:75675361-75675632(-)$1	271	134	137	9.0000
JJJ	chr1:228284678-228285029(+)$1	351	5	8	9.0000
ggg	chr2:74438225-74438518(+)$1	293	211	214	9.0000
ccc	chr16:89627247-89627571(+)$1	324	21	24	9.0000
]dd	chr11:75115615-75116012(+)$1	397	36	39	9.0000
ddd	chr17:7481044-7481334(+)$1	290	7	10	9.0000
bff	chr17:65336841-65337197(-)$1	356	149	152	9.0000
HHH	chr3:12626527-12626828(-)$1	301	5	8	9.0000
]dd	chr19:3982143-3982522(-)$1	379	122	125	9.0000
HHH	chr11:118472240-118472511(+)$1	271	17	20	9.0000
C::	chr16:87867919-87868242(-)$1	323	3	6	9.0000
EEE	chr19:51301287-51301671(-)$1	384	7	10	9.0000
MEE	chr1:228295281-228295518(-)$1	237	12	15	9.0000
eee	chr22:19035913-19036171(-)$1	258	45	48	9.0000
::e	chr19:39924204-39924501(-)$1	297	7	10	9.0000
D:d	chr20:377050-377459(+)$1	409	78	81	9.0000
iii	chr9:131455816-131456187(+)$1	371	16	19	9.0000
FFF	chr16:29827840-29828101(+)$1	261	0	3	9.0000
DDD	chr6:74229505-74229878(-)$1	373	16	19	9.0000
ddd	chr5:149825071-149825347(-)$1	276	27	30	9.0000
DDD	chr12:56511182-56511484(+)$1	302	7	10	9.0000
eeb	chrX:71494802-71495100(-)$1	298	3	6	9.0000
cc:	chr15:68582611-68582859(+)$1	248	25	28	9.0000
]cc	chr22:29191097-29191377(-)$1	280	24	27	9.0000
:::	chr14:103986705-103987029(-)$1	324	1	4	9.0000
NNN	chr1:32505015-32505274(+)$1	259	29	32	9.0000

#DB
.))	chr5:176764620-176764886(-)$1	1	22	25	9.0000
)))	chr2:130948134-130948397(+)$1	1	34	37	9.0000
.((	chr17:8108506-8108790(-)$1	1	1	4	9.0000
((.	chr10:43882688-43882934(-)$1	1	2	5	9.0000
(.(	chr20:60963264-60963520(+)$1	1	16	19	9.0000
).)	chr5:14758560-14758798(-)$1	1	136	139	9.0000
)))	chr17:79826165-79826559(-)$1	1	47	50	9.0000
(.(	chr16:449526-449839(+)$1	1	1	4	9.0000
.))	chrX:100646347-100646652(+)$1	1	10	13	9.0000
(((	chr8:38034343-38034728(+)$1	1	4	7	9.0000
(..	chr16:30747479-30747807(+)$1	1	35	38	9.0000
...	chr2:232324817-232325098(-)$1	1	37	40	9.0000
(((	chr19:49993633-49993933(+)$1	1	0	3	9.0000
.((	chr17:47126661-47127101(+)$1	1	11	14	9.0000
..)	chr12:124114860-124115172(-)$1	1	49	52	9.0000
.((	chr6:33243641-33243943(+)$1	1	39	42	9.0000
(((	chr19:39924061-39924309(-)$1	1	3	6	9.0000
(((	chr12:21794895-21795159(-)$1	1	3	6	9.0000
...	chr1:116932009-116932356(+)$1	1	61	64	9.0000
(((	chr4:109543014-109543280(+)$1	1	57	60	9.0000
(((	chr3:128888977-128889409(-)$1	1	8	11	9.0000
(((	chr13:27829305-27829563(+)$1	1	45	48	9.0000
(((	chr6:31498730-31499074(-)$1	1	14	17	9.0000
(((	chr19:59058863-59059157(+)$1	1	33	36	9.0000
.((	chr6:44217311-44217665(+)$1	1	50	53	9.0000
((.	chr12:98991533-98991826(+)$1	1	12	15	9.0000
(((	chr1:213181549-213181797(-)$1	1	6	9	9.0000
((.	chr8:26227720-26228068(+)$1	1	64	67	9.0000
)))	chr3:47162342-47162697(-)$1	1	69	72	9.0000
(((	chr10:62539798-62540047(+)$1	1	10	13	9.0000
(((	chr16:47487823-47488104(-)$1	1	68	71	9.0000
(((	chr6:26158438-26158929(+)$1	1	137	140	9.0000
(((	chr3:113442793-113443024(-)$1	1	6	9	9.0000
(((	chr11:94231566-94231932(+)$1	1	34	37	9.0000
(((	chr19:39923755-39924158(-)$1	1	8	11	9.0000
)))	chr6:160206317-160206565(-)$1	1	87	90	9.0000
(((	chr7:25163010-25163466(-)$1	1	6	9	9.0000
(((	chr1:23637120-23637390(-)$1	1	26	29	9.0000
).)	chr9:86585711-86585927(-)$1	1	102	105	9.0000
.))	chr22:41320323-41320586(+)$1	1	71	74	9.0000
(((	chr12:95365016-95365389(-)$1	1	0	3	9.0000
).)	chr20:34542012-34542321(-)$1	1	108	111	9.0000
.))	chr5:180663829-180664084(-)$1	1	53	56	9.0000
)))	chr17:75199590-75199840(+)$1	1	20	23	9.0000
(((	chr3:49166115-49166352(-)$1	1	12	15	9.0000
)..	chr9:91929985-91930312(+)$1	1	68	71	9.0000
(((	chr21:34923442-34923861(+)$1	1	2	5	9.0000
(((	chr2:32639932-32640194(+)$1	1	40	43	9.0000
((.	chr14:102548506-102548801(-)$1	1	21	24	9.0000
)))	chr7:97481352-97481850(-)$1	1	86	89	9.0000
.))	chr11:66393965-66394385(+)$1	1	61	64	9.0000
(((	chr4:99993410-99993675(-)$1	1	8	11	9.0000
.((	chr12:6646166-6646482(+)$1	1	6	9	9.0000
...	chr16:2011961-2012371(-)$1	1	6	9	9.0000
)))	chr16:74670143-74670390(-)$1	1	78	81	9.0000
)))	chr15:66792293-66792574(-)$1	1	186	189	9.0000
(((	chr18:47016756-47017022(-)$1	1	42	45	9.0000
.((	chr9:135554035-135554290(+)$1	1	57	60	9.0000
...	chr10:70100830-70101166(+)$1	1	0	3	9.0000
(((	chr22:21272240-21272633(+)$1	1	21	24	9.0000
.((	chr1:1509789-1510170(-)$1	1	71	74	9.0000
...	chr6:31593752-31594039(+)$1	1	0	3	9.0000
...	chr6:116600049-116600308(-)$1	1	0	3	9.0000
(((	chr19:55915657-55915946(-)$1	1	22	25	9.0000
(((	chr6:27419224-27419476(-)$1	1	133	136	9.0000
.((	chr8:42977726-42977970(+)$1	1	1	4	9.0000
.))	chrX:24024484-24024917(-)$1	1	61	64	9.0000
(((	chr7:157177460-157177780(+)$1	1	113	116	9.0000
(((	chr1:161070313-161070649(-)$1	1	91	94	9.0000
)))	chr16:1828045-1828307(-)$1	1	66	69	9.0000
).)	chr19:47278632-47279104(-)$1	1	34	37	9.0000
.((	chr1:44441873-44442146(+)$1	1	14	17	9.0000
(((	chr6:137524698-137524922(-)$1	1	32	35	9.0000
(((	chr1:35652560-35652823(-)$1	1	14	17	9.0000
)))	chr16:75675361-75675632(-)$1	1	134	137	9.0000
(((	chr1:228284678-228285029(+)$1	1	5	8	9.0000
(((	chr2:74438225-74438518(+)$1	1	211	214	9.0000
)))	chr16:89627247-89627571(+)$1	1	21	24	9.0000
.))	chr11:75115615-75116012(+)$1	1	36	39	9.0000
(((	chr17:7481044-7481334(+)$1	1	7	10	9.0000
)))	chr17:65336841-65337197(-)$1	1	149	152	9.0000
(((	chr3:12626527-12626828(-)$1	1	5	8	9.0000
.))	chr19:3982143-3982522(-)$1	1	122	125	9.0000
(((	chr11:118472240-118472511(+)$1	1	17	20	9.0000
(..	chr16:87867919-87868242(-)$1	1	3	6	9.0000
(((	chr19:51301287-51301671(-)$1	1	7	10	9.0000
.((	chr1:228295281-228295518(-)$1	1	12	15	9.0000
)))	chr22:19035913-19036171(-)$1	1	45	48	9.0000
..(	chr19:39924204-39924501(-)$1	1	7	10	9.0000
(.(	chr20:377050-377459(+)$1	1	78	81	9.0000
(((	chr9:131455816-131456187(+)$1	1	16	19	9.0000
(((	chr16:29827840-29828101(+)$1	1	0	3	9.0000
(((	chr6:74229505-74229878(-)$1	1	16	19	9.0000
(((	chr5:149825071-149825347(-)$1	1	27	30	9.0000
(((	chr12:56511182-56511484(+)$1	1	7	10	9.0000
(((	chrX:71494802-71495100(-)$1	1	3	6	9.0000
)).	chr15:68582611-68582859(+)$1	1	25	28	9.0000
.))	chr22:29191097-29191377(-)$1	1	24	27	9.0000
...	chr14:103986705-103987029(-)$1	1	1	4	9.0000
...	chr1:32505015-32505274(+)$1	1	29	32	9.0000

#PSSM
U : 0.99	u : 0.01	
G : 0.99	g : 0.01	
G : 0.99	g : 0.01	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m1_run2.nuc.txt

#NT
CCCA	chr16:2011601-2011824(+)$1	223	6	10	11.9999
CCCA	chr1:201122920-201123145(-)$1	225	75	79	11.9999
CCCA	chrM:5357-5592(+)$1	235	28	32	11.9999
CCCA	chr6:33385197-33385442(-)$1	245	79	83	11.9999
CCCA	chr3:49770244-49770466(-)$1	222	6	10	11.9999
CCCA	chr19:34859417-34859645(+)$1	228	3	7	11.9999
CCCA	chr3:47870413-47870673(+)$1	260	95	99	11.9999
CCCA	chr16:29708609-29708842(+)$1	233	46	50	11.9999
CCCA	chr2:85276560-85276801(+)$1	241	48	52	11.9999
CCCA	chr1:9795901-9796122(-)$1	221	15	19	11.9999
CCCA	chr19:19626975-19627215(+)$1	240	123	127	11.9999
CCCA	chr20:34288682-34288950(+)$1	268	174	178	11.9999
CCCA	chr10:43882197-43882438(-)$1	241	71	75	11.9999
CCCA	chr19:38866936-38867176(+)$1	240	48	52	11.9999
CCCA	chr21:34901112-34901333(-)$1	221	23	27	11.9999
ccca	chr17:80445699-80445945(+)$1	246	59	63	11.9999
CCCA	chr19:8376324-8376554(-)$1	230	121	125	11.9999
CCCA	chr2:217012810-217013031(+)$1	221	36	40	11.9999
CCCA	chr11:122928385-122928621(-)$1	236	51	55	11.9999
CCCA	chr16:30096203-30096514(+)$1	311	124	128	11.9999
CCCA	chr19:59060391-59060654(+)$1	263	80	84	11.9999
CCCA	chr19:34887386-34887632(+)$1	246	55	59	11.9999
CCCA	chr19:49299638-49299859(-)$1	221	95	99	11.9999
CCCA	chr2:70315452-70315675(+)$1	223	45	49	11.9999
CCCA	chr12:58145348-58145572(-)$1	224	148	152	11.9999
CCCA	chr9:127623695-127623927(-)$1	232	175	179	11.9999
CCCA	chr5:10256004-10256247(+)$1	243	117	121	11.9999
CCCA	chr17:4578997-4579232(-)$1	235	220	224	11.9999
CCCA	chr19:9958606-9958834(+)$1	228	55	59	11.9999
CCCA	chr16:449578-449826(+)$1	248	14	18	11.9999
CCCA	chrX:153590952-153591176(-)$1	224	48	52	11.9999
CCCA	chr19:42738674-42738904(-)$1	230	117	121	11.9999
CCCA	chr19:41895646-41895867(-)$1	221	111	115	11.9999
CCCA	chr2:232321285-232321507(-)$1	222	138	142	11.9999
CCCA	chr19:2811553-2811799(+)$1	246	37	41	11.9999
CCCA	chr20:2638682-2638927(+)$1	245	66	70	11.9999
CCCA	chr3:23929030-23929290(+)$1	260	34	38	11.9999
CCCA	chr15:91517273-91517509(-)$1	236	117	121	11.9999
CCCA	chr16:29820829-29821056(+)$1	227	6	10	11.9999
CCCA	chr14:104208187-104208412(-)$1	225	45	49	11.9999
CCCA	chr20:49575719-49575947(+)$1	228	209	213	11.9999
CCCA	chr11:763692-763925(+)$1	233	185	189	11.9999
CCCA	chr8:26267797-26268025(+)$1	228	223	227	11.9999
CCCA	chr12:57625490-57625743(+)$1	253	125	129	11.9999
CCCA	chr19:2759158-2759386(-)$1	228	116	120	11.9999
CCCA	chr10:27412395-27412631(-)$1	236	22	26	11.9999
CCCA	chr12:6958811-6959036(-)$1	225	18	22	11.9999
CCCA	chr1:151371972-151372221(+)$1	249	141	145	11.9999
CCCA	chr1:226552652-226552930(-)$1	278	190	194	11.9999
CCCA	chr11:60667986-60668233(-)$1	247	175	179	11.9999
CCCA	chr16:30435550-30435799(-)$1	249	119	123	11.9999
CCCA	chr19:39663457-39663688(+)$1	231	55	59	11.9999
CCCA	chr1:8074187-8074410(-)$1	223	45	49	11.9999
CCCA	chr1:36641752-36641974(+)$1	222	9	13	11.9999
CCCA	chr12:12977400-12977631(+)$1	231	200	204	11.9999
CCCA	chr17:6916926-6917157(+)$1	231	40	44	11.9999
CCCA	chr1:228285527-228285811(+)$1	284	1	5	11.9999
CCCA	chr3:47458727-47458953(-)$1	226	17	21	11.9999
CCCA	chr15:89169777-89170010(+)$1	233	116	120	11.9999
CCCA	chr19:10254349-10254592(-)$1	243	86	90	11.9999
CCCA	chr17:40049292-40049520(-)$1	228	85	89	11.9999
CCCA	chr5:92923831-92924057(+)$1	226	121	125	11.9999
CCCA	chr19:39924085-39924308(-)$1	223	10	14	11.9999
CCCA	chr17:7834256-7834484(-)$1	228	75	79	11.9999
CCCA	chr17:5336957-5337216(-)$1	259	124	128	11.9999
CCCA	chr17:80011745-80011966(+)$1	221	73	77	11.9999
CCCA	chr19:41247915-41248149(-)$1	234	166	170	11.9999
CCCA	chr12:49952960-49953184(-)$1	224	23	27	11.9999
CCCA	chr19:50166370-50166591(-)$1	221	28	32	11.9999
CCCA	chrM:11543-11787(+)$1	244	169	173	11.9999
CCCA	chr6:26056169-26056394(-)$1	225	89	93	11.9999
CCCA	chrX:53458313-53458555(-)$1	242	26	30	11.9999
CCCA	chr12:57036436-57036714(-)$1	278	241	245	11.9999
CCCA	chr7:150069548-150069774(+)$1	226	103	107	11.9999

#otherMatches

#Struct PSSM
GGZZ	chr7:156799107-156799332(-)$1	225	112	116	11.9999
:bb[	chr16:2011601-2011824(+)$1	223	6	10	11.9999
cggg	chr1:201122920-201123145(-)$1	225	75	79	11.9999
::::	chrM:5357-5592(+)$1	235	28	32	11.9999
c!!d	chr6:33385197-33385442(-)$1	245	79	83	11.9999
F:cc	chr3:49770244-49770466(-)$1	222	6	10	11.9999
cccm	chr19:34859417-34859645(+)$1	228	3	7	11.9999
^^cc	chr3:47870413-47870673(+)$1	260	95	99	11.9999
6666	chr16:29708609-29708842(+)$1	233	46	50	11.9999
c444	chr2:85276560-85276801(+)$1	241	48	52	11.9999
DDDD	chr1:9795901-9796122(-)$1	221	15	19	11.9999
eee:	chr19:19626975-19627215(+)$1	240	123	127	11.9999
22ee	chr20:34288682-34288950(+)$1	268	174	178	11.9999
GGGM	chr10:43882197-43882438(-)$1	241	71	75	11.9999
ffmm	chr19:38866936-38867176(+)$1	240	48	52	11.9999
{DDD	chr21:34901112-34901333(-)$1	221	23	27	11.9999
cbbi	chr17:80445699-80445945(+)$1	246	59	63	11.9999
[bbp	chr19:8376324-8376554(-)$1	230	121	125	11.9999
++++	chr2:217012810-217013031(+)$1	221	36	40	11.9999
SSSS	chr11:122928385-122928621(-)$1	236	51	55	11.9999
fttt	chr16:30096203-30096514(+)$1	311	124	128	11.9999
c:::	chr19:59060391-59060654(+)$1	263	80	84	11.9999
TTTT	chr19:34887386-34887632(+)$1	246	55	59	11.9999
cc55	chr19:49299638-49299859(-)$1	221	95	99	11.9999
ccdd	chr2:70315452-70315675(+)$1	223	45	49	11.9999
CDDD	chr12:58145348-58145572(-)$1	224	148	152	11.9999
22dd	chr9:127623695-127623927(-)$1	232	175	179	11.9999
bbGG	chr5:10256004-10256247(+)$1	243	117	121	11.9999
c:::	chr17:4578997-4579232(-)$1	235	220	224	11.9999
uuuu	chr19:9958606-9958834(+)$1	228	55	59	11.9999
::::	chr16:449578-449826(+)$1	248	14	18	11.9999
FFBB	chrX:153590952-153591176(-)$1	224	48	52	11.9999
pppp	chr19:42738674-42738904(-)$1	230	117	121	11.9999
ddd!	chr19:41895646-41895867(-)$1	221	111	115	11.9999
cc[d	chr2:232321285-232321507(-)$1	222	138	142	11.9999
FFFF	chr19:2811553-2811799(+)$1	246	37	41	11.9999
ddnn	chr20:2638682-2638927(+)$1	245	66	70	11.9999
cc""	chr3:23929030-23929290(+)$1	260	34	38	11.9999
III:	chr15:91517273-91517509(-)$1	236	117	121	11.9999
::::	chr16:29820829-29821056(+)$1	227	6	10	11.9999
vvvv	chr14:104208187-104208412(-)$1	225	45	49	11.9999
C}BB	chr20:49575719-49575947(+)$1	228	209	213	11.9999
dddd	chr11:763692-763925(+)$1	233	185	189	11.9999
bccc	chr8:26267797-26268025(+)$1	228	223	227	11.9999
eee:	chr12:57625490-57625743(+)$1	253	125	129	11.9999
EEEE	chr19:2759158-2759386(-)$1	228	116	120	11.9999
cccc	chr10:27412395-27412631(-)$1	236	22	26	11.9999
::::	chr12:6958811-6959036(-)$1	225	18	22	11.9999
eee:	chr1:151371972-151372221(+)$1	249	141	145	11.9999
ffff	chr1:226552652-226552930(-)$1	278	190	194	11.9999
qqqq	chr11:60667986-60668233(-)$1	247	175	179	11.9999
ZZZC	chr16:30435550-30435799(-)$1	249	119	123	11.9999
cccc	chr19:39663457-39663688(+)$1	231	55	59	11.9999
gggg	chr1:8074187-8074410(-)$1	223	45	49	11.9999
FFNN	chr1:36641752-36641974(+)$1	222	9	13	11.9999
ccdd	chr12:12977400-12977631(+)$1	231	200	204	11.9999
bb""	chr17:6916926-6917157(+)$1	231	40	44	11.9999
::::	chr1:228285527-228285811(+)$1	284	1	5	11.9999
[bb!	chr3:47458727-47458953(-)$1	226	17	21	11.9999
ffff	chr15:89169777-89170010(+)$1	233	116	120	11.9999
OOOO	chr19:10254349-10254592(-)$1	243	86	90	11.9999
ddd8	chr17:40049292-40049520(-)$1	228	85	89	11.9999
eccc	chr5:92923831-92924057(+)$1	226	121	125	11.9999
FFLL	chr19:39924085-39924308(-)$1	223	10	14	11.9999
gggg	chr17:7834256-7834484(-)$1	228	75	79	11.9999
!!bb	chr17:5336957-5337216(-)$1	259	124	128	11.9999
]bb]	chr17:80011745-80011966(+)$1	221	73	77	11.9999
EEEE	chr19:41247915-41248149(-)$1	234	166	170	11.9999
"ccc	chr12:49952960-49953184(-)$1	224	23	27	11.9999
ggll	chr19:50166370-50166591(-)$1	221	28	32	11.9999
dd::	chrM:11543-11787(+)$1	244	169	173	11.9999
DDDY	chr6:26056169-26056394(-)$1	225	89	93	11.9999
mccc	chrX:53458313-53458555(-)$1	242	26	30	11.9999
EEEE	chr12:57036436-57036714(-)$1	278	241	245	11.9999
oooo	chr7:150069548-150069774(+)$1	226	103	107	11.9999

#DB
))..	chr7:156799107-156799332(-)$1	1	112	116	11.9999
.((.	chr16:2011601-2011824(+)$1	1	6	10	11.9999
((((	chr1:201122920-201123145(-)$1	1	75	79	11.9999
....	chrM:5357-5592(+)$1	1	28	32	11.9999
(..(	chr6:33385197-33385442(-)$1	1	79	83	11.9999
(.((	chr3:49770244-49770466(-)$1	1	6	10	11.9999
(((.	chr19:34859417-34859645(+)$1	1	3	7	11.9999
..))	chr3:47870413-47870673(+)$1	1	95	99	11.9999
....	chr16:29708609-29708842(+)$1	1	46	50	11.9999
)...	chr2:85276560-85276801(+)$1	1	48	52	11.9999
((((	chr1:9795901-9796122(-)$1	1	15	19	11.9999
))).	chr19:19626975-19627215(+)$1	1	123	127	11.9999
..))	chr20:34288682-34288950(+)$1	1	174	178	11.9999
(((.	chr10:43882197-43882438(-)$1	1	71	75	11.9999
((..	chr19:38866936-38867176(+)$1	1	48	52	11.9999
.(((	chr21:34901112-34901333(-)$1	1	23	27	11.9999
)(((	chr17:80445699-80445945(+)$1	1	59	63	11.9999
.((.	chr19:8376324-8376554(-)$1	1	121	125	11.9999
....	chr2:217012810-217013031(+)$1	1	36	40	11.9999
....	chr11:122928385-122928621(-)$1	1	51	55	11.9999
(...	chr16:30096203-30096514(+)$1	1	124	128	11.9999
)...	chr19:59060391-59060654(+)$1	1	80	84	11.9999
....	chr19:34887386-34887632(+)$1	1	55	59	11.9999
))..	chr19:49299638-49299859(-)$1	1	95	99	11.9999
))((	chr2:70315452-70315675(+)$1	1	45	49	11.9999
((((	chr12:58145348-58145572(-)$1	1	148	152	11.9999
..))	chr9:127623695-127623927(-)$1	1	175	179	11.9999
))))	chr5:10256004-10256247(+)$1	1	117	121	11.9999
)...	chr17:4578997-4579232(-)$1	1	220	224	11.9999
....	chr19:9958606-9958834(+)$1	1	55	59	11.9999
....	chr16:449578-449826(+)$1	1	14	18	11.9999
((((	chrX:153590952-153591176(-)$1	1	48	52	11.9999
....	chr19:42738674-42738904(-)$1	1	117	121	11.9999
(((.	chr19:41895646-41895867(-)$1	1	111	115	11.9999
((.(	chr2:232321285-232321507(-)$1	1	138	142	11.9999
((((	chr19:2811553-2811799(+)$1	1	37	41	11.9999
((..	chr20:2638682-2638927(+)$1	1	66	70	11.9999
((..	chr3:23929030-23929290(+)$1	1	34	38	11.9999
(((.	chr15:91517273-91517509(-)$1	1	117	121	11.9999
....	chr16:29820829-29821056(+)$1	1	6	10	11.9999
....	chr14:104208187-104208412(-)$1	1	45	49	11.9999
).))	chr20:49575719-49575947(+)$1	1	209	213	11.9999
((((	chr11:763692-763925(+)$1	1	185	189	11.9999
))))	chr8:26267797-26268025(+)$1	1	223	227	11.9999
))).	chr12:57625490-57625743(+)$1	1	125	129	11.9999
))))	chr19:2759158-2759386(-)$1	1	116	120	11.9999
((((	chr10:27412395-27412631(-)$1	1	22	26	11.9999
....	chr12:6958811-6959036(-)$1	1	18	22	11.9999
))).	chr1:151371972-151372221(+)$1	1	141	145	11.9999
))))	chr1:226552652-226552930(-)$1	1	190	194	11.9999
....	chr11:60667986-60668233(-)$1	1	175	179	11.9999
...)	chr16:30435550-30435799(-)$1	1	119	123	11.9999
((((	chr19:39663457-39663688(+)$1	1	55	59	11.9999
((((	chr1:8074187-8074410(-)$1	1	45	49	11.9999
((..	chr1:36641752-36641974(+)$1	1	9	13	11.9999
))))	chr12:12977400-12977631(+)$1	1	200	204	11.9999
((..	chr17:6916926-6917157(+)$1	1	40	44	11.9999
....	chr1:228285527-228285811(+)$1	1	1	5	11.9999
.((.	chr3:47458727-47458953(-)$1	1	17	21	11.9999
((((	chr15:89169777-89170010(+)$1	1	116	120	11.9999
....	chr19:10254349-10254592(-)$1	1	86	90	11.9999
))).	chr17:40049292-40049520(-)$1	1	85	89	11.9999
((((	chr5:92923831-92924057(+)$1	1	121	125	11.9999
((..	chr19:39924085-39924308(-)$1	1	10	14	11.9999
((((	chr17:7834256-7834484(-)$1	1	75	79	11.9999
..((	chr17:5336957-5337216(-)$1	1	124	128	11.9999
.)).	chr17:80011745-80011966(+)$1	1	73	77	11.9999
))))	chr19:41247915-41248149(-)$1	1	166	170	11.9999
.(((	chr12:49952960-49953184(-)$1	1	23	27	11.9999
((..	chr19:50166370-50166591(-)$1	1	28	32	11.9999
))..	chrM:11543-11787(+)$1	1	169	173	11.9999
))).	chr6:26056169-26056394(-)$1	1	89	93	11.9999
.)))	chrX:53458313-53458555(-)$1	1	26	30	11.9999
))))	chr12:57036436-57036714(-)$1	1	241	245	11.9999
....	chr7:150069548-150069774(+)$1	1	103	107	11.9999

#PSSM
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
A : 0.98	a : 0.01	

#score	899.9999999999995
#seq	75
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m2_run2.nuc.txt

#NT
UGUAAAAA	chr15:44706940-44707162(+)$1	222	9	17	15.9090
UUUAAAAA	chr12:49413005-49413224(-)$1	219	176	184	20.2727
UUUAAAAA	chr3:45785473-45785703(+)$1	230	16	24	20.2727
uuuuaaaa	chr8:91636513-91636734(-)$1	221	73	81	16.0000
AUUAAAAA	chr13:32975838-32976050(-)$1	212	153	161	16.0909
UUUAAAAC	chr1:205684908-205685130(-)$1	222	40	48	16.1818
UAUAAAAA	chr3:41281796-41282026(+)$1	230	100	108	16.1818
UUGAAAAA	chr10:858564-858781(-)$1	217	76	84	15.5454
UUUUAAAA	chr1:193057885-193058130(+)$1	245	124	132	16.0000
UUUAUAAA	chr8:41787523-41787754(-)$1	231	104	112	15.8181
UUUAAAUA	chr14:88399949-88400168(-)$1	219	64	72	16.0000
UCUAAAAA	chr1:114305543-114305773(-)$1	230	122	130	15.9090
UUUAAAAA	chr4:40427628-40427850(-)$1	222	175	183	20.2727
UUUACAAA	chr17:47367242-47367466(-)$1	224	168	176	15.8181
UUUAAAAC	chr1:167391521-167391751(+)$1	230	114	122	16.1818
UUUAAAAA	chr4:128759933-128760154(+)$1	221	35	43	20.2727
UUUAACAA	chr17:27590603-27590824(-)$1	221	22	30	15.9090
UUUAAACA	chr10:70863783-70864014(+)$1	231	192	200	15.9090
UUUAACAA	chr8:101533758-101533983(-)$1	225	147	155	15.9090
UUUAAAAA	chr16:18819638-18819867(-)$1	229	30	38	20.2727
UUUGAAAA	chr15:78792886-78793116(+)$1	230	111	119	16.0000
UUUAAAAA	chr4:148556179-148556398(+)$1	219	7	15	20.2727
CUUAAAAA	chr6:7251921-7252151(+)$1	230	101	109	16.0000
UUUAAAAG	chr15:55473442-55473662(-)$1	220	36	44	16.2727
UUUAAAAA	chr13:42893994-42894213(+)$1	219	168	176	20.2727
UUUCAAAA	chr1:203277306-203277535(+)$1	229	219	227	16.0000
UUUAAAAA	chr18:29648285-29648504(+)$1	219	207	215	20.2727
UUUAAAUA	chrX:103439487-103439717(+)$1	230	42	50	16.0000
CUUAAAAA	chr2:29406257-29406479(+)$1	222	106	114	16.0000
UUCAAAAA	chr6:117055224-117055444(+)$1	220	43	51	15.5454
UUUAAAAU	chr2:48035011-48035241(-)$1	230	53	61	16.2727
UUUAAAAA	chr16:18817361-18817585(-)$1	224	106	114	20.2727
UUUAAAAG	chr14:31085686-31085916(+)$1	230	82	90	16.2727
UUUAAAAU	chr14:60752658-60752875(+)$1	217	67	75	16.2727
UUUAAAAG	chr7:90043098-90043321(+)$1	223	192	200	16.2727
UUUAAAAA	chr15:52203847-52204099(+)$1	252	11	19	20.2727
UUUGAAAA	chr12:117153951-117154173(-)$1	222	171	179	16.0000
UUUAAUAA	chr10:105357458-105357688(-)$1	230	23	31	15.7272
UUUAAAAA	chr10:23730111-23730331(+)$1	220	56	64	20.2727
UUUAAAAA	chr14:69254288-69254512(-)$1	224	100	108	20.2727
AUUAAAAA	chr3:141164867-141165101(+)$1	234	55	63	16.0909
UUUACAAA	chr6:159056099-159056343(+)$1	244	125	133	15.8181
UAUAAAAA	chr10:134596528-134596753(+)$1	225	20	28	16.1818
UUUAACAA	chr3:196313147-196313365(+)$1	218	140	148	15.9090
UAUAAAAA	chr17:30551670-30551894(+)$1	224	82	90	16.1818
UAUAAAAA	chrY:15030418-15030637(+)$1	219	88	96	16.1818
uuuaaaua	chr3:193413385-193413607(+)$1	222	31	39	16.0000
UUUAAACA	chr1:39329446-39329669(-)$1	223	37	45	15.9090
UUUAUAAA	chr12:30862485-30862715(-)$1	230	72	80	15.8181
UUUAAAAA	chr10:75135233-75135463(-)$1	230	34	42	20.2727
UUUAAAAU	chr1:67453224-67453454(+)$1	230	3	11	16.2727
GUUAAAAA	chr1:91380830-91381051(-)$1	221	63	71	15.9090
UUUAAAAA	chr14:54943126-54943356(-)$1	230	163	171	20.2727
AUUAAAAA	chrX:107377515-107377738(+)$1	223	42	50	16.0909

#otherMatches

#Struct PSSM
eeeooooo	chr5:142658832-142659050(-)$1	218	30	38	16.0000
DDDDKKGG	chr15:44706940-44707162(+)$1	222	9	17	15.9090
^^^^^^^^	chr12:49413005-49413224(-)$1	219	176	184	20.2727
IIII{DDD	chr3:45785473-45785703(+)$1	230	16	24	20.2727
fff4444f	chr8:91636513-91636734(-)$1	221	73	81	16.0000
eeee::::	chr13:32975838-32976050(-)$1	212	153	161	16.0909
ggg^^^^^	chr1:205684908-205685130(-)$1	222	40	48	16.1818
cooooooc	chr3:41281796-41282026(+)$1	230	100	108	16.1818
22ccc22=	chr10:858564-858781(-)$1	217	76	84	15.5454
oooodddd	chr1:193057885-193058130(+)$1	245	124	132	16.0000
oooeeeee	chr8:41787523-41787754(-)$1	231	104	112	15.8181
##eeeeee	chr14:88399949-88400168(-)$1	219	64	72	16.0000
#ggggggg	chr1:114305543-114305773(-)$1	230	122	130	15.9090
fff22ccc	chr4:40427628-40427850(-)$1	222	175	183	20.2727
ff4444dd	chr17:47367242-47367466(-)$1	224	168	176	15.8181
?????EEE	chr1:167391521-167391751(+)$1	230	114	122	16.1818
KDDDD:::	chr4:128759933-128760154(+)$1	221	35	43	20.2727
zzzzzzhh	chr17:27590603-27590824(-)$1	221	22	30	15.9090
iii:::::	chr10:70863783-70864014(+)$1	231	192	200	15.9090
mffffff:	chr8:101533758-101533983(-)$1	225	147	155	15.9090
HHHHHHH{	chr16:18819638-18819867(-)$1	229	30	38	20.2727
hhhhhhhb	chr15:78792886-78793116(+)$1	230	111	119	16.0000
NNGGGGGG	chr4:148556179-148556398(+)$1	219	7	15	20.2727
::::::::	chr6:7251921-7252151(+)$1	230	101	109	16.0000
iiiiiiii	chr15:55473442-55473662(-)$1	220	36	44	16.2727
========	chr13:42893994-42894213(+)$1	219	168	176	20.2727
::::::::	chr1:203277306-203277535(+)$1	229	219	227	16.0000
FFF}CCCY	chr18:29648285-29648504(+)$1	219	207	215	20.2727
e:::dddd	chrX:103439487-103439717(+)$1	230	42	50	16.0000
iii:::::	chr2:29406257-29406479(+)$1	222	106	114	16.0000
GGeeeee"	chr6:117055224-117055444(+)$1	220	43	51	15.5454
::::::::	chr2:48035011-48035241(-)$1	230	53	61	16.2727
3ggggggg	chr16:18817361-18817585(-)$1	224	106	114	20.2727
eeeee333	chr14:31085686-31085916(+)$1	230	82	90	16.2727
b::::eee	chr14:60752658-60752875(+)$1	217	67	75	16.2727
FFYYFFFF	chr7:90043098-90043321(+)$1	223	192	200	16.2727
D:::::::	chr15:52203847-52204099(+)$1	252	11	19	20.2727
ZHHHHHHH	chr12:117153951-117154173(-)$1	222	171	179	16.0000
:::::::e	chr10:105357458-105357688(-)$1	230	23	31	15.7272
iiii]ccc	chr10:23730111-23730331(+)$1	220	56	64	20.2727
eeeeqqqq	chr14:69254288-69254512(-)$1	224	100	108	20.2727
======::	chr3:141164867-141165101(+)$1	234	55	63	16.0909
iiiiiiii	chr6:159056099-159056343(+)$1	244	125	133	15.8181
++++++++	chr10:134596528-134596753(+)$1	225	20	28	16.1818
eee99999	chr3:196313147-196313365(+)$1	218	140	148	15.9090
g:::::::	chr17:30551670-30551894(+)$1	224	82	90	16.1818
:::::::c	chrY:15030418-15030637(+)$1	219	88	96	16.1818
e:::::::	chr3:193413385-193413607(+)$1	222	31	39	16.0000
:::::ddd	chr1:39329446-39329669(-)$1	223	37	45	15.9090
PPPPPPPH	chr12:30862485-30862715(-)$1	230	72	80	15.8181
eeHHHHHH	chr10:75135233-75135463(-)$1	230	34	42	20.2727
hhhhhrrr	chr1:67453224-67453454(+)$1	230	3	11	16.2727
eeee::::	chr1:91380830-91381051(-)$1	221	63	71	15.9090
ggggggnn	chr14:54943126-54943356(-)$1	230	163	171	20.2727
ddduuuuu	chrX:107377515-107377738(+)$1	223	42	50	16.0909

#DB
(((.....	chr5:142658832-142659050(-)$1	1	30	38	16.0000
((((..((	chr15:44706940-44707162(+)$1	1	9	17	15.9090
........	chr12:49413005-49413224(-)$1	1	176	184	20.2727
((((.(((	chr3:45785473-45785703(+)$1	1	16	24	20.2727
)))....)	chr8:91636513-91636734(-)$1	1	73	81	16.0000
))))....	chr13:32975838-32976050(-)$1	1	153	161	16.0909
(((.....	chr1:205684908-205685130(-)$1	1	40	48	16.1818
(......)	chr3:41281796-41282026(+)$1	1	100	108	16.1818
..)))..)	chr10:858564-858781(-)$1	1	76	84	15.5454
....))))	chr1:193057885-193058130(+)$1	1	124	132	16.0000
...)))))	chr8:41787523-41787754(-)$1	1	104	112	15.8181
..((((((	chr14:88399949-88400168(-)$1	1	64	72	16.0000
.(((((((	chr1:114305543-114305773(-)$1	1	122	130	15.9090
)))..)))	chr4:40427628-40427850(-)$1	1	175	183	20.2727
))....))	chr17:47367242-47367466(-)$1	1	168	176	15.8181
.....)))	chr1:167391521-167391751(+)$1	1	114	122	16.1818
.((((...	chr4:128759933-128760154(+)$1	1	35	43	20.2727
......))	chr17:27590603-27590824(-)$1	1	22	30	15.9090
))).....	chr10:70863783-70864014(+)$1	1	192	200	15.9090
.)))))).	chr8:101533758-101533983(-)$1	1	147	155	15.9090
(((((((.	chr16:18819638-18819867(-)$1	1	30	38	20.2727
))))))))	chr15:78792886-78793116(+)$1	1	111	119	16.0000
..((((((	chr4:148556179-148556398(+)$1	1	7	15	20.2727
........	chr6:7251921-7252151(+)$1	1	101	109	16.0000
((((((((	chr15:55473442-55473662(-)$1	1	36	44	16.2727
))))))))	chr13:42893994-42894213(+)$1	1	168	176	20.2727
........	chr1:203277306-203277535(+)$1	1	219	227	16.0000
))).))).	chr18:29648285-29648504(+)$1	1	207	215	20.2727
)...((((	chrX:103439487-103439717(+)$1	1	42	50	16.0000
))).....	chr2:29406257-29406479(+)$1	1	106	114	16.0000
(((((((.	chr6:117055224-117055444(+)$1	1	43	51	15.5454
........	chr2:48035011-48035241(-)$1	1	53	61	16.2727
.)))))))	chr16:18817361-18817585(-)$1	1	106	114	20.2727
)))))...	chr14:31085686-31085916(+)$1	1	82	90	16.2727
)....(((	chr14:60752658-60752875(+)$1	1	67	75	16.2727
))..))))	chr7:90043098-90043321(+)$1	1	192	200	16.2727
(.......	chr15:52203847-52204099(+)$1	1	11	19	20.2727
.)))))))	chr12:117153951-117154173(-)$1	1	171	179	16.0000
.......(	chr10:105357458-105357688(-)$1	1	23	31	15.7272
)))).)))	chr10:23730111-23730331(+)$1	1	56	64	20.2727
((((....	chr14:69254288-69254512(-)$1	1	100	108	20.2727
))))))..	chr3:141164867-141165101(+)$1	1	55	63	16.0909
((((((((	chr6:159056099-159056343(+)$1	1	125	133	15.8181
........	chr10:134596528-134596753(+)$1	1	20	28	16.1818
))).....	chr3:196313147-196313365(+)$1	1	140	148	15.9090
).......	chr17:30551670-30551894(+)$1	1	82	90	16.1818
.......(	chrY:15030418-15030637(+)$1	1	88	96	16.1818
).......	chr3:193413385-193413607(+)$1	1	31	39	16.0000
.....(((	chr1:39329446-39329669(-)$1	1	37	45	15.9090
.......(	chr12:30862485-30862715(-)$1	1	72	80	15.8181
))((((((	chr10:75135233-75135463(-)$1	1	34	42	20.2727
(((((...	chr1:67453224-67453454(+)$1	1	3	11	16.2727
))))....	chr1:91380830-91381051(-)$1	1	63	71	15.9090
((((((..	chr14:54943126-54943356(-)$1	1	163	171	20.2727
(((.....	chrX:107377515-107377738(+)$1	1	42	50	16.0909

#PSSM
U : 0.85	A : 0.05	u : 0.03	C : 0.03	G : 0.01	
U : 0.85	A : 0.07	u : 0.03	G : 0.01	C : 0.01	
U : 0.92	u : 0.03	G : 0.01	C : 0.01	
A : 0.87	C : 0.03	G : 0.03	u : 0.01	U : 0.01	a : 0.01	
A : 0.89	a : 0.03	U : 0.03	C : 0.03	
A : 0.89	C : 0.05	a : 0.03	U : 0.01	
A : 0.89	U : 0.03	C : 0.03	a : 0.01	u : 0.01	
A : 0.81	G : 0.05	U : 0.05	a : 0.03	C : 0.03	

#score	940.181818181818
#seq	55
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_UTR_m1_run2.nuc.txt

#NT
AUUUUUUUUUUUU	chr14:99978651-99978891(-)$1	240	113	126	30.6326
CUUUUCUUGUUUU	chr17:7757286-7757526(+)$1	240	86	99	25.8367
CUUUUUUUUUUUU	chr1:109474136-109474376(-)$1	240	110	123	33.6938
CUUUUUUUGUUUU	chr15:23043874-23044114(-)$1	240	122	135	29.9183
GUUUUUUUUUUUU	chr4:26433105-26433345(+)$1	240	93	106	30.4285
CUUUUUUUUUUUU	chr17:46024677-46024919(+)$1	242	113	126	33.6938
AUUUUUUUCUUUU	chr5:68505685-68505927(+)$1	242	104	117	26.6530
CUUUUCUUUCUUU	chrX:16779277-16779517(+)$1	240	108	121	25.0204
CUUUUUUUUUUUU	chr11:9610700-9610940(+)$1	240	120	133	33.6938
Cuuuuuuuuuuuu	chr11:118619952-118620232(-)$1	280	141	154	33.6938
Cuuuuuauuuuuu	chr19:8023833-8024073(-)$1	240	113	126	29.2040
CUUUUUUUUUUUC	chr8:61778635-61778875(+)$1	240	122	135	29.1020
AUUUUUUCUUUUU	chr1:53290815-53291055(+)$1	240	78	91	25.8367
CUUUUUUUUUCUU	chr16:23077614-23077856(-)$1	242	107	120	29.3061
cuuuuuuuuuuuu	chr1:204521826-204522066(+)$1	240	173	186	33.6938
cuuuuuuuuuuuu	chr1:151023699-151023939(-)$1	240	42	55	33.6938
CUCUUUUUUCUUU	chr18:45364259-45364499(-)$1	240	114	127	24.7142
Auuuuuuuuuuuu	chr3:141464697-141464941(+)$1	244	117	130	30.6326
cuuuuuuuuuuuu	chr10:71898749-71898989(-)$1	240	113	126	33.6938
cuuuuuuuuuuuu	chr6:118636481-118636721(+)$1	240	114	127	33.6938
CUUUUUCUUUUUU	chr14:103808286-103808526(+)$1	240	185	198	29.4081
cuuuuuuuuuuuu	chr17:4173741-4173999(-)$1	258	136	149	33.6938
CUUUUAUUAUUUU	chr22:28249030-28249354(-)$1	324	145	158	25.3265
Cuuuuuuuuuuuu	chr8:25269472-25269712(+)$1	240	121	134	33.6938
CUUGUUUUGUUUU	chr2:29022539-29022789(+)$1	250	13	26	25.3265
CAGUUUUUUUUUU	chr1:10240475-10240715(+)$1	240	196	209	25.0204
auuuuuuuuuuuu	chr1:114306451-114306691(-)$1	240	115	128	30.6326
cuuuuuuuuuuuu	chr3:113163236-113163478(-)$1	242	116	129	33.6938
GUUUUUUUUUUUU	chr8:37612241-37612481(+)$1	240	111	124	30.4285
cuuuuuuucuuuu	chr1:155884209-155884488(-)$1	279	112	125	29.7142
GUUUUUUUUUUUU	chr20:57609832-57610112(-)$1	280	147	160	30.4285
Cauuuuuuuuuuu	chr12:56295132-56295374(-)$1	242	120	133	29.3061
Cuuuuuuuuuuuu	chr10:72637406-72637646(+)$1	240	158	171	33.6938
guuguuuuuuuuu	chr1:46093348-46093601(-)$1	253	181	194	25.8367
AUUUUCUUUUUUU	chr1:57179493-57179734(+)$1	241	113	126	26.5510
CUuuuucuuuucu	chr7:155256466-155256706(+)$1	240	91	104	25.0204
CUAUUUUUUUUUC	chr7:112115489-112115729(+)$1	240	117	130	24.8163
CAUUUUUUUUCUU	chr8:101270175-101270415(-)$1	240	121	134	24.9183
CUUUUUCUUUUCU	chr5:156820144-156820384(+)$1	240	107	120	25.0204
auuuuuuuuuuuu	chr8:33356716-33356956(+)$1	240	108	121	30.6326
CUUUUUUUGUUUU	chr6:117883619-117883859(-)$1	240	120	133	29.9183
GUUUAUUUUUUUU	chr2:102508625-102508865(+)$1	240	29	42	25.7346
CUAUUUUUUUUUU	chr16:67132944-67133184(+)$1	240	121	134	29.4081
CUUUUCUUUUUCU	chr10:35860427-35860667(+)$1	240	122	135	25.2244
CUUUUUUUUUUUU	chr6:32153182-32153422(-)$1	240	103	116	33.6938
CUUUCUUUUUCUU	chr18:71920583-71920823(-)$1	240	124	137	24.6122
cuuuuuuuuuuuu	chr5:90666713-90666956(-)$1	243	109	122	33.6938
CUGUUUUUAUUUU	chr3:5026423-5026663(+)$1	240	126	139	25.4285

#otherMatches

#Struct PSSM
dd:::::::::::	chr8:26513250-26513490(+)$1	240	48	61	33.6938
yyyydddd]iiii	chr14:99978651-99978891(-)$1	240	113	126	30.6326
::::::::bb###	chr17:7757286-7757526(+)$1	240	86	99	25.8367
gg[ggggggghhh	chr1:109474136-109474376(-)$1	240	110	123	33.6938
iiiiiiiiooooo	chr15:23043874-23044114(-)$1	240	122	135	29.9183
eee999999999e	chr4:26433105-26433345(+)$1	240	93	106	30.4285
^^^^^^^^^^^ff	chr17:46024677-46024919(+)$1	242	113	126	33.6938
mdddd22dddd]e	chr5:68505685-68505927(+)$1	242	104	117	26.6530
^^^^^^^^^^^^^	chrX:16779277-16779517(+)$1	240	108	121	25.0204
:::::::::gggg	chr11:9610700-9610940(+)$1	240	120	133	33.6938
====666666ggg	chr11:118619952-118620232(-)$1	280	141	154	33.6938
ffffff]======	chr19:8023833-8024073(-)$1	240	113	126	29.2040
d>>>>>>>>>>>>	chr8:61778635-61778875(+)$1	240	122	135	29.1020
ggg:::::::::i	chr1:53290815-53291055(+)$1	240	78	91	25.8367
DDD::::::::::	chr16:23077614-23077856(-)$1	242	107	120	29.3061
^^^^^^^^^^^hh	chr1:204521826-204522066(+)$1	240	173	186	33.6938
:::::::::::::	chr1:151023699-151023939(-)$1	240	42	55	33.6938
cc::::::::fff	chr18:45364259-45364499(-)$1	240	114	127	24.7142
:::::::::::::	chr3:141464697-141464941(+)$1	244	117	130	30.6326
^^^^^^^^^^^^^	chr10:71898749-71898989(-)$1	240	113	126	33.6938
ffffff:::::::	chr6:118636481-118636721(+)$1	240	114	127	33.6938
eeeee[=======	chr14:103808286-103808526(+)$1	240	185	198	29.4081
:::::::ffffff	chr17:4173741-4173999(-)$1	258	136	149	33.6938
bb22ffffff>>>	chr22:28249030-28249354(-)$1	324	145	158	25.3265
c^^^^^^^^^^^^	chr8:25269472-25269712(+)$1	240	121	134	33.6938
B{FFFFFFbb[ff	chr2:29022539-29022789(+)$1	250	13	26	25.3265
YYFFFFFFYYJJJ	chr1:10240475-10240715(+)$1	240	196	209	25.0204
mmmmdddd]gggg	chr1:114306451-114306691(-)$1	240	115	128	30.6326
dyyyyyyyyyyyy	chr3:113163236-113163478(-)$1	242	116	129	33.6938
:::::::::::::	chr8:37612241-37612481(+)$1	240	111	124	30.4285
^^^^^^^^^^^^^	chr1:155884209-155884488(-)$1	279	112	125	29.7142
fff4444eeeee7	chr20:57609832-57610112(-)$1	280	147	160	30.4285
iiiiiii[ggggg	chr12:56295132-56295374(-)$1	242	120	133	29.3061
d^^^^^^^^^^^^	chr10:72637406-72637646(+)$1	240	158	171	33.6938
IIIIIII@@@@@@	chr1:46093348-46093601(-)$1	253	181	194	25.8367
55555hhhhhhhh	chr1:57179493-57179734(+)$1	241	113	126	26.5510
a666666ffffff	chr7:155256466-155256706(+)$1	240	91	104	25.0204
cc]ggggggg:::	chr7:112115489-112115729(+)$1	240	117	130	24.8163
:::::::::ccc"	chr8:101270175-101270415(-)$1	240	121	134	24.9183
hhhhhh]dddd::	chr5:156820144-156820384(+)$1	240	107	120	25.0204
:::::::::::::	chr8:33356716-33356956(+)$1	240	108	121	30.6326
fccc[eeeee[dd	chr6:117883619-117883859(-)$1	240	120	133	29.9183
dddd=========	chr2:102508625-102508865(+)$1	240	29	42	25.7346
33ggggggg22ee	chr16:67132944-67133184(+)$1	240	121	134	29.4081
:::::::::::::	chr10:35860427-35860667(+)$1	240	122	135	25.2244
=========''''	chr6:32153182-32153422(-)$1	240	103	116	33.6938
:::BB}JJJJJJJ	chr18:71920583-71920823(-)$1	240	124	137	24.6122
LGGGGGGGQQQQQ	chr5:90666713-90666956(-)$1	243	109	122	33.6938
vvccc22ccc]ff	chr3:5026423-5026663(+)$1	240	126	139	25.4285

#DB
))...........	chr8:26513250-26513490(+)$1	1	48	61	33.6938
....)))).))))	chr14:99978651-99978891(-)$1	1	113	126	30.6326
........((...	chr17:7757286-7757526(+)$1	1	86	99	25.8367
((.((((((((((	chr1:109474136-109474376(-)$1	1	110	123	33.6938
((((((((.....	chr15:23043874-23044114(-)$1	1	122	135	29.9183
))).........)	chr4:26433105-26433345(+)$1	1	93	106	30.4285
...........))	chr17:46024677-46024919(+)$1	1	113	126	33.6938
.))))..)))).)	chr5:68505685-68505927(+)$1	1	104	117	26.6530
.............	chrX:16779277-16779517(+)$1	1	108	121	25.0204
.........((((	chr11:9610700-9610940(+)$1	1	120	133	33.6938
))))......)))	chr11:118619952-118620232(-)$1	1	141	154	33.6938
)))))).))))))	chr19:8023833-8024073(-)$1	1	113	126	29.2040
)............	chr8:61778635-61778875(+)$1	1	122	135	29.1020
))).........(	chr1:53290815-53291055(+)$1	1	78	91	25.8367
(((..........	chr16:23077614-23077856(-)$1	1	107	120	29.3061
...........))	chr1:204521826-204522066(+)$1	1	173	186	33.6938
.............	chr1:151023699-151023939(-)$1	1	42	55	33.6938
))........(((	chr18:45364259-45364499(-)$1	1	114	127	24.7142
.............	chr3:141464697-141464941(+)$1	1	117	130	30.6326
.............	chr10:71898749-71898989(-)$1	1	113	126	33.6938
)))))).......	chr6:118636481-118636721(+)$1	1	114	127	33.6938
(((((.(((((((	chr14:103808286-103808526(+)$1	1	185	198	29.4081
.......((((((	chr17:4173741-4173999(-)$1	1	136	149	33.6938
))..))))))...	chr22:28249030-28249354(-)$1	1	145	158	25.3265
(............	chr8:25269472-25269712(+)$1	1	121	134	33.6938
(.((((((((.((	chr2:29022539-29022789(+)$1	1	13	26	25.3265
..))))))..)))	chr1:10240475-10240715(+)$1	1	196	209	25.0204
....)))).))))	chr1:114306451-114306691(-)$1	1	115	128	30.6326
(............	chr3:113163236-113163478(-)$1	1	116	129	33.6938
.............	chr8:37612241-37612481(+)$1	1	111	124	30.4285
.............	chr1:155884209-155884488(-)$1	1	112	125	29.7142
)))....))))).	chr20:57609832-57610112(-)$1	1	147	160	30.4285
(((((((.(((((	chr12:56295132-56295374(-)$1	1	120	133	29.3061
(............	chr10:72637406-72637646(+)$1	1	158	171	33.6938
)))))))......	chr1:46093348-46093601(-)$1	1	181	194	25.8367
.....))))))))	chr1:57179493-57179734(+)$1	1	113	126	26.5510
)......))))))	chr7:155256466-155256706(+)$1	1	91	104	25.0204
)).)))))))...	chr7:112115489-112115729(+)$1	1	117	130	24.8163
.........(((.	chr8:101270175-101270415(-)$1	1	121	134	24.9183
)))))).))))..	chr5:156820144-156820384(+)$1	1	107	120	25.0204
.............	chr8:33356716-33356956(+)$1	1	108	121	30.6326
((((.(((((.((	chr6:117883619-117883859(-)$1	1	120	133	29.9183
)))))))))))))	chr2:102508625-102508865(+)$1	1	29	42	25.7346
..)))))))..))	chr16:67132944-67133184(+)$1	1	121	134	29.4081
.............	chr10:35860427-35860667(+)$1	1	122	135	25.2244
(((((((((....	chr6:32153182-32153422(-)$1	1	103	116	33.6938
...)).)))))))	chr18:71920583-71920823(-)$1	1	124	137	24.6122
.(((((((.....	chr5:90666713-90666956(-)$1	1	109	122	33.6938
..)))..))).))	chr3:5026423-5026663(+)$1	1	126	139	25.4285

#PSSM
C : 0.57	c : 0.18	A : 0.10	G : 0.08	a : 0.04	g : 0.02	
U : 0.59	u : 0.34	A : 0.04	a : 0.02	
U : 0.51	u : 0.38	G : 0.04	A : 0.04	C : 0.02	
U : 0.59	u : 0.36	G : 0.02	g : 0.02	
U : 0.57	u : 0.38	A : 0.02	C : 0.02	
U : 0.51	u : 0.38	C : 0.08	A : 0.02	
U : 0.57	u : 0.34	C : 0.04	a : 0.02	c : 0.02	
U : 0.59	u : 0.38	C : 0.02	
U : 0.46	u : 0.36	G : 0.08	A : 0.04	C : 0.02	c : 0.02	
U : 0.57	u : 0.38	C : 0.04	
U : 0.55	u : 0.38	C : 0.06	
U : 0.57	u : 0.36	C : 0.04	c : 0.02	
U : 0.57	u : 0.38	C : 0.04	

#score	1441.4081632653076
#seq	49
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m3_run2.nuc.txt

#NT
UUUC	chr14:89042158-89042384(+)$1	226	8	12	12.0000
UUUC	chr12:40344960-40345190(-)$1	230	2	6	12.0000
UUUC	chr6:71245921-71246151(+)$1	230	28	32	12.0000
UUUC	chr1:110553789-110554019(+)$1	230	12	16	12.0000
UUUC	chr3:101284316-101284546(+)$1	230	28	32	12.0000
UUUC	chr9:108226463-108226693(+)$1	230	39	43	12.0000
UUUC	chr13:48934116-48934346(+)$1	230	6	10	12.0000
UUUC	chr8:68115300-68115530(-)$1	230	35	39	12.0000
UUUC	chr2:217005895-217006120(+)$1	225	99	103	12.0000
UUUC	chr1:116206615-116206844(+)$1	229	14	18	12.0000
UUUC	chr12:12630356-12630582(-)$1	226	37	41	12.0000
UUUC	chr8:90921726-90921953(+)$1	227	204	208	12.0000
UUUC	chr15:52874269-52874499(-)$1	230	132	136	12.0000
UUUC	chr2:27551290-27551519(-)$1	229	46	50	12.0000
UUUC	chr5:36181822-36182057(+)$1	235	51	55	12.0000
UUUC	chr11:47254298-47254521(+)$1	223	48	52	12.0000
UUUC	chr6:43322692-43322919(-)$1	227	12	16	12.0000
UUUC	chr3:148741886-148742111(+)$1	225	77	81	12.0000
UUUC	chr21:34889315-34889540(-)$1	225	46	50	12.0000
UUUC	chr2:220366632-220366859(+)$1	227	105	109	12.0000
UUUC	chr2:27659515-27659745(+)$1	230	202	206	12.0000
UUUC	chr2:160661499-160661724(-)$1	225	100	104	12.0000
UUUC	chr1:150974591-150974816(-)$1	225	58	62	12.0000
UUUC	chr3:186503933-186504155(+)$1	222	9	13	12.0000
UUUC	chr1:197112523-197112753(-)$1	230	52	56	12.0000
UUUC	chr11:33369984-33370214(+)$1	230	1	5	12.0000
UUUC	chr3:130653366-130653593(+)$1	227	93	97	12.0000
UUUC	chr19:20002999-20003229(+)$1	230	101	105	12.0000
UUUC	chr5:72168394-72168625(+)$1	231	11	15	12.0000
UUUC	chr19:1418151-1418381(+)$1	230	29	33	12.0000
UUUC	chr9:86584188-86584415(-)$1	227	43	47	12.0000
UUUC	chr8:38677045-38677269(+)$1	224	118	122	12.0000
UUUC	chr1:70742382-70742612(-)$1	230	39	43	12.0000
UUUC	chr17:1326295-1326525(-)$1	230	89	93	12.0000
UUUC	chr19:3976158-3976388(-)$1	230	4	8	12.0000
UUUC	chr13:23908573-23908811(-)$1	238	110	114	12.0000
UUUC	chr6:407367-407605(+)$1	238	143	147	12.0000
UUUC	chr2:62110530-62110760(-)$1	230	70	74	12.0000
UUUC	chr5:88018581-88018811(-)$1	230	51	55	12.0000
UUUC	chr4:123109011-123109241(+)$1	230	100	104	12.0000
UUUC	chr9:125582686-125582916(-)$1	230	52	56	12.0000
UUUC	chr1:28233388-28233615(-)$1	227	12	16	12.0000
UUUC	chr15:41961518-41961748(+)$1	230	41	45	12.0000
UUUC	chr12:125466988-125467213(-)$1	225	31	35	12.0000
UUUC	chr4:187510168-187510383(+)$1	215	47	51	12.0000
UUUC	chr16:69200891-69201121(+)$1	230	122	126	12.0000
UUUC	chr2:242275374-242275604(+)$1	230	3	7	12.0000
UUUC	chr5:36177233-36177463(+)$1	230	21	25	12.0000
UUUC	chr2:32713631-32713854(+)$1	223	7	11	12.0000
UUUC	chr2:213878490-213878716(-)$1	226	39	43	12.0000
UUUC	chr12:65082079-65082309(+)$1	230	90	94	12.0000
UUUC	chr21:47704883-47705107(-)$1	224	61	65	12.0000
UUUC	chr3:110611888-110612105(+)$1	217	52	56	12.0000
UUUC	chr11:57576727-57576953(+)$1	226	7	11	12.0000
UUUC	chr17:57744065-57744288(+)$1	223	26	30	12.0000
UUUC	chr10:97443255-97443485(-)$1	230	2	6	12.0000
UUUC	chr10:127451787-127452017(+)$1	230	11	15	12.0000
UUUC	chr11:64876219-64876449(+)$1	230	121	125	12.0000
UUUC	chr12:69652553-69652783(+)$1	230	88	92	12.0000
UUUC	chr9:98002888-98003118(-)$1	230	10	14	12.0000
UUUC	chr5:40767576-40767806(-)$1	230	1	5	12.0000
UUUC	chr7:30656649-30656879(+)$1	230	40	44	12.0000
UUUC	chr3:56667771-56668001(-)$1	230	57	61	12.0000
UUUC	chr9:88967759-88967989(-)$1	230	89	93	12.0000
UUUC	chr1:175958484-175958714(-)$1	230	51	55	12.0000
UUUC	chr6:90409256-90409486(-)$1	230	219	223	12.0000
UUUC	chr7:156971376-156971596(+)$1	220	72	76	12.0000
UUUC	chr7:99170651-99170878(+)$1	227	201	205	12.0000
UUUC	chr1:90058332-90058559(+)$1	227	21	25	12.0000
UUUC	chrX:154490354-154490575(-)$1	221	46	50	12.0000
UUUC	chr3:48040164-48040390(-)$1	226	6	10	12.0000
UUUC	chr3:193332448-193332678(+)$1	230	7	11	12.0000
UUUC	chr22:37637555-37637785(-)$1	230	81	85	12.0000
UUUC	chr6:27419676-27419902(-)$1	226	94	98	12.0000
UUUC	chr5:134231990-134232220(+)$1	230	39	43	12.0000
UUUC	chr19:58772455-58772680(+)$1	225	65	69	12.0000
UUUC	chr7:65419251-65419481(+)$1	230	72	76	12.0000
UUUC	chr6:109690054-109690273(-)$1	219	31	35	12.0000
UUUC	chr17:79536017-79536239(-)$1	222	60	64	12.0000
UUUC	chr15:59344437-59344667(+)$1	230	4	8	12.0000

#otherMatches

#Struct PSSM
nnnn	chr10:101996586-101996816(-)$1	230	65	69	12.0000
GGGM	chr14:89042158-89042384(+)$1	226	8	12	12.0000
:GGG	chr12:40344960-40345190(-)$1	230	2	6	12.0000
gggg	chr6:71245921-71246151(+)$1	230	28	32	12.0000
FFFF	chr1:110553789-110554019(+)$1	230	12	16	12.0000
nnbb	chr3:101284316-101284546(+)$1	230	28	32	12.0000
:fff	chr9:108226463-108226693(+)$1	230	39	43	12.0000
iiii	chr13:48934116-48934346(+)$1	230	6	10	12.0000
JJJJ	chr8:68115300-68115530(-)$1	230	35	39	12.0000
ggg7	chr2:217005895-217006120(+)$1	225	99	103	12.0000
c"""	chr1:116206615-116206844(+)$1	229	14	18	12.0000
ccc]	chr12:12630356-12630582(-)$1	226	37	41	12.0000
iiii	chr8:90921726-90921953(+)$1	227	204	208	12.0000
^^^^	chr15:52874269-52874499(-)$1	230	132	136	12.0000
3ccc	chr2:27551290-27551519(-)$1	229	46	50	12.0000
d[bb	chr5:36181822-36182057(+)$1	235	51	55	12.0000
iiii	chr11:47254298-47254521(+)$1	223	48	52	12.0000
cc""	chr6:43322692-43322919(-)$1	227	12	16	12.0000
++++	chr3:148741886-148742111(+)$1	225	77	81	12.0000
e###	chr21:34889315-34889540(-)$1	225	46	50	12.0000
gggg	chr2:220366632-220366859(+)$1	227	105	109	12.0000
ffdd	chr2:27659515-27659745(+)$1	230	202	206	12.0000
22bb	chr2:160661499-160661724(-)$1	225	100	104	12.0000
""ff	chr1:150974591-150974816(-)$1	225	58	62	12.0000
hhhh	chr3:186503933-186504155(+)$1	222	9	13	12.0000
[ccc	chr1:197112523-197112753(-)$1	230	52	56	12.0000
FFFF	chr11:33369984-33370214(+)$1	230	1	5	12.0000
FF{C	chr3:130653366-130653593(+)$1	227	93	97	12.0000
rrdd	chr19:20002999-20003229(+)$1	230	101	105	12.0000
HHHH	chr5:72168394-72168625(+)$1	231	11	15	12.0000
::::	chr19:1418151-1418381(+)$1	230	29	33	12.0000
^^^^	chr9:86584188-86584415(-)$1	227	43	47	12.0000
:eee	chr8:38677045-38677269(+)$1	224	118	122	12.0000
::::	chr1:70742382-70742612(-)$1	230	39	43	12.0000
::::	chr17:1326295-1326525(-)$1	230	89	93	12.0000
IIII	chr19:3976158-3976388(-)$1	230	4	8	12.0000
''''	chr13:23908573-23908811(-)$1	238	110	114	12.0000
YYA}	chr6:407367-407605(+)$1	238	143	147	12.0000
ddd2	chr2:62110530-62110760(-)$1	230	70	74	12.0000
pppp	chr5:88018581-88018811(-)$1	230	51	55	12.0000
::::	chr4:123109011-123109241(+)$1	230	100	104	12.0000
FFFF	chr9:125582686-125582916(-)$1	230	52	56	12.0000
JJJJ	chr1:28233388-28233615(-)$1	227	12	16	12.0000
gggg	chr15:41961518-41961748(+)$1	230	41	45	12.0000
eeee	chr12:125466988-125467213(-)$1	225	31	35	12.0000
oooo	chr4:187510168-187510383(+)$1	215	47	51	12.0000
eeeq	chr16:69200891-69201121(+)$1	230	122	126	12.0000
eeee	chr2:242275374-242275604(+)$1	230	3	7	12.0000
ggg2	chr5:36177233-36177463(+)$1	230	21	25	12.0000
GGGG	chr2:32713631-32713854(+)$1	223	7	11	12.0000
====	chr2:213878490-213878716(-)$1	226	39	43	12.0000
22ee	chr12:65082079-65082309(+)$1	230	90	94	12.0000
ssss	chr21:47704883-47705107(-)$1	224	61	65	12.0000
eeee	chr3:110611888-110612105(+)$1	217	52	56	12.0000
::::	chr11:57576727-57576953(+)$1	226	7	11	12.0000
ddd2	chr17:57744065-57744288(+)$1	223	26	30	12.0000
:::C	chr10:97443255-97443485(-)$1	230	2	6	12.0000
mmmf	chr10:127451787-127452017(+)$1	230	11	15	12.0000
iiiq	chr11:64876219-64876449(+)$1	230	121	125	12.0000
d:::	chr12:69652553-69652783(+)$1	230	88	92	12.0000
D{CC	chr9:98002888-98003118(-)$1	230	10	14	12.0000
::::	chr5:40767576-40767806(-)$1	230	1	5	12.0000
^^^^	chr7:30656649-30656879(+)$1	230	40	44	12.0000
EEEE	chr3:56667771-56668001(-)$1	230	57	61	12.0000
mmmm	chr9:88967759-88967989(-)$1	230	89	93	12.0000
RRRR	chr1:175958484-175958714(-)$1	230	51	55	12.0000
ccc2	chr6:90409256-90409486(-)$1	230	219	223	12.0000
====	chr7:156971376-156971596(+)$1	220	72	76	12.0000
eeee	chr7:99170651-99170878(+)$1	227	201	205	12.0000
:::b	chr1:90058332-90058559(+)$1	227	21	25	12.0000
"hhh	chrX:154490354-154490575(-)$1	221	46	50	12.0000
EEEE	chr3:48040164-48040390(-)$1	226	6	10	12.0000
SSSS	chr3:193332448-193332678(+)$1	230	7	11	12.0000
5555	chr22:37637555-37637785(-)$1	230	81	85	12.0000
fff6	chr6:27419676-27419902(-)$1	226	94	98	12.0000
dd33	chr5:134231990-134232220(+)$1	230	39	43	12.0000
gggg	chr19:58772455-58772680(+)$1	225	65	69	12.0000
HHHS	chr7:65419251-65419481(+)$1	230	72	76	12.0000
))))	chr6:109690054-109690273(-)$1	219	31	35	12.0000
::::	chr17:79536017-79536239(-)$1	222	60	64	12.0000
EEEE	chr15:59344437-59344667(+)$1	230	4	8	12.0000

#DB
....	chr10:101996586-101996816(-)$1	1	65	69	12.0000
(((.	chr14:89042158-89042384(+)$1	1	8	12	12.0000
.(((	chr12:40344960-40345190(-)$1	1	2	6	12.0000
))))	chr6:71245921-71246151(+)$1	1	28	32	12.0000
((((	chr1:110553789-110554019(+)$1	1	12	16	12.0000
..))	chr3:101284316-101284546(+)$1	1	28	32	12.0000
.(((	chr9:108226463-108226693(+)$1	1	39	43	12.0000
((((	chr13:48934116-48934346(+)$1	1	6	10	12.0000
((((	chr8:68115300-68115530(-)$1	1	35	39	12.0000
))).	chr2:217005895-217006120(+)$1	1	99	103	12.0000
(...	chr1:116206615-116206844(+)$1	1	14	18	12.0000
))).	chr12:12630356-12630582(-)$1	1	37	41	12.0000
))))	chr8:90921726-90921953(+)$1	1	204	208	12.0000
....	chr15:52874269-52874499(-)$1	1	132	136	12.0000
.)))	chr2:27551290-27551519(-)$1	1	46	50	12.0000
(.((	chr5:36181822-36182057(+)$1	1	51	55	12.0000
((((	chr11:47254298-47254521(+)$1	1	48	52	12.0000
((..	chr6:43322692-43322919(-)$1	1	12	16	12.0000
....	chr3:148741886-148742111(+)$1	1	77	81	12.0000
(...	chr21:34889315-34889540(-)$1	1	46	50	12.0000
((((	chr2:220366632-220366859(+)$1	1	105	109	12.0000
))))	chr2:27659515-27659745(+)$1	1	202	206	12.0000
..))	chr2:160661499-160661724(-)$1	1	100	104	12.0000
..((	chr1:150974591-150974816(-)$1	1	58	62	12.0000
((((	chr3:186503933-186504155(+)$1	1	9	13	12.0000
.(((	chr1:197112523-197112753(-)$1	1	52	56	12.0000
((((	chr11:33369984-33370214(+)$1	1	1	5	12.0000
((.(	chr3:130653366-130653593(+)$1	1	93	97	12.0000
..))	chr19:20002999-20003229(+)$1	1	101	105	12.0000
((((	chr5:72168394-72168625(+)$1	1	11	15	12.0000
....	chr19:1418151-1418381(+)$1	1	29	33	12.0000
....	chr9:86584188-86584415(-)$1	1	43	47	12.0000
.(((	chr8:38677045-38677269(+)$1	1	118	122	12.0000
....	chr1:70742382-70742612(-)$1	1	39	43	12.0000
....	chr17:1326295-1326525(-)$1	1	89	93	12.0000
((((	chr19:3976158-3976388(-)$1	1	4	8	12.0000
....	chr13:23908573-23908811(-)$1	1	110	114	12.0000
..).	chr6:407367-407605(+)$1	1	143	147	12.0000
))).	chr2:62110530-62110760(-)$1	1	70	74	12.0000
....	chr5:88018581-88018811(-)$1	1	51	55	12.0000
....	chr4:123109011-123109241(+)$1	1	100	104	12.0000
((((	chr9:125582686-125582916(-)$1	1	52	56	12.0000
((((	chr1:28233388-28233615(-)$1	1	12	16	12.0000
))))	chr15:41961518-41961748(+)$1	1	41	45	12.0000
((((	chr12:125466988-125467213(-)$1	1	31	35	12.0000
....	chr4:187510168-187510383(+)$1	1	47	51	12.0000
(((.	chr16:69200891-69201121(+)$1	1	122	126	12.0000
((((	chr2:242275374-242275604(+)$1	1	3	7	12.0000
))).	chr5:36177233-36177463(+)$1	1	21	25	12.0000
((((	chr2:32713631-32713854(+)$1	1	7	11	12.0000
((((	chr2:213878490-213878716(-)$1	1	39	43	12.0000
..))	chr12:65082079-65082309(+)$1	1	90	94	12.0000
....	chr21:47704883-47705107(-)$1	1	61	65	12.0000
((((	chr3:110611888-110612105(+)$1	1	52	56	12.0000
....	chr11:57576727-57576953(+)$1	1	7	11	12.0000
))).	chr17:57744065-57744288(+)$1	1	26	30	12.0000
...(	chr10:97443255-97443485(-)$1	1	2	6	12.0000
...)	chr10:127451787-127452017(+)$1	1	11	15	12.0000
(((.	chr11:64876219-64876449(+)$1	1	121	125	12.0000
)...	chr12:69652553-69652783(+)$1	1	88	92	12.0000
(.((	chr9:98002888-98003118(-)$1	1	10	14	12.0000
....	chr5:40767576-40767806(-)$1	1	1	5	12.0000
....	chr7:30656649-30656879(+)$1	1	40	44	12.0000
((((	chr3:56667771-56668001(-)$1	1	57	61	12.0000
....	chr9:88967759-88967989(-)$1	1	89	93	12.0000
....	chr1:175958484-175958714(-)$1	1	51	55	12.0000
))).	chr6:90409256-90409486(-)$1	1	219	223	12.0000
((((	chr7:156971376-156971596(+)$1	1	72	76	12.0000
))))	chr7:99170651-99170878(+)$1	1	201	205	12.0000
...(	chr1:90058332-90058559(+)$1	1	21	25	12.0000
.(((	chrX:154490354-154490575(-)$1	1	46	50	12.0000
((((	chr3:48040164-48040390(-)$1	1	6	10	12.0000
....	chr3:193332448-193332678(+)$1	1	7	11	12.0000
....	chr22:37637555-37637785(-)$1	1	81	85	12.0000
))).	chr6:27419676-27419902(-)$1	1	94	98	12.0000
))..	chr5:134231990-134232220(+)$1	1	39	43	12.0000
((((	chr19:58772455-58772680(+)$1	1	65	69	12.0000
(((.	chr7:65419251-65419481(+)$1	1	72	76	12.0000
....	chr6:109690054-109690273(-)$1	1	31	35	12.0000
....	chr17:79536017-79536239(-)$1	1	60	64	12.0000
((((	chr15:59344437-59344667(+)$1	1	4	8	12.0000

#PSSM
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	

#score	972.0000000000006
#seq	81
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m2_run1.nuc.txt

#NT
AGU	chr3:145788758-145788981(-)$1	223	50	53	9.0000
AGU	chr7:148700908-148701127(-)$1	219	15	18	9.0000
AGU	chr3:41275223-41275445(+)$1	222	62	65	9.0000
AGU	chr2:145157127-145157346(-)$1	219	46	49	9.0000
AGU	chr1:91404870-91405092(-)$1	222	36	39	9.0000
AGU	chr8:91643806-91644028(-)$1	222	9	12	9.0000
AGU	chr1:224553547-224553793(+)$1	246	0	3	9.0000
AGU	chr10:17756581-17756810(+)$1	229	8	11	9.0000
AGU	chr3:31621314-31621538(+)$1	224	207	210	9.0000
AGU	chrX:40993925-40994155(+)$1	230	66	69	9.0000
AGU	chr6:11134553-11134776(+)$1	223	121	124	9.0000
AGU	chr19:47712332-47712561(+)$1	229	156	159	9.0000
AGU	chr19:3976161-3976388(-)$1	227	27	30	9.0000
AGU	chr6:82914512-82914736(-)$1	224	32	35	9.0000
AGU	chr1:63955729-63955952(-)$1	223	61	64	9.0000
AGU	chr4:187584353-187584578(-)$1	225	83	86	9.0000
AGU	chr5:95124412-95124633(+)$1	221	6	9	9.0000
AGU	chr10:90974500-90974725(-)$1	225	136	139	9.0000
AGU	chr5:153830573-153830795(+)$1	222	122	125	9.0000
AGU	chr1:20981019-20981252(-)$1	233	10	13	9.0000
AGU	chr6:159058703-159058922(-)$1	219	40	43	9.0000
AGU	chr17:29482966-29483190(+)$1	224	72	75	9.0000
AGU	chr10:92982560-92982781(+)$1	221	50	53	9.0000
AGU	chr10:88220898-88221123(-)$1	225	31	34	9.0000
AGU	chr10:70666623-70666844(+)$1	221	24	27	9.0000
AGU	chr5:137735506-137735730(+)$1	224	46	49	9.0000
AGU	chr13:23909318-23909547(-)$1	229	14	17	9.0000
AGU	chr21:34926437-34926660(+)$1	223	35	38	9.0000
AGU	chr1:224377686-224377908(+)$1	222	67	70	9.0000
AGU	chr4:185599409-185599634(+)$1	225	78	81	9.0000
AGU	chr4:25915897-25916118(+)$1	221	141	144	9.0000
AGU	chr8:19680721-19680947(+)$1	226	88	91	9.0000
AGU	chr1:113459868-113460092(-)$1	224	53	56	9.0000
AGU	chr12:50236655-50236875(-)$1	220	35	38	9.0000
AGU	chr2:197662439-197662661(-)$1	222	29	32	9.0000
AGU	chr8:97285474-97285698(+)$1	224	19	22	9.0000
AGU	chr3:142754787-142755011(+)$1	224	7	10	9.0000
AGU	chr10:124793848-124794071(+)$1	223	90	93	9.0000
AGU	chr16:2817719-2817940(+)$1	221	119	122	9.0000
AGU	chr2:69581526-69581747(-)$1	221	78	81	9.0000
AGU	chr6:26104142-26104389(+)$1	247	4	7	9.0000
AGU	chr7:116550215-116550442(+)$1	227	97	100	9.0000
AGU	chr1:90400655-90400878(+)$1	223	3	6	9.0000
AGU	chr5:149826275-149826509(-)$1	234	150	153	9.0000
AGU	chr3:52723102-52723322(+)$1	220	80	83	9.0000
AGU	chr10:119043756-119043975(-)$1	219	26	29	9.0000
AGU	chr5:41917261-41917501(+)$1	240	19	22	9.0000
AGU	chr15:73854183-73854410(-)$1	227	7	10	9.0000
AGU	chr7:148526802-148527024(-)$1	222	23	26	9.0000
AGU	chr12:72092737-72092968(+)$1	231	65	68	9.0000
AGU	chr16:2811838-2812065(+)$1	227	8	11	9.0000
AGU	chr17:38557125-38557345(-)$1	220	59	62	9.0000
AGU	chr4:185552819-185553043(-)$1	224	89	92	9.0000
AGU	chr14:32562266-32562496(+)$1	230	24	27	9.0000
AGU	chr5:157162755-157162980(+)$1	225	25	28	9.0000
AGU	chr1:33292234-33292463(+)$1	229	156	159	9.0000
AGU	chr2:55900023-55900244(-)$1	221	28	31	9.0000
AGU	chr9:86297810-86298034(-)$1	224	123	126	9.0000
AGU	chr5:134235172-134235396(+)$1	224	80	83	9.0000
AGU	chr5:43505885-43506109(-)$1	224	46	49	9.0000
AGU	chr14:67841142-67841365(+)$1	223	67	70	9.0000
AGU	chr4:57265262-57265496(-)$1	234	37	40	9.0000
AGU	chr1:214818226-214818455(+)$1	229	74	77	9.0000
agu	chr9:135917565-135917792(+)$1	227	215	218	9.0000
AGU	chr9:115567005-115567229(+)$1	224	6	9	9.0000
AGU	chr2:73680879-73681102(+)$1	223	11	14	9.0000
AGU	chr8:27660816-27661035(+)$1	219	77	80	9.0000
AGU	chr5:151170461-151170681(+)$1	220	2	5	9.0000
AGU	chr3:9483728-9483949(+)$1	221	22	25	9.0000
AGU	chr1:243858799-243859028(-)$1	229	128	131	9.0000
AGU	chr5:178310290-178310514(+)$1	224	6	9	9.0000
AGU	chr12:25380087-25380310(-)$1	223	40	43	9.0000
AGU	chr10:86130952-86131175(+)$1	223	0	3	9.0000
AGU	chr20:43115206-43115428(+)$1	222	55	58	9.0000
AGU	chr11:3712483-3712706(-)$1	223	122	125	9.0000
AGU	chr19:3976117-3976345(-)$1	228	12	15	9.0000
AGU	chr18:9561942-9562166(-)$1	224	4	7	9.0000
AGU	chr14:104027255-104027481(-)$1	226	10	13	9.0000
AGU	chr5:150075008-150075231(-)$1	223	177	180	9.0000
AGU	chr12:69983210-69983447(+)$1	237	11	14	9.0000
AGU	chr5:68463934-68464154(+)$1	220	91	94	9.0000
AGU	chr6:116599824-116600046(-)$1	222	11	14	9.0000
AGU	chr1:76260099-76260319(+)$1	220	9	12	9.0000
AGU	chr12:42503355-42503581(-)$1	226	52	55	9.0000
AGU	chr16:29822244-29822466(+)$1	222	54	57	9.0000
AGU	chr17:52982784-52983008(+)$1	224	46	49	9.0000
AGU	chr3:25661263-25661489(-)$1	226	97	100	9.0000
AGU	chr12:98927329-98927552(+)$1	223	2	5	9.0000
AGU	chr5:74877057-74877289(+)$1	232	5	8	9.0000
AGU	chr1:193045036-193045261(+)$1	225	12	15	9.0000
AGU	chr15:83698918-83699141(-)$1	223	6	9	9.0000
AGU	chr12:88542119-88542355(+)$1	236	8	11	9.0000
AGU	chr1:67889860-67890082(-)$1	222	79	82	9.0000
AGU	chr5:14758570-14758791(-)$1	221	89	92	9.0000
AGU	chr21:44520482-44520703(-)$1	221	21	24	9.0000
AGU	chr14:45565241-45565459(+)$1	218	140	143	9.0000
AGU	chr1:109952485-109952709(-)$1	224	71	74	9.0000

#otherMatches

#Struct PSSM
ggg	chr2:183867881-183868101(-)$1	220	177	180	9.0000
eee	chr3:145788758-145788981(-)$1	223	50	53	9.0000
[a[	chr7:148700908-148701127(-)$1	219	15	18	9.0000
FFF	chr3:41275223-41275445(+)$1	222	62	65	9.0000
mmm	chr2:145157127-145157346(-)$1	219	46	49	9.0000
eee	chr1:91404870-91405092(-)$1	222	36	39	9.0000
ccc	chr8:91643806-91644028(-)$1	222	9	12	9.0000
:ee	chr1:224553547-224553793(+)$1	246	0	3	9.0000
{FF	chr10:17756581-17756810(+)$1	229	8	11	9.0000
ggg	chr3:31621314-31621538(+)$1	224	207	210	9.0000
cc:	chrX:40993925-40994155(+)$1	230	66	69	9.0000
fff	chr6:11134553-11134776(+)$1	223	121	124	9.0000
dd:	chr19:47712332-47712561(+)$1	229	156	159	9.0000
fff	chr19:3976161-3976388(-)$1	227	27	30	9.0000
hhG	chr6:82914512-82914736(-)$1	224	32	35	9.0000
FFF	chr1:63955729-63955952(-)$1	223	61	64	9.0000
:dd	chr4:187584353-187584578(-)$1	225	83	86	9.0000
HHH	chr5:95124412-95124633(+)$1	221	6	9	9.0000
ddd	chr10:90974500-90974725(-)$1	225	136	139	9.0000
:::	chr5:153830573-153830795(+)$1	222	122	125	9.0000
GGG	chr1:20981019-20981252(-)$1	233	10	13	9.0000
%%%	chr6:159058703-159058922(-)$1	219	40	43	9.0000
::c	chr17:29482966-29483190(+)$1	224	72	75	9.0000
eee	chr10:92982560-92982781(+)$1	221	50	53	9.0000
G::	chr10:88220898-88221123(-)$1	225	31	34	9.0000
ddd	chr10:70666623-70666844(+)$1	221	24	27	9.0000
qdd	chr5:137735506-137735730(+)$1	224	46	49	9.0000
mmm	chr13:23909318-23909547(-)$1	229	14	17	9.0000
dcc	chr21:34926437-34926660(+)$1	223	35	38	9.0000
{CC	chr1:224377686-224377908(+)$1	222	67	70	9.0000
:::	chr4:185599409-185599634(+)$1	225	78	81	9.0000
bb:	chr4:25915897-25916118(+)$1	221	141	144	9.0000
cqq	chr8:19680721-19680947(+)$1	226	88	91	9.0000
qqq	chr1:113459868-113460092(-)$1	224	53	56	9.0000
ggg	chr12:50236655-50236875(-)$1	220	35	38	9.0000
ggg	chr2:197662439-197662661(-)$1	222	29	32	9.0000
FFF	chr8:97285474-97285698(+)$1	224	19	22	9.0000
:::	chr3:142754787-142755011(+)$1	224	7	10	9.0000
555	chr10:124793848-124794071(+)$1	223	90	93	9.0000
2cc	chr16:2817719-2817940(+)$1	221	119	122	9.0000
fff	chr2:69581526-69581747(-)$1	221	78	81	9.0000
:::	chr6:26104142-26104389(+)$1	247	4	7	9.0000
[bb	chr7:116550215-116550442(+)$1	227	97	100	9.0000
:::	chr1:90400655-90400878(+)$1	223	3	6	9.0000
>>>	chr5:149826275-149826509(-)$1	234	150	153	9.0000
bb[	chr3:52723102-52723322(+)$1	220	80	83	9.0000
mcc	chr10:119043756-119043975(-)$1	219	26	29	9.0000
:::	chr5:41917261-41917501(+)$1	240	19	22	9.0000
{FF	chr15:73854183-73854410(-)$1	227	7	10	9.0000
hh[	chr7:148526802-148527024(-)$1	222	23	26	9.0000
fff	chr12:72092737-72092968(+)$1	231	65	68	9.0000
:::	chr16:2811838-2812065(+)$1	227	8	11	9.0000
!cc	chr17:38557125-38557345(-)$1	220	59	62	9.0000
ggg	chr4:185552819-185553043(-)$1	224	89	92	9.0000
ddd	chr14:32562266-32562496(+)$1	230	24	27	9.0000
ggg	chr5:157162755-157162980(+)$1	225	25	28	9.0000
fff	chr1:33292234-33292463(+)$1	229	156	159	9.0000
dd[	chr2:55900023-55900244(-)$1	221	28	31	9.0000
ggg	chr9:86297810-86298034(-)$1	224	123	126	9.0000
ggg	chr5:134235172-134235396(+)$1	224	80	83	9.0000
eee	chr5:43505885-43506109(-)$1	224	46	49	9.0000
YEE	chr14:67841142-67841365(+)$1	223	67	70	9.0000
hhh	chr4:57265262-57265496(-)$1	234	37	40	9.0000
occ	chr1:214818226-214818455(+)$1	229	74	77	9.0000
EEE	chr9:135917565-135917792(+)$1	227	215	218	9.0000
:CC	chr9:115567005-115567229(+)$1	224	6	9	9.0000
+++	chr2:73680879-73681102(+)$1	223	11	14	9.0000
:::	chr8:27660816-27661035(+)$1	219	77	80	9.0000
bb[	chr5:151170461-151170681(+)$1	220	2	5	9.0000
ee]	chr3:9483728-9483949(+)$1	221	22	25	9.0000
''d	chr1:243858799-243859028(-)$1	229	128	131	9.0000
f[f	chr5:178310290-178310514(+)$1	224	6	9	9.0000
dd]	chr12:25380087-25380310(-)$1	223	40	43	9.0000
:::	chr10:86130952-86131175(+)$1	223	0	3	9.0000
]dd	chr20:43115206-43115428(+)$1	222	55	58	9.0000
CCY	chr11:3712483-3712706(-)$1	223	122	125	9.0000
ddd	chr19:3976117-3976345(-)$1	228	12	15	9.0000
[ff	chr18:9561942-9562166(-)$1	224	4	7	9.0000
%%%	chr14:104027255-104027481(-)$1	226	10	13	9.0000
hhh	chr5:150075008-150075231(-)$1	223	177	180	9.0000
:gg	chr12:69983210-69983447(+)$1	237	11	14	9.0000
BB{	chr5:68463934-68464154(+)$1	220	91	94	9.0000
ddd	chr6:116599824-116600046(-)$1	222	11	14	9.0000
[hh	chr1:76260099-76260319(+)$1	220	9	12	9.0000
[bb	chr12:42503355-42503581(-)$1	226	52	55	9.0000
ncc	chr16:29822244-29822466(+)$1	222	54	57	9.0000
e[g	chr17:52982784-52983008(+)$1	224	46	49	9.0000
ggg	chr3:25661263-25661489(-)$1	226	97	100	9.0000
c[a	chr12:98927329-98927552(+)$1	223	2	5	9.0000
KKC	chr5:74877057-74877289(+)$1	232	5	8	9.0000
LBB	chr1:193045036-193045261(+)$1	225	12	15	9.0000
:::	chr15:83698918-83699141(-)$1	223	6	9	9.0000
===	chr12:88542119-88542355(+)$1	236	8	11	9.0000
ddd	chr1:67889860-67890082(-)$1	222	79	82	9.0000
[ee	chr5:14758570-14758791(-)$1	221	89	92	9.0000
iii	chr21:44520482-44520703(-)$1	221	21	24	9.0000
f33	chr14:45565241-45565459(+)$1	218	140	143	9.0000
fcc	chr1:109952485-109952709(-)$1	224	71	74	9.0000

#DB
)))	chr2:183867881-183868101(-)$1	1	177	180	9.0000
)))	chr3:145788758-145788981(-)$1	1	50	53	9.0000
.(.	chr7:148700908-148701127(-)$1	1	15	18	9.0000
(((	chr3:41275223-41275445(+)$1	1	62	65	9.0000
...	chr2:145157127-145157346(-)$1	1	46	49	9.0000
(((	chr1:91404870-91405092(-)$1	1	36	39	9.0000
(((	chr8:91643806-91644028(-)$1	1	9	12	9.0000
.((	chr1:224553547-224553793(+)$1	1	0	3	9.0000
.((	chr10:17756581-17756810(+)$1	1	8	11	9.0000
)))	chr3:31621314-31621538(+)$1	1	207	210	9.0000
)).	chrX:40993925-40994155(+)$1	1	66	69	9.0000
(((	chr6:11134553-11134776(+)$1	1	121	124	9.0000
)).	chr19:47712332-47712561(+)$1	1	156	159	9.0000
(((	chr19:3976161-3976388(-)$1	1	27	30	9.0000
))(	chr6:82914512-82914736(-)$1	1	32	35	9.0000
(((	chr1:63955729-63955952(-)$1	1	61	64	9.0000
.((	chr4:187584353-187584578(-)$1	1	83	86	9.0000
(((	chr5:95124412-95124633(+)$1	1	6	9	9.0000
(((	chr10:90974500-90974725(-)$1	1	136	139	9.0000
...	chr5:153830573-153830795(+)$1	1	122	125	9.0000
(((	chr1:20981019-20981252(-)$1	1	10	13	9.0000
...	chr6:159058703-159058922(-)$1	1	40	43	9.0000
..(	chr17:29482966-29483190(+)$1	1	72	75	9.0000
)))	chr10:92982560-92982781(+)$1	1	50	53	9.0000
(..	chr10:88220898-88221123(-)$1	1	31	34	9.0000
(((	chr10:70666623-70666844(+)$1	1	24	27	9.0000
.))	chr5:137735506-137735730(+)$1	1	46	49	9.0000
...	chr13:23909318-23909547(-)$1	1	14	17	9.0000
)))	chr21:34926437-34926660(+)$1	1	35	38	9.0000
.((	chr1:224377686-224377908(+)$1	1	67	70	9.0000
...	chr4:185599409-185599634(+)$1	1	78	81	9.0000
)).	chr4:25915897-25916118(+)$1	1	141	144	9.0000
(..	chr8:19680721-19680947(+)$1	1	88	91	9.0000
...	chr1:113459868-113460092(-)$1	1	53	56	9.0000
(((	chr12:50236655-50236875(-)$1	1	35	38	9.0000
(((	chr2:197662439-197662661(-)$1	1	29	32	9.0000
(((	chr8:97285474-97285698(+)$1	1	19	22	9.0000
...	chr3:142754787-142755011(+)$1	1	7	10	9.0000
...	chr10:124793848-124794071(+)$1	1	90	93	9.0000
.))	chr16:2817719-2817940(+)$1	1	119	122	9.0000
(((	chr2:69581526-69581747(-)$1	1	78	81	9.0000
...	chr6:26104142-26104389(+)$1	1	4	7	9.0000
.((	chr7:116550215-116550442(+)$1	1	97	100	9.0000
...	chr1:90400655-90400878(+)$1	1	3	6	9.0000
...	chr5:149826275-149826509(-)$1	1	150	153	9.0000
((.	chr3:52723102-52723322(+)$1	1	80	83	9.0000
.))	chr10:119043756-119043975(-)$1	1	26	29	9.0000
...	chr5:41917261-41917501(+)$1	1	19	22	9.0000
.((	chr15:73854183-73854410(-)$1	1	7	10	9.0000
((.	chr7:148526802-148527024(-)$1	1	23	26	9.0000
(((	chr12:72092737-72092968(+)$1	1	65	68	9.0000
...	chr16:2811838-2812065(+)$1	1	8	11	9.0000
.((	chr17:38557125-38557345(-)$1	1	59	62	9.0000
)))	chr4:185552819-185553043(-)$1	1	89	92	9.0000
(((	chr14:32562266-32562496(+)$1	1	24	27	9.0000
(((	chr5:157162755-157162980(+)$1	1	25	28	9.0000
)))	chr1:33292234-33292463(+)$1	1	156	159	9.0000
((.	chr2:55900023-55900244(-)$1	1	28	31	9.0000
)))	chr9:86297810-86298034(-)$1	1	123	126	9.0000
)))	chr5:134235172-134235396(+)$1	1	80	83	9.0000
(((	chr5:43505885-43506109(-)$1	1	46	49	9.0000
.))	chr14:67841142-67841365(+)$1	1	67	70	9.0000
(((	chr4:57265262-57265496(-)$1	1	37	40	9.0000
.))	chr1:214818226-214818455(+)$1	1	74	77	9.0000
)))	chr9:135917565-135917792(+)$1	1	215	218	9.0000
.((	chr9:115567005-115567229(+)$1	1	6	9	9.0000
...	chr2:73680879-73681102(+)$1	1	11	14	9.0000
...	chr8:27660816-27661035(+)$1	1	77	80	9.0000
((.	chr5:151170461-151170681(+)$1	1	2	5	9.0000
)).	chr3:9483728-9483949(+)$1	1	22	25	9.0000
..(	chr1:243858799-243859028(-)$1	1	128	131	9.0000
(.(	chr5:178310290-178310514(+)$1	1	6	9	9.0000
)).	chr12:25380087-25380310(-)$1	1	40	43	9.0000
...	chr10:86130952-86131175(+)$1	1	0	3	9.0000
.))	chr20:43115206-43115428(+)$1	1	55	58	9.0000
)).	chr11:3712483-3712706(-)$1	1	122	125	9.0000
(((	chr19:3976117-3976345(-)$1	1	12	15	9.0000
.((	chr18:9561942-9562166(-)$1	1	4	7	9.0000
...	chr14:104027255-104027481(-)$1	1	10	13	9.0000
(((	chr5:150075008-150075231(-)$1	1	177	180	9.0000
.((	chr12:69983210-69983447(+)$1	1	11	14	9.0000
((.	chr5:68463934-68464154(+)$1	1	91	94	9.0000
(((	chr6:116599824-116600046(-)$1	1	11	14	9.0000
.((	chr1:76260099-76260319(+)$1	1	9	12	9.0000
.((	chr12:42503355-42503581(-)$1	1	52	55	9.0000
.))	chr16:29822244-29822466(+)$1	1	54	57	9.0000
(.(	chr17:52982784-52983008(+)$1	1	46	49	9.0000
)))	chr3:25661263-25661489(-)$1	1	97	100	9.0000
(.(	chr12:98927329-98927552(+)$1	1	2	5	9.0000
..(	chr5:74877057-74877289(+)$1	1	5	8	9.0000
.((	chr1:193045036-193045261(+)$1	1	12	15	9.0000
...	chr15:83698918-83699141(-)$1	1	6	9	9.0000
(((	chr12:88542119-88542355(+)$1	1	8	11	9.0000
(((	chr1:67889860-67890082(-)$1	1	79	82	9.0000
.((	chr5:14758570-14758791(-)$1	1	89	92	9.0000
(((	chr21:44520482-44520703(-)$1	1	21	24	9.0000
)..	chr14:45565241-45565459(+)$1	1	140	143	9.0000
(((	chr1:109952485-109952709(-)$1	1	71	74	9.0000

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
U : 0.98	u : 0.01	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m3_run1.nuc.txt

#NT
auuuu	chr1:115312448-115312673(-)$1	225	0	5	15.0000
AUUUU	chr1:155851772-155851998(+)$1	226	193	198	15.0000
AUUUU	chr19:21305328-21305554(+)$1	226	107	112	15.0000
AUUUU	chr12:95645616-95645851(+)$1	235	81	86	15.0000
AUUUU	chr1:93619627-93619851(-)$1	224	182	187	15.0000
AUUUU	chr4:2231131-2231360(-)$1	229	110	115	15.0000
AUUUU	chr12:16056057-16056298(+)$1	241	191	196	15.0000
AUUUU	chr3:57307009-57307238(+)$1	229	15	20	15.0000
AUUUU	chr19:40576999-40577219(-)$1	220	86	91	15.0000
AUUUU	chrX:46918740-46918962(+)$1	222	1	6	15.0000
AUUUU	chr4:16164980-16165200(-)$1	220	28	33	15.0000
AUUUU	chr1:204526715-204526956(+)$1	241	185	190	15.0000
AUUUU	chr5:41917517-41917751(+)$1	234	170	175	15.0000
AUUUU	chr5:77773203-77773434(+)$1	231	64	69	15.0000
AUUUU	chr14:32624870-32625101(+)$1	231	15	20	15.0000
AUUUU	chr5:34906990-34907218(-)$1	228	118	123	15.0000
auuuu	chr5:135513355-135513583(+)$1	228	107	112	15.0000
AUUUU	chr6:24777113-24777341(+)$1	228	26	31	15.0000
AUUUU	chr2:113289406-113289637(+)$1	231	146	151	15.0000
AUUUU	chr7:75956759-75957005(-)$1	246	122	127	15.0000
AUUUU	chr1:54298060-54298288(-)$1	228	101	106	15.0000
AUUUU	chr10:70506911-70507132(+)$1	221	204	209	15.0000
AUUUU	chr1:91990633-91990873(+)$1	240	193	198	15.0000
AUUUU	chr5:37289933-37290175(-)$1	242	126	131	15.0000
AUUUU	chr2:207177906-207178131(+)$1	225	216	221	15.0000
AUUUU	chr3:122143622-122143854(-)$1	232	4	9	15.0000
AUUUU	chr12:49083898-49084124(-)$1	226	117	122	15.0000
AUUUU	chr4:48425901-48426123(+)$1	222	145	150	15.0000
AUUUU	chr1:85016098-85016321(-)$1	223	54	59	15.0000
AUUUU	chr5:132214515-132214742(-)$1	227	100	105	15.0000
AUUUU	chr12:46578093-46578313(-)$1	220	13	18	15.0000
AUUUU	chr2:187628825-187629059(+)$1	234	26	31	15.0000
AUUUU	chr12:100691766-100692000(+)$1	234	54	59	15.0000
AUUUU	chr12:54628513-54628744(-)$1	231	54	59	15.0000
AUUUU	chr1:205686164-205686406(-)$1	242	7	12	15.0000
AUUUU	chr11:18630689-18630909(-)$1	220	143	148	15.0000
AUUUU	chr2:198256355-198256573(-)$1	218	154	159	15.0000
AUUUU	chr10:30304126-30304360(-)$1	234	159	164	15.0000
AUUUU	chr21:34930577-34930801(+)$1	224	76	81	15.0000
AUUUU	chr1:179068600-179068823(-)$1	223	178	183	15.0000
AUUUU	chr6:11134949-11135174(+)$1	225	137	142	15.0000
AUUUU	chr3:113437829-113438060(-)$1	231	171	176	15.0000
AUUUU	chr7:138991016-138991244(+)$1	228	219	224	15.0000
AUUUU	chr11:130014517-130014747(+)$1	230	10	15	15.0000
AUUUU	chr2:172821869-172822090(+)$1	221	33	38	15.0000
AUUUU	chr10:61551109-61551350(-)$1	241	59	64	15.0000
AUUUU	chr17:30700085-30700328(+)$1	243	25	30	15.0000
AUUUU	chr12:12630704-12630922(-)$1	218	14	19	15.0000
AUUUU	chr2:208466169-208466395(+)$1	226	109	114	15.0000
AUUUU	chr11:74548691-74548915(+)$1	224	185	190	15.0000
AUUUU	chrX:103435542-103435767(+)$1	225	200	205	15.0000
AUUUU	chr8:6616915-6617145(+)$1	230	66	71	15.0000
AUUUU	chr1:205682793-205683032(-)$1	239	26	31	15.0000
AUUUU	chr7:134654330-134654560(+)$1	230	165	170	15.0000
AUUUU	chr16:1749433-1749671(+)$1	238	47	52	15.0000

#otherMatches

#Struct PSSM
::::E	chr13:77457941-77458172(-)$1	231	13	18	15.0000
:::::	chr1:115312448-115312673(-)$1	225	0	5	15.0000
333ee	chr1:155851772-155851998(+)$1	226	193	198	15.0000
hhhhh	chr19:21305328-21305554(+)$1	226	107	112	15.0000
::ggg	chr12:95645616-95645851(+)$1	235	81	86	15.0000
ffff3	chr1:93619627-93619851(-)$1	224	182	187	15.0000
tthhh	chr4:2231131-2231360(-)$1	229	110	115	15.0000
::CCC	chr12:16056057-16056298(+)$1	241	191	196	15.0000
:::::	chr3:57307009-57307238(+)$1	229	15	20	15.0000
fffff	chr19:40576999-40577219(-)$1	220	86	91	15.0000
::::E	chrX:46918740-46918962(+)$1	222	1	6	15.0000
+++++	chr4:16164980-16165200(-)$1	220	28	33	15.0000
peeee	chr1:204526715-204526956(+)$1	241	185	190	15.0000
cnnnn	chr5:41917517-41917751(+)$1	234	170	175	15.0000
'''''	chr5:77773203-77773434(+)$1	231	64	69	15.0000
ggggg	chr14:32624870-32625101(+)$1	231	15	20	15.0000
ccc22	chr5:34906990-34907218(-)$1	228	118	123	15.0000
::fff	chr5:135513355-135513583(+)$1	228	107	112	15.0000
GGGGG	chr6:24777113-24777341(+)$1	228	26	31	15.0000
:::::	chr2:113289406-113289637(+)$1	231	146	151	15.0000
ee!!g	chr7:75956759-75957005(-)$1	246	122	127	15.0000
e6666	chr1:54298060-54298288(-)$1	228	101	106	15.0000
cccmm	chr10:70506911-70507132(+)$1	221	204	209	15.0000
fffff	chr1:91990633-91990873(+)$1	240	193	198	15.0000
:::::	chr5:37289933-37290175(-)$1	242	126	131	15.0000
D}GGG	chr2:207177906-207178131(+)$1	225	216	221	15.0000
CC:gg	chr3:122143622-122143854(-)$1	232	4	9	15.0000
:iiii	chr12:49083898-49084124(-)$1	226	117	122	15.0000
meeee	chr4:48425901-48426123(+)$1	222	145	150	15.0000
((fff	chr1:85016098-85016321(-)$1	223	54	59	15.0000
cc[bb	chr5:132214515-132214742(-)$1	227	100	105	15.0000
=====	chr12:46578093-46578313(-)$1	220	13	18	15.0000
EEEEK	chr2:187628825-187629059(+)$1	234	26	31	15.0000
:::::	chr12:100691766-100692000(+)$1	234	54	59	15.0000
dllld	chr12:54628513-54628744(-)$1	231	54	59	15.0000
eeeee	chr1:205686164-205686406(-)$1	242	7	12	15.0000
:::::	chr11:18630689-18630909(-)$1	220	143	148	15.0000
333dd	chr2:198256355-198256573(-)$1	218	154	159	15.0000
ddlll	chr10:30304126-30304360(-)$1	234	159	164	15.0000
+++++	chr21:34930577-34930801(+)$1	224	76	81	15.0000
ooobb	chr1:179068600-179068823(-)$1	223	178	183	15.0000
gg:::	chr6:11134949-11135174(+)$1	225	137	142	15.0000
EE:::	chr3:113437829-113438060(-)$1	231	171	176	15.0000
:::::	chr7:138991016-138991244(+)$1	228	219	224	15.0000
LLLDD	chr11:130014517-130014747(+)$1	230	10	15	15.0000
hhhhh	chr2:172821869-172822090(+)$1	221	33	38	15.0000
:::::	chr10:61551109-61551350(-)$1	241	59	64	15.0000
ffff:	chr17:30700085-30700328(+)$1	243	25	30	15.0000
!eeee	chr12:12630704-12630922(-)$1	218	14	19	15.0000
]====	chr2:208466169-208466395(+)$1	226	109	114	15.0000
HYYFF	chr11:74548691-74548915(+)$1	224	185	190	15.0000
BB|||	chrX:103435542-103435767(+)$1	225	200	205	15.0000
%%%dd	chr8:6616915-6617145(+)$1	230	66	71	15.0000
NNNEE	chr1:205682793-205683032(-)$1	239	26	31	15.0000
CYYCC	chr7:134654330-134654560(+)$1	230	165	170	15.0000
GTTTT	chr16:1749433-1749671(+)$1	238	47	52	15.0000

#DB
....(	chr13:77457941-77458172(-)$1	1	13	18	15.0000
.....	chr1:115312448-115312673(-)$1	1	0	5	15.0000
...))	chr1:155851772-155851998(+)$1	1	193	198	15.0000
)))))	chr19:21305328-21305554(+)$1	1	107	112	15.0000
..(((	chr12:95645616-95645851(+)$1	1	81	86	15.0000
)))).	chr1:93619627-93619851(-)$1	1	182	187	15.0000
..)))	chr4:2231131-2231360(-)$1	1	110	115	15.0000
..)))	chr12:16056057-16056298(+)$1	1	191	196	15.0000
.....	chr3:57307009-57307238(+)$1	1	15	20	15.0000
(((((	chr19:40576999-40577219(-)$1	1	86	91	15.0000
....(	chrX:46918740-46918962(+)$1	1	1	6	15.0000
.....	chr4:16164980-16165200(-)$1	1	28	33	15.0000
.))))	chr1:204526715-204526956(+)$1	1	185	190	15.0000
(....	chr5:41917517-41917751(+)$1	1	170	175	15.0000
.....	chr5:77773203-77773434(+)$1	1	64	69	15.0000
)))))	chr14:32624870-32625101(+)$1	1	15	20	15.0000
)))..	chr5:34906990-34907218(-)$1	1	118	123	15.0000
..(((	chr5:135513355-135513583(+)$1	1	107	112	15.0000
(((((	chr6:24777113-24777341(+)$1	1	26	31	15.0000
.....	chr2:113289406-113289637(+)$1	1	146	151	15.0000
((..(	chr7:75956759-75957005(-)$1	1	122	127	15.0000
)....	chr1:54298060-54298288(-)$1	1	101	106	15.0000
(((..	chr10:70506911-70507132(+)$1	1	204	209	15.0000
)))))	chr1:91990633-91990873(+)$1	1	193	198	15.0000
.....	chr5:37289933-37290175(-)$1	1	126	131	15.0000
).)))	chr2:207177906-207178131(+)$1	1	216	221	15.0000
((.((	chr3:122143622-122143854(-)$1	1	4	9	15.0000
.((((	chr12:49083898-49084124(-)$1	1	117	122	15.0000
.))))	chr4:48425901-48426123(+)$1	1	145	150	15.0000
..(((	chr1:85016098-85016321(-)$1	1	54	59	15.0000
((.((	chr5:132214515-132214742(-)$1	1	100	105	15.0000
(((((	chr12:46578093-46578313(-)$1	1	13	18	15.0000
((((.	chr2:187628825-187629059(+)$1	1	26	31	15.0000
.....	chr12:100691766-100692000(+)$1	1	54	59	15.0000
(...)	chr12:54628513-54628744(-)$1	1	54	59	15.0000
(((((	chr1:205686164-205686406(-)$1	1	7	12	15.0000
.....	chr11:18630689-18630909(-)$1	1	143	148	15.0000
...))	chr2:198256355-198256573(-)$1	1	154	159	15.0000
((...	chr10:30304126-30304360(-)$1	1	159	164	15.0000
.....	chr21:34930577-34930801(+)$1	1	76	81	15.0000
...))	chr1:179068600-179068823(-)$1	1	178	183	15.0000
))...	chr6:11134949-11135174(+)$1	1	137	142	15.0000
))...	chr3:113437829-113438060(-)$1	1	171	176	15.0000
.....	chr7:138991016-138991244(+)$1	1	219	224	15.0000
...((	chr11:130014517-130014747(+)$1	1	10	15	15.0000
)))))	chr2:172821869-172822090(+)$1	1	33	38	15.0000
.....	chr10:61551109-61551350(-)$1	1	59	64	15.0000
)))).	chr17:30700085-30700328(+)$1	1	25	30	15.0000
.((((	chr12:12630704-12630922(-)$1	1	14	19	15.0000
.))))	chr2:208466169-208466395(+)$1	1	109	114	15.0000
)..))	chr11:74548691-74548915(+)$1	1	185	190	15.0000
))...	chrX:103435542-103435767(+)$1	1	200	205	15.0000
...((	chr8:6616915-6617145(+)$1	1	66	71	15.0000
...((	chr1:205682793-205683032(-)$1	1	26	31	15.0000
)..))	chr7:134654330-134654560(+)$1	1	165	170	15.0000
(....	chr16:1749433-1749671(+)$1	1	47	52	15.0000

#PSSM
A : 0.96	a : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	

#score	840.0000000000005
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_CDS_m3_run1.nuc.txt

#NT
CUUCU	chr16:19554122-19554354(+)$1	232	63	68	15.0000
CUUCU	chr16:20810020-20810244(-)$1	224	132	137	15.0000
CUUCU	chr5:150071248-150071493(-)$1	245	125	130	15.0000
CUUCU	chr6:49459809-49460031(+)$1	222	83	88	15.0000
CUUCU	chr14:32561379-32561607(+)$1	228	116	121	15.0000
CUUCU	chr20:33027915-33028152(+)$1	237	71	76	15.0000
CUUCU	chr12:49435785-49436010(-)$1	225	207	212	15.0000
CUUCU	chr5:112178706-112178926(+)$1	220	191	196	15.0000
CUUCU	chr5:158588308-158588535(-)$1	227	163	168	15.0000
CUUCU	chr2:201434388-201434615(+)$1	227	200	205	15.0000
CUUCU	chr17:60140328-60140559(-)$1	231	180	185	15.0000
CUUCU	chr22:39710069-39710313(-)$1	244	11	16	15.0000
CUUCU	chr13:25881883-25882108(+)$1	225	65	70	15.0000
CUUCU	chr15:59910664-59910893(-)$1	229	30	35	15.0000
CUUCU	chr15:32929904-32930127(+)$1	223	14	19	15.0000
CUUCU	chr11:118376728-118376966(+)$1	238	212	217	15.0000
CUUCU	chr2:201436600-201436828(+)$1	228	66	71	15.0000
CUUCU	chr16:15705396-15705621(-)$1	225	111	116	15.0000
CUUCU	chr1:171546480-171546701(+)$1	221	113	118	15.0000
CUUCU	chr1:113471818-113472048(-)$1	230	210	215	15.0000
CUUCU	chr5:32364170-32364399(-)$1	229	55	60	15.0000
CUUCU	chr5:132227886-132228106(-)$1	220	51	56	15.0000
CUUCU	chr5:176715726-176715949(+)$1	223	178	183	15.0000
CUUCU	chr15:91510267-91510490(-)$1	223	92	97	15.0000
cuucu	chr17:7416619-7416860(+)$1	241	110	115	15.0000
CUUCU	chrX:14883061-14883287(-)$1	226	104	109	15.0000
CUUCU	chrM:12397-12770(-)$1	373	252	257	15.0000
CUUCU	chr16:70605506-70605735(+)$1	229	203	208	15.0000
CUUCU	chrM:4606-4870(+)$1	264	71	76	15.0000
CUUCU	chr9:136917436-136917664(-)$1	228	65	70	15.0000
CUUCU	chr1:108703748-108703977(-)$1	229	113	118	15.0000
CUUCU	chr15:68473519-68473744(+)$1	225	20	25	15.0000
CUUCU	chr12:995000-995225(+)$1	225	80	85	15.0000
CUUCU	chr9:79929403-79929635(+)$1	232	32	37	15.0000
CUUCU	chr5:112176034-112176255(+)$1	221	105	110	15.0000
CUUCU	chr5:112176518-112176741(+)$1	223	39	44	15.0000
CUUCU	chr8:30706286-30706509(-)$1	223	61	66	15.0000
CUUCU	chr2:73678805-73679041(+)$1	236	8	13	15.0000
CUUCU	chr13:21955550-21955782(-)$1	232	83	88	15.0000
CUUCU	chr19:9676703-9676924(-)$1	221	187	192	15.0000
CUUCU	chr7:97770706-97770926(+)$1	220	138	143	15.0000
CUUCU	chr8:95523655-95523875(-)$1	220	106	111	15.0000

#otherMatches

#Struct PSSM
%%%%%	chr7:6388136-6388361(-)$1	225	40	45	15.0000
dd>>>	chr16:19554122-19554354(+)$1	232	63	68	15.0000
emmmm	chr16:20810020-20810244(-)$1	224	132	137	15.0000
ddmmm	chr5:150071248-150071493(-)$1	245	125	130	15.0000
dddd!	chr6:49459809-49460031(+)$1	222	83	88	15.0000
ddbb:	chr14:32561379-32561607(+)$1	228	116	121	15.0000
eeemm	chr20:33027915-33028152(+)$1	237	71	76	15.0000
doooo	chr12:49435785-49436010(-)$1	225	207	212	15.0000
ooooo	chr5:112178706-112178926(+)$1	220	191	196	15.0000
eeeoo	chr5:158588308-158588535(-)$1	227	163	168	15.0000
fff::	chr2:201434388-201434615(+)$1	227	200	205	15.0000
EEEEE	chr17:60140328-60140559(-)$1	231	180	185	15.0000
cc###	chr22:39710069-39710313(-)$1	244	11	16	15.0000
coooo	chr13:25881883-25882108(+)$1	225	65	70	15.0000
ccccc	chr15:59910664-59910893(-)$1	229	30	35	15.0000
KEEEE	chr15:32929904-32930127(+)$1	223	14	19	15.0000
bmmmm	chr11:118376728-118376966(+)$1	238	212	217	15.0000
:eeee	chr2:201436600-201436828(+)$1	228	66	71	15.0000
vvvvv	chr16:15705396-15705621(-)$1	225	111	116	15.0000
:::::	chr1:171546480-171546701(+)$1	221	113	118	15.0000
cc:EE	chr1:113471818-113472048(-)$1	230	210	215	15.0000
d%%%%	chr5:32364170-32364399(-)$1	229	55	60	15.0000
e:EEE	chr5:132227886-132228106(-)$1	220	51	56	15.0000
ffffE	chr5:176715726-176715949(+)$1	223	178	183	15.0000
yyyye	chr15:91510267-91510490(-)$1	223	92	97	15.0000
:::::	chr17:7416619-7416860(+)$1	241	110	115	15.0000
III::	chrX:14883061-14883287(-)$1	226	104	109	15.0000
qqfff	chrM:12397-12770(-)$1	373	252	257	15.0000
nnnnb	chr16:70605506-70605735(+)$1	229	203	208	15.0000
c^^^^	chrM:4606-4870(+)$1	264	71	76	15.0000
FFFFF	chr9:136917436-136917664(-)$1	228	65	70	15.0000
ccc]g	chr1:108703748-108703977(-)$1	229	113	118	15.0000
TTTTT	chr15:68473519-68473744(+)$1	225	20	25	15.0000
TTTTT	chr12:995000-995225(+)$1	225	80	85	15.0000
!hhhh	chr9:79929403-79929635(+)$1	232	32	37	15.0000
^^^^^	chr5:112176034-112176255(+)$1	221	105	110	15.0000
[dddd	chr5:112176518-112176741(+)$1	223	39	44	15.0000
EEE{G	chr8:30706286-30706509(-)$1	223	61	66	15.0000
GGGGG	chr2:73678805-73679041(+)$1	236	8	13	15.0000
e22bb	chr13:21955550-21955782(-)$1	232	83	88	15.0000
fff]f	chr19:9676703-9676924(-)$1	221	187	192	15.0000
$$$ee	chr7:97770706-97770926(+)$1	220	138	143	15.0000
:::::	chr8:95523655-95523875(-)$1	220	106	111	15.0000

#DB
.....	chr7:6388136-6388361(-)$1	1	40	45	15.0000
))...	chr16:19554122-19554354(+)$1	1	63	68	15.0000
(....	chr16:20810020-20810244(-)$1	1	132	137	15.0000
((...	chr5:150071248-150071493(-)$1	1	125	130	15.0000
((((.	chr6:49459809-49460031(+)$1	1	83	88	15.0000
)))).	chr14:32561379-32561607(+)$1	1	116	121	15.0000
(((..	chr20:33027915-33028152(+)$1	1	71	76	15.0000
(....	chr12:49435785-49436010(-)$1	1	207	212	15.0000
.....	chr5:112178706-112178926(+)$1	1	191	196	15.0000
(((..	chr5:158588308-158588535(-)$1	1	163	168	15.0000
)))..	chr2:201434388-201434615(+)$1	1	200	205	15.0000
)))))	chr17:60140328-60140559(-)$1	1	180	185	15.0000
((...	chr22:39710069-39710313(-)$1	1	11	16	15.0000
(....	chr13:25881883-25882108(+)$1	1	65	70	15.0000
)))((	chr15:59910664-59910893(-)$1	1	30	35	15.0000
.((((	chr15:32929904-32930127(+)$1	1	14	19	15.0000
(....	chr11:118376728-118376966(+)$1	1	212	217	15.0000
.((((	chr2:201436600-201436828(+)$1	1	66	71	15.0000
.....	chr16:15705396-15705621(-)$1	1	111	116	15.0000
.....	chr1:171546480-171546701(+)$1	1	113	118	15.0000
)).))	chr1:113471818-113472048(-)$1	1	210	215	15.0000
(....	chr5:32364170-32364399(-)$1	1	55	60	15.0000
).(((	chr5:132227886-132228106(-)$1	1	51	56	15.0000
)))))	chr5:176715726-176715949(+)$1	1	178	183	15.0000
....)	chr15:91510267-91510490(-)$1	1	92	97	15.0000
.....	chr17:7416619-7416860(+)$1	1	110	115	15.0000
(((..	chrX:14883061-14883287(-)$1	1	104	109	15.0000
..)))	chrM:12397-12770(-)$1	1	252	257	15.0000
....)	chr16:70605506-70605735(+)$1	1	203	208	15.0000
(....	chrM:4606-4870(+)$1	1	71	76	15.0000
(((((	chr9:136917436-136917664(-)$1	1	65	70	15.0000
))).)	chr1:108703748-108703977(-)$1	1	113	118	15.0000
.....	chr15:68473519-68473744(+)$1	1	20	25	15.0000
.....	chr12:995000-995225(+)$1	1	80	85	15.0000
.((((	chr9:79929403-79929635(+)$1	1	32	37	15.0000
.....	chr5:112176034-112176255(+)$1	1	105	110	15.0000
.((((	chr5:112176518-112176741(+)$1	1	39	44	15.0000
(((.(	chr8:30706286-30706509(-)$1	1	61	66	15.0000
(((((	chr2:73678805-73679041(+)$1	1	8	13	15.0000
)..))	chr13:21955550-21955782(-)$1	1	83	88	15.0000
))).)	chr19:9676703-9676924(-)$1	1	187	192	15.0000
...((	chr7:97770706-97770926(+)$1	1	138	143	15.0000
.....	chr8:95523655-95523875(-)$1	1	106	111	15.0000

#PSSM
C : 0.97	c : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
C : 0.97	c : 0.02	
U : 0.97	u : 0.02	

#score	645.0000000000001
#seq	43
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m3_run2.nuc.txt

#NT
UGGCAAGGUCUUUAAGCAGUCCCCAACCCUUACUAAACAUCAGAUAAUUUAUACUGGAGAGGAACCAUACAAAUGUGAGGAAUGUGGCAAAGCUUUUAACCUAUCUUAACAACUUACUGAACAUAAGAAAAUUUACACUAGAGAGAAAGCCUACAAAUGUGAAGAAUGUGGCAAAGCCUUUAACCAGUUUUCAACCCUUAUUACACAUAAGAUAAUUCAUAG	chr7:64292459-64292694(+)$1	235	12	234	301.0000

#otherMatches

#Struct PSSM
:::ddddnnnnndddd:ddddnnnnndddd:::IIIIIIIIIEEEEE::EEEEE:::::eeeee!!bbddddeeeeeooooooeeeee666666dddd]bb]eeeee::::::::ddddnnnnnddddeeeee####iiiiiiiiillliiiiiiiii4444eeeee::::EEEEEeeeeeooooooeeeee::EEEEEYYIIIIIIIII}FFFFFFZZZCC	chr2:86992180-86992416(+)$1	236	11	233	301.0000
cbb!!dddd####dddd####bbbb!!ffffff####a[ddddccclllccc]dddd]a>>>>>>>>>>>>>>>ffffff22bb]bb4444dddd333dddd22bb22ccc:::::::::::::::ggggggg$$$$$eeeee[a"""ccc[ccctttttttttttcccccc4444aeeeee333ggggggg::::eeeeennnnneeeee::::FFFFFF:	chr7:64292459-64292694(+)$1	235	12	234	301.0000

#DB
...((((.....)))).((((.....))))...((((((((((((((..(((((.....(((((..(((((((((((......)))))......)))).)).)))))........((((.....))))(((((....(((((((((...)))))))))....)))))....)))))(((((......)))))..)))))..))))))))).))))))...))	chr2:86992180-86992416(+)$1	1	11	233	301.0000
(((..((((....((((....((((..((((((....(.(((((((...))).)))).)...............))))))..)).))....))))...))))..))..)))...............(((((((.....(((((.(...(((.(((...........))))))....))))))...)))))))....(((((.....)))))....)))))).	chr7:64292459-64292694(+)$1	1	12	234	301.0000

#PSSM
C : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
U : 0.50	A : 0.50	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
U : 1.00	
A : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
A : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	C : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
G : 1.00	
A : 1.00	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
G : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
C : 0.50	G : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
G : 1.00	

#score	602.0
#seq	2
#width	222
#escape	false
#onStep	13013
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m2_run2.nuc.txt

#NT
UAUUGCUAUUUUA	chr17:29663692-29663921(+)$1	229	43	56	14.4000
cuauucuuuuuug	chr1:100659441-100659663(-)$1	222	70	83	14.8000
uauauauauuuuu	chr7:123324415-123324636(-)$1	221	81	94	15.7000
ACUUUGUUUUUUA	chr5:110097580-110097815(+)$1	235	44	57	16.9000
GAUUUUUUCUUUU	chr12:72307512-72307750(+)$1	238	72	85	17.5000
GAUUUCUUUUUUU	chrX:103435803-103436023(+)$1	220	40	53	23.5000
UACCUAUUUUUUA	chr18:32916050-32916283(-)$1	233	47	60	13.4000
AAUUUUUUUUUUG	chr6:44414951-44415184(+)$1	233	50	63	21.1000
AAGUUCUUAUUUU	chr2:128057355-128057587(-)$1	232	97	110	16.6000
UAUAUAAUUUUUU	chr5:133292214-133292439(-)$1	225	41	54	15.2000
GGUUUUUUUUUUC	chr1:92978190-92978426(-)$1	236	29	42	15.6000
AAUUUAUUUUUAU	chr21:46645267-46645512(+)$1	245	99	112	18.7000
UAUUUGUAUUUUA	chr1:225684171-225684412(-)$1	241	59	72	16.3000
uauauuuuuuuua	chr9:125611721-125611952(-)$1	231	132	145	17.4000
uuuuucuuuuuuu	chr1:204373593-204373819(-)$1	226	191	204	21.0000
AAUAUCCUUUUUG	chr1:224573869-224574098(-)$1	229	52	65	15.5000
AAUUUGAUUUUUU	chr15:66181654-66181878(+)$1	224	69	82	18.0000
AAUGACUUUUUUU	chr9:91092209-91092456(+)$1	247	118	131	16.7000
CAUUUCUUUUCUU	chr20:60755250-60755492(+)$1	242	2	15	19.1000
UCUAUCUUUUUUG	chr1:203771169-203771404(+)$1	235	122	135	16.1000
GAUUUCUUUAUUU	chr1:193220221-193220455(+)$1	234	191	204	19.2000
AAUUUAUUUUUCA	chr3:182989605-182989837(+)$1	232	214	227	16.7000
UCUUUCUUCUUUC	chr5:134192745-134192968(+)$1	223	6	19	14.7000
CACUUAUUUUUUU	chr6:149912507-149912740(+)$1	233	185	198	18.1000
UAUCUCCUUUUUU	chr11:32999231-32999456(+)$1	225	110	123	16.5000
UCUUCCUUUUUUU	chr9:77598205-77598428(-)$1	223	110	123	16.6000
AAUUUCUuuuuau	chr9:114982555-114982790(-)$1	235	103	116	20.5000
uAuuuuuauuuuu	chr14:61440269-61440491(-)$1	222	104	117	18.8000
CAUAUUUUUUUUC	chr18:43845181-43845417(+)$1	236	106	119	16.3000
AACuucuuuuuuu	chr1:173867087-173867312(+)$1	225	150	163	21.0000
AAUUUCUCUUUUU	chr8:64124790-64125015(+)$1	225	104	117	20.5000
GAUUUCUAUUUUG	chr12:105196757-105196992(-)$1	235	48	61	18.1000
GAUAUCUUUUUAU	chr10:70530891-70531111(+)$1	220	56	69	16.1000
UAAUACUUUUUUG	chr4:76406559-76406782(-)$1	223	73	86	14.8000
UAUUUAUUUAUUC	chr17:5393670-5393905(+)$1	235	111	124	16.1000
AAUUUAUUAUUUU	chr5:137541644-137541868(-)$1	224	71	84	18.8000
AACUUCUUGUUUG	chr15:43037471-43037697(-)$1	226	85	98	15.3000
AAuuuuuuuuuuu	chr6:150047502-150047745(-)$1	243	190	203	22.8000
Cuucucuuuuuug	chr17:30700739-30700976(+)$1	237	181	194	14.9000
CCUUUCUUUUUUU	chr18:723999-724237(-)$1	238	118	131	20.2000
CAUUUUAUUUUUU	chr17:4848951-4849207(-)$1	256	84	97	17.5000
GAAUUCUUUGUUG	chr1:173857827-173858054(+)$1	227	48	61	13.6000
CAUUUUUUUUAUU	chr21:43409174-43409409(-)$1	235	8	21	17.1000
UAUUUCUAGUUUG	chr15:64459141-64459364(-)$1	223	186	199	15.0000
AUUUUCUUUUUUU	chr13:98119358-98119581(+)$1	223	36	49	21.3000
uauuuauuuauua	chr6:111590288-111590514(+)$1	226	112	125	16.4000
AAUUUCUUUUCCU	chr12:96672716-96672939(-)$1	223	185	198	15.9000
aaauacuuuuuuc	chr6:44416247-44416472(+)$1	225	110	123	14.6000
AUUUUCUUGUUUU	chr2:120735874-120736095(+)$1	221	124	137	17.3000

#otherMatches

#Struct PSSM
ddd[bbnnnnnbb	chr6:151790984-151791216(+)$1	232	99	112	21.0000
GGGGddddllldd	chr17:29663692-29663921(+)$1	229	43	56	14.4000
ff]ggggggg:gg	chr1:100659441-100659663(-)$1	222	70	83	14.8000
gggg::ffffffo	chr7:123324415-123324636(-)$1	221	81	94	15.7000
EEEEERRRRRRRR	chr5:110097580-110097815(+)$1	235	44	57	16.9000
bbnnnnnbb]eee	chr12:72307512-72307750(+)$1	238	72	85	17.5000
%%%%=========	chrX:103435803-103436023(+)$1	220	40	53	23.5000
fffff::::dddd	chr18:32916050-32916283(-)$1	233	47	60	13.4000
:::::::ffffff	chr6:44414951-44415184(+)$1	233	50	63	21.1000
d!!ggggggg"""	chr2:128057355-128057587(-)$1	232	97	110	16.6000
FNNNNNHHHHHHH	chr5:133292214-133292439(-)$1	225	41	54	15.2000
ggggggg####ff	chr1:92978190-92978426(-)$1	236	29	42	15.6000
"""ffffffoooo	chr21:46645267-46645512(+)$1	245	99	112	18.7000
eeee"""cccrrr	chr1:225684171-225684412(-)$1	241	59	72	16.3000
cciiiiiiiiimm	chr9:125611721-125611952(-)$1	231	132	145	17.4000
:::::::::::::	chr1:204373593-204373819(-)$1	226	191	204	21.0000
4444eeeee::::	chr1:224573869-224574098(-)$1	229	52	65	15.5000
IIIIII:::::::	chr15:66181654-66181878(+)$1	224	69	82	18.0000
DDDDEEEEE}CCC	chr9:91092209-91092456(+)$1	247	118	131	16.7000
hhhhhhhqqqqqq	chr20:60755250-60755492(+)$1	242	2	15	19.1000
D}EEEEE?????B	chr1:203771169-203771404(+)$1	235	122	135	16.1000
:::::::::::::	chr1:193220221-193220455(+)$1	234	191	204	19.2000
gggggg333ccc:	chr3:182989605-182989837(+)$1	232	214	227	16.7000
::::::::eeeee	chr5:134192745-134192968(+)$1	223	6	19	14.7000
eeeeddddrrrrr	chr6:149912507-149912740(+)$1	233	185	198	18.1000
eeeee:iiiiiii	chr11:32999231-32999456(+)$1	225	110	123	16.5000
fuuuuuuuuuuuu	chr9:77598205-77598428(-)$1	223	110	123	16.6000
^^^^^^^^^^^^^	chr9:114982555-114982790(-)$1	235	103	116	20.5000
f[ffffffqqqqq	chr14:61440269-61440491(-)$1	222	104	117	18.8000
ee+++++++++++	chr18:43845181-43845417(+)$1	236	106	119	16.3000
eettttttttttt	chr1:173867087-173867312(+)$1	225	150	163	21.0000
ggwwwwwwwwwww	chr8:64124790-64125015(+)$1	225	104	117	20.5000
eee&&&&&&&fff	chr12:105196757-105196992(-)$1	235	48	61	18.1000
::IIIIIIIIINN	chr10:70530891-70531111(+)$1	220	56	69	16.1000
i!!cccwwwwwww	chr4:76406559-76406782(-)$1	223	73	86	14.8000
JJJJJ::::::::	chr17:5393670-5393905(+)$1	235	111	124	16.1000
l==========::	chr5:137541644-137541868(-)$1	224	71	84	18.8000
#ggggggg=====	chr15:43037471-43037697(-)$1	226	85	98	15.3000
==========:::	chr6:150047502-150047745(-)$1	243	190	203	22.8000
b[ddddooooood	chr17:30700739-30700976(+)$1	237	181	194	14.9000
bb333bb333bb]	chr18:723999-724237(-)$1	238	118	131	20.2000
::::::::::::d	chr17:4848951-4849207(-)$1	256	84	97	17.5000
FFFFF:::::::h	chr1:173857827-173858054(+)$1	227	48	61	13.6000
::::::ffffff[	chr21:43409174-43409409(-)$1	235	8	21	17.1000
ee!!bb!!eeeee	chr15:64459141-64459364(-)$1	223	186	199	15.0000
doooooodddd]d	chr13:98119358-98119581(+)$1	223	36	49	21.3000
oooooa22bb22=	chr6:111590288-111590514(+)$1	226	112	125	16.4000
::::::::::fff	chr12:96672716-96672939(-)$1	223	185	198	15.9000
cccnnnnnccc44	chr6:44416247-44416472(+)$1	225	110	123	14.6000
eeee!!ddddsss	chr2:120735874-120736095(+)$1	221	124	137	17.3000

#DB
(((.((.....))	chr6:151790984-151791216(+)$1	1	99	112	21.0000
((((((((...))	chr17:29663692-29663921(+)$1	1	43	56	14.4000
)).))))))).((	chr1:100659441-100659663(-)$1	1	70	83	14.8000
))))..((((((.	chr7:123324415-123324636(-)$1	1	81	94	15.7000
(((((........	chr5:110097580-110097815(+)$1	1	44	57	16.9000
((.....)).)))	chr12:72307512-72307750(+)$1	1	72	85	17.5000
....(((((((((	chrX:103435803-103436023(+)$1	1	40	53	23.5000
)))))....((((	chr18:32916050-32916283(-)$1	1	47	60	13.4000
.......((((((	chr6:44414951-44415184(+)$1	1	50	63	21.1000
(..(((((((...	chr2:128057355-128057587(-)$1	1	97	110	16.6000
(.....(((((((	chr5:133292214-133292439(-)$1	1	41	54	15.2000
(((((((....((	chr1:92978190-92978426(-)$1	1	29	42	15.6000
...((((((....	chr21:46645267-46645512(+)$1	1	99	112	18.7000
((((...(((...	chr1:225684171-225684412(-)$1	1	59	72	16.3000
(((((((((((..	chr9:125611721-125611952(-)$1	1	132	145	17.4000
.............	chr1:204373593-204373819(-)$1	1	191	204	21.0000
....)))))....	chr1:224573869-224574098(-)$1	1	52	65	15.5000
((((((.......	chr15:66181654-66181878(+)$1	1	69	82	18.0000
))))))))).)))	chr9:91092209-91092456(+)$1	1	118	131	16.7000
(((((((......	chr20:60755250-60755492(+)$1	1	2	15	19.1000
).))))).....)	chr1:203771169-203771404(+)$1	1	122	135	16.1000
.............	chr1:193220221-193220455(+)$1	1	191	204	19.2000
))))))...))).	chr3:182989605-182989837(+)$1	1	214	227	16.7000
........(((((	chr5:134192745-134192968(+)$1	1	6	19	14.7000
((((((((.....	chr6:149912507-149912740(+)$1	1	185	198	18.1000
))))).(((((((	chr11:32999231-32999456(+)$1	1	110	123	16.5000
(............	chr9:77598205-77598428(-)$1	1	110	123	16.6000
.............	chr9:114982555-114982790(-)$1	1	103	116	20.5000
(.((((((.....	chr14:61440269-61440491(-)$1	1	104	117	18.8000
((...........	chr18:43845181-43845417(+)$1	1	106	119	16.3000
((...........	chr1:173867087-173867312(+)$1	1	150	163	21.0000
((...........	chr8:64124790-64125015(+)$1	1	104	117	20.5000
(((.......(((	chr12:105196757-105196992(-)$1	1	48	61	18.1000
..(((((((((..	chr10:70530891-70531111(+)$1	1	56	69	16.1000
(..(((.......	chr4:76406559-76406782(-)$1	1	73	86	14.8000
(((((........	chr17:5393670-5393905(+)$1	1	111	124	16.1000
.))))))))))..	chr5:137541644-137541868(-)$1	1	71	84	18.8000
.((((((((((((	chr15:43037471-43037697(-)$1	1	85	98	15.3000
))))))))))...	chr6:150047502-150047745(-)$1	1	190	203	22.8000
(.((((......)	chr17:30700739-30700976(+)$1	1	181	194	14.9000
))...))...)).	chr18:723999-724237(-)$1	1	118	131	20.2000
............(	chr17:4848951-4849207(-)$1	1	84	97	17.5000
(((((.......(	chr1:173857827-173858054(+)$1	1	48	61	13.6000
......((((((.	chr21:43409174-43409409(-)$1	1	8	21	17.1000
((..((..(((((	chr15:64459141-64459364(-)$1	1	186	199	15.0000
(......)))).)	chr13:98119358-98119581(+)$1	1	36	49	21.3000
.....)..))..)	chr6:111590288-111590514(+)$1	1	112	125	16.4000
..........(((	chr12:96672716-96672939(-)$1	1	185	198	15.9000
(((.....)))..	chr6:44416247-44416472(+)$1	1	110	123	14.6000
((((..((((...	chr2:120735874-120736095(+)$1	1	124	137	17.3000

#PSSM
A : 0.36	U : 0.21	G : 0.14	C : 0.14	u : 0.10	c : 0.02	a : 0.02	
A : 0.70	C : 0.10	a : 0.08	u : 0.06	U : 0.04	G : 0.02	
U : 0.68	u : 0.14	C : 0.08	a : 0.04	A : 0.04	G : 0.02	
U : 0.64	u : 0.14	A : 0.10	a : 0.04	C : 0.04	G : 0.02	c : 0.02	
U : 0.72	u : 0.18	A : 0.04	G : 0.02	C : 0.02	a : 0.02	
C : 0.46	A : 0.16	U : 0.12	c : 0.10	G : 0.06	u : 0.06	a : 0.04	
U : 0.70	u : 0.19	A : 0.06	C : 0.04	
U : 0.68	u : 0.18	A : 0.08	a : 0.04	C : 0.02	
U : 0.64	u : 0.21	G : 0.06	C : 0.04	A : 0.04	
U : 0.72	u : 0.19	A : 0.04	G : 0.02	a : 0.02	
U : 0.72	u : 0.21	C : 0.04	A : 0.02	
U : 0.70	u : 0.19	A : 0.04	C : 0.04	a : 0.02	
U : 0.42	G : 0.16	A : 0.12	u : 0.12	C : 0.08	g : 0.04	a : 0.04	c : 0.02	

#score	869.2000000000008
#seq	50
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m1_run1.nuc.txt

#NT
UUGUUGUUUUUA	chr1:26451581-26451829(+)$1	248	209	221	19.9534
uuaauuuuuuua	chr14:45397198-45397431(-)$1	233	49	61	20.6511
UUGUUCUUUUUA	chr2:101622738-101622968(+)$1	230	152	164	20.0697
UUUAUUUUUUUA	chr13:79886000-79886220(-)$1	220	41	53	24.3720
UUUUAUUUUUUA	chr15:73595510-73595746(+)$1	236	79	91	23.9069
CUUUUUUUUUUC	chr1:225590808-225591030(-)$1	222	132	144	20.7674
uauuuuuauuua	chr1:235335887-235336108(-)$1	221	192	204	19.0232
UUUUACUUUUUA	chr1:145586283-145586507(+)$1	224	200	212	19.9534
CUUUUUUCUUUA	chr11:19261588-19261810(-)$1	222	19	31	20.4186
UUUUAAUUUUUA	chr12:49413207-49413422(-)$1	215	154	166	20.1860
GUUGAUUUUUUA	chr12:133345406-133345641(-)$1	235	68	80	17.7441
UUGAUUUUUUUA	chr2:235402742-235402972(-)$1	230	97	109	21.0000
UUUUGUUUAUUA	chr1:100547915-100548142(+)$1	227	54	66	19.1395
UGUUUUUUCUUA	chrX:24095925-24096155(+)$1	230	61	73	19.0232
UUUUGUUGUUUA	chr21:38886890-38887110(+)$1	220	53	65	19.7209
UUGUUAUUUUUA	chr1:65298245-65298462(+)$1	217	4	16	20.3023
CUUUAUUUUUUA	chr14:65390687-65390911(+)$1	224	166	178	21.1162
UUUUUUCUUUGA	chr4:88082505-88082735(-)$1	230	28	40	18.0930
UUCUUUUUCUUA	chr12:27951374-27951594(+)$1	220	129	141	19.2558
UUUUGUUUUUUA	chr22:21801474-21801694(+)$1	220	182	194	23.6744
GUUUUUUUUUUA	chr8:30536637-30536855(-)$1	218	51	63	24.4883
uguguuuuuuua	chr19:12741316-12741546(+)$1	230	53	65	20.1860
UUUAUUUAUUUA	chr6:42712136-42712380(-)$1	244	19	31	20.3023
UUUCUUUGUUUA	chr14:32627140-32627357(+)$1	217	83	95	19.8372
CUUGUUUUUUUA	chr1:101706932-101707162(+)$1	230	34	46	21.3488
AUUUUUUUUUUG	chr7:128411170-128411388(+)$1	218	162	174	20.6511
UUUUUUGUUUUA	chr4:71686423-71686632(-)$1	209	35	47	22.9767
UUUUUUUUUUUG	chr14:92527510-92527723(-)$1	213	121	133	23.9069
UUUUUUUUUUUA	chr7:104753985-104754211(+)$1	226	65	77	27.3953
UUCUUAUUUUUA	chr1:91380828-91381051(-)$1	223	207	219	19.9534
UUUAUUGUUUUA	chr13:25906000-25906230(+)$1	230	28	40	19.9534
GUUGUUUUUUUA	chr7:32628141-32628367(+)$1	226	64	76	21.2325
UUUUUUUGUUUG	chr12:42479518-42479750(-)$1	232	82	94	19.9534
AUAAUUUUUUUA	chr2:74333739-74333959(+)$1	220	126	138	17.3953
GUUUUUUUUUUG	chr5:145667611-145667830(+)$1	219	13	25	20.9999
UUUUUUUUUUUG	chr12:53873448-53873678(+)$1	230	8	20	23.9069
UUUUUUUUUUUC	chr15:65738272-65738495(-)$1	223	69	81	23.5581
CUUUUUUUUUUA	chr1:211487538-211487768(+)$1	230	137	149	24.6046
CUUUUAUUUUUA	chr5:54964981-54965208(-)$1	227	42	54	20.8837
UUUUUUUUUUUA	chr20:60711720-60711945(-)$1	225	161	173	27.3953
GGUUUUUUUUUA	chr1:42643630-42643870(-)$1	240	168	180	20.5348
UUUUUUUUUUUU	chr1:32799437-32799662(-)$1	225	136	148	23.4418

#otherMatches

#Struct PSSM
CC?????CCC}G	chr4:185550379-185550615(-)$1	236	206	218	20.0697
""dddd####ee	chr1:26451581-26451829(+)$1	248	209	221	19.9534
eeee$$$$$eee	chr14:45397198-45397431(-)$1	233	49	61	20.6511
======::::::	chr2:101622738-101622968(+)$1	230	152	164	20.0697
===========!	chr13:79886000-79886220(-)$1	220	41	53	24.3720
""cccnnnnncc	chr15:73595510-73595746(+)$1	236	79	91	23.9069
7777777dddd6	chr1:225590808-225591030(-)$1	222	132	144	20.7674
h]eeeee:::::	chr1:235335887-235336108(-)$1	221	192	204	19.0232
::::eeeeeqqq	chr1:145586283-145586507(+)$1	224	200	212	19.9534
eeeqqqqqqqqe	chr11:19261588-19261810(-)$1	222	19	31	20.4186
eeeccc]fffff	chr12:49413207-49413422(-)$1	215	154	166	20.1860
g&&&&&&&eeee	chr12:133345406-133345641(-)$1	235	68	80	17.7441
::GGGGGGG:::	chr2:235402742-235402972(-)$1	230	97	109	21.0000
::::eeeee"""	chr1:100547915-100548142(+)$1	227	54	66	19.1395
ddxxxxxxxxxx	chrX:24095925-24096155(+)$1	230	61	73	19.0232
eeeggggggg!!	chr21:38886890-38887110(+)$1	220	53	65	19.7209
ff!!bb[bb!!c	chr1:65298245-65298462(+)$1	217	4	16	20.3023
33iiiiiiiii2	chr14:65390687-65390911(+)$1	224	166	178	21.1162
ssssssseeeee	chr4:88082505-88082735(-)$1	230	28	40	18.0930
nneeeee]dddd	chr12:27951374-27951594(+)$1	220	129	141	19.2558
qqqqqqqbb22c	chr22:21801474-21801694(+)$1	220	182	194	23.6744
HHHHHLLLFFFF	chr8:30536637-30536855(-)$1	218	51	63	24.4883
dddrrrrrrrrr	chr19:12741316-12741546(+)$1	230	53	65	20.1860
ee::::::::::	chr6:42712136-42712380(-)$1	244	19	31	20.3023
GGGGGGFFFFFF	chr14:32627140-32627357(+)$1	217	83	95	19.8372
CCC:::======	chr1:101706932-101707162(+)$1	230	34	46	21.3488
dooooooddddH	chr7:128411170-128411388(+)$1	218	162	174	20.6511
oooodddd22ee	chr4:71686423-71686632(-)$1	209	35	47	22.9767
fffff::eeeee	chr14:92527510-92527723(-)$1	213	121	133	23.9069
++++++++++cc	chr7:104753985-104754211(+)$1	226	65	77	27.3953
JJJJJJJJJJ::	chr1:91380828-91381051(-)$1	223	207	219	19.9534
======bb[ccc	chr13:25906000-25906230(+)$1	230	28	40	19.9534
%%ccc!!ccc!!	chr7:32628141-32628367(+)$1	226	64	76	21.2325
:::::::JJJJJ	chr12:42479518-42479750(-)$1	232	82	94	19.9534
e:::::::::::	chr2:74333739-74333959(+)$1	220	126	138	17.3953
D{HHHHHHHH{A	chr5:145667611-145667830(+)$1	219	13	25	20.9999
:::::::::::C	chr12:53873448-53873678(+)$1	230	8	20	23.9069
b####=======	chr15:65738272-65738495(-)$1	223	69	81	23.5581
iiiii!!=====	chr1:211487538-211487768(+)$1	230	137	149	24.6046
xxxxxxxxxxxf	chr5:54964981-54965208(-)$1	227	42	54	20.8837
JJJJJJJJJJJ:	chr20:60711720-60711945(-)$1	225	161	173	27.3953
gggg!!ccc!!c	chr1:42643630-42643870(-)$1	240	168	180	20.5348
[ccc[=======	chr1:32799437-32799662(-)$1	225	136	148	23.4418

#DB
)).....))).)	chr4:185550379-185550615(-)$1	1	206	218	20.0697
..((((....((	chr1:26451581-26451829(+)$1	1	209	221	19.9534
((((.....(((	chr14:45397198-45397431(-)$1	1	49	61	20.6511
))))))......	chr2:101622738-101622968(+)$1	1	152	164	20.0697
(((((((((((.	chr13:79886000-79886220(-)$1	1	41	53	24.3720
..(((.....))	chr15:73595510-73595746(+)$1	1	79	91	23.9069
.......)))).	chr1:225590808-225591030(-)$1	1	132	144	20.7674
).))))).....	chr1:235335887-235336108(-)$1	1	192	204	19.0232
....(((((...	chr1:145586283-145586507(+)$1	1	200	212	19.9534
(((........)	chr11:19261588-19261810(-)$1	1	19	31	20.4186
)))))).)))))	chr12:49413207-49413422(-)$1	1	154	166	20.1860
(.......((((	chr12:133345406-133345641(-)$1	1	68	80	17.7441
..)))))))...	chr2:235402742-235402972(-)$1	1	97	109	21.0000
....(((((...	chr1:100547915-100548142(+)$1	1	54	66	19.1395
((..........	chrX:24095925-24096155(+)$1	1	61	73	19.0232
((((((((((..	chr21:38886890-38887110(+)$1	1	53	65	19.7209
((..((.((..(	chr1:65298245-65298462(+)$1	1	4	16	20.3023
..))))))))).	chr14:65390687-65390911(+)$1	1	166	178	21.1162
.......)))))	chr4:88082505-88082735(-)$1	1	28	40	18.0930
..))))).))))	chr12:27951374-27951594(+)$1	1	129	141	19.2558
.......))..)	chr22:21801474-21801694(+)$1	1	182	194	23.6744
(((((...((((	chr8:30536637-30536855(-)$1	1	51	63	24.4883
(((.........	chr19:12741316-12741546(+)$1	1	53	65	20.1860
))..........	chr6:42712136-42712380(-)$1	1	19	31	20.3023
((((((((((((	chr14:32627140-32627357(+)$1	1	83	95	19.8372
(((...((((((	chr1:101706932-101707162(+)$1	1	34	46	21.3488
(......)))))	chr7:128411170-128411388(+)$1	1	162	174	20.6511
....))))..))	chr4:71686423-71686632(-)$1	1	35	47	22.9767
)))))..(((((	chr14:92527510-92527723(-)$1	1	121	133	23.9069
..........((	chr7:104753985-104754211(+)$1	1	65	77	27.3953
))))))))))..	chr1:91380828-91381051(-)$1	1	207	219	19.9534
((((((((.(((	chr13:25906000-25906230(+)$1	1	28	40	19.9534
..(((..(((..	chr7:32628141-32628367(+)$1	1	64	76	21.2325
.......(((((	chr12:42479518-42479750(-)$1	1	82	94	19.9534
)...........	chr2:74333739-74333959(+)$1	1	126	138	17.3953
(.((((((((.(	chr5:145667611-145667830(+)$1	1	13	25	20.9999
...........(	chr12:53873448-53873678(+)$1	1	8	20	23.9069
(....(((((((	chr15:65738272-65738495(-)$1	1	69	81	23.5581
(((((..(((((	chr1:211487538-211487768(+)$1	1	137	149	24.6046
...........)	chr5:54964981-54965208(-)$1	1	42	54	20.8837
))))))))))).	chr20:60711720-60711945(-)$1	1	161	173	27.3953
((((..(((..(	chr1:42643630-42643870(-)$1	1	168	180	20.5348
.(((.(((((((	chr1:32799437-32799662(-)$1	1	136	148	23.4418

#PSSM
U : 0.62	C : 0.13	G : 0.11	u : 0.06	A : 0.04	
U : 0.86	G : 0.06	u : 0.02	a : 0.02	g : 0.02	
U : 0.74	G : 0.11	u : 0.04	C : 0.04	a : 0.02	A : 0.02	
U : 0.72	A : 0.11	G : 0.06	a : 0.02	u : 0.02	g : 0.02	C : 0.02	
U : 0.74	A : 0.11	u : 0.06	G : 0.06	
U : 0.76	A : 0.09	u : 0.06	C : 0.04	G : 0.02	
U : 0.86	u : 0.06	G : 0.04	C : 0.02	
U : 0.81	G : 0.06	u : 0.04	a : 0.02	C : 0.02	A : 0.02	
U : 0.86	u : 0.06	C : 0.04	A : 0.02	
U : 0.93	u : 0.06	
U : 0.90	u : 0.06	G : 0.02	
A : 0.74	G : 0.11	a : 0.06	C : 0.04	U : 0.02	

#score	913.3488372093025
#seq	43
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m3_run1.nuc.txt

#NT
UUUUUUUU	chr2:38522989-38523244(-)$1	255	138	146	14.3076
UUUUUAUU	chr8:131065841-131066080(-)$1	239	116	124	16.4615
UUUAUAUU	chr1:21070903-21071219(-)$1	316	280	288	18.8461
UCUAUAUU	chr4:115598278-115598552(+)$1	274	201	209	14.7692
UUUAUUUU	chr12:93802973-93803202(-)$1	229	86	94	16.6923
UUUAUUUU	chr5:135513867-135514134(+)$1	267	140	148	16.6923
UUUUUAUU	chr1:200520925-200521158(-)$1	233	170	178	16.4615
UUUAAAUU	chr7:116199345-116199637(+)$1	292	207	215	14.5384
UUGAUAUU	chr13:98045386-98045697(+)$1	311	59	67	14.3076
UUCAUAUU	chr10:116736005-116736233(+)$1	228	213	221	14.3846
UCUAUAUU	chr9:135564865-135565126(+)$1	261	52	60	14.7692
UUUAUAUU	chr2:196999999-197000326(-)$1	327	144	152	18.8461
UUUAUGUU	chr17:39910814-39911048(-)$1	234	122	130	16.1538
GUUAUAUU	chr3:58305388-58305638(+)$1	250	55	63	14.2307
UUUAUACU	chr17:48940029-48940325(-)$1	296	160	168	13.9999
UUUUUAUU	chr5:137088392-137088783(-)$1	391	198	206	16.4615
UUUUUAUU	chr5:57749834-57750086(-)$1	252	172	180	16.4615
UUAAUAUU	chr15:45009828-45010063(+)$1	235	31	39	14.3846
UUUAUGUU	chr17:79845705-79845960(-)$1	255	59	67	16.1538
uuuauguu	chr1:78482861-78483089(+)$1	228	122	130	16.1538
UUUAUUUU	chr1:46093329-46093588(-)$1	259	104	112	16.6923
UUUAUCUU	chr2:36777577-36777865(+)$1	288	256	264	15.7692
UUUACAUU	chr18:21062655-21062922(+)$1	267	81	89	14.4615
UUUAUGUU	chr5:114949476-114949760(-)$1	284	63	71	16.1538
UUUAUUUU	chr8:81432630-81432856(+)$1	226	15	23	16.6923
UUUACAUU	chr1:91381459-91381738(-)$1	279	137	145	14.4615
UUUUUAUU	chr9:7797985-7798235(-)$1	250	129	137	16.4615
UUUUUAUU	chr15:49935675-49935934(+)$1	259	122	130	16.4615
UUUAGAUU	chr6:151686304-151686534(-)$1	230	134	142	14.3846
UCUAUAUU	chr1:234742506-234742894(-)$1	388	166	174	14.7692
UUUAUUUU	chr11:57584127-57584358(+)$1	231	114	122	16.6923
UUUCUAUU	chr6:82456501-82456744(-)$1	243	127	135	15.6923
UUUUUUUU	chr3:111710648-111710945(+)$1	297	133	141	14.3076
UUUAUGUU	chr8:124511591-124511867(-)$1	276	5	13	16.1538
uuuauauu	chr1:29474174-29474482(-)$1	308	110	118	18.8461
UUUGUAUU	chr1:68947115-68947340(-)$1	225	33	41	15.5384
UUUAUAUC	chr1:155708117-155708355(+)$1	238	121	129	13.9999
UAUAUAUU	chr11:62283775-62284036(-)$1	261	74	82	14.6153
UCUAUAUU	chr13:100037683-100037914(+)$1	231	113	121	14.7692
UGUAUAUU	chr12:98943295-98943562(+)$1	267	204	212	14.6153
UUUAAAUU	chr5:65118893-65119135(+)$1	242	170	178	14.5384
UUUGUAUU	chr1:61924063-61924300(+)$1	237	75	83	15.5384
UUUCUAUU	chr7:54819847-54820113(-)$1	266	133	141	15.6923
GUUAUAUU	chr7:72855070-72855311(-)$1	241	40	48	14.2307
AUUAUAUU	chr4:123818307-123818577(+)$1	270	43	51	14.1538
UUUUUAUU	chr2:136872152-136872395(-)$1	243	49	57	16.4615
UAUAUAUU	chr5:14695891-14696151(+)$1	260	145	153	14.6153
UUAAUAUU	chr12:12272973-12273244(-)$1	271	21	29	14.3846
UUUAUUUU	chr15:29993277-29993508(-)$1	231	113	121	16.6923
UUUUUAUU	chr9:127573336-127573568(+)$1	232	104	112	16.4615
UUUUUAUU	chr2:206860475-206860707(-)$1	232	17	25	16.4615
UUCAUAUU	chr17:7474788-7475060(+)$1	272	128	136	14.3846
UUUAUUUU	chr1:110564233-110564552(+)$1	319	137	145	16.6923
UUUAUUUU	chrX:24003846-24004120(-)$1	274	75	83	16.6923
UUUCUAUU	chr10:32298328-32298573(-)$1	245	126	134	15.6923
UUUUUUUU	chr13:95673614-95673840(-)$1	226	85	93	14.3076
UUUAUGUU	chr15:44063557-44063813(+)$1	256	51	59	16.1538
UUUAAAUU	chr9:123521899-123522130(-)$1	231	40	48	14.5384
UUUAUUUU	chr8:64124750-64125040(+)$1	290	6	14	16.6923
UUUUUGUU	chr19:6414566-6414869(-)$1	303	144	152	13.7692
UUUUUCUU	chr2:70107435-70107675(+)$1	240	9	17	13.3846
UGUAUAUU	chr3:55501609-55501926(-)$1	317	229	237	14.6153
UUUAUUUU	chr10:94113291-94113548(+)$1	257	114	122	16.6923
UUUCUAUU	chr15:63358199-63358447(+)$1	248	38	46	15.6923

#otherMatches

#Struct PSSM
+++++++f	chr1:65880193-65880431(+)$1	238	113	121	16.6923
:::::ggg	chr2:38522989-38523244(-)$1	255	138	146	14.3076
::::::::	chr8:131065841-131066080(-)$1	239	116	124	16.4615
?????EEE	chr1:21070903-21071219(-)$1	316	280	288	18.8461
BB}CCC}D	chr4:115598278-115598552(+)$1	274	201	209	14.7692
fppppppp	chr12:93802973-93803202(-)$1	229	86	94	16.6923
::::::cc	chr5:135513867-135514134(+)$1	267	140	148	16.6923
++++++++	chr1:200520925-200521158(-)$1	233	170	178	16.4615
ffffff22	chr7:116199345-116199637(+)$1	292	207	215	14.5384
ffGGGGGG	chr13:98045386-98045697(+)$1	311	59	67	14.3076
c]ccc:::	chr10:116736005-116736233(+)$1	228	213	221	14.3846
::::::::	chr9:135564865-135565126(+)$1	261	52	60	14.7692
hhhhhhhb	chr2:196999999-197000326(-)$1	327	144	152	18.8461
eeeee[ee	chr17:39910814-39911048(-)$1	234	122	130	16.1538
fffff[cc	chr3:58305388-58305638(+)$1	250	55	63	14.2307
::ccc[dd	chr17:48940029-48940325(-)$1	296	160	168	13.9999
:::::ddd	chr5:137088392-137088783(-)$1	391	198	206	16.4615
ggggg:::	chr5:57749834-57750086(-)$1	252	172	180	16.4615
I:::::::	chr15:45009828-45010063(+)$1	235	31	39	14.3846
!ccc%%%%	chr17:79845705-79845960(-)$1	255	59	67	16.1538
mmmfffff	chr1:78482861-78483089(+)$1	228	122	130	16.1538
2ggggggg	chr1:46093329-46093588(-)$1	259	104	112	16.6923
////FFFF	chr2:36777577-36777865(+)$1	288	256	264	15.7692
qqqqqqqq	chr18:21062655-21062922(+)$1	267	81	89	14.4615
g[ccc[ee	chr5:114949476-114949760(-)$1	284	63	71	16.1538
::::::::	chr8:81432630-81432856(+)$1	226	15	23	16.6923
qa22iiii	chr1:91381459-91381738(-)$1	279	137	145	14.4615
sssssssf	chr9:7797985-7798235(-)$1	250	129	137	16.4615
c:ffffff	chr15:49935675-49935934(+)$1	259	122	130	16.4615
eee[bbmm	chr6:151686304-151686534(-)$1	230	134	142	14.3846
========	chr1:234742506-234742894(-)$1	388	166	174	14.7692
c[======	chr11:57584127-57584358(+)$1	231	114	122	16.6923
ffff####	chr6:82456501-82456744(-)$1	243	127	135	15.6923
========	chr3:111710648-111710945(+)$1	297	133	141	14.3076
GGGG{CCC	chr8:124511591-124511867(-)$1	276	5	13	16.1538
oodddd::	chr1:29474174-29474482(-)$1	308	110	118	18.8461
&&&&&ccc	chr1:68947115-68947340(-)$1	225	33	41	15.5384
eppppppp	chr1:155708117-155708355(+)$1	238	121	129	13.9999
vvvvveee	chr11:62283775-62284036(-)$1	261	74	82	14.6153
$$gggggg	chr13:100037683-100037914(+)$1	231	113	121	14.7692
hhhhh:::	chr12:98943295-98943562(+)$1	267	204	212	14.6153
)hhhhhhh	chr5:65118893-65119135(+)$1	242	170	178	14.5384
gg[cccww	chr1:61924063-61924300(+)$1	237	75	83	15.5384
ee]bbhhh	chr7:54819847-54820113(-)$1	266	133	141	15.6923
ee777777	chr7:72855070-72855311(-)$1	241	40	48	14.2307
wwwwwwww	chr4:123818307-123818577(+)$1	270	43	51	14.1538
hhhhh:::	chr2:136872152-136872395(-)$1	243	49	57	16.4615
:ggggggg	chr5:14695891-14696151(+)$1	260	145	153	14.6153
GG::::::	chr12:12272973-12273244(-)$1	271	21	29	14.3846
[iiiiiii	chr15:29993277-29993508(-)$1	231	113	121	16.6923
:::::JJJ	chr9:127573336-127573568(+)$1	232	104	112	16.4615
::::::::	chr2:206860475-206860707(-)$1	232	17	25	16.4615
ddd:::::	chr17:7474788-7475060(+)$1	272	128	136	14.3846
xxxxxxxx	chr1:110564233-110564552(+)$1	319	137	145	16.6923
qqgggggg	chrX:24003846-24004120(-)$1	274	75	83	16.6923
eee22a>>	chr10:32298328-32298573(-)$1	245	126	134	15.6923
::::::::	chr13:95673614-95673840(-)$1	226	85	93	14.3076
tttttttt	chr15:44063557-44063813(+)$1	256	51	59	16.1538
%%%%%%ee	chr9:123521899-123522130(-)$1	231	40	48	14.5384
eee[====	chr8:64124750-64125040(+)$1	290	6	14	16.6923
++++++++	chr19:6414566-6414869(-)$1	303	144	152	13.7692
::::::::	chr2:70107435-70107675(+)$1	240	9	17	13.3846
ssssssss	chr3:55501609-55501926(-)$1	317	229	237	14.6153
gggggggc	chr10:94113291-94113548(+)$1	257	114	122	16.6923
FFFFLLLC	chr15:63358199-63358447(+)$1	248	38	46	15.6923

#DB
.......(	chr1:65880193-65880431(+)$1	1	113	121	16.6923
.....(((	chr2:38522989-38523244(-)$1	1	138	146	14.3076
........	chr8:131065841-131066080(-)$1	1	116	124	16.4615
.....)))	chr1:21070903-21071219(-)$1	1	280	288	18.8461
)).))).)	chr4:115598278-115598552(+)$1	1	201	209	14.7692
(.......	chr12:93802973-93803202(-)$1	1	86	94	16.6923
......((	chr5:135513867-135514134(+)$1	1	140	148	16.6923
........	chr1:200520925-200521158(-)$1	1	170	178	16.4615
))))))..	chr7:116199345-116199637(+)$1	1	207	215	14.5384
))((((((	chr13:98045386-98045697(+)$1	1	59	67	14.3076
).)))...	chr10:116736005-116736233(+)$1	1	213	221	14.3846
........	chr9:135564865-135565126(+)$1	1	52	60	14.7692
))))))))	chr2:196999999-197000326(-)$1	1	144	152	18.8461
(((((.((	chr17:39910814-39911048(-)$1	1	122	130	16.1538
(((((.((	chr3:58305388-58305638(+)$1	1	55	63	14.2307
..(((.((	chr17:48940029-48940325(-)$1	1	160	168	13.9999
.....(((	chr5:137088392-137088783(-)$1	1	198	206	16.4615
)))))...	chr5:57749834-57750086(-)$1	1	172	180	16.4615
(.......	chr15:45009828-45010063(+)$1	1	31	39	14.3846
.(((....	chr17:79845705-79845960(-)$1	1	59	67	16.1538
...)))))	chr1:78482861-78483089(+)$1	1	122	130	16.1538
.)))))))	chr1:46093329-46093588(-)$1	1	104	112	16.6923
....))))	chr2:36777577-36777865(+)$1	1	256	264	15.7692
........	chr18:21062655-21062922(+)$1	1	81	89	14.4615
(.(((.((	chr5:114949476-114949760(-)$1	1	63	71	16.1538
........	chr8:81432630-81432856(+)$1	1	15	23	16.6923
.)..))))	chr1:91381459-91381738(-)$1	1	137	145	14.4615
.......)	chr9:7797985-7798235(-)$1	1	129	137	16.4615
).((((((	chr15:49935675-49935934(+)$1	1	122	130	16.4615
(((.((..	chr6:151686304-151686534(-)$1	1	134	142	14.3846
))))))))	chr1:234742506-234742894(-)$1	1	166	174	14.7692
(.((((((	chr11:57584127-57584358(+)$1	1	114	122	16.6923
((((....	chr6:82456501-82456744(-)$1	1	127	135	15.6923
((((((((	chr3:111710648-111710945(+)$1	1	133	141	14.3076
((((.(((	chr8:124511591-124511867(-)$1	1	5	13	16.1538
..))))..	chr1:29474174-29474482(-)$1	1	110	118	18.8461
.....(((	chr1:68947115-68947340(-)$1	1	33	41	15.5384
(.......	chr1:155708117-155708355(+)$1	1	121	129	13.9999
.....)))	chr11:62283775-62284036(-)$1	1	74	82	14.6153
..((((((	chr13:100037683-100037914(+)$1	1	113	121	14.7692
)))))...	chr12:98943295-98943562(+)$1	1	204	212	14.6153
.(((((((	chr5:65118893-65119135(+)$1	1	170	178	14.5384
((.(((..	chr1:61924063-61924300(+)$1	1	75	83	15.5384
)).)))))	chr7:54819847-54820113(-)$1	1	133	141	15.6923
))......	chr7:72855070-72855311(-)$1	1	40	48	14.2307
........	chr4:123818307-123818577(+)$1	1	43	51	14.1538
)))))...	chr2:136872152-136872395(-)$1	1	49	57	16.4615
.(((((((	chr5:14695891-14696151(+)$1	1	145	153	14.6153
((......	chr12:12272973-12273244(-)$1	1	21	29	14.3846
.(((((((	chr15:29993277-29993508(-)$1	1	113	121	16.6923
.....)))	chr9:127573336-127573568(+)$1	1	104	112	16.4615
........	chr2:206860475-206860707(-)$1	1	17	25	16.4615
))).....	chr17:7474788-7475060(+)$1	1	128	136	14.3846
........	chr1:110564233-110564552(+)$1	1	137	145	16.6923
..))))))	chrX:24003846-24004120(-)$1	1	75	83	16.6923
)))..)..	chr10:32298328-32298573(-)$1	1	126	134	15.6923
........	chr13:95673614-95673840(-)$1	1	85	93	14.3076
........	chr15:44063557-44063813(+)$1	1	51	59	16.1538
......((	chr9:123521899-123522130(-)$1	1	40	48	14.5384
(((.((((	chr8:64124750-64125040(+)$1	1	6	14	16.6923
........	chr19:6414566-6414869(-)$1	1	144	152	13.7692
........	chr2:70107435-70107675(+)$1	1	9	17	13.3846
........	chr3:55501609-55501926(-)$1	1	229	237	14.6153
))))))))	chr10:94113291-94113548(+)$1	1	114	122	16.6923
((((...(	chr15:63358199-63358447(+)$1	1	38	46	15.6923

#PSSM
U : 0.92	G : 0.03	u : 0.03	A : 0.01	
U : 0.84	C : 0.06	u : 0.03	A : 0.03	G : 0.03	
U : 0.89	C : 0.03	A : 0.03	u : 0.03	G : 0.01	
A : 0.66	U : 0.21	C : 0.06	a : 0.03	G : 0.03	
U : 0.87	A : 0.04	u : 0.03	C : 0.03	G : 0.01	
A : 0.63	U : 0.21	G : 0.09	C : 0.03	g : 0.01	a : 0.01	
U : 0.95	u : 0.03	C : 0.01	
U : 0.95	u : 0.03	C : 0.01	

#score	1011.8461538461522
#seq	65
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m2_run2.nuc.txt

#NT
UUU	chr7:94166818-94167044(+)$1	226	2	5	9.0000
UUU	chr12:88443023-88443245(+)$1	222	36	39	9.0000
UUU	chr15:78789495-78789718(+)$1	223	22	25	9.0000
UUU	chr5:61847015-61847232(+)$1	217	4	7	9.0000
UUU	chr2:227731913-227732133(+)$1	220	1	4	9.0000
UUU	chr2:114493254-114493475(-)$1	221	3	6	9.0000
UUU	chr1:172542990-172543213(+)$1	223	0	3	9.0000
UUU	chr2:32523238-32523459(+)$1	221	23	26	9.0000
UUU	chr6:64422096-64422321(+)$1	225	36	39	9.0000
UUU	chr8:124031391-124031612(-)$1	221	40	43	9.0000
UUU	chr13:96579240-96579460(-)$1	220	24	27	9.0000
UUU	chr12:70206658-70206878(+)$1	220	19	22	9.0000
UUU	chr2:85769943-85770178(+)$1	235	6	9	9.0000
UUU	chr21:38131928-38132147(-)$1	219	0	3	9.0000
UUU	chr6:4937799-4938017(+)$1	218	101	104	9.0000
UUU	chr2:32249177-32249398(-)$1	221	14	17	9.0000
UUU	chr19:23927677-23927911(-)$1	234	10	13	9.0000
UUU	chr6:119150120-119150341(-)$1	221	49	52	9.0000
UUU	chr2:70131362-70131582(+)$1	220	4	7	9.0000
UUU	chr11:121177753-121177990(+)$1	237	0	3	9.0000
UUU	chr6:153312197-153312422(+)$1	225	12	15	9.0000
UUU	chr4:85730962-85731185(-)$1	223	30	33	9.0000
UUU	chr7:156619267-156619488(-)$1	221	9	12	9.0000
UUU	chr2:61528051-61528271(-)$1	220	82	85	9.0000
UUU	chr14:45644731-45644947(+)$1	216	10	13	9.0000
UUU	chr18:28667574-28667794(-)$1	220	1	4	9.0000
UUU	chr3:130452767-130452988(-)$1	221	49	52	9.0000
UUU	chr12:11139320-11139555(-)$1	235	20	23	9.0000
UUU	chr20:17950486-17950706(+)$1	220	31	34	9.0000
UUU	chr13:23911480-23911702(-)$1	222	5	8	9.0000
UUU	chr8:119122594-119122820(-)$1	226	14	17	9.0000
UUU	chr12:11091337-11091572(-)$1	235	47	50	9.0000
UUU	chr16:58585052-58585272(-)$1	220	4	7	9.0000
UUU	chr6:64421574-64421797(+)$1	223	66	69	9.0000
UUU	chr17:67309306-67309535(-)$1	229	5	8	9.0000
UUU	chr12:88442984-88443208(+)$1	224	2	5	9.0000
UUU	chr3:179306602-179306821(-)$1	219	0	3	9.0000
UUU	chr5:130940256-130940485(-)$1	229	13	16	9.0000
uuu	chr6:112395868-112396093(-)$1	225	12	15	9.0000
UUU	chr11:57457459-57457686(+)$1	227	32	35	9.0000
UUU	chrM:10374-10601(+)$1	227	41	44	9.0000
UUU	chrX:76814189-76814411(-)$1	222	44	47	9.0000
UUU	chr18:44656529-44656751(-)$1	222	8	11	9.0000
UUU	chr6:31604215-31604434(+)$1	219	31	34	9.0000
UUU	chr14:60611599-60611823(-)$1	224	72	75	9.0000
UUU	chr17:27008212-27008438(+)$1	226	18	21	9.0000
UUU	chr17:42745479-42745705(-)$1	226	94	97	9.0000
UUU	chr2:149449229-149449447(+)$1	218	0	3	9.0000
UUU	chr16:20810020-20810243(-)$1	223	14	17	9.0000
UUU	chr7:86825894-86826129(-)$1	235	16	19	9.0000
UUU	chr10:5791604-5791824(+)$1	220	42	45	9.0000
UUU	chr7:82543763-82543984(-)$1	221	32	35	9.0000
UUU	chr1:40735616-40735846(+)$1	230	1	4	9.0000
UUU	chr3:44448993-44449212(+)$1	219	20	23	9.0000
UUU	chr17:16052690-16052914(-)$1	224	44	47	9.0000
UUU	chr3:31641775-31641999(+)$1	224	5	8	9.0000
UUU	chr6:74331497-74331715(-)$1	218	1	4	9.0000
UUU	chr10:88220898-88221122(-)$1	224	4	7	9.0000
UUU	chr19:19135890-19136114(-)$1	224	6	9	9.0000
UUU	chr19:32945820-32946046(+)$1	226	11	14	9.0000
UUU	chr13:52598466-52598687(+)$1	221	48	51	9.0000
UUU	chr1:224377622-224377845(+)$1	223	14	17	9.0000
UUU	chr19:58489683-58489906(-)$1	223	7	10	9.0000
UUU	chr2:102509100-102509325(+)$1	225	37	40	9.0000
UUU	chr17:34893559-34893780(+)$1	221	7	10	9.0000
UUU	chr11:118344146-118344369(+)$1	223	72	75	9.0000
UUU	chr22:32883633-32883852(+)$1	219	69	72	9.0000
UUU	chr5:134079587-134079810(+)$1	223	0	3	9.0000
UUU	chr4:17805058-17805279(-)$1	221	35	38	9.0000
UUU	chr2:114482952-114483173(-)$1	221	27	30	9.0000
UUU	chr19:58268108-58268340(+)$1	232	111	114	9.0000
UUU	chr1:224377448-224377671(+)$1	223	36	39	9.0000
UUU	chr1:109779333-109779556(+)$1	223	9	12	9.0000
UUU	chr13:33110271-33110491(-)$1	220	92	95	9.0000
UUU	chr11:32637455-32637690(+)$1	235	18	21	9.0000
UUU	chr16:15138090-15138317(-)$1	227	45	48	9.0000
UUU	chr15:23012311-23012537(-)$1	226	3	6	9.0000
UUU	chr7:94166794-94167016(+)$1	222	26	29	9.0000
UUU	chr13:100211670-100211888(+)$1	218	27	30	9.0000
UUU	chr21:47711238-47711460(-)$1	222	28	31	9.0000
UUU	chr1:227841937-227842160(+)$1	223	27	30	9.0000
UUU	chrX:99890568-99890788(-)$1	220	19	22	9.0000
UUU	chr19:56896150-56896377(+)$1	227	8	11	9.0000
UUU	chr6:117023047-117023282(+)$1	235	31	34	9.0000
UUU	chr12:75893495-75893720(+)$1	225	8	11	9.0000
UUU	chr19:44680608-44680829(+)$1	221	92	95	9.0000
UUU	chr5:58571126-58571357(-)$1	231	9	12	9.0000
UUU	chr7:87170573-87170803(-)$1	230	4	7	9.0000
UUU	chr2:179429126-179429351(+)$1	225	14	17	9.0000
UUU	chr12:57464465-57464688(-)$1	223	0	3	9.0000
UUU	chr5:133295549-133295778(-)$1	229	8	11	9.0000
UUU	chr9:14658656-14658879(-)$1	223	31	34	9.0000
UUU	chr3:155571440-155571658(-)$1	218	95	98	9.0000
UUU	chr2:190323381-190323599(+)$1	218	25	28	9.0000
UUU	chr11:121177017-121177242(+)$1	225	43	46	9.0000
UUU	chrM:10402-10621(+)$1	219	13	16	9.0000
UUU	chr10:70721768-70721989(+)$1	221	21	24	9.0000

#otherMatches

#Struct PSSM
>>>	chr16:29822244-29822463(+)$1	219	101	104	9.0000
:::	chr7:94166818-94167044(+)$1	226	2	5	9.0000
HHH	chr12:88443023-88443245(+)$1	222	36	39	9.0000
f[b	chr15:78789495-78789718(+)$1	223	22	25	9.0000
:DD	chr5:61847015-61847232(+)$1	217	4	7	9.0000
:::	chr2:227731913-227732133(+)$1	220	1	4	9.0000
D::	chr2:114493254-114493475(-)$1	221	3	6	9.0000
:::	chr1:172542990-172543213(+)$1	223	0	3	9.0000
$gg	chr2:32523238-32523459(+)$1	221	23	26	9.0000
III	chr6:64422096-64422321(+)$1	225	36	39	9.0000
c[c	chr8:124031391-124031612(-)$1	221	40	43	9.0000
f##	chr13:96579240-96579460(-)$1	220	24	27	9.0000
hhh	chr12:70206658-70206878(+)$1	220	19	22	9.0000
g""	chr2:85769943-85770178(+)$1	235	6	9	9.0000
:::	chr21:38131928-38132147(-)$1	219	0	3	9.0000
CC:	chr6:4937799-4938017(+)$1	218	101	104	9.0000
ddo	chr2:32249177-32249398(-)$1	221	14	17	9.0000
ggg	chr19:23927677-23927911(-)$1	234	10	13	9.0000
!!c	chr6:119150120-119150341(-)$1	221	49	52	9.0000
:dd	chr2:70131362-70131582(+)$1	220	4	7	9.0000
:::	chr11:121177753-121177990(+)$1	237	0	3	9.0000
nne	chr6:153312197-153312422(+)$1	225	12	15	9.0000
^^^	chr4:85730962-85731185(-)$1	223	30	33	9.0000
:::	chr7:156619267-156619488(-)$1	221	9	12	9.0000
ggg	chr2:61528051-61528271(-)$1	220	82	85	9.0000
eee	chr14:45644731-45644947(+)$1	216	10	13	9.0000
:::	chr18:28667574-28667794(-)$1	220	1	4	9.0000
GGG	chr3:130452767-130452988(-)$1	221	49	52	9.0000
:::	chr12:11139320-11139555(-)$1	235	20	23	9.0000
%%%	chr20:17950486-17950706(+)$1	220	31	34	9.0000
hhh	chr13:23911480-23911702(-)$1	222	5	8	9.0000
:::	chr8:119122594-119122820(-)$1	226	14	17	9.0000
d::	chr12:11091337-11091572(-)$1	235	47	50	9.0000
:::	chr16:58585052-58585272(-)$1	220	4	7	9.0000
fff	chr6:64421574-64421797(+)$1	223	66	69	9.0000
b!!	chr17:67309306-67309535(-)$1	229	5	8	9.0000
:::	chr12:88442984-88443208(+)$1	224	2	5	9.0000
:::	chr3:179306602-179306821(-)$1	219	0	3	9.0000
KKB	chr5:130940256-130940485(-)$1	229	13	16	9.0000
GGG	chr6:112395868-112396093(-)$1	225	12	15	9.0000
###	chr11:57457459-57457686(+)$1	227	32	35	9.0000
===	chrM:10374-10601(+)$1	227	41	44	9.0000
eee	chrX:76814189-76814411(-)$1	222	44	47	9.0000
EE:	chr18:44656529-44656751(-)$1	222	8	11	9.0000
LLL	chr6:31604215-31604434(+)$1	219	31	34	9.0000
GGG	chr14:60611599-60611823(-)$1	224	72	75	9.0000
:::	chr17:27008212-27008438(+)$1	226	18	21	9.0000
22f	chr17:42745479-42745705(-)$1	226	94	97	9.0000
:::	chr2:149449229-149449447(+)$1	218	0	3	9.0000
"ff	chr16:20810020-20810243(-)$1	223	14	17	9.0000
ddd	chr7:86825894-86826129(-)$1	235	16	19	9.0000
::g	chr10:5791604-5791824(+)$1	220	42	45	9.0000
DDD	chr7:82543763-82543984(-)$1	221	32	35	9.0000
:::	chr1:40735616-40735846(+)$1	230	1	4	9.0000
FFF	chr3:44448993-44449212(+)$1	219	20	23	9.0000
:::	chr17:16052690-16052914(-)$1	224	44	47	9.0000
===	chr3:31641775-31641999(+)$1	224	5	8	9.0000
:::	chr6:74331497-74331715(-)$1	218	1	4	9.0000
:::	chr10:88220898-88221122(-)$1	224	4	7	9.0000
EEN	chr19:19135890-19136114(-)$1	224	6	9	9.0000
:::	chr19:32945820-32946046(+)$1	226	11	14	9.0000
ccm	chr13:52598466-52598687(+)$1	221	48	51	9.0000
EKK	chr1:224377622-224377845(+)$1	223	14	17	9.0000
fff	chr19:58489683-58489906(-)$1	223	7	10	9.0000
d::	chr2:102509100-102509325(+)$1	225	37	40	9.0000
::d	chr17:34893559-34893780(+)$1	221	7	10	9.0000
dd"	chr11:118344146-118344369(+)$1	223	72	75	9.0000
hhh	chr22:32883633-32883852(+)$1	219	69	72	9.0000
:::	chr5:134079587-134079810(+)$1	223	0	3	9.0000
eee	chr4:17805058-17805279(-)$1	221	35	38	9.0000
ndd	chr2:114482952-114483173(-)$1	221	27	30	9.0000
hhh	chr19:58268108-58268340(+)$1	232	111	114	9.0000
lll	chr1:224377448-224377671(+)$1	223	36	39	9.0000
:::	chr1:109779333-109779556(+)$1	223	9	12	9.0000
+++	chr13:33110271-33110491(-)$1	220	92	95	9.0000
:::	chr11:32637455-32637690(+)$1	235	18	21	9.0000
333	chr16:15138090-15138317(-)$1	227	45	48	9.0000
ee"	chr15:23012311-23012537(-)$1	226	3	6	9.0000
EEE	chr7:94166794-94167016(+)$1	222	26	29	9.0000
^^^	chr13:100211670-100211888(+)$1	218	27	30	9.0000
:::	chr21:47711238-47711460(-)$1	222	28	31	9.0000
ssg	chr1:227841937-227842160(+)$1	223	27	30	9.0000
e22	chrX:99890568-99890788(-)$1	220	19	22	9.0000
:::	chr19:56896150-56896377(+)$1	227	8	11	9.0000
xxx	chr6:117023047-117023282(+)$1	235	31	34	9.0000
:::	chr12:75893495-75893720(+)$1	225	8	11	9.0000
qqq	chr19:44680608-44680829(+)$1	221	92	95	9.0000
DMM	chr5:58571126-58571357(-)$1	231	9	12	9.0000
:::	chr7:87170573-87170803(-)$1	230	4	7	9.0000
MFF	chr2:179429126-179429351(+)$1	225	14	17	9.0000
HHH	chr12:57464465-57464688(-)$1	223	0	3	9.0000
E::	chr5:133295549-133295778(-)$1	229	8	11	9.0000
EEE	chr9:14658656-14658879(-)$1	223	31	34	9.0000
HHH	chr3:155571440-155571658(-)$1	218	95	98	9.0000
ff^	chr2:190323381-190323599(+)$1	218	25	28	9.0000
vvv	chr11:121177017-121177242(+)$1	225	43	46	9.0000
D{B	chrM:10402-10621(+)$1	219	13	16	9.0000
"""	chr10:70721768-70721989(+)$1	221	21	24	9.0000

#DB
...	chr16:29822244-29822463(+)$1	1	101	104	9.0000
...	chr7:94166818-94167044(+)$1	1	2	5	9.0000
(((	chr12:88443023-88443245(+)$1	1	36	39	9.0000
(.(	chr15:78789495-78789718(+)$1	1	22	25	9.0000
.((	chr5:61847015-61847232(+)$1	1	4	7	9.0000
...	chr2:227731913-227732133(+)$1	1	1	4	9.0000
(..	chr2:114493254-114493475(-)$1	1	3	6	9.0000
...	chr1:172542990-172543213(+)$1	1	0	3	9.0000
.((	chr2:32523238-32523459(+)$1	1	23	26	9.0000
(((	chr6:64422096-64422321(+)$1	1	36	39	9.0000
(.(	chr8:124031391-124031612(-)$1	1	40	43	9.0000
(..	chr13:96579240-96579460(-)$1	1	24	27	9.0000
(((	chr12:70206658-70206878(+)$1	1	19	22	9.0000
(..	chr2:85769943-85770178(+)$1	1	6	9	9.0000
...	chr21:38131928-38132147(-)$1	1	0	3	9.0000
)).	chr6:4937799-4938017(+)$1	1	101	104	9.0000
((.	chr2:32249177-32249398(-)$1	1	14	17	9.0000
)))	chr19:23927677-23927911(-)$1	1	10	13	9.0000
..(	chr6:119150120-119150341(-)$1	1	49	52	9.0000
.((	chr2:70131362-70131582(+)$1	1	4	7	9.0000
...	chr11:121177753-121177990(+)$1	1	0	3	9.0000
..)	chr6:153312197-153312422(+)$1	1	12	15	9.0000
...	chr4:85730962-85731185(-)$1	1	30	33	9.0000
...	chr7:156619267-156619488(-)$1	1	9	12	9.0000
(((	chr2:61528051-61528271(-)$1	1	82	85	9.0000
(((	chr14:45644731-45644947(+)$1	1	10	13	9.0000
...	chr18:28667574-28667794(-)$1	1	1	4	9.0000
(((	chr3:130452767-130452988(-)$1	1	49	52	9.0000
...	chr12:11139320-11139555(-)$1	1	20	23	9.0000
...	chr20:17950486-17950706(+)$1	1	31	34	9.0000
(((	chr13:23911480-23911702(-)$1	1	5	8	9.0000
...	chr8:119122594-119122820(-)$1	1	14	17	9.0000
)..	chr12:11091337-11091572(-)$1	1	47	50	9.0000
...	chr16:58585052-58585272(-)$1	1	4	7	9.0000
(((	chr6:64421574-64421797(+)$1	1	66	69	9.0000
(..	chr17:67309306-67309535(-)$1	1	5	8	9.0000
...	chr12:88442984-88443208(+)$1	1	2	5	9.0000
...	chr3:179306602-179306821(-)$1	1	0	3	9.0000
..(	chr5:130940256-130940485(-)$1	1	13	16	9.0000
(((	chr6:112395868-112396093(-)$1	1	12	15	9.0000
...	chr11:57457459-57457686(+)$1	1	32	35	9.0000
(((	chrM:10374-10601(+)$1	1	41	44	9.0000
(((	chrX:76814189-76814411(-)$1	1	44	47	9.0000
((.	chr18:44656529-44656751(-)$1	1	8	11	9.0000
...	chr6:31604215-31604434(+)$1	1	31	34	9.0000
(((	chr14:60611599-60611823(-)$1	1	72	75	9.0000
...	chr17:27008212-27008438(+)$1	1	18	21	9.0000
..)	chr17:42745479-42745705(-)$1	1	94	97	9.0000
...	chr2:149449229-149449447(+)$1	1	0	3	9.0000
.((	chr16:20810020-20810243(-)$1	1	14	17	9.0000
(((	chr7:86825894-86826129(-)$1	1	16	19	9.0000
..(	chr10:5791604-5791824(+)$1	1	42	45	9.0000
(((	chr7:82543763-82543984(-)$1	1	32	35	9.0000
...	chr1:40735616-40735846(+)$1	1	1	4	9.0000
(((	chr3:44448993-44449212(+)$1	1	20	23	9.0000
...	chr17:16052690-16052914(-)$1	1	44	47	9.0000
(((	chr3:31641775-31641999(+)$1	1	5	8	9.0000
...	chr6:74331497-74331715(-)$1	1	1	4	9.0000
...	chr10:88220898-88221122(-)$1	1	4	7	9.0000
((.	chr19:19135890-19136114(-)$1	1	6	9	9.0000
...	chr19:32945820-32946046(+)$1	1	11	14	9.0000
((.	chr13:52598466-52598687(+)$1	1	48	51	9.0000
(..	chr1:224377622-224377845(+)$1	1	14	17	9.0000
(((	chr19:58489683-58489906(-)$1	1	7	10	9.0000
)..	chr2:102509100-102509325(+)$1	1	37	40	9.0000
..(	chr17:34893559-34893780(+)$1	1	7	10	9.0000
((.	chr11:118344146-118344369(+)$1	1	72	75	9.0000
)))	chr22:32883633-32883852(+)$1	1	69	72	9.0000
...	chr5:134079587-134079810(+)$1	1	0	3	9.0000
)))	chr4:17805058-17805279(-)$1	1	35	38	9.0000
.))	chr2:114482952-114483173(-)$1	1	27	30	9.0000
(((	chr19:58268108-58268340(+)$1	1	111	114	9.0000
...	chr1:224377448-224377671(+)$1	1	36	39	9.0000
...	chr1:109779333-109779556(+)$1	1	9	12	9.0000
...	chr13:33110271-33110491(-)$1	1	92	95	9.0000
...	chr11:32637455-32637690(+)$1	1	18	21	9.0000
...	chr16:15138090-15138317(-)$1	1	45	48	9.0000
((.	chr15:23012311-23012537(-)$1	1	3	6	9.0000
(((	chr7:94166794-94167016(+)$1	1	26	29	9.0000
...	chr13:100211670-100211888(+)$1	1	27	30	9.0000
...	chr21:47711238-47711460(-)$1	1	28	31	9.0000
..)	chr1:227841937-227842160(+)$1	1	27	30	9.0000
)..	chrX:99890568-99890788(-)$1	1	19	22	9.0000
...	chr19:56896150-56896377(+)$1	1	8	11	9.0000
...	chr6:117023047-117023282(+)$1	1	31	34	9.0000
...	chr12:75893495-75893720(+)$1	1	8	11	9.0000
...	chr19:44680608-44680829(+)$1	1	92	95	9.0000
(..	chr5:58571126-58571357(-)$1	1	9	12	9.0000
...	chr7:87170573-87170803(-)$1	1	4	7	9.0000
.((	chr2:179429126-179429351(+)$1	1	14	17	9.0000
(((	chr12:57464465-57464688(-)$1	1	0	3	9.0000
(..	chr5:133295549-133295778(-)$1	1	8	11	9.0000
(((	chr9:14658656-14658879(-)$1	1	31	34	9.0000
(((	chr3:155571440-155571658(-)$1	1	95	98	9.0000
((.	chr2:190323381-190323599(+)$1	1	25	28	9.0000
...	chr11:121177017-121177242(+)$1	1	43	46	9.0000
(.(	chrM:10402-10621(+)$1	1	13	16	9.0000
...	chr10:70721768-70721989(+)$1	1	21	24	9.0000

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_CDS_m3_run2.nuc.txt

#NT
GUGAAU	chr1:115279291-115279534(-)$1	243	9	15	10.8448
GUAAAA	chr5:167988314-167988589(-)$1	275	14	20	9.9827
GUGAAA	chr16:2820919-2821164(+)$1	245	114	120	14.4655
UUGAAA	chr15:66625406-66625651(-)$1	245	18	24	11.7068
GUGAAA	chr1:203818982-203819222(+)$1	240	132	138	14.4655
GUGAAU	chr14:71570042-71570287(+)$1	245	16	22	10.8448
GUAAAA	chr8:26221256-26221493(+)$1	237	48	54	9.9827
GUGAAC	chr11:32955833-32956073(+)$1	240	139	145	11.0172
UUGAAA	chr6:17646197-17646426(-)$1	229	3	9	11.7068
GUGAAA	chr5:40832475-40832722(-)$1	247	215	221	14.4655
GUGAAG	chr7:151874214-151874457(-)$1	243	5	11	11.0172
AUGAAA	chr12:123798066-123798290(-)$1	224	51	57	11.5344
GGGAAA	chr1:113232001-113232220(+)$1	219	51	57	10.6724
GUGAAA	chr13:25671139-25671352(+)$1	213	88	94	14.4655
GUGAAA	chr20:17930869-17931115(-)$1	246	147	153	14.4655
GUGAAG	chr17:7474115-7474351(+)$1	236	54	60	11.0172
AUGAAA	chr17:65944100-65944349(+)$1	249	54	60	11.5344
AUGAAA	chr10:119042721-119042955(-)$1	234	97	103	11.5344
GUGAAA	chr21:44513077-44513318(-)$1	241	84	90	14.4655
GUGAAC	chr15:75212653-75212883(-)$1	230	140	146	11.0172
UUGAAA	chr10:30625826-30626052(-)$1	226	21	27	11.7068
GUGAAA	chr1:193060647-193060921(+)$1	274	108	114	14.4655
GUGAAA	chr17:27614235-27614466(-)$1	231	155	161	14.4655
AUGAAA	chr1:115266481-115266723(-)$1	242	59	65	11.5344
GUGAAG	chr10:103546121-103546347(-)$1	226	21	27	11.0172
CUGAAA	chrX:107976387-107976619(-)$1	232	163	169	11.3620
GUGAAU	chr1:16255782-16256028(+)$1	246	230	236	10.8448
GUGAAA	chr1:203816282-203816512(+)$1	230	19	25	14.4655
GGGAAA	chr1:16255390-16255631(+)$1	241	5	11	10.6724
GGGAAA	chr1:16254524-16254753(+)$1	229	192	198	10.6724
UUGAAA	chr12:67700136-67700367(+)$1	231	97	103	11.7068
GUGAAA	chrX:71492981-71493198(-)$1	217	54	60	14.4655
GGGAAA	chr19:3976124-3976356(-)$1	232	97	103	10.6724
GUGAAA	chr4:1976518-1976760(+)$1	242	2	8	14.4655
GUGAAG	chr1:16262184-16262406(+)$1	222	199	205	11.0172
GUGAAG	chr5:37303309-37303529(-)$1	220	189	195	11.0172
GUGAAC	chr13:25671962-25672203(+)$1	241	46	52	11.0172
GGGAAA	chr6:87968198-87968427(+)$1	229	17	23	10.6724
AUGAAA	chr1:16256114-16256333(+)$1	219	33	39	11.5344
UUGAAA	chr19:24009993-24010228(+)$1	235	172	178	11.7068
UUGAAA	chr11:102269511-102269742(-)$1	231	21	27	11.7068
CUGAAA	chrX:53561399-53561635(-)$1	236	111	117	11.3620
GGGAAA	chr15:66791589-66791854(-)$1	265	16	22	10.6724
GUGAAC	chr17:37006577-37006800(-)$1	223	161	167	11.0172
GUGAAA	chr1:183522224-183522469(+)$1	245	19	25	14.4655
GUAAAA	chr2:152298328-152298558(+)$1	230	67	73	9.9827
GUGAAA	chr13:25670763-25671001(+)$1	238	230	236	14.4655
CUGAAA	chr14:59830393-59830614(-)$1	221	49	55	11.3620
UUGAAA	chr8:101718870-101719133(-)$1	263	57	63	11.7068
GUGAAC	chr2:61483906-61484157(-)$1	251	76	82	11.0172
UUGAAA	chr3:133306716-133306951(+)$1	235	136	142	11.7068
GUGAAA	chr2:48033858-48034090(+)$1	232	76	82	14.4655
AUGAAA	chr9:125613370-125613596(+)$1	226	167	173	11.5344
GGGAAA	chr12:53848518-53848748(+)$1	230	149	155	10.6724
CUGAAA	chr1:40035452-40035691(-)$1	239	132	138	11.3620
GUGAAA	chr1:62905381-62905641(+)$1	260	176	182	14.4655
GUGAAA	chr1:115263202-115263430(-)$1	228	53	59	14.4655

#otherMatches

#Struct PSSM
::::::	chr1:244217765-244217998(+)$1	233	226	232	14.4655
c!!bb[	chr1:115279291-115279534(-)$1	243	9	15	10.8448
ddddmm	chr5:167988314-167988589(-)$1	275	14	20	9.9827
ttdddd	chr16:2820919-2821164(+)$1	245	114	120	14.4655
c!!ggg	chr15:66625406-66625651(-)$1	245	18	24	11.7068
dddd::	chr1:203818982-203819222(+)$1	240	132	138	14.4655
::dddd	chr14:71570042-71570287(+)$1	245	16	22	10.8448
::IIII	chr8:26221256-26221493(+)$1	237	48	54	9.9827
dddddl	chr11:32955833-32956073(+)$1	240	139	145	11.0172
::::::	chr6:17646197-17646426(-)$1	229	3	9	11.7068
ppppp=	chr5:40832475-40832722(-)$1	247	215	221	14.4655
HHH{CC	chr7:151874214-151874457(-)$1	243	5	11	11.0172
::bbff	chr12:123798066-123798290(-)$1	224	51	57	11.5344
ccc555	chr1:113232001-113232220(+)$1	219	51	57	10.6724
pppppc	chr13:25671139-25671352(+)$1	213	88	94	14.4655
eeee]b	chr20:17930869-17931115(-)$1	246	147	153	14.4655
a]a]ee	chr17:7474115-7474351(+)$1	236	54	60	11.0172
leeeee	chr17:65944100-65944349(+)$1	249	54	60	11.5344
BBNNNN	chr10:119042721-119042955(-)$1	234	97	103	11.5344
ff6666	chr21:44513077-44513318(-)$1	241	84	90	14.4655
ee]bb]	chr15:75212653-75212883(-)$1	230	140	146	11.0172
::gggg	chr10:30625826-30626052(-)$1	226	21	27	11.7068
ffffff	chr1:193060647-193060921(+)$1	274	108	114	14.4655
nnnnnf	chr17:27614235-27614466(-)$1	231	155	161	14.4655
======	chr1:115266481-115266723(-)$1	242	59	65	11.5344
iiiiii	chr10:103546121-103546347(-)$1	226	21	27	11.0172
b:dddd	chrX:107976387-107976619(-)$1	232	163	169	11.3620
FFZZZC	chr1:16255782-16256028(+)$1	246	230	236	10.8448
ddmmmm	chr1:203816282-203816512(+)$1	230	19	25	14.4655
DDBB{B	chr1:16255390-16255631(+)$1	241	5	11	10.6724
ttgggg	chr1:16254524-16254753(+)$1	229	192	198	10.6724
eellle	chr12:67700136-67700367(+)$1	231	97	103	11.7068
eegggg	chrX:71492981-71493198(-)$1	217	54	60	14.4655
cnnnnn	chr19:3976124-3976356(-)$1	232	97	103	10.6724
::::::	chr4:1976518-1976760(+)$1	242	2	8	14.4655
ffoooo	chr1:16262184-16262406(+)$1	222	199	205	11.0172
ggg:::	chr5:37303309-37303529(-)$1	220	189	195	11.0172
ddd"""	chr13:25671962-25672203(+)$1	241	46	52	11.0172
DDDDLL	chr6:87968198-87968427(+)$1	229	17	23	10.6724
fff:::	chr1:16256114-16256333(+)$1	219	33	39	11.5344
::::::	chr19:24009993-24010228(+)$1	235	172	178	11.7068
{A{BB{	chr11:102269511-102269742(-)$1	231	21	27	11.7068
ggggg&	chrX:53561399-53561635(-)$1	236	111	117	11.3620
ddd'''	chr15:66791589-66791854(-)$1	265	16	22	10.6724
]ccc>>	chr17:37006577-37006800(-)$1	223	161	167	11.0172
FFFFFK	chr1:183522224-183522469(+)$1	245	19	25	14.4655
c"""ee	chr2:152298328-152298558(+)$1	230	67	73	9.9827
EEEEEE	chr13:25670763-25671001(+)$1	238	230	236	14.4655
ccc:::	chr14:59830393-59830614(-)$1	221	49	55	11.3620
ff]ddd	chr8:101718870-101719133(-)$1	263	57	63	11.7068
eeeee=	chr2:61483906-61484157(-)$1	251	76	82	11.0172
ddddll	chr3:133306716-133306951(+)$1	235	136	142	11.7068
bb[a[i	chr2:48033858-48034090(+)$1	232	76	82	14.4655
Eggggg	chr9:125613370-125613596(+)$1	226	167	173	11.5344
ccbb::	chr12:53848518-53848748(+)$1	230	149	155	10.6724
eeeeep	chr1:40035452-40035691(-)$1	239	132	138	11.3620
!ggggg	chr1:62905381-62905641(+)$1	260	176	182	14.4655
fccc44	chr1:115263202-115263430(-)$1	228	53	59	14.4655

#DB
......	chr1:244217765-244217998(+)$1	1	226	232	14.4655
(..((.	chr1:115279291-115279534(-)$1	1	9	15	10.8448
((((..	chr5:167988314-167988589(-)$1	1	14	20	9.9827
..))))	chr16:2820919-2821164(+)$1	1	114	120	14.4655
(..(((	chr15:66625406-66625651(-)$1	1	18	24	11.7068
))))..	chr1:203818982-203819222(+)$1	1	132	138	14.4655
..((((	chr14:71570042-71570287(+)$1	1	16	22	10.8448
..((((	chr8:26221256-26221493(+)$1	1	48	54	9.9827
(((((.	chr11:32955833-32956073(+)$1	1	139	145	11.0172
......	chr6:17646197-17646426(-)$1	1	3	9	11.7068
.....)	chr5:40832475-40832722(-)$1	1	215	221	14.4655
(((.((	chr7:151874214-151874457(-)$1	1	5	11	11.0172
..((((	chr12:123798066-123798290(-)$1	1	51	57	11.5344
)))...	chr1:113232001-113232220(+)$1	1	51	57	10.6724
.....)	chr13:25671139-25671352(+)$1	1	88	94	14.4655
)))).)	chr20:17930869-17931115(-)$1	1	147	153	14.4655
).).))	chr17:7474115-7474351(+)$1	1	54	60	11.0172
.)))))	chr17:65944100-65944349(+)$1	1	54	60	11.5344
((....	chr10:119042721-119042955(-)$1	1	97	103	11.5344
))....	chr21:44513077-44513318(-)$1	1	84	90	14.4655
)).)).	chr15:75212653-75212883(-)$1	1	140	146	11.0172
..((((	chr10:30625826-30626052(-)$1	1	21	27	11.7068
))))))	chr1:193060647-193060921(+)$1	1	108	114	14.4655
.....)	chr17:27614235-27614466(-)$1	1	155	161	14.4655
((((((	chr1:115266481-115266723(-)$1	1	59	65	11.5344
((((((	chr10:103546121-103546347(-)$1	1	21	27	11.0172
).((((	chrX:107976387-107976619(-)$1	1	163	169	11.3620
))...)	chr1:16255782-16256028(+)$1	1	230	236	10.8448
((....	chr1:203816282-203816512(+)$1	1	19	25	14.4655
((((.(	chr1:16255390-16255631(+)$1	1	5	11	10.6724
..))))	chr1:16254524-16254753(+)$1	1	192	198	10.6724
((...)	chr12:67700136-67700367(+)$1	1	97	103	11.7068
))))))	chrX:71492981-71493198(-)$1	1	54	60	14.4655
(.....	chr19:3976124-3976356(-)$1	1	97	103	10.6724
......	chr4:1976518-1976760(+)$1	1	2	8	14.4655
((....	chr1:16262184-16262406(+)$1	1	199	205	11.0172
)))...	chr5:37303309-37303529(-)$1	1	189	195	11.0172
(((...	chr13:25671962-25672203(+)$1	1	46	52	11.0172
((((..	chr6:87968198-87968427(+)$1	1	17	23	10.6724
)))...	chr1:16256114-16256333(+)$1	1	33	39	11.5344
......	chr19:24009993-24010228(+)$1	1	172	178	11.7068
.(.((.	chr11:102269511-102269742(-)$1	1	21	27	11.7068
(((((.	chrX:53561399-53561635(-)$1	1	111	117	11.3620
(((...	chr15:66791589-66791854(-)$1	1	16	22	10.6724
.)))..	chr17:37006577-37006800(-)$1	1	161	167	11.0172
(((((.	chr1:183522224-183522469(+)$1	1	19	25	14.4655
(...((	chr2:152298328-152298558(+)$1	1	67	73	9.9827
))))))	chr13:25670763-25671001(+)$1	1	230	236	14.4655
)))...	chr14:59830393-59830614(-)$1	1	49	55	11.3620
)).)))	chr8:101718870-101719133(-)$1	1	57	63	11.7068
)))))(	chr2:61483906-61484157(-)$1	1	76	82	11.0172
((((..	chr3:133306716-133306951(+)$1	1	136	142	11.7068
((.(.(	chr2:48033858-48034090(+)$1	1	76	82	14.4655
)(((((	chr9:125613370-125613596(+)$1	1	167	173	11.5344
))))..	chr12:53848518-53848748(+)$1	1	149	155	10.6724
(((((.	chr1:40035452-40035691(-)$1	1	132	138	11.3620
.(((((	chr1:62905381-62905641(+)$1	1	176	182	14.4655
))))..	chr1:115263202-115263430(-)$1	1	53	59	14.4655

#PSSM
G : 0.68	U : 0.13	A : 0.10	C : 0.06	
U : 0.87	G : 0.12	
G : 0.94	A : 0.05	
A : 1.00	
A : 1.00	
A : 0.77	C : 0.08	G : 0.08	U : 0.05	

#score	701.586206896552
#seq	58
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m3_run2.nuc.txt

#NT
auaaaagu	chr8:101165671-101165908(+)$1	237	150	158	15.7647
AUAAAACU	chr6:88384867-88385095(-)$1	228	103	111	15.9607
auaaaacu	chr19:36729019-36729249(+)$1	230	154	162	15.9607
AUAAAAUG	chr2:74444466-74444697(+)$1	231	3	11	15.6666
AUAAAAAU	chr3:169712739-169712990(+)$1	251	114	122	16.1568
AUAAAAUU	chr12:42475731-42475956(-)$1	225	160	168	19.7843
CUAAAAUU	chr5:145890287-145890531(+)$1	244	159	167	15.4705
ACAAAAUU	chr11:118620846-118621069(-)$1	223	174	182	15.6666
AAAAAAUU	chr5:151184248-151184524(+)$1	276	156	164	15.8627
AUAUAAUU	chr13:26787222-26787447(-)$1	225	17	25	15.4705
aaaaaauu	chr19:44679229-44679441(+)$1	212	156	164	15.8627
AUGAAAUU	chr6:138412400-138412634(-)$1	234	131	139	15.5686
AGAAAAUU	chr1:245015259-245015497(-)$1	238	36	44	15.5686
UUAAAAUU	chr12:12271195-12271409(-)$1	214	72	80	15.5686
AUAAAAUG	chrX:119392039-119392263(+)$1	224	194	202	15.6666
AUAAUAUU	chr1:167395270-167395492(+)$1	222	53	61	15.1764
AUUAAAUU	chr1:109605131-109605364(-)$1	233	55	63	15.7647
AUAAAAUU	chr15:43034421-43034658(-)$1	237	41	49	19.7843
AAAAAAUU	chr10:27036531-27036769(-)$1	238	64	72	15.8627
GUAAAAUU	chr6:11138817-11139059(+)$1	242	6	14	15.6666
AUAAAACU	chr11:27517814-27518055(-)$1	241	131	139	15.9607
AUAAAAUU	chr9:91092534-91092764(+)$1	230	170	178	19.7843
AUAAAAUU	chr13:77457041-77457308(-)$1	267	38	46	19.7843
AUAAAAUA	chr5:133307513-133307753(-)$1	240	129	137	15.3725
augaaauu	chr8:101931887-101932125(-)$1	238	111	119	15.5686
AUAAAUUU	chr1:173866571-173866804(+)$1	233	26	34	15.4705
AUAAAUUU	chr10:93040521-93040742(+)$1	221	67	75	15.4705
GUAAAAUU	chr2:37074722-37074953(-)$1	231	66	74	15.6666
auuaaauu	chrX:77382136-77382365(+)$1	229	169	177	15.7647
AUAAAAUG	chr2:38971837-38972114(-)$1	277	60	68	15.6666
AUAAAAAU	chr15:35270448-35270684(-)$1	236	49	57	16.1568
AUUAAAUU	chr5:72206638-72206869(+)$1	231	77	85	15.7647
AUAAAAUU	chr20:49369793-49370024(+)$1	231	166	174	19.7843
AUAAACUU	chr12:50871725-50872005(+)$1	280	47	55	15.2745
AUAAUAUU	chr12:124146920-124147149(+)$1	229	11	19	15.1764
ACAAAAUU	chr12:69237792-69238018(+)$1	226	60	68	15.6666
UUAAAAUU	chr6:29913504-29913743(+)$1	239	22	30	15.5686
AUAAAAUG	chr10:97819701-97819954(+)$1	253	30	38	15.6666
AUAGAAUU	chrX:123235415-123235640(+)$1	225	195	203	15.2745
AUAUAAUU	chr1:36391076-36391302(+)$1	226	103	111	15.4705
AUAAAUUU	chr12:79985735-79985964(-)$1	229	156	164	15.4705
GUAAAAUU	chr21:43407596-43407824(-)$1	228	35	43	15.6666
AUUAAAUU	chr14:51442057-51442287(-)$1	230	163	171	15.7647
AAAAAAUU	chr6:75965473-75965721(-)$1	248	90	98	15.8627
AUAAAAUU	chr7:94296844-94297094(+)$1	250	240	248	19.7843
AUAUAAUU	chr5:133292213-133292439(-)$1	226	42	50	15.4705
AUAAAAAU	chr5:167978688-167978913(-)$1	225	112	120	16.1568
AUAAAAUU	chr7:107401635-107401881(+)$1	246	100	108	19.7843
AUAAAAAU	chr2:74379810-74380059(-)$1	249	202	210	16.1568
AUAAAAUU	chr3:152182185-152182408(+)$1	223	168	176	19.7843

#otherMatches

#Struct PSSM
::::::::	chr3:120044810-120045036(-)$1	226	7	15	16.1568
qqqqqbb]	chr8:101165671-101165908(+)$1	237	150	158	15.7647
dddd$$$$	chr6:88384867-88385095(-)$1	228	103	111	15.9607
b]dddd]c	chr19:36729019-36729249(+)$1	230	154	162	15.9607
eessssss	chr2:74444466-74444697(+)$1	231	3	11	15.6666
::::::::	chr3:169712739-169712990(+)$1	251	114	122	16.1568
::::::::	chr12:42475731-42475956(-)$1	225	160	168	19.7843
ddd55555	chr5:145890287-145890531(+)$1	244	159	167	15.4705
:::ggggg	chr11:118620846-118621069(-)$1	223	174	182	15.6666
hhhhhhhh	chr5:151184248-151184524(+)$1	276	156	164	15.8627
:::::JJJ	chr13:26787222-26787447(-)$1	225	17	25	15.4705
@@@@@@@@	chr19:44679229-44679441(+)$1	212	156	164	15.8627
IIII::::	chr6:138412400-138412634(-)$1	234	131	139	15.5686
cbbiiiii	chr1:245015259-245015497(-)$1	238	36	44	15.5686
::::::::	chr12:12271195-12271409(-)$1	214	72	80	15.5686
::::::::	chrX:119392039-119392263(+)$1	224	194	202	15.6666
fflllfff	chr1:167395270-167395492(+)$1	222	53	61	15.1764
cggggggg	chr1:109605131-109605364(-)$1	233	55	63	15.7647
::::::::	chr15:43034421-43034658(-)$1	237	41	49	19.7843
BBPPPPPP	chr10:27036531-27036769(-)$1	238	64	72	15.8627
EEELLLFF	chr6:11138817-11139059(+)$1	242	6	14	15.6666
%%%%%ddd	chr11:27517814-27518055(-)$1	241	131	139	15.9607
::::::::	chr9:91092534-91092764(+)$1	230	170	178	19.7843
CCMMMMGG	chr13:77457041-77457308(-)$1	267	38	46	19.7843
eee]dddd	chr5:133307513-133307753(-)$1	240	129	137	15.3725
wwwwwwww	chr8:101931887-101932125(-)$1	238	111	119	15.5686
qqqqqeee	chr1:173866571-173866804(+)$1	233	26	34	15.4705
RRRRREEE	chr10:93040521-93040742(+)$1	221	67	75	15.4705
cc22dddd	chr2:37074722-37074953(-)$1	231	66	74	15.6666
ccdddd[d	chrX:77382136-77382365(+)$1	229	169	177	15.7647
e%%%%%%c	chr2:38971837-38972114(-)$1	277	60	68	15.6666
++++++++	chr15:35270448-35270684(-)$1	236	49	57	16.1568
ffoooooo	chr5:72206638-72206869(+)$1	231	77	85	15.7647
iiiiiiii	chr20:49369793-49370024(+)$1	231	166	174	19.7843
::::::HH	chr12:50871725-50872005(+)$1	280	47	55	15.2745
JJJJSSSS	chr12:124146920-124147149(+)$1	229	11	19	15.1764
B{IIIIII	chr12:69237792-69238018(+)$1	226	60	68	15.6666
MMMGGGGG	chr6:29913504-29913743(+)$1	239	22	30	15.5686
dd22ffff	chr10:97819701-97819954(+)$1	253	30	38	15.6666
ggg:::CC	chrX:123235415-123235640(+)$1	225	195	203	15.2745
zzzzzzzz	chr1:36391076-36391302(+)$1	226	103	111	15.4705
:::hhhhh	chr12:79985735-79985964(-)$1	229	156	164	15.4705
oooooobb	chr21:43407596-43407824(-)$1	228	35	43	15.6666
iiiiiiii	chr14:51442057-51442287(-)$1	230	163	171	15.7647
tttttttt	chr6:75965473-75965721(-)$1	248	90	98	15.8627
::::::::	chr7:94296844-94297094(+)$1	250	240	248	19.7843
NNNNNHHH	chr5:133292213-133292439(-)$1	226	42	50	15.4705
DDZZZGGG	chr5:167978688-167978913(-)$1	225	112	120	16.1568
EIIIIIII	chr7:107401635-107401881(+)$1	246	100	108	19.7843
dd::DDDD	chr2:74379810-74380059(-)$1	249	202	210	16.1568
ettttttt	chr3:152182185-152182408(+)$1	223	168	176	19.7843

#DB
........	chr3:120044810-120045036(-)$1	1	7	15	16.1568
.....)).	chr8:101165671-101165908(+)$1	1	150	158	15.7647
((((....	chr6:88384867-88385095(-)$1	1	103	111	15.9607
).)))).)	chr19:36729019-36729249(+)$1	1	154	162	15.9607
((......	chr2:74444466-74444697(+)$1	1	3	11	15.6666
........	chr3:169712739-169712990(+)$1	1	114	122	16.1568
........	chr12:42475731-42475956(-)$1	1	160	168	19.7843
))).....	chr5:145890287-145890531(+)$1	1	159	167	15.4705
...(((((	chr11:118620846-118621069(-)$1	1	174	182	15.6666
))))))))	chr5:151184248-151184524(+)$1	1	156	164	15.8627
.....(((	chr13:26787222-26787447(-)$1	1	17	25	15.4705
........	chr19:44679229-44679441(+)$1	1	156	164	15.8627
))))....	chr6:138412400-138412634(-)$1	1	131	139	15.5686
((((((((	chr1:245015259-245015497(-)$1	1	36	44	15.5686
........	chr12:12271195-12271409(-)$1	1	72	80	15.5686
........	chrX:119392039-119392263(+)$1	1	194	202	15.6666
((...)))	chr1:167395270-167395492(+)$1	1	53	61	15.1764
)(((((((	chr1:109605131-109605364(-)$1	1	55	63	15.7647
........	chr15:43034421-43034658(-)$1	1	41	49	19.7843
((......	chr10:27036531-27036769(-)$1	1	64	72	15.8627
(((...((	chr6:11138817-11139059(+)$1	1	6	14	15.6666
.....(((	chr11:27517814-27518055(-)$1	1	131	139	15.9607
........	chr9:91092534-91092764(+)$1	1	170	178	19.7843
((....((	chr13:77457041-77457308(-)$1	1	38	46	19.7843
))).))))	chr5:133307513-133307753(-)$1	1	129	137	15.3725
........	chr8:101931887-101932125(-)$1	1	111	119	15.5686
.....)))	chr1:173866571-173866804(+)$1	1	26	34	15.4705
.....(((	chr10:93040521-93040742(+)$1	1	67	75	15.4705
))..))))	chr2:37074722-37074953(-)$1	1	66	74	15.6666
((((((.(	chrX:77382136-77382365(+)$1	1	169	177	15.7647
(......(	chr2:38971837-38972114(-)$1	1	60	68	15.6666
........	chr15:35270448-35270684(-)$1	1	49	57	16.1568
((......	chr5:72206638-72206869(+)$1	1	77	85	15.7647
((((((((	chr20:49369793-49370024(+)$1	1	166	174	19.7843
......((	chr12:50871725-50872005(+)$1	1	47	55	15.2745
((((....	chr12:124146920-124147149(+)$1	1	11	19	15.1764
(.((((((	chr12:69237792-69238018(+)$1	1	60	68	15.6666
...(((((	chr6:29913504-29913743(+)$1	1	22	30	15.5686
))..))))	chr10:97819701-97819954(+)$1	1	30	38	15.6666
)))...))	chrX:123235415-123235640(+)$1	1	195	203	15.2745
........	chr1:36391076-36391302(+)$1	1	103	111	15.4705
...(((((	chr12:79985735-79985964(-)$1	1	156	164	15.4705
......))	chr21:43407596-43407824(-)$1	1	35	43	15.6666
))))))))	chr14:51442057-51442287(-)$1	1	163	171	15.7647
........	chr6:75965473-75965721(-)$1	1	90	98	15.8627
........	chr7:94296844-94297094(+)$1	1	240	248	19.7843
.....(((	chr5:133292213-133292439(-)$1	1	42	50	15.4705
))...)))	chr5:167978688-167978913(-)$1	1	112	120	16.1568
((((((((	chr7:107401635-107401881(+)$1	1	100	108	19.7843
))..))))	chr2:74379810-74380059(-)$1	1	202	210	16.1568
(.......	chr3:152182185-152182408(+)$1	1	168	176	19.7843

#PSSM
A : 0.76	a : 0.11	G : 0.05	U : 0.03	C : 0.01	
U : 0.76	u : 0.09	A : 0.05	C : 0.03	a : 0.01	G : 0.01	
A : 0.80	a : 0.07	U : 0.05	G : 0.01	g : 0.01	u : 0.01	
A : 0.80	a : 0.11	U : 0.05	G : 0.01	
A : 0.84	a : 0.11	U : 0.03	
A : 0.80	a : 0.11	U : 0.05	C : 0.01	
U : 0.76	A : 0.07	u : 0.05	C : 0.03	a : 0.01	g : 0.01	c : 0.01	
U : 0.78	u : 0.11	G : 0.07	A : 0.01	

#score	832.6274509803924
#seq	51
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m1_run1.nuc.txt

#NT
GCAG	chr10:103825607-103825845(+)$1	238	11	15	11.9999
GCAG	chr4:44680647-44680868(+)$1	221	145	149	11.9999
GCAG	chr15:74742211-74742432(-)$1	221	80	84	11.9999
GCAG	chr16:2815273-2815533(+)$1	260	39	43	11.9999
GCAG	chr1:6704540-6704757(-)$1	217	19	23	11.9999
GCAG	chr9:135163902-135164120(-)$1	218	40	44	11.9999
GCAG	chr5:126154575-126154786(+)$1	211	157	161	11.9999
GCAG	chr17:3628355-3628578(+)$1	223	81	85	11.9999
GCAG	chr15:42032103-42032323(+)$1	220	20	24	11.9999
GCAG	chr1:151378014-151378238(-)$1	224	19	23	11.9999
GCAG	chr1:242023841-242024062(+)$1	221	162	166	11.9999
GCAG	chr17:40485630-40485852(-)$1	222	87	91	11.9999
GCAG	chr22:36745008-36745226(-)$1	218	203	207	11.9999
GCAG	chr17:80044944-80045178(-)$1	234	67	71	11.9999
GCAG	chr9:35403374-35403598(+)$1	224	58	62	11.9999
GCAG	chrX:47045603-47045823(+)$1	220	16	20	11.9999
GCAG	chr9:131749842-131750065(+)$1	223	40	44	11.9999
GCAG	chr3:127324888-127325129(+)$1	241	14	18	11.9999
GCAG	chr6:7404649-7404873(+)$1	224	61	65	11.9999
GCAG	chr14:24655528-24655745(-)$1	217	49	53	11.9999
GCAG	chr14:21870407-21870654(-)$1	247	18	22	11.9999
GCAG	chr20:47641887-47642110(+)$1	223	60	64	11.9999
GCAG	chr13:100635078-100635303(+)$1	225	127	131	11.9999
GCAG	chr5:620187-620403(+)$1	216	59	63	11.9999
GCAG	chr9:103090102-103090328(-)$1	226	199	203	11.9999
GCAG	chr6:31603644-31603869(+)$1	225	95	99	11.9999
GCAG	chr22:26849179-26849395(-)$1	216	82	86	11.9999
GCAG	chr1:237025464-237025679(+)$1	215	18	22	11.9999
GCAG	chr5:138651682-138651933(+)$1	251	100	104	11.9999
GCAG	chr9:138376426-138376649(+)$1	223	70	74	11.9999
GCAG	chr9:136913220-136913444(-)$1	224	57	61	11.9999
GCAG	chr6:7581491-7581736(+)$1	245	9	13	11.9999
GCAG	chr12:6707078-6707320(-)$1	242	184	188	11.9999
GCAG	chr19:13051570-13051796(+)$1	226	4	8	11.9999
GCAG	chr1:16255650-16255941(+)$1	291	49	53	11.9999
GCAG	chr15:66618263-66618484(+)$1	221	11	15	11.9999
GCAG	chr17:78290933-78291156(+)$1	223	50	54	11.9999
GCAG	chr17:26943886-26944116(-)$1	230	26	30	11.9999
GCAG	chr11:64034592-64034809(+)$1	217	81	85	11.9999
GCAG	chr3:9483238-9483471(+)$1	233	207	211	11.9999
GCAG	chr4:129782768-129783021(+)$1	253	25	29	11.9999
GCAG	chr2:85553659-85553883(-)$1	224	161	165	11.9999
GCAG	chr21:33043626-33043847(-)$1	221	40	44	11.9999
GCAG	chr11:113672238-113672457(-)$1	219	72	76	11.9999
GCAG	chr2:65299578-65299797(+)$1	219	196	200	11.9999
GCAG	chr1:29641881-29642095(+)$1	214	57	61	11.9999
GCAG	chr17:73316470-73316688(-)$1	218	50	54	11.9999
GCAG	chr6:138655894-138656104(+)$1	210	137	141	11.9999
GCAG	chr19:47492811-47493029(+)$1	218	6	10	11.9999
GCAG	chr8:67547385-67547599(-)$1	214	90	94	11.9999
gcag	chr7:27223980-27224203(-)$1	223	55	59	11.9999
GCAG	chr5:6754887-6755104(+)$1	217	163	167	11.9999
GCAG	chr19:10906647-10906868(+)$1	221	137	141	11.9999
GCAG	chrX:53239815-53240033(-)$1	218	66	70	11.9999
GCAG	chr13:21396235-21396463(-)$1	228	82	86	11.9999
GCAG	chr2:128079549-128079766(-)$1	217	40	44	11.9999
GCAG	chr11:62371387-62371613(-)$1	226	0	4	11.9999
GCAG	chr2:73676779-73677008(+)$1	229	4	8	11.9999
GCAG	chr9:131763727-131763998(+)$1	271	76	80	11.9999
GCAG	chr19:36275032-36275250(+)$1	218	101	105	11.9999
GCAG	chr16:4908981-4909205(+)$1	224	0	4	11.9999
GCAG	chr10:134219131-134219345(+)$1	214	140	144	11.9999
GCAG	chr2:96948894-96949119(-)$1	225	164	168	11.9999
GCAG	chr2:241706630-241706857(-)$1	227	91	95	11.9999
GCAG	chr8:18725170-18725385(-)$1	215	92	96	11.9999
GCAG	chr22:50960830-50961050(+)$1	220	7	11	11.9999
GCAG	chr15:101775210-101775427(-)$1	217	111	115	11.9999
GCAG	chr8:28360446-28360656(+)$1	210	12	16	11.9999
GCAG	chr17:42284556-42284780(-)$1	224	115	119	11.9999
GCAG	chr16:30535856-30536086(-)$1	230	128	132	11.9999
GCAG	chr2:230633849-230634091(-)$1	242	69	73	11.9999
GCAG	chr10:79571919-79572140(-)$1	221	38	42	11.9999
GCAG	chr20:34053508-34053729(+)$1	221	55	59	11.9999
GCAG	chr3:62187092-62187309(+)$1	217	187	191	11.9999
GCAG	chr17:20916071-20916289(-)$1	218	117	121	11.9999
GCAG	chr17:26711810-26712024(+)$1	214	49	53	11.9999
GCAG	chr9:131747162-131747386(+)$1	224	157	161	11.9999
GCAG	chr5:133897854-133898075(+)$1	221	66	70	11.9999

#otherMatches

#Struct PSSM
ccqq	chr4:6862861-6863073(+)$1	212	130	134	11.9999
d:::	chr10:103825607-103825845(+)$1	238	11	15	11.9999
"ddd	chr4:44680647-44680868(+)$1	221	145	149	11.9999
ooob	chr15:74742211-74742432(-)$1	221	80	84	11.9999
bb##	chr16:2815273-2815533(+)$1	260	39	43	11.9999
eell	chr1:6704540-6704757(-)$1	217	19	23	11.9999
bppp	chr9:135163902-135164120(-)$1	218	40	44	11.9999
ddd[	chr5:126154575-126154786(+)$1	211	157	161	11.9999
A{CC	chr17:3628355-3628578(+)$1	223	81	85	11.9999
d!!c	chr15:42032103-42032323(+)$1	220	20	24	11.9999
BBKK	chr1:151378014-151378238(-)$1	224	19	23	11.9999
????	chr1:242023841-242024062(+)$1	221	162	166	11.9999
DDDC	chr17:40485630-40485852(-)$1	222	87	91	11.9999
cc::	chr22:36745008-36745226(-)$1	218	203	207	11.9999
f333	chr17:80044944-80045178(-)$1	234	67	71	11.9999
ffff	chr9:35403374-35403598(+)$1	224	58	62	11.9999
dddd	chrX:47045603-47045823(+)$1	220	16	20	11.9999
ffff	chr9:131749842-131750065(+)$1	223	40	44	11.9999
EEEE	chr3:127324888-127325129(+)$1	241	14	18	11.9999
gggg	chr6:7404649-7404873(+)$1	224	61	65	11.9999
2bb]	chr14:24655528-24655745(-)$1	217	49	53	11.9999
CCC{	chr14:21870407-21870654(-)$1	247	18	22	11.9999
GG:e	chr20:47641887-47642110(+)$1	223	60	64	11.9999
eeee	chr13:100635078-100635303(+)$1	225	127	131	11.9999
b]cc	chr5:620187-620403(+)$1	216	59	63	11.9999
mmmb	chr9:103090102-103090328(-)$1	226	199	203	11.9999
$ccc	chr6:31603644-31603869(+)$1	225	95	99	11.9999
hhhh	chr22:26849179-26849395(-)$1	216	82	86	11.9999
dd!!	chr1:237025464-237025679(+)$1	215	18	22	11.9999
f]dd	chr5:138651682-138651933(+)$1	251	100	104	11.9999
ff[c	chr9:138376426-138376649(+)$1	223	70	74	11.9999
bb!!	chr9:136913220-136913444(-)$1	224	57	61	11.9999
DDDD	chr6:7581491-7581736(+)$1	245	9	13	11.9999
]ddd	chr12:6707078-6707320(-)$1	242	184	188	11.9999
###d	chr19:13051570-13051796(+)$1	226	4	8	11.9999
]ggg	chr1:16255650-16255941(+)$1	291	49	53	11.9999
qqqq	chr15:66618263-66618484(+)$1	221	11	15	11.9999
hhhh	chr17:78290933-78291156(+)$1	223	50	54	11.9999
b]ff	chr17:26943886-26944116(-)$1	230	26	30	11.9999
cccd	chr11:64034592-64034809(+)$1	217	81	85	11.9999
qqee	chr3:9483238-9483471(+)$1	233	207	211	11.9999
]bb:	chr4:129782768-129783021(+)$1	253	25	29	11.9999
dd[b	chr2:85553659-85553883(-)$1	224	161	165	11.9999
ssss	chr21:33043626-33043847(-)$1	221	40	44	11.9999
2hhh	chr11:113672238-113672457(-)$1	219	72	76	11.9999
ffff	chr2:65299578-65299797(+)$1	219	196	200	11.9999
EEEE	chr1:29641881-29642095(+)$1	214	57	61	11.9999
d22b	chr17:73316470-73316688(-)$1	218	50	54	11.9999
bbb!	chr6:138655894-138656104(+)$1	210	137	141	11.9999
GGGG	chr19:47492811-47493029(+)$1	218	6	10	11.9999
:fff	chr8:67547385-67547599(-)$1	214	90	94	11.9999
bb::	chr7:27223980-27224203(-)$1	223	55	59	11.9999
uuuu	chr5:6754887-6755104(+)$1	217	163	167	11.9999
ff]d	chr19:10906647-10906868(+)$1	221	137	141	11.9999
gggg	chrX:53239815-53240033(-)$1	218	66	70	11.9999
333e	chr13:21396235-21396463(-)$1	228	82	86	11.9999
:::b	chr2:128079549-128079766(-)$1	217	40	44	11.9999
::::	chr11:62371387-62371613(-)$1	226	0	4	11.9999
:DDD	chr2:73676779-73677008(+)$1	229	4	8	11.9999
hhhh	chr9:131763727-131763998(+)$1	271	76	80	11.9999
ffdd	chr19:36275032-36275250(+)$1	218	101	105	11.9999
:::h	chr16:4908981-4909205(+)$1	224	0	4	11.9999
[a$$	chr10:134219131-134219345(+)$1	214	140	144	11.9999
bb]a	chr2:96948894-96949119(-)$1	225	164	168	11.9999
DKKB	chr2:241706630-241706857(-)$1	227	91	95	11.9999
b[ff	chr8:18725170-18725385(-)$1	215	92	96	11.9999
FEEE	chr22:50960830-50961050(+)$1	220	7	11	11.9999
ee44	chr15:101775210-101775427(-)$1	217	111	115	11.9999
#eee	chr8:28360446-28360656(+)$1	210	12	16	11.9999
ddmm	chr17:42284556-42284780(-)$1	224	115	119	11.9999
FFFF	chr16:30535856-30536086(-)$1	230	128	132	11.9999
!a##	chr2:230633849-230634091(-)$1	242	69	73	11.9999
HHHH	chr10:79571919-79572140(-)$1	221	38	42	11.9999
hhhh	chr20:34053508-34053729(+)$1	221	55	59	11.9999
ppff	chr3:62187092-62187309(+)$1	217	187	191	11.9999
iiii	chr17:20916071-20916289(-)$1	218	117	121	11.9999
ddgg	chr17:26711810-26712024(+)$1	214	49	53	11.9999
hhhh	chr9:131747162-131747386(+)$1	224	157	161	11.9999
ddd]	chr5:133897854-133898075(+)$1	221	66	70	11.9999

#DB
((..	chr4:6862861-6863073(+)$1	1	130	134	11.9999
)...	chr10:103825607-103825845(+)$1	1	11	15	11.9999
.(((	chr4:44680647-44680868(+)$1	1	145	149	11.9999
...)	chr15:74742211-74742432(-)$1	1	80	84	11.9999
((..	chr16:2815273-2815533(+)$1	1	39	43	11.9999
((..	chr1:6704540-6704757(-)$1	1	19	23	11.9999
(...	chr9:135163902-135164120(-)$1	1	40	44	11.9999
(((.	chr5:126154575-126154786(+)$1	1	157	161	11.9999
(.((	chr17:3628355-3628578(+)$1	1	81	85	11.9999
(..(	chr15:42032103-42032323(+)$1	1	20	24	11.9999
((..	chr1:151378014-151378238(-)$1	1	19	23	11.9999
....	chr1:242023841-242024062(+)$1	1	162	166	11.9999
((((	chr17:40485630-40485852(-)$1	1	87	91	11.9999
))..	chr22:36745008-36745226(-)$1	1	203	207	11.9999
)...	chr17:80044944-80045178(-)$1	1	67	71	11.9999
((((	chr9:35403374-35403598(+)$1	1	58	62	11.9999
((((	chrX:47045603-47045823(+)$1	1	16	20	11.9999
((((	chr9:131749842-131750065(+)$1	1	40	44	11.9999
((((	chr3:127324888-127325129(+)$1	1	14	18	11.9999
))))	chr6:7404649-7404873(+)$1	1	61	65	11.9999
.)).	chr14:24655528-24655745(-)$1	1	49	53	11.9999
(((.	chr14:21870407-21870654(-)$1	1	18	22	11.9999
((.(	chr20:47641887-47642110(+)$1	1	60	64	11.9999
((((	chr13:100635078-100635303(+)$1	1	127	131	11.9999
).))	chr5:620187-620403(+)$1	1	59	63	11.9999
...)	chr9:103090102-103090328(-)$1	1	199	203	11.9999
.(((	chr6:31603644-31603869(+)$1	1	95	99	11.9999
((((	chr22:26849179-26849395(-)$1	1	82	86	11.9999
((..	chr1:237025464-237025679(+)$1	1	18	22	11.9999
).))	chr5:138651682-138651933(+)$1	1	100	104	11.9999
((.(	chr9:138376426-138376649(+)$1	1	70	74	11.9999
((..	chr9:136913220-136913444(-)$1	1	57	61	11.9999
((((	chr6:7581491-7581736(+)$1	1	9	13	11.9999
.)))	chr12:6707078-6707320(-)$1	1	184	188	11.9999
...(	chr19:13051570-13051796(+)$1	1	4	8	11.9999
.)))	chr1:16255650-16255941(+)$1	1	49	53	11.9999
....	chr15:66618263-66618484(+)$1	1	11	15	11.9999
))))	chr17:78290933-78291156(+)$1	1	50	54	11.9999
).))	chr17:26943886-26944116(-)$1	1	26	30	11.9999
((((	chr11:64034592-64034809(+)$1	1	81	85	11.9999
..))	chr3:9483238-9483471(+)$1	1	207	211	11.9999
.)).	chr4:129782768-129783021(+)$1	1	25	29	11.9999
((.(	chr2:85553659-85553883(-)$1	1	161	165	11.9999
....	chr21:33043626-33043847(-)$1	1	40	44	11.9999
.)))	chr11:113672238-113672457(-)$1	1	72	76	11.9999
))))	chr2:65299578-65299797(+)$1	1	196	200	11.9999
((((	chr1:29641881-29642095(+)$1	1	57	61	11.9999
)..)	chr17:73316470-73316688(-)$1	1	50	54	11.9999
(((.	chr6:138655894-138656104(+)$1	1	137	141	11.9999
((((	chr19:47492811-47493029(+)$1	1	6	10	11.9999
.(((	chr8:67547385-67547599(-)$1	1	90	94	11.9999
))..	chr7:27223980-27224203(-)$1	1	55	59	11.9999
....	chr5:6754887-6755104(+)$1	1	163	167	11.9999
)).)	chr19:10906647-10906868(+)$1	1	137	141	11.9999
))))	chrX:53239815-53240033(-)$1	1	66	70	11.9999
...)	chr13:21396235-21396463(-)$1	1	82	86	11.9999
...(	chr2:128079549-128079766(-)$1	1	40	44	11.9999
....	chr11:62371387-62371613(-)$1	1	0	4	11.9999
.(((	chr2:73676779-73677008(+)$1	1	4	8	11.9999
))))	chr9:131763727-131763998(+)$1	1	76	80	11.9999
))))	chr19:36275032-36275250(+)$1	1	101	105	11.9999
...(	chr16:4908981-4909205(+)$1	1	0	4	11.9999
.(..	chr10:134219131-134219345(+)$1	1	140	144	11.9999
)).)	chr2:96948894-96949119(-)$1	1	164	168	11.9999
(..(	chr2:241706630-241706857(-)$1	1	91	95	11.9999
(.((	chr8:18725170-18725385(-)$1	1	92	96	11.9999
((((	chr22:50960830-50961050(+)$1	1	7	11	11.9999
))..	chr15:101775210-101775427(-)$1	1	111	115	11.9999
.(((	chr8:28360446-28360656(+)$1	1	12	16	11.9999
((..	chr17:42284556-42284780(-)$1	1	115	119	11.9999
))))	chr16:30535856-30536086(-)$1	1	128	132	11.9999
.(..	chr2:230633849-230634091(-)$1	1	69	73	11.9999
((((	chr10:79571919-79572140(-)$1	1	38	42	11.9999
))))	chr20:34053508-34053729(+)$1	1	55	59	11.9999
..))	chr3:62187092-62187309(+)$1	1	187	191	11.9999
))))	chr17:20916071-20916289(-)$1	1	117	121	11.9999
((((	chr17:26711810-26712024(+)$1	1	49	53	11.9999
))))	chr9:131747162-131747386(+)$1	1	157	161	11.9999
))).	chr5:133897854-133898075(+)$1	1	66	70	11.9999

#PSSM
G : 0.98	g : 0.01	
C : 0.98	c : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m1_run1.nuc.txt

#NT
UAUUUCU	chr19:2273060-2273308(+)$1	248	189	196	12.9863
CUUUUCU	chr17:17174131-17174371(-)$1	240	31	38	13.5342
UUUUUCU	chr12:94071050-94071290(+)$1	240	161	168	17.2328
UUUUUAU	chr1:150445810-150446050(+)$1	240	72	79	13.2602
AUUUUCU	chr9:91090592-91090841(+)$1	249	120	127	13.2602
CUUUUCU	chr12:6438139-6438379(-)$1	240	44	51	13.5342
CUUUUCU	chr3:49547767-49548007(+)$1	240	66	73	13.5342
UUUUUCU	chr7:6062875-6063115(+)$1	240	45	52	17.2328
UUUUUCC	chr12:122716811-122717051(-)$1	240	109	116	12.7808
UUGUUCU	chr19:47567489-47567729(-)$1	240	54	61	12.6438
uuuuuCU	chr8:26268706-26268946(+)$1	240	117	124	17.2328
UUUUGCU	chr14:74181737-74182044(-)$1	307	39	46	13.1232
UUUUUCU	chr3:66429795-66430035(-)$1	240	209	216	17.2328
UUUUUCU	chr16:74485804-74486044(-)$1	240	198	205	17.2328
UUUAUCU	chr17:7362592-7362832(-)$1	240	73	80	12.7808
UAUUUCU	chr7:99632036-99632316(+)$1	280	213	220	12.9863
UUUUUCU	chr12:21669393-21669633(+)$1	240	128	135	17.2328
UUUCUCU	chr3:129034924-129035164(-)$1	240	113	120	12.8493
GUUUUCU	chr12:53806555-53806795(+)$1	240	217	224	13.4657
UUUUUUU	chr6:34557943-34558183(-)$1	240	229	236	13.3287
UUUUUCU	chr12:26225440-26225680(+)$1	240	98	105	17.2328
UUUUUCC	chr16:11643107-11643347(-)$1	240	186	193	12.7808
UUUUUAU	chr10:114925807-114926047(+)$1	240	153	160	13.2602
UUUCUCU	chr15:66180081-66180321(+)$1	240	101	108	12.8493
UUUUCCU	chr1:44443701-44443981(+)$1	280	24	31	13.2602
UUUUUUU	chr2:10269403-10269643(+)$1	240	141	148	13.3287
UUUUUAU	chr3:122927991-122928231(+)$1	240	19	26	13.2602
UUUUUCU	chr6:83878736-83878976(-)$1	240	156	163	17.2328
UCUUUCU	chr4:761470-761710(+)$1	240	40	47	13.0547
UUUUUCU	chr14:71576947-71577187(+)$1	240	51	58	17.2328
UUUUCCU	chr12:120882300-120882582(-)$1	282	44	51	13.2602
CUUUUCU	chr5:134086932-134087172(+)$1	240	164	171	13.5342
GUUUUCU	chr17:79524312-79524552(-)$1	240	139	146	13.4657
UUUUACU	chr7:23351311-23351551(-)$1	240	120	127	13.0547
UUUUUCU	chr17:27207244-27207484(-)$1	240	171	178	17.2328
uuuuccu	chr5:179156469-179156804(+)$1	335	51	58	13.2602
UUUUUGU	chr22:41575109-41575349(+)$1	240	50	57	13.1232
AUUUUCU	chr10:22616842-22617082(+)$1	240	204	211	13.2602
UUUGUCU	chr12:120638786-120639026(-)$1	240	9	16	12.7123
UUUAUCU	chr3:184085972-184086212(+)$1	240	78	85	12.7808
UUUUUCC	chr19:47113676-47113916(+)$1	240	6	13	12.7808
UUGUUCU	chr16:56501729-56501969(+)$1	240	217	224	12.6438
uuuugcu	chr2:153512089-153512329(-)$1	240	3	10	13.1232
UCUUUCU	chr4:57327266-57327514(+)$1	248	65	72	13.0547
UUUUUCU	chr5:162945910-162946150(+)$1	240	66	73	17.2328
GUUUUCU	chr17:27233051-27233291(-)$1	240	173	180	13.4657
UUUUUAU	chr4:77955861-77956101(+)$1	240	46	53	13.2602
UUUUACU	chr22:30728192-30728432(-)$1	240	223	230	13.0547
UUGUUCU	chr22:21304114-21304404(+)$1	290	48	55	12.6438
UUUUGCU	chr5:137842883-137843123(-)$1	240	19	26	13.1232
UUUUUCU	chr15:25582351-25582591(-)$1	240	18	25	17.2328
CUUUUCU	chr17:40128610-40128850(-)$1	240	48	55	13.5342
UUUUUCC	chr20:62571225-62571465(-)$1	240	48	55	12.7808
UUUUUUU	chr1:53692523-53692763(-)$1	240	113	120	13.3287
UUUUUCU	chr7:44618538-44618778(-)$1	240	171	178	17.2328
UAUUUCU	chr2:66799351-66799591(+)$1	240	129	136	12.9863
GUUUUCU	chr1:1718091-1718331(-)$1	240	76	83	13.4657
GUUUUCU	chr6:30558964-30559204(+)$1	240	188	195	13.4657
UUUUCCU	chr5:172752851-172753091(-)$1	240	66	73	13.2602
UGUUUCU	chr6:4061480-4061720(+)$1	240	125	132	12.8493
UUUUUUU	chr20:2446262-2446542(-)$1	280	47	54	13.3287
UUUUUCU	chr8:26228469-26228709(+)$1	240	190	197	17.2328
UUUUUGU	chr22:32080572-32080812(-)$1	240	1	8	13.1232
UUUUUCU	chr14:38059329-38059599(-)$1	270	220	227	17.2328
UUUUUUU	chr11:121178272-121178512(+)$1	240	4	11	13.3287
UCUUUCU	chr15:91463695-91463935(+)$1	240	149	156	13.0547
UUUUUCU	chr17:76987831-76988071(-)$1	240	172	179	17.2328
UUUUUCU	chr2:128620376-128620675(-)$1	299	144	151	17.2328
UUUCUCU	chr19:39327076-39327336(-)$1	260	14	21	12.8493
UCUUUCU	chr16:85812936-85813176(-)$1	240	122	129	13.0547
UUUUUCU	chr7:56131320-56131560(+)$1	240	205	212	17.2328
CUUUUCU	chr8:102211231-102211471(-)$1	240	67	74	13.5342

#otherMatches

#Struct PSSM
GGGGGGc	chr15:49171197-49171437(+)$1	240	16	23	13.2602
EE::::g	chr19:2273060-2273308(+)$1	248	189	196	12.9863
MEEEEE:	chr17:17174131-17174371(-)$1	240	31	38	13.5342
%%%%ccc	chr12:94071050-94071290(+)$1	240	161	168	17.2328
+++++++	chr1:150445810-150446050(+)$1	240	72	79	13.2602
"""ffff	chr9:91090592-91090841(+)$1	249	120	127	13.2602
eeooooo	chr12:6438139-6438379(-)$1	240	44	51	13.5342
:::::::	chr3:49547767-49548007(+)$1	240	66	73	13.5342
e%%%%%%	chr7:6062875-6063115(+)$1	240	45	52	17.2328
uuuubbe	chr12:122716811-122717051(-)$1	240	109	116	12.7808
22dddd:	chr19:47567489-47567729(-)$1	240	54	61	12.6438
^^^^^^^	chr8:26268706-26268946(+)$1	240	117	124	17.2328
d[ddddr	chr14:74181737-74182044(-)$1	307	39	46	13.1232
mmmmfff	chr3:66429795-66430035(-)$1	240	209	216	17.2328
==::::F	chr16:74485804-74486044(-)$1	240	198	205	17.2328
ssssbb6	chr17:7362592-7362832(-)$1	240	73	80	12.7808
::fffff	chr7:99632036-99632316(+)$1	280	213	220	12.9863
eee^^^^	chr12:21669393-21669633(+)$1	240	128	135	17.2328
333a]dd	chr3:129034924-129035164(-)$1	240	113	120	12.8493
JJJJJJJ	chr12:53806555-53806795(+)$1	240	217	224	13.4657
JJJJJJJ	chr6:34557943-34558183(-)$1	240	229	236	13.3287
=======	chr12:26225440-26225680(+)$1	240	98	105	17.2328
zzzzzzz	chr16:11643107-11643347(-)$1	240	186	193	12.7808
JJJJJ::	chr10:114925807-114926047(+)$1	240	153	160	13.2602
e:::fff	chr15:66180081-66180321(+)$1	240	101	108	12.8493
dd$$$$$	chr1:44443701-44443981(+)$1	280	24	31	13.2602
=======	chr2:10269403-10269643(+)$1	240	141	148	13.3287
bmmmmbb	chr3:122927991-122928231(+)$1	240	19	26	13.2602
ffvvvvv	chr6:83878736-83878976(-)$1	240	156	163	17.2328
bb[dddd	chr4:761470-761710(+)$1	240	40	47	13.0547
::::::e	chr14:71576947-71577187(+)$1	240	51	58	17.2328
b22eeee	chr12:120882300-120882582(-)$1	282	44	51	13.2602
xxxxxxx	chr5:134086932-134087172(+)$1	240	164	171	13.5342
:======	chr17:79524312-79524552(-)$1	240	139	146	13.4657
::eeeee	chr7:23351311-23351551(-)$1	240	120	127	13.0547
^^^^^^^	chr17:27207244-27207484(-)$1	240	171	178	17.2328
d22ccc:	chr5:179156469-179156804(+)$1	335	51	58	13.2602
wiiiiii	chr22:41575109-41575349(+)$1	240	50	57	13.1232
hpppppp	chr10:22616842-22617082(+)$1	240	204	211	13.2602
ooooocc	chr12:120638786-120639026(-)$1	240	9	16	12.7123
=======	chr3:184085972-184086212(+)$1	240	78	85	12.7808
ooooocc	chr19:47113676-47113916(+)$1	240	6	13	12.7808
eeooooo	chr16:56501729-56501969(+)$1	240	217	224	12.6438
DLLLBBP	chr2:153512089-153512329(-)$1	240	3	10	13.1232
hhsssss	chr4:57327266-57327514(+)$1	248	65	72	13.0547
BB{CCC:	chr5:162945910-162946150(+)$1	240	66	73	17.2328
ffnnnnn	chr17:27233051-27233291(-)$1	240	173	180	13.4657
hhh"""d	chr4:77955861-77956101(+)$1	240	46	53	13.2602
c22dddd	chr22:30728192-30728432(-)$1	240	223	230	13.0547
::::::c	chr22:21304114-21304404(+)$1	290	48	55	12.6438
dddnnnn	chr5:137842883-137843123(-)$1	240	19	26	13.1232
eeee"""	chr15:25582351-25582591(-)$1	240	18	25	17.2328
+++ffff	chr17:40128610-40128850(-)$1	240	48	55	13.5342
doooooo	chr20:62571225-62571465(-)$1	240	48	55	12.7808
gggggg:	chr1:53692523-53692763(-)$1	240	113	120	13.3287
ooooccc	chr7:44618538-44618778(-)$1	240	171	178	17.2328
dssssss	chr2:66799351-66799591(+)$1	240	129	136	12.9863
=======	chr1:1718091-1718331(-)$1	240	76	83	13.4657
DYYCCC}	chr6:30558964-30559204(+)$1	240	188	195	13.4657
ffffccc	chr5:172752851-172753091(-)$1	240	66	73	13.2602
ggggggg	chr6:4061480-4061720(+)$1	240	125	132	12.8493
:gggggg	chr20:2446262-2446542(-)$1	280	47	54	13.3287
g22ffff	chr8:26228469-26228709(+)$1	240	190	197	17.2328
:::::::	chr22:32080572-32080812(-)$1	240	1	8	13.1232
!!ddddr	chr14:38059329-38059599(-)$1	270	220	227	17.2328
gggqqqq	chr11:121178272-121178512(+)$1	240	4	11	13.3287
e[fffff	chr15:91463695-91463935(+)$1	240	149	156	13.0547
::::FFF	chr17:76987831-76988071(-)$1	240	172	179	17.2328
JJJJDDD	chr2:128620376-128620675(-)$1	299	144	151	17.2328
:JJJJJJ	chr19:39327076-39327336(-)$1	260	14	21	12.8493
ppppppp	chr16:85812936-85813176(-)$1	240	122	129	13.0547
??FFFFF	chr7:56131320-56131560(+)$1	240	205	212	17.2328
dd!!bb[	chr8:102211231-102211471(-)$1	240	67	74	13.5342

#DB
(((((((	chr15:49171197-49171437(+)$1	1	16	23	13.2602
))....(	chr19:2273060-2273308(+)$1	1	189	196	12.9863
.(((((.	chr17:17174131-17174371(-)$1	1	31	38	13.5342
....(((	chr12:94071050-94071290(+)$1	1	161	168	17.2328
.......	chr1:150445810-150446050(+)$1	1	72	79	13.2602
...((((	chr9:91090592-91090841(+)$1	1	120	127	13.2602
((.....	chr12:6438139-6438379(-)$1	1	44	51	13.5342
.......	chr3:49547767-49548007(+)$1	1	66	73	13.5342
(......	chr7:6062875-6063115(+)$1	1	45	52	17.2328
....)))	chr12:122716811-122717051(-)$1	1	109	116	12.7808
..)))).	chr19:47567489-47567729(-)$1	1	54	61	12.6438
.......	chr8:26268706-26268946(+)$1	1	117	124	17.2328
(.((((.	chr14:74181737-74182044(-)$1	1	39	46	13.1232
....)))	chr3:66429795-66430035(-)$1	1	209	216	17.2328
))....)	chr16:74485804-74486044(-)$1	1	198	205	17.2328
....)).	chr17:7362592-7362832(-)$1	1	73	80	12.7808
..(((((	chr7:99632036-99632316(+)$1	1	213	220	12.9863
(((....	chr12:21669393-21669633(+)$1	1	128	135	17.2328
...).))	chr3:129034924-129035164(-)$1	1	113	120	12.8493
)))))))	chr12:53806555-53806795(+)$1	1	217	224	13.4657
)))))))	chr6:34557943-34558183(-)$1	1	229	236	13.3287
)))))))	chr12:26225440-26225680(+)$1	1	98	105	17.2328
.......	chr16:11643107-11643347(-)$1	1	186	193	12.7808
)))))..	chr10:114925807-114926047(+)$1	1	153	160	13.2602
)...(((	chr15:66180081-66180321(+)$1	1	101	108	12.8493
((.....	chr1:44443701-44443981(+)$1	1	24	31	13.2602
(((((((	chr2:10269403-10269643(+)$1	1	141	148	13.3287
(....))	chr3:122927991-122928231(+)$1	1	19	26	13.2602
((.....	chr6:83878736-83878976(-)$1	1	156	163	17.2328
((.((((	chr4:761470-761710(+)$1	1	40	47	13.0547
......(	chr14:71576947-71577187(+)$1	1	51	58	17.2328
)..))))	chr12:120882300-120882582(-)$1	1	44	51	13.2602
.......	chr5:134086932-134087172(+)$1	1	164	171	13.5342
.((((((	chr17:79524312-79524552(-)$1	1	139	146	13.4657
..(((((	chr7:23351311-23351551(-)$1	1	120	127	13.0547
.......	chr17:27207244-27207484(-)$1	1	171	178	17.2328
)..))).	chr5:179156469-179156804(+)$1	1	51	58	13.2602
.))))))	chr22:41575109-41575349(+)$1	1	50	57	13.1232
(......	chr10:22616842-22617082(+)$1	1	204	211	13.2602
.....))	chr12:120638786-120639026(-)$1	1	9	16	12.7123
)))))))	chr3:184085972-184086212(+)$1	1	78	85	12.7808
.....))	chr19:47113676-47113916(+)$1	1	6	13	12.7808
((.....	chr16:56501729-56501969(+)$1	1	217	224	12.6438
(...((.	chr2:153512089-153512329(-)$1	1	3	10	13.1232
((.....	chr4:57327266-57327514(+)$1	1	65	72	13.0547
((.(((.	chr5:162945910-162946150(+)$1	1	66	73	17.2328
((.....	chr17:27233051-27233291(-)$1	1	173	180	13.4657
(((...(	chr4:77955861-77956101(+)$1	1	46	53	13.2602
)..))))	chr22:30728192-30728432(-)$1	1	223	230	13.0547
......(	chr22:21304114-21304404(+)$1	1	48	55	12.6438
(((....	chr5:137842883-137843123(-)$1	1	19	26	13.1232
((((...	chr15:25582351-25582591(-)$1	1	18	25	17.2328
...((((	chr17:40128610-40128850(-)$1	1	48	55	13.5342
(......	chr20:62571225-62571465(-)$1	1	48	55	12.7808
)))))).	chr1:53692523-53692763(-)$1	1	113	120	13.3287
....)))	chr7:44618538-44618778(-)$1	1	171	178	17.2328
(......	chr2:66799351-66799591(+)$1	1	129	136	12.9863
(((((((	chr1:1718091-1718331(-)$1	1	76	83	13.4657
)..))).	chr6:30558964-30559204(+)$1	1	188	195	13.4657
)))))))	chr5:172752851-172753091(-)$1	1	66	73	13.2602
(((((((	chr6:4061480-4061720(+)$1	1	125	132	12.8493
.((((((	chr20:2446262-2446542(-)$1	1	47	54	13.3287
)..))))	chr8:26228469-26228709(+)$1	1	190	197	17.2328
.......	chr22:32080572-32080812(-)$1	1	1	8	13.1232
..((((.	chr14:38059329-38059599(-)$1	1	220	227	17.2328
(((....	chr11:121178272-121178512(+)$1	1	4	11	13.3287
(.(((((	chr15:91463695-91463935(+)$1	1	149	156	13.0547
....)))	chr17:76987831-76988071(-)$1	1	172	179	17.2328
)))))))	chr2:128620376-128620675(-)$1	1	144	151	17.2328
.((((((	chr19:39327076-39327336(-)$1	1	14	21	12.8493
.......	chr16:85812936-85813176(-)$1	1	122	129	13.0547
..)))))	chr7:56131320-56131560(+)$1	1	205	212	17.2328
((..((.	chr8:102211231-102211471(-)$1	1	67	74	13.5342

#PSSM
U : 0.78	C : 0.08	G : 0.06	u : 0.04	A : 0.02	
U : 0.84	C : 0.05	A : 0.04	u : 0.04	G : 0.01	
U : 0.91	G : 0.04	u : 0.04	
U : 0.87	u : 0.04	C : 0.04	A : 0.02	G : 0.01	
U : 0.84	C : 0.05	G : 0.02	A : 0.02	u : 0.01	c : 0.01	g : 0.01	
C : 0.82	U : 0.06	A : 0.05	c : 0.02	G : 0.02	
U : 0.91	C : 0.05	u : 0.02	

#score	1032.863013698632
#seq	73
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m2_run1.nuc.txt

#NT
UUUCU	chr1:246829043-246829268(+)$1	225	214	219	15.0000
UUUCU	chr3:19923986-19924202(-)$1	216	194	199	15.0000
UUUCU	chr11:6631096-6631319(+)$1	223	56	61	15.0000
UUUCU	chr1:162535762-162535983(+)$1	221	27	32	15.0000
UUUCU	chr11:92881740-92881964(-)$1	224	107	112	15.0000
UUUCU	chr16:18864865-18865089(-)$1	224	89	94	15.0000
UUUCU	chr2:197872484-197872703(-)$1	219	185	190	15.0000
UUUCU	chr11:62491078-62491298(-)$1	220	89	94	15.0000
UUUCU	chr1:169446845-169447067(-)$1	222	56	61	15.0000
UUUCU	chr22:29181983-29182206(+)$1	223	143	148	15.0000
UUUCU	chr6:36070303-36070525(+)$1	222	196	201	15.0000
UUUCU	chr11:18422299-18422524(+)$1	225	75	80	15.0000
UUUCU	chr17:2233717-2233937(-)$1	220	5	10	15.0000
UUUCU	chr19:33482630-33482860(-)$1	230	145	150	15.0000
UUUCU	chr20:47768144-47768364(-)$1	220	73	78	15.0000
UUUCU	chr15:78789394-78789613(+)$1	219	206	211	15.0000
UUUCU	chr6:86223691-86223911(-)$1	220	132	137	15.0000
UUUCU	chr4:56726569-56726791(+)$1	222	68	73	15.0000
UUUCU	chr1:154246203-154246426(+)$1	223	37	42	15.0000
UUUCU	chr12:132522213-132522433(+)$1	220	112	117	15.0000
UUUCU	chr2:44174358-44174578(-)$1	220	43	48	15.0000
UUUCU	chr12:40668325-40668550(+)$1	225	102	107	15.0000
UUUCU	chr18:12725409-12725629(+)$1	220	114	119	15.0000
UUUCU	chr19:3980539-3980769(-)$1	230	46	51	15.0000
UUUCU	chr3:111603720-111603944(+)$1	224	114	119	15.0000
UUUCU	chr6:43170795-43171025(+)$1	230	5	10	15.0000
UUUCU	chr1:12065828-12066046(+)$1	218	75	80	15.0000
UUUCU	chr17:3618104-3618331(-)$1	227	36	41	15.0000
UUUCU	chr14:69853628-69853851(-)$1	223	43	48	15.0000
UUUCU	chr9:5069908-5070130(+)$1	222	52	57	15.0000
UUUCU	chr2:24475250-24475480(-)$1	230	37	42	15.0000
UUUCU	chr1:67516039-67516259(-)$1	220	154	159	15.0000
UUUCU	chr2:170785148-170785374(+)$1	226	68	73	15.0000
UUUCU	chr10:102039783-102040013(-)$1	230	11	16	15.0000
UUUCU	chr11:47189463-47189683(-)$1	220	20	25	15.0000
UUUCU	chr5:72189229-72189447(+)$1	218	168	173	15.0000
UUUCU	chr3:167413335-167413553(-)$1	218	153	158	15.0000
UUUCU	chr5:68467007-68467233(+)$1	226	160	165	15.0000
UUUCU	chr3:113442754-113442977(-)$1	223	205	210	15.0000
UUUCU	chr16:68107850-68108080(+)$1	230	73	78	15.0000
UUUCU	chr1:186106948-186107169(+)$1	221	193	198	15.0000
UUUCU	chr8:67488219-67488443(+)$1	224	137	142	15.0000
UUUCU	chr15:55621869-55622107(+)$1	238	44	49	15.0000
UUUCU	chr2:20885284-20885514(-)$1	230	87	92	15.0000
UUUCU	chr15:87097557-87097780(-)$1	223	117	122	15.0000
UUUCU	chr3:113524238-113524463(+)$1	225	144	149	15.0000
uuucu	chr10:22828834-22829064(-)$1	230	195	200	15.0000
UUUCU	chr1:84961510-84961740(+)$1	230	47	52	15.0000
UUUCU	chr1:91382360-91382581(-)$1	221	25	30	15.0000
UUUCU	chr9:108226471-108226704(+)$1	233	31	36	15.0000
UUUCU	chr13:111919862-111920092(+)$1	230	23	28	15.0000
UUUCU	chr5:77423828-77424048(-)$1	220	206	211	15.0000
UUUCU	chr14:31062658-31062882(+)$1	224	209	214	15.0000
UUUCU	chr14:99871530-99871747(-)$1	217	13	18	15.0000
UUUCU	chr2:136872726-136872944(-)$1	218	187	192	15.0000
UUUCU	chr9:127920499-127920725(-)$1	226	219	224	15.0000
UUUCU	chr12:53854757-53854979(+)$1	222	7	12	15.0000
UUUCU	chr1:220206833-220207054(-)$1	221	27	32	15.0000
UUUCU	chr19:23543982-23544212(-)$1	230	197	202	15.0000

#otherMatches

#Struct PSSM
ffff!	chr7:128585822-128586041(+)$1	219	60	65	15.0000
H::::	chr1:246829043-246829268(+)$1	225	214	219	15.0000
e]eee	chr3:19923986-19924202(-)$1	216	194	199	15.0000
uuuuu	chr11:6631096-6631319(+)$1	223	56	61	15.0000
:::::	chr1:162535762-162535983(+)$1	221	27	32	15.0000
dddd3	chr11:92881740-92881964(-)$1	224	107	112	15.0000
HHHHH	chr16:18864865-18865089(-)$1	224	89	94	15.0000
:::::	chr2:197872484-197872703(-)$1	219	185	190	15.0000
:::::	chr11:62491078-62491298(-)$1	220	89	94	15.0000
:::::	chr1:169446845-169447067(-)$1	222	56	61	15.0000
::::C	chr22:29181983-29182206(+)$1	223	143	148	15.0000
GGGGG	chr6:36070303-36070525(+)$1	222	196	201	15.0000
GGGKK	chr11:18422299-18422524(+)$1	225	75	80	15.0000
fpppp	chr17:2233717-2233937(-)$1	220	5	10	15.0000
d333d	chr19:33482630-33482860(-)$1	230	145	150	15.0000
:::::	chr20:47768144-47768364(-)$1	220	73	78	15.0000
ggggg	chr15:78789394-78789613(+)$1	219	206	211	15.0000
$$$$$	chr6:86223691-86223911(-)$1	220	132	137	15.0000
ggggg	chr4:56726569-56726791(+)$1	222	68	73	15.0000
rrrrr	chr1:154246203-154246426(+)$1	223	37	42	15.0000
d:ddd	chr12:132522213-132522433(+)$1	220	112	117	15.0000
88888	chr2:44174358-44174578(-)$1	220	43	48	15.0000
ooocc	chr12:40668325-40668550(+)$1	225	102	107	15.0000
7777f	chr18:12725409-12725629(+)$1	220	114	119	15.0000
sssss	chr19:3980539-3980769(-)$1	230	46	51	15.0000
::eee	chr3:111603720-111603944(+)$1	224	114	119	15.0000
:::DD	chr6:43170795-43171025(+)$1	230	5	10	15.0000
gggpp	chr1:12065828-12066046(+)$1	218	75	80	15.0000
JJJJJ	chr17:3618104-3618331(-)$1	227	36	41	15.0000
+++++	chr14:69853628-69853851(-)$1	223	43	48	15.0000
33eee	chr9:5069908-5070130(+)$1	222	52	57	15.0000
reeee	chr2:24475250-24475480(-)$1	230	37	42	15.0000
GGGGG	chr1:67516039-67516259(-)$1	220	154	159	15.0000
fffff	chr2:170785148-170785374(+)$1	226	68	73	15.0000
OOOOO	chr10:102039783-102040013(-)$1	230	11	16	15.0000
KAMMM	chr11:47189463-47189683(-)$1	220	20	25	15.0000
eeeeg	chr5:72189229-72189447(+)$1	218	168	173	15.0000
ddd]c	chr3:167413335-167413553(-)$1	218	153	158	15.0000
ddd]d	chr5:68467007-68467233(+)$1	226	160	165	15.0000
:::::	chr3:113442754-113442977(-)$1	223	205	210	15.0000
MMMBB	chr16:68107850-68108080(+)$1	230	73	78	15.0000
vvvvg	chr1:186106948-186107169(+)$1	221	193	198	15.0000
#eeee	chr8:67488219-67488443(+)$1	224	137	142	15.0000
IIIII	chr15:55621869-55622107(+)$1	238	44	49	15.0000
eeeee	chr2:20885284-20885514(-)$1	230	87	92	15.0000
eeeee	chr15:87097557-87097780(-)$1	223	117	122	15.0000
bmmmm	chr3:113524238-113524463(+)$1	225	144	149	15.0000
:::::	chr10:22828834-22829064(-)$1	230	195	200	15.0000
G:ccc	chr1:84961510-84961740(+)$1	230	47	52	15.0000
IIIII	chr1:91382360-91382581(-)$1	221	25	30	15.0000
:ffff	chr9:108226471-108226704(+)$1	233	31	36	15.0000
d$$$$	chr13:111919862-111920092(+)$1	230	23	28	15.0000
:::::	chr5:77423828-77424048(-)$1	220	206	211	15.0000
22fff	chr14:31062658-31062882(+)$1	224	209	214	15.0000
:::::	chr14:99871530-99871747(-)$1	217	13	18	15.0000
fff33	chr2:136872726-136872944(-)$1	218	187	192	15.0000
88eee	chr9:127920499-127920725(-)$1	226	219	224	15.0000
HHHee	chr12:53854757-53854979(+)$1	222	7	12	15.0000
gggg:	chr1:220206833-220207054(-)$1	221	27	32	15.0000
hhhhh	chr19:23543982-23544212(-)$1	230	197	202	15.0000

#DB
((((.	chr7:128585822-128586041(+)$1	1	60	65	15.0000
)....	chr1:246829043-246829268(+)$1	1	214	219	15.0000
).)))	chr3:19923986-19924202(-)$1	1	194	199	15.0000
.....	chr11:6631096-6631319(+)$1	1	56	61	15.0000
.....	chr1:162535762-162535983(+)$1	1	27	32	15.0000
)))).	chr11:92881740-92881964(-)$1	1	107	112	15.0000
)))))	chr16:18864865-18865089(-)$1	1	89	94	15.0000
.....	chr2:197872484-197872703(-)$1	1	185	190	15.0000
.....	chr11:62491078-62491298(-)$1	1	89	94	15.0000
.....	chr1:169446845-169447067(-)$1	1	56	61	15.0000
....)	chr22:29181983-29182206(+)$1	1	143	148	15.0000
)))))	chr6:36070303-36070525(+)$1	1	196	201	15.0000
(((..	chr11:18422299-18422524(+)$1	1	75	80	15.0000
(....	chr17:2233717-2233937(-)$1	1	5	10	15.0000
)...)	chr19:33482630-33482860(-)$1	1	145	150	15.0000
.....	chr20:47768144-47768364(-)$1	1	73	78	15.0000
)))))	chr15:78789394-78789613(+)$1	1	206	211	15.0000
.....	chr6:86223691-86223911(-)$1	1	132	137	15.0000
)))))	chr4:56726569-56726791(+)$1	1	68	73	15.0000
.....	chr1:154246203-154246426(+)$1	1	37	42	15.0000
).(((	chr12:132522213-132522433(+)$1	1	112	117	15.0000
.....	chr2:44174358-44174578(-)$1	1	43	48	15.0000
...))	chr12:40668325-40668550(+)$1	1	102	107	15.0000
....)	chr18:12725409-12725629(+)$1	1	114	119	15.0000
.....	chr19:3980539-3980769(-)$1	1	46	51	15.0000
..(((	chr3:111603720-111603944(+)$1	1	114	119	15.0000
...((	chr6:43170795-43171025(+)$1	1	5	10	15.0000
(((..	chr1:12065828-12066046(+)$1	1	75	80	15.0000
(((((	chr17:3618104-3618331(-)$1	1	36	41	15.0000
.....	chr14:69853628-69853851(-)$1	1	43	48	15.0000
..)))	chr9:5069908-5070130(+)$1	1	52	57	15.0000
.))))	chr2:24475250-24475480(-)$1	1	37	42	15.0000
)))))	chr1:67516039-67516259(-)$1	1	154	159	15.0000
(((((	chr2:170785148-170785374(+)$1	1	68	73	15.0000
.....	chr10:102039783-102040013(-)$1	1	11	16	15.0000
.(...	chr11:47189463-47189683(-)$1	1	20	25	15.0000
)))))	chr5:72189229-72189447(+)$1	1	168	173	15.0000
))).)	chr3:167413335-167413553(-)$1	1	153	158	15.0000
))).)	chr5:68467007-68467233(+)$1	1	160	165	15.0000
.....	chr3:113442754-113442977(-)$1	1	205	210	15.0000
...((	chr16:68107850-68108080(+)$1	1	73	78	15.0000
....)	chr1:186106948-186107169(+)$1	1	193	198	15.0000
.((((	chr8:67488219-67488443(+)$1	1	137	142	15.0000
(((((	chr15:55621869-55622107(+)$1	1	44	49	15.0000
)))))	chr2:20885284-20885514(-)$1	1	87	92	15.0000
)((((	chr15:87097557-87097780(-)$1	1	117	122	15.0000
(....	chr3:113524238-113524463(+)$1	1	144	149	15.0000
.....	chr10:22828834-22829064(-)$1	1	195	200	15.0000
(.(((	chr1:84961510-84961740(+)$1	1	47	52	15.0000
(((((	chr1:91382360-91382581(-)$1	1	25	30	15.0000
.((((	chr9:108226471-108226704(+)$1	1	31	36	15.0000
(....	chr13:111919862-111920092(+)$1	1	23	28	15.0000
.....	chr5:77423828-77424048(-)$1	1	206	211	15.0000
..)))	chr14:31062658-31062882(+)$1	1	209	214	15.0000
.....	chr14:99871530-99871747(-)$1	1	13	18	15.0000
)))..	chr2:136872726-136872944(-)$1	1	187	192	15.0000
..)))	chr9:127920499-127920725(-)$1	1	219	224	15.0000
(((((	chr12:53854757-53854979(+)$1	1	7	12	15.0000
)))).	chr1:220206833-220207054(-)$1	1	27	32	15.0000
(((((	chr19:23543982-23544212(-)$1	1	197	202	15.0000

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	

#score	900.0000000000005
#seq	60
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_CDS_m3_run2.nuc.txt

#NT
cuacucaccuaccucuccaagcuauucacccaccucccccagcuacucacccacuuccccaaguuacucacccaccagcccGAACUAUUCUCCAACCAGUCCCAAUUACACCCCAACAUCACCCAGCUACAGCCCGACAUCACCCAGCUAUUCACCUACUAGUCCCAACUACACACCUACCAGCCCUAACUACAGCCCAACCUCUCCAAGCUACUCUCCAACAUCACCCAGC	chr17:7416738-7416980(+)$1	242	1	233	488.5000

#otherMatches

#Struct PSSM
::::::DDDD::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff:bboooooobb::::::::::::::::::::::::::DDDD::::::::::::::::::::::eeeeerrrrrrrrreee	chr17:7417184-7417439(+)$1	255	17	249	488.5000
CC:::::::::::::::::ddddzzzzzzzzzzzzzzzzzdddd::::::::ddddmmmmdddd:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::bbmmmmbb:::::::::::::ccc))))))))))ddddmmmmdddd0000000000ccc:::::::::cccvvvvvvvvvvvvvccc:::::::::::::::::CCC	chr17:7416738-7416980(+)$1	242	1	233	488.5000

#DB
......((((..............................................................................................((((((....................................)))))).((......))..........................))))......................(((((.........)))	chr17:7417184-7417439(+)$1	1	17	249	488.5000
((.................((((.................))))........((((....)))).............................................................((....)).............(((..........((((....))))..........))).........(((.............))).................)))	chr17:7416738-7416980(+)$1	1	1	233	488.5000

#PSSM
G : 0.50	c : 0.50	
U : 0.50	u : 0.50	
A : 0.50	a : 0.50	
C : 0.50	c : 0.50	
U : 0.50	u : 0.50	
C : 0.50	c : 0.50	
G : 0.50	a : 0.50	
C : 0.50	c : 0.50	
C : 0.50	c : 0.50	
U : 0.50	u : 0.50	
A : 0.50	a : 0.50	
C : 0.50	c : 0.50	
C : 0.50	c : 0.50	
A : 0.50	u : 0.50	
G : 0.50	c : 0.50	
U : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
c : 0.50	a : 0.50	
a : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
u : 1.00	
a : 1.00	
u : 1.00	
u : 1.00	
c : 1.00	
a : 1.00	
c : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 1.00	
c : 1.00	
a : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
c : 1.00	
c : 1.00	
a : 0.50	c : 0.50	
a : 1.00	
a : 0.50	g : 0.50	
a : 0.50	c : 0.50	
u : 1.00	
a : 1.00	
c : 1.00	
u : 1.00	
c : 1.00	
c : 0.50	a : 0.50	
c : 1.00	
c : 1.00	
a : 0.50	c : 0.50	
a : 1.00	
c : 1.00	
a : 0.50	u : 0.50	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
c : 1.00	
u : 0.50	a : 0.50	
a : 1.00	
c : 0.50	g : 0.50	
u : 1.00	
u : 1.00	
a : 1.00	
u : 0.50	c : 0.50	
u : 1.00	
c : 1.00	
c : 0.50	a : 0.50	
c : 1.00	
c : 1.00	
a : 0.50	c : 0.50	
a : 1.00	
c : 1.00	
c : 1.00	
u : 0.50	a : 0.50	
c : 0.50	g : 0.50	
u : 0.50	c : 0.50	
c : 1.00	
c : 1.00	
a : 0.50	G : 0.50	
g : 0.50	A : 0.50	
u : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	U : 0.50	
a : 0.50	U : 0.50	
c : 0.50	C : 0.50	
c : 0.50	U : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
a : 0.50	A : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
c : 0.50	G : 0.50	
u : 0.50	U : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
a : 0.50	A : 0.50	
a : 0.50	A : 0.50	
g : 0.50	U : 0.50	
u : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
c : 0.50	C : 0.50	
a : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
a : 0.50	U : 0.50	
g : 0.50	C : 0.50	
c : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
a : 0.50	A : 0.50	
c : 0.50	G : 0.50	
u : 0.50	C : 0.50	
u : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
c : 0.50	G : 0.50	
g : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	G : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
u : 0.50	U : 0.50	
c : 0.50	C : 0.50	
c : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
a : 0.50	A : 0.50	
a : 0.50	G : 0.50	
g : 0.50	C : 0.50	
u : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	U : 0.50	
u : 0.50	U : 0.50	
c : 0.50	C : 0.50	
g : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	U : 0.50	
a : 0.50	A : 0.50	
g : 0.50	G : 0.50	
c : 0.50	U : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
a : 0.50	A : 0.50	
c : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
c : 0.50	C : 0.50	
g : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	U : 0.50	
a : 0.50	A : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
u : 0.50	A : 0.50	
c : 0.50	G : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
c : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
C : 0.50	A : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
C : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
C : 1.00	
G : 0.50	A : 0.50	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
C : 0.50	G : 0.50	
C : 1.00	

#score	977.0
#seq	2
#width	232
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m1_run1.nuc.txt

#NT
UUAUU	chr19:58490764-58490994(-)$1	230	8	13	15.0000
UUAUU	chr7:151265739-151265969(-)$1	230	94	99	15.0000
UUAUU	chr9:108226463-108226693(+)$1	230	111	116	15.0000
UUAUU	chr7:43635486-43635703(-)$1	217	94	99	15.0000
UUAUU	chr3:101284383-101284613(+)$1	230	82	87	15.0000
UUAUU	chr21:34827932-34828162(-)$1	230	15	20	15.0000
UUAUU	chr12:112486042-112486266(-)$1	224	32	37	15.0000
UUAUU	chr1:205588992-205589222(-)$1	230	169	174	15.0000
UUAUU	chr4:110446430-110446666(+)$1	236	28	33	15.0000
UUAUU	chr14:45414455-45414677(-)$1	222	1	6	15.0000
UUAUU	chr2:225727321-225727551(-)$1	230	23	28	15.0000
UUAUU	chr21:15745848-15746078(-)$1	230	159	164	15.0000
UUAUU	chr12:46598028-46598258(-)$1	230	2	7	15.0000
uuauu	chr2:128528269-128528494(-)$1	225	182	187	15.0000
UUAUU	chr2:170678434-170678659(-)$1	225	11	16	15.0000
UUAUU	chr15:78780973-78781203(+)$1	230	191	196	15.0000
UUAUU	chr3:186503933-186504155(+)$1	222	171	176	15.0000
UUAUU	chr6:135514889-135515112(+)$1	223	216	221	15.0000
UUAUU	chr20:52188171-52188396(-)$1	225	70	75	15.0000
UUAUU	chr2:231940161-231940380(+)$1	219	41	46	15.0000
UUAUU	chr5:138654543-138654769(+)$1	226	57	62	15.0000
UUAUU	chr17:45740409-45740639(+)$1	230	7	12	15.0000
UUAUU	chr16:23096110-23096333(-)$1	223	24	29	15.0000
UUAUU	chr13:48934116-48934346(+)$1	230	105	110	15.0000
UUAUU	chr20:43615692-43615922(+)$1	230	65	70	15.0000
UUAUU	chr16:11066698-11066924(+)$1	226	49	54	15.0000
UUAUU	chr5:175921108-175921329(+)$1	221	99	104	15.0000
UUAUU	chr1:155447635-155447865(-)$1	230	198	203	15.0000
UUAUU	chr15:78453929-78454159(+)$1	230	204	209	15.0000
UUAUU	chr13:39588499-39588724(-)$1	225	4	9	15.0000
UUAUU	chr11:108119573-108119820(+)$1	247	69	74	15.0000
UUAUU	chr16:69727760-69727990(+)$1	230	215	220	15.0000
UUAUU	chr16:57241878-57242108(+)$1	230	31	36	15.0000
UUAUU	chr16:24560221-24560451(+)$1	230	28	33	15.0000
UUAUU	chr20:43129749-43129970(-)$1	221	192	197	15.0000
UUAUU	chr6:13639721-13639943(-)$1	222	169	174	15.0000
UUAUU	chr1:114942035-114942265(-)$1	230	7	12	15.0000
UUAUU	chr3:23573962-23574185(+)$1	223	4	9	15.0000
UUAUU	chr2:24471432-24471662(-)$1	230	195	200	15.0000
UUAUU	chr20:52194782-52195012(-)$1	230	78	83	15.0000
UUAUU	chr17:2583431-2583661(+)$1	230	78	83	15.0000
UUAUU	chr17:56428696-56428926(-)$1	230	36	41	15.0000
UUAUU	chr13:98658309-98658535(+)$1	226	173	178	15.0000
UUAUU	chr2:135848538-135848761(+)$1	223	13	18	15.0000
UUAUU	chr17:48941238-48941468(-)$1	230	121	126	15.0000
UUAUU	chr8:86021768-86021998(+)$1	230	7	12	15.0000
UUAUU	chr8:124132236-124132466(+)$1	230	13	18	15.0000
UUAUU	chr15:49426497-49426727(-)$1	230	55	60	15.0000
UUAUU	chr8:30037938-30038168(+)$1	230	56	61	15.0000
UUAUU	chr17:27957745-27957988(-)$1	243	207	212	15.0000
UUAUU	chr2:63170862-63171085(+)$1	223	181	186	15.0000
UUAUU	chr7:120606615-120606845(+)$1	230	181	186	15.0000
UUAUU	chr6:116756673-116756903(+)$1	230	25	30	15.0000
UUAUU	chr2:160604264-160604486(+)$1	222	13	18	15.0000

#otherMatches

#Struct PSSM
ddddf	chr5:158698977-158699215(+)$1	238	28	33	15.0000
:::FF	chr19:58490764-58490994(-)$1	230	8	13	15.0000
cclll	chr7:151265739-151265969(-)$1	230	94	99	15.0000
fffff	chr9:108226463-108226693(+)$1	230	111	116	15.0000
ddddb	chr7:43635486-43635703(-)$1	217	94	99	15.0000
[dddd	chr3:101284383-101284613(+)$1	230	82	87	15.0000
leeee	chr21:34827932-34828162(-)$1	230	15	20	15.0000
leeee	chr12:112486042-112486266(-)$1	224	32	37	15.0000
::fff	chr1:205588992-205589222(-)$1	230	169	174	15.0000
mmmme	chr4:110446430-110446666(+)$1	236	28	33	15.0000
:::gg	chr14:45414455-45414677(-)$1	222	1	6	15.0000
ee]hh	chr2:225727321-225727551(-)$1	230	23	28	15.0000
ee]hh	chr21:15745848-15746078(-)$1	230	159	164	15.0000
:::::	chr12:46598028-46598258(-)$1	230	2	7	15.0000
=====	chr2:128528269-128528494(-)$1	225	182	187	15.0000
g%%%%	chr2:170678434-170678659(-)$1	225	11	16	15.0000
ii:::	chr15:78780973-78781203(+)$1	230	191	196	15.0000
55555	chr3:186503933-186504155(+)$1	222	171	176	15.0000
ee:::	chr6:135514889-135515112(+)$1	223	216	221	15.0000
EE:dd	chr20:52188171-52188396(-)$1	225	70	75	15.0000
ggggg	chr2:231940161-231940380(+)$1	219	41	46	15.0000
pppgg	chr5:138654543-138654769(+)$1	226	57	62	15.0000
ggggg	chr17:45740409-45740639(+)$1	230	7	12	15.0000
ooooo	chr16:23096110-23096333(-)$1	223	24	29	15.0000
2dddd	chr13:48934116-48934346(+)$1	230	105	110	15.0000
22eee	chr20:43615692-43615922(+)$1	230	65	70	15.0000
nnnnn	chr16:11066698-11066924(+)$1	226	49	54	15.0000
eeeee	chr5:175921108-175921329(+)$1	221	99	104	15.0000
uuuuu	chr1:155447635-155447865(-)$1	230	198	203	15.0000
==:::	chr15:78453929-78454159(+)$1	230	204	209	15.0000
:::::	chr13:39588499-39588724(-)$1	225	4	9	15.0000
e====	chr11:108119573-108119820(+)$1	247	69	74	15.0000
:::::	chr16:69727760-69727990(+)$1	230	215	220	15.0000
vvvve	chr16:57241878-57242108(+)$1	230	31	36	15.0000
iiii#	chr16:24560221-24560451(+)$1	230	28	33	15.0000
gg]cc	chr20:43129749-43129970(-)$1	221	192	197	15.0000
~~~DD	chr6:13639721-13639943(-)$1	222	169	174	15.0000
EE{EE	chr1:114942035-114942265(-)$1	230	7	12	15.0000
eeee[	chr3:23573962-23574185(+)$1	223	4	9	15.0000
eeell	chr2:24471432-24471662(-)$1	230	195	200	15.0000
e!!cc	chr20:52194782-52195012(-)$1	230	78	83	15.0000
eeeee	chr17:2583431-2583661(+)$1	230	78	83	15.0000
JJJJJ	chr17:56428696-56428926(-)$1	230	36	41	15.0000
ee]cc	chr13:98658309-98658535(+)$1	226	173	178	15.0000
&&&&&	chr2:135848538-135848761(+)$1	223	13	18	15.0000
:::::	chr17:48941238-48941468(-)$1	230	121	126	15.0000
IIIII	chr8:86021768-86021998(+)$1	230	7	12	15.0000
H:fff	chr8:124132236-124132466(+)$1	230	13	18	15.0000
fffff	chr15:49426497-49426727(-)$1	230	55	60	15.0000
xxhhh	chr8:30037938-30038168(+)$1	230	56	61	15.0000
f::FF	chr17:27957745-27957988(-)$1	243	207	212	15.0000
e::::	chr2:63170862-63171085(+)$1	223	181	186	15.0000
::::I	chr7:120606615-120606845(+)$1	230	181	186	15.0000
::::e	chr6:116756673-116756903(+)$1	230	25	30	15.0000
:::::	chr2:160604264-160604486(+)$1	222	13	18	15.0000

#DB
)))))	chr5:158698977-158699215(+)$1	1	28	33	15.0000
...((	chr19:58490764-58490994(-)$1	1	8	13	15.0000
((...	chr7:151265739-151265969(-)$1	1	94	99	15.0000
)))))	chr9:108226463-108226693(+)$1	1	111	116	15.0000
)))))	chr7:43635486-43635703(-)$1	1	94	99	15.0000
.((((	chr3:101284383-101284613(+)$1	1	82	87	15.0000
.))))	chr21:34827932-34828162(-)$1	1	15	20	15.0000
.))))	chr12:112486042-112486266(-)$1	1	32	37	15.0000
..(((	chr1:205588992-205589222(-)$1	1	169	174	15.0000
....)	chr4:110446430-110446666(+)$1	1	28	33	15.0000
...((	chr14:45414455-45414677(-)$1	1	1	6	15.0000
)).))	chr2:225727321-225727551(-)$1	1	23	28	15.0000
)).))	chr21:15745848-15746078(-)$1	1	159	164	15.0000
.....	chr12:46598028-46598258(-)$1	1	2	7	15.0000
)))))	chr2:128528269-128528494(-)$1	1	182	187	15.0000
(....	chr2:170678434-170678659(-)$1	1	11	16	15.0000
))...	chr15:78780973-78781203(+)$1	1	191	196	15.0000
.....	chr3:186503933-186504155(+)$1	1	171	176	15.0000
))...	chr6:135514889-135515112(+)$1	1	216	221	15.0000
((.((	chr20:52188171-52188396(-)$1	1	70	75	15.0000
(((((	chr2:231940161-231940380(+)$1	1	41	46	15.0000
...))	chr5:138654543-138654769(+)$1	1	57	62	15.0000
(((((	chr17:45740409-45740639(+)$1	1	7	12	15.0000
.....	chr16:23096110-23096333(-)$1	1	24	29	15.0000
.))))	chr13:48934116-48934346(+)$1	1	105	110	15.0000
..)))	chr20:43615692-43615922(+)$1	1	65	70	15.0000
.....	chr16:11066698-11066924(+)$1	1	49	54	15.0000
(((((	chr5:175921108-175921329(+)$1	1	99	104	15.0000
.....	chr1:155447635-155447865(-)$1	1	198	203	15.0000
))...	chr15:78453929-78454159(+)$1	1	204	209	15.0000
.....	chr13:39588499-39588724(-)$1	1	4	9	15.0000
(((((	chr11:108119573-108119820(+)$1	1	69	74	15.0000
.....	chr16:69727760-69727990(+)$1	1	215	220	15.0000
....)	chr16:57241878-57242108(+)$1	1	31	36	15.0000
((((.	chr16:24560221-24560451(+)$1	1	28	33	15.0000
)).))	chr20:43129749-43129970(-)$1	1	192	197	15.0000
...))	chr6:13639721-13639943(-)$1	1	169	174	15.0000
((.((	chr1:114942035-114942265(-)$1	1	7	12	15.0000
((((.	chr3:23573962-23574185(+)$1	1	4	9	15.0000
(((..	chr2:24471432-24471662(-)$1	1	195	200	15.0000
(..((	chr20:52194782-52195012(-)$1	1	78	83	15.0000
(((((	chr17:2583431-2583661(+)$1	1	78	83	15.0000
(((((	chr17:56428696-56428926(-)$1	1	36	41	15.0000
)).))	chr13:98658309-98658535(+)$1	1	173	178	15.0000
.....	chr2:135848538-135848761(+)$1	1	13	18	15.0000
.....	chr17:48941238-48941468(-)$1	1	121	126	15.0000
(((((	chr8:86021768-86021998(+)$1	1	7	12	15.0000
(.(((	chr8:124132236-124132466(+)$1	1	13	18	15.0000
(((((	chr15:49426497-49426727(-)$1	1	55	60	15.0000
..)))	chr8:30037938-30038168(+)$1	1	56	61	15.0000
)..))	chr17:27957745-27957988(-)$1	1	207	212	15.0000
)....	chr2:63170862-63171085(+)$1	1	181	186	15.0000
....)	chr7:120606615-120606845(+)$1	1	181	186	15.0000
....(	chr6:116756673-116756903(+)$1	1	25	30	15.0000
.....	chr2:160604264-160604486(+)$1	1	13	18	15.0000

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
A : 0.98	a : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	

#score	825.0000000000001
#seq	55
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m3_run2.nuc.txt

#NT
AUUUCAUACAAUCAUAUUUCCCAGUACUUUUCACAAUCAUUUUUUACCCAUCUAACUCUAUGUUUUGUGGCUUCCCGGUCUCUUAGAACUUUGAAAACAUGAUAUACAAUAAUGUUUAUUUAUUAUACAUCCAGAUUCUGAAAUAAUUUUCCUACUGAUGUUCAGCUCACACUAUCUGUACCUUUUUAGAAGAGAAAAGAAUCUUGAAUUGUAUAUAUUUAUUUUGCUUUACAGAAAAAAAUGGUUUCGUAAAUAAUUUGCCUAUUUUGGUUAACAUA	chr12:46582238-46582557(-)$1	319	30	308	406.5000

#otherMatches

#Struct PSSM
qqqqqhhhhhhhhBBKKHHHHHHHH:hhhhhhhh$$$$$eeeee$$$$$iiiiiiiiiccc[eeeee!!eeeee"""ddddoooooodddd]eeeeeeeeee]ccc88888888iiiiiiiiieeeee4444hhhhhhhh:::::cccffffffmmmmffffff4444cccHHHHHHHHYYBB:::::::eeeeennnnneeeee:EEEEE|||||||BB}FFFFFF}EEEEE}FFFFFF::eeeeevvvvvvvvvvvvveeeeeHHHHHHHH}BB::	chr15:52203718-52204140(+)$1	422	135	413	406.5000
^^^^^^^^^^^^^^^^^^^^^^^^^^^^==========:::::::::::::::::HHHHHHHH{EEEEE:::bb!!cccbblllbb]ccc22bbfffffftttttttttttffffff::::::FFFFFFBB{GGGGGGGddddmmmmdddd:::ddddllldddd::::::bb[ddddqqqqqqqqdddd22bb:::GGGGGGG}BBYYFFFFFFggggggg"""cccwwwwwwwwwwwwwwccc333ggggggg::::cccooooooccc:::EEEE	chr12:46582238-46582557(-)$1	319	30	308	406.5000

#DB
.....))))))))((..((((((((.((((((((.....(((((.....((((((((((((.(((((..(((((...((((......)))).)))))))))).)))........))))))))))))))....)))))))).....(((((((((....))))))....)))))))))))..)).......(((((.....))))).))))).......)).)))))).))))).))))))..(((((.............))))))))))))).))..	chr15:52203718-52204140(+)$1	1	135	413	406.5000
............................)))))))))).................((((((((.(((((...((..(((((...)).)))..))((((((...........))))))......((((((((.(((((((((((....))))...((((...))))......((.((((........))))..))...))))))).))..))))))(((((((...(((..............)))...)))))))....(((......)))...))))	chr12:46582238-46582557(-)$1	1	30	308	406.5000

#PSSM
C : 0.50	A : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
U : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
C : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
A : 1.00	
U : 1.00	
A : 0.50	C : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
C : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
C : 1.00	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
U : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
U : 0.50	G : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
U : 1.00	
U : 1.00	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
U : 1.00	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
U : 0.50	A : 0.50	

#score	813.0
#seq	2
#width	278
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m2_run1.nuc.txt

#NT
UUUUUUUCCU	chr3:100013892-100014143(+)$1	251	185	195	18.0833
UGUUUUUCAU	chr8:26218450-26218690(+)$1	240	14	24	17.7500
UUUUUUACAU	chr8:29961732-29961973(+)$1	241	109	119	17.6666
UCCUUUUCAU	chr5:74893735-74893975(+)$1	240	8	18	13.8333
UUUUCUGCAU	chr15:48434387-48434667(-)$1	280	93	103	14.8333
UUUUUUUCAU	chr20:10389237-10389477(-)$1	240	117	127	21.7500
UUAUUUUCUU	chr8:97285458-97285698(+)$1	240	115	125	14.3333
AUUUAUUCAU	chr1:54262328-54262568(-)$1	240	174	184	14.3333
UUUCUUUCAU	chr20:47686670-47686910(+)$1	240	196	206	17.4166
UCUUUUUCUU	chr14:74429638-74429878(+)$1	240	180	190	15.4166
UUUUAUUUAU	chr15:76209549-76209789(+)$1	240	195	205	14.7500
UUUUUUUAAU	chr11:9812011-9812251(-)$1	240	5	15	18.5000
UUUCUUUCUU	chr6:109689987-109690227(-)$1	240	119	129	14.5833
UUUUCUUCAU	chr1:202302524-202302764(-)$1	240	225	235	19.0833
UUUUUUUCAC	chr5:131039695-131039935(-)$1	240	115	125	17.8333
UUUUACUCAU	chr17:65074249-65074489(-)$1	240	101	111	14.5000
UUUUUUUAAA	chr3:15288160-15288400(+)$1	240	63	73	14.9166
UUCUUUUCUU	chr11:9307995-9308235(-)$1	240	74	84	14.5000
UUUUUUACAU	chr5:90106226-90106466(+)$1	240	116	126	17.6666
UCUUUUACAU	chr6:99819315-99819555(-)$1	240	52	62	14.1666
UCUUUUUCUU	chr2:223773428-223773709(+)$1	281	4	14	15.4166
CCUUUUUCAU	chr14:57698233-57698473(-)$1	240	24	34	14.5000
UUUUUUACAA	chr6:108370416-108370656(-)$1	240	205	215	14.0833
UUUUUUUGUU	chr14:39536342-39536582(-)$1	240	60	70	15.1666
GUUUUUUGAU	chr2:37428757-37428997(-)$1	240	152	162	13.8333
UUUUUUUCCU	chr12:57458340-57458580(-)$1	240	44	54	18.0833
UUUUUUUUUU	chr16:58584953-58585193(-)$1	240	3	13	15.2500
CCUUUUUCAU	chr5:61778838-61779078(+)$1	240	113	123	14.5000
UUUUUUUCUC	chr13:79189940-79190180(-)$1	240	117	127	15.0000
UUUUUUUAAA	chr3:156262052-156262292(-)$1	240	13	23	14.9166
UUUUCUUCAU	chrX:138901401-138901641(-)$1	240	14	24	19.0833
UAUUGUUCAU	chr11:32954039-32954279(+)$1	240	213	223	14.5833
UUUUCUUCAU	chr20:5155763-5156003(+)$1	240	115	125	19.0833
UUUAUUUCUU	chr4:166254616-166254856(+)$1	240	87	97	14.5000
UUUUCUUCAU	chr12:102590680-102590920(+)$1	240	108	118	19.0833
UUUUGCUCAU	chr2:148709897-148710139(-)$1	242	98	108	14.5000
CUUUUAUCAu	chr19:44501478-44501718(+)$1	240	118	128	13.9166
UUCUCUUCAU	chr12:44337974-44338214(+)$1	240	113	123	14.6666
UUUUUGUCAU	chr14:31171436-31171676(+)$1	240	34	44	17.7500
UUUUCCUCAU	chr7:73096986-73097226(-)$1	240	107	117	15.1666
UUUUCUUCAU	chr4:87685674-87685914(+)$1	240	119	129	19.0833
UUUUUGUCAU	chr4:83276372-83276613(-)$1	241	178	188	17.7500
uuucuuucuu	chr11:118267018-118267258(+)$1	240	222	232	14.5833
AUUUUUUCAU	chr2:190742011-190742251(+)$1	240	111	121	17.6666
CUUUUUUCAA	chr3:37032980-37033220(-)$1	240	110	120	14.4166
UUUUUAUAAU	chr6:107361017-107361258(+)$1	241	120	130	14.4166
UUUUUUUCAA	chr5:54948256-54948496(-)$1	240	115	125	18.1666
UUUUUGUCUU	chr8:95780589-95780829(+)$1	240	17	27	14.9166
UUUUUUUUAA	chr9:34398153-34398393(-)$1	240	119	129	14.5000
UAUUUUUAAU	chr16:57282410-57282650(+)$1	240	129	139	14.6666
UUUACUUCAU	chr10:32328177-32328417(-)$1	240	4	14	14.6666
UUUUCUUCAC	chr16:53190694-53190934(+)$1	240	114	124	15.1666
CUUUUUUCAU	chr14:91947843-91948083(-)$1	240	180	190	18.0000
UUUUUCUAAU	chr3:108298112-108298352(-)$1	240	58	68	14.5833
UCUUUUUCAU	chr5:133725938-133726178(+)$1	240	125	135	18.2500
UUUUUUUAaa	chr17:10595126-10595366(-)$1	240	181	191	14.9166
UAUUUUGCAU	chr12:27156098-27156338(-)$1	240	82	92	13.6666
UUUUCUCCAU	chr14:60585107-60585347(+)$1	240	74	84	14.7500
UUUUGUUAAU	chr10:32097839-32098079(-)$1	240	141	151	15.1666

#otherMatches

#Struct PSSM
'''''eeeee	chr4:122737863-122738113(-)$1	250	120	130	15.1666
]ccc]dddd4	chr3:100013892-100014143(+)$1	251	185	195	18.0833
J:::::::::	chr8:26218450-26218690(+)$1	240	14	24	17.7500
::::::::::	chr8:29961732-29961973(+)$1	241	109	119	17.6666
::::::EEEE	chr5:74893735-74893975(+)$1	240	8	18	13.8333
HHH{FFFFFF	chr15:48434387-48434667(-)$1	280	93	103	14.8333
d]hhhhhhhh	chr20:10389237-10389477(-)$1	240	117	127	21.7500
777777ffff	chr8:97285458-97285698(+)$1	240	115	125	14.3333
ffff:fffff	chr1:54262328-54262568(-)$1	240	174	184	14.3333
"eeeeennnn	chr20:47686670-47686910(+)$1	240	196	206	17.4166
dddd999999	chr14:74429638-74429878(+)$1	240	180	190	15.4166
wwwwwwwwww	chr15:76209549-76209789(+)$1	240	195	205	14.7500
ffnnnnnfff	chr11:9812011-9812251(-)$1	240	5	15	18.5000
dddd[ggggg	chr6:109689987-109690227(-)$1	240	119	129	14.5833
d::DDDDYYB	chr1:202302524-202302764(-)$1	240	225	235	19.0833
JJJJJJJDDD	chr5:131039695-131039935(-)$1	240	115	125	17.8333
d:::::::::	chr17:65074249-65074489(-)$1	240	101	111	14.5000
GGGQQQQQQQ	chr3:15288160-15288400(+)$1	240	63	73	14.9166
::::::::ee	chr11:9307995-9308235(-)$1	240	74	84	14.5000
mffffff22c	chr5:90106226-90106466(+)$1	240	116	126	17.6666
c88888888c	chr6:99819315-99819555(-)$1	240	52	62	14.1666
::ccc!!ddd	chr2:223773428-223773709(+)$1	281	4	14	15.4166
:::::::::b	chr14:57698233-57698473(-)$1	240	24	34	14.5000
ffffff::::	chr6:108370416-108370656(-)$1	240	205	215	14.0833
DDDEEEEEKK	chr14:39536342-39536582(-)$1	240	60	70	15.1666
iiiiiiiii:	chr2:37428757-37428997(-)$1	240	152	162	13.8333
+++++iiiii	chr12:57458340-57458580(-)$1	240	44	54	18.0833
::::::::::	chr16:58584953-58585193(-)$1	240	3	13	15.2500
::::::::::	chr5:61778838-61779078(+)$1	240	113	123	14.5000
ccc[eeeee#	chr13:79189940-79190180(-)$1	240	117	127	15.0000
fff"""eeee	chr3:156262052-156262292(-)$1	240	13	23	14.9166
""ffffff[c	chrX:138901401-138901641(-)$1	240	14	24	19.0833
::::::::::	chr11:32954039-32954279(+)$1	240	213	223	14.5833
ff%%%%%%gg	chr20:5155763-5156003(+)$1	240	115	125	19.0833
Jhhhhhhhh!	chr4:166254616-166254856(+)$1	240	87	97	14.5000
::EEEEEEEE	chr12:102590680-102590920(+)$1	240	108	118	19.0833
333bb333ee	chr2:148709897-148710139(-)$1	242	98	108	14.5000
oooodddd55	chr19:44501478-44501718(+)$1	240	118	128	13.9166
e!!ddddbb"	chr12:44337974-44338214(+)$1	240	113	123	14.6666
dd]ffffff:	chr14:31171436-31171676(+)$1	240	34	44	17.7500
$$ffffff[g	chr7:73096986-73097226(-)$1	240	107	117	15.1666
HHHHHHH:::	chr4:87685674-87685914(+)$1	240	119	129	19.0833
:ffffff$$$	chr4:83276372-83276613(-)$1	241	178	188	17.7500
JJJ}BBYYII	chr11:118267018-118267258(+)$1	240	222	232	14.5833
hhhhhhh22e	chr2:190742011-190742251(+)$1	240	111	121	17.6666
YHHHHHHHH:	chr3:37032980-37033220(-)$1	240	110	120	14.4166
niiiiiiiii	chr6:107361017-107361258(+)$1	241	120	130	14.4166
++++++++++	chr5:54948256-54948496(-)$1	240	115	125	18.1666
EELLLGGGGG	chr8:95780589-95780829(+)$1	240	17	27	14.9166
qqqqqqcccd	chr9:34398153-34398393(-)$1	240	119	129	14.5000
eeeeennnnn	chr16:57282410-57282650(+)$1	240	129	139	14.6666
gggg[eeeee	chr10:32328177-32328417(-)$1	240	4	14	14.6666
JJJJJJJJ::	chr16:53190694-53190934(+)$1	240	114	124	15.1666
:::::::::e	chr14:91947843-91948083(-)$1	240	180	190	18.0000
::::::::::	chr3:108298112-108298352(-)$1	240	58	68	14.5833
BBHHHHHHHH	chr5:133725938-133726178(+)$1	240	125	135	18.2500
&&&&&&gggg	chr17:10595126-10595366(-)$1	240	181	191	14.9166
::::dddd[c	chr12:27156098-27156338(-)$1	240	82	92	13.6666
ggggggg22f	chr14:60585107-60585347(+)$1	240	74	84	14.7500
ff55555ddd	chr10:32097839-32098079(-)$1	240	141	151	15.1666

#DB
.....(((((	chr4:122737863-122738113(-)$1	1	120	130	15.1666
.))).)))).	chr3:100013892-100014143(+)$1	1	185	195	18.0833
(.........	chr8:26218450-26218690(+)$1	1	14	24	17.7500
..........	chr8:29961732-29961973(+)$1	1	109	119	17.6666
......((((	chr5:74893735-74893975(+)$1	1	8	18	13.8333
(((.((((((	chr15:48434387-48434667(-)$1	1	93	103	14.8333
).))))))))	chr20:10389237-10389477(-)$1	1	117	127	21.7500
......))))	chr8:97285458-97285698(+)$1	1	115	125	14.3333
)))).(((((	chr1:54262328-54262568(-)$1	1	174	184	14.3333
.(((((....	chr20:47686670-47686910(+)$1	1	196	206	17.4166
))))......	chr14:74429638-74429878(+)$1	1	180	190	15.4166
..........	chr15:76209549-76209789(+)$1	1	195	205	14.7500
((.....)))	chr11:9812011-9812251(-)$1	1	5	15	18.5000
((((.(((((	chr6:109689987-109690227(-)$1	1	119	129	14.5833
)..))))..)	chr1:202302524-202302764(-)$1	1	225	235	19.0833
))))))))))	chr5:131039695-131039935(-)$1	1	115	125	17.8333
).........	chr17:65074249-65074489(-)$1	1	101	111	14.5000
(((.......	chr3:15288160-15288400(+)$1	1	63	73	14.9166
........((	chr11:9307995-9308235(-)$1	1	74	84	14.5000
.))))))..)	chr5:90106226-90106466(+)$1	1	116	126	17.6666
)........)	chr6:99819315-99819555(-)$1	1	52	62	14.1666
..(((..(((	chr2:223773428-223773709(+)$1	1	4	14	15.4166
.........(	chr14:57698233-57698473(-)$1	1	24	34	14.5000
))))))....	chr6:108370416-108370656(-)$1	1	205	215	14.0833
((((((((..	chr14:39536342-39536582(-)$1	1	60	70	15.1666
))))))))).	chr2:37428757-37428997(-)$1	1	152	162	13.8333
.....(((((	chr12:57458340-57458580(-)$1	1	44	54	18.0833
..........	chr16:58584953-58585193(-)$1	1	3	13	15.2500
..........	chr5:61778838-61779078(+)$1	1	113	123	14.5000
(((.(((((.	chr13:79189940-79190180(-)$1	1	117	127	15.0000
(((...((((	chr3:156262052-156262292(-)$1	1	13	23	14.9166
..((((((.(	chrX:138901401-138901641(-)$1	1	14	24	19.0833
..........	chr11:32954039-32954279(+)$1	1	213	223	14.5833
((......((	chr20:5155763-5156003(+)$1	1	115	125	19.0833
(((((((((.	chr4:166254616-166254856(+)$1	1	87	97	14.5000
..))))))))	chr12:102590680-102590920(+)$1	1	108	118	19.0833
...))...))	chr2:148709897-148710139(-)$1	1	98	108	14.5000
....))))..	chr19:44501478-44501718(+)$1	1	118	128	13.9166
(..((((((.	chr12:44337974-44338214(+)$1	1	113	123	14.6666
)).)))))).	chr14:31171436-31171676(+)$1	1	34	44	17.7500
..((((((.(	chr7:73096986-73097226(-)$1	1	107	117	15.1666
)))))))...	chr4:87685674-87685914(+)$1	1	119	129	19.0833
.((((((...	chr4:83276372-83276613(-)$1	1	178	188	17.7500
))).))..))	chr11:118267018-118267258(+)$1	1	222	232	14.5833
)))))))..)	chr2:190742011-190742251(+)$1	1	111	121	17.6666
.)))))))).	chr3:37032980-37033220(-)$1	1	110	120	14.4166
.)))))))))	chr6:107361017-107361258(+)$1	1	120	130	14.4166
..........	chr5:54948256-54948496(-)$1	1	115	125	18.1666
((...(((((	chr8:95780589-95780829(+)$1	1	17	27	14.9166
......))))	chr9:34398153-34398393(-)$1	1	119	129	14.5000
(((((.....	chr16:57282410-57282650(+)$1	1	129	139	14.6666
((((.(((((	chr10:32328177-32328417(-)$1	1	4	14	14.6666
))))))))..	chr16:53190694-53190934(+)$1	1	114	124	15.1666
.........(	chr14:91947843-91948083(-)$1	1	180	190	18.0000
..........	chr3:108298112-108298352(-)$1	1	58	68	14.5833
))))))))))	chr5:133725938-133726178(+)$1	1	125	135	18.2500
......((((	chr17:10595126-10595366(-)$1	1	181	191	14.9166
....((((.(	chr12:27156098-27156338(-)$1	1	82	92	13.6666
)))))))..)	chr14:60585107-60585347(+)$1	1	74	84	14.7500
)).....)))	chr10:32097839-32098079(-)$1	1	141	151	15.1666

#PSSM
U : 0.83	C : 0.09	A : 0.03	G : 0.01	u : 0.01	
U : 0.80	C : 0.11	A : 0.05	G : 0.01	u : 0.01	
U : 0.91	C : 0.05	A : 0.01	u : 0.01	
U : 0.91	C : 0.03	A : 0.03	c : 0.01	
U : 0.70	C : 0.18	A : 0.05	G : 0.05	u : 0.01	
U : 0.83	C : 0.06	G : 0.05	A : 0.03	u : 0.01	
U : 0.86	A : 0.06	G : 0.03	u : 0.01	C : 0.01	
C : 0.76	A : 0.13	U : 0.05	G : 0.03	c : 0.01	
A : 0.75	U : 0.18	C : 0.03	u : 0.01	a : 0.01	
U : 0.80	A : 0.09	C : 0.05	u : 0.03	a : 0.01	

#score	953.5000000000019
#seq	60
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m3_run1.nuc.txt

#NT
AAU	chr4:17843513-17843743(+)$1	230	52	55	8.9999
AAU	chr1:87209516-87209741(+)$1	225	5	8	8.9999
AAU	chr1:67875625-67875859(-)$1	234	5	8	8.9999
AAU	chr14:103808590-103808834(+)$1	244	162	165	8.9999
AAU	chr1:214522257-214522486(-)$1	229	116	119	8.9999
AAU	chrX:70794175-70794413(+)$1	238	52	55	8.9999
AAU	chr22:30728825-30729050(-)$1	225	50	53	8.9999
AAU	chr1:229458454-229458673(-)$1	219	10	13	8.9999
AAU	chr10:18968960-18969202(+)$1	242	11	14	8.9999
AAU	chr2:128460243-128460469(-)$1	226	70	73	8.9999
AAU	chr3:49758826-49759055(-)$1	229	100	103	8.9999
AAU	chr10:13360973-13361202(-)$1	229	28	31	8.9999
AAU	chr19:58774716-58774940(+)$1	224	107	110	8.9999
AAU	chr13:77455181-77455411(-)$1	230	6	9	8.9999
AAU	chr21:43409413-43409637(-)$1	224	49	52	8.9999
AAU	chr17:27587949-27588184(-)$1	235	7	10	8.9999
AAU	chr2:61150351-61150581(+)$1	230	36	39	8.9999
AAU	chr11:8017908-8018131(+)$1	223	19	22	8.9999
AAU	chrX:24002703-24002958(-)$1	255	67	70	8.9999
AAU	chrX:24229455-24229683(+)$1	228	4	7	8.9999
aau	chr19:52517047-52517277(-)$1	230	25	28	8.9999
AAU	chr4:110633892-110634115(-)$1	223	76	79	8.9999
AAU	chr20:43122126-43122358(+)$1	232	5	8	8.9999
AAU	chr2:208466198-208466426(+)$1	228	57	60	8.9999
AAU	chr7:104722058-104722290(+)$1	232	8	11	8.9999
AAU	chr22:40724644-40724869(+)$1	225	18	21	8.9999
AAU	chr1:244572010-244572241(-)$1	231	4	7	8.9999
AAU	chrX:48761194-48761428(-)$1	234	100	103	8.9999
AAU	chr13:21548604-21548834(-)$1	230	20	23	8.9999
AAU	chr2:113496043-113496263(-)$1	220	12	15	8.9999
AAU	chr18:9547003-9547227(-)$1	224	75	78	8.9999
AAU	chr18:32821278-32821504(+)$1	226	7	10	8.9999
aau	chr5:78619808-78620043(+)$1	235	6	9	8.9999
AAU	chr13:25907509-25907749(+)$1	240	5	8	8.9999
AAU	chr19:34306044-34306275(+)$1	231	29	32	8.9999
AAU	chr6:71235578-71235800(+)$1	222	75	78	8.9999
AAU	chr17:48211071-48211295(-)$1	224	113	116	8.9999
aau	chr1:200828126-200828352(+)$1	226	16	19	8.9999
AAU	chr5:133531134-133531377(-)$1	243	9	12	8.9999
aau	chr5:37290155-37290377(-)$1	222	67	70	8.9999
AAU	chr1:245016532-245016760(-)$1	228	28	31	8.9999
AAU	chr5:151188982-151189212(+)$1	230	31	34	8.9999
AAU	chr22:24742971-24743195(+)$1	224	2	5	8.9999
AAU	chr2:120740506-120740734(+)$1	228	29	32	8.9999
AAU	chr3:100082893-100083115(-)$1	222	84	87	8.9999
AAU	chr12:123639709-123639932(-)$1	223	102	105	8.9999
AAU	chr10:18967520-18967752(+)$1	232	9	12	8.9999
AAU	chr4:123817159-123817382(+)$1	223	37	40	8.9999
AAU	chr6:36455440-36455691(+)$1	251	21	24	8.9999
AAU	chr7:155570789-155571012(+)$1	223	2	5	8.9999
aau	chr10:70516985-70517206(+)$1	221	3	6	8.9999
AAU	chr10:127452573-127452808(+)$1	235	88	91	8.9999
AAU	chr1:197127833-197128057(-)$1	224	38	41	8.9999
aau	chr16:81420675-81420904(+)$1	229	40	43	8.9999
AAU	chr6:24705538-24705781(-)$1	243	159	162	8.9999
AAU	chr12:72179911-72180136(+)$1	225	73	76	8.9999
AAU	chr5:143538728-143538959(-)$1	231	6	9	8.9999
AAU	chr1:229457211-229457439(-)$1	228	56	59	8.9999
AAU	chrX:73808324-73808545(-)$1	221	61	64	8.9999
AAU	chr3:30735384-30735615(+)$1	231	2	5	8.9999
AAU	chr6:136580745-136580972(-)$1	227	26	29	8.9999
AAU	chr2:152332501-152332732(+)$1	231	56	59	8.9999
AAU	chr1:85116000-85116224(-)$1	224	28	31	8.9999
AAU	chr2:153511919-153512140(-)$1	221	3	6	8.9999
AAU	chr8:42692037-42692274(-)$1	237	30	33	8.9999
AAU	chr2:148685304-148685528(+)$1	224	5	8	8.9999
AAU	chr20:61509139-61509363(-)$1	224	23	26	8.9999
AAU	chr3:188608058-188608291(+)$1	233	8	11	8.9999
AAU	chr11:73116542-73116765(-)$1	223	95	98	8.9999
AAU	chr7:92242858-92243080(-)$1	222	31	34	8.9999
AAU	chr6:97590164-97590385(-)$1	221	5	8	8.9999
AAU	chr20:464129-464351(-)$1	222	8	11	8.9999
AAU	chr18:19781648-19781870(+)$1	222	9	12	8.9999
AAU	chr10:115670260-115670485(+)$1	225	11	14	8.9999
AAU	chr2:100899924-100900152(-)$1	228	8	11	8.9999
AAU	chr15:59955205-59955437(-)$1	232	61	64	8.9999
AAU	chr1:207222131-207222349(-)$1	218	47	50	8.9999
AAU	chr1:151263942-151264166(+)$1	224	113	116	8.9999
AAU	chr12:29487756-29487985(+)$1	229	18	21	8.9999
AAU	chr3:55499650-55499875(-)$1	225	2	5	8.9999
AAU	chr17:47131222-47131485(+)$1	263	80	83	8.9999
AAU	chr17:47126765-47127029(+)$1	264	86	89	8.9999
AAU	chrX:122747905-122748140(-)$1	235	9	12	8.9999
AAU	chr19:44679880-44680105(+)$1	225	3	6	8.9999
AAU	chr12:69968813-69969039(+)$1	226	28	31	8.9999
AAU	chr5:132213026-132213254(-)$1	228	2	5	8.9999
AAU	chr10:101465696-101465920(+)$1	224	29	32	8.9999
AAU	chr15:91463339-91463566(+)$1	227	99	102	8.9999
aau	chr19:13884718-13884962(+)$1	244	48	51	8.9999
aau	chr19:24312075-24312305(+)$1	230	11	14	8.9999
AAU	chr1:227844471-227844704(+)$1	233	9	12	8.9999
AAU	chr8:64122332-64122559(+)$1	227	76	79	8.9999
AAU	chr12:69233721-69233965(+)$1	244	1	4	8.9999
AAU	chr9:80031661-80031886(+)$1	225	26	29	8.9999
AAU	chr7:44917930-44918153(-)$1	223	24	27	8.9999

#otherMatches

#Struct PSSM
mmm	chr17:47131624-47131846(+)$1	222	9	12	8.9999
:::	chr4:17843513-17843743(+)$1	230	52	55	8.9999
:ee	chr1:87209516-87209741(+)$1	225	5	8	8.9999
::D	chr1:67875625-67875859(-)$1	234	5	8	8.9999
eee	chr14:103808590-103808834(+)$1	244	162	165	8.9999
:::	chr1:214522257-214522486(-)$1	229	116	119	8.9999
qqq	chrX:70794175-70794413(+)$1	238	52	55	8.9999
::e	chr22:30728825-30729050(-)$1	225	50	53	8.9999
:::	chr1:229458454-229458673(-)$1	219	10	13	8.9999
ppp	chr10:18968960-18969202(+)$1	242	11	14	8.9999
fff	chr2:128460243-128460469(-)$1	226	70	73	8.9999
:::	chr3:49758826-49759055(-)$1	229	100	103	8.9999
$$d	chr10:13360973-13361202(-)$1	229	28	31	8.9999
:::	chr19:58774716-58774940(+)$1	224	107	110	8.9999
EE:	chr13:77455181-77455411(-)$1	230	6	9	8.9999
:::	chr21:43409413-43409637(-)$1	224	49	52	8.9999
:::	chr17:27587949-27588184(-)$1	235	7	10	8.9999
!!g	chr2:61150351-61150581(+)$1	230	36	39	8.9999
fff	chr11:8017908-8018131(+)$1	223	19	22	8.9999
::h	chrX:24002703-24002958(-)$1	255	67	70	8.9999
DDD	chrX:24229455-24229683(+)$1	228	4	7	8.9999
OOO	chr19:52517047-52517277(-)$1	230	25	28	8.9999
ooo	chr4:110633892-110634115(-)$1	223	76	79	8.9999
:::	chr20:43122126-43122358(+)$1	232	5	8	8.9999
eee	chr2:208466198-208466426(+)$1	228	57	60	8.9999
I::	chr7:104722058-104722290(+)$1	232	8	11	8.9999
:::	chr22:40724644-40724869(+)$1	225	18	21	8.9999
[dd	chr1:244572010-244572241(-)$1	231	4	7	8.9999
mmm	chrX:48761194-48761428(-)$1	234	100	103	8.9999
nnn	chr13:21548604-21548834(-)$1	230	20	23	8.9999
:hh	chr2:113496043-113496263(-)$1	220	12	15	8.9999
ddd	chr18:9547003-9547227(-)$1	224	75	78	8.9999
:==	chr18:32821278-32821504(+)$1	226	7	10	8.9999
:::	chr5:78619808-78620043(+)$1	235	6	9	8.9999
:::	chr13:25907509-25907749(+)$1	240	5	8	8.9999
d!!	chr19:34306044-34306275(+)$1	231	29	32	8.9999
vvv	chr6:71235578-71235800(+)$1	222	75	78	8.9999
===	chr17:48211071-48211295(-)$1	224	113	116	8.9999
hhh	chr1:200828126-200828352(+)$1	226	16	19	8.9999
===	chr5:133531134-133531377(-)$1	243	9	12	8.9999
dpp	chr5:37290155-37290377(-)$1	222	67	70	8.9999
H::	chr1:245016532-245016760(-)$1	228	28	31	8.9999
MME	chr5:151188982-151189212(+)$1	230	31	34	8.9999
:::	chr22:24742971-24743195(+)$1	224	2	5	8.9999
ndd	chr2:120740506-120740734(+)$1	228	29	32	8.9999
eee	chr3:100082893-100083115(-)$1	222	84	87	8.9999
:::	chr12:123639709-123639932(-)$1	223	102	105	8.9999
qqq	chr10:18967520-18967752(+)$1	232	9	12	8.9999
{BB	chr4:123817159-123817382(+)$1	223	37	40	8.9999
d:F	chr6:36455440-36455691(+)$1	251	21	24	8.9999
:::	chr7:155570789-155571012(+)$1	223	2	5	8.9999
hhh	chr10:70516985-70517206(+)$1	221	3	6	8.9999
agg	chr10:127452573-127452808(+)$1	235	88	91	8.9999
===	chr1:197127833-197128057(-)$1	224	38	41	8.9999
zzz	chr16:81420675-81420904(+)$1	229	40	43	8.9999
JKK	chr6:24705538-24705781(-)$1	243	159	162	8.9999
%%d	chr12:72179911-72180136(+)$1	225	73	76	8.9999
:::	chr5:143538728-143538959(-)$1	231	6	9	8.9999
''i	chr1:229457211-229457439(-)$1	228	56	59	8.9999
^^c	chrX:73808324-73808545(-)$1	221	61	64	8.9999
:::	chr3:30735384-30735615(+)$1	231	2	5	8.9999
KKG	chr6:136580745-136580972(-)$1	227	26	29	8.9999
^^^	chr2:152332501-152332732(+)$1	231	56	59	8.9999
!dd	chr1:85116000-85116224(-)$1	224	28	31	8.9999
:::	chr2:153511919-153512140(-)$1	221	3	6	8.9999
rrr	chr8:42692037-42692274(-)$1	237	30	33	8.9999
:::	chr2:148685304-148685528(+)$1	224	5	8	8.9999
DD{	chr20:61509139-61509363(-)$1	224	23	26	8.9999
DDD	chr3:188608058-188608291(+)$1	233	8	11	8.9999
mmm	chr11:73116542-73116765(-)$1	223	95	98	8.9999
:::	chr7:92242858-92243080(-)$1	222	31	34	8.9999
HHH	chr6:97590164-97590385(-)$1	221	5	8	8.9999
::J	chr20:464129-464351(-)$1	222	8	11	8.9999
JJJ	chr18:19781648-19781870(+)$1	222	9	12	8.9999
ffv	chr10:115670260-115670485(+)$1	225	11	14	8.9999
$$c	chr2:100899924-100900152(-)$1	228	8	11	8.9999
b!!	chr15:59955205-59955437(-)$1	232	61	64	8.9999
cqq	chr1:207222131-207222349(-)$1	218	47	50	8.9999
444	chr1:151263942-151264166(+)$1	224	113	116	8.9999
ffn	chr12:29487756-29487985(+)$1	229	18	21	8.9999
III	chr3:55499650-55499875(-)$1	225	2	5	8.9999
sss	chr17:47131222-47131485(+)$1	263	80	83	8.9999
:::	chr17:47126765-47127029(+)$1	264	86	89	8.9999
ppp	chrX:122747905-122748140(-)$1	235	9	12	8.9999
:::	chr19:44679880-44680105(+)$1	225	3	6	8.9999
hh[	chr12:69968813-69969039(+)$1	226	28	31	8.9999
EEE	chr5:132213026-132213254(-)$1	228	2	5	8.9999
^^^	chr10:101465696-101465920(+)$1	224	29	32	8.9999
:gg	chr15:91463339-91463566(+)$1	227	99	102	8.9999
""c	chr19:13884718-13884962(+)$1	244	48	51	8.9999
KKD	chr19:24312075-24312305(+)$1	230	11	14	8.9999
HHH	chr1:227844471-227844704(+)$1	233	9	12	8.9999
333	chr8:64122332-64122559(+)$1	227	76	79	8.9999
:::	chr12:69233721-69233965(+)$1	244	1	4	8.9999
eee	chr9:80031661-80031886(+)$1	225	26	29	8.9999
MMF	chr7:44917930-44918153(-)$1	223	24	27	8.9999

#DB
...	chr17:47131624-47131846(+)$1	1	9	12	8.9999
...	chr4:17843513-17843743(+)$1	1	52	55	8.9999
.((	chr1:87209516-87209741(+)$1	1	5	8	8.9999
..(	chr1:67875625-67875859(-)$1	1	5	8	8.9999
(((	chr14:103808590-103808834(+)$1	1	162	165	8.9999
...	chr1:214522257-214522486(-)$1	1	116	119	8.9999
...	chrX:70794175-70794413(+)$1	1	52	55	8.9999
..(	chr22:30728825-30729050(-)$1	1	50	53	8.9999
...	chr1:229458454-229458673(-)$1	1	10	13	8.9999
...	chr10:18968960-18969202(+)$1	1	11	14	8.9999
(((	chr2:128460243-128460469(-)$1	1	70	73	8.9999
...	chr3:49758826-49759055(-)$1	1	100	103	8.9999
..(	chr10:13360973-13361202(-)$1	1	28	31	8.9999
...	chr19:58774716-58774940(+)$1	1	107	110	8.9999
((.	chr13:77455181-77455411(-)$1	1	6	9	8.9999
...	chr21:43409413-43409637(-)$1	1	49	52	8.9999
...	chr17:27587949-27588184(-)$1	1	7	10	8.9999
..(	chr2:61150351-61150581(+)$1	1	36	39	8.9999
)))	chr11:8017908-8018131(+)$1	1	19	22	8.9999
..(	chrX:24002703-24002958(-)$1	1	67	70	8.9999
(((	chrX:24229455-24229683(+)$1	1	4	7	8.9999
...	chr19:52517047-52517277(-)$1	1	25	28	8.9999
...	chr4:110633892-110634115(-)$1	1	76	79	8.9999
...	chr20:43122126-43122358(+)$1	1	5	8	8.9999
(((	chr2:208466198-208466426(+)$1	1	57	60	8.9999
(..	chr7:104722058-104722290(+)$1	1	8	11	8.9999
...	chr22:40724644-40724869(+)$1	1	18	21	8.9999
.((	chr1:244572010-244572241(-)$1	1	4	7	8.9999
...	chrX:48761194-48761428(-)$1	1	100	103	8.9999
...	chr13:21548604-21548834(-)$1	1	20	23	8.9999
.((	chr2:113496043-113496263(-)$1	1	12	15	8.9999
)))	chr18:9547003-9547227(-)$1	1	75	78	8.9999
.((	chr18:32821278-32821504(+)$1	1	7	10	8.9999
...	chr5:78619808-78620043(+)$1	1	6	9	8.9999
...	chr13:25907509-25907749(+)$1	1	5	8	8.9999
(..	chr19:34306044-34306275(+)$1	1	29	32	8.9999
...	chr6:71235578-71235800(+)$1	1	75	78	8.9999
(((	chr17:48211071-48211295(-)$1	1	113	116	8.9999
(((	chr1:200828126-200828352(+)$1	1	16	19	8.9999
(((	chr5:133531134-133531377(-)$1	1	9	12	8.9999
(..	chr5:37290155-37290377(-)$1	1	67	70	8.9999
(..	chr1:245016532-245016760(-)$1	1	28	31	8.9999
..(	chr5:151188982-151189212(+)$1	1	31	34	8.9999
...	chr22:24742971-24743195(+)$1	1	2	5	8.9999
.))	chr2:120740506-120740734(+)$1	1	29	32	8.9999
(((	chr3:100082893-100083115(-)$1	1	84	87	8.9999
...	chr12:123639709-123639932(-)$1	1	102	105	8.9999
...	chr10:18967520-18967752(+)$1	1	9	12	8.9999
.((	chr4:123817159-123817382(+)$1	1	37	40	8.9999
).(	chr6:36455440-36455691(+)$1	1	21	24	8.9999
...	chr7:155570789-155571012(+)$1	1	2	5	8.9999
(((	chr10:70516985-70517206(+)$1	1	3	6	8.9999
)))	chr10:127452573-127452808(+)$1	1	88	91	8.9999
(((	chr1:197127833-197128057(-)$1	1	38	41	8.9999
...	chr16:81420675-81420904(+)$1	1	40	43	8.9999
(..	chr6:24705538-24705781(-)$1	1	159	162	8.9999
..(	chr12:72179911-72180136(+)$1	1	73	76	8.9999
...	chr5:143538728-143538959(-)$1	1	6	9	8.9999
..(	chr1:229457211-229457439(-)$1	1	56	59	8.9999
..)	chrX:73808324-73808545(-)$1	1	61	64	8.9999
...	chr3:30735384-30735615(+)$1	1	2	5	8.9999
..(	chr6:136580745-136580972(-)$1	1	26	29	8.9999
...	chr2:152332501-152332732(+)$1	1	56	59	8.9999
.((	chr1:85116000-85116224(-)$1	1	28	31	8.9999
...	chr2:153511919-153512140(-)$1	1	3	6	8.9999
...	chr8:42692037-42692274(-)$1	1	30	33	8.9999
...	chr2:148685304-148685528(+)$1	1	5	8	8.9999
((.	chr20:61509139-61509363(-)$1	1	23	26	8.9999
(((	chr3:188608058-188608291(+)$1	1	8	11	8.9999
...	chr11:73116542-73116765(-)$1	1	95	98	8.9999
...	chr7:92242858-92243080(-)$1	1	31	34	8.9999
(((	chr6:97590164-97590385(-)$1	1	5	8	8.9999
..(	chr20:464129-464351(-)$1	1	8	11	8.9999
(((	chr18:19781648-19781870(+)$1	1	9	12	8.9999
((.	chr10:115670260-115670485(+)$1	1	11	14	8.9999
..(	chr2:100899924-100900152(-)$1	1	8	11	8.9999
(..	chr15:59955205-59955437(-)$1	1	61	64	8.9999
(..	chr1:207222131-207222349(-)$1	1	47	50	8.9999
...	chr1:151263942-151264166(+)$1	1	113	116	8.9999
((.	chr12:29487756-29487985(+)$1	1	18	21	8.9999
(((	chr3:55499650-55499875(-)$1	1	2	5	8.9999
...	chr17:47131222-47131485(+)$1	1	80	83	8.9999
...	chr17:47126765-47127029(+)$1	1	86	89	8.9999
...	chrX:122747905-122748140(-)$1	1	9	12	8.9999
...	chr19:44679880-44680105(+)$1	1	3	6	8.9999
((.	chr12:69968813-69969039(+)$1	1	28	31	8.9999
(((	chr5:132213026-132213254(-)$1	1	2	5	8.9999
...	chr10:101465696-101465920(+)$1	1	29	32	8.9999
.((	chr15:91463339-91463566(+)$1	1	99	102	8.9999
..(	chr19:13884718-13884962(+)$1	1	48	51	8.9999
..(	chr19:24312075-24312305(+)$1	1	11	14	8.9999
(((	chr1:227844471-227844704(+)$1	1	9	12	8.9999
...	chr8:64122332-64122559(+)$1	1	76	79	8.9999
...	chr12:69233721-69233965(+)$1	1	1	4	8.9999
(((	chr9:80031661-80031886(+)$1	1	26	29	8.9999
..(	chr7:44917930-44918153(-)$1	1	24	27	8.9999

#PSSM
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	
U : 0.91	u : 0.08	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m3_run1.nuc.txt

#NT
CUGUCUCUGCUGGGCUUUUCCGGCCCCGUCCCAGCUCCUCCUCAGGCAGAGGCUGCAGCCCUCAGCUCUGCUGCUGGAUGGAACAUUUCAACCCCCUCCGGGAAGGUGGGCAGGGUGGAGGGCCCAGGGCUAGGCCUGCCAUGCACCAUGAGCAGGGGUGCUACCUGGGUGUGUGAAGUUGGGCUGGCUUUUCCUGGAGGUGGGUGAGAAGGCUCUCCGGGCAAAUCAGAAGGCCACGAGAGAGAGAGGAGCGGGGAGAGUGGUGAGGAGGAUUCGUCUCUGACUGAUG	chr7:4807980-4808436(+)$1	456	148	437	387.0000

#otherMatches

#Struct PSSM
dddooooooddddddddlllddddddddmmmmddddJJJJJJJJJJJKKHHHHHHHHMMMMCCC{BBCCCKKDDDDEEEEEgggggggccc[cccmmmmcccccc]ggggggg:::bb[bboooooobb]bb::::::::EEEEE}DDDDYYCCCgggggggnnnnngggggggBBCCCHHHHHHHHJJJJJJJJJJJ::::::dddd[eeeeerrrrrrrrreeeee]dddd:::::eeeeemmmmeeeeeCCCYYGGGGGGG::::::::::gggggggvvvvvvvv	chr17:54969251-54969571(-)$1	320	16	305	387.0000
lleeeeeddddeeeeennnnneeeee:HHHHHHHHcccccc"""ggggggg[cccpppppppcccggggggg333ccc]ccc:::eeeee[ccc===========bb[ccc[bb[a"""a[gggggggbb####eeeeeddddllldddd]eeeee333bb22ggggggg]a4444a]bb22ccc]bb]===========]ccceeeeeEEEEEZZZEEEEEYYDDDDYYCCC}BB}DDDDYYDDDD:::eeeee[a"""hhhhhhhh####ffffffpppppppffff	chr7:4807980-4808436(+)$1	456	148	437	387.0000

#DB
(((......))))((((...))))((((....))))(((((((((((..((((((((....(((.(((((..(((((((((((((((((((.(((....)))))).)))))))...((.((......)).))........))))).))))..)))(((((((.....)))))))))))))))))))))))))))))))......((((.(((((.........))))).)))).....(((((....))))))))..)))))))..........(((((((........	chr17:54969251-54969571(-)$1	1	16	305	387.0000
..)))))))))(((((.....))))).))))))))((((((...(((((((.(((.......))))))))))...))).)))...(((((.((((((((((((((((.(((.((.(...(.(((((((((....(((((((((...)))).)))))...))..))))))).)....).))..))).)).))))))))))).)))))))))))))...)))))..))))..))).)).))))..))))...(((((.(...((((((((....((((((.......))))	chr7:4807980-4808436(+)$1	1	148	437	387.0000

#PSSM
C : 1.00	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
A : 0.50	C : 0.50	
G : 1.00	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
A : 1.00	
G : 1.00	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
C : 1.00	
U : 0.50	C : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 1.00	
G : 1.00	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 0.50	G : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
C : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 1.00	
C : 1.00	
A : 0.50	C : 0.50	
A : 1.00	
C : 1.00	
A : 0.50	G : 0.50	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
C : 1.00	
G : 1.00	
U : 0.50	G : 0.50	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
C : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
G : 0.50	C : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	

#score	774.0
#seq	2
#width	289
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012a_hg19_UTR_m3_run2.nuc.txt

#NT
ACAUUUUG	chr19:23835507-23835737(-)$1	230	157	165	12.5294
AUAAUUUU	chr9:111780777-111781000(-)$1	223	49	57	14.3921
AAAUUUUU	chr2:158287327-158287545(-)$1	218	181	189	15.5686
AUAUUCUU	chr8:82712774-82713001(-)$1	227	48	56	13.4117
AUAUUUUG	chr21:35472577-35472800(+)$1	223	31	39	13.9019
ACAGUUUU	chr15:83685991-83686214(-)$1	223	28	36	12.8235
ACAUUCUU	chr21:42767539-42767769(+)$1	230	144	152	12.0392
ACAUUUUU	chr12:88590052-88590269(+)$1	217	36	44	16.6470
CUAUUUUU	chr12:27181330-27181556(+)$1	226	193	201	13.5098
ACAUGUUU	chr5:145667120-145667343(+)$1	223	126	134	12.6274
AUCUUUUU	chrX:110463988-110464206(-)$1	218	76	84	13.6078
ACGUUUUU	chr18:60793190-60793450(-)$1	260	223	231	12.2352
ACAUUUAU	chrX:41379382-41379612(-)$1	230	60	68	13.0196
AUAUUUUA	chr14:74181930-74182160(-)$1	230	6	14	13.9019
AUAUUUAU	chr10:126674068-126674293(+)$1	225	195	203	14.3921
GUAUUUUU	chr6:118781952-118782182(-)$1	230	173	181	13.6078
AUAUUUAU	chr6:79647862-79648080(-)$1	218	91	99	14.3921
AUAUCUUU	chr5:172563238-172563460(+)$1	222	29	37	13.8039
AUAUUUUU	chr4:146057902-146058132(-)$1	230	218	226	18.0196
AUAUUUGU	chr8:48973901-48974122(+)$1	221	87	95	14.1960
auauguuu	chr12:93166296-93166522(-)$1	226	196	204	14.0000
ACCUUUUU	chr14:55309008-55309231(-)$1	223	28	36	12.2352
ACAAUUUU	chr9:5468303-5468540(+)$1	237	101	109	13.0196
acauuuua	chr6:97002462-97002682(+)$1	220	57	65	12.5294
AUAUUUAU	chr8:94744309-94744534(-)$1	225	6	14	14.3921
AUAGUUUU	chr12:12874046-12874271(+)$1	225	172	180	14.1960
AAAUGUUU	chr19:53570679-53570909(-)$1	230	21	29	11.5490
AUAUUUGU	chr3:193856193-193856418(+)$1	225	15	23	14.1960
AUAUUUGU	chr6:159056099-159056343(+)$1	244	143	151	14.1960
GUAUUUUU	chr2:173435397-173435618(+)$1	221	25	33	13.6078
ACAUUUUU	chr1:26449960-26450178(+)$1	218	47	55	16.6470
acaauuuu	chr5:78073089-78073312(-)$1	223	181	189	13.0196
AUAUUUUU	chr6:109689606-109689831(-)$1	225	33	41	18.0196
AUGUUUUU	chr7:2400245-2400467(+)$1	222	51	59	13.6078
AAAUUUUU	chr11:93528096-93528326(+)$1	230	34	42	15.5686
ACAUUUUU	chr18:43464655-43464875(-)$1	220	73	81	16.6470
ACAUUUUU	chr17:27953128-27953347(-)$1	219	190	198	16.6470
AUACUUUU	chr17:1326178-1326408(-)$1	230	177	185	14.0000
AUAUCUUU	chr17:63010143-63010412(-)$1	269	61	69	13.8039
AUAUUUUG	chr12:42475776-42475997(-)$1	221	35	43	13.9019
AUAUUUUU	chr12:77415025-77415245(-)$1	220	158	166	18.0196
AAAUUUCU	chr12:75892749-75892979(-)$1	230	72	80	11.5490
UUAUUUUU	chr12:93802186-93802406(-)$1	220	41	49	13.5098
AUAAUUUU	chr1:173754474-173754696(+)$1	222	75	83	14.3921
AUAUUUAU	chr9:114696712-114696932(+)$1	220	135	143	14.3921
AAAGUUUU	chr6:42175419-42175643(-)$1	224	36	44	11.7450
ACAUUUUA	chr5:135516873-135517091(+)$1	218	102	110	12.5294
AUAAUUUU	chr7:77268977-77269197(+)$1	220	164	172	14.3921
ACAUGUUU	chr9:125670291-125670514(-)$1	223	138	146	12.6274
AUAUUUUU	chr13:21548664-21548889(-)$1	225	110	118	18.0196

#otherMatches

#Struct PSSM
llhhhhhh	chr14:77806556-77806778(-)$1	222	153	161	18.0196
ffCCCYYF	chr19:23835507-23835737(-)$1	230	157	165	12.5294
pppfffff	chr9:111780777-111781000(-)$1	223	49	57	14.3921
>>>>ffff	chr2:158287327-158287545(-)$1	218	181	189	15.5686
nnnndddd	chr8:82712774-82713001(-)$1	227	48	56	13.4117
cnnnnncc	chr21:35472577-35472800(+)$1	223	31	39	13.9019
DDDD::::	chr15:83685991-83686214(-)$1	223	28	36	12.8235
oooggggg	chr21:42767539-42767769(+)$1	230	144	152	12.0392
[ddddlll	chr12:88590052-88590269(+)$1	217	36	44	16.6470
====::::	chr12:27181330-27181556(+)$1	226	193	201	13.5098
::ccc"""	chr5:145667120-145667343(+)$1	223	126	134	12.6274
[ffffff#	chrX:110463988-110464206(-)$1	218	76	84	13.6078
ddeeeeeo	chr18:60793190-60793450(-)$1	260	223	231	12.2352
GGGGGGLL	chrX:41379382-41379612(-)$1	230	60	68	13.0196
KJJJJJJJ	chr14:74181930-74182160(-)$1	230	6	14	13.9019
::::::EE	chr10:126674068-126674293(+)$1	225	195	203	14.3921
eeqqqqqq	chr6:118781952-118782182(-)$1	230	173	181	13.6078
========	chr6:79647862-79648080(-)$1	218	91	99	14.3921
a22eeeee	chr5:172563238-172563460(+)$1	222	29	37	13.8039
HH::::::	chr4:146057902-146058132(-)$1	230	218	226	18.0196
HHHH:::F	chr8:48973901-48974122(+)$1	221	87	95	14.1960
=====rrr	chr12:93166296-93166522(-)$1	226	196	204	14.0000
{DDDDfff	chr14:55309008-55309231(-)$1	223	28	36	12.2352
ggggg22d	chr9:5468303-5468540(+)$1	237	101	109	13.0196
e]bb>>>>	chr6:97002462-97002682(+)$1	220	57	65	12.5294
:JJJJJJJ	chr8:94744309-94744534(-)$1	225	6	14	14.3921
e:::::::	chr12:12874046-12874271(+)$1	225	172	180	14.1960
NDDDDGGG	chr19:53570679-53570909(-)$1	230	21	29	11.5490
c####bb[	chr3:193856193-193856418(+)$1	225	15	23	14.1960
bb]iiiii	chr6:159056099-159056343(+)$1	244	143	151	14.1960
hhhhhhh[	chr2:173435397-173435618(+)$1	221	25	33	13.6078
ddd::hhh	chr1:26449960-26450178(+)$1	218	47	55	16.6470
ee::::::	chr5:78073089-78073312(-)$1	223	181	189	13.0196
aooooooa	chr6:109689606-109689831(-)$1	225	33	41	18.0196
bb[a[hhh	chr7:2400245-2400467(+)$1	222	51	59	13.6078
mmmmffff	chr11:93528096-93528326(+)$1	230	34	42	15.5686
qq======	chr18:43464655-43464875(-)$1	220	73	81	16.6470
d::::DDD	chr17:27953128-27953347(-)$1	219	190	198	16.6470
7777777=	chr17:1326178-1326408(-)$1	230	177	185	14.0000
ii[ccc!!	chr17:63010143-63010412(-)$1	269	61	69	13.8039
:::::::h	chr12:42475776-42475997(-)$1	221	35	43	13.9019
:::::::J	chr12:77415025-77415245(-)$1	220	158	166	18.0196
]bb]ccc]	chr12:75892749-75892979(-)$1	230	72	80	11.5490
eeee[ddd	chr12:93802186-93802406(-)$1	220	41	49	13.5098
wwwwwwww	chr1:173754474-173754696(+)$1	222	75	83	14.3921
iiiii:::	chr9:114696712-114696932(+)$1	220	135	143	14.3921
rrrrrrre	chr6:42175419-42175643(-)$1	224	36	44	11.7450
gggggggq	chr5:135516873-135517091(+)$1	218	102	110	12.5294
fff$$$$$	chr7:77268977-77269197(+)$1	220	164	172	14.3921
[bb[eeee	chr9:125670291-125670514(-)$1	223	138	146	12.6274
ooooffff	chr13:21548664-21548889(-)$1	225	110	118	18.0196

#DB
..))))))	chr14:77806556-77806778(-)$1	1	153	161	18.0196
)))))..)	chr19:23835507-23835737(-)$1	1	157	165	12.5294
...)))))	chr9:111780777-111781000(-)$1	1	49	57	14.3921
....))))	chr2:158287327-158287545(-)$1	1	181	189	15.5686
....))))	chr8:82712774-82713001(-)$1	1	48	56	13.4117
(.....))	chr21:35472577-35472800(+)$1	1	31	39	13.9019
((((....	chr15:83685991-83686214(-)$1	1	28	36	12.8235
...)))))	chr21:42767539-42767769(+)$1	1	144	152	12.0392
.((((...	chr12:88590052-88590269(+)$1	1	36	44	16.6470
))))....	chr12:27181330-27181556(+)$1	1	193	201	13.5098
..(((...	chr5:145667120-145667343(+)$1	1	126	134	12.6274
.((((((.	chrX:110463988-110464206(-)$1	1	76	84	13.6078
(((((((.	chr18:60793190-60793450(-)$1	1	223	231	12.2352
((((((..	chrX:41379382-41379612(-)$1	1	60	68	13.0196
.(((((((	chr14:74181930-74182160(-)$1	1	6	14	13.9019
......))	chr10:126674068-126674293(+)$1	1	195	203	14.3921
((......	chr6:118781952-118782182(-)$1	1	173	181	13.6078
))))))))	chr6:79647862-79648080(-)$1	1	91	99	14.3921
)..)))))	chr5:172563238-172563460(+)$1	1	29	37	13.8039
))......	chr4:146057902-146058132(-)$1	1	218	226	18.0196
))))...(	chr8:48973901-48974122(+)$1	1	87	95	14.1960
(((((...	chr12:93166296-93166522(-)$1	1	196	204	14.0000
.(((((((	chr14:55309008-55309231(-)$1	1	28	36	12.2352
)))))..)	chr9:5468303-5468540(+)$1	1	101	109	13.0196
).))....	chr6:97002462-97002682(+)$1	1	57	65	12.5294
.(((((((	chr8:94744309-94744534(-)$1	1	6	14	14.3921
).......	chr12:12874046-12874271(+)$1	1	172	180	14.1960
.(((((((	chr19:53570679-53570909(-)$1	1	21	29	11.5490
(....((.	chr3:193856193-193856418(+)$1	1	15	23	14.1960
)).)))))	chr6:159056099-159056343(+)$1	1	143	151	14.1960
(((((((.	chr2:173435397-173435618(+)$1	1	25	33	13.6078
)))..(((	chr1:26449960-26450178(+)$1	1	47	55	16.6470
))......	chr5:78073089-78073312(-)$1	1	181	189	13.0196
(......)	chr6:109689606-109689831(-)$1	1	33	41	18.0196
((.(.(((	chr7:2400245-2400467(+)$1	1	51	59	13.6078
....))))	chr11:93528096-93528326(+)$1	1	34	42	15.5686
..))))))	chr18:43464655-43464875(-)$1	1	73	81	16.6470
)....)))	chr17:27953128-27953347(-)$1	1	190	198	16.6470
.......)	chr17:1326178-1326408(-)$1	1	177	185	14.0000
((.(((..	chr17:63010143-63010412(-)$1	1	61	69	13.8039
.......(	chr12:42475776-42475997(-)$1	1	35	43	13.9019
.......)	chr12:77415025-77415245(-)$1	1	158	166	18.0196
.)).))).	chr12:75892749-75892979(-)$1	1	72	80	11.5490
((((.(((	chr12:93802186-93802406(-)$1	1	41	49	13.5098
........	chr1:173754474-173754696(+)$1	1	75	83	14.3921
)))))...	chr9:114696712-114696932(+)$1	1	135	143	14.3921
.......)	chr6:42175419-42175643(-)$1	1	36	44	11.7450
(((((((.	chr5:135516873-135517091(+)$1	1	102	110	12.5294
(((.....	chr7:77268977-77269197(+)$1	1	164	172	14.3921
.((.((((	chr9:125670291-125670514(-)$1	1	138	146	12.6274
....))))	chr13:21548664-21548889(-)$1	1	110	118	18.0196

#PSSM
A : 0.86	a : 0.05	G : 0.03	C : 0.01	U : 0.01	
U : 0.56	C : 0.27	A : 0.09	c : 0.03	u : 0.01	
A : 0.86	a : 0.05	C : 0.03	G : 0.03	
U : 0.78	A : 0.07	G : 0.05	u : 0.03	a : 0.01	C : 0.01	
U : 0.84	G : 0.05	C : 0.03	u : 0.03	g : 0.01	
U : 0.90	u : 0.05	C : 0.03	
U : 0.76	A : 0.09	G : 0.05	u : 0.05	C : 0.01	
U : 0.84	G : 0.05	A : 0.03	u : 0.03	a : 0.01	

#score	723.6078431372549
#seq	51
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m1_run1.nuc.txt

#NT
CUUU	chr11:86658464-86658704(-)$1	240	79	83	11.9999
CUUU	chr18:25530902-25531142(-)$1	240	99	103	11.9999
CUUU	chr22:38337719-38337959(+)$1	240	39	43	11.9999
CUUU	chr1:235275023-235275263(-)$1	240	18	22	11.9999
CUUU	chr5:33467913-33468199(+)$1	286	160	164	11.9999
CUUU	chr4:39826570-39826810(-)$1	240	90	94	11.9999
CUUU	chr7:913539-913800(+)$1	261	159	163	11.9999
CUUU	chr5:14697083-14697363(+)$1	280	129	133	11.9999
CUUU	chr5:171638289-171638529(-)$1	240	47	51	11.9999
CUUU	chr6:56323609-56323849(-)$1	240	187	191	11.9999
CUUU	chr17:75211285-75211525(+)$1	240	65	69	11.9999
cuuu	chr10:89512999-89513239(-)$1	240	76	80	11.9999
CUUU	chr6:38137915-38138155(-)$1	240	56	60	11.9999
CUUU	chr15:25583657-25583897(-)$1	240	75	79	11.9999
CUUU	chr21:40567890-40568130(-)$1	240	118	122	11.9999
CUUU	chr19:46206268-46206508(+)$1	240	139	143	11.9999
CUUU	chr15:31668228-31668468(+)$1	240	108	112	11.9999
CUUU	chrX:102005556-102005797(+)$1	241	93	97	11.9999
CUUU	chr12:80239001-80239242(-)$1	241	8	12	11.9999
CUUU	chr19:21907801-21908042(-)$1	241	105	109	11.9999
CUUU	chr1:206907340-206907607(+)$1	267	107	111	11.9999
CUUU	chr11:78147702-78147946(-)$1	244	196	200	11.9999
CUUU	chr6:33161749-33161989(-)$1	240	51	55	11.9999
cuuu	chr7:25161084-25161324(-)$1	240	184	188	11.9999
CUUU	chr18:28572213-28572493(-)$1	280	2	6	11.9999
CUUU	chr7:154753144-154753384(-)$1	240	13	17	11.9999
CUUU	chr5:143538509-143538755(-)$1	246	10	14	11.9999
CUUU	chr1:233388288-233388528(-)$1	240	213	217	11.9999
CUUU	chr11:8124107-8124359(+)$1	252	69	73	11.9999
CUUU	chr9:125866646-125866886(+)$1	240	46	50	11.9999
CUUU	chr1:226333248-226333532(-)$1	284	23	27	11.9999
CUUU	chr12:6857833-6858113(-)$1	280	267	271	11.9999
CUUU	chr6:86318500-86318780(-)$1	280	90	94	11.9999
CUUU	chr5:76358918-76359192(+)$1	274	148	152	11.9999
CUUU	chr14:93705084-93705330(-)$1	246	39	43	11.9999
CUUU	chr3:150459085-150459325(-)$1	240	12	16	11.9999
CUUU	chr12:122626996-122627276(+)$1	280	79	83	11.9999
CUUU	chr20:35221019-35221339(+)$1	320	78	82	11.9999
CUUU	chrX:129299491-129299731(-)$1	240	132	136	11.9999
CUUU	chr1:192984979-192985223(-)$1	244	160	164	11.9999
CUUU	chr2:201345688-201345928(+)$1	240	101	105	11.9999
CUUU	chr5:127524502-127524742(+)$1	240	43	47	11.9999
CUUU	chr17:61666951-61667240(+)$1	289	19	23	11.9999
CUUU	chr14:71196165-71196405(-)$1	240	48	52	11.9999
CUUU	chr17:78442591-78442838(-)$1	247	92	96	11.9999
CUUU	chr3:57912983-57913223(+)$1	240	27	31	11.9999
CUUU	chr10:102120938-102121178(+)$1	240	12	16	11.9999
CUUU	chr14:61176238-61176478(-)$1	240	16	20	11.9999
CUUU	chr13:113540728-113540968(+)$1	240	59	63	11.9999
CUUU	chr1:202909995-202910275(-)$1	280	10	14	11.9999
CUUU	chr19:37266368-37266609(+)$1	241	56	60	11.9999
CUUU	chr3:9404665-9405005(+)$1	340	300	304	11.9999
CUUU	chr5:150070268-150070525(-)$1	257	203	207	11.9999
cuuu	chr12:131275797-131276037(-)$1	240	129	133	11.9999
CUUU	chr15:43668634-43668874(+)$1	240	9	13	11.9999
CUUU	chr6:108250554-108250797(-)$1	243	67	71	11.9999
CUUU	chr15:75193232-75193520(-)$1	288	16	20	11.9999
CUUU	chr12:110788386-110788634(+)$1	248	155	159	11.9999
CUUU	chr7:45758071-45758311(+)$1	240	108	112	11.9999
CUUU	chr6:105527690-105527930(+)$1	240	223	227	11.9999
CUUU	chr3:150301553-150301793(+)$1	240	70	74	11.9999
CUUU	chr14:67800939-67801179(+)$1	240	62	66	11.9999
CUUU	chr22:41322484-41322724(+)$1	240	21	25	11.9999
CUUU	chr12:117583150-117583390(-)$1	240	116	120	11.9999
CUUU	chr1:44170374-44170614(+)$1	240	52	56	11.9999
CUUU	chr16:57505845-57506085(-)$1	240	106	110	11.9999
CUUU	chr8:28610866-28611106(+)$1	240	174	178	11.9999
CUUU	chr4:174244771-174245011(+)$1	240	118	122	11.9999
CUUU	chr14:31425289-31425529(-)$1	240	66	70	11.9999
CUUU	chr1:87209461-87209701(+)$1	240	68	72	11.9999
CUUU	chr5:176722574-176722814(+)$1	240	10	14	11.9999
CUUU	chr8:95500914-95501158(-)$1	244	57	61	11.9999
CUUU	chr17:40994408-40994769(+)$1	361	81	85	11.9999
CUUU	chr10:22618340-22618581(+)$1	241	69	73	11.9999
CUUU	chr5:66463635-66463875(+)$1	240	41	45	11.9999
CUUU	chr7:120989966-120990249(-)$1	283	113	117	11.9999
CUUU	chr14:73586341-73586621(+)$1	280	73	77	11.9999
CUUU	chr1:36389637-36389877(+)$1	240	8	12	11.9999
CUUU	chr8:48889745-48890065(+)$1	320	166	170	11.9999
CUUU	chr5:34831630-34831870(+)$1	240	59	63	11.9999
CUUU	chr22:29184392-29184632(+)$1	240	232	236	11.9999
CUUU	chr11:20529893-20530174(+)$1	281	169	173	11.9999
CUUU	chr7:148877758-148878024(+)$1	266	31	35	11.9999
CUUU	chr17:74267170-74267418(+)$1	248	25	29	11.9999
CUUU	chr5:137842468-137842709(-)$1	241	61	65	11.9999
CUUU	chr11:96086407-96086647(-)$1	240	14	18	11.9999
CUUU	chr2:3502291-3502537(-)$1	246	188	192	11.9999
CUUU	chr12:118474105-118474385(-)$1	280	29	33	11.9999
CUUU	chr3:133878051-133878301(-)$1	250	75	79	11.9999
CUUU	chr1:228682361-228682693(+)$1	332	16	20	11.9999

#otherMatches

#Struct PSSM
::::	chr4:73941543-73941783(-)$1	240	63	67	11.9999
lggg	chr11:86658464-86658704(-)$1	240	79	83	11.9999
ff''	chr18:25530902-25531142(-)$1	240	99	103	11.9999
eeee	chr22:38337719-38337959(+)$1	240	39	43	11.9999
ffff	chr1:235275023-235275263(-)$1	240	18	22	11.9999
eeee	chr5:33467913-33468199(+)$1	286	160	164	11.9999
dqqq	chr4:39826570-39826810(-)$1	240	90	94	11.9999
nnnn	chr7:913539-913800(+)$1	261	159	163	11.9999
oooo	chr5:14697083-14697363(+)$1	280	129	133	11.9999
DDDL	chr5:171638289-171638529(-)$1	240	47	51	11.9999
JJJJ	chr6:56323609-56323849(-)$1	240	187	191	11.9999
gggg	chr17:75211285-75211525(+)$1	240	65	69	11.9999
[ccc	chr10:89512999-89513239(-)$1	240	76	80	11.9999
HHHH	chr6:38137915-38138155(-)$1	240	56	60	11.9999
d:::	chr15:25583657-25583897(-)$1	240	75	79	11.9999
""cc	chr21:40567890-40568130(-)$1	240	118	122	11.9999
c:::	chr19:46206268-46206508(+)$1	240	139	143	11.9999
[eee	chr15:31668228-31668468(+)$1	240	108	112	11.9999
::::	chrX:102005556-102005797(+)$1	241	93	97	11.9999
FFFF	chr12:80239001-80239242(-)$1	241	8	12	11.9999
ooog	chr19:21907801-21908042(-)$1	241	105	109	11.9999
====	chr1:206907340-206907607(+)$1	267	107	111	11.9999
EYYJ	chr11:78147702-78147946(-)$1	244	196	200	11.9999
iiii	chr6:33161749-33161989(-)$1	240	51	55	11.9999
::::	chr7:25161084-25161324(-)$1	240	184	188	11.9999
eeee	chr18:28572213-28572493(-)$1	280	2	6	11.9999
::::	chr7:154753144-154753384(-)$1	240	13	17	11.9999
ddxx	chr5:143538509-143538755(-)$1	246	10	14	11.9999
ffff	chr1:233388288-233388528(-)$1	240	213	217	11.9999
ffff	chr11:8124107-8124359(+)$1	252	69	73	11.9999
nnff	chr9:125866646-125866886(+)$1	240	46	50	11.9999
::::	chr1:226333248-226333532(-)$1	284	23	27	11.9999
G:::	chr12:6857833-6858113(-)$1	280	267	271	11.9999
::::	chr6:86318500-86318780(-)$1	280	90	94	11.9999
ii!!	chr5:76358918-76359192(+)$1	274	148	152	11.9999
g:::	chr14:93705084-93705330(-)$1	246	39	43	11.9999
brrr	chr3:150459085-150459325(-)$1	240	12	16	11.9999
%%%%	chr12:122626996-122627276(+)$1	280	79	83	11.9999
((((	chr20:35221019-35221339(+)$1	320	78	82	11.9999
gg##	chrX:129299491-129299731(-)$1	240	132	136	11.9999
ffff	chr1:192984979-192985223(-)$1	244	160	164	11.9999
ttdd	chr2:201345688-201345928(+)$1	240	101	105	11.9999
b===	chr5:127524502-127524742(+)$1	240	43	47	11.9999
6666	chr17:61666951-61667240(+)$1	289	19	23	11.9999
c:::	chr14:71196165-71196405(-)$1	240	48	52	11.9999
e:::	chr17:78442591-78442838(-)$1	247	92	96	11.9999
ggqq	chr3:57912983-57913223(+)$1	240	27	31	11.9999
::::	chr10:102120938-102121178(+)$1	240	12	16	11.9999
eeee	chr14:61176238-61176478(-)$1	240	16	20	11.9999
qqqe	chr13:113540728-113540968(+)$1	240	59	63	11.9999
JJJJ	chr1:202909995-202910275(-)$1	280	10	14	11.9999
gggl	chr19:37266368-37266609(+)$1	241	56	60	11.9999
EE::	chr3:9404665-9405005(+)$1	340	300	304	11.9999
bb##	chr5:150070268-150070525(-)$1	257	203	207	11.9999
bbmm	chr12:131275797-131276037(-)$1	240	129	133	11.9999
GGGC	chr15:43668634-43668874(+)$1	240	9	13	11.9999
iiee	chr6:108250554-108250797(-)$1	243	67	71	11.9999
::::	chr15:75193232-75193520(-)$1	288	16	20	11.9999
c[hh	chr12:110788386-110788634(+)$1	248	155	159	11.9999
bb[c	chr7:45758071-45758311(+)$1	240	108	112	11.9999
GGG:	chr6:105527690-105527930(+)$1	240	223	227	11.9999
[iii	chr3:150301553-150301793(+)$1	240	70	74	11.9999
dddd	chr14:67800939-67801179(+)$1	240	62	66	11.9999
f"""	chr22:41322484-41322724(+)$1	240	21	25	11.9999
0000	chr12:117583150-117583390(-)$1	240	116	120	11.9999
cmmm	chr1:44170374-44170614(+)$1	240	52	56	11.9999
HHHH	chr16:57505845-57506085(-)$1	240	106	110	11.9999
===]	chr8:28610866-28611106(+)$1	240	174	178	11.9999
eeee	chr4:174244771-174245011(+)$1	240	118	122	11.9999
DDDD	chr14:31425289-31425529(-)$1	240	66	70	11.9999
dddd	chr1:87209461-87209701(+)$1	240	68	72	11.9999
C::g	chr5:176722574-176722814(+)$1	240	10	14	11.9999
====	chr8:95500914-95501158(-)$1	244	57	61	11.9999
gggg	chr17:40994408-40994769(+)$1	361	81	85	11.9999
'''d	chr10:22618340-22618581(+)$1	241	69	73	11.9999
a[cc	chr5:66463635-66463875(+)$1	240	41	45	11.9999
ffff	chr7:120989966-120990249(-)$1	283	113	117	11.9999
b[dd	chr14:73586341-73586621(+)$1	280	73	77	11.9999
::::	chr1:36389637-36389877(+)$1	240	8	12	11.9999
YDDD	chr8:48889745-48890065(+)$1	320	166	170	11.9999
yyyd	chr5:34831630-34831870(+)$1	240	59	63	11.9999
EE::	chr22:29184392-29184632(+)$1	240	232	236	11.9999
$eee	chr11:20529893-20530174(+)$1	281	169	173	11.9999
::::	chr7:148877758-148878024(+)$1	266	31	35	11.9999
MMMM	chr17:74267170-74267418(+)$1	248	25	29	11.9999
ffff	chr5:137842468-137842709(-)$1	241	61	65	11.9999
!!bb	chr11:96086407-96086647(-)$1	240	14	18	11.9999
hhhh	chr2:3502291-3502537(-)$1	246	188	192	11.9999
::::	chr12:118474105-118474385(-)$1	280	29	33	11.9999
bbnn	chr3:133878051-133878301(-)$1	250	75	79	11.9999
KGGG	chr1:228682361-228682693(+)$1	332	16	20	11.9999

#DB
....	chr4:73941543-73941783(-)$1	1	63	67	11.9999
.)))	chr11:86658464-86658704(-)$1	1	79	83	11.9999
((..	chr18:25530902-25531142(-)$1	1	99	103	11.9999
((((	chr22:38337719-38337959(+)$1	1	39	43	11.9999
))))	chr1:235275023-235275263(-)$1	1	18	22	11.9999
))))	chr5:33467913-33468199(+)$1	1	160	164	11.9999
(...	chr4:39826570-39826810(-)$1	1	90	94	11.9999
....	chr7:913539-913800(+)$1	1	159	163	11.9999
....	chr5:14697083-14697363(+)$1	1	129	133	11.9999
(((.	chr5:171638289-171638529(-)$1	1	47	51	11.9999
))))	chr6:56323609-56323849(-)$1	1	187	191	11.9999
((((	chr17:75211285-75211525(+)$1	1	65	69	11.9999
.(((	chr10:89512999-89513239(-)$1	1	76	80	11.9999
((((	chr6:38137915-38138155(-)$1	1	56	60	11.9999
)...	chr15:25583657-25583897(-)$1	1	75	79	11.9999
..((	chr21:40567890-40568130(-)$1	1	118	122	11.9999
)...	chr19:46206268-46206508(+)$1	1	139	143	11.9999
.(((	chr15:31668228-31668468(+)$1	1	108	112	11.9999
....	chrX:102005556-102005797(+)$1	1	93	97	11.9999
((((	chr12:80239001-80239242(-)$1	1	8	12	11.9999
...)	chr19:21907801-21908042(-)$1	1	105	109	11.9999
))))	chr1:206907340-206907607(+)$1	1	107	111	11.9999
)..)	chr11:78147702-78147946(-)$1	1	196	200	11.9999
((((	chr6:33161749-33161989(-)$1	1	51	55	11.9999
....	chr7:25161084-25161324(-)$1	1	184	188	11.9999
((((	chr18:28572213-28572493(-)$1	1	2	6	11.9999
....	chr7:154753144-154753384(-)$1	1	13	17	11.9999
((..	chr5:143538509-143538755(-)$1	1	10	14	11.9999
))))	chr1:233388288-233388528(-)$1	1	213	217	11.9999
))))	chr11:8124107-8124359(+)$1	1	69	73	11.9999
..))	chr9:125866646-125866886(+)$1	1	46	50	11.9999
....	chr1:226333248-226333532(-)$1	1	23	27	11.9999
)...	chr12:6857833-6858113(-)$1	1	267	271	11.9999
....	chr6:86318500-86318780(-)$1	1	90	94	11.9999
((..	chr5:76358918-76359192(+)$1	1	148	152	11.9999
)...	chr14:93705084-93705330(-)$1	1	39	43	11.9999
(...	chr3:150459085-150459325(-)$1	1	12	16	11.9999
....	chr12:122626996-122627276(+)$1	1	79	83	11.9999
....	chr20:35221019-35221339(+)$1	1	78	82	11.9999
((..	chrX:129299491-129299731(-)$1	1	132	136	11.9999
((((	chr1:192984979-192985223(-)$1	1	160	164	11.9999
..))	chr2:201345688-201345928(+)$1	1	101	105	11.9999
((((	chr5:127524502-127524742(+)$1	1	43	47	11.9999
....	chr17:61666951-61667240(+)$1	1	19	23	11.9999
)...	chr14:71196165-71196405(-)$1	1	48	52	11.9999
)...	chr17:78442591-78442838(-)$1	1	92	96	11.9999
((..	chr3:57912983-57913223(+)$1	1	27	31	11.9999
....	chr10:102120938-102121178(+)$1	1	12	16	11.9999
((((	chr14:61176238-61176478(-)$1	1	16	20	11.9999
...)	chr13:113540728-113540968(+)$1	1	59	63	11.9999
((((	chr1:202909995-202910275(-)$1	1	10	14	11.9999
(((.	chr19:37266368-37266609(+)$1	1	56	60	11.9999
))..	chr3:9404665-9405005(+)$1	1	300	304	11.9999
((..	chr5:150070268-150070525(-)$1	1	203	207	11.9999
((..	chr12:131275797-131276037(-)$1	1	129	133	11.9999
((((	chr15:43668634-43668874(+)$1	1	9	13	11.9999
((((	chr6:108250554-108250797(-)$1	1	67	71	11.9999
....	chr15:75193232-75193520(-)$1	1	16	20	11.9999
(.((	chr12:110788386-110788634(+)$1	1	155	159	11.9999
((.(	chr7:45758071-45758311(+)$1	1	108	112	11.9999
))).	chr6:105527690-105527930(+)$1	1	223	227	11.9999
.(((	chr3:150301553-150301793(+)$1	1	70	74	11.9999
))))	chr14:67800939-67801179(+)$1	1	62	66	11.9999
(...	chr22:41322484-41322724(+)$1	1	21	25	11.9999
....	chr12:117583150-117583390(-)$1	1	116	120	11.9999
(...	chr1:44170374-44170614(+)$1	1	52	56	11.9999
))))	chr16:57505845-57506085(-)$1	1	106	110	11.9999
))).	chr8:28610866-28611106(+)$1	1	174	178	11.9999
))))	chr4:174244771-174245011(+)$1	1	118	122	11.9999
((((	chr14:31425289-31425529(-)$1	1	66	70	11.9999
((((	chr1:87209461-87209701(+)$1	1	68	72	11.9999
(..(	chr5:176722574-176722814(+)$1	1	10	14	11.9999
))))	chr8:95500914-95501158(-)$1	1	57	61	11.9999
))))	chr17:40994408-40994769(+)$1	1	81	85	11.9999
...(	chr10:22618340-22618581(+)$1	1	69	73	11.9999
(.((	chr5:66463635-66463875(+)$1	1	41	45	11.9999
))))	chr7:120989966-120990249(-)$1	1	113	117	11.9999
(.((	chr14:73586341-73586621(+)$1	1	73	77	11.9999
....	chr1:36389637-36389877(+)$1	1	8	12	11.9999
.)))	chr8:48889745-48890065(+)$1	1	166	170	11.9999
...)	chr5:34831630-34831870(+)$1	1	59	63	11.9999
))..	chr22:29184392-29184632(+)$1	1	232	236	11.9999
.(((	chr11:20529893-20530174(+)$1	1	169	173	11.9999
....	chr7:148877758-148878024(+)$1	1	31	35	11.9999
....	chr17:74267170-74267418(+)$1	1	25	29	11.9999
((((	chr5:137842468-137842709(-)$1	1	61	65	11.9999
..((	chr11:96086407-96086647(-)$1	1	14	18	11.9999
((((	chr2:3502291-3502537(-)$1	1	188	192	11.9999
....	chr12:118474105-118474385(-)$1	1	29	33	11.9999
((..	chr3:133878051-133878301(-)$1	1	75	79	11.9999
.(((	chr1:228682361-228682693(+)$1	1	16	20	11.9999

#PSSM
C : 0.96	c : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	

#score	1091.9999999999995
#seq	91
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_CDS_m2_run2.nuc.txt

#NT
GAAAA	chr2:44428653-44428883(+)$1	230	17	22	15.0000
GAAAA	chr17:58365863-58366088(-)$1	225	48	53	15.0000
GAAAA	chr5:159520693-159520918(-)$1	225	137	142	15.0000
GAAAA	chr2:61433072-61433302(-)$1	230	162	167	15.0000
GAAAA	chr10:31137859-31138082(-)$1	223	38	43	15.0000
GAAAA	chr2:160604264-160604486(+)$1	222	98	103	15.0000
GAAAA	chr3:130653366-130653593(+)$1	227	193	198	15.0000
GAAAA	chr6:79607843-79608073(+)$1	230	17	22	15.0000
GAAAA	chr10:28824540-28824766(+)$1	226	1	6	15.0000
GAAAA	chr1:160456805-160457035(-)$1	230	94	99	15.0000
GAAAA	chr2:178095723-178095953(-)$1	230	33	38	15.0000
GAAAA	chr3:51477732-51477962(-)$1	230	133	138	15.0000
GAAAA	chr1:54508979-54509209(-)$1	230	144	149	15.0000
GAAAA	chr8:64099668-64099891(+)$1	223	17	22	15.0000
GAAAA	chr13:25886994-25887224(+)$1	230	188	193	15.0000
GAAAA	chr18:59925762-59925986(+)$1	224	132	137	15.0000
GAAAA	chr9:2039509-2039739(+)$1	230	224	229	15.0000
GAAAA	chrX:117578238-117578468(+)$1	230	158	163	15.0000
GAAAA	chr1:111494646-111494873(-)$1	227	81	86	15.0000
GAAAA	chr21:33038678-33038901(+)$1	223	122	127	15.0000
GAAAA	chr4:174298299-174298529(+)$1	230	92	97	15.0000
GAAAA	chr6:149699821-149700051(+)$1	230	194	199	15.0000
GAAAA	chr22:26890687-26890908(-)$1	221	116	121	15.0000
GAAAA	chr14:106321182-106321412(-)$1	230	224	229	15.0000
GAAAA	chr10:97605090-97605320(+)$1	230	22	27	15.0000
GAAAA	chrX:30577827-30578049(-)$1	222	161	166	15.0000
GAAAA	chr4:154517412-154517638(+)$1	226	59	64	15.0000
GAAAA	chr11:32994966-32995196(+)$1	230	86	91	15.0000
GAAAA	chr11:11374342-11374567(-)$1	225	28	33	15.0000
GAAAA	chr4:113540244-113540469(-)$1	225	196	201	15.0000
GAAAA	chr9:21334412-21334636(-)$1	224	89	94	15.0000
GAAAA	chr5:145610267-145610490(+)$1	223	110	115	15.0000
GAAAA	chr14:35480698-35480921(+)$1	223	74	79	15.0000
GAAAA	chr1:175958484-175958714(-)$1	230	17	22	15.0000
GAAAA	chr11:10820798-10821021(-)$1	223	7	12	15.0000
GAAAA	chr13:39603354-39603581(-)$1	227	5	10	15.0000
GAAAA	chr17:56572650-56572880(-)$1	230	3	8	15.0000
GAAAA	chr14:57741322-57741546(+)$1	224	158	163	15.0000
GAAAA	chrX:51488236-51488457(+)$1	221	184	189	15.0000
GAAAA	chr8:26196327-26196551(+)$1	224	37	42	15.0000
GAAAA	chr3:43384755-43384985(+)$1	230	150	155	15.0000
GAAAA	chr6:2890601-2890828(-)$1	227	27	32	15.0000
GAAAA	chr1:7527818-7528040(-)$1	222	163	168	15.0000
GAAAA	chr1:193018841-193019068(-)$1	227	213	218	15.0000
GAAAA	chr1:158987947-158988177(+)$1	230	76	81	15.0000
GAAAA	chr7:7273834-7274064(+)$1	230	212	217	15.0000
GAAAA	chr12:123098119-123098349(+)$1	230	164	169	15.0000
GAAAA	chr9:114694510-114694729(+)$1	219	145	150	15.0000
GAAAA	chr11:102195490-102195720(+)$1	230	134	139	15.0000
GAAAA	chr15:65982780-65983010(-)$1	230	190	195	15.0000
GAAAA	chr21:34117043-34117265(-)$1	222	49	54	15.0000
GAAAA	chr12:57144798-57145028(-)$1	230	144	149	15.0000
GAAAA	chr10:120921786-120922016(-)$1	230	99	104	15.0000
GAAAA	chr6:31632112-31632331(+)$1	219	161	166	15.0000
GAAAA	chr8:38146813-38147038(-)$1	225	86	91	15.0000
GAAAA	chr6:32820070-32820300(-)$1	230	147	152	15.0000
GAAAA	chr1:14108140-14108373(+)$1	233	165	170	15.0000

#otherMatches

#Struct PSSM
EE~~~	chr3:48730401-48730631(-)$1	230	189	194	15.0000
hhhhh	chr2:44428653-44428883(+)$1	230	17	22	15.0000
bb[hh	chr17:58365863-58366088(-)$1	225	48	53	15.0000
EZZZB	chr5:159520693-159520918(-)$1	225	137	142	15.0000
=====	chr2:61433072-61433302(-)$1	230	162	167	15.0000
cc(((	chr10:31137859-31138082(-)$1	223	38	43	15.0000
:::::	chr2:160604264-160604486(+)$1	222	98	103	15.0000
qqqqq	chr3:130653366-130653593(+)$1	227	193	198	15.0000
)))))	chr6:79607843-79608073(+)$1	230	17	22	15.0000
DDDDL	chr10:28824540-28824766(+)$1	226	1	6	15.0000
ee:ff	chr1:160456805-160457035(-)$1	230	94	99	15.0000
:::::	chr2:178095723-178095953(-)$1	230	33	38	15.0000
ttttt	chr3:51477732-51477962(-)$1	230	133	138	15.0000
EEEEZ	chr1:54508979-54509209(-)$1	230	144	149	15.0000
{CCC{	chr8:64099668-64099891(+)$1	223	17	22	15.0000
eeeeh	chr13:25886994-25887224(+)$1	230	188	193	15.0000
ccc[e	chr18:59925762-59925986(+)$1	224	132	137	15.0000
ee:::	chr9:2039509-2039739(+)$1	230	224	229	15.0000
eemmm	chrX:117578238-117578468(+)$1	230	158	163	15.0000
bb:ff	chr1:111494646-111494873(-)$1	227	81	86	15.0000
sssss	chr21:33038678-33038901(+)$1	223	122	127	15.0000
b]bb]	chr4:174298299-174298529(+)$1	230	92	97	15.0000
:::::	chr6:149699821-149700051(+)$1	230	194	199	15.0000
:::::	chr22:26890687-26890908(-)$1	221	116	121	15.0000
D::::	chr14:106321182-106321412(-)$1	230	224	229	15.0000
:::::	chr10:97605090-97605320(+)$1	230	22	27	15.0000
yyyyy	chrX:30577827-30578049(-)$1	222	161	166	15.0000
dddd[	chr4:154517412-154517638(+)$1	226	59	64	15.0000
ddd""	chr11:32994966-32995196(+)$1	230	86	91	15.0000
F::::	chr11:11374342-11374567(-)$1	225	28	33	15.0000
:::::	chr4:113540244-113540469(-)$1	225	196	201	15.0000
Fffff	chr9:21334412-21334636(-)$1	224	89	94	15.0000
:::::	chr5:145610267-145610490(+)$1	223	110	115	15.0000
mmmme	chr14:35480698-35480921(+)$1	223	74	79	15.0000
BBNNN	chr1:175958484-175958714(-)$1	230	17	22	15.0000
DDDD:	chr11:10820798-10821021(-)$1	223	7	12	15.0000
ggggp	chr13:39603354-39603581(-)$1	227	5	10	15.0000
CMMMM	chr17:56572650-56572880(-)$1	230	3	8	15.0000
II:::	chr14:57741322-57741546(+)$1	224	158	163	15.0000
ff:::	chrX:51488236-51488457(+)$1	221	184	189	15.0000
bb333	chr8:26196327-26196551(+)$1	224	37	42	15.0000
A}HHH	chr3:43384755-43384985(+)$1	230	150	155	15.0000
bbooo	chr6:2890601-2890828(-)$1	227	27	32	15.0000
ooooo	chr1:7527818-7528040(-)$1	222	163	168	15.0000
::::D	chr1:193018841-193019068(-)$1	227	213	218	15.0000
:::::	chr1:158987947-158988177(+)$1	230	76	81	15.0000
h::HH	chr7:7273834-7274064(+)$1	230	212	217	15.0000
fnnnn	chr12:123098119-123098349(+)$1	230	164	169	15.0000
iiiii	chr9:114694510-114694729(+)$1	219	145	150	15.0000
bb555	chr11:102195490-102195720(+)$1	230	134	139	15.0000
nnnnb	chr15:65982780-65983010(-)$1	230	190	195	15.0000
eeeee	chr21:34117043-34117265(-)$1	222	49	54	15.0000
eJJJJ	chr12:57144798-57145028(-)$1	230	144	149	15.0000
:::::	chr10:120921786-120922016(-)$1	230	99	104	15.0000
b4444	chr6:31632112-31632331(+)$1	219	161	166	15.0000
nnnnn	chr8:38146813-38147038(-)$1	225	86	91	15.0000
cc]ff	chr6:32820070-32820300(-)$1	230	147	152	15.0000
fff33	chr1:14108140-14108373(+)$1	233	165	170	15.0000

#DB
))...	chr3:48730401-48730631(-)$1	1	189	194	15.0000
(((((	chr2:44428653-44428883(+)$1	1	17	22	15.0000
((.((	chr17:58365863-58366088(-)$1	1	48	53	15.0000
)...)	chr5:159520693-159520918(-)$1	1	137	142	15.0000
(((((	chr2:61433072-61433302(-)$1	1	162	167	15.0000
((...	chr10:31137859-31138082(-)$1	1	38	43	15.0000
.....	chr2:160604264-160604486(+)$1	1	98	103	15.0000
.....	chr3:130653366-130653593(+)$1	1	193	198	15.0000
.....	chr6:79607843-79608073(+)$1	1	17	22	15.0000
((((.	chr10:28824540-28824766(+)$1	1	1	6	15.0000
)).((	chr1:160456805-160457035(-)$1	1	94	99	15.0000
.....	chr2:178095723-178095953(-)$1	1	33	38	15.0000
.....	chr3:51477732-51477962(-)$1	1	133	138	15.0000
)))).	chr1:54508979-54509209(-)$1	1	144	149	15.0000
.(((.	chr8:64099668-64099891(+)$1	1	17	22	15.0000
(((((	chr13:25886994-25887224(+)$1	1	188	193	15.0000
(((.(	chr18:59925762-59925986(+)$1	1	132	137	15.0000
))...	chr9:2039509-2039739(+)$1	1	224	229	15.0000
((...	chrX:117578238-117578468(+)$1	1	158	163	15.0000
)).((	chr1:111494646-111494873(-)$1	1	81	86	15.0000
.....	chr21:33038678-33038901(+)$1	1	122	127	15.0000
).)).	chr4:174298299-174298529(+)$1	1	92	97	15.0000
.....	chr6:149699821-149700051(+)$1	1	194	199	15.0000
.....	chr22:26890687-26890908(-)$1	1	116	121	15.0000
)....	chr14:106321182-106321412(-)$1	1	224	229	15.0000
.....	chr10:97605090-97605320(+)$1	1	22	27	15.0000
.....	chrX:30577827-30578049(-)$1	1	161	166	15.0000
((((.	chr4:154517412-154517638(+)$1	1	59	64	15.0000
(((..	chr11:32994966-32995196(+)$1	1	86	91	15.0000
(....	chr11:11374342-11374567(-)$1	1	28	33	15.0000
.....	chr4:113540244-113540469(-)$1	1	196	201	15.0000
(((((	chr9:21334412-21334636(-)$1	1	89	94	15.0000
.....	chr5:145610267-145610490(+)$1	1	110	115	15.0000
....)	chr14:35480698-35480921(+)$1	1	74	79	15.0000
((...	chr1:175958484-175958714(-)$1	1	17	22	15.0000
((((.	chr11:10820798-10821021(-)$1	1	7	12	15.0000
((((.	chr13:39603354-39603581(-)$1	1	5	10	15.0000
(....	chr17:56572650-56572880(-)$1	1	3	8	15.0000
))...	chr14:57741322-57741546(+)$1	1	158	163	15.0000
))...	chrX:51488236-51488457(+)$1	1	184	189	15.0000
))...	chr8:26196327-26196551(+)$1	1	37	42	15.0000
).)))	chr3:43384755-43384985(+)$1	1	150	155	15.0000
((...	chr6:2890601-2890828(-)$1	1	27	32	15.0000
.....	chr1:7527818-7528040(-)$1	1	163	168	15.0000
....)	chr1:193018841-193019068(-)$1	1	213	218	15.0000
.....	chr1:158987947-158988177(+)$1	1	76	81	15.0000
)..))	chr7:7273834-7274064(+)$1	1	212	217	15.0000
(....	chr12:123098119-123098349(+)$1	1	164	169	15.0000
)))))	chr9:114694510-114694729(+)$1	1	145	150	15.0000
))...	chr11:102195490-102195720(+)$1	1	134	139	15.0000
....)	chr15:65982780-65983010(-)$1	1	190	195	15.0000
)))))	chr21:34117043-34117265(-)$1	1	49	54	15.0000
)((((	chr12:57144798-57145028(-)$1	1	144	149	15.0000
.....	chr10:120921786-120922016(-)$1	1	99	104	15.0000
)....	chr6:31632112-31632331(+)$1	1	161	166	15.0000
.....	chr8:38146813-38147038(-)$1	1	86	91	15.0000
)).))	chr6:32820070-32820300(-)$1	1	147	152	15.0000
)))..	chr1:14108140-14108373(+)$1	1	165	170	15.0000

#PSSM
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	

#score	870.0000000000001
#seq	58
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUU	chr1:205686028-205686256(-)$1	228	184	189	14.9999
UUUUU	chr14:23033769-23034001(-)$1	232	59	64	14.9999
UUUUU	chr15:65737814-65738043(-)$1	229	145	150	14.9999
UUUUU	chr3:14528431-14528663(+)$1	232	4	9	14.9999
UUUUU	chr7:39612341-39612566(+)$1	225	136	141	14.9999
UUUUU	chr5:125829825-125830058(+)$1	233	78	83	14.9999
UUUUU	chr6:137518607-137518833(-)$1	226	29	34	14.9999
UUUUU	chr18:723131-723364(-)$1	233	117	122	14.9999
UUUUU	chr15:65441182-65441414(-)$1	232	10	15	14.9999
UUUUU	chr12:96673133-96673363(-)$1	230	46	51	14.9999
UUUUU	chr10:115671402-115671632(+)$1	230	208	213	14.9999
UUUUU	chr1:213166035-213166267(-)$1	232	38	43	14.9999
UUUUU	chr1:113673397-113673623(+)$1	226	146	151	14.9999
UUUUU	chr12:66357254-66357481(+)$1	227	105	110	14.9999
uuuuu	chr4:3273331-3273563(+)$1	232	150	155	14.9999
UUUUU	chr2:100016497-100016730(+)$1	233	165	170	14.9999
UUUUU	chr5:68473458-68473690(+)$1	232	110	115	14.9999
UUUUU	chr8:79515199-79515423(+)$1	224	25	30	14.9999
UUUUU	chr17:57777965-57778191(-)$1	226	190	195	14.9999
uuuuu	chr6:144146761-144146993(+)$1	232	30	35	14.9999
UUUUU	chr11:47799571-47799803(-)$1	232	68	73	14.9999
UUUUU	chr15:83686243-83686475(-)$1	232	3	8	14.9999
UUUUU	chr6:1612872-1613104(+)$1	232	71	76	14.9999
UUUUU	chr17:46669248-46669480(+)$1	232	0	5	14.9999
uuuuu	chr11:6504879-6505111(+)$1	232	58	63	14.9999
UUUUU	chr5:37206426-37206658(-)$1	232	29	34	14.9999
UUUUU	chr1:47142056-47142282(-)$1	226	102	107	14.9999
UUUUU	chr12:98928456-98928679(+)$1	223	78	83	14.9999
UUUUU	chrX:147031426-147031656(+)$1	230	115	120	14.9999
UUUUU	chr5:95131334-95131562(+)$1	228	185	190	14.9999
UUUUU	chr2:24290445-24290691(-)$1	246	112	117	14.9999
UUUUU	chr17:56082502-56082726(-)$1	224	30	35	14.9999
uuuuu	chr3:123330177-123330421(+)$1	244	210	215	14.9999
UUUUU	chr21:16336189-16336422(-)$1	233	92	97	14.9999
UUUUU	chr2:170668429-170668661(+)$1	232	148	153	14.9999
uuuuu	chr19:24312011-24312245(+)$1	234	69	74	14.9999
UUUUU	chr12:133160887-133161119(+)$1	232	0	5	14.9999
UUUUU	chr2:70676620-70676845(-)$1	225	3	8	14.9999
uuuuu	chr2:37329325-37329556(-)$1	231	124	129	14.9999
UUUUU	chr16:2553150-2553395(+)$1	245	75	80	14.9999
UUUUU	chr4:71657713-71657956(+)$1	243	155	160	14.9999
UUUUU	chr8:146106393-146106624(-)$1	231	79	84	14.9999
UUUUU	chr3:120407424-120407654(-)$1	230	32	37	14.9999
UUUUU	chr21:43410265-43410500(-)$1	235	60	65	14.9999
UUUUU	chr4:85593414-85593643(-)$1	229	64	69	14.9999
UUUUU	chr14:93669588-93669814(-)$1	226	51	56	14.9999
UUUUU	chr12:100733414-100733647(+)$1	233	53	58	14.9999
UUUUU	chr10:3820879-3821111(-)$1	232	184	189	14.9999
UUUUU	chrX:107965415-107965641(-)$1	226	133	138	14.9999
uuuuu	chr3:41281495-41281729(+)$1	234	0	5	14.9999
uuuuu	chr11:6617476-6617708(-)$1	232	151	156	14.9999
UUUUU	chr1:115312351-115312577(-)$1	226	197	202	14.9999
UUUUU	chr10:115668533-115668765(+)$1	232	114	119	14.9999
UUUUU	chr15:71173724-71173954(-)$1	230	175	180	14.9999
UUUUU	chrX:103436894-103437146(+)$1	252	109	114	14.9999
UUUUU	chr17:65336531-65336769(-)$1	238	63	68	14.9999
UUUUU	chr9:133513580-133513811(+)$1	231	64	69	14.9999
UUUUU	chr6:136581715-136581937(-)$1	222	167	172	14.9999
UUUUU	chr5:133291104-133291334(-)$1	230	58	63	14.9999
UUUUU	chr18:19447987-19448220(+)$1	233	68	73	14.9999
UUUUU	chr1:59123904-59124136(-)$1	232	139	144	14.9999
UUUUU	chr22:17618521-17618753(-)$1	232	10	15	14.9999
UUUUU	chr5:142659928-142660157(-)$1	229	223	228	14.9999
UUUUU	chr4:175240780-175241012(+)$1	232	165	170	14.9999
UUUUU	chr9:91090380-91090623(+)$1	243	182	187	14.9999
UUUUU	chr1:52882424-52882650(+)$1	226	41	46	14.9999
UUUUU	chr12:50569599-50569821(-)$1	222	0	5	14.9999
UUUUU	chr8:82570782-82571007(-)$1	225	76	81	14.9999
uuuuu	chr2:71634588-71634813(+)$1	225	59	64	14.9999
UUUUU	chr7:44874883-44875129(-)$1	246	200	205	14.9999
UUUUU	chr7:12269209-12269441(+)$1	232	53	58	14.9999

#otherMatches

#Struct PSSM
$$$$f	chr13:111372459-111372686(+)$1	227	151	156	14.9999
::::G	chr1:205686028-205686256(-)$1	228	184	189	14.9999
ggggg	chr14:23033769-23034001(-)$1	232	59	64	14.9999
55bb2	chr15:65737814-65738043(-)$1	229	145	150	14.9999
cc[gg	chr3:14528431-14528663(+)$1	232	4	9	14.9999
qqqqq	chr7:39612341-39612566(+)$1	225	136	141	14.9999
rrrdd	chr5:125829825-125830058(+)$1	233	78	83	14.9999
cccmm	chr6:137518607-137518833(-)$1	226	29	34	14.9999
iiiii	chr18:723131-723364(-)$1	233	117	122	14.9999
DDDLL	chr15:65441182-65441414(-)$1	232	10	15	14.9999
:ffff	chr12:96673133-96673363(-)$1	230	46	51	14.9999
iiiii	chr10:115671402-115671632(+)$1	230	208	213	14.9999
essss	chr1:213166035-213166267(-)$1	232	38	43	14.9999
ccc22	chr1:113673397-113673623(+)$1	226	146	151	14.9999
:::FF	chr12:66357254-66357481(+)$1	227	105	110	14.9999
cpppp	chr4:3273331-3273563(+)$1	232	150	155	14.9999
eesss	chr2:100016497-100016730(+)$1	233	165	170	14.9999
HHHHH	chr5:68473458-68473690(+)$1	232	110	115	14.9999
e!!cc	chr8:79515199-79515423(+)$1	224	25	30	14.9999
22ccc	chr17:57777965-57778191(-)$1	226	190	195	14.9999
:FFFF	chr6:144146761-144146993(+)$1	232	30	35	14.9999
nnnnb	chr11:47799571-47799803(-)$1	232	68	73	14.9999
:dddd	chr15:83686243-83686475(-)$1	232	3	8	14.9999
22ccc	chr6:1612872-1613104(+)$1	232	71	76	14.9999
:JJJJ	chr17:46669248-46669480(+)$1	232	0	5	14.9999
bnnnn	chr11:6504879-6505111(+)$1	232	58	63	14.9999
:::::	chr5:37206426-37206658(-)$1	232	29	34	14.9999
f::::	chr1:47142056-47142282(-)$1	226	102	107	14.9999
e::::	chr12:98928456-98928679(+)$1	223	78	83	14.9999
4dddd	chrX:147031426-147031656(+)$1	230	115	120	14.9999
nnnnn	chr5:95131334-95131562(+)$1	228	185	190	14.9999
:::::	chr2:24290445-24290691(-)$1	246	112	117	14.9999
:::::	chr17:56082502-56082726(-)$1	224	30	35	14.9999
nnnnn	chr3:123330177-123330421(+)$1	244	210	215	14.9999
bb22e	chr21:16336189-16336422(-)$1	233	92	97	14.9999
ddlll	chr2:170668429-170668661(+)$1	232	148	153	14.9999
cc22d	chr19:24312011-24312245(+)$1	234	69	74	14.9999
:::::	chr12:133160887-133161119(+)$1	232	0	5	14.9999
:::::	chr2:70676620-70676845(-)$1	225	3	8	14.9999
zzzzc	chr2:37329325-37329556(-)$1	231	124	129	14.9999
hhhh:	chr16:2553150-2553395(+)$1	245	75	80	14.9999
ggggg	chr4:71657713-71657956(+)$1	243	155	160	14.9999
ffnnn	chr8:146106393-146106624(-)$1	231	79	84	14.9999
:::::	chr3:120407424-120407654(-)$1	230	32	37	14.9999
c"""c	chr21:43410265-43410500(-)$1	235	60	65	14.9999
:::dd	chr4:85593414-85593643(-)$1	229	64	69	14.9999
4ffff	chr14:93669588-93669814(-)$1	226	51	56	14.9999
hhhhh	chr12:100733414-100733647(+)$1	233	53	58	14.9999
uuuuu	chr10:3820879-3821111(-)$1	232	184	189	14.9999
ee22c	chrX:107965415-107965641(-)$1	226	133	138	14.9999
:::::	chr3:41281495-41281729(+)$1	234	0	5	14.9999
ddsss	chr11:6617476-6617708(-)$1	232	151	156	14.9999
GGGG~	chr1:115312351-115312577(-)$1	226	197	202	14.9999
7hhhh	chr10:115668533-115668765(+)$1	232	114	119	14.9999
ggddd	chr15:71173724-71173954(-)$1	230	175	180	14.9999
mmmmf	chrX:103436894-103437146(+)$1	252	109	114	14.9999
EEddd	chr17:65336531-65336769(-)$1	238	63	68	14.9999
EELLL	chr9:133513580-133513811(+)$1	231	64	69	14.9999
C~~~~	chr6:136581715-136581937(-)$1	222	167	172	14.9999
f"""e	chr5:133291104-133291334(-)$1	230	58	63	14.9999
fffff	chr18:19447987-19448220(+)$1	233	68	73	14.9999
6666d	chr1:59123904-59124136(-)$1	232	139	144	14.9999
:::::	chr22:17618521-17618753(-)$1	232	10	15	14.9999
=====	chr5:142659928-142660157(-)$1	229	223	228	14.9999
qqqcc	chr4:175240780-175241012(+)$1	232	165	170	14.9999
:::::	chr9:91090380-91090623(+)$1	243	182	187	14.9999
vvvvv	chr1:52882424-52882650(+)$1	226	41	46	14.9999
:::::	chr12:50569599-50569821(-)$1	222	0	5	14.9999
b22==	chr8:82570782-82571007(-)$1	225	76	81	14.9999
mdddd	chr2:71634588-71634813(+)$1	225	59	64	14.9999
:::::	chr7:44874883-44875129(-)$1	246	200	205	14.9999
2hhhh	chr7:12269209-12269441(+)$1	232	53	58	14.9999

#DB
....(	chr13:111372459-111372686(+)$1	1	151	156	14.9999
....)	chr1:205686028-205686256(-)$1	1	184	189	14.9999
(((((	chr14:23033769-23034001(-)$1	1	59	64	14.9999
..)).	chr15:65737814-65738043(-)$1	1	145	150	14.9999
((.((	chr3:14528431-14528663(+)$1	1	4	9	14.9999
.....	chr7:39612341-39612566(+)$1	1	136	141	14.9999
...))	chr5:125829825-125830058(+)$1	1	78	83	14.9999
(((..	chr6:137518607-137518833(-)$1	1	29	34	14.9999
)))))	chr18:723131-723364(-)$1	1	117	122	14.9999
(((..	chr15:65441182-65441414(-)$1	1	10	15	14.9999
.((((	chr12:96673133-96673363(-)$1	1	46	51	14.9999
)))))	chr10:115671402-115671632(+)$1	1	208	213	14.9999
(....	chr1:213166035-213166267(-)$1	1	38	43	14.9999
)))..	chr1:113673397-113673623(+)$1	1	146	151	14.9999
...((	chr12:66357254-66357481(+)$1	1	105	110	14.9999
(....	chr4:3273331-3273563(+)$1	1	150	155	14.9999
((...	chr2:100016497-100016730(+)$1	1	165	170	14.9999
(((((	chr5:68473458-68473690(+)$1	1	110	115	14.9999
(..((	chr8:79515199-79515423(+)$1	1	25	30	14.9999
..)))	chr17:57777965-57778191(-)$1	1	190	195	14.9999
.((((	chr6:144146761-144146993(+)$1	1	30	35	14.9999
....)	chr11:47799571-47799803(-)$1	1	68	73	14.9999
.((((	chr15:83686243-83686475(-)$1	1	3	8	14.9999
..)))	chr6:1612872-1613104(+)$1	1	71	76	14.9999
.((((	chr17:46669248-46669480(+)$1	1	0	5	14.9999
(....	chr11:6504879-6505111(+)$1	1	58	63	14.9999
.....	chr5:37206426-37206658(-)$1	1	29	34	14.9999
)....	chr1:47142056-47142282(-)$1	1	102	107	14.9999
)....	chr12:98928456-98928679(+)$1	1	78	83	14.9999
.))))	chrX:147031426-147031656(+)$1	1	115	120	14.9999
.....	chr5:95131334-95131562(+)$1	1	185	190	14.9999
.....	chr2:24290445-24290691(-)$1	1	112	117	14.9999
.....	chr17:56082502-56082726(-)$1	1	30	35	14.9999
.....	chr3:123330177-123330421(+)$1	1	210	215	14.9999
))..)	chr21:16336189-16336422(-)$1	1	92	97	14.9999
((...	chr2:170668429-170668661(+)$1	1	148	153	14.9999
))..)	chr19:24312011-24312245(+)$1	1	69	74	14.9999
.....	chr12:133160887-133161119(+)$1	1	0	5	14.9999
.....	chr2:70676620-70676845(-)$1	1	3	8	14.9999
....)	chr2:37329325-37329556(-)$1	1	124	129	14.9999
)))).	chr16:2553150-2553395(+)$1	1	75	80	14.9999
)))))	chr4:71657713-71657956(+)$1	1	155	160	14.9999
((...	chr8:146106393-146106624(-)$1	1	79	84	14.9999
.....	chr3:120407424-120407654(-)$1	1	32	37	14.9999
(...(	chr21:43410265-43410500(-)$1	1	60	65	14.9999
...((	chr4:85593414-85593643(-)$1	1	64	69	14.9999
.))))	chr14:93669588-93669814(-)$1	1	51	56	14.9999
)))))	chr12:100733414-100733647(+)$1	1	53	58	14.9999
.....	chr10:3820879-3821111(-)$1	1	184	189	14.9999
))..)	chrX:107965415-107965641(-)$1	1	133	138	14.9999
.....	chr3:41281495-41281729(+)$1	1	0	5	14.9999
((...	chr11:6617476-6617708(-)$1	1	151	156	14.9999
)))).	chr1:115312351-115312577(-)$1	1	197	202	14.9999
.))))	chr10:115668533-115668765(+)$1	1	114	119	14.9999
(((((	chr15:71173724-71173954(-)$1	1	175	180	14.9999
....)	chrX:103436894-103437146(+)$1	1	109	114	14.9999
(((((	chr17:65336531-65336769(-)$1	1	63	68	14.9999
((...	chr9:133513580-133513811(+)$1	1	64	69	14.9999
)....	chr6:136581715-136581937(-)$1	1	167	172	14.9999
(...(	chr5:133291104-133291334(-)$1	1	58	63	14.9999
(((((	chr18:19447987-19448220(+)$1	1	68	73	14.9999
....)	chr1:59123904-59124136(-)$1	1	139	144	14.9999
.....	chr22:17618521-17618753(-)$1	1	10	15	14.9999
)))))	chr5:142659928-142660157(-)$1	1	223	228	14.9999
...))	chr4:175240780-175241012(+)$1	1	165	170	14.9999
.....	chr9:91090380-91090623(+)$1	1	182	187	14.9999
.....	chr1:52882424-52882650(+)$1	1	41	46	14.9999
.....	chr12:50569599-50569821(-)$1	1	0	5	14.9999
)..))	chr8:82570782-82571007(-)$1	1	76	81	14.9999
.))))	chr2:71634588-71634813(+)$1	1	59	64	14.9999
.....	chr7:44874883-44875129(-)$1	1	200	205	14.9999
.))))	chr7:12269209-12269441(+)$1	1	53	58	14.9999

#PSSM
U : 0.87	u : 0.12	
U : 0.87	u : 0.12	
U : 0.87	u : 0.12	
U : 0.87	u : 0.12	
U : 0.87	u : 0.12	

#score	1079.9999999999995
#seq	72
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m2_run1.nuc.txt

#NT

#otherMatches

#Struct PSSM
dd[cccmmmmccc]dddd]ccc::JJJJJJJJJJJJKKCCCWWWWWWWWWWWWWWHHHHHHHHLLLEEEEE:::eeeee!!cccqqqqqqqqccc22eeeeeffffff^^^^^^^^^^^^^^^^^^^^^^^^ffffff:ffffffnnnnnffffff:::::::::::::::::::::::::EEEEEHHHHHHHH@@@@@@@@@@@@@CCCYYJJJJJJJJJJJJeeeee%%%%%%bboooooobb666666eeeee	chr2:198256869-198257170(-)$1	301	19	275	768.0000

#DB
((.(((....))).)))).)))..((((((((((((..(((..............((((((((...(((((...(((((..(((........)))..)))))((((((........................)))))).((((((.....)))))).........................))))))))))))).............)))..))))))))))))(((((......((......))......)))))	chr2:198256869-198257170(-)$1	1	19	275	768.0000

#PSSM
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	

#score	768.0
#seq	1
#width	256
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_UTR_m2_run1.nuc.txt

#NT
UUUUUUUUUA	chr12:42841491-42841718(+)$1	227	168	178	17.1000
UUUUAUUUUU	chr5:179041452-179041679(-)$1	227	202	212	18.2000
UUCUCUGUUU	chr1:228682196-228682419(+)$1	223	64	74	14.3000
UUUUCAUUUC	chr1:26901259-26901501(+)$1	242	184	194	14.2000
UUGUCUUUCA	chr19:47713168-47713430(+)$1	262	52	62	13.3000
UUUUCUUUUU	chr22:24761499-24761724(+)$1	225	201	211	21.2000
UGUUCUUUUA	chrX:73806023-73806252(-)$1	229	171	181	15.8000
CUUUCUUUCA	chr11:68658789-68659016(-)$1	227	142	152	13.3000
uuuucuguau	chr6:170890203-170890425(-)$1	222	197	207	14.3000
UUUUAUUUUG	chr12:49082974-49083208(-)$1	234	35	45	15.8000
UUUUCUUUAA	chr2:153511963-153512186(-)$1	223	155	165	16.7000
UUUUUUUUUU	chr11:118964581-118964810(-)$1	229	214	224	18.2000
UUUUCUCUUA	chr2:62069156-62069393(-)$1	237	219	229	16.6000
UUCUCUUUCU	chr7:30638308-30638554(+)$1	246	86	96	14.8000
CUUUCUUUCA	chr4:139104271-139104494(-)$1	223	21	31	13.3000
UUUUCUUAUU	chr12:132428157-132428397(+)$1	240	210	220	16.6000
UUUUUUUUUU	chr19:36259374-36259600(+)$1	226	106	116	18.2000
UUUUCUUUCU	chr3:66413209-66413432(+)$1	223	52	62	18.2000
UUGUAUUUUA	chr17:56082398-56082657(-)$1	259	68	78	13.3000
AUUUCUUUAU	chr2:174228470-174228712(+)$1	242	231	241	13.8000
UUUUCUUUCU	chr7:135612347-135612610(-)$1	263	95	105	18.2000
CAUUCUUUUU	chr15:72553867-72554104(-)$1	237	36	46	13.3000
UUUUUUUUUA	chr17:42283801-42284026(-)$1	225	22	32	17.1000
UUUUUUUUUA	chr2:9629818-9630049(-)$1	231	97	107	17.1000
UUUUGUUUUA	chr1:59124409-59124640(-)$1	231	122	132	16.7000
UUCUCUUUUC	chr10:79793523-79793752(+)$1	229	95	105	15.5000
UUUUUUGUUU	chr6:109688167-109688395(-)$1	228	57	67	14.7000
cuuucuuuuu	chr2:232786887-232787118(-)$1	231	194	204	17.4000
UUAUCUUUAU	chr12:50152079-50152299(+)$1	220	9	19	14.0000
UUAUCUUUUG	chr12:131362065-131362292(+)$1	227	216	226	15.0000
UUUUCUUUUA	chr1:1717342-1717575(-)$1	233	171	181	20.1000
UUUUAUUUUU	chr8:48890277-48890519(+)$1	242	45	55	18.2000
UUCUCUAUUA	chrX:150157052-150157294(+)$1	242	193	203	13.1000
GUUUCUUUCU	chr7:135333202-135333430(+)$1	228	169	179	14.2000
UUUUCUUUUC	chr17:73228912-73229140(+)$1	228	13	23	18.9000
UUCUAUUUUA	chrX:23803948-23804191(+)$1	243	53	63	13.7000
UCUUCUAUUU	chr19:41263144-41263417(+)$1	273	26	36	13.4000
UAUUCUUUUU	chr1:111661332-111661561(-)$1	229	18	28	17.1000
UUUUCUCUUU	chr2:29170408-29170635(+)$1	227	94	104	17.7000
UUUUCUUAUG	chr2:61705786-61706017(-)$1	231	181	191	14.2000
uuuucuuuuu	chr19:15348209-15348467(-)$1	258	21	31	21.2000
UUUUCCUUUU	chr10:104417468-104417694(+)$1	226	75	85	16.5000
UCUUCUUUUA	chrX:117928094-117928340(+)$1	246	16	26	15.9000
UAUUAUUUUU	chr19:12242400-12242629(-)$1	229	79	89	14.1000
GUUUCUGUUU	chr10:75506535-75506802(+)$1	267	231	241	13.7000
AUUUCUAUUU	chr1:67877221-67877461(-)$1	240	74	84	13.6000
UUUUGUUUUA	chr1:114976202-114976428(-)$1	226	38	48	16.7000
UUUUCUCUCU	chrX:48750715-48750944(-)$1	229	106	116	14.7000
uuuucuuuuu	chr1:35649830-35650080(-)$1	250	236	246	21.2000

#otherMatches

#Struct PSSM
88888888ff	chr15:89169297-89169531(+)$1	234	67	77	12.0000
ee22gggggg	chr12:42841491-42841718(+)$1	227	168	178	17.1000
ffffffoooo	chr5:179041452-179041679(-)$1	227	202	212	18.2000
ssssssffff	chr1:228682196-228682419(+)$1	223	64	74	14.3000
++++++++++	chr1:26901259-26901501(+)$1	242	184	194	14.2000
======mmmm	chr19:47713168-47713430(+)$1	262	52	62	13.3000
444bb]ccc]	chr22:24761499-24761724(+)$1	225	201	211	21.2000
[dddd$$$$$	chrX:73806023-73806252(-)$1	229	171	181	15.8000
gggggg22ff	chr11:68658789-68659016(-)$1	227	142	152	13.3000
HHHHHHHHZZ	chr6:170890203-170890425(-)$1	222	197	207	14.3000
CMMMMDDDD{	chr12:49082974-49083208(-)$1	234	35	45	15.8000
pppppdddd2	chr2:153511963-153512186(-)$1	223	155	165	16.7000
mffffff22d	chr11:118964581-118964810(-)$1	229	214	224	18.2000
HHHHHH::::	chr2:62069156-62069393(-)$1	237	219	229	16.6000
ddd666666d	chr7:30638308-30638554(+)$1	246	86	96	14.8000
:::cccoooo	chr4:139104271-139104494(-)$1	223	21	31	13.3000
meeeee22ee	chr12:132428157-132428397(+)$1	240	210	220	16.6000
==========	chr19:36259374-36259600(+)$1	226	106	116	18.2000
JJJJJJJJJJ	chr3:66413209-66413432(+)$1	223	52	62	18.2000
ccqqqqqqqq	chr17:56082398-56082657(-)$1	259	68	78	13.3000
IIIIII::::	chr2:174228470-174228712(+)$1	242	231	241	13.8000
c::::FFFFF	chr7:135612347-135612610(-)$1	263	95	105	18.2000
EE::::::::	chr15:72553867-72554104(-)$1	237	36	46	13.3000
JJJJJJJJJJ	chr17:42283801-42284026(-)$1	225	22	32	17.1000
e::::::ddd	chr2:9629818-9630049(-)$1	231	97	107	17.1000
====dddd[b	chr1:59124409-59124640(-)$1	231	122	132	16.7000
++++++++++	chr10:79793523-79793752(+)$1	229	95	105	15.5000
44eeeee333	chr6:109688167-109688395(-)$1	228	57	67	14.7000
JJJJ::::::	chr2:232786887-232787118(-)$1	231	194	204	17.4000
eeee[dddd[	chr12:50152079-50152299(+)$1	220	9	19	14.0000
mmdddd::::	chr12:131362065-131362292(+)$1	227	216	226	15.0000
eqqqqqqqqe	chr1:1717342-1717575(-)$1	233	171	181	20.1000
GGGGGGG{GG	chr8:48890277-48890519(+)$1	242	45	55	18.2000
ccc22dddd2	chrX:150157052-150157294(+)$1	242	193	203	13.1000
dpppppppdd	chr7:135333202-135333430(+)$1	228	169	179	14.2000
::::::::::	chr17:73228912-73229140(+)$1	228	13	23	18.9000
]eeeee333b	chrX:23803948-23804191(+)$1	243	53	63	13.7000
IIIIII:hhh	chr19:41263144-41263417(+)$1	273	26	36	13.4000
::::::::::	chr1:111661332-111661561(-)$1	229	18	28	17.1000
c22ccc22ee	chr2:29170408-29170635(+)$1	227	94	104	17.7000
:=========	chr2:61705786-61706017(-)$1	231	181	191	14.2000
::::::::FF	chr19:15348209-15348467(-)$1	258	21	31	21.2000
KKDDDD{FFF	chr10:104417468-104417694(+)$1	226	75	85	16.5000
d[========	chrX:117928094-117928340(+)$1	246	16	26	15.9000
fffffnnnnn	chr19:12242400-12242629(-)$1	229	79	89	14.1000
ddddccc:::	chr10:75506535-75506802(+)$1	267	231	241	13.7000
JJJJJJJ:EE	chr1:67877221-67877461(-)$1	240	74	84	13.6000
fffff333dd	chr1:114976202-114976428(-)$1	226	38	48	16.7000
qqcccccc]h	chrX:48750715-48750944(-)$1	229	106	116	14.7000
7777777ggg	chr1:35649830-35650080(-)$1	250	236	246	21.2000

#DB
........))	chr15:89169297-89169531(+)$1	1	67	77	12.0000
))..))))))	chr12:42841491-42841718(+)$1	1	168	178	17.1000
((((((....	chr5:179041452-179041679(-)$1	1	202	212	18.2000
......))))	chr1:228682196-228682419(+)$1	1	64	74	14.3000
..........	chr1:26901259-26901501(+)$1	1	184	194	14.2000
((((((....	chr19:47713168-47713430(+)$1	1	52	62	13.3000
...)).))).	chr22:24761499-24761724(+)$1	1	201	211	21.2000
.((((.....	chrX:73806023-73806252(-)$1	1	171	181	15.8000
))))))..))	chr11:68658789-68659016(-)$1	1	142	152	13.3000
))))))))..	chr6:170890203-170890425(-)$1	1	197	207	14.3000
(....((((.	chr12:49082974-49083208(-)$1	1	35	45	15.8000
.....)))).	chr2:153511963-153512186(-)$1	1	155	165	16.7000
.))))))..)	chr11:118964581-118964810(-)$1	1	214	224	18.2000
))))))....	chr2:62069156-62069393(-)$1	1	219	229	16.6000
)))......)	chr7:30638308-30638554(+)$1	1	86	96	14.8000
...(((....	chr4:139104271-139104494(-)$1	1	21	31	13.3000
.)))))..))	chr12:132428157-132428397(+)$1	1	210	220	16.6000
))))))))))	chr19:36259374-36259600(+)$1	1	106	116	18.2000
((((((((((	chr3:66413209-66413432(+)$1	1	52	62	18.2000
((........	chr17:56082398-56082657(-)$1	1	68	78	13.3000
))))))....	chr2:174228470-174228712(+)$1	1	231	241	13.8000
)....(((((	chr7:135612347-135612610(-)$1	1	95	105	18.2000
((........	chr15:72553867-72554104(-)$1	1	36	46	13.3000
((((((((((	chr17:42283801-42284026(-)$1	1	22	32	17.1000
)......(((	chr2:9629818-9630049(-)$1	1	97	107	17.1000
))))((((.(	chr1:59124409-59124640(-)$1	1	122	132	16.7000
..........	chr10:79793523-79793752(+)$1	1	95	105	15.5000
..)))))...	chr6:109688167-109688395(-)$1	1	57	67	14.7000
))))......	chr2:232786887-232787118(-)$1	1	194	204	17.4000
((((.((((.	chr12:50152079-50152299(+)$1	1	9	19	14.0000
..))))....	chr12:131362065-131362292(+)$1	1	216	226	15.0000
(........)	chr1:1717342-1717575(-)$1	1	171	181	20.1000
(((((((.((	chr8:48890277-48890519(+)$1	1	45	55	18.2000
)))..)))).	chrX:150157052-150157294(+)$1	1	193	203	13.1000
(.......))	chr7:135333202-135333430(+)$1	1	169	179	14.2000
..........	chr17:73228912-73229140(+)$1	1	13	23	18.9000
.)))))...)	chrX:23803948-23804191(+)$1	1	53	63	13.7000
((((((.(((	chr19:41263144-41263417(+)$1	1	26	36	13.4000
..........	chr1:111661332-111661561(-)$1	1	18	28	17.1000
)..)))..))	chr2:29170408-29170635(+)$1	1	94	104	17.7000
.(((((((((	chr2:61705786-61706017(-)$1	1	181	191	14.2000
........((	chr19:15348209-15348467(-)$1	1	21	31	21.2000
..((((.(((	chr10:104417468-104417694(+)$1	1	75	85	16.5000
(.((((((((	chrX:117928094-117928340(+)$1	1	16	26	15.9000
(((((.....	chr19:12242400-12242629(-)$1	1	79	89	14.1000
)))))))...	chr10:75506535-75506802(+)$1	1	231	241	13.7000
))))))).((	chr1:67877221-67877461(-)$1	1	74	84	13.6000
)))))...))	chr1:114976202-114976428(-)$1	1	38	48	16.7000
..)))))).)	chrX:48750715-48750944(-)$1	1	106	116	14.7000
.......)))	chr1:35649830-35650080(-)$1	1	236	246	21.2000

#PSSM
U : 0.78	C : 0.06	u : 0.06	A : 0.04	G : 0.04	c : 0.02	
U : 0.80	u : 0.08	A : 0.06	C : 0.04	G : 0.02	
U : 0.72	C : 0.12	u : 0.08	G : 0.04	A : 0.04	
U : 0.92	u : 0.08	
C : 0.64	U : 0.12	A : 0.12	c : 0.08	G : 0.04	
U : 0.88	u : 0.08	A : 0.02	C : 0.02	
U : 0.72	C : 0.08	G : 0.06	u : 0.06	A : 0.06	g : 0.02	
U : 0.88	u : 0.08	A : 0.04	
U : 0.70	C : 0.16	A : 0.06	u : 0.06	a : 0.02	
U : 0.46	A : 0.32	C : 0.08	u : 0.08	G : 0.06	

#score	796.4000000000008
#seq	50
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m1_run2.nuc.txt

#NT
UCAUUUUUU	chr15:57578896-57579117(+)$1	221	89	98	18.7460
UCUUUUUUU	chr6:114181773-114181999(+)$1	226	99	108	22.7936
ucuuuuuua	chr4:119635636-119635864(+)$1	228	106	115	18.5079
UCUAUUUUU	chr7:66105181-66105406(+)$1	225	115	124	18.5873
UUUUUUUUU	chr3:107762163-107762382(-)$1	219	83	92	19.8571
ACuuuuuuu	chr4:122737400-122737617(+)$1	217	85	94	18.5079
UAUUUUUUU	chr14:35180805-35181025(-)$1	220	149	158	20.0158
UCUUUUUUC	chr5:114949477-114949697(-)$1	220	167	176	18.5079
uauuuuuuu	chrX:153295589-153295815(-)$1	226	109	118	20.0158
GCUUUUUUU	chrX:11140906-11141136(+)$1	230	81	90	18.2698
UCUCUUUUU	chr2:170494767-170494988(+)$1	221	187	196	18.5873
UCUUUUUUA	chr5:64014691-64014910(-)$1	219	103	112	18.5079
UCUUUUUCU	chrX:24003936-24004174(-)$1	238	100	109	18.5873
UAUUUUUUU	chr3:136667955-136668179(+)$1	224	104	113	20.0158
UCUUUUUUU	chr4:114900156-114900380(-)$1	224	108	117	22.7936
UUUUUUUUU	chr9:114985799-114986019(-)$1	220	35	44	19.8571
UCUUUAUUU	chr1:65692953-65693180(+)$1	227	108	117	18.1111
UUUUUUUUU	chr13:107194588-107194808(-)$1	220	144	153	19.8571
UCUUUUUAU	chr1:155852011-155852240(+)$1	229	17	26	18.4285
UGUUUUUUU	chr11:8126380-8126602(+)$1	222	95	104	19.5396
UCUGUUUUU	chr6:107474671-107474893(-)$1	222	48	57	18.4285
ucauuuuuu	chr19:46358672-46358918(-)$1	246	56	65	18.7460
UAUUUUUUU	chr8:95805205-95805431(+)$1	226	141	150	20.0158
UUUUUUUUU	chr11:108342944-108343179(-)$1	235	126	135	19.8571
UGUUUUUUU	chr6:161552093-161552316(-)$1	223	122	131	19.5396
uauuuuuuu	chr4:153243091-153243318(-)$1	227	105	114	20.0158
uauuuuuuu	chr2:105474413-105474653(+)$1	240	103	112	20.0158
UAUUUUUUU	chr15:35148666-35148884(-)$1	218	41	50	20.0158
UCUUUUUUC	chr5:78620980-78621199(+)$1	219	74	83	18.5079
UCUUUUUCU	chr3:33189128-33189351(+)$1	223	5	14	18.5873
UGUUUUUUU	chrX:76762511-76762746(-)$1	235	72	81	19.5396
UCUUUUUCU	chr19:33871590-33871828(+)$1	238	157	166	18.5873
UUUUUUUUU	chr5:180001633-180001853(+)$1	220	104	113	19.8571
UCUUUUUUU	chr6:56970569-56970804(+)$1	235	64	73	22.7936
UUUUUUUUU	chr6:167453511-167453742(+)$1	231	8	17	19.8571
UAUUUUUUU	chr14:21732513-21732737(-)$1	224	140	149	20.0158
UCUUUUUUU	chr14:20754590-20754814(-)$1	224	199	208	22.7936
UCAUUUUUU	chr5:173386987-173387206(+)$1	219	103	112	18.7460
UCUUUCUUU	chr9:112709072-112709300(+)$1	228	116	125	18.1904
UCAUUUUUU	chr19:19793357-19793584(+)$1	227	131	140	18.7460
ucuuuuuuu	chr17:27953198-27953427(-)$1	229	110	119	22.7936
UCUAUUUUU	chr4:157683406-157683627(-)$1	221	161	170	18.5873
UCUUUUUUU	chr15:45653825-45654050(-)$1	225	199	208	22.7936
uauuuuuuu	chr2:60685958-60686182(-)$1	224	171	180	20.0158
ACUUUUUUU	chr3:178736886-178737106(-)$1	220	27	36	18.5079
UCUUUUUUU	chr3:156260310-156260539(-)$1	229	101	110	22.7936
UCUUUUUUC	chr4:73940777-73941000(-)$1	223	148	157	18.5079
UCAUUUUUU	chr1:54513068-54513289(-)$1	221	105	114	18.7460
ACUUUUUUU	chr4:140428809-140429032(-)$1	223	144	153	18.5079
UCAUUUUUU	chr13:29252875-29253098(+)$1	223	36	45	18.7460
ACUUUUUUU	chr9:101913521-101913743(+)$1	222	131	140	18.5079
UUUUUUUUU	chr1:207218750-207218969(-)$1	219	12	21	19.8571
UCUUUUUUU	chr17:44107564-44107787(-)$1	223	38	47	22.7936
UCUCUUUUU	chr12:95415579-95415814(-)$1	235	131	140	18.5873
UCUUUUUCU	chr9:126795235-126795462(+)$1	227	115	124	18.5873
UCUCUUUUU	chr1:46744300-46744532(-)$1	232	110	119	18.5873
UCUUUUUUU	chr1:1595130-1595350(-)$1	220	109	118	22.7936
UCUUUCUUU	chr11:105967612-105967830(+)$1	218	207	216	18.1904
UCUUUUAUU	chr5:115357309-115357534(+)$1	225	99	108	17.9523
UCuuuuuua	chr2:32531120-32531355(+)$1	235	106	115	18.5079
UCUUUUuau	chr1:171562204-171562422(+)$1	218	177	186	18.4285
ucuuuuuuu	chr12:72184502-72184735(+)$1	233	150	159	22.7936

#otherMatches

#Struct PSSM
ccc!!eeee	chr19:15348001-15348248(-)$1	247	125	134	18.5873
cccnnnnnc	chr15:57578896-57579117(+)$1	221	89	98	18.7460
oooofffff	chr6:114181773-114181999(+)$1	226	99	108	22.7936
^^^^^^^^^	chr4:119635636-119635864(+)$1	228	106	115	18.5079
e7777777=	chr7:66105181-66105406(+)$1	225	115	124	18.5873
c::::dddd	chr3:107762163-107762382(-)$1	219	83	92	19.8571
(((((eeee	chr4:122737400-122737617(+)$1	217	85	94	18.5079
::::hhhhh	chr14:35180805-35181025(-)$1	220	149	158	20.0158
::::JJJJJ	chr5:114949477-114949697(-)$1	220	167	176	18.5079
nnnnnffff	chrX:153295589-153295815(-)$1	226	109	118	20.0158
eee::::::	chrX:11140906-11141136(+)$1	230	81	90	18.2698
qqqqqqfff	chr2:170494767-170494988(+)$1	221	187	196	18.5873
ffffff999	chr5:64014691-64014910(-)$1	219	103	112	18.5079
:cccfffff	chrX:24003936-24004174(-)$1	238	100	109	18.5873
^^^^^^^^^	chr3:136667955-136668179(+)$1	224	104	113	20.0158
=========	chr4:114900156-114900380(-)$1	224	108	117	22.7936
yyyyyyyyy	chr9:114985799-114986019(-)$1	220	35	44	19.8571
eeee:::::	chr1:65692953-65693180(+)$1	227	108	117	18.1111
55555ffff	chr13:107194588-107194808(-)$1	220	144	153	19.8571
:::::::::	chr1:155852011-155852240(+)$1	229	17	26	18.4285
hhhhhhh44	chr11:8126380-8126602(+)$1	222	95	104	19.5396
rrrrrrrrr	chr6:107474671-107474893(-)$1	222	48	57	18.4285
3dddd::::	chr19:46358672-46358918(-)$1	246	56	65	18.7460
:::::::::	chr8:95805205-95805431(+)$1	226	141	150	20.0158
=========	chr11:108342944-108343179(-)$1	235	126	135	19.8571
ccc:::::i	chr6:161552093-161552316(-)$1	223	122	131	19.5396
qqiiiiiii	chr4:153243091-153243318(-)$1	227	105	114	20.0158
eeppppppp	chr2:105474413-105474653(+)$1	240	103	112	20.0158
hh:::::::	chr15:35148666-35148884(-)$1	218	41	50	20.0158
+++++++++	chr5:78620980-78621199(+)$1	219	74	83	18.5079
:::::::CC	chr3:33189128-33189351(+)$1	223	5	14	18.5873
ffwwwwwww	chrX:76762511-76762746(-)$1	235	72	81	19.5396
=====:eee	chr19:33871590-33871828(+)$1	238	157	166	18.5873
ooooooddd	chr5:180001633-180001853(+)$1	220	104	113	19.8571
eeeeeelll	chr6:56970569-56970804(+)$1	235	64	73	22.7936
::::::::G	chr6:167453511-167453742(+)$1	231	8	17	19.8571
zzzzzzzzz	chr14:21732513-21732737(-)$1	224	140	149	20.0158
ddppppppp	chr14:20754590-20754814(-)$1	224	199	208	22.7936
ee"""eeee	chr5:173386987-173387206(+)$1	219	103	112	18.7460
::=======	chr9:112709072-112709300(+)$1	228	116	125	18.1904
[ffffffww	chr19:19793357-19793584(+)$1	227	131	140	18.7460
:::::::::	chr17:27953198-27953427(-)$1	229	110	119	22.7936
zzzzzzzzz	chr4:157683406-157683627(-)$1	221	161	170	18.5873
=========	chr15:45653825-45654050(-)$1	225	199	208	22.7936
gg:::BBYY	chr2:60685958-60686182(-)$1	224	171	180	20.0158
:::::::::	chr3:178736886-178737106(-)$1	220	27	36	18.5079
LLLFFFFFF	chr3:156260310-156260539(-)$1	229	101	110	22.7936
:::::::::	chr4:73940777-73941000(-)$1	223	148	157	18.5079
:::======	chr1:54513068-54513289(-)$1	221	105	114	18.7460
b[ccceeee	chr4:140428809-140429032(-)$1	223	144	153	18.5079
:eeeee[bb	chr13:29252875-29253098(+)$1	223	36	45	18.7460
dccc$$$$$	chr9:101913521-101913743(+)$1	222	131	140	18.5079
+++++++++	chr1:207218750-207218969(-)$1	219	12	21	19.8571
=========	chr17:44107564-44107787(-)$1	223	38	47	22.7936
:::::::gg	chr12:95415579-95415814(-)$1	235	131	140	18.5873
bb^^^^^^^	chr9:126795235-126795462(+)$1	227	115	124	18.5873
:::::::::	chr1:46744300-46744532(-)$1	232	110	119	18.5873
!!eeeeevv	chr1:1595130-1595350(-)$1	220	109	118	22.7936
YYDDDD:::	chr11:105967612-105967830(+)$1	218	207	216	18.1904
f^^^^^^^^	chr5:115357309-115357534(+)$1	225	99	108	17.9523
:::::::::	chr2:32531120-32531355(+)$1	235	106	115	18.5079
f::::::::	chr1:171562204-171562422(+)$1	218	177	186	18.4285
d^^^^^^^^	chr12:72184502-72184735(+)$1	233	150	159	22.7936

#DB
(((..((((	chr19:15348001-15348248(-)$1	1	125	134	18.5873
(((.....)	chr15:57578896-57579117(+)$1	1	89	98	18.7460
....)))))	chr6:114181773-114181999(+)$1	1	99	108	22.7936
.........	chr4:119635636-119635864(+)$1	1	106	115	18.5079
).......)	chr7:66105181-66105406(+)$1	1	115	124	18.5873
)....((((	chr3:107762163-107762382(-)$1	1	83	92	19.8571
.....((((	chr4:122737400-122737617(+)$1	1	85	94	18.5079
....(((((	chr14:35180805-35181025(-)$1	1	149	158	20.0158
....)))))	chr5:114949477-114949697(-)$1	1	167	176	18.5079
.....))))	chrX:153295589-153295815(-)$1	1	109	118	20.0158
)))......	chrX:11140906-11141136(+)$1	1	81	90	18.2698
......)))	chr2:170494767-170494988(+)$1	1	187	196	18.5873
))))))...	chr5:64014691-64014910(-)$1	1	103	112	18.5079
.((((((((	chrX:24003936-24004174(-)$1	1	100	109	18.5873
.........	chr3:136667955-136668179(+)$1	1	104	113	20.0158
(((((((((	chr4:114900156-114900380(-)$1	1	108	117	22.7936
.........	chr9:114985799-114986019(-)$1	1	35	44	19.8571
)))).....	chr1:65692953-65693180(+)$1	1	108	117	18.1111
.....))))	chr13:107194588-107194808(-)$1	1	144	153	19.8571
.........	chr1:155852011-155852240(+)$1	1	17	26	18.4285
)))))))..	chr11:8126380-8126602(+)$1	1	95	104	19.5396
.........	chr6:107474671-107474893(-)$1	1	48	57	18.4285
.))))....	chr19:46358672-46358918(-)$1	1	56	65	18.7460
.........	chr8:95805205-95805431(+)$1	1	141	150	20.0158
(((((((((	chr11:108342944-108343179(-)$1	1	126	135	19.8571
))).....(	chr6:161552093-161552316(-)$1	1	122	131	19.5396
..)))))))	chr4:153243091-153243318(-)$1	1	105	114	20.0158
((.......	chr2:105474413-105474653(+)$1	1	103	112	20.0158
)).......	chr15:35148666-35148884(-)$1	1	41	50	20.0158
.........	chr5:78620980-78621199(+)$1	1	74	83	18.5079
.......((	chr3:33189128-33189351(+)$1	1	5	14	18.5873
((.......	chrX:76762511-76762746(-)$1	1	72	81	19.5396
))))).(((	chr19:33871590-33871828(+)$1	1	157	166	18.5873
......)))	chr5:180001633-180001853(+)$1	1	104	113	19.8571
((((((...	chr6:56970569-56970804(+)$1	1	64	73	22.7936
........(	chr6:167453511-167453742(+)$1	1	8	17	19.8571
.........	chr14:21732513-21732737(-)$1	1	140	149	20.0158
((.......	chr14:20754590-20754814(-)$1	1	199	208	22.7936
((...((((	chr5:173386987-173387206(+)$1	1	103	112	18.7460
..(((((((	chr9:112709072-112709300(+)$1	1	116	125	18.1904
.((((((..	chr19:19793357-19793584(+)$1	1	131	140	18.7460
.........	chr17:27953198-27953427(-)$1	1	110	119	22.7936
.........	chr4:157683406-157683627(-)$1	1	161	170	18.5873
(((((((((	chr15:45653825-45654050(-)$1	1	199	208	22.7936
))...))..	chr2:60685958-60686182(-)$1	1	171	180	20.0158
.........	chr3:178736886-178737106(-)$1	1	27	36	18.5079
...((((((	chr3:156260310-156260539(-)$1	1	101	110	22.7936
.........	chr4:73940777-73941000(-)$1	1	148	157	18.5079
...((((((	chr1:54513068-54513289(-)$1	1	105	114	18.7460
(.(((((((	chr4:140428809-140429032(-)$1	1	144	153	18.5079
.(((((.((	chr13:29252875-29253098(+)$1	1	36	45	18.7460
((((.....	chr9:101913521-101913743(+)$1	1	131	140	18.5079
.........	chr1:207218750-207218969(-)$1	1	12	21	19.8571
)))))))))	chr17:44107564-44107787(-)$1	1	38	47	22.7936
.......((	chr12:95415579-95415814(-)$1	1	131	140	18.5873
((.......	chr9:126795235-126795462(+)$1	1	115	124	18.5873
.........	chr1:46744300-46744532(-)$1	1	110	119	18.5873
..(((((..	chr1:1595130-1595350(-)$1	1	109	118	22.7936
..))))...	chr11:105967612-105967830(+)$1	1	207	216	18.1904
(........	chr5:115357309-115357534(+)$1	1	99	108	17.9523
.........	chr2:32531120-32531355(+)$1	1	106	115	18.5079
)........	chr1:171562204-171562422(+)$1	1	177	186	18.4285
(........	chr12:72184502-72184735(+)$1	1	150	159	22.7936

#PSSM
U : 0.79	u : 0.12	A : 0.06	G : 0.01	
C : 0.63	U : 0.11	A : 0.07	c : 0.06	a : 0.06	G : 0.04	
U : 0.76	u : 0.14	A : 0.07	a : 0.01	
U : 0.73	u : 0.15	A : 0.04	C : 0.04	G : 0.01	
U : 0.84	u : 0.15	
U : 0.79	u : 0.15	C : 0.03	A : 0.01	
U : 0.80	u : 0.17	A : 0.01	
U : 0.74	u : 0.15	C : 0.06	A : 0.01	a : 0.01	
U : 0.76	u : 0.14	C : 0.04	a : 0.03	A : 0.01	

#score	1235.1269841269823
#seq	63
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m1_run2.nuc.txt

#NT
CCU	chr7:98575824-98576045(+)$1	221	19	22	8.9999
CCU	chr18:20793877-20794099(+)$1	222	69	72	8.9999
CCU	chr12:121205100-121205336(-)$1	236	12	15	8.9999
CCU	chr17:45198224-45198447(-)$1	223	206	209	8.9999
CCU	chr17:40052782-40052996(-)$1	214	12	15	8.9999
CCU	chr17:74036920-74037138(-)$1	218	37	40	8.9999
CCU	chr18:43667271-43667499(-)$1	228	77	80	8.9999
CCU	chr6:136599321-136599553(-)$1	232	174	177	8.9999
CCU	chr9:115060074-115060286(-)$1	212	132	135	8.9999
CCU	chr1:11082480-11082717(+)$1	237	82	85	8.9999
CCU	chr12:49432504-49432762(-)$1	258	31	34	8.9999
ccu	chr7:99145687-99145901(-)$1	214	49	52	8.9999
CCU	chr6:97615936-97616158(-)$1	222	161	164	8.9999
CCU	chr12:90017959-90018179(-)$1	220	62	65	8.9999
CCU	chr1:210010116-210010343(+)$1	227	24	27	8.9999
CCU	chr1:154574192-154574426(-)$1	234	38	41	8.9999
CCU	chr14:94519258-94519543(-)$1	285	25	28	8.9999
CCU	chr1:179100443-179100689(-)$1	246	50	53	8.9999
CCU	chr10:31809191-31809415(+)$1	224	79	82	8.9999
CCU	chr6:151789895-151790128(+)$1	233	38	41	8.9999
CCU	chr13:46533532-46533773(-)$1	241	168	171	8.9999
CCU	chr7:116397619-116397873(+)$1	254	65	68	8.9999
CCU	chr15:66021390-66021614(-)$1	224	8	11	8.9999
CCU	chr1:82415853-82416092(+)$1	239	21	24	8.9999
CCU	chr7:40127732-40127956(+)$1	224	194	197	8.9999
CCU	chr6:111702438-111702658(-)$1	220	66	69	8.9999
ccu	chr4:1818512-1818731(-)$1	219	34	37	8.9999
CCU	chr22:36914804-36915022(-)$1	218	21	24	8.9999
CCU	chr6:30627865-30628088(-)$1	223	28	31	8.9999
CCU	chr1:179961130-179961341(+)$1	211	5	8	8.9999
CCU	chr1:210415068-210415288(+)$1	220	0	3	8.9999
CCU	chr12:993979-994202(+)$1	223	2	5	8.9999
CCU	chr16:8988882-8989106(-)$1	224	6	9	8.9999
CCU	chr11:65055165-65055389(+)$1	224	2	5	8.9999
CCU	chr13:23911535-23911787(-)$1	252	67	70	8.9999
CCU	chr8:103230961-103231188(-)$1	227	28	31	8.9999
CCU	chr10:76910529-76910775(+)$1	246	51	54	8.9999
CCU	chr17:2570293-2570513(+)$1	220	49	52	8.9999
CCU	chr15:68582734-68582973(+)$1	239	71	74	8.9999
CCU	chr1:114945335-114945555(-)$1	220	33	36	8.9999
CCU	chr12:463186-463409(-)$1	223	111	114	8.9999
CCU	chrX:47099121-47099354(+)$1	233	38	41	8.9999
CCU	chr5:158585679-158585899(-)$1	220	12	15	8.9999
CCU	chr3:38565513-38565739(+)$1	226	36	39	8.9999
CCU	chr14:35245360-35245581(-)$1	221	16	19	8.9999
CCU	chr12:118480549-118480803(-)$1	254	10	13	8.9999
CCU	chr20:30381579-30381804(+)$1	225	66	69	8.9999
CCU	chr7:819677-819902(+)$1	225	14	17	8.9999
CCU	chr17:15971232-15971450(-)$1	218	68	71	8.9999
CCU	chr12:12629600-12629947(-)$1	347	35	38	8.9999
CCU	chr10:12126487-12126708(+)$1	221	31	34	8.9999
CCU	chr11:65396023-65396246(+)$1	223	3	6	8.9999
CCU	chr14:92622774-92623029(+)$1	255	133	136	8.9999
CCU	chr12:6623632-6623842(+)$1	210	40	43	8.9999
CCU	chr17:65918876-65919099(+)$1	223	68	71	8.9999
CCU	chr1:222800971-222801191(+)$1	220	95	98	8.9999
CCU	chr12:437964-438191(-)$1	227	34	37	8.9999
CCU	chr6:44394265-44394485(+)$1	220	60	63	8.9999
CCU	chr2:136623669-136623935(-)$1	266	44	47	8.9999
CCU	chr1:214815427-214815687(+)$1	260	33	36	8.9999
CCU	chr7:105205929-105206154(+)$1	225	119	122	8.9999
CCU	chr1:61869690-61869909(+)$1	219	62	65	8.9999
CCU	chr10:75525526-75525770(+)$1	244	53	56	8.9999
CCU	chr17:38140566-38140819(+)$1	253	50	53	8.9999
CCU	chr5:32400114-32400369(-)$1	255	132	135	8.9999
CCU	chr8:71069315-71069564(-)$1	249	51	54	8.9999
CCU	chr17:39983735-39983964(-)$1	229	46	49	8.9999
CCU	chr12:32902820-32903046(-)$1	226	17	20	8.9999
CCU	chr10:94274599-94274821(-)$1	222	4	7	8.9999
CCU	chr1:46736266-46736482(+)$1	216	22	25	8.9999
CCU	chr13:23914938-23915159(-)$1	221	192	195	8.9999
CCU	chr14:96998601-96998839(+)$1	238	54	57	8.9999
CCU	chr10:25313677-25313899(+)$1	222	72	75	8.9999
CCU	chr11:108381714-108381937(-)$1	223	144	147	8.9999
CCU	chr5:171766212-171766434(-)$1	222	33	36	8.9999
CCU	chrX:39933685-39933954(-)$1	269	14	17	8.9999
CCU	chr19:9271675-9271904(+)$1	229	25	28	8.9999
CCU	chr2:109382996-109383226(+)$1	230	3	6	8.9999
CCU	chr11:118252040-118252259(+)$1	219	81	84	8.9999
CCU	chr11:106647126-106647344(-)$1	218	55	58	8.9999
CCU	chr10:70333794-70334023(+)$1	229	12	15	8.9999
CCU	chr3:88104792-88105016(-)$1	224	72	75	8.9999
CCU	chr8:104076882-104077098(+)$1	216	204	207	8.9999
CCU	chr4:24577772-24578005(-)$1	233	5	8	8.9999
CCU	chr7:128388620-128388844(+)$1	224	22	25	8.9999
CCU	chr1:197144075-197144302(-)$1	227	11	14	8.9999
CCU	chr8:37732460-37732687(-)$1	227	7	10	8.9999
CCU	chr8:95900069-95900302(-)$1	233	119	122	8.9999
CCU	chr10:14938785-14939053(+)$1	268	119	122	8.9999
CCU	chr4:122742120-122742344(-)$1	224	19	22	8.9999
CCU	chr15:42742153-42742370(-)$1	217	101	104	8.9999
CCU	chr6:64395446-64395680(+)$1	234	4	7	8.9999
CCU	chr17:57767954-57768166(+)$1	212	135	138	8.9999
CCU	chr11:9168503-9168723(-)$1	220	10	13	8.9999
CCU	chr17:57057916-57058129(+)$1	213	59	62	8.9999
CCU	chr6:30571282-30571530(-)$1	248	61	64	8.9999

#otherMatches

#Struct PSSM
:::	chr1:151214817-151215036(+)$1	219	7	10	8.9999
FFK	chr7:98575824-98576045(+)$1	221	19	22	8.9999
:::	chr18:20793877-20794099(+)$1	222	69	72	8.9999
err	chr12:121205100-121205336(-)$1	236	12	15	8.9999
:cc	chr17:45198224-45198447(-)$1	223	206	209	8.9999
:::	chr17:40052782-40052996(-)$1	214	12	15	8.9999
JJ:	chr17:74036920-74037138(-)$1	218	37	40	8.9999
cc:	chr18:43667271-43667499(-)$1	228	77	80	8.9999
???	chr6:136599321-136599553(-)$1	232	174	177	8.9999
ccc	chr9:115060074-115060286(-)$1	212	132	135	8.9999
bbl	chr1:11082480-11082717(+)$1	237	82	85	8.9999
ddo	chr12:49432504-49432762(-)$1	258	31	34	8.9999
nnn	chr7:99145687-99145901(-)$1	214	49	52	8.9999
B//	chr6:97615936-97616158(-)$1	222	161	164	8.9999
III	chr12:90017959-90018179(-)$1	220	62	65	8.9999
BBK	chr1:210010116-210010343(+)$1	227	24	27	8.9999
KCC	chr1:154574192-154574426(-)$1	234	38	41	8.9999
Eee	chr14:94519258-94519543(-)$1	285	25	28	8.9999
DDD	chr1:179100443-179100689(-)$1	246	50	53	8.9999
qqc	chr10:31809191-31809415(+)$1	224	79	82	8.9999
eee	chr6:151789895-151790128(+)$1	233	38	41	8.9999
a[c	chr13:46533532-46533773(-)$1	241	168	171	8.9999
BB{	chr7:116397619-116397873(+)$1	254	65	68	8.9999
:::	chr15:66021390-66021614(-)$1	224	8	11	8.9999
F::	chr1:82415853-82416092(+)$1	239	21	24	8.9999
B}A	chr7:40127732-40127956(+)$1	224	194	197	8.9999
:ee	chr6:111702438-111702658(-)$1	220	66	69	8.9999
ddd	chr4:1818512-1818731(-)$1	219	34	37	8.9999
!!f	chr22:36914804-36915022(-)$1	218	21	24	8.9999
gg!	chr6:30627865-30628088(-)$1	223	28	31	8.9999
ddd	chr1:179961130-179961341(+)$1	211	5	8	8.9999
:::	chr1:210415068-210415288(+)$1	220	0	3	8.9999
III	chr12:993979-994202(+)$1	223	2	5	8.9999
ddl	chr16:8988882-8989106(-)$1	224	6	9	8.9999
EEE	chr11:65055165-65055389(+)$1	224	2	5	8.9999
dgg	chr13:23911535-23911787(-)$1	252	67	70	8.9999
e##	chr8:103230961-103231188(-)$1	227	28	31	8.9999
ooo	chr10:76910529-76910775(+)$1	246	51	54	8.9999
ddm	chr17:2570293-2570513(+)$1	220	49	52	8.9999
ddd	chr15:68582734-68582973(+)$1	239	71	74	8.9999
:::	chr1:114945335-114945555(-)$1	220	33	36	8.9999
fff	chr12:463186-463409(-)$1	223	111	114	8.9999
$$$	chrX:47099121-47099354(+)$1	233	38	41	8.9999
ccc	chr5:158585679-158585899(-)$1	220	12	15	8.9999
EBB	chr3:38565513-38565739(+)$1	226	36	39	8.9999
[ff	chr14:35245360-35245581(-)$1	221	16	19	8.9999
CCC	chr12:118480549-118480803(-)$1	254	10	13	8.9999
iii	chr20:30381579-30381804(+)$1	225	66	69	8.9999
:::	chr7:819677-819902(+)$1	225	14	17	8.9999
ddd	chr17:15971232-15971450(-)$1	218	68	71	8.9999
:::	chr12:12629600-12629947(-)$1	347	35	38	8.9999
dd&	chr10:12126487-12126708(+)$1	221	31	34	8.9999
DDD	chr11:65396023-65396246(+)$1	223	3	6	8.9999
ccc	chr14:92622774-92623029(+)$1	255	133	136	8.9999
ccc	chr12:6623632-6623842(+)$1	210	40	43	8.9999
JJJ	chr17:65918876-65919099(+)$1	223	68	71	8.9999
===	chr1:222800971-222801191(+)$1	220	95	98	8.9999
ddl	chr12:437964-438191(-)$1	227	34	37	8.9999
DDD	chr6:44394265-44394485(+)$1	220	60	63	8.9999
HH:	chr2:136623669-136623935(-)$1	266	44	47	8.9999
e::	chr1:214815427-214815687(+)$1	260	33	36	8.9999
d:d	chr7:105205929-105206154(+)$1	225	119	122	8.9999
ooc	chr1:61869690-61869909(+)$1	219	62	65	8.9999
bb[	chr10:75525526-75525770(+)$1	244	53	56	8.9999
===	chr17:38140566-38140819(+)$1	253	50	53	8.9999
ddd	chr5:32400114-32400369(-)$1	255	132	135	8.9999
cc[	chr8:71069315-71069564(-)$1	249	51	54	8.9999
===	chr17:39983735-39983964(-)$1	229	46	49	8.9999
FFF	chr12:32902820-32903046(-)$1	226	17	20	8.9999
BBK	chr10:94274599-94274821(-)$1	222	4	7	8.9999
qqh	chr1:46736266-46736482(+)$1	216	22	25	8.9999
ddd	chr13:23914938-23915159(-)$1	221	192	195	8.9999
fcc	chr14:96998601-96998839(+)$1	238	54	57	8.9999
edd	chr10:25313677-25313899(+)$1	222	72	75	8.9999
ddd	chr11:108381714-108381937(-)$1	223	144	147	8.9999
:ii	chr5:171766212-171766434(-)$1	222	33	36	8.9999
D:e	chrX:39933685-39933954(-)$1	269	14	17	8.9999
DDD	chr19:9271675-9271904(+)$1	229	25	28	8.9999
DDN	chr2:109382996-109383226(+)$1	230	3	6	8.9999
ncc	chr11:118252040-118252259(+)$1	219	81	84	8.9999
eee	chr11:106647126-106647344(-)$1	218	55	58	8.9999
DDD	chr10:70333794-70334023(+)$1	229	12	15	8.9999
qqq	chr3:88104792-88105016(-)$1	224	72	75	8.9999
bbp	chr8:104076882-104077098(+)$1	216	204	207	8.9999
::b	chr4:24577772-24578005(-)$1	233	5	8	8.9999
d!!	chr7:128388620-128388844(+)$1	224	22	25	8.9999
ccc	chr1:197144075-197144302(-)$1	227	11	14	8.9999
!gg	chr8:37732460-37732687(-)$1	227	7	10	8.9999
fff	chr8:95900069-95900302(-)$1	233	119	122	8.9999
"""	chr10:14938785-14939053(+)$1	268	119	122	8.9999
DDD	chr4:122742120-122742344(-)$1	224	19	22	8.9999
cmm	chr15:42742153-42742370(-)$1	217	101	104	8.9999
:FF	chr6:64395446-64395680(+)$1	234	4	7	8.9999
add	chr17:57767954-57768166(+)$1	212	135	138	8.9999
bee	chr11:9168503-9168723(-)$1	220	10	13	8.9999
bbn	chr17:57057916-57058129(+)$1	213	59	62	8.9999
mmd	chr6:30571282-30571530(-)$1	248	61	64	8.9999

#DB
...	chr1:151214817-151215036(+)$1	1	7	10	8.9999
((.	chr7:98575824-98576045(+)$1	1	19	22	8.9999
...	chr18:20793877-20794099(+)$1	1	69	72	8.9999
(..	chr12:121205100-121205336(-)$1	1	12	15	8.9999
.((	chr17:45198224-45198447(-)$1	1	206	209	8.9999
...	chr17:40052782-40052996(-)$1	1	12	15	8.9999
((.	chr17:74036920-74037138(-)$1	1	37	40	8.9999
)).	chr18:43667271-43667499(-)$1	1	77	80	8.9999
...	chr6:136599321-136599553(-)$1	1	174	177	8.9999
)))	chr9:115060074-115060286(-)$1	1	132	135	8.9999
((.	chr1:11082480-11082717(+)$1	1	82	85	8.9999
((.	chr12:49432504-49432762(-)$1	1	31	34	8.9999
...	chr7:99145687-99145901(-)$1	1	49	52	8.9999
)..	chr6:97615936-97616158(-)$1	1	161	164	8.9999
(((	chr12:90017959-90018179(-)$1	1	62	65	8.9999
((.	chr1:210010116-210010343(+)$1	1	24	27	8.9999
.((	chr1:154574192-154574426(-)$1	1	38	41	8.9999
(((	chr14:94519258-94519543(-)$1	1	25	28	8.9999
(((	chr1:179100443-179100689(-)$1	1	50	53	8.9999
..)	chr10:31809191-31809415(+)$1	1	79	82	8.9999
(((	chr6:151789895-151790128(+)$1	1	38	41	8.9999
(.(	chr13:46533532-46533773(-)$1	1	168	171	8.9999
((.	chr7:116397619-116397873(+)$1	1	65	68	8.9999
...	chr15:66021390-66021614(-)$1	1	8	11	8.9999
(..	chr1:82415853-82416092(+)$1	1	21	24	8.9999
).)	chr7:40127732-40127956(+)$1	1	194	197	8.9999
.((	chr6:111702438-111702658(-)$1	1	66	69	8.9999
)))	chr4:1818512-1818731(-)$1	1	34	37	8.9999
..(	chr22:36914804-36915022(-)$1	1	21	24	8.9999
((.	chr6:30627865-30628088(-)$1	1	28	31	8.9999
(((	chr1:179961130-179961341(+)$1	1	5	8	8.9999
...	chr1:210415068-210415288(+)$1	1	0	3	8.9999
(((	chr12:993979-994202(+)$1	1	2	5	8.9999
((.	chr16:8988882-8989106(-)$1	1	6	9	8.9999
(((	chr11:65055165-65055389(+)$1	1	2	5	8.9999
)((	chr13:23911535-23911787(-)$1	1	67	70	8.9999
(..	chr8:103230961-103231188(-)$1	1	28	31	8.9999
...	chr10:76910529-76910775(+)$1	1	51	54	8.9999
((.	chr17:2570293-2570513(+)$1	1	49	52	8.9999
(((	chr15:68582734-68582973(+)$1	1	71	74	8.9999
...	chr1:114945335-114945555(-)$1	1	33	36	8.9999
)))	chr12:463186-463409(-)$1	1	111	114	8.9999
...	chrX:47099121-47099354(+)$1	1	38	41	8.9999
(((	chr5:158585679-158585899(-)$1	1	12	15	8.9999
(((	chr3:38565513-38565739(+)$1	1	36	39	8.9999
.((	chr14:35245360-35245581(-)$1	1	16	19	8.9999
(((	chr12:118480549-118480803(-)$1	1	10	13	8.9999
)))	chr20:30381579-30381804(+)$1	1	66	69	8.9999
...	chr7:819677-819902(+)$1	1	14	17	8.9999
(((	chr17:15971232-15971450(-)$1	1	68	71	8.9999
...	chr12:12629600-12629947(-)$1	1	35	38	8.9999
((.	chr10:12126487-12126708(+)$1	1	31	34	8.9999
(((	chr11:65396023-65396246(+)$1	1	3	6	8.9999
(((	chr14:92622774-92623029(+)$1	1	133	136	8.9999
(((	chr12:6623632-6623842(+)$1	1	40	43	8.9999
(((	chr17:65918876-65919099(+)$1	1	68	71	8.9999
)))	chr1:222800971-222801191(+)$1	1	95	98	8.9999
((.	chr12:437964-438191(-)$1	1	34	37	8.9999
(((	chr6:44394265-44394485(+)$1	1	60	63	8.9999
((.	chr2:136623669-136623935(-)$1	1	44	47	8.9999
)..	chr1:214815427-214815687(+)$1	1	33	36	8.9999
).(	chr7:105205929-105206154(+)$1	1	119	122	8.9999
..)	chr1:61869690-61869909(+)$1	1	62	65	8.9999
((.	chr10:75525526-75525770(+)$1	1	53	56	8.9999
(((	chr17:38140566-38140819(+)$1	1	50	53	8.9999
)))	chr5:32400114-32400369(-)$1	1	132	135	8.9999
((.	chr8:71069315-71069564(-)$1	1	51	54	8.9999
(((	chr17:39983735-39983964(-)$1	1	46	49	8.9999
(((	chr12:32902820-32903046(-)$1	1	17	20	8.9999
((.	chr10:94274599-94274821(-)$1	1	4	7	8.9999
..)	chr1:46736266-46736482(+)$1	1	22	25	8.9999
)))	chr13:23914938-23915159(-)$1	1	192	195	8.9999
(((	chr14:96998601-96998839(+)$1	1	54	57	8.9999
(((	chr10:25313677-25313899(+)$1	1	72	75	8.9999
(((	chr11:108381714-108381937(-)$1	1	144	147	8.9999
.((	chr5:171766212-171766434(-)$1	1	33	36	8.9999
(.(	chrX:39933685-39933954(-)$1	1	14	17	8.9999
(((	chr19:9271675-9271904(+)$1	1	25	28	8.9999
((.	chr2:109382996-109383226(+)$1	1	3	6	8.9999
.))	chr11:118252040-118252259(+)$1	1	81	84	8.9999
)))	chr11:106647126-106647344(-)$1	1	55	58	8.9999
(((	chr10:70333794-70334023(+)$1	1	12	15	8.9999
...	chr3:88104792-88105016(-)$1	1	72	75	8.9999
((.	chr8:104076882-104077098(+)$1	1	204	207	8.9999
..(	chr4:24577772-24578005(-)$1	1	5	8	8.9999
(..	chr7:128388620-128388844(+)$1	1	22	25	8.9999
)))	chr1:197144075-197144302(-)$1	1	11	14	8.9999
.((	chr8:37732460-37732687(-)$1	1	7	10	8.9999
(((	chr8:95900069-95900302(-)$1	1	119	122	8.9999
...	chr10:14938785-14939053(+)$1	1	119	122	8.9999
(((	chr4:122742120-122742344(-)$1	1	19	22	8.9999
(..	chr15:42742153-42742370(-)$1	1	101	104	8.9999
.((	chr6:64395446-64395680(+)$1	1	4	7	8.9999
)))	chr17:57767954-57768166(+)$1	1	135	138	8.9999
(((	chr11:9168503-9168723(-)$1	1	10	13	8.9999
((.	chr17:57057916-57058129(+)$1	1	59	62	8.9999
..)	chr6:30571282-30571530(-)$1	1	61	64	8.9999

#PSSM
C : 0.97	c : 0.02	
C : 0.97	c : 0.02	
U : 0.97	u : 0.02	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m1_run2.nuc.txt

#NT
CUU	chr17:40140734-40140958(-)$1	224	1	4	8.9999
CUU	chrX:100383629-100383859(+)$1	230	23	26	8.9999
CUU	chr2:152311438-152311672(+)$1	234	27	30	8.9999
CUU	chr12:98925438-98925668(+)$1	230	9	12	8.9999
CUU	chr1:169953646-169953869(-)$1	223	5	8	8.9999
CUU	chr19:21719560-21719783(+)$1	223	24	27	8.9999
CUU	chr15:65739134-65739359(-)$1	225	78	81	8.9999
CUU	chr1:24022743-24022984(+)$1	241	78	81	8.9999
CUU	chr3:189608524-189608754(+)$1	230	7	10	8.9999
CUU	chr15:83805203-83805428(+)$1	225	56	59	8.9999
CUU	chr5:134010638-134010868(+)$1	230	16	19	8.9999
CUU	chr2:211019017-211019247(-)$1	230	72	75	8.9999
CUU	chr6:34725600-34725826(+)$1	226	12	15	8.9999
CUU	chr3:172533357-172533579(+)$1	222	42	45	8.9999
CUU	chr7:107546633-107546863(+)$1	230	60	63	8.9999
CUU	chr12:50386238-50386457(-)$1	219	1	4	8.9999
CUU	chrM:15408-15638(+)$1	230	3	6	8.9999
CUU	chr8:124266467-124266697(-)$1	230	91	94	8.9999
CUU	chr5:88056772-88057002(-)$1	230	19	22	8.9999
CUU	chr9:72338403-72338633(-)$1	230	43	46	8.9999
CUU	chr10:17756570-17756798(+)$1	228	121	124	8.9999
CUU	chr20:52188171-52188396(-)$1	225	29	32	8.9999
CUU	chr10:31137857-31138082(-)$1	225	85	88	8.9999
CUU	chr2:191760295-191760525(+)$1	230	15	18	8.9999
CUU	chrX:16759778-16760008(+)$1	230	29	32	8.9999
cuu	chr9:32558821-32559051(-)$1	230	9	12	8.9999
CUU	chr5:61673398-61673621(+)$1	223	30	33	8.9999
CUU	chr14:24642121-24642351(+)$1	230	52	55	8.9999
CUU	chr3:121410385-121410615(-)$1	230	79	82	8.9999
CUU	chr2:220089736-220089960(-)$1	224	8	11	8.9999
CUU	chr2:61710034-61710264(-)$1	230	10	13	8.9999
CUU	chr1:41236044-41236267(+)$1	223	8	11	8.9999
CUU	chr12:2983507-2983733(-)$1	226	18	21	8.9999
CUU	chr12:49445698-49445928(-)$1	230	19	22	8.9999
CUU	chr5:114860506-114860730(-)$1	224	17	20	8.9999
CUU	chrX:41084265-41084490(+)$1	225	21	24	8.9999
CUU	chr12:70150136-70150356(+)$1	220	40	43	8.9999
CUU	chr10:22839571-22839794(-)$1	223	7	10	8.9999
CUU	chr14:78182070-78182293(+)$1	223	19	22	8.9999
CUU	chr1:154573953-154574176(-)$1	223	28	31	8.9999
CUU	chr3:170078238-170078468(+)$1	230	39	42	8.9999
CUU	chr20:33233010-33233240(-)$1	230	66	69	8.9999
CUU	chr20:42232379-42232602(+)$1	223	2	5	8.9999
CUU	chr8:64098838-64099068(+)$1	230	85	88	8.9999
CUU	chr13:20346491-20346721(-)$1	230	8	11	8.9999
CUU	chr20:44049089-44049315(+)$1	226	46	49	8.9999
CUU	chr3:63967866-63968096(+)$1	230	94	97	8.9999
CUU	chr7:129842321-129842551(-)$1	230	19	22	8.9999
CUU	chr18:3253132-3253359(+)$1	227	15	18	8.9999
CUU	chr3:114070558-114070785(-)$1	227	107	110	8.9999
CUU	chr1:154229463-154229693(+)$1	230	6	9	8.9999
CUU	chr9:127951861-127952087(-)$1	226	15	18	8.9999
CUU	chr3:179287835-179288065(+)$1	230	12	15	8.9999
CUU	chr1:155874011-155874232(-)$1	221	50	53	8.9999
CUU	chr16:70605506-70605736(+)$1	230	1	4	8.9999
CUU	chr17:38572634-38572864(-)$1	230	14	17	8.9999
CUU	chr19:46020927-46021157(+)$1	230	30	33	8.9999
CUU	chr1:54262325-54262562(-)$1	237	55	58	8.9999
CUU	chr5:180277076-180277300(-)$1	224	92	95	8.9999
CUU	chr13:113889338-113889560(+)$1	222	50	53	8.9999
CUU	chr2:180818836-180819066(-)$1	230	17	20	8.9999
CUU	chr10:103869258-103869483(-)$1	225	17	20	8.9999
cuU	chr9:106878425-106878655(+)$1	230	172	175	8.9999
CUU	chr1:212245346-212245576(+)$1	230	11	14	8.9999
CUU	chr19:21990484-21990714(-)$1	230	16	19	8.9999
CUU	chr12:49418261-49418486(-)$1	225	49	52	8.9999
CUU	chr20:44049120-44049350(+)$1	230	15	18	8.9999
CUU	chr3:178927983-178928209(+)$1	226	22	25	8.9999
CUU	chr12:112701851-112702077(-)$1	226	14	17	8.9999
CUU	chr20:34242929-34243159(-)$1	230	42	45	8.9999
CUU	chr3:150262095-150262325(-)$1	230	8	11	8.9999
CUU	chr5:149826351-149826573(-)$1	222	4	7	8.9999
CUU	chr5:93807283-93807503(+)$1	220	0	3	8.9999
CUU	chr12:112691835-112692060(-)$1	225	27	30	8.9999
CUU	chr1:183513446-183513670(+)$1	224	25	28	8.9999
CUU	chr3:119133264-119133486(-)$1	222	39	42	8.9999
CUU	chr10:115636402-115636632(+)$1	230	2	5	8.9999
CUU	chr17:80583199-80583422(-)$1	223	25	28	8.9999
CUU	chr2:61710088-61710318(-)$1	230	16	19	8.9999
CUU	chr15:78575723-78575953(-)$1	230	72	75	8.9999
CUU	chrM:10162-10392(+)$1	230	3	6	8.9999
CUU	chr3:97705452-97705675(+)$1	223	43	46	8.9999
CUU	chr1:200818552-200818778(+)$1	226	44	47	8.9999
CUU	chrM:13030-13260(-)$1	230	0	3	8.9999
CUU	chr7:65419098-65419328(+)$1	230	53	56	8.9999
CUU	chr6:144262739-144262969(-)$1	230	15	18	8.9999
CUU	chr19:9949020-9949244(+)$1	224	19	22	8.9999
CUU	chr20:33328479-33328698(-)$1	219	24	27	8.9999
CUU	chr20:46262158-46262380(+)$1	222	35	38	8.9999
CUU	chr9:95040430-95040652(-)$1	222	12	15	8.9999
CUU	chr8:76476147-76476377(+)$1	230	53	56	8.9999
CUU	chr5:162868788-162869011(+)$1	223	7	10	8.9999
CUU	chr1:234743191-234743416(-)$1	225	56	59	8.9999
CUU	chr6:42827956-42828181(+)$1	225	21	24	8.9999
CUU	chr15:74703175-74703405(-)$1	230	38	41	8.9999
CUU	chr1:21137161-21137387(-)$1	226	4	7	8.9999
CUU	chr11:17118649-17118874(-)$1	225	64	67	8.9999
CUU	chr20:61299319-61299544(+)$1	225	6	9	8.9999

#otherMatches

#Struct PSSM
{HH	chr2:20451357-20451581(-)$1	224	41	44	8.9999
DDD	chr17:40140734-40140958(-)$1	224	1	4	8.9999
ooo	chrX:100383629-100383859(+)$1	230	23	26	8.9999
ggg	chr2:152311438-152311672(+)$1	234	27	30	8.9999
ddd	chr12:98925438-98925668(+)$1	230	9	12	8.9999
HHH	chr1:169953646-169953869(-)$1	223	5	8	8.9999
CCC	chr19:21719560-21719783(+)$1	223	24	27	8.9999
nnn	chr15:65739134-65739359(-)$1	225	78	81	8.9999
+++	chr1:24022743-24022984(+)$1	241	78	81	8.9999
FF:	chr3:189608524-189608754(+)$1	230	7	10	8.9999
'''	chr15:83805203-83805428(+)$1	225	56	59	8.9999
FFF	chr5:134010638-134010868(+)$1	230	16	19	8.9999
eee	chr2:211019017-211019247(-)$1	230	72	75	8.9999
::f	chr6:34725600-34725826(+)$1	226	12	15	8.9999
22e	chr3:172533357-172533579(+)$1	222	42	45	8.9999
dde	chr7:107546633-107546863(+)$1	230	60	63	8.9999
EEE	chr12:50386238-50386457(-)$1	219	1	4	8.9999
:::	chrM:15408-15638(+)$1	230	3	6	8.9999
uuu	chr8:124266467-124266697(-)$1	230	91	94	8.9999
GGG	chr5:88056772-88057002(-)$1	230	19	22	8.9999
$$$	chr9:72338403-72338633(-)$1	230	43	46	8.9999
:::	chr10:17756570-17756798(+)$1	228	121	124	8.9999
CCC	chr20:52188171-52188396(-)$1	225	29	32	8.9999
ccc	chr10:31137857-31138082(-)$1	225	85	88	8.9999
:::	chr2:191760295-191760525(+)$1	230	15	18	8.9999
:::	chrX:16759778-16760008(+)$1	230	29	32	8.9999
:::	chr9:32558821-32559051(-)$1	230	9	12	8.9999
^^^	chr5:61673398-61673621(+)$1	223	30	33	8.9999
c::	chr14:24642121-24642351(+)$1	230	52	55	8.9999
ggg	chr3:121410385-121410615(-)$1	230	79	82	8.9999
:::	chr2:220089736-220089960(-)$1	224	8	11	8.9999
OOO	chr2:61710034-61710264(-)$1	230	10	13	8.9999
:::	chr1:41236044-41236267(+)$1	223	8	11	8.9999
:::	chr12:2983507-2983733(-)$1	226	18	21	8.9999
ooo	chr12:49445698-49445928(-)$1	230	19	22	8.9999
CKK	chr5:114860506-114860730(-)$1	224	17	20	8.9999
DDL	chrX:41084265-41084490(+)$1	225	21	24	8.9999
b[b	chr12:70150136-70150356(+)$1	220	40	43	8.9999
JJJ	chr10:22839571-22839794(-)$1	223	7	10	8.9999
eee	chr14:78182070-78182293(+)$1	223	19	22	8.9999
fff	chr1:154573953-154574176(-)$1	223	28	31	8.9999
ccc	chr3:170078238-170078468(+)$1	230	39	42	8.9999
:::	chr20:33233010-33233240(-)$1	230	66	69	8.9999
:::	chr20:42232379-42232602(+)$1	223	2	5	8.9999
===	chr8:64098838-64099068(+)$1	230	85	88	8.9999
DDD	chr13:20346491-20346721(-)$1	230	8	11	8.9999
HHH	chr20:44049089-44049315(+)$1	226	46	49	8.9999
&&&	chr3:63967866-63968096(+)$1	230	94	97	8.9999
DDD	chr7:129842321-129842551(-)$1	230	19	22	8.9999
GGG	chr18:3253132-3253359(+)$1	227	15	18	8.9999
:::	chr3:114070558-114070785(-)$1	227	107	110	8.9999
TTT	chr1:154229463-154229693(+)$1	230	6	9	8.9999
d!!	chr9:127951861-127952087(-)$1	226	15	18	8.9999
ddd	chr3:179287835-179288065(+)$1	230	12	15	8.9999
ggg	chr1:155874011-155874232(-)$1	221	50	53	8.9999
fff	chr16:70605506-70605736(+)$1	230	1	4	8.9999
OOD	chr17:38572634-38572864(-)$1	230	14	17	8.9999
dds	chr19:46020927-46021157(+)$1	230	30	33	8.9999
PJJ	chr1:54262325-54262562(-)$1	237	55	58	8.9999
cc2	chr5:180277076-180277300(-)$1	224	92	95	8.9999
ddd	chr13:113889338-113889560(+)$1	222	50	53	8.9999
ggg	chr2:180818836-180819066(-)$1	230	17	20	8.9999
^^^	chr10:103869258-103869483(-)$1	225	17	20	8.9999
sss	chr9:106878425-106878655(+)$1	230	172	175	8.9999
:::	chr1:212245346-212245576(+)$1	230	11	14	8.9999
fff	chr19:21990484-21990714(-)$1	230	16	19	8.9999
:::	chr12:49418261-49418486(-)$1	225	49	52	8.9999
b!!	chr20:44049120-44049350(+)$1	230	15	18	8.9999
::f	chr3:178927983-178928209(+)$1	226	22	25	8.9999
ddd	chr12:112701851-112702077(-)$1	226	14	17	8.9999
nnn	chr20:34242929-34243159(-)$1	230	42	45	8.9999
DDD	chr3:150262095-150262325(-)$1	230	8	11	8.9999
ggg	chr5:149826351-149826573(-)$1	222	4	7	8.9999
FFF	chr5:93807283-93807503(+)$1	220	0	3	8.9999
===	chr12:112691835-112692060(-)$1	225	27	30	8.9999
ggg	chr1:183513446-183513670(+)$1	224	25	28	8.9999
c[b	chr3:119133264-119133486(-)$1	222	39	42	8.9999
CKK	chr10:115636402-115636632(+)$1	230	2	5	8.9999
d::	chr17:80583199-80583422(-)$1	223	25	28	8.9999
{JJ	chr2:61710088-61710318(-)$1	230	16	19	8.9999
qqq	chr15:78575723-78575953(-)$1	230	72	75	8.9999
:::	chrM:10162-10392(+)$1	230	3	6	8.9999
LLL	chr3:97705452-97705675(+)$1	223	43	46	8.9999
cc[	chr1:200818552-200818778(+)$1	226	44	47	8.9999
CCC	chrM:13030-13260(-)$1	230	0	3	8.9999
dll	chr7:65419098-65419328(+)$1	230	53	56	8.9999
nnn	chr6:144262739-144262969(-)$1	230	15	18	8.9999
FFL	chr19:9949020-9949244(+)$1	224	19	22	8.9999
LLD	chr20:33328479-33328698(-)$1	219	24	27	8.9999
cc:	chr20:46262158-46262380(+)$1	222	35	38	8.9999
EKK	chr9:95040430-95040652(-)$1	222	12	15	8.9999
:::	chr8:76476147-76476377(+)$1	230	53	56	8.9999
BMM	chr5:162868788-162869011(+)$1	223	7	10	8.9999
EEE	chr1:234743191-234743416(-)$1	225	56	59	8.9999
GGG	chr6:42827956-42828181(+)$1	225	21	24	8.9999
555	chr15:74703175-74703405(-)$1	230	38	41	8.9999
FFF	chr1:21137161-21137387(-)$1	226	4	7	8.9999
$$$	chr11:17118649-17118874(-)$1	225	64	67	8.9999
:::	chr20:61299319-61299544(+)$1	225	6	9	8.9999

#DB
.((	chr2:20451357-20451581(-)$1	1	41	44	8.9999
(((	chr17:40140734-40140958(-)$1	1	1	4	8.9999
...	chrX:100383629-100383859(+)$1	1	23	26	8.9999
(((	chr2:152311438-152311672(+)$1	1	27	30	8.9999
(((	chr12:98925438-98925668(+)$1	1	9	12	8.9999
(((	chr1:169953646-169953869(-)$1	1	5	8	8.9999
(((	chr19:21719560-21719783(+)$1	1	24	27	8.9999
...	chr15:65739134-65739359(-)$1	1	78	81	8.9999
...	chr1:24022743-24022984(+)$1	1	78	81	8.9999
((.	chr3:189608524-189608754(+)$1	1	7	10	8.9999
...	chr15:83805203-83805428(+)$1	1	56	59	8.9999
(((	chr5:134010638-134010868(+)$1	1	16	19	8.9999
)))	chr2:211019017-211019247(-)$1	1	72	75	8.9999
..(	chr6:34725600-34725826(+)$1	1	12	15	8.9999
..)	chr3:172533357-172533579(+)$1	1	42	45	8.9999
(((	chr7:107546633-107546863(+)$1	1	60	63	8.9999
(((	chr12:50386238-50386457(-)$1	1	1	4	8.9999
...	chrM:15408-15638(+)$1	1	3	6	8.9999
...	chr8:124266467-124266697(-)$1	1	91	94	8.9999
(((	chr5:88056772-88057002(-)$1	1	19	22	8.9999
...	chr9:72338403-72338633(-)$1	1	43	46	8.9999
...	chr10:17756570-17756798(+)$1	1	121	124	8.9999
(((	chr20:52188171-52188396(-)$1	1	29	32	8.9999
(((	chr10:31137857-31138082(-)$1	1	85	88	8.9999
...	chr2:191760295-191760525(+)$1	1	15	18	8.9999
...	chrX:16759778-16760008(+)$1	1	29	32	8.9999
...	chr9:32558821-32559051(-)$1	1	9	12	8.9999
...	chr5:61673398-61673621(+)$1	1	30	33	8.9999
)..	chr14:24642121-24642351(+)$1	1	52	55	8.9999
(((	chr3:121410385-121410615(-)$1	1	79	82	8.9999
...	chr2:220089736-220089960(-)$1	1	8	11	8.9999
...	chr2:61710034-61710264(-)$1	1	10	13	8.9999
...	chr1:41236044-41236267(+)$1	1	8	11	8.9999
...	chr12:2983507-2983733(-)$1	1	18	21	8.9999
...	chr12:49445698-49445928(-)$1	1	19	22	8.9999
(..	chr5:114860506-114860730(-)$1	1	17	20	8.9999
((.	chrX:41084265-41084490(+)$1	1	21	24	8.9999
(.(	chr12:70150136-70150356(+)$1	1	40	43	8.9999
(((	chr10:22839571-22839794(-)$1	1	7	10	8.9999
(((	chr14:78182070-78182293(+)$1	1	19	22	8.9999
(((	chr1:154573953-154574176(-)$1	1	28	31	8.9999
)))	chr3:170078238-170078468(+)$1	1	39	42	8.9999
...	chr20:33233010-33233240(-)$1	1	66	69	8.9999
...	chr20:42232379-42232602(+)$1	1	2	5	8.9999
)))	chr8:64098838-64099068(+)$1	1	85	88	8.9999
(((	chr13:20346491-20346721(-)$1	1	8	11	8.9999
(((	chr20:44049089-44049315(+)$1	1	46	49	8.9999
...	chr3:63967866-63968096(+)$1	1	94	97	8.9999
(((	chr7:129842321-129842551(-)$1	1	19	22	8.9999
(((	chr18:3253132-3253359(+)$1	1	15	18	8.9999
...	chr3:114070558-114070785(-)$1	1	107	110	8.9999
...	chr1:154229463-154229693(+)$1	1	6	9	8.9999
(..	chr9:127951861-127952087(-)$1	1	15	18	8.9999
(((	chr3:179287835-179288065(+)$1	1	12	15	8.9999
)))	chr1:155874011-155874232(-)$1	1	50	53	8.9999
(((	chr16:70605506-70605736(+)$1	1	1	4	8.9999
..(	chr17:38572634-38572864(-)$1	1	14	17	8.9999
((.	chr19:46020927-46021157(+)$1	1	30	33	8.9999
.((	chr1:54262325-54262562(-)$1	1	55	58	8.9999
)).	chr5:180277076-180277300(-)$1	1	92	95	8.9999
(((	chr13:113889338-113889560(+)$1	1	50	53	8.9999
(((	chr2:180818836-180819066(-)$1	1	17	20	8.9999
...	chr10:103869258-103869483(-)$1	1	17	20	8.9999
...	chr9:106878425-106878655(+)$1	1	172	175	8.9999
...	chr1:212245346-212245576(+)$1	1	11	14	8.9999
(((	chr19:21990484-21990714(-)$1	1	16	19	8.9999
...	chr12:49418261-49418486(-)$1	1	49	52	8.9999
(..	chr20:44049120-44049350(+)$1	1	15	18	8.9999
..(	chr3:178927983-178928209(+)$1	1	22	25	8.9999
(((	chr12:112701851-112702077(-)$1	1	14	17	8.9999
...	chr20:34242929-34243159(-)$1	1	42	45	8.9999
(((	chr3:150262095-150262325(-)$1	1	8	11	8.9999
(((	chr5:149826351-149826573(-)$1	1	4	7	8.9999
(((	chr5:93807283-93807503(+)$1	1	0	3	8.9999
(((	chr12:112691835-112692060(-)$1	1	27	30	8.9999
(((	chr1:183513446-183513670(+)$1	1	25	28	8.9999
(.(	chr3:119133264-119133486(-)$1	1	39	42	8.9999
(..	chr10:115636402-115636632(+)$1	1	2	5	8.9999
)..	chr17:80583199-80583422(-)$1	1	25	28	8.9999
.((	chr2:61710088-61710318(-)$1	1	16	19	8.9999
...	chr15:78575723-78575953(-)$1	1	72	75	8.9999
...	chrM:10162-10392(+)$1	1	3	6	8.9999
...	chr3:97705452-97705675(+)$1	1	43	46	8.9999
((.	chr1:200818552-200818778(+)$1	1	44	47	8.9999
(((	chrM:13030-13260(-)$1	1	0	3	8.9999
(..	chr7:65419098-65419328(+)$1	1	53	56	8.9999
...	chr6:144262739-144262969(-)$1	1	15	18	8.9999
((.	chr19:9949020-9949244(+)$1	1	19	22	8.9999
..(	chr20:33328479-33328698(-)$1	1	24	27	8.9999
)).	chr20:46262158-46262380(+)$1	1	35	38	8.9999
(..	chr9:95040430-95040652(-)$1	1	12	15	8.9999
...	chr8:76476147-76476377(+)$1	1	53	56	8.9999
(..	chr5:162868788-162869011(+)$1	1	7	10	8.9999
(((	chr1:234743191-234743416(-)$1	1	56	59	8.9999
(((	chr6:42827956-42828181(+)$1	1	21	24	8.9999
...	chr15:74703175-74703405(-)$1	1	38	41	8.9999
(((	chr1:21137161-21137387(-)$1	1	4	7	8.9999
...	chr11:17118649-17118874(-)$1	1	64	67	8.9999
...	chr20:61299319-61299544(+)$1	1	6	9	8.9999

#PSSM
C : 0.97	c : 0.02	
U : 0.97	u : 0.02	
U : 0.98	u : 0.01	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_transcript_m1_run1.nuc.txt

#NT
AAUUUUUUUU	chr6:5301832-5302064(+)$1	232	115	125	18.7704
ACUUUAUUUA	chr1:92802005-92802237(+)$1	232	19	29	14.6721
ACAUUUUUCU	chr15:67889500-67889732(+)$1	232	109	119	13.7704
GCUUUUUCUU	chr22:31562357-31562583(+)$1	226	99	109	14.2622
UCUUUUUUUU	chr1:114307981-114308209(-)$1	228	204	214	18.8524
ACUUUUAAUU	chr2:24817407-24817631(+)$1	224	103	113	13.6885
ACUUUGUUUG	chr3:32362319-32362551(+)$1	232	38	48	14.6721
AUUUUUUUUU	chr20:33973864-33974110(-)$1	246	64	74	18.6885
auuuuuuuuu	chr2:233081185-233081417(+)$1	232	110	120	18.6885
aauuuuguuu	chr10:131464798-131465043(+)$1	245	156	166	14.5081
AUUUUUUUUU	chr19:30832540-30832771(+)$1	231	23	33	18.6885
CCuuucuuuu	chr11:96019605-96019831(-)$1	226	169	179	14.8360
ACUUUCUUUU	chrX:107972017-107972239(-)$1	222	187	197	18.4426
UCUUUUUUUU	chr11:68338313-68338538(+)$1	225	176	186	18.8524
ACUGUUAUUU	chr14:100829270-100829493(-)$1	223	46	56	14.0163
ucuuguuuuu	chr20:33957423-33957652(-)$1	229	184	194	14.5081
ACUUUUGUGU	chr14:90071924-90072157(-)$1	233	18	28	14.2622
GCUUUGUUUU	chr12:116630017-116630249(-)$1	232	22	32	15.0819
ACUAUUUUUU	chr4:20261131-20261365(+)$1	234	175	185	18.1967
CCUUUUUUGU	chr1:90101919-90102158(+)$1	239	45	55	14.9180
acuauguuuu	chr8:95515792-95516014(-)$1	222	181	191	14.8360
ucuuuuuucu	chr1:68956223-68956454(-)$1	231	26	36	15.0819
acuuuuucau	chr1:180365171-180365419(-)$1	248	79	89	14.0983
acuuuuuguu	chr13:41199086-41199325(-)$1	239	194	204	17.7049
CCUUUAUUUU	chrX:73464089-73464315(-)$1	226	36	46	15.3278
UGuuuuuuuu	chr10:49636672-49636904(+)$1	232	183	193	15.0819
ACUUUUUUGG	chrX:73059043-73059271(-)$1	228	55	65	14.5081
acuuuuuuua	chr20:58957286-58957518(+)$1	232	114	124	17.7868
ACAUUUUUUU	chr19:2140963-2141195(-)$1	232	119	129	17.5409
auuuuuuauu	chr2:114693966-114694216(+)$1	250	2	12	14.5081
AAUUUUUUUG	chr6:8427970-8428198(-)$1	228	72	82	14.7540
ACUUUUUUUU	chr13:50615911-50616143(-)$1	232	126	136	22.0491
acuuauuugu	chr18:257295-257519(-)$1	224	159	169	14.5081
ACUUUUUAUG	chr7:126513880-126514112(-)$1	232	203	213	13.8524
ACUUUUUUUU	chr9:91062077-91062309(+)$1	232	212	222	22.0491
GCUUUUUUUU	chr18:29489048-29489272(-)$1	224	210	220	18.4426
ucuguuuuuu	chr6:45133199-45133431(-)$1	232	0	10	15.0000
accuuuuuuu	chr8:14407305-14407535(-)$1	230	29	39	17.5409
aaucuuuuuu	chr1:22035812-22036044(-)$1	232	44	54	14.7540
ucuuauuuuu	chr11:74339214-74339446(+)$1	232	154	164	14.8360
ACUAUUUUUG	chr14:93779622-93779854(-)$1	232	221	231	14.1803
UCUUUGUUUU	chr22:26119608-26119830(+)$1	222	184	194	15.4918
AUUUUAUUUU	chr1:64552087-64552320(+)$1	233	169	179	15.5737
ACUCAUUUUU	chr7:26881571-26881803(-)$1	232	4	14	14.0163
ACUUAUCUUU	chr1:241499170-241499402(-)$1	232	25	35	13.7704
aauuuuuucu	chr4:164420075-164420305(+)$1	230	140	150	15.0000
ACUUUAUUUU	chr14:67313762-67313994(+)$1	232	117	127	18.9344
aauuuauuuu	chr6:37267746-37267993(+)$1	247	132	142	15.6557
ACUUCUUUUU	chr11:36336925-36337157(+)$1	232	168	178	17.7049
AUUUUAUUUU	chr8:15432790-15433022(+)$1	232	41	51	15.5737
acuuaauuuu	chr8:25870460-25870692(-)$1	232	98	108	14.9180
ACCUUAUUUU	chr8:17502464-17502707(-)$1	243	182	192	14.4262
ACUUUUAUAU	chrX:102043136-102043362(+)$1	226	87	97	14.0983
ACUGUUUUGU	chr4:85591597-85591827(-)$1	230	203	213	14.6721
AAUUUUUUUU	chr8:130910534-130910765(-)$1	231	156	166	18.7704
aCUUUUUUGU	chr1:109945091-109945324(-)$1	233	8	18	18.5245
ACUUUGUCUU	chr3:6624958-6625190(+)$1	232	203	213	14.5081
ACUUUUCUUU	chr1:58934582-58934814(-)$1	232	120	130	17.7868
acuguuuuuu	chr10:3131923-3132155(+)$1	232	96	106	18.1967
ACUAUUUUUU	chr5:137295815-137296047(-)$1	232	199	209	18.1967

#otherMatches

#Struct PSSM
3=========	chr5:151180986-151181221(+)$1	235	83	93	18.2786
>>>>>>>>>>	chr6:5301832-5302064(+)$1	232	115	125	18.7704
::::::::::	chr1:92802005-92802237(+)$1	232	19	29	14.6721
>>>>>>ccc2	chr15:67889500-67889732(+)$1	232	109	119	13.7704
eeee++++++	chr22:31562357-31562583(+)$1	226	99	109	14.2622
DDEEEEE}EE	chr1:114307981-114308209(-)$1	228	204	214	18.8524
::::::::::	chr2:24817407-24817631(+)$1	224	103	113	13.6885
DDDKKCCC{C	chr3:32362319-32362551(+)$1	232	38	48	14.6721
=[bb[dddd[	chr20:33973864-33974110(-)$1	246	64	74	18.6885
^^^^^^^^^^	chr2:233081185-233081417(+)$1	232	110	120	18.6885
ee"""ddddt	chr10:131464798-131465043(+)$1	245	156	166	14.5081
iiiiiiisss	chr19:30832540-30832771(+)$1	231	23	33	18.6885
ddd22bb>>>	chr11:96019605-96019831(-)$1	226	169	179	14.8360
ssssdddd]c	chrX:107972017-107972239(-)$1	222	187	197	18.4426
xxxxxxxxxx	chr11:68338313-68338538(+)$1	225	176	186	18.8524
##cccqqqqq	chr14:100829270-100829493(-)$1	223	46	56	14.0163
bb"""hhhhh	chr20:33957423-33957652(-)$1	229	184	194	14.5081
ddmmmmdddd	chr14:90071924-90072157(-)$1	233	18	28	14.2622
EEEggggggg	chr12:116630017-116630249(-)$1	232	22	32	15.0819
lffffff22g	chr4:20261131-20261365(+)$1	234	175	185	18.1967
99999999a]	chr1:90101919-90102158(+)$1	239	45	55	14.9180
::ffffff""	chr8:95515792-95516014(-)$1	222	181	191	14.8360
:::::IIIII	chr1:68956223-68956454(-)$1	231	26	36	15.0819
::::eeeeet	chr1:180365171-180365419(-)$1	248	79	89	14.0983
DDDD::eeee	chr13:41199086-41199325(-)$1	239	194	204	17.7049
ddd::::::f	chrX:73464089-73464315(-)$1	226	36	46	15.3278
GGGGGGG:::	chr10:49636672-49636904(+)$1	232	183	193	15.0819
mdddd]dddd	chrX:73059043-73059271(-)$1	228	55	65	14.5081
zbb]gggggg	chr20:58957286-58957518(+)$1	232	114	124	17.7868
:::::::::f	chr19:2140963-2141195(-)$1	232	119	129	17.5409
DDLLLHHHHH	chr2:114693966-114694216(+)$1	250	2	12	14.5081
33hhhhhhhh	chr6:8427970-8428198(-)$1	228	72	82	14.7540
^^^^^^^^^^	chr13:50615911-50616143(-)$1	232	126	136	22.0491
bboooooobb	chr18:257295-257519(-)$1	224	159	169	14.5081
e]bb55555h	chr7:126513880-126514112(-)$1	232	203	213	13.8524
ccqqqqqqqq	chr9:91062077-91062309(+)$1	232	212	222	22.0491
BB::::::::	chr18:29489048-29489272(-)$1	224	210	220	18.4426
::::::::::	chr6:45133199-45133431(-)$1	232	0	10	15.0000
::::::::::	chr8:14407305-14407535(-)$1	230	29	39	17.5409
gg[ccc%%%%	chr1:22035812-22036044(-)$1	232	44	54	14.7540
::::::::::	chr11:74339214-74339446(+)$1	232	154	164	14.8360
ee]ffffff:	chr14:93779622-93779854(-)$1	232	221	231	14.1803
2a22dddd44	chr22:26119608-26119830(+)$1	222	184	194	15.4918
mmmccc22dd	chr1:64552087-64552320(+)$1	233	169	179	15.5737
::cccmmmmc	chr7:26881571-26881803(-)$1	232	4	14	14.0163
dgggggggGG	chr1:241499170-241499402(-)$1	232	25	35	13.7704
::::::::::	chr4:164420075-164420305(+)$1	230	140	150	15.0000
&dddd[hhhh	chr14:67313762-67313994(+)$1	232	117	127	18.9344
eeeee"""gg	chr6:37267746-37267993(+)$1	247	132	142	15.6557
GGGGGG}CCC	chr11:36336925-36337157(+)$1	232	168	178	17.7049
E:::::::cc	chr8:15432790-15433022(+)$1	232	41	51	15.5737
cqqqqqqqqc	chr8:25870460-25870692(-)$1	232	98	108	14.9180
22ccc]gggg	chr8:17502464-17502707(-)$1	243	182	192	14.4262
::::::::::	chrX:102043136-102043362(+)$1	226	87	97	14.0983
fnnnnnffff	chr4:85591597-85591827(-)$1	230	203	213	14.6721
=========:	chr8:130910534-130910765(-)$1	231	156	166	18.7704
ggggpppppp	chr1:109945091-109945324(-)$1	233	8	18	18.5245
bb::eeeeeq	chr3:6624958-6625190(+)$1	232	203	213	14.5081
!a"""ddddn	chr1:58934582-58934814(-)$1	232	120	130	17.7868
::::::::::	chr10:3131923-3132155(+)$1	232	96	106	18.1967
hnnnnnhhhh	chr5:137295815-137296047(-)$1	232	199	209	18.1967

#DB
.)))))))))	chr5:151180986-151181221(+)$1	1	83	93	18.2786
..........	chr6:5301832-5302064(+)$1	1	115	125	18.7704
..........	chr1:92802005-92802237(+)$1	1	19	29	14.6721
......))).	chr15:67889500-67889732(+)$1	1	109	119	13.7704
((((......	chr22:31562357-31562583(+)$1	1	99	109	14.2622
))))))).))	chr1:114307981-114308209(-)$1	1	204	214	18.8524
..........	chr2:24817407-24817631(+)$1	1	103	113	13.6885
(((..(((.(	chr3:32362319-32362551(+)$1	1	38	48	14.6721
(.((.((((.	chr20:33973864-33974110(-)$1	1	64	74	18.6885
..........	chr2:233081185-233081417(+)$1	1	110	120	18.6885
((...((((.	chr10:131464798-131465043(+)$1	1	156	166	14.5081
(((((((...	chr19:30832540-30832771(+)$1	1	23	33	18.6885
)))..))...	chr11:96019605-96019831(-)$1	1	169	179	14.8360
....)))).)	chrX:107972017-107972239(-)$1	1	187	197	18.4426
..........	chr11:68338313-68338538(+)$1	1	176	186	18.8524
..(((.....	chr14:100829270-100829493(-)$1	1	46	56	14.0163
((...(((((	chr20:33957423-33957652(-)$1	1	184	194	14.5081
((....))))	chr14:90071924-90072157(-)$1	1	18	28	14.2622
((((((((((	chr12:116630017-116630249(-)$1	1	22	32	15.0819
.))))))..)	chr4:20261131-20261365(+)$1	1	175	185	18.1967
........).	chr1:90101919-90102158(+)$1	1	45	55	14.9180
..((((((..	chr8:95515792-95516014(-)$1	1	181	191	14.8360
.....(((((	chr1:68956223-68956454(-)$1	1	26	36	15.0819
....(((((.	chr1:180365171-180365419(-)$1	1	79	89	14.0983
))))..((((	chr13:41199086-41199325(-)$1	1	194	204	17.7049
)))......(	chrX:73464089-73464315(-)$1	1	36	46	15.3278
)))))))...	chr10:49636672-49636904(+)$1	1	183	193	15.0819
.)))).))))	chrX:73059043-73059271(-)$1	1	55	65	14.5081
.)).))))))	chr20:58957286-58957518(+)$1	1	114	124	17.7868
.........(	chr19:2140963-2141195(-)$1	1	119	129	17.5409
((...(((((	chr2:114693966-114694216(+)$1	1	2	12	14.5081
..))))))))	chr6:8427970-8428198(-)$1	1	72	82	14.7540
..........	chr13:50615911-50616143(-)$1	1	126	136	22.0491
((......))	chr18:257295-257519(-)$1	1	159	169	14.5081
).)).....)	chr7:126513880-126514112(-)$1	1	203	213	13.8524
((........	chr9:91062077-91062309(+)$1	1	212	222	22.0491
))........	chr18:29489048-29489272(-)$1	1	210	220	18.4426
..........	chr6:45133199-45133431(-)$1	1	0	10	15.0000
..........	chr8:14407305-14407535(-)$1	1	29	39	17.5409
((.(((....	chr1:22035812-22036044(-)$1	1	44	54	14.7540
..........	chr11:74339214-74339446(+)$1	1	154	164	14.8360
)).)))))).	chr14:93779622-93779854(-)$1	1	221	231	14.1803
.)..))))..	chr22:26119608-26119830(+)$1	1	184	194	15.4918
...)))..))	chr1:64552087-64552320(+)$1	1	169	179	15.5737
..(((....)	chr7:26881571-26881803(-)$1	1	4	14	14.0163
))))))))((	chr1:241499170-241499402(-)$1	1	25	35	13.7704
..........	chr4:164420075-164420305(+)$1	1	140	150	15.0000
.((((.((((	chr14:67313762-67313994(+)$1	1	117	127	18.9344
(((((...((	chr6:37267746-37267993(+)$1	1	132	142	15.6557
)))))).)))	chr11:36336925-36337157(+)$1	1	168	178	17.7049
(.......((	chr8:15432790-15433022(+)$1	1	41	51	15.5737
(........)	chr8:25870460-25870692(-)$1	1	98	108	14.9180
..))).))))	chr8:17502464-17502707(-)$1	1	182	192	14.4262
..........	chrX:102043136-102043362(+)$1	1	87	97	14.0983
(.....))))	chr4:85591597-85591827(-)$1	1	203	213	14.6721
))))))))).	chr8:130910534-130910765(-)$1	1	156	166	18.7704
((((......	chr1:109945091-109945324(-)$1	1	8	18	18.5245
))..(((((.	chr3:6624958-6625190(+)$1	1	203	213	14.5081
.(...((((.	chr1:58934582-58934814(-)$1	1	120	130	17.7868
..........	chr10:3131923-3132155(+)$1	1	96	106	18.1967
(.....))))	chr5:137295815-137296047(-)$1	1	199	209	18.1967

#PSSM
A : 0.52	a : 0.24	U : 0.06	u : 0.06	G : 0.04	C : 0.04	
C : 0.57	c : 0.19	U : 0.06	a : 0.06	A : 0.04	u : 0.03	G : 0.01	
U : 0.60	u : 0.32	A : 0.03	c : 0.01	C : 0.01	
U : 0.55	u : 0.27	A : 0.04	G : 0.03	g : 0.03	a : 0.01	c : 0.01	C : 0.01	
U : 0.60	u : 0.27	a : 0.04	A : 0.03	g : 0.01	C : 0.01	
U : 0.47	u : 0.27	A : 0.09	G : 0.06	a : 0.03	c : 0.01	C : 0.01	g : 0.01	
U : 0.55	u : 0.32	A : 0.04	C : 0.03	g : 0.01	G : 0.01	
U : 0.59	u : 0.29	C : 0.03	A : 0.03	c : 0.01	g : 0.01	a : 0.01	
U : 0.54	u : 0.26	G : 0.08	a : 0.03	c : 0.03	C : 0.01	g : 0.01	A : 0.01	
U : 0.55	u : 0.32	G : 0.08	A : 0.01	a : 0.01	

#score	984.918032786886
#seq	61
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m1_run1.nuc.txt

#NT
UCCUGG	chr17:57287500-57287740(+)$1	240	163	169	15.3750
UCCUGG	chr16:698083-698323(+)$1	240	78	84	15.3750
UCCUGG	chr22:50280430-50280670(+)$1	240	207	213	15.3750
UCCUGA	chr12:124081163-124081456(+)$1	293	122	128	14.3750
UCCUGC	chr9:135562560-135562800(+)$1	240	84	90	13.6250
UCCUGU	chr17:76181102-76181342(-)$1	240	228	234	13.6250
UCCUGU	chr7:139288763-139289003(-)$1	240	19	25	13.6250
UCCUGA	chr21:45194013-45194253(-)$1	240	171	177	14.3750
UCCUGG	chr2:169622083-169622323(+)$1	240	70	76	15.3750
UCCUGA	chr11:33093927-33094167(+)$1	240	101	107	14.3750
UCCUGA	chrX:53588732-53588972(-)$1	240	161	167	14.3750
UCCUGG	chr1:68948349-68948589(-)$1	240	0	6	15.3750
UCCUGA	chr17:6546225-6546465(+)$1	240	143	149	14.3750
UCCUGG	chr1:67442182-67442422(+)$1	240	211	217	15.3750
UCCUGG	chr6:41908142-41908416(-)$1	274	196	202	15.3750
UCCUGC	chr17:73808189-73808437(+)$1	248	11	17	13.6250
UCCUGA	chr1:6293475-6293715(-)$1	240	101	107	14.3750
UCCUGG	chr10:30611256-30611496(-)$1	240	67	73	15.3750
UCCUGU	chr3:101370253-101370493(-)$1	240	69	75	13.6250
UCCUGA	chr3:49064154-49064394(-)$1	240	46	52	14.3750
UCCUGG	chr15:85326351-85326591(+)$1	240	99	105	15.3750
UCCUGA	chr5:179047817-179048060(-)$1	243	82	88	14.3750
UCCUGG	chr11:64900338-64900578(-)$1	240	48	54	15.3750
UCCUGG	chr6:53372176-53372416(-)$1	240	217	223	15.3750
UCCUGG	chr6:150048121-150048361(-)$1	240	98	104	15.3750
UCCUGC	chr9:124103406-124103686(-)$1	280	71	77	13.6250
UCCUGG	chr2:233433587-233433840(+)$1	253	229	235	15.3750
UCCUGG	chr9:33944364-33944606(-)$1	242	57	63	15.3750
UCCUGU	chr14:50249563-50249803(+)$1	240	151	157	13.6250
UCCUGU	chr3:49148970-49149210(-)$1	240	177	183	13.6250
UCCUGG	chr1:94639401-94639641(-)$1	240	3	9	15.3750
UCCUGC	chr1:202920076-202920316(-)$1	240	162	168	13.6250
UCCUGA	chr1:149876424-149876714(-)$1	290	226	232	14.3750
UCCUGG	chr3:66550574-66550821(-)$1	247	191	197	15.3750
UCCUGG	chr2:27263550-27263790(+)$1	240	164	170	15.3750
UCCUGG	chr5:176025654-176025894(-)$1	240	8	14	15.3750
UCCUGA	chr8:77765396-77765636(+)$1	240	188	194	14.3750
UCCUGA	chr3:130698069-130698309(+)$1	240	42	48	14.3750
UCCUGC	chr9:131107497-131107737(+)$1	240	124	130	13.6250

#otherMatches

#Struct PSSM
:::DDD	chr1:224612127-224612407(-)$1	280	109	115	15.3750
ffffff	chr17:57287500-57287740(+)$1	240	163	169	15.3750
dHHHHH	chr16:698083-698323(+)$1	240	78	84	15.3750
FFFFff	chr22:50280430-50280670(+)$1	240	207	213	15.3750
ffdddd	chr12:124081163-124081456(+)$1	293	122	128	14.3750
4444a]	chr9:135562560-135562800(+)$1	240	84	90	13.6250
:::EEE	chr17:76181102-76181342(-)$1	240	228	234	13.6250
e:dddd	chr7:139288763-139289003(-)$1	240	19	25	13.6250
4444bb	chr21:45194013-45194253(-)$1	240	171	177	14.3750
cccmmm	chr2:169622083-169622323(+)$1	240	70	76	15.3750
dddd55	chr11:33093927-33094167(+)$1	240	101	107	14.3750
@@@@@@	chrX:53588732-53588972(-)$1	240	161	167	14.3750
FFFFFF	chr1:68948349-68948589(-)$1	240	0	6	15.3750
CCYYEE	chr17:6546225-6546465(+)$1	240	143	149	14.3750
ccca]d	chr1:67442182-67442422(+)$1	240	211	217	15.3750
bb!!ee	chr6:41908142-41908416(-)$1	274	196	202	15.3750
^^^^^^	chr17:73808189-73808437(+)$1	248	11	17	13.6250
rrrree	chr1:6293475-6293715(-)$1	240	101	107	14.3750
cccqqq	chr10:30611256-30611496(-)$1	240	67	73	15.3750
ccc[ee	chr3:101370253-101370493(-)$1	240	69	75	13.6250
JJJJJJ	chr3:49064154-49064394(-)$1	240	46	52	14.3750
BDDDDK	chr15:85326351-85326591(+)$1	240	99	105	15.3750
dd"""c	chr5:179047817-179048060(-)$1	243	82	88	14.3750
HHHHHH	chr11:64900338-64900578(-)$1	240	48	54	15.3750
EEEEEZ	chr6:53372176-53372416(-)$1	240	217	223	15.3750
dllldd	chr6:150048121-150048361(-)$1	240	98	104	15.3750
%%ffff	chr9:124103406-124103686(-)$1	280	71	77	13.6250
ccc]bb	chr2:233433587-233433840(+)$1	253	229	235	15.3750
:eeeee	chr9:33944364-33944606(-)$1	242	57	63	15.3750
ccceee	chr14:50249563-50249803(+)$1	240	151	157	13.6250
e4444f	chr3:49148970-49149210(-)$1	240	177	183	13.6250
BBHHHH	chr1:94639401-94639641(-)$1	240	3	9	15.3750
dddeee	chr1:202920076-202920316(-)$1	240	162	168	13.6250
gggggg	chr1:149876424-149876714(-)$1	290	226	232	14.3750
d4444g	chr3:66550574-66550821(-)$1	247	191	197	15.3750
5555hh	chr2:27263550-27263790(+)$1	240	164	170	15.3750
DDDDAD	chr5:176025654-176025894(-)$1	240	8	14	15.3750
ccclll	chr8:77765396-77765636(+)$1	240	188	194	14.3750
c!!ccc	chr3:130698069-130698309(+)$1	240	42	48	14.3750
qqdddd	chr9:131107497-131107737(+)$1	240	124	130	13.6250

#DB
...(((	chr1:224612127-224612407(-)$1	1	109	115	15.3750
((((((	chr17:57287500-57287740(+)$1	1	163	169	15.3750
)(((((	chr16:698083-698323(+)$1	1	78	84	15.3750
))))((	chr22:50280430-50280670(+)$1	1	207	213	15.3750
))((((	chr12:124081163-124081456(+)$1	1	122	128	14.3750
....).	chr9:135562560-135562800(+)$1	1	84	90	13.6250
...)))	chr17:76181102-76181342(-)$1	1	228	234	13.6250
).((((	chr7:139288763-139289003(-)$1	1	19	25	13.6250
....))	chr21:45194013-45194253(-)$1	1	171	177	14.3750
(((...	chr2:169622083-169622323(+)$1	1	70	76	15.3750
))))..	chr11:33093927-33094167(+)$1	1	101	107	14.3750
......	chrX:53588732-53588972(-)$1	1	161	167	14.3750
((((((	chr1:68948349-68948589(-)$1	1	0	6	15.3750
))..))	chr17:6546225-6546465(+)$1	1	143	149	14.3750
)))).)	chr1:67442182-67442422(+)$1	1	211	217	15.3750
((..((	chr6:41908142-41908416(-)$1	1	196	202	15.3750
......	chr17:73808189-73808437(+)$1	1	11	17	13.6250
....))	chr1:6293475-6293715(-)$1	1	101	107	14.3750
(((...	chr10:30611256-30611496(-)$1	1	67	73	15.3750
(((.((	chr3:101370253-101370493(-)$1	1	69	75	13.6250
((((((	chr3:49064154-49064394(-)$1	1	46	52	14.3750
(((((.	chr15:85326351-85326591(+)$1	1	99	105	15.3750
((...(	chr5:179047817-179048060(-)$1	1	82	88	14.3750
((((((	chr11:64900338-64900578(-)$1	1	48	54	15.3750
))))).	chr6:53372176-53372416(-)$1	1	217	223	15.3750
(...))	chr6:150048121-150048361(-)$1	1	98	104	15.3750
..((((	chr9:124103406-124103686(-)$1	1	71	77	13.6250
))).))	chr2:233433587-233433840(+)$1	1	229	235	15.3750
.(((((	chr9:33944364-33944606(-)$1	1	57	63	15.3750
))))))	chr14:50249563-50249803(+)$1	1	151	157	13.6250
)....)	chr3:49148970-49149210(-)$1	1	177	183	13.6250
((((((	chr1:94639401-94639641(-)$1	1	3	9	15.3750
))))))	chr1:202920076-202920316(-)$1	1	162	168	13.6250
))))))	chr1:149876424-149876714(-)$1	1	226	232	14.3750
)....)	chr3:66550574-66550821(-)$1	1	191	197	15.3750
....))	chr2:27263550-27263790(+)$1	1	164	170	15.3750
((((((	chr5:176025654-176025894(-)$1	1	8	14	15.3750
(((...	chr8:77765396-77765636(+)$1	1	188	194	14.3750
(..(((	chr3:130698069-130698309(+)$1	1	42	48	14.3750
..))))	chr9:131107497-131107737(+)$1	1	124	130	13.6250

#PSSM
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 0.47	A : 0.27	C : 0.12	U : 0.12	

#score	586.5000000000001
#seq	40
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m1_run2.nuc.txt

#NT
UUU	chr10:121356097-121356298(-)$1	201	85	88	9.0000
UUU	chr8:99718716-99718917(-)$1	201	4	7	9.0000
UUU	chr17:61499387-61499588(+)$1	201	16	19	9.0000
UUU	chr16:70286266-70286467(-)$1	201	4	7	9.0000
uuu	chr19:54970361-54970562(+)$1	201	3	6	9.0000
UUU	chr5:37226926-37227127(-)$1	201	8	11	9.0000
UUU	chr1:26881986-26882187(+)$1	201	35	38	9.0000
UUU	chr2:135703868-135704069(+)$1	201	10	13	9.0000
UUU	chr2:61725759-61725960(-)$1	201	10	13	9.0000
UUU	chr17:30707910-30708111(+)$1	201	99	102	9.0000
uuu	chr3:49155054-49155255(-)$1	201	131	134	9.0000
UUU	chr22:31363862-31364063(-)$1	201	20	23	9.0000
UUU	chr12:53565174-53565375(-)$1	201	56	59	9.0000
UUU	chr20:36719992-36720193(+)$1	201	14	17	9.0000
UUU	chr2:198284664-198284865(-)$1	201	17	20	9.0000
uuu	chr8:42934947-42935148(+)$1	201	48	51	9.0000
UUU	chr1:204523977-204524178(+)$1	201	3	6	9.0000
UUU	chr8:23116501-23116702(+)$1	201	7	10	9.0000
UUU	chr11:58386351-58386552(+)$1	201	51	54	9.0000
UUU	chr1:1228050-1228251(-)$1	201	19	22	9.0000
UUU	chr4:4238171-4238372(-)$1	201	76	79	9.0000
UUU	chr9:97222545-97222746(+)$1	201	14	17	9.0000
UUU	chr17:34860253-34860454(-)$1	201	37	40	9.0000
UUU	chr1:27734542-27734743(-)$1	201	34	37	9.0000
UUU	chr3:169700385-169700586(+)$1	201	9	12	9.0000
UUU	chr17:76399604-76399805(+)$1	201	6	9	9.0000
uuu	chr19:36729137-36729338(+)$1	201	5	8	9.0000
UUU	chr9:131582822-131583023(+)$1	201	36	39	9.0000
UUU	chr6:56328438-56328639(-)$1	201	31	34	9.0000
uuu	chr1:92853922-92854123(+)$1	201	103	106	9.0000
UUU	chr3:32769102-32769303(+)$1	201	44	47	9.0000
UUU	chr16:66855329-66855530(-)$1	201	6	9	9.0000
UUU	chr21:34707778-34707979(+)$1	201	13	16	9.0000
UUU	chr6:52935813-52936014(+)$1	201	3	6	9.0000
UUU	chr3:136192307-136192508(-)$1	201	9	12	9.0000
UUU	chr15:52970217-52970418(-)$1	201	37	40	9.0000
UUU	chr17:2570238-2570439(+)$1	201	1	4	9.0000
UUU	chr19:48608551-48608752(-)$1	201	4	7	9.0000
UUU	chr6:56371220-56371421(-)$1	201	14	17	9.0000
UUU	chr17:2586533-2586734(+)$1	201	2	5	9.0000
UUU	chr16:30995783-30995984(+)$1	201	116	119	9.0000
uuu	chr16:57207601-57207802(-)$1	201	1	4	9.0000
UUU	chr15:78758536-78758737(+)$1	201	7	10	9.0000
UUU	chr12:53846857-53847058(+)$1	201	14	17	9.0000
UUU	chr12:121746370-121746571(-)$1	201	15	18	9.0000
UUU	chr19:1611013-1611214(-)$1	201	12	15	9.0000
UUU	chr5:179663317-179663518(-)$1	201	46	49	9.0000
UUU	chr4:52765396-52765597(+)$1	201	15	18	9.0000
UUU	chr10:129895791-129895992(-)$1	201	55	58	9.0000
UUU	chr4:103644949-103645150(-)$1	201	0	3	9.0000
UUU	chr17:65733542-65733743(+)$1	201	62	65	9.0000
UUU	chr15:42556269-42556470(-)$1	201	23	26	9.0000
UUU	chr22:41605742-41605943(+)$1	201	11	14	9.0000
UUU	chr19:35175051-35175252(+)$1	201	11	14	9.0000
UUU	chr16:66850432-66850633(-)$1	201	31	34	9.0000
UUU	chr22:35820457-35820658(+)$1	201	46	49	9.0000
UUU	chr1:162492142-162492343(+)$1	201	28	31	9.0000
UUU	chr7:99951467-99951668(+)$1	201	53	56	9.0000
UUU	chr7:131186497-131186698(-)$1	201	14	17	9.0000
UUU	chr12:57108316-57108517(-)$1	201	7	10	9.0000
UUU	chr1:167385294-167385495(+)$1	201	14	17	9.0000
UUU	chr1:211452508-211452709(+)$1	201	54	57	9.0000
UUU	chr1:203766250-203766451(+)$1	201	4	7	9.0000
UUU	chr19:58003586-58003787(+)$1	201	65	68	9.0000
UUU	chr13:77742626-77742827(-)$1	201	2	5	9.0000
UUU	chr2:55899956-55900157(-)$1	201	92	95	9.0000
UUU	chr7:42949758-42949959(-)$1	201	115	118	9.0000
UUU	chr12:57453655-57453856(-)$1	201	6	9	9.0000
UUU	chr15:28508116-28508317(-)$1	201	133	136	9.0000
UUU	chr12:124105862-124106063(-)$1	201	5	8	9.0000
UUU	chr12:57906582-57906783(+)$1	201	4	7	9.0000
UUU	chr3:124946235-124946436(-)$1	201	27	30	9.0000
UUU	chr9:115927949-115928150(-)$1	201	9	12	9.0000
UUU	chr5:134193533-134193734(+)$1	201	0	3	9.0000
UUU	chr1:116915989-116916190(+)$1	201	87	90	9.0000
uuu	chr16:70284157-70284358(-)$1	201	76	79	9.0000
UUU	chr1:1296914-1297115(+)$1	201	167	170	9.0000
UUU	chr16:30709552-30709753(+)$1	201	0	3	9.0000
UUU	chr1:160249170-160249371(-)$1	201	42	45	9.0000
UUU	chr19:33620999-33621200(+)$1	201	2	5	9.0000
UUU	chr6:111695482-111695683(-)$1	201	11	14	9.0000
UUU	chr11:62407028-62407229(-)$1	201	7	10	9.0000
UUU	chr8:110566012-110566213(+)$1	201	25	28	9.0000
UUU	chr14:102550667-102550868(-)$1	201	9	12	9.0000
UUU	chr10:103916705-103916906(+)$1	201	10	13	9.0000
UUU	chr5:72207433-72207634(+)$1	201	0	3	9.0000
uuu	chr19:37672651-37672852(-)$1	201	60	63	9.0000
UUU	chr8:145171499-145171700(+)$1	201	143	146	9.0000
UUU	chr17:7146832-7147033(-)$1	201	2	5	9.0000
UUU	chr19:47222755-47222956(-)$1	201	50	53	9.0000
uuu	chr7:89866289-89866490(+)$1	201	97	100	9.0000
UUU	chr15:91456088-91456289(+)$1	201	9	12	9.0000
UUU	chr12:69084398-69084599(+)$1	201	0	3	9.0000
UUU	chr5:112176858-112177059(+)$1	201	15	18	9.0000
UUU	chr13:40175367-40175568(-)$1	201	8	11	9.0000
UUU	chr2:27806209-27806410(+)$1	201	16	19	9.0000
UUU	chr7:150930546-150930747(+)$1	201	112	115	9.0000
UUU	chr12:110933901-110934102(-)$1	201	38	41	9.0000
UUU	chr19:44559208-44559409(+)$1	201	15	18	9.0000

#otherMatches

#Struct PSSM
e22	chr3:12882619-12882820(-)$1	201	49	52	9.0000
cc2	chr10:121356097-121356298(-)$1	201	85	88	9.0000
III	chr8:99718716-99718917(-)$1	201	4	7	9.0000
ggg	chr17:61499387-61499588(+)$1	201	16	19	9.0000
GGG	chr16:70286266-70286467(-)$1	201	4	7	9.0000
DDK	chr19:54970361-54970562(+)$1	201	3	6	9.0000
HHH	chr5:37226926-37227127(-)$1	201	8	11	9.0000
33g	chr1:26881986-26882187(+)$1	201	35	38	9.0000
""b	chr2:135703868-135704069(+)$1	201	10	13	9.0000
::g	chr2:61725759-61725960(-)$1	201	10	13	9.0000
:::	chr17:30707910-30708111(+)$1	201	99	102	9.0000
===	chr3:49155054-49155255(-)$1	201	131	134	9.0000
ff$	chr22:31363862-31364063(-)$1	201	20	23	9.0000
&&&	chr12:53565174-53565375(-)$1	201	56	59	9.0000
D::	chr20:36719992-36720193(+)$1	201	14	17	9.0000
:::	chr2:198284664-198284865(-)$1	201	17	20	9.0000
:ff	chr8:42934947-42935148(+)$1	201	48	51	9.0000
JJJ	chr1:204523977-204524178(+)$1	201	3	6	9.0000
:::	chr8:23116501-23116702(+)$1	201	7	10	9.0000
555	chr11:58386351-58386552(+)$1	201	51	54	9.0000
===	chr1:1228050-1228251(-)$1	201	19	22	9.0000
:::	chr4:4238171-4238372(-)$1	201	76	79	9.0000
ccc	chr9:97222545-97222746(+)$1	201	14	17	9.0000
!!c	chr17:34860253-34860454(-)$1	201	37	40	9.0000
sss	chr1:27734542-27734743(-)$1	201	34	37	9.0000
qqq	chr3:169700385-169700586(+)$1	201	9	12	9.0000
:::	chr17:76399604-76399805(+)$1	201	6	9	9.0000
ggg	chr19:36729137-36729338(+)$1	201	5	8	9.0000
[==	chr9:131582822-131583023(+)$1	201	36	39	9.0000
:::	chr6:56328438-56328639(-)$1	201	31	34	9.0000
ooo	chr1:92853922-92854123(+)$1	201	103	106	9.0000
hhh	chr3:32769102-32769303(+)$1	201	44	47	9.0000
mmm	chr16:66855329-66855530(-)$1	201	6	9	9.0000
c''	chr21:34707778-34707979(+)$1	201	13	16	9.0000
:DD	chr6:52935813-52936014(+)$1	201	3	6	9.0000
BKK	chr3:136192307-136192508(-)$1	201	9	12	9.0000
EEE	chr15:52970217-52970418(-)$1	201	37	40	9.0000
:::	chr17:2570238-2570439(+)$1	201	1	4	9.0000
JJJ	chr19:48608551-48608752(-)$1	201	4	7	9.0000
ttt	chr6:56371220-56371421(-)$1	201	14	17	9.0000
iii	chr17:2586533-2586734(+)$1	201	2	5	9.0000
ee5	chr16:30995783-30995984(+)$1	201	116	119	9.0000
GGG	chr16:57207601-57207802(-)$1	201	1	4	9.0000
III	chr15:78758536-78758737(+)$1	201	7	10	9.0000
c""	chr12:53846857-53847058(+)$1	201	14	17	9.0000
ggg	chr12:121746370-121746571(-)$1	201	15	18	9.0000
:::	chr19:1611013-1611214(-)$1	201	12	15	9.0000
obb	chr5:179663317-179663518(-)$1	201	46	49	9.0000
nnb	chr4:52765396-52765597(+)$1	201	15	18	9.0000
eeD	chr10:129895791-129895992(-)$1	201	55	58	9.0000
:::	chr4:103644949-103645150(-)$1	201	0	3	9.0000
cc#	chr17:65733542-65733743(+)$1	201	62	65	9.0000
HHH	chr15:42556269-42556470(-)$1	201	23	26	9.0000
eee	chr22:41605742-41605943(+)$1	201	11	14	9.0000
JJJ	chr19:35175051-35175252(+)$1	201	11	14	9.0000
fff	chr16:66850432-66850633(-)$1	201	31	34	9.0000
eee	chr22:35820457-35820658(+)$1	201	46	49	9.0000
ooo	chr1:162492142-162492343(+)$1	201	28	31	9.0000
:::	chr7:99951467-99951668(+)$1	201	53	56	9.0000
GGG	chr7:131186497-131186698(-)$1	201	14	17	9.0000
qqq	chr12:57108316-57108517(-)$1	201	7	10	9.0000
mff	chr1:167385294-167385495(+)$1	201	14	17	9.0000
ddd	chr1:211452508-211452709(+)$1	201	54	57	9.0000
:II	chr1:203766250-203766451(+)$1	201	4	7	9.0000
eee	chr19:58003586-58003787(+)$1	201	65	68	9.0000
b!!	chr13:77742626-77742827(-)$1	201	2	5	9.0000
CCC	chr2:55899956-55900157(-)$1	201	92	95	9.0000
hhh	chr7:42949758-42949959(-)$1	201	115	118	9.0000
f!!	chr12:57453655-57453856(-)$1	201	6	9	9.0000
ngg	chr15:28508116-28508317(-)$1	201	133	136	9.0000
:::	chr12:124105862-124106063(-)$1	201	5	8	9.0000
fff	chr12:57906582-57906783(+)$1	201	4	7	9.0000
"""	chr3:124946235-124946436(-)$1	201	27	30	9.0000
ggg	chr9:115927949-115928150(-)$1	201	9	12	9.0000
:::	chr5:134193533-134193734(+)$1	201	0	3	9.0000
444	chr1:116915989-116916190(+)$1	201	87	90	9.0000
rrr	chr16:70284157-70284358(-)$1	201	76	79	9.0000
fff	chr1:1296914-1297115(+)$1	201	167	170	9.0000
:::	chr16:30709552-30709753(+)$1	201	0	3	9.0000
e::	chr1:160249170-160249371(-)$1	201	42	45	9.0000
:::	chr19:33620999-33621200(+)$1	201	2	5	9.0000
::e	chr6:111695482-111695683(-)$1	201	11	14	9.0000
JJJ	chr11:62407028-62407229(-)$1	201	7	10	9.0000
CKK	chr8:110566012-110566213(+)$1	201	25	28	9.0000
SSS	chr14:102550667-102550868(-)$1	201	9	12	9.0000
:::	chr10:103916705-103916906(+)$1	201	10	13	9.0000
:::	chr5:72207433-72207634(+)$1	201	0	3	9.0000
"""	chr19:37672651-37672852(-)$1	201	60	63	9.0000
HHH	chr8:145171499-145171700(+)$1	201	143	146	9.0000
:::	chr17:7146832-7147033(-)$1	201	2	5	9.0000
:::	chr19:47222755-47222956(-)$1	201	50	53	9.0000
%%%	chr7:89866289-89866490(+)$1	201	97	100	9.0000
FFF	chr15:91456088-91456289(+)$1	201	9	12	9.0000
:::	chr12:69084398-69084599(+)$1	201	0	3	9.0000
===	chr5:112176858-112177059(+)$1	201	15	18	9.0000
:::	chr13:40175367-40175568(-)$1	201	8	11	9.0000
NNN	chr2:27806209-27806410(+)$1	201	16	19	9.0000
:::	chr7:150930546-150930747(+)$1	201	112	115	9.0000
ooo	chr12:110933901-110934102(-)$1	201	38	41	9.0000
DD{	chr19:44559208-44559409(+)$1	201	15	18	9.0000

#DB
)..	chr3:12882619-12882820(-)$1	1	49	52	9.0000
)).	chr10:121356097-121356298(-)$1	1	85	88	9.0000
(((	chr8:99718716-99718917(-)$1	1	4	7	9.0000
(((	chr17:61499387-61499588(+)$1	1	16	19	9.0000
(((	chr16:70286266-70286467(-)$1	1	4	7	9.0000
((.	chr19:54970361-54970562(+)$1	1	3	6	9.0000
(((	chr5:37226926-37227127(-)$1	1	8	11	9.0000
..)	chr1:26881986-26882187(+)$1	1	35	38	9.0000
..(	chr2:135703868-135704069(+)$1	1	10	13	9.0000
..(	chr2:61725759-61725960(-)$1	1	10	13	9.0000
...	chr17:30707910-30708111(+)$1	1	99	102	9.0000
)))	chr3:49155054-49155255(-)$1	1	131	134	9.0000
((.	chr22:31363862-31364063(-)$1	1	20	23	9.0000
...	chr12:53565174-53565375(-)$1	1	56	59	9.0000
(..	chr20:36719992-36720193(+)$1	1	14	17	9.0000
...	chr2:198284664-198284865(-)$1	1	17	20	9.0000
.((	chr8:42934947-42935148(+)$1	1	48	51	9.0000
(((	chr1:204523977-204524178(+)$1	1	3	6	9.0000
...	chr8:23116501-23116702(+)$1	1	7	10	9.0000
...	chr11:58386351-58386552(+)$1	1	51	54	9.0000
(((	chr1:1228050-1228251(-)$1	1	19	22	9.0000
...	chr4:4238171-4238372(-)$1	1	76	79	9.0000
)))	chr9:97222545-97222746(+)$1	1	14	17	9.0000
..(	chr17:34860253-34860454(-)$1	1	37	40	9.0000
...	chr1:27734542-27734743(-)$1	1	34	37	9.0000
...	chr3:169700385-169700586(+)$1	1	9	12	9.0000
...	chr17:76399604-76399805(+)$1	1	6	9	9.0000
(((	chr19:36729137-36729338(+)$1	1	5	8	9.0000
.((	chr9:131582822-131583023(+)$1	1	36	39	9.0000
...	chr6:56328438-56328639(-)$1	1	31	34	9.0000
...	chr1:92853922-92854123(+)$1	1	103	106	9.0000
(((	chr3:32769102-32769303(+)$1	1	44	47	9.0000
...	chr16:66855329-66855530(-)$1	1	6	9	9.0000
(..	chr21:34707778-34707979(+)$1	1	13	16	9.0000
.((	chr6:52935813-52936014(+)$1	1	3	6	9.0000
(..	chr3:136192307-136192508(-)$1	1	9	12	9.0000
(((	chr15:52970217-52970418(-)$1	1	37	40	9.0000
...	chr17:2570238-2570439(+)$1	1	1	4	9.0000
(((	chr19:48608551-48608752(-)$1	1	4	7	9.0000
...	chr6:56371220-56371421(-)$1	1	14	17	9.0000
(((	chr17:2586533-2586734(+)$1	1	2	5	9.0000
)).	chr16:30995783-30995984(+)$1	1	116	119	9.0000
(((	chr16:57207601-57207802(-)$1	1	1	4	9.0000
(((	chr15:78758536-78758737(+)$1	1	7	10	9.0000
(..	chr12:53846857-53847058(+)$1	1	14	17	9.0000
(((	chr12:121746370-121746571(-)$1	1	15	18	9.0000
...	chr19:1611013-1611214(-)$1	1	12	15	9.0000
.))	chr5:179663317-179663518(-)$1	1	46	49	9.0000
..)	chr4:52765396-52765597(+)$1	1	15	18	9.0000
))(	chr10:129895791-129895992(-)$1	1	55	58	9.0000
...	chr4:103644949-103645150(-)$1	1	0	3	9.0000
((.	chr17:65733542-65733743(+)$1	1	62	65	9.0000
(((	chr15:42556269-42556470(-)$1	1	23	26	9.0000
(((	chr22:41605742-41605943(+)$1	1	11	14	9.0000
(((	chr19:35175051-35175252(+)$1	1	11	14	9.0000
)))	chr16:66850432-66850633(-)$1	1	31	34	9.0000
)))	chr22:35820457-35820658(+)$1	1	46	49	9.0000
...	chr1:162492142-162492343(+)$1	1	28	31	9.0000
...	chr7:99951467-99951668(+)$1	1	53	56	9.0000
(((	chr7:131186497-131186698(-)$1	1	14	17	9.0000
...	chr12:57108316-57108517(-)$1	1	7	10	9.0000
.))	chr1:167385294-167385495(+)$1	1	14	17	9.0000
)))	chr1:211452508-211452709(+)$1	1	54	57	9.0000
.((	chr1:203766250-203766451(+)$1	1	4	7	9.0000
(((	chr19:58003586-58003787(+)$1	1	65	68	9.0000
(..	chr13:77742626-77742827(-)$1	1	2	5	9.0000
(((	chr2:55899956-55900157(-)$1	1	92	95	9.0000
(((	chr7:42949758-42949959(-)$1	1	115	118	9.0000
(..	chr12:57453655-57453856(-)$1	1	6	9	9.0000
.))	chr15:28508116-28508317(-)$1	1	133	136	9.0000
...	chr12:124105862-124106063(-)$1	1	5	8	9.0000
(((	chr12:57906582-57906783(+)$1	1	4	7	9.0000
...	chr3:124946235-124946436(-)$1	1	27	30	9.0000
(((	chr9:115927949-115928150(-)$1	1	9	12	9.0000
...	chr5:134193533-134193734(+)$1	1	0	3	9.0000
...	chr1:116915989-116916190(+)$1	1	87	90	9.0000
...	chr16:70284157-70284358(-)$1	1	76	79	9.0000
)))	chr1:1296914-1297115(+)$1	1	167	170	9.0000
...	chr16:30709552-30709753(+)$1	1	0	3	9.0000
)..	chr1:160249170-160249371(-)$1	1	42	45	9.0000
...	chr19:33620999-33621200(+)$1	1	2	5	9.0000
..(	chr6:111695482-111695683(-)$1	1	11	14	9.0000
(((	chr11:62407028-62407229(-)$1	1	7	10	9.0000
(..	chr8:110566012-110566213(+)$1	1	25	28	9.0000
...	chr14:102550667-102550868(-)$1	1	9	12	9.0000
...	chr10:103916705-103916906(+)$1	1	10	13	9.0000
...	chr5:72207433-72207634(+)$1	1	0	3	9.0000
...	chr19:37672651-37672852(-)$1	1	60	63	9.0000
)))	chr8:145171499-145171700(+)$1	1	143	146	9.0000
...	chr17:7146832-7147033(-)$1	1	2	5	9.0000
...	chr19:47222755-47222956(-)$1	1	50	53	9.0000
...	chr7:89866289-89866490(+)$1	1	97	100	9.0000
(((	chr15:91456088-91456289(+)$1	1	9	12	9.0000
...	chr12:69084398-69084599(+)$1	1	0	3	9.0000
(((	chr5:112176858-112177059(+)$1	1	15	18	9.0000
...	chr13:40175367-40175568(-)$1	1	8	11	9.0000
...	chr2:27806209-27806410(+)$1	1	16	19	9.0000
...	chr7:150930546-150930747(+)$1	1	112	115	9.0000
...	chr12:110933901-110934102(-)$1	1	38	41	9.0000
((.	chr19:44559208-44559409(+)$1	1	15	18	9.0000

#PSSM
U : 0.91	u : 0.09	
U : 0.91	u : 0.09	
U : 0.91	u : 0.09	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m2_run2.nuc.txt

#NT
UUUACUUUU	chr15:77241424-77241677(+)$1	253	192	201	13.5454
UUUUUUUUU	chr3:156260209-156260503(-)$1	294	67	76	16.9090
UUUUGUUUU	chr7:90492428-90492647(+)$1	219	48	57	17.0909
GUUUAUUUU	chr4:144391828-144392049(+)$1	221	145	154	17.2727
UUAUAUUUU	chr14:95552952-95553207(-)$1	255	13	22	16.9090
uuuuguuuu	chr3:196075612-196075863(-)$1	251	27	36	17.0909
AUUUAUUUU	chr6:11582790-11583027(+)$1	237	157	166	16.7272
GAUUAUUUU	chr5:126888082-126888296(+)$1	214	94	103	13.3636
UAAUAUUUU	chr7:22982290-22982529(-)$1	239	215	224	13.0000
UUUUCUUUU	chr8:26269585-26269803(+)$1	218	25	34	17.0909
UUUUAUUUU	chr18:66342597-66342820(-)$1	223	159	168	20.4545
UUUCAUUUG	chr16:23477136-23477357(-)$1	221	10	19	13.1818
UUUUACUUU	chr1:31425023-31425251(-)$1	228	23	32	16.5454
UUUUAGUUU	chr12:107367384-107367609(+)$1	225	75	84	16.3636
UUUCAUGUU	chr8:57872805-57873017(-)$1	212	169	178	12.9090
UUUUGCUUU	chr14:52196408-52196621(+)$1	213	184	193	13.1818
CUUUACUUU	chr17:41844339-41844604(-)$1	265	119	128	12.8181
UGUUAUUUU	chr3:107526683-107526921(+)$1	238	197	206	16.1818
UUUUGUUUU	chr6:99724354-99724573(-)$1	219	178	187	17.0909
UUUCAGUUU	chr21:30717685-30717896(+)$1	211	15	24	13.5454
uuuuauuuu	chr1:32636819-32637042(+)$1	223	7	16	20.4545
UUUUAuuuu	chr16:22330141-22330359(+)$1	218	138	147	20.4545
UUUUAUUUU	chr15:44816622-44816856(+)$1	234	101	110	20.4545
UUAGAUUUU	chr10:96361504-96361733(+)$1	229	66	75	13.7272
GUUUCUUUU	chr12:123779823-123780038(-)$1	215	50	59	13.9090
GUAUAUUUU	chr11:13750436-13750662(+)$1	226	16	25	13.7272
UUACAUUUU	chr10:89727542-89727792(+)$1	250	27	36	14.0909
AUUUACUUU	chr9:114982829-114983050(-)$1	221	16	25	12.8181
UUUCAUUUU	chr18:72997363-72997585(+)$1	222	20	29	17.6363
GUUUAUUUU	chr3:10321227-10321449(+)$1	222	134	143	17.2727
UUUUGUUUU	chr8:53536079-53536331(-)$1	252	195	204	17.0909
UUUUUUUUU	chrX:133905688-133905906(-)$1	218	139	148	16.9090
UUAUAUUUU	chr1:24799157-24799378(+)$1	221	200	209	16.9090
UUUUAUUUA	chr5:157186886-157187112(+)$1	226	159	168	15.9090
UAUGAUUUU	chrX:119391783-119392008(+)$1	225	130	139	13.3636
GUUUAUUCU	chr15:23005495-23005720(-)$1	225	183	192	12.5454
UUUUAUUUU	chr12:64842473-64842699(+)$1	226	30	39	20.4545
guuuauugu	chr4:156266998-156267224(-)$1	226	176	185	12.5454
UCUUAUUUU	chrX:48435753-48435988(+)$1	235	181	190	16.1818
UUUGAUUUU	chr1:35885621-35885847(+)$1	226	189	198	17.2727
UUAUAUUUU	chr20:4681983-4682196(+)$1	213	146	155	16.9090
UUUUAUAUU	chr9:72327911-72328144(-)$1	233	205	214	15.7272
UUUGAUUUU	chr1:243665924-243666155(-)$1	231	157	166	17.2727
UUUUAAUUU	chr20:43128177-43128393(-)$1	216	32	41	16.3636
GUUCAUUUU	chr4:140311487-140311713(+)$1	226	12	21	14.4545
UUUCCUUUU	chr17:2226945-2227196(-)$1	251	13	22	14.2727
UUUGAUUUC	chr2:148691658-148691890(-)$1	232	37	46	12.7272
UAUUAUUUU	chr2:210885627-210885856(+)$1	229	135	144	16.5454
UUUCAUUUG	chr4:103716091-103716320(-)$1	229	14	23	13.1818
UUCUAAUUU	chr4:88091246-88091464(-)$1	218	0	9	12.2727
UUUUUUUUU	chr11:32998332-32998607(+)$1	275	39	48	16.9090
UUUUCUUUU	chr2:170917769-170917997(+)$1	228	39	48	17.0909
CUUCAUUUU	chr15:83698850-83699071(-)$1	221	41	50	13.9090
uuuuauuuu	chr6:75964510-75964727(-)$1	217	103	112	20.4545

#otherMatches

#Struct PSSM
=========	chr21:34930870-34931089(+)$1	219	44	53	12.4545
HHHHHH:::	chr15:77241424-77241677(+)$1	253	192	201	13.5454
=========	chr3:156260209-156260503(-)$1	294	67	76	16.9090
:::::::::	chr7:90492428-90492647(+)$1	219	48	57	17.0909
gggggg+++	chr4:144391828-144392049(+)$1	221	145	154	17.2727
:::::::::	chr14:95552952-95553207(-)$1	255	13	22	16.9090
333eeeee]	chr3:196075612-196075863(-)$1	251	27	36	17.0909
JJJJJJJJJ	chr6:11582790-11583027(+)$1	237	157	166	16.7272
rrrrrrrdd	chr5:126888082-126888296(+)$1	214	94	103	13.3636
dddnnnnnd	chr7:22982290-22982529(-)$1	239	215	224	13.0000
+++++++++	chr8:26269585-26269803(+)$1	218	25	34	17.0909
ttttttttt	chr18:66342597-66342820(-)$1	223	159	168	20.4545
ooooooeee	chr16:23477136-23477357(-)$1	221	10	19	13.1818
NNNCCC:::	chr1:31425023-31425251(-)$1	228	23	32	16.5454
iii[bbmmm	chr12:107367384-107367609(+)$1	225	75	84	16.3636
[ddddllld	chr8:57872805-57873017(-)$1	212	169	178	12.9090
dddd]ffff	chr14:52196408-52196621(+)$1	213	184	193	13.1818
ffff]bb::	chr17:41844339-41844604(-)$1	265	119	128	12.8181
=======mm	chr3:107526683-107526921(+)$1	238	197	206	16.1818
eeeeBBYYH	chr6:99724354-99724573(-)$1	219	178	187	17.0909
FFFFFFDDD	chr21:30717685-30717896(+)$1	211	15	24	13.5454
^^^^^^^^^	chr1:32636819-32637042(+)$1	223	7	16	20.4545
q========	chr16:22330141-22330359(+)$1	218	138	147	20.4545
mmhhhhhhh	chr15:44816622-44816856(+)$1	234	101	110	20.4545
!bb####gg	chr10:96361504-96361733(+)$1	229	66	75	13.7272
drrrrrrrr	chr12:123779823-123780038(-)$1	215	50	59	13.9090
bb]hhhhhh	chr11:13750436-13750662(+)$1	226	16	25	13.7272
ccc[iiiii	chr10:89727542-89727792(+)$1	250	27	36	14.0909
ffff::::b	chr9:114982829-114983050(-)$1	221	16	25	12.8181
eeeeeffff	chr18:72997363-72997585(+)$1	222	20	29	17.6363
cqqqqqqqq	chr3:10321227-10321449(+)$1	222	134	143	17.2727
GGGGG:::h	chr8:53536079-53536331(-)$1	252	195	204	17.0909
]eeeee::c	chrX:133905688-133905906(-)$1	218	139	148	16.9090
GGGG@@@@@	chr1:24799157-24799378(+)$1	221	200	209	16.9090
dgggggggn	chr5:157186886-157187112(+)$1	226	159	168	15.9090
eeee::::g	chrX:119391783-119392008(+)$1	225	130	139	13.3636
FFFF}CCCF	chr15:23005495-23005720(-)$1	225	183	192	12.5454
FFFFFKKDD	chr12:64842473-64842699(+)$1	226	30	39	20.4545
c!!dddd""	chr4:156266998-156267224(-)$1	226	176	185	12.5454
ccc22hhhh	chrX:48435753-48435988(+)$1	235	181	190	16.1818
dddd22fff	chr1:35885621-35885847(+)$1	226	189	198	17.2727
JJJJJ::::	chr20:4681983-4682196(+)$1	213	146	155	16.9090
GG}EEEEE}	chr9:72327911-72328144(-)$1	233	205	214	15.7272
[eeeee!!g	chr1:243665924-243666155(-)$1	231	157	166	17.2727
fffff[ddd	chr20:43128177-43128393(-)$1	216	32	41	16.3636
eee::::::	chr4:140311487-140311713(+)$1	226	12	21	14.4545
::::::ggg	chr17:2226945-2227196(-)$1	251	13	22	14.2727
odddd::::	chr2:148691658-148691890(-)$1	232	37	46	12.7272
qqqqqqqqe	chr2:210885627-210885856(+)$1	229	135	144	16.5454
DDNNNNNDD	chr4:103716091-103716320(-)$1	229	14	23	13.1818
:::::::::	chr4:88091246-88091464(-)$1	218	0	9	12.2727
eeee66666	chr11:32998332-32998607(+)$1	275	39	48	16.9090
ffffff'''	chr2:170917769-170917997(+)$1	228	39	48	17.0909
JJJJJJJJJ	chr15:83698850-83699071(-)$1	221	41	50	13.9090
JJJJ:::::	chr6:75964510-75964727(-)$1	217	103	112	20.4545

#DB
)))))))))	chr21:34930870-34931089(+)$1	1	44	53	12.4545
))))))...	chr15:77241424-77241677(+)$1	1	192	201	13.5454
)))))))))	chr3:156260209-156260503(-)$1	1	67	76	16.9090
.........	chr7:90492428-90492647(+)$1	1	48	57	17.0909
((((((...	chr4:144391828-144392049(+)$1	1	145	154	17.2727
.........	chr14:95552952-95553207(-)$1	1	13	22	16.9090
...))))).	chr3:196075612-196075863(-)$1	1	27	36	17.0909
(((((((((	chr6:11582790-11583027(+)$1	1	157	166	16.7272
.......))	chr5:126888082-126888296(+)$1	1	94	103	13.3636
(((.....)	chr7:22982290-22982529(-)$1	1	215	224	13.0000
.........	chr8:26269585-26269803(+)$1	1	25	34	17.0909
.........	chr18:66342597-66342820(-)$1	1	159	168	20.4545
......)))	chr16:23477136-23477357(-)$1	1	10	19	13.1818
...(((...	chr1:31425023-31425251(-)$1	1	23	32	16.5454
(((.((...	chr12:107367384-107367609(+)$1	1	75	84	16.3636
.((((...)	chr8:57872805-57873017(-)$1	1	169	178	12.9090
)))).))))	chr14:52196408-52196621(+)$1	1	184	193	13.1818
)))).))..	chr17:41844339-41844604(-)$1	1	119	128	12.8181
(((((((..	chr3:107526683-107526921(+)$1	1	197	206	16.1818
))))))..)	chr6:99724354-99724573(-)$1	1	178	187	17.0909
(((((((((	chr21:30717685-30717896(+)$1	1	15	24	13.5454
.........	chr1:32636819-32637042(+)$1	1	7	16	20.4545
.))))))))	chr16:22330141-22330359(+)$1	1	138	147	20.4545
..)))))))	chr15:44816622-44816856(+)$1	1	101	110	20.4545
.((....((	chr10:96361504-96361733(+)$1	1	66	75	13.7272
(........	chr12:123779823-123780038(-)$1	1	50	59	13.9090
)).))))))	chr11:13750436-13750662(+)$1	1	16	25	13.7272
(((.(((((	chr10:89727542-89727792(+)$1	1	27	36	14.0909
))))....(	chr9:114982829-114983050(-)$1	1	16	25	12.8181
(((((((((	chr18:72997363-72997585(+)$1	1	20	29	17.6363
(........	chr3:10321227-10321449(+)$1	1	134	143	17.2727
)))))...(	chr8:53536079-53536331(-)$1	1	195	204	17.0909
.)))))..(	chrX:133905688-133905906(-)$1	1	139	148	16.9090
)))).....	chr1:24799157-24799378(+)$1	1	200	209	16.9090
)(((((((.	chr5:157186886-157187112(+)$1	1	159	168	15.9090
))))....(	chrX:119391783-119392008(+)$1	1	130	139	13.3636
)))).))))	chr15:23005495-23005720(-)$1	1	183	192	12.5454
(((((..((	chr12:64842473-64842699(+)$1	1	30	39	20.4545
(..((((..	chr4:156266998-156267224(-)$1	1	176	185	12.5454
)))..))))	chrX:48435753-48435988(+)$1	1	181	190	16.1818
))))..)))	chr1:35885621-35885847(+)$1	1	189	198	17.2727
)))))....	chr20:4681983-4682196(+)$1	1	146	155	16.9090
)).))))).	chr9:72327911-72328144(-)$1	1	205	214	15.7272
.(((((..(	chr1:243665924-243666155(-)$1	1	157	166	17.2727
(((((.(((	chr20:43128177-43128393(-)$1	1	32	41	16.3636
)))......	chr4:140311487-140311713(+)$1	1	12	21	14.4545
......(((	chr17:2226945-2227196(-)$1	1	13	22	14.2727
.))))....	chr2:148691658-148691890(-)$1	1	37	46	12.7272
........)	chr2:210885627-210885856(+)$1	1	135	144	16.5454
((.....((	chr4:103716091-103716320(-)$1	1	14	23	13.1818
.........	chr4:88091246-88091464(-)$1	1	0	9	12.2727
)))).....	chr11:32998332-32998607(+)$1	1	39	48	16.9090
((((((...	chr2:170917769-170917997(+)$1	1	39	48	17.0909
(((((((((	chr15:83698850-83699071(-)$1	1	41	50	13.9090
((((.....	chr6:75964510-75964727(-)$1	1	103	112	20.4545

#PSSM
U : 0.72	G : 0.12	u : 0.05	A : 0.03	C : 0.03	g : 0.01	
U : 0.80	A : 0.09	u : 0.07	G : 0.01	C : 0.01	
U : 0.76	A : 0.12	u : 0.07	G : 0.01	C : 0.01	
U : 0.65	C : 0.16	G : 0.09	u : 0.07	A : 0.01	
A : 0.70	C : 0.09	G : 0.07	U : 0.05	a : 0.05	g : 0.01	
U : 0.76	u : 0.09	C : 0.07	G : 0.03	A : 0.03	
U : 0.87	u : 0.09	G : 0.01	A : 0.01	
U : 0.89	u : 0.07	C : 0.01	g : 0.01	
U : 0.83	u : 0.09	G : 0.03	A : 0.01	C : 0.01	

#score	865.5454545454546
#seq	55
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m3_run2.nuc.txt

#NT
UCCUGC	chr6:26158286-26158529(+)$1	243	134	140	11.2031
cccugc	chr3:129034508-129034848(-)$1	340	15	21	14.5625
CCCUGC	chr17:40997326-40997616(+)$1	290	63	69	14.5625
CCCUAC	chr5:150076000-150076311(-)$1	311	134	140	11.0468
UCCUGC	chr6:112408357-112408597(-)$1	240	41	47	11.2031
UCCUGC	chr6:150048035-150048277(-)$1	242	31	37	11.2031
CCCUGC	chrX:54569596-54569851(+)$1	255	35	41	14.5625
CCCUGC	chr1:39903359-39903639(+)$1	280	163	169	14.5625
CACUGC	chr2:97017541-97017781(+)$1	240	102	108	10.8906
cacugc	chr15:83499607-83499847(+)$1	240	11	17	10.8906
CACUGC	chrX:154754122-154754362(-)$1	240	122	128	10.8906
CCCUGC	chr5:162905604-162905849(+)$1	245	132	138	14.5625
CCCUAC	chr7:72861495-72861735(-)$1	240	0	6	11.0468
CCCUGC	chr17:18137063-18137303(+)$1	240	20	26	14.5625
cccucc	chr5:74046355-74046595(-)$1	240	16	22	11.0468
ACCUGC	chr1:43308293-43308533(+)$1	240	150	156	10.8125
CCCUAC	chr17:35583161-35583401(-)$1	240	48	54	11.0468
CCCUCC	chrX:40513600-40513848(-)$1	248	66	72	11.0468
GCCUGC	chr19:1407569-1407875(+)$1	306	251	257	11.0468
CCCUCC	chr19:39322027-39322471(-)$1	444	3	9	11.0468
CCCUGC	chr17:1582010-1582250(-)$1	240	216	222	14.5625
CCAUGC	chr5:162943522-162943805(+)$1	283	245	251	10.0312
CCCUGC	chr17:40996929-40997209(+)$1	280	189	195	14.5625
CCCUGC	chr19:6213051-6213457(-)$1	406	241	247	14.5625
gccugc	chr1:39466546-39466795(+)$1	249	15	21	11.0468
CCUUGC	chr15:86125150-86125439(+)$1	289	111	117	10.2656
CCCUGC	chr1:232574869-232575156(-)$1	287	82	88	14.5625
GCCUGC	chr12:56114986-56115226(+)$1	240	49	55	11.0468
CCCUCC	chr1:212161155-212161395(-)$1	240	66	72	11.0468
CCCUGC	chr12:10862573-10862814(-)$1	241	154	160	14.5625
CCUUGC	chr15:89169529-89169861(+)$1	332	44	50	10.2656
CCCUGC	chr20:32264811-32265051(-)$1	240	209	215	14.5625
CGCUGC	chr19:19603088-19603332(+)$1	244	175	181	10.5781
UCCUGC	chrX:137785100-137785340(-)$1	240	18	24	11.2031
CCCUGC	chr5:174953536-174953856(+)$1	320	33	39	14.5625
GCCUGC	chr19:40698419-40698659(+)$1	240	5	11	11.0468
CCCUGC	chr5:137680471-137680711(+)$1	240	232	238	14.5625
CGCUGC	chr3:8590318-8590558(+)$1	240	55	61	10.5781
CCCUAC	chr1:156106021-156106261(+)$1	240	1	7	11.0468
UCCUGC	chr17:61735120-61735360(+)$1	240	40	46	11.2031
CUCUGC	chr21:48069418-48069658(+)$1	240	54	60	10.6562
UCCUGC	chr3:127325507-127325747(+)$1	240	4	10	11.2031
CACUGC	chr1:36823772-36824012(-)$1	240	114	120	10.8906
CUCUGC	chr13:99992598-99992844(+)$1	246	23	29	10.6562
CUCUGC	chr2:74595067-74595310(-)$1	243	11	17	10.6562
CCCUAC	chr1:27219792-27220032(-)$1	240	85	91	11.0468
CCCUGC	chr17:76410966-76411208(+)$1	242	119	125	14.5625
CACUGC	chr12:124106236-124106476(-)$1	240	80	86	10.8906
CCCUGC	chr9:22006046-22006289(-)$1	243	114	120	14.5625
CCCUCC	chr19:5653291-5653531(+)$1	240	144	150	11.0468
UCCUGC	chr1:94360121-94360361(-)$1	240	110	116	11.2031
CCCUUC	chr17:38552552-38552792(-)$1	240	64	70	10.9687
ACCUGC	chr19:5705800-5706040(-)$1	240	71	77	10.8125
CACUGC	chr19:57839958-57840198(+)$1	240	171	177	10.8906
CCUUGC	chr19:44423655-44423935(-)$1	280	146	152	10.2656
CCCUGC	chr8:28209035-28209275(-)$1	240	190	196	14.5625
GCCUGC	chr6:31607938-31608178(-)$1	240	184	190	11.0468
CCCUGC	chr5:159840408-159840690(-)$1	282	240	246	14.5625
CCCUUC	chr5:112178596-112178836(+)$1	240	154	160	10.9687
CCCUGC	chr19:40316534-40316785(-)$1	251	124	130	14.5625
CCUUGC	chr7:6509160-6509400(-)$1	240	23	29	10.2656
CCCUUC	chr19:15366221-15366461(-)$1	240	48	54	10.9687
CCCUUC	chr3:101481266-101481506(+)$1	240	23	29	10.9687

#otherMatches

#Struct PSSM
hhhhcc	chr6:41903693-41903933(-)$1	240	22	28	14.5625
iiiiii	chr6:26158286-26158529(+)$1	243	134	140	11.2031
MMMCCC	chr3:129034508-129034848(-)$1	340	15	21	14.5625
eeeee:	chr17:40997326-40997616(+)$1	290	63	69	14.5625
CCC{CC	chr5:150076000-150076311(-)$1	311	134	140	11.0468
JJJJJJ	chr6:112408357-112408597(-)$1	240	41	47	11.2031
LLLBBF	chr6:150048035-150048277(-)$1	242	31	37	11.2031
dllldd	chrX:54569596-54569851(+)$1	255	35	41	14.5625
B:dddd	chr1:39903359-39903639(+)$1	280	163	169	14.5625
CCC{CC	chr2:97017541-97017781(+)$1	240	102	108	10.8906
ssssss	chr15:83499607-83499847(+)$1	240	11	17	10.8906
NNNNND	chrX:154754122-154754362(-)$1	240	122	128	10.8906
]ccc]e	chr5:162905604-162905849(+)$1	245	132	138	14.5625
::bb[=	chr7:72861495-72861735(-)$1	240	0	6	11.0468
::ccc[	chr17:18137063-18137303(+)$1	240	20	26	14.5625
[cccmm	chr5:74046355-74046595(-)$1	240	16	22	11.0468
2ccc]b	chr1:43308293-43308533(+)$1	240	150	156	10.8125
E::::c	chr17:35583161-35583401(-)$1	240	48	54	11.0468
D:::::	chrX:40513600-40513848(-)$1	248	66	72	11.0468
FFFF}A	chr19:1407569-1407875(+)$1	306	251	257	11.0468
[bb!!d	chr19:39322027-39322471(-)$1	444	3	9	11.0468
d22ggg	chr17:1582010-1582250(-)$1	240	216	222	14.5625
FFFFF:	chr5:162943522-162943805(+)$1	283	245	251	10.0312
mmeeee	chr17:40996929-40997209(+)$1	280	189	195	14.5625
DDD:::	chr19:6213051-6213457(-)$1	406	241	247	14.5625
CC{EEE	chr1:39466546-39466795(+)$1	249	15	21	11.0468
KDDDD{	chr15:86125150-86125439(+)$1	289	111	117	10.2656
ffdddd	chr1:232574869-232575156(-)$1	287	82	88	14.5625
CCC{FF	chr12:56114986-56115226(+)$1	240	49	55	11.0468
666666	chr1:212161155-212161395(-)$1	240	66	72	11.0468
ddeeee	chr12:10862573-10862814(-)$1	241	154	160	14.5625
c[bb[c	chr15:89169529-89169861(+)$1	332	44	50	10.2656
2ggggg	chr20:32264811-32265051(-)$1	240	209	215	14.5625
ddmmmm	chr19:19603088-19603332(+)$1	244	175	181	10.5781
eeee]a	chrX:137785100-137785340(-)$1	240	18	24	11.2031
ddd:::	chr5:174953536-174953856(+)$1	320	33	39	14.5625
mmmmee	chr19:40698419-40698659(+)$1	240	5	11	11.0468
::::::	chr5:137680471-137680711(+)$1	240	232	238	14.5625
oooooo	chr3:8590318-8590558(+)$1	240	55	61	10.5781
:IIIII	chr1:156106021-156106261(+)$1	240	1	7	11.0468
ssssdd	chr17:61735120-61735360(+)$1	240	40	46	11.2031
HHHHHH	chr21:48069418-48069658(+)$1	240	54	60	10.6562
nnnncc	chr3:127325507-127325747(+)$1	240	4	10	11.2031
qqqqqq	chr1:36823772-36824012(-)$1	240	114	120	10.8906
EEEEE{	chr13:99992598-99992844(+)$1	246	23	29	10.6562
KKBB{C	chr2:74595067-74595310(-)$1	243	11	17	10.6562
mmmmee	chr1:27219792-27220032(-)$1	240	85	91	11.0468
4444dd	chr17:76410966-76411208(+)$1	242	119	125	14.5625
::::::	chr12:124106236-124106476(-)$1	240	80	86	10.8906
lldddd	chr9:22006046-22006289(-)$1	243	114	120	14.5625
ddddbb	chr19:5653291-5653531(+)$1	240	144	150	11.0468
555fff	chr1:94360121-94360361(-)$1	240	110	116	11.2031
ffGGGG	chr17:38552552-38552792(-)$1	240	64	70	10.9687
[ccc[b	chr19:5705800-5706040(-)$1	240	71	77	10.8125
ffffff	chr19:57839958-57840198(+)$1	240	171	177	10.8906
IIIIII	chr19:44423655-44423935(-)$1	280	146	152	10.2656
:::ddd	chr8:28209035-28209275(-)$1	240	190	196	14.5625
:EEEEE	chr6:31607938-31608178(-)$1	240	184	190	11.0468
EEEE}F	chr5:159840408-159840690(-)$1	282	240	246	14.5625
D?????	chr5:112178596-112178836(+)$1	240	154	160	10.9687
iiiiii	chr19:40316534-40316785(-)$1	251	124	130	14.5625
EE{FFF	chr7:6509160-6509400(-)$1	240	23	29	10.2656
[eeeee	chr19:15366221-15366461(-)$1	240	48	54	10.9687
i^^^^^	chr3:101481266-101481506(+)$1	240	23	29	10.9687

#DB
((((((	chr6:41903693-41903933(-)$1	1	22	28	14.5625
))))))	chr6:26158286-26158529(+)$1	1	134	140	11.2031
...(((	chr3:129034508-129034848(-)$1	1	15	21	14.5625
))))).	chr17:40997326-40997616(+)$1	1	63	69	14.5625
(((.((	chr5:150076000-150076311(-)$1	1	134	140	11.0468
((((((	chr6:112408357-112408597(-)$1	1	41	47	11.2031
...(((	chr6:150048035-150048277(-)$1	1	31	37	11.2031
(...))	chrX:54569596-54569851(+)$1	1	35	41	14.5625
).((((	chr1:39903359-39903639(+)$1	1	163	169	14.5625
(((.((	chr2:97017541-97017781(+)$1	1	102	108	10.8906
......	chr15:83499607-83499847(+)$1	1	11	17	10.8906
.....(	chrX:154754122-154754362(-)$1	1	122	128	10.8906
.))).)	chr5:162905604-162905849(+)$1	1	132	138	14.5625
..((.(	chr7:72861495-72861735(-)$1	1	0	6	11.0468
..(((.	chr17:18137063-18137303(+)$1	1	20	26	14.5625
.(((..	chr5:74046355-74046595(-)$1	1	16	22	11.0468
.))).)	chr1:43308293-43308533(+)$1	1	150	156	10.8125
(....(	chr17:35583161-35583401(-)$1	1	48	54	11.0468
(.....	chrX:40513600-40513848(-)$1	1	66	72	11.0468
)))).)	chr19:1407569-1407875(+)$1	1	251	257	11.0468
.((..(	chr19:39322027-39322471(-)$1	1	3	9	11.0468
)..)))	chr17:1582010-1582250(-)$1	1	216	222	14.5625
))))).	chr5:162943522-162943805(+)$1	1	245	251	10.0312
..))))	chr17:40996929-40997209(+)$1	1	189	195	14.5625
)))...	chr19:6213051-6213457(-)$1	1	241	247	14.5625
((.(((	chr1:39466546-39466795(+)$1	1	15	21	11.0468
.((((.	chr15:86125150-86125439(+)$1	1	111	117	10.2656
))((((	chr1:232574869-232575156(-)$1	1	82	88	14.5625
(((.((	chr12:56114986-56115226(+)$1	1	49	55	11.0468
......	chr1:212161155-212161395(-)$1	1	66	72	11.0468
((((((	chr12:10862573-10862814(-)$1	1	154	160	14.5625
(.((.(	chr15:89169529-89169861(+)$1	1	44	50	10.2656
.)))))	chr20:32264811-32265051(-)$1	1	209	215	14.5625
((....	chr19:19603088-19603332(+)$1	1	175	181	10.5781
)))).)	chrX:137785100-137785340(-)$1	1	18	24	11.2031
)))...	chr5:174953536-174953856(+)$1	1	33	39	14.5625
....))	chr19:40698419-40698659(+)$1	1	5	11	11.0468
......	chr5:137680471-137680711(+)$1	1	232	238	14.5625
......	chr3:8590318-8590558(+)$1	1	55	61	10.5781
.(((((	chr1:156106021-156106261(+)$1	1	1	7	11.0468
....))	chr17:61735120-61735360(+)$1	1	40	46	11.2031
((((((	chr21:48069418-48069658(+)$1	1	54	60	10.6562
....))	chr3:127325507-127325747(+)$1	1	4	10	11.2031
......	chr1:36823772-36824012(-)$1	1	114	120	10.8906
(((((.	chr13:99992598-99992844(+)$1	1	23	29	10.6562
..((.(	chr2:74595067-74595310(-)$1	1	11	17	10.6562
....))	chr1:27219792-27220032(-)$1	1	85	91	11.0468
....))	chr17:76410966-76411208(+)$1	1	119	125	14.5625
......	chr12:124106236-124106476(-)$1	1	80	86	10.8906
..))))	chr9:22006046-22006289(-)$1	1	114	120	14.5625
((((((	chr19:5653291-5653531(+)$1	1	144	150	11.0468
...)))	chr1:94360121-94360361(-)$1	1	110	116	11.2031
))((((	chr17:38552552-38552792(-)$1	1	64	70	10.9687
.(((.(	chr19:5705800-5706040(-)$1	1	71	77	10.8125
))))))	chr19:57839958-57840198(+)$1	1	171	177	10.8906
((((((	chr19:44423655-44423935(-)$1	1	146	152	10.2656
...(((	chr8:28209035-28209275(-)$1	1	190	196	14.5625
.)))))	chr6:31607938-31608178(-)$1	1	184	190	11.0468
)))).)	chr5:159840408-159840690(-)$1	1	240	246	14.5625
).....	chr5:112178596-112178836(+)$1	1	154	160	10.9687
))))))	chr19:40316534-40316785(-)$1	1	124	130	14.5625
((.(((	chr7:6509160-6509400(-)$1	1	23	29	10.2656
.(((((	chr19:15366221-15366461(-)$1	1	48	54	10.9687
(.....	chr3:101481266-101481506(+)$1	1	23	29	10.9687

#PSSM
C : 0.73	U : 0.10	G : 0.06	c : 0.04	A : 0.03	g : 0.01	
C : 0.78	A : 0.07	c : 0.04	U : 0.04	G : 0.03	a : 0.01	
C : 0.85	c : 0.06	U : 0.06	A : 0.01	
U : 0.93	u : 0.06	
G : 0.73	A : 0.07	C : 0.06	U : 0.06	g : 0.04	c : 0.01	
C : 0.93	c : 0.06	

#score	770.4375
#seq	64
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_CDS_m2_run2.nuc.txt

#NT
CAA	chr17:34934348-34934578(+)$1	230	11	14	8.9999
CAA	chr7:135263445-135263666(+)$1	221	64	67	8.9999
CAA	chr7:881504-881724(+)$1	220	13	16	8.9999
CAA	chr1:229738271-229738501(-)$1	230	17	20	8.9999
CAA	chr2:38812782-38813012(-)$1	230	52	55	8.9999
CAA	chr8:48697671-48697899(-)$1	228	95	98	8.9999
CAA	chr17:27614347-27614567(-)$1	220	8	11	8.9999
caa	chr2:135696500-135696730(+)$1	230	44	47	8.9999
CAA	chr13:31729651-31729878(-)$1	227	70	73	8.9999
CAA	chr16:24581120-24581350(+)$1	230	14	17	8.9999
CAA	chr1:24134679-24134901(-)$1	222	9	12	8.9999
CAA	chr7:38247181-38247414(+)$1	233	7	10	8.9999
CAA	chr19:53383906-53384133(-)$1	227	11	14	8.9999
CAA	chr13:25016650-25016875(-)$1	225	61	64	8.9999
CAA	chr11:14535265-14535488(-)$1	223	33	36	8.9999
CAA	chr7:116869852-116870063(+)$1	211	114	117	8.9999
CAA	chr8:101541708-101541927(-)$1	219	94	97	8.9999
CAA	chr3:100091424-100091645(-)$1	221	102	105	8.9999
CAA	chr19:10334674-10334895(-)$1	221	9	12	8.9999
CAA	chr22:40662827-40663060(+)$1	233	0	3	8.9999
CAA	chr1:41457352-41457569(+)$1	217	100	103	8.9999
CAA	chr9:74489602-74489826(-)$1	224	57	60	8.9999
CAA	chr1:19410921-19411129(-)$1	208	6	9	8.9999
CAA	chr15:23811985-23812204(+)$1	219	17	20	8.9999
CAA	chr9:19049757-19049982(+)$1	225	136	139	8.9999
CAA	chr19:47503644-47503861(+)$1	217	68	71	8.9999
CAA	chr5:140744696-140744918(+)$1	222	46	49	8.9999
CAA	chr1:156912438-156912663(-)$1	225	122	125	8.9999
CAA	chr19:38897514-38897731(+)$1	217	38	41	8.9999
CAA	chr1:100546019-100546242(+)$1	223	24	27	8.9999
CAA	chr17:56083077-56083299(-)$1	222	203	206	8.9999
CAA	chr22:19036034-19036255(-)$1	221	80	83	8.9999
CAA	chr12:123466470-123466691(+)$1	221	82	85	8.9999
CAA	chr14:92554992-92555215(-)$1	223	40	43	8.9999
CAA	chrX:129349121-129349347(-)$1	226	58	61	8.9999
CAA	chrX:16876747-16876977(-)$1	230	57	60	8.9999
CAA	chr7:64168199-64168427(+)$1	228	1	4	8.9999
CAA	chr22:38692992-38693222(-)$1	230	30	33	8.9999
CAA	chr14:93760914-93761140(-)$1	226	23	26	8.9999
CAA	chr9:33911863-33912088(+)$1	225	137	140	8.9999
CAA	chr1:161721615-161721834(+)$1	219	62	65	8.9999
CAA	chr8:6302557-6302789(+)$1	232	43	46	8.9999
CAA	chr17:45748035-45748261(+)$1	226	203	206	8.9999
CAA	chr10:75010618-75010839(-)$1	221	129	132	8.9999
CAA	chr3:107938171-107938394(-)$1	223	78	81	8.9999
CAA	chr16:70304025-70304249(-)$1	224	36	39	8.9999
CAA	chr21:34922399-34922615(+)$1	216	27	30	8.9999
CAA	chr19:40542162-40542387(-)$1	225	24	27	8.9999
CAA	chr17:27957744-27957974(-)$1	230	29	32	8.9999
CAA	chr7:1197213-1197438(-)$1	225	84	87	8.9999
CAA	chr10:38344060-38344282(+)$1	222	63	66	8.9999
CAA	chr5:133535988-133536211(-)$1	223	28	31	8.9999
CAA	chr6:31506442-31506667(-)$1	225	85	88	8.9999
CAA	chr19:1037534-1037771(+)$1	237	133	136	8.9999
CAA	chr17:37564186-37564405(-)$1	219	14	17	8.9999
CAA	chr5:125960199-125960419(+)$1	220	88	91	8.9999
CAA	chr11:72420891-72421117(-)$1	226	38	41	8.9999
CAA	chr11:31653805-31654025(+)$1	220	47	50	8.9999
CAA	chr10:17756581-17756808(+)$1	227	46	49	8.9999
CAA	chr15:73566160-73566385(+)$1	225	83	86	8.9999
caa	chr3:40574350-40574567(+)$1	217	147	150	8.9999
CAA	chr15:40300247-40300478(+)$1	231	10	13	8.9999
CAA	chr9:94800492-94800719(-)$1	227	25	28	8.9999
CAA	chr2:170806341-170806562(+)$1	221	46	49	8.9999
CAA	chr6:157256553-157256783(+)$1	230	79	82	8.9999
CAA	chr3:101298552-101298771(+)$1	219	28	31	8.9999
CAA	chr10:14939070-14939287(+)$1	217	17	20	8.9999
CAA	chr12:51088968-51089192(+)$1	224	5	8	8.9999
CAA	chr4:57883675-57883895(+)$1	220	109	112	8.9999
CAA	chr12:56740274-56740500(-)$1	226	40	43	8.9999
CAA	chr22:42273879-42274100(+)$1	221	23	26	8.9999
CAA	chr12:50570862-50571092(-)$1	230	47	50	8.9999
CAA	chr15:75140917-75141137(-)$1	220	30	33	8.9999
CAA	chr7:91948689-91948915(+)$1	226	29	32	8.9999
CAA	chr20:5098105-5098322(-)$1	217	112	115	8.9999
CAA	chr10:115609398-115609618(-)$1	220	28	31	8.9999
CAA	chr1:19481312-19481537(-)$1	225	49	52	8.9999
CAA	chr20:34220691-34220915(-)$1	224	126	129	8.9999
CAA	chr16:4910606-4910832(+)$1	226	70	73	8.9999
CAA	chr6:150004653-150004877(-)$1	224	15	18	8.9999
CAA	chr4:103723618-103723889(-)$1	271	28	31	8.9999
CAA	chr3:12610340-12610570(+)$1	230	92	95	8.9999
CAA	chr9:14658656-14658886(-)$1	230	7	10	8.9999
CAA	chr16:50783804-50784026(+)$1	222	33	36	8.9999
CAA	chr11:107965114-107965341(+)$1	227	32	35	8.9999
CAA	chr7:86824247-86824469(+)$1	222	110	113	8.9999
CAA	chr15:95019855-95020078(+)$1	223	115	118	8.9999
CAA	chrX:39931672-39931890(-)$1	218	43	46	8.9999
CAA	chr12:69968142-69968380(+)$1	238	73	76	8.9999
CAA	chr1:97243327-97243541(+)$1	214	107	110	8.9999
CAA	chr4:125593436-125593656(-)$1	220	13	16	8.9999
caa	chr17:57721598-57721816(+)$1	218	55	58	8.9999
CAA	chr1:226566769-226566993(-)$1	224	103	106	8.9999
CAA	chr11:14535117-14535337(-)$1	220	47	50	8.9999
CAA	chr17:2202683-2202909(-)$1	226	20	23	8.9999
CAA	chr9:131029385-131029609(-)$1	224	17	20	8.9999
CAA	chr14:35871639-35871869(-)$1	230	45	48	8.9999
CAA	chr3:139067041-139067265(+)$1	224	30	33	8.9999

#otherMatches

#Struct PSSM
:::	chr10:27059109-27059333(-)$1	224	17	20	8.9999
CCC	chr17:34934348-34934578(+)$1	230	11	14	8.9999
b]e	chr7:135263445-135263666(+)$1	221	64	67	8.9999
iii	chr7:881504-881724(+)$1	220	13	16	8.9999
:::	chr1:229738271-229738501(-)$1	230	17	20	8.9999
"dd	chr2:38812782-38813012(-)$1	230	52	55	8.9999
f00	chr8:48697671-48697899(-)$1	228	95	98	8.9999
DD:	chr17:27614347-27614567(-)$1	220	8	11	8.9999
zzz	chr2:135696500-135696730(+)$1	230	44	47	8.9999
^^^	chr13:31729651-31729878(-)$1	227	70	73	8.9999
:::	chr16:24581120-24581350(+)$1	230	14	17	8.9999
BB{	chr1:24134679-24134901(-)$1	222	9	12	8.9999
HHH	chr7:38247181-38247414(+)$1	233	7	10	8.9999
ooo	chr19:53383906-53384133(-)$1	227	11	14	8.9999
::H	chr13:25016650-25016875(-)$1	225	61	64	8.9999
eee	chr11:14535265-14535488(-)$1	223	33	36	8.9999
###	chr7:116869852-116870063(+)$1	211	114	117	8.9999
%%d	chr8:101541708-101541927(-)$1	219	94	97	8.9999
"""	chr3:100091424-100091645(-)$1	221	102	105	8.9999
""g	chr19:10334674-10334895(-)$1	221	9	12	8.9999
:::	chr22:40662827-40663060(+)$1	233	0	3	8.9999
qqq	chr1:41457352-41457569(+)$1	217	100	103	8.9999
ddd	chr9:74489602-74489826(-)$1	224	57	60	8.9999
:::	chr1:19410921-19411129(-)$1	208	6	9	8.9999
ooo	chr15:23811985-23812204(+)$1	219	17	20	8.9999
ccc	chr9:19049757-19049982(+)$1	225	136	139	8.9999
###	chr19:47503644-47503861(+)$1	217	68	71	8.9999
ppp	chr5:140744696-140744918(+)$1	222	46	49	8.9999
!!b	chr1:156912438-156912663(-)$1	225	122	125	8.9999
qqq	chr19:38897514-38897731(+)$1	217	38	41	8.9999
MMM	chr1:100546019-100546242(+)$1	223	24	27	8.9999
EYY	chr17:56083077-56083299(-)$1	222	203	206	8.9999
ggg	chr22:19036034-19036255(-)$1	221	80	83	8.9999
bnn	chr12:123466470-123466691(+)$1	221	82	85	8.9999
:::	chr14:92554992-92555215(-)$1	223	40	43	8.9999
:ee	chrX:129349121-129349347(-)$1	226	58	61	8.9999
uuu	chrX:16876747-16876977(-)$1	230	57	60	8.9999
:::	chr7:64168199-64168427(+)$1	228	1	4	8.9999
c::	chr22:38692992-38693222(-)$1	230	30	33	8.9999
DD:	chr14:93760914-93761140(-)$1	226	23	26	8.9999
:::	chr9:33911863-33912088(+)$1	225	137	140	8.9999
bb:	chr1:161721615-161721834(+)$1	219	62	65	8.9999
bb[	chr8:6302557-6302789(+)$1	232	43	46	8.9999
~~~	chr17:45748035-45748261(+)$1	226	203	206	8.9999
333	chr10:75010618-75010839(-)$1	221	129	132	8.9999
fff	chr3:107938171-107938394(-)$1	223	78	81	8.9999
f::	chr16:70304025-70304249(-)$1	224	36	39	8.9999
eem	chr21:34922399-34922615(+)$1	216	27	30	8.9999
:::	chr19:40542162-40542387(-)$1	225	24	27	8.9999
b22	chr17:27957744-27957974(-)$1	230	29	32	8.9999
ee:	chr7:1197213-1197438(-)$1	225	84	87	8.9999
22d	chr10:38344060-38344282(+)$1	222	63	66	8.9999
BB:	chr5:133535988-133536211(-)$1	223	28	31	8.9999
e::	chr6:31506442-31506667(-)$1	225	85	88	8.9999
555	chr19:1037534-1037771(+)$1	237	133	136	8.9999
qqq	chr17:37564186-37564405(-)$1	219	14	17	8.9999
ccc	chr5:125960199-125960419(+)$1	220	88	91	8.9999
+++	chr11:72420891-72421117(-)$1	226	38	41	8.9999
css	chr11:31653805-31654025(+)$1	220	47	50	8.9999
ppp	chr10:17756581-17756808(+)$1	227	46	49	8.9999
fff	chr15:73566160-73566385(+)$1	225	83	86	8.9999
666	chr3:40574350-40574567(+)$1	217	147	150	8.9999
::C	chr15:40300247-40300478(+)$1	231	10	13	8.9999
dd:	chr9:94800492-94800719(-)$1	227	25	28	8.9999
sss	chr2:170806341-170806562(+)$1	221	46	49	8.9999
ggg	chr6:157256553-157256783(+)$1	230	79	82	8.9999
'''	chr3:101298552-101298771(+)$1	219	28	31	8.9999
GG:	chr10:14939070-14939287(+)$1	217	17	20	8.9999
iii	chr12:51088968-51089192(+)$1	224	5	8	8.9999
:::	chr4:57883675-57883895(+)$1	220	109	112	8.9999
##d	chr12:56740274-56740500(-)$1	226	40	43	8.9999
KKE	chr22:42273879-42274100(+)$1	221	23	26	8.9999
G::	chr12:50570862-50571092(-)$1	230	47	50	8.9999
EEE	chr15:75140917-75141137(-)$1	220	30	33	8.9999
dd4	chr7:91948689-91948915(+)$1	226	29	32	8.9999
:::	chr20:5098105-5098322(-)$1	217	112	115	8.9999
www	chr10:115609398-115609618(-)$1	220	28	31	8.9999
###	chr1:19481312-19481537(-)$1	225	49	52	8.9999
c!!	chr20:34220691-34220915(-)$1	224	126	129	8.9999
666	chr16:4910606-4910832(+)$1	226	70	73	8.9999
D:d	chr6:150004653-150004877(-)$1	224	15	18	8.9999
eee	chr4:103723618-103723889(-)$1	271	28	31	8.9999
bnn	chr3:12610340-12610570(+)$1	230	92	95	8.9999
hhh	chr9:14658656-14658886(-)$1	230	7	10	8.9999
dd[	chr16:50783804-50784026(+)$1	222	33	36	8.9999
:gg	chr11:107965114-107965341(+)$1	227	32	35	8.9999
:::	chr7:86824247-86824469(+)$1	222	110	113	8.9999
:::	chr15:95019855-95020078(+)$1	223	115	118	8.9999
ggg	chrX:39931672-39931890(-)$1	218	43	46	8.9999
d::	chr12:69968142-69968380(+)$1	238	73	76	8.9999
f''	chr1:97243327-97243541(+)$1	214	107	110	8.9999
::c	chr4:125593436-125593656(-)$1	220	13	16	8.9999
mmf	chr17:57721598-57721816(+)$1	218	55	58	8.9999
ooo	chr1:226566769-226566993(-)$1	224	103	106	8.9999
::d	chr11:14535117-14535337(-)$1	220	47	50	8.9999
%%%	chr17:2202683-2202909(-)$1	226	20	23	8.9999
:::	chr9:131029385-131029609(-)$1	224	17	20	8.9999
cc3	chr14:35871639-35871869(-)$1	230	45	48	8.9999
bb:	chr3:139067041-139067265(+)$1	224	30	33	8.9999

#DB
...	chr10:27059109-27059333(-)$1	1	17	20	8.9999
(((	chr17:34934348-34934578(+)$1	1	11	14	8.9999
).)	chr7:135263445-135263666(+)$1	1	64	67	8.9999
(((	chr7:881504-881724(+)$1	1	13	16	8.9999
...	chr1:229738271-229738501(-)$1	1	17	20	8.9999
.((	chr2:38812782-38813012(-)$1	1	52	55	8.9999
)..	chr8:48697671-48697899(-)$1	1	95	98	8.9999
((.	chr17:27614347-27614567(-)$1	1	8	11	8.9999
...	chr2:135696500-135696730(+)$1	1	44	47	8.9999
...	chr13:31729651-31729878(-)$1	1	70	73	8.9999
...	chr16:24581120-24581350(+)$1	1	14	17	8.9999
((.	chr1:24134679-24134901(-)$1	1	9	12	8.9999
(((	chr7:38247181-38247414(+)$1	1	7	10	8.9999
...	chr19:53383906-53384133(-)$1	1	11	14	8.9999
..(	chr13:25016650-25016875(-)$1	1	61	64	8.9999
)))	chr11:14535265-14535488(-)$1	1	33	36	8.9999
...	chr7:116869852-116870063(+)$1	1	114	117	8.9999
..(	chr8:101541708-101541927(-)$1	1	94	97	8.9999
...	chr3:100091424-100091645(-)$1	1	102	105	8.9999
..(	chr19:10334674-10334895(-)$1	1	9	12	8.9999
...	chr22:40662827-40663060(+)$1	1	0	3	8.9999
...	chr1:41457352-41457569(+)$1	1	100	103	8.9999
(((	chr9:74489602-74489826(-)$1	1	57	60	8.9999
...	chr1:19410921-19411129(-)$1	1	6	9	8.9999
...	chr15:23811985-23812204(+)$1	1	17	20	8.9999
(((	chr9:19049757-19049982(+)$1	1	136	139	8.9999
...	chr19:47503644-47503861(+)$1	1	68	71	8.9999
...	chr5:140744696-140744918(+)$1	1	46	49	8.9999
..(	chr1:156912438-156912663(-)$1	1	122	125	8.9999
...	chr19:38897514-38897731(+)$1	1	38	41	8.9999
...	chr1:100546019-100546242(+)$1	1	24	27	8.9999
)..	chr17:56083077-56083299(-)$1	1	203	206	8.9999
)))	chr22:19036034-19036255(-)$1	1	80	83	8.9999
(..	chr12:123466470-123466691(+)$1	1	82	85	8.9999
...	chr14:92554992-92555215(-)$1	1	40	43	8.9999
.((	chrX:129349121-129349347(-)$1	1	58	61	8.9999
...	chrX:16876747-16876977(-)$1	1	57	60	8.9999
...	chr7:64168199-64168427(+)$1	1	1	4	8.9999
)..	chr22:38692992-38693222(-)$1	1	30	33	8.9999
((.	chr14:93760914-93761140(-)$1	1	23	26	8.9999
...	chr9:33911863-33912088(+)$1	1	137	140	8.9999
)).	chr1:161721615-161721834(+)$1	1	62	65	8.9999
((.	chr8:6302557-6302789(+)$1	1	43	46	8.9999
...	chr17:45748035-45748261(+)$1	1	203	206	8.9999
...	chr10:75010618-75010839(-)$1	1	129	132	8.9999
)))	chr3:107938171-107938394(-)$1	1	78	81	8.9999
)..	chr16:70304025-70304249(-)$1	1	36	39	8.9999
((.	chr21:34922399-34922615(+)$1	1	27	30	8.9999
...	chr19:40542162-40542387(-)$1	1	24	27	8.9999
)..	chr17:27957744-27957974(-)$1	1	29	32	8.9999
)).	chr7:1197213-1197438(-)$1	1	84	87	8.9999
..)	chr10:38344060-38344282(+)$1	1	63	66	8.9999
((.	chr5:133535988-133536211(-)$1	1	28	31	8.9999
)..	chr6:31506442-31506667(-)$1	1	85	88	8.9999
...	chr19:1037534-1037771(+)$1	1	133	136	8.9999
...	chr17:37564186-37564405(-)$1	1	14	17	8.9999
)))	chr5:125960199-125960419(+)$1	1	88	91	8.9999
...	chr11:72420891-72421117(-)$1	1	38	41	8.9999
(..	chr11:31653805-31654025(+)$1	1	47	50	8.9999
...	chr10:17756581-17756808(+)$1	1	46	49	8.9999
(((	chr15:73566160-73566385(+)$1	1	83	86	8.9999
...	chr3:40574350-40574567(+)$1	1	147	150	8.9999
..(	chr15:40300247-40300478(+)$1	1	10	13	8.9999
)).	chr9:94800492-94800719(-)$1	1	25	28	8.9999
...	chr2:170806341-170806562(+)$1	1	46	49	8.9999
)))	chr6:157256553-157256783(+)$1	1	79	82	8.9999
...	chr3:101298552-101298771(+)$1	1	28	31	8.9999
((.	chr10:14939070-14939287(+)$1	1	17	20	8.9999
(((	chr12:51088968-51089192(+)$1	1	5	8	8.9999
...	chr4:57883675-57883895(+)$1	1	109	112	8.9999
..(	chr12:56740274-56740500(-)$1	1	40	43	8.9999
..(	chr22:42273879-42274100(+)$1	1	23	26	8.9999
(..	chr12:50570862-50571092(-)$1	1	47	50	8.9999
(((	chr15:75140917-75141137(-)$1	1	30	33	8.9999
)).	chr7:91948689-91948915(+)$1	1	29	32	8.9999
...	chr20:5098105-5098322(-)$1	1	112	115	8.9999
...	chr10:115609398-115609618(-)$1	1	28	31	8.9999
...	chr1:19481312-19481537(-)$1	1	49	52	8.9999
(..	chr20:34220691-34220915(-)$1	1	126	129	8.9999
...	chr16:4910606-4910832(+)$1	1	70	73	8.9999
(.(	chr6:150004653-150004877(-)$1	1	15	18	8.9999
(((	chr4:103723618-103723889(-)$1	1	28	31	8.9999
(..	chr3:12610340-12610570(+)$1	1	92	95	8.9999
(((	chr9:14658656-14658886(-)$1	1	7	10	8.9999
((.	chr16:50783804-50784026(+)$1	1	33	36	8.9999
.((	chr11:107965114-107965341(+)$1	1	32	35	8.9999
...	chr7:86824247-86824469(+)$1	1	110	113	8.9999
...	chr15:95019855-95020078(+)$1	1	115	118	8.9999
)))	chrX:39931672-39931890(-)$1	1	43	46	8.9999
)..	chr12:69968142-69968380(+)$1	1	73	76	8.9999
(..	chr1:97243327-97243541(+)$1	1	107	110	8.9999
..(	chr4:125593436-125593656(-)$1	1	13	16	8.9999
..)	chr17:57721598-57721816(+)$1	1	55	58	8.9999
...	chr1:226566769-226566993(-)$1	1	103	106	8.9999
..(	chr11:14535117-14535337(-)$1	1	47	50	8.9999
...	chr17:2202683-2202909(-)$1	1	20	23	8.9999
...	chr9:131029385-131029609(-)$1	1	17	20	8.9999
)).	chr14:35871639-35871869(-)$1	1	45	48	8.9999
)).	chr3:139067041-139067265(+)$1	1	30	33	8.9999

#PSSM
C : 0.96	c : 0.03	
A : 0.96	a : 0.03	
A : 0.96	a : 0.03	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m3_run1.nuc.txt

#NT
GCAGUU	chr1:101455978-101456218(-)$1	240	30	36	10.2463
GCAGCU	chr10:73588694-73588934(-)$1	240	180	186	14.0144
GCAGCC	chr17:2226897-2227138(-)$1	241	119	125	10.7536
GCAGCC	chr2:174227921-174228161(+)$1	240	66	72	10.7536
GCAGCA	chr1:60338408-60338663(+)$1	255	159	165	10.8260
GCAGCC	chr2:45806962-45807202(-)$1	240	119	125	10.7536
GCAGCU	chr6:90340122-90340362(+)$1	240	64	70	14.0144
GCAGUU	chr7:36366283-36366563(-)$1	280	72	78	10.2463
GCAGUU	chr9:134369728-134369974(+)$1	246	103	109	10.2463
GGAGCU	chr6:33257545-33257785(+)$1	240	16	22	10.5362
CCAGCU	chr19:38895601-38895841(+)$1	240	124	130	10.1739
GUAGCU	chr6:41874871-41875113(-)$1	242	109	115	10.3913
GCAGGU	chr7:102716166-102716406(+)$1	240	53	59	9.9565
GCAGCA	chr2:128631514-128631759(-)$1	245	120	126	10.8260
GCAGCU	chr3:9796299-9796607(+)$1	308	200	206	14.0144
ACAGCU	chr12:122745774-122746014(-)$1	240	142	148	10.1014
GCAGCA	chr7:149171339-149171579(-)$1	240	161	167	10.8260
GCAGCU	chr5:154346177-154346433(+)$1	256	243	249	14.0144
GAAGCU	chr9:114184135-114184375(-)$1	240	82	88	10.7536
GAAGCU	chr8:103664308-103664548(-)$1	240	4	10	10.7536
GGAGCU	chr18:32826102-32826342(+)$1	240	41	47	10.5362
GCAGCU	chr5:82834686-82834926(+)$1	240	191	197	14.0144
GCAGCA	chr17:41113116-41113356(-)$1	240	134	140	10.8260
GCAGCU	chr5:914485-914725(+)$1	240	117	123	14.0144
GGAGCU	chr6:43540146-43540386(-)$1	240	128	134	10.5362
GAAGCU	chr4:54325370-54325610(+)$1	240	225	231	10.7536
GCAGCA	chr1:2340139-2340379(-)$1	240	40	46	10.8260
ACAGCU	chrX:131188675-131188918(+)$1	243	173	179	10.1014
GAAGCU	chr1:179089265-179089505(-)$1	240	5	11	10.7536
GCAGCU	chr20:58519948-58520190(+)$1	242	34	40	14.0144
GCAGUU	chr1:214792400-214792640(+)$1	240	195	201	10.2463
GUAGCU	chr3:9880684-9880927(-)$1	243	32	38	10.3913
UCAGCU	chr11:82868442-82868682(+)$1	240	2	8	10.2463
GGAGCU	chr5:137895526-137895806(-)$1	280	101	107	10.5362
GCAGCC	chr8:59492170-59492410(+)$1	240	111	117	10.7536
GCAGCG	chr20:34797579-34797819(+)$1	240	50	56	10.3913
UCAGCU	chr19:58698246-58698494(+)$1	248	71	77	10.2463
GCAGCU	chr6:47220904-47221145(-)$1	241	25	31	14.0144
GUAGCU	chr8:77763194-77763434(+)$1	240	167	173	10.3913
GCAGCU	chr12:57167655-57167895(+)$1	240	181	187	14.0144
GGAGCU	chr12:133697883-133698123(-)$1	240	173	179	10.5362
ucAGCU	chr5:159832000-159832240(-)$1	240	58	64	10.2463
GAAGCU	chr6:79911892-79912172(-)$1	280	123	129	10.7536
GCAGCC	chr12:122618383-122618623(+)$1	240	74	80	10.7536
UCAGCU	chr1:43824925-43825165(+)$1	240	2	8	10.2463
GCAGCC	chr12:133360752-133360993(-)$1	241	5	11	10.7536
CCAGCU	chr3:170945861-170946101(-)$1	240	111	117	10.1739
GCAGCA	chr6:13620421-13620661(+)$1	240	82	88	10.8260
UCAGCU	chr4:139966093-139966333(+)$1	240	130	136	10.2463
GCAGCA	chr17:56435694-56435936(-)$1	242	2	8	10.8260
GCAGCU	chr2:182786841-182787086(+)$1	245	160	166	14.0144
GAAGCU	chr1:6697193-6697435(-)$1	242	150	156	10.7536
GCAGCC	chr13:23929054-23929294(-)$1	240	8	14	10.7536
GCAGCU	chr1:151378505-151378790(-)$1	285	192	198	14.0144
GCAGCU	chr19:56600035-56600275(-)$1	240	204	210	14.0144
GCAGCA	chr20:31021373-31021613(+)$1	240	41	47	10.8260
GCAGUU	chr3:141164161-141164401(+)$1	240	119	125	10.2463
GCAGGU	chr12:56607691-56607931(-)$1	240	206	212	9.9565
GCAGCU	chr3:196118604-196118844(-)$1	240	147	153	14.0144
ACAGCU	chr9:99521930-99522170(-)$1	240	124	130	10.1014
GCAGCU	chr6:43029125-43029365(+)$1	240	154	160	14.0144
GAAGCU	chr16:89348192-89348450(-)$1	258	210	216	10.7536
CCAGCU	chr3:44700421-44700661(+)$1	240	78	84	10.1739
GCAGUU	chr3:37368132-37368372(+)$1	240	203	209	10.2463
CCAGCU	chr12:51458292-51458532(-)$1	240	6	12	10.1739
GCAGUU	chr10:51581182-51581422(+)$1	240	92	98	10.2463
GAAGCU	chr3:9934560-9934800(+)$1	240	62	68	10.7536
GCAGGU	chr6:136597471-136597711(-)$1	240	61	67	9.9565

#otherMatches

#Struct PSSM
GGGGG:	chr2:71220743-71220983(-)$1	240	74	80	10.3913
mmmddd	chr1:101455978-101456218(-)$1	240	30	36	10.2463
cc!!dd	chr10:73588694-73588934(-)$1	240	180	186	14.0144
ffff%%	chr17:2226897-2227138(-)$1	241	119	125	10.7536
ffffff	chr2:174227921-174228161(+)$1	240	66	72	10.7536
ffff55	chr1:60338408-60338663(+)$1	255	159	165	10.8260
eeee[a	chr2:45806962-45807202(-)$1	240	119	125	10.7536
dccc##	chr6:90340122-90340362(+)$1	240	64	70	14.0144
cccccc	chr7:36366283-36366563(-)$1	280	72	78	10.2463
eeee66	chr9:134369728-134369974(+)$1	246	103	109	10.2463
CC::cc	chr6:33257545-33257785(+)$1	240	16	22	10.5362
cccccc	chr19:38895601-38895841(+)$1	240	124	130	10.1739
gg[bbc	chr6:41874871-41875113(-)$1	242	109	115	10.3913
[ddddl	chr7:102716166-102716406(+)$1	240	53	59	9.9565
HHHHH:	chr2:128631514-128631759(-)$1	245	120	126	10.8260
lfffff	chr3:9796299-9796607(+)$1	308	200	206	14.0144
[bb[bb	chr12:122745774-122746014(-)$1	240	142	148	10.1014
eeee22	chr7:149171339-149171579(-)$1	240	161	167	10.8260
CCCEEE	chr5:154346177-154346433(+)$1	256	243	249	14.0144
f!!fff	chr9:114184135-114184375(-)$1	240	82	88	10.7536
::CCCB	chr8:103664308-103664548(-)$1	240	4	10	10.7536
:FFFFF	chr18:32826102-32826342(+)$1	240	41	47	10.5362
cnnnnn	chr5:82834686-82834926(+)$1	240	191	197	14.0144
d22bbb	chr17:41113116-41113356(-)$1	240	134	140	10.8260
nnnbb:	chr5:914485-914725(+)$1	240	117	123	14.0144
$$$ccc	chr6:43540146-43540386(-)$1	240	128	134	10.5362
oooccc	chr4:54325370-54325610(+)$1	240	225	231	10.7536
EE{EEE	chr1:2340139-2340379(-)$1	240	40	46	10.8260
dd:ggg	chrX:131188675-131188918(+)$1	243	173	179	10.1014
D{FFFF	chr1:179089265-179089505(-)$1	240	5	11	10.7536
b]cccd	chr20:58519948-58520190(+)$1	242	34	40	14.0144
tttttt	chr1:214792400-214792640(+)$1	240	195	201	10.2463
bb]hhh	chr3:9880684-9880927(-)$1	243	32	38	10.3913
:::bbm	chr11:82868442-82868682(+)$1	240	2	8	10.2463
b[a[bb	chr5:137895526-137895806(-)$1	280	101	107	10.5362
GGGGG{	chr8:59492170-59492410(+)$1	240	111	117	10.7536
eeee[b	chr20:34797579-34797819(+)$1	240	50	56	10.3913
eewwww	chr19:58698246-58698494(+)$1	248	71	77	10.2463
cc::JJ	chr6:47220904-47221145(-)$1	241	25	31	14.0144
ffffa]	chr8:77763194-77763434(+)$1	240	167	173	10.3913
ddd]bb	chr12:57167655-57167895(+)$1	240	181	187	14.0144
ddddbb	chr12:133697883-133698123(-)$1	240	173	179	10.5362
ff:::=	chr5:159832000-159832240(-)$1	240	58	64	10.2463
mmmmcc	chr6:79911892-79912172(-)$1	280	123	129	10.7536
eeee""	chr12:122618383-122618623(+)$1	240	74	80	10.7536
:::DDD	chr1:43824925-43825165(+)$1	240	2	8	10.2463
fmmmmf	chr12:133360752-133360993(-)$1	241	5	11	10.7536
crrrrr	chr3:170945861-170946101(-)$1	240	111	117	10.1739
dddd++	chr6:13620421-13620661(+)$1	240	82	88	10.8260
GYYA}C	chr4:139966093-139966333(+)$1	240	130	136	10.2463
CKKBBB	chr17:56435694-56435936(-)$1	242	2	8	10.8260
ffffff	chr2:182786841-182787086(+)$1	245	160	166	14.0144
tttttt	chr1:6697193-6697435(-)$1	242	150	156	10.7536
GGGGGM	chr13:23929054-23929294(-)$1	240	8	14	10.7536
DJJJJJ	chr1:151378505-151378790(-)$1	285	192	198	14.0144
dddd::	chr19:56600035-56600275(-)$1	240	204	210	14.0144
dddd[b	chr20:31021373-31021613(+)$1	240	41	47	10.8260
b]eeee	chr3:141164161-141164401(+)$1	240	119	125	10.2463
IIIII_	chr12:56607691-56607931(-)$1	240	206	212	9.9565
rrrbb]	chr3:196118604-196118844(-)$1	240	147	153	14.0144
DDDDgg	chr9:99521930-99522170(-)$1	240	124	130	10.1014
{A{CCC	chr6:43029125-43029365(+)$1	240	154	160	14.0144
ooooog	chr16:89348192-89348450(-)$1	258	210	216	10.7536
DDDddd	chr3:44700421-44700661(+)$1	240	78	84	10.1739
gggggg	chr3:37368132-37368372(+)$1	240	203	209	10.2463
D::DDD	chr12:51458292-51458532(-)$1	240	6	12	10.1739
hhhhhh	chr10:51581182-51581422(+)$1	240	92	98	10.2463
oooood	chr3:9934560-9934800(+)$1	240	62	68	10.7536
"""eee	chr6:136597471-136597711(-)$1	240	61	67	9.9565

#DB
))))).	chr2:71220743-71220983(-)$1	1	74	80	10.3913
...)))	chr1:101455978-101456218(-)$1	1	30	36	10.2463
((..((	chr10:73588694-73588934(-)$1	1	180	186	14.0144
((((..	chr17:2226897-2227138(-)$1	1	119	125	10.7536
))))))	chr2:174227921-174228161(+)$1	1	66	72	10.7536
))))..	chr1:60338408-60338663(+)$1	1	159	165	10.8260
((((.(	chr2:45806962-45807202(-)$1	1	119	125	10.7536
((((..	chr6:90340122-90340362(+)$1	1	64	70	14.0144
)))(((	chr7:36366283-36366563(-)$1	1	72	78	10.2463
))))..	chr9:134369728-134369974(+)$1	1	103	109	10.2463
((..((	chr6:33257545-33257785(+)$1	1	16	22	10.5362
((((((	chr19:38895601-38895841(+)$1	1	124	130	10.1739
((.(((	chr6:41874871-41875113(-)$1	1	109	115	10.3913
.((((.	chr7:102716166-102716406(+)$1	1	53	59	9.9565
))))).	chr2:128631514-128631759(-)$1	1	120	126	10.8260
.)))))	chr3:9796299-9796607(+)$1	1	200	206	14.0144
.((.((	chr12:122745774-122746014(-)$1	1	142	148	10.1014
))))..	chr7:149171339-149171579(-)$1	1	161	167	10.8260
))))))	chr5:154346177-154346433(+)$1	1	243	249	14.0144
(..(((	chr9:114184135-114184375(-)$1	1	82	88	10.7536
..((((	chr8:103664308-103664548(-)$1	1	4	10	10.7536
.(((((	chr18:32826102-32826342(+)$1	1	41	47	10.5362
(.....	chr5:82834686-82834926(+)$1	1	191	197	14.0144
)..)))	chr17:41113116-41113356(-)$1	1	134	140	10.8260
...)).	chr5:914485-914725(+)$1	1	117	123	14.0144
...(((	chr6:43540146-43540386(-)$1	1	128	134	10.5362
...)))	chr4:54325370-54325610(+)$1	1	225	231	10.7536
((.(((	chr1:2340139-2340379(-)$1	1	40	46	10.8260
)).(((	chrX:131188675-131188918(+)$1	1	173	179	10.1014
(.((((	chr1:179089265-179089505(-)$1	1	5	11	10.7536
).)))(	chr20:58519948-58520190(+)$1	1	34	40	14.0144
......	chr1:214792400-214792640(+)$1	1	195	201	10.2463
)).)))	chr3:9880684-9880927(-)$1	1	32	38	10.3913
...((.	chr11:82868442-82868682(+)$1	1	2	8	10.2463
(.(.((	chr5:137895526-137895806(-)$1	1	101	107	10.5362
(((((.	chr8:59492170-59492410(+)$1	1	111	117	10.7536
((((.(	chr20:34797579-34797819(+)$1	1	50	56	10.3913
((....	chr19:58698246-58698494(+)$1	1	71	77	10.2463
))..((	chr6:47220904-47221145(-)$1	1	25	31	14.0144
))))).	chr8:77763194-77763434(+)$1	1	167	173	10.3913
))).))	chr12:57167655-57167895(+)$1	1	181	187	14.0144
))))))	chr12:133697883-133698123(-)$1	1	173	179	10.5362
))...(	chr5:159832000-159832240(-)$1	1	58	64	10.2463
....))	chr6:79911892-79912172(-)$1	1	123	129	10.7536
((((..	chr12:122618383-122618623(+)$1	1	74	80	10.7536
...(((	chr1:43824925-43825165(+)$1	1	2	8	10.2463
(....)	chr12:133360752-133360993(-)$1	1	5	11	10.7536
(.....	chr3:170945861-170946101(-)$1	1	111	117	10.1739
((((..	chr6:13620421-13620661(+)$1	1	82	88	10.8260
)..).)	chr4:139966093-139966333(+)$1	1	130	136	10.2463
(..(((	chr17:56435694-56435936(-)$1	1	2	8	10.8260
((((((	chr2:182786841-182787086(+)$1	1	160	166	14.0144
......	chr1:6697193-6697435(-)$1	1	150	156	10.7536
(((((.	chr13:23929054-23929294(-)$1	1	8	14	10.7536
)(((((	chr1:151378505-151378790(-)$1	1	192	198	14.0144
))))..	chr19:56600035-56600275(-)$1	1	204	210	14.0144
((((.(	chr20:31021373-31021613(+)$1	1	41	47	10.8260
).))))	chr3:141164161-141164401(+)$1	1	119	125	10.2463
))))).	chr12:56607691-56607931(-)$1	1	206	212	9.9565
...)).	chr3:196118604-196118844(-)$1	1	147	153	14.0144
))))((	chr9:99521930-99522170(-)$1	1	124	130	10.1014
.(.(((	chr6:43029125-43029365(+)$1	1	154	160	14.0144
.....)	chr16:89348192-89348450(-)$1	1	210	216	10.7536
((((((	chr3:44700421-44700661(+)$1	1	78	84	10.1739
))))))	chr3:37368132-37368372(+)$1	1	203	209	10.2463
(..(((	chr12:51458292-51458532(-)$1	1	6	12	10.1739
((((((	chr10:51581182-51581422(+)$1	1	92	98	10.2463
.....)	chr3:9934560-9934800(+)$1	1	62	68	10.7536
...(((	chr6:136597471-136597711(-)$1	1	61	67	9.9565

#PSSM
G : 0.82	C : 0.05	U : 0.05	A : 0.04	u : 0.01	
C : 0.75	A : 0.11	G : 0.07	U : 0.04	c : 0.01	
A : 0.99	
G : 0.99	
C : 0.85	U : 0.10	G : 0.04	
U : 0.75	A : 0.11	C : 0.10	G : 0.02	

#score	772.5797101449266
#seq	69
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m1_run1.nuc.txt

#NT
AUAUUUUUUG	chr20:36146251-36146481(-)$1	230	68	78	19.2857
GUAAUUUUUU	chr12:99007114-99007366(-)$1	252	30	40	17.6190
UUAUUUUUGU	chr2:174771777-174772008(-)$1	231	18	28	18.0952
AUAUAUUUUU	chr7:151832088-151832343(-)$1	255	84	94	19.7619
UUAUGUUUUU	chr14:100748803-100749027(+)$1	224	38	48	18.4523
UUGUUUUUUu	chr15:64977316-64977549(+)$1	233	39	49	17.8571
GUAUUUUUUU	chr5:133726219-133726460(+)$1	241	53	63	22.1428
CUAUUUUAUU	chr1:206762192-206762424(+)$1	232	70	80	16.7857
AGAUUUUUUU	chr1:150237767-150238043(-)$1	276	98	108	19.4047
UUAUCUUUUU	chr3:183530235-183530472(+)$1	237	50	60	18.3333
uuauuauuuu	chr11:28042160-28042428(-)$1	268	22	32	17.6190
GUAUUUUUUU	chr1:45976821-45977056(-)$1	235	115	125	22.1428
GUAUGUUUUU	chr3:196079391-196079623(-)$1	232	94	104	18.3333
AUAUAUUUUU	chr8:42032676-42032929(-)$1	253	153	163	19.7619
GUAUUUUUUA	chrX:118605108-118605332(+)$1	224	108	118	17.7380
uuauuuuuuu	chr22:41575255-41575484(+)$1	229	34	44	22.2619
UUACUUUUUU	chr5:126888453-126888685(+)$1	232	102	112	17.8571
auauuuauuu	chr15:73043614-73043844(-)$1	230	65	75	18.9285
AUAUUCUUUU	chr10:94414581-94414817(+)$1	236	125	135	19.0476
guauuuuguu	chr6:43304563-43304796(-)$1	233	138	148	17.8571
AUACUUUUUU	chr15:38645329-38645567(+)$1	238	207	217	19.2857
AUAUUUUUUU	chr10:61552196-61552422(-)$1	226	111	121	23.6904
AAAUUUUUUU	chr5:157213316-157213552(-)$1	236	169	179	19.5238
GUAUCUUUUU	chr12:76739162-76739394(-)$1	232	117	127	18.2142
AUAUGUUUUU	chr10:90973250-90973496(-)$1	246	25	35	19.8809
auauuuuuuu	chr6:15520403-15520646(+)$1	243	108	118	23.6904
auauuuuguu	chr4:186284839-186285073(+)$1	234	75	85	19.4047
AUAUUUUUUU	chr18:74681748-74681977(+)$1	229	142	152	23.6904
AAAUUUUUUU	chr12:69968698-69968931(+)$1	233	142	152	19.5238
UUAUUUUUGU	chr3:98512643-98512878(+)$1	235	0	10	18.0952
ACAUUUUUUU	chr5:54720586-54720838(+)$1	252	187	197	19.5238
AUGUUUUUUU	chr19:12903767-12904004(+)$1	237	61	71	19.2857
GUAUUUUUUC	chr20:54944603-54944833(-)$1	230	116	126	17.8571
uuauuuucuu	chr3:188597028-188597251(+)$1	223	50	60	17.8571
ACAUUUUUUU	chr5:137088142-137088366(-)$1	224	69	79	19.5238
AUAUUUUUUC	chr1:91990705-91990946(+)$1	241	119	129	19.4047
GUAUUUUUUU	chr10:49643211-49643433(+)$1	222	68	78	22.1428
UUAUUUUUUU	chr1:63790385-63790616(+)$1	231	152	162	22.2619
AUAUUUUUGU	chrX:119570529-119570769(-)$1	240	103	113	19.5238
AUAUUUUUUU	chr12:110784502-110784741(+)$1	239	8	18	23.6904
AUUUUUUUUU	chr5:79276182-79276409(-)$1	227	5	15	19.1666

#otherMatches

#Struct PSSM
C~~~~DDDD}	chr1:94351044-94351276(-)$1	232	215	225	19.2857
+++++++++g	chr20:36146251-36146481(-)$1	230	68	78	19.2857
FFFFF:::::	chr12:99007114-99007366(-)$1	252	30	40	17.6190
fffff!!ccc	chr2:174771777-174772008(-)$1	231	18	28	18.0952
HHHeeeee[b	chr7:151832088-151832343(-)$1	255	84	94	19.7619
flllffffff	chr14:100748803-100749027(+)$1	224	38	48	18.4523
ddd::::::=	chr15:64977316-64977549(+)$1	233	39	49	17.8571
BB{JJJJJJJ	chr5:133726219-133726460(+)$1	241	53	63	22.1428
ff[dddd[ee	chr1:206762192-206762424(+)$1	232	70	80	16.7857
D{DDDD::::	chr1:150237767-150238043(-)$1	276	98	108	19.4047
:::ffffffl	chr3:183530235-183530472(+)$1	237	50	60	18.3333
f=========	chr11:28042160-28042428(-)$1	268	22	32	17.6190
GG::::::::	chr1:45976821-45977056(-)$1	235	115	125	22.1428
hhhhhttttt	chr3:196079391-196079623(-)$1	232	94	104	18.3333
]dddd66666	chr8:42032676-42032929(-)$1	253	153	163	19.7619
iiiiiiiicc	chrX:118605108-118605332(+)$1	224	108	118	17.7380
ggg[cccmmm	chr22:41575255-41575484(+)$1	229	34	44	22.2619
::::::::::	chr5:126888453-126888685(+)$1	232	102	112	17.8571
I:ffffffoo	chr15:73043614-73043844(-)$1	230	65	75	18.9285
ttttttttdd	chr10:94414581-94414817(+)$1	236	125	135	19.0476
eee22fffff	chr6:43304563-43304796(-)$1	233	138	148	17.8571
dnnnnndddd	chr15:38645329-38645567(+)$1	238	207	217	19.2857
cc]hhhhhhh	chr10:61552196-61552422(-)$1	226	111	121	23.6904
dd####hhhh	chr5:157213316-157213552(-)$1	236	169	179	19.5238
::::::::::	chr12:76739162-76739394(-)$1	232	117	127	18.2142
:ffffffnnn	chr10:90973250-90973496(-)$1	246	25	35	19.8809
dddooooood	chr6:15520403-15520646(+)$1	243	108	118	23.6904
#gggggggll	chr4:186284839-186285073(+)$1	234	75	85	19.4047
^^^^^^^^^^	chr18:74681748-74681977(+)$1	229	142	152	23.6904
dddd[cccmm	chr12:69968698-69968931(+)$1	233	142	152	19.5238
::::::::::	chr3:98512643-98512878(+)$1	235	0	10	18.0952
iiiiiiiinn	chr5:54720586-54720838(+)$1	252	187	197	19.5238
::dddd[eee	chr19:12903767-12904004(+)$1	237	61	71	19.2857
iiiiiiii::	chr20:54944603-54944833(-)$1	230	116	126	17.8571
::::::::GG	chr3:188597028-188597251(+)$1	223	50	60	17.8571
eeee::HHHH	chr5:137088142-137088366(-)$1	224	69	79	19.5238
dffffff666	chr1:91990705-91990946(+)$1	241	119	129	19.4047
bb333ccc]g	chr10:49643211-49643433(+)$1	222	68	78	22.1428
cc[ffffffm	chr1:63790385-63790616(+)$1	231	152	162	22.2619
2dddd333ii	chrX:119570529-119570769(-)$1	240	103	113	19.5238
foooooofff	chr12:110784502-110784741(+)$1	239	8	18	23.6904
E:::::::::	chr5:79276182-79276409(-)$1	227	5	15	19.1666

#DB
)....)))).	chr1:94351044-94351276(-)$1	1	215	225	19.2857
.........(	chr20:36146251-36146481(-)$1	1	68	78	19.2857
(((((.....	chr12:99007114-99007366(-)$1	1	30	40	17.6190
(((((..(((	chr2:174771777-174772008(-)$1	1	18	28	18.0952
((((((((.(	chr7:151832088-151832343(-)$1	1	84	94	19.7619
(...))))))	chr14:100748803-100749027(+)$1	1	38	48	18.4523
)))......(	chr15:64977316-64977549(+)$1	1	39	49	17.8571
((.(((((((	chr5:133726219-133726460(+)$1	1	53	63	22.1428
((.((((.((	chr1:206762192-206762424(+)$1	1	70	80	16.7857
(.((((....	chr1:150237767-150238043(-)$1	1	98	108	19.4047
...((((((.	chr3:183530235-183530472(+)$1	1	50	60	18.3333
((((((((((	chr11:28042160-28042428(-)$1	1	22	32	17.6190
))........	chr1:45976821-45977056(-)$1	1	115	125	22.1428
(((((.....	chr3:196079391-196079623(-)$1	1	94	104	18.3333
.)))).....	chr8:42032676-42032929(-)$1	1	153	163	19.7619
((((((((((	chrX:118605108-118605332(+)$1	1	108	118	17.7380
(((.(((...	chr22:41575255-41575484(+)$1	1	34	44	22.2619
..........	chr5:126888453-126888685(+)$1	1	102	112	17.8571
(.((((((..	chr15:73043614-73043844(-)$1	1	65	75	18.9285
........))	chr10:94414581-94414817(+)$1	1	125	135	19.0476
)))..)))))	chr6:43304563-43304796(-)$1	1	138	148	17.8571
(.....))))	chr15:38645329-38645567(+)$1	1	207	217	19.2857
)).)))))))	chr10:61552196-61552422(-)$1	1	111	121	23.6904
((....((((	chr5:157213316-157213552(-)$1	1	169	179	19.5238
..........	chr12:76739162-76739394(-)$1	1	117	127	18.2142
.((((((...	chr10:90973250-90973496(-)$1	1	25	35	19.8809
(((......)	chr6:15520403-15520646(+)$1	1	108	118	23.6904
.(((((((..	chr4:186284839-186285073(+)$1	1	75	85	19.4047
..........	chr18:74681748-74681977(+)$1	1	142	152	23.6904
((((.(((..	chr12:69968698-69968931(+)$1	1	142	152	19.5238
..........	chr3:98512643-98512878(+)$1	1	0	10	18.0952
((((((((..	chr5:54720586-54720838(+)$1	1	187	197	19.5238
..((((.(((	chr19:12903767-12904004(+)$1	1	61	71	19.2857
))))))))..	chr20:54944603-54944833(-)$1	1	116	126	17.8571
........((	chr3:188597028-188597251(+)$1	1	50	60	17.8571
))))..((((	chr5:137088142-137088366(-)$1	1	69	79	19.5238
)))))))...	chr1:91990705-91990946(+)$1	1	119	129	19.4047
))...))).)	chr10:49643211-49643433(+)$1	1	68	78	22.1428
((.((((((.	chr1:63790385-63790616(+)$1	1	152	162	22.2619
.))))...))	chrX:119570529-119570769(-)$1	1	103	113	19.5238
(......)))	chr12:110784502-110784741(+)$1	1	8	18	23.6904
(.........	chr5:79276182-79276409(-)$1	1	5	15	19.1666

#PSSM
A : 0.45	G : 0.19	U : 0.16	u : 0.07	a : 0.07	C : 0.02	g : 0.02	
U : 0.71	u : 0.16	A : 0.04	C : 0.04	G : 0.02	
A : 0.76	a : 0.16	G : 0.04	U : 0.02	
U : 0.76	u : 0.16	C : 0.04	A : 0.02	
U : 0.66	u : 0.16	G : 0.07	A : 0.04	C : 0.04	
U : 0.80	u : 0.14	a : 0.02	C : 0.02	
U : 0.83	u : 0.14	a : 0.02	
U : 0.80	u : 0.09	g : 0.04	A : 0.02	c : 0.02	
U : 0.73	u : 0.16	G : 0.07	A : 0.02	
U : 0.71	u : 0.19	C : 0.04	G : 0.02	A : 0.02	

#score	823.8095238095245
#seq	42
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m1_run1.nuc.txt

#NT
UUAUUUUA	chrX:24230248-24230475(+)$1	227	143	151	17.7804
UUUUUUUU	chr17:65720106-65720333(+)$1	227	44	52	16.4390
UUGUUUUA	chr1:245006942-245007171(-)$1	229	43	51	14.8536
UUAUUUUA	chr1:224348652-224348899(+)$1	247	51	59	17.7804
UUAUUUUC	chr14:52196774-52197001(+)$1	227	141	149	17.0487
UUAUUUUU	chr5:132215869-132216099(-)$1	230	204	212	19.7317
UUAAUUUU	chr17:30699891-30700118(+)$1	227	173	181	15.4634
UCAUUUUU	chr8:28431307-28431531(+)$1	224	9	17	15.7073
uuauuuuu	chr16:70607931-70608171(+)$1	240	147	155	19.7317
UUUUUUUU	chr12:110760726-110760954(+)$1	228	51	59	16.4390
UUAAUUUU	chr13:73283943-73284169(-)$1	226	118	126	15.4634
uuauuuuu	chr4:52887765-52887986(-)$1	221	148	156	19.7317
UUCUUUUU	chr1:29096132-29096367(+)$1	235	102	110	16.3170
UUAUUUUU	chr12:54632568-54632801(-)$1	233	142	150	19.7317
UAAUUUUU	chr5:135516267-135516489(+)$1	222	107	115	15.9512
UUAAUUUU	chr12:65090527-65090755(+)$1	228	45	53	15.4634
UUAUUUUA	chr16:69736728-69736951(+)$1	223	171	179	17.7804
UUAUUUUA	chr1:114516515-114516773(+)$1	258	123	131	17.7804
UUAUUUUU	chr5:77782107-77782333(-)$1	226	108	116	19.7317
UUAUUUUC	chr10:62553851-62554076(+)$1	225	185	193	17.0487
UAAUUUUU	chr3:169814515-169814746(-)$1	231	13	21	15.9512
UUGUUUUU	chr5:153435053-153435279(+)$1	226	41	49	16.8048
UCAUUUUU	chr7:44916633-44916878(-)$1	245	21	29	15.7073
UUGUUUUU	chr4:108835119-108835341(+)$1	222	133	141	16.8048
UUGUUUUU	chr14:93695396-93695618(+)$1	222	178	186	16.8048
uuauuuua	chr11:8020903-8021126(+)$1	223	55	63	17.7804
UUAUUUUU	chr1:15994883-15995109(+)$1	226	60	68	19.7317
UUUUUUUU	chr3:56656888-56657124(-)$1	236	70	78	16.4390
UUAUUUUU	chr8:74704821-74705046(-)$1	225	149	157	19.7317
UAAUUUUU	chr1:23633731-23633965(-)$1	234	32	40	15.9512
UUGUUUUU	chr16:81078747-81078973(+)$1	226	35	43	16.8048
UUGUUUUA	chr8:133859337-133859593(+)$1	256	68	76	14.8536
uuauuuuc	chr6:28195976-28196201(+)$1	225	103	111	17.0487
UAAUUUUU	chr3:101369178-101369411(-)$1	233	66	74	15.9512
UUAUUUUC	chrX:73806338-73806559(-)$1	221	19	27	17.0487
UUAUUUUG	chr2:152691879-152692102(-)$1	223	42	50	16.6829
UUAUUUUU	chr2:180809744-180809969(-)$1	225	164	172	19.7317
UUAUUUUA	chr6:4061340-4061567(+)$1	227	79	87	17.7804
UUAUUUUA	chr6:165744758-165744982(-)$1	224	103	111	17.7804
UUAUUUUA	chr3:37032242-37032466(-)$1	224	63	71	17.7804

#otherMatches

#Struct PSSM
^^^^^^^^	chr14:81940805-81941046(-)$1	241	48	56	16.3170
#cccnnnn	chrX:24230248-24230475(+)$1	227	143	151	17.7804
c::::::f	chr17:65720106-65720333(+)$1	227	44	52	16.4390
ppa22iii	chr1:245006942-245007171(-)$1	229	43	51	14.8536
22ffffff	chr1:224348652-224348899(+)$1	247	51	59	17.7804
f22fffff	chr14:52196774-52197001(+)$1	227	141	149	17.0487
ee55555e	chr5:132215869-132216099(-)$1	230	204	212	19.7317
qqqqqqqq	chr17:30699891-30700118(+)$1	227	173	181	15.4634
ddd"""cc	chr8:28431307-28431531(+)$1	224	9	17	15.7073
^^^^^^^^	chr16:70607931-70608171(+)$1	240	147	155	19.7317
##dddd[b	chr12:110760726-110760954(+)$1	228	51	59	16.4390
pdddd333	chr13:73283943-73284169(-)$1	226	118	126	15.4634
::::::::	chr4:52887765-52887986(-)$1	221	148	156	19.7317
iiiiii::	chr1:29096132-29096367(+)$1	235	102	110	16.3170
dd999999	chr12:54632568-54632801(-)$1	233	142	150	19.7317
ppeeeee]	chr5:135516267-135516489(+)$1	222	107	115	15.9512
KDDDD:::	chr12:65090527-65090755(+)$1	228	45	53	15.4634
ccc22hhh	chr16:69736728-69736951(+)$1	223	171	179	17.7804
eeelllee	chr1:114516515-114516773(+)$1	258	123	131	17.7804
c:::::::	chr5:77782107-77782333(-)$1	226	108	116	19.7317
}FFFFFFY	chr10:62553851-62554076(+)$1	225	185	193	17.0487
EEKKHHHH	chr3:169814515-169814746(-)$1	231	13	21	15.9512
========	chr5:153435053-153435279(+)$1	226	41	49	16.8048
FLLLEEEE	chr7:44916633-44916878(-)$1	245	21	29	15.7073
rrrrrrdd	chr4:108835119-108835341(+)$1	222	133	141	16.8048
22ccc333	chr14:93695396-93695618(+)$1	222	178	186	16.8048
))))iiii	chr11:8020903-8021126(+)$1	223	55	63	17.7804
==::::dd	chr1:15994883-15995109(+)$1	226	60	68	19.7317
hhhhh[dd	chr3:56656888-56657124(-)$1	236	70	78	16.4390
[ddddooo	chr8:74704821-74705046(-)$1	225	149	157	19.7317
::::::::	chr1:23633731-23633965(-)$1	234	32	40	15.9512
dddd"""d	chr16:81078747-81078973(+)$1	226	35	43	16.8048
cccxxxxx	chr8:133859337-133859593(+)$1	256	68	76	14.8536
nnnneeee	chr6:28195976-28196201(+)$1	225	103	111	17.0487
:GGGGGGG	chr3:101369178-101369411(-)$1	233	66	74	15.9512
ff"""ddd	chrX:73806338-73806559(-)$1	221	19	27	17.0487
ffff!!gg	chr2:152691879-152692102(-)$1	223	42	50	16.6829
========	chr2:180809744-180809969(-)$1	225	164	172	19.7317
ddssssss	chr6:4061340-4061567(+)$1	227	79	87	17.7804
:ccc"""f	chr6:165744758-165744982(-)$1	224	103	111	17.7804
::::eeee	chr3:37032242-37032466(-)$1	224	63	71	17.7804

#DB
........	chr14:81940805-81941046(-)$1	1	48	56	16.3170
.(((....	chrX:24230248-24230475(+)$1	1	143	151	17.7804
)......(	chr17:65720106-65720333(+)$1	1	44	52	16.4390
..)..)))	chr1:245006942-245007171(-)$1	1	43	51	14.8536
..))))))	chr1:224348652-224348899(+)$1	1	51	59	17.7804
)..)))))	chr14:52196774-52197001(+)$1	1	141	149	17.0487
)).....)	chr5:132215869-132216099(-)$1	1	204	212	19.7317
........	chr17:30699891-30700118(+)$1	1	173	181	15.4634
(((...((	chr8:28431307-28431531(+)$1	1	9	17	15.7073
........	chr16:70607931-70608171(+)$1	1	147	155	19.7317
..((((.(	chr12:110760726-110760954(+)$1	1	51	59	16.4390
.))))...	chr13:73283943-73284169(-)$1	1	118	126	15.4634
........	chr4:52887765-52887986(-)$1	1	148	156	19.7317
))))))..	chr1:29096132-29096367(+)$1	1	102	110	16.3170
))......	chr12:54632568-54632801(-)$1	1	142	150	19.7317
..))))).	chr5:135516267-135516489(+)$1	1	107	115	15.9512
.((((...	chr12:65090527-65090755(+)$1	1	45	53	15.4634
)))..)))	chr16:69736728-69736951(+)$1	1	171	179	17.7804
(((...))	chr1:114516515-114516773(+)$1	1	123	131	17.7804
).......	chr5:77782107-77782333(-)$1	1	108	116	19.7317
.)))))).	chr10:62553851-62554076(+)$1	1	185	193	17.0487
((..((((	chr3:169814515-169814746(-)$1	1	13	21	15.9512
((((((((	chr5:153435053-153435279(+)$1	1	41	49	16.8048
(...((((	chr7:44916633-44916878(-)$1	1	21	29	15.7073
......))	chr4:108835119-108835341(+)$1	1	133	141	16.8048
..)))...	chr14:93695396-93695618(+)$1	1	178	186	16.8048
....((((	chr11:8020903-8021126(+)$1	1	55	63	17.7804
))....((	chr1:15994883-15995109(+)$1	1	60	68	19.7317
(((((.((	chr3:56656888-56657124(-)$1	1	70	78	16.4390
.((((...	chr8:74704821-74705046(-)$1	1	149	157	19.7317
........	chr1:23633731-23633965(-)$1	1	32	40	15.9512
((((...(	chr16:81078747-81078973(+)$1	1	35	43	16.8048
(((.....	chr8:133859337-133859593(+)$1	1	68	76	14.8536
....))))	chr6:28195976-28196201(+)$1	1	103	111	17.0487
.(((((((	chr3:101369178-101369411(-)$1	1	66	74	15.9512
((...(((	chrX:73806338-73806559(-)$1	1	19	27	17.0487
((((..((	chr2:152691879-152692102(-)$1	1	42	50	16.6829
))))))))	chr2:180809744-180809969(-)$1	1	164	172	19.7317
((......	chr6:4061340-4061567(+)$1	1	79	87	17.7804
.(((...(	chr6:165744758-165744982(-)$1	1	103	111	17.7804
....((((	chr3:37032242-37032466(-)$1	1	63	71	17.7804

#PSSM
U : 0.90	u : 0.09	
U : 0.75	u : 0.09	A : 0.09	C : 0.04	
A : 0.63	G : 0.14	a : 0.09	U : 0.07	C : 0.04	
U : 0.82	u : 0.09	A : 0.07	
U : 0.90	u : 0.09	
U : 0.90	u : 0.09	
U : 0.90	u : 0.09	
U : 0.58	A : 0.21	C : 0.07	u : 0.04	a : 0.02	c : 0.02	G : 0.02	

#score	705.4634146341471
#seq	41
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m2_run2.nuc.txt

#NT
CCUCC	chr12:49522412-49522667(-)$1	255	19	24	15.0000
CCUCC	chr4:3501951-3502173(-)$1	222	19	24	15.0000
CCUCC	chr1:173456874-173457099(+)$1	225	103	108	15.0000
CCUCC	chr22:40742452-40742679(+)$1	227	46	51	15.0000
CCUCC	chr20:30149372-30149630(+)$1	258	32	37	15.0000
CCUCC	chr12:49427384-49427609(-)$1	225	60	65	15.0000
CCUCC	chr17:7403954-7404178(+)$1	224	17	22	15.0000
CCUCC	chr12:7048136-7048365(+)$1	229	212	217	15.0000
CCUCC	chrX:152244480-152244728(+)$1	248	48	53	15.0000
ccuCC	chr21:40762568-40762801(+)$1	233	3	8	15.0000
CCUCC	chr17:36884157-36884413(+)$1	256	110	115	15.0000
CCUCC	chr15:41021965-41022213(-)$1	248	71	76	15.0000
CCUCC	chr12:121174698-121174924(+)$1	226	208	213	15.0000
CCUCC	chr18:46190039-46190264(+)$1	225	161	166	15.0000
CCUCC	chr15:101562012-101562244(+)$1	232	46	51	15.0000
CCUCC	chr1:156737765-156737987(+)$1	222	32	37	15.0000
CCUCC	chr1:153924383-153924615(-)$1	232	44	49	15.0000
ccucc	chr2:43451477-43451705(-)$1	228	10	15	15.0000
CCUCC	chr2:74466518-74466748(-)$1	230	91	96	15.0000
CCUCC	chr3:49568947-49569179(+)$1	232	41	46	15.0000
CCUCC	chr19:6374478-6374700(+)$1	222	125	130	15.0000
CCUCC	chr22:31495631-31495859(+)$1	228	82	87	15.0000
CCUCC	chr11:134212594-134212816(+)$1	222	20	25	15.0000
CCUCC	chr22:38620797-38621028(-)$1	231	29	34	15.0000
CCUCC	chr20:32880077-32880327(-)$1	250	7	12	15.0000
CCUCC	chr19:18685784-18686027(+)$1	243	64	69	15.0000
CCUCC	chr14:89069158-89069389(+)$1	231	178	183	15.0000
CCUCC	chr4:119606599-119606852(-)$1	253	67	72	15.0000
CCUCC	chr21:47642450-47642677(-)$1	227	26	31	15.0000
CCUCC	chr3:49049818-49050056(+)$1	238	15	20	15.0000
CCUCC	chr12:106461448-106461683(-)$1	235	74	79	15.0000
CCUCC	chr2:74590021-74590261(-)$1	240	180	185	15.0000
CCUCC	chr14:21966347-21966613(-)$1	266	79	84	15.0000
CCUCC	chr22:21983844-21984068(-)$1	224	36	41	15.0000
CCUCC	chr17:46993338-46993563(+)$1	225	72	77	15.0000
CCUCC	chr11:65766728-65766951(-)$1	223	215	220	15.0000
CCUCC	chr1:205767734-205767962(-)$1	228	0	5	15.0000
CCUCC	chr17:36884217-36884455(+)$1	238	50	55	15.0000
CCUCC	chr14:24626401-24626646(+)$1	245	218	223	15.0000

#otherMatches

#Struct PSSM
:BBKK	chr19:42462369-42462588(-)$1	219	31	36	15.0000
:::::	chr12:49522412-49522667(-)$1	255	19	24	15.0000
FFFFF	chr4:3501951-3502173(-)$1	222	19	24	15.0000
dddd[	chr1:173456874-173457099(+)$1	225	103	108	15.0000
"""ee	chr22:40742452-40742679(+)$1	227	46	51	15.0000
EEEE:	chr20:30149372-30149630(+)$1	258	32	37	15.0000
iiiii	chr12:49427384-49427609(-)$1	225	60	65	15.0000
PPPPP	chr17:7403954-7404178(+)$1	224	17	22	15.0000
:::::	chr12:7048136-7048365(+)$1	229	212	217	15.0000
qqqqq	chrX:152244480-152244728(+)$1	248	48	53	15.0000
:CCCG	chr21:40762568-40762801(+)$1	233	3	8	15.0000
b:::h	chr17:36884157-36884413(+)$1	256	110	115	15.0000
b]ddd	chr15:41021965-41022213(-)$1	248	71	76	15.0000
:dddd	chr12:121174698-121174924(+)$1	226	208	213	15.0000
eeeea	chr18:46190039-46190264(+)$1	225	161	166	15.0000
g"""f	chr15:101562012-101562244(+)$1	232	46	51	15.0000
{A{GG	chr1:156737765-156737987(+)$1	222	32	37	15.0000
FFFFF	chr1:153924383-153924615(-)$1	232	44	49	15.0000
:::::	chr2:43451477-43451705(-)$1	228	10	15	15.0000
bffff	chr2:74466518-74466748(-)$1	230	91	96	15.0000
Bcccn	chr3:49568947-49569179(+)$1	232	41	46	15.0000
rrrrr	chr19:6374478-6374700(+)$1	222	125	130	15.0000
:::DD	chr22:31495631-31495859(+)$1	228	82	87	15.0000
iiiii	chr11:134212594-134212816(+)$1	222	20	25	15.0000
gggqq	chr22:38620797-38621028(-)$1	231	29	34	15.0000
CCCDD	chr20:32880077-32880327(-)$1	250	7	12	15.0000
ccc[b	chr19:18685784-18686027(+)$1	243	64	69	15.0000
dddd:	chr14:89069158-89069389(+)$1	231	178	183	15.0000
eeeoo	chr4:119606599-119606852(-)$1	253	67	72	15.0000
III:f	chr21:47642450-47642677(-)$1	227	26	31	15.0000
HH{CC	chr3:49049818-49050056(+)$1	238	15	20	15.0000
d[bb[	chr12:106461448-106461683(-)$1	235	74	79	15.0000
zzzzb	chr2:74590021-74590261(-)$1	240	180	185	15.0000
ccccc	chr14:21966347-21966613(-)$1	266	79	84	15.0000
dddd[	chr22:21983844-21984068(-)$1	224	36	41	15.0000
d22dd	chr17:46993338-46993563(+)$1	225	72	77	15.0000
gggg:	chr11:65766728-65766951(-)$1	223	215	220	15.0000
:EEEE	chr1:205767734-205767962(-)$1	228	0	5	15.0000
::::h	chr17:36884217-36884455(+)$1	238	50	55	15.0000
FFFF}	chr14:24626401-24626646(+)$1	245	218	223	15.0000

#DB
.((..	chr19:42462369-42462588(-)$1	1	31	36	15.0000
.....	chr12:49522412-49522667(-)$1	1	19	24	15.0000
(((((	chr4:3501951-3502173(-)$1	1	19	24	15.0000
((((.	chr1:173456874-173457099(+)$1	1	103	108	15.0000
...((	chr22:40742452-40742679(+)$1	1	46	51	15.0000
((((.	chr20:30149372-30149630(+)$1	1	32	37	15.0000
(((((	chr12:49427384-49427609(-)$1	1	60	65	15.0000
.....	chr17:7403954-7404178(+)$1	1	17	22	15.0000
.....	chr12:7048136-7048365(+)$1	1	212	217	15.0000
.....	chrX:152244480-152244728(+)$1	1	48	53	15.0000
.((((	chr21:40762568-40762801(+)$1	1	3	8	15.0000
)...(	chr17:36884157-36884413(+)$1	1	110	115	15.0000
).)))	chr15:41021965-41022213(-)$1	1	71	76	15.0000
.((((	chr12:121174698-121174924(+)$1	1	208	213	15.0000
(((((	chr18:46190039-46190264(+)$1	1	161	166	15.0000
(...(	chr15:101562012-101562244(+)$1	1	46	51	15.0000
.(.((	chr1:156737765-156737987(+)$1	1	32	37	15.0000
(((((	chr1:153924383-153924615(-)$1	1	44	49	15.0000
.....	chr2:43451477-43451705(-)$1	1	10	15	15.0000
(((((	chr2:74466518-74466748(-)$1	1	91	96	15.0000
((((.	chr3:49568947-49569179(+)$1	1	41	46	15.0000
.....	chr19:6374478-6374700(+)$1	1	125	130	15.0000
...))	chr22:31495631-31495859(+)$1	1	82	87	15.0000
(((((	chr11:134212594-134212816(+)$1	1	20	25	15.0000
(((..	chr22:38620797-38621028(-)$1	1	29	34	15.0000
(((((	chr20:32880077-32880327(-)$1	1	7	12	15.0000
(((.(	chr19:18685784-18686027(+)$1	1	64	69	15.0000
)))).	chr14:89069158-89069389(+)$1	1	178	183	15.0000
(((..	chr4:119606599-119606852(-)$1	1	67	72	15.0000
(((.(	chr21:47642450-47642677(-)$1	1	26	31	15.0000
((.((	chr3:49049818-49050056(+)$1	1	15	20	15.0000
(.((.	chr12:106461448-106461683(-)$1	1	74	79	15.0000
....)	chr2:74590021-74590261(-)$1	1	180	185	15.0000
(((((	chr14:21966347-21966613(-)$1	1	79	84	15.0000
((((.	chr22:21983844-21984068(-)$1	1	36	41	15.0000
)..))	chr17:46993338-46993563(+)$1	1	72	77	15.0000
)))).	chr11:65766728-65766951(-)$1	1	215	220	15.0000
.((((	chr1:205767734-205767962(-)$1	1	0	5	15.0000
....(	chr17:36884217-36884455(+)$1	1	50	55	15.0000
)))).	chr14:24626401-24626646(+)$1	1	218	223	15.0000

#PSSM
C : 0.95	c : 0.05	
C : 0.95	c : 0.05	
U : 0.95	u : 0.05	
C : 0.97	c : 0.02	
C : 0.97	c : 0.02	

#score	600.0000000000001
#seq	40
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m3_run2.nuc.txt

#NT
UUUUA	chr12:44188442-44188670(-)$1	228	42	47	14.9999
UUUUA	chr17:27586007-27586246(-)$1	239	196	201	14.9999
UUUUA	chr6:89794005-89794237(+)$1	232	61	66	14.9999
UUUUA	chr9:111777996-111778226(-)$1	230	113	118	14.9999
UUUUA	chr2:242291489-242291722(+)$1	233	9	14	14.9999
UUUUA	chr5:173383647-173383906(+)$1	259	8	13	14.9999
UUUUA	chr8:124027354-124027594(-)$1	240	199	204	14.9999
UUUUA	chr1:205682446-205682666(-)$1	220	23	28	14.9999
UUUUA	chr13:37583380-37583633(+)$1	253	119	124	14.9999
UUUUA	chr6:163994104-163994360(+)$1	256	8	13	14.9999
UUUUA	chr10:116622457-116622689(+)$1	232	60	65	14.9999
uuuua	chr19:2273055-2273358(+)$1	303	264	269	14.9999
UUUUA	chrX:19378006-19378234(+)$1	228	212	217	14.9999
UUUUA	chr7:26231394-26231633(-)$1	239	18	23	14.9999
UUUUA	chr11:74352892-74353113(+)$1	221	48	53	14.9999
UUUUA	chr6:3272719-3272952(-)$1	233	137	142	14.9999
UUUUA	chr4:123815925-123816150(+)$1	225	82	87	14.9999
UUUUA	chr19:18417929-18418151(-)$1	222	11	16	14.9999
UUUUA	chr13:79189451-79189697(-)$1	246	176	181	14.9999
UUUUA	chr11:18428740-18428995(+)$1	255	82	87	14.9999
UUUUA	chr8:103660911-103661206(-)$1	295	100	105	14.9999
UUUUA	chr6:131923374-131923599(-)$1	225	45	50	14.9999
UUUUA	chr15:45900034-45900297(+)$1	263	163	168	14.9999
UUUUA	chr15:82334154-82334381(-)$1	227	65	70	14.9999
UUUUA	chr1:227844340-227844573(+)$1	233	18	23	14.9999
UUUUA	chr12:122989758-122989994(-)$1	236	148	153	14.9999
UUUUA	chrX:131208440-131208663(+)$1	223	1	6	14.9999
UUUUA	chr11:118622433-118622655(-)$1	222	86	91	14.9999
UUUUA	chr9:85594419-85594662(-)$1	243	80	85	14.9999
UUUUA	chr15:76587892-76588126(-)$1	234	42	47	14.9999
UUUUA	chr18:29128287-29128569(+)$1	282	70	75	14.9999
UUUUA	chr15:40913482-40913724(+)$1	242	68	73	14.9999
UUUUA	chr3:51436013-51436248(-)$1	235	147	152	14.9999
UUUUA	chr1:108114137-108114362(-)$1	225	58	63	14.9999
UUUUA	chr11:47489818-47490087(-)$1	269	86	91	14.9999
UUUUA	chr10:96093833-96094080(-)$1	247	25	30	14.9999
UUUUA	chr19:3976092-3976388(-)$1	296	153	158	14.9999
UUUUA	chr5:143539653-143539891(-)$1	238	84	89	14.9999
uuuua	chr2:200136771-200137011(-)$1	240	203	208	14.9999
UUUUA	chr17:56082662-56082915(-)$1	253	221	226	14.9999
UUUUA	chr13:114295276-114295514(+)$1	238	92	97	14.9999
UUUUA	chr17:5344138-5344391(-)$1	253	61	66	14.9999
UUUUA	chr2:176959615-176959841(+)$1	226	36	41	14.9999
UUUUA	chr1:51738629-51738853(+)$1	224	185	190	14.9999
UUUUA	chr2:74437009-74437245(+)$1	236	30	35	14.9999
UUUUA	chr3:67059003-67059249(+)$1	246	52	57	14.9999
UUUUA	chr15:96881824-96882056(+)$1	232	67	72	14.9999
UUUUA	chr1:11082945-11083199(+)$1	254	63	68	14.9999
uuuua	chr2:170429426-170429653(-)$1	227	85	90	14.9999
uuuuA	chr7:23544892-23545152(-)$1	260	29	34	14.9999
UUUUA	chr13:53261972-53262193(+)$1	221	179	184	14.9999
UUUUA	chr6:86318029-86318250(-)$1	221	129	134	14.9999
UUUUA	chr11:102269486-102269720(-)$1	234	82	87	14.9999
UUUUA	chr5:172461691-172461939(+)$1	248	231	236	14.9999
UUUUA	chr12:32902823-32903046(-)$1	223	191	196	14.9999
UUUUA	chr6:47592056-47592286(+)$1	230	138	143	14.9999
UUUUA	chr2:202902092-202902321(+)$1	229	6	11	14.9999
UUUUA	chr6:8015750-8015978(-)$1	228	91	96	14.9999
UUUUA	chr2:216198029-216198259(+)$1	230	23	28	14.9999
UUUUA	chr12:27908513-27908738(+)$1	225	33	38	14.9999
UUUUA	chr14:77935655-77935879(+)$1	224	118	123	14.9999
UUUUA	chr17:55758428-55758666(+)$1	238	25	30	14.9999
UUUUA	chr2:171822895-171823122(+)$1	227	201	206	14.9999
UUUUA	chr1:20978523-20978747(-)$1	224	38	43	14.9999

#otherMatches

#Struct PSSM
CC{CC	chr13:25914473-25914742(+)$1	269	3	8	14.9999
DDDDD	chr12:44188442-44188670(-)$1	228	42	47	14.9999
ddd!!	chr17:27586007-27586246(-)$1	239	196	201	14.9999
5eeee	chr6:89794005-89794237(+)$1	232	61	66	14.9999
rrfff	chr9:111777996-111778226(-)$1	230	113	118	14.9999
F::::	chr2:242291489-242291722(+)$1	233	9	14	14.9999
EEEE{	chr5:173383647-173383906(+)$1	259	8	13	14.9999
qeeee	chr8:124027354-124027594(-)$1	240	199	204	14.9999
sseee	chr1:205682446-205682666(-)$1	220	23	28	14.9999
=====	chr13:37583380-37583633(+)$1	253	119	124	14.9999
PPPPP	chr6:163994104-163994360(+)$1	256	8	13	14.9999
cmmmm	chr10:116622457-116622689(+)$1	232	60	65	14.9999
nnnbb	chr19:2273055-2273358(+)$1	303	264	269	14.9999
EEEEE	chrX:19378006-19378234(+)$1	228	212	217	14.9999
=====	chr7:26231394-26231633(-)$1	239	18	23	14.9999
:::::	chr11:74352892-74353113(+)$1	221	48	53	14.9999
hhhhh	chr6:3272719-3272952(-)$1	233	137	142	14.9999
[ffff	chr4:123815925-123816150(+)$1	225	82	87	14.9999
CLLLE	chr19:18417929-18418151(-)$1	222	11	16	14.9999
eee!!	chr13:79189451-79189697(-)$1	246	176	181	14.9999
eeee4	chr11:18428740-18428995(+)$1	255	82	87	14.9999
eeee:	chr8:103660911-103661206(-)$1	295	100	105	14.9999
22eee	chr6:131923374-131923599(-)$1	225	45	50	14.9999
}CCC:	chr15:45900034-45900297(+)$1	263	163	168	14.9999
iffff	chr15:82334154-82334381(-)$1	227	65	70	14.9999
FOOOO	chr1:227844340-227844573(+)$1	233	18	23	14.9999
dd]ff	chr12:122989758-122989994(-)$1	236	148	153	14.9999
:ffff	chrX:131208440-131208663(+)$1	223	1	6	14.9999
fffff	chr11:118622433-118622655(-)$1	222	86	91	14.9999
h]ccc	chr9:85594419-85594662(-)$1	243	80	85	14.9999
:::::	chr15:76587892-76588126(-)$1	234	42	47	14.9999
iiiii	chr18:29128287-29128569(+)$1	282	70	75	14.9999
eee[g	chr15:40913482-40913724(+)$1	242	68	73	14.9999
ddlll	chr3:51436013-51436248(-)$1	235	147	152	14.9999
e"""c	chr1:108114137-108114362(-)$1	225	58	63	14.9999
eeeee	chr11:47489818-47490087(-)$1	269	86	91	14.9999
mmddd	chr10:96093833-96094080(-)$1	247	25	30	14.9999
fffff	chr19:3976092-3976388(-)$1	296	153	158	14.9999
hhhhh	chr5:143539653-143539891(-)$1	238	84	89	14.9999
gccc]	chr2:200136771-200137011(-)$1	240	203	208	14.9999
^^^cc	chr17:56082662-56082915(-)$1	253	221	226	14.9999
GGGGG	chr13:114295276-114295514(+)$1	238	92	97	14.9999
]iiii	chr17:5344138-5344391(-)$1	253	61	66	14.9999
rrddd	chr2:176959615-176959841(+)$1	226	36	41	14.9999
HHHHH	chr1:51738629-51738853(+)$1	224	185	190	14.9999
))))f	chr2:74437009-74437245(+)$1	236	30	35	14.9999
wwwww	chr3:67059003-67059249(+)$1	246	52	57	14.9999
ee!!i	chr15:96881824-96882056(+)$1	232	67	72	14.9999
mmddd	chr1:11082945-11083199(+)$1	254	63	68	14.9999
mmmmb	chr2:170429426-170429653(-)$1	227	85	90	14.9999
)))))	chr7:23544892-23545152(-)$1	260	29	34	14.9999
hhhhh	chr13:53261972-53262193(+)$1	221	179	184	14.9999
:::ee	chr6:86318029-86318250(-)$1	221	129	134	14.9999
qqqqq	chr11:102269486-102269720(-)$1	234	82	87	14.9999
FFFFF	chr5:172461691-172461939(+)$1	248	231	236	14.9999
ftttt	chr12:32902823-32903046(-)$1	223	191	196	14.9999
dddll	chr6:47592056-47592286(+)$1	230	138	143	14.9999
flllf	chr2:202902092-202902321(+)$1	229	6	11	14.9999
bmmmm	chr6:8015750-8015978(-)$1	228	91	96	14.9999
:::::	chr2:216198029-216198259(+)$1	230	23	28	14.9999
uuuuu	chr12:27908513-27908738(+)$1	225	33	38	14.9999
$$fff	chr14:77935655-77935879(+)$1	224	118	123	14.9999
KKEEE	chr17:55758428-55758666(+)$1	238	25	30	14.9999
frrrr	chr2:171822895-171823122(+)$1	227	201	206	14.9999
ggggp	chr1:20978523-20978747(-)$1	224	38	43	14.9999

#DB
((.((	chr13:25914473-25914742(+)$1	1	3	8	14.9999
(((((	chr12:44188442-44188670(-)$1	1	42	47	14.9999
(((..	chr17:27586007-27586246(-)$1	1	196	201	14.9999
.))))	chr6:89794005-89794237(+)$1	1	61	66	14.9999
..)))	chr9:111777996-111778226(-)$1	1	113	118	14.9999
(....	chr2:242291489-242291722(+)$1	1	9	14	14.9999
((((.	chr5:173383647-173383906(+)$1	1	8	13	14.9999
.))))	chr8:124027354-124027594(-)$1	1	199	204	14.9999
..)))	chr1:205682446-205682666(-)$1	1	23	28	14.9999
)))))	chr13:37583380-37583633(+)$1	1	119	124	14.9999
.....	chr6:163994104-163994360(+)$1	1	8	13	14.9999
(....	chr10:116622457-116622689(+)$1	1	60	65	14.9999
...))	chr19:2273055-2273358(+)$1	1	264	269	14.9999
)))))	chrX:19378006-19378234(+)$1	1	212	217	14.9999
(((((	chr7:26231394-26231633(-)$1	1	18	23	14.9999
.....	chr11:74352892-74353113(+)$1	1	48	53	14.9999
(((((	chr6:3272719-3272952(-)$1	1	137	142	14.9999
.((((	chr4:123815925-123816150(+)$1	1	82	87	14.9999
(...(	chr19:18417929-18418151(-)$1	1	11	16	14.9999
(((..	chr13:79189451-79189697(-)$1	1	176	181	14.9999
)))).	chr11:18428740-18428995(+)$1	1	82	87	14.9999
)))).	chr8:103660911-103661206(-)$1	1	100	105	14.9999
..)))	chr6:131923374-131923599(-)$1	1	45	50	14.9999
.))).	chr15:45900034-45900297(+)$1	1	163	168	14.9999
)((((	chr15:82334154-82334381(-)$1	1	65	70	14.9999
(....	chr1:227844340-227844573(+)$1	1	18	23	14.9999
)).))	chr12:122989758-122989994(-)$1	1	148	153	14.9999
.((((	chrX:131208440-131208663(+)$1	1	1	6	14.9999
(((((	chr11:118622433-118622655(-)$1	1	86	91	14.9999
).)))	chr9:85594419-85594662(-)$1	1	80	85	14.9999
.....	chr15:76587892-76588126(-)$1	1	42	47	14.9999
)))))	chr18:29128287-29128569(+)$1	1	70	75	14.9999
(((.(	chr15:40913482-40913724(+)$1	1	68	73	14.9999
((...	chr3:51436013-51436248(-)$1	1	147	152	14.9999
(...(	chr1:108114137-108114362(-)$1	1	58	63	14.9999
(((((	chr11:47489818-47490087(-)$1	1	86	91	14.9999
..)))	chr10:96093833-96094080(-)$1	1	25	30	14.9999
(((((	chr19:3976092-3976388(-)$1	1	153	158	14.9999
)))))	chr5:143539653-143539891(-)$1	1	84	89	14.9999
)))).	chr2:200136771-200137011(-)$1	1	203	208	14.9999
...))	chr17:56082662-56082915(-)$1	1	221	226	14.9999
)))))	chr13:114295276-114295514(+)$1	1	92	97	14.9999
.))))	chr17:5344138-5344391(-)$1	1	61	66	14.9999
..)))	chr2:176959615-176959841(+)$1	1	36	41	14.9999
)))))	chr1:51738629-51738853(+)$1	1	185	190	14.9999
....(	chr2:74437009-74437245(+)$1	1	30	35	14.9999
.....	chr3:67059003-67059249(+)$1	1	52	57	14.9999
((..(	chr15:96881824-96882056(+)$1	1	67	72	14.9999
..)))	chr1:11082945-11083199(+)$1	1	63	68	14.9999
....)	chr2:170429426-170429653(-)$1	1	85	90	14.9999
.....	chr7:23544892-23545152(-)$1	1	29	34	14.9999
(((((	chr13:53261972-53262193(+)$1	1	179	184	14.9999
...((	chr6:86318029-86318250(-)$1	1	129	134	14.9999
.....	chr11:102269486-102269720(-)$1	1	82	87	14.9999
)))))	chr5:172461691-172461939(+)$1	1	231	236	14.9999
(....	chr12:32902823-32903046(-)$1	1	191	196	14.9999
(((..	chr6:47592056-47592286(+)$1	1	138	143	14.9999
(...)	chr2:202902092-202902321(+)$1	1	6	11	14.9999
(....	chr6:8015750-8015978(-)$1	1	91	96	14.9999
.....	chr2:216198029-216198259(+)$1	1	23	28	14.9999
.....	chr12:27908513-27908738(+)$1	1	33	38	14.9999
..(((	chr14:77935655-77935879(+)$1	1	118	123	14.9999
..(((	chr17:55758428-55758666(+)$1	1	25	30	14.9999
(....	chr2:171822895-171823122(+)$1	1	201	206	14.9999
((((.	chr1:20978523-20978747(-)$1	1	38	43	14.9999

#PSSM
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
A : 0.95	a : 0.04	

#score	974.9999999999995
#seq	65
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m3_run1.nuc.txt

#NT
UAC	chr1:161201053-161201293(-)$1	240	94	97	8.9999
UAC	chr17:16456110-16456350(-)$1	240	32	35	8.9999
UAC	chr3:184040560-184040800(+)$1	240	86	89	8.9999
UAC	chr16:28113080-28113320(-)$1	240	111	114	8.9999
UAC	chr1:153788719-153788959(-)$1	240	121	124	8.9999
UAC	chr3:154027473-154027713(-)$1	240	178	181	8.9999
UAC	chr12:112492198-112492438(-)$1	240	164	167	8.9999
UAC	chr17:74729278-74729518(+)$1	240	41	44	8.9999
UAC	chr1:203276168-203276414(+)$1	246	68	71	8.9999
UAC	chr9:128728059-128728328(+)$1	269	100	103	8.9999
UAC	chr20:42697191-42697431(+)$1	240	20	23	8.9999
UAC	chr4:57204681-57204921(-)$1	240	8	11	8.9999
UAC	chr2:191523841-191524081(+)$1	240	18	21	8.9999
UAC	chrX:152959518-152959758(+)$1	240	120	123	8.9999
UAC	chrX:49850889-49851129(+)$1	240	101	104	8.9999
UAC	chr17:47394974-47395214(-)$1	240	65	68	8.9999
UAC	chr14:93760115-93760355(-)$1	240	109	112	8.9999
UAC	chr6:33255650-33255890(-)$1	240	46	49	8.9999
UAC	chr4:183676022-183676262(+)$1	240	8	11	8.9999
UAC	chr11:20515613-20515853(+)$1	240	41	44	8.9999
UAC	chr6:41755365-41755605(+)$1	240	31	34	8.9999
UAC	chr6:138794404-138794644(-)$1	240	26	29	8.9999
UAC	chr19:53571333-53571573(-)$1	240	12	15	8.9999
UAC	chr11:120355041-120355281(+)$1	240	4	7	8.9999
UAC	chr20:14306197-14306437(-)$1	240	74	77	8.9999
UAC	chr7:17374474-17374714(+)$1	240	14	17	8.9999
UAC	chr16:21181764-21182004(+)$1	240	26	29	8.9999
UAC	chr13:115090820-115091060(+)$1	240	62	65	8.9999
UAC	chr19:30313072-30313312(+)$1	240	126	129	8.9999
UAC	chr6:101311846-101312086(-)$1	240	126	129	8.9999
UAC	chr2:202488862-202489102(-)$1	240	11	14	8.9999
UAC	chr12:50615999-50616239(-)$1	240	74	77	8.9999
UAC	chr9:125836550-125836790(+)$1	240	16	19	8.9999
UAC	chr2:42530221-42530461(+)$1	240	5	8	8.9999
UAC	chr12:121855491-121855731(+)$1	240	29	32	8.9999
UAC	chr20:43583665-43583905(-)$1	240	117	120	8.9999
UAC	chr9:37780653-37780893(-)$1	240	42	45	8.9999
UAC	chr7:100469118-100469358(+)$1	240	118	121	8.9999
UAC	chr14:31598397-31598637(-)$1	240	24	27	8.9999
UAC	chr19:37382731-37382971(-)$1	240	109	112	8.9999
UAC	chr8:12955914-12956154(-)$1	240	132	135	8.9999
UAC	chr3:125298642-125298882(-)$1	240	35	38	8.9999
UAC	chr1:47717320-47717560(-)$1	240	185	188	8.9999
UAC	chr1:236180407-236180647(-)$1	240	169	172	8.9999
UAC	chrX:100400033-100400273(+)$1	240	88	91	8.9999
UAC	chr11:130131373-130131613(-)$1	240	75	78	8.9999
UAC	chr1:247264353-247264593(-)$1	240	71	74	8.9999
UAC	chr11:74716667-74716907(+)$1	240	119	122	8.9999
UAC	chr1:173772337-173772577(-)$1	240	218	221	8.9999
UAC	chr5:126889444-126889684(+)$1	240	27	30	8.9999
UAC	chr2:180846442-180846682(-)$1	240	93	96	8.9999
UAC	chr17:40383939-40384179(-)$1	240	47	50	8.9999
UAC	chr19:19757889-19758129(-)$1	240	40	43	8.9999
UAC	chr2:71649889-71650129(+)$1	240	45	48	8.9999
UAC	chr2:48026027-48026267(+)$1	240	99	102	8.9999
UAC	chr14:95579347-95579587(-)$1	240	27	30	8.9999
UAC	chr3:135870278-135870522(-)$1	244	1	4	8.9999
UAC	chr10:77159038-77159278(-)$1	240	121	124	8.9999
UAC	chr13:50589986-50590226(+)$1	240	62	65	8.9999
UAC	chr7:139299059-139299299(-)$1	240	71	74	8.9999
UAC	chr3:160142572-160142812(+)$1	240	149	152	8.9999
UAC	chrX:24006687-24006927(-)$1	240	18	21	8.9999
UAC	chr14:75230718-75230958(+)$1	240	20	23	8.9999
UAC	chr17:79575708-79575948(-)$1	240	82	85	8.9999
uac	chr17:6917365-6917699(+)$1	334	0	3	8.9999
UAC	chr11:85711670-85711910(-)$1	240	36	39	8.9999
UAC	chr1:183498463-183498703(+)$1	240	142	145	8.9999
UAC	chr16:10631768-10632008(-)$1	240	17	20	8.9999
UAC	chr6:64420999-64421239(+)$1	240	13	16	8.9999
UAC	chr6:30576509-30576789(-)$1	280	44	47	8.9999
UAC	chr2:48573676-48573916(+)$1	240	19	22	8.9999
UAC	chr5:139946824-139947064(+)$1	240	17	20	8.9999
UAC	chr3:73114080-73114326(+)$1	246	156	159	8.9999
UAC	chr5:54456894-54457134(+)$1	240	110	113	8.9999
UAC	chrX:68382748-68382988(-)$1	240	128	131	8.9999
UAC	chr12:57397762-57398002(-)$1	240	39	42	8.9999
UAC	chr17:8280802-8281042(-)$1	240	125	128	8.9999
UAC	chr2:17860083-17860323(-)$1	240	103	106	8.9999
UAC	chrX:152037414-152037654(+)$1	240	0	3	8.9999
UAC	chr19:53343902-53344142(-)$1	240	62	65	8.9999
UAC	chr10:43882289-43882529(-)$1	240	22	25	8.9999
UAC	chr19:52447504-52447744(+)$1	240	12	15	8.9999
UAC	chr19:44660781-44661054(+)$1	273	128	131	8.9999
UAC	chr13:111545297-111545617(-)$1	320	2	5	8.9999
UAC	chr10:104228740-104228980(+)$1	240	151	154	8.9999
UAC	chr2:84668324-84668564(-)$1	240	120	123	8.9999
UAC	chr16:75681895-75682135(+)$1	240	131	134	8.9999
UAC	chr10:77158894-77159144(-)$1	250	92	95	8.9999
UAC	chr19:52090269-52090509(+)$1	240	52	55	8.9999
UAC	chr16:4921053-4921293(+)$1	240	10	13	8.9999
UAC	chr7:26242496-26242736(+)$1	240	4	7	8.9999
UAC	chr17:57759580-57759820(+)$1	240	44	47	8.9999
UAC	chr11:82644926-82645166(+)$1	240	4	7	8.9999
UAC	chr7:65444651-65444891(-)$1	240	32	35	8.9999
UAC	chr9:114686960-114687200(+)$1	240	36	39	8.9999
UAC	chr3:32495855-32496101(+)$1	246	180	183	8.9999
UAC	chr12:22213711-22213951(+)$1	240	42	45	8.9999
UAC	chr16:46724870-46725110(+)$1	240	45	48	8.9999

#otherMatches

#Struct PSSM
:dd	chr22:26892642-26892882(-)$1	240	158	161	8.9999
:::	chr1:161201053-161201293(-)$1	240	94	97	8.9999
uuu	chr17:16456110-16456350(-)$1	240	32	35	8.9999
ppp	chr3:184040560-184040800(+)$1	240	86	89	8.9999
ppp	chr16:28113080-28113320(-)$1	240	111	114	8.9999
666	chr1:153788719-153788959(-)$1	240	121	124	8.9999
eee	chr3:154027473-154027713(-)$1	240	178	181	8.9999
ddd	chr12:112492198-112492438(-)$1	240	164	167	8.9999
qqq	chr17:74729278-74729518(+)$1	240	41	44	8.9999
cc:	chr1:203276168-203276414(+)$1	246	68	71	8.9999
iii	chr9:128728059-128728328(+)$1	269	100	103	8.9999
b[c	chr20:42697191-42697431(+)$1	240	20	23	8.9999
nnn	chr4:57204681-57204921(-)$1	240	8	11	8.9999
F::	chr2:191523841-191524081(+)$1	240	18	21	8.9999
[cc	chrX:152959518-152959758(+)$1	240	120	123	8.9999
II:	chrX:49850889-49851129(+)$1	240	101	104	8.9999
dd#	chr17:47394974-47395214(-)$1	240	65	68	8.9999
gcc	chr14:93760115-93760355(-)$1	240	109	112	8.9999
bnn	chr6:33255650-33255890(-)$1	240	46	49	8.9999
ood	chr4:183676022-183676262(+)$1	240	8	11	8.9999
goo	chr11:20515613-20515853(+)$1	240	41	44	8.9999
::E	chr6:41755365-41755605(+)$1	240	31	34	8.9999
!!b	chr6:138794404-138794644(-)$1	240	26	29	8.9999
C{C	chr19:53571333-53571573(-)$1	240	12	15	8.9999
EKK	chr11:120355041-120355281(+)$1	240	4	7	8.9999
###	chr20:14306197-14306437(-)$1	240	74	77	8.9999
HHH	chr7:17374474-17374714(+)$1	240	14	17	8.9999
###	chr16:21181764-21182004(+)$1	240	26	29	8.9999
dde	chr13:115090820-115091060(+)$1	240	62	65	8.9999
:gg	chr19:30313072-30313312(+)$1	240	126	129	8.9999
f""	chr6:101311846-101312086(-)$1	240	126	129	8.9999
III	chr2:202488862-202489102(-)$1	240	11	14	8.9999
:::	chr12:50615999-50616239(-)$1	240	74	77	8.9999
mmm	chr9:125836550-125836790(+)$1	240	16	19	8.9999
:::	chr2:42530221-42530461(+)$1	240	5	8	8.9999
ppp	chr12:121855491-121855731(+)$1	240	29	32	8.9999
888	chr20:43583665-43583905(-)$1	240	117	120	8.9999
:::	chr9:37780653-37780893(-)$1	240	42	45	8.9999
rrr	chr7:100469118-100469358(+)$1	240	118	121	8.9999
ppp	chr14:31598397-31598637(-)$1	240	24	27	8.9999
dmm	chr19:37382731-37382971(-)$1	240	109	112	8.9999
fff	chr8:12955914-12956154(-)$1	240	132	135	8.9999
ccc	chr3:125298642-125298882(-)$1	240	35	38	8.9999
@@@	chr1:47717320-47717560(-)$1	240	185	188	8.9999
ccc	chr1:236180407-236180647(-)$1	240	169	172	8.9999
e]e	chrX:100400033-100400273(+)$1	240	88	91	8.9999
ddl	chr11:130131373-130131613(-)$1	240	75	78	8.9999
ggg	chr1:247264353-247264593(-)$1	240	71	74	8.9999
:::	chr11:74716667-74716907(+)$1	240	119	122	8.9999
ggc	chr1:173772337-173772577(-)$1	240	218	221	8.9999
:CC	chr5:126889444-126889684(+)$1	240	27	30	8.9999
ccc	chr2:180846442-180846682(-)$1	240	93	96	8.9999
RHH	chr17:40383939-40384179(-)$1	240	47	50	8.9999
:::	chr19:19757889-19758129(-)$1	240	40	43	8.9999
hhh	chr2:71649889-71650129(+)$1	240	45	48	8.9999
e!!	chr2:48026027-48026267(+)$1	240	99	102	8.9999
lld	chr14:95579347-95579587(-)$1	240	27	30	8.9999
:::	chr3:135870278-135870522(-)$1	244	1	4	8.9999
HHH	chr10:77159038-77159278(-)$1	240	121	124	8.9999
:::	chr13:50589986-50590226(+)$1	240	62	65	8.9999
B{C	chr7:139299059-139299299(-)$1	240	71	74	8.9999
G~~	chr3:160142572-160142812(+)$1	240	149	152	8.9999
:::	chrX:24006687-24006927(-)$1	240	18	21	8.9999
:::	chr14:75230718-75230958(+)$1	240	20	23	8.9999
GGG	chr17:79575708-79575948(-)$1	240	82	85	8.9999
:::	chr17:6917365-6917699(+)$1	334	0	3	8.9999
:::	chr11:85711670-85711910(-)$1	240	36	39	8.9999
cc:	chr1:183498463-183498703(+)$1	240	142	145	8.9999
nnn	chr16:10631768-10632008(-)$1	240	17	20	8.9999
III	chr6:64420999-64421239(+)$1	240	13	16	8.9999
c[f	chr6:30576509-30576789(-)$1	280	44	47	8.9999
ttt	chr2:48573676-48573916(+)$1	240	19	22	8.9999
iii	chr5:139946824-139947064(+)$1	240	17	20	8.9999
enn	chr3:73114080-73114326(+)$1	246	156	159	8.9999
ccc	chr5:54456894-54457134(+)$1	240	110	113	8.9999
eee	chrX:68382748-68382988(-)$1	240	128	131	8.9999
D{A	chr12:57397762-57398002(-)$1	240	39	42	8.9999
:::	chr17:8280802-8281042(-)$1	240	125	128	8.9999
qqq	chr2:17860083-17860323(-)$1	240	103	106	8.9999
:::	chrX:152037414-152037654(+)$1	240	0	3	8.9999
eee	chr19:53343902-53344142(-)$1	240	62	65	8.9999
GGG	chr10:43882289-43882529(-)$1	240	22	25	8.9999
:::	chr19:52447504-52447744(+)$1	240	12	15	8.9999
ddd	chr19:44660781-44661054(+)$1	273	128	131	8.9999
B{E	chr13:111545297-111545617(-)$1	320	2	5	8.9999
ccc	chr10:104228740-104228980(+)$1	240	151	154	8.9999
CYY	chr2:84668324-84668564(-)$1	240	120	123	8.9999
=[b	chr16:75681895-75682135(+)$1	240	131	134	8.9999
:::	chr10:77158894-77159144(-)$1	250	92	95	8.9999
zzd	chr19:52090269-52090509(+)$1	240	52	55	8.9999
eee	chr16:4921053-4921293(+)$1	240	10	13	8.9999
:GG	chr7:26242496-26242736(+)$1	240	4	7	8.9999
HHK	chr17:57759580-57759820(+)$1	240	44	47	8.9999
:::	chr11:82644926-82645166(+)$1	240	4	7	8.9999
nnn	chr7:65444651-65444891(-)$1	240	32	35	8.9999
GGG	chr9:114686960-114687200(+)$1	240	36	39	8.9999
dd[	chr3:32495855-32496101(+)$1	246	180	183	8.9999
c:f	chr12:22213711-22213951(+)$1	240	42	45	8.9999
H::	chr16:46724870-46725110(+)$1	240	45	48	8.9999

#DB
.((	chr22:26892642-26892882(-)$1	1	158	161	8.9999
...	chr1:161201053-161201293(-)$1	1	94	97	8.9999
...	chr17:16456110-16456350(-)$1	1	32	35	8.9999
...	chr3:184040560-184040800(+)$1	1	86	89	8.9999
...	chr16:28113080-28113320(-)$1	1	111	114	8.9999
...	chr1:153788719-153788959(-)$1	1	121	124	8.9999
)))	chr3:154027473-154027713(-)$1	1	178	181	8.9999
(((	chr12:112492198-112492438(-)$1	1	164	167	8.9999
...	chr17:74729278-74729518(+)$1	1	41	44	8.9999
)).	chr1:203276168-203276414(+)$1	1	68	71	8.9999
)))	chr9:128728059-128728328(+)$1	1	100	103	8.9999
(.(	chr20:42697191-42697431(+)$1	1	20	23	8.9999
...	chr4:57204681-57204921(-)$1	1	8	11	8.9999
(..	chr2:191523841-191524081(+)$1	1	18	21	8.9999
.((	chrX:152959518-152959758(+)$1	1	120	123	8.9999
)).	chrX:49850889-49851129(+)$1	1	101	104	8.9999
((.	chr17:47394974-47395214(-)$1	1	65	68	8.9999
(((	chr14:93760115-93760355(-)$1	1	109	112	8.9999
(..	chr6:33255650-33255890(-)$1	1	46	49	8.9999
..)	chr4:183676022-183676262(+)$1	1	8	11	8.9999
(..	chr11:20515613-20515853(+)$1	1	41	44	8.9999
..(	chr6:41755365-41755605(+)$1	1	31	34	8.9999
..(	chr6:138794404-138794644(-)$1	1	26	29	8.9999
(.(	chr19:53571333-53571573(-)$1	1	12	15	8.9999
(..	chr11:120355041-120355281(+)$1	1	4	7	8.9999
...	chr20:14306197-14306437(-)$1	1	74	77	8.9999
(((	chr7:17374474-17374714(+)$1	1	14	17	8.9999
...	chr16:21181764-21182004(+)$1	1	26	29	8.9999
)))	chr13:115090820-115091060(+)$1	1	62	65	8.9999
.((	chr19:30313072-30313312(+)$1	1	126	129	8.9999
(..	chr6:101311846-101312086(-)$1	1	126	129	8.9999
(((	chr2:202488862-202489102(-)$1	1	11	14	8.9999
...	chr12:50615999-50616239(-)$1	1	74	77	8.9999
...	chr9:125836550-125836790(+)$1	1	16	19	8.9999
...	chr2:42530221-42530461(+)$1	1	5	8	8.9999
...	chr12:121855491-121855731(+)$1	1	29	32	8.9999
...	chr20:43583665-43583905(-)$1	1	117	120	8.9999
...	chr9:37780653-37780893(-)$1	1	42	45	8.9999
...	chr7:100469118-100469358(+)$1	1	118	121	8.9999
...	chr14:31598397-31598637(-)$1	1	24	27	8.9999
(..	chr19:37382731-37382971(-)$1	1	109	112	8.9999
)))	chr8:12955914-12956154(-)$1	1	132	135	8.9999
(((	chr3:125298642-125298882(-)$1	1	35	38	8.9999
...	chr1:47717320-47717560(-)$1	1	185	188	8.9999
(((	chr1:236180407-236180647(-)$1	1	169	172	8.9999
).)	chrX:100400033-100400273(+)$1	1	88	91	8.9999
((.	chr11:130131373-130131613(-)$1	1	75	78	8.9999
(((	chr1:247264353-247264593(-)$1	1	71	74	8.9999
...	chr11:74716667-74716907(+)$1	1	119	122	8.9999
)))	chr1:173772337-173772577(-)$1	1	218	221	8.9999
.((	chr5:126889444-126889684(+)$1	1	27	30	8.9999
)))	chr2:180846442-180846682(-)$1	1	93	96	8.9999
.((	chr17:40383939-40384179(-)$1	1	47	50	8.9999
...	chr19:19757889-19758129(-)$1	1	40	43	8.9999
(((	chr2:71649889-71650129(+)$1	1	45	48	8.9999
(..	chr2:48026027-48026267(+)$1	1	99	102	8.9999
..)	chr14:95579347-95579587(-)$1	1	27	30	8.9999
...	chr3:135870278-135870522(-)$1	1	1	4	8.9999
)))	chr10:77159038-77159278(-)$1	1	121	124	8.9999
...	chr13:50589986-50590226(+)$1	1	62	65	8.9999
(.(	chr7:139299059-139299299(-)$1	1	71	74	8.9999
)..	chr3:160142572-160142812(+)$1	1	149	152	8.9999
...	chrX:24006687-24006927(-)$1	1	18	21	8.9999
...	chr14:75230718-75230958(+)$1	1	20	23	8.9999
(((	chr17:79575708-79575948(-)$1	1	82	85	8.9999
...	chr17:6917365-6917699(+)$1	1	0	3	8.9999
...	chr11:85711670-85711910(-)$1	1	36	39	8.9999
)).	chr1:183498463-183498703(+)$1	1	142	145	8.9999
...	chr16:10631768-10632008(-)$1	1	17	20	8.9999
(((	chr6:64420999-64421239(+)$1	1	13	16	8.9999
(.(	chr6:30576509-30576789(-)$1	1	44	47	8.9999
...	chr2:48573676-48573916(+)$1	1	19	22	8.9999
(((	chr5:139946824-139947064(+)$1	1	17	20	8.9999
(..	chr3:73114080-73114326(+)$1	1	156	159	8.9999
(((	chr5:54456894-54457134(+)$1	1	110	113	8.9999
(((	chrX:68382748-68382988(-)$1	1	128	131	8.9999
(.(	chr12:57397762-57398002(-)$1	1	39	42	8.9999
...	chr17:8280802-8281042(-)$1	1	125	128	8.9999
...	chr2:17860083-17860323(-)$1	1	103	106	8.9999
...	chrX:152037414-152037654(+)$1	1	0	3	8.9999
(((	chr19:53343902-53344142(-)$1	1	62	65	8.9999
(((	chr10:43882289-43882529(-)$1	1	22	25	8.9999
...	chr19:52447504-52447744(+)$1	1	12	15	8.9999
)))	chr19:44660781-44661054(+)$1	1	128	131	8.9999
(.(	chr13:111545297-111545617(-)$1	1	2	5	8.9999
(((	chr10:104228740-104228980(+)$1	1	151	154	8.9999
)..	chr2:84668324-84668564(-)$1	1	120	123	8.9999
(.(	chr16:75681895-75682135(+)$1	1	131	134	8.9999
...	chr10:77158894-77159144(-)$1	1	92	95	8.9999
..)	chr19:52090269-52090509(+)$1	1	52	55	8.9999
(((	chr16:4921053-4921293(+)$1	1	10	13	8.9999
.((	chr7:26242496-26242736(+)$1	1	4	7	8.9999
((.	chr17:57759580-57759820(+)$1	1	44	47	8.9999
...	chr11:82644926-82645166(+)$1	1	4	7	8.9999
...	chr7:65444651-65444891(-)$1	1	32	35	8.9999
(((	chr9:114686960-114687200(+)$1	1	36	39	8.9999
((.	chr3:32495855-32496101(+)$1	1	180	183	8.9999
).(	chr12:22213711-22213951(+)$1	1	42	45	8.9999
(..	chr16:46724870-46725110(+)$1	1	45	48	8.9999

#PSSM
U : 0.98	u : 0.01	
A : 0.98	a : 0.01	
C : 0.98	c : 0.01	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_UTR_m2_run1.nuc.txt

#NT
UUUCA	chr6:10402728-10402929(-)$1	201	9	14	15.0000
UUUCA	chr2:97372350-97372551(-)$1	201	75	80	15.0000
UUUCA	chr10:102120848-102121049(+)$1	201	78	83	15.0000
UUUCA	chr17:30706098-30706299(+)$1	201	35	40	15.0000
UUUCA	chr5:179249724-179249925(+)$1	201	147	152	15.0000
UUUCA	chr1:28864548-28864749(+)$1	201	191	196	15.0000
UUUCA	chr3:52312206-52312407(-)$1	201	113	118	15.0000
UUUCA	chr14:55429662-55429863(-)$1	201	170	175	15.0000
UUUCA	chrX:48380519-48380720(+)$1	201	35	40	15.0000
UUUCA	chr8:103218029-103218230(-)$1	201	35	40	15.0000
UUUCA	chr17:73314708-73314909(-)$1	201	11	16	15.0000
UUUCA	chr1:1499243-1499444(-)$1	201	12	17	15.0000
UUUCA	chr19:47113241-47113442(+)$1	201	89	94	15.0000
uuuca	chr6:112165960-112166161(-)$1	201	10	15	15.0000
UUUCA	chr10:105787584-105787785(+)$1	201	99	104	15.0000
UUUCA	chr11:63721946-63722147(+)$1	201	19	24	15.0000
UUUCA	chr1:112305478-112305679(+)$1	201	156	161	15.0000
UUUCA	chr2:24150260-24150461(+)$1	201	153	158	15.0000
UUUCA	chr15:43724385-43724586(-)$1	201	34	39	15.0000
UUUCA	chr7:140507748-140507949(-)$1	201	10	15	15.0000
UUUCA	chr4:76415722-76415923(-)$1	201	6	11	15.0000
UUUCA	chr13:45607333-45607534(+)$1	201	18	23	15.0000
UUUCA	chr6:111697068-111697269(-)$1	201	46	51	15.0000
UUUCA	chr20:34131343-34131544(+)$1	201	57	62	15.0000
UUUCA	chr2:170440846-170441047(+)$1	201	192	197	15.0000
UUUCA	chr6:161455235-161455436(+)$1	201	47	52	15.0000
UUUCA	chr17:76818049-76818250(-)$1	201	158	163	15.0000
UUUCA	chr15:52841839-52842040(-)$1	201	73	78	15.0000
UUUCA	chr5:6715019-6715220(+)$1	201	152	157	15.0000
UUUCA	chr20:56806604-56806805(-)$1	201	10	15	15.0000
UUUCA	chr1:46713429-46713630(+)$1	201	76	81	15.0000
UUUCA	chr11:47861436-47861637(-)$1	201	76	81	15.0000
UUUCA	chr12:104487068-104487269(+)$1	201	48	53	15.0000
UUUCA	chr12:72291560-72291761(+)$1	201	26	31	15.0000
UUUCA	chr9:123232347-123232548(-)$1	201	59	64	15.0000
UUUCA	chrX:16867150-16867351(-)$1	201	93	98	15.0000
UUUCA	chr1:173793316-173793517(-)$1	201	42	47	15.0000
UUUCA	chr2:8919057-8919258(-)$1	201	2	7	15.0000
UUUCA	chr19:33600547-33600748(+)$1	201	43	48	15.0000
UUUCA	chr12:27058307-27058508(-)$1	201	33	38	15.0000
UUUCA	chr7:44921927-44922128(-)$1	201	87	92	15.0000

#otherMatches

#Struct PSSM
ZEEEE	chr15:67483390-67483591(+)$1	201	192	197	15.0000
:::::	chr6:10402728-10402929(-)$1	201	9	14	15.0000
d5555	chr2:97372350-97372551(-)$1	201	75	80	15.0000
:::::	chr10:102120848-102121049(+)$1	201	78	83	15.0000
uuuuu	chr17:30706098-30706299(+)$1	201	35	40	15.0000
ppppf	chr5:179249724-179249925(+)$1	201	147	152	15.0000
5555f	chr1:28864548-28864749(+)$1	201	191	196	15.0000
33eee	chr3:52312206-52312407(-)$1	201	113	118	15.0000
+eeee	chr14:55429662-55429863(-)$1	201	170	175	15.0000
ccc%%	chrX:48380519-48380720(+)$1	201	35	40	15.0000
:eeee	chr8:103218029-103218230(-)$1	201	35	40	15.0000
:::::	chr17:73314708-73314909(-)$1	201	11	16	15.0000
::::B	chr1:1499243-1499444(-)$1	201	12	17	15.0000
b''''	chr19:47113241-47113442(+)$1	201	89	94	15.0000
HH:::	chr6:112165960-112166161(-)$1	201	10	15	15.0000
:::::	chr10:105787584-105787785(+)$1	201	99	104	15.0000
:::::	chr11:63721946-63722147(+)$1	201	19	24	15.0000
gggg5	chr1:112305478-112305679(+)$1	201	156	161	15.0000
::eee	chr2:24150260-24150461(+)$1	201	153	158	15.0000
FFFFF	chr15:43724385-43724586(-)$1	201	34	39	15.0000
Hgggg	chr7:140507748-140507949(-)$1	201	10	15	15.0000
:::::	chr4:76415722-76415923(-)$1	201	6	11	15.0000
^^^^^	chr13:45607333-45607534(+)$1	201	18	23	15.0000
mdddd	chr6:111697068-111697269(-)$1	201	46	51	15.0000
HHHHH	chr20:34131343-34131544(+)$1	201	57	62	15.0000
:::::	chr2:170440846-170441047(+)$1	201	192	197	15.0000
FFFFF	chr6:161455235-161455436(+)$1	201	47	52	15.0000
555dd	chr17:76818049-76818250(-)$1	201	158	163	15.0000
iiiii	chr15:52841839-52842040(-)$1	201	73	78	15.0000
gggg!	chr5:6715019-6715220(+)$1	201	152	157	15.0000
::ccc	chr20:56806604-56806805(-)$1	201	10	15	15.0000
hhhhh	chr1:46713429-46713630(+)$1	201	76	81	15.0000
gg]bb	chr11:47861436-47861637(-)$1	201	76	81	15.0000
JJJJJ	chr12:104487068-104487269(+)$1	201	48	53	15.0000
fpppp	chr12:72291560-72291761(+)$1	201	26	31	15.0000
&&eee	chr9:123232347-123232548(-)$1	201	59	64	15.0000
ffffo	chrX:16867150-16867351(-)$1	201	93	98	15.0000
DDD::	chr1:173793316-173793517(-)$1	201	42	47	15.0000
FFFF:	chr2:8919057-8919258(-)$1	201	2	7	15.0000
LCCC{	chr19:33600547-33600748(+)$1	201	43	48	15.0000
nnnnd	chr12:27058307-27058508(-)$1	201	33	38	15.0000
ffff2	chr7:44921927-44922128(-)$1	201	87	92	15.0000

#DB
.))))	chr15:67483390-67483591(+)$1	1	192	197	15.0000
.....	chr6:10402728-10402929(-)$1	1	9	14	15.0000
)....	chr2:97372350-97372551(-)$1	1	75	80	15.0000
.....	chr10:102120848-102121049(+)$1	1	78	83	15.0000
.....	chr17:30706098-30706299(+)$1	1	35	40	15.0000
....)	chr5:179249724-179249925(+)$1	1	147	152	15.0000
....)	chr1:28864548-28864749(+)$1	1	191	196	15.0000
..)))	chr3:52312206-52312407(-)$1	1	113	118	15.0000
.((((	chr14:55429662-55429863(-)$1	1	170	175	15.0000
(((..	chrX:48380519-48380720(+)$1	1	35	40	15.0000
.((((	chr8:103218029-103218230(-)$1	1	35	40	15.0000
.....	chr17:73314708-73314909(-)$1	1	11	16	15.0000
....(	chr1:1499243-1499444(-)$1	1	12	17	15.0000
(....	chr19:47113241-47113442(+)$1	1	89	94	15.0000
((...	chr6:112165960-112166161(-)$1	1	10	15	15.0000
.....	chr10:105787584-105787785(+)$1	1	99	104	15.0000
.....	chr11:63721946-63722147(+)$1	1	19	24	15.0000
)))).	chr1:112305478-112305679(+)$1	1	156	161	15.0000
..(((	chr2:24150260-24150461(+)$1	1	153	158	15.0000
(((((	chr15:43724385-43724586(-)$1	1	34	39	15.0000
(((((	chr7:140507748-140507949(-)$1	1	10	15	15.0000
.....	chr4:76415722-76415923(-)$1	1	6	11	15.0000
.....	chr13:45607333-45607534(+)$1	1	18	23	15.0000
.))))	chr6:111697068-111697269(-)$1	1	46	51	15.0000
(((((	chr20:34131343-34131544(+)$1	1	57	62	15.0000
.....	chr2:170440846-170441047(+)$1	1	192	197	15.0000
(((((	chr6:161455235-161455436(+)$1	1	47	52	15.0000
...))	chr17:76818049-76818250(-)$1	1	158	163	15.0000
(((((	chr15:52841839-52842040(-)$1	1	73	78	15.0000
((((.	chr5:6715019-6715220(+)$1	1	152	157	15.0000
..(((	chr20:56806604-56806805(-)$1	1	10	15	15.0000
)))))	chr1:46713429-46713630(+)$1	1	76	81	15.0000
)).))	chr11:47861436-47861637(-)$1	1	76	81	15.0000
(((((	chr12:104487068-104487269(+)$1	1	48	53	15.0000
(....	chr12:72291560-72291761(+)$1	1	26	31	15.0000
..(((	chr9:123232347-123232548(-)$1	1	59	64	15.0000
((((.	chrX:16867150-16867351(-)$1	1	93	98	15.0000
(((..	chr1:173793316-173793517(-)$1	1	42	47	15.0000
((((.	chr2:8919057-8919258(-)$1	1	2	7	15.0000
.(((.	chr19:33600547-33600748(+)$1	1	43	48	15.0000
....)	chr12:27058307-27058508(-)$1	1	33	38	15.0000
)))).	chr7:44921927-44922128(-)$1	1	87	92	15.0000

#PSSM
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
C : 0.97	c : 0.02	
A : 0.97	a : 0.02	

#score	630.0000000000001
#seq	42
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m1_run2.nuc.txt

#NT
AGAAG	chr14:67831448-67831696(+)$1	248	192	197	15.0000
AGAAG	chr8:37702295-37702569(-)$1	274	252	257	15.0000
AGAAG	chr1:93819360-93819610(+)$1	250	147	152	15.0000
AGAAG	chr22:30144422-30144662(-)$1	240	193	198	15.0000
AGAAG	chrX:53629427-53629674(-)$1	247	114	119	15.0000
AGAAG	chr13:73336027-73336267(-)$1	240	202	207	15.0000
AGAAG	chr11:93401875-93402115(+)$1	240	0	5	15.0000
AGAAG	chr19:47672988-47673232(+)$1	244	15	20	15.0000
AGAAG	chr16:56485528-56485768(+)$1	240	51	56	15.0000
AGAAG	chr19:42752804-42753086(-)$1	282	0	5	15.0000
AGAAG	chr2:220404907-220405147(-)$1	240	45	50	15.0000
AGAAG	chr15:66633445-66633685(-)$1	240	92	97	15.0000
AGAAG	chr7:44245888-44246168(+)$1	280	40	45	15.0000
AGAAG	chr14:104026341-104026621(-)$1	280	116	121	15.0000
AGAAG	chr16:15967273-15967513(-)$1	240	150	155	15.0000
AGAAG	chr6:56347465-56347706(-)$1	241	102	107	15.0000
AGAAG	chrX:53224450-53224691(-)$1	241	226	231	15.0000
AGAAG	chr3:51971592-51971832(-)$1	240	86	91	15.0000
AGAAG	chr3:50327751-50327991(-)$1	240	58	63	15.0000
AGAAG	chr10:30637951-30638247(-)$1	296	94	99	15.0000
AGAAG	chrX:71788536-71788776(-)$1	240	116	121	15.0000
AGAAG	chr15:52356699-52356939(+)$1	240	86	91	15.0000
AGAAG	chr9:77562918-77563158(-)$1	240	140	145	15.0000
AGAAG	chr1:97278857-97279100(+)$1	243	13	18	15.0000
AGAAG	chr19:58017970-58018210(+)$1	240	7	12	15.0000
AGAAG	chr8:103664308-103664548(-)$1	240	12	17	15.0000
AGAAG	chr1:27094300-27094540(+)$1	240	8	13	15.0000
AGAAG	chr11:45883522-45883762(+)$1	240	137	142	15.0000
AGAAG	chr3:49570246-49570487(+)$1	241	27	32	15.0000
AGAAG	chr3:88104563-88104809(-)$1	246	38	43	15.0000
AGAAG	chr19:18652504-18652744(-)$1	240	233	238	15.0000
AGAAG	chr19:2233923-2234163(-)$1	240	119	124	15.0000
AGAAG	chr17:7509331-7509571(-)$1	240	197	202	15.0000
AGAAG	chr6:116979889-116980129(-)$1	240	97	102	15.0000
AGAAG	chr7:129297206-129297446(+)$1	240	29	34	15.0000
AGAAG	chr4:129783189-129783429(+)$1	240	226	231	15.0000
AGAAG	chr3:15127309-15127549(-)$1	240	89	94	15.0000
AGAAG	chr5:108714088-108714328(-)$1	240	161	166	15.0000
AGAAG	chr19:44571236-44571476(+)$1	240	48	53	15.0000
AGAAG	chr1:153909013-153909253(-)$1	240	57	62	15.0000
AGAAG	chr16:2263693-2263933(-)$1	240	137	142	15.0000
AGAAG	chr6:87968844-87969084(+)$1	240	25	30	15.0000
AGAAG	chr17:74722327-74722567(-)$1	240	26	31	15.0000
AGAAG	chr5:132096539-132096779(-)$1	240	102	107	15.0000
AGAAG	chr21:37758304-37758544(+)$1	240	79	84	15.0000
AGAAG	chr4:7056149-7056414(+)$1	265	78	83	15.0000
agaag	chr17:7217758-7217998(-)$1	240	86	91	15.0000
AGAAG	chr17:18197919-18198159(-)$1	240	67	72	15.0000
AGAAG	chr5:68463993-68464244(+)$1	251	146	151	15.0000
AGAAG	chr5:114860811-114861066(-)$1	255	122	127	15.0000
AGAAG	chr17:2573475-2573715(+)$1	240	200	205	15.0000
AGAAG	chr1:168148181-168148421(+)$1	240	234	239	15.0000
AGAAG	chr12:64823914-64824154(+)$1	240	53	58	15.0000
AGAAG	chr2:55470623-55470903(-)$1	280	176	181	15.0000

#otherMatches

#Struct PSSM
ttttt	chr13:33110999-33111239(-)$1	240	116	121	15.0000
::::E	chr14:67831448-67831696(+)$1	248	192	197	15.0000
ZEEEE	chr8:37702295-37702569(-)$1	274	252	257	15.0000
:::::	chr1:93819360-93819610(+)$1	250	147	152	15.0000
YCCCB	chr22:30144422-30144662(-)$1	240	193	198	15.0000
FFFFF	chrX:53629427-53629674(-)$1	247	114	119	15.0000
qdddd	chr13:73336027-73336267(-)$1	240	202	207	15.0000
eeeee	chr11:93401875-93402115(+)$1	240	0	5	15.0000
fffff	chr19:47672988-47673232(+)$1	244	15	20	15.0000
+++++	chr16:56485528-56485768(+)$1	240	51	56	15.0000
:::::	chr19:42752804-42753086(-)$1	282	0	5	15.0000
:::::	chr2:220404907-220405147(-)$1	240	45	50	15.0000
[a!!b	chr15:66633445-66633685(-)$1	240	92	97	15.0000
rrrrr	chr7:44245888-44246168(+)$1	280	40	45	15.0000
!!bb$	chr14:104026341-104026621(-)$1	280	116	121	15.0000
GGGG}	chr16:15967273-15967513(-)$1	240	150	155	15.0000
ooobb	chr6:56347465-56347706(-)$1	241	102	107	15.0000
ee:CC	chrX:53224450-53224691(-)$1	241	226	231	15.0000
)))dd	chr3:51971592-51971832(-)$1	240	86	91	15.0000
qqqqq	chr3:50327751-50327991(-)$1	240	58	63	15.0000
FOOOO	chr10:30637951-30638247(-)$1	296	94	99	15.0000
4ffff	chrX:71788536-71788776(-)$1	240	116	121	15.0000
b22bb	chr15:52356699-52356939(+)$1	240	86	91	15.0000
bbqqq	chr9:77562918-77563158(-)$1	240	140	145	15.0000
HHHHH	chr1:97278857-97279100(+)$1	243	13	18	15.0000
yyyyy	chr19:58017970-58018210(+)$1	240	7	12	15.0000
EEEEE	chr8:103664308-103664548(-)$1	240	12	17	15.0000
bb"""	chr1:27094300-27094540(+)$1	240	8	13	15.0000
ggggg	chr11:45883522-45883762(+)$1	240	137	142	15.0000
nnnnd	chr3:49570246-49570487(+)$1	241	27	32	15.0000
:bb!!	chr3:88104563-88104809(-)$1	246	38	43	15.0000
H::::	chr19:18652504-18652744(-)$1	240	233	238	15.0000
G:::c	chr19:2233923-2234163(-)$1	240	119	124	15.0000
JJJJC	chr17:7509331-7509571(-)$1	240	197	202	15.0000
qqqqd	chr6:116979889-116980129(-)$1	240	97	102	15.0000
::::b	chr7:129297206-129297446(+)$1	240	29	34	15.0000
:::::	chr4:129783189-129783429(+)$1	240	226	231	15.0000
ooobb	chr3:15127309-15127549(-)$1	240	89	94	15.0000
|||||	chr5:108714088-108714328(-)$1	240	161	166	15.0000
::::B	chr19:44571236-44571476(+)$1	240	48	53	15.0000
gg!!a	chr1:153909013-153909253(-)$1	240	57	62	15.0000
mmmcc	chr16:2263693-2263933(-)$1	240	137	142	15.0000
!!bb^	chr6:87968844-87969084(+)$1	240	25	30	15.0000
::::d	chr17:74722327-74722567(-)$1	240	26	31	15.0000
eeeee	chr5:132096539-132096779(-)$1	240	102	107	15.0000
ii!!a	chr21:37758304-37758544(+)$1	240	79	84	15.0000
]eeee	chr4:7056149-7056414(+)$1	265	78	83	15.0000
=====	chr17:7217758-7217998(-)$1	240	86	91	15.0000
lleee	chr17:18197919-18198159(-)$1	240	67	72	15.0000
:dddd	chr5:68463993-68464244(+)$1	251	146	151	15.0000
c5555	chr5:114860811-114861066(-)$1	255	122	127	15.0000
:====	chr17:2573475-2573715(+)$1	240	200	205	15.0000
b::::	chr1:168148181-168148421(+)$1	240	234	239	15.0000
ee:::	chr12:64823914-64824154(+)$1	240	53	58	15.0000
DDYYH	chr2:55470623-55470903(-)$1	280	176	181	15.0000

#DB
.....	chr13:33110999-33111239(-)$1	1	116	121	15.0000
....)	chr14:67831448-67831696(+)$1	1	192	197	15.0000
.))))	chr8:37702295-37702569(-)$1	1	252	257	15.0000
.....	chr1:93819360-93819610(+)$1	1	147	152	15.0000
.))))	chr22:30144422-30144662(-)$1	1	193	198	15.0000
)))))	chrX:53629427-53629674(-)$1	1	114	119	15.0000
.))))	chr13:73336027-73336267(-)$1	1	202	207	15.0000
(((((	chr11:93401875-93402115(+)$1	1	0	5	15.0000
(((((	chr19:47672988-47673232(+)$1	1	15	20	15.0000
.....	chr16:56485528-56485768(+)$1	1	51	56	15.0000
.....	chr19:42752804-42753086(-)$1	1	0	5	15.0000
.....	chr2:220404907-220405147(-)$1	1	45	50	15.0000
.(..(	chr15:66633445-66633685(-)$1	1	92	97	15.0000
.....	chr7:44245888-44246168(+)$1	1	40	45	15.0000
..((.	chr14:104026341-104026621(-)$1	1	116	121	15.0000
)))).	chr16:15967273-15967513(-)$1	1	150	155	15.0000
...))	chr6:56347465-56347706(-)$1	1	102	107	15.0000
)).))	chrX:53224450-53224691(-)$1	1	226	231	15.0000
...((	chr3:51971592-51971832(-)$1	1	86	91	15.0000
.....	chr3:50327751-50327991(-)$1	1	58	63	15.0000
(....	chr10:30637951-30638247(-)$1	1	94	99	15.0000
.))))	chrX:71788536-71788776(-)$1	1	116	121	15.0000
)..))	chr15:52356699-52356939(+)$1	1	86	91	15.0000
((...	chr9:77562918-77563158(-)$1	1	140	145	15.0000
(((((	chr1:97278857-97279100(+)$1	1	13	18	15.0000
.....	chr19:58017970-58018210(+)$1	1	7	12	15.0000
(((((	chr8:103664308-103664548(-)$1	1	12	17	15.0000
((...	chr1:27094300-27094540(+)$1	1	8	13	15.0000
(((((	chr11:45883522-45883762(+)$1	1	137	142	15.0000
....)	chr3:49570246-49570487(+)$1	1	27	32	15.0000
.((..	chr3:88104563-88104809(-)$1	1	38	43	15.0000
)....	chr19:18652504-18652744(-)$1	1	233	238	15.0000
)...(	chr19:2233923-2234163(-)$1	1	119	124	15.0000
)))))	chr17:7509331-7509571(-)$1	1	197	202	15.0000
....)	chr6:116979889-116980129(-)$1	1	97	102	15.0000
....(	chr7:129297206-129297446(+)$1	1	29	34	15.0000
.....	chr4:129783189-129783429(+)$1	1	226	231	15.0000
...))	chr3:15127309-15127549(-)$1	1	89	94	15.0000
.....	chr5:108714088-108714328(-)$1	1	161	166	15.0000
....(	chr19:44571236-44571476(+)$1	1	48	53	15.0000
((..(	chr1:153909013-153909253(-)$1	1	57	62	15.0000
...))	chr16:2263693-2263933(-)$1	1	137	142	15.0000
..((.	chr6:87968844-87969084(+)$1	1	25	30	15.0000
....(	chr17:74722327-74722567(-)$1	1	26	31	15.0000
)))))	chr5:132096539-132096779(-)$1	1	102	107	15.0000
((..(	chr21:37758304-37758544(+)$1	1	79	84	15.0000
.))))	chr4:7056149-7056414(+)$1	1	78	83	15.0000
)))))	chr17:7217758-7217998(-)$1	1	86	91	15.0000
..)))	chr17:18197919-18198159(-)$1	1	67	72	15.0000
.((((	chr5:68463993-68464244(+)$1	1	146	151	15.0000
)....	chr5:114860811-114861066(-)$1	1	122	127	15.0000
.((((	chr17:2573475-2573715(+)$1	1	200	205	15.0000
)....	chr1:168148181-168148421(+)$1	1	234	239	15.0000
))...	chr12:64823914-64824154(+)$1	1	53	58	15.0000
))..)	chr2:55470623-55470903(-)$1	1	176	181	15.0000

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	

#score	825.0000000000001
#seq	55
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m1_run1.nuc.txt

#NT
GCGGAA	chr6:36177940-36178196(+)$1	256	105	111	10.0833
GUGGAA	chr3:98568227-98568467(-)$1	240	103	109	10.0833
GAGGAC	chr4:129193517-129193757(-)$1	240	124	130	10.2222
CAGGAA	chr10:33218774-33219014(-)$1	240	51	57	9.7361
GAGAAA	chr17:60677963-60678203(+)$1	240	121	127	9.8055
GAGGAA	chr3:14199951-14200192(-)$1	241	7	13	13.8333
GAGGAA	chr2:128477273-128477513(-)$1	240	154	160	13.8333
AAGGAA	chr14:76121175-76121419(-)$1	244	202	208	9.8749
GAGAAA	chr17:35913215-35913466(-)$1	251	24	30	9.8055
AAGGAA	chr20:57567960-57568250(+)$1	290	66	72	9.8749
GAGGAA	chr16:30750732-30751070(+)$1	338	169	175	13.8333
GAGAAA	chr11:65828060-65828300(+)$1	240	25	31	9.8055
GAGGAG	chr1:15987749-15987989(+)$1	240	111	117	10.7083
GAUGAA	chrX:134166590-134166849(+)$1	259	122	128	10.0833
GAUGAA	chr1:165865425-165865669(+)$1	244	94	100	10.0833
GAGGAU	chr11:77340793-77341037(-)$1	244	47	53	10.5694
GUGGAA	chr3:4816856-4817096(+)$1	240	145	151	10.0833
CAGGAA	chr15:77025498-77025738(-)$1	240	112	118	9.7361
GAUGAA	chr17:76420045-76420286(+)$1	241	106	112	10.0833
GAUGAA	chr5:137750727-137751007(+)$1	280	110	116	10.0833
GUGGAA	chr7:912017-912257(+)$1	240	15	21	10.0833
GAGGAA	chr11:62487424-62487681(-)$1	257	102	108	13.8333
GAGGAG	chr3:154042010-154042250(-)$1	240	154	160	10.7083
GAGGAG	chr16:599683-599923(+)$1	240	159	165	10.7083
GGGGAA	chr21:32639047-32639287(-)$1	240	130	136	9.9444
GAGGAA	chr1:243589690-243589930(+)$1	240	120	126	13.8333
GAGGAA	chr13:113914821-113915061(+)$1	240	102	108	13.8333
GCGGAA	chrX:154004381-154004624(+)$1	243	79	85	10.0833
GAGCAA	chr17:5286384-5286624(+)$1	240	186	192	9.7361
AAGGAA	chr17:65134030-65134310(-)$1	280	115	121	9.8749
GAGGAU	chr5:71495056-71495301(+)$1	245	108	114	10.5694
GAGCAA	chr4:183696100-183696340(+)$1	240	161	167	9.7361
GAGGAG	chr8:71060578-71060818(-)$1	240	124	130	10.7083
GAGGAG	chr22:50169634-50169874(-)$1	240	210	216	10.7083
GAGGAG	chr22:43272050-43272291(-)$1	241	176	182	10.7083
GAGGAU	chr7:99077203-99077443(+)$1	240	95	101	10.5694
GAGGAA	chr6:42980845-42981205(-)$1	360	212	218	13.8333
GAGGAA	chr22:45595659-45595979(-)$1	320	134	140	13.8333
GAUGAA	chr19:34685286-34685543(+)$1	257	149	155	10.0833
GAUGAA	chr21:17246675-17246915(+)$1	240	128	134	10.0833
GAGGAA	chr12:49239357-49239597(-)$1	240	83	89	13.8333
GAGGAA	chr19:58904673-58904930(+)$1	257	3	9	13.8333
GAAGAA	chr10:95276810-95277050(+)$1	240	156	162	9.6666
GAUGAA	chr8:67968690-67968930(-)$1	240	106	112	10.0833
GCGGAA	chr8:123965465-123965745(+)$1	280	24	30	10.0833
GAGGAG	chr16:19725639-19725959(-)$1	320	16	22	10.7083
GAGAAA	chr4:57856819-57857063(+)$1	244	107	113	9.8055
GAUGAA	chr18:12794210-12794450(-)$1	240	26	32	10.0833
GAGCAA	chr16:2327932-2328172(-)$1	240	189	195	9.7361
GCGGAA	chr14:20923649-20923950(+)$1	301	185	191	10.0833
GAGGAG	chr3:139062899-139063139(+)$1	240	10	16	10.7083
UAGGAA	chrX:119066031-119066271(-)$1	240	49	55	9.6666
GAGGAU	chr9:138773387-138773627(-)$1	240	119	125	10.5694
GAGCAA	chr7:75511072-75511312(+)$1	240	32	38	9.7361
AAGGAA	chr16:20809287-20809527(-)$1	240	4	10	9.8749
GAGGAA	chr3:49020597-49020901(+)$1	304	130	136	13.8333
GAGGAU	chr20:13463789-13464029(-)$1	240	107	113	10.5694
GAGAAA	chr4:106892131-106892372(+)$1	241	223	229	9.8055
GAGGAC	chr1:89298950-89299230(+)$1	280	38	44	10.2222
GAGGAG	chr11:6423779-6424019(-)$1	240	103	109	10.7083
CAGGAA	chr6:24423721-24424007(+)$1	286	172	178	9.7361
GAAGAA	chr15:91524024-91524344(-)$1	320	168	174	9.6666
GCGGAA	chr11:111582938-111583178(+)$1	240	116	122	10.0833
GAGGAU	chr19:5667066-5667558(+)$1	492	70	76	10.5694
UAGGAA	chr2:54864747-54864999(+)$1	252	105	111	9.6666
GAGGAA	chr1:24483572-24483812(-)$1	240	73	79	13.8333
GUGGAA	chr6:126342204-126342444(+)$1	240	6	12	10.0833
GUGGAA	chr6:53380834-53381074(-)$1	240	100	106	10.0833
GGGGAA	chr15:29560855-29561106(-)$1	251	177	183	9.9444
AAGGAA	chr17:75202213-75202453(+)$1	240	24	30	9.8749
GGGGAA	chr3:184041153-184041473(+)$1	320	195	201	9.9444

#otherMatches

#Struct PSSM
d4444f	chr11:64888940-64889180(-)$1	240	133	139	10.5694
dddd[b	chr6:36177940-36178196(+)$1	256	105	111	10.0833
eeebb!	chr3:98568227-98568467(-)$1	240	103	109	10.0833
dmmmmd	chr4:129193517-129193757(-)$1	240	124	130	10.2222
eeeeec	chr10:33218774-33219014(-)$1	240	51	57	9.7361
3bb22e	chr17:60677963-60678203(+)$1	240	121	127	9.8055
EEEEE:	chr3:14199951-14200192(-)$1	241	7	13	13.8333
dddd""	chr2:128477273-128477513(-)$1	240	154	160	13.8333
DCCCYY	chr14:76121175-76121419(-)$1	244	202	208	9.8749
::ffff	chr17:35913215-35913466(-)$1	251	24	30	9.8055
hhhhhc	chr20:57567960-57568250(+)$1	290	66	72	9.8749
EEEE{E	chr16:30750732-30751070(+)$1	338	169	175	13.8333
JJJJJJ	chr11:65828060-65828300(+)$1	240	25	31	9.8055
bb[ccc	chr1:15987749-15987989(+)$1	240	111	117	10.7083
cc&&&&	chrX:134166590-134166849(+)$1	259	122	128	10.0833
[assss	chr1:165865425-165865669(+)$1	244	94	100	10.0833
{AKKBB	chr11:77340793-77341037(-)$1	244	47	53	10.5694
eeemmm	chr3:4816856-4817096(+)$1	240	145	151	10.0833
qqqqqq	chr15:77025498-77025738(-)$1	240	112	118	9.7361
YYFFFF	chr17:76420045-76420286(+)$1	241	106	112	10.0833
[dddd[	chr5:137750727-137751007(+)$1	280	110	116	10.0833
eeeee[	chr7:912017-912257(+)$1	240	15	21	10.0833
pppppp	chr11:62487424-62487681(-)$1	257	102	108	13.8333
EEEE:a	chr3:154042010-154042250(-)$1	240	154	160	10.7083
""a[bb	chr16:599683-599923(+)$1	240	159	165	10.7083
mmeeee	chr21:32639047-32639287(-)$1	240	130	136	9.9444
gggg::	chr1:243589690-243589930(+)$1	240	120	126	13.8333
ccccc:	chr13:113914821-113915061(+)$1	240	102	108	13.8333
bbmmmm	chrX:154004381-154004624(+)$1	243	79	85	10.0833
g'''''	chr17:5286384-5286624(+)$1	240	186	192	9.7361
ddd333	chr17:65134030-65134310(-)$1	280	115	121	9.8749
!dddd!	chr5:71495056-71495301(+)$1	245	108	114	10.5694
c:bb""	chr4:183696100-183696340(+)$1	240	161	167	9.7361
ffffff	chr8:71060578-71060818(-)$1	240	124	130	10.7083
22dddd	chr22:50169634-50169874(-)$1	240	210	216	10.7083
JJJJJJ	chr22:43272050-43272291(-)$1	241	176	182	10.7083
ddddDD	chr7:99077203-99077443(+)$1	240	95	101	10.5694
nnnnnb	chr6:42980845-42981205(-)$1	360	212	218	13.8333
======	chr22:45595659-45595979(-)$1	320	134	140	13.8333
FFFF::	chr19:34685286-34685543(+)$1	257	149	155	10.0833
eeeee]	chr21:17246675-17246915(+)$1	240	128	134	10.0833
nndddd	chr12:49239357-49239597(-)$1	240	83	89	13.8333
gggg$$	chr19:58904673-58904930(+)$1	257	3	9	13.8333
::::::	chr10:95276810-95277050(+)$1	240	156	162	9.6666
eeeee:	chr8:67968690-67968930(-)$1	240	106	112	10.0833
KKBBKK	chr8:123965465-123965745(+)$1	280	24	30	10.0833
GGGGGG	chr16:19725639-19725959(-)$1	320	16	22	10.7083
eeeee[	chr4:57856819-57857063(+)$1	244	107	113	9.8055
::::::	chr18:12794210-12794450(-)$1	240	26	32	10.0833
66bb]b	chr16:2327932-2328172(-)$1	240	189	195	9.7361
eeffff	chr14:20923649-20923950(+)$1	301	185	191	10.0833
MMFFFF	chr3:139062899-139063139(+)$1	240	10	16	10.7083
eeee!!	chrX:119066031-119066271(-)$1	240	49	55	9.6666
ffff::	chr9:138773387-138773627(-)$1	240	119	125	10.5694
ddbbnn	chr7:75511072-75511312(+)$1	240	32	38	9.7361
::DDDD	chr16:20809287-20809527(-)$1	240	4	10	9.8749
{AEEEE	chr3:49020597-49020901(+)$1	304	130	136	13.8333
fffff]	chr20:13463789-13464029(-)$1	240	107	113	10.5694
FFFFYY	chr4:106892131-106892372(+)$1	241	223	229	9.8055
wwwwww	chr1:89298950-89299230(+)$1	280	38	44	10.2222
:eeeee	chr11:6423779-6424019(-)$1	240	103	109	10.7083
DDDFFF	chr6:24423721-24424007(+)$1	286	172	178	9.7361
e:::::	chr15:91524024-91524344(-)$1	320	168	174	9.6666
FFFFF}	chr11:111582938-111583178(+)$1	240	116	122	10.0833
cc::::	chr19:5667066-5667558(+)$1	492	70	76	10.5694
bddddf	chr2:54864747-54864999(+)$1	252	105	111	9.6666
======	chr1:24483572-24483812(-)$1	240	73	79	13.8333
fffvvv	chr6:126342204-126342444(+)$1	240	6	12	10.0833
g=====	chr6:53380834-53381074(-)$1	240	100	106	10.0833
GGGG::	chr15:29560855-29561106(-)$1	251	177	183	9.9444
::::::	chr17:75202213-75202453(+)$1	240	24	30	9.8749
hhhhhh	chr3:184041153-184041473(+)$1	320	195	201	9.9444

#DB
)....)	chr11:64888940-64889180(-)$1	1	133	139	10.5694
((((.(	chr6:36177940-36178196(+)$1	1	105	111	10.0833
(((((.	chr3:98568227-98568467(-)$1	1	103	109	10.0833
(....)	chr4:129193517-129193757(-)$1	1	124	130	10.2222
((((((	chr10:33218774-33219014(-)$1	1	51	57	9.7361
.))..)	chr17:60677963-60678203(+)$1	1	121	127	9.8055
(((((.	chr3:14199951-14200192(-)$1	1	7	13	13.8333
((((..	chr2:128477273-128477513(-)$1	1	154	160	13.8333
))))..	chr14:76121175-76121419(-)$1	1	202	208	9.8749
..((((	chr17:35913215-35913466(-)$1	1	24	30	9.8055
)))))(	chr20:57567960-57568250(+)$1	1	66	72	9.8749
((((.(	chr16:30750732-30751070(+)$1	1	169	175	13.8333
((((((	chr11:65828060-65828300(+)$1	1	25	31	9.8055
((.(((	chr1:15987749-15987989(+)$1	1	111	117	10.7083
((....	chrX:134166590-134166849(+)$1	1	122	128	10.0833
.(....	chr1:165865425-165865669(+)$1	1	94	100	10.0833
.(..((	chr11:77340793-77341037(-)$1	1	47	53	10.5694
(((...	chr3:4816856-4817096(+)$1	1	145	151	10.0833
......	chr15:77025498-77025738(-)$1	1	112	118	9.7361
..))))	chr17:76420045-76420286(+)$1	1	106	112	10.0833
.((((.	chr5:137750727-137751007(+)$1	1	110	116	10.0833
(((((.	chr7:912017-912257(+)$1	1	15	21	10.0833
......	chr11:62487424-62487681(-)$1	1	102	108	13.8333
)))).(	chr3:154042010-154042250(-)$1	1	154	160	10.7083
..(.((	chr16:599683-599923(+)$1	1	159	165	10.7083
..))))	chr21:32639047-32639287(-)$1	1	130	136	9.9444
))))..	chr1:243589690-243589930(+)$1	1	120	126	13.8333
))))).	chr13:113914821-113915061(+)$1	1	102	108	13.8333
((....	chrX:154004381-154004624(+)$1	1	79	85	10.0833
(.....	chr17:5286384-5286624(+)$1	1	186	192	9.7361
)))...	chr17:65134030-65134310(-)$1	1	115	121	9.8749
.((((.	chr5:71495056-71495301(+)$1	1	108	114	10.5694
).((..	chr4:183696100-183696340(+)$1	1	161	167	9.7361
((((((	chr8:71060578-71060818(-)$1	1	124	130	10.7083
..))))	chr22:50169634-50169874(-)$1	1	210	216	10.7083
))))))	chr22:43272050-43272291(-)$1	1	176	182	10.7083
))))))	chr7:99077203-99077443(+)$1	1	95	101	10.5694
.....)	chr6:42980845-42981205(-)$1	1	212	218	13.8333
))))))	chr22:45595659-45595979(-)$1	1	134	140	13.8333
))))..	chr19:34685286-34685543(+)$1	1	149	155	10.0833
))))).	chr21:17246675-17246915(+)$1	1	128	134	10.0833
..))))	chr12:49239357-49239597(-)$1	1	83	89	13.8333
((((..	chr19:58904673-58904930(+)$1	1	3	9	13.8333
......	chr10:95276810-95277050(+)$1	1	156	162	9.6666
))))).	chr8:67968690-67968930(-)$1	1	106	112	10.0833
..((..	chr8:123965465-123965745(+)$1	1	24	30	10.0833
((((((	chr16:19725639-19725959(-)$1	1	16	22	10.7083
(((((.	chr4:57856819-57857063(+)$1	1	107	113	9.8055
......	chr18:12794210-12794450(-)$1	1	26	32	10.0833
..)).)	chr16:2327932-2328172(-)$1	1	189	195	9.7361
((((((	chr14:20923649-20923950(+)$1	1	185	191	10.0833
..((((	chr3:139062899-139063139(+)$1	1	10	16	10.7083
((((..	chrX:119066031-119066271(-)$1	1	49	55	9.6666
))))..	chr9:138773387-138773627(-)$1	1	119	125	10.5694
))((..	chr7:75511072-75511312(+)$1	1	32	38	9.7361
..((((	chr16:20809287-20809527(-)$1	1	4	10	9.8749
.(((((	chr3:49020597-49020901(+)$1	1	130	136	13.8333
))))).	chr20:13463789-13464029(-)$1	1	107	113	10.5694
))))..	chr4:106892131-106892372(+)$1	1	223	229	9.8055
......	chr1:89298950-89299230(+)$1	1	38	44	10.2222
.(((((	chr11:6423779-6424019(-)$1	1	103	109	10.7083
))))))	chr6:24423721-24424007(+)$1	1	172	178	9.7361
).....	chr15:91524024-91524344(-)$1	1	168	174	9.6666
))))).	chr11:111582938-111583178(+)$1	1	116	122	10.0833
))....	chr19:5667066-5667558(+)$1	1	70	76	10.5694
))))))	chr2:54864747-54864999(+)$1	1	105	111	9.6666
))))))	chr1:24483572-24483812(-)$1	1	73	79	13.8333
(((...	chr6:126342204-126342444(+)$1	1	6	12	10.0833
)(((((	chr6:53380834-53381074(-)$1	1	100	106	10.0833
))))..	chr15:29560855-29561106(-)$1	1	177	183	9.9444
......	chr17:75202213-75202453(+)$1	1	24	30	9.8749
((((((	chr3:184041153-184041473(+)$1	1	195	201	9.9444

#PSSM
G : 0.86	A : 0.06	C : 0.04	U : 0.02	
A : 0.81	C : 0.06	U : 0.06	G : 0.04	
G : 0.86	U : 0.11	A : 0.02	
G : 0.87	A : 0.06	C : 0.05	
A : 0.99	
A : 0.74	G : 0.12	U : 0.09	C : 0.02	

#score	773.36111111111
#seq	72
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m3_run1.nuc.txt

#NT
GAAA	chr13:30778065-30778294(-)$1	229	29	33	12.0000
GAAA	chr2:37075094-37075311(-)$1	217	6	10	12.0000
GAAA	chr8:97245290-97245512(-)$1	222	90	94	12.0000
GAAA	chr1:20236947-20237169(+)$1	222	64	68	12.0000
GAAA	chr1:218505387-218505618(+)$1	231	39	43	12.0000
GAAA	chr7:65420352-65420607(+)$1	255	201	205	12.0000
GAAA	chr1:27107402-27107620(+)$1	218	93	97	12.0000
GAAA	chr15:70386786-70387015(-)$1	229	30	34	12.0000
GAAA	chr11:117038588-117038818(+)$1	230	14	18	12.0000
GAAA	chr11:65111174-65111396(+)$1	222	117	121	12.0000
GAAA	chr2:128044457-128044685(-)$1	228	98	102	12.0000
GAAA	chr5:159829204-159829427(-)$1	223	45	49	12.0000
GAAA	chrX:131510483-131510707(-)$1	224	182	186	12.0000
GAAA	chr9:72999976-73000219(-)$1	243	97	101	12.0000
GAAA	chr1:179075674-179075929(-)$1	255	99	103	12.0000
GAAA	chr21:37758268-37758492(+)$1	224	135	139	12.0000
gaaa	chr11:73114940-73115158(-)$1	218	30	34	12.0000
GAAA	chr6:52962812-52963032(+)$1	220	60	64	12.0000
GAAA	chr13:95279512-95279736(+)$1	224	4	8	12.0000
GAAA	chr1:166821064-166821296(+)$1	232	43	47	12.0000
GAAA	chr1:173900769-173900997(-)$1	228	175	179	12.0000
GAAA	chr12:110734353-110734581(+)$1	228	50	54	12.0000
GAAA	chr4:57799995-57800221(+)$1	226	4	8	12.0000
GAAA	chr3:58310175-58310388(+)$1	213	133	137	12.0000
GAAA	chr12:54625312-54625562(-)$1	250	99	103	12.0000
GAAA	chr22:20098618-20098840(+)$1	222	93	97	12.0000
GAAA	chr4:48039373-48039591(+)$1	218	186	190	12.0000
GAAA	chr11:74550439-74550656(+)$1	217	72	76	12.0000
GAAA	chr1:33146305-33146515(+)$1	210	93	97	12.0000
GAAA	chr20:42091748-42092063(+)$1	315	302	306	12.0000
GAAA	chr8:68110963-68111182(-)$1	219	90	94	12.0000
GAAA	chr10:103567531-103567751(-)$1	220	213	217	12.0000
gaaa	chr14:61439280-61439504(-)$1	224	10	14	12.0000
GAAA	chr12:12795644-12795859(+)$1	215	64	68	12.0000
GAAA	chr1:204374073-204374356(-)$1	283	15	19	12.0000
GAAA	chr1:227845959-227846191(+)$1	232	45	49	12.0000
GAAA	chr3:142777220-142777448(+)$1	228	92	96	12.0000
GAAA	chr17:49039487-49039716(-)$1	229	3	7	12.0000
GAAA	chr7:139247152-139247374(-)$1	222	140	144	12.0000
gaaa	chr17:8279559-8279776(-)$1	217	124	128	12.0000
GAAA	chr6:64404388-64404682(+)$1	294	98	102	12.0000
GAAA	chr18:9954227-9954447(+)$1	220	29	33	12.0000
GAAA	chr3:48674463-48674691(-)$1	228	77	81	12.0000
GAAA	chr10:857261-857496(-)$1	235	148	152	12.0000
GAAA	chr11:118267224-118267446(+)$1	222	81	85	12.0000
GAAA	chr17:49040181-49040410(-)$1	229	188	192	12.0000
GAAA	chrX:103436983-103437211(+)$1	228	139	143	12.0000
GAAA	chr12:24969324-24969538(-)$1	214	18	22	12.0000
GAAA	chr14:61180384-61180611(-)$1	227	199	203	12.0000
GAAA	chr16:20809045-20809257(-)$1	212	10	14	12.0000
GAAA	chr3:112722832-112723052(+)$1	220	102	106	12.0000
GAAA	chr21:19165628-19165852(-)$1	224	194	198	12.0000
GAAA	chr12:123351145-123351364(-)$1	219	83	87	12.0000
GAAA	chr7:97922196-97922407(-)$1	211	59	63	12.0000
GAAA	chr6:56358829-56359040(-)$1	211	92	96	12.0000
GAAA	chr20:42089622-42089891(+)$1	269	181	185	12.0000
GAAA	chr1:210416086-210416307(+)$1	221	68	72	12.0000
GAAA	chrX:14938514-14938724(+)$1	210	89	93	12.0000
GAAA	chr1:223983875-223984094(-)$1	219	3	7	12.0000
GAAA	chr1:168215133-168215369(+)$1	236	63	67	12.0000
GAAA	chr2:149882567-149882797(+)$1	230	11	15	12.0000
GAAA	chr17:29550450-29550663(+)$1	213	38	42	12.0000
GAAA	chr21:35473470-35473710(+)$1	240	224	228	12.0000
GAAA	chr7:27202615-27202828(-)$1	213	176	180	12.0000
GAAA	chr9:22002854-22003071(-)$1	217	41	45	12.0000
GAAA	chr12:124496214-124496623(+)$1	409	295	299	12.0000
GAAA	chr1:120163801-120164023(-)$1	222	208	212	12.0000
GAAA	chr18:13665750-13665977(-)$1	227	40	44	12.0000
GAAA	chr1:57174359-57174623(+)$1	264	98	102	12.0000
GAAA	chr5:132440358-132440609(+)$1	251	69	73	12.0000
GAAA	chr12:106459969-106460201(-)$1	232	203	207	12.0000
GAAA	chr3:188594718-188594944(+)$1	226	115	119	12.0000
GAAA	chr11:123494711-123494929(+)$1	218	119	123	12.0000
GAAA	chr21:35470535-35470784(+)$1	249	33	37	12.0000
GAAA	chr4:39779995-39780233(+)$1	238	197	201	12.0000
GAAA	chr7:140156521-140156741(-)$1	220	173	177	12.0000
GAAA	chr14:75515442-75515683(-)$1	241	143	147	12.0000
GAAA	chr22:35689904-35690164(+)$1	260	163	167	12.0000
GAAA	chr14:23780246-23780475(+)$1	229	79	83	12.0000
GAAA	chr1:153779983-153780206(-)$1	223	77	81	12.0000
GAAA	chr5:112177401-112177626(+)$1	225	39	43	12.0000
gaaa	chr1:115249072-115249397(-)$1	325	2	6	12.0000
GAAA	chr16:50830370-50830589(+)$1	219	62	66	12.0000
GAAA	chr3:142777539-142777752(+)$1	213	148	152	12.0000
GAAA	chr6:149826336-149826585(-)$1	249	59	63	12.0000

#otherMatches

#Struct PSSM
::::	chr10:59953281-59953503(-)$1	222	1	5	12.0000
))))	chr13:30778065-30778294(-)$1	229	29	33	12.0000
hhh!	chr2:37075094-37075311(-)$1	217	6	10	12.0000
dddd	chr8:97245290-97245512(-)$1	222	90	94	12.0000
d]ff	chr1:20236947-20237169(+)$1	222	64	68	12.0000
ee22	chr1:218505387-218505618(+)$1	231	39	43	12.0000
ZZEE	chr7:65420352-65420607(+)$1	255	201	205	12.0000
eooo	chr1:27107402-27107620(+)$1	218	93	97	12.0000
eerr	chr15:70386786-70387015(-)$1	229	30	34	12.0000
::::	chr11:117038588-117038818(+)$1	230	14	18	12.0000
h444	chr11:65111174-65111396(+)$1	222	117	121	12.0000
[a[d	chr2:128044457-128044685(-)$1	228	98	102	12.0000
HHHH	chr5:159829204-159829427(-)$1	223	45	49	12.0000
eebb	chrX:131510483-131510707(-)$1	224	182	186	12.0000
::::	chr9:72999976-73000219(-)$1	243	97	101	12.0000
>>>>	chr1:179075674-179075929(-)$1	255	99	103	12.0000
uuuu	chr21:37758268-37758492(+)$1	224	135	139	12.0000
ee::	chr11:73114940-73115158(-)$1	218	30	34	12.0000
GGGG	chr6:52962812-52963032(+)$1	220	60	64	12.0000
EE::	chr13:95279512-95279736(+)$1	224	4	8	12.0000
hhhh	chr1:166821064-166821296(+)$1	232	43	47	12.0000
grrr	chr1:173900769-173900997(-)$1	228	175	179	12.0000
gggg	chr12:110734353-110734581(+)$1	228	50	54	12.0000
{GGG	chr4:57799995-57800221(+)$1	226	4	8	12.0000
qqqq	chr3:58310175-58310388(+)$1	213	133	137	12.0000
cc33	chr12:54625312-54625562(-)$1	250	99	103	12.0000
dddn	chr22:20098618-20098840(+)$1	222	93	97	12.0000
}JJJ	chr4:48039373-48039591(+)$1	218	186	190	12.0000
HHKK	chr11:74550439-74550656(+)$1	217	72	76	12.0000
eepp	chr1:33146305-33146515(+)$1	210	93	97	12.0000
FFFF	chr20:42091748-42092063(+)$1	315	302	306	12.0000
dddd	chr8:68110963-68111182(-)$1	219	90	94	12.0000
GGGG	chr10:103567531-103567751(-)$1	220	213	217	12.0000
FFKK	chr14:61439280-61439504(-)$1	224	10	14	12.0000
dddd	chr12:12795644-12795859(+)$1	215	64	68	12.0000
cc!!	chr1:204374073-204374356(-)$1	283	15	19	12.0000
gggg	chr1:227845959-227846191(+)$1	232	45	49	12.0000
ggg:	chr3:142777220-142777448(+)$1	228	92	96	12.0000
FFFF	chr17:49039487-49039716(-)$1	229	3	7	12.0000
:DDD	chr7:139247152-139247374(-)$1	222	140	144	12.0000
gg:h	chr17:8279559-8279776(-)$1	217	124	128	12.0000
qqqq	chr6:64404388-64404682(+)$1	294	98	102	12.0000
iiii	chr18:9954227-9954447(+)$1	220	29	33	12.0000
ggg:	chr3:48674463-48674691(-)$1	228	77	81	12.0000
gggg	chr10:857261-857496(-)$1	235	148	152	12.0000
CCKK	chr11:118267224-118267446(+)$1	222	81	85	12.0000
5555	chr17:49040181-49040410(-)$1	229	188	192	12.0000
IIII	chrX:103436983-103437211(+)$1	228	139	143	12.0000
FFKK	chr12:24969324-24969538(-)$1	214	18	22	12.0000
ee22	chr14:61180384-61180611(-)$1	227	199	203	12.0000
ddd!	chr16:20809045-20809257(-)$1	212	10	14	12.0000
fff3	chr3:112722832-112723052(+)$1	220	102	106	12.0000
B}GG	chr21:19165628-19165852(-)$1	224	194	198	12.0000
:::e	chr12:123351145-123351364(-)$1	219	83	87	12.0000
hccc	chr7:97922196-97922407(-)$1	211	59	63	12.0000
xxxx	chr6:56358829-56359040(-)$1	211	92	96	12.0000
f:::	chr20:42089622-42089891(+)$1	269	181	185	12.0000
pppp	chr1:210416086-210416307(+)$1	221	68	72	12.0000
ee&&	chrX:14938514-14938724(+)$1	210	89	93	12.0000
::::	chr1:223983875-223984094(-)$1	219	3	7	12.0000
gggg	chr1:168215133-168215369(+)$1	236	63	67	12.0000
::::	chr2:149882567-149882797(+)$1	230	11	15	12.0000
::::	chr17:29550450-29550663(+)$1	213	38	42	12.0000
4444	chr21:35473470-35473710(+)$1	240	224	228	12.0000
::::	chr7:27202615-27202828(-)$1	213	176	180	12.0000
c+++	chr9:22002854-22003071(-)$1	217	41	45	12.0000
emmm	chr12:124496214-124496623(+)$1	409	295	299	12.0000
cc33	chr1:120163801-120164023(-)$1	222	208	212	12.0000
hhhh	chr18:13665750-13665977(-)$1	227	40	44	12.0000
ff&&	chr1:57174359-57174623(+)$1	264	98	102	12.0000
dd[d	chr5:132440358-132440609(+)$1	251	69	73	12.0000
DDYY	chr12:106459969-106460201(-)$1	232	203	207	12.0000
ffff	chr3:188594718-188594944(+)$1	226	115	119	12.0000
6666	chr11:123494711-123494929(+)$1	218	119	123	12.0000
ff$$	chr21:35470535-35470784(+)$1	249	33	37	12.0000
gggg	chr4:39779995-39780233(+)$1	238	197	201	12.0000
))))	chr7:140156521-140156741(-)$1	220	173	177	12.0000
DDDD	chr14:75515442-75515683(-)$1	241	143	147	12.0000
xxxx	chr22:35689904-35690164(+)$1	260	163	167	12.0000
b555	chr14:23780246-23780475(+)$1	229	79	83	12.0000
cmmm	chr1:153779983-153780206(-)$1	223	77	81	12.0000
CCCL	chr5:112177401-112177626(+)$1	225	39	43	12.0000
::::	chr1:115249072-115249397(-)$1	325	2	6	12.0000
MHHH	chr16:50830370-50830589(+)$1	219	62	66	12.0000
b]==	chr3:142777539-142777752(+)$1	213	148	152	12.0000
gggg	chr6:149826336-149826585(-)$1	249	59	63	12.0000

#DB
....	chr10:59953281-59953503(-)$1	1	1	5	12.0000
....	chr13:30778065-30778294(-)$1	1	29	33	12.0000
(((.	chr2:37075094-37075311(-)$1	1	6	10	12.0000
))))	chr8:97245290-97245512(-)$1	1	90	94	12.0000
).))	chr1:20236947-20237169(+)$1	1	64	68	12.0000
))..	chr1:218505387-218505618(+)$1	1	39	43	12.0000
..))	chr7:65420352-65420607(+)$1	1	201	205	12.0000
(...	chr1:27107402-27107620(+)$1	1	93	97	12.0000
((..	chr15:70386786-70387015(-)$1	1	30	34	12.0000
....	chr11:117038588-117038818(+)$1	1	14	18	12.0000
)...	chr11:65111174-65111396(+)$1	1	117	121	12.0000
.(.(	chr2:128044457-128044685(-)$1	1	98	102	12.0000
((((	chr5:159829204-159829427(-)$1	1	45	49	12.0000
))))	chrX:131510483-131510707(-)$1	1	182	186	12.0000
....	chr9:72999976-73000219(-)$1	1	97	101	12.0000
....	chr1:179075674-179075929(-)$1	1	99	103	12.0000
....	chr21:37758268-37758492(+)$1	1	135	139	12.0000
))..	chr11:73114940-73115158(-)$1	1	30	34	12.0000
((((	chr6:52962812-52963032(+)$1	1	60	64	12.0000
((..	chr13:95279512-95279736(+)$1	1	4	8	12.0000
))))	chr1:166821064-166821296(+)$1	1	43	47	12.0000
(...	chr1:173900769-173900997(-)$1	1	175	179	12.0000
))))	chr12:110734353-110734581(+)$1	1	50	54	12.0000
.(((	chr4:57799995-57800221(+)$1	1	4	8	12.0000
....	chr3:58310175-58310388(+)$1	1	133	137	12.0000
))..	chr12:54625312-54625562(-)$1	1	99	103	12.0000
(((.	chr22:20098618-20098840(+)$1	1	93	97	12.0000
.)))	chr4:48039373-48039591(+)$1	1	186	190	12.0000
((..	chr11:74550439-74550656(+)$1	1	72	76	12.0000
((..	chr1:33146305-33146515(+)$1	1	93	97	12.0000
))))	chr20:42091748-42092063(+)$1	1	302	306	12.0000
((((	chr8:68110963-68111182(-)$1	1	90	94	12.0000
))))	chr10:103567531-103567751(-)$1	1	213	217	12.0000
((..	chr14:61439280-61439504(-)$1	1	10	14	12.0000
((((	chr12:12795644-12795859(+)$1	1	64	68	12.0000
((..	chr1:204374073-204374356(-)$1	1	15	19	12.0000
((((	chr1:227845959-227846191(+)$1	1	45	49	12.0000
))).	chr3:142777220-142777448(+)$1	1	92	96	12.0000
((((	chr17:49039487-49039716(-)$1	1	3	7	12.0000
.)))	chr7:139247152-139247374(-)$1	1	140	144	12.0000
)).(	chr17:8279559-8279776(-)$1	1	124	128	12.0000
....	chr6:64404388-64404682(+)$1	1	98	102	12.0000
))))	chr18:9954227-9954447(+)$1	1	29	33	12.0000
))).	chr3:48674463-48674691(-)$1	1	77	81	12.0000
))))	chr10:857261-857496(-)$1	1	148	152	12.0000
((..	chr11:118267224-118267446(+)$1	1	81	85	12.0000
....	chr17:49040181-49040410(-)$1	1	188	192	12.0000
))))	chrX:103436983-103437211(+)$1	1	139	143	12.0000
((..	chr12:24969324-24969538(-)$1	1	18	22	12.0000
))..	chr14:61180384-61180611(-)$1	1	199	203	12.0000
(((.	chr16:20809045-20809257(-)$1	1	10	14	12.0000
))).	chr3:112722832-112723052(+)$1	1	102	106	12.0000
).))	chr21:19165628-19165852(-)$1	1	194	198	12.0000
...(	chr12:123351145-123351364(-)$1	1	83	87	12.0000
)(((	chr7:97922196-97922407(-)$1	1	59	63	12.0000
....	chr6:56358829-56359040(-)$1	1	92	96	12.0000
)...	chr20:42089622-42089891(+)$1	1	181	185	12.0000
....	chr1:210416086-210416307(+)$1	1	68	72	12.0000
((..	chrX:14938514-14938724(+)$1	1	89	93	12.0000
....	chr1:223983875-223984094(-)$1	1	3	7	12.0000
((((	chr1:168215133-168215369(+)$1	1	63	67	12.0000
....	chr2:149882567-149882797(+)$1	1	11	15	12.0000
....	chr17:29550450-29550663(+)$1	1	38	42	12.0000
....	chr21:35473470-35473710(+)$1	1	224	228	12.0000
....	chr7:27202615-27202828(-)$1	1	176	180	12.0000
(...	chr9:22002854-22003071(-)$1	1	41	45	12.0000
(...	chr12:124496214-124496623(+)$1	1	295	299	12.0000
))..	chr1:120163801-120164023(-)$1	1	208	212	12.0000
((((	chr18:13665750-13665977(-)$1	1	40	44	12.0000
((..	chr1:57174359-57174623(+)$1	1	98	102	12.0000
((.(	chr5:132440358-132440609(+)$1	1	69	73	12.0000
))..	chr12:106459969-106460201(-)$1	1	203	207	12.0000
((((	chr3:188594718-188594944(+)$1	1	115	119	12.0000
....	chr11:123494711-123494929(+)$1	1	119	123	12.0000
((..	chr21:35470535-35470784(+)$1	1	33	37	12.0000
))))	chr4:39779995-39780233(+)$1	1	197	201	12.0000
....	chr7:140156521-140156741(-)$1	1	173	177	12.0000
))))	chr14:75515442-75515683(-)$1	1	143	147	12.0000
....	chr22:35689904-35690164(+)$1	1	163	167	12.0000
)...	chr14:23780246-23780475(+)$1	1	79	83	12.0000
(...	chr1:153779983-153780206(-)$1	1	77	81	12.0000
(((.	chr5:112177401-112177626(+)$1	1	39	43	12.0000
....	chr1:115249072-115249397(-)$1	1	2	6	12.0000
.(((	chr16:50830370-50830589(+)$1	1	62	66	12.0000
).))	chr3:142777539-142777752(+)$1	1	148	152	12.0000
((((	chr6:149826336-149826585(-)$1	1	59	63	12.0000

#PSSM
G : 0.95	g : 0.04	
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m3_run1.nuc.txt

#NT
AAG	chr19:58453424-58453656(-)$1	232	3	6	8.9999
AAG	chr13:21721371-21721598(+)$1	227	23	26	8.9999
AAG	chrM:11097-11374(+)$1	277	213	216	8.9999
AAG	chr19:50003987-50004211(-)$1	224	22	25	8.9999
AAG	chr1:175956103-175956333(-)$1	230	95	98	8.9999
AAG	chrM:14564-14796(+)$1	232	40	43	8.9999
AAG	chr14:64989905-64990128(+)$1	223	3	6	8.9999
AAG	chr21:28210676-28210899(-)$1	223	15	18	8.9999
AAG	chr10:63851756-63851977(+)$1	221	92	95	8.9999
AAG	chr1:165712315-165712549(-)$1	234	23	26	8.9999
AAG	chr12:49086895-49087130(-)$1	235	55	58	8.9999
AAG	chr5:114859941-114860173(-)$1	232	25	28	8.9999
AAG	chr7:6731102-6731325(-)$1	223	13	16	8.9999
AAG	chr11:70229074-70229306(+)$1	232	83	86	8.9999
AAG	chr1:231411778-231412003(+)$1	225	8	11	8.9999
AAG	chr2:37517979-37518211(-)$1	232	66	69	8.9999
AAG	chr10:60128417-60128653(+)$1	236	77	80	8.9999
AAG	chr20:42825627-42825848(-)$1	221	44	47	8.9999
AAG	chr1:155316055-155316278(-)$1	223	89	92	8.9999
AAG	chr1:40705480-40705707(+)$1	227	17	20	8.9999
AAG	chr2:24483951-24484184(-)$1	233	17	20	8.9999
AAG	chr9:5921578-5921807(-)$1	229	3	6	8.9999
AAG	chr9:78808124-78808363(+)$1	239	25	28	8.9999
AAG	chr13:31232110-31232361(+)$1	251	30	33	8.9999
AAG	chrX:138879342-138879566(-)$1	224	1	4	8.9999
AAG	chr5:122724025-122724249(-)$1	224	6	9	8.9999
AAG	chr11:9459297-9459536(+)$1	239	22	25	8.9999
AAG	chr18:77893409-77893655(+)$1	246	0	3	8.9999
AAG	chr1:231509639-231509864(-)$1	225	90	93	8.9999
AAG	chr2:55479527-55479755(-)$1	228	131	134	8.9999
AAG	chr13:76432032-76432254(+)$1	222	50	53	8.9999
AAG	chr7:64292463-64292695(+)$1	232	12	15	8.9999
AAG	chr12:50847262-50847486(+)$1	224	13	16	8.9999
AAG	chr20:31025037-31025275(+)$1	238	9	12	8.9999
AAG	chr15:41672279-41672572(+)$1	293	13	16	8.9999
AAG	chr11:61188861-61189094(-)$1	233	94	97	8.9999
AAG	chr7:6441849-6442081(+)$1	232	1	4	8.9999
AAG	chr5:36183943-36184165(+)$1	222	7	10	8.9999
AAG	chr17:56082278-56082513(-)$1	235	69	72	8.9999
AAG	chr8:48752496-48752719(-)$1	223	9	12	8.9999
AAG	chr6:56919214-56919447(+)$1	233	7	10	8.9999
AAG	chr12:57652632-57652858(-)$1	226	147	150	8.9999
AAG	chr14:101349270-101349494(+)$1	224	9	12	8.9999
AAG	chr4:146576481-146576722(+)$1	241	30	33	8.9999
AAG	chr6:168311928-168312152(+)$1	224	38	41	8.9999
AAG	chr19:49657604-49657839(-)$1	235	9	12	8.9999
AAG	chrM:4326-4571(+)$1	245	75	78	8.9999
AAG	chr12:42853505-42853741(-)$1	236	86	89	8.9999
AAG	chr7:6730514-6730751(-)$1	237	12	15	8.9999
AAG	chr19:3976123-3976345(-)$1	222	126	129	8.9999
AAG	chr1:54678086-54678318(+)$1	232	7	10	8.9999
AAG	chr15:55474225-55474457(-)$1	232	1	4	8.9999
AAG	chr1:85790371-85790605(-)$1	234	130	133	8.9999
AAG	chr3:32754657-32754881(+)$1	224	61	64	8.9999
aaG	chr5:132203090-132203318(+)$1	228	5	8	8.9999
AAG	chr9:125672953-125673185(-)$1	232	7	10	8.9999
AAG	chr16:30681338-30681565(+)$1	227	8	11	8.9999
AAG	chr8:26227779-26228017(+)$1	238	2	5	8.9999
AAG	chr16:47733159-47733381(+)$1	222	21	24	8.9999
AAG	chr10:119044242-119044474(-)$1	232	17	20	8.9999
AAG	chr13:45007945-45008224(-)$1	279	88	91	8.9999
AAG	chr14:20825756-20826008(+)$1	252	70	73	8.9999
AAG	chrX:84526269-84526493(+)$1	224	32	35	8.9999
AAG	chr3:179051424-179051656(+)$1	232	3	6	8.9999
AAG	chr4:79844931-79845155(-)$1	224	21	24	8.9999
AAG	chr16:19518945-19519176(-)$1	231	90	93	8.9999
AAG	chr4:74277710-74277944(+)$1	234	34	37	8.9999
AAG	chr16:23646844-23647065(-)$1	221	1	4	8.9999
AAG	chr6:18226306-18226530(-)$1	224	92	95	8.9999
AAG	chr13:98043545-98043778(+)$1	233	69	72	8.9999
AAG	chrX:18264707-18264939(-)$1	232	13	16	8.9999
AAG	chr7:135612228-135612460(-)$1	232	35	38	8.9999
AAG	chr19:37210742-37210962(+)$1	220	12	15	8.9999
AAG	chr9:74489520-74489745(-)$1	225	166	169	8.9999
AAG	chr4:184930616-184930838(+)$1	222	19	22	8.9999
AAG	chr19:37210229-37210457(+)$1	228	59	62	8.9999
AAG	chr3:122133611-122133838(-)$1	227	216	219	8.9999
AAG	chr6:83863181-83863407(+)$1	226	90	93	8.9999
AAG	chr13:108881591-108881824(+)$1	233	10	13	8.9999
AAG	chr19:37618917-37619139(+)$1	222	72	75	8.9999
AAG	chr3:41280725-41280946(+)$1	221	122	125	8.9999
AAG	chr15:32929903-32930156(+)$1	253	55	58	8.9999
aag	chr14:24408825-24409062(-)$1	237	147	150	8.9999
AAG	chr12:104326060-104326294(+)$1	234	2	5	8.9999
AAG	chr8:25364803-25365036(+)$1	233	44	47	8.9999
AAG	chr1:109952484-109952709(-)$1	225	1	4	8.9999
AAG	chr20:35695536-35695757(-)$1	221	34	37	8.9999
AAG	chr1:214828487-214828713(+)$1	226	54	57	8.9999
AAG	chr18:77737561-77737785(-)$1	224	35	38	8.9999
AAG	chr4:77977001-77977228(-)$1	227	63	66	8.9999
AAG	chr15:34395323-34395566(+)$1	243	60	63	8.9999
AAG	chrX:23725860-23726096(-)$1	236	65	68	8.9999
AAG	chr1:242015494-242015740(+)$1	246	46	49	8.9999
AAG	chr19:38190281-38190502(-)$1	221	39	42	8.9999
AAG	chr22:46725152-46725378(+)$1	226	30	33	8.9999
AAG	chr12:120534657-120534878(-)$1	221	1	4	8.9999

#otherMatches

#Struct PSSM
!cc	chr10:38407622-38407845(+)$1	223	59	62	8.9999
:CC	chr19:58453424-58453656(-)$1	232	3	6	8.9999
bb[	chr13:21721371-21721598(+)$1	227	23	26	8.9999
^^^	chrM:11097-11374(+)$1	277	213	216	8.9999
pcc	chr19:50003987-50004211(-)$1	224	22	25	8.9999
dd2	chr1:175956103-175956333(-)$1	230	95	98	8.9999
::b	chrM:14564-14796(+)$1	232	40	43	8.9999
::e	chr14:64989905-64990128(+)$1	223	3	6	8.9999
qqf	chr21:28210676-28210899(-)$1	223	15	18	8.9999
#cc	chr10:63851756-63851977(+)$1	221	92	95	8.9999
:::	chr1:165712315-165712549(-)$1	234	23	26	8.9999
###	chr12:49086895-49087130(-)$1	235	55	58	8.9999
^^^	chr5:114859941-114860173(-)$1	232	25	28	8.9999
OOB	chr7:6731102-6731325(-)$1	223	13	16	8.9999
vvv	chr11:70229074-70229306(+)$1	232	83	86	8.9999
::d	chr1:231411778-231412003(+)$1	225	8	11	8.9999
ddd	chr2:37517979-37518211(-)$1	232	66	69	8.9999
===	chr10:60128417-60128653(+)$1	236	77	80	8.9999
22b	chr20:42825627-42825848(-)$1	221	44	47	8.9999
c22	chr1:155316055-155316278(-)$1	223	89	92	8.9999
:::	chr1:40705480-40705707(+)$1	227	17	20	8.9999
ddd	chr2:24483951-24484184(-)$1	233	17	20	8.9999
{FF	chr9:5921578-5921807(-)$1	229	3	6	8.9999
eee	chr9:78808124-78808363(+)$1	239	25	28	8.9999
iii	chr13:31232110-31232361(+)$1	251	30	33	8.9999
fff	chrX:138879342-138879566(-)$1	224	1	4	8.9999
::H	chr5:122724025-122724249(-)$1	224	6	9	8.9999
E::	chr11:9459297-9459536(+)$1	239	22	25	8.9999
III	chr18:77893409-77893655(+)$1	246	0	3	8.9999
d22	chr1:231509639-231509864(-)$1	225	90	93	8.9999
%%%	chr2:55479527-55479755(-)$1	228	131	134	8.9999
eee	chr13:76432032-76432254(+)$1	222	50	53	8.9999
:dd	chr7:64292463-64292695(+)$1	232	12	15	8.9999
::f	chr12:50847262-50847486(+)$1	224	13	16	8.9999
##b	chr20:31025037-31025275(+)$1	238	9	12	8.9999
e:D	chr15:41672279-41672572(+)$1	293	13	16	8.9999
55b	chr11:61188861-61189094(-)$1	233	94	97	8.9999
b!!	chr7:6441849-6442081(+)$1	232	1	4	8.9999
EEE	chr5:36183943-36184165(+)$1	222	7	10	8.9999
!!g	chr17:56082278-56082513(-)$1	235	69	72	8.9999
:::	chr8:48752496-48752719(-)$1	223	9	12	8.9999
::g	chr6:56919214-56919447(+)$1	233	7	10	8.9999
444	chr12:57652632-57652858(-)$1	226	147	150	8.9999
:II	chr14:101349270-101349494(+)$1	224	9	12	8.9999
::f	chr4:146576481-146576722(+)$1	241	30	33	8.9999
Edd	chr6:168311928-168312152(+)$1	224	38	41	8.9999
OOO	chr19:49657604-49657839(-)$1	235	9	12	8.9999
ooo	chrM:4326-4571(+)$1	245	75	78	8.9999
KKH	chr12:42853505-42853741(-)$1	236	86	89	8.9999
FFF	chr7:6730514-6730751(-)$1	237	12	15	8.9999
sss	chr19:3976123-3976345(-)$1	222	126	129	8.9999
FFF	chr1:54678086-54678318(+)$1	232	7	10	8.9999
:::	chr15:55474225-55474457(-)$1	232	1	4	8.9999
MCC	chr1:85790371-85790605(-)$1	234	130	133	8.9999
===	chr3:32754657-32754881(+)$1	224	61	64	8.9999
ggg	chr5:132203090-132203318(+)$1	228	5	8	8.9999
PPP	chr9:125672953-125673185(-)$1	232	7	10	8.9999
{GG	chr16:30681338-30681565(+)$1	227	8	11	8.9999
::D	chr8:26227779-26228017(+)$1	238	2	5	8.9999
bb!	chr16:47733159-47733381(+)$1	222	21	24	8.9999
:BB	chr10:119044242-119044474(-)$1	232	17	20	8.9999
555	chr13:45007945-45008224(-)$1	279	88	91	8.9999
BKK	chr14:20825756-20826008(+)$1	252	70	73	8.9999
FFF	chrX:84526269-84526493(+)$1	224	32	35	8.9999
HHH	chr3:179051424-179051656(+)$1	232	3	6	8.9999
DDD	chr4:79844931-79845155(-)$1	224	21	24	8.9999
fff	chr16:19518945-19519176(-)$1	231	90	93	8.9999
ddo	chr4:74277710-74277944(+)$1	234	34	37	8.9999
::E	chr16:23646844-23647065(-)$1	221	1	4	8.9999
eee	chr6:18226306-18226530(-)$1	224	92	95	8.9999
(((	chr13:98043545-98043778(+)$1	233	69	72	8.9999
G{C	chrX:18264707-18264939(-)$1	232	13	16	8.9999
eee	chr7:135612228-135612460(-)$1	232	35	38	8.9999
ddd	chr19:37210742-37210962(+)$1	220	12	15	8.9999
GGG	chr9:74489520-74489745(-)$1	225	166	169	8.9999
::D	chr4:184930616-184930838(+)$1	222	19	22	8.9999
nnn	chr19:37210229-37210457(+)$1	228	59	62	8.9999
:::	chr3:122133611-122133838(-)$1	227	216	219	8.9999
::H	chr6:83863181-83863407(+)$1	226	90	93	8.9999
dd[	chr13:108881591-108881824(+)$1	233	10	13	8.9999
ttt	chr19:37618917-37619139(+)$1	222	72	75	8.9999
444	chr3:41280725-41280946(+)$1	221	122	125	8.9999
:::	chr15:32929903-32930156(+)$1	253	55	58	8.9999
:FF	chr14:24408825-24409062(-)$1	237	147	150	8.9999
::E	chr12:104326060-104326294(+)$1	234	2	5	8.9999
LLL	chr8:25364803-25365036(+)$1	233	44	47	8.9999
eee	chr1:109952484-109952709(-)$1	225	1	4	8.9999
{DD	chr20:35695536-35695757(-)$1	221	34	37	8.9999
eee	chr1:214828487-214828713(+)$1	226	54	57	8.9999
fff	chr18:77737561-77737785(-)$1	224	35	38	8.9999
##d	chr4:77977001-77977228(-)$1	227	63	66	8.9999
QQE	chr15:34395323-34395566(+)$1	243	60	63	8.9999
33c	chrX:23725860-23726096(-)$1	236	65	68	8.9999
eee	chr1:242015494-242015740(+)$1	246	46	49	8.9999
mmm	chr19:38190281-38190502(-)$1	221	39	42	8.9999
lle	chr22:46725152-46725378(+)$1	226	30	33	8.9999
III	chr12:120534657-120534878(-)$1	221	1	4	8.9999

#DB
.((	chr10:38407622-38407845(+)$1	1	59	62	8.9999
.((	chr19:58453424-58453656(-)$1	1	3	6	8.9999
((.	chr13:21721371-21721598(+)$1	1	23	26	8.9999
...	chrM:11097-11374(+)$1	1	213	216	8.9999
.))	chr19:50003987-50004211(-)$1	1	22	25	8.9999
)).	chr1:175956103-175956333(-)$1	1	95	98	8.9999
..(	chrM:14564-14796(+)$1	1	40	43	8.9999
..(	chr14:64989905-64990128(+)$1	1	3	6	8.9999
..)	chr21:28210676-28210899(-)$1	1	15	18	8.9999
.((	chr10:63851756-63851977(+)$1	1	92	95	8.9999
...	chr1:165712315-165712549(-)$1	1	23	26	8.9999
...	chr12:49086895-49087130(-)$1	1	55	58	8.9999
...	chr5:114859941-114860173(-)$1	1	25	28	8.9999
..(	chr7:6731102-6731325(-)$1	1	13	16	8.9999
...	chr11:70229074-70229306(+)$1	1	83	86	8.9999
..(	chr1:231411778-231412003(+)$1	1	8	11	8.9999
)))	chr2:37517979-37518211(-)$1	1	66	69	8.9999
)))	chr10:60128417-60128653(+)$1	1	77	80	8.9999
..)	chr20:42825627-42825848(-)$1	1	44	47	8.9999
)..	chr1:155316055-155316278(-)$1	1	89	92	8.9999
...	chr1:40705480-40705707(+)$1	1	17	20	8.9999
(((	chr2:24483951-24484184(-)$1	1	17	20	8.9999
.((	chr9:5921578-5921807(-)$1	1	3	6	8.9999
(((	chr9:78808124-78808363(+)$1	1	25	28	8.9999
(((	chr13:31232110-31232361(+)$1	1	30	33	8.9999
(((	chrX:138879342-138879566(-)$1	1	1	4	8.9999
..(	chr5:122724025-122724249(-)$1	1	6	9	8.9999
(..	chr11:9459297-9459536(+)$1	1	22	25	8.9999
(((	chr18:77893409-77893655(+)$1	1	0	3	8.9999
)..	chr1:231509639-231509864(-)$1	1	90	93	8.9999
...	chr2:55479527-55479755(-)$1	1	131	134	8.9999
)))	chr13:76432032-76432254(+)$1	1	50	53	8.9999
.((	chr7:64292463-64292695(+)$1	1	12	15	8.9999
..(	chr12:50847262-50847486(+)$1	1	13	16	8.9999
..(	chr20:31025037-31025275(+)$1	1	9	12	8.9999
).(	chr15:41672279-41672572(+)$1	1	13	16	8.9999
..)	chr11:61188861-61189094(-)$1	1	94	97	8.9999
(..	chr7:6441849-6442081(+)$1	1	1	4	8.9999
(((	chr5:36183943-36184165(+)$1	1	7	10	8.9999
..(	chr17:56082278-56082513(-)$1	1	69	72	8.9999
...	chr8:48752496-48752719(-)$1	1	9	12	8.9999
..(	chr6:56919214-56919447(+)$1	1	7	10	8.9999
...	chr12:57652632-57652858(-)$1	1	147	150	8.9999
.((	chr14:101349270-101349494(+)$1	1	9	12	8.9999
..(	chr4:146576481-146576722(+)$1	1	30	33	8.9999
(((	chr6:168311928-168312152(+)$1	1	38	41	8.9999
...	chr19:49657604-49657839(-)$1	1	9	12	8.9999
...	chrM:4326-4571(+)$1	1	75	78	8.9999
..(	chr12:42853505-42853741(-)$1	1	86	89	8.9999
(((	chr7:6730514-6730751(-)$1	1	12	15	8.9999
...	chr19:3976123-3976345(-)$1	1	126	129	8.9999
(((	chr1:54678086-54678318(+)$1	1	7	10	8.9999
...	chr15:55474225-55474457(-)$1	1	1	4	8.9999
.((	chr1:85790371-85790605(-)$1	1	130	133	8.9999
)))	chr3:32754657-32754881(+)$1	1	61	64	8.9999
(((	chr5:132203090-132203318(+)$1	1	5	8	8.9999
...	chr9:125672953-125673185(-)$1	1	7	10	8.9999
.((	chr16:30681338-30681565(+)$1	1	8	11	8.9999
..(	chr8:26227779-26228017(+)$1	1	2	5	8.9999
((.	chr16:47733159-47733381(+)$1	1	21	24	8.9999
.((	chr10:119044242-119044474(-)$1	1	17	20	8.9999
...	chr13:45007945-45008224(-)$1	1	88	91	8.9999
(..	chr14:20825756-20826008(+)$1	1	70	73	8.9999
(((	chrX:84526269-84526493(+)$1	1	32	35	8.9999
(((	chr3:179051424-179051656(+)$1	1	3	6	8.9999
(((	chr4:79844931-79845155(-)$1	1	21	24	8.9999
)))	chr16:19518945-19519176(-)$1	1	90	93	8.9999
((.	chr4:74277710-74277944(+)$1	1	34	37	8.9999
..(	chr16:23646844-23647065(-)$1	1	1	4	8.9999
)))	chr6:18226306-18226530(-)$1	1	92	95	8.9999
...	chr13:98043545-98043778(+)$1	1	69	72	8.9999
(.(	chrX:18264707-18264939(-)$1	1	13	16	8.9999
(((	chr7:135612228-135612460(-)$1	1	35	38	8.9999
)))	chr19:37210742-37210962(+)$1	1	12	15	8.9999
)))	chr9:74489520-74489745(-)$1	1	166	169	8.9999
..(	chr4:184930616-184930838(+)$1	1	19	22	8.9999
...	chr19:37210229-37210457(+)$1	1	59	62	8.9999
...	chr3:122133611-122133838(-)$1	1	216	219	8.9999
..(	chr6:83863181-83863407(+)$1	1	90	93	8.9999
((.	chr13:108881591-108881824(+)$1	1	10	13	8.9999
...	chr19:37618917-37619139(+)$1	1	72	75	8.9999
...	chr3:41280725-41280946(+)$1	1	122	125	8.9999
...	chr15:32929903-32930156(+)$1	1	55	58	8.9999
.((	chr14:24408825-24409062(-)$1	1	147	150	8.9999
..(	chr12:104326060-104326294(+)$1	1	2	5	8.9999
...	chr8:25364803-25365036(+)$1	1	44	47	8.9999
(((	chr1:109952484-109952709(-)$1	1	1	4	8.9999
.((	chr20:35695536-35695757(-)$1	1	34	37	8.9999
(((	chr1:214828487-214828713(+)$1	1	54	57	8.9999
)))	chr18:77737561-77737785(-)$1	1	35	38	8.9999
..(	chr4:77977001-77977228(-)$1	1	63	66	8.9999
..(	chr15:34395323-34395566(+)$1	1	60	63	8.9999
..)	chrX:23725860-23726096(-)$1	1	65	68	8.9999
)))	chr1:242015494-242015740(+)$1	1	46	49	8.9999
...	chr19:38190281-38190502(-)$1	1	39	42	8.9999
..)	chr22:46725152-46725378(+)$1	1	30	33	8.9999
(((	chr12:120534657-120534878(-)$1	1	1	4	8.9999

#PSSM
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
G : 0.98	g : 0.01	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m3_run2.nuc.txt

#NT
AAAAAUAGUAUA	chr21:30378428-30378652(-)$1	224	41	53	16.9000
AAAAAUAAAAUA	chr1:155708037-155708359(+)$1	322	261	273	24.5000
GAAAUGAAAAUA	chr2:99813394-99813636(+)$1	242	49	61	14.9000
UAAAACAGAAUA	chr19:34719994-34720249(+)$1	255	169	181	15.0000
AAAAAUAAAACU	chr5:140024912-140025139(-)$1	227	157	169	18.2000
AUAACUAAAAUA	chr1:68167884-68168123(-)$1	239	80	92	16.2000
AAAAAUAAAUAA	chr1:203839407-203839632(+)$1	225	10	22	19.2000
AAAAAGAACAGA	chr15:78841070-78841321(+)$1	251	187	199	17.2000
AAAAAGAAAAAA	chr7:156797605-156797898(-)$1	293	138	150	21.3000
UGAAAUAAAAUA	chr17:36920295-36920554(+)$1	259	159	171	17.3000
AAAAAAAAAAAA	chr7:27868436-27868687(+)$1	251	47	59	21.6000
AAAAAUACAAGA	chr19:47653371-47653601(+)$1	230	47	59	20.0000
AGAAUUAAAAUA	chr7:141450074-141450356(+)$1	282	160	172	16.8000
AGAAAUAUAAUA	chr10:94111065-94111307(+)$1	242	17	29	17.7000
AAAAUUAAAACA	chr7:155255591-155255821(+)$1	230	135	147	18.3000
AAAAAAAAAAGA	chr6:149912507-149912740(+)$1	233	37	49	21.5000
aaaaaaaaaaaa	chr22:40719568-40719821(+)$1	253	222	234	21.6000
AAAAAAAAAAAA	chr12:54627992-54628239(-)$1	247	185	197	21.6000
AAAAAAACAAGA	chr2:122493159-122493386(-)$1	227	62	74	18.3000
GGAAAUAAAAUA	chr12:46753908-46754174(-)$1	266	142	154	17.4000
UAAAAGAAAAUA	chr9:97222929-97223156(+)$1	227	151	163	18.9000
AAACAUACAAAA	chr10:120927172-120927437(-)$1	265	176	188	15.5000
AAAAAUACAGGA	chr1:205685451-205685871(-)$1	420	214	226	15.8000
AAGAAUAGAAAA	chr14:57877066-57877318(+)$1	252	70	82	15.7000
AAAAAUUaaaaa	chr1:167385317-167385560(+)$1	243	0	12	19.0000
AAGAACAAAAUA	chr7:92086897-92087164(+)$1	267	70	82	17.8000
AAAAAGAAAAUC	chr19:4047638-4047863(-)$1	225	200	212	18.3000
AGAAAUAUAAUA	chr13:100638729-100639018(+)$1	289	260	272	17.7000
UAAAAUAAACUA	chr5:167982693-167982914(-)$1	221	102	114	16.6000
AAACAUUAAACA	chr21:33040815-33041126(+)$1	311	149	161	13.5000
AAAAAGAAAAGA	chr16:18804478-18804715(-)$1	237	119	131	21.2000
AAAAAUAUGAGA	chr1:183596078-183596302(-)$1	224	58	70	16.0000
AACAAAAAAAGA	chr14:96010799-96011042(+)$1	243	66	78	17.2000
AAAAGAAAAAGA	chr12:112845993-112846233(-)$1	240	95	107	17.3000
AAGAAAAAGAUA	chr12:54628747-54629068(-)$1	321	122	134	14.6000
GAAAAUCUAAUA	chr5:142659749-142660007(-)$1	258	36	48	13.3000
AAAAAUAACAUG	chrX:15338251-15338502(-)$1	251	222	234	16.3000
AAAAAUAAAGUA	chr6:111697302-111697526(-)$1	224	114	126	20.3000
AAAAAUACCAAA	chr17:5336095-5336345(-)$1	250	125	137	16.1000
GAAAAAAAAAUC	chr13:28519447-28519668(+)$1	221	197	209	15.1000
AAAAAAAAAAAA	chr3:107526364-107526616(+)$1	252	193	205	21.6000
AGAAGUAAAAUA	chr18:13666290-13666546(-)$1	256	193	205	16.7000
AAAAAUAAAAGU	chr15:71174054-71174284(-)$1	230	206	218	19.0000
CACAAUAAAAUA	chr5:71505197-71505438(+)$1	241	169	181	16.3000
AUAAACAUAAUA	chr22:42479200-42479437(+)$1	237	138	150	14.8000
GAAAAUAAAUUA	chr6:44081283-44081562(-)$1	279	162	174	16.9000
AAAAAGAAAAGG	chr9:134371845-134372073(+)$1	228	64	76	17.0000
AAAAAGUAGAUA	chr15:52843245-52843515(-)$1	270	161	173	14.2000
AAAAAUAAAUAA	chr12:14939382-14939612(-)$1	230	175	187	19.2000

#otherMatches

#Struct PSSM
HHHHHHHZZZDD	chr14:100744281-100744506(+)$1	225	189	201	21.6000
:::::::ccc##	chr21:30378428-30378652(-)$1	224	41	53	16.9000
:::::dddd"""	chr1:155708037-155708359(+)$1	322	261	273	24.5000
GGGGGG::::::	chr2:99813394-99813636(+)$1	242	49	61	14.9000
""iiiiiiiii"	chr19:34719994-34720249(+)$1	255	169	181	15.0000
mmmmccc55555	chr5:140024912-140025139(-)$1	227	157	169	18.2000
333eeeee:GGG	chr1:68167884-68168123(-)$1	239	80	92	16.2000
hh!!ddddbbdd	chr1:203839407-203839632(+)$1	225	10	22	19.2000
::::::::::::	chr15:78841070-78841321(+)$1	251	187	199	17.2000
333ccc::::::	chr7:156797605-156797898(-)$1	293	138	150	21.3000
pdddd]dddd22	chr17:36920295-36920554(+)$1	259	159	171	17.3000
::::::::::::	chr7:27868436-27868687(+)$1	251	47	59	21.6000
d!!dddd!!a[b	chr19:47653371-47653601(+)$1	230	47	59	20.0000
ddd[ccc"""ee	chr7:141450074-141450356(+)$1	282	160	172	16.8000
mhhhhhhhh444	chr10:94111065-94111307(+)$1	242	17	29	17.7000
hhhhhh%%%%%%	chr7:155255591-155255821(+)$1	230	135	147	18.3000
^^^^^^^^^^^^	chr6:149912507-149912740(+)$1	233	37	49	21.5000
vvvvvvvvvvvv	chr22:40719568-40719821(+)$1	253	222	234	21.6000
c+++++++++++	chr12:54627992-54628239(-)$1	247	185	197	21.6000
:::::::FFFFF	chr2:122493159-122493386(-)$1	227	62	74	18.3000
b####ffffffn	chr12:46753908-46754174(-)$1	266	142	154	17.4000
JJJJJJJJJJ__	chr9:97222929-97223156(+)$1	227	151	163	18.9000
nnnnneeeee::	chr10:120927172-120927437(-)$1	265	176	188	15.5000
MMFFFFFFCCC{	chr1:205685451-205685871(-)$1	420	214	226	15.8000
neeeee::::::	chr14:57877066-57877318(+)$1	252	70	82	15.7000
::::::::::::	chr1:167385317-167385560(+)$1	243	0	12	19.0000
3dddd22eeeee	chr7:92086897-92087164(+)$1	267	70	82	17.8000
^^^^^^^^^^cc	chr19:4047638-4047863(-)$1	225	200	212	18.3000
ffffff666666	chr13:100638729-100639018(+)$1	289	260	272	17.7000
nniiiiiiiiiF	chr5:167982693-167982914(-)$1	221	102	114	16.6000
::ccc####eee	chr21:33040815-33041126(+)$1	311	149	161	13.5000
::::::::::::	chr16:18804478-18804715(-)$1	237	119	131	21.2000
nnffffff]a44	chr1:183596078-183596302(-)$1	224	58	70	16.0000
::::::::::::	chr14:96010799-96011042(+)$1	243	66	78	17.2000
cc22a22bb22d	chr12:112845993-112846233(-)$1	240	95	107	17.3000
EEE______DDD	chr12:54628747-54629068(-)$1	321	122	134	14.6000
ffff!!dddd""	chr5:142659749-142660007(-)$1	258	36	48	13.3000
:::::::::::c	chrX:15338251-15338502(-)$1	251	222	234	16.3000
::::::::::::	chr6:111697302-111697526(-)$1	224	114	126	20.3000
%%%%%%dddd++	chr17:5336095-5336345(-)$1	250	125	137	16.1000
::::::::::::	chr13:28519447-28519668(+)$1	221	197	209	15.1000
pppppppggggg	chr3:107526364-107526616(+)$1	252	193	205	21.6000
==::DDDDYYFF	chr18:13666290-13666546(-)$1	256	193	205	16.7000
::::::::::::	chr15:71174054-71174284(-)$1	230	206	218	19.0000
eeeee&&&&&&&	chr5:71505197-71505438(+)$1	241	169	181	16.3000
oooooffffff>	chr22:42479200-42479437(+)$1	237	138	150	14.8000
=======:IIII	chr6:44081283-44081562(-)$1	279	162	174	16.9000
ssssssssssa]	chr9:134371845-134372073(+)$1	228	64	76	17.0000
:::::dddd###	chr15:52843245-52843515(-)$1	270	161	173	14.2000
gwwwwwwwwwww	chr12:14939382-14939612(-)$1	230	175	187	19.2000

#DB
)))))))...))	chr14:100744281-100744506(+)$1	1	189	201	21.6000
.......(((..	chr21:30378428-30378652(-)$1	1	41	53	16.9000
.....((((...	chr1:155708037-155708359(+)$1	1	261	273	24.5000
((((((......	chr2:99813394-99813636(+)$1	1	49	61	14.9000
..(((((((((.	chr19:34719994-34720249(+)$1	1	169	181	15.0000
....))).....	chr5:140024912-140025139(-)$1	1	157	169	18.2000
...))))).(((	chr1:68167884-68168123(-)$1	1	80	92	16.2000
((..((((((((	chr1:203839407-203839632(+)$1	1	10	22	19.2000
............	chr15:78841070-78841321(+)$1	1	187	199	17.2000
...)))......	chr7:156797605-156797898(-)$1	1	138	150	21.3000
.)))).))))..	chr17:36920295-36920554(+)$1	1	159	171	17.3000
............	chr7:27868436-27868687(+)$1	1	47	59	21.6000
(..((((..(.(	chr19:47653371-47653601(+)$1	1	47	59	20.0000
(((.(((...((	chr7:141450074-141450356(+)$1	1	160	172	16.8000
.))))))))...	chr10:94111065-94111307(+)$1	1	17	29	17.7000
((((((......	chr7:155255591-155255821(+)$1	1	135	147	18.3000
............	chr6:149912507-149912740(+)$1	1	37	49	21.5000
............	chr22:40719568-40719821(+)$1	1	222	234	21.6000
(...........	chr12:54627992-54628239(-)$1	1	185	197	21.6000
.......(((((	chr2:122493159-122493386(-)$1	1	62	74	18.3000
(....((((((.	chr12:46753908-46754174(-)$1	1	142	154	17.4000
))))))))))..	chr9:97222929-97223156(+)$1	1	151	163	18.9000
.....)))))..	chr10:120927172-120927437(-)$1	1	176	188	15.5000
..(((((((((.	chr1:205685451-205685871(-)$1	1	214	226	15.8000
.)))))......	chr14:57877066-57877318(+)$1	1	70	82	15.7000
............	chr1:167385317-167385560(+)$1	1	0	12	19.0000
.))))..)))))	chr7:92086897-92087164(+)$1	1	70	82	17.8000
..........))	chr19:4047638-4047863(-)$1	1	200	212	18.3000
))))))......	chr13:100638729-100639018(+)$1	1	260	272	17.7000
..))))))))))	chr5:167982693-167982914(-)$1	1	102	114	16.6000
..(((....(((	chr21:33040815-33041126(+)$1	1	149	161	13.5000
............	chr16:18804478-18804715(-)$1	1	119	131	21.2000
..)))))).)..	chr1:183596078-183596302(-)$1	1	58	70	16.0000
............	chr14:96010799-96011042(+)$1	1	66	78	17.2000
))..)..))..)	chr12:112845993-112846233(-)$1	1	95	107	17.3000
)))......)))	chr12:54628747-54629068(-)$1	1	122	134	14.6000
((((..((((..	chr5:142659749-142660007(-)$1	1	36	48	13.3000
...........(	chrX:15338251-15338502(-)$1	1	222	234	16.3000
............	chr6:111697302-111697526(-)$1	1	114	126	20.3000
......((((..	chr17:5336095-5336345(-)$1	1	125	137	16.1000
............	chr13:28519447-28519668(+)$1	1	197	209	15.1000
.......)))))	chr3:107526364-107526616(+)$1	1	193	205	21.6000
))..))))..))	chr18:13666290-13666546(-)$1	1	193	205	16.7000
............	chr15:71174054-71174284(-)$1	1	206	218	19.0000
(((((.......	chr5:71505197-71505438(+)$1	1	169	181	16.3000
.....)))))).	chr22:42479200-42479437(+)$1	1	138	150	14.8000
))))))).))))	chr6:44081283-44081562(-)$1	1	162	174	16.9000
..........).	chr9:134371845-134372073(+)$1	1	64	76	17.0000
.....((((...	chr15:52843245-52843515(-)$1	1	161	173	14.2000
(...........	chr12:14939382-14939612(-)$1	1	175	187	19.2000

#PSSM
A : 0.78	G : 0.10	U : 0.08	a : 0.02	C : 0.02	
A : 0.82	G : 0.12	U : 0.04	a : 0.02	
A : 0.88	G : 0.06	C : 0.04	a : 0.02	
A : 0.94	C : 0.04	a : 0.02	
A : 0.86	U : 0.06	G : 0.04	C : 0.02	a : 0.02	
U : 0.56	A : 0.19	G : 0.16	C : 0.06	a : 0.02	
A : 0.90	U : 0.06	a : 0.02	C : 0.02	
A : 0.70	C : 0.10	U : 0.10	G : 0.06	a : 0.04	
A : 0.82	C : 0.06	G : 0.06	a : 0.04	U : 0.02	
A : 0.84	U : 0.06	a : 0.04	G : 0.04	C : 0.02	
U : 0.48	G : 0.21	A : 0.19	C : 0.06	a : 0.04	
A : 0.84	U : 0.04	a : 0.04	C : 0.04	G : 0.04	

#score	889.0000000000013
#seq	50
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m1_run1.nuc.txt

#NT
GAA	chr8:67485537-67485738(-)$1	201	21	24	9.0000
GAA	chr6:138733925-138734126(+)$1	201	121	124	9.0000
GAA	chr14:105920478-105920679(+)$1	201	89	92	9.0000
GAA	chr15:51828365-51828566(-)$1	201	12	15	9.0000
GAA	chr5:64082261-64082462(+)$1	201	14	17	9.0000
GAA	chr1:156721046-156721247(-)$1	201	46	49	9.0000
GAA	chr8:48885444-48885645(+)$1	201	9	12	9.0000
GAA	chr4:83784402-83784603(-)$1	201	36	39	9.0000
GAA	chr15:64419834-64420035(+)$1	201	5	8	9.0000
GAA	chr2:223499061-223499262(-)$1	201	2	5	9.0000
GAA	chr2:183866797-183866998(-)$1	201	24	27	9.0000
GAA	chr9:121393-121594(-)$1	201	24	27	9.0000
GAA	chr12:133372584-133372785(-)$1	201	47	50	9.0000
GAA	chr5:89949597-89949798(+)$1	201	41	44	9.0000
GAA	chr16:57250797-57250998(+)$1	201	20	23	9.0000
GAA	chr2:179410048-179410249(+)$1	201	4	7	9.0000
GAA	chr3:142122483-142122684(-)$1	201	18	21	9.0000
GAA	chr5:16758169-16758370(-)$1	201	60	63	9.0000
GAA	chr2:197595515-197595716(+)$1	201	5	8	9.0000
GAA	chr16:28883902-28884103(+)$1	201	169	172	9.0000
GAA	chr10:103281347-103281548(+)$1	201	95	98	9.0000
GAA	chr2:38812888-38813089(-)$1	201	22	25	9.0000
GAA	chr12:44176113-44176314(+)$1	201	15	18	9.0000
GAA	chr10:116606821-116607022(+)$1	201	34	37	9.0000
GAA	chr2:160076210-160076411(+)$1	201	50	53	9.0000
GAA	chr8:145164927-145165128(+)$1	201	4	7	9.0000
GAA	chr17:35627552-35627753(-)$1	201	10	13	9.0000
gaa	chr20:62896845-62897046(+)$1	201	46	49	9.0000
GAA	chr16:248996-249197(-)$1	201	118	121	9.0000
GAA	chr4:82361968-82362169(-)$1	201	36	39	9.0000
GAA	chr13:52598550-52598751(+)$1	201	122	125	9.0000
GAA	chr20:32265244-32265445(-)$1	201	63	66	9.0000
GAA	chr16:30972675-30972876(+)$1	201	26	29	9.0000
GAA	chr22:24133936-24134137(+)$1	201	10	13	9.0000
GAA	chr14:105929465-105929666(+)$1	201	63	66	9.0000
GAA	chr5:68425258-68425459(+)$1	201	22	25	9.0000
GAA	chr12:123095326-123095527(+)$1	201	86	89	9.0000
GAA	chr6:88318798-88318999(+)$1	201	14	17	9.0000
GAA	chr7:156685548-156685749(-)$1	201	54	57	9.0000
GAA	chr2:54853154-54853355(+)$1	201	45	48	9.0000
GAA	chr17:17179341-17179542(-)$1	201	33	36	9.0000
GAA	chr14:77925993-77926194(+)$1	201	4	7	9.0000
GAA	chr12:102547608-102547809(+)$1	201	86	89	9.0000
GAA	chr2:197654591-197654792(-)$1	201	60	63	9.0000
GAA	chr14:35255286-35255487(-)$1	201	35	38	9.0000
GAA	chr3:127788295-127788496(+)$1	201	109	112	9.0000
gaa	chr12:56999563-56999764(-)$1	201	1	4	9.0000
GAA	chr18:18546833-18547034(-)$1	201	6	9	9.0000
GAA	chr10:103908918-103909119(+)$1	201	132	135	9.0000
GAA	chrX:48791984-48792185(-)$1	201	47	50	9.0000
GAA	chr17:49337870-49338071(+)$1	201	97	100	9.0000
GAA	chr3:87298949-87299150(+)$1	201	42	45	9.0000
GAA	chr15:99251167-99251368(+)$1	201	41	44	9.0000
GAA	chr12:27841889-27842090(+)$1	201	82	85	9.0000
GAA	chr5:71500886-71501087(+)$1	201	51	54	9.0000
GAA	chr17:80045208-80045409(-)$1	201	51	54	9.0000
GAA	chr5:134010237-134010438(+)$1	201	41	44	9.0000
GAA	chr16:419061-419262(-)$1	201	2	5	9.0000
GAA	chr16:29822251-29822452(+)$1	201	37	40	9.0000
gaa	chr12:6878931-6879132(+)$1	201	163	166	9.0000
GAA	chr5:64892164-64892365(-)$1	201	18	21	9.0000
GAA	chr6:83834350-83834551(+)$1	201	56	59	9.0000
GAA	chr1:151378705-151378906(-)$1	201	5	8	9.0000
GAA	chr1:113460437-113460638(-)$1	201	137	140	9.0000
GAA	chr2:15674605-15674806(-)$1	201	46	49	9.0000
GAA	chr15:44892704-44892905(-)$1	201	21	24	9.0000
GAA	chr4:48569224-48569425(-)$1	201	10	13	9.0000
GAA	chr16:75338879-75339080(-)$1	201	36	39	9.0000
GAA	chr14:92623926-92624127(+)$1	201	32	35	9.0000
GAA	chr16:30731453-30731654(+)$1	201	65	68	9.0000
GAA	chr14:90770340-90770541(-)$1	201	25	28	9.0000
GAA	chr16:2135194-2135395(+)$1	201	120	123	9.0000
GAA	chr22:50684011-50684212(-)$1	201	96	99	9.0000
GAA	chr17:16029415-16029616(-)$1	201	65	68	9.0000
GAA	chr22:24175753-24175954(+)$1	201	8	11	9.0000
GAA	chr11:95582780-95582981(-)$1	201	28	31	9.0000
GAA	chr1:146763110-146763311(+)$1	201	10	13	9.0000
GAA	chr18:76856404-76856605(+)$1	201	10	13	9.0000
GAA	chr1:110888111-110888312(+)$1	201	12	15	9.0000
GAA	chr8:21844565-21844766(+)$1	201	62	65	9.0000
GAA	chr3:49343160-49343361(-)$1	201	4	7	9.0000
GAA	chr6:160482507-160482708(+)$1	201	36	39	9.0000
GAA	chr15:90986554-90986755(+)$1	201	74	77	9.0000
GAA	chr11:59367879-59368080(-)$1	201	10	13	9.0000
GAA	chr7:102952410-102952611(+)$1	201	66	69	9.0000
GAA	chr17:7149272-7149473(-)$1	201	137	140	9.0000
GAA	chr4:129782866-129783067(+)$1	201	0	3	9.0000
GAA	chr15:52510716-52510917(-)$1	201	40	43	9.0000
GAA	chr1:61553967-61554168(+)$1	201	0	3	9.0000
GAA	chr11:65826214-65826415(+)$1	201	4	7	9.0000
GAA	chr3:127335779-127335980(+)$1	201	19	22	9.0000
GAA	chr14:104173423-104173624(-)$1	201	91	94	9.0000
GAA	chr2:38975670-38975871(-)$1	201	67	70	9.0000
GAA	chr3:9786593-9786794(+)$1	201	4	7	9.0000
GAA	chr2:97297062-97297263(-)$1	201	2	5	9.0000
GAA	chr5:140908672-140908873(-)$1	201	32	35	9.0000
GAA	chr12:67701100-67701301(+)$1	201	91	94	9.0000
GAA	chr8:23112766-23112967(+)$1	201	25	28	9.0000
GAA	chr6:26388284-26388485(+)$1	201	92	95	9.0000

#otherMatches

#Struct PSSM
:::	chr14:64545098-64545299(+)$1	201	23	26	9.0000
CCD	chr8:67485537-67485738(-)$1	201	21	24	9.0000
fuu	chr6:138733925-138734126(+)$1	201	121	124	9.0000
foo	chr14:105920478-105920679(+)$1	201	89	92	9.0000
EEE	chr15:51828365-51828566(-)$1	201	12	15	9.0000
sss	chr5:64082261-64082462(+)$1	201	14	17	9.0000
d!!	chr1:156721046-156721247(-)$1	201	46	49	9.0000
MMM	chr8:48885444-48885645(+)$1	201	9	12	9.0000
DD{	chr4:83784402-83784603(-)$1	201	36	39	9.0000
e%%	chr15:64419834-64420035(+)$1	201	5	8	9.0000
:::	chr2:223499061-223499262(-)$1	201	2	5	9.0000
BOO	chr2:183866797-183866998(-)$1	201	24	27	9.0000
:::	chr9:121393-121594(-)$1	201	24	27	9.0000
OOO	chr12:133372584-133372785(-)$1	201	47	50	9.0000
bhh	chr5:89949597-89949798(+)$1	201	41	44	9.0000
[bb	chr16:57250797-57250998(+)$1	201	20	23	9.0000
BB:	chr2:179410048-179410249(+)$1	201	4	7	9.0000
iii	chr3:142122483-142122684(-)$1	201	18	21	9.0000
cc:	chr5:16758169-16758370(-)$1	201	60	63	9.0000
EEE	chr2:197595515-197595716(+)$1	201	5	8	9.0000
FFF	chr16:28883902-28884103(+)$1	201	169	172	9.0000
b22	chr10:103281347-103281548(+)$1	201	95	98	9.0000
D:c	chr2:38812888-38813089(-)$1	201	22	25	9.0000
III	chr12:44176113-44176314(+)$1	201	15	18	9.0000
ooo	chr10:116606821-116607022(+)$1	201	34	37	9.0000
:::	chr2:160076210-160076411(+)$1	201	50	53	9.0000
:::	chr8:145164927-145165128(+)$1	201	4	7	9.0000
f""	chr17:35627552-35627753(-)$1	201	10	13	9.0000
fff	chr20:62896845-62897046(+)$1	201	46	49	9.0000
a]f	chr16:248996-249197(-)$1	201	118	121	9.0000
hhh	chr4:82361968-82362169(-)$1	201	36	39	9.0000
ddd	chr13:52598550-52598751(+)$1	201	122	125	9.0000
rrr	chr20:32265244-32265445(-)$1	201	63	66	9.0000
ff[	chr16:30972675-30972876(+)$1	201	26	29	9.0000
ddd	chr22:24133936-24134137(+)$1	201	10	13	9.0000
d22	chr14:105929465-105929666(+)$1	201	63	66	9.0000
^^^	chr5:68425258-68425459(+)$1	201	22	25	9.0000
E{C	chr12:123095326-123095527(+)$1	201	86	89	9.0000
eee	chr6:88318798-88318999(+)$1	201	14	17	9.0000
i!!	chr7:156685548-156685749(-)$1	201	54	57	9.0000
a22	chr2:54853154-54853355(+)$1	201	45	48	9.0000
ooo	chr17:17179341-17179542(-)$1	201	33	36	9.0000
:GG	chr14:77925993-77926194(+)$1	201	4	7	9.0000
g$$	chr12:102547608-102547809(+)$1	201	86	89	9.0000
bbm	chr2:197654591-197654792(-)$1	201	60	63	9.0000
ggg	chr14:35255286-35255487(-)$1	201	35	38	9.0000
ddd	chr3:127788295-127788496(+)$1	201	109	112	9.0000
:::	chr12:56999563-56999764(-)$1	201	1	4	9.0000
BBM	chr18:18546833-18547034(-)$1	201	6	9	9.0000
]gg	chr10:103908918-103909119(+)$1	201	132	135	9.0000
fff	chrX:48791984-48792185(-)$1	201	47	50	9.0000
:::	chr17:49337870-49338071(+)$1	201	97	100	9.0000
:::	chr3:87298949-87299150(+)$1	201	42	45	9.0000
dpp	chr15:99251167-99251368(+)$1	201	41	44	9.0000
eee	chr12:27841889-27842090(+)$1	201	82	85	9.0000
mmc	chr5:71500886-71501087(+)$1	201	51	54	9.0000
)))	chr17:80045208-80045409(-)$1	201	51	54	9.0000
$dd	chr5:134010237-134010438(+)$1	201	41	44	9.0000
c""	chr16:419061-419262(-)$1	201	2	5	9.0000
ff[	chr16:29822251-29822452(+)$1	201	37	40	9.0000
d:H	chr12:6878931-6879132(+)$1	201	163	166	9.0000
JJJ	chr5:64892164-64892365(-)$1	201	18	21	9.0000
e::	chr6:83834350-83834551(+)$1	201	56	59	9.0000
c!!	chr1:151378705-151378906(-)$1	201	5	8	9.0000
ggg	chr1:113460437-113460638(-)$1	201	137	140	9.0000
iii	chr2:15674605-15674806(-)$1	201	46	49	9.0000
:::	chr15:44892704-44892905(-)$1	201	21	24	9.0000
J::	chr4:48569224-48569425(-)$1	201	10	13	9.0000
c44	chr16:75338879-75339080(-)$1	201	36	39	9.0000
ooo	chr14:92623926-92624127(+)$1	201	32	35	9.0000
:::	chr16:30731453-30731654(+)$1	201	65	68	9.0000
hhh	chr14:90770340-90770541(-)$1	201	25	28	9.0000
bb:	chr16:2135194-2135395(+)$1	201	120	123	9.0000
[bb	chr22:50684011-50684212(-)$1	201	96	99	9.0000
fff	chr17:16029415-16029616(-)$1	201	65	68	9.0000
:::	chr22:24175753-24175954(+)$1	201	8	11	9.0000
eee	chr11:95582780-95582981(-)$1	201	28	31	9.0000
DDE	chr1:146763110-146763311(+)$1	201	10	13	9.0000
BPP	chr18:76856404-76856605(+)$1	201	10	13	9.0000
ff&	chr1:110888111-110888312(+)$1	201	12	15	9.0000
]dd	chr8:21844565-21844766(+)$1	201	62	65	9.0000
eee	chr3:49343160-49343361(-)$1	201	4	7	9.0000
fff	chr6:160482507-160482708(+)$1	201	36	39	9.0000
qqq	chr15:90986554-90986755(+)$1	201	74	77	9.0000
CMM	chr11:59367879-59368080(-)$1	201	10	13	9.0000
ddd	chr7:102952410-102952611(+)$1	201	66	69	9.0000
III	chr17:7149272-7149473(-)$1	201	137	140	9.0000
:::	chr4:129782866-129783067(+)$1	201	0	3	9.0000
ppp	chr15:52510716-52510917(-)$1	201	40	43	9.0000
:::	chr1:61553967-61554168(+)$1	201	0	3	9.0000
D::	chr11:65826214-65826415(+)$1	201	4	7	9.0000
hhh	chr3:127335779-127335980(+)$1	201	19	22	9.0000
d::	chr14:104173423-104173624(-)$1	201	91	94	9.0000
fff	chr2:38975670-38975871(-)$1	201	67	70	9.0000
FFF	chr3:9786593-9786794(+)$1	201	4	7	9.0000
:::	chr2:97297062-97297263(-)$1	201	2	5	9.0000
I::	chr5:140908672-140908873(-)$1	201	32	35	9.0000
a[d	chr12:67701100-67701301(+)$1	201	91	94	9.0000
:::	chr8:23112766-23112967(+)$1	201	25	28	9.0000
44c	chr6:26388284-26388485(+)$1	201	92	95	9.0000

#DB
...	chr14:64545098-64545299(+)$1	1	23	26	9.0000
(((	chr8:67485537-67485738(-)$1	1	21	24	9.0000
(..	chr6:138733925-138734126(+)$1	1	121	124	9.0000
(..	chr14:105920478-105920679(+)$1	1	89	92	9.0000
(((	chr15:51828365-51828566(-)$1	1	12	15	9.0000
...	chr5:64082261-64082462(+)$1	1	14	17	9.0000
(..	chr1:156721046-156721247(-)$1	1	46	49	9.0000
...	chr8:48885444-48885645(+)$1	1	9	12	9.0000
((.	chr4:83784402-83784603(-)$1	1	36	39	9.0000
(..	chr15:64419834-64420035(+)$1	1	5	8	9.0000
...	chr2:223499061-223499262(-)$1	1	2	5	9.0000
(..	chr2:183866797-183866998(-)$1	1	24	27	9.0000
...	chr9:121393-121594(-)$1	1	24	27	9.0000
...	chr12:133372584-133372785(-)$1	1	47	50	9.0000
)((	chr5:89949597-89949798(+)$1	1	41	44	9.0000
.((	chr16:57250797-57250998(+)$1	1	20	23	9.0000
((.	chr2:179410048-179410249(+)$1	1	4	7	9.0000
)))	chr3:142122483-142122684(-)$1	1	18	21	9.0000
)).	chr5:16758169-16758370(-)$1	1	60	63	9.0000
(((	chr2:197595515-197595716(+)$1	1	5	8	9.0000
)))	chr16:28883902-28884103(+)$1	1	169	172	9.0000
)..	chr10:103281347-103281548(+)$1	1	95	98	9.0000
(.(	chr2:38812888-38813089(-)$1	1	22	25	9.0000
(((	chr12:44176113-44176314(+)$1	1	15	18	9.0000
...	chr10:116606821-116607022(+)$1	1	34	37	9.0000
...	chr2:160076210-160076411(+)$1	1	50	53	9.0000
...	chr8:145164927-145165128(+)$1	1	4	7	9.0000
(..	chr17:35627552-35627753(-)$1	1	10	13	9.0000
)))	chr20:62896845-62897046(+)$1	1	46	49	9.0000
).)	chr16:248996-249197(-)$1	1	118	121	9.0000
)))	chr4:82361968-82362169(-)$1	1	36	39	9.0000
(((	chr13:52598550-52598751(+)$1	1	122	125	9.0000
...	chr20:32265244-32265445(-)$1	1	63	66	9.0000
((.	chr16:30972675-30972876(+)$1	1	26	29	9.0000
(((	chr22:24133936-24134137(+)$1	1	10	13	9.0000
)..	chr14:105929465-105929666(+)$1	1	63	66	9.0000
...	chr5:68425258-68425459(+)$1	1	22	25	9.0000
(.(	chr12:123095326-123095527(+)$1	1	86	89	9.0000
(((	chr6:88318798-88318999(+)$1	1	14	17	9.0000
(..	chr7:156685548-156685749(-)$1	1	54	57	9.0000
)..	chr2:54853154-54853355(+)$1	1	45	48	9.0000
...	chr17:17179341-17179542(-)$1	1	33	36	9.0000
.((	chr14:77925993-77926194(+)$1	1	4	7	9.0000
(..	chr12:102547608-102547809(+)$1	1	86	89	9.0000
((.	chr2:197654591-197654792(-)$1	1	60	63	9.0000
(((	chr14:35255286-35255487(-)$1	1	35	38	9.0000
)))	chr3:127788295-127788496(+)$1	1	109	112	9.0000
...	chr12:56999563-56999764(-)$1	1	1	4	9.0000
((.	chr18:18546833-18547034(-)$1	1	6	9	9.0000
.))	chr10:103908918-103909119(+)$1	1	132	135	9.0000
)))	chrX:48791984-48792185(-)$1	1	47	50	9.0000
...	chr17:49337870-49338071(+)$1	1	97	100	9.0000
...	chr3:87298949-87299150(+)$1	1	42	45	9.0000
(..	chr15:99251167-99251368(+)$1	1	41	44	9.0000
)))	chr12:27841889-27842090(+)$1	1	82	85	9.0000
..)	chr5:71500886-71501087(+)$1	1	51	54	9.0000
...	chr17:80045208-80045409(-)$1	1	51	54	9.0000
.((	chr5:134010237-134010438(+)$1	1	41	44	9.0000
(..	chr16:419061-419262(-)$1	1	2	5	9.0000
((.	chr16:29822251-29822452(+)$1	1	37	40	9.0000
).)	chr12:6878931-6879132(+)$1	1	163	166	9.0000
(((	chr5:64892164-64892365(-)$1	1	18	21	9.0000
)..	chr6:83834350-83834551(+)$1	1	56	59	9.0000
(..	chr1:151378705-151378906(-)$1	1	5	8	9.0000
)))	chr1:113460437-113460638(-)$1	1	137	140	9.0000
(((	chr2:15674605-15674806(-)$1	1	46	49	9.0000
...	chr15:44892704-44892905(-)$1	1	21	24	9.0000
(..	chr4:48569224-48569425(-)$1	1	10	13	9.0000
)..	chr16:75338879-75339080(-)$1	1	36	39	9.0000
...	chr14:92623926-92624127(+)$1	1	32	35	9.0000
...	chr16:30731453-30731654(+)$1	1	65	68	9.0000
)))	chr14:90770340-90770541(-)$1	1	25	28	9.0000
)).	chr16:2135194-2135395(+)$1	1	120	123	9.0000
.((	chr22:50684011-50684212(-)$1	1	96	99	9.0000
(((	chr17:16029415-16029616(-)$1	1	65	68	9.0000
...	chr22:24175753-24175954(+)$1	1	8	11	9.0000
(((	chr11:95582780-95582981(-)$1	1	28	31	9.0000
(((	chr1:146763110-146763311(+)$1	1	10	13	9.0000
(..	chr18:76856404-76856605(+)$1	1	10	13	9.0000
((.	chr1:110888111-110888312(+)$1	1	12	15	9.0000
.))	chr8:21844565-21844766(+)$1	1	62	65	9.0000
(((	chr3:49343160-49343361(-)$1	1	4	7	9.0000
)))	chr6:160482507-160482708(+)$1	1	36	39	9.0000
...	chr15:90986554-90986755(+)$1	1	74	77	9.0000
(..	chr11:59367879-59368080(-)$1	1	10	13	9.0000
)))	chr7:102952410-102952611(+)$1	1	66	69	9.0000
)))	chr17:7149272-7149473(-)$1	1	137	140	9.0000
...	chr4:129782866-129783067(+)$1	1	0	3	9.0000
...	chr15:52510716-52510917(-)$1	1	40	43	9.0000
...	chr1:61553967-61554168(+)$1	1	0	3	9.0000
(..	chr11:65826214-65826415(+)$1	1	4	7	9.0000
)))	chr3:127335779-127335980(+)$1	1	19	22	9.0000
)..	chr14:104173423-104173624(-)$1	1	91	94	9.0000
)))	chr2:38975670-38975871(-)$1	1	67	70	9.0000
(((	chr3:9786593-9786794(+)$1	1	4	7	9.0000
...	chr2:97297062-97297263(-)$1	1	2	5	9.0000
(..	chr5:140908672-140908873(-)$1	1	32	35	9.0000
(.(	chr12:67701100-67701301(+)$1	1	91	94	9.0000
...	chr8:23112766-23112967(+)$1	1	25	28	9.0000
..)	chr6:26388284-26388485(+)$1	1	92	95	9.0000

#PSSM
G : 0.97	g : 0.03	
A : 0.97	a : 0.03	
A : 0.97	a : 0.03	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m1_run2.nuc.txt

#NT
CCUG	chr16:447128-447352(+)$1	224	162	166	11.9999
CCUG	chr20:60740995-60741217(+)$1	222	22	26	11.9999
ccug	chr2:242524339-242524572(+)$1	233	60	64	11.9999
CCUG	chr16:54145650-54145919(+)$1	269	51	55	11.9999
CCUG	chr10:108363328-108363549(-)$1	221	178	182	11.9999
CCUG	chr22:39709726-39710014(-)$1	288	115	119	11.9999
CCUG	chr9:111754700-111754927(-)$1	227	201	205	11.9999
ccug	chr16:47539003-47539230(+)$1	227	179	183	11.9999
CCUG	chr2:242695143-242695375(+)$1	232	10	14	11.9999
CCUG	chr12:125431896-125432137(-)$1	241	84	88	11.9999
ccug	chr22:28818555-28818774(-)$1	219	63	67	11.9999
CCUG	chr14:21968545-21968916(-)$1	371	115	119	11.9999
CCUG	chr6:116914091-116914314(+)$1	223	140	144	11.9999
ccug	chr16:19889176-19889425(-)$1	249	131	135	11.9999
CCUG	chr17:75085289-75085526(+)$1	237	13	17	11.9999
CCUG	chr17:7790076-7790301(+)$1	225	3	7	11.9999
CCUG	chr6:26217280-26217505(+)$1	225	74	78	11.9999
CCUG	chr19:10912955-10913186(+)$1	231	197	201	11.9999
ccug	chr7:40035449-40035680(+)$1	231	33	37	11.9999
CCUG	chr20:3898088-3898311(+)$1	223	192	196	11.9999
CCUG	chr20:37055849-37056081(-)$1	232	24	28	11.9999
ccug	chr9:21699379-21699604(+)$1	225	56	60	11.9999
ccug	chr3:79667996-79668218(-)$1	222	103	107	11.9999
ccug	chr4:1704633-1704869(-)$1	236	10	14	11.9999
CCUG	chr2:219866271-219866491(-)$1	220	91	95	11.9999
CCUG	chr11:8705674-8705893(+)$1	219	93	97	11.9999
ccug	chr11:58646066-58646285(+)$1	219	75	79	11.9999
CCUG	chr17:54990973-54991194(-)$1	221	72	76	11.9999
CCUG	chr1:198828098-198828319(-)$1	221	208	212	11.9999
CCUG	chr11:661030-661251(-)$1	221	42	46	11.9999
CCUG	chr11:61061953-61062179(-)$1	226	7	11	11.9999
ccug	chr7:22311756-22311987(+)$1	231	10	14	11.9999
CCUG	chr14:97227131-97227351(+)$1	220	112	116	11.9999
CCUG	chr21:33104028-33104248(-)$1	220	22	26	11.9999
CCUG	chr14:91541878-91542104(+)$1	226	61	65	11.9999
CCUG	chr16:89474570-89474789(-)$1	219	22	26	11.9999
CCUG	chr3:49168244-49168464(-)$1	220	154	158	11.9999
CCUG	chr1:17198974-17199248(+)$1	274	95	99	11.9999
CCUG	chr14:95999837-96000065(-)$1	228	191	195	11.9999
ccug	chr7:65422378-65422602(+)$1	224	61	65	11.9999
ccug	chr1:145969206-145969525(-)$1	319	99	103	11.9999
CCUG	chrX:153581584-153581807(-)$1	223	64	68	11.9999
CCUG	chr1:52879534-52879756(+)$1	222	34	38	11.9999
CCUG	chr20:43882998-43883219(-)$1	221	23	27	11.9999
CCUG	chr8:41517862-41518083(+)$1	221	13	17	11.9999
CCUG	chr11:46783917-46784147(-)$1	230	86	90	11.9999
CCUG	chr7:94635961-94636181(-)$1	220	98	102	11.9999
CCUG	chr2:172703946-172704170(-)$1	224	202	206	11.9999
CCUG	chr5:180687234-180687468(-)$1	234	74	78	11.9999
CCUG	chr13:92003399-92003620(+)$1	221	13	17	11.9999
ccug	chr1:16948806-16949034(-)$1	228	70	74	11.9999
CCUG	chr20:48808037-48808256(+)$1	219	9	13	11.9999
CCUG	chr3:131197842-131198062(-)$1	220	5	9	11.9999
ccug	chr7:128665996-128666243(-)$1	247	155	159	11.9999
ccug	chr13:34486875-34487100(+)$1	225	31	35	11.9999
CCUG	chr19:1426111-1426334(+)$1	223	33	37	11.9999
CCUG	chr1:11969778-11970077(-)$1	299	42	46	11.9999
CCUG	chr17:41172437-41172657(+)$1	220	86	90	11.9999
CCUG	chr22:46474983-46475202(+)$1	219	80	84	11.9999
CCUG	chr17:33923535-33923756(+)$1	221	72	76	11.9999
CCUG	chr8:37553408-37553637(+)$1	229	211	215	11.9999
CCUG	chr16:66982638-66982869(+)$1	231	89	93	11.9999
CCUG	chr1:6631509-6631731(+)$1	222	32	36	11.9999
CCUG	chr8:107709801-107710026(-)$1	225	73	77	11.9999
ccug	chr17:38382661-38382885(+)$1	224	32	36	11.9999
ccug	chrX:19394792-19395013(+)$1	221	14	18	11.9999
CCUG	chr17:1552318-1552537(+)$1	219	13	17	11.9999
CCUG	chr17:79846989-79847219(-)$1	230	121	125	11.9999
cCUG	chr17:71820212-71820438(+)$1	226	55	59	11.9999
CCUG	chr7:121513694-121513917(+)$1	223	204	208	11.9999
CCUG	chr1:1492137-1492364(-)$1	227	27	31	11.9999
CCUG	chr19:4361302-4361523(-)$1	221	5	9	11.9999
CCUG	chr16:29818819-29819047(+)$1	228	125	129	11.9999
CCUG	chr3:170858103-170858323(+)$1	220	67	71	11.9999
ccug	chr2:115695252-115695479(+)$1	227	6	10	11.9999
ccug	chr16:22118313-22118532(+)$1	219	27	31	11.9999
CCUG	chr16:3749054-3749277(-)$1	223	12	16	11.9999
CCUG	chr20:62701072-62701294(+)$1	222	79	83	11.9999
CCUG	chr7:99007562-99007786(+)$1	224	18	22	11.9999
CCUG	chr3:15106620-15106844(-)$1	224	9	13	11.9999
ccug	chr3:48102460-48102692(-)$1	232	79	83	11.9999
ccug	chr3:129310279-129310503(+)$1	224	142	146	11.9999
CCUG	chr19:12912510-12912740(-)$1	230	17	21	11.9999
ccug	chr22:40025155-40025398(-)$1	243	34	38	11.9999
CCUG	chr2:99171684-99171920(+)$1	236	43	47	11.9999
CCUG	chr17:46136890-46137121(+)$1	231	114	118	11.9999
CCUG	chr8:12647309-12647528(+)$1	219	22	26	11.9999

#otherMatches

#Struct PSSM
FFFF	chr13:41767537-41767758(-)$1	221	18	22	11.9999
iicc	chr16:447128-447352(+)$1	224	162	166	11.9999
HH{D	chr20:60740995-60741217(+)$1	222	22	26	11.9999
eeee	chr2:242524339-242524572(+)$1	233	60	64	11.9999
a!!c	chr16:54145650-54145919(+)$1	269	51	55	11.9999
teee	chr10:108363328-108363549(-)$1	221	178	182	11.9999
ffff	chr22:39709726-39710014(-)$1	288	115	119	11.9999
====	chr9:111754700-111754927(-)$1	227	201	205	11.9999
:eee	chr16:47539003-47539230(+)$1	227	179	183	11.9999
gggg	chr2:242695143-242695375(+)$1	232	10	14	11.9999
:FFF	chr12:125431896-125432137(-)$1	241	84	88	11.9999
HHHH	chr22:28818555-28818774(-)$1	219	63	67	11.9999
d:::	chr14:21968545-21968916(-)$1	371	115	119	11.9999
bccc	chr6:116914091-116914314(+)$1	223	140	144	11.9999
DDDD	chr16:19889176-19889425(-)$1	249	131	135	11.9999
DDDD	chr17:75085289-75085526(+)$1	237	13	17	11.9999
fffm	chr17:7790076-7790301(+)$1	225	3	7	11.9999
nddd	chr6:26217280-26217505(+)$1	225	74	78	11.9999
}FFF	chr19:10912955-10913186(+)$1	231	197	201	11.9999
dd44	chr7:40035449-40035680(+)$1	231	33	37	11.9999
::::	chr20:3898088-3898311(+)$1	223	192	196	11.9999
pppp	chr20:37055849-37056081(-)$1	232	24	28	11.9999
2bb]	chr9:21699379-21699604(+)$1	225	56	60	11.9999
ggg:	chr3:79667996-79668218(-)$1	222	103	107	11.9999
ammm	chr4:1704633-1704869(-)$1	236	10	14	11.9999
qqqq	chr2:219866271-219866491(-)$1	220	91	95	11.9999
FFFF	chr11:8705674-8705893(+)$1	219	93	97	11.9999
====	chr11:58646066-58646285(+)$1	219	75	79	11.9999
gggg	chr17:54990973-54991194(-)$1	221	72	76	11.9999
:CCC	chr1:198828098-198828319(-)$1	221	208	212	11.9999
b22e	chr11:661030-661251(-)$1	221	42	46	11.9999
IIIF	chr11:61061953-61062179(-)$1	226	7	11	11.9999
EEEE	chr7:22311756-22311987(+)$1	231	10	14	11.9999
++++	chr14:97227131-97227351(+)$1	220	112	116	11.9999
eeee	chr21:33104028-33104248(-)$1	220	22	26	11.9999
hhhh	chr14:91541878-91542104(+)$1	226	61	65	11.9999
mmee	chr16:89474570-89474789(-)$1	219	22	26	11.9999
ffff	chr3:49168244-49168464(-)$1	220	154	158	11.9999
]bb]	chr1:17198974-17199248(+)$1	274	95	99	11.9999
D:cc	chr14:95999837-96000065(-)$1	228	191	195	11.9999
bccc	chr7:65422378-65422602(+)$1	224	61	65	11.9999
ccc[	chr1:145969206-145969525(-)$1	319	99	103	11.9999
FF{C	chrX:153581584-153581807(-)$1	223	64	68	11.9999
"""d	chr1:52879534-52879756(+)$1	222	34	38	11.9999
ee[b	chr20:43882998-43883219(-)$1	221	23	27	11.9999
]ddd	chr8:41517862-41518083(+)$1	221	13	17	11.9999
GGGG	chr11:46783917-46784147(-)$1	230	86	90	11.9999
HHHH	chr7:94635961-94636181(-)$1	220	98	102	11.9999
c]cc	chr2:172703946-172704170(-)$1	224	202	206	11.9999
eeee	chr5:180687234-180687468(-)$1	234	74	78	11.9999
DDNN	chr13:92003399-92003620(+)$1	221	13	17	11.9999
eee:	chr1:16948806-16949034(-)$1	228	70	74	11.9999
{DDD	chr20:48808037-48808256(+)$1	219	9	13	11.9999
iiii	chr3:131197842-131198062(-)$1	220	5	9	11.9999
ppcc	chr7:128665996-128666243(-)$1	247	155	159	11.9999
III:	chr13:34486875-34487100(+)$1	225	31	35	11.9999
EEEE	chr19:1426111-1426334(+)$1	223	33	37	11.9999
]fff	chr1:11969778-11970077(-)$1	299	42	46	11.9999
eIII	chr17:41172437-41172657(+)$1	220	86	90	11.9999
pppb	chr22:46474983-46475202(+)$1	219	80	84	11.9999
dddl	chr17:33923535-33923756(+)$1	221	72	76	11.9999
nna]	chr8:37553408-37553637(+)$1	229	211	215	11.9999
ffff	chr16:66982638-66982869(+)$1	231	89	93	11.9999
:::b	chr1:6631509-6631731(+)$1	222	32	36	11.9999
5ddd	chr8:107709801-107710026(-)$1	225	73	77	11.9999
CKKC	chr17:38382661-38382885(+)$1	224	32	36	11.9999
[eee	chrX:19394792-19395013(+)$1	221	14	18	11.9999
EEEE	chr17:1552318-1552537(+)$1	219	13	17	11.9999
hhhh	chr17:79846989-79847219(-)$1	230	121	125	11.9999
ffff	chr17:71820212-71820438(+)$1	226	55	59	11.9999
hhcc	chr7:121513694-121513917(+)$1	223	204	208	11.9999
ffdd	chr1:1492137-1492364(-)$1	227	27	31	11.9999
ffff	chr19:4361302-4361523(-)$1	221	5	9	11.9999
ddcc	chr16:29818819-29819047(+)$1	228	125	129	11.9999
gggg	chr3:170858103-170858323(+)$1	220	67	71	11.9999
{BBK	chr2:115695252-115695479(+)$1	227	6	10	11.9999
gggg	chr16:22118313-22118532(+)$1	219	27	31	11.9999
eee:	chr16:3749054-3749277(-)$1	223	12	16	11.9999
ee::	chr20:62701072-62701294(+)$1	222	79	83	11.9999
dddd	chr7:99007562-99007786(+)$1	224	18	22	11.9999
FFFF	chr3:15106620-15106844(-)$1	224	9	13	11.9999
eeeg	chr3:48102460-48102692(-)$1	232	79	83	11.9999
dddd	chr3:129310279-129310503(+)$1	224	142	146	11.9999
:::g	chr19:12912510-12912740(-)$1	230	17	21	11.9999
cnnn	chr22:40025155-40025398(-)$1	243	34	38	11.9999
c!!=	chr2:99171684-99171920(+)$1	236	43	47	11.9999
D:DD	chr17:46136890-46137121(+)$1	231	114	118	11.9999
eee[	chr8:12647309-12647528(+)$1	219	22	26	11.9999

#DB
((((	chr13:41767537-41767758(-)$1	1	18	22	11.9999
((((	chr16:447128-447352(+)$1	1	162	166	11.9999
((.(	chr20:60740995-60741217(+)$1	1	22	26	11.9999
))))	chr2:242524339-242524572(+)$1	1	60	64	11.9999
(..(	chr16:54145650-54145919(+)$1	1	51	55	11.9999
.)))	chr10:108363328-108363549(-)$1	1	178	182	11.9999
((((	chr22:39709726-39710014(-)$1	1	115	119	11.9999
((((	chr9:111754700-111754927(-)$1	1	201	205	11.9999
.(((	chr16:47539003-47539230(+)$1	1	179	183	11.9999
((((	chr2:242695143-242695375(+)$1	1	10	14	11.9999
.(((	chr12:125431896-125432137(-)$1	1	84	88	11.9999
((((	chr22:28818555-28818774(-)$1	1	63	67	11.9999
)...	chr14:21968545-21968916(-)$1	1	115	119	11.9999
((((	chr6:116914091-116914314(+)$1	1	140	144	11.9999
((((	chr16:19889176-19889425(-)$1	1	131	135	11.9999
((((	chr17:75085289-75085526(+)$1	1	13	17	11.9999
(((.	chr17:7790076-7790301(+)$1	1	3	7	11.9999
.)))	chr6:26217280-26217505(+)$1	1	74	78	11.9999
.)))	chr19:10912955-10913186(+)$1	1	197	201	11.9999
))..	chr7:40035449-40035680(+)$1	1	33	37	11.9999
....	chr20:3898088-3898311(+)$1	1	192	196	11.9999
....	chr20:37055849-37056081(-)$1	1	24	28	11.9999
.)).	chr9:21699379-21699604(+)$1	1	56	60	11.9999
))).	chr3:79667996-79668218(-)$1	1	103	107	11.9999
(...	chr4:1704633-1704869(-)$1	1	10	14	11.9999
....	chr2:219866271-219866491(-)$1	1	91	95	11.9999
((((	chr11:8705674-8705893(+)$1	1	93	97	11.9999
((((	chr11:58646066-58646285(+)$1	1	75	79	11.9999
((((	chr17:54990973-54991194(-)$1	1	72	76	11.9999
.)))	chr1:198828098-198828319(-)$1	1	208	212	11.9999
)..)	chr11:661030-661251(-)$1	1	42	46	11.9999
((((	chr11:61061953-61062179(-)$1	1	7	11	11.9999
((((	chr7:22311756-22311987(+)$1	1	10	14	11.9999
....	chr14:97227131-97227351(+)$1	1	112	116	11.9999
((((	chr21:33104028-33104248(-)$1	1	22	26	11.9999
((((	chr14:91541878-91542104(+)$1	1	61	65	11.9999
..))	chr16:89474570-89474789(-)$1	1	22	26	11.9999
))))	chr3:49168244-49168464(-)$1	1	154	158	11.9999
.)).	chr1:17198974-17199248(+)$1	1	95	99	11.9999
).((	chr14:95999837-96000065(-)$1	1	191	195	11.9999
((((	chr7:65422378-65422602(+)$1	1	61	65	11.9999
(((.	chr1:145969206-145969525(-)$1	1	99	103	11.9999
((.(	chrX:153581584-153581807(-)$1	1	64	68	11.9999
...(	chr1:52879534-52879756(+)$1	1	34	38	11.9999
((.(	chr20:43882998-43883219(-)$1	1	23	27	11.9999
.)))	chr8:41517862-41518083(+)$1	1	13	17	11.9999
((((	chr11:46783917-46784147(-)$1	1	86	90	11.9999
))))	chr7:94635961-94636181(-)$1	1	98	102	11.9999
).))	chr2:172703946-172704170(-)$1	1	202	206	11.9999
))))	chr5:180687234-180687468(-)$1	1	74	78	11.9999
((..	chr13:92003399-92003620(+)$1	1	13	17	11.9999
))).	chr1:16948806-16949034(-)$1	1	70	74	11.9999
.(((	chr20:48808037-48808256(+)$1	1	9	13	11.9999
((((	chr3:131197842-131198062(-)$1	1	5	9	11.9999
..))	chr7:128665996-128666243(-)$1	1	155	159	11.9999
(((.	chr13:34486875-34487100(+)$1	1	31	35	11.9999
((((	chr19:1426111-1426334(+)$1	1	33	37	11.9999
.)))	chr1:11969778-11970077(-)$1	1	42	46	11.9999
))))	chr17:41172437-41172657(+)$1	1	86	90	11.9999
...)	chr22:46474983-46475202(+)$1	1	80	84	11.9999
(((.	chr17:33923535-33923756(+)$1	1	72	76	11.9999
..).	chr8:37553408-37553637(+)$1	1	211	215	11.9999
((((	chr16:66982638-66982869(+)$1	1	89	93	11.9999
...(	chr1:6631509-6631731(+)$1	1	32	36	11.9999
.)))	chr8:107709801-107710026(-)$1	1	73	77	11.9999
(..(	chr17:38382661-38382885(+)$1	1	32	36	11.9999
.(((	chrX:19394792-19395013(+)$1	1	14	18	11.9999
((((	chr17:1552318-1552537(+)$1	1	13	17	11.9999
((((	chr17:79846989-79847219(-)$1	1	121	125	11.9999
((((	chr17:71820212-71820438(+)$1	1	55	59	11.9999
))))	chr7:121513694-121513917(+)$1	1	204	208	11.9999
))))	chr1:1492137-1492364(-)$1	1	27	31	11.9999
((((	chr19:4361302-4361523(-)$1	1	5	9	11.9999
((((	chr16:29818819-29819047(+)$1	1	125	129	11.9999
))))	chr3:170858103-170858323(+)$1	1	67	71	11.9999
.((.	chr2:115695252-115695479(+)$1	1	6	10	11.9999
((((	chr16:22118313-22118532(+)$1	1	27	31	11.9999
))).	chr16:3749054-3749277(-)$1	1	12	16	11.9999
))..	chr20:62701072-62701294(+)$1	1	79	83	11.9999
((((	chr7:99007562-99007786(+)$1	1	18	22	11.9999
((((	chr3:15106620-15106844(-)$1	1	9	13	11.9999
)))(	chr3:48102460-48102692(-)$1	1	79	83	11.9999
))))	chr3:129310279-129310503(+)$1	1	142	146	11.9999
...(	chr19:12912510-12912740(-)$1	1	17	21	11.9999
(...	chr22:40025155-40025398(-)$1	1	34	38	11.9999
(..(	chr2:99171684-99171920(+)$1	1	43	47	11.9999
).((	chr17:46136890-46137121(+)$1	1	114	118	11.9999
(((.	chr8:12647309-12647528(+)$1	1	22	26	11.9999

#PSSM
C : 0.73	c : 0.26	
C : 0.74	c : 0.24	
U : 0.74	u : 0.24	
G : 0.74	g : 0.24	

#score	1055.9999999999998
#seq	88
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m2_run1.nuc.txt

#NT
AAAGGA	chr6:20781375-20781595(+)$1	220	28	34	14.3281
AAAGUA	chr16:69972866-69973085(+)$1	219	9	15	10.7343
AAAGGA	chr11:129992201-129992424(+)$1	223	119	125	14.3281
AAAGCA	chr11:9607896-9608117(+)$1	221	117	123	10.6562
AAAGGA	chr1:242023795-242024017(+)$1	222	141	147	14.3281
AAAGCA	chr1:229577536-229577760(-)$1	224	71	77	10.6562
AGAGGA	chr14:24606845-24607075(-)$1	230	18	24	11.1250
UAAGGA	chr10:15820887-15821109(-)$1	222	135	141	10.5000
AAAGUA	chr3:127774290-127774513(+)$1	223	28	34	10.7343
AGAGGA	chr10:27112077-27112297(-)$1	220	86	92	11.1250
AGAGGA	chrM:6107-6411(-)$1	304	36	42	11.1250
GAAGGA	chr1:214820282-214820505(+)$1	223	187	193	10.5000
AGAGGa	chr14:23794372-23794601(+)$1	229	147	153	11.1250
AAAGUA	chr7:99091069-99091303(-)$1	234	72	78	10.7343
AAAGGA	chr8:30361706-30362051(+)$1	345	53	59	14.3281
AAAGUA	chr6:79668091-79668317(-)$1	226	123	129	10.7343
GAAGGA	chr12:112371596-112371824(-)$1	228	212	218	10.5000
AAAAGA	chr7:156629424-156629645(-)$1	221	17	23	9.9531
AGAGGA	chr10:111628348-111628570(-)$1	222	61	67	11.1250
AGAGGA	chr7:150935474-150935695(+)$1	221	55	61	11.1250
UAAGGA	chr12:106500094-106500322(-)$1	228	39	45	10.5000
AAAGGA	chr6:49459809-49460031(+)$1	222	88	94	14.3281
AAAAGA	chr10:91163312-91163545(-)$1	233	10	16	9.9531
AAAAGA	chr17:66039121-66039341(+)$1	220	54	60	9.9531
AAAGGC	chr10:103921878-103922111(+)$1	233	43	49	10.2656
AAAGAA	chr4:113539007-113539226(-)$1	219	3	9	10.6562
AAAGGA	chr9:86617106-86617335(+)$1	229	152	158	14.3281
UAAGGA	chr12:12630357-12630582(-)$1	225	200	206	10.5000
AAAGGC	chr19:37619422-37619643(+)$1	221	81	87	10.2656
AAAGGU	chr6:119215515-119215740(+)$1	225	67	73	10.0312
AAAGGA	chr7:124481038-124481259(-)$1	221	151	157	14.3281
AAAGAA	chr2:74399746-74399970(-)$1	224	121	127	10.6562
UAAGGA	chr19:36883903-36884127(-)$1	224	73	79	10.5000
AAAAGA	chr16:31200973-31201201(-)$1	228	0	6	9.9531
AAAGGA	chr11:18428741-18428961(+)$1	220	68	74	14.3281
AGAGGA	chrX:48791944-48792171(-)$1	227	66	72	11.1250
AAAGCA	chrX:53432085-53432318(-)$1	233	88	94	10.6562
AAAGGC	chr15:75694132-75694361(-)$1	229	55	61	10.2656
AAAGGA	chr11:105950220-105950447(+)$1	227	54	60	14.3281
AAAGCA	chr7:39729980-39730207(+)$1	227	24	30	10.6562
AAAGGA	chr3:160155802-160156039(-)$1	237	30	36	14.3281
AAAGGA	chr5:38511920-38512140(-)$1	220	13	19	14.3281
CAAGGA	chr2:38527349-38527569(-)$1	220	117	123	10.4218
aaagua	chr6:82941413-82941632(-)$1	219	45	51	10.7343
GAAGGA	chr3:150906077-150906298(+)$1	221	92	98	10.5000
AAAGAA	chr10:88277228-88277447(-)$1	219	47	53	10.6562
AAAGAA	chr1:231377039-231377261(+)$1	222	8	14	10.6562
AAAGGA	chr5:5468877-5469111(+)$1	234	176	182	14.3281
AAAGGA	chr10:17278257-17278478(+)$1	221	77	83	14.3281
AAAGGC	chr8:61742998-61743236(+)$1	238	50	56	10.2656
AAAGGA	chr11:10821033-10821256(-)$1	223	129	135	14.3281
AGAGGA	chr5:157162755-157162980(+)$1	225	4	10	11.1250
AGAGGA	chr21:34901113-34901333(-)$1	220	133	139	11.1250
AAAGGA	chr17:65907180-65907410(+)$1	230	13	19	14.3281
AAAGGA	chr19:40478310-40478541(+)$1	231	36	42	14.3281
AGAGGA	chr3:196626758-196626979(+)$1	221	212	218	11.1250
AAAGGU	chr11:93540649-93540868(+)$1	219	30	36	10.0312
CAAGGA	chr1:26752641-26752893(+)$1	252	124	130	10.4218
CAAGGA	chr6:10404749-10404969(-)$1	220	52	58	10.4218
AGAGGA	chr1:203766642-203766862(+)$1	220	136	142	11.1250
GAAGGA	chr2:20508172-20508391(-)$1	219	119	125	10.5000
ACAGGA	chr14:64679442-64679664(+)$1	222	94	100	10.3437
AAAGGA	chr1:11082162-11082388(+)$1	226	54	60	14.3281

#otherMatches

#Struct PSSM
tteeee	chr20:46268344-46268565(+)$1	221	43	49	10.2656
JJJJJJ	chr6:20781375-20781595(+)$1	220	28	34	14.3281
Fdddd[	chr16:69972866-69973085(+)$1	219	9	15	10.7343
((((((	chr11:129992201-129992424(+)$1	223	119	125	14.3281
:::eee	chr11:9607896-9608117(+)$1	221	117	123	10.6562
ffeeee	chr1:242023795-242024017(+)$1	222	141	147	14.3281
liiiii	chr1:229577536-229577760(-)$1	224	71	77	10.6562
rrrrrr	chr14:24606845-24607075(-)$1	230	18	24	11.1250
pppppp	chr10:15820887-15821109(-)$1	222	135	141	10.5000
mfffff	chr3:127774290-127774513(+)$1	223	28	34	10.7343
ccc]dd	chr10:27112077-27112297(-)$1	220	86	92	11.1250
::::::	chrM:6107-6411(-)$1	304	36	42	11.1250
::::::	chr1:214820282-214820505(+)$1	223	187	193	10.5000
J}DDDD	chr14:23794372-23794601(+)$1	229	147	153	11.1250
e22ccc	chr7:99091069-99091303(-)$1	234	72	78	10.7343
:::fff	chr8:30361706-30362051(+)$1	345	53	59	14.3281
QQDDDD	chr6:79668091-79668317(-)$1	226	123	129	10.7343
??A}DD	chr12:112371596-112371824(-)$1	228	212	218	10.5000
RRRRRF	chr7:156629424-156629645(-)$1	221	17	23	9.9531
gggggg	chr10:111628348-111628570(-)$1	222	61	67	11.1250
hhhhh[	chr7:150935474-150935695(+)$1	221	55	61	11.1250
qqqccc	chr12:106500094-106500322(-)$1	228	39	45	10.5000
!dddd$	chr6:49459809-49460031(+)$1	222	88	94	14.3281
MMMDDD	chr10:91163312-91163545(-)$1	233	10	16	9.9531
mmmccc	chr17:66039121-66039341(+)$1	220	54	60	9.9531
MMMMBB	chr10:103921878-103922111(+)$1	233	43	49	10.2656
::::::	chr4:113539007-113539226(-)$1	219	3	9	10.6562
::gggg	chr9:86617106-86617335(+)$1	229	152	158	14.3281
22ccc]	chr12:12630357-12630582(-)$1	225	200	206	10.5000
!!eeee	chr19:37619422-37619643(+)$1	221	81	87	10.2656
eeeee2	chr6:119215515-119215740(+)$1	225	67	73	10.0312
ee[ddd	chr7:124481038-124481259(-)$1	221	151	157	14.3281
yyffff	chr2:74399746-74399970(-)$1	224	121	127	10.6562
fffff:	chr19:36883903-36884127(-)$1	224	73	79	10.5000
::::::	chr16:31200973-31201201(-)$1	228	0	6	9.9531
dddd33	chr11:18428741-18428961(+)$1	220	68	74	14.3281
oooocc	chrX:48791944-48792171(-)$1	227	66	72	11.1250
WWWWWW	chrX:53432085-53432318(-)$1	233	88	94	10.6562
ffoooo	chr15:75694132-75694361(-)$1	229	55	61	10.2656
uuuuuu	chr11:105950220-105950447(+)$1	227	54	60	14.3281
333eee	chr7:39729980-39730207(+)$1	227	24	30	10.6562
IIIIII	chr3:160155802-160156039(-)$1	237	30	36	14.3281
ff[a""	chr5:38511920-38512140(-)$1	220	13	19	14.3281
2bbhhh	chr2:38527349-38527569(-)$1	220	117	123	10.4218
e22fff	chr6:82941413-82941632(-)$1	219	45	51	10.7343
dd[ccc	chr3:150906077-150906298(+)$1	221	92	98	10.5000
eeEEEE	chr10:88277228-88277447(-)$1	219	47	53	10.6562
NNNNND	chr1:231377039-231377261(+)$1	222	8	14	10.6562
::====	chr5:5468877-5469111(+)$1	234	176	182	14.3281
!!dddd	chr10:17278257-17278478(+)$1	221	77	83	14.3281
cc:EEE	chr8:61742998-61743236(+)$1	238	50	56	10.2656
%%%%%f	chr11:10821033-10821256(-)$1	223	129	135	14.3281
:FFFFF	chr5:157162755-157162980(+)$1	225	4	10	11.1250
mmiiii	chr21:34901113-34901333(-)$1	220	133	139	11.1250
mmeeee	chr17:65907180-65907410(+)$1	230	13	19	14.3281
nnccc:	chr19:40478310-40478541(+)$1	231	36	42	14.3281
hhhhhh	chr3:196626758-196626979(+)$1	221	212	218	11.1250
NDDDD:	chr11:93540649-93540868(+)$1	219	30	36	10.0312
qqqqqq	chr1:26752641-26752893(+)$1	252	124	130	10.4218
ppccc:	chr6:10404749-10404969(-)$1	220	52	58	10.4218
eeee55	chr1:203766642-203766862(+)$1	220	136	142	11.1250
ttbb33	chr2:20508172-20508391(-)$1	219	119	125	10.5000
mmmccc	chr14:64679442-64679664(+)$1	222	94	100	10.3437
::ccc!	chr1:11082162-11082388(+)$1	226	54	60	14.3281

#DB
..))))	chr20:46268344-46268565(+)$1	1	43	49	10.2656
((((((	chr6:20781375-20781595(+)$1	1	28	34	14.3281
(((((.	chr16:69972866-69973085(+)$1	1	9	15	10.7343
......	chr11:129992201-129992424(+)$1	1	119	125	14.3281
...(((	chr11:9607896-9608117(+)$1	1	117	123	10.6562
))))))	chr1:242023795-242024017(+)$1	1	141	147	14.3281
.)))))	chr1:229577536-229577760(-)$1	1	71	77	10.6562
......	chr14:24606845-24607075(-)$1	1	18	24	11.1250
......	chr10:15820887-15821109(-)$1	1	135	141	10.5000
.)))))	chr3:127774290-127774513(+)$1	1	28	34	10.7343
))).))	chr10:27112077-27112297(-)$1	1	86	92	11.1250
......	chrM:6107-6411(-)$1	1	36	42	11.1250
......	chr1:214820282-214820505(+)$1	1	187	193	10.5000
).))))	chr14:23794372-23794601(+)$1	1	147	153	11.1250
)..)))	chr7:99091069-99091303(-)$1	1	72	78	10.7343
...(((	chr8:30361706-30362051(+)$1	1	53	59	14.3281
..((((	chr6:79668091-79668317(-)$1	1	123	129	10.7343
..).))	chr12:112371596-112371824(-)$1	1	212	218	10.5000
.....(	chr7:156629424-156629645(-)$1	1	17	23	9.9531
((((((	chr10:111628348-111628570(-)$1	1	61	67	11.1250
(((((.	chr7:150935474-150935695(+)$1	1	55	61	11.1250
...)))	chr12:106500094-106500322(-)$1	1	39	45	10.5000
.((((.	chr6:49459809-49460031(+)$1	1	88	94	14.3281
...(((	chr10:91163312-91163545(-)$1	1	10	16	9.9531
...)))	chr17:66039121-66039341(+)$1	1	54	60	9.9531
....((	chr10:103921878-103922111(+)$1	1	43	49	10.2656
......	chr4:113539007-113539226(-)$1	1	3	9	10.6562
..((((	chr9:86617106-86617335(+)$1	1	152	158	14.3281
..))).	chr12:12630357-12630582(-)$1	1	200	206	10.5000
..((((	chr19:37619422-37619643(+)$1	1	81	87	10.2656
))))).	chr6:119215515-119215740(+)$1	1	67	73	10.0312
((.(((	chr7:124481038-124481259(-)$1	1	151	157	14.3281
..))))	chr2:74399746-74399970(-)$1	1	121	127	10.6562
))))).	chr19:36883903-36884127(-)$1	1	73	79	10.5000
......	chr16:31200973-31201201(-)$1	1	0	6	9.9531
))))..	chr11:18428741-18428961(+)$1	1	68	74	14.3281
....))	chrX:48791944-48792171(-)$1	1	66	72	11.1250
......	chrX:53432085-53432318(-)$1	1	88	94	10.6562
((....	chr15:75694132-75694361(-)$1	1	55	61	10.2656
......	chr11:105950220-105950447(+)$1	1	54	60	14.3281
...)))	chr7:39729980-39730207(+)$1	1	24	30	10.6562
((((((	chr3:160155802-160156039(-)$1	1	30	36	14.3281
((.(..	chr5:38511920-38512140(-)$1	1	13	19	14.3281
.)))))	chr2:38527349-38527569(-)$1	1	117	123	10.4218
)..)))	chr6:82941413-82941632(-)$1	1	45	51	10.7343
((.(((	chr3:150906077-150906298(+)$1	1	92	98	10.5000
))((((	chr10:88277228-88277447(-)$1	1	47	53	10.6562
.....(	chr1:231377039-231377261(+)$1	1	8	14	10.6562
..((((	chr5:5468877-5469111(+)$1	1	176	182	14.3281
..((((	chr10:17278257-17278478(+)$1	1	77	83	14.3281
)).(((	chr8:61742998-61743236(+)$1	1	50	56	10.2656
.....(	chr11:10821033-10821256(-)$1	1	129	135	14.3281
.(((((	chr5:157162755-157162980(+)$1	1	4	10	11.1250
..))))	chr21:34901113-34901333(-)$1	1	133	139	11.1250
..))))	chr17:65907180-65907410(+)$1	1	13	19	14.3281
..))).	chr19:40478310-40478541(+)$1	1	36	42	14.3281
))))))	chr3:196626758-196626979(+)$1	1	212	218	11.1250
.((((.	chr11:93540649-93540868(+)$1	1	30	36	10.0312
......	chr1:26752641-26752893(+)$1	1	124	130	10.4218
..))).	chr6:10404749-10404969(-)$1	1	52	58	10.4218
))))..	chr1:203766642-203766862(+)$1	1	136	142	11.1250
..))..	chr2:20508172-20508391(-)$1	1	119	125	10.5000
...)))	chr14:64679442-64679664(+)$1	1	94	100	10.3437
..(((.	chr1:11082162-11082388(+)$1	1	54	60	14.3281

#PSSM
A : 0.81	U : 0.06	G : 0.06	C : 0.04	a : 0.01	
A : 0.79	G : 0.17	a : 0.01	C : 0.01	
A : 0.98	a : 0.01	
G : 0.92	A : 0.06	g : 0.01	
G : 0.79	U : 0.06	C : 0.06	A : 0.06	u : 0.01	
A : 0.85	C : 0.07	a : 0.03	U : 0.03	

#score	741.6875
#seq	64
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m3_run2.nuc.txt

#NT
AGCU	chr22:17629311-17629540(-)$1	229	130	134	12.0000
AGCU	chr11:66391658-66391894(+)$1	236	80	84	12.0000
AGCU	chr12:57006893-57007117(-)$1	224	139	143	12.0000
AGCU	chr10:62551621-62551883(+)$1	262	70	74	12.0000
AGCU	chr20:35835695-35835922(+)$1	227	63	67	12.0000
AGCU	chr13:100634383-100634614(+)$1	231	116	120	12.0000
AGCU	chr17:56083710-56083972(-)$1	262	33	37	12.0000
AGCU	chr7:5352897-5353127(-)$1	230	112	116	12.0000
AGCU	chr3:170108775-170109013(+)$1	238	118	122	12.0000
AGCU	chr19:41807417-41807668(+)$1	251	85	89	12.0000
AGCU	chr20:3128728-3128948(-)$1	220	70	74	12.0000
AGCU	chr10:77160887-77161115(-)$1	228	55	59	12.0000
AGCU	chr17:62499451-62499683(-)$1	232	44	48	12.0000
AGCU	chr12:133281143-133281374(+)$1	231	87	91	12.0000
AGCU	chr3:184048955-184049192(+)$1	237	37	41	12.0000
AGCU	chr12:57006797-57007018(-)$1	221	40	44	12.0000
AGCU	chr15:80988065-80988307(+)$1	242	12	16	12.0000
AGCU	chr22:29176952-29177175(+)$1	223	18	22	12.0000
AGCU	chr3:15686538-15686769(+)$1	231	131	135	12.0000
AGCU	chr16:4491350-4491584(+)$1	234	109	113	12.0000
AGCU	chr7:99694841-99695094(-)$1	253	135	139	12.0000
AGCU	chr2:242099751-242099979(+)$1	228	135	139	12.0000
AGCU	chr19:19033424-19033664(+)$1	240	5	9	12.0000
AGCU	chrX:153669350-153669573(+)$1	223	75	79	12.0000
AGCU	chr19:39207715-39207936(+)$1	221	8	12	12.0000
AGCU	chr6:142519509-142519753(+)$1	244	208	212	12.0000
AGCU	chr19:52705156-52705387(+)$1	231	38	42	12.0000
AGCU	chr19:58197813-58198064(+)$1	251	66	70	12.0000
AGCU	chr5:465185-465405(+)$1	220	170	174	12.0000
AGCU	chr8:29194586-29194811(-)$1	225	47	51	12.0000
AGCU	chr11:47602346-47602571(+)$1	225	1	5	12.0000
AGCU	chr10:15255475-15255705(-)$1	230	128	132	12.0000
AGCU	chr8:21890531-21890751(+)$1	220	128	132	12.0000
AGCU	chr16:28844041-28844288(+)$1	247	181	185	12.0000
AGCU	chr19:40329690-40329921(-)$1	231	125	129	12.0000
AGCU	chr22:39908136-39908383(+)$1	247	41	45	12.0000
AGCU	chr17:80012481-80012727(+)$1	246	5	9	12.0000
AGCU	chr15:89169777-89170010(+)$1	233	45	49	12.0000
AGCU	chr16:31200397-31200638(+)$1	241	171	175	12.0000
AGCU	chr19:34942831-34943083(+)$1	252	131	135	12.0000
AGCU	chr12:125444772-125444995(-)$1	223	213	217	12.0000
AGCU	chr19:50412194-50412424(-)$1	230	128	132	12.0000
AGCU	chrX:118604783-118605037(+)$1	254	78	82	12.0000
AGCU	chr12:7083703-7083926(+)$1	223	45	49	12.0000
AGCU	chr12:7362561-7362791(+)$1	230	21	25	12.0000
AGCU	chr12:57036358-57036629(-)$1	271	67	71	12.0000
AGCU	chr14:90870162-90870399(+)$1	237	20	24	12.0000
AGCU	chr6:26032046-26032280(-)$1	234	12	16	12.0000
AGCU	chr15:74925146-74925369(-)$1	223	170	174	12.0000
AGCU	chr2:170666711-170666942(+)$1	231	2	6	12.0000
AGCU	chr10:14987022-14987242(-)$1	220	52	56	12.0000
AGCU	chr12:131360325-131360556(+)$1	231	152	156	12.0000
AGCU	chr1:245027286-245027539(-)$1	253	27	31	12.0000
AGCU	chr9:37436559-37436781(+)$1	222	39	43	12.0000
AGCU	chr19:15534896-15535121(-)$1	225	10	14	12.0000
AGCU	chr5:175959283-175959511(-)$1	228	132	136	12.0000
AGCU	chr1:55319617-55319845(-)$1	228	17	21	12.0000
AGCU	chrM:6336-6576(+)$1	240	173	177	12.0000
AGCU	chr11:129991439-129991681(+)$1	242	99	103	12.0000
AGCU	chr20:2443640-2443914(-)$1	274	82	86	12.0000
AGCU	chr6:44219649-44219871(+)$1	222	114	118	12.0000
AGCU	chr7:156799185-156799419(-)$1	234	149	153	12.0000
AGCU	chr10:104486686-104486905(+)$1	219	92	96	12.0000
AGCU	chr19:13248262-13248483(+)$1	221	45	49	12.0000
AGCU	chrM:6455-6693(+)$1	238	54	58	12.0000
AGCU	chr10:129901091-129901322(-)$1	231	39	43	12.0000
AGCU	chr12:56575452-56575696(-)$1	244	27	31	12.0000
AGCU	chr16:28855194-28855414(-)$1	220	181	185	12.0000
AGCU	chr12:110929747-110929966(-)$1	219	104	108	12.0000
AGCU	chr7:142997262-142997487(+)$1	225	32	36	12.0000
AGCU	chrX:13773181-13773408(+)$1	227	92	96	12.0000
AGCU	chr11:61732075-61732306(-)$1	231	102	106	12.0000
AGCU	chr8:67341446-67341673(+)$1	227	5	9	12.0000
AGCU	chr19:39408412-39408666(-)$1	254	155	159	12.0000
AGCU	chr3:128205545-128205778(-)$1	233	16	20	12.0000
AGCU	chr10:12240631-12240865(+)$1	234	209	213	12.0000

#otherMatches

#Struct PSSM
IIII	chr19:2433829-2434068(-)$1	239	32	36	12.0000
!ddd	chr22:17629311-17629540(-)$1	229	130	134	12.0000
[ddd	chr11:66391658-66391894(+)$1	236	80	84	12.0000
cbb#	chr12:57006893-57007117(-)$1	224	139	143	12.0000
eee!	chr10:62551621-62551883(+)$1	262	70	74	12.0000
]bb]	chr20:35835695-35835922(+)$1	227	63	67	12.0000
eeee	chr13:100634383-100634614(+)$1	231	116	120	12.0000
ccc4	chr17:56083710-56083972(-)$1	262	33	37	12.0000
bb""	chr7:5352897-5353127(-)$1	230	112	116	12.0000
eppp	chr3:170108775-170109013(+)$1	238	118	122	12.0000
eeee	chr19:41807417-41807668(+)$1	251	85	89	12.0000
CC::	chr20:3128728-3128948(-)$1	220	70	74	12.0000
777c	chr10:77160887-77161115(-)$1	228	55	59	12.0000
HHHH	chr17:62499451-62499683(-)$1	232	44	48	12.0000
DDDH	chr12:133281143-133281374(+)$1	231	87	91	12.0000
ffff	chr3:184048955-184049192(+)$1	237	37	41	12.0000
cbb#	chr12:57006797-57007018(-)$1	221	40	44	12.0000
GGGG	chr15:80988065-80988307(+)$1	242	12	16	12.0000
KDDD	chr22:29176952-29177175(+)$1	223	18	22	12.0000
f[bb	chr3:15686538-15686769(+)$1	231	131	135	12.0000
qqqq	chr16:4491350-4491584(+)$1	234	109	113	12.0000
:a[g	chr7:99694841-99695094(-)$1	253	135	139	12.0000
]bbd	chr2:242099751-242099979(+)$1	228	135	139	12.0000
EEEE	chr19:19033424-19033664(+)$1	240	5	9	12.0000
QQQQ	chrX:153669350-153669573(+)$1	223	75	79	12.0000
::hh	chr19:39207715-39207936(+)$1	221	8	12	12.0000
:ccc	chr6:142519509-142519753(+)$1	244	208	212	12.0000
WWWW	chr19:52705156-52705387(+)$1	231	38	42	12.0000
====	chr19:58197813-58198064(+)$1	251	66	70	12.0000
nndd	chr5:465185-465405(+)$1	220	170	174	12.0000
eee[	chr8:29194586-29194811(-)$1	225	47	51	12.0000
:FFF	chr11:47602346-47602571(+)$1	225	1	5	12.0000
::::	chr10:15255475-15255705(-)$1	230	128	132	12.0000
BB}F	chr8:21890531-21890751(+)$1	220	128	132	12.0000
aeee	chr16:28844041-28844288(+)$1	247	181	185	12.0000
3ccc	chr19:40329690-40329921(-)$1	231	125	129	12.0000
f$$$	chr22:39908136-39908383(+)$1	247	41	45	12.0000
:FFF	chr17:80012481-80012727(+)$1	246	5	9	12.0000
occc	chr15:89169777-89170010(+)$1	233	45	49	12.0000
dddd	chr16:31200397-31200638(+)$1	241	171	175	12.0000
eeee	chr19:34942831-34943083(+)$1	252	131	135	12.0000
HHHH	chr12:125444772-125444995(-)$1	223	213	217	12.0000
cc::	chr19:50412194-50412424(-)$1	230	128	132	12.0000
!!bb	chrX:118604783-118605037(+)$1	254	78	82	12.0000
ddmm	chr12:7083703-7083926(+)$1	223	45	49	12.0000
fddd	chr12:7362561-7362791(+)$1	230	21	25	12.0000
eeee	chr12:57036358-57036629(-)$1	271	67	71	12.0000
dddn	chr14:90870162-90870399(+)$1	237	20	24	12.0000
HHHH	chr6:26032046-26032280(-)$1	234	12	16	12.0000
ff]b	chr15:74925146-74925369(-)$1	223	170	174	12.0000
:EEE	chr2:170666711-170666942(+)$1	231	2	6	12.0000
c"""	chr10:14987022-14987242(-)$1	220	52	56	12.0000
:eee	chr12:131360325-131360556(+)$1	231	152	156	12.0000
:ddd	chr1:245027286-245027539(-)$1	253	27	31	12.0000
lddd	chr9:37436559-37436781(+)$1	222	39	43	12.0000
mddd	chr19:15534896-15535121(-)$1	225	10	14	12.0000
ee!!	chr5:175959283-175959511(-)$1	228	132	136	12.0000
rrrr	chr1:55319617-55319845(-)$1	228	17	21	12.0000
4ggg	chrM:6336-6576(+)$1	240	173	177	12.0000
:bbm	chr11:129991439-129991681(+)$1	242	99	103	12.0000
cddd	chr20:2443640-2443914(-)$1	274	82	86	12.0000
[eee	chr6:44219649-44219871(+)$1	222	114	118	12.0000
mmmm	chr7:156799185-156799419(-)$1	234	149	153	12.0000
dbbm	chr10:104486686-104486905(+)$1	219	92	96	12.0000
H{BB	chr19:13248262-13248483(+)$1	221	45	49	12.0000
4ggg	chrM:6455-6693(+)$1	238	54	58	12.0000
MEEE	chr10:129901091-129901322(-)$1	231	39	43	12.0000
cc[c	chr12:56575452-56575696(-)$1	244	27	31	12.0000
"ccc	chr16:28855194-28855414(-)$1	220	181	185	12.0000
dddd	chr12:110929747-110929966(-)$1	219	104	108	12.0000
"""b	chr7:142997262-142997487(+)$1	225	32	36	12.0000
bmmm	chrX:13773181-13773408(+)$1	227	92	96	12.0000
6hhh	chr11:61732075-61732306(-)$1	231	102	106	12.0000
FFFF	chr8:67341446-67341673(+)$1	227	5	9	12.0000
eeee	chr19:39408412-39408666(-)$1	254	155	159	12.0000
CCC:	chr3:128205545-128205778(-)$1	233	16	20	12.0000
EEZZ	chr10:12240631-12240865(+)$1	234	209	213	12.0000

#DB
((((	chr19:2433829-2434068(-)$1	1	32	36	12.0000
.(((	chr22:17629311-17629540(-)$1	1	130	134	12.0000
.(((	chr11:66391658-66391894(+)$1	1	80	84	12.0000
(((.	chr12:57006893-57007117(-)$1	1	139	143	12.0000
(((.	chr10:62551621-62551883(+)$1	1	70	74	12.0000
.)).	chr20:35835695-35835922(+)$1	1	63	67	12.0000
((((	chr13:100634383-100634614(+)$1	1	116	120	12.0000
))).	chr17:56083710-56083972(-)$1	1	33	37	12.0000
((..	chr7:5352897-5353127(-)$1	1	112	116	12.0000
(...	chr3:170108775-170109013(+)$1	1	118	122	12.0000
))))	chr19:41807417-41807668(+)$1	1	85	89	12.0000
((..	chr20:3128728-3128948(-)$1	1	70	74	12.0000
...)	chr10:77160887-77161115(-)$1	1	55	59	12.0000
((((	chr17:62499451-62499683(-)$1	1	44	48	12.0000
)))(	chr12:133281143-133281374(+)$1	1	87	91	12.0000
((((	chr3:184048955-184049192(+)$1	1	37	41	12.0000
(((.	chr12:57006797-57007018(-)$1	1	40	44	12.0000
((((	chr15:80988065-80988307(+)$1	1	12	16	12.0000
.(((	chr22:29176952-29177175(+)$1	1	18	22	12.0000
(.((	chr3:15686538-15686769(+)$1	1	131	135	12.0000
....	chr16:4491350-4491584(+)$1	1	109	113	12.0000
.(.(	chr7:99694841-99695094(-)$1	1	135	139	12.0000
.)))	chr2:242099751-242099979(+)$1	1	135	139	12.0000
((((	chr19:19033424-19033664(+)$1	1	5	9	12.0000
....	chrX:153669350-153669573(+)$1	1	75	79	12.0000
..((	chr19:39207715-39207936(+)$1	1	8	12	12.0000
.(((	chr6:142519509-142519753(+)$1	1	208	212	12.0000
....	chr19:52705156-52705387(+)$1	1	38	42	12.0000
))))	chr19:58197813-58198064(+)$1	1	66	70	12.0000
..))	chr5:465185-465405(+)$1	1	170	174	12.0000
(((.	chr8:29194586-29194811(-)$1	1	47	51	12.0000
.(((	chr11:47602346-47602571(+)$1	1	1	5	12.0000
....	chr10:15255475-15255705(-)$1	1	128	132	12.0000
)).)	chr8:21890531-21890751(+)$1	1	128	132	12.0000
)(((	chr16:28844041-28844288(+)$1	1	181	185	12.0000
.)))	chr19:40329690-40329921(-)$1	1	125	129	12.0000
(...	chr22:39908136-39908383(+)$1	1	41	45	12.0000
.(((	chr17:80012481-80012727(+)$1	1	5	9	12.0000
.)))	chr15:89169777-89170010(+)$1	1	45	49	12.0000
((((	chr16:31200397-31200638(+)$1	1	171	175	12.0000
((((	chr19:34942831-34943083(+)$1	1	131	135	12.0000
))))	chr12:125444772-125444995(-)$1	1	213	217	12.0000
))..	chr19:50412194-50412424(-)$1	1	128	132	12.0000
..((	chrX:118604783-118605037(+)$1	1	78	82	12.0000
((..	chr12:7083703-7083926(+)$1	1	45	49	12.0000
((((	chr12:7362561-7362791(+)$1	1	21	25	12.0000
((((	chr12:57036358-57036629(-)$1	1	67	71	12.0000
(((.	chr14:90870162-90870399(+)$1	1	20	24	12.0000
((((	chr6:26032046-26032280(-)$1	1	12	16	12.0000
)).)	chr15:74925146-74925369(-)$1	1	170	174	12.0000
.(((	chr2:170666711-170666942(+)$1	1	2	6	12.0000
(...	chr10:14987022-14987242(-)$1	1	52	56	12.0000
.(((	chr12:131360325-131360556(+)$1	1	152	156	12.0000
.(((	chr1:245027286-245027539(-)$1	1	27	31	12.0000
.)))	chr9:37436559-37436781(+)$1	1	39	43	12.0000
.)))	chr19:15534896-15535121(-)$1	1	10	14	12.0000
((..	chr5:175959283-175959511(-)$1	1	132	136	12.0000
....	chr1:55319617-55319845(-)$1	1	17	21	12.0000
.)))	chrM:6336-6576(+)$1	1	173	177	12.0000
.((.	chr11:129991439-129991681(+)$1	1	99	103	12.0000
((((	chr20:2443640-2443914(-)$1	1	82	86	12.0000
.(((	chr6:44219649-44219871(+)$1	1	114	118	12.0000
....	chr7:156799185-156799419(-)$1	1	149	153	12.0000
)((.	chr10:104486686-104486905(+)$1	1	92	96	12.0000
(.((	chr19:13248262-13248483(+)$1	1	45	49	12.0000
.)))	chrM:6455-6693(+)$1	1	54	58	12.0000
.(((	chr10:129901091-129901322(-)$1	1	39	43	12.0000
((.(	chr12:56575452-56575696(-)$1	1	27	31	12.0000
.(((	chr16:28855194-28855414(-)$1	1	181	185	12.0000
))))	chr12:110929747-110929966(-)$1	1	104	108	12.0000
...(	chr7:142997262-142997487(+)$1	1	32	36	12.0000
(...	chrX:13773181-13773408(+)$1	1	92	96	12.0000
.)))	chr11:61732075-61732306(-)$1	1	102	106	12.0000
((((	chr8:67341446-67341673(+)$1	1	5	9	12.0000
))))	chr19:39408412-39408666(-)$1	1	155	159	12.0000
(((.	chr3:128205545-128205778(-)$1	1	16	20	12.0000
))..	chr10:12240631-12240865(+)$1	1	209	213	12.0000

#PSSM
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	

#score	924.0000000000001
#seq	77
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m2_run1.nuc.txt

#NT
UUUUAUAA	chr8:22879780-22880005(-)$1	225	7	15	15.9000
AUUUAAAA	chr14:103808362-103808583(+)$1	221	141	149	16.3000
UUGUAAAA	chr17:1324642-1324863(-)$1	221	44	52	15.5000
AUUUAAAA	chr6:66041816-66042036(+)$1	220	135	143	16.3000
UUUUGAAA	chr8:66621495-66621721(+)$1	226	41	49	15.9000
UUUUAUAA	chr8:95939012-95939242(-)$1	230	0	8	15.9000
UUUUAAAA	chr11:110041343-110041565(+)$1	222	188	196	20.1000
UUUUAAAA	chr17:29110800-29111030(-)$1	230	167	175	20.1000
uuuuaaaa	chr17:56051110-56051334(-)$1	224	211	219	20.1000
UAUUAAAA	chr1:200828755-200828980(+)$1	225	114	122	15.9000
UUUGAAAA	chrX:106956679-106956909(-)$1	230	175	183	15.4000
UUUUAAGA	chr17:27954150-27954380(-)$1	230	75	83	15.7000
UUUUAAGA	chr1:161721584-161721808(+)$1	224	31	39	15.7000
uuuuagaa	chr5:110465158-110465393(+)$1	235	41	49	16.0000
UUUUAAAA	chr4:8368090-8368320(-)$1	230	219	227	20.1000
UGUUAAAA	chr4:6644304-6644528(+)$1	224	97	105	15.9000
UUUUAGAA	chr3:148745116-148745363(+)$1	247	15	23	16.0000
UCUUAAAA	chr7:19737228-19737458(-)$1	230	59	67	15.9000
UUUUAAAU	chrX:76761578-76761808(-)$1	230	157	165	16.3000
UUUUAAAC	chr3:42266488-42266718(+)$1	230	66	74	15.9000
AUUUAAAA	chr10:113911605-113911835(-)$1	230	118	126	16.3000
CUUUAAAA	chr6:33054424-33054654(+)$1	230	139	147	16.0000
UUUUAAAU	chr16:71890913-71891143(+)$1	230	99	107	16.3000
uuuuacaa	chr3:137880042-137880272(-)$1	230	107	115	15.8000
UUUUAAAA	chr11:113668508-113668730(-)$1	222	7	15	20.1000
UUUUAAAA	chr15:43036384-43036608(-)$1	224	177	185	20.1000
AUUUAAAA	chr7:139107583-139107802(+)$1	219	40	48	16.3000
UUUUAAAG	chr3:160969903-160970133(+)$1	230	141	149	15.9000
UUUUAAAU	chr9:125611427-125611678(-)$1	251	90	98	16.3000
UAUUAAAA	chr5:137842790-137843020(-)$1	230	2	10	15.9000
UCUUAAAA	chr10:63853162-63853393(+)$1	231	169	177	15.9000
UUUUAGAA	chr5:130727981-130728211(+)$1	230	207	215	16.0000
UUUUAAAA	chr15:77338454-77338671(-)$1	217	133	141	20.1000
UUUUAAAA	chr8:79514518-79514748(+)$1	230	128	136	20.1000
UUUUAAAU	chr18:56997328-56997558(-)$1	230	185	193	16.3000
UUUUAAAA	chr3:123213421-123213651(-)$1	230	23	31	20.1000
UUGUAAAA	chr1:44170070-44170300(+)$1	230	70	78	15.5000
uuuuaaau	chr2:28639186-28639408(+)$1	222	52	60	16.3000
UUUUCAAA	chr20:23335261-23335491(+)$1	230	47	55	15.8000
AUUUAAAA	chr14:77935647-77935877(+)$1	230	156	164	16.3000
UGUUAAAA	chr12:131361193-131361423(+)$1	230	97	105	15.9000
UUUUAAAA	chr6:33268919-33269139(-)$1	220	83	91	20.1000
CUUUAAAA	chr14:54896917-54897146(-)$1	229	210	218	16.0000
UUUUGAAA	chr14:54942459-54942689(-)$1	230	219	227	15.9000
UUUUAAAA	chr9:108152571-108152801(+)$1	230	53	61	20.1000
UUUUUAAA	chr13:49783434-49783677(+)$1	243	133	141	16.0000
UUUUUAAA	chr10:3820715-3820945(-)$1	230	185	193	16.0000
UUUUUAAA	chr5:64885804-64886027(-)$1	223	202	210	16.0000
UUUUAAGA	chr1:65299307-65299537(-)$1	230	75	83	15.7000

#otherMatches

#Struct PSSM
GGGeeeee	chr7:131173803-131174026(+)$1	223	113	121	15.4000
mmmmdddd	chr8:22879780-22880005(-)$1	225	7	15	15.9000
5555====	chr14:103808362-103808583(+)$1	221	141	149	16.3000
::::::ee	chr17:1324642-1324863(-)$1	221	44	52	15.5000
oooooccc	chr6:66041816-66042036(+)$1	220	135	143	16.3000
:::::FFF	chr8:66621495-66621721(+)$1	226	41	49	15.9000
:::::::h	chr8:95939012-95939242(-)$1	230	0	8	15.9000
drrrrrrr	chr11:110041343-110041565(+)$1	222	188	196	20.1000
IIIIII::	chr17:29110800-29111030(-)$1	230	167	175	20.1000
::::::::	chr17:56051110-56051334(-)$1	224	211	219	20.1000
e55555ff	chr1:200828755-200828980(+)$1	225	114	122	15.9000
=======!	chrX:106956679-106956909(-)$1	230	175	183	15.4000
fffff]hh	chr17:27954150-27954380(-)$1	230	75	83	15.7000
=====%%%	chr1:161721584-161721808(+)$1	224	31	39	15.7000
ooooo===	chr5:110465158-110465393(+)$1	235	41	49	16.0000
44eeeee:	chr4:8368090-8368320(-)$1	230	219	227	20.1000
ddddoooo	chr4:6644304-6644528(+)$1	224	97	105	15.9000
####hhhh	chr3:148745116-148745363(+)$1	247	15	23	16.0000
dddd::::	chr7:19737228-19737458(-)$1	230	59	67	15.9000
===55555	chrX:76761578-76761808(-)$1	230	157	165	16.3000
e!!ddddo	chr3:42266488-42266718(+)$1	230	66	74	15.9000
E::::::g	chr10:113911605-113911835(-)$1	230	118	126	16.3000
ooooofff	chr6:33054424-33054654(+)$1	230	139	147	16.0000
::::::::	chr16:71890913-71891143(+)$1	230	99	107	16.3000
:FFFFFF:	chr3:137880042-137880272(-)$1	230	107	115	15.8000
::::::::	chr11:113668508-113668730(-)$1	222	7	15	20.1000
@@@@@@@@	chr15:43036384-43036608(-)$1	224	177	185	20.1000
hhhhrrrr	chr7:139107583-139107802(+)$1	219	40	48	16.3000
mmbb333e	chr3:160969903-160970133(+)$1	230	141	149	15.9000
qqqqgggg	chr9:125611427-125611678(-)$1	251	90	98	16.3000
::::::::	chr5:137842790-137843020(-)$1	230	2	10	15.9000
====::==	chr10:63853162-63853393(+)$1	231	169	177	15.9000
FFFFFHHH	chr5:130727981-130728211(+)$1	230	207	215	16.0000
ddd"""dd	chr15:77338454-77338671(-)$1	217	133	141	20.1000
&&&&&&&g	chr8:79514518-79514748(+)$1	230	128	136	20.1000
fffooooo	chr18:56997328-56997558(-)$1	230	185	193	16.3000
::::::::	chr3:123213421-123213651(-)$1	230	23	31	20.1000
ddd^^^^^	chr1:44170070-44170300(+)$1	230	70	78	15.5000
333hhhhh	chr2:28639186-28639408(+)$1	222	52	60	16.3000
LLLCCC:e	chr20:23335261-23335491(+)$1	230	47	55	15.8000
f55555cc	chr14:77935647-77935877(+)$1	230	156	164	16.3000
===:::::	chr12:131361193-131361423(+)$1	230	97	105	15.9000
^^^^^^^^	chr6:33268919-33269139(-)$1	220	83	91	20.1000
DD______	chr14:54896917-54897146(-)$1	229	210	218	16.0000
::::::::	chr14:54942459-54942689(-)$1	230	219	227	15.9000
"iiiiiii	chr9:108152571-108152801(+)$1	230	53	61	20.1000
FFFFFF{E	chr13:49783434-49783677(+)$1	243	133	141	16.0000
==mmmm==	chr10:3820715-3820945(-)$1	230	185	193	16.0000
:::::::e	chr5:64885804-64886027(-)$1	223	202	210	16.0000
ccclllcc	chr1:65299307-65299537(-)$1	230	75	83	15.7000

#DB
)))(((((	chr7:131173803-131174026(+)$1	1	113	121	15.4000
....))))	chr8:22879780-22880005(-)$1	1	7	15	15.9000
....))))	chr14:103808362-103808583(+)$1	1	141	149	16.3000
......((	chr17:1324642-1324863(-)$1	1	44	52	15.5000
.....)))	chr6:66041816-66042036(+)$1	1	135	143	16.3000
.....(((	chr8:66621495-66621721(+)$1	1	41	49	15.9000
.......(	chr8:95939012-95939242(-)$1	1	0	8	15.9000
(.......	chr11:110041343-110041565(+)$1	1	188	196	20.1000
))))))..	chr17:29110800-29111030(-)$1	1	167	175	20.1000
........	chr17:56051110-56051334(-)$1	1	211	219	20.1000
).....))	chr1:200828755-200828980(+)$1	1	114	122	15.9000
(((((((.	chrX:106956679-106956909(-)$1	1	175	183	15.4000
))))).))	chr17:27954150-27954380(-)$1	1	75	83	15.7000
(((((...	chr1:161721584-161721808(+)$1	1	31	39	15.7000
.....)))	chr5:110465158-110465393(+)$1	1	41	49	16.0000
..))))).	chr4:8368090-8368320(-)$1	1	219	227	20.1000
((((....	chr4:6644304-6644528(+)$1	1	97	105	15.9000
....((((	chr3:148745116-148745363(+)$1	1	15	23	16.0000
))))....	chr7:19737228-19737458(-)$1	1	59	67	15.9000
))).....	chrX:76761578-76761808(-)$1	1	157	165	16.3000
(..((((.	chr3:42266488-42266718(+)$1	1	66	74	15.9000
(......(	chr10:113911605-113911835(-)$1	1	118	126	16.3000
.....)))	chr6:33054424-33054654(+)$1	1	139	147	16.0000
........	chr16:71890913-71891143(+)$1	1	99	107	16.3000
.((((((.	chr3:137880042-137880272(-)$1	1	107	115	15.8000
........	chr11:113668508-113668730(-)$1	1	7	15	20.1000
........	chr15:43036384-43036608(-)$1	1	177	185	20.1000
((((....	chr7:139107583-139107802(+)$1	1	40	48	16.3000
..))...)	chr3:160969903-160970133(+)$1	1	141	149	15.9000
....))))	chr9:125611427-125611678(-)$1	1	90	98	16.3000
........	chr5:137842790-137843020(-)$1	1	2	10	15.9000
))))..((	chr10:63853162-63853393(+)$1	1	169	177	15.9000
))))))))	chr5:130727981-130728211(+)$1	1	207	215	16.0000
(((...((	chr15:77338454-77338671(-)$1	1	133	141	20.1000
.......(	chr8:79514518-79514748(+)$1	1	128	136	20.1000
(((.....	chr18:56997328-56997558(-)$1	1	185	193	16.3000
........	chr3:123213421-123213651(-)$1	1	23	31	20.1000
(((.....	chr1:44170070-44170300(+)$1	1	70	78	15.5000
...)))))	chr2:28639186-28639408(+)$1	1	52	60	16.3000
...(((.(	chr20:23335261-23335491(+)$1	1	47	55	15.8000
).....))	chr14:77935647-77935877(+)$1	1	156	164	16.3000
))).....	chr12:131361193-131361423(+)$1	1	97	105	15.9000
........	chr6:33268919-33269139(-)$1	1	83	91	20.1000
))......	chr14:54896917-54897146(-)$1	1	210	218	16.0000
........	chr14:54942459-54942689(-)$1	1	219	227	15.9000
.(((((((	chr9:108152571-108152801(+)$1	1	53	61	20.1000
((((((.(	chr13:49783434-49783677(+)$1	1	133	141	16.0000
((....))	chr10:3820715-3820945(-)$1	1	185	193	16.0000
.......(	chr5:64885804-64886027(-)$1	1	202	210	16.0000
(((...))	chr1:65299307-65299537(-)$1	1	75	83	15.7000

#PSSM
U : 0.78	A : 0.10	u : 0.08	C : 0.04	
U : 0.80	u : 0.08	A : 0.04	G : 0.04	C : 0.04	
U : 0.88	u : 0.08	G : 0.04	
U : 0.88	u : 0.08	C : 0.02	G : 0.02	
A : 0.80	a : 0.08	U : 0.06	G : 0.04	C : 0.02	
A : 0.84	U : 0.04	a : 0.04	G : 0.04	g : 0.02	c : 0.02	
A : 0.86	a : 0.08	G : 0.06	
A : 0.80	U : 0.08	a : 0.06	C : 0.02	G : 0.02	u : 0.02	

#score	843.4000000000007
#seq	50
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_UTR_m1_run2.nuc.txt

#NT
UCUU	chr16:22345352-22345655(+)$1	303	10	14	11.9999
UCUU	chr19:4794873-4795127(+)$1	254	123	127	11.9999
UCUu	chr19:45910505-45910789(-)$1	284	88	92	11.9999
UCUU	chr2:61726751-61727129(-)$1	378	33	37	11.9999
UCUU	chr16:69943276-69943553(+)$1	277	70	74	11.9999
UCUU	chr1:54417562-54417826(+)$1	264	113	117	11.9999
UCUU	chr6:136581109-136581430(-)$1	321	108	112	11.9999
UCUU	chr20:43955433-43955813(-)$1	380	62	66	11.9999
UCUU	chr21:43410323-43410676(-)$1	353	33	37	11.9999
UCUU	chr1:202300832-202301184(-)$1	352	89	93	11.9999
UCUU	chr22:40725966-40726218(+)$1	252	5	9	11.9999
UCUU	chr10:101151823-101152282(+)$1	459	181	185	11.9999
UCUU	chr18:20876664-20876913(-)$1	249	161	165	11.9999
UCUU	chr3:58279680-58279972(+)$1	292	69	73	11.9999
UCUU	chr14:103196236-103196553(+)$1	317	88	92	11.9999
UCUU	chr3:197510591-197510919(+)$1	328	26	30	11.9999
UCUU	chr14:55534407-55534747(+)$1	340	19	23	11.9999
UCUU	chr3:39137437-39137813(+)$1	376	115	119	11.9999
UCUU	chr14:64938482-64938730(+)$1	248	46	50	11.9999
UCUU	chr15:63556669-63556902(+)$1	233	65	69	11.9999
UCUU	chr6:7249302-7249576(+)$1	274	179	183	11.9999
UCUU	chr9:135569949-135570270(+)$1	321	125	129	11.9999
UCUU	chr13:74264514-74264935(-)$1	421	109	113	11.9999
UCUU	chr3:120115443-120115777(-)$1	334	13	17	11.9999
UCUU	chr17:45197747-45197995(-)$1	248	7	11	11.9999
UCUU	chr2:38971834-38972121(-)$1	287	115	119	11.9999
ucuu	chr1:52378194-52378564(-)$1	370	32	36	11.9999
UCUU	chr12:49522519-49522762(-)$1	243	58	62	11.9999
UCUU	chr14:54944535-54944891(-)$1	356	212	216	11.9999
UCUU	chr6:90343644-90344093(-)$1	449	110	114	11.9999
ucuu	chr11:107833556-107833883(+)$1	327	261	265	11.9999
UCUU	chr1:157091381-157091814(-)$1	433	2	6	11.9999
ucuu	chr1:36067275-36067735(-)$1	460	2	6	11.9999
UCUU	chr3:73115909-73116251(+)$1	342	108	112	11.9999
UCUU	chr10:101153249-101153532(+)$1	283	139	143	11.9999
UCUU	chr20:43705761-43706185(+)$1	424	114	118	11.9999
ucuu	chr19:37236582-37236992(-)$1	410	117	121	11.9999
UCUU	chr17:65073008-65073378(-)$1	370	49	53	11.9999
UCUU	chr17:32965550-32965909(+)$1	359	118	122	11.9999
UCUU	chr12:70747615-70747951(+)$1	336	114	118	11.9999
UCUU	chr12:6623342-6623605(+)$1	263	74	78	11.9999
UCUU	chr1:180854188-180854519(+)$1	331	118	122	11.9999
UCUU	chr19:18306969-18307357(+)$1	388	367	371	11.9999
UCUU	chr22:39912906-39913374(+)$1	468	65	69	11.9999
UCUU	chr17:58524228-58524565(-)$1	337	23	27	11.9999
UCUU	chr3:167727852-167728153(-)$1	301	134	138	11.9999
UCUU	chr2:109492448-109492787(+)$1	339	109	113	11.9999
UCUU	chr2:120020932-120021231(+)$1	299	46	50	11.9999
UCUU	chr7:99704693-99705057(-)$1	364	306	310	11.9999
UCUU	chr8:77777885-77778178(+)$1	293	262	266	11.9999
UCUU	chr13:111291879-111292219(+)$1	340	37	41	11.9999
UCUU	chr17:28793485-28793833(+)$1	348	124	128	11.9999
UCUU	chr8:91634275-91634520(-)$1	245	234	238	11.9999
UCUU	chr3:57304947-57305440(+)$1	493	221	225	11.9999
UCUU	chr8:104080940-104081251(+)$1	311	138	142	11.9999
UCUU	chr1:27181017-27181344(+)$1	327	36	40	11.9999
UCUU	chr12:57450587-57450934(-)$1	347	54	58	11.9999
UCUU	chr11:117038979-117039254(+)$1	275	4	8	11.9999
UCUU	chrX:48929151-48929613(-)$1	462	292	296	11.9999
UCUU	chr15:77401081-77401463(-)$1	382	274	278	11.9999
UCUU	chr1:169433435-169433681(-)$1	246	144	148	11.9999
UCUU	chr2:73479879-73480223(+)$1	344	213	217	11.9999
UCUU	chr6:132780818-132781211(-)$1	393	86	90	11.9999
UCUU	chr4:108535036-108535308(-)$1	272	102	106	11.9999
UCUU	chr11:95504434-95504683(-)$1	249	239	243	11.9999
UCUU	chr13:26787472-26787815(-)$1	343	169	173	11.9999
UCUU	chrX:77082104-77082546(-)$1	442	223	227	11.9999
UCUU	chr16:4013499-4013769(-)$1	270	131	135	11.9999
UCUU	chr3:150176165-150176458(+)$1	293	84	88	11.9999
UCUU	chr5:112355316-112355683(+)$1	367	3	7	11.9999
UCUU	chr20:58521279-58521596(+)$1	317	16	20	11.9999
UCUU	chr1:110943862-110944262(-)$1	400	41	45	11.9999
UCUU	chr12:121135708-121135999(+)$1	291	70	74	11.9999
UCUU	chr12:115108370-115108660(-)$1	290	51	55	11.9999
UCUU	chr15:52104943-52105240(+)$1	297	30	34	11.9999
UCUU	chr4:143094770-143095006(-)$1	236	29	33	11.9999
UCUU	chr19:17535963-17536239(+)$1	276	218	222	11.9999
UCUU	chr2:136664675-136664911(-)$1	236	114	118	11.9999
UCUU	chr12:96672577-96672863(-)$1	286	23	27	11.9999
UCUU	chr1:85111090-85111499(-)$1	409	249	253	11.9999
UCUU	chr10:72640305-72640664(+)$1	359	38	42	11.9999
UCUU	chr19:1609192-1609523(-)$1	331	159	163	11.9999
UCUU	chr6:53132881-53133212(-)$1	331	30	34	11.9999
UCUU	chr10:123501279-123501525(-)$1	246	19	23	11.9999
UCUU	chr3:12623936-12624289(+)$1	353	128	132	11.9999
UCUU	chrX:47430946-47431269(+)$1	323	64	68	11.9999
UCUU	chr10:72181584-72182051(+)$1	467	50	54	11.9999
UCUU	chr12:56635033-56635287(-)$1	254	19	23	11.9999
UCUU	chr7:77410239-77410530(+)$1	291	69	73	11.9999
UCUU	chr8:26269092-26269436(+)$1	344	30	34	11.9999
UCUU	chr9:35757965-35758432(+)$1	467	47	51	11.9999
UCUU	chr11:69466372-69466748(+)$1	376	180	184	11.9999

#otherMatches

#Struct PSSM
bb22	chr19:46214516-46214814(-)$1	298	62	66	11.9999
hhhh	chr16:22345352-22345655(+)$1	303	10	14	11.9999
oooo	chr19:4794873-4795127(+)$1	254	123	127	11.9999
::::	chr19:45910505-45910789(-)$1	284	88	92	11.9999
ffll	chr2:61726751-61727129(-)$1	378	33	37	11.9999
:::F	chr16:69943276-69943553(+)$1	277	70	74	11.9999
eeee	chr1:54417562-54417826(+)$1	264	113	117	11.9999
::::	chr6:136581109-136581430(-)$1	321	108	112	11.9999
eeee	chr20:43955433-43955813(-)$1	380	62	66	11.9999
!eee	chr21:43410323-43410676(-)$1	353	33	37	11.9999
ffff	chr1:202300832-202301184(-)$1	352	89	93	11.9999
ffff	chr22:40725966-40726218(+)$1	252	5	9	11.9999
eeee	chr10:101151823-101152282(+)$1	459	181	185	11.9999
bccc	chr18:20876664-20876913(-)$1	249	161	165	11.9999
IIII	chr3:58279680-58279972(+)$1	292	69	73	11.9999
i###	chr14:103196236-103196553(+)$1	317	88	92	11.9999
]ddd	chr3:197510591-197510919(+)$1	328	26	30	11.9999
rrrr	chr14:55534407-55534747(+)$1	340	19	23	11.9999
>>>>	chr3:39137437-39137813(+)$1	376	115	119	11.9999
[ccc	chr14:64938482-64938730(+)$1	248	46	50	11.9999
333d	chr15:63556669-63556902(+)$1	233	65	69	11.9999
!ddd	chr6:7249302-7249576(+)$1	274	179	183	11.9999
eeee	chr9:135569949-135570270(+)$1	321	125	129	11.9999
hhh]	chr13:74264514-74264935(-)$1	421	109	113	11.9999
MMMM	chr3:120115443-120115777(-)$1	334	13	17	11.9999
HHHH	chr17:45197747-45197995(-)$1	248	7	11	11.9999
gggg	chr2:38971834-38972121(-)$1	287	115	119	11.9999
qqdd	chr1:52378194-52378564(-)$1	370	32	36	11.9999
qqqq	chr12:49522519-49522762(-)$1	243	58	62	11.9999
eeee	chr14:54944535-54944891(-)$1	356	212	216	11.9999
"""d	chr6:90343644-90344093(-)$1	449	110	114	11.9999
dttt	chr11:107833556-107833883(+)$1	327	261	265	11.9999
::::	chr1:157091381-157091814(-)$1	433	2	6	11.9999
::::	chr1:36067275-36067735(-)$1	460	2	6	11.9999
!!ee	chr3:73115909-73116251(+)$1	342	108	112	11.9999
eeee	chr10:101153249-101153532(+)$1	283	139	143	11.9999
fddd	chr20:43705761-43706185(+)$1	424	114	118	11.9999
gggg	chr19:37236582-37236992(-)$1	410	117	121	11.9999
dddd	chr17:65073008-65073378(-)$1	370	49	53	11.9999
]a::	chr17:32965550-32965909(+)$1	359	118	122	11.9999
e:::	chr12:70747615-70747951(+)$1	336	114	118	11.9999
fttt	chr12:6623342-6623605(+)$1	263	74	78	11.9999
gggg	chr1:180854188-180854519(+)$1	331	118	122	11.9999
||||	chr19:18306969-18307357(+)$1	388	367	371	11.9999
::::	chr22:39912906-39913374(+)$1	468	65	69	11.9999
FFFF	chr17:58524228-58524565(-)$1	337	23	27	11.9999
ffff	chr3:167727852-167728153(-)$1	301	134	138	11.9999
bb!!	chr2:109492448-109492787(+)$1	339	109	113	11.9999
JJJJ	chr2:120020932-120021231(+)$1	299	46	50	11.9999
e!!d	chr7:99704693-99705057(-)$1	364	306	310	11.9999
3a22	chr8:77777885-77778178(+)$1	293	262	266	11.9999
dddm	chr13:111291879-111292219(+)$1	340	37	41	11.9999
gggg	chr17:28793485-28793833(+)$1	348	124	128	11.9999
BYYD	chr8:91634275-91634520(-)$1	245	234	238	11.9999
====	chr3:57304947-57305440(+)$1	493	221	225	11.9999
2bb:	chr8:104080940-104081251(+)$1	311	138	142	11.9999
meee	chr1:27181017-27181344(+)$1	327	36	40	11.9999
::::	chr12:57450587-57450934(-)$1	347	54	58	11.9999
::::	chr11:117038979-117039254(+)$1	275	4	8	11.9999
bqqq	chrX:48929151-48929613(-)$1	462	292	296	11.9999
ccc]	chr15:77401081-77401463(-)$1	382	274	278	11.9999
::==	chr1:169433435-169433681(-)$1	246	144	148	11.9999
uuuu	chr2:73479879-73480223(+)$1	344	213	217	11.9999
ffff	chr6:132780818-132781211(-)$1	393	86	90	11.9999
''''	chr4:108535036-108535308(-)$1	272	102	106	11.9999
iiii	chr11:95504434-95504683(-)$1	249	239	243	11.9999
uuuu	chr13:26787472-26787815(-)$1	343	169	173	11.9999
c[ff	chrX:77082104-77082546(-)$1	442	223	227	11.9999
ETTT	chr16:4013499-4013769(-)$1	270	131	135	11.9999
bb[b	chr3:150176165-150176458(+)$1	293	84	88	11.9999
:fff	chr5:112355316-112355683(+)$1	367	3	7	11.9999
DKKG	chr20:58521279-58521596(+)$1	317	16	20	11.9999
JJJJ	chr1:110943862-110944262(-)$1	400	41	45	11.9999
BLLL	chr12:121135708-121135999(+)$1	291	70	74	11.9999
!ddd	chr12:115108370-115108660(-)$1	290	51	55	11.9999
EEEE	chr15:52104943-52105240(+)$1	297	30	34	11.9999
:::C	chr4:143094770-143095006(-)$1	236	29	33	11.9999
[eee	chr19:17535963-17536239(+)$1	276	218	222	11.9999
gggg	chr2:136664675-136664911(-)$1	236	114	118	11.9999
!!ee	chr12:96672577-96672863(-)$1	286	23	27	11.9999
DDDD	chr1:85111090-85111499(-)$1	409	249	253	11.9999
KDDD	chr10:72640305-72640664(+)$1	359	38	42	11.9999
qqqq	chr19:1609192-1609523(-)$1	331	159	163	11.9999
hhh"	chr6:53132881-53133212(-)$1	331	30	34	11.9999
JJJJ	chr10:123501279-123501525(-)$1	246	19	23	11.9999
8888	chr3:12623936-12624289(+)$1	353	128	132	11.9999
nnnn	chrX:47430946-47431269(+)$1	323	64	68	11.9999
^^^^	chr10:72181584-72182051(+)$1	467	50	54	11.9999
VVVV	chr12:56635033-56635287(-)$1	254	19	23	11.9999
::::	chr7:77410239-77410530(+)$1	291	69	73	11.9999
oooo	chr8:26269092-26269436(+)$1	344	30	34	11.9999
uuuu	chr9:35757965-35758432(+)$1	467	47	51	11.9999
dddh	chr11:69466372-69466748(+)$1	376	180	184	11.9999

#DB
))..	chr19:46214516-46214814(-)$1	1	62	66	11.9999
((((	chr16:22345352-22345655(+)$1	1	10	14	11.9999
....	chr19:4794873-4795127(+)$1	1	123	127	11.9999
....	chr19:45910505-45910789(-)$1	1	88	92	11.9999
((..	chr2:61726751-61727129(-)$1	1	33	37	11.9999
...(	chr16:69943276-69943553(+)$1	1	70	74	11.9999
))))	chr1:54417562-54417826(+)$1	1	113	117	11.9999
....	chr6:136581109-136581430(-)$1	1	108	112	11.9999
))))	chr20:43955433-43955813(-)$1	1	62	66	11.9999
.(((	chr21:43410323-43410676(-)$1	1	33	37	11.9999
((((	chr1:202300832-202301184(-)$1	1	89	93	11.9999
((((	chr22:40725966-40726218(+)$1	1	5	9	11.9999
((((	chr10:101151823-101152282(+)$1	1	181	185	11.9999
))))	chr18:20876664-20876913(-)$1	1	161	165	11.9999
((((	chr3:58279680-58279972(+)$1	1	69	73	11.9999
(...	chr14:103196236-103196553(+)$1	1	88	92	11.9999
.)))	chr3:197510591-197510919(+)$1	1	26	30	11.9999
....	chr14:55534407-55534747(+)$1	1	19	23	11.9999
....	chr3:39137437-39137813(+)$1	1	115	119	11.9999
.(((	chr14:64938482-64938730(+)$1	1	46	50	11.9999
...)	chr15:63556669-63556902(+)$1	1	65	69	11.9999
.(((	chr6:7249302-7249576(+)$1	1	179	183	11.9999
))))	chr9:135569949-135570270(+)$1	1	125	129	11.9999
))).	chr13:74264514-74264935(-)$1	1	109	113	11.9999
....	chr3:120115443-120115777(-)$1	1	13	17	11.9999
((((	chr17:45197747-45197995(-)$1	1	7	11	11.9999
((((	chr2:38971834-38972121(-)$1	1	115	119	11.9999
..))	chr1:52378194-52378564(-)$1	1	32	36	11.9999
....	chr12:49522519-49522762(-)$1	1	58	62	11.9999
((((	chr14:54944535-54944891(-)$1	1	212	216	11.9999
...(	chr6:90343644-90344093(-)$1	1	110	114	11.9999
(...	chr11:107833556-107833883(+)$1	1	261	265	11.9999
....	chr1:157091381-157091814(-)$1	1	2	6	11.9999
....	chr1:36067275-36067735(-)$1	1	2	6	11.9999
..((	chr3:73115909-73116251(+)$1	1	108	112	11.9999
))))	chr10:101153249-101153532(+)$1	1	139	143	11.9999
)(((	chr20:43705761-43706185(+)$1	1	114	118	11.9999
((((	chr19:37236582-37236992(-)$1	1	117	121	11.9999
((((	chr17:65073008-65073378(-)$1	1	49	53	11.9999
.)..	chr17:32965550-32965909(+)$1	1	118	122	11.9999
)...	chr12:70747615-70747951(+)$1	1	114	118	11.9999
(...	chr12:6623342-6623605(+)$1	1	74	78	11.9999
))))	chr1:180854188-180854519(+)$1	1	118	122	11.9999
....	chr19:18306969-18307357(+)$1	1	367	371	11.9999
....	chr22:39912906-39913374(+)$1	1	65	69	11.9999
((((	chr17:58524228-58524565(-)$1	1	23	27	11.9999
))))	chr3:167727852-167728153(-)$1	1	134	138	11.9999
((..	chr2:109492448-109492787(+)$1	1	109	113	11.9999
((((	chr2:120020932-120021231(+)$1	1	46	50	11.9999
(..(	chr7:99704693-99705057(-)$1	1	306	310	11.9999
.)..	chr8:77777885-77778178(+)$1	1	262	266	11.9999
(((.	chr13:111291879-111292219(+)$1	1	37	41	11.9999
((((	chr17:28793485-28793833(+)$1	1	124	128	11.9999
)..)	chr8:91634275-91634520(-)$1	1	234	238	11.9999
))))	chr3:57304947-57305440(+)$1	1	221	225	11.9999
.)).	chr8:104080940-104081251(+)$1	1	138	142	11.9999
.)))	chr1:27181017-27181344(+)$1	1	36	40	11.9999
....	chr12:57450587-57450934(-)$1	1	54	58	11.9999
....	chr11:117038979-117039254(+)$1	1	4	8	11.9999
(...	chrX:48929151-48929613(-)$1	1	292	296	11.9999
))).	chr15:77401081-77401463(-)$1	1	274	278	11.9999
..((	chr1:169433435-169433681(-)$1	1	144	148	11.9999
....	chr2:73479879-73480223(+)$1	1	213	217	11.9999
))))	chr6:132780818-132781211(-)$1	1	86	90	11.9999
....	chr4:108535036-108535308(-)$1	1	102	106	11.9999
))))	chr11:95504434-95504683(-)$1	1	239	243	11.9999
....	chr13:26787472-26787815(-)$1	1	169	173	11.9999
(.((	chrX:77082104-77082546(-)$1	1	223	227	11.9999
(...	chr16:4013499-4013769(-)$1	1	131	135	11.9999
((.(	chr3:150176165-150176458(+)$1	1	84	88	11.9999
.(((	chr5:112355316-112355683(+)$1	1	3	7	11.9999
(..(	chr20:58521279-58521596(+)$1	1	16	20	11.9999
((((	chr1:110943862-110944262(-)$1	1	41	45	11.9999
(...	chr12:121135708-121135999(+)$1	1	70	74	11.9999
.(((	chr12:115108370-115108660(-)$1	1	51	55	11.9999
((((	chr15:52104943-52105240(+)$1	1	30	34	11.9999
...(	chr4:143094770-143095006(-)$1	1	29	33	11.9999
.(((	chr19:17535963-17536239(+)$1	1	218	222	11.9999
))))	chr2:136664675-136664911(-)$1	1	114	118	11.9999
..((	chr12:96672577-96672863(-)$1	1	23	27	11.9999
))))	chr1:85111090-85111499(-)$1	1	249	253	11.9999
.(((	chr10:72640305-72640664(+)$1	1	38	42	11.9999
....	chr19:1609192-1609523(-)$1	1	159	163	11.9999
(((.	chr6:53132881-53133212(-)$1	1	30	34	11.9999
((((	chr10:123501279-123501525(-)$1	1	19	23	11.9999
....	chr3:12623936-12624289(+)$1	1	128	132	11.9999
....	chrX:47430946-47431269(+)$1	1	64	68	11.9999
....	chr10:72181584-72182051(+)$1	1	50	54	11.9999
....	chr12:56635033-56635287(-)$1	1	19	23	11.9999
....	chr7:77410239-77410530(+)$1	1	69	73	11.9999
....	chr8:26269092-26269436(+)$1	1	30	34	11.9999
....	chr9:35757965-35758432(+)$1	1	47	51	11.9999
)))(	chr11:69466372-69466748(+)$1	1	180	184	11.9999

#PSSM
U : 0.95	u : 0.04	
C : 0.95	c : 0.04	
U : 0.95	u : 0.04	
U : 0.94	u : 0.05	

#score	1115.9999999999998
#seq	93
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m2_run2.nuc.txt

#NT
GAGCAG	chr19:10218680-10218910(+)$1	230	10	16	11.7068
GAGAAG	chr12:133327205-133327462(-)$1	257	114	120	15.0689
GAGAAG	chr17:76989669-76989922(-)$1	253	9	15	15.0689
GAGAAG	chr1:32495878-32496106(+)$1	228	25	31	15.0689
gagcag	chr20:42320694-42320923(+)$1	229	9	15	11.7068
GAGAAG	chr2:47388796-47389022(-)$1	226	82	88	15.0689
GAGAAG	chr11:3039600-3039836(-)$1	236	184	190	15.0689
GAGAAG	chr17:4083019-4083247(-)$1	228	116	122	15.0689
GAGGAG	chr1:229789967-229790218(+)$1	251	108	114	11.6206
GAGAAG	chrX:53432193-53432423(-)$1	230	214	220	15.0689
GAGAAG	chr22:35819193-35819419(+)$1	226	63	69	15.0689
AAGAAG	chr12:57906441-57906684(+)$1	243	13	19	12.3103
CAGAAG	chr2:174228470-174228712(+)$1	242	4	10	12.2241
GAGAAG	chr1:26230131-26230366(-)$1	235	82	88	15.0689
UAGAAG	chr15:35149083-35149313(-)$1	230	34	40	11.8793
GAGAAG	chr7:155457821-155458047(+)$1	226	93	99	15.0689
GAGCAG	chr6:43483667-43483903(-)$1	236	7	13	11.7068
GAGAAG	chr5:33457373-33457596(+)$1	223	84	90	15.0689
GAGAAG	chr5:179048220-179048449(-)$1	229	99	105	15.0689
GAGAAG	chr1:226027536-226027771(+)$1	235	129	135	15.0689
AAGAAG	chr19:41800223-41800453(+)$1	230	94	100	12.3103
GAGAAG	chr17:42225329-42225558(+)$1	229	183	189	15.0689
GAGUAG	chrM:7944-8173(+)$1	229	63	69	11.3620
UAGAAG	chr8:103359138-103359393(-)$1	255	70	76	11.8793
GAGGAG	chrM:14245-14483(-)$1	238	34	40	11.6206
GAGAAG	chr19:10781976-10782242(+)$1	266	175	181	15.0689
CAGAAG	chr5:36958192-36958419(+)$1	227	45	51	12.2241
CAGAAG	chr11:124496707-124496931(+)$1	224	188	194	12.2241
GAGAAG	chr17:1268166-1268395(-)$1	229	202	208	15.0689
GAGAGG	chr16:2806359-2806585(+)$1	226	118	124	10.5862
AAGAAG	chr16:11940478-11940707(-)$1	229	28	34	12.3103
CAGAAG	chr10:62551654-62551908(+)$1	254	18	24	12.2241
GAGCAG	chr7:99690471-99690713(-)$1	242	39	45	11.7068
AAGAAG	chr10:5803178-5803406(+)$1	228	93	99	12.3103
GAGAAG	chrX:53409155-53409385(-)$1	230	189	195	15.0689
GAGAAG	chr6:26056399-26056630(-)$1	231	19	25	15.0689
GAGAAG	chr16:30750743-30750994(+)$1	251	17	23	15.0689
GAGCAG	chr1:211751403-211751627(-)$1	224	185	191	11.7068
CAGAAG	chr13:114152671-114152901(+)$1	230	215	221	12.2241
GAGAGG	chr19:18120521-18120742(+)$1	221	70	76	10.5862
AAGAAG	chr2:54856440-54856666(+)$1	226	39	45	12.3103
UAGAAG	chrM:7599-7832(+)$1	233	36	42	11.8793
GAGCAG	chr21:45209509-45209734(+)$1	225	61	67	11.7068
CAGAAG	chr7:150911893-150912145(-)$1	252	7	13	12.2241
GAGGAG	chr22:50356496-50356720(+)$1	224	0	6	11.6206
GAGAAG	chr16:89347357-89347597(-)$1	240	168	174	15.0689
GAGAAG	chr19:6383225-6383458(-)$1	233	31	37	15.0689
GAGGAG	chr12:120427641-120427862(+)$1	221	199	205	11.6206
AAGAAG	chr12:49666064-49666288(+)$1	224	82	88	12.3103
GAGGAG	chr22:35799379-35799618(+)$1	239	84	90	11.6206
GAGAAG	chr1:35580648-35580876(+)$1	228	92	98	15.0689
AAGAAG	chr22:43529139-43529366(-)$1	227	15	21	12.3103
GAGAGG	chrX:71493077-71493311(-)$1	234	134	140	10.5862
AAGAAG	chr12:6787262-6787484(-)$1	222	1	7	12.3103
GAGUAG	chr1:182827633-182827864(+)$1	231	16	22	11.3620
CAGAAG	chr9:125673984-125674212(-)$1	228	93	99	12.2241
GAGAAG	chr11:64536878-64537111(-)$1	233	52	58	15.0689

#otherMatches

#Struct PSSM
bb333g	chr19:5657201-5657442(+)$1	241	86	92	15.0689
mmcccb	chr19:10218680-10218910(+)$1	230	10	16	11.7068
dddd%%	chr12:133327205-133327462(-)$1	257	114	120	15.0689
BBIIII	chr17:76989669-76989922(-)$1	253	9	15	15.0689
eee###	chr1:32495878-32496106(+)$1	228	25	31	15.0689
{FFFFF	chr20:42320694-42320923(+)$1	229	9	15	11.7068
xxxxxd	chr2:47388796-47389022(-)$1	226	82	88	15.0689
IIIIII	chr11:3039600-3039836(-)$1	236	184	190	15.0689
c:::::	chr17:4083019-4083247(-)$1	228	116	122	15.0689
d[bb""	chr1:229789967-229790218(+)$1	251	108	114	11.6206
2ccc]c	chrX:53432193-53432423(-)$1	230	214	220	15.0689
qqqqqb	chr22:35819193-35819419(+)$1	226	63	69	15.0689
{EEEEE	chr12:57906441-57906684(+)$1	243	13	19	12.3103
:IIIII	chr2:174228470-174228712(+)$1	242	4	10	12.2241
eeeeee	chr1:26230131-26230366(-)$1	235	82	88	15.0689
fff:::	chr15:35149083-35149313(-)$1	230	34	40	11.8793
DKKCCC	chr7:155457821-155458047(+)$1	226	93	99	15.0689
pppccc	chr6:43483667-43483903(-)$1	236	7	13	11.7068
eeeeee	chr5:33457373-33457596(+)$1	223	84	90	15.0689
$$$$$b	chr5:179048220-179048449(-)$1	229	99	105	15.0689
bddddm	chr1:226027536-226027771(+)$1	235	129	135	15.0689
^^^^^^	chr19:41800223-41800453(+)$1	230	94	100	12.3103
CCC}BB	chr17:42225329-42225558(+)$1	229	183	189	15.0689
BDDDD{	chrM:7944-8173(+)$1	229	63	69	11.3620
e"""a[	chr8:103359138-103359393(-)$1	255	70	76	11.8793
4bb22f	chrM:14245-14483(-)$1	238	34	40	11.6206
]a22cc	chr19:10781976-10782242(+)$1	266	175	181	15.0689
"""bb[	chr5:36958192-36958419(+)$1	227	45	51	12.2241
[bb!!d	chr11:124496707-124496931(+)$1	224	188	194	12.2241
JJJ}DD	chr17:1268166-1268395(-)$1	229	202	208	15.0689
ee]ccc	chr16:2806359-2806585(+)$1	226	118	124	10.5862
ttbb]c	chr16:11940478-11940707(-)$1	229	28	34	12.3103
ddd]cc	chr10:62551654-62551908(+)$1	254	18	24	12.2241
FFFFFF	chr7:99690471-99690713(-)$1	242	39	45	11.7068
66eeee	chr10:5803178-5803406(+)$1	228	93	99	12.3103
iii###	chrX:53409155-53409385(-)$1	230	189	195	15.0689
ddd::d	chr6:26056399-26056630(-)$1	231	19	25	15.0689
mmmmdd	chr16:30750743-30750994(+)$1	251	17	23	15.0689
f[bb[c	chr1:211751403-211751627(-)$1	224	185	191	11.7068
6eeeee	chr13:114152671-114152901(+)$1	230	215	221	12.2241
bb[ccc	chr19:18120521-18120742(+)$1	221	70	76	10.5862
mmccc2	chr2:54856440-54856666(+)$1	226	39	45	12.3103
ssdddd	chrM:7599-7832(+)$1	233	36	42	11.8793
oooooo	chr21:45209509-45209734(+)$1	225	61	67	11.7068
ddmmmm	chr7:150911893-150912145(-)$1	252	7	13	12.2241
::dddd	chr22:50356496-50356720(+)$1	224	0	6	11.6206
ddd[cc	chr16:89347357-89347597(-)$1	240	168	174	15.0689
++++++	chr19:6383225-6383458(-)$1	233	31	37	15.0689
CC}DDD	chr12:120427641-120427862(+)$1	221	199	205	11.6206
!dddd[	chr12:49666064-49666288(+)$1	224	82	88	12.3103
f:dddd	chr22:35799379-35799618(+)$1	239	84	90	11.6206
ccc::c	chr1:35580648-35580876(+)$1	228	92	98	15.0689
##ffff	chr22:43529139-43529366(-)$1	227	15	21	12.3103
FFYYBB	chrX:71493077-71493311(-)$1	234	134	140	10.5862
:::::F	chr12:6787262-6787484(-)$1	222	1	7	12.3103
CCC{CC	chr1:182827633-182827864(+)$1	231	16	22	11.3620
ee####	chr9:125673984-125674212(-)$1	228	93	99	12.2241
ccc]gg	chr11:64536878-64537111(-)$1	233	52	58	15.0689

#DB
))...)	chr19:5657201-5657442(+)$1	1	86	92	15.0689
..))))	chr19:10218680-10218910(+)$1	1	10	16	11.7068
((((..	chr12:133327205-133327462(-)$1	1	114	120	15.0689
((((((	chr17:76989669-76989922(-)$1	1	9	15	15.0689
(((...	chr1:32495878-32496106(+)$1	1	25	31	15.0689
.(((((	chr20:42320694-42320923(+)$1	1	9	15	11.7068
.....)	chr2:47388796-47389022(-)$1	1	82	88	15.0689
))))))	chr11:3039600-3039836(-)$1	1	184	190	15.0689
).....	chr17:4083019-4083247(-)$1	1	116	122	15.0689
(.((..	chr1:229789967-229790218(+)$1	1	108	114	11.6206
.))).)	chrX:53432193-53432423(-)$1	1	214	220	15.0689
.....)	chr22:35819193-35819419(+)$1	1	63	69	15.0689
.(((((	chr12:57906441-57906684(+)$1	1	13	19	12.3103
.(((((	chr2:174228470-174228712(+)$1	1	4	10	12.2241
))((((	chr1:26230131-26230366(-)$1	1	82	88	15.0689
)))...	chr15:35149083-35149313(-)$1	1	34	40	11.8793
(..(((	chr7:155457821-155458047(+)$1	1	93	99	15.0689
...)))	chr6:43483667-43483903(-)$1	1	7	13	11.7068
))))))	chr5:33457373-33457596(+)$1	1	84	90	15.0689
.....(	chr5:179048220-179048449(-)$1	1	99	105	15.0689
(((((.	chr1:226027536-226027771(+)$1	1	129	135	15.0689
......	chr19:41800223-41800453(+)$1	1	94	100	12.3103
))).))	chr17:42225329-42225558(+)$1	1	183	189	15.0689
(((((.	chrM:7944-8173(+)$1	1	63	69	11.3620
(...(.	chr8:103359138-103359393(-)$1	1	70	76	11.8793
.))..)	chrM:14245-14483(-)$1	1	34	40	11.6206
.)..))	chr19:10781976-10782242(+)$1	1	175	181	15.0689
...((.	chr5:36958192-36958419(+)$1	1	45	51	12.2241
.((..(	chr11:124496707-124496931(+)$1	1	188	194	12.2241
))).))	chr17:1268166-1268395(-)$1	1	202	208	15.0689
)).)))	chr16:2806359-2806585(+)$1	1	118	124	10.5862
..)).)	chr16:11940478-11940707(-)$1	1	28	34	12.3103
))).))	chr10:62551654-62551908(+)$1	1	18	24	12.2241
((((((	chr7:99690471-99690713(-)$1	1	39	45	11.7068
..))))	chr10:5803178-5803406(+)$1	1	93	99	12.3103
(((...	chrX:53409155-53409385(-)$1	1	189	195	15.0689
)))..(	chr6:26056399-26056630(-)$1	1	19	25	15.0689
....))	chr16:30750743-30750994(+)$1	1	17	23	15.0689
(.((.(	chr1:211751403-211751627(-)$1	1	185	191	11.7068
.)))))	chr13:114152671-114152901(+)$1	1	215	221	12.2241
((.(((	chr19:18120521-18120742(+)$1	1	70	76	10.5862
..))).	chr2:54856440-54856666(+)$1	1	39	45	12.3103
..))))	chrM:7599-7832(+)$1	1	36	42	11.8793
......	chr21:45209509-45209734(+)$1	1	61	67	11.7068
((....	chr7:150911893-150912145(-)$1	1	7	13	12.2241
..((((	chr22:50356496-50356720(+)$1	1	0	6	11.6206
(((.((	chr16:89347357-89347597(-)$1	1	168	174	15.0689
......	chr19:6383225-6383458(-)$1	1	31	37	15.0689
)).)))	chr12:120427641-120427862(+)$1	1	199	205	11.6206
.((((.	chr12:49666064-49666288(+)$1	1	82	88	12.3103
).((((	chr22:35799379-35799618(+)$1	1	84	90	11.6206
)))..(	chr1:35580648-35580876(+)$1	1	92	98	15.0689
..((((	chr22:43529139-43529366(-)$1	1	15	21	12.3103
))..))	chrX:71493077-71493311(-)$1	1	134	140	10.5862
.....(	chr12:6787262-6787484(-)$1	1	1	7	12.3103
(((.((	chr1:182827633-182827864(+)$1	1	16	22	11.3620
((....	chr9:125673984-125674212(-)$1	1	93	99	12.2241
))).))	chr11:64536878-64537111(-)$1	1	52	58	15.0689

#PSSM
G : 0.67	A : 0.13	C : 0.12	U : 0.05	g : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.77	C : 0.08	G : 0.08	U : 0.03	c : 0.01	
A : 0.93	G : 0.05	a : 0.01	
G : 0.98	g : 0.01	

#score	764.172413793104
#seq	58
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m1_run2.nuc.txt

#NT
UGG	chr15:75091568-75091792(+)$1	224	8	11	9.0000
UGG	chr16:58616664-58616894(-)$1	230	45	48	9.0000
UGG	chr7:150776622-150776846(-)$1	224	20	23	9.0000
ugg	chr10:103871146-103871379(-)$1	233	14	17	9.0000
UGG	chr7:135612347-135612610(-)$1	263	16	19	9.0000
UGG	chr16:23546198-23546452(-)$1	254	1	4	9.0000
UGG	chr16:2569620-2569843(+)$1	223	5	8	9.0000
UGG	chr5:44809196-44809419(+)$1	223	10	13	9.0000
UGG	chr16:24828145-24828378(+)$1	233	1	4	9.0000
UGG	chr10:43292237-43292465(+)$1	228	83	86	9.0000
UGG	chr9:95036612-95036834(-)$1	222	42	45	9.0000
UGG	chr17:42225329-42225558(+)$1	229	56	59	9.0000
UGG	chr17:80363132-80363361(-)$1	229	31	34	9.0000
UGG	chr8:48885435-48885668(+)$1	233	4	7	9.0000
UGG	chr9:139277761-139277988(-)$1	227	61	64	9.0000
UGG	chr17:1557124-1557352(-)$1	228	50	53	9.0000
ugg	chr3:127816209-127816433(-)$1	224	1	4	9.0000
UGG	chr12:113596655-113596897(-)$1	242	101	104	9.0000
UGG	chr1:40627071-40627300(+)$1	229	1	4	9.0000
UGG	chr1:16273464-16273692(-)$1	228	3	6	9.0000
UGG	chr5:36958192-36958419(+)$1	227	31	34	9.0000
UGG	chr1:35580648-35580876(+)$1	228	8	11	9.0000
UGG	chr9:33466820-33467061(-)$1	241	10	13	9.0000
UGG	chr7:90895022-90895243(+)$1	221	44	47	9.0000
UGG	chr19:4432997-4433227(+)$1	230	9	12	9.0000
UGG	chr19:39961902-39962176(+)$1	274	116	119	9.0000
UGG	chr11:46392946-46393174(+)$1	228	29	32	9.0000
UGG	chr1:23650022-23650265(-)$1	243	11	14	9.0000
UGG	chr8:145748272-145748496(+)$1	224	83	86	9.0000
UGG	chr7:56022549-56022804(+)$1	255	14	17	9.0000
UGG	chr7:44608629-44608855(-)$1	226	24	27	9.0000
UGG	chr11:62648368-62648598(+)$1	230	50	53	9.0000
UGG	chr17:1554448-1554679(-)$1	231	0	3	9.0000
UGG	chr16:30750743-30750994(+)$1	251	52	55	9.0000
UGG	chr21:45209509-45209734(+)$1	225	2	5	9.0000
UGG	chr19:10250257-10250481(-)$1	224	23	26	9.0000
UGG	chr18:12814105-12814332(-)$1	227	39	42	9.0000
UGG	chr7:72891670-72891913(-)$1	243	35	38	9.0000
UGG	chr20:62340357-62340584(+)$1	227	8	11	9.0000
UGG	chr19:15367821-15368057(-)$1	236	31	34	9.0000
UGG	chr17:76415569-76415808(+)$1	239	3	6	9.0000
UGG	chr12:6636874-6637109(+)$1	235	7	10	9.0000
UGG	chr20:57485740-57485968(+)$1	228	14	17	9.0000
UGG	chr3:122087032-122087258(-)$1	226	93	96	9.0000
UGG	chrM:14957-15211(+)$1	254	14	17	9.0000
UGG	chrX:47073899-47074138(+)$1	239	127	130	9.0000
UGG	chr16:67914532-67914787(+)$1	255	91	94	9.0000
UGG	chr16:3077154-3077400(+)$1	246	21	24	9.0000
UGG	chrX:70516755-70516984(+)$1	229	9	12	9.0000
UGG	chr2:47630363-47630607(+)$1	244	121	124	9.0000
UGG	chr16:58587595-58587826(-)$1	231	39	42	9.0000
UGG	chr5:139914874-139915107(+)$1	233	2	5	9.0000
UGG	chr19:1428742-1428972(+)$1	230	54	57	9.0000
UGG	chrM:6103-6350(+)$1	247	34	37	9.0000
UGG	chr19:3526913-3527149(+)$1	236	0	3	9.0000
UGG	chr15:86123764-86124008(+)$1	244	12	15	9.0000
UGG	chrM:8935-9173(+)$1	238	58	61	9.0000
UGG	chr1:35656973-35657203(-)$1	230	14	17	9.0000
UGG	chrX:71493679-71493904(-)$1	225	12	15	9.0000
UGG	chr2:62069156-62069393(-)$1	237	43	46	9.0000
UGG	chr12:6626945-6627220(+)$1	275	8	11	9.0000
UGG	chr15:75693089-75693317(-)$1	228	20	23	9.0000
UGG	chr20:34322867-34323094(-)$1	227	19	22	9.0000
UGG	chr10:103559073-103559300(-)$1	227	107	110	9.0000
UGG	chr1:155903430-155903682(-)$1	252	9	12	9.0000
UGG	chrM:14245-14483(-)$1	238	9	12	9.0000
UGG	chr17:80040726-80040953(-)$1	227	66	69	9.0000
UGG	chr14:96810950-96811178(-)$1	228	24	27	9.0000
UGG	chr22:41572393-41572630(+)$1	237	22	25	9.0000
UGG	chr1:35656240-35656464(-)$1	224	10	13	9.0000
UGG	chr20:30897508-30897737(+)$1	229	56	59	9.0000
UGG	chr7:99690471-99690713(-)$1	242	1	4	9.0000
UGG	chr12:39155826-39156062(-)$1	236	96	99	9.0000
UGG	chr22:38897125-38897377(-)$1	252	31	34	9.0000
UGG	chr17:26687713-26687942(+)$1	229	28	31	9.0000
Ugg	chr19:46295812-46296038(-)$1	226	25	28	9.0000
UGG	chr17:4787605-4787837(+)$1	232	41	44	9.0000
UGG	chr17:2577254-2577483(+)$1	229	43	46	9.0000
UGG	chr19:36595390-36595663(+)$1	273	36	39	9.0000
UGG	chr15:90168552-90168786(+)$1	234	10	13	9.0000
UGG	chr17:47075103-47075325(+)$1	222	56	59	9.0000
UGG	chr1:19490171-19490417(-)$1	246	39	42	9.0000
UGG	chrX:18278229-18278476(-)$1	247	130	133	9.0000
UGG	chr16:19528377-19528611(-)$1	234	25	28	9.0000
UGG	chr22:30951573-30951802(-)$1	229	45	48	9.0000
UGG	chr2:109405281-109405509(+)$1	228	5	8	9.0000
UGG	chr22:36912438-36912687(-)$1	249	43	46	9.0000
UGG	chr1:24082351-24082579(+)$1	228	8	11	9.0000
UGG	chr8:48874592-48874843(+)$1	251	99	102	9.0000
UGG	chr10:5788965-5789209(+)$1	244	35	38	9.0000
UGG	chr19:41800223-41800453(+)$1	230	29	32	9.0000
UGG	chr1:31531958-31532187(-)$1	229	12	15	9.0000
UGG	chr4:57896403-57896636(+)$1	233	17	20	9.0000
UGG	chr6:149833190-149833419(-)$1	229	155	158	9.0000
UGG	chr1:155232903-155233134(-)$1	231	34	37	9.0000
UGG	chr17:40761046-40761270(-)$1	224	12	15	9.0000
UGG	chr9:104322980-104323207(+)$1	227	21	24	9.0000
UGG	chr3:197009462-197009691(-)$1	229	5	8	9.0000
UGG	chr17:38175965-38176208(-)$1	243	52	55	9.0000

#otherMatches

#Struct PSSM
[bb	chr2:61717767-61718001(-)$1	234	32	35	9.0000
ccc	chr15:75091568-75091792(+)$1	224	8	11	9.0000
&gg	chr16:58616664-58616894(-)$1	230	45	48	9.0000
=##	chr7:150776622-150776846(-)$1	224	20	23	9.0000
cbb	chr10:103871146-103871379(-)$1	233	14	17	9.0000
eee	chr7:135612347-135612610(-)$1	263	16	19	9.0000
:DD	chr16:23546198-23546452(-)$1	254	1	4	9.0000
{DD	chr16:2569620-2569843(+)$1	223	5	8	9.0000
fff	chr5:44809196-44809419(+)$1	223	10	13	9.0000
DDD	chr16:24828145-24828378(+)$1	233	1	4	9.0000
eee	chr10:43292237-43292465(+)$1	228	83	86	9.0000
!ee	chr9:95036612-95036834(-)$1	222	42	45	9.0000
"dd	chr17:42225329-42225558(+)$1	229	56	59	9.0000
ooo	chr17:80363132-80363361(-)$1	229	31	34	9.0000
DDM	chr8:48885435-48885668(+)$1	233	4	7	9.0000
ddq	chr9:139277761-139277988(-)$1	227	61	64	9.0000
CC:	chr17:1557124-1557352(-)$1	228	50	53	9.0000
ggg	chr3:127816209-127816433(-)$1	224	1	4	9.0000
ood	chr12:113596655-113596897(-)$1	242	101	104	9.0000
:EE	chr1:40627071-40627300(+)$1	229	1	4	9.0000
EEC	chr1:16273464-16273692(-)$1	228	3	6	9.0000
ee[	chr5:36958192-36958419(+)$1	227	31	34	9.0000
:::	chr1:35580648-35580876(+)$1	228	8	11	9.0000
MMD	chr9:33466820-33467061(-)$1	241	10	13	9.0000
ccc	chr7:90895022-90895243(+)$1	221	44	47	9.0000
:BB	chr19:4432997-4433227(+)$1	230	9	12	9.0000
]bb	chr19:39961902-39962176(+)$1	274	116	119	9.0000
]ff	chr11:46392946-46393174(+)$1	228	29	32	9.0000
:::	chr1:23650022-23650265(-)$1	243	11	14	9.0000
!!c	chr8:145748272-145748496(+)$1	224	83	86	9.0000
e[b	chr7:56022549-56022804(+)$1	255	14	17	9.0000
OOO	chr7:44608629-44608855(-)$1	226	24	27	9.0000
d]d	chr11:62648368-62648598(+)$1	230	50	53	9.0000
:a[	chr17:1554448-1554679(-)$1	231	0	3	9.0000
===	chr16:30750743-30750994(+)$1	251	52	55	9.0000
:BB	chr21:45209509-45209734(+)$1	225	2	5	9.0000
fff	chr19:10250257-10250481(-)$1	224	23	26	9.0000
:ff	chr18:12814105-12814332(-)$1	227	39	42	9.0000
mbb	chr7:72891670-72891913(-)$1	243	35	38	9.0000
a[d	chr20:62340357-62340584(+)$1	227	8	11	9.0000
ddd	chr19:15367821-15368057(-)$1	236	31	34	9.0000
EEE	chr17:76415569-76415808(+)$1	239	3	6	9.0000
:DD	chr12:6636874-6637109(+)$1	235	7	10	9.0000
dd2	chr20:57485740-57485968(+)$1	228	14	17	9.0000
eee	chr3:122087032-122087258(-)$1	226	93	96	9.0000
ddd	chrM:14957-15211(+)$1	254	14	17	9.0000
ggl	chrX:47073899-47074138(+)$1	239	127	130	9.0000
fff	chr16:67914532-67914787(+)$1	255	91	94	9.0000
hhh	chr16:3077154-3077400(+)$1	246	21	24	9.0000
dd$	chrX:70516755-70516984(+)$1	229	9	12	9.0000
ccc	chr2:47630363-47630607(+)$1	244	121	124	9.0000
hhh	chr16:58587595-58587826(-)$1	231	39	42	9.0000
iii	chr5:139914874-139915107(+)$1	233	2	5	9.0000
[bb	chr19:1428742-1428972(+)$1	230	54	57	9.0000
JJJ	chrM:6103-6350(+)$1	247	34	37	9.0000
eee	chr19:3526913-3527149(+)$1	236	0	3	9.0000
EEE	chr15:86123764-86124008(+)$1	244	12	15	9.0000
"cc	chrM:8935-9173(+)$1	238	58	61	9.0000
$ii	chr1:35656973-35657203(-)$1	230	14	17	9.0000
lgg	chrX:71493679-71493904(-)$1	225	12	15	9.0000
ee:	chr2:62069156-62069393(-)$1	237	43	46	9.0000
:::	chr12:6626945-6627220(+)$1	275	8	11	9.0000
JJJ	chr15:75693089-75693317(-)$1	228	20	23	9.0000
{DD	chr20:34322867-34323094(-)$1	227	19	22	9.0000
cc]	chr10:103559073-103559300(-)$1	227	107	110	9.0000
FFF	chr1:155903430-155903682(-)$1	252	9	12	9.0000
[ff	chrM:14245-14483(-)$1	238	9	12	9.0000
c]d	chr17:80040726-80040953(-)$1	227	66	69	9.0000
CCC	chr14:96810950-96811178(-)$1	228	24	27	9.0000
HHH	chr22:41572393-41572630(+)$1	237	22	25	9.0000
{FF	chr1:35656240-35656464(-)$1	224	10	13	9.0000
!!c	chr20:30897508-30897737(+)$1	229	56	59	9.0000
::=	chr7:99690471-99690713(-)$1	242	1	4	9.0000
fff	chr12:39155826-39156062(-)$1	236	96	99	9.0000
[dd	chr22:38897125-38897377(-)$1	252	31	34	9.0000
EEE	chr17:26687713-26687942(+)$1	229	28	31	9.0000
PBB	chr19:46295812-46296038(-)$1	226	25	28	9.0000
ddd	chr17:4787605-4787837(+)$1	232	41	44	9.0000
fff	chr17:2577254-2577483(+)$1	229	43	46	9.0000
eee	chr19:36595390-36595663(+)$1	273	36	39	9.0000
DDD	chr15:90168552-90168786(+)$1	234	10	13	9.0000
:II	chr17:47075103-47075325(+)$1	222	56	59	9.0000
scc	chr1:19490171-19490417(-)$1	246	39	42	9.0000
ggg	chrX:18278229-18278476(-)$1	247	130	133	9.0000
mbb	chr16:19528377-19528611(-)$1	234	25	28	9.0000
eee	chr22:30951573-30951802(-)$1	229	45	48	9.0000
EEE	chr2:109405281-109405509(+)$1	228	5	8	9.0000
2gg	chr22:36912438-36912687(-)$1	249	43	46	9.0000
:::	chr1:24082351-24082579(+)$1	228	8	11	9.0000
DDD	chr8:48874592-48874843(+)$1	251	99	102	9.0000
ccm	chr10:5788965-5789209(+)$1	244	35	38	9.0000
HHH	chr19:41800223-41800453(+)$1	230	29	32	9.0000
III	chr1:31531958-31532187(-)$1	229	12	15	9.0000
LCC	chr4:57896403-57896636(+)$1	233	17	20	9.0000
DDC	chr6:149833190-149833419(-)$1	229	155	158	9.0000
llc	chr1:155232903-155233134(-)$1	231	34	37	9.0000
mmm	chr17:40761046-40761270(-)$1	224	12	15	9.0000
KFF	chr9:104322980-104323207(+)$1	227	21	24	9.0000
::C	chr3:197009462-197009691(-)$1	229	5	8	9.0000
:ff	chr17:38175965-38176208(-)$1	243	52	55	9.0000

#DB
.((	chr2:61717767-61718001(-)$1	1	32	35	9.0000
(((	chr15:75091568-75091792(+)$1	1	8	11	9.0000
.((	chr16:58616664-58616894(-)$1	1	45	48	9.0000
(..	chr7:150776622-150776846(-)$1	1	20	23	9.0000
(((	chr10:103871146-103871379(-)$1	1	14	17	9.0000
(((	chr7:135612347-135612610(-)$1	1	16	19	9.0000
.((	chr16:23546198-23546452(-)$1	1	1	4	9.0000
.((	chr16:2569620-2569843(+)$1	1	5	8	9.0000
(((	chr5:44809196-44809419(+)$1	1	10	13	9.0000
(((	chr16:24828145-24828378(+)$1	1	1	4	9.0000
(((	chr10:43292237-43292465(+)$1	1	83	86	9.0000
.((	chr9:95036612-95036834(-)$1	1	42	45	9.0000
.((	chr17:42225329-42225558(+)$1	1	56	59	9.0000
...	chr17:80363132-80363361(-)$1	1	31	34	9.0000
((.	chr8:48885435-48885668(+)$1	1	4	7	9.0000
((.	chr9:139277761-139277988(-)$1	1	61	64	9.0000
((.	chr17:1557124-1557352(-)$1	1	50	53	9.0000
(((	chr3:127816209-127816433(-)$1	1	1	4	9.0000
..)	chr12:113596655-113596897(-)$1	1	101	104	9.0000
.((	chr1:40627071-40627300(+)$1	1	1	4	9.0000
(((	chr1:16273464-16273692(-)$1	1	3	6	9.0000
((.	chr5:36958192-36958419(+)$1	1	31	34	9.0000
...	chr1:35580648-35580876(+)$1	1	8	11	9.0000
..(	chr9:33466820-33467061(-)$1	1	10	13	9.0000
)))	chr7:90895022-90895243(+)$1	1	44	47	9.0000
.((	chr19:4432997-4433227(+)$1	1	9	12	9.0000
.))	chr19:39961902-39962176(+)$1	1	116	119	9.0000
.))	chr11:46392946-46393174(+)$1	1	29	32	9.0000
...	chr1:23650022-23650265(-)$1	1	11	14	9.0000
..(	chr8:145748272-145748496(+)$1	1	83	86	9.0000
(.(	chr7:56022549-56022804(+)$1	1	14	17	9.0000
...	chr7:44608629-44608855(-)$1	1	24	27	9.0000
).)	chr11:62648368-62648598(+)$1	1	50	53	9.0000
.(.	chr17:1554448-1554679(-)$1	1	0	3	9.0000
(((	chr16:30750743-30750994(+)$1	1	52	55	9.0000
.((	chr21:45209509-45209734(+)$1	1	2	5	9.0000
(((	chr19:10250257-10250481(-)$1	1	23	26	9.0000
.((	chr18:12814105-12814332(-)$1	1	39	42	9.0000
.))	chr7:72891670-72891913(-)$1	1	35	38	9.0000
(.(	chr20:62340357-62340584(+)$1	1	8	11	9.0000
(((	chr19:15367821-15368057(-)$1	1	31	34	9.0000
(((	chr17:76415569-76415808(+)$1	1	3	6	9.0000
.((	chr12:6636874-6637109(+)$1	1	7	10	9.0000
)).	chr20:57485740-57485968(+)$1	1	14	17	9.0000
(((	chr3:122087032-122087258(-)$1	1	93	96	9.0000
(((	chrM:14957-15211(+)$1	1	14	17	9.0000
((.	chrX:47073899-47074138(+)$1	1	127	130	9.0000
(((	chr16:67914532-67914787(+)$1	1	91	94	9.0000
(((	chr16:3077154-3077400(+)$1	1	21	24	9.0000
((.	chrX:70516755-70516984(+)$1	1	9	12	9.0000
)))	chr2:47630363-47630607(+)$1	1	121	124	9.0000
(((	chr16:58587595-58587826(-)$1	1	39	42	9.0000
(((	chr5:139914874-139915107(+)$1	1	2	5	9.0000
.((	chr19:1428742-1428972(+)$1	1	54	57	9.0000
(((	chrM:6103-6350(+)$1	1	34	37	9.0000
(((	chr19:3526913-3527149(+)$1	1	0	3	9.0000
(((	chr15:86123764-86124008(+)$1	1	12	15	9.0000
.((	chrM:8935-9173(+)$1	1	58	61	9.0000
.((	chr1:35656973-35657203(-)$1	1	14	17	9.0000
.))	chrX:71493679-71493904(-)$1	1	12	15	9.0000
)).	chr2:62069156-62069393(-)$1	1	43	46	9.0000
...	chr12:6626945-6627220(+)$1	1	8	11	9.0000
(((	chr15:75693089-75693317(-)$1	1	20	23	9.0000
.((	chr20:34322867-34323094(-)$1	1	19	22	9.0000
)).	chr10:103559073-103559300(-)$1	1	107	110	9.0000
(((	chr1:155903430-155903682(-)$1	1	9	12	9.0000
.((	chrM:14245-14483(-)$1	1	9	12	9.0000
).)	chr17:80040726-80040953(-)$1	1	66	69	9.0000
(((	chr14:96810950-96811178(-)$1	1	24	27	9.0000
(((	chr22:41572393-41572630(+)$1	1	22	25	9.0000
.((	chr1:35656240-35656464(-)$1	1	10	13	9.0000
..(	chr20:30897508-30897737(+)$1	1	56	59	9.0000
..(	chr7:99690471-99690713(-)$1	1	1	4	9.0000
)))	chr12:39155826-39156062(-)$1	1	96	99	9.0000
.((	chr22:38897125-38897377(-)$1	1	31	34	9.0000
(((	chr17:26687713-26687942(+)$1	1	28	31	9.0000
.((	chr19:46295812-46296038(-)$1	1	25	28	9.0000
(((	chr17:4787605-4787837(+)$1	1	41	44	9.0000
)))	chr17:2577254-2577483(+)$1	1	43	46	9.0000
)))	chr19:36595390-36595663(+)$1	1	36	39	9.0000
(((	chr15:90168552-90168786(+)$1	1	10	13	9.0000
.((	chr17:47075103-47075325(+)$1	1	56	59	9.0000
.))	chr1:19490171-19490417(-)$1	1	39	42	9.0000
(((	chrX:18278229-18278476(-)$1	1	130	133	9.0000
.))	chr16:19528377-19528611(-)$1	1	25	28	9.0000
(((	chr22:30951573-30951802(-)$1	1	45	48	9.0000
(((	chr2:109405281-109405509(+)$1	1	5	8	9.0000
.))	chr22:36912438-36912687(-)$1	1	43	46	9.0000
...	chr1:24082351-24082579(+)$1	1	8	11	9.0000
(((	chr8:48874592-48874843(+)$1	1	99	102	9.0000
((.	chr10:5788965-5789209(+)$1	1	35	38	9.0000
(((	chr19:41800223-41800453(+)$1	1	29	32	9.0000
(((	chr1:31531958-31532187(-)$1	1	12	15	9.0000
.((	chr4:57896403-57896636(+)$1	1	17	20	9.0000
)))	chr6:149833190-149833419(-)$1	1	155	158	9.0000
..)	chr1:155232903-155233134(-)$1	1	34	37	9.0000
...	chr17:40761046-40761270(-)$1	1	12	15	9.0000
.((	chr9:104322980-104323207(+)$1	1	21	24	9.0000
..(	chr3:197009462-197009691(-)$1	1	5	8	9.0000
.((	chr17:38175965-38176208(-)$1	1	52	55	9.0000

#PSSM
U : 0.98	u : 0.02	
G : 0.97	g : 0.03	
G : 0.97	g : 0.03	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m2_run1.nuc.txt

#NT
UUUUAUUU	chr17:56172360-56172595(+)$1	235	103	111	20.8461
UUUUAUUU	chr11:33163076-33163311(-)$1	235	106	114	20.8461
uuuuauuu	chr9:33045742-33045978(-)$1	236	124	132	20.8461
UUUUAUUU	chr18:29128673-29128900(+)$1	227	157	165	20.8461
UUUUAUUU	chr16:11966539-11966768(-)$1	229	105	113	20.8461
UUCUAUUU	chr15:83659601-83659819(+)$1	218	124	132	16.6153
UUUUAUUU	chr12:98929186-98929406(+)$1	220	101	109	20.8461
UUUUGUUU	chr5:108671261-108671487(-)$1	226	205	213	17.2307
UUUUGUUU	chr6:109785448-109785669(-)$1	221	80	88	17.2307
UUGUAUUU	chr4:110609691-110609919(-)$1	228	34	42	16.6153
uuuuaauu	chr2:118588494-118588719(+)$1	225	61	69	16.6153
UUUUAAUU	chr12:124498951-124499183(+)$1	232	6	14	16.6153
UUUCAUUU	chr17:53797406-53797638(-)$1	232	101	109	16.7692
uuuuaauu	chr17:65987574-65987793(-)$1	219	70	78	16.6153
uuuuauuu	chr6:109484979-109485195(+)$1	216	45	53	20.8461
UUUUAUAU	chr20:18541349-18541572(+)$1	223	149	157	16.1538
UUUUAUUU	chr13:79189101-79189331(-)$1	230	120	128	20.8461
UUUCAUUU	chr5:133726443-133726663(+)$1	220	99	107	16.7692
UUUUAAUU	chr6:144151662-144151880(+)$1	218	107	115	16.6153
UUUUCUUU	chr6:106632961-106633182(-)$1	221	105	113	17.3076
UUUUAUUU	chr15:35159654-35159873(-)$1	219	51	59	20.8461
UUUUCUUU	chr6:71270305-71270532(+)$1	227	105	113	17.3076
AUUUAUUU	chr9:106902355-106902579(+)$1	224	109	117	16.6153
UUUUAUUU	chr15:91509974-91510199(-)$1	225	147	155	20.8461
UUUUAUUU	chr1:67451222-67451443(+)$1	221	171	179	20.8461
UUUCAUUU	chr1:94017088-94017307(+)$1	219	99	107	16.7692
UUUUAUUU	chr8:86194825-86195049(+)$1	224	113	121	20.8461
uuuuauuu	chr15:43031174-43031399(-)$1	225	181	189	20.8461
UUUUUUUU	chr7:117351347-117351566(-)$1	219	154	162	16.9999
UUUUCUUU	chr1:151376465-151376684(-)$1	219	21	29	17.3076
uuuuauuu	chr6:87973120-87973348(+)$1	228	130	138	20.8461
UUUUGUUU	chr11:9468780-9469003(+)$1	223	40	48	17.2307
UUUUAUUU	chr10:94113364-94113591(+)$1	227	40	48	20.8461
UUUUAUUU	chr11:47593725-47593950(-)$1	225	32	40	20.8461
uuuucuuu	chr5:58264991-58265219(-)$1	228	105	113	17.3076
UUUUAUUU	chr10:93043829-93044049(+)$1	220	17	25	20.8461
UUUCAUUU	chr16:67232561-67232783(+)$1	222	102	110	16.7692
UUUUCUUU	chr2:74091345-74091569(+)$1	224	104	112	17.3076
uuuuauau	chr18:32840487-32840707(+)$1	220	104	112	16.1538
UUUCAUUU	chr6:64424066-64424288(+)$1	222	141	149	16.7692
CUUUAUUU	chr7:107224227-107224445(+)$1	218	52	60	16.4615
UUUUGUUU	chr8:101166019-101166251(+)$1	232	50	58	17.2307
UUUUUUUU	chr1:197477735-197477957(-)$1	222	101	109	16.9999
auuuauuu	chr16:69338339-69338564(+)$1	225	64	72	16.6153
UUUUAUUU	chrX:133561040-133561274(+)$1	234	139	147	20.8461
auuuauuu	chr8:28927149-28927379(-)$1	230	101	109	16.6153
UUGUAUUU	chr3:185348658-185348876(+)$1	218	81	89	16.6153
uuuuauuu	chr1:28087585-28087808(+)$1	223	101	109	20.8461
UUUUCUUU	chr15:78789495-78789718(+)$1	223	104	112	17.3076
UUUUAUUU	chr14:55535306-55535526(+)$1	220	108	116	20.8461
UUUAAUUU	chr2:70523106-70523328(-)$1	222	205	213	16.4615
uuauauuu	chr19:2273195-2273435(+)$1	240	119	127	16.7692
AUUUAUUU	chr12:117583153-117583380(-)$1	227	60	68	16.6153
uuuuauuu	chr7:30052654-30052881(-)$1	227	84	92	20.8461
UUUUGUUU	chr3:33132022-33132240(-)$1	218	124	132	17.2307
UUAUAUUU	chr18:11852738-11852966(+)$1	228	104	112	16.7692
UUUUAUUU	chr4:155457576-155457797(-)$1	221	145	153	20.8461
UUUUAAUU	chr8:124358763-124358984(-)$1	221	103	111	16.6153
UUAUAUUU	chr5:142660767-142660998(-)$1	231	77	85	16.7692
UUUUAUUU	chr14:81645720-81645944(-)$1	224	196	204	20.8461
uuuuauuu	chr6:44418052-44418278(+)$1	226	169	177	20.8461
uuauauuu	chr4:55606489-55606719(+)$1	230	100	108	16.7692
CUUUAUUU	chr2:135714856-135715081(+)$1	225	203	211	16.4615
UUUGAUUU	chr11:18630155-18630385(-)$1	230	18	26	16.4615

#otherMatches

#Struct PSSM
GGGGGGOO	chr5:162879420-162879655(-)$1	235	121	129	16.6153
::::::::	chr17:56172360-56172595(+)$1	235	103	111	20.8461
eeeee[cc	chr11:33163076-33163311(-)$1	235	106	114	20.8461
::::::::	chr9:33045742-33045978(-)$1	236	124	132	20.8461
g!!ggggg	chr18:29128673-29128900(+)$1	227	157	165	20.8461
>>>>>>hh	chr16:11966539-11966768(-)$1	229	105	113	20.8461
ii[bb$$$	chr15:83659601-83659819(+)$1	218	124	132	16.6153
HHHHHHHD	chr12:98929186-98929406(+)$1	220	101	109	20.8461
]bb]eeee	chr5:108671261-108671487(-)$1	226	205	213	17.2307
gggg[hhh	chr6:109785448-109785669(-)$1	221	80	88	17.2307
ddd[ffff	chr4:110609691-110609919(-)$1	228	34	42	16.6153
fffppppp	chr2:118588494-118588719(+)$1	225	61	69	16.6153
::::::::	chr12:124498951-124499183(+)$1	232	6	14	16.6153
:::::ddd	chr17:53797406-53797638(-)$1	232	101	109	16.7692
hhhh"""d	chr17:65987574-65987793(-)$1	219	70	78	16.6153
:::::::e	chr6:109484979-109485195(+)$1	216	45	53	20.8461
ff:::::e	chr20:18541349-18541572(+)$1	223	149	157	16.1538
::::::::	chr13:79189101-79189331(-)$1	230	120	128	20.8461
++++++++	chr5:133726443-133726663(+)$1	220	99	107	16.7692
gggg::::	chr6:144151662-144151880(+)$1	218	107	115	16.6153
^^^^^^^^	chr6:106632961-106633182(-)$1	221	105	113	17.3076
NNNNEEEE	chr15:35159654-35159873(-)$1	219	51	59	20.8461
^^^^^^^^	chr6:71270305-71270532(+)$1	227	105	113	17.3076
ccc>>>>>	chr9:106902355-106902579(+)$1	224	109	117	16.6153
EEEE????	chr15:91509974-91510199(-)$1	225	147	155	20.8461
g55555ff	chr1:67451222-67451443(+)$1	221	171	179	20.8461
::======	chr1:94017088-94017307(+)$1	219	99	107	16.7692
^^^^^^^^	chr8:86194825-86195049(+)$1	224	113	121	20.8461
=======[	chr15:43031174-43031399(-)$1	225	181	189	20.8461
DD\\\\\\	chr7:117351347-117351566(-)$1	219	154	162	16.9999
::::::::	chr1:151376465-151376684(-)$1	219	21	29	17.3076
eeee::::	chr6:87973120-87973348(+)$1	228	130	138	20.8461
HHH{HHHH	chr11:9468780-9469003(+)$1	223	40	48	17.2307
ee!!a[gg	chr10:94113364-94113591(+)$1	227	40	48	20.8461
eeee[===	chr11:47593725-47593950(-)$1	225	32	40	20.8461
GGGGGG__	chr5:58264991-58265219(-)$1	228	105	113	17.3076
::::::::	chr10:93043829-93044049(+)$1	220	17	25	20.8461
fzzzzzzz	chr16:67232561-67232783(+)$1	222	102	110	16.7692
++++++ee	chr2:74091345-74091569(+)$1	224	104	112	17.3076
%eeeee[d	chr18:32840487-32840707(+)$1	220	104	112	16.1538
@@@@@DDD	chr6:64424066-64424288(+)$1	222	141	149	16.7692
ffpppppp	chr7:107224227-107224445(+)$1	218	52	60	16.4615
hh[a[iii	chr8:101166019-101166251(+)$1	232	50	58	17.2307
======!!	chr1:197477735-197477957(-)$1	222	101	109	16.9999
hhhhhhvv	chr16:69338339-69338564(+)$1	225	64	72	16.6153
::::::::	chrX:133561040-133561274(+)$1	234	139	147	20.8461
goooooog	chr8:28927149-28927379(-)$1	230	101	109	16.6153
gppppppp	chr3:185348658-185348876(+)$1	218	81	89	16.6153
a[eeeee[	chr1:28087585-28087808(+)$1	223	101	109	20.8461
lhhhhhhh	chr15:78789495-78789718(+)$1	223	104	112	17.3076
nccc]fff	chr14:55535306-55535526(+)$1	220	108	116	20.8461
H:::::::	chr2:70523106-70523328(-)$1	222	205	213	16.4615
ccc]ffff	chr19:2273195-2273435(+)$1	240	119	127	16.7692
=====+++	chr12:117583153-117583380(-)$1	227	60	68	16.6153
fffooooo	chr7:30052654-30052881(-)$1	227	84	92	20.8461
HHHHHHHG	chr3:33132022-33132240(-)$1	218	124	132	17.2307
eee22ggg	chr18:11852738-11852966(+)$1	228	104	112	16.7692
====((((	chr4:155457576-155457797(-)$1	221	145	153	20.8461
::::::::	chr8:124358763-124358984(-)$1	221	103	111	16.6153
=ggggggg	chr5:142660767-142660998(-)$1	231	77	85	16.7692
fff:::::	chr14:81645720-81645944(-)$1	224	196	204	20.8461
ffffa22e	chr6:44418052-44418278(+)$1	226	169	177	20.8461
ggggg555	chr4:55606489-55606719(+)$1	230	100	108	16.7692
~~~~EEEE	chr2:135714856-135715081(+)$1	225	203	211	16.4615
ddddmmmm	chr11:18630155-18630385(-)$1	230	18	26	16.4615

#DB
((((((..	chr5:162879420-162879655(-)$1	1	121	129	16.6153
........	chr17:56172360-56172595(+)$1	1	103	111	20.8461
(((((.((	chr11:33163076-33163311(-)$1	1	106	114	20.8461
........	chr9:33045742-33045978(-)$1	1	124	132	20.8461
(..(((((	chr18:29128673-29128900(+)$1	1	157	165	20.8461
......))	chr16:11966539-11966768(-)$1	1	105	113	20.8461
((.((...	chr15:83659601-83659819(+)$1	1	124	132	16.6153
))))))))	chr12:98929186-98929406(+)$1	1	101	109	20.8461
.)).))))	chr5:108671261-108671487(-)$1	1	205	213	17.2307
((((.(((	chr6:109785448-109785669(-)$1	1	80	88	17.2307
(((.((((	chr4:110609691-110609919(-)$1	1	34	42	16.6153
(((.....	chr2:118588494-118588719(+)$1	1	61	69	16.6153
........	chr12:124498951-124499183(+)$1	1	6	14	16.6153
.....(((	chr17:53797406-53797638(-)$1	1	101	109	16.7692
((((...(	chr17:65987574-65987793(-)$1	1	70	78	16.6153
.......(	chr6:109484979-109485195(+)$1	1	45	53	20.8461
)).....(	chr20:18541349-18541572(+)$1	1	149	157	16.1538
........	chr13:79189101-79189331(-)$1	1	120	128	20.8461
........	chr5:133726443-133726663(+)$1	1	99	107	16.7692
))))....	chr6:144151662-144151880(+)$1	1	107	115	16.6153
........	chr6:106632961-106633182(-)$1	1	105	113	17.3076
....((((	chr15:35159654-35159873(-)$1	1	51	59	20.8461
........	chr6:71270305-71270532(+)$1	1	105	113	17.3076
))).....	chr9:106902355-106902579(+)$1	1	109	117	16.6153
))))....	chr15:91509974-91510199(-)$1	1	147	155	20.8461
).....))	chr1:67451222-67451443(+)$1	1	171	179	20.8461
..((((((	chr1:94017088-94017307(+)$1	1	99	107	16.7692
........	chr8:86194825-86195049(+)$1	1	113	121	20.8461
(((((((.	chr15:43031174-43031399(-)$1	1	181	189	20.8461
))......	chr7:117351347-117351566(-)$1	1	154	162	16.9999
........	chr1:151376465-151376684(-)$1	1	21	29	17.3076
))))....	chr6:87973120-87973348(+)$1	1	130	138	20.8461
(((.((((	chr11:9468780-9469003(+)$1	1	40	48	17.2307
((..(.((	chr10:94113364-94113591(+)$1	1	40	48	20.8461
((((.(((	chr11:47593725-47593950(-)$1	1	32	40	20.8461
))))))..	chr5:58264991-58265219(-)$1	1	105	113	17.3076
........	chr10:93043829-93044049(+)$1	1	17	25	20.8461
(.......	chr16:67232561-67232783(+)$1	1	102	110	16.7692
......((	chr2:74091345-74091569(+)$1	1	104	112	17.3076
.(((((.(	chr18:32840487-32840707(+)$1	1	104	112	16.1538
.....)))	chr6:64424066-64424288(+)$1	1	141	149	16.7692
((......	chr7:107224227-107224445(+)$1	1	52	60	16.4615
((.(.(((	chr8:101166019-101166251(+)$1	1	50	58	17.2307
((((((..	chr1:197477735-197477957(-)$1	1	101	109	16.9999
((((((..	chr16:69338339-69338564(+)$1	1	64	72	16.6153
........	chrX:133561040-133561274(+)$1	1	139	147	20.8461
(......)	chr8:28927149-28927379(-)$1	1	101	109	16.6153
(.......	chr3:185348658-185348876(+)$1	1	81	89	16.6153
(.(((((.	chr1:28087585-28087808(+)$1	1	101	109	20.8461
.)))))))	chr15:78789495-78789718(+)$1	1	104	112	17.3076
.))).)))	chr14:55535306-55535526(+)$1	1	108	116	20.8461
).......	chr2:70523106-70523328(-)$1	1	205	213	16.4615
))).))))	chr19:2273195-2273435(+)$1	1	119	127	16.7692
(((((...	chr12:117583153-117583380(-)$1	1	60	68	16.6153
(((.....	chr7:30052654-30052881(-)$1	1	84	92	20.8461
))))))))	chr3:33132022-33132240(-)$1	1	124	132	17.2307
)))..)))	chr18:11852738-11852966(+)$1	1	104	112	16.7692
((((....	chr4:155457576-155457797(-)$1	1	145	153	20.8461
........	chr8:124358763-124358984(-)$1	1	103	111	16.6153
))))))))	chr5:142660767-142660998(-)$1	1	77	85	16.7692
))).....	chr14:81645720-81645944(-)$1	1	196	204	20.8461
)))))..)	chr6:44418052-44418278(+)$1	1	169	177	20.8461
)))))...	chr4:55606489-55606719(+)$1	1	100	108	16.7692
....))))	chr2:135714856-135715081(+)$1	1	203	211	16.4615
((((....	chr11:18630155-18630385(-)$1	1	18	26	16.4615

#PSSM
U : 0.69	u : 0.21	A : 0.03	C : 0.03	a : 0.03	
U : 0.75	u : 0.24	
U : 0.67	u : 0.20	G : 0.03	a : 0.03	A : 0.03	c : 0.01	C : 0.01	
U : 0.64	u : 0.24	C : 0.07	A : 0.01	G : 0.01	
A : 0.56	a : 0.23	G : 0.07	C : 0.07	U : 0.03	c : 0.01	
U : 0.70	u : 0.21	A : 0.04	a : 0.03	
U : 0.73	u : 0.23	A : 0.01	a : 0.01	
U : 0.75	u : 0.24	

#score	1189.3846153846139
#seq	65
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_CDS_m1_run1.nuc.txt

#NT
UCACAACUUACCCGACAUCAAAAAGUUCAUACUGGUGAGAAACCUUAUGAAUGUAAAGAAUGUGGGAAGGCCUUUACUCAGAAUUCACAACUUACACUACACCAGAGACUUCAUACUGGUGAAAAGCUCUAUGAAUGUAAAGAAUGUAGGAAGGUCUUUACUC	chr19:37618569-37618804(+)$1	235	29	192	263.0909
UCGUCUCUUGUUCUGCACUAUAGAUUUCACACUGGAGAGAAACCCUACAAAUGUAAUGAAUGUGGACGAGCCUUUGGUCACACUUCAUCCCUUAUUAAGCAUCAGAGGACUCAUACUGGAGAAAAGCCCUAUGAAUGCCGGGAAUGUGGGAGAACCUUCAGCC	chr2:95815209-95815436(-)$1	227	23	186	257.1818
UCAACCCUUAAGAAACAUAAGAUAAUUCAUACUGGAGAGAAACCCUACAAAUGUAAAGAAUGUGGGAAAGCCUUUGCCUUCUCCUCAACUCUUAAUACUCAUAAGAGGAUUCAUACUGGAGAGGAACCCUACAAAUGUGAAGAAUGUGACAAAGCUUUUAAGU	chr7:63726991-63727220(+)$1	229	28	191	315.8181
UCAACCCUUACAAAACAUAAAAGAAUUCAUAAUGGAGAAAAACCCUACAAAUGUGAAGAAUGUGGCAAAGCUUUUAACCGAUCCUCAACCCUUAAUAGACAUAAGAUAACUCAUACUGGAGGGAAACCCUACAAAUAUAAAGAAUGUGGUAAAGCUUUUAACC	chr19:23328794-23329014(+)$1	220	24	187	318.5454
UCAACCCUUACUAAACAUAAGAUAAUUCAUACUGGAGAGAAGCCUUACAAAUGUAAAGAAUGUGAAAAAGCUUUUAACCAAUCCUCAAAACUUACUGAACAUAAGAAAAUUCAUACUGGAGAGAAACCCUAUGAAUGUGAAAAAUGUGGCAAAGCUUUUAACC	chr19:21132521-21132747(+)$1	226	29	192	324.9090
UCAGCUUUUACUAAACAUAAGAGAAAUCAUAUGGAAGAUAAACCCUACAAAUGUGAAGAAUGUGGCAAAGCCUUUAGUGUAUUCUCAACCCUUACUAAACAUAAAAUAAUUCAUACUAGAGAAAAACCCUACAAAUGUGAAGAAUGUGGCAAAGCCUUUAACC	chr7:64864318-64864558(+)$1	240	20	183	313.5454
UCAACCCUUACUGAACAUAAGAGAAUUCAUACCAGAGAGAAAACCUACAAAUGUGAAGAAUGUGGCAAAGCAUUUAGCCAGCCUUCACACCUUACUACACAUAAGAGGAUGCACACUGGAGAGAAACCCUACAAAUGUGAAGAAUGUGGCAAAGCUUUUAGCC	chr19:23542894-23543117(-)$1	223	19	182	321.2727
UCAAACCUCACUCAGCAUCAAAAAACUCAUACUGGGGAGAAACCCUAUGAUUGUGCAGAAUGUGGAAAAUCUUUUAGUUACUGGUCAUCCCUUGCUCAACACCUGAAAAUUCAUACUGGAGAAAAACCUUACAAAUGCAAUGAAUGUGGAAAGGCCUUCAGUU	chr6:27419857-27420077(-)$1	220	30	193	273.5454
UCACACCUUACUAAUCAUAAGGUAAUUCAUACUGGAGAGAAACCCUACAAAUGUGAAGAAUGUGGUAAAGCCUUUACCAAGUCCUCAACUCUUACUUAUCAUAAGGUAAUUCAUACUGGAAAGAAACCCUACAAAUGUGAAGAAUGUGGUAAAGCCUUUAGUA	chr19:21476435-21476658(-)$1	223	19	182	320.3636
UCAGACCUUAUUGAACACCAGAGAAUUCACACCGGAGAGAGACCCUUUGAAUGCAAUGAGUGUGGGAAAGCCUUUAUUCGGAGUUCAAAGCUCAUUCAGCAUCAGAGGAUCCAUACUGGGGAGAGGCCUUACGUAUGCAAUGAGUGUGGGAAGCGCUUCAGCC	chr8:144732942-144733172(+)$1	230	9	172	248.5454

#otherMatches

#Struct PSSM
CC:::::dddd$$$$$eeeee$$$$$ddddmmmmdddd55555eeeee4444dddd:::::::ccclllccc:::::a[a[ccc))))))))))cccpppppppccc0000000000ccc]a]a::::ddddmmmmdddd:CCCYYCCC}EEEEEBB:::::d	chr19:23405876-23406098(-)$1	222	18	181	332.1818
qqqqqqqddddbb[dddda$$$$$ggggggg!!cccnnnnnccc]ggggggg55555a]dddd]bbDDDD}DDDD}DDDDYYDDDD::::::::DDDD:ffffffssssssssssffffff::::::::ggggggg&&&&&&&hhhhhhhhdddd^^^^^^^^	chr19:37618569-37618804(+)$1	235	29	192	263.0909
bb%%%%%%ccclllccc55555bb]ccc333ffffff]a4444eeeee:::gggggggdddd[abb[dddd[ffffff$$$$$ccc[dddd[dddd!!ddddbb[ccc[cccooooooccc666666ccc]bb]dddd4444dddd]ddddccc666666fff	chr2:95815209-95815436(-)$1	227	23	186	257.1818
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ddddbb::::fffffftttttttttttffffffDDDD}GGGGGGGDDDD:::::GGGGGGG::::::::::ffffff"""dddd[eeeee%%%%%%ddddtttttttttttdddd666666eeeee]ddd	chr7:63726991-63727220(+)$1	229	28	191	315.8181
nnncccdddd:::::::ffffff!!ffffff[bb[bbpppppppbb]bb22ffffff>>>>>>>>>>>>>ffffff::::::::::::eeeee!!ccczzzzzzzzzzzzzzzzzccceeeee:::::eeeeettttttttttteeeee:HHHHHHHHZZZCC	chr19:23328794-23329014(+)$1	220	24	187	318.5454
DDD:::ddddpppppppdddd:::::::::::ccc!!ffffff[eeeeettttttttttteeeee4444ffffff22ccc::::cccqqqqqqqqccc::::::::::ggggggg!!bbqqqqqqqqbbggggggg:DDDDZZZCCCZZZHHHHHHHHYYDDD	chr19:21132521-21132747(+)$1	226	29	192	324.9090
neeeeeddddbb"""dddd[bbmmmmbb]dddd22bb]ddddDDDD{BBKKFFFFFF:::eeeee%%%%%%iiiiiiiii^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^iiiiiiiii7777777eeeee:::ggggggg[bb[bbawwwwwwwwwwwww	chr7:64864318-64864558(+)$1	240	20	183	313.5454
&&&&&addddpppppppdddd]a7777777ffffff::::::::::::::EEEEE{BBMMMMDDDDEEEEE{CCC{DDDDKKGGGGGGGddddtttttttttttdddd:::::::::bbqqqqqqqqbb::::::GGGGGGG~~~~DDDDCCCEEEEEYYDDD	chr19:23542894-23543117(-)$1	223	19	182	321.2727
c[cccbb[bb[bb[ccc[ccc$$$$$eeeee!!cccooooooccceeeeecccccc]bb]bb]bb666666ccc]ccc22eeeee::::::::::cccnnnnnccc::::::::ggggggg$$$$$dddd[bb[bbpppppppbb]bb22dddd]ggggggg:	chr6:27419857-27420077(-)$1	220	30	193	273.5454
%%%%ffffffpppppppffffff7777777eeeee22dddd::::::::::EEEEEHHHHHHHH{EEEEE{HHHHHHHH{BB{BBKKBB::ffffffooooooffffff::::::::bbqqqqqqqqbb:::::::BBYYBB}BB}HHHHHHHH}EEEEE}HH	chr19:21476435-21476658(-)$1	223	19	182	320.3636
qqqccc:::::::::::DDDD{FFFFFF::::::::::::bb[ggggggg[cccggggggg####ccc!!bbpppppppbb22ccc333ggggggg22cccggggggg]bb::::eeeee!!dddd####dddd[bb"""cccddddnnnnndddd]ccc22b	chr8:144732942-144733172(+)$1	230	9	172	248.5454

#DB
((.....((((.....(((((.....((((....)))).....)))))....)))).......(((...))).....(.(.(((..........(((.......)))..........))).).)....((((....)))).)))..))).))))))).....(	chr19:23405876-23406098(-)$1	1	18	181	332.1818
.......))))((.(((((.....(((((((..(((.....))).))))))).....).)))).)))))).)))).))))..))))........((((.((((((..........))))))........(((((((.......((((((((((((........	chr19:37618569-37618804(+)$1	1	29	192	263.0909
((......(((...))).....)).)))...)))))).)....)))))...(((((((((((.(((.((((.((((((.....(((.((((.((((..((((((.(((.(((......)))......))).)).))))....)))).)))))))......)))	chr2:95815209-95815436(-)$1	1	23	186	257.1818
.................................))))))....((((((...........)))))))))).))))))))))).....(((((((..........((((((...((((.(((((......((((...........))))......))))).)))	chr7:63726991-63727220(+)$1	1	28	191	315.8181
...))))))).......((((((..((((((.((.((.......)).))..)))))).............))))))............(((((..(((.................)))))))).....(((((...........))))).))))))))...))	chr19:23328794-23329014(+)$1	1	24	187	318.5454
(((...((((.......))))...........(((..((((((.(((((...........)))))....))))))..)))....(((........)))..........(((((((..((........))))))))).))))...)))...))))))))..)))	chr19:21132521-21132747(+)$1	1	29	192	324.9090
.)))))((((((...((((.((....)).))))..)).))))((((.((..((((((...(((((......(((((((((................................))))))))).......)))))...(((((((.((.(((.............	chr7:64864318-64864558(+)$1	1	20	183	313.5454
.....(((((.......)))).).......))))))..............(((((.((....(((((((((.(((.((((..(((((((((((...........)))).........((........))......)))))))....))))))))))))..)))	chr19:23542894-23543117(-)$1	1	19	182	321.2727
(.(((((.((.((.(((.(((.....(((((..(((......)))))))))))))).)).)).))......))).)))..)))))..........(((.....)))........(((((((.....((((.((.((.......)).))..)))).))))))).	chr6:27419857-27420077(-)$1	1	30	193	273.5454
....((((((.......)))))).......)))))..))))..........(((((((((((((.(((((.((((((((.((.((..((..((((((......))))))........((........)).......))..)).)).)))))))).))))).))	chr19:21476435-21476658(-)$1	1	19	182	320.3636
...)))...........((((.((((((............((.(((((((.((((((((((....(((..((.......))..)))...)))))))..)))))))))).))....(((((..((((....((((.((...(((((((.....)))).)))..)	chr8:144732942-144733172(+)$1	1	9	172	248.5454

#PSSM
U : 1.00	
C : 1.00	
A : 0.81	G : 0.18	
A : 0.54	C : 0.18	G : 0.18	U : 0.09	
C : 0.54	A : 0.45	
C : 0.72	U : 0.18	A : 0.09	
C : 0.90	U : 0.09	
U : 1.00	
U : 0.90	C : 0.09	
A : 0.90	G : 0.09	
C : 0.72	U : 0.18	A : 0.09	
U : 0.72	C : 0.09	G : 0.09	A : 0.09	
A : 0.54	C : 0.27	G : 0.18	
A : 0.81	G : 0.09	U : 0.09	
A : 0.72	G : 0.18	U : 0.09	
C : 1.00	
A : 1.00	
U : 0.81	C : 0.18	
A : 0.63	C : 0.27	U : 0.09	
A : 1.00	
G : 0.63	A : 0.27	U : 0.09	
A : 0.90	G : 0.09	
G : 0.54	U : 0.27	A : 0.18	
A : 1.00	
A : 0.81	G : 0.09	U : 0.09	
U : 0.81	A : 0.09	C : 0.09	
U : 1.00	
C : 1.00	
A : 1.00	
U : 0.81	C : 0.18	
A : 1.00	
C : 0.81	A : 0.09	U : 0.09	
U : 0.72	C : 0.18	G : 0.09	
G : 0.90	A : 0.09	
G : 0.90	A : 0.09	
A : 0.72	U : 0.18	G : 0.09	
G : 1.00	
A : 1.00	
G : 0.72	U : 0.18	A : 0.09	
A : 1.00	
A : 0.90	G : 0.09	
A : 0.90	G : 0.09	
C : 0.90	A : 0.09	
C : 1.00	
C : 0.72	U : 0.27	
U : 1.00	
A : 0.90	U : 0.09	
C : 0.63	U : 0.36	
A : 0.72	G : 0.27	
A : 1.00	
A : 0.90	U : 0.09	
U : 1.00	
G : 1.00	
U : 0.90	C : 0.09	
G : 0.54	A : 0.45	
A : 0.90	C : 0.09	
A : 0.81	U : 0.18	
G : 1.00	
A : 1.00	
A : 0.90	G : 0.09	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 0.90	A : 0.09	
C : 0.36	G : 0.27	A : 0.27	U : 0.09	
A : 0.90	C : 0.09	
A : 0.90	G : 0.09	
A : 0.90	G : 0.09	
G : 0.90	U : 0.09	
C : 1.00	
C : 0.63	U : 0.27	A : 0.09	
U : 1.00	
U : 1.00	
U : 1.00	
A : 0.81	G : 0.18	
G : 0.36	A : 0.27	C : 0.27	U : 0.09	
U : 0.54	C : 0.45	
C : 0.54	G : 0.18	U : 0.18	A : 0.09	
A : 0.54	U : 0.27	G : 0.18	
G : 0.45	C : 0.27	A : 0.27	
U : 0.63	A : 0.27	C : 0.09	
C : 0.63	G : 0.18	A : 0.09	U : 0.09	
C : 0.54	U : 0.36	G : 0.09	
U : 1.00	
C : 1.00	
A : 1.00	
A : 0.63	C : 0.18	U : 0.18	
C : 0.63	A : 0.36	
C : 0.54	A : 0.18	U : 0.18	G : 0.09	
C : 1.00	
U : 1.00	
U : 0.90	C : 0.09	
A : 0.90	G : 0.09	
C : 0.63	U : 0.18	A : 0.18	
U : 0.90	A : 0.09	
A : 0.45	C : 0.36	G : 0.09	U : 0.09	
A : 0.63	C : 0.18	U : 0.09	G : 0.09	
A : 0.63	G : 0.18	U : 0.18	
C : 1.00	
A : 1.00	
U : 0.81	C : 0.18	
A : 0.63	C : 0.36	
A : 0.90	U : 0.09	
G : 0.90	A : 0.09	
A : 0.90	G : 0.09	
G : 0.54	U : 0.27	A : 0.18	
A : 0.63	G : 0.36	
A : 0.90	C : 0.09	
U : 0.81	C : 0.18	
U : 0.81	G : 0.09	C : 0.09	
C : 1.00	
A : 1.00	
U : 0.90	C : 0.09	
A : 1.00	
C : 1.00	
U : 1.00	
G : 0.90	A : 0.09	
G : 1.00	
A : 0.81	U : 0.09	G : 0.09	
G : 0.90	A : 0.09	
A : 0.90	G : 0.09	
G : 0.63	A : 0.36	
A : 0.90	G : 0.09	
A : 0.90	G : 0.09	
A : 0.72	G : 0.27	
C : 1.00	
C : 0.90	U : 0.09	
C : 0.72	U : 0.27	
U : 1.00	
A : 1.00	
C : 0.72	U : 0.27	
A : 0.63	G : 0.36	
A : 0.90	U : 0.09	
A : 1.00	
U : 1.00	
G : 0.90	A : 0.09	
U : 0.72	C : 0.27	
G : 0.54	A : 0.36	C : 0.09	
A : 0.90	G : 0.09	
A : 0.72	U : 0.18	G : 0.09	
G : 0.90	A : 0.09	
A : 1.00	
A : 0.81	G : 0.18	
U : 1.00	
G : 1.00	
U : 1.00	
G : 0.90	A : 0.09	
G : 0.90	A : 0.09	
C : 0.45	G : 0.27	U : 0.18	A : 0.09	
A : 1.00	
A : 0.90	G : 0.09	
A : 0.72	G : 0.27	
G : 0.81	A : 0.09	C : 0.09	
C : 0.81	U : 0.09	G : 0.09	
C : 0.63	U : 0.36	
U : 1.00	
U : 1.00	
U : 0.72	C : 0.27	
A : 1.00	
A : 0.45	G : 0.45	C : 0.09	
C : 0.63	U : 0.27	G : 0.09	
C : 0.63	U : 0.18	G : 0.09	A : 0.09	

#score	3288.9999999999955
#seq	11
#width	163
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m2_run2.nuc.txt

#NT
CUUU	chr19:53057289-53057507(+)$1	218	15	19	12.0000
CUUU	chr2:73678240-73678471(+)$1	231	165	169	12.0000
CUUU	chr17:35992122-35992340(-)$1	218	4	8	12.0000
CUUU	chr12:46594835-46595054(-)$1	219	112	116	12.0000
CUUU	chr16:58565861-58566079(-)$1	218	93	97	12.0000
CUUU	chr4:187540940-187541160(-)$1	220	88	92	12.0000
CUUU	chr1:85136369-85136594(-)$1	225	20	24	12.0000
CUUU	chr10:129905891-129906113(-)$1	222	53	57	12.0000
CUUU	chr14:102550168-102550390(-)$1	222	191	195	12.0000
CUUU	chr5:71490469-71490687(+)$1	218	124	128	12.0000
CUUU	chr8:37732670-37732888(-)$1	218	23	27	12.0000
CUUU	chr19:37241205-37241427(-)$1	222	15	19	12.0000
CUUU	chr2:207172489-207172713(+)$1	224	4	8	12.0000
CUUU	chr1:16256551-16256771(+)$1	220	100	104	12.0000
CUUU	chr21:38852907-38853124(+)$1	217	211	215	12.0000
CUUU	chr18:43674923-43675145(-)$1	222	7	11	12.0000
CUUU	chr6:56336827-56337048(-)$1	221	35	39	12.0000
CUUU	chr8:145999004-145999219(-)$1	215	82	86	12.0000
CUUU	chr19:53855763-53855983(+)$1	220	92	96	12.0000
CUUU	chr10:27459216-27459435(+)$1	219	206	210	12.0000
CUUU	chr17:28769243-28769462(+)$1	219	19	23	12.0000
CUUU	chr19:44470844-44471061(+)$1	217	34	38	12.0000
CUUU	chr1:93599565-93599785(+)$1	220	10	14	12.0000
CUUU	chr7:30656671-30656889(+)$1	218	21	25	12.0000
CUUU	chr19:16652645-16652861(-)$1	216	120	124	12.0000
CUUU	chr15:32928385-32928602(+)$1	217	61	65	12.0000
CUUU	chr7:64864572-64864795(+)$1	223	4	8	12.0000
CUUU	chr4:113538609-113538830(-)$1	221	87	91	12.0000
CUUU	chr9:88611366-88611585(+)$1	219	208	212	12.0000
CUUU	chr17:1584136-1584356(-)$1	220	85	89	12.0000
CUUU	chr2:152311365-152311586(+)$1	221	103	107	12.0000
CUUU	chr1:214794002-214794225(+)$1	223	103	107	12.0000
CUUU	chr1:184772651-184772871(-)$1	220	33	37	12.0000
CUUU	chr13:32912764-32912985(+)$1	221	74	78	12.0000
CUUU	chr13:32915138-32915358(+)$1	220	19	23	12.0000
CUUU	chr5:79279420-79279638(-)$1	218	3	7	12.0000
CUUU	chr21:37736407-37736626(+)$1	219	16	20	12.0000
CUUU	chr11:108381875-108382095(-)$1	220	149	153	12.0000
CUUU	chr11:32996736-32996959(+)$1	223	40	44	12.0000
CUUU	chr19:38126378-38126600(-)$1	222	76	80	12.0000
CUUU	chr14:102551628-102551848(-)$1	220	64	68	12.0000
CUUU	chr4:24541767-24541987(-)$1	220	5	9	12.0000
CUUU	chr12:46243355-46243574(+)$1	219	13	17	12.0000
CUUU	chr10:18957376-18957596(+)$1	220	56	60	12.0000
CUUU	chr19:30501922-30502141(+)$1	219	27	31	12.0000
CUUU	chr7:97484565-97484783(-)$1	218	193	197	12.0000
CUUU	chr6:122767869-122768090(-)$1	221	109	113	12.0000
CUUU	chr2:73680426-73680648(+)$1	222	20	24	12.0000
CUUU	chr10:7841921-7842142(+)$1	221	104	108	12.0000
CUUU	chrX:53243835-53244053(-)$1	218	1	5	12.0000
CUUU	chr4:24577766-24577989(-)$1	223	81	85	12.0000
CUUU	chr17:29214274-29214491(+)$1	217	0	4	12.0000
CUUU	chr7:138960769-138960988(+)$1	219	57	61	12.0000
CUUU	chr21:34923185-34923402(+)$1	217	209	213	12.0000
CUUU	chr19:23542734-23542952(-)$1	218	8	12	12.0000
CUUU	chr10:88202946-88203166(-)$1	220	26	30	12.0000
CUUU	chr17:1554905-1555120(-)$1	215	26	30	12.0000
CUUU	chr19:23837069-23837285(-)$1	216	6	10	12.0000
CUUU	chr22:32883632-32883852(+)$1	220	69	73	12.0000
CUUU	chr17:73205843-73206063(+)$1	220	20	24	12.0000
CUUU	chr16:75203585-75203801(+)$1	216	4	8	12.0000
CUUU	chr11:108044002-108044221(-)$1	219	107	111	12.0000
CUUU	chr5:41917261-41917488(+)$1	227	118	122	12.0000
CUUU	chr20:37144771-37144989(+)$1	218	44	48	12.0000
CUUU	chr6:31765705-31765926(-)$1	221	91	95	12.0000
CUUU	chr8:103323457-103323676(-)$1	219	82	86	12.0000
CUUU	chr2:201438393-201438613(+)$1	220	65	69	12.0000
CUUU	chr7:150554568-150554783(+)$1	215	188	192	12.0000
CUUU	chr13:108862003-108862219(-)$1	216	185	189	12.0000
CUUU	chr17:1564531-1564749(-)$1	218	32	36	12.0000
CUUU	chr2:61710094-61710318(-)$1	224	16	20	12.0000
CUUU	chr12:6691967-6692182(-)$1	215	2	6	12.0000
CUUU	chr6:126248770-126248991(+)$1	221	28	32	12.0000
CUUU	chr4:17818921-17819140(+)$1	219	173	177	12.0000
CUUU	chr12:57626490-57626709(+)$1	219	78	82	12.0000
CUUU	chr18:13746148-13746367(+)$1	219	40	44	12.0000
CUUU	chr1:11078812-11079030(+)$1	218	18	22	12.0000
cuuu	chr3:108298344-108298562(-)$1	218	12	16	12.0000
CUUU	chr6:149826578-149826797(-)$1	219	122	126	12.0000
CUUU	chr6:75969056-75969273(-)$1	217	47	51	12.0000
CUUU	chr6:12125070-12125289(+)$1	219	44	48	12.0000

#otherMatches

#Struct PSSM
:ccc	chr19:37903917-37904141(-)$1	224	3	7	12.0000
IIII	chr19:53057289-53057507(+)$1	218	15	19	12.0000
====	chr2:73678240-73678471(+)$1	231	165	169	12.0000
::::	chr17:35992122-35992340(-)$1	218	4	8	12.0000
]fff	chr12:46594835-46595054(-)$1	219	112	116	12.0000
333d	chr16:58565861-58566079(-)$1	218	93	97	12.0000
&&&&	chr4:187540940-187541160(-)$1	220	88	92	12.0000
(eee	chr1:85136369-85136594(-)$1	225	20	24	12.0000
dddm	chr10:129905891-129906113(-)$1	222	53	57	12.0000
eeee	chr14:102550168-102550390(-)$1	222	191	195	12.0000
FFFF	chr5:71490469-71490687(+)$1	218	124	128	12.0000
ccc[	chr8:37732670-37732888(-)$1	218	23	27	12.0000
GGGG	chr19:37241205-37241427(-)$1	222	15	19	12.0000
ee$$	chr2:207172489-207172713(+)$1	224	4	8	12.0000
ff::	chr1:16256551-16256771(+)$1	220	100	104	12.0000
eeee	chr21:38852907-38853124(+)$1	217	211	215	12.0000
!!bb	chr18:43674923-43675145(-)$1	222	7	11	12.0000
meee	chr6:56336827-56337048(-)$1	221	35	39	12.0000
ffff	chr8:145999004-145999219(-)$1	215	82	86	12.0000
ggll	chr19:53855763-53855983(+)$1	220	92	96	12.0000
gggg	chr10:27459216-27459435(+)$1	219	206	210	12.0000
WWWD	chr17:28769243-28769462(+)$1	219	19	23	12.0000
:::d	chr19:44470844-44471061(+)$1	217	34	38	12.0000
####	chr1:93599565-93599785(+)$1	220	10	14	12.0000
LLLD	chr7:30656671-30656889(+)$1	218	21	25	12.0000
hhmm	chr19:16652645-16652861(-)$1	216	120	124	12.0000
DDD{	chr15:32928385-32928602(+)$1	217	61	65	12.0000
FFFF	chr7:64864572-64864795(+)$1	223	4	8	12.0000
]eee	chr4:113538609-113538830(-)$1	221	87	91	12.0000
ZZZG	chr9:88611366-88611585(+)$1	219	208	212	12.0000
wwww	chr17:1584136-1584356(-)$1	220	85	89	12.0000
gggg	chr2:152311365-152311586(+)$1	221	103	107	12.0000
gggg	chr1:214794002-214794225(+)$1	223	103	107	12.0000
booo	chr1:184772651-184772871(-)$1	220	33	37	12.0000
ffff	chr13:32912764-32912985(+)$1	221	74	78	12.0000
pfff	chr13:32915138-32915358(+)$1	220	19	23	12.0000
eeff	chr5:79279420-79279638(-)$1	218	3	7	12.0000
EENN	chr21:37736407-37736626(+)$1	219	16	20	12.0000
ee[c	chr11:108381875-108382095(-)$1	220	149	153	12.0000
e%%%	chr11:32996736-32996959(+)$1	223	40	44	12.0000
ff!!	chr19:38126378-38126600(-)$1	222	76	80	12.0000
:::F	chr14:102551628-102551848(-)$1	220	64	68	12.0000
OOOO	chr4:24541767-24541987(-)$1	220	5	9	12.0000
nnnn	chr12:46243355-46243574(+)$1	219	13	17	12.0000
gggg	chr10:18957376-18957596(+)$1	220	56	60	12.0000
:fff	chr19:30501922-30502141(+)$1	219	27	31	12.0000
bb[c	chr7:97484565-97484783(-)$1	218	193	197	12.0000
CC}G	chr6:122767869-122768090(-)$1	221	109	113	12.0000
mmee	chr2:73680426-73680648(+)$1	222	20	24	12.0000
ffff	chr10:7841921-7842142(+)$1	221	104	108	12.0000
::::	chrX:53243835-53244053(-)$1	218	1	5	12.0000
bqqq	chr4:24577766-24577989(-)$1	223	81	85	12.0000
EEEE	chr17:29214274-29214491(+)$1	217	0	4	12.0000
]fff	chr7:138960769-138960988(+)$1	219	57	61	12.0000
cc::	chr21:34923185-34923402(+)$1	217	209	213	12.0000
EEEE	chr19:23542734-23542952(-)$1	218	8	12	12.0000
RRRR	chr10:88202946-88203166(-)$1	220	26	30	12.0000
e"""	chr17:1554905-1555120(-)$1	215	26	30	12.0000
EEEE	chr19:23837069-23837285(-)$1	216	6	10	12.0000
hhhh	chr22:32883632-32883852(+)$1	220	69	73	12.0000
NNNN	chr17:73205843-73206063(+)$1	220	20	24	12.0000
e!!b	chr16:75203585-75203801(+)$1	216	4	8	12.0000
ffff	chr11:108044002-108044221(-)$1	219	107	111	12.0000
yccc	chr5:41917261-41917488(+)$1	227	118	122	12.0000
>>>>	chr20:37144771-37144989(+)$1	218	44	48	12.0000
{EEE	chr6:31765705-31765926(-)$1	221	91	95	12.0000
++++	chr8:103323457-103323676(-)$1	219	82	86	12.0000
:eee	chr2:201438393-201438613(+)$1	220	65	69	12.0000
2eee	chr7:150554568-150554783(+)$1	215	188	192	12.0000
b333	chr13:108862003-108862219(-)$1	216	185	189	12.0000
ffff	chr17:1564531-1564749(-)$1	218	32	36	12.0000
meee	chr2:61710094-61710318(-)$1	224	16	20	12.0000
CKKA	chr12:6691967-6692182(-)$1	215	2	6	12.0000
pppp	chr6:126248770-126248991(+)$1	221	28	32	12.0000
eeee	chr4:17818921-17819140(+)$1	219	173	177	12.0000
ggg:	chr12:57626490-57626709(+)$1	219	78	82	12.0000
$$$f	chr18:13746148-13746367(+)$1	219	40	44	12.0000
dddd	chr1:11078812-11079030(+)$1	218	18	22	12.0000
::::	chr3:108298344-108298562(-)$1	218	12	16	12.0000
GGGG	chr6:149826578-149826797(-)$1	219	122	126	12.0000
###b	chr6:75969056-75969273(-)$1	217	47	51	12.0000
eeee	chr6:12125070-12125289(+)$1	219	44	48	12.0000

#DB
.(((	chr19:37903917-37904141(-)$1	1	3	7	12.0000
((((	chr19:53057289-53057507(+)$1	1	15	19	12.0000
))))	chr2:73678240-73678471(+)$1	1	165	169	12.0000
....	chr17:35992122-35992340(-)$1	1	4	8	12.0000
.)))	chr12:46594835-46595054(-)$1	1	112	116	12.0000
...)	chr16:58565861-58566079(-)$1	1	93	97	12.0000
....	chr4:187540940-187541160(-)$1	1	88	92	12.0000
.(((	chr1:85136369-85136594(-)$1	1	20	24	12.0000
(((.	chr10:129905891-129906113(-)$1	1	53	57	12.0000
))))	chr14:102550168-102550390(-)$1	1	191	195	12.0000
))))	chr5:71490469-71490687(+)$1	1	124	128	12.0000
(((.	chr8:37732670-37732888(-)$1	1	23	27	12.0000
((((	chr19:37241205-37241427(-)$1	1	15	19	12.0000
((..	chr2:207172489-207172713(+)$1	1	4	8	12.0000
))..	chr1:16256551-16256771(+)$1	1	100	104	12.0000
))))	chr21:38852907-38853124(+)$1	1	211	215	12.0000
..((	chr18:43674923-43675145(-)$1	1	7	11	12.0000
.)))	chr6:56336827-56337048(-)$1	1	35	39	12.0000
((((	chr8:145999004-145999219(-)$1	1	82	86	12.0000
((..	chr19:53855763-53855983(+)$1	1	92	96	12.0000
))))	chr10:27459216-27459435(+)$1	1	206	210	12.0000
...(	chr17:28769243-28769462(+)$1	1	19	23	12.0000
...(	chr19:44470844-44471061(+)$1	1	34	38	12.0000
....	chr1:93599565-93599785(+)$1	1	10	14	12.0000
...(	chr7:30656671-30656889(+)$1	1	21	25	12.0000
((..	chr19:16652645-16652861(-)$1	1	120	124	12.0000
(((.	chr15:32928385-32928602(+)$1	1	61	65	12.0000
((((	chr7:64864572-64864795(+)$1	1	4	8	12.0000
.)))	chr4:113538609-113538830(-)$1	1	87	91	12.0000
...)	chr9:88611366-88611585(+)$1	1	208	212	12.0000
....	chr17:1584136-1584356(-)$1	1	85	89	12.0000
))))	chr2:152311365-152311586(+)$1	1	103	107	12.0000
((((	chr1:214794002-214794225(+)$1	1	103	107	12.0000
(...	chr1:184772651-184772871(-)$1	1	33	37	12.0000
((((	chr13:32912764-32912985(+)$1	1	74	78	12.0000
.)))	chr13:32915138-32915358(+)$1	1	19	23	12.0000
((((	chr5:79279420-79279638(-)$1	1	3	7	12.0000
((..	chr21:37736407-37736626(+)$1	1	16	20	12.0000
((.(	chr11:108381875-108382095(-)$1	1	149	153	12.0000
(...	chr11:32996736-32996959(+)$1	1	40	44	12.0000
((..	chr19:38126378-38126600(-)$1	1	76	80	12.0000
...(	chr14:102551628-102551848(-)$1	1	64	68	12.0000
....	chr4:24541767-24541987(-)$1	1	5	9	12.0000
....	chr12:46243355-46243574(+)$1	1	13	17	12.0000
))))	chr10:18957376-18957596(+)$1	1	56	60	12.0000
.(((	chr19:30501922-30502141(+)$1	1	27	31	12.0000
((.(	chr7:97484565-97484783(-)$1	1	193	197	12.0000
)).)	chr6:122767869-122768090(-)$1	1	109	113	12.0000
..))	chr2:73680426-73680648(+)$1	1	20	24	12.0000
))))	chr10:7841921-7842142(+)$1	1	104	108	12.0000
....	chrX:53243835-53244053(-)$1	1	1	5	12.0000
(...	chr4:24577766-24577989(-)$1	1	81	85	12.0000
((((	chr17:29214274-29214491(+)$1	1	0	4	12.0000
.)))	chr7:138960769-138960988(+)$1	1	57	61	12.0000
))..	chr21:34923185-34923402(+)$1	1	209	213	12.0000
((((	chr19:23542734-23542952(-)$1	1	8	12	12.0000
....	chr10:88202946-88203166(-)$1	1	26	30	12.0000
(...	chr17:1554905-1555120(-)$1	1	26	30	12.0000
((((	chr19:23837069-23837285(-)$1	1	6	10	12.0000
))))	chr22:32883632-32883852(+)$1	1	69	73	12.0000
....	chr17:73205843-73206063(+)$1	1	20	24	12.0000
(..(	chr16:75203585-75203801(+)$1	1	4	8	12.0000
))))	chr11:108044002-108044221(-)$1	1	107	111	12.0000
.)))	chr5:41917261-41917488(+)$1	1	118	122	12.0000
....	chr20:37144771-37144989(+)$1	1	44	48	12.0000
.(((	chr6:31765705-31765926(-)$1	1	91	95	12.0000
....	chr8:103323457-103323676(-)$1	1	82	86	12.0000
.(((	chr2:201438393-201438613(+)$1	1	65	69	12.0000
.)))	chr7:150554568-150554783(+)$1	1	188	192	12.0000
)...	chr13:108862003-108862219(-)$1	1	185	189	12.0000
((((	chr17:1564531-1564749(-)$1	1	32	36	12.0000
.)))	chr2:61710094-61710318(-)$1	1	16	20	12.0000
(..(	chr12:6691967-6692182(-)$1	1	2	6	12.0000
....	chr6:126248770-126248991(+)$1	1	28	32	12.0000
))))	chr4:17818921-17819140(+)$1	1	173	177	12.0000
))).	chr12:57626490-57626709(+)$1	1	78	82	12.0000
...(	chr18:13746148-13746367(+)$1	1	40	44	12.0000
((((	chr1:11078812-11079030(+)$1	1	18	22	12.0000
....	chr3:108298344-108298562(-)$1	1	12	16	12.0000
((((	chr6:149826578-149826797(-)$1	1	122	126	12.0000
...(	chr6:75969056-75969273(-)$1	1	47	51	12.0000
((((	chr6:12125070-12125289(+)$1	1	44	48	12.0000

#PSSM
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m1_run1.nuc.txt

#NT
AGAA	chr10:112724591-112724815(+)$1	224	30	34	12.0000
AGAA	chr1:62913026-62913246(+)$1	220	15	19	12.0000
AGAA	chr8:103664100-103664320(-)$1	220	171	175	12.0000
AGAA	chr10:11259347-11259566(+)$1	219	5	9	12.0000
AGAA	chr22:21083656-21083877(-)$1	221	43	47	12.0000
AGAA	chr1:14105860-14106078(+)$1	218	13	17	12.0000
AGAA	chr1:91403288-91403518(-)$1	230	46	50	12.0000
AGAA	chr15:42855926-42856144(+)$1	218	68	72	12.0000
AGAA	chr13:96577840-96578064(-)$1	224	98	102	12.0000
AGAA	chr11:3720254-3720471(-)$1	217	6	10	12.0000
AGAA	chr19:6362426-6362647(+)$1	221	94	98	12.0000
AGAA	chrM:10501-10721(+)$1	220	67	71	12.0000
AGAA	chr2:48692590-48692814(+)$1	224	124	128	12.0000
AGAA	chrX:149901021-149901240(+)$1	219	202	206	12.0000
AGAA	chr3:48730448-48730666(-)$1	218	76	80	12.0000
AGAA	chr11:18317551-18317771(+)$1	220	32	36	12.0000
AGAA	chr8:53570285-53570506(-)$1	221	122	126	12.0000
AGAA	chr4:73964018-73964237(-)$1	219	19	23	12.0000
AGAA	chr3:135870032-135870250(-)$1	218	47	51	12.0000
AGAA	chr7:98961071-98961290(+)$1	219	201	205	12.0000
AGAA	chr15:64967920-64968150(+)$1	230	150	154	12.0000
AGAA	chr10:5804443-5804666(+)$1	223	70	74	12.0000
AGAA	chr2:213914421-213914640(-)$1	219	81	85	12.0000
AGAA	chr11:130131364-130131594(-)$1	230	25	29	12.0000
AGAA	chr10:64974274-64974495(-)$1	221	58	62	12.0000
AGAA	chr22:29939375-29939592(-)$1	217	66	70	12.0000
AGAA	chr1:79116004-79116230(+)$1	226	70	74	12.0000
AGAA	chr12:57006744-57006966(-)$1	222	191	195	12.0000
AGAA	chr4:153831117-153831336(+)$1	219	165	169	12.0000
AGAA	chr6:135357840-135358062(-)$1	222	44	48	12.0000
AGAA	chr9:114304339-114304562(+)$1	223	8	12	12.0000
AGAA	chr5:149225317-149225538(-)$1	221	85	89	12.0000
AGAA	chr7:112101984-112102214(+)$1	230	129	133	12.0000
AGAA	chr4:39747305-39747523(+)$1	218	97	101	12.0000
AGAA	chr2:135027954-135028178(+)$1	224	8	12	12.0000
AGAA	chr1:40703357-40703578(+)$1	221	46	50	12.0000
AGAA	chr2:198288443-198288661(-)$1	218	178	182	12.0000
AGAA	chr2:135711437-135711667(+)$1	230	147	151	12.0000
AGAA	chr15:77241438-77241668(+)$1	230	25	29	12.0000
AGAA	chr20:5539319-5539537(-)$1	218	86	90	12.0000
AGAA	chr2:219445331-219445549(+)$1	218	58	62	12.0000
AGAA	chr3:101284316-101284546(+)$1	230	11	15	12.0000
AGAA	chr4:139993038-139993257(-)$1	219	13	17	12.0000
AGAA	chr4:1725449-1725675(+)$1	226	138	142	12.0000
AGAA	chr6:116973147-116973377(-)$1	230	52	56	12.0000
AGAA	chr6:33371458-33371680(+)$1	222	77	81	12.0000
AGAA	chr1:38228385-38228608(+)$1	223	154	158	12.0000
AGAA	chr1:220275819-220276038(+)$1	219	35	39	12.0000
AGAA	chr6:56564351-56564568(-)$1	217	43	47	12.0000
AGAA	chr1:24680781-24681005(+)$1	224	23	27	12.0000
AGAA	chrX:53578210-53578430(-)$1	220	64	68	12.0000
AGAA	chr16:56976021-56976251(+)$1	230	63	67	12.0000
AGAA	chr1:2321299-2321520(-)$1	221	131	135	12.0000
AGAA	chr22:40661250-40661476(+)$1	226	69	73	12.0000
AGAA	chr10:115636402-115636632(+)$1	230	10	14	12.0000
AGAA	chr17:57741116-57741338(+)$1	222	100	104	12.0000
AGAA	chr2:100055262-100055486(-)$1	224	4	8	12.0000
AGAA	chr1:151377828-151378048(-)$1	220	178	182	12.0000
AGAA	chr14:77901529-77901755(-)$1	226	36	40	12.0000
AGAA	chr14:72055955-72056177(+)$1	222	36	40	12.0000
AGAA	chr12:69968142-69968372(+)$1	230	66	70	12.0000
AGAA	chr4:104097997-104098227(-)$1	230	30	34	12.0000
AGAA	chr6:82914512-82914730(-)$1	218	20	24	12.0000
AGAA	chr3:44685514-44685744(+)$1	230	15	19	12.0000
AGAA	chr17:53471599-53471825(-)$1	226	215	219	12.0000
AGAA	chr11:110007903-110008137(+)$1	234	53	57	12.0000
AGAA	chr11:30352446-30352666(+)$1	220	39	43	12.0000
AGAA	chr5:138723483-138723709(-)$1	226	138	142	12.0000
AGAA	chr10:43088797-43089017(-)$1	220	0	4	12.0000
AGAA	chr2:47705480-47705703(+)$1	223	20	24	12.0000
AGAA	chr10:129910470-129910688(-)$1	218	17	21	12.0000
AGAA	chr5:140951398-140951628(-)$1	230	82	86	12.0000
AGAA	chr11:102195914-102196134(+)$1	220	30	34	12.0000
AGAA	chr5:138643612-138643831(+)$1	219	28	32	12.0000
AGAA	chr12:31632624-31632846(-)$1	222	33	37	12.0000
AGAA	chr18:12337285-12337504(-)$1	219	46	50	12.0000
AGAA	chr3:69073159-69073379(-)$1	220	50	54	12.0000
AGAA	chr12:132508233-132508453(+)$1	220	10	14	12.0000
AGAA	chr11:34910203-34910433(-)$1	230	78	82	12.0000
AGAA	chr3:170928838-170929063(-)$1	225	7	11	12.0000
AGAA	chr2:67630822-67631041(+)$1	219	83	87	12.0000
AGAA	chr9:96326616-96326859(+)$1	243	21	25	12.0000
AGAA	chr3:107491691-107491912(+)$1	221	46	50	12.0000
AGAA	chr9:5457200-5457424(+)$1	224	10	14	12.0000
AGAA	chr14:95570080-95570303(-)$1	223	30	34	12.0000
AGAA	chr11:118625380-118625606(-)$1	226	98	102	12.0000
AGAA	chr20:42826176-42826397(-)$1	221	49	53	12.0000
AGAA	chrX:76872066-76872291(-)$1	225	27	31	12.0000

#otherMatches

#Struct PSSM
eeee	chr2:39283748-39283971(-)$1	223	20	24	12.0000
NNDD	chr10:112724591-112724815(+)$1	224	30	34	12.0000
bxxx	chr1:62913026-62913246(+)$1	220	15	19	12.0000
IIII	chr8:103664100-103664320(-)$1	220	171	175	12.0000
:ddd	chr10:11259347-11259566(+)$1	219	5	9	12.0000
pppp	chr22:21083656-21083877(-)$1	221	43	47	12.0000
::::	chr1:14105860-14106078(+)$1	218	13	17	12.0000
^^^^	chr1:91403288-91403518(-)$1	230	46	50	12.0000
eeee	chr15:42855926-42856144(+)$1	218	68	72	12.0000
GGGG	chr13:96577840-96578064(-)$1	224	98	102	12.0000
dddd	chr11:3720254-3720471(-)$1	217	6	10	12.0000
::::	chr19:6362426-6362647(+)$1	221	94	98	12.0000
hhhh	chrM:10501-10721(+)$1	220	67	71	12.0000
5iii	chr2:48692590-48692814(+)$1	224	124	128	12.0000
cc22	chrX:149901021-149901240(+)$1	219	202	206	12.0000
dd22	chr3:48730448-48730666(-)$1	218	76	80	12.0000
%%%%	chr11:18317551-18317771(+)$1	220	32	36	12.0000
ddd!	chr8:53570285-53570506(-)$1	221	122	126	12.0000
gggg	chr4:73964018-73964237(-)$1	219	19	23	12.0000
F:::	chr3:135870032-135870250(-)$1	218	47	51	12.0000
gggg	chr7:98961071-98961290(+)$1	219	201	205	12.0000
^^^^	chr15:64967920-64968150(+)$1	230	150	154	12.0000
eemm	chr10:5804443-5804666(+)$1	223	70	74	12.0000
iiii	chr2:213914421-213914640(-)$1	219	81	85	12.0000
ee!!	chr11:130131364-130131594(-)$1	230	25	29	12.0000
"""e	chr10:64974274-64974495(-)$1	221	58	62	12.0000
2ggg	chr22:29939375-29939592(-)$1	217	66	70	12.0000
hhhh	chr1:79116004-79116230(+)$1	226	70	74	12.0000
ddoo	chr12:57006744-57006966(-)$1	222	191	195	12.0000
bb]a	chr4:153831117-153831336(+)$1	219	165	169	12.0000
IIII	chr6:135357840-135358062(-)$1	222	44	48	12.0000
::::	chr9:114304339-114304562(+)$1	223	8	12	12.0000
:ggg	chr5:149225317-149225538(-)$1	221	85	89	12.0000
ddd]	chr7:112101984-112102214(+)$1	230	129	133	12.0000
::::	chr4:39747305-39747523(+)$1	218	97	101	12.0000
::::	chr2:135027954-135028178(+)$1	224	8	12	12.0000
ddss	chr1:40703357-40703578(+)$1	221	46	50	12.0000
gggg	chr2:198288443-198288661(-)$1	218	178	182	12.0000
hhhh	chr2:135711437-135711667(+)$1	230	147	151	12.0000
nnne	chr15:77241438-77241668(+)$1	230	25	29	12.0000
]ddd	chr20:5539319-5539537(-)$1	218	86	90	12.0000
wwwf	chr2:219445331-219445549(+)$1	218	58	62	12.0000
ffff	chr3:101284316-101284546(+)$1	230	11	15	12.0000
hhhh	chr4:139993038-139993257(-)$1	219	13	17	12.0000
wwww	chr4:1725449-1725675(+)$1	226	138	142	12.0000
dd::	chr6:116973147-116973377(-)$1	230	52	56	12.0000
oooo	chr6:33371458-33371680(+)$1	222	77	81	12.0000
::::	chr1:38228385-38228608(+)$1	223	154	158	12.0000
!ccc	chr1:220275819-220276038(+)$1	219	35	39	12.0000
emmm	chr6:56564351-56564568(-)$1	217	43	47	12.0000
CCC{	chr1:24680781-24681005(+)$1	224	23	27	12.0000
mddd	chrX:53578210-53578430(-)$1	220	64	68	12.0000
cuuu	chr16:56976021-56976251(+)$1	230	63	67	12.0000
gg22	chr1:2321299-2321520(-)$1	221	131	135	12.0000
ccoo	chr22:40661250-40661476(+)$1	226	69	73	12.0000
F:::	chr10:115636402-115636632(+)$1	230	10	14	12.0000
cc[=	chr17:57741116-57741338(+)$1	222	100	104	12.0000
EDDD	chr2:100055262-100055486(-)$1	224	4	8	12.0000
BB::	chr1:151377828-151378048(-)$1	220	178	182	12.0000
::::	chr14:77901529-77901755(-)$1	226	36	40	12.0000
nnnn	chr14:72055955-72056177(+)$1	222	36	40	12.0000
pppp	chr12:69968142-69968372(+)$1	230	66	70	12.0000
cc!!	chr4:104097997-104098227(-)$1	230	30	34	12.0000
ccc:	chr6:82914512-82914730(-)$1	218	20	24	12.0000
::::	chr3:44685514-44685744(+)$1	230	15	19	12.0000
::::	chr17:53471599-53471825(-)$1	226	215	219	12.0000
::::	chr11:110007903-110008137(+)$1	234	53	57	12.0000
:::d	chr11:30352446-30352666(+)$1	220	39	43	12.0000
oooo	chr5:138723483-138723709(-)$1	226	138	142	12.0000
::::	chr10:43088797-43089017(-)$1	220	0	4	12.0000
::::	chr2:47705480-47705703(+)$1	223	20	24	12.0000
::::	chr10:129910470-129910688(-)$1	218	17	21	12.0000
ffff	chr5:140951398-140951628(-)$1	230	82	86	12.0000
KGGG	chr11:102195914-102196134(+)$1	220	30	34	12.0000
::::	chr5:138643612-138643831(+)$1	219	28	32	12.0000
]ccc	chr12:31632624-31632846(-)$1	222	33	37	12.0000
EEEE	chr18:12337285-12337504(-)$1	219	46	50	12.0000
f"""	chr3:69073159-69073379(-)$1	220	50	54	12.0000
::::	chr12:132508233-132508453(+)$1	220	10	14	12.0000
ee::	chr11:34910203-34910433(-)$1	230	78	82	12.0000
::::	chr3:170928838-170929063(-)$1	225	7	11	12.0000
pppp	chr2:67630822-67631041(+)$1	219	83	87	12.0000
"""a	chr9:96326616-96326859(+)$1	243	21	25	12.0000
::::	chr3:107491691-107491912(+)$1	221	46	50	12.0000
fnnn	chr9:5457200-5457424(+)$1	224	10	14	12.0000
[ccc	chr14:95570080-95570303(-)$1	223	30	34	12.0000
bbrr	chr11:118625380-118625606(-)$1	226	98	102	12.0000
ddd[	chr20:42826176-42826397(-)$1	221	49	53	12.0000
ceee	chrX:76872066-76872291(-)$1	225	27	31	12.0000

#DB
((((	chr2:39283748-39283971(-)$1	1	20	24	12.0000
..((	chr10:112724591-112724815(+)$1	1	30	34	12.0000
(...	chr1:62913026-62913246(+)$1	1	15	19	12.0000
))))	chr8:103664100-103664320(-)$1	1	171	175	12.0000
.(((	chr10:11259347-11259566(+)$1	1	5	9	12.0000
....	chr22:21083656-21083877(-)$1	1	43	47	12.0000
....	chr1:14105860-14106078(+)$1	1	13	17	12.0000
....	chr1:91403288-91403518(-)$1	1	46	50	12.0000
))))	chr15:42855926-42856144(+)$1	1	68	72	12.0000
((((	chr13:96577840-96578064(-)$1	1	98	102	12.0000
((((	chr11:3720254-3720471(-)$1	1	6	10	12.0000
....	chr19:6362426-6362647(+)$1	1	94	98	12.0000
))))	chrM:10501-10721(+)$1	1	67	71	12.0000
.)))	chr2:48692590-48692814(+)$1	1	124	128	12.0000
))..	chrX:149901021-149901240(+)$1	1	202	206	12.0000
))..	chr3:48730448-48730666(-)$1	1	76	80	12.0000
....	chr11:18317551-18317771(+)$1	1	32	36	12.0000
(((.	chr8:53570285-53570506(-)$1	1	122	126	12.0000
((((	chr4:73964018-73964237(-)$1	1	19	23	12.0000
(...	chr3:135870032-135870250(-)$1	1	47	51	12.0000
((((	chr7:98961071-98961290(+)$1	1	201	205	12.0000
....	chr15:64967920-64968150(+)$1	1	150	154	12.0000
((..	chr10:5804443-5804666(+)$1	1	70	74	12.0000
((((	chr2:213914421-213914640(-)$1	1	81	85	12.0000
((..	chr11:130131364-130131594(-)$1	1	25	29	12.0000
...(	chr10:64974274-64974495(-)$1	1	58	62	12.0000
.)))	chr22:29939375-29939592(-)$1	1	66	70	12.0000
((((	chr1:79116004-79116230(+)$1	1	70	74	12.0000
((..	chr12:57006744-57006966(-)$1	1	191	195	12.0000
)).)	chr4:153831117-153831336(+)$1	1	165	169	12.0000
((((	chr6:135357840-135358062(-)$1	1	44	48	12.0000
....	chr9:114304339-114304562(+)$1	1	8	12	12.0000
.(((	chr5:149225317-149225538(-)$1	1	85	89	12.0000
))).	chr7:112101984-112102214(+)$1	1	129	133	12.0000
....	chr4:39747305-39747523(+)$1	1	97	101	12.0000
....	chr2:135027954-135028178(+)$1	1	8	12	12.0000
((..	chr1:40703357-40703578(+)$1	1	46	50	12.0000
))))	chr2:198288443-198288661(-)$1	1	178	182	12.0000
((((	chr2:135711437-135711667(+)$1	1	147	151	12.0000
...)	chr15:77241438-77241668(+)$1	1	25	29	12.0000
.)))	chr20:5539319-5539537(-)$1	1	86	90	12.0000
...)	chr2:219445331-219445549(+)$1	1	58	62	12.0000
((((	chr3:101284316-101284546(+)$1	1	11	15	12.0000
((((	chr4:139993038-139993257(-)$1	1	13	17	12.0000
....	chr4:1725449-1725675(+)$1	1	138	142	12.0000
))..	chr6:116973147-116973377(-)$1	1	52	56	12.0000
....	chr6:33371458-33371680(+)$1	1	77	81	12.0000
....	chr1:38228385-38228608(+)$1	1	154	158	12.0000
.(((	chr1:220275819-220276038(+)$1	1	35	39	12.0000
(...	chr6:56564351-56564568(-)$1	1	43	47	12.0000
(((.	chr1:24680781-24681005(+)$1	1	23	27	12.0000
.)))	chrX:53578210-53578430(-)$1	1	64	68	12.0000
(...	chr16:56976021-56976251(+)$1	1	63	67	12.0000
))..	chr1:2321299-2321520(-)$1	1	131	135	12.0000
((..	chr22:40661250-40661476(+)$1	1	69	73	12.0000
(...	chr10:115636402-115636632(+)$1	1	10	14	12.0000
((.(	chr17:57741116-57741338(+)$1	1	100	104	12.0000
((((	chr2:100055262-100055486(-)$1	1	4	8	12.0000
))..	chr1:151377828-151378048(-)$1	1	178	182	12.0000
....	chr14:77901529-77901755(-)$1	1	36	40	12.0000
....	chr14:72055955-72056177(+)$1	1	36	40	12.0000
....	chr12:69968142-69968372(+)$1	1	66	70	12.0000
((..	chr4:104097997-104098227(-)$1	1	30	34	12.0000
))).	chr6:82914512-82914730(-)$1	1	20	24	12.0000
....	chr3:44685514-44685744(+)$1	1	15	19	12.0000
....	chr17:53471599-53471825(-)$1	1	215	219	12.0000
....	chr11:110007903-110008137(+)$1	1	53	57	12.0000
...(	chr11:30352446-30352666(+)$1	1	39	43	12.0000
....	chr5:138723483-138723709(-)$1	1	138	142	12.0000
....	chr10:43088797-43089017(-)$1	1	0	4	12.0000
....	chr2:47705480-47705703(+)$1	1	20	24	12.0000
....	chr10:129910470-129910688(-)$1	1	17	21	12.0000
((((	chr5:140951398-140951628(-)$1	1	82	86	12.0000
.(((	chr11:102195914-102196134(+)$1	1	30	34	12.0000
....	chr5:138643612-138643831(+)$1	1	28	32	12.0000
.)))	chr12:31632624-31632846(-)$1	1	33	37	12.0000
((((	chr18:12337285-12337504(-)$1	1	46	50	12.0000
(...	chr3:69073159-69073379(-)$1	1	50	54	12.0000
....	chr12:132508233-132508453(+)$1	1	10	14	12.0000
))..	chr11:34910203-34910433(-)$1	1	78	82	12.0000
....	chr3:170928838-170929063(-)$1	1	7	11	12.0000
....	chr2:67630822-67631041(+)$1	1	83	87	12.0000
...(	chr9:96326616-96326859(+)$1	1	21	25	12.0000
....	chr3:107491691-107491912(+)$1	1	46	50	12.0000
(...	chr9:5457200-5457424(+)$1	1	10	14	12.0000
.(((	chr14:95570080-95570303(-)$1	1	30	34	12.0000
((..	chr11:118625380-118625606(-)$1	1	98	102	12.0000
(((.	chr20:42826176-42826397(-)$1	1	49	53	12.0000
)(((	chrX:76872066-76872291(-)$1	1	27	31	12.0000

#PSSM
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	

#score	1068.0000000000007
#seq	89
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m3_run2.nuc.txt

#NT
UUCUUCUU	chr13:50586512-50586743(-)$1	231	74	82	15.3636
UAUUUCUU	chr21:34707734-34707959(+)$1	225	74	82	15.8181
UUUUUUUU	chr9:125617996-125618213(-)$1	217	41	49	17.2954
UUGUUCUU	chr4:57265269-57265496(-)$1	227	69	77	15.2499
UUUCUCUU	chr11:32955492-32955727(+)$1	235	181	189	14.9090
UUUUUCCU	chr19:41257234-41257468(+)$1	234	41	49	14.7954
UUUUUGUU	chr22:28254366-28254583(-)$1	217	65	73	16.7272
UUUUUCUU	chr10:70243159-70243378(-)$1	219	207	215	19.5681
UUUAUCUU	chr10:27437812-27438038(-)$1	226	54	62	14.9090
UUUUUCUU	chr10:27422868-27423093(-)$1	225	24	32	19.5681
UUUUUUUU	chr15:23012307-23012530(-)$1	223	69	77	17.2954
UUAUUCUU	chr21:43413825-43414056(-)$1	231	112	120	15.3636
UCUUUCUU	chr3:31661073-31661296(+)$1	223	158	166	15.8181
UUUUUGUU	chr1:197108797-197109021(-)$1	224	207	215	16.7272
UCUUUUUU	chr2:210905061-210905288(+)$1	227	148	156	13.5454
UUAUUCUU	chr1:202302525-202302756(-)$1	231	59	67	15.3636
UAUUUUUU	chrM:10633-10902(+)$1	269	245	253	13.5454
UUUUUUUU	chr7:152346070-152346300(-)$1	230	73	81	17.2954
UUUUUCUU	chrX:21871422-21871646(+)$1	224	49	57	19.5681
UUUUUAUU	chr7:112424520-112424743(-)$1	223	62	70	16.4999
UGUUUCUU	chr14:97022562-97022785(+)$1	223	28	36	15.7045
UUUUUCUA	chr4:52765395-52765622(+)$1	227	31	39	15.4772
UUUUUCUG	chr2:85848541-85848766(+)$1	225	44	52	15.2499
UCUUUCUU	chr7:107408199-107408430(+)$1	231	42	50	15.8181
UUUUUGUU	chr10:70721766-70721989(+)$1	223	210	218	16.7272
UGUUUCUU	chr1:173780271-173780500(-)$1	229	39	47	15.7045
UUUUUCUU	chr7:36463422-36463653(+)$1	231	164	172	19.5681
UUUUUUUU	chr17:41329874-41330097(+)$1	223	15	23	17.2954
UAUUUUUU	chr7:120610670-120610905(+)$1	235	59	67	13.5454
CUUUUCUU	chr18:32920463-32920689(-)$1	226	49	57	14.9090
UUUUUGUU	chr2:232322956-232323176(-)$1	220	9	17	16.7272
UUUUUCUU	chr12:6788557-6788779(-)$1	222	77	85	19.5681
UUUUUCUA	chrX:153197423-153197652(-)$1	229	144	152	15.4772
UUUUUCUC	chr1:154226278-154226506(+)$1	228	75	83	15.2499
AUUUUCUU	chr2:219452239-219452462(+)$1	223	58	66	14.9090
UUUUUAUU	chr2:153535474-153535695(-)$1	221	41	49	16.4999
uuuuuuuu	chr2:217057317-217057541(+)$1	224	158	166	17.2954
UUUUUUUU	chr4:128904046-128904272(+)$1	226	164	172	17.2954
UUUUACUU	chr7:6513733-6513957(-)$1	224	103	111	14.7954
UUUUUCUU	chr1:115282378-115282600(-)$1	222	71	79	19.5681
UUUUUCUA	chr1:162469660-162469896(+)$1	236	75	83	15.4772
UUUUUCUU	chr21:33038678-33038901(+)$1	223	61	69	19.5681
UUCUUCUU	chrX:17768264-17768486(+)$1	222	57	65	15.3636

#otherMatches

#Struct PSSM
::::::::	chrX:16870600-16870827(-)$1	227	65	73	19.5681
eeee::::	chr13:50586512-50586743(-)$1	231	74	82	15.3636
7777777e	chr21:34707734-34707959(+)$1	225	74	82	15.8181
^^^^^^^^	chr9:125617996-125618213(-)$1	217	41	49	17.2954
hhhhhooo	chr4:57265269-57265496(-)$1	227	69	77	15.2499
iiii]bbc	chr11:32955492-32955727(+)$1	235	181	189	14.9090
hhhhhhhf	chr19:41257234-41257468(+)$1	234	41	49	14.7954
eeeee[ee	chr22:28254366-28254583(-)$1	217	65	73	16.7272
hhhhh:::	chr10:70243159-70243378(-)$1	219	207	215	19.5681
"""ddddo	chr10:27437812-27438038(-)$1	226	54	62	14.9090
IIIIIIII	chr10:27422868-27423093(-)$1	225	24	32	19.5681
IIIIGGGG	chr15:23012307-23012530(-)$1	223	69	77	17.2954
e:::::cc	chr21:43413825-43414056(-)$1	231	112	120	15.3636
::::::::	chr3:31661073-31661296(+)$1	223	158	166	15.8181
gEEEEE}F	chr1:197108797-197109021(-)$1	224	207	215	16.7272
FFFFF:::	chr2:210905061-210905288(+)$1	227	148	156	13.5454
8888888c	chr1:202302525-202302756(-)$1	231	59	67	15.3636
::::::::	chrM:10633-10902(+)$1	269	245	253	13.5454
((((((((	chr7:152346070-152346300(-)$1	230	73	81	17.2954
::::::::	chrX:21871422-21871646(+)$1	224	49	57	19.5681
g'''''''	chr7:112424520-112424743(-)$1	223	62	70	16.4999
ddddnnnn	chr14:97022562-97022785(+)$1	223	28	36	15.7045
hhhhhhh[	chr4:52765395-52765622(+)$1	227	31	39	15.4772
::::::::	chr2:85848541-85848766(+)$1	225	44	52	15.2499
vvvvveee	chr7:107408199-107408430(+)$1	231	42	50	15.8181
========	chr10:70721766-70721989(+)$1	223	210	218	16.7272
NNGGGGGG	chr1:173780271-173780500(-)$1	229	39	47	15.7045
++++++++	chr7:36463422-36463653(+)$1	231	164	172	19.5681
gg$$$$$c	chr17:41329874-41330097(+)$1	223	15	23	17.2954
GGGGGLLL	chr7:120610670-120610905(+)$1	235	59	67	13.5454
EEEE}A::	chr18:32920463-32920689(-)$1	226	49	57	14.9090
EEE:DDDD	chr2:232322956-232323176(-)$1	220	9	17	16.7272
ggg[bbmm	chr12:6788557-6788779(-)$1	222	77	85	19.5681
:::dddd[	chrX:153197423-153197652(-)$1	229	144	152	15.4772
mmmmdddd	chr1:154226278-154226506(+)$1	228	75	83	15.2499
#eeeee[e	chr2:219452239-219452462(+)$1	223	58	66	14.9090
mmmhhhhh	chr2:153535474-153535695(-)$1	221	41	49	16.4999
ii::::::	chr2:217057317-217057541(+)$1	224	158	166	17.2954
dddqqqqq	chr4:128904046-128904272(+)$1	226	164	172	17.2954
::::::::	chr7:6513733-6513957(-)$1	224	103	111	14.7954
c:::::::	chr1:115282378-115282600(-)$1	222	71	79	19.5681
::::ccc[	chr1:162469660-162469896(+)$1	236	75	83	15.4772
cccvvvvv	chr21:33038678-33038901(+)$1	223	61	69	19.5681
FFFFFF{C	chrX:17768264-17768486(+)$1	222	57	65	15.3636

#DB
........	chrX:16870600-16870827(-)$1	1	65	73	19.5681
))))....	chr13:50586512-50586743(-)$1	1	74	82	15.3636
.......)	chr21:34707734-34707959(+)$1	1	74	82	15.8181
........	chr9:125617996-125618213(-)$1	1	41	49	17.2954
(((((...	chr4:57265269-57265496(-)$1	1	69	77	15.2499
)))).)))	chr11:32955492-32955727(+)$1	1	181	189	14.9090
))))))))	chr19:41257234-41257468(+)$1	1	41	49	14.7954
(((((.((	chr22:28254366-28254583(-)$1	1	65	73	16.7272
)))))...	chr10:70243159-70243378(-)$1	1	207	215	19.5681
...((((.	chr10:27437812-27438038(-)$1	1	54	62	14.9090
((((((((	chr10:27422868-27423093(-)$1	1	24	32	19.5681
((((((((	chr15:23012307-23012530(-)$1	1	69	77	17.2954
).....((	chr21:43413825-43414056(-)$1	1	112	120	15.3636
........	chr3:31661073-31661296(+)$1	1	158	166	15.8181
)))))).)	chr1:197108797-197109021(-)$1	1	207	215	16.7272
)))))...	chr2:210905061-210905288(+)$1	1	148	156	13.5454
.......)	chr1:202302525-202302756(-)$1	1	59	67	15.3636
........	chrM:10633-10902(+)$1	1	245	253	13.5454
........	chr7:152346070-152346300(-)$1	1	73	81	17.2954
........	chrX:21871422-21871646(+)$1	1	49	57	19.5681
(.......	chr7:112424520-112424743(-)$1	1	62	70	16.4999
((((....	chr14:97022562-97022785(+)$1	1	28	36	15.7045
(((((((.	chr4:52765395-52765622(+)$1	1	31	39	15.4772
........	chr2:85848541-85848766(+)$1	1	44	52	15.2499
.....)))	chr7:107408199-107408430(+)$1	1	42	50	15.8181
))))))))	chr10:70721766-70721989(+)$1	1	210	218	16.7272
..((((((	chr1:173780271-173780500(-)$1	1	39	47	15.7045
........	chr7:36463422-36463653(+)$1	1	164	172	19.5681
((.....(	chr17:41329874-41330097(+)$1	1	15	23	17.2954
(((((...	chr7:120610670-120610905(+)$1	1	59	67	13.5454
)))).)..	chr18:32920463-32920689(-)$1	1	49	57	14.9090
(((.((((	chr2:232322956-232323176(-)$1	1	9	17	16.7272
(((.((..	chr12:6788557-6788779(-)$1	1	77	85	19.5681
...((((.	chrX:153197423-153197652(-)$1	1	144	152	15.4772
....))))	chr1:154226278-154226506(+)$1	1	75	83	15.2499
.(((((.(	chr2:219452239-219452462(+)$1	1	58	66	14.9090
...)))))	chr2:153535474-153535695(-)$1	1	41	49	16.4999
))......	chr2:217057317-217057541(+)$1	1	158	166	17.2954
(((.....	chr4:128904046-128904272(+)$1	1	164	172	17.2954
........	chr7:6513733-6513957(-)$1	1	103	111	14.7954
).......	chr1:115282378-115282600(-)$1	1	71	79	19.5681
....(((.	chr1:162469660-162469896(+)$1	1	75	83	15.4772
(((.....	chr21:33038678-33038901(+)$1	1	61	69	19.5681
((((((.(	chrX:17768264-17768486(+)$1	1	57	65	15.3636

#PSSM
U : 0.93	C : 0.02	A : 0.02	u : 0.02	
U : 0.79	A : 0.06	C : 0.06	G : 0.04	u : 0.02	
U : 0.86	C : 0.04	A : 0.04	G : 0.02	u : 0.02	
U : 0.93	C : 0.02	A : 0.02	u : 0.02	
U : 0.95	u : 0.02	A : 0.02	
C : 0.65	U : 0.18	G : 0.09	A : 0.04	u : 0.02	
U : 0.95	C : 0.02	u : 0.02	
U : 0.86	A : 0.06	G : 0.02	C : 0.02	u : 0.02	

#score	722.5909090909084
#seq	44
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ALKBH5_Baltz2012a_hg19_CDS_m3_run1.nuc.txt

#NT
CUUCUUC	chr13:114152671-114152901(+)$1	230	186	193	12.2962
CUUCUCC	chr11:6661853-6662090(-)$1	237	157	164	16.6481
CUACUCC	chr5:137089426-137089674(-)$1	248	80	87	13.0370
CUGCUCC	chr1:1334391-1334617(-)$1	226	201	208	13.0370
CUUCCCC	chr7:2411380-2411605(+)$1	225	9	16	13.2222
CUUUUCC	chr22:29191097-29191324(-)$1	227	184	191	12.1111
CUUCCCC	chr21:40720734-40720960(-)$1	226	75	82	13.2222
CUUCUUC	chr13:114138079-114138303(-)$1	224	57	64	12.2962
CUUCCCC	chrM:7894-8125(+)$1	231	58	65	13.2222
UUUCUCC	chr22:35799379-35799618(+)$1	239	18	25	12.6666
CUUCACC	chr19:49119242-49119471(-)$1	229	189	196	13.1296
uuucucc	chr19:30106093-30106334(+)$1	241	26	33	12.6666
CUCCUCC	chr1:226027536-226027771(+)$1	235	54	61	12.9444
CUGCUCC	chr7:30634619-30634845(+)$1	226	8	15	13.0370
CGUCUCC	chr16:23695159-23695396(+)$1	237	151	158	12.2962
CUUCUCU	chr18:74587482-74587721(+)$1	239	86	93	12.4814
CUUCACC	chr17:38175965-38176208(-)$1	243	161	168	13.1296
CUGCUCC	chr16:74660266-74660516(-)$1	250	137	144	13.0370
CUUCUCC	chrM:6381-6622(+)$1	241	105	112	16.6481
UUUCUCC	chr12:57905365-57905619(+)$1	254	98	105	12.6666
CUUCACC	chr22:35819193-35819419(+)$1	226	23	30	13.1296
AUUCUCC	chr12:57906441-57906684(+)$1	243	76	83	12.3888
CUUCUCC	chr22:30975737-30975983(-)$1	246	110	117	16.6481
CCUCUCC	chr6:2948470-2948708(-)$1	238	203	210	12.2962
CUUCUGC	chr17:40925407-40925647(+)$1	240	12	19	12.1111
CUUCUUC	chr5:138650265-138650504(+)$1	239	146	153	12.2962
UUUCUCC	chr19:1434667-1434921(+)$1	254	56	63	12.6666
CUUCACC	chr19:54966543-54966790(+)$1	247	77	84	13.1296
CUCCUCC	chr15:90166842-90167076(+)$1	234	175	182	12.9444
GUUCUCC	chr12:49666064-49666288(+)$1	224	99	106	12.4814
CUCCUCC	chr19:34890801-34891031(+)$1	230	191	198	12.9444
CUUCUCC	chr22:41924464-41924695(+)$1	231	5	12	16.6481
CUACUCC	chr19:46295812-46296038(-)$1	226	126	133	13.0370
GUUCUCC	chr5:33459758-33459991(+)$1	233	145	152	12.4814
CUUCUCC	chr16:87870091-87870318(-)$1	227	88	95	16.6481
CUUAUCC	chr12:6636874-6637109(+)$1	235	35	42	12.0185
CAUCUCC	chr16:2814252-2814482(+)$1	230	85	92	12.5740
CUACUCC	chr5:137089509-137089735(-)$1	226	141	148	13.0370
CAUCUCC	chr8:48874072-48874309(+)$1	237	24	31	12.5740
CUGCUCC	chr16:23546198-23546452(-)$1	254	57	64	13.0370
CUUCUCC	chr9:135919043-135919270(+)$1	227	213	220	16.6481
CUUCUCU	chr8:28574331-28574560(+)$1	229	103	110	12.4814
CUUUUCC	chr1:214828604-214828830(+)$1	226	179	186	12.1111
CUACUCC	chrM:12991-13217(+)$1	226	81	88	13.0370
CUUCUCC	chr14:103988705-103988934(-)$1	229	109	116	16.6481
CAUCUCC	chr9:106896725-106896954(+)$1	229	182	189	12.5740
CAUCUCC	chr22:29191959-29192207(-)$1	248	128	135	12.5740
CUUCACC	chr7:30655510-30655735(+)$1	225	80	87	13.1296
CUUCUCU	chr3:184035018-184035255(+)$1	237	49	56	12.4814
CUUCUCA	chr11:3039600-3039836(-)$1	236	23	30	12.2037
CUUCCCC	chr22:35660668-35660897(+)$1	229	62	69	13.2222
CUUCCCC	chr1:52704665-52704892(+)$1	227	105	112	13.2222
CUUCUCU	chr20:30533498-30533729(-)$1	231	25	32	12.4814

#otherMatches

#Struct PSSM
dddd[dd	chr17:3627299-3627538(+)$1	239	139	146	13.2222
eeeee''	chr13:114152671-114152901(+)$1	230	186	193	12.2962
fff:EEE	chr11:6661853-6662090(-)$1	237	157	164	16.6481
cc[eeee	chr5:137089426-137089674(-)$1	248	80	87	13.0370
FFFF::f	chr1:1334391-1334617(-)$1	226	201	208	13.0370
!ccc[ee	chr7:2411380-2411605(+)$1	225	9	16	13.2222
555ffff	chr22:29191097-29191324(-)$1	227	184	191	12.1111
hhhhh[a	chr21:40720734-40720960(-)$1	226	75	82	13.2222
=======	chr13:114138079-114138303(-)$1	224	57	64	12.2962
^^^^^^^	chrM:7894-8125(+)$1	231	58	65	13.2222
:ffffff	chr22:35799379-35799618(+)$1	239	18	25	12.6666
cc####b	chr19:49119242-49119471(-)$1	229	189	196	13.1296
EEEEKKC	chr19:30106093-30106334(+)$1	241	26	33	12.6666
cpppppp	chr1:226027536-226027771(+)$1	235	54	61	12.9444
mmbbCCC	chr7:30634619-30634845(+)$1	226	8	15	13.0370
:DDDDZZ	chr16:23695159-23695396(+)$1	237	151	158	12.2962
:ffffff	chr18:74587482-74587721(+)$1	239	86	93	12.4814
ee[eeee	chr17:38175965-38176208(-)$1	243	161	168	13.1296
DDDD}BB	chr16:74660266-74660516(-)$1	250	137	144	13.0370
ccxxxxx	chrM:6381-6622(+)$1	241	105	112	16.6481
gggg!!d	chr12:57905365-57905619(+)$1	254	98	105	12.6666
EE{DDDD	chr22:35819193-35819419(+)$1	226	23	30	13.1296
]iiiiii	chr12:57906441-57906684(+)$1	243	76	83	12.3888
DD{HHHH	chr22:30975737-30975983(-)$1	246	110	117	16.6481
BBZZZCC	chr6:2948470-2948708(-)$1	238	203	210	12.2962
bqqqqqq	chr17:40925407-40925647(+)$1	240	12	19	12.1111
ddddddd	chr5:138650265-138650504(+)$1	239	146	153	12.2962
%%%%%ee	chr19:1434667-1434921(+)$1	254	56	63	12.6666
JJJKKII	chr19:54966543-54966790(+)$1	247	77	84	13.1296
gggggbb	chr15:90166842-90167076(+)$1	234	175	182	12.9444
]dddddd	chr12:49666064-49666288(+)$1	224	99	106	12.4814
::::::b	chr19:34890801-34891031(+)$1	230	191	198	12.9444
::fffff	chr22:41924464-41924695(+)$1	231	5	12	16.6481
22dddd]	chr19:46295812-46296038(-)$1	226	126	133	13.0370
(ffffff	chr5:33459758-33459991(+)$1	233	145	152	12.4814
dddmmmm	chr16:87870091-87870318(-)$1	227	88	95	16.6481
CCSSSSS	chr12:6636874-6637109(+)$1	235	35	42	12.0185
::ccc[c	chr16:2814252-2814482(+)$1	230	85	92	12.5740
:::eeee	chr5:137089509-137089735(-)$1	226	141	148	13.0370
DD:ccce	chr8:48874072-48874309(+)$1	237	24	31	12.5740
mmccc::	chr16:23546198-23546452(-)$1	254	57	64	13.0370
:::::::	chr9:135919043-135919270(+)$1	227	213	220	16.6481
hhhhhhh	chr8:28574331-28574560(+)$1	229	103	110	12.4814
&&dddda	chr1:214828604-214828830(+)$1	226	179	186	12.1111
ddd((((	chrM:12991-13217(+)$1	226	81	88	13.0370
ggggccc	chr14:103988705-103988934(-)$1	229	109	116	16.6481
5555===	chr9:106896725-106896954(+)$1	229	182	189	12.5740
####ccc	chr22:29191959-29192207(-)$1	248	128	135	12.5740
6eeeee:	chr7:30655510-30655735(+)$1	225	80	87	13.1296
a333fff	chr3:184035018-184035255(+)$1	237	49	56	12.4814
IIIIIII	chr11:3039600-3039836(-)$1	236	23	30	12.2037
wwwwwww	chr22:35660668-35660897(+)$1	229	62	69	13.2222
dddabbd	chr1:52704665-52704892(+)$1	227	105	112	13.2222
ssssssc	chr20:30533498-30533729(-)$1	231	25	32	12.4814

#DB
((((.((	chr17:3627299-3627538(+)$1	1	139	146	13.2222
(((((..	chr13:114152671-114152901(+)$1	1	186	193	12.2962
))).)))	chr11:6661853-6662090(-)$1	1	157	164	16.6481
((.((((	chr5:137089426-137089674(-)$1	1	80	87	13.0370
))))..(	chr1:1334391-1334617(-)$1	1	201	208	13.0370
.(((.((	chr7:2411380-2411605(+)$1	1	9	16	13.2222
...))))	chr22:29191097-29191324(-)$1	1	184	191	12.1111
(((((.(	chr21:40720734-40720960(-)$1	1	75	82	13.2222
(((((((	chr13:114138079-114138303(-)$1	1	57	64	12.2962
.......	chrM:7894-8125(+)$1	1	58	65	13.2222
.((((((	chr22:35799379-35799618(+)$1	1	18	25	12.6666
((....(	chr19:49119242-49119471(-)$1	1	189	196	13.1296
((((..(	chr19:30106093-30106334(+)$1	1	26	33	12.6666
(......	chr1:226027536-226027771(+)$1	1	54	61	12.9444
..))(((	chr7:30634619-30634845(+)$1	1	8	15	13.0370
.))))..	chr16:23695159-23695396(+)$1	1	151	158	12.2962
.((((((	chr18:74587482-74587721(+)$1	1	86	93	12.4814
((.((((	chr17:38175965-38176208(-)$1	1	161	168	13.1296
)))).))	chr16:74660266-74660516(-)$1	1	137	144	13.0370
((.....	chrM:6381-6622(+)$1	1	105	112	16.6481
((((..(	chr12:57905365-57905619(+)$1	1	98	105	12.6666
((.((((	chr22:35819193-35819419(+)$1	1	23	30	13.1296
.))))))	chr12:57906441-57906684(+)$1	1	76	83	12.3888
((.((((	chr22:30975737-30975983(-)$1	1	110	117	16.6481
))...))	chr6:2948470-2948708(-)$1	1	203	210	12.2962
(......	chr17:40925407-40925647(+)$1	1	12	19	12.1111
)))))))	chr5:138650265-138650504(+)$1	1	146	153	12.2962
.....((	chr19:1434667-1434921(+)$1	1	56	63	12.6666
(((..((	chr19:54966543-54966790(+)$1	1	77	84	13.1296
)))))((	chr15:90166842-90167076(+)$1	1	175	182	12.9444
.))))))	chr12:49666064-49666288(+)$1	1	99	106	12.4814
......(	chr19:34890801-34891031(+)$1	1	191	198	12.9444
..(((((	chr22:41924464-41924695(+)$1	1	5	12	16.6481
..)))).	chr19:46295812-46296038(-)$1	1	126	133	13.0370
.((((((	chr5:33459758-33459991(+)$1	1	145	152	12.4814
(((....	chr16:87870091-87870318(-)$1	1	88	95	16.6481
((.....	chr12:6636874-6637109(+)$1	1	35	42	12.0185
..(((.(	chr16:2814252-2814482(+)$1	1	85	92	12.5740
...((((	chr5:137089509-137089735(-)$1	1	141	148	13.0370
((.((((	chr8:48874072-48874309(+)$1	1	24	31	12.5740
..)))..	chr16:23546198-23546452(-)$1	1	57	64	13.0370
.......	chr9:135919043-135919270(+)$1	1	213	220	16.6481
)))))))	chr8:28574331-28574560(+)$1	1	103	110	12.4814
..(((((	chr1:214828604-214828830(+)$1	1	179	186	12.1111
(((....	chrM:12991-13217(+)$1	1	81	88	13.0370
))))(((	chr14:103988705-103988934(-)$1	1	109	116	16.6481
....)))	chr9:106896725-106896954(+)$1	1	182	189	12.5740
....(((	chr22:29191959-29192207(-)$1	1	128	135	12.5740
.))))).	chr7:30655510-30655735(+)$1	1	80	87	13.1296
)...)))	chr3:184035018-184035255(+)$1	1	49	56	12.4814
(((((((	chr11:3039600-3039836(-)$1	1	23	30	12.2037
.......	chr22:35660668-35660897(+)$1	1	62	69	13.2222
(((((((	chr1:52704665-52704892(+)$1	1	105	112	13.2222
......)	chr20:30533498-30533729(-)$1	1	25	32	12.4814

#PSSM
C : 0.87	U : 0.05	G : 0.03	u : 0.01	A : 0.01	
U : 0.87	A : 0.07	u : 0.01	G : 0.01	C : 0.01	
U : 0.77	A : 0.07	G : 0.07	C : 0.05	u : 0.01	
C : 0.92	U : 0.03	c : 0.01	A : 0.01	
U : 0.77	C : 0.11	A : 0.09	u : 0.01	
C : 0.90	U : 0.05	c : 0.01	G : 0.01	
C : 0.88	U : 0.07	c : 0.01	A : 0.01	

#score	714.9259259259252
#seq	54
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m2_run2.nuc.txt

#NT
uuuuuuucuuu	chr5:179041678-179041958(-)$1	280	166	177	25.1052
UUUAUUACUUU	chrX:70756051-70756291(+)$1	240	112	123	16.5964
UUUUUUUCUGU	chr3:132153307-132153547(+)$1	240	175	186	20.8070
UUUUGUUUUUU	chr4:71895044-71895284(+)$1	240	228	239	17.9122
UUUUUCACUUU	chr7:94166804-94167044(+)$1	240	90	101	17.0350
UGUUUUUGUUU	chr3:57647129-57647369(-)$1	240	71	82	18.1754
UCAUUUUCUUU	chr7:94167019-94167261(+)$1	242	194	205	18.1754
UUUCUUUCUUU	chr6:109689987-109690227(-)$1	240	119	130	20.5438
CUUUUAUCUUU	chr14:91947843-91948083(-)$1	240	120	131	16.8596
UUUUUUACAUU	chr5:90106226-90106466(+)$1	240	116	127	16.9473
UUCUUUUCUUU	chr11:9307995-9308235(-)$1	240	74	85	21.1578
UUUUUUUCUUU	chrX:100880844-100881084(+)$1	240	122	133	25.1052
UUUUGUUCUUC	chr11:62348556-62348975(-)$1	419	234	245	17.6491
UAUUUGUCUUU	chr14:90870955-90871195(+)$1	240	62	73	17.5614
UUUUUUUUUUU	chr14:53513436-53513676(-)$1	240	225	236	21.4210
UUAUUUUCUUA	chr8:56675194-56675440(-)$1	246	124	135	17.2105
UCUUUUACUUU	chr3:169801936-169802176(+)$1	240	21	32	17.7368
UUUUUUUAUUU	chr20:52835585-52835825(+)$1	240	118	129	21.5964
GUUUUUUAUUU	chr12:112568218-112568458(+)$1	240	16	27	17.2982
UUAUCUUCUUU	chr10:98287068-98287308(-)$1	240	27	38	17.7368
UCUUUUUCUUU	chr19:32945806-32946046(+)$1	240	213	224	21.8596
AUUUUUUCUUU	chr2:191300868-191301108(+)$1	240	110	121	20.8947
UACUUUUCUUU	chr4:103226081-103226321(-)$1	240	123	134	17.6491
UGUUUCUCUUU	chr5:81571793-81572033(-)$1	240	54	65	17.8245
UUUUUUUCAUC	chr20:10389237-10389477(-)$1	240	117	128	17.1228
AUUUUUUCAUU	chr7:107224221-107224464(+)$1	243	115	126	16.8596
UGUUUUUGUUU	chr9:108123461-108123701(+)$1	240	184	195	18.1754
UUUUUUUGUUU	chr1:170004494-170004743(-)$1	249	132	143	21.5087
UUUUUUUCCUU	chr1:109472457-109472697(+)$1	240	120	131	20.7192
UUAUUUACUUU	chr11:62344063-62344541(-)$1	478	304	315	17.2982
UUUUUUUUUUU	chr6:17602761-17603010(+)$1	249	36	47	21.4210
UUUUUUUAUCU	chr10:32097839-32098079(-)$1	240	227	238	17.3859
UUUUUUUCUUA	chr8:27680565-27680805(-)$1	240	71	82	20.8947
CCUUUUUCUUU	chr9:19096605-19096845(-)$1	240	37	48	17.8245
UUUUUCUCUCU	chr20:18526506-18526746(+)$1	240	37	48	16.9473
UUCUAUUCUUU	chr19:37726559-37726799(+)$1	240	115	126	17.5614
UUAUUUUCUUU	chr1:63884940-63885180(+)$1	240	124	135	21.4210
UUUUUCUCUCU	chr15:48434387-48434667(-)$1	280	62	73	16.9473
UUUUCUUCAUU	chrX:41055464-41055704(+)$1	240	113	124	17.3859
UUUUUUUCUUC	chr12:75893480-75893720(+)$1	240	113	124	21.1578
UUUUUUUGUUU	chrX:133927780-133928020(-)$1	240	65	76	21.5087
uuuuauuauuu	chrX:40456415-40456655(+)$1	240	224	235	18.0000
CUUUUGUCUUU	chrX:135080182-135080424(+)$1	242	169	180	17.0350
UAUUUUUCUUU	chr12:85695145-85695419(+)$1	274	123	134	21.5964
CUUAUUUCUUU	chr5:37052517-37052757(+)$1	240	115	126	16.6842
UUUUAUUCUAU	chr6:96034241-96034481(+)$1	240	115	126	17.1228
UUAUUUUCUGU	chr5:110441692-110441932(+)$1	240	216	227	17.1228
UUUUUUUAUUU	chr8:95392363-95392605(-)$1	242	121	132	21.5964
UGUUCUUCUUU	chr15:42823574-42823814(+)$1	240	111	122	18.0877
UUUUGGUCUUU	chr3:145806271-145806511(-)$1	240	178	189	17.5614
UUUUGUUCUUU	chr14:39536342-39536582(-)$1	240	63	74	21.5964
UUUAUUUCUUU	chr3:169802047-169802287(+)$1	240	125	136	20.7192
UCUUUUUCUUU	chr5:70860605-70860845(+)$1	240	119	130	21.8596
UCUUUUUCAUU	chr7:108155191-108155431(-)$1	240	59	70	17.8245
UUUUAUUCUUC	chr14:74363092-74363332(+)$1	240	116	127	17.5614
UGUUUUUCUUC	chr17:79535989-79536229(-)$1	240	76	87	17.8245

#otherMatches

#Struct PSSM
5555dddd22d	chr1:82435902-82436142(+)$1	240	74	85	21.5964
:::::::GGGG	chr5:179041678-179041958(-)$1	280	166	177	25.1052
:::::::bb!!	chrX:70756051-70756291(+)$1	240	112	123	16.5964
ccc]eeeee33	chr3:132153307-132153547(+)$1	240	175	186	20.8070
:::::::::::	chr4:71895044-71895284(+)$1	240	228	239	17.9122
==========!	chr7:94166804-94167044(+)$1	240	90	101	17.0350
zzzzzgggggg	chr3:57647129-57647369(-)$1	240	71	82	18.1754
[bb((((((((	chr7:94167019-94167261(+)$1	242	194	205	18.1754
dddd[gggggg	chr6:109689987-109690227(-)$1	240	119	130	20.5438
eeee[eeeeep	chr14:91947843-91948083(-)$1	240	120	131	16.8596
mffffff22cc	chr5:90106226-90106466(+)$1	240	116	127	16.9473
::::::::eee	chr11:9307995-9308235(-)$1	240	74	85	21.1578
iiiiiiiii::	chrX:100880844-100881084(+)$1	240	122	133	25.1052
qqqqbb]a:::	chr11:62348556-62348975(-)$1	419	234	245	17.6491
^^^hhhhhhhh	chr14:90870955-90871195(+)$1	240	62	73	17.5614
:::::::::::	chr14:53513436-53513676(-)$1	240	225	236	21.4210
cc[hhhhhhhh	chr8:56675194-56675440(-)$1	246	124	135	17.2105
:::ffffffll	chr3:169801936-169802176(+)$1	240	21	32	17.7368
ccc[ffffffn	chr20:52835585-52835825(+)$1	240	118	129	21.5964
HHHdddd[ccc	chr12:112568218-112568458(+)$1	240	16	27	17.2982
ppppppeeeee	chr10:98287068-98287308(-)$1	240	27	38	17.7368
EE}EEEEEGGG	chr19:32945806-32946046(+)$1	240	213	224	21.8596
:::::::::ii	chr2:191300868-191301108(+)$1	240	110	121	20.8947
eeeeddddooo	chr4:103226081-103226321(-)$1	240	123	134	17.6491
::dddd[eeee	chr5:81571793-81572033(-)$1	240	54	65	17.8245
d]hhhhhhhh4	chr20:10389237-10389477(-)$1	240	117	128	17.1228
mmmmdddd:EE	chr7:107224221-107224464(+)$1	243	115	126	16.8596
cccqqqqqqqq	chr9:108123461-108123701(+)$1	240	184	195	18.1754
5555iiiiiii	chr1:170004494-170004743(-)$1	249	132	143	21.5087
7==========	chr1:109472457-109472697(+)$1	240	120	131	20.7192
>>>>>>>>>gg	chr11:62344063-62344541(-)$1	478	304	315	17.2982
:::::::::JJ	chr6:17602761-17603010(+)$1	249	36	47	21.4210
gggg22eeeee	chr10:32097839-32098079(-)$1	240	227	238	17.3859
iiiiiii!!cc	chr8:27680565-27680805(-)$1	240	71	82	20.8947
[a"""eeeee^	chr9:19096605-19096845(-)$1	240	37	48	17.8245
mmmmccc::::	chr20:18526506-18526746(+)$1	240	37	48	16.9473
ddd!!ccc%%%	chr19:37726559-37726799(+)$1	240	115	126	17.5614
:::::::::::	chr1:63884940-63885180(+)$1	240	124	135	21.4210
ooeeeee]bb:	chr15:48434387-48434667(-)$1	280	62	73	16.9473
cc[ffffff!!	chrX:41055464-41055704(+)$1	240	113	124	17.3859
IIIIIII::::	chr12:75893480-75893720(+)$1	240	113	124	21.1578
hhhhhDDDDFF	chrX:133927780-133928020(-)$1	240	65	76	21.5087
ggg::::::::	chrX:40456415-40456655(+)$1	240	224	235	18.0000
fffff::::dd	chrX:135080182-135080424(+)$1	242	169	180	17.0350
%%%%%%hhhhh	chr12:85695145-85695419(+)$1	274	123	134	21.5964
NNNNFFFFFF:	chr5:37052517-37052757(+)$1	240	115	126	16.6842
fffff!!bb!!	chr6:96034241-96034481(+)$1	240	115	126	17.1228
d]ggggggg:J	chr5:110441692-110441932(+)$1	240	216	227	17.1228
b]eeeee::::	chr8:95392363-95392605(-)$1	242	121	132	21.5964
B{GGGGGGG{C	chr15:42823574-42823814(+)$1	240	111	122	18.0877
ffffffbbiii	chr3:145806271-145806511(-)$1	240	178	189	17.5614
EEEEEKKBB{H	chr14:39536342-39536582(-)$1	240	63	74	21.5964
i[bboooooob	chr3:169802047-169802287(+)$1	240	125	136	20.7192
ccc]dddd:::	chr5:70860605-70860845(+)$1	240	119	130	21.8596
iiiiiiii:::	chr7:108155191-108155431(-)$1	240	59	70	17.8245
000000000dd	chr14:74363092-74363332(+)$1	240	116	127	17.5614
=======&&&&	chr17:79535989-79536229(-)$1	240	76	87	17.8245

#DB
....))))..)	chr1:82435902-82436142(+)$1	1	74	85	21.5964
.......((((	chr5:179041678-179041958(-)$1	1	166	177	25.1052
.......((..	chrX:70756051-70756291(+)$1	1	112	123	16.5964
))).)))))..	chr3:132153307-132153547(+)$1	1	175	186	20.8070
...........	chr4:71895044-71895284(+)$1	1	228	239	17.9122
((((((((((.	chr7:94166804-94167044(+)$1	1	90	101	17.0350
.....))))))	chr3:57647129-57647369(-)$1	1	71	82	18.1754
.((........	chr7:94167019-94167261(+)$1	1	194	205	18.1754
((((.((((((	chr6:109689987-109690227(-)$1	1	119	130	20.5438
((((.(((((.	chr14:91947843-91948083(-)$1	1	120	131	16.8596
.))))))..))	chr5:90106226-90106466(+)$1	1	116	127	16.9473
........(((	chr11:9307995-9308235(-)$1	1	74	85	21.1578
)))))))))..	chrX:100880844-100881084(+)$1	1	122	133	25.1052
....)).)...	chr11:62348556-62348975(-)$1	1	234	245	17.6491
...))))))))	chr14:90870955-90871195(+)$1	1	62	73	17.5614
...........	chr14:53513436-53513676(-)$1	1	225	236	21.4210
((.((((((((	chr8:56675194-56675440(-)$1	1	124	135	17.2105
...((((((..	chr3:169801936-169802176(+)$1	1	21	32	17.7368
(((.((((((.	chr20:52835585-52835825(+)$1	1	118	129	21.5964
(((((((.(((	chr12:112568218-112568458(+)$1	1	16	27	17.2982
......)))))	chr10:98287068-98287308(-)$1	1	27	38	17.7368
)).))))))))	chr19:32945806-32946046(+)$1	1	213	224	21.8596
.........((	chr2:191300868-191301108(+)$1	1	110	121	20.8947
))))((((...	chr4:103226081-103226321(-)$1	1	123	134	17.6491
..((((.((((	chr5:81571793-81572033(-)$1	1	54	65	17.8245
).)))))))).	chr20:10389237-10389477(-)$1	1	117	128	17.1228
....)))).))	chr7:107224221-107224464(+)$1	1	115	126	16.8596
(((........	chr9:108123461-108123701(+)$1	1	184	195	18.1754
....)))))))	chr1:170004494-170004743(-)$1	1	132	143	21.5087
.))))))))))	chr1:109472457-109472697(+)$1	1	120	131	20.7192
.........))	chr11:62344063-62344541(-)$1	1	304	315	17.2982
.........((	chr6:17602761-17603010(+)$1	1	36	47	21.4210
))))..)))))	chr10:32097839-32098079(-)$1	1	227	238	17.3859
(((((((..((	chr8:27680565-27680805(-)$1	1	71	82	20.8947
.(...(((((.	chr9:19096605-19096845(-)$1	1	37	48	17.8245
....)))....	chr20:18526506-18526746(+)$1	1	37	48	16.9473
(((..(((...	chr19:37726559-37726799(+)$1	1	115	126	17.5614
...........	chr1:63884940-63885180(+)$1	1	124	135	21.4210
..))))).)).	chr15:48434387-48434667(-)$1	1	62	73	16.9473
((.((((((..	chrX:41055464-41055704(+)$1	1	113	124	17.3859
)))))))....	chr12:75893480-75893720(+)$1	1	113	124	21.1578
)))))((((((	chrX:133927780-133928020(-)$1	1	65	76	21.5087
)))........	chrX:40456415-40456655(+)$1	1	224	235	18.0000
)))))....((	chrX:135080182-135080424(+)$1	1	169	180	17.0350
......(((((	chr12:85695145-85695419(+)$1	1	123	134	21.5964
....((((((.	chr5:37052517-37052757(+)$1	1	115	126	16.6842
(((((..((..	chr6:96034241-96034481(+)$1	1	115	126	17.1228
).))))))).)	chr5:110441692-110441932(+)$1	1	216	227	17.1228
).)))))....	chr8:95392363-95392605(-)$1	1	121	132	21.5964
(.(((((((.(	chr15:42823574-42823814(+)$1	1	111	122	18.0877
)))))))))))	chr3:145806271-145806511(-)$1	1	178	189	17.5614
(((((..((.(	chr14:39536342-39536582(-)$1	1	63	74	21.5964
(.((......)	chr3:169802047-169802287(+)$1	1	125	136	20.7192
))).))))...	chr5:70860605-70860845(+)$1	1	119	130	21.8596
))))))))...	chr7:108155191-108155431(-)$1	1	59	70	17.8245
.........))	chr14:74363092-74363332(+)$1	1	116	127	17.5614
(((((((....	chr17:79535989-79536229(-)$1	1	76	87	17.8245

#PSSM
U : 0.84	C : 0.07	u : 0.03	A : 0.03	G : 0.01	
U : 0.71	C : 0.10	G : 0.08	A : 0.05	u : 0.03	
U : 0.80	A : 0.10	C : 0.05	u : 0.03	
U : 0.89	A : 0.05	u : 0.03	C : 0.01	
U : 0.77	G : 0.08	C : 0.05	A : 0.05	u : 0.01	a : 0.01	
U : 0.82	C : 0.07	G : 0.05	u : 0.03	A : 0.01	
U : 0.87	A : 0.08	u : 0.03	
C : 0.77	G : 0.07	A : 0.07	U : 0.05	c : 0.01	a : 0.01	
U : 0.85	A : 0.08	u : 0.03	C : 0.01	
U : 0.85	C : 0.05	u : 0.03	G : 0.03	A : 0.01	
U : 0.84	C : 0.08	u : 0.03	A : 0.03	

#score	1086.789473684212
#seq	57
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m2_run2.nuc.txt

#NT
CUG	chr8:27591620-27591840(-)$1	220	22	25	9.0000
CUG	chr9:95077888-95078118(-)$1	230	17	20	9.0000
CUG	chr19:13888974-13889193(+)$1	219	6	9	9.0000
CUG	chr16:89727314-89727548(+)$1	234	72	75	9.0000
CUG	chr11:117160063-117160291(+)$1	228	22	25	9.0000
CUG	chr15:45028762-45028985(+)$1	223	26	29	9.0000
CUG	chr20:43438840-43439067(+)$1	227	46	49	9.0000
CUG	chr19:59062855-59063076(-)$1	221	8	11	9.0000
CUG	chr17:26898179-26898408(-)$1	229	109	112	9.0000
CUG	chr3:33450867-33451090(-)$1	223	2	5	9.0000
CUG	chr5:176730721-176730952(+)$1	231	54	57	9.0000
CUG	chr17:27209560-27209789(-)$1	229	34	37	9.0000
CUG	chr9:134360010-134360236(+)$1	226	18	21	9.0000
CUG	chr21:43160540-43160775(-)$1	235	3	6	9.0000
CUG	chr12:123646600-123646825(-)$1	225	89	92	9.0000
CUG	chr5:71516379-71516612(-)$1	233	27	30	9.0000
CUG	chr1:228286386-228286618(+)$1	232	80	83	9.0000
CUG	chr17:56082424-56082657(-)$1	233	131	134	9.0000
CUG	chr18:9535967-9536188(+)$1	221	0	3	9.0000
CUG	chr9:106860694-106860920(+)$1	226	106	109	9.0000
Cug	chr5:79924202-79924445(-)$1	243	20	23	9.0000
CUG	chr19:16629367-16629594(-)$1	227	15	18	9.0000
CUG	chr12:50157455-50157691(+)$1	236	30	33	9.0000
cug	chr1:33067763-33067987(+)$1	224	40	43	9.0000
CUG	chr19:49468475-49468704(+)$1	229	36	39	9.0000
CUG	chr1:153931632-153931887(-)$1	255	21	24	9.0000
CUG	chr3:126755598-126755821(+)$1	223	8	11	9.0000
CUG	chr22:38620797-38621028(-)$1	231	50	53	9.0000
CUG	chr12:105538422-105538643(+)$1	221	39	42	9.0000
CUG	chr8:98740802-98741062(+)$1	260	16	19	9.0000
CUG	chr17:79976802-79977022(-)$1	220	19	22	9.0000
CUG	chr1:202848903-202849132(-)$1	229	52	55	9.0000
CUG	chr17:35837834-35838069(+)$1	235	38	41	9.0000
CUG	chr6:17763907-17764128(-)$1	221	90	93	9.0000
cug	chrX:77083449-77083699(-)$1	250	12	15	9.0000
CUG	chr14:21851342-21851565(-)$1	223	29	32	9.0000
cug	chr20:3909197-3909440(+)$1	243	12	15	9.0000
CUG	chr7:128410429-128410657(+)$1	228	58	61	9.0000
CUG	chr11:95646037-95646257(+)$1	220	2	5	9.0000
CUG	chr10:99192181-99192402(+)$1	221	74	77	9.0000
CUG	chr3:25705851-25706075(-)$1	224	28	31	9.0000
cug	chr12:102173529-102173765(+)$1	236	0	3	9.0000
CUG	chr3:48638704-48638928(-)$1	224	12	15	9.0000
CUG	chr11:61197250-61197477(-)$1	227	191	194	9.0000
CUG	chr2:38971766-38971985(-)$1	219	163	166	9.0000
CUG	chr18:23969835-23970063(+)$1	228	12	15	9.0000
CUG	chrX:153664172-153664413(+)$1	241	67	70	9.0000
cug	chr7:25160424-25160668(-)$1	244	18	21	9.0000
cug	chr1:235272741-235272964(-)$1	223	121	124	9.0000
CUG	chr5:72742150-72742375(-)$1	225	42	45	9.0000
CUG	chr7:120497970-120498191(-)$1	221	12	15	9.0000
CUG	chr7:150068143-150068372(+)$1	229	91	94	9.0000
CUG	chr16:4559922-4560147(+)$1	225	23	26	9.0000
CUG	chr22:21242814-21243037(+)$1	223	0	3	9.0000
CUG	chr19:10506632-10506873(-)$1	241	39	42	9.0000
CUG	chr6:146875621-146875840(+)$1	219	116	119	9.0000
CUG	chr2:238939120-238939354(+)$1	234	32	35	9.0000
CUG	chr11:95522689-95522926(-)$1	237	62	65	9.0000
cug	chr19:16683079-16683298(-)$1	219	46	49	9.0000
cug	chr18:60383375-60383610(+)$1	235	1	4	9.0000
CUG	chr1:155300651-155300877(+)$1	226	32	35	9.0000
CUG	chr5:175935768-175935990(+)$1	222	39	42	9.0000
CUG	chr5:175773159-175773382(-)$1	223	18	21	9.0000
CUG	chr1:155979037-155979263(-)$1	226	61	64	9.0000
cug	chr16:848350-848585(+)$1	235	44	47	9.0000
CUG	chr6:26198986-26199246(-)$1	260	24	27	9.0000
CUG	chr1:169337323-169337549(+)$1	226	12	15	9.0000
CUG	chr4:7058188-7058417(+)$1	229	94	97	9.0000
cug	chr9:129460680-129460901(+)$1	221	30	33	9.0000
CUG	chr19:41786969-41787194(+)$1	225	47	50	9.0000
CUG	chr12:12045662-12045894(+)$1	232	190	193	9.0000
CUG	chr14:23346715-23346940(+)$1	225	9	12	9.0000
CUG	chr12:49666090-49666345(+)$1	255	3	6	9.0000
CUG	chr5:170814801-170815036(+)$1	235	44	47	9.0000
CUG	chr17:42827040-42827261(+)$1	221	46	49	9.0000
CUG	chr12:113623672-113623902(+)$1	230	24	27	9.0000
CUG	chr17:73885404-73885630(-)$1	226	22	25	9.0000
CUG	chr17:16345521-16345744(+)$1	223	4	7	9.0000
CUG	chr17:3714394-3714622(-)$1	228	62	65	9.0000
CUG	chr9:125636081-125636332(-)$1	251	24	27	9.0000
CUG	chr8:10969258-10969482(-)$1	224	158	161	9.0000
CUG	chr17:80200895-80201115(-)$1	220	11	14	9.0000
CUG	chr12:14956202-14956430(-)$1	228	41	44	9.0000
CUG	chr1:160248608-160248847(-)$1	239	30	33	9.0000
CUG	chrX:47509275-47509497(-)$1	222	12	15	9.0000
CUG	chr13:79174827-79175054(-)$1	227	34	37	9.0000
CUG	chr14:100331816-100332054(+)$1	238	6	9	9.0000
CUG	chr5:176873518-176873754(+)$1	236	2	5	9.0000
CUG	chr22:24813318-24813542(+)$1	224	8	11	9.0000
CUG	chr2:128604569-128604795(-)$1	226	32	35	9.0000
CUG	chr11:93463630-93463912(-)$1	282	36	39	9.0000
CUG	chr2:106761592-106761819(-)$1	227	30	33	9.0000
CUG	chr19:2430375-2430606(-)$1	231	40	43	9.0000
CUG	chr15:76136254-76136487(+)$1	233	12	15	9.0000
CUG	chr12:93881207-93881437(+)$1	230	14	17	9.0000
CUG	chr17:47130351-47130571(+)$1	220	4	7	9.0000
CUG	chr5:159505038-159505258(-)$1	220	101	104	9.0000
CUG	chr1:45975875-45976107(+)$1	232	2	5	9.0000
cug	chr11:62440149-62440374(-)$1	225	37	40	9.0000

#otherMatches

#Struct PSSM
ccc	chr15:100347097-100347330(+)$1	233	73	76	9.0000
occ	chr8:27591620-27591840(-)$1	220	22	25	9.0000
OOO	chr9:95077888-95078118(-)$1	230	17	20	9.0000
mmc	chr19:13888974-13889193(+)$1	219	6	9	9.0000
EEE	chr16:89727314-89727548(+)$1	234	72	75	9.0000
eee	chr11:117160063-117160291(+)$1	228	22	25	9.0000
ccf	chr15:45028762-45028985(+)$1	223	26	29	9.0000
:::	chr20:43438840-43439067(+)$1	227	46	49	9.0000
{GG	chr19:59062855-59063076(-)$1	221	8	11	9.0000
ooo	chr17:26898179-26898408(-)$1	229	109	112	9.0000
EEE	chr3:33450867-33451090(-)$1	223	2	5	9.0000
ooo	chr5:176730721-176730952(+)$1	231	54	57	9.0000
ccc	chr17:27209560-27209789(-)$1	229	34	37	9.0000
##d	chr9:134360010-134360236(+)$1	226	18	21	9.0000
fff	chr21:43160540-43160775(-)$1	235	3	6	9.0000
dd:	chr12:123646600-123646825(-)$1	225	89	92	9.0000
pdd	chr5:71516379-71516612(-)$1	233	27	30	9.0000
ddd	chr1:228286386-228286618(+)$1	232	80	83	9.0000
###	chr17:56082424-56082657(-)$1	233	131	134	9.0000
BBK	chr18:9535967-9536188(+)$1	221	0	3	9.0000
2cc	chr9:106860694-106860920(+)$1	226	106	109	9.0000
EE{	chr5:79924202-79924445(-)$1	243	20	23	9.0000
""a	chr19:16629367-16629594(-)$1	227	15	18	9.0000
d!!	chr12:50157455-50157691(+)$1	236	30	33	9.0000
hhh	chr1:33067763-33067987(+)$1	224	40	43	9.0000
PPP	chr19:49468475-49468704(+)$1	229	36	39	9.0000
GGG	chr1:153931632-153931887(-)$1	255	21	24	9.0000
ggg	chr3:126755598-126755821(+)$1	223	8	11	9.0000
::d	chr22:38620797-38621028(-)$1	231	50	53	9.0000
ccq	chr12:105538422-105538643(+)$1	221	39	42	9.0000
eee	chr8:98740802-98741062(+)$1	260	16	19	9.0000
ffm	chr17:79976802-79977022(-)$1	220	19	22	9.0000
dd$	chr1:202848903-202849132(-)$1	229	52	55	9.0000
{CC	chr17:35837834-35838069(+)$1	235	38	41	9.0000
:ff	chr6:17763907-17764128(-)$1	221	90	93	9.0000
ddq	chrX:77083449-77083699(-)$1	250	12	15	9.0000
dbb	chr14:21851342-21851565(-)$1	223	29	32	9.0000
BBF	chr20:3909197-3909440(+)$1	243	12	15	9.0000
ddd	chr7:128410429-128410657(+)$1	228	58	61	9.0000
:cc	chr11:95646037-95646257(+)$1	220	2	5	9.0000
hh5	chr10:99192181-99192402(+)$1	221	74	77	9.0000
DDD	chr3:25705851-25706075(-)$1	224	28	31	9.0000
::G	chr12:102173529-102173765(+)$1	236	0	3	9.0000
ccc	chr3:48638704-48638928(-)$1	224	12	15	9.0000
hhh	chr11:61197250-61197477(-)$1	227	191	194	9.0000
44h	chr2:38971766-38971985(-)$1	219	163	166	9.0000
:bb	chr18:23969835-23970063(+)$1	228	12	15	9.0000
cdd	chrX:153664172-153664413(+)$1	241	67	70	9.0000
TTC	chr7:25160424-25160668(-)$1	244	18	21	9.0000
>>d	chr1:235272741-235272964(-)$1	223	121	124	9.0000
nne	chr5:72742150-72742375(-)$1	225	42	45	9.0000
KDD	chr7:120497970-120498191(-)$1	221	12	15	9.0000
gg:	chr7:150068143-150068372(+)$1	229	91	94	9.0000
EEE	chr16:4559922-4560147(+)$1	225	23	26	9.0000
DDD	chr22:21242814-21243037(+)$1	223	0	3	9.0000
ddd	chr19:10506632-10506873(-)$1	241	39	42	9.0000
ddd	chr6:146875621-146875840(+)$1	219	116	119	9.0000
{DD	chr2:238939120-238939354(+)$1	234	32	35	9.0000
[dd	chr11:95522689-95522926(-)$1	237	62	65	9.0000
e:g	chr19:16683079-16683298(-)$1	219	46	49	9.0000
:::	chr18:60383375-60383610(+)$1	235	1	4	9.0000
ccc	chr1:155300651-155300877(+)$1	226	32	35	9.0000
ee[	chr5:175935768-175935990(+)$1	222	39	42	9.0000
CC{	chr5:175773159-175773382(-)$1	223	18	21	9.0000
ddd	chr1:155979037-155979263(-)$1	226	61	64	9.0000
bbp	chr16:848350-848585(+)$1	235	44	47	9.0000
ddf	chr6:26198986-26199246(-)$1	260	24	27	9.0000
bbs	chr1:169337323-169337549(+)$1	226	12	15	9.0000
eeD	chr4:7058188-7058417(+)$1	229	94	97	9.0000
ncc	chr9:129460680-129460901(+)$1	221	30	33	9.0000
iii	chr19:41786969-41787194(+)$1	225	47	50	9.0000
ddd	chr12:12045662-12045894(+)$1	232	190	193	9.0000
mme	chr14:23346715-23346940(+)$1	225	9	12	9.0000
::D	chr12:49666090-49666345(+)$1	255	3	6	9.0000
!dd	chr5:170814801-170815036(+)$1	235	44	47	9.0000
iii	chr17:42827040-42827261(+)$1	221	46	49	9.0000
{BB	chr12:113623672-113623902(+)$1	230	24	27	9.0000
c[e	chr17:73885404-73885630(-)$1	226	22	25	9.0000
LLL	chr17:16345521-16345744(+)$1	223	4	7	9.0000
ttt	chr17:3714394-3714622(-)$1	228	62	65	9.0000
EEE	chr9:125636081-125636332(-)$1	251	24	27	9.0000
:gg	chr8:10969258-10969482(-)$1	224	158	161	9.0000
qqq	chr17:80200895-80201115(-)$1	220	11	14	9.0000
cc:	chr12:14956202-14956430(-)$1	228	41	44	9.0000
fff	chr1:160248608-160248847(-)$1	239	30	33	9.0000
ccc	chrX:47509275-47509497(-)$1	222	12	15	9.0000
[cc	chr13:79174827-79175054(-)$1	227	34	37	9.0000
:GG	chr14:100331816-100332054(+)$1	238	6	9	9.0000
EEE	chr5:176873518-176873754(+)$1	236	2	5	9.0000
DDD	chr22:24813318-24813542(+)$1	224	8	11	9.0000
#ee	chr2:128604569-128604795(-)$1	226	32	35	9.0000
ggg	chr11:93463630-93463912(-)$1	282	36	39	9.0000
yyy	chr2:106761592-106761819(-)$1	227	30	33	9.0000
FFC	chr19:2430375-2430606(-)$1	231	40	43	9.0000
===	chr15:76136254-76136487(+)$1	233	12	15	9.0000
DDD	chr12:93881207-93881437(+)$1	230	14	17	9.0000
ggg	chr17:47130351-47130571(+)$1	220	4	7	9.0000
ccc	chr5:159505038-159505258(-)$1	220	101	104	9.0000
:BB	chr1:45975875-45976107(+)$1	232	2	5	9.0000
fff	chr11:62440149-62440374(-)$1	225	37	40	9.0000

#DB
(((	chr15:100347097-100347330(+)$1	1	73	76	9.0000
.))	chr8:27591620-27591840(-)$1	1	22	25	9.0000
...	chr9:95077888-95078118(-)$1	1	17	20	9.0000
..)	chr19:13888974-13889193(+)$1	1	6	9	9.0000
(((	chr16:89727314-89727548(+)$1	1	72	75	9.0000
(((	chr11:117160063-117160291(+)$1	1	22	25	9.0000
(((	chr15:45028762-45028985(+)$1	1	26	29	9.0000
...	chr20:43438840-43439067(+)$1	1	46	49	9.0000
.((	chr19:59062855-59063076(-)$1	1	8	11	9.0000
...	chr17:26898179-26898408(-)$1	1	109	112	9.0000
(((	chr3:33450867-33451090(-)$1	1	2	5	9.0000
...	chr5:176730721-176730952(+)$1	1	54	57	9.0000
(((	chr17:27209560-27209789(-)$1	1	34	37	9.0000
..(	chr9:134360010-134360236(+)$1	1	18	21	9.0000
(((	chr21:43160540-43160775(-)$1	1	3	6	9.0000
)).	chr12:123646600-123646825(-)$1	1	89	92	9.0000
.))	chr5:71516379-71516612(-)$1	1	27	30	9.0000
(((	chr1:228286386-228286618(+)$1	1	80	83	9.0000
...	chr17:56082424-56082657(-)$1	1	131	134	9.0000
((.	chr18:9535967-9536188(+)$1	1	0	3	9.0000
.))	chr9:106860694-106860920(+)$1	1	106	109	9.0000
((.	chr5:79924202-79924445(-)$1	1	20	23	9.0000
..(	chr19:16629367-16629594(-)$1	1	15	18	9.0000
(..	chr12:50157455-50157691(+)$1	1	30	33	9.0000
)))	chr1:33067763-33067987(+)$1	1	40	43	9.0000
...	chr19:49468475-49468704(+)$1	1	36	39	9.0000
(((	chr1:153931632-153931887(-)$1	1	21	24	9.0000
(((	chr3:126755598-126755821(+)$1	1	8	11	9.0000
..(	chr22:38620797-38621028(-)$1	1	50	53	9.0000
((.	chr12:105538422-105538643(+)$1	1	39	42	9.0000
(((	chr8:98740802-98741062(+)$1	1	16	19	9.0000
((.	chr17:79976802-79977022(-)$1	1	19	22	9.0000
((.	chr1:202848903-202849132(-)$1	1	52	55	9.0000
.((	chr17:35837834-35838069(+)$1	1	38	41	9.0000
.((	chr6:17763907-17764128(-)$1	1	90	93	9.0000
((.	chrX:77083449-77083699(-)$1	1	12	15	9.0000
(((	chr14:21851342-21851565(-)$1	1	29	32	9.0000
(((	chr20:3909197-3909440(+)$1	1	12	15	9.0000
(((	chr7:128410429-128410657(+)$1	1	58	61	9.0000
.((	chr11:95646037-95646257(+)$1	1	2	5	9.0000
)).	chr10:99192181-99192402(+)$1	1	74	77	9.0000
(((	chr3:25705851-25706075(-)$1	1	28	31	9.0000
..(	chr12:102173529-102173765(+)$1	1	0	3	9.0000
(((	chr3:48638704-48638928(-)$1	1	12	15	9.0000
(((	chr11:61197250-61197477(-)$1	1	191	194	9.0000
..)	chr2:38971766-38971985(-)$1	1	163	166	9.0000
.((	chr18:23969835-23970063(+)$1	1	12	15	9.0000
)))	chrX:153664172-153664413(+)$1	1	67	70	9.0000
..(	chr7:25160424-25160668(-)$1	1	18	21	9.0000
..)	chr1:235272741-235272964(-)$1	1	121	124	9.0000
..)	chr5:72742150-72742375(-)$1	1	42	45	9.0000
.((	chr7:120497970-120498191(-)$1	1	12	15	9.0000
)).	chr7:150068143-150068372(+)$1	1	91	94	9.0000
(((	chr16:4559922-4560147(+)$1	1	23	26	9.0000
(((	chr22:21242814-21243037(+)$1	1	0	3	9.0000
(((	chr19:10506632-10506873(-)$1	1	39	42	9.0000
)))	chr6:146875621-146875840(+)$1	1	116	119	9.0000
.((	chr2:238939120-238939354(+)$1	1	32	35	9.0000
.((	chr11:95522689-95522926(-)$1	1	62	65	9.0000
).(	chr19:16683079-16683298(-)$1	1	46	49	9.0000
...	chr18:60383375-60383610(+)$1	1	1	4	9.0000
(((	chr1:155300651-155300877(+)$1	1	32	35	9.0000
((.	chr5:175935768-175935990(+)$1	1	39	42	9.0000
((.	chr5:175773159-175773382(-)$1	1	18	21	9.0000
(((	chr1:155979037-155979263(-)$1	1	61	64	9.0000
((.	chr16:848350-848585(+)$1	1	44	47	9.0000
(((	chr6:26198986-26199246(-)$1	1	24	27	9.0000
((.	chr1:169337323-169337549(+)$1	1	12	15	9.0000
))(	chr4:7058188-7058417(+)$1	1	94	97	9.0000
.))	chr9:129460680-129460901(+)$1	1	30	33	9.0000
)))	chr19:41786969-41787194(+)$1	1	47	50	9.0000
(((	chr12:12045662-12045894(+)$1	1	190	193	9.0000
..)	chr14:23346715-23346940(+)$1	1	9	12	9.0000
..(	chr12:49666090-49666345(+)$1	1	3	6	9.0000
.((	chr5:170814801-170815036(+)$1	1	44	47	9.0000
(((	chr17:42827040-42827261(+)$1	1	46	49	9.0000
.((	chr12:113623672-113623902(+)$1	1	24	27	9.0000
(.(	chr17:73885404-73885630(-)$1	1	22	25	9.0000
...	chr17:16345521-16345744(+)$1	1	4	7	9.0000
...	chr17:3714394-3714622(-)$1	1	62	65	9.0000
(((	chr9:125636081-125636332(-)$1	1	24	27	9.0000
.((	chr8:10969258-10969482(-)$1	1	158	161	9.0000
...	chr17:80200895-80201115(-)$1	1	11	14	9.0000
)).	chr12:14956202-14956430(-)$1	1	41	44	9.0000
)))	chr1:160248608-160248847(-)$1	1	30	33	9.0000
(((	chrX:47509275-47509497(-)$1	1	12	15	9.0000
.((	chr13:79174827-79175054(-)$1	1	34	37	9.0000
.((	chr14:100331816-100332054(+)$1	1	6	9	9.0000
(((	chr5:176873518-176873754(+)$1	1	2	5	9.0000
(((	chr22:24813318-24813542(+)$1	1	8	11	9.0000
.((	chr2:128604569-128604795(-)$1	1	32	35	9.0000
(((	chr11:93463630-93463912(-)$1	1	36	39	9.0000
...	chr2:106761592-106761819(-)$1	1	30	33	9.0000
(((	chr19:2430375-2430606(-)$1	1	40	43	9.0000
(((	chr15:76136254-76136487(+)$1	1	12	15	9.0000
(((	chr12:93881207-93881437(+)$1	1	14	17	9.0000
(((	chr17:47130351-47130571(+)$1	1	4	7	9.0000
(((	chr5:159505038-159505258(-)$1	1	101	104	9.0000
.((	chr1:45975875-45976107(+)$1	1	2	5	9.0000
)))	chr11:62440149-62440374(-)$1	1	37	40	9.0000

#PSSM
C : 0.89	c : 0.10	
U : 0.88	u : 0.11	
G : 0.88	g : 0.11	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m1_run1.nuc.txt

#NT
UGGG	chr15:93568222-93568441(+)$1	219	4	8	11.9999
UGGG	chr19:8553568-8553819(+)$1	251	40	44	11.9999
UGGG	chr22:39916868-39917097(+)$1	229	27	31	11.9999
UGGG	chr17:37618090-37618316(+)$1	226	95	99	11.9999
uggg	chr9:125636081-125636332(-)$1	251	74	78	11.9999
UGGG	chrX:48761884-48762109(-)$1	225	119	123	11.9999
UGGG	chr1:39470293-39470539(+)$1	246	138	142	11.9999
UGGG	chr8:41400151-41400371(+)$1	220	153	157	11.9999
UGGG	chr17:73775697-73775921(-)$1	224	87	91	11.9999
UGGG	chr18:74240779-74240999(+)$1	220	16	20	11.9999
UGGG	chr17:7606290-7606530(+)$1	240	69	73	11.9999
UGGG	chr17:73773763-73773997(-)$1	234	62	66	11.9999
UGGG	chr5:175935768-175935990(+)$1	222	178	182	11.9999
UGGG	chrX:114869102-114869333(+)$1	231	128	132	11.9999
uggg	chr19:16662538-16662789(-)$1	251	98	102	11.9999
UGGG	chr1:228681690-228681931(+)$1	241	5	9	11.9999
UGGG	chr18:46385894-46386120(+)$1	226	71	75	11.9999
UGGG	chr10:5945027-5945247(+)$1	220	155	159	11.9999
UGGG	chr5:180287470-180287691(-)$1	221	77	81	11.9999
UGGG	chr1:43312194-43312425(+)$1	231	57	61	11.9999
UGGG	chr22:37766010-37766231(-)$1	221	149	153	11.9999
UGGG	chr12:121138701-121138924(+)$1	223	34	38	11.9999
UGGG	chr11:65746508-65746739(+)$1	231	100	104	11.9999
UGGG	chr12:4413767-4413987(+)$1	220	18	22	11.9999
UGGG	chr1:32098016-32098259(-)$1	243	188	192	11.9999
UGGG	chr11:46695369-46695594(+)$1	225	0	4	11.9999
UGGG	chr7:72854865-72855100(-)$1	235	93	97	11.9999
UGGG	chr9:135933435-135933687(+)$1	252	204	208	11.9999
UGGG	chr17:79668861-79669111(+)$1	250	2	6	11.9999
UGGG	chrX:48336264-48336495(+)$1	231	35	39	11.9999
UGGG	chr16:27472405-27472628(-)$1	223	46	50	11.9999
UGGG	chr2:10923686-10923907(-)$1	221	145	149	11.9999
UGGG	chr3:129033679-129033921(-)$1	242	207	211	11.9999
UGGG	chr12:132406663-132406896(+)$1	233	99	103	11.9999
UGGG	chr19:47278095-47278339(-)$1	244	118	122	11.9999
UGGG	chr11:118620326-118620563(-)$1	237	50	54	11.9999
uggg	chr3:58305771-58305993(+)$1	222	180	184	11.9999
UGGG	chr1:228346904-228347134(+)$1	230	61	65	11.9999
UGGG	chr19:49121886-49122124(-)$1	238	89	93	11.9999
UGGG	chr6:52905983-52906207(-)$1	224	31	35	11.9999
UGGG	chr7:135358993-135359237(+)$1	244	73	77	11.9999
UGGG	chr22:25589512-25589733(+)$1	221	105	109	11.9999
UGGG	chr11:62327115-62327370(-)$1	255	13	17	11.9999
UGGG	chr12:6958180-6958400(-)$1	220	134	138	11.9999
UGGG	chr7:129685120-129685340(-)$1	220	70	74	11.9999
UGGG	chr19:3209385-3209623(+)$1	238	34	38	11.9999
UGGG	chr1:174975801-174976028(+)$1	227	81	85	11.9999
UGGG	chr15:51296668-51296907(+)$1	239	96	100	11.9999
UGGG	chr11:118967844-118968071(-)$1	227	171	175	11.9999
UGGG	chr2:220074374-220074593(-)$1	219	20	24	11.9999
UGGG	chr12:56078747-56078970(-)$1	223	24	28	11.9999
UGGG	chr17:38296696-38296916(-)$1	220	176	180	11.9999
UGGG	chr17:79825826-79826047(+)$1	221	53	57	11.9999
UGGG	chr1:155300651-155300877(+)$1	226	189	193	11.9999
UGGG	chr16:85813246-85813472(-)$1	226	176	180	11.9999
UGGG	chr8:134249416-134249645(-)$1	229	2	6	11.9999
UGGG	chr16:2564267-2564490(+)$1	223	189	193	11.9999
UGGG	chr17:42826891-42827116(+)$1	225	39	43	11.9999
UGGG	chr3:136062593-136062816(-)$1	223	82	86	11.9999
UGGG	chr2:220151001-220151225(+)$1	224	15	19	11.9999
UGGG	chr17:22022551-22022786(+)$1	235	169	173	11.9999
UGGG	chr7:96746921-96747151(+)$1	230	105	109	11.9999
UGGG	chr12:85254665-85254897(-)$1	232	76	80	11.9999
UGGG	chr2:8998369-8998589(-)$1	220	7	11	11.9999
UGGG	chr6:3751974-3752200(-)$1	226	23	27	11.9999
UGGG	chr12:122627587-122627843(+)$1	256	165	169	11.9999
UGGG	chr1:228286641-228286871(+)$1	230	111	115	11.9999
UGGG	chr3:25705851-25706075(-)$1	224	153	157	11.9999
UGGG	chr20:31033466-31033689(-)$1	223	8	12	11.9999
UGGG	chr17:15587407-15587631(-)$1	224	153	157	11.9999
UGGG	chr12:51453841-51454065(+)$1	224	74	78	11.9999
UGGG	chr7:92462773-92462992(-)$1	219	16	20	11.9999
UGGG	chr6:150093205-150093454(+)$1	249	6	10	11.9999

#otherMatches

#Struct PSSM
C{JJ	chr16:450515-450735(+)$1	220	62	66	11.9999
::::	chr15:93568222-93568441(+)$1	219	4	8	11.9999
ssss	chr19:8553568-8553819(+)$1	251	40	44	11.9999
ffff	chr22:39916868-39917097(+)$1	229	27	31	11.9999
2bbb	chr17:37618090-37618316(+)$1	226	95	99	11.9999
gggg	chr9:125636081-125636332(-)$1	251	74	78	11.9999
JJJJ	chrX:48761884-48762109(-)$1	225	119	123	11.9999
'ddd	chr1:39470293-39470539(+)$1	246	138	142	11.9999
]ccc	chr8:41400151-41400371(+)$1	220	153	157	11.9999
qqcc	chr17:73775697-73775921(-)$1	224	87	91	11.9999
EEEE	chr18:74240779-74240999(+)$1	220	16	20	11.9999
nfff	chr17:7606290-7606530(+)$1	240	69	73	11.9999
===e	chr17:73773763-73773997(-)$1	234	62	66	11.9999
ffff	chr5:175935768-175935990(+)$1	222	178	182	11.9999
a[ee	chrX:114869102-114869333(+)$1	231	128	132	11.9999
ffff	chr19:16662538-16662789(-)$1	251	98	102	11.9999
HHHH	chr1:228681690-228681931(+)$1	241	5	9	11.9999
c::g	chr18:46385894-46386120(+)$1	226	71	75	11.9999
BYYD	chr10:5945027-5945247(+)$1	220	155	159	11.9999
gggg	chr5:180287470-180287691(-)$1	221	77	81	11.9999
EEEE	chr1:43312194-43312425(+)$1	231	57	61	11.9999
DA}H	chr22:37766010-37766231(-)$1	221	149	153	11.9999
===3	chr12:121138701-121138924(+)$1	223	34	38	11.9999
hh!!	chr11:65746508-65746739(+)$1	231	100	104	11.9999
ffff	chr12:4413767-4413987(+)$1	220	18	22	11.9999
EECC	chr1:32098016-32098259(-)$1	243	188	192	11.9999
::::	chr11:46695369-46695594(+)$1	225	0	4	11.9999
333h	chr7:72854865-72855100(-)$1	235	93	97	11.9999
[eee	chr9:135933435-135933687(+)$1	252	204	208	11.9999
DDhh	chr17:79668861-79669111(+)$1	250	2	6	11.9999
[bb[	chrX:48336264-48336495(+)$1	231	35	39	11.9999
2===	chr16:27472405-27472628(-)$1	223	46	50	11.9999
ffff	chr2:10923686-10923907(-)$1	221	145	149	11.9999
teee	chr3:129033679-129033921(-)$1	242	207	211	11.9999
====	chr12:132406663-132406896(+)$1	233	99	103	11.9999
hhhh	chr19:47278095-47278339(-)$1	244	118	122	11.9999
[ggg	chr11:118620326-118620563(-)$1	237	50	54	11.9999
:::E	chr3:58305771-58305993(+)$1	222	180	184	11.9999
lbbg	chr1:228346904-228347134(+)$1	230	61	65	11.9999
iiii	chr19:49121886-49122124(-)$1	238	89	93	11.9999
c]ee	chr6:52905983-52906207(-)$1	224	31	35	11.9999
FFFF	chr7:135358993-135359237(+)$1	244	73	77	11.9999
^ccc	chr22:25589512-25589733(+)$1	221	105	109	11.9999
G:::	chr11:62327115-62327370(-)$1	255	13	17	11.9999
ZEEE	chr12:6958180-6958400(-)$1	220	134	138	11.9999
eeee	chr7:129685120-129685340(-)$1	220	70	74	11.9999
mccc	chr19:3209385-3209623(+)$1	238	34	38	11.9999
====	chr1:174975801-174976028(+)$1	227	81	85	11.9999
eeee	chr15:51296668-51296907(+)$1	239	96	100	11.9999
4ccc	chr11:118967844-118968071(-)$1	227	171	175	11.9999
d!!a	chr2:220074374-220074593(-)$1	219	20	24	11.9999
b]bb	chr12:56078747-56078970(-)$1	223	24	28	11.9999
}GGG	chr17:38296696-38296916(-)$1	220	176	180	11.9999
b]dd	chr17:79825826-79826047(+)$1	221	53	57	11.9999
}GGG	chr1:155300651-155300877(+)$1	226	189	193	11.9999
CCA}	chr16:85813246-85813472(-)$1	226	176	180	11.9999
EEEN	chr8:134249416-134249645(-)$1	229	2	6	11.9999
eee[	chr16:2564267-2564490(+)$1	223	189	193	11.9999
ffff	chr17:42826891-42827116(+)$1	225	39	43	11.9999
cc]c	chr3:136062593-136062816(-)$1	223	82	86	11.9999
ffff	chr2:220151001-220151225(+)$1	224	15	19	11.9999
dddd	chr17:22022551-22022786(+)$1	235	169	173	11.9999
ggFF	chr7:96746921-96747151(+)$1	230	105	109	11.9999
d[a[	chr12:85254665-85254897(-)$1	232	76	80	11.9999
dddd	chr2:8998369-8998589(-)$1	220	7	11	11.9999
qqqq	chr6:3751974-3752200(-)$1	226	23	27	11.9999
hnnn	chr12:122627587-122627843(+)$1	256	165	169	11.9999
ffff	chr1:228286641-228286871(+)$1	230	111	115	11.9999
oooo	chr3:25705851-25706075(-)$1	224	153	157	11.9999
FFFF	chr20:31033466-31033689(-)$1	223	8	12	11.9999
""cc	chr17:15587407-15587631(-)$1	224	153	157	11.9999
$ggg	chr12:51453841-51454065(+)$1	224	74	78	11.9999
HHHH	chr7:92462773-92462992(-)$1	219	16	20	11.9999
ffff	chr6:150093205-150093454(+)$1	249	6	10	11.9999

#DB
(.((	chr16:450515-450735(+)$1	1	62	66	11.9999
....	chr15:93568222-93568441(+)$1	1	4	8	11.9999
....	chr19:8553568-8553819(+)$1	1	40	44	11.9999
((((	chr22:39916868-39917097(+)$1	1	27	31	11.9999
.))(	chr17:37618090-37618316(+)$1	1	95	99	11.9999
((((	chr9:125636081-125636332(-)$1	1	74	78	11.9999
))))	chrX:48761884-48762109(-)$1	1	119	123	11.9999
.(((	chr1:39470293-39470539(+)$1	1	138	142	11.9999
.)))	chr8:41400151-41400371(+)$1	1	153	157	11.9999
..))	chr17:73775697-73775921(-)$1	1	87	91	11.9999
((((	chr18:74240779-74240999(+)$1	1	16	20	11.9999
.)))	chr17:7606290-7606530(+)$1	1	69	73	11.9999
((((	chr17:73773763-73773997(-)$1	1	62	66	11.9999
))))	chr5:175935768-175935990(+)$1	1	178	182	11.9999
(.((	chrX:114869102-114869333(+)$1	1	128	132	11.9999
))))	chr19:16662538-16662789(-)$1	1	98	102	11.9999
((((	chr1:228681690-228681931(+)$1	1	5	9	11.9999
)..(	chr18:46385894-46386120(+)$1	1	71	75	11.9999
)..)	chr10:5945027-5945247(+)$1	1	155	159	11.9999
))))	chr5:180287470-180287691(-)$1	1	77	81	11.9999
((((	chr1:43312194-43312425(+)$1	1	57	61	11.9999
)).)	chr22:37766010-37766231(-)$1	1	149	153	11.9999
))).	chr12:121138701-121138924(+)$1	1	34	38	11.9999
((..	chr11:65746508-65746739(+)$1	1	100	104	11.9999
((((	chr12:4413767-4413987(+)$1	1	18	22	11.9999
))))	chr1:32098016-32098259(-)$1	1	188	192	11.9999
....	chr11:46695369-46695594(+)$1	1	0	4	11.9999
...)	chr7:72854865-72855100(-)$1	1	93	97	11.9999
.(((	chr9:135933435-135933687(+)$1	1	204	208	11.9999
((((	chr17:79668861-79669111(+)$1	1	2	6	11.9999
.((.	chrX:48336264-48336495(+)$1	1	35	39	11.9999
.)))	chr16:27472405-27472628(-)$1	1	46	50	11.9999
))))	chr2:10923686-10923907(-)$1	1	145	149	11.9999
.)))	chr3:129033679-129033921(-)$1	1	207	211	11.9999
))))	chr12:132406663-132406896(+)$1	1	99	103	11.9999
))))	chr19:47278095-47278339(-)$1	1	118	122	11.9999
.(((	chr11:118620326-118620563(-)$1	1	50	54	11.9999
...)	chr3:58305771-58305993(+)$1	1	180	184	11.9999
.)))	chr1:228346904-228347134(+)$1	1	61	65	11.9999
))))	chr19:49121886-49122124(-)$1	1	89	93	11.9999
).))	chr6:52905983-52906207(-)$1	1	31	35	11.9999
))))	chr7:135358993-135359237(+)$1	1	73	77	11.9999
.)))	chr22:25589512-25589733(+)$1	1	105	109	11.9999
(...	chr11:62327115-62327370(-)$1	1	13	17	11.9999
.)))	chr12:6958180-6958400(-)$1	1	134	138	11.9999
))))	chr7:129685120-129685340(-)$1	1	70	74	11.9999
.)))	chr19:3209385-3209623(+)$1	1	34	38	11.9999
))))	chr1:174975801-174976028(+)$1	1	81	85	11.9999
((((	chr15:51296668-51296907(+)$1	1	96	100	11.9999
.)))	chr11:118967844-118968071(-)$1	1	171	175	11.9999
(..(	chr2:220074374-220074593(-)$1	1	20	24	11.9999
).))	chr12:56078747-56078970(-)$1	1	24	28	11.9999
.)))	chr17:38296696-38296916(-)$1	1	176	180	11.9999
).))	chr17:79825826-79826047(+)$1	1	53	57	11.9999
.)))	chr1:155300651-155300877(+)$1	1	189	193	11.9999
))).	chr16:85813246-85813472(-)$1	1	176	180	11.9999
(((.	chr8:134249416-134249645(-)$1	1	2	6	11.9999
(((.	chr16:2564267-2564490(+)$1	1	189	193	11.9999
))))	chr17:42826891-42827116(+)$1	1	39	43	11.9999
)).)	chr3:136062593-136062816(-)$1	1	82	86	11.9999
((((	chr2:220151001-220151225(+)$1	1	15	19	11.9999
))))	chr17:22022551-22022786(+)$1	1	169	173	11.9999
))))	chr7:96746921-96747151(+)$1	1	105	109	11.9999
(.(.	chr12:85254665-85254897(-)$1	1	76	80	11.9999
((((	chr2:8998369-8998589(-)$1	1	7	11	11.9999
....	chr6:3751974-3752200(-)$1	1	23	27	11.9999
(...	chr12:122627587-122627843(+)$1	1	165	169	11.9999
((((	chr1:228286641-228286871(+)$1	1	111	115	11.9999
....	chr3:25705851-25706075(-)$1	1	153	157	11.9999
((((	chr20:31033466-31033689(-)$1	1	8	12	11.9999
..((	chr17:15587407-15587631(-)$1	1	153	157	11.9999
.(((	chr12:51453841-51454065(+)$1	1	74	78	11.9999
((((	chr7:92462773-92462992(-)$1	1	16	20	11.9999
((((	chr6:150093205-150093454(+)$1	1	6	10	11.9999

#PSSM
U : 0.95	u : 0.04	
G : 0.95	g : 0.04	
G : 0.95	g : 0.04	
G : 0.95	g : 0.04	

#score	887.9999999999995
#seq	74
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m2_run2.nuc.txt

#NT
ACCCGAUGACAAAAAGAAGAAUCGGGGGUUCUGCUUCCUUGAAUAUGAGGAUCACAAGUCAGCAGCACAAGCCAGACGCCGGCUGAUGAGUGGAAAAGUAAAAGUGUGGGGAAAUGUAGUUACAGUUGAAUGGGCUGACCCUGUGGAAGAACCAGAUCCAGAAGUCAUGGCUAAGGUAAAUACAGUUGCUUGGAAUGGGCAUAGGGUCAUCAUUUAAAUUUUGUACUCAGAAUAAAGCUCAAAUAUUUUGAGUUUUAUGAUAAAUAGAA	chr1:23644875-23645269(-)$1	394	119	388	374.5000

#otherMatches

#Struct PSSM
JJJJJ{A{BB:eeeeebboooooobb]eeeeeeeeee[ccc[ccc[cccbbmmmmbb]ccc]ccc]ccc22eeeee::BB}A}JJJJJJJJJJJ:::ffffffhhhhhhhhnnnnnhhhhhhhh4444ffffff:::::DDDD::::::::::::ffffff"""eeeee####ccc%%%%%%eeeee!!ccc!!gggggggeeeeedddd[assssssssssadddd]eeeee333gggggggccc22eeeee666666ccc4444eee	chr20:34241697-34242002(-)$1	305	14	283	374.5000
eeee22bb::::::bb[fffffflllffffff]bbeeeeeooooooeeeee:ccc!!ffffff[bbtttttttttttbb22ffffff22ccc:::::::::::AYYDDDD}A}BB}CCCZZZBB}DDDDFFFFFF==========%%%%%%ccc!!dddd''''''''ccc####bbmmmmbb4444cccdddd]ccc]==========:::::::ffffff(((((((((============lll============88888888fff	chr1:23644875-23645269(-)$1	394	119	388	374.5000

#DB
(((((.(.((.(((((((......)).)))))(((((.(((.(((.(((((....)).))).))).)))..)))))..)).).)))))))))))...((((((((((((((.....))))))))....)))))).....))))............((((((...(((((....(((......(((((..(((..((((((((((((((((.(..........))))).)))))...))))))))))..)))))......)))....)))	chr20:34241697-34242002(-)$1	1	14	283	374.5000
))))..))......((.((((((...)))))).))(((((......))))).(((..((((((.((...........))..))))))..)))...........)..)))).).)).)))...)).))))))))))((((((((((......(((..((((........(((....((....))....))))))).))).)))))))))).......((((((.........((((((((((((...))))))))))))........)))	chr1:23644875-23645269(-)$1	1	119	388	374.5000

#PSSM
A : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
A : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
U : 1.00	
U : 0.50	G : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
G : 0.50	U : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
A : 0.50	C : 0.50	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
C : 1.00	
A : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
G : 1.00	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
U : 0.50	G : 0.50	
U : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
G : 1.00	
C : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
G : 1.00	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
C : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 1.00	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 1.00	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
U : 1.00	
U : 0.50	G : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	U : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
G : 0.50	A : 0.50	

#score	749.0
#seq	2
#width	269
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m2_run1.nuc.txt

#NT
UUUAAAGAAUAAAGUC	chr20:5095686-5095907(-)$1	221	144	160	12.6739
UUAAAAAAAAAUCUAU	chr2:37072474-37072696(-)$1	222	185	201	17.7826
UUAUAAAAAGCAAAUA	chr3:156424038-156424264(+)$1	226	33	49	14.8478
CCAAAAAAAAAAAAAA	chr4:77969102-77969325(-)$1	223	145	161	17.6739
uuaaaaaaaaaaaauu	chr12:120899625-120899851(+)$1	226	75	91	24.1956
UUAAAAACACUAAAAA	chr10:76941718-76941941(+)$1	223	127	143	15.3913
UUUACAAAUAAAAUUG	chr5:68473419-68473641(+)$1	222	66	82	13.4347
UGAAAAAAAAAAAGAA	chr9:125611632-125611852(-)$1	220	119	135	20.8260
UCAAACAACAAAAACU	chr5:5489618-5489841(+)$1	223	81	97	11.5869
auaaaaaaauaaauaa	chr19:11243823-11244041(+)$1	218	61	77	18.1086
GUGAAAAUAAAAAUGC	chr6:71270595-71270816(+)$1	221	107	123	12.6739
uuaaaaaaaaaaaGGU	chr10:69676430-69676654(+)$1	224	127	143	22.3478
GUACAGAAAAAAAAAA	chr18:74727159-74727380(-)$1	221	143	159	15.6086
GUAAAAAUAAAUAAUC	chr15:66641316-66641536(-)$1	220	44	60	14.0869
UUAUAAGUACAAAUUU	chr22:46239588-46239809(+)$1	221	53	69	11.9130
UUAAAAGAAAUUAAAC	chr4:40427179-40427405(-)$1	226	93	109	14.5217
UUAUUAAAAAAGAAUU	chr5:96366837-96367059(+)$1	222	43	59	14.6304
UUGUAAAAUAAAAUAA	chr6:159056150-159056376(+)$1	226	96	112	16.6956
UUUCAAAGGAAAAGAA	chr19:6439976-6440195(-)$1	219	77	93	13.1086
UUACUGAUAAAAAUGA	chr4:71895604-71895826(+)$1	222	205	221	11.6956
UUGUAAAAAUAAACUU	chr8:11182513-11182736(+)$1	223	155	171	13.1086
UUAAAAACAAUAAUAG	chr2:61725796-61726026(-)$1	230	49	65	17.9999
UUAAAAUAAACAGUUG	chr14:71050717-71050947(-)$1	230	117	133	12.3478
UUACAAAAGGAAAUAA	chr10:85912680-85912901(+)$1	221	155	171	16.0434
AUAGAAAAAAAAAACA	chr1:184659899-184660118(-)$1	219	169	185	16.9130
UUAAAAACAAACAAAC	chr11:17109143-17109363(-)$1	220	164	180	17.7826
UGCaaaaaaaaaaaaa	chr5:82876942-82877163(+)$1	221	191	207	17.8913
UUAUGAAGAAAAAGAG	chr15:68583803-68584025(+)$1	222	175	191	14.3043
UUAGUGAGAAAAAAUG	chr8:104411659-104411889(-)$1	230	65	81	10.7173
UUAAUGGAGAAAAUAA	chr3:124948515-124948735(-)$1	220	115	131	11.9130
UUAAAAAGAAACAGAA	chr17:37077574-37077793(+)$1	219	178	194	18.6521
UUAAAAGACAAAAGCA	chr1:25168744-25168968(+)$1	224	66	82	16.2608
UUAAAAAUAAAAACUA	chr1:226548600-226548830(-)$1	230	100	116	21.1521
UUUAAUUAAAAAAUUU	chr15:64657995-64658225(-)$1	230	102	118	13.8695
UUAAAAUACAAGAUUU	chr5:134193227-134193450(+)$1	223	62	78	13.8695
UUAAAAUAAAAUUUUA	chr14:24635572-24635831(+)$1	259	174	190	14.7391
UUUAAAAAAAUAGCAA	chr7:99635673-99635903(+)$1	230	47	63	13.8695
UUAAACAAAAAUUAGA	chr6:24706096-24706321(-)$1	225	129	145	13.1086
uuaauaaauaaauaag	chr6:34253735-34253962(-)$1	227	84	100	13.6521
CUACAAAUAAAAAGUG	chr22:32015279-32015500(-)$1	221	127	143	13.6521
UCUAAAAGAAAAAGAU	chr1:169356543-169356764(+)$1	221	139	155	14.1956
uuucaaaauaaaaugu	chr16:77236083-77236299(+)$1	216	186	202	14.3043
UUAAUAAAAAUAAUAC	chr4:89182490-89182709(-)$1	219	188	204	17.5652
UUAAAAAUUAAUACCA	chr4:52781375-52781599(+)$1	224	192	208	13.6521
UUAGACAAAGAAAAAC	chr3:101486219-101486444(+)$1	225	65	81	13.8695

#otherMatches

#Struct PSSM
c[cccqqqqqqqqccc	chr3:130720895-130721125(+)$1	230	100	116	12.6739
c4444ffffff]bb::	chr20:5095686-5095907(-)$1	221	144	160	12.6739
::::dddd!!cccooo	chr2:37072474-37072696(-)$1	222	185	201	17.7826
ccnnnnnccc4444gg	chr3:156424038-156424264(+)$1	226	33	49	14.8478
:::::::::hhhhhhh	chr4:77969102-77969325(-)$1	223	145	161	17.6739
tttttt==========	chr12:120899625-120899851(+)$1	226	75	91	24.1956
hhyyyyyyyyyyyyyy	chr10:76941718-76941941(+)$1	223	127	143	15.3913
d[dddd''''''''ff	chr5:68473419-68473641(+)$1	222	66	82	13.4347
HHHHHH::::::::::	chr9:125611632-125611852(-)$1	220	119	135	20.8260
CC{HHHHHHHHLLLCC	chr5:5489618-5489841(+)$1	223	81	97	11.5869
ccooooooccc:::::	chr19:11243823-11244041(+)$1	218	61	77	18.1086
:==========[eeee	chr6:71270595-71270816(+)$1	221	107	123	12.6739
lll===========dd	chr10:69676430-69676654(+)$1	224	127	143	22.3478
gggggttttttttttt	chr18:74727159-74727380(-)$1	221	143	159	15.6086
gggg::::::::::::	chr15:66641316-66641536(-)$1	220	44	60	14.0869
ffqqqqqqqqffffff	chr22:46239588-46239809(+)$1	221	53	69	11.9130
hhhh%%%%%%dddd$$	chr4:40427179-40427405(-)$1	226	93	109	14.5217
cc!!ccc&&&&&&&ee	chr5:96366837-96367059(+)$1	222	43	59	14.6304
iiiiiiii::::::ee	chr6:159056150-159056376(+)$1	226	96	112	16.6956
ddddmmmmdddd22dd	chr19:6439976-6440195(-)$1	219	77	93	13.1086
qqqdddd]dddd22bb	chr4:71895604-71895826(+)$1	222	205	221	11.6956
ff::::::::::eeee	chr8:11182513-11182736(+)$1	223	155	171	13.1086
iiiiiiiiieeeee[a	chr2:61725796-61726026(-)$1	230	49	65	17.9999
wwwwwwwwwwwwwwff	chr14:71050717-71050947(-)$1	230	117	133	12.3478
cc"""ddddppppppp	chr10:85912680-85912901(+)$1	221	155	171	16.0434
ggg[bb''''''''ee	chr1:184659899-184660118(-)$1	219	169	185	16.9130
EEEE:::::::::::c	chr11:17109143-17109363(-)$1	220	164	180	17.7826
::::::::::::::::	chr5:82876942-82877163(+)$1	221	191	207	17.8913
2dddd22bb333bb]c	chr15:68583803-68584025(+)$1	222	175	191	14.3043
hhhh:JJJJJJJJJJC	chr8:104411659-104411889(-)$1	230	65	81	10.7173
tttttbbeeeee]===	chr3:124948515-124948735(-)$1	220	115	131	11.9130
ccmmmmccc]dddd::	chr17:37077574-37077793(+)$1	219	178	194	18.6521
qdddd22ccc22ffff	chr1:25168744-25168968(+)$1	224	66	82	16.2608
qqqqqqqffffffDDD	chr1:226548600-226548830(-)$1	230	100	116	21.1521
=:::::::::::::::	chr15:64657995-64658225(-)$1	230	102	118	13.8695
Deeeeeqqqqqqqqee	chr5:134193227-134193450(+)$1	223	62	78	13.8695
:fffffflllffffff	chr14:24635572-24635831(+)$1	259	174	190	14.7391
^^^^^^^^^^^^^^^^	chr7:99635673-99635903(+)$1	230	47	63	13.8695
c+++++++++++++ee	chr6:24706096-24706321(-)$1	225	129	145	13.1086
dddrrrrrrrrrdddd	chr6:34253735-34253962(-)$1	227	84	100	13.6521
HH:::::::::::III	chr22:32015279-32015500(-)$1	221	127	143	13.6521
&&&&&&ddddnnnnnd	chr1:169356543-169356764(+)$1	221	139	155	14.1956
cc22ffffff4444cc	chr16:77236083-77236299(+)$1	216	186	202	14.3043
eeooooooeeeee:::	chr4:89182490-89182709(-)$1	219	188	204	17.5652
::::::::::::::::	chr4:52781375-52781599(+)$1	224	192	208	13.6521
EEEEE{EEEEE:::::	chr3:101486219-101486444(+)$1	225	65	81	13.8695

#DB
(.(((........)))	chr3:130720895-130721125(+)$1	1	100	116	12.6739
)....)))))).))..	chr20:5095686-5095907(-)$1	1	144	160	12.6739
....((((..(((...	chr2:37072474-37072696(-)$1	1	185	201	17.7826
((.....)))....))	chr3:156424038-156424264(+)$1	1	33	49	14.8478
.........(((((((	chr4:77969102-77969325(-)$1	1	145	161	17.6739
......))))))))))	chr12:120899625-120899851(+)$1	1	75	91	24.1956
((..............	chr10:76941718-76941941(+)$1	1	127	143	15.3913
(.((((........((	chr5:68473419-68473641(+)$1	1	66	82	13.4347
))))))..........	chr9:125611632-125611852(-)$1	1	119	135	20.8260
((.((((((((...((	chr5:5489618-5489841(+)$1	1	81	97	11.5869
((......))).....	chr19:11243823-11244041(+)$1	1	61	77	18.1086
.((((((((((.((((	chr6:71270595-71270816(+)$1	1	107	123	12.6739
...)))))))))))))	chr10:69676430-69676654(+)$1	1	127	143	22.3478
(((((...........	chr18:74727159-74727380(-)$1	1	143	159	15.6086
))))............	chr15:66641316-66641536(-)$1	1	44	60	14.0869
((........))))))	chr22:46239588-46239809(+)$1	1	53	69	11.9130
((((......((((..	chr4:40427179-40427405(-)$1	1	93	109	14.5217
((..(((.......((	chr5:96366837-96367059(+)$1	1	43	59	14.6304
))))))))......((	chr6:159056150-159056376(+)$1	1	96	112	16.6956
((((....))))..))	chr19:6439976-6440195(-)$1	1	77	93	13.1086
...)))).))))..))	chr4:71895604-71895826(+)$1	1	205	221	11.6956
))..........((((	chr8:11182513-11182736(+)$1	1	155	171	13.1086
)))))))))(((((.(	chr2:61725796-61726026(-)$1	1	49	65	17.9999
..............))	chr14:71050717-71050947(-)$1	1	117	133	12.3478
((...((((.......	chr10:85912680-85912901(+)$1	1	155	171	16.0434
(((.((........((	chr1:184659899-184660118(-)$1	1	169	185	16.9130
))))...........(	chr11:17109143-17109363(-)$1	1	164	180	17.7826
................	chr5:82876942-82877163(+)$1	1	191	207	17.8913
.))))..))...)).)	chr15:68583803-68584025(+)$1	1	175	191	14.3043
)))).(((((((((((	chr8:104411659-104411889(-)$1	1	65	81	10.7173
.....))))))).)))	chr3:124948515-124948735(-)$1	1	115	131	11.9130
((....))).))))..	chr17:37077574-37077793(+)$1	1	178	194	18.6521
.))))..)))..))))	chr1:25168744-25168968(+)$1	1	66	82	16.2608
.......)))))))))	chr1:226548600-226548830(-)$1	1	100	116	21.1521
)...............	chr15:64657995-64658225(-)$1	1	102	118	13.8695
((((((........))	chr5:134193227-134193450(+)$1	1	62	78	13.8695
.((((((...))))))	chr14:24635572-24635831(+)$1	1	174	190	14.7391
................	chr7:99635673-99635903(+)$1	1	47	63	13.8695
(.............((	chr6:24706096-24706321(-)$1	1	129	145	13.1086
(((.........))))	chr6:34253735-34253962(-)$1	1	84	100	13.6521
))...........(((	chr22:32015279-32015500(-)$1	1	127	143	13.6521
......((((.....)	chr1:169356543-169356764(+)$1	1	139	155	14.1956
))..))))))....))	chr16:77236083-77236299(+)$1	1	186	202	14.3043
((......)))))...	chr4:89182490-89182709(-)$1	1	188	204	17.5652
................	chr4:52781375-52781599(+)$1	1	192	208	13.6521
(((((.(((((.....	chr3:101486219-101486444(+)$1	1	65	81	13.8695

#PSSM
U : 0.76	u : 0.08	G : 0.06	C : 0.04	a : 0.02	A : 0.02	
U : 0.78	u : 0.10	C : 0.06	G : 0.04	
A : 0.67	U : 0.13	a : 0.08	G : 0.06	C : 0.02	u : 0.02	
A : 0.54	U : 0.15	a : 0.10	C : 0.10	G : 0.06	c : 0.02	
A : 0.71	a : 0.10	U : 0.10	C : 0.02	G : 0.02	u : 0.02	
A : 0.69	a : 0.13	G : 0.08	C : 0.06	U : 0.02	
A : 0.65	a : 0.13	U : 0.10	G : 0.10	
A : 0.54	U : 0.15	a : 0.13	G : 0.10	C : 0.06	
A : 0.67	a : 0.08	U : 0.06	C : 0.06	G : 0.06	u : 0.04	
A : 0.71	a : 0.10	G : 0.06	U : 0.04	C : 0.04	u : 0.02	
A : 0.69	U : 0.13	a : 0.13	C : 0.04	
A : 0.63	U : 0.15	a : 0.13	G : 0.04	C : 0.04	
A : 0.76	a : 0.10	G : 0.04	U : 0.04	C : 0.02	u : 0.02	
U : 0.32	A : 0.28	G : 0.19	C : 0.08	a : 0.06	u : 0.04	
A : 0.41	U : 0.30	C : 0.08	G : 0.08	a : 0.06	u : 0.02	g : 0.02	
A : 0.39	U : 0.21	C : 0.15	G : 0.13	u : 0.04	a : 0.04	g : 0.02	

#score	701.9130434782603
#seq	46
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m1_run1.nuc.txt

#NT
UCUU	chr6:150001184-150001403(-)$1	219	4	8	11.9999
UCUU	chr10:88277228-88277447(-)$1	219	134	138	11.9999
UCUU	chr10:60548920-60549317(-)$1	397	36	40	11.9999
UCUU	chr1:153640883-153641123(-)$1	240	50	54	11.9999
UCUU	chr19:33695545-33695809(+)$1	264	150	154	11.9999
UCUU	chr19:41928094-41928317(+)$1	223	109	113	11.9999
UCUU	chr16:1741771-1741992(+)$1	221	90	94	11.9999
UCUU	chr15:78789495-78789718(+)$1	223	107	111	11.9999
UCUU	chr13:45841358-45841581(+)$1	223	116	120	11.9999
UCUU	chr12:24982711-24982931(-)$1	220	36	40	11.9999
UCUU	chr17:42883028-42883249(-)$1	221	152	156	11.9999
UCUU	chrM:10371-10635(+)$1	264	259	263	11.9999
UCUU	chr3:156262055-156262290(-)$1	235	64	68	11.9999
UCUU	chr18:29100695-29100920(+)$1	225	81	85	11.9999
UCUU	chr1:160314444-160314668(+)$1	224	55	59	11.9999
UCUU	chr10:115606914-115607140(-)$1	226	2	6	11.9999
UCUU	chr11:93540649-93540868(+)$1	219	110	114	11.9999
UCUU	chr17:5302778-5303002(-)$1	224	120	124	11.9999
UCUU	chr5:71491943-71492162(-)$1	219	12	16	11.9999
UCUU	chrM:8007-8320(+)$1	313	54	58	11.9999
UCUU	chr19:37619422-37619643(+)$1	221	21	25	11.9999
UCUU	chr20:43135457-43135681(-)$1	224	52	56	11.9999
UCUU	chrX:107977016-107977257(-)$1	241	80	84	11.9999
UCUU	chr16:31201987-31202206(+)$1	219	9	13	11.9999
UCUU	chr8:30361706-30362051(+)$1	345	69	73	11.9999
UCUU	chr19:37239430-37239668(-)$1	238	19	23	11.9999
UCUU	chr5:134688563-134688783(-)$1	220	39	43	11.9999
UCUU	chr5:159841355-159841577(-)$1	222	5	9	11.9999
UCUU	chr12:402113-402348(-)$1	235	58	62	11.9999
UCUU	chr5:90079704-90079923(+)$1	219	153	157	11.9999
UCUU	chr10:60556042-60556291(+)$1	249	208	212	11.9999
UCUU	chr14:60574537-60574757(+)$1	220	144	148	11.9999
UCUU	chr10:91163101-91163323(-)$1	222	21	25	11.9999
UCUU	chr16:29821422-29821660(+)$1	238	199	203	11.9999
UCUU	chr16:2225293-2225514(+)$1	221	96	100	11.9999
UCUU	chr2:74000863-74001084(-)$1	221	11	15	11.9999
UCUU	chr11:10821033-10821256(-)$1	223	10	14	11.9999
UCUU	chr6:75968426-75968646(-)$1	220	80	84	11.9999
UCUU	chr10:127520026-127520247(+)$1	221	171	175	11.9999
UCUU	chr8:67576649-67576874(-)$1	225	57	61	11.9999
UCUU	chr1:24019071-24019291(+)$1	220	12	16	11.9999
UCUU	chr12:69990923-69991143(+)$1	220	170	174	11.9999
UCUU	chr6:30153586-30153805(-)$1	219	196	200	11.9999
UCUU	chr10:33475290-33475509(-)$1	219	78	82	11.9999
UCUU	chrX:18283719-18283945(-)$1	226	55	59	11.9999
UCUU	chr17:38991020-38991241(+)$1	221	32	36	11.9999
UCUU	chr7:26724269-26724490(-)$1	221	7	11	11.9999
UCUU	chr7:104748081-104748303(+)$1	222	15	19	11.9999
UCUU	chr15:66794904-66795125(-)$1	221	19	23	11.9999
UCUU	chr1:153634802-153635036(-)$1	234	5	9	11.9999
UCUU	chr1:36380944-36381180(-)$1	236	149	153	11.9999
UCUU	chr10:79743600-79743825(-)$1	225	2	6	11.9999
UCUU	chr7:117420517-117420744(-)$1	227	13	17	11.9999
UCUU	chr2:61709524-61709747(+)$1	223	98	102	11.9999
UCUU	chr10:99132711-99132930(-)$1	219	24	28	11.9999
UCUU	chr9:35102651-35102870(-)$1	219	35	39	11.9999
UCUU	chr16:66976569-66976788(+)$1	219	101	105	11.9999
UCUU	chr2:11922422-11922650(+)$1	228	124	128	11.9999
UCUU	chr6:64422096-64422331(+)$1	235	29	33	11.9999
UCUU	chr5:153432557-153432779(+)$1	222	48	52	11.9999
UCUU	chr10:60558726-60558962(+)$1	236	52	56	11.9999
UCUU	chr2:242195587-242195807(-)$1	220	141	145	11.9999
UCUU	chr19:42753608-42753831(-)$1	223	63	67	11.9999
UCUU	chr4:6864738-6864962(+)$1	224	157	161	11.9999
UCUU	chr1:231403400-231403628(+)$1	228	13	17	11.9999
UCUU	chr1:26440960-26441184(+)$1	224	106	110	11.9999
UCUU	chr10:105838240-105838459(-)$1	219	93	97	11.9999
UCUU	chr1:244586073-244586304(-)$1	231	62	66	11.9999
UCUU	chr11:61069653-61069873(-)$1	220	35	39	11.9999
UCUU	chr2:136677981-136678201(-)$1	220	12	16	11.9999
UCUU	chr9:111812574-111812796(-)$1	222	31	35	11.9999
UCUU	chr12:70206658-70206878(+)$1	220	163	167	11.9999
UCUU	chr11:92531416-92531636(+)$1	220	71	75	11.9999
UCUU	chr13:98668920-98669144(+)$1	224	199	203	11.9999
UCUU	chr10:60577222-60577580(+)$1	358	179	183	11.9999
UCUU	chr9:37126583-37126808(+)$1	225	99	103	11.9999
UCUU	chr16:14758708-14758927(+)$1	219	19	23	11.9999
UCUU	chr7:73101255-73101479(+)$1	224	42	46	11.9999
UCUU	chr10:60548028-60548284(+)$1	256	93	97	11.9999

#otherMatches

#Struct PSSM
FFFF	chr15:91010625-91010846(+)$1	221	27	31	11.9999
::ff	chr6:150001184-150001403(-)$1	219	4	8	11.9999
::::	chr10:88277228-88277447(-)$1	219	134	138	11.9999
GGGG	chr10:60548920-60549317(-)$1	397	36	40	11.9999
RRRF	chr1:153640883-153641123(-)$1	240	50	54	11.9999
oood	chr19:33695545-33695809(+)$1	264	150	154	11.9999
::::	chr19:41928094-41928317(+)$1	223	109	113	11.9999
oooo	chr16:1741771-1741992(+)$1	221	90	94	11.9999
hhhh	chr15:78789495-78789718(+)$1	223	107	111	11.9999
bb!!	chr13:45841358-45841581(+)$1	223	116	120	11.9999
b444	chr12:24982711-24982931(-)$1	220	36	40	11.9999
b333	chr17:42883028-42883249(-)$1	221	152	156	11.9999
::::	chrM:10371-10635(+)$1	264	259	263	11.9999
]a==	chr3:156262055-156262290(-)$1	235	64	68	11.9999
ddd]	chr18:29100695-29100920(+)$1	225	81	85	11.9999
ccmm	chr1:160314444-160314668(+)$1	224	55	59	11.9999
::::	chr10:115606914-115607140(-)$1	226	2	6	11.9999
d(((	chr11:93540649-93540868(+)$1	219	110	114	11.9999
eee[	chr17:5302778-5303002(-)$1	224	120	124	11.9999
::::	chr5:71491943-71492162(-)$1	219	12	16	11.9999
hhhd	chrM:8007-8320(+)$1	313	54	58	11.9999
:HHH	chr19:37619422-37619643(+)$1	221	21	25	11.9999
nnnn	chr20:43135457-43135681(-)$1	224	52	56	11.9999
::::	chrX:107977016-107977257(-)$1	241	80	84	11.9999
LIII	chr16:31201987-31202206(+)$1	219	9	13	11.9999
rrrr	chr8:30361706-30362051(+)$1	345	69	73	11.9999
rrrr	chr19:37239430-37239668(-)$1	238	19	23	11.9999
FFDD	chr5:134688563-134688783(-)$1	220	39	43	11.9999
KBBM	chr5:159841355-159841577(-)$1	222	5	9	11.9999
JJJJ	chr12:402113-402348(-)$1	235	58	62	11.9999
bb[d	chr5:90079704-90079923(+)$1	219	153	157	11.9999
fbb2	chr10:60556042-60556291(+)$1	249	208	212	11.9999
GGGG	chr14:60574537-60574757(+)$1	220	144	148	11.9999
ffHH	chr10:91163101-91163323(-)$1	222	21	25	11.9999
====	chr16:29821422-29821660(+)$1	238	199	203	11.9999
[ccc	chr16:2225293-2225514(+)$1	221	96	100	11.9999
eeee	chr2:74000863-74001084(-)$1	221	11	15	11.9999
GGGG	chr11:10821033-10821256(-)$1	223	10	14	11.9999
DDDD	chr6:75968426-75968646(-)$1	220	80	84	11.9999
:DDD	chr10:127520026-127520247(+)$1	221	171	175	11.9999
ffff	chr8:67576649-67576874(-)$1	225	57	61	11.9999
tttt	chr1:24019071-24019291(+)$1	220	12	16	11.9999
eee]	chr12:69990923-69991143(+)$1	220	170	174	11.9999
ccc2	chr6:30153586-30153805(-)$1	219	196	200	11.9999
mmmd	chr10:33475290-33475509(-)$1	219	78	82	11.9999
{BB{	chrX:18283719-18283945(-)$1	226	55	59	11.9999
qqqq	chr17:38991020-38991241(+)$1	221	32	36	11.9999
eeee	chr7:26724269-26724490(-)$1	221	7	11	11.9999
DDcc	chr7:104748081-104748303(+)$1	222	15	19	11.9999
FKKB	chr15:66794904-66795125(-)$1	221	19	23	11.9999
DDDD	chr1:153634802-153635036(-)$1	234	5	9	11.9999
ccoo	chr1:36380944-36381180(-)$1	236	149	153	11.9999
EEE:	chr10:79743600-79743825(-)$1	225	2	6	11.9999
DKKG	chr7:117420517-117420744(-)$1	227	13	17	11.9999
ddde	chr2:61709524-61709747(+)$1	223	98	102	11.9999
D{CC	chr10:99132711-99132930(-)$1	219	24	28	11.9999
ccc:	chr9:35102651-35102870(-)$1	219	35	39	11.9999
JJJJ	chr16:66976569-66976788(+)$1	219	101	105	11.9999
eeee	chr2:11922422-11922650(+)$1	228	124	128	11.9999
EEEE	chr6:64422096-64422331(+)$1	235	29	33	11.9999
pppp	chr5:153432557-153432779(+)$1	222	48	52	11.9999
::::	chr10:60558726-60558962(+)$1	236	52	56	11.9999
eeed	chr2:242195587-242195807(-)$1	220	141	145	11.9999
^^^^	chr19:42753608-42753831(-)$1	223	63	67	11.9999
ffff	chr4:6864738-6864962(+)$1	224	157	161	11.9999
cccp	chr1:231403400-231403628(+)$1	228	13	17	11.9999
dddd	chr1:26440960-26441184(+)$1	224	106	110	11.9999
qqqq	chr10:105838240-105838459(-)$1	219	93	97	11.9999
iibb	chr1:244586073-244586304(-)$1	231	62	66	11.9999
wwww	chr11:61069653-61069873(-)$1	220	35	39	11.9999
JJJJ	chr2:136677981-136678201(-)$1	220	12	16	11.9999
dooo	chr9:111812574-111812796(-)$1	222	31	35	11.9999
iii4	chr12:70206658-70206878(+)$1	220	163	167	11.9999
22ee	chr11:92531416-92531636(+)$1	220	71	75	11.9999
]ddd	chr13:98668920-98669144(+)$1	224	199	203	11.9999
f:::	chr10:60577222-60577580(+)$1	358	179	183	11.9999
JJJJ	chr9:37126583-37126808(+)$1	225	99	103	11.9999
lfff	chr16:14758708-14758927(+)$1	219	19	23	11.9999
ffff	chr7:73101255-73101479(+)$1	224	42	46	11.9999
cnnn	chr10:60548028-60548284(+)$1	256	93	97	11.9999

#DB
((((	chr15:91010625-91010846(+)$1	1	27	31	11.9999
..((	chr6:150001184-150001403(-)$1	1	4	8	11.9999
....	chr10:88277228-88277447(-)$1	1	134	138	11.9999
((((	chr10:60548920-60549317(-)$1	1	36	40	11.9999
...(	chr1:153640883-153641123(-)$1	1	50	54	11.9999
...)	chr19:33695545-33695809(+)$1	1	150	154	11.9999
....	chr19:41928094-41928317(+)$1	1	109	113	11.9999
....	chr16:1741771-1741992(+)$1	1	90	94	11.9999
))))	chr15:78789495-78789718(+)$1	1	107	111	11.9999
((..	chr13:45841358-45841581(+)$1	1	116	120	11.9999
)...	chr12:24982711-24982931(-)$1	1	36	40	11.9999
)...	chr17:42883028-42883249(-)$1	1	152	156	11.9999
....	chrM:10371-10635(+)$1	1	259	263	11.9999
.)((	chr3:156262055-156262290(-)$1	1	64	68	11.9999
))).	chr18:29100695-29100920(+)$1	1	81	85	11.9999
((..	chr1:160314444-160314668(+)$1	1	55	59	11.9999
....	chr10:115606914-115607140(-)$1	1	2	6	11.9999
(...	chr11:93540649-93540868(+)$1	1	110	114	11.9999
(((.	chr17:5302778-5303002(-)$1	1	120	124	11.9999
....	chr5:71491943-71492162(-)$1	1	12	16	11.9999
((((	chrM:8007-8320(+)$1	1	54	58	11.9999
.(((	chr19:37619422-37619643(+)$1	1	21	25	11.9999
....	chr20:43135457-43135681(-)$1	1	52	56	11.9999
....	chrX:107977016-107977257(-)$1	1	80	84	11.9999
.(((	chr16:31201987-31202206(+)$1	1	9	13	11.9999
....	chr8:30361706-30362051(+)$1	1	69	73	11.9999
....	chr19:37239430-37239668(-)$1	1	19	23	11.9999
((((	chr5:134688563-134688783(-)$1	1	39	43	11.9999
.((.	chr5:159841355-159841577(-)$1	1	5	9	11.9999
))))	chr12:402113-402348(-)$1	1	58	62	11.9999
((.(	chr5:90079704-90079923(+)$1	1	153	157	11.9999
))).	chr10:60556042-60556291(+)$1	1	208	212	11.9999
((((	chr14:60574537-60574757(+)$1	1	144	148	11.9999
))((	chr10:91163101-91163323(-)$1	1	21	25	11.9999
))))	chr16:29821422-29821660(+)$1	1	199	203	11.9999
.(((	chr16:2225293-2225514(+)$1	1	96	100	11.9999
((((	chr2:74000863-74001084(-)$1	1	11	15	11.9999
((((	chr11:10821033-10821256(-)$1	1	10	14	11.9999
((((	chr6:75968426-75968646(-)$1	1	80	84	11.9999
.)))	chr10:127520026-127520247(+)$1	1	171	175	11.9999
))))	chr8:67576649-67576874(-)$1	1	57	61	11.9999
....	chr1:24019071-24019291(+)$1	1	12	16	11.9999
))).	chr12:69990923-69991143(+)$1	1	170	174	11.9999
))).	chr6:30153586-30153805(-)$1	1	196	200	11.9999
...)	chr10:33475290-33475509(-)$1	1	78	82	11.9999
.((.	chrX:18283719-18283945(-)$1	1	55	59	11.9999
....	chr17:38991020-38991241(+)$1	1	32	36	11.9999
((((	chr7:26724269-26724490(-)$1	1	7	11	11.9999
((((	chr7:104748081-104748303(+)$1	1	15	19	11.9999
(..(	chr15:66794904-66795125(-)$1	1	19	23	11.9999
((((	chr1:153634802-153635036(-)$1	1	5	9	11.9999
((..	chr1:36380944-36381180(-)$1	1	149	153	11.9999
(((.	chr10:79743600-79743825(-)$1	1	2	6	11.9999
(..(	chr7:117420517-117420744(-)$1	1	13	17	11.9999
((((	chr2:61709524-61709747(+)$1	1	98	102	11.9999
(.((	chr10:99132711-99132930(-)$1	1	24	28	11.9999
))).	chr9:35102651-35102870(-)$1	1	35	39	11.9999
((((	chr16:66976569-66976788(+)$1	1	101	105	11.9999
))))	chr2:11922422-11922650(+)$1	1	124	128	11.9999
((((	chr6:64422096-64422331(+)$1	1	29	33	11.9999
....	chr5:153432557-153432779(+)$1	1	48	52	11.9999
....	chr10:60558726-60558962(+)$1	1	52	56	11.9999
))))	chr2:242195587-242195807(-)$1	1	141	145	11.9999
....	chr19:42753608-42753831(-)$1	1	63	67	11.9999
))))	chr4:6864738-6864962(+)$1	1	157	161	11.9999
(((.	chr1:231403400-231403628(+)$1	1	13	17	11.9999
((((	chr1:26440960-26441184(+)$1	1	106	110	11.9999
....	chr10:105838240-105838459(-)$1	1	93	97	11.9999
))))	chr1:244586073-244586304(-)$1	1	62	66	11.9999
....	chr11:61069653-61069873(-)$1	1	35	39	11.9999
((((	chr2:136677981-136678201(-)$1	1	12	16	11.9999
(...	chr9:111812574-111812796(-)$1	1	31	35	11.9999
))).	chr12:70206658-70206878(+)$1	1	163	167	11.9999
..))	chr11:92531416-92531636(+)$1	1	71	75	11.9999
.)))	chr13:98668920-98669144(+)$1	1	199	203	11.9999
)...	chr10:60577222-60577580(+)$1	1	179	183	11.9999
((((	chr9:37126583-37126808(+)$1	1	99	103	11.9999
.)))	chr16:14758708-14758927(+)$1	1	19	23	11.9999
((((	chr7:73101255-73101479(+)$1	1	42	46	11.9999
(...	chr10:60548028-60548284(+)$1	1	93	97	11.9999

#PSSM
U : 0.99	
C : 0.99	
U : 0.99	
U : 0.99	

#score	959.9999999999995
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m1_run2.nuc.txt

#NT
UGUUUUAUUCUUA	chr5:33448689-33448924(+)$1	235	218	231	17.3673
UCUUUUCAUCUUU	chr5:40777446-40777663(-)$1	217	151	164	14.4081
UGUUUUCUUUUUC	chr5:122729026-122729249(-)$1	223	32	45	23.4897
UGAUUAUUUUUUA	chr10:12126487-12126708(+)$1	221	10	23	13.5918
UGUUUUCUUGAUC	chr18:25589635-25589859(-)$1	224	5	18	15.1224
UCUUUUAGUUUUA	chr3:180666126-180666350(+)$1	224	0	13	15.5306
UGUUUUCUGUAUU	chr2:97372924-97373144(-)$1	220	72	85	15.2244
AUUUUUCUUUUCC	chr20:43115206-43115428(+)$1	222	166	179	14.2040
UUAUUUAUUUUUA	chr1:243858799-243859028(-)$1	229	170	183	16.3469
UGUAUUAUUUUAU	chr5:5468892-5469111(+)$1	219	26	39	14.2040
UGUUAUCAUUUUU	chr1:77627218-77627439(-)$1	221	23	36	15.7346
GACUUUAUUUUUU	chr12:42768742-42768963(+)$1	221	147	160	13.1836
UGUUUUCUGUUUG	chr17:58365800-58366025(-)$1	225	161	174	18.0816
UCAUUUCUUUUUC	chr8:97243476-97243694(-)$1	218	100	113	18.3877
UAUUUUACUUUUA	chr4:56329789-56330013(-)$1	224	12	25	16.4489
UGGUUUAUUUUUU	chr4:57876870-57877091(+)$1	221	28	41	18.4897
UGUUUUUCUUCUU	chr17:45741488-45741710(+)$1	222	20	33	13.7959
UGUUUUCUUCUUA	chr14:45566038-45566265(+)$1	227	37	50	19.1020
AUGUUUCUUUUUC	chr6:49427026-49427256(-)$1	230	22	35	14.2040
UAUUUUAUUGUUG	chr9:82188520-82188746(+)$1	226	62	75	15.3265
UUUAUUUUUUUUU	chr11:18104994-18105215(-)$1	221	198	211	15.8367
UGUUUCCUCUUUC	chr5:137735506-137735730(+)$1	224	23	36	15.5306
UGUUUGCUCUUCU	chr13:21955550-21955782(-)$1	232	75	88	12.2653
UGUUUUUCCUUUC	chr16:46726195-46726415(+)$1	220	81	94	13.7959
UGUUUUAUCUUAC	chr1:202742164-202742390(-)$1	226	170	183	14.1020
UAUAUUCUUUUUA	chr6:97717730-97717950(-)$1	220	195	208	17.7755
uuuuuuuuuuuuu	chr12:97311315-97311537(+)$1	222	61	74	19.9183
UACUUGCUUUUUC	chr10:62547782-62548004(+)$1	222	19	32	14.9183
UGAUUUCAUUUUU	chr10:70669991-70670214(+)$1	223	54	67	17.0612
UCUUUUCUUUCUG	chr5:14755913-14756132(-)$1	219	62	75	16.1428
UGCUUUUUUUUCC	chr6:53761230-53761451(+)$1	221	36	49	14.5102
GAUUUUCUUUUUC	chr17:17158135-17158359(-)$1	224	194	207	18.1836
UAAUUUCUUUUUC	chr1:203769485-203769713(+)$1	228	102	115	19.2040
UAUUUUCUUAUUA	chr3:182545863-182546091(+)$1	228	107	120	17.6734
UGUUUUAUUUUUA	chr14:45565241-45565459(+)$1	218	47	60	21.2448
UGUUUCUUUUUUG	chr4:123813306-123813530(+)$1	224	77	90	16.2448
UGUUUCCUUUUCU	chr12:27156099-27156328(-)$1	229	144	157	16.2448
UUAUUUCAUUUUC	chr12:123738136-123738360(+)$1	224	100	113	15.1224
UAUUUUGUUUUAU	chr10:98286904-98287137(-)$1	233	73	86	16.6530
UGGUUUGUUCUUU	chr1:160000193-160000417(-)$1	224	63	76	14.1020
UGUUUUGGUUUCA	chr19:30501922-30502141(+)$1	219	14	27	13.4897
UGUUUGGUUUUUA	chr5:110097203-110097424(+)$1	221	166	179	16.7551
UUUGUUCUUUUGC	chr1:23399756-23399984(+)$1	228	13	26	13.6938
CAUUUUCUUUUGC	chr5:68469995-68470220(+)$1	225	67	80	14.3061
UGUUCUGUUUUUU	chr1:193044864-193045086(+)$1	222	26	39	16.8571
UAUCUUCUUUUUU	chr15:35230875-35231096(-)$1	221	160	173	18.3877
ACUUUUCUUUCUU	chr2:38527349-38527569(-)$1	220	27	40	13.4897
UAUUAUCUUUUUU	chr4:102001622-102001849(-)$1	227	14	27	18.0816

#otherMatches

#Struct PSSM
==========ppp	chr11:32956762-32956985(+)$1	223	105	118	14.7142
HHHHHHZZZCCC:	chr5:33448689-33448924(+)$1	235	218	231	17.3673
f[eeeee[bb"""	chr5:40777446-40777663(-)$1	217	151	164	14.4081
hhhhhhhh55555	chr5:122729026-122729249(-)$1	223	32	45	23.4897
:::ffffffmmmm	chr10:12126487-12126708(+)$1	221	10	23	13.5918
eeee!!ggggggg	chr18:25589635-25589859(-)$1	224	5	18	15.1224
:::::::EEEEEN	chr3:180666126-180666350(+)$1	224	0	13	15.5306
dddd####dddd[	chr2:97372924-97373144(-)$1	220	72	85	15.2244
duuuuuuuuuuuu	chr20:43115206-43115428(+)$1	222	166	179	14.2040
CC}EEEEEHHHHH	chr1:243858799-243859028(-)$1	229	170	183	16.3469
:::::::::::::	chr5:5468892-5469111(+)$1	219	26	39	14.2040
ggmmmmggggggg	chr1:77627218-77627439(-)$1	221	23	36	15.7346
eeee:::::::::	chr12:42768742-42768963(+)$1	221	147	160	13.1836
ggggggg"""eee	chr17:58365800-58366025(-)$1	225	161	174	18.0816
III::gggggggo	chr8:97243476-97243694(-)$1	218	100	113	18.3877
EEEEE{FFFFFF:	chr4:56329789-56330013(-)$1	224	12	25	16.4489
B{FFFFFFPPPPP	chr4:57876870-57877091(+)$1	221	28	41	18.4897
e"""ffffff"""	chr17:45741488-45741710(+)$1	222	20	33	13.7959
ddddddd:GGGGG	chr14:45566038-45566265(+)$1	227	37	50	19.1020
:bb[eeeee))))	chr6:49427026-49427256(-)$1	230	22	35	14.2040
FF:::::::dddd	chr9:82188520-82188746(+)$1	226	62	75	15.3265
22===========	chr11:18104994-18105215(-)$1	221	198	211	15.8367
ggggggg$$$$$d	chr5:137735506-137735730(+)$1	224	23	36	15.5306
d333eeeee22bb	chr13:21955550-21955782(-)$1	232	75	88	12.2653
gggg!!eeeee""	chr16:46726195-46726415(+)$1	220	81	94	13.7959
E~~~~FFFFFFYY	chr1:202742164-202742390(-)$1	226	170	183	14.1020
hhhh22bbEEEEE	chr6:97717730-97717950(-)$1	220	195	208	17.7755
cc22ccc::::::	chr12:97311315-97311537(+)$1	222	61	74	19.9183
JJJJJJJJJJ:FF	chr10:62547782-62548004(+)$1	222	19	32	14.9183
b!!dddd"""eee	chr10:70669991-70670214(+)$1	223	54	67	17.0612
wwwwwwwwwwwee	chr5:14755913-14756132(-)$1	219	62	75	16.1428
2a]hhhhhhhh]e	chr6:53761230-53761451(+)$1	221	36	49	14.5102
cc:::::::::::	chr17:17158135-17158359(-)$1	224	194	207	18.1836
rr===========	chr1:203769485-203769713(+)$1	228	102	115	19.2040
+++++++++++++	chr3:182545863-182546091(+)$1	228	107	120	17.6734
ccc333ffffff]	chr14:45565241-45565459(+)$1	218	47	60	21.2448
=========&&&&	chr4:123813306-123813530(+)$1	224	77	90	16.2448
:IIIIIIIII:::	chr12:27156099-27156328(-)$1	229	144	157	16.2448
f^^^^^^^^^^^^	chr12:123738136-123738360(+)$1	224	100	113	15.1224
=======qqqqqq	chr10:98286904-98287137(-)$1	233	73	86	16.6530
b[ccc%%%%%%hh	chr1:160000193-160000417(-)$1	224	63	76	14.1020
KDDDD{FFFFFF:	chr19:30501922-30502141(+)$1	219	14	27	13.4897
GGGZZZCCC::::	chr5:110097203-110097424(+)$1	221	166	179	16.7551
uuuuuuuuuffff	chr1:23399756-23399984(+)$1	228	13	26	13.6938
b[gggggggmmmm	chr5:68469995-68470220(+)$1	225	67	80	14.3061
nnnnn========	chr1:193044864-193045086(+)$1	222	26	39	16.8571
ccssssssssssc	chr15:35230875-35231096(-)$1	221	160	173	18.3877
cccJJJJJJJJJJ	chr2:38527349-38527569(-)$1	220	27	40	13.4897
c::::::::::::	chr4:102001622-102001849(-)$1	227	14	27	18.0816

#DB
((((((((((...	chr11:32956762-32956985(+)$1	1	105	118	14.7142
))))))...))).	chr5:33448689-33448924(+)$1	1	218	231	17.3673
(.(((((.((...	chr5:40777446-40777663(-)$1	1	151	164	14.4081
)))))))).....	chr5:122729026-122729249(-)$1	1	32	45	23.4897
...((((((....	chr10:12126487-12126708(+)$1	1	10	23	13.5918
((((..(((((((	chr18:25589635-25589859(-)$1	1	5	18	15.1224
.......(((((.	chr3:180666126-180666350(+)$1	1	0	13	15.5306
((((....((((.	chr2:97372924-97373144(-)$1	1	72	85	15.2244
(............	chr20:43115206-43115428(+)$1	1	166	179	14.2040
)).))))))))))	chr1:243858799-243859028(-)$1	1	170	183	16.3469
.............	chr5:5468892-5469111(+)$1	1	26	39	14.2040
((....)))))))	chr1:77627218-77627439(-)$1	1	23	36	15.7346
)))).........	chr12:42768742-42768963(+)$1	1	147	160	13.1836
(((((((...(((	chr17:58365800-58366025(-)$1	1	161	174	18.0816
)))..(((((((.	chr8:97243476-97243694(-)$1	1	100	113	18.3877
(((((.((((((.	chr4:56329789-56330013(-)$1	1	12	25	16.4489
(.((((((.....	chr4:57876870-57877091(+)$1	1	28	41	18.4897
(...((((((...	chr17:45741488-45741710(+)$1	1	20	33	13.7959
))))))).(((((	chr14:45566038-45566265(+)$1	1	37	50	19.1020
.((.(((((....	chr6:49427026-49427256(-)$1	1	22	35	14.2040
((.......((((	chr9:82188520-82188746(+)$1	1	62	75	15.3265
..)))))))))))	chr11:18104994-18105215(-)$1	1	198	211	15.8367
(((((((.....(	chr5:137735506-137735730(+)$1	1	23	36	15.5306
)...)))))..))	chr13:21955550-21955782(-)$1	1	75	88	12.2653
((((..(((((..	chr16:46726195-46726415(+)$1	1	81	94	13.7959
)....))))))..	chr1:202742164-202742390(-)$1	1	170	183	14.1020
))))..)))))))	chr6:97717730-97717950(-)$1	1	195	208	17.7755
))..)))......	chr12:97311315-97311537(+)$1	1	61	74	19.9183
((((((((((.((	chr10:62547782-62548004(+)$1	1	19	32	14.9183
(..((((...(((	chr10:70669991-70670214(+)$1	1	54	67	17.0612
...........))	chr5:14755913-14756132(-)$1	1	62	75	16.1428
.).)))))))).)	chr6:53761230-53761451(+)$1	1	36	49	14.5102
))...........	chr17:17158135-17158359(-)$1	1	194	207	18.1836
..)))))))))))	chr1:203769485-203769713(+)$1	1	102	115	19.2040
.............	chr3:182545863-182546091(+)$1	1	107	120	17.6734
)))...)))))).	chr14:45565241-45565459(+)$1	1	47	60	21.2448
(((((((((....	chr4:123813306-123813530(+)$1	1	77	90	16.2448
.)))))))))...	chr12:27156099-27156328(-)$1	1	144	157	16.2448
(............	chr12:123738136-123738360(+)$1	1	100	113	15.1224
(((((((......	chr10:98286904-98287137(-)$1	1	73	86	16.6530
(.(((......((	chr1:160000193-160000417(-)$1	1	63	76	14.1020
.((((.((((((.	chr19:30501922-30502141(+)$1	1	14	27	13.4897
)))...)))....	chr5:110097203-110097424(+)$1	1	166	179	16.7551
.........))))	chr1:23399756-23399984(+)$1	1	13	26	13.6938
(.(((((((....	chr5:68469995-68470220(+)$1	1	67	80	14.3061
.....))))))))	chr1:193044864-193045086(+)$1	1	26	39	16.8571
((..........)	chr15:35230875-35231096(-)$1	1	160	173	18.3877
)))((((((((((	chr2:38527349-38527569(-)$1	1	27	40	13.4897
)............	chr4:102001622-102001849(-)$1	1	14	27	18.0816

#PSSM
U : 0.85	A : 0.06	G : 0.04	u : 0.02	C : 0.02	
G : 0.48	A : 0.26	U : 0.12	C : 0.10	u : 0.02	
U : 0.73	A : 0.12	C : 0.06	G : 0.06	u : 0.02	
U : 0.85	A : 0.06	C : 0.04	u : 0.02	G : 0.02	
U : 0.91	A : 0.04	u : 0.02	C : 0.02	
U : 0.83	C : 0.06	G : 0.06	A : 0.02	u : 0.02	
C : 0.55	A : 0.20	U : 0.12	G : 0.10	u : 0.02	
U : 0.77	A : 0.10	C : 0.06	G : 0.04	u : 0.02	
U : 0.85	C : 0.08	G : 0.04	u : 0.02	
U : 0.83	C : 0.08	G : 0.04	u : 0.02	A : 0.02	
U : 0.87	C : 0.06	A : 0.04	u : 0.02	
U : 0.77	C : 0.10	A : 0.06	G : 0.04	u : 0.02	
U : 0.34	C : 0.32	A : 0.22	G : 0.08	u : 0.02	

#score	788.5510204081645
#seq	49
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m1_run1.nuc.txt

#NT
uuuuuuu	chr19:44591538-44591762(+)$1	224	207	214	18.1296
uuuuuau	chr14:45669141-45669372(+)$1	231	197	204	14.2407
UUUUUGU	chr1:91381530-91381760(-)$1	230	165	172	14.5185
UUUUUUU	chr12:9092886-9093115(-)$1	229	2	9	18.1296
UGUUUUU	chr1:19234701-19234931(-)$1	230	219	226	13.6851
CUUUUUU	chr6:163992297-163992527(+)$1	230	14	21	13.8703
uuuuuuu	chr8:26513317-26513547(+)$1	230	0	7	18.1296
uuuuuuu	chr18:33716188-33716411(+)$1	223	184	191	18.1296
UUUUUCU	chr9:26840668-26840893(-)$1	225	40	47	14.3333
CUUUUUU	chr8:22879746-22879957(-)$1	211	63	70	13.8703
UUUUUUU	chr10:23730822-23731066(+)$1	244	173	180	18.1296
UAUUUUU	chr14:74182117-74182347(-)$1	230	28	35	13.6851
UUUUUCU	chr14:24658338-24658553(-)$1	215	156	163	14.3333
UUUUUUU	chr12:69968789-69969037(+)$1	248	54	61	18.1296
uuuuuuu	chr2:152976841-152977066(-)$1	225	137	144	18.1296
uuuuuuu	chr3:41281494-41281726(+)$1	232	0	7	18.1296
UUUUUUU	chr1:52811882-52812112(+)$1	230	26	33	18.1296
UUUAUUU	chr7:141357994-141358224(-)$1	230	210	217	13.7777
UUUUUGU	chr19:57804801-57805023(+)$1	222	47	54	14.5185
uuuuuuu	chr12:65090658-65090882(+)$1	224	182	189	18.1296
UUUUUGU	chr1:10043083-10043309(+)$1	226	126	133	14.5185
UUUUUUU	chr6:36569933-36570163(+)$1	230	148	155	18.1296
uuuuuuu	chr2:74442364-74442594(+)$1	230	186	193	18.1296
UUAUUUU	chr2:24464713-24464943(-)$1	230	14	21	13.7777
UUUCUUU	chr5:95128775-95129018(+)$1	243	125	132	13.5925
UUAUUUU	chr14:53238607-53238834(+)$1	227	121	128	13.7777
uuuuuuu	chr11:82924461-82924691(+)$1	230	134	141	18.1296
UUUUUGU	chr9:464736-464952(+)$1	216	79	86	14.5185
UUUUUUU	chr7:138992056-138992280(+)$1	224	3	10	18.1296
UAUUUUU	chr18:46446572-46446797(-)$1	225	183	190	13.6851
UUUUAUU	chr12:30781951-30782171(-)$1	220	49	56	13.8703
UUUUUUU	chr5:150088906-150089130(-)$1	224	79	86	18.1296
UUUAUUU	chr10:32299246-32299472(-)$1	226	114	121	13.7777
UGUUUUU	chr11:9467372-9467611(+)$1	239	218	225	13.6851
UUUAUUU	chr9:86276468-86276698(-)$1	230	26	33	13.7777
UUUUUUU	chr1:184660284-184660508(-)$1	224	60	67	18.1296
UUUUUGU	chr3:56657399-56657622(-)$1	223	8	15	14.5185
UUCUUUU	chr10:115668347-115668577(+)$1	230	111	118	13.5925
CUUUUUU	chr15:38645331-38645561(+)$1	230	8	15	13.8703
CUUUUUU	chr14:23494960-23495191(-)$1	231	8	15	13.8703
UUUUUUU	chr1:89300946-89301169(+)$1	223	198	205	18.1296
uuuuuuu	chr11:65404770-65405000(+)$1	230	78	85	18.1296
UUUUUAU	chr6:36653640-36653847(+)$1	207	164	171	14.2407
UUUUUUU	chr14:24635572-24635819(+)$1	247	17	24	18.1296
UUUUGUU	chr17:1326295-1326525(-)$1	230	83	90	13.7777
UUUUUUU	chr12:53908689-53908919(-)$1	230	205	212	18.1296
UUUUGUU	chr11:117038696-117038922(+)$1	226	161	168	13.7777
uuuuuuu	chr12:4410752-4410976(+)$1	224	98	105	18.1296
uuuuauu	chr5:112214104-112214324(+)$1	220	84	91	13.8703
UUUUUUU	chr12:4410310-4410540(+)$1	230	209	216	18.1296
UUUUAUU	chrX:108886035-108886265(-)$1	230	20	27	13.8703
UUUUUUU	chr2:174773620-174773845(-)$1	225	195	202	18.1296
UUUUUCU	chr2:55515085-55515315(-)$1	230	9	16	14.3333

#otherMatches

#Struct PSSM
ggggggg	chr1:150192541-150192771(-)$1	230	194	201	13.7777
:::::::	chr19:44591538-44591762(+)$1	224	207	214	18.1296
>======	chr14:45669141-45669372(+)$1	231	197	204	14.2407
iiiiiii	chr1:91381530-91381760(-)$1	230	165	172	14.5185
EEEE{DD	chr12:9092886-9093115(-)$1	229	2	9	18.1296
DD:::::	chr1:19234701-19234931(-)$1	230	219	226	13.6851
EEEIIII	chr6:163992297-163992527(+)$1	230	14	21	13.8703
:::::::	chr8:26513317-26513547(+)$1	230	0	7	18.1296
ddJJJJJ	chr18:33716188-33716411(+)$1	223	184	191	18.1296
cc22ccc	chr9:26840668-26840893(-)$1	225	40	47	14.3333
IIIIII{	chr8:22879746-22879957(-)$1	211	63	70	13.8703
666eeee	chr10:23730822-23731066(+)$1	244	173	180	18.1296
HHH{EEE	chr14:74182117-74182347(-)$1	230	28	35	13.6851
hhhhhhh	chr14:24658338-24658553(-)$1	215	156	163	14.3333
:::::::	chr12:69968789-69969037(+)$1	248	54	61	18.1296
hhhhh::	chr2:152976841-152977066(-)$1	225	137	144	18.1296
:::::::	chr3:41281494-41281726(+)$1	232	0	7	18.1296
o======	chr1:52811882-52812112(+)$1	230	26	33	18.1296
YCCC~~~	chr7:141357994-141358224(-)$1	230	210	217	13.7777
h:::GGG	chr19:57804801-57805023(+)$1	222	47	54	14.5185
:::::::	chr12:65090658-65090882(+)$1	224	182	189	18.1296
mmmffff	chr1:10043083-10043309(+)$1	226	126	133	14.5185
eeee!!e	chr6:36569933-36570163(+)$1	230	148	155	18.1296
ggg>>>>	chr2:74442364-74442594(+)$1	230	186	193	18.1296
:::::::	chr2:24464713-24464943(-)$1	230	14	21	13.7777
eeeehhh	chr5:95128775-95129018(+)$1	243	125	132	13.5925
=======	chr14:53238607-53238834(+)$1	227	121	128	13.7777
JJJJJJJ	chr11:82924461-82924691(+)$1	230	134	141	18.1296
!!bbccc	chr9:464736-464952(+)$1	216	79	86	14.5185
qqqqqqq	chr7:138992056-138992280(+)$1	224	3	10	18.1296
^^^^^^^	chr18:46446572-46446797(-)$1	225	183	190	13.6851
eeee[dd	chr12:30781951-30782171(-)$1	220	49	56	13.8703
4444ggg	chr5:150088906-150089130(-)$1	224	79	86	18.1296
:hhhhhh	chr10:32299246-32299472(-)$1	226	114	121	13.7777
Deeeeem	chr11:9467372-9467611(+)$1	239	218	225	13.6851
:::::::	chr9:86276468-86276698(-)$1	230	26	33	13.7777
:::::::	chr1:184660284-184660508(-)$1	224	60	67	18.1296
FFFFF==	chr3:56657399-56657622(-)$1	223	8	15	14.5185
^^^^^^^	chr10:115668347-115668577(+)$1	230	111	118	13.5925
cc&&&&&	chr15:38645331-38645561(+)$1	230	8	15	13.8703
JJJJJJJ	chr14:23494960-23495191(-)$1	231	8	15	13.8703
@@@@@@@	chr1:89300946-89301169(+)$1	223	198	205	18.1296
G::::::	chr11:65404770-65405000(+)$1	230	78	85	18.1296
iiiiii:	chr6:36653640-36653847(+)$1	207	164	171	14.2407
JJJJJJJ	chr14:24635572-24635819(+)$1	247	17	24	18.1296
c::::::	chr17:1326295-1326525(-)$1	230	83	90	13.7777
:::::::	chr12:53908689-53908919(-)$1	230	205	212	18.1296
c!!dddd	chr11:117038696-117038922(+)$1	226	161	168	13.7777
======z	chr12:4410752-4410976(+)$1	224	98	105	18.1296
[ddddll	chr5:112214104-112214324(+)$1	220	84	91	13.8703
:::::::	chr12:4410310-4410540(+)$1	230	209	216	18.1296
iiqqqqq	chrX:108886035-108886265(-)$1	230	20	27	13.8703
@@@@@@@	chr2:174773620-174773845(-)$1	225	195	202	18.1296
LLFFFFF	chr2:55515085-55515315(-)$1	230	9	16	14.3333

#DB
(((((((	chr1:150192541-150192771(-)$1	1	194	201	13.7777
.......	chr19:44591538-44591762(+)$1	1	207	214	18.1296
.))))))	chr14:45669141-45669372(+)$1	1	197	204	14.2407
)))))))	chr1:91381530-91381760(-)$1	1	165	172	14.5185
((((.((	chr12:9092886-9093115(-)$1	1	2	9	18.1296
)).....	chr1:19234701-19234931(-)$1	1	219	226	13.6851
(((((((	chr6:163992297-163992527(+)$1	1	14	21	13.8703
.......	chr8:26513317-26513547(+)$1	1	0	7	18.1296
)))))))	chr18:33716188-33716411(+)$1	1	184	191	18.1296
))..)))	chr9:26840668-26840893(-)$1	1	40	47	14.3333
((((((.	chr8:22879746-22879957(-)$1	1	63	70	13.8703
...))))	chr10:23730822-23731066(+)$1	1	173	180	18.1296
(((.(((	chr14:74182117-74182347(-)$1	1	28	35	13.6851
(((((((	chr14:24658338-24658553(-)$1	1	156	163	14.3333
.......	chr12:69968789-69969037(+)$1	1	54	61	18.1296
)))))..	chr2:152976841-152977066(-)$1	1	137	144	18.1296
.......	chr3:41281494-41281726(+)$1	1	0	7	18.1296
.))))))	chr1:52811882-52812112(+)$1	1	26	33	18.1296
.)))...	chr7:141357994-141358224(-)$1	1	210	217	13.7777
)...(((	chr19:57804801-57805023(+)$1	1	47	54	14.5185
.......	chr12:65090658-65090882(+)$1	1	182	189	18.1296
...))))	chr1:10043083-10043309(+)$1	1	126	133	14.5185
((((..(	chr6:36569933-36570163(+)$1	1	148	155	18.1296
)))....	chr2:74442364-74442594(+)$1	1	186	193	18.1296
.......	chr2:24464713-24464943(-)$1	1	14	21	13.7777
(((((((	chr5:95128775-95129018(+)$1	1	125	132	13.5925
(((((((	chr14:53238607-53238834(+)$1	1	121	128	13.7777
)))))))	chr11:82924461-82924691(+)$1	1	134	141	18.1296
..(((((	chr9:464736-464952(+)$1	1	79	86	14.5185
.......	chr7:138992056-138992280(+)$1	1	3	10	18.1296
.......	chr18:46446572-46446797(-)$1	1	183	190	13.6851
((((.((	chr12:30781951-30782171(-)$1	1	49	56	13.8703
....)))	chr5:150088906-150089130(-)$1	1	79	86	18.1296
.((((((	chr10:32299246-32299472(-)$1	1	114	121	13.7777
)(((((.	chr11:9467372-9467611(+)$1	1	218	225	13.6851
.......	chr9:86276468-86276698(-)$1	1	26	33	13.7777
.......	chr1:184660284-184660508(-)$1	1	60	67	18.1296
(((((((	chr3:56657399-56657622(-)$1	1	8	15	14.5185
.......	chr10:115668347-115668577(+)$1	1	111	118	13.5925
((.....	chr15:38645331-38645561(+)$1	1	8	15	13.8703
(((((((	chr14:23494960-23495191(-)$1	1	8	15	13.8703
.......	chr1:89300946-89301169(+)$1	1	198	205	18.1296
(......	chr11:65404770-65405000(+)$1	1	78	85	18.1296
)))))).	chr6:36653640-36653847(+)$1	1	164	171	14.2407
(((((((	chr14:24635572-24635819(+)$1	1	17	24	18.1296
)......	chr17:1326295-1326525(-)$1	1	83	90	13.7777
.......	chr12:53908689-53908919(-)$1	1	205	212	18.1296
(..((((	chr11:117038696-117038922(+)$1	1	161	168	13.7777
((((((.	chr12:4410752-4410976(+)$1	1	98	105	18.1296
.((((..	chr5:112214104-112214324(+)$1	1	84	91	13.8703
.......	chr12:4410310-4410540(+)$1	1	209	216	18.1296
((.....	chrX:108886035-108886265(-)$1	1	20	27	13.8703
.......	chr2:174773620-174773845(-)$1	1	195	202	18.1296
..(((((	chr2:55515085-55515315(-)$1	1	9	16	14.3333

#PSSM
U : 0.70	u : 0.22	C : 0.07	
U : 0.70	u : 0.22	G : 0.03	A : 0.03	
U : 0.70	u : 0.22	A : 0.05	C : 0.01	
U : 0.70	u : 0.22	A : 0.05	C : 0.01	
U : 0.70	u : 0.20	A : 0.03	G : 0.03	a : 0.01	
U : 0.61	u : 0.20	G : 0.09	C : 0.05	a : 0.01	A : 0.01	
U : 0.77	u : 0.22	

#score	850.2962962962957
#seq	54
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m3_run1.nuc.txt

#NT
CUUCUG	chr1:67451971-67452199(+)$1	228	187	193	11.2786
CUCCUG	chr9:35060316-35060562(-)$1	246	113	119	10.7868
AUGCUG	chr17:2237830-2238051(-)$1	221	71	77	10.9508
UUGCUG	chr4:174254238-174254465(-)$1	227	65	71	11.1147
CUGCUG	chr7:42966881-42967148(-)$1	267	128	134	13.9016
AUGCUG	chr13:31721995-31722239(-)$1	244	36	42	10.9508
CUACUG	chr5:162868131-162868418(+)$1	287	142	148	10.5409
CUUCUG	chr1:116931981-116932226(+)$1	245	145	151	11.2786
GUGCUG	chr15:66179994-66180225(+)$1	231	165	171	11.1967
CAGCUG	chr6:28359378-28359607(-)$1	229	15	21	9.8852
CUUCUG	chr1:32096195-32096447(-)$1	252	48	54	11.2786
AUGCUG	chr13:42876659-42876956(+)$1	297	94	100	10.9508
UUGCUG	chr10:51585206-51585443(+)$1	237	139	145	11.1147
CUCCUG	chr11:59434273-59434509(-)$1	236	220	226	10.7868
GUGCUG	chr22:38355273-38355493(+)$1	220	181	187	11.1967
CAGCUG	chr22:42052863-42053114(+)$1	251	48	54	9.8852
CUUCUG	chr8:17094751-17094977(-)$1	226	85	91	11.2786
AUGCUG	chrX:17767988-17768213(+)$1	225	2	8	10.9508
UUGCUG	chr3:183962357-183962605(-)$1	248	4	10	11.1147
CAGCUG	chr19:58319782-58320001(-)$1	219	5	11	9.8852
CAGCUG	chr19:3061070-3061357(-)$1	287	15	21	9.8852
CUGCUG	chr20:368679-368959(+)$1	280	153	159	13.9016
CUUCUG	chr17:61890487-61890720(+)$1	233	50	56	11.2786
CUGGUG	chr16:2312648-2312875(-)$1	227	8	14	9.7213
GUGCUG	chr3:196529862-196530083(+)$1	221	103	109	11.1967
UUGCUG	chr14:89075621-89075847(+)$1	226	9	15	11.1147
CUGCUG	chr19:3979705-3980164(-)$1	459	74	80	13.9016
CUCCUG	chr1:45242304-45242547(+)$1	243	125	131	10.7868
GUGCUG	chr14:103988675-103988942(-)$1	267	208	214	11.1967
GUGCUG	chr1:28527271-28527522(-)$1	251	13	19	11.1967
UUGCUG	chr12:50385743-50385983(-)$1	240	53	59	11.1147
CUGGUG	chr17:42284510-42284780(-)$1	270	13	19	9.7213
CUGCUG	chr11:14539092-14539360(-)$1	268	151	157	13.9016
CUGCUG	chr7:157000091-157000319(+)$1	228	183	189	13.9016
CUGCUG	chr22:29191942-29192207(-)$1	265	55	61	13.9016
CUGCUG	chr7:127230042-127230271(+)$1	229	126	132	13.9016
CUCCUG	chr19:580615-580838(+)$1	223	20	26	10.7868
CUGCUG	chr16:2011116-2011354(+)$1	238	218	224	13.9016
CUUCUG	chr3:53265383-53265612(-)$1	229	1	7	11.2786
CUGCUG	chr1:193110914-193111143(+)$1	229	30	36	13.9016
CUGAUG	chr7:50513128-50513356(-)$1	228	169	175	9.5573
GUGCUG	chr2:232320685-232320945(-)$1	260	244	250	11.1967
GUGCUG	chr1:3697596-3697876(-)$1	280	88	94	11.1967
UUGCUG	chr12:131357506-131357758(+)$1	252	182	188	11.1147
CUGCUG	chr19:50376400-50376628(-)$1	228	163	169	13.9016
CUGGUG	chrX:118724293-118724520(-)$1	227	81	87	9.7213
CUUCUG	chr8:67547016-67547251(-)$1	235	52	58	11.2786
UUGCUG	chrX:107976718-107977096(-)$1	378	364	370	11.1147
CUGCUG	chr12:58217673-58217897(-)$1	224	46	52	13.9016
CUGAUG	chr19:56172359-56172653(+)$1	294	7	13	9.5573
CUUCUG	chr1:45981229-45981453(-)$1	224	94	100	11.2786
CAGCUG	chr17:7158002-7158271(+)$1	269	40	46	9.8852
CUUCUG	chr16:31089796-31090033(+)$1	237	197	203	11.2786
CUACUG	chr5:122940370-122940608(+)$1	238	123	129	10.5409
CUUCUG	chr17:55038192-55038417(-)$1	225	111	117	11.2786
CUUCUG	chr15:89021026-89021278(+)$1	252	60	66	11.2786
AUGCUG	chr1:43852532-43852763(-)$1	231	203	209	10.9508
GUGCUG	chr10:77160789-77161079(-)$1	290	127	133	11.1967
CUCCUG	chr1:227170284-227170510(+)$1	226	80	86	10.7868
CAGCUG	chrX:118603742-118603998(+)$1	256	194	200	9.8852

#otherMatches

#Struct PSSM
ZZDDDD	chr16:68055622-68055868(-)$1	246	153	159	9.7213
bbnnnn	chr1:67451971-67452199(+)$1	228	187	193	11.2786
ff!!cc	chr9:35060316-35060562(-)$1	246	113	119	10.7868
gg"""d	chr17:2237830-2238051(-)$1	221	71	77	10.9508
======	chr4:174254238-174254465(-)$1	227	65	71	11.1147
JJJJJJ	chr7:42966881-42967148(-)$1	267	128	134	13.9016
PDDDD=	chr13:31721995-31722239(-)$1	244	36	42	10.9508
666666	chr5:162868131-162868418(+)$1	287	142	148	10.5409
YYEEEE	chr1:116931981-116932226(+)$1	245	145	151	11.2786
"bbmmm	chr15:66179994-66180225(+)$1	231	165	171	11.1967
:::fff	chr6:28359378-28359607(-)$1	229	15	21	9.8852
uuuddd	chr1:32096195-32096447(-)$1	252	48	54	11.2786
]dddd5	chr13:42876659-42876956(+)$1	297	94	100	10.9508
::dddd	chr10:51585206-51585443(+)$1	237	139	145	11.1147
22dddd	chr11:59434273-59434509(-)$1	236	220	226	10.7868
eeeee:	chr22:38355273-38355493(+)$1	220	181	187	11.1967
ddddhh	chr22:42052863-42053114(+)$1	251	48	54	9.8852
bb22ff	chr8:17094751-17094977(-)$1	226	85	91	11.2786
::CCC{	chrX:17767988-17768213(+)$1	225	2	8	10.9508
KKAMMM	chr3:183962357-183962605(-)$1	248	4	10	11.1147
EFFFFF	chr19:58319782-58320001(-)$1	219	5	11	9.8852
eooooo	chr19:3061070-3061357(-)$1	287	15	21	9.8852
e]bb]a	chr20:368679-368959(+)$1	280	153	159	13.9016
eeeett	chr17:61890487-61890720(+)$1	233	50	56	11.2786
hhdddd	chr16:2312648-2312875(-)$1	227	8	14	9.7213
fff[dd	chr3:196529862-196530083(+)$1	221	103	109	11.1967
DD{FFF	chr14:89075621-89075847(+)$1	226	9	15	11.1147
IIII{E	chr19:3979705-3980164(-)$1	459	74	80	13.9016
eeee:c	chr1:45242304-45242547(+)$1	243	125	131	10.7868
EEEEZZ	chr14:103988675-103988942(-)$1	267	208	214	11.1967
gggggF	chr1:28527271-28527522(-)$1	251	13	19	11.1967
gg]a]d	chr12:50385743-50385983(-)$1	240	53	59	11.1147
lllccc	chr17:42284510-42284780(-)$1	270	13	19	9.7213
dddd]h	chr11:14539092-14539360(-)$1	268	151	157	13.9016
nneeee	chr7:157000091-157000319(+)$1	228	183	189	13.9016
ddddpp	chr22:29191942-29192207(-)$1	265	55	61	13.9016
dd[ccc	chr7:127230042-127230271(+)$1	229	126	132	13.9016
EEEEE:	chr19:580615-580838(+)$1	223	20	26	10.7868
JJJJJe	chr16:2011116-2011354(+)$1	238	218	224	13.9016
fffffe	chr3:53265383-53265612(-)$1	229	1	7	11.2786
ddd22c	chr1:193110914-193111143(+)$1	229	30	36	13.9016
hhhbb3	chr7:50513128-50513356(-)$1	228	169	175	9.5573
}DDDDC	chr2:232320685-232320945(-)$1	260	244	250	11.1967
bb22cc	chr1:3697596-3697876(-)$1	280	88	94	11.1967
?????G	chr12:131357506-131357758(+)$1	252	182	188	11.1147
b]ccc]	chr19:50376400-50376628(-)$1	228	163	169	13.9016
hhhhhh	chrX:118724293-118724520(-)$1	227	81	87	9.7213
dd[ddd	chr8:67547016-67547251(-)$1	235	52	58	11.2786
YDDDD:	chrX:107976718-107977096(-)$1	378	364	370	11.1147
[ccc[d	chr12:58217673-58217897(-)$1	224	46	52	13.9016
::HHHH	chr19:56172359-56172653(+)$1	294	7	13	9.5573
ee!!bb	chr1:45981229-45981453(-)$1	224	94	100	11.2786
::EEEE	chr17:7158002-7158271(+)$1	269	40	46	9.8852
ddddCC	chr16:31089796-31090033(+)$1	237	197	203	11.2786
ddddmm	chr5:122940370-122940608(+)$1	238	123	129	10.5409
!!bb[c	chr17:55038192-55038417(-)$1	225	111	117	11.2786
::eeee	chr15:89021026-89021278(+)$1	252	60	66	11.2786
]dddd:	chr1:43852532-43852763(-)$1	231	203	209	10.9508
ffffff	chr10:77160789-77161079(-)$1	290	127	133	11.1967
a[eeee	chr1:227170284-227170510(+)$1	226	80	86	10.7868
qqqqqd	chrX:118603742-118603998(+)$1	256	194	200	9.8852

#DB
..))))	chr16:68055622-68055868(-)$1	1	153	159	9.7213
((....	chr1:67451971-67452199(+)$1	1	187	193	11.2786
((..((	chr9:35060316-35060562(-)$1	1	113	119	10.7868
((...(	chr17:2237830-2238051(-)$1	1	71	77	10.9508
((((((	chr4:174254238-174254465(-)$1	1	65	71	11.1147
((((((	chr7:42966881-42967148(-)$1	1	128	134	13.9016
.(((((	chr13:31721995-31722239(-)$1	1	36	42	10.9508
......	chr5:162868131-162868418(+)$1	1	142	148	10.5409
..))))	chr1:116931981-116932226(+)$1	1	145	151	11.2786
.((...	chr15:66179994-66180225(+)$1	1	165	171	11.1967
...(((	chr6:28359378-28359607(-)$1	1	15	21	9.8852
...)))	chr1:32096195-32096447(-)$1	1	48	54	11.2786
.)))).	chr13:42876659-42876956(+)$1	1	94	100	10.9508
..((((	chr10:51585206-51585443(+)$1	1	139	145	11.1147
..))))	chr11:59434273-59434509(-)$1	1	220	226	10.7868
))))).	chr22:38355273-38355493(+)$1	1	181	187	11.1967
((((((	chr22:42052863-42053114(+)$1	1	48	54	9.8852
))..))	chr8:17094751-17094977(-)$1	1	85	91	11.2786
..(((.	chrX:17767988-17768213(+)$1	1	2	8	10.9508
..(...	chr3:183962357-183962605(-)$1	1	4	10	11.1147
((((((	chr19:58319782-58320001(-)$1	1	5	11	9.8852
(.....	chr19:3061070-3061357(-)$1	1	15	21	9.8852
).)).)	chr20:368679-368959(+)$1	1	153	159	13.9016
((((..	chr17:61890487-61890720(+)$1	1	50	56	11.2786
((((((	chr16:2312648-2312875(-)$1	1	8	14	9.7213
(((.((	chr3:196529862-196530083(+)$1	1	103	109	11.1967
((.(((	chr14:89075621-89075847(+)$1	1	9	15	11.1147
((((.(	chr19:3979705-3980164(-)$1	1	74	80	13.9016
)))).(	chr1:45242304-45242547(+)$1	1	125	131	10.7868
))))..	chr14:103988675-103988942(-)$1	1	208	214	11.1967
)))))(	chr1:28527271-28527522(-)$1	1	13	19	11.1967
)).).)	chr12:50385743-50385983(-)$1	1	53	59	11.1147
...)))	chr17:42284510-42284780(-)$1	1	13	19	9.7213
)))).)	chr11:14539092-14539360(-)$1	1	151	157	13.9016
..))))	chr7:157000091-157000319(+)$1	1	183	189	13.9016
((((..	chr22:29191942-29192207(-)$1	1	55	61	13.9016
((.(((	chr7:127230042-127230271(+)$1	1	126	132	13.9016
(((((.	chr19:580615-580838(+)$1	1	20	26	10.7868
)))))(	chr16:2011116-2011354(+)$1	1	218	224	13.9016
((((((	chr3:53265383-53265612(-)$1	1	1	7	11.2786
)))..)	chr1:193110914-193111143(+)$1	1	30	36	13.9016
))))).	chr7:50513128-50513356(-)$1	1	169	175	9.5573
.)))))	chr2:232320685-232320945(-)$1	1	244	250	11.1967
))..))	chr1:3697596-3697876(-)$1	1	88	94	11.1967
.....)	chr12:131357506-131357758(+)$1	1	182	188	11.1147
).))).	chr19:50376400-50376628(-)$1	1	163	169	13.9016
))))))	chrX:118724293-118724520(-)$1	1	81	87	9.7213
((.(((	chr8:67547016-67547251(-)$1	1	52	58	11.2786
.)))).	chrX:107976718-107977096(-)$1	1	364	370	11.1147
.(((.(	chr12:58217673-58217897(-)$1	1	46	52	13.9016
..((((	chr19:56172359-56172653(+)$1	1	7	13	9.5573
((..((	chr1:45981229-45981453(-)$1	1	94	100	11.2786
..((((	chr17:7158002-7158271(+)$1	1	40	46	9.8852
))))))	chr16:31089796-31090033(+)$1	1	197	203	11.2786
((((..	chr5:122940370-122940608(+)$1	1	123	129	10.5409
..((.(	chr17:55038192-55038417(-)$1	1	111	117	11.2786
..((((	chr15:89021026-89021278(+)$1	1	60	66	11.2786
.)))).	chr1:43852532-43852763(-)$1	1	203	209	10.9508
))))))	chr10:77160789-77161079(-)$1	1	127	133	11.1967
(.((((	chr1:227170284-227170510(+)$1	1	80	86	10.7868
.....)	chrX:118603742-118603998(+)$1	1	194	200	9.8852

#PSSM
C : 0.67	G : 0.13	U : 0.11	A : 0.08	
U : 0.90	A : 0.09	
G : 0.70	U : 0.18	C : 0.08	A : 0.03	
C : 0.90	G : 0.06	A : 0.03	
U : 1.00	
G : 1.00	

#score	691.4426229508202
#seq	61
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m2_run1.nuc.txt

#NT
AUUUUU	chr10:5804892-5805172(+)$1	280	243	249	18.0000
AUUUUU	chr3:142729561-142729785(+)$1	224	78	84	18.0000
AUUUUU	chr10:79800331-79800557(+)$1	226	88	94	18.0000
AUUUUU	chr10:85912794-85913030(+)$1	236	154	160	18.0000
AUUUUU	chr1:51738141-51738365(+)$1	224	193	199	18.0000
AUUUUU	chr7:94296657-94296908(+)$1	251	143	149	18.0000
AUUUUU	chr6:160176841-160177069(+)$1	228	66	72	18.0000
AUUUUU	chr12:46580446-46580673(-)$1	227	131	137	18.0000
AUUUUU	chr12:120899627-120899874(-)$1	247	67	73	18.0000
AUUUUU	chr6:79646466-79646694(-)$1	228	133	139	18.0000
AUUUUU	chr13:113918448-113918684(+)$1	236	33	39	18.0000
AUUUUU	chr1:33475862-33476111(-)$1	249	0	6	18.0000
AUUUUU	chr21:40768802-40769028(+)$1	226	171	177	18.0000
AUUUUU	chr2:175939171-175939433(-)$1	262	197	203	18.0000
AUUUUU	chr14:90871511-90871767(+)$1	256	225	231	18.0000
AUUUUU	chr1:113455529-113455755(-)$1	226	39	45	18.0000
AUUUUU	chr1:210416210-210416445(+)$1	235	139	145	18.0000
AUUUUU	chr11:93212296-93212525(-)$1	229	1	7	18.0000
AUUUUU	chr12:54627992-54628239(-)$1	247	77	83	18.0000
AUUUUU	chr1:25169489-25169745(+)$1	256	170	176	18.0000
AUUUUU	chrX:147031241-147031466(+)$1	225	102	108	18.0000
auuuuu	chr12:56295240-56295494(-)$1	254	241	247	18.0000
AUUUUU	chr13:49783446-49783676(+)$1	230	64	70	18.0000
AUUUUU	chr21:43407105-43407347(-)$1	242	77	83	18.0000
AUUUUU	chr22:22841248-22841482(-)$1	234	53	59	18.0000
AUUUUU	chr1:224577102-224577382(-)$1	280	136	142	18.0000
AUUUUU	chr19:44681893-44682133(+)$1	240	129	135	18.0000
AUUUUU	chr12:122499007-122499235(+)$1	228	17	23	18.0000
AUUUUU	chr11:58386131-58386354(+)$1	223	192	198	18.0000
auuuuu	chrX:56592370-56592603(+)$1	233	4	10	18.0000
AUUUUU	chr1:8482692-8482957(-)$1	265	200	206	18.0000
AUUUUU	chr12:120899398-120899664(-)$1	266	62	68	18.0000
AUUUUU	chr18:32918217-32918445(-)$1	228	48	54	18.0000
AUUUUU	chr7:139030358-139030585(+)$1	227	166	172	18.0000
auuuuu	chr10:102724480-102724701(+)$1	221	38	44	18.0000

#otherMatches

#Struct PSSM
JJJJJJ	chr1:245017552-245017830(-)$1	278	219	225	18.0000
ddd"""	chr10:5804892-5805172(+)$1	280	243	249	18.0000
WWWWWW	chr3:142729561-142729785(+)$1	224	78	84	18.0000
IIII::	chr10:79800331-79800557(+)$1	226	88	94	18.0000
55eeee	chr10:85912794-85913030(+)$1	236	154	160	18.0000
ssssss	chr1:51738141-51738365(+)$1	224	193	199	18.0000
fffqqq	chr7:94296657-94296908(+)$1	251	143	149	18.0000
::hhhh	chr6:160176841-160177069(+)$1	228	66	72	18.0000
666666	chr12:46580446-46580673(-)$1	227	131	137	18.0000
mmmmdd	chr12:120899627-120899874(-)$1	247	67	73	18.0000
^^^^^h	chr6:79646466-79646694(-)$1	228	133	139	18.0000
ggggnn	chr13:113918448-113918684(+)$1	236	33	39	18.0000
:::eee	chr1:33475862-33476111(-)$1	249	0	6	18.0000
iiiii:	chr21:40768802-40769028(+)$1	226	171	177	18.0000
5ccc22	chr2:175939171-175939433(-)$1	262	197	203	18.0000
::::::	chr14:90871511-90871767(+)$1	256	225	231	18.0000
fggggg	chr1:113455529-113455755(-)$1	226	39	45	18.0000
qqqqqq	chr1:210416210-210416445(+)$1	235	139	145	18.0000
::::EE	chr11:93212296-93212525(-)$1	229	1	7	18.0000
ssssss	chr12:54627992-54628239(-)$1	247	77	83	18.0000
ii::::	chr1:25169489-25169745(+)$1	256	170	176	18.0000
gggttt	chrX:147031241-147031466(+)$1	225	102	108	18.0000
f:::::	chr12:56295240-56295494(-)$1	254	241	247	18.0000
::::::	chr13:49783446-49783676(+)$1	230	64	70	18.0000
bmmmmb	chr21:43407105-43407347(-)$1	242	77	83	18.0000
ggggg:	chr22:22841248-22841482(-)$1	234	53	59	18.0000
::::::	chr1:224577102-224577382(-)$1	280	136	142	18.0000
qqqqdd	chr19:44681893-44682133(+)$1	240	129	135	18.0000
CCOOOO	chr12:122499007-122499235(+)$1	228	17	23	18.0000
======	chr11:58386131-58386354(+)$1	223	192	198	18.0000
::::::	chrX:56592370-56592603(+)$1	233	4	10	18.0000
ccc]ff	chr1:8482692-8482957(-)$1	265	200	206	18.0000
ffffff	chr12:120899398-120899664(-)$1	266	62	68	18.0000
qqqiii	chr18:32918217-32918445(-)$1	228	48	54	18.0000
hhhhnn	chr7:139030358-139030585(+)$1	227	166	172	18.0000
hhhhhh	chr10:102724480-102724701(+)$1	221	38	44	18.0000

#DB
))))))	chr1:245017552-245017830(-)$1	1	219	225	18.0000
(((...	chr10:5804892-5805172(+)$1	1	243	249	18.0000
......	chr3:142729561-142729785(+)$1	1	78	84	18.0000
((((..	chr10:79800331-79800557(+)$1	1	88	94	18.0000
..))))	chr10:85912794-85913030(+)$1	1	154	160	18.0000
......	chr1:51738141-51738365(+)$1	1	193	199	18.0000
(((...	chr7:94296657-94296908(+)$1	1	143	149	18.0000
..((((	chr6:160176841-160177069(+)$1	1	66	72	18.0000
......	chr12:46580446-46580673(-)$1	1	131	137	18.0000
....))	chr12:120899627-120899874(-)$1	1	67	73	18.0000
.....)	chr6:79646466-79646694(-)$1	1	133	139	18.0000
((((..	chr13:113918448-113918684(+)$1	1	33	39	18.0000
...(((	chr1:33475862-33476111(-)$1	1	0	6	18.0000
))))).	chr21:40768802-40769028(+)$1	1	171	177	18.0000
.)))..	chr2:175939171-175939433(-)$1	1	197	203	18.0000
......	chr14:90871511-90871767(+)$1	1	225	231	18.0000
((((((	chr1:113455529-113455755(-)$1	1	39	45	18.0000
......	chr1:210416210-210416445(+)$1	1	139	145	18.0000
....((	chr11:93212296-93212525(-)$1	1	1	7	18.0000
......	chr12:54627992-54628239(-)$1	1	77	83	18.0000
))....	chr1:25169489-25169745(+)$1	1	170	176	18.0000
(((...	chrX:147031241-147031466(+)$1	1	102	108	18.0000
).....	chr12:56295240-56295494(-)$1	1	241	247	18.0000
......	chr13:49783446-49783676(+)$1	1	64	70	18.0000
(....)	chr21:43407105-43407347(-)$1	1	77	83	18.0000
))))).	chr22:22841248-22841482(-)$1	1	53	59	18.0000
......	chr1:224577102-224577382(-)$1	1	136	142	18.0000
....))	chr19:44681893-44682133(+)$1	1	129	135	18.0000
((....	chr12:122499007-122499235(+)$1	1	17	23	18.0000
((((((	chr11:58386131-58386354(+)$1	1	192	198	18.0000
......	chrX:56592370-56592603(+)$1	1	4	10	18.0000
))).))	chr1:8482692-8482957(-)$1	1	200	206	18.0000
((((((	chr12:120899398-120899664(-)$1	1	62	68	18.0000
...)))	chr18:32918217-32918445(-)$1	1	48	54	18.0000
((((..	chr7:139030358-139030585(+)$1	1	166	172	18.0000
((((((	chr10:102724480-102724701(+)$1	1	38	44	18.0000

#PSSM
A : 0.91	a : 0.08	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	

#score	648.0000000000001
#seq	36
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_UTR_m3_run2.nuc.txt

#NT
UAAAA	chr3:145788050-145788278(-)$1	228	74	79	14.9999
UAAAA	chr16:69737330-69737542(+)$1	212	164	169	14.9999
UAAAA	chr8:9635514-9635738(+)$1	224	139	144	14.9999
UAAAA	chr3:136056605-136056827(-)$1	222	29	34	14.9999
UAAAA	chr14:53238284-53238531(+)$1	247	229	234	14.9999
UAAAA	chr12:76439601-76439819(-)$1	218	46	51	14.9999
uaaaa	chr12:96672446-96672674(-)$1	228	103	108	14.9999
UAAAA	chr10:18969474-18969694(+)$1	220	123	128	14.9999
UAAAA	chr7:106843762-106843981(-)$1	219	187	192	14.9999
uaaaa	chr7:148700432-148700656(-)$1	224	102	107	14.9999
UAAAA	chr14:55309283-55309512(-)$1	229	19	24	14.9999
UAAAA	chr8:67542653-67542881(-)$1	228	39	44	14.9999
UAAAA	chr6:71269619-71269841(+)$1	222	7	12	14.9999
UAAAA	chr3:33191861-33192096(-)$1	235	6	11	14.9999
UAAAA	chr12:27118723-27118941(+)$1	218	26	31	14.9999
UAAAA	chr12:1018641-1018861(+)$1	220	6	11	14.9999
UAAAA	chr2:68406671-68406892(-)$1	221	70	75	14.9999
UAAAA	chr14:103809274-103809494(+)$1	220	48	53	14.9999
UAAAA	chr15:45010146-45010371(+)$1	225	187	192	14.9999
UAAAA	chr19:40575929-40576164(-)$1	235	111	116	14.9999
uaaaa	chr11:111846420-111846655(+)$1	235	114	119	14.9999
UAAAA	chr17:47373322-47373541(-)$1	219	154	159	14.9999
UAAAA	chr19:38029807-38030027(+)$1	220	77	82	14.9999
UAAAA	chr14:20754428-20754646(-)$1	218	81	86	14.9999
UAAAA	chr15:68586025-68586257(+)$1	232	14	19	14.9999
uAAAA	chr6:44123119-44123345(+)$1	226	110	115	14.9999
UAAAA	chr1:171283322-171283548(+)$1	226	154	159	14.9999
UAAAA	chr6:8079644-8079868(-)$1	224	13	18	14.9999
UAAAA	chr4:77968462-77968682(-)$1	220	16	21	14.9999
UAAAA	chr2:54001933-54002159(+)$1	226	137	142	14.9999
UAAAA	chr6:139500323-139500549(+)$1	226	80	85	14.9999
UAAAA	chr10:97629309-97629546(-)$1	237	88	93	14.9999
UAAAA	chr12:57488882-57489103(+)$1	221	3	8	14.9999
UAAAA	chr3:73114975-73115206(+)$1	231	8	13	14.9999
UAAAA	chr5:43706076-43706307(+)$1	231	57	62	14.9999
UAAAA	chr17:17969239-17969465(+)$1	226	87	92	14.9999
UAAAA	chr4:40157728-40157948(+)$1	220	48	53	14.9999
UAAAA	chr1:109513324-109513543(-)$1	219	157	162	14.9999
UAAAA	chr3:190023414-190023635(-)$1	221	132	137	14.9999
UAAAA	chr12:54632284-54632519(-)$1	235	143	148	14.9999
uaaaa	chr19:21304046-21304282(+)$1	236	129	134	14.9999
UAAAA	chr7:64433412-64433633(-)$1	221	27	32	14.9999
UAAAA	chr12:88442117-88442339(+)$1	222	79	84	14.9999
UAAAA	chr21:33043453-33043674(-)$1	221	184	189	14.9999
UAAAA	chr3:44450495-44450716(+)$1	221	64	69	14.9999
UAAAA	chr3:113528331-113528556(+)$1	225	106	111	14.9999
UAAAA	chr5:40715224-40715446(-)$1	222	53	58	14.9999
UAAAA	chr1:214209973-214210209(+)$1	236	36	41	14.9999
UAAAA	chr16:4560660-4560883(-)$1	223	127	132	14.9999
UAAAA	chr5:38941992-38942216(-)$1	224	119	124	14.9999
uaaaa	chr5:79275643-79275866(-)$1	223	63	68	14.9999
UAAAA	chr12:132197643-132197869(+)$1	226	23	28	14.9999
UAAAA	chr12:109179662-109179891(-)$1	229	105	110	14.9999
UAAAA	chr1:192987450-192987675(-)$1	225	32	37	14.9999
UAAAA	chr1:230972845-230973074(-)$1	229	198	203	14.9999
uaaaa	chr2:191798103-191798323(+)$1	220	57	62	14.9999
UAAAA	chr18:723128-723363(-)$1	235	107	112	14.9999
UAAAA	chr19:44741257-44741475(+)$1	218	112	117	14.9999
UAAAA	chr13:30777257-30777485(-)$1	228	102	107	14.9999
UAAAA	chr5:52099006-52099227(+)$1	221	72	77	14.9999
UAAAA	chr12:66741923-66742148(-)$1	225	115	120	14.9999
UAAAA	chr13:77574999-77575222(+)$1	223	44	49	14.9999
UAAAA	chr1:20235190-20235414(+)$1	224	92	97	14.9999
UAAAA	chr17:28795024-28795246(+)$1	222	30	35	14.9999
UAAAA	chr13:73283564-73283784(-)$1	220	9	14	14.9999
UAAAA	chr5:133942057-133942280(-)$1	223	138	143	14.9999
UAAAA	chr4:140309296-140309521(+)$1	225	105	110	14.9999
UAAAA	chr17:5336043-5336290(-)$1	247	171	176	14.9999
UAAAA	chr13:25914443-25914671(+)$1	228	106	111	14.9999

#otherMatches

#Struct PSSM
((===	chr3:194123438-194123659(-)$1	221	18	23	14.9999
ccJJJ	chr3:145788050-145788278(-)$1	228	74	79	14.9999
GGG//	chr16:69737330-69737542(+)$1	212	164	169	14.9999
ggggu	chr8:9635514-9635738(+)$1	224	139	144	14.9999
hhhhe	chr3:136056605-136056827(-)$1	222	29	34	14.9999
:::::	chr14:53238284-53238531(+)$1	247	229	234	14.9999
qqeee	chr12:76439601-76439819(-)$1	218	46	51	14.9999
fffff	chr12:96672446-96672674(-)$1	228	103	108	14.9999
ddddg	chr10:18969474-18969694(+)$1	220	123	128	14.9999
hnnnn	chr7:106843762-106843981(-)$1	219	187	192	14.9999
fffff	chr7:148700432-148700656(-)$1	224	102	107	14.9999
^^^^^	chr14:55309283-55309512(-)$1	229	19	24	14.9999
mmmdd	chr8:67542653-67542881(-)$1	228	39	44	14.9999
hhh==	chr6:71269619-71269841(+)$1	222	7	12	14.9999
:::FF	chr3:33191861-33192096(-)$1	235	6	11	14.9999
hhhhh	chr12:27118723-27118941(+)$1	218	26	31	14.9999
IIIII	chr12:1018641-1018861(+)$1	220	6	11	14.9999
hhppp	chr2:68406671-68406892(-)$1	221	70	75	14.9999
:::::	chr14:103809274-103809494(+)$1	220	48	53	14.9999
:::::	chr15:45010146-45010371(+)$1	225	187	192	14.9999
:::::	chr19:40575929-40576164(-)$1	235	111	116	14.9999
^^^^^	chr11:111846420-111846655(+)$1	235	114	119	14.9999
5555c	chr17:47373322-47373541(-)$1	219	154	159	14.9999
WWWWW	chr19:38029807-38030027(+)$1	220	77	82	14.9999
UUUUU	chr14:20754428-20754646(-)$1	218	81	86	14.9999
####g	chr15:68586025-68586257(+)$1	232	14	19	14.9999
uuuuu	chr6:44123119-44123345(+)$1	226	110	115	14.9999
gmmmm	chr1:171283322-171283548(+)$1	226	154	159	14.9999
e####	chr6:8079644-8079868(-)$1	224	13	18	14.9999
eeeem	chr4:77968462-77968682(-)$1	220	16	21	14.9999
HHH::	chr2:54001933-54002159(+)$1	226	137	142	14.9999
cc666	chr6:139500323-139500549(+)$1	226	80	85	14.9999
ggggg	chr10:97629309-97629546(-)$1	237	88	93	14.9999
DD:ee	chr12:57488882-57489103(+)$1	221	3	8	14.9999
:::::	chr3:73114975-73115206(+)$1	231	8	13	14.9999
ffff"	chr5:43706076-43706307(+)$1	231	57	62	14.9999
:::::	chr17:17969239-17969465(+)$1	226	87	92	14.9999
'''''	chr4:40157728-40157948(+)$1	220	48	53	14.9999
GGG}E	chr1:109513324-109513543(-)$1	219	157	162	14.9999
gg22g	chr3:190023414-190023635(-)$1	221	132	137	14.9999
:====	chr12:54632284-54632519(-)$1	235	143	148	14.9999
:::::	chr19:21304046-21304282(+)$1	236	129	134	14.9999
SIIII	chr7:64433412-64433633(-)$1	221	27	32	14.9999
ellle	chr12:88442117-88442339(+)$1	222	79	84	14.9999
iiii[	chr21:33043453-33043674(-)$1	221	184	189	14.9999
FFFFF	chr3:44450495-44450716(+)$1	221	64	69	14.9999
eee[b	chr3:113528331-113528556(+)$1	225	106	111	14.9999
eeeee	chr5:40715224-40715446(-)$1	222	53	58	14.9999
''''e	chr1:214209973-214210209(+)$1	236	36	41	14.9999
ooooo	chr16:4560660-4560883(-)$1	223	127	132	14.9999
d4444	chr5:38941992-38942216(-)$1	224	119	124	14.9999
JJJJJ	chr5:79275643-79275866(-)$1	223	63	68	14.9999
ccooo	chr12:132197643-132197869(+)$1	226	23	28	14.9999
g22cc	chr12:109179662-109179891(-)$1	229	105	110	14.9999
:::::	chr1:192987450-192987675(-)$1	225	32	37	14.9999
dd22c	chr1:230972845-230973074(-)$1	229	198	203	14.9999
####f	chr2:191798103-191798323(+)$1	220	57	62	14.9999
cc444	chr18:723128-723363(-)$1	235	107	112	14.9999
^^^^^	chr19:44741257-44741475(+)$1	218	112	117	14.9999
fffff	chr13:30777257-30777485(-)$1	228	102	107	14.9999
:::::	chr5:52099006-52099227(+)$1	221	72	77	14.9999
dpppp	chr12:66741923-66742148(-)$1	225	115	120	14.9999
ggggg	chr13:77574999-77575222(+)$1	223	44	49	14.9999
eee::	chr1:20235190-20235414(+)$1	224	92	97	14.9999
ggggg	chr17:28795024-28795246(+)$1	222	30	35	14.9999
::::d	chr13:73283564-73283784(-)$1	220	9	14	14.9999
:::::	chr5:133942057-133942280(-)$1	223	138	143	14.9999
+++++	chr4:140309296-140309521(+)$1	225	105	110	14.9999
=====	chr17:5336043-5336290(-)$1	247	171	176	14.9999
eeeee	chr13:25914443-25914671(+)$1	228	106	111	14.9999

#DB
..(((	chr3:194123438-194123659(-)$1	1	18	23	14.9999
)))))	chr3:145788050-145788278(-)$1	1	74	79	14.9999
)))..	chr16:69737330-69737542(+)$1	1	164	169	14.9999
((((.	chr8:9635514-9635738(+)$1	1	139	144	14.9999
(((((	chr3:136056605-136056827(-)$1	1	29	34	14.9999
.....	chr14:53238284-53238531(+)$1	1	229	234	14.9999
..)))	chr12:76439601-76439819(-)$1	1	46	51	14.9999
(((((	chr12:96672446-96672674(-)$1	1	103	108	14.9999
)))))	chr10:18969474-18969694(+)$1	1	123	128	14.9999
(....	chr7:106843762-106843981(-)$1	1	187	192	14.9999
)))))	chr7:148700432-148700656(-)$1	1	102	107	14.9999
.....	chr14:55309283-55309512(-)$1	1	19	24	14.9999
...))	chr8:67542653-67542881(-)$1	1	39	44	14.9999
(((((	chr6:71269619-71269841(+)$1	1	7	12	14.9999
...((	chr3:33191861-33192096(-)$1	1	6	11	14.9999
(((((	chr12:27118723-27118941(+)$1	1	26	31	14.9999
(((((	chr12:1018641-1018861(+)$1	1	6	11	14.9999
((...	chr2:68406671-68406892(-)$1	1	70	75	14.9999
.....	chr14:103809274-103809494(+)$1	1	48	53	14.9999
.....	chr15:45010146-45010371(+)$1	1	187	192	14.9999
.....	chr19:40575929-40576164(-)$1	1	111	116	14.9999
.....	chr11:111846420-111846655(+)$1	1	114	119	14.9999
....)	chr17:47373322-47373541(-)$1	1	154	159	14.9999
.....	chr19:38029807-38030027(+)$1	1	77	82	14.9999
.....	chr14:20754428-20754646(-)$1	1	81	86	14.9999
....(	chr15:68586025-68586257(+)$1	1	14	19	14.9999
.....	chr6:44123119-44123345(+)$1	1	110	115	14.9999
(....	chr1:171283322-171283548(+)$1	1	154	159	14.9999
(....	chr6:8079644-8079868(-)$1	1	13	18	14.9999
((((.	chr4:77968462-77968682(-)$1	1	16	21	14.9999
)))..	chr2:54001933-54002159(+)$1	1	137	142	14.9999
))...	chr6:139500323-139500549(+)$1	1	80	85	14.9999
(((((	chr10:97629309-97629546(-)$1	1	88	93	14.9999
((.((	chr12:57488882-57489103(+)$1	1	3	8	14.9999
.....	chr3:73114975-73115206(+)$1	1	8	13	14.9999
((((.	chr5:43706076-43706307(+)$1	1	57	62	14.9999
.....	chr17:17969239-17969465(+)$1	1	87	92	14.9999
.....	chr4:40157728-40157948(+)$1	1	48	53	14.9999
))).)	chr1:109513324-109513543(-)$1	1	157	162	14.9999
))..)	chr3:190023414-190023635(-)$1	1	132	137	14.9999
.((((	chr12:54632284-54632519(-)$1	1	143	148	14.9999
.....	chr19:21304046-21304282(+)$1	1	129	134	14.9999
.((((	chr7:64433412-64433633(-)$1	1	27	32	14.9999
(...)	chr12:88442117-88442339(+)$1	1	79	84	14.9999
((((.	chr21:33043453-33043674(-)$1	1	184	189	14.9999
(((((	chr3:44450495-44450716(+)$1	1	64	69	14.9999
(((.(	chr3:113528331-113528556(+)$1	1	106	111	14.9999
)))))	chr5:40715224-40715446(-)$1	1	53	58	14.9999
....(	chr1:214209973-214210209(+)$1	1	36	41	14.9999
.....	chr16:4560660-4560883(-)$1	1	127	132	14.9999
)....	chr5:38941992-38942216(-)$1	1	119	124	14.9999
(((((	chr5:79275643-79275866(-)$1	1	63	68	14.9999
((...	chr12:132197643-132197869(+)$1	1	23	28	14.9999
)..))	chr12:109179662-109179891(-)$1	1	105	110	14.9999
.....	chr1:192987450-192987675(-)$1	1	32	37	14.9999
))..)	chr1:230972845-230973074(-)$1	1	198	203	14.9999
....(	chr2:191798103-191798323(+)$1	1	57	62	14.9999
))...	chr18:723128-723363(-)$1	1	107	112	14.9999
.....	chr19:44741257-44741475(+)$1	1	112	117	14.9999
)))))	chr13:30777257-30777485(-)$1	1	102	107	14.9999
.....	chr5:52099006-52099227(+)$1	1	72	77	14.9999
(....	chr12:66741923-66742148(-)$1	1	115	120	14.9999
)))))	chr13:77574999-77575222(+)$1	1	44	49	14.9999
)))..	chr1:20235190-20235414(+)$1	1	92	97	14.9999
(((((	chr17:28795024-28795246(+)$1	1	30	35	14.9999
....(	chr13:73283564-73283784(-)$1	1	9	14	14.9999
.....	chr5:133942057-133942280(-)$1	1	138	143	14.9999
.....	chr4:140309296-140309521(+)$1	1	105	110	14.9999
)))))	chr17:5336043-5336290(-)$1	1	171	176	14.9999
(((((	chr13:25914443-25914671(+)$1	1	106	111	14.9999

#PSSM
U : 0.89	u : 0.10	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	

#score	1049.9999999999995
#seq	70
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_UTR_m2_run1.nuc.txt

#NT
UCUU	chr2:192288749-192288969(+)$1	220	48	52	12.0000
ucuu	chr8:81434954-81435187(+)$1	233	8	12	12.0000
UCUU	chr8:48890586-48890809(+)$1	223	28	32	12.0000
ucuu	chr6:44416629-44416853(+)$1	224	118	122	12.0000
UCUU	chr11:93430982-93431206(+)$1	224	75	79	12.0000
UCUU	chr5:125960484-125960702(+)$1	218	174	178	12.0000
UCUU	chr2:87004575-87004792(+)$1	217	112	116	12.0000
UCUU	chrX:123234523-123234744(+)$1	221	139	143	12.0000
UCUU	chr5:71501722-71501954(+)$1	232	18	22	12.0000
UCUU	chr3:38532700-38532926(+)$1	226	204	208	12.0000
UCUU	chrX:53402548-53402772(-)$1	224	105	109	12.0000
UCUU	chr5:70810705-70810925(+)$1	220	9	13	12.0000
UCUU	chr14:103810047-103810267(+)$1	220	174	178	12.0000
UCUU	chr13:25906666-25906884(+)$1	218	100	104	12.0000
UCUU	chr4:87735626-87735853(+)$1	227	29	33	12.0000
UCUU	chr2:128461986-128462209(-)$1	223	104	108	12.0000
UCUU	chr2:87003471-87003695(+)$1	224	146	150	12.0000
UCUU	chr6:64292704-64292928(+)$1	224	18	22	12.0000
UCUU	chr3:48200209-48200428(-)$1	219	48	52	12.0000
UCUU	chr11:130100966-130101184(-)$1	218	113	117	12.0000
UCUU	chr6:139501050-139501273(+)$1	223	91	95	12.0000
UCUU	chr10:8056857-8057079(+)$1	222	154	158	12.0000
UCUU	chr5:143538113-143538340(-)$1	227	132	136	12.0000
UCUU	chr17:47131292-47131510(+)$1	218	150	154	12.0000
UCUU	chr7:6442842-6443063(+)$1	221	92	96	12.0000
UCUU	chr10:105786953-105787175(+)$1	222	4	8	12.0000
UCUU	chr12:57627441-57627660(+)$1	219	75	79	12.0000
UCUU	chr19:2101080-2101300(-)$1	220	85	89	12.0000
UCUU	chr16:69693675-69693898(+)$1	223	108	112	12.0000
UCUU	chr10:99946188-99946409(+)$1	221	65	69	12.0000
UCUU	chr5:71501458-71501676(+)$1	218	145	149	12.0000
UCUU	chr2:224740663-224740884(-)$1	221	25	29	12.0000
UCUU	chr19:32875548-32875768(+)$1	220	47	51	12.0000
UCUU	chr9:91091214-91091432(+)$1	218	184	188	12.0000
UCUU	chr5:81570017-81570237(-)$1	220	92	96	12.0000
UCUU	chr1:99225577-99225795(+)$1	218	133	137	12.0000
UCUU	chr1:32641789-32642007(+)$1	218	123	127	12.0000
UCUU	chr6:64421120-64421340(+)$1	220	3	7	12.0000
UCUU	chr2:30785018-30785239(+)$1	221	20	24	12.0000
UCUU	chr8:87573010-87573231(+)$1	221	63	67	12.0000
UCUU	chr2:37326470-37326688(-)$1	218	20	24	12.0000
UCUU	chr5:56217996-56218216(-)$1	220	103	107	12.0000
UCUU	chr2:113496308-113496527(-)$1	219	28	32	12.0000
UCUU	chr10:70744019-70744238(+)$1	219	5	9	12.0000
UCUU	chr18:67994958-67995177(+)$1	219	61	65	12.0000
UCUU	chr5:167977378-167977602(-)$1	224	2	6	12.0000
UCUU	chr13:41701751-41701972(-)$1	221	95	99	12.0000
UCUU	chr2:159514600-159514823(+)$1	223	46	50	12.0000
UCUU	chr17:33951469-33951687(+)$1	218	169	173	12.0000
UCUU	chr13:79888697-79888920(-)$1	223	16	20	12.0000
UCUU	chr3:113439666-113439888(-)$1	222	116	120	12.0000
UCUU	chr20:47730762-47730981(-)$1	219	125	129	12.0000
ucuu	chrX:51234196-51234414(-)$1	218	17	21	12.0000
UCUU	chr10:32299935-32300155(-)$1	220	94	98	12.0000
UCUU	chrX:76763123-76763343(-)$1	220	6	10	12.0000
UCUU	chr16:29822203-29822426(+)$1	223	26	30	12.0000
UCUU	chr14:32626532-32626774(+)$1	242	45	49	12.0000
UCUU	chr3:142778601-142778820(+)$1	219	102	106	12.0000
UCUU	chr2:231685035-231685259(+)$1	224	114	118	12.0000
UCUU	chr12:124242616-124242833(+)$1	217	57	61	12.0000
UCUU	chr14:75601459-75601678(-)$1	219	2	6	12.0000
UCUU	chr14:36340176-36340398(+)$1	222	35	39	12.0000
UCUU	chr19:3976075-3976313(-)$1	238	46	50	12.0000
UCUU	chr13:25907516-25907749(+)$1	233	48	52	12.0000
UCUU	chr1:211745597-211745815(-)$1	218	114	118	12.0000
UCUU	chr5:151184303-151184523(+)$1	220	31	35	12.0000
UCUU	chr1:99157097-99157320(+)$1	223	187	191	12.0000
UCUU	chr12:57452173-57452390(-)$1	217	45	49	12.0000
UCUU	chr8:95900069-95900288(-)$1	219	25	29	12.0000
UCUU	chr1:32371925-32372147(-)$1	222	124	128	12.0000
UCUU	chr1:200521714-200521936(-)$1	222	110	114	12.0000
UCUU	chr8:67545373-67545593(-)$1	220	43	47	12.0000
UCUU	chr9:91092315-91092534(+)$1	219	171	175	12.0000
UCUU	chr7:105731735-105731953(-)$1	218	13	17	12.0000
UCUU	chr2:48033360-48033584(+)$1	224	189	193	12.0000
UCUU	chr10:5759525-5759749(+)$1	224	13	17	12.0000

#otherMatches

#Struct PSSM
qqqq	chr1:46828391-46828612(+)$1	221	61	65	12.0000
gggg	chr2:192288749-192288969(+)$1	220	48	52	12.0000
FFFF	chr8:81434954-81435187(+)$1	233	8	12	12.0000
cc::	chr8:48890586-48890809(+)$1	223	28	32	12.0000
::::	chr6:44416629-44416853(+)$1	224	118	122	12.0000
ffff	chr11:93430982-93431206(+)$1	224	75	79	12.0000
ff]f	chr5:125960484-125960702(+)$1	218	174	178	12.0000
DD}E	chr2:87004575-87004792(+)$1	217	112	116	12.0000
DD::	chrX:123234523-123234744(+)$1	221	139	143	12.0000
f:::	chr5:71501722-71501954(+)$1	232	18	22	12.0000
EEEE	chr3:38532700-38532926(+)$1	226	204	208	12.0000
i333	chrX:53402548-53402772(-)$1	224	105	109	12.0000
wwww	chr5:70810705-70810925(+)$1	220	9	13	12.0000
nnnn	chr14:103810047-103810267(+)$1	220	174	178	12.0000
ffff	chr13:25906666-25906884(+)$1	218	100	104	12.0000
eeee	chr4:87735626-87735853(+)$1	227	29	33	12.0000
dddd	chr2:128461986-128462209(-)$1	223	104	108	12.0000
ff]c	chr2:87003471-87003695(+)$1	224	146	150	12.0000
irrr	chr6:64292704-64292928(+)$1	224	18	22	12.0000
====	chr3:48200209-48200428(-)$1	219	48	52	12.0000
ddd[	chr11:130100966-130101184(-)$1	218	113	117	12.0000
==::	chr6:139501050-139501273(+)$1	223	91	95	12.0000
dddd	chr10:8056857-8057079(+)$1	222	154	158	12.0000
!!gg	chr5:143538113-143538340(-)$1	227	132	136	12.0000
]ddd	chr17:47131292-47131510(+)$1	218	150	154	12.0000
mmmm	chr7:6442842-6443063(+)$1	221	92	96	12.0000
:::d	chr10:105786953-105787175(+)$1	222	4	8	12.0000
::::	chr12:57627441-57627660(+)$1	219	75	79	12.0000
pppd	chr19:2101080-2101300(-)$1	220	85	89	12.0000
:::e	chr16:69693675-69693898(+)$1	223	108	112	12.0000
{CCC	chr10:99946188-99946409(+)$1	221	65	69	12.0000
GGGG	chr5:71501458-71501676(+)$1	218	145	149	12.0000
eeee	chr2:224740663-224740884(-)$1	221	25	29	12.0000
!!ff	chr19:32875548-32875768(+)$1	220	47	51	12.0000
bbhh	chr9:91091214-91091432(+)$1	218	184	188	12.0000
eee2	chr5:81570017-81570237(-)$1	220	92	96	12.0000
::::	chr1:99225577-99225795(+)$1	218	133	137	12.0000
dddd	chr1:32641789-32642007(+)$1	218	123	127	12.0000
nnnn	chr6:64421120-64421340(+)$1	220	3	7	12.0000
:GGG	chr2:30785018-30785239(+)$1	221	20	24	12.0000
mmmd	chr8:87573010-87573231(+)$1	221	63	67	12.0000
::::	chr2:37326470-37326688(-)$1	218	20	24	12.0000
^^^^	chr5:56217996-56218216(-)$1	220	103	107	12.0000
IIII	chr2:113496308-113496527(-)$1	219	28	32	12.0000
::::	chr10:70744019-70744238(+)$1	219	5	9	12.0000
====	chr18:67994958-67995177(+)$1	219	61	65	12.0000
EEEE	chr5:167977378-167977602(-)$1	224	2	6	12.0000
dddd	chr13:41701751-41701972(-)$1	221	95	99	12.0000
6666	chr2:159514600-159514823(+)$1	223	46	50	12.0000
f:DD	chr17:33951469-33951687(+)$1	218	169	173	12.0000
DDMM	chr13:79888697-79888920(-)$1	223	16	20	12.0000
g22e	chr3:113439666-113439888(-)$1	222	116	120	12.0000
::::	chr20:47730762-47730981(-)$1	219	125	129	12.0000
[add	chrX:51234196-51234414(-)$1	218	17	21	12.0000
::::	chr10:32299935-32300155(-)$1	220	94	98	12.0000
::hh	chrX:76763123-76763343(-)$1	220	6	10	12.0000
NNNN	chr16:29822203-29822426(+)$1	223	26	30	12.0000
eeee	chr14:32626532-32626774(+)$1	242	45	49	12.0000
uuuu	chr3:142778601-142778820(+)$1	219	102	106	12.0000
eeed	chr2:231685035-231685259(+)$1	224	114	118	12.0000
444d	chr12:124242616-124242833(+)$1	217	57	61	12.0000
::::	chr14:75601459-75601678(-)$1	219	2	6	12.0000
GG::	chr14:36340176-36340398(+)$1	222	35	39	12.0000
tttt	chr19:3976075-3976313(-)$1	238	46	50	12.0000
++++	chr13:25907516-25907749(+)$1	233	48	52	12.0000
ccc$	chr1:211745597-211745815(-)$1	218	114	118	12.0000
uuuu	chr5:151184303-151184523(+)$1	220	31	35	12.0000
iii[	chr1:99157097-99157320(+)$1	223	187	191	12.0000
::ff	chr12:57452173-57452390(-)$1	217	45	49	12.0000
dddd	chr8:95900069-95900288(-)$1	219	25	29	12.0000
ffff	chr1:32371925-32372147(-)$1	222	124	128	12.0000
hhhh	chr1:200521714-200521936(-)$1	222	110	114	12.0000
$$$b	chr8:67545373-67545593(-)$1	220	43	47	12.0000
ddd:	chr9:91092315-91092534(+)$1	219	171	175	12.0000
ccco	chr7:105731735-105731953(-)$1	218	13	17	12.0000
ff::	chr2:48033360-48033584(+)$1	224	189	193	12.0000
))))	chr10:5759525-5759749(+)$1	224	13	17	12.0000

#DB
....	chr1:46828391-46828612(+)$1	1	61	65	12.0000
))))	chr2:192288749-192288969(+)$1	1	48	52	12.0000
((((	chr8:81434954-81435187(+)$1	1	8	12	12.0000
))..	chr8:48890586-48890809(+)$1	1	28	32	12.0000
....	chr6:44416629-44416853(+)$1	1	118	122	12.0000
))))	chr11:93430982-93431206(+)$1	1	75	79	12.0000
)).)	chr5:125960484-125960702(+)$1	1	174	178	12.0000
)).)	chr2:87004575-87004792(+)$1	1	112	116	12.0000
))..	chrX:123234523-123234744(+)$1	1	139	143	12.0000
)...	chr5:71501722-71501954(+)$1	1	18	22	12.0000
))))	chr3:38532700-38532926(+)$1	1	204	208	12.0000
)...	chrX:53402548-53402772(-)$1	1	105	109	12.0000
....	chr5:70810705-70810925(+)$1	1	9	13	12.0000
....	chr14:103810047-103810267(+)$1	1	174	178	12.0000
((((	chr13:25906666-25906884(+)$1	1	100	104	12.0000
((((	chr4:87735626-87735853(+)$1	1	29	33	12.0000
((((	chr2:128461986-128462209(-)$1	1	104	108	12.0000
)).)	chr2:87003471-87003695(+)$1	1	146	150	12.0000
(...	chr6:64292704-64292928(+)$1	1	18	22	12.0000
((((	chr3:48200209-48200428(-)$1	1	48	52	12.0000
(((.	chr11:130100966-130101184(-)$1	1	113	117	12.0000
))..	chr6:139501050-139501273(+)$1	1	91	95	12.0000
))))	chr10:8056857-8057079(+)$1	1	154	158	12.0000
..((	chr5:143538113-143538340(-)$1	1	132	136	12.0000
.)))	chr17:47131292-47131510(+)$1	1	150	154	12.0000
....	chr7:6442842-6443063(+)$1	1	92	96	12.0000
...(	chr10:105786953-105787175(+)$1	1	4	8	12.0000
....	chr12:57627441-57627660(+)$1	1	75	79	12.0000
...)	chr19:2101080-2101300(-)$1	1	85	89	12.0000
...(	chr16:69693675-69693898(+)$1	1	108	112	12.0000
.(((	chr10:99946188-99946409(+)$1	1	65	69	12.0000
))))	chr5:71501458-71501676(+)$1	1	145	149	12.0000
))))	chr2:224740663-224740884(-)$1	1	25	29	12.0000
..((	chr19:32875548-32875768(+)$1	1	47	51	12.0000
))))	chr9:91091214-91091432(+)$1	1	184	188	12.0000
))).	chr5:81570017-81570237(-)$1	1	92	96	12.0000
....	chr1:99225577-99225795(+)$1	1	133	137	12.0000
))))	chr1:32641789-32642007(+)$1	1	123	127	12.0000
....	chr6:64421120-64421340(+)$1	1	3	7	12.0000
.(((	chr2:30785018-30785239(+)$1	1	20	24	12.0000
...)	chr8:87573010-87573231(+)$1	1	63	67	12.0000
....	chr2:37326470-37326688(-)$1	1	20	24	12.0000
....	chr5:56217996-56218216(-)$1	1	103	107	12.0000
((((	chr2:113496308-113496527(-)$1	1	28	32	12.0000
....	chr10:70744019-70744238(+)$1	1	5	9	12.0000
((((	chr18:67994958-67995177(+)$1	1	61	65	12.0000
((((	chr5:167977378-167977602(-)$1	1	2	6	12.0000
))))	chr13:41701751-41701972(-)$1	1	95	99	12.0000
....	chr2:159514600-159514823(+)$1	1	46	50	12.0000
).))	chr17:33951469-33951687(+)$1	1	169	173	12.0000
((..	chr13:79888697-79888920(-)$1	1	16	20	12.0000
)..)	chr3:113439666-113439888(-)$1	1	116	120	12.0000
....	chr20:47730762-47730981(-)$1	1	125	129	12.0000
.(((	chrX:51234196-51234414(-)$1	1	17	21	12.0000
....	chr10:32299935-32300155(-)$1	1	94	98	12.0000
..((	chrX:76763123-76763343(-)$1	1	6	10	12.0000
....	chr16:29822203-29822426(+)$1	1	26	30	12.0000
((((	chr14:32626532-32626774(+)$1	1	45	49	12.0000
....	chr3:142778601-142778820(+)$1	1	102	106	12.0000
((((	chr2:231685035-231685259(+)$1	1	114	118	12.0000
...)	chr12:124242616-124242833(+)$1	1	57	61	12.0000
....	chr14:75601459-75601678(-)$1	1	2	6	12.0000
((..	chr14:36340176-36340398(+)$1	1	35	39	12.0000
....	chr19:3976075-3976313(-)$1	1	46	50	12.0000
....	chr13:25907516-25907749(+)$1	1	48	52	12.0000
(((.	chr1:211745597-211745815(-)$1	1	114	118	12.0000
....	chr5:151184303-151184523(+)$1	1	31	35	12.0000
(((.	chr1:99157097-99157320(+)$1	1	187	191	12.0000
..((	chr12:57452173-57452390(-)$1	1	45	49	12.0000
((((	chr8:95900069-95900288(-)$1	1	25	29	12.0000
((((	chr1:32371925-32372147(-)$1	1	124	128	12.0000
((((	chr1:200521714-200521936(-)$1	1	110	114	12.0000
...(	chr8:67545373-67545593(-)$1	1	43	47	12.0000
))).	chr9:91092315-91092534(+)$1	1	171	175	12.0000
(((.	chr7:105731735-105731953(-)$1	1	13	17	12.0000
))..	chr2:48033360-48033584(+)$1	1	189	193	12.0000
....	chr10:5759525-5759749(+)$1	1	13	17	12.0000

#PSSM
U : 0.96	u : 0.03	
C : 0.96	c : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	

#score	924.0000000000001
#seq	77
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m1_run2.nuc.txt

#NT
GAUUUUCUU	chr18:29128569-29128799(+)$1	230	129	138	15.1818
GAUUUUGUU	chr11:82996373-82996593(-)$1	220	50	59	15.1818
GGUUUUUUU	chr8:81550753-81550972(-)$1	219	134	143	14.5454
GAUCUUUUU	chr3:63988447-63988677(+)$1	230	43	52	14.9090
GAUUUUUUC	chr12:79985123-79985350(-)$1	227	30	39	14.5454
AAUGUUUUU	chr18:19103716-19103937(+)$1	221	95	104	14.7272
AAGUUUUUU	chr17:38291922-38292152(+)$1	230	59	68	14.1818
UAUAUUUUU	chr2:70506494-70506730(+)$1	236	100	109	16.1818
AAAUUUUUU	chr9:125670575-125670799(-)$1	224	39	48	14.1818
GAUUUUUGU	chr5:41731371-41731596(-)$1	225	150	159	14.8181
uacuuuuuu	chr7:148879048-148879275(+)$1	227	110	119	15.3636
UAUUUUAUU	chr15:82334428-82334657(-)$1	229	102	111	16.0909
CAUUUAUUU	chr2:206861643-206861862(-)$1	219	9	18	14.6363
AAUUUUUAU	chr3:120048633-120048854(-)$1	221	109	118	14.6363
CAUUUAUUU	chr15:89859569-89859798(-)$1	229	105	114	14.6363
GAUGUUUUU	chrX:53402277-53402503(-)$1	226	70	79	15.0000
UAUUUUUUU	chr2:224622821-224623047(-)$1	226	177	186	19.8181
UAUUUUGUU	chr21:34949631-34949853(+)$1	222	4	13	16.0000
GAUUAUUUU	chr5:151170455-151170681(+)$1	226	182	191	14.5454
GAUAUUUUU	chr11:17108376-17108599(-)$1	223	33	42	15.3636
CACUUUUUU	chrX:47495715-47495937(-)$1	222	54	63	14.6363
UAUUUUUUU	chrX:128580417-128580645(-)$1	228	16	25	19.8181
CAUUUUUUA	chr2:214182212-214182441(+)$1	229	101	110	14.5454
UAUUUUAUU	chr4:145916242-145916470(-)$1	228	66	75	16.0909
uguuuuuuu	chr15:52839559-52839781(-)$1	222	212	221	15.3636
UAUUCUUUU	chr8:30401916-30402240(+)$1	324	78	87	15.3636
AAUUUUUGU	chr11:77377223-77377449(-)$1	226	119	128	14.5454
UAUUUUUUU	chr8:81432875-81433102(+)$1	227	30	39	19.8181
UAUUUUUUU	chr7:155255555-155255779(+)$1	224	17	26	19.8181
AAUAUUUUU	chr5:77771546-77771766(+)$1	220	10	19	15.0909
CAUUUUUUU	chr7:128409915-128410140(+)$1	225	112	121	19.0909
AAUUUUUAU	chr12:25361826-25362053(-)$1	227	106	115	14.6363
CAUUUUCUU	chr15:43016191-43016411(-)$1	220	150	159	15.2727
CAUUUAUUU	chr12:118469729-118469953(+)$1	224	110	119	14.6363
CAUUUUUUU	chr5:71515580-71515818(-)$1	238	103	112	19.0909
AAUUUUCUU	chr19:44662237-44662462(+)$1	225	102	111	14.9090
GAUUUUUUU	chr4:71587785-71588005(+)$1	220	11	20	19.0000
UAUUUUUAU	chr9:35661367-35661590(-)$1	223	80	89	15.7272
UAUAUUUUU	chr12:53906081-53906303(-)$1	222	82	91	16.1818
GAUUUUUUU	chr19:32875446-32875671(+)$1	225	165	174	19.0000
UCUUUUUUU	chr4:3513082-3513304(-)$1	222	101	110	15.3636
CAUUUUUUU	chr10:102122025-102122246(+)$1	221	109	118	19.0909
UAUUUUGUU	chr1:178886603-178886834(+)$1	231	2	11	16.0000
CAUUUUUUC	chr4:79839528-79839749(-)$1	221	109	118	14.6363
GAUUUUUUU	chr16:11964138-11964357(-)$1	219	66	75	19.0000
CAUUUUUCU	chr2:224741123-224741344(-)$1	221	143	152	14.9090
UAUAUUUUU	chr3:31678151-31678373(+)$1	222	131	140	16.1818
UAUUUUAUU	chr3:143710124-143710358(+)$1	234	181	190	16.0909
UCUUUUUUU	chr3:69104348-69104568(-)$1	220	83	92	15.3636
AAUUAUUUU	chr21:34932512-34932735(+)$1	223	102	111	14.2727
UAUUUUAUU	chr4:129190778-129191010(-)$1	232	66	75	16.0909
UAUUCUUUU	chr3:170113077-170113312(+)$1	235	43	52	15.3636
CAUUUUUCU	chr4:7062013-7062239(-)$1	226	103	112	14.9090
CAUAUUUUU	chr1:179075177-179075400(-)$1	223	140	149	15.4545

#otherMatches

#Struct PSSM
ee666666f	chr19:40578896-40579121(-)$1	225	50	59	15.2727
eeooooooe	chr18:29128569-29128799(+)$1	230	129	138	15.1818
pppdddd::	chr11:82996373-82996593(-)$1	220	50	59	15.1818
ccc>>>>>>	chr8:81550753-81550972(-)$1	219	134	143	14.5454
ggggggg]e	chr3:63988447-63988677(+)$1	230	43	52	14.9090
ccqqqqqqq	chr12:79985123-79985350(-)$1	227	30	39	14.5454
oooohhhhh	chr18:19103716-19103937(+)$1	221	95	104	14.7272
bb]ffffff	chr17:38291922-38292152(+)$1	230	59	68	14.1818
f++++++++	chr2:70506494-70506730(+)$1	236	100	109	16.1818
pffffff44	chr9:125670575-125670799(-)$1	224	39	48	14.1818
]ffffff]a	chr5:41731371-41731596(-)$1	225	150	159	14.8181
ooooooddd	chr7:148879048-148879275(+)$1	227	110	119	15.3636
::::::ggg	chr15:82334428-82334657(-)$1	229	102	111	16.0909
ddd"""ggg	chr2:206861643-206861862(-)$1	219	9	18	14.6363
hhhhhhhh:	chr3:120048633-120048854(-)$1	221	109	118	14.6363
dddd[====	chr15:89859569-89859798(-)$1	229	105	114	14.6363
nnnnnhhhh	chrX:53402277-53402503(-)$1	226	70	79	15.0000
ddd666666	chr2:224622821-224623047(-)$1	226	177	186	19.8181
FFFFFFFFF	chr21:34949631-34949853(+)$1	222	4	13	16.0000
[eeeeelll	chr5:151170455-151170681(+)$1	226	182	191	14.5454
eeeemmmme	chr11:17108376-17108599(-)$1	223	33	42	15.3636
BBMMMMJJJ	chrX:47495715-47495937(-)$1	222	54	63	14.6363
:::::HHHH	chrX:128580417-128580645(-)$1	228	16	25	19.8181
iiiiiiiii	chr2:214182212-214182441(+)$1	229	101	110	14.5454
ff"""bb[c	chr4:145916242-145916470(-)$1	228	66	75	16.0909
:::::::::	chr15:52839559-52839781(-)$1	222	212	221	15.3636
+++++++++	chr8:30401916-30402240(+)$1	324	78	87	15.3636
::::eeeee	chr11:77377223-77377449(-)$1	226	119	128	14.5454
III::::cc	chr8:81432875-81433102(+)$1	227	30	39	19.8181
mmmmdddd2	chr7:155255555-155255779(+)$1	224	17	26	19.8181
:::::::::	chr5:77771546-77771766(+)$1	220	10	19	15.0909
+++++++++	chr7:128409915-128410140(+)$1	225	112	121	19.0909
YYHHHHHHH	chr12:25361826-25362053(-)$1	227	106	115	14.6363
EE:::::::	chr15:43016191-43016411(-)$1	220	150	159	15.2727
:::::::::	chr12:118469729-118469953(+)$1	224	110	119	14.6363
44iiiiiii	chr5:71515580-71515818(-)$1	238	103	112	19.0909
^^^^^^^^^	chr19:44662237-44662462(+)$1	225	102	111	14.9090
LLJJJJJJJ	chr4:71587785-71588005(+)$1	220	11	20	19.0000
fff::::::	chr9:35661367-35661590(-)$1	223	80	89	15.7272
:::::::::	chr12:53906081-53906303(-)$1	222	82	91	16.1818
hhhhhhh::	chr19:32875446-32875671(+)$1	225	165	174	19.0000
eee::::dd	chr4:3513082-3513304(-)$1	222	101	110	15.3636
ddqqqqqqq	chr10:102122025-102122246(+)$1	221	109	118	19.0909
hhhhhhhhs	chr1:178886603-178886834(+)$1	231	2	11	16.0000
fffff[ddd	chr4:79839528-79839749(-)$1	221	109	118	14.6363
G::::::::	chr16:11964138-11964357(-)$1	219	66	75	19.0000
FFF::::::	chr2:224741123-224741344(-)$1	221	143	152	14.9090
oobb]hhhh	chr3:31678151-31678373(+)$1	222	131	140	16.1818
ffftttttt	chr3:143710124-143710358(+)$1	234	181	190	16.0909
c]bb]dddd	chr3:69104348-69104568(-)$1	220	83	92	15.3636
^^^^^^^^^	chr21:34932512-34932735(+)$1	223	102	111	14.2727
wwwhhhhhh	chr4:129190778-129191010(-)$1	232	66	75	16.0909
qqqqqqqqi	chr3:170113077-170113312(+)$1	235	43	52	15.3636
+++++++ff	chr4:7062013-7062239(-)$1	226	103	112	14.9090
:::::::::	chr1:179075177-179075400(-)$1	223	140	149	15.4545

#DB
))......)	chr19:40578896-40579121(-)$1	1	50	59	15.2727
((......)	chr18:29128569-29128799(+)$1	1	129	138	15.1818
...))))..	chr11:82996373-82996593(-)$1	1	50	59	15.1818
)))......	chr8:81550753-81550972(-)$1	1	134	143	14.5454
))))))).)	chr3:63988447-63988677(+)$1	1	43	52	14.9090
((.......	chr12:79985123-79985350(-)$1	1	30	39	14.5454
....)))))	chr18:19103716-19103937(+)$1	1	95	104	14.7272
)).))))))	chr17:38291922-38292152(+)$1	1	59	68	14.1818
(........	chr2:70506494-70506730(+)$1	1	100	109	16.1818
.))))))..	chr9:125670575-125670799(-)$1	1	39	48	14.1818
.)))))).)	chr5:41731371-41731596(-)$1	1	150	159	14.8181
......)))	chr7:148879048-148879275(+)$1	1	110	119	15.3636
......(((	chr15:82334428-82334657(-)$1	1	102	111	16.0909
(((...(((	chr2:206861643-206861862(-)$1	1	9	18	14.6363
)))))))).	chr3:120048633-120048854(-)$1	1	109	118	14.6363
((((.((((	chr15:89859569-89859798(-)$1	1	105	114	14.6363
.....))))	chrX:53402277-53402503(-)$1	1	70	79	15.0000
)))......	chr2:224622821-224623047(-)$1	1	177	186	19.8181
(((((((((	chr21:34949631-34949853(+)$1	1	4	13	16.0000
.(((((...	chr5:151170455-151170681(+)$1	1	182	191	14.5454
((((....)	chr11:17108376-17108599(-)$1	1	33	42	15.3636
((....(((	chrX:47495715-47495937(-)$1	1	54	63	14.6363
.....((((	chrX:128580417-128580645(-)$1	1	16	25	19.8181
)))))))))	chr2:214182212-214182441(+)$1	1	101	110	14.5454
((...((.(	chr4:145916242-145916470(-)$1	1	66	75	16.0909
.........	chr15:52839559-52839781(-)$1	1	212	221	15.3636
.........	chr8:30401916-30402240(+)$1	1	78	87	15.3636
....(((((	chr11:77377223-77377449(-)$1	1	119	128	14.5454
(((....((	chr8:81432875-81433102(+)$1	1	30	39	19.8181
....)))).	chr7:155255555-155255779(+)$1	1	17	26	19.8181
.........	chr5:77771546-77771766(+)$1	1	10	19	15.0909
.........	chr7:128409915-128410140(+)$1	1	112	121	19.0909
..)))))))	chr12:25361826-25362053(-)$1	1	106	115	14.6363
)).......	chr15:43016191-43016411(-)$1	1	150	159	15.2727
.........	chr12:118469729-118469953(+)$1	1	110	119	14.6363
..)))))))	chr5:71515580-71515818(-)$1	1	103	112	19.0909
.........	chr19:44662237-44662462(+)$1	1	102	111	14.9090
..(((((((	chr4:71587785-71588005(+)$1	1	11	20	19.0000
)))......	chr9:35661367-35661590(-)$1	1	80	89	15.7272
.........	chr12:53906081-53906303(-)$1	1	82	91	16.1818
)))))))..	chr19:32875446-32875671(+)$1	1	165	174	19.0000
)))....((	chr4:3513082-3513304(-)$1	1	101	110	15.3636
((.......	chr10:102122025-102122246(+)$1	1	109	118	19.0909
((((((((.	chr1:178886603-178886834(+)$1	1	2	11	16.0000
(((((.(((	chr4:79839528-79839749(-)$1	1	109	118	14.6363
(........	chr16:11964138-11964357(-)$1	1	66	75	19.0000
(((......	chr2:224741123-224741344(-)$1	1	143	152	14.9090
..)).))))	chr3:31678151-31678373(+)$1	1	131	140	16.1818
(((......	chr3:143710124-143710358(+)$1	1	181	190	16.0909
).)).))))	chr3:69104348-69104568(-)$1	1	83	92	15.3636
.........	chr21:34932512-34932735(+)$1	1	102	111	14.2727
...))))))	chr4:129190778-129191010(-)$1	1	66	75	16.0909
........)	chr3:170113077-170113312(+)$1	1	43	52	15.3636
.......((	chr4:7062013-7062239(-)$1	1	103	112	14.9090
.........	chr1:179075177-179075400(-)$1	1	140	149	15.4545

#PSSM
U : 0.32	C : 0.23	G : 0.21	A : 0.16	u : 0.05	
A : 0.89	a : 0.03	C : 0.03	G : 0.01	g : 0.01	
U : 0.89	u : 0.03	G : 0.01	A : 0.01	c : 0.01	C : 0.01	
U : 0.78	A : 0.10	u : 0.05	G : 0.03	C : 0.01	
U : 0.87	u : 0.05	A : 0.03	C : 0.03	
U : 0.89	u : 0.05	A : 0.05	
U : 0.76	A : 0.07	u : 0.05	C : 0.05	G : 0.05	
U : 0.81	u : 0.05	A : 0.05	G : 0.03	C : 0.03	
U : 0.89	C : 0.03	u : 0.03	g : 0.01	A : 0.01	

#score	875.1818181818186
#seq	55
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_UTR_m1_run1.nuc.txt

#NT
UUUU	chr12:51636555-51636776(+)$1	221	141	145	11.9999
uuuu	chr15:71188114-71188329(+)$1	215	0	4	11.9999
UUUU	chr3:122143019-122143249(-)$1	230	17	21	11.9999
UUUU	chr18:29711082-29711301(+)$1	219	48	52	11.9999
UUUU	chr15:35154998-35155219(-)$1	221	61	65	11.9999
UUUU	chr3:122449546-122449776(+)$1	230	103	107	11.9999
UUUU	chr8:94744366-94744584(-)$1	218	17	21	11.9999
UUUU	chr3:183637768-183637985(-)$1	217	17	21	11.9999
UUUU	chr11:47800129-47800348(-)$1	219	74	78	11.9999
UUUU	chr4:177251060-177251290(+)$1	230	41	45	11.9999
uuuu	chr1:200828100-200828317(+)$1	217	56	60	11.9999
UUUU	chr4:15606483-15606713(-)$1	230	15	19	11.9999
UUUU	chr15:49281281-49281502(-)$1	221	66	70	11.9999
UUUU	chr13:33677274-33677504(-)$1	230	55	59	11.9999
UUUU	chr2:114472461-114472683(-)$1	222	27	31	11.9999
UUUU	chr6:116597945-116598165(-)$1	220	125	129	11.9999
uuuu	chr7:139254451-139254681(-)$1	230	16	20	11.9999
uuuu	chr11:85989606-85989836(+)$1	230	149	153	11.9999
UUUU	chr6:31545709-31545927(+)$1	218	175	179	11.9999
UUUU	chr1:203651831-203652053(+)$1	222	8	12	11.9999
UUUU	chr8:74704290-74704511(-)$1	221	11	15	11.9999
UUUU	chr7:17383135-17383365(+)$1	230	10	14	11.9999
UUUU	chr9:5470290-5470543(+)$1	253	79	83	11.9999
UUUU	chr3:138015553-138015772(+)$1	219	35	39	11.9999
UUUU	chr4:40425414-40425644(-)$1	230	156	160	11.9999
UUUU	chr4:139086659-139086879(-)$1	220	9	13	11.9999
UUUU	chrX:77386708-77386933(-)$1	225	79	83	11.9999
UUUU	chr15:42834676-42834906(-)$1	230	3	7	11.9999
UUUU	chr2:65313891-65314111(-)$1	220	76	80	11.9999
UUUU	chr7:102738997-102739224(+)$1	227	12	16	11.9999
UUUU	chr10:98719030-98719251(+)$1	221	5	9	11.9999
UUUU	chr1:193057905-193058115(+)$1	210	26	30	11.9999
UUUU	chr3:124947204-124947434(-)$1	230	164	168	11.9999
UUUU	chr5:112170680-112170901(+)$1	221	66	70	11.9999
UUUU	chr14:53238281-53238506(+)$1	225	7	11	11.9999
UUUU	chr8:37720117-37720337(-)$1	220	103	107	11.9999
UUUU	chr5:95131738-95131978(+)$1	240	105	109	11.9999
UUUU	chr6:97594537-97594760(-)$1	223	14	18	11.9999
UUUU	chr5:114951518-114951748(-)$1	230	6	10	11.9999
UUUU	chr2:178405272-178405495(+)$1	223	114	118	11.9999
UUUU	chr4:120977073-120977296(-)$1	223	3	7	11.9999
UUUU	chrX:72900831-72901051(+)$1	220	13	17	11.9999
UUUU	chr12:77246044-77246269(+)$1	225	128	132	11.9999
UUUU	chr2:174091419-174091651(+)$1	232	14	18	11.9999
UUUU	chr1:9989734-9989964(-)$1	230	82	86	11.9999
UUUU	chr3:113163854-113164074(+)$1	220	203	207	11.9999
UUUU	chr5:78075994-78076219(-)$1	225	50	54	11.9999
UUUU	chr5:72209686-72209918(+)$1	232	10	14	11.9999
UUUU	chr17:62539182-62539403(-)$1	221	207	211	11.9999
UUUU	chr1:229440174-229440399(+)$1	225	6	10	11.9999
UUUU	chr3:141230963-141231188(+)$1	225	20	24	11.9999
UUUU	chr9:27547735-27547959(-)$1	224	28	32	11.9999
UUUU	chr4:53497145-53497375(-)$1	230	8	12	11.9999
UUUU	chr7:135612240-135612460(-)$1	220	53	57	11.9999
UUUU	chr2:47387350-47387578(-)$1	228	113	117	11.9999
UUUU	chr8:95893597-95893815(-)$1	218	27	31	11.9999
UUUU	chr7:44921237-44921459(-)$1	222	141	145	11.9999
UUUU	chr13:39622911-39623148(+)$1	237	27	31	11.9999
UUUU	chr5:110836053-110836283(-)$1	230	13	17	11.9999
UUUU	chr9:101979577-101979799(-)$1	222	40	44	11.9999
UUUU	chr2:201844873-201845092(-)$1	219	29	33	11.9999
UUUU	chr8:64123145-64123370(+)$1	225	72	76	11.9999
UUUU	chr18:45359833-45360063(-)$1	230	101	105	11.9999
UUUU	chr1:47142142-47142372(-)$1	230	65	69	11.9999
UUUU	chr4:186283708-186283938(+)$1	230	48	52	11.9999
UUUU	chr14:54942505-54942728(-)$1	223	49	53	11.9999
UUUU	chr14:55512607-55512872(+)$1	265	4	8	11.9999
UUUU	chr17:38989291-38989521(+)$1	230	52	56	11.9999
UUUU	chr20:61510203-61510433(-)$1	230	25	29	11.9999
UUUU	chr20:32441876-32442095(+)$1	219	160	164	11.9999
uuuu	chr10:82284888-82285110(+)$1	222	18	22	11.9999
UUUU	chr2:61417443-61417673(-)$1	230	92	96	11.9999
UUUU	chr14:81667843-81668064(-)$1	221	51	55	11.9999
UUUU	chr2:200797654-200797874(-)$1	220	147	151	11.9999
UUUU	chr3:185225901-185226122(-)$1	221	39	43	11.9999
UUUU	chr6:24705241-24705458(-)$1	217	20	24	11.9999
UUUU	chr4:139100404-139100624(-)$1	220	54	58	11.9999
UUUU	chr12:21788260-21788480(-)$1	220	65	69	11.9999
UUUU	chr10:98723569-98723831(+)$1	262	222	226	11.9999
UUUU	chr11:9467760-9467985(+)$1	225	35	39	11.9999
UUUU	chr10:81114276-81114493(+)$1	217	81	85	11.9999
UUUU	chr3:172116784-172117006(+)$1	222	10	14	11.9999
UUUU	chr10:27399622-27399857(-)$1	235	92	96	11.9999
uuuu	chr13:28197454-28197676(+)$1	222	121	125	11.9999
UUUU	chr2:223807339-223807565(+)$1	226	20	24	11.9999
UUUU	chr20:56935192-56935412(+)$1	220	114	118	11.9999
UUUU	chr11:60236056-60236271(+)$1	215	92	96	11.9999
UUUU	chr12:27955406-27955627(+)$1	221	1	5	11.9999
UUUU	chr5:89689723-89689946(-)$1	223	4	8	11.9999
UUUU	chr11:62392485-62392715(-)$1	230	17	21	11.9999
uuuu	chr4:1387463-1387688(+)$1	225	21	25	11.9999
UUUU	chr10:74035334-74035559(+)$1	225	87	91	11.9999
UUUU	chr4:39782160-39782390(+)$1	230	146	150	11.9999
UUUU	chr16:85812140-85812362(-)$1	222	63	67	11.9999
UUUU	chr6:116914255-116914485(+)$1	230	77	81	11.9999
UUUU	chr3:39438524-39438757(+)$1	233	74	78	11.9999

#otherMatches

#Struct PSSM
::::	chr1:93826830-93827054(+)$1	224	0	4	11.9999
b22a	chr12:51636555-51636776(+)$1	221	141	145	11.9999
::::	chr15:71188114-71188329(+)$1	215	0	4	11.9999
EEE{	chr3:122143019-122143249(-)$1	230	17	21	11.9999
::::	chr18:29711082-29711301(+)$1	219	48	52	11.9999
GGGG	chr15:35154998-35155219(-)$1	221	61	65	11.9999
GGKK	chr3:122449546-122449776(+)$1	230	103	107	11.9999
pppd	chr8:94744366-94744584(-)$1	218	17	21	11.9999
DDDK	chr3:183637768-183637985(-)$1	217	17	21	11.9999
::::	chr11:47800129-47800348(-)$1	219	74	78	11.9999
nnnn	chr4:177251060-177251290(+)$1	230	41	45	11.9999
hhhh	chr1:200828100-200828317(+)$1	217	56	60	11.9999
GGGK	chr4:15606483-15606713(-)$1	230	15	19	11.9999
hhh]	chr15:49281281-49281502(-)$1	221	66	70	11.9999
fff:	chr13:33677274-33677504(-)$1	230	55	59	11.9999
::::	chr2:114472461-114472683(-)$1	222	27	31	11.9999
fffb	chr6:116597945-116598165(-)$1	220	125	129	11.9999
::dd	chr7:139254451-139254681(-)$1	230	16	20	11.9999
HHHH	chr11:85989606-85989836(+)$1	230	149	153	11.9999
ddde	chr6:31545709-31545927(+)$1	218	175	179	11.9999
::::	chr1:203651831-203652053(+)$1	222	8	12	11.9999
BLLL	chr8:74704290-74704511(-)$1	221	11	15	11.9999
rrrr	chr7:17383135-17383365(+)$1	230	10	14	11.9999
hhhh	chr9:5470290-5470543(+)$1	253	79	83	11.9999
gggg	chr3:138015553-138015772(+)$1	219	35	39	11.9999
ggg=	chr4:40425414-40425644(-)$1	230	156	160	11.9999
:ggg	chr4:139086659-139086879(-)$1	220	9	13	11.9999
cc22	chrX:77386708-77386933(-)$1	225	79	83	11.9999
::::	chr15:42834676-42834906(-)$1	230	3	7	11.9999
rrcc	chr2:65313891-65314111(-)$1	220	76	80	11.9999
gggg	chr7:102738997-102739224(+)$1	227	12	16	11.9999
emmm	chr10:98719030-98719251(+)$1	221	5	9	11.9999
vvvv	chr1:193057905-193058115(+)$1	210	26	30	11.9999
GGGG	chr3:124947204-124947434(-)$1	230	164	168	11.9999
eedd	chr5:112170680-112170901(+)$1	221	66	70	11.9999
::::	chr14:53238281-53238506(+)$1	225	7	11	11.9999
h>>>	chr8:37720117-37720337(-)$1	220	103	107	11.9999
GGGG	chr5:95131738-95131978(+)$1	240	105	109	11.9999
====	chr6:97594537-97594760(-)$1	223	14	18	11.9999
####	chr5:114951518-114951748(-)$1	230	6	10	11.9999
::::	chr2:178405272-178405495(+)$1	223	114	118	11.9999
bb[c	chr4:120977073-120977296(-)$1	223	3	7	11.9999
b%%%	chrX:72900831-72901051(+)$1	220	13	17	11.9999
EE{G	chr12:77246044-77246269(+)$1	225	128	132	11.9999
::::	chr2:174091419-174091651(+)$1	232	14	18	11.9999
hhhh	chr1:9989734-9989964(-)$1	230	82	86	11.9999
gggg	chr3:113163854-113164074(+)$1	220	203	207	11.9999
c444	chr5:78075994-78076219(-)$1	225	50	54	11.9999
dddd	chr5:72209686-72209918(+)$1	232	10	14	11.9999
CYYF	chr17:62539182-62539403(-)$1	221	207	211	11.9999
eeee	chr1:229440174-229440399(+)$1	225	6	10	11.9999
qqff	chr3:141230963-141231188(+)$1	225	20	24	11.9999
HHHH	chr9:27547735-27547959(-)$1	224	28	32	11.9999
D:::	chr4:53497145-53497375(-)$1	230	8	12	11.9999
++++	chr7:135612240-135612460(-)$1	220	53	57	11.9999
rrrr	chr2:47387350-47387578(-)$1	228	113	117	11.9999
hhhh	chr8:95893597-95893815(-)$1	218	27	31	11.9999
llee	chr7:44921237-44921459(-)$1	222	141	145	11.9999
e###	chr13:39622911-39623148(+)$1	237	27	31	11.9999
hhhh	chr5:110836053-110836283(-)$1	230	13	17	11.9999
iiii	chr9:101979577-101979799(-)$1	222	40	44	11.9999
oiii	chr2:201844873-201845092(-)$1	219	29	33	11.9999
::::	chr8:64123145-64123370(+)$1	225	72	76	11.9999
pppp	chr18:45359833-45360063(-)$1	230	101	105	11.9999
::::	chr1:47142142-47142372(-)$1	230	65	69	11.9999
GGGD	chr4:186283708-186283938(+)$1	230	48	52	11.9999
d!!c	chr14:54942505-54942728(-)$1	223	49	53	11.9999
ffoo	chr14:55512607-55512872(+)$1	265	4	8	11.9999
rrrr	chr17:38989291-38989521(+)$1	230	52	56	11.9999
JJJJ	chr20:61510203-61510433(-)$1	230	25	29	11.9999
44gg	chr20:32441876-32442095(+)$1	219	160	164	11.9999
EE{D	chr10:82284888-82285110(+)$1	222	18	22	11.9999
::::	chr2:61417443-61417673(-)$1	230	92	96	11.9999
tttt	chr14:81667843-81668064(-)$1	221	51	55	11.9999
xxff	chr2:200797654-200797874(-)$1	220	147	151	11.9999
fffm	chr3:185225901-185226122(-)$1	221	39	43	11.9999
DDDD	chr6:24705241-24705458(-)$1	217	20	24	11.9999
6666	chr4:139100404-139100624(-)$1	220	54	58	11.9999
eee[	chr12:21788260-21788480(-)$1	220	65	69	11.9999
mmmm	chr10:98723569-98723831(+)$1	262	222	226	11.9999
ddpp	chr11:9467760-9467985(+)$1	225	35	39	11.9999
!!ee	chr10:81114276-81114493(+)$1	217	81	85	11.9999
DKKC	chr3:172116784-172117006(+)$1	222	10	14	11.9999
gggg	chr10:27399622-27399857(-)$1	235	92	96	11.9999
::::	chr13:28197454-28197676(+)$1	222	121	125	11.9999
IIII	chr2:223807339-223807565(+)$1	226	20	24	11.9999
E___	chr20:56935192-56935412(+)$1	220	114	118	11.9999
qqqq	chr11:60236056-60236271(+)$1	215	92	96	11.9999
::::	chr12:27955406-27955627(+)$1	221	1	5	11.9999
::::	chr5:89689723-89689946(-)$1	223	4	8	11.9999
::::	chr11:62392485-62392715(-)$1	230	17	21	11.9999
^^^f	chr4:1387463-1387688(+)$1	225	21	25	11.9999
gggg	chr10:74035334-74035559(+)$1	225	87	91	11.9999
::::	chr4:39782160-39782390(+)$1	230	146	150	11.9999
eeee	chr16:85812140-85812362(-)$1	222	63	67	11.9999
c22c	chr6:116914255-116914485(+)$1	230	77	81	11.9999
ddd3	chr3:39438524-39438757(+)$1	233	74	78	11.9999

#DB
....	chr1:93826830-93827054(+)$1	1	0	4	11.9999
)..)	chr12:51636555-51636776(+)$1	1	141	145	11.9999
....	chr15:71188114-71188329(+)$1	1	0	4	11.9999
(((.	chr3:122143019-122143249(-)$1	1	17	21	11.9999
....	chr18:29711082-29711301(+)$1	1	48	52	11.9999
((((	chr15:35154998-35155219(-)$1	1	61	65	11.9999
((..	chr3:122449546-122449776(+)$1	1	103	107	11.9999
...)	chr8:94744366-94744584(-)$1	1	17	21	11.9999
(((.	chr3:183637768-183637985(-)$1	1	17	21	11.9999
....	chr11:47800129-47800348(-)$1	1	74	78	11.9999
....	chr4:177251060-177251290(+)$1	1	41	45	11.9999
))))	chr1:200828100-200828317(+)$1	1	56	60	11.9999
(((.	chr4:15606483-15606713(-)$1	1	15	19	11.9999
))).	chr15:49281281-49281502(-)$1	1	66	70	11.9999
))).	chr13:33677274-33677504(-)$1	1	55	59	11.9999
....	chr2:114472461-114472683(-)$1	1	27	31	11.9999
((((	chr6:116597945-116598165(-)$1	1	125	129	11.9999
..((	chr7:139254451-139254681(-)$1	1	16	20	11.9999
))))	chr11:85989606-85989836(+)$1	1	149	153	11.9999
((((	chr6:31545709-31545927(+)$1	1	175	179	11.9999
....	chr1:203651831-203652053(+)$1	1	8	12	11.9999
(...	chr8:74704290-74704511(-)$1	1	11	15	11.9999
....	chr7:17383135-17383365(+)$1	1	10	14	11.9999
((((	chr9:5470290-5470543(+)$1	1	79	83	11.9999
((((	chr3:138015553-138015772(+)$1	1	35	39	11.9999
((((	chr4:40425414-40425644(-)$1	1	156	160	11.9999
.(((	chr4:139086659-139086879(-)$1	1	9	13	11.9999
))..	chrX:77386708-77386933(-)$1	1	79	83	11.9999
....	chr15:42834676-42834906(-)$1	1	3	7	11.9999
..))	chr2:65313891-65314111(-)$1	1	76	80	11.9999
((((	chr7:102738997-102739224(+)$1	1	12	16	11.9999
(...	chr10:98719030-98719251(+)$1	1	5	9	11.9999
....	chr1:193057905-193058115(+)$1	1	26	30	11.9999
))))	chr3:124947204-124947434(-)$1	1	164	168	11.9999
))((	chr5:112170680-112170901(+)$1	1	66	70	11.9999
....	chr14:53238281-53238506(+)$1	1	7	11	11.9999
)...	chr8:37720117-37720337(-)$1	1	103	107	11.9999
((((	chr5:95131738-95131978(+)$1	1	105	109	11.9999
((((	chr6:97594537-97594760(-)$1	1	14	18	11.9999
....	chr5:114951518-114951748(-)$1	1	6	10	11.9999
....	chr2:178405272-178405495(+)$1	1	114	118	11.9999
((.(	chr4:120977073-120977296(-)$1	1	3	7	11.9999
(...	chrX:72900831-72901051(+)$1	1	13	17	11.9999
((.(	chr12:77246044-77246269(+)$1	1	128	132	11.9999
....	chr2:174091419-174091651(+)$1	1	14	18	11.9999
((((	chr1:9989734-9989964(-)$1	1	82	86	11.9999
))))	chr3:113163854-113164074(+)$1	1	203	207	11.9999
)...	chr5:78075994-78076219(-)$1	1	50	54	11.9999
((((	chr5:72209686-72209918(+)$1	1	10	14	11.9999
)..)	chr17:62539182-62539403(-)$1	1	207	211	11.9999
((((	chr1:229440174-229440399(+)$1	1	6	10	11.9999
..))	chr3:141230963-141231188(+)$1	1	20	24	11.9999
((((	chr9:27547735-27547959(-)$1	1	28	32	11.9999
(...	chr4:53497145-53497375(-)$1	1	8	12	11.9999
....	chr7:135612240-135612460(-)$1	1	53	57	11.9999
....	chr2:47387350-47387578(-)$1	1	113	117	11.9999
((((	chr8:95893597-95893815(-)$1	1	27	31	11.9999
..))	chr7:44921237-44921459(-)$1	1	141	145	11.9999
(...	chr13:39622911-39623148(+)$1	1	27	31	11.9999
))))	chr5:110836053-110836283(-)$1	1	13	17	11.9999
((((	chr9:101979577-101979799(-)$1	1	40	44	11.9999
.)))	chr2:201844873-201845092(-)$1	1	29	33	11.9999
....	chr8:64123145-64123370(+)$1	1	72	76	11.9999
....	chr18:45359833-45360063(-)$1	1	101	105	11.9999
....	chr1:47142142-47142372(-)$1	1	65	69	11.9999
((((	chr4:186283708-186283938(+)$1	1	48	52	11.9999
(..(	chr14:54942505-54942728(-)$1	1	49	53	11.9999
((..	chr14:55512607-55512872(+)$1	1	4	8	11.9999
....	chr17:38989291-38989521(+)$1	1	52	56	11.9999
((((	chr20:61510203-61510433(-)$1	1	25	29	11.9999
..))	chr20:32441876-32442095(+)$1	1	160	164	11.9999
((.(	chr10:82284888-82285110(+)$1	1	18	22	11.9999
....	chr2:61417443-61417673(-)$1	1	92	96	11.9999
....	chr14:81667843-81668064(-)$1	1	51	55	11.9999
..))	chr2:200797654-200797874(-)$1	1	147	151	11.9999
(((.	chr3:185225901-185226122(-)$1	1	39	43	11.9999
((((	chr6:24705241-24705458(-)$1	1	20	24	11.9999
....	chr4:139100404-139100624(-)$1	1	54	58	11.9999
(((.	chr12:21788260-21788480(-)$1	1	65	69	11.9999
....	chr10:98723569-98723831(+)$1	1	222	226	11.9999
((..	chr11:9467760-9467985(+)$1	1	35	39	11.9999
..((	chr10:81114276-81114493(+)$1	1	81	85	11.9999
(..(	chr3:172116784-172117006(+)$1	1	10	14	11.9999
))))	chr10:27399622-27399857(-)$1	1	92	96	11.9999
....	chr13:28197454-28197676(+)$1	1	121	125	11.9999
((((	chr2:223807339-223807565(+)$1	1	20	24	11.9999
)...	chr20:56935192-56935412(+)$1	1	114	118	11.9999
....	chr11:60236056-60236271(+)$1	1	92	96	11.9999
....	chr12:27955406-27955627(+)$1	1	1	5	11.9999
....	chr5:89689723-89689946(-)$1	1	4	8	11.9999
....	chr11:62392485-62392715(-)$1	1	17	21	11.9999
...)	chr4:1387463-1387688(+)$1	1	21	25	11.9999
((((	chr10:74035334-74035559(+)$1	1	87	91	11.9999
....	chr4:39782160-39782390(+)$1	1	146	150	11.9999
((((	chr16:85812140-85812362(-)$1	1	63	67	11.9999
)..)	chr6:116914255-116914485(+)$1	1	77	81	11.9999
))).	chr3:39438524-39438757(+)$1	1	74	78	11.9999

#PSSM
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	

#score	1163.9999999999998
#seq	97
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m2_run1.nuc.txt

#NT
UUU	chr15:101811338-101811599(-)$1	261	81	84	9.0000
UUU	chr3:5260040-5260311(+)$1	271	56	59	9.0000
UUU	chr6:36822580-36822905(-)$1	325	0	3	9.0000
UUU	chr2:71413097-71413357(-)$1	260	15	18	9.0000
UUU	chr14:93695092-93695408(+)$1	316	35	38	9.0000
UUU	chr16:18818067-18818357(-)$1	290	18	21	9.0000
UUU	chr6:56323569-56323847(-)$1	278	79	82	9.0000
UUU	chr12:4668301-4668650(+)$1	349	44	47	9.0000
UUU	chr5:121363653-121363911(+)$1	258	5	8	9.0000
UUU	chr16:3777121-3777394(-)$1	273	28	31	9.0000
UUU	chr12:57057080-57057361(-)$1	281	15	18	9.0000
UUU	chr8:28610223-28610465(+)$1	242	25	28	9.0000
UUU	chr9:101912428-101912745(+)$1	317	57	60	9.0000
UUU	chr17:64802962-64803198(+)$1	236	71	74	9.0000
UUU	chr12:54679101-54679348(+)$1	247	91	94	9.0000
UUU	chr9:35056461-35056684(-)$1	223	18	21	9.0000
UUU	chr5:71489918-71490147(+)$1	229	23	26	9.0000
UUU	chr12:4410237-4410563(+)$1	326	44	47	9.0000
UUU	chr7:64389926-64390157(+)$1	231	44	47	9.0000
UUU	chr12:69972206-69972512(+)$1	306	40	43	9.0000
UUU	chr1:120164047-120164304(-)$1	257	18	21	9.0000
UUU	chr22:45581084-45581324(+)$1	240	68	71	9.0000
UUU	chr20:50215429-50215689(-)$1	260	22	25	9.0000
UUU	chr18:211378-211659(+)$1	281	1	4	9.0000
UUU	chr20:30389009-30389332(+)$1	323	34	37	9.0000
UUU	chr2:131808491-131808778(-)$1	287	53	56	9.0000
UUU	chr20:61576608-61576892(+)$1	284	32	35	9.0000
UUU	chr1:205583138-205583382(-)$1	244	81	84	9.0000
UUU	chr8:117655968-117656199(-)$1	231	31	34	9.0000
UUU	chr22:35691446-35691849(+)$1	403	54	57	9.0000
UUU	chr7:112424826-112425047(-)$1	221	55	58	9.0000
UUU	chrX:111003098-111003327(+)$1	229	162	165	9.0000
UUU	chr1:224348738-224349015(+)$1	277	52	55	9.0000
UUU	chr4:83274237-83274465(-)$1	228	0	3	9.0000
UUU	chr17:34165339-34165582(+)$1	243	16	19	9.0000
UUU	chr3:47628510-47628738(-)$1	228	34	37	9.0000
UUU	chr18:77898010-77898291(+)$1	281	33	36	9.0000
UUU	chr3:150289704-150289945(+)$1	241	4	7	9.0000
UUU	chr1:156712449-156712709(-)$1	260	42	45	9.0000
UUU	chr1:22418922-22419199(+)$1	277	12	15	9.0000
UUU	chr1:165877258-165877577(+)$1	319	92	95	9.0000
UUU	chr20:57252112-57252383(+)$1	271	0	3	9.0000
UUU	chr5:172742535-172742931(-)$1	396	235	238	9.0000
UUU	chr16:1751015-1751423(+)$1	408	11	14	9.0000
UUU	chr19:37003077-37003302(-)$1	225	12	15	9.0000
UUU	chr21:46225925-46226168(-)$1	243	53	56	9.0000
UUU	chr1:235274112-235274389(-)$1	277	0	3	9.0000
UUU	chr12:109889031-109889293(-)$1	262	8	11	9.0000
UUU	chr1:2238298-2238528(+)$1	230	41	44	9.0000
UUU	chr16:3351702-3351939(-)$1	237	22	25	9.0000
UUU	chr1:116235365-116235636(+)$1	271	52	55	9.0000
UUU	chr7:129472853-129473082(-)$1	229	12	15	9.0000
UUU	chr12:79983259-79983539(-)$1	280	4	7	9.0000
UUU	chr15:76209513-76209789(+)$1	276	13	16	9.0000
UUU	chr6:133135774-133136005(+)$1	231	18	21	9.0000
UUU	chr22:22118316-22118546(-)$1	230	2	5	9.0000
UUU	chr6:107388535-107388778(-)$1	243	28	31	9.0000
UUU	chr20:61576697-61576959(+)$1	262	3	6	9.0000
UUU	chr6:34557889-34558160(-)$1	271	60	63	9.0000
UUU	chr7:39746217-39746465(+)$1	248	62	65	9.0000
UUU	chr6:24705863-24706201(-)$1	338	56	59	9.0000
UUU	chr5:142782738-142782962(-)$1	224	9	12	9.0000
UUU	chr7:26231107-26231391(-)$1	284	10	13	9.0000
UUU	chr12:76441539-76441811(-)$1	272	10	13	9.0000
UUU	chr4:77956562-77956887(+)$1	325	24	27	9.0000
UUU	chr5:65458208-65458444(+)$1	236	3	6	9.0000
UUU	chr16:23077704-23077969(-)$1	265	31	34	9.0000
UUU	chr20:3904304-3904573(+)$1	269	37	40	9.0000
UUU	chr4:76419210-76419450(-)$1	240	36	39	9.0000
UUU	chr4:77968656-77968959(-)$1	303	1	4	9.0000
uuu	chr5:52098439-52098707(+)$1	268	48	51	9.0000
UUU	chr1:87379798-87380025(-)$1	227	23	26	9.0000
UUU	chr4:89442562-89442802(-)$1	240	37	40	9.0000
UUU	chr16:84157441-84157740(-)$1	299	0	3	9.0000
UUU	chr2:38971935-38972204(-)$1	269	88	91	9.0000
uuu	chr11:74551005-74551274(+)$1	269	5	8	9.0000
UUU	chrX:20144771-20145032(-)$1	261	39	42	9.0000
UUU	chr2:89049791-89050027(+)$1	236	10	13	9.0000
UUU	chr11:1977517-1977753(+)$1	236	1	4	9.0000
UUU	chr2:170496467-170496717(+)$1	250	1	4	9.0000
UUU	chr2:38970835-38971209(-)$1	374	4	7	9.0000
UUU	chrX:62569724-62569953(-)$1	229	9	12	9.0000
UUU	chr2:131906128-131906367(+)$1	239	9	12	9.0000
UUU	chr20:16721657-16721935(+)$1	278	10	13	9.0000
UUU	chr11:62480309-62480551(-)$1	242	34	37	9.0000
UUU	chr12:133303490-133303794(-)$1	304	0	3	9.0000
UUU	chr7:42977221-42977478(+)$1	257	17	20	9.0000
UUU	chr10:22619830-22620178(+)$1	348	19	22	9.0000
UUU	chr11:12964472-12964809(+)$1	337	79	82	9.0000
UUU	chr19:49120535-49120780(-)$1	245	7	10	9.0000
UUU	chr14:56765409-56765718(+)$1	309	6	9	9.0000
UUU	chr1:204523561-204523833(+)$1	272	2	5	9.0000
UUU	chr7:50658039-50658285(-)$1	246	1	4	9.0000
UUU	chr14:81646188-81646430(-)$1	242	67	70	9.0000
UUU	chr7:44873756-44874032(-)$1	276	12	15	9.0000
UUU	chr1:217782315-217782638(-)$1	323	13	16	9.0000
UUU	chr1:179070350-179070610(-)$1	260	109	112	9.0000

#otherMatches

#Struct PSSM
iii	chr2:28638781-28639008(+)$1	227	74	77	9.0000
HOO	chr15:101811338-101811599(-)$1	261	81	84	9.0000
33h	chr3:5260040-5260311(+)$1	271	56	59	9.0000
:::	chr6:36822580-36822905(-)$1	325	0	3	9.0000
ggg	chr2:71413097-71413357(-)$1	260	15	18	9.0000
DD:	chr14:93695092-93695408(+)$1	316	35	38	9.0000
LLL	chr16:18818067-18818357(-)$1	290	18	21	9.0000
rrr	chr6:56323569-56323847(-)$1	278	79	82	9.0000
"""	chr12:4668301-4668650(+)$1	349	44	47	9.0000
:::	chr5:121363653-121363911(+)$1	258	5	8	9.0000
:::	chr16:3777121-3777394(-)$1	273	28	31	9.0000
uuu	chr12:57057080-57057361(-)$1	281	15	18	9.0000
dmm	chr8:28610223-28610465(+)$1	242	25	28	9.0000
GGG	chr9:101912428-101912745(+)$1	317	57	60	9.0000
fff	chr17:64802962-64803198(+)$1	236	71	74	9.0000
HHH	chr12:54679101-54679348(+)$1	247	91	94	9.0000
ddd	chr9:35056461-35056684(-)$1	223	18	21	9.0000
EEE	chr5:71489918-71490147(+)$1	229	23	26	9.0000
ttt	chr12:4410237-4410563(+)$1	326	44	47	9.0000
FFF	chr7:64389926-64390157(+)$1	231	44	47	9.0000
:::	chr12:69972206-69972512(+)$1	306	40	43	9.0000
FFF	chr1:120164047-120164304(-)$1	257	18	21	9.0000
::f	chr22:45581084-45581324(+)$1	240	68	71	9.0000
www	chr20:50215429-50215689(-)$1	260	22	25	9.0000
cc!	chr18:211378-211659(+)$1	281	1	4	9.0000
33h	chr20:30389009-30389332(+)$1	323	34	37	9.0000
ooa	chr2:131808491-131808778(-)$1	287	53	56	9.0000
dff	chr20:61576608-61576892(+)$1	284	32	35	9.0000
rrd	chr1:205583138-205583382(-)$1	244	81	84	9.0000
ggg	chr8:117655968-117656199(-)$1	231	31	34	9.0000
ccc	chr22:35691446-35691849(+)$1	403	54	57	9.0000
##c	chr7:112424826-112425047(-)$1	221	55	58	9.0000
H??	chrX:111003098-111003327(+)$1	229	162	165	9.0000
vvv	chr1:224348738-224349015(+)$1	277	52	55	9.0000
:::	chr4:83274237-83274465(-)$1	228	0	3	9.0000
!!b	chr17:34165339-34165582(+)$1	243	16	19	9.0000
lff	chr3:47628510-47628738(-)$1	228	34	37	9.0000
h[c	chr18:77898010-77898291(+)$1	281	33	36	9.0000
e!!	chr3:150289704-150289945(+)$1	241	4	7	9.0000
ggg	chr1:156712449-156712709(-)$1	260	42	45	9.0000
ooc	chr1:22418922-22419199(+)$1	277	12	15	9.0000
===	chr1:165877258-165877577(+)$1	319	92	95	9.0000
:::	chr20:57252112-57252383(+)$1	271	0	3	9.0000
eee	chr5:172742535-172742931(-)$1	396	235	238	9.0000
b""	chr16:1751015-1751423(+)$1	408	11	14	9.0000
&&&	chr19:37003077-37003302(-)$1	225	12	15	9.0000
444	chr21:46225925-46226168(-)$1	243	53	56	9.0000
:::	chr1:235274112-235274389(-)$1	277	0	3	9.0000
{EE	chr12:109889031-109889293(-)$1	262	8	11	9.0000
eee	chr1:2238298-2238528(+)$1	230	41	44	9.0000
iii	chr16:3351702-3351939(-)$1	237	22	25	9.0000
ggg	chr1:116235365-116235636(+)$1	271	52	55	9.0000
mmc	chr7:129472853-129473082(-)$1	229	12	15	9.0000
EEE	chr12:79983259-79983539(-)$1	280	4	7	9.0000
JJJ	chr15:76209513-76209789(+)$1	276	13	16	9.0000
dd#	chr6:133135774-133136005(+)$1	231	18	21	9.0000
:::	chr22:22118316-22118546(-)$1	230	2	5	9.0000
ppp	chr6:107388535-107388778(-)$1	243	28	31	9.0000
eee	chr20:61576697-61576959(+)$1	262	3	6	9.0000
tth	chr6:34557889-34558160(-)$1	271	60	63	9.0000
JJJ	chr7:39746217-39746465(+)$1	248	62	65	9.0000
ddd	chr6:24705863-24706201(-)$1	338	56	59	9.0000
eee	chr5:142782738-142782962(-)$1	224	9	12	9.0000
iii	chr7:26231107-26231391(-)$1	284	10	13	9.0000
QQQ	chr12:76441539-76441811(-)$1	272	10	13	9.0000
iii	chr4:77956562-77956887(+)$1	325	24	27	9.0000
:::	chr5:65458208-65458444(+)$1	236	3	6	9.0000
888	chr16:23077704-23077969(-)$1	265	31	34	9.0000
!gg	chr20:3904304-3904573(+)$1	269	37	40	9.0000
g!!	chr4:76419210-76419450(-)$1	240	36	39	9.0000
HHH	chr4:77968656-77968959(-)$1	303	1	4	9.0000
JJJ	chr5:52098439-52098707(+)$1	268	48	51	9.0000
:ff	chr1:87379798-87380025(-)$1	227	23	26	9.0000
mmd	chr4:89442562-89442802(-)$1	240	37	40	9.0000
:::	chr16:84157441-84157740(-)$1	299	0	3	9.0000
:::	chr2:38971935-38972204(-)$1	269	88	91	9.0000
:::	chr11:74551005-74551274(+)$1	269	5	8	9.0000
:::	chrX:20144771-20145032(-)$1	261	39	42	9.0000
:::	chr2:89049791-89050027(+)$1	236	10	13	9.0000
::E	chr11:1977517-1977753(+)$1	236	1	4	9.0000
:::	chr2:170496467-170496717(+)$1	250	1	4	9.0000
GGG	chr2:38970835-38971209(-)$1	374	4	7	9.0000
:::	chrX:62569724-62569953(-)$1	229	9	12	9.0000
H::	chr2:131906128-131906367(+)$1	239	9	12	9.0000
eel	chr20:16721657-16721935(+)$1	278	10	13	9.0000
CBB	chr11:62480309-62480551(-)$1	242	34	37	9.0000
:::	chr12:133303490-133303794(-)$1	304	0	3	9.0000
HHH	chr7:42977221-42977478(+)$1	257	17	20	9.0000
qqq	chr10:22619830-22620178(+)$1	348	19	22	9.0000
[cc	chr11:12964472-12964809(+)$1	337	79	82	9.0000
:::	chr19:49120535-49120780(-)$1	245	7	10	9.0000
fff	chr14:56765409-56765718(+)$1	309	6	9	9.0000
eee	chr1:204523561-204523833(+)$1	272	2	5	9.0000
:::	chr7:50658039-50658285(-)$1	246	1	4	9.0000
nnn	chr14:81646188-81646430(-)$1	242	67	70	9.0000
F{E	chr7:44873756-44874032(-)$1	276	12	15	9.0000
KKD	chr1:217782315-217782638(-)$1	323	13	16	9.0000
b]c	chr1:179070350-179070610(-)$1	260	109	112	9.0000

#DB
)))	chr2:28638781-28639008(+)$1	1	74	77	9.0000
(..	chr15:101811338-101811599(-)$1	1	81	84	9.0000
..)	chr3:5260040-5260311(+)$1	1	56	59	9.0000
...	chr6:36822580-36822905(-)$1	1	0	3	9.0000
(((	chr2:71413097-71413357(-)$1	1	15	18	9.0000
((.	chr14:93695092-93695408(+)$1	1	35	38	9.0000
...	chr16:18818067-18818357(-)$1	1	18	21	9.0000
...	chr6:56323569-56323847(-)$1	1	79	82	9.0000
...	chr12:4668301-4668650(+)$1	1	44	47	9.0000
...	chr5:121363653-121363911(+)$1	1	5	8	9.0000
...	chr16:3777121-3777394(-)$1	1	28	31	9.0000
...	chr12:57057080-57057361(-)$1	1	15	18	9.0000
(..	chr8:28610223-28610465(+)$1	1	25	28	9.0000
(((	chr9:101912428-101912745(+)$1	1	57	60	9.0000
(((	chr17:64802962-64803198(+)$1	1	71	74	9.0000
)))	chr12:54679101-54679348(+)$1	1	91	94	9.0000
(((	chr9:35056461-35056684(-)$1	1	18	21	9.0000
(((	chr5:71489918-71490147(+)$1	1	23	26	9.0000
...	chr12:4410237-4410563(+)$1	1	44	47	9.0000
(((	chr7:64389926-64390157(+)$1	1	44	47	9.0000
...	chr12:69972206-69972512(+)$1	1	40	43	9.0000
(((	chr1:120164047-120164304(-)$1	1	18	21	9.0000
..(	chr22:45581084-45581324(+)$1	1	68	71	9.0000
...	chr20:50215429-50215689(-)$1	1	22	25	9.0000
((.	chr18:211378-211659(+)$1	1	1	4	9.0000
..)	chr20:30389009-30389332(+)$1	1	34	37	9.0000
..)	chr2:131808491-131808778(-)$1	1	53	56	9.0000
)))	chr20:61576608-61576892(+)$1	1	32	35	9.0000
..)	chr1:205583138-205583382(-)$1	1	81	84	9.0000
)))	chr8:117655968-117656199(-)$1	1	31	34	9.0000
)))	chr22:35691446-35691849(+)$1	1	54	57	9.0000
..(	chr7:112424826-112425047(-)$1	1	55	58	9.0000
)..	chrX:111003098-111003327(+)$1	1	162	165	9.0000
...	chr1:224348738-224349015(+)$1	1	52	55	9.0000
...	chr4:83274237-83274465(-)$1	1	0	3	9.0000
..(	chr17:34165339-34165582(+)$1	1	16	19	9.0000
.))	chr3:47628510-47628738(-)$1	1	34	37	9.0000
(.(	chr18:77898010-77898291(+)$1	1	33	36	9.0000
(..	chr3:150289704-150289945(+)$1	1	4	7	9.0000
)))	chr1:156712449-156712709(-)$1	1	42	45	9.0000
..)	chr1:22418922-22419199(+)$1	1	12	15	9.0000
)))	chr1:165877258-165877577(+)$1	1	92	95	9.0000
...	chr20:57252112-57252383(+)$1	1	0	3	9.0000
(((	chr5:172742535-172742931(-)$1	1	235	238	9.0000
(..	chr16:1751015-1751423(+)$1	1	11	14	9.0000
...	chr19:37003077-37003302(-)$1	1	12	15	9.0000
...	chr21:46225925-46226168(-)$1	1	53	56	9.0000
...	chr1:235274112-235274389(-)$1	1	0	3	9.0000
.((	chr12:109889031-109889293(-)$1	1	8	11	9.0000
)))	chr1:2238298-2238528(+)$1	1	41	44	9.0000
(((	chr16:3351702-3351939(-)$1	1	22	25	9.0000
)))	chr1:116235365-116235636(+)$1	1	52	55	9.0000
..)	chr7:129472853-129473082(-)$1	1	12	15	9.0000
(((	chr12:79983259-79983539(-)$1	1	4	7	9.0000
(((	chr15:76209513-76209789(+)$1	1	13	16	9.0000
((.	chr6:133135774-133136005(+)$1	1	18	21	9.0000
...	chr22:22118316-22118546(-)$1	1	2	5	9.0000
...	chr6:107388535-107388778(-)$1	1	28	31	9.0000
(((	chr20:61576697-61576959(+)$1	1	3	6	9.0000
..)	chr6:34557889-34558160(-)$1	1	60	63	9.0000
(((	chr7:39746217-39746465(+)$1	1	62	65	9.0000
)))	chr6:24705863-24706201(-)$1	1	56	59	9.0000
(((	chr5:142782738-142782962(-)$1	1	9	12	9.0000
(((	chr7:26231107-26231391(-)$1	1	10	13	9.0000
...	chr12:76441539-76441811(-)$1	1	10	13	9.0000
(((	chr4:77956562-77956887(+)$1	1	24	27	9.0000
...	chr5:65458208-65458444(+)$1	1	3	6	9.0000
...	chr16:23077704-23077969(-)$1	1	31	34	9.0000
.((	chr20:3904304-3904573(+)$1	1	37	40	9.0000
(..	chr4:76419210-76419450(-)$1	1	36	39	9.0000
(((	chr4:77968656-77968959(-)$1	1	1	4	9.0000
(((	chr5:52098439-52098707(+)$1	1	48	51	9.0000
.((	chr1:87379798-87380025(-)$1	1	23	26	9.0000
..)	chr4:89442562-89442802(-)$1	1	37	40	9.0000
...	chr16:84157441-84157740(-)$1	1	0	3	9.0000
...	chr2:38971935-38972204(-)$1	1	88	91	9.0000
...	chr11:74551005-74551274(+)$1	1	5	8	9.0000
...	chrX:20144771-20145032(-)$1	1	39	42	9.0000
...	chr2:89049791-89050027(+)$1	1	10	13	9.0000
..(	chr11:1977517-1977753(+)$1	1	1	4	9.0000
...	chr2:170496467-170496717(+)$1	1	1	4	9.0000
(((	chr2:38970835-38971209(-)$1	1	4	7	9.0000
...	chrX:62569724-62569953(-)$1	1	9	12	9.0000
(..	chr2:131906128-131906367(+)$1	1	9	12	9.0000
((.	chr20:16721657-16721935(+)$1	1	10	13	9.0000
(((	chr11:62480309-62480551(-)$1	1	34	37	9.0000
...	chr12:133303490-133303794(-)$1	1	0	3	9.0000
(((	chr7:42977221-42977478(+)$1	1	17	20	9.0000
...	chr10:22619830-22620178(+)$1	1	19	22	9.0000
.((	chr11:12964472-12964809(+)$1	1	79	82	9.0000
...	chr19:49120535-49120780(-)$1	1	7	10	9.0000
(((	chr14:56765409-56765718(+)$1	1	6	9	9.0000
(((	chr1:204523561-204523833(+)$1	1	2	5	9.0000
...	chr7:50658039-50658285(-)$1	1	1	4	9.0000
...	chr14:81646188-81646430(-)$1	1	67	70	9.0000
(.(	chr7:44873756-44874032(-)$1	1	12	15	9.0000
..(	chr1:217782315-217782638(-)$1	1	13	16	9.0000
).)	chr1:179070350-179070610(-)$1	1	109	112	9.0000

#PSSM
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012c_hg19_UTR_m3_run1.nuc.txt

#NT
UUU	chr11:85669159-85669389(-)$1	230	53	56	8.9999
uuu	chr18:33716188-33716411(+)$1	223	1	4	8.9999
UUU	chr12:109041132-109041362(-)$1	230	0	3	8.9999
uuu	chr5:102544248-102544478(+)$1	230	48	51	8.9999
UUU	chr12:57392696-57392922(-)$1	226	1	4	8.9999
UUU	chr9:86276468-86276698(-)$1	230	2	5	8.9999
UUU	chr2:8823724-8823961(+)$1	237	68	71	8.9999
UUU	chr3:69154233-69154463(+)$1	230	13	16	8.9999
UUU	chr16:56504358-56504587(+)$1	229	7	10	8.9999
UUU	chr13:40297438-40297668(+)$1	230	0	3	8.9999
UUU	chr11:244624-244862(+)$1	238	22	25	8.9999
UUU	chr19:1038850-1039065(+)$1	215	32	35	8.9999
UUU	chr11:77376462-77376692(-)$1	230	43	46	8.9999
UUU	chr1:10479733-10479963(+)$1	230	10	13	8.9999
UUU	chr7:20455106-20455322(+)$1	216	42	45	8.9999
UUU	chr1:236372067-236372297(+)$1	230	19	22	8.9999
UUU	chr10:105357458-105357681(-)$1	223	0	3	8.9999
uuu	chr15:64459317-64459547(-)$1	230	0	3	8.9999
UUU	chr4:89306599-89306829(+)$1	230	29	32	8.9999
UUU	chr21:35476316-35476546(+)$1	230	34	37	8.9999
UUU	chr10:14913577-14913807(+)$1	230	30	33	8.9999
UUU	chr6:108365084-108365297(-)$1	213	9	12	8.9999
UUU	chr1:100548241-100548465(+)$1	224	28	31	8.9999
UUU	chr5:43289595-43289816(-)$1	221	14	17	8.9999
UUU	chr3:158383036-158383266(+)$1	230	1	4	8.9999
uUU	chr1:115125985-115126215(-)$1	230	100	103	8.9999
UUU	chr6:56972099-56972323(+)$1	224	10	13	8.9999
UUU	chr11:32999040-32999270(+)$1	230	22	25	8.9999
UUU	chr1:162493329-162493559(+)$1	230	11	14	8.9999
UUU	chr14:71139257-71139487(+)$1	230	26	29	8.9999
UUU	chr3:38296240-38296470(+)$1	230	3	6	8.9999
UUU	chr5:36181822-36182057(+)$1	235	23	26	8.9999
UUU	chr16:14045173-14045399(+)$1	226	8	11	8.9999
UUU	chr4:129794487-129794710(+)$1	223	92	95	8.9999
UUU	chr20:5919001-5919231(-)$1	230	54	57	8.9999
UUU	chr1:10043083-10043309(+)$1	226	94	97	8.9999
UUU	chr12:77416036-77416268(-)$1	232	7	10	8.9999
UUU	chr16:87443299-87443529(-)$1	230	80	83	8.9999
UUU	chr1:25568854-25569076(-)$1	222	19	22	8.9999
UUU	chr3:197510674-197510904(+)$1	230	29	32	8.9999
UUU	chr18:23597366-23597592(-)$1	226	5	8	8.9999
UUU	chr18:44390301-44390520(-)$1	219	18	21	8.9999
UUU	chr1:193056251-193056476(+)$1	225	112	115	8.9999
UUU	chr3:52248180-52248410(+)$1	230	31	34	8.9999
UUU	chr11:96086524-96086750(-)$1	226	62	65	8.9999
UUU	chr3:196460605-196460831(+)$1	226	139	142	8.9999
UUU	chr2:191798342-191798565(+)$1	223	58	61	8.9999
UUU	chrX:103435897-103436127(+)$1	230	52	55	8.9999
UUU	chr10:60156343-60156573(+)$1	230	108	111	8.9999
UUU	chr5:142660690-142660927(-)$1	237	0	3	8.9999
UUU	chr18:722268-722498(-)$1	230	22	25	8.9999
UUU	chr2:48698342-48698566(+)$1	224	1	4	8.9999
UUU	chr14:31085686-31085925(+)$1	239	58	61	8.9999
UUU	chr12:67703694-67703918(+)$1	224	2	5	8.9999
UUU	chr15:56384864-56385087(-)$1	223	16	19	8.9999
UUU	chr1:167395514-167395744(+)$1	230	53	56	8.9999
UUU	chr5:74100305-74100530(-)$1	225	20	23	8.9999
UUU	chr1:85717755-85717985(-)$1	230	1	4	8.9999
UUU	chr13:21721425-21721655(+)$1	230	62	65	8.9999
UUU	chr1:33765726-33765947(+)$1	221	81	84	8.9999
UUU	chr18:12725442-12725672(+)$1	230	55	58	8.9999
UUU	chr2:198338754-198338978(+)$1	224	2	5	8.9999
UUU	chr11:82684261-82684491(-)$1	230	5	8	8.9999
UUU	chr2:26512843-26513069(+)$1	226	3	6	8.9999
UUU	chr5:180002287-180002513(+)$1	226	15	18	8.9999
UUU	chr5:72208551-72208781(+)$1	230	52	55	8.9999
UUU	chr14:93705312-93705542(-)$1	230	2	5	8.9999
UUU	chr4:42411897-42412127(-)$1	230	12	15	8.9999
UUU	chr3:172118261-172118487(+)$1	226	27	30	8.9999
uuu	chr7:17383240-17383470(+)$1	230	60	63	8.9999
UUU	chr3:185335218-185335448(+)$1	230	37	40	8.9999
uuu	chr12:113410754-113411005(+)$1	251	62	65	8.9999
UUU	chr1:203771499-203771729(+)$1	230	7	10	8.9999
UUU	chr15:83685984-83686214(-)$1	230	32	35	8.9999
UUU	chr22:37621277-37621507(-)$1	230	43	46	8.9999
UUU	chr12:51214609-51214839(+)$1	230	20	23	8.9999
uuu	chr12:44180796-44181020(+)$1	224	69	72	8.9999
UUU	chr16:24801209-24801439(+)$1	230	63	66	8.9999
UUU	chr2:231684634-231684852(+)$1	218	23	26	8.9999
UUU	chr14:50360945-50361175(+)$1	230	112	115	8.9999
UUU	chr20:32233614-32233844(+)$1	230	47	50	8.9999
UUU	chr2:70053411-70053641(+)$1	230	30	33	8.9999
UUU	chr5:94040698-94040928(-)$1	230	2	5	8.9999
uuu	chr6:90346646-90346873(-)$1	227	57	60	8.9999
UUU	chr3:156422988-156423222(+)$1	234	41	44	8.9999
UUU	chr4:17626715-17626945(+)$1	230	40	43	8.9999
UUU	chr18:55268062-55268305(-)$1	243	32	35	8.9999
UUU	chr11:110100859-110101089(-)$1	230	10	13	8.9999
UUU	chr3:122143020-122143247(-)$1	227	15	18	8.9999
UUU	chr1:156209706-156209930(+)$1	224	0	3	8.9999
UUU	chr13:50274010-50274235(-)$1	225	0	3	8.9999
UUU	chr1:246830236-246830466(+)$1	230	28	31	8.9999
UUU	chr4:26434634-26434852(+)$1	218	23	26	8.9999
UUU	chr14:88892819-88893045(+)$1	226	20	23	8.9999
UUU	chr4:88059325-88059547(+)$1	222	6	9	8.9999

#otherMatches

#Struct PSSM
fff	chr5:173034948-173035178(-)$1	230	87	90	8.9999
::f	chr11:85669159-85669389(-)$1	230	53	56	8.9999
:::	chr18:33716188-33716411(+)$1	223	1	4	8.9999
:::	chr12:109041132-109041362(-)$1	230	0	3	8.9999
:::	chr5:102544248-102544478(+)$1	230	48	51	8.9999
fff	chr12:57392696-57392922(-)$1	226	1	4	8.9999
ddd	chr9:86276468-86276698(-)$1	230	2	5	8.9999
LFF	chr2:8823724-8823961(+)$1	237	68	71	8.9999
ggg	chr3:69154233-69154463(+)$1	230	13	16	8.9999
fff	chr16:56504358-56504587(+)$1	229	7	10	8.9999
:::	chr13:40297438-40297668(+)$1	230	0	3	8.9999
!!b	chr11:244624-244862(+)$1	238	22	25	8.9999
$$$	chr19:1038850-1039065(+)$1	215	32	35	8.9999
cc4	chr11:77376462-77376692(-)$1	230	43	46	8.9999
:::	chr1:10479733-10479963(+)$1	230	10	13	8.9999
$$$	chr7:20455106-20455322(+)$1	216	42	45	8.9999
fff	chr1:236372067-236372297(+)$1	230	19	22	8.9999
III	chr10:105357458-105357681(-)$1	223	0	3	8.9999
:::	chr15:64459317-64459547(-)$1	230	0	3	8.9999
(==	chr4:89306599-89306829(+)$1	230	29	32	8.9999
###	chr21:35476316-35476546(+)$1	230	34	37	8.9999
###	chr10:14913577-14913807(+)$1	230	30	33	8.9999
hhh	chr6:108365084-108365297(-)$1	213	9	12	8.9999
KKC	chr1:100548241-100548465(+)$1	224	28	31	8.9999
::=	chr5:43289595-43289816(-)$1	221	14	17	8.9999
hhh	chr3:158383036-158383266(+)$1	230	1	4	8.9999
qqq	chr1:115125985-115126215(-)$1	230	100	103	8.9999
D{C	chr6:56972099-56972323(+)$1	224	10	13	8.9999
III	chr11:32999040-32999270(+)$1	230	22	25	8.9999
DKK	chr1:162493329-162493559(+)$1	230	11	14	8.9999
!!g	chr14:71139257-71139487(+)$1	230	26	29	8.9999
:::	chr3:38296240-38296470(+)$1	230	3	6	8.9999
fff	chr5:36181822-36182057(+)$1	235	23	26	8.9999
:::	chr16:14045173-14045399(+)$1	226	8	11	8.9999
999	chr4:129794487-129794710(+)$1	223	92	95	8.9999
nnf	chr20:5919001-5919231(-)$1	230	54	57	8.9999
+++	chr1:10043083-10043309(+)$1	226	94	97	8.9999
JJJ	chr12:77416036-77416268(-)$1	232	7	10	8.9999
{BB	chr16:87443299-87443529(-)$1	230	80	83	8.9999
%%d	chr1:25568854-25569076(-)$1	222	19	22	8.9999
"""	chr3:197510674-197510904(+)$1	230	29	32	8.9999
JJJ	chr18:23597366-23597592(-)$1	226	5	8	8.9999
DD{	chr18:44390301-44390520(-)$1	219	18	21	8.9999
fff	chr1:193056251-193056476(+)$1	225	112	115	8.9999
:::	chr3:52248180-52248410(+)$1	230	31	34	8.9999
e66	chr11:96086524-96086750(-)$1	226	62	65	8.9999
c88	chr3:196460605-196460831(+)$1	226	139	142	8.9999
]gg	chr2:191798342-191798565(+)$1	223	58	61	8.9999
d[d	chrX:103435897-103436127(+)$1	230	52	55	8.9999
fff	chr10:60156343-60156573(+)$1	230	108	111	8.9999
:::	chr5:142660690-142660927(-)$1	237	0	3	8.9999
:::	chr18:722268-722498(-)$1	230	22	25	8.9999
:::	chr2:48698342-48698566(+)$1	224	1	4	8.9999
eee	chr14:31085686-31085925(+)$1	239	58	61	8.9999
eee	chr12:67703694-67703918(+)$1	224	2	5	8.9999
III	chr15:56384864-56385087(-)$1	223	16	19	8.9999
hhh	chr1:167395514-167395744(+)$1	230	53	56	8.9999
555	chr5:74100305-74100530(-)$1	225	20	23	8.9999
:::	chr1:85717755-85717985(-)$1	230	1	4	8.9999
xxx	chr13:21721425-21721655(+)$1	230	62	65	8.9999
ddd	chr1:33765726-33765947(+)$1	221	81	84	8.9999
c::	chr18:12725442-12725672(+)$1	230	55	58	8.9999
"""	chr2:198338754-198338978(+)$1	224	2	5	8.9999
EEE	chr11:82684261-82684491(-)$1	230	5	8	8.9999
:::	chr2:26512843-26513069(+)$1	226	3	6	8.9999
:::	chr5:180002287-180002513(+)$1	226	15	18	8.9999
pee	chr5:72208551-72208781(+)$1	230	52	55	8.9999
:::	chr14:93705312-93705542(-)$1	230	2	5	8.9999
:::	chr4:42411897-42412127(-)$1	230	12	15	8.9999
ccc	chr3:172118261-172118487(+)$1	226	27	30	8.9999
qqq	chr7:17383240-17383470(+)$1	230	60	63	8.9999
qqq	chr3:185335218-185335448(+)$1	230	37	40	8.9999
22g	chr12:113410754-113411005(+)$1	251	62	65	8.9999
:::	chr1:203771499-203771729(+)$1	230	7	10	8.9999
:::	chr15:83685984-83686214(-)$1	230	32	35	8.9999
ee:	chr22:37621277-37621507(-)$1	230	43	46	8.9999
fff	chr12:51214609-51214839(+)$1	230	20	23	8.9999
)))	chr12:44180796-44181020(+)$1	224	69	72	8.9999
dde	chr16:24801209-24801439(+)$1	230	63	66	8.9999
GGG	chr2:231684634-231684852(+)$1	218	23	26	8.9999
>>>	chr14:50360945-50361175(+)$1	230	112	115	8.9999
"""	chr20:32233614-32233844(+)$1	230	47	50	8.9999
d::	chr2:70053411-70053641(+)$1	230	30	33	8.9999
:::	chr5:94040698-94040928(-)$1	230	2	5	8.9999
fff	chr6:90346646-90346873(-)$1	227	57	60	8.9999
hhh	chr3:156422988-156423222(+)$1	234	41	44	8.9999
sss	chr4:17626715-17626945(+)$1	230	40	43	8.9999
eee	chr18:55268062-55268305(-)$1	243	32	35	8.9999
fff	chr11:110100859-110101089(-)$1	230	10	13	8.9999
EEE	chr3:122143020-122143247(-)$1	227	15	18	8.9999
fff	chr1:156209706-156209930(+)$1	224	0	3	8.9999
:::	chr13:50274010-50274235(-)$1	225	0	3	8.9999
ee!	chr1:246830236-246830466(+)$1	230	28	31	8.9999
gqq	chr4:26434634-26434852(+)$1	218	23	26	8.9999
JJJ	chr14:88892819-88893045(+)$1	226	20	23	8.9999
GGG	chr4:88059325-88059547(+)$1	222	6	9	8.9999

#DB
)))	chr5:173034948-173035178(-)$1	1	87	90	8.9999
..(	chr11:85669159-85669389(-)$1	1	53	56	8.9999
...	chr18:33716188-33716411(+)$1	1	1	4	8.9999
...	chr12:109041132-109041362(-)$1	1	0	3	8.9999
...	chr5:102544248-102544478(+)$1	1	48	51	8.9999
(((	chr12:57392696-57392922(-)$1	1	1	4	8.9999
(((	chr9:86276468-86276698(-)$1	1	2	5	8.9999
.((	chr2:8823724-8823961(+)$1	1	68	71	8.9999
(((	chr3:69154233-69154463(+)$1	1	13	16	8.9999
(((	chr16:56504358-56504587(+)$1	1	7	10	8.9999
...	chr13:40297438-40297668(+)$1	1	0	3	8.9999
..(	chr11:244624-244862(+)$1	1	22	25	8.9999
...	chr19:1038850-1039065(+)$1	1	32	35	8.9999
)).	chr11:77376462-77376692(-)$1	1	43	46	8.9999
...	chr1:10479733-10479963(+)$1	1	10	13	8.9999
...	chr7:20455106-20455322(+)$1	1	42	45	8.9999
(((	chr1:236372067-236372297(+)$1	1	19	22	8.9999
(((	chr10:105357458-105357681(-)$1	1	0	3	8.9999
...	chr15:64459317-64459547(-)$1	1	0	3	8.9999
.((	chr4:89306599-89306829(+)$1	1	29	32	8.9999
...	chr21:35476316-35476546(+)$1	1	34	37	8.9999
...	chr10:14913577-14913807(+)$1	1	30	33	8.9999
(((	chr6:108365084-108365297(-)$1	1	9	12	8.9999
..(	chr1:100548241-100548465(+)$1	1	28	31	8.9999
..(	chr5:43289595-43289816(-)$1	1	14	17	8.9999
(((	chr3:158383036-158383266(+)$1	1	1	4	8.9999
...	chr1:115125985-115126215(-)$1	1	100	103	8.9999
(.(	chr6:56972099-56972323(+)$1	1	10	13	8.9999
(((	chr11:32999040-32999270(+)$1	1	22	25	8.9999
(..	chr1:162493329-162493559(+)$1	1	11	14	8.9999
..(	chr14:71139257-71139487(+)$1	1	26	29	8.9999
...	chr3:38296240-38296470(+)$1	1	3	6	8.9999
)))	chr5:36181822-36182057(+)$1	1	23	26	8.9999
...	chr16:14045173-14045399(+)$1	1	8	11	8.9999
...	chr4:129794487-129794710(+)$1	1	92	95	8.9999
..)	chr20:5919001-5919231(-)$1	1	54	57	8.9999
...	chr1:10043083-10043309(+)$1	1	94	97	8.9999
(((	chr12:77416036-77416268(-)$1	1	7	10	8.9999
.((	chr16:87443299-87443529(-)$1	1	80	83	8.9999
..(	chr1:25568854-25569076(-)$1	1	19	22	8.9999
...	chr3:197510674-197510904(+)$1	1	29	32	8.9999
(((	chr18:23597366-23597592(-)$1	1	5	8	8.9999
((.	chr18:44390301-44390520(-)$1	1	18	21	8.9999
(((	chr1:193056251-193056476(+)$1	1	112	115	8.9999
...	chr3:52248180-52248410(+)$1	1	31	34	8.9999
)..	chr11:96086524-96086750(-)$1	1	62	65	8.9999
)..	chr3:196460605-196460831(+)$1	1	139	142	8.9999
.))	chr2:191798342-191798565(+)$1	1	58	61	8.9999
(.(	chrX:103435897-103436127(+)$1	1	52	55	8.9999
(((	chr10:60156343-60156573(+)$1	1	108	111	8.9999
...	chr5:142660690-142660927(-)$1	1	0	3	8.9999
...	chr18:722268-722498(-)$1	1	22	25	8.9999
...	chr2:48698342-48698566(+)$1	1	1	4	8.9999
(((	chr14:31085686-31085925(+)$1	1	58	61	8.9999
(((	chr12:67703694-67703918(+)$1	1	2	5	8.9999
(((	chr15:56384864-56385087(-)$1	1	16	19	8.9999
)))	chr1:167395514-167395744(+)$1	1	53	56	8.9999
...	chr5:74100305-74100530(-)$1	1	20	23	8.9999
...	chr1:85717755-85717985(-)$1	1	1	4	8.9999
...	chr13:21721425-21721655(+)$1	1	62	65	8.9999
)))	chr1:33765726-33765947(+)$1	1	81	84	8.9999
)..	chr18:12725442-12725672(+)$1	1	55	58	8.9999
...	chr2:198338754-198338978(+)$1	1	2	5	8.9999
(((	chr11:82684261-82684491(-)$1	1	5	8	8.9999
...	chr2:26512843-26513069(+)$1	1	3	6	8.9999
...	chr5:180002287-180002513(+)$1	1	15	18	8.9999
.))	chr5:72208551-72208781(+)$1	1	52	55	8.9999
...	chr14:93705312-93705542(-)$1	1	2	5	8.9999
...	chr4:42411897-42412127(-)$1	1	12	15	8.9999
(((	chr3:172118261-172118487(+)$1	1	27	30	8.9999
...	chr7:17383240-17383470(+)$1	1	60	63	8.9999
...	chr3:185335218-185335448(+)$1	1	37	40	8.9999
..)	chr12:113410754-113411005(+)$1	1	62	65	8.9999
...	chr1:203771499-203771729(+)$1	1	7	10	8.9999
...	chr15:83685984-83686214(-)$1	1	32	35	8.9999
)).	chr22:37621277-37621507(-)$1	1	43	46	8.9999
)))	chr12:51214609-51214839(+)$1	1	20	23	8.9999
...	chr12:44180796-44181020(+)$1	1	69	72	8.9999
(((	chr16:24801209-24801439(+)$1	1	63	66	8.9999
(((	chr2:231684634-231684852(+)$1	1	23	26	8.9999
...	chr14:50360945-50361175(+)$1	1	112	115	8.9999
...	chr20:32233614-32233844(+)$1	1	47	50	8.9999
)..	chr2:70053411-70053641(+)$1	1	30	33	8.9999
...	chr5:94040698-94040928(-)$1	1	2	5	8.9999
(((	chr6:90346646-90346873(-)$1	1	57	60	8.9999
(((	chr3:156422988-156423222(+)$1	1	41	44	8.9999
...	chr4:17626715-17626945(+)$1	1	40	43	8.9999
)))	chr18:55268062-55268305(-)$1	1	32	35	8.9999
(((	chr11:110100859-110101089(-)$1	1	10	13	8.9999
(((	chr3:122143020-122143247(-)$1	1	15	18	8.9999
(((	chr1:156209706-156209930(+)$1	1	0	3	8.9999
...	chr13:50274010-50274235(-)$1	1	0	3	8.9999
((.	chr1:246830236-246830466(+)$1	1	28	31	8.9999
(..	chr4:26434634-26434852(+)$1	1	23	26	8.9999
(((	chr14:88892819-88893045(+)$1	1	20	23	8.9999
(((	chr4:88059325-88059547(+)$1	1	6	9	8.9999

#PSSM
U : 0.91	u : 0.08	
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_CDS_m1_run1.nuc.txt

#NT
AUU	chr19:52394276-52394496(-)$1	220	89	92	9.0000
AUU	chr2:179407143-179407366(+)$1	223	63	66	9.0000
AUU	chr10:95266662-95266890(+)$1	228	7	10	9.0000
AUU	chr2:183817784-183818008(-)$1	224	70	73	9.0000
AUU	chr14:57858285-57858509(+)$1	224	110	113	9.0000
AUU	chr13:53254017-53254238(+)$1	221	33	36	9.0000
AUU	chr1:214818236-214818455(+)$1	219	24	27	9.0000
AUU	chr3:186503933-186504155(+)$1	222	99	102	9.0000
AUU	chrM:10192-10411(+)$1	219	28	31	9.0000
AUU	chr5:43502388-43502612(-)$1	224	0	3	9.0000
AUU	chr22:30035075-30035301(+)$1	226	59	62	9.0000
AUU	chr5:61778849-61779078(+)$1	229	5	8	9.0000
AUU	chr2:85769943-85770178(+)$1	235	20	23	9.0000
AUU	chr19:34951334-34951553(+)$1	219	11	14	9.0000
AUU	chr6:7402779-7403007(+)$1	228	12	15	9.0000
AUU	chr19:24309867-24310102(+)$1	235	45	48	9.0000
AUU	chr6:35841949-35842169(-)$1	220	45	48	9.0000
AUU	chr1:70761752-70761995(-)$1	243	19	22	9.0000
AUU	chr19:44513138-44513369(+)$1	231	24	27	9.0000
AUU	chr11:32955492-32955727(+)$1	235	21	24	9.0000
AUU	chr6:116968529-116968756(-)$1	227	40	43	9.0000
AUU	chr20:54974212-54974448(+)$1	236	25	28	9.0000
AUU	chr18:13681974-13682198(-)$1	224	19	22	9.0000
AUU	chr21:33038678-33038901(+)$1	223	30	33	9.0000
AUU	chr2:26461702-26461922(-)$1	220	61	64	9.0000
AUU	chr2:190719485-190719707(+)$1	222	29	32	9.0000
AUU	chr12:109525896-109526122(-)$1	226	91	94	9.0000
AUU	chr19:38125969-38126193(-)$1	224	5	8	9.0000
AUU	chr1:206646533-206646750(-)$1	217	162	165	9.0000
AUU	chr7:103002336-103002556(+)$1	220	12	15	9.0000
AUU	chr16:47733158-47733378(+)$1	220	39	42	9.0000
AUU	chr3:193343796-193344023(+)$1	227	34	37	9.0000
AUU	chr5:145863052-145863281(+)$1	229	2	5	9.0000
AUU	chr6:114267163-114267388(-)$1	225	0	3	9.0000
AUU	chr1:115269509-115269731(-)$1	222	35	38	9.0000
AUU	chrX:123217260-123217481(+)$1	221	22	25	9.0000
AUU	chr6:116599824-116600046(-)$1	222	58	61	9.0000
AUU	chr17:40997852-40998082(+)$1	230	17	20	9.0000
AUU	chr2:198256919-198257140(-)$1	221	0	3	9.0000
AUU	chr21:34926035-34926255(+)$1	220	14	17	9.0000
AUU	chrM:8548-8798(+)$1	250	2	5	9.0000
AUU	chr15:66786737-66786965(-)$1	228	5	8	9.0000
AUU	chr11:111941104-111941331(+)$1	227	28	31	9.0000
AUU	chr12:123006628-123006848(-)$1	220	111	114	9.0000
AUU	chr19:44376892-44377118(-)$1	226	46	49	9.0000
AUU	chr17:46622060-46622283(-)$1	223	0	3	9.0000
AUU	chr5:112154786-112155011(+)$1	225	46	49	9.0000
AUU	chr10:124921791-124922023(+)$1	232	3	6	9.0000
AUU	chr9:138847104-138847328(-)$1	224	11	14	9.0000
AUU	chr12:21796818-21797040(-)$1	222	1	4	9.0000
AUU	chr17:41329874-41330097(+)$1	223	5	8	9.0000
AUU	chr16:29822321-29822585(+)$1	264	136	139	9.0000
AUU	chr16:68156016-68156245(+)$1	229	43	46	9.0000
AUU	chr1:186348845-186349081(+)$1	236	1	4	9.0000
AUU	chr10:62547720-62547941(+)$1	221	0	3	9.0000
AUU	chr5:159851209-159851437(+)$1	228	14	17	9.0000
AUU	chr2:55825497-55825717(-)$1	220	58	61	9.0000
AUU	chr8:144733544-144733769(+)$1	225	59	62	9.0000
AUU	chr7:148494978-148495201(+)$1	223	21	24	9.0000
AUU	chr19:36940130-36940351(-)$1	221	41	44	9.0000
AUU	chr17:3623533-3623758(-)$1	225	41	44	9.0000
AUU	chr19:40542037-40542255(-)$1	218	30	33	9.0000
AUU	chr15:44097482-44097709(-)$1	227	22	25	9.0000
AUU	chr10:98312678-98312907(-)$1	229	6	9	9.0000
AUU	chr19:44739745-44739964(+)$1	219	102	105	9.0000
AUU	chr4:79847689-79847909(-)$1	220	9	12	9.0000
AUU	chr9:88293176-88293403(-)$1	227	0	3	9.0000
AUU	chr19:48893589-48893824(-)$1	235	45	48	9.0000
AUU	chr11:93471181-93471403(-)$1	222	44	47	9.0000
AUU	chr20:47679744-47679968(+)$1	224	1	4	9.0000
AUU	chr5:43505885-43506104(-)$1	219	101	104	9.0000
AUU	chr3:128356671-128356900(-)$1	229	4	7	9.0000
AUU	chr2:219452239-219452462(+)$1	223	43	46	9.0000
AUU	chr2:54114303-54114531(-)$1	228	15	18	9.0000
AUU	chr11:93471507-93471726(-)$1	219	1	4	9.0000
AUU	chrM:9209-9430(+)$1	221	99	102	9.0000
AUU	chr1:26440960-26441184(+)$1	224	40	43	9.0000
AUU	chr5:72856980-72857206(-)$1	226	0	3	9.0000
AUU	chr12:98927401-98927636(+)$1	235	33	36	9.0000
AUU	chr2:219093367-219093599(+)$1	232	42	45	9.0000
AUU	chr20:43615692-43615917(+)$1	225	12	15	9.0000
AUU	chr21:18966518-18966743(-)$1	225	50	53	9.0000
AUU	chr1:19948518-19948742(+)$1	224	0	3	9.0000
AUU	chr10:119043756-119043979(-)$1	223	72	75	9.0000
AUU	chr10:5784255-5784485(+)$1	230	48	51	9.0000
AUU	chr2:176981675-176981893(+)$1	218	204	207	9.0000
AUU	chr4:166262811-166263036(+)$1	225	0	3	9.0000
AUU	chr22:36913263-36913491(-)$1	228	64	67	9.0000
AUU	chr7:107543832-107544055(+)$1	223	14	17	9.0000
AUU	chr19:37368274-37368494(+)$1	220	25	28	9.0000
AUU	chr20:43532544-43532764(+)$1	220	57	60	9.0000
auu	chr7:99144614-99144840(-)$1	226	12	15	9.0000
AUU	chr1:220197639-220197858(-)$1	219	40	43	9.0000
AUU	chr8:29921240-29921458(-)$1	218	8	11	9.0000
AUU	chr19:37038875-37039092(-)$1	217	17	20	9.0000
AUU	chr2:183790311-183790534(-)$1	223	5	8	9.0000
AUU	chr10:70721766-70721989(+)$1	223	18	21	9.0000
AUU	chr9:6015051-6015271(-)$1	220	21	24	9.0000
AUU	chr1:82408743-82408972(+)$1	229	19	22	9.0000

#otherMatches

#Struct PSSM
:::	chrX:153197423-153197652(-)$1	229	107	110	9.0000
:::	chr19:52394276-52394496(-)$1	220	89	92	9.0000
sss	chr2:179407143-179407366(+)$1	223	63	66	9.0000
EKK	chr10:95266662-95266890(+)$1	228	7	10	9.0000
]bb	chr2:183817784-183818008(-)$1	224	70	73	9.0000
:ee	chr14:57858285-57858509(+)$1	224	110	113	9.0000
:::	chr13:53254017-53254238(+)$1	221	33	36	9.0000
III	chr1:214818236-214818455(+)$1	219	24	27	9.0000
fff	chr3:186503933-186504155(+)$1	222	99	102	9.0000
EEE	chrM:10192-10411(+)$1	219	28	31	9.0000
:ee	chr5:43502388-43502612(-)$1	224	0	3	9.0000
uuu	chr22:30035075-30035301(+)$1	226	59	62	9.0000
[hh	chr5:61778849-61779078(+)$1	229	5	8	9.0000
dd3	chr2:85769943-85770178(+)$1	235	20	23	9.0000
)))	chr19:34951334-34951553(+)$1	219	11	14	9.0000
sss	chr6:7402779-7403007(+)$1	228	12	15	9.0000
999	chr19:24309867-24310102(+)$1	235	45	48	9.0000
777	chr6:35841949-35842169(-)$1	220	45	48	9.0000
HHH	chr1:70761752-70761995(-)$1	243	19	22	9.0000
off	chr19:44513138-44513369(+)$1	231	24	27	9.0000
:DD	chr11:32955492-32955727(+)$1	235	21	24	9.0000
!ff	chr6:116968529-116968756(-)$1	227	40	43	9.0000
:::	chr20:54974212-54974448(+)$1	236	25	28	9.0000
:::	chr18:13681974-13682198(-)$1	224	19	22	9.0000
FFF	chr21:33038678-33038901(+)$1	223	30	33	9.0000
enn	chr2:26461702-26461922(-)$1	220	61	64	9.0000
!dd	chr2:190719485-190719707(+)$1	222	29	32	9.0000
qqq	chr12:109525896-109526122(-)$1	226	91	94	9.0000
iii	chr19:38125969-38126193(-)$1	224	5	8	9.0000
44e	chr1:206646533-206646750(-)$1	217	162	165	9.0000
C{B	chr7:103002336-103002556(+)$1	220	12	15	9.0000
ddd	chr16:47733158-47733378(+)$1	220	39	42	9.0000
^^^	chr3:193343796-193344023(+)$1	227	34	37	9.0000
:::	chr5:145863052-145863281(+)$1	229	2	5	9.0000
:::	chr6:114267163-114267388(-)$1	225	0	3	9.0000
fff	chr1:115269509-115269731(-)$1	222	35	38	9.0000
E{J	chrX:123217260-123217481(+)$1	221	22	25	9.0000
B{B	chr6:116599824-116600046(-)$1	222	58	61	9.0000
:::	chr17:40997852-40998082(+)$1	230	17	20	9.0000
:::	chr2:198256919-198257140(-)$1	221	0	3	9.0000
b[c	chr21:34926035-34926255(+)$1	220	14	17	9.0000
:::	chrM:8548-8798(+)$1	250	2	5	9.0000
:::	chr15:66786737-66786965(-)$1	228	5	8	9.0000
:::	chr11:111941104-111941331(+)$1	227	28	31	9.0000
[bb	chr12:123006628-123006848(-)$1	220	111	114	9.0000
ggg	chr19:44376892-44377118(-)$1	226	46	49	9.0000
:::	chr17:46622060-46622283(-)$1	223	0	3	9.0000
fff	chr5:112154786-112155011(+)$1	225	46	49	9.0000
:::	chr10:124921791-124922023(+)$1	232	3	6	9.0000
:::	chr9:138847104-138847328(-)$1	224	11	14	9.0000
:dd	chr12:21796818-21797040(-)$1	222	1	4	9.0000
e##	chr17:41329874-41330097(+)$1	223	5	8	9.0000
:::	chr16:29822321-29822585(+)$1	264	136	139	9.0000
JJJ	chr16:68156016-68156245(+)$1	229	43	46	9.0000
FFF	chr1:186348845-186349081(+)$1	236	1	4	9.0000
:::	chr10:62547720-62547941(+)$1	221	0	3	9.0000
DPP	chr5:159851209-159851437(+)$1	228	14	17	9.0000
33b	chr2:55825497-55825717(-)$1	220	58	61	9.0000
ooo	chr8:144733544-144733769(+)$1	225	59	62	9.0000
GGd	chr7:148494978-148495201(+)$1	223	21	24	9.0000
::d	chr19:36940130-36940351(-)$1	221	41	44	9.0000
EEE	chr17:3623533-3623758(-)$1	225	41	44	9.0000
bbn	chr19:40542037-40542255(-)$1	218	30	33	9.0000
:::	chr15:44097482-44097709(-)$1	227	22	25	9.0000
KKB	chr10:98312678-98312907(-)$1	229	6	9	9.0000
2ii	chr19:44739745-44739964(+)$1	219	102	105	9.0000
:::	chr4:79847689-79847909(-)$1	220	9	12	9.0000
:::	chr9:88293176-88293403(-)$1	227	0	3	9.0000
444	chr19:48893589-48893824(-)$1	235	45	48	9.0000
GGG	chr11:93471181-93471403(-)$1	222	44	47	9.0000
:::	chr20:47679744-47679968(+)$1	224	1	4	9.0000
:::	chr5:43505885-43506104(-)$1	219	101	104	9.0000
:::	chr3:128356671-128356900(-)$1	229	4	7	9.0000
:==	chr2:219452239-219452462(+)$1	223	43	46	9.0000
!dd	chr2:54114303-54114531(-)$1	228	15	18	9.0000
:II	chr11:93471507-93471726(-)$1	219	1	4	9.0000
e^^	chrM:9209-9430(+)$1	221	99	102	9.0000
nnn	chr1:26440960-26441184(+)$1	224	40	43	9.0000
:::	chr5:72856980-72857206(-)$1	226	0	3	9.0000
:::	chr12:98927401-98927636(+)$1	235	33	36	9.0000
fff	chr2:219093367-219093599(+)$1	232	42	45	9.0000
KKH	chr20:43615692-43615917(+)$1	225	12	15	9.0000
GGG	chr21:18966518-18966743(-)$1	225	50	53	9.0000
:::	chr1:19948518-19948742(+)$1	224	0	3	9.0000
[cc	chr10:119043756-119043979(-)$1	223	72	75	9.0000
rff	chr10:5784255-5784485(+)$1	230	48	51	9.0000
vvv	chr2:176981675-176981893(+)$1	218	204	207	9.0000
:::	chr4:166262811-166263036(+)$1	225	0	3	9.0000
###	chr22:36913263-36913491(-)$1	228	64	67	9.0000
FFh	chr7:107543832-107544055(+)$1	223	14	17	9.0000
:::	chr19:37368274-37368494(+)$1	220	25	28	9.0000
qqq	chr20:43532544-43532764(+)$1	220	57	60	9.0000
ee:	chr7:99144614-99144840(-)$1	226	12	15	9.0000
www	chr1:220197639-220197858(-)$1	219	40	43	9.0000
:::	chr8:29921240-29921458(-)$1	218	8	11	9.0000
qcc	chr19:37038875-37039092(-)$1	217	17	20	9.0000
fff	chr2:183790311-183790534(-)$1	223	5	8	9.0000
ggg	chr10:70721766-70721989(+)$1	223	18	21	9.0000
HHH	chr9:6015051-6015271(-)$1	220	21	24	9.0000
BB{	chr1:82408743-82408972(+)$1	229	19	22	9.0000

#DB
...	chrX:153197423-153197652(-)$1	1	107	110	9.0000
...	chr19:52394276-52394496(-)$1	1	89	92	9.0000
...	chr2:179407143-179407366(+)$1	1	63	66	9.0000
(..	chr10:95266662-95266890(+)$1	1	7	10	9.0000
.))	chr2:183817784-183818008(-)$1	1	70	73	9.0000
.((	chr14:57858285-57858509(+)$1	1	110	113	9.0000
...	chr13:53254017-53254238(+)$1	1	33	36	9.0000
(((	chr1:214818236-214818455(+)$1	1	24	27	9.0000
)))	chr3:186503933-186504155(+)$1	1	99	102	9.0000
(((	chrM:10192-10411(+)$1	1	28	31	9.0000
.((	chr5:43502388-43502612(-)$1	1	0	3	9.0000
...	chr22:30035075-30035301(+)$1	1	59	62	9.0000
.((	chr5:61778849-61779078(+)$1	1	5	8	9.0000
)).	chr2:85769943-85770178(+)$1	1	20	23	9.0000
...	chr19:34951334-34951553(+)$1	1	11	14	9.0000
...	chr6:7402779-7403007(+)$1	1	12	15	9.0000
...	chr19:24309867-24310102(+)$1	1	45	48	9.0000
...	chr6:35841949-35842169(-)$1	1	45	48	9.0000
(((	chr1:70761752-70761995(-)$1	1	19	22	9.0000
.))	chr19:44513138-44513369(+)$1	1	24	27	9.0000
.((	chr11:32955492-32955727(+)$1	1	21	24	9.0000
.((	chr6:116968529-116968756(-)$1	1	40	43	9.0000
...	chr20:54974212-54974448(+)$1	1	25	28	9.0000
...	chr18:13681974-13682198(-)$1	1	19	22	9.0000
(((	chr21:33038678-33038901(+)$1	1	30	33	9.0000
(..	chr2:26461702-26461922(-)$1	1	61	64	9.0000
.((	chr2:190719485-190719707(+)$1	1	29	32	9.0000
...	chr12:109525896-109526122(-)$1	1	91	94	9.0000
(((	chr19:38125969-38126193(-)$1	1	5	8	9.0000
..)	chr1:206646533-206646750(-)$1	1	162	165	9.0000
(.(	chr7:103002336-103002556(+)$1	1	12	15	9.0000
(((	chr16:47733158-47733378(+)$1	1	39	42	9.0000
...	chr3:193343796-193344023(+)$1	1	34	37	9.0000
...	chr5:145863052-145863281(+)$1	1	2	5	9.0000
...	chr6:114267163-114267388(-)$1	1	0	3	9.0000
(((	chr1:115269509-115269731(-)$1	1	35	38	9.0000
(.(	chrX:123217260-123217481(+)$1	1	22	25	9.0000
(.(	chr6:116599824-116600046(-)$1	1	58	61	9.0000
...	chr17:40997852-40998082(+)$1	1	17	20	9.0000
...	chr2:198256919-198257140(-)$1	1	0	3	9.0000
(.(	chr21:34926035-34926255(+)$1	1	14	17	9.0000
...	chrM:8548-8798(+)$1	1	2	5	9.0000
...	chr15:66786737-66786965(-)$1	1	5	8	9.0000
...	chr11:111941104-111941331(+)$1	1	28	31	9.0000
.((	chr12:123006628-123006848(-)$1	1	111	114	9.0000
(((	chr19:44376892-44377118(-)$1	1	46	49	9.0000
...	chr17:46622060-46622283(-)$1	1	0	3	9.0000
(((	chr5:112154786-112155011(+)$1	1	46	49	9.0000
...	chr10:124921791-124922023(+)$1	1	3	6	9.0000
...	chr9:138847104-138847328(-)$1	1	11	14	9.0000
.((	chr12:21796818-21797040(-)$1	1	1	4	9.0000
(..	chr17:41329874-41330097(+)$1	1	5	8	9.0000
...	chr16:29822321-29822585(+)$1	1	136	139	9.0000
(((	chr16:68156016-68156245(+)$1	1	43	46	9.0000
(((	chr1:186348845-186349081(+)$1	1	1	4	9.0000
...	chr10:62547720-62547941(+)$1	1	0	3	9.0000
(..	chr5:159851209-159851437(+)$1	1	14	17	9.0000
..)	chr2:55825497-55825717(-)$1	1	58	61	9.0000
...	chr8:144733544-144733769(+)$1	1	59	62	9.0000
(((	chr7:148494978-148495201(+)$1	1	21	24	9.0000
..(	chr19:36940130-36940351(-)$1	1	41	44	9.0000
(((	chr17:3623533-3623758(-)$1	1	41	44	9.0000
((.	chr19:40542037-40542255(-)$1	1	30	33	9.0000
...	chr15:44097482-44097709(-)$1	1	22	25	9.0000
..(	chr10:98312678-98312907(-)$1	1	6	9	9.0000
.))	chr19:44739745-44739964(+)$1	1	102	105	9.0000
...	chr4:79847689-79847909(-)$1	1	9	12	9.0000
...	chr9:88293176-88293403(-)$1	1	0	3	9.0000
...	chr19:48893589-48893824(-)$1	1	45	48	9.0000
(((	chr11:93471181-93471403(-)$1	1	44	47	9.0000
...	chr20:47679744-47679968(+)$1	1	1	4	9.0000
...	chr5:43505885-43506104(-)$1	1	101	104	9.0000
...	chr3:128356671-128356900(-)$1	1	4	7	9.0000
.((	chr2:219452239-219452462(+)$1	1	43	46	9.0000
.((	chr2:54114303-54114531(-)$1	1	15	18	9.0000
.((	chr11:93471507-93471726(-)$1	1	1	4	9.0000
(..	chrM:9209-9430(+)$1	1	99	102	9.0000
...	chr1:26440960-26441184(+)$1	1	40	43	9.0000
...	chr5:72856980-72857206(-)$1	1	0	3	9.0000
...	chr12:98927401-98927636(+)$1	1	33	36	9.0000
)))	chr2:219093367-219093599(+)$1	1	42	45	9.0000
..(	chr20:43615692-43615917(+)$1	1	12	15	9.0000
(((	chr21:18966518-18966743(-)$1	1	50	53	9.0000
...	chr1:19948518-19948742(+)$1	1	0	3	9.0000
.((	chr10:119043756-119043979(-)$1	1	72	75	9.0000
.))	chr10:5784255-5784485(+)$1	1	48	51	9.0000
...	chr2:176981675-176981893(+)$1	1	204	207	9.0000
...	chr4:166262811-166263036(+)$1	1	0	3	9.0000
...	chr22:36913263-36913491(-)$1	1	64	67	9.0000
(((	chr7:107543832-107544055(+)$1	1	14	17	9.0000
...	chr19:37368274-37368494(+)$1	1	25	28	9.0000
...	chr20:43532544-43532764(+)$1	1	57	60	9.0000
)).	chr7:99144614-99144840(-)$1	1	12	15	9.0000
...	chr1:220197639-220197858(-)$1	1	40	43	9.0000
...	chr8:29921240-29921458(-)$1	1	8	11	9.0000
.))	chr19:37038875-37039092(-)$1	1	17	20	9.0000
(((	chr2:183790311-183790534(-)$1	1	5	8	9.0000
(((	chr10:70721766-70721989(+)$1	1	18	21	9.0000
(((	chr9:6015051-6015271(-)$1	1	21	24	9.0000
((.	chr1:82408743-82408972(+)$1	1	19	22	9.0000

#PSSM
A : 0.99	a : 0.01	
U : 0.99	u : 0.01	
U : 0.99	u : 0.01	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_UTR_m2_run1.nuc.txt

#NT
AAAGAAA	chr3:12571991-12572274(+)$1	283	14	21	14.2539
AAAUACA	chr6:39072829-39073086(-)$1	257	68	75	12.6666
aaaaaaa	chr4:31144690-31144930(+)$1	240	44	51	13.8571
AAAUAAA	chr11:66112780-66113020(-)$1	240	153	160	17.1111
UAAUAAA	chr11:9004654-9004894(-)$1	240	177	184	12.5873
AAAUAGA	chr1:57176531-57176771(+)$1	240	110	117	12.6666
AAAUAAA	chr17:35990065-35990305(-)$1	240	191	198	17.1111
AAAUAAA	chr1:26161117-26161357(-)$1	240	17	24	17.1111
AAAUCAA	chr10:102034736-102035021(-)$1	285	99	106	12.7460
AAAUAUA	chr4:6710102-6710344(-)$1	242	158	165	12.9047
AAAUAAA	chr14:55833829-55834071(-)$1	242	23	30	17.1111
AAAUGAA	chr3:182989046-182989326(+)$1	280	23	30	13.1428
AAAUGAA	chrX:99884605-99884845(-)$1	240	146	153	13.1428
AAAUAUA	chr8:124027237-124027540(-)$1	303	6	13	12.9047
AAAUAAA	chr8:62414922-62415175(-)$1	253	95	102	17.1111
CAAUAAA	chr17:70122384-70122624(+)$1	240	148	155	12.7460
CAAUAAA	chr19:41807373-41807613(+)$1	240	173	180	12.7460
AAAUGAA	chr5:68669751-68669991(+)$1	240	123	130	13.1428
AAAAAAA	chr9:37357561-37357803(+)$1	242	16	23	13.8571
AAAUGAA	chr2:55515545-55515785(-)$1	240	173	180	13.1428
CAAUAAA	chr3:9427998-9428238(+)$1	240	219	226	12.7460
AACUAAA	chr3:141122672-141122912(+)$1	240	203	210	12.7460
AAAUAAG	chr18:722471-722711(-)$1	240	53	60	12.6666
aaaaaaa	chr1:24797993-24798383(+)$1	390	75	82	13.8571
AAAUAAA	chr1:70716936-70717183(+)$1	247	200	207	17.1111
AAGUAAA	chr14:50750539-50750779(-)$1	240	140	147	12.5873
AACUAAA	chr2:101893512-101893768(-)$1	256	111	118	12.7460
AAAUAAA	chr3:128902550-128902792(-)$1	242	89	96	17.1111
AUAUAAA	chr11:107396104-107396344(-)$1	240	222	229	12.5079
AAAUAAC	chr1:21545891-21546137(-)$1	246	144	151	12.8253
AAAUAAA	chr3:156424330-156424584(+)$1	254	201	208	17.1111
AAAGAAA	chr6:7285352-7285592(-)$1	240	35	42	14.2539
AAAUAAU	chr13:115089203-115089443(+)$1	240	32	39	12.7460
AAUUAAA	chr9:98247934-98248174(-)$1	240	39	46	12.5873
AAAGAAA	chr1:113002521-113002762(+)$1	241	10	17	14.2539
AAAUAAU	chr3:5260436-5260678(+)$1	242	201	208	12.7460
AAAGAAA	chr17:42477203-42477443(-)$1	240	26	33	14.2539
AAAUAAA	chr5:142657990-142658230(-)$1	240	107	114	17.1111
AAAGAAA	chr14:81940439-81940759(-)$1	320	241	248	14.2539
AAAUGAA	chr2:178404504-178404744(+)$1	240	15	22	13.1428
AAACAAA	chr12:93803238-93803479(-)$1	241	204	211	13.6190
AACUAAA	chr2:70889753-70889993(-)$1	240	197	204	12.7460
AAAAAAA	chr7:106848476-106848717(-)$1	241	99	106	13.8571
AAAGAAA	chr7:44923361-44923601(-)$1	240	147	154	14.2539
AAAUAAA	chr1:230973978-230974258(-)$1	280	56	63	17.1111
AAAUAAC	chr7:98610327-98610567(+)$1	240	33	40	12.8253
AAAUAAA	chr8:41479400-41479640(+)$1	240	9	16	17.1111
AAAUAUA	chr1:235274510-235274846(-)$1	336	90	97	12.9047
GAAUAAA	chr6:31765106-31765346(-)$1	240	153	160	12.5873
AUAUAAA	chr20:33097825-33098072(+)$1	247	230	237	12.5079
AAAGAAA	chr6:88050370-88050610(+)$1	240	55	62	14.2539
AAAUAUA	chr7:108214819-108215059(+)$1	240	4	11	12.9047
AAAUAAA	chr1:149912866-149913107(-)$1	241	91	98	17.1111
AAACAAA	chr6:170881345-170881625(+)$1	280	57	64	13.6190
AAAGAAA	chr3:183529061-183529375(+)$1	314	266	273	14.2539
AAAUAAA	chr10:75135731-75135971(-)$1	240	9	16	17.1111
AAAUGAA	chr17:44833181-44833461(+)$1	280	8	15	13.1428
AAAAAAA	chr5:149366065-149366306(+)$1	241	41	48	13.8571
AAAUAAA	chr4:113570675-113570915(+)$1	240	95	102	17.1111
ACAUAAA	chr18:9861375-9861615(+)$1	240	144	151	12.4285
AAAGAAA	chr2:30863284-30863524(+)$1	240	185	192	14.2539
AAAGAAA	chr5:70806637-70806877(+)$1	240	44	51	14.2539

#otherMatches

#Struct PSSM
UUUUUUU	chr12:54632667-54633033(-)$1	366	20	27	12.8253
RRRRRRR	chr3:12571991-12572274(+)$1	283	14	21	14.2539
IIII:::	chr6:39072829-39073086(-)$1	257	68	75	12.6666
^^^^^^^	chr4:31144690-31144930(+)$1	240	44	51	13.8571
ooooooe	chr11:66112780-66113020(-)$1	240	153	160	17.1111
ggggggg	chr11:9004654-9004894(-)$1	240	177	184	12.5873
wwwwwww	chr1:57176531-57176771(+)$1	240	110	117	12.6666
ZZEEEEE	chr17:35990065-35990305(-)$1	240	191	198	17.1111
I::::::	chr1:26161117-26161357(-)$1	240	17	24	17.1111
:::::::	chr10:102034736-102035021(-)$1	285	99	106	12.7460
ggggggg	chr4:6710102-6710344(-)$1	242	158	165	12.9047
wwwwwww	chr14:55833829-55834071(-)$1	242	23	30	17.1111
:::::::	chr3:182989046-182989326(+)$1	280	23	30	13.1428
qqqqqqc	chrX:99884605-99884845(-)$1	240	146	153	13.1428
&&&&&&f	chr8:124027237-124027540(-)$1	303	6	13	12.9047
gggggg2	chr8:62414922-62415175(-)$1	253	95	102	17.1111
dddd]hh	chr17:70122384-70122624(+)$1	240	148	155	12.7460
:::::CC	chr19:41807373-41807613(+)$1	240	173	180	12.7460
d22====	chr5:68669751-68669991(+)$1	240	123	130	13.1428
:::::CC	chr9:37357561-37357803(+)$1	242	16	23	13.8571
dddd]a2	chr2:55515545-55515785(-)$1	240	173	180	13.1428
:::::::	chr3:9427998-9428238(+)$1	240	219	226	12.7460
:::::GG	chr3:141122672-141122912(+)$1	240	203	210	12.7460
::::::e	chr18:722471-722711(-)$1	240	53	60	12.6666
i::::::	chr1:24797993-24798383(+)$1	390	75	82	13.8571
IIII:::	chr1:70716936-70717183(+)$1	247	200	207	17.1111
hhh++++	chr14:50750539-50750779(-)$1	240	140	147	12.5873
!!fffff	chr2:101893512-101893768(-)$1	256	111	118	12.7460
^^^^^^^	chr3:128902550-128902792(-)$1	242	89	96	17.1111
CC:::::	chr11:107396104-107396344(-)$1	240	222	229	12.5079
:::::::	chr1:21545891-21546137(-)$1	246	144	151	12.8253
[ffffff	chr3:156424330-156424584(+)$1	254	201	208	17.1111
xxxxxxx	chr6:7285352-7285592(-)$1	240	35	42	14.2539
d::::::	chr13:115089203-115089443(+)$1	240	32	39	12.7460
zzzzzzz	chr9:98247934-98248174(-)$1	240	39	46	12.5873
DDDCCC{	chr1:113002521-113002762(+)$1	241	10	17	14.2539
>>>>>>>	chr3:5260436-5260678(+)$1	242	201	208	12.7460
:::::::	chr17:42477203-42477443(-)$1	240	26	33	14.2539
$$$$$gg	chr5:142657990-142658230(-)$1	240	107	114	17.1111
^^^^^^^	chr14:81940439-81940759(-)$1	320	241	248	14.2539
hhhhhhh	chr2:178404504-178404744(+)$1	240	15	22	13.1428
:::::::	chr12:93803238-93803479(-)$1	241	204	211	13.6190
:::::::	chr2:70889753-70889993(-)$1	240	197	204	12.7460
ooooocc	chr7:106848476-106848717(-)$1	241	99	106	13.8571
sssssss	chr7:44923361-44923601(-)$1	240	147	154	14.2539
:::::::	chr1:230973978-230974258(-)$1	280	56	63	17.1111
dd:::::	chr7:98610327-98610567(+)$1	240	33	40	12.8253
RRRRRRR	chr8:41479400-41479640(+)$1	240	9	16	17.1111
lffffff	chr1:235274510-235274846(-)$1	336	90	97	12.9047
ddddlll	chr6:31765106-31765346(-)$1	240	153	160	12.5873
gggggg3	chr20:33097825-33098072(+)$1	247	230	237	12.5079
mmmmggg	chr6:88050370-88050610(+)$1	240	55	62	14.2539
:::::::	chr7:108214819-108215059(+)$1	240	4	11	12.9047
mffffff	chr1:149912866-149913107(-)$1	241	91	98	17.1111
ggggggg	chr6:170881345-170881625(+)$1	280	57	64	13.6190
nnnnfff	chr3:183529061-183529375(+)$1	314	266	273	14.2539
C::::::	chr10:75135731-75135971(-)$1	240	9	16	17.1111
KKA{CCC	chr17:44833181-44833461(+)$1	280	8	15	13.1428
fffffhh	chr5:149366065-149366306(+)$1	241	41	48	13.8571
:EEEEEK	chr4:113570675-113570915(+)$1	240	95	102	17.1111
cccpppp	chr18:9861375-9861615(+)$1	240	144	151	12.4285
:::::::	chr2:30863284-30863524(+)$1	240	185	192	14.2539
^^^^^^^	chr5:70806637-70806877(+)$1	240	44	51	14.2539

#DB
.......	chr12:54632667-54633033(-)$1	1	20	27	12.8253
.......	chr3:12571991-12572274(+)$1	1	14	21	14.2539
((((...	chr6:39072829-39073086(-)$1	1	68	75	12.6666
.......	chr4:31144690-31144930(+)$1	1	44	51	13.8571
......)	chr11:66112780-66113020(-)$1	1	153	160	17.1111
)))))))	chr11:9004654-9004894(-)$1	1	177	184	12.5873
.......	chr1:57176531-57176771(+)$1	1	110	117	12.6666
..)))))	chr17:35990065-35990305(-)$1	1	191	198	17.1111
(......	chr1:26161117-26161357(-)$1	1	17	24	17.1111
.......	chr10:102034736-102035021(-)$1	1	99	106	12.7460
)))))))	chr4:6710102-6710344(-)$1	1	158	165	12.9047
.......	chr14:55833829-55834071(-)$1	1	23	30	17.1111
.......	chr3:182989046-182989326(+)$1	1	23	30	13.1428
......)	chrX:99884605-99884845(-)$1	1	146	153	13.1428
......(	chr8:124027237-124027540(-)$1	1	6	13	12.9047
)))))).	chr8:62414922-62415175(-)$1	1	95	102	17.1111
)))).))	chr17:70122384-70122624(+)$1	1	148	155	12.7460
.....))	chr19:41807373-41807613(+)$1	1	173	180	12.7460
)..))))	chr5:68669751-68669991(+)$1	1	123	130	13.1428
.....((	chr9:37357561-37357803(+)$1	1	16	23	13.8571
)))).).	chr2:55515545-55515785(-)$1	1	173	180	13.1428
.......	chr3:9427998-9428238(+)$1	1	219	226	12.7460
.....))	chr3:141122672-141122912(+)$1	1	203	210	12.7460
......(	chr18:722471-722711(-)$1	1	53	60	12.6666
)......	chr1:24797993-24798383(+)$1	1	75	82	13.8571
))))...	chr1:70716936-70717183(+)$1	1	200	207	17.1111
(((....	chr14:50750539-50750779(-)$1	1	140	147	12.5873
..(((((	chr2:101893512-101893768(-)$1	1	111	118	12.7460
.......	chr3:128902550-128902792(-)$1	1	89	96	17.1111
)).....	chr11:107396104-107396344(-)$1	1	222	229	12.5079
.......	chr1:21545891-21546137(-)$1	1	144	151	12.8253
.((((((	chr3:156424330-156424584(+)$1	1	201	208	17.1111
.......	chr6:7285352-7285592(-)$1	1	35	42	14.2539
)......	chr13:115089203-115089443(+)$1	1	32	39	12.7460
.......	chr9:98247934-98248174(-)$1	1	39	46	12.5873
((((((.	chr1:113002521-113002762(+)$1	1	10	17	14.2539
.......	chr3:5260436-5260678(+)$1	1	201	208	12.7460
.......	chr17:42477203-42477443(-)$1	1	26	33	14.2539
.....((	chr5:142657990-142658230(-)$1	1	107	114	17.1111
.......	chr14:81940439-81940759(-)$1	1	241	248	14.2539
(((((((	chr2:178404504-178404744(+)$1	1	15	22	13.1428
.......	chr12:93803238-93803479(-)$1	1	204	211	13.6190
.......	chr2:70889753-70889993(-)$1	1	197	204	12.7460
.....))	chr7:106848476-106848717(-)$1	1	99	106	13.8571
.......	chr7:44923361-44923601(-)$1	1	147	154	14.2539
.......	chr1:230973978-230974258(-)$1	1	56	63	17.1111
)).....	chr7:98610327-98610567(+)$1	1	33	40	12.8253
.......	chr8:41479400-41479640(+)$1	1	9	16	17.1111
.))))))	chr1:235274510-235274846(-)$1	1	90	97	12.9047
((((...	chr6:31765106-31765346(-)$1	1	153	160	12.5873
)))))).	chr20:33097825-33098072(+)$1	1	230	237	12.5079
....)))	chr6:88050370-88050610(+)$1	1	55	62	14.2539
.......	chr7:108214819-108215059(+)$1	1	4	11	12.9047
.))))))	chr1:149912866-149913107(-)$1	1	91	98	17.1111
(((((((	chr6:170881345-170881625(+)$1	1	57	64	13.6190
....)))	chr3:183529061-183529375(+)$1	1	266	273	14.2539
(......	chr10:75135731-75135971(-)$1	1	9	16	17.1111
..(.(((	chr17:44833181-44833461(+)$1	1	8	15	13.1428
)))))((	chr5:149366065-149366306(+)$1	1	41	48	13.8571
.(((((.	chr4:113570675-113570915(+)$1	1	95	102	17.1111
(((....	chr18:9861375-9861615(+)$1	1	144	151	12.4285
.......	chr2:30863284-30863524(+)$1	1	185	192	14.2539
.......	chr5:70806637-70806877(+)$1	1	44	51	14.2539

#PSSM
A : 0.88	C : 0.04	a : 0.03	U : 0.01	G : 0.01	
A : 0.92	a : 0.03	U : 0.03	C : 0.01	
A : 0.88	C : 0.04	a : 0.03	G : 0.01	U : 0.01	
U : 0.73	G : 0.15	A : 0.04	a : 0.03	C : 0.03	
A : 0.85	G : 0.09	a : 0.03	C : 0.01	
A : 0.87	U : 0.06	a : 0.03	C : 0.01	G : 0.01	
A : 0.87	C : 0.04	a : 0.03	U : 0.03	G : 0.01	

#score	888.0793650793637
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m1_run1.nuc.txt

#NT
CUUUAAAUU	chr1:53679511-53679741(+)$1	230	186	195	13.6346
UUUUAAUAU	chr1:162496523-162496753(+)$1	230	97	106	14.5961
UUUUAAGUG	chr9:114984794-114985016(-)$1	222	72	81	16.0384
UUGUAAGUU	chr12:22842151-22842392(+)$1	241	79	88	14.9807
UUUUAAAAU	chr5:74100306-74100530(-)$1	224	77	86	14.3076
UUUUCUGUU	chr16:48576517-48576747(-)$1	230	143	152	13.2500
UUUUAAUUU	chr16:66756202-66756426(-)$1	224	108	117	18.3461
UUUUCAGUG	chr7:32908401-32908631(-)$1	230	91	100	13.4423
UUUUAAAUU	chr8:17914112-17914342(-)$1	230	100	109	18.0576
UUUUUAGUU	chr11:121178962-121179183(+)$1	221	92	101	17.0000
UUUUUUGUU	chr1:41236588-41236818(+)$1	230	92	101	13.3461
UUUUAAGUA	chrX:77305428-77305658(+)$1	230	56	65	15.7500
UUUUAAAUU	chr15:52605148-52605371(-)$1	223	102	111	18.0576
UUUUAACAU	chr14:51187082-51187319(-)$1	237	181	190	13.7307
UUUuuuguu	chr1:92974801-92975023(-)$1	222	27	36	13.3461
UUUUAAGuu	chr1:36067499-36067726(-)$1	227	84	93	19.5000
UUUUAAUCU	chr8:17092216-17092446(-)$1	230	19	28	14.2115
UUUUCAUUU	chr8:103216946-103217168(-)$1	222	136	145	15.7500
UUUUACAUU	chr15:100253721-100253951(+)$1	230	13	22	13.9230
UUAUAAUUU	chrX:103344704-103344926(-)$1	222	110	119	13.7307
UUUUAAUGU	chr5:82352573-82352803(-)$1	230	38	47	14.3076
UUUUGAGUU	chr9:72325911-72326134(-)$1	223	58	67	16.5192
UUUUAAGGU	chr1:85733058-85733288(-)$1	230	204	213	15.4615
UUUUAAGUC	chr10:70931949-70932179(+)$1	230	135	144	15.5576
UUUUGAGUA	chr11:82692180-82692410(-)$1	230	132	141	12.7692
UUUUAAAUA	chr19:1434976-1435206(+)$1	230	100	109	14.3076
UUUUUAAUU	chr9:123617887-123618111(-)$1	224	97	106	15.5576
UUGUAAUUU	chr17:57189239-57189469(-)$1	230	96	105	13.8269
UUUUAUGUU	chr2:61610329-61610559(-)$1	230	69	78	15.8461
UUUUAAUUU	chr1:247462948-247463178(-)$1	230	106	115	18.3461
CUUUAAUUU	chr2:74380698-74380924(-)$1	226	114	123	13.9230
uuuuuacuu	chr1:167388160-167388390(+)$1	230	7	16	14.9807
UUUUCAGUG	chr3:186791863-186792088(+)$1	225	76	85	13.4423
UUUUCAGUU	chr15:44093936-44094161(+)$1	225	129	138	16.9038
UUUUUAGAU	chr7:26231144-26231370(-)$1	226	93	102	13.2500
UUUUCUGUU	chr15:79189496-79189719(+)$1	223	27	36	13.2500
AUUUAAGUU	chrX:131337642-131337872(-)$1	230	87	96	15.0769
UUUUAAUUU	chr6:57034320-57034543(+)$1	223	180	189	18.3461
UUUUAAGAU	chr4:185309010-185309235(-)$1	225	194	203	15.7500
UUUUUAUUU	chr6:109688398-109688637(-)$1	239	13	22	15.8461
UUUUAAUUU	chr4:88061352-88061577(+)$1	225	191	200	18.3461
UUUUAAAUU	chr17:40467200-40467419(-)$1	219	165	174	18.0576
UUUUAUGUU	chr6:11136626-11136849(+)$1	223	18	27	15.8461
UUUUAAGUU	chr7:7646975-7647205(+)$1	230	164	173	19.5000
AUUUAAUUU	chr4:26435650-26435890(+)$1	240	12	21	13.9230
UUUUAGCUU	chr5:77772404-77772634(+)$1	230	93	102	13.3461
UUUUAAGUG	chr11:67023710-67023934(+)$1	224	161	170	16.0384
UUUUAAGUU	chr8:130854281-130854511(-)$1	230	17	26	19.5000
UUUUAAAUG	chr11:58976723-58976947(-)$1	224	91	100	14.5961
UUUUUACUU	chr19:41813383-41813607(+)$1	224	64	73	14.9807
UUUUGAAUU	chr5:167978204-167978429(-)$1	225	31	40	15.0769

#otherMatches

#Struct PSSM
GGGG{BB{B	chr1:101706925-101707155(+)$1	230	13	22	13.4423
iiiiiiiqq	chr1:53679511-53679741(+)$1	230	186	195	13.6346
i22dddd]b	chr1:162496523-162496753(+)$1	230	97	106	14.5961
qqqqqqeee	chr9:114984794-114985016(-)$1	222	72	81	16.0384
IIIIggggg	chr12:22842151-22842392(+)$1	241	79	88	14.9807
eee####ee	chr5:74100306-74100530(-)$1	224	77	86	14.3076
nnnnngggg	chr16:48576517-48576747(-)$1	230	143	152	13.2500
GGGGG}GGG	chr16:66756202-66756426(-)$1	224	108	117	18.3461
:::::ffff	chr7:32908401-32908631(-)$1	230	91	100	13.4423
ffffHHHHH	chr8:17914112-17914342(-)$1	230	100	109	18.0576
mmmeeeee8	chr11:121178962-121179183(+)$1	221	92	101	17.0000
oooodddd]	chr1:41236588-41236818(+)$1	230	92	101	13.3461
qqqqqqccc	chrX:77305428-77305658(+)$1	230	56	65	15.7500
hhhh:GGGG	chr15:52605148-52605371(-)$1	223	102	111	18.0576
:::::eeee	chr14:51187082-51187319(-)$1	237	181	190	13.7307
^^^^^^^^^	chr1:92974801-92975023(-)$1	222	27	36	13.3461
:::::CCC{	chr1:36067499-36067726(-)$1	227	84	93	19.5000
gggg:::::	chr8:17092216-17092446(-)$1	230	19	28	14.2115
b22======	chr8:103216946-103217168(-)$1	222	136	145	15.7500
eee]bb:::	chr15:100253721-100253951(+)$1	230	13	22	13.9230
$$$$$eeee	chrX:103344704-103344926(-)$1	222	110	119	13.7307
FFMMMMCCC	chr5:82352573-82352803(-)$1	230	38	47	14.3076
dddd!!ccc	chr9:72325911-72326134(-)$1	223	58	67	16.5192
ddd]hhhhh	chr1:85733058-85733288(-)$1	230	204	213	15.4615
22bb]ccc3	chr10:70931949-70932179(+)$1	230	135	144	15.5576
ttttdddd:	chr11:82692180-82692410(-)$1	230	132	141	12.7692
qqqqqqqqe	chr19:1434976-1435206(+)$1	230	100	109	14.3076
d7777777c	chr9:123617887-123618111(-)$1	224	97	106	15.5576
dd'''''''	chr17:57189239-57189469(-)$1	230	96	105	13.8269
GGKKDDDDL	chr2:61610329-61610559(-)$1	230	69	78	15.8461
vvvvvveee	chr1:247462948-247463178(-)$1	230	106	115	18.3461
c22ffffff	chr2:74380698-74380924(-)$1	226	114	123	13.9230
:::::gggg	chr1:167388160-167388390(+)$1	230	7	16	14.9807
88888eeee	chr3:186791863-186792088(+)$1	225	76	85	13.4423
33ffffff:	chr15:44093936-44094161(+)$1	225	129	138	16.9038
dd:ccc!!f	chr7:26231144-26231370(-)$1	226	93	102	13.2500
=========	chr15:79189496-79189719(+)$1	223	27	36	13.2500
'========	chrX:131337642-131337872(-)$1	230	87	96	15.0769
JJJJJJCCC	chr6:57034320-57034543(+)$1	223	180	189	18.3461
EEEEE}CCC	chr4:185309010-185309235(-)$1	225	194	203	15.7500
:::::::::	chr6:109688398-109688637(-)$1	239	13	22	15.8461
:::::::::	chr4:88061352-88061577(+)$1	225	191	200	18.3461
gqqqqqqqq	chr17:40467200-40467419(-)$1	219	165	174	18.0576
JJJJKKBB{	chr6:11136626-11136849(+)$1	223	18	27	15.8461
DDDCCC}HH	chr7:7646975-7647205(+)$1	230	164	173	19.5000
BLLLDDDD{	chr4:26435650-26435890(+)$1	240	12	21	13.9230
fffHHHHHH	chr5:77772404-77772634(+)$1	230	93	102	13.3461
||||||CCC	chr11:67023710-67023934(+)$1	224	161	170	16.0384
::::::bb[	chr8:130854281-130854511(-)$1	230	17	26	19.5000
:::::hhhh	chr11:58976723-58976947(-)$1	224	91	100	14.5961
uuueeeee:	chr19:41813383-41813607(+)$1	224	64	73	14.9807
ggHHHHHHH	chr5:167978204-167978429(-)$1	225	31	40	15.0769

#DB
((((.((.(	chr1:101706925-101707155(+)$1	1	13	22	13.4423
(((((((..	chr1:53679511-53679741(+)$1	1	186	195	13.6346
)..)))).)	chr1:162496523-162496753(+)$1	1	97	106	14.5961
......)))	chr9:114984794-114985016(-)$1	1	72	81	16.0384
(((((((((	chr12:22842151-22842392(+)$1	1	79	88	14.9807
(((....((	chr5:74100306-74100530(-)$1	1	77	86	14.3076
.....))))	chr16:48576517-48576747(-)$1	1	143	152	13.2500
))))).)))	chr16:66756202-66756426(-)$1	1	108	117	18.3461
.....((((	chr7:32908401-32908631(-)$1	1	91	100	13.4423
))))(((((	chr8:17914112-17914342(-)$1	1	100	109	18.0576
...))))).	chr11:121178962-121179183(+)$1	1	92	101	17.0000
....)))).	chr1:41236588-41236818(+)$1	1	92	101	13.3461
......)))	chrX:77305428-77305658(+)$1	1	56	65	15.7500
)))).))))	chr15:52605148-52605371(-)$1	1	102	111	18.0576
.....((((	chr14:51187082-51187319(-)$1	1	181	190	13.7307
.........	chr1:92974801-92975023(-)$1	1	27	36	13.3461
.....(((.	chr1:36067499-36067726(-)$1	1	84	93	19.5000
)))).....	chr8:17092216-17092446(-)$1	1	19	28	14.2115
)..))))))	chr8:103216946-103217168(-)$1	1	136	145	15.7500
))).))...	chr15:100253721-100253951(+)$1	1	13	22	13.9230
.....((((	chrX:103344704-103344926(-)$1	1	110	119	13.7307
((....(((	chr5:82352573-82352803(-)$1	1	38	47	14.3076
((((..(((	chr9:72325911-72326134(-)$1	1	58	67	16.5192
))).)))))	chr1:85733058-85733288(-)$1	1	204	213	15.4615
..)).))).	chr10:70931949-70932179(+)$1	1	135	144	15.5576
....)))).	chr11:82692180-82692410(-)$1	1	132	141	12.7692
........)	chr19:1434976-1435206(+)$1	1	100	109	14.3076
).......)	chr9:123617887-123618111(-)$1	1	97	106	15.5576
((.......	chr17:57189239-57189469(-)$1	1	96	105	13.8269
((..((((.	chr2:61610329-61610559(-)$1	1	69	78	15.8461
......)))	chr1:247462948-247463178(-)$1	1	106	115	18.3461
)..))))))	chr2:74380698-74380924(-)$1	1	114	123	13.9230
.....((((	chr1:167388160-167388390(+)$1	1	7	16	14.9807
.....))))	chr3:186791863-186792088(+)$1	1	76	85	13.4423
..)))))).	chr15:44093936-44094161(+)$1	1	129	138	16.9038
)).(((..(	chr7:26231144-26231370(-)$1	1	93	102	13.2500
(((((((((	chr15:79189496-79189719(+)$1	1	27	36	13.2500
.((((((((	chrX:131337642-131337872(-)$1	1	87	96	15.0769
)))))))))	chr6:57034320-57034543(+)$1	1	180	189	18.3461
))))).)))	chr4:185309010-185309235(-)$1	1	194	203	15.7500
.........	chr6:109688398-109688637(-)$1	1	13	22	15.8461
.........	chr4:88061352-88061577(+)$1	1	191	200	18.3461
(........	chr17:40467200-40467419(-)$1	1	165	174	18.0576
((((..((.	chr6:11136626-11136849(+)$1	1	18	27	15.8461
)))))).))	chr7:7646975-7647205(+)$1	1	164	173	19.5000
(...((((.	chr4:26435650-26435890(+)$1	1	12	21	13.9230
)))))))))	chr5:77772404-77772634(+)$1	1	93	102	13.3461
......)))	chr11:67023710-67023934(+)$1	1	161	170	16.0384
......((.	chr8:130854281-130854511(-)$1	1	17	26	19.5000
.....((((	chr11:58976723-58976947(-)$1	1	91	100	14.5961
...))))).	chr19:41813383-41813607(+)$1	1	64	73	14.9807
))(((((((	chr5:167978204-167978429(-)$1	1	31	40	15.0769

#PSSM
U : 0.90	C : 0.03	A : 0.03	u : 0.01	
U : 0.98	u : 0.01	
U : 0.92	G : 0.03	A : 0.01	u : 0.01	
U : 0.96	u : 0.03	
A : 0.65	C : 0.13	U : 0.11	G : 0.05	u : 0.03	
A : 0.82	U : 0.09	u : 0.01	C : 0.01	a : 0.01	G : 0.01	
G : 0.46	U : 0.24	A : 0.19	C : 0.05	g : 0.01	c : 0.01	
U : 0.78	A : 0.09	u : 0.05	G : 0.03	C : 0.01	
U : 0.75	G : 0.11	A : 0.05	u : 0.05	C : 0.01	

#score	800.9230769230772
#seq	52
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m2_run2.nuc.txt

#NT
AUUUUUCU	chr9:32540782-32541076(-)$1	294	109	117	16.4038
auuuuuuu	chr3:196557589-196557813(+)$1	224	177	185	20.0576
auauuuuu	chrX:37315182-37315415(+)$1	233	26	34	16.2115
AUUUUCUU	chr12:4796389-4796617(+)$1	228	19	27	15.8269
AUUUUUUU	chr4:140427318-140427544(-)$1	226	126	134	20.0576
AUUUUUUU	chr12:117583200-117583430(-)$1	230	114	122	20.0576
aucuuuuu	chrX:153213817-153214046(-)$1	229	59	67	16.2115
AUUUUUGU	chr2:192289642-192289872(+)$1	230	25	33	16.5000
GUUUUUUU	chr1:54562872-54563100(+)$1	228	77	85	15.4423
AUCUUUUU	chr2:10193138-10193364(+)$1	226	37	45	16.2115
AUUUUUUC	chr2:20449739-20449968(-)$1	229	210	218	15.8269
AUCUUUUU	chr15:67494801-67495034(-)$1	233	39	47	16.2115
AUUUUUCU	chr4:139092666-139092920(-)$1	254	156	164	16.4038
AUUUUUUU	chr5:122359205-122359431(-)$1	226	134	142	20.0576
AUUUUUAU	chr17:58520749-58520972(-)$1	223	104	112	16.1153
AUUUCUUU	chr6:45518465-45518737(+)$1	272	35	43	15.7307
AUUUUUUC	chr3:15709909-15710140(-)$1	231	109	117	15.8269
AUGUUUUU	chrX:153295588-153295816(-)$1	228	178	186	16.2115
auuuuuuu	chr17:1323995-1324225(-)$1	230	145	153	20.0576
AUUUUUGU	chr16:18817153-18817399(-)$1	246	55	63	16.5000
AUAUUUUU	chr12:42553109-42553336(-)$1	227	76	84	16.2115
AUUUUCUU	chr2:215590452-215590709(-)$1	257	225	233	15.8269
AUUUUUUU	chr5:175934415-175934705(+)$1	290	111	119	20.0576
auuuuauu	chr4:186081765-186082039(-)$1	274	0	8	15.7307
AGUUUUUU	chr1:61921555-61921800(+)$1	245	122	130	15.7307
AUUUUUCU	chr17:56167268-56167522(+)$1	254	140	148	16.4038
AUUUUUGU	chr4:15068136-15068369(+)$1	233	66	74	16.5000
AGUUUUUU	chr4:41957816-41958054(+)$1	238	105	113	15.7307
AUGUUUUU	chr3:140696980-140697252(+)$1	272	42	50	16.2115
AUUUUCUU	chr4:123814438-123814684(+)$1	246	112	120	15.8269
AUUUUUUU	chr11:96126398-96126624(+)$1	226	169	177	20.0576
AUUUCUUU	chr5:90664783-90665027(-)$1	244	145	153	15.7307
ACUUUUUU	chr7:27871512-27871772(-)$1	260	166	174	15.7307
auauuuuu	chr3:110853478-110853708(+)$1	230	58	66	16.2115
AUUUUUUC	chr3:23631542-23631778(+)$1	236	26	34	15.8269
AUUAUUUU	chr9:36677326-36677550(+)$1	224	165	173	15.2500
CUUUUUUU	chr5:1462846-1463112(-)$1	266	151	159	15.5384
AUUUUUCU	chr11:76737577-76737803(+)$1	226	140	148	16.4038
AUUUUUGU	chr4:139085198-139085439(-)$1	241	119	127	16.5000
AUUUUUUU	chr4:17609317-17609575(+)$1	258	39	47	20.0576
auuuauuu	chr20:43707348-43707598(+)$1	250	73	81	15.5384
AUUUCUUU	chr3:141167525-141167770(+)$1	245	48	56	15.7307
AUUUUUGU	chr3:101485142-101485392(+)$1	250	67	75	16.5000
AUUUUUUU	chr3:52937594-52937818(-)$1	224	101	109	20.0576
AAUUUUUU	chr5:158584539-158584767(-)$1	228	159	167	15.6346
CUUUUUUU	chr5:82351554-82351784(-)$1	230	142	150	15.5384
AUUUUUUU	chr11:117040281-117040528(+)$1	247	174	182	20.0576
acuuuuuu	chr3:111632891-111633121(+)$1	230	46	54	15.7307
AUUUUUUU	chr17:43226389-43226644(+)$1	255	108	116	20.0576
AUUUUAUU	chr2:175938492-175938761(-)$1	269	122	130	15.7307
AUUUUUUC	chr4:52752901-52753132(+)$1	231	102	110	15.8269

#otherMatches

#Struct PSSM
gggggg55	chr8:124261076-124261335(-)$1	259	48	56	16.2115
ffffffoo	chr9:32540782-32541076(-)$1	294	109	117	16.4038
::::::::	chr3:196557589-196557813(+)$1	224	177	185	20.0576
dddmmmmd	chrX:37315182-37315415(+)$1	233	26	34	16.2115
JJJJJKKF	chr12:4796389-4796617(+)$1	228	19	27	15.8269
====mmmm	chr4:140427318-140427544(-)$1	226	126	134	20.0576
=+++++++	chr12:117583200-117583430(-)$1	230	114	122	20.0576
d^^^^^^^	chrX:153213817-153214046(-)$1	229	59	67	16.2115
f[eeeeee	chr2:192289642-192289872(+)$1	230	25	33	16.5000
ssssssss	chr1:54562872-54563100(+)$1	228	77	85	15.4423
beeeee##	chr2:10193138-10193364(+)$1	226	37	45	16.2115
::::::cc	chr2:20449739-20449968(-)$1	229	210	218	15.8269
======""	chr15:67494801-67495034(-)$1	233	39	47	16.2115
c55555hh	chr4:139092666-139092920(-)$1	254	156	164	16.4038
qqqqqqee	chr5:122359205-122359431(-)$1	226	134	142	20.0576
gggggg::	chr17:58520749-58520972(-)$1	223	104	112	16.1153
dddd22ff	chr6:45518465-45518737(+)$1	272	35	43	15.7307
bb!!eeee	chr3:15709909-15710140(-)$1	231	109	117	15.8269
gggggghh	chrX:153295588-153295816(-)$1	228	178	186	16.2115
ffffffdd	chr17:1323995-1324225(-)$1	230	145	153	20.0576
66======	chr16:18817153-18817399(-)$1	246	55	63	16.5000
flllffff	chr12:42553109-42553336(-)$1	227	76	84	16.2115
DD::::dd	chr2:215590452-215590709(-)$1	257	225	233	15.8269
::::::::	chr5:175934415-175934705(+)$1	290	111	119	20.0576
:JJJJJJJ	chr4:186081765-186082039(-)$1	274	0	8	15.7307
ddd[gggg	chr1:61921555-61921800(+)$1	245	122	130	15.7307
^^^^^^^^	chr17:56167268-56167522(+)$1	254	140	148	16.4038
66eeeeee	chr4:15068136-15068369(+)$1	233	66	74	16.5000
hggggggg	chr4:41957816-41958054(+)$1	238	105	113	15.7307
EKKBBLLL	chr3:140696980-140697252(+)$1	272	42	50	16.2115
::::::dd	chr4:123814438-123814684(+)$1	246	112	120	15.8269
::::::::	chr11:96126398-96126624(+)$1	226	169	177	20.0576
rrrrrhhh	chr5:90664783-90665027(-)$1	244	145	153	15.7307
oooooddd	chr7:27871512-27871772(-)$1	260	166	174	15.7307
fffffmmm	chr3:110853478-110853708(+)$1	230	58	66	16.2115
ennnnnee	chr3:23631542-23631778(+)$1	236	26	34	15.8269
ggg::HHH	chr9:36677326-36677550(+)$1	224	165	173	15.2500
^^^^^^^^	chr5:1462846-1463112(-)$1	266	151	159	15.5384
e:::::::	chr11:76737577-76737803(+)$1	226	140	148	16.4038
ffff%%%%	chr4:139085198-139085439(-)$1	241	119	127	16.5000
cqqqqqqq	chr4:17609317-17609575(+)$1	258	39	47	20.0576
yyyyyyyy	chr20:43707348-43707598(+)$1	250	73	81	15.5384
>>>>>>>>	chr3:141167525-141167770(+)$1	245	48	56	15.7307
ddmmmmdd	chr3:101485142-101485392(+)$1	250	67	75	16.5000
&&&&&&gg	chr3:52937594-52937818(-)$1	224	101	109	20.0576
hh000000	chr5:158584539-158584767(-)$1	228	159	167	15.6346
:ggggggg	chr5:82351554-82351784(-)$1	230	142	150	15.5384
d7777777	chr11:117040281-117040528(+)$1	247	174	182	20.0576
]bb]ccc>	chr3:111632891-111633121(+)$1	230	46	54	15.7307
::::::::	chr17:43226389-43226644(+)$1	255	108	116	20.0576
=======[	chr2:175938492-175938761(-)$1	269	122	130	15.7307
e>>>>>>>	chr4:52752901-52753132(+)$1	231	102	110	15.8269

#DB
))))))..	chr8:124261076-124261335(-)$1	1	48	56	16.2115
((((((..	chr9:32540782-32541076(-)$1	1	109	117	16.4038
........	chr3:196557589-196557813(+)$1	1	177	185	20.0576
(((....)	chrX:37315182-37315415(+)$1	1	26	34	16.2115
(((((..(	chr12:4796389-4796617(+)$1	1	19	27	15.8269
((((....	chr4:140427318-140427544(-)$1	1	126	134	20.0576
(.......	chr12:117583200-117583430(-)$1	1	114	122	20.0576
(.......	chrX:153213817-153214046(-)$1	1	59	67	16.2115
(.((((((	chr2:192289642-192289872(+)$1	1	25	33	16.5000
........	chr1:54562872-54563100(+)$1	1	77	85	15.4423
((((((..	chr2:10193138-10193364(+)$1	1	37	45	16.2115
......((	chr2:20449739-20449968(-)$1	1	210	218	15.8269
((((((..	chr15:67494801-67495034(-)$1	1	39	47	16.2115
).....))	chr4:139092666-139092920(-)$1	1	156	164	16.4038
......))	chr5:122359205-122359431(-)$1	1	134	142	20.0576
))))))..	chr17:58520749-58520972(-)$1	1	104	112	16.1153
))))..))	chr6:45518465-45518737(+)$1	1	35	43	15.7307
((..((((	chr3:15709909-15710140(-)$1	1	109	117	15.8269
))))))))	chrX:153295588-153295816(-)$1	1	178	186	16.2115
((((((((	chr17:1323995-1324225(-)$1	1	145	153	20.0576
..))))))	chr16:18817153-18817399(-)$1	1	55	63	16.5000
(...))))	chr12:42553109-42553336(-)$1	1	76	84	16.2115
))....((	chr2:215590452-215590709(-)$1	1	225	233	15.8269
........	chr5:175934415-175934705(+)$1	1	111	119	20.0576
.(((((((	chr4:186081765-186082039(-)$1	1	0	8	15.7307
(((.((((	chr1:61921555-61921800(+)$1	1	122	130	15.7307
........	chr17:56167268-56167522(+)$1	1	140	148	16.4038
..))))))	chr4:15068136-15068369(+)$1	1	66	74	16.5000
))))))))	chr4:41957816-41958054(+)$1	1	105	113	15.7307
(..((...	chr3:140696980-140697252(+)$1	1	42	50	16.2115
......((	chr4:123814438-123814684(+)$1	1	112	120	15.8269
........	chr11:96126398-96126624(+)$1	1	169	177	20.0576
.....)))	chr5:90664783-90665027(-)$1	1	145	153	15.7307
.....)))	chr7:27871512-27871772(-)$1	1	166	174	15.7307
(((((...	chr3:110853478-110853708(+)$1	1	58	66	16.2115
(.....))	chr3:23631542-23631778(+)$1	1	26	34	15.8269
)))..)))	chr9:36677326-36677550(+)$1	1	165	173	15.2500
........	chr5:1462846-1463112(-)$1	1	151	159	15.5384
).......	chr11:76737577-76737803(+)$1	1	140	148	16.4038
((((....	chr4:139085198-139085439(-)$1	1	119	127	16.5000
(.......	chr4:17609317-17609575(+)$1	1	39	47	20.0576
........	chr20:43707348-43707598(+)$1	1	73	81	15.5384
........	chr3:141167525-141167770(+)$1	1	48	56	15.7307
((....))	chr3:101485142-101485392(+)$1	1	67	75	16.5000
......((	chr3:52937594-52937818(-)$1	1	101	109	20.0576
))......	chr5:158584539-158584767(-)$1	1	159	167	15.6346
.(((((((	chr5:82351554-82351784(-)$1	1	142	150	15.5384
).......	chr11:117040281-117040528(+)$1	1	174	182	20.0576
.)).))).	chr3:111632891-111633121(+)$1	1	46	54	15.7307
........	chr17:43226389-43226644(+)$1	1	108	116	20.0576
(((((((.	chr2:175938492-175938761(-)$1	1	122	130	15.7307
).......	chr4:52752901-52753132(+)$1	1	102	110	15.8269

#PSSM
A : 0.78	a : 0.15	C : 0.03	G : 0.01	
U : 0.76	u : 0.13	G : 0.03	C : 0.01	A : 0.01	c : 0.01	
U : 0.73	u : 0.09	G : 0.05	a : 0.03	C : 0.03	c : 0.01	A : 0.01	
U : 0.82	u : 0.15	A : 0.01	
U : 0.78	u : 0.13	C : 0.05	a : 0.01	
U : 0.76	u : 0.13	C : 0.05	a : 0.01	A : 0.01	
U : 0.65	u : 0.15	G : 0.09	C : 0.07	A : 0.01	
U : 0.76	u : 0.15	C : 0.07	

#score	876.0769230769234
#seq	52
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m2_run1.nuc.txt

#NT
AAA	chr1:29446428-29446651(+)$1	223	107	110	8.9999
AAA	chr1:59247103-59247329(-)$1	226	127	130	8.9999
AAA	chr1:879903-880124(-)$1	221	198	201	8.9999
AAA	chr4:120219176-120219407(-)$1	231	0	3	8.9999
AAA	chr17:40467525-40467748(-)$1	223	9	12	8.9999
AAA	chr7:112460662-112460890(-)$1	228	32	35	8.9999
AAA	chr2:175937203-175937431(-)$1	228	4	7	8.9999
AAA	chr1:52382728-52382957(-)$1	229	3	6	8.9999
AAA	chr17:5335894-5336115(+)$1	221	99	102	8.9999
AAA	chrX:152140620-152140839(+)$1	219	8	11	8.9999
AAA	chr2:207024327-207024553(+)$1	226	121	124	8.9999
AAA	chr11:73113002-73113221(-)$1	219	120	123	8.9999
AAA	chr4:79836173-79836398(+)$1	225	8	11	8.9999
AAA	chr8:8994571-8994798(-)$1	227	8	11	8.9999
AAA	chr3:9519356-9519575(+)$1	219	29	32	8.9999
AAA	chr8:26229880-26230100(+)$1	220	53	56	8.9999
AAA	chr10:127524874-127525099(+)$1	225	5	8	8.9999
AAA	chr12:117582548-117582786(-)$1	238	43	46	8.9999
AAA	chr12:25360655-25360887(-)$1	232	99	102	8.9999
AAA	chr8:74704557-74704777(-)$1	220	2	5	8.9999
AAA	chr15:67494868-67495097(-)$1	229	20	23	8.9999
AAA	chr15:35272105-35272329(-)$1	224	22	25	8.9999
AAA	chr2:203426449-203426672(+)$1	223	8	11	8.9999
AAA	chr18:32916944-32917167(-)$1	223	19	22	8.9999
AAA	chr1:228880541-228880767(+)$1	226	34	37	8.9999
aaa	chr13:52605804-52606025(+)$1	221	54	57	8.9999
AAA	chr8:127567098-127567326(-)$1	228	2	5	8.9999
AAA	chr12:112460652-112460877(+)$1	225	27	30	8.9999
AAA	chr9:135569347-135569568(+)$1	221	50	53	8.9999
AAA	chr16:3023012-3023241(+)$1	229	85	88	8.9999
AAA	chr3:30735294-30735518(+)$1	224	55	58	8.9999
AAA	chr16:1750352-1750576(+)$1	224	78	81	8.9999
AAA	chr22:21976251-21976478(+)$1	227	26	29	8.9999
AAA	chr1:205578747-205578982(-)$1	235	26	29	8.9999
AAA	chr3:133876459-133876679(-)$1	220	85	88	8.9999
AAA	chr7:139253306-139253525(-)$1	219	55	58	8.9999
aaa	chr10:102121512-102121735(+)$1	223	72	75	8.9999
AAA	chr2:29023649-29023873(+)$1	224	59	62	8.9999
AAA	chr1:201852993-201853217(+)$1	224	5	8	8.9999
AAA	chr12:69235226-69235456(+)$1	230	28	31	8.9999
AAA	chr2:201768473-201768702(+)$1	229	69	72	8.9999
AAA	chr1:101445079-101445310(+)$1	231	22	25	8.9999
AAA	chr1:205683224-205683458(-)$1	234	42	45	8.9999
AAA	chr8:38961598-38961820(+)$1	222	48	51	8.9999
AAA	chrX:24231450-24231674(+)$1	224	31	34	8.9999
AAA	chr5:162871219-162871442(+)$1	223	36	39	8.9999
AAA	chr5:14695177-14695396(+)$1	219	41	44	8.9999
AAA	chr18:722117-722343(-)$1	226	15	18	8.9999
AAA	chr1:47842911-47843149(+)$1	238	17	20	8.9999
AAA	chr9:88641541-88641776(-)$1	235	0	3	8.9999
AAA	chr20:34238145-34238374(-)$1	229	10	13	8.9999
aaa	chr8:27142893-27143113(-)$1	220	25	28	8.9999
AAA	chr1:36805555-36805780(-)$1	225	126	129	8.9999
AAA	chr1:9989273-9989495(-)$1	222	24	27	8.9999
AAA	chr2:110374594-110374817(+)$1	223	10	13	8.9999
AAA	chr3:53262218-53262438(-)$1	220	94	97	8.9999
AAA	chr19:58376330-58376549(+)$1	219	17	20	8.9999
AAA	chr6:108532779-108533018(-)$1	239	140	143	8.9999
AAA	chr5:95131335-95131562(+)$1	227	55	58	8.9999
AAA	chr12:110355585-110355805(+)$1	220	19	22	8.9999
AAA	chr17:44107564-44107787(-)$1	223	14	17	8.9999
AAA	chr22:29190764-29190986(-)$1	222	36	39	8.9999
AAA	chr17:38784437-38784670(-)$1	233	26	29	8.9999
AAA	chr12:105197086-105197319(-)$1	233	8	11	8.9999
AAA	chr7:99637080-99637304(+)$1	224	78	81	8.9999
AAA	chr16:1822064-1822283(-)$1	219	19	22	8.9999
AAA	chr7:94298524-94298756(+)$1	232	95	98	8.9999
AAA	chr9:125672965-125673186(-)$1	221	26	29	8.9999
AAA	chr12:75891923-75892145(-)$1	222	0	3	8.9999
AAA	chrX:39956368-39956592(-)$1	224	67	70	8.9999
AAA	chr17:35873375-35873597(+)$1	222	101	104	8.9999
AAA	chr11:102268539-102268758(-)$1	219	83	86	8.9999
AAA	chr1:224573146-224573369(-)$1	223	8	11	8.9999
AAA	chrX:25014677-25014900(+)$1	223	42	45	8.9999
AAA	chr6:44214800-44215032(+)$1	232	82	85	8.9999
AAA	chr1:67877050-67877287(-)$1	237	46	49	8.9999
AAA	chr6:136580286-136580508(-)$1	222	17	20	8.9999
AAA	chr17:71244349-71244575(+)$1	226	7	10	8.9999
AAA	chr2:201841710-201841933(-)$1	223	18	21	8.9999
AAA	chr13:21548215-21548454(-)$1	239	123	126	8.9999
AAA	chr5:175788611-175788832(-)$1	221	99	102	8.9999
AAA	chr2:32248957-32249188(-)$1	231	113	116	8.9999
AAA	chr4:110972796-110973015(-)$1	219	31	34	8.9999
AAA	chr15:59955483-59955709(-)$1	226	117	120	8.9999
aaa	chr19:7086169-7086392(+)$1	223	0	3	8.9999
AAA	chr14:31917465-31917687(-)$1	222	40	43	8.9999
AAA	chr12:109547742-109547977(+)$1	235	99	102	8.9999
AAA	chr4:762377-762614(+)$1	237	45	48	8.9999
AAA	chr1:215792155-215792377(+)$1	222	24	27	8.9999
AAA	chr1:166822867-166823091(+)$1	224	5	8	8.9999
AAA	chr15:83424687-83424923(+)$1	236	21	24	8.9999
AAA	chr12:102467929-102468150(-)$1	221	17	20	8.9999
AAA	chr20:334431-334650(+)$1	219	55	58	8.9999
AAA	chr17:57292451-57292670(+)$1	219	5	8	8.9999
aaa	chr1:222906655-222906877(+)$1	222	27	30	8.9999
AAA	chr3:49022522-49022749(+)$1	227	86	89	8.9999
AAA	chr10:112657868-112658091(+)$1	223	9	12	8.9999
AAA	chr7:123324204-123324427(-)$1	223	20	23	8.9999

#otherMatches

#Struct PSSM
g[h	chr22:42393452-42393674(+)$1	222	61	64	8.9999
:::	chr1:29446428-29446651(+)$1	223	107	110	8.9999
ee[	chr1:59247103-59247329(-)$1	226	127	130	8.9999
ggg	chr1:879903-880124(-)$1	221	198	201	8.9999
:::	chr4:120219176-120219407(-)$1	231	0	3	8.9999
LLE	chr17:40467525-40467748(-)$1	223	9	12	8.9999
::c	chr7:112460662-112460890(-)$1	228	32	35	8.9999
:::	chr2:175937203-175937431(-)$1	228	4	7	8.9999
:::	chr1:52382728-52382957(-)$1	229	3	6	8.9999
ttt	chr17:5335894-5336115(+)$1	221	99	102	8.9999
ddd	chrX:152140620-152140839(+)$1	219	8	11	8.9999
h::	chr2:207024327-207024553(+)$1	226	121	124	8.9999
ttt	chr11:73113002-73113221(-)$1	219	120	123	8.9999
dd$	chr4:79836173-79836398(+)$1	225	8	11	8.9999
::e	chr8:8994571-8994798(-)$1	227	8	11	8.9999
:::	chr3:9519356-9519575(+)$1	219	29	32	8.9999
d33	chr8:26229880-26230100(+)$1	220	53	56	8.9999
:GG	chr10:127524874-127525099(+)$1	225	5	8	8.9999
hhh	chr12:117582548-117582786(-)$1	238	43	46	8.9999
:::	chr12:25360655-25360887(-)$1	232	99	102	8.9999
:::	chr8:74704557-74704777(-)$1	220	2	5	8.9999
:::	chr15:67494868-67495097(-)$1	229	20	23	8.9999
b33	chr15:35272105-35272329(-)$1	224	22	25	8.9999
eee	chr2:203426449-203426672(+)$1	223	8	11	8.9999
mmm	chr18:32916944-32917167(-)$1	223	19	22	8.9999
ddd	chr1:228880541-228880767(+)$1	226	34	37	8.9999
''c	chr13:52605804-52606025(+)$1	221	54	57	8.9999
:::	chr8:127567098-127567326(-)$1	228	2	5	8.9999
ooo	chr12:112460652-112460877(+)$1	225	27	30	8.9999
ppp	chr9:135569347-135569568(+)$1	221	50	53	8.9999
:::	chr16:3023012-3023241(+)$1	229	85	88	8.9999
===	chr3:30735294-30735518(+)$1	224	55	58	8.9999
c!!	chr16:1750352-1750576(+)$1	224	78	81	8.9999
eee	chr22:21976251-21976478(+)$1	227	26	29	8.9999
:::	chr1:205578747-205578982(-)$1	235	26	29	8.9999
F::	chr3:133876459-133876679(-)$1	220	85	88	8.9999
qqq	chr7:139253306-139253525(-)$1	219	55	58	8.9999
cc#	chr10:102121512-102121735(+)$1	223	72	75	8.9999
b22	chr2:29023649-29023873(+)$1	224	59	62	8.9999
!dd	chr1:201852993-201853217(+)$1	224	5	8	8.9999
qqq	chr12:69235226-69235456(+)$1	230	28	31	8.9999
eee	chr2:201768473-201768702(+)$1	229	69	72	8.9999
QQQ	chr1:101445079-101445310(+)$1	231	22	25	8.9999
eee	chr1:205683224-205683458(-)$1	234	42	45	8.9999
:::	chr8:38961598-38961820(+)$1	222	48	51	8.9999
:::	chrX:24231450-24231674(+)$1	224	31	34	8.9999
DKK	chr5:162871219-162871442(+)$1	223	36	39	8.9999
iii	chr5:14695177-14695396(+)$1	219	41	44	8.9999
DDD	chr18:722117-722343(-)$1	226	15	18	8.9999
FFF	chr1:47842911-47843149(+)$1	238	17	20	8.9999
:::	chr9:88641541-88641776(-)$1	235	0	3	8.9999
fff	chr20:34238145-34238374(-)$1	229	10	13	8.9999
ddd	chr8:27142893-27143113(-)$1	220	25	28	8.9999
hhh	chr1:36805555-36805780(-)$1	225	126	129	8.9999
ooe	chr1:9989273-9989495(-)$1	222	24	27	8.9999
hh[	chr2:110374594-110374817(+)$1	223	10	13	8.9999
cc#	chr3:53262218-53262438(-)$1	220	94	97	8.9999
J::	chr19:58376330-58376549(+)$1	219	17	20	8.9999
:::	chr6:108532779-108533018(-)$1	239	140	143	8.9999
:::	chr5:95131335-95131562(+)$1	227	55	58	8.9999
$$$	chr12:110355585-110355805(+)$1	220	19	22	8.9999
===	chr17:44107564-44107787(-)$1	223	14	17	8.9999
ooo	chr22:29190764-29190986(-)$1	222	36	39	8.9999
D:c	chr17:38784437-38784670(-)$1	233	26	29	8.9999
LGG	chr12:105197086-105197319(-)$1	233	8	11	8.9999
c::	chr7:99637080-99637304(+)$1	224	78	81	8.9999
B{D	chr16:1822064-1822283(-)$1	219	19	22	8.9999
ooo	chr7:94298524-94298756(+)$1	232	95	98	8.9999
:::	chr9:125672965-125673186(-)$1	221	26	29	8.9999
:::	chr12:75891923-75892145(-)$1	222	0	3	8.9999
g%%	chrX:39956368-39956592(-)$1	224	67	70	8.9999
iii	chr17:35873375-35873597(+)$1	222	101	104	8.9999
:::	chr11:102268539-102268758(-)$1	219	83	86	8.9999
:::	chr1:224573146-224573369(-)$1	223	8	11	8.9999
:::	chrX:25014677-25014900(+)$1	223	42	45	8.9999
!!e	chr6:44214800-44215032(+)$1	232	82	85	8.9999
::c	chr1:67877050-67877287(-)$1	237	46	49	8.9999
SSS	chr6:136580286-136580508(-)$1	222	17	20	8.9999
:::	chr17:71244349-71244575(+)$1	226	7	10	8.9999
sss	chr2:201841710-201841933(-)$1	223	18	21	8.9999
:::	chr13:21548215-21548454(-)$1	239	123	126	8.9999
e##	chr5:175788611-175788832(-)$1	221	99	102	8.9999
dd:	chr2:32248957-32249188(-)$1	231	113	116	8.9999
fmm	chr4:110972796-110973015(-)$1	219	31	34	8.9999
::d	chr15:59955483-59955709(-)$1	226	117	120	8.9999
:::	chr19:7086169-7086392(+)$1	223	0	3	8.9999
qqq	chr14:31917465-31917687(-)$1	222	40	43	8.9999
bb!	chr12:109547742-109547977(+)$1	235	99	102	8.9999
DDD	chr4:762377-762614(+)$1	237	45	48	8.9999
:::	chr1:215792155-215792377(+)$1	222	24	27	8.9999
:::	chr1:166822867-166823091(+)$1	224	5	8	8.9999
f""	chr15:83424687-83424923(+)$1	236	21	24	8.9999
JKK	chr12:102467929-102468150(-)$1	221	17	20	8.9999
^^^	chr20:334431-334650(+)$1	219	55	58	8.9999
:::	chr17:57292451-57292670(+)$1	219	5	8	8.9999
&&&	chr1:222906655-222906877(+)$1	222	27	30	8.9999
!cc	chr3:49022522-49022749(+)$1	227	86	89	8.9999
cmm	chr10:112657868-112658091(+)$1	223	9	12	8.9999
:ff	chr7:123324204-123324427(-)$1	223	20	23	8.9999

#DB
(.(	chr22:42393452-42393674(+)$1	1	61	64	8.9999
...	chr1:29446428-29446651(+)$1	1	107	110	8.9999
((.	chr1:59247103-59247329(-)$1	1	127	130	8.9999
)))	chr1:879903-880124(-)$1	1	198	201	8.9999
...	chr4:120219176-120219407(-)$1	1	0	3	8.9999
..(	chr17:40467525-40467748(-)$1	1	9	12	8.9999
..(	chr7:112460662-112460890(-)$1	1	32	35	8.9999
...	chr2:175937203-175937431(-)$1	1	4	7	8.9999
...	chr1:52382728-52382957(-)$1	1	3	6	8.9999
...	chr17:5335894-5336115(+)$1	1	99	102	8.9999
(((	chrX:152140620-152140839(+)$1	1	8	11	8.9999
)..	chr2:207024327-207024553(+)$1	1	121	124	8.9999
...	chr11:73113002-73113221(-)$1	1	120	123	8.9999
((.	chr4:79836173-79836398(+)$1	1	8	11	8.9999
..(	chr8:8994571-8994798(-)$1	1	8	11	8.9999
...	chr3:9519356-9519575(+)$1	1	29	32	8.9999
)..	chr8:26229880-26230100(+)$1	1	53	56	8.9999
.((	chr10:127524874-127525099(+)$1	1	5	8	8.9999
(((	chr12:117582548-117582786(-)$1	1	43	46	8.9999
...	chr12:25360655-25360887(-)$1	1	99	102	8.9999
...	chr8:74704557-74704777(-)$1	1	2	5	8.9999
...	chr15:67494868-67495097(-)$1	1	20	23	8.9999
)..	chr15:35272105-35272329(-)$1	1	22	25	8.9999
(((	chr2:203426449-203426672(+)$1	1	8	11	8.9999
...	chr18:32916944-32917167(-)$1	1	19	22	8.9999
)))	chr1:228880541-228880767(+)$1	1	34	37	8.9999
..(	chr13:52605804-52606025(+)$1	1	54	57	8.9999
...	chr8:127567098-127567326(-)$1	1	2	5	8.9999
...	chr12:112460652-112460877(+)$1	1	27	30	8.9999
...	chr9:135569347-135569568(+)$1	1	50	53	8.9999
...	chr16:3023012-3023241(+)$1	1	85	88	8.9999
)))	chr3:30735294-30735518(+)$1	1	55	58	8.9999
(..	chr16:1750352-1750576(+)$1	1	78	81	8.9999
)))	chr22:21976251-21976478(+)$1	1	26	29	8.9999
...	chr1:205578747-205578982(-)$1	1	26	29	8.9999
(..	chr3:133876459-133876679(-)$1	1	85	88	8.9999
...	chr7:139253306-139253525(-)$1	1	55	58	8.9999
((.	chr10:102121512-102121735(+)$1	1	72	75	8.9999
)..	chr2:29023649-29023873(+)$1	1	59	62	8.9999
.((	chr1:201852993-201853217(+)$1	1	5	8	8.9999
...	chr12:69235226-69235456(+)$1	1	28	31	8.9999
)))	chr2:201768473-201768702(+)$1	1	69	72	8.9999
...	chr1:101445079-101445310(+)$1	1	22	25	8.9999
(((	chr1:205683224-205683458(-)$1	1	42	45	8.9999
...	chr8:38961598-38961820(+)$1	1	48	51	8.9999
...	chrX:24231450-24231674(+)$1	1	31	34	8.9999
(..	chr5:162871219-162871442(+)$1	1	36	39	8.9999
(((	chr5:14695177-14695396(+)$1	1	41	44	8.9999
(((	chr18:722117-722343(-)$1	1	15	18	8.9999
(((	chr1:47842911-47843149(+)$1	1	17	20	8.9999
...	chr9:88641541-88641776(-)$1	1	0	3	8.9999
(((	chr20:34238145-34238374(-)$1	1	10	13	8.9999
(((	chr8:27142893-27143113(-)$1	1	25	28	8.9999
)))	chr1:36805555-36805780(-)$1	1	126	129	8.9999
..)	chr1:9989273-9989495(-)$1	1	24	27	8.9999
((.	chr2:110374594-110374817(+)$1	1	10	13	8.9999
((.	chr3:53262218-53262438(-)$1	1	94	97	8.9999
(..	chr19:58376330-58376549(+)$1	1	17	20	8.9999
...	chr6:108532779-108533018(-)$1	1	140	143	8.9999
...	chr5:95131335-95131562(+)$1	1	55	58	8.9999
...	chr12:110355585-110355805(+)$1	1	19	22	8.9999
(((	chr17:44107564-44107787(-)$1	1	14	17	8.9999
...	chr22:29190764-29190986(-)$1	1	36	39	8.9999
(.(	chr17:38784437-38784670(-)$1	1	26	29	8.9999
.((	chr12:105197086-105197319(-)$1	1	8	11	8.9999
)..	chr7:99637080-99637304(+)$1	1	78	81	8.9999
(.(	chr16:1822064-1822283(-)$1	1	19	22	8.9999
...	chr7:94298524-94298756(+)$1	1	95	98	8.9999
...	chr9:125672965-125673186(-)$1	1	26	29	8.9999
...	chr12:75891923-75892145(-)$1	1	0	3	8.9999
(..	chrX:39956368-39956592(-)$1	1	67	70	8.9999
(((	chr17:35873375-35873597(+)$1	1	101	104	8.9999
...	chr11:102268539-102268758(-)$1	1	83	86	8.9999
...	chr1:224573146-224573369(-)$1	1	8	11	8.9999
...	chrX:25014677-25014900(+)$1	1	42	45	8.9999
..(	chr6:44214800-44215032(+)$1	1	82	85	8.9999
..(	chr1:67877050-67877287(-)$1	1	46	49	8.9999
...	chr6:136580286-136580508(-)$1	1	17	20	8.9999
...	chr17:71244349-71244575(+)$1	1	7	10	8.9999
...	chr2:201841710-201841933(-)$1	1	18	21	8.9999
...	chr13:21548215-21548454(-)$1	1	123	126	8.9999
(..	chr5:175788611-175788832(-)$1	1	99	102	8.9999
)).	chr2:32248957-32249188(-)$1	1	113	116	8.9999
(..	chr4:110972796-110973015(-)$1	1	31	34	8.9999
..(	chr15:59955483-59955709(-)$1	1	117	120	8.9999
...	chr19:7086169-7086392(+)$1	1	0	3	8.9999
...	chr14:31917465-31917687(-)$1	1	40	43	8.9999
((.	chr12:109547742-109547977(+)$1	1	99	102	8.9999
(((	chr4:762377-762614(+)$1	1	45	48	8.9999
...	chr1:215792155-215792377(+)$1	1	24	27	8.9999
...	chr1:166822867-166823091(+)$1	1	5	8	8.9999
(..	chr15:83424687-83424923(+)$1	1	21	24	8.9999
(..	chr12:102467929-102468150(-)$1	1	17	20	8.9999
...	chr20:334431-334650(+)$1	1	55	58	8.9999
...	chr17:57292451-57292670(+)$1	1	5	8	8.9999
...	chr1:222906655-222906877(+)$1	1	27	30	8.9999
.((	chr3:49022522-49022749(+)$1	1	86	89	8.9999
(..	chr10:112657868-112658091(+)$1	1	9	12	8.9999
.((	chr7:123324204-123324427(-)$1	1	20	23	8.9999

#PSSM
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	

#score	890.9999999999998
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_CDS_m2_run1.nuc.txt

#NT
CUUCAUUUU	chr1:165712315-165712549(-)$1	234	103	112	15.7288
CUGUAUUUU	chr11:124908832-124909063(+)$1	231	107	116	15.8135
AUUUAUUUU	chr1:231509639-231509864(-)$1	225	158	167	19.2881
UAUUAUUUU	chr14:97000807-97001037(+)$1	230	100	109	14.6271
CUUUUUUUU	chr2:191797435-191797660(+)$1	225	209	218	16.5762
CUUUAUUUG	chr8:98735042-98735265(+)$1	223	12	21	15.5593
GUUUGUUUU	chr8:21857037-21857269(+)$1	232	181	190	15.7288
UUUUAUUUU	chr1:243827980-243828203(-)$1	223	1	10	19.3728
AUUUGUUUU	chr14:101350950-101351175(+)$1	225	107	116	15.8983
AUUUAUUUC	chr19:12127125-12127364(-)$1	239	216	225	14.8813
AUUUACUUU	chr14:31055894-31056117(+)$1	223	9	18	14.8813
AUUCAUUUU	chr7:35006411-35006643(-)$1	232	16	25	15.0508
UUUUAUUUU	chr3:149638886-149639110(+)$1	224	22	31	19.3728
AUUUAUUCU	chrM:3526-3771(+)$1	245	89	98	14.7966
UUUUAUUGU	chr1:109952484-109952709(-)$1	225	170	179	15.0508
GUUGAUUUU	chr3:56660975-56661204(-)$1	229	171	180	14.9661
CUUUAUUUC	chr12:88442984-88443222(+)$1	238	195	204	15.5593
UUUUCUUUU	chr15:83686713-83686938(-)$1	225	37	46	15.8983
CUGUAUUUU	chr5:36183943-36184165(+)$1	222	118	127	15.8135
GUUUCUUUU	chr7:135612377-135612603(-)$1	226	191	200	15.6440
GUAUAUUUU	chr5:114956096-114956332(-)$1	236	126	135	14.7966
CUUUGUUUU	chr5:162868193-162868418(+)$1	225	153	162	16.5762
UUUUAUUUA	chr12:50535760-50535987(-)$1	227	107	116	14.8813
CUUUUUUUU	chr3:152017853-152018085(+)$1	232	43	52	16.5762
UUUUAUUAU	chr14:32560333-32560568(+)$1	235	17	26	14.8813
GUGUAUUUU	chr8:126034041-126034264(+)$1	223	11	20	14.9661
UUUUAUUUU	chr18:54281688-54281920(-)$1	232	67	76	19.3728
CUUGAUUUU	chr1:93312662-93312885(-)$1	223	35	44	15.8135
CUUUCUUUU	chr18:77893409-77893655(+)$1	246	66	75	16.4915
AUUUUUUUU	chr5:32397297-32397521(-)$1	224	58	67	15.8983
UUUUAUCUU	chr14:45571682-45571914(+)$1	232	6	15	14.6271
AUUUAUAUU	chr20:39833211-39833435(-)$1	224	102	111	14.5423
Cuuuauuuu	chr8:27685583-27685808(-)$1	225	43	52	19.9661
AUUUAUUUU	chr13:21721371-21721598(+)$1	227	131	140	19.2881
UGuuauuuu	chr12:12277407-12277637(-)$1	230	5	14	14.6271
GUUUCUUUU	chr7:135612228-135612460(-)$1	232	48	57	15.6440
AUUUAUUUU	chr5:118582808-118583052(+)$1	244	218	227	19.2881
GUUUAUUUU	chr11:62156509-62156728(+)$1	219	80	89	19.1186
CUGUAUUUU	chr5:114859941-114860173(-)$1	232	177	186	15.8135
UUAUAUUUU	chr9:125672953-125673185(-)$1	232	213	222	15.0508
CUUAAUUUU	chr14:95592845-95593072(-)$1	227	84	93	15.7288
GUUUAUUUU	chr6:127794360-127794599(-)$1	239	214	223	19.1186
UUUUAUUUU	chr1:214828487-214828713(+)$1	226	83	92	19.3728
CUUUUUUUU	chr5:132203090-132203318(+)$1	228	27	36	16.5762
CUUUGUUUU	chr6:168311928-168312152(+)$1	224	10	19	16.5762
AUUUAUUUG	chr5:64926018-64926247(+)$1	229	108	117	14.8813
CUUGAUUUU	chr2:113079283-113079504(+)$1	221	9	18	15.8135
GUUUAUUUU	chr2:198256908-198257140(-)$1	232	121	130	19.1186
CUUUACUUU	chr21:26957879-26958135(-)$1	256	221	230	15.5593
UUUUAUUGU	chrX:21534536-21534755(+)$1	219	36	45	15.0508
AUUAAUUUU	chr10:60128417-60128653(+)$1	236	17	26	15.0508
GUUUAUUUU	chr11:70229074-70229306(+)$1	232	21	30	19.1186
UUUUAAUUU	chr12:66539546-66539770(-)$1	224	18	27	14.7966
CUUUAUUUU	chr13:108881591-108881824(+)$1	233	167	176	19.9661
CUUUAUUGU	chr11:77780801-77781029(-)$1	228	140	149	15.6440
GUUUAUUUU	chr15:55474225-55474457(-)$1	232	6	15	19.1186
CUUUUUUUU	chr13:76432032-76432254(+)$1	222	140	149	16.5762
CUUUACUUU	chr3:32754657-32754881(+)$1	224	13	22	15.5593

#otherMatches

#Struct PSSM
b333bb]bb	chr1:175956103-175956333(-)$1	230	82	91	15.8983
44iiiiiii	chr1:165712315-165712549(-)$1	234	103	112	15.7288
'ddddnnnn	chr11:124908832-124909063(+)$1	231	107	116	15.8135
eeeevvvvv	chr1:231509639-231509864(-)$1	225	158	167	19.2881
ee####eee	chr14:97000807-97001037(+)$1	230	100	109	14.6271
========C	chr2:191797435-191797660(+)$1	225	209	218	16.5762
B{FFFFFFe	chr8:98735042-98735265(+)$1	223	12	21	15.5593
fpppppppf	chr8:21857037-21857269(+)$1	232	181	190	15.7288
:::gggggg	chr1:243827980-243828203(-)$1	223	1	10	19.3728
eeeee"""=	chr14:101350950-101351175(+)$1	225	107	116	15.8983
qqqqqeeee	chr19:12127125-12127364(-)$1	239	216	225	14.8813
:::::::::	chr14:31055894-31056117(+)$1	223	9	18	14.8813
:::::::::	chr7:35006411-35006643(-)$1	232	16	25	15.0508
dhhhhhhhh	chr3:149638886-149639110(+)$1	224	22	31	19.3728
^^^^^^^^^	chrM:3526-3771(+)$1	245	89	98	14.7966
66666ffff	chr1:109952484-109952709(-)$1	225	170	179	15.0508
g]bb]ffff	chr3:56660975-56661204(-)$1	229	171	180	14.9661
:::::eeee	chr12:88442984-88443222(+)$1	238	195	204	15.5593
ffffff[bb	chr15:83686713-83686938(-)$1	225	37	46	15.8983
sssssseee	chr5:36183943-36184165(+)$1	222	118	127	15.8135
FFFFFF@@@	chr7:135612377-135612603(-)$1	226	191	200	15.6440
cc7777777	chr5:114956096-114956332(-)$1	236	126	135	14.7966
:::ffffff	chr5:162868193-162868418(+)$1	225	153	162	16.5762
dpppppppd	chr12:50535760-50535987(-)$1	227	107	116	14.8813
=========	chr3:152017853-152018085(+)$1	232	43	52	16.5762
JJJJJJJJJ	chr14:32560333-32560568(+)$1	235	17	26	14.8813
JJJJJJJJJ	chr8:126034041-126034264(+)$1	223	11	20	14.9661
+++++++++	chr18:54281688-54281920(-)$1	232	67	76	19.3728
ddd!!ffff	chr1:93312662-93312885(-)$1	223	35	44	15.8135
c::::::::	chr18:77893409-77893655(+)$1	246	66	75	16.4915
dddd22hhh	chr5:32397297-32397521(-)$1	224	58	67	15.8983
::ggggggg	chr14:45571682-45571914(+)$1	232	6	15	14.6271
ddeeeeemm	chr20:39833211-39833435(-)$1	224	102	111	14.5423
:::::::::	chr8:27685583-27685808(-)$1	225	43	52	19.9661
GGGGG::::	chr13:21721371-21721598(+)$1	227	131	140	19.2881
ffoooooof	chr12:12277407-12277637(-)$1	230	5	14	14.6271
+++++++++	chr7:135612228-135612460(-)$1	232	48	57	15.6440
?????FFFF	chr5:118582808-118583052(+)$1	244	218	227	19.2881
gggpppppp	chr11:62156509-62156728(+)$1	219	80	89	19.1186
FFFF:gggg	chr5:114859941-114860173(-)$1	232	177	186	15.8135
:::::::::	chr9:125672953-125673185(-)$1	232	213	222	15.0508
r========	chr14:95592845-95593072(-)$1	227	84	93	15.7288
eeeee22ee	chr6:127794360-127794599(-)$1	239	214	223	19.1186
eeee22a22	chr1:214828487-214828713(+)$1	226	83	92	19.3728
fffff]ggg	chr5:132203090-132203318(+)$1	228	27	36	16.5762
FFFFFFLLL	chr6:168311928-168312152(+)$1	224	10	19	16.5762
{IIIIIIII	chr5:64926018-64926247(+)$1	229	108	117	14.8813
e!!aooooo	chr2:113079283-113079504(+)$1	221	9	18	15.8135
eeeee"""d	chr2:198256908-198257140(-)$1	232	121	130	19.1186
$$$ffffff	chr21:26957879-26958135(-)$1	256	221	230	15.5593
'''''''ee	chrX:21534536-21534755(+)$1	219	36	45	15.0508
ddd!!====	chr10:60128417-60128653(+)$1	236	17	26	15.0508
dd^^^^^^^	chr11:70229074-70229306(+)$1	232	21	30	19.1186
crrrrrrrr	chr12:66539546-66539770(-)$1	224	18	27	14.7966
ee:::::::	chr13:108881591-108881824(+)$1	233	167	176	19.9661
d:::JJJJJ	chr11:77780801-77781029(-)$1	228	140	149	15.6440
ffff[eeee	chr15:55474225-55474457(-)$1	232	6	15	19.1186
vvvvvvvvv	chr13:76432032-76432254(+)$1	222	140	149	16.5762
:::::GGGG	chr3:32754657-32754881(+)$1	224	13	22	15.5593

#DB
)...)).))	chr1:175956103-175956333(-)$1	1	82	91	15.8983
..)))))))	chr1:165712315-165712549(-)$1	1	103	112	15.7288
.((((....	chr11:124908832-124909063(+)$1	1	107	116	15.8135
((((.....	chr1:231509639-231509864(-)$1	1	158	167	19.2881
((....(((	chr14:97000807-97001037(+)$1	1	100	109	14.6271
)))))))))	chr2:191797435-191797660(+)$1	1	209	218	16.5762
(.(((((((	chr8:98735042-98735265(+)$1	1	12	21	15.5593
(.......)	chr8:21857037-21857269(+)$1	1	181	190	15.7288
...((((((	chr1:243827980-243828203(-)$1	1	1	10	19.3728
(((((...(	chr14:101350950-101351175(+)$1	1	107	116	15.8983
.....))))	chr19:12127125-12127364(-)$1	1	216	225	14.8813
.........	chr14:31055894-31056117(+)$1	1	9	18	14.8813
.........	chr7:35006411-35006643(-)$1	1	16	25	15.0508
(((((((((	chr3:149638886-149639110(+)$1	1	22	31	19.3728
.........	chrM:3526-3771(+)$1	1	89	98	14.7966
.....))))	chr1:109952484-109952709(-)$1	1	170	179	15.0508
).)).))))	chr3:56660975-56661204(-)$1	1	171	180	14.9661
.....((((	chr12:88442984-88443222(+)$1	1	195	204	15.5593
((((((.((	chr15:83686713-83686938(-)$1	1	37	46	15.8983
......)))	chr5:36183943-36184165(+)$1	1	118	127	15.8135
))))))...	chr7:135612377-135612603(-)$1	1	191	200	15.6440
)).......	chr5:114956096-114956332(-)$1	1	126	135	14.7966
...((((((	chr5:162868193-162868418(+)$1	1	153	162	16.5762
(.......)	chr12:50535760-50535987(-)$1	1	107	116	14.8813
)))))))))	chr3:152017853-152018085(+)$1	1	43	52	16.5762
(((((((((	chr14:32560333-32560568(+)$1	1	17	26	14.8813
(((((((((	chr8:126034041-126034264(+)$1	1	11	20	14.9661
.........	chr18:54281688-54281920(-)$1	1	67	76	19.3728
(((..((((	chr1:93312662-93312885(-)$1	1	35	44	15.8135
)........	chr18:77893409-77893655(+)$1	1	66	75	16.4915
))))..)))	chr5:32397297-32397521(-)$1	1	58	67	15.8983
..(((((((	chr14:45571682-45571914(+)$1	1	6	15	14.6271
))(((((..	chr20:39833211-39833435(-)$1	1	102	111	14.5423
.........	chr8:27685583-27685808(-)$1	1	43	52	19.9661
(((((....	chr13:21721371-21721598(+)$1	1	131	140	19.2881
((......)	chr12:12277407-12277637(-)$1	1	5	14	14.6271
.........	chr7:135612228-135612460(-)$1	1	48	57	15.6440
.....))))	chr5:118582808-118583052(+)$1	1	218	227	19.2881
(((......	chr11:62156509-62156728(+)$1	1	80	89	19.1186
((((.((((	chr5:114859941-114860173(-)$1	1	177	186	15.8135
.........	chr9:125672953-125673185(-)$1	1	213	222	15.0508
.))))))))	chr14:95592845-95593072(-)$1	1	84	93	15.7288
)))))..))	chr6:127794360-127794599(-)$1	1	214	223	19.1186
))))..)..	chr1:214828487-214828713(+)$1	1	83	92	19.3728
))))).)))	chr5:132203090-132203318(+)$1	1	27	36	16.5762
((((((...	chr6:168311928-168312152(+)$1	1	10	19	16.5762
.((((((((	chr5:64926018-64926247(+)$1	1	108	117	14.8813
(..(.....	chr2:113079283-113079504(+)$1	1	9	18	15.8135
(((((...(	chr2:198256908-198257140(-)$1	1	121	130	19.1186
...((((((	chr21:26957879-26958135(-)$1	1	221	230	15.5593
.......((	chrX:21534536-21534755(+)$1	1	36	45	15.0508
(((..((((	chr10:60128417-60128653(+)$1	1	17	26	15.0508
((.......	chr11:70229074-70229306(+)$1	1	21	30	19.1186
(........	chr12:66539546-66539770(-)$1	1	18	27	14.7966
)).......	chr13:108881591-108881824(+)$1	1	167	176	19.9661
)...)))))	chr11:77780801-77781029(-)$1	1	140	149	15.6440
((((.((((	chr15:55474225-55474457(-)$1	1	6	15	19.1186
.........	chr13:76432032-76432254(+)$1	1	140	149	16.5762
.....((((	chr3:32754657-32754881(+)$1	1	13	22	15.5593

#PSSM
C : 0.35	U : 0.23	A : 0.22	G : 0.18	
U : 0.94	A : 0.01	u : 0.01	G : 0.01	
U : 0.86	G : 0.06	A : 0.03	u : 0.03	
U : 0.84	G : 0.05	C : 0.03	u : 0.03	A : 0.03	
A : 0.72	G : 0.08	U : 0.08	C : 0.06	a : 0.03	
U : 0.89	C : 0.05	u : 0.03	A : 0.01	
U : 0.93	u : 0.03	C : 0.01	A : 0.01	
U : 0.88	G : 0.05	u : 0.03	C : 0.01	A : 0.01	
U : 0.88	G : 0.03	C : 0.03	u : 0.03	A : 0.01	

#score	968.2542372881342
#seq	59
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m1_run2.nuc.txt

#NT
AGAAGUU	chr16:15818389-15818610(+)$1	221	67	74	12.6964
UGAAGAU	chr19:2271367-2271593(+)$1	226	94	101	13.8571
AGAAGAC	chr17:7495548-7495770(-)$1	222	174	181	13.3214
AGAAGAU	chr1:93825989-93826216(+)$1	227	185	192	17.1607
AGAAAAU	chr3:56657011-56657232(-)$1	221	50	57	12.8750
AGAAGAU	chr16:23634274-23634494(-)$1	220	193	200	17.1607
UGAAGAU	chr10:119044004-119044223(-)$1	219	187	194	13.8571
AAAAGAU	chr17:40986747-40986974(+)$1	227	7	14	12.6964
AGAAGAG	chr12:121001173-121001408(+)$1	235	68	75	13.1428
AAAAGAU	chr6:7583838-7584062(+)$1	224	88	95	12.6964
AGAAGAC	chr1:27022836-27023060(+)$1	224	8	15	13.3214
AGAAGAA	chr13:50108228-50108449(-)$1	221	56	63	13.5892
AGAAGAU	chr10:116590560-116590780(+)$1	220	73	80	17.1607
AGGAGAU	chr7:149576619-149576842(+)$1	223	65	72	12.8750
AGAAGAU	chr1:205739394-205739616(-)$1	222	68	75	17.1607
AGAGGAU	chr12:104714968-104715195(+)$1	227	36	43	12.6964
AGAAGAA	chr6:159058093-159058314(-)$1	221	95	102	13.5892
AGAAGAU	chrM:12895-13143(-)$1	248	31	38	17.1607
UGAAGAU	chr6:148855830-148856052(+)$1	222	88	95	13.8571
GGAAGAU	chr5:149109833-149110078(+)$1	245	67	74	13.4107
AGAAAAU	chr10:71990020-71990242(-)$1	222	85	92	12.8750
ACAAGAU	chr3:44489098-44489324(-)$1	226	123	130	12.6964
AGACGAU	chr10:34985158-34985383(-)$1	225	122	129	12.6964
AGAAGUU	chr7:134849253-134849479(-)$1	226	129	136	12.6964
AGAAGAU	chr3:32200390-32200613(-)$1	223	131	138	17.1607
UGAAGAU	chr6:30522527-30522768(-)$1	241	35	42	13.8571
GGAAGAU	chr2:224828424-224828647(+)$1	223	94	101	13.4107
AGCAGAU	chrX:24483551-24483771(+)$1	220	61	68	13.0535
AGAAGAU	chr19:30499907-30500128(+)$1	221	31	38	17.1607
AGAAGAU	chr8:41789664-41789883(-)$1	219	152	159	17.1607
GGAAGAU	chr15:72185240-72185470(-)$1	230	50	57	13.4107
AGAAAAU	chr10:5799407-5799628(+)$1	221	21	28	12.8750
AGAAGAA	chr21:28210181-28210403(-)$1	222	129	136	13.5892
AGAAGAA	chr3:49154646-49154879(-)$1	233	83	90	13.5892
UGAAGAU	chr2:190660480-190660701(+)$1	221	124	131	13.8571
AGACGAU	chr3:128526321-128526543(+)$1	222	164	171	12.6964
AGAAGAU	chr16:23695140-23695366(+)$1	226	81	88	17.1607
AGAAGAU	chr19:48284049-48284268(+)$1	219	94	101	17.1607
UGAAGAU	chr21:30927416-30927654(+)$1	238	45	52	13.8571
AGAAAAU	chr6:52142233-52142453(-)$1	220	74	81	12.8750
UGAAGAU	chr20:39832896-39833123(-)$1	227	126	133	13.8571
AGAAGAU	chr14:69847152-69847374(-)$1	222	70	77	17.1607
AGAAGCU	chr11:9833999-9834220(-)$1	221	47	54	12.6964
AGAAGAA	chr8:90992891-90993123(-)$1	232	113	120	13.5892
AGGAGAU	chr2:85533343-85533568(+)$1	225	68	75	12.8750
AGAAGAC	chr3:179462811-179463031(+)$1	220	66	73	13.3214
ACAAGAU	chr17:57775123-57775355(-)$1	232	209	216	12.6964
AGAAGAU	chr4:7042971-7043191(-)$1	220	156	163	17.1607
AGAAGAU	chr2:225342888-225343115(-)$1	227	167	174	17.1607
AGAAGAA	chr8:61742998-61743236(+)$1	238	0	7	13.5892
AGCAGAU	chr12:88584237-88584464(+)$1	227	96	103	13.0535
AGAGGAU	chr21:33651085-33651324(-)$1	239	29	36	12.6964
AGCAGAU	chrM:12605-12857(+)$1	252	214	221	13.0535
UGAAGAU	chr1:182353439-182353660(-)$1	221	9	16	13.8571
AGCAGAU	chr7:99123346-99123568(+)$1	222	125	132	13.0535

#otherMatches

#Struct PSSM
ddllldd	chr1:225591019-225591248(-)$1	229	144	151	12.6964
qqqqggg	chr16:15818389-15818610(+)$1	221	67	74	12.6964
"bblllb	chr19:2271367-2271593(+)$1	226	94	101	13.8571
]a]gggg	chr17:7495548-7495770(-)$1	222	174	181	13.3214
ggggggg	chr1:93825989-93826216(+)$1	227	185	192	17.1607
FFFFFF{	chr3:56657011-56657232(-)$1	221	50	57	12.8750
::::DDD	chr16:23634274-23634494(-)$1	220	193	200	17.1607
:::::hh	chr10:119044004-119044223(-)$1	219	187	194	13.8571
FF::ddd	chr17:40986747-40986974(+)$1	227	7	14	12.6964
bbfffff	chr12:121001173-121001408(+)$1	235	68	75	13.1428
eettttt	chr6:7583838-7584062(+)$1	224	88	95	12.6964
KA:::::	chr1:27022836-27023060(+)$1	224	8	15	13.3214
===bbmm	chr13:50108228-50108449(-)$1	221	56	63	13.5892
ffflllf	chr10:116590560-116590780(+)$1	220	73	80	17.1607
bb[bbll	chr7:149576619-149576842(+)$1	223	65	72	12.8750
hhhhhhh	chr1:205739394-205739616(-)$1	222	68	75	17.1607
ccc====	chr12:104714968-104715195(+)$1	227	36	43	12.6964
ff:DDDD	chr6:159058093-159058314(-)$1	221	95	102	13.5892
{BBMMMM	chrM:12895-13143(-)$1	248	31	38	17.1607
]dddd33	chr6:148855830-148856052(+)$1	222	88	95	13.8571
ffffff[	chr5:149109833-149110078(+)$1	245	67	74	13.4107
:BBLLLD	chr10:71990020-71990242(-)$1	222	85	92	12.8750
uuuuuuu	chr3:44489098-44489324(-)$1	226	123	130	12.6964
FFFccc[	chr10:34985158-34985383(-)$1	225	122	129	12.6964
[bb[ccc	chr7:134849253-134849479(-)$1	226	129	136	12.6964
bbooooo	chr3:32200390-32200613(-)$1	223	131	138	17.1607
e55555g	chr6:30522527-30522768(-)$1	241	35	42	13.8571
eeeee::	chr2:224828424-224828647(+)$1	223	94	101	13.4107
eeeee]c	chrX:24483551-24483771(+)$1	220	61	68	13.0535
ggggggg	chr19:30499907-30500128(+)$1	221	31	38	17.1607
dd::ccc	chr8:41789664-41789883(-)$1	219	152	159	17.1607
bb!!fff	chr15:72185240-72185470(-)$1	230	50	57	13.4107
PPPPPPB	chr10:5799407-5799628(+)$1	221	21	28	12.8750
qqqqddd	chr21:28210181-28210403(-)$1	222	129	136	13.5892
meeeee]	chr3:49154646-49154879(-)$1	233	83	90	13.5892
zzzzzzz	chr2:190660480-190660701(+)$1	221	124	131	13.8571
uuuuuuu	chr3:128526321-128526543(+)$1	222	164	171	12.6964
CCKKDDD	chr16:23695140-23695366(+)$1	226	81	88	17.1607
]gggggg	chr19:48284049-48284268(+)$1	219	94	101	17.1607
======[	chr21:30927416-30927654(+)$1	238	45	52	13.8571
:::::::	chr6:52142233-52142453(-)$1	220	74	81	12.8750
dpppppp	chr20:39832896-39833123(-)$1	227	126	133	13.8571
qqqqfff	chr14:69847152-69847374(-)$1	222	70	77	17.1607
]ccc:::	chr11:9833999-9834220(-)$1	221	47	54	12.6964
d[fffff	chr8:90992891-90993123(-)$1	232	113	120	13.5892
a]bb]hh	chr2:85533343-85533568(+)$1	225	68	75	12.8750
:ddddmm	chr3:179462811-179463031(+)$1	220	66	73	13.3214
ggggggm	chr17:57775123-57775355(-)$1	232	209	216	12.6964
::::::G	chr4:7042971-7043191(-)$1	220	156	163	17.1607
8888888	chr2:225342888-225343115(-)$1	227	167	174	17.1607
:::::::	chr8:61742998-61743236(+)$1	238	0	7	13.5892
''''ccc	chr12:88584237-88584464(+)$1	227	96	103	13.0535
cnnnnnc	chr21:33651085-33651324(-)$1	239	29	36	12.6964
FFFF}DD	chrM:12605-12857(+)$1	252	214	221	13.0535
!dddd""	chr1:182353439-182353660(-)$1	221	9	16	13.8571
II::hhh	chr7:99123346-99123568(+)$1	222	125	132	13.0535

#DB
((...))	chr1:225591019-225591248(-)$1	1	144	151	12.6964
....)))	chr16:15818389-15818610(+)$1	1	67	74	12.6964
.((...)	chr19:2271367-2271593(+)$1	1	94	101	13.8571
.).))))	chr17:7495548-7495770(-)$1	1	174	181	13.3214
)))))))	chr1:93825989-93826216(+)$1	1	185	192	17.1607
((((((.	chr3:56657011-56657232(-)$1	1	50	57	12.8750
....)))	chr16:23634274-23634494(-)$1	1	193	200	17.1607
.....((	chr10:119044004-119044223(-)$1	1	187	194	13.8571
((..(((	chr17:40986747-40986974(+)$1	1	7	14	12.6964
)))))))	chr12:121001173-121001408(+)$1	1	68	75	13.1428
((.....	chr6:7583838-7584062(+)$1	1	88	95	12.6964
.(.....	chr1:27022836-27023060(+)$1	1	8	15	13.3214
(((((..	chr13:50108228-50108449(-)$1	1	56	63	13.5892
(((...)	chr10:116590560-116590780(+)$1	1	73	80	17.1607
((.((..	chr7:149576619-149576842(+)$1	1	65	72	12.8750
)))))))	chr1:205739394-205739616(-)$1	1	68	75	17.1607
)))))))	chr12:104714968-104715195(+)$1	1	36	43	12.6964
)).))))	chr6:159058093-159058314(-)$1	1	95	102	13.5892
.((....	chrM:12895-13143(-)$1	1	31	38	17.1607
.))))..	chr6:148855830-148856052(+)$1	1	88	95	13.8571
((((((.	chr5:149109833-149110078(+)$1	1	67	74	13.4107
.((...(	chr10:71990020-71990242(-)$1	1	85	92	12.8750
.......	chr3:44489098-44489324(-)$1	1	123	130	12.6964
((((((.	chr10:34985158-34985383(-)$1	1	122	129	12.6964
.((.(((	chr7:134849253-134849479(-)$1	1	129	136	12.6964
((.....	chr3:32200390-32200613(-)$1	1	131	138	17.1607
).....)	chr6:30522527-30522768(-)$1	1	35	42	13.8571
)))))..	chr2:224828424-224828647(+)$1	1	94	101	13.4107
))))).)	chrX:24483551-24483771(+)$1	1	61	68	13.0535
(((((((	chr19:30499907-30500128(+)$1	1	31	38	17.1607
))..(((	chr8:41789664-41789883(-)$1	1	152	159	17.1607
((..(((	chr15:72185240-72185470(-)$1	1	50	57	13.4107
......(	chr10:5799407-5799628(+)$1	1	21	28	12.8750
....)))	chr21:28210181-28210403(-)$1	1	129	136	13.5892
.))))).	chr3:49154646-49154879(-)$1	1	83	90	13.5892
.......	chr2:190660480-190660701(+)$1	1	124	131	13.8571
.......	chr3:128526321-128526543(+)$1	1	164	171	12.6964
((..(((	chr16:23695140-23695366(+)$1	1	81	88	17.1607
.))))))	chr19:48284049-48284268(+)$1	1	94	101	17.1607
((((((.	chr21:30927416-30927654(+)$1	1	45	52	13.8571
.......	chr6:52142233-52142453(-)$1	1	74	81	12.8750
(......	chr20:39832896-39833123(-)$1	1	126	133	13.8571
....)))	chr14:69847152-69847374(-)$1	1	70	77	17.1607
.)))...	chr11:9833999-9834220(-)$1	1	47	54	12.6964
(.(((((	chr8:90992891-90993123(-)$1	1	113	120	13.5892
).)).))	chr2:85533343-85533568(+)$1	1	68	75	12.8750
.((((..	chr3:179462811-179463031(+)$1	1	66	73	13.3214
((((((.	chr17:57775123-57775355(-)$1	1	209	216	12.6964
......)	chr4:7042971-7043191(-)$1	1	156	163	17.1607
.......	chr2:225342888-225343115(-)$1	1	167	174	17.1607
.......	chr8:61742998-61743236(+)$1	1	0	7	13.5892
....(((	chr12:88584237-88584464(+)$1	1	96	103	13.0535
(.....)	chr21:33651085-33651324(-)$1	1	29	36	12.6964
)))).))	chrM:12605-12857(+)$1	1	214	221	13.0535
.((((..	chr1:182353439-182353660(-)$1	1	9	16	13.8571
))..(((	chr7:99123346-99123568(+)$1	1	125	132	13.0535

#PSSM
A : 0.80	U : 0.14	G : 0.05	
G : 0.92	A : 0.03	C : 0.03	
A : 0.89	C : 0.07	G : 0.03	
A : 0.92	G : 0.03	C : 0.03	
G : 0.92	A : 0.07	
A : 0.92	C : 0.03	U : 0.03	
U : 0.82	A : 0.10	C : 0.05	G : 0.01	

#score	790.6428571428579
#seq	56
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m3_run1.nuc.txt

#NT
UUUGAAAA	chr3:160155264-160155591(-)$1	327	41	49	16.6000
UUUUAAAA	chr18:55269486-55269784(-)$1	298	263	271	20.6000
UUUGAAAA	chr11:9610295-9610532(+)$1	237	217	225	16.6000
UUCUAAAA	chr15:66180329-66180783(+)$1	454	357	365	16.2000
UUUUAUAA	chr2:29025217-29025459(+)$1	242	174	182	16.3000
UUUUAAAA	chr9:37865816-37866140(+)$1	324	133	141	20.6000
UAUUAAAA	chr12:94763577-94763816(-)$1	239	179	187	16.1000
CUUUAAAA	chr12:42478555-42478844(-)$1	289	152	160	16.4000
UUGUAAAA	chr15:83807259-83807555(-)$1	296	62	70	16.2000
CUUUAAAA	chr4:110736638-110736886(+)$1	248	212	220	16.4000
UUUUAAAA	chr21:40668786-40669036(-)$1	250	174	182	20.6000
uuuuuaaa	chr22:39080163-39080432(+)$1	269	55	63	16.3000
AUUUAAAA	chr13:21722575-21722804(+)$1	229	49	57	16.6000
UUUUAAAA	chr19:58268421-58268728(+)$1	307	156	164	20.6000
UUUUAAAA	chr4:115598365-115598623(+)$1	258	67	75	20.6000
UUUUAAAA	chr5:64813692-64814043(-)$1	351	163	171	20.6000
UUUUAAAA	chr1:178887319-178887548(+)$1	229	108	116	20.6000
UUUUAUAA	chr2:217367937-217368168(+)$1	231	165	173	16.3000
UUAUAAAA	chr6:16147620-16147908(+)$1	288	51	59	16.4000
AUUUAAAA	chr6:149397637-149397868(+)$1	231	172	180	16.6000
UUUUAUAA	chr8:28420688-28420950(+)$1	262	103	111	16.3000
UUUUUAAA	chr10:75535536-75535806(+)$1	270	184	192	16.3000
AUUUAAAA	chr10:98718178-98718419(+)$1	241	142	150	16.6000
AUUUAAAA	chr5:173384449-173384695(+)$1	246	121	129	16.6000
UAUUAAAA	chr10:89727278-89727618(+)$1	340	127	135	16.1000
UUUUAAAA	chr7:103766704-103767016(-)$1	312	173	181	20.6000
UUUUAAAA	chr1:168221837-168222071(+)$1	234	120	128	20.6000
UUUUAAAA	chr6:75963930-75964396(-)$1	466	72	80	20.6000
UGUUAAAA	chr7:19737547-19737778(-)$1	231	31	39	16.0000
UUAUAAAA	chr2:74435637-74435941(+)$1	304	247	255	16.4000
UUUCAAAA	chr20:34238190-34238555(-)$1	365	51	59	16.4000
UUUUAAAG	chr13:42806404-42806633(+)$1	229	107	115	16.2000
UUUUAACA	chr1:22416690-22416917(+)$1	227	155	163	15.9000
UUUGAAAA	chr5:68473681-68473972(+)$1	291	96	104	16.6000
UUUUAAAU	chr12:72179402-72179769(+)$1	367	169	177	16.2000
UUUUAAAU	chr15:68586435-68586703(+)$1	268	185	193	16.2000
UUUUAGAA	chr3:142778704-142778982(+)$1	278	20	28	16.1000
UUUUGAAA	chr12:69646782-69647006(+)$1	224	119	127	16.1000
UUUUAAAA	chr2:85548944-85549213(-)$1	269	153	161	20.6000
UUUUAAUA	chr1:204373663-204374083(-)$1	420	41	49	15.9000
uuuuuAAA	chr12:19671100-19671324(+)$1	224	67	75	16.3000
UUUUAAAG	chr4:17846146-17846373(+)$1	227	135	143	16.2000
UUUUAAAA	chr1:93619383-93619857(-)$1	474	411	419	20.6000
UUUUAAAA	chr17:30327164-30327544(+)$1	380	109	117	20.6000
UUAUAAAA	chr6:34248522-34248927(-)$1	405	53	61	16.4000
UUUUAAAA	chr1:25167437-25167668(+)$1	231	173	181	20.6000
UUUUAAAA	chr2:206859016-206859243(-)$1	227	104	112	20.6000
UUUUAAAA	chr5:77773935-77774237(+)$1	302	260	268	20.6000
UUUGAAAA	chr21:38888463-38888692(+)$1	229	94	102	16.6000

#otherMatches

#Struct PSSM
ddmmmmdd	chr5:56191341-56191575(+)$1	234	91	99	16.4000
c!!bb!!c	chr3:160155264-160155591(-)$1	327	41	49	16.6000
44ccc22b	chr18:55269486-55269784(-)$1	298	263	271	20.6000
ffmmmmff	chr11:9610295-9610532(+)$1	237	217	225	16.6000
++++++++	chr15:66180329-66180783(+)$1	454	357	365	16.2000
gggggqqq	chr2:29025217-29025459(+)$1	242	174	182	16.3000
ccmmmmcc	chr9:37865816-37866140(+)$1	324	133	141	20.6000
wwwwwwww	chr12:94763577-94763816(-)$1	239	179	187	16.1000
rrrrrrrr	chr12:42478555-42478844(-)$1	289	152	160	16.4000
eemmmmee	chr15:83807259-83807555(-)$1	296	62	70	16.2000
22hhhhhh	chr4:110736638-110736886(+)$1	248	212	220	16.4000
:::::::c	chr21:40668786-40669036(-)$1	250	174	182	20.6000
sssssfff	chr22:39080163-39080432(+)$1	269	55	63	16.3000
::::::::	chr13:21722575-21722804(+)$1	229	49	57	16.6000
emmmmeee	chr19:58268421-58268728(+)$1	307	156	164	20.6000
PPPPPPPE	chr4:115598365-115598623(+)$1	258	67	75	20.6000
}FFFFFFY	chr5:64813692-64814043(-)$1	351	163	171	20.6000
e[hhhhhh	chr1:178887319-178887548(+)$1	229	108	116	20.6000
ffff::::	chr2:217367937-217368168(+)$1	231	165	173	16.3000
MMHHHHHH	chr6:16147620-16147908(+)$1	288	51	59	16.4000
hxxxxxxx	chr6:149397637-149397868(+)$1	231	172	180	16.6000
ggggg:::	chr8:28420688-28420950(+)$1	262	103	111	16.3000
drrrrrrr	chr10:75535536-75535806(+)$1	270	184	192	16.3000
^^^^^^^^	chr10:98718178-98718419(+)$1	241	142	150	16.6000
xxxxxxxx	chr5:173384449-173384695(+)$1	246	121	129	16.6000
gggg!!dd	chr10:89727278-89727618(+)$1	340	127	135	16.1000
d::::::B	chr7:103766704-103767016(-)$1	312	173	181	20.6000
hhhhhhee	chr1:168221837-168222071(+)$1	234	120	128	20.6000
fffqqqqq	chr6:75963930-75964396(-)$1	466	72	80	20.6000
ennnnnee	chr7:19737547-19737778(-)$1	231	31	39	16.0000
ffffmmmm	chr2:74435637-74435941(+)$1	304	247	255	16.4000
EEEEE::d	chr20:34238190-34238555(-)$1	365	51	59	16.4000
eeee22ff	chr13:42806404-42806633(+)$1	229	107	115	16.2000
ffffff55	chr1:22416690-22416917(+)$1	227	155	163	15.9000
tttttttt	chr5:68473681-68473972(+)$1	291	96	104	16.6000
fffffccc	chr12:72179402-72179769(+)$1	367	169	177	16.2000
44ccc444	chr15:68586435-68586703(+)$1	268	185	193	16.2000
FFFFFFKK	chr3:142778704-142778982(+)$1	278	20	28	16.1000
iiiiiiii	chr12:69646782-69647006(+)$1	224	119	127	16.1000
fffff&&&	chr2:85548944-85549213(-)$1	269	153	161	20.6000
ggggggg[	chr1:204373663-204374083(-)$1	420	41	49	15.9000
:::::::d	chr12:19671100-19671324(+)$1	224	67	75	16.3000
qqqqqqqf	chr4:17846146-17846373(+)$1	227	135	143	16.2000
:::::::f	chr1:93619383-93619857(-)$1	474	411	419	20.6000
fffffggg	chr17:30327164-30327544(+)$1	380	109	117	20.6000
++++++++	chr6:34248522-34248927(-)$1	405	53	61	16.4000
hhhhhhcc	chr1:25167437-25167668(+)$1	231	173	181	20.6000
tttttttt	chr2:206859016-206859243(-)$1	227	104	112	20.6000
rrrrrggg	chr5:77773935-77774237(+)$1	302	260	268	20.6000
======""	chr21:38888463-38888692(+)$1	229	94	102	16.6000

#DB
((....))	chr5:56191341-56191575(+)$1	1	91	99	16.4000
(..((..(	chr3:160155264-160155591(-)$1	1	41	49	16.6000
..)))..)	chr18:55269486-55269784(-)$1	1	263	271	20.6000
((....))	chr11:9610295-9610532(+)$1	1	217	225	16.6000
........	chr15:66180329-66180783(+)$1	1	357	365	16.2000
(((((...	chr2:29025217-29025459(+)$1	1	174	182	16.3000
((....))	chr9:37865816-37866140(+)$1	1	133	141	20.6000
........	chr12:94763577-94763816(-)$1	1	179	187	16.1000
........	chr12:42478555-42478844(-)$1	1	152	160	16.4000
((....))	chr15:83807259-83807555(-)$1	1	62	70	16.2000
..))))))	chr4:110736638-110736886(+)$1	1	212	220	16.4000
.......(	chr21:40668786-40669036(-)$1	1	174	182	20.6000
.....)))	chr22:39080163-39080432(+)$1	1	55	63	16.3000
........	chr13:21722575-21722804(+)$1	1	49	57	16.6000
(....)))	chr19:58268421-58268728(+)$1	1	156	164	20.6000
.......(	chr4:115598365-115598623(+)$1	1	67	75	20.6000
.)))))).	chr5:64813692-64814043(-)$1	1	163	171	20.6000
(.((((((	chr1:178887319-178887548(+)$1	1	108	116	20.6000
))))....	chr2:217367937-217368168(+)$1	1	165	173	16.3000
..((((((	chr6:16147620-16147908(+)$1	1	51	59	16.4000
(.......	chr6:149397637-149397868(+)$1	1	172	180	16.6000
)))))...	chr8:28420688-28420950(+)$1	1	103	111	16.3000
(.......	chr10:75535536-75535806(+)$1	1	184	192	16.3000
........	chr10:98718178-98718419(+)$1	1	142	150	16.6000
........	chr5:173384449-173384695(+)$1	1	121	129	16.6000
((((..((	chr10:89727278-89727618(+)$1	1	127	135	16.1000
)......)	chr7:103766704-103767016(-)$1	1	173	181	20.6000
((((((((	chr1:168221837-168222071(+)$1	1	120	128	20.6000
(((.....	chr6:75963930-75964396(-)$1	1	72	80	20.6000
(.....))	chr7:19737547-19737778(-)$1	1	31	39	16.0000
((((....	chr2:74435637-74435941(+)$1	1	247	255	16.4000
(((((..(	chr20:34238190-34238555(-)$1	1	51	59	16.4000
))))..))	chr13:42806404-42806633(+)$1	1	107	115	16.2000
))))))..	chr1:22416690-22416917(+)$1	1	155	163	15.9000
........	chr5:68473681-68473972(+)$1	1	96	104	16.6000
))))))))	chr12:72179402-72179769(+)$1	1	169	177	16.2000
..)))...	chr15:68586435-68586703(+)$1	1	185	193	16.2000
((((((..	chr3:142778704-142778982(+)$1	1	20	28	16.1000
))))))))	chr12:69646782-69647006(+)$1	1	119	127	16.1000
(((((...	chr2:85548944-85549213(-)$1	1	153	161	20.6000
(((((((.	chr1:204373663-204374083(-)$1	1	41	49	15.9000
.......(	chr12:19671100-19671324(+)$1	1	67	75	16.3000
.......)	chr4:17846146-17846373(+)$1	1	135	143	16.2000
.......(	chr1:93619383-93619857(-)$1	1	411	419	20.6000
((((((((	chr17:30327164-30327544(+)$1	1	109	117	20.6000
........	chr6:34248522-34248927(-)$1	1	53	61	16.4000
))))))))	chr1:25167437-25167668(+)$1	1	173	181	20.6000
........	chr2:206859016-206859243(-)$1	1	104	112	20.6000
.....)))	chr5:77773935-77774237(+)$1	1	260	268	20.6000
((((((..	chr21:38888463-38888692(+)$1	1	94	102	16.6000

#PSSM
U : 0.84	A : 0.08	C : 0.04	u : 0.04	
U : 0.90	A : 0.04	u : 0.04	G : 0.02	
U : 0.86	A : 0.06	u : 0.04	C : 0.02	G : 0.02	
U : 0.84	G : 0.08	C : 0.04	u : 0.04	
A : 0.92	u : 0.04	U : 0.02	G : 0.02	
A : 0.90	U : 0.06	a : 0.02	G : 0.02	
A : 0.94	a : 0.02	C : 0.02	U : 0.02	
A : 0.90	G : 0.04	U : 0.04	a : 0.02	

#score	884.4000000000009
#seq	50
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_UTR_m1_run1.nuc.txt

#NT
CAG	chr20:5171979-5172200(+)$1	221	16	19	9.0000
CAG	chr7:129658202-129658420(-)$1	218	57	60	9.0000
CAG	chr17:78795957-78796180(+)$1	223	0	3	9.0000
CAG	chr2:233194565-233194782(+)$1	217	27	30	9.0000
CAG	chr6:56323673-56323892(-)$1	219	13	16	9.0000
CAG	chr11:67925689-67925917(-)$1	228	32	35	9.0000
CAG	chr1:16893635-16893870(-)$1	235	21	24	9.0000
CAG	chr10:75531447-75531674(+)$1	227	5	8	9.0000
CAG	chr8:11167028-11167245(+)$1	217	20	23	9.0000
CAG	chr5:72742326-72742552(-)$1	226	44	47	9.0000
CAG	chr20:418810-419021(-)$1	211	17	20	9.0000
CAG	chr19:39435510-39435729(-)$1	219	19	22	9.0000
CAG	chr7:131173202-131173415(+)$1	213	33	36	9.0000
CAG	chr17:38545364-38545575(-)$1	211	107	110	9.0000
CAG	chr8:8888553-8888772(+)$1	219	55	58	9.0000
CAG	chr19:42798709-42798919(+)$1	210	14	17	9.0000
CAG	chr12:125515187-125515415(+)$1	228	16	19	9.0000
CAG	chr1:44088611-44088854(+)$1	243	63	66	9.0000
CAG	chr1:15983040-15983267(+)$1	227	68	71	9.0000
CAG	chr4:2069296-2069520(+)$1	224	18	21	9.0000
CAG	chr1:231472929-231473176(-)$1	247	90	93	9.0000
CAG	chr19:50315790-50316022(-)$1	232	77	80	9.0000
CAG	chr12:6438598-6438828(-)$1	230	37	40	9.0000
CAG	chr6:31498987-31499276(-)$1	289	91	94	9.0000
CAG	chr9:130697666-130697887(-)$1	221	6	9	9.0000
CAG	chr15:89173890-89174125(+)$1	235	144	147	9.0000
CAG	chrX:135292003-135292221(+)$1	218	23	26	9.0000
CAG	chr9:114154966-114155189(-)$1	223	95	98	9.0000
CAG	chr1:214542759-214542980(-)$1	221	4	7	9.0000
CAG	chr1:231502003-231502219(-)$1	216	34	37	9.0000
CAG	chr8:22994320-22994539(-)$1	219	26	29	9.0000
CAG	chr6:26158286-26158528(+)$1	242	44	47	9.0000
CAG	chr12:53680361-53680581(+)$1	220	41	44	9.0000
CAG	chr6:91261741-91261963(-)$1	222	145	148	9.0000
CAG	chr1:38002612-38002840(-)$1	228	59	62	9.0000
CAG	chr2:43783550-43783768(-)$1	218	46	49	9.0000
CAG	chr10:120444717-120444948(-)$1	231	16	19	9.0000
CAG	chr14:23502565-23502786(-)$1	221	27	30	9.0000
CAG	chr15:78765521-78765759(+)$1	238	5	8	9.0000
CAG	chr8:28610749-28610972(+)$1	223	44	47	9.0000
CAG	chr2:12863370-12863586(+)$1	216	26	29	9.0000
CAG	chr19:33168570-33168790(+)$1	220	28	31	9.0000
CAG	chr15:78290151-78290371(-)$1	220	31	34	9.0000
CAG	chr2:215593531-215593756(-)$1	225	21	24	9.0000
CAG	chr16:75269241-75269527(-)$1	286	20	23	9.0000
CAG	chr19:2101510-2101771(-)$1	261	82	85	9.0000
CAG	chr20:62563585-62563810(+)$1	225	178	181	9.0000
CAG	chr16:88697606-88697832(+)$1	226	4	7	9.0000
CAG	chr11:46639750-46639976(+)$1	226	121	124	9.0000
CAG	chr8:81883201-81883413(-)$1	212	24	27	9.0000
CAG	chr1:212208716-212208945(-)$1	229	6	9	9.0000
CAG	chr1:174983271-174983491(-)$1	220	77	80	9.0000
CAG	chrX:153585721-153585975(-)$1	254	42	45	9.0000
CAG	chr11:9406192-9406420(+)$1	228	52	55	9.0000
CAG	chr7:1580298-1580516(+)$1	218	67	70	9.0000
CAG	chr17:56168093-56168311(+)$1	218	119	122	9.0000
cag	chr3:185764814-185765033(-)$1	219	167	170	9.0000
CAG	chr3:67059499-67059721(+)$1	222	17	20	9.0000
CAG	chr3:179506084-179506299(+)$1	215	45	48	9.0000
CAG	chr6:43473156-43473375(+)$1	219	5	8	9.0000
CAG	chr17:63525277-63525497(-)$1	220	5	8	9.0000
CAG	chr19:2430135-2430373(-)$1	238	15	18	9.0000
CAG	chr2:131810369-131810585(-)$1	216	69	72	9.0000
CAG	chr6:31236815-31237044(-)$1	229	34	37	9.0000
CAG	chr12:121159829-121160053(+)$1	224	34	37	9.0000
CAG	chr7:32623982-32624196(+)$1	214	71	74	9.0000
CAG	chr17:75494840-75495071(+)$1	231	32	35	9.0000
CAG	chr15:75137374-75137603(-)$1	229	13	16	9.0000
CAG	chr14:75150044-75150259(-)$1	215	20	23	9.0000
CAG	chr10:72186765-72186995(+)$1	230	33	36	9.0000
CAG	chr2:242027321-242027535(-)$1	214	65	68	9.0000
CAG	chr4:76582682-76582917(-)$1	235	35	38	9.0000
CAG	chr12:133291357-133291579(+)$1	222	26	29	9.0000
CAG	chr6:82935192-82935428(-)$1	236	113	116	9.0000
CAG	chr5:7889117-7889339(+)$1	222	15	18	9.0000
CAG	chr6:150059772-150059998(-)$1	226	90	93	9.0000
CAG	chr7:99006710-99006924(+)$1	214	17	20	9.0000
CAG	chr3:49155096-49155310(-)$1	214	2	5	9.0000
CAG	chr10:129895677-129895903(-)$1	226	22	25	9.0000
CAG	chr1:226822083-226822308(-)$1	225	104	107	9.0000
CAG	chr4:2010382-2010603(-)$1	221	68	71	9.0000
CAG	chr15:52842671-52842894(-)$1	223	51	54	9.0000
CAG	chr14:64434393-64434623(+)$1	230	30	33	9.0000
CAG	chr1:120457382-120457660(-)$1	278	36	39	9.0000
CAG	chr1:38277252-38277474(-)$1	222	5	8	9.0000
CAG	chr1:173807233-173807454(+)$1	221	101	104	9.0000
CAG	chr6:15520854-15521080(+)$1	226	21	24	9.0000
CAG	chr12:110972881-110973109(-)$1	228	40	43	9.0000
CAG	chr12:58145917-58146178(-)$1	261	21	24	9.0000
CAG	chr17:77760305-77760530(+)$1	225	25	28	9.0000
CAG	chr14:70237851-70238073(+)$1	222	71	74	9.0000
CAG	chr7:116418752-116418977(+)$1	225	74	77	9.0000
CAG	chr1:245014511-245014722(-)$1	211	104	107	9.0000
CAG	chr1:92161213-92161434(-)$1	221	13	16	9.0000
CAG	chr5:137501535-137501760(-)$1	225	33	36	9.0000
CAG	chr12:122717259-122717471(-)$1	212	0	3	9.0000
CAG	chr22:38061864-38062093(+)$1	229	28	31	9.0000
CAG	chr4:7033127-7033352(+)$1	225	16	19	9.0000
CAG	chr17:37688502-37688741(+)$1	239	15	18	9.0000

#otherMatches

#Struct PSSM
nna	chr19:58193316-58193548(+)$1	232	14	17	9.0000
CCQ	chr20:5171979-5172200(+)$1	221	16	19	9.0000
ddd	chr7:129658202-129658420(-)$1	218	57	60	9.0000
::c	chr17:78795957-78796180(+)$1	223	0	3	9.0000
III	chr2:233194565-233194782(+)$1	217	27	30	9.0000
CCC	chr6:56323673-56323892(-)$1	219	13	16	9.0000
ddd	chr11:67925689-67925917(-)$1	228	32	35	9.0000
e!!	chr1:16893635-16893870(-)$1	235	21	24	9.0000
FFF	chr10:75531447-75531674(+)$1	227	5	8	9.0000
HHH	chr8:11167028-11167245(+)$1	217	20	23	9.0000
c]f	chr5:72742326-72742552(-)$1	226	44	47	9.0000
CCC	chr20:418810-419021(-)$1	211	17	20	9.0000
eee	chr19:39435510-39435729(-)$1	219	19	22	9.0000
edd	chr7:131173202-131173415(+)$1	213	33	36	9.0000
ddd	chr17:38545364-38545575(-)$1	211	107	110	9.0000
ddd	chr8:8888553-8888772(+)$1	219	55	58	9.0000
DDD	chr19:42798709-42798919(+)$1	210	14	17	9.0000
ggg	chr12:125515187-125515415(+)$1	228	16	19	9.0000
cc[	chr1:44088611-44088854(+)$1	243	63	66	9.0000
EEE	chr1:15983040-15983267(+)$1	227	68	71	9.0000
hhh	chr4:2069296-2069520(+)$1	224	18	21	9.0000
c22	chr1:231472929-231473176(-)$1	247	90	93	9.0000
e44	chr19:50315790-50316022(-)$1	232	77	80	9.0000
c:D	chr12:6438598-6438828(-)$1	230	37	40	9.0000
##i	chr6:31498987-31499276(-)$1	289	91	94	9.0000
FFF	chr9:130697666-130697887(-)$1	221	6	9	9.0000
eee	chr15:89173890-89174125(+)$1	235	144	147	9.0000
mmc	chrX:135292003-135292221(+)$1	218	23	26	9.0000
ccc	chr9:114154966-114155189(-)$1	223	95	98	9.0000
FFF	chr1:214542759-214542980(-)$1	221	4	7	9.0000
[cc	chr1:231502003-231502219(-)$1	216	34	37	9.0000
c::	chr8:22994320-22994539(-)$1	219	26	29	9.0000
##f	chr6:26158286-26158528(+)$1	242	44	47	9.0000
ggg	chr12:53680361-53680581(+)$1	220	41	44	9.0000
eee	chr6:91261741-91261963(-)$1	222	145	148	9.0000
===	chr1:38002612-38002840(-)$1	228	59	62	9.0000
eee	chr2:43783550-43783768(-)$1	218	46	49	9.0000
ddd	chr10:120444717-120444948(-)$1	231	16	19	9.0000
DDD	chr14:23502565-23502786(-)$1	221	27	30	9.0000
C{D	chr15:78765521-78765759(+)$1	238	5	8	9.0000
hhh	chr8:28610749-28610972(+)$1	223	44	47	9.0000
bb]	chr2:12863370-12863586(+)$1	216	26	29	9.0000
cdd	chr19:33168570-33168790(+)$1	220	28	31	9.0000
ff:	chr15:78290151-78290371(-)$1	220	31	34	9.0000
:::	chr2:215593531-215593756(-)$1	225	21	24	9.0000
ggg	chr16:75269241-75269527(-)$1	286	20	23	9.0000
=::	chr19:2101510-2101771(-)$1	261	82	85	9.0000
qqq	chr20:62563585-62563810(+)$1	225	178	181	9.0000
d!!	chr16:88697606-88697832(+)$1	226	4	7	9.0000
fff	chr11:46639750-46639976(+)$1	226	121	124	9.0000
NJJ	chr8:81883201-81883413(-)$1	212	24	27	9.0000
b$$	chr1:212208716-212208945(-)$1	229	6	9	9.0000
HHH	chr1:174983271-174983491(-)$1	220	77	80	9.0000
Ahh	chrX:153585721-153585975(-)$1	254	42	45	9.0000
GGG	chr11:9406192-9406420(+)$1	228	52	55	9.0000
sss	chr7:1580298-1580516(+)$1	218	67	70	9.0000
ggg	chr17:56168093-56168311(+)$1	218	119	122	9.0000
fff	chr3:185764814-185765033(-)$1	219	167	170	9.0000
GGG	chr3:67059499-67059721(+)$1	222	17	20	9.0000
ooo	chr3:179506084-179506299(+)$1	215	45	48	9.0000
iii	chr6:43473156-43473375(+)$1	219	5	8	9.0000
fff	chr17:63525277-63525497(-)$1	220	5	8	9.0000
GGG	chr19:2430135-2430373(-)$1	238	15	18	9.0000
ddd	chr2:131810369-131810585(-)$1	216	69	72	9.0000
fff	chr6:31236815-31237044(-)$1	229	34	37	9.0000
ee!	chr12:121159829-121160053(+)$1	224	34	37	9.0000
:cc	chr7:32623982-32624196(+)$1	214	71	74	9.0000
^^^	chr17:75494840-75495071(+)$1	231	32	35	9.0000
EEE	chr15:75137374-75137603(-)$1	229	13	16	9.0000
]bb	chr14:75150044-75150259(-)$1	215	20	23	9.0000
::c	chr10:72186765-72186995(+)$1	230	33	36	9.0000
[ee	chr2:242027321-242027535(-)$1	214	65	68	9.0000
GGG	chr4:76582682-76582917(-)$1	235	35	38	9.0000
ggg	chr12:133291357-133291579(+)$1	222	26	29	9.0000
GGG	chr6:82935192-82935428(-)$1	236	113	116	9.0000
ccc	chr5:7889117-7889339(+)$1	222	15	18	9.0000
:::	chr6:150059772-150059998(-)$1	226	90	93	9.0000
qqq	chr7:99006710-99006924(+)$1	214	17	20	9.0000
FFF	chr3:49155096-49155310(-)$1	214	2	5	9.0000
bb[	chr10:129895677-129895903(-)$1	226	22	25	9.0000
een	chr1:226822083-226822308(-)$1	225	104	107	9.0000
c]b	chr4:2010382-2010603(-)$1	221	68	71	9.0000
DDD	chr15:52842671-52842894(-)$1	223	51	54	9.0000
ddd	chr14:64434393-64434623(+)$1	230	30	33	9.0000
)))	chr1:120457382-120457660(-)$1	278	36	39	9.0000
:==	chr1:38277252-38277474(-)$1	222	5	8	9.0000
b[b	chr1:173807233-173807454(+)$1	221	101	104	9.0000
cco	chr6:15520854-15521080(+)$1	226	21	24	9.0000
ggg	chr12:110972881-110973109(-)$1	228	40	43	9.0000
ccb	chr12:58145917-58146178(-)$1	261	21	24	9.0000
B{C	chr17:77760305-77760530(+)$1	225	25	28	9.0000
22e	chr14:70237851-70238073(+)$1	222	71	74	9.0000
%%%	chr7:116418752-116418977(+)$1	225	74	77	9.0000
eee	chr1:245014511-245014722(-)$1	211	104	107	9.0000
FFF	chr1:92161213-92161434(-)$1	221	13	16	9.0000
FFF	chr5:137501535-137501760(-)$1	225	33	36	9.0000
::c	chr12:122717259-122717471(-)$1	212	0	3	9.0000
eee	chr22:38061864-38062093(+)$1	229	28	31	9.0000
nne	chr4:7033127-7033352(+)$1	225	16	19	9.0000
:cc	chr17:37688502-37688741(+)$1	239	15	18	9.0000

#DB
..)	chr19:58193316-58193548(+)$1	1	14	17	9.0000
((.	chr20:5171979-5172200(+)$1	1	16	19	9.0000
(((	chr7:129658202-129658420(-)$1	1	57	60	9.0000
..(	chr17:78795957-78796180(+)$1	1	0	3	9.0000
(((	chr2:233194565-233194782(+)$1	1	27	30	9.0000
(((	chr6:56323673-56323892(-)$1	1	13	16	9.0000
(((	chr11:67925689-67925917(-)$1	1	32	35	9.0000
(..	chr1:16893635-16893870(-)$1	1	21	24	9.0000
(((	chr10:75531447-75531674(+)$1	1	5	8	9.0000
(((	chr8:11167028-11167245(+)$1	1	20	23	9.0000
).)	chr5:72742326-72742552(-)$1	1	44	47	9.0000
(((	chr20:418810-419021(-)$1	1	17	20	9.0000
)))	chr19:39435510-39435729(-)$1	1	19	22	9.0000
(((	chr7:131173202-131173415(+)$1	1	33	36	9.0000
)))	chr17:38545364-38545575(-)$1	1	107	110	9.0000
(((	chr8:8888553-8888772(+)$1	1	55	58	9.0000
(((	chr19:42798709-42798919(+)$1	1	14	17	9.0000
(((	chr12:125515187-125515415(+)$1	1	16	19	9.0000
((.	chr1:44088611-44088854(+)$1	1	63	66	9.0000
(((	chr1:15983040-15983267(+)$1	1	68	71	9.0000
)))	chr4:2069296-2069520(+)$1	1	18	21	9.0000
)..	chr1:231472929-231473176(-)$1	1	90	93	9.0000
)..	chr19:50315790-50316022(-)$1	1	77	80	9.0000
).(	chr12:6438598-6438828(-)$1	1	37	40	9.0000
..(	chr6:31498987-31499276(-)$1	1	91	94	9.0000
(((	chr9:130697666-130697887(-)$1	1	6	9	9.0000
(((	chr15:89173890-89174125(+)$1	1	144	147	9.0000
..)	chrX:135292003-135292221(+)$1	1	23	26	9.0000
(((	chr9:114154966-114155189(-)$1	1	95	98	9.0000
(((	chr1:214542759-214542980(-)$1	1	4	7	9.0000
.((	chr1:231502003-231502219(-)$1	1	34	37	9.0000
)..	chr8:22994320-22994539(-)$1	1	26	29	9.0000
..(	chr6:26158286-26158528(+)$1	1	44	47	9.0000
)))	chr12:53680361-53680581(+)$1	1	41	44	9.0000
)))	chr6:91261741-91261963(-)$1	1	145	148	9.0000
(((	chr1:38002612-38002840(-)$1	1	59	62	9.0000
(((	chr2:43783550-43783768(-)$1	1	46	49	9.0000
)))	chr10:120444717-120444948(-)$1	1	16	19	9.0000
(((	chr14:23502565-23502786(-)$1	1	27	30	9.0000
(.(	chr15:78765521-78765759(+)$1	1	5	8	9.0000
(((	chr8:28610749-28610972(+)$1	1	44	47	9.0000
)).	chr2:12863370-12863586(+)$1	1	26	29	9.0000
)((	chr19:33168570-33168790(+)$1	1	28	31	9.0000
)).	chr15:78290151-78290371(-)$1	1	31	34	9.0000
...	chr2:215593531-215593756(-)$1	1	21	24	9.0000
(((	chr16:75269241-75269527(-)$1	1	20	23	9.0000
)..	chr19:2101510-2101771(-)$1	1	82	85	9.0000
...	chr20:62563585-62563810(+)$1	1	178	181	9.0000
(..	chr16:88697606-88697832(+)$1	1	4	7	9.0000
)))	chr11:46639750-46639976(+)$1	1	121	124	9.0000
.((	chr8:81883201-81883413(-)$1	1	24	27	9.0000
(..	chr1:212208716-212208945(-)$1	1	6	9	9.0000
(((	chr1:174983271-174983491(-)$1	1	77	80	9.0000
(((	chrX:153585721-153585975(-)$1	1	42	45	9.0000
(((	chr11:9406192-9406420(+)$1	1	52	55	9.0000
...	chr7:1580298-1580516(+)$1	1	67	70	9.0000
)))	chr17:56168093-56168311(+)$1	1	119	122	9.0000
)))	chr3:185764814-185765033(-)$1	1	167	170	9.0000
(((	chr3:67059499-67059721(+)$1	1	17	20	9.0000
...	chr3:179506084-179506299(+)$1	1	45	48	9.0000
(((	chr6:43473156-43473375(+)$1	1	5	8	9.0000
(((	chr17:63525277-63525497(-)$1	1	5	8	9.0000
(((	chr19:2430135-2430373(-)$1	1	15	18	9.0000
(((	chr2:131810369-131810585(-)$1	1	69	72	9.0000
(((	chr6:31236815-31237044(-)$1	1	34	37	9.0000
((.	chr12:121159829-121160053(+)$1	1	34	37	9.0000
.((	chr7:32623982-32624196(+)$1	1	71	74	9.0000
...	chr17:75494840-75495071(+)$1	1	32	35	9.0000
(((	chr15:75137374-75137603(-)$1	1	13	16	9.0000
.))	chr14:75150044-75150259(-)$1	1	20	23	9.0000
..(	chr10:72186765-72186995(+)$1	1	33	36	9.0000
.((	chr2:242027321-242027535(-)$1	1	65	68	9.0000
(((	chr4:76582682-76582917(-)$1	1	35	38	9.0000
)))	chr12:133291357-133291579(+)$1	1	26	29	9.0000
(((	chr6:82935192-82935428(-)$1	1	113	116	9.0000
(((	chr5:7889117-7889339(+)$1	1	15	18	9.0000
...	chr6:150059772-150059998(-)$1	1	90	93	9.0000
...	chr7:99006710-99006924(+)$1	1	17	20	9.0000
(((	chr3:49155096-49155310(-)$1	1	2	5	9.0000
((.	chr10:129895677-129895903(-)$1	1	22	25	9.0000
((.	chr1:226822083-226822308(-)$1	1	104	107	9.0000
).)	chr4:2010382-2010603(-)$1	1	68	71	9.0000
(((	chr15:52842671-52842894(-)$1	1	51	54	9.0000
(((	chr14:64434393-64434623(+)$1	1	30	33	9.0000
...	chr1:120457382-120457660(-)$1	1	36	39	9.0000
.((	chr1:38277252-38277474(-)$1	1	5	8	9.0000
(.(	chr1:173807233-173807454(+)$1	1	101	104	9.0000
((.	chr6:15520854-15521080(+)$1	1	21	24	9.0000
)))	chr12:110972881-110973109(-)$1	1	40	43	9.0000
(((	chr12:58145917-58146178(-)$1	1	21	24	9.0000
(.(	chr17:77760305-77760530(+)$1	1	25	28	9.0000
..)	chr14:70237851-70238073(+)$1	1	71	74	9.0000
...	chr7:116418752-116418977(+)$1	1	74	77	9.0000
(((	chr1:245014511-245014722(-)$1	1	104	107	9.0000
(((	chr1:92161213-92161434(-)$1	1	13	16	9.0000
(((	chr5:137501535-137501760(-)$1	1	33	36	9.0000
..(	chr12:122717259-122717471(-)$1	1	0	3	9.0000
)))	chr22:38061864-38062093(+)$1	1	28	31	9.0000
..)	chr4:7033127-7033352(+)$1	1	16	19	9.0000
.((	chr17:37688502-37688741(+)$1	1	15	18	9.0000

#PSSM
C : 0.99	c : 0.01	
A : 0.99	a : 0.01	
G : 0.99	g : 0.01	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_UTR_m3_run2.nuc.txt

#NT
AUUAAA	chr5:90664555-90664795(-)$1	240	64	70	16.8888
auuaaa	chr16:4012621-4012873(-)$1	252	197	203	16.8888
AUUAAA	chr12:27477667-27477907(+)$1	240	19	25	16.8888
AUUAAA	chr1:193220215-193220455(+)$1	240	23	29	16.8888
AUGAAA	chr8:74704820-74705060(-)$1	240	9	15	14.1111
AUGAAA	chr15:55651035-55651275(-)$1	240	147	153	14.1111
AUUAAA	chrX:118717250-118717490(+)$1	240	57	63	16.8888
AUUAAA	chr20:34238652-34238892(-)$1	240	118	124	16.8888
AUUAAA	chr10:3820872-3821112(-)$1	240	23	29	16.8888
AUUAAA	chr10:119766655-119766895(-)$1	240	79	85	16.8888
AUUAAA	chr4:68482538-68482778(-)$1	240	7	13	16.8888
AUUAAA	chr10:8116683-8116923(+)$1	240	232	238	16.8888
AUUAAA	chr1:67452398-67452638(+)$1	240	132	138	16.8888
AUUAAA	chr14:54941957-54942197(-)$1	240	218	224	16.8888
AUUAAA	chr8:17078624-17078864(+)$1	240	114	120	16.8888
AUUAAA	chr17:9147079-9147319(+)$1	240	215	221	16.8888
AUGAAA	chr1:224346497-224346737(+)$1	240	38	44	14.1111
AUGAAA	chr1:243666390-243666630(-)$1	240	18	24	14.1111
AUUAAA	chr1:86116670-86116910(-)$1	240	85	91	16.8888
AUUAAA	chr13:41657899-41658139(+)$1	240	219	225	16.8888
AUUAAA	chr4:99799630-99799870(-)$1	240	99	105	16.8888
AUUAAA	chrX:24230893-24231133(+)$1	240	18	24	16.8888
AUUAAA	chr12:76748437-76748681(-)$1	244	41	47	16.8888
AUUAAA	chr20:56936342-56936582(+)$1	240	71	77	16.8888
AUUAAA	chr12:69665967-69666207(+)$1	240	181	187	16.8888
AUUAAA	chr11:130098232-130098472(-)$1	240	182	188	16.8888
AUUAAA	chr12:112330828-112331068(+)$1	240	140	146	16.8888
AUGAAA	chr12:112465003-112465243(-)$1	240	25	31	14.1111
AUGAAA	chr5:41917892-41918132(+)$1	240	18	24	14.1111
AUUAAA	chr18:20876577-20876818(-)$1	241	230	236	16.8888
AUUAAA	chr11:13751464-13751704(+)$1	240	113	119	16.8888
AUUAAA	chr8:94937939-94938179(+)$1	240	67	73	16.8888
AUGAAA	chr1:101446448-101446688(+)$1	240	25	31	14.1111
AUUAAA	chr4:153832798-153833078(+)$1	280	242	248	16.8888
AUUAAA	chr12:88590609-88590849(+)$1	240	106	112	16.8888

#otherMatches

#Struct PSSM
oooooo	chr2:30864963-30865203(+)$1	240	37	43	14.1111
ssssss	chr5:90664555-90664795(-)$1	240	64	70	16.8888
eeee!!	chr16:4012621-4012873(-)$1	252	197	203	16.8888
:GGGGG	chr12:27477667-27477907(+)$1	240	19	25	16.8888
HHHHHH	chr1:193220215-193220455(+)$1	240	23	29	16.8888
dqqqqq	chr8:74704820-74705060(-)$1	240	9	15	14.1111
ffffff	chr15:55651035-55651275(-)$1	240	147	153	14.1111
KKBB::	chrX:118717250-118717490(+)$1	240	57	63	16.8888
ccqqqq	chr20:34238652-34238892(-)$1	240	118	124	16.8888
%%%%%%	chr10:3820872-3821112(-)$1	240	23	29	16.8888
555eee	chr10:119766655-119766895(-)$1	240	79	85	16.8888
EEEEEM	chr4:68482538-68482778(-)$1	240	7	13	16.8888
::::::	chr10:8116683-8116923(+)$1	240	232	238	16.8888
ooofff	chr1:67452398-67452638(+)$1	240	132	138	16.8888
gglllg	chr14:54941957-54942197(-)$1	240	218	224	16.8888
::::::	chr8:17078624-17078864(+)$1	240	114	120	16.8888
JJJJJJ	chr17:9147079-9147319(+)$1	240	215	221	16.8888
c[dddd	chr1:224346497-224346737(+)$1	240	38	44	14.1111
HHH:::	chr1:243666390-243666630(-)$1	240	18	24	14.1111
''''''	chr1:86116670-86116910(-)$1	240	85	91	16.8888
JJJJJJ	chr13:41657899-41658139(+)$1	240	219	225	16.8888
h22fff	chr4:99799630-99799870(-)$1	240	99	105	16.8888
[bb!!d	chrX:24230893-24231133(+)$1	240	18	24	16.8888
d!!bbo	chr12:76748437-76748681(-)$1	244	41	47	16.8888
f####h	chr20:56936342-56936582(+)$1	240	71	77	16.8888
dddd::	chr12:69665967-69666207(+)$1	240	181	187	16.8888
>>>>>>	chr11:130098232-130098472(-)$1	240	182	188	16.8888
:::::E	chr12:112330828-112331068(+)$1	240	140	146	16.8888
vvvvff	chr12:112465003-112465243(-)$1	240	25	31	14.1111
::GGGG	chr5:41917892-41918132(+)$1	240	18	24	14.1111
::::::	chr18:20876577-20876818(-)$1	241	230	236	16.8888
iiiii2	chr11:13751464-13751704(+)$1	240	113	119	16.8888
::::::	chr8:94937939-94938179(+)$1	240	67	73	16.8888
QQBB{E	chr1:101446448-101446688(+)$1	240	25	31	14.1111
eeeedd	chr4:153832798-153833078(+)$1	280	242	248	16.8888
qqqqcc	chr12:88590609-88590849(+)$1	240	106	112	16.8888

#DB
......	chr2:30864963-30865203(+)$1	1	37	43	14.1111
......	chr5:90664555-90664795(-)$1	1	64	70	16.8888
((((..	chr16:4012621-4012873(-)$1	1	197	203	16.8888
.(((((	chr12:27477667-27477907(+)$1	1	19	25	16.8888
((((((	chr1:193220215-193220455(+)$1	1	23	29	16.8888
(.....	chr8:74704820-74705060(-)$1	1	9	15	14.1111
))))))	chr15:55651035-55651275(-)$1	1	147	153	14.1111
..((..	chrX:118717250-118717490(+)$1	1	57	63	16.8888
((....	chr20:34238652-34238892(-)$1	1	118	124	16.8888
......	chr10:3820872-3821112(-)$1	1	23	29	16.8888
...)))	chr10:119766655-119766895(-)$1	1	79	85	16.8888
(((((.	chr4:68482538-68482778(-)$1	1	7	13	16.8888
......	chr10:8116683-8116923(+)$1	1	232	238	16.8888
...)))	chr1:67452398-67452638(+)$1	1	132	138	16.8888
((...)	chr14:54941957-54942197(-)$1	1	218	224	16.8888
......	chr8:17078624-17078864(+)$1	1	114	120	16.8888
))))))	chr17:9147079-9147319(+)$1	1	215	221	16.8888
(.((((	chr1:224346497-224346737(+)$1	1	38	44	14.1111
(((...	chr1:243666390-243666630(-)$1	1	18	24	14.1111
......	chr1:86116670-86116910(-)$1	1	85	91	16.8888
))))))	chr13:41657899-41658139(+)$1	1	219	225	16.8888
)..)))	chr4:99799630-99799870(-)$1	1	99	105	16.8888
.((..(	chrX:24230893-24231133(+)$1	1	18	24	16.8888
(..((.	chr12:76748437-76748681(-)$1	1	41	47	16.8888
(....(	chr20:56936342-56936582(+)$1	1	71	77	16.8888
))))..	chr12:69665967-69666207(+)$1	1	181	187	16.8888
......	chr11:130098232-130098472(-)$1	1	182	188	16.8888
.....)	chr12:112330828-112331068(+)$1	1	140	146	16.8888
....))	chr12:112465003-112465243(-)$1	1	25	31	14.1111
..((((	chr5:41917892-41918132(+)$1	1	18	24	14.1111
......	chr18:20876577-20876818(-)$1	1	230	236	16.8888
))))).	chr11:13751464-13751704(+)$1	1	113	119	16.8888
......	chr8:94937939-94938179(+)$1	1	67	73	16.8888
..((.(	chr1:101446448-101446688(+)$1	1	25	31	14.1111
))))((	chr4:153832798-153833078(+)$1	1	242	248	16.8888
....))	chr12:88590609-88590849(+)$1	1	106	112	16.8888

#PSSM
A : 0.97	a : 0.02	
U : 0.97	u : 0.02	
U : 0.75	G : 0.22	u : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	

#score	585.7777777777783
#seq	36
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_mukherjee2011_hg19_CDS_m3_run1.nuc.txt

#NT
UUUUUCUG	chr3:155560262-155560484(-)$1	222	84	92	15.8518
UUUUGCUU	chr10:70922089-70922308(+)$1	219	21	29	16.4074
UUUUUCUU	chr2:178095614-178095840(+)$1	226	87	95	20.4814
AUUUUCUU	chr20:18526555-18526777(+)$1	222	29	37	16.6851
UUUUUGUU	chr11:32616404-32616627(+)$1	223	36	44	15.8518
AUUUUCUU	chr12:62721342-62721568(+)$1	226	77	85	16.6851
UUGUUCUU	chr17:55028183-55028401(-)$1	218	29	37	16.0370
AUUUUCUU	chr11:32956762-32956985(+)$1	223	112	120	16.6851
UUUUUCUU	chr14:24658560-24658795(-)$1	235	120	128	20.4814
UUUUUCAU	chr20:10389238-10389469(-)$1	231	111	119	16.3148
UUUGUCUU	chr3:196083547-196083768(-)$1	221	27	35	15.7592
UUUUUCUU	chr20:47686684-47686910(+)$1	226	180	188	20.4814
UUUUUCUC	chr6:56918710-56918931(+)$1	221	101	109	15.9444
UUUUGCUU	chr12:102542147-102542382(+)$1	235	191	199	16.4074
UUUUUCUU	chrX:21871422-21871646(+)$1	224	49	57	20.4814
UUUUUCUU	chr8:17089935-17090166(-)$1	231	83	91	20.4814
UUUUUCUU	chr2:188361597-188361820(-)$1	223	101	109	20.4814
UUUCUCUU	chr14:50626267-50626487(-)$1	220	105	113	15.7592
UUUUUCAU	chr2:207171908-207172131(+)$1	223	111	119	16.3148
UUUUCCUU	chr2:183790311-183790534(-)$1	223	35	43	16.4074
UUUUUCUU	chr22:31851098-31851326(+)$1	228	36	44	20.4814
UUUUUCUU	chrX:23412090-23412316(-)$1	226	99	107	20.4814
UUCUUCUU	chrM:9970-10244(+)$1	274	251	259	16.2222
UUUUUCUU	chr10:15145385-15145603(-)$1	218	93	101	20.4814
UUUUUCUC	chr11:107920596-107920817(+)$1	221	206	214	15.9444
GUUUUCUU	chr12:27070185-27070406(-)$1	221	15	23	16.4074
UUUUUCUU	chr12:123078702-123078937(+)$1	235	101	109	20.4814
uuuuccuu	chr7:99144656-99144886(+)$1	230	28	36	16.4074
AUUUUCUU	chr21:34962012-34962238(-)$1	226	167	175	16.6851
UUUUACUU	chr4:185618755-185618980(-)$1	225	190	198	16.5925
AUUUUCUU	chr12:11138621-11138842(-)$1	221	100	108	16.6851
UUCUUCUU	chrM:10168-10389(+)$1	221	53	61	16.2222
uuuuucuu	chr6:31502185-31502426(-)$1	241	104	112	20.4814
UUUUACUU	chr8:26227565-26227785(+)$1	220	22	30	16.5925
UUUUUCAU	chr13:108862986-108863207(-)$1	221	207	215	16.3148
UUUUUCUU	chr2:86344137-86344355(+)$1	218	25	33	20.4814
UAUUUCUU	chr2:75891766-75891987(+)$1	221	124	132	15.9444
UCUUUCUU	chr3:155571440-155571658(-)$1	218	107	115	16.1296
UUUUACUU	chr2:102509100-102509325(+)$1	225	113	121	16.5925
UUCUUCUU	chr15:34521927-34522149(+)$1	222	14	22	16.2222
GUUUUCUU	chr12:46327868-46328085(-)$1	217	73	81	16.4074
UUUUUCAU	chr5:72351769-72351991(+)$1	222	59	67	16.3148
UUUUUAUU	chrX:123171335-123171557(+)$1	222	111	119	15.8518
UCUUUCUU	chr8:29961736-29961972(+)$1	236	198	206	16.1296
UUUUACUU	chr1:193094183-193094409(+)$1	226	178	186	16.5925
UCUUUCUU	chrM:13918-14139(+)$1	221	186	194	16.1296
UUAUUCUU	chr7:32598072-32598292(+)$1	220	0	8	16.0370
UUUUUCUU	chr7:112423937-112424158(-)$1	221	209	217	20.4814
UUUUUCCU	chr12:57464465-57464688(-)$1	223	104	112	16.0370
UUUUUUUU	chr2:73957757-73957989(-)$1	232	111	119	15.8518
UUUUUCUU	chr22:24967863-24968093(+)$1	230	110	118	20.4814
CUUUUCUU	chr7:102952521-102952753(+)$1	232	70	78	16.3148
UUUUUCUU	chr7:156589050-156589271(-)$1	221	53	61	20.4814

#otherMatches

#Struct PSSM
@@@@@@EE	chr14:96998749-96998974(+)$1	225	214	222	20.4814
GGGGGGGN	chr3:155560262-155560484(-)$1	222	84	92	15.8518
((((((((	chr10:70922089-70922308(+)$1	219	21	29	16.4074
c:::::::	chr2:178095614-178095840(+)$1	226	87	95	20.4814
!hhhhhhh	chr20:18526555-18526777(+)$1	222	29	37	16.6851
dd:::EEE	chr11:32616404-32616627(+)$1	223	36	44	15.8518
::::::::	chr12:62721342-62721568(+)$1	226	77	85	16.6851
ii[a"""f	chr17:55028183-55028401(-)$1	218	29	37	16.0370
===ppppp	chr11:32956762-32956985(+)$1	223	112	120	16.6851
::::::::	chr14:24658560-24658795(-)$1	235	120	128	20.4814
hhhhhhhh	chr20:10389238-10389469(-)$1	231	111	119	16.3148
:::A{AKK	chr3:196083547-196083768(-)$1	221	27	35	15.7592
eeeerrrr	chr20:47686684-47686910(+)$1	226	180	188	20.4814
h:::FFFF	chr6:56918710-56918931(+)$1	221	101	109	15.9444
GGGGccc!	chr12:102542147-102542382(+)$1	235	191	199	16.4074
::::::::	chrX:21871422-21871646(+)$1	224	49	57	20.4814
pppppppd	chr8:17089935-17090166(-)$1	231	83	91	20.4814
::::eeee	chr2:188361597-188361820(-)$1	223	101	109	20.4814
dd]bb]cc	chr14:50626267-50626487(-)$1	220	105	113	15.7592
iiiiii::	chr2:207171908-207172131(+)$1	223	111	119	16.3148
DKKCCCCC	chr2:183790311-183790534(-)$1	223	35	43	16.4074
e:::::II	chr22:31851098-31851326(+)$1	228	36	44	20.4814
^^^^^^^^	chrX:23412090-23412316(-)$1	226	99	107	20.4814
cc]dddd2	chrM:9970-10244(+)$1	274	251	259	16.2222
qqqqqa44	chr10:15145385-15145603(-)$1	218	93	101	20.4814
::::::::	chr11:107920596-107920817(+)$1	221	206	214	15.9444
ee[ddddq	chr12:27070185-27070406(-)$1	221	15	23	16.4074
4444gggg	chr12:123078702-123078937(+)$1	235	101	109	20.4814
hhhhhh%%	chr7:99144656-99144886(+)$1	230	28	36	16.4074
========	chr21:34962012-34962238(-)$1	226	167	175	16.6851
qqeeeee]	chr4:185618755-185618980(-)$1	225	190	198	16.5925
####dddd	chr12:11138621-11138842(-)$1	221	100	108	16.6851
::::::::	chrM:10168-10389(+)$1	221	53	61	16.2222
====mmmm	chr6:31502185-31502426(-)$1	241	104	112	20.4814
pppppppc	chr8:26227565-26227785(+)$1	220	22	30	16.5925
J:::::::	chr13:108862986-108863207(-)$1	221	207	215	16.3148
eee[bb!!	chr2:86344137-86344355(+)$1	218	25	33	20.4814
::::::::	chr2:75891766-75891987(+)$1	221	124	132	15.9444
:::eeeee	chr3:155571440-155571658(-)$1	218	107	115	16.1296
::JJJJJJ	chr2:102509100-102509325(+)$1	225	113	121	16.5925
:ffffff[	chr15:34521927-34522149(+)$1	222	14	22	16.2222
ccc!!amm	chr12:46327868-46328085(-)$1	217	73	81	16.4074
IIIII:::	chr5:72351769-72351991(+)$1	222	59	67	16.3148
++++++++	chrX:123171335-123171557(+)$1	222	111	119	15.8518
rr======	chr8:29961736-29961972(+)$1	236	198	206	16.1296
GGGGGGGY	chr1:193094183-193094409(+)$1	226	178	186	16.5925
::::::::	chrM:13918-14139(+)$1	221	186	194	16.1296
:::::::d	chr7:32598072-32598292(+)$1	220	0	8	16.0370
ggg:CCC}	chr7:112423937-112424158(-)$1	221	209	217	20.4814
eegggggg	chr12:57464465-57464688(-)$1	223	104	112	16.0370
HJJJJJJJ	chr2:73957757-73957989(-)$1	232	111	119	15.8518
iiieeeee	chr22:24967863-24968093(+)$1	230	110	118	20.4814
ee888888	chr7:102952521-102952753(+)$1	232	70	78	16.3148
g^^^^^^^	chr7:156589050-156589271(-)$1	221	53	61	20.4814

#DB
......))	chr14:96998749-96998974(+)$1	1	214	222	20.4814
(((((((.	chr3:155560262-155560484(-)$1	1	84	92	15.8518
........	chr10:70922089-70922308(+)$1	1	21	29	16.4074
).......	chr2:178095614-178095840(+)$1	1	87	95	20.4814
.(((((((	chr20:18526555-18526777(+)$1	1	29	37	16.6851
))...(((	chr11:32616404-32616627(+)$1	1	36	44	15.8518
........	chr12:62721342-62721568(+)$1	1	77	85	16.6851
((.(...(	chr17:55028183-55028401(-)$1	1	29	37	16.0370
(((.....	chr11:32956762-32956985(+)$1	1	112	120	16.6851
........	chr14:24658560-24658795(-)$1	1	120	128	20.4814
))))))))	chr20:10389238-10389469(-)$1	1	111	119	16.3148
...(.(..	chr3:196083547-196083768(-)$1	1	27	35	15.7592
((((....	chr20:47686684-47686910(+)$1	1	180	188	20.4814
)...))))	chr6:56918710-56918931(+)$1	1	101	109	15.9444
))))(((.	chr12:102542147-102542382(+)$1	1	191	199	16.4074
........	chrX:21871422-21871646(+)$1	1	49	57	20.4814
.......)	chr8:17089935-17090166(-)$1	1	83	91	20.4814
....((((	chr2:188361597-188361820(-)$1	1	101	109	20.4814
)).)).))	chr14:50626267-50626487(-)$1	1	105	113	15.7592
))))))..	chr2:207171908-207172131(+)$1	1	111	119	16.3148
(..(((((	chr2:183790311-183790534(-)$1	1	35	43	16.4074
).....((	chr22:31851098-31851326(+)$1	1	36	44	20.4814
........	chrX:23412090-23412316(-)$1	1	99	107	20.4814
)).)))).	chrM:9970-10244(+)$1	1	251	259	16.2222
.....)..	chr10:15145385-15145603(-)$1	1	93	101	20.4814
........	chr11:107920596-107920817(+)$1	1	206	214	15.9444
((.((((.	chr12:27070185-27070406(-)$1	1	15	23	16.4074
....))))	chr12:123078702-123078937(+)$1	1	101	109	20.4814
((((((..	chr7:99144656-99144886(+)$1	1	28	36	16.4074
((((((((	chr21:34962012-34962238(-)$1	1	167	175	16.6851
..))))).	chr4:185618755-185618980(-)$1	1	190	198	16.5925
....((((	chr12:11138621-11138842(-)$1	1	100	108	16.6851
........	chrM:10168-10389(+)$1	1	53	61	16.2222
((((....	chr6:31502185-31502426(-)$1	1	104	112	20.4814
.......)	chr8:26227565-26227785(+)$1	1	22	30	16.5925
).......	chr13:108862986-108863207(-)$1	1	207	215	16.3148
(((.((..	chr2:86344137-86344355(+)$1	1	25	33	20.4814
........	chr2:75891766-75891987(+)$1	1	124	132	15.9444
...(((((	chr3:155571440-155571658(-)$1	1	107	115	16.1296
..))))))	chr2:102509100-102509325(+)$1	1	113	121	16.5925
.((((((.	chr15:34521927-34522149(+)$1	1	14	22	16.2222
(((..(..	chr12:46327868-46328085(-)$1	1	73	81	16.4074
(((((...	chr5:72351769-72351991(+)$1	1	59	67	16.3148
........	chrX:123171335-123171557(+)$1	1	111	119	15.8518
..))))))	chr8:29961736-29961972(+)$1	1	198	206	16.1296
))))))).	chr1:193094183-193094409(+)$1	1	178	186	16.5925
........	chrM:13918-14139(+)$1	1	186	194	16.1296
.......(	chr7:32598072-32598292(+)$1	1	0	8	16.0370
))).))).	chr7:112423937-112424158(-)$1	1	209	217	20.4814
))))))))	chr12:57464465-57464688(-)$1	1	104	112	16.0370
)(((((((	chr2:73957757-73957989(-)$1	1	111	119	15.8518
))))))))	chr22:24967863-24968093(+)$1	1	110	118	20.4814
))......	chr7:102952521-102952753(+)$1	1	70	78	16.3148
(.......	chr7:156589050-156589271(-)$1	1	53	61	20.4814

#PSSM
U : 0.81	A : 0.09	G : 0.03	u : 0.03	C : 0.01	
U : 0.88	C : 0.05	u : 0.03	A : 0.01	
U : 0.87	C : 0.05	u : 0.03	G : 0.01	A : 0.01	
U : 0.92	u : 0.03	G : 0.01	C : 0.01	
U : 0.83	A : 0.07	G : 0.03	C : 0.01	c : 0.01	u : 0.01	
C : 0.90	c : 0.03	G : 0.01	A : 0.01	U : 0.01	
U : 0.87	A : 0.07	u : 0.03	C : 0.01	
U : 0.90	C : 0.03	u : 0.03	G : 0.01	

#score	945.4444444444434
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m3_run2.nuc.txt

#NT
CAAA	chr7:64167337-64167570(+)$1	233	10	14	12.0000
caaa	chr10:70765399-70765624(+)$1	225	60	64	12.0000
CAAA	chrM:10597-10918(+)$1	321	216	220	12.0000
CAAA	chr17:80529587-80529822(+)$1	235	19	23	12.0000
CAAA	chr6:97634411-97634640(-)$1	229	3	7	12.0000
CAAA	chr17:27024824-27025053(+)$1	229	119	123	12.0000
CAAA	chrM:10063-10340(-)$1	277	85	89	12.0000
CAAA	chr11:92531216-92531440(+)$1	224	77	81	12.0000
CAAA	chr5:79770407-79770635(+)$1	228	132	136	12.0000
CAAA	chr2:128479313-128479544(-)$1	231	16	20	12.0000
CAAA	chr5:44811967-44812196(+)$1	229	108	112	12.0000
CAAA	chr1:35915456-35915687(-)$1	231	124	128	12.0000
CAAA	chrX:123185111-123185337(+)$1	226	79	83	12.0000
CAAA	chr1:220197639-220197858(-)$1	219	20	24	12.0000
CAAA	chr12:108145782-108146008(-)$1	226	216	220	12.0000
CAAA	chr11:10821617-10821877(-)$1	260	11	15	12.0000
CAAA	chr11:10821997-10822230(-)$1	233	73	77	12.0000
CAAA	chr7:27832685-27832923(+)$1	238	104	108	12.0000
CAAA	chr3:56682929-56683156(-)$1	227	61	65	12.0000
CAAA	chr4:114378553-114378806(-)$1	253	94	98	12.0000
CAAA	chr10:32560556-32560804(-)$1	248	52	56	12.0000
CAAA	chr6:12125564-12125785(+)$1	221	178	182	12.0000
CAAA	chr2:55252294-55252525(-)$1	231	68	72	12.0000
CAAA	chr1:214819502-214819726(+)$1	224	57	61	12.0000
CAAA	chr1:173916458-173916691(-)$1	233	105	109	12.0000
CAAA	chr6:170627958-170628187(+)$1	229	31	35	12.0000
CAAA	chr5:132403027-132403249(+)$1	222	94	98	12.0000
CAAA	chr2:70315623-70315884(+)$1	261	86	90	12.0000
CAAA	chr17:65908210-65908445(+)$1	235	5	9	12.0000
CAAA	chr8:95550446-95550670(-)$1	224	61	65	12.0000
CAAA	chrM:14733-15002(+)$1	269	28	32	12.0000
CAAA	chr4:26431986-26432205(+)$1	219	109	113	12.0000
CAAA	chrX:48433106-48433335(+)$1	229	197	201	12.0000
CAAA	chr15:50867011-50867241(-)$1	230	0	4	12.0000
CAAA	chr21:16338106-16338329(-)$1	223	60	64	12.0000
caaa	chr16:24576033-24576276(+)$1	243	90	94	12.0000
CAAA	chr19:52519904-52520132(-)$1	228	49	53	12.0000
CAAA	chr3:20027266-20027496(+)$1	230	115	119	12.0000
CAAA	chr10:129900758-129901019(-)$1	261	32	36	12.0000
CAAA	chr15:44811341-44811564(+)$1	223	105	109	12.0000
CAAA	chr4:187530317-187530539(-)$1	222	172	176	12.0000
CAAA	chr22:32108002-32108228(-)$1	226	184	188	12.0000
CAAA	chr8:67963437-67963659(-)$1	222	110	114	12.0000
CAAA	chr8:95862185-95862410(+)$1	225	156	160	12.0000
CAAA	chr5:154336614-154336843(+)$1	229	130	134	12.0000
CAAA	chr8:48875479-48875699(+)$1	220	72	76	12.0000
CAAA	chr1:115269504-115269731(-)$1	227	113	117	12.0000
CAAA	chr2:162036078-162036307(+)$1	229	188	192	12.0000
CAAA	chr6:27420082-27420316(-)$1	234	119	123	12.0000
CAAA	chr9:80868051-80868271(+)$1	220	62	66	12.0000
CAAA	chr14:31576156-31576383(-)$1	227	64	68	12.0000
CAAA	chr19:37879619-37879846(+)$1	227	86	90	12.0000
CAAA	chr5:139908925-139909145(+)$1	220	48	52	12.0000
CAAA	chr21:37705856-37706078(+)$1	222	39	43	12.0000
CAAA	chr2:64778687-64778906(+)$1	219	105	109	12.0000
CAAA	chr11:18104994-18105216(-)$1	222	130	134	12.0000
CAAA	chr1:85116000-85116224(-)$1	224	55	59	12.0000
CAAA	chr7:158447760-158447988(-)$1	228	100	104	12.0000
CAAA	chr17:7411635-7411867(+)$1	232	94	98	12.0000
CAAA	chrX:119387872-119388111(+)$1	239	8	12	12.0000
CAAA	chr17:7804170-7804400(+)$1	230	8	12	12.0000
CAAA	chr14:61444186-61444429(-)$1	243	89	93	12.0000
CAAA	chr17:60088168-60088395(-)$1	227	0	4	12.0000
CAAA	chr1:90400614-90400840(+)$1	226	91	95	12.0000
CAAA	chr8:48793936-48794168(-)$1	232	53	57	12.0000
CAAA	chr18:9257118-9257347(+)$1	229	106	110	12.0000
CAAA	chr3:160150074-160150314(+)$1	240	31	35	12.0000
CAAA	chr2:219362717-219362944(-)$1	227	135	139	12.0000
CAAA	chr11:108032055-108032275(-)$1	220	13	17	12.0000
CAAA	chr1:19451004-19451232(-)$1	228	30	34	12.0000
CAAA	chrX:123220459-123220681(+)$1	222	107	111	12.0000
CAAA	chr6:114267163-114267388(-)$1	225	58	62	12.0000
CAAA	chr14:94528418-94528641(-)$1	223	8	12	12.0000
CAAA	chr19:37239921-37240145(-)$1	224	28	32	12.0000
CAAA	chr11:14854205-14854436(+)$1	231	11	15	12.0000
CAAA	chr12:1005706-1005961(+)$1	255	59	63	12.0000
CAAA	chr3:113376273-113376493(-)$1	220	72	76	12.0000
CAAA	chr6:105474111-105474351(+)$1	240	63	67	12.0000
CAAA	chr14:31585421-31585662(-)$1	241	144	148	12.0000
CAAA	chr9:95078238-95078465(-)$1	227	50	54	12.0000
CAAA	chr6:97609860-97610099(-)$1	239	38	42	12.0000
CAAA	chr11:32953329-32953562(+)$1	233	127	131	12.0000
CAAA	chrX:153197423-153197647(-)$1	224	40	44	12.0000
CAAA	chr5:5461373-5461602(+)$1	229	99	103	12.0000
CAAA	chr11:33362470-33362703(+)$1	233	102	106	12.0000

#otherMatches

#Struct PSSM
ccc:	chr1:220206795-220207054(-)$1	259	82	86	12.0000
dsss	chr7:64167337-64167570(+)$1	233	10	14	12.0000
oooo	chr10:70765399-70765624(+)$1	225	60	64	12.0000
mmmd	chrM:10597-10918(+)$1	321	216	220	12.0000
MMMF	chr17:80529587-80529822(+)$1	235	19	23	12.0000
::::	chr6:97634411-97634640(-)$1	229	3	7	12.0000
bqqq	chr17:27024824-27025053(+)$1	229	119	123	12.0000
hhhh	chrM:10063-10340(-)$1	277	85	89	12.0000
bb]d	chr11:92531216-92531440(+)$1	224	77	81	12.0000
bb!!	chr5:79770407-79770635(+)$1	228	132	136	12.0000
CMMM	chr2:128479313-128479544(-)$1	231	16	20	12.0000
::::	chr5:44811967-44812196(+)$1	229	108	112	12.0000
iiio	chr1:35915456-35915687(-)$1	231	124	128	12.0000
iiii	chrX:123185111-123185337(+)$1	226	79	83	12.0000
dd:f	chr1:220197639-220197858(-)$1	219	20	24	12.0000
::::	chr12:108145782-108146008(-)$1	226	216	220	12.0000
pppe	chr11:10821617-10821877(-)$1	260	11	15	12.0000
::::	chr11:10821997-10822230(-)$1	233	73	77	12.0000
clll	chr7:27832685-27832923(+)$1	238	104	108	12.0000
qqqq	chr3:56682929-56683156(-)$1	227	61	65	12.0000
nnee	chr4:114378553-114378806(-)$1	253	94	98	12.0000
::::	chr10:32560556-32560804(-)$1	248	52	56	12.0000
????	chr6:12125564-12125785(+)$1	221	178	182	12.0000
uuuu	chr2:55252294-55252525(-)$1	231	68	72	12.0000
e^^^	chr1:214819502-214819726(+)$1	224	57	61	12.0000
e+++	chr1:173916458-173916691(-)$1	233	105	109	12.0000
cnnn	chr6:170627958-170628187(+)$1	229	31	35	12.0000
3fff	chr5:132403027-132403249(+)$1	222	94	98	12.0000
ccrr	chr2:70315623-70315884(+)$1	261	86	90	12.0000
iiii	chr17:65908210-65908445(+)$1	235	5	9	12.0000
&&&&	chr8:95550446-95550670(-)$1	224	61	65	12.0000
::::	chrM:14733-15002(+)$1	269	28	32	12.0000
hhhh	chr4:26431986-26432205(+)$1	219	109	113	12.0000
6666	chrX:48433106-48433335(+)$1	229	197	201	12.0000
::::	chr15:50867011-50867241(-)$1	230	0	4	12.0000
oooo	chr21:16338106-16338329(-)$1	223	60	64	12.0000
nnnn	chr16:24576033-24576276(+)$1	243	90	94	12.0000
nnnn	chr19:52519904-52520132(-)$1	228	49	53	12.0000
iiii	chr3:20027266-20027496(+)$1	230	115	119	12.0000
''''	chr10:129900758-129901019(-)$1	261	32	36	12.0000
::::	chr15:44811341-44811564(+)$1	223	105	109	12.0000
uuuu	chr4:187530317-187530539(-)$1	222	172	176	12.0000
9999	chr22:32108002-32108228(-)$1	226	184	188	12.0000
'''d	chr8:67963437-67963659(-)$1	222	110	114	12.0000
eeem	chr8:95862185-95862410(+)$1	225	156	160	12.0000
ccc5	chr5:154336614-154336843(+)$1	229	130	134	12.0000
::::	chr8:48875479-48875699(+)$1	220	72	76	12.0000
nnnn	chr1:115269504-115269731(-)$1	227	113	117	12.0000
bbnn	chr2:162036078-162036307(+)$1	229	188	192	12.0000
^^^^	chr6:27420082-27420316(-)$1	234	119	123	12.0000
ff::	chr9:80868051-80868271(+)$1	220	62	66	12.0000
nnnn	chr14:31576156-31576383(-)$1	227	64	68	12.0000
d:ee	chr19:37879619-37879846(+)$1	227	86	90	12.0000
''''	chr5:139908925-139909145(+)$1	220	48	52	12.0000
llcc	chr21:37705856-37706078(+)$1	222	39	43	12.0000
eeee	chr2:64778687-64778906(+)$1	219	105	109	12.0000
::::	chr11:18104994-18105216(-)$1	222	130	134	12.0000
vvvv	chr1:85116000-85116224(-)$1	224	55	59	12.0000
>>>>	chr7:158447760-158447988(-)$1	228	100	104	12.0000
::::	chr17:7411635-7411867(+)$1	232	94	98	12.0000
eeee	chrX:119387872-119388111(+)$1	239	8	12	12.0000
DLLL	chr17:7804170-7804400(+)$1	230	8	12	12.0000
oooo	chr14:61444186-61444429(-)$1	243	89	93	12.0000
::::	chr17:60088168-60088395(-)$1	227	0	4	12.0000
77ff	chr1:90400614-90400840(+)$1	226	91	95	12.0000
dmmm	chr8:48793936-48794168(-)$1	232	53	57	12.0000
^^^^	chr18:9257118-9257347(+)$1	229	106	110	12.0000
GGKK	chr3:160150074-160150314(+)$1	240	31	35	12.0000
ddee	chr2:219362717-219362944(-)$1	227	135	139	12.0000
::ee	chr11:108032055-108032275(-)$1	220	13	17	12.0000
cc##	chr1:19451004-19451232(-)$1	228	30	34	12.0000
:::f	chrX:123220459-123220681(+)$1	222	107	111	12.0000
####	chr6:114267163-114267388(-)$1	225	58	62	12.0000
%%%%	chr14:94528418-94528641(-)$1	223	8	12	12.0000
::::	chr19:37239921-37240145(-)$1	224	28	32	12.0000
EEEL	chr11:14854205-14854436(+)$1	231	11	15	12.0000
dlll	chr12:1005706-1005961(+)$1	255	59	63	12.0000
gg""	chr3:113376273-113376493(-)$1	220	72	76	12.0000
ff99	chr6:105474111-105474351(+)$1	240	63	67	12.0000
::::	chr14:31585421-31585662(-)$1	241	144	148	12.0000
nnnn	chr9:95078238-95078465(-)$1	227	50	54	12.0000
JJJJ	chr6:97609860-97610099(-)$1	239	38	42	12.0000
^^^^	chr11:32953329-32953562(+)$1	233	127	131	12.0000
d&&&	chrX:153197423-153197647(-)$1	224	40	44	12.0000
::::	chr5:5461373-5461602(+)$1	229	99	103	12.0000
gggg	chr11:33362470-33362703(+)$1	233	102	106	12.0000

#DB
))).	chr1:220206795-220207054(-)$1	1	82	86	12.0000
(...	chr7:64167337-64167570(+)$1	1	10	14	12.0000
....	chr10:70765399-70765624(+)$1	1	60	64	12.0000
...)	chrM:10597-10918(+)$1	1	216	220	12.0000
...(	chr17:80529587-80529822(+)$1	1	19	23	12.0000
....	chr6:97634411-97634640(-)$1	1	3	7	12.0000
(...	chr17:27024824-27025053(+)$1	1	119	123	12.0000
))))	chrM:10063-10340(-)$1	1	85	89	12.0000
)).)	chr11:92531216-92531440(+)$1	1	77	81	12.0000
((..	chr5:79770407-79770635(+)$1	1	132	136	12.0000
(...	chr2:128479313-128479544(-)$1	1	16	20	12.0000
....	chr5:44811967-44812196(+)$1	1	108	112	12.0000
(((.	chr1:35915456-35915687(-)$1	1	124	128	12.0000
))))	chrX:123185111-123185337(+)$1	1	79	83	12.0000
)).(	chr1:220197639-220197858(-)$1	1	20	24	12.0000
....	chr12:108145782-108146008(-)$1	1	216	220	12.0000
...)	chr11:10821617-10821877(-)$1	1	11	15	12.0000
....	chr11:10821997-10822230(-)$1	1	73	77	12.0000
(...	chr7:27832685-27832923(+)$1	1	104	108	12.0000
....	chr3:56682929-56683156(-)$1	1	61	65	12.0000
..))	chr4:114378553-114378806(-)$1	1	94	98	12.0000
....	chr10:32560556-32560804(-)$1	1	52	56	12.0000
....	chr6:12125564-12125785(+)$1	1	178	182	12.0000
....	chr2:55252294-55252525(-)$1	1	68	72	12.0000
(...	chr1:214819502-214819726(+)$1	1	57	61	12.0000
(...	chr1:173916458-173916691(-)$1	1	105	109	12.0000
(...	chr6:170627958-170628187(+)$1	1	31	35	12.0000
.)))	chr5:132403027-132403249(+)$1	1	94	98	12.0000
((..	chr2:70315623-70315884(+)$1	1	86	90	12.0000
((((	chr17:65908210-65908445(+)$1	1	5	9	12.0000
....	chr8:95550446-95550670(-)$1	1	61	65	12.0000
....	chrM:14733-15002(+)$1	1	28	32	12.0000
((((	chr4:26431986-26432205(+)$1	1	109	113	12.0000
....	chrX:48433106-48433335(+)$1	1	197	201	12.0000
....	chr15:50867011-50867241(-)$1	1	0	4	12.0000
....	chr21:16338106-16338329(-)$1	1	60	64	12.0000
....	chr16:24576033-24576276(+)$1	1	90	94	12.0000
....	chr19:52519904-52520132(-)$1	1	49	53	12.0000
))))	chr3:20027266-20027496(+)$1	1	115	119	12.0000
....	chr10:129900758-129901019(-)$1	1	32	36	12.0000
....	chr15:44811341-44811564(+)$1	1	105	109	12.0000
....	chr4:187530317-187530539(-)$1	1	172	176	12.0000
....	chr22:32108002-32108228(-)$1	1	184	188	12.0000
...(	chr8:67963437-67963659(-)$1	1	110	114	12.0000
(((.	chr8:95862185-95862410(+)$1	1	156	160	12.0000
))).	chr5:154336614-154336843(+)$1	1	130	134	12.0000
....	chr8:48875479-48875699(+)$1	1	72	76	12.0000
....	chr1:115269504-115269731(-)$1	1	113	117	12.0000
((..	chr2:162036078-162036307(+)$1	1	188	192	12.0000
....	chr6:27420082-27420316(-)$1	1	119	123	12.0000
))..	chr9:80868051-80868271(+)$1	1	62	66	12.0000
....	chr14:31576156-31576383(-)$1	1	64	68	12.0000
).((	chr19:37879619-37879846(+)$1	1	86	90	12.0000
....	chr5:139908925-139909145(+)$1	1	48	52	12.0000
..))	chr21:37705856-37706078(+)$1	1	39	43	12.0000
))))	chr2:64778687-64778906(+)$1	1	105	109	12.0000
....	chr11:18104994-18105216(-)$1	1	130	134	12.0000
....	chr1:85116000-85116224(-)$1	1	55	59	12.0000
....	chr7:158447760-158447988(-)$1	1	100	104	12.0000
....	chr17:7411635-7411867(+)$1	1	94	98	12.0000
((((	chrX:119387872-119388111(+)$1	1	8	12	12.0000
(...	chr17:7804170-7804400(+)$1	1	8	12	12.0000
....	chr14:61444186-61444429(-)$1	1	89	93	12.0000
....	chr17:60088168-60088395(-)$1	1	0	4	12.0000
..))	chr1:90400614-90400840(+)$1	1	91	95	12.0000
(...	chr8:48793936-48794168(-)$1	1	53	57	12.0000
....	chr18:9257118-9257347(+)$1	1	106	110	12.0000
((..	chr3:160150074-160150314(+)$1	1	31	35	12.0000
((((	chr2:219362717-219362944(-)$1	1	135	139	12.0000
..((	chr11:108032055-108032275(-)$1	1	13	17	12.0000
((..	chr1:19451004-19451232(-)$1	1	30	34	12.0000
...(	chrX:123220459-123220681(+)$1	1	107	111	12.0000
....	chr6:114267163-114267388(-)$1	1	58	62	12.0000
....	chr14:94528418-94528641(-)$1	1	8	12	12.0000
....	chr19:37239921-37240145(-)$1	1	28	32	12.0000
(((.	chr11:14854205-14854436(+)$1	1	11	15	12.0000
(...	chr12:1005706-1005961(+)$1	1	59	63	12.0000
((..	chr3:113376273-113376493(-)$1	1	72	76	12.0000
))..	chr6:105474111-105474351(+)$1	1	63	67	12.0000
....	chr14:31585421-31585662(-)$1	1	144	148	12.0000
....	chr9:95078238-95078465(-)$1	1	50	54	12.0000
((((	chr6:97609860-97610099(-)$1	1	38	42	12.0000
....	chr11:32953329-32953562(+)$1	1	127	131	12.0000
(...	chrX:153197423-153197647(-)$1	1	40	44	12.0000
....	chr5:5461373-5461602(+)$1	1	99	103	12.0000
))))	chr11:33362470-33362703(+)$1	1	102	106	12.0000

#PSSM
C : 0.97	c : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m3_run2.nuc.txt

#NT
CCAG	chr20:20006227-20006451(+)$1	224	132	136	11.9999
CCAG	chr17:36876647-36876884(+)$1	237	20	24	11.9999
CCAG	chr15:64506051-64506275(-)$1	224	6	10	11.9999
CCAG	chr16:30975499-30975724(+)$1	225	7	11	11.9999
CCAG	chrM:6577-6809(+)$1	232	71	75	11.9999
CCAG	chr12:32908043-32908264(-)$1	221	118	122	11.9999
CCAG	chr3:49137563-49137786(-)$1	223	76	80	11.9999
CCAG	chr16:1748861-1749100(+)$1	239	118	122	11.9999
CCAG	chr1:184020899-184021124(+)$1	225	156	160	11.9999
CCAG	chr15:41102290-41102511(+)$1	221	57	61	11.9999
CCAG	chr4:79772072-79772302(+)$1	230	95	99	11.9999
CCAG	chr4:39207133-39207359(+)$1	226	168	172	11.9999
CCAG	chr19:18480585-18480808(+)$1	223	39	43	11.9999
CCAG	chr11:2424021-2424253(+)$1	232	61	65	11.9999
CCAG	chr3:133969169-133969397(+)$1	228	51	55	11.9999
CCAG	chr9:140349983-140350208(-)$1	225	211	215	11.9999
CCAG	chr16:74942719-74942939(-)$1	220	19	23	11.9999
CCAG	chr13:23914402-23914625(-)$1	223	82	86	11.9999
CCAG	chr16:450081-450311(+)$1	230	151	155	11.9999
CCAG	chr10:60566668-60566914(-)$1	246	88	92	11.9999
CCAG	chr16:30976175-30976402(+)$1	227	15	19	11.9999
CCAG	chr17:21086980-21087202(+)$1	222	124	128	11.9999
CCAG	chr3:192516879-192517099(-)$1	220	57	61	11.9999
CCAG	chr7:100175760-100175981(-)$1	221	17	21	11.9999
CCAG	chrX:37701006-37701230(-)$1	224	122	126	11.9999
CCAG	chr10:119134020-119134247(-)$1	227	1	5	11.9999
CCAG	chr16:30667507-30667732(+)$1	225	21	25	11.9999
CCAG	chr17:4789783-4790005(+)$1	222	61	65	11.9999
CCAG	chr3:47165468-47165689(-)$1	221	21	25	11.9999
CCAG	chr19:2271770-2271991(+)$1	221	72	76	11.9999
CCAG	chr19:12907788-12908017(-)$1	229	212	216	11.9999
CCAG	chr19:35424440-35424659(-)$1	219	183	187	11.9999
CCAG	chr17:48469710-48469942(-)$1	232	203	207	11.9999
CCAG	chr2:43798792-43799017(-)$1	225	126	130	11.9999
CCAG	chr1:23636974-23637217(-)$1	243	105	109	11.9999
CCAG	chr3:120121995-120122220(-)$1	225	215	219	11.9999
CCAG	chr17:65942135-65942367(+)$1	232	14	18	11.9999
CCAG	chr17:27051494-27051720(-)$1	226	45	49	11.9999
CCAG	chr17:8380122-8380355(-)$1	233	27	31	11.9999
CCAG	chr9:131767533-131767757(+)$1	224	83	87	11.9999
CCAG	chr18:28602247-28602471(-)$1	224	123	127	11.9999
CCAG	chr19:2477386-2477607(+)$1	221	8	12	11.9999
CCAG	chr1:16242616-16242836(+)$1	220	136	140	11.9999
CCAG	chr6:144171176-144171395(+)$1	219	169	173	11.9999
CCAG	chr5:180036877-180037107(-)$1	230	117	121	11.9999
CCAG	chr2:232321251-232321470(-)$1	219	102	106	11.9999
CCAG	chr11:1977518-1977749(+)$1	231	112	116	11.9999
CCAG	chr6:1391027-1391259(+)$1	232	11	15	11.9999
CCAG	chr15:90808882-90809111(+)$1	229	149	153	11.9999
CCAG	chr10:43881991-43882236(-)$1	245	3	7	11.9999
CCAG	chr12:115109530-115109754(-)$1	224	29	33	11.9999
CCAG	chr19:18054288-18054511(+)$1	223	24	28	11.9999
CCAG	chr10:60548928-60549315(-)$1	387	250	254	11.9999
CCAG	chr6:1394895-1395126(+)$1	231	51	55	11.9999
CCAG	chr15:78337287-78337510(-)$1	223	139	143	11.9999
CCAG	chr19:47287695-47287916(-)$1	221	31	35	11.9999
CCAG	chr8:38145950-38146180(-)$1	230	59	63	11.9999
CCAG	chr14:31852759-31852987(-)$1	228	6	10	11.9999
CCAG	chr3:126180806-126181033(-)$1	227	9	13	11.9999
CCAG	chr8:30704153-30704384(-)$1	231	144	148	11.9999
CCAG	chr11:63742114-63742336(+)$1	222	95	99	11.9999
CCAG	chr20:49575758-49575981(+)$1	223	22	26	11.9999
CCAG	chr1:39457150-39457370(+)$1	220	154	158	11.9999
CCAG	chr6:132175971-132176199(+)$1	228	90	94	11.9999
CCAG	chr11:62559223-62559448(-)$1	225	143	147	11.9999
CCAG	chr19:36595716-36595952(+)$1	236	33	37	11.9999
CCAG	chrM:4622-4870(+)$1	248	193	197	11.9999
CCAG	chr18:28576752-28576979(-)$1	227	87	91	11.9999
CCAG	chr20:60963271-60963513(+)$1	242	198	202	11.9999
CCAG	chr19:14076380-14076600(-)$1	220	113	117	11.9999
CCAG	chr22:29517313-29517538(+)$1	225	88	92	11.9999
CCAG	chr12:48367834-48368061(-)$1	227	30	34	11.9999
CCAG	chr3:9514822-9515045(+)$1	223	52	56	11.9999
CCAG	chr19:2271394-2271630(+)$1	236	75	79	11.9999
CCAG	chr10:119044004-119044223(-)$1	219	66	70	11.9999
CCAG	chr16:31088783-31089005(+)$1	222	49	53	11.9999
CCAG	chr6:31127242-31127467(+)$1	225	141	145	11.9999
CCAG	chr17:76046740-76046962(+)$1	222	170	174	11.9999

#otherMatches

#Struct PSSM
hhhh	chr13:80911557-80911778(-)$1	221	26	30	11.9999
c]bb	chr20:20006227-20006451(+)$1	224	132	136	11.9999
LFFF	chr17:36876647-36876884(+)$1	237	20	24	11.9999
ffff	chr15:64506051-64506275(-)$1	224	6	10	11.9999
###c	chr16:30975499-30975724(+)$1	225	7	11	11.9999
F:::	chrM:6577-6809(+)$1	232	71	75	11.9999
nncc	chr12:32908043-32908264(-)$1	221	118	122	11.9999
ffff	chr3:49137563-49137786(-)$1	223	76	80	11.9999
::::	chr16:1748861-1749100(+)$1	239	118	122	11.9999
gaee	chr1:184020899-184021124(+)$1	225	156	160	11.9999
nnnd	chr15:41102290-41102511(+)$1	221	57	61	11.9999
HHHH	chr4:79772072-79772302(+)$1	230	95	99	11.9999
DDDD	chr4:39207133-39207359(+)$1	226	168	172	11.9999
Bccc	chr19:18480585-18480808(+)$1	223	39	43	11.9999
f:::	chr11:2424021-2424253(+)$1	232	61	65	11.9999
g!!c	chr3:133969169-133969397(+)$1	228	51	55	11.9999
IIII	chr9:140349983-140350208(-)$1	225	211	215	11.9999
eee#	chr16:74942719-74942939(-)$1	220	19	23	11.9999
$$$d	chr13:23914402-23914625(-)$1	223	82	86	11.9999
c!!a	chr16:450081-450311(+)$1	230	151	155	11.9999
bccc	chr10:60566668-60566914(-)$1	246	88	92	11.9999
eeee	chr16:30976175-30976402(+)$1	227	15	19	11.9999
ff::	chr17:21086980-21087202(+)$1	222	124	128	11.9999
NNNN	chr3:192516879-192517099(-)$1	220	57	61	11.9999
FFFF	chr7:100175760-100175981(-)$1	221	17	21	11.9999
bbb]	chrX:37701006-37701230(-)$1	224	122	126	11.9999
ddd[	chr10:119134020-119134247(-)$1	227	1	5	11.9999
ffff	chr16:30667507-30667732(+)$1	225	21	25	11.9999
:::C	chr17:4789783-4790005(+)$1	222	61	65	11.9999
))))	chr3:47165468-47165689(-)$1	221	21	25	11.9999
BB{D	chr19:2271770-2271991(+)$1	221	72	76	11.9999
gggg	chr19:12907788-12908017(-)$1	229	212	216	11.9999
[bb#	chr19:35424440-35424659(-)$1	219	183	187	11.9999
ba22	chr17:48469710-48469942(-)$1	232	203	207	11.9999
cc[b	chr2:43798792-43799017(-)$1	225	126	130	11.9999
cccd	chr1:23636974-23637217(-)$1	243	105	109	11.9999
:EEE	chr3:120121995-120122220(-)$1	225	215	219	11.9999
DD:b	chr17:65942135-65942367(+)$1	232	14	18	11.9999
caff	chr17:27051494-27051720(-)$1	226	45	49	11.9999
bFFF	chr17:8380122-8380355(-)$1	233	27	31	11.9999
nddd	chr9:131767533-131767757(+)$1	224	83	87	11.9999
((((	chr18:28602247-28602471(-)$1	224	123	127	11.9999
:ccc	chr19:2477386-2477607(+)$1	221	8	12	11.9999
dddd	chr1:16242616-16242836(+)$1	220	136	140	11.9999
eeee	chr6:144171176-144171395(+)$1	219	169	173	11.9999
ddd!	chr5:180036877-180037107(-)$1	230	117	121	11.9999
c[dd	chr2:232321251-232321470(-)$1	219	102	106	11.9999
bbmm	chr11:1977518-1977749(+)$1	231	112	116	11.9999
C::e	chr6:1391027-1391259(+)$1	232	11	15	11.9999
FFFF	chr15:90808882-90809111(+)$1	229	149	153	11.9999
EEEE	chr10:43881991-43882236(-)$1	245	3	7	11.9999
::cc	chr12:115109530-115109754(-)$1	224	29	33	11.9999
rrre	chr19:18054288-18054511(+)$1	223	24	28	11.9999
qddd	chr10:60548928-60549315(-)$1	387	250	254	11.9999
{A:c	chr6:1394895-1395126(+)$1	231	51	55	11.9999
bccc	chr15:78337287-78337510(-)$1	223	139	143	11.9999
DDD{	chr19:47287695-47287916(-)$1	221	31	35	11.9999
bb""	chr8:38145950-38146180(-)$1	230	59	63	11.9999
llcc	chr14:31852759-31852987(-)$1	228	6	10	11.9999
oooo	chr3:126180806-126181033(-)$1	227	9	13	11.9999
CCC}	chr8:30704153-30704384(-)$1	231	144	148	11.9999
3eee	chr11:63742114-63742336(+)$1	222	95	99	11.9999
dddd	chr20:49575758-49575981(+)$1	223	22	26	11.9999
====	chr1:39457150-39457370(+)$1	220	154	158	11.9999
gggg	chr6:132175971-132176199(+)$1	228	90	94	11.9999
ee[c	chr11:62559223-62559448(-)$1	225	143	147	11.9999
gggg	chr19:36595716-36595952(+)$1	236	33	37	11.9999
nggg	chrM:4622-4870(+)$1	248	193	197	11.9999
bb33	chr18:28576752-28576979(-)$1	227	87	91	11.9999
gg::	chr20:60963271-60963513(+)$1	242	198	202	11.9999
IIII	chr19:14076380-14076600(-)$1	220	113	117	11.9999
mddd	chr22:29517313-29517538(+)$1	225	88	92	11.9999
++++	chr12:48367834-48368061(-)$1	227	30	34	11.9999
dddd	chr3:9514822-9515045(+)$1	223	52	56	11.9999
333f	chr19:2271394-2271630(+)$1	236	75	79	11.9999
ccc5	chr10:119044004-119044223(-)$1	219	66	70	11.9999
dddd	chr16:31088783-31089005(+)$1	222	49	53	11.9999
e]cc	chr6:31127242-31127467(+)$1	225	141	145	11.9999
eeee	chr17:76046740-76046962(+)$1	222	170	174	11.9999

#DB
((((	chr13:80911557-80911778(-)$1	1	26	30	11.9999
).))	chr20:20006227-20006451(+)$1	1	132	136	11.9999
.(((	chr17:36876647-36876884(+)$1	1	20	24	11.9999
((((	chr15:64506051-64506275(-)$1	1	6	10	11.9999
...(	chr16:30975499-30975724(+)$1	1	7	11	11.9999
(...	chrM:6577-6809(+)$1	1	71	75	11.9999
..))	chr12:32908043-32908264(-)$1	1	118	122	11.9999
))))	chr3:49137563-49137786(-)$1	1	76	80	11.9999
....	chr16:1748861-1749100(+)$1	1	118	122	11.9999
))))	chr1:184020899-184021124(+)$1	1	156	160	11.9999
...)	chr15:41102290-41102511(+)$1	1	57	61	11.9999
))))	chr4:79772072-79772302(+)$1	1	95	99	11.9999
))))	chr4:39207133-39207359(+)$1	1	168	172	11.9999
((((	chr19:18480585-18480808(+)$1	1	39	43	11.9999
)...	chr11:2424021-2424253(+)$1	1	61	65	11.9999
(..(	chr3:133969169-133969397(+)$1	1	51	55	11.9999
))))	chr9:140349983-140350208(-)$1	1	211	215	11.9999
(((.	chr16:74942719-74942939(-)$1	1	19	23	11.9999
...(	chr13:23914402-23914625(-)$1	1	82	86	11.9999
(..(	chr16:450081-450311(+)$1	1	151	155	11.9999
((((	chr10:60566668-60566914(-)$1	1	88	92	11.9999
))))	chr16:30976175-30976402(+)$1	1	15	19	11.9999
))..	chr17:21086980-21087202(+)$1	1	124	128	11.9999
....	chr3:192516879-192517099(-)$1	1	57	61	11.9999
((((	chr7:100175760-100175981(-)$1	1	17	21	11.9999
))).	chrX:37701006-37701230(-)$1	1	122	126	11.9999
(((.	chr10:119134020-119134247(-)$1	1	1	5	11.9999
((((	chr16:30667507-30667732(+)$1	1	21	25	11.9999
...(	chr17:4789783-4790005(+)$1	1	61	65	11.9999
....	chr3:47165468-47165689(-)$1	1	21	25	11.9999
((.(	chr19:2271770-2271991(+)$1	1	72	76	11.9999
))))	chr19:12907788-12908017(-)$1	1	212	216	11.9999
.((.	chr19:35424440-35424659(-)$1	1	183	187	11.9999
))..	chr17:48469710-48469942(-)$1	1	203	207	11.9999
((.(	chr2:43798792-43799017(-)$1	1	126	130	11.9999
))))	chr1:23636974-23637217(-)$1	1	105	109	11.9999
.)))	chr3:120121995-120122220(-)$1	1	215	219	11.9999
((.(	chr17:65942135-65942367(+)$1	1	14	18	11.9999
))))	chr17:27051494-27051720(-)$1	1	45	49	11.9999
)(((	chr17:8380122-8380355(-)$1	1	27	31	11.9999
.)))	chr9:131767533-131767757(+)$1	1	83	87	11.9999
....	chr18:28602247-28602471(-)$1	1	123	127	11.9999
.(((	chr19:2477386-2477607(+)$1	1	8	12	11.9999
((((	chr1:16242616-16242836(+)$1	1	136	140	11.9999
))))	chr6:144171176-144171395(+)$1	1	169	173	11.9999
(((.	chr5:180036877-180037107(-)$1	1	117	121	11.9999
(.((	chr2:232321251-232321470(-)$1	1	102	106	11.9999
((..	chr11:1977518-1977749(+)$1	1	112	116	11.9999
(..(	chr6:1391027-1391259(+)$1	1	11	15	11.9999
))))	chr15:90808882-90809111(+)$1	1	149	153	11.9999
((((	chr10:43881991-43882236(-)$1	1	3	7	11.9999
..((	chr12:115109530-115109754(-)$1	1	29	33	11.9999
...)	chr19:18054288-18054511(+)$1	1	24	28	11.9999
.)))	chr10:60548928-60549315(-)$1	1	250	254	11.9999
.(.(	chr6:1394895-1395126(+)$1	1	51	55	11.9999
((((	chr15:78337287-78337510(-)$1	1	139	143	11.9999
(((.	chr19:47287695-47287916(-)$1	1	31	35	11.9999
((..	chr8:38145950-38146180(-)$1	1	59	63	11.9999
..))	chr14:31852759-31852987(-)$1	1	6	10	11.9999
....	chr3:126180806-126181033(-)$1	1	9	13	11.9999
))).	chr8:30704153-30704384(-)$1	1	144	148	11.9999
.)))	chr11:63742114-63742336(+)$1	1	95	99	11.9999
((((	chr20:49575758-49575981(+)$1	1	22	26	11.9999
))))	chr1:39457150-39457370(+)$1	1	154	158	11.9999
((((	chr6:132175971-132176199(+)$1	1	90	94	11.9999
((.(	chr11:62559223-62559448(-)$1	1	143	147	11.9999
))))	chr19:36595716-36595952(+)$1	1	33	37	11.9999
.)))	chrM:4622-4870(+)$1	1	193	197	11.9999
))..	chr18:28576752-28576979(-)$1	1	87	91	11.9999
))..	chr20:60963271-60963513(+)$1	1	198	202	11.9999
))))	chr19:14076380-14076600(-)$1	1	113	117	11.9999
.)))	chr22:29517313-29517538(+)$1	1	88	92	11.9999
....	chr12:48367834-48368061(-)$1	1	30	34	11.9999
((((	chr3:9514822-9515045(+)$1	1	52	56	11.9999
...)	chr19:2271394-2271630(+)$1	1	75	79	11.9999
))).	chr10:119044004-119044223(-)$1	1	66	70	11.9999
))))	chr16:31088783-31089005(+)$1	1	49	53	11.9999
).))	chr6:31127242-31127467(+)$1	1	141	145	11.9999
))))	chr17:76046740-76046962(+)$1	1	170	174	11.9999

#PSSM
C : 0.99	
C : 0.99	
A : 0.99	
G : 0.99	

#score	947.9999999999995
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_UTR_m1_run1.nuc.txt

#NT
auuuuuauuuuu	chr4:5502376-5502613(+)$1	237	5	17	24.7068
UAUUUAAUUUUU	chr5:36099192-36099420(-)$1	228	42	54	19.8793
uuuuuuguuuuu	chr6:43129244-43129472(+)$1	228	148	160	25.9999
uuuuauguuuuu	chr2:241082-241310(-)$1	228	93	105	21.8620
AUUUUUAUUUCU	chr18:66341861-66342092(-)$1	231	82	94	19.9655
UUAUAUAUUUUU	chrX:131209003-131209259(+)$1	256	113	125	20.3965
CUUUUGAUUUUU	chr9:34088163-34088425(-)$1	262	135	147	19.9655
uuuuuuaauuua	chr8:116423064-116423354(-)$1	290	149	161	20.3103
uuuuuuguuuuu	chr10:115675247-115675505(+)$1	258	151	163	25.9999
gUGUUUAUUUUU	chr12:120899094-120899324(+)$1	230	97	109	20.3965
UUUUUUUUUUUU	chr2:44999533-44999758(+)$1	225	70	82	26.2586
CUUUUUAAUUUU	chr10:18965435-18965718(+)$1	283	134	146	20.4827
UUUUUUGUUUUU	chr7:20452199-20452440(+)$1	241	106	118	25.9999
auuuuuauuuau	chr1:150937766-150938000(-)$1	234	112	124	19.9655
UUUUUUAUUUUU	chr7:7284580-7284810(+)$1	230	107	119	28.4137
uuuuuuuuuuuu	chr1:185070807-185071035(+)$1	228	157	169	26.2586
uuucuuaauuuu	chr3:32032915-32033140(+)$1	225	101	113	19.9655
UCUUUUAUUUUU	chr8:86194816-86195049(+)$1	233	120	132	24.4482
UUUUUUCUUGUU	chr14:58838826-58839058(+)$1	232	37	49	21.7758
uuauuuauuuua	chr8:22110304-22110560(+)$1	256	131	143	20.3965
uuuuuuauuuua	chr3:120048354-120048585(-)$1	231	115	127	24.2758
uuuuguaguuuu	chr20:25428845-25429075(+)$1	230	122	134	19.7068
uuauuuauuuuu	chr5:70861636-70861867(+)$1	231	101	113	24.5344
UUUUUUUUUUUU	chr3:172115401-172115757(+)$1	356	189	201	26.2586
guuuuuguuuuu	chr15:52203310-52203562(+)$1	252	87	99	22.1206
UCUUUUAUUAUU	chr7:137560855-137561086(-)$1	231	113	125	20.0517
guuuuuauuuuu	chr4:140396464-140396774(+)$1	310	184	196	24.5344
UUUCCUAUUUUU	chr12:22840970-22841197(+)$1	227	81	93	19.5344
UGUUUGAUUUUU	chr2:179968969-179969206(-)$1	237	80	92	20.0517
uuuuuucuuuuu	chr2:30865192-30865460(+)$1	268	56	68	25.9137
UGUUUUUUUUUU	chr6:134490403-134490626(-)$1	223	0	12	22.3793
UCUUUUAUUGUU	chr9:91092959-91093235(+)$1	276	147	159	20.3103
UUUUUUAUUGUC	chr3:185635303-185635552(-)$1	249	106	118	19.9655
UUUUUUUUUUUU	chr1:193054474-193054720(+)$1	246	101	113	26.2586
UUUUUUCCUUUU	chr2:24290370-24290593(-)$1	223	15	27	21.6034
UUUUUUAAUUUC	chr2:28616090-28616331(+)$1	241	120	132	20.1379
AUUUUUUUUUUU	chr13:38935137-38935390(+)$1	253	76	88	22.5517
UGUUUUUUUUUU	chr16:23582311-23582567(+)$1	256	42	54	22.3793
UUUUUUCUUUUU	chr13:39611400-39611639(-)$1	239	40	52	25.9137
uuauauauuuuu	chr22:45582387-45582647(+)$1	260	141	153	20.3965
UUUUUUUUAUUU	chr8:82570782-82571050(-)$1	268	119	131	21.6896
AUUGUUAUUUUU	chr13:50273450-50273693(-)$1	243	101	113	20.1379
UUUUUUGUUUUU	chrX:77082288-77082547(-)$1	259	94	106	25.9999
uuauuaauuuuu	chr3:146233287-146233532(-)$1	245	11	23	20.0517
UUGUUUAAUUUU	chr6:34255785-34256035(-)$1	250	44	56	20.3103
UUUUUUGUAUUU	chr14:64951340-64951573(-)$1	233	27	39	21.4310
uuuuuuuuuuuu	chr6:24719338-24719565(-)$1	227	162	174	26.2586
UGCUUUAUUUUU	chr12:69666012-69666263(+)$1	251	105	117	20.3103
UUUUUUCUUUUU	chrX:24095433-24095699(+)$1	266	138	150	25.9137
uuuuuuauucuu	chr22:28146308-28146533(-)$1	225	49	61	24.0172
uuuuuuauuuuu	chr11:66407776-66408011(+)$1	235	110	122	28.4137
UUUUUUAUUUUU	chr6:163992667-163992918(+)$1	251	184	196	28.4137
UUUUUUCUGUUU	chr18:48609805-48610044(+)$1	239	17	29	21.2586
uuuuuuuuuuuu	chr1:173905608-173905853(-)$1	245	176	188	26.2586
UAUUUUAUUUUU	chr5:154194245-154194509(+)$1	264	132	144	24.3620
UUUUAUAUUGUU	chrX:123235392-123235636(+)$1	244	115	127	20.1379
UUUAUUAUUUUA	chr15:66181491-66181758(+)$1	267	152	164	19.7068

#otherMatches

#Struct PSSM
HHHHH::::ggg	chr10:93043819-93044112(+)$1	293	25	37	28.4137
:ffffffnnnnn	chr4:5502376-5502613(+)$1	237	5	17	24.7068
hhhhhhpppppp	chr5:36099192-36099420(-)$1	228	42	54	19.8793
((((((bb"""c	chr6:43129244-43129472(+)$1	228	148	160	25.9999
f"""ggggggg#	chr2:241082-241310(-)$1	228	93	105	21.8620
h####hhhhhhh	chr18:66341861-66342092(-)$1	231	82	94	19.9655
:::::::::::g	chrX:131209003-131209259(+)$1	256	113	125	20.3965
wwwdddd::::J	chr9:34088163-34088425(-)$1	262	135	147	19.9655
""bb[=======	chr8:116423064-116423354(-)$1	290	149	161	20.3103
gggggggmmmmg	chr10:115675247-115675505(+)$1	258	151	163	25.9999
GGGGG______D	chr12:120899094-120899324(+)$1	230	97	109	20.3965
::::::::::::	chr2:44999533-44999758(+)$1	225	70	82	26.2586
:::::::iiiii	chr10:18965435-18965718(+)$1	283	134	146	20.4827
fff"""ffffff	chr7:20452199-20452440(+)$1	241	106	118	25.9999
::::::::::::	chr1:150937766-150938000(-)$1	234	112	124	19.9655
::::::::::::	chr7:7284580-7284810(+)$1	230	107	119	28.4137
CCC:::::::::	chr1:185070807-185071035(+)$1	228	157	169	26.2586
==::::::::::	chr3:32032915-32033140(+)$1	225	101	113	19.9655
^^^^^^^^^^^^	chr8:86194816-86195049(+)$1	233	120	132	24.4482
bb!!bbffffff	chr14:58838826-58839058(+)$1	232	37	49	21.7758
gg:::::fffff	chr8:22110304-22110560(+)$1	256	131	143	20.3965
pppppccc4444	chr3:120048354-120048585(-)$1	231	115	127	24.2758
ggggggg333gg	chr20:25428845-25429075(+)$1	230	122	134	19.7068
f[bb"""iiiii	chr5:70861636-70861867(+)$1	231	101	113	24.5344
ee++++++++++	chr3:172115401-172115757(+)$1	356	189	201	26.2586
cc####dddd++	chr15:52203310-52203562(+)$1	252	87	99	22.1206
dd[ddddmmmmd	chr7:137560855-137561086(-)$1	231	113	125	20.0517
iiiiiipppppp	chr4:140396464-140396774(+)$1	310	184	196	24.5344
iiiiii::====	chr12:22840970-22841197(+)$1	227	81	93	19.5344
D{JJJJJJJJJJ	chr2:179968969-179969206(-)$1	237	80	92	20.0517
hhhhhh^^^^^^	chr2:30865192-30865460(+)$1	268	56	68	25.9137
::::::DDDD{E	chr6:134490403-134490626(-)$1	223	0	12	22.3793
YEEEEE}BBBB}	chr9:91092959-91093235(+)$1	276	147	159	20.3103
dddd55555ccc	chr3:185635303-185635552(-)$1	249	106	118	19.9655
ggggg&&&&&&&	chr1:193054474-193054720(+)$1	246	101	113	26.2586
::::::::::::	chr2:24290370-24290593(-)$1	223	15	27	21.6034
::::::::::gg	chr2:28616090-28616331(+)$1	241	120	132	20.1379
========gggg	chr13:38935137-38935390(+)$1	253	76	88	22.5517
gggg::::::::	chr16:23582311-23582567(+)$1	256	42	54	22.3793
::::hhhhhhhh	chr13:39611400-39611639(-)$1	239	40	52	25.9137
gggqqqqqqqqg	chr22:45582387-45582647(+)$1	260	141	153	20.3965
b22=========	chr8:82570782-82571050(-)$1	268	119	131	21.6896
hhhhhh:::===	chr13:50273450-50273693(-)$1	243	101	113	20.1379
ggggggg66666	chrX:77082288-77082547(-)$1	259	94	106	25.9999
$$$$ffffffoo	chr3:146233287-146233532(-)$1	245	11	23	20.0517
^^^^^^^^^^^^	chr6:34255785-34256035(-)$1	250	44	56	20.3103
&&&dddd[ccc!	chr14:64951340-64951573(-)$1	233	27	39	21.4310
fffff[ffffff	chr6:24719338-24719565(-)$1	227	162	174	26.2586
ooooo=======	chr12:69666012-69666263(+)$1	251	105	117	20.3103
ii]dddd66666	chrX:24095433-24095699(+)$1	266	138	150	25.9137
eeggggggg:::	chr22:28146308-28146533(-)$1	225	49	61	24.0172
hhh>>>>>>>>>	chr11:66407776-66408011(+)$1	235	110	122	28.4137
2eeeee666666	chr6:163992667-163992918(+)$1	251	184	196	28.4137
''''''''iiii	chr18:48609805-48610044(+)$1	239	17	29	21.2586
hhh^^^^^^^^^	chr1:173905608-173905853(-)$1	245	176	188	26.2586
qqqqqhhhhhhh	chr5:154194245-154194509(+)$1	264	132	144	24.3620
:::::ggggggg	chrX:123235392-123235636(+)$1	244	115	127	20.1379
$$eeeeelllee	chr15:66181491-66181758(+)$1	267	152	164	19.7068

#DB
(((((....(((	chr10:93043819-93044112(+)$1	1	25	37	28.4137
.((((((.....	chr4:5502376-5502613(+)$1	1	5	17	24.7068
((((((......	chr5:36099192-36099420(-)$1	1	42	54	19.8793
......((...(	chr6:43129244-43129472(+)$1	1	148	160	25.9999
(...(((((((.	chr2:241082-241310(-)$1	1	93	105	21.8620
(....(((((((	chr18:66341861-66342092(-)$1	1	82	94	19.9655
...........(	chrX:131209003-131209259(+)$1	1	113	125	20.3965
...))))....(	chr9:34088163-34088425(-)$1	1	135	147	19.9655
..((.(((((((	chr8:116423064-116423354(-)$1	1	149	161	20.3103
(((((((....)	chr10:115675247-115675505(+)$1	1	151	163	25.9999
)))))......)	chr12:120899094-120899324(+)$1	1	97	109	20.3965
............	chr2:44999533-44999758(+)$1	1	70	82	26.2586
.......(((((	chr10:18965435-18965718(+)$1	1	134	146	20.4827
(((...((((((	chr7:20452199-20452440(+)$1	1	106	118	25.9999
............	chr1:150937766-150938000(-)$1	1	112	124	19.9655
............	chr7:7284580-7284810(+)$1	1	107	119	28.4137
))).........	chr1:185070807-185071035(+)$1	1	157	169	26.2586
))..........	chr3:32032915-32033140(+)$1	1	101	113	19.9655
............	chr8:86194816-86195049(+)$1	1	120	132	24.4482
((..((((((((	chr14:58838826-58839058(+)$1	1	37	49	21.7758
)).....(((((	chr8:22110304-22110560(+)$1	1	131	143	20.3965
.....)))....	chr3:120048354-120048585(-)$1	1	115	127	24.2758
)))))))...))	chr20:25428845-25429075(+)$1	1	122	134	19.7068
(.((...(((((	chr5:70861636-70861867(+)$1	1	101	113	24.5344
((..........	chr3:172115401-172115757(+)$1	1	189	201	26.2586
((....((((..	chr15:52203310-52203562(+)$1	1	87	99	22.1206
((.((((....)	chr7:137560855-137561086(-)$1	1	113	125	20.0517
((((((......	chr4:140396464-140396774(+)$1	1	184	196	24.5344
))))))..((((	chr12:22840970-22841197(+)$1	1	81	93	19.5344
(.((((((((((	chr2:179968969-179969206(-)$1	1	80	92	20.0517
((((((......	chr2:30865192-30865460(+)$1	1	56	68	25.9137
......((((.(	chr6:134490403-134490626(-)$1	1	0	12	22.3793
.))))).)))).	chr9:91092959-91093235(+)$1	1	147	159	20.3103
)))).....)))	chr3:185635303-185635552(-)$1	1	106	118	19.9655
(((((.......	chr1:193054474-193054720(+)$1	1	101	113	26.2586
............	chr2:24290370-24290593(-)$1	1	15	27	21.6034
..........((	chr2:28616090-28616331(+)$1	1	120	132	20.1379
((((((((((((	chr13:38935137-38935390(+)$1	1	76	88	22.5517
))))........	chr16:23582311-23582567(+)$1	1	42	54	22.3793
....((((((((	chr13:39611400-39611639(-)$1	1	40	52	25.9137
(((........)	chr22:45582387-45582647(+)$1	1	141	153	20.3965
)..)))))))))	chr8:82570782-82571050(-)$1	1	119	131	21.6896
))))))...(((	chr13:50273450-50273693(-)$1	1	101	113	20.1379
))))))).....	chrX:77082288-77082547(-)$1	1	94	106	25.9999
....((((((..	chr3:146233287-146233532(-)$1	1	11	23	20.0517
............	chr6:34255785-34256035(-)$1	1	44	56	20.3103
...((((.(((.	chr14:64951340-64951573(-)$1	1	27	39	21.4310
(((((.((((((	chr6:24719338-24719565(-)$1	1	162	174	26.2586
.....)))))))	chr12:69666012-69666263(+)$1	1	105	117	20.3103
)).)))).....	chrX:24095433-24095699(+)$1	1	138	150	25.9137
)))))))))...	chr22:28146308-28146533(-)$1	1	49	61	24.0172
))).........	chr11:66407776-66408011(+)$1	1	110	122	28.4137
.)))))......	chr6:163992667-163992918(+)$1	1	184	196	28.4137
........((((	chr18:48609805-48610044(+)$1	1	17	29	21.2586
(((.........	chr1:173905608-173905853(-)$1	1	176	188	26.2586
.....)))))))	chr5:154194245-154194509(+)$1	1	132	144	24.3620
.....(((((((	chrX:123235392-123235636(+)$1	1	115	127	20.1379
..(((((...))	chr15:66181491-66181758(+)$1	1	152	164	19.7068

#PSSM
U : 0.53	u : 0.29	A : 0.05	g : 0.05	a : 0.03	C : 0.03	
U : 0.48	u : 0.36	G : 0.06	C : 0.05	A : 0.03	
U : 0.56	u : 0.29	a : 0.06	G : 0.03	A : 0.01	C : 0.01	
U : 0.58	u : 0.34	c : 0.01	C : 0.01	G : 0.01	A : 0.01	
U : 0.58	u : 0.31	a : 0.03	A : 0.03	g : 0.01	C : 0.01	
U : 0.58	u : 0.34	G : 0.03	A : 0.01	a : 0.01	
A : 0.37	a : 0.22	U : 0.12	C : 0.08	g : 0.06	G : 0.05	u : 0.05	c : 0.01	
U : 0.56	u : 0.31	A : 0.05	a : 0.03	g : 0.01	C : 0.01	
U : 0.58	u : 0.36	A : 0.03	G : 0.01	
U : 0.55	u : 0.34	G : 0.06	A : 0.01	c : 0.01	
U : 0.62	u : 0.34	C : 0.01	a : 0.01	
U : 0.58	u : 0.31	a : 0.05	C : 0.03	A : 0.01	

#score	1325.4137931034475
#seq	58
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m2_run2.nuc.txt

#NT
UUAGUUUU	chr21:43409709-43409926(-)$1	217	165	173	15.0344
UUCUUUUU	chr7:139107381-139107609(+)$1	228	69	77	15.9827
UUAUUUUU	chr6:57033903-57034125(+)$1	222	106	114	19.6896
UUAUUUUC	chr1:178889094-178889314(+)$1	220	79	87	15.8103
UUACUUUU	chr1:111495256-111495475(-)$1	219	202	210	15.1206
UUAUUUAU	chr10:18964599-18964817(+)$1	218	179	187	15.4655
UUAUGUUU	chr5:112351508-112351726(+)$1	218	168	176	15.6379
UGAUUUUU	chrX:123164851-123165072(+)$1	221	196	204	15.4655
UUAUGUUU	chr12:53807151-53807373(+)$1	222	156	164	15.6379
UUAUUUUG	chr5:64886515-64886735(-)$1	220	140	148	15.7241
UUAUGUUU	chr21:34950431-34950647(+)$1	216	75	83	15.6379
auauuuuu	chr6:64412343-64412567(+)$1	224	26	34	15.5517
uuguuuuU	chr8:12942305-12942527(-)$1	222	61	69	16.1551
uuguuuuu	chr19:52517935-52518152(-)$1	217	2	10	16.1551
UUAUUCUU	chr11:18629819-18630041(-)$1	222	126	134	15.0344
cuauuuuu	chr19:57911630-57911851(+)$1	221	163	171	15.3793
UGAUUUUU	chr4:57799144-57799368(+)$1	224	65	73	15.4655
UCAUUUUU	chr8:117859495-117859719(-)$1	224	111	119	15.4655
UUAUUUUU	chr3:101487850-101488074(+)$1	224	40	48	19.6896
UUACUUUU	chr1:54233222-54233441(-)$1	219	123	131	15.1206
UUCUUUUU	chr16:20808165-20808385(-)$1	220	126	134	15.9827
UUAUUUUG	chr8:38128436-38128657(-)$1	221	65	73	15.7241
UUAUUUAU	chr12:24968783-24969000(-)$1	217	200	208	15.4655
UUAUUUUU	chr1:162495607-162495833(+)$1	226	85	93	19.6896
UUAUUUUA	chr10:22619443-22619674(+)$1	231	169	177	15.9827
UUAUUUUC	chr1:167386107-167386333(+)$1	226	175	183	15.8103
UUAUUUAU	chr8:67546222-67546440(-)$1	218	183	191	15.4655
AUAUUUUU	chr1:24087604-24087822(+)$1	218	79	87	15.5517
UUAUUUUA	chr8:27970558-27970780(+)$1	222	63	71	15.9827
UUAUUCUU	chr17:57737677-57737903(+)$1	226	56	64	15.0344
UCAUUUUU	chr1:231468575-231468793(-)$1	218	91	99	15.4655
AUAUUUUU	chr17:28794865-28795087(+)$1	222	82	90	15.5517
UUGUUUUU	chr4:52894875-52895094(-)$1	219	8	16	16.1551
UUCUUUUU	chr13:73333808-73334032(-)$1	224	131	139	15.9827
AUAUUUUU	chr10:103922626-103922843(+)$1	217	86	94	15.5517
UCAUUUUU	chr7:44917931-44918153(-)$1	222	107	115	15.4655
UUAUUUUU	chr10:72184132-72184343(+)$1	211	114	122	19.6896
UUUUUUUU	chr17:1326625-1326847(-)$1	222	79	87	16.0689
UUUUUUUU	chr12:27955354-27955579(+)$1	225	71	79	16.0689
UUAUGUUU	chr1:198291350-198291570(+)$1	220	0	8	15.6379
UUAUUUAU	chr7:135613781-135613999(-)$1	218	3	11	15.4655
UUAUUUUC	chr16:15154205-15154424(-)$1	219	37	45	15.8103
UUAUUUUU	chr21:34930083-34930313(+)$1	230	121	129	19.6896
UUAUUUUU	chr2:20450687-20450906(-)$1	219	5	13	19.6896
UUAUGUUU	chr7:44869330-44869547(-)$1	217	56	64	15.6379
UGAUUUUU	chr14:60760420-60760640(+)$1	220	6	14	15.4655
UUAUUUUU	chrX:73809130-73809357(-)$1	227	54	62	19.6896
uuuuuuuu	chr22:45582923-45583142(+)$1	219	124	132	16.0689
CUAUUUUU	chr3:182659766-182659990(-)$1	224	179	187	15.3793
UUAUUUUA	chr6:109688785-109689003(-)$1	218	31	39	15.9827
uuauuuua	chr11:13751908-13752132(+)$1	224	28	36	15.9827
UUGUUUUU	chr11:117038676-117038895(+)$1	219	183	191	16.1551
uuuuuuuu	chrX:134022075-134022299(-)$1	224	44	52	16.0689
UUGUUUUU	chr4:125586371-125586596(-)$1	225	14	22	16.1551
UUAUUUUA	chr15:45901256-45901477(+)$1	221	23	31	15.9827
UUAUUUGU	chr17:58525018-58525243(-)$1	225	5	13	15.2068
UUAUUUUU	chr18:9561942-9562166(-)$1	224	76	84	19.6896

#otherMatches

#Struct PSSM
eeee::::	chr3:101486069-101486291(+)$1	222	128	136	15.2931
==%%%%%%	chr21:43409709-43409926(-)$1	217	165	173	15.0344
::::::::	chr7:139107381-139107609(+)$1	228	69	77	15.9827
]ffffff:	chr6:57033903-57034125(+)$1	222	106	114	19.6896
::::::::	chr1:178889094-178889314(+)$1	220	79	87	15.8103
>>>>>>>>	chr1:111495256-111495475(-)$1	219	202	210	15.1206
~GGGGGGG	chr10:18964599-18964817(+)$1	218	179	187	15.4655
]ddddddd	chr5:112351508-112351726(+)$1	218	168	176	15.6379
EEEEE}CC	chrX:123164851-123165072(+)$1	221	196	204	15.4655
:dddd[dd	chr12:53807151-53807373(+)$1	222	156	164	15.6379
hhhhhhhh	chr5:64886515-64886735(-)$1	220	140	148	15.7241
JJJJJJJJ	chr21:34950431-34950647(+)$1	216	75	83	15.6379
rrrrrggg	chr6:64412343-64412567(+)$1	224	26	34	15.5517
e[ffffff	chr8:12942305-12942527(-)$1	222	61	69	16.1551
CCC{EEEE	chr19:52517935-52518152(-)$1	217	2	10	16.1551
::::::::	chr11:18629819-18630041(-)$1	222	126	134	15.0344
::::::::	chr19:57911630-57911851(+)$1	221	163	171	15.3793
"cccoooo	chr4:57799144-57799368(+)$1	224	65	73	15.4655
hhhh&&&&	chr8:117859495-117859719(-)$1	224	111	119	15.4655
d:::::dd	chr3:101487850-101488074(+)$1	224	40	48	19.6896
i!!eeeee	chr1:54233222-54233441(-)$1	219	123	131	15.1206
dd&&&&&&	chr16:20808165-20808385(-)$1	220	126	134	15.9827
(((fffff	chr8:38128436-38128657(-)$1	221	65	73	15.7241
F:::::::	chr12:24968783-24969000(-)$1	217	200	208	15.4655
g+++++++	chr1:162495607-162495833(+)$1	226	85	93	19.6896
uuuuuuuu	chr10:22619443-22619674(+)$1	231	169	177	15.9827
hhhnnnnn	chr1:167386107-167386333(+)$1	226	175	183	15.8103
33dddd]b	chr8:67546222-67546440(-)$1	218	183	191	15.4655
::::::::	chr1:24087604-24087822(+)$1	218	79	87	15.5517
========	chr8:27970558-27970780(+)$1	222	63	71	15.9827
dddnnnnn	chr17:57737677-57737903(+)$1	226	56	64	15.0344
qqqqqqqq	chr1:231468575-231468793(-)$1	218	91	99	15.4655
rreeeee]	chr17:28794865-28795087(+)$1	222	82	90	15.5517
mmmmgggg	chr4:52894875-52895094(-)$1	219	8	16	16.1551
}CCC::hh	chr13:73333808-73334032(-)$1	224	131	139	15.9827
::::::::	chr10:103922626-103922843(+)$1	217	86	94	15.5517
:eeeeeqq	chr7:44917931-44918153(-)$1	222	107	115	15.4655
========	chr10:72184132-72184343(+)$1	211	114	122	19.6896
ssssssss	chr17:1326625-1326847(-)$1	222	79	87	16.0689
ssssssss	chr12:27955354-27955579(+)$1	225	71	79	16.0689
::::::::	chr1:198291350-198291570(+)$1	220	0	8	15.6379
IIIIIILL	chr7:135613781-135613999(-)$1	218	3	11	15.4655
::::::::	chr16:15154205-15154424(-)$1	219	37	45	15.8103
qqqqqqqc	chr21:34930083-34930313(+)$1	230	121	129	19.6896
GGGGGG{B	chr2:20450687-20450906(-)$1	219	5	13	19.6896
iiiiii22	chr7:44869330-44869547(-)$1	217	56	64	15.6379
FFFFFFFF	chr14:60760420-60760640(+)$1	220	6	14	15.4655
++++++++	chrX:73809130-73809357(-)$1	227	54	62	19.6896
&&&&&&gg	chr22:45582923-45583142(+)$1	219	124	132	16.0689
@@@@@@@@	chr3:182659766-182659990(-)$1	224	179	187	15.3793
DDKKEEEE	chr6:109688785-109689003(-)$1	218	31	39	15.9827
oooohhhh	chr11:13751908-13752132(+)$1	224	28	36	15.9827
ddd55555	chr11:117038676-117038895(+)$1	219	183	191	16.1551
iiiiii!!	chrX:134022075-134022299(-)$1	224	44	52	16.0689
:FFFFFFK	chr4:125586371-125586596(-)$1	225	14	22	16.1551
gggggg::	chr15:45901256-45901477(+)$1	221	23	31	15.9827
::::::::	chr17:58525018-58525243(-)$1	225	5	13	15.2068
EE{IIIII	chr18:9561942-9562166(-)$1	224	76	84	19.6896

#DB
))))....	chr3:101486069-101486291(+)$1	1	128	136	15.2931
((......	chr21:43409709-43409926(-)$1	1	165	173	15.0344
........	chr7:139107381-139107609(+)$1	1	69	77	15.9827
.)))))).	chr6:57033903-57034125(+)$1	1	106	114	19.6896
........	chr1:178889094-178889314(+)$1	1	79	87	15.8103
........	chr1:111495256-111495475(-)$1	1	202	210	15.1206
.)))))))	chr10:18964599-18964817(+)$1	1	179	187	15.4655
.)))))))	chr5:112351508-112351726(+)$1	1	168	176	15.6379
))))).))	chrX:123164851-123165072(+)$1	1	196	204	15.4655
.((((.((	chr12:53807151-53807373(+)$1	1	156	164	15.6379
))))))))	chr5:64886515-64886735(-)$1	1	140	148	15.7241
((((((((	chr21:34950431-34950647(+)$1	1	75	83	15.6379
.....)))	chr6:64412343-64412567(+)$1	1	26	34	15.5517
(.((((((	chr8:12942305-12942527(-)$1	1	61	69	16.1551
(((.((((	chr19:52517935-52518152(-)$1	1	2	10	16.1551
........	chr11:18629819-18630041(-)$1	1	126	134	15.0344
........	chr19:57911630-57911851(+)$1	1	163	171	15.3793
.(((....	chr4:57799144-57799368(+)$1	1	65	73	15.4655
((((....	chr8:117859495-117859719(-)$1	1	111	119	15.4655
).....((	chr3:101487850-101488074(+)$1	1	40	48	19.6896
(..(((((	chr1:54233222-54233441(-)$1	1	123	131	15.1206
((......	chr16:20808165-20808385(-)$1	1	126	134	15.9827
...(((((	chr8:38128436-38128657(-)$1	1	65	73	15.7241
).......	chr12:24968783-24969000(-)$1	1	200	208	15.4655
(.......	chr1:162495607-162495833(+)$1	1	85	93	19.6896
........	chr10:22619443-22619674(+)$1	1	169	177	15.9827
(((.....	chr1:167386107-167386333(+)$1	1	175	183	15.8103
..)))).)	chr8:67546222-67546440(-)$1	1	183	191	15.4655
........	chr1:24087604-24087822(+)$1	1	79	87	15.5517
))))))))	chr8:27970558-27970780(+)$1	1	63	71	15.9827
(((.....	chr17:57737677-57737903(+)$1	1	56	64	15.0344
........	chr1:231468575-231468793(-)$1	1	91	99	15.4655
..))))).	chr17:28794865-28795087(+)$1	1	82	90	15.5517
....))))	chr4:52894875-52895094(-)$1	1	8	16	16.1551
.)))..((	chr13:73333808-73334032(-)$1	1	131	139	15.9827
........	chr10:103922626-103922843(+)$1	1	86	94	15.5517
.(((((..	chr7:44917931-44918153(-)$1	1	107	115	15.4655
))))))))	chr10:72184132-72184343(+)$1	1	114	122	19.6896
........	chr17:1326625-1326847(-)$1	1	79	87	16.0689
........	chr12:27955354-27955579(+)$1	1	71	79	16.0689
........	chr1:198291350-198291570(+)$1	1	0	8	15.6379
((((((..	chr7:135613781-135613999(-)$1	1	3	11	15.4655
........	chr16:15154205-15154424(-)$1	1	37	45	15.8103
.......)	chr21:34930083-34930313(+)$1	1	121	129	19.6896
((((((.(	chr2:20450687-20450906(-)$1	1	5	13	19.6896
))))))..	chr7:44869330-44869547(-)$1	1	56	64	15.6379
((((((((	chr14:60760420-60760640(+)$1	1	6	14	15.4655
........	chrX:73809130-73809357(-)$1	1	54	62	19.6896
......((	chr22:45582923-45583142(+)$1	1	124	132	16.0689
........	chr3:182659766-182659990(-)$1	1	179	187	15.3793
((..((((	chr6:109688785-109689003(-)$1	1	31	39	15.9827
....))))	chr11:13751908-13752132(+)$1	1	28	36	15.9827
))).....	chr11:117038676-117038895(+)$1	1	183	191	16.1551
((((((..	chrX:134022075-134022299(-)$1	1	44	52	16.0689
.((((((.	chr4:125586371-125586596(-)$1	1	14	22	16.1551
))))))..	chr15:45901256-45901477(+)$1	1	23	31	15.9827
........	chr17:58525018-58525243(-)$1	1	5	13	15.2068
((.(((((	chr18:9561942-9562166(-)$1	1	76	84	19.6896

#PSSM
U : 0.81	u : 0.08	A : 0.05	a : 0.01	c : 0.01	C : 0.01	
U : 0.77	u : 0.12	G : 0.05	C : 0.05	
A : 0.74	C : 0.05	a : 0.05	G : 0.05	g : 0.03	U : 0.03	u : 0.03	
U : 0.82	u : 0.12	C : 0.03	G : 0.01	
U : 0.77	u : 0.12	G : 0.08	C : 0.01	
U : 0.84	u : 0.12	C : 0.03	
U : 0.79	u : 0.12	A : 0.06	G : 0.01	
U : 0.74	u : 0.08	A : 0.06	C : 0.05	G : 0.03	a : 0.01	

#score	940.9655172413798
#seq	58
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_CDS_m2_run1.nuc.txt

#NT
UUU	chr17:35550228-35550452(-)$1	224	23	26	8.9999
UUU	chr12:67701115-67701348(+)$1	233	14	17	8.9999
UUU	chr3:56707579-56707805(-)$1	226	1	4	8.9999
UUU	chr17:42750742-42750966(-)$1	224	45	48	8.9999
UUU	chr5:37060917-37061142(+)$1	225	2	5	8.9999
UUU	chr15:49301328-49301555(-)$1	227	135	138	8.9999
UUU	chrM:11754-12017(+)$1	263	73	76	8.9999
UUU	chr10:51027342-51027563(-)$1	221	10	13	8.9999
UUU	chr6:87942989-87943216(+)$1	227	43	46	8.9999
UUU	chr13:28197274-28197507(+)$1	233	50	53	8.9999
UUU	chr6:64422084-64422321(+)$1	237	48	51	8.9999
UUU	chr3:113373859-113374088(-)$1	229	0	3	8.9999
UUU	chr10:18964014-18964253(+)$1	239	27	30	8.9999
UUU	chr17:60088110-60088341(-)$1	231	140	143	8.9999
UUU	chr10:70719634-70719855(+)$1	221	102	105	8.9999
UUU	chr1:193045036-193045261(+)$1	225	105	108	8.9999
UUU	chr1:243809098-243809320(-)$1	222	162	165	8.9999
UUU	chr6:36437879-36438119(+)$1	240	66	69	8.9999
UUU	chr10:30630305-30630530(-)$1	225	36	39	8.9999
UUU	chr1:245023646-245023867(-)$1	221	23	26	8.9999
UUU	chr13:42874383-42874617(+)$1	234	79	82	8.9999
UUU	chr10:32560556-32560804(-)$1	248	38	41	8.9999
UUU	chr12:67699372-67699593(+)$1	221	4	7	8.9999
UUU	chr19:21719640-21719867(+)$1	227	10	13	8.9999
UUU	chr19:41257229-41257468(+)$1	239	18	21	8.9999
UUU	chrM:11157-11384(-)$1	227	7	10	8.9999
UUU	chr22:39267388-39267612(-)$1	224	31	34	8.9999
UUU	chr5:145648992-145649230(+)$1	238	58	61	8.9999
UUU	chr2:47606023-47606248(+)$1	225	9	12	8.9999
UUU	chr6:17649313-17649557(-)$1	244	20	23	8.9999
UUU	chr21:34929413-34929647(+)$1	234	10	13	8.9999
UUU	chr1:204378960-204379205(-)$1	245	33	36	8.9999
UUU	chr15:35274902-35275138(-)$1	236	7	10	8.9999
uuu	chr3:170107914-170108138(+)$1	224	8	11	8.9999
UUU	chr17:65889501-65889733(+)$1	232	12	15	8.9999
UUU	chr1:111490745-111490965(-)$1	220	80	83	8.9999
UUU	chr17:63049588-63049808(-)$1	220	51	54	8.9999
UUU	chr6:33669023-33669252(-)$1	229	20	23	8.9999
UUU	chr5:10405642-10405870(+)$1	228	9	12	8.9999
UUU	chr2:73761918-73762149(+)$1	231	17	20	8.9999
UUU	chrM:10371-10601(+)$1	230	44	47	8.9999
UUU	chr13:73354894-73355115(-)$1	221	102	105	8.9999
UUU	chr10:116606246-116606469(+)$1	223	37	40	8.9999
UUU	chr1:70703012-70703243(+)$1	231	0	3	8.9999
UUU	chr15:50867011-50867241(-)$1	230	10	13	8.9999
UUU	chr1:91382273-91382494(-)$1	221	107	110	8.9999
UUU	chr13:23906006-23906223(-)$1	217	77	80	8.9999
UUU	chr2:26461702-26461923(-)$1	221	1	4	8.9999
UUU	chr1:115266476-115266708(-)$1	232	11	14	8.9999
UUU	chr1:32622922-32623146(+)$1	224	11	14	8.9999
UUU	chr7:44161434-44161679(-)$1	245	30	33	8.9999
UUU	chr2:73467471-73467702(+)$1	231	52	55	8.9999
UUU	chr1:214830364-214830583(+)$1	219	128	131	8.9999
UUU	chr10:5791258-5791505(+)$1	247	47	50	8.9999
UUU	chr6:149900989-149901226(+)$1	237	11	14	8.9999
UUU	chr12:67698856-67699082(+)$1	226	8	11	8.9999
UUU	chr1:101431350-101431574(+)$1	224	0	3	8.9999
UUU	chr6:100965792-100966021(-)$1	229	148	151	8.9999
UUU	chr8:48883895-48884128(+)$1	233	121	124	8.9999
UUU	chr3:56649877-56650098(+)$1	221	19	22	8.9999
UUU	chr5:54456014-54456257(+)$1	243	60	63	8.9999
UUU	chr12:994626-994859(+)$1	233	25	28	8.9999
UUU	chr12:67700067-67700287(+)$1	220	60	63	8.9999
UUU	chr20:35852186-35852420(+)$1	234	23	26	8.9999
UUU	chr10:70101447-70101681(+)$1	234	0	3	8.9999
UUU	chr1:243675604-243675824(-)$1	220	7	10	8.9999
UUU	chr5:71490308-71490534(+)$1	226	68	71	8.9999
UUU	chr8:48875479-48875699(+)$1	220	11	14	8.9999
UUU	chr7:44874033-44874256(-)$1	223	14	17	8.9999
UUU	chr10:96099949-96100178(-)$1	229	11	14	8.9999
UUU	chr14:45644376-45644608(+)$1	232	5	8	8.9999
UUU	chr14:45645111-45645331(+)$1	220	42	45	8.9999
UUU	chr11:10820748-10820982(-)$1	234	0	3	8.9999
UUU	chr6:56472142-56472371(-)$1	229	122	125	8.9999
UUU	chr11:34111977-34112197(+)$1	220	3	6	8.9999
UUU	chr4:166215492-166215712(+)$1	220	0	3	8.9999
UUU	chr11:93460606-93460841(+)$1	235	76	79	8.9999
UUU	chr9:131721025-131721253(+)$1	228	5	8	8.9999
UUU	chr17:1582281-1582510(-)$1	229	13	16	8.9999
UUU	chr1:155450543-155450778(-)$1	235	82	85	8.9999
UUU	chr16:28187119-28187337(-)$1	218	26	29	8.9999
UUU	chr19:21720053-21720279(+)$1	226	15	18	8.9999
uuu	chr6:64412343-64412567(+)$1	224	15	18	8.9999
UUU	chr2:30862921-30863145(+)$1	224	39	42	8.9999
UUU	chr3:12626528-12626753(-)$1	225	42	45	8.9999
UUU	chr16:27549025-27549248(-)$1	223	35	38	8.9999
UUU	chr17:38554985-38555211(-)$1	226	4	7	8.9999
UUU	chr2:242179367-242179597(-)$1	230	51	54	8.9999
UUU	chr14:50249015-50249246(-)$1	231	12	15	8.9999
UUU	chr3:129150285-129150508(-)$1	223	6	9	8.9999
UUU	chr10:28872280-28872504(+)$1	224	10	13	8.9999
UUU	chr3:130424435-130424659(-)$1	224	1	4	8.9999
UUU	chr7:94898446-94898678(+)$1	232	1	4	8.9999
UUU	chr10:88939826-88940051(+)$1	225	29	32	8.9999
UUU	chr9:125613561-125613784(-)$1	223	59	62	8.9999
UUU	chr7:98582483-98582711(+)$1	228	16	19	8.9999
UUU	chr13:113963965-113964189(+)$1	224	1	4	8.9999
UUU	chr2:24261383-24261614(-)$1	231	73	76	8.9999

#otherMatches

#Struct PSSM
d]d	chr14:91947843-91948079(-)$1	236	85	88	8.9999
b::	chr17:35550228-35550452(-)$1	224	23	26	8.9999
hhh	chr12:67701115-67701348(+)$1	233	14	17	8.9999
:==	chr3:56707579-56707805(-)$1	226	1	4	8.9999
fff	chr17:42750742-42750966(-)$1	224	45	48	8.9999
JJJ	chr5:37060917-37061142(+)$1	225	2	5	8.9999
ggg	chr15:49301328-49301555(-)$1	227	135	138	8.9999
2bb	chrM:11754-12017(+)$1	263	73	76	8.9999
fff	chr10:51027342-51027563(-)$1	221	10	13	8.9999
qqq	chr6:87942989-87943216(+)$1	227	43	46	8.9999
44d	chr13:28197274-28197507(+)$1	233	50	53	8.9999
hhh	chr6:64422084-64422321(+)$1	237	48	51	8.9999
:::	chr3:113373859-113374088(-)$1	229	0	3	8.9999
!!b	chr10:18964014-18964253(+)$1	239	27	30	8.9999
:::	chr17:60088110-60088341(-)$1	231	140	143	8.9999
fff	chr10:70719634-70719855(+)$1	221	102	105	8.9999
ggg	chr1:193045036-193045261(+)$1	225	105	108	8.9999
pdd	chr1:243809098-243809320(-)$1	222	162	165	8.9999
d]f	chr6:36437879-36438119(+)$1	240	66	69	8.9999
coo	chr10:30630305-30630530(-)$1	225	36	39	8.9999
HHH	chr1:245023646-245023867(-)$1	221	23	26	8.9999
ddd	chr13:42874383-42874617(+)$1	234	79	82	8.9999
TTT	chr10:32560556-32560804(-)$1	248	38	41	8.9999
{DD	chr12:67699372-67699593(+)$1	221	4	7	8.9999
:::	chr19:21719640-21719867(+)$1	227	10	13	8.9999
"""	chr19:41257229-41257468(+)$1	239	18	21	8.9999
mmd	chrM:11157-11384(-)$1	227	7	10	8.9999
iii	chr22:39267388-39267612(-)$1	224	31	34	8.9999
EEE	chr5:145648992-145649230(+)$1	238	58	61	8.9999
E{D	chr2:47606023-47606248(+)$1	225	9	12	8.9999
LLL	chr6:17649313-17649557(-)$1	244	20	23	8.9999
:::	chr21:34929413-34929647(+)$1	234	10	13	8.9999
[==	chr1:204378960-204379205(-)$1	245	33	36	8.9999
mmm	chr15:35274902-35275138(-)$1	236	7	10	8.9999
GGG	chr3:170107914-170108138(+)$1	224	8	11	8.9999
eee	chr17:65889501-65889733(+)$1	232	12	15	8.9999
fff	chr1:111490745-111490965(-)$1	220	80	83	8.9999
fff	chr17:63049588-63049808(-)$1	220	51	54	8.9999
eJJ	chr6:33669023-33669252(-)$1	229	20	23	8.9999
HHH	chr5:10405642-10405870(+)$1	228	9	12	8.9999
HHH	chr2:73761918-73762149(+)$1	231	17	20	8.9999
hhh	chrM:10371-10601(+)$1	230	44	47	8.9999
FFF	chr13:73354894-73355115(-)$1	221	102	105	8.9999
d55	chr10:116606246-116606469(+)$1	223	37	40	8.9999
:::	chr1:70703012-70703243(+)$1	231	0	3	8.9999
EEE	chr15:50867011-50867241(-)$1	230	10	13	8.9999
oee	chr1:91382273-91382494(-)$1	221	107	110	8.9999
ggg	chr13:23906006-23906223(-)$1	217	77	80	8.9999
fff	chr2:26461702-26461923(-)$1	221	1	4	8.9999
hhh	chr1:115266476-115266708(-)$1	232	11	14	8.9999
rrr	chr1:32622922-32623146(+)$1	224	11	14	8.9999
hhh	chr7:44161434-44161679(-)$1	245	30	33	8.9999
fff	chr2:73467471-73467702(+)$1	231	52	55	8.9999
fff	chr1:214830364-214830583(+)$1	219	128	131	8.9999
ooo	chr10:5791258-5791505(+)$1	247	47	50	8.9999
OOO	chr6:149900989-149901226(+)$1	237	11	14	8.9999
EEL	chr12:67698856-67699082(+)$1	226	8	11	8.9999
:::	chr1:101431350-101431574(+)$1	224	0	3	8.9999
eee	chr6:100965792-100966021(-)$1	229	148	151	8.9999
ggg	chr8:48883895-48884128(+)$1	233	121	124	8.9999
:::	chr3:56649877-56650098(+)$1	221	19	22	8.9999
eee	chr5:54456014-54456257(+)$1	243	60	63	8.9999
%%%	chr12:994626-994859(+)$1	233	25	28	8.9999
ddd	chr12:67700067-67700287(+)$1	220	60	63	8.9999
&&&	chr20:35852186-35852420(+)$1	234	23	26	8.9999
:::	chr10:70101447-70101681(+)$1	234	0	3	8.9999
:::	chr1:243675604-243675824(-)$1	220	7	10	8.9999
:::	chr5:71490308-71490534(+)$1	226	68	71	8.9999
C::	chr8:48875479-48875699(+)$1	220	11	14	8.9999
^^^	chr7:44874033-44874256(-)$1	223	14	17	8.9999
!cc	chr10:96099949-96100178(-)$1	229	11	14	8.9999
iii	chr14:45644376-45644608(+)$1	232	5	8	8.9999
[cc	chr14:45645111-45645331(+)$1	220	42	45	8.9999
:::	chr11:10820748-10820982(-)$1	234	0	3	8.9999
ccc	chr6:56472142-56472371(-)$1	229	122	125	8.9999
:::	chr11:34111977-34112197(+)$1	220	3	6	8.9999
:::	chr4:166215492-166215712(+)$1	220	0	3	8.9999
iii	chr11:93460606-93460841(+)$1	235	76	79	8.9999
"""	chr9:131721025-131721253(+)$1	228	5	8	8.9999
{CC	chr17:1582281-1582510(-)$1	229	13	16	8.9999
ee[	chr1:155450543-155450778(-)$1	235	82	85	8.9999
eee	chr16:28187119-28187337(-)$1	218	26	29	8.9999
hhh	chr19:21720053-21720279(+)$1	226	15	18	8.9999
ggg	chr6:64412343-64412567(+)$1	224	15	18	8.9999
:dd	chr2:30862921-30863145(+)$1	224	39	42	8.9999
ggg	chr3:12626528-12626753(-)$1	225	42	45	8.9999
ddd	chr16:27549025-27549248(-)$1	223	35	38	8.9999
ddo	chr17:38554985-38555211(-)$1	226	4	7	8.9999
fff	chr2:242179367-242179597(-)$1	230	51	54	8.9999
ff!	chr14:50249015-50249246(-)$1	231	12	15	8.9999
ggg	chr3:129150285-129150508(-)$1	223	6	9	8.9999
nnn	chr10:28872280-28872504(+)$1	224	10	13	8.9999
:::	chr3:130424435-130424659(-)$1	224	1	4	8.9999
:::	chr7:94898446-94898678(+)$1	232	1	4	8.9999
wwe	chr10:88939826-88940051(+)$1	225	29	32	8.9999
hhh	chr9:125613561-125613784(-)$1	223	59	62	8.9999
'''	chr7:98582483-98582711(+)$1	228	16	19	8.9999
EEE	chr13:113963965-113964189(+)$1	224	1	4	8.9999
gg]	chr2:24261383-24261614(-)$1	231	73	76	8.9999

#DB
).)	chr14:91947843-91948079(-)$1	1	85	88	8.9999
)..	chr17:35550228-35550452(-)$1	1	23	26	8.9999
(((	chr12:67701115-67701348(+)$1	1	14	17	8.9999
.((	chr3:56707579-56707805(-)$1	1	1	4	8.9999
)))	chr17:42750742-42750966(-)$1	1	45	48	8.9999
(((	chr5:37060917-37061142(+)$1	1	2	5	8.9999
(((	chr15:49301328-49301555(-)$1	1	135	138	8.9999
.))	chrM:11754-12017(+)$1	1	73	76	8.9999
(((	chr10:51027342-51027563(-)$1	1	10	13	8.9999
...	chr6:87942989-87943216(+)$1	1	43	46	8.9999
..)	chr13:28197274-28197507(+)$1	1	50	53	8.9999
)))	chr6:64422084-64422321(+)$1	1	48	51	8.9999
...	chr3:113373859-113374088(-)$1	1	0	3	8.9999
..(	chr10:18964014-18964253(+)$1	1	27	30	8.9999
...	chr17:60088110-60088341(-)$1	1	140	143	8.9999
(((	chr10:70719634-70719855(+)$1	1	102	105	8.9999
)))	chr1:193045036-193045261(+)$1	1	105	108	8.9999
.))	chr1:243809098-243809320(-)$1	1	162	165	8.9999
).)	chr6:36437879-36438119(+)$1	1	66	69	8.9999
(..	chr10:30630305-30630530(-)$1	1	36	39	8.9999
(((	chr1:245023646-245023867(-)$1	1	23	26	8.9999
(((	chr13:42874383-42874617(+)$1	1	79	82	8.9999
...	chr10:32560556-32560804(-)$1	1	38	41	8.9999
.((	chr12:67699372-67699593(+)$1	1	4	7	8.9999
...	chr19:21719640-21719867(+)$1	1	10	13	8.9999
...	chr19:41257229-41257468(+)$1	1	18	21	8.9999
..)	chrM:11157-11384(-)$1	1	7	10	8.9999
(((	chr22:39267388-39267612(-)$1	1	31	34	8.9999
(((	chr5:145648992-145649230(+)$1	1	58	61	8.9999
(.(	chr2:47606023-47606248(+)$1	1	9	12	8.9999
...	chr6:17649313-17649557(-)$1	1	20	23	8.9999
...	chr21:34929413-34929647(+)$1	1	10	13	8.9999
.((	chr1:204378960-204379205(-)$1	1	33	36	8.9999
...	chr15:35274902-35275138(-)$1	1	7	10	8.9999
(((	chr3:170107914-170108138(+)$1	1	8	11	8.9999
(((	chr17:65889501-65889733(+)$1	1	12	15	8.9999
(((	chr1:111490745-111490965(-)$1	1	80	83	8.9999
)))	chr17:63049588-63049808(-)$1	1	51	54	8.9999
)((	chr6:33669023-33669252(-)$1	1	20	23	8.9999
(((	chr5:10405642-10405870(+)$1	1	9	12	8.9999
(((	chr2:73761918-73762149(+)$1	1	17	20	8.9999
)))	chrM:10371-10601(+)$1	1	44	47	8.9999
)))	chr13:73354894-73355115(-)$1	1	102	105	8.9999
)..	chr10:116606246-116606469(+)$1	1	37	40	8.9999
...	chr1:70703012-70703243(+)$1	1	0	3	8.9999
(((	chr15:50867011-50867241(-)$1	1	10	13	8.9999
.))	chr1:91382273-91382494(-)$1	1	107	110	8.9999
)))	chr13:23906006-23906223(-)$1	1	77	80	8.9999
(((	chr2:26461702-26461923(-)$1	1	1	4	8.9999
(((	chr1:115266476-115266708(-)$1	1	11	14	8.9999
...	chr1:32622922-32623146(+)$1	1	11	14	8.9999
(((	chr7:44161434-44161679(-)$1	1	30	33	8.9999
)))	chr2:73467471-73467702(+)$1	1	52	55	8.9999
)))	chr1:214830364-214830583(+)$1	1	128	131	8.9999
...	chr10:5791258-5791505(+)$1	1	47	50	8.9999
...	chr6:149900989-149901226(+)$1	1	11	14	8.9999
((.	chr12:67698856-67699082(+)$1	1	8	11	8.9999
...	chr1:101431350-101431574(+)$1	1	0	3	8.9999
)))	chr6:100965792-100966021(-)$1	1	148	151	8.9999
(((	chr8:48883895-48884128(+)$1	1	121	124	8.9999
...	chr3:56649877-56650098(+)$1	1	19	22	8.9999
)))	chr5:54456014-54456257(+)$1	1	60	63	8.9999
...	chr12:994626-994859(+)$1	1	25	28	8.9999
(((	chr12:67700067-67700287(+)$1	1	60	63	8.9999
...	chr20:35852186-35852420(+)$1	1	23	26	8.9999
...	chr10:70101447-70101681(+)$1	1	0	3	8.9999
...	chr1:243675604-243675824(-)$1	1	7	10	8.9999
...	chr5:71490308-71490534(+)$1	1	68	71	8.9999
(..	chr8:48875479-48875699(+)$1	1	11	14	8.9999
...	chr7:44874033-44874256(-)$1	1	14	17	8.9999
.((	chr10:96099949-96100178(-)$1	1	11	14	8.9999
(((	chr14:45644376-45644608(+)$1	1	5	8	8.9999
.((	chr14:45645111-45645331(+)$1	1	42	45	8.9999
...	chr11:10820748-10820982(-)$1	1	0	3	8.9999
(((	chr6:56472142-56472371(-)$1	1	122	125	8.9999
...	chr11:34111977-34112197(+)$1	1	3	6	8.9999
...	chr4:166215492-166215712(+)$1	1	0	3	8.9999
)))	chr11:93460606-93460841(+)$1	1	76	79	8.9999
...	chr9:131721025-131721253(+)$1	1	5	8	8.9999
.((	chr17:1582281-1582510(-)$1	1	13	16	8.9999
((.	chr1:155450543-155450778(-)$1	1	82	85	8.9999
(((	chr16:28187119-28187337(-)$1	1	26	29	8.9999
(((	chr19:21720053-21720279(+)$1	1	15	18	8.9999
(((	chr6:64412343-64412567(+)$1	1	15	18	8.9999
.((	chr2:30862921-30863145(+)$1	1	39	42	8.9999
(((	chr3:12626528-12626753(-)$1	1	42	45	8.9999
(((	chr16:27549025-27549248(-)$1	1	35	38	8.9999
((.	chr17:38554985-38555211(-)$1	1	4	7	8.9999
(((	chr2:242179367-242179597(-)$1	1	51	54	8.9999
((.	chr14:50249015-50249246(-)$1	1	12	15	8.9999
(((	chr3:129150285-129150508(-)$1	1	6	9	8.9999
...	chr10:28872280-28872504(+)$1	1	10	13	8.9999
...	chr3:130424435-130424659(-)$1	1	1	4	8.9999
...	chr7:94898446-94898678(+)$1	1	1	4	8.9999
..)	chr10:88939826-88940051(+)$1	1	29	32	8.9999
(((	chr9:125613561-125613784(-)$1	1	59	62	8.9999
...	chr7:98582483-98582711(+)$1	1	16	19	8.9999
(((	chr13:113963965-113964189(+)$1	1	1	4	8.9999
)).	chr2:24261383-24261614(-)$1	1	73	76	8.9999

#PSSM
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m2_run2.nuc.txt

#NT
UUUCUG	chr9:80944110-80944556(+)$1	446	224	230	18.0000
UUUCUG	chr6:26027027-26027513(-)$1	486	216	222	18.0000
UUUCUG	chr19:16302598-16302834(+)$1	236	145	151	18.0000
UUUCUG	chr12:111159839-111160146(-)$1	307	124	130	18.0000
UUUCUG	chr1:67876597-67876932(-)$1	335	257	263	18.0000
UUUCUG	chr18:55268301-55268797(-)$1	496	20	26	18.0000
UUUCUG	chr1:203839004-203839302(+)$1	298	280	286	18.0000
UUUCUG	chr19:19617055-19617514(+)$1	459	129	135	18.0000
UUUCUG	chr12:50869881-50870194(+)$1	313	171	177	18.0000
UUUCUG	chr20:35240314-35240610(+)$1	296	289	295	18.0000
UUUCUG	chr2:176960462-176960738(+)$1	276	30	36	18.0000
UUUCUG	chr5:142657935-142658223(-)$1	288	253	259	18.0000
UUUCUG	chr19:18679582-18679967(+)$1	385	361	367	18.0000
UUUCUG	chr6:32945920-32946249(+)$1	329	281	287	18.0000
UUUCUG	chr8:30643558-30643923(-)$1	365	267	273	18.0000
uuucug	chr17:42112742-42113043(-)$1	301	83	89	18.0000
UUUCUG	chr17:42283925-42284248(-)$1	323	312	318	18.0000
UUUCUG	chr6:43608356-43608686(+)$1	330	224	230	18.0000
UUUCUG	chr2:131806159-131806633(-)$1	474	265	271	18.0000
UUUCUG	chr19:49993388-49993646(+)$1	258	139	145	18.0000
UUUCUG	chr7:99633348-99633591(+)$1	243	2	8	18.0000
UUUCUG	chr11:27519929-27520208(-)$1	279	194	200	18.0000
UUUCUG	chrX:77381217-77381636(+)$1	419	161	167	18.0000
UUUCUG	chr12:56668685-56668935(-)$1	250	204	210	18.0000
UUUCUG	chr7:108203996-108204291(-)$1	295	120	126	18.0000
UUUCUG	chr5:137683216-137683701(+)$1	485	208	214	18.0000
UUUCUG	chr4:1981206-1981636(+)$1	430	266	272	18.0000
UUUCUG	chr15:44816997-44817275(+)$1	278	75	81	18.0000
UUUCUG	chr1:59246871-59247176(-)$1	305	129	135	18.0000
UUUCUG	chr17:5346925-5347164(-)$1	239	114	120	18.0000
UUUCUG	chr2:64686065-64686319(+)$1	254	159	165	18.0000
UUUCUG	chr20:17971472-17971795(+)$1	323	164	170	18.0000
UUUCUG	chr7:6509189-6509446(-)$1	257	157	163	18.0000
uuucug	chr3:196313689-196313991(+)$1	302	2	8	18.0000
UUUCUG	chr2:70523845-70524221(-)$1	376	290	296	18.0000

#otherMatches

#Struct PSSM
eeeeoo	chrX:100646642-100646910(+)$1	268	14	20	18.0000
:::::B	chr9:80944110-80944556(+)$1	446	224	230	18.0000
mmccc]	chr6:26027027-26027513(-)$1	486	216	222	18.0000
dggggg	chr19:16302598-16302834(+)$1	236	145	151	18.0000
"ggggg	chr12:111159839-111160146(-)$1	307	124	130	18.0000
ddllld	chr1:67876597-67876932(-)$1	335	257	263	18.0000
FBB{HH	chr18:55268301-55268797(-)$1	496	20	26	18.0000
fffccc	chr1:203839004-203839302(+)$1	298	280	286	18.0000
::::::	chr19:19617055-19617514(+)$1	459	129	135	18.0000
gggggg	chr12:50869881-50870194(+)$1	313	171	177	18.0000
oooccc	chr20:35240314-35240610(+)$1	296	289	295	18.0000
CC{CCC	chr2:176960462-176960738(+)$1	276	30	36	18.0000
hhhhhh	chr5:142657935-142658223(-)$1	288	253	259	18.0000
:::::e	chr19:18679582-18679967(+)$1	385	361	367	18.0000
gggggg	chr6:32945920-32946249(+)$1	329	281	287	18.0000
eeeFFF	chr8:30643558-30643923(-)$1	365	267	273	18.0000
hhhddd	chr17:42112742-42113043(-)$1	301	83	89	18.0000
333bb]	chr17:42283925-42284248(-)$1	323	312	318	18.0000
ccc]dd	chr6:43608356-43608686(+)$1	330	224	230	18.0000
nnbb]g	chr2:131806159-131806633(-)$1	474	265	271	18.0000
hhhhhh	chr19:49993388-49993646(+)$1	258	139	145	18.0000
JJJJJJ	chr7:99633348-99633591(+)$1	243	2	8	18.0000
hhhhhm	chr11:27519929-27520208(-)$1	279	194	200	18.0000
::::hh	chrX:77381217-77381636(+)$1	419	161	167	18.0000
qqqqqq	chr12:56668685-56668935(-)$1	250	204	210	18.0000
oeeeee	chr7:108203996-108204291(-)$1	295	120	126	18.0000
QEEEEE	chr5:137683216-137683701(+)$1	485	208	214	18.0000
IIIII:	chr4:1981206-1981636(+)$1	430	266	272	18.0000
c333dd	chr15:44816997-44817275(+)$1	278	75	81	18.0000
ffffff	chr1:59246871-59247176(-)$1	305	129	135	18.0000
)eeeee	chr17:5346925-5347164(-)$1	239	114	120	18.0000
ggggww	chr2:64686065-64686319(+)$1	254	159	165	18.0000
GGG:::	chr20:17971472-17971795(+)$1	323	164	170	18.0000
appppp	chr7:6509189-6509446(-)$1	257	157	163	18.0000
EEE:dd	chr3:196313689-196313991(+)$1	302	2	8	18.0000
======	chr2:70523845-70524221(-)$1	376	290	296	18.0000

#DB
((((..	chrX:100646642-100646910(+)$1	1	14	20	18.0000
.....)	chr9:80944110-80944556(+)$1	1	224	230	18.0000
..))).	chr6:26027027-26027513(-)$1	1	216	222	18.0000
)(((((	chr19:16302598-16302834(+)$1	1	145	151	18.0000
.(((((	chr12:111159839-111160146(-)$1	1	124	130	18.0000
((...)	chr1:67876597-67876932(-)$1	1	257	263	18.0000
(((.((	chr18:55268301-55268797(-)$1	1	20	26	18.0000
))))))	chr1:203839004-203839302(+)$1	1	280	286	18.0000
......	chr19:19617055-19617514(+)$1	1	129	135	18.0000
((((((	chr12:50869881-50870194(+)$1	1	171	177	18.0000
...)))	chr20:35240314-35240610(+)$1	1	289	295	18.0000
((.(((	chr2:176960462-176960738(+)$1	1	30	36	18.0000
))))))	chr5:142657935-142658223(-)$1	1	253	259	18.0000
.....(	chr19:18679582-18679967(+)$1	1	361	367	18.0000
))))))	chr6:32945920-32946249(+)$1	1	281	287	18.0000
))))))	chr8:30643558-30643923(-)$1	1	267	273	18.0000
)))(((	chr17:42112742-42113043(-)$1	1	83	89	18.0000
...)).	chr17:42283925-42284248(-)$1	1	312	318	18.0000
))).))	chr6:43608356-43608686(+)$1	1	224	230	18.0000
..)).)	chr2:131806159-131806633(-)$1	1	265	271	18.0000
))))))	chr19:49993388-49993646(+)$1	1	139	145	18.0000
((((((	chr7:99633348-99633591(+)$1	1	2	8	18.0000
(((((.	chr11:27519929-27520208(-)$1	1	194	200	18.0000
....((	chrX:77381217-77381636(+)$1	1	161	167	18.0000
......	chr12:56668685-56668935(-)$1	1	204	210	18.0000
.)))))	chr7:108203996-108204291(-)$1	1	120	126	18.0000
.(((((	chr5:137683216-137683701(+)$1	1	208	214	18.0000
))))).	chr4:1981206-1981636(+)$1	1	266	272	18.0000
)...))	chr15:44816997-44817275(+)$1	1	75	81	18.0000
((((((	chr1:59246871-59247176(-)$1	1	129	135	18.0000
.(((((	chr17:5346925-5347164(-)$1	1	114	120	18.0000
((((..	chr2:64686065-64686319(+)$1	1	159	165	18.0000
)))...	chr20:17971472-17971795(+)$1	1	164	170	18.0000
(.....	chr7:6509189-6509446(-)$1	1	157	163	18.0000
(((.((	chr3:196313689-196313991(+)$1	1	2	8	18.0000
))))))	chr2:70523845-70524221(-)$1	1	290	296	18.0000

#PSSM
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	
G : 0.94	g : 0.05	

#score	648.0000000000001
#seq	36
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m3_run1.nuc.txt

#NT
UUUUAGA	chr11:102267029-102267258(-)$1	229	166	173	12.9285
UUUUUAA	chr7:44918481-44918713(-)$1	232	121	128	13.3571
UUUUAAA	chr2:111925890-111926120(+)$1	230	80	87	17.2857
AUUUAAA	chr22:26118604-26118830(+)$1	226	132	139	13.0714
UUUUAAA	chr3:101504338-101504575(+)$1	237	44	51	17.2857
UUGUAAA	chr13:25910230-25910450(+)$1	220	90	97	12.9999
UUUUUAA	chr5:79276183-79276409(-)$1	226	17	24	13.3571
GUUUAAA	chr3:188595619-188595845(+)$1	226	164	171	13.0714
UGUUAAA	chr16:81078810-81079041(+)$1	231	19	26	13.2142
UUUUCAA	chr7:50658536-50658755(-)$1	219	37	44	12.9999
UUUUAAG	chr15:25583930-25584165(-)$1	235	195	202	12.8571
UUUUAUA	chr17:29701749-29701973(+)$1	224	32	39	13.1428
UAUUAAA	chr6:151678694-151678930(+)$1	236	105	112	13.1428
uuuuaaa	chr16:70607931-70608171(+)$1	240	160	167	17.2857
UUUGAAA	chr4:56236258-56236480(+)$1	222	95	102	12.7857
UUGUAAA	chr7:77584965-77585196(+)$1	231	210	217	12.9999
UUUUAAU	chr12:49083898-49084124(-)$1	226	171	178	13.0714
UUUUAAA	chr5:1463062-1463287(-)$1	225	81	88	17.2857
UUUCAAA	chr1:23635361-23635584(-)$1	223	106	113	12.7857
UUUUAAA	chr5:40715224-40715446(-)$1	222	168	175	17.2857
UUGUAAA	chr21:45115613-45115834(+)$1	221	24	31	12.9999
UUUUAAU	chr17:20903946-20904171(-)$1	225	89	96	13.0714
UUUUAAA	chr1:225589785-225590016(-)$1	231	35	42	17.2857
UUUUAAC	chr5:133938136-133938371(-)$1	235	153	160	12.9285
UUUUAAA	chr15:59930966-59931198(-)$1	232	120	127	17.2857
UUUUAAA	chr5:78620565-78620787(+)$1	222	45	52	17.2857
UUUGAAA	chr13:98116947-98117180(+)$1	233	13	20	12.7857
UUUUAAC	chr3:140697327-140697548(+)$1	221	169	176	12.9285
uuuuaua	chr21:34730650-34730878(+)$1	228	105	112	13.1428
UUUUGAA	chr16:67323239-67323472(+)$1	233	5	12	13.0714
GUUUAAA	chr9:74481016-74481242(-)$1	226	51	58	13.0714
UGUUAAA	chr7:120427996-120428223(-)$1	227	182	189	13.2142
AUUUAAA	chr17:39847268-39847525(+)$1	257	7	14	13.0714
UUUUUAA	chr15:91347442-91347679(+)$1	237	114	121	13.3571
UGuuaaa	chr19:12810466-12810688(-)$1	222	198	205	13.2142
UUUUAAA	chr1:244572010-244572241(-)$1	231	167	174	17.2857
UUUUAUA	chr19:2430772-2431016(-)$1	244	161	168	13.1428
UUUUAAA	chr16:50264466-50264696(+)$1	230	118	125	17.2857
uuuuaaa	chr3:179052223-179052451(+)$1	228	105	112	17.2857
uuuuaaa	chr2:139329790-139330025(+)$1	235	61	68	17.2857
UCUUAAA	chr13:73283496-73283727(-)$1	231	35	42	13.0714
UUUUUAA	chr12:53805304-53805526(+)$1	222	105	112	13.3571
UUUUAAU	chr13:52989715-52989944(-)$1	229	108	115	13.0714
UUUUGAA	chr3:5258431-5258656(+)$1	225	12	19	13.0714
UUUUAAA	chr12:92537443-92537677(-)$1	234	126	133	17.2857
UUAUAAA	chr4:2229692-2229918(-)$1	226	111	118	12.9285
UUUUAAA	chr6:11134905-11135128(+)$1	223	40	47	17.2857
UUUUAAA	chr3:140697638-140697884(+)$1	246	79	86	17.2857
UUUUAAA	chr1:68168026-68168251(-)$1	225	24	31	17.2857
AUUUAAA	chrX:24003936-24004174(-)$1	238	111	118	13.0714
UUUUAUA	chrX:150573792-150574012(+)$1	220	26	33	13.1428
UUUUAAU	chr10:70551862-70552089(+)$1	227	144	151	13.0714
UCUUAAA	chr21:15745505-15745734(-)$1	229	43	50	13.0714
UUUAAAA	chr12:99019562-99019785(-)$1	223	29	36	12.7142
UUUUAAA	chr5:110824378-110824605(-)$1	227	162	169	17.2857
UGUUAAA	chr1:205686023-205686271(-)$1	248	159	166	13.2142
UAUUAAA	chr5:61684556-61684786(+)$1	230	85	92	13.1428
UUCUAAA	chr12:75891923-75892142(-)$1	219	6	13	12.9285
UUUUAAA	chr1:85731833-85732058(-)$1	225	118	125	17.2857
GUUUAAA	chr15:98515552-98515778(+)$1	226	66	73	13.0714
UUUCAAA	chr18:48701605-48701838(-)$1	233	109	116	12.7857
UUAUAAA	chr7:139255221-139255458(-)$1	237	131	138	12.9285
UUUUUAA	chr8:64123299-64123528(+)$1	229	80	87	13.3571
UUUUUAA	chr12:42479640-42479863(-)$1	223	87	94	13.3571
CUUUAAA	chr22:20098831-20099062(+)$1	231	157	164	12.9999
UUUUAGA	chrX:133560718-133560938(+)$1	220	60	67	12.9285
UUCUAAA	chr11:114278914-114279135(+)$1	221	196	203	12.9285
cuuuaaa	chr2:103332416-103332648(-)$1	232	140	147	12.9999
UUUUAUA	chr21:43409174-43409409(-)$1	235	32	39	13.1428

#otherMatches

#Struct PSSM
eee$$$$	chr7:131179295-131179528(+)$1	233	14	21	13.1428
mmmffff	chr11:102267029-102267258(-)$1	229	166	173	12.9285
:::::::	chr7:44918481-44918713(-)$1	232	121	128	13.3571
:::::::	chr2:111925890-111926120(+)$1	230	80	87	17.2857
]ccc]gg	chr22:26118604-26118830(+)$1	226	132	139	13.0714
''''''d	chr3:101504338-101504575(+)$1	237	44	51	17.2857
g:bb"""	chr13:25910230-25910450(+)$1	220	90	97	12.9999
hhhhhhq	chr5:79276183-79276409(-)$1	226	17	24	13.3571
/////EE	chr3:188595619-188595845(+)$1	226	164	171	13.0714
:::::::	chr16:81078810-81079041(+)$1	231	19	26	13.2142
&&&&&gg	chr7:50658536-50658755(-)$1	219	37	44	12.9999
%%%gggg	chr15:25583930-25584165(-)$1	235	195	202	12.8571
EEEEEFF	chr17:29701749-29701973(+)$1	224	32	39	13.1428
fffff::	chr6:151678694-151678930(+)$1	236	105	112	13.1428
^^=====	chr16:70607931-70608171(+)$1	240	160	167	17.2857
g888888	chr4:56236258-56236480(+)$1	222	95	102	12.7857
gggg:::	chr7:77584965-77585196(+)$1	231	210	217	12.9999
2ccc:GG	chr12:49083898-49084124(-)$1	226	171	178	13.0714
fffffnn	chr5:1463062-1463287(-)$1	225	81	88	17.2857
fff5555	chr1:23635361-23635584(-)$1	223	106	113	12.7857
:::::gg	chr5:40715224-40715446(-)$1	222	168	175	17.2857
HHHHHHH	chr21:45115613-45115834(+)$1	221	24	31	12.9999
ffff[ee	chr17:20903946-20904171(-)$1	225	89	96	13.0714
:::::::	chr1:225589785-225590016(-)$1	231	35	42	17.2857
ooeeeee	chr5:133938136-133938371(-)$1	235	153	160	12.9285
:::::::	chr15:59930966-59931198(-)$1	232	120	127	17.2857
(((((((	chr5:78620565-78620787(+)$1	222	45	52	17.2857
DDDD:::	chr13:98116947-98117180(+)$1	233	13	20	12.7857
ffff!!f	chr3:140697327-140697548(+)$1	221	169	176	12.9285
hhhhhhh	chr21:34730650-34730878(+)$1	228	105	112	13.1428
d####gg	chr16:67323239-67323472(+)$1	233	5	12	13.0714
geeeee[	chr9:74481016-74481242(-)$1	226	51	58	13.0714
bb:::::	chr7:120427996-120428223(-)$1	227	182	189	13.2142
rrrrrrr	chr17:39847268-39847525(+)$1	257	7	14	13.0714
HHHHHZZ	chr15:91347442-91347679(+)$1	237	114	121	13.3571
:::::::	chr19:12810466-12810688(-)$1	222	198	205	13.2142
sssssss	chr1:244572010-244572241(-)$1	231	167	174	17.2857
wwwwwww	chr19:2430772-2431016(-)$1	244	161	168	13.1428
::::eee	chr16:50264466-50264696(+)$1	230	118	125	17.2857
dddqqqq	chr3:179052223-179052451(+)$1	228	105	112	17.2857
=======	chr2:139329790-139330025(+)$1	235	61	68	17.2857
gggggg:	chr13:73283496-73283727(-)$1	231	35	42	13.0714
mffffff	chr12:53805304-53805526(+)$1	222	105	112	13.3571
c22ccc]	chr13:52989715-52989944(-)$1	229	108	115	13.0714
qqqqfff	chr3:5258431-5258656(+)$1	225	12	19	13.0714
::::::c	chr12:92537443-92537677(-)$1	234	126	133	17.2857
2ccc333	chr4:2229692-2229918(-)$1	226	111	118	12.9285
ggggmmm	chr6:11134905-11135128(+)$1	223	40	47	17.2857
iiiiiii	chr3:140697638-140697884(+)$1	246	79	86	17.2857
[ffffff	chr1:68168026-68168251(-)$1	225	24	31	17.2857
!ccc[gg	chrX:24003936-24004174(-)$1	238	111	118	13.0714
ff####i	chrX:150573792-150574012(+)$1	220	26	33	13.1428
eeepppp	chr10:70551862-70552089(+)$1	227	144	151	13.0714
ddd####	chr21:15745505-15745734(-)$1	229	43	50	13.0714
#dddd$$	chr12:99019562-99019785(-)$1	223	29	36	12.7142
>>>>>>>	chr5:110824378-110824605(-)$1	227	162	169	17.2857
:::::::	chr1:205686023-205686271(-)$1	248	159	166	13.2142
ggggggg	chr5:61684556-61684786(+)$1	230	85	92	13.1428
EENNNNN	chr12:75891923-75892142(-)$1	219	6	13	12.9285
=======	chr1:85731833-85732058(-)$1	225	118	125	17.2857
c4444ee	chr15:98515552-98515778(+)$1	226	66	73	13.0714
tttttee	chr18:48701605-48701838(-)$1	233	109	116	12.7857
pppppee	chr7:139255221-139255458(-)$1	237	131	138	12.9285
ooooddd	chr8:64123299-64123528(+)$1	229	80	87	13.3571
iiiiiii	chr12:42479640-42479863(-)$1	223	87	94	13.3571
~~~~JJJ	chr22:20098831-20099062(+)$1	231	157	164	12.9999
=======	chrX:133560718-133560938(+)$1	220	60	67	12.9285
ffffffl	chr11:114278914-114279135(+)$1	221	196	203	12.9285
zzzgggg	chr2:103332416-103332648(-)$1	232	140	147	12.9999
ccc]fff	chr21:43409174-43409409(-)$1	235	32	39	13.1428

#DB
(((....	chr7:131179295-131179528(+)$1	1	14	21	13.1428
...))))	chr11:102267029-102267258(-)$1	1	166	173	12.9285
.......	chr7:44918481-44918713(-)$1	1	121	128	13.3571
.......	chr2:111925890-111926120(+)$1	1	80	87	17.2857
.))).))	chr22:26118604-26118830(+)$1	1	132	139	13.0714
......(	chr3:101504338-101504575(+)$1	1	44	51	17.2857
).((...	chr13:25910230-25910450(+)$1	1	90	97	12.9999
((((((.	chr5:79276183-79276409(-)$1	1	17	24	13.3571
.....))	chr3:188595619-188595845(+)$1	1	164	171	13.0714
.......	chr16:81078810-81079041(+)$1	1	19	26	13.2142
.....((	chr7:50658536-50658755(-)$1	1	37	44	12.9999
...((((	chr15:25583930-25584165(-)$1	1	195	202	12.8571
(((((((	chr17:29701749-29701973(+)$1	1	32	39	13.1428
)))))..	chr6:151678694-151678930(+)$1	1	105	112	13.1428
..)))))	chr16:70607931-70608171(+)$1	1	160	167	17.2857
)......	chr4:56236258-56236480(+)$1	1	95	102	12.7857
))))...	chr7:77584965-77585196(+)$1	1	210	217	12.9999
.))).))	chr12:49083898-49084124(-)$1	1	171	178	13.0714
(((((..	chr5:1463062-1463287(-)$1	1	81	88	17.2857
)))....	chr1:23635361-23635584(-)$1	1	106	113	12.7857
.....((	chr5:40715224-40715446(-)$1	1	168	175	17.2857
(((((((	chr21:45115613-45115834(+)$1	1	24	31	12.9999
((((.((	chr17:20903946-20904171(-)$1	1	89	96	13.0714
.......	chr1:225589785-225590016(-)$1	1	35	42	17.2857
..)))))	chr5:133938136-133938371(-)$1	1	153	160	12.9285
.......	chr15:59930966-59931198(-)$1	1	120	127	17.2857
.......	chr5:78620565-78620787(+)$1	1	45	52	17.2857
((((...	chr13:98116947-98117180(+)$1	1	13	20	12.7857
((((..(	chr3:140697327-140697548(+)$1	1	169	176	12.9285
)))))))	chr21:34730650-34730878(+)$1	1	105	112	13.1428
(....((	chr16:67323239-67323472(+)$1	1	5	12	13.0714
((((((.	chr9:74481016-74481242(-)$1	1	51	58	13.0714
)).....	chr7:120427996-120428223(-)$1	1	182	189	13.2142
.......	chr17:39847268-39847525(+)$1	1	7	14	13.0714
)))))..	chr15:91347442-91347679(+)$1	1	114	121	13.3571
.......	chr19:12810466-12810688(-)$1	1	198	205	13.2142
.......	chr1:244572010-244572241(-)$1	1	167	174	17.2857
.......	chr19:2430772-2431016(-)$1	1	161	168	13.1428
....(((	chr16:50264466-50264696(+)$1	1	118	125	17.2857
(((....	chr3:179052223-179052451(+)$1	1	105	112	17.2857
)))))))	chr2:139329790-139330025(+)$1	1	61	68	17.2857
)))))).	chr13:73283496-73283727(-)$1	1	35	42	13.0714
.))))))	chr12:53805304-53805526(+)$1	1	105	112	13.3571
)..))).	chr13:52989715-52989944(-)$1	1	108	115	13.0714
....)))	chr3:5258431-5258656(+)$1	1	12	19	13.0714
......(	chr12:92537443-92537677(-)$1	1	126	133	17.2857
.)))...	chr4:2229692-2229918(-)$1	1	111	118	12.9285
((((...	chr6:11134905-11135128(+)$1	1	40	47	17.2857
(((((((	chr3:140697638-140697884(+)$1	1	79	86	17.2857
.((((((	chr1:68168026-68168251(-)$1	1	24	31	17.2857
.(((.((	chrX:24003936-24004174(-)$1	1	111	118	13.0714
((....(	chrX:150573792-150574012(+)$1	1	26	33	13.1428
(((....	chr10:70551862-70552089(+)$1	1	144	151	13.0714
(((....	chr21:15745505-15745734(-)$1	1	43	50	13.0714
.((((..	chr12:99019562-99019785(-)$1	1	29	36	12.7142
.......	chr5:110824378-110824605(-)$1	1	162	169	17.2857
.......	chr1:205686023-205686271(-)$1	1	159	166	13.2142
(((((((	chr5:61684556-61684786(+)$1	1	85	92	13.1428
((.....	chr12:75891923-75892142(-)$1	1	6	13	12.9285
(((((((	chr1:85731833-85732058(-)$1	1	118	125	17.2857
)....))	chr15:98515552-98515778(+)$1	1	66	73	13.0714
.....))	chr18:48701605-48701838(-)$1	1	109	116	12.7857
.....))	chr7:139255221-139255458(-)$1	1	131	138	12.9285
....)))	chr8:64123299-64123528(+)$1	1	80	87	13.3571
(((((((	chr12:42479640-42479863(-)$1	1	87	94	13.3571
....)))	chr22:20098831-20099062(+)$1	1	157	164	12.9999
)))))))	chrX:133560718-133560938(+)$1	1	60	67	12.9285
((((((.	chr11:114278914-114279135(+)$1	1	196	203	12.9285
...))))	chr2:103332416-103332648(-)$1	1	140	147	12.9999
))).)))	chr21:43409174-43409409(-)$1	1	32	39	13.1428

#PSSM
U : 0.82	u : 0.05	A : 0.04	G : 0.04	C : 0.01	c : 0.01	
U : 0.79	u : 0.07	G : 0.05	A : 0.04	C : 0.02	
U : 0.81	u : 0.08	G : 0.04	A : 0.02	C : 0.02	
U : 0.84	u : 0.08	G : 0.02	C : 0.02	A : 0.01	
A : 0.78	U : 0.08	a : 0.08	G : 0.02	C : 0.01	
A : 0.82	a : 0.07	U : 0.05	G : 0.02	u : 0.01	
A : 0.81	a : 0.08	U : 0.05	C : 0.02	G : 0.01	

#score	990.4285714285702
#seq	70
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_UTR_m2_run1.nuc.txt

#NT
AUUUCUUUAA	chr1:108678820-108679060(-)$1	240	200	210	18.1355
AUUUUUCUAU	chr10:115883287-115883567(-)$1	280	19	29	14.6610
AUUUUUUCAA	chr7:133976849-133977090(-)$1	241	124	134	18.3898
AUUUUUUUGU	chr17:74712102-74712342(-)$1	240	175	185	15.7627
AUUUGUUUAA	chr1:202102525-202102776(-)$1	251	81	91	18.2203
AUUUUUUUUA	chr5:32125282-32125526(-)$1	244	104	114	19.4067
uuuuuuuuga	chr12:133349026-133349272(-)$1	246	135	145	15.9322
AUAUUUUAAA	chr10:120450764-120451004(-)$1	240	4	14	15.4237
UUUUUUUUGA	chr20:48808978-48809218(+)$1	240	208	218	15.9322
AUAUUUCuaa	chr1:85019127-85019370(-)$1	243	37	47	15.2542
AUUUUUUUUG	chr1:173826927-173827167(+)$1	240	114	124	15.5084
aucuuuuuaa	chr14:61435136-61435376(+)$1	240	227	237	18.8983
AUUUUUUUCC	chr3:196662674-196662914(-)$1	240	111	121	15.6779
AUUUUGUUAA	chr6:146119337-146119577(-)$1	240	180	190	17.6271
AUUUUUUUCA	chr12:76738920-76739160(-)$1	240	49	59	19.5762
AUUUUUUUAA	chr1:113455012-113455252(-)$1	240	111	121	22.3728
AUUUUUUUUA	chr7:27146842-27147128(-)$1	286	273	283	19.4067
AUUUUUUCCA	chr17:7093421-7093661(-)$1	240	112	122	15.5932
AUUUUUUAAA	chr12:76738275-76738515(-)$1	240	150	160	18.3050
GUUUAUUUAA	chr2:201448297-201448537(+)$1	240	129	139	14.5762
AGUUUUUUAU	chr1:227846681-227846962(+)$1	281	35	45	14.5762
AUUUUUAUAA	chr3:180328594-180328834(+)$1	240	106	116	18.3050
GUUUUUUUAA	chr7:66421896-66422185(+)$1	289	178	188	18.4745
UUUUUUUUAA	chr3:63985427-63985672(+)$1	245	130	140	19.0677
UUAUUUUUAA	chr2:153617083-153617326(+)$1	243	15	25	16.1864
AUUUAUUUUA	chr6:32948808-32949109(+)$1	301	45	55	15.5084
AUUAUUUUCA	chr6:17610397-17610645(+)$1	248	110	120	15.2542
AUUUUUUUCA	chr15:86292377-86292617(+)$1	240	67	77	19.5762
AUAUUUUUAA	chr7:108214466-108214706(+)$1	240	208	218	19.4915
auuuauuuau	chr12:104743658-104743907(+)$1	249	115	125	14.9999
auauuuuuaa	chr1:92146890-92147130(-)$1	240	70	80	19.4915
AAAUUUUUAA	chr17:18231219-18231459(-)$1	240	165	175	14.9999
AUUAUUUUAA	chr10:120927280-120927524(-)$1	244	41	51	18.0508
UUCUUUUUAA	chr5:132030083-132030323(-)$1	240	7	17	15.5932
AUUUUUUCCA	chr6:20492634-20492874(+)$1	240	197	207	15.5932
AUUUUUGUAA	chr22:40724407-40724647(+)$1	240	152	162	18.0508
AUUUUUUUCU	chr6:89872009-89872249(+)$1	240	12	22	16.1016
UUAUUUUUAA	chr15:60713630-60713870(-)$1	240	3	13	16.1864
UUUUUUUUAA	chr2:128462084-128462324(-)$1	240	125	135	19.0677
AUAUUUUUAU	chr20:33097845-33098085(+)$1	240	39	49	16.0169
AUGUUUUUAC	chr2:231743646-231743896(+)$1	250	141	151	14.9152
AUUUUCUUAA	chr18:29203333-29203573(-)$1	240	168	178	17.6271
AUUUAUAUAA	chr15:100253711-100253951(+)$1	240	160	170	14.4067
AUUUUUUCAU	chr12:40150553-40150793(-)$1	240	112	122	14.9152
AUUUAUUUUA	chr17:35872980-35873220(+)$1	240	123	133	15.5084
AUUCUUUUAA	chr1:75669092-75669332(-)$1	240	210	220	17.9661
ACUUUUUUAA	chrX:117582910-117583150(+)$1	240	121	131	17.8813
UUUCUUUUAA	chr8:57875668-57875908(-)$1	240	117	127	14.6610
AUUUUUUGAA	chr13:73283495-73283735(-)$1	240	223	233	18.1355
AUGUUUUAAA	chr12:39046678-39046918(-)$1	240	108	118	14.7457
AUUUUUUUGG	chr5:112350911-112351151(+)$1	240	131	141	15.3389
AUAUUUAUAA	chr10:120794615-120794855(-)$1	240	74	84	15.4237
auuuuuuuaa	chr2:203633498-203633738(+)$1	240	1	11	22.3728
AGUUUUUUAA	chr2:89049683-89049923(+)$1	240	138	148	18.0508
AGCUUUUUAA	chr18:21061729-21061969(+)$1	240	180	190	14.5762
AUUAUUUUAA	chr2:202152270-202152510(+)$1	240	67	77	18.0508
AUUUUUAUCA	chr1:90182833-90183073(+)$1	240	127	137	15.5084
UUAUUUUUAA	chr17:37689730-37689971(+)$1	241	125	135	16.1864

#otherMatches

#Struct PSSM
ffffffoooo	chr3:119212139-119212379(+)$1	240	82	92	15.2542
dd333fffff	chr1:108678820-108679060(-)$1	240	200	210	18.1355
QQQQQQQJJJ	chr10:115883287-115883567(-)$1	280	19	29	14.6610
ggggggg:::	chr7:133976849-133977090(-)$1	241	124	134	18.3898
GG~~~~GGGG	chr17:74712102-74712342(-)$1	240	175	185	15.7627
::::::::::	chr1:202102525-202102776(-)$1	251	81	91	18.2203
d!!bb####d	chr5:32125282-32125526(-)$1	244	104	114	19.4067
::::::::cc	chr12:133349026-133349272(-)$1	246	135	145	15.9322
gggggeeeee	chr10:120450764-120451004(-)$1	240	4	14	15.4237
99999ggggg	chr20:48808978-48809218(+)$1	240	208	218	15.9322
eeee22ccc4	chr1:85019127-85019370(-)$1	243	37	47	15.2542
ffff::::::	chr1:173826927-173827167(+)$1	240	114	124	15.5084
YYDDDD::::	chr14:61435136-61435376(+)$1	240	227	237	18.8983
eeee:ggggg	chr3:196662674-196662914(-)$1	240	111	121	15.6779
b:dddd"""i	chr6:146119337-146119577(-)$1	240	180	190	17.6271
DDLLLEEEEE	chr12:76738920-76739160(-)$1	240	49	59	19.5762
$$ffffff!!	chr1:113455012-113455252(-)$1	240	111	121	22.3728
}HHHHHHHH:	chr7:27146842-27147128(-)$1	286	273	283	19.4067
+++++++hhh	chr17:7093421-7093661(-)$1	240	112	122	15.5932
fffff:::dd	chr12:76738275-76738515(-)$1	240	150	160	18.3050
eeee!!dddd	chr2:201448297-201448537(+)$1	240	129	139	14.5762
JDDDDKKDDD	chr1:227846681-227846962(+)$1	281	35	45	14.5762
nnndddd666	chr3:180328594-180328834(+)$1	240	106	116	18.3050
eee'''''''	chr7:66421896-66422185(+)$1	289	178	188	18.4745
::::::::::	chr3:63985427-63985672(+)$1	245	130	140	19.0677
ggggg"""gg	chr2:153617083-153617326(+)$1	243	15	25	16.1864
cc22hhhhhh	chr6:32948808-32949109(+)$1	301	45	55	15.5084
ggggg22ccc	chr6:17610397-17610645(+)$1	248	110	120	15.2542
:::::::===	chr15:86292377-86292617(+)$1	240	67	77	19.5762
EEEZZZDDDD	chr7:108214466-108214706(+)$1	240	208	218	19.4915
::::::::::	chr12:104743658-104743907(+)$1	249	115	125	14.9999
ggggg4444c	chr1:92146890-92147130(-)$1	240	70	80	19.4915
&ggggggg##	chr17:18231219-18231459(-)$1	240	165	175	14.9999
+++++++++d	chr10:120927280-120927524(-)$1	244	41	51	18.0508
JJJJ:=====	chr5:132030083-132030323(-)$1	240	7	17	15.5932
::::::::::	chr6:20492634-20492874(+)$1	240	197	207	15.5932
f333ffffff	chr22:40724407-40724647(+)$1	240	152	162	18.0508
dddsssssss	chr6:89872009-89872249(+)$1	240	12	22	16.1016
======="""	chr15:60713630-60713870(-)$1	240	3	13	16.1864
hhhhh4444e	chr2:128462084-128462324(-)$1	240	125	135	19.0677
:JJJJJJJJJ	chr20:33097845-33098085(+)$1	240	39	49	16.0169
gggggwwwww	chr2:231743646-231743896(+)$1	250	141	151	14.9152
dooooooddd	chr18:29203333-29203573(-)$1	240	168	178	17.6271
f%%%%%%hhh	chr15:100253711-100253951(+)$1	240	160	170	14.4067
ttthhhhhhh	chr12:40150553-40150793(-)$1	240	112	122	14.9152
33ffffff]f	chr17:35872980-35873220(+)$1	240	123	133	15.5084
ffff::::::	chr1:75669092-75669332(-)$1	240	210	220	17.9661
22ffffff::	chrX:117582910-117583150(+)$1	240	121	131	17.8813
nnbb22iiii	chr8:57875668-57875908(-)$1	240	117	127	14.6610
==========	chr13:73283495-73283735(-)$1	240	223	233	18.1355
DDDNNNNNCC	chr12:39046678-39046918(-)$1	240	108	118	14.7457
::::::::==	chr5:112350911-112351151(+)$1	240	131	141	15.3389
ggggggg]ff	chr10:120794615-120794855(-)$1	240	74	84	15.4237
:::ffffffo	chr2:203633498-203633738(+)$1	240	1	11	22.3728
eeeeeetttt	chr2:89049683-89049923(+)$1	240	138	148	18.0508
xxffffff::	chr18:21061729-21061969(+)$1	240	180	190	14.5762
d:::::::::	chr2:202152270-202152510(+)$1	240	67	77	18.0508
hhhhhhhhnn	chr1:90182833-90183073(+)$1	240	127	137	15.5084
:::::::::g	chr17:37689730-37689971(+)$1	241	125	135	16.1864

#DB
((((((....	chr3:119212139-119212379(+)$1	1	82	92	15.2542
))...)))))	chr1:108678820-108679060(-)$1	1	200	210	18.1355
.......(((	chr10:115883287-115883567(-)$1	1	19	29	14.6610
)))))))...	chr7:133976849-133977090(-)$1	1	124	134	18.3898
))....))))	chr17:74712102-74712342(-)$1	1	175	185	15.7627
..........	chr1:202102525-202102776(-)$1	1	81	91	18.2203
(..((....(	chr5:32125282-32125526(-)$1	1	104	114	19.4067
........((	chr12:133349026-133349272(-)$1	1	135	145	15.9322
((((((((((	chr10:120450764-120451004(-)$1	1	4	14	15.4237
.....)))))	chr20:48808978-48809218(+)$1	1	208	218	15.9322
))))..))).	chr1:85019127-85019370(-)$1	1	37	47	15.2542
))))......	chr1:173826927-173827167(+)$1	1	114	124	15.5084
..))))....	chr14:61435136-61435376(+)$1	1	227	237	18.8983
)))).(((((	chr3:196662674-196662914(-)$1	1	111	121	15.6779
).((((...(	chr6:146119337-146119577(-)$1	1	180	190	17.6271
((...(((((	chr12:76738920-76739160(-)$1	1	49	59	19.5762
..((((((..	chr1:113455012-113455252(-)$1	1	111	121	22.3728
.)))))))).	chr7:27146842-27147128(-)$1	1	273	283	19.4067
.......(((	chr17:7093421-7093661(-)$1	1	112	122	15.5932
)))))...((	chr12:76738275-76738515(-)$1	1	150	160	18.3050
((((..((((	chr2:201448297-201448537(+)$1	1	129	139	14.5762
(((((..(((	chr1:227846681-227846962(+)$1	1	35	45	14.5762
...))))...	chr3:180328594-180328834(+)$1	1	106	116	18.3050
(((.......	chr7:66421896-66422185(+)$1	1	178	188	18.4745
..........	chr3:63985427-63985672(+)$1	1	130	140	19.0677
(((((...((	chr2:153617083-153617326(+)$1	1	15	25	16.1864
))..))))))	chr6:32948808-32949109(+)$1	1	45	55	15.5084
)))))..)))	chr6:17610397-17610645(+)$1	1	110	120	15.2542
.......(((	chr15:86292377-86292617(+)$1	1	67	77	19.5762
)))...))))	chr7:108214466-108214706(+)$1	1	208	218	19.4915
..........	chr12:104743658-104743907(+)$1	1	115	125	14.9999
)))))....)	chr1:92146890-92147130(-)$1	1	70	80	19.4915
.(((((((..	chr17:18231219-18231459(-)$1	1	165	175	14.9999
.........(	chr10:120927280-120927524(-)$1	1	41	51	18.0508
((((.(((((	chr5:132030083-132030323(-)$1	1	7	17	15.5932
..........	chr6:20492634-20492874(+)$1	1	197	207	15.5932
)...))))))	chr22:40724407-40724647(+)$1	1	152	162	18.0508
(((.......	chr6:89872009-89872249(+)$1	1	12	22	16.1016
(((((((...	chr15:60713630-60713870(-)$1	1	3	13	16.1864
)))))....)	chr2:128462084-128462324(-)$1	1	125	135	19.0677
.(((((((((	chr20:33097845-33098085(+)$1	1	39	49	16.0169
(((((.....	chr2:231743646-231743896(+)$1	1	141	151	14.9152
(......)))	chr18:29203333-29203573(-)$1	1	168	178	17.6271
(......(((	chr15:100253711-100253951(+)$1	1	160	170	14.4067
...)))))))	chr12:40150553-40150793(-)$1	1	112	122	14.9152
..)))))).)	chr17:35872980-35873220(+)$1	1	123	133	15.5084
))))......	chr1:75669092-75669332(-)$1	1	210	220	17.9661
..))))))..	chrX:117582910-117583150(+)$1	1	121	131	17.8813
..))..))))	chr8:57875668-57875908(-)$1	1	117	127	14.6610
))))))))))	chr13:73283495-73283735(-)$1	1	223	233	18.1355
(((.....((	chr12:39046678-39046918(-)$1	1	108	118	14.7457
........((	chr5:112350911-112351151(+)$1	1	131	141	15.3389
))))))).))	chr10:120794615-120794855(-)$1	1	74	84	15.4237
...((((((.	chr2:203633498-203633738(+)$1	1	1	11	22.3728
((((((....	chr2:89049683-89049923(+)$1	1	138	148	18.0508
..))))))..	chr18:21061729-21061969(+)$1	1	180	190	14.5762
).........	chr2:202152270-202152510(+)$1	1	67	77	18.0508
((((((((..	chr1:90182833-90183073(+)$1	1	127	137	15.5084
.........(	chr17:37689730-37689971(+)$1	1	125	135	16.1864

#PSSM
A : 0.74	U : 0.13	a : 0.06	G : 0.03	u : 0.01	
U : 0.83	u : 0.08	G : 0.05	A : 0.01	C : 0.01	
U : 0.69	A : 0.15	u : 0.05	C : 0.03	G : 0.03	c : 0.01	a : 0.01	
U : 0.83	u : 0.08	A : 0.05	C : 0.03	
U : 0.79	u : 0.06	A : 0.06	G : 0.03	C : 0.01	a : 0.01	
U : 0.88	u : 0.08	G : 0.01	C : 0.01	
U : 0.79	u : 0.08	A : 0.06	C : 0.03	G : 0.01	
U : 0.76	u : 0.10	C : 0.06	A : 0.05	G : 0.01	
A : 0.61	C : 0.13	U : 0.10	a : 0.08	G : 0.05	g : 0.01	
A : 0.72	U : 0.10	a : 0.08	G : 0.03	C : 0.03	u : 0.01	

#score	996.7796610169484
#seq	59
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m2_run1.nuc.txt

#NT
AAACUUA	chr8:64099155-64099493(+)$1	338	164	171	11.8333
AAAAUGA	chr1:91404771-91405100(-)$1	329	69	76	13.2727
AAAAAUA	chr2:74362515-74362872(-)$1	357	14	21	12.3636
UAAAUUA	chr11:118656689-118656937(-)$1	248	190	197	12.2121
AAAAUCA	chr19:33870408-33870847(+)$1	439	55	62	13.1212
AAAAUGA	chr8:41801171-41801439(-)$1	268	62	69	13.2727
AAUAUUA	chr12:49522519-49522762(-)$1	243	13	20	12.1363
AAAAUUC	chr2:171912877-171913141(-)$1	264	126	133	12.6666
AAAAAUA	chrM:4606-4868(+)$1	262	1	8	12.3636
aaaauaa	chr5:134192871-134193177(+)$1	306	70	77	13.1969
AAAAUUG	chr3:127786164-127786547(+)$1	383	3	10	12.5909
AAAAUUC	chr5:134164248-134164534(+)$1	286	101	108	12.6666
AAAAUUC	chr19:9677255-9677593(-)$1	338	254	261	12.6666
AUAAUUA	chr14:71485720-71485979(+)$1	259	246	253	11.9848
AAAAUUG	chr6:43481005-43481315(-)$1	310	126	133	12.5909
AAAAGUA	chr12:31632659-31632944(-)$1	285	85	92	12.1363
AAAAUGA	chr5:37052391-37052704(+)$1	313	51	58	13.2727
AAAAUUA	chr3:179046004-179046239(+)$1	235	180	187	16.3787
AAAAUUG	chr13:21961600-21961873(-)$1	273	25	32	12.5909
AAAAUAA	chr5:112179438-112179757(+)$1	319	77	84	13.1969
AAAAUUA	chr11:9431445-9431718(+)$1	273	178	185	16.3787
AAAAUUA	chr12:111923462-111923769(-)$1	307	8	15	16.3787
AAGAUUA	chr20:33045106-33045358(+)$1	252	208	215	11.9848
CAAAUUA	chr21:38538176-38538470(+)$1	294	196	203	12.2121
AAAAUCA	chr20:10393128-10393478(-)$1	350	17	24	13.1212
AAAUUUA	chr6:105606254-105606556(-)$1	302	224	231	11.7575
AAAAUUC	chr16:50069245-50069586(+)$1	341	56	63	12.6666
GAAAUUA	chr11:105950141-105950452(+)$1	311	72	79	12.1363
AGAAUUA	chr1:236713940-236714375(-)$1	435	10	17	11.9090
AAAAUUU	chr6:90039504-90039769(-)$1	265	81	88	12.5151
AAAAUAA	chr3:10089561-10089811(+)$1	250	219	226	13.1969
AAAAAUA	chr13:31231685-31232046(+)$1	361	25	32	12.3636
AAAAUUA	chr1:115276508-115276837(-)$1	329	21	28	16.3787
CAAAUUA	chr17:34149557-34149841(+)$1	284	193	200	12.2121
AAAACUA	chr5:137853176-137853441(-)$1	265	4	11	12.0606
AAAAUCA	chr10:38344957-38345220(+)$1	263	122	129	13.1212
AAAAUAA	chr12:133294496-133294799(+)$1	303	239	246	13.1969
AAAAUUU	chr16:27549024-27549272(-)$1	248	55	62	12.5151
AAAAUCA	chr5:177632786-177633061(+)$1	275	0	7	13.1212
AAAAUUC	chr4:24556286-24556659(-)$1	373	125	132	12.6666
AUAAUUA	chr1:242020577-242020885(+)$1	308	162	169	11.9848
AAAAUUU	chr7:98524697-98524980(+)$1	283	12	19	12.5151
AAAAUUG	chr1:242023712-242024114(+)$1	402	115	122	12.5909
AAAAUAA	chr2:24290433-24290764(-)$1	331	126	133	13.1969
AAAGUUA	chr17:1264284-1264594(-)$1	310	244	251	11.7575
AGAAUUA	chrX:77387037-77387389(-)$1	352	20	27	11.9090
AAAAUGA	chr15:66179938-66180172(+)$1	234	145	152	13.2727
AAUAUUA	chr16:11978939-11979228(-)$1	289	7	14	12.1363
uaaauua	chr17:41361856-41362267(+)$1	411	11	18	12.2121
AAAAUGA	chr17:38324355-38324696(+)$1	341	53	60	13.2727
UAAAUUA	chr10:127529770-127530193(+)$1	423	155	162	12.2121
GAAAUUA	chr19:9075189-9075583(-)$1	394	285	292	12.1363
AAAAUGA	chr14:24707857-24708289(+)$1	432	346	353	13.2727
AAAAUAA	chr5:170341111-170341344(+)$1	233	39	46	13.1969
aagauua	chr15:44672903-44673275(+)$1	372	51	58	11.9848
AAAAUCA	chr4:77969251-77969575(-)$1	324	266	273	13.1212
CAAAUUA	chr3:160146440-160146802(+)$1	362	70	77	12.2121
AAAAAUA	chr10:5803180-5803534(+)$1	354	37	44	12.3636
AAAAUUA	chr19:38190507-38190749(-)$1	242	201	208	16.3787
AAAAUGA	chr11:18317454-18317724(-)$1	270	260	267	13.2727
AAAAGUA	chr4:6863308-6863641(+)$1	333	49	56	12.1363
AAAAAUA	chr2:25982299-25982590(-)$1	291	267	274	12.3636
AAUAUUA	chr5:137680457-137680787(+)$1	330	26	33	12.1363
AAACUUA	chr3:98530232-98530497(-)$1	265	110	117	11.8333
AUAAUUA	chrX:40531019-40531309(-)$1	290	10	17	11.9848

#otherMatches

#Struct PSSM
ttttfff	chr2:225338745-225339101(-)$1	356	213	220	12.1363
:::::::	chr8:64099155-64099493(+)$1	338	164	171	11.8333
:::DDDD	chr1:91404771-91405100(-)$1	329	69	76	13.2727
mmmmddd	chr2:74362515-74362872(-)$1	357	14	21	12.3636
ddllldd	chr11:118656689-118656937(-)$1	248	190	197	12.2121
eqqqqqq	chr19:33870408-33870847(+)$1	439	55	62	13.1212
OOOODDD	chr8:41801171-41801439(-)$1	268	62	69	13.2727
:::::::	chr12:49522519-49522762(-)$1	243	13	20	12.1363
DDDDKKA	chr2:171912877-171913141(-)$1	264	126	133	12.6666
:::::::	chrM:4606-4868(+)$1	262	1	8	12.3636
=====pp	chr5:134192871-134193177(+)$1	306	70	77	13.1969
:::::::	chr3:127786164-127786547(+)$1	383	3	10	12.5909
hhhhhcc	chr5:134164248-134164534(+)$1	286	101	108	12.6666
pppgggg	chr19:9677255-9677593(-)$1	338	254	261	12.6666
:::::::	chr14:71485720-71485979(+)$1	259	246	253	11.9848
333ccc]	chr6:43481005-43481315(-)$1	310	126	133	12.5909
hhddddm	chr12:31632659-31632944(-)$1	285	85	92	12.1363
LHHHHHH	chr5:37052391-37052704(+)$1	313	51	58	13.2727
:::::::	chr3:179046004-179046239(+)$1	235	180	187	16.3787
:::::::	chr13:21961600-21961873(-)$1	273	25	32	12.5909
qqqqqqq	chr5:112179438-112179757(+)$1	319	77	84	13.1969
YYCCCDD	chr11:9431445-9431718(+)$1	273	178	185	16.3787
)))))))	chr12:111923462-111923769(-)$1	307	8	15	16.3787
nffffff	chr20:33045106-33045358(+)$1	252	208	215	11.9848
::ggggg	chr21:38538176-38538470(+)$1	294	196	203	12.2121
::::::F	chr20:10393128-10393478(-)$1	350	17	24	13.1212
]eeeee:	chr6:105606254-105606556(-)$1	302	224	231	11.7575
::::hhh	chr16:50069245-50069586(+)$1	341	56	63	12.6666
e"""fff	chr11:105950141-105950452(+)$1	311	72	79	12.1363
=======	chr1:236713940-236714375(-)$1	435	10	17	11.9090
::::::c	chr6:90039504-90039769(-)$1	265	81	88	12.5151
HHHH}BB	chr3:10089561-10089811(+)$1	250	219	226	13.1969
oooooa]	chr13:31231685-31232046(+)$1	361	25	32	12.3636
''''''c	chr1:115276508-115276837(-)$1	329	21	28	16.3787
0000000	chr17:34149557-34149841(+)$1	284	193	200	12.2121
:::::::	chr5:137853176-137853441(-)$1	265	4	11	12.0606
qqqqqee	chr10:38344957-38345220(+)$1	263	122	129	13.1212
:::::::	chr12:133294496-133294799(+)$1	303	239	246	13.1969
$$$$ddd	chr16:27549024-27549272(-)$1	248	55	62	12.5151
:EEEEE:	chr5:177632786-177633061(+)$1	275	0	7	13.1212
d%%%%%%	chr4:24556286-24556659(-)$1	373	125	132	12.6666
}BB????	chr1:242020577-242020885(+)$1	308	162	169	11.9848
:::::::	chr7:98524697-98524980(+)$1	283	12	19	12.5151
JJJJJJL	chr1:242023712-242024114(+)$1	402	115	122	12.5909
:::::ff	chr2:24290433-24290764(-)$1	331	126	133	13.1969
qqqqqqq	chr17:1264284-1264594(-)$1	310	244	251	11.7575
::::FFF	chrX:77387037-77387389(-)$1	352	20	27	11.9090
wwwweee	chr15:66179938-66180172(+)$1	234	145	152	13.2727
EEQQQQQ	chr16:11978939-11979228(-)$1	289	7	14	12.1363
:::::::	chr17:41361856-41362267(+)$1	411	11	18	12.2121
hhhhhhh	chr17:38324355-38324696(+)$1	341	53	60	13.2727
yyyyyyy	chr10:127529770-127530193(+)$1	423	155	162	12.2121
cc333cc	chr19:9075189-9075583(-)$1	394	285	292	12.1363
CCC}GGG	chr14:24707857-24708289(+)$1	432	346	353	13.2727
eeeeppp	chr5:170341111-170341344(+)$1	233	39	46	13.1969
dd[====	chr15:44672903-44673275(+)$1	372	51	58	11.9848
d4444ff	chr4:77969251-77969575(-)$1	324	266	273	13.1212
aoooooo	chr3:160146440-160146802(+)$1	362	70	77	12.2121
fff"""=	chr10:5803180-5803534(+)$1	354	37	44	12.3636
sssssss	chr19:38190507-38190749(-)$1	242	201	208	16.3787
]hhhhhh	chr11:18317454-18317724(-)$1	270	260	267	13.2727
h::::::	chr4:6863308-6863641(+)$1	333	49	56	12.1363
_____EE	chr2:25982299-25982590(-)$1	291	267	274	12.3636
eeeeppp	chr5:137680457-137680787(+)$1	330	26	33	12.1363
ddd::::	chr3:98530232-98530497(-)$1	265	110	117	11.8333
EE:::::	chrX:40531019-40531309(-)$1	290	10	17	11.9848

#DB
....)))	chr2:225338745-225339101(-)$1	1	213	220	12.1363
.......	chr8:64099155-64099493(+)$1	1	164	171	11.8333
...((((	chr1:91404771-91405100(-)$1	1	69	76	13.2727
....)))	chr2:74362515-74362872(-)$1	1	14	21	12.3636
((...))	chr11:118656689-118656937(-)$1	1	190	197	12.2121
(......	chr19:33870408-33870847(+)$1	1	55	62	13.1212
....(((	chr8:41801171-41801439(-)$1	1	62	69	13.2727
.......	chr12:49522519-49522762(-)$1	1	13	20	12.1363
((((..(	chr2:171912877-171913141(-)$1	1	126	133	12.6666
.......	chrM:4606-4868(+)$1	1	1	8	12.3636
(((((..	chr5:134192871-134193177(+)$1	1	70	77	13.1969
.......	chr3:127786164-127786547(+)$1	1	3	10	12.5909
)))))))	chr5:134164248-134164534(+)$1	1	101	108	12.6666
...))))	chr19:9677255-9677593(-)$1	1	254	261	12.6666
.......	chr14:71485720-71485979(+)$1	1	246	253	11.9848
...))).	chr6:43481005-43481315(-)$1	1	126	133	12.5909
))((((.	chr12:31632659-31632944(-)$1	1	85	92	12.1363
.((((((	chr5:37052391-37052704(+)$1	1	51	58	13.2727
.......	chr3:179046004-179046239(+)$1	1	180	187	16.3787
.......	chr13:21961600-21961873(-)$1	1	25	32	12.5909
.......	chr5:112179438-112179757(+)$1	1	77	84	13.1969
..)))))	chr11:9431445-9431718(+)$1	1	178	185	16.3787
.......	chr12:111923462-111923769(-)$1	1	8	15	16.3787
.))))))	chr20:33045106-33045358(+)$1	1	208	215	11.9848
..(((((	chr21:38538176-38538470(+)$1	1	196	203	12.2121
......(	chr20:10393128-10393478(-)$1	1	17	24	13.1212
.))))).	chr6:105606254-105606556(-)$1	1	224	231	11.7575
....(((	chr16:50069245-50069586(+)$1	1	56	63	12.6666
(...(((	chr11:105950141-105950452(+)$1	1	72	79	12.1363
(((((((	chr1:236713940-236714375(-)$1	1	10	17	11.9090
......(	chr6:90039504-90039769(-)$1	1	81	88	12.5151
)))).))	chr3:10089561-10089811(+)$1	1	219	226	13.1969
.....).	chr13:31231685-31232046(+)$1	1	25	32	12.3636
......(	chr1:115276508-115276837(-)$1	1	21	28	16.3787
.......	chr17:34149557-34149841(+)$1	1	193	200	12.2121
.......	chr5:137853176-137853441(-)$1	1	4	11	12.0606
.....))	chr10:38344957-38345220(+)$1	1	122	129	13.1212
.......	chr12:133294496-133294799(+)$1	1	239	246	13.1969
....(((	chr16:27549024-27549272(-)$1	1	55	62	12.5151
.(((((.	chr5:177632786-177633061(+)$1	1	0	7	13.1212
(......	chr4:24556286-24556659(-)$1	1	125	132	12.6666
.))....	chr1:242020577-242020885(+)$1	1	162	169	11.9848
.......	chr7:98524697-98524980(+)$1	1	12	19	12.5151
((((((.	chr1:242023712-242024114(+)$1	1	115	122	12.5909
.....((	chr2:24290433-24290764(-)$1	1	126	133	13.1969
.......	chr17:1264284-1264594(-)$1	1	244	251	11.7575
....(((	chrX:77387037-77387389(-)$1	1	20	27	11.9090
....)))	chr15:66179938-66180172(+)$1	1	145	152	13.2727
((.....	chr16:11978939-11979228(-)$1	1	7	14	12.1363
.......	chr17:41361856-41362267(+)$1	1	11	18	12.2121
(((((((	chr17:38324355-38324696(+)$1	1	53	60	13.2727
.......	chr10:127529770-127530193(+)$1	1	155	162	12.2121
))...))	chr19:9075189-9075583(-)$1	1	285	292	12.1363
))).)))	chr14:24707857-24708289(+)$1	1	346	353	13.2727
((((...	chr5:170341111-170341344(+)$1	1	39	46	13.1969
((.((((	chr15:44672903-44673275(+)$1	1	51	58	11.9848
)....))	chr4:77969251-77969575(-)$1	1	266	273	13.1212
(......	chr3:160146440-160146802(+)$1	1	70	77	12.2121
(((...(	chr10:5803180-5803534(+)$1	1	37	44	12.3636
.......	chr19:38190507-38190749(-)$1	1	201	208	16.3787
.))))))	chr11:18317454-18317724(-)$1	1	260	267	13.2727
)......	chr4:6863308-6863641(+)$1	1	49	56	12.1363
.....))	chr2:25982299-25982590(-)$1	1	267	274	12.3636
((((...	chr5:137680457-137680787(+)$1	1	26	33	12.1363
)))....	chr3:98530232-98530497(-)$1	1	110	117	11.8333
((.....	chrX:40531019-40531309(-)$1	1	10	17	11.9848

#PSSM
A : 0.84	C : 0.04	U : 0.03	a : 0.03	G : 0.03	u : 0.01	
A : 0.87	a : 0.04	U : 0.04	G : 0.03	
A : 0.87	U : 0.06	a : 0.03	G : 0.01	g : 0.01	
A : 0.89	a : 0.04	C : 0.03	U : 0.01	G : 0.01	
U : 0.83	A : 0.07	u : 0.04	G : 0.03	C : 0.01	
U : 0.69	G : 0.10	C : 0.07	A : 0.07	u : 0.03	a : 0.01	
A : 0.77	C : 0.07	G : 0.06	a : 0.04	U : 0.04	

#score	845.9999999999994
#seq	66
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m1_run2.nuc.txt

#NT
UUUUUUUUU	chr17:5386025-5386258(-)$1	233	42	51	19.1052
UUCUUUUCU	chr12:76446896-76447126(-)$1	230	216	225	18.5789
UUUUUUUCU	chr16:66592077-66592311(+)$1	234	1	10	22.6140
UUCUUUUCU	chr16:19680490-19680716(+)$1	226	104	113	18.5789
GUUUUUUCU	chr10:35857954-35858203(+)$1	249	228	237	18.1403
UUUUUUUUU	chr1:32384562-32384836(-)$1	274	109	118	19.1052
UUUUUGUCU	chr16:20808164-20808411(-)$1	247	155	164	18.3157
UUGUUUUCU	chr17:58365799-58366025(-)$1	226	160	169	18.4035
UUUUAUUCU	chr4:129891522-129891748(-)$1	226	70	79	18.2280
UUUUCUUCU	chr17:34173964-34174190(+)$1	226	131	140	18.2280
UGUUUUUCU	chr13:113459225-113459454(+)$1	229	27	36	18.1403
UCUUUUUCU	chr2:110301723-110301947(-)$1	224	31	40	18.0526
UUUUUUUCU	chr16:2820897-2821151(+)$1	254	119	128	22.6140
auuuuuucu	chr12:25362062-25362298(-)$1	236	163	172	18.4035
UUUUUUUCC	chrX:123171325-123171559(+)$1	234	31	40	18.2280
UUUAUUUCU	chr1:90400613-90400840(+)$1	227	145	154	18.3157
UUUUUUUCU	chr18:33740769-33740999(+)$1	230	103	112	22.6140
UUUUUUUCU	chr6:5260863-5261088(-)$1	225	106	115	22.6140
UUUUUUUUU	chr5:889662-889892(-)$1	230	107	116	19.1052
UUUUUGUCU	chr14:35222740-35222995(-)$1	255	62	71	18.3157
UUUUUUUCG	chr1:156714992-156715228(-)$1	236	118	127	18.1403
UUUUUUUCU	chr7:102960021-102960252(-)$1	231	114	123	22.6140
UUUGUUUCU	chr7:135276131-135276366(+)$1	235	46	55	18.2280
UUAUUUUCU	chr12:42554265-42554501(-)$1	236	114	123	18.6666
UUAUUUUCU	chr9:33258926-33259157(-)$1	231	102	111	18.6666
UUUAUUUCU	chr12:46760961-46761204(-)$1	243	201	210	18.3157
UAUUUUUCU	chr5:145543932-145544158(-)$1	226	102	111	18.0526
UUUUUGUCU	chr15:49421573-49421798(-)$1	225	28	37	18.3157
UUUUUUUCA	chr14:57696497-57696734(-)$1	237	105	114	18.2280
UUUUUAUCU	chr2:162247537-162247767(+)$1	230	163	172	18.2280
UUAUUUUCU	chr12:102313839-102314071(+)$1	232	102	111	18.6666
uuuuuuuuu	chr18:9124775-9125019(+)$1	244	24	33	19.1052
UUUUUUACU	chr15:64458148-64458407(-)$1	259	105	114	18.0526
UUUUUUUCA	chr3:149682873-149683099(-)$1	226	85	94	18.2280
AUUUUUUCU	chr2:223773601-223773839(+)$1	238	13	22	18.4035
UUUUUUCCU	chr11:57457458-57457686(+)$1	228	103	112	18.2280
UUCUUUUCU	chr20:48330046-48330273(-)$1	227	106	115	18.5789
UUUGUUUCU	chr14:31108883-31109115(+)$1	232	88	97	18.2280
UUUUUUUUU	chr1:40756456-40756679(+)$1	223	86	95	19.1052
UUUUUUUUU	chr16:66651141-66651361(-)$1	220	82	91	19.1052
UUUUUUCCU	chr17:40962653-40962903(-)$1	250	127	136	18.2280
UGUUUUUCU	chr16:56973953-56974213(+)$1	260	123	132	18.1403
AUUUUUUCU	chr1:54273302-54273536(-)$1	234	224	233	18.4035
UUUUUUUCU	chr12:124144457-124144697(+)$1	240	45	54	22.6140
UUUUUUUGU	chr12:16516825-16517047(+)$1	222	80	89	18.4912
UUUUUUUCU	chr9:86584253-86584496(-)$1	243	120	129	22.6140
UUUAUUUCU	chr3:140694975-140695204(+)$1	229	106	115	18.3157
UUUUAUUCU	chr6:96034252-96034482(+)$1	230	104	113	18.2280
uuuuuuuuu	chr5:94005828-94006056(+)$1	228	213	222	19.1052
uuuuuuuuu	chr9:134138884-134139112(-)$1	228	110	119	19.1052
UUAUUUUCU	chr15:48626488-48626715(+)$1	227	100	109	18.6666
AUUUUUUCU	chr13:100214819-100215045(+)$1	226	109	118	18.4035
UUUUCUUCU	chr4:129028416-129028648(+)$1	232	60	69	18.2280
UUUUUUUCC	chr11:9444498-9444740(+)$1	242	42	51	18.2280
UUUUGUUCU	chr10:5042652-5042876(-)$1	224	167	176	18.1403
UUUUUUCCU	chr2:32530538-32530777(+)$1	239	0	9	18.2280

#otherMatches

#Struct PSSM
iiiiiiiii	chr9:79874920-79875148(+)$1	228	61	70	18.2280
c:::::::F	chr17:5386025-5386258(-)$1	233	42	51	19.1052
IIIIIIIII	chr12:76446896-76447126(-)$1	230	216	225	18.5789
:::::::::	chr16:66592077-66592311(+)$1	234	1	10	22.6140
3ggggggg2	chr16:19680490-19680716(+)$1	226	104	113	18.5789
BYYGGGGGG	chr10:35857954-35858203(+)$1	249	228	237	18.1403
HHHHHHHH}	chr1:32384562-32384836(-)$1	274	109	118	19.1052
F:::::ggg	chr16:20808164-20808411(-)$1	247	155	164	18.3157
dggggggg"	chr17:58365799-58366025(-)$1	226	160	169	18.4035
===333ccc	chr4:129891522-129891748(-)$1	226	70	79	18.2280
+++++++++	chr17:34173964-34174190(+)$1	226	131	140	18.2280
:::::IIII	chr13:113459225-113459454(+)$1	229	27	36	18.1403
{GGGGGGG:	chr2:110301723-110301947(-)$1	224	31	40	18.0526
::::ddddt	chr16:2820897-2821151(+)$1	254	119	128	22.6140
:========	chr12:25362062-25362298(-)$1	236	163	172	18.4035
:::::::::	chrX:123171325-123171559(+)$1	234	31	40	18.2280
f^^^^^^^^	chr1:90400613-90400840(+)$1	227	145	154	18.3157
cc####ccc	chr18:33740769-33740999(+)$1	230	103	112	22.6140
>>>>>>>>>	chr6:5260863-5261088(-)$1	225	106	115	22.6140
eeee4444e	chr5:889662-889892(-)$1	230	107	116	19.1052
::::bb[bb	chr14:35222740-35222995(-)$1	255	62	71	18.3157
epppppppe	chr1:156714992-156715228(-)$1	236	118	127	18.1403
::GGGGGGG	chr7:102960021-102960252(-)$1	231	114	123	22.6140
=======!!	chr7:135276131-135276366(+)$1	235	46	55	18.2280
zzzzzgggg	chr12:42554265-42554501(-)$1	236	114	123	18.6666
^^^^^^^^^	chr9:33258926-33259157(-)$1	231	102	111	18.6666
666666iii	chr12:46760961-46761204(-)$1	243	201	210	18.3157
E::::::::	chr5:145543932-145544158(-)$1	226	102	111	18.0526
::ddddnnn	chr15:49421573-49421798(-)$1	225	28	37	18.3157
=========	chr14:57696497-57696734(-)$1	237	105	114	18.2280
i++++++++	chr2:162247537-162247767(+)$1	230	163	172	18.2280
::::::::e	chr12:102313839-102314071(+)$1	232	102	111	18.6666
:::::::::	chr18:9124775-9125019(+)$1	244	24	33	19.1052
:::::::::	chr15:64458148-64458407(-)$1	259	105	114	18.0526
d::::::::	chr3:149682873-149683099(-)$1	226	85	94	18.2280
IIIIII{CC	chr2:223773601-223773839(+)$1	238	13	22	18.4035
ggg::::::	chr11:57457458-57457686(+)$1	228	103	112	18.2280
=========	chr20:48330046-48330273(-)$1	227	106	115	18.5789
wwwwwwwww	chr14:31108883-31109115(+)$1	232	88	97	18.2280
cc:::::::	chr1:40756456-40756679(+)$1	223	86	95	19.1052
###======	chr16:66651141-66651361(-)$1	220	82	91	19.1052
c333=====	chr17:40962653-40962903(-)$1	250	127	136	18.2280
]dddd7777	chr16:56973953-56974213(+)$1	260	123	132	18.1403
:::::::::	chr1:54273302-54273536(-)$1	234	224	233	18.4035
^^^bb22bb	chr12:124144457-124144697(+)$1	240	45	54	22.6140
DNNNNNCCC	chr12:16516825-16517047(+)$1	222	80	89	18.4912
^^^^^^^^^	chr9:86584253-86584496(-)$1	243	120	129	22.6140
%%%ffffff	chr3:140694975-140695204(+)$1	229	106	115	18.3157
fffff!!bb	chr6:96034252-96034482(+)$1	230	104	113	18.2280
:::::::::	chr5:94005828-94006056(+)$1	228	213	222	19.1052
:::::::::	chr9:134138884-134139112(-)$1	228	110	119	19.1052
4========	chr15:48626488-48626715(+)$1	227	100	109	18.6666
ff:::::::	chr13:100214819-100215045(+)$1	226	109	118	18.4035
cqqqqqqqq	chr4:129028416-129028648(+)$1	232	60	69	18.2280
::HHHHHHH	chr11:9444498-9444740(+)$1	242	42	51	18.2280
4444ccc:H	chr10:5042652-5042876(-)$1	224	167	176	18.1403
HHHHHHHHK	chr2:32530538-32530777(+)$1	239	0	9	18.2280

#DB
(((((((((	chr9:79874920-79875148(+)$1	1	61	70	18.2280
).......(	chr17:5386025-5386258(-)$1	1	42	51	19.1052
)))))))))	chr12:76446896-76447126(-)$1	1	216	225	18.5789
.........	chr16:66592077-66592311(+)$1	1	1	10	22.6140
.))))))).	chr16:19680490-19680716(+)$1	1	104	113	18.5789
)..))))))	chr10:35857954-35858203(+)$1	1	228	237	18.1403
)))))))).	chr1:32384562-32384836(-)$1	1	109	118	19.1052
).....(((	chr16:20808164-20808411(-)$1	1	155	164	18.3157
)(((((((.	chr17:58365799-58366025(-)$1	1	160	169	18.4035
)))...)))	chr4:129891522-129891748(-)$1	1	70	79	18.2280
.........	chr17:34173964-34174190(+)$1	1	131	140	18.2280
.....((((	chr13:113459225-113459454(+)$1	1	27	36	18.1403
.(((((((.	chr2:110301723-110301947(-)$1	1	31	40	18.0526
....((((.	chr16:2820897-2821151(+)$1	1	119	128	22.6140
.((((((((	chr12:25362062-25362298(-)$1	1	163	172	18.4035
.........	chrX:123171325-123171559(+)$1	1	31	40	18.2280
(........	chr1:90400613-90400840(+)$1	1	145	154	18.3157
((....(((	chr18:33740769-33740999(+)$1	1	103	112	22.6140
.........	chr6:5260863-5261088(-)$1	1	106	115	22.6140
))))....)	chr5:889662-889892(-)$1	1	107	116	19.1052
....((.((	chr14:35222740-35222995(-)$1	1	62	71	18.3157
(.......)	chr1:156714992-156715228(-)$1	1	118	127	18.1403
..(((((((	chr7:102960021-102960252(-)$1	1	114	123	22.6140
(((((((..	chr7:135276131-135276366(+)$1	1	46	55	18.2280
.....))))	chr12:42554265-42554501(-)$1	1	114	123	18.6666
.........	chr9:33258926-33259157(-)$1	1	102	111	18.6666
......)))	chr12:46760961-46761204(-)$1	1	201	210	18.3157
(........	chr5:145543932-145544158(-)$1	1	102	111	18.0526
..((((...	chr15:49421573-49421798(-)$1	1	28	37	18.3157
(((((((((	chr14:57696497-57696734(-)$1	1	105	114	18.2280
(........	chr2:162247537-162247767(+)$1	1	163	172	18.2280
........(	chr12:102313839-102314071(+)$1	1	102	111	18.6666
.........	chr18:9124775-9125019(+)$1	1	24	33	19.1052
.........	chr15:64458148-64458407(-)$1	1	105	114	18.0526
)........	chr3:149682873-149683099(-)$1	1	85	94	18.2280
((((((.((	chr2:223773601-223773839(+)$1	1	13	22	18.4035
)))......	chr11:57457458-57457686(+)$1	1	103	112	18.2280
(((((((((	chr20:48330046-48330273(-)$1	1	106	115	18.5789
.........	chr14:31108883-31109115(+)$1	1	88	97	18.2280
)).......	chr1:40756456-40756679(+)$1	1	86	95	19.1052
...((((((	chr16:66651141-66651361(-)$1	1	82	91	19.1052
)...)))))	chr17:40962653-40962903(-)$1	1	127	136	18.2280
.))))....	chr16:56973953-56974213(+)$1	1	123	132	18.1403
.........	chr1:54273302-54273536(-)$1	1	224	233	18.4035
...))..))	chr12:124144457-124144697(+)$1	1	45	54	22.6140
(.....(((	chr12:16516825-16517047(+)$1	1	80	89	18.4912
.........	chr9:86584253-86584496(-)$1	1	120	129	22.6140
...((((((	chr3:140694975-140695204(+)$1	1	106	115	18.3157
(((((..((	chr6:96034252-96034482(+)$1	1	104	113	18.2280
.........	chr5:94005828-94006056(+)$1	1	213	222	19.1052
.........	chr9:134138884-134139112(-)$1	1	110	119	19.1052
.))))))))	chr15:48626488-48626715(+)$1	1	100	109	18.6666
)).......	chr13:100214819-100215045(+)$1	1	109	118	18.4035
(........	chr4:129028416-129028648(+)$1	1	60	69	18.2280
..(((((((	chr11:9444498-9444740(+)$1	1	42	51	18.2280
....))).)	chr10:5042652-5042876(-)$1	1	167	176	18.1403
((((((((.	chr2:32530538-32530777(+)$1	1	0	9	18.2280

#PSSM
U : 0.85	u : 0.05	A : 0.05	G : 0.01	a : 0.01	
U : 0.85	u : 0.07	G : 0.03	C : 0.01	A : 0.01	
U : 0.78	u : 0.07	A : 0.07	C : 0.05	G : 0.01	
U : 0.84	u : 0.07	A : 0.05	G : 0.03	
U : 0.84	u : 0.07	A : 0.03	C : 0.03	G : 0.01	
U : 0.84	u : 0.07	G : 0.05	A : 0.03	
U : 0.85	u : 0.07	C : 0.05	A : 0.01	
C : 0.82	U : 0.08	u : 0.05	c : 0.01	G : 0.01	
U : 0.84	u : 0.07	C : 0.03	A : 0.03	G : 0.01	

#score	1080.2280701754403
#seq	57
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m3_run1.nuc.txt

#NT
UUUUGAU	chr4:1944604-1944826(+)$1	222	36	43	14.1666
uuuugau	chr19:58005873-58006103(+)$1	230	40	47	14.1666
UUUUGUU	chr1:28824959-28825185(+)$1	226	46	53	14.1666
UUUUGAA	chr21:46190611-46190836(-)$1	225	147	154	14.0833
UUUUGAG	chr10:101474103-101474328(-)$1	225	20	27	13.5000
UUUUGAC	chr1:47842394-47842624(+)$1	230	4	11	13.5833
UUUUGUC	chr7:106842493-106842719(+)$1	226	176	183	13.5833
UUUUGAG	chr9:73002042-73002264(-)$1	222	128	135	13.5000
UUUUGCU	chrX:48771105-48771326(-)$1	221	181	188	13.3333
UUUUGAC	chr16:47115946-47116176(-)$1	230	131	138	13.5833
UUUUGCA	chr22:41831315-41831532(-)$1	217	177	184	13.2500
UUUUGUA	chr6:149732449-149732678(+)$1	229	27	34	14.0833
UUUUGUU	chr11:93429784-93430002(+)$1	218	48	55	14.1666
UUUUGCA	chr19:17160540-17160762(-)$1	222	179	186	13.2500
UUUUGAG	chr10:89727543-89727774(+)$1	231	10	17	13.5000
UUUUGUA	chr17:80721810-80722040(+)$1	230	164	171	14.0833
UUUUGAU	chr2:209222437-209222667(+)$1	230	222	229	14.1666
UUUUGUU	chr10:70546309-70546539(+)$1	230	43	50	14.1666
uuuuggu	chr9:125581365-125581595(-)$1	230	151	158	13.6666
UUUUGGG	chr17:62504616-62504846(+)$1	230	201	208	13.0000
UUUUGGA	chr6:15521974-15522204(+)$1	230	22	29	13.5833
UUUUGUG	chr14:75549768-75549994(-)$1	226	70	77	13.5000
UUUUGGA	chr6:25620092-25620318(+)$1	226	73	80	13.5833
UUUUGAU	chr1:204374792-204375022(-)$1	230	28	35	14.1666
UUUUGGC	chr6:52365009-52365230(-)$1	221	148	155	13.0833
UUUUGUA	chr10:127431703-127431933(+)$1	230	198	205	14.0833
UUUUGUA	chr5:148874309-148874527(-)$1	218	104	111	14.0833
UUUUGAC	chr18:48702221-48702446(-)$1	225	168	175	13.5833
UUUUGUA	chr16:87442642-87442863(-)$1	221	65	72	14.0833
UUUUGAA	chr5:36099311-36099541(-)$1	230	23	30	14.0833
UUUUGUU	chr1:36067123-36067340(-)$1	217	71	78	14.1666
UUUUGGU	chr14:35870649-35870869(-)$1	220	105	112	13.6666
UUUUGAC	chr19:21301391-21301621(+)$1	230	184	191	13.5833
UUUUGGG	chr6:86215578-86215799(-)$1	221	182	189	13.0000
UUUUGUG	chr13:79887074-79887298(-)$1	224	17	24	13.5000
UUUUGCA	chr5:14704838-14705062(-)$1	224	24	31	13.2500
UUUUGAU	chr2:191799569-191799799(+)$1	230	94	101	14.1666
UUUUGUU	chr15:72875588-72875805(+)$1	217	175	182	14.1666
UUUUGGA	chr1:145498877-145499107(+)$1	230	78	85	13.5833
UUUUGAA	chr8:92098707-92098930(+)$1	223	28	35	14.0833
UUUUGAA	chr11:120359346-120359575(+)$1	229	203	210	14.0833
UUUUGCC	chrX:53406924-53407149(-)$1	225	132	139	12.7500
UUUUGUG	chr18:51904637-51904864(+)$1	227	80	87	13.5000
UUUUGCA	chr7:50517189-50517419(-)$1	230	113	120	13.2500
UUUUGGC	chr9:93659824-93660054(+)$1	230	93	100	13.0833
UUUUGCU	chr13:28121329-28121551(-)$1	222	130	137	13.3333
UUUUGAG	chr15:42835914-42836134(-)$1	220	68	75	13.5000
UUUUGGU	chr5:66463298-66463523(+)$1	225	66	73	13.6666
UUUUGUU	chr4:6644017-6644244(+)$1	227	37	44	14.1666
UUUUGGA	chr11:124503132-124503364(+)$1	232	66	73	13.5833
uuuuguc	chr16:30565413-30565642(+)$1	229	24	31	13.5833
UUUUGUG	chr12:42835331-42835561(+)$1	230	65	72	13.5000
UUUUGGU	chr10:70744475-70744705(+)$1	230	149	156	13.6666
UUUUGAA	chr12:121202290-121202505(-)$1	215	59	66	14.0833
UUUUGUC	chr12:110013780-110014001(+)$1	221	2	9	13.5833
UUUUGUU	chr3:88102267-88102496(-)$1	229	64	71	14.1666
UUUUGCU	chr4:71555779-71555998(+)$1	219	58	65	13.3333
UUUUGCC	chr12:89983990-89984209(-)$1	219	45	52	12.7500
UUUUGGG	chr6:109687746-109687976(-)$1	230	25	32	13.0000

#otherMatches

#Struct PSSM
cc[bbee	chr21:27253671-27253893(-)$1	222	35	42	13.5833
emmmmee	chr4:1944604-1944826(+)$1	222	36	43	14.1666
offffff	chr19:58005873-58006103(+)$1	230	40	47	14.1666
ee[ccc[	chr1:28824959-28825185(+)$1	226	46	53	14.1666
fffff]g	chr21:46190611-46190836(-)$1	225	147	154	14.0833
::::hhh	chr10:101474103-101474328(-)$1	225	20	27	13.5000
ee####f	chr1:47842394-47842624(+)$1	230	4	11	13.5833
f::::ii	chr7:106842493-106842719(+)$1	226	176	183	13.5833
tgggggg	chr9:73002042-73002264(-)$1	222	128	135	13.5000
ttttttt	chrX:48771105-48771326(-)$1	221	181	188	13.3333
"""ccc"	chr16:47115946-47116176(-)$1	230	131	138	13.5833
:::::::	chr22:41831315-41831532(-)$1	217	177	184	13.2500
cpppppp	chr6:149732449-149732678(+)$1	229	27	34	14.0833
::ggggg	chr11:93429784-93430002(+)$1	218	48	55	14.1666
:::::ff	chr19:17160540-17160762(-)$1	222	179	186	13.2500
{CCC{BB	chr10:89727543-89727774(+)$1	231	10	17	13.5000
((((eee	chr17:80721810-80722040(+)$1	230	164	171	14.0833
FFFFF::	chr2:209222437-209222667(+)$1	230	222	229	14.1666
hhh[ccc	chr10:70546309-70546539(+)$1	230	43	50	14.1666
======[	chr9:125581365-125581595(-)$1	230	151	158	13.6666
:::::::	chr17:62504616-62504846(+)$1	230	201	208	13.0000
G::::::	chr6:15521974-15522204(+)$1	230	22	29	13.5833
:::dddd	chr14:75549768-75549994(-)$1	226	70	77	13.5000
dd]ccc]	chr6:25620092-25620318(+)$1	226	73	80	13.5833
JJJJ:::	chr1:204374792-204375022(-)$1	230	28	35	14.1666
:FFFFFF	chr6:52365009-52365230(-)$1	221	148	155	13.0833
ppppfff	chr10:127431703-127431933(+)$1	230	198	205	14.0833
ffffff:	chr5:148874309-148874527(-)$1	218	104	111	14.0833
eeeelll	chr18:48702221-48702446(-)$1	225	168	175	13.5833
hhhhhh2	chr16:87442642-87442863(-)$1	221	65	72	14.0833
rrriiii	chr5:36099311-36099541(-)$1	230	23	30	14.0833
[ffffff	chr1:36067123-36067340(-)$1	217	71	78	14.1666
nnccc]a	chr14:35870649-35870869(-)$1	220	105	112	13.6666
:eeeeep	chr19:21301391-21301621(+)$1	230	184	191	13.5833
555eeee	chr6:86215578-86215799(-)$1	221	182	189	13.0000
oobb]dd	chr13:79887074-79887298(-)$1	224	17	24	13.5000
SSSEEEE	chr5:14704838-14705062(-)$1	224	24	31	13.2500
88888dd	chr2:191799569-191799799(+)$1	230	94	101	14.1666
IIIIIII	chr15:72875588-72875805(+)$1	217	175	182	14.1666
EFFFFFF	chr1:145498877-145499107(+)$1	230	78	85	13.5833
=======	chr8:92098707-92098930(+)$1	223	28	35	14.0833
ZZZCCCY	chr11:120359346-120359575(+)$1	229	203	210	14.0833
::::bbo	chrX:53406924-53407149(-)$1	225	132	139	12.7500
ooooccc	chr18:51904637-51904864(+)$1	227	80	87	13.5000
eeeeooo	chr7:50517189-50517419(-)$1	230	113	120	13.2500
5555ccc	chr9:93659824-93660054(+)$1	230	93	100	13.0833
((fffff	chr13:28121329-28121551(-)$1	222	130	137	13.3333
eeee333	chr15:42835914-42836134(-)$1	220	68	75	13.5000
"""ffff	chr5:66463298-66463523(+)$1	225	66	73	13.6666
d%%%%%%	chr4:6644017-6644244(+)$1	227	37	44	14.1666
FFFFFKK	chr11:124503132-124503364(+)$1	232	66	73	13.5833
g!!eeee	chr16:30565413-30565642(+)$1	229	24	31	13.5833
=====]b	chr12:42835331-42835561(+)$1	230	65	72	13.5000
nnnccc]	chr10:70744475-70744705(+)$1	230	149	156	13.6666
ddd%%%%	chr12:121202290-121202505(-)$1	215	59	66	14.0833
FFFFRRR	chr12:110013780-110014001(+)$1	221	2	9	13.5833
mmmmeee	chr3:88102267-88102496(-)$1	229	64	71	14.1666
::FFFFF	chr4:71555779-71555998(+)$1	219	58	65	13.3333
eeee::g	chr12:89983990-89984209(-)$1	219	45	52	12.7500
:::hhhh	chr6:109687746-109687976(-)$1	230	25	32	13.0000

#DB
((.((((	chr21:27253671-27253893(-)$1	1	35	42	13.5833
(....))	chr4:1944604-1944826(+)$1	1	36	43	14.1666
.))))))	chr19:58005873-58006103(+)$1	1	40	47	14.1666
((.(((.	chr1:28824959-28825185(+)$1	1	46	53	14.1666
))))).)	chr21:46190611-46190836(-)$1	1	147	154	14.0833
....(((	chr10:101474103-101474328(-)$1	1	20	27	13.5000
((....(	chr1:47842394-47842624(+)$1	1	4	11	13.5833
)....((	chr7:106842493-106842719(+)$1	1	176	183	13.5833
.))))))	chr9:73002042-73002264(-)$1	1	128	135	13.5000
.......	chrX:48771105-48771326(-)$1	1	181	188	13.3333
...(((.	chr16:47115946-47116176(-)$1	1	131	138	13.5833
.......	chr22:41831315-41831532(-)$1	1	177	184	13.2500
(......	chr6:149732449-149732678(+)$1	1	27	34	14.0833
..(((((	chr11:93429784-93430002(+)$1	1	48	55	14.1666
.....((	chr19:17160540-17160762(-)$1	1	179	186	13.2500
.(((.((	chr10:89727543-89727774(+)$1	1	10	17	13.5000
....(((	chr17:80721810-80722040(+)$1	1	164	171	14.0833
)))))..	chr2:209222437-209222667(+)$1	1	222	229	14.1666
(((.(((	chr10:70546309-70546539(+)$1	1	43	50	14.1666
((((((.	chr9:125581365-125581595(-)$1	1	151	158	13.6666
.......	chr17:62504616-62504846(+)$1	1	201	208	13.0000
(......	chr6:15521974-15522204(+)$1	1	22	29	13.5833
...((((	chr14:75549768-75549994(-)$1	1	70	77	13.5000
)).))).	chr6:25620092-25620318(+)$1	1	73	80	13.5833
((((...	chr1:204374792-204375022(-)$1	1	28	35	14.1666
.((((((	chr6:52365009-52365230(-)$1	1	148	155	13.0833
....)))	chr10:127431703-127431933(+)$1	1	198	205	14.0833
)))))).	chr5:148874309-148874527(-)$1	1	104	111	14.0833
((((...	chr18:48702221-48702446(-)$1	1	168	175	13.5833
)))))).	chr16:87442642-87442863(-)$1	1	65	72	14.0833
...))))	chr5:36099311-36099541(-)$1	1	23	30	14.0833
.((((((	chr1:36067123-36067340(-)$1	1	71	78	14.1666
..))).)	chr14:35870649-35870869(-)$1	1	105	112	13.6666
.(((((.	chr19:21301391-21301621(+)$1	1	184	191	13.5833
...))))	chr6:86215578-86215799(-)$1	1	182	189	13.0000
..)).))	chr13:79887074-79887298(-)$1	1	17	24	13.5000
...((((	chr5:14704838-14705062(-)$1	1	24	31	13.2500
.....))	chr2:191799569-191799799(+)$1	1	94	101	14.1666
)))))))	chr15:72875588-72875805(+)$1	1	175	182	14.1666
(((((((	chr1:145498877-145499107(+)$1	1	78	85	13.5833
(((((((	chr8:92098707-92098930(+)$1	1	28	35	14.0833
...))).	chr11:120359346-120359575(+)$1	1	203	210	14.0833
....((.	chrX:53406924-53407149(-)$1	1	132	139	12.7500
....)))	chr18:51904637-51904864(+)$1	1	80	87	13.5000
((((...	chr7:50517189-50517419(-)$1	1	113	120	13.2500
....)))	chr9:93659824-93660054(+)$1	1	93	100	13.0833
..(((((	chr13:28121329-28121551(-)$1	1	130	137	13.3333
))))...	chr15:42835914-42836134(-)$1	1	68	75	13.5000
...((((	chr5:66463298-66463523(+)$1	1	66	73	13.6666
(......	chr4:6644017-6644244(+)$1	1	37	44	14.1666
(((((..	chr11:124503132-124503364(+)$1	1	66	73	13.5833
(..((((	chr16:30565413-30565642(+)$1	1	24	31	13.5833
))))).)	chr12:42835331-42835561(+)$1	1	65	72	13.5000
...))).	chr10:70744475-70744705(+)$1	1	149	156	13.6666
(((....	chr12:121202290-121202505(-)$1	1	59	66	14.0833
((((...	chr12:110013780-110014001(+)$1	1	2	9	13.5833
....)))	chr3:88102267-88102496(-)$1	1	64	71	14.1666
..(((((	chr4:71555779-71555998(+)$1	1	58	65	13.3333
))))..(	chr12:89983990-89984209(-)$1	1	45	52	12.7500
...((((	chr6:109687746-109687976(-)$1	1	25	32	13.0000

#PSSM
U : 0.95	u : 0.05	
U : 0.95	u : 0.05	
U : 0.95	u : 0.05	
U : 0.95	u : 0.05	
G : 0.95	g : 0.05	
A : 0.30	U : 0.30	G : 0.19	C : 0.15	a : 0.01	g : 0.01	u : 0.01	
A : 0.30	U : 0.28	C : 0.18	G : 0.18	u : 0.03	c : 0.01	

#score	820.1666666666682
#seq	60
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m3_run1.nuc.txt

#NT
AAUU	chr7:6513731-6513989(-)$1	258	235	239	12.0000
AAUU	chrM:9058-9283(+)$1	225	50	54	12.0000
AAUU	chr16:69752182-69752409(-)$1	227	164	168	12.0000
AAUU	chr8:26221161-26221401(+)$1	240	147	151	12.0000
AAUU	chr3:148767926-148768151(-)$1	225	28	32	12.0000
AAUU	chr2:101885549-101885779(+)$1	230	4	8	12.0000
AAUU	chr9:135554037-135554261(+)$1	224	211	215	12.0000
AAUU	chr1:213037081-213037305(+)$1	224	125	129	12.0000
AAUU	chr4:186083776-186084057(-)$1	281	170	174	12.0000
aauu	chr12:2970363-2970591(-)$1	228	166	170	12.0000
AAUU	chr12:46757408-46757681(-)$1	273	17	21	12.0000
AAUU	chr14:36781081-36781304(-)$1	223	62	66	12.0000
AAUU	chr1:245023643-245023869(-)$1	226	10	14	12.0000
AAUU	chr5:145543932-145544158(-)$1	226	40	44	12.0000
AAUU	chr4:56283950-56284199(+)$1	249	180	184	12.0000
AAUU	chr5:864404-864693(-)$1	289	2	6	12.0000
AAUU	chr5:178047552-178047790(-)$1	238	5	9	12.0000
AAUU	chr18:25568507-25568733(-)$1	226	77	81	12.0000
AAUU	chr7:152345652-152345883(-)$1	231	68	72	12.0000
AAUU	chr18:10786986-10787210(-)$1	224	51	55	12.0000
AAUU	chr9:115014911-115015138(-)$1	227	80	84	12.0000
AAUU	chr1:22007223-22007453(-)$1	230	93	97	12.0000
AAUU	chr1:169356197-169356427(+)$1	230	45	49	12.0000
AAUU	chr6:109689956-109690212(-)$1	256	71	75	12.0000
AAUU	chr1:227441735-227441956(-)$1	221	3	7	12.0000
AAUU	chr7:114655876-114656109(+)$1	233	94	98	12.0000
AAUU	chr2:198256869-198257170(-)$1	301	29	33	12.0000
AAUU	chr15:83686714-83686938(-)$1	224	92	96	12.0000
AAUU	chr4:103723639-103723872(-)$1	233	45	49	12.0000
AAUU	chr4:38691226-38691455(+)$1	229	76	80	12.0000
AAUU	chr8:42262791-42263034(+)$1	243	50	54	12.0000
AAUU	chr1:7838105-7838329(+)$1	224	210	214	12.0000
AAUU	chr4:108831415-108831645(+)$1	230	18	22	12.0000
AAUU	chr14:50092153-50092392(-)$1	239	85	89	12.0000
AAUU	chr9:19056300-19056534(-)$1	234	0	4	12.0000
AAUU	chr6:149900965-149901184(+)$1	219	27	31	12.0000
AAUU	chr12:38714832-38715062(+)$1	230	1	5	12.0000
aauu	chr11:18428534-18428764(+)$1	230	25	29	12.0000
AAUU	chrX:70280830-70281054(-)$1	224	35	39	12.0000
AAUU	chr4:39501643-39501904(-)$1	261	12	16	12.0000
AAUU	chr20:52835585-52835870(+)$1	285	19	23	12.0000
AAUU	chr2:162247537-162247767(+)$1	230	43	47	12.0000
AAUU	chr16:66592077-66592311(+)$1	234	197	201	12.0000
AAUU	chr12:31632602-31632846(-)$1	244	36	40	12.0000
AAUU	chr7:156974754-156974981(+)$1	227	8	12	12.0000
aAUU	chr13:107196209-107196479(-)$1	270	72	76	12.0000
AAUU	chr1:225600088-225600336(-)$1	248	194	198	12.0000
AAUU	chr13:48934115-48934345(+)$1	230	158	162	12.0000
AAUU	chr10:30602726-30602991(-)$1	265	194	198	12.0000
AAUU	chr6:5260863-5261088(-)$1	225	200	204	12.0000
AAUU	chr2:114482951-114483174(-)$1	223	26	30	12.0000
AAUU	chr2:61430241-61430464(-)$1	223	28	32	12.0000
AAUU	chr19:49118490-49118722(-)$1	232	170	174	12.0000
AAUU	chr6:36489493-36489716(-)$1	223	19	23	12.0000
AAUU	chr12:20801602-20801830(+)$1	228	111	115	12.0000
AAUU	chr3:120320995-120321218(+)$1	223	90	94	12.0000
AAUU	chr2:189876386-189876616(+)$1	230	76	80	12.0000
AAUU	chr11:125483968-125484188(+)$1	220	75	79	12.0000
AAUU	chr21:34901112-34901342(-)$1	230	122	126	12.0000
AAUU	chr10:98292798-98293027(-)$1	229	5	9	12.0000
AAUU	chr9:86584253-86584496(-)$1	243	1	5	12.0000
AAUU	chr12:46758071-46758302(-)$1	231	13	17	12.0000
AAUU	chr1:179012925-179013154(+)$1	229	89	93	12.0000
AAUU	chr12:111157906-111158191(-)$1	285	84	88	12.0000
AAUU	chr17:56780489-56780720(+)$1	231	12	16	12.0000
AAUU	chr1:45981346-45981570(-)$1	224	178	182	12.0000
AAUU	chr5:36122281-36122513(-)$1	232	138	142	12.0000
AAUU	chr4:139093069-139093330(-)$1	261	9	13	12.0000
AAUU	chr6:64286617-64286893(+)$1	276	58	62	12.0000
AAUU	chr13:45010577-45010808(-)$1	231	38	42	12.0000
AAUU	chr3:128890238-128890479(-)$1	241	22	26	12.0000
AAUU	chr3:3182205-3182432(+)$1	227	0	4	12.0000
AAUU	chr3:158261839-158262081(+)$1	242	78	82	12.0000
AAUU	chr1:215749168-215749396(+)$1	228	35	39	12.0000
AAUU	chr8:95392368-95392596(-)$1	228	181	185	12.0000
AAUU	chr12:16516825-16517047(+)$1	222	136	140	12.0000
AAUU	chr7:105205737-105205961(+)$1	224	115	119	12.0000
AAUU	chr4:139100298-139100525(-)$1	227	160	164	12.0000
AAUU	chr3:145806339-145806562(-)$1	223	5	9	12.0000
AAUU	chr1:62148993-62149222(-)$1	229	101	105	12.0000
AAUU	chr5:41917260-41917494(+)$1	234	107	111	12.0000

#otherMatches

#Struct PSSM
gggg	chr3:170078527-170078746(+)$1	219	105	109	12.0000
@@@@	chr7:6513731-6513989(-)$1	258	235	239	12.0000
::::	chrM:9058-9283(+)$1	225	50	54	12.0000
oooo	chr16:69752182-69752409(-)$1	227	164	168	12.0000
eee:	chr8:26221161-26221401(+)$1	240	147	151	12.0000
d]cc	chr3:148767926-148768151(-)$1	225	28	32	12.0000
::::	chr2:101885549-101885779(+)$1	230	4	8	12.0000
ZZBB	chr9:135554037-135554261(+)$1	224	211	215	12.0000
::::	chr1:213037081-213037305(+)$1	224	125	129	12.0000
hhhh	chr4:186083776-186084057(-)$1	281	170	174	12.0000
:DDD	chr12:2970363-2970591(-)$1	228	166	170	12.0000
b"""	chr12:46757408-46757681(-)$1	273	17	21	12.0000
]ddd	chr14:36781081-36781304(-)$1	223	62	66	12.0000
::::	chr1:245023643-245023869(-)$1	226	10	14	12.0000
nnhh	chr5:145543932-145544158(-)$1	226	40	44	12.0000
""dd	chr4:56283950-56284199(+)$1	249	180	184	12.0000
::::	chr5:864404-864693(-)$1	289	2	6	12.0000
HHH{	chr5:178047552-178047790(-)$1	238	5	9	12.0000
ddtt	chr18:25568507-25568733(-)$1	226	77	81	12.0000
^^^^	chr7:152345652-152345883(-)$1	231	68	72	12.0000
###g	chr18:10786986-10787210(-)$1	224	51	55	12.0000
rfff	chr9:115014911-115015138(-)$1	227	80	84	12.0000
ggg:	chr1:22007223-22007453(-)$1	230	93	97	12.0000
nnnn	chr1:169356197-169356427(+)$1	230	45	49	12.0000
::::	chr6:109689956-109690212(-)$1	256	71	75	12.0000
::::	chr1:227441735-227441956(-)$1	221	3	7	12.0000
ddoo	chr7:114655876-114656109(+)$1	233	94	98	12.0000
ccc]	chr2:198256869-198257170(-)$1	301	29	33	12.0000
nnnd	chr15:83686714-83686938(-)$1	224	92	96	12.0000
2eee	chr4:103723639-103723872(-)$1	233	45	49	12.0000
dd!!	chr4:38691226-38691455(+)$1	229	76	80	12.0000
####	chr8:42262791-42263034(+)$1	243	50	54	12.0000
@@@@	chr1:7838105-7838329(+)$1	224	210	214	12.0000
::::	chr4:108831415-108831645(+)$1	230	18	22	12.0000
333g	chr14:50092153-50092392(-)$1	239	85	89	12.0000
::::	chr9:19056300-19056534(-)$1	234	0	4	12.0000
ffff	chr6:149900965-149901184(+)$1	219	27	31	12.0000
::::	chr12:38714832-38715062(+)$1	230	1	5	12.0000
ccc[	chr11:18428534-18428764(+)$1	230	25	29	12.0000
::::	chrX:70280830-70281054(-)$1	224	35	39	12.0000
%%%%	chr4:39501643-39501904(-)$1	261	12	16	12.0000
::::	chr20:52835585-52835870(+)$1	285	19	23	12.0000
mddd	chr2:162247537-162247767(+)$1	230	43	47	12.0000
:hhh	chr16:66592077-66592311(+)$1	234	197	201	12.0000
c:::	chr12:31632602-31632846(-)$1	244	36	40	12.0000
====	chr7:156974754-156974981(+)$1	227	8	12	12.0000
JJJJ	chr13:107196209-107196479(-)$1	270	72	76	12.0000
ccc[	chr1:225600088-225600336(-)$1	248	194	198	12.0000
nfff	chr13:48934115-48934345(+)$1	230	158	162	12.0000
mmmf	chr10:30602726-30602991(-)$1	265	194	198	12.0000
::::	chr6:5260863-5261088(-)$1	225	200	204	12.0000
++++	chr2:114482951-114483174(-)$1	223	26	30	12.0000
^^^^	chr2:61430241-61430464(-)$1	223	28	32	12.0000
YYFF	chr19:49118490-49118722(-)$1	232	170	174	12.0000
%%%g	chr6:36489493-36489716(-)$1	223	19	23	12.0000
::::	chr12:20801602-20801830(+)$1	228	111	115	12.0000
bb[b	chr3:120320995-120321218(+)$1	223	90	94	12.0000
mmme	chr2:189876386-189876616(+)$1	230	76	80	12.0000
:fff	chr11:125483968-125484188(+)$1	220	75	79	12.0000
::::	chr21:34901112-34901342(-)$1	230	122	126	12.0000
::::	chr10:98292798-98293027(-)$1	229	5	9	12.0000
:::C	chr9:86584253-86584496(-)$1	243	1	5	12.0000
qqqq	chr12:46758071-46758302(-)$1	231	13	17	12.0000
22cc	chr1:179012925-179013154(+)$1	229	89	93	12.0000
EEEf	chr12:111157906-111158191(-)$1	285	84	88	12.0000
::ee	chr17:56780489-56780720(+)$1	231	12	16	12.0000
F???	chr1:45981346-45981570(-)$1	224	178	182	12.0000
444d	chr5:36122281-36122513(-)$1	232	138	142	12.0000
::DD	chr4:139093069-139093330(-)$1	261	9	13	12.0000
nnnn	chr6:64286617-64286893(+)$1	276	58	62	12.0000
B{DD	chr13:45010577-45010808(-)$1	231	38	42	12.0000
offf	chr3:128890238-128890479(-)$1	241	22	26	12.0000
:GGG	chr3:3182205-3182432(+)$1	227	0	4	12.0000
::::	chr3:158261839-158262081(+)$1	242	78	82	12.0000
!hhh	chr1:215749168-215749396(+)$1	228	35	39	12.0000
qggg	chr8:95392368-95392596(-)$1	228	181	185	12.0000
6666	chr12:16516825-16517047(+)$1	222	136	140	12.0000
::gg	chr7:105205737-105205961(+)$1	224	115	119	12.0000
[ccc	chr4:139100298-139100525(-)$1	227	160	164	12.0000
GGG:	chr3:145806339-145806562(-)$1	223	5	9	12.0000
^^^^	chr1:62148993-62149222(-)$1	229	101	105	12.0000
yyyy	chr5:41917260-41917494(+)$1	234	107	111	12.0000

#DB
((((	chr3:170078527-170078746(+)$1	1	105	109	12.0000
....	chr7:6513731-6513989(-)$1	1	235	239	12.0000
....	chrM:9058-9283(+)$1	1	50	54	12.0000
....	chr16:69752182-69752409(-)$1	1	164	168	12.0000
))).	chr8:26221161-26221401(+)$1	1	147	151	12.0000
).))	chr3:148767926-148768151(-)$1	1	28	32	12.0000
....	chr2:101885549-101885779(+)$1	1	4	8	12.0000
..))	chr9:135554037-135554261(+)$1	1	211	215	12.0000
....	chr1:213037081-213037305(+)$1	1	125	129	12.0000
((((	chr4:186083776-186084057(-)$1	1	170	174	12.0000
.)))	chr12:2970363-2970591(-)$1	1	166	170	12.0000
(...	chr12:46757408-46757681(-)$1	1	17	21	12.0000
.)))	chr14:36781081-36781304(-)$1	1	62	66	12.0000
....	chr1:245023643-245023869(-)$1	1	10	14	12.0000
..))	chr5:145543932-145544158(-)$1	1	40	44	12.0000
..((	chr4:56283950-56284199(+)$1	1	180	184	12.0000
....	chr5:864404-864693(-)$1	1	2	6	12.0000
(((.	chr5:178047552-178047790(-)$1	1	5	9	12.0000
((..	chr18:25568507-25568733(-)$1	1	77	81	12.0000
....	chr7:152345652-152345883(-)$1	1	68	72	12.0000
...(	chr18:10786986-10787210(-)$1	1	51	55	12.0000
.)))	chr9:115014911-115015138(-)$1	1	80	84	12.0000
))).	chr1:22007223-22007453(-)$1	1	93	97	12.0000
....	chr1:169356197-169356427(+)$1	1	45	49	12.0000
....	chr6:109689956-109690212(-)$1	1	71	75	12.0000
....	chr1:227441735-227441956(-)$1	1	3	7	12.0000
((..	chr7:114655876-114656109(+)$1	1	94	98	12.0000
))).	chr2:198256869-198257170(-)$1	1	29	33	12.0000
...)	chr15:83686714-83686938(-)$1	1	92	96	12.0000
.)))	chr4:103723639-103723872(-)$1	1	45	49	12.0000
((..	chr4:38691226-38691455(+)$1	1	76	80	12.0000
....	chr8:42262791-42263034(+)$1	1	50	54	12.0000
....	chr1:7838105-7838329(+)$1	1	210	214	12.0000
....	chr4:108831415-108831645(+)$1	1	18	22	12.0000
...)	chr14:50092153-50092392(-)$1	1	85	89	12.0000
....	chr9:19056300-19056534(-)$1	1	0	4	12.0000
((((	chr6:149900965-149901184(+)$1	1	27	31	12.0000
....	chr12:38714832-38715062(+)$1	1	1	5	12.0000
(((.	chr11:18428534-18428764(+)$1	1	25	29	12.0000
....	chrX:70280830-70281054(-)$1	1	35	39	12.0000
....	chr4:39501643-39501904(-)$1	1	12	16	12.0000
....	chr20:52835585-52835870(+)$1	1	19	23	12.0000
.)))	chr2:162247537-162247767(+)$1	1	43	47	12.0000
.(((	chr16:66592077-66592311(+)$1	1	197	201	12.0000
)...	chr12:31632602-31632846(-)$1	1	36	40	12.0000
((((	chr7:156974754-156974981(+)$1	1	8	12	12.0000
((((	chr13:107196209-107196479(-)$1	1	72	76	12.0000
(((.	chr1:225600088-225600336(-)$1	1	194	198	12.0000
.)))	chr13:48934115-48934345(+)$1	1	158	162	12.0000
...)	chr10:30602726-30602991(-)$1	1	194	198	12.0000
....	chr6:5260863-5261088(-)$1	1	200	204	12.0000
....	chr2:114482951-114483174(-)$1	1	26	30	12.0000
....	chr2:61430241-61430464(-)$1	1	28	32	12.0000
..))	chr19:49118490-49118722(-)$1	1	170	174	12.0000
...(	chr6:36489493-36489716(-)$1	1	19	23	12.0000
....	chr12:20801602-20801830(+)$1	1	111	115	12.0000
((.(	chr3:120320995-120321218(+)$1	1	90	94	12.0000
...)	chr2:189876386-189876616(+)$1	1	76	80	12.0000
.(((	chr11:125483968-125484188(+)$1	1	75	79	12.0000
....	chr21:34901112-34901342(-)$1	1	122	126	12.0000
....	chr10:98292798-98293027(-)$1	1	5	9	12.0000
...(	chr9:86584253-86584496(-)$1	1	1	5	12.0000
....	chr12:46758071-46758302(-)$1	1	13	17	12.0000
..))	chr1:179012925-179013154(+)$1	1	89	93	12.0000
((((	chr12:111157906-111158191(-)$1	1	84	88	12.0000
..((	chr17:56780489-56780720(+)$1	1	12	16	12.0000
)...	chr1:45981346-45981570(-)$1	1	178	182	12.0000
...)	chr5:36122281-36122513(-)$1	1	138	142	12.0000
..((	chr4:139093069-139093330(-)$1	1	9	13	12.0000
....	chr6:64286617-64286893(+)$1	1	58	62	12.0000
(.((	chr13:45010577-45010808(-)$1	1	38	42	12.0000
.)))	chr3:128890238-128890479(-)$1	1	22	26	12.0000
.(((	chr3:3182205-3182432(+)$1	1	0	4	12.0000
....	chr3:158261839-158262081(+)$1	1	78	82	12.0000
.(((	chr1:215749168-215749396(+)$1	1	35	39	12.0000
.)))	chr8:95392368-95392596(-)$1	1	181	185	12.0000
....	chr12:16516825-16517047(+)$1	1	136	140	12.0000
..((	chr7:105205737-105205961(+)$1	1	115	119	12.0000
.(((	chr4:139100298-139100525(-)$1	1	160	164	12.0000
(((.	chr3:145806339-145806562(-)$1	1	5	9	12.0000
....	chr1:62148993-62149222(-)$1	1	101	105	12.0000
....	chr5:41917260-41917494(+)$1	1	107	111	12.0000

#PSSM
A : 0.96	a : 0.03	
A : 0.97	a : 0.02	
U : 0.97	u : 0.02	
U : 0.97	u : 0.02	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUUGUA	chr18:19208977-19209476(+)$1	499	162	170	15.6037
UUUUGUUA	chrX:77082163-77082440(-)$1	277	63	71	15.6037
UUUUUUUA	chr3:14239555-14239939(+)$1	384	375	383	20.1320
UUUCUUUA	chr1:25170622-25170865(+)$1	243	1	9	16.1698
AUUUUUUA	chr18:47014757-47015036(-)$1	279	247	255	16.2641
GUUUUUUA	chr6:87971960-87972218(+)$1	258	22	30	15.9811
AUUUUUUA	chr19:30500095-30500349(+)$1	254	224	232	16.2641
UUUUUUUA	chr2:278121-278376(+)$1	255	177	185	20.1320
UAUUUUUA	chr13:27262168-27262571(+)$1	403	115	123	15.8867
UGUUUUUA	chr10:126086103-126086349(-)$1	246	151	159	15.9811
UUUUUUUA	chr7:44921828-44922237(-)$1	409	247	255	20.1320
UUUCUUUA	chr1:24292871-24293135(-)$1	264	238	246	16.1698
UUUUUUUA	chr7:26231607-26232058(-)$1	451	70	78	20.1320
UUUUUUUG	chr19:10795822-10796249(+)$1	427	89	97	16.1698
uuuuuuuA	chr19:47567953-47568280(-)$1	327	295	303	20.1320
UUUUUCUA	chr1:68944871-68945103(-)$1	232	91	99	15.5094
AUUUUUUA	chr17:37008784-37009085(-)$1	301	69	77	16.2641
UUUGUUUA	chr14:74178634-74178940(-)$1	306	96	104	15.9811
UUUUUGUA	chrX:38665137-38665406(+)$1	269	117	125	15.6037
UAUUUUUA	chr19:39889073-39889449(+)$1	376	75	83	15.8867
UUUUUUUA	chr11:94231566-94231932(+)$1	366	343	351	20.1320
UUCUUUUA	chr17:1326172-1326476(-)$1	304	261	269	15.6037
UUUUUUUA	chr6:89872015-89872500(+)$1	485	208	216	20.1320
AUUUUUUA	chr4:100869447-100869780(-)$1	333	53	61	16.2641
UCUUUUUA	chr17:36922537-36922858(-)$1	321	194	202	15.7924
GUUUUUUA	chr16:4930727-4931077(+)$1	350	266	274	15.9811
UUUUUUUG	chr7:4807366-4807657(+)$1	291	32	40	16.1698
UUUUUUUA	chr14:100744157-100744530(+)$1	373	149	157	20.1320
UUUUUUUC	chr15:69071835-69072223(-)$1	388	19	27	16.1698
UUUUUUUA	chr19:2430491-2430899(-)$1	408	382	390	20.1320
UUCUUUUA	chr5:148730758-148731094(+)$1	336	135	143	15.6037
UUUUUUUC	chr3:120320991-120321222(+)$1	231	44	52	16.1698
UUUUUUUA	chr10:124924462-124924762(+)$1	300	26	34	20.1320
UUUUUUUA	chr5:108670558-108670872(-)$1	314	181	189	20.1320
UUUCUUUA	chr12:50158409-50158831(+)$1	422	48	56	16.1698
UUUAUUUA	chr6:87972019-87972286(+)$1	267	57	65	15.8867
UUUUUUGA	chr9:80943890-80944209(+)$1	319	236	244	15.7924
UUUUUUUU	chr8:48973575-48973873(+)$1	298	10	18	16.0754
UUUUUUCA	chr1:22418894-22419357(+)$1	463	366	374	15.6037
UUUUCUUA	chr1:193054206-193054480(+)$1	274	16	24	15.5094
UUUUUUGA	chr1:28607725-28608174(+)$1	449	158	166	15.7924
UGUUUUUA	chr12:123892338-123892582(+)$1	244	25	33	15.9811
UGUUUUUA	chr19:994287-994620(+)$1	333	241	249	15.9811
UUUUUUUC	chr5:157214297-157214561(-)$1	264	118	126	16.1698
UUUGUUUA	chr1:234741701-234741994(-)$1	293	92	100	15.9811
AUUUUUUA	chr17:45760214-45760531(+)$1	317	83	91	16.2641
UUUUUUUU	chr1:234742689-234742983(-)$1	294	233	241	16.0754
UUAUUUUA	chr12:98992199-98992581(+)$1	382	319	327	15.5094
UUUUGUUA	chr7:6442184-6442476(+)$1	292	16	24	15.6037
UUUCUUUA	chr2:30866435-30866726(+)$1	291	161	169	16.1698
UUUUUUUA	chr10:60154980-60155292(+)$1	312	141	149	20.1320
UUUUUUUG	chr12:31944457-31944694(-)$1	237	66	74	16.1698

#otherMatches

#Struct PSSM
GGGGGGGZ	chr1:162498337-162498600(+)$1	263	220	228	15.7924
h22dddd:	chr18:19208977-19209476(+)$1	499	162	170	15.6037
dddd]bb:	chrX:77082163-77082440(-)$1	277	63	71	15.6037
::::::::	chr3:14239555-14239939(+)$1	384	375	383	20.1320
::::::::	chr1:25170622-25170865(+)$1	243	1	9	16.1698
GGgggggg	chr18:47014757-47015036(-)$1	279	247	255	16.2641
dddd::::	chr6:87971960-87972218(+)$1	258	22	30	15.9811
88888ggg	chr19:30500095-30500349(+)$1	254	224	232	16.2641
========	chr2:278121-278376(+)$1	255	177	185	20.1320
i####hhh	chr13:27262168-27262571(+)$1	403	115	123	15.8867
oooooodd	chr10:126086103-126086349(-)$1	246	151	159	15.9811
####gggg	chr7:44921828-44922237(-)$1	409	247	255	20.1320
GGGGGGFF	chr1:24292871-24293135(-)$1	264	238	246	16.1698
::::::::	chr7:26231607-26232058(-)$1	451	70	78	20.1320
:eeeee[i	chr19:10795822-10796249(+)$1	427	89	97	16.1698
:::::::c	chr19:47567953-47568280(-)$1	327	295	303	20.1320
mmbb333e	chr1:68944871-68945103(-)$1	232	91	99	15.5094
========	chr17:37008784-37009085(-)$1	301	69	77	16.2641
e[bbnnnn	chr14:74178634-74178940(-)$1	306	96	104	15.9811
::eeeee[	chrX:38665137-38665406(+)$1	269	117	125	15.6037
)))))bb!	chr19:39889073-39889449(+)$1	376	75	83	15.8867
ssseeeee	chr11:94231566-94231932(+)$1	366	343	351	20.1320
=====:::	chr17:1326172-1326476(-)$1	304	261	269	15.6037
^^^^^^^^	chr6:89872015-89872500(+)$1	485	208	216	20.1320
fffffmmm	chr4:100869447-100869780(-)$1	333	53	61	16.2641
rrrrrrrr	chr17:36922537-36922858(-)$1	321	194	202	15.7924
ggggggg:	chr16:4930727-4931077(+)$1	350	266	274	15.9811
oooooodd	chr7:4807366-4807657(+)$1	291	32	40	16.1698
HHHHHHHH	chr14:100744157-100744530(+)$1	373	149	157	20.1320
::::::::	chr15:69071835-69072223(-)$1	388	19	27	16.1698
E______D	chr19:2430491-2430899(-)$1	408	382	390	20.1320
dd!!aooo	chr5:148730758-148731094(+)$1	336	135	143	15.6037
========	chr3:120320991-120321222(+)$1	231	44	52	16.1698
cc"""fff	chr10:124924462-124924762(+)$1	300	26	34	20.1320
:::::ccc	chr5:108670558-108670872(-)$1	314	181	189	20.1320
h22eeeee	chr12:50158409-50158831(+)$1	422	48	56	16.1698
eeeppppp	chr6:87972019-87972286(+)$1	267	57	65	15.8867
fffmmmmf	chr9:80943890-80944209(+)$1	319	236	244	15.7924
FFFFFFff	chr8:48973575-48973873(+)$1	298	10	18	16.0754
I:::::ee	chr1:22418894-22419357(+)$1	463	366	374	15.6037
bggggggg	chr1:193054206-193054480(+)$1	274	16	24	15.5094
]ffffff:	chr1:28607725-28608174(+)$1	449	158	166	15.7924
DDDMMMMJ	chr12:123892338-123892582(+)$1	244	25	33	15.9811
>>>>>>>>	chr19:994287-994620(+)$1	333	241	249	15.9811
eepppppp	chr5:157214297-157214561(-)$1	264	118	126	16.1698
555ggggg	chr1:234741701-234741994(-)$1	293	92	100	15.9811
EEffffff	chr17:45760214-45760531(+)$1	317	83	91	16.2641
oooooodd	chr1:234742689-234742983(-)$1	294	233	241	16.0754
444iiiii	chr12:98992199-98992581(+)$1	382	319	327	15.5094
::::eeee	chr7:6442184-6442476(+)$1	292	16	24	15.6037
ffvvvvvv	chr2:30866435-30866726(+)$1	291	161	169	16.1698
mmmfffff	chr10:60154980-60155292(+)$1	312	141	149	20.1320
d::::::I	chr12:31944457-31944694(-)$1	237	66	74	16.1698

#DB
))))))).	chr1:162498337-162498600(+)$1	1	220	228	15.7924
)..)))).	chr18:19208977-19209476(+)$1	1	162	170	15.6037
)))).)).	chrX:77082163-77082440(-)$1	1	63	71	15.6037
........	chr3:14239555-14239939(+)$1	1	375	383	20.1320
........	chr1:25170622-25170865(+)$1	1	1	9	16.1698
))((((((	chr18:47014757-47015036(-)$1	1	247	255	16.2641
))))....	chr6:87971960-87972218(+)$1	1	22	30	15.9811
.....)))	chr19:30500095-30500349(+)$1	1	224	232	16.2641
((((((((	chr2:278121-278376(+)$1	1	177	185	20.1320
(....(((	chr13:27262168-27262571(+)$1	1	115	123	15.8867
......))	chr10:126086103-126086349(-)$1	1	151	159	15.9811
....((((	chr7:44921828-44922237(-)$1	1	247	255	20.1320
))))))))	chr1:24292871-24293135(-)$1	1	238	246	16.1698
........	chr7:26231607-26232058(-)$1	1	70	78	20.1320
.(((((.(	chr19:10795822-10796249(+)$1	1	89	97	16.1698
.......(	chr19:47567953-47568280(-)$1	1	295	303	20.1320
..))...)	chr1:68944871-68945103(-)$1	1	91	99	15.5094
))))))))	chr17:37008784-37009085(-)$1	1	69	77	16.2641
(.((....	chr14:74178634-74178940(-)$1	1	96	104	15.9811
..(((((.	chrX:38665137-38665406(+)$1	1	117	125	15.6037
.....((.	chr19:39889073-39889449(+)$1	1	75	83	15.8867
...)))))	chr11:94231566-94231932(+)$1	1	343	351	20.1320
)))))...	chr17:1326172-1326476(-)$1	1	261	269	15.6037
........	chr6:89872015-89872500(+)$1	1	208	216	20.1320
(((((...	chr4:100869447-100869780(-)$1	1	53	61	16.2641
........	chr17:36922537-36922858(-)$1	1	194	202	15.7924
))))))).	chr16:4930727-4931077(+)$1	1	266	274	15.9811
......))	chr7:4807366-4807657(+)$1	1	32	40	16.1698
((((((((	chr14:100744157-100744530(+)$1	1	149	157	20.1320
........	chr15:69071835-69072223(-)$1	1	19	27	16.1698
)......)	chr19:2430491-2430899(-)$1	1	382	390	20.1320
((..(...	chr5:148730758-148731094(+)$1	1	135	143	15.6037
((((((((	chr3:120320991-120321222(+)$1	1	44	52	16.1698
((...(((	chr10:124924462-124924762(+)$1	1	26	34	20.1320
.....(((	chr5:108670558-108670872(-)$1	1	181	189	20.1320
)..)))))	chr12:50158409-50158831(+)$1	1	48	56	16.1698
(((.....	chr6:87972019-87972286(+)$1	1	57	65	15.8867
(((....)	chr9:80943890-80944209(+)$1	1	236	244	15.7924
((((((((	chr8:48973575-48973873(+)$1	1	10	18	16.0754
).....((	chr1:22418894-22419357(+)$1	1	366	374	15.6037
))))))))	chr1:193054206-193054480(+)$1	1	16	24	15.5094
.)))))).	chr1:28607725-28608174(+)$1	1	158	166	15.7924
(((....(	chr12:123892338-123892582(+)$1	1	25	33	15.9811
........	chr19:994287-994620(+)$1	1	241	249	15.9811
((......	chr5:157214297-157214561(-)$1	1	118	126	16.1698
...)))))	chr1:234741701-234741994(-)$1	1	92	100	15.9811
))((((((	chr17:45760214-45760531(+)$1	1	83	91	16.2641
......))	chr1:234742689-234742983(-)$1	1	233	241	16.0754
...)))))	chr12:98992199-98992581(+)$1	1	319	327	15.5094
....((((	chr7:6442184-6442476(+)$1	1	16	24	15.6037
((......	chr2:30866435-30866726(+)$1	1	161	169	16.1698
...)))))	chr10:60154980-60155292(+)$1	1	141	149	20.1320
)......(	chr12:31944457-31944694(-)$1	1	66	74	16.1698

#PSSM
U : 0.84	A : 0.09	G : 0.03	u : 0.01	
U : 0.86	G : 0.05	A : 0.03	u : 0.01	C : 0.01	
U : 0.92	C : 0.03	u : 0.01	A : 0.01	
U : 0.84	C : 0.07	G : 0.03	u : 0.01	A : 0.01	
U : 0.92	G : 0.03	u : 0.01	C : 0.01	
U : 0.92	G : 0.03	u : 0.01	C : 0.01	
U : 0.90	G : 0.05	u : 0.01	C : 0.01	
A : 0.84	G : 0.05	C : 0.05	U : 0.03	

#score	895.2075471698108
#seq	53
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_UTR_m2_run1.nuc.txt

#NT
AAAUU	chr22:40724644-40724869(+)$1	225	186	191	15.0000
AAAUU	chrX:131510473-131510707(-)$1	234	25	30	15.0000
AAAUU	chr1:82457506-82457734(+)$1	228	175	180	15.0000
aaauu	chr7:150070975-150071205(+)$1	230	0	5	15.0000
AAAUU	chr11:105879927-105880152(-)$1	225	173	178	15.0000
AAAUU	chr1:115250045-115250300(-)$1	255	44	49	15.0000
AAAUU	chr7:65423043-65423267(+)$1	224	170	175	15.0000
AAAUU	chr10:74646652-74646896(+)$1	244	83	88	15.0000
AAAUU	chr14:62214166-62214393(+)$1	227	24	29	15.0000
aaauu	chr2:196998508-196998745(-)$1	237	157	162	15.0000
AAAUU	chr1:86118796-86119023(-)$1	227	188	193	15.0000
AAAUU	chr5:133291583-133291827(-)$1	244	51	56	15.0000
AAAUU	chrX:46740627-46740851(+)$1	224	12	17	15.0000
AAAUU	chr7:44921844-44922079(-)$1	235	110	115	15.0000
AAAUU	chr13:36877997-36878224(-)$1	227	93	98	15.0000
AAAUU	chr2:110374594-110374817(+)$1	223	23	28	15.0000
AAAUU	chrX:133561040-133561274(+)$1	234	27	32	15.0000
AAAUU	chr5:114949477-114949697(-)$1	220	109	114	15.0000
AAAUU	chr5:162871334-162871564(+)$1	230	37	42	15.0000
AAAUU	chr20:57608560-57608785(-)$1	225	117	122	15.0000
AAAUU	chr3:196076940-196077164(-)$1	224	10	15	15.0000
AAAUU	chr10:60156970-60157191(+)$1	221	85	90	15.0000
AAAUU	chr1:162493192-162493425(+)$1	233	29	34	15.0000
AAAUU	chr6:90345369-90345592(-)$1	223	118	123	15.0000
AAAUU	chr8:81433791-81434040(+)$1	249	159	164	15.0000
AAAUU	chr18:29205174-29205401(-)$1	227	93	98	15.0000
AAAUU	chr5:145667329-145667555(+)$1	226	126	131	15.0000
AAAUU	chr19:37001767-37001998(-)$1	231	185	190	15.0000
AAAUU	chr6:42175729-42175959(-)$1	230	191	196	15.0000
AAAUU	chr19:44979905-44980133(-)$1	228	45	50	15.0000
AAAUU	chr1:23634377-23634606(-)$1	229	58	63	15.0000
AAAUU	chr12:22841079-22841309(+)$1	230	18	23	15.0000
AAAUU	chrX:73809982-73810203(-)$1	221	130	135	15.0000
AAAUU	chr11:33162526-33162765(-)$1	239	180	185	15.0000
aaauu	chr5:71503255-71503491(+)$1	236	65	70	15.0000
AAAUU	chr6:71298392-71298619(+)$1	227	196	201	15.0000
AAAUU	chr5:167979046-167979271(-)$1	225	5	10	15.0000
AAAUU	chr9:135567643-135567873(+)$1	230	1	6	15.0000
AAAUU	chr12:26223366-26223601(+)$1	235	52	57	15.0000
AAAUU	chr10:27475414-27475639(+)$1	225	56	61	15.0000
AAAUU	chr16:20808847-20809088(-)$1	241	6	11	15.0000
AAAUU	chr13:100616774-100617005(-)$1	231	221	226	15.0000
AAAUU	chr10:93040990-93041214(+)$1	224	130	135	15.0000
AAAUU	chr5:64017565-64017801(-)$1	236	128	133	15.0000
AAAUU	chr10:96370139-96370365(+)$1	226	99	104	15.0000
AAAUU	chr14:55514823-55515078(+)$1	255	213	218	15.0000
AAAUU	chr4:39781595-39781818(+)$1	223	55	60	15.0000
AAAUU	chr12:72182236-72182467(+)$1	231	88	93	15.0000
AAAUU	chr21:43410058-43410282(-)$1	224	78	83	15.0000
AAAUU	chr7:128144068-128144297(+)$1	229	26	31	15.0000
AAAUU	chr11:58921790-58922019(+)$1	229	44	49	15.0000
AAAUU	chr10:86277598-86277829(+)$1	231	147	152	15.0000
AAAUU	chr12:42479640-42479863(-)$1	223	99	104	15.0000
AAAUU	chr10:28872280-28872504(+)$1	224	69	74	15.0000
AAAUU	chr7:32625285-32625511(+)$1	226	2	7	15.0000
AAAUU	chr10:93623161-93623385(+)$1	224	79	84	15.0000

#otherMatches

#Struct PSSM
dddxx	chr11:130097731-130097958(-)$1	227	119	124	15.0000
:::::	chr22:40724644-40724869(+)$1	225	186	191	15.0000
EEEEE	chrX:131510473-131510707(-)$1	234	25	30	15.0000
^^^^^	chr1:82457506-82457734(+)$1	228	175	180	15.0000
:::EE	chr7:150070975-150071205(+)$1	230	0	5	15.0000
:::::	chr11:105879927-105880152(-)$1	225	173	178	15.0000
ddddd	chr1:115250045-115250300(-)$1	255	44	49	15.0000
eeeff	chr7:65423043-65423267(+)$1	224	170	175	15.0000
qqqqi	chr10:74646652-74646896(+)$1	244	83	88	15.0000
gggvv	chr14:62214166-62214393(+)$1	227	24	29	15.0000
ggg]b	chr2:196998508-196998745(-)$1	237	157	162	15.0000
ee333	chr1:86118796-86119023(-)$1	227	188	193	15.0000
ttttt	chr5:133291583-133291827(-)$1	244	51	56	15.0000
G::::	chrX:46740627-46740851(+)$1	224	12	17	15.0000
ggg44	chr7:44921844-44922079(-)$1	235	110	115	15.0000
qqqqq	chr13:36877997-36878224(-)$1	227	93	98	15.0000
dccc[	chr2:110374594-110374817(+)$1	223	23	28	15.0000
ggggg	chrX:133561040-133561274(+)$1	234	27	32	15.0000
:::::	chr5:114949477-114949697(-)$1	220	109	114	15.0000
mmccc	chr5:162871334-162871564(+)$1	230	37	42	15.0000
CCCKK	chr20:57608560-57608785(-)$1	225	117	122	15.0000
::GGG	chr3:196076940-196077164(-)$1	224	10	15	15.0000
]cccH	chr10:60156970-60157191(+)$1	221	85	90	15.0000
GKKFF	chr1:162493192-162493425(+)$1	233	29	34	15.0000
:::bb	chr6:90345369-90345592(-)$1	223	118	123	15.0000
===vv	chr8:81433791-81434040(+)$1	249	159	164	15.0000
c$$$$	chr18:29205174-29205401(-)$1	227	93	98	15.0000
b::::	chr5:145667329-145667555(+)$1	226	126	131	15.0000
dd:::	chr19:37001767-37001998(-)$1	231	185	190	15.0000
mmeee	chr6:42175729-42175959(-)$1	230	191	196	15.0000
bb$$$	chr19:44979905-44980133(-)$1	228	45	50	15.0000
wwwww	chr1:23634377-23634606(-)$1	229	58	63	15.0000
DDLLL	chr12:22841079-22841309(+)$1	230	18	23	15.0000
d::::	chrX:73809982-73810203(-)$1	221	130	135	15.0000
ttttt	chr11:33162526-33162765(-)$1	239	180	185	15.0000
'''gg	chr5:71503255-71503491(+)$1	236	65	70	15.0000
dd:ee	chr6:71298392-71298619(+)$1	227	196	201	15.0000
ggggg	chr5:167979046-167979271(-)$1	225	5	10	15.0000
:::::	chr9:135567643-135567873(+)$1	230	1	6	15.0000
dllld	chr12:26223366-26223601(+)$1	235	52	57	15.0000
TTTTT	chr10:27475414-27475639(+)$1	225	56	61	15.0000
::ddd	chr16:20808847-20809088(-)$1	241	6	11	15.0000
a22dd	chr13:100616774-100617005(-)$1	231	221	226	15.0000
uuuuu	chr10:93040990-93041214(+)$1	224	130	135	15.0000
~~~~E	chr5:64017565-64017801(-)$1	236	128	133	15.0000
^^^^^	chr10:96370139-96370365(+)$1	226	99	104	15.0000
00000	chr14:55514823-55515078(+)$1	255	213	218	15.0000
:::::	chr4:39781595-39781818(+)$1	223	55	60	15.0000
ddmmm	chr12:72182236-72182467(+)$1	231	88	93	15.0000
"""ff	chr21:43410058-43410282(-)$1	224	78	83	15.0000
fflll	chr7:128144068-128144297(+)$1	229	26	31	15.0000
c"""c	chr11:58921790-58922019(+)$1	229	44	49	15.0000
ccc!!	chr10:86277598-86277829(+)$1	231	147	152	15.0000
rrrri	chr12:42479640-42479863(-)$1	223	99	104	15.0000
FF:::	chr10:28872280-28872504(+)$1	224	69	74	15.0000
:::::	chr7:32625285-32625511(+)$1	226	2	7	15.0000
:::::	chr10:93623161-93623385(+)$1	224	79	84	15.0000

#DB
(((..	chr11:130097731-130097958(-)$1	1	119	124	15.0000
.....	chr22:40724644-40724869(+)$1	1	186	191	15.0000
(((((	chrX:131510473-131510707(-)$1	1	25	30	15.0000
.....	chr1:82457506-82457734(+)$1	1	175	180	15.0000
...((	chr7:150070975-150071205(+)$1	1	0	5	15.0000
.....	chr11:105879927-105880152(-)$1	1	173	178	15.0000
(((((	chr1:115250045-115250300(-)$1	1	44	49	15.0000
(((((	chr7:65423043-65423267(+)$1	1	170	175	15.0000
....)	chr10:74646652-74646896(+)$1	1	83	88	15.0000
(((..	chr14:62214166-62214393(+)$1	1	24	29	15.0000
))).)	chr2:196998508-196998745(-)$1	1	157	162	15.0000
))...	chr1:86118796-86119023(-)$1	1	188	193	15.0000
.....	chr5:133291583-133291827(-)$1	1	51	56	15.0000
(....	chrX:46740627-46740851(+)$1	1	12	17	15.0000
)))..	chr7:44921844-44922079(-)$1	1	110	115	15.0000
.....	chr13:36877997-36878224(-)$1	1	93	98	15.0000
((((.	chr2:110374594-110374817(+)$1	1	23	28	15.0000
(((((	chrX:133561040-133561274(+)$1	1	27	32	15.0000
.....	chr5:114949477-114949697(-)$1	1	109	114	15.0000
..)))	chr5:162871334-162871564(+)$1	1	37	42	15.0000
(((..	chr20:57608560-57608785(-)$1	1	117	122	15.0000
..(((	chr3:196076940-196077164(-)$1	1	10	15	15.0000
.))))	chr10:60156970-60157191(+)$1	1	85	90	15.0000
(..((	chr1:162493192-162493425(+)$1	1	29	34	15.0000
...((	chr6:90345369-90345592(-)$1	1	118	123	15.0000
(((..	chr8:81433791-81434040(+)$1	1	159	164	15.0000
(....	chr18:29205174-29205401(-)$1	1	93	98	15.0000
)....	chr5:145667329-145667555(+)$1	1	126	131	15.0000
))...	chr19:37001767-37001998(-)$1	1	185	190	15.0000
..)))	chr6:42175729-42175959(-)$1	1	191	196	15.0000
((...	chr19:44979905-44980133(-)$1	1	45	50	15.0000
.....	chr1:23634377-23634606(-)$1	1	58	63	15.0000
((...	chr12:22841079-22841309(+)$1	1	18	23	15.0000
)....	chrX:73809982-73810203(-)$1	1	130	135	15.0000
.....	chr11:33162526-33162765(-)$1	1	180	185	15.0000
...((	chr5:71503255-71503491(+)$1	1	65	70	15.0000
)).((	chr6:71298392-71298619(+)$1	1	196	201	15.0000
(((((	chr5:167979046-167979271(-)$1	1	5	10	15.0000
.....	chr9:135567643-135567873(+)$1	1	1	6	15.0000
(...)	chr12:26223366-26223601(+)$1	1	52	57	15.0000
.....	chr10:27475414-27475639(+)$1	1	56	61	15.0000
..(((	chr16:20808847-20809088(-)$1	1	6	11	15.0000
)..))	chr13:100616774-100617005(-)$1	1	221	226	15.0000
.....	chr10:93040990-93041214(+)$1	1	130	135	15.0000
....)	chr5:64017565-64017801(-)$1	1	128	133	15.0000
.....	chr10:96370139-96370365(+)$1	1	99	104	15.0000
.....	chr14:55514823-55515078(+)$1	1	213	218	15.0000
.....	chr4:39781595-39781818(+)$1	1	55	60	15.0000
((...	chr12:72182236-72182467(+)$1	1	88	93	15.0000
...((	chr21:43410058-43410282(-)$1	1	78	83	15.0000
((...	chr7:128144068-128144297(+)$1	1	26	31	15.0000
(...(	chr11:58921790-58922019(+)$1	1	44	49	15.0000
(((..	chr10:86277598-86277829(+)$1	1	147	152	15.0000
....)	chr12:42479640-42479863(-)$1	1	99	104	15.0000
((...	chr10:28872280-28872504(+)$1	1	69	74	15.0000
.....	chr7:32625285-32625511(+)$1	1	2	7	15.0000
.....	chr10:93623161-93623385(+)$1	1	79	84	15.0000

#PSSM
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	

#score	855.0000000000005
#seq	57
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m2_run2.nuc.txt

#NT
GGCUG	chr7:75695505-75695736(+)$1	231	9	14	15.0000
GGCUG	chr19:5695479-5695705(+)$1	226	14	19	15.0000
GGCUG	chr10:116434147-116434370(-)$1	223	180	185	15.0000
GGCUG	chr16:88678258-88678485(+)$1	227	183	188	15.0000
GGCUG	chr19:4065525-4065745(+)$1	220	51	56	15.0000
GGCUG	chr10:125664535-125664768(-)$1	233	19	24	15.0000
GGCUG	chr5:14405447-14405666(+)$1	219	42	47	15.0000
ggcug	chr1:210987996-210988217(+)$1	221	21	26	15.0000
GGCUG	chr11:62621038-62621268(-)$1	230	94	99	15.0000
GGCUG	chr11:66372897-66373117(+)$1	220	191	196	15.0000
ggcug	chr5:149112292-149112513(+)$1	221	35	40	15.0000
GGCUG	chr16:81592085-81592305(-)$1	220	41	46	15.0000
GGCUG	chr1:204210238-204210460(-)$1	222	58	63	15.0000
GGCUG	chr1:155532786-155533007(+)$1	221	204	209	15.0000
GGCUG	chr19:18257566-18257798(-)$1	232	75	80	15.0000
GGCUG	chr1:32197575-32197810(-)$1	235	188	193	15.0000
GGCUG	chr1:162670288-162670516(+)$1	228	131	136	15.0000
GGCUG	chr13:100634817-100635043(+)$1	226	45	50	15.0000
GGCUG	chr17:62206926-62207155(-)$1	229	68	73	15.0000
GGCUG	chr6:43591613-43591838(-)$1	225	195	200	15.0000
GGCUG	chr11:130297598-130297819(+)$1	221	143	148	15.0000
GGCUG	chr1:1425332-1425553(+)$1	221	41	46	15.0000
GGCUG	chr4:6359161-6359383(-)$1	222	50	55	15.0000
GGCUG	chr1:156209272-156209497(+)$1	225	209	214	15.0000
GGCUG	chr10:70091794-70092049(+)$1	255	206	211	15.0000
GGCUG	chr19:2110192-2110412(-)$1	220	70	75	15.0000
ggcug	chr14:50320244-50320725(-)$1	481	136	141	15.0000
GGCUG	chr7:26241396-26241620(+)$1	224	210	215	15.0000
GGCUG	chr12:69112961-69113185(+)$1	224	213	218	15.0000
GGCUG	chr17:8159477-8159702(+)$1	225	10	15	15.0000
GGCUG	chr7:72286943-72287166(-)$1	223	65	70	15.0000
ggcug	chr17:18967174-18967407(-)$1	233	93	98	15.0000
GGCUG	chr17:1617108-1617329(-)$1	221	48	53	15.0000
GGCUG	chr19:48287537-48287757(+)$1	220	105	110	15.0000
GGCUG	chr19:2338166-2338386(+)$1	220	84	89	15.0000
ggcug	chr9:127970605-127970829(+)$1	224	90	95	15.0000
GGCUG	chr5:138941609-138941836(+)$1	227	17	22	15.0000
ggcug	chr1:168218706-168218930(+)$1	224	184	189	15.0000
GGCUG	chr19:10671789-10672015(-)$1	226	218	223	15.0000
ggcug	chr22:32122085-32122336(-)$1	251	99	104	15.0000
GGCUG	chrX:129139083-129139310(+)$1	227	117	122	15.0000
ggcug	chrX:117048173-117048408(-)$1	235	100	105	15.0000
GGCUG	chr20:62331482-62331711(+)$1	229	81	86	15.0000
GGCUG	chr1:226026380-226026608(+)$1	228	54	59	15.0000
GGCUg	chr4:109088935-109089155(-)$1	220	64	69	15.0000
ggcug	chr2:204389888-204390124(-)$1	236	133	138	15.0000
GGCUG	chr12:65193491-65193716(+)$1	225	103	108	15.0000
ggcug	chr7:65422378-65422602(+)$1	224	159	164	15.0000
GGCUG	chrX:154003040-154003264(+)$1	224	198	203	15.0000
GGCUG	chr9:137641822-137642043(+)$1	221	22	27	15.0000
GGCUG	chr3:171011025-171011248(-)$1	223	103	108	15.0000
GGCUG	chr1:19557250-19557489(+)$1	239	189	194	15.0000
GGCUG	chr12:49048101-49048401(-)$1	300	133	138	15.0000
GGCUG	chr14:21152133-21152360(+)$1	227	198	203	15.0000
GGCUG	chr14:33507781-33508003(+)$1	222	129	134	15.0000

#otherMatches

#Struct PSSM
bbbb[	chr16:30566767-30567001(-)$1	234	37	42	15.0000
DDDDG	chr7:75695505-75695736(+)$1	231	9	14	15.0000
Dffff	chr19:5695479-5695705(+)$1	226	14	19	15.0000
ggggg	chr10:116434147-116434370(-)$1	223	180	185	15.0000
}CCC?	chr16:88678258-88678485(+)$1	227	183	188	15.0000
ggggg	chr19:4065525-4065745(+)$1	220	51	56	15.0000
DDDDF	chr10:125664535-125664768(-)$1	233	19	24	15.0000
hhh##	chr5:14405447-14405666(+)$1	219	42	47	15.0000
EEKKC	chr1:210987996-210988217(+)$1	221	21	26	15.0000
dddrr	chr11:62621038-62621268(-)$1	230	94	99	15.0000
GGYYF	chr11:66372897-66373117(+)$1	220	191	196	15.0000
eeeee	chr5:149112292-149112513(+)$1	221	35	40	15.0000
ccccc	chr16:81592085-81592305(-)$1	220	41	46	15.0000
ddd]a	chr1:204210238-204210460(-)$1	222	58	63	15.0000
}EEEE	chr1:155532786-155533007(+)$1	221	204	209	15.0000
HHHHH	chr19:18257566-18257798(-)$1	232	75	80	15.0000
ccc::	chr1:32197575-32197810(-)$1	235	188	193	15.0000
iiiii	chr1:162670288-162670516(+)$1	228	131	136	15.0000
fff[f	chr13:100634817-100635043(+)$1	226	45	50	15.0000
ee!!c	chr17:62206926-62207155(-)$1	229	68	73	15.0000
DDDYY	chr6:43591613-43591838(-)$1	225	195	200	15.0000
bb22=	chr11:130297598-130297819(+)$1	221	143	148	15.0000
oooee	chr1:1425332-1425553(+)$1	221	41	46	15.0000
IIIII	chr4:6359161-6359383(-)$1	222	50	55	15.0000
eeeee	chr1:156209272-156209497(+)$1	225	209	214	15.0000
DCCC}	chr10:70091794-70092049(+)$1	255	206	211	15.0000
hhhhh	chr19:2110192-2110412(-)$1	220	70	75	15.0000
gggg:	chr14:50320244-50320725(-)$1	481	136	141	15.0000
EEE~~	chr7:26241396-26241620(+)$1	224	210	215	15.0000
FFFFF	chr12:69112961-69113185(+)$1	224	213	218	15.0000
hhhhh	chr17:8159477-8159702(+)$1	225	10	15	15.0000
eeeed	chr7:72286943-72287166(-)$1	223	65	70	15.0000
ooooe	chr17:18967174-18967407(-)$1	233	93	98	15.0000
ccc[c	chr17:1617108-1617329(-)$1	221	48	53	15.0000
c]fff	chr19:48287537-48287757(+)$1	220	105	110	15.0000
!!fff	chr19:2338166-2338386(+)$1	220	84	89	15.0000
DDD{D	chr9:127970605-127970829(+)$1	224	90	95	15.0000
tcccc	chr5:138941609-138941836(+)$1	227	17	22	15.0000
gggg2	chr1:168218706-168218930(+)$1	224	184	189	15.0000
22bb:	chr19:10671789-10672015(-)$1	226	218	223	15.0000
ccca[	chr22:32122085-32122336(-)$1	251	99	104	15.0000
Beeee	chrX:129139083-129139310(+)$1	227	117	122	15.0000
HHHHH	chrX:117048173-117048408(-)$1	235	100	105	15.0000
bblll	chr20:62331482-62331711(+)$1	229	81	86	15.0000
cc]ee	chr1:226026380-226026608(+)$1	228	54	59	15.0000
ddd22	chr4:109088935-109089155(-)$1	220	64	69	15.0000
d!!gg	chr2:204389888-204390124(-)$1	236	133	138	15.0000
:::::	chr12:65193491-65193716(+)$1	225	103	108	15.0000
ff###	chr7:65422378-65422602(+)$1	224	159	164	15.0000
EEECC	chrX:154003040-154003264(+)$1	224	198	203	15.0000
ccc[d	chr9:137641822-137642043(+)$1	221	22	27	15.0000
99999	chr3:171011025-171011248(-)$1	223	103	108	15.0000
oooee	chr1:19557250-19557489(+)$1	239	189	194	15.0000
=====	chr12:49048101-49048401(-)$1	300	133	138	15.0000
edddd	chr14:21152133-21152360(+)$1	227	198	203	15.0000
wwbb]	chr14:33507781-33508003(+)$1	222	129	134	15.0000

#DB
((((.	chr16:30566767-30567001(-)$1	1	37	42	15.0000
(((((	chr7:75695505-75695736(+)$1	1	9	14	15.0000
(((((	chr19:5695479-5695705(+)$1	1	14	19	15.0000
(((((	chr10:116434147-116434370(-)$1	1	180	185	15.0000
.))).	chr16:88678258-88678485(+)$1	1	183	188	15.0000
(((((	chr19:4065525-4065745(+)$1	1	51	56	15.0000
(((((	chr10:125664535-125664768(-)$1	1	19	24	15.0000
(((..	chr5:14405447-14405666(+)$1	1	42	47	15.0000
((..(	chr1:210987996-210988217(+)$1	1	21	26	15.0000
(((..	chr11:62621038-62621268(-)$1	1	94	99	15.0000
))..)	chr11:66372897-66373117(+)$1	1	191	196	15.0000
)))))	chr5:149112292-149112513(+)$1	1	35	40	15.0000
(((((	chr16:81592085-81592305(-)$1	1	41	46	15.0000
))).)	chr1:204210238-204210460(-)$1	1	58	63	15.0000
.))))	chr1:155532786-155533007(+)$1	1	204	209	15.0000
)))))	chr19:18257566-18257798(-)$1	1	75	80	15.0000
)))..	chr1:32197575-32197810(-)$1	1	188	193	15.0000
)))))	chr1:162670288-162670516(+)$1	1	131	136	15.0000
(((.(	chr13:100634817-100635043(+)$1	1	45	50	15.0000
((..(	chr17:62206926-62207155(-)$1	1	68	73	15.0000
)))..	chr6:43591613-43591838(-)$1	1	195	200	15.0000
))..)	chr11:130297598-130297819(+)$1	1	143	148	15.0000
...))	chr1:1425332-1425553(+)$1	1	41	46	15.0000
(((((	chr4:6359161-6359383(-)$1	1	50	55	15.0000
)))))	chr1:156209272-156209497(+)$1	1	209	214	15.0000
)))).	chr10:70091794-70092049(+)$1	1	206	211	15.0000
(((((	chr19:2110192-2110412(-)$1	1	70	75	15.0000
)))).	chr14:50320244-50320725(-)$1	1	136	141	15.0000
)))..	chr7:26241396-26241620(+)$1	1	210	215	15.0000
)))))	chr12:69112961-69113185(+)$1	1	213	218	15.0000
(((((	chr17:8159477-8159702(+)$1	1	10	15	15.0000
))))(	chr7:72286943-72287166(-)$1	1	65	70	15.0000
....)	chr17:18967174-18967407(-)$1	1	93	98	15.0000
(((.(	chr17:1617108-1617329(-)$1	1	48	53	15.0000
).)))	chr19:48287537-48287757(+)$1	1	105	110	15.0000
..(((	chr19:2338166-2338386(+)$1	1	84	89	15.0000
(((.(	chr9:127970605-127970829(+)$1	1	90	95	15.0000
.)))(	chr5:138941609-138941836(+)$1	1	17	22	15.0000
)))).	chr1:168218706-168218930(+)$1	1	184	189	15.0000
..)).	chr19:10671789-10672015(-)$1	1	218	223	15.0000
)))(.	chr22:32122085-32122336(-)$1	1	99	104	15.0000
(((((	chrX:129139083-129139310(+)$1	1	117	122	15.0000
(((((	chrX:117048173-117048408(-)$1	1	100	105	15.0000
((...	chr20:62331482-62331711(+)$1	1	81	86	15.0000
)).))	chr1:226026380-226026608(+)$1	1	54	59	15.0000
)))..	chr4:109088935-109089155(-)$1	1	64	69	15.0000
(..((	chr2:204389888-204390124(-)$1	1	133	138	15.0000
.....	chr12:65193491-65193716(+)$1	1	103	108	15.0000
((...	chr7:65422378-65422602(+)$1	1	159	164	15.0000
)))))	chrX:154003040-154003264(+)$1	1	198	203	15.0000
(((.(	chr9:137641822-137642043(+)$1	1	22	27	15.0000
.....	chr3:171011025-171011248(-)$1	1	103	108	15.0000
...))	chr1:19557250-19557489(+)$1	1	189	194	15.0000
)))))	chr12:49048101-49048401(-)$1	1	133	138	15.0000
)((((	chr14:21152133-21152360(+)$1	1	198	203	15.0000
..)).	chr14:33507781-33508003(+)$1	1	129	134	15.0000

#PSSM
G : 0.82	g : 0.17	
G : 0.82	g : 0.17	
C : 0.82	c : 0.17	
U : 0.82	u : 0.17	
G : 0.80	g : 0.19	

#score	840.0000000000001
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m1_run2.nuc.txt

#NT
GGAAGA	chr15:23811248-23811449(+)$1	201	51	57	14.3492
GGAAGU	chr3:142499712-142499913(+)$1	201	44	50	10.2222
AGAAGA	chr2:223488925-223489126(-)$1	201	60	66	11.5714
GGAAGA	chr14:21876853-21877054(-)$1	201	92	98	14.3492
GGAAGG	chr18:20570883-20571084(+)$1	201	66	72	10.0634
UGAAGA	chr12:8290772-8290973(+)$1	201	94	100	11.8095
GGAUGA	chr2:10584632-10584833(-)$1	201	59	65	10.6984
GGAUGA	chr12:54422285-54422486(+)$1	201	18	24	10.6984
GGAAGA	chr2:239164380-239164581(-)$1	201	36	42	14.3492
GGCAGA	chr16:67228549-67228750(+)$1	201	49	55	9.9841
CGAAGA	chr5:137666751-137666952(-)$1	201	75	81	11.0158
UGAAGA	chr20:42893045-42893246(+)$1	201	73	79	11.8095
GGAAGC	chr15:44918487-44918688(-)$1	201	132	138	10.3015
GGAAGA	chr1:35656286-35656487(-)$1	201	34	40	14.3492
UGAAGA	chr1:89237433-89237634(+)$1	201	22	28	11.8095
GGACGA	chr18:77896284-77896485(+)$1	201	107	113	10.3809
GGGAGA	chr19:50105019-50105220(+)$1	201	58	64	10.1428
GGAAGC	chr5:137902272-137902473(-)$1	201	113	119	10.3015
AGAAGA	chr1:19449385-19449586(-)$1	201	175	181	11.5714
GGAAGA	chr15:43653881-43654082(-)$1	201	92	98	14.3492
UGAAGA	chr14:31613342-31613543(-)$1	201	114	120	11.8095
AGAAGA	chr9:136301887-136302088(+)$1	201	68	74	11.5714
GGAGGA	chr13:25067718-25067919(-)$1	201	56	62	10.7777
AGAAGA	chr1:19445976-19446177(-)$1	201	119	125	11.5714
AGAAGA	chr1:54670878-54671079(+)$1	201	14	20	11.5714
GGAAGA	chr15:48633660-48633861(+)$1	201	136	142	14.3492
GGAAGA	chr17:40933021-40933222(+)$1	201	51	57	14.3492
AGAAGA	chr2:128247343-128247544(-)$1	201	80	86	11.5714
GGAAGC	chr17:73489549-73489750(+)$1	201	133	139	10.3015
GGAAGA	chr9:139290081-139290282(-)$1	201	59	65	14.3492
GGAGGA	chr1:23420636-23420837(-)$1	201	172	178	10.7777
UGAAGA	chr2:9727490-9727691(-)$1	201	91	97	11.8095
GGAAGU	chr4:146080587-146080788(-)$1	201	77	83	10.2222
GGAAGA	chr1:150463990-150464191(+)$1	201	8	14	14.3492
GGGAGA	chr19:39395865-39396066(+)$1	201	4	10	10.1428
UGAAGA	chr4:153243946-153244147(-)$1	201	66	72	11.8095
GGAGGA	chrX:53643897-53644098(-)$1	201	141	147	10.7777
AGAAGA	chr1:201970425-201970626(+)$1	201	15	21	11.5714
GGAAGA	chr15:91333931-91334132(+)$1	201	64	70	14.3492
GGCAGA	chr1:220156076-220156277(-)$1	201	126	132	9.9841
GGAAGA	chr2:234761155-234761356(-)$1	201	107	113	14.3492
ggagga	chr19:41292477-41292678(+)$1	201	3	9	10.7777
GGAAGC	chr5:138260230-138260431(+)$1	201	140	146	10.3015
GGAGGA	chr16:419906-420107(-)$1	201	74	80	10.7777
GGAUGA	chr6:100960549-100960750(-)$1	201	18	24	10.6984
GGAAGU	chr6:79735743-79735944(-)$1	201	189	195	10.2222
GGAAGA	chr10:8005938-8006139(+)$1	201	8	14	14.3492
GGAAGA	chr9:98242705-98242906(-)$1	201	84	90	14.3492
GGGAGA	chr10:103901526-103901727(+)$1	201	67	73	10.1428
UGAAGA	chr11:63756049-63756250(+)$1	201	141	147	11.8095
GGAUGA	chr13:25051843-25052044(-)$1	201	48	54	10.6984
GGAAGA	chr10:97387146-97387347(-)$1	201	107	113	14.3492
GGGAGA	chr5:54640302-54640503(+)$1	201	112	118	10.1428
GGAAGA	chr3:52964947-52965148(-)$1	201	155	161	14.3492
UGAAGA	chr2:39053612-39053813(-)$1	201	18	24	11.8095
UGAAGA	chr16:75663255-75663456(-)$1	201	64	70	11.8095
UGAAGA	chr6:34952886-34953087(+)$1	201	24	30	11.8095
GGAAGA	chr12:72017908-72018109(-)$1	201	193	199	14.3492
GGAGGA	chr15:73048638-73048839(-)$1	201	52	58	10.7777
AGAAGA	chrX:131205072-131205273(+)$1	201	76	82	11.5714
UGAAGA	chr5:38962999-38963200(-)$1	201	101	107	11.8095
GGAAGA	chr6:149721653-149721854(+)$1	201	107	113	14.3492

#otherMatches

#Struct PSSM
dd:ggg	chr6:112024041-112024242(-)$1	201	33	39	10.6984
ea22ff	chr15:23811248-23811449(+)$1	201	51	57	14.3492
ffffmm	chr3:142499712-142499913(+)$1	201	44	50	10.2222
dbb]dd	chr2:223488925-223489126(-)$1	201	60	66	11.5714
eCCC}C	chr14:21876853-21877054(-)$1	201	92	98	14.3492
cc]ccc	chr18:20570883-20571084(+)$1	201	66	72	10.0634
cmmmmc	chr12:8290772-8290973(+)$1	201	94	100	11.8095
{DDDD:	chr2:10584632-10584833(-)$1	201	59	65	10.6984
ee[ddd	chr12:54422285-54422486(+)$1	201	18	24	10.6984
CNNNNN	chr2:239164380-239164581(-)$1	201	36	42	14.3492
ii))))	chr16:67228549-67228750(+)$1	201	49	55	9.9841
dd[ddd	chr5:137666751-137666952(-)$1	201	75	81	11.0158
eee[bb	chr20:42893045-42893246(+)$1	201	73	79	11.8095
::::GG	chr15:44918487-44918688(-)$1	201	132	138	10.3015
g[bb!!	chr1:35656286-35656487(-)$1	201	34	40	14.3492
MMMFFF	chr1:89237433-89237634(+)$1	201	22	28	11.8095
ffff!!	chr18:77896284-77896485(+)$1	201	107	113	10.3809
oooooo	chr19:50105019-50105220(+)$1	201	58	64	10.1428
"""ddd	chr5:137902272-137902473(-)$1	201	113	119	10.3015
ZFFFFF	chr1:19449385-19449586(-)$1	201	175	181	11.5714
cEEEEE	chr15:43653881-43654082(-)$1	201	92	98	14.3492
=====3	chr14:31613342-31613543(-)$1	201	114	120	11.8095
e[a[cc	chr9:136301887-136302088(+)$1	201	68	74	11.5714
gg[ccc	chr13:25067718-25067919(-)$1	201	56	62	10.7777
iiiiii	chr1:19445976-19446177(-)$1	201	119	125	11.5714
:eeeee	chr1:54670878-54671079(+)$1	201	14	20	11.5714
^^^^^^	chr15:48633660-48633861(+)$1	201	136	142	14.3492
777777	chr17:40933021-40933222(+)$1	201	51	57	14.3492
JJJJJJ	chr2:128247343-128247544(-)$1	201	80	86	11.5714
a22ccc	chr17:73489549-73489750(+)$1	201	133	139	10.3015
vvvvvv	chr9:139290081-139290282(-)$1	201	59	65	14.3492
gggggv	chr1:23420636-23420837(-)$1	201	172	178	10.7777
[eeeee	chr2:9727490-9727691(-)$1	201	91	97	11.8095
ppppbb	chr4:146080587-146080788(-)$1	201	77	83	10.2222
gggggg	chr1:150463990-150464191(+)$1	201	8	14	14.3492
EEEEEB	chr19:39395865-39396066(+)$1	201	4	10	10.1428
:dddd"	chr4:153243946-153244147(-)$1	201	66	72	11.8095
ddddFF	chrX:53643897-53644098(-)$1	201	141	147	10.7777
dd[ddd	chr1:201970425-201970626(+)$1	201	15	21	11.5714
bb!!ff	chr15:91333931-91334132(+)$1	201	64	70	14.3492
eeeeqq	chr1:220156076-220156277(-)$1	201	126	132	9.9841
xxbb22	chr2:234761155-234761356(-)$1	201	107	113	14.3492
DD{BBO	chr19:41292477-41292678(+)$1	201	3	9	10.7777
dddccc	chr5:138260230-138260431(+)$1	201	140	146	10.3015
FFFFF{	chr16:419906-420107(-)$1	201	74	80	10.7777
{BB{A{	chr6:100960549-100960750(-)$1	201	18	24	10.6984
}FFFFF	chr6:79735743-79735944(-)$1	201	189	195	10.2222
LLLBBM	chr10:8005938-8006139(+)$1	201	8	14	14.3492
CCC}CC	chr9:98242705-98242906(-)$1	201	84	90	14.3492
dddqqq	chr10:103901526-103901727(+)$1	201	67	73	10.1428
ccceee	chr11:63756049-63756250(+)$1	201	141	147	11.8095
IIIIII	chr13:25051843-25052044(-)$1	201	48	54	10.6984
cc6666	chr10:97387146-97387347(-)$1	201	107	113	14.3492
2dddd2	chr5:54640302-54640503(+)$1	201	112	118	10.1428
bb[bb[	chr3:52964947-52965148(-)$1	201	155	161	14.3492
:::::D	chr2:39053612-39053813(-)$1	201	18	24	11.8095
{DDDD:	chr16:75663255-75663456(-)$1	201	64	70	11.8095
bppppp	chr6:34952886-34953087(+)$1	201	24	30	11.8095
\\\\DD	chr12:72017908-72018109(-)$1	201	193	199	14.3492
======	chr15:73048638-73048839(-)$1	201	52	58	10.7777
eeeee2	chrX:131205072-131205273(+)$1	201	76	82	11.5714
iiiiii	chr5:38962999-38963200(-)$1	201	101	107	11.8095
::::::	chr6:149721653-149721854(+)$1	201	107	113	14.3492

#DB
)).(((	chr6:112024041-112024242(-)$1	1	33	39	10.6984
))..))	chr15:23811248-23811449(+)$1	1	51	57	14.3492
((((..	chr3:142499712-142499913(+)$1	1	44	50	10.2222
))).))	chr2:223488925-223489126(-)$1	1	60	66	11.5714
)))).)	chr14:21876853-21877054(-)$1	1	92	98	14.3492
)).)))	chr18:20570883-20571084(+)$1	1	66	72	10.0634
(....)	chr12:8290772-8290973(+)$1	1	94	100	11.8095
.((((.	chr2:10584632-10584833(-)$1	1	59	65	10.6984
((.(((	chr12:54422285-54422486(+)$1	1	18	24	10.6984
(.....	chr2:239164380-239164581(-)$1	1	36	42	14.3492
((....	chr16:67228549-67228750(+)$1	1	49	55	9.9841
((.(((	chr5:137666751-137666952(-)$1	1	75	81	11.0158
(((.((	chr20:42893045-42893246(+)$1	1	73	79	11.8095
....))	chr15:44918487-44918688(-)$1	1	132	138	10.3015
(.((..	chr1:35656286-35656487(-)$1	1	34	40	14.3492
...(((	chr1:89237433-89237634(+)$1	1	22	28	11.8095
((((..	chr18:77896284-77896485(+)$1	1	107	113	10.3809
......	chr19:50105019-50105220(+)$1	1	58	64	10.1428
...(((	chr5:137902272-137902473(-)$1	1	113	119	10.3015
.)))))	chr1:19449385-19449586(-)$1	1	175	181	11.5714
))))))	chr15:43653881-43654082(-)$1	1	92	98	14.3492
))))).	chr14:31613342-31613543(-)$1	1	114	120	11.8095
(.(.((	chr9:136301887-136302088(+)$1	1	68	74	11.5714
((.(((	chr13:25067718-25067919(-)$1	1	56	62	10.7777
((((((	chr1:19445976-19446177(-)$1	1	119	125	11.5714
.(((((	chr1:54670878-54671079(+)$1	1	14	20	11.5714
......	chr15:48633660-48633861(+)$1	1	136	142	14.3492
......	chr17:40933021-40933222(+)$1	1	51	57	14.3492
))))))	chr2:128247343-128247544(-)$1	1	80	86	11.5714
)..)))	chr17:73489549-73489750(+)$1	1	133	139	10.3015
......	chr9:139290081-139290282(-)$1	1	59	65	14.3492
(((((.	chr1:23420636-23420837(-)$1	1	172	178	10.7777
.(((((	chr2:9727490-9727691(-)$1	1	91	97	11.8095
....))	chr4:146080587-146080788(-)$1	1	77	83	10.2222
((((((	chr1:150463990-150464191(+)$1	1	8	14	14.3492
((((((	chr19:39395865-39396066(+)$1	1	4	10	10.1428
.((((.	chr4:153243946-153244147(-)$1	1	66	72	11.8095
))))))	chrX:53643897-53644098(-)$1	1	141	147	10.7777
((.(((	chr1:201970425-201970626(+)$1	1	15	21	11.5714
((..((	chr15:91333931-91334132(+)$1	1	64	70	14.3492
((((..	chr1:220156076-220156277(-)$1	1	126	132	9.9841
..))..	chr2:234761155-234761356(-)$1	1	107	113	14.3492
((.((.	chr19:41292477-41292678(+)$1	1	3	9	10.7777
((((((	chr5:138260230-138260431(+)$1	1	140	146	10.3015
(((((.	chr16:419906-420107(-)$1	1	74	80	10.7777
.((.(.	chr6:100960549-100960750(-)$1	1	18	24	10.6984
.)))))	chr6:79735743-79735944(-)$1	1	189	195	10.2222
...((.	chr10:8005938-8006139(+)$1	1	8	14	14.3492
))).))	chr9:98242705-98242906(-)$1	1	84	90	14.3492
(((...	chr10:103901526-103901727(+)$1	1	67	73	10.1428
((((((	chr11:63756049-63756250(+)$1	1	141	147	11.8095
((((((	chr13:25051843-25052044(-)$1	1	48	54	10.6984
))....	chr10:97387146-97387347(-)$1	1	107	113	14.3492
.)))).	chr5:54640302-54640503(+)$1	1	112	118	10.1428
((.((.	chr3:52964947-52965148(-)$1	1	155	161	14.3492
.....(	chr2:39053612-39053813(-)$1	1	18	24	11.8095
.((((.	chr16:75663255-75663456(-)$1	1	64	70	11.8095
(.....	chr6:34952886-34953087(+)$1	1	24	30	11.8095
....))	chr12:72017908-72018109(-)$1	1	193	199	14.3492
))))))	chr15:73048638-73048839(-)$1	1	52	58	10.7777
))))).	chrX:131205072-131205273(+)$1	1	76	82	11.5714
((((((	chr5:38962999-38963200(-)$1	1	101	107	11.8095
......	chr6:149721653-149721854(+)$1	1	107	113	14.3492

#PSSM
G : 0.66	U : 0.17	A : 0.12	C : 0.01	g : 0.01	
G : 0.98	g : 0.01	
A : 0.88	G : 0.06	C : 0.03	a : 0.01	
A : 0.80	U : 0.07	G : 0.07	C : 0.01	g : 0.01	
G : 0.98	g : 0.01	
A : 0.85	C : 0.06	U : 0.04	G : 0.01	a : 0.01	

#score	748.4444444444428
#seq	63
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m1_run2.nuc.txt

#NT
CUUC	chr14:69847172-69847395(-)$1	223	108	112	11.9999
CUUC	chr15:43814148-43814365(+)$1	217	89	93	11.9999
CUUC	chr1:201957934-201958163(+)$1	229	32	36	11.9999
CUUC	chr2:85553655-85553888(-)$1	233	185	189	11.9999
CUUC	chr1:24077640-24077874(+)$1	234	194	198	11.9999
CUUC	chr1:29508084-29508309(-)$1	225	104	108	11.9999
CUUC	chr16:27506030-27506274(-)$1	244	103	107	11.9999
CUUC	chr11:64535495-64535768(-)$1	273	4	8	11.9999
CUUC	chr11:10827411-10827665(-)$1	254	194	198	11.9999
CUUC	chr12:49433905-49434154(-)$1	249	61	65	11.9999
CUUC	chrX:153589635-153589869(-)$1	234	82	86	11.9999
CUUC	chr14:104151238-104151448(+)$1	210	176	180	11.9999
CUUC	chr19:42754523-42754743(-)$1	220	33	37	11.9999
CUUC	chr17:35310387-35310604(+)$1	217	147	151	11.9999
CUUC	chr18:29210952-29211172(-)$1	220	107	111	11.9999
CUUC	chrX:53659354-53659577(-)$1	223	199	203	11.9999
CUUC	chr15:72501073-72501317(-)$1	244	27	31	11.9999
CUUC	chr11:62482721-62482938(-)$1	217	34	38	11.9999
CUUC	chr3:170781606-170781833(-)$1	227	59	63	11.9999
CUUC	chr20:57566314-57566538(+)$1	224	41	45	11.9999
CUUC	chr22:50169189-50169412(-)$1	223	7	11	11.9999
CUUC	chr17:26964931-26965150(-)$1	219	6	10	11.9999
CUUC	chr16:87870032-87870252(-)$1	220	22	26	11.9999
CUUC	chr11:66460709-66460932(-)$1	223	156	160	11.9999
CUUC	chr12:121764812-121765046(-)$1	234	173	177	11.9999
CUUC	chr9:136913143-136913384(-)$1	241	92	96	11.9999
CUUC	chr16:29818050-29818295(+)$1	245	10	14	11.9999
CUUC	chr16:2506463-2506706(+)$1	243	1	5	11.9999
CUUC	chr21:38845049-38845266(+)$1	217	7	11	11.9999
CUUC	chr17:37627432-37627653(+)$1	221	76	80	11.9999
CUUC	chr1:111495029-111495246(-)$1	217	0	4	11.9999
CUUC	chr14:103336651-103336873(+)$1	222	99	103	11.9999
CUUC	chr19:39913742-39913966(+)$1	224	125	129	11.9999
CUUC	chr12:77423521-77423739(-)$1	218	178	182	11.9999
CUUC	chr13:42876100-42876328(+)$1	228	194	198	11.9999
CUUC	chr14:69392199-69392425(-)$1	226	18	22	11.9999
CUUC	chr1:32622402-32622644(+)$1	242	108	112	11.9999
CUUC	chr3:47890672-47890936(+)$1	264	46	50	11.9999
CUUC	chr10:70333395-70333627(+)$1	232	36	40	11.9999
CUUC	chr17:73499167-73499391(-)$1	224	37	41	11.9999
CUUC	chr12:120574317-120574549(-)$1	232	28	32	11.9999
CUUC	chr1:24125055-24125271(-)$1	216	157	161	11.9999
CUUC	chr16:70296227-70296449(-)$1	222	215	219	11.9999
CUUC	chr17:47117270-47117502(+)$1	232	207	211	11.9999
CUUC	chr1:33318585-33318802(+)$1	217	163	167	11.9999
CUUC	chr8:48883033-48883319(+)$1	286	46	50	11.9999
CUUC	chr6:43015843-43016062(-)$1	219	92	96	11.9999
CUUC	chr17:4442668-4442890(-)$1	222	34	38	11.9999
CUUC	chr9:98677952-98678165(+)$1	213	118	122	11.9999
CUUC	chr6:36454718-36454950(+)$1	232	20	24	11.9999
CUUC	chr16:2814871-2815110(+)$1	239	102	106	11.9999
CUUC	chr12:13142161-13142380(-)$1	219	16	20	11.9999
CUUC	chr9:6014134-6014365(-)$1	231	3	7	11.9999
CUUC	chrX:14038306-14038520(-)$1	214	5	9	11.9999
CUUC	chr5:14378029-14378257(+)$1	228	107	111	11.9999
CUUC	chr16:2369691-2369914(-)$1	223	89	93	11.9999
CUUC	chr4:170618523-170618742(+)$1	219	124	128	11.9999
CUUC	chr1:224345087-224345312(+)$1	225	3	7	11.9999
CUUC	chr20:33345023-33345246(-)$1	223	82	86	11.9999
CUUC	chrX:71424970-71425207(-)$1	237	27	31	11.9999
CUUC	chr11:70208106-70208327(+)$1	221	80	84	11.9999
CUUC	chr21:45535071-45535333(+)$1	262	184	188	11.9999
CUUC	chr7:32914598-32914817(-)$1	219	31	35	11.9999
CUUC	chrX:153219669-153219902(-)$1	233	62	66	11.9999
CUUC	chr14:102805398-102805629(+)$1	231	19	23	11.9999
CUUC	chr2:54864795-54865011(+)$1	216	14	18	11.9999
CUUC	chr7:5541078-5541299(-)$1	221	95	99	11.9999
CUUC	chr13:52548247-52548470(-)$1	223	22	26	11.9999

#otherMatches

#Struct PSSM
dddd	chr11:71726621-71726847(-)$1	226	168	172	11.9999
b!!b	chr14:69847172-69847395(-)$1	223	108	112	11.9999
vvvv	chr15:43814148-43814365(+)$1	217	89	93	11.9999
bbnn	chr1:201957934-201958163(+)$1	229	32	36	11.9999
HHHH	chr2:85553655-85553888(-)$1	233	185	189	11.9999
qddd	chr1:24077640-24077874(+)$1	234	194	198	11.9999
hhhh	chr1:29508084-29508309(-)$1	225	104	108	11.9999
ee22	chr16:27506030-27506274(-)$1	244	103	107	11.9999
:::G	chr11:64535495-64535768(-)$1	273	4	8	11.9999
ffff	chr11:10827411-10827665(-)$1	254	194	198	11.9999
FFFF	chr12:49433905-49434154(-)$1	249	61	65	11.9999
ffff	chrX:153589635-153589869(-)$1	234	82	86	11.9999
oooo	chr14:104151238-104151448(+)$1	210	176	180	11.9999
CFFF	chr19:42754523-42754743(-)$1	220	33	37	11.9999
FFFF	chr17:35310387-35310604(+)$1	217	147	151	11.9999
ffff	chr18:29210952-29211172(-)$1	220	107	111	11.9999
}DDD	chrX:53659354-53659577(-)$1	223	199	203	11.9999
e:GG	chr15:72501073-72501317(-)$1	244	27	31	11.9999
gg::	chr11:62482721-62482938(-)$1	217	34	38	11.9999
iiii	chr3:170781606-170781833(-)$1	227	59	63	11.9999
eee:	chr20:57566314-57566538(+)$1	224	41	45	11.9999
nnne	chr22:50169189-50169412(-)$1	223	7	11	11.9999
FFFF	chr17:26964931-26965150(-)$1	219	6	10	11.9999
dddm	chr16:87870032-87870252(-)$1	220	22	26	11.9999
"ddd	chr11:66460709-66460932(-)$1	223	156	160	11.9999
dddl	chr12:121764812-121765046(-)$1	234	173	177	11.9999
""ee	chr9:136913143-136913384(-)$1	241	92	96	11.9999
aooo	chr16:29818050-29818295(+)$1	245	10	14	11.9999
::::	chr16:2506463-2506706(+)$1	243	1	5	11.9999
$$$$	chr21:38845049-38845266(+)$1	217	7	11	11.9999
dggg	chr17:37627432-37627653(+)$1	221	76	80	11.9999
::::	chr1:111495029-111495246(-)$1	217	0	4	11.9999
22ee	chr14:103336651-103336873(+)$1	222	99	103	11.9999
eeel	chr19:39913742-39913966(+)$1	224	125	129	11.9999
GGee	chr12:77423521-77423739(-)$1	218	178	182	11.9999
>>>>	chr13:42876100-42876328(+)$1	228	194	198	11.9999
::cc	chr14:69392199-69392425(-)$1	226	18	22	11.9999
oobb	chr1:32622402-32622644(+)$1	242	108	112	11.9999
PPPP	chr3:47890672-47890936(+)$1	264	46	50	11.9999
bqqq	chr10:70333395-70333627(+)$1	232	36	40	11.9999
dddd	chr17:73499167-73499391(-)$1	224	37	41	11.9999
ffff	chr12:120574317-120574549(-)$1	232	28	32	11.9999
EEE_	chr1:24125055-24125271(-)$1	216	157	161	11.9999
eeee	chr16:70296227-70296449(-)$1	222	215	219	11.9999
====	chr17:47117270-47117502(+)$1	232	207	211	11.9999
hhhh	chr1:33318585-33318802(+)$1	217	163	167	11.9999
::FF	chr8:48883033-48883319(+)$1	286	46	50	11.9999
dddd	chr6:43015843-43016062(-)$1	219	92	96	11.9999
iiiq	chr17:4442668-4442890(-)$1	222	34	38	11.9999
ffff	chr9:98677952-98678165(+)$1	213	118	122	11.9999
ffff	chr6:36454718-36454950(+)$1	232	20	24	11.9999
gggg	chr16:2814871-2815110(+)$1	239	102	106	11.9999
EEEE	chr12:13142161-13142380(-)$1	219	16	20	11.9999
:::d	chr9:6014134-6014365(-)$1	231	3	7	11.9999
FFFF	chrX:14038306-14038520(-)$1	214	5	9	11.9999
ffff	chr5:14378029-14378257(+)$1	228	107	111	11.9999
lggg	chr16:2369691-2369914(-)$1	223	89	93	11.9999
ffzz	chr4:170618523-170618742(+)$1	219	124	128	11.9999
EELL	chr1:224345087-224345312(+)$1	225	3	7	11.9999
%%%%	chr20:33345023-33345246(-)$1	223	82	86	11.9999
dddd	chrX:71424970-71425207(-)$1	237	27	31	11.9999
:fff	chr11:70208106-70208327(+)$1	221	80	84	11.9999
bb::	chr21:45535071-45535333(+)$1	262	184	188	11.9999
BEEE	chr7:32914598-32914817(-)$1	219	31	35	11.9999
::bb	chrX:153219669-153219902(-)$1	233	62	66	11.9999
iiii	chr14:102805398-102805629(+)$1	231	19	23	11.9999
$$dd	chr2:54864795-54865011(+)$1	216	14	18	11.9999
cc22	chr7:5541078-5541299(-)$1	221	95	99	11.9999
oooo	chr13:52548247-52548470(-)$1	223	22	26	11.9999

#DB
))))	chr11:71726621-71726847(-)$1	1	168	172	11.9999
(..(	chr14:69847172-69847395(-)$1	1	108	112	11.9999
....	chr15:43814148-43814365(+)$1	1	89	93	11.9999
((..	chr1:201957934-201958163(+)$1	1	32	36	11.9999
))))	chr2:85553655-85553888(-)$1	1	185	189	11.9999
.)))	chr1:24077640-24077874(+)$1	1	194	198	11.9999
))))	chr1:29508084-29508309(-)$1	1	104	108	11.9999
))..	chr16:27506030-27506274(-)$1	1	103	107	11.9999
...(	chr11:64535495-64535768(-)$1	1	4	8	11.9999
((((	chr11:10827411-10827665(-)$1	1	194	198	11.9999
))))	chr12:49433905-49434154(-)$1	1	61	65	11.9999
((((	chrX:153589635-153589869(-)$1	1	82	86	11.9999
....	chr14:104151238-104151448(+)$1	1	176	180	11.9999
((((	chr19:42754523-42754743(-)$1	1	33	37	11.9999
))))	chr17:35310387-35310604(+)$1	1	147	151	11.9999
((((	chr18:29210952-29211172(-)$1	1	107	111	11.9999
.)))	chrX:53659354-53659577(-)$1	1	199	203	11.9999
).((	chr15:72501073-72501317(-)$1	1	27	31	11.9999
))..	chr11:62482721-62482938(-)$1	1	34	38	11.9999
))))	chr3:170781606-170781833(-)$1	1	59	63	11.9999
))).	chr20:57566314-57566538(+)$1	1	41	45	11.9999
...)	chr22:50169189-50169412(-)$1	1	7	11	11.9999
((((	chr17:26964931-26965150(-)$1	1	6	10	11.9999
(((.	chr16:87870032-87870252(-)$1	1	22	26	11.9999
.(((	chr11:66460709-66460932(-)$1	1	156	160	11.9999
(((.	chr12:121764812-121765046(-)$1	1	173	177	11.9999
..((	chr9:136913143-136913384(-)$1	1	92	96	11.9999
(...	chr16:29818050-29818295(+)$1	1	10	14	11.9999
....	chr16:2506463-2506706(+)$1	1	1	5	11.9999
....	chr21:38845049-38845266(+)$1	1	7	11	11.9999
)(((	chr17:37627432-37627653(+)$1	1	76	80	11.9999
....	chr1:111495029-111495246(-)$1	1	0	4	11.9999
..))	chr14:103336651-103336873(+)$1	1	99	103	11.9999
(((.	chr19:39913742-39913966(+)$1	1	125	129	11.9999
))((	chr12:77423521-77423739(-)$1	1	178	182	11.9999
....	chr13:42876100-42876328(+)$1	1	194	198	11.9999
..((	chr14:69392199-69392425(-)$1	1	18	22	11.9999
..))	chr1:32622402-32622644(+)$1	1	108	112	11.9999
....	chr3:47890672-47890936(+)$1	1	46	50	11.9999
(...	chr10:70333395-70333627(+)$1	1	36	40	11.9999
((((	chr17:73499167-73499391(-)$1	1	37	41	11.9999
((((	chr12:120574317-120574549(-)$1	1	28	32	11.9999
))).	chr1:24125055-24125271(-)$1	1	157	161	11.9999
))))	chr16:70296227-70296449(-)$1	1	215	219	11.9999
))))	chr17:47117270-47117502(+)$1	1	207	211	11.9999
))))	chr1:33318585-33318802(+)$1	1	163	167	11.9999
..((	chr8:48883033-48883319(+)$1	1	46	50	11.9999
((((	chr6:43015843-43016062(-)$1	1	92	96	11.9999
(((.	chr17:4442668-4442890(-)$1	1	34	38	11.9999
((((	chr9:98677952-98678165(+)$1	1	118	122	11.9999
((((	chr6:36454718-36454950(+)$1	1	20	24	11.9999
))))	chr16:2814871-2815110(+)$1	1	102	106	11.9999
((((	chr12:13142161-13142380(-)$1	1	16	20	11.9999
...(	chr9:6014134-6014365(-)$1	1	3	7	11.9999
((((	chrX:14038306-14038520(-)$1	1	5	9	11.9999
((((	chr5:14378029-14378257(+)$1	1	107	111	11.9999
.)))	chr16:2369691-2369914(-)$1	1	89	93	11.9999
((..	chr4:170618523-170618742(+)$1	1	124	128	11.9999
((..	chr1:224345087-224345312(+)$1	1	3	7	11.9999
....	chr20:33345023-33345246(-)$1	1	82	86	11.9999
))))	chrX:71424970-71425207(-)$1	1	27	31	11.9999
.(((	chr11:70208106-70208327(+)$1	1	80	84	11.9999
))..	chr21:45535071-45535333(+)$1	1	184	188	11.9999
((((	chr7:32914598-32914817(-)$1	1	31	35	11.9999
..((	chrX:153219669-153219902(-)$1	1	62	66	11.9999
((((	chr14:102805398-102805629(+)$1	1	19	23	11.9999
..((	chr2:54864795-54865011(+)$1	1	14	18	11.9999
))..	chr7:5541078-5541299(-)$1	1	95	99	11.9999
....	chr13:52548247-52548470(-)$1	1	22	26	11.9999

#PSSM
C : 0.99	
U : 0.99	
U : 0.99	
C : 0.99	

#score	827.9999999999995
#seq	69
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m2_run1.nuc.txt

#NT
AGC	chr17:18154584-18154807(-)$1	223	19	22	8.9999
AGC	chr8:144996699-144996918(-)$1	219	3	6	8.9999
AGC	chr17:17116931-17117155(-)$1	224	47	50	8.9999
AGC	chr17:18144041-18144273(+)$1	232	57	60	8.9999
agc	chr12:21788500-21788718(-)$1	218	5	8	8.9999
AGC	chr5:5463947-5464164(+)$1	217	3	6	8.9999
AGC	chr14:103371801-103372031(+)$1	230	84	87	8.9999
AGC	chr19:44612056-44612277(-)$1	221	145	148	8.9999
AGC	chr11:118390295-118390517(+)$1	222	94	97	8.9999
AGC	chr8:48706854-48707089(-)$1	235	12	15	8.9999
AGC	chr14:69350857-69351082(-)$1	225	55	58	8.9999
AGC	chr8:48751614-48751831(-)$1	217	19	22	8.9999
AGC	chr12:57398249-57398472(-)$1	223	23	26	8.9999
AGC	chrX:39930147-39930382(-)$1	235	26	29	8.9999
AGC	chr22:43563899-43564142(-)$1	243	31	34	8.9999
AGC	chr11:6652228-6652453(-)$1	225	24	27	8.9999
AGC	chr16:74670181-74670400(-)$1	219	12	15	8.9999
AGC	chr2:85866343-85866564(+)$1	221	103	106	8.9999
AGC	chr8:81431548-81431768(+)$1	220	36	39	8.9999
AGC	chr1:179851942-179852209(+)$1	267	23	26	8.9999
AGC	chr9:34107278-34107503(-)$1	225	1	4	8.9999
AGC	chr10:75855336-75855564(+)$1	228	182	185	8.9999
AGC	chr7:82585053-82585269(-)$1	216	12	15	8.9999
AGC	chr3:136019778-136019998(+)$1	220	110	113	8.9999
AGC	chr14:21874914-21875133(-)$1	219	58	61	8.9999
AGC	chr5:150080421-150080647(-)$1	226	23	26	8.9999
AGC	chr10:99416545-99416766(+)$1	221	45	48	8.9999
AGC	chr6:31762679-31762908(-)$1	229	18	21	8.9999
AGC	chr8:144894397-144894621(-)$1	224	37	40	8.9999
AGC	chr15:90168754-90168978(+)$1	224	2	5	8.9999
AGC	chr2:128480144-128480357(-)$1	213	188	191	8.9999
AGC	chr9:138376301-138376530(+)$1	229	0	3	8.9999
AGC	chr1:16464394-16464612(-)$1	218	12	15	8.9999
AGC	chr16:2049915-2050163(-)$1	248	97	100	8.9999
AGC	chr22:50304007-50304227(-)$1	220	152	155	8.9999
AGC	chr19:45494451-45494670(+)$1	219	10	13	8.9999
AGC	chr16:30740376-30740603(+)$1	227	51	54	8.9999
AGC	chr16:2998802-2999016(+)$1	214	13	16	8.9999
AGC	chr17:76210305-76210558(+)$1	253	123	126	8.9999
AGC	chr1:113239253-113239485(+)$1	232	37	40	8.9999
AGC	chr18:29118783-29119038(+)$1	255	26	29	8.9999
AGC	chr9:132400392-132400618(-)$1	226	43	46	8.9999
AGC	chr5:133895539-133895754(+)$1	215	23	26	8.9999
AGC	chr1:1246272-1246490(+)$1	218	94	97	8.9999
AGC	chr16:2053569-2053800(-)$1	231	0	3	8.9999
AGC	chr15:41828614-41828833(-)$1	219	5	8	8.9999
AGC	chr9:95018899-95019127(-)$1	228	90	93	8.9999
AGC	chr22:41523451-41523675(+)$1	224	46	49	8.9999
AGC	chr6:31112849-31113067(-)$1	218	19	22	8.9999
AGC	chr2:73302620-73302843(-)$1	223	43	46	8.9999
AGC	chr22:40742592-40742803(+)$1	211	3	6	8.9999
AGC	chr1:38338627-38338844(-)$1	217	31	34	8.9999
AGC	chr17:41345323-41345553(+)$1	230	1	4	8.9999
AGC	chr13:111134791-111135011(+)$1	220	46	49	8.9999
AGC	chr14:102453834-102454051(+)$1	217	65	68	8.9999
AGC	chr12:125465118-125465363(-)$1	245	22	25	8.9999
AGC	chr19:34791658-34791881(+)$1	223	23	26	8.9999
AGC	chr12:53775812-53776035(+)$1	223	36	39	8.9999
AGC	chr9:131581068-131581288(+)$1	220	38	41	8.9999
AGC	chr8:144941914-144942142(-)$1	228	149	152	8.9999
AGC	chr1:33248010-33248235(-)$1	225	200	203	8.9999
AGC	chr6:43017672-43017890(-)$1	218	128	131	8.9999
AGC	chr15:76632576-76632799(+)$1	223	58	61	8.9999
AGC	chr22:50946665-50946891(+)$1	226	7	10	8.9999
AGC	chr13:37393944-37394154(+)$1	210	0	3	8.9999
AGC	chr1:115275232-115275455(-)$1	223	166	169	8.9999
AGC	chr19:59058644-59058882(+)$1	238	74	77	8.9999
AGC	chr2:232326363-232326670(-)$1	307	37	40	8.9999
AGC	chr12:49956686-49956935(-)$1	249	16	19	8.9999
AGC	chr1:24077315-24077529(+)$1	214	27	30	8.9999
AGC	chr17:42949737-42949961(-)$1	224	21	24	8.9999
AGC	chrX:53410051-53410272(-)$1	221	0	3	8.9999
AGC	chr17:8354052-8354274(+)$1	222	61	64	8.9999
AGC	chr9:138714613-138714826(-)$1	213	29	32	8.9999
AGC	chr1:200376558-200376800(-)$1	242	167	170	8.9999
AGC	chr15:74315572-74315786(+)$1	214	81	84	8.9999
AGC	chr10:77159799-77160021(-)$1	222	61	64	8.9999
AGC	chr17:74053401-74053626(-)$1	225	22	25	8.9999
AGC	chr1:115251069-115251311(-)$1	242	0	3	8.9999
agc	chr5:137088965-137089193(-)$1	228	92	95	8.9999
AGC	chr17:80048154-80048383(-)$1	229	98	101	8.9999
AGC	chr6:31747711-31747951(-)$1	240	19	22	8.9999
AGC	chr8:144944819-144945042(-)$1	223	15	18	8.9999
AGC	chr19:50882214-50882435(+)$1	221	42	45	8.9999
AGC	chr19:17835756-17836086(+)$1	330	99	102	8.9999
AGC	chr2:207174506-207174732(+)$1	226	30	33	8.9999
AGC	chr2:70315383-70315622(+)$1	239	42	45	8.9999
AGC	chr19:2810217-2810434(+)$1	217	8	11	8.9999
AGC	chr16:85694875-85695104(+)$1	229	39	42	8.9999
AGC	chr3:58116491-58116711(+)$1	220	17	20	8.9999
AGC	chr16:19722632-19722855(-)$1	223	69	72	8.9999
AGC	chr19:50124685-50124910(+)$1	225	99	102	8.9999
AGC	chr7:5396448-5396730(-)$1	282	0	3	8.9999
AGC	chr21:46689721-46689949(-)$1	228	19	22	8.9999
AGC	chr5:71489610-71489828(+)$1	218	9	12	8.9999
AGC	chr5:123984327-123984551(-)$1	224	11	14	8.9999

#otherMatches

#Struct PSSM
##d	chr6:88391247-88391465(-)$1	218	89	92	8.9999
ddc	chr17:18154584-18154807(-)$1	223	19	22	8.9999
{BB	chr8:144996699-144996918(-)$1	219	3	6	8.9999
ooo	chr17:17116931-17117155(-)$1	224	47	50	8.9999
[cc	chr17:18144041-18144273(+)$1	232	57	60	8.9999
CCM	chr12:21788500-21788718(-)$1	218	5	8	8.9999
eeo	chr5:5463947-5464164(+)$1	217	3	6	8.9999
fff	chr14:103371801-103372031(+)$1	230	84	87	8.9999
"bb	chr19:44612056-44612277(-)$1	221	145	148	8.9999
uhh	chr11:118390295-118390517(+)$1	222	94	97	8.9999
FFF	chr8:48706854-48707089(-)$1	235	12	15	8.9999
CC{	chr14:69350857-69351082(-)$1	225	55	58	8.9999
nnn	chr8:48751614-48751831(-)$1	217	19	22	8.9999
hh"	chr12:57398249-57398472(-)$1	223	23	26	8.9999
obb	chrX:39930147-39930382(-)$1	235	26	29	8.9999
ee"	chr22:43563899-43564142(-)$1	243	31	34	8.9999
DDD	chr11:6652228-6652453(-)$1	225	24	27	8.9999
ooo	chr16:74670181-74670400(-)$1	219	12	15	8.9999
22d	chr2:85866343-85866564(+)$1	221	103	106	8.9999
[cc	chr8:81431548-81431768(+)$1	220	36	39	8.9999
!dd	chr1:179851942-179852209(+)$1	267	23	26	8.9999
ccc	chr9:34107278-34107503(-)$1	225	1	4	8.9999
ggg	chr10:75855336-75855564(+)$1	228	182	185	8.9999
[cc	chr7:82585053-82585269(-)$1	216	12	15	8.9999
cc"	chr3:136019778-136019998(+)$1	220	110	113	8.9999
ggg	chr14:21874914-21875133(-)$1	219	58	61	8.9999
KKC	chr5:150080421-150080647(-)$1	226	23	26	8.9999
fff	chr10:99416545-99416766(+)$1	221	45	48	8.9999
DDD	chr6:31762679-31762908(-)$1	229	18	21	8.9999
3ff	chr8:144894397-144894621(-)$1	224	37	40	8.9999
:dd	chr15:90168754-90168978(+)$1	224	2	5	8.9999
fff	chr2:128480144-128480357(-)$1	213	188	191	8.9999
:bb	chr9:138376301-138376530(+)$1	229	0	3	8.9999
:EE	chr1:16464394-16464612(-)$1	218	12	15	8.9999
ppp	chr16:2049915-2050163(-)$1	248	97	100	8.9999
qqd	chr22:50304007-50304227(-)$1	220	152	155	8.9999
EEE	chr19:45494451-45494670(+)$1	219	10	13	8.9999
FFF	chr16:30740376-30740603(+)$1	227	51	54	8.9999
:::	chr16:2998802-2999016(+)$1	214	13	16	8.9999
iii	chr17:76210305-76210558(+)$1	253	123	126	8.9999
III	chr1:113239253-113239485(+)$1	232	37	40	8.9999
::E	chr18:29118783-29119038(+)$1	255	26	29	8.9999
]a3	chr9:132400392-132400618(-)$1	226	43	46	8.9999
fff	chr5:133895539-133895754(+)$1	215	23	26	8.9999
mmc	chr1:1246272-1246490(+)$1	218	94	97	8.9999
:::	chr16:2053569-2053800(-)$1	231	0	3	8.9999
ggg	chr15:41828614-41828833(-)$1	219	5	8	8.9999
DYY	chr9:95018899-95019127(-)$1	228	90	93	8.9999
{CC	chr22:41523451-41523675(+)$1	224	46	49	8.9999
d]b	chr6:31112849-31113067(-)$1	218	19	22	8.9999
[ee	chr2:73302620-73302843(-)$1	223	43	46	8.9999
fff	chr22:40742592-40742803(+)$1	211	3	6	8.9999
ddd	chr1:38338627-38338844(-)$1	217	31	34	8.9999
ddd	chr17:41345323-41345553(+)$1	230	1	4	8.9999
EEE	chr13:111134791-111135011(+)$1	220	46	49	8.9999
555	chr14:102453834-102454051(+)$1	217	65	68	8.9999
4dd	chr12:125465118-125465363(-)$1	245	22	25	8.9999
BB{	chr19:34791658-34791881(+)$1	223	23	26	8.9999
:ff	chr12:53775812-53776035(+)$1	223	36	39	8.9999
ggg	chr9:131581068-131581288(+)$1	220	38	41	8.9999
ccc	chr8:144941914-144942142(-)$1	228	149	152	8.9999
cc:	chr1:33248010-33248235(-)$1	225	200	203	8.9999
:ee	chr6:43017672-43017890(-)$1	218	128	131	8.9999
bb3	chr15:76632576-76632799(+)$1	223	58	61	8.9999
ddd	chr22:50946665-50946891(+)$1	226	7	10	8.9999
:cc	chr13:37393944-37394154(+)$1	210	0	3	8.9999
ddd	chr1:115275232-115275455(-)$1	223	166	169	8.9999
lee	chr19:59058644-59058882(+)$1	238	74	77	8.9999
%cc	chr2:232326363-232326670(-)$1	307	37	40	8.9999
DDD	chr12:49956686-49956935(-)$1	249	16	19	8.9999
:EE	chr1:24077315-24077529(+)$1	214	27	30	8.9999
GGG	chr17:42949737-42949961(-)$1	224	21	24	8.9999
:::	chrX:53410051-53410272(-)$1	221	0	3	8.9999
dd[	chr17:8354052-8354274(+)$1	222	61	64	8.9999
obb	chr9:138714613-138714826(-)$1	213	29	32	8.9999
ffn	chr1:200376558-200376800(-)$1	242	167	170	8.9999
:bb	chr15:74315572-74315786(+)$1	214	81	84	8.9999
KCC	chr10:77159799-77160021(-)$1	222	61	64	8.9999
GGG	chr17:74053401-74053626(-)$1	225	22	25	8.9999
:CC	chr1:115251069-115251311(-)$1	242	0	3	8.9999
[bb	chr5:137088965-137089193(-)$1	228	92	95	8.9999
]bb	chr17:80048154-80048383(-)$1	229	98	101	8.9999
GGG	chr6:31747711-31747951(-)$1	240	19	22	8.9999
KBB	chr8:144944819-144945042(-)$1	223	15	18	8.9999
:::	chr19:50882214-50882435(+)$1	221	42	45	8.9999
ggg	chr19:17835756-17836086(+)$1	330	99	102	8.9999
III	chr2:207174506-207174732(+)$1	226	30	33	8.9999
DDD	chr2:70315383-70315622(+)$1	239	42	45	8.9999
{CC	chr19:2810217-2810434(+)$1	217	8	11	8.9999
:bb	chr16:85694875-85695104(+)$1	229	39	42	8.9999
EEN	chr3:58116491-58116711(+)$1	220	17	20	8.9999
"dd	chr16:19722632-19722855(-)$1	223	69	72	8.9999
ff:	chr19:50124685-50124910(+)$1	225	99	102	8.9999
:BB	chr7:5396448-5396730(-)$1	282	0	3	8.9999
%%%	chr21:46689721-46689949(-)$1	228	19	22	8.9999
:::	chr5:71489610-71489828(+)$1	218	9	12	8.9999
cc:	chr5:123984327-123984551(-)$1	224	11	14	8.9999

#DB
..(	chr6:88391247-88391465(-)$1	1	89	92	8.9999
)))	chr17:18154584-18154807(-)$1	1	19	22	8.9999
.((	chr8:144996699-144996918(-)$1	1	3	6	8.9999
...	chr17:17116931-17117155(-)$1	1	47	50	8.9999
.((	chr17:18144041-18144273(+)$1	1	57	60	8.9999
((.	chr12:21788500-21788718(-)$1	1	5	8	8.9999
((.	chr5:5463947-5464164(+)$1	1	3	6	8.9999
)))	chr14:103371801-103372031(+)$1	1	84	87	8.9999
.((	chr19:44612056-44612277(-)$1	1	145	148	8.9999
.))	chr11:118390295-118390517(+)$1	1	94	97	8.9999
(((	chr8:48706854-48707089(-)$1	1	12	15	8.9999
((.	chr14:69350857-69351082(-)$1	1	55	58	8.9999
...	chr8:48751614-48751831(-)$1	1	19	22	8.9999
((.	chr12:57398249-57398472(-)$1	1	23	26	8.9999
.))	chrX:39930147-39930382(-)$1	1	26	29	8.9999
((.	chr22:43563899-43564142(-)$1	1	31	34	8.9999
(((	chr11:6652228-6652453(-)$1	1	24	27	8.9999
...	chr16:74670181-74670400(-)$1	1	12	15	8.9999
..)	chr2:85866343-85866564(+)$1	1	103	106	8.9999
.((	chr8:81431548-81431768(+)$1	1	36	39	8.9999
.((	chr1:179851942-179852209(+)$1	1	23	26	8.9999
(((	chr9:34107278-34107503(-)$1	1	1	4	8.9999
(((	chr10:75855336-75855564(+)$1	1	182	185	8.9999
.((	chr7:82585053-82585269(-)$1	1	12	15	8.9999
((.	chr3:136019778-136019998(+)$1	1	110	113	8.9999
)))	chr14:21874914-21875133(-)$1	1	58	61	8.9999
..(	chr5:150080421-150080647(-)$1	1	23	26	8.9999
)))	chr10:99416545-99416766(+)$1	1	45	48	8.9999
(((	chr6:31762679-31762908(-)$1	1	18	21	8.9999
.))	chr8:144894397-144894621(-)$1	1	37	40	8.9999
.((	chr15:90168754-90168978(+)$1	1	2	5	8.9999
)))	chr2:128480144-128480357(-)$1	1	188	191	8.9999
.((	chr9:138376301-138376530(+)$1	1	0	3	8.9999
.((	chr1:16464394-16464612(-)$1	1	12	15	8.9999
...	chr16:2049915-2050163(-)$1	1	97	100	8.9999
..)	chr22:50304007-50304227(-)$1	1	152	155	8.9999
(((	chr19:45494451-45494670(+)$1	1	10	13	8.9999
(((	chr16:30740376-30740603(+)$1	1	51	54	8.9999
...	chr16:2998802-2999016(+)$1	1	13	16	8.9999
(((	chr17:76210305-76210558(+)$1	1	123	126	8.9999
(((	chr1:113239253-113239485(+)$1	1	37	40	8.9999
..(	chr18:29118783-29119038(+)$1	1	26	29	8.9999
.).	chr9:132400392-132400618(-)$1	1	43	46	8.9999
(((	chr5:133895539-133895754(+)$1	1	23	26	8.9999
..)	chr1:1246272-1246490(+)$1	1	94	97	8.9999
...	chr16:2053569-2053800(-)$1	1	0	3	8.9999
(((	chr15:41828614-41828833(-)$1	1	5	8	8.9999
)..	chr9:95018899-95019127(-)$1	1	90	93	8.9999
.((	chr22:41523451-41523675(+)$1	1	46	49	8.9999
).)	chr6:31112849-31113067(-)$1	1	19	22	8.9999
.((	chr2:73302620-73302843(-)$1	1	43	46	8.9999
(((	chr22:40742592-40742803(+)$1	1	3	6	8.9999
(((	chr1:38338627-38338844(-)$1	1	31	34	8.9999
(((	chr17:41345323-41345553(+)$1	1	1	4	8.9999
(((	chr13:111134791-111135011(+)$1	1	46	49	8.9999
...	chr14:102453834-102454051(+)$1	1	65	68	8.9999
.))	chr12:125465118-125465363(-)$1	1	22	25	8.9999
((.	chr19:34791658-34791881(+)$1	1	23	26	8.9999
.((	chr12:53775812-53776035(+)$1	1	36	39	8.9999
)))	chr9:131581068-131581288(+)$1	1	38	41	8.9999
(((	chr8:144941914-144942142(-)$1	1	149	152	8.9999
)).	chr1:33248010-33248235(-)$1	1	200	203	8.9999
.((	chr6:43017672-43017890(-)$1	1	128	131	8.9999
)).	chr15:76632576-76632799(+)$1	1	58	61	8.9999
(((	chr22:50946665-50946891(+)$1	1	7	10	8.9999
.((	chr13:37393944-37394154(+)$1	1	0	3	8.9999
)))	chr1:115275232-115275455(-)$1	1	166	169	8.9999
.))	chr19:59058644-59058882(+)$1	1	74	77	8.9999
.((	chr2:232326363-232326670(-)$1	1	37	40	8.9999
(((	chr12:49956686-49956935(-)$1	1	16	19	8.9999
.((	chr1:24077315-24077529(+)$1	1	27	30	8.9999
(((	chr17:42949737-42949961(-)$1	1	21	24	8.9999
...	chrX:53410051-53410272(-)$1	1	0	3	8.9999
((.	chr17:8354052-8354274(+)$1	1	61	64	8.9999
.))	chr9:138714613-138714826(-)$1	1	29	32	8.9999
((.	chr1:200376558-200376800(-)$1	1	167	170	8.9999
.((	chr15:74315572-74315786(+)$1	1	81	84	8.9999
.((	chr10:77159799-77160021(-)$1	1	61	64	8.9999
(((	chr17:74053401-74053626(-)$1	1	22	25	8.9999
.((	chr1:115251069-115251311(-)$1	1	0	3	8.9999
.((	chr5:137088965-137089193(-)$1	1	92	95	8.9999
.))	chr17:80048154-80048383(-)$1	1	98	101	8.9999
(((	chr6:31747711-31747951(-)$1	1	19	22	8.9999
.((	chr8:144944819-144945042(-)$1	1	15	18	8.9999
...	chr19:50882214-50882435(+)$1	1	42	45	8.9999
(((	chr19:17835756-17836086(+)$1	1	99	102	8.9999
(((	chr2:207174506-207174732(+)$1	1	30	33	8.9999
(((	chr2:70315383-70315622(+)$1	1	42	45	8.9999
.((	chr19:2810217-2810434(+)$1	1	8	11	8.9999
.((	chr16:85694875-85695104(+)$1	1	39	42	8.9999
((.	chr3:58116491-58116711(+)$1	1	17	20	8.9999
.((	chr16:19722632-19722855(-)$1	1	69	72	8.9999
)).	chr19:50124685-50124910(+)$1	1	99	102	8.9999
.((	chr7:5396448-5396730(-)$1	1	0	3	8.9999
...	chr21:46689721-46689949(-)$1	1	19	22	8.9999
...	chr5:71489610-71489828(+)$1	1	9	12	8.9999
)).	chr5:123984327-123984551(-)$1	1	11	14	8.9999

#PSSM
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	
C : 0.97	c : 0.02	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_UTR_m3_run2.nuc.txt

#NT
UGCC	chr7:148921642-148921894(+)$1	252	162	166	12.0000
UGCC	chr13:77458313-77458536(-)$1	223	58	62	12.0000
UGCC	chrX:70519875-70520099(+)$1	224	23	27	12.0000
UGCC	chr19:58609459-58609681(-)$1	222	75	79	12.0000
ugcc	chr16:30680522-30680743(+)$1	221	5	9	12.0000
UGCC	chr16:69362828-69363075(-)$1	247	82	86	12.0000
UGCC	chr15:31666334-31666563(+)$1	229	57	61	12.0000
UGCC	chr7:99634809-99635038(+)$1	229	115	119	12.0000
UGCC	chr17:7157869-7158095(+)$1	226	210	214	12.0000
UGCC	chr2:232673135-232673350(+)$1	215	3	7	12.0000
UGCC	chr22:50282942-50283166(+)$1	224	155	159	12.0000
UGCC	chr1:47143367-47143615(-)$1	248	90	94	12.0000
UGCC	chr17:79801497-79801718(-)$1	221	142	146	12.0000
UGCC	chr16:30081430-30081661(+)$1	231	18	22	12.0000
UGCC	chr5:65222188-65222421(+)$1	233	3	7	12.0000
UGCC	chr8:21862695-21862915(+)$1	220	208	212	12.0000
UGCC	chr6:75962870-75963099(-)$1	229	185	189	12.0000
ugcc	chr11:17394028-17394253(+)$1	225	32	36	12.0000
UGCC	chr15:91463659-91463873(+)$1	214	133	137	12.0000
UGCC	chr3:47882469-47882692(+)$1	223	9	13	12.0000
UGCC	chrX:49143449-49143662(+)$1	213	76	80	12.0000
UGCC	chr1:1189540-1189772(-)$1	232	72	76	12.0000
UGCC	chr1:117531750-117531974(+)$1	224	148	152	12.0000
ugcc	chr10:127530950-127531169(+)$1	219	150	154	12.0000
UGCC	chr12:69753617-69753843(+)$1	226	191	195	12.0000
UGCC	chr19:42751673-42751896(-)$1	223	11	15	12.0000
UGCC	chr17:21454676-21454897(-)$1	221	95	99	12.0000
UGCC	chr21:45113532-45113763(+)$1	231	210	214	12.0000
UGCC	chr1:151317497-151317728(-)$1	231	40	44	12.0000
UGCC	chr19:41096877-41097115(+)$1	238	110	114	12.0000
UGCC	chr4:2067853-2068079(+)$1	226	42	46	12.0000
UGCC	chr9:132995594-132995811(+)$1	217	97	101	12.0000
UGCC	chr1:2451669-2451900(-)$1	231	28	32	12.0000
UGCC	chr20:34135092-34135320(+)$1	228	44	48	12.0000
UGCC	chr9:95018899-95019127(-)$1	228	14	18	12.0000
UGCC	chr5:175954683-175954904(-)$1	221	187	191	12.0000
UGCC	chr1:6653556-6653801(-)$1	245	33	37	12.0000
UGCC	chr2:96850796-96851014(-)$1	218	9	13	12.0000
UGCC	chr3:24019301-24019536(+)$1	235	159	163	12.0000
UGCC	chr12:122497849-122498083(+)$1	234	46	50	12.0000
UGCC	chr5:112170661-112170887(+)$1	226	12	16	12.0000
UGCC	chr14:77254963-77255217(-)$1	254	34	38	12.0000
UGCC	chr7:44920003-44920230(-)$1	227	23	27	12.0000
UGCC	chr2:20550292-20550507(-)$1	215	46	50	12.0000
UGCC	chr19:33872098-33872337(+)$1	239	120	124	12.0000
UGCC	chr6:43147383-43147599(+)$1	216	9	13	12.0000
UGCC	chr6:4954298-4954532(+)$1	234	1	5	12.0000
UGCC	chr19:55739488-55739712(-)$1	224	2	6	12.0000
UGCC	chr15:43656150-43656371(-)$1	221	65	69	12.0000
UGCC	chr19:1576836-1577182(-)$1	346	1	5	12.0000
UGCC	chr1:179074174-179074444(-)$1	270	83	87	12.0000
UGCC	chr10:64893117-64893337(+)$1	220	178	182	12.0000
UGCC	chr20:34515623-34515849(+)$1	226	87	91	12.0000
UGCC	chr7:75958593-75958820(-)$1	227	85	89	12.0000
UGCC	chr17:47367080-47367290(-)$1	210	69	73	12.0000
UGCC	chr9:140098482-140098706(-)$1	224	105	109	12.0000
UGCC	chr5:32174250-32174488(-)$1	238	28	32	12.0000
UGCC	chr14:78140231-78140459(-)$1	228	36	40	12.0000
UGCC	chr7:143079614-143079848(+)$1	234	12	16	12.0000
UGCC	chr12:122499144-122499366(+)$1	222	32	36	12.0000
UGCC	chr15:79178391-79178614(+)$1	223	17	21	12.0000
UGCC	chr12:1896287-1896512(+)$1	225	13	17	12.0000
UGCC	chr19:1985423-1985658(-)$1	235	6	10	12.0000
UGCC	chr12:132406311-132406534(+)$1	223	172	176	12.0000
UGCC	chr19:13862476-13862705(+)$1	229	48	52	12.0000
UGCC	chr11:33083069-33083282(+)$1	213	81	85	12.0000
UGCC	chr6:33165572-33165809(-)$1	237	171	175	12.0000
UGCC	chr9:136901152-136901374(-)$1	222	44	48	12.0000
UGCC	chr2:242617815-242618045(-)$1	230	70	74	12.0000
UGCC	chr19:44662688-44662939(+)$1	251	30	34	12.0000
UGCC	chr19:18978281-18978503(+)$1	222	149	153	12.0000
UGCC	chr2:74333270-74333489(+)$1	219	113	117	12.0000
UGCC	chr3:196081441-196081663(-)$1	222	139	143	12.0000
UGCC	chr7:100867126-100867354(+)$1	228	150	154	12.0000
UGCC	chr2:207026000-207026210(+)$1	210	71	75	12.0000
UGCC	chr10:99218348-99218574(-)$1	226	74	78	12.0000
UGCC	chr14:60749362-60749587(+)$1	225	100	104	12.0000
UGCC	chr5:112175990-112176211(+)$1	221	43	47	12.0000
UGCC	chr14:77974731-77974977(-)$1	246	150	154	12.0000
UGCC	chr21:45179915-45180144(+)$1	229	73	77	12.0000

#otherMatches

#Struct PSSM
eeeb	chr12:110971794-110972011(-)$1	217	58	62	12.0000
hh!!	chr7:148921642-148921894(+)$1	252	162	166	12.0000
ffff	chr13:77458313-77458536(-)$1	223	58	62	12.0000
:EEE	chrX:70519875-70520099(+)$1	224	23	27	12.0000
mmmm	chr19:58609459-58609681(-)$1	222	75	79	12.0000
[a!!	chr16:30680522-30680743(+)$1	221	5	9	12.0000
Gbb[	chr16:69362828-69363075(-)$1	247	82	86	12.0000
##ee	chr15:31666334-31666563(+)$1	229	57	61	12.0000
iiii	chr7:99634809-99635038(+)$1	229	115	119	12.0000
bb]d	chr17:7157869-7158095(+)$1	226	210	214	12.0000
gggg	chr2:232673135-232673350(+)$1	215	3	7	12.0000
EEcc	chr22:50282942-50283166(+)$1	224	155	159	12.0000
====	chr1:47143367-47143615(-)$1	248	90	94	12.0000
dggg	chr17:79801497-79801718(-)$1	221	142	146	12.0000
[ccc	chr16:30081430-30081661(+)$1	231	18	22	12.0000
C{FF	chr5:65222188-65222421(+)$1	233	3	7	12.0000
EEEE	chr8:21862695-21862915(+)$1	220	208	212	12.0000
EEEE	chr6:75962870-75963099(-)$1	229	185	189	12.0000
JJJJ	chr11:17394028-17394253(+)$1	225	32	36	12.0000
gggg	chr15:91463659-91463873(+)$1	214	133	137	12.0000
BBBB	chr3:47882469-47882692(+)$1	223	9	13	12.0000
:ccc	chrX:49143449-49143662(+)$1	213	76	80	12.0000
]fff	chr1:1189540-1189772(-)$1	232	72	76	12.0000
DDDD	chr1:117531750-117531974(+)$1	224	148	152	12.0000
oocc	chr10:127530950-127531169(+)$1	219	150	154	12.0000
]ddd	chr12:69753617-69753843(+)$1	226	191	195	12.0000
CCC{	chr19:42751673-42751896(-)$1	223	11	15	12.0000
ggg2	chr17:21454676-21454897(-)$1	221	95	99	12.0000
EEEE	chr21:45113532-45113763(+)$1	231	210	214	12.0000
:III	chr1:151317497-151317728(-)$1	231	40	44	12.0000
dd::	chr19:41096877-41097115(+)$1	238	110	114	12.0000
eeee	chr4:2067853-2068079(+)$1	226	42	46	12.0000
h###	chr9:132995594-132995811(+)$1	217	97	101	12.0000
ffff	chr1:2451669-2451900(-)$1	231	28	32	12.0000
:eee	chr20:34135092-34135320(+)$1	228	44	48	12.0000
EMMM	chr9:95018899-95019127(-)$1	228	14	18	12.0000
mfff	chr5:175954683-175954904(-)$1	221	187	191	12.0000
FFFF	chr1:6653556-6653801(-)$1	245	33	37	12.0000
==!!	chr2:96850796-96851014(-)$1	218	9	13	12.0000
uuuu	chr3:24019301-24019536(+)$1	235	159	163	12.0000
EEEE	chr12:122497849-122498083(+)$1	234	46	50	12.0000
CCFF	chr5:112170661-112170887(+)$1	226	12	16	12.0000
qa33	chr14:77254963-77255217(-)$1	254	34	38	12.0000
:ccc	chr7:44920003-44920230(-)$1	227	23	27	12.0000
eeee	chr2:20550292-20550507(-)$1	215	46	50	12.0000
:BBK	chr19:33872098-33872337(+)$1	239	120	124	12.0000
!eee	chr6:43147383-43147599(+)$1	216	9	13	12.0000
DDD:	chr6:4954298-4954532(+)$1	234	1	5	12.0000
C{CC	chr19:55739488-55739712(-)$1	224	2	6	12.0000
mddd	chr15:43656150-43656371(-)$1	221	65	69	12.0000
FFFF	chr19:1576836-1577182(-)$1	346	1	5	12.0000
====	chr1:179074174-179074444(-)$1	270	83	87	12.0000
[bbm	chr10:64893117-64893337(+)$1	220	178	182	12.0000
eeee	chr20:34515623-34515849(+)$1	226	87	91	12.0000
gggv	chr7:75958593-75958820(-)$1	227	85	89	12.0000
ff""	chr17:47367080-47367290(-)$1	210	69	73	12.0000
]ddd	chr9:140098482-140098706(-)$1	224	105	109	12.0000
::::	chr5:32174250-32174488(-)$1	238	28	32	12.0000
ffff	chr14:78140231-78140459(-)$1	228	36	40	12.0000
b[cc	chr7:143079614-143079848(+)$1	234	12	16	12.0000
lccc	chr12:122499144-122499366(+)$1	222	32	36	12.0000
a22f	chr15:79178391-79178614(+)$1	223	17	21	12.0000
:::b	chr12:1896287-1896512(+)$1	225	13	17	12.0000
[bbd	chr19:1985423-1985658(-)$1	235	6	10	12.0000
ccc!	chr12:132406311-132406534(+)$1	223	172	176	12.0000
B{EE	chr19:13862476-13862705(+)$1	229	48	52	12.0000
2ddd	chr11:33083069-33083282(+)$1	213	81	85	12.0000
d22c	chr6:33165572-33165809(-)$1	237	171	175	12.0000
mmmd	chr9:136901152-136901374(-)$1	222	44	48	12.0000
]ddd	chr2:242617815-242618045(-)$1	230	70	74	12.0000
eee+	chr19:44662688-44662939(+)$1	251	30	34	12.0000
"ddd	chr19:18978281-18978503(+)$1	222	149	153	12.0000
ffff	chr2:74333270-74333489(+)$1	219	113	117	12.0000
4ggg	chr3:196081441-196081663(-)$1	222	139	143	12.0000
3ddd	chr7:100867126-100867354(+)$1	228	150	154	12.0000
dddd	chr2:207026000-207026210(+)$1	210	71	75	12.0000
gggg	chr10:99218348-99218574(-)$1	226	74	78	12.0000
:eee	chr14:60749362-60749587(+)$1	225	100	104	12.0000
d000	chr5:112175990-112176211(+)$1	221	43	47	12.0000
bDDD	chr14:77974731-77974977(-)$1	246	150	154	12.0000
obb]	chr21:45179915-45180144(+)$1	229	73	77	12.0000

#DB
((((	chr12:110971794-110972011(-)$1	1	58	62	12.0000
((..	chr7:148921642-148921894(+)$1	1	162	166	12.0000
))))	chr13:77458313-77458536(-)$1	1	58	62	12.0000
.(((	chrX:70519875-70520099(+)$1	1	23	27	12.0000
....	chr19:58609459-58609681(-)$1	1	75	79	12.0000
.(..	chr16:30680522-30680743(+)$1	1	5	9	12.0000
(((.	chr16:69362828-69363075(-)$1	1	82	86	12.0000
..((	chr15:31666334-31666563(+)$1	1	57	61	12.0000
((((	chr7:99634809-99635038(+)$1	1	115	119	12.0000
)).)	chr17:7157869-7158095(+)$1	1	210	214	12.0000
((((	chr2:232673135-232673350(+)$1	1	3	7	12.0000
))((	chr22:50282942-50283166(+)$1	1	155	159	12.0000
((((	chr1:47143367-47143615(-)$1	1	90	94	12.0000
)(((	chr17:79801497-79801718(-)$1	1	142	146	12.0000
.(((	chr16:30081430-30081661(+)$1	1	18	22	12.0000
(.((	chr5:65222188-65222421(+)$1	1	3	7	12.0000
))))	chr8:21862695-21862915(+)$1	1	208	212	12.0000
))))	chr6:75962870-75963099(-)$1	1	185	189	12.0000
((((	chr11:17394028-17394253(+)$1	1	32	36	12.0000
))))	chr15:91463659-91463873(+)$1	1	133	137	12.0000
((((	chr3:47882469-47882692(+)$1	1	9	13	12.0000
.(((	chrX:49143449-49143662(+)$1	1	76	80	12.0000
.)))	chr1:1189540-1189772(-)$1	1	72	76	12.0000
))))	chr1:117531750-117531974(+)$1	1	148	152	12.0000
..))	chr10:127530950-127531169(+)$1	1	150	154	12.0000
.)))	chr12:69753617-69753843(+)$1	1	191	195	12.0000
(((.	chr19:42751673-42751896(-)$1	1	11	15	12.0000
))).	chr17:21454676-21454897(-)$1	1	95	99	12.0000
))))	chr21:45113532-45113763(+)$1	1	210	214	12.0000
.(((	chr1:151317497-151317728(-)$1	1	40	44	12.0000
))..	chr19:41096877-41097115(+)$1	1	110	114	12.0000
))))	chr4:2067853-2068079(+)$1	1	42	46	12.0000
(...	chr9:132995594-132995811(+)$1	1	97	101	12.0000
))))	chr1:2451669-2451900(-)$1	1	28	32	12.0000
.(((	chr20:34135092-34135320(+)$1	1	44	48	12.0000
(...	chr9:95018899-95019127(-)$1	1	14	18	12.0000
.)))	chr5:175954683-175954904(-)$1	1	187	191	12.0000
((((	chr1:6653556-6653801(-)$1	1	33	37	12.0000
((..	chr2:96850796-96851014(-)$1	1	9	13	12.0000
....	chr3:24019301-24019536(+)$1	1	159	163	12.0000
((((	chr12:122497849-122498083(+)$1	1	46	50	12.0000
((((	chr5:112170661-112170887(+)$1	1	12	16	12.0000
.)..	chr14:77254963-77255217(-)$1	1	34	38	12.0000
.(((	chr7:44920003-44920230(-)$1	1	23	27	12.0000
))))	chr2:20550292-20550507(-)$1	1	46	50	12.0000
.((.	chr19:33872098-33872337(+)$1	1	120	124	12.0000
.(((	chr6:43147383-43147599(+)$1	1	9	13	12.0000
(((.	chr6:4954298-4954532(+)$1	1	1	5	12.0000
(.((	chr19:55739488-55739712(-)$1	1	2	6	12.0000
.)))	chr15:43656150-43656371(-)$1	1	65	69	12.0000
((((	chr19:1576836-1577182(-)$1	1	1	5	12.0000
((((	chr1:179074174-179074444(-)$1	1	83	87	12.0000
.((.	chr10:64893117-64893337(+)$1	1	178	182	12.0000
((((	chr20:34515623-34515849(+)$1	1	87	91	12.0000
(((.	chr7:75958593-75958820(-)$1	1	85	89	12.0000
((..	chr17:47367080-47367290(-)$1	1	69	73	12.0000
.)))	chr9:140098482-140098706(-)$1	1	105	109	12.0000
....	chr5:32174250-32174488(-)$1	1	28	32	12.0000
((((	chr14:78140231-78140459(-)$1	1	36	40	12.0000
(.((	chr7:143079614-143079848(+)$1	1	12	16	12.0000
.)))	chr12:122499144-122499366(+)$1	1	32	36	12.0000
)..)	chr15:79178391-79178614(+)$1	1	17	21	12.0000
...(	chr12:1896287-1896512(+)$1	1	13	17	12.0000
.(((	chr19:1985423-1985658(-)$1	1	6	10	12.0000
(((.	chr12:132406311-132406534(+)$1	1	172	176	12.0000
(.((	chr19:13862476-13862705(+)$1	1	48	52	12.0000
.)))	chr11:33083069-33083282(+)$1	1	81	85	12.0000
)..)	chr6:33165572-33165809(-)$1	1	171	175	12.0000
...)	chr9:136901152-136901374(-)$1	1	44	48	12.0000
.)))	chr2:242617815-242618045(-)$1	1	70	74	12.0000
(((.	chr19:44662688-44662939(+)$1	1	30	34	12.0000
.(((	chr19:18978281-18978503(+)$1	1	149	153	12.0000
))))	chr2:74333270-74333489(+)$1	1	113	117	12.0000
.)))	chr3:196081441-196081663(-)$1	1	139	143	12.0000
.)))	chr7:100867126-100867354(+)$1	1	150	154	12.0000
((((	chr2:207026000-207026210(+)$1	1	71	75	12.0000
((((	chr10:99218348-99218574(-)$1	1	74	78	12.0000
.(((	chr14:60749362-60749587(+)$1	1	100	104	12.0000
)...	chr5:112175990-112176211(+)$1	1	43	47	12.0000
))))	chr14:77974731-77974977(-)$1	1	150	154	12.0000
.)).	chr21:45179915-45180144(+)$1	1	73	77	12.0000

#PSSM
U : 0.96	u : 0.03	
G : 0.96	g : 0.03	
C : 0.96	c : 0.03	
C : 0.96	c : 0.03	

#score	972.0000000000006
#seq	81
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m1_run2.nuc.txt

#NT
GCUG	chr19:49510229-49510466(+)$1	237	133	137	11.9999
GCUG	chr17:8159477-8159702(+)$1	225	11	15	11.9999
GCUG	chr3:52002717-52002958(-)$1	241	134	138	11.9999
gcug	chr5:108745549-108745785(+)$1	236	96	100	11.9999
GCUG	chr17:80861200-80861427(+)$1	227	96	100	11.9999
GCUG	chr10:120863559-120863805(+)$1	246	72	76	11.9999
GCUG	chr4:119609021-119609264(+)$1	243	62	66	11.9999
GCUG	chr17:74733754-74733983(-)$1	229	103	107	11.9999
GCUG	chr8:56986856-56987082(-)$1	226	44	48	11.9999
gcug	chr10:111985742-111985974(+)$1	232	28	32	11.9999
GCUG	chr7:129771443-129771697(+)$1	254	138	142	11.9999
GCUG	chr1:1271123-1271342(-)$1	219	117	121	11.9999
GCUG	chr7:150759744-150759969(+)$1	225	82	86	11.9999
GCUG	chr19:49993164-49993404(+)$1	240	10	14	11.9999
GCUG	chr19:1383456-1383687(+)$1	231	15	19	11.9999
GCUG	chr19:50311852-50312075(+)$1	223	70	74	11.9999
GCUG	chr3:155588460-155588686(+)$1	226	11	15	11.9999
GCUG	chr6:34557226-34557456(-)$1	230	42	46	11.9999
GCUG	chr19:1578263-1578518(-)$1	255	17	21	11.9999
GCUG	chr6:26273091-26273314(+)$1	223	103	107	11.9999
GCUG	chr1:934311-934539(-)$1	228	10	14	11.9999
GCUG	chr6:37787493-37787720(+)$1	227	49	53	11.9999
GCUG	chr14:23794523-23794760(+)$1	237	136	140	11.9999
GCUG	chr14:21968545-21968916(-)$1	371	155	159	11.9999
GCUG	chr19:38865652-38865893(+)$1	241	68	72	11.9999
GCUG	chr1:55207904-55208125(-)$1	221	185	189	11.9999
GCUG	chr7:103629706-103629934(-)$1	228	144	148	11.9999
gcug	chrX:17168764-17168984(+)$1	220	38	42	11.9999
GCUG	chr20:418111-418341(-)$1	230	153	157	11.9999
GCUG	chr1:1284579-1284812(-)$1	233	92	96	11.9999
gcug	chr17:42836354-42836573(+)$1	219	45	49	11.9999
gcug	chr12:102173531-102173764(+)$1	233	12	16	11.9999
GCUG	chr15:40998302-40998551(-)$1	249	166	170	11.9999
GCUG	chr2:71558835-71559055(+)$1	220	46	50	11.9999
GCUG	chr19:1095194-1095422(-)$1	228	102	106	11.9999
GCUG	chr22:42455781-42456010(-)$1	229	43	47	11.9999
GCUG	chr3:171177891-171178115(-)$1	224	35	39	11.9999
gcug	chr10:73995015-73995271(+)$1	256	92	96	11.9999
gcug	chr9:127951837-127952060(-)$1	223	2	6	11.9999
GCUG	chr14:21793883-21794104(+)$1	221	3	7	11.9999
GCUG	chr17:1613444-1613675(-)$1	231	4	8	11.9999
GCUG	chr21:46237849-46238071(-)$1	222	146	150	11.9999
GCUG	chr3:49757877-49758103(-)$1	226	49	53	11.9999
GCUG	chr14:21979166-21979466(-)$1	300	42	46	11.9999
GCUG	chr19:4065525-4065745(+)$1	220	52	56	11.9999
GCUG	chr14:21971816-21972039(+)$1	223	105	109	11.9999
GCUG	chr5:180687812-180688040(-)$1	228	0	4	11.9999
GCUG	chr22:39259522-39259743(-)$1	221	9	13	11.9999
GCUG	chr15:75940264-75940489(-)$1	225	156	160	11.9999
GCUG	chr1:226107762-226107986(-)$1	224	63	67	11.9999
GCUG	chr17:74077955-74078176(-)$1	221	82	86	11.9999
GCUG	chr16:28074419-28074647(+)$1	228	62	66	11.9999
GCUG	chr15:41023198-41023431(+)$1	233	124	128	11.9999
GCUG	chr19:1434834-1435069(+)$1	235	216	220	11.9999
GCUG	chr9:127631410-127631631(+)$1	221	18	22	11.9999
GCUG	chr19:37180270-37180498(+)$1	228	55	59	11.9999
GCUG	chr7:16736543-16736766(+)$1	223	83	87	11.9999
GCUG	chr6:43970400-43970626(+)$1	226	47	51	11.9999
GCUG	chr4:174253128-174253386(-)$1	258	3	7	11.9999
gcug	chr19:7978305-7978531(+)$1	226	103	107	11.9999
GCUG	chr17:1962085-1962306(+)$1	221	70	74	11.9999
GCUG	chr15:41001160-41001400(+)$1	240	139	143	11.9999
GCUG	chr2:130939309-130939540(-)$1	231	154	158	11.9999
GCUG	chr3:129033570-129033791(-)$1	221	1	5	11.9999
GCUG	chr7:26241396-26241620(+)$1	224	10	14	11.9999
GCUG	chr16:30709506-30709732(+)$1	226	80	84	11.9999
GCUG	chr14:21971713-21972033(-)$1	320	197	201	11.9999
GCUG	chr12:48138482-48138701(-)$1	219	16	20	11.9999
GCUg	chr7:65422378-65422602(+)$1	224	156	160	11.9999
GCUG	chr12:57453353-57453578(-)$1	225	125	129	11.9999
GCUG	chr5:79946505-79946748(-)$1	243	226	230	11.9999
GCUG	chr3:119886218-119886438(+)$1	220	10	14	11.9999
GCUG	chr1:1007839-1008065(+)$1	226	8	12	11.9999
GCUG	chr20:3804881-3805100(-)$1	219	69	73	11.9999
GCUG	chr19:13029956-13030180(-)$1	224	45	49	11.9999
gcug	chr16:53843950-53844207(+)$1	257	249	253	11.9999
GCUG	chr13:41885485-41885704(+)$1	219	29	33	11.9999
GCUG	chr1:117452663-117452888(-)$1	225	139	143	11.9999
GCUG	chr16:69362891-69363115(-)$1	224	14	18	11.9999
GCUG	chr6:163835768-163835995(+)$1	227	71	75	11.9999
GCUG	chr14:21971870-21972125(+)$1	255	51	55	11.9999
GCUG	chr1:156209272-156209497(+)$1	225	89	93	11.9999
GCUG	chr5:138941609-138941836(+)$1	227	18	22	11.9999
GCUG	chr22:21802675-21802896(+)$1	221	68	72	11.9999
GCUG	chr19:49611477-49611704(+)$1	227	114	118	11.9999
GCUG	chr19:1582586-1582805(-)$1	219	111	115	11.9999
GCUG	chr20:17608061-17608284(-)$1	223	12	16	11.9999

#otherMatches

#Struct PSSM
EEEE	chr7:44808944-44809167(-)$1	223	3	7	11.9999
[ccc	chr19:49510229-49510466(+)$1	237	133	137	11.9999
hhhh	chr17:8159477-8159702(+)$1	225	11	15	11.9999
!all	chr3:52002717-52002958(-)$1	241	134	138	11.9999
22ff	chr5:108745549-108745785(+)$1	236	96	100	11.9999
b:dd	chr17:80861200-80861427(+)$1	227	96	100	11.9999
"ddd	chr10:120863559-120863805(+)$1	246	72	76	11.9999
qqqq	chr4:119609021-119609264(+)$1	243	62	66	11.9999
:ccc	chr17:74733754-74733983(-)$1	229	103	107	11.9999
hhhh	chr8:56986856-56987082(-)$1	226	44	48	11.9999
FKKB	chr10:111985742-111985974(+)$1	232	28	32	11.9999
bbdd	chr7:129771443-129771697(+)$1	254	138	142	11.9999
EEEE	chr1:1271123-1271342(-)$1	219	117	121	11.9999
cnnn	chr7:150759744-150759969(+)$1	225	82	86	11.9999
CCDD	chr19:49993164-49993404(+)$1	240	10	14	11.9999
dduu	chr19:1383456-1383687(+)$1	231	15	19	11.9999
[bbq	chr19:50311852-50312075(+)$1	223	70	74	11.9999
GGGG	chr3:155588460-155588686(+)$1	226	11	15	11.9999
ffff	chr6:34557226-34557456(-)$1	230	42	46	11.9999
eeee	chr19:1578263-1578518(-)$1	255	17	21	11.9999
mmmm	chr6:26273091-26273314(+)$1	223	103	107	11.9999
ee[c	chr1:934311-934539(-)$1	228	10	14	11.9999
ebbm	chr6:37787493-37787720(+)$1	227	49	53	11.9999
mmmm	chr14:23794523-23794760(+)$1	237	136	140	11.9999
&&&&	chr14:21968545-21968916(-)$1	371	155	159	11.9999
DDD}	chr19:38865652-38865893(+)$1	241	68	72	11.9999
bbff	chr1:55207904-55208125(-)$1	221	185	189	11.9999
dddd	chr7:103629706-103629934(-)$1	228	144	148	11.9999
D:ee	chrX:17168764-17168984(+)$1	220	38	42	11.9999
GGGG	chr20:418111-418341(-)$1	230	153	157	11.9999
qqqq	chr1:1284579-1284812(-)$1	233	92	96	11.9999
d!!c	chr17:42836354-42836573(+)$1	219	45	49	11.9999
ffff	chr12:102173531-102173764(+)$1	233	12	16	11.9999
::dd	chr15:40998302-40998551(-)$1	249	166	170	11.9999
hhhh	chr2:71558835-71559055(+)$1	220	46	50	11.9999
ffff	chr19:1095194-1095422(-)$1	228	102	106	11.9999
::BB	chr22:42455781-42456010(-)$1	229	43	47	11.9999
dd!!	chr3:171177891-171178115(-)$1	224	35	39	11.9999
dddg	chr10:73995015-73995271(+)$1	256	92	96	11.9999
DDDD	chr9:127951837-127952060(-)$1	223	2	6	11.9999
ffff	chr14:21793883-21794104(+)$1	221	3	7	11.9999
dddr	chr17:1613444-1613675(-)$1	231	4	8	11.9999
gggg	chr21:46237849-46238071(-)$1	222	146	150	11.9999
ddd:	chr3:49757877-49758103(-)$1	226	49	53	11.9999
ccc:	chr14:21979166-21979466(-)$1	300	42	46	11.9999
gggg	chr19:4065525-4065745(+)$1	220	52	56	11.9999
gggg	chr14:21971816-21972039(+)$1	223	105	109	11.9999
ccc"	chr5:180687812-180688040(-)$1	228	0	4	11.9999
cccH	chr22:39259522-39259743(-)$1	221	9	13	11.9999
====	chr15:75940264-75940489(-)$1	225	156	160	11.9999
444f	chr1:226107762-226107986(-)$1	224	63	67	11.9999
GGGG	chr17:74077955-74078176(-)$1	221	82	86	11.9999
cccm	chr16:28074419-28074647(+)$1	228	62	66	11.9999
''''	chr15:41023198-41023431(+)$1	233	124	128	11.9999
ddd4	chr19:1434834-1435069(+)$1	235	216	220	11.9999
!ddd	chr9:127631410-127631631(+)$1	221	18	22	11.9999
hhhd	chr19:37180270-37180498(+)$1	228	55	59	11.9999
ffff	chr7:16736543-16736766(+)$1	223	83	87	11.9999
dddd	chr6:43970400-43970626(+)$1	226	47	51	11.9999
GGGG	chr4:174253128-174253386(-)$1	258	3	7	11.9999
g"""	chr19:7978305-7978531(+)$1	226	103	107	11.9999
::cc	chr17:1962085-1962306(+)$1	221	70	74	11.9999
ee[a	chr15:41001160-41001400(+)$1	240	139	143	11.9999
FFFF	chr2:130939309-130939540(-)$1	231	154	158	11.9999
::::	chr3:129033570-129033791(-)$1	221	1	5	11.9999
EEEE	chr7:26241396-26241620(+)$1	224	10	14	11.9999
eeee	chr16:30709506-30709732(+)$1	226	80	84	11.9999
ccc[	chr14:21971713-21972033(-)$1	320	197	201	11.9999
FFFc	chr12:48138482-48138701(-)$1	219	16	20	11.9999
ffff	chr7:65422378-65422602(+)$1	224	156	160	11.9999
!!dd	chr12:57453353-57453578(-)$1	225	125	129	11.9999
DDEE	chr5:79946505-79946748(-)$1	243	226	230	11.9999
BKKD	chr3:119886218-119886438(+)$1	220	10	14	11.9999
GBBL	chr1:1007839-1008065(+)$1	226	8	12	11.9999
ffff	chr20:3804881-3805100(-)$1	219	69	73	11.9999
!bb[	chr19:13029956-13030180(-)$1	224	45	49	11.9999
FFFF	chr16:53843950-53844207(+)$1	257	249	253	11.9999
FFFF	chr13:41885485-41885704(+)$1	219	29	33	11.9999
dddd	chr1:117452663-117452888(-)$1	225	139	143	11.9999
!fff	chr16:69362891-69363115(-)$1	224	14	18	11.9999
bb""	chr6:163835768-163835995(+)$1	227	71	75	11.9999
oddd	chr14:21971870-21972125(+)$1	255	51	55	11.9999
occc	chr1:156209272-156209497(+)$1	225	89	93	11.9999
cccc	chr5:138941609-138941836(+)$1	227	18	22	11.9999
====	chr22:21802675-21802896(+)$1	221	68	72	11.9999
fff:	chr19:49611477-49611704(+)$1	227	114	118	11.9999
d###	chr19:1582586-1582805(-)$1	219	111	115	11.9999
FFFF	chr20:17608061-17608284(-)$1	223	12	16	11.9999

#DB
((((	chr7:44808944-44809167(-)$1	1	3	7	11.9999
.(((	chr19:49510229-49510466(+)$1	1	133	137	11.9999
((((	chr17:8159477-8159702(+)$1	1	11	15	11.9999
.(..	chr3:52002717-52002958(-)$1	1	134	138	11.9999
..))	chr5:108745549-108745785(+)$1	1	96	100	11.9999
).((	chr17:80861200-80861427(+)$1	1	96	100	11.9999
.(((	chr10:120863559-120863805(+)$1	1	72	76	11.9999
....	chr4:119609021-119609264(+)$1	1	62	66	11.9999
.(((	chr17:74733754-74733983(-)$1	1	103	107	11.9999
((((	chr8:56986856-56987082(-)$1	1	44	48	11.9999
(..(	chr10:111985742-111985974(+)$1	1	28	32	11.9999
))))	chr7:129771443-129771697(+)$1	1	138	142	11.9999
))))	chr1:1271123-1271342(-)$1	1	117	121	11.9999
(...	chr7:150759744-150759969(+)$1	1	82	86	11.9999
((((	chr19:49993164-49993404(+)$1	1	10	14	11.9999
((..	chr19:1383456-1383687(+)$1	1	15	19	11.9999
.((.	chr19:50311852-50312075(+)$1	1	70	74	11.9999
((((	chr3:155588460-155588686(+)$1	1	11	15	11.9999
((((	chr6:34557226-34557456(-)$1	1	42	46	11.9999
((((	chr19:1578263-1578518(-)$1	1	17	21	11.9999
....	chr6:26273091-26273314(+)$1	1	103	107	11.9999
((.(	chr1:934311-934539(-)$1	1	10	14	11.9999
(((.	chr6:37787493-37787720(+)$1	1	49	53	11.9999
....	chr14:23794523-23794760(+)$1	1	136	140	11.9999
....	chr14:21968545-21968916(-)$1	1	155	159	11.9999
))).	chr19:38865652-38865893(+)$1	1	68	72	11.9999
))((	chr1:55207904-55208125(-)$1	1	185	189	11.9999
((((	chr7:103629706-103629934(-)$1	1	144	148	11.9999
(.((	chrX:17168764-17168984(+)$1	1	38	42	11.9999
))))	chr20:418111-418341(-)$1	1	153	157	11.9999
....	chr1:1284579-1284812(-)$1	1	92	96	11.9999
(..(	chr17:42836354-42836573(+)$1	1	45	49	11.9999
((((	chr12:102173531-102173764(+)$1	1	12	16	11.9999
..((	chr15:40998302-40998551(-)$1	1	166	170	11.9999
((((	chr2:71558835-71559055(+)$1	1	46	50	11.9999
))))	chr19:1095194-1095422(-)$1	1	102	106	11.9999
..((	chr22:42455781-42456010(-)$1	1	43	47	11.9999
((..	chr3:171177891-171178115(-)$1	1	35	39	11.9999
)))(	chr10:73995015-73995271(+)$1	1	92	96	11.9999
((((	chr9:127951837-127952060(-)$1	1	2	6	11.9999
((((	chr14:21793883-21794104(+)$1	1	3	7	11.9999
(((.	chr17:1613444-1613675(-)$1	1	4	8	11.9999
))))	chr21:46237849-46238071(-)$1	1	146	150	11.9999
))).	chr3:49757877-49758103(-)$1	1	49	53	11.9999
))).	chr14:21979166-21979466(-)$1	1	42	46	11.9999
((((	chr19:4065525-4065745(+)$1	1	52	56	11.9999
))))	chr14:21971816-21972039(+)$1	1	105	109	11.9999
(((.	chr5:180687812-180688040(-)$1	1	0	4	11.9999
)))(	chr22:39259522-39259743(-)$1	1	9	13	11.9999
((((	chr15:75940264-75940489(-)$1	1	156	160	11.9999
...)	chr1:226107762-226107986(-)$1	1	63	67	11.9999
((((	chr17:74077955-74078176(-)$1	1	82	86	11.9999
(((.	chr16:28074419-28074647(+)$1	1	62	66	11.9999
....	chr15:41023198-41023431(+)$1	1	124	128	11.9999
))).	chr19:1434834-1435069(+)$1	1	216	220	11.9999
.(((	chr9:127631410-127631631(+)$1	1	18	22	11.9999
))))	chr19:37180270-37180498(+)$1	1	55	59	11.9999
))))	chr7:16736543-16736766(+)$1	1	83	87	11.9999
((((	chr6:43970400-43970626(+)$1	1	47	51	11.9999
((((	chr4:174253128-174253386(-)$1	1	3	7	11.9999
(...	chr19:7978305-7978531(+)$1	1	103	107	11.9999
..((	chr17:1962085-1962306(+)$1	1	70	74	11.9999
((.(	chr15:41001160-41001400(+)$1	1	139	143	11.9999
((((	chr2:130939309-130939540(-)$1	1	154	158	11.9999
....	chr3:129033570-129033791(-)$1	1	1	5	11.9999
((((	chr7:26241396-26241620(+)$1	1	10	14	11.9999
((((	chr16:30709506-30709732(+)$1	1	80	84	11.9999
(((.	chr14:21971713-21972033(-)$1	1	197	201	11.9999
((((	chr12:48138482-48138701(-)$1	1	16	20	11.9999
((((	chr7:65422378-65422602(+)$1	1	156	160	11.9999
..((	chr12:57453353-57453578(-)$1	1	125	129	11.9999
))))	chr5:79946505-79946748(-)$1	1	226	230	11.9999
(..(	chr3:119886218-119886438(+)$1	1	10	14	11.9999
(((.	chr1:1007839-1008065(+)$1	1	8	12	11.9999
))))	chr20:3804881-3805100(-)$1	1	69	73	11.9999
.((.	chr19:13029956-13030180(-)$1	1	45	49	11.9999
))))	chr16:53843950-53844207(+)$1	1	249	253	11.9999
((((	chr13:41885485-41885704(+)$1	1	29	33	11.9999
))))	chr1:117452663-117452888(-)$1	1	139	143	11.9999
.(((	chr16:69362891-69363115(-)$1	1	14	18	11.9999
((..	chr6:163835768-163835995(+)$1	1	71	75	11.9999
.)))	chr14:21971870-21972125(+)$1	1	51	55	11.9999
.)))	chr1:156209272-156209497(+)$1	1	89	93	11.9999
)))(	chr5:138941609-138941836(+)$1	1	18	22	11.9999
((((	chr22:21802675-21802896(+)$1	1	68	72	11.9999
))).	chr19:49611477-49611704(+)$1	1	114	118	11.9999
(...	chr19:1582586-1582805(-)$1	1	111	115	11.9999
((((	chr20:17608061-17608284(-)$1	1	12	16	11.9999

#PSSM
G : 0.89	g : 0.10	
C : 0.89	c : 0.10	
U : 0.89	u : 0.10	
G : 0.88	g : 0.11	

#score	1055.9999999999998
#seq	88
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m1_run1.nuc.txt

#NT
GAA	chr16:23478522-23478751(-)$1	229	89	92	9.0000
GAA	chr15:49172000-49172225(+)$1	225	80	83	9.0000
GAA	chr4:177249427-177249659(+)$1	232	33	36	9.0000
GAA	chr20:21369889-21370117(+)$1	228	33	36	9.0000
GAA	chr5:78982295-78982518(+)$1	223	196	199	9.0000
GAA	chr1:204372607-204372830(-)$1	223	94	97	9.0000
GAA	chr17:56050632-56050857(-)$1	225	86	89	9.0000
GAA	chr6:79650274-79650493(-)$1	219	16	19	9.0000
GAA	chr1:87571007-87571232(+)$1	225	53	56	9.0000
GAA	chr10:70742699-70742923(+)$1	224	87	90	9.0000
GAA	chr6:19840426-19840651(+)$1	225	12	15	9.0000
GAA	chr1:203765501-203765724(+)$1	223	84	87	9.0000
GAA	chr2:74441340-74441563(+)$1	223	74	77	9.0000
GAA	chr15:45900594-45900814(+)$1	220	1	4	9.0000
gaa	chr7:112101550-112101785(+)$1	235	67	70	9.0000
GAA	chr15:77338283-77338505(-)$1	222	1	4	9.0000
GAA	chr4:17845643-17845868(+)$1	225	26	29	9.0000
GAA	chr21:31851995-31852222(-)$1	227	14	17	9.0000
GAA	chr11:85372547-85372775(-)$1	228	23	26	9.0000
GAA	chr1:115250064-115250293(-)$1	229	0	3	9.0000
GAA	chr6:163987959-163988185(+)$1	226	211	214	9.0000
gaa	chr16:74339561-74339788(+)$1	227	9	12	9.0000
GAA	chr19:33871132-33871357(+)$1	225	59	62	9.0000
GAA	chr11:105968503-105968730(+)$1	227	16	19	9.0000
GAA	chr2:183790311-183790534(-)$1	223	27	30	9.0000
GAA	chr22:29184916-29185142(+)$1	226	71	74	9.0000
GAA	chr9:32973259-32973485(-)$1	226	65	68	9.0000
GAA	chr12:124498951-124499183(+)$1	232	47	50	9.0000
GAA	chr3:133876517-133876741(-)$1	224	75	78	9.0000
GAA	chr13:98116947-98117180(+)$1	233	16	19	9.0000
GAA	chr9:77562522-77562747(-)$1	225	43	46	9.0000
GAA	chr8:6616763-6616987(+)$1	224	23	26	9.0000
gaa	chr3:10193307-10193527(+)$1	220	200	203	9.0000
GAA	chr20:30157218-30157442(+)$1	224	15	18	9.0000
GAA	chr11:94608374-94608596(+)$1	222	21	24	9.0000
GAA	chr5:175773918-175774152(-)$1	234	3	6	9.0000
GAA	chr5:114949477-114949697(-)$1	220	9	12	9.0000
GAA	chr3:15483568-15483797(+)$1	229	36	39	9.0000
GAA	chr7:27210643-27210874(-)$1	231	23	26	9.0000
GAA	chrX:70520884-70521110(+)$1	226	77	80	9.0000
GAA	chr18:12986195-12986418(+)$1	223	64	67	9.0000
GAA	chr9:86553240-86553464(-)$1	224	71	74	9.0000
GAA	chr19:37673021-37673251(-)$1	230	57	60	9.0000
GAA	chr7:94297494-94297718(+)$1	224	128	131	9.0000
GAA	chr6:7288874-7289092(-)$1	218	41	44	9.0000
GAA	chr9:123940765-123940993(-)$1	228	69	72	9.0000
GAA	chr5:54460230-54460452(+)$1	222	35	38	9.0000
GAA	chr5:10435271-10435503(+)$1	232	219	222	9.0000
GAA	chr20:62219694-62219916(-)$1	222	197	200	9.0000
GAA	chr8:26365011-26365237(-)$1	226	4	7	9.0000
GAA	chr1:67877051-67877281(-)$1	230	11	14	9.0000
GAA	chr5:148731926-148732147(+)$1	221	211	214	9.0000
GAA	chr1:205577224-205577447(-)$1	223	27	30	9.0000
GAA	chr19:37238463-37238688(-)$1	225	0	3	9.0000
GAA	chrX:153063814-153064035(+)$1	221	52	55	9.0000
GAA	chr21:18966144-18966368(-)$1	224	0	3	9.0000
GAA	chr17:74730277-74730507(-)$1	230	157	160	9.0000
gaa	chr18:72909264-72909495(-)$1	231	140	143	9.0000
GAA	chr20:49507538-49507758(-)$1	220	32	35	9.0000
GAA	chr19:16756861-16757083(-)$1	222	6	9	9.0000
GAA	chr2:170494483-170494710(+)$1	227	12	15	9.0000
GAA	chr1:192985207-192985436(-)$1	229	5	8	9.0000
GAA	chr8:33354050-33354273(+)$1	223	6	9	9.0000
GAA	chr15:65410636-65410858(-)$1	222	1	4	9.0000
GAA	chr1:193220222-193220455(+)$1	233	9	12	9.0000
GAA	chr21:27143068-27143292(+)$1	224	24	27	9.0000
GAA	chr3:23961811-23962052(+)$1	241	40	43	9.0000
GAA	chr10:89513169-89513395(-)$1	226	88	91	9.0000
GAA	chr20:57608261-57608479(-)$1	218	25	28	9.0000
GAA	chr1:171673429-171673665(-)$1	236	4	7	9.0000
GAA	chr15:91509974-91510199(-)$1	225	55	58	9.0000
GAA	chr7:66453223-66453457(-)$1	234	1	4	9.0000
GAA	chr12:95645616-95645842(+)$1	226	17	20	9.0000
GAA	chr12:64844284-64844507(+)$1	223	6	9	9.0000
GAA	chr15:98515552-98515778(+)$1	226	158	161	9.0000
GAA	chr10:112052960-112053182(-)$1	222	10	13	9.0000
GAA	chr16:66756940-66757161(-)$1	221	5	8	9.0000
gaa	chr19:23521455-23521682(-)$1	227	127	130	9.0000
GAA	chr11:105881559-105881785(-)$1	226	20	23	9.0000
GAA	chr2:8992854-8993078(-)$1	224	12	15	9.0000
GAA	chr14:69925461-69925690(+)$1	229	8	11	9.0000
GAA	chr1:67877466-67877692(-)$1	226	28	31	9.0000
GAA	chr14:64151437-64151673(-)$1	236	6	9	9.0000
GAA	chr22:41832092-41832313(-)$1	221	40	43	9.0000
GAA	chr1:161128246-161128469(+)$1	223	20	23	9.0000
GAA	chr11:108028945-108029163(-)$1	218	15	18	9.0000
GAA	chr12:57449337-57449561(-)$1	224	54	57	9.0000
GAA	chr3:195776558-195776786(-)$1	228	2	5	9.0000
GAA	chr16:20808819-20809039(-)$1	220	9	12	9.0000
GAA	chr18:9955107-9955337(+)$1	230	44	47	9.0000
GAA	chr2:46988722-46988945(+)$1	223	74	77	9.0000
GAA	chr17:17095204-17095429(+)$1	225	38	41	9.0000
GAA	chr1:234741747-234741966(-)$1	219	7	10	9.0000
GAA	chr4:140394905-140395133(+)$1	228	8	11	9.0000
GAA	chr12:69667627-69667848(+)$1	221	68	71	9.0000
GAA	chr6:151686307-151686533(-)$1	226	57	60	9.0000
GAA	chr1:228682257-228682483(+)$1	226	131	134	9.0000
GAA	chr6:105528862-105529109(+)$1	247	8	11	9.0000
GAA	chr19:36727174-36727392(+)$1	218	53	56	9.0000

#otherMatches

#Struct PSSM
gg[	chr5:179155904-179156130(+)$1	226	36	39	9.0000
===	chr16:23478522-23478751(-)$1	229	89	92	9.0000
ee:	chr15:49172000-49172225(+)$1	225	80	83	9.0000
!!f	chr4:177249427-177249659(+)$1	232	33	36	9.0000
ccc	chr20:21369889-21370117(+)$1	228	33	36	9.0000
eee	chr5:78982295-78982518(+)$1	223	196	199	9.0000
fff	chr1:204372607-204372830(-)$1	223	94	97	9.0000
ee%	chr17:56050632-56050857(-)$1	225	86	89	9.0000
==[	chr6:79650274-79650493(-)$1	219	16	19	9.0000
i##	chr1:87571007-87571232(+)$1	225	53	56	9.0000
eee	chr10:70742699-70742923(+)$1	224	87	90	9.0000
f[c	chr6:19840426-19840651(+)$1	225	12	15	9.0000
lll	chr1:203765501-203765724(+)$1	223	84	87	9.0000
sss	chr2:74441340-74441563(+)$1	223	74	77	9.0000
eee	chr15:45900594-45900814(+)$1	220	1	4	9.0000
G::	chr7:112101550-112101785(+)$1	235	67	70	9.0000
::F	chr15:77338283-77338505(-)$1	222	1	4	9.0000
NNH	chr4:17845643-17845868(+)$1	225	26	29	9.0000
JJJ	chr21:31851995-31852222(-)$1	227	14	17	9.0000
FMM	chr11:85372547-85372775(-)$1	228	23	26	9.0000
:::	chr1:115250064-115250293(-)$1	229	0	3	9.0000
:GG	chr6:163987959-163988185(+)$1	226	211	214	9.0000
:::	chr16:74339561-74339788(+)$1	227	9	12	9.0000
:::	chr19:33871132-33871357(+)$1	225	59	62	9.0000
oob	chr11:105968503-105968730(+)$1	227	16	19	9.0000
DDD	chr2:183790311-183790534(-)$1	223	27	30	9.0000
===	chr22:29184916-29185142(+)$1	226	71	74	9.0000
fff	chr9:32973259-32973485(-)$1	226	65	68	9.0000
ddd	chr12:124498951-124499183(+)$1	232	47	50	9.0000
eee	chr3:133876517-133876741(-)$1	224	75	78	9.0000
D::	chr13:98116947-98117180(+)$1	233	16	19	9.0000
===	chr9:77562522-77562747(-)$1	225	43	46	9.0000
e[b	chr8:6616763-6616987(+)$1	224	23	26	9.0000
hmm	chr3:10193307-10193527(+)$1	220	200	203	9.0000
FF:	chr20:30157218-30157442(+)$1	224	15	18	9.0000
(((	chr11:94608374-94608596(+)$1	222	21	24	9.0000
fff	chr5:175773918-175774152(-)$1	234	3	6	9.0000
mmf	chr5:114949477-114949697(-)$1	220	9	12	9.0000
ddd	chr3:15483568-15483797(+)$1	229	36	39	9.0000
+++	chr7:27210643-27210874(-)$1	231	23	26	9.0000
fff	chrX:70520884-70521110(+)$1	226	77	80	9.0000
"""	chr18:12986195-12986418(+)$1	223	64	67	9.0000
ddd	chr9:86553240-86553464(-)$1	224	71	74	9.0000
e$$	chr19:37673021-37673251(-)$1	230	57	60	9.0000
:==	chr7:94297494-94297718(+)$1	224	128	131	9.0000
ggg	chr6:7288874-7289092(-)$1	218	41	44	9.0000
ddd	chr9:123940765-123940993(-)$1	228	69	72	9.0000
FFF	chr5:54460230-54460452(+)$1	222	35	38	9.0000
HHH	chr5:10435271-10435503(+)$1	232	219	222	9.0000
DD|	chr20:62219694-62219916(-)$1	222	197	200	9.0000
:::	chr8:26365011-26365237(-)$1	226	4	7	9.0000
ggg	chr1:67877051-67877281(-)$1	230	11	14	9.0000
E__	chr5:148731926-148732147(+)$1	221	211	214	9.0000
GGG	chr1:205577224-205577447(-)$1	223	27	30	9.0000
:EE	chr19:37238463-37238688(-)$1	225	0	3	9.0000
444	chrX:153063814-153064035(+)$1	221	52	55	9.0000
:::	chr21:18966144-18966368(-)$1	224	0	3	9.0000
ff:	chr17:74730277-74730507(-)$1	230	157	160	9.0000
hhh	chr18:72909264-72909495(-)$1	231	140	143	9.0000
:::	chr20:49507538-49507758(-)$1	220	32	35	9.0000
qqq	chr19:16756861-16757083(-)$1	222	6	9	9.0000
DEE	chr2:170494483-170494710(+)$1	227	12	15	9.0000
dll	chr1:192985207-192985436(-)$1	229	5	8	9.0000
hh&	chr8:33354050-33354273(+)$1	223	6	9	9.0000
:::	chr15:65410636-65410858(-)$1	222	1	4	9.0000
HHH	chr1:193220222-193220455(+)$1	233	9	12	9.0000
CCC	chr21:27143068-27143292(+)$1	224	24	27	9.0000
ee:	chr3:23961811-23962052(+)$1	241	40	43	9.0000
g::	chr10:89513169-89513395(-)$1	226	88	91	9.0000
:::	chr20:57608261-57608479(-)$1	218	25	28	9.0000
DDD	chr1:171673429-171673665(-)$1	236	4	7	9.0000
bb[	chr15:91509974-91510199(-)$1	225	55	58	9.0000
EEE	chr7:66453223-66453457(-)$1	234	1	4	9.0000
dd3	chr12:95645616-95645842(+)$1	226	17	20	9.0000
BB:	chr12:64844284-64844507(+)$1	223	6	9	9.0000
eee	chr15:98515552-98515778(+)$1	226	158	161	9.0000
KKE	chr10:112052960-112053182(-)$1	222	10	13	9.0000
KKD	chr16:66756940-66757161(-)$1	221	5	8	9.0000
ca]	chr19:23521455-23521682(-)$1	227	127	130	9.0000
BBC	chr11:105881559-105881785(-)$1	226	20	23	9.0000
ggg	chr2:8992854-8993078(-)$1	224	12	15	9.0000
D::	chr14:69925461-69925690(+)$1	229	8	11	9.0000
nnn	chr1:67877466-67877692(-)$1	226	28	31	9.0000
HHH	chr14:64151437-64151673(-)$1	236	6	9	9.0000
E::	chr22:41832092-41832313(-)$1	221	40	43	9.0000
^^^	chr1:161128246-161128469(+)$1	223	20	23	9.0000
:::	chr11:108028945-108029163(-)$1	218	15	18	9.0000
ggg	chr12:57449337-57449561(-)$1	224	54	57	9.0000
c!!	chr3:195776558-195776786(-)$1	228	2	5	9.0000
b^^	chr16:20808819-20809039(-)$1	220	9	12	9.0000
ddd	chr18:9955107-9955337(+)$1	230	44	47	9.0000
:::	chr2:46988722-46988945(+)$1	223	74	77	9.0000
ppp	chr17:17095204-17095429(+)$1	225	38	41	9.0000
###	chr1:234741747-234741966(-)$1	219	7	10	9.0000
iii	chr4:140394905-140395133(+)$1	228	8	11	9.0000
^^^	chr12:69667627-69667848(+)$1	221	68	71	9.0000
sgg	chr6:151686307-151686533(-)$1	226	57	60	9.0000
EE{	chr1:228682257-228682483(+)$1	226	131	134	9.0000
eee	chr6:105528862-105529109(+)$1	247	8	11	9.0000
EEE	chr19:36727174-36727392(+)$1	218	53	56	9.0000

#DB
((.	chr5:179155904-179156130(+)$1	1	36	39	9.0000
(((	chr16:23478522-23478751(-)$1	1	89	92	9.0000
)).	chr15:49172000-49172225(+)$1	1	80	83	9.0000
..(	chr4:177249427-177249659(+)$1	1	33	36	9.0000
)))	chr20:21369889-21370117(+)$1	1	33	36	9.0000
(((	chr5:78982295-78982518(+)$1	1	196	199	9.0000
(((	chr1:204372607-204372830(-)$1	1	94	97	9.0000
((.	chr17:56050632-56050857(-)$1	1	86	89	9.0000
((.	chr6:79650274-79650493(-)$1	1	16	19	9.0000
(..	chr1:87571007-87571232(+)$1	1	53	56	9.0000
)))	chr10:70742699-70742923(+)$1	1	87	90	9.0000
(.(	chr6:19840426-19840651(+)$1	1	12	15	9.0000
...	chr1:203765501-203765724(+)$1	1	84	87	9.0000
...	chr2:74441340-74441563(+)$1	1	74	77	9.0000
(((	chr15:45900594-45900814(+)$1	1	1	4	9.0000
(..	chr7:112101550-112101785(+)$1	1	67	70	9.0000
..(	chr15:77338283-77338505(-)$1	1	1	4	9.0000
..(	chr4:17845643-17845868(+)$1	1	26	29	9.0000
(((	chr21:31851995-31852222(-)$1	1	14	17	9.0000
(..	chr11:85372547-85372775(-)$1	1	23	26	9.0000
...	chr1:115250064-115250293(-)$1	1	0	3	9.0000
.))	chr6:163987959-163988185(+)$1	1	211	214	9.0000
...	chr16:74339561-74339788(+)$1	1	9	12	9.0000
...	chr19:33871132-33871357(+)$1	1	59	62	9.0000
..)	chr11:105968503-105968730(+)$1	1	16	19	9.0000
(((	chr2:183790311-183790534(-)$1	1	27	30	9.0000
)))	chr22:29184916-29185142(+)$1	1	71	74	9.0000
(((	chr9:32973259-32973485(-)$1	1	65	68	9.0000
(((	chr12:124498951-124499183(+)$1	1	47	50	9.0000
)))	chr3:133876517-133876741(-)$1	1	75	78	9.0000
(..	chr13:98116947-98117180(+)$1	1	16	19	9.0000
(((	chr9:77562522-77562747(-)$1	1	43	46	9.0000
(.(	chr8:6616763-6616987(+)$1	1	23	26	9.0000
(..	chr3:10193307-10193527(+)$1	1	200	203	9.0000
((.	chr20:30157218-30157442(+)$1	1	15	18	9.0000
...	chr11:94608374-94608596(+)$1	1	21	24	9.0000
(((	chr5:175773918-175774152(-)$1	1	3	6	9.0000
..)	chr5:114949477-114949697(-)$1	1	9	12	9.0000
(((	chr3:15483568-15483797(+)$1	1	36	39	9.0000
...	chr7:27210643-27210874(-)$1	1	23	26	9.0000
)))	chrX:70520884-70521110(+)$1	1	77	80	9.0000
...	chr18:12986195-12986418(+)$1	1	64	67	9.0000
(((	chr9:86553240-86553464(-)$1	1	71	74	9.0000
(..	chr19:37673021-37673251(-)$1	1	57	60	9.0000
.((	chr7:94297494-94297718(+)$1	1	128	131	9.0000
)))	chr6:7288874-7289092(-)$1	1	41	44	9.0000
)))	chr9:123940765-123940993(-)$1	1	69	72	9.0000
(((	chr5:54460230-54460452(+)$1	1	35	38	9.0000
)))	chr5:10435271-10435503(+)$1	1	219	222	9.0000
)).	chr20:62219694-62219916(-)$1	1	197	200	9.0000
...	chr8:26365011-26365237(-)$1	1	4	7	9.0000
(((	chr1:67877051-67877281(-)$1	1	11	14	9.0000
)..	chr5:148731926-148732147(+)$1	1	211	214	9.0000
(((	chr1:205577224-205577447(-)$1	1	27	30	9.0000
.((	chr19:37238463-37238688(-)$1	1	0	3	9.0000
...	chrX:153063814-153064035(+)$1	1	52	55	9.0000
...	chr21:18966144-18966368(-)$1	1	0	3	9.0000
)).	chr17:74730277-74730507(-)$1	1	157	160	9.0000
)))	chr18:72909264-72909495(-)$1	1	140	143	9.0000
...	chr20:49507538-49507758(-)$1	1	32	35	9.0000
...	chr19:16756861-16757083(-)$1	1	6	9	9.0000
(((	chr2:170494483-170494710(+)$1	1	12	15	9.0000
(..	chr1:192985207-192985436(-)$1	1	5	8	9.0000
((.	chr8:33354050-33354273(+)$1	1	6	9	9.0000
...	chr15:65410636-65410858(-)$1	1	1	4	9.0000
(((	chr1:193220222-193220455(+)$1	1	9	12	9.0000
(((	chr21:27143068-27143292(+)$1	1	24	27	9.0000
)).	chr3:23961811-23962052(+)$1	1	40	43	9.0000
)..	chr10:89513169-89513395(-)$1	1	88	91	9.0000
...	chr20:57608261-57608479(-)$1	1	25	28	9.0000
(((	chr1:171673429-171673665(-)$1	1	4	7	9.0000
((.	chr15:91509974-91510199(-)$1	1	55	58	9.0000
(((	chr7:66453223-66453457(-)$1	1	1	4	9.0000
)).	chr12:95645616-95645842(+)$1	1	17	20	9.0000
((.	chr12:64844284-64844507(+)$1	1	6	9	9.0000
)))	chr15:98515552-98515778(+)$1	1	158	161	9.0000
..(	chr10:112052960-112053182(-)$1	1	10	13	9.0000
..(	chr16:66756940-66757161(-)$1	1	5	8	9.0000
)).	chr19:23521455-23521682(-)$1	1	127	130	9.0000
(((	chr11:105881559-105881785(-)$1	1	20	23	9.0000
)))	chr2:8992854-8993078(-)$1	1	12	15	9.0000
(..	chr14:69925461-69925690(+)$1	1	8	11	9.0000
...	chr1:67877466-67877692(-)$1	1	28	31	9.0000
(((	chr14:64151437-64151673(-)$1	1	6	9	9.0000
(..	chr22:41832092-41832313(-)$1	1	40	43	9.0000
...	chr1:161128246-161128469(+)$1	1	20	23	9.0000
...	chr11:108028945-108029163(-)$1	1	15	18	9.0000
(((	chr12:57449337-57449561(-)$1	1	54	57	9.0000
(..	chr3:195776558-195776786(-)$1	1	2	5	9.0000
(..	chr16:20808819-20809039(-)$1	1	9	12	9.0000
)))	chr18:9955107-9955337(+)$1	1	44	47	9.0000
...	chr2:46988722-46988945(+)$1	1	74	77	9.0000
...	chr17:17095204-17095429(+)$1	1	38	41	9.0000
...	chr1:234741747-234741966(-)$1	1	7	10	9.0000
(((	chr4:140394905-140395133(+)$1	1	8	11	9.0000
...	chr12:69667627-69667848(+)$1	1	68	71	9.0000
.))	chr6:151686307-151686533(-)$1	1	57	60	9.0000
((.	chr1:228682257-228682483(+)$1	1	131	134	9.0000
(((	chr6:105528862-105529109(+)$1	1	8	11	9.0000
(((	chr19:36727174-36727392(+)$1	1	53	56	9.0000

#PSSM
G : 0.95	g : 0.05	
A : 0.95	a : 0.05	
A : 0.95	a : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m3_run1.nuc.txt

#NT
UUUA	chr9:86584253-86584496(-)$1	243	44	48	12.0000
UUUA	chr9:123367816-123368090(-)$1	274	20	24	12.0000
UUUA	chr17:48941213-48941459(-)$1	246	111	115	12.0000
UUUA	chr10:98292798-98293027(-)$1	229	1	5	12.0000
UUUA	chrX:48435824-48436083(+)$1	259	78	82	12.0000
UUUA	chr5:86705034-86705269(-)$1	235	33	37	12.0000
UUUA	chr6:122777572-122777804(-)$1	232	122	126	12.0000
UUUA	chr4:108829724-108829954(+)$1	230	24	28	12.0000
UUUA	chr18:54278163-54278397(-)$1	234	120	124	12.0000
UUUA	chr4:123814223-123814474(+)$1	251	0	4	12.0000
UUUA	chr5:14758562-14758791(-)$1	229	6	10	12.0000
UUUA	chr7:112423936-112424159(-)$1	223	0	4	12.0000
UUUA	chr17:5386025-5386258(-)$1	233	12	16	12.0000
UUUA	chr6:170105105-170105331(+)$1	226	49	53	12.0000
UUUA	chr11:9459623-9459853(+)$1	230	72	76	12.0000
UUUA	chr5:131008402-131008634(-)$1	232	121	125	12.0000
UUUA	chr15:41643036-41643288(+)$1	252	53	57	12.0000
UUUA	chr1:63884952-63885186(+)$1	234	9	13	12.0000
UUUA	chr17:34893889-34894126(+)$1	237	89	93	12.0000
UUUA	chrM:10104-10389(+)$1	285	170	174	12.0000
UUUA	chr2:38522989-38523244(-)$1	255	191	195	12.0000
UUUA	chr17:29551989-29552215(+)$1	226	26	30	12.0000
UUUA	chr13:45010577-45010808(-)$1	231	87	91	12.0000
UUUA	chr1:93298970-93299204(+)$1	234	8	12	12.0000
UUUA	chr8:71499064-71499290(-)$1	226	35	39	12.0000
UUUA	chr2:42936144-42936371(+)$1	227	102	106	12.0000
UUUA	chr5:134235167-134235401(+)$1	234	120	124	12.0000
UUUA	chr20:34213906-34214176(-)$1	270	127	131	12.0000
UUUA	chr1:203786117-203786345(+)$1	228	150	154	12.0000
uuua	chr5:864404-864693(-)$1	289	132	136	12.0000
UUUA	chr8:38961084-38961386(+)$1	302	113	117	12.0000
UUUA	chr7:91743055-91743284(-)$1	229	12	16	12.0000
UUUA	chr14:57698232-57698463(-)$1	231	61	65	12.0000
uuua	chr2:182766402-182766665(+)$1	263	26	30	12.0000
UUUA	chr7:112423829-112424057(-)$1	228	8	12	12.0000
UUUA	chr17:56082278-56082559(-)$1	281	2	6	12.0000
UUUA	chr2:198256869-198257170(-)$1	301	284	288	12.0000
UUUA	chr17:48940650-48940874(-)$1	224	17	21	12.0000
UUUA	chr2:188361596-188361823(-)$1	227	0	4	12.0000
UUUA	chr11:62291708-62291936(-)$1	228	101	105	12.0000
UUUA	chrM:14381-14653(-)$1	272	11	15	12.0000
UUUA	chr12:69995124-69995392(+)$1	268	68	72	12.0000
UUUA	chr1:28177069-28177295(+)$1	226	187	191	12.0000
UUUA	chr6:64289828-64290064(+)$1	236	149	153	12.0000
UUUA	chr13:96443144-96443447(+)$1	303	113	117	12.0000
UUUA	chr1:160247861-160248110(-)$1	249	57	61	12.0000
UUUA	chr1:32384562-32384836(-)$1	274	57	61	12.0000
UUUA	chr14:54896879-54897115(-)$1	236	103	107	12.0000
uuua	chr2:38523149-38523459(-)$1	310	80	84	12.0000
UUUA	chr14:73959656-73959886(+)$1	230	108	112	12.0000
UUUA	chr11:9444498-9444740(+)$1	242	56	60	12.0000
UUUA	chr2:128521990-128522277(-)$1	287	138	142	12.0000
UUUA	chr5:92956669-92956901(-)$1	232	122	126	12.0000
UUUA	chr15:64458148-64458407(-)$1	259	22	26	12.0000
UUUA	chr4:123813799-123814102(+)$1	303	17	21	12.0000
UUUA	chr7:148523495-148523722(-)$1	227	137	141	12.0000
uuua	chr5:134192921-134193147(+)$1	226	17	21	12.0000
UUUA	chr12:111157906-111158191(-)$1	285	103	107	12.0000
UUUA	chr8:62574384-62574646(-)$1	262	83	87	12.0000
UUUA	chr16:66592077-66592311(+)$1	234	42	46	12.0000
UUUA	chr11:32954264-32954491(+)$1	227	5	9	12.0000
UUUA	chr1:68947115-68947340(-)$1	225	61	65	12.0000
UUUA	chr17:34893429-34893666(+)$1	237	115	119	12.0000
UUUA	chr19:11256947-11257172(-)$1	225	28	32	12.0000
UUUA	chr7:94166789-94167016(+)$1	227	113	117	12.0000
uuua	chr19:18390706-18390940(-)$1	234	52	56	12.0000

#otherMatches

#Struct PSSM
eeee	chr5:58571073-58571357(-)$1	284	44	48	12.0000
eee!	chr9:86584253-86584496(-)$1	243	44	48	12.0000
::::	chr9:123367816-123368090(-)$1	274	20	24	12.0000
::::	chr17:48941213-48941459(-)$1	246	111	115	12.0000
::::	chr10:98292798-98293027(-)$1	229	1	5	12.0000
GGG:	chrX:48435824-48436083(+)$1	259	78	82	12.0000
!ddd	chr5:86705034-86705269(-)$1	235	33	37	12.0000
iiii	chr6:122777572-122777804(-)$1	232	122	126	12.0000
J:::	chr4:108829724-108829954(+)$1	230	24	28	12.0000
ii!!	chr18:54278163-54278397(-)$1	234	120	124	12.0000
::::	chr4:123814223-123814474(+)$1	251	0	4	12.0000
hhhh	chr5:14758562-14758791(-)$1	229	6	10	12.0000
::::	chr7:112423936-112424159(-)$1	223	0	4	12.0000
oooo	chr17:5386025-5386258(-)$1	233	12	16	12.0000
22dd	chr6:170105105-170105331(+)$1	226	49	53	12.0000
ffff	chr11:9459623-9459853(+)$1	230	72	76	12.0000
eeee	chr5:131008402-131008634(-)$1	232	121	125	12.0000
::::	chr15:41643036-41643288(+)$1	252	53	57	12.0000
JJJJ	chr1:63884952-63885186(+)$1	234	9	13	12.0000
ssss	chr17:34893889-34894126(+)$1	237	89	93	12.0000
::::	chrM:10104-10389(+)$1	285	170	174	12.0000
eeee	chr2:38522989-38523244(-)$1	255	191	195	12.0000
fffG	chr17:29551989-29552215(+)$1	226	26	30	12.0000
G:::	chr13:45010577-45010808(-)$1	231	87	91	12.0000
::::	chr1:93298970-93299204(+)$1	234	8	12	12.0000
tfff	chr8:71499064-71499290(-)$1	226	35	39	12.0000
^^^^	chr2:42936144-42936371(+)$1	227	102	106	12.0000
GGKK	chr5:134235167-134235401(+)$1	234	120	124	12.0000
::::	chr20:34213906-34214176(-)$1	270	127	131	12.0000
ssss	chr1:203786117-203786345(+)$1	228	150	154	12.0000
KFFF	chr5:864404-864693(-)$1	289	132	136	12.0000
::::	chr8:38961084-38961386(+)$1	302	113	117	12.0000
::::	chr7:91743055-91743284(-)$1	229	12	16	12.0000
eeee	chr14:57698232-57698463(-)$1	231	61	65	12.0000
::ff	chr2:182766402-182766665(+)$1	263	26	30	12.0000
::::	chr7:112423829-112424057(-)$1	228	8	12	12.0000
::::	chr17:56082278-56082559(-)$1	281	2	6	12.0000
HHH:	chr2:198256869-198257170(-)$1	301	284	288	12.0000
::::	chr17:48940650-48940874(-)$1	224	17	21	12.0000
::::	chr2:188361596-188361823(-)$1	227	0	4	12.0000
2hhh	chr11:62291708-62291936(-)$1	228	101	105	12.0000
:FFF	chrM:14381-14653(-)$1	272	11	15	12.0000
NNNN	chr12:69995124-69995392(+)$1	268	68	72	12.0000
::ee	chr1:28177069-28177295(+)$1	226	187	191	12.0000
iii]	chr6:64289828-64290064(+)$1	236	149	153	12.0000
eeee	chr13:96443144-96443447(+)$1	303	113	117	12.0000
++++	chr1:160247861-160248110(-)$1	249	57	61	12.0000
2fff	chr1:32384562-32384836(-)$1	274	57	61	12.0000
ddd]	chr14:54896879-54897115(-)$1	236	103	107	12.0000
JJJJ	chr2:38523149-38523459(-)$1	310	80	84	12.0000
::::	chr14:73959656-73959886(+)$1	230	108	112	12.0000
::ff	chr11:9444498-9444740(+)$1	242	56	60	12.0000
mmmm	chr2:128521990-128522277(-)$1	287	138	142	12.0000
oooo	chr5:92956669-92956901(-)$1	232	122	126	12.0000
e###	chr15:64458148-64458407(-)$1	259	22	26	12.0000
eeer	chr4:123813799-123814102(+)$1	303	17	21	12.0000
^^^^	chr7:148523495-148523722(-)$1	227	137	141	12.0000
====	chr5:134192921-134193147(+)$1	226	17	21	12.0000
e+++	chr12:111157906-111158191(-)$1	285	103	107	12.0000
pppp	chr8:62574384-62574646(-)$1	262	83	87	12.0000
ffff	chr16:66592077-66592311(+)$1	234	42	46	12.0000
::::	chr11:32954264-32954491(+)$1	227	5	9	12.0000
pppp	chr1:68947115-68947340(-)$1	225	61	65	12.0000
>>>>	chr17:34893429-34893666(+)$1	237	115	119	12.0000
::::	chr19:11256947-11257172(-)$1	225	28	32	12.0000
==!!	chr7:94166789-94167016(+)$1	227	113	117	12.0000
::::	chr19:18390706-18390940(-)$1	234	52	56	12.0000

#DB
((((	chr5:58571073-58571357(-)$1	1	44	48	12.0000
(((.	chr9:86584253-86584496(-)$1	1	44	48	12.0000
....	chr9:123367816-123368090(-)$1	1	20	24	12.0000
....	chr17:48941213-48941459(-)$1	1	111	115	12.0000
....	chr10:98292798-98293027(-)$1	1	1	5	12.0000
))).	chrX:48435824-48436083(+)$1	1	78	82	12.0000
.(((	chr5:86705034-86705269(-)$1	1	33	37	12.0000
((((	chr6:122777572-122777804(-)$1	1	122	126	12.0000
(...	chr4:108829724-108829954(+)$1	1	24	28	12.0000
((..	chr18:54278163-54278397(-)$1	1	120	124	12.0000
....	chr4:123814223-123814474(+)$1	1	0	4	12.0000
((((	chr5:14758562-14758791(-)$1	1	6	10	12.0000
....	chr7:112423936-112424159(-)$1	1	0	4	12.0000
....	chr17:5386025-5386258(-)$1	1	12	16	12.0000
..))	chr6:170105105-170105331(+)$1	1	49	53	12.0000
))))	chr11:9459623-9459853(+)$1	1	72	76	12.0000
((((	chr5:131008402-131008634(-)$1	1	121	125	12.0000
....	chr15:41643036-41643288(+)$1	1	53	57	12.0000
((((	chr1:63884952-63885186(+)$1	1	9	13	12.0000
....	chr17:34893889-34894126(+)$1	1	89	93	12.0000
....	chrM:10104-10389(+)$1	1	170	174	12.0000
))))	chr2:38522989-38523244(-)$1	1	191	195	12.0000
)))(	chr17:29551989-29552215(+)$1	1	26	30	12.0000
(...	chr13:45010577-45010808(-)$1	1	87	91	12.0000
....	chr1:93298970-93299204(+)$1	1	8	12	12.0000
.)))	chr8:71499064-71499290(-)$1	1	35	39	12.0000
....	chr2:42936144-42936371(+)$1	1	102	106	12.0000
((..	chr5:134235167-134235401(+)$1	1	120	124	12.0000
....	chr20:34213906-34214176(-)$1	1	127	131	12.0000
....	chr1:203786117-203786345(+)$1	1	150	154	12.0000
.(((	chr5:864404-864693(-)$1	1	132	136	12.0000
....	chr8:38961084-38961386(+)$1	1	113	117	12.0000
....	chr7:91743055-91743284(-)$1	1	12	16	12.0000
((((	chr14:57698232-57698463(-)$1	1	61	65	12.0000
..((	chr2:182766402-182766665(+)$1	1	26	30	12.0000
....	chr7:112423829-112424057(-)$1	1	8	12	12.0000
....	chr17:56082278-56082559(-)$1	1	2	6	12.0000
))).	chr2:198256869-198257170(-)$1	1	284	288	12.0000
....	chr17:48940650-48940874(-)$1	1	17	21	12.0000
....	chr2:188361596-188361823(-)$1	1	0	4	12.0000
.)))	chr11:62291708-62291936(-)$1	1	101	105	12.0000
.(((	chrM:14381-14653(-)$1	1	11	15	12.0000
....	chr12:69995124-69995392(+)$1	1	68	72	12.0000
..((	chr1:28177069-28177295(+)$1	1	187	191	12.0000
))).	chr6:64289828-64290064(+)$1	1	149	153	12.0000
((((	chr13:96443144-96443447(+)$1	1	113	117	12.0000
....	chr1:160247861-160248110(-)$1	1	57	61	12.0000
.)))	chr1:32384562-32384836(-)$1	1	57	61	12.0000
))).	chr14:54896879-54897115(-)$1	1	103	107	12.0000
))))	chr2:38523149-38523459(-)$1	1	80	84	12.0000
....	chr14:73959656-73959886(+)$1	1	108	112	12.0000
..((	chr11:9444498-9444740(+)$1	1	56	60	12.0000
....	chr2:128521990-128522277(-)$1	1	138	142	12.0000
....	chr5:92956669-92956901(-)$1	1	122	126	12.0000
(...	chr15:64458148-64458407(-)$1	1	22	26	12.0000
(((.	chr4:123813799-123814102(+)$1	1	17	21	12.0000
....	chr7:148523495-148523722(-)$1	1	137	141	12.0000
((((	chr5:134192921-134193147(+)$1	1	17	21	12.0000
(...	chr12:111157906-111158191(-)$1	1	103	107	12.0000
....	chr8:62574384-62574646(-)$1	1	83	87	12.0000
((((	chr16:66592077-66592311(+)$1	1	42	46	12.0000
....	chr11:32954264-32954491(+)$1	1	5	9	12.0000
....	chr1:68947115-68947340(-)$1	1	61	65	12.0000
....	chr17:34893429-34893666(+)$1	1	115	119	12.0000
....	chr19:11256947-11257172(-)$1	1	28	32	12.0000
((..	chr7:94166789-94167016(+)$1	1	113	117	12.0000
....	chr19:18390706-18390940(-)$1	1	52	56	12.0000

#PSSM
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	
A : 0.92	a : 0.07	

#score	804.0000000000002
#seq	67
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m3_run2.nuc.txt

#NT
UAAUUAACUAA	chr1:118067121-118067339(+)$1	218	102	113	10.9464
UAACAAAAUAA	chr4:17845645-17845866(+)$1	221	99	110	13.6250
UUAUAAAAAAC	chr10:115884547-115884765(-)$1	218	157	168	13.8035
UAUUAAAAAUC	chr2:152657897-152658119(-)$1	222	137	148	10.8571
UUAUAAAUAAA	chr1:229653394-229653612(-)$1	218	36	47	14.0714
UUAUCAAAACA	chr2:20451160-20451385(-)$1	225	102	113	11.3928
UAAUGCAAAAC	chr1:229653729-229653948(-)$1	219	55	66	10.5892
UGAGAAAAGAA	chr12:27181372-27181589(+)$1	217	43	54	10.5000
uauuaaaucaa	chr1:235272714-235272932(-)$1	218	104	115	11.3035
UAAUGAAAAGU	chrX:24230354-24230574(+)$1	220	89	100	10.2321
UUAGAAAACAA	chr1:229458923-229459143(-)$1	220	96	107	11.5714
UAUUUAAAAAA	chr12:100733133-100733357(+)$1	224	151	162	16.5714
UAAAGAAAAAA	chr2:197705162-197705381(-)$1	219	161	172	15.1428
uaaaaaacaaa	chr5:151188655-151188886(+)$1	231	81	92	13.9821
UUUUAAAAAAA	chr9:73000237-73000458(-)$1	221	87	98	15.9464
UAUUUACAAAA	chr1:227845220-227845442(+)$1	222	44	55	12.3750
UAAGCAAAAAA	chr22:22115793-22116011(-)$1	218	196	207	15.3214
UAAUGCAUAAA	chr12:21670012-21670231(+)$1	219	14	25	10.8571
UAAAACAAAAA	chr10:76937606-76937826(+)$1	220	168	179	14.1607
UAUUAAAUAGA	chr16:87443064-87443282(-)$1	218	120	131	11.1250
UACUCAAAUAA	chr12:64844351-64844570(+)$1	219	123	134	11.3928
UAAUUGAAAUA	chr6:122764700-122764918(-)$1	218	171	182	11.1250
UUAUCGAAAAA	chr1:114516963-114517184(+)$1	221	18	29	11.8392
UGACAAAAAAA	chr1:114516554-114516773(+)$1	219	29	40	14.2500
UGGUCAAAAAA	chr14:102550168-102550390(-)$1	222	169	180	11.6607
UAACAGAGAAA	chr7:17915275-17915494(-)$1	219	176	187	10.1428
UAAGUAUAAAA	chr4:120980717-120980938(-)$1	221	38	49	11.7500
UUCUAAGAAAA	chr8:104344240-104344459(+)$1	219	1	12	11.1250
aaagaaaaaaa	chr7:101893191-101893409(+)$1	218	137	148	13.1785
GAAUAAGAAAA	chr6:89320102-89320323(-)$1	221	143	154	11.9285
CAUUACAAAAA	chr4:140428546-140428772(-)$1	226	111	122	10.5892
UAUUAAACAGA	chr2:54896120-54896338(+)$1	218	53	64	11.2142
UACUAAAACUA	chr19:52520177-52520396(-)$1	219	67	78	10.3214
UAAAAAAAAAA	chr17:60021678-60021897(-)$1	219	147	158	17.5535
UAACUAAAAAC	chr1:179068600-179068823(-)$1	223	103	114	11.5714
UAAAACAAAAA	chr1:67877763-67877983(-)$1	220	124	135	14.1607
UUUUAUAAAAA	chr9:123523830-123524051(-)$1	221	151	162	12.1071
UAUUUCAAAAA	chr21:43409690-43409908(-)$1	218	105	116	13.1785
UUAGAAGAAAA	chr14:93706882-93707108(-)$1	226	136	147	11.2142
UAAAAGAAAAA	chr4:108835430-108835649(+)$1	219	76	87	14.0714
UUAUUGAAAAA	chrX:24229991-24230216(+)$1	225	179	190	12.2857
UCUUAAAAACA	chr1:93619439-93619657(-)$1	218	84	95	11.1250
UAAUGAAAAAU	chr5:78622374-78622600(+)$1	226	63	74	13.9821
UGAUUAAAAUA	chrX:20144295-20144512(-)$1	217	47	58	11.3928
UAAUAAUCCAA	chr11:119176517-119176734(+)$1	217	104	115	9.1607
UACUAAAGAAU	chr7:99637867-99638089(+)$1	222	114	125	9.8750
GAUUUAAAAAA	chr6:160100965-160101183(-)$1	218	22	33	12.1071
UAUGAAUAAAA	chr7:138984543-138984761(+)$1	218	29	40	11.9285
uaauuaaaaaa	chr6:80625158-80625376(-)$1	218	12	23	18.3571
UUUUAAAAAAA	chr13:100616774-100616999(-)$1	225	82	93	15.9464
UAUGAAAAAAA	chr10:70666623-70666841(+)$1	218	65	76	15.9464
UACUAAACCAA	chr4:186082104-186082325(-)$1	221	46	57	10.5000
UAAUAAGAAGA	chr16:11935509-11935728(-)$1	219	161	172	12.6428
UAAUGAAAAAU	chr12:46754153-46754377(-)$1	224	136	147	13.9821
UAAUAAAAAAA	chr6:149979232-149979455(-)$1	223	141	152	20.3214

#otherMatches

#Struct PSSM
ddd22eeeee:	chr2:201448305-201448527(+)$1	222	154	165	11.4821
!!cccmmmmcc	chr1:118067121-118067339(+)$1	218	102	113	10.9464
::::::HHHHH	chr4:17845645-17845866(+)$1	221	99	110	13.6250
ddmmmmdddde	chr10:115884547-115884765(-)$1	218	157	168	13.8035
:::::::::::	chr2:152657897-152658119(-)$1	222	137	148	10.8571
GGGGG::::::	chr1:229653394-229653612(-)$1	218	36	47	14.0714
mmmccc22fff	chr2:20451160-20451385(-)$1	225	102	113	11.3928
=::eeeeeppp	chr1:229653729-229653948(-)$1	219	55	66	10.5892
======%%%%%	chr12:27181372-27181589(+)$1	217	43	54	10.5000
mmmmbb]ccc4	chr1:235272714-235272932(-)$1	218	104	115	11.3035
""ccc####cc	chrX:24230354-24230574(+)$1	220	89	100	10.2321
ggggg::::::	chr1:229458923-229459143(-)$1	220	96	107	11.5714
=======::::	chr12:100733133-100733357(+)$1	224	151	162	16.5714
d:GGGGGGG}C	chr2:197705162-197705381(-)$1	219	161	172	15.1428
:::::::::::	chr5:151188655-151188886(+)$1	231	81	92	13.9821
qqqqqqqbb22	chr9:73000237-73000458(-)$1	221	87	98	15.9464
:::::::::::	chr1:227845220-227845442(+)$1	222	44	55	12.3750
::ddddrrrrr	chr22:22115793-22116011(-)$1	218	196	207	15.3214
qqqqbb:hhhh	chr12:21670012-21670231(+)$1	219	14	25	10.8571
::::::::::E	chr10:76937606-76937826(+)$1	220	168	179	14.1607
eee::::gggg	chr16:87443064-87443282(-)$1	218	120	131	11.1250
H{HHHHHHHH:	chr12:64844351-64844570(+)$1	219	123	134	11.3928
a22eeeee555	chr6:122764700-122764918(-)$1	218	171	182	11.1250
:::::dddd!!	chr1:114516963-114517184(+)$1	221	18	29	11.8392
[ffffff[eee	chr1:114516554-114516773(+)$1	219	29	40	14.2500
ccccqqqqqqq	chr14:102550168-102550390(-)$1	222	169	180	11.6607
:::::cccggg	chr7:17915275-17915494(-)$1	219	176	187	10.1428
:::ddddllld	chr4:120980717-120980938(-)$1	221	38	49	11.7500
:CCCKKDDDD{	chr8:104344240-104344459(+)$1	219	1	12	11.1250
:::::::::::	chr7:101893191-101893409(+)$1	218	137	148	13.1785
ttttt======	chr6:89320102-89320323(-)$1	221	143	154	11.9285
=====333fff	chr4:140428546-140428772(-)$1	226	111	122	10.5892
::::::::fff	chr2:54896120-54896338(+)$1	218	53	64	11.2142
DPPPPPPPBB{	chr19:52520177-52520396(-)$1	219	67	78	10.3214
====^^^^^^^	chr17:60021678-60021897(-)$1	219	147	158	17.5535
""ccc"""eee	chr1:179068600-179068823(-)$1	223	103	114	11.5714
mmmeeeee:ee	chr1:67877763-67877983(-)$1	220	124	135	14.1607
]hhhhhhhh::	chr9:123523830-123524051(-)$1	221	151	162	12.1071
gggggpppppp	chr21:43409690-43409908(-)$1	218	105	116	13.1785
:::::======	chr14:93706882-93707108(-)$1	226	136	147	11.2142
frrrrrrrrrf	chr4:108835430-108835649(+)$1	219	76	87	14.0714
^^^^^^^^^^^	chrX:24229991-24230216(+)$1	225	179	190	12.2857
ffff&&&&&&&	chr1:93619439-93619657(-)$1	218	84	95	11.1250
gwwwwwwwwww	chr5:78622374-78622600(+)$1	226	63	74	13.9821
eeeee777777	chrX:20144295-20144512(-)$1	217	47	58	11.3928
cc:::cccmmm	chr11:119176517-119176734(+)$1	217	104	115	9.1607
^^^^^^^^^^^	chr7:99637867-99638089(+)$1	222	114	125	9.8750
[ccc[bboooo	chr6:160100965-160101183(-)$1	218	22	33	12.1071
ppdddd22bb]	chr7:138984543-138984761(+)$1	218	29	40	11.9285
!!dddd^^^^^	chr6:80625158-80625376(-)$1	218	12	23	18.3571
:::::::::::	chr13:100616774-100616999(-)$1	225	82	93	15.9464
"ccc[dddd[b	chr10:70666623-70666841(+)$1	218	65	76	15.9464
yyyyyyyyyyf	chr4:186082104-186082325(-)$1	221	46	57	10.5000
rrrrrreeeee	chr16:11935509-11935728(-)$1	219	161	172	12.6428
fddddiiiiii	chr12:46754153-46754377(-)$1	224	136	147	13.9821
]dddd]ccc]b	chr6:149979232-149979455(-)$1	223	141	152	20.3214

#DB
)))..))))).	chr2:201448305-201448527(+)$1	1	154	165	11.4821
..(((....))	chr1:118067121-118067339(+)$1	1	102	113	10.9464
......)))))	chr4:17845645-17845866(+)$1	1	99	110	13.6250
((....)))))	chr10:115884547-115884765(-)$1	1	157	168	13.8035
...........	chr2:152657897-152658119(-)$1	1	137	148	10.8571
(((((......	chr1:229653394-229653612(-)$1	1	36	47	14.0714
...)))..)))	chr2:20451160-20451385(-)$1	1	102	113	11.3928
)..(((((...	chr1:229653729-229653948(-)$1	1	55	66	10.5892
((((((.....	chr12:27181372-27181589(+)$1	1	43	54	10.5000
....)).))).	chr1:235272714-235272932(-)$1	1	104	115	11.3035
..(((....((	chrX:24230354-24230574(+)$1	1	89	100	10.2321
)))))......	chr1:229458923-229459143(-)$1	1	96	107	11.5714
)))))))....	chr12:100733133-100733357(+)$1	1	151	162	16.5714
).))))))).)	chr2:197705162-197705381(-)$1	1	161	172	15.1428
...........	chr5:151188655-151188886(+)$1	1	81	92	13.9821
.......))..	chr9:73000237-73000458(-)$1	1	87	98	15.9464
...........	chr1:227845220-227845442(+)$1	1	44	55	12.3750
..((((.....	chr22:22115793-22116011(-)$1	1	196	207	15.3214
....)).((((	chr12:21670012-21670231(+)$1	1	14	25	10.8571
..........)	chr10:76937606-76937826(+)$1	1	168	179	14.1607
)))....((((	chr16:87443064-87443282(-)$1	1	120	131	11.1250
(.((((((((.	chr12:64844351-64844570(+)$1	1	123	134	11.3928
)..)))))...	chr6:122764700-122764918(-)$1	1	171	182	11.1250
.....((((..	chr1:114516963-114517184(+)$1	1	18	29	11.8392
.((((((.(((	chr1:114516554-114516773(+)$1	1	29	40	14.2500
((((.......	chr14:102550168-102550390(-)$1	1	169	180	11.6607
.....((((((	chr7:17915275-17915494(-)$1	1	176	187	10.1428
...((((...)	chr4:120980717-120980938(-)$1	1	38	49	11.7500
.(((..((((.	chr8:104344240-104344459(+)$1	1	1	12	11.1250
...........	chr7:101893191-101893409(+)$1	1	137	148	13.1785
.....))))))	chr6:89320102-89320323(-)$1	1	143	154	11.9285
)))))...)))	chr4:140428546-140428772(-)$1	1	111	122	10.5892
........(((	chr2:54896120-54896338(+)$1	1	53	64	11.2142
(.......((.	chr19:52520177-52520396(-)$1	1	67	78	10.3214
((((.......	chr17:60021678-60021897(-)$1	1	147	158	17.5535
..(((...(((	chr1:179068600-179068823(-)$1	1	103	114	11.5714
...))))).((	chr1:67877763-67877983(-)$1	1	124	135	14.1607
.))))))))..	chr9:123523830-123524051(-)$1	1	151	162	12.1071
(((((......	chr21:43409690-43409908(-)$1	1	105	116	13.1785
.....((((((	chr14:93706882-93707108(-)$1	1	136	147	11.2142
(.........)	chr4:108835430-108835649(+)$1	1	76	87	14.0714
...........	chrX:24229991-24230216(+)$1	1	179	190	12.2857
((((.......	chr1:93619439-93619657(-)$1	1	84	95	11.1250
(..........	chr5:78622374-78622600(+)$1	1	63	74	13.9821
)))))......	chrX:20144295-20144512(-)$1	1	47	58	11.3928
))...(((...	chr11:119176517-119176734(+)$1	1	104	115	9.1607
...........	chr7:99637867-99638089(+)$1	1	114	125	9.8750
.(((.((....	chr6:160100965-160101183(-)$1	1	22	33	12.1071
..))))..)).	chr7:138984543-138984761(+)$1	1	29	40	11.9285
..((((.....	chr6:80625158-80625376(-)$1	1	12	23	18.3571
...........	chr13:100616774-100616999(-)$1	1	82	93	15.9464
.(((.((((.(	chr10:70666623-70666841(+)$1	1	65	76	15.9464
..........)	chr4:186082104-186082325(-)$1	1	46	57	10.5000
......)))))	chr16:11935509-11935728(-)$1	1	161	172	12.6428
(((((((((((	chr12:46754153-46754377(-)$1	1	136	147	13.9821
.)))).))).)	chr6:149979232-149979455(-)$1	1	141	152	20.3214

#PSSM
U : 0.87	u : 0.05	G : 0.03	a : 0.01	C : 0.01	
A : 0.64	U : 0.19	G : 0.07	a : 0.07	C : 0.01	
A : 0.57	U : 0.24	C : 0.08	a : 0.05	u : 0.01	G : 0.01	
U : 0.62	G : 0.12	C : 0.08	A : 0.08	u : 0.03	a : 0.01	g : 0.01	
A : 0.53	U : 0.17	C : 0.10	G : 0.10	a : 0.05	u : 0.01	
A : 0.71	C : 0.10	G : 0.08	a : 0.07	U : 0.01	
A : 0.78	a : 0.07	G : 0.07	U : 0.05	C : 0.01	
A : 0.76	C : 0.07	U : 0.05	G : 0.03	a : 0.03	u : 0.01	c : 0.01	
A : 0.76	C : 0.08	U : 0.05	a : 0.05	G : 0.01	c : 0.01	
A : 0.75	U : 0.07	a : 0.07	G : 0.07	C : 0.03	
A : 0.78	C : 0.07	a : 0.07	U : 0.07	

#score	709.7857142857147
#seq	56
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m3_run1.nuc.txt

#NT
GGCAGGA	chr6:47251727-47251950(-)$1	223	178	185	12.7924
AGCAGGG	chr14:102505901-102506134(+)$1	233	20	27	12.7924
AGCAGUA	chr1:214560105-214560328(-)$1	223	195	202	12.8867
GGCAGGA	chr10:123846207-123846431(+)$1	224	97	104	12.7924
AGAAGGA	chr1:33058861-33059076(+)$1	215	138	145	12.6037
AGCUGGA	chr21:33727712-33727938(-)$1	226	104	111	11.9433
AGCAGGA	chr1:202976823-202977056(+)$1	233	159	166	16.5660
AGCAGGG	chr1:228645320-228645543(-)$1	223	41	48	12.7924
AACAGGA	chr15:28356840-28357058(-)$1	218	137	144	12.2264
AGCAGGA	chr8:144942438-144942669(-)$1	231	137	144	16.5660
AGCAAGA	chr16:30678560-30678786(+)$1	226	20	27	12.2264
AUCAGGA	chr3:155642999-155643216(+)$1	217	76	83	12.5094
AGCAGAA	chr4:187629805-187630025(-)$1	220	162	169	12.6981
AGCAGCA	chr22:50169678-50169889(-)$1	211	93	100	13.2641
AGCAGCA	chr1:12336441-12336663(+)$1	222	28	35	13.2641
AGAAGGA	chr6:12125112-12125335(+)$1	223	17	24	12.6037
GGCAGGA	chr2:75061615-75061831(+)$1	216	86	93	12.7924
AGCAGCA	chr12:49427855-49428080(-)$1	225	196	203	13.2641
AGCUGGA	chr8:145009977-145010191(-)$1	214	129	136	11.9433
AGGAGGA	chr1:31478626-31478848(-)$1	222	139	146	12.5094
AGCAGGC	chr15:41820012-41820234(-)$1	222	38	45	12.6981
AGCAGCA	chr1:19486570-19486798(-)$1	228	116	123	13.2641
GGCAGGA	chr19:1429871-1430084(+)$1	213	107	114	12.7924
CGCAGGA	chr19:38643435-38643665(+)$1	230	216	223	12.4150
AGCAGGA	chr9:94984742-94984958(-)$1	216	114	121	16.5660
AGCAGGG	chr22:26894761-26894981(-)$1	220	158	165	12.7924
AGCAGGU	chr8:144944296-144944515(-)$1	219	146	153	12.6037
ACCAGGA	chr3:127336078-127336324(+)$1	246	50	57	12.2264
UGCAGGA	chr22:24718709-24718930(+)$1	221	115	122	12.5094
AGCAGGC	chr14:51237017-51237234(-)$1	217	31	38	12.6981
AGGAGGA	chr22:50180941-50181162(-)$1	221	92	99	12.5094
GGCAGGA	chr19:39218531-39218754(+)$1	223	49	56	12.7924
AGCAGCA	chr15:72119166-72119388(-)$1	222	82	89	13.2641
AGCAGCA	chr13:77459919-77460144(-)$1	225	57	64	13.2641
AGCAGGA	chr1:10381741-10381970(+)$1	229	180	187	16.5660
AGCAGUA	chr10:77161072-77161292(-)$1	220	148	155	12.8867
AGCAGGA	chr17:3985652-3985874(-)$1	222	86	93	16.5660
AGCAGUA	chr11:130108239-130108457(-)$1	218	4	11	12.8867
AGCAGGU	chr5:176637056-176637297(+)$1	241	218	225	12.6037
AGCAUGA	chr12:65004360-65004584(+)$1	224	49	56	12.0377
AGCAGGA	chr1:117146214-117146426(-)$1	212	57	64	16.5660
AUCAGGA	chrX:39930138-39930377(-)$1	239	83	90	12.5094
AUCAGGA	chr1:214818118-214818340(+)$1	222	88	95	12.5094
AGGAGGA	chr19:11118557-11118787(+)$1	230	18	25	12.5094
AGCAGCA	chr1:24083448-24083667(+)$1	219	124	131	13.2641
AGAAGGA	chr10:105201986-105202210(+)$1	224	29	36	12.6037
UGCAGGA	chr10:18962863-18963079(+)$1	216	44	51	12.5094
AGCAGGG	chr9:101552589-101552808(-)$1	219	113	120	12.7924
AGCAAGA	chr14:21896204-21896428(-)$1	224	169	176	12.2264
AGAAGGA	chr1:171519234-171519463(+)$1	229	122	129	12.6037
AGCAAGA	chr3:98235448-98235662(-)$1	214	159	166	12.2264
AUCAGGA	chr9:139350028-139350276(-)$1	248	50	57	12.5094

#otherMatches

#Struct PSSM
EHHHHHH	chr10:12123432-12123654(+)$1	222	209	216	12.6981
bbb4444	chr6:47251727-47251950(-)$1	223	178	185	12.7924
=====mm	chr14:102505901-102506134(+)$1	233	20	27	12.7924
DDDD???	chr1:214560105-214560328(-)$1	223	195	202	12.8867
ggggggg	chr10:123846207-123846431(+)$1	224	97	104	12.7924
cc]dddd	chr1:33058861-33059076(+)$1	215	138	145	12.6037
ee]ccc]	chr21:33727712-33727938(-)$1	226	104	111	11.9433
lddddff	chr1:202976823-202977056(+)$1	233	159	166	16.5660
KKDDDDe	chr1:228645320-228645543(-)$1	223	41	48	12.7924
^^^^ccc	chr15:28356840-28357058(-)$1	218	137	144	12.2264
eeeee!!	chr8:144942438-144942669(-)$1	231	137	144	16.5660
FFF:ggg	chr16:30678560-30678786(+)$1	226	20	27	12.2264
eeeeeoo	chr3:155642999-155643216(+)$1	217	76	83	12.5094
ggggggs	chr4:187629805-187630025(-)$1	220	162	169	12.6981
:ccc[bb	chr22:50169678-50169889(-)$1	211	93	100	13.2641
mhhhhhh	chr1:12336441-12336663(+)$1	222	28	35	13.2641
eeEEEEE	chr6:12125112-12125335(+)$1	223	17	24	12.6037
ccc]ccc	chr2:75061615-75061831(+)$1	216	86	93	12.7924
b]dddd]	chr12:49427855-49428080(-)$1	225	196	203	13.2641
mmmmddd	chr8:145009977-145010191(-)$1	214	129	136	11.9433
cccdddd	chr1:31478626-31478848(-)$1	222	139	146	12.5094
cc[ccc[	chr15:41820012-41820234(-)$1	222	38	45	12.6981
fff:ddd	chr1:19486570-19486798(-)$1	228	116	123	13.2641
g:::ggg	chr19:1429871-1430084(+)$1	213	107	114	12.7924
qeeeee:	chr19:38643435-38643665(+)$1	230	216	223	12.4150
ooooccc	chr9:94984742-94984958(-)$1	216	114	121	16.5660
ggglllg	chr22:26894761-26894981(-)$1	220	158	165	12.7924
[ddddmm	chr8:144944296-144944515(-)$1	219	146	153	12.6037
GGG::cc	chr3:127336078-127336324(+)$1	246	50	57	12.2264
:::::::	chr22:24718709-24718930(+)$1	221	115	122	12.5094
nnnnnee	chr14:51237017-51237234(-)$1	217	31	38	12.6981
ttttfff	chr22:50180941-50181162(-)$1	221	92	99	12.5094
ffffff5	chr19:39218531-39218754(+)$1	223	49	56	12.7924
:EEEEE:	chr15:72119166-72119388(-)$1	222	82	89	13.2641
EE::bbm	chr13:77459919-77460144(-)$1	225	57	64	13.2641
}CCC:::	chr1:10381741-10381970(+)$1	229	180	187	16.5660
qdddd]d	chr10:77161072-77161292(-)$1	220	148	155	12.8867
dddbbdd	chr17:3985652-3985874(-)$1	222	86	93	16.5660
HHHHH::	chr11:130108239-130108457(-)$1	218	4	11	12.8867
E}AZZZB	chr5:176637056-176637297(+)$1	241	218	225	12.6037
:bb[bbc	chr12:65004360-65004584(+)$1	224	49	56	12.0377
wwdddd5	chr1:117146214-117146426(-)$1	212	57	64	16.5660
%%%%bbq	chrX:39930138-39930377(-)$1	239	83	90	12.5094
mgggggg	chr1:214818118-214818340(+)$1	222	88	95	12.5094
fff!!a[	chr19:11118557-11118787(+)$1	230	18	25	12.5094
+++++++	chr1:24083448-24083667(+)$1	219	124	131	13.2641
:::dddd	chr10:105201986-105202210(+)$1	224	29	36	12.6037
mmfffff	chr10:18962863-18963079(+)$1	216	44	51	12.5094
FFFdddd	chr9:101552589-101552808(-)$1	219	113	120	12.7924
CCC}A}C	chr14:21896204-21896428(-)$1	224	169	176	12.2264
ppppbb:	chr1:171519234-171519463(+)$1	229	122	129	12.6037
[cccooo	chr3:98235448-98235662(-)$1	214	159	166	12.2264
{EEEEE:	chr9:139350028-139350276(-)$1	248	50	57	12.5094

#DB
)))))))	chr10:12123432-12123654(+)$1	1	209	216	12.6981
)))....	chr6:47251727-47251950(-)$1	1	178	185	12.7924
(((((..	chr14:102505901-102506134(+)$1	1	20	27	12.7924
))))...	chr1:214560105-214560328(-)$1	1	195	202	12.8867
(((((((	chr10:123846207-123846431(+)$1	1	97	104	12.7924
)).))))	chr1:33058861-33059076(+)$1	1	138	145	12.6037
)).))).	chr21:33727712-33727938(-)$1	1	104	111	11.9433
.))))((	chr1:202976823-202977056(+)$1	1	159	166	16.5660
..(((((	chr1:228645320-228645543(-)$1	1	41	48	12.7924
....)))	chr15:28356840-28357058(-)$1	1	137	144	12.2264
(((((..	chr8:144942438-144942669(-)$1	1	137	144	16.5660
(((.(((	chr16:30678560-30678786(+)$1	1	20	27	12.2264
(((((..	chr3:155642999-155643216(+)$1	1	76	83	12.5094
((((((.	chr4:187629805-187630025(-)$1	1	162	169	12.6981
.(((.((	chr22:50169678-50169889(-)$1	1	93	100	13.2641
.))))))	chr1:12336441-12336663(+)$1	1	28	35	13.2641
))(((((	chr6:12125112-12125335(+)$1	1	17	24	12.6037
))).)))	chr2:75061615-75061831(+)$1	1	86	93	12.7924
).)))).	chr12:49427855-49428080(-)$1	1	196	203	13.2641
....)))	chr8:145009977-145010191(-)$1	1	129	136	11.9433
)))))))	chr1:31478626-31478848(-)$1	1	139	146	12.5094
((.(((.	chr15:41820012-41820234(-)$1	1	38	45	12.6981
))).(((	chr1:19486570-19486798(-)$1	1	116	123	13.2641
)...(((	chr19:1429871-1430084(+)$1	1	107	114	12.7924
.))))).	chr19:38643435-38643665(+)$1	1	216	223	12.4150
....)))	chr9:94984742-94984958(-)$1	1	114	121	16.5660
(((...)	chr22:26894761-26894981(-)$1	1	158	165	12.7924
.((((..	chr8:144944296-144944515(-)$1	1	146	153	12.6037
(((..((	chr3:127336078-127336324(+)$1	1	50	57	12.2264
.......	chr22:24718709-24718930(+)$1	1	115	122	12.5094
.....))	chr14:51237017-51237234(-)$1	1	31	38	12.6981
....)))	chr22:50180941-50181162(-)$1	1	92	99	12.5094
)))))).	chr19:39218531-39218754(+)$1	1	49	56	12.7924
.(((((.	chr15:72119166-72119388(-)$1	1	82	89	13.2641
((..((.	chr13:77459919-77460144(-)$1	1	57	64	13.2641
.)))...	chr1:10381741-10381970(+)$1	1	180	187	16.5660
.)))).)	chr10:77161072-77161292(-)$1	1	148	155	12.8867
(((((((	chr17:3985652-3985874(-)$1	1	86	93	16.5660
(((((..	chr11:130108239-130108457(-)$1	1	4	11	12.8867
).)...)	chr5:176637056-176637297(+)$1	1	218	225	12.6037
.((.(((	chr12:65004360-65004584(+)$1	1	49	56	12.0377
..)))).	chr1:117146214-117146426(-)$1	1	57	64	16.5660
....((.	chrX:39930138-39930377(-)$1	1	83	90	12.5094
.))))))	chr1:214818118-214818340(+)$1	1	88	95	12.5094
(((..(.	chr19:11118557-11118787(+)$1	1	18	25	12.5094
.......	chr1:24083448-24083667(+)$1	1	124	131	13.2641
...((((	chr10:105201986-105202210(+)$1	1	29	36	12.6037
..)))))	chr10:18962863-18963079(+)$1	1	44	51	12.5094
(((((((	chr9:101552589-101552808(-)$1	1	113	120	12.7924
))).).)	chr14:21896204-21896428(-)$1	1	169	176	12.2264
....)).	chr1:171519234-171519463(+)$1	1	122	129	12.6037
.(((...	chr3:98235448-98235662(-)$1	1	159	166	12.2264
.(((((.	chr9:139350028-139350276(-)$1	1	50	57	12.5094

#PSSM
A : 0.84	G : 0.09	U : 0.03	C : 0.01	
G : 0.88	U : 0.07	A : 0.01	C : 0.01	
C : 0.86	A : 0.07	G : 0.05	
A : 0.96	U : 0.03	
G : 0.92	A : 0.05	U : 0.01	
G : 0.79	C : 0.13	U : 0.05	A : 0.01	
A : 0.83	G : 0.07	C : 0.05	U : 0.03	

#score	694.5094339622636
#seq	53
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m2_run1.nuc.txt

#NT
AAAAUUUC	chr6:80412996-80413236(+)$1	240	88	96	15.4423
AAAAUUUU	chr10:98723804-98724046(+)$1	242	166	174	16.5000
AAGAUUUU	chr7:155099958-155100198(+)$1	240	53	61	12.4615
AGAAUUUU	chr6:108364461-108364701(-)$1	240	11	19	12.1730
UAAAUUUA	chr3:185643159-185643399(-)$1	240	185	193	12.0769
AAAAUCUG	chr5:74656129-74656369(+)$1	240	93	101	11.5000
aaaaauua	chr5:96109099-96109339(+)$1	240	200	208	12.6538
ACAAUUUA	chr3:57611487-57611727(-)$1	240	29	37	11.9807
AAAAUUUA	chr15:64658025-64658323(-)$1	298	209	217	16.5000
AAAAUUUA	chr1:39471448-39471737(+)$1	289	207	215	16.5000
AAGAUUUA	chr15:44817105-44817345(+)$1	240	52	60	12.4615
AAAAGUUA	chr1:231155002-231155242(-)$1	240	189	197	12.7500
AAAAGUUA	chr21:35469617-35469870(+)$1	253	93	101	12.7500
AAAACUUA	chr2:153616254-153616534(+)$1	280	126	134	12.5576
AAAAUUGU	chr12:69047802-69048042(+)$1	240	26	34	12.7500
AAAAUAUU	chr9:14086632-14086872(-)$1	240	174	182	12.4615
aaaauuaG	chr2:207176466-207176706(+)$1	240	5	13	11.8846
AAAGUUUC	chr19:19414437-19414677(-)$1	240	17	25	10.9230
AAAAGUUG	chr5:56189949-56190189(+)$1	240	59	67	11.8846
AGAAUUUA	chr12:49413216-49413456(-)$1	240	160	168	12.1730
AAAAUGUG	chr9:140729956-140730196(+)$1	240	4	12	11.5000
AAAAUUAU	chr21:38886141-38886381(+)$1	240	83	91	12.7500
UAAAUUUG	chr6:90077269-90077509(-)$1	240	193	201	11.2115
AACAUUUC	chr11:107662051-107662325(-)$1	274	27	35	11.5000
AAAAUUUG	chr15:65312444-65312684(-)$1	240	90	98	15.6346
AAAGUUUA	chr7:129772960-129773240(+)$1	280	184	192	11.9807
AAAAUUGU	chrX:65817463-65817703(-)$1	240	104	112	12.7500
AAAAUUUU	chr13:77580218-77580458(-)$1	240	168	176	16.5000
CAAAUUUU	chr11:113668511-113668751(-)$1	240	64	72	12.0769
AAAAUUGA	chr3:100083751-100083991(-)$1	240	81	89	12.7500
AAAAUUUA	chr15:48634244-48634484(+)$1	240	29	37	16.5000
AAAAUUUU	chr17:61671408-61671688(+)$1	280	2	10	16.5000
AAAAUAUA	chr20:36719983-36720223(+)$1	240	204	212	12.4615
AGAAUUUU	chr14:35777149-35777389(+)$1	240	186	194	12.1730
AACAUUUG	chr1:226332597-226332837(-)$1	240	62	70	11.6923
AAAAAUUC	chr22:30094432-30094672(+)$1	240	135	143	11.5961
aaaauuau	chr8:86393509-86393753(+)$1	244	0	8	12.7500
AAUAUUUC	chr1:45976797-45977037(-)$1	240	14	22	11.5000
AAAAAUUG	chr12:89982016-89982266(-)$1	250	24	32	11.7884
AAAAUGUA	chr17:73316337-73316577(-)$1	240	160	168	12.3653
AAAAUUCU	chr17:28851334-28851574(+)$1	240	29	37	12.4615
AAAAUAUU	chr7:117831966-117832206(+)$1	240	221	229	12.4615
CAAAUUUU	chr9:73000613-73000853(-)$1	240	169	177	12.0769
aaaauuau	chr3:135868994-135869234(-)$1	240	23	31	12.7500
AAAAGUUC	chr17:47007671-47007911(-)$1	240	165	173	11.6923
AACAUUUU	chr7:112406896-112407136(-)$1	240	55	63	12.5576
AAUAUUUU	chr14:64938878-64939118(+)$1	240	226	234	12.5576
AAAAUUGG	chr17:19580697-19580937(+)$1	240	94	102	11.8846
AAAAUCUA	chr7:129127274-129127514(+)$1	240	76	84	12.3653
AAACUUUA	chr22:39913093-39913333(+)$1	240	116	124	11.8846
AAAACUUC	chr20:55949614-55949854(+)$1	240	147	155	11.5000

#otherMatches

#Struct PSSM
::::::::	chr12:56214896-56215137(-)$1	241	35	43	12.5576
mccc]ddd	chr6:80412996-80413236(+)$1	240	88	96	15.4423
dddd]fff	chr10:98723804-98724046(+)$1	242	166	174	16.5000
!ggggggg	chr7:155099958-155100198(+)$1	240	53	61	12.4615
:ggggggg	chr6:108364461-108364701(-)$1	240	11	19	12.1730
dddd]ccc	chr3:185643159-185643399(-)$1	240	185	193	12.0769
:::FFFFF	chr5:74656129-74656369(+)$1	240	93	101	11.5000
g$$$$$dd	chr5:96109099-96109339(+)$1	240	200	208	12.6538
========	chr3:57611487-57611727(-)$1	240	29	37	11.9807
:::::GGG	chr15:64658025-64658323(-)$1	298	209	217	16.5000
ee::::::	chr1:39471448-39471737(+)$1	289	207	215	16.5000
^^^^^^^^	chr15:44817105-44817345(+)$1	240	52	60	12.4615
hhhhhhh:	chr1:231155002-231155242(-)$1	240	189	197	12.7500
JFFFFFF{	chr21:35469617-35469870(+)$1	253	93	101	12.7500
ggggguuu	chr2:153616254-153616534(+)$1	280	126	134	12.5576
yyyyyyyy	chr12:69047802-69048042(+)$1	240	26	34	12.7500
:::::::e	chr9:14086632-14086872(-)$1	240	174	182	12.4615
::::::::	chr2:207176466-207176706(+)$1	240	5	13	11.8846
&&&&&&bb	chr19:19414437-19414677(-)$1	240	17	25	10.9230
::ddddmm	chr5:56189949-56190189(+)$1	240	59	67	11.8846
gggg[ccc	chr12:49413216-49413456(-)$1	240	160	168	12.1730
:::ggggg	chr9:140729956-140730196(+)$1	240	4	12	11.5000
((((((((	chr21:38886141-38886381(+)$1	240	83	91	12.7500
::::::BB	chr6:90077269-90077509(-)$1	240	193	201	11.2115
eeee9999	chr11:107662051-107662325(-)$1	274	27	35	11.5000
xxxxxxxx	chr15:65312444-65312684(-)$1	240	90	98	15.6346
gg::::::	chr7:129772960-129773240(+)$1	280	184	192	11.9807
bmmmmbb]	chrX:65817463-65817703(-)$1	240	104	112	12.7500
::::::::	chr13:77580218-77580458(-)$1	240	168	176	16.5000
99999999	chr11:113668511-113668751(-)$1	240	64	72	12.0769
lllccc22	chr3:100083751-100083991(-)$1	240	81	89	12.7500
mmmdddd3	chr15:48634244-48634484(+)$1	240	29	37	16.5000
::::::::	chr17:61671408-61671688(+)$1	280	2	10	16.5000
:::::::E	chr20:36719983-36720223(+)$1	240	204	212	12.4615
:ccclllc	chr14:35777149-35777389(+)$1	240	186	194	12.1730
cc"""ccc	chr1:226332597-226332837(-)$1	240	62	70	11.6923
:::::eee	chr22:30094432-30094672(+)$1	240	135	143	11.5961
::::::::	chr8:86393509-86393753(+)$1	244	0	8	12.7500
ddlllddd	chr1:45976797-45977037(-)$1	240	14	22	11.5000
::::::cc	chr12:89982016-89982266(-)$1	250	24	32	11.7884
:::ddddn	chr17:73316337-73316577(-)$1	240	160	168	12.3653
g:::::::	chr17:28851334-28851574(+)$1	240	29	37	12.4615
::::::::	chr7:117831966-117832206(+)$1	240	221	229	12.4615
bbuuuuuu	chr9:73000613-73000853(-)$1	240	169	177	12.0769
=oooooo=	chr3:135868994-135869234(-)$1	240	23	31	12.7500
ddd333dd	chr17:47007671-47007911(-)$1	240	165	173	11.6923
]ccc8888	chr7:112406896-112407136(-)$1	240	55	63	12.5576
_____HHH	chr14:64938878-64939118(+)$1	240	226	234	12.5576
gggggggm	chr17:19580697-19580937(+)$1	240	94	102	11.8846
c&&&&&&&	chr7:129127274-129127514(+)$1	240	76	84	12.3653
""bbpppp	chr22:39913093-39913333(+)$1	240	116	124	11.8846
::::::::	chr20:55949614-55949854(+)$1	240	147	155	11.5000

#DB
........	chr12:56214896-56215137(-)$1	1	35	43	12.5576
.))).)))	chr6:80412996-80413236(+)$1	1	88	96	15.4423
)))).)))	chr10:98723804-98724046(+)$1	1	166	174	16.5000
.(((((((	chr7:155099958-155100198(+)$1	1	53	61	12.4615
.(((((((	chr6:108364461-108364701(-)$1	1	11	19	12.1730
)))).)))	chr3:185643159-185643399(-)$1	1	185	193	12.0769
...(((((	chr5:74656129-74656369(+)$1	1	93	101	11.5000
(.....((	chr5:96109099-96109339(+)$1	1	200	208	12.6538
((((((((	chr3:57611487-57611727(-)$1	1	29	37	11.9807
.....)))	chr15:64658025-64658323(-)$1	1	209	217	16.5000
))......	chr1:39471448-39471737(+)$1	1	207	215	16.5000
........	chr15:44817105-44817345(+)$1	1	52	60	12.4615
))))))).	chr1:231155002-231155242(-)$1	1	189	197	12.7500
(((((((.	chr21:35469617-35469870(+)$1	1	93	101	12.7500
(((((...	chr2:153616254-153616534(+)$1	1	126	134	12.5576
........	chr12:69047802-69048042(+)$1	1	26	34	12.7500
.......(	chr9:14086632-14086872(-)$1	1	174	182	12.4615
........	chr2:207176466-207176706(+)$1	1	5	13	11.8846
......((	chr19:19414437-19414677(-)$1	1	17	25	10.9230
..((((..	chr5:56189949-56190189(+)$1	1	59	67	11.8846
((((.(((	chr12:49413216-49413456(-)$1	1	160	168	12.1730
...(((((	chr9:140729956-140730196(+)$1	1	4	12	11.5000
........	chr21:38886141-38886381(+)$1	1	83	91	12.7500
......))	chr6:90077269-90077509(-)$1	1	193	201	11.2115
))))....	chr11:107662051-107662325(-)$1	1	27	35	11.5000
........	chr15:65312444-65312684(-)$1	1	90	98	15.6346
))......	chr7:129772960-129773240(+)$1	1	184	192	11.9807
(....)).	chrX:65817463-65817703(-)$1	1	104	112	12.7500
........	chr13:77580218-77580458(-)$1	1	168	176	16.5000
........	chr11:113668511-113668751(-)$1	1	64	72	12.0769
...)))..	chr3:100083751-100083991(-)$1	1	81	89	12.7500
...)))).	chr15:48634244-48634484(+)$1	1	29	37	16.5000
........	chr17:61671408-61671688(+)$1	1	2	10	16.5000
.......)	chr20:36719983-36720223(+)$1	1	204	212	12.4615
.(((...)	chr14:35777149-35777389(+)$1	1	186	194	12.1730
((...(((	chr1:226332597-226332837(-)$1	1	62	70	11.6923
.....(((	chr22:30094432-30094672(+)$1	1	135	143	11.5961
........	chr8:86393509-86393753(+)$1	1	0	8	12.7500
((...)))	chr1:45976797-45977037(-)$1	1	14	22	11.5000
......((	chr12:89982016-89982266(-)$1	1	24	32	11.7884
...((((.	chr17:73316337-73316577(-)$1	1	160	168	12.3653
).......	chr17:28851334-28851574(+)$1	1	29	37	12.4615
........	chr7:117831966-117832206(+)$1	1	221	229	12.4615
((......	chr9:73000613-73000853(-)$1	1	169	177	12.0769
(......)	chr3:135868994-135869234(-)$1	1	23	31	12.7500
)))...))	chr17:47007671-47007911(-)$1	1	165	173	11.6923
.)))....	chr7:112406896-112407136(-)$1	1	55	63	12.5576
.....)))	chr14:64938878-64939118(+)$1	1	226	234	12.5576
(((((((.	chr17:19580697-19580937(+)$1	1	94	102	11.8846
(.......	chr7:129127274-129127514(+)$1	1	76	84	12.3653
..((....	chr22:39913093-39913333(+)$1	1	116	124	11.8846
........	chr20:55949614-55949854(+)$1	1	147	155	11.5000

#PSSM
A : 0.84	a : 0.07	U : 0.03	C : 0.03	
A : 0.84	a : 0.07	G : 0.05	C : 0.01	
A : 0.76	a : 0.07	U : 0.05	C : 0.05	G : 0.03	
A : 0.86	a : 0.07	G : 0.03	C : 0.01	
U : 0.76	G : 0.07	u : 0.05	C : 0.03	A : 0.03	a : 0.01	
U : 0.78	u : 0.07	A : 0.05	C : 0.03	G : 0.03	
U : 0.80	G : 0.07	a : 0.05	u : 0.01	A : 0.01	C : 0.01	
A : 0.32	U : 0.30	G : 0.17	C : 0.13	u : 0.03	a : 0.01	

#score	665.1153846153849
#seq	52
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m3_run1.nuc.txt

#NT
UAUGAAUAAA	chr13:96233475-96233705(-)$1	230	10	20	13.3928
UCAAAGUAAA	chr5:60454706-60454929(-)$1	223	87	97	13.8392
AAAAAAGAAA	chr3:23962136-23962359(+)$1	223	116	126	14.4642
uaaaaauauu	chr2:203427337-203427559(+)$1	222	23	33	13.9285
GAAAAAAAAA	chr18:56995594-56995817(-)$1	223	6	16	15.0000
UACAAAUACA	chr12:51214192-51214417(+)$1	225	105	115	13.7500
uaaaaauaga	chr10:75001795-75002016(-)$1	221	82	92	17.4107
UGAAACUAAA	chr4:128753931-128754162(+)$1	231	25	35	13.4821
UCAAAAAAAA	chr1:23636772-23636996(-)$1	224	109	119	14.9107
uuaaaauaau	chr21:40195167-40195392(+)$1	225	175	185	14.4642
CAAUAAUAAA	chr1:227846792-227847013(+)$1	221	6	16	14.2857
UAACAAUAAA	chr6:21232492-21232716(+)$1	224	111	121	16.9642
AAAUAAUAAA	chr22:38363654-38363879(+)$1	225	128	138	14.3750
UGAAAAUAAA	chr3:14530665-14530891(+)$1	226	161	171	17.8571
uauaaauaua	chr1:160186376-160186597(-)$1	221	39	49	13.9285
UAUUAAUAAA	chr19:10942410-10942662(+)$1	252	131	141	13.7500
UAGAAAUGAA	chr5:55247196-55247418(-)$1	222	173	183	13.1250
AAAAAAUAAA	chr17:73148923-73149150(-)$1	227	160	170	18.3035
UCAAUAUAAA	chr14:69254971-69255190(-)$1	219	85	95	14.0178
UAAUAACAAA	chr12:96672240-96672464(-)$1	224	106	116	13.7500
UAAAAAUAAU	chr13:30339117-30339339(-)$1	222	49	59	17.6785
UAAAAUUACA	chr13:103492357-103492589(+)$1	232	118	128	12.9464
uuaaaauaau	chr5:134192922-134193146(+)$1	224	17	27	14.4642
UAAAACUAAC	chr5:135516196-135516418(+)$1	222	100	110	13.0357
uaaauauaac	chr17:57187392-57187617(-)$1	225	104	114	13.2142
CAAAAACAAA	chr8:105502082-105502307(-)$1	225	16	26	14.6428
UAUAAAUCAA	chr15:41669324-41669547(+)$1	223	20	30	13.2142
UAAAAAUAAU	chr12:88589561-88589784(+)$1	223	165	175	17.6785
AAAACAUAAA	chr21:15744003-15744233(-)$1	230	140	150	13.9285
UUAAUAUAAA	chr12:125515455-125515677(+)$1	222	9	19	13.8392
UAAAAAUUAA	chrX:103435803-103436023(+)$1	220	203	213	16.7857
UAAUAGUAAA	chr5:64017438-64017659(-)$1	221	29	39	12.9464
UAAAAACAAC	chr17:46626528-46626749(-)$1	221	28	38	13.8392
UAUAAAUAAA	chr1:198290925-198291150(+)$1	225	213	223	17.6785
UAGAGAUAAA	chr3:52745367-52745587(-)$1	220	160	170	13.1250
AAAAAAUAUA	chr7:44867571-44867791(-)$1	220	104	114	14.5535
UAAAAAUAAA	chr12:120532818-120533044(-)$1	226	116	126	21.2500
CAAAAAUACA	chr11:43877644-43877868(+)$1	224	106	116	14.3750
UCAAAAUAUA	chr1:212910890-212911110(-)$1	220	122	132	14.4642
UAAAAAAAAA	chr5:173315549-173315772(+)$1	223	52	62	17.9464
UAAAAAUAAU	chr6:139501810-139502032(+)$1	222	102	112	17.6785
UUCAAAUAAA	chr5:10434819-10435052(+)$1	233	107	117	14.3750
GAAAGAUAAA	chrX:15339385-15339606(-)$1	221	127	137	14.0178
UCAAAAUAAG	chr12:72072595-72072819(+)$1	224	196	206	14.1964
UAAAAAAGAA	chr10:13482990-13483212(-)$1	222	3	13	13.6607
GAAAAAAAAA	chr7:141360496-141360721(-)$1	225	70	80	15.0000
UACAAAUAGA	chr11:88026896-88027129(-)$1	233	53	63	13.7500
AAAAAAUAGA	chr2:48602500-48602728(+)$1	228	73	83	14.4642
GAAAAAAAAA	chr11:8711032-8711260(+)$1	228	28	38	15.0000
GAAAAAUAAA	chr1:173902164-173902386(-)$1	222	143	153	18.3035
UCAAAAUGAA	chr20:18541810-18542032(+)$1	222	50	60	13.9285
UGAAAACAAA	chr11:108343123-108343349(-)$1	226	176	186	14.2857
CAAAAAUAAA	chr18:45367525-45367747(-)$1	222	107	117	18.2142
UUCAAAUAAA	chr3:56761351-56761576(-)$1	225	103	113	14.3750
CCAAAAUAAA	chr2:239308978-239309210(+)$1	232	117	127	15.1785

#otherMatches

#Struct PSSM
eeeeeooooo	chr17:5335866-5336088(+)$1	222	148	158	15.0000
hhmmmmhhhh	chr13:96233475-96233705(-)$1	230	10	20	13.3928
d]eeeee555	chr5:60454706-60454929(-)$1	223	87	97	13.8392
qqqqffffff	chr3:23962136-23962359(+)$1	223	116	126	14.4642
::::gggggg	chr2:203427337-203427559(+)$1	222	23	33	13.9285
ELLLDDDD{C	chr18:56995594-56995817(-)$1	223	6	16	15.0000
$$$ccc[ccc	chr12:51214192-51214417(+)$1	225	105	115	13.7500
iiiiinnnnn	chr10:75001795-75002016(-)$1	221	82	92	17.4107
dddppppppp	chr4:128753931-128754162(+)$1	231	25	35	13.4821
::::::::::	chr1:23636772-23636996(-)$1	224	109	119	14.9107
qqqqqdddd]	chr21:40195167-40195392(+)$1	225	175	185	14.4642
!!ddddgggg	chr1:227846792-227847013(+)$1	221	6	16	14.2857
uuuuuuuuuu	chr6:21232492-21232716(+)$1	224	111	121	16.9642
2ccc333eee	chr22:38363654-38363879(+)$1	225	128	138	14.3750
++++++++ee	chr3:14530665-14530891(+)$1	226	161	171	17.8571
oooooeeeee	chr1:160186376-160186597(-)$1	221	39	49	13.9285
d^^^^^^^^^	chr19:10942410-10942662(+)$1	252	131	141	13.7500
eeeee]dddd	chr5:55247196-55247418(-)$1	222	173	183	13.1250
!!bboooooo	chr17:73148923-73149150(-)$1	227	160	170	18.3035
::dddd[hhh	chr14:69254971-69255190(-)$1	219	85	95	14.0178
hhhhhhhhrr	chr12:96672240-96672464(-)$1	224	106	116	13.7500
+++++++++=	chr13:30339117-30339339(-)$1	222	49	59	17.6785
::::::::::	chr13:103492357-103492589(+)$1	232	118	128	12.9464
=======ppp	chr5:134192922-134193146(+)$1	224	17	27	14.4642
eee]ccc]bb	chr5:135516196-135516418(+)$1	222	100	110	13.0357
xxxxxxxxxx	chr17:57187392-57187617(-)$1	225	104	114	13.2142
MMMMCCC:::	chr8:105502082-105502307(-)$1	225	16	26	14.6428
ppppppbb::	chr15:41669324-41669547(+)$1	223	20	30	13.2142
uuuuuuuuuu	chr12:88589561-88589784(+)$1	223	165	175	17.6785
:::::::::c	chr21:15744003-15744233(-)$1	230	140	150	13.9285
e$$$$$ffff	chr12:125515455-125515677(+)$1	222	9	19	13.8392
eeeee]dddd	chrX:103435803-103436023(+)$1	220	203	213	16.7857
iiiiiii::i	chr5:64017438-64017659(-)$1	221	29	39	12.9464
iiii::::::	chr17:46626528-46626749(-)$1	221	28	38	13.8392
d:::::::::	chr1:198290925-198291150(+)$1	225	213	223	17.6785
gggg:::::I	chr3:52745367-52745587(-)$1	220	160	170	13.1250
55555fffff	chr7:44867571-44867791(-)$1	220	104	114	14.5535
g:::::::::	chr12:120532818-120533044(-)$1	226	116	126	21.2500
dffffff:::	chr11:43877644-43877868(+)$1	224	106	116	14.3750
eeeee]ccc:	chr1:212910890-212911110(-)$1	220	122	132	14.4642
::::::::::	chr5:173315549-173315772(+)$1	223	52	62	17.9464
fffff333cc	chr6:139501810-139502032(+)$1	222	102	112	17.6785
::gggggggs	chr5:10434819-10435052(+)$1	233	107	117	14.3750
bb:::::::F	chrX:15339385-15339606(-)$1	221	127	137	14.0178
ppffffff:E	chr12:72072595-72072819(+)$1	224	196	206	14.1964
::::::::DD	chr10:13482990-13483212(-)$1	222	3	13	13.6607
ccqqqqqqqq	chr7:141360496-141360721(-)$1	225	70	80	15.0000
HHHHHHH{DD	chr11:88026896-88027129(-)$1	233	53	63	13.7500
FFF:::::a!	chr2:48602500-48602728(+)$1	228	73	83	14.4642
hh"""dddd#	chr11:8711032-8711260(+)$1	228	28	38	15.0000
g[hhhhhhhh	chr1:173902164-173902386(-)$1	222	143	153	18.3035
ccclllccc2	chr20:18541810-18542032(+)$1	222	50	60	13.9285
odddd:::::	chr11:108343123-108343349(-)$1	226	176	186	14.2857
dddsssssss	chr18:45367525-45367747(-)$1	222	107	117	18.2142
LLHHHHHHHH	chr3:56761351-56761576(-)$1	225	103	113	14.3750
^^^^^^^^^^	chr2:239308978-239309210(+)$1	232	117	127	15.1785

#DB
(((((.....	chr17:5335866-5336088(+)$1	1	148	158	15.0000
((....))))	chr13:96233475-96233705(-)$1	1	10	20	13.3928
).)))))...	chr5:60454706-60454929(-)$1	1	87	97	13.8392
....))))))	chr3:23962136-23962359(+)$1	1	116	126	14.4642
....((((((	chr2:203427337-203427559(+)$1	1	23	33	13.9285
(...((((.(	chr18:56995594-56995817(-)$1	1	6	16	15.0000
...(((.(((	chr12:51214192-51214417(+)$1	1	105	115	13.7500
(((((.....	chr10:75001795-75002016(-)$1	1	82	92	17.4107
(((.......	chr4:128753931-128754162(+)$1	1	25	35	13.4821
..........	chr1:23636772-23636996(-)$1	1	109	119	14.9107
.....)))).	chr21:40195167-40195392(+)$1	1	175	185	14.4642
..((((((((	chr1:227846792-227847013(+)$1	1	6	16	14.2857
..........	chr6:21232492-21232716(+)$1	1	111	121	16.9642
.)))...)))	chr22:38363654-38363879(+)$1	1	128	138	14.3750
........((	chr3:14530665-14530891(+)$1	1	161	171	17.8571
.....)))))	chr1:160186376-160186597(-)$1	1	39	49	13.9285
(.........	chr19:10942410-10942662(+)$1	1	131	141	13.7500
))))).))))	chr5:55247196-55247418(-)$1	1	173	183	13.1250
..((......	chr17:73148923-73149150(-)$1	1	160	170	18.3035
..((((.(((	chr14:69254971-69255190(-)$1	1	85	95	14.0178
((((((((..	chr12:96672240-96672464(-)$1	1	106	116	13.7500
.........(	chr13:30339117-30339339(-)$1	1	49	59	17.6785
..........	chr13:103492357-103492589(+)$1	1	118	128	12.9464
(((((((...	chr5:134192922-134193146(+)$1	1	17	27	14.4642
))).))).))	chr5:135516196-135516418(+)$1	1	100	110	13.0357
..........	chr17:57187392-57187617(-)$1	1	104	114	13.2142
....(((...	chr8:105502082-105502307(-)$1	1	16	26	14.6428
......))..	chr15:41669324-41669547(+)$1	1	20	30	13.2142
..........	chr12:88589561-88589784(+)$1	1	165	175	17.6785
.........(	chr21:15744003-15744233(-)$1	1	140	150	13.9285
(.....((((	chr12:125515455-125515677(+)$1	1	9	19	13.8392
))))).))))	chrX:103435803-103436023(+)$1	1	203	213	16.7857
)))))))..(	chr5:64017438-64017659(-)$1	1	29	39	12.9464
))))......	chr17:46626528-46626749(-)$1	1	28	38	13.8392
).........	chr1:198290925-198291150(+)$1	1	213	223	17.6785
)))).....)	chr3:52745367-52745587(-)$1	1	160	170	13.1250
.....)))))	chr7:44867571-44867791(-)$1	1	104	114	14.5535
).........	chr12:120532818-120533044(-)$1	1	116	126	21.2500
)))))))...	chr11:43877644-43877868(+)$1	1	106	116	14.3750
))))).))).	chr1:212910890-212911110(-)$1	1	122	132	14.4642
..........	chr5:173315549-173315772(+)$1	1	52	62	17.9464
)))))...))	chr6:139501810-139502032(+)$1	1	102	112	17.6785
..(((((((.	chr5:10434819-10435052(+)$1	1	107	117	14.3750
)).......)	chrX:15339385-15339606(-)$1	1	127	137	14.0178
..)))))).)	chr12:72072595-72072819(+)$1	1	196	206	14.1964
........((	chr10:13482990-13483212(-)$1	1	3	13	13.6607
((........	chr7:141360496-141360721(-)$1	1	70	80	15.0000
(((((((.((	chr11:88026896-88027129(-)$1	1	53	63	13.7500
(((.....(.	chr2:48602500-48602728(+)$1	1	73	83	14.4642
((...((((.	chr11:8711032-8711260(+)$1	1	28	38	15.0000
(.((((((((	chr1:173902164-173902386(-)$1	1	143	153	18.3035
(((...))).	chr20:18541810-18542032(+)$1	1	50	60	13.9285
.)))).....	chr11:108343123-108343349(-)$1	1	176	186	14.2857
(((.......	chr18:45367525-45367747(-)$1	1	107	117	18.2142
..((((((((	chr3:56761351-56761576(-)$1	1	103	113	14.3750
..........	chr2:239308978-239309210(+)$1	1	117	127	15.1785

#PSSM
U : 0.58	G : 0.10	A : 0.10	u : 0.10	C : 0.08	
A : 0.66	C : 0.12	a : 0.07	G : 0.05	U : 0.05	u : 0.03	
A : 0.71	a : 0.08	U : 0.07	C : 0.07	G : 0.03	u : 0.01	
A : 0.76	a : 0.10	U : 0.08	G : 0.01	C : 0.01	
A : 0.80	a : 0.08	U : 0.03	G : 0.03	u : 0.01	C : 0.01	
A : 0.80	a : 0.10	G : 0.03	C : 0.03	U : 0.01	
U : 0.67	A : 0.12	u : 0.10	C : 0.07	G : 0.01	
A : 0.80	a : 0.10	G : 0.05	C : 0.01	U : 0.01	
A : 0.76	C : 0.05	a : 0.05	u : 0.03	U : 0.03	G : 0.03	g : 0.01	
A : 0.78	u : 0.05	U : 0.05	a : 0.03	C : 0.03	c : 0.01	G : 0.01	

#score	838.0357142857144
#seq	56
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m1_run2.nuc.txt

#NT
AAGAA	chr5:33461714-33461949(+)$1	235	5	10	15.0000
AAGAA	chr6:99850362-99850602(-)$1	240	97	102	15.0000
AAGAA	chr8:67974128-67974359(-)$1	231	224	229	15.0000
AAGAA	chr19:3762650-3762896(+)$1	246	156	161	15.0000
AAGAA	chr7:129760515-129760754(+)$1	239	201	206	15.0000
AAGAA	chr9:125673665-125673897(-)$1	232	81	86	15.0000
AAGAA	chr4:113189316-113189543(+)$1	227	63	68	15.0000
AAGAA	chr8:12947751-12947985(-)$1	234	151	156	15.0000
AAGAA	chr17:33968810-33969040(+)$1	230	127	132	15.0000
AAGAA	chr5:72182797-72183029(+)$1	232	180	185	15.0000
AAGAA	chr19:44732619-44732879(+)$1	260	87	92	15.0000
AAGAA	chr1:228284797-228285063(+)$1	266	64	69	15.0000
AAGAA	chr19:49377142-49377395(+)$1	253	52	57	15.0000
AAGAA	chr19:5691442-5691666(+)$1	224	13	18	15.0000
AAGAA	chr9:112900489-112900757(+)$1	268	126	131	15.0000
AAGAA	chrX:73812432-73812657(-)$1	225	140	145	15.0000
AAGAA	chr18:47016789-47017021(-)$1	232	11	16	15.0000
AAGAA	chr7:50513693-50513915(-)$1	222	58	63	15.0000
AAGAA	chr3:139078023-139078267(-)$1	244	177	182	15.0000
AAGAA	chr7:115891774-115892001(+)$1	227	67	72	15.0000
AAGAA	chr20:17581463-17581686(+)$1	223	3	8	15.0000
AAGAA	chr6:26204749-26204999(+)$1	250	62	67	15.0000
AAGAA	chr3:167414715-167414944(-)$1	229	37	42	15.0000
AAGAA	chr10:129905992-129906281(-)$1	289	256	261	15.0000
AAGAA	chr1:8425829-8426057(-)$1	228	53	58	15.0000
AAGAA	chr2:74399630-74399876(-)$1	246	28	33	15.0000
AAGAA	chr6:43488590-43488846(+)$1	256	153	158	15.0000
AAGAA	chr10:75896349-75896590(-)$1	241	96	101	15.0000
AAGAA	chr2:217005841-217006086(+)$1	245	117	122	15.0000
AAGAA	chr2:232326478-232326722(-)$1	244	9	14	15.0000
AAGAA	chr1:149859227-149859453(-)$1	226	209	214	15.0000
AAGAA	chr14:62204890-62205128(+)$1	238	79	84	15.0000
AAGAA	chr5:32403209-32403442(-)$1	233	198	203	15.0000
AAGAA	chr5:41911114-41911359(+)$1	245	124	129	15.0000
AAGAA	chr1:91404184-91404417(-)$1	233	51	56	15.0000
AAGAA	chr9:35068211-35068445(-)$1	234	126	131	15.0000
AAGAA	chr16:2812452-2812692(+)$1	240	233	238	15.0000
AAGAA	chr12:58142157-58142420(-)$1	263	138	143	15.0000
AAGAA	chr1:111494595-111494824(-)$1	229	48	53	15.0000
AAGAA	chr10:71899638-71899887(-)$1	249	229	234	15.0000
AAGAA	chr16:29821580-29821956(+)$1	376	100	105	15.0000
AAGAA	chr17:37360789-37361028(+)$1	239	58	63	15.0000
AAGAA	chr3:179316404-179316631(-)$1	227	86	91	15.0000
AAGAA	chrX:102931196-102931418(-)$1	222	22	27	15.0000
AAGAA	chr1:115280496-115280775(-)$1	279	157	162	15.0000
AAGAA	chr3:47957580-47957812(-)$1	232	89	94	15.0000
AAGAA	chr14:94528771-94529059(-)$1	288	13	18	15.0000
AAGAA	chr1:20976867-20977104(+)$1	237	128	133	15.0000
AAGAA	chrX:71492986-71493272(-)$1	286	70	75	15.0000
AAGAA	chr13:52604560-52604787(+)$1	227	27	32	15.0000
AAGAA	chr4:140282808-140283030(+)$1	222	203	208	15.0000
AAGAA	chr12:120903343-120903575(-)$1	232	9	14	15.0000
AAGAA	chr17:40280237-40280500(-)$1	263	117	122	15.0000
AAGAA	chr2:47705456-47705704(+)$1	248	195	200	15.0000
AAGAA	chr15:66794975-66795215(-)$1	240	65	70	15.0000

#otherMatches

#Struct PSSM
ggggg	chr16:31200894-31201128(+)$1	234	27	32	15.0000
::::D	chr5:33461714-33461949(+)$1	235	5	10	15.0000
c333b	chr6:99850362-99850602(-)$1	240	97	102	15.0000
:::::	chr8:67974128-67974359(-)$1	231	224	229	15.0000
rrrrr	chr19:3762650-3762896(+)$1	246	156	161	15.0000
HHHHH	chr7:129760515-129760754(+)$1	239	201	206	15.0000
mmmbb	chr9:125673665-125673897(-)$1	232	81	86	15.0000
:DDDD	chr4:113189316-113189543(+)$1	227	63	68	15.0000
66eee	chr8:12947751-12947985(-)$1	234	151	156	15.0000
2ccc:	chr17:33968810-33969040(+)$1	230	127	132	15.0000
eeenn	chr5:72182797-72183029(+)$1	232	180	185	15.0000
FFF::	chr19:44732619-44732879(+)$1	260	87	92	15.0000
dddd3	chr1:228284797-228285063(+)$1	266	64	69	15.0000
^^^^^	chr19:49377142-49377395(+)$1	253	52	57	15.0000
qqqqq	chr19:5691442-5691666(+)$1	224	13	18	15.0000
\\\\\	chr9:112900489-112900757(+)$1	268	126	131	15.0000
ttttt	chrX:73812432-73812657(-)$1	225	140	145	15.0000
:::::	chr18:47016789-47017021(-)$1	232	11	16	15.0000
]bb:c	chr7:50513693-50513915(-)$1	222	58	63	15.0000
eeenn	chr3:139078023-139078267(-)$1	244	177	182	15.0000
999dd	chr7:115891774-115892001(+)$1	227	67	72	15.0000
:::::	chr20:17581463-17581686(+)$1	223	3	8	15.0000
22ddd	chr6:26204749-26204999(+)$1	250	62	67	15.0000
2gggg	chr3:167414715-167414944(-)$1	229	37	42	15.0000
ooooo	chr10:129905992-129906281(-)$1	289	256	261	15.0000
fff22	chr1:8425829-8426057(-)$1	228	53	58	15.0000
yffff	chr2:74399630-74399876(-)$1	246	28	33	15.0000
!bb''	chr6:43488590-43488846(+)$1	256	153	158	15.0000
::===	chr10:75896349-75896590(-)$1	241	96	101	15.0000
=====	chr2:217005841-217006086(+)$1	245	117	122	15.0000
:::::	chr2:232326478-232326722(-)$1	244	9	14	15.0000
22bb]	chr1:149859227-149859453(-)$1	226	209	214	15.0000
77eee	chr14:62204890-62205128(+)$1	238	79	84	15.0000
dd[dd	chr5:32403209-32403442(-)$1	233	198	203	15.0000
qqq==	chr5:41911114-41911359(+)$1	245	124	129	15.0000
pcccD	chr1:91404184-91404417(-)$1	233	51	56	15.0000
eeeee	chr9:35068211-35068445(-)$1	234	126	131	15.0000
:::::	chr16:2812452-2812692(+)$1	240	233	238	15.0000
]ccc:	chr12:58142157-58142420(-)$1	263	138	143	15.0000
ooodd	chr1:111494595-111494824(-)$1	229	48	53	15.0000
nnddd	chr10:71899638-71899887(-)$1	249	229	234	15.0000
fffff	chr16:29821580-29821956(+)$1	376	100	105	15.0000
ccc!!	chr17:37360789-37361028(+)$1	239	58	63	15.0000
44fff	chr3:179316404-179316631(-)$1	227	86	91	15.0000
ooooo	chrX:102931196-102931418(-)$1	222	22	27	15.0000
ODDDD	chr1:115280496-115280775(-)$1	279	157	162	15.0000
neeee	chr3:47957580-47957812(-)$1	232	89	94	15.0000
::ddd	chr14:94528771-94529059(-)$1	288	13	18	15.0000
DDD::	chr1:20976867-20977104(+)$1	237	128	133	15.0000
HHHHH	chrX:71492986-71493272(-)$1	286	70	75	15.0000
yyyyy	chr13:52604560-52604787(+)$1	227	27	32	15.0000
eelll	chr4:140282808-140283030(+)$1	222	203	208	15.0000
GGGG:	chr12:120903343-120903575(-)$1	232	9	14	15.0000
:::::	chr17:40280237-40280500(-)$1	263	117	122	15.0000
e::::	chr2:47705456-47705704(+)$1	248	195	200	15.0000
77777	chr15:66794975-66795215(-)$1	240	65	70	15.0000

#DB
(((((	chr16:31200894-31201128(+)$1	1	27	32	15.0000
....(	chr5:33461714-33461949(+)$1	1	5	10	15.0000
)...)	chr6:99850362-99850602(-)$1	1	97	102	15.0000
.....	chr8:67974128-67974359(-)$1	1	224	229	15.0000
.....	chr19:3762650-3762896(+)$1	1	156	161	15.0000
)))))	chr7:129760515-129760754(+)$1	1	201	206	15.0000
...))	chr9:125673665-125673897(-)$1	1	81	86	15.0000
.((((	chr4:113189316-113189543(+)$1	1	63	68	15.0000
..)))	chr8:12947751-12947985(-)$1	1	151	156	15.0000
.))).	chr17:33968810-33969040(+)$1	1	127	132	15.0000
(((..	chr5:72182797-72183029(+)$1	1	180	185	15.0000
(((..	chr19:44732619-44732879(+)$1	1	87	92	15.0000
)))).	chr1:228284797-228285063(+)$1	1	64	69	15.0000
.....	chr19:49377142-49377395(+)$1	1	52	57	15.0000
.....	chr19:5691442-5691666(+)$1	1	13	18	15.0000
.....	chr9:112900489-112900757(+)$1	1	126	131	15.0000
.....	chrX:73812432-73812657(-)$1	1	140	145	15.0000
.....	chr18:47016789-47017021(-)$1	1	11	16	15.0000
.)).(	chr7:50513693-50513915(-)$1	1	58	63	15.0000
(((..	chr3:139078023-139078267(-)$1	1	177	182	15.0000
...))	chr7:115891774-115892001(+)$1	1	67	72	15.0000
.....	chr20:17581463-17581686(+)$1	1	3	8	15.0000
..)))	chr6:26204749-26204999(+)$1	1	62	67	15.0000
.))))	chr3:167414715-167414944(-)$1	1	37	42	15.0000
.....	chr10:129905992-129906281(-)$1	1	256	261	15.0000
)))..	chr1:8425829-8426057(-)$1	1	53	58	15.0000
.))))	chr2:74399630-74399876(-)$1	1	28	33	15.0000
.((..	chr6:43488590-43488846(+)$1	1	153	158	15.0000
..(((	chr10:75896349-75896590(-)$1	1	96	101	15.0000
)))))	chr2:217005841-217006086(+)$1	1	117	122	15.0000
.....	chr2:232326478-232326722(-)$1	1	9	14	15.0000
..)).	chr1:149859227-149859453(-)$1	1	209	214	15.0000
..)))	chr14:62204890-62205128(+)$1	1	79	84	15.0000
((.((	chr5:32403209-32403442(-)$1	1	198	203	15.0000
...))	chr5:41911114-41911359(+)$1	1	124	129	15.0000
.)))(	chr1:91404184-91404417(-)$1	1	51	56	15.0000
)))((	chr9:35068211-35068445(-)$1	1	126	131	15.0000
.....	chr16:2812452-2812692(+)$1	1	233	238	15.0000
.))).	chr12:58142157-58142420(-)$1	1	138	143	15.0000
...))	chr1:111494595-111494824(-)$1	1	48	53	15.0000
..)))	chr10:71899638-71899887(-)$1	1	229	234	15.0000
(((((	chr16:29821580-29821956(+)$1	1	100	105	15.0000
(((..	chr17:37360789-37361028(+)$1	1	58	63	15.0000
..)))	chr3:179316404-179316631(-)$1	1	86	91	15.0000
.....	chrX:102931196-102931418(-)$1	1	22	27	15.0000
.((((	chr1:115280496-115280775(-)$1	1	157	162	15.0000
.))))	chr3:47957580-47957812(-)$1	1	89	94	15.0000
..(((	chr14:94528771-94529059(-)$1	1	13	18	15.0000
)))..	chr1:20976867-20977104(+)$1	1	128	133	15.0000
)))))	chrX:71492986-71493272(-)$1	1	70	75	15.0000
.....	chr13:52604560-52604787(+)$1	1	27	32	15.0000
((...	chr4:140282808-140283030(+)$1	1	203	208	15.0000
((((.	chr12:120903343-120903575(-)$1	1	9	14	15.0000
.....	chr17:40280237-40280500(-)$1	1	117	122	15.0000
)....	chr2:47705456-47705704(+)$1	1	195	200	15.0000
.....	chr15:66794975-66795215(-)$1	1	65	70	15.0000

#PSSM
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	

#score	840.0000000000005
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_UTR_m2_run2.nuc.txt

#NT
GGAGUU	chr22:42998718-42998919(-)$1	201	67	73	10.3611
GGAGCC	chr11:61116379-61116580(-)$1	201	53	59	9.8055
GGAGAU	chr6:83878239-83878440(-)$1	201	37	43	10.2916
GGACCU	chr1:241799006-241799207(-)$1	201	18	24	10.1527
GGAGCU	chr17:73237631-73237832(-)$1	201	54	60	13.9027
AGAGCU	chr15:78461205-78461406(+)$1	201	56	62	9.6666
GGAGCU	chrX:133930797-133930998(-)$1	201	66	72	13.9027
GGACCU	chr17:46052898-46053099(+)$1	201	19	25	10.1527
GGAGUU	chr19:39904123-39904324(+)$1	201	32	38	10.3611
ggaacu	chr14:102549374-102549575(-)$1	201	96	102	10.0138
GCAGCU	chr12:123462360-123462561(+)$1	201	13	19	9.5972
GGAGGU	chr13:30087377-30087578(-)$1	201	150	156	10.4999
gcagcu	chr13:100637848-100638049(+)$1	201	11	17	9.5972
GGAGCC	chr3:37107227-37107428(-)$1	201	61	67	9.8055
GGCGCU	chr16:8952079-8952280(-)$1	201	112	118	9.5277
GGAGUU	chr1:24022347-24022548(+)$1	201	101	107	10.3611
GGAGGU	chr9:139316712-139316913(+)$1	201	151	157	10.4999
GGAGCU	chr12:122975443-122975644(-)$1	201	171	177	13.9027
GAAGCU	chr13:30084323-30084524(-)$1	201	11	17	9.5972
GCAGCU	chr18:47017869-47018070(-)$1	201	32	38	9.5972
UGAGCU	chr16:70606814-70607015(+)$1	201	21	27	9.8749
GGAGCC	chr17:1946155-1946356(+)$1	201	144	150	9.8055
ggaucu	chr16:87364240-87364441(-)$1	201	89	95	9.8749
UGAGCU	chr11:64882746-64882947(+)$1	201	121	127	9.8749
GGAGGU	chr14:24679787-24679988(-)$1	201	62	68	10.4999
GGAGCC	chr12:110811717-110811918(-)$1	201	40	46	9.8055
GAAGCU	chr17:38573785-38573986(-)$1	201	38	44	9.5972
GGGGCU	chrX:64743390-64743591(-)$1	201	49	55	9.4583
GGAGAU	chr2:20166416-20166617(-)$1	201	85	91	10.2916
GGAGCU	chr6:43639775-43639976(-)$1	201	87	93	13.9027
GGAGCU	chr17:45727652-45727853(+)$1	201	106	112	13.9027
GGAACU	chr19:4117387-4117588(-)$1	201	0	6	10.0138
UGAGCU	chr11:67201605-67201806(+)$1	201	25	31	9.8749
GGAGCG	chr21:44473778-44473979(-)$1	201	12	18	9.6666
GGAGGU	chr19:12826411-12826612(-)$1	201	1	7	10.4999
GGAGCU	chr17:41150200-41150401(+)$1	201	69	75	13.9027
GGAGCU	chr12:49226213-49226414(-)$1	201	107	113	13.9027
GGAGCG	chr9:131465043-131465244(+)$1	201	140	146	9.6666
GGAGCU	chr17:74057114-74057315(-)$1	201	182	188	13.9027
GGAGGU	chr11:62361151-62361352(-)$1	201	21	27	10.4999
GGGGCU	chr17:1373680-1373881(-)$1	201	175	181	9.4583
UGAGCU	chr1:6651408-6651609(-)$1	201	27	33	9.8749
GGAGCU	chr8:145693018-145693219(+)$1	201	83	89	13.9027
GGCGCU	chr19:48620822-48621023(-)$1	201	27	33	9.5277
GAAGCU	chr12:53685737-53685938(+)$1	201	38	44	9.5972
GGAGCU	chr11:62437037-62437238(-)$1	201	52	58	13.9027
GGACCU	chr16:2047804-2048005(-)$1	201	33	39	10.1527
GGCGCU	chr12:65088474-65088675(+)$1	201	153	159	9.5277
CGAGCU	chr10:856537-856738(-)$1	201	90	96	9.6666
GGAGCA	chr5:138650279-138650480(+)$1	201	105	111	9.7361
CGAGCU	chr15:56152541-56152742(-)$1	201	130	136	9.6666
GGAGCU	chr11:118923024-118923225(-)$1	201	41	47	13.9027
GGAGUU	chr17:30800874-30801075(+)$1	201	170	176	10.3611
ugagcu	chr8:22465393-22465594(+)$1	201	26	32	9.8749
GGAGUU	chr3:108288220-108288421(-)$1	201	161	167	10.3611
GGAGGU	chr19:47230653-47230854(-)$1	201	82	88	10.4999
GGAGGU	chr9:139342230-139342431(-)$1	201	123	129	10.4999
GGAGCU	chr6:86246515-86246716(-)$1	201	159	165	13.9027
GGACCU	chr1:1169558-1169759(+)$1	201	37	43	10.1527
GGAGAU	chr3:122145838-122146039(-)$1	201	60	66	10.2916
GGAGCA	chr11:72553683-72553884(-)$1	201	63	69	9.7361
GGUGCU	chr20:32247865-32248066(-)$1	201	11	17	9.3888
GGAACU	chr3:15711523-15711724(-)$1	201	123	129	10.0138
GGACCU	chr15:90378542-90378743(-)$1	201	104	110	10.1527
GGAACU	chr2:241536002-241536203(+)$1	201	36	42	10.0138
GGACCU	chr17:42478355-42478556(-)$1	201	88	94	10.1527
AGAGCU	chr3:72873503-72873704(-)$1	201	0	6	9.6666
GGAGCA	chr17:4794683-4794884(+)$1	201	29	35	9.7361
GUAGCU	chr1:28374799-28375000(-)$1	201	0	6	9.4583
GGAGAU	chr6:56381936-56382137(-)$1	201	45	51	10.2916
GGAGCU	chr17:3716102-3716303(-)$1	201	47	53	13.9027

#otherMatches

#Struct PSSM
!bb[ee	chr12:49916459-49916660(+)$1	201	103	109	9.8749
2bb]cc	chr22:42998718-42998919(-)$1	201	67	73	10.3611
::eeee	chr11:61116379-61116580(-)$1	201	53	59	9.8055
ddd$$$	chr6:83878239-83878440(-)$1	201	37	43	10.2916
++++++	chr1:241799006-241799207(-)$1	201	18	24	10.1527
ddddff	chr17:73237631-73237832(-)$1	201	54	60	13.9027
ggg[cc	chr15:78461205-78461406(+)$1	201	56	62	9.6666
eee]dd	chrX:133930797-133930998(-)$1	201	66	72	13.9027
cc]bb]	chr17:46052898-46053099(+)$1	201	19	25	10.1527
CCCGGG	chr19:39904123-39904324(+)$1	201	32	38	10.3611
eeelll	chr14:102549374-102549575(-)$1	201	96	102	10.0138
iiiiii	chr12:123462360-123462561(+)$1	201	13	19	9.5972
ii]ccc	chr13:30087377-30087578(-)$1	201	150	156	10.4999
bb[bb[	chr13:100637848-100638049(+)$1	201	11	17	9.5972
hh333=	chr3:37107227-37107428(-)$1	201	61	67	9.8055
=66666	chr16:8952079-8952280(-)$1	201	112	118	9.5277
DDDCCC	chr1:24022347-24022548(+)$1	201	101	107	10.3611
iiiiii	chr9:139316712-139316913(+)$1	201	151	157	10.4999
HHH???	chr12:122975443-122975644(-)$1	201	171	177	13.9027
((((((	chr13:30084323-30084524(-)$1	201	11	17	9.5972
dddd!!	chr18:47017869-47018070(-)$1	201	32	38	9.5972
CFFFFF	chr16:70606814-70607015(+)$1	201	21	27	9.8749
EE:ggg	chr17:1946155-1946356(+)$1	201	144	150	9.8055
Jbbddd	chr16:87364240-87364441(-)$1	201	89	95	9.8749
JJJJEE	chr11:64882746-64882947(+)$1	201	121	127	9.8749
a22ddd	chr14:24679787-24679988(-)$1	201	62	68	10.4999
EEEEEd	chr12:110811717-110811918(-)$1	201	40	46	9.8055
f::HHH	chr17:38573785-38573986(-)$1	201	38	44	9.5972
eeeee[	chrX:64743390-64743591(-)$1	201	49	55	9.4583
ccceee	chr2:20166416-20166617(-)$1	201	85	91	10.2916
eeee33	chr6:43639775-43639976(-)$1	201	87	93	13.9027
CCCKKC	chr17:45727652-45727853(+)$1	201	106	112	13.9027
::::::	chr19:4117387-4117588(-)$1	201	0	6	10.0138
B{BBKK	chr11:67201605-67201806(+)$1	201	25	31	9.8749
bboooo	chr21:44473778-44473979(-)$1	201	12	18	9.6666
ccccc[	chr19:12826411-12826612(-)$1	201	1	7	10.4999
gggggg	chr17:41150200-41150401(+)$1	201	69	75	13.9027
[a[ccc	chr12:49226213-49226414(-)$1	201	107	113	13.9027
JJJJJJ	chr9:131465043-131465244(+)$1	201	140	146	9.6666
EEEddd	chr17:74057114-74057315(-)$1	201	182	188	13.9027
======	chr11:62361151-62361352(-)$1	201	21	27	10.4999
""ammm	chr17:1373680-1373881(-)$1	201	175	181	9.4583
qqqqee	chr1:6651408-6651609(-)$1	201	27	33	9.8749
##eeee	chr8:145693018-145693219(+)$1	201	83	89	13.9027
eeeee$	chr19:48620822-48621023(-)$1	201	27	33	9.5277
bb[ddd	chr12:53685737-53685938(+)$1	201	38	44	9.5972
dhhhhh	chr11:62437037-62437238(-)$1	201	52	58	13.9027
[eeeee	chr16:2047804-2048005(-)$1	201	33	39	10.1527
dddqqq	chr12:65088474-65088675(+)$1	201	153	159	9.5277
dddd]c	chr10:856537-856738(-)$1	201	90	96	9.6666
dddd[d	chr5:138650279-138650480(+)$1	201	105	111	9.7361
f!!bbl	chr15:56152541-56152742(-)$1	201	130	136	9.6666
bccc22	chr11:118923024-118923225(-)$1	201	41	47	13.9027
cfffff	chr17:30800874-30801075(+)$1	201	170	176	10.3611
gggmmm	chr8:22465393-22465594(+)$1	201	26	32	9.8749
EEEEII	chr3:108288220-108288421(-)$1	201	161	167	10.3611
ggggg]	chr19:47230653-47230854(-)$1	201	82	88	10.4999
[bbooo	chr9:139342230-139342431(-)$1	201	123	129	10.4999
::ffff	chr6:86246515-86246716(-)$1	201	159	165	13.9027
======	chr1:1169558-1169759(+)$1	201	37	43	10.1527
[fffff	chr3:122145838-122146039(-)$1	201	60	66	10.2916
fffff#	chr11:72553683-72553884(-)$1	201	63	69	9.7361
offfff	chr20:32247865-32248066(-)$1	201	11	17	9.3888
dddd[d	chr3:15711523-15711724(-)$1	201	123	129	10.0138
ggg22c	chr15:90378542-90378743(-)$1	201	104	110	10.1527
drrrrr	chr2:241536002-241536203(+)$1	201	36	42	10.0138
ooofff	chr17:42478355-42478556(-)$1	201	88	94	10.1527
::::::	chr3:72873503-72873704(-)$1	201	0	6	9.6666
EE{BBH	chr17:4794683-4794884(+)$1	201	29	35	9.7361
:DDDDM	chr1:28374799-28375000(-)$1	201	0	6	9.4583
D:ffff	chr6:56381936-56382137(-)$1	201	45	51	10.2916
ddddcc	chr17:3716102-3716303(-)$1	201	47	53	13.9027

#DB
.((.((	chr12:49916459-49916660(+)$1	1	103	109	9.8749
.)).))	chr22:42998718-42998919(-)$1	1	67	73	10.3611
..((((	chr11:61116379-61116580(-)$1	1	53	59	9.8055
(((...	chr6:83878239-83878440(-)$1	1	37	43	10.2916
......	chr1:241799006-241799207(-)$1	1	18	24	10.1527
((((((	chr17:73237631-73237832(-)$1	1	54	60	13.9027
(((.((	chr15:78461205-78461406(+)$1	1	56	62	9.6666
))).))	chrX:133930797-133930998(-)$1	1	66	72	13.9027
)).)).	chr17:46052898-46053099(+)$1	1	19	25	10.1527
((((((	chr19:39904123-39904324(+)$1	1	32	38	10.3611
(((...	chr14:102549374-102549575(-)$1	1	96	102	10.0138
((((((	chr12:123462360-123462561(+)$1	1	13	19	9.5972
)).)))	chr13:30087377-30087578(-)$1	1	150	156	10.4999
((.((.	chr13:100637848-100638049(+)$1	1	11	17	9.5972
))...)	chr3:37107227-37107428(-)$1	1	61	67	9.8055
).....	chr16:8952079-8952280(-)$1	1	112	118	9.5277
((((((	chr1:24022347-24022548(+)$1	1	101	107	10.3611
((((((	chr9:139316712-139316913(+)$1	1	151	157	10.4999
)))...	chr12:122975443-122975644(-)$1	1	171	177	13.9027
......	chr13:30084323-30084524(-)$1	1	11	17	9.5972
((((..	chr18:47017869-47018070(-)$1	1	32	38	9.5972
((((((	chr16:70606814-70607015(+)$1	1	21	27	9.8749
)).(((	chr17:1946155-1946356(+)$1	1	144	150	9.8055
((((((	chr16:87364240-87364441(-)$1	1	89	95	9.8749
))))))	chr11:64882746-64882947(+)$1	1	121	127	9.8749
)..)))	chr14:24679787-24679988(-)$1	1	62	68	10.4999
((((((	chr12:110811717-110811918(-)$1	1	40	46	9.8055
)..(((	chr17:38573785-38573986(-)$1	1	38	44	9.5972
(((((.	chrX:64743390-64743591(-)$1	1	49	55	9.4583
((((((	chr2:20166416-20166617(-)$1	1	85	91	10.2916
))))..	chr6:43639775-43639976(-)$1	1	87	93	13.9027
(((..(	chr17:45727652-45727853(+)$1	1	106	112	13.9027
......	chr19:4117387-4117588(-)$1	1	0	6	10.0138
(.((..	chr11:67201605-67201806(+)$1	1	25	31	9.8749
((....	chr21:44473778-44473979(-)$1	1	12	18	9.6666
(((((.	chr19:12826411-12826612(-)$1	1	1	7	10.4999
((((((	chr17:41150200-41150401(+)$1	1	69	75	13.9027
.(.(((	chr12:49226213-49226414(-)$1	1	107	113	13.9027
))))))	chr9:131465043-131465244(+)$1	1	140	146	9.6666
)))(((	chr17:74057114-74057315(-)$1	1	182	188	13.9027
((((((	chr11:62361151-62361352(-)$1	1	21	27	10.4999
..(...	chr17:1373680-1373881(-)$1	1	175	181	9.4583
....))	chr1:6651408-6651609(-)$1	1	27	33	9.8749
..((((	chr8:145693018-145693219(+)$1	1	83	89	13.9027
(((((.	chr19:48620822-48621023(-)$1	1	27	33	9.5277
((.(((	chr12:53685737-53685938(+)$1	1	38	44	9.5972
((((((	chr11:62437037-62437238(-)$1	1	52	58	13.9027
.(((((	chr16:2047804-2048005(-)$1	1	33	39	10.1527
(((...	chr12:65088474-65088675(+)$1	1	153	159	9.5277
)))).)	chr10:856537-856738(-)$1	1	90	96	9.6666
((((.(	chr5:138650279-138650480(+)$1	1	105	111	9.7361
(..((.	chr15:56152541-56152742(-)$1	1	130	136	9.6666
))))..	chr11:118923024-118923225(-)$1	1	41	47	13.9027
))))))	chr17:30800874-30801075(+)$1	1	170	176	10.3611
(((...	chr8:22465393-22465594(+)$1	1	26	32	9.8749
))))))	chr3:108288220-108288421(-)$1	1	161	167	10.3611
))))).	chr19:47230653-47230854(-)$1	1	82	88	10.4999
.((...	chr9:139342230-139342431(-)$1	1	123	129	10.4999
..((((	chr6:86246515-86246716(-)$1	1	159	165	13.9027
))))))	chr1:1169558-1169759(+)$1	1	37	43	10.1527
.(((((	chr3:122145838-122146039(-)$1	1	60	66	10.2916
(((((.	chr11:72553683-72553884(-)$1	1	63	69	9.7361
.)))))	chr20:32247865-32248066(-)$1	1	11	17	9.3888
((((.(	chr3:15711523-15711724(-)$1	1	123	129	10.0138
)))..)	chr15:90378542-90378743(-)$1	1	104	110	10.1527
(.....	chr2:241536002-241536203(+)$1	1	36	42	10.0138
...)))	chr17:42478355-42478556(-)$1	1	88	94	10.1527
......	chr3:72873503-72873704(-)$1	1	0	6	9.6666
((.(((	chr17:4794683-4794884(+)$1	1	29	35	9.7361
.((((.	chr1:28374799-28375000(-)$1	1	0	6	9.4583
(.((((	chr6:56381936-56382137(-)$1	1	45	51	10.2916
))))))	chr17:3716102-3716303(-)$1	1	47	53	13.9027

#PSSM
G : 0.83	U : 0.05	g : 0.04	A : 0.02	C : 0.02	u : 0.01	
G : 0.86	g : 0.04	A : 0.04	C : 0.02	c : 0.01	U : 0.01	
A : 0.86	a : 0.05	C : 0.04	G : 0.02	U : 0.01	
G : 0.80	C : 0.08	A : 0.04	g : 0.02	U : 0.01	a : 0.01	u : 0.01	
C : 0.72	G : 0.09	U : 0.06	A : 0.05	c : 0.05	
U : 0.81	C : 0.05	u : 0.05	A : 0.04	G : 0.02	

#score	767.6666666666654
#seq	72
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m3_run2.nuc.txt

#NT
UCUUGUUUUUGUGUUUU	chr20:47689079-47689306(+)$1	227	1	18	14.6538
AAGUUCUAUUUUUCUUU	chr2:70454777-70455003(-)$1	226	5	22	17.0576
UUUUUUUUUUUUUCUUA	chr2:152293243-152293466(+)$1	223	77	94	26.7692
UUGUUCUUUUUUUUUUC	chr1:151955563-151955820(-)$1	257	1	18	18.0192
UUUUAUUGUUUAUAUUU	chr3:15288171-15288400(+)$1	229	202	219	18.6923
AUUUUGUUUUGUUUUUU	chr11:94924594-94924816(-)$1	222	23	40	20.9038
GAUUUUUUUUUUUCUUU	chr12:31633004-31633232(-)$1	228	17	34	25.6153
UAAUUACUUGUUUCUUU	chr17:57746034-57746264(+)$1	230	83	100	14.2692
auuaauuuuuuuuaauu	chr6:53156561-53156801(-)$1	240	17	34	17.5384
ACUGCAUUUUUUUCUAU	chr5:133537569-133537812(-)$1	243	12	29	13.8846
UUCUUAUAUUUUUCUCU	chr11:76637513-76637741(+)$1	228	65	82	16.7692
CAUUCUUCUUUUUGUUU	chr19:35996519-35996767(-)$1	248	74	91	16.3846
ACUUAUCUUUUUGCUUU	chr14:96998623-96998858(+)$1	235	193	210	19.0769
AUUAAUUAUUUUACUUU	chr1:220170536-220170761(-)$1	225	41	58	17.3461
CUUUAAGGUUUUUCUUU	chr17:45201156-45201380(-)$1	224	26	43	17.9230
UCUUAAAUCUUUUCUUU	chr8:48866086-48866318(-)$1	232	19	36	15.6153
AUUUUACUUUUUACUUU	chr10:120489732-120489978(-)$1	246	36	53	21.6730
CUUUUUUUUUUUUCUUU	chr1:28233388-28233615(-)$1	227	30	47	28.9807
GUUUCUGUUUUGUUUUU	chr2:48066492-48066717(-)$1	225	57	74	17.5384
GUUUUUGUGUUUACUUG	chr20:34241900-34242148(-)$1	248	189	206	15.6153
AUUUUUAUUUUAGAUUU	chr14:55004364-55004595(+)$1	231	62	79	17.9230
AUUACUUUGUUUUAUUU	chr12:48081630-48081867(-)$1	237	43	60	18.1153
UUUUCUUUUUGUUCUUU	chr1:244855154-244855383(+)$1	229	6	23	24.0769
UUUCUUUUUCUUUCUUU	chr1:67889849-67890083(-)$1	234	55	72	22.0576
AUUUUUUUUUAAUCUUU	chr10:70497519-70497742(+)$1	223	62	79	22.9230
AUUUAUUAUGUUGCUUC	chr6:88234207-88234449(-)$1	242	38	55	13.5000
UUCUUUGUUUUUAAUUC	chr8:125520654-125520876(-)$1	222	100	117	15.1346
GUUUUUUUUUUUUUUUU	chr20:47770392-47770648(-)$1	256	185	202	26.6730
AUCCCUUUGUUUGCUUU	chr1:153789747-153789971(-)$1	224	161	178	14.1730
GUUUAUUGUUUUACUAU	chr3:142753660-142753916(+)$1	256	161	178	15.9038
uuuuuuuuuuuuuuuAA	chrX:48382048-48382309(+)$1	261	54	71	20.4230
CUUUUCUUGUUUUAUUA	chr3:25835528-25835771(+)$1	243	36	53	16.6730
AGCUUUUGUUUUUCUUG	chr1:27059079-27059305(+)$1	226	64	81	16.1923
AUUUCUUCCUUUUCUUU	chr15:70368343-70368576(-)$1	233	160	177	20.6153
UUUUUUGUCGUUUCUCU	chr18:53070616-53070840(-)$1	224	68	85	15.8076
CUUUAUUUAUCUUCUAU	chr8:42212959-42213183(+)$1	224	53	70	15.2307
AUCUUCGUUUUUCCUUU	chr2:44203230-44203464(-)$1	234	75	92	18.0192
UUAUUUUUUUUAUCCUA	chr5:81571776-81572034(-)$1	258	222	239	15.5192
ACUUUUCUCUUUUUUUU	chr9:19300120-19300341(+)$1	221	41	58	18.5961
AUUUUGCUUUUUUUUUU	chr8:67759327-67759549(+)$1	222	77	94	22.1538
uuuuuuuuuucuucuuu	chr12:104516941-104517166(-)$1	225	188	205	26.4807
AUAUAUUUUUAAUCUUU	chr6:53372261-53372487(-)$1	226	52	69	17.6346
AUUGACCUCUUUUCUUU	chr15:65868541-65868773(+)$1	232	77	94	15.4230
UUCUUUCUUUUCUCUUA	chr1:118462854-118463090(-)$1	236	23	40	17.2500
UGAUUUUUUUUUUAUUU	chr14:67831404-67831632(+)$1	228	17	34	21.0000
GUUUUCUUUUUUUCCUU	chr19:12921072-12921303(+)$1	231	208	225	21.6730
AUUUUUCUUCUUUGUUU	chr12:76446926-76447169(-)$1	243	16	33	20.5192
UACUGUUUGUUCUCUUU	chr2:224831557-224831777(+)$1	220	1	18	13.6923
uuuuuuuuuuCUGUUUU	chr4:140270590-140270811(+)$1	221	1	18	20.9038
UUGUUAUUUUAUUCAUU	chr17:38564649-38564884(-)$1	235	182	199	16.0000
CUUGUAUUUAUUUAUUU	chr1:243858798-243859031(-)$1	233	166	183	15.6153

#otherMatches

#Struct PSSM
::::::::::eeeeell	chr8:6582296-6582522(+)$1	226	74	91	24.0769
:FFFFFFKKIIIIIIII	chr20:47689079-47689306(+)$1	227	1	18	14.6538
F{CCC{EEEEE{FFFFF	chr2:70454777-70455003(-)$1	226	5	22	17.0576
]dddd::::::eeeee"	chr2:152293243-152293466(+)$1	223	77	94	26.7692
::::ggggggg!!bbmm	chr1:151955563-151955820(-)$1	257	1	18	18.0192
:::::CCCYYIIIIIII	chr3:15288171-15288400(+)$1	229	202	219	18.6923
bqqqqqqqqbb666666	chr11:94924594-94924816(-)$1	222	23	40	20.9038
bboooooobb>>>>>>>	chr12:31633004-31633232(-)$1	228	17	34	25.6153
cc::::ddddooooood	chr17:57746034-57746264(+)$1	230	83	100	14.2692
JJJJJKKFFFFFFWWWW	chr6:53156561-53156801(-)$1	240	17	34	17.5384
KCCCOOOOOOFFFFFF:	chr5:133537569-133537812(-)$1	243	12	29	13.8846
oooooffffffffffff	chr11:76637513-76637741(+)$1	228	65	82	16.7692
)))))))))ffffffpp	chr19:35996519-35996767(-)$1	248	74	91	16.3846
::::::::::DDDD@@@	chr14:96998623-96998858(+)$1	235	193	210	19.0769
::::::FFFFFF{HHHH	chr1:220170536-220170761(-)$1	225	41	58	17.3461
u==========:JJJJJ	chr17:45201156-45201380(-)$1	224	26	43	17.9230
ccc[cccqqqqqqqqcc	chr8:48866086-48866318(-)$1	232	19	36	15.6153
==!!ddddsssssssss	chr10:120489732-120489978(-)$1	246	36	53	21.6730
:::::::::========	chr1:28233388-28233615(-)$1	227	30	47	28.9807
ccdddd:ffffff!!ff	chr2:48066492-48066717(-)$1	225	57	74	17.5384
gggggCCC}CCC}BBBB	chr20:34241900-34242148(-)$1	248	189	206	15.6153
eeeepppppppeeeee2	chr14:55004364-55004595(+)$1	231	62	79	17.9230
GGGGGGG{EEEEE{DDD	chr12:48081630-48081867(-)$1	237	43	60	18.1153
hhhhhh%%%%%%eeeee	chr1:244855154-244855383(+)$1	229	6	23	24.0769
LFFFFFFKKEEEEEIII	chr1:67889849-67890083(-)$1	234	55	72	22.0576
fff!!hhhhhhhh''''	chr10:70497519-70497742(+)$1	223	62	79	22.9230
g:::::::::eeeee[c	chr6:88234207-88234449(-)$1	242	38	55	13.5000
iiiiiBB}JJJJJJJJJ	chr8:125520654-125520876(-)$1	222	100	117	15.1346
JJJJJJJJJJ:======	chr20:47770392-47770648(-)$1	256	185	202	26.6730
oooohhhhhhhhDDDD}	chr1:153789747-153789971(-)$1	224	161	178	14.1730
ndddd22eeeee>>>>>	chr3:142753660-142753916(+)$1	256	161	178	15.9038
:::::::::::::::::	chrX:48382048-48382309(+)$1	261	54	71	20.4230
vvvvvvvvvviiiiiii	chr3:25835528-25835771(+)$1	243	36	53	16.6730
eeevvvvvvvvvvvvve	chr1:27059079-27059305(+)$1	226	64	81	16.1923
xxxddddffffff::::	chr15:70368343-70368576(-)$1	233	160	177	20.6153
ttttdddd]cccfffff	chr18:53070616-53070840(-)$1	224	68	85	15.8076
%%%%eeeee[ccc[ddd	chr8:42212959-42213183(+)$1	224	53	70	15.2307
mmmffffff::::JJJJ	chr2:44203230-44203464(-)$1	234	75	92	18.0192
:::::::::::::::::	chr5:81571776-81572034(-)$1	258	222	239	15.5192
qqqqqbb::::::::::	chr9:19300120-19300341(+)$1	221	41	58	18.5961
::::::HHHHHHHHIII	chr8:67759327-67759549(+)$1	222	77	94	22.1538
EEEEEGGGGGGGFFFFF	chr12:104516941-104517166(-)$1	225	188	205	26.4807
===========:fffff	chr6:53372261-53372487(-)$1	226	52	69	17.6346
eeebb]eeeee:HHHHH	chr15:65868541-65868773(+)$1	232	77	94	15.4230
ee"""iiiiiiiii'''	chr1:118462854-118463090(-)$1	236	23	40	17.2500
[bbpppppppbb]hhhh	chr14:67831404-67831632(+)$1	228	17	34	21.0000
JJJJJJJJJJJJJJJJJ	chr19:12921072-12921303(+)$1	231	208	225	21.6730
'''iiiiiiiii[eeee	chr12:76446926-76447169(-)$1	243	16	33	20.5192
hhhhhhhh[cccggggg	chr2:224831557-224831777(+)$1	220	1	18	13.6923
:::::::::::GGGGGG	chr4:140270590-140270811(+)$1	221	1	18	20.9038
ccc0000000000eeee	chr17:38564649-38564884(-)$1	235	182	199	16.0000
GGGGYYCCC}EEEEEHH	chr1:243858798-243859031(-)$1	233	166	183	15.6153

#DB
..........(((((..	chr8:6582296-6582522(+)$1	1	74	91	24.0769
.((((((..((((((((	chr20:47689079-47689306(+)$1	1	1	18	14.6538
(.(((.(((((.(((((	chr2:70454777-70455003(-)$1	1	5	22	17.0576
.))))......(((((.	chr2:152293243-152293466(+)$1	1	77	94	26.7692
....(((((((..((..	chr1:151955563-151955820(-)$1	1	1	18	18.0192
.....)))..)))))))	chr3:15288171-15288400(+)$1	1	202	219	18.6923
(........))......	chr11:94924594-94924816(-)$1	1	23	40	20.9038
((......)).......	chr12:31633004-31633232(-)$1	1	17	34	25.6153
))....((((......)	chr17:57746034-57746264(+)$1	1	83	100	14.2692
(((((..((((((....	chr6:53156561-53156801(-)$1	1	17	34	17.5384
.(((......((((((.	chr5:133537569-133537812(-)$1	1	12	29	13.8846
.....))))))((((((	chr11:76637513-76637741(+)$1	1	65	82	16.7692
.........((((((..	chr19:35996519-35996767(-)$1	1	74	91	16.3846
..........))))...	chr14:96998623-96998858(+)$1	1	193	210	19.0769
......((((((.((((	chr1:220170536-220170761(-)$1	1	41	58	17.3461
.)))))))))).(((((	chr17:45201156-45201380(-)$1	1	26	43	17.9230
(((.(((........))	chr8:48866086-48866318(-)$1	1	19	36	15.6153
((..((((.........	chr10:120489732-120489978(-)$1	1	36	53	21.6730
.........((((((((	chr1:28233388-28233615(-)$1	1	30	47	28.9807
)))))).((((((..((	chr2:48066492-48066717(-)$1	1	57	74	17.5384
)))))))).))).))))	chr20:34241900-34242148(-)$1	1	189	206	15.6153
((((.......))))).	chr14:55004364-55004595(+)$1	1	62	79	17.9230
(((((((.(((((.(((	chr12:48081630-48081867(-)$1	1	43	60	18.1153
((((((......(((((	chr1:244855154-244855383(+)$1	1	6	23	24.0769
.((((((..((((((((	chr1:67889849-67890083(-)$1	1	55	72	22.0576
(((..((((((((....	chr10:70497519-70497742(+)$1	1	62	79	22.9230
).........(((((.(	chr6:88234207-88234449(-)$1	1	38	55	13.5000
))))))).)))))))))	chr8:125520654-125520876(-)$1	1	100	117	15.1346
)))))))))).((((((	chr20:47770392-47770648(-)$1	1	185	202	26.6730
....)))))))))))).	chr1:153789747-153789971(-)$1	1	161	178	14.1730
.))))..))))).....	chr3:142753660-142753916(+)$1	1	161	178	15.9038
.................	chrX:48382048-48382309(+)$1	1	54	71	20.4230
..........)))))))	chr3:25835528-25835771(+)$1	1	36	53	16.6730
(((.............)	chr1:27059079-27059305(+)$1	1	64	81	16.1923
...))))))))))....	chr15:70368343-70368576(-)$1	1	160	177	20.6153
....)))).))))))))	chr18:53070616-53070840(-)$1	1	68	85	15.8076
....(((((.(((.(((	chr8:42212959-42213183(+)$1	1	53	70	15.2307
...))))))....))))	chr2:44203230-44203464(-)$1	1	75	92	18.0192
.................	chr5:81571776-81572034(-)$1	1	222	239	15.5192
.....))..........	chr9:19300120-19300341(+)$1	1	41	58	18.5961
......(((((((((((	chr8:67759327-67759549(+)$1	1	77	94	22.1538
)))))))))))))))))	chr12:104516941-104517166(-)$1	1	188	205	26.4807
))))))))))).(((((	chr6:53372261-53372487(-)$1	1	52	69	17.6346
))))).))))).(((((	chr15:65868541-65868773(+)$1	1	77	94	15.4230
((...(((((((((...	chr1:118462854-118463090(-)$1	1	23	40	17.2500
.((.......)).))))	chr14:67831404-67831632(+)$1	1	17	34	21.0000
)))))))))))))))))	chr19:12921072-12921303(+)$1	1	208	225	21.6730
...(((((((((.((((	chr12:76446926-76447169(-)$1	1	16	33	20.5192
((((((((.((((((((	chr2:224831557-224831777(+)$1	1	1	18	13.6923
...........((((((	chr4:140270590-140270811(+)$1	1	1	18	20.9038
)))..........))))	chr17:38564649-38564884(-)$1	1	182	199	16.0000
))))..))).)))))))	chr1:243858798-243859031(-)$1	1	166	183	15.6153

#PSSM
A : 0.36	U : 0.32	G : 0.11	C : 0.11	u : 0.05	a : 0.01	
U : 0.69	C : 0.09	A : 0.09	u : 0.07	G : 0.03	
U : 0.65	C : 0.13	A : 0.07	u : 0.07	G : 0.05	
U : 0.78	G : 0.05	u : 0.05	A : 0.03	C : 0.03	a : 0.01	
U : 0.55	A : 0.19	C : 0.13	u : 0.05	G : 0.03	a : 0.01	
U : 0.61	A : 0.15	C : 0.11	u : 0.07	G : 0.03	
U : 0.59	C : 0.15	G : 0.13	u : 0.07	A : 0.03	
U : 0.73	A : 0.07	G : 0.07	u : 0.07	C : 0.03	
U : 0.71	C : 0.09	G : 0.09	u : 0.07	A : 0.01	
U : 0.80	u : 0.07	G : 0.05	C : 0.03	A : 0.01	
U : 0.78	G : 0.05	A : 0.05	u : 0.03	C : 0.03	c : 0.01	
U : 0.76	A : 0.11	u : 0.05	C : 0.03	G : 0.01	
U : 0.71	G : 0.11	A : 0.09	u : 0.05	C : 0.01	
C : 0.61	U : 0.15	A : 0.13	G : 0.03	a : 0.01	u : 0.01	c : 0.01	
U : 0.88	u : 0.03	C : 0.03	a : 0.01	A : 0.01	
U : 0.84	A : 0.07	u : 0.03	C : 0.03	
U : 0.76	A : 0.09	C : 0.05	u : 0.03	G : 0.03	

#score	974.3076923076933
#seq	52
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m1_run2.nuc.txt

#NT
AGGAG	chr16:2813516-2813741(+)$1	225	123	128	15.0000
AGGAG	chr1:28559374-28559611(-)$1	237	30	35	15.0000
AGGAG	chr17:10542906-10543135(-)$1	229	95	100	15.0000
AGGAG	chr19:39329457-39329706(-)$1	249	220	225	15.0000
AGGAG	chr20:35812621-35812861(+)$1	240	191	196	15.0000
AGGAG	chr3:156422509-156422730(+)$1	221	179	184	15.0000
AGGAG	chr16:72821494-72821735(-)$1	241	1	6	15.0000
AGGAG	chr18:55103201-55103440(+)$1	239	12	17	15.0000
AGGAG	chr20:30784233-30784462(-)$1	229	18	23	15.0000
AGGAG	chr12:122242603-122242829(+)$1	226	109	114	15.0000
AGGAG	chr11:111896250-111896470(+)$1	220	22	27	15.0000
AGGAG	chr10:97366535-97366761(-)$1	226	59	64	15.0000
AGGAG	chr1:155938950-155939184(-)$1	234	103	108	15.0000
AGGAG	chr6:32947605-32947854(+)$1	249	58	63	15.0000
AGGAG	chr4:146823354-146823576(-)$1	222	40	45	15.0000
AGGAG	chr17:38278838-38279064(+)$1	226	184	189	15.0000
AGGAG	chr19:56155935-56156159(+)$1	224	207	212	15.0000
AGGAG	chr19:46282962-46283184(-)$1	222	81	86	15.0000
AGGAG	chr19:47280439-47280658(-)$1	219	31	36	15.0000
AGGAG	chr17:47117322-47117554(+)$1	232	13	18	15.0000
AGGAG	chr19:3977432-3977662(-)$1	230	67	72	15.0000
AGGAG	chr4:20619049-20619280(+)$1	231	101	106	15.0000
AGGAG	chr9:139340044-139340270(-)$1	226	167	172	15.0000
AGGAG	chr19:6213045-6213275(-)$1	230	12	17	15.0000
AGGAG	chrX:69385626-69385886(+)$1	260	101	106	15.0000
AGGAG	chr12:6645560-6645789(+)$1	229	56	61	15.0000
AGGAG	chr6:160176305-160176524(+)$1	219	99	104	15.0000
AGGAG	chr1:32694084-32694310(+)$1	226	40	45	15.0000
AGGAG	chr20:62128957-62129201(-)$1	244	92	97	15.0000
AGGAG	chr17:16285490-16285768(+)$1	278	146	151	15.0000
AGGAG	chr1:27087269-27087507(+)$1	238	118	123	15.0000
AGGAG	chr19:14262001-14262223(-)$1	222	135	140	15.0000
aggag	chr10:96162393-96162625(+)$1	232	125	130	15.0000
AGGAG	chr12:124114698-124114919(-)$1	221	138	143	15.0000
AGGAG	chr12:6958180-6958400(-)$1	220	85	90	15.0000
AGGAG	chr3:38647468-38647702(-)$1	234	172	177	15.0000
AGGAG	chr14:105927029-105927251(+)$1	222	175	180	15.0000
AGGAG	chr19:4445946-4446172(-)$1	226	143	148	15.0000
AGGAG	chr17:27400998-27401227(-)$1	229	74	79	15.0000
aggag	chr4:42145469-42145690(-)$1	221	129	134	15.0000
AGGAG	chr2:219515063-219515291(-)$1	228	58	63	15.0000
AGGAG	chr2:169721241-169721460(-)$1	219	191	196	15.0000
AGGAG	chr9:116048965-116049194(+)$1	229	35	40	15.0000
AGGAG	chr1:46032517-46032777(+)$1	260	36	41	15.0000
AGGAG	chr16:68156126-68156346(+)$1	220	176	181	15.0000
AGGAG	chr19:47996591-47996810(-)$1	219	15	20	15.0000
AGGAG	chrX:1409210-1409435(+)$1	225	17	22	15.0000
agGAG	chr22:50886936-50887155(-)$1	219	74	79	15.0000

#otherMatches

#Struct PSSM
$$$cc	chr10:7844199-7844421(+)$1	222	123	128	15.0000
[ccco	chr16:2813516-2813741(+)$1	225	123	128	15.0000
nnncc	chr1:28559374-28559611(-)$1	237	30	35	15.0000
ttttc	chr17:10542906-10543135(-)$1	229	95	100	15.0000
BBYYA	chr19:39329457-39329706(-)$1	249	220	225	15.0000
JJCCC	chr20:35812621-35812861(+)$1	240	191	196	15.0000
ldddd	chr3:156422509-156422730(+)$1	221	179	184	15.0000
ddd[b	chr16:72821494-72821735(-)$1	241	1	6	15.0000
KDDDD	chr18:55103201-55103440(+)$1	239	12	17	15.0000
"dddd	chr20:30784233-30784462(-)$1	229	18	23	15.0000
ccc!!	chr12:122242603-122242829(+)$1	226	109	114	15.0000
FFKKD	chr11:111896250-111896470(+)$1	220	22	27	15.0000
cc333	chr10:97366535-97366761(-)$1	226	59	64	15.0000
2ccc2	chr1:155938950-155939184(-)$1	234	103	108	15.0000
:BB}D	chr6:32947605-32947854(+)$1	249	58	63	15.0000
iii[b	chr4:146823354-146823576(-)$1	222	40	45	15.0000
sbb]f	chr17:38278838-38279064(+)$1	226	184	189	15.0000
FFFFF	chr19:56155935-56156159(+)$1	224	207	212	15.0000
mmmee	chr19:46282962-46283184(-)$1	222	81	86	15.0000
dddd#	chr19:47280439-47280658(-)$1	219	31	36	15.0000
KDDDD	chr17:47117322-47117554(+)$1	232	13	18	15.0000
:EEEE	chr19:3977432-3977662(-)$1	230	67	72	15.0000
:eeee	chr4:20619049-20619280(+)$1	231	101	106	15.0000
2cccd	chr9:139340044-139340270(-)$1	226	167	172	15.0000
EEECC	chr19:6213045-6213275(-)$1	230	12	17	15.0000
]eeee	chrX:69385626-69385886(+)$1	260	101	106	15.0000
cc]ee	chr12:6645560-6645789(+)$1	229	56	61	15.0000
ooooc	chr6:160176305-160176524(+)$1	219	99	104	15.0000
HHHHH	chr1:32694084-32694310(+)$1	226	40	45	15.0000
2bb44	chr20:62128957-62129201(-)$1	244	92	97	15.0000
=====	chr17:16285490-16285768(+)$1	278	146	151	15.0000
DDDDD	chr1:27087269-27087507(+)$1	238	118	123	15.0000
]bb]g	chr19:14262001-14262223(-)$1	222	135	140	15.0000
""ddd	chr10:96162393-96162625(+)$1	232	125	130	15.0000
::FFF	chr12:124114698-124114919(-)$1	221	138	143	15.0000
ee!!a	chr12:6958180-6958400(-)$1	220	85	90	15.0000
!!a[b	chr3:38647468-38647702(-)$1	234	172	177	15.0000
YBB}D	chr14:105927029-105927251(+)$1	222	175	180	15.0000
=::CC	chr19:4445946-4446172(-)$1	226	143	148	15.0000
GGGGG	chr17:27400998-27401227(-)$1	229	74	79	15.0000
EEEYY	chr4:42145469-42145690(-)$1	221	129	134	15.0000
ddd[c	chr2:219515063-219515291(-)$1	228	58	63	15.0000
GGGGG	chr2:169721241-169721460(-)$1	219	191	196	15.0000
eeeee	chr9:116048965-116049194(+)$1	229	35	40	15.0000
!!a[a	chr1:46032517-46032777(+)$1	260	36	41	15.0000
ffff]	chr16:68156126-68156346(+)$1	220	176	181	15.0000
:eeee	chr19:47996591-47996810(-)$1	219	15	20	15.0000
mmmme	chrX:1409210-1409435(+)$1	225	17	22	15.0000
###dd	chr22:50886936-50887155(-)$1	219	74	79	15.0000

#DB
...((	chr10:7844199-7844421(+)$1	1	123	128	15.0000
.(((.	chr16:2813516-2813741(+)$1	1	123	128	15.0000
...))	chr1:28559374-28559611(-)$1	1	30	35	15.0000
....)	chr17:10542906-10543135(-)$1	1	95	100	15.0000
))..)	chr19:39329457-39329706(-)$1	1	220	225	15.0000
)))))	chr20:35812621-35812861(+)$1	1	191	196	15.0000
.))))	chr3:156422509-156422730(+)$1	1	179	184	15.0000
(((.(	chr16:72821494-72821735(-)$1	1	1	6	15.0000
.((((	chr18:55103201-55103440(+)$1	1	12	17	15.0000
.((((	chr20:30784233-30784462(-)$1	1	18	23	15.0000
(((..	chr12:122242603-122242829(+)$1	1	109	114	15.0000
((..(	chr11:111896250-111896470(+)$1	1	22	27	15.0000
))...	chr10:97366535-97366761(-)$1	1	59	64	15.0000
.))).	chr1:155938950-155939184(-)$1	1	103	108	15.0000
.)).)	chr6:32947605-32947854(+)$1	1	58	63	15.0000
(((.(	chr4:146823354-146823576(-)$1	1	40	45	15.0000
.)).)	chr17:38278838-38279064(+)$1	1	184	189	15.0000
)))))	chr19:56155935-56156159(+)$1	1	207	212	15.0000
...))	chr19:46282962-46283184(-)$1	1	81	86	15.0000
((((.	chr19:47280439-47280658(-)$1	1	31	36	15.0000
.((((	chr17:47117322-47117554(+)$1	1	13	18	15.0000
.))))	chr19:3977432-3977662(-)$1	1	67	72	15.0000
.((((	chr4:20619049-20619280(+)$1	1	101	106	15.0000
.))))	chr9:139340044-139340270(-)$1	1	167	172	15.0000
(((((	chr19:6213045-6213275(-)$1	1	12	17	15.0000
.))))	chrX:69385626-69385886(+)$1	1	101	106	15.0000
)).))	chr12:6645560-6645789(+)$1	1	56	61	15.0000
....)	chr6:160176305-160176524(+)$1	1	99	104	15.0000
(((((	chr1:32694084-32694310(+)$1	1	40	45	15.0000
.))..	chr20:62128957-62129201(-)$1	1	92	97	15.0000
)))))	chr17:16285490-16285768(+)$1	1	146	151	15.0000
(((((	chr1:27087269-27087507(+)$1	1	118	123	15.0000
.)).)	chr19:14262001-14262223(-)$1	1	135	140	15.0000
..(((	chr10:96162393-96162625(+)$1	1	125	130	15.0000
..)))	chr12:124114698-124114919(-)$1	1	138	143	15.0000
((..(	chr12:6958180-6958400(-)$1	1	85	90	15.0000
..(.(	chr3:38647468-38647702(-)$1	1	172	177	15.0000
.)).)	chr14:105927029-105927251(+)$1	1	175	180	15.0000
)..))	chr19:4445946-4446172(-)$1	1	143	148	15.0000
(((((	chr17:27400998-27401227(-)$1	1	74	79	15.0000
)))..	chr4:42145469-42145690(-)$1	1	129	134	15.0000
(((.(	chr2:219515063-219515291(-)$1	1	58	63	15.0000
)))))	chr2:169721241-169721460(-)$1	1	191	196	15.0000
(((((	chr9:116048965-116049194(+)$1	1	35	40	15.0000
..(.(	chr1:46032517-46032777(+)$1	1	36	41	15.0000
)))).	chr16:68156126-68156346(+)$1	1	176	181	15.0000
.((((	chr19:47996591-47996810(-)$1	1	15	20	15.0000
....)	chrX:1409210-1409435(+)$1	1	17	22	15.0000
...((	chr22:50886936-50887155(-)$1	1	74	79	15.0000

#PSSM
A : 0.93	a : 0.06	
G : 0.93	g : 0.06	
G : 0.95	g : 0.04	
A : 0.95	a : 0.04	
G : 0.95	g : 0.04	

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_UTR_m1_run1.nuc.txt

#NT
AAUUU	chr5:78622627-78622845(+)$1	218	78	83	14.9999
AAUUU	chr8:81435691-81435910(+)$1	219	5	10	14.9999
AAUUU	chr13:30781280-30781497(-)$1	217	166	171	14.9999
AAUUU	chr17:47366678-47366903(-)$1	225	141	146	14.9999
AAUUU	chr1:16200041-16200265(+)$1	224	188	193	14.9999
AAUUU	chr19:21907905-21908129(-)$1	224	8	13	14.9999
AAUUU	chr3:120049024-120049243(-)$1	219	141	146	14.9999
AAUUU	chr12:46580483-46580705(-)$1	222	45	50	14.9999
AAUUU	chr1:180083377-180083596(+)$1	219	9	14	14.9999
AAUUU	chr5:114949477-114949697(-)$1	220	110	115	14.9999
AAUUU	chr19:37035704-37035925(-)$1	221	102	107	14.9999
AAUUU	chr10:63853867-63854090(+)$1	223	46	51	14.9999
AAUUU	chr3:101487155-101487374(+)$1	219	166	171	14.9999
AAUUU	chr1:198290345-198290569(+)$1	224	38	43	14.9999
AAUUU	chr21:43409709-43409926(-)$1	217	49	54	14.9999
AAUUU	chr1:229458454-229458676(-)$1	222	93	98	14.9999
AAUUU	chr21:18941338-18941557(+)$1	219	5	10	14.9999
AAUUU	chr22:29184548-29184768(+)$1	220	103	108	14.9999
AAUUU	chr12:98928295-98928518(+)$1	223	34	39	14.9999
AAUUU	chr17:15619687-15619907(+)$1	220	203	208	14.9999
AAUUU	chr3:170112275-170112498(+)$1	223	24	29	14.9999
AAUUU	chr1:59124962-59125182(-)$1	220	167	172	14.9999
AAUUU	chr5:167977378-167977602(-)$1	224	114	119	14.9999
AAUUU	chr11:18630776-18630994(-)$1	218	100	105	14.9999
AAUUU	chr4:124240139-124240358(+)$1	219	38	43	14.9999
AAUUU	chrX:24003826-24004046(-)$1	220	36	41	14.9999
AAUUU	chr8:87572882-87573098(+)$1	216	67	72	14.9999
AAUUU	chr1:202910072-202910289(-)$1	217	166	171	14.9999
AAUUU	chrX:24005774-24005993(-)$1	219	80	85	14.9999
AAUUU	chr21:30715060-30715291(+)$1	231	122	127	14.9999
AAUUU	chr9:125610672-125610893(-)$1	221	131	136	14.9999
AAUUU	chr16:75478774-75478997(-)$1	223	101	106	14.9999
AAUUU	chr21:16334413-16334632(-)$1	219	10	15	14.9999
AAUUU	chr4:39782071-39782297(+)$1	226	203	208	14.9999
AAUUU	chr21:18941546-18941764(+)$1	218	102	107	14.9999
AAUUU	chr1:229458632-229458856(-)$1	224	72	77	14.9999
AAUUU	chr2:42558031-42558248(+)$1	217	185	190	14.9999
AAUUU	chr5:173385853-173386073(+)$1	220	163	168	14.9999
AAUUU	chr6:114257167-114257388(-)$1	221	112	117	14.9999
AAUUU	chr10:5759525-5759745(+)$1	220	169	174	14.9999
AAUUU	chr14:55515554-55515776(+)$1	222	171	176	14.9999
AAUUU	chr3:148748683-148748904(-)$1	221	38	43	14.9999
AAUUU	chr7:135612513-135612732(-)$1	219	23	28	14.9999
AAUUU	chr3:107526603-107526825(+)$1	222	133	138	14.9999
AAUUU	chr13:53049472-53049691(+)$1	219	40	45	14.9999
AAUUU	chr10:120927582-120927800(-)$1	218	56	61	14.9999
AAUUU	chr1:227845547-227845764(+)$1	217	23	28	14.9999
AAUUU	chr5:167978204-167978426(-)$1	222	33	38	14.9999
AAUUU	chrX:133559964-133560182(+)$1	218	101	106	14.9999
AAUUU	chr10:98983222-98983444(-)$1	222	155	160	14.9999
AAUUU	chr13:50107227-50107448(-)$1	221	170	175	14.9999
AAUUU	chr6:24650858-24651079(-)$1	221	107	112	14.9999
AAUUU	chr16:87440252-87440477(-)$1	225	65	70	14.9999
AAUUU	chr12:68054266-68054484(+)$1	218	41	46	14.9999
AAUUU	chr19:44741296-44741519(+)$1	223	36	41	14.9999
AAUUU	chr5:151189450-151189671(+)$1	221	100	105	14.9999
AAUUU	chr12:54628659-54628878(-)$1	219	187	192	14.9999
AAUUU	chr12:101019712-101019932(+)$1	220	135	140	14.9999
AAUUU	chr1:162499057-162499275(+)$1	218	78	83	14.9999
AAUUU	chr1:227845220-227845442(+)$1	222	141	146	14.9999
aauuu	chr1:9989976-9990199(-)$1	223	170	175	14.9999
AAUUU	chr16:19563056-19563279(+)$1	223	217	222	14.9999
AAUUU	chr3:9483728-9483949(+)$1	221	63	68	14.9999
AAUUU	chr15:35152143-35152363(-)$1	220	165	170	14.9999
AAUUU	chr11:13751663-13751884(+)$1	221	123	128	14.9999
AAUUU	chr6:109689880-109690099(-)$1	219	156	161	14.9999
AAUUU	chr7:141358904-141359129(-)$1	225	188	193	14.9999
AAUUU	chrX:24005203-24005427(-)$1	224	84	89	14.9999
AAUUU	chr10:119766478-119766700(-)$1	222	187	192	14.9999

#otherMatches

#Struct PSSM
LLLII	chr6:127610590-127610811(-)$1	221	139	144	14.9999
22===	chr5:78622627-78622845(+)$1	218	78	83	14.9999
JJJJJ	chr8:81435691-81435910(+)$1	219	5	10	14.9999
cnnnn	chr13:30781280-30781497(-)$1	217	166	171	14.9999
88888	chr17:47366678-47366903(-)$1	225	141	146	14.9999
]ffff	chr1:16200041-16200265(+)$1	224	188	193	14.9999
:::::	chr19:21907905-21908129(-)$1	224	8	13	14.9999
iiiii	chr3:120049024-120049243(-)$1	219	141	146	14.9999
fff[e	chr12:46580483-46580705(-)$1	222	45	50	14.9999
EEEE{	chr1:180083377-180083596(+)$1	219	9	14	14.9999
:::::	chr5:114949477-114949697(-)$1	220	110	115	14.9999
fffrr	chr19:37035704-37035925(-)$1	221	102	107	14.9999
::ggg	chr10:63853867-63854090(+)$1	223	46	51	14.9999
eeeeg	chr3:101487155-101487374(+)$1	219	166	171	14.9999
JJJJJ	chr1:198290345-198290569(+)$1	224	38	43	14.9999
ee[dd	chr21:43409709-43409926(-)$1	217	49	54	14.9999
::hhh	chr1:229458454-229458676(-)$1	222	93	98	14.9999
DD{FF	chr21:18941338-18941557(+)$1	219	5	10	14.9999
JJJJJ	chr22:29184548-29184768(+)$1	220	103	108	14.9999
=====	chr12:98928295-98928518(+)$1	223	34	39	14.9999
ee:::	chr17:15619687-15619907(+)$1	220	203	208	14.9999
:::::	chr3:170112275-170112498(+)$1	223	24	29	14.9999
:::::	chr1:59124962-59125182(-)$1	220	167	172	14.9999
qqqqq	chr5:167977378-167977602(-)$1	224	114	119	14.9999
oofff	chr11:18630776-18630994(-)$1	218	100	105	14.9999
:::::	chr4:124240139-124240358(+)$1	219	38	43	14.9999
UUUUU	chrX:24003826-24004046(-)$1	220	36	41	14.9999
>>>>>	chr8:87572882-87573098(+)$1	216	67	72	14.9999
:::::	chr1:202910072-202910289(-)$1	217	166	171	14.9999
dddd2	chrX:24005774-24005993(-)$1	219	80	85	14.9999
^^^^^	chr21:30715060-30715291(+)$1	231	122	127	14.9999
hh555	chr9:125610672-125610893(-)$1	221	131	136	14.9999
:::::	chr16:75478774-75478997(-)$1	223	101	106	14.9999
::::g	chr21:16334413-16334632(-)$1	219	10	15	14.9999
JJJJ}	chr4:39782071-39782297(+)$1	226	203	208	14.9999
gCCCK	chr21:18941546-18941764(+)$1	218	102	107	14.9999
lllbb	chr1:229458632-229458856(-)$1	224	72	77	14.9999
ooooo	chr2:42558031-42558248(+)$1	217	185	190	14.9999
:::::	chr5:173385853-173386073(+)$1	220	163	168	14.9999
:::CC	chr6:114257167-114257388(-)$1	221	112	117	14.9999
ppppp	chr10:5759525-5759745(+)$1	220	169	174	14.9999
ooocc	chr14:55515554-55515776(+)$1	222	171	176	14.9999
::::E	chr3:148748683-148748904(-)$1	221	38	43	14.9999
cclll	chr7:135612513-135612732(-)$1	219	23	28	14.9999
fflll	chr3:107526603-107526825(+)$1	222	133	138	14.9999
:::::	chr13:53049472-53049691(+)$1	219	40	45	14.9999
777ee	chr10:120927582-120927800(-)$1	218	56	61	14.9999
b[eee	chr1:227845547-227845764(+)$1	217	23	28	14.9999
HHHHH	chr5:167978204-167978426(-)$1	222	33	38	14.9999
444hh	chrX:133559964-133560182(+)$1	218	101	106	14.9999
!!eee	chr10:98983222-98983444(-)$1	222	155	160	14.9999
dd]gg	chr13:50107227-50107448(-)$1	221	170	175	14.9999
fffee	chr6:24650858-24651079(-)$1	221	107	112	14.9999
d"""f	chr16:87440252-87440477(-)$1	225	65	70	14.9999
DKKJJ	chr12:68054266-68054484(+)$1	218	41	46	14.9999
JJJJJ	chr19:44741296-44741519(+)$1	223	36	41	14.9999
:::::	chr5:151189450-151189671(+)$1	221	100	105	14.9999
:::::	chr12:54628659-54628878(-)$1	219	187	192	14.9999
:::::	chr12:101019712-101019932(+)$1	220	135	140	14.9999
dd"""	chr1:162499057-162499275(+)$1	218	78	83	14.9999
gggg3	chr1:227845220-227845442(+)$1	222	141	146	14.9999
ffffm	chr1:9989976-9990199(-)$1	223	170	175	14.9999
fff::	chr16:19563056-19563279(+)$1	223	217	222	14.9999
ddd88	chr3:9483728-9483949(+)$1	221	63	68	14.9999
rrrrr	chr15:35152143-35152363(-)$1	220	165	170	14.9999
:::::	chr11:13751663-13751884(+)$1	221	123	128	14.9999
ZZZCC	chr6:109689880-109690099(-)$1	219	156	161	14.9999
GGGGG	chr7:141358904-141359129(-)$1	225	188	193	14.9999
ffff:	chrX:24005203-24005427(-)$1	224	84	89	14.9999
:::::	chr10:119766478-119766700(-)$1	222	187	192	14.9999

#DB
...((	chr6:127610590-127610811(-)$1	1	139	144	14.9999
..)))	chr5:78622627-78622845(+)$1	1	78	83	14.9999
(((((	chr8:81435691-81435910(+)$1	1	5	10	14.9999
(....	chr13:30781280-30781497(-)$1	1	166	171	14.9999
.....	chr17:47366678-47366903(-)$1	1	141	146	14.9999
.))))	chr1:16200041-16200265(+)$1	1	188	193	14.9999
.....	chr19:21907905-21908129(-)$1	1	8	13	14.9999
(((((	chr3:120049024-120049243(-)$1	1	141	146	14.9999
(((.(	chr12:46580483-46580705(-)$1	1	45	50	14.9999
((((.	chr1:180083377-180083596(+)$1	1	9	14	14.9999
.....	chr5:114949477-114949697(-)$1	1	110	115	14.9999
(((..	chr19:37035704-37035925(-)$1	1	102	107	14.9999
..(((	chr10:63853867-63854090(+)$1	1	46	51	14.9999
)))))	chr3:101487155-101487374(+)$1	1	166	171	14.9999
(((((	chr1:198290345-198290569(+)$1	1	38	43	14.9999
((.((	chr21:43409709-43409926(-)$1	1	49	54	14.9999
..(((	chr1:229458454-229458676(-)$1	1	93	98	14.9999
((.((	chr21:18941338-18941557(+)$1	1	5	10	14.9999
(((((	chr22:29184548-29184768(+)$1	1	103	108	14.9999
(((((	chr12:98928295-98928518(+)$1	1	34	39	14.9999
))...	chr17:15619687-15619907(+)$1	1	203	208	14.9999
.....	chr3:170112275-170112498(+)$1	1	24	29	14.9999
.....	chr1:59124962-59125182(-)$1	1	167	172	14.9999
.....	chr5:167977378-167977602(-)$1	1	114	119	14.9999
..)))	chr11:18630776-18630994(-)$1	1	100	105	14.9999
.....	chr4:124240139-124240358(+)$1	1	38	43	14.9999
.....	chrX:24003826-24004046(-)$1	1	36	41	14.9999
.....	chr8:87572882-87573098(+)$1	1	67	72	14.9999
.....	chr1:202910072-202910289(-)$1	1	166	171	14.9999
)))).	chrX:24005774-24005993(-)$1	1	80	85	14.9999
.....	chr21:30715060-30715291(+)$1	1	122	127	14.9999
))...	chr9:125610672-125610893(-)$1	1	131	136	14.9999
.....	chr16:75478774-75478997(-)$1	1	101	106	14.9999
....(	chr21:16334413-16334632(-)$1	1	10	15	14.9999
)))).	chr4:39782071-39782297(+)$1	1	203	208	14.9999
)(((.	chr21:18941546-18941764(+)$1	1	102	107	14.9999
...))	chr1:229458632-229458856(-)$1	1	72	77	14.9999
.....	chr2:42558031-42558248(+)$1	1	185	190	14.9999
.....	chr5:173385853-173386073(+)$1	1	163	168	14.9999
...))	chr6:114257167-114257388(-)$1	1	112	117	14.9999
.....	chr10:5759525-5759745(+)$1	1	169	174	14.9999
...))	chr14:55515554-55515776(+)$1	1	171	176	14.9999
....(	chr3:148748683-148748904(-)$1	1	38	43	14.9999
((...	chr7:135612513-135612732(-)$1	1	23	28	14.9999
((...	chr3:107526603-107526825(+)$1	1	133	138	14.9999
.....	chr13:53049472-53049691(+)$1	1	40	45	14.9999
...))	chr10:120927582-120927800(-)$1	1	56	61	14.9999
(.(((	chr1:227845547-227845764(+)$1	1	23	28	14.9999
(((((	chr5:167978204-167978426(-)$1	1	33	38	14.9999
...))	chrX:133559964-133560182(+)$1	1	101	106	14.9999
..(((	chr10:98983222-98983444(-)$1	1	155	160	14.9999
)).))	chr13:50107227-50107448(-)$1	1	170	175	14.9999
)))((	chr6:24650858-24651079(-)$1	1	107	112	14.9999
(...(	chr16:87440252-87440477(-)$1	1	65	70	14.9999
(..((	chr12:68054266-68054484(+)$1	1	41	46	14.9999
(((((	chr19:44741296-44741519(+)$1	1	36	41	14.9999
.....	chr5:151189450-151189671(+)$1	1	100	105	14.9999
.....	chr12:54628659-54628878(-)$1	1	187	192	14.9999
.....	chr12:101019712-101019932(+)$1	1	135	140	14.9999
((...	chr1:162499057-162499275(+)$1	1	78	83	14.9999
)))).	chr1:227845220-227845442(+)$1	1	141	146	14.9999
((((.	chr1:9989976-9990199(-)$1	1	170	175	14.9999
)))..	chr16:19563056-19563279(+)$1	1	217	222	14.9999
)))..	chr3:9483728-9483949(+)$1	1	63	68	14.9999
.....	chr15:35152143-35152363(-)$1	1	165	170	14.9999
.....	chr11:13751663-13751884(+)$1	1	123	128	14.9999
...))	chr6:109689880-109690099(-)$1	1	156	161	14.9999
)))))	chr7:141358904-141359129(-)$1	1	188	193	14.9999
)))).	chrX:24005203-24005427(-)$1	1	84	89	14.9999
.....	chr10:119766478-119766700(-)$1	1	187	192	14.9999

#PSSM
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	

#score	1049.9999999999995
#seq	70
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_CDS_m2_run1.nuc.txt

#NT
CAC	chr1:173952592-173952793(-)$1	201	14	17	9.0000
CAC	chr17:7365444-7365645(-)$1	201	89	92	9.0000
CAC	chr6:44107979-44108180(+)$1	201	28	31	9.0000
CAC	chr14:51273396-51273597(-)$1	201	127	130	9.0000
CAC	chr10:123279537-123279738(-)$1	201	25	28	9.0000
CAC	chr2:86268980-86269181(-)$1	201	190	193	9.0000
CAC	chr10:127519074-127519275(+)$1	201	154	157	9.0000
CAC	chr9:88207395-88207596(-)$1	201	60	63	9.0000
CAC	chr1:206776274-206776475(-)$1	201	13	16	9.0000
CAC	chr1:1452462-1452663(+)$1	201	111	114	9.0000
cac	chr3:170098943-170099144(+)$1	201	25	28	9.0000
CAC	chr21:46945719-46945920(-)$1	201	105	108	9.0000
CAC	chr11:608857-609058(+)$1	201	1	4	9.0000
CAC	chr19:44739351-44739552(+)$1	201	76	79	9.0000
CAC	chr5:61778910-61779111(+)$1	201	72	75	9.0000
CAC	chr9:88233901-88234102(-)$1	201	7	10	9.0000
CAC	chr8:124369780-124369981(-)$1	201	25	28	9.0000
CAC	chr6:111621183-111621384(-)$1	201	58	61	9.0000
cac	chr2:27455852-27456053(+)$1	201	5	8	9.0000
CAC	chr5:178310074-178310275(+)$1	201	51	54	9.0000
CAC	chr19:45176023-45176224(+)$1	201	10	13	9.0000
CAC	chr15:41276427-41276628(-)$1	201	44	47	9.0000
CAC	chr20:35812586-35812787(+)$1	201	3	6	9.0000
CAC	chr1:16257944-16258145(+)$1	201	63	66	9.0000
CAC	chrX:71787745-71787946(-)$1	201	30	33	9.0000
CAC	chr9:88628596-88628797(+)$1	201	9	12	9.0000
CAC	chr11:34093219-34093420(+)$1	201	153	156	9.0000
CAC	chr1:84961605-84961806(+)$1	201	17	20	9.0000
CAC	chr12:416849-417050(-)$1	201	183	186	9.0000
CAC	chr2:197641229-197641430(-)$1	201	146	149	9.0000
CAC	chr6:34256594-34256795(-)$1	201	82	85	9.0000
CAC	chr10:75597155-75597356(-)$1	201	1	4	9.0000
CAC	chr7:1510736-1510937(-)$1	201	48	51	9.0000
CAC	chr17:7474626-7474827(+)$1	201	13	16	9.0000
CAC	chr1:54417954-54418155(+)$1	201	24	27	9.0000
CAC	chr5:159834711-159834912(-)$1	201	125	128	9.0000
CAC	chr2:100019450-100019651(-)$1	201	160	163	9.0000
CAC	chr19:39913798-39913999(+)$1	201	16	19	9.0000
CAC	chr13:111562977-111563178(-)$1	201	96	99	9.0000
CAC	chr12:104496865-104497066(+)$1	201	58	61	9.0000
CAC	chr5:7899950-7900151(+)$1	201	175	178	9.0000
cac	chr19:45495417-45495618(+)$1	201	18	21	9.0000
CAC	chr4:68374539-68374740(-)$1	201	34	37	9.0000
CAC	chr22:39066822-39067023(+)$1	201	45	48	9.0000
CAC	chr12:49442801-49443002(-)$1	201	161	164	9.0000
CAC	chr12:51399092-51399293(-)$1	201	109	112	9.0000
CAC	chr1:197112626-197112827(-)$1	201	17	20	9.0000
CAC	chr1:179961143-179961344(+)$1	201	31	34	9.0000
CAC	chr6:43538564-43538765(-)$1	201	119	122	9.0000
CAC	chr10:70946117-70946318(+)$1	201	48	51	9.0000
CAC	chr14:64484336-64484537(+)$1	201	174	177	9.0000
CAC	chr10:70958149-70958350(+)$1	201	24	27	9.0000
CAC	chr1:54690754-54690955(+)$1	201	14	17	9.0000
CAC	chr19:40841947-40842148(-)$1	201	123	126	9.0000
CAC	chr6:53156614-53156815(-)$1	201	97	100	9.0000
CAC	chr1:186324514-186324715(-)$1	201	128	131	9.0000
CAC	chr17:36523666-36523867(+)$1	201	36	39	9.0000
CAC	chr4:123270514-123270715(+)$1	201	125	128	9.0000
CAC	chr12:48468172-48468373(-)$1	201	24	27	9.0000
CAC	chr13:42768945-42769146(+)$1	201	84	87	9.0000
CAC	chr18:685870-686071(-)$1	201	164	167	9.0000
CAC	chr12:109687703-109687904(+)$1	201	29	32	9.0000
CAC	chr9:79910437-79910638(+)$1	201	114	117	9.0000
CAC	chr17:28772882-28773083(+)$1	201	134	137	9.0000
cac	chr19:5654016-5654217(+)$1	201	21	24	9.0000
CAC	chr5:37305080-37305281(-)$1	201	157	160	9.0000
CAC	chr17:65908429-65908630(+)$1	201	108	111	9.0000
CAC	chr14:69925019-69925220(+)$1	201	55	58	9.0000
CAC	chr12:120534951-120535152(-)$1	201	67	70	9.0000
CAC	chr10:96109833-96110034(-)$1	201	91	94	9.0000
CAC	chr1:52847241-52847442(-)$1	201	135	138	9.0000
CAC	chr2:29135406-29135607(+)$1	201	39	42	9.0000
CAC	chr17:1380728-1380929(-)$1	201	27	30	9.0000
CAC	chr7:98567767-98567968(+)$1	201	5	8	9.0000
CAC	chr17:26900669-26900870(-)$1	201	47	50	9.0000
CAC	chr2:32706353-32706554(+)$1	201	3	6	9.0000
CAC	chr1:19439096-19439297(-)$1	201	25	28	9.0000
cac	chr19:17387099-17387300(+)$1	201	0	3	9.0000
CAC	chr15:64506011-64506212(-)$1	201	48	51	9.0000
CAC	chr1:151150452-151150653(-)$1	201	105	108	9.0000
CAC	chr20:61906833-61907034(+)$1	201	175	178	9.0000
CAC	chr2:160303271-160303472(-)$1	201	38	41	9.0000
CAC	chr11:47317011-47317212(+)$1	201	2	5	9.0000
CAC	chr2:33810639-33810840(-)$1	201	59	62	9.0000
CAC	chr1:150443798-150443999(+)$1	201	75	78	9.0000
CAC	chr16:1498922-1499123(-)$1	201	47	50	9.0000
CAC	chr20:47688744-47688945(+)$1	201	136	139	9.0000
CAC	chr9:35389792-35389993(+)$1	201	29	32	9.0000
CAC	chr12:120582089-120582290(-)$1	201	20	23	9.0000
CAC	chr6:79713446-79713647(-)$1	201	140	143	9.0000
CAC	chr17:73008729-73008930(+)$1	201	60	63	9.0000
CAC	chr6:110064256-110064457(+)$1	201	41	44	9.0000
CAC	chr17:71199115-71199316(+)$1	201	40	43	9.0000
CAC	chr1:240371881-240372082(+)$1	201	0	3	9.0000
CAC	chr15:44903035-44903236(-)$1	201	33	36	9.0000
CAC	chr15:101152435-101152636(+)$1	201	67	70	9.0000
CAC	chr22:46724520-46724721(+)$1	201	0	3	9.0000

#otherMatches

#Struct PSSM
fff	chr17:7470210-7470411(+)$1	201	28	31	9.0000
ccc	chr1:173952592-173952793(-)$1	201	14	17	9.0000
^^^	chr17:7365444-7365645(-)$1	201	89	92	9.0000
{CC	chr6:44107979-44108180(+)$1	201	28	31	9.0000
d]b	chr14:51273396-51273597(-)$1	201	127	130	9.0000
::G	chr10:123279537-123279738(-)$1	201	25	28	9.0000
ddd	chr2:86268980-86269181(-)$1	201	190	193	9.0000
b]e	chr10:127519074-127519275(+)$1	201	154	157	9.0000
KKC	chr9:88207395-88207596(-)$1	201	60	63	9.0000
c[d	chr1:206776274-206776475(-)$1	201	13	16	9.0000
:::	chr1:1452462-1452663(+)$1	201	111	114	9.0000
rrr	chr3:170098943-170099144(+)$1	201	25	28	9.0000
cc]	chr21:46945719-46945920(-)$1	201	105	108	9.0000
bmm	chr11:608857-609058(+)$1	201	1	4	9.0000
DDD	chr19:44739351-44739552(+)$1	201	76	79	9.0000
ggg	chr5:61778910-61779111(+)$1	201	72	75	9.0000
{BB	chr9:88233901-88234102(-)$1	201	7	10	9.0000
C::	chr8:124369780-124369981(-)$1	201	25	28	9.0000
ggg	chr6:111621183-111621384(-)$1	201	58	61	9.0000
::D	chr2:27455852-27456053(+)$1	201	5	8	9.0000
fff	chr5:178310074-178310275(+)$1	201	51	54	9.0000
]cc	chr19:45176023-45176224(+)$1	201	10	13	9.0000
fff	chr15:41276427-41276628(-)$1	201	44	47	9.0000
DDK	chr20:35812586-35812787(+)$1	201	3	6	9.0000
qcc	chr1:16257944-16258145(+)$1	201	63	66	9.0000
JJJ	chrX:71787745-71787946(-)$1	201	30	33	9.0000
:::	chr9:88628596-88628797(+)$1	201	9	12	9.0000
b::	chr11:34093219-34093420(+)$1	201	153	156	9.0000
uuu	chr1:84961605-84961806(+)$1	201	17	20	9.0000
c]b	chr12:416849-417050(-)$1	201	183	186	9.0000
ccp	chr2:197641229-197641430(-)$1	201	146	149	9.0000
bll	chr6:34256594-34256795(-)$1	201	82	85	9.0000
BMM	chr10:75597155-75597356(-)$1	201	1	4	9.0000
d::	chr7:1510736-1510937(-)$1	201	48	51	9.0000
ddd	chr17:7474626-7474827(+)$1	201	13	16	9.0000
ggg	chr1:54417954-54418155(+)$1	201	24	27	9.0000
hh]	chr5:159834711-159834912(-)$1	201	125	128	9.0000
mmd	chr2:100019450-100019651(-)$1	201	160	163	9.0000
::h	chr19:39913798-39913999(+)$1	201	16	19	9.0000
nnn	chr13:111562977-111563178(-)$1	201	96	99	9.0000
cc7	chr12:104496865-104497066(+)$1	201	58	61	9.0000
FFE	chr5:7899950-7900151(+)$1	201	175	178	9.0000
D{E	chr19:45495417-45495618(+)$1	201	18	21	9.0000
d>>	chr4:68374539-68374740(-)$1	201	34	37	9.0000
lll	chr22:39066822-39067023(+)$1	201	45	48	9.0000
HYY	chr12:49442801-49443002(-)$1	201	161	164	9.0000
ddb	chr12:51399092-51399293(-)$1	201	109	112	9.0000
RRR	chr1:197112626-197112827(-)$1	201	17	20	9.0000
CCC	chr1:179961143-179961344(+)$1	201	31	34	9.0000
cc"	chr6:43538564-43538765(-)$1	201	119	122	9.0000
www	chr10:70946117-70946318(+)$1	201	48	51	9.0000
BBC	chr14:64484336-64484537(+)$1	201	174	177	9.0000
ddd	chr10:70958149-70958350(+)$1	201	24	27	9.0000
C{A	chr1:54690754-54690955(+)$1	201	14	17	9.0000
eee	chr19:40841947-40842148(-)$1	201	123	126	9.0000
DDD	chr6:53156614-53156815(-)$1	201	97	100	9.0000
:::	chr1:186324514-186324715(-)$1	201	128	131	9.0000
666	chr17:36523666-36523867(+)$1	201	36	39	9.0000
:::	chr4:123270514-123270715(+)$1	201	125	128	9.0000
nnn	chr12:48468172-48468373(-)$1	201	24	27	9.0000
[bb	chr13:42768945-42769146(+)$1	201	84	87	9.0000
:::	chr18:685870-686071(-)$1	201	164	167	9.0000
:::	chr12:109687703-109687904(+)$1	201	29	32	9.0000
qqq	chr9:79910437-79910638(+)$1	201	114	117	9.0000
ttt	chr17:28772882-28773083(+)$1	201	134	137	9.0000
c66	chr19:5654016-5654217(+)$1	201	21	24	9.0000
]ee	chr5:37305080-37305281(-)$1	201	157	160	9.0000
qqe	chr17:65908429-65908630(+)$1	201	108	111	9.0000
sss	chr14:69925019-69925220(+)$1	201	55	58	9.0000
ddd	chr12:120534951-120535152(-)$1	201	67	70	9.0000
ecc	chr10:96109833-96110034(-)$1	201	91	94	9.0000
5hh	chr1:52847241-52847442(-)$1	201	135	138	9.0000
OOO	chr2:29135406-29135607(+)$1	201	39	42	9.0000
C{B	chr17:1380728-1380929(-)$1	201	27	30	9.0000
ffn	chr7:98567767-98567968(+)$1	201	5	8	9.0000
ccc	chr17:26900669-26900870(-)$1	201	47	50	9.0000
DOO	chr2:32706353-32706554(+)$1	201	3	6	9.0000
)))	chr1:19439096-19439297(-)$1	201	25	28	9.0000
:::	chr19:17387099-17387300(+)$1	201	0	3	9.0000
:::	chr15:64506011-64506212(-)$1	201	48	51	9.0000
b[d	chr1:151150452-151150653(-)$1	201	105	108	9.0000
CCC	chr20:61906833-61907034(+)$1	201	175	178	9.0000
e""	chr2:160303271-160303472(-)$1	201	38	41	9.0000
::E	chr11:47317011-47317212(+)$1	201	2	5	9.0000
:::	chr2:33810639-33810840(-)$1	201	59	62	9.0000
gg:	chr1:150443798-150443999(+)$1	201	75	78	9.0000
22b	chr16:1498922-1499123(-)$1	201	47	50	9.0000
:EE	chr20:47688744-47688945(+)$1	201	136	139	9.0000
:::	chr9:35389792-35389993(+)$1	201	29	32	9.0000
eee	chr12:120582089-120582290(-)$1	201	20	23	9.0000
bb3	chr6:79713446-79713647(-)$1	201	140	143	9.0000
d[d	chr17:73008729-73008930(+)$1	201	60	63	9.0000
fff	chr6:110064256-110064457(+)$1	201	41	44	9.0000
&&&	chr17:71199115-71199316(+)$1	201	40	43	9.0000
:::	chr1:240371881-240372082(+)$1	201	0	3	9.0000
]dd	chr15:44903035-44903236(-)$1	201	33	36	9.0000
'''	chr15:101152435-101152636(+)$1	201	67	70	9.0000
:::	chr22:46724520-46724721(+)$1	201	0	3	9.0000

#DB
)))	chr17:7470210-7470411(+)$1	1	28	31	9.0000
)))	chr1:173952592-173952793(-)$1	1	14	17	9.0000
...	chr17:7365444-7365645(-)$1	1	89	92	9.0000
.((	chr6:44107979-44108180(+)$1	1	28	31	9.0000
).)	chr14:51273396-51273597(-)$1	1	127	130	9.0000
..(	chr10:123279537-123279738(-)$1	1	25	28	9.0000
(((	chr2:86268980-86269181(-)$1	1	190	193	9.0000
).)	chr10:127519074-127519275(+)$1	1	154	157	9.0000
..(	chr9:88207395-88207596(-)$1	1	60	63	9.0000
(.(	chr1:206776274-206776475(-)$1	1	13	16	9.0000
...	chr1:1452462-1452663(+)$1	1	111	114	9.0000
...	chr3:170098943-170099144(+)$1	1	25	28	9.0000
)).	chr21:46945719-46945920(-)$1	1	105	108	9.0000
(..	chr11:608857-609058(+)$1	1	1	4	9.0000
(((	chr19:44739351-44739552(+)$1	1	76	79	9.0000
(((	chr5:61778910-61779111(+)$1	1	72	75	9.0000
.((	chr9:88233901-88234102(-)$1	1	7	10	9.0000
(..	chr8:124369780-124369981(-)$1	1	25	28	9.0000
(((	chr6:111621183-111621384(-)$1	1	58	61	9.0000
..(	chr2:27455852-27456053(+)$1	1	5	8	9.0000
)))	chr5:178310074-178310275(+)$1	1	51	54	9.0000
.))	chr19:45176023-45176224(+)$1	1	10	13	9.0000
(((	chr15:41276427-41276628(-)$1	1	44	47	9.0000
((.	chr20:35812586-35812787(+)$1	1	3	6	9.0000
.))	chr1:16257944-16258145(+)$1	1	63	66	9.0000
(((	chrX:71787745-71787946(-)$1	1	30	33	9.0000
...	chr9:88628596-88628797(+)$1	1	9	12	9.0000
)..	chr11:34093219-34093420(+)$1	1	153	156	9.0000
...	chr1:84961605-84961806(+)$1	1	17	20	9.0000
).)	chr12:416849-417050(-)$1	1	183	186	9.0000
((.	chr2:197641229-197641430(-)$1	1	146	149	9.0000
(..	chr6:34256594-34256795(-)$1	1	82	85	9.0000
(..	chr10:75597155-75597356(-)$1	1	1	4	9.0000
)..	chr7:1510736-1510937(-)$1	1	48	51	9.0000
)))	chr17:7474626-7474827(+)$1	1	13	16	9.0000
)))	chr1:54417954-54418155(+)$1	1	24	27	9.0000
)).	chr5:159834711-159834912(-)$1	1	125	128	9.0000
..)	chr2:100019450-100019651(-)$1	1	160	163	9.0000
..(	chr19:39913798-39913999(+)$1	1	16	19	9.0000
...	chr13:111562977-111563178(-)$1	1	96	99	9.0000
)).	chr12:104496865-104497066(+)$1	1	58	61	9.0000
)))	chr5:7899950-7900151(+)$1	1	175	178	9.0000
(.(	chr19:45495417-45495618(+)$1	1	18	21	9.0000
)..	chr4:68374539-68374740(-)$1	1	34	37	9.0000
...	chr22:39066822-39067023(+)$1	1	45	48	9.0000
)..	chr12:49442801-49443002(-)$1	1	161	164	9.0000
(((	chr12:51399092-51399293(-)$1	1	109	112	9.0000
...	chr1:197112626-197112827(-)$1	1	17	20	9.0000
(((	chr1:179961143-179961344(+)$1	1	31	34	9.0000
((.	chr6:43538564-43538765(-)$1	1	119	122	9.0000
...	chr10:70946117-70946318(+)$1	1	48	51	9.0000
)))	chr14:64484336-64484537(+)$1	1	174	177	9.0000
)))	chr10:70958149-70958350(+)$1	1	24	27	9.0000
(.(	chr1:54690754-54690955(+)$1	1	14	17	9.0000
(((	chr19:40841947-40842148(-)$1	1	123	126	9.0000
(((	chr6:53156614-53156815(-)$1	1	97	100	9.0000
...	chr1:186324514-186324715(-)$1	1	128	131	9.0000
...	chr17:36523666-36523867(+)$1	1	36	39	9.0000
...	chr4:123270514-123270715(+)$1	1	125	128	9.0000
...	chr12:48468172-48468373(-)$1	1	24	27	9.0000
.((	chr13:42768945-42769146(+)$1	1	84	87	9.0000
...	chr18:685870-686071(-)$1	1	164	167	9.0000
...	chr12:109687703-109687904(+)$1	1	29	32	9.0000
...	chr9:79910437-79910638(+)$1	1	114	117	9.0000
...	chr17:28772882-28773083(+)$1	1	134	137	9.0000
)..	chr19:5654016-5654217(+)$1	1	21	24	9.0000
.))	chr5:37305080-37305281(-)$1	1	157	160	9.0000
..)	chr17:65908429-65908630(+)$1	1	108	111	9.0000
...	chr14:69925019-69925220(+)$1	1	55	58	9.0000
)))	chr12:120534951-120535152(-)$1	1	67	70	9.0000
)))	chr10:96109833-96110034(-)$1	1	91	94	9.0000
.))	chr1:52847241-52847442(-)$1	1	135	138	9.0000
...	chr2:29135406-29135607(+)$1	1	39	42	9.0000
(.(	chr17:1380728-1380929(-)$1	1	27	30	9.0000
((.	chr7:98567767-98567968(+)$1	1	5	8	9.0000
(((	chr17:26900669-26900870(-)$1	1	47	50	9.0000
(..	chr2:32706353-32706554(+)$1	1	3	6	9.0000
...	chr1:19439096-19439297(-)$1	1	25	28	9.0000
...	chr19:17387099-17387300(+)$1	1	0	3	9.0000
...	chr15:64506011-64506212(-)$1	1	48	51	9.0000
(.(	chr1:151150452-151150653(-)$1	1	105	108	9.0000
)))	chr20:61906833-61907034(+)$1	1	175	178	9.0000
(..	chr2:160303271-160303472(-)$1	1	38	41	9.0000
..(	chr11:47317011-47317212(+)$1	1	2	5	9.0000
...	chr2:33810639-33810840(-)$1	1	59	62	9.0000
)).	chr1:150443798-150443999(+)$1	1	75	78	9.0000
..)	chr16:1498922-1499123(-)$1	1	47	50	9.0000
.))	chr20:47688744-47688945(+)$1	1	136	139	9.0000
...	chr9:35389792-35389993(+)$1	1	29	32	9.0000
)))	chr12:120582089-120582290(-)$1	1	20	23	9.0000
)).	chr6:79713446-79713647(-)$1	1	140	143	9.0000
(.(	chr17:73008729-73008930(+)$1	1	60	63	9.0000
(((	chr6:110064256-110064457(+)$1	1	41	44	9.0000
...	chr17:71199115-71199316(+)$1	1	40	43	9.0000
...	chr1:240371881-240372082(+)$1	1	0	3	9.0000
.))	chr15:44903035-44903236(-)$1	1	33	36	9.0000
...	chr15:101152435-101152636(+)$1	1	67	70	9.0000
...	chr22:46724520-46724721(+)$1	1	0	3	9.0000

#PSSM
C : 0.94	c : 0.05	
A : 0.94	a : 0.05	
C : 0.94	c : 0.05	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m2_run1.nuc.txt

#NT
UUC	chr16:68391006-68391246(+)$1	240	62	65	8.9999
UUC	chr2:170666704-170666944(+)$1	240	0	3	8.9999
UUC	chr7:105205912-105206152(+)$1	240	51	54	8.9999
UUC	chr20:62226931-62227171(-)$1	240	3	6	8.9999
UUC	chr1:44437598-44437838(+)$1	240	25	28	8.9999
UUC	chrX:107937952-107938193(+)$1	241	9	12	8.9999
UUC	chr3:122145756-122145996(-)$1	240	57	60	8.9999
UUC	chr8:37635415-37635655(+)$1	240	10	13	8.9999
UUC	chr1:153789770-153790010(-)$1	240	9	12	8.9999
UUC	chr19:531813-532053(+)$1	240	199	202	8.9999
UUC	chrX:40523478-40523718(-)$1	240	116	119	8.9999
UUC	chr18:9516797-9517037(+)$1	240	34	37	8.9999
UUC	chr2:216992257-216992497(+)$1	240	2	5	8.9999
UUC	chr13:42875133-42875374(+)$1	241	67	70	8.9999
UUC	chr12:57626136-57626376(+)$1	240	60	63	8.9999
UUC	chr16:686119-686359(-)$1	240	201	204	8.9999
UUC	chr19:57066424-57066664(+)$1	240	66	69	8.9999
UUC	chr20:5100224-5100464(-)$1	240	23	26	8.9999
UUC	chr9:123301222-123301462(-)$1	240	174	177	8.9999
UUC	chr16:81077681-81077921(+)$1	240	123	126	8.9999
UUC	chr9:108366493-108366733(+)$1	240	12	15	8.9999
UUC	chr18:9570328-9570568(-)$1	240	39	42	8.9999
UUC	chr6:90042748-90042988(-)$1	240	13	16	8.9999
UUC	chr16:3339625-3339865(+)$1	240	39	42	8.9999
UUC	chr1:110134632-110134872(+)$1	240	33	36	8.9999
UUC	chr1:226455615-226455855(-)$1	240	18	21	8.9999
UUC	chr1:179077684-179077924(-)$1	240	20	23	8.9999
UUC	chr19:36939787-36940027(-)$1	240	19	22	8.9999
UUC	chr19:7592651-7592891(+)$1	240	120	123	8.9999
UUC	chr13:36909314-36909554(-)$1	240	57	60	8.9999
UUC	chr7:127342401-127342641(+)$1	240	74	77	8.9999
UUC	chr11:118897636-118897876(-)$1	240	12	15	8.9999
UUC	chr14:30132826-30133066(-)$1	240	86	89	8.9999
UUC	chr3:58486939-58487179(+)$1	240	10	13	8.9999
UUC	chr10:103569924-103570164(-)$1	240	19	22	8.9999
UUC	chr4:501137-501377(+)$1	240	43	46	8.9999
UUC	chr1:41462972-41463212(+)$1	240	12	15	8.9999
UUC	chr10:31809556-31809796(+)$1	240	44	47	8.9999
UUC	chr17:16455477-16455717(-)$1	240	0	3	8.9999
UUC	chr10:117824993-117825233(-)$1	240	53	56	8.9999
UUC	chr8:17412015-17412295(+)$1	280	48	51	8.9999
UUC	chr10:43882419-43882678(-)$1	259	108	111	8.9999
UUC	chr15:78461233-78461473(+)$1	240	17	20	8.9999
UUC	chr2:55253053-55253293(-)$1	240	118	121	8.9999
UUC	chr13:31232442-31232688(+)$1	246	75	78	8.9999
UUC	chr19:59060840-59061080(+)$1	240	133	136	8.9999
UUC	chr16:89294813-89295053(+)$1	240	102	105	8.9999
UUC	chr10:27459854-27460094(+)$1	240	61	64	8.9999
UUC	chr3:130743857-130744097(-)$1	240	52	55	8.9999
UUC	chr5:134192874-134193154(+)$1	280	153	156	8.9999
UUC	chr12:57929465-57929710(-)$1	245	31	34	8.9999
UUC	chr1:205138458-205138698(-)$1	240	121	124	8.9999
UUC	chr16:69374004-69374244(+)$1	240	56	59	8.9999
UUC	chr17:1798227-1798467(+)$1	240	41	44	8.9999
UUC	chr11:102272633-102272918(-)$1	285	0	3	8.9999
UUC	chr17:57128476-57128716(-)$1	240	17	20	8.9999
UUC	chr2:196544656-196544936(+)$1	280	25	28	8.9999
UUC	chr19:35434066-35434306(+)$1	240	0	3	8.9999
UUC	chr1:26440884-26441124(+)$1	240	30	33	8.9999
UUC	chr6:34622318-34622558(-)$1	240	152	155	8.9999
UUC	chr14:51239663-51239903(-)$1	240	84	87	8.9999
UUC	chr17:37566262-37566502(-)$1	240	44	47	8.9999
UUC	chr19:18311064-18311304(-)$1	240	30	33	8.9999
UUC	chr5:139908949-139909189(+)$1	240	4	7	8.9999
UUC	chr5:150274899-150275139(-)$1	240	12	15	8.9999
UUC	chr14:72125013-72125253(+)$1	240	55	58	8.9999
UUC	chr12:120436403-120436643(+)$1	240	48	51	8.9999
UUC	chr5:82837365-82837605(+)$1	240	45	48	8.9999
UUC	chr16:72821101-72821383(-)$1	282	32	35	8.9999
UUC	chr19:54627867-54628107(+)$1	240	96	99	8.9999
UUC	chr22:41936635-41936875(-)$1	240	142	145	8.9999
UUC	chr4:39459740-39459985(-)$1	245	13	16	8.9999
UUC	chr10:120931846-120932086(-)$1	240	59	62	8.9999
UUC	chr11:85361186-85361426(+)$1	240	10	13	8.9999
UUC	chr1:183519791-183520044(+)$1	253	35	38	8.9999
UUC	chr5:134050607-134050847(+)$1	240	6	9	8.9999
UUC	chr16:51174370-51174619(-)$1	249	145	148	8.9999
UUC	chr12:70150169-70150409(+)$1	240	17	20	8.9999
UUC	chr6:83933383-83933623(-)$1	240	17	20	8.9999
UUC	chr7:44425513-44425753(-)$1	240	21	24	8.9999
UUC	chr14:62233890-62234130(+)$1	240	23	26	8.9999
UUC	chr11:124506932-124507172(-)$1	240	20	23	8.9999
UUC	chr3:41280622-41280862(+)$1	240	15	18	8.9999
UUC	chr16:11944090-11944330(-)$1	240	24	27	8.9999
UUC	chr1:113159354-113159594(-)$1	240	59	62	8.9999
UUC	chr19:58084470-58084710(-)$1	240	61	64	8.9999
UUC	chr12:48543071-48543311(-)$1	240	20	23	8.9999
UUC	chr19:45593627-45593867(+)$1	240	48	51	8.9999
UUC	chr9:74319536-74319776(-)$1	240	18	21	8.9999
UUC	chr1:23636993-23637233(-)$1	240	55	58	8.9999
UUC	chr18:51809245-51809485(+)$1	240	31	34	8.9999
UUC	chr6:26373412-26373742(+)$1	330	17	20	8.9999
UUC	chr1:156012464-156012704(-)$1	240	5	8	8.9999
UUC	chr9:129641692-129641932(+)$1	240	17	20	8.9999
UUC	chr6:37336680-37336920(+)$1	240	8	11	8.9999
UUC	chr2:62991356-62991596(+)$1	240	2	5	8.9999
uuc	chr6:26545297-26545537(+)$1	240	8	11	8.9999
UUC	chr19:2933621-2933861(-)$1	240	4	7	8.9999

#otherMatches

#Struct PSSM
&&&	chr8:57078739-57079019(-)$1	280	46	49	8.9999
"bb	chr16:68391006-68391246(+)$1	240	62	65	8.9999
:::	chr2:170666704-170666944(+)$1	240	0	3	8.9999
hhs	chr7:105205912-105206152(+)$1	240	51	54	8.9999
lll	chr20:62226931-62227171(-)$1	240	3	6	8.9999
G::	chr1:44437598-44437838(+)$1	240	25	28	8.9999
eee	chrX:107937952-107938193(+)$1	241	9	12	8.9999
dd:	chr3:122145756-122145996(-)$1	240	57	60	8.9999
qqq	chr8:37635415-37635655(+)$1	240	10	13	8.9999
:::	chr1:153789770-153790010(-)$1	240	9	12	8.9999
ddd	chr19:531813-532053(+)$1	240	199	202	8.9999
ggg	chrX:40523478-40523718(-)$1	240	116	119	8.9999
fff	chr18:9516797-9517037(+)$1	240	34	37	8.9999
!gg	chr2:216992257-216992497(+)$1	240	2	5	8.9999
ccd	chr13:42875133-42875374(+)$1	241	67	70	8.9999
rrr	chr12:57626136-57626376(+)$1	240	60	63	8.9999
nnn	chr16:686119-686359(-)$1	240	201	204	8.9999
eee	chr19:57066424-57066664(+)$1	240	66	69	8.9999
:::	chr20:5100224-5100464(-)$1	240	23	26	8.9999
3dd	chr9:123301222-123301462(-)$1	240	174	177	8.9999
xxx	chr16:81077681-81077921(+)$1	240	123	126	8.9999
iif	chr9:108366493-108366733(+)$1	240	12	15	8.9999
lll	chr18:9570328-9570568(-)$1	240	39	42	8.9999
{EE	chr6:90042748-90042988(-)$1	240	13	16	8.9999
GGG	chr16:3339625-3339865(+)$1	240	39	42	8.9999
hh[	chr1:110134632-110134872(+)$1	240	33	36	8.9999
EEE	chr1:226455615-226455855(-)$1	240	18	21	8.9999
Ccc	chr1:179077684-179077924(-)$1	240	20	23	8.9999
DMM	chr19:36939787-36940027(-)$1	240	19	22	8.9999
iii	chr19:7592651-7592891(+)$1	240	120	123	8.9999
dd"	chr13:36909314-36909554(-)$1	240	57	60	8.9999
55b	chr7:127342401-127342641(+)$1	240	74	77	8.9999
"""	chr11:118897636-118897876(-)$1	240	12	15	8.9999
)dd	chr14:30132826-30133066(-)$1	240	86	89	8.9999
LLD	chr3:58486939-58487179(+)$1	240	10	13	8.9999
EEE	chr10:103569924-103570164(-)$1	240	19	22	8.9999
EEE	chr4:501137-501377(+)$1	240	43	46	8.9999
doo	chr1:41462972-41463212(+)$1	240	12	15	8.9999
EEE	chr10:31809556-31809796(+)$1	240	44	47	8.9999
CCC	chr17:16455477-16455717(-)$1	240	0	3	8.9999
ooo	chr10:117824993-117825233(-)$1	240	53	56	8.9999
:::	chr8:17412015-17412295(+)$1	280	48	51	8.9999
cdd	chr10:43882419-43882678(-)$1	259	108	111	8.9999
$$b	chr15:78461233-78461473(+)$1	240	17	20	8.9999
ff]	chr2:55253053-55253293(-)$1	240	118	121	8.9999
rrr	chr13:31232442-31232688(+)$1	246	75	78	8.9999
:::	chr19:59060840-59061080(+)$1	240	133	136	8.9999
ddd	chr16:89294813-89295053(+)$1	240	102	105	8.9999
fff	chr10:27459854-27460094(+)$1	240	61	64	8.9999
LCC	chr3:130743857-130744097(-)$1	240	52	55	8.9999
eee	chr5:134192874-134193154(+)$1	280	153	156	8.9999
eee	chr12:57929465-57929710(-)$1	245	31	34	8.9999
$bb	chr1:205138458-205138698(-)$1	240	121	124	8.9999
c44	chr16:69374004-69374244(+)$1	240	56	59	8.9999
III	chr17:1798227-1798467(+)$1	240	41	44	8.9999
:EE	chr11:102272633-102272918(-)$1	285	0	3	8.9999
d[b	chr17:57128476-57128716(-)$1	240	17	20	8.9999
rdd	chr2:196544656-196544936(+)$1	280	25	28	8.9999
:::	chr19:35434066-35434306(+)$1	240	0	3	8.9999
ddd	chr1:26440884-26441124(+)$1	240	30	33	8.9999
DDD	chr6:34622318-34622558(-)$1	240	152	155	8.9999
ccc	chr14:51239663-51239903(-)$1	240	84	87	8.9999
c]b	chr17:37566262-37566502(-)$1	240	44	47	8.9999
GGG	chr19:18311064-18311304(-)$1	240	30	33	8.9999
e++	chr5:139908949-139909189(+)$1	240	4	7	8.9999
JJJ	chr5:150274899-150275139(-)$1	240	12	15	8.9999
ccc	chr14:72125013-72125253(+)$1	240	55	58	8.9999
ddd	chr12:120436403-120436643(+)$1	240	48	51	8.9999
III	chr5:82837365-82837605(+)$1	240	45	48	8.9999
:::	chr16:72821101-72821383(-)$1	282	32	35	8.9999
FF{	chr19:54627867-54628107(+)$1	240	96	99	8.9999
##=	chr22:41936635-41936875(-)$1	240	142	145	8.9999
FFF	chr4:39459740-39459985(-)$1	245	13	16	8.9999
hhh	chr10:120931846-120932086(-)$1	240	59	62	8.9999
h!!	chr11:85361186-85361426(+)$1	240	10	13	8.9999
f""	chr1:183519791-183520044(+)$1	253	35	38	8.9999
FFF	chr5:134050607-134050847(+)$1	240	6	9	8.9999
:::	chr16:51174370-51174619(-)$1	249	145	148	8.9999
eee	chr12:70150169-70150409(+)$1	240	17	20	8.9999
:cc	chr6:83933383-83933623(-)$1	240	17	20	8.9999
hhh	chr7:44425513-44425753(-)$1	240	21	24	8.9999
::d	chr14:62233890-62234130(+)$1	240	23	26	8.9999
:::	chr11:124506932-124507172(-)$1	240	20	23	8.9999
eee	chr3:41280622-41280862(+)$1	240	15	18	8.9999
fff	chr16:11944090-11944330(-)$1	240	24	27	8.9999
444	chr1:113159354-113159594(-)$1	240	59	62	8.9999
fff	chr19:58084470-58084710(-)$1	240	61	64	8.9999
GGG	chr12:48543071-48543311(-)$1	240	20	23	8.9999
555	chr19:45593627-45593867(+)$1	240	48	51	8.9999
:::	chr9:74319536-74319776(-)$1	240	18	21	8.9999
Dee	chr1:23636993-23637233(-)$1	240	55	58	8.9999
vdd	chr18:51809245-51809485(+)$1	240	31	34	8.9999
yyy	chr6:26373412-26373742(+)$1	330	17	20	8.9999
:::	chr1:156012464-156012704(-)$1	240	5	8	8.9999
{CC	chr9:129641692-129641932(+)$1	240	17	20	8.9999
OOO	chr6:37336680-37336920(+)$1	240	8	11	8.9999
:::	chr2:62991356-62991596(+)$1	240	2	5	8.9999
:::	chr6:26545297-26545537(+)$1	240	8	11	8.9999
ddb	chr19:2933621-2933861(-)$1	240	4	7	8.9999

#DB
...	chr8:57078739-57079019(-)$1	1	46	49	8.9999
.((	chr16:68391006-68391246(+)$1	1	62	65	8.9999
...	chr2:170666704-170666944(+)$1	1	0	3	8.9999
((.	chr7:105205912-105206152(+)$1	1	51	54	8.9999
...	chr20:62226931-62227171(-)$1	1	3	6	8.9999
(..	chr1:44437598-44437838(+)$1	1	25	28	8.9999
(((	chrX:107937952-107938193(+)$1	1	9	12	8.9999
)).	chr3:122145756-122145996(-)$1	1	57	60	8.9999
...	chr8:37635415-37635655(+)$1	1	10	13	8.9999
...	chr1:153789770-153790010(-)$1	1	9	12	8.9999
)))	chr19:531813-532053(+)$1	1	199	202	8.9999
)))	chrX:40523478-40523718(-)$1	1	116	119	8.9999
(((	chr18:9516797-9517037(+)$1	1	34	37	8.9999
.((	chr2:216992257-216992497(+)$1	1	2	5	8.9999
)))	chr13:42875133-42875374(+)$1	1	67	70	8.9999
...	chr12:57626136-57626376(+)$1	1	60	63	8.9999
...	chr16:686119-686359(-)$1	1	201	204	8.9999
(((	chr19:57066424-57066664(+)$1	1	66	69	8.9999
...	chr20:5100224-5100464(-)$1	1	23	26	8.9999
.))	chr9:123301222-123301462(-)$1	1	174	177	8.9999
...	chr16:81077681-81077921(+)$1	1	123	126	8.9999
(((	chr9:108366493-108366733(+)$1	1	12	15	8.9999
...	chr18:9570328-9570568(-)$1	1	39	42	8.9999
.((	chr6:90042748-90042988(-)$1	1	13	16	8.9999
(((	chr16:3339625-3339865(+)$1	1	39	42	8.9999
((.	chr1:110134632-110134872(+)$1	1	33	36	8.9999
(((	chr1:226455615-226455855(-)$1	1	18	21	8.9999
(((	chr1:179077684-179077924(-)$1	1	20	23	8.9999
(..	chr19:36939787-36940027(-)$1	1	19	22	8.9999
)))	chr19:7592651-7592891(+)$1	1	120	123	8.9999
((.	chr13:36909314-36909554(-)$1	1	57	60	8.9999
..)	chr7:127342401-127342641(+)$1	1	74	77	8.9999
...	chr11:118897636-118897876(-)$1	1	12	15	8.9999
.((	chr14:30132826-30133066(-)$1	1	86	89	8.9999
..(	chr3:58486939-58487179(+)$1	1	10	13	8.9999
(((	chr10:103569924-103570164(-)$1	1	19	22	8.9999
(((	chr4:501137-501377(+)$1	1	43	46	8.9999
(..	chr1:41462972-41463212(+)$1	1	12	15	8.9999
(((	chr10:31809556-31809796(+)$1	1	44	47	8.9999
(((	chr17:16455477-16455717(-)$1	1	0	3	8.9999
...	chr10:117824993-117825233(-)$1	1	53	56	8.9999
...	chr8:17412015-17412295(+)$1	1	48	51	8.9999
)))	chr10:43882419-43882678(-)$1	1	108	111	8.9999
..(	chr15:78461233-78461473(+)$1	1	17	20	8.9999
)).	chr2:55253053-55253293(-)$1	1	118	121	8.9999
...	chr13:31232442-31232688(+)$1	1	75	78	8.9999
...	chr19:59060840-59061080(+)$1	1	133	136	8.9999
)))	chr16:89294813-89295053(+)$1	1	102	105	8.9999
)))	chr10:27459854-27460094(+)$1	1	61	64	8.9999
.((	chr3:130743857-130744097(-)$1	1	52	55	8.9999
)))	chr5:134192874-134193154(+)$1	1	153	156	8.9999
(((	chr12:57929465-57929710(-)$1	1	31	34	8.9999
.((	chr1:205138458-205138698(-)$1	1	121	124	8.9999
)..	chr16:69374004-69374244(+)$1	1	56	59	8.9999
(((	chr17:1798227-1798467(+)$1	1	41	44	8.9999
.((	chr11:102272633-102272918(-)$1	1	0	3	8.9999
(.(	chr17:57128476-57128716(-)$1	1	17	20	8.9999
.))	chr2:196544656-196544936(+)$1	1	25	28	8.9999
...	chr19:35434066-35434306(+)$1	1	0	3	8.9999
)))	chr1:26440884-26441124(+)$1	1	30	33	8.9999
)))	chr6:34622318-34622558(-)$1	1	152	155	8.9999
)))	chr14:51239663-51239903(-)$1	1	84	87	8.9999
).)	chr17:37566262-37566502(-)$1	1	44	47	8.9999
(((	chr19:18311064-18311304(-)$1	1	30	33	8.9999
(..	chr5:139908949-139909189(+)$1	1	4	7	8.9999
(((	chr5:150274899-150275139(-)$1	1	12	15	8.9999
(((	chr14:72125013-72125253(+)$1	1	55	58	8.9999
)))	chr12:120436403-120436643(+)$1	1	48	51	8.9999
(((	chr5:82837365-82837605(+)$1	1	45	48	8.9999
...	chr16:72821101-72821383(-)$1	1	32	35	8.9999
((.	chr19:54627867-54628107(+)$1	1	96	99	8.9999
..(	chr22:41936635-41936875(-)$1	1	142	145	8.9999
(((	chr4:39459740-39459985(-)$1	1	13	16	8.9999
(((	chr10:120931846-120932086(-)$1	1	59	62	8.9999
(..	chr11:85361186-85361426(+)$1	1	10	13	8.9999
(..	chr1:183519791-183520044(+)$1	1	35	38	8.9999
(((	chr5:134050607-134050847(+)$1	1	6	9	8.9999
...	chr16:51174370-51174619(-)$1	1	145	148	8.9999
(((	chr12:70150169-70150409(+)$1	1	17	20	8.9999
.((	chr6:83933383-83933623(-)$1	1	17	20	8.9999
(((	chr7:44425513-44425753(-)$1	1	21	24	8.9999
..(	chr14:62233890-62234130(+)$1	1	23	26	8.9999
...	chr11:124506932-124507172(-)$1	1	20	23	8.9999
(((	chr3:41280622-41280862(+)$1	1	15	18	8.9999
)))	chr16:11944090-11944330(-)$1	1	24	27	8.9999
...	chr1:113159354-113159594(-)$1	1	59	62	8.9999
)))	chr19:58084470-58084710(-)$1	1	61	64	8.9999
(((	chr12:48543071-48543311(-)$1	1	20	23	8.9999
...	chr19:45593627-45593867(+)$1	1	48	51	8.9999
...	chr9:74319536-74319776(-)$1	1	18	21	8.9999
(((	chr1:23636993-23637233(-)$1	1	55	58	8.9999
.))	chr18:51809245-51809485(+)$1	1	31	34	8.9999
...	chr6:26373412-26373742(+)$1	1	17	20	8.9999
...	chr1:156012464-156012704(-)$1	1	5	8	8.9999
.((	chr9:129641692-129641932(+)$1	1	17	20	8.9999
...	chr6:37336680-37336920(+)$1	1	8	11	8.9999
...	chr2:62991356-62991596(+)$1	1	2	5	8.9999
...	chr6:26545297-26545537(+)$1	1	8	11	8.9999
(((	chr19:2933621-2933861(-)$1	1	4	7	8.9999

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
C : 0.98	c : 0.01	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m1_run1.nuc.txt

#NT
AGU	chr8:110586996-110587247(-)$1	251	118	121	9.0000
AGU	chrM:9969-10253(+)$1	284	30	33	9.0000
AGU	chr14:51100788-51101040(-)$1	252	18	21	9.0000
AGU	chr22:39917730-39917958(+)$1	228	98	101	9.0000
AGU	chr19:36884423-36884662(-)$1	239	146	149	9.0000
AGU	chr10:85909717-85910087(+)$1	370	16	19	9.0000
AGU	chr6:41039243-41039491(-)$1	248	0	3	9.0000
AGU	chr3:120469356-120469584(+)$1	228	11	14	9.0000
AGU	chr19:34942857-34943093(+)$1	236	67	70	9.0000
AGU	chr2:230923914-230924152(-)$1	238	93	96	9.0000
AGU	chr3:141163669-141163921(+)$1	252	51	54	9.0000
AGU	chr17:30205174-30205398(-)$1	224	125	128	9.0000
AGU	chr17:46700166-46700391(-)$1	225	27	30	9.0000
AGU	chr16:67000527-67000758(+)$1	231	27	30	9.0000
AGU	chr3:133375423-133375686(-)$1	263	23	26	9.0000
AGU	chr15:85191684-85191926(-)$1	242	9	12	9.0000
AGU	chr22:42017923-42018151(+)$1	228	68	71	9.0000
AGU	chr1:8925369-8925627(-)$1	258	4	7	9.0000
AGU	chr7:56125961-56126196(+)$1	235	2	5	9.0000
AGU	chr12:111160175-111160486(-)$1	311	128	131	9.0000
AGU	chr18:48444418-48444658(+)$1	240	119	122	9.0000
AGU	chr15:29997637-29997932(-)$1	295	74	77	9.0000
AGU	chr2:95773851-95774081(-)$1	230	57	60	9.0000
AGU	chr18:39600533-39600769(+)$1	236	26	29	9.0000
AGU	chr2:242102606-242102841(+)$1	235	62	65	9.0000
AGU	chr6:109796537-109796784(-)$1	247	2	5	9.0000
AGU	chr19:38126618-38126882(-)$1	264	30	33	9.0000
AGU	chr17:45742332-45742591(+)$1	259	38	41	9.0000
agu	chr1:156252297-156252535(-)$1	238	11	14	9.0000
AGU	chr16:30364716-30364958(-)$1	242	41	44	9.0000
AGU	chr9:127622405-127622638(-)$1	233	32	35	9.0000
AGU	chr19:30505835-30506116(+)$1	281	62	65	9.0000
agU	chr17:2583358-2583617(+)$1	259	21	24	9.0000
agu	chrX:70782593-70782901(+)$1	308	10	13	9.0000
AGU	chr14:93684913-93685150(+)$1	237	23	26	9.0000
AGU	chr6:105733311-105733535(-)$1	224	43	46	9.0000
AGU	chr11:65822905-65823147(+)$1	242	39	42	9.0000
AGU	chr20:49508006-49508278(-)$1	272	23	26	9.0000
AGU	chr9:32543051-32543283(-)$1	232	90	93	9.0000
AGU	chr17:48826500-48826731(+)$1	231	110	113	9.0000
AGU	chr16:58608830-58609060(-)$1	230	118	121	9.0000
AGU	chr7:105733377-105733673(-)$1	296	13	16	9.0000
AGU	chr3:47868768-47869026(+)$1	258	16	19	9.0000
AGU	chr14:55510434-55510666(+)$1	232	0	3	9.0000
AGU	chr17:78113386-78113623(-)$1	237	49	52	9.0000
AGU	chr3:52724897-52725175(+)$1	278	28	31	9.0000
AGU	chr5:126141162-126141395(+)$1	233	98	101	9.0000
AGU	chrX:19379572-19379814(+)$1	242	79	82	9.0000
AGU	chr1:225594274-225594621(-)$1	347	21	24	9.0000
AGU	chrX:102471227-102471475(+)$1	248	15	18	9.0000
AGU	chr2:217279805-217280040(+)$1	235	6	9	9.0000
AGU	chr4:1976940-1977178(+)$1	238	160	163	9.0000
AGU	chr21:34923459-34923830(+)$1	371	44	47	9.0000
AGU	chr17:27614383-27614668(-)$1	285	43	46	9.0000
AGU	chr6:52141845-52142081(-)$1	236	48	51	9.0000
AGU	chr12:72004200-72004447(-)$1	247	69	72	9.0000
AGU	chr5:31472192-31472419(-)$1	227	11	14	9.0000
AGU	chr7:135300569-135300840(+)$1	271	20	23	9.0000
AGU	chr1:231474038-231474268(+)$1	230	0	3	9.0000
AGU	chr1:116939165-116939397(+)$1	232	20	23	9.0000
AGU	chr3:64004162-64004401(-)$1	239	44	47	9.0000
AGU	chr21:34941261-34941493(+)$1	232	52	55	9.0000
AGU	chr12:42499558-42499818(-)$1	260	9	12	9.0000
AGU	chr3:141163018-141163263(+)$1	245	1	4	9.0000
AGU	chr13:53035778-53036022(+)$1	244	74	77	9.0000
AGU	chr13:23915429-23915722(-)$1	293	182	185	9.0000
AGU	chr16:46637904-46638133(-)$1	229	17	20	9.0000
AGU	chr19:9677066-9677438(-)$1	372	130	133	9.0000
AGU	chr20:2443702-2443933(-)$1	231	3	6	9.0000
AGU	chr1:154184813-154185132(-)$1	319	118	121	9.0000
AGU	chr16:30435550-30435788(-)$1	238	10	13	9.0000
AGU	chrX:106882483-106882721(+)$1	238	39	42	9.0000
AGU	chrX:17771314-17771540(+)$1	226	45	48	9.0000
AGU	chr17:38548818-38549075(-)$1	257	40	43	9.0000
AGU	chr12:26217566-26217802(+)$1	236	13	16	9.0000
AGU	chr7:141478278-141478507(+)$1	229	3	6	9.0000
AGU	chr6:26031915-26032148(-)$1	233	29	32	9.0000
AGU	chr11:64532812-64533038(-)$1	226	85	88	9.0000
AGU	chr1:24077837-24078087(+)$1	250	32	35	9.0000
AGU	chr3:38017118-38017361(+)$1	243	20	23	9.0000
AGU	chr11:62557344-62557580(+)$1	236	71	74	9.0000
AGU	chr20:1146788-1147061(+)$1	273	105	108	9.0000
AGU	chr21:38884198-38884427(+)$1	229	156	159	9.0000
AGU	chr19:37383067-37383370(-)$1	303	50	53	9.0000
AGU	chr2:192278675-192278931(+)$1	256	44	47	9.0000
AGU	chr21:26973588-26973818(-)$1	230	131	134	9.0000
AGU	chr10:5827028-5827328(-)$1	300	90	93	9.0000
AGU	chr2:152320039-152320308(+)$1	269	77	80	9.0000
AGU	chr15:76225232-76225458(+)$1	226	38	41	9.0000
AGU	chr13:115010297-115010528(+)$1	231	15	18	9.0000
AGU	chr13:34410125-34410386(+)$1	261	18	21	9.0000
AGU	chr5:71489918-71490147(+)$1	229	91	94	9.0000
AGU	chrX:108911332-108911595(-)$1	263	1	4	9.0000
AGU	chr10:11998259-11998510(-)$1	251	29	32	9.0000
AGU	chr1:17755533-17755768(-)$1	235	89	92	9.0000
AGU	chr15:48451808-48452100(-)$1	292	56	59	9.0000
AGU	chr5:145863051-145863281(+)$1	230	79	82	9.0000
AGU	chr1:245021980-245022237(-)$1	257	25	28	9.0000
AGU	chr10:27437771-27438038(-)$1	267	43	46	9.0000

#otherMatches

#Struct PSSM
EE:	chr20:34242548-34242783(-)$1	235	90	93	9.0000
a[b	chr8:110586996-110587247(-)$1	251	118	121	9.0000
:dd	chrM:9969-10253(+)$1	284	30	33	9.0000
:hh	chr14:51100788-51101040(-)$1	252	18	21	9.0000
{GG	chr22:39917730-39917958(+)$1	228	98	101	9.0000
fff	chr19:36884423-36884662(-)$1	239	146	149	9.0000
hhh	chr10:85909717-85910087(+)$1	370	16	19	9.0000
III	chr6:41039243-41039491(-)$1	248	0	3	9.0000
ppp	chr3:120469356-120469584(+)$1	228	11	14	9.0000
b[e	chr19:34942857-34943093(+)$1	236	67	70	9.0000
eee	chr2:230923914-230924152(-)$1	238	93	96	9.0000
:cc	chr3:141163669-141163921(+)$1	252	51	54	9.0000
pgg	chr17:30205174-30205398(-)$1	224	125	128	9.0000
MMD	chr17:46700166-46700391(-)$1	225	27	30	9.0000
mmm	chr16:67000527-67000758(+)$1	231	27	30	9.0000
GGG	chr3:133375423-133375686(-)$1	263	23	26	9.0000
FFF	chr15:85191684-85191926(-)$1	242	9	12	9.0000
!!c	chr22:42017923-42018151(+)$1	228	68	71	9.0000
EEN	chr1:8925369-8925627(-)$1	258	4	7	9.0000
EEE	chr7:56125961-56126196(+)$1	235	2	5	9.0000
IIZ	chr12:111160175-111160486(-)$1	311	128	131	9.0000
obb	chr18:48444418-48444658(+)$1	240	119	122	9.0000
:ee	chr15:29997637-29997932(-)$1	295	74	77	9.0000
:::	chr2:95773851-95774081(-)$1	230	57	60	9.0000
GGG	chr18:39600533-39600769(+)$1	236	26	29	9.0000
dd[	chr2:242102606-242102841(+)$1	235	62	65	9.0000
:::	chr6:109796537-109796784(-)$1	247	2	5	9.0000
bb]	chr19:38126618-38126882(-)$1	264	30	33	9.0000
nff	chr17:45742332-45742591(+)$1	259	38	41	9.0000
fff	chr1:156252297-156252535(-)$1	238	11	14	9.0000
EEK	chr16:30364716-30364958(-)$1	242	41	44	9.0000
:::	chr9:127622405-127622638(-)$1	233	32	35	9.0000
3bb	chr19:30505835-30506116(+)$1	281	62	65	9.0000
"""	chr17:2583358-2583617(+)$1	259	21	24	9.0000
eee	chrX:70782593-70782901(+)$1	308	10	13	9.0000
KFF	chr14:93684913-93685150(+)$1	237	23	26	9.0000
===	chr6:105733311-105733535(-)$1	224	43	46	9.0000
OOO	chr11:65822905-65823147(+)$1	242	39	42	9.0000
DDD	chr20:49508006-49508278(-)$1	272	23	26	9.0000
ddd	chr9:32543051-32543283(-)$1	232	90	93	9.0000
fff	chr17:48826500-48826731(+)$1	231	110	113	9.0000
ddd	chr16:58608830-58609060(-)$1	230	118	121	9.0000
dd[	chr7:105733377-105733673(-)$1	296	13	16	9.0000
fff	chr3:47868768-47869026(+)$1	258	16	19	9.0000
ddd	chr14:55510434-55510666(+)$1	232	0	3	9.0000
xxx	chr17:78113386-78113623(-)$1	237	49	52	9.0000
[dd	chr3:52724897-52725175(+)$1	278	28	31	9.0000
cGG	chr5:126141162-126141395(+)$1	233	98	101	9.0000
EEE	chrX:19379572-19379814(+)$1	242	79	82	9.0000
FFF	chr1:225594274-225594621(-)$1	347	21	24	9.0000
===	chrX:102471227-102471475(+)$1	248	15	18	9.0000
:::	chr2:217279805-217280040(+)$1	235	6	9	9.0000
ppd	chr4:1976940-1977178(+)$1	238	160	163	9.0000
cc[	chr21:34923459-34923830(+)$1	371	44	47	9.0000
2dd	chr17:27614383-27614668(-)$1	285	43	46	9.0000
b[d	chr6:52141845-52142081(-)$1	236	48	51	9.0000
CCC	chr12:72004200-72004447(-)$1	247	69	72	9.0000
ddd	chr5:31472192-31472419(-)$1	227	11	14	9.0000
IIL	chr7:135300569-135300840(+)$1	271	20	23	9.0000
A{D	chr1:231474038-231474268(+)$1	230	0	3	9.0000
:dd	chr1:116939165-116939397(+)$1	232	20	23	9.0000
c[e	chr3:64004162-64004401(-)$1	239	44	47	9.0000
rrr	chr21:34941261-34941493(+)$1	232	52	55	9.0000
:II	chr12:42499558-42499818(-)$1	260	9	12	9.0000
CC{	chr3:141163018-141163263(+)$1	245	1	4	9.0000
ccc	chr13:53035778-53036022(+)$1	244	74	77	9.0000
sss	chr13:23915429-23915722(-)$1	293	182	185	9.0000
eee	chr16:46637904-46638133(-)$1	229	17	20	9.0000
FF}	chr19:9677066-9677438(-)$1	372	130	133	9.0000
fff	chr20:2443702-2443933(-)$1	231	3	6	9.0000
:ii	chr1:154184813-154185132(-)$1	319	118	121	9.0000
EEE	chr16:30435550-30435788(-)$1	238	10	13	9.0000
mcc	chrX:106882483-106882721(+)$1	238	39	42	9.0000
g[f	chrX:17771314-17771540(+)$1	226	45	48	9.0000
:DD	chr17:38548818-38549075(-)$1	257	40	43	9.0000
nnn	chr12:26217566-26217802(+)$1	236	13	16	9.0000
DDD	chr7:141478278-141478507(+)$1	229	3	6	9.0000
EEE	chr6:26031915-26032148(-)$1	233	29	32	9.0000
fff	chr11:64532812-64533038(-)$1	226	85	88	9.0000
:CC	chr1:24077837-24078087(+)$1	250	32	35	9.0000
cff	chr3:38017118-38017361(+)$1	243	20	23	9.0000
KKB	chr11:62557344-62557580(+)$1	236	71	74	9.0000
qqq	chr20:1146788-1147061(+)$1	273	105	108	9.0000
^^^	chr21:38884198-38884427(+)$1	229	156	159	9.0000
!!c	chr19:37383067-37383370(-)$1	303	50	53	9.0000
JJJ	chr2:192278675-192278931(+)$1	256	44	47	9.0000
YBB	chr21:26973588-26973818(-)$1	230	131	134	9.0000
^^^	chr10:5827028-5827328(-)$1	300	90	93	9.0000
ttt	chr2:152320039-152320308(+)$1	269	77	80	9.0000
KGG	chr15:76225232-76225458(+)$1	226	38	41	9.0000
a[d	chr13:115010297-115010528(+)$1	231	15	18	9.0000
=[b	chr13:34410125-34410386(+)$1	261	18	21	9.0000
c[d	chr5:71489918-71490147(+)$1	229	91	94	9.0000
:::	chrX:108911332-108911595(-)$1	263	1	4	9.0000
fff	chr10:11998259-11998510(-)$1	251	29	32	9.0000
:::	chr1:17755533-17755768(-)$1	235	89	92	9.0000
C{E	chr15:48451808-48452100(-)$1	292	56	59	9.0000
e[a	chr5:145863051-145863281(+)$1	230	79	82	9.0000
pdd	chr1:245021980-245022237(-)$1	257	25	28	9.0000
ggg	chr10:27437771-27438038(-)$1	267	43	46	9.0000

#DB
((.	chr20:34242548-34242783(-)$1	1	90	93	9.0000
(.(	chr8:110586996-110587247(-)$1	1	118	121	9.0000
.((	chrM:9969-10253(+)$1	1	30	33	9.0000
.((	chr14:51100788-51101040(-)$1	1	18	21	9.0000
.((	chr22:39917730-39917958(+)$1	1	98	101	9.0000
)))	chr19:36884423-36884662(-)$1	1	146	149	9.0000
(((	chr10:85909717-85910087(+)$1	1	16	19	9.0000
(((	chr6:41039243-41039491(-)$1	1	0	3	9.0000
...	chr3:120469356-120469584(+)$1	1	11	14	9.0000
(.(	chr19:34942857-34943093(+)$1	1	67	70	9.0000
(((	chr2:230923914-230924152(-)$1	1	93	96	9.0000
.((	chr3:141163669-141163921(+)$1	1	51	54	9.0000
.))	chr17:30205174-30205398(-)$1	1	125	128	9.0000
..(	chr17:46700166-46700391(-)$1	1	27	30	9.0000
...	chr16:67000527-67000758(+)$1	1	27	30	9.0000
(((	chr3:133375423-133375686(-)$1	1	23	26	9.0000
(((	chr15:85191684-85191926(-)$1	1	9	12	9.0000
..(	chr22:42017923-42018151(+)$1	1	68	71	9.0000
((.	chr1:8925369-8925627(-)$1	1	4	7	9.0000
(((	chr7:56125961-56126196(+)$1	1	2	5	9.0000
)).	chr12:111160175-111160486(-)$1	1	128	131	9.0000
.))	chr18:48444418-48444658(+)$1	1	119	122	9.0000
.((	chr15:29997637-29997932(-)$1	1	74	77	9.0000
...	chr2:95773851-95774081(-)$1	1	57	60	9.0000
(((	chr18:39600533-39600769(+)$1	1	26	29	9.0000
((.	chr2:242102606-242102841(+)$1	1	62	65	9.0000
...	chr6:109796537-109796784(-)$1	1	2	5	9.0000
)).	chr19:38126618-38126882(-)$1	1	30	33	9.0000
.))	chr17:45742332-45742591(+)$1	1	38	41	9.0000
(((	chr1:156252297-156252535(-)$1	1	11	14	9.0000
((.	chr16:30364716-30364958(-)$1	1	41	44	9.0000
...	chr9:127622405-127622638(-)$1	1	32	35	9.0000
.))	chr19:30505835-30506116(+)$1	1	62	65	9.0000
...	chr17:2583358-2583617(+)$1	1	21	24	9.0000
(((	chrX:70782593-70782901(+)$1	1	10	13	9.0000
.((	chr14:93684913-93685150(+)$1	1	23	26	9.0000
(((	chr6:105733311-105733535(-)$1	1	43	46	9.0000
...	chr11:65822905-65823147(+)$1	1	39	42	9.0000
(((	chr20:49508006-49508278(-)$1	1	23	26	9.0000
(((	chr9:32543051-32543283(-)$1	1	90	93	9.0000
)))	chr17:48826500-48826731(+)$1	1	110	113	9.0000
)))	chr16:58608830-58609060(-)$1	1	118	121	9.0000
((.	chr7:105733377-105733673(-)$1	1	13	16	9.0000
(((	chr3:47868768-47869026(+)$1	1	16	19	9.0000
(((	chr14:55510434-55510666(+)$1	1	0	3	9.0000
...	chr17:78113386-78113623(-)$1	1	49	52	9.0000
.((	chr3:52724897-52725175(+)$1	1	28	31	9.0000
)))	chr5:126141162-126141395(+)$1	1	98	101	9.0000
(((	chrX:19379572-19379814(+)$1	1	79	82	9.0000
(((	chr1:225594274-225594621(-)$1	1	21	24	9.0000
(((	chrX:102471227-102471475(+)$1	1	15	18	9.0000
...	chr2:217279805-217280040(+)$1	1	6	9	9.0000
..)	chr4:1976940-1977178(+)$1	1	160	163	9.0000
((.	chr21:34923459-34923830(+)$1	1	44	47	9.0000
.))	chr17:27614383-27614668(-)$1	1	43	46	9.0000
(.(	chr6:52141845-52142081(-)$1	1	48	51	9.0000
(((	chr12:72004200-72004447(-)$1	1	69	72	9.0000
(((	chr5:31472192-31472419(-)$1	1	11	14	9.0000
((.	chr7:135300569-135300840(+)$1	1	20	23	9.0000
(.(	chr1:231474038-231474268(+)$1	1	0	3	9.0000
.((	chr1:116939165-116939397(+)$1	1	20	23	9.0000
(.(	chr3:64004162-64004401(-)$1	1	44	47	9.0000
...	chr21:34941261-34941493(+)$1	1	52	55	9.0000
.((	chr12:42499558-42499818(-)$1	1	9	12	9.0000
((.	chr3:141163018-141163263(+)$1	1	1	4	9.0000
)))	chr13:53035778-53036022(+)$1	1	74	77	9.0000
...	chr13:23915429-23915722(-)$1	1	182	185	9.0000
(((	chr16:46637904-46638133(-)$1	1	17	20	9.0000
)).	chr19:9677066-9677438(-)$1	1	130	133	9.0000
(((	chr20:2443702-2443933(-)$1	1	3	6	9.0000
.((	chr1:154184813-154185132(-)$1	1	118	121	9.0000
(((	chr16:30435550-30435788(-)$1	1	10	13	9.0000
.))	chrX:106882483-106882721(+)$1	1	39	42	9.0000
(.(	chrX:17771314-17771540(+)$1	1	45	48	9.0000
.((	chr17:38548818-38549075(-)$1	1	40	43	9.0000
...	chr12:26217566-26217802(+)$1	1	13	16	9.0000
(((	chr7:141478278-141478507(+)$1	1	3	6	9.0000
(((	chr6:26031915-26032148(-)$1	1	29	32	9.0000
(((	chr11:64532812-64533038(-)$1	1	85	88	9.0000
.((	chr1:24077837-24078087(+)$1	1	32	35	9.0000
)))	chr3:38017118-38017361(+)$1	1	20	23	9.0000
..(	chr11:62557344-62557580(+)$1	1	71	74	9.0000
...	chr20:1146788-1147061(+)$1	1	105	108	9.0000
...	chr21:38884198-38884427(+)$1	1	156	159	9.0000
..(	chr19:37383067-37383370(-)$1	1	50	53	9.0000
(((	chr2:192278675-192278931(+)$1	1	44	47	9.0000
.))	chr21:26973588-26973818(-)$1	1	131	134	9.0000
...	chr10:5827028-5827328(-)$1	1	90	93	9.0000
...	chr2:152320039-152320308(+)$1	1	77	80	9.0000
.((	chr15:76225232-76225458(+)$1	1	38	41	9.0000
(.(	chr13:115010297-115010528(+)$1	1	15	18	9.0000
(.(	chr13:34410125-34410386(+)$1	1	18	21	9.0000
(.(	chr5:71489918-71490147(+)$1	1	91	94	9.0000
...	chrX:108911332-108911595(-)$1	1	1	4	9.0000
(((	chr10:11998259-11998510(-)$1	1	29	32	9.0000
...	chr1:17755533-17755768(-)$1	1	89	92	9.0000
(.(	chr15:48451808-48452100(-)$1	1	56	59	9.0000
(.(	chr5:145863051-145863281(+)$1	1	79	82	9.0000
.))	chr1:245021980-245022237(-)$1	1	25	28	9.0000
)))	chr10:27437771-27438038(-)$1	1	43	46	9.0000

#PSSM
A : 0.97	a : 0.03	
G : 0.97	g : 0.03	
U : 0.98	u : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m2_run1.nuc.txt

#NT
UCU	chr3:16411655-16411878(-)$1	223	57	60	8.9999
UCU	chr11:32953327-32953562(+)$1	235	32	35	8.9999
UCU	chr2:32819990-32820226(+)$1	236	24	27	8.9999
UCU	chr12:120984153-120984373(+)$1	220	20	23	8.9999
UCU	chr16:18804491-18804715(-)$1	224	111	114	8.9999
UCU	chr19:44738797-44739020(+)$1	223	24	27	8.9999
UCU	chr10:115606875-115607096(-)$1	221	63	66	8.9999
UCU	chr1:155450555-155450776(-)$1	221	57	60	8.9999
UCU	chr1:214819507-214819726(+)$1	219	33	36	8.9999
UCU	chr10:129909831-129910060(-)$1	229	28	31	8.9999
UCU	chr22:35799116-35799338(+)$1	222	36	39	8.9999
UCU	chr15:71211411-71211630(+)$1	219	27	30	8.9999
UCU	chr20:20006227-20006451(+)$1	224	88	91	8.9999
UCU	chr17:7810130-7810348(+)$1	218	6	9	8.9999
UCU	chr16:58577289-58577520(-)$1	231	58	61	8.9999
UCU	chr16:11940577-11940800(-)$1	223	43	46	8.9999
UCU	chr8:90801575-90801798(+)$1	223	44	47	8.9999
UCU	chr19:6415578-6415803(-)$1	225	22	25	8.9999
UCU	chr6:153296291-153296522(-)$1	231	113	116	8.9999
UCU	chr19:36728104-36728331(+)$1	227	5	8	8.9999
UCU	chr1:155938916-155939150(-)$1	234	36	39	8.9999
UCU	chr11:118889474-118889703(+)$1	229	141	144	8.9999
UCU	chr2:169727830-169728051(-)$1	221	5	8	8.9999
UCU	chr9:102784361-102784580(-)$1	219	64	67	8.9999
UCU	chr19:36219801-36220023(+)$1	222	53	56	8.9999
UCU	chr1:111490745-111490965(-)$1	220	114	117	8.9999
UCU	chr5:112203033-112203252(+)$1	219	22	25	8.9999
UCU	chr17:28512003-28512227(+)$1	224	38	41	8.9999
UCU	chr1:186307160-186307395(-)$1	235	30	33	8.9999
UCU	chr10:112341704-112341923(+)$1	219	34	37	8.9999
UCU	chr5:36177222-36177461(+)$1	239	0	3	8.9999
UCU	chr5:38502716-38502944(-)$1	228	81	84	8.9999
UCU	chr19:24309447-24309671(+)$1	224	90	93	8.9999
UCU	chr9:110068627-110068850(+)$1	223	15	18	8.9999
UCU	chr5:64867700-64867928(+)$1	228	14	17	8.9999
UCU	chr10:112724591-112724815(+)$1	224	14	17	8.9999
UCU	chr11:85977134-85977358(+)$1	224	38	41	8.9999
UCU	chr12:106740192-106740410(+)$1	218	10	13	8.9999
UCU	chr12:88554498-88554718(+)$1	220	23	26	8.9999
UCU	chr19:36940043-36940267(-)$1	224	179	182	8.9999
UCU	chr6:24412498-24412722(+)$1	224	50	53	8.9999
UCU	chr1:186370131-186370363(+)$1	232	104	107	8.9999
UCU	chr7:77423359-77423581(-)$1	222	15	18	8.9999
UCU	chr11:10821065-10821292(-)$1	227	46	49	8.9999
UCU	chrM:10000-10227(+)$1	227	210	213	8.9999
UCU	chr4:113502756-113502981(-)$1	225	119	122	8.9999
UCU	chr11:64054115-64054341(+)$1	226	2	5	8.9999
UCU	chr10:5768774-5769002(+)$1	228	222	225	8.9999
UCU	chr11:11373734-11373955(-)$1	221	32	35	8.9999
UCU	chr6:36485410-36485630(-)$1	220	42	45	8.9999
UCU	chr1:27623486-27623708(+)$1	222	8	11	8.9999
UCU	chr12:11091128-11091351(-)$1	223	43	46	8.9999
UCU	chr11:18536264-18536487(-)$1	223	13	16	8.9999
UCU	chr19:42740732-42740959(-)$1	227	50	53	8.9999
UCU	chr2:170416923-170417147(-)$1	224	110	113	8.9999
UCU	chr8:37555208-37555434(+)$1	226	99	102	8.9999
UCU	chr8:26221169-26221401(+)$1	232	118	121	8.9999
UCU	chr15:76209559-76209789(+)$1	230	4	7	8.9999
UCU	chr12:11090986-11091207(-)$1	221	5	8	8.9999
UCU	chr19:34890783-34891014(+)$1	231	13	16	8.9999
UCU	chr15:75165469-75165689(-)$1	220	15	18	8.9999
UCU	chr11:94917484-94917706(-)$1	222	29	32	8.9999
UCU	chr5:7866756-7866991(-)$1	235	19	22	8.9999
UCu	chr6:127647541-127647768(-)$1	227	1	4	8.9999
UCU	chr2:223787419-223787644(+)$1	225	17	20	8.9999
UCU	chr1:100524132-100524356(+)$1	224	82	85	8.9999
UCU	chr10:98336376-98336611(-)$1	235	1	4	8.9999
UCU	chr1:42656950-42657176(-)$1	226	106	109	8.9999
UCU	chr12:48543594-48543814(-)$1	220	3	6	8.9999
UCU	chrX:71495412-71495635(-)$1	223	102	105	8.9999
UCU	chr7:135635298-135635523(-)$1	225	10	13	8.9999
UCU	chr12:1005706-1005930(+)$1	224	81	84	8.9999
UCU	chr19:37309209-37309441(+)$1	232	8	11	8.9999
UCU	chr6:26156490-26156731(+)$1	241	84	87	8.9999
UCU	chr13:73336086-73336317(-)$1	231	19	22	8.9999
UCU	chr4:166254629-166254856(+)$1	227	80	83	8.9999
UCU	chr1:16259800-16260023(+)$1	223	132	135	8.9999
UCU	chr1:169279122-169279345(-)$1	223	170	173	8.9999
ucu	chr1:227841937-227842160(+)$1	223	10	13	8.9999
UCU	chr11:35006109-35006331(+)$1	222	2	5	8.9999
UCU	chr9:132591693-132591918(-)$1	225	4	7	8.9999
UCU	chr4:57891469-57891710(+)$1	241	15	18	8.9999
UCU	chr2:109381283-109381504(+)$1	221	8	11	8.9999
UCU	chr12:65564702-65564941(+)$1	239	32	35	8.9999
UCU	chr13:73293029-73293253(-)$1	224	7	10	8.9999
ucu	chr11:125523567-125523789(+)$1	222	3	6	8.9999
UCU	chr18:52942789-52943010(-)$1	221	11	14	8.9999
UCU	chr2:201726333-201726554(-)$1	221	113	116	8.9999
UCU	chr1:54262616-54262839(-)$1	223	7	10	8.9999
UCU	chr1:85724987-85725222(-)$1	235	118	121	8.9999
UCU	chr2:105893988-105894209(-)$1	221	71	74	8.9999
UCU	chr21:30433554-30433773(-)$1	219	116	119	8.9999
UCU	chr20:47686684-47686910(+)$1	226	11	14	8.9999
UCU	chrX:107977028-107977257(-)$1	229	80	83	8.9999
UCU	chr9:129594729-129594957(+)$1	228	22	25	8.9999
UCU	chr6:97246740-97246960(-)$1	220	91	94	8.9999
UCU	chr8:124042767-124042989(-)$1	222	24	27	8.9999
UCU	chr2:166768924-166769152(-)$1	228	4	7	8.9999

#otherMatches

#Struct PSSM
:::	chr1:85331500-85331727(-)$1	227	42	45	8.9999
:::	chr3:16411655-16411878(-)$1	223	57	60	8.9999
QQQ	chr11:32953327-32953562(+)$1	235	32	35	8.9999
nnd	chr2:32819990-32820226(+)$1	236	24	27	8.9999
www	chr12:120984153-120984373(+)$1	220	20	23	8.9999
ddd	chr16:18804491-18804715(-)$1	224	111	114	8.9999
:::	chr19:44738797-44739020(+)$1	223	24	27	8.9999
66c	chr10:115606875-115607096(-)$1	221	63	66	8.9999
vvv	chr1:155450555-155450776(-)$1	221	57	60	8.9999
===	chr1:214819507-214819726(+)$1	219	33	36	8.9999
::g	chr10:129909831-129910060(-)$1	229	28	31	8.9999
888	chr22:35799116-35799338(+)$1	222	36	39	8.9999
eee	chr15:71211411-71211630(+)$1	219	27	30	8.9999
KEE	chr20:20006227-20006451(+)$1	224	88	91	8.9999
DKK	chr17:7810130-7810348(+)$1	218	6	9	8.9999
ooo	chr16:58577289-58577520(-)$1	231	58	61	8.9999
===	chr16:11940577-11940800(-)$1	223	43	46	8.9999
3cc	chr8:90801575-90801798(+)$1	223	44	47	8.9999
ddd	chr19:6415578-6415803(-)$1	225	22	25	8.9999
cc[	chr6:153296291-153296522(-)$1	231	113	116	8.9999
[cc	chr19:36728104-36728331(+)$1	227	5	8	8.9999
f[b	chr1:155938916-155939150(-)$1	234	36	39	8.9999
KKE	chr11:118889474-118889703(+)$1	229	141	144	8.9999
lll	chr2:169727830-169728051(-)$1	221	5	8	8.9999
eee	chr9:102784361-102784580(-)$1	219	64	67	8.9999
ddd	chr19:36219801-36220023(+)$1	222	53	56	8.9999
fff	chr1:111490745-111490965(-)$1	220	114	117	8.9999
DDD	chr5:112203033-112203252(+)$1	219	22	25	8.9999
ddd	chr17:28512003-28512227(+)$1	224	38	41	8.9999
hhh	chr1:186307160-186307395(-)$1	235	30	33	8.9999
ddd	chr10:112341704-112341923(+)$1	219	34	37	8.9999
EEE	chr5:36177222-36177461(+)$1	239	0	3	8.9999
[gg	chr5:38502716-38502944(-)$1	228	81	84	8.9999
777	chr19:24309447-24309671(+)$1	224	90	93	8.9999
:::	chr9:110068627-110068850(+)$1	223	15	18	8.9999
nnn	chr5:64867700-64867928(+)$1	228	14	17	8.9999
HHH	chr10:112724591-112724815(+)$1	224	14	17	8.9999
===	chr11:85977134-85977358(+)$1	224	38	41	8.9999
DUU	chr12:106740192-106740410(+)$1	218	10	13	8.9999
sss	chr12:88554498-88554718(+)$1	220	23	26	8.9999
iii	chr19:36940043-36940267(-)$1	224	179	182	8.9999
mcc	chr6:24412498-24412722(+)$1	224	50	53	8.9999
ccc	chr1:186370131-186370363(+)$1	232	104	107	8.9999
d!!	chr7:77423359-77423581(-)$1	222	15	18	8.9999
DDD	chr11:10821065-10821292(-)$1	227	46	49	8.9999
:::	chrM:10000-10227(+)$1	227	210	213	8.9999
:::	chr4:113502756-113502981(-)$1	225	119	122	8.9999
hhh	chr11:64054115-64054341(+)$1	226	2	5	8.9999
:::	chr10:5768774-5769002(+)$1	228	222	225	8.9999
ecc	chr11:11373734-11373955(-)$1	221	32	35	8.9999
fff	chr6:36485410-36485630(-)$1	220	42	45	8.9999
DDK	chr1:27623486-27623708(+)$1	222	8	11	8.9999
d]b	chr12:11091128-11091351(-)$1	223	43	46	8.9999
G::	chr11:18536264-18536487(-)$1	223	13	16	8.9999
dqq	chr19:42740732-42740959(-)$1	227	50	53	8.9999
LLC	chr2:170416923-170417147(-)$1	224	110	113	8.9999
uuu	chr8:37555208-37555434(+)$1	226	99	102	8.9999
sss	chr8:26221169-26221401(+)$1	232	118	121	8.9999
::G	chr15:76209559-76209789(+)$1	230	4	7	8.9999
hhh	chr12:11090986-11091207(-)$1	221	5	8	8.9999
nnn	chr19:34890783-34891014(+)$1	231	13	16	8.9999
EEE	chr15:75165469-75165689(-)$1	220	15	18	8.9999
EEE	chr11:94917484-94917706(-)$1	222	29	32	8.9999
MMB	chr5:7866756-7866991(-)$1	235	19	22	8.9999
ddd	chr6:127647541-127647768(-)$1	227	1	4	8.9999
iii	chr2:223787419-223787644(+)$1	225	17	20	8.9999
zzz	chr1:100524132-100524356(+)$1	224	82	85	8.9999
FFF	chr10:98336376-98336611(-)$1	235	1	4	8.9999
:::	chr1:42656950-42657176(-)$1	226	106	109	8.9999
EEE	chr12:48543594-48543814(-)$1	220	3	6	8.9999
lcc	chrX:71495412-71495635(-)$1	223	102	105	8.9999
LLJ	chr7:135635298-135635523(-)$1	225	10	13	8.9999
dee	chr12:1005706-1005930(+)$1	224	81	84	8.9999
EEO	chr19:37309209-37309441(+)$1	232	8	11	8.9999
ncc	chr6:26156490-26156731(+)$1	241	84	87	8.9999
::d	chr13:73336086-73336317(-)$1	231	19	22	8.9999
hhh	chr4:166254629-166254856(+)$1	227	80	83	8.9999
cbb	chr1:16259800-16260023(+)$1	223	132	135	8.9999
22c	chr1:169279122-169279345(-)$1	223	170	173	8.9999
DDg	chr1:227841937-227842160(+)$1	223	10	13	8.9999
::E	chr11:35006109-35006331(+)$1	222	2	5	8.9999
FFF	chr9:132591693-132591918(-)$1	225	4	7	8.9999
:::	chr4:57891469-57891710(+)$1	241	15	18	8.9999
FF{	chr2:109381283-109381504(+)$1	221	8	11	8.9999
ggg	chr12:65564702-65564941(+)$1	239	32	35	8.9999
fff	chr13:73293029-73293253(-)$1	224	7	10	8.9999
:::	chr11:125523567-125523789(+)$1	222	3	6	8.9999
e""	chr18:52942789-52943010(-)$1	221	11	14	8.9999
[ao	chr2:201726333-201726554(-)$1	221	113	116	8.9999
"""	chr1:54262616-54262839(-)$1	223	7	10	8.9999
iii	chr1:85724987-85725222(-)$1	235	118	121	8.9999
ddd	chr2:105893988-105894209(-)$1	221	71	74	8.9999
55c	chr21:30433554-30433773(-)$1	219	116	119	8.9999
DDD	chr20:47686684-47686910(+)$1	226	11	14	8.9999
:::	chrX:107977028-107977257(-)$1	229	80	83	8.9999
:::	chr9:129594729-129594957(+)$1	228	22	25	8.9999
ttt	chr6:97246740-97246960(-)$1	220	91	94	8.9999
!!b	chr8:124042767-124042989(-)$1	222	24	27	8.9999
bb[	chr2:166768924-166769152(-)$1	228	4	7	8.9999

#DB
...	chr1:85331500-85331727(-)$1	1	42	45	8.9999
...	chr3:16411655-16411878(-)$1	1	57	60	8.9999
...	chr11:32953327-32953562(+)$1	1	32	35	8.9999
..)	chr2:32819990-32820226(+)$1	1	24	27	8.9999
...	chr12:120984153-120984373(+)$1	1	20	23	8.9999
)))	chr16:18804491-18804715(-)$1	1	111	114	8.9999
...	chr19:44738797-44739020(+)$1	1	24	27	8.9999
..)	chr10:115606875-115607096(-)$1	1	63	66	8.9999
...	chr1:155450555-155450776(-)$1	1	57	60	8.9999
)))	chr1:214819507-214819726(+)$1	1	33	36	8.9999
..(	chr10:129909831-129910060(-)$1	1	28	31	8.9999
...	chr22:35799116-35799338(+)$1	1	36	39	8.9999
(((	chr15:71211411-71211630(+)$1	1	27	30	8.9999
.((	chr20:20006227-20006451(+)$1	1	88	91	8.9999
(..	chr17:7810130-7810348(+)$1	1	6	9	8.9999
...	chr16:58577289-58577520(-)$1	1	58	61	8.9999
(((	chr16:11940577-11940800(-)$1	1	43	46	8.9999
.))	chr8:90801575-90801798(+)$1	1	44	47	8.9999
)))	chr19:6415578-6415803(-)$1	1	22	25	8.9999
((.	chr6:153296291-153296522(-)$1	1	113	116	8.9999
.((	chr19:36728104-36728331(+)$1	1	5	8	8.9999
(.(	chr1:155938916-155939150(-)$1	1	36	39	8.9999
..(	chr11:118889474-118889703(+)$1	1	141	144	8.9999
...	chr2:169727830-169728051(-)$1	1	5	8	8.9999
(((	chr9:102784361-102784580(-)$1	1	64	67	8.9999
)))	chr19:36219801-36220023(+)$1	1	53	56	8.9999
(((	chr1:111490745-111490965(-)$1	1	114	117	8.9999
(((	chr5:112203033-112203252(+)$1	1	22	25	8.9999
(((	chr17:28512003-28512227(+)$1	1	38	41	8.9999
)))	chr1:186307160-186307395(-)$1	1	30	33	8.9999
)))	chr10:112341704-112341923(+)$1	1	34	37	8.9999
(((	chr5:36177222-36177461(+)$1	1	0	3	8.9999
.((	chr5:38502716-38502944(-)$1	1	81	84	8.9999
...	chr19:24309447-24309671(+)$1	1	90	93	8.9999
...	chr9:110068627-110068850(+)$1	1	15	18	8.9999
...	chr5:64867700-64867928(+)$1	1	14	17	8.9999
(((	chr10:112724591-112724815(+)$1	1	14	17	8.9999
(((	chr11:85977134-85977358(+)$1	1	38	41	8.9999
(..	chr12:106740192-106740410(+)$1	1	10	13	8.9999
...	chr12:88554498-88554718(+)$1	1	23	26	8.9999
)))	chr19:36940043-36940267(-)$1	1	179	182	8.9999
.))	chr6:24412498-24412722(+)$1	1	50	53	8.9999
)))	chr1:186370131-186370363(+)$1	1	104	107	8.9999
(..	chr7:77423359-77423581(-)$1	1	15	18	8.9999
(((	chr11:10821065-10821292(-)$1	1	46	49	8.9999
...	chrM:10000-10227(+)$1	1	210	213	8.9999
...	chr4:113502756-113502981(-)$1	1	119	122	8.9999
(((	chr11:64054115-64054341(+)$1	1	2	5	8.9999
...	chr10:5768774-5769002(+)$1	1	222	225	8.9999
(((	chr11:11373734-11373955(-)$1	1	32	35	8.9999
(((	chr6:36485410-36485630(-)$1	1	42	45	8.9999
((.	chr1:27623486-27623708(+)$1	1	8	11	8.9999
).)	chr12:11091128-11091351(-)$1	1	43	46	8.9999
(..	chr11:18536264-18536487(-)$1	1	13	16	8.9999
(..	chr19:42740732-42740959(-)$1	1	50	53	8.9999
..(	chr2:170416923-170417147(-)$1	1	110	113	8.9999
...	chr8:37555208-37555434(+)$1	1	99	102	8.9999
...	chr8:26221169-26221401(+)$1	1	118	121	8.9999
..(	chr15:76209559-76209789(+)$1	1	4	7	8.9999
(((	chr12:11090986-11091207(-)$1	1	5	8	8.9999
...	chr19:34890783-34891014(+)$1	1	13	16	8.9999
(((	chr15:75165469-75165689(-)$1	1	15	18	8.9999
(((	chr11:94917484-94917706(-)$1	1	29	32	8.9999
..(	chr5:7866756-7866991(-)$1	1	19	22	8.9999
(((	chr6:127647541-127647768(-)$1	1	1	4	8.9999
(((	chr2:223787419-223787644(+)$1	1	17	20	8.9999
...	chr1:100524132-100524356(+)$1	1	82	85	8.9999
(((	chr10:98336376-98336611(-)$1	1	1	4	8.9999
...	chr1:42656950-42657176(-)$1	1	106	109	8.9999
(((	chr12:48543594-48543814(-)$1	1	3	6	8.9999
.))	chrX:71495412-71495635(-)$1	1	102	105	8.9999
..(	chr7:135635298-135635523(-)$1	1	10	13	8.9999
(((	chr12:1005706-1005930(+)$1	1	81	84	8.9999
((.	chr19:37309209-37309441(+)$1	1	8	11	8.9999
.))	chr6:26156490-26156731(+)$1	1	84	87	8.9999
..(	chr13:73336086-73336317(-)$1	1	19	22	8.9999
(((	chr4:166254629-166254856(+)$1	1	80	83	8.9999
(((	chr1:16259800-16260023(+)$1	1	132	135	8.9999
..)	chr1:169279122-169279345(-)$1	1	170	173	8.9999
(((	chr1:227841937-227842160(+)$1	1	10	13	8.9999
..(	chr11:35006109-35006331(+)$1	1	2	5	8.9999
(((	chr9:132591693-132591918(-)$1	1	4	7	8.9999
...	chr4:57891469-57891710(+)$1	1	15	18	8.9999
((.	chr2:109381283-109381504(+)$1	1	8	11	8.9999
(((	chr12:65564702-65564941(+)$1	1	32	35	8.9999
(((	chr13:73293029-73293253(-)$1	1	7	10	8.9999
...	chr11:125523567-125523789(+)$1	1	3	6	8.9999
(..	chr18:52942789-52943010(-)$1	1	11	14	8.9999
.(.	chr2:201726333-201726554(-)$1	1	113	116	8.9999
...	chr1:54262616-54262839(-)$1	1	7	10	8.9999
(((	chr1:85724987-85725222(-)$1	1	118	121	8.9999
(((	chr2:105893988-105894209(-)$1	1	71	74	8.9999
..)	chr21:30433554-30433773(-)$1	1	116	119	8.9999
(((	chr20:47686684-47686910(+)$1	1	11	14	8.9999
...	chrX:107977028-107977257(-)$1	1	80	83	8.9999
...	chr9:129594729-129594957(+)$1	1	22	25	8.9999
...	chr6:97246740-97246960(-)$1	1	91	94	8.9999
..(	chr8:124042767-124042989(-)$1	1	24	27	8.9999
((.	chr2:166768924-166769152(-)$1	1	4	7	8.9999

#PSSM
U : 0.97	u : 0.02	
C : 0.97	c : 0.02	
U : 0.96	u : 0.03	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m3_run2.nuc.txt

#NT
GAG	chr6:32944335-32944561(+)$1	226	89	92	9.0000
GAG	chr17:38457020-38457239(+)$1	219	73	76	9.0000
GAG	chr17:38289782-38289999(+)$1	217	16	19	9.0000
GAG	chr12:113596702-113596913(-)$1	211	38	41	9.0000
GAG	chr17:78305774-78305995(+)$1	221	40	43	9.0000
GAG	chr1:153914332-153914549(-)$1	217	14	17	9.0000
GAG	chr7:56120035-56120252(+)$1	217	96	99	9.0000
GAG	chr6:31600442-31600659(+)$1	217	4	7	9.0000
GAG	chr3:182987974-182988196(+)$1	222	23	26	9.0000
GAG	chr11:763817-764034(+)$1	217	18	21	9.0000
GAG	chr10:88277228-88277447(-)$1	219	29	32	9.0000
GAG	chr18:55283065-55283285(-)$1	220	9	12	9.0000
GAG	chr3:172534391-172534615(+)$1	224	167	170	9.0000
GAG	chr5:108713821-108714038(-)$1	217	46	49	9.0000
GAG	chr3:47887823-47888044(+)$1	221	9	12	9.0000
GAG	chr5:112178665-112178882(+)$1	217	171	174	9.0000
GAG	chr12:116424036-116424253(-)$1	217	57	60	9.0000
GAG	chr1:214803878-214804094(+)$1	216	40	43	9.0000
GAG	chr17:7405210-7405436(+)$1	226	38	41	9.0000
GAG	chr7:30634604-30634822(+)$1	218	88	91	9.0000
GAG	chr14:95581904-95582122(-)$1	218	3	6	9.0000
GAG	chr1:54238005-54238224(-)$1	219	165	168	9.0000
GAG	chr16:47117570-47117788(-)$1	218	91	94	9.0000
GAG	chr16:71319239-71319465(-)$1	226	84	87	9.0000
GAG	chr19:33183065-33183275(+)$1	210	158	161	9.0000
GAG	chr13:77661622-77661843(-)$1	221	0	3	9.0000
GAG	chr13:67800998-67801217(-)$1	219	22	25	9.0000
GAG	chr7:72873903-72874123(-)$1	220	8	11	9.0000
GAG	chr2:61558339-61558556(-)$1	217	119	122	9.0000
GAG	chr19:24309867-24310098(+)$1	231	55	58	9.0000
GAG	chr11:120348783-120348999(+)$1	216	84	87	9.0000
GAG	chr6:52144264-52144488(-)$1	224	30	33	9.0000
GAG	chr13:31205338-31205558(+)$1	220	47	50	9.0000
GAG	chr9:35060950-35061165(-)$1	215	43	46	9.0000
GAG	chr15:70960152-70960377(-)$1	225	115	118	9.0000
GAG	chr1:19518621-19518839(-)$1	218	91	94	9.0000
GAG	chr17:7406386-7406607(+)$1	221	15	18	9.0000
GAG	chr14:53325062-53325282(-)$1	220	23	26	9.0000
GAG	chr2:10187679-10187899(+)$1	220	27	30	9.0000
GAG	chr19:13051060-13051278(+)$1	218	2	5	9.0000
GAG	chr19:56179781-56180002(+)$1	221	11	14	9.0000
GAG	chr1:197059272-197059488(-)$1	216	57	60	9.0000
gag	chr18:9256288-9256507(+)$1	219	65	68	9.0000
GAG	chr16:58577594-58577816(-)$1	222	78	81	9.0000
GAG	chr21:34926248-34926499(+)$1	251	57	60	9.0000
GAG	chr12:7079302-7079525(-)$1	223	42	45	9.0000
GAG	chr5:56180522-56180741(+)$1	219	23	26	9.0000
GAG	chr12:49440024-49440244(-)$1	220	204	207	9.0000
GAG	chr2:48026200-48026420(+)$1	220	44	47	9.0000
GAG	chrX:41202897-41203127(+)$1	230	61	64	9.0000
GAG	chr8:145011056-145011275(-)$1	219	17	20	9.0000
GAG	chr1:229772501-229772713(+)$1	212	9	12	9.0000
GAG	chr19:39214588-39214806(+)$1	218	6	9	9.0000
GAG	chr17:37006607-37006828(-)$1	221	10	13	9.0000
GAG	chrX:153590826-153591043(-)$1	217	2	5	9.0000
GAG	chr15:75498412-75498637(+)$1	225	40	43	9.0000
GAG	chr10:32582533-32582753(-)$1	220	32	35	9.0000
GAG	chr2:73476131-73476356(+)$1	225	11	14	9.0000
GAG	chr12:14613742-14613960(+)$1	218	2	5	9.0000
GAG	chr1:39926249-39926470(+)$1	221	7	10	9.0000
GAG	chr2:61722569-61722788(-)$1	219	196	199	9.0000
GAG	chr14:60073996-60074214(-)$1	218	56	59	9.0000
GAG	chr6:31508067-31508291(-)$1	224	6	9	9.0000
GAG	chr19:37643373-37643595(-)$1	222	11	14	9.0000
GAG	chr1:227842924-227843149(+)$1	225	60	63	9.0000
GAG	chr10:63852366-63852589(+)$1	223	3	6	9.0000
GAG	chr21:34923617-34923860(+)$1	243	11	14	9.0000
GAG	chr19:1556446-1556662(-)$1	216	87	90	9.0000
GAG	chr11:57564098-57564315(+)$1	217	121	124	9.0000
GAG	chr1:19420355-19420576(-)$1	221	73	76	9.0000
GAG	chr1:40697142-40697367(+)$1	225	64	67	9.0000
GAG	chr10:75305262-75305481(-)$1	219	177	180	9.0000
GAG	chr2:60689014-60689237(-)$1	223	0	3	9.0000
GAG	chr20:35661087-35661310(-)$1	223	49	52	9.0000
GAG	chr17:59878534-59878753(-)$1	219	66	69	9.0000
GAG	chr7:129761905-129762124(+)$1	219	25	28	9.0000
GAG	chr10:88220090-88220309(-)$1	219	83	86	9.0000
GAG	chr12:49433621-49433841(-)$1	220	95	98	9.0000
GAG	chr15:42742783-42743001(-)$1	218	51	54	9.0000
GAG	chr1:28601269-28601487(+)$1	218	117	120	9.0000
GAG	chr5:167985977-167986195(-)$1	218	43	46	9.0000
GAG	chr19:40318890-40319116(-)$1	226	66	69	9.0000
GAG	chr1:16260114-16260335(+)$1	221	96	99	9.0000
GAG	chr19:37238756-37238967(-)$1	211	41	44	9.0000
GAG	chr6:7189368-7189591(+)$1	223	39	42	9.0000
GAG	chr10:28884805-28885024(+)$1	219	96	99	9.0000
GAG	chr14:55510114-55510332(+)$1	218	157	160	9.0000
GAG	chr12:116420258-116420484(-)$1	226	4	7	9.0000
GAG	chr16:4029048-4029266(-)$1	218	6	9	9.0000
GAG	chr19:42583607-42583827(+)$1	220	32	35	9.0000
GAG	chr13:108862488-108862714(-)$1	226	88	91	9.0000
GAG	chr19:47646659-47646884(+)$1	225	168	171	9.0000
GAG	chr17:8169089-8169308(+)$1	219	26	29	9.0000
GAG	chr17:7405172-7405405(+)$1	233	9	12	9.0000

#otherMatches

#Struct PSSM
!cc	chr12:51074385-51074607(+)$1	222	12	15	9.0000
ggg	chr6:32944335-32944561(+)$1	226	89	92	9.0000
HHH	chr17:38457020-38457239(+)$1	219	73	76	9.0000
III	chr17:38289782-38289999(+)$1	217	16	19	9.0000
ddd	chr12:113596702-113596913(-)$1	211	38	41	9.0000
eee	chr17:78305774-78305995(+)$1	221	40	43	9.0000
d$$	chr1:153914332-153914549(-)$1	217	14	17	9.0000
fff	chr7:56120035-56120252(+)$1	217	96	99	9.0000
A{G	chr6:31600442-31600659(+)$1	217	4	7	9.0000
cce	chr3:182987974-182988196(+)$1	222	23	26	9.0000
QQQ	chr11:763817-764034(+)$1	217	18	21	9.0000
eee	chr10:88277228-88277447(-)$1	219	29	32	9.0000
===	chr18:55283065-55283285(-)$1	220	9	12	9.0000
hhh	chr3:172534391-172534615(+)$1	224	167	170	9.0000
fff	chr5:108713821-108714038(-)$1	217	46	49	9.0000
III	chr3:47887823-47888044(+)$1	221	9	12	9.0000
ddd	chr5:112178665-112178882(+)$1	217	171	174	9.0000
fff	chr12:116424036-116424253(-)$1	217	57	60	9.0000
ddd	chr1:214803878-214804094(+)$1	216	40	43	9.0000
ccc	chr17:7405210-7405436(+)$1	226	38	41	9.0000
c]b	chr7:30634604-30634822(+)$1	218	88	91	9.0000
ddd	chr14:95581904-95582122(-)$1	218	3	6	9.0000
ppc	chr1:54238005-54238224(-)$1	219	165	168	9.0000
ggg	chr16:47117570-47117788(-)$1	218	91	94	9.0000
fff	chr16:71319239-71319465(-)$1	226	84	87	9.0000
oob	chr19:33183065-33183275(+)$1	210	158	161	9.0000
iii	chr13:77661622-77661843(-)$1	221	0	3	9.0000
EEE	chr13:67800998-67801217(-)$1	219	22	25	9.0000
ddd	chr7:72873903-72874123(-)$1	220	8	11	9.0000
]ff	chr2:61558339-61558556(-)$1	217	119	122	9.0000
{DD	chr19:24309867-24310098(+)$1	231	55	58	9.0000
CCC	chr11:120348783-120348999(+)$1	216	84	87	9.0000
hhh	chr6:52144264-52144488(-)$1	224	30	33	9.0000
iii	chr13:31205338-31205558(+)$1	220	47	50	9.0000
c]g	chr9:35060950-35061165(-)$1	215	43	46	9.0000
fff	chr15:70960152-70960377(-)$1	225	115	118	9.0000
!cc	chr1:19518621-19518839(-)$1	218	91	94	9.0000
DDD	chr17:7406386-7406607(+)$1	221	15	18	9.0000
FFF	chr14:53325062-53325282(-)$1	220	23	26	9.0000
GGG	chr2:10187679-10187899(+)$1	220	27	30	9.0000
:::	chr19:13051060-13051278(+)$1	218	2	5	9.0000
fff	chr19:56179781-56180002(+)$1	221	11	14	9.0000
:::	chr1:197059272-197059488(-)$1	216	57	60	9.0000
FFF	chr18:9256288-9256507(+)$1	219	65	68	9.0000
G{B	chr16:58577594-58577816(-)$1	222	78	81	9.0000
eee	chr21:34926248-34926499(+)$1	251	57	60	9.0000
ccc	chr12:7079302-7079525(-)$1	223	42	45	9.0000
:::	chr5:56180522-56180741(+)$1	219	23	26	9.0000
BBY	chr12:49440024-49440244(-)$1	220	204	207	9.0000
c%%	chr2:48026200-48026420(+)$1	220	44	47	9.0000
hhh	chrX:41202897-41203127(+)$1	230	61	64	9.0000
ddd	chr8:145011056-145011275(-)$1	219	17	20	9.0000
OOO	chr1:229772501-229772713(+)$1	212	9	12	9.0000
f!!	chr19:39214588-39214806(+)$1	218	6	9	9.0000
!cc	chr17:37006607-37006828(-)$1	221	10	13	9.0000
C{C	chrX:153590826-153591043(-)$1	217	2	5	9.0000
GGf	chr15:75498412-75498637(+)$1	225	40	43	9.0000
###	chr10:32582533-32582753(-)$1	220	32	35	9.0000
cc[	chr2:73476131-73476356(+)$1	225	11	14	9.0000
eee	chr12:14613742-14613960(+)$1	218	2	5	9.0000
mmd	chr1:39926249-39926470(+)$1	221	7	10	9.0000
EEE	chr2:61722569-61722788(-)$1	219	196	199	9.0000
bb4	chr14:60073996-60074214(-)$1	218	56	59	9.0000
FFF	chr6:31508067-31508291(-)$1	224	6	9	9.0000
::C	chr19:37643373-37643595(-)$1	222	11	14	9.0000
eee	chr1:227842924-227843149(+)$1	225	60	63	9.0000
GGG	chr10:63852366-63852589(+)$1	223	3	6	9.0000
"""	chr21:34923617-34923860(+)$1	243	11	14	9.0000
a]c	chr19:1556446-1556662(-)$1	216	87	90	9.0000
}EE	chr11:57564098-57564315(+)$1	217	121	124	9.0000
hhh	chr1:19420355-19420576(-)$1	221	73	76	9.0000
[bb	chr1:40697142-40697367(+)$1	225	64	67	9.0000
eee	chr10:75305262-75305481(-)$1	219	177	180	9.0000
:::	chr2:60689014-60689237(-)$1	223	0	3	9.0000
mmm	chr20:35661087-35661310(-)$1	223	49	52	9.0000
]bb	chr17:59878534-59878753(-)$1	219	66	69	9.0000
[dd	chr7:129761905-129762124(+)$1	219	25	28	9.0000
666	chr10:88220090-88220309(-)$1	219	83	86	9.0000
f::	chr12:49433621-49433841(-)$1	220	95	98	9.0000
ccc	chr15:42742783-42743001(-)$1	218	51	54	9.0000
llf	chr1:28601269-28601487(+)$1	218	117	120	9.0000
ggg	chr5:167985977-167986195(-)$1	218	43	46	9.0000
ddd	chr19:40318890-40319116(-)$1	226	66	69	9.0000
bb]	chr1:16260114-16260335(+)$1	221	96	99	9.0000
eee	chr19:37238756-37238967(-)$1	211	41	44	9.0000
[a[	chr6:7189368-7189591(+)$1	223	39	42	9.0000
[hh	chr10:28884805-28885024(+)$1	219	96	99	9.0000
ee]	chr14:55510114-55510332(+)$1	218	157	160	9.0000
:DD	chr12:116420258-116420484(-)$1	226	4	7	9.0000
EEE	chr16:4029048-4029266(-)$1	218	6	9	9.0000
e[b	chr19:42583607-42583827(+)$1	220	32	35	9.0000
[an	chr13:108862488-108862714(-)$1	226	88	91	9.0000
::D	chr19:47646659-47646884(+)$1	225	168	171	9.0000
ddd	chr17:8169089-8169308(+)$1	219	26	29	9.0000
GGe	chr17:7405172-7405405(+)$1	233	9	12	9.0000

#DB
.((	chr12:51074385-51074607(+)$1	1	12	15	9.0000
(((	chr6:32944335-32944561(+)$1	1	89	92	9.0000
(((	chr17:38457020-38457239(+)$1	1	73	76	9.0000
(((	chr17:38289782-38289999(+)$1	1	16	19	9.0000
(((	chr12:113596702-113596913(-)$1	1	38	41	9.0000
(((	chr17:78305774-78305995(+)$1	1	40	43	9.0000
(..	chr1:153914332-153914549(-)$1	1	14	17	9.0000
(((	chr7:56120035-56120252(+)$1	1	96	99	9.0000
(.(	chr6:31600442-31600659(+)$1	1	4	7	9.0000
)))	chr3:182987974-182988196(+)$1	1	23	26	9.0000
...	chr11:763817-764034(+)$1	1	18	21	9.0000
(((	chr10:88277228-88277447(-)$1	1	29	32	9.0000
(((	chr18:55283065-55283285(-)$1	1	9	12	9.0000
(((	chr3:172534391-172534615(+)$1	1	167	170	9.0000
(((	chr5:108713821-108714038(-)$1	1	46	49	9.0000
(((	chr3:47887823-47888044(+)$1	1	9	12	9.0000
)))	chr5:112178665-112178882(+)$1	1	171	174	9.0000
)))	chr12:116424036-116424253(-)$1	1	57	60	9.0000
)))	chr1:214803878-214804094(+)$1	1	40	43	9.0000
(((	chr17:7405210-7405436(+)$1	1	38	41	9.0000
).)	chr7:30634604-30634822(+)$1	1	88	91	9.0000
(((	chr14:95581904-95582122(-)$1	1	3	6	9.0000
..)	chr1:54238005-54238224(-)$1	1	165	168	9.0000
(((	chr16:47117570-47117788(-)$1	1	91	94	9.0000
)))	chr16:71319239-71319465(-)$1	1	84	87	9.0000
..)	chr19:33183065-33183275(+)$1	1	158	161	9.0000
(((	chr13:77661622-77661843(-)$1	1	0	3	9.0000
(((	chr13:67800998-67801217(-)$1	1	22	25	9.0000
(((	chr7:72873903-72874123(-)$1	1	8	11	9.0000
.))	chr2:61558339-61558556(-)$1	1	119	122	9.0000
.((	chr19:24309867-24310098(+)$1	1	55	58	9.0000
)))	chr11:120348783-120348999(+)$1	1	84	87	9.0000
)))	chr6:52144264-52144488(-)$1	1	30	33	9.0000
(((	chr13:31205338-31205558(+)$1	1	47	50	9.0000
).)	chr9:35060950-35061165(-)$1	1	43	46	9.0000
)))	chr15:70960152-70960377(-)$1	1	115	118	9.0000
.((	chr1:19518621-19518839(-)$1	1	91	94	9.0000
(((	chr17:7406386-7406607(+)$1	1	15	18	9.0000
(((	chr14:53325062-53325282(-)$1	1	23	26	9.0000
(((	chr2:10187679-10187899(+)$1	1	27	30	9.0000
...	chr19:13051060-13051278(+)$1	1	2	5	9.0000
(((	chr19:56179781-56180002(+)$1	1	11	14	9.0000
...	chr1:197059272-197059488(-)$1	1	57	60	9.0000
(((	chr18:9256288-9256507(+)$1	1	65	68	9.0000
(.(	chr16:58577594-58577816(-)$1	1	78	81	9.0000
(((	chr21:34926248-34926499(+)$1	1	57	60	9.0000
)))	chr12:7079302-7079525(-)$1	1	42	45	9.0000
...	chr5:56180522-56180741(+)$1	1	23	26	9.0000
)).	chr12:49440024-49440244(-)$1	1	204	207	9.0000
(..	chr2:48026200-48026420(+)$1	1	44	47	9.0000
(((	chrX:41202897-41203127(+)$1	1	61	64	9.0000
(((	chr8:145011056-145011275(-)$1	1	17	20	9.0000
...	chr1:229772501-229772713(+)$1	1	9	12	9.0000
(..	chr19:39214588-39214806(+)$1	1	6	9	9.0000
.((	chr17:37006607-37006828(-)$1	1	10	13	9.0000
(.(	chrX:153590826-153591043(-)$1	1	2	5	9.0000
(((	chr15:75498412-75498637(+)$1	1	40	43	9.0000
...	chr10:32582533-32582753(-)$1	1	32	35	9.0000
((.	chr2:73476131-73476356(+)$1	1	11	14	9.0000
(((	chr12:14613742-14613960(+)$1	1	2	5	9.0000
..)	chr1:39926249-39926470(+)$1	1	7	10	9.0000
)))	chr2:61722569-61722788(-)$1	1	196	199	9.0000
)).	chr14:60073996-60074214(-)$1	1	56	59	9.0000
(((	chr6:31508067-31508291(-)$1	1	6	9	9.0000
..(	chr19:37643373-37643595(-)$1	1	11	14	9.0000
(((	chr1:227842924-227843149(+)$1	1	60	63	9.0000
(((	chr10:63852366-63852589(+)$1	1	3	6	9.0000
...	chr21:34923617-34923860(+)$1	1	11	14	9.0000
).)	chr19:1556446-1556662(-)$1	1	87	90	9.0000
.))	chr11:57564098-57564315(+)$1	1	121	124	9.0000
)))	chr1:19420355-19420576(-)$1	1	73	76	9.0000
.((	chr1:40697142-40697367(+)$1	1	64	67	9.0000
)))	chr10:75305262-75305481(-)$1	1	177	180	9.0000
...	chr2:60689014-60689237(-)$1	1	0	3	9.0000
...	chr20:35661087-35661310(-)$1	1	49	52	9.0000
.))	chr17:59878534-59878753(-)$1	1	66	69	9.0000
.((	chr7:129761905-129762124(+)$1	1	25	28	9.0000
...	chr10:88220090-88220309(-)$1	1	83	86	9.0000
)..	chr12:49433621-49433841(-)$1	1	95	98	9.0000
(((	chr15:42742783-42743001(-)$1	1	51	54	9.0000
..)	chr1:28601269-28601487(+)$1	1	117	120	9.0000
(((	chr5:167985977-167986195(-)$1	1	43	46	9.0000
(((	chr19:40318890-40319116(-)$1	1	66	69	9.0000
)).	chr1:16260114-16260335(+)$1	1	96	99	9.0000
)))	chr19:37238756-37238967(-)$1	1	41	44	9.0000
.(.	chr6:7189368-7189591(+)$1	1	39	42	9.0000
.((	chr10:28884805-28885024(+)$1	1	96	99	9.0000
)).	chr14:55510114-55510332(+)$1	1	157	160	9.0000
.((	chr12:116420258-116420484(-)$1	1	4	7	9.0000
(((	chr16:4029048-4029266(-)$1	1	6	9	9.0000
(.(	chr19:42583607-42583827(+)$1	1	32	35	9.0000
.(.	chr13:108862488-108862714(-)$1	1	88	91	9.0000
..)	chr19:47646659-47646884(+)$1	1	168	171	9.0000
(((	chr17:8169089-8169308(+)$1	1	26	29	9.0000
(((	chr17:7405172-7405405(+)$1	1	9	12	9.0000

#PSSM
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	

#score	855.0000000000002
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUUUUUU	chr17:17714661-17714901(-)$1	240	166	175	19.6851
UUUACUUUU	chr3:179110162-179110402(+)$1	240	214	223	18.1111
UUUAUAUUU	chr12:4668757-4669097(+)$1	340	279	288	17.5555
UUUAUUAUU	chr2:27664774-27665022(+)$1	248	14	23	17.9259
UGUAUUUUU	chr13:96234036-96234276(-)$1	240	84	93	17.4629
UUUUUUUUU	chr17:45699631-45699876(+)$1	245	160	169	19.6851
UUUGUGUUU	chr8:104343484-104343764(+)$1	280	37	46	14.9629
UUUUUUUUU	chr1:65878939-65879214(+)$1	275	246	255	19.6851
UUUUUUUUU	chr18:59712791-59713032(-)$1	241	113	122	19.6851
GUUAUUUUU	chr5:130538390-130538637(+)$1	247	1	10	17.6481
UUUACUUUU	chr17:57075525-57075765(-)$1	240	147	156	18.1111
UUUGUCUUU	chrX:53964051-53964291(-)$1	240	178	187	15.0555
UUUAUUAUU	chr13:25822400-25822640(-)$1	240	17	26	17.9259
Uuuauuauu	chr17:46652967-46653247(-)$1	280	176	185	17.9259
UUGAUUUUU	chr7:25161440-25161680(-)$1	240	21	30	17.4629
UUUUUUUUU	chr14:56766112-56766352(+)$1	240	215	224	19.6851
UUUAGUUUU	chr4:10443572-10443815(-)$1	243	8	17	17.7407
UUUUCUUUU	chrX:153214182-153214522(-)$1	340	165	174	15.8888
UUUAUUUUA	chr6:108365582-108365854(-)$1	272	137	146	17.1851
UCUAUUUUU	chrX:47495313-47495553(-)$1	240	155	164	17.6481
UUUACUUUU	chr20:11906599-11906852(+)$1	253	134	143	18.1111
UUGAUUUUU	chr8:57875578-57875819(-)$1	241	21	30	17.4629
UUUGAUUUU	chr9:36677219-36677459(+)$1	240	186	195	15.3333
UUUUUUUUU	chr5:122359278-122359518(-)$1	240	39	48	19.6851
UUUAUUUUG	chr1:226819729-226819969(-)$1	240	163	172	17.1851
UUUUUUUUU	chr1:236371995-236372235(+)$1	240	43	52	19.6851
UUUAAUUUU	chr3:45719428-45719708(+)$1	280	240	249	17.8333
UUUUUUUUU	chr10:71911623-71911868(-)$1	245	58	67	19.6851
UUUAUUUUU	chr2:203425448-203425693(+)$1	245	119	128	21.9074
UUUUUUUUU	chr11:68458442-68458723(+)$1	281	150	159	19.6851
UUUAUUCUU	chr3:120115072-120115392(-)$1	320	279	288	17.8333
CUUAUUUUU	chr6:10982420-10982660(-)$1	240	10	19	17.5555
UUUAUUUUU	chr12:50872506-50872787(+)$1	281	227	236	21.9074
UCUAUUUUU	chr10:30305979-30306220(-)$1	241	117	126	17.6481
UUUAUUUUU	chrX:133560351-133560633(+)$1	282	252	261	21.9074
AUUAUUUUU	chr17:29110685-29110925(-)$1	240	57	66	17.7407
UUUGUUUUU	chr10:90974367-90974607(-)$1	240	123	132	19.4074
UUUAUUCUU	chr14:70838562-70838813(-)$1	251	4	13	17.8333
UUUAUAUUU	chr3:9515042-9515303(+)$1	261	184	193	17.5555
UUUAUUUUU	chr5:137841946-137842187(-)$1	241	129	138	21.9074
UUUACUUUU	chr10:27484513-27484753(-)$1	240	45	54	18.1111
AUUAUUUUU	chr21:18938298-18938538(+)$1	240	99	108	17.7407
UUUAUUAUU	chr17:691178-691418(+)$1	240	93	102	17.9259
UCUGUUUUU	chr18:45366879-45367123(-)$1	244	140	149	15.1481
AUUAUUUUU	chr12:56507094-56507334(+)$1	240	64	73	17.7407
UUGAUUUUU	chr1:67468303-67468543(-)$1	240	121	130	17.4629
UUUAUUUUU	chr13:113139768-113140008(-)$1	240	190	199	21.9074
uuuauuuuu	chr8:30643076-30643332(-)$1	256	235	244	21.9074
UAUAUUUUU	chr14:96986358-96986603(+)$1	245	221	230	17.4629
UUUAUUCUU	chr17:2938389-2938630(+)$1	241	58	67	17.8333
GUUGUUUUU	chr6:34556312-34556636(-)$1	324	4	13	15.1481
UUUGUCUUU	chr3:150126986-150127226(+)$1	240	59	68	15.0555
uuuuuuuuu	chr2:128604217-128604458(-)$1	241	226	235	19.6851

#otherMatches

#Struct PSSM
DDD}IIIII	chr14:50885481-50885723(-)$1	242	123	132	19.4074
^^^^^^^^^	chr17:17714661-17714901(-)$1	240	166	175	19.6851
::::::::J	chr3:179110162-179110402(+)$1	240	214	223	18.1111
lllgggggg	chr12:4668757-4669097(+)$1	340	279	288	17.5555
grrrrrrrr	chr2:27664774-27665022(+)$1	248	14	23	17.9259
]iiiiiiii	chr13:96234036-96234276(-)$1	240	84	93	17.4629
vvvvvvvvv	chr17:45699631-45699876(+)$1	245	160	169	19.6851
gggqqqqqq	chr8:104343484-104343764(+)$1	280	37	46	14.9629
:::::::::	chr1:65878939-65879214(+)$1	275	246	255	19.6851
gggggg]hh	chr18:59712791-59713032(-)$1	241	113	122	19.6851
:::::::::	chr5:130538390-130538637(+)$1	247	1	10	17.6481
EE}FFFFFF	chr17:57075525-57075765(-)$1	240	147	156	18.1111
^^^^^^^^^	chrX:53964051-53964291(-)$1	240	178	187	15.0555
[ccc[eeee	chr13:25822400-25822640(-)$1	240	17	26	17.9259
::hhhhhhh	chr17:46652967-46653247(-)$1	280	176	185	17.9259
HHHUUUUUU	chr7:25161440-25161680(-)$1	240	21	30	17.4629
ooooooeee	chr14:56766112-56766352(+)$1	240	215	224	19.6851
::::JJJJJ	chr4:10443572-10443815(-)$1	243	8	17	17.7407
^^^^^^^^^	chrX:153214182-153214522(-)$1	340	165	174	15.8888
eeeeellle	chr6:108365582-108365854(-)$1	272	137	146	17.1851
oeeeee333	chrX:47495313-47495553(-)$1	240	155	164	17.6481
:ddddmmmm	chr20:11906599-11906852(+)$1	253	134	143	18.1111
nn=======	chr8:57875578-57875819(-)$1	241	21	30	17.4629
ffffmmmmf	chr9:36677219-36677459(+)$1	240	186	195	15.3333
::::eeeee	chr5:122359278-122359518(-)$1	240	39	48	19.6851
eeeeooooo	chr1:226819729-226819969(-)$1	240	163	172	17.1851
nnnnngggg	chr1:236371995-236372235(+)$1	240	43	52	19.6851
:::::::::	chr3:45719428-45719708(+)$1	280	240	249	17.8333
[bb!!cccm	chr10:71911623-71911868(-)$1	245	58	67	19.6851
^^^^^^^^^	chr2:203425448-203425693(+)$1	245	119	128	21.9074
mmmmdddd3	chr11:68458442-68458723(+)$1	281	150	159	19.6851
:::::::::	chr3:120115072-120115392(-)$1	320	279	288	17.8333
gggggggmm	chr6:10982420-10982660(-)$1	240	10	19	17.5555
gg:::::::	chr12:50872506-50872787(+)$1	281	227	236	21.9074
cc666666f	chr10:30305979-30306220(-)$1	241	117	126	17.6481
4444=====	chrX:133560351-133560633(+)$1	282	252	261	21.9074
[cccmmmmc	chr17:29110685-29110925(-)$1	240	57	66	17.7407
F========	chr10:90974367-90974607(-)$1	240	123	132	19.4074
fffff[ggg	chr14:70838562-70838813(-)$1	251	4	13	17.8333
d::::gggg	chr3:9515042-9515303(+)$1	261	184	193	17.5555
sssssssss	chr5:137841946-137842187(-)$1	241	129	138	21.9074
vvhhhhhhh	chr10:27484513-27484753(-)$1	240	45	54	18.1111
ff333eeee	chr21:18938298-18938538(+)$1	240	99	108	17.7407
GGGGGG{CC	chr17:691178-691418(+)$1	240	93	102	17.9259
dddd!!ddd	chr18:45366879-45367123(-)$1	244	140	149	15.1481
g::::::::	chr12:56507094-56507334(+)$1	240	64	73	17.7407
"ccc####=	chr1:67468303-67468543(-)$1	240	121	130	17.4629
ggggg%%%%	chr13:113139768-113140008(-)$1	240	190	199	21.9074
ggggggg]b	chr8:30643076-30643332(-)$1	256	235	244	21.9074
eee:GGGGG	chr14:96986358-96986603(+)$1	245	221	230	17.4629
::::ddddm	chr17:2938389-2938630(+)$1	241	58	67	17.8333
:::::::::	chr6:34556312-34556636(-)$1	324	4	13	15.1481
rrrddddff	chr3:150126986-150127226(+)$1	240	59	68	15.0555
ffff]hhhh	chr2:128604217-128604458(-)$1	241	226	235	19.6851

#DB
))).)))))	chr14:50885481-50885723(-)$1	1	123	132	19.4074
.........	chr17:17714661-17714901(-)$1	1	166	175	19.6851
........)	chr3:179110162-179110402(+)$1	1	214	223	18.1111
...))))))	chr12:4668757-4669097(+)$1	1	279	288	17.5555
(........	chr2:27664774-27665022(+)$1	1	14	23	17.9259
.))))))))	chr13:96234036-96234276(-)$1	1	84	93	17.4629
.........	chr17:45699631-45699876(+)$1	1	160	169	19.6851
(((......	chr8:104343484-104343764(+)$1	1	37	46	14.9629
.........	chr1:65878939-65879214(+)$1	1	246	255	19.6851
)))))).))	chr18:59712791-59713032(-)$1	1	113	122	19.6851
.........	chr5:130538390-130538637(+)$1	1	1	10	17.6481
)).))))))	chr17:57075525-57075765(-)$1	1	147	156	18.1111
.........	chrX:53964051-53964291(-)$1	1	178	187	15.0555
.(((.((((	chr13:25822400-25822640(-)$1	1	17	26	17.9259
..(((((((	chr17:46652967-46653247(-)$1	1	176	185	17.9259
(((......	chr7:25161440-25161680(-)$1	1	21	30	17.4629
......)))	chr14:56766112-56766352(+)$1	1	215	224	19.6851
....(((((	chr4:10443572-10443815(-)$1	1	8	17	17.7407
.........	chrX:153214182-153214522(-)$1	1	165	174	15.8888
(((((...)	chr6:108365582-108365854(-)$1	1	137	146	17.1851
.)))))...	chrX:47495313-47495553(-)$1	1	155	164	17.6481
.((((....	chr20:11906599-11906852(+)$1	1	134	143	18.1111
..)))))))	chr8:57875578-57875819(-)$1	1	21	30	17.4629
((((....)	chr9:36677219-36677459(+)$1	1	186	195	15.3333
....(((((	chr5:122359278-122359518(-)$1	1	39	48	19.6851
((((.....	chr1:226819729-226819969(-)$1	1	163	172	17.1851
.....))))	chr1:236371995-236372235(+)$1	1	43	52	19.6851
.........	chr3:45719428-45719708(+)$1	1	240	249	17.8333
.((..(((.	chr10:71911623-71911868(-)$1	1	58	67	19.6851
.........	chr2:203425448-203425693(+)$1	1	119	128	21.9074
....)))).	chr11:68458442-68458723(+)$1	1	150	159	19.6851
.........	chr3:120115072-120115392(-)$1	1	279	288	17.8333
(((((((..	chr6:10982420-10982660(-)$1	1	10	19	17.5555
)).......	chr12:50872506-50872787(+)$1	1	227	236	21.9074
))......)	chr10:30305979-30306220(-)$1	1	117	126	17.6481
....)))))	chrX:133560351-133560633(+)$1	1	252	261	21.9074
.(((....)	chr17:29110685-29110925(-)$1	1	57	66	17.7407
(((((((((	chr10:90974367-90974607(-)$1	1	123	132	19.4074
(((((.(((	chr14:70838562-70838813(-)$1	1	4	13	17.8333
)....((((	chr3:9515042-9515303(+)$1	1	184	193	17.5555
.........	chr5:137841946-137842187(-)$1	1	129	138	21.9074
..)))))))	chr10:27484513-27484753(-)$1	1	45	54	18.1111
))...))))	chr21:18938298-18938538(+)$1	1	99	108	17.7407
((((((.((	chr17:691178-691418(+)$1	1	93	102	17.9259
((((..(((	chr18:45366879-45367123(-)$1	1	140	149	15.1481
)........	chr12:56507094-56507334(+)$1	1	64	73	17.7407
.(((....(	chr1:67468303-67468543(-)$1	1	121	130	17.4629
(((((....	chr13:113139768-113140008(-)$1	1	190	199	21.9074
))))))).)	chr8:30643076-30643332(-)$1	1	235	244	21.9074
))).)))))	chr14:96986358-96986603(+)$1	1	221	230	17.4629
....((((.	chr17:2938389-2938630(+)$1	1	58	67	17.8333
.........	chr6:34556312-34556636(-)$1	1	4	13	15.1481
...))))))	chr3:150126986-150127226(+)$1	1	59	68	15.0555
)))).))))	chr2:128604217-128604458(-)$1	1	226	235	19.6851

#PSSM
U : 0.85	A : 0.05	G : 0.03	u : 0.03	C : 0.01	
U : 0.85	u : 0.05	C : 0.05	G : 0.01	A : 0.01	
U : 0.88	u : 0.05	G : 0.05	
A : 0.61	U : 0.18	G : 0.14	a : 0.03	u : 0.01	
U : 0.79	C : 0.09	u : 0.05	A : 0.03	G : 0.01	
U : 0.85	u : 0.05	A : 0.03	C : 0.03	G : 0.01	
U : 0.83	A : 0.05	C : 0.05	u : 0.03	a : 0.01	
U : 0.94	u : 0.05	
U : 0.90	u : 0.05	A : 0.01	G : 0.01	

#score	987.4444444444434
#seq	54
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m2_run2.nuc.txt

#NT
aaga	chr8:26365929-26366187(-)$1	258	75	79	11.9999
AAGA	chr5:149385952-149386169(+)$1	217	62	66	11.9999
AAGA	chr17:1747851-1748078(+)$1	227	59	63	11.9999
AAGA	chr1:16257211-16257544(+)$1	333	12	16	11.9999
AAGA	chr13:26789393-26789616(-)$1	223	97	101	11.9999
AAGA	chr14:39502336-39502557(-)$1	221	85	89	11.9999
AAGA	chr1:155931377-155931607(-)$1	230	131	135	11.9999
AAGA	chr4:53497134-53497353(-)$1	219	67	71	11.9999
AAGA	chrX:39932204-39932432(-)$1	228	49	53	11.9999
AAGA	chr11:118923010-118923237(-)$1	227	10	14	11.9999
AAGA	chr3:24009387-24009611(+)$1	224	85	89	11.9999
AAGA	chr1:246823447-246823664(+)$1	217	22	26	11.9999
AAGA	chr4:140281593-140281820(+)$1	227	165	169	11.9999
AAGA	chr8:38153345-38153577(-)$1	232	31	35	11.9999
AAGA	chr3:196214194-196214419(-)$1	225	1	5	11.9999
AAGA	chr12:104337416-104337666(+)$1	250	34	38	11.9999
AAGA	chr14:91791129-91791339(-)$1	210	87	91	11.9999
AAGA	chr20:55803219-55803439(-)$1	220	27	31	11.9999
AAGA	chrX:41073730-41073985(+)$1	255	101	105	11.9999
AAGA	chr5:65466655-65466866(+)$1	211	17	21	11.9999
AAGA	chr4:71691791-71692020(-)$1	229	166	170	11.9999
AAGA	chr15:91512671-91512892(-)$1	221	66	70	11.9999
AAGA	chr7:91948663-91948886(+)$1	223	26	30	11.9999
AAGA	chr3:178748590-178748816(-)$1	226	44	48	11.9999
AAGA	chr20:34060422-34060644(+)$1	222	85	89	11.9999
AAGA	chr7:114655653-114655892(+)$1	239	85	89	11.9999
AAGA	chr8:21832116-21832379(+)$1	263	210	214	11.9999
AAGA	chr17:26943645-26943864(-)$1	219	178	182	11.9999
AAGA	chr14:45579817-45580030(+)$1	213	10	14	11.9999
AAGA	chr5:16673762-16673994(-)$1	232	60	64	11.9999
AAGA	chr7:127979710-127979936(-)$1	226	139	143	11.9999
AAGA	chr14:71540172-71540390(+)$1	218	140	144	11.9999
AAGA	chr4:141580724-141580953(-)$1	229	134	138	11.9999
AAGA	chr9:135201790-135202005(-)$1	215	128	132	11.9999
AAGA	chr20:17950482-17950706(+)$1	224	23	27	11.9999
AAGA	chr21:35469337-35469572(+)$1	235	84	88	11.9999
AAGA	chr17:61908612-61908837(+)$1	225	35	39	11.9999
AAGA	chr5:90119163-90119386(+)$1	223	86	90	11.9999
AAGA	chr10:75530675-75530953(+)$1	278	56	60	11.9999
AAGA	chr10:22880532-22880751(-)$1	219	38	42	11.9999
AAGA	chr17:41244777-41244998(-)$1	221	86	90	11.9999
AAGA	chr16:78148928-78149141(+)$1	213	28	32	11.9999
AAGA	chr17:60088049-60088278(-)$1	229	127	131	11.9999
AAGA	chr4:126369696-126369909(+)$1	213	96	100	11.9999
AAGA	chr12:76739686-76739910(-)$1	224	19	23	11.9999
AAGA	chr7:128655007-128655249(-)$1	242	119	123	11.9999
AAGA	chrX:69521774-69521994(+)$1	220	124	128	11.9999
AAGA	chr5:71492540-71492803(+)$1	263	90	94	11.9999
AAGA	chr10:120817449-120817675(-)$1	226	2	6	11.9999
AAGA	chr5:78586866-78587081(+)$1	215	115	119	11.9999
AAGA	chr5:179044917-179045133(-)$1	216	139	143	11.9999
AAGA	chr9:32542803-32543065(-)$1	262	82	86	11.9999
AAGA	chr17:27778564-27778793(+)$1	229	63	67	11.9999
AAGA	chr20:40050382-40050633(-)$1	251	215	219	11.9999
AAGA	chrX:70469374-70469597(-)$1	223	197	201	11.9999
AAGA	chr14:21862051-21862265(-)$1	214	31	35	11.9999
AAGA	chr1:90049896-90050126(+)$1	230	59	63	11.9999
AAGA	chr5:132216557-132216859(-)$1	302	201	205	11.9999
AAGA	chr1:173772462-173772680(-)$1	218	143	147	11.9999
AAGA	chr12:88479732-88479947(-)$1	215	1	5	11.9999
AAGA	chr19:2853118-2853341(+)$1	223	12	16	11.9999
AAGA	chr4:87655834-87656067(+)$1	233	26	30	11.9999
AAGA	chr1:186310305-186310525(-)$1	220	32	36	11.9999
AAGA	chr3:49070463-49070678(-)$1	215	167	171	11.9999
AAGA	chr7:135302285-135302497(+)$1	212	204	208	11.9999
AAGA	chr11:9202407-9202629(-)$1	222	166	170	11.9999
AAGA	chr21:33074087-33074306(-)$1	219	6	10	11.9999
AAGA	chr2:232325131-232325343(-)$1	212	77	81	11.9999
AAGA	chr6:170870821-170871039(+)$1	218	160	164	11.9999
AAGA	chr2:64779869-64780090(+)$1	221	24	28	11.9999
AAGA	chr4:128812645-128812871(+)$1	226	28	32	11.9999
AAGA	chr17:42953264-42953523(-)$1	259	127	131	11.9999
AAGA	chr19:34900099-34900317(+)$1	218	90	94	11.9999
AAGA	chr21:45472125-45472343(+)$1	218	63	67	11.9999
AAGA	chr11:65298115-65298334(+)$1	219	29	33	11.9999
AAGA	chr10:79581584-79581812(-)$1	228	5	9	11.9999
AAGA	chr14:31604213-31604435(-)$1	222	97	101	11.9999
AAGA	chr12:125396185-125396407(-)$1	222	5	9	11.9999
AAGA	chr10:126686568-126686798(-)$1	230	95	99	11.9999
AAGA	chr15:78758627-78758859(+)$1	232	64	68	11.9999
AAGA	chr14:51381350-51381566(-)$1	216	192	196	11.9999
AAGA	chr16:3738964-3739190(-)$1	226	87	91	11.9999
AAGA	chr5:96066439-96066659(+)$1	220	54	58	11.9999

#otherMatches

#Struct PSSM
ccc"	chr7:151843607-151843831(-)$1	224	22	26	11.9999
2ddd	chr8:26365929-26366187(-)$1	258	75	79	11.9999
f[ee	chr5:149385952-149386169(+)$1	217	62	66	11.9999
>>>>	chr17:1747851-1748078(+)$1	227	59	63	11.9999
::DD	chr1:16257211-16257544(+)$1	333	12	16	11.9999
::dd	chr13:26789393-26789616(-)$1	223	97	101	11.9999
cccl	chr14:39502336-39502557(-)$1	221	85	89	11.9999
qbb]	chr1:155931377-155931607(-)$1	230	131	135	11.9999
bbmm	chr4:53497134-53497353(-)$1	219	67	71	11.9999
::::	chrX:39932204-39932432(-)$1	228	49	53	11.9999
DDKK	chr11:118923010-118923237(-)$1	227	10	14	11.9999
uuuu	chr3:24009387-24009611(+)$1	224	85	89	11.9999
oooo	chr1:246823447-246823664(+)$1	217	22	26	11.9999
e$$$	chr4:140281593-140281820(+)$1	227	165	169	11.9999
eeee	chr8:38153345-38153577(-)$1	232	31	35	11.9999
::::	chr3:196214194-196214419(-)$1	225	1	5	11.9999
eeee	chr12:104337416-104337666(+)$1	250	34	38	11.9999
"bb"	chr14:91791129-91791339(-)$1	210	87	91	11.9999
:fff	chr20:55803219-55803439(-)$1	220	27	31	11.9999
IIII	chrX:41073730-41073985(+)$1	255	101	105	11.9999
:::D	chr5:65466655-65466866(+)$1	211	17	21	11.9999
!a[d	chr4:71691791-71692020(-)$1	229	166	170	11.9999
ssss	chr15:91512671-91512892(-)$1	221	66	70	11.9999
IILL	chr7:91948663-91948886(+)$1	223	26	30	11.9999
hhuu	chr3:178748590-178748816(-)$1	226	44	48	11.9999
ffff	chr20:34060422-34060644(+)$1	222	85	89	11.9999
deee	chr7:114655653-114655892(+)$1	239	85	89	11.9999
oooo	chr8:21832116-21832379(+)$1	263	210	214	11.9999
iiii	chr17:26943645-26943864(-)$1	219	178	182	11.9999
ddA{	chr14:45579817-45580030(+)$1	213	10	14	11.9999
yyyy	chr5:16673762-16673994(-)$1	232	60	64	11.9999
$$cc	chr7:127979710-127979936(-)$1	226	139	143	11.9999
ffdd	chr14:71540172-71540390(+)$1	218	140	144	11.9999
gggg	chr4:141580724-141580953(-)$1	229	134	138	11.9999
:EEE	chr9:135201790-135202005(-)$1	215	128	132	11.9999
dddd	chr20:17950482-17950706(+)$1	224	23	27	11.9999
::::	chr21:35469337-35469572(+)$1	235	84	88	11.9999
:eee	chr17:61908612-61908837(+)$1	225	35	39	11.9999
ffff	chr5:90119163-90119386(+)$1	223	86	90	11.9999
a"""	chr10:75530675-75530953(+)$1	278	56	60	11.9999
gggg	chr10:22880532-22880751(-)$1	219	38	42	11.9999
e###	chr17:41244777-41244998(-)$1	221	86	90	11.9999
rrrr	chr16:78148928-78149141(+)$1	213	28	32	11.9999
cddd	chr17:60088049-60088278(-)$1	229	127	131	11.9999
6666	chr4:126369696-126369909(+)$1	213	96	100	11.9999
FFFF	chr12:76739686-76739910(-)$1	224	19	23	11.9999
b22=	chr7:128655007-128655249(-)$1	242	119	123	11.9999
555e	chrX:69521774-69521994(+)$1	220	124	128	11.9999
JJJJ	chr5:71492540-71492803(+)$1	263	90	94	11.9999
::::	chr10:120817449-120817675(-)$1	226	2	6	11.9999
A}CC	chr5:78586866-78587081(+)$1	215	115	119	11.9999
eeee	chr5:179044917-179045133(-)$1	216	139	143	11.9999
6666	chr9:32542803-32543065(-)$1	262	82	86	11.9999
llee	chr17:27778564-27778793(+)$1	229	63	67	11.9999
8888	chr20:40050382-40050633(-)$1	251	215	219	11.9999
B:::	chrX:70469374-70469597(-)$1	223	197	201	11.9999
JJJ:	chr14:21862051-21862265(-)$1	214	31	35	11.9999
::::	chr1:90049896-90050126(+)$1	230	59	63	11.9999
d::h	chr5:132216557-132216859(-)$1	302	201	205	11.9999
====	chr1:173772462-173772680(-)$1	218	143	147	11.9999
GGGG	chr12:88479732-88479947(-)$1	215	1	5	11.9999
qqqq	chr19:2853118-2853341(+)$1	223	12	16	11.9999
:a[e	chr4:87655834-87656067(+)$1	233	26	30	11.9999
annn	chr1:186310305-186310525(-)$1	220	32	36	11.9999
AFFF	chr3:49070463-49070678(-)$1	215	167	171	11.9999
GGGG	chr7:135302285-135302497(+)$1	212	204	208	11.9999
!ggg	chr11:9202407-9202629(-)$1	222	166	170	11.9999
iiii	chr21:33074087-33074306(-)$1	219	6	10	11.9999
::::	chr2:232325131-232325343(-)$1	212	77	81	11.9999
IIII	chr6:170870821-170871039(+)$1	218	160	164	11.9999
FFFF	chr2:64779869-64780090(+)$1	221	24	28	11.9999
uuuu	chr4:128812645-128812871(+)$1	226	28	32	11.9999
c]ee	chr17:42953264-42953523(-)$1	259	127	131	11.9999
tttt	chr19:34900099-34900317(+)$1	218	90	94	11.9999
::::	chr21:45472125-45472343(+)$1	218	63	67	11.9999
nbb2	chr11:65298115-65298334(+)$1	219	29	33	11.9999
pppp	chr10:79581584-79581812(-)$1	228	5	9	11.9999
[bbm	chr14:31604213-31604435(-)$1	222	97	101	11.9999
DDNN	chr12:125396185-125396407(-)$1	222	5	9	11.9999
[ddd	chr10:126686568-126686798(-)$1	230	95	99	11.9999
3ccc	chr15:78758627-78758859(+)$1	232	64	68	11.9999
ZZII	chr14:51381350-51381566(-)$1	216	192	196	11.9999
e$$$	chr16:3738964-3739190(-)$1	226	87	91	11.9999
ffff	chr5:96066439-96066659(+)$1	220	54	58	11.9999

#DB
(((.	chr7:151843607-151843831(-)$1	1	22	26	11.9999
.)))	chr8:26365929-26366187(-)$1	1	75	79	11.9999
(.((	chr5:149385952-149386169(+)$1	1	62	66	11.9999
....	chr17:1747851-1748078(+)$1	1	59	63	11.9999
..((	chr1:16257211-16257544(+)$1	1	12	16	11.9999
..((	chr13:26789393-26789616(-)$1	1	97	101	11.9999
(((.	chr14:39502336-39502557(-)$1	1	85	89	11.9999
.)).	chr1:155931377-155931607(-)$1	1	131	135	11.9999
((..	chr4:53497134-53497353(-)$1	1	67	71	11.9999
....	chrX:39932204-39932432(-)$1	1	49	53	11.9999
((..	chr11:118923010-118923237(-)$1	1	10	14	11.9999
....	chr3:24009387-24009611(+)$1	1	85	89	11.9999
....	chr1:246823447-246823664(+)$1	1	22	26	11.9999
(...	chr4:140281593-140281820(+)$1	1	165	169	11.9999
((((	chr8:38153345-38153577(-)$1	1	31	35	11.9999
....	chr3:196214194-196214419(-)$1	1	1	5	11.9999
))))	chr12:104337416-104337666(+)$1	1	34	38	11.9999
.((.	chr14:91791129-91791339(-)$1	1	87	91	11.9999
.(((	chr20:55803219-55803439(-)$1	1	27	31	11.9999
((((	chrX:41073730-41073985(+)$1	1	101	105	11.9999
...(	chr5:65466655-65466866(+)$1	1	17	21	11.9999
.(.(	chr4:71691791-71692020(-)$1	1	166	170	11.9999
....	chr15:91512671-91512892(-)$1	1	66	70	11.9999
((..	chr7:91948663-91948886(+)$1	1	26	30	11.9999
((..	chr3:178748590-178748816(-)$1	1	44	48	11.9999
((((	chr20:34060422-34060644(+)$1	1	85	89	11.9999
))))	chr7:114655653-114655892(+)$1	1	85	89	11.9999
....	chr8:21832116-21832379(+)$1	1	210	214	11.9999
))))	chr17:26943645-26943864(-)$1	1	178	182	11.9999
))(.	chr14:45579817-45580030(+)$1	1	10	14	11.9999
....	chr5:16673762-16673994(-)$1	1	60	64	11.9999
..((	chr7:127979710-127979936(-)$1	1	139	143	11.9999
))))	chr14:71540172-71540390(+)$1	1	140	144	11.9999
))))	chr4:141580724-141580953(-)$1	1	134	138	11.9999
.)))	chr9:135201790-135202005(-)$1	1	128	132	11.9999
((((	chr20:17950482-17950706(+)$1	1	23	27	11.9999
....	chr21:35469337-35469572(+)$1	1	84	88	11.9999
.(((	chr17:61908612-61908837(+)$1	1	35	39	11.9999
((((	chr5:90119163-90119386(+)$1	1	86	90	11.9999
(...	chr10:75530675-75530953(+)$1	1	56	60	11.9999
))))	chr10:22880532-22880751(-)$1	1	38	42	11.9999
(...	chr17:41244777-41244998(-)$1	1	86	90	11.9999
....	chr16:78148928-78149141(+)$1	1	28	32	11.9999
)(((	chr17:60088049-60088278(-)$1	1	127	131	11.9999
....	chr4:126369696-126369909(+)$1	1	96	100	11.9999
((((	chr12:76739686-76739910(-)$1	1	19	23	11.9999
)..)	chr7:128655007-128655249(-)$1	1	119	123	11.9999
...)	chrX:69521774-69521994(+)$1	1	124	128	11.9999
((((	chr5:71492540-71492803(+)$1	1	90	94	11.9999
....	chr10:120817449-120817675(-)$1	1	2	6	11.9999
).))	chr5:78586866-78587081(+)$1	1	115	119	11.9999
((((	chr5:179044917-179045133(-)$1	1	139	143	11.9999
....	chr9:32542803-32543065(-)$1	1	82	86	11.9999
..))	chr17:27778564-27778793(+)$1	1	63	67	11.9999
....	chr20:40050382-40050633(-)$1	1	215	219	11.9999
)...	chrX:70469374-70469597(-)$1	1	197	201	11.9999
(((.	chr14:21862051-21862265(-)$1	1	31	35	11.9999
....	chr1:90049896-90050126(+)$1	1	59	63	11.9999
)..(	chr5:132216557-132216859(-)$1	1	201	205	11.9999
))))	chr1:173772462-173772680(-)$1	1	143	147	11.9999
((((	chr12:88479732-88479947(-)$1	1	1	5	11.9999
....	chr19:2853118-2853341(+)$1	1	12	16	11.9999
.(.(	chr4:87655834-87656067(+)$1	1	26	30	11.9999
(...	chr1:186310305-186310525(-)$1	1	32	36	11.9999
))))	chr3:49070463-49070678(-)$1	1	167	171	11.9999
))))	chr7:135302285-135302497(+)$1	1	204	208	11.9999
.(((	chr11:9202407-9202629(-)$1	1	166	170	11.9999
((((	chr21:33074087-33074306(-)$1	1	6	10	11.9999
....	chr2:232325131-232325343(-)$1	1	77	81	11.9999
))))	chr6:170870821-170871039(+)$1	1	160	164	11.9999
((((	chr2:64779869-64780090(+)$1	1	24	28	11.9999
....	chr4:128812645-128812871(+)$1	1	28	32	11.9999
).))	chr17:42953264-42953523(-)$1	1	127	131	11.9999
....	chr19:34900099-34900317(+)$1	1	90	94	11.9999
....	chr21:45472125-45472343(+)$1	1	63	67	11.9999
.)).	chr11:65298115-65298334(+)$1	1	29	33	11.9999
....	chr10:79581584-79581812(-)$1	1	5	9	11.9999
.((.	chr14:31604213-31604435(-)$1	1	97	101	11.9999
((..	chr12:125396185-125396407(-)$1	1	5	9	11.9999
.(((	chr10:126686568-126686798(-)$1	1	95	99	11.9999
.)))	chr15:78758627-78758859(+)$1	1	64	68	11.9999
..))	chr14:51381350-51381566(-)$1	1	192	196	11.9999
(...	chr16:3738964-3739190(-)$1	1	87	91	11.9999
))))	chr5:96066439-96066659(+)$1	1	54	58	11.9999

#PSSM
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	

#score	1007.9999999999995
#seq	84
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m2_run2.nuc.txt

#NT
cug	chr1:227849210-227849433(+)$1	223	51	54	8.9999
CUG	chr17:34070147-34070371(+)$1	224	5	8	8.9999
cug	chr17:65334580-65334808(-)$1	228	33	36	8.9999
CUG	chr12:98943457-98943685(+)$1	228	2	5	8.9999
CUG	chr6:34555403-34555628(-)$1	225	16	19	8.9999
CUG	chr9:132998371-132998602(+)$1	231	38	41	8.9999
CUG	chr12:54576273-54576496(-)$1	223	121	124	8.9999
CUG	chr17:4701250-4701479(+)$1	229	24	27	8.9999
CUG	chr1:11355270-11355497(+)$1	227	52	55	8.9999
CUG	chr22:20909273-20909492(+)$1	219	0	3	8.9999
CUG	chr17:26941549-26941776(-)$1	227	63	66	8.9999
CUG	chr1:233398735-233398961(-)$1	226	32	35	8.9999
CUG	chr12:125512767-125512995(+)$1	228	12	15	8.9999
CUG	chr9:134371463-134371682(+)$1	219	39	42	8.9999
CUG	chr8:110355835-110356059(+)$1	224	175	178	8.9999
CUG	chr22:38881543-38881767(-)$1	224	1	4	8.9999
CUG	chrX:153276792-153277013(-)$1	221	1	4	8.9999
CUG	chr6:90343899-90344128(-)$1	229	6	9	8.9999
CUG	chr10:7201172-7201402(-)$1	230	140	143	8.9999
cug	chr8:26364690-26364915(-)$1	225	21	24	8.9999
CUG	chr7:5570055-5570306(-)$1	251	237	240	8.9999
CUG	chr1:145281984-145282212(+)$1	228	16	19	8.9999
CUG	chr11:4133105-4133325(+)$1	220	27	30	8.9999
CUG	chr3:194408727-194408947(+)$1	220	20	23	8.9999
CUG	chr3:38527259-38527479(+)$1	220	154	157	8.9999
CUG	chr13:38935839-38936061(+)$1	222	131	134	8.9999
CUG	chr3:186507050-186507272(+)$1	222	11	14	8.9999
CUG	chr12:120882074-120882294(-)$1	220	55	58	8.9999
CUG	chr12:118480933-118481158(-)$1	225	55	58	8.9999
CUG	chr21:37791161-37791389(+)$1	228	34	37	8.9999
CUG	chr17:79525599-79525826(-)$1	227	3	6	8.9999
CUG	chr1:24296561-24296788(-)$1	227	0	3	8.9999
CUG	chr1:32508249-32508487(+)$1	238	20	23	8.9999
CUG	chr19:7979117-7979338(+)$1	221	5	8	8.9999
CUG	chr3:45962308-45962532(-)$1	224	41	44	8.9999
CUG	chr17:27871455-27871682(+)$1	227	17	20	8.9999
CUG	chr15:68586505-68586759(+)$1	254	27	30	8.9999
CUG	chr2:191556927-191557158(+)$1	231	1	4	8.9999
CUG	chr4:129192137-129192364(-)$1	227	66	69	8.9999
cug	chr11:70053266-70053487(+)$1	221	3	6	8.9999
CUG	chr15:43236912-43237148(-)$1	236	4	7	8.9999
CUG	chr22:41221699-41221918(-)$1	219	15	18	8.9999
cug	chr8:59363015-59363239(+)$1	224	125	128	8.9999
CUG	chr10:50223556-50223798(-)$1	242	12	15	8.9999
CUG	chr7:931918-932154(+)$1	236	2	5	8.9999
CUG	chr17:74266493-74266726(+)$1	233	95	98	8.9999
CUG	chr3:101368470-101368692(-)$1	222	114	117	8.9999
CUG	chr4:90165745-90165967(-)$1	222	46	49	8.9999
cug	chr3:176914905-176915135(-)$1	230	19	22	8.9999
CUG	chr2:98272832-98273052(-)$1	220	13	16	8.9999
CUG	chr22:50702419-50702649(-)$1	230	13	16	8.9999
CUG	chr18:45365051-45365271(-)$1	220	1	4	8.9999
CUG	chr5:133492736-133492966(-)$1	230	26	29	8.9999
CUG	chr11:120204140-120204367(+)$1	227	26	29	8.9999
CUG	chr17:73059715-73059946(+)$1	231	59	62	8.9999
CUG	chr1:238107416-238107637(-)$1	221	31	34	8.9999
CUG	chr9:123943248-123943473(-)$1	225	12	15	8.9999
CUG	chr17:7364645-7364866(-)$1	221	10	13	8.9999
CUG	chr17:73773763-73773984(-)$1	221	29	32	8.9999
cUG	chr15:74006282-74006518(+)$1	236	23	26	8.9999
CUG	chr7:128098039-128098268(+)$1	229	19	22	8.9999
CUG	chr3:196074599-196074824(-)$1	225	5	8	8.9999
CUG	chr19:42376384-42376614(+)$1	230	24	27	8.9999
CUG	chr17:21086980-21087202(+)$1	222	4	7	8.9999
CUG	chr20:30920464-30920694(+)$1	230	30	33	8.9999
CUG	chr1:36023115-36023334(+)$1	219	13	16	8.9999
CUG	chr7:66420908-66421138(+)$1	230	16	19	8.9999
CUG	chr1:151732069-151732291(-)$1	222	29	32	8.9999
CUG	chr18:74726006-74726230(-)$1	224	65	68	8.9999
CUG	chr8:22478398-22478627(-)$1	229	74	77	8.9999
CUG	chr19:48260187-48260411(+)$1	224	58	61	8.9999
CUG	chr3:23932609-23932839(+)$1	230	33	36	8.9999
CUG	chr2:10270280-10270499(+)$1	219	7	10	8.9999
CUG	chr11:102932946-102933165(-)$1	219	25	28	8.9999
cug	chr14:92526013-92526242(-)$1	229	79	82	8.9999
CUG	chr7:33066379-33066601(-)$1	222	4	7	8.9999
CUG	chr3:12875693-12875915(+)$1	222	63	66	8.9999
CUG	chr14:91924815-91925041(-)$1	226	41	44	8.9999
cug	chr21:44330054-44330278(+)$1	224	6	9	8.9999
CUG	chr6:157529464-157529685(+)$1	221	25	28	8.9999
CUG	chr10:22825404-22825641(-)$1	237	136	139	8.9999
CUG	chrX:46741275-46741506(+)$1	231	150	153	8.9999
CUG	chr7:44424735-44424964(-)$1	229	5	8	8.9999
CUG	chr10:97365660-97365890(-)$1	230	3	6	8.9999
CUG	chr7:99705009-99705231(-)$1	222	112	115	8.9999
CUG	chr11:105967714-105967937(+)$1	223	69	72	8.9999
CUG	chr10:72183064-72183294(+)$1	230	29	32	8.9999
CUG	chr17:27401181-27401414(-)$1	233	5	8	8.9999
CUG	chr12:6659816-6660037(-)$1	221	6	9	8.9999
CUG	chr1:228363714-228363935(+)$1	221	7	10	8.9999
CUG	chr16:2821857-2822076(-)$1	219	23	26	8.9999
CUG	chr17:40986690-40986909(+)$1	219	7	10	8.9999
CUG	chr11:22303175-22303403(+)$1	228	7	10	8.9999
CUG	chr1:1263149-1263368(+)$1	219	24	27	8.9999
CUG	chr20:52185478-52185698(-)$1	220	18	21	8.9999
CUG	chr16:51169854-51170073(-)$1	219	41	44	8.9999
CUG	chr22:29450359-29450589(+)$1	230	17	20	8.9999
CUG	chr6:97711140-97711360(-)$1	220	46	49	8.9999

#otherMatches

#Struct PSSM
GGG	chr16:46731917-46732137(+)$1	220	8	11	8.9999
ccc	chr1:227849210-227849433(+)$1	223	51	54	8.9999
{HH	chr17:34070147-34070371(+)$1	224	5	8	8.9999
HHH	chr17:65334580-65334808(-)$1	228	33	36	8.9999
ccc	chr12:98943457-98943685(+)$1	228	2	5	8.9999
eee	chr6:34555403-34555628(-)$1	225	16	19	8.9999
FFF	chr9:132998371-132998602(+)$1	231	38	41	8.9999
hhh	chr12:54576273-54576496(-)$1	223	121	124	8.9999
nnn	chr17:4701250-4701479(+)$1	229	24	27	8.9999
cc]	chr1:11355270-11355497(+)$1	227	52	55	8.9999
CCC	chr22:20909273-20909492(+)$1	219	0	3	8.9999
ddd	chr17:26941549-26941776(-)$1	227	63	66	8.9999
DDF	chr1:233398735-233398961(-)$1	226	32	35	8.9999
CCM	chr12:125512767-125512995(+)$1	228	12	15	8.9999
fff	chr9:134371463-134371682(+)$1	219	39	42	8.9999
e[b	chr8:110355835-110356059(+)$1	224	175	178	8.9999
:::	chr22:38881543-38881767(-)$1	224	1	4	8.9999
eee	chrX:153276792-153277013(-)$1	221	1	4	8.9999
hhh	chr6:90343899-90344128(-)$1	229	6	9	8.9999
!!c	chr10:7201172-7201402(-)$1	230	140	143	8.9999
C{C	chr8:26364690-26364915(-)$1	225	21	24	8.9999
GYY	chr7:5570055-5570306(-)$1	251	237	240	8.9999
DDD	chr1:145281984-145282212(+)$1	228	16	19	8.9999
c]f	chr11:4133105-4133325(+)$1	220	27	30	8.9999
ttt	chr3:194408727-194408947(+)$1	220	20	23	8.9999
eee	chr3:38527259-38527479(+)$1	220	154	157	8.9999
!bb	chr13:38935839-38936061(+)$1	222	131	134	8.9999
:JJ	chr3:186507050-186507272(+)$1	222	11	14	8.9999
ddm	chr12:120882074-120882294(-)$1	220	55	58	8.9999
boo	chr12:118480933-118481158(-)$1	225	55	58	8.9999
ccc	chr21:37791161-37791389(+)$1	228	34	37	8.9999
GGG	chr17:79525599-79525826(-)$1	227	3	6	8.9999
BBK	chr1:24296561-24296788(-)$1	227	0	3	8.9999
::c	chr1:32508249-32508487(+)$1	238	20	23	8.9999
ggg	chr19:7979117-7979338(+)$1	221	5	8	8.9999
qcc	chr3:45962308-45962532(-)$1	224	41	44	8.9999
::D	chr17:27871455-27871682(+)$1	227	17	20	8.9999
DDD	chr15:68586505-68586759(+)$1	254	27	30	8.9999
:::	chr2:191556927-191557158(+)$1	231	1	4	8.9999
eee	chr4:129192137-129192364(-)$1	227	66	69	8.9999
EEE	chr11:70053266-70053487(+)$1	221	3	6	8.9999
:::	chr15:43236912-43237148(-)$1	236	4	7	8.9999
rrr	chr22:41221699-41221918(-)$1	219	15	18	8.9999
ddd	chr8:59363015-59363239(+)$1	224	125	128	8.9999
qqq	chr10:50223556-50223798(-)$1	242	12	15	8.9999
:::	chr7:931918-932154(+)$1	236	2	5	8.9999
ccc	chr17:74266493-74266726(+)$1	233	95	98	8.9999
fff	chr3:101368470-101368692(-)$1	222	114	117	8.9999
mdd	chr4:90165745-90165967(-)$1	222	46	49	8.9999
JJJ	chr3:176914905-176915135(-)$1	230	19	22	8.9999
[a[	chr2:98272832-98273052(-)$1	220	13	16	8.9999
JJJ	chr22:50702419-50702649(-)$1	230	13	16	8.9999
:::	chr18:45365051-45365271(-)$1	220	1	4	8.9999
{FF	chr5:133492736-133492966(-)$1	230	26	29	8.9999
c22	chr11:120204140-120204367(+)$1	227	26	29	8.9999
!!a	chr17:73059715-73059946(+)$1	231	59	62	8.9999
LLG	chr1:238107416-238107637(-)$1	221	31	34	8.9999
BBL	chr9:123943248-123943473(-)$1	225	12	15	8.9999
LLF	chr17:7364645-7364866(-)$1	221	10	13	8.9999
eee	chr17:73773763-73773984(-)$1	221	29	32	8.9999
++b	chr15:74006282-74006518(+)$1	236	23	26	8.9999
::c	chr7:128098039-128098268(+)$1	229	19	22	8.9999
FFh	chr3:196074599-196074824(-)$1	225	5	8	8.9999
LFF	chr19:42376384-42376614(+)$1	230	24	27	8.9999
EBB	chr17:21086980-21087202(+)$1	222	4	7	8.9999
qhh	chr20:30920464-30920694(+)$1	230	30	33	8.9999
B:h	chr1:36023115-36023334(+)$1	219	13	16	8.9999
ggg	chr7:66420908-66421138(+)$1	230	16	19	8.9999
a]e	chr1:151732069-151732291(-)$1	222	29	32	8.9999
HHH	chr18:74726006-74726230(-)$1	224	65	68	8.9999
:ee	chr8:22478398-22478627(-)$1	229	74	77	8.9999
EEE	chr19:48260187-48260411(+)$1	224	58	61	8.9999
ffo	chr3:23932609-23932839(+)$1	230	33	36	8.9999
{DD	chr2:10270280-10270499(+)$1	219	7	10	8.9999
d:f	chr11:102932946-102933165(-)$1	219	25	28	8.9999
:dd	chr14:92526013-92526242(-)$1	229	79	82	8.9999
FF{	chr7:33066379-33066601(-)$1	222	4	7	8.9999
eee	chr3:12875693-12875915(+)$1	222	63	66	8.9999
ddd	chr14:91924815-91925041(-)$1	226	41	44	8.9999
EEE	chr21:44330054-44330278(+)$1	224	6	9	8.9999
:cc	chr6:157529464-157529685(+)$1	221	25	28	8.9999
:::	chr10:22825404-22825641(-)$1	237	136	139	8.9999
eee	chrX:46741275-46741506(+)$1	231	150	153	8.9999
GGG	chr7:44424735-44424964(-)$1	229	5	8	8.9999
:DD	chr10:97365660-97365890(-)$1	230	3	6	8.9999
ccr	chr7:99705009-99705231(-)$1	222	112	115	8.9999
dd]	chr11:105967714-105967937(+)$1	223	69	72	8.9999
qqg	chr10:72183064-72183294(+)$1	230	29	32	8.9999
EEQ	chr17:27401181-27401414(-)$1	233	5	8	8.9999
BBK	chr12:6659816-6660037(-)$1	221	6	9	8.9999
GGG	chr1:228363714-228363935(+)$1	221	7	10	8.9999
ddd	chr16:2821857-2822076(-)$1	219	23	26	8.9999
:::	chr17:40986690-40986909(+)$1	219	7	10	8.9999
FFL	chr11:22303175-22303403(+)$1	228	7	10	8.9999
ood	chr1:1263149-1263368(+)$1	219	24	27	8.9999
:HH	chr20:52185478-52185698(-)$1	220	18	21	8.9999
==[	chr16:51169854-51170073(-)$1	219	41	44	8.9999
:::	chr22:29450359-29450589(+)$1	230	17	20	8.9999
bb]	chr6:97711140-97711360(-)$1	220	46	49	8.9999

#DB
(((	chr16:46731917-46732137(+)$1	1	8	11	8.9999
)))	chr1:227849210-227849433(+)$1	1	51	54	8.9999
.((	chr17:34070147-34070371(+)$1	1	5	8	8.9999
(((	chr17:65334580-65334808(-)$1	1	33	36	8.9999
(((	chr12:98943457-98943685(+)$1	1	2	5	8.9999
(((	chr6:34555403-34555628(-)$1	1	16	19	8.9999
(((	chr9:132998371-132998602(+)$1	1	38	41	8.9999
(((	chr12:54576273-54576496(-)$1	1	121	124	8.9999
...	chr17:4701250-4701479(+)$1	1	24	27	8.9999
)).	chr1:11355270-11355497(+)$1	1	52	55	8.9999
(((	chr22:20909273-20909492(+)$1	1	0	3	8.9999
(((	chr17:26941549-26941776(-)$1	1	63	66	8.9999
(((	chr1:233398735-233398961(-)$1	1	32	35	8.9999
((.	chr12:125512767-125512995(+)$1	1	12	15	8.9999
)))	chr9:134371463-134371682(+)$1	1	39	42	8.9999
(.(	chr8:110355835-110356059(+)$1	1	175	178	8.9999
...	chr22:38881543-38881767(-)$1	1	1	4	8.9999
(((	chrX:153276792-153277013(-)$1	1	1	4	8.9999
(((	chr6:90343899-90344128(-)$1	1	6	9	8.9999
..(	chr10:7201172-7201402(-)$1	1	140	143	8.9999
(.(	chr8:26364690-26364915(-)$1	1	21	24	8.9999
)..	chr7:5570055-5570306(-)$1	1	237	240	8.9999
(((	chr1:145281984-145282212(+)$1	1	16	19	8.9999
).)	chr11:4133105-4133325(+)$1	1	27	30	8.9999
...	chr3:194408727-194408947(+)$1	1	20	23	8.9999
)))	chr3:38527259-38527479(+)$1	1	154	157	8.9999
.((	chr13:38935839-38936061(+)$1	1	131	134	8.9999
.((	chr3:186507050-186507272(+)$1	1	11	14	8.9999
((.	chr12:120882074-120882294(-)$1	1	55	58	8.9999
(..	chr12:118480933-118481158(-)$1	1	55	58	8.9999
)))	chr21:37791161-37791389(+)$1	1	34	37	8.9999
(((	chr17:79525599-79525826(-)$1	1	3	6	8.9999
((.	chr1:24296561-24296788(-)$1	1	0	3	8.9999
..(	chr1:32508249-32508487(+)$1	1	20	23	8.9999
(((	chr19:7979117-7979338(+)$1	1	5	8	8.9999
.))	chr3:45962308-45962532(-)$1	1	41	44	8.9999
..(	chr17:27871455-27871682(+)$1	1	17	20	8.9999
(((	chr15:68586505-68586759(+)$1	1	27	30	8.9999
...	chr2:191556927-191557158(+)$1	1	1	4	8.9999
(((	chr4:129192137-129192364(-)$1	1	66	69	8.9999
(((	chr11:70053266-70053487(+)$1	1	3	6	8.9999
...	chr15:43236912-43237148(-)$1	1	4	7	8.9999
...	chr22:41221699-41221918(-)$1	1	15	18	8.9999
(((	chr8:59363015-59363239(+)$1	1	125	128	8.9999
...	chr10:50223556-50223798(-)$1	1	12	15	8.9999
...	chr7:931918-932154(+)$1	1	2	5	8.9999
)))	chr17:74266493-74266726(+)$1	1	95	98	8.9999
(((	chr3:101368470-101368692(-)$1	1	114	117	8.9999
.))	chr4:90165745-90165967(-)$1	1	46	49	8.9999
(((	chr3:176914905-176915135(-)$1	1	19	22	8.9999
.(.	chr2:98272832-98273052(-)$1	1	13	16	8.9999
(((	chr22:50702419-50702649(-)$1	1	13	16	8.9999
...	chr18:45365051-45365271(-)$1	1	1	4	8.9999
.((	chr5:133492736-133492966(-)$1	1	26	29	8.9999
)..	chr11:120204140-120204367(+)$1	1	26	29	8.9999
..(	chr17:73059715-73059946(+)$1	1	59	62	8.9999
..(	chr1:238107416-238107637(-)$1	1	31	34	8.9999
((.	chr9:123943248-123943473(-)$1	1	12	15	8.9999
..(	chr17:7364645-7364866(-)$1	1	10	13	8.9999
(((	chr17:73773763-73773984(-)$1	1	29	32	8.9999
..(	chr15:74006282-74006518(+)$1	1	23	26	8.9999
..(	chr7:128098039-128098268(+)$1	1	19	22	8.9999
(((	chr3:196074599-196074824(-)$1	1	5	8	8.9999
.((	chr19:42376384-42376614(+)$1	1	24	27	8.9999
(((	chr17:21086980-21087202(+)$1	1	4	7	8.9999
.))	chr20:30920464-30920694(+)$1	1	30	33	8.9999
(.(	chr1:36023115-36023334(+)$1	1	13	16	8.9999
(((	chr7:66420908-66421138(+)$1	1	16	19	8.9999
).)	chr1:151732069-151732291(-)$1	1	29	32	8.9999
(((	chr18:74726006-74726230(-)$1	1	65	68	8.9999
.((	chr8:22478398-22478627(-)$1	1	74	77	8.9999
(((	chr19:48260187-48260411(+)$1	1	58	61	8.9999
((.	chr3:23932609-23932839(+)$1	1	33	36	8.9999
.((	chr2:10270280-10270499(+)$1	1	7	10	8.9999
).(	chr11:102932946-102933165(-)$1	1	25	28	8.9999
.((	chr14:92526013-92526242(-)$1	1	79	82	8.9999
((.	chr7:33066379-33066601(-)$1	1	4	7	8.9999
(((	chr3:12875693-12875915(+)$1	1	63	66	8.9999
(((	chr14:91924815-91925041(-)$1	1	41	44	8.9999
(((	chr21:44330054-44330278(+)$1	1	6	9	8.9999
.((	chr6:157529464-157529685(+)$1	1	25	28	8.9999
...	chr10:22825404-22825641(-)$1	1	136	139	8.9999
(((	chrX:46741275-46741506(+)$1	1	150	153	8.9999
(((	chr7:44424735-44424964(-)$1	1	5	8	8.9999
.((	chr10:97365660-97365890(-)$1	1	3	6	8.9999
((.	chr7:99705009-99705231(-)$1	1	112	115	8.9999
)).	chr11:105967714-105967937(+)$1	1	69	72	8.9999
..)	chr10:72183064-72183294(+)$1	1	29	32	8.9999
((.	chr17:27401181-27401414(-)$1	1	5	8	8.9999
((.	chr12:6659816-6660037(-)$1	1	6	9	8.9999
(((	chr1:228363714-228363935(+)$1	1	7	10	8.9999
)))	chr16:2821857-2822076(-)$1	1	23	26	8.9999
...	chr17:40986690-40986909(+)$1	1	7	10	8.9999
((.	chr11:22303175-22303403(+)$1	1	7	10	8.9999
..)	chr1:1263149-1263368(+)$1	1	24	27	8.9999
.((	chr20:52185478-52185698(-)$1	1	18	21	8.9999
((.	chr16:51169854-51170073(-)$1	1	41	44	8.9999
...	chr22:29450359-29450589(+)$1	1	17	20	8.9999
)).	chr6:97711140-97711360(-)$1	1	46	49	8.9999

#PSSM
C : 0.89	c : 0.10	
U : 0.90	u : 0.09	
G : 0.90	g : 0.09	

#score	890.9999999999998
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_UTR_m3_run1.nuc.txt

#NT
CUUU	chr19:21988492-21988722(-)$1	230	27	31	11.9999
CUUU	chr10:103923481-103923711(+)$1	230	207	211	11.9999
CUUU	chr14:104152428-104152657(+)$1	229	54	58	11.9999
CUUU	chr12:57392695-57392922(-)$1	227	12	16	11.9999
CUUU	chr2:669144-669376(-)$1	232	12	16	11.9999
CUUU	chr1:40539503-40539730(-)$1	227	162	166	11.9999
CUUU	chr12:125585650-125585882(+)$1	232	90	94	11.9999
cuuu	chr7:25160009-25160241(-)$1	232	5	9	11.9999
CUUU	chr17:38291054-38291286(+)$1	232	34	38	11.9999
cuuu	chr2:228423522-228423751(+)$1	229	57	61	11.9999
CUUU	chr14:55535141-55535373(+)$1	232	82	86	11.9999
CUUU	chr6:74303997-74304228(-)$1	231	33	37	11.9999
cuuu	chr11:94230293-94230527(+)$1	234	192	196	11.9999
CUUU	chr11:74550290-74550517(+)$1	227	37	41	11.9999
CUUU	chr11:18388461-18388693(+)$1	232	61	65	11.9999
CUUU	chr13:95059029-95059262(+)$1	233	8	12	11.9999
CUUU	chr11:13742305-13742537(+)$1	232	19	23	11.9999
CUUU	chr15:66183865-66184091(+)$1	226	162	166	11.9999
CUUU	chr9:80944466-80944699(+)$1	233	37	41	11.9999
CUUU	chr10:105153955-105154179(-)$1	224	170	174	11.9999
CUUU	chr1:115259922-115260154(-)$1	232	38	42	11.9999
CUUU	chr16:54147027-54147252(+)$1	225	118	122	11.9999
CUUU	chr5:34954867-34955099(+)$1	232	91	95	11.9999
CUUU	chr3:52745102-52745334(-)$1	232	81	85	11.9999
CUUU	chr5:137771324-137771548(+)$1	224	101	105	11.9999
CUUU	chr18:673997-674222(-)$1	225	79	83	11.9999
CUUU	chr15:62145356-62145584(-)$1	228	9	13	11.9999
CUUU	chr2:169628876-169629108(+)$1	232	119	123	11.9999
CUUU	chr15:63901124-63901356(-)$1	232	145	149	11.9999
cuuu	chr19:40535939-40536171(-)$1	232	10	14	11.9999
CUUU	chr22:38686857-38687088(-)$1	231	61	65	11.9999
CUUU	chr1:47143953-47144202(-)$1	249	56	60	11.9999
CUUU	chr1:101444609-101444840(+)$1	231	64	68	11.9999
CUUU	chr3:27414661-27414897(-)$1	236	32	36	11.9999
CUUU	chr17:7560490-7560725(+)$1	235	24	28	11.9999
CUUU	chr7:64292463-64292690(+)$1	227	17	21	11.9999
CUUU	chrX:49030992-49031223(+)$1	231	3	7	11.9999
CUUU	chr3:16299611-16299841(-)$1	230	42	46	11.9999
CUUU	chr2:178407015-178407247(+)$1	232	26	30	11.9999
CUUU	chr1:150237947-150238188(-)$1	241	33	37	11.9999
CUUU	chr1:75171789-75172021(-)$1	232	51	55	11.9999
CUUU	chr11:96086270-96086502(-)$1	232	82	86	11.9999
CUUU	chr2:37329325-37329556(-)$1	231	19	23	11.9999
CUUU	chr12:69968696-69968928(+)$1	232	66	70	11.9999
cuuu	chr1:115249126-115249358(-)$1	232	69	73	11.9999
cUUU	chr2:86438522-86438746(+)$1	224	21	25	11.9999
CUUU	chr1:162492336-162492568(+)$1	232	102	106	11.9999
CUUU	chr9:95177215-95177447(+)$1	232	133	137	11.9999
CUUU	chr19:8920285-8920517(-)$1	232	9	13	11.9999
CUUU	chr9:21969464-21969697(-)$1	233	142	146	11.9999
cuuu	chr1:28148847-28149080(+)$1	233	134	138	11.9999
CUUU	chr14:24783593-24783825(+)$1	232	47	51	11.9999
CUUU	chr9:115449182-115449414(-)$1	232	52	56	11.9999
CUUU	chr3:15288787-15289019(+)$1	232	30	34	11.9999
CUUU	chr13:20712378-20712610(-)$1	232	148	152	11.9999
CUUU	chr2:209170025-209170254(+)$1	229	10	14	11.9999
CUUU	chr5:162870921-162871146(+)$1	225	46	50	11.9999
cuuu	chr19:46142166-46142390(-)$1	224	45	49	11.9999
CUUU	chr7:120428105-120428332(-)$1	227	113	117	11.9999
CUUU	chr15:75713332-75713569(-)$1	237	81	85	11.9999
CUUU	chr4:85593414-85593643(-)$1	229	21	25	11.9999
CUUU	chr1:75171416-75171651(-)$1	235	38	42	11.9999
CUUU	chr7:94921490-94921722(+)$1	232	38	42	11.9999
CUUU	chr14:69256071-69256304(-)$1	233	34	38	11.9999
CUUU	chr5:133492257-133492487(-)$1	230	102	106	11.9999
CUUU	chr5:137776630-137776862(+)$1	232	80	84	11.9999
CUUU	chr18:66342873-66343096(-)$1	223	85	89	11.9999
CUUU	chr19:21476274-21476506(-)$1	232	22	26	11.9999
CUUU	chr3:120321114-120321344(+)$1	230	73	77	11.9999
CUUU	chr18:22032396-22032633(+)$1	237	81	85	11.9999
CUUU	chr12:70738898-70739133(+)$1	235	82	86	11.9999
CUUU	chr6:159396757-159396988(-)$1	231	142	146	11.9999
CUUU	chr10:72181818-72182048(+)$1	230	187	191	11.9999
CUUU	chr17:56081655-56081889(-)$1	234	92	96	11.9999
CUUU	chr7:92029349-92029582(+)$1	233	105	109	11.9999
CUUU	chr7:108112301-108112533(-)$1	232	39	43	11.9999
CUUU	chr17:27047579-27047810(+)$1	231	128	132	11.9999
CUUU	chr4:26434921-26435150(+)$1	229	8	12	11.9999
CUUU	chr2:135816014-135816251(+)$1	237	10	14	11.9999

#otherMatches

#Struct PSSM
ssss	chr6:109688649-109688882(-)$1	233	60	64	11.9999
::::	chr19:21988492-21988722(-)$1	230	27	31	11.9999
nfff	chr10:103923481-103923711(+)$1	230	207	211	11.9999
gg++	chr14:104152428-104152657(+)$1	229	54	58	11.9999
ppff	chr12:57392695-57392922(-)$1	227	12	16	11.9999
:::e	chr2:669144-669376(-)$1	232	12	16	11.9999
dddd	chr1:40539503-40539730(-)$1	227	162	166	11.9999
cc44	chr12:125585650-125585882(+)$1	232	90	94	11.9999
eeee	chr7:25160009-25160241(-)$1	232	5	9	11.9999
ffff	chr17:38291054-38291286(+)$1	232	34	38	11.9999
eeem	chr2:228423522-228423751(+)$1	229	57	61	11.9999
EEEE	chr14:55535141-55535373(+)$1	232	82	86	11.9999
ee""	chr6:74303997-74304228(-)$1	231	33	37	11.9999
dfff	chr11:94230293-94230527(+)$1	234	192	196	11.9999
::::	chr11:74550290-74550517(+)$1	227	37	41	11.9999
fppp	chr11:18388461-18388693(+)$1	232	61	65	11.9999
JJJJ	chr13:95059029-95059262(+)$1	233	8	12	11.9999
JJJJ	chr11:13742305-13742537(+)$1	232	19	23	11.9999
5555	chr15:66183865-66184091(+)$1	226	162	166	11.9999
dddd	chr9:80944466-80944699(+)$1	233	37	41	11.9999
::::	chr10:105153955-105154179(-)$1	224	170	174	11.9999
ddd[	chr1:115259922-115260154(-)$1	232	38	42	11.9999
!eee	chr16:54147027-54147252(+)$1	225	118	122	11.9999
aooo	chr5:34954867-34955099(+)$1	232	91	95	11.9999
eeee	chr3:52745102-52745334(-)$1	232	81	85	11.9999
offf	chr5:137771324-137771548(+)$1	224	101	105	11.9999
iii:	chr18:673997-674222(-)$1	225	79	83	11.9999
GGGG	chr15:62145356-62145584(-)$1	228	9	13	11.9999
::::	chr2:169628876-169629108(+)$1	232	119	123	11.9999
a[ff	chr15:63901124-63901356(-)$1	232	145	149	11.9999
b[ee	chr19:40535939-40536171(-)$1	232	10	14	11.9999
dddl	chr22:38686857-38687088(-)$1	231	61	65	11.9999
====	chr1:47143953-47144202(-)$1	249	56	60	11.9999
::::	chr1:101444609-101444840(+)$1	231	64	68	11.9999
C{EE	chr3:27414661-27414897(-)$1	236	32	36	11.9999
G:::	chr17:7560490-7560725(+)$1	235	24	28	11.9999
####	chr7:64292463-64292690(+)$1	227	17	21	11.9999
:ddd	chrX:49030992-49031223(+)$1	231	3	7	11.9999
2eee	chr3:16299611-16299841(-)$1	230	42	46	11.9999
eeee	chr2:178407015-178407247(+)$1	232	26	30	11.9999
====	chr1:150237947-150238188(-)$1	241	33	37	11.9999
b::g	chr1:75171789-75172021(-)$1	232	51	55	11.9999
''''	chr11:96086270-96086502(-)$1	232	82	86	11.9999
"""e	chr2:37329325-37329556(-)$1	231	19	23	11.9999
mmmm	chr12:69968696-69968928(+)$1	232	66	70	11.9999
dddd	chr1:115249126-115249358(-)$1	232	69	73	11.9999
ccpp	chr2:86438522-86438746(+)$1	224	21	25	11.9999
]ccc	chr1:162492336-162492568(+)$1	232	102	106	11.9999
ggll	chr9:95177215-95177447(+)$1	232	133	137	11.9999
DDDD	chr19:8920285-8920517(-)$1	232	9	13	11.9999
22gg	chr9:21969464-21969697(-)$1	233	142	146	11.9999
!!cc	chr1:28148847-28149080(+)$1	233	134	138	11.9999
::::	chr14:24783593-24783825(+)$1	232	47	51	11.9999
cc55	chr9:115449182-115449414(-)$1	232	52	56	11.9999
]===	chr3:15288787-15289019(+)$1	232	30	34	11.9999
!!bb	chr13:20712378-20712610(-)$1	232	148	152	11.9999
oooc	chr2:209170025-209170254(+)$1	229	10	14	11.9999
rrrr	chr5:162870921-162871146(+)$1	225	46	50	11.9999
hh::	chr19:46142166-46142390(-)$1	224	45	49	11.9999
hhhh	chr7:120428105-120428332(-)$1	227	113	117	11.9999
d:::	chr15:75713332-75713569(-)$1	237	81	85	11.9999
rggg	chr4:85593414-85593643(-)$1	229	21	25	11.9999
eeem	chr1:75171416-75171651(-)$1	235	38	42	11.9999
=ccc	chr7:94921490-94921722(+)$1	232	38	42	11.9999
::::	chr14:69256071-69256304(-)$1	233	34	38	11.9999
44dd	chr5:133492257-133492487(-)$1	230	102	106	11.9999
a]ee	chr5:137776630-137776862(+)$1	232	80	84	11.9999
mmdd	chr18:66342873-66343096(-)$1	223	85	89	11.9999
lddd	chr19:21476274-21476506(-)$1	232	22	26	11.9999
bb22	chr3:120321114-120321344(+)$1	230	73	77	11.9999
zeee	chr18:22032396-22032633(+)$1	237	81	85	11.9999
lldd	chr12:70738898-70739133(+)$1	235	82	86	11.9999
nnnn	chr6:159396757-159396988(-)$1	231	142	146	11.9999
444e	chr10:72181818-72182048(+)$1	230	187	191	11.9999
tttt	chr17:56081655-56081889(-)$1	234	92	96	11.9999
d22b	chr7:92029349-92029582(+)$1	233	105	109	11.9999
IIII	chr7:108112301-108112533(-)$1	232	39	43	11.9999
>>>>	chr17:27047579-27047810(+)$1	231	128	132	11.9999
::GG	chr4:26434921-26435150(+)$1	229	8	12	11.9999
e[ff	chr2:135816014-135816251(+)$1	237	10	14	11.9999

#DB
....	chr6:109688649-109688882(-)$1	1	60	64	11.9999
....	chr19:21988492-21988722(-)$1	1	27	31	11.9999
.)))	chr10:103923481-103923711(+)$1	1	207	211	11.9999
((..	chr14:104152428-104152657(+)$1	1	54	58	11.9999
..))	chr12:57392695-57392922(-)$1	1	12	16	11.9999
...(	chr2:669144-669376(-)$1	1	12	16	11.9999
))))	chr1:40539503-40539730(-)$1	1	162	166	11.9999
))..	chr12:125585650-125585882(+)$1	1	90	94	11.9999
((((	chr7:25160009-25160241(-)$1	1	5	9	11.9999
((((	chr17:38291054-38291286(+)$1	1	34	38	11.9999
(((.	chr2:228423522-228423751(+)$1	1	57	61	11.9999
((((	chr14:55535141-55535373(+)$1	1	82	86	11.9999
((..	chr6:74303997-74304228(-)$1	1	33	37	11.9999
((((	chr11:94230293-94230527(+)$1	1	192	196	11.9999
....	chr11:74550290-74550517(+)$1	1	37	41	11.9999
(...	chr11:18388461-18388693(+)$1	1	61	65	11.9999
((((	chr13:95059029-95059262(+)$1	1	8	12	11.9999
((((	chr11:13742305-13742537(+)$1	1	19	23	11.9999
....	chr15:66183865-66184091(+)$1	1	162	166	11.9999
((((	chr9:80944466-80944699(+)$1	1	37	41	11.9999
....	chr10:105153955-105154179(-)$1	1	170	174	11.9999
(((.	chr1:115259922-115260154(-)$1	1	38	42	11.9999
.(((	chr16:54147027-54147252(+)$1	1	118	122	11.9999
(...	chr5:34954867-34955099(+)$1	1	91	95	11.9999
))))	chr3:52745102-52745334(-)$1	1	81	85	11.9999
.)))	chr5:137771324-137771548(+)$1	1	101	105	11.9999
))).	chr18:673997-674222(-)$1	1	79	83	11.9999
((((	chr15:62145356-62145584(-)$1	1	9	13	11.9999
....	chr2:169628876-169629108(+)$1	1	119	123	11.9999
(.((	chr15:63901124-63901356(-)$1	1	145	149	11.9999
(.((	chr19:40535939-40536171(-)$1	1	10	14	11.9999
(((.	chr22:38686857-38687088(-)$1	1	61	65	11.9999
))))	chr1:47143953-47144202(-)$1	1	56	60	11.9999
....	chr1:101444609-101444840(+)$1	1	64	68	11.9999
(.((	chr3:27414661-27414897(-)$1	1	32	36	11.9999
(...	chr17:7560490-7560725(+)$1	1	24	28	11.9999
....	chr7:64292463-64292690(+)$1	1	17	21	11.9999
.(((	chrX:49030992-49031223(+)$1	1	3	7	11.9999
.)))	chr3:16299611-16299841(-)$1	1	42	46	11.9999
((((	chr2:178407015-178407247(+)$1	1	26	30	11.9999
((((	chr1:150237947-150238188(-)$1	1	33	37	11.9999
)..(	chr1:75171789-75172021(-)$1	1	51	55	11.9999
....	chr11:96086270-96086502(-)$1	1	82	86	11.9999
...(	chr2:37329325-37329556(-)$1	1	19	23	11.9999
....	chr12:69968696-69968928(+)$1	1	66	70	11.9999
))))	chr1:115249126-115249358(-)$1	1	69	73	11.9999
((..	chr2:86438522-86438746(+)$1	1	21	25	11.9999
.)))	chr1:162492336-162492568(+)$1	1	102	106	11.9999
((..	chr9:95177215-95177447(+)$1	1	133	137	11.9999
((((	chr19:8920285-8920517(-)$1	1	9	13	11.9999
..))	chr9:21969464-21969697(-)$1	1	142	146	11.9999
..((	chr1:28148847-28149080(+)$1	1	134	138	11.9999
....	chr14:24783593-24783825(+)$1	1	47	51	11.9999
))..	chr9:115449182-115449414(-)$1	1	52	56	11.9999
.)))	chr3:15288787-15289019(+)$1	1	30	34	11.9999
..((	chr13:20712378-20712610(-)$1	1	148	152	11.9999
...)	chr2:209170025-209170254(+)$1	1	10	14	11.9999
....	chr5:162870921-162871146(+)$1	1	46	50	11.9999
))..	chr19:46142166-46142390(-)$1	1	45	49	11.9999
))))	chr7:120428105-120428332(-)$1	1	113	117	11.9999
)...	chr15:75713332-75713569(-)$1	1	81	85	11.9999
.)))	chr4:85593414-85593643(-)$1	1	21	25	11.9999
(((.	chr1:75171416-75171651(-)$1	1	38	42	11.9999
)(((	chr7:94921490-94921722(+)$1	1	38	42	11.9999
....	chr14:69256071-69256304(-)$1	1	34	38	11.9999
..))	chr5:133492257-133492487(-)$1	1	102	106	11.9999
).))	chr5:137776630-137776862(+)$1	1	80	84	11.9999
..))	chr18:66342873-66343096(-)$1	1	85	89	11.9999
.)))	chr19:21476274-21476506(-)$1	1	22	26	11.9999
))..	chr3:120321114-120321344(+)$1	1	73	77	11.9999
.)))	chr18:22032396-22032633(+)$1	1	81	85	11.9999
..))	chr12:70738898-70739133(+)$1	1	82	86	11.9999
....	chr6:159396757-159396988(-)$1	1	142	146	11.9999
...)	chr10:72181818-72182048(+)$1	1	187	191	11.9999
....	chr17:56081655-56081889(-)$1	1	92	96	11.9999
)..)	chr7:92029349-92029582(+)$1	1	105	109	11.9999
((((	chr7:108112301-108112533(-)$1	1	39	43	11.9999
....	chr17:27047579-27047810(+)$1	1	128	132	11.9999
..((	chr4:26434921-26435150(+)$1	1	8	12	11.9999
(.((	chr2:135816014-135816251(+)$1	1	10	14	11.9999

#PSSM
C : 0.89	c : 0.09	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	

#score	959.9999999999998
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_CDS_m2_run1.nuc.txt

#NT
UCC	chr14:23793317-23793591(+)$1	274	33	36	8.9999
UCC	chr8:67577932-67578180(-)$1	248	34	37	8.9999
UCC	chr2:152289490-152289750(+)$1	260	150	153	8.9999
UCC	chr19:57802407-57802630(+)$1	223	9	12	8.9999
UCC	chr12:57032786-57033095(-)$1	309	13	16	8.9999
UCC	chr11:75115129-75115354(+)$1	225	8	11	8.9999
UCC	chr1:100547592-100547827(+)$1	235	43	46	8.9999
UCC	chr7:27211437-27211684(-)$1	247	51	54	8.9999
UCC	chr19:39923774-39924107(-)$1	333	24	27	8.9999
UCC	chr14:103988675-103988942(-)$1	267	72	75	8.9999
UCC	chr12:49953993-49954242(-)$1	249	10	13	8.9999
UCC	chrX:118726250-118726556(-)$1	306	39	42	8.9999
UCC	chr6:43193433-43193689(-)$1	256	2	5	8.9999
UCC	chr11:82644523-82644749(+)$1	226	39	42	8.9999
UCC	chr7:26236838-26237181(-)$1	343	111	114	8.9999
UCC	chr4:83347517-83347861(-)$1	344	47	50	8.9999
UCC	chr16:29820828-29821116(+)$1	288	11	14	8.9999
UCC	chr4:174298298-174298525(+)$1	227	32	35	8.9999
UCC	chr2:101622321-101622551(+)$1	230	116	119	8.9999
UCC	chr15:66792386-66792610(-)$1	224	104	107	8.9999
UCC	chr8:37555733-37556014(+)$1	281	228	231	8.9999
UCC	chr1:28527271-28527522(-)$1	251	27	30	8.9999
UCC	chr17:73888083-73888315(-)$1	232	3	6	8.9999
UCC	chr1:225155082-225155308(+)$1	226	88	91	8.9999
UCC	chr7:26251621-26251850(+)$1	229	134	137	8.9999
UCC	chr16:31191426-31191648(+)$1	222	39	42	8.9999
UCC	chrX:153284038-153284282(-)$1	244	24	27	8.9999
UCC	chr17:61890487-61890720(+)$1	233	116	119	8.9999
UCC	chr22:22142932-22143176(-)$1	244	29	32	8.9999
UCC	chr10:27400809-27401059(-)$1	250	234	237	8.9999
UCC	chr2:38973188-38973418(-)$1	230	107	110	8.9999
UCC	chr7:140080015-140080239(-)$1	224	60	63	8.9999
UCC	chr20:13747358-13747586(-)$1	228	120	123	8.9999
UCC	chrX:119007176-119007405(+)$1	229	10	13	8.9999
UCC	chr15:69708281-69708502(+)$1	221	91	94	8.9999
UCC	chr16:2821410-2821638(-)$1	228	5	8	8.9999
UCC	chr12:133291348-133291663(+)$1	315	162	165	8.9999
UCC	chr1:227174123-227174349(+)$1	226	10	13	8.9999
UCC	chr6:26156740-26157105(+)$1	365	28	31	8.9999
UCC	chr17:7158002-7158271(+)$1	269	7	10	8.9999
UCC	chr5:140027049-140027288(-)$1	239	52	55	8.9999
UCC	chr10:94100395-94100623(+)$1	228	35	38	8.9999
UCC	chr19:35996519-35996752(-)$1	233	75	78	8.9999
UCC	chr16:2816731-2817018(+)$1	287	10	13	8.9999
UCC	chr9:134351438-134351666(+)$1	228	15	18	8.9999
UCC	chr1:27736085-27736321(-)$1	236	5	8	8.9999
ucc	chr7:27149658-27149908(-)$1	250	11	14	8.9999
UCC	chr17:40734678-40734924(-)$1	246	59	62	8.9999
UCC	chr13:52604560-52604787(+)$1	227	64	67	8.9999
UCC	chr17:38140489-38140760(+)$1	271	143	146	8.9999
UCC	chr6:24716281-24716532(-)$1	251	50	53	8.9999
UCC	chr3:197680781-197681012(+)$1	231	44	47	8.9999
UCC	chrX:71492986-71493272(-)$1	286	23	26	8.9999
UCC	chr5:71491637-71491941(+)$1	304	26	29	8.9999
UCC	chr2:32517239-32517476(+)$1	237	47	50	8.9999
UCC	chrX:53240894-53241179(-)$1	285	3	6	8.9999
UCC	chr15:69080011-69080279(-)$1	268	34	37	8.9999
UCC	chr1:62910418-62910654(+)$1	236	82	85	8.9999
UCC	chr19:44605254-44605478(+)$1	224	43	46	8.9999
UCC	chr19:14551906-14552129(+)$1	223	13	16	8.9999
UCC	chr12:4771626-4771867(+)$1	241	104	107	8.9999
UCC	chr1:43212849-43213070(-)$1	221	177	180	8.9999
UCC	chr6:53139836-53140081(-)$1	245	13	16	8.9999
UCC	chr17:45754328-45754561(+)$1	233	40	43	8.9999
UCC	chr1:214814088-214814313(+)$1	225	55	58	8.9999
UCC	chr8:42798410-42798664(+)$1	254	26	29	8.9999
UCC	chr22:20109780-20110016(+)$1	236	20	23	8.9999
UCC	chr7:75695566-75695805(+)$1	239	15	18	8.9999
UCC	chr21:44514705-44514948(-)$1	243	120	123	8.9999
UCC	chrX:47058358-47058606(+)$1	248	33	36	8.9999
UCC	chr12:115112435-115112665(-)$1	230	8	11	8.9999
UCC	chr1:153635122-153635359(-)$1	237	45	48	8.9999
UCC	chr12:53715079-53715303(-)$1	224	8	11	8.9999
UCC	chr19:39308021-39308248(-)$1	227	12	15	8.9999
UCC	chr17:46700159-46700391(-)$1	232	38	41	8.9999
UCC	chr9:134340212-134340441(+)$1	229	30	33	8.9999
UCC	chr19:41800365-41800642(+)$1	277	21	24	8.9999
UCC	chr12:131357506-131357758(+)$1	252	12	15	8.9999
UCC	chr1:109241737-109241975(+)$1	238	28	31	8.9999
UCC	chr5:175812159-175812391(-)$1	232	31	34	8.9999
UCC	chr8:30037929-30038158(+)$1	229	152	155	8.9999
UCC	chr19:58904392-58904652(+)$1	260	23	26	8.9999
UCC	chr8:110283135-110283358(-)$1	223	1	4	8.9999
UCC	chr4:83348284-83348541(-)$1	257	225	228	8.9999
UCC	chr6:116909920-116910159(+)$1	239	57	60	8.9999
ucc	chr12:21788484-21788743(-)$1	259	2	5	8.9999
UCC	chr1:153640893-153641129(-)$1	236	44	47	8.9999
UCC	chr1:202912862-202913157(-)$1	295	45	48	8.9999
UCC	chr14:90770214-90770444(-)$1	230	21	24	8.9999
UCC	chr10:53459124-53459357(-)$1	233	17	20	8.9999
UCC	chr19:34890371-34890632(+)$1	261	28	31	8.9999
UCC	chr7:65418989-65419225(+)$1	236	3	6	8.9999
UCC	chr16:31195136-31195394(+)$1	258	1	4	8.9999
UCC	chrX:39916365-39916595(-)$1	230	3	6	8.9999
UCC	chr10:1046818-1047042(+)$1	224	21	24	8.9999

#otherMatches

#Struct PSSM
FFF	chr15:41188147-41188386(+)$1	239	56	59	8.9999
h]b	chr14:23793317-23793591(+)$1	274	33	36	8.9999
III	chr8:67577932-67578180(-)$1	248	34	37	8.9999
ddc	chr2:152289490-152289750(+)$1	260	150	153	8.9999
ddd	chr19:57802407-57802630(+)$1	223	9	12	8.9999
ddd	chr12:57032786-57033095(-)$1	309	13	16	8.9999
ccq	chr11:75115129-75115354(+)$1	225	8	11	8.9999
ooo	chr1:100547592-100547827(+)$1	235	43	46	8.9999
ddd	chr7:27211437-27211684(-)$1	247	51	54	8.9999
ddd	chr19:39923774-39924107(-)$1	333	24	27	8.9999
ddd	chr14:103988675-103988942(-)$1	267	72	75	8.9999
[ee	chr12:49953993-49954242(-)$1	249	10	13	8.9999
nnc	chrX:118726250-118726556(-)$1	306	39	42	8.9999
eee	chr6:43193433-43193689(-)$1	256	2	5	8.9999
ooo	chr11:82644523-82644749(+)$1	226	39	42	8.9999
fff	chr7:26236838-26237181(-)$1	343	111	114	8.9999
!cc	chr4:83347517-83347861(-)$1	344	47	50	8.9999
LLC	chr16:29820828-29821116(+)$1	288	11	14	8.9999
NNI	chr4:174298298-174298525(+)$1	227	32	35	8.9999
mmb	chr2:101622321-101622551(+)$1	230	116	119	8.9999
mmm	chr15:66792386-66792610(-)$1	224	104	107	8.9999
33e	chr8:37555733-37556014(+)$1	281	228	231	8.9999
:::	chr1:28527271-28527522(-)$1	251	27	30	8.9999
ooo	chr17:73888083-73888315(-)$1	232	3	6	8.9999
ccm	chr1:225155082-225155308(+)$1	226	88	91	8.9999
aee	chr7:26251621-26251850(+)$1	229	134	137	8.9999
]ee	chr16:31191426-31191648(+)$1	222	39	42	8.9999
ccc	chrX:153284038-153284282(-)$1	244	24	27	8.9999
bbs	chr17:61890487-61890720(+)$1	233	116	119	8.9999
ggg	chr22:22142932-22143176(-)$1	244	29	32	8.9999
iii	chr10:27400809-27401059(-)$1	250	234	237	8.9999
GGG	chr2:38973188-38973418(-)$1	230	107	110	8.9999
g!!	chr7:140080015-140080239(-)$1	224	60	63	8.9999
ggg	chr20:13747358-13747586(-)$1	228	120	123	8.9999
[cc	chrX:119007176-119007405(+)$1	229	10	13	8.9999
eey	chr15:69708281-69708502(+)$1	221	91	94	8.9999
GGG	chr16:2821410-2821638(-)$1	228	5	8	8.9999
eee	chr12:133291348-133291663(+)$1	315	162	165	8.9999
DDD	chr1:227174123-227174349(+)$1	226	10	13	8.9999
bbm	chr6:26156740-26157105(+)$1	365	28	31	8.9999
rrr	chr17:7158002-7158271(+)$1	269	7	10	8.9999
ba!	chr5:140027049-140027288(-)$1	239	52	55	8.9999
GGG	chr10:94100395-94100623(+)$1	228	35	38	8.9999
ppp	chr19:35996519-35996752(-)$1	233	75	78	8.9999
ELL	chr16:2816731-2817018(+)$1	287	10	13	8.9999
fff	chr9:134351438-134351666(+)$1	228	15	18	8.9999
GGA	chr1:27736085-27736321(-)$1	236	5	8	8.9999
:::	chr7:27149658-27149908(-)$1	250	11	14	8.9999
[bb	chr17:40734678-40734924(-)$1	246	59	62	8.9999
FFF	chr13:52604560-52604787(+)$1	227	64	67	8.9999
nnb	chr17:38140489-38140760(+)$1	271	143	146	8.9999
:::	chr6:24716281-24716532(-)$1	251	50	53	8.9999
EEE	chr3:197680781-197681012(+)$1	231	44	47	8.9999
HHH	chrX:71492986-71493272(-)$1	286	23	26	8.9999
C{E	chr5:71491637-71491941(+)$1	304	26	29	8.9999
vvv	chr2:32517239-32517476(+)$1	237	47	50	8.9999
:::	chrX:53240894-53241179(-)$1	285	3	6	8.9999
DDD	chr15:69080011-69080279(-)$1	268	34	37	8.9999
c[b	chr1:62910418-62910654(+)$1	236	82	85	8.9999
:::	chr19:44605254-44605478(+)$1	224	43	46	8.9999
KKB	chr19:14551906-14552129(+)$1	223	13	16	8.9999
eee	chr12:4771626-4771867(+)$1	241	104	107	8.9999
hh:	chr1:43212849-43213070(-)$1	221	177	180	8.9999
HHH	chr6:53139836-53140081(-)$1	245	13	16	8.9999
ooo	chr17:45754328-45754561(+)$1	233	40	43	8.9999
ccc	chr1:214814088-214814313(+)$1	225	55	58	8.9999
FFF	chr8:42798410-42798664(+)$1	254	26	29	8.9999
ddd	chr22:20109780-20110016(+)$1	236	20	23	8.9999
dd"	chr7:75695566-75695805(+)$1	239	15	18	8.9999
HHH	chr21:44514705-44514948(-)$1	243	120	123	8.9999
JJJ	chrX:47058358-47058606(+)$1	248	33	36	8.9999
[gg	chr12:115112435-115112665(-)$1	230	8	11	8.9999
{JJ	chr1:153635122-153635359(-)$1	237	45	48	8.9999
GGG	chr12:53715079-53715303(-)$1	224	8	11	8.9999
ggg	chr19:39308021-39308248(-)$1	227	12	15	8.9999
BB{	chr17:46700159-46700391(-)$1	232	38	41	8.9999
HHA	chr9:134340212-134340441(+)$1	229	30	33	8.9999
5ff	chr19:41800365-41800642(+)$1	277	21	24	8.9999
eee	chr12:131357506-131357758(+)$1	252	12	15	8.9999
JJJ	chr1:109241737-109241975(+)$1	238	28	31	8.9999
CCC	chr5:175812159-175812391(-)$1	232	31	34	8.9999
:::	chr8:30037929-30038158(+)$1	229	152	155	8.9999
dnn	chr19:58904392-58904652(+)$1	260	23	26	8.9999
:::	chr8:110283135-110283358(-)$1	223	1	4	8.9999
iii	chr4:83348284-83348541(-)$1	257	225	228	8.9999
ooc	chr6:116909920-116910159(+)$1	239	57	60	8.9999
:::	chr12:21788484-21788743(-)$1	259	2	5	8.9999
xxd	chr1:153640893-153641129(-)$1	236	44	47	8.9999
bbp	chr1:202912862-202913157(-)$1	295	45	48	8.9999
eee	chr14:90770214-90770444(-)$1	230	21	24	8.9999
::B	chr10:53459124-53459357(-)$1	233	17	20	8.9999
b[=	chr19:34890371-34890632(+)$1	261	28	31	8.9999
:::	chr7:65418989-65419225(+)$1	236	3	6	8.9999
::E	chr16:31195136-31195394(+)$1	258	1	4	8.9999
eee	chrX:39916365-39916595(-)$1	230	3	6	8.9999
:::	chr10:1046818-1047042(+)$1	224	21	24	8.9999

#DB
(((	chr15:41188147-41188386(+)$1	1	56	59	8.9999
).)	chr14:23793317-23793591(+)$1	1	33	36	8.9999
(((	chr8:67577932-67578180(-)$1	1	34	37	8.9999
(((	chr2:152289490-152289750(+)$1	1	150	153	8.9999
)))	chr19:57802407-57802630(+)$1	1	9	12	8.9999
(((	chr12:57032786-57033095(-)$1	1	13	16	8.9999
((.	chr11:75115129-75115354(+)$1	1	8	11	8.9999
...	chr1:100547592-100547827(+)$1	1	43	46	8.9999
(((	chr7:27211437-27211684(-)$1	1	51	54	8.9999
(((	chr19:39923774-39924107(-)$1	1	24	27	8.9999
)))	chr14:103988675-103988942(-)$1	1	72	75	8.9999
.((	chr12:49953993-49954242(-)$1	1	10	13	8.9999
..)	chrX:118726250-118726556(-)$1	1	39	42	8.9999
(((	chr6:43193433-43193689(-)$1	1	2	5	8.9999
...	chr11:82644523-82644749(+)$1	1	39	42	8.9999
(((	chr7:26236838-26237181(-)$1	1	111	114	8.9999
.((	chr4:83347517-83347861(-)$1	1	47	50	8.9999
..(	chr16:29820828-29821116(+)$1	1	11	14	8.9999
..(	chr4:174298298-174298525(+)$1	1	32	35	8.9999
..)	chr2:101622321-101622551(+)$1	1	116	119	8.9999
...	chr15:66792386-66792610(-)$1	1	104	107	8.9999
..)	chr8:37555733-37556014(+)$1	1	228	231	8.9999
...	chr1:28527271-28527522(-)$1	1	27	30	8.9999
...	chr17:73888083-73888315(-)$1	1	3	6	8.9999
((.	chr1:225155082-225155308(+)$1	1	88	91	8.9999
)))	chr7:26251621-26251850(+)$1	1	134	137	8.9999
.))	chr16:31191426-31191648(+)$1	1	39	42	8.9999
)))	chrX:153284038-153284282(-)$1	1	24	27	8.9999
((.	chr17:61890487-61890720(+)$1	1	116	119	8.9999
)))	chr22:22142932-22143176(-)$1	1	29	32	8.9999
)))	chr10:27400809-27401059(-)$1	1	234	237	8.9999
)))	chr2:38973188-38973418(-)$1	1	107	110	8.9999
(..	chr7:140080015-140080239(-)$1	1	60	63	8.9999
(((	chr20:13747358-13747586(-)$1	1	120	123	8.9999
.((	chrX:119007176-119007405(+)$1	1	10	13	8.9999
((.	chr15:69708281-69708502(+)$1	1	91	94	8.9999
(((	chr16:2821410-2821638(-)$1	1	5	8	8.9999
(((	chr12:133291348-133291663(+)$1	1	162	165	8.9999
(((	chr1:227174123-227174349(+)$1	1	10	13	8.9999
((.	chr6:26156740-26157105(+)$1	1	28	31	8.9999
...	chr17:7158002-7158271(+)$1	1	7	10	8.9999
((.	chr5:140027049-140027288(-)$1	1	52	55	8.9999
(((	chr10:94100395-94100623(+)$1	1	35	38	8.9999
...	chr19:35996519-35996752(-)$1	1	75	78	8.9999
(..	chr16:2816731-2817018(+)$1	1	10	13	8.9999
(((	chr9:134351438-134351666(+)$1	1	15	18	8.9999
(((	chr1:27736085-27736321(-)$1	1	5	8	8.9999
...	chr7:27149658-27149908(-)$1	1	11	14	8.9999
.((	chr17:40734678-40734924(-)$1	1	59	62	8.9999
(((	chr13:52604560-52604787(+)$1	1	64	67	8.9999
..)	chr17:38140489-38140760(+)$1	1	143	146	8.9999
...	chr6:24716281-24716532(-)$1	1	50	53	8.9999
(((	chr3:197680781-197681012(+)$1	1	44	47	8.9999
(((	chrX:71492986-71493272(-)$1	1	23	26	8.9999
(.(	chr5:71491637-71491941(+)$1	1	26	29	8.9999
...	chr2:32517239-32517476(+)$1	1	47	50	8.9999
...	chrX:53240894-53241179(-)$1	1	3	6	8.9999
(((	chr15:69080011-69080279(-)$1	1	34	37	8.9999
(.(	chr1:62910418-62910654(+)$1	1	82	85	8.9999
...	chr19:44605254-44605478(+)$1	1	43	46	8.9999
..(	chr19:14551906-14552129(+)$1	1	13	16	8.9999
(((	chr12:4771626-4771867(+)$1	1	104	107	8.9999
)).	chr1:43212849-43213070(-)$1	1	177	180	8.9999
(((	chr6:53139836-53140081(-)$1	1	13	16	8.9999
...	chr17:45754328-45754561(+)$1	1	40	43	8.9999
)))	chr1:214814088-214814313(+)$1	1	55	58	8.9999
(((	chr8:42798410-42798664(+)$1	1	26	29	8.9999
)))	chr22:20109780-20110016(+)$1	1	20	23	8.9999
((.	chr7:75695566-75695805(+)$1	1	15	18	8.9999
)))	chr21:44514705-44514948(-)$1	1	120	123	8.9999
(((	chrX:47058358-47058606(+)$1	1	33	36	8.9999
.((	chr12:115112435-115112665(-)$1	1	8	11	8.9999
.((	chr1:153635122-153635359(-)$1	1	45	48	8.9999
(((	chr12:53715079-53715303(-)$1	1	8	11	8.9999
(((	chr19:39308021-39308248(-)$1	1	12	15	8.9999
((.	chr17:46700159-46700391(-)$1	1	38	41	8.9999
(((	chr9:134340212-134340441(+)$1	1	30	33	8.9999
.))	chr19:41800365-41800642(+)$1	1	21	24	8.9999
)))	chr12:131357506-131357758(+)$1	1	12	15	8.9999
(((	chr1:109241737-109241975(+)$1	1	28	31	8.9999
(((	chr5:175812159-175812391(-)$1	1	31	34	8.9999
...	chr8:30037929-30038158(+)$1	1	152	155	8.9999
(..	chr19:58904392-58904652(+)$1	1	23	26	8.9999
...	chr8:110283135-110283358(-)$1	1	1	4	8.9999
)))	chr4:83348284-83348541(-)$1	1	225	228	8.9999
..)	chr6:116909920-116910159(+)$1	1	57	60	8.9999
...	chr12:21788484-21788743(-)$1	1	2	5	8.9999
..)	chr1:153640893-153641129(-)$1	1	44	47	8.9999
((.	chr1:202912862-202913157(-)$1	1	45	48	8.9999
)))	chr14:90770214-90770444(-)$1	1	21	24	8.9999
..(	chr10:53459124-53459357(-)$1	1	17	20	8.9999
(.(	chr19:34890371-34890632(+)$1	1	28	31	8.9999
...	chr7:65418989-65419225(+)$1	1	3	6	8.9999
..(	chr16:31195136-31195394(+)$1	1	1	4	8.9999
(((	chrX:39916365-39916595(-)$1	1	3	6	8.9999
...	chr10:1046818-1047042(+)$1	1	21	24	8.9999

#PSSM
U : 0.97	u : 0.02	
C : 0.97	c : 0.02	
C : 0.97	c : 0.02	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_UTR_m2_run1.nuc.txt

#NT
UGU	chr17:49239238-49239483(+)$1	245	34	37	8.9999
UGU	chr1:150547755-150547975(-)$1	220	21	24	8.9999
UGU	chr1:217781672-217781904(-)$1	232	3	6	8.9999
UGU	chr4:122725695-122725941(+)$1	246	8	11	8.9999
UGU	chr12:133780668-133780935(+)$1	267	31	34	8.9999
UGU	chr2:70443524-70443754(-)$1	230	0	3	8.9999
UGU	chr20:3888493-3888736(+)$1	243	14	17	8.9999
UGU	chr11:57586105-57586332(+)$1	227	29	32	8.9999
UGU	chr16:71962602-71962847(+)$1	245	67	70	8.9999
UGU	chr19:36237674-36237903(+)$1	229	139	142	8.9999
UGU	chr1:7826638-7826860(+)$1	222	92	95	8.9999
UGU	chr11:94863640-94863868(+)$1	228	24	27	8.9999
UGU	chr1:162498316-162498541(+)$1	225	130	133	8.9999
ugu	chr1:161184043-161184268(+)$1	225	16	19	8.9999
UGU	chr7:138745355-138745579(-)$1	224	66	69	8.9999
UGU	chr3:107525864-107526096(+)$1	232	9	12	8.9999
UGU	chr6:56969244-56969481(+)$1	237	7	10	8.9999
UGU	chr7:44252373-44252602(+)$1	229	90	93	8.9999
UGU	chr12:49413640-49413891(-)$1	251	115	118	8.9999
UGU	chr1:150191010-150191249(-)$1	239	20	23	8.9999
UGU	chr2:172821863-172822091(+)$1	228	3	6	8.9999
UGU	chr19:8530268-8530498(+)$1	230	121	124	8.9999
UGU	chr10:103545989-103546243(-)$1	254	8	11	8.9999
UGU	chr20:4682025-4682255(+)$1	230	32	35	8.9999
UGU	chr2:96918373-96918597(-)$1	224	55	58	8.9999
UGU	chr2:135714816-135715042(+)$1	226	5	8	8.9999
UGU	chr12:64895309-64895551(+)$1	242	24	27	8.9999
UGU	chr12:109548564-109548810(+)$1	246	152	155	8.9999
UGU	chr9:14088141-14088379(-)$1	238	3	6	8.9999
UGU	chr5:134086977-134087204(+)$1	227	26	29	8.9999
UGU	chr2:27016578-27016808(+)$1	230	72	75	8.9999
UGU	chr14:70838838-70839063(-)$1	225	7	10	8.9999
UGU	chr7:123324106-123324337(-)$1	231	6	9	8.9999
UGU	chr10:89511571-89511808(-)$1	237	31	34	8.9999
UGU	chr12:116397177-116397403(-)$1	226	90	93	8.9999
UGU	chr16:71780407-71780637(-)$1	230	25	28	8.9999
UGU	chr16:24815944-24816167(+)$1	223	7	10	8.9999
UGU	chr12:69054234-69054471(+)$1	237	6	9	8.9999
UGU	chr17:17088750-17088999(+)$1	249	2	5	8.9999
UGU	chr2:160623920-160624179(+)$1	259	7	10	8.9999
UGU	chr1:59247063-59247329(-)$1	266	37	40	8.9999
UGU	chr2:86333168-86333386(-)$1	218	37	40	8.9999
UGU	chr2:27550814-27551041(-)$1	227	98	101	8.9999
UGU	chr12:102542610-102542831(+)$1	221	4	7	8.9999
UGU	chr1:230991336-230991563(-)$1	227	54	57	8.9999
UGU	chr14:69257077-69257307(-)$1	230	16	19	8.9999
UGU	chr2:74334368-74334594(+)$1	226	144	147	8.9999
UGU	chr8:12580457-12580692(-)$1	235	8	11	8.9999
UGU	chr11:125526682-125526921(+)$1	239	51	54	8.9999
UGU	chr13:42896394-42896617(+)$1	223	12	15	8.9999
UGU	chr12:77417180-77417402(-)$1	222	66	69	8.9999
UGU	chr11:57471143-57471378(-)$1	235	46	49	8.9999
UGU	chr14:35181344-35181577(-)$1	233	20	23	8.9999
UGU	chr12:68056773-68057011(+)$1	238	50	53	8.9999
UGU	chr10:51590276-51590506(+)$1	230	19	22	8.9999
UGU	chr7:158526407-158526646(-)$1	239	0	3	8.9999
UGU	chr16:732181-732403(+)$1	222	5	8	8.9999
UGU	chr6:74225684-74225912(-)$1	228	91	94	8.9999
UGU	chr7:101893975-101894212(+)$1	237	25	28	8.9999
ugu	chr21:30716991-30717243(+)$1	252	0	3	8.9999
UGU	chr14:65542077-65542311(-)$1	234	2	5	8.9999
UGU	chrX:123042077-123042385(+)$1	308	7	10	8.9999
UGU	chr19:53302434-53302676(-)$1	242	0	3	8.9999
UGU	chr8:11185030-11185255(+)$1	225	16	19	8.9999
UGU	chr6:117883671-117883897(-)$1	226	40	43	8.9999
UGU	chr5:151187952-151188199(+)$1	247	50	53	8.9999
UGU	chr2:32843369-32843599(+)$1	230	34	37	8.9999
UGU	chr11:102269276-102269515(-)$1	239	40	43	8.9999
UGU	chr10:61548850-61549072(-)$1	222	1	4	8.9999
UGU	chr17:38189545-38189797(-)$1	252	48	51	8.9999
UGU	chr19:2429102-2429342(-)$1	240	5	8	8.9999
UGU	chr7:115898651-115898935(+)$1	284	2	5	8.9999
UGU	chr5:175816622-175816854(+)$1	232	9	12	8.9999
UGU	chr1:147097645-147097880(+)$1	235	60	63	8.9999
UGU	chr9:134373572-134373837(+)$1	265	62	65	8.9999
UGU	chr11:14891263-14891488(+)$1	225	19	22	8.9999
UGU	chr1:224344953-224345200(+)$1	247	37	40	8.9999
UGU	chr3:31678720-31678966(+)$1	246	98	101	8.9999
UGU	chr17:17150696-17150931(-)$1	235	41	44	8.9999
UGU	chr14:104025856-104026079(-)$1	223	71	74	8.9999
UGU	chr15:73004511-73004733(+)$1	222	2	5	8.9999
UGU	chrX:24002874-24003111(-)$1	237	54	57	8.9999
UGU	chr7:154777660-154777888(-)$1	228	1	4	8.9999
UGU	chr2:10923567-10923794(-)$1	227	26	29	8.9999
UGU	chrX:18258053-18258300(-)$1	247	49	52	8.9999
ugu	chr14:67853088-67853308(+)$1	220	16	19	8.9999
UGU	chr5:64961770-64962003(-)$1	233	131	134	8.9999
UGU	chr7:27868442-27868676(+)$1	234	152	155	8.9999
UGU	chr19:3976038-3976274(-)$1	236	27	30	8.9999
UGU	chr16:69389384-69389612(-)$1	228	2	5	8.9999
UGU	chr5:82876808-82877041(+)$1	233	95	98	8.9999
UGU	chr17:6547586-6547811(-)$1	225	56	59	8.9999
UGU	chr3:141167545-141167785(+)$1	240	16	19	8.9999
UGu	chr10:28908366-28908637(+)$1	271	5	8	8.9999
ugu	chr5:96367570-96367804(+)$1	234	10	13	8.9999
UGU	chr5:38479742-38479976(-)$1	234	33	36	8.9999

#otherMatches

#Struct PSSM
DDD	chr1:200374103-200374342(-)$1	239	26	29	8.9999
DDD	chr17:49239238-49239483(+)$1	245	34	37	8.9999
ooo	chr1:150547755-150547975(-)$1	220	21	24	8.9999
:ee	chr1:217781672-217781904(-)$1	232	3	6	8.9999
III	chr4:122725695-122725941(+)$1	246	8	11	8.9999
ff:	chr12:133780668-133780935(+)$1	267	31	34	8.9999
:::	chr2:70443524-70443754(-)$1	230	0	3	8.9999
FFF	chr20:3888493-3888736(+)$1	243	14	17	8.9999
d]a	chr11:57586105-57586332(+)$1	227	29	32	8.9999
!ee	chr16:71962602-71962847(+)$1	245	67	70	8.9999
===	chr19:36237674-36237903(+)$1	229	139	142	8.9999
III	chr1:7826638-7826860(+)$1	222	92	95	8.9999
eee	chr11:94863640-94863868(+)$1	228	24	27	8.9999
ddd	chr1:162498316-162498541(+)$1	225	130	133	8.9999
:::	chr1:161184043-161184268(+)$1	225	16	19	8.9999
goo	chr7:138745355-138745579(-)$1	224	66	69	8.9999
===	chr3:107525864-107526096(+)$1	232	9	12	8.9999
HKK	chr6:56969244-56969481(+)$1	237	7	10	8.9999
bbf	chr7:44252373-44252602(+)$1	229	90	93	8.9999
c[f	chr12:49413640-49413891(-)$1	251	115	118	8.9999
ncc	chr1:150191010-150191249(-)$1	239	20	23	8.9999
:CC	chr2:172821863-172822091(+)$1	228	3	6	8.9999
c]d	chr19:8530268-8530498(+)$1	230	121	124	8.9999
hhh	chr10:103545989-103546243(-)$1	254	8	11	8.9999
rrr	chr20:4682025-4682255(+)$1	230	32	35	8.9999
""a	chr2:96918373-96918597(-)$1	224	55	58	8.9999
EEE	chr2:135714816-135715042(+)$1	226	5	8	8.9999
D::	chr12:64895309-64895551(+)$1	242	24	27	8.9999
:::	chr12:109548564-109548810(+)$1	246	152	155	8.9999
EEE	chr9:14088141-14088379(-)$1	238	3	6	8.9999
ppp	chr5:134086977-134087204(+)$1	227	26	29	8.9999
zzz	chr2:27016578-27016808(+)$1	230	72	75	8.9999
::D	chr14:70838838-70839063(-)$1	225	7	10	8.9999
!ee	chr7:123324106-123324337(-)$1	231	6	9	8.9999
eee	chr10:89511571-89511808(-)$1	237	31	34	8.9999
eee	chr12:116397177-116397403(-)$1	226	90	93	8.9999
ddd	chr16:71780407-71780637(-)$1	230	25	28	8.9999
ccc	chr16:24815944-24816167(+)$1	223	7	10	8.9999
ddd	chr12:69054234-69054471(+)$1	237	6	9	8.9999
:dd	chr17:17088750-17088999(+)$1	249	2	5	8.9999
::d	chr2:160623920-160624179(+)$1	259	7	10	8.9999
fff	chr1:59247063-59247329(-)$1	266	37	40	8.9999
ccc	chr2:86333168-86333386(-)$1	218	37	40	8.9999
ddd	chr2:27550814-27551041(-)$1	227	98	101	8.9999
{AK	chr12:102542610-102542831(+)$1	221	4	7	8.9999
[gg	chr1:230991336-230991563(-)$1	227	54	57	8.9999
LGG	chr14:69257077-69257307(-)$1	230	16	19	8.9999
nbb	chr2:74334368-74334594(+)$1	226	144	147	8.9999
ffe	chr8:12580457-12580692(-)$1	235	8	11	8.9999
nnn	chr11:125526682-125526921(+)$1	239	51	54	8.9999
GGG	chr13:42896394-42896617(+)$1	223	12	15	8.9999
HHH	chr12:77417180-77417402(-)$1	222	66	69	8.9999
mmm	chr11:57471143-57471378(-)$1	235	46	49	8.9999
c[a	chr14:35181344-35181577(-)$1	233	20	23	8.9999
CC{	chr12:68056773-68057011(+)$1	238	50	53	8.9999
:A{	chr10:51590276-51590506(+)$1	230	19	22	8.9999
BB{	chr7:158526407-158526646(-)$1	239	0	3	8.9999
DDD	chr16:732181-732403(+)$1	222	5	8	8.9999
mcc	chr6:74225684-74225912(-)$1	228	91	94	8.9999
===	chr7:101893975-101894212(+)$1	237	25	28	8.9999
hhh	chr21:30716991-30717243(+)$1	252	0	3	8.9999
:::	chr14:65542077-65542311(-)$1	234	2	5	8.9999
G:D	chrX:123042077-123042385(+)$1	308	7	10	8.9999
::D	chr19:53302434-53302676(-)$1	242	0	3	8.9999
MCC	chr8:11185030-11185255(+)$1	225	16	19	8.9999
ggg	chr6:117883671-117883897(-)$1	226	40	43	8.9999
DDD	chr5:151187952-151188199(+)$1	247	50	53	8.9999
RRR	chr2:32843369-32843599(+)$1	230	34	37	8.9999
eee	chr11:102269276-102269515(-)$1	239	40	43	8.9999
:::	chr10:61548850-61549072(-)$1	222	1	4	8.9999
CLL	chr17:38189545-38189797(-)$1	252	48	51	8.9999
HHH	chr19:2429102-2429342(-)$1	240	5	8	8.9999
:::	chr7:115898651-115898935(+)$1	284	2	5	8.9999
dd"	chr5:175816622-175816854(+)$1	232	9	12	8.9999
:::	chr1:147097645-147097880(+)$1	235	60	63	8.9999
ddd	chr9:134373572-134373837(+)$1	265	62	65	8.9999
HHH	chr11:14891263-14891488(+)$1	225	19	22	8.9999
b[a	chr1:224344953-224345200(+)$1	247	37	40	8.9999
HHH	chr3:31678720-31678966(+)$1	246	98	101	8.9999
ggg	chr17:17150696-17150931(-)$1	235	41	44	8.9999
:::	chr14:104025856-104026079(-)$1	223	71	74	8.9999
:::	chr15:73004511-73004733(+)$1	222	2	5	8.9999
HHH	chrX:24002874-24003111(-)$1	237	54	57	8.9999
:::	chr7:154777660-154777888(-)$1	228	1	4	8.9999
rrr	chr2:10923567-10923794(-)$1	227	26	29	8.9999
mmm	chrX:18258053-18258300(-)$1	247	49	52	8.9999
$$$	chr14:67853088-67853308(+)$1	220	16	19	8.9999
cc&	chr5:64961770-64962003(-)$1	233	131	134	8.9999
d::	chr7:27868442-27868676(+)$1	234	152	155	8.9999
ii#	chr19:3976038-3976274(-)$1	236	27	30	8.9999
[dd	chr16:69389384-69389612(-)$1	228	2	5	8.9999
occ	chr5:82876808-82877041(+)$1	233	95	98	8.9999
gpp	chr17:6547586-6547811(-)$1	225	56	59	8.9999
FFF	chr3:141167545-141167785(+)$1	240	16	19	8.9999
:::	chr10:28908366-28908637(+)$1	271	5	8	8.9999
hhh	chr5:96367570-96367804(+)$1	234	10	13	8.9999
FFF	chr5:38479742-38479976(-)$1	234	33	36	8.9999

#DB
(((	chr1:200374103-200374342(-)$1	1	26	29	8.9999
(((	chr17:49239238-49239483(+)$1	1	34	37	8.9999
...	chr1:150547755-150547975(-)$1	1	21	24	8.9999
.((	chr1:217781672-217781904(-)$1	1	3	6	8.9999
(((	chr4:122725695-122725941(+)$1	1	8	11	8.9999
)).	chr12:133780668-133780935(+)$1	1	31	34	8.9999
...	chr2:70443524-70443754(-)$1	1	0	3	8.9999
(((	chr20:3888493-3888736(+)$1	1	14	17	8.9999
).)	chr11:57586105-57586332(+)$1	1	29	32	8.9999
.((	chr16:71962602-71962847(+)$1	1	67	70	8.9999
)))	chr19:36237674-36237903(+)$1	1	139	142	8.9999
(((	chr1:7826638-7826860(+)$1	1	92	95	8.9999
(((	chr11:94863640-94863868(+)$1	1	24	27	8.9999
)))	chr1:162498316-162498541(+)$1	1	130	133	8.9999
...	chr1:161184043-161184268(+)$1	1	16	19	8.9999
(..	chr7:138745355-138745579(-)$1	1	66	69	8.9999
(((	chr3:107525864-107526096(+)$1	1	9	12	8.9999
(..	chr6:56969244-56969481(+)$1	1	7	10	8.9999
)))	chr7:44252373-44252602(+)$1	1	90	93	8.9999
(.(	chr12:49413640-49413891(-)$1	1	115	118	8.9999
.))	chr1:150191010-150191249(-)$1	1	20	23	8.9999
.((	chr2:172821863-172822091(+)$1	1	3	6	8.9999
).)	chr19:8530268-8530498(+)$1	1	121	124	8.9999
(((	chr10:103545989-103546243(-)$1	1	8	11	8.9999
...	chr20:4682025-4682255(+)$1	1	32	35	8.9999
..(	chr2:96918373-96918597(-)$1	1	55	58	8.9999
(((	chr2:135714816-135715042(+)$1	1	5	8	8.9999
(..	chr12:64895309-64895551(+)$1	1	24	27	8.9999
...	chr12:109548564-109548810(+)$1	1	152	155	8.9999
(((	chr9:14088141-14088379(-)$1	1	3	6	8.9999
...	chr5:134086977-134087204(+)$1	1	26	29	8.9999
...	chr2:27016578-27016808(+)$1	1	72	75	8.9999
..(	chr14:70838838-70839063(-)$1	1	7	10	8.9999
.((	chr7:123324106-123324337(-)$1	1	6	9	8.9999
(((	chr10:89511571-89511808(-)$1	1	31	34	8.9999
(((	chr12:116397177-116397403(-)$1	1	90	93	8.9999
(((	chr16:71780407-71780637(-)$1	1	25	28	8.9999
(((	chr16:24815944-24816167(+)$1	1	7	10	8.9999
(((	chr12:69054234-69054471(+)$1	1	6	9	8.9999
.((	chr17:17088750-17088999(+)$1	1	2	5	8.9999
..(	chr2:160623920-160624179(+)$1	1	7	10	8.9999
(((	chr1:59247063-59247329(-)$1	1	37	40	8.9999
)))	chr2:86333168-86333386(-)$1	1	37	40	8.9999
(((	chr2:27550814-27551041(-)$1	1	98	101	8.9999
.(.	chr12:102542610-102542831(+)$1	1	4	7	8.9999
.((	chr1:230991336-230991563(-)$1	1	54	57	8.9999
.((	chr14:69257077-69257307(-)$1	1	16	19	8.9999
.))	chr2:74334368-74334594(+)$1	1	144	147	8.9999
(((	chr8:12580457-12580692(-)$1	1	8	11	8.9999
...	chr11:125526682-125526921(+)$1	1	51	54	8.9999
(((	chr13:42896394-42896617(+)$1	1	12	15	8.9999
(((	chr12:77417180-77417402(-)$1	1	66	69	8.9999
...	chr11:57471143-57471378(-)$1	1	46	49	8.9999
(.(	chr14:35181344-35181577(-)$1	1	20	23	8.9999
((.	chr12:68056773-68057011(+)$1	1	50	53	8.9999
.(.	chr10:51590276-51590506(+)$1	1	19	22	8.9999
((.	chr7:158526407-158526646(-)$1	1	0	3	8.9999
(((	chr16:732181-732403(+)$1	1	5	8	8.9999
.))	chr6:74225684-74225912(-)$1	1	91	94	8.9999
(((	chr7:101893975-101894212(+)$1	1	25	28	8.9999
(((	chr21:30716991-30717243(+)$1	1	0	3	8.9999
...	chr14:65542077-65542311(-)$1	1	2	5	8.9999
(.(	chrX:123042077-123042385(+)$1	1	7	10	8.9999
..(	chr19:53302434-53302676(-)$1	1	0	3	8.9999
.((	chr8:11185030-11185255(+)$1	1	16	19	8.9999
(((	chr6:117883671-117883897(-)$1	1	40	43	8.9999
(((	chr5:151187952-151188199(+)$1	1	50	53	8.9999
...	chr2:32843369-32843599(+)$1	1	34	37	8.9999
(((	chr11:102269276-102269515(-)$1	1	40	43	8.9999
...	chr10:61548850-61549072(-)$1	1	1	4	8.9999
(..	chr17:38189545-38189797(-)$1	1	48	51	8.9999
(((	chr19:2429102-2429342(-)$1	1	5	8	8.9999
...	chr7:115898651-115898935(+)$1	1	2	5	8.9999
((.	chr5:175816622-175816854(+)$1	1	9	12	8.9999
...	chr1:147097645-147097880(+)$1	1	60	63	8.9999
(((	chr9:134373572-134373837(+)$1	1	62	65	8.9999
(((	chr11:14891263-14891488(+)$1	1	19	22	8.9999
(.(	chr1:224344953-224345200(+)$1	1	37	40	8.9999
(((	chr3:31678720-31678966(+)$1	1	98	101	8.9999
(((	chr17:17150696-17150931(-)$1	1	41	44	8.9999
...	chr14:104025856-104026079(-)$1	1	71	74	8.9999
...	chr15:73004511-73004733(+)$1	1	2	5	8.9999
(((	chrX:24002874-24003111(-)$1	1	54	57	8.9999
...	chr7:154777660-154777888(-)$1	1	1	4	8.9999
...	chr2:10923567-10923794(-)$1	1	26	29	8.9999
...	chrX:18258053-18258300(-)$1	1	49	52	8.9999
...	chr14:67853088-67853308(+)$1	1	16	19	8.9999
((.	chr5:64961770-64962003(-)$1	1	131	134	8.9999
)..	chr7:27868442-27868676(+)$1	1	152	155	8.9999
((.	chr19:3976038-3976274(-)$1	1	27	30	8.9999
.((	chr16:69389384-69389612(-)$1	1	2	5	8.9999
.))	chr5:82876808-82877041(+)$1	1	95	98	8.9999
(..	chr17:6547586-6547811(-)$1	1	56	59	8.9999
(((	chr3:141167545-141167785(+)$1	1	16	19	8.9999
...	chr10:28908366-28908637(+)$1	1	5	8	8.9999
(((	chr5:96367570-96367804(+)$1	1	10	13	8.9999
(((	chr5:38479742-38479976(-)$1	1	33	36	8.9999

#PSSM
U : 0.95	u : 0.04	
G : 0.95	g : 0.04	
U : 0.94	u : 0.05	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_CDS_m1_run2.nuc.txt

#NT
AUUUUUUU	chr17:5386025-5386258(-)$1	233	41	49	17.2407
CUUUUUCU	chr14:57698232-57698463(-)$1	231	3	11	16.4074
CUUUCUUU	chr12:111157906-111158191(-)$1	285	262	270	16.4074
CUUUUUUU	chr6:170105105-170105331(+)$1	226	106	114	20.5740
CUUUUUUU	chrX:48435824-48436083(+)$1	259	188	196	20.5740
GUUUUUUU	chrM:14381-14653(-)$1	272	141	149	16.9629
CUUUUCUU	chr15:41643036-41643288(+)$1	252	43	51	16.3148
cUUUUUUU	chr19:11256947-11257172(-)$1	225	12	20	20.5740
CUUUUUUU	chr7:91743055-91743284(-)$1	229	116	124	20.5740
CUAUUUUU	chr1:203786117-203786345(+)$1	228	104	112	16.0370
CUUUUAUU	chr9:123367816-123368090(-)$1	274	105	113	16.4999
Cuuuuauu	chr5:864404-864693(-)$1	289	130	138	16.4999
CUUGUUUU	chr14:62203523-62203750(+)$1	227	70	78	16.0370
AUUUUUUU	chr1:32384562-32384836(-)$1	274	108	116	17.2407
CUUUUUCU	chr9:19096605-19096838(-)$1	233	31	39	16.4074
CUUUUUUU	chr1:160247861-160248110(-)$1	249	138	146	20.5740
AUUUUUUU	chr6:64286617-64286893(+)$1	276	117	125	17.2407
CUUUGUUU	chr2:128521990-128522277(-)$1	287	14	22	16.4074
GUUUUUUU	chr8:97285473-97285703(+)$1	230	194	202	16.9629
CUUUUUUU	chr8:38961084-38961386(+)$1	302	183	191	20.5740
AUUUUUUU	chr8:62574384-62574646(-)$1	262	122	130	17.2407
CUUUUUUU	chr9:86584253-86584496(-)$1	243	118	126	20.5740
CUUUAUUU	chr11:33163074-33163311(-)$1	237	213	221	16.4999
CUUUAUUU	chr5:131008402-131008634(-)$1	232	103	111	16.4999
CUUUUUUU	chr13:45010577-45010808(-)$1	231	8	16	20.5740
CUUUUUAU	chr14:54896879-54897115(-)$1	236	100	108	16.2222
CUGUUUUU	chr13:96443144-96443447(+)$1	303	145	153	16.2222
CUUUUUUU	chr1:156714992-156715228(-)$1	236	116	124	20.5740
CUUUUCUU	chr4:108829724-108829954(+)$1	230	193	201	16.3148
CUGUUUUU	chrX:48432839-48433062(+)$1	223	61	69	16.2222
CUUGUUUU	chr7:94166789-94167016(+)$1	227	100	108	16.0370
AUUUUUUU	chr5:86705034-86705269(-)$1	235	71	79	17.2407
cuuuuuuu	chr19:18390706-18390940(-)$1	234	62	70	20.5740
CUUAUUUU	chr5:58571073-58571357(-)$1	284	101	109	15.9444
Cuuuuuuu	chr17:48941213-48941459(-)$1	246	19	27	20.5740
AUUUUUUU	chr17:29551989-29552215(+)$1	226	111	119	17.2407
CUUUUAUU	chr11:9459623-9459853(+)$1	230	112	120	16.4999
CUUUUUGU	chr7:112423936-112424159(-)$1	223	40	48	16.3148
CUUUUAUU	chr10:98292798-98293027(-)$1	229	15	23	16.4999
AUUUUUUU	chr11:9444498-9444740(+)$1	242	41	49	17.2407
CUGUUUUU	chr2:135711881-135712106(+)$1	225	122	130	16.2222
CUUUUUGU	chr1:93298970-93299204(+)$1	234	55	63	16.3148
CUUUGUUU	chr17:34893429-34893666(+)$1	237	39	47	16.4074
CUUUUUUU	chr14:73959656-73959886(+)$1	230	46	54	20.5740
cuuuuuuu	chr2:38523149-38523459(-)$1	310	154	162	20.5740
CUUUCUUU	chr1:28177069-28177295(+)$1	226	158	166	16.4074
CUUUUUUU	chr2:38522989-38523244(-)$1	255	137	145	20.5740
CUUUUUUU	chr15:64458148-64458407(-)$1	259	103	111	20.5740
cuuuuuuu	chr2:42936144-42936371(+)$1	227	160	168	20.5740
CUUUUUCU	chr11:32954264-32954491(+)$1	227	56	64	16.4074
CUUUUUUU	chr18:54278163-54278397(-)$1	234	55	63	20.5740
GUUUUUUU	chr16:66592077-66592311(+)$1	234	0	8	16.9629
CUUUAUUU	chr2:242276798-242277025(+)$1	227	109	117	16.4999

#otherMatches

#Struct PSSM
ffffffdd	chr12:46756783-46757013(-)$1	230	62	70	16.9629
cc::::::	chr17:5386025-5386258(-)$1	233	41	49	17.2407
HHHHHH::	chr14:57698232-57698463(-)$1	231	3	11	16.4074
gggggg::	chr12:111157906-111158191(-)$1	285	262	270	16.4074
[dddd###	chr6:170105105-170105331(+)$1	226	106	114	20.5740
!!ccciii	chrX:48435824-48436083(+)$1	259	188	196	20.5740
2iiiiiii	chrM:14381-14653(-)$1	272	141	149	16.9629
FFFFFF::	chr15:41643036-41643288(+)$1	252	43	51	16.3148
::::::::	chr19:11256947-11257172(-)$1	225	12	20	20.5740
hhhhhh::	chr7:91743055-91743284(-)$1	229	116	124	20.5740
qqqqqiii	chr1:203786117-203786345(+)$1	228	104	112	16.0370
::::::::	chr9:123367816-123368090(-)$1	274	105	113	16.4999
BKKFFFFF	chr5:864404-864693(-)$1	289	130	138	16.4999
rrrrrrrr	chr14:62203523-62203750(+)$1	227	70	78	16.0370
:HHHHHHH	chr1:32384562-32384836(-)$1	274	108	116	17.2407
a"""eeee	chr9:19096605-19096838(-)$1	233	31	39	16.4074
DDD{GGGG	chr1:160247861-160248110(-)$1	249	138	146	20.5740
ee^^^^^^	chr6:64286617-64286893(+)$1	276	117	125	17.2407
DDHHHHHH	chr2:128521990-128522277(-)$1	287	14	22	16.4074
cc666666	chr8:97285473-97285703(+)$1	230	194	202	16.9629
HHHHH:::	chr8:38961084-38961386(+)$1	302	183	191	20.5740
fppppppp	chr8:62574384-62574646(-)$1	262	122	130	17.2407
hh^^^^^^	chr9:86584253-86584496(-)$1	243	118	126	20.5740
B~~~~FFF	chr11:33163074-33163311(-)$1	237	213	221	16.4999
""======	chr5:131008402-131008634(-)$1	232	103	111	16.4999
::::::II	chr13:45010577-45010808(-)$1	231	8	16	20.5740
ccdddd]f	chr14:54896879-54897115(-)$1	236	100	108	16.2222
:::::GGG	chr13:96443144-96443447(+)$1	303	145	153	16.2222
eeeppppp	chr1:156714992-156715228(-)$1	236	116	124	20.5740
cc22ffff	chr4:108829724-108829954(+)$1	230	193	201	16.3148
f:::::::	chrX:48432839-48433062(+)$1	223	61	69	16.2222
ddd:====	chr7:94166789-94167016(+)$1	227	100	108	16.0370
IIII::::	chr5:86705034-86705269(-)$1	235	71	79	17.2407
:::=====	chr19:18390706-18390940(-)$1	234	62	70	20.5740
mmmmeeee	chr5:58571073-58571357(-)$1	284	101	109	15.9444
d^^^^^^^	chr17:48941213-48941459(-)$1	246	19	27	20.5740
:::::fff	chr17:29551989-29552215(+)$1	226	111	119	17.2407
d[bbnnnn	chr11:9459623-9459853(+)$1	230	112	120	16.4999
b::dddd#	chr7:112423936-112424159(-)$1	223	40	48	16.3148
GGGGEEEE	chr10:98292798-98293027(-)$1	229	15	23	16.4999
:::HHHHH	chr11:9444498-9444740(+)$1	242	41	49	17.2407
dddd22ee	chr2:135711881-135712106(+)$1	225	122	130	16.2222
eee]dddd	chr1:93298970-93299204(+)$1	234	55	63	16.3148
HHHHHHHK	chr17:34893429-34893666(+)$1	237	39	47	16.4074
HHHHKKJJ	chr14:73959656-73959886(+)$1	230	46	54	20.5740
::::::::	chr2:38523149-38523459(-)$1	310	154	162	20.5740
dd^^^^^^	chr1:28177069-28177295(+)$1	226	158	166	16.4074
::::::gg	chr2:38522989-38523244(-)$1	255	137	145	20.5740
cc::::::	chr15:64458148-64458407(-)$1	259	103	111	20.5740
::::::::	chr2:42936144-42936371(+)$1	227	160	168	20.5740
fffnnnnn	chr11:32954264-32954491(+)$1	227	56	64	16.4074
hhhhhhhh	chr18:54278163-54278397(-)$1	234	55	63	20.5740
::::::::	chr16:66592077-66592311(+)$1	234	0	8	16.9629
hhhhhhhc	chr2:242276798-242277025(+)$1	227	109	117	16.4999

#DB
))))))))	chr12:46756783-46757013(-)$1	1	62	70	16.9629
))......	chr17:5386025-5386258(-)$1	1	41	49	17.2407
((((((..	chr14:57698232-57698463(-)$1	1	3	11	16.4074
))))))..	chr12:111157906-111158191(-)$1	1	262	270	16.4074
.((((...	chr6:170105105-170105331(+)$1	1	106	114	20.5740
..((((((	chrX:48435824-48436083(+)$1	1	188	196	20.5740
.)))))))	chrM:14381-14653(-)$1	1	141	149	16.9629
((((((..	chr15:41643036-41643288(+)$1	1	43	51	16.3148
........	chr19:11256947-11257172(-)$1	1	12	20	20.5740
))))))..	chr7:91743055-91743284(-)$1	1	116	124	20.5740
.....)))	chr1:203786117-203786345(+)$1	1	104	112	16.0370
........	chr9:123367816-123368090(-)$1	1	105	113	16.4999
(..(((((	chr5:864404-864693(-)$1	1	130	138	16.4999
........	chr14:62203523-62203750(+)$1	1	70	78	16.0370
.)))))))	chr1:32384562-32384836(-)$1	1	108	116	17.2407
(...((((	chr9:19096605-19096838(-)$1	1	31	39	16.4074
(((.((((	chr1:160247861-160248110(-)$1	1	138	146	20.5740
((......	chr6:64286617-64286893(+)$1	1	117	125	17.2407
((((((((	chr2:128521990-128522277(-)$1	1	14	22	16.4074
))......	chr8:97285473-97285703(+)$1	1	194	202	16.9629
)))))...	chr8:38961084-38961386(+)$1	1	183	191	20.5740
(.......	chr8:62574384-62574646(-)$1	1	122	130	17.2407
((......	chr9:86584253-86584496(-)$1	1	118	126	20.5740
)....)))	chr11:33163074-33163311(-)$1	1	213	221	16.4999
..((((((	chr5:131008402-131008634(-)$1	1	103	111	16.4999
......((	chr13:45010577-45010808(-)$1	1	8	16	20.5740
)))))).)	chr14:54896879-54897115(-)$1	1	100	108	16.2222
.....)))	chr13:96443144-96443447(+)$1	1	145	153	16.2222
(((.....	chr1:156714992-156715228(-)$1	1	116	124	20.5740
))..))))	chr4:108829724-108829954(+)$1	1	193	201	16.3148
).......	chrX:48432839-48433062(+)$1	1	61	69	16.2222
))).((((	chr7:94166789-94167016(+)$1	1	100	108	16.0370
((((....	chr5:86705034-86705269(-)$1	1	71	79	17.2407
...(((((	chr19:18390706-18390940(-)$1	1	62	70	20.5740
....))))	chr5:58571073-58571357(-)$1	1	101	109	15.9444
(.......	chr17:48941213-48941459(-)$1	1	19	27	20.5740
.....(((	chr17:29551989-29552215(+)$1	1	111	119	17.2407
(.((....	chr11:9459623-9459853(+)$1	1	112	120	16.4999
)..((((.	chr7:112423936-112424159(-)$1	1	40	48	16.3148
((((((((	chr10:98292798-98293027(-)$1	1	15	23	16.4999
...(((((	chr11:9444498-9444740(+)$1	1	41	49	17.2407
))))..))	chr2:135711881-135712106(+)$1	1	122	130	16.2222
))).))))	chr1:93298970-93299204(+)$1	1	55	63	16.3148
(((((((.	chr17:34893429-34893666(+)$1	1	39	47	16.4074
((((..((	chr14:73959656-73959886(+)$1	1	46	54	20.5740
........	chr2:38523149-38523459(-)$1	1	154	162	20.5740
((......	chr1:28177069-28177295(+)$1	1	158	166	16.4074
......((	chr2:38522989-38523244(-)$1	1	137	145	20.5740
))......	chr15:64458148-64458407(-)$1	1	103	111	20.5740
........	chr2:42936144-42936371(+)$1	1	160	168	20.5740
(((.....	chr11:32954264-32954491(+)$1	1	56	64	16.4074
))))))))	chr18:54278163-54278397(-)$1	1	55	63	20.5740
........	chr16:66592077-66592311(+)$1	1	0	8	16.9629
))))))))	chr2:242276798-242277025(+)$1	1	109	117	16.4999

#PSSM
C : 0.72	A : 0.12	G : 0.07	c : 0.07	
U : 0.90	u : 0.09	
U : 0.83	u : 0.09	G : 0.05	A : 0.01	
U : 0.85	u : 0.09	G : 0.03	A : 0.01	
U : 0.77	u : 0.09	A : 0.05	C : 0.03	G : 0.03	
U : 0.81	u : 0.07	A : 0.05	C : 0.03	a : 0.01	
U : 0.79	u : 0.09	C : 0.05	G : 0.03	A : 0.01	
U : 0.90	u : 0.09	

#score	962.8518518518508
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_CDS_m2_run2.nuc.txt

#NT
UUUCU	chr12:988855-989085(+)$1	230	80	85	15.0000
UUUCU	chr2:198324579-198324809(+)$1	230	8	13	15.0000
UUUCU	chr1:32768184-32768414(+)$1	230	223	228	15.0000
UUUCU	chr2:28626915-28627131(-)$1	216	155	160	15.0000
UUUCU	chr7:138252252-138252478(+)$1	226	119	124	15.0000
UUUCU	chr3:196674765-196674983(-)$1	218	52	57	15.0000
UUUCU	chr1:153640907-153641137(-)$1	230	4	9	15.0000
UUUCU	chr2:219362648-219362873(-)$1	225	206	211	15.0000
UUUCU	chr9:100678497-100678717(-)$1	220	85	90	15.0000
UUUCU	chrM:9965-10195(-)$1	230	39	44	15.0000
UUUCU	chr14:69853627-69853862(-)$1	235	54	59	15.0000
UUUCU	chr17:27957742-27957977(-)$1	235	140	145	15.0000
UUUCU	chr7:77423251-77423473(-)$1	222	205	210	15.0000
UUUCU	chr11:77618662-77618892(-)$1	230	87	92	15.0000
UUUCU	chr16:21979848-21980078(+)$1	230	16	21	15.0000
UUUCU	chr12:109046023-109046248(-)$1	225	45	50	15.0000
UUUCU	chr5:118469849-118470079(+)$1	230	106	111	15.0000
UUUCU	chr16:24826410-24826640(+)$1	230	31	36	15.0000
UUUCU	chr2:174820119-174820343(-)$1	224	50	55	15.0000
UUUCU	chr1:183513446-183513670(+)$1	224	203	208	15.0000
UUUCU	chr11:102272771-102273001(-)$1	230	45	50	15.0000
UUUCU	chr6:71269486-71269716(+)$1	230	105	110	15.0000
UUUCU	chr16:69200891-69201121(+)$1	230	180	185	15.0000
UUUCU	chr16:72822640-72822863(-)$1	223	94	99	15.0000
UUUCU	chr5:114860506-114860730(-)$1	224	196	201	15.0000
UUUCU	chr17:48941234-48941464(-)$1	230	1	6	15.0000
UUUCU	chr22:22160047-22160277(-)$1	230	31	36	15.0000
UUUCU	chr2:228419087-228419317(+)$1	230	114	119	15.0000
UUUCU	chr17:33591136-33591366(+)$1	230	32	37	15.0000
UUUCU	chr14:24649262-24649489(+)$1	227	123	128	15.0000
UUUCU	chr12:44165901-44166121(+)$1	220	10	15	15.0000
UUUCU	chr17:27613569-27613802(-)$1	233	31	36	15.0000
UUUCU	chr14:21878013-21878243(-)$1	230	65	70	15.0000
UUUCU	chr9:72338403-72338633(-)$1	230	73	78	15.0000
UUUCU	chr20:33233010-33233240(-)$1	230	20	25	15.0000
UUUCU	chr9:88293173-88293403(-)$1	230	165	170	15.0000
UUUCU	chr7:150775032-150775250(+)$1	218	185	190	15.0000
UUUCU	chr10:75897865-75898095(-)$1	230	0	5	15.0000
UUUCU	chr3:122331833-122332063(+)$1	230	104	109	15.0000
UUUCU	chr4:76714790-76715015(+)$1	225	100	105	15.0000
UUUCU	chr2:213878490-213878716(-)$1	226	39	44	15.0000
UUUCU	chr6:135514889-135515119(+)$1	230	219	224	15.0000
UUUCU	chr11:6630739-6630961(+)$1	222	6	11	15.0000
UUUCU	chr1:25669389-25669619(+)$1	230	34	39	15.0000
UUUCU	chr6:34725600-34725826(+)$1	226	62	67	15.0000
UUUCU	chr2:61726752-61726972(-)$1	220	74	79	15.0000

#otherMatches

#Struct PSSM
+++++	chr1:154227555-154227785(+)$1	230	34	39	15.0000
:::::	chr12:988855-989085(+)$1	230	80	85	15.0000
lllff	chr2:198324579-198324809(+)$1	230	8	13	15.0000
:::::	chr1:32768184-32768414(+)$1	230	223	228	15.0000
eeeee	chr2:28626915-28627131(-)$1	216	155	160	15.0000
ggg::	chr7:138252252-138252478(+)$1	226	119	124	15.0000
ppppp	chr3:196674765-196674983(-)$1	218	52	57	15.0000
:::::	chr1:153640907-153641137(-)$1	230	4	9	15.0000
vvddd	chr2:219362648-219362873(-)$1	225	206	211	15.0000
:eeee	chr9:100678497-100678717(-)$1	220	85	90	15.0000
ooooo	chrM:9965-10195(-)$1	230	39	44	15.0000
+++++	chr14:69853627-69853862(-)$1	235	54	59	15.0000
eeeee	chr17:27957742-27957977(-)$1	235	140	145	15.0000
::::F	chr7:77423251-77423473(-)$1	222	205	210	15.0000
d^^^^	chr11:77618662-77618892(-)$1	230	87	92	15.0000
zzzzz	chr16:21979848-21980078(+)$1	230	16	21	15.0000
EEE{D	chr12:109046023-109046248(-)$1	225	45	50	15.0000
c!!cc	chr5:118469849-118470079(+)$1	230	106	111	15.0000
:::::	chr16:24826410-24826640(+)$1	230	31	36	15.0000
FFFF{	chr2:174820119-174820343(-)$1	224	50	55	15.0000
H::::	chr1:183513446-183513670(+)$1	224	203	208	15.0000
ggmmm	chr11:102272771-102273001(-)$1	230	45	50	15.0000
+++++	chr6:71269486-71269716(+)$1	230	105	110	15.0000
ZZZA}	chr16:69200891-69201121(+)$1	230	180	185	15.0000
bb]cc	chr16:72822640-72822863(-)$1	223	94	99	15.0000
@@@@@	chr5:114860506-114860730(-)$1	224	196	201	15.0000
CC{BB	chr17:48941234-48941464(-)$1	230	1	6	15.0000
DDDDW	chr22:22160047-22160277(-)$1	230	31	36	15.0000
::::e	chr2:228419087-228419317(+)$1	230	114	119	15.0000
III::	chr17:33591136-33591366(+)$1	230	32	37	15.0000
::DDD	chr14:24649262-24649489(+)$1	227	123	128	15.0000
eeqqq	chr12:44165901-44166121(+)$1	220	10	15	15.0000
vvvvv	chr17:27613569-27613802(-)$1	233	31	36	15.0000
ndddd	chr14:21878013-21878243(-)$1	230	65	70	15.0000
4hhhh	chr9:72338403-72338633(-)$1	230	73	78	15.0000
hhhhz	chr20:33233010-33233240(-)$1	230	20	25	15.0000
DDD~~	chr9:88293173-88293403(-)$1	230	165	170	15.0000
:::II	chr7:150775032-150775250(+)$1	218	185	190	15.0000
:::::	chr10:75897865-75898095(-)$1	230	0	5	15.0000
ddd22	chr3:122331833-122332063(+)$1	230	104	109	15.0000
ggggg	chr4:76714790-76715015(+)$1	225	100	105	15.0000
=====	chr2:213878490-213878716(-)$1	226	39	44	15.0000
DDDD}	chr6:135514889-135515119(+)$1	230	219	224	15.0000
KCCCK	chr11:6630739-6630961(+)$1	222	6	11	15.0000
^^===	chr1:25669389-25669619(+)$1	230	34	39	15.0000
+++++	chr6:34725600-34725826(+)$1	226	62	67	15.0000
hh&&&	chr2:61726752-61726972(-)$1	220	74	79	15.0000

#DB
.....	chr1:154227555-154227785(+)$1	1	34	39	15.0000
.....	chr12:988855-989085(+)$1	1	80	85	15.0000
...))	chr2:198324579-198324809(+)$1	1	8	13	15.0000
.....	chr1:32768184-32768414(+)$1	1	223	228	15.0000
(((((	chr2:28626915-28627131(-)$1	1	155	160	15.0000
)))..	chr7:138252252-138252478(+)$1	1	119	124	15.0000
.....	chr3:196674765-196674983(-)$1	1	52	57	15.0000
.....	chr1:153640907-153641137(-)$1	1	4	9	15.0000
..)))	chr2:219362648-219362873(-)$1	1	206	211	15.0000
.((((	chr9:100678497-100678717(-)$1	1	85	90	15.0000
.....	chrM:9965-10195(-)$1	1	39	44	15.0000
.....	chr14:69853627-69853862(-)$1	1	54	59	15.0000
(((((	chr17:27957742-27957977(-)$1	1	140	145	15.0000
....)	chr7:77423251-77423473(-)$1	1	205	210	15.0000
(....	chr11:77618662-77618892(-)$1	1	87	92	15.0000
.....	chr16:21979848-21980078(+)$1	1	16	21	15.0000
(((.(	chr12:109046023-109046248(-)$1	1	45	50	15.0000
(..((	chr5:118469849-118470079(+)$1	1	106	111	15.0000
.....	chr16:24826410-24826640(+)$1	1	31	36	15.0000
((((.	chr2:174820119-174820343(-)$1	1	50	55	15.0000
)....	chr1:183513446-183513670(+)$1	1	203	208	15.0000
((...	chr11:102272771-102273001(-)$1	1	45	50	15.0000
.....	chr6:71269486-71269716(+)$1	1	105	110	15.0000
...).	chr16:69200891-69201121(+)$1	1	180	185	15.0000
)).))	chr16:72822640-72822863(-)$1	1	94	99	15.0000
.....	chr5:114860506-114860730(-)$1	1	196	201	15.0000
((.((	chr17:48941234-48941464(-)$1	1	1	6	15.0000
((((.	chr22:22160047-22160277(-)$1	1	31	36	15.0000
....(	chr2:228419087-228419317(+)$1	1	114	119	15.0000
(((..	chr17:33591136-33591366(+)$1	1	32	37	15.0000
..(((	chr14:24649262-24649489(+)$1	1	123	128	15.0000
((...	chr12:44165901-44166121(+)$1	1	10	15	15.0000
.....	chr17:27613569-27613802(-)$1	1	31	36	15.0000
.))))	chr14:21878013-21878243(-)$1	1	65	70	15.0000
.))))	chr9:72338403-72338633(-)$1	1	73	78	15.0000
((((.	chr20:33233010-33233240(-)$1	1	20	25	15.0000
)))..	chr9:88293173-88293403(-)$1	1	165	170	15.0000
...))	chr7:150775032-150775250(+)$1	1	185	190	15.0000
.....	chr10:75897865-75898095(-)$1	1	0	5	15.0000
)))..	chr3:122331833-122332063(+)$1	1	104	109	15.0000
)))))	chr4:76714790-76715015(+)$1	1	100	105	15.0000
(((((	chr2:213878490-213878716(-)$1	1	39	44	15.0000
)))).	chr6:135514889-135515119(+)$1	1	219	224	15.0000
.(((.	chr11:6630739-6630961(+)$1	1	6	11	15.0000
..)))	chr1:25669389-25669619(+)$1	1	34	39	15.0000
.....	chr6:34725600-34725826(+)$1	1	62	67	15.0000
((...	chr2:61726752-61726972(-)$1	1	74	79	15.0000

#PSSM
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	

#score	705.0000000000001
#seq	47
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m1_run1.nuc.txt

#NT
UUUCAUUU	chr17:47129204-47129445(+)$1	241	10	18	16.0895
CUUUAUUU	chr12:24969943-24970163(-)$1	220	76	84	15.6417
UUUUCUUU	chr7:112461315-112461551(-)$1	236	209	217	16.4626
UUUCAUUU	chr1:93618553-93618785(-)$1	232	195	203	16.0895
UUUUAUUU	chr17:30326754-30326973(+)$1	219	201	209	19.8208
UUUUAUUG	chr11:94904204-94904471(-)$1	267	1	9	15.3432
UCUUAUUU	chr6:109689714-109689942(-)$1	228	113	121	15.1194
UUUUAUUU	chr6:20493249-20493473(+)$1	224	61	69	19.8208
UUUUCUUU	chr20:280715-280942(+)$1	227	128	136	16.4626
uuuuuuuu	chr22:45583020-45583249(+)$1	229	27	35	16.6865
UUUUAUAU	chr15:101716055-101716289(-)$1	234	5	13	15.2686
UGUUAUUU	chr12:46752544-46752825(-)$1	281	238	246	15.1194
UUCUAUUU	chr13:53050379-53050626(+)$1	247	18	26	15.1940
UUUCAUUU	chr2:198256540-198256769(-)$1	229	152	160	16.0895
UUUUUUUU	chr5:112212436-112212665(-)$1	229	132	140	16.6865
uuuuauuu	chr2:178088041-178088271(+)$1	230	18	26	19.8208
UUUUGUUU	chr7:107401265-107401522(+)$1	257	83	91	16.3880
CUUUAUUU	chr11:95532330-95532559(+)$1	229	52	60	15.6417
CUUUAUUU	chr1:205682636-205682865(-)$1	229	86	94	15.6417
uuuuuuuu	chr1:67451430-67451688(+)$1	258	67	75	16.6865
UUUUAUUU	chrX:20145033-20145250(-)$1	217	140	148	19.8208
UUUAAUUU	chr6:146120277-146120526(-)$1	249	19	27	15.7164
UUGUAUUU	chr15:66181653-66181886(+)$1	233	48	56	15.2686
UUUUAAUU	chr5:174954292-174954505(+)$1	213	115	123	15.6417
UUUUAUUU	chr1:218510946-218511176(+)$1	230	131	139	19.8208
UUUUAUUU	chr12:98942309-98942533(+)$1	224	88	96	19.8208
uuuuguuu	chr1:6582480-6582717(-)$1	237	83	91	16.3880
UUUUAUUU	chr10:18967971-18968182(+)$1	211	28	36	19.8208
UUUUAUUC	chr1:67877461-67877692(-)$1	231	160	168	15.3432
GUUUAUUU	chr5:98131645-98131898(+)$1	253	159	167	15.4925
CUUUAUUU	chrX:119390170-119390410(+)$1	240	131	139	15.6417
GUUUAUUU	chr10:32298035-32298259(-)$1	224	191	199	15.4925
UUUUACUU	chr21:16335236-16335498(-)$1	262	65	73	15.4179
UUUUAUUU	chr12:4409628-4409858(+)$1	230	187	195	19.8208
UUUUAUUU	chr2:70316071-70316298(+)$1	227	116	124	19.8208
UUUUAUUC	chr1:33145647-33145883(+)$1	236	62	70	15.3432
UUUUAAUU	chr12:110788354-110788581(+)$1	227	189	197	15.6417
UUUUAUAU	chr20:61509306-61509538(-)$1	232	11	19	15.2686
UUUAAUUU	chr17:28793485-28793717(+)$1	232	109	117	15.7164
UUUGAUUU	chr17:38545167-38545435(-)$1	268	19	27	15.6417
UUUUAUAU	chr14:105362924-105363153(+)$1	229	103	111	15.2686
UUUCAUUU	chr18:56996211-56996432(-)$1	221	167	175	16.0895
UUUUAUUU	chr12:69236532-69236747(+)$1	215	42	50	19.8208
UUAUAUUU	chr18:47309802-47310101(-)$1	299	247	255	15.1940
UUUUUUUU	chr1:205684571-205684810(-)$1	239	72	80	16.6865
AUUUAUUU	chr10:105787152-105787406(+)$1	254	207	215	15.4179
UUGUAUUU	chr11:27516431-27516663(-)$1	232	187	195	15.2686
UUUUCUUU	chr1:184660196-184660451(-)$1	255	133	141	16.4626
UUUUUUUU	chr2:128062475-128062704(-)$1	229	39	47	16.6865
UUUUAUUA	chr10:31816640-31816894(+)$1	254	19	27	15.2686
UUUUCUUU	chr6:109002360-109002571(+)$1	211	115	123	16.4626
UUUUUUUU	chr17:39847621-39847845(+)$1	224	198	206	16.6865
UUUUUUUU	chr21:44513077-44513318(-)$1	241	179	187	16.6865
UUUUAAUU	chr12:53873323-53873585(+)$1	262	49	57	15.6417
UUUUAAUU	chr8:81435690-81435919(+)$1	229	2	10	15.6417
uuuuguuu	chr10:98715972-98716220(+)$1	248	11	19	16.3880
UUUUUUUU	chr18:29710507-29710736(+)$1	229	133	141	16.6865
UUUUAUUU	chr9:136897264-136897530(-)$1	266	27	35	19.8208
UUUUCUUU	chr2:47387435-47387646(-)$1	211	44	52	16.4626
UUUUAUUG	chr10:119041192-119041418(-)$1	226	74	82	15.3432
UUUCAUUU	chr9:135565027-135565252(+)$1	225	184	192	16.0895
UUUUAGUU	chr3:38529450-38529699(+)$1	249	137	145	15.4925
UUUUGUUU	chr17:17971555-17971776(+)$1	221	43	51	16.3880
UUUUAGUU	chr1:162493119-162493345(+)$1	226	166	174	15.4925
UUUCAUUU	chr12:76746036-76746280(-)$1	244	30	38	16.0895
UAUUAUUU	chr1:113455565-113455793(-)$1	228	73	81	15.1194

#otherMatches

#Struct PSSM
ooooffff	chr2:200790998-200791224(+)$1	226	15	23	16.0895
:::::HHH	chr17:47129204-47129445(+)$1	241	10	18	16.0895
i:::::::	chr12:24969943-24970163(-)$1	220	76	84	15.6417
IIII::::	chr7:112461315-112461551(-)$1	236	209	217	16.4626
oooooodd	chr1:93618553-93618785(-)$1	232	195	203	16.0895
::::::::	chr17:30326754-30326973(+)$1	219	201	209	19.8208
EEEEE{GG	chr11:94904204-94904471(-)$1	267	1	9	15.3432
hsssssss	chr6:109689714-109689942(-)$1	228	113	121	15.1194
uuuuuuuu	chr6:20493249-20493473(+)$1	224	61	69	19.8208
ggggggff	chr20:280715-280942(+)$1	227	128	136	16.4626
LLLGGGGG	chr22:45583020-45583249(+)$1	229	27	35	16.6865
::::::::	chr15:101716055-101716289(-)$1	234	5	13	15.2686
gggg[ccc	chr12:46752544-46752825(-)$1	281	238	246	15.1194
:bbqqqqq	chr13:53050379-53050626(+)$1	247	18	26	15.1940
dd!!iiii	chr2:198256540-198256769(-)$1	229	152	160	16.0895
eee66666	chr5:112212436-112212665(-)$1	229	132	140	16.6865
hhhhhh22	chr2:178088041-178088271(+)$1	230	18	26	19.8208
f22ggggg	chr7:107401265-107401522(+)$1	257	83	91	16.3880
ccrrrrrr	chr11:95532330-95532559(+)$1	229	52	60	15.6417
!=======	chr1:205682636-205682865(-)$1	229	86	94	15.6417
hhhhhh::	chr1:67451430-67451688(+)$1	258	67	75	16.6865
JJJJJJJJ	chrX:20145033-20145250(-)$1	217	140	148	19.8208
ccc!!hhh	chr6:146120277-146120526(-)$1	249	19	27	15.7164
ggggg]bb	chr15:66181653-66181886(+)$1	233	48	56	15.2686
====::==	chr5:174954292-174954505(+)$1	213	115	123	15.6417
ggggggg3	chr1:218510946-218511176(+)$1	230	131	139	19.8208
rrrrrrre	chr12:98942309-98942533(+)$1	224	88	96	19.8208
iiiiii00	chr1:6582480-6582717(-)$1	237	83	91	16.3880
bb[eeeee	chr10:18967971-18968182(+)$1	211	28	36	19.8208
d]eeeee]	chr1:67877461-67877692(-)$1	231	160	168	15.3432
::::::::	chr5:98131645-98131898(+)$1	253	159	167	15.4925
cc22bb]d	chrX:119390170-119390410(+)$1	240	131	139	15.6417
D}FFFFFF	chr10:32298035-32298259(-)$1	224	191	199	15.4925
qqqqqqee	chr21:16335236-16335498(-)$1	262	65	73	15.4179
lllfffff	chr12:4409628-4409858(+)$1	230	187	195	19.8208
d::ggggg	chr2:70316071-70316298(+)$1	227	116	124	19.8208
qqbb]eee	chr1:33145647-33145883(+)$1	236	62	70	15.3432
|||GGGGG	chr12:110788354-110788581(+)$1	227	189	197	15.6417
FFFFFKKE	chr20:61509306-61509538(-)$1	232	11	19	15.2686
cc++++++	chr17:28793485-28793717(+)$1	232	109	117	15.7164
FFPPPPPP	chr17:38545167-38545435(-)$1	268	19	27	15.6417
))))))ii	chr14:105362924-105363153(+)$1	229	103	111	15.2686
"dddd###	chr18:56996211-56996432(-)$1	221	167	175	16.0895
ooffffff	chr12:69236532-69236747(+)$1	215	42	50	19.8208
FFFFF::f	chr18:47309802-47310101(-)$1	299	247	255	15.1940
^^^^^^^^	chr1:205684571-205684810(-)$1	239	72	80	16.6865
EYYDDDDY	chr10:105787152-105787406(+)$1	254	207	215	15.4179
HHHHH:cc	chr11:27516431-27516663(-)$1	232	187	195	15.2686
fff^^^^^	chr1:184660196-184660451(-)$1	255	133	141	16.4626
ffff]ddd	chr2:128062475-128062704(-)$1	229	39	47	16.6865
HHHHHHHH	chr10:31816640-31816894(+)$1	254	19	27	15.2686
ooofffff	chr6:109002360-109002571(+)$1	211	115	123	16.4626
::::::::	chr17:39847621-39847845(+)$1	224	198	206	16.6865
hhhhhhhh	chr21:44513077-44513318(-)$1	241	179	187	16.6865
JJJJJJJJ	chr12:53873323-53873585(+)$1	262	49	57	15.6417
GGGGGGKK	chr8:81435690-81435919(+)$1	229	2	10	15.6417
qqqccc::	chr10:98715972-98716220(+)$1	248	11	19	16.3880
iiiii[dd	chr18:29710507-29710736(+)$1	229	133	141	16.6865
::::::::	chr9:136897264-136897530(-)$1	266	27	35	19.8208
FLLLDDDD	chr2:47387435-47387646(-)$1	211	44	52	16.4626
pppppppd	chr10:119041192-119041418(-)$1	226	74	82	15.3432
}IIIIIII	chr9:135565027-135565252(+)$1	225	184	192	16.0895
mddddddd	chr3:38529450-38529699(+)$1	249	137	145	15.4925
hhhhhhdd	chr17:17971555-17971776(+)$1	221	43	51	16.3880
IIIIIIII	chr1:162493119-162493345(+)$1	226	166	174	15.4925
HHHHHHMM	chr12:76746036-76746280(-)$1	244	30	38	16.0895
fffffggg	chr1:113455565-113455793(-)$1	228	73	81	15.1194

#DB
....))))	chr2:200790998-200791224(+)$1	1	15	23	16.0895
.....(((	chr17:47129204-47129445(+)$1	1	10	18	16.0895
).......	chr12:24969943-24970163(-)$1	1	76	84	15.6417
))))....	chr7:112461315-112461551(-)$1	1	209	217	16.4626
......))	chr1:93618553-93618785(-)$1	1	195	203	16.0895
........	chr17:30326754-30326973(+)$1	1	201	209	19.8208
(((((.((	chr11:94904204-94904471(-)$1	1	1	9	15.3432
(.......	chr6:109689714-109689942(-)$1	1	113	121	15.1194
........	chr6:20493249-20493473(+)$1	1	61	69	19.8208
))))))))	chr20:280715-280942(+)$1	1	128	136	16.4626
...(((((	chr22:45583020-45583249(+)$1	1	27	35	16.6865
........	chr15:101716055-101716289(-)$1	1	5	13	15.2686
((((.(((	chr12:46752544-46752825(-)$1	1	238	246	15.1194
.((.....	chr13:53050379-53050626(+)$1	1	18	26	15.1940
((..((((	chr2:198256540-198256769(-)$1	1	152	160	16.0895
))).....	chr5:112212436-112212665(-)$1	1	132	140	16.6865
))))))..	chr2:178088041-178088271(+)$1	1	18	26	19.8208
)..)))))	chr7:107401265-107401522(+)$1	1	83	91	16.3880
((......	chr11:95532330-95532559(+)$1	1	52	60	15.6417
.(((((((	chr1:205682636-205682865(-)$1	1	86	94	15.6417
))))))..	chr1:67451430-67451688(+)$1	1	67	75	16.6865
))))))))	chrX:20145033-20145250(-)$1	1	140	148	19.8208
(((..(((	chr6:146120277-146120526(-)$1	1	19	27	15.7164
))))).))	chr15:66181653-66181886(+)$1	1	48	56	15.2686
))))..((	chr5:174954292-174954505(+)$1	1	115	123	15.6417
))))))).	chr1:218510946-218511176(+)$1	1	131	139	19.8208
.......)	chr12:98942309-98942533(+)$1	1	88	96	19.8208
))))))..	chr1:6582480-6582717(-)$1	1	83	91	16.3880
((.(((((	chr10:18967971-18968182(+)$1	1	28	36	19.8208
).))))).	chr1:67877461-67877692(-)$1	1	160	168	15.3432
........	chr5:98131645-98131898(+)$1	1	159	167	15.4925
))..)).)	chrX:119390170-119390410(+)$1	1	131	139	15.6417
).))))))	chr10:32298035-32298259(-)$1	1	191	199	15.4925
......))	chr21:16335236-16335498(-)$1	1	65	73	15.4179
...)))))	chr12:4409628-4409858(+)$1	1	187	195	19.8208
)..(((((	chr2:70316071-70316298(+)$1	1	116	124	19.8208
..)).)))	chr1:33145647-33145883(+)$1	1	62	70	15.3432
...)))))	chr12:110788354-110788581(+)$1	1	189	197	15.6417
(((((..(	chr20:61509306-61509538(-)$1	1	11	19	15.2686
((......	chr17:28793485-28793717(+)$1	1	109	117	15.7164
((......	chr17:38545167-38545435(-)$1	1	19	27	15.6417
......((	chr14:105362924-105363153(+)$1	1	103	111	15.2686
.((((...	chr18:56996211-56996432(-)$1	1	167	175	16.0895
..))))))	chr12:69236532-69236747(+)$1	1	42	50	19.8208
)))))..(	chr18:47309802-47310101(-)$1	1	247	255	15.1940
........	chr1:205684571-205684810(-)$1	1	72	80	16.6865
)..)))).	chr10:105787152-105787406(+)$1	1	207	215	15.4179
))))).((	chr11:27516431-27516663(-)$1	1	187	195	15.2686
(((.....	chr1:184660196-184660451(-)$1	1	133	141	16.4626
)))).)))	chr2:128062475-128062704(-)$1	1	39	47	16.6865
((((((((	chr10:31816640-31816894(+)$1	1	19	27	15.2686
...)))))	chr6:109002360-109002571(+)$1	1	115	123	16.4626
........	chr17:39847621-39847845(+)$1	1	198	206	16.6865
((((((((	chr21:44513077-44513318(-)$1	1	179	187	16.6865
((((((((	chr12:53873323-53873585(+)$1	1	49	57	15.6417
((((((..	chr8:81435690-81435919(+)$1	1	2	10	15.6417
...)))..	chr10:98715972-98716220(+)$1	1	11	19	16.3880
(((((.((	chr18:29710507-29710736(+)$1	1	133	141	16.6865
........	chr9:136897264-136897530(-)$1	1	27	35	19.8208
(...((((	chr2:47387435-47387646(-)$1	1	44	52	16.4626
.......)	chr10:119041192-119041418(-)$1	1	74	82	15.3432
.)))))))	chr9:135565027-135565252(+)$1	1	184	192	16.0895
.)))))))	chr3:38529450-38529699(+)$1	1	137	145	15.4925
))))))((	chr17:17971555-17971776(+)$1	1	43	51	16.3880
))))))))	chr1:162493119-162493345(+)$1	1	166	174	15.4925
((((((..	chr12:76746036-76746280(-)$1	1	30	38	16.0895
((((((((	chr1:113455565-113455793(-)$1	1	73	81	15.1194

#PSSM
U : 0.82	u : 0.07	C : 0.05	G : 0.02	A : 0.01	
U : 0.88	u : 0.07	C : 0.01	G : 0.01	A : 0.01	
U : 0.86	u : 0.07	G : 0.02	C : 0.01	A : 0.01	
U : 0.77	C : 0.10	u : 0.07	A : 0.02	G : 0.01	
A : 0.73	U : 0.08	C : 0.07	u : 0.02	G : 0.02	g : 0.02	a : 0.01	
U : 0.82	u : 0.07	A : 0.05	G : 0.02	C : 0.01	
U : 0.88	u : 0.07	A : 0.04	
U : 0.85	u : 0.07	G : 0.02	C : 0.02	A : 0.01	

#score	1105.7611940298518
#seq	67
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_CDS_m1_run2.nuc.txt

#NT
UUUCU	chr5:180669073-180669425(-)$1	352	56	61	15.0000
UUUCU	chr1:45225871-45226120(+)$1	249	66	71	15.0000
UUUCU	chrX:152958617-152958891(+)$1	274	126	131	15.0000
UUUCU	chrX:71492354-71492722(-)$1	368	88	93	15.0000
UUUCU	chr8:87568335-87568626(+)$1	291	135	140	15.0000
UUUCU	chrX:84510627-84510907(+)$1	280	240	245	15.0000
UUUCU	chr7:97482533-97482772(-)$1	239	53	58	15.0000
UUUCU	chr17:30795971-30796286(+)$1	315	270	275	15.0000
UUUCU	chrX:41002455-41002684(+)$1	229	51	56	15.0000
UUUCU	chr6:32945920-32946249(+)$1	329	281	286	15.0000
UUUCU	chr1:28169608-28169857(+)$1	249	28	33	15.0000
UUUCU	chr5:137904546-137904838(-)$1	292	70	75	15.0000
UUUCU	chr12:98993632-98993890(+)$1	258	27	32	15.0000
UUUCU	chr12:7044650-7044931(+)$1	281	50	55	15.0000
UUUCU	chr22:36141874-36142119(-)$1	245	41	46	15.0000
UUUCU	chr12:12873927-12874227(+)$1	300	30	35	15.0000
UUUCU	chr11:118886459-118886734(-)$1	275	33	38	15.0000
UUUCU	chr10:124923235-124923515(+)$1	280	82	87	15.0000
UUUCU	chr12:98941486-98941951(+)$1	465	117	122	15.0000
UUUCU	chr12:95889697-95889951(+)$1	254	70	75	15.0000
UUUCU	chr5:149825071-149825347(-)$1	276	92	97	15.0000
UUUCU	chr12:98992199-98992581(+)$1	382	25	30	15.0000
UUUCU	chr1:231509625-231509866(-)$1	241	169	174	15.0000
UUUCU	chr16:30747479-30747807(+)$1	328	13	18	15.0000
UUUCU	chr6:32944479-32944795(+)$1	316	146	151	15.0000
UUUCU	chr20:5095663-5096102(-)$1	439	250	255	15.0000
UUUCU	chrX:15339564-15339797(-)$1	233	34	39	15.0000
UUUCU	chr15:82821061-82821389(-)$1	328	34	39	15.0000
UUUCU	chr19:34685303-34685646(+)$1	343	68	73	15.0000
UUUCU	chr17:26888461-26888713(-)$1	252	24	29	15.0000
UUUCU	chr11:75115615-75116012(+)$1	397	350	355	15.0000
UUUCU	chr6:32943060-32943398(+)$1	338	65	70	15.0000
UUUCU	chr1:45241605-45241912(+)$1	307	298	303	15.0000
UUUCU	chr17:75199590-75199840(+)$1	250	198	203	15.0000
UUUCU	chr12:110874312-110874555(-)$1	243	236	241	15.0000
UUUCU	chr8:74203926-74204245(-)$1	319	248	253	15.0000
UUUCU	chr5:74695952-74696211(-)$1	259	147	152	15.0000
UUUCU	chr19:34832690-34832937(+)$1	247	102	107	15.0000
UUUCU	chr6:137524698-137524922(-)$1	224	83	88	15.0000
UUUCU	chr6:74228959-74229339(-)$1	380	304	309	15.0000
UUUCU	chr1:28598084-28598403(+)$1	319	4	9	15.0000
UUUCU	chr11:62338339-62338679(-)$1	340	171	176	15.0000
UUUCU	chr14:21699016-21699250(-)$1	234	195	200	15.0000
UUUCU	chr1:205683199-205683573(-)$1	374	134	139	15.0000
UUUCU	chr3:160151345-160151656(+)$1	311	80	85	15.0000
UUUCU	chr19:57838971-57839219(+)$1	248	48	53	15.0000
UUUCU	chr14:102549782-102550094(-)$1	312	278	283	15.0000
UUUCU	chr19:59067981-59068214(-)$1	233	38	43	15.0000
UUUCU	chr1:153920833-153921185(-)$1	352	123	128	15.0000
uuucu	chr14:50050202-50050489(-)$1	287	252	257	15.0000
UUUCU	chr10:135214934-135215162(+)$1	228	80	85	15.0000
UUUCU	chr17:38151115-38151399(+)$1	284	33	38	15.0000
UUUCU	chr19:44738872-44739198(+)$1	326	147	152	15.0000
UUUCU	chr19:3980411-3980806(-)$1	395	83	88	15.0000
UUUCU	chr6:36940390-36940640(-)$1	250	101	106	15.0000

#otherMatches

#Struct PSSM
ssss=	chr12:57036141-57036464(-)$1	323	90	95	15.0000
:::::	chr5:180669073-180669425(-)$1	352	56	61	15.0000
d7777	chr1:45225871-45226120(+)$1	249	66	71	15.0000
+++++	chrX:152958617-152958891(+)$1	274	126	131	15.0000
FFF:B	chrX:71492354-71492722(-)$1	368	88	93	15.0000
CYYEE	chr8:87568335-87568626(+)$1	291	135	140	15.0000
=====	chrX:84510627-84510907(+)$1	280	240	245	15.0000
)))))	chr7:97482533-97482772(-)$1	239	53	58	15.0000
eeell	chr17:30795971-30796286(+)$1	315	270	275	15.0000
:gggg	chrX:41002455-41002684(+)$1	229	51	56	15.0000
ggggg	chr6:32945920-32946249(+)$1	329	281	286	15.0000
:DDDD	chr1:28169608-28169857(+)$1	249	28	33	15.0000
ooooo	chr5:137904546-137904838(-)$1	292	70	75	15.0000
mmeee	chr12:98993632-98993890(+)$1	258	27	32	15.0000
hhhhh	chr12:7044650-7044931(+)$1	281	50	55	15.0000
aoooo	chr22:36141874-36142119(-)$1	245	41	46	15.0000
qqqqq	chr12:12873927-12874227(+)$1	300	30	35	15.0000
IIIII	chr11:118886459-118886734(-)$1	275	33	38	15.0000
uuuuu	chr10:124923235-124923515(+)$1	280	82	87	15.0000
:::::	chr12:98941486-98941951(+)$1	465	117	122	15.0000
lgggg	chr12:95889697-95889951(+)$1	254	70	75	15.0000
>hhhh	chr5:149825071-149825347(-)$1	276	92	97	15.0000
FFFFC	chr12:98992199-98992581(+)$1	382	25	30	15.0000
vvvvv	chr1:231509625-231509866(-)$1	241	169	174	15.0000
=====	chr16:30747479-30747807(+)$1	328	13	18	15.0000
""eee	chr6:32944479-32944795(+)$1	316	146	151	15.0000
||||F	chr20:5095663-5096102(-)$1	439	250	255	15.0000
ooooo	chrX:15339564-15339797(-)$1	233	34	39	15.0000
sssii	chr15:82821061-82821389(-)$1	328	34	39	15.0000
=====	chr19:34685303-34685646(+)$1	343	68	73	15.0000
qqqqq	chr17:26888461-26888713(-)$1	252	24	29	15.0000
bbooo	chr11:75115615-75116012(+)$1	397	350	355	15.0000
!bb[f	chr6:32943060-32943398(+)$1	338	65	70	15.0000
:::::	chr1:45241605-45241912(+)$1	307	298	303	15.0000
::::D	chr17:75199590-75199840(+)$1	250	198	203	15.0000
mdddd	chr12:110874312-110874555(-)$1	243	236	241	15.0000
c]eee	chr8:74203926-74204245(-)$1	319	248	253	15.0000
hhhhh	chr5:74695952-74696211(-)$1	259	147	152	15.0000
ppbbd	chr19:34832690-34832937(+)$1	247	102	107	15.0000
c[iii	chr6:137524698-137524922(-)$1	224	83	88	15.0000
qbb]b	chr6:74228959-74229339(-)$1	380	304	309	15.0000
:::::	chr1:28598084-28598403(+)$1	319	4	9	15.0000
eeee]	chr11:62338339-62338679(-)$1	340	171	176	15.0000
ZZHHH	chr14:21699016-21699250(-)$1	234	195	200	15.0000
ggggg	chr1:205683199-205683573(-)$1	374	134	139	15.0000
ddd[i	chr3:160151345-160151656(+)$1	311	80	85	15.0000
:::::	chr19:57838971-57839219(+)$1	248	48	53	15.0000
===:c	chr14:102549782-102550094(-)$1	312	278	283	15.0000
ttttt	chr19:59067981-59068214(-)$1	233	38	43	15.0000
HHHHH	chr1:153920833-153921185(-)$1	352	123	128	15.0000
!!ddd	chr14:50050202-50050489(-)$1	287	252	257	15.0000
:::::	chr10:135214934-135215162(+)$1	228	80	85	15.0000
:::::	chr17:38151115-38151399(+)$1	284	33	38	15.0000
Hdddd	chr19:44738872-44739198(+)$1	326	147	152	15.0000
sssss	chr19:3980411-3980806(-)$1	395	83	88	15.0000
KDDDD	chr6:36940390-36940640(-)$1	250	101	106	15.0000

#DB
....)	chr12:57036141-57036464(-)$1	1	90	95	15.0000
.....	chr5:180669073-180669425(-)$1	1	56	61	15.0000
)....	chr1:45225871-45226120(+)$1	1	66	71	15.0000
.....	chrX:152958617-152958891(+)$1	1	126	131	15.0000
(((.(	chrX:71492354-71492722(-)$1	1	88	93	15.0000
)..))	chr8:87568335-87568626(+)$1	1	135	140	15.0000
)))))	chrX:84510627-84510907(+)$1	1	240	245	15.0000
.....	chr7:97482533-97482772(-)$1	1	53	58	15.0000
(((..	chr17:30795971-30796286(+)$1	1	270	275	15.0000
.((((	chrX:41002455-41002684(+)$1	1	51	56	15.0000
)))))	chr6:32945920-32946249(+)$1	1	281	286	15.0000
.((((	chr1:28169608-28169857(+)$1	1	28	33	15.0000
.....	chr5:137904546-137904838(-)$1	1	70	75	15.0000
..)))	chr12:98993632-98993890(+)$1	1	27	32	15.0000
)))))	chr12:7044650-7044931(+)$1	1	50	55	15.0000
(....	chr22:36141874-36142119(-)$1	1	41	46	15.0000
.....	chr12:12873927-12874227(+)$1	1	30	35	15.0000
(((((	chr11:118886459-118886734(-)$1	1	33	38	15.0000
.....	chr10:124923235-124923515(+)$1	1	82	87	15.0000
.....	chr12:98941486-98941951(+)$1	1	117	122	15.0000
.))))	chr12:95889697-95889951(+)$1	1	70	75	15.0000
.))))	chr5:149825071-149825347(-)$1	1	92	97	15.0000
(((((	chr12:98992199-98992581(+)$1	1	25	30	15.0000
.....	chr1:231509625-231509866(-)$1	1	169	174	15.0000
(((((	chr16:30747479-30747807(+)$1	1	13	18	15.0000
..(((	chr6:32944479-32944795(+)$1	1	146	151	15.0000
....)	chr20:5095663-5096102(-)$1	1	250	255	15.0000
.....	chrX:15339564-15339797(-)$1	1	34	39	15.0000
...))	chr15:82821061-82821389(-)$1	1	34	39	15.0000
(((((	chr19:34685303-34685646(+)$1	1	68	73	15.0000
.....	chr17:26888461-26888713(-)$1	1	24	29	15.0000
((...	chr11:75115615-75116012(+)$1	1	350	355	15.0000
.((.(	chr6:32943060-32943398(+)$1	1	65	70	15.0000
.....	chr1:45241605-45241912(+)$1	1	298	303	15.0000
....)	chr17:75199590-75199840(+)$1	1	198	203	15.0000
.))))	chr12:110874312-110874555(-)$1	1	236	241	15.0000
).)))	chr8:74203926-74204245(-)$1	1	248	253	15.0000
)))))	chr5:74695952-74696211(-)$1	1	147	152	15.0000
..)))	chr19:34832690-34832937(+)$1	1	102	107	15.0000
(.(((	chr6:137524698-137524922(-)$1	1	83	88	15.0000
.)).)	chr6:74228959-74229339(-)$1	1	304	309	15.0000
.....	chr1:28598084-28598403(+)$1	1	4	9	15.0000
)))).	chr11:62338339-62338679(-)$1	1	171	176	15.0000
..)))	chr14:21699016-21699250(-)$1	1	195	200	15.0000
(((((	chr1:205683199-205683573(-)$1	1	134	139	15.0000
(((.(	chr3:160151345-160151656(+)$1	1	80	85	15.0000
.....	chr19:57838971-57839219(+)$1	1	48	53	15.0000
))).(	chr14:102549782-102550094(-)$1	1	278	283	15.0000
.....	chr19:59067981-59068214(-)$1	1	38	43	15.0000
(((((	chr1:153920833-153921185(-)$1	1	123	128	15.0000
..(((	chr14:50050202-50050489(-)$1	1	252	257	15.0000
.....	chr10:135214934-135215162(+)$1	1	80	85	15.0000
.....	chr17:38151115-38151399(+)$1	1	33	38	15.0000
(((((	chr19:44738872-44739198(+)$1	1	147	152	15.0000
.....	chr19:3980411-3980806(-)$1	1	83	88	15.0000
.((((	chr6:36940390-36940640(-)$1	1	101	106	15.0000

#PSSM
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
U : 0.98	u : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	

#score	840.0000000000005
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m2_run2.nuc.txt

#NT
GCAG	chr1:19711977-19712208(-)$1	231	14	18	12.0000
GCAG	chr14:103438351-103438570(-)$1	219	134	138	12.0000
GCAG	chr7:45148405-45148632(-)$1	227	5	9	12.0000
GCAG	chrX:123194990-123195247(+)$1	257	95	99	12.0000
GCAG	chr4:6863715-6863944(+)$1	229	38	42	12.0000
GCAG	chr5:37305135-37305358(-)$1	223	188	192	12.0000
GCAG	chr1:242020643-242020877(+)$1	234	56	60	12.0000
GCAG	chr8:28206101-28206362(-)$1	261	11	15	12.0000
GCAG	chr6:36189907-36190129(+)$1	222	33	37	12.0000
GCAG	chr11:65545899-65546122(-)$1	223	25	29	12.0000
GCAG	chr1:38034783-38034999(-)$1	216	132	136	12.0000
GCAG	chrX:49127116-49127337(+)$1	221	118	122	12.0000
GCAG	chr8:125463645-125463866(+)$1	221	84	88	12.0000
GCAG	chrX:48792014-48792227(-)$1	213	30	34	12.0000
gcag	chr8:17815067-17815288(+)$1	221	58	62	12.0000
GCAG	chr9:131502139-131502384(-)$1	245	181	185	12.0000
GCAG	chr22:41572394-41572633(+)$1	239	56	60	12.0000
GCAG	chr7:148921260-148921473(+)$1	213	3	7	12.0000
GCAG	chr4:1730256-1730511(+)$1	255	6	10	12.0000
GCAG	chr3:47891027-47891253(+)$1	226	27	31	12.0000
GCAG	chr1:27056075-27056368(+)$1	293	134	138	12.0000
GCAG	chr3:78666860-78667086(-)$1	226	75	79	12.0000
GCAG	chr9:135553444-135553691(+)$1	247	94	98	12.0000
GCAG	chr20:57484725-57484946(+)$1	221	43	47	12.0000
GCAG	chr6:43499190-43499410(-)$1	220	161	165	12.0000
GCAG	chr2:173356102-173356319(+)$1	217	137	141	12.0000
GCAG	chr7:2394869-2395136(+)$1	267	16	20	12.0000
GCAG	chr4:4285260-4285483(-)$1	223	87	91	12.0000
GCAG	chr6:41562563-41562795(+)$1	232	208	212	12.0000
GCAG	chr16:75263378-75263604(-)$1	226	8	12	12.0000
GCAG	chr1:232539121-232539340(-)$1	219	60	64	12.0000
GCAG	chr2:174819856-174820075(-)$1	219	47	51	12.0000
GCAG	chr10:119134183-119134478(-)$1	295	132	136	12.0000
GCAG	chr21:16339794-16340015(-)$1	221	147	151	12.0000
GCAG	chr15:77346442-77346672(-)$1	230	70	74	12.0000
gcag	chr19:36209141-36209361(+)$1	220	116	120	12.0000
GCAG	chr19:42861484-42861704(+)$1	220	181	185	12.0000
GCAG	chr12:110719550-110719774(+)$1	224	168	172	12.0000
GCAG	chr19:52521549-52521766(-)$1	217	69	73	12.0000
GCAG	chr19:622523-622756(-)$1	233	0	4	12.0000
GCAG	chr15:69745927-69746148(+)$1	221	85	89	12.0000
GCAG	chr10:105178189-105178407(+)$1	218	148	152	12.0000
GCAG	chr1:232650574-232650794(-)$1	220	50	54	12.0000
GCAG	chr11:57076857-57077075(-)$1	218	13	17	12.0000
GCAG	chr6:90660309-90660558(-)$1	249	88	92	12.0000
GCAG	chr16:69402248-69402467(-)$1	219	23	27	12.0000
GCAG	chr17:27901695-27901923(-)$1	228	53	57	12.0000
GCAG	chr19:36120416-36120673(+)$1	257	11	15	12.0000
GCAG	chr19:49489119-49489343(-)$1	224	108	112	12.0000
GCAG	chr3:9475956-9476186(+)$1	230	209	213	12.0000
GCAG	chr12:49431634-49431858(-)$1	224	204	208	12.0000
GCAG	chr17:1631100-1631327(+)$1	227	143	147	12.0000
GCAG	chr17:74716356-74716596(-)$1	240	44	48	12.0000
GCAG	chr15:22928353-22928582(+)$1	229	69	73	12.0000
GCAG	chr12:49436498-49436750(-)$1	252	117	121	12.0000
GCAG	chr16:3819155-3819373(-)$1	218	28	32	12.0000
GCAG	chr8:77763520-77763743(+)$1	223	47	51	12.0000
GCAG	chr14:75295819-75296043(+)$1	224	156	160	12.0000
GCAG	chr3:47888218-47888514(+)$1	296	77	81	12.0000
GCAG	chr20:35294606-35294825(-)$1	219	107	111	12.0000
GCAG	chr1:171553032-171553258(+)$1	226	85	89	12.0000
GCAG	chr17:38508124-38508357(+)$1	233	2	6	12.0000
GCAG	chr1:27098891-27099137(+)$1	246	115	119	12.0000
GCAG	chr9:110250232-110250443(-)$1	211	181	185	12.0000
GCAG	chr1:150471292-150471598(+)$1	306	86	90	12.0000
GCAG	chr5:150497249-150497487(-)$1	238	57	61	12.0000
GCAG	chr11:47296337-47296566(+)$1	229	53	57	12.0000
GCAG	chr12:124241276-124241487(+)$1	211	64	68	12.0000
GCAG	chr6:4037636-4037859(+)$1	223	128	132	12.0000
GCAG	chr13:32929199-32929419(+)$1	220	183	187	12.0000
GCAG	chr19:40486118-40486360(+)$1	242	39	43	12.0000
GCAG	chr18:29848485-29848706(-)$1	221	181	185	12.0000
GCAG	chr6:159188293-159188503(-)$1	210	81	85	12.0000
GCAG	chr19:50910189-50910447(+)$1	258	208	212	12.0000
GCAG	chr12:12317263-12317485(-)$1	222	144	148	12.0000
GCAG	chr11:57077161-57077394(-)$1	233	31	35	12.0000
GCAG	chr16:69370392-69370630(-)$1	238	169	173	12.0000
GCAG	chr19:6381082-6381292(-)$1	210	15	19	12.0000
GCAG	chr1:16263694-16263957(+)$1	263	7	11	12.0000
GCAG	chr16:11439427-11439651(+)$1	224	80	84	12.0000
GCAG	chr10:72297977-72298205(+)$1	228	54	58	12.0000

#otherMatches

#Struct PSSM
GGGG	chr6:7580154-7580372(+)$1	218	51	55	12.0000
pppg	chr1:19711977-19712208(-)$1	231	14	18	12.0000
&ddd	chr14:103438351-103438570(-)$1	219	134	138	12.0000
::::	chr7:45148405-45148632(-)$1	227	5	9	12.0000
[bbd	chrX:123194990-123195247(+)$1	257	95	99	12.0000
{DDD	chr4:6863715-6863944(+)$1	229	38	42	12.0000
GYYC	chr5:37305135-37305358(-)$1	223	188	192	12.0000
iiii	chr1:242020643-242020877(+)$1	234	56	60	12.0000
bboo	chr8:28206101-28206362(-)$1	261	11	15	12.0000
EEEE	chr6:36189907-36190129(+)$1	222	33	37	12.0000
]eee	chr11:65545899-65546122(-)$1	223	25	29	12.0000
eeee	chr1:38034783-38034999(-)$1	216	132	136	12.0000
ee[b	chrX:49127116-49127337(+)$1	221	118	122	12.0000
hhhh	chr8:125463645-125463866(+)$1	221	84	88	12.0000
""cc	chrX:48792014-48792227(-)$1	213	30	34	12.0000
'aoo	chr8:17815067-17815288(+)$1	221	58	62	12.0000
H}BB	chr9:131502139-131502384(-)$1	245	181	185	12.0000
dddd	chr22:41572394-41572633(+)$1	239	56	60	12.0000
bbnn	chr7:148921260-148921473(+)$1	213	3	7	12.0000
::::	chr4:1730256-1730511(+)$1	255	6	10	12.0000
CCC{	chr3:47891027-47891253(+)$1	226	27	31	12.0000
::DD	chr1:27056075-27056368(+)$1	293	134	138	12.0000
ccc5	chr3:78666860-78667086(-)$1	226	75	79	12.0000
ccmm	chr9:135553444-135553691(+)$1	247	94	98	12.0000
c22c	chr20:57484725-57484946(+)$1	221	43	47	12.0000
hhhh	chr6:43499190-43499410(-)$1	220	161	165	12.0000
pppd	chr2:173356102-173356319(+)$1	217	137	141	12.0000
dd!!	chr7:2394869-2395136(+)$1	267	16	20	12.0000
hhhh	chr4:4285260-4285483(-)$1	223	87	91	12.0000
e"""	chr6:41562563-41562795(+)$1	232	208	212	12.0000
gggg	chr16:75263378-75263604(-)$1	226	8	12	12.0000
dd::	chr1:232539121-232539340(-)$1	219	60	64	12.0000
b22b	chr2:174819856-174820075(-)$1	219	47	51	12.0000
DDDD	chr10:119134183-119134478(-)$1	295	132	136	12.0000
g:::	chr21:16339794-16340015(-)$1	221	147	151	12.0000
gggg	chr15:77346442-77346672(-)$1	230	70	74	12.0000
eeee	chr19:36209141-36209361(+)$1	220	116	120	12.0000
iiii	chr19:42861484-42861704(+)$1	220	181	185	12.0000
DD}A	chr12:110719550-110719774(+)$1	224	168	172	12.0000
mmmf	chr19:52521549-52521766(-)$1	217	69	73	12.0000
dddd	chr19:622523-622756(-)$1	233	0	4	12.0000
$$$c	chr15:69745927-69746148(+)$1	221	85	89	12.0000
da[e	chr10:105178189-105178407(+)$1	218	148	152	12.0000
qqqq	chr1:232650574-232650794(-)$1	220	50	54	12.0000
bqqq	chr11:57076857-57077075(-)$1	218	13	17	12.0000
2bb]	chr6:90660309-90660558(-)$1	249	88	92	12.0000
fbb[	chr16:69402248-69402467(-)$1	219	23	27	12.0000
bb]a	chr17:27901695-27901923(-)$1	228	53	57	12.0000
bb[c	chr19:36120416-36120673(+)$1	257	11	15	12.0000
Efff	chr19:49489119-49489343(-)$1	224	108	112	12.0000
EEEE	chr3:9475956-9476186(+)$1	230	209	213	12.0000
FFFF	chr12:49431634-49431858(-)$1	224	204	208	12.0000
bbee	chr17:1631100-1631327(+)$1	227	143	147	12.0000
G{BB	chr17:74716356-74716596(-)$1	240	44	48	12.0000
cccd	chr15:22928353-22928582(+)$1	229	69	73	12.0000
c::g	chr12:49436498-49436750(-)$1	252	117	121	12.0000
ccmm	chr16:3819155-3819373(-)$1	218	28	32	12.0000
eee[	chr8:77763520-77763743(+)$1	223	47	51	12.0000
deee	chr14:75295819-75296043(+)$1	224	156	160	12.0000
dddd	chr3:47888218-47888514(+)$1	296	77	81	12.0000
D}JJ	chr20:35294606-35294825(-)$1	219	107	111	12.0000
ffff	chr1:171553032-171553258(+)$1	226	85	89	12.0000
bbmm	chr17:38508124-38508357(+)$1	233	2	6	12.0000
dd[b	chr1:27098891-27099137(+)$1	246	115	119	12.0000
dbbf	chr9:110250232-110250443(-)$1	211	181	185	12.0000
BBGG	chr1:150471292-150471598(+)$1	306	86	90	12.0000
dddd	chr5:150497249-150497487(-)$1	238	57	61	12.0000
BB{B	chr11:47296337-47296566(+)$1	229	53	57	12.0000
gggg	chr12:124241276-124241487(+)$1	211	64	68	12.0000
b22b	chr6:4037636-4037859(+)$1	223	128	132	12.0000
6666	chr13:32929199-32929419(+)$1	220	183	187	12.0000
[ccc	chr19:40486118-40486360(+)$1	242	39	43	12.0000
gggg	chr18:29848485-29848706(-)$1	221	181	185	12.0000
gg::	chr6:159188293-159188503(-)$1	210	81	85	12.0000
FFFD	chr19:50910189-50910447(+)$1	258	208	212	12.0000
iiii	chr12:12317263-12317485(-)$1	222	144	148	12.0000
cc!!	chr11:57077161-57077394(-)$1	233	31	35	12.0000
ccpp	chr16:69370392-69370630(-)$1	238	169	173	12.0000
a]bb	chr19:6381082-6381292(-)$1	210	15	19	12.0000
dddd	chr1:16263694-16263957(+)$1	263	7	11	12.0000
"""i	chr16:11439427-11439651(+)$1	224	80	84	12.0000
FFCC	chr10:72297977-72298205(+)$1	228	54	58	12.0000

#DB
((((	chr6:7580154-7580372(+)$1	1	51	55	12.0000
...)	chr1:19711977-19712208(-)$1	1	14	18	12.0000
.(((	chr14:103438351-103438570(-)$1	1	134	138	12.0000
....	chr7:45148405-45148632(-)$1	1	5	9	12.0000
.(((	chrX:123194990-123195247(+)$1	1	95	99	12.0000
.(((	chr4:6863715-6863944(+)$1	1	38	42	12.0000
)..)	chr5:37305135-37305358(-)$1	1	188	192	12.0000
((((	chr1:242020643-242020877(+)$1	1	56	60	12.0000
((..	chr8:28206101-28206362(-)$1	1	11	15	12.0000
((((	chr6:36189907-36190129(+)$1	1	33	37	12.0000
.)))	chr11:65545899-65546122(-)$1	1	25	29	12.0000
))))	chr1:38034783-38034999(-)$1	1	132	136	12.0000
((.(	chrX:49127116-49127337(+)$1	1	118	122	12.0000
((((	chr8:125463645-125463866(+)$1	1	84	88	12.0000
..((	chrX:48792014-48792227(-)$1	1	30	34	12.0000
.(..	chr8:17815067-17815288(+)$1	1	58	62	12.0000
).))	chr9:131502139-131502384(-)$1	1	181	185	12.0000
))))	chr22:41572394-41572633(+)$1	1	56	60	12.0000
((..	chr7:148921260-148921473(+)$1	1	3	7	12.0000
....	chr4:1730256-1730511(+)$1	1	6	10	12.0000
(((.	chr3:47891027-47891253(+)$1	1	27	31	12.0000
..))	chr1:27056075-27056368(+)$1	1	134	138	12.0000
))).	chr3:78666860-78667086(-)$1	1	75	79	12.0000
((..	chr9:135553444-135553691(+)$1	1	94	98	12.0000
)..)	chr20:57484725-57484946(+)$1	1	43	47	12.0000
((((	chr6:43499190-43499410(-)$1	1	161	165	12.0000
...)	chr2:173356102-173356319(+)$1	1	137	141	12.0000
((..	chr7:2394869-2395136(+)$1	1	16	20	12.0000
((((	chr4:4285260-4285483(-)$1	1	87	91	12.0000
(...	chr6:41562563-41562795(+)$1	1	208	212	12.0000
((((	chr16:75263378-75263604(-)$1	1	8	12	12.0000
))..	chr1:232539121-232539340(-)$1	1	60	64	12.0000
)..)	chr2:174819856-174820075(-)$1	1	47	51	12.0000
))))	chr10:119134183-119134478(-)$1	1	132	136	12.0000
)...	chr21:16339794-16340015(-)$1	1	147	151	12.0000
((((	chr15:77346442-77346672(-)$1	1	70	74	12.0000
))))	chr19:36209141-36209361(+)$1	1	116	120	12.0000
))))	chr19:42861484-42861704(+)$1	1	181	185	12.0000
)).)	chr12:110719550-110719774(+)$1	1	168	172	12.0000
...)	chr19:52521549-52521766(-)$1	1	69	73	12.0000
((((	chr19:622523-622756(-)$1	1	0	4	12.0000
...(	chr15:69745927-69746148(+)$1	1	85	89	12.0000
((.(	chr10:105178189-105178407(+)$1	1	148	152	12.0000
....	chr1:232650574-232650794(-)$1	1	50	54	12.0000
(...	chr11:57076857-57077075(-)$1	1	13	17	12.0000
.)).	chr6:90660309-90660558(-)$1	1	88	92	12.0000
(((.	chr16:69402248-69402467(-)$1	1	23	27	12.0000
)).)	chr17:27901695-27901923(-)$1	1	53	57	12.0000
((.(	chr19:36120416-36120673(+)$1	1	11	15	12.0000
)(((	chr19:49489119-49489343(-)$1	1	108	112	12.0000
))))	chr3:9475956-9476186(+)$1	1	209	213	12.0000
))))	chr12:49431634-49431858(-)$1	1	204	208	12.0000
))))	chr17:1631100-1631327(+)$1	1	143	147	12.0000
(.((	chr17:74716356-74716596(-)$1	1	44	48	12.0000
))))	chr15:22928353-22928582(+)$1	1	69	73	12.0000
)..(	chr12:49436498-49436750(-)$1	1	117	121	12.0000
((..	chr16:3819155-3819373(-)$1	1	28	32	12.0000
(((.	chr8:77763520-77763743(+)$1	1	47	51	12.0000
((((	chr14:75295819-75296043(+)$1	1	156	160	12.0000
((((	chr3:47888218-47888514(+)$1	1	77	81	12.0000
).))	chr20:35294606-35294825(-)$1	1	107	111	12.0000
((((	chr1:171553032-171553258(+)$1	1	85	89	12.0000
((..	chr17:38508124-38508357(+)$1	1	2	6	12.0000
((.(	chr1:27098891-27099137(+)$1	1	115	119	12.0000
))))	chr9:110250232-110250443(-)$1	1	181	185	12.0000
))))	chr1:150471292-150471598(+)$1	1	86	90	12.0000
((((	chr5:150497249-150497487(-)$1	1	57	61	12.0000
((.(	chr11:47296337-47296566(+)$1	1	53	57	12.0000
))))	chr12:124241276-124241487(+)$1	1	64	68	12.0000
)..)	chr6:4037636-4037859(+)$1	1	128	132	12.0000
....	chr13:32929199-32929419(+)$1	1	183	187	12.0000
.(((	chr19:40486118-40486360(+)$1	1	39	43	12.0000
))))	chr18:29848485-29848706(-)$1	1	181	185	12.0000
))..	chr6:159188293-159188503(-)$1	1	81	85	12.0000
))))	chr19:50910189-50910447(+)$1	1	208	212	12.0000
))))	chr12:12317263-12317485(-)$1	1	144	148	12.0000
((..	chr11:57077161-57077394(-)$1	1	31	35	12.0000
((..	chr16:69370392-69370630(-)$1	1	169	173	12.0000
).))	chr19:6381082-6381292(-)$1	1	15	19	12.0000
((((	chr1:16263694-16263957(+)$1	1	7	11	12.0000
...(	chr16:11439427-11439651(+)$1	1	80	84	12.0000
((((	chr10:72297977-72298205(+)$1	1	54	58	12.0000

#PSSM
G : 0.97	g : 0.02	
C : 0.97	c : 0.02	
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_CDS_m2_run1.nuc.txt

#NT
CAGAACA	chr12:133381296-133381516(-)$1	220	79	86	12.5178
UAGAAGA	chr14:24900809-24901040(+)$1	231	61	68	12.5178
CAGAAGA	chr1:200818863-200819080(+)$1	217	203	210	16.4464
CAGAAGA	chr17:7798568-7798783(+)$1	215	112	119	16.4464
CUGAAGA	chr1:1250140-1250360(-)$1	220	118	125	13.0535
CUGAAGA	chr17:41242874-41243104(-)$1	230	94	101	13.0535
CAGAAAA	chr2:219319577-219319806(-)$1	229	92	99	12.5178
AAGAAGA	chr6:159046659-159046881(+)$1	222	129	136	12.6964
CAGAAAA	chrX:68381886-68382106(-)$1	220	28	35	12.5178
CGGAAGA	chr12:2973467-2973688(-)$1	221	29	36	12.5178
CAGGAGA	chr14:61924182-61924396(+)$1	214	66	73	12.1607
CAGAUGA	chr15:74948214-74948431(-)$1	217	84	91	12.1607
GAGAAGA	chr7:100482297-100482517(+)$1	220	126	133	12.6964
CUGAAGA	chr6:30679362-30679594(-)$1	232	94	101	13.0535
CAGAACA	chr17:78280865-78281099(+)$1	234	86	93	12.5178
CAGAUGA	chr17:2598099-2598328(-)$1	229	218	225	12.1607
CAGAAGU	chr13:41705846-41706063(-)$1	217	191	198	12.3392
AAGAAGA	chr17:61907166-61907382(+)$1	216	122	129	12.6964
CAGAACA	chr15:85326486-85326713(+)$1	227	86	93	12.5178
CAGAACA	chr3:10312525-10312743(+)$1	218	160	167	12.5178
CAGAAGG	chr8:1904864-1905082(+)$1	218	184	191	12.3392
CGGAAGA	chr21:47836372-47836603(+)$1	231	93	100	12.5178
GAGAAGA	chr15:30024589-30024806(-)$1	217	140	147	12.6964
CAGAAGC	chr1:861251-861477(+)$1	226	2	9	12.5178
CAGAGGA	chr6:143093344-143093559(-)$1	215	4	11	12.3392
AAGAAGA	chr19:39664431-39664655(+)$1	224	168	175	12.6964
CUGAAGA	chr14:77273685-77273903(-)$1	218	188	195	13.0535
CAGAAGC	chr15:78765525-78765752(+)$1	227	76	83	12.5178
CAUAAGA	chr18:77896422-77896645(+)$1	223	60	67	11.8928
CAGAAGC	chr9:134459629-134459868(-)$1	239	153	160	12.5178
GAGAAGA	chr8:18432550-18432775(-)$1	225	73	80	12.6964
CAGGAGA	chr12:6708928-6709184(-)$1	256	3	10	12.1607
CACAAGA	chr17:62589508-62589727(-)$1	219	79	86	11.8928
CUGAAGA	chr12:57135224-57135437(-)$1	213	185	192	13.0535
GAGAAGA	chr7:98534697-98534907(+)$1	210	15	22	12.6964
CAAAAGA	chr9:71831243-71831466(+)$1	223	16	23	11.9821
CAGCAGA	chr14:23532145-23532363(-)$1	218	118	125	12.0714
CAGAGGA	chr10:119043053-119043291(-)$1	238	133	140	12.3392
CAGAAGG	chr1:203818983-203819205(+)$1	222	83	90	12.3392
CUGAAGA	chr12:133331413-133331633(-)$1	220	187	194	13.0535
CUGAAGA	chr1:25824801-25825021(+)$1	220	144	151	13.0535
CAGAAAA	chr16:71724466-71724685(-)$1	219	70	77	12.5178
CAGAAGA	chr18:13736953-13737172(+)$1	219	78	85	16.4464
CAGAAGC	chr5:78573745-78573963(+)$1	218	72	79	12.5178
CAGAGGA	chr15:29346194-29346418(+)$1	224	65	72	12.3392
CAAAAGA	chr3:124952482-124952704(-)$1	222	54	61	11.9821
CAGGAGA	chr8:103307373-103307595(-)$1	222	147	154	12.1607
CAGCAGA	chr6:138751455-138751686(-)$1	231	23	30	12.0714
AAGAAGA	chr10:129905054-129905275(-)$1	221	99	106	12.6964
CAGAAGA	chr16:46705562-46705784(-)$1	222	85	92	16.4464
CAGAAAA	chr17:29509447-29509664(+)$1	217	84	91	12.5178
CUGAAGA	chr22:24480444-24480664(+)$1	220	201	208	13.0535
CAGAAGU	chr19:38126160-38126376(-)$1	216	96	103	12.3392
CAGAGGA	chr6:116600782-116601005(-)$1	223	205	212	12.3392
CAGAAGA	chr1:203769015-203769237(+)$1	222	21	28	16.4464

#otherMatches

#Struct PSSM
####eee	chr17:48457617-48457840(+)$1	223	8	15	12.5178
HHH::::	chr12:133381296-133381516(-)$1	220	79	86	12.5178
annnnna	chr14:24900809-24901040(+)$1	231	61	68	12.5178
dd:::CC	chr1:200818863-200819080(+)$1	217	203	210	16.4464
ddddddd	chr17:7798568-7798783(+)$1	215	112	119	16.4464
qqqqqqq	chr1:1250140-1250360(-)$1	220	118	125	13.0535
ffff[bb	chr17:41242874-41243104(-)$1	230	94	101	13.0535
ddddfff	chr2:219319577-219319806(-)$1	229	92	99	12.5178
fbb!!cc	chr6:159046659-159046881(+)$1	222	129	136	12.6964
bb:::::	chrX:68381886-68382106(-)$1	220	28	35	12.5178
]eeeeed	chr12:2973467-2973688(-)$1	221	29	36	12.5178
55dddd]	chr14:61924182-61924396(+)$1	214	66	73	12.1607
ee:::::	chr15:74948214-74948431(-)$1	217	84	91	12.1607
:::::::	chr7:100482297-100482517(+)$1	220	126	133	12.6964
nnnnnee	chr6:30679362-30679594(-)$1	232	94	101	13.0535
b]eeeee	chr17:78280865-78281099(+)$1	234	86	93	12.5178
EYYCCC}	chr17:2598099-2598328(-)$1	229	218	225	12.1607
]bb22a]	chr13:41705846-41706063(-)$1	217	191	198	12.3392
g::::::	chr17:61907166-61907382(+)$1	216	122	129	12.6964
GGGKKA{	chr15:85326486-85326713(+)$1	227	86	93	12.5178
eeee444	chr3:10312525-10312743(+)$1	218	160	167	12.5178
bmmmmbb	chr8:1904864-1905082(+)$1	218	184	191	12.3392
:ffffff	chr21:47836372-47836603(+)$1	231	93	100	12.5178
gggggg3	chr15:30024589-30024806(-)$1	217	140	147	12.6964
eeee!!b	chr1:861251-861477(+)$1	226	2	9	12.5178
DD{IIII	chr6:143093344-143093559(-)$1	215	4	11	12.3392
nnnnnee	chr19:39664431-39664655(+)$1	224	168	175	12.6964
oobb:BB	chr14:77273685-77273903(-)$1	218	188	195	13.0535
ddddddd	chr15:78765525-78765752(+)$1	227	76	83	12.5178
hhhhhhh	chr18:77896422-77896645(+)$1	223	60	67	11.8928
ccc22ee	chr9:134459629-134459868(-)$1	239	153	160	12.5178
[ccciii	chr8:18432550-18432775(-)$1	225	73	80	12.6964
:::::::	chr12:6708928-6709184(-)$1	256	3	10	12.1607
bpppppp	chr17:62589508-62589727(-)$1	219	79	86	11.8928
DDD::dd	chr12:57135224-57135437(-)$1	213	185	192	13.0535
F::::::	chr7:98534697-98534907(+)$1	210	15	22	12.6964
DDD::ff	chr9:71831243-71831466(+)$1	223	16	23	11.9821
:::::::	chr14:23532145-23532363(-)$1	218	118	125	12.0714
ccccc""	chr10:119043053-119043291(-)$1	238	133	140	12.3392
oobb22b	chr1:203818983-203819205(+)$1	222	83	90	12.3392
fffmmmm	chr12:133331413-133331633(-)$1	220	187	194	13.0535
ccc22cc	chr1:25824801-25825021(+)$1	220	144	151	13.0535
hhhhh22	chr16:71724466-71724685(-)$1	219	70	77	12.5178
cc!!bb!	chr18:13736953-13737172(+)$1	219	78	85	16.4464
DDDKKEE	chr5:78573745-78573963(+)$1	218	72	79	12.5178
eeeee$$	chr15:29346194-29346418(+)$1	224	65	72	12.3392
^^^^^^^	chr3:124952482-124952704(-)$1	222	54	61	11.9821
vvvvvvv	chr8:103307373-103307595(-)$1	222	147	154	12.1607
ooooccc	chr6:138751455-138751686(-)$1	231	23	30	12.0714
dddd:ee	chr10:129905054-129905275(-)$1	221	99	106	12.6964
dd[ccc[	chr16:46705562-46705784(-)$1	222	85	92	16.4464
ddfffff	chr17:29509447-29509664(+)$1	217	84	91	12.5178
::::::D	chr22:24480444-24480664(+)$1	220	201	208	13.0535
!ccclll	chr19:38126160-38126376(-)$1	216	96	103	12.3392
ttdddd2	chr6:116600782-116601005(-)$1	223	205	212	12.3392
!!eeeee	chr1:203769015-203769237(+)$1	222	21	28	16.4464

#DB
....(((	chr17:48457617-48457840(+)$1	1	8	15	12.5178
(((....	chr12:133381296-133381516(-)$1	1	79	86	12.5178
(.....)	chr14:24900809-24901040(+)$1	1	61	68	12.5178
))...))	chr1:200818863-200819080(+)$1	1	203	210	16.4464
)))))))	chr17:7798568-7798783(+)$1	1	112	119	16.4464
.......	chr1:1250140-1250360(-)$1	1	118	125	13.0535
((((.((	chr17:41242874-41243104(-)$1	1	94	101	13.0535
)))))))	chr2:219319577-219319806(-)$1	1	92	99	12.5178
)((..((	chr6:159046659-159046881(+)$1	1	129	136	12.6964
)).....	chrX:68381886-68382106(-)$1	1	28	35	12.5178
.))))))	chr12:2973467-2973688(-)$1	1	29	36	12.5178
..)))).	chr14:61924182-61924396(+)$1	1	66	73	12.1607
)).....	chr15:74948214-74948431(-)$1	1	84	91	12.1607
.......	chr7:100482297-100482517(+)$1	1	126	133	12.6964
.....))	chr6:30679362-30679594(-)$1	1	94	101	13.0535
).)))))	chr17:78280865-78281099(+)$1	1	86	93	12.5178
)..))).	chr17:2598099-2598328(-)$1	1	218	225	12.1607
.))..).	chr13:41705846-41706063(-)$1	1	191	198	12.3392
)......	chr17:61907166-61907382(+)$1	1	122	129	12.6964
(((..(.	chr15:85326486-85326713(+)$1	1	86	93	12.5178
))))...	chr3:10312525-10312743(+)$1	1	160	167	12.5178
(....))	chr8:1904864-1905082(+)$1	1	184	191	12.3392
.((((((	chr21:47836372-47836603(+)$1	1	93	100	12.5178
)))))).	chr15:30024589-30024806(-)$1	1	140	147	12.6964
((((..(	chr1:861251-861477(+)$1	1	2	9	12.5178
((.((((	chr6:143093344-143093559(-)$1	1	4	11	12.3392
.....))	chr19:39664431-39664655(+)$1	1	168	175	12.6964
..)).))	chr14:77273685-77273903(-)$1	1	188	195	13.0535
(((((((	chr15:78765525-78765752(+)$1	1	76	83	12.5178
)))))))	chr18:77896422-77896645(+)$1	1	60	67	11.8928
)))..))	chr9:134459629-134459868(-)$1	1	153	160	12.5178
.((((((	chr8:18432550-18432775(-)$1	1	73	80	12.6964
.......	chr12:6708928-6709184(-)$1	1	3	10	12.1607
(......	chr17:62589508-62589727(-)$1	1	79	86	11.8928
)))..((	chr12:57135224-57135437(-)$1	1	185	192	13.0535
(......	chr7:98534697-98534907(+)$1	1	15	22	12.6964
(((..((	chr9:71831243-71831466(+)$1	1	16	23	11.9821
.......	chr14:23532145-23532363(-)$1	1	118	125	12.0714
(((((..	chr10:119043053-119043291(-)$1	1	133	140	12.3392
..))..)	chr1:203818983-203819205(+)$1	1	83	90	12.3392
(((....	chr12:133331413-133331633(-)$1	1	187	194	13.0535
)))..))	chr1:25824801-25825021(+)$1	1	144	151	13.0535
)))))..	chr16:71724466-71724685(-)$1	1	70	77	12.5178
((..((.	chr18:13736953-13737172(+)$1	1	78	85	16.4464
(((..((	chr5:78573745-78573963(+)$1	1	72	79	12.5178
(((((..	chr15:29346194-29346418(+)$1	1	65	72	12.3392
.......	chr3:124952482-124952704(-)$1	1	54	61	11.9821
.......	chr8:103307373-103307595(-)$1	1	147	154	12.1607
....)))	chr6:138751455-138751686(-)$1	1	23	30	12.0714
)))).((	chr10:129905054-129905275(-)$1	1	99	106	12.6964
((.(((.	chr16:46705562-46705784(-)$1	1	85	92	16.4464
)))))))	chr17:29509447-29509664(+)$1	1	84	91	12.5178
......)	chr22:24480444-24480664(+)$1	1	201	208	13.0535
.(((...	chr19:38126160-38126376(-)$1	1	96	103	12.3392
..)))).	chr6:116600782-116601005(-)$1	1	205	212	12.3392
..(((((	chr1:203769015-203769237(+)$1	1	21	28	16.4464

#PSSM
C : 0.82	A : 0.07	G : 0.07	U : 0.03	
A : 0.82	U : 0.14	G : 0.03	
G : 0.92	A : 0.03	U : 0.01	C : 0.01	
A : 0.91	G : 0.05	C : 0.03	
A : 0.89	G : 0.07	U : 0.03	
G : 0.85	C : 0.07	A : 0.07	
A : 0.85	C : 0.07	U : 0.03	G : 0.03	

#score	719.9285714285724
#seq	56
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_CDS_m3_run1.nuc.txt

#NT
UUUCUUUU	chr8:75272380-75272627(+)$1	247	205	213	19.8474
UGUCUUUU	chr12:111158683-111159024(-)$1	341	36	44	16.2033
UUUCUUGU	chr12:64878005-64878315(+)$1	310	287	295	15.3559
UUUCUUUG	chr9:100756891-100757144(+)$1	253	3	11	15.6949
UUUCCUUU	chr15:41643088-41643336(+)$1	248	77	85	15.4406
UUUCUUCU	chr1:94941071-94941340(+)$1	269	79	87	15.4406
UUUCUUUC	chr5:132202550-132202816(+)$1	266	157	165	16.0338
UUUAUUUU	chr1:55575761-55575997(-)$1	236	26	34	15.8644
UUUCUAUU	chr6:34263328-34263558(-)$1	230	7	15	15.2711
UUUCUUUU	chr2:54150384-54150640(-)$1	256	13	21	19.8474
UUGCUUUU	chr12:54448602-54448870(+)$1	268	10	18	16.0338
UAUCUUUU	chr14:104378848-104379177(-)$1	329	38	46	16.0338
UUGCUUUU	chr20:48565731-48565981(+)$1	250	35	43	16.0338
UUUCUUUC	chr4:160260214-160260466(+)$1	252	37	45	16.0338
UUUUUUUU	chr12:104732817-104733071(+)$1	254	83	91	16.0338
UUUCUUUU	chrX:153994096-153994331(+)$1	235	211	219	19.8474
UUUCUUUU	chr2:10937123-10937426(-)$1	303	73	81	19.8474
CUUCUUUU	chr10:1052926-1053156(+)$1	230	11	19	15.1864
UGUCUUUU	chr2:207175878-207176132(+)$1	254	66	74	16.2033
UUGCUUUU	chr5:10426415-10426691(+)$1	276	65	73	16.0338
UUUUUUUU	chr7:56126031-56126283(+)$1	252	5	13	16.0338
UUGCUUUU	chr7:112424192-112424434(-)$1	242	224	232	16.0338
UUUCUUUC	chr7:116528085-116528322(+)$1	237	79	87	16.0338
UUUCUUUU	chr1:197102545-197102793(-)$1	248	48	56	19.8474
UUUCUUAU	chr19:1555204-1555435(-)$1	231	160	168	15.4406
UUUUUUUU	chr20:49520336-49520590(-)$1	254	36	44	16.0338
UUUCUUUU	chr15:69715396-69715752(+)$1	356	88	96	19.8474
UAUCUUUU	chr18:12706465-12706799(+)$1	334	65	73	16.0338
UUUCUUUC	chr12:21661244-21661531(+)$1	287	56	64	16.0338
UUUCUUUU	chr10:75896304-75896660(-)$1	356	52	60	19.8474
uuuauuuu	chr12:440916-441165(-)$1	249	18	26	15.8644
UUGCUUUU	chr3:56600655-56600892(+)$1	237	183	191	16.0338
UUUCUUUU	chr10:102015945-102016200(-)$1	255	246	254	19.8474
CUUCUUUU	chr11:10825616-10825842(-)$1	226	80	88	15.1864
UUUCUUAU	chr8:67971417-67971675(-)$1	258	242	250	15.4406
UUUCUUUG	chr11:3039011-3039262(-)$1	251	190	198	15.6949
UUUCCUUU	chr16:46726189-46726457(+)$1	268	91	99	15.4406
UUUAUUUU	chr10:133760978-133761239(+)$1	261	38	46	15.8644
UUGCUUUU	chr2:61715202-61715489(-)$1	287	206	214	16.0338
UGUCUUUU	chr7:157000091-157000349(+)$1	258	44	52	16.2033
UUUUUUUU	chr14:56078698-56078975(+)$1	277	1	9	16.0338
UUUCUUCU	chr1:36101841-36102133(-)$1	292	84	92	15.4406
UUUCUUUC	chr19:58371082-58371315(+)$1	233	198	206	16.0338
UUUGUUUU	chr7:128398846-128399104(+)$1	258	66	74	15.6949
UUUCUCUU	chr16:23637524-23637760(-)$1	236	139	147	15.4406
UUUCCUUU	chr12:90010659-90010913(-)$1	254	86	94	15.4406
UUUCAUUU	chr17:78109129-78109399(-)$1	270	44	52	15.2711
UAUCUUUU	chr20:25405743-25406050(+)$1	307	227	235	16.0338
UUUCUCUU	chrX:53570720-53570963(-)$1	243	18	26	15.4406
UGUCUUUU	chr8:94748059-94748300(-)$1	241	177	185	16.2033
UUUCUUUU	chr6:35840281-35840539(-)$1	258	206	214	19.8474
UAUCUUUU	chr2:71592482-71592723(+)$1	241	62	70	16.0338
UUUCUUUC	chr15:44085119-44085362(+)$1	243	40	48	16.0338
UGUCUUUU	chr8:48873968-48874252(+)$1	284	80	88	16.2033
UUGCUUUU	chr11:3800306-3800529(-)$1	223	30	38	16.0338
UUUUUUUU	chr13:111932588-111932816(+)$1	228	0	8	16.0338
UGUCUUUU	chr1:204375107-204375410(-)$1	303	241	249	16.2033
UUUCUCUU	chr1:244572756-244573025(-)$1	269	64	72	15.4406

#otherMatches

#Struct PSSM
88888888	chr6:26027329-26027601(-)$1	272	79	87	19.8474
HHHHHHH:	chr8:75272380-75272627(+)$1	247	205	213	19.8474
::ffffff	chr12:111158683-111159024(-)$1	341	36	44	16.2033
mmccc:II	chr12:64878005-64878315(+)$1	310	287	295	15.3559
GGGG:eee	chr9:100756891-100757144(+)$1	253	3	11	15.6949
ffffff[c	chr15:41643088-41643336(+)$1	248	77	85	15.4406
:::::::b	chr1:94941071-94941340(+)$1	269	79	87	15.4406
c::::hhh	chr5:132202550-132202816(+)$1	266	157	165	16.0338
EEKKEEEE	chr1:55575761-55575997(-)$1	236	26	34	15.8644
ggggg!!e	chr6:34263328-34263558(-)$1	230	7	15	15.2711
E:::::::	chr2:54150384-54150640(-)$1	256	13	21	19.8474
:eeeeeii	chr12:54448602-54448870(+)$1	268	10	18	16.0338
hhhhhhhh	chr14:104378848-104379177(-)$1	329	38	46	16.0338
qqqqqqqq	chr20:48565731-48565981(+)$1	250	35	43	16.0338
:::::::c	chr4:160260214-160260466(+)$1	252	37	45	16.0338
3hhhhhhh	chr12:104732817-104733071(+)$1	254	83	91	16.0338
gggggg::	chrX:153994096-153994331(+)$1	235	211	219	19.8474
$$$dddd[	chr2:10937123-10937426(-)$1	303	73	81	19.8474
ssssssss	chr10:1052926-1053156(+)$1	230	11	19	15.1864
::gggggg	chr2:207175878-207176132(+)$1	254	66	74	16.2033
"dddd[ee	chr5:10426415-10426691(+)$1	276	65	73	16.0338
GGG{EEEE	chr7:56126031-56126283(+)$1	252	5	13	16.0338
I:bbmmmm	chr7:112424192-112424434(-)$1	242	224	232	16.0338
4444hhhh	chr7:116528085-116528322(+)$1	237	79	87	16.0338
eeeee22h	chr1:197102545-197102793(-)$1	248	48	56	19.8474
eeeccc[c	chr19:1555204-1555435(-)$1	231	160	168	15.4406
mmmmccc3	chr20:49520336-49520590(-)$1	254	36	44	16.0338
DDDDPPPP	chr15:69715396-69715752(+)$1	356	88	96	19.8474
ccnnnnnc	chr18:12706465-12706799(+)$1	334	65	73	16.0338
:hhhhhhh	chr12:21661244-21661531(+)$1	287	56	64	16.0338
::::::::	chr10:75896304-75896660(-)$1	356	52	60	19.8474
E{BB::::	chr12:440916-441165(-)$1	249	18	26	15.8644
GGGGGG::	chr3:56600655-56600892(+)$1	237	183	191	16.0338
::::::::	chr10:102015945-102016200(-)$1	255	246	254	19.8474
ccc:::::	chr11:10825616-10825842(-)$1	226	80	88	15.1864
BYYDDDD}	chr8:67971417-67971675(-)$1	258	242	250	15.4406
ggggggg:	chr11:3039011-3039262(-)$1	251	190	198	15.6949
!!eeeee"	chr16:46726189-46726457(+)$1	268	91	99	15.4406
qqqqqqqb	chr10:133760978-133761239(+)$1	261	38	46	15.8644
uuuuuuuu	chr2:61715202-61715489(-)$1	287	206	214	16.0338
[eeeeell	chr7:157000091-157000349(+)$1	258	44	52	16.2033
JJJJJJJJ	chr14:56078698-56078975(+)$1	277	1	9	16.0338
&&&&&eee	chr1:36101841-36102133(-)$1	292	84	92	15.4406
qqqqffff	chr19:58371082-58371315(+)$1	233	198	206	16.0338
ggggggg!	chr7:128398846-128399104(+)$1	258	66	74	15.6949
oooaffff	chr16:23637524-23637760(-)$1	236	139	147	15.4406
c####ccc	chr12:90010659-90010913(-)$1	254	86	94	15.4406
ppppppff	chr17:78109129-78109399(-)$1	270	44	52	15.2711
fttttttt	chr20:25405743-25406050(+)$1	307	227	235	16.0338
B{EEEEEK	chrX:53570720-53570963(-)$1	243	18	26	15.4406
occc]eee	chr8:94748059-94748300(-)$1	241	177	185	16.2033
hhhhhhhh	chr6:35840281-35840539(-)$1	258	206	214	19.8474
ccc22eee	chr2:71592482-71592723(+)$1	241	62	70	16.0338
[ffffff$	chr15:44085119-44085362(+)$1	243	40	48	16.0338
ee]hhhhh	chr8:48873968-48874252(+)$1	284	80	88	16.2033
ddd::::C	chr11:3800306-3800529(-)$1	223	30	38	16.0338
::::::::	chr13:111932588-111932816(+)$1	228	0	8	16.0338
hh::::::	chr1:204375107-204375410(-)$1	303	241	249	16.2033
44eeeee]	chr1:244572756-244573025(-)$1	269	64	72	15.4406

#DB
........	chr6:26027329-26027601(-)$1	1	79	87	19.8474
))))))).	chr8:75272380-75272627(+)$1	1	205	213	19.8474
..((((((	chr12:111158683-111159024(-)$1	1	36	44	16.2033
..))).))	chr12:64878005-64878315(+)$1	1	287	295	15.3559
((((.(((	chr9:100756891-100757144(+)$1	1	3	11	15.6949
((((((.(	chr15:41643088-41643336(+)$1	1	77	85	15.4406
.......(	chr1:94941071-94941340(+)$1	1	79	87	15.4406
)....(((	chr5:132202550-132202816(+)$1	1	157	165	16.0338
((..((((	chr1:55575761-55575997(-)$1	1	26	34	15.8644
(((((..(	chr6:34263328-34263558(-)$1	1	7	15	15.2711
(.......	chr2:54150384-54150640(-)$1	1	13	21	19.8474
.(((((((	chr12:54448602-54448870(+)$1	1	10	18	16.0338
))))))))	chr14:104378848-104379177(-)$1	1	38	46	16.0338
........	chr20:48565731-48565981(+)$1	1	35	43	16.0338
.......(	chr4:160260214-160260466(+)$1	1	37	45	16.0338
.)))))))	chr12:104732817-104733071(+)$1	1	83	91	16.0338
))))))..	chrX:153994096-153994331(+)$1	1	211	219	19.8474
...((((.	chr2:10937123-10937426(-)$1	1	73	81	19.8474
........	chr10:1052926-1053156(+)$1	1	11	19	15.1864
..((((((	chr2:207175878-207176132(+)$1	1	66	74	16.2033
.((((.((	chr5:10426415-10426691(+)$1	1	65	73	16.0338
(((.((((	chr7:56126031-56126283(+)$1	1	5	13	16.0338
).((....	chr7:112424192-112424434(-)$1	1	224	232	16.0338
....))))	chr7:116528085-116528322(+)$1	1	79	87	16.0338
)))))..)	chr1:197102545-197102793(-)$1	1	48	56	19.8474
((((((.(	chr19:1555204-1555435(-)$1	1	160	168	15.4406
....))).	chr20:49520336-49520590(-)$1	1	36	44	16.0338
((((....	chr15:69715396-69715752(+)$1	1	88	96	19.8474
((.....)	chr18:12706465-12706799(+)$1	1	65	73	16.0338
.(((((((	chr12:21661244-21661531(+)$1	1	56	64	16.0338
........	chr10:75896304-75896660(-)$1	1	52	60	19.8474
(.((....	chr12:440916-441165(-)$1	1	18	26	15.8644
))))))..	chr3:56600655-56600892(+)$1	1	183	191	16.0338
........	chr10:102015945-102016200(-)$1	1	246	254	19.8474
))).....	chr11:10825616-10825842(-)$1	1	80	88	15.1864
)..)))).	chr8:67971417-67971675(-)$1	1	242	250	15.4406
))))))).	chr11:3039011-3039262(-)$1	1	190	198	15.6949
..(((((.	chr16:46726189-46726457(+)$1	1	91	99	15.4406
.......)	chr10:133760978-133761239(+)$1	1	38	46	15.8644
........	chr2:61715202-61715489(-)$1	1	206	214	16.0338
.(((((..	chr7:157000091-157000349(+)$1	1	44	52	16.2033
((((((((	chr14:56078698-56078975(+)$1	1	1	9	16.0338
.....(((	chr1:36101841-36102133(-)$1	1	84	92	15.4406
....))))	chr19:58371082-58371315(+)$1	1	198	206	16.0338
(((((((.	chr7:128398846-128399104(+)$1	1	66	74	15.6949
...)))))	chr16:23637524-23637760(-)$1	1	139	147	15.4406
(....(((	chr12:90010659-90010913(-)$1	1	86	94	15.4406
......))	chr17:78109129-78109399(-)$1	1	44	52	15.2711
(.......	chr20:25405743-25406050(+)$1	1	227	235	16.0338
(.(((((.	chrX:53570720-53570963(-)$1	1	18	26	15.4406
.))).)))	chr8:94748059-94748300(-)$1	1	177	185	16.2033
((((((((	chr6:35840281-35840539(-)$1	1	206	214	19.8474
)))..)))	chr2:71592482-71592723(+)$1	1	62	70	16.0338
.((((((.	chr15:44085119-44085362(+)$1	1	40	48	16.0338
)).)))))	chr8:48873968-48874252(+)$1	1	80	88	16.2033
)))....(	chr11:3800306-3800529(-)$1	1	30	38	16.0338
........	chr13:111932588-111932816(+)$1	1	0	8	16.0338
))......	chr1:204375107-204375410(-)$1	1	241	249	16.2033
..))))).	chr1:244572756-244573025(-)$1	1	64	72	15.4406

#PSSM
U : 0.94	C : 0.03	u : 0.01	
U : 0.81	G : 0.10	A : 0.06	u : 0.01	
U : 0.86	G : 0.11	u : 0.01	
C : 0.84	U : 0.08	A : 0.03	a : 0.01	G : 0.01	
U : 0.91	C : 0.05	u : 0.01	A : 0.01	
U : 0.91	C : 0.05	A : 0.01	u : 0.01	
U : 0.89	C : 0.03	A : 0.03	G : 0.01	u : 0.01	
U : 0.84	C : 0.10	G : 0.03	u : 0.01	

#score	973.7966101694908
#seq	59
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m2_run2.nuc.txt

#NT
ACUUCAG	chr12:133683094-133683326(+)$1	232	205	212	16.5769
ACUUCAG	chr15:35274061-35274286(-)$1	225	18	25	16.5769
AAUUCAG	chr2:231683315-231683538(+)$1	223	132	139	12.7307
AUUUCAG	chr10:31809570-31809796(+)$1	226	61	68	13.0192
ACUUAAG	chr12:104378491-104378721(+)$1	230	123	130	12.0576
AAUUCAG	chr1:171537299-171537524(+)$1	225	43	50	12.7307
gcuucag	chr1:82456544-82456775(+)$1	231	158	165	12.5384
UCUUCAG	chr3:196666125-196666347(-)$1	222	141	148	12.7307
ACUUCGG	chrM:14733-15002(+)$1	269	108	115	11.9615
ACAUCAG	chr5:173317732-173317961(+)$1	229	219	226	12.9230
ACUUCAC	chr21:38496845-38497074(+)$1	229	113	120	12.7307
ACUUCAA	chr3:129150285-129150508(-)$1	223	206	213	12.8269
ACAUCAG	chr19:37240018-37240243(-)$1	225	35	42	12.9230
ACUUCAU	chr19:37618401-37618637(+)$1	236	52	59	13.0192
ACUACAG	chr3:98309402-98309626(-)$1	224	118	125	12.3461
UCUUCAG	chr3:48594091-48594309(+)$1	218	79	86	12.7307
ACUUCAG	chr14:97022554-97022784(+)$1	230	91	98	16.5769
ACUCCAG	chr2:70315623-70315884(+)$1	261	33	40	12.1538
ACAUCAG	chr19:53884324-53884546(+)$1	222	203	210	12.9230
ACUUCAA	chr10:32560556-32560804(-)$1	248	66	73	12.8269
ACUUCAA	chr2:170402804-170403059(-)$1	255	67	74	12.8269
ACUUCGG	chr11:4130805-4131033(+)$1	228	114	121	11.9615
ACAUCAG	chr1:27087269-27087504(+)$1	235	143	150	12.9230
GCUUCAG	chr2:166768924-166769152(-)$1	228	193	200	12.5384
ACUUUAG	chr18:9254754-9254986(+)$1	232	69	76	12.1538
ACUUCAU	chr17:27613750-27613988(-)$1	238	108	115	13.0192
ACUUCAU	chr21:43413502-43413740(-)$1	238	126	133	13.0192
ACUUCAC	chr6:17616763-17617001(-)$1	238	114	121	12.7307
AUUUCAG	chr9:106878425-106878656(+)$1	231	124	131	13.0192
ACUUUAG	chr20:40033432-40033655(-)$1	223	18	25	12.1538
ACUUCAU	chr19:38125803-38126037(-)$1	234	23	30	13.0192
ACUGCAG	chr1:8418175-8418410(-)$1	235	63	70	12.1538
AUUUCAG	chr15:93515516-93515747(+)$1	231	139	146	13.0192
ACUUCAG	chr7:98601745-98601965(+)$1	220	73	80	16.5769
ACUUCAU	chr7:26235370-26235610(-)$1	240	206	213	13.0192
ACCUCAG	chr17:17158135-17158359(-)$1	224	153	160	12.4423
ACUUGAG	chr2:206869526-206869754(-)$1	228	203	210	12.0576
ACAUCAG	chr15:23006462-23006682(-)$1	220	150	157	12.9230
CCUUCAG	chr6:12125564-12125785(+)$1	221	92	99	12.5384
UCUUCAG	chr2:61719089-61719310(-)$1	221	125	132	12.7307
ACUACAG	chr2:170806236-170806462(+)$1	226	28	35	12.3461
UCUUCAG	chr12:46319885-46320111(-)$1	226	132	139	12.7307
ACUUCAG	chr4:106196298-106196525(+)$1	227	121	128	16.5769
CCUUCAG	chr8:95523655-95523875(-)$1	220	172	179	12.5384
AUUUCAG	chr8:48772195-48772416(-)$1	221	89	96	13.0192
AUUUCAG	chr6:128561174-128561395(-)$1	221	161	168	13.0192
ACGUCAG	chr10:119043222-119043450(-)$1	228	126	133	12.4423
ACAUCAG	chr3:169504343-169504565(+)$1	222	45	52	12.9230
AUUUCAG	chr16:53272191-53272422(+)$1	231	56	63	13.0192
ACUUCAG	chr3:184018024-184018249(+)$1	225	118	125	16.5769
ACUACAG	chr16:72827669-72827890(-)$1	221	47	54	12.3461

#otherMatches

#Struct PSSM
qqqqggg	chr2:232320700-232320926(-)$1	226	22	29	12.7307
fffff::	chr12:133683094-133683326(+)$1	232	205	212	16.5769
ee####e	chr15:35274061-35274286(-)$1	225	18	25	16.5769
444bb:b	chr2:231683315-231683538(+)$1	223	132	139	12.7307
:::gggg	chr10:31809570-31809796(+)$1	226	61	68	13.0192
ffff:GG	chr12:104378491-104378721(+)$1	230	123	130	12.0576
ddd!!bb	chr1:171537299-171537524(+)$1	225	43	50	12.7307
gggggdd	chr1:82456544-82456775(+)$1	231	158	165	12.5384
ggggggg	chr3:196666125-196666347(-)$1	222	141	148	12.7307
h####cc	chrM:14733-15002(+)$1	269	108	115	11.9615
333ffff	chr5:173317732-173317961(+)$1	229	219	226	12.9230
[ffffff	chr21:38496845-38497074(+)$1	229	113	120	12.7307
sssssss	chr3:129150285-129150508(-)$1	223	206	213	12.8269
rrrrrrr	chr19:37240018-37240243(-)$1	225	35	42	12.9230
fff:::h	chr19:37618401-37618637(+)$1	236	52	59	13.0192
!dddduu	chr3:98309402-98309626(-)$1	224	118	125	12.3461
eeellle	chr3:48594091-48594309(+)$1	218	79	86	12.7307
ttttttt	chr14:97022554-97022784(+)$1	230	91	98	16.5769
EEELLLC	chr2:70315623-70315884(+)$1	261	33	40	12.1538
}DDDDEE	chr19:53884324-53884546(+)$1	222	203	210	12.9230
:::::::	chr10:32560556-32560804(-)$1	248	66	73	12.8269
:DDDDOO	chr2:170402804-170403059(-)$1	255	67	74	12.8269
zzeeeee	chr11:4130805-4131033(+)$1	228	114	121	11.9615
bb]eeee	chr1:27087269-27087504(+)$1	235	143	150	12.9230
mmmbb22	chr2:166768924-166769152(-)$1	228	193	200	12.5384
!bb!!cc	chr18:9254754-9254986(+)$1	232	69	76	12.1538
:::::::	chr17:27613750-27613988(-)$1	238	108	115	13.0192
###bb##	chr21:43413502-43413740(-)$1	238	126	133	13.0192
::::::d	chr6:17616763-17617001(-)$1	238	114	121	12.7307
^^^^^^^	chr9:106878425-106878656(+)$1	231	124	131	13.0192
cc]cccc	chr20:40033432-40033655(-)$1	223	18	25	12.1538
LDDDD::	chr19:38125803-38126037(-)$1	234	23	30	13.0192
eeeebb#	chr1:8418175-8418410(-)$1	235	63	70	12.1538
fffnnnn	chr15:93515516-93515747(+)$1	231	139	146	13.0192
ceeeee#	chr7:98601745-98601965(+)$1	220	73	80	16.5769
cc:::::	chr7:26235370-26235610(-)$1	240	206	213	13.0192
g22ccc]	chr17:17158135-17158359(-)$1	224	153	160	12.4423
\\\FFFF	chr2:206869526-206869754(-)$1	228	203	210	12.0576
ccc!!cc	chr15:23006462-23006682(-)$1	220	150	157	12.9230
FFFKKCC	chr6:12125564-12125785(+)$1	221	92	99	12.5384
:IIIIII	chr2:61719089-61719310(-)$1	221	125	132	12.7307
:::::::	chr2:170806236-170806462(+)$1	226	28	35	12.3461
eeee22f	chr12:46319885-46320111(-)$1	226	132	139	12.7307
:::::::	chr4:106196298-106196525(+)$1	227	121	128	16.5769
:::::dd	chr8:95523655-95523875(-)$1	220	172	179	12.5384
>>=====	chr8:48772195-48772416(-)$1	221	89	96	13.0192
pppppdd	chr6:128561174-128561395(-)$1	221	161	168	13.0192
#cccooo	chr10:119043222-119043450(-)$1	228	126	133	12.4423
cccdddd	chr3:169504343-169504565(+)$1	222	45	52	12.9230
FFNNNNN	chr16:53272191-53272422(+)$1	231	56	63	13.0192
2iiiiii	chr3:184018024-184018249(+)$1	225	118	125	16.5769
nnnnbb]	chr16:72827669-72827890(-)$1	221	47	54	12.3461

#DB
....)))	chr2:232320700-232320926(-)$1	1	22	29	12.7307
)))))..	chr12:133683094-133683326(+)$1	1	205	212	16.5769
((....(	chr15:35274061-35274286(-)$1	1	18	25	16.5769
...)).(	chr2:231683315-231683538(+)$1	1	132	139	12.7307
...((((	chr10:31809570-31809796(+)$1	1	61	68	13.0192
)))).))	chr12:104378491-104378721(+)$1	1	123	130	12.0576
(((..((	chr1:171537299-171537524(+)$1	1	43	50	12.7307
)))))))	chr1:82456544-82456775(+)$1	1	158	165	12.5384
)))))))	chr3:196666125-196666347(-)$1	1	141	148	12.7307
(....((	chrM:14733-15002(+)$1	1	108	115	11.9615
...))))	chr5:173317732-173317961(+)$1	1	219	226	12.9230
.((((((	chr21:38496845-38497074(+)$1	1	113	120	12.7307
.......	chr3:129150285-129150508(-)$1	1	206	213	12.8269
.......	chr19:37240018-37240243(-)$1	1	35	42	12.9230
)))...(	chr19:37618401-37618637(+)$1	1	52	59	13.0192
.((((..	chr3:98309402-98309626(-)$1	1	118	125	12.3461
(((...)	chr3:48594091-48594309(+)$1	1	79	86	12.7307
.......	chr14:97022554-97022784(+)$1	1	91	98	16.5769
(((...(	chr2:70315623-70315884(+)$1	1	33	40	12.1538
.))))))	chr19:53884324-53884546(+)$1	1	203	210	12.9230
.......	chr10:32560556-32560804(-)$1	1	66	73	12.8269
.((((..	chr2:170402804-170403059(-)$1	1	67	74	12.8269
..)))))	chr11:4130805-4131033(+)$1	1	114	121	11.9615
)).))))	chr1:27087269-27087504(+)$1	1	143	150	12.9230
...))..	chr2:166768924-166769152(-)$1	1	193	200	12.5384
.((..((	chr18:9254754-9254986(+)$1	1	69	76	12.1538
.......	chr17:27613750-27613988(-)$1	1	108	115	13.0192
...((..	chr21:43413502-43413740(-)$1	1	126	133	13.0192
......(	chr6:17616763-17617001(-)$1	1	114	121	12.7307
.......	chr9:106878425-106878656(+)$1	1	124	131	13.0192
)).)))(	chr20:40033432-40033655(-)$1	1	18	25	12.1538
.((((..	chr19:38125803-38126037(-)$1	1	23	30	13.0192
((((((.	chr1:8418175-8418410(-)$1	1	63	70	12.1538
(((....	chr15:93515516-93515747(+)$1	1	139	146	13.0192
((((((.	chr7:98601745-98601965(+)$1	1	73	80	16.5769
)).....	chr7:26235370-26235610(-)$1	1	206	213	13.0192
)..))).	chr17:17158135-17158359(-)$1	1	153	160	12.4423
...))))	chr2:206869526-206869754(-)$1	1	203	210	12.0576
(((..((	chr15:23006462-23006682(-)$1	1	150	157	12.9230
(((..((	chr6:12125564-12125785(+)$1	1	92	99	12.5384
.))))))	chr2:61719089-61719310(-)$1	1	125	132	12.7307
.......	chr2:170806236-170806462(+)$1	1	28	35	12.3461
))))..)	chr12:46319885-46320111(-)$1	1	132	139	12.7307
.......	chr4:106196298-106196525(+)$1	1	121	128	16.5769
.....((	chr8:95523655-95523875(-)$1	1	172	179	12.5384
..)))))	chr8:48772195-48772416(-)$1	1	89	96	13.0192
.....))	chr6:128561174-128561395(-)$1	1	161	168	13.0192
.(((...	chr10:119043222-119043450(-)$1	1	126	133	12.4423
(((((((	chr3:169504343-169504565(+)$1	1	45	52	12.9230
((.....	chr16:53272191-53272422(+)$1	1	56	63	13.0192
.))))))	chr3:184018024-184018249(+)$1	1	118	125	16.5769
....)).	chr16:72827669-72827890(-)$1	1	47	54	12.3461

#PSSM
A : 0.84	U : 0.07	C : 0.03	g : 0.01	G : 0.01	
C : 0.80	U : 0.11	A : 0.05	c : 0.01	
U : 0.82	A : 0.11	u : 0.01	C : 0.01	G : 0.01	
U : 0.88	A : 0.05	u : 0.01	C : 0.01	G : 0.01	
C : 0.90	U : 0.03	A : 0.01	c : 0.01	G : 0.01	
A : 0.94	G : 0.03	a : 0.01	
G : 0.78	U : 0.09	A : 0.05	C : 0.03	g : 0.01	

#score	682.0000000000009
#seq	52
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m1_run2.nuc.txt

#NT
UGG	chr16:58572584-58572804(-)$1	220	15	18	9.0000
UGG	chr5:37314217-37314437(-)$1	220	52	55	9.0000
UGG	chr1:200376947-200377190(-)$1	243	35	38	9.0000
UGG	chrX:100910974-100911208(-)$1	234	51	54	9.0000
UGG	chr7:116339632-116339860(+)$1	228	32	35	9.0000
UGG	chr16:71319239-71319465(-)$1	226	46	49	9.0000
UGG	chr15:72191940-72192162(-)$1	222	14	17	9.0000
UGG	chr19:21606174-21606406(+)$1	232	12	15	9.0000
UGG	chr15:91304344-91304575(+)$1	231	139	142	9.0000
UGG	chr5:32415070-32415295(-)$1	225	165	168	9.0000
UGG	chr1:233398735-233398961(-)$1	226	125	128	9.0000
UGG	chr16:24801219-24801443(+)$1	224	1	4	9.0000
UGG	chr16:2814256-2814482(+)$1	226	150	153	9.0000
UGG	chr10:120795483-120795711(-)$1	228	77	80	9.0000
UGG	chr1:226566775-226567014(-)$1	239	31	34	9.0000
UGG	chr1:179815195-179815443(-)$1	248	5	8	9.0000
UGG	chr6:87968235-87968464(+)$1	229	51	54	9.0000
UGG	chr5:178309945-178310178(+)$1	233	218	221	9.0000
UGG	chr11:118373104-118373338(+)$1	234	66	69	9.0000
UGG	chr16:58581369-58581595(-)$1	226	70	73	9.0000
UGG	chr19:6414024-6414260(-)$1	236	12	15	9.0000
UGG	chr14:96779597-96779831(-)$1	234	96	99	9.0000
UGG	chr6:87966870-87967101(+)$1	231	1	4	9.0000
Ugg	chr1:54269533-54269754(-)$1	221	210	213	9.0000
UGG	chr2:191760295-191760517(+)$1	222	86	89	9.0000
UGG	chr1:203768579-203768805(+)$1	226	5	8	9.0000
UGG	chr1:235969628-235969858(-)$1	230	50	53	9.0000
UGG	chr7:40102536-40102765(+)$1	229	9	12	9.0000
UGG	chr6:126249239-126249459(+)$1	220	89	92	9.0000
UGG	chr16:67645765-67645984(+)$1	219	148	151	9.0000
UGG	chr8:8875791-8876012(+)$1	221	69	72	9.0000
UGG	chr6:83891442-83891668(-)$1	226	29	32	9.0000
UGG	chr5:180670594-180670862(-)$1	268	85	88	9.0000
UGG	chr7:97821862-97822090(+)$1	228	170	173	9.0000
UGG	chr5:139908925-139909145(+)$1	220	42	45	9.0000
UGG	chr17:42750742-42750966(-)$1	224	63	66	9.0000
UGG	chr19:14199410-14199644(-)$1	234	26	29	9.0000
UGG	chr14:92609436-92609671(+)$1	235	11	14	9.0000
UGG	chr16:20809490-20809714(-)$1	224	157	160	9.0000
UGG	chr17:1556781-1557018(-)$1	237	3	6	9.0000
UGG	chr10:76744865-76745099(+)$1	234	33	36	9.0000
UGG	chr14:103958227-103958468(+)$1	241	33	36	9.0000
UGG	chr2:61726886-61727116(-)$1	230	102	105	9.0000
UGG	chr12:76788363-76788586(-)$1	223	7	10	9.0000
UGG	chr11:108384522-108384751(-)$1	229	52	55	9.0000
UGG	chr12:69652654-69652878(+)$1	224	13	16	9.0000
UGG	chr17:38562751-38562979(-)$1	228	60	63	9.0000
UGG	chrM:4606-4870(+)$1	264	162	165	9.0000
UGG	chr2:111395504-111395726(-)$1	222	1	4	9.0000
ugg	chr21:37705856-37706078(+)$1	222	26	29	9.0000
UGG	chr1:91406135-91406363(-)$1	228	52	55	9.0000
UGG	chr19:23405204-23405427(-)$1	223	51	54	9.0000
UGG	chr11:34118656-34118882(+)$1	226	96	99	9.0000
UGG	chr7:106938640-106938858(-)$1	218	61	64	9.0000
uGG	chr11:4130805-4131033(+)$1	228	44	47	9.0000
UGG	chr9:134471600-134471837(-)$1	237	59	62	9.0000
UGG	chr12:56994670-56994892(-)$1	222	24	27	9.0000
UGG	chr3:196866937-196867164(-)$1	227	43	46	9.0000
UGG	chr20:39813464-39813692(-)$1	228	64	67	9.0000
UGG	chr11:43428594-43428824(+)$1	230	140	143	9.0000
UGG	chr21:40552111-40552337(-)$1	226	10	13	9.0000
UGG	chr3:15269262-15269498(+)$1	236	24	27	9.0000
UGG	chr12:49436424-49436652(-)$1	228	3	6	9.0000
UGG	chrM:6286-6605(+)$1	319	34	37	9.0000
UGG	chr17:41329874-41330097(+)$1	223	11	14	9.0000
UGG	chr17:37680909-37681131(+)$1	222	27	30	9.0000
UGG	chr13:108862200-108862425(-)$1	225	97	100	9.0000
UGG	chr1:220197639-220197858(-)$1	219	35	38	9.0000
UGG	chr9:135917557-135917792(+)$1	235	58	61	9.0000
UGG	chr2:170806236-170806462(+)$1	226	9	12	9.0000
UGG	chr1:82447487-82447719(+)$1	232	8	11	9.0000
UGG	chr1:210412754-210412981(+)$1	227	28	31	9.0000
UGG	chr7:64167673-64167899(+)$1	226	7	10	9.0000
UGG	chr21:30338975-30339201(-)$1	226	84	87	9.0000
UGG	chr19:57803159-57803382(+)$1	223	24	27	9.0000
UGG	chr1:235331828-235332061(-)$1	233	70	73	9.0000
UGG	chr2:152319539-152319781(+)$1	242	118	121	9.0000
UGG	chr10:25313746-25313969(+)$1	223	141	144	9.0000
UGG	chr17:41244487-41244711(-)$1	224	52	55	9.0000
UGG	chr10:64973464-64973726(-)$1	262	151	154	9.0000
UGG	chr6:56472142-56472371(-)$1	229	69	72	9.0000
UGG	chr5:112176034-112176255(+)$1	221	70	73	9.0000
UGG	chr18:47352795-47353024(-)$1	229	10	13	9.0000
UGG	chr5:90106864-90107090(+)$1	226	18	21	9.0000
UGG	chr19:39860314-39860538(+)$1	224	19	22	9.0000
UGG	chr16:19548049-19548277(+)$1	228	164	167	9.0000
UGG	chr16:89347849-89348090(-)$1	241	44	47	9.0000
UGG	chr2:230657702-230657943(-)$1	241	182	185	9.0000
UGG	chr1:14105906-14106141(+)$1	235	50	53	9.0000
UGG	chr3:47162233-47162458(-)$1	225	21	24	9.0000
UGG	chr10:102703738-102703959(+)$1	221	139	142	9.0000
UGG	chr20:34240315-34240556(-)$1	241	13	16	9.0000
UGG	chr5:178311124-178311353(+)$1	229	47	50	9.0000
UGG	chr6:149983055-149983287(-)$1	232	26	29	9.0000
UGG	chr1:227843173-227843397(+)$1	224	7	10	9.0000
UGG	chr17:1564187-1564438(-)$1	251	3	6	9.0000
UGG	chr5:89933590-89933816(+)$1	226	2	5	9.0000
UGG	chr5:37333549-37333774(-)$1	225	47	50	9.0000
UGG	chr19:40478308-40478547(+)$1	239	91	94	9.0000

#otherMatches

#Struct PSSM
!!b	chr1:233362927-233363151(-)$1	224	21	24	9.0000
EEE	chr16:58572584-58572804(-)$1	220	15	18	9.0000
DDD	chr5:37314217-37314437(-)$1	220	52	55	9.0000
ccc	chr1:200376947-200377190(-)$1	243	35	38	9.0000
HHH	chrX:100910974-100911208(-)$1	234	51	54	9.0000
mcc	chr7:116339632-116339860(+)$1	228	32	35	9.0000
rrr	chr16:71319239-71319465(-)$1	226	46	49	9.0000
:dd	chr15:72191940-72192162(-)$1	222	14	17	9.0000
DDD	chr19:21606174-21606406(+)$1	232	12	15	9.0000
ggg	chr15:91304344-91304575(+)$1	231	139	142	9.0000
ggc	chr5:32415070-32415295(-)$1	225	165	168	9.0000
ccc	chr1:233398735-233398961(-)$1	226	125	128	9.0000
GGG	chr16:24801219-24801443(+)$1	224	1	4	9.0000
e55	chr16:2814256-2814482(+)$1	226	150	153	9.0000
bbh	chr10:120795483-120795711(-)$1	228	77	80	9.0000
i::	chr1:226566775-226567014(-)$1	239	31	34	9.0000
EEL	chr1:179815195-179815443(-)$1	248	5	8	9.0000
eem	chr6:87968235-87968464(+)$1	229	51	54	9.0000
EEE	chr5:178309945-178310178(+)$1	233	218	221	9.0000
ccd	chr11:118373104-118373338(+)$1	234	66	69	9.0000
ddd	chr16:58581369-58581595(-)$1	226	70	73	9.0000
ddd	chr19:6414024-6414260(-)$1	236	12	15	9.0000
===	chr14:96779597-96779831(-)$1	234	96	99	9.0000
eee	chr6:87966870-87967101(+)$1	231	1	4	9.0000
C}B	chr1:54269533-54269754(-)$1	221	210	213	9.0000
buu	chr2:191760295-191760517(+)$1	222	86	89	9.0000
:gg	chr1:203768579-203768805(+)$1	226	5	8	9.0000
eea	chr1:235969628-235969858(-)$1	230	50	53	9.0000
===	chr7:40102536-40102765(+)$1	229	9	12	9.0000
hhh	chr6:126249239-126249459(+)$1	220	89	92	9.0000
eee	chr16:67645765-67645984(+)$1	219	148	151	9.0000
2bb	chr8:8875791-8876012(+)$1	221	69	72	9.0000
eee	chr6:83891442-83891668(-)$1	226	29	32	9.0000
eee	chr5:180670594-180670862(-)$1	268	85	88	9.0000
sff	chr7:97821862-97822090(+)$1	228	170	173	9.0000
ccc	chr5:139908925-139909145(+)$1	220	42	45	9.0000
fff	chr17:42750742-42750966(-)$1	224	63	66	9.0000
]gg	chr19:14199410-14199644(-)$1	234	26	29	9.0000
ddd	chr14:92609436-92609671(+)$1	235	11	14	9.0000
[ee	chr16:20809490-20809714(-)$1	224	157	160	9.0000
::G	chr17:1556781-1557018(-)$1	237	3	6	9.0000
ccc	chr10:76744865-76745099(+)$1	234	33	36	9.0000
:cc	chr14:103958227-103958468(+)$1	241	33	36	9.0000
eee	chr2:61726886-61727116(-)$1	230	102	105	9.0000
ccc	chr12:76788363-76788586(-)$1	223	7	10	9.0000
ddd	chr11:108384522-108384751(-)$1	229	52	55	9.0000
LEE	chr12:69652654-69652878(+)$1	224	13	16	9.0000
ddd	chr17:38562751-38562979(-)$1	228	60	63	9.0000
:ff	chrM:4606-4870(+)$1	264	162	165	9.0000
:::	chr2:111395504-111395726(-)$1	222	1	4	9.0000
Iff	chr21:37705856-37706078(+)$1	222	26	29	9.0000
cc"	chr1:91406135-91406363(-)$1	228	52	55	9.0000
bb2	chr19:23405204-23405427(-)$1	223	51	54	9.0000
[cc	chr11:34118656-34118882(+)$1	226	96	99	9.0000
ccb	chr7:106938640-106938858(-)$1	218	61	64	9.0000
gdd	chr11:4130805-4131033(+)$1	228	44	47	9.0000
obb	chr9:134471600-134471837(-)$1	237	59	62	9.0000
JJJ	chr12:56994670-56994892(-)$1	222	24	27	9.0000
CCC	chr3:196866937-196867164(-)$1	227	43	46	9.0000
!hh	chr20:39813464-39813692(-)$1	228	64	67	9.0000
ppp	chr11:43428594-43428824(+)$1	230	140	143	9.0000
HHH	chr21:40552111-40552337(-)$1	226	10	13	9.0000
===	chr3:15269262-15269498(+)$1	236	24	27	9.0000
GGG	chr12:49436424-49436652(-)$1	228	3	6	9.0000
odd	chrM:6286-6605(+)$1	319	34	37	9.0000
ggg	chr17:41329874-41330097(+)$1	223	11	14	9.0000
eee	chr17:37680909-37681131(+)$1	222	27	30	9.0000
zzz	chr13:108862200-108862425(-)$1	225	97	100	9.0000
ddd	chr1:220197639-220197858(-)$1	219	35	38	9.0000
fff	chr9:135917557-135917792(+)$1	235	58	61	9.0000
:CC	chr2:170806236-170806462(+)$1	226	9	12	9.0000
"dd	chr1:82447487-82447719(+)$1	232	8	11	9.0000
FFF	chr1:210412754-210412981(+)$1	227	28	31	9.0000
eee	chr7:64167673-64167899(+)$1	226	7	10	9.0000
ghh	chr21:30338975-30339201(-)$1	226	84	87	9.0000
III	chr19:57803159-57803382(+)$1	223	24	27	9.0000
lhh	chr1:235331828-235332061(-)$1	233	70	73	9.0000
==e	chr2:152319539-152319781(+)$1	242	118	121	9.0000
ggg	chr10:25313746-25313969(+)$1	223	141	144	9.0000
ggg	chr17:41244487-41244711(-)$1	224	52	55	9.0000
fff	chr10:64973464-64973726(-)$1	262	151	154	9.0000
d]a	chr6:56472142-56472371(-)$1	229	69	72	9.0000
JJJ	chr5:112176034-112176255(+)$1	221	70	73	9.0000
EEE	chr18:47352795-47353024(-)$1	229	10	13	9.0000
PPP	chr5:90106864-90107090(+)$1	226	18	21	9.0000
hhh	chr19:39860314-39860538(+)$1	224	19	22	9.0000
FFF	chr16:19548049-19548277(+)$1	228	164	167	9.0000
hhh	chr16:89347849-89348090(-)$1	241	44	47	9.0000
ecc	chr2:230657702-230657943(-)$1	241	182	185	9.0000
f55	chr1:14105906-14106141(+)$1	235	50	53	9.0000
::h	chr3:47162233-47162458(-)$1	225	21	24	9.0000
eee	chr10:102703738-102703959(+)$1	221	139	142	9.0000
::e	chr20:34240315-34240556(-)$1	241	13	16	9.0000
hhh	chr5:178311124-178311353(+)$1	229	47	50	9.0000
hhh	chr6:149983055-149983287(-)$1	232	26	29	9.0000
fff	chr1:227843173-227843397(+)$1	224	7	10	9.0000
fff	chr17:1564187-1564438(-)$1	251	3	6	9.0000
:DD	chr5:89933590-89933816(+)$1	226	2	5	9.0000
!bb	chr5:37333549-37333774(-)$1	225	47	50	9.0000
ddd	chr19:40478308-40478547(+)$1	239	91	94	9.0000

#DB
..(	chr1:233362927-233363151(-)$1	1	21	24	9.0000
(((	chr16:58572584-58572804(-)$1	1	15	18	9.0000
(((	chr5:37314217-37314437(-)$1	1	52	55	9.0000
(((	chr1:200376947-200377190(-)$1	1	35	38	9.0000
(((	chrX:100910974-100911208(-)$1	1	51	54	9.0000
.))	chr7:116339632-116339860(+)$1	1	32	35	9.0000
...	chr16:71319239-71319465(-)$1	1	46	49	9.0000
.((	chr15:72191940-72192162(-)$1	1	14	17	9.0000
(((	chr19:21606174-21606406(+)$1	1	12	15	9.0000
)))	chr15:91304344-91304575(+)$1	1	139	142	9.0000
(((	chr5:32415070-32415295(-)$1	1	165	168	9.0000
(((	chr1:233398735-233398961(-)$1	1	125	128	9.0000
(((	chr16:24801219-24801443(+)$1	1	1	4	9.0000
)..	chr16:2814256-2814482(+)$1	1	150	153	9.0000
)))	chr10:120795483-120795711(-)$1	1	77	80	9.0000
)..	chr1:226566775-226567014(-)$1	1	31	34	9.0000
((.	chr1:179815195-179815443(-)$1	1	5	8	9.0000
((.	chr6:87968235-87968464(+)$1	1	51	54	9.0000
)))	chr5:178309945-178310178(+)$1	1	218	221	9.0000
)))	chr11:118373104-118373338(+)$1	1	66	69	9.0000
(((	chr16:58581369-58581595(-)$1	1	70	73	9.0000
(((	chr19:6414024-6414260(-)$1	1	12	15	9.0000
)))	chr14:96779597-96779831(-)$1	1	96	99	9.0000
(((	chr6:87966870-87967101(+)$1	1	1	4	9.0000
).)	chr1:54269533-54269754(-)$1	1	210	213	9.0000
(..	chr2:191760295-191760517(+)$1	1	86	89	9.0000
.((	chr1:203768579-203768805(+)$1	1	5	8	9.0000
)))	chr1:235969628-235969858(-)$1	1	50	53	9.0000
(((	chr7:40102536-40102765(+)$1	1	9	12	9.0000
(((	chr6:126249239-126249459(+)$1	1	89	92	9.0000
)))	chr16:67645765-67645984(+)$1	1	148	151	9.0000
.))	chr8:8875791-8876012(+)$1	1	69	72	9.0000
(((	chr6:83891442-83891668(-)$1	1	29	32	9.0000
(((	chr5:180670594-180670862(-)$1	1	85	88	9.0000
.))	chr7:97821862-97822090(+)$1	1	170	173	9.0000
(((	chr5:139908925-139909145(+)$1	1	42	45	9.0000
(((	chr17:42750742-42750966(-)$1	1	63	66	9.0000
.))	chr19:14199410-14199644(-)$1	1	26	29	9.0000
(((	chr14:92609436-92609671(+)$1	1	11	14	9.0000
.((	chr16:20809490-20809714(-)$1	1	157	160	9.0000
..(	chr17:1556781-1557018(-)$1	1	3	6	9.0000
(((	chr10:76744865-76745099(+)$1	1	33	36	9.0000
.((	chr14:103958227-103958468(+)$1	1	33	36	9.0000
(((	chr2:61726886-61727116(-)$1	1	102	105	9.0000
(((	chr12:76788363-76788586(-)$1	1	7	10	9.0000
(((	chr11:108384522-108384751(-)$1	1	52	55	9.0000
.((	chr12:69652654-69652878(+)$1	1	13	16	9.0000
)))	chr17:38562751-38562979(-)$1	1	60	63	9.0000
.((	chrM:4606-4870(+)$1	1	162	165	9.0000
...	chr2:111395504-111395726(-)$1	1	1	4	9.0000
(((	chr21:37705856-37706078(+)$1	1	26	29	9.0000
((.	chr1:91406135-91406363(-)$1	1	52	55	9.0000
)).	chr19:23405204-23405427(-)$1	1	51	54	9.0000
.((	chr11:34118656-34118882(+)$1	1	96	99	9.0000
))(	chr7:106938640-106938858(-)$1	1	61	64	9.0000
)((	chr11:4130805-4131033(+)$1	1	44	47	9.0000
.))	chr9:134471600-134471837(-)$1	1	59	62	9.0000
(((	chr12:56994670-56994892(-)$1	1	24	27	9.0000
(((	chr3:196866937-196867164(-)$1	1	43	46	9.0000
.((	chr20:39813464-39813692(-)$1	1	64	67	9.0000
...	chr11:43428594-43428824(+)$1	1	140	143	9.0000
(((	chr21:40552111-40552337(-)$1	1	10	13	9.0000
(((	chr3:15269262-15269498(+)$1	1	24	27	9.0000
(((	chr12:49436424-49436652(-)$1	1	3	6	9.0000
.))	chrM:6286-6605(+)$1	1	34	37	9.0000
(((	chr17:41329874-41330097(+)$1	1	11	14	9.0000
(((	chr17:37680909-37681131(+)$1	1	27	30	9.0000
...	chr13:108862200-108862425(-)$1	1	97	100	9.0000
(((	chr1:220197639-220197858(-)$1	1	35	38	9.0000
)))	chr9:135917557-135917792(+)$1	1	58	61	9.0000
.((	chr2:170806236-170806462(+)$1	1	9	12	9.0000
.((	chr1:82447487-82447719(+)$1	1	8	11	9.0000
(((	chr1:210412754-210412981(+)$1	1	28	31	9.0000
(((	chr7:64167673-64167899(+)$1	1	7	10	9.0000
(((	chr21:30338975-30339201(-)$1	1	84	87	9.0000
(((	chr19:57803159-57803382(+)$1	1	24	27	9.0000
.))	chr1:235331828-235332061(-)$1	1	70	73	9.0000
))(	chr2:152319539-152319781(+)$1	1	118	121	9.0000
)))	chr10:25313746-25313969(+)$1	1	141	144	9.0000
)))	chr17:41244487-41244711(-)$1	1	52	55	9.0000
)))	chr10:64973464-64973726(-)$1	1	151	154	9.0000
).)	chr6:56472142-56472371(-)$1	1	69	72	9.0000
(((	chr5:112176034-112176255(+)$1	1	70	73	9.0000
(((	chr18:47352795-47353024(-)$1	1	10	13	9.0000
...	chr5:90106864-90107090(+)$1	1	18	21	9.0000
(((	chr19:39860314-39860538(+)$1	1	19	22	9.0000
)))	chr16:19548049-19548277(+)$1	1	164	167	9.0000
(((	chr16:89347849-89348090(-)$1	1	44	47	9.0000
)))	chr2:230657702-230657943(-)$1	1	182	185	9.0000
)..	chr1:14105906-14106141(+)$1	1	50	53	9.0000
..(	chr3:47162233-47162458(-)$1	1	21	24	9.0000
)))	chr10:102703738-102703959(+)$1	1	139	142	9.0000
..(	chr20:34240315-34240556(-)$1	1	13	16	9.0000
(((	chr5:178311124-178311353(+)$1	1	47	50	9.0000
(((	chr6:149983055-149983287(-)$1	1	26	29	9.0000
(((	chr1:227843173-227843397(+)$1	1	7	10	9.0000
(((	chr17:1564187-1564438(-)$1	1	3	6	9.0000
.((	chr5:89933590-89933816(+)$1	1	2	5	9.0000
.((	chr5:37333549-37333774(-)$1	1	47	50	9.0000
)))	chr19:40478308-40478547(+)$1	1	91	94	9.0000

#PSSM
U : 0.98	u : 0.02	
G : 0.98	g : 0.02	
G : 0.98	g : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m1_run2.nuc.txt

#NT
ACA	chr20:23334887-23335111(+)$1	224	43	46	9.0000
ACA	chr14:61445972-61446214(-)$1	242	96	99	9.0000
ACA	chr17:76988580-76988843(-)$1	263	49	52	9.0000
ACA	chr7:2412207-2412436(+)$1	229	28	31	9.0000
ACA	chr15:43668295-43668521(+)$1	226	69	72	9.0000
ACA	chr6:26189186-26189438(-)$1	252	51	54	9.0000
ACA	chr1:150915257-150915495(+)$1	238	2	5	9.0000
ACA	chr7:102957199-102957431(-)$1	232	29	32	9.0000
ACA	chr22:32352527-32352798(+)$1	271	104	107	9.0000
ACA	chr5:180670593-180670862(-)$1	269	41	44	9.0000
ACA	chr8:71078805-71079046(-)$1	241	96	99	9.0000
ACA	chr14:21829237-21829470(-)$1	233	43	46	9.0000
ACA	chr2:228197087-228197337(+)$1	250	130	133	9.0000
ACA	chr17:7807804-7808027(+)$1	223	44	47	9.0000
ACA	chr11:64573119-64573343(-)$1	224	77	80	9.0000
ACA	chr14:39511894-39512138(-)$1	244	114	117	9.0000
ACA	chr3:127327124-127327359(+)$1	235	55	58	9.0000
ACA	chr5:74980987-74981224(-)$1	237	22	25	9.0000
ACA	chr9:100417082-100417305(+)$1	223	25	28	9.0000
ACA	chr10:70733209-70733433(+)$1	224	104	107	9.0000
ACA	chr15:59350620-59350846(+)$1	226	68	71	9.0000
ACA	chr13:48522978-48523234(-)$1	256	9	12	9.0000
ACA	chr3:120449471-120449713(-)$1	242	27	30	9.0000
ACA	chr2:43453323-43453548(-)$1	225	92	95	9.0000
ACA	chr14:31424762-31424997(-)$1	235	4	7	9.0000
ACA	chr1:43826420-43826651(+)$1	231	0	3	9.0000
ACA	chr22:38028357-38028608(+)$1	251	8	11	9.0000
ACA	chr14:24658515-24658750(-)$1	235	0	3	9.0000
ACA	chrX:53622192-53622415(-)$1	223	23	26	9.0000
ACA	chr7:100479680-100479917(+)$1	237	118	121	9.0000
ACA	chr12:133281268-133281488(+)$1	220	19	22	9.0000
ACA	chr6:64395205-64395429(+)$1	224	67	70	9.0000
ACA	chr7:141441899-141442123(+)$1	224	89	92	9.0000
ACA	chr9:35066592-35066833(-)$1	241	78	81	9.0000
ACA	chr13:113975812-113976046(+)$1	234	106	109	9.0000
ACA	chr19:10793236-10793475(+)$1	239	150	153	9.0000
ACA	chr17:27844489-27844710(+)$1	221	19	22	9.0000
ACA	chr19:58491105-58491331(-)$1	226	7	10	9.0000
ACA	chr12:56638792-56639016(-)$1	224	43	46	9.0000
ACA	chrX:152861411-152861635(-)$1	224	152	155	9.0000
ACA	chr5:102611928-102612150(+)$1	222	95	98	9.0000
ACA	chr22:29696023-29696267(+)$1	244	223	226	9.0000
ACA	chr12:21807420-21807656(-)$1	236	102	105	9.0000
ACA	chr10:133757508-133757736(+)$1	228	30	33	9.0000
ACA	chr2:9581889-9582111(+)$1	222	25	28	9.0000
ACA	chr18:29488823-29489069(-)$1	246	0	3	9.0000
ACA	chr12:6837004-6837232(+)$1	228	20	23	9.0000
ACA	chr5:32414996-32415234(-)$1	238	0	3	9.0000
ACA	chr3:12626579-12626828(-)$1	249	68	71	9.0000
ACA	chr8:37635456-37635684(+)$1	228	30	33	9.0000
ACA	chr4:1976564-1976793(+)$1	229	21	24	9.0000
ACA	chr17:5009572-5009805(-)$1	233	9	12	9.0000
ACA	chrM:11147-11510(+)$1	363	51	54	9.0000
ACA	chr14:67847320-67847547(+)$1	227	139	142	9.0000
ACA	chr5:61690240-61690468(-)$1	228	122	125	9.0000
ACA	chr10:129913537-129913764(-)$1	227	22	25	9.0000
ACA	chr19:37879705-37879930(+)$1	225	34	37	9.0000
ACA	chr19:1278959-1279182(+)$1	223	90	93	9.0000
ACA	chr19:40486488-40486721(+)$1	233	1	4	9.0000
ACA	chr1:25551441-25551679(-)$1	238	107	110	9.0000
ACA	chr11:10823161-10823409(-)$1	248	144	147	9.0000
ACA	chr3:49775693-49775918(-)$1	225	30	33	9.0000
aca	chr19:49506438-49506661(+)$1	223	7	10	9.0000
ACA	chr2:118753766-118753995(-)$1	229	81	84	9.0000
ACA	chr20:3765301-3765524(-)$1	223	102	105	9.0000
ACA	chr15:65956836-65957067(-)$1	231	3	6	9.0000
ACA	chr19:6364480-6364730(+)$1	250	15	18	9.0000
ACA	chr22:41646946-41647192(-)$1	246	48	51	9.0000
ACA	chr21:45107730-45107955(+)$1	225	11	14	9.0000
ACA	chr5:74016856-74017081(+)$1	225	4	7	9.0000
ACA	chr14:95574155-95574385(-)$1	230	38	41	9.0000
ACA	chr10:13217537-13217759(+)$1	222	21	24	9.0000
ACA	chr6:126210453-126210682(+)$1	229	38	41	9.0000
ACA	chr17:31102786-31103008(-)$1	222	32	35	9.0000
ACA	chr8:94745720-94745948(-)$1	228	152	155	9.0000
ACA	chr22:35804322-35804594(+)$1	272	74	77	9.0000
ACA	chr10:73056274-73056497(+)$1	223	10	13	9.0000
ACA	chr22:40757465-40757688(+)$1	223	16	19	9.0000
ACA	chr15:35198748-35198973(-)$1	225	2	5	9.0000
ACA	chr15:78575643-78575902(-)$1	259	35	38	9.0000
ACA	chr6:12120464-12120689(+)$1	225	46	49	9.0000
ACA	chr1:226173055-226173302(-)$1	247	11	14	9.0000
ACA	chr1:51204490-51204722(-)$1	232	3	6	9.0000
ACA	chr12:6646709-6646979(+)$1	270	43	46	9.0000
ACA	chr5:54579155-54579375(-)$1	220	54	57	9.0000
ACA	chr1:75214364-75214588(+)$1	224	14	17	9.0000
ACA	chr7:77402374-77402602(+)$1	228	85	88	9.0000
ACA	chr5:132425164-132425400(+)$1	236	6	9	9.0000
ACA	chr19:11256947-11257167(-)$1	220	127	130	9.0000
ACA	chr10:32635644-32635868(-)$1	224	128	131	9.0000
ACA	chr12:69232986-69233262(+)$1	276	33	36	9.0000
ACA	chr1:36492617-36492906(+)$1	289	62	65	9.0000
ACA	chr4:152679828-152680061(-)$1	233	192	195	9.0000
ACA	chr21:38844932-38845154(+)$1	222	1	4	9.0000
ACA	chr19:56172406-56172653(+)$1	247	100	103	9.0000
ACA	chr7:102952554-102952798(+)$1	244	127	130	9.0000
ACA	chr6:149700043-149700279(+)$1	236	6	9	9.0000
ACA	chr20:47841589-47841822(+)$1	233	118	121	9.0000
ACA	chr11:66475164-66475388(-)$1	224	34	37	9.0000

#otherMatches

#Struct PSSM
:::	chr19:40486203-40486439(+)$1	236	1	4	9.0000
EE{	chr20:23334887-23335111(+)$1	224	43	46	9.0000
%%b	chr14:61445972-61446214(-)$1	242	96	99	9.0000
EEE	chr17:76988580-76988843(-)$1	263	49	52	9.0000
II:	chr7:2412207-2412436(+)$1	229	28	31	9.0000
e]b	chr15:43668295-43668521(+)$1	226	69	72	9.0000
:EE	chr6:26189186-26189438(-)$1	252	51	54	9.0000
BEE	chr1:150915257-150915495(+)$1	238	2	5	9.0000
nnn	chr7:102957199-102957431(-)$1	232	29	32	9.0000
ddd	chr22:32352527-32352798(+)$1	271	104	107	9.0000
eeF	chr5:180670593-180670862(-)$1	269	41	44	9.0000
333	chr8:71078805-71079046(-)$1	241	96	99	9.0000
cc:	chr14:21829237-21829470(-)$1	233	43	46	9.0000
ddd	chr2:228197087-228197337(+)$1	250	130	133	9.0000
2ff	chr17:7807804-7808027(+)$1	223	44	47	9.0000
:::	chr11:64573119-64573343(-)$1	224	77	80	9.0000
dqq	chr14:39511894-39512138(-)$1	244	114	117	9.0000
ddp	chr3:127327124-127327359(+)$1	235	55	58	9.0000
uuu	chr5:74980987-74981224(-)$1	237	22	25	9.0000
:::	chr9:100417082-100417305(+)$1	223	25	28	9.0000
hhh	chr10:70733209-70733433(+)$1	224	104	107	9.0000
>>=	chr15:59350620-59350846(+)$1	226	68	71	9.0000
FFF	chr13:48522978-48523234(-)$1	256	9	12	9.0000
NNN	chr3:120449471-120449713(-)$1	242	27	30	9.0000
"""	chr2:43453323-43453548(-)$1	225	92	95	9.0000
:::	chr14:31424762-31424997(-)$1	235	4	7	9.0000
:::	chr1:43826420-43826651(+)$1	231	0	3	9.0000
{CC	chr22:38028357-38028608(+)$1	251	8	11	9.0000
:BB	chr14:24658515-24658750(-)$1	235	0	3	9.0000
ooo	chrX:53622192-53622415(-)$1	223	23	26	9.0000
:::	chr7:100479680-100479917(+)$1	237	118	121	9.0000
obb	chr12:133281268-133281488(+)$1	220	19	22	9.0000
zzz	chr6:64395205-64395429(+)$1	224	67	70	9.0000
ccm	chr7:141441899-141442123(+)$1	224	89	92	9.0000
ooo	chr9:35066592-35066833(-)$1	241	78	81	9.0000
ooo	chr13:113975812-113976046(+)$1	234	106	109	9.0000
c22	chr19:10793236-10793475(+)$1	239	150	153	9.0000
!bb	chr17:27844489-27844710(+)$1	221	19	22	9.0000
:ee	chr19:58491105-58491331(-)$1	226	7	10	9.0000
!!h	chr12:56638792-56639016(-)$1	224	43	46	9.0000
bnn	chrX:152861411-152861635(-)$1	224	152	155	9.0000
!!c	chr5:102611928-102612150(+)$1	222	95	98	9.0000
m==	chr22:29696023-29696267(+)$1	244	223	226	9.0000
ee:	chr12:21807420-21807656(-)$1	236	102	105	9.0000
:::	chr10:133757508-133757736(+)$1	228	30	33	9.0000
LLL	chr2:9581889-9582111(+)$1	222	25	28	9.0000
:cc	chr18:29488823-29489069(-)$1	246	0	3	9.0000
LEE	chr12:6837004-6837232(+)$1	228	20	23	9.0000
:DD	chr5:32414996-32415234(-)$1	238	0	3	9.0000
f::	chr3:12626579-12626828(-)$1	249	68	71	9.0000
mmm	chr8:37635456-37635684(+)$1	228	30	33	9.0000
KEE	chr4:1976564-1976793(+)$1	229	21	24	9.0000
+++	chr17:5009572-5009805(-)$1	233	9	12	9.0000
:::	chrM:11147-11510(+)$1	363	51	54	9.0000
oee	chr14:67847320-67847547(+)$1	227	139	142	9.0000
\\C	chr5:61690240-61690468(-)$1	228	122	125	9.0000
c22	chr10:129913537-129913764(-)$1	227	22	25	9.0000
:dd	chr19:37879705-37879930(+)$1	225	34	37	9.0000
3a]	chr19:1278959-1279182(+)$1	223	90	93	9.0000
:EE	chr19:40486488-40486721(+)$1	233	1	4	9.0000
"ee	chr1:25551441-25551679(-)$1	238	107	110	9.0000
[bb	chr11:10823161-10823409(-)$1	248	144	147	9.0000
e##	chr3:49775693-49775918(-)$1	225	30	33	9.0000
CC:	chr19:49506438-49506661(+)$1	223	7	10	9.0000
e]f	chr2:118753766-118753995(-)$1	229	81	84	9.0000
}DD	chr20:3765301-3765524(-)$1	223	102	105	9.0000
:::	chr15:65956836-65957067(-)$1	231	3	6	9.0000
[cc	chr19:6364480-6364730(+)$1	250	15	18	9.0000
333	chr22:41646946-41647192(-)$1	246	48	51	9.0000
e!!	chr21:45107730-45107955(+)$1	225	11	14	9.0000
===	chr5:74016856-74017081(+)$1	225	4	7	9.0000
[cc	chr14:95574155-95574385(-)$1	230	38	41	9.0000
hhh	chr10:13217537-13217759(+)$1	222	21	24	9.0000
yyy	chr6:126210453-126210682(+)$1	229	38	41	9.0000
cmm	chr17:31102786-31103008(-)$1	222	32	35	9.0000
:::	chr8:94745720-94745948(-)$1	228	152	155	9.0000
444	chr22:35804322-35804594(+)$1	272	74	77	9.0000
ee[	chr10:73056274-73056497(+)$1	223	10	13	9.0000
:::	chr22:40757465-40757688(+)$1	223	16	19	9.0000
:::	chr15:35198748-35198973(-)$1	225	2	5	9.0000
GGG	chr15:78575643-78575902(-)$1	259	35	38	9.0000
fff	chr6:12120464-12120689(+)$1	225	46	49	9.0000
FFF	chr1:226173055-226173302(-)$1	247	11	14	9.0000
:::	chr1:51204490-51204722(-)$1	232	3	6	9.0000
ggg	chr12:6646709-6646979(+)$1	270	43	46	9.0000
qqq	chr5:54579155-54579375(-)$1	220	54	57	9.0000
fff	chr1:75214364-75214588(+)$1	224	14	17	9.0000
e]d	chr7:77402374-77402602(+)$1	228	85	88	9.0000
:::	chr5:132425164-132425400(+)$1	236	6	9	9.0000
[ee	chr19:11256947-11257167(-)$1	220	127	130	9.0000
qqq	chr10:32635644-32635868(-)$1	224	128	131	9.0000
hhh	chr12:69232986-69233262(+)$1	276	33	36	9.0000
fff	chr1:36492617-36492906(+)$1	289	62	65	9.0000
ggg	chr4:152679828-152680061(-)$1	233	192	195	9.0000
:::	chr21:38844932-38845154(+)$1	222	1	4	9.0000
e""	chr19:56172406-56172653(+)$1	247	100	103	9.0000
e]c	chr7:102952554-102952798(+)$1	244	127	130	9.0000
:::	chr6:149700043-149700279(+)$1	236	6	9	9.0000
FKK	chr20:47841589-47841822(+)$1	233	118	121	9.0000
dd[	chr11:66475164-66475388(-)$1	224	34	37	9.0000

#DB
...	chr19:40486203-40486439(+)$1	1	1	4	9.0000
((.	chr20:23334887-23335111(+)$1	1	43	46	9.0000
..(	chr14:61445972-61446214(-)$1	1	96	99	9.0000
(((	chr17:76988580-76988843(-)$1	1	49	52	9.0000
((.	chr7:2412207-2412436(+)$1	1	28	31	9.0000
).)	chr15:43668295-43668521(+)$1	1	69	72	9.0000
.((	chr6:26189186-26189438(-)$1	1	51	54	9.0000
(((	chr1:150915257-150915495(+)$1	1	2	5	9.0000
...	chr7:102957199-102957431(-)$1	1	29	32	9.0000
)))	chr22:32352527-32352798(+)$1	1	104	107	9.0000
))(	chr5:180670593-180670862(-)$1	1	41	44	9.0000
...	chr8:71078805-71079046(-)$1	1	96	99	9.0000
)).	chr14:21829237-21829470(-)$1	1	43	46	9.0000
(((	chr2:228197087-228197337(+)$1	1	130	133	9.0000
.))	chr17:7807804-7808027(+)$1	1	44	47	9.0000
...	chr11:64573119-64573343(-)$1	1	77	80	9.0000
(..	chr14:39511894-39512138(-)$1	1	114	117	9.0000
((.	chr3:127327124-127327359(+)$1	1	55	58	9.0000
...	chr5:74980987-74981224(-)$1	1	22	25	9.0000
...	chr9:100417082-100417305(+)$1	1	25	28	9.0000
)))	chr10:70733209-70733433(+)$1	1	104	107	9.0000
..)	chr15:59350620-59350846(+)$1	1	68	71	9.0000
(((	chr13:48522978-48523234(-)$1	1	9	12	9.0000
...	chr3:120449471-120449713(-)$1	1	27	30	9.0000
...	chr2:43453323-43453548(-)$1	1	92	95	9.0000
...	chr14:31424762-31424997(-)$1	1	4	7	9.0000
...	chr1:43826420-43826651(+)$1	1	0	3	9.0000
.((	chr22:38028357-38028608(+)$1	1	8	11	9.0000
.((	chr14:24658515-24658750(-)$1	1	0	3	9.0000
...	chrX:53622192-53622415(-)$1	1	23	26	9.0000
...	chr7:100479680-100479917(+)$1	1	118	121	9.0000
.))	chr12:133281268-133281488(+)$1	1	19	22	9.0000
...	chr6:64395205-64395429(+)$1	1	67	70	9.0000
((.	chr7:141441899-141442123(+)$1	1	89	92	9.0000
...	chr9:35066592-35066833(-)$1	1	78	81	9.0000
...	chr13:113975812-113976046(+)$1	1	106	109	9.0000
)..	chr19:10793236-10793475(+)$1	1	150	153	9.0000
.((	chr17:27844489-27844710(+)$1	1	19	22	9.0000
.((	chr19:58491105-58491331(-)$1	1	7	10	9.0000
..(	chr12:56638792-56639016(-)$1	1	43	46	9.0000
(..	chrX:152861411-152861635(-)$1	1	152	155	9.0000
..(	chr5:102611928-102612150(+)$1	1	95	98	9.0000
.))	chr22:29696023-29696267(+)$1	1	223	226	9.0000
)).	chr12:21807420-21807656(-)$1	1	102	105	9.0000
...	chr10:133757508-133757736(+)$1	1	30	33	9.0000
...	chr2:9581889-9582111(+)$1	1	25	28	9.0000
.((	chr18:29488823-29489069(-)$1	1	0	3	9.0000
.((	chr12:6837004-6837232(+)$1	1	20	23	9.0000
.((	chr5:32414996-32415234(-)$1	1	0	3	9.0000
)..	chr3:12626579-12626828(-)$1	1	68	71	9.0000
...	chr8:37635456-37635684(+)$1	1	30	33	9.0000
.((	chr4:1976564-1976793(+)$1	1	21	24	9.0000
...	chr17:5009572-5009805(-)$1	1	9	12	9.0000
...	chrM:11147-11510(+)$1	1	51	54	9.0000
.))	chr14:67847320-67847547(+)$1	1	139	142	9.0000
..)	chr5:61690240-61690468(-)$1	1	122	125	9.0000
)..	chr10:129913537-129913764(-)$1	1	22	25	9.0000
.((	chr19:37879705-37879930(+)$1	1	34	37	9.0000
.).	chr19:1278959-1279182(+)$1	1	90	93	9.0000
.((	chr19:40486488-40486721(+)$1	1	1	4	9.0000
.((	chr1:25551441-25551679(-)$1	1	107	110	9.0000
.((	chr11:10823161-10823409(-)$1	1	144	147	9.0000
(..	chr3:49775693-49775918(-)$1	1	30	33	9.0000
((.	chr19:49506438-49506661(+)$1	1	7	10	9.0000
).)	chr2:118753766-118753995(-)$1	1	81	84	9.0000
.))	chr20:3765301-3765524(-)$1	1	102	105	9.0000
...	chr15:65956836-65957067(-)$1	1	3	6	9.0000
.((	chr19:6364480-6364730(+)$1	1	15	18	9.0000
...	chr22:41646946-41647192(-)$1	1	48	51	9.0000
(..	chr21:45107730-45107955(+)$1	1	11	14	9.0000
(((	chr5:74016856-74017081(+)$1	1	4	7	9.0000
.((	chr14:95574155-95574385(-)$1	1	38	41	9.0000
(((	chr10:13217537-13217759(+)$1	1	21	24	9.0000
...	chr6:126210453-126210682(+)$1	1	38	41	9.0000
(..	chr17:31102786-31103008(-)$1	1	32	35	9.0000
...	chr8:94745720-94745948(-)$1	1	152	155	9.0000
...	chr22:35804322-35804594(+)$1	1	74	77	9.0000
((.	chr10:73056274-73056497(+)$1	1	10	13	9.0000
...	chr22:40757465-40757688(+)$1	1	16	19	9.0000
...	chr15:35198748-35198973(-)$1	1	2	5	9.0000
(((	chr15:78575643-78575902(-)$1	1	35	38	9.0000
(((	chr6:12120464-12120689(+)$1	1	46	49	9.0000
(((	chr1:226173055-226173302(-)$1	1	11	14	9.0000
...	chr1:51204490-51204722(-)$1	1	3	6	9.0000
(((	chr12:6646709-6646979(+)$1	1	43	46	9.0000
...	chr5:54579155-54579375(-)$1	1	54	57	9.0000
)))	chr1:75214364-75214588(+)$1	1	14	17	9.0000
).)	chr7:77402374-77402602(+)$1	1	85	88	9.0000
...	chr5:132425164-132425400(+)$1	1	6	9	9.0000
.((	chr19:11256947-11257167(-)$1	1	127	130	9.0000
...	chr10:32635644-32635868(-)$1	1	128	131	9.0000
)))	chr12:69232986-69233262(+)$1	1	33	36	9.0000
)))	chr1:36492617-36492906(+)$1	1	62	65	9.0000
)))	chr4:152679828-152680061(-)$1	1	192	195	9.0000
...	chr21:38844932-38845154(+)$1	1	1	4	9.0000
(..	chr19:56172406-56172653(+)$1	1	100	103	9.0000
).)	chr7:102952554-102952798(+)$1	1	127	130	9.0000
...	chr6:149700043-149700279(+)$1	1	6	9	9.0000
(..	chr20:47841589-47841822(+)$1	1	118	121	9.0000
((.	chr11:66475164-66475388(-)$1	1	34	37	9.0000

#PSSM
A : 0.99	a : 0.01	
C : 0.99	c : 0.01	
A : 0.99	a : 0.01	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m3_run1.nuc.txt

#NT
CUG	chr9:34241133-34241541(+)$1	408	11	14	9.0000
CUG	chr9:124751555-124751889(-)$1	334	1	4	9.0000
CUG	chr9:138712842-138713082(-)$1	240	18	21	9.0000
CUG	chr17:7480891-7481130(+)$1	239	4	7	9.0000
CUG	chr5:137519058-137519319(+)$1	261	14	17	9.0000
CUG	chr1:111506166-111506537(-)$1	371	22	25	9.0000
CUG	chr7:135277739-135278039(+)$1	300	25	28	9.0000
CUG	chr16:3823664-3824031(-)$1	367	4	7	9.0000
CUG	chr7:140710118-140710413(-)$1	295	85	88	9.0000
CUG	chr19:9061538-9061869(-)$1	331	0	3	9.0000
CUG	chr16:30369385-30369720(-)$1	335	16	19	9.0000
CUG	chr15:65261490-65261732(-)$1	242	15	18	9.0000
CUG	chr7:77256486-77256784(+)$1	298	0	3	9.0000
CUG	chr2:149447741-149448043(+)$1	302	111	114	9.0000
CUG	chrX:53573296-53573625(-)$1	329	38	41	9.0000
CUG	chr17:38151572-38151873(+)$1	301	62	65	9.0000
CUG	chr13:21383863-21384186(-)$1	323	19	22	9.0000
CUG	chr1:44121204-44121517(+)$1	313	2	5	9.0000
CUG	chr6:64422073-64422353(+)$1	280	62	65	9.0000
CUG	chr19:42365090-42365397(+)$1	307	56	59	9.0000
CUG	chr1:53513427-53513677(+)$1	250	2	5	9.0000
CUG	chr4:106196433-106196747(+)$1	314	44	47	9.0000
CUG	chr12:21807410-21807711(-)$1	301	179	182	9.0000
CUG	chr17:26950707-26951015(-)$1	308	10	13	9.0000
CUG	chr17:66246228-66246539(+)$1	311	23	26	9.0000
CUG	chr17:34894083-34894521(+)$1	438	10	13	9.0000
CUG	chr16:50813517-50813813(+)$1	296	34	37	9.0000
CUG	chr12:116445224-116445541(-)$1	317	133	136	9.0000
CUG	chr17:80202356-80202807(-)$1	451	16	19	9.0000
CUG	chr19:9056153-9056495(-)$1	342	19	22	9.0000
CUG	chrX:118726244-118726556(-)$1	312	7	10	9.0000
CUG	chr1:14106243-14106660(+)$1	417	13	16	9.0000
CUG	chr12:88439375-88439652(+)$1	277	20	23	9.0000
CUG	chr8:74893555-74893888(+)$1	333	172	175	9.0000
CUG	chr12:2968453-2968742(-)$1	289	43	46	9.0000
CUG	chr20:47686672-47686932(+)$1	260	63	66	9.0000
CUG	chr15:35273834-35274156(-)$1	322	13	16	9.0000
CUG	chr1:90400247-90400616(+)$1	369	19	22	9.0000
CUG	chr6:159004885-159005174(+)$1	289	130	133	9.0000
CUG	chr8:41790968-41791248(-)$1	280	18	21	9.0000
CUG	chr1:156256038-156256346(+)$1	308	17	20	9.0000
CUG	chr12:6637240-6637594(+)$1	354	5	8	9.0000
CUG	chr17:45746983-45747323(+)$1	340	45	48	9.0000
CUG	chr14:91338333-91338664(-)$1	331	175	178	9.0000
CUG	chr1:46096051-46096356(-)$1	305	51	54	9.0000
CUG	chr1:193181420-193181705(+)$1	285	78	81	9.0000
CUG	chr12:93792967-93793202(+)$1	235	45	48	9.0000
CUG	chrX:47496341-47496598(-)$1	257	0	3	9.0000
CUG	chr12:133153360-133153617(+)$1	257	33	36	9.0000
CUG	chr9:137293468-137293784(+)$1	316	66	69	9.0000
CUG	chr3:9879564-9879870(-)$1	306	12	15	9.0000
CUG	chr15:84286924-84287193(+)$1	269	33	36	9.0000
CUG	chr12:46321090-46321336(-)$1	246	44	47	9.0000
CUG	chr15:78337148-78337417(-)$1	269	34	37	9.0000
CUG	chr8:21839143-21839481(+)$1	338	85	88	9.0000
CUG	chr12:121783596-121783923(-)$1	327	41	44	9.0000
CUG	chr6:52144092-52144462(-)$1	370	39	42	9.0000
CUG	chr2:149541067-149541414(+)$1	347	111	114	9.0000
CUG	chr19:37677299-37677538(-)$1	239	5	8	9.0000
CUG	chr12:70150092-70150491(+)$1	399	22	25	9.0000
CUG	chr16:75673977-75674347(-)$1	370	22	25	9.0000
CUG	chr1:44086409-44086748(+)$1	339	11	14	9.0000
CUG	chr15:58889477-58889785(-)$1	308	40	43	9.0000
CUG	chr2:232326150-232326549(-)$1	399	5	8	9.0000
CUG	chr19:37733730-37733991(+)$1	261	69	72	9.0000
CUG	chr19:31767949-31768271(-)$1	322	55	58	9.0000
CUG	chr15:82335867-82336178(-)$1	311	32	35	9.0000
CUG	chr11:60665513-60665842(-)$1	329	61	64	9.0000
CUG	chr1:183497927-183498277(+)$1	350	25	28	9.0000
CUG	chr3:184046326-184046610(+)$1	284	54	57	9.0000
CUG	chr22:46712023-46712311(+)$1	288	6	9	9.0000
CUG	chr7:42079650-42079937(-)$1	287	46	49	9.0000
CUG	chr2:200137027-200137410(-)$1	383	94	97	9.0000
CUG	chrX:109414547-109414848(+)$1	301	13	16	9.0000
CUG	chr7:43680070-43680348(-)$1	278	42	45	9.0000
CUG	chr17:30795985-30796307(+)$1	322	39	42	9.0000
CUG	chr22:42981660-42982059(-)$1	399	48	51	9.0000
CUG	chr5:37060897-37061217(+)$1	320	71	74	9.0000
CUG	chr1:153914243-153914550(-)$1	307	33	36	9.0000
CUG	chr16:2998688-2998952(+)$1	264	19	22	9.0000
CUG	chr3:12632254-12632573(-)$1	319	24	27	9.0000
CUG	chr1:93298959-93299325(+)$1	366	59	62	9.0000
CUG	chr7:21940495-21940785(-)$1	290	42	45	9.0000
CUG	chr12:57625893-57626176(+)$1	283	4	7	9.0000
CUG	chr2:148692842-148693283(-)$1	441	94	97	9.0000
CUG	chr19:2765083-2765362(-)$1	279	21	24	9.0000
CUG	chr2:128479309-128479565(-)$1	256	31	34	9.0000
CUG	chr11:18424323-18424612(+)$1	289	137	140	9.0000
CUG	chr6:7571647-7571915(+)$1	268	130	133	9.0000
CUG	chr1:27099203-27099571(+)$1	368	8	11	9.0000
CUG	chr7:70227895-70228226(+)$1	331	66	69	9.0000
CUG	chr12:50149322-50149638(+)$1	316	82	85	9.0000
CUG	chr19:34929468-34929758(+)$1	290	38	41	9.0000
CUG	chr8:145537101-145537403(+)$1	302	56	59	9.0000
CUG	chr12:102547547-102547849(+)$1	302	6	9	9.0000
CUG	chrX:47102720-47103084(+)$1	364	31	34	9.0000
CUG	chr9:125627591-125627863(-)$1	272	4	7	9.0000
CUG	chr1:32691912-32692224(+)$1	312	16	19	9.0000
CUG	chr8:145151387-145151735(+)$1	348	19	22	9.0000

#otherMatches

#Struct PSSM
:ee	chr17:26966246-26966581(-)$1	335	85	88	9.0000
KFF	chr9:34241133-34241541(+)$1	408	11	14	9.0000
:::	chr9:124751555-124751889(-)$1	334	1	4	9.0000
ccc	chr9:138712842-138713082(-)$1	240	18	21	9.0000
KKF	chr17:7480891-7481130(+)$1	239	4	7	9.0000
DDD	chr5:137519058-137519319(+)$1	261	14	17	9.0000
hhh	chr1:111506166-111506537(-)$1	371	22	25	9.0000
===	chr7:135277739-135278039(+)$1	300	25	28	9.0000
::f	chr16:3823664-3824031(-)$1	367	4	7	9.0000
ccm	chr7:140710118-140710413(-)$1	295	85	88	9.0000
::=	chr19:9061538-9061869(-)$1	331	0	3	9.0000
c[f	chr16:30369385-30369720(-)$1	335	16	19	9.0000
eee	chr15:65261490-65261732(-)$1	242	15	18	9.0000
CCC	chr7:77256486-77256784(+)$1	298	0	3	9.0000
%ee	chr2:149447741-149448043(+)$1	302	111	114	9.0000
KEE	chrX:53573296-53573625(-)$1	329	38	41	9.0000
bb]	chr17:38151572-38151873(+)$1	301	62	65	9.0000
BBK	chr13:21383863-21384186(-)$1	323	19	22	9.0000
:::	chr1:44121204-44121517(+)$1	313	2	5	9.0000
III	chr6:64422073-64422353(+)$1	280	62	65	9.0000
ooo	chr19:42365090-42365397(+)$1	307	56	59	9.0000
:::	chr1:53513427-53513677(+)$1	250	2	5	9.0000
DDD	chr4:106196433-106196747(+)$1	314	44	47	9.0000
EEE	chr12:21807410-21807711(-)$1	301	179	182	9.0000
iii	chr17:26950707-26951015(-)$1	308	10	13	9.0000
EE:	chr17:66246228-66246539(+)$1	311	23	26	9.0000
CCC	chr17:34894083-34894521(+)$1	438	10	13	9.0000
===	chr16:50813517-50813813(+)$1	296	34	37	9.0000
eee	chr12:116445224-116445541(-)$1	317	133	136	9.0000
EEE	chr17:80202356-80202807(-)$1	451	16	19	9.0000
ddd	chr19:9056153-9056495(-)$1	342	19	22	9.0000
nnn	chrX:118726244-118726556(-)$1	312	7	10	9.0000
DDd	chr1:14106243-14106660(+)$1	417	13	16	9.0000
ddd	chr12:88439375-88439652(+)$1	277	20	23	9.0000
FFF	chr8:74893555-74893888(+)$1	333	172	175	9.0000
c[g	chr12:2968453-2968742(-)$1	289	43	46	9.0000
ggg	chr20:47686672-47686932(+)$1	260	63	66	9.0000
::F	chr15:35273834-35274156(-)$1	322	13	16	9.0000
cmm	chr1:90400247-90400616(+)$1	369	19	22	9.0000
888	chr6:159004885-159005174(+)$1	289	130	133	9.0000
FFF	chr8:41790968-41791248(-)$1	280	18	21	9.0000
HHH	chr1:156256038-156256346(+)$1	308	17	20	9.0000
ddd	chr12:6637240-6637594(+)$1	354	5	8	9.0000
:::	chr17:45746983-45747323(+)$1	340	45	48	9.0000
EEE	chr14:91338333-91338664(-)$1	331	175	178	9.0000
EEE	chr1:46096051-46096356(-)$1	305	51	54	9.0000
hhh	chr1:193181420-193181705(+)$1	285	78	81	9.0000
ddd	chr12:93792967-93793202(+)$1	235	45	48	9.0000
::E	chrX:47496341-47496598(-)$1	257	0	3	9.0000
c]b	chr12:133153360-133153617(+)$1	257	33	36	9.0000
ddd	chr9:137293468-137293784(+)$1	316	66	69	9.0000
ddd	chr3:9879564-9879870(-)$1	306	12	15	9.0000
4dd	chr15:84286924-84287193(+)$1	269	33	36	9.0000
=GG	chr12:46321090-46321336(-)$1	246	44	47	9.0000
bb[	chr15:78337148-78337417(-)$1	269	34	37	9.0000
b[a	chr8:21839143-21839481(+)$1	338	85	88	9.0000
:::	chr12:121783596-121783923(-)$1	327	41	44	9.0000
hhh	chr6:52144092-52144462(-)$1	370	39	42	9.0000
&&c	chr2:149541067-149541414(+)$1	347	111	114	9.0000
:ff	chr19:37677299-37677538(-)$1	239	5	8	9.0000
ggg	chr12:70150092-70150491(+)$1	399	22	25	9.0000
fff	chr16:75673977-75674347(-)$1	370	22	25	9.0000
FFF	chr1:44086409-44086748(+)$1	339	11	14	9.0000
nnb	chr15:58889477-58889785(-)$1	308	40	43	9.0000
:dd	chr2:232326150-232326549(-)$1	399	5	8	9.0000
3bb	chr19:37733730-37733991(+)$1	261	69	72	9.0000
qff	chr19:31767949-31768271(-)$1	322	55	58	9.0000
cdd	chr15:82335867-82336178(-)$1	311	32	35	9.0000
##g	chr11:60665513-60665842(-)$1	329	61	64	9.0000
]bb	chr1:183497927-183498277(+)$1	350	25	28	9.0000
DDK	chr3:184046326-184046610(+)$1	284	54	57	9.0000
F:f	chr22:46712023-46712311(+)$1	288	6	9	9.0000
EEE	chr7:42079650-42079937(-)$1	287	46	49	9.0000
fff	chr2:200137027-200137410(-)$1	383	94	97	9.0000
{BB	chrX:109414547-109414848(+)$1	301	13	16	9.0000
:==	chr7:43680070-43680348(-)$1	278	42	45	9.0000
ff[	chr17:30795985-30796307(+)$1	322	39	42	9.0000
:::	chr22:42981660-42982059(-)$1	399	48	51	9.0000
ggg	chr5:37060897-37061217(+)$1	320	71	74	9.0000
ddd	chr1:153914243-153914550(-)$1	307	33	36	9.0000
EEF	chr16:2998688-2998952(+)$1	264	19	22	9.0000
eee	chr3:12632254-12632573(-)$1	319	24	27	9.0000
ooo	chr1:93298959-93299325(+)$1	366	59	62	9.0000
eee	chr7:21940495-21940785(-)$1	290	42	45	9.0000
JJJ	chr12:57625893-57626176(+)$1	283	4	7	9.0000
bss	chr2:148692842-148693283(-)$1	441	94	97	9.0000
FFF	chr19:2765083-2765362(-)$1	279	21	24	9.0000
GGG	chr2:128479309-128479565(-)$1	256	31	34	9.0000
:::	chr11:18424323-18424612(+)$1	289	137	140	9.0000
eee	chr6:7571647-7571915(+)$1	268	130	133	9.0000
:::	chr1:27099203-27099571(+)$1	368	8	11	9.0000
::c	chr7:70227895-70228226(+)$1	331	66	69	9.0000
:::	chr12:50149322-50149638(+)$1	316	82	85	9.0000
cc[	chr19:34929468-34929758(+)$1	290	38	41	9.0000
::J	chr8:145537101-145537403(+)$1	302	56	59	9.0000
:::	chr12:102547547-102547849(+)$1	302	6	9	9.0000
mmm	chrX:47102720-47103084(+)$1	364	31	34	9.0000
HHH	chr9:125627591-125627863(-)$1	272	4	7	9.0000
b[d	chr1:32691912-32692224(+)$1	312	16	19	9.0000
LLL	chr8:145151387-145151735(+)$1	348	19	22	9.0000

#DB
.((	chr17:26966246-26966581(-)$1	1	85	88	9.0000
.((	chr9:34241133-34241541(+)$1	1	11	14	9.0000
...	chr9:124751555-124751889(-)$1	1	1	4	9.0000
(((	chr9:138712842-138713082(-)$1	1	18	21	9.0000
..(	chr17:7480891-7481130(+)$1	1	4	7	9.0000
(((	chr5:137519058-137519319(+)$1	1	14	17	9.0000
)))	chr1:111506166-111506537(-)$1	1	22	25	9.0000
)))	chr7:135277739-135278039(+)$1	1	25	28	9.0000
..(	chr16:3823664-3824031(-)$1	1	4	7	9.0000
((.	chr7:140710118-140710413(-)$1	1	85	88	9.0000
..(	chr19:9061538-9061869(-)$1	1	0	3	9.0000
(.(	chr16:30369385-30369720(-)$1	1	16	19	9.0000
(((	chr15:65261490-65261732(-)$1	1	15	18	9.0000
(((	chr7:77256486-77256784(+)$1	1	0	3	9.0000
.((	chr2:149447741-149448043(+)$1	1	111	114	9.0000
.((	chrX:53573296-53573625(-)$1	1	38	41	9.0000
)).	chr17:38151572-38151873(+)$1	1	62	65	9.0000
((.	chr13:21383863-21384186(-)$1	1	19	22	9.0000
...	chr1:44121204-44121517(+)$1	1	2	5	9.0000
(((	chr6:64422073-64422353(+)$1	1	62	65	9.0000
...	chr19:42365090-42365397(+)$1	1	56	59	9.0000
...	chr1:53513427-53513677(+)$1	1	2	5	9.0000
(((	chr4:106196433-106196747(+)$1	1	44	47	9.0000
(((	chr12:21807410-21807711(-)$1	1	179	182	9.0000
(((	chr17:26950707-26951015(-)$1	1	10	13	9.0000
((.	chr17:66246228-66246539(+)$1	1	23	26	9.0000
(((	chr17:34894083-34894521(+)$1	1	10	13	9.0000
(((	chr16:50813517-50813813(+)$1	1	34	37	9.0000
)))	chr12:116445224-116445541(-)$1	1	133	136	9.0000
(((	chr17:80202356-80202807(-)$1	1	16	19	9.0000
)))	chr19:9056153-9056495(-)$1	1	19	22	9.0000
...	chrX:118726244-118726556(-)$1	1	7	10	9.0000
(((	chr1:14106243-14106660(+)$1	1	13	16	9.0000
)))	chr12:88439375-88439652(+)$1	1	20	23	9.0000
(((	chr8:74893555-74893888(+)$1	1	172	175	9.0000
(.(	chr12:2968453-2968742(-)$1	1	43	46	9.0000
(((	chr20:47686672-47686932(+)$1	1	63	66	9.0000
..(	chr15:35273834-35274156(-)$1	1	13	16	9.0000
(..	chr1:90400247-90400616(+)$1	1	19	22	9.0000
...	chr6:159004885-159005174(+)$1	1	130	133	9.0000
(((	chr8:41790968-41791248(-)$1	1	18	21	9.0000
(((	chr1:156256038-156256346(+)$1	1	17	20	9.0000
(((	chr12:6637240-6637594(+)$1	1	5	8	9.0000
...	chr17:45746983-45747323(+)$1	1	45	48	9.0000
)))	chr14:91338333-91338664(-)$1	1	175	178	9.0000
(((	chr1:46096051-46096356(-)$1	1	51	54	9.0000
(((	chr1:193181420-193181705(+)$1	1	78	81	9.0000
(((	chr12:93792967-93793202(+)$1	1	45	48	9.0000
..(	chrX:47496341-47496598(-)$1	1	0	3	9.0000
).)	chr12:133153360-133153617(+)$1	1	33	36	9.0000
(((	chr9:137293468-137293784(+)$1	1	66	69	9.0000
(((	chr3:9879564-9879870(-)$1	1	12	15	9.0000
.))	chr15:84286924-84287193(+)$1	1	33	36	9.0000
)((	chr12:46321090-46321336(-)$1	1	44	47	9.0000
((.	chr15:78337148-78337417(-)$1	1	34	37	9.0000
(.(	chr8:21839143-21839481(+)$1	1	85	88	9.0000
...	chr12:121783596-121783923(-)$1	1	41	44	9.0000
)))	chr6:52144092-52144462(-)$1	1	39	42	9.0000
..(	chr2:149541067-149541414(+)$1	1	111	114	9.0000
.((	chr19:37677299-37677538(-)$1	1	5	8	9.0000
(((	chr12:70150092-70150491(+)$1	1	22	25	9.0000
)))	chr16:75673977-75674347(-)$1	1	22	25	9.0000
(((	chr1:44086409-44086748(+)$1	1	11	14	9.0000
..)	chr15:58889477-58889785(-)$1	1	40	43	9.0000
.((	chr2:232326150-232326549(-)$1	1	5	8	9.0000
.))	chr19:37733730-37733991(+)$1	1	69	72	9.0000
.))	chr19:31767949-31768271(-)$1	1	55	58	9.0000
)((	chr15:82335867-82336178(-)$1	1	32	35	9.0000
..(	chr11:60665513-60665842(-)$1	1	61	64	9.0000
.))	chr1:183497927-183498277(+)$1	1	25	28	9.0000
((.	chr3:184046326-184046610(+)$1	1	54	57	9.0000
(.(	chr22:46712023-46712311(+)$1	1	6	9	9.0000
(((	chr7:42079650-42079937(-)$1	1	46	49	9.0000
(((	chr2:200137027-200137410(-)$1	1	94	97	9.0000
.((	chrX:109414547-109414848(+)$1	1	13	16	9.0000
.((	chr7:43680070-43680348(-)$1	1	42	45	9.0000
((.	chr17:30795985-30796307(+)$1	1	39	42	9.0000
...	chr22:42981660-42982059(-)$1	1	48	51	9.0000
)))	chr5:37060897-37061217(+)$1	1	71	74	9.0000
)))	chr1:153914243-153914550(-)$1	1	33	36	9.0000
(((	chr16:2998688-2998952(+)$1	1	19	22	9.0000
)))	chr3:12632254-12632573(-)$1	1	24	27	9.0000
...	chr1:93298959-93299325(+)$1	1	59	62	9.0000
(((	chr7:21940495-21940785(-)$1	1	42	45	9.0000
(((	chr12:57625893-57626176(+)$1	1	4	7	9.0000
(..	chr2:148692842-148693283(-)$1	1	94	97	9.0000
(((	chr19:2765083-2765362(-)$1	1	21	24	9.0000
(((	chr2:128479309-128479565(-)$1	1	31	34	9.0000
...	chr11:18424323-18424612(+)$1	1	137	140	9.0000
)))	chr6:7571647-7571915(+)$1	1	130	133	9.0000
...	chr1:27099203-27099571(+)$1	1	8	11	9.0000
..(	chr7:70227895-70228226(+)$1	1	66	69	9.0000
...	chr12:50149322-50149638(+)$1	1	82	85	9.0000
((.	chr19:34929468-34929758(+)$1	1	38	41	9.0000
..(	chr8:145537101-145537403(+)$1	1	56	59	9.0000
...	chr12:102547547-102547849(+)$1	1	6	9	9.0000
...	chrX:47102720-47103084(+)$1	1	31	34	9.0000
(((	chr9:125627591-125627863(-)$1	1	4	7	9.0000
(.(	chr1:32691912-32692224(+)$1	1	16	19	9.0000
...	chr8:145151387-145151735(+)$1	1	19	22	9.0000

#PSSM
C : 1.00	
U : 1.00	
G : 1.00	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoel2011_hg19_CDS_m1_run2.nuc.txt

#NT
GAAG	chr10:121602700-121602920(-)$1	220	93	97	11.9999
GAAG	chr4:113502756-113502981(-)$1	225	65	69	11.9999
GAAG	chrM:8007-8242(+)$1	235	17	21	11.9999
GAAG	chr2:128479313-128479544(-)$1	231	42	46	11.9999
GAAG	chr4:39918597-39918817(-)$1	220	34	38	11.9999
GAAG	chr17:58533593-58533818(-)$1	225	122	126	11.9999
GAAG	chr19:53572029-53572252(-)$1	223	123	127	11.9999
GAAG	chrM:6533-6815(+)$1	282	94	98	11.9999
GAAG	chr10:5790426-5790657(+)$1	231	55	59	11.9999
GAAG	chr13:23908523-23908744(-)$1	221	74	78	11.9999
GAAG	chr10:116606246-116606469(+)$1	223	14	18	11.9999
GAAG	chr19:36883567-36883793(-)$1	226	3	7	11.9999
GAAG	chr6:153296299-153296521(-)$1	222	61	65	11.9999
GAAG	chr5:71490461-71490698(+)$1	237	92	96	11.9999
GAAG	chr15:42743364-42743590(-)$1	226	84	88	11.9999
GAAG	chrM:14178-14446(-)$1	268	136	140	11.9999
GAAG	chr16:2813153-2813384(+)$1	231	132	136	11.9999
GAAG	chr1:200377432-200377655(-)$1	223	75	79	11.9999
GAAG	chr1:36380941-36381174(+)$1	233	85	89	11.9999
GAAG	chr19:49120536-49120778(-)$1	242	42	46	11.9999
GAAG	chr19:57802433-57802675(+)$1	242	54	58	11.9999
GAAG	chr17:7415515-7415745(+)$1	230	8	12	11.9999
GAAG	chr5:56509877-56510120(+)$1	243	42	46	11.9999
GAAG	chr17:65909119-65909339(+)$1	220	31	35	11.9999
GAAG	chr1:70697924-70698160(+)$1	236	40	44	11.9999
GAAG	chr1:40705951-40706188(+)$1	237	157	161	11.9999
GAAG	chr1:185275998-185276224(-)$1	226	61	65	11.9999
GAAG	chr2:61710094-61710318(-)$1	224	133	137	11.9999
GAAG	chr3:25661263-25661488(-)$1	225	55	59	11.9999
GAAG	chr1:235875346-235875572(-)$1	226	212	216	11.9999
GAAG	chr10:120489709-120489929(-)$1	220	27	31	11.9999
GAAG	chr19:16652609-16652828(-)$1	219	41	45	11.9999
GAAG	chr19:37130019-37130240(-)$1	221	166	170	11.9999
GAAG	chr16:57265041-57265269(+)$1	228	167	171	11.9999
GAAG	chr3:160149425-160149645(+)$1	220	32	36	11.9999
GAAG	chr9:35720343-35720564(-)$1	221	85	89	11.9999
GAAG	chr16:30733413-30733637(+)$1	224	34	38	11.9999
gaag	chr19:58145105-58145328(+)$1	223	59	63	11.9999
GAAG	chr1:82415806-82416038(+)$1	232	182	186	11.9999
GAAG	chr12:1005706-1005961(+)$1	255	148	152	11.9999
GAAG	chr1:171560872-171561112(+)$1	240	15	19	11.9999
GAAG	chr1:116932072-116932294(+)$1	222	36	40	11.9999
GAAG	chr2:48027672-48027920(+)$1	248	5	9	11.9999
GAAG	chr5:145857979-145858209(+)$1	230	13	17	11.9999
GAAG	chr4:123855608-123855836(+)$1	228	29	33	11.9999
GAAG	chr6:76380174-76380398(+)$1	224	212	216	11.9999
GAAG	chr10:115609850-115610089(-)$1	239	144	148	11.9999
GAAG	chr15:42005250-42005485(+)$1	235	205	209	11.9999
GAAG	chr6:36437879-36438119(+)$1	240	88	92	11.9999
GAAG	chr2:152320418-152320670(+)$1	252	60	64	11.9999
GAAG	chr22:26854335-26854557(-)$1	222	47	51	11.9999
GAAG	chr2:202272106-202272336(-)$1	230	42	46	11.9999
GAAG	chr1:91404129-91404351(-)$1	222	6	10	11.9999
GAAG	chr4:110441470-110441694(+)$1	224	124	128	11.9999
GAAG	chrX:84526618-84526836(+)$1	218	14	18	11.9999
GAAG	chr15:52900725-52900947(-)$1	222	30	34	11.9999
GAAG	chr6:87971101-87971330(+)$1	229	19	23	11.9999
GAAG	chr5:71492678-71492921(+)$1	243	65	69	11.9999
GAAG	chr8:37554619-37554891(+)$1	272	54	58	11.9999
GAAG	chr13:103387696-103387931(-)$1	235	65	69	11.9999
GAAG	chr19:53057781-53058020(+)$1	239	179	183	11.9999
GAAG	chr11:32956293-32956510(+)$1	217	75	79	11.9999
GAAG	chrX:119387872-119388111(+)$1	239	185	189	11.9999
GAAG	chr1:155327052-155327271(-)$1	219	141	145	11.9999
GAAG	chr21:34926074-34926324(+)$1	250	149	153	11.9999
GAAG	chr16:20809490-20809714(-)$1	224	54	58	11.9999
GAAG	chr7:104742453-104742686(+)$1	233	44	48	11.9999
GAAG	chr21:37705856-37706078(+)$1	222	95	99	11.9999
GAAG	chr2:74437010-74437234(+)$1	224	74	78	11.9999
GAAG	chr13:23913739-23913963(-)$1	224	124	128	11.9999
GAAG	chr18:72343722-72343956(+)$1	234	15	19	11.9999
GAAG	chrX:119388318-119388547(+)$1	229	70	74	11.9999
GAAG	chr19:37239765-37239987(-)$1	222	82	86	11.9999
GAAG	chr5:79746271-79746491(+)$1	220	70	74	11.9999
GAAG	chr17:33690048-33690275(-)$1	227	214	218	11.9999
GAAG	chr19:9676517-9676752(-)$1	235	135	139	11.9999
GAAG	chr5:71493072-71493306(+)$1	234	19	23	11.9999
GAAG	chr4:13582667-13582887(-)$1	220	56	60	11.9999

#otherMatches

#Struct PSSM
gggg	chr10:70666623-70666844(+)$1	221	30	34	11.9999
:::d	chr10:121602700-121602920(-)$1	220	93	97	11.9999
nnee	chr4:113502756-113502981(-)$1	225	65	69	11.9999
C{CC	chrM:8007-8242(+)$1	235	17	21	11.9999
^^^^	chr2:128479313-128479544(-)$1	231	42	46	11.9999
CC{C	chr4:39918597-39918817(-)$1	220	34	38	11.9999
ffff	chr17:58533593-58533818(-)$1	225	122	126	11.9999
bbnn	chr19:53572029-53572252(-)$1	223	123	127	11.9999
iiii	chrM:6533-6815(+)$1	282	94	98	11.9999
e[a[	chr10:5790426-5790657(+)$1	231	55	59	11.9999
ff88	chr13:23908523-23908744(-)$1	221	74	78	11.9999
gg[a	chr10:116606246-116606469(+)$1	223	14	18	11.9999
iiii	chr19:36883567-36883793(-)$1	226	3	7	11.9999
::dd	chr6:153296299-153296521(-)$1	222	61	65	11.9999
:fff	chr5:71490461-71490698(+)$1	237	92	96	11.9999
====	chr15:42743364-42743590(-)$1	226	84	88	11.9999
444f	chrM:14178-14446(-)$1	268	136	140	11.9999
c]cc	chr16:2813153-2813384(+)$1	231	132	136	11.9999
FFFF	chr1:200377432-200377655(-)$1	223	75	79	11.9999
b!!g	chr1:36380941-36381174(+)$1	233	85	89	11.9999
ff[b	chr19:49120536-49120778(-)$1	242	42	46	11.9999
E::c	chr19:57802433-57802675(+)$1	242	54	58	11.9999
B::I	chr17:7415515-7415745(+)$1	230	8	12	11.9999
ffff	chr5:56509877-56510120(+)$1	243	42	46	11.9999
gggn	chr17:65909119-65909339(+)$1	220	31	35	11.9999
hhhh	chr1:70697924-70698160(+)$1	236	40	44	11.9999
iiii	chr1:40705951-40706188(+)$1	237	157	161	11.9999
C:ii	chr1:185275998-185276224(-)$1	226	61	65	11.9999
qqqq	chr2:61710094-61710318(-)$1	224	133	137	11.9999
eeee	chr3:25661263-25661488(-)$1	225	55	59	11.9999
B}DD	chr1:235875346-235875572(-)$1	226	212	216	11.9999
dddd	chr10:120489709-120489929(-)$1	220	27	31	11.9999
JJJJ	chr19:16652609-16652828(-)$1	219	41	45	11.9999
iiii	chr19:37130019-37130240(-)$1	221	166	170	11.9999
E}BB	chr16:57265041-57265269(+)$1	228	167	171	11.9999
eee"	chr3:160149425-160149645(+)$1	220	32	36	11.9999
c22e	chr9:35720343-35720564(-)$1	221	85	89	11.9999
ccc2	chr16:30733413-30733637(+)$1	224	34	38	11.9999
cccc	chr19:58145105-58145328(+)$1	223	59	63	11.9999
:::f	chr1:82415806-82416038(+)$1	232	182	186	11.9999
llld	chr12:1005706-1005961(+)$1	255	148	152	11.9999
::::	chr1:171560872-171561112(+)$1	240	15	19	11.9999
[bbl	chr1:116932072-116932294(+)$1	222	36	40	11.9999
====	chr2:48027672-48027920(+)$1	248	5	9	11.9999
IIII	chr5:145857979-145858209(+)$1	230	13	17	11.9999
ssss	chr4:123855608-123855836(+)$1	228	29	33	11.9999
====	chr6:76380174-76380398(+)$1	224	212	216	11.9999
ccc:	chr10:115609850-115610089(-)$1	239	144	148	11.9999
f444	chr15:42005250-42005485(+)$1	235	205	209	11.9999
eeee	chr6:36437879-36438119(+)$1	240	88	92	11.9999
22gg	chr2:152320418-152320670(+)$1	252	60	64	11.9999
eeee	chr22:26854335-26854557(-)$1	222	47	51	11.9999
]a::	chr2:202272106-202272336(-)$1	230	42	46	11.9999
::::	chr1:91404129-91404351(-)$1	222	6	10	11.9999
""cc	chr4:110441470-110441694(+)$1	224	124	128	11.9999
EKKB	chrX:84526618-84526836(+)$1	218	14	18	11.9999
:::D	chr15:52900725-52900947(-)$1	222	30	34	11.9999
d[ee	chr6:87971101-87971330(+)$1	229	19	23	11.9999
ffff	chr5:71492678-71492921(+)$1	243	65	69	11.9999
gqqq	chr8:37554619-37554891(+)$1	272	54	58	11.9999
::::	chr13:103387696-103387931(-)$1	235	65	69	11.9999
EE::	chr19:53057781-53058020(+)$1	239	179	183	11.9999
ffff	chr11:32956293-32956510(+)$1	217	75	79	11.9999
gggg	chrX:119387872-119388111(+)$1	239	185	189	11.9999
||||	chr1:155327052-155327271(-)$1	219	141	145	11.9999
tttt	chr21:34926074-34926324(+)$1	250	149	153	11.9999
eeee	chr16:20809490-20809714(-)$1	224	54	58	11.9999
eeee	chr7:104742453-104742686(+)$1	233	44	48	11.9999
ffff	chr21:37705856-37706078(+)$1	222	95	99	11.9999
hhhh	chr2:74437010-74437234(+)$1	224	74	78	11.9999
dddd	chr13:23913739-23913963(-)$1	224	124	128	11.9999
RRRR	chr18:72343722-72343956(+)$1	234	15	19	11.9999
eeee	chrX:119388318-119388547(+)$1	229	70	74	11.9999
hhhh	chr19:37239765-37239987(-)$1	222	82	86	11.9999
gggg	chr5:79746271-79746491(+)$1	220	70	74	11.9999
gg]b	chr17:33690048-33690275(-)$1	227	214	218	11.9999
^^^^	chr19:9676517-9676752(-)$1	235	135	139	11.9999
::dd	chr5:71493072-71493306(+)$1	234	19	23	11.9999
ddd:	chr4:13582667-13582887(-)$1	220	56	60	11.9999

#DB
((((	chr10:70666623-70666844(+)$1	1	30	34	11.9999
...(	chr10:121602700-121602920(-)$1	1	93	97	11.9999
..))	chr4:113502756-113502981(-)$1	1	65	69	11.9999
(.((	chrM:8007-8242(+)$1	1	17	21	11.9999
....	chr2:128479313-128479544(-)$1	1	42	46	11.9999
((.(	chr4:39918597-39918817(-)$1	1	34	38	11.9999
((((	chr17:58533593-58533818(-)$1	1	122	126	11.9999
((..	chr19:53572029-53572252(-)$1	1	123	127	11.9999
((((	chrM:6533-6815(+)$1	1	94	98	11.9999
(.(.	chr10:5790426-5790657(+)$1	1	55	59	11.9999
))..	chr13:23908523-23908744(-)$1	1	74	78	11.9999
((.(	chr10:116606246-116606469(+)$1	1	14	18	11.9999
((((	chr19:36883567-36883793(-)$1	1	3	7	11.9999
..((	chr6:153296299-153296521(-)$1	1	61	65	11.9999
.(((	chr5:71490461-71490698(+)$1	1	92	96	11.9999
((((	chr15:42743364-42743590(-)$1	1	84	88	11.9999
...)	chrM:14178-14446(-)$1	1	136	140	11.9999
).))	chr16:2813153-2813384(+)$1	1	132	136	11.9999
((((	chr1:200377432-200377655(-)$1	1	75	79	11.9999
(..(	chr1:36380941-36381174(+)$1	1	85	89	11.9999
((.(	chr19:49120536-49120778(-)$1	1	42	46	11.9999
(..(	chr19:57802433-57802675(+)$1	1	54	58	11.9999
(..(	chr17:7415515-7415745(+)$1	1	8	12	11.9999
((((	chr5:56509877-56510120(+)$1	1	42	46	11.9999
(((.	chr17:65909119-65909339(+)$1	1	31	35	11.9999
((((	chr1:70697924-70698160(+)$1	1	40	44	11.9999
))))	chr1:40705951-40706188(+)$1	1	157	161	11.9999
(.((	chr1:185275998-185276224(-)$1	1	61	65	11.9999
....	chr2:61710094-61710318(-)$1	1	133	137	11.9999
((((	chr3:25661263-25661488(-)$1	1	55	59	11.9999
).))	chr1:235875346-235875572(-)$1	1	212	216	11.9999
))))	chr10:120489709-120489929(-)$1	1	27	31	11.9999
((((	chr19:16652609-16652828(-)$1	1	41	45	11.9999
((((	chr19:37130019-37130240(-)$1	1	166	170	11.9999
).))	chr16:57265041-57265269(+)$1	1	167	171	11.9999
(((.	chr3:160149425-160149645(+)$1	1	32	36	11.9999
)..)	chr9:35720343-35720564(-)$1	1	85	89	11.9999
))).	chr16:30733413-30733637(+)$1	1	34	38	11.9999
))))	chr19:58145105-58145328(+)$1	1	59	63	11.9999
...(	chr1:82415806-82416038(+)$1	1	182	186	11.9999
...)	chr12:1005706-1005961(+)$1	1	148	152	11.9999
....	chr1:171560872-171561112(+)$1	1	15	19	11.9999
.((.	chr1:116932072-116932294(+)$1	1	36	40	11.9999
((((	chr2:48027672-48027920(+)$1	1	5	9	11.9999
((((	chr5:145857979-145858209(+)$1	1	13	17	11.9999
....	chr4:123855608-123855836(+)$1	1	29	33	11.9999
))))	chr6:76380174-76380398(+)$1	1	212	216	11.9999
))).	chr10:115609850-115610089(-)$1	1	144	148	11.9999
)...	chr15:42005250-42005485(+)$1	1	205	209	11.9999
((((	chr6:36437879-36438119(+)$1	1	88	92	11.9999
..))	chr2:152320418-152320670(+)$1	1	60	64	11.9999
((((	chr22:26854335-26854557(-)$1	1	47	51	11.9999
.)..	chr2:202272106-202272336(-)$1	1	42	46	11.9999
....	chr1:91404129-91404351(-)$1	1	6	10	11.9999
..((	chr4:110441470-110441694(+)$1	1	124	128	11.9999
(..(	chrX:84526618-84526836(+)$1	1	14	18	11.9999
...(	chr15:52900725-52900947(-)$1	1	30	34	11.9999
(.((	chr6:87971101-87971330(+)$1	1	19	23	11.9999
((((	chr5:71492678-71492921(+)$1	1	65	69	11.9999
(...	chr8:37554619-37554891(+)$1	1	54	58	11.9999
....	chr13:103387696-103387931(-)$1	1	65	69	11.9999
))..	chr19:53057781-53058020(+)$1	1	179	183	11.9999
((((	chr11:32956293-32956510(+)$1	1	75	79	11.9999
))))	chrX:119387872-119388111(+)$1	1	185	189	11.9999
....	chr1:155327052-155327271(-)$1	1	141	145	11.9999
....	chr21:34926074-34926324(+)$1	1	149	153	11.9999
))))	chr16:20809490-20809714(-)$1	1	54	58	11.9999
))))	chr7:104742453-104742686(+)$1	1	44	48	11.9999
))))	chr21:37705856-37706078(+)$1	1	95	99	11.9999
))))	chr2:74437010-74437234(+)$1	1	74	78	11.9999
))))	chr13:23913739-23913963(-)$1	1	124	128	11.9999
....	chr18:72343722-72343956(+)$1	1	15	19	11.9999
((((	chrX:119388318-119388547(+)$1	1	70	74	11.9999
((((	chr19:37239765-37239987(-)$1	1	82	86	11.9999
((((	chr5:79746271-79746491(+)$1	1	70	74	11.9999
)).)	chr17:33690048-33690275(-)$1	1	214	218	11.9999
....	chr19:9676517-9676752(-)$1	1	135	139	11.9999
..((	chr5:71493072-71493306(+)$1	1	19	23	11.9999
))).	chr4:13582667-13582887(-)$1	1	56	60	11.9999

#PSSM
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO1234_Hafner2010a_hg19_CDS_m2_run1.nuc.txt

#NT
CCU	chr16:71784056-71784307(-)$1	251	64	67	9.0000
CCU	chr1:114449602-114449827(+)$1	225	38	41	9.0000
CCU	chr14:45579816-45580053(+)$1	237	155	158	9.0000
CCU	chr8:124359237-124359459(-)$1	222	4	7	9.0000
CCU	chr11:14907301-14907540(-)$1	239	145	148	9.0000
CCU	chr4:73944460-73944689(-)$1	229	2	5	9.0000
CCU	chr19:1612174-1612402(-)$1	228	6	9	9.0000
CCU	chr20:54978539-54978796(+)$1	257	117	120	9.0000
CCU	chr1:110173519-110173745(+)$1	226	18	21	9.0000
CCU	chr20:31954623-31954847(-)$1	224	145	148	9.0000
CCU	chr12:6631058-6631303(+)$1	245	3	6	9.0000
CCU	chr19:58087152-58087389(-)$1	237	44	47	9.0000
CCU	chrX:135581697-135581941(+)$1	244	170	173	9.0000
CCU	chr3:113522406-113522626(+)$1	220	85	88	9.0000
CCU	chr13:53048934-53049176(+)$1	242	228	231	9.0000
ccu	chr12:57167526-57167750(+)$1	224	0	3	9.0000
ccu	chr4:146085249-146085473(-)$1	224	15	18	9.0000
CCU	chr1:245019262-245019490(-)$1	228	23	26	9.0000
CCU	chr10:65357718-65357948(+)$1	230	71	74	9.0000
CCU	chr19:40478309-40478558(+)$1	249	31	34	9.0000
ccu	chr14:93649911-93650132(-)$1	221	7	10	9.0000
CCU	chr1:109766503-109766749(+)$1	246	3	6	9.0000
CCU	chr4:88370245-88370471(+)$1	226	85	88	9.0000
CCU	chr9:132396341-132396568(+)$1	227	16	19	9.0000
CCU	chr8:144899402-144899643(-)$1	241	39	42	9.0000
CCU	chr19:9676758-9677005(-)$1	247	7	10	9.0000
CCU	chr18:48703616-48703841(-)$1	225	19	22	9.0000
CCU	chr12:109536893-109537115(+)$1	222	167	170	9.0000
CCU	chr12:57626212-57626438(+)$1	226	34	37	9.0000
CCU	chr1:94639725-94639964(-)$1	239	20	23	9.0000
CCU	chr1:15987236-15987458(+)$1	222	12	15	9.0000
CCU	chr18:43669440-43669681(-)$1	241	40	43	9.0000
CCU	chr1:54273302-54273542(-)$1	240	44	47	9.0000
CCU	chr2:69642229-69642464(-)$1	235	16	19	9.0000
CCU	chr12:14650755-14650988(+)$1	233	67	70	9.0000
CCU	chr11:19258796-19259028(-)$1	232	2	5	9.0000
CCU	chr5:137502242-137502482(-)$1	240	50	53	9.0000
CCU	chr1:109957858-109958080(-)$1	222	60	63	9.0000
CCU	chr5:64867699-64867928(+)$1	229	117	120	9.0000
CCU	chr19:47342645-47342865(-)$1	220	14	17	9.0000
CCU	chr5:33455041-33455276(+)$1	235	118	121	9.0000
ccu	chr16:2818113-2818335(+)$1	222	13	16	9.0000
CCU	chr10:70098237-70098463(+)$1	226	1	4	9.0000
CCU	chr12:50482212-50482435(+)$1	223	16	19	9.0000
CCU	chr16:2811547-2811796(+)$1	249	29	32	9.0000
CCU	chr16:57286061-57286291(+)$1	230	120	123	9.0000
CCU	chr7:139315868-139316093(-)$1	225	34	37	9.0000
CCU	chr17:74035829-74036056(-)$1	227	42	45	9.0000
CCU	chr5:169021100-169021323(+)$1	223	22	25	9.0000
CCU	chr11:46774855-46775082(-)$1	227	7	10	9.0000
CCU	chr11:118343597-118343819(+)$1	222	0	3	9.0000
CCU	chr20:32664457-32664691(+)$1	234	5	8	9.0000
CCU	chr11:46784460-46784681(-)$1	221	14	17	9.0000
CCU	chr12:48442634-48442869(-)$1	235	30	33	9.0000
CCU	chrX:100667652-100667884(+)$1	232	27	30	9.0000
CCU	chr5:98231899-98232130(-)$1	231	17	20	9.0000
CCU	chr12:57037086-57037345(-)$1	259	151	154	9.0000
CCU	chr4:44700577-44700815(+)$1	238	226	229	9.0000
CCU	chr3:184039089-184039329(+)$1	240	24	27	9.0000
CCU	chr19:8921880-8922132(-)$1	252	6	9	9.0000
CCU	chr7:43917800-43918027(-)$1	227	29	32	9.0000
CCU	chr7:150554566-150554786(+)$1	220	31	34	9.0000
CCU	chr10:15255548-15255772(-)$1	224	74	77	9.0000
CCU	chr22:24236602-24236825(+)$1	223	26	29	9.0000
ccu	chr19:39191580-39191822(+)$1	242	2	5	9.0000
CCU	chr17:7144097-7144322(-)$1	225	118	121	9.0000
CCU	chr17:57758608-57758837(+)$1	229	59	62	9.0000
CCU	chr5:37333548-37333774(-)$1	226	64	67	9.0000
CCU	chr17:27085485-27085714(-)$1	229	12	15	9.0000
CCU	chr9:112018616-112018851(-)$1	235	29	32	9.0000
CCU	chr17:47115601-47115831(+)$1	230	13	16	9.0000
CCU	chr3:154017562-154017805(-)$1	243	60	63	9.0000
CCU	chr20:34213984-34214239(-)$1	255	39	42	9.0000
CCU	chr17:31094648-31094870(-)$1	222	14	17	9.0000
CCU	chr11:66392132-66392354(+)$1	222	26	29	9.0000
CCU	chr1:150129043-150129284(+)$1	241	20	23	9.0000
CCU	chr10:79785302-79785521(-)$1	219	35	38	9.0000
CCU	chr2:54028782-54029010(+)$1	228	55	58	9.0000
CCU	chr13:50306432-50306700(-)$1	268	12	15	9.0000
CCU	chr17:48222479-48222702(-)$1	223	13	16	9.0000
CCU	chr11:47828521-47828749(-)$1	228	44	47	9.0000
CCU	chr1:111494979-111495209(-)$1	230	160	163	9.0000
CCU	chr6:42986054-42986302(+)$1	248	15	18	9.0000
CCU	chr19:44680482-44680702(+)$1	220	16	19	9.0000
CCU	chr17:42426773-42426999(+)$1	226	7	10	9.0000
CCU	chr12:123751697-123751920(-)$1	223	2	5	9.0000
CCU	chr5:176637503-176637727(+)$1	224	0	3	9.0000
CCU	chrX:40999821-41000051(+)$1	230	43	46	9.0000
CCU	chr19:44242215-44242444(-)$1	229	17	20	9.0000
CCU	chr17:80041348-80041570(-)$1	222	40	43	9.0000
CCU	chr5:894853-895081(+)$1	228	72	75	9.0000
CCU	chr8:17089876-17090099(-)$1	223	6	9	9.0000
CCU	chr7:102988041-102988291(+)$1	250	128	131	9.0000
CCU	chr2:114482872-114483118(-)$1	246	125	128	9.0000
CCU	chr3:194151821-194152045(-)$1	224	56	59	9.0000
CCU	chr17:37359199-37359430(+)$1	231	3	6	9.0000
CCU	chr12:112470971-112471198(-)$1	227	18	21	9.0000

#otherMatches

#Struct PSSM
ddd	chr12:2983262-2983487(-)$1	225	163	166	9.0000
)))	chr16:71784056-71784307(-)$1	251	64	67	9.0000
{DD	chr1:114449602-114449827(+)$1	225	38	41	9.0000
nnc	chr14:45579816-45580053(+)$1	237	155	158	9.0000
::g	chr8:124359237-124359459(-)$1	222	4	7	9.0000
ddd	chr11:14907301-14907540(-)$1	239	145	148	9.0000
GGG	chr4:73944460-73944689(-)$1	229	2	5	9.0000
:::	chr19:1612174-1612402(-)$1	228	6	9	9.0000
abb	chr20:54978539-54978796(+)$1	257	117	120	9.0000
:EE	chr1:110173519-110173745(+)$1	226	18	21	9.0000
b""	chr20:31954623-31954847(-)$1	224	145	148	9.0000
EE{	chr12:6631058-6631303(+)$1	245	3	6	9.0000
:::	chr19:58087152-58087389(-)$1	237	44	47	9.0000
mcc	chrX:135581697-135581941(+)$1	244	170	173	9.0000
:::	chr3:113522406-113522626(+)$1	220	85	88	9.0000
@II	chr13:53048934-53049176(+)$1	242	228	231	9.0000
::e	chr12:57167526-57167750(+)$1	224	0	3	9.0000
ccc	chr4:146085249-146085473(-)$1	224	15	18	9.0000
ffm	chr1:245019262-245019490(-)$1	228	23	26	9.0000
6dd	chr10:65357718-65357948(+)$1	230	71	74	9.0000
ccc	chr19:40478309-40478558(+)$1	249	31	34	9.0000
ggg	chr14:93649911-93650132(-)$1	221	7	10	9.0000
iii	chr1:109766503-109766749(+)$1	246	3	6	9.0000
ddd	chr4:88370245-88370471(+)$1	226	85	88	9.0000
fff	chr9:132396341-132396568(+)$1	227	16	19	9.0000
"ee	chr8:144899402-144899643(-)$1	241	39	42	9.0000
cc:	chr19:9676758-9677005(-)$1	247	7	10	9.0000
===	chr18:48703616-48703841(-)$1	225	19	22	9.0000
ooo	chr12:109536893-109537115(+)$1	222	167	170	9.0000
c66	chr12:57626212-57626438(+)$1	226	34	37	9.0000
[bb	chr1:94639725-94639964(-)$1	239	20	23	9.0000
zzz	chr1:15987236-15987458(+)$1	222	12	15	9.0000
II:	chr18:43669440-43669681(-)$1	241	40	43	9.0000
ccm	chr1:54273302-54273542(-)$1	240	44	47	9.0000
ee:	chr2:69642229-69642464(-)$1	235	16	19	9.0000
mmm	chr12:14650755-14650988(+)$1	233	67	70	9.0000
eee	chr11:19258796-19259028(-)$1	232	2	5	9.0000
fff	chr5:137502242-137502482(-)$1	240	50	53	9.0000
ccp	chr1:109957858-109958080(-)$1	222	60	63	9.0000
::c	chr5:64867699-64867928(+)$1	229	117	120	9.0000
HHH	chr19:47342645-47342865(-)$1	220	14	17	9.0000
HHH	chr5:33455041-33455276(+)$1	235	118	121	9.0000
qqq	chr16:2818113-2818335(+)$1	222	13	16	9.0000
DDD	chr10:70098237-70098463(+)$1	226	1	4	9.0000
{CC	chr12:50482212-50482435(+)$1	223	16	19	9.0000
:::	chr16:2811547-2811796(+)$1	249	29	32	9.0000
GGY	chr16:57286061-57286291(+)$1	230	120	123	9.0000
hhh	chr7:139315868-139316093(-)$1	225	34	37	9.0000
eel	chr17:74035829-74036056(-)$1	227	42	45	9.0000
DHH	chr5:169021100-169021323(+)$1	223	22	25	9.0000
EEE	chr11:46774855-46775082(-)$1	227	7	10	9.0000
:::	chr11:118343597-118343819(+)$1	222	0	3	9.0000
:::	chr20:32664457-32664691(+)$1	234	5	8	9.0000
PHH	chr11:46784460-46784681(-)$1	221	14	17	9.0000
HHH	chr12:48442634-48442869(-)$1	235	30	33	9.0000
JJJ	chrX:100667652-100667884(+)$1	232	27	30	9.0000
BBc	chr5:98231899-98232130(-)$1	231	17	20	9.0000
ddd	chr12:57037086-57037345(-)$1	259	151	154	9.0000
III	chr4:44700577-44700815(+)$1	238	226	229	9.0000
ggg	chr3:184039089-184039329(+)$1	240	24	27	9.0000
:::	chr19:8921880-8922132(-)$1	252	6	9	9.0000
JOO	chr7:43917800-43918027(-)$1	227	29	32	9.0000
hhh	chr7:150554566-150554786(+)$1	220	31	34	9.0000
:::	chr10:15255548-15255772(-)$1	224	74	77	9.0000
cc]	chr22:24236602-24236825(+)$1	223	26	29	9.0000
FFF	chr19:39191580-39191822(+)$1	242	2	5	9.0000
mmm	chr17:7144097-7144322(-)$1	225	118	121	9.0000
^^^	chr17:57758608-57758837(+)$1	229	59	62	9.0000
bba	chr5:37333548-37333774(-)$1	226	64	67	9.0000
FFF	chr17:27085485-27085714(-)$1	229	12	15	9.0000
dd!	chr9:112018616-112018851(-)$1	235	29	32	9.0000
GGG	chr17:47115601-47115831(+)$1	230	13	16	9.0000
eee	chr3:154017562-154017805(-)$1	243	60	63	9.0000
ccc	chr20:34213984-34214239(-)$1	255	39	42	9.0000
OOO	chr17:31094648-31094870(-)$1	222	14	17	9.0000
bqq	chr11:66392132-66392354(+)$1	222	26	29	9.0000
eee	chr1:150129043-150129284(+)$1	241	20	23	9.0000
JJJ	chr10:79785302-79785521(-)$1	219	35	38	9.0000
ccc	chr2:54028782-54029010(+)$1	228	55	58	9.0000
KKJ	chr13:50306432-50306700(-)$1	268	12	15	9.0000
fff	chr17:48222479-48222702(-)$1	223	13	16	9.0000
ddd	chr11:47828521-47828749(-)$1	228	44	47	9.0000
44c	chr1:111494979-111495209(-)$1	230	160	163	9.0000
MMM	chr6:42986054-42986302(+)$1	248	15	18	9.0000
fff	chr19:44680482-44680702(+)$1	220	16	19	9.0000
ddd	chr17:42426773-42426999(+)$1	226	7	10	9.0000
bb[	chr12:123751697-123751920(-)$1	223	2	5	9.0000
:::	chr5:176637503-176637727(+)$1	224	0	3	9.0000
rrr	chrX:40999821-41000051(+)$1	230	43	46	9.0000
]bb	chr19:44242215-44242444(-)$1	229	17	20	9.0000
bb:	chr17:80041348-80041570(-)$1	222	40	43	9.0000
d:e	chr5:894853-895081(+)$1	228	72	75	9.0000
:::	chr8:17089876-17090099(-)$1	223	6	9	9.0000
f22	chr7:102988041-102988291(+)$1	250	128	131	9.0000
b]g	chr2:114482872-114483118(-)$1	246	125	128	9.0000
B::	chr3:194151821-194152045(-)$1	224	56	59	9.0000
:II	chr17:37359199-37359430(+)$1	231	3	6	9.0000
b!!	chr12:112470971-112471198(-)$1	227	18	21	9.0000

#DB
(((	chr12:2983262-2983487(-)$1	1	163	166	9.0000
...	chr16:71784056-71784307(-)$1	1	64	67	9.0000
.((	chr1:114449602-114449827(+)$1	1	38	41	9.0000
..)	chr14:45579816-45580053(+)$1	1	155	158	9.0000
..(	chr8:124359237-124359459(-)$1	1	4	7	9.0000
)))	chr11:14907301-14907540(-)$1	1	145	148	9.0000
(((	chr4:73944460-73944689(-)$1	1	2	5	9.0000
...	chr19:1612174-1612402(-)$1	1	6	9	9.0000
)))	chr20:54978539-54978796(+)$1	1	117	120	9.0000
.((	chr1:110173519-110173745(+)$1	1	18	21	9.0000
(..	chr20:31954623-31954847(-)$1	1	145	148	9.0000
((.	chr12:6631058-6631303(+)$1	1	3	6	9.0000
...	chr19:58087152-58087389(-)$1	1	44	47	9.0000
.))	chrX:135581697-135581941(+)$1	1	170	173	9.0000
...	chr3:113522406-113522626(+)$1	1	85	88	9.0000
.))	chr13:53048934-53049176(+)$1	1	228	231	9.0000
..(	chr12:57167526-57167750(+)$1	1	0	3	9.0000
)((	chr4:146085249-146085473(-)$1	1	15	18	9.0000
((.	chr1:245019262-245019490(-)$1	1	23	26	9.0000
.))	chr10:65357718-65357948(+)$1	1	71	74	9.0000
(((	chr19:40478309-40478558(+)$1	1	31	34	9.0000
(((	chr14:93649911-93650132(-)$1	1	7	10	9.0000
(((	chr1:109766503-109766749(+)$1	1	3	6	9.0000
(((	chr4:88370245-88370471(+)$1	1	85	88	9.0000
)))	chr9:132396341-132396568(+)$1	1	16	19	9.0000
.((	chr8:144899402-144899643(-)$1	1	39	42	9.0000
)).	chr19:9676758-9677005(-)$1	1	7	10	9.0000
(((	chr18:48703616-48703841(-)$1	1	19	22	9.0000
...	chr12:109536893-109537115(+)$1	1	167	170	9.0000
)..	chr12:57626212-57626438(+)$1	1	34	37	9.0000
.((	chr1:94639725-94639964(-)$1	1	20	23	9.0000
...	chr1:15987236-15987458(+)$1	1	12	15	9.0000
((.	chr18:43669440-43669681(-)$1	1	40	43	9.0000
((.	chr1:54273302-54273542(-)$1	1	44	47	9.0000
)).	chr2:69642229-69642464(-)$1	1	16	19	9.0000
...	chr12:14650755-14650988(+)$1	1	67	70	9.0000
(((	chr11:19258796-19259028(-)$1	1	2	5	9.0000
(((	chr5:137502242-137502482(-)$1	1	50	53	9.0000
((.	chr1:109957858-109958080(-)$1	1	60	63	9.0000
..(	chr5:64867699-64867928(+)$1	1	117	120	9.0000
(((	chr19:47342645-47342865(-)$1	1	14	17	9.0000
)))	chr5:33455041-33455276(+)$1	1	118	121	9.0000
...	chr16:2818113-2818335(+)$1	1	13	16	9.0000
(((	chr10:70098237-70098463(+)$1	1	1	4	9.0000
.((	chr12:50482212-50482435(+)$1	1	16	19	9.0000
...	chr16:2811547-2811796(+)$1	1	29	32	9.0000
)).	chr16:57286061-57286291(+)$1	1	120	123	9.0000
(((	chr7:139315868-139316093(-)$1	1	34	37	9.0000
((.	chr17:74035829-74036056(-)$1	1	42	45	9.0000
(((	chr5:169021100-169021323(+)$1	1	22	25	9.0000
(((	chr11:46774855-46775082(-)$1	1	7	10	9.0000
...	chr11:118343597-118343819(+)$1	1	0	3	9.0000
...	chr20:32664457-32664691(+)$1	1	5	8	9.0000
.((	chr11:46784460-46784681(-)$1	1	14	17	9.0000
(((	chr12:48442634-48442869(-)$1	1	30	33	9.0000
(((	chrX:100667652-100667884(+)$1	1	27	30	9.0000
(((	chr5:98231899-98232130(-)$1	1	17	20	9.0000
(((	chr12:57037086-57037345(-)$1	1	151	154	9.0000
)))	chr4:44700577-44700815(+)$1	1	226	229	9.0000
)))	chr3:184039089-184039329(+)$1	1	24	27	9.0000
...	chr19:8921880-8922132(-)$1	1	6	9	9.0000
(..	chr7:43917800-43918027(-)$1	1	29	32	9.0000
(((	chr7:150554566-150554786(+)$1	1	31	34	9.0000
...	chr10:15255548-15255772(-)$1	1	74	77	9.0000
)).	chr22:24236602-24236825(+)$1	1	26	29	9.0000
(((	chr19:39191580-39191822(+)$1	1	2	5	9.0000
...	chr17:7144097-7144322(-)$1	1	118	121	9.0000
...	chr17:57758608-57758837(+)$1	1	59	62	9.0000
)))	chr5:37333548-37333774(-)$1	1	64	67	9.0000
(((	chr17:27085485-27085714(-)$1	1	12	15	9.0000
((.	chr9:112018616-112018851(-)$1	1	29	32	9.0000
(((	chr17:47115601-47115831(+)$1	1	13	16	9.0000
(((	chr3:154017562-154017805(-)$1	1	60	63	9.0000
(((	chr20:34213984-34214239(-)$1	1	39	42	9.0000
...	chr17:31094648-31094870(-)$1	1	14	17	9.0000
(..	chr11:66392132-66392354(+)$1	1	26	29	9.0000
)))	chr1:150129043-150129284(+)$1	1	20	23	9.0000
(((	chr10:79785302-79785521(-)$1	1	35	38	9.0000
(((	chr2:54028782-54029010(+)$1	1	55	58	9.0000
..(	chr13:50306432-50306700(-)$1	1	12	15	9.0000
)))	chr17:48222479-48222702(-)$1	1	13	16	9.0000
(((	chr11:47828521-47828749(-)$1	1	44	47	9.0000
..)	chr1:111494979-111495209(-)$1	1	160	163	9.0000
...	chr6:42986054-42986302(+)$1	1	15	18	9.0000
(((	chr19:44680482-44680702(+)$1	1	16	19	9.0000
(((	chr17:42426773-42426999(+)$1	1	7	10	9.0000
((.	chr12:123751697-123751920(-)$1	1	2	5	9.0000
...	chr5:176637503-176637727(+)$1	1	0	3	9.0000
...	chrX:40999821-41000051(+)$1	1	43	46	9.0000
.))	chr19:44242215-44242444(-)$1	1	17	20	9.0000
)).	chr17:80041348-80041570(-)$1	1	40	43	9.0000
).(	chr5:894853-895081(+)$1	1	72	75	9.0000
...	chr8:17089876-17090099(-)$1	1	6	9	9.0000
)..	chr7:102988041-102988291(+)$1	1	128	131	9.0000
).)	chr2:114482872-114483118(-)$1	1	125	128	9.0000
(..	chr3:194151821-194152045(-)$1	1	56	59	9.0000
.((	chr17:37359199-37359430(+)$1	1	3	6	9.0000
(..	chr12:112470971-112471198(-)$1	1	18	21	9.0000

#PSSM
C : 0.94	c : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_CDS_m2_run1.nuc.txt

#NT
GGA	chr7:102988036-102988261(+)$1	225	40	43	8.9999
GGA	chr15:63433779-63434004(+)$1	225	39	42	8.9999
GGA	chr16:31927655-31927875(+)$1	220	34	37	8.9999
GGA	chr6:43322490-43322711(-)$1	221	98	101	8.9999
GGA	chr11:71718135-71718358(-)$1	223	2	5	8.9999
GGA	chr1:156290699-156290916(-)$1	217	208	211	8.9999
GGA	chr4:128910811-128911029(+)$1	218	97	100	8.9999
GGA	chr2:44204274-44204496(-)$1	222	34	37	8.9999
GGA	chr5:74484332-74484562(-)$1	230	131	134	8.9999
GGA	chr12:27654818-27655044(+)$1	226	36	39	8.9999
GGA	chr16:66836878-66837103(-)$1	225	81	84	8.9999
GGA	chr7:77423317-77423537(-)$1	220	54	57	8.9999
GGA	chr22:30734747-30734966(-)$1	219	14	17	8.9999
GGA	chr17:41577321-41577549(+)$1	228	64	67	8.9999
GGA	chr3:182576887-182577117(+)$1	230	161	164	8.9999
GGA	chr3:69096755-69096976(-)$1	221	130	133	8.9999
GGA	chr3:142753682-142753906(+)$1	224	0	3	8.9999
GGA	chr17:45742393-45742625(+)$1	232	41	44	8.9999
GGA	chr1:152006072-152006292(-)$1	220	88	91	8.9999
GGA	chr17:61498644-61498874(+)$1	230	122	125	8.9999
GGA	chr8:126071587-126071817(-)$1	230	53	56	8.9999
GGA	chr12:12483128-12483351(-)$1	223	27	30	8.9999
GGA	chr3:136085688-136085907(-)$1	219	34	37	8.9999
GGA	chr8:101299957-101300187(-)$1	230	2	5	8.9999
GGA	chrX:53658436-53658666(-)$1	230	29	32	8.9999
GGA	chr12:124870239-124870459(-)$1	220	33	36	8.9999
GGA	chr10:81111998-81112211(+)$1	213	176	179	8.9999
GGA	chr19:37488135-37488351(-)$1	216	129	132	8.9999
GGA	chr4:128715138-128715355(+)$1	217	24	27	8.9999
GGA	chr12:49883230-49883452(+)$1	222	97	100	8.9999
GGA	chr2:201846299-201846523(-)$1	224	25	28	8.9999
GGA	chr12:89864046-89864264(-)$1	218	4	7	8.9999
GGA	chr19:44738779-44739020(+)$1	241	97	100	8.9999
GGA	chr4:151849652-151849868(-)$1	216	120	123	8.9999
GGA	chr16:23096111-23096334(-)$1	223	42	45	8.9999
GGA	chr9:123955550-123955772(-)$1	222	2	5	8.9999
GGA	chrX:30872503-30872733(-)$1	230	81	84	8.9999
GGA	chr16:24816318-24816538(+)$1	220	43	46	8.9999
GGA	chr9:134405773-134405991(-)$1	218	6	9	8.9999
GGA	chr1:115275139-115275362(-)$1	223	20	23	8.9999
GGA	chr7:2414995-2415221(+)$1	226	52	55	8.9999
GGA	chr19:44237413-44237638(-)$1	225	33	36	8.9999
GGA	chr18:13742428-13742650(+)$1	222	43	46	8.9999
GGA	chr10:104128031-104128249(+)$1	218	2	5	8.9999
GGA	chr5:94813902-94814119(-)$1	217	0	3	8.9999
GGA	chr17:5336316-5336541(-)$1	225	77	80	8.9999
GGA	chr11:3781724-3781945(-)$1	221	122	125	8.9999
GGA	chr7:92163736-92163965(+)$1	229	28	31	8.9999
GGA	chr9:35068220-35068445(-)$1	225	53	56	8.9999
GGA	chr1:90400655-90400875(+)$1	220	95	98	8.9999
GGA	chr5:173317092-173317318(+)$1	226	3	6	8.9999
GGA	chr2:202151191-202151410(+)$1	219	44	47	8.9999
GGA	chr11:3038237-3038468(-)$1	231	9	12	8.9999
GGA	chr2:219510907-219511126(-)$1	219	146	149	8.9999
GGA	chr17:46998438-46998668(+)$1	230	54	57	8.9999
GGA	chr9:2097303-2097523(+)$1	220	19	22	8.9999
GGA	chr12:133778699-133778925(+)$1	226	39	42	8.9999
GGA	chr3:69220932-69221154(-)$1	222	46	49	8.9999
GGA	chr12:53696787-53697013(+)$1	226	65	68	8.9999
GGA	chr14:60585045-60585265(+)$1	220	77	80	8.9999
GGA	chrX:117530905-117531145(+)$1	240	26	29	8.9999
GGA	chr2:219114040-219114287(+)$1	247	113	116	8.9999
GGA	chr5:173382910-173383131(+)$1	221	4	7	8.9999
GGA	chrX:110970078-110970300(+)$1	222	12	15	8.9999
GGA	chrX:70282673-70282899(-)$1	226	17	20	8.9999
GGA	chr11:125466871-125467101(+)$1	230	180	183	8.9999
GGA	chr16:11940577-11940800(-)$1	223	2	5	8.9999
GGA	chr5:112871320-112871546(+)$1	226	17	20	8.9999
GGA	chr1:42693508-42693734(-)$1	226	25	28	8.9999
GGA	chr6:28200808-28201038(+)$1	230	48	51	8.9999
GGA	chr7:38805121-38805351(-)$1	230	4	7	8.9999
GGA	chr3:184018058-184018272(+)$1	214	8	11	8.9999
GGA	chr3:170078378-170078603(+)$1	225	47	50	8.9999
GGA	chr11:6630739-6630962(+)$1	223	2	5	8.9999
GGA	chr8:91054893-91055123(+)$1	230	90	93	8.9999
GGA	chr8:11667167-11667398(+)$1	231	47	50	8.9999
GGA	chr3:52014752-52014973(+)$1	221	8	11	8.9999
GGA	chrX:51640791-51641021(+)$1	230	4	7	8.9999
GGA	chr14:78182070-78182296(+)$1	226	43	46	8.9999
GGA	chr7:77423344-77423581(-)$1	237	18	21	8.9999
GGA	chr8:38187192-38187422(-)$1	230	15	18	8.9999
GGA	chr7:92764240-92764462(-)$1	222	32	35	8.9999
GGA	chr22:21354362-21354585(-)$1	223	153	156	8.9999
GGA	chr6:42179511-42179733(-)$1	222	43	46	8.9999
GGA	chr19:2207545-2207765(+)$1	220	52	55	8.9999
GGA	chr12:64587695-64587915(-)$1	220	62	65	8.9999
GGA	chr6:109319799-109320021(-)$1	222	63	66	8.9999
GGA	chr1:161761903-161762133(+)$1	230	15	18	8.9999
GGA	chr10:111879179-111879409(+)$1	230	57	60	8.9999
GGA	chr10:52103341-52103562(-)$1	221	4	7	8.9999
GGA	chr3:107517315-107517547(+)$1	232	82	85	8.9999
GGA	chr8:26218454-26218684(+)$1	230	55	58	8.9999
GGA	chr7:23017860-23018079(-)$1	219	57	60	8.9999
GGA	chr12:16507082-16507304(+)$1	222	127	130	8.9999
GGA	chr6:146121139-146121360(-)$1	221	25	28	8.9999
GGA	chr12:25398128-25398358(-)$1	230	67	70	8.9999
GGA	chr9:136230401-136230627(-)$1	226	116	119	8.9999
GGA	chr8:117869451-117869681(-)$1	230	21	24	8.9999

#otherMatches

#Struct PSSM
eev	chr12:12673723-12673944(-)$1	221	16	19	8.9999
^^^	chr7:102988036-102988261(+)$1	225	40	43	8.9999
hhh	chr15:63433779-63434004(+)$1	225	39	42	8.9999
!ab	chr16:31927655-31927875(+)$1	220	34	37	8.9999
ee:	chr6:43322490-43322711(-)$1	221	98	101	8.9999
fff	chr11:71718135-71718358(-)$1	223	2	5	8.9999
eee	chr1:156290699-156290916(-)$1	217	208	211	8.9999
ddw	chr4:128910811-128911029(+)$1	218	97	100	8.9999
bbm	chr2:44204274-44204496(-)$1	222	34	37	8.9999
>>d	chr5:74484332-74484562(-)$1	230	131	134	8.9999
EEL	chr12:27654818-27655044(+)$1	226	36	39	8.9999
"dd	chr16:66836878-66837103(-)$1	225	81	84	8.9999
bb]	chr7:77423317-77423537(-)$1	220	54	57	8.9999
FF{	chr22:30734747-30734966(-)$1	219	14	17	8.9999
cc]	chr17:41577321-41577549(+)$1	228	64	67	8.9999
fff	chr3:182576887-182577117(+)$1	230	161	164	8.9999
:DD	chr3:69096755-69096976(-)$1	221	130	133	8.9999
ggg	chr3:142753682-142753906(+)$1	224	0	3	8.9999
qqq	chr17:45742393-45742625(+)$1	232	41	44	8.9999
eee	chr1:152006072-152006292(-)$1	220	88	91	8.9999
FFF	chr17:61498644-61498874(+)$1	230	122	125	8.9999
fff	chr8:126071587-126071817(-)$1	230	53	56	8.9999
a22	chr12:12483128-12483351(-)$1	223	27	30	8.9999
dd2	chr3:136085688-136085907(-)$1	219	34	37	8.9999
:::	chr8:101299957-101300187(-)$1	230	2	5	8.9999
bb:	chrX:53658436-53658666(-)$1	230	29	32	8.9999
d::	chr12:124870239-124870459(-)$1	220	33	36	8.9999
FFF	chr10:81111998-81112211(+)$1	213	176	179	8.9999
ggg	chr19:37488135-37488351(-)$1	216	129	132	8.9999
DKK	chr4:128715138-128715355(+)$1	217	24	27	8.9999
]a]	chr12:49883230-49883452(+)$1	222	97	100	8.9999
bbo	chr2:201846299-201846523(-)$1	224	25	28	8.9999
hhh	chr12:89864046-89864264(-)$1	218	4	7	8.9999
d::	chr19:44738779-44739020(+)$1	241	97	100	8.9999
eee	chr4:151849652-151849868(-)$1	216	120	123	8.9999
[ee	chr16:23096111-23096334(-)$1	223	42	45	8.9999
ddd	chr9:123955550-123955772(-)$1	222	2	5	8.9999
eee	chrX:30872503-30872733(-)$1	230	81	84	8.9999
eoo	chr16:24816318-24816538(+)$1	220	43	46	8.9999
BBK	chr9:134405773-134405991(-)$1	218	6	9	8.9999
GGG	chr1:115275139-115275362(-)$1	223	20	23	8.9999
gg#	chr7:2414995-2415221(+)$1	226	52	55	8.9999
[dd	chr19:44237413-44237638(-)$1	225	33	36	8.9999
III	chr18:13742428-13742650(+)$1	222	43	46	8.9999
DD:	chr10:104128031-104128249(+)$1	218	2	5	8.9999
:EE	chr5:94813902-94814119(-)$1	217	0	3	8.9999
bb:	chr17:5336316-5336541(-)$1	225	77	80	8.9999
:dd	chr11:3781724-3781945(-)$1	221	122	125	8.9999
DDD	chr7:92163736-92163965(+)$1	229	28	31	8.9999
eee	chr9:35068220-35068445(-)$1	225	53	56	8.9999
fff	chr1:90400655-90400875(+)$1	220	95	98	8.9999
eee	chr5:173317092-173317318(+)$1	226	3	6	8.9999
fff	chr2:202151191-202151410(+)$1	219	44	47	8.9999
DDK	chr11:3038237-3038468(-)$1	231	9	12	8.9999
bb]	chr2:219510907-219511126(-)$1	219	146	149	8.9999
hhh	chr17:46998438-46998668(+)$1	230	54	57	8.9999
bb[	chr9:2097303-2097523(+)$1	220	19	22	8.9999
iii	chr12:133778699-133778925(+)$1	226	39	42	8.9999
cpp	chr3:69220932-69221154(-)$1	222	46	49	8.9999
cc]	chr12:53696787-53697013(+)$1	226	65	68	8.9999
fff	chr14:60585045-60585265(+)$1	220	77	80	8.9999
CJJ	chrX:117530905-117531145(+)$1	240	26	29	8.9999
FFF	chr2:219114040-219114287(+)$1	247	113	116	8.9999
FFF	chr5:173382910-173383131(+)$1	221	4	7	8.9999
EEK	chrX:110970078-110970300(+)$1	222	12	15	8.9999
::g	chrX:70282673-70282899(-)$1	226	17	20	8.9999
ccc	chr11:125466871-125467101(+)$1	230	180	183	8.9999
dd[	chr16:11940577-11940800(-)$1	223	2	5	8.9999
fff	chr5:112871320-112871546(+)$1	226	17	20	8.9999
eee	chr1:42693508-42693734(-)$1	226	25	28	8.9999
bEE	chr6:28200808-28201038(+)$1	230	48	51	8.9999
EEM	chr7:38805121-38805351(-)$1	230	4	7	8.9999
dd[	chr3:184018058-184018272(+)$1	214	8	11	8.9999
nnn	chr3:170078378-170078603(+)$1	225	47	50	8.9999
DDD	chr11:6630739-6630962(+)$1	223	2	5	8.9999
rrr	chr8:91054893-91055123(+)$1	230	90	93	8.9999
ccc	chr8:11667167-11667398(+)$1	231	47	50	8.9999
fff	chr3:52014752-52014973(+)$1	221	8	11	8.9999
HHH	chrX:51640791-51641021(+)$1	230	4	7	8.9999
eee	chr14:78182070-78182296(+)$1	226	43	46	8.9999
eee	chr7:77423344-77423581(-)$1	237	18	21	8.9999
ddn	chr8:38187192-38187422(-)$1	230	15	18	8.9999
[dd	chr7:92764240-92764462(-)$1	222	32	35	8.9999
bbc	chr22:21354362-21354585(-)$1	223	153	156	8.9999
EE:	chr6:42179511-42179733(-)$1	222	43	46	8.9999
EEE	chr19:2207545-2207765(+)$1	220	52	55	8.9999
ggg	chr12:64587695-64587915(-)$1	220	62	65	8.9999
iii	chr6:109319799-109320021(-)$1	222	63	66	8.9999
ddd	chr1:161761903-161762133(+)$1	230	15	18	8.9999
ccc	chr10:111879179-111879409(+)$1	230	57	60	8.9999
bmm	chr10:52103341-52103562(-)$1	221	4	7	8.9999
::e	chr3:107517315-107517547(+)$1	232	82	85	8.9999
"dd	chr8:26218454-26218684(+)$1	230	55	58	8.9999
f!!	chr7:23017860-23018079(-)$1	219	57	60	8.9999
ddd	chr12:16507082-16507304(+)$1	222	127	130	8.9999
ddd	chr6:146121139-146121360(-)$1	221	25	28	8.9999
::e	chr12:25398128-25398358(-)$1	230	67	70	8.9999
bb[	chr9:136230401-136230627(-)$1	226	116	119	8.9999
b[c	chr8:117869451-117869681(-)$1	230	21	24	8.9999

#DB
((.	chr12:12673723-12673944(-)$1	1	16	19	8.9999
...	chr7:102988036-102988261(+)$1	1	40	43	8.9999
(((	chr15:63433779-63434004(+)$1	1	39	42	8.9999
.((	chr16:31927655-31927875(+)$1	1	34	37	8.9999
)).	chr6:43322490-43322711(-)$1	1	98	101	8.9999
(((	chr11:71718135-71718358(-)$1	1	2	5	8.9999
)))	chr1:156290699-156290916(-)$1	1	208	211	8.9999
((.	chr4:128910811-128911029(+)$1	1	97	100	8.9999
((.	chr2:44204274-44204496(-)$1	1	34	37	8.9999
..)	chr5:74484332-74484562(-)$1	1	131	134	8.9999
((.	chr12:27654818-27655044(+)$1	1	36	39	8.9999
.((	chr16:66836878-66837103(-)$1	1	81	84	8.9999
)).	chr7:77423317-77423537(-)$1	1	54	57	8.9999
((.	chr22:30734747-30734966(-)$1	1	14	17	8.9999
)).	chr17:41577321-41577549(+)$1	1	64	67	8.9999
)))	chr3:182576887-182577117(+)$1	1	161	164	8.9999
.))	chr3:69096755-69096976(-)$1	1	130	133	8.9999
(((	chr3:142753682-142753906(+)$1	1	0	3	8.9999
...	chr17:45742393-45742625(+)$1	1	41	44	8.9999
)))	chr1:152006072-152006292(-)$1	1	88	91	8.9999
(((	chr17:61498644-61498874(+)$1	1	122	125	8.9999
)))	chr8:126071587-126071817(-)$1	1	53	56	8.9999
)..	chr12:12483128-12483351(-)$1	1	27	30	8.9999
)).	chr3:136085688-136085907(-)$1	1	34	37	8.9999
...	chr8:101299957-101300187(-)$1	1	2	5	8.9999
)).	chrX:53658436-53658666(-)$1	1	29	32	8.9999
)..	chr12:124870239-124870459(-)$1	1	33	36	8.9999
)))	chr10:81111998-81112211(+)$1	1	176	179	8.9999
)))	chr19:37488135-37488351(-)$1	1	129	132	8.9999
(..	chr4:128715138-128715355(+)$1	1	24	27	8.9999
.).	chr12:49883230-49883452(+)$1	1	97	100	8.9999
((.	chr2:201846299-201846523(-)$1	1	25	28	8.9999
(((	chr12:89864046-89864264(-)$1	1	4	7	8.9999
)..	chr19:44738779-44739020(+)$1	1	97	100	8.9999
(((	chr4:151849652-151849868(-)$1	1	120	123	8.9999
.((	chr16:23096111-23096334(-)$1	1	42	45	8.9999
(((	chr9:123955550-123955772(-)$1	1	2	5	8.9999
(((	chrX:30872503-30872733(-)$1	1	81	84	8.9999
(..	chr16:24816318-24816538(+)$1	1	43	46	8.9999
((.	chr9:134405773-134405991(-)$1	1	6	9	8.9999
(((	chr1:115275139-115275362(-)$1	1	20	23	8.9999
((.	chr7:2414995-2415221(+)$1	1	52	55	8.9999
.((	chr19:44237413-44237638(-)$1	1	33	36	8.9999
(((	chr18:13742428-13742650(+)$1	1	43	46	8.9999
((.	chr10:104128031-104128249(+)$1	1	2	5	8.9999
.((	chr5:94813902-94814119(-)$1	1	0	3	8.9999
)).	chr17:5336316-5336541(-)$1	1	77	80	8.9999
.((	chr11:3781724-3781945(-)$1	1	122	125	8.9999
(((	chr7:92163736-92163965(+)$1	1	28	31	8.9999
(((	chr9:35068220-35068445(-)$1	1	53	56	8.9999
(((	chr1:90400655-90400875(+)$1	1	95	98	8.9999
(((	chr5:173317092-173317318(+)$1	1	3	6	8.9999
)))	chr2:202151191-202151410(+)$1	1	44	47	8.9999
((.	chr11:3038237-3038468(-)$1	1	9	12	8.9999
)).	chr2:219510907-219511126(-)$1	1	146	149	8.9999
(((	chr17:46998438-46998668(+)$1	1	54	57	8.9999
((.	chr9:2097303-2097523(+)$1	1	19	22	8.9999
)))	chr12:133778699-133778925(+)$1	1	39	42	8.9999
(..	chr3:69220932-69221154(-)$1	1	46	49	8.9999
)).	chr12:53696787-53697013(+)$1	1	65	68	8.9999
(((	chr14:60585045-60585265(+)$1	1	77	80	8.9999
(((	chrX:117530905-117531145(+)$1	1	26	29	8.9999
(((	chr2:219114040-219114287(+)$1	1	113	116	8.9999
(((	chr5:173382910-173383131(+)$1	1	4	7	8.9999
((.	chrX:110970078-110970300(+)$1	1	12	15	8.9999
..(	chrX:70282673-70282899(-)$1	1	17	20	8.9999
)))	chr11:125466871-125467101(+)$1	1	180	183	8.9999
((.	chr16:11940577-11940800(-)$1	1	2	5	8.9999
)))	chr5:112871320-112871546(+)$1	1	17	20	8.9999
(((	chr1:42693508-42693734(-)$1	1	25	28	8.9999
)))	chr6:28200808-28201038(+)$1	1	48	51	8.9999
((.	chr7:38805121-38805351(-)$1	1	4	7	8.9999
((.	chr3:184018058-184018272(+)$1	1	8	11	8.9999
...	chr3:170078378-170078603(+)$1	1	47	50	8.9999
(((	chr11:6630739-6630962(+)$1	1	2	5	8.9999
...	chr8:91054893-91055123(+)$1	1	90	93	8.9999
)))	chr8:11667167-11667398(+)$1	1	47	50	8.9999
(((	chr3:52014752-52014973(+)$1	1	8	11	8.9999
(((	chrX:51640791-51641021(+)$1	1	4	7	8.9999
)))	chr14:78182070-78182296(+)$1	1	43	46	8.9999
(((	chr7:77423344-77423581(-)$1	1	18	21	8.9999
((.	chr8:38187192-38187422(-)$1	1	15	18	8.9999
.((	chr7:92764240-92764462(-)$1	1	32	35	8.9999
(((	chr22:21354362-21354585(-)$1	1	153	156	8.9999
((.	chr6:42179511-42179733(-)$1	1	43	46	8.9999
(((	chr19:2207545-2207765(+)$1	1	52	55	8.9999
(((	chr12:64587695-64587915(-)$1	1	62	65	8.9999
(((	chr6:109319799-109320021(-)$1	1	63	66	8.9999
)))	chr1:161761903-161762133(+)$1	1	15	18	8.9999
(((	chr10:111879179-111879409(+)$1	1	57	60	8.9999
(..	chr10:52103341-52103562(-)$1	1	4	7	8.9999
..(	chr3:107517315-107517547(+)$1	1	82	85	8.9999
.((	chr8:26218454-26218684(+)$1	1	55	58	8.9999
(..	chr7:23017860-23018079(-)$1	1	57	60	8.9999
)))	chr12:16507082-16507304(+)$1	1	127	130	8.9999
(((	chr6:146121139-146121360(-)$1	1	25	28	8.9999
..(	chr12:25398128-25398358(-)$1	1	67	70	8.9999
((.	chr9:136230401-136230627(-)$1	1	116	119	8.9999
(.(	chr8:117869451-117869681(-)$1	1	21	24	8.9999

#PSSM
G : 0.99	
G : 0.99	
A : 0.99	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C17ORF85_Baltz2012b_hg19_CDS_m2_run1.nuc.txt

#NT
UCCU	chr17:3721470-3721698(-)$1	228	207	211	11.9999
UCCU	chr12:46760952-46761182(-)$1	230	44	48	11.9999
UCCU	chrX:107976850-107977076(-)$1	226	8	12	11.9999
UCCU	chrM:3397-3627(+)$1	230	214	218	11.9999
UCCU	chr17:3527282-3527515(-)$1	233	86	90	11.9999
UCCU	chr1:32110351-32110572(-)$1	221	118	122	11.9999
UCCU	chr9:134353194-134353421(+)$1	227	150	154	11.9999
UCCU	chr12:4385193-4385423(+)$1	230	80	84	11.9999
UCCU	chr22:39714956-39715186(-)$1	230	9	13	11.9999
UCCU	chr10:121652172-121652403(+)$1	231	15	19	11.9999
UCCU	chr12:56578536-56578772(-)$1	236	18	22	11.9999
UCCU	chr4:56262312-56262575(+)$1	263	3	7	11.9999
uccu	chr12:124156519-124156757(+)$1	238	6	10	11.9999
UCCU	chr17:47119601-47119822(+)$1	221	166	170	11.9999
UCCU	chr2:230675760-230675983(-)$1	223	44	48	11.9999
UCCU	chr8:48690294-48690514(-)$1	220	56	60	11.9999
UCCU	chr11:66136811-66137035(-)$1	224	78	82	11.9999
UCCU	chr1:19426786-19427007(-)$1	221	112	116	11.9999
UCCU	chr9:135525530-135525758(-)$1	228	165	169	11.9999
UCCU	chr13:28854483-28854703(+)$1	220	45	49	11.9999
UCCU	chrM:9804-10067(+)$1	263	43	47	11.9999
UCCU	chr12:62965153-62965375(+)$1	222	29	33	11.9999
UCCU	chr4:108565859-108566088(-)$1	229	13	17	11.9999
UCCU	chr10:102268669-102268890(-)$1	221	38	42	11.9999
UCCU	chr1:162467696-162467920(+)$1	224	190	194	11.9999
UCCU	chr2:44222880-44223123(-)$1	243	113	117	11.9999
UCCU	chr11:65820443-65820672(+)$1	229	37	41	11.9999
UCCU	chr1:241798748-241798969(-)$1	221	69	73	11.9999
UCCU	chr17:41150710-41150943(+)$1	233	39	43	11.9999
UCCU	chr9:135926075-135926298(+)$1	223	63	67	11.9999
UCCU	chr11:47663866-47664093(-)$1	227	101	105	11.9999
UCCU	chr19:36579848-36580070(+)$1	222	77	81	11.9999
UCCU	chr11:62396637-62396867(-)$1	230	58	62	11.9999
uccu	chr3:49155298-49155524(-)$1	226	26	30	11.9999
UCCU	chr11:801432-801668(-)$1	236	14	18	11.9999
UCCU	chr19:42797648-42797871(+)$1	223	172	176	11.9999
UCCU	chrX:70755998-70756256(+)$1	258	49	53	11.9999
UCCU	chr6:88321750-88321975(+)$1	225	107	111	11.9999
UCCU	chr22:35811817-35812051(+)$1	234	104	108	11.9999
UCCU	chr16:58557186-58557413(-)$1	227	180	184	11.9999
UCCU	chr20:43252756-43252979(-)$1	223	142	146	11.9999
UCCU	chr18:33647251-33647480(-)$1	229	62	66	11.9999
UCCU	chr17:58469158-58469385(-)$1	227	113	117	11.9999
UCCU	chr22:50955918-50956155(+)$1	237	52	56	11.9999
UCCU	chr22:22319586-22319820(-)$1	234	35	39	11.9999
UCCU	chr1:120269589-120269822(+)$1	233	14	18	11.9999
UCCU	chr17:61869790-61870010(+)$1	220	32	36	11.9999
UCCU	chr21:37783732-37783956(+)$1	224	111	115	11.9999
UCCU	chr2:20939687-20939909(-)$1	222	78	82	11.9999
UCCU	chr19:10789245-10789471(+)$1	226	175	179	11.9999
UCCU	chr20:47860257-47860487(+)$1	230	60	64	11.9999
UCCU	chr1:97189024-97189246(+)$1	222	16	20	11.9999
UCCU	chr13:111929847-111930070(+)$1	223	145	149	11.9999
UCCU	chr10:91464979-91465204(+)$1	225	195	199	11.9999
UCCU	chr17:62499219-62499440(-)$1	221	61	65	11.9999
UCCU	chr19:1434639-1434880(+)$1	241	157	161	11.9999
UCCU	chr20:2083588-2083848(+)$1	260	84	88	11.9999
UCCU	chr1:203691541-203691763(+)$1	222	49	53	11.9999
uccu	chr8:94805329-94805553(+)$1	224	19	23	11.9999
UCCU	chr8:141595276-141595504(-)$1	228	104	108	11.9999
UCCU	chr13:30109936-30110177(-)$1	241	6	10	11.9999
UCCU	chr16:30718551-30718789(+)$1	238	158	162	11.9999
UCCU	chr3:49728539-49728764(+)$1	225	169	173	11.9999
UCCU	chr17:45734225-45734467(+)$1	242	107	111	11.9999
UCCU	chr6:44197555-44197780(+)$1	225	19	23	11.9999
UCCU	chr2:162036138-162036366(+)$1	228	3	7	11.9999
UCCU	chr7:128843299-128843530(+)$1	231	90	94	11.9999
UCCU	chr15:52074837-52075074(+)$1	237	65	69	11.9999
UCCU	chr2:223507473-223507697(-)$1	224	79	83	11.9999
UCCU	chr12:112884072-112884298(+)$1	226	154	158	11.9999
UCCU	chr12:57036447-57036669(-)$1	222	15	19	11.9999
UCCU	chr3:49737016-49737258(+)$1	242	44	48	11.9999
UCCU	chr2:232326444-232326698(-)$1	254	197	201	11.9999
UCCU	chr19:36106156-36106383(+)$1	227	26	30	11.9999
UCCU	chr1:115272789-115273028(-)$1	239	113	117	11.9999
UCCU	chr22:50666235-50666465(-)$1	230	57	61	11.9999
UCCU	chr13:75923272-75923500(-)$1	228	54	58	11.9999

#otherMatches

#Struct PSSM
cccc	chr2:198285066-198285288(-)$1	222	123	127	11.9999
::::	chr17:3721470-3721698(-)$1	228	207	211	11.9999
::::	chr12:46760952-46761182(-)$1	230	44	48	11.9999
HKKD	chrX:107976850-107977076(-)$1	226	8	12	11.9999
E:::	chrM:3397-3627(+)$1	230	214	218	11.9999
EEEE	chr17:3527282-3527515(-)$1	233	86	90	11.9999
rrrr	chr1:32110351-32110572(-)$1	221	118	122	11.9999
eeee	chr9:134353194-134353421(+)$1	227	150	154	11.9999
HHHH	chr12:4385193-4385423(+)$1	230	80	84	11.9999
eeee	chr22:39714956-39715186(-)$1	230	9	13	11.9999
gggg	chr10:121652172-121652403(+)$1	231	15	19	11.9999
::::	chr12:56578536-56578772(-)$1	236	18	22	11.9999
::::	chr4:56262312-56262575(+)$1	263	3	7	11.9999
::::	chr12:124156519-124156757(+)$1	238	6	10	11.9999
g::G	chr17:47119601-47119822(+)$1	221	166	170	11.9999
=ttt	chr2:230675760-230675983(-)$1	223	44	48	11.9999
nnnn	chr8:48690294-48690514(-)$1	220	56	60	11.9999
fffb	chr11:66136811-66137035(-)$1	224	78	82	11.9999
ffff	chr1:19426786-19427007(-)$1	221	112	116	11.9999
rbb2	chr9:135525530-135525758(-)$1	228	165	169	11.9999
f:a[	chr13:28854483-28854703(+)$1	220	45	49	11.9999
^^^^	chrM:9804-10067(+)$1	263	43	47	11.9999
lldd	chr12:62965153-62965375(+)$1	222	29	33	11.9999
dddd	chr4:108565859-108566088(-)$1	229	13	17	11.9999
c:gg	chr10:102268669-102268890(-)$1	221	38	42	11.9999
HHHY	chr1:162467696-162467920(+)$1	224	190	194	11.9999
qqqq	chr2:44222880-44223123(-)$1	243	113	117	11.9999
eee=	chr11:65820443-65820672(+)$1	229	37	41	11.9999
ffff	chr1:241798748-241798969(-)$1	221	69	73	11.9999
9999	chr17:41150710-41150943(+)$1	233	39	43	11.9999
ggcc	chr9:135926075-135926298(+)$1	223	63	67	11.9999
2eee	chr11:47663866-47664093(-)$1	227	101	105	11.9999
ccbb	chr19:36579848-36580070(+)$1	222	77	81	11.9999
eeee	chr11:62396637-62396867(-)$1	230	58	62	11.9999
::::	chr3:49155298-49155524(-)$1	226	26	30	11.9999
c[cc	chr11:801432-801668(-)$1	236	14	18	11.9999
:bb!	chr19:42797648-42797871(+)$1	223	172	176	11.9999
!ddd	chrX:70755998-70756256(+)$1	258	49	53	11.9999
::::	chr6:88321750-88321975(+)$1	225	107	111	11.9999
cmmm	chr22:35811817-35812051(+)$1	234	104	108	11.9999
qqqq	chr16:58557186-58557413(-)$1	227	180	184	11.9999
dddd	chr20:43252756-43252979(-)$1	223	142	146	11.9999
cc]g	chr18:33647251-33647480(-)$1	229	62	66	11.9999
hhhh	chr17:58469158-58469385(-)$1	227	113	117	11.9999
hhhh	chr22:50955918-50956155(+)$1	237	52	56	11.9999
obb]	chr22:22319586-22319820(-)$1	234	35	39	11.9999
JJJJ	chr1:120269589-120269822(+)$1	233	14	18	11.9999
SSGG	chr17:61869790-61870010(+)$1	220	32	36	11.9999
ggcc	chr21:37783732-37783956(+)$1	224	111	115	11.9999
ddmm	chr2:20939687-20939909(-)$1	222	78	82	11.9999
##ff	chr19:10789245-10789471(+)$1	226	175	179	11.9999
eeee	chr20:47860257-47860487(+)$1	230	60	64	11.9999
EEEE	chr1:97189024-97189246(+)$1	222	16	20	11.9999
bbpp	chr13:111929847-111930070(+)$1	223	145	149	11.9999
[ggg	chr10:91464979-91465204(+)$1	225	195	199	11.9999
F:::	chr17:62499219-62499440(-)$1	221	61	65	11.9999
D{A{	chr19:1434639-1434880(+)$1	241	157	161	11.9999
mccc	chr20:2083588-2083848(+)$1	260	84	88	11.9999
dddd	chr1:203691541-203691763(+)$1	222	49	53	11.9999
EEEE	chr8:94805329-94805553(+)$1	224	19	23	11.9999
f333	chr8:141595276-141595504(-)$1	228	104	108	11.9999
{A{F	chr13:30109936-30110177(-)$1	241	6	10	11.9999
gfff	chr16:30718551-30718789(+)$1	238	158	162	11.9999
hhhh	chr3:49728539-49728764(+)$1	225	169	173	11.9999
4bb:	chr17:45734225-45734467(+)$1	242	107	111	11.9999
cc::	chr6:44197555-44197780(+)$1	225	19	23	11.9999
deee	chr2:162036138-162036366(+)$1	228	3	7	11.9999
FFFF	chr7:128843299-128843530(+)$1	231	90	94	11.9999
:::e	chr15:52074837-52075074(+)$1	237	65	69	11.9999
cccp	chr2:223507473-223507697(-)$1	224	79	83	11.9999
^ccc	chr12:112884072-112884298(+)$1	226	154	158	11.9999
:EEE	chr12:57036447-57036669(-)$1	222	15	19	11.9999
====	chr3:49737016-49737258(+)$1	242	44	48	11.9999
[ccc	chr2:232326444-232326698(-)$1	254	197	201	11.9999
::::	chr19:36106156-36106383(+)$1	227	26	30	11.9999
:::g	chr1:115272789-115273028(-)$1	239	113	117	11.9999
dddd	chr22:50666235-50666465(-)$1	230	57	61	11.9999
$ccc	chr13:75923272-75923500(-)$1	228	54	58	11.9999

#DB
))))	chr2:198285066-198285288(-)$1	1	123	127	11.9999
....	chr17:3721470-3721698(-)$1	1	207	211	11.9999
....	chr12:46760952-46761182(-)$1	1	44	48	11.9999
(..(	chrX:107976850-107977076(-)$1	1	8	12	11.9999
)...	chrM:3397-3627(+)$1	1	214	218	11.9999
))))	chr17:3527282-3527515(-)$1	1	86	90	11.9999
....	chr1:32110351-32110572(-)$1	1	118	122	11.9999
((((	chr9:134353194-134353421(+)$1	1	150	154	11.9999
((((	chr12:4385193-4385423(+)$1	1	80	84	11.9999
((((	chr22:39714956-39715186(-)$1	1	9	13	11.9999
((((	chr10:121652172-121652403(+)$1	1	15	19	11.9999
....	chr12:56578536-56578772(-)$1	1	18	22	11.9999
....	chr4:56262312-56262575(+)$1	1	3	7	11.9999
....	chr12:124156519-124156757(+)$1	1	6	10	11.9999
)..)	chr17:47119601-47119822(+)$1	1	166	170	11.9999
(...	chr2:230675760-230675983(-)$1	1	44	48	11.9999
....	chr8:48690294-48690514(-)$1	1	56	60	11.9999
((((	chr11:66136811-66137035(-)$1	1	78	82	11.9999
))))	chr1:19426786-19427007(-)$1	1	112	116	11.9999
.)).	chr9:135525530-135525758(-)$1	1	165	169	11.9999
).(.	chr13:28854483-28854703(+)$1	1	45	49	11.9999
....	chrM:9804-10067(+)$1	1	43	47	11.9999
..))	chr12:62965153-62965375(+)$1	1	29	33	11.9999
))))	chr4:108565859-108566088(-)$1	1	13	17	11.9999
).((	chr10:102268669-102268890(-)$1	1	38	42	11.9999
))).	chr1:162467696-162467920(+)$1	1	190	194	11.9999
....	chr2:44222880-44223123(-)$1	1	113	117	11.9999
)))(	chr11:65820443-65820672(+)$1	1	37	41	11.9999
))))	chr1:241798748-241798969(-)$1	1	69	73	11.9999
....	chr17:41150710-41150943(+)$1	1	39	43	11.9999
))))	chr9:135926075-135926298(+)$1	1	63	67	11.9999
.)))	chr11:47663866-47664093(-)$1	1	101	105	11.9999
((((	chr19:36579848-36580070(+)$1	1	77	81	11.9999
))))	chr11:62396637-62396867(-)$1	1	58	62	11.9999
....	chr3:49155298-49155524(-)$1	1	26	30	11.9999
(.((	chr11:801432-801668(-)$1	1	14	18	11.9999
.((.	chr19:42797648-42797871(+)$1	1	172	176	11.9999
.(((	chrX:70755998-70756256(+)$1	1	49	53	11.9999
....	chr6:88321750-88321975(+)$1	1	107	111	11.9999
(...	chr22:35811817-35812051(+)$1	1	104	108	11.9999
....	chr16:58557186-58557413(-)$1	1	180	184	11.9999
((((	chr20:43252756-43252979(-)$1	1	142	146	11.9999
)).)	chr18:33647251-33647480(-)$1	1	62	66	11.9999
((((	chr17:58469158-58469385(-)$1	1	113	117	11.9999
((((	chr22:50955918-50956155(+)$1	1	52	56	11.9999
.)).	chr22:22319586-22319820(-)$1	1	35	39	11.9999
((((	chr1:120269589-120269822(+)$1	1	14	18	11.9999
..((	chr17:61869790-61870010(+)$1	1	32	36	11.9999
((((	chr21:37783732-37783956(+)$1	1	111	115	11.9999
((..	chr2:20939687-20939909(-)$1	1	78	82	11.9999
..((	chr19:10789245-10789471(+)$1	1	175	179	11.9999
((((	chr20:47860257-47860487(+)$1	1	60	64	11.9999
((((	chr1:97189024-97189246(+)$1	1	16	20	11.9999
((..	chr13:111929847-111930070(+)$1	1	145	149	11.9999
.(((	chr10:91464979-91465204(+)$1	1	195	199	11.9999
(...	chr17:62499219-62499440(-)$1	1	61	65	11.9999
(.(.	chr19:1434639-1434880(+)$1	1	157	161	11.9999
.)))	chr20:2083588-2083848(+)$1	1	84	88	11.9999
((((	chr1:203691541-203691763(+)$1	1	49	53	11.9999
((((	chr8:94805329-94805553(+)$1	1	19	23	11.9999
)...	chr8:141595276-141595504(-)$1	1	104	108	11.9999
.(.(	chr13:30109936-30110177(-)$1	1	6	10	11.9999
))))	chr16:30718551-30718789(+)$1	1	158	162	11.9999
((((	chr3:49728539-49728764(+)$1	1	169	173	11.9999
.)).	chr17:45734225-45734467(+)$1	1	107	111	11.9999
))..	chr6:44197555-44197780(+)$1	1	19	23	11.9999
((((	chr2:162036138-162036366(+)$1	1	3	7	11.9999
((((	chr7:128843299-128843530(+)$1	1	90	94	11.9999
...(	chr15:52074837-52075074(+)$1	1	65	69	11.9999
(((.	chr2:223507473-223507697(-)$1	1	79	83	11.9999
.)))	chr12:112884072-112884298(+)$1	1	154	158	11.9999
.(((	chr12:57036447-57036669(-)$1	1	15	19	11.9999
))))	chr3:49737016-49737258(+)$1	1	44	48	11.9999
.(((	chr2:232326444-232326698(-)$1	1	197	201	11.9999
....	chr19:36106156-36106383(+)$1	1	26	30	11.9999
...(	chr1:115272789-115273028(-)$1	1	113	117	11.9999
))))	chr22:50666235-50666465(-)$1	1	57	61	11.9999
.(((	chr13:75923272-75923500(-)$1	1	54	58	11.9999

#PSSM
U : 0.96	u : 0.03	
C : 0.96	c : 0.03	
C : 0.96	c : 0.03	
U : 0.96	u : 0.03	

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m3_run2.nuc.txt

#NT
auuuuu	chr3:32523037-32523259(-)$1	222	185	191	18.0000
AUUUUU	chr9:101914786-101915010(+)$1	224	142	148	18.0000
AUUUUU	chr3:38530809-38531031(+)$1	222	13	19	18.0000
AUUUUU	chr12:110784201-110784429(+)$1	228	116	122	18.0000
AUUUUU	chr1:233398735-233398961(-)$1	226	24	30	18.0000
AUUUUU	chr12:69973155-69973382(+)$1	227	105	111	18.0000
AUUUUU	chr1:213166665-213166892(-)$1	227	108	114	18.0000
AUUUUU	chr5:126888852-126889071(+)$1	219	128	134	18.0000
AUUUUU	chr12:46636950-46637191(-)$1	241	40	46	18.0000
AUUUUU	chrX:135951604-135951826(-)$1	222	6	12	18.0000
AUUUUU	chr3:182804387-182804616(-)$1	229	216	222	18.0000
AUUUUU	chr19:17402943-17403166(-)$1	223	136	142	18.0000
auuuuu	chr10:14950097-14950329(+)$1	232	215	221	18.0000
AUUUUU	chrX:133903825-133904049(-)$1	224	65	71	18.0000
AUUUUU	chrX:103435273-103435499(+)$1	226	31	37	18.0000
AUUUUU	chr1:19401092-19401315(-)$1	223	114	120	18.0000
AUUUUU	chr14:105477116-105477338(-)$1	222	131	137	18.0000
AUUUUU	chr1:210416238-210416457(+)$1	219	111	117	18.0000
AUUUUU	chr21:47610612-47610840(-)$1	228	8	14	18.0000
AUUUUU	chr2:47388762-47388984(-)$1	222	160	166	18.0000
AUUUUU	chr9:36336355-36336575(-)$1	220	34	40	18.0000
AUUUUU	chr3:196662677-196662912(-)$1	235	109	115	18.0000
AUUUUU	chr8:33405336-33405558(-)$1	222	131	137	18.0000
AUUUUU	chr11:102102298-102102520(+)$1	222	44	50	18.0000
AUUUUU	chr10:22823982-22824201(-)$1	219	152	158	18.0000
AUUUUU	chr8:103217410-103217633(-)$1	223	29	35	18.0000
AUUUUU	chr18:28573896-28574121(-)$1	225	75	81	18.0000
AUUUUU	chr8:1952086-1952309(+)$1	223	165	171	18.0000
auuuuu	chr1:32636658-32636877(+)$1	219	172	178	18.0000
AUUUUU	chr1:15994889-15995109(+)$1	220	56	62	18.0000
AUUUUU	chr7:132469720-132469942(-)$1	222	209	215	18.0000
AUUUUU	chr5:173383680-173383905(+)$1	225	11	17	18.0000
AUUUUU	chr3:160137191-160137427(+)$1	236	149	155	18.0000
AUUUUU	chr12:88568324-88568555(+)$1	231	25	31	18.0000
auuuuu	chr3:56654924-56655151(-)$1	227	129	135	18.0000
auuuuu	chr19:45913816-45914041(+)$1	225	141	147	18.0000
AUUUUU	chr7:116436530-116436751(+)$1	221	107	113	18.0000
AUUUUU	chr18:45365051-45365271(-)$1	220	75	81	18.0000
AUUUUU	chr8:17423783-17424007(+)$1	224	168	174	18.0000
Auuuuu	chr9:20342993-20343235(-)$1	242	22	28	18.0000
auuuuu	chr17:18111782-18112013(+)$1	231	58	64	18.0000

#otherMatches

#Struct PSSM
$$$eee	chr1:244219056-244219284(+)$1	228	43	49	18.0000
mmiiii	chr3:32523037-32523259(-)$1	222	185	191	18.0000
ff!!bb	chr9:101914786-101915010(+)$1	224	142	148	18.0000
::::==	chr3:38530809-38531031(+)$1	222	13	19	18.0000
bmmmmb	chr12:110784201-110784429(+)$1	228	116	122	18.0000
gggggg	chr1:233398735-233398961(-)$1	226	24	30	18.0000
SSSSSS	chr12:69973155-69973382(+)$1	227	105	111	18.0000
::::::	chr1:213166665-213166892(-)$1	227	108	114	18.0000
:hhhhh	chr5:126888852-126889071(+)$1	219	128	134	18.0000
bmmmmb	chr12:46636950-46637191(-)$1	241	40	46	18.0000
::::::	chrX:135951604-135951826(-)$1	222	6	12	18.0000
ff333d	chr3:182804387-182804616(-)$1	229	216	222	18.0000
pppppp	chr19:17402943-17403166(-)$1	223	136	142	18.0000
::::::	chr10:14950097-14950329(+)$1	232	215	221	18.0000
qqqqqq	chrX:133903825-133904049(-)$1	224	65	71	18.0000
e::::g	chrX:103435273-103435499(+)$1	226	31	37	18.0000
++++++	chr1:19401092-19401315(-)$1	223	114	120	18.0000
g:::::	chr14:105477116-105477338(-)$1	222	131	137	18.0000
hhhhhh	chr1:210416238-210416457(+)$1	219	111	117	18.0000
!hhhhh	chr21:47610612-47610840(-)$1	228	8	14	18.0000
vvvvvv	chr2:47388762-47388984(-)$1	222	160	166	18.0000
iiiiim	chr9:36336355-36336575(-)$1	220	34	40	18.0000
eeee:g	chr3:196662677-196662912(-)$1	235	109	115	18.0000
eemmmm	chr8:33405336-33405558(-)$1	222	131	137	18.0000
dddd%%	chr11:102102298-102102520(+)$1	222	44	50	18.0000
:::eee	chr10:22823982-22824201(-)$1	219	152	158	18.0000
sssfff	chr8:103217410-103217633(-)$1	223	29	35	18.0000
c>>>>>	chr18:28573896-28574121(-)$1	225	75	81	18.0000
meeeee	chr8:1952086-1952309(+)$1	223	165	171	18.0000
^^^^gg	chr1:32636658-32636877(+)$1	219	172	178	18.0000
::::dd	chr1:15994889-15995109(+)$1	220	56	62	18.0000
ff]ccc	chr7:132469720-132469942(-)$1	222	209	215	18.0000
##bb[e	chr5:173383680-173383905(+)$1	225	11	17	18.0000
hhhhhh	chr3:160137191-160137427(+)$1	236	149	155	18.0000
fooooo	chr12:88568324-88568555(+)$1	231	25	31	18.0000
4444ee	chr3:56654924-56655151(-)$1	227	129	135	18.0000
d::::B	chr19:45913816-45914041(+)$1	225	141	147	18.0000
::::::	chr7:116436530-116436751(+)$1	221	107	113	18.0000
IIIIII	chr18:45365051-45365271(-)$1	220	75	81	18.0000
ccc444	chr8:17423783-17424007(+)$1	224	168	174	18.0000
++++++	chr9:20342993-20343235(-)$1	242	22	28	18.0000
"ccc!!	chr17:18111782-18112013(+)$1	231	58	64	18.0000

#DB
...(((	chr1:244219056-244219284(+)$1	1	43	49	18.0000
..))))	chr3:32523037-32523259(-)$1	1	185	191	18.0000
((..((	chr9:101914786-101915010(+)$1	1	142	148	18.0000
....((	chr3:38530809-38531031(+)$1	1	13	19	18.0000
(....)	chr12:110784201-110784429(+)$1	1	116	122	18.0000
))))))	chr1:233398735-233398961(-)$1	1	24	30	18.0000
......	chr12:69973155-69973382(+)$1	1	105	111	18.0000
......	chr1:213166665-213166892(-)$1	1	108	114	18.0000
.(((((	chr5:126888852-126889071(+)$1	1	128	134	18.0000
(....)	chr12:46636950-46637191(-)$1	1	40	46	18.0000
......	chrX:135951604-135951826(-)$1	1	6	12	18.0000
))...)	chr3:182804387-182804616(-)$1	1	216	222	18.0000
......	chr19:17402943-17403166(-)$1	1	136	142	18.0000
......	chr10:14950097-14950329(+)$1	1	215	221	18.0000
......	chrX:133903825-133904049(-)$1	1	65	71	18.0000
)....(	chrX:103435273-103435499(+)$1	1	31	37	18.0000
......	chr1:19401092-19401315(-)$1	1	114	120	18.0000
).....	chr14:105477116-105477338(-)$1	1	131	137	18.0000
((((((	chr1:210416238-210416457(+)$1	1	111	117	18.0000
.(((((	chr21:47610612-47610840(-)$1	1	8	14	18.0000
......	chr2:47388762-47388984(-)$1	1	160	166	18.0000
(((((.	chr9:36336355-36336575(-)$1	1	34	40	18.0000
)))).(	chr3:196662677-196662912(-)$1	1	109	115	18.0000
((....	chr8:33405336-33405558(-)$1	1	131	137	18.0000
((((..	chr11:102102298-102102520(+)$1	1	44	50	18.0000
...(((	chr10:22823982-22824201(-)$1	1	152	158	18.0000
...)))	chr8:103217410-103217633(-)$1	1	29	35	18.0000
).....	chr18:28573896-28574121(-)$1	1	75	81	18.0000
.)))))	chr8:1952086-1952309(+)$1	1	165	171	18.0000
....))	chr1:32636658-32636877(+)$1	1	172	178	18.0000
....((	chr1:15994889-15995109(+)$1	1	56	62	18.0000
)).)))	chr7:132469720-132469942(-)$1	1	209	215	18.0000
..((.(	chr5:173383680-173383905(+)$1	1	11	17	18.0000
))))))	chr3:160137191-160137427(+)$1	1	149	155	18.0000
(.....	chr12:88568324-88568555(+)$1	1	25	31	18.0000
....))	chr3:56654924-56655151(-)$1	1	129	135	18.0000
)....)	chr19:45913816-45914041(+)$1	1	141	147	18.0000
......	chr7:116436530-116436751(+)$1	1	107	113	18.0000
((((((	chr18:45365051-45365271(-)$1	1	75	81	18.0000
)))...	chr8:17423783-17424007(+)$1	1	168	174	18.0000
......	chr9:20342993-20343235(-)$1	1	22	28	18.0000
.(((..	chr17:18111782-18112013(+)$1	1	58	64	18.0000

#PSSM
A : 0.85	a : 0.14	
U : 0.83	u : 0.16	
U : 0.83	u : 0.16	
U : 0.83	u : 0.16	
U : 0.83	u : 0.16	
U : 0.83	u : 0.16	

#score	756.0000000000001
#seq	42
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_UTR_m2_run1.nuc.txt

#NT
UUAAAAAU	chr5:34956383-34956612(+)$1	229	7	15	16.6470
uuaauuau	chr6:144146761-144146993(+)$1	232	21	29	14.0000
UCAAAAAU	chr4:26434921-26435150(+)$1	229	173	181	13.3137
uuaaaaau	chr1:93618829-93619061(-)$1	232	110	118	16.6470
UUAAAAAU	chr10:115671402-115671632(+)$1	230	67	75	16.6470
UGAAUAAU	chr2:149882670-149882902(+)$1	232	142	150	14.4901
UUACUAAU	chr6:153326412-153326640(-)$1	228	142	150	14.4901
UUAGUAAU	chr2:203426032-203426264(+)$1	232	53	61	14.3921
UUAAUGAU	chr5:118583220-118583452(+)$1	232	128	136	13.8039
UUAAUCAU	chr5:173387838-173388061(+)$1	223	45	53	13.9019
auaaaaau	chr19:37656218-37656450(-)$1	232	52	60	12.7254
UUAAUAAA	chr5:175816629-175816855(+)$1	226	101	109	13.6078
UUAGAAAU	chr15:65737814-65738043(-)$1	229	11	19	12.9215
UCAAUAAU	chr18:32833143-32833375(+)$1	232	107	115	14.7843
ugaaaaau	chr1:67874558-67874787(-)$1	229	131	139	13.0196
AUAAAAAU	chr7:44920588-44920838(-)$1	250	161	169	12.7254
uuaauacu	chr2:228422248-228422500(+)$1	252	33	41	13.7058
AUAAAAAU	chr12:49087315-49087563(-)$1	248	4	12	12.7254
UUAAAAAU	chr22:43266473-43266695(-)$1	222	53	61	16.6470
UUAAUAAG	chr7:94295148-94295374(+)$1	226	118	126	13.6078
UUAAAAAU	chr14:53241823-53242050(-)$1	227	112	120	16.6470
auaauaau	chr17:46669248-46669480(+)$1	232	103	111	14.1960
UUAAUAAC	chr16:72820901-72821133(-)$1	232	116	124	13.7058
UUAGUAAU	chr12:4598668-4598895(-)$1	227	175	183	14.3921
uuauuaau	chr5:133307525-133307750(-)$1	225	162	170	14.3921
UUAAUAAC	chr1:180854599-180854835(+)$1	236	154	162	13.7058
UCAAUAAU	chr6:90343175-90343407(-)$1	232	91	99	14.7843
UGAAUAAU	chr6:125596927-125597158(-)$1	231	207	215	14.4901
GUAAUAAU	chr18:19447987-19448220(+)$1	233	43	51	13.8039
uuaaauau	chr1:150937767-150938000(-)$1	233	123	131	12.5294
UUAAUAUU	chr12:11149183-11149409(-)$1	226	79	87	13.7058
UUAACAAU	chr11:47799571-47799803(-)$1	232	127	135	15.1764
UUAAUACU	chr16:51169852-51170089(-)$1	237	117	125	13.7058
AUAAAAAU	chr1:15992494-15992726(+)$1	232	70	78	12.7254
UUACUAAU	chr22:41697569-41697801(+)$1	232	115	123	14.4901
UUACUAAU	chr7:94214543-94214782(-)$1	239	130	138	14.4901
UUAAUAUU	chr6:79646466-79646694(-)$1	228	108	116	13.7058
UUAAUAAU	chr9:8317621-8317852(-)$1	231	160	168	18.1176
uaaauaau	chr18:22032396-22032633(+)$1	237	16	24	14.3921
UUAAUCAU	chr1:150594652-150594878(-)$1	226	109	117	13.9019
UUAAAUAU	chr1:89401603-89401830(-)$1	227	70	78	12.5294
UUACUAAU	chr1:85732590-85732833(-)$1	243	123	131	14.4901
UCAAUAAU	chr11:33162533-33162765(-)$1	232	40	48	14.7843
UUAAUAAU	chr2:153591415-153591640(+)$1	225	54	62	18.1176
UAAAUAAU	chr9:135564273-135564495(+)$1	222	56	64	14.3921
UUAAAAAU	chr15:49417717-49417949(-)$1	232	215	223	16.6470
UCAAAAAU	chr17:48772164-48772391(-)$1	227	147	155	13.3137
UUAACAAU	chrX:107965415-107965641(-)$1	226	108	116	15.1764
UCAAUAAU	chr4:41958543-41958768(+)$1	225	70	78	14.7843
uuauaaau	chr1:211917897-211918126(-)$1	229	77	85	12.9215

#otherMatches

#Struct PSSM
xxxxxxxx	chr1:109427926-109428153(+)$1	227	63	71	14.3921
KBB{DDDD	chr5:34956383-34956612(+)$1	229	7	15	16.6470
::::::::	chr6:144146761-144146993(+)$1	232	21	29	14.0000
nggggggg	chr4:26434921-26435150(+)$1	229	173	181	13.3137
>>>>>>>>	chr1:93618829-93619061(-)$1	232	110	118	16.6470
HHHHHH::	chr10:115671402-115671632(+)$1	230	67	75	16.6470
::::::::	chr2:149882670-149882902(+)$1	232	142	150	14.4901
444fffff	chr6:153326412-153326640(-)$1	228	142	150	14.4901
SSFFFFFF	chr2:203426032-203426264(+)$1	232	53	61	14.3921
rrrrrbb]	chr5:118583220-118583452(+)$1	232	128	136	13.8039
dppppppp	chr5:173387838-173388061(+)$1	223	45	53	13.9019
:::::::g	chr19:37656218-37656450(-)$1	232	52	60	12.7254
!!cccccc	chr5:175816629-175816855(+)$1	226	101	109	13.6078
IIIIIII:	chr15:65737814-65738043(-)$1	229	11	19	12.9215
''''''''	chr18:32833143-32833375(+)$1	232	107	115	14.7843
eeeerrrr	chr1:67874558-67874787(-)$1	229	131	139	13.0196
yyyyyyye	chr7:44920588-44920838(-)$1	250	161	169	12.7254
mffffff:	chr2:228422248-228422500(+)$1	252	33	41	13.7058
:::::::c	chr12:49087315-49087563(-)$1	248	4	12	12.7254
::::::::	chr22:43266473-43266695(-)$1	222	53	61	16.6470
^^^^^^dd	chr7:94295148-94295374(+)$1	226	118	126	13.6078
^^^^^^^^	chr14:53241823-53242050(-)$1	227	112	120	16.6470
iiiiiiii	chr17:46669248-46669480(+)$1	232	103	111	14.1960
^^^^^^^^	chr16:72820901-72821133(-)$1	232	116	124	13.7058
!!cccqqq	chr12:4598668-4598895(-)$1	227	175	183	14.3921
::::::::	chr5:133307525-133307750(-)$1	225	162	170	14.3921
hh::::::	chr1:180854599-180854835(+)$1	236	154	162	13.7058
::::::::	chr6:90343175-90343407(-)$1	232	91	99	14.7843
eee4444e	chr6:125596927-125597158(-)$1	231	207	215	14.4901
d22dddd3	chr18:19447987-19448220(+)$1	233	43	51	13.8039
::::::::	chr1:150937767-150938000(-)$1	233	123	131	12.5294
^^^^^^^^	chr12:11149183-11149409(-)$1	226	79	87	13.7058
yyyyyiii	chr11:47799571-47799803(-)$1	232	127	135	15.1764
888ggggg	chr16:51169852-51170089(-)$1	237	117	125	13.7058
+++++++d	chr1:15992494-15992726(+)$1	232	70	78	12.7254
iiimmmmi	chr22:41697569-41697801(+)$1	232	115	123	14.4901
ffff"""c	chr7:94214543-94214782(-)$1	239	130	138	14.4901
hhhhhh^^	chr6:79646466-79646694(-)$1	228	108	116	13.7058
ee55555c	chr9:8317621-8317852(-)$1	231	160	168	18.1176
::HHHHHH	chr18:22032396-22032633(+)$1	237	16	24	14.3921
::::bb[e	chr1:150594652-150594878(-)$1	226	109	117	13.9019
::::::::	chr1:89401603-89401830(-)$1	227	70	78	12.5294
ppppffff	chr1:85732590-85732833(-)$1	243	123	131	14.4901
cbb!!bbs	chr11:33162533-33162765(-)$1	232	40	48	14.7843
eee[ccc[	chr2:153591415-153591640(+)$1	225	54	62	18.1176
bqqqqqqq	chr9:135564273-135564495(+)$1	222	56	64	14.3921
}DDDD///	chr15:49417717-49417949(-)$1	232	215	223	16.6470
l=======	chr17:48772164-48772391(-)$1	227	147	155	13.3137
!!eeeeex	chrX:107965415-107965641(-)$1	226	108	116	15.1764
:eeeeenn	chr4:41958543-41958768(+)$1	225	70	78	14.7843
ggggg!!g	chr1:211917897-211918126(-)$1	229	77	85	12.9215

#DB
........	chr1:109427926-109428153(+)$1	1	63	71	14.3921
.((.((((	chr5:34956383-34956612(+)$1	1	7	15	16.6470
........	chr6:144146761-144146993(+)$1	1	21	29	14.0000
.)))))))	chr4:26434921-26435150(+)$1	1	173	181	13.3137
........	chr1:93618829-93619061(-)$1	1	110	118	16.6470
((((((..	chr10:115671402-115671632(+)$1	1	67	75	16.6470
........	chr2:149882670-149882902(+)$1	1	142	150	14.4901
...)))))	chr6:153326412-153326640(-)$1	1	142	150	14.4901
..((((((	chr2:203426032-203426264(+)$1	1	53	61	14.3921
.....)).	chr5:118583220-118583452(+)$1	1	128	136	13.8039
(.......	chr5:173387838-173388061(+)$1	1	45	53	13.9019
.......(	chr19:37656218-37656450(-)$1	1	52	60	12.7254
..((((((	chr5:175816629-175816855(+)$1	1	101	109	13.6078
(((((((.	chr15:65737814-65738043(-)$1	1	11	19	12.9215
........	chr18:32833143-32833375(+)$1	1	107	115	14.7843
((((....	chr1:67874558-67874787(-)$1	1	131	139	13.0196
.......)	chr7:44920588-44920838(-)$1	1	161	169	12.7254
.)))))).	chr2:228422248-228422500(+)$1	1	33	41	13.7058
.......(	chr12:49087315-49087563(-)$1	1	4	12	12.7254
........	chr22:43266473-43266695(-)$1	1	53	61	16.6470
......))	chr7:94295148-94295374(+)$1	1	118	126	13.6078
........	chr14:53241823-53242050(-)$1	1	112	120	16.6470
((((((((	chr17:46669248-46669480(+)$1	1	103	111	14.1960
........	chr16:72820901-72821133(-)$1	1	116	124	13.7058
..(((...	chr12:4598668-4598895(-)$1	1	175	183	14.3921
........	chr5:133307525-133307750(-)$1	1	162	170	14.3921
))......	chr1:180854599-180854835(+)$1	1	154	162	13.7058
........	chr6:90343175-90343407(-)$1	1	91	99	14.7843
)))....)	chr6:125596927-125597158(-)$1	1	207	215	14.4901
)..)))).	chr18:19447987-19448220(+)$1	1	43	51	13.8039
........	chr1:150937767-150938000(-)$1	1	123	131	12.5294
........	chr12:11149183-11149409(-)$1	1	79	87	13.7058
.....)))	chr11:47799571-47799803(-)$1	1	127	135	15.1764
...)))))	chr16:51169852-51170089(-)$1	1	117	125	13.7058
.......(	chr1:15992494-15992726(+)$1	1	70	78	12.7254
(((....)	chr22:41697569-41697801(+)$1	1	115	123	14.4901
((((...(	chr7:94214543-94214782(-)$1	1	130	138	14.4901
((((((..	chr6:79646466-79646694(-)$1	1	108	116	13.7058
)).....)	chr9:8317621-8317852(-)$1	1	160	168	18.1176
..((((((	chr18:22032396-22032633(+)$1	1	16	24	14.3921
....((.(	chr1:150594652-150594878(-)$1	1	109	117	13.9019
........	chr1:89401603-89401830(-)$1	1	70	78	12.5294
....))))	chr1:85732590-85732833(-)$1	1	123	131	14.4901
(((..((.	chr11:33162533-33162765(-)$1	1	40	48	14.7843
(((.(((.	chr2:153591415-153591640(+)$1	1	54	62	18.1176
(.......	chr9:135564273-135564495(+)$1	1	56	64	14.3921
.))))...	chr15:49417717-49417949(-)$1	1	215	223	16.6470
.)))))))	chr17:48772164-48772391(-)$1	1	147	155	13.3137
..(((((.	chrX:107965415-107965641(-)$1	1	108	116	15.1764
.(((((..	chr4:41958543-41958768(+)$1	1	70	78	14.7843
(((((..(	chr1:211917897-211918126(-)$1	1	77	85	12.9215

#PSSM
U : 0.72	u : 0.15	A : 0.05	a : 0.03	G : 0.01	
U : 0.62	u : 0.15	C : 0.11	G : 0.03	g : 0.01	a : 0.01	A : 0.01	
A : 0.80	a : 0.19	
A : 0.64	a : 0.15	C : 0.07	G : 0.05	u : 0.03	U : 0.01	
U : 0.52	A : 0.23	u : 0.09	a : 0.09	C : 0.03	
A : 0.72	a : 0.15	u : 0.03	C : 0.03	G : 0.01	U : 0.01	
A : 0.74	a : 0.17	U : 0.03	c : 0.01	C : 0.01	
U : 0.72	u : 0.19	C : 0.03	A : 0.01	G : 0.01	

#score	733.4117647058824
#seq	51
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_CDS_m3_run2.nuc.txt

#NT
ACAAUUUCACAGCACCAAAUCUCCACCUCCAUCAUCACCUCAACCCAAAAAGGCAUAAUUAAACUUUACUUCCUCUCUUUCUUCUUCCCACUCAUCCUAACCCUACUCCUAAUCACAUAACCUAUUCCCCCGAGCAAUCUCAAUUACAAUAUAUACACCAACAAACAAUGUUCAACCAGUAACCACUACUAAUCAACGCCCAUAAUCAUACAAAGCCCCCGCACCAAUAGGAUCCUCCCGAAUCAACCCUGACCCCUCUCCUUCAUAA	chrM:14017-14299(+)$1	282	12	280	354.0000

#otherMatches

#Struct PSSM
::CCCLLLCCC:::::::::::::::::::ddddnnnnndddd:::::ddddnnnnndddd::::::::::::::::::::::::bbmmmmbb:::::eeeee!!bb"""dddd%%%%%%cccssssssssssccc666666ddddbb22eeeee:cccnnnnnccc::::::::::::::::::::::::::::::::::::::ccc^^^^^^^^^^^^^^^^^^ccc::::::::::::::::::::::CCC}CCC::::::::::	chrM:14144-14431(+)$1	287	14	282	354.0000
::::::::::::::::::::::::::::::::::::::::::::::::ddddtttttttttttdddd:::::::::::::::::CCCOOOOOOFFFFFF::::::::::::::::::::::::::::::::cccmmmmccc::::::::::::::::::ddddnnnnndddd:::::ddddnnnnndddd::::::::::::::::::::::::bbmmmmbb:::::FFFFFF______CCC::::::::::::::::::::::::::	chrM:14017-14299(+)$1	282	12	280	354.0000

#DB
..(((...(((...................((((.....)))).....((((.....))))........................((....)).....(((((..((...((((......(((..........)))......))))))..))))).(((.....)))......................................(((..................)))......................))).)))..........	chrM:14144-14431(+)$1	1	14	282	354.0000
................................................((((...........)))).................(((......((((((................................(((....)))..................((((.....)))).....((((.....))))........................((....)).....))))))......)))..........................	chrM:14017-14299(+)$1	1	12	280	354.0000

#PSSM
C : 0.50	A : 0.50	
C : 1.00	
G : 0.50	A : 0.50	
A : 1.00	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
C : 1.00	
C : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
C : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
G : 0.50	C : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
C : 0.50	A : 0.50	
C : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
C : 1.00	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
U : 1.00	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 0.50	A : 0.50	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 0.50	C : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
C : 0.50	U : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
A : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 1.00	
U : 0.50	G : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
C : 0.50	A : 0.50	

#score	708.0
#seq	2
#width	268
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_CDS_m2_run2.nuc.txt

#NT
GGGCAG	chr21:44323854-44324083(+)$1	229	179	185	11.7288
GGGCCG	chr19:56185284-56185530(+)$1	246	71	77	14.3559
GGGCCG	chr14:38061690-38061929(-)$1	239	161	167	14.3559
GGGCCU	chr1:8044939-8045205(+)$1	266	73	79	10.2881
GGGCAG	chr17:1561513-1561737(-)$1	224	128	134	11.7288
GGGCUG	chr17:7399744-7399975(+)$1	231	195	201	11.9830
GGGCUG	chr15:72499078-72499300(-)$1	222	116	122	11.9830
GGGCCG	chr12:4409067-4409305(+)$1	238	119	125	14.3559
GGGACG	chr19:39976964-39977235(+)$1	271	133	139	10.2033
GGGCCG	chr19:56614446-56614677(-)$1	231	121	127	14.3559
GGGCAG	chr16:30435647-30435922(-)$1	275	121	127	11.7288
GGACCG	chr17:1564505-1564749(-)$1	244	121	127	9.6949
GGGCCG	chr19:47349263-47349493(-)$1	230	22	28	14.3559
GGGCAG	chr17:7402645-7402872(+)$1	227	197	203	11.7288
GGGCUG	chr19:19031287-19031514(+)$1	227	114	120	11.9830
GGGCCG	chr22:19163848-19164095(-)$1	247	11	17	14.3559
GGGCAG	chr1:44442768-44442988(+)$1	220	2	8	11.7288
GGGCCA	chr1:36558704-36558929(+)$1	225	158	164	10.6271
GGGCCG	chr8:144102700-144102921(+)$1	221	203	209	14.3559
GGGCUG	chr17:79990173-79990418(+)$1	245	21	27	11.9830
GGGCUG	chr11:117165781-117166008(-)$1	227	135	141	11.9830
gggccg	chr18:77748261-77748486(-)$1	225	6	12	14.3559
GAGCCG	chr9:135546119-135546339(+)$1	220	28	34	10.1186
GGGCCG	chr12:120899764-120899993(-)$1	229	105	111	14.3559
GGGCCA	chr19:10469735-10469959(-)$1	224	42	48	10.6271
GGGCCC	chr11:122928385-122928621(-)$1	236	153	159	10.5423
GGGCUG	chr19:39880613-39880865(-)$1	252	6	12	11.9830
GGGCUG	chr16:2820782-2821016(+)$1	234	31	37	11.9830
GGACCG	chrX:48340765-48340991(+)$1	226	107	113	9.6949
GGGCCC	chr1:35658182-35658416(-)$1	234	184	190	10.5423
GGGCCG	chr7:40173844-40174098(-)$1	254	156	162	14.3559
GGGACG	chr7:127229527-127229748(+)$1	221	59	65	10.2033
GGGACG	chr19:5713108-5713332(-)$1	224	114	120	10.2033
gggccg	chr12:6976690-6976918(+)$1	228	184	190	14.3559
GGGCAG	chr19:47349202-47349440(-)$1	238	66	72	11.7288
GGGCCA	chr22:29752314-29752560(-)$1	246	80	86	10.6271
GGGCCC	chr16:2049939-2050211(-)$1	272	47	53	10.5423
GGGCUG	chr19:18685590-18685850(+)$1	260	48	54	11.9830
GAGCCG	chr19:36222872-36223109(+)$1	237	195	201	10.1186
GGGCCG	chr5:139493957-139494182(+)$1	225	54	60	14.3559
GGGCCG	chr22:32870943-32871167(+)$1	224	28	34	14.3559
GGGCAG	chr3:193855540-193855783(+)$1	243	107	113	11.7288
GGGCGG	chr11:77348642-77348871(-)$1	229	40	46	11.1355
GGGCUG	chr17:73845687-73845922(-)$1	235	57	63	11.9830
GGGCCA	chr20:60882677-60882924(+)$1	247	185	191	10.6271
GGGCCG	chr11:118965809-118966262(-)$1	453	163	169	14.3559
GUGCCG	chr12:110841338-110841568(-)$1	230	16	22	10.1186
GGGCCG	chr20:279173-279399(+)$1	226	15	21	14.3559
GGGACG	chr7:100473181-100473413(+)$1	232	133	139	10.2033
GUGCCG	chr19:5785580-5785810(-)$1	230	191	197	10.1186
GGGCCA	chr11:62396156-62396387(-)$1	231	69	75	10.6271
GUGCCG	chr22:24236606-24236855(+)$1	249	97	103	10.1186
GGGCAG	chr15:72502049-72502273(-)$1	224	204	210	11.7288
GGGACG	chr1:207532885-207533110(+)$1	225	37	43	10.2033
GGGCUG	chr20:270819-271041(-)$1	222	48	54	11.9830
GAGCCG	chr19:5690433-5690684(+)$1	251	4	10	10.1186
GGGCCC	chr16:30081145-30081369(+)$1	224	92	98	10.5423
GGGCCG	chr8:74888598-74888819(+)$1	221	56	62	14.3559

#otherMatches

#Struct PSSM
JJJJJJ	chr16:8889855-8890080(-)$1	225	73	79	11.9830
bbdddd	chr21:44323854-44324083(+)$1	229	179	185	11.7288
eeeeec	chr19:56185284-56185530(+)$1	246	71	77	14.3559
EEEYYE	chr14:38061690-38061929(-)$1	239	161	167	14.3559
mmmmdd	chr1:8044939-8045205(+)$1	266	73	79	10.2881
ddbb!!	chr17:1561513-1561737(-)$1	224	128	134	11.7288
HHH~~~	chr17:7399744-7399975(+)$1	231	195	201	11.9830
dddd44	chr15:72499078-72499300(-)$1	222	116	122	11.9830
]bbbbf	chr12:4409067-4409305(+)$1	238	119	125	14.3559
ccc]bb	chr19:39976964-39977235(+)$1	271	133	139	10.2033
eeee[b	chr19:56614446-56614677(-)$1	231	121	127	14.3559
DDDD{B	chr16:30435647-30435922(-)$1	275	121	127	11.7288
d22a]c	chr17:1564505-1564749(-)$1	244	121	127	9.6949
!!cccm	chr19:47349263-47349493(-)$1	230	22	28	14.3559
bb]ccc	chr17:7402645-7402872(+)$1	227	197	203	11.7288
h!!bbo	chr19:19031287-19031514(+)$1	227	114	120	11.9830
FF{JJJ	chr22:19163848-19164095(-)$1	247	11	17	14.3559
BB{FFF	chr1:44442768-44442988(+)$1	220	2	8	11.7288
cccc]b	chr1:36558704-36558929(+)$1	225	158	164	10.6271
33eeee	chr8:144102700-144102921(+)$1	221	203	209	14.3559
C::fff	chr17:79990173-79990418(+)$1	245	21	27	11.9830
hhhhhh	chr11:117165781-117166008(-)$1	227	135	141	11.9830
gghhhh	chr18:77748261-77748486(-)$1	225	6	12	14.3559
EEE{DD	chr9:135546119-135546339(+)$1	220	28	34	10.1186
======	chr12:120899764-120899993(-)$1	229	105	111	14.3559
dddbb2	chr19:10469735-10469959(-)$1	224	42	48	10.6271
ddddee	chr11:122928385-122928621(-)$1	236	153	159	10.5423
cdddd$	chr19:39880613-39880865(-)$1	252	6	12	11.9830
eeeedd	chr16:2820782-2821016(+)$1	234	31	37	11.9830
ccc]a]	chrX:48340765-48340991(+)$1	226	107	113	9.6949
ffff33	chr1:35658182-35658416(-)$1	234	184	190	10.5423
hhhhhd	chr7:40173844-40174098(-)$1	254	156	162	14.3559
GGG:::	chr7:127229527-127229748(+)$1	221	59	65	10.2033
dd4444	chr19:5713108-5713332(-)$1	224	114	120	10.2033
3fffff	chr12:6976690-6976918(+)$1	228	184	190	14.3559
bb[eee	chr19:47349202-47349440(-)$1	238	66	72	11.7288
ee22ff	chr22:29752314-29752560(-)$1	246	80	86	10.6271
gppppp	chr16:2049939-2050211(-)$1	272	47	53	10.5423
gggggi	chr19:18685590-18685850(+)$1	260	48	54	11.9830
YYCCCC	chr19:36222872-36223109(+)$1	237	195	201	10.1186
cc:::D	chr5:139493957-139494182(+)$1	225	54	60	14.3559
JJJJJJ	chr22:32870943-32871167(+)$1	224	28	34	14.3559
======	chr3:193855540-193855783(+)$1	243	107	113	11.7288
ffffff	chr11:77348642-77348871(-)$1	229	40	46	11.1355
pp====	chr17:73845687-73845922(-)$1	235	57	63	11.9830
fff:ee	chr20:60882677-60882924(+)$1	247	185	191	10.6271
ennnnn	chr11:118965809-118966262(-)$1	453	163	169	14.3559
ggg[cc	chr12:110841338-110841568(-)$1	230	16	22	10.1186
ggggg:	chr20:279173-279399(+)$1	226	15	21	14.3559
gggggg	chr7:100473181-100473413(+)$1	232	133	139	10.2033
eeeeem	chr19:5785580-5785810(-)$1	230	191	197	10.1186
dddd[e	chr11:62396156-62396387(-)$1	231	69	75	10.6271
#ccc[b	chr22:24236606-24236855(+)$1	249	97	103	10.1186
@GGGGG	chr15:72502049-72502273(-)$1	224	204	210	11.7288
]ccc:C	chr1:207532885-207533110(+)$1	225	37	43	10.2033
eeeggg	chr20:270819-271041(-)$1	222	48	54	11.9830
EEEEE:	chr19:5690433-5690684(+)$1	251	4	10	10.1186
ddddCC	chr16:30081145-30081369(+)$1	224	92	98	10.5423
eeeee]	chr8:74888598-74888819(+)$1	221	56	62	14.3559

#DB
((((((	chr16:8889855-8890080(-)$1	1	73	79	11.9830
))))))	chr21:44323854-44324083(+)$1	1	179	185	11.7288
))))))	chr19:56185284-56185530(+)$1	1	71	77	14.3559
)))..)	chr14:38061690-38061929(-)$1	1	161	167	14.3559
....))	chr1:8044939-8045205(+)$1	1	73	79	10.2881
((((..	chr17:1561513-1561737(-)$1	1	128	134	11.7288
)))...	chr17:7399744-7399975(+)$1	1	195	201	11.9830
))))..	chr15:72499078-72499300(-)$1	1	116	122	11.9830
.))))(	chr12:4409067-4409305(+)$1	1	119	125	14.3559
))).))	chr19:39976964-39977235(+)$1	1	133	139	10.2033
((((.(	chr19:56614446-56614677(-)$1	1	121	127	14.3559
((((.(	chr16:30435647-30435922(-)$1	1	121	127	11.7288
)..).)	chr17:1564505-1564749(-)$1	1	121	127	9.6949
..(((.	chr19:47349263-47349493(-)$1	1	22	28	14.3559
)).)))	chr17:7402645-7402872(+)$1	1	197	203	11.7288
(..((.	chr19:19031287-19031514(+)$1	1	114	120	11.9830
((.(((	chr22:19163848-19164095(-)$1	1	11	17	14.3559
((.(((	chr1:44442768-44442988(+)$1	1	2	8	11.7288
)))).)	chr1:36558704-36558929(+)$1	1	158	164	10.6271
..))))	chr8:144102700-144102921(+)$1	1	203	209	14.3559
(..(((	chr17:79990173-79990418(+)$1	1	21	27	11.9830
))))))	chr11:117165781-117166008(-)$1	1	135	141	11.9830
((((((	chr18:77748261-77748486(-)$1	1	6	12	14.3559
(((.((	chr9:135546119-135546339(+)$1	1	28	34	10.1186
))))))	chr12:120899764-120899993(-)$1	1	105	111	14.3559
))))).	chr19:10469735-10469959(-)$1	1	42	48	10.6271
))))))	chr11:122928385-122928621(-)$1	1	153	159	10.5423
(((((.	chr19:39880613-39880865(-)$1	1	6	12	11.9830
((((((	chr16:2820782-2821016(+)$1	1	31	37	11.9830
))).).	chrX:48340765-48340991(+)$1	1	107	113	9.6949
))))..	chr1:35658182-35658416(-)$1	1	184	190	10.5423
((((((	chr7:40173844-40174098(-)$1	1	156	162	14.3559
(((...	chr7:127229527-127229748(+)$1	1	59	65	10.2033
))....	chr19:5713108-5713332(-)$1	1	114	120	10.2033
.)))))	chr12:6976690-6976918(+)$1	1	184	190	14.3559
((.(((	chr19:47349202-47349440(-)$1	1	66	72	11.7288
))..))	chr22:29752314-29752560(-)$1	1	80	86	10.6271
(.....	chr16:2049939-2050211(-)$1	1	47	53	10.5423
)))))(	chr19:18685590-18685850(+)$1	1	48	54	11.9830
..))))	chr19:36222872-36223109(+)$1	1	195	201	10.1186
))...(	chr5:139493957-139494182(+)$1	1	54	60	14.3559
((((((	chr22:32870943-32871167(+)$1	1	28	34	14.3559
))))))	chr3:193855540-193855783(+)$1	1	107	113	11.7288
))))))	chr11:77348642-77348871(-)$1	1	40	46	11.1355
..))))	chr17:73845687-73845922(-)$1	1	57	63	11.9830
))).((	chr20:60882677-60882924(+)$1	1	185	191	10.6271
(.....	chr11:118965809-118966262(-)$1	1	163	169	14.3559
(((.((	chr12:110841338-110841568(-)$1	1	16	22	10.1186
))))).	chr20:279173-279399(+)$1	1	15	21	14.3559
))))))	chr7:100473181-100473413(+)$1	1	133	139	10.2033
(((((.	chr19:5785580-5785810(-)$1	1	191	197	10.1186
((((.(	chr11:62396156-62396387(-)$1	1	69	75	10.6271
.(((.(	chr22:24236606-24236855(+)$1	1	97	103	10.1186
.)))))	chr15:72502049-72502273(-)$1	1	204	210	11.7288
.))).(	chr1:207532885-207533110(+)$1	1	37	43	10.2033
((((((	chr20:270819-271041(-)$1	1	48	54	11.9830
(((((.	chr19:5690433-5690684(+)$1	1	4	10	10.1186
))))((	chr16:30081145-30081369(+)$1	1	92	98	10.5423
))))).	chr8:74888598-74888819(+)$1	1	56	62	14.3559

#PSSM
G : 0.96	g : 0.03	
G : 0.86	A : 0.05	U : 0.05	g : 0.03	
G : 0.93	A : 0.03	g : 0.03	
C : 0.88	A : 0.08	c : 0.03	
C : 0.62	U : 0.18	A : 0.13	c : 0.03	G : 0.01	
G : 0.79	A : 0.08	C : 0.06	g : 0.03	U : 0.01	

#score	703.1864406779654
#seq	59
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_Hoell2011b_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUAAAU	chr15:49419660-49419881(-)$1	221	44	52	19.9558
UUUUACAU	chrX:24230248-24230475(+)$1	227	146	154	15.6911
uuauaaau	chr6:125407055-125407280(+)$1	225	22	30	15.3970
UUUUAUAU	chr20:8864782-8865013(+)$1	231	14	22	15.6911
UUUUAUAU	chr10:93624486-93624713(+)$1	227	26	34	15.6911
UUUUAAAU	chr19:37037120-37037348(-)$1	228	51	59	19.9558
UUUGAAAU	chr8:90938365-90938594(+)$1	229	15	23	15.9852
UUUUAAAA	chr14:57115329-57115563(+)$1	234	124	132	16.5735
UUUUAAAU	chr12:69233721-69233965(+)$1	244	123	131	19.9558
UUUUAAAU	chr2:136664412-136664648(-)$1	236	175	183	19.9558
UUUUAAAU	chr5:32125620-32125853(-)$1	233	25	33	19.9558
UUUUAAAG	chr10:30599051-30599276(-)$1	225	66	74	16.2058
UUUUAAAU	chr1:118068878-118069114(+)$1	236	72	80	19.9558
UUUUAUAU	chr9:125608248-125608472(-)$1	224	22	30	15.6911
UUUUGAAU	chr1:109179106-109179331(+)$1	225	35	43	16.0588
UUCUAAAU	chr6:116956724-116956947(-)$1	223	0	8	15.3970
UUUUAAAU	chr6:137518608-137518833(-)$1	225	187	195	19.9558
UUUUAAAA	chr1:67877375-67877610(-)$1	235	117	125	16.5735
auuuaaau	chr13:23903538-23903771(-)$1	233	114	122	15.2499
UUUUUAAU	chrX:37316301-37316529(+)$1	228	17	25	15.7647
UUUUAAAA	chr3:142776528-142776753(+)$1	225	101	109	16.5735
UUUUGAAU	chr11:17110908-17111141(-)$1	233	50	58	16.0588
UUUUCAAU	chr11:82644524-82644749(+)$1	225	114	122	15.6911
UUUGAAAU	chr5:133938136-133938371(-)$1	235	132	140	15.9852
UUUUGAAU	chr2:196998508-196998745(-)$1	237	6	14	16.0588
UUUUAAAG	chr1:1716782-1717002(-)$1	220	178	186	16.2058
CUUUAAAU	chr1:150619456-150619700(-)$1	244	20	28	15.2499
UUUUUAAU	chr12:16056057-16056298(+)$1	241	90	98	15.7647
UUUUAAAA	chr2:182794368-182794598(+)$1	230	63	71	16.5735
UUUUGAAU	chr6:111543464-111543684(+)$1	220	7	15	16.0588
UUUUAAAA	chr6:21597329-21597555(+)$1	226	22	30	16.5735
UUUCAAAU	chr17:29578321-29578551(+)$1	230	77	85	15.7647
UUUAAAAU	chr12:22839226-22839466(+)$1	240	198	206	15.7647
UUUGAAAU	chr9:116025443-116025670(+)$1	227	39	47	15.9852
UUUUAAAA	chr2:69549449-69549670(-)$1	221	144	152	16.5735
UUUUAAGU	chr5:162871334-162871564(+)$1	230	202	210	15.5441
UUUUAAAU	chr5:180001747-180001967(+)$1	220	110	118	19.9558
UUUUAAAG	chr1:179075177-179075400(-)$1	223	85	93	16.2058
UUUUAAAA	chr6:109484722-109484953(+)$1	231	83	91	16.5735
UGUUAAAU	chr12:42480705-42480929(-)$1	224	80	88	15.6176
UUUCAAAU	chr8:8889703-8889926(+)$1	223	189	197	15.7647
GUUUAAAU	chr3:170111091-170111333(+)$1	242	72	80	15.2499
UUUGAAAU	chr7:99639165-99639406(+)$1	241	74	82	15.9852
UUUUACAU	chr1:225684171-225684412(-)$1	241	39	47	15.6911
UUUAAAAU	chr5:36101469-36101694(-)$1	225	196	204	15.7647
UUUUAAAU	chr5:132215097-132215327(-)$1	230	113	121	19.9558
UAUUAAAU	chr2:62095471-62095695(-)$1	224	32	40	15.5441
UGUUAAAU	chr2:74442016-74442235(+)$1	219	118	126	15.6176
UUUUAAAA	chr3:122143622-122143854(-)$1	232	200	208	16.5735
UAUUAAAU	chr19:37379003-37379233(-)$1	230	61	69	15.5441
UUUUAGAU	chr2:239358173-239358409(+)$1	236	54	62	15.5441
UUUUACAU	chr3:156256225-156256457(-)$1	232	3	11	15.6911
UGUUAAAU	chr12:133498967-133499187(-)$1	220	15	23	15.6176
UUUUGAAU	chr1:205683507-205683752(-)$1	245	88	96	16.0588
UCUUAAAU	chr11:85373966-85374187(-)$1	221	104	112	15.4705
UUUUAAAA	chr21:38885983-38886211(+)$1	228	43	51	16.5735
UUUUAAAU	chr10:88195973-88196202(-)$1	229	113	121	19.9558
UUUUAAAU	chr16:75478594-75478831(-)$1	237	227	235	19.9558
UUCUAAAU	chr17:27954534-27954765(-)$1	231	89	97	15.3970
UUUUGAAU	chr10:119042412-119042661(-)$1	249	222	230	16.0588
UUUUAAGU	chr7:44916215-44916437(-)$1	222	72	80	15.5441
UUUGAAAU	chrX:39910519-39910745(-)$1	226	137	145	15.9852
UUUUAAGU	chr17:41567660-41567900(+)$1	240	34	42	15.5441
UUUUAAGU	chr3:101369253-101369487(-)$1	234	34	42	15.5441
UUUUAAAG	chr17:34894941-34895165(+)$1	224	45	53	16.2058
uuuuaaau	chr5:36183567-36183800(+)$1	233	213	221	19.9558
UUUUAAAU	chr15:68586574-68586808(+)$1	234	46	54	19.9558

#otherMatches

#Struct PSSM
::::::::	chr22:38686961-38687201(-)$1	240	114	122	15.3970
!ggggggg	chr15:49419660-49419881(-)$1	221	44	52	19.9558
cnnnnncc	chrX:24230248-24230475(+)$1	227	146	154	15.6911
::::::::	chr6:125407055-125407280(+)$1	225	22	30	15.3970
GG:dddd[	chr20:8864782-8865013(+)$1	231	14	22	15.6911
JJJJJJJJ	chr10:93624486-93624713(+)$1	227	26	34	15.6911
::::::::	chr19:37037120-37037348(-)$1	228	51	59	19.9558
:ddddnnn	chr8:90938365-90938594(+)$1	229	15	23	15.9852
0000000c	chr14:57115329-57115563(+)$1	234	124	132	16.5735
::::::::	chr12:69233721-69233965(+)$1	244	123	131	19.9558
qggggggg	chr2:136664412-136664648(-)$1	236	175	183	19.9558
eeeee[ee	chr5:32125620-32125853(-)$1	233	25	33	19.9558
d::::::f	chr10:30599051-30599276(-)$1	225	66	74	16.2058
iiiiii::	chr1:118068878-118069114(+)$1	236	72	80	19.9558
========	chr9:125608248-125608472(-)$1	224	22	30	15.6911
:::DDDD{	chr1:109179106-109179331(+)$1	225	35	43	16.0588
DDDDJJJJ	chr6:116956724-116956947(-)$1	223	0	8	15.3970
gggggggq	chr6:137518608-137518833(-)$1	225	187	195	19.9558
iiilllii	chr1:67877375-67877610(-)$1	235	117	125	16.5735
III:::::	chr13:23903538-23903771(-)$1	233	114	122	15.2499
ee$$$$$c	chrX:37316301-37316529(+)$1	228	17	25	15.7647
vvffffff	chr3:142776528-142776753(+)$1	225	101	109	16.5735
::GGGGGG	chr11:17110908-17111141(-)$1	233	50	58	16.0588
?????HHH	chr11:82644524-82644749(+)$1	225	114	122	15.6911
iiii"""b	chr5:133938136-133938371(-)$1	235	132	140	15.9852
::::::::	chr2:196998508-196998745(-)$1	237	6	14	16.0588
mmmdddd2	chr1:1716782-1717002(-)$1	220	178	186	16.2058
""dddddd	chr1:150619456-150619700(-)$1	244	20	28	15.2499
::::::gg	chr12:16056057-16056298(+)$1	241	90	98	15.7647
HHHHHHHH	chr2:182794368-182794598(+)$1	230	63	71	16.5735
hsssssss	chr6:111543464-111543684(+)$1	220	7	15	16.0588
hhh4444d	chr6:21597329-21597555(+)$1	226	22	30	16.5735
2ffffff:	chr17:29578321-29578551(+)$1	230	77	85	15.7647
iiiiiii!	chr12:22839226-22839466(+)$1	240	198	206	15.7647
dddttttt	chr9:116025443-116025670(+)$1	227	39	47	15.9852
::::HHHH	chr2:69549449-69549670(-)$1	221	144	152	16.5735
ee333ddd	chr5:162871334-162871564(+)$1	230	202	210	15.5441
eqqqqqqq	chr5:180001747-180001967(+)$1	220	110	118	19.9558
000000ee	chr1:179075177-179075400(-)$1	223	85	93	16.2058
dd]eeeee	chr6:109484722-109484953(+)$1	231	83	91	16.5735
tttttttd	chr12:42480705-42480929(-)$1	224	80	88	15.6176
oocccggg	chr8:8889703-8889926(+)$1	223	189	197	15.7647
gggggg::	chr3:170111091-170111333(+)$1	242	72	80	15.2499
fppppppp	chr7:99639165-99639406(+)$1	241	74	82	15.9852
DDD:::gg	chr1:225684171-225684412(-)$1	241	39	47	15.6911
cffffff]	chr5:36101469-36101694(-)$1	225	196	204	15.7647
gggdddd]	chr5:132215097-132215327(-)$1	230	113	121	19.9558
hhhhhhhh	chr2:62095471-62095695(-)$1	224	32	40	15.5441
offffff:	chr2:74442016-74442235(+)$1	219	118	126	15.6176
!ddddooo	chr3:122143622-122143854(-)$1	232	200	208	16.5735
:::::::e	chr19:37379003-37379233(-)$1	230	61	69	15.5441
fffnnnnn	chr2:239358173-239358409(+)$1	236	54	62	15.5441
eee!!bbm	chr3:156256225-156256457(-)$1	232	3	11	15.6911
iiiiiiii	chr12:133498967-133499187(-)$1	220	15	23	15.6176
nnnneeee	chr1:205683507-205683752(-)$1	245	88	96	16.0588
ff::::::	chr11:85373966-85374187(-)$1	221	104	112	15.4705
::::::::	chr21:38885983-38886211(+)$1	228	43	51	16.5735
eeeee%%%	chr10:88195973-88196202(-)$1	229	113	121	19.9558
===:::::	chr16:75478594-75478831(-)$1	237	227	235	19.9558
hhhhhhmm	chr17:27954534-27954765(-)$1	231	89	97	15.3970
::::::::	chr10:119042412-119042661(-)$1	249	222	230	16.0588
iiii++++	chr7:44916215-44916437(-)$1	222	72	80	15.5441
cccdddd5	chrX:39910519-39910745(-)$1	226	137	145	15.9852
c####eee	chr17:41567660-41567900(+)$1	240	34	42	15.5441
^^^=====	chr3:101369253-101369487(-)$1	234	34	42	15.5441
i$$$$$ee	chr17:34894941-34895165(+)$1	224	45	53	16.2058
e:::::::	chr5:36183567-36183800(+)$1	233	213	221	19.9558
JJJJJJJJ	chr15:68586574-68586808(+)$1	234	46	54	19.9558

#DB
........	chr22:38686961-38687201(-)$1	1	114	122	15.3970
.(((((((	chr15:49419660-49419881(-)$1	1	44	52	19.9558
(.....))	chrX:24230248-24230475(+)$1	1	146	154	15.6911
........	chr6:125407055-125407280(+)$1	1	22	30	15.3970
((.((((.	chr20:8864782-8865013(+)$1	1	14	22	15.6911
((((((((	chr10:93624486-93624713(+)$1	1	26	34	15.6911
........	chr19:37037120-37037348(-)$1	1	51	59	19.9558
.((((...	chr8:90938365-90938594(+)$1	1	15	23	15.9852
.......)	chr14:57115329-57115563(+)$1	1	124	132	16.5735
........	chr12:69233721-69233965(+)$1	1	123	131	19.9558
.)))))))	chr2:136664412-136664648(-)$1	1	175	183	19.9558
(((((.((	chr5:32125620-32125853(-)$1	1	25	33	19.9558
)......(	chr10:30599051-30599276(-)$1	1	66	74	16.2058
))))))..	chr1:118068878-118069114(+)$1	1	72	80	19.9558
))))))))	chr9:125608248-125608472(-)$1	1	22	30	15.6911
...((((.	chr1:109179106-109179331(+)$1	1	35	43	16.0588
((((((((	chr6:116956724-116956947(-)$1	1	0	8	15.3970
(((((((.	chr6:137518608-137518833(-)$1	1	187	195	19.9558
(((...))	chr1:67877375-67877610(-)$1	1	117	125	16.5735
(((.....	chr13:23903538-23903771(-)$1	1	114	122	15.2499
((.....(	chrX:37316301-37316529(+)$1	1	17	25	15.7647
..))))))	chr3:142776528-142776753(+)$1	1	101	109	16.5735
..((((((	chr11:17110908-17111141(-)$1	1	50	58	16.0588
.....)))	chr11:82644524-82644749(+)$1	1	114	122	15.6911
((((...(	chr5:133938136-133938371(-)$1	1	132	140	15.9852
........	chr2:196998508-196998745(-)$1	1	6	14	16.0588
...)))).	chr1:1716782-1717002(-)$1	1	178	186	16.2058
..((((((	chr1:150619456-150619700(-)$1	1	20	28	15.2499
......((	chr12:16056057-16056298(+)$1	1	90	98	15.7647
((((((((	chr2:182794368-182794598(+)$1	1	63	71	16.5735
(.......	chr6:111543464-111543684(+)$1	1	7	15	16.0588
)))....)	chr6:21597329-21597555(+)$1	1	22	30	16.5735
.)))))).	chr17:29578321-29578551(+)$1	1	77	85	15.7647
(((((((.	chr12:22839226-22839466(+)$1	1	198	206	15.7647
(((.....	chr9:116025443-116025670(+)$1	1	39	47	15.9852
....))))	chr2:69549449-69549670(-)$1	1	144	152	16.5735
))...)))	chr5:162871334-162871564(+)$1	1	202	210	15.5441
(.......	chr5:180001747-180001967(+)$1	1	110	118	19.9558
......))	chr1:179075177-179075400(-)$1	1	85	93	16.2058
)).)))))	chr6:109484722-109484953(+)$1	1	83	91	16.5735
.......)	chr12:42480705-42480929(-)$1	1	80	88	15.6176
..))))))	chr8:8889703-8889926(+)$1	1	189	197	15.7647
))))))..	chr3:170111091-170111333(+)$1	1	72	80	15.2499
(.......	chr7:99639165-99639406(+)$1	1	74	82	15.9852
(((...((	chr1:225684171-225684412(-)$1	1	39	47	15.6911
))))))).	chr5:36101469-36101694(-)$1	1	196	204	15.7647
))))))).	chr5:132215097-132215327(-)$1	1	113	121	19.9558
))))))))	chr2:62095471-62095695(-)$1	1	32	40	15.5441
.)))))).	chr2:74442016-74442235(+)$1	1	118	126	15.6176
.((((...	chr3:122143622-122143854(-)$1	1	200	208	16.5735
.......(	chr19:37379003-37379233(-)$1	1	61	69	15.5441
(((.....	chr2:239358173-239358409(+)$1	1	54	62	15.5441
(((..((.	chr3:156256225-156256457(-)$1	1	3	11	15.6911
((((((((	chr12:133498967-133499187(-)$1	1	15	23	15.6176
....))))	chr1:205683507-205683752(-)$1	1	88	96	16.0588
))......	chr11:85373966-85374187(-)$1	1	104	112	15.4705
........	chr21:38885983-38886211(+)$1	1	43	51	16.5735
(((((...	chr10:88195973-88196202(-)$1	1	113	121	19.9558
))).....	chr16:75478594-75478831(-)$1	1	227	235	19.9558
((((((..	chr17:27954534-27954765(-)$1	1	89	97	15.3970
........	chr10:119042412-119042661(-)$1	1	222	230	16.0588
((((....	chr7:44916215-44916437(-)$1	1	72	80	15.5441
))))))).	chrX:39910519-39910745(-)$1	1	137	145	15.9852
(....(((	chr17:41567660-41567900(+)$1	1	34	42	15.5441
...)))))	chr3:101369253-101369487(-)$1	1	34	42	15.5441
(.....((	chr17:34894941-34895165(+)$1	1	45	53	16.2058
).......	chr5:36183567-36183800(+)$1	1	213	221	19.9558
((((((((	chr15:68586574-68586808(+)$1	1	46	54	19.9558

#PSSM
U : 0.92	u : 0.02	a : 0.01	C : 0.01	G : 0.01	
U : 0.86	u : 0.04	G : 0.04	A : 0.02	C : 0.01	
U : 0.91	C : 0.02	u : 0.02	A : 0.01	a : 0.01	
U : 0.82	G : 0.07	u : 0.04	C : 0.02	A : 0.02	
A : 0.82	G : 0.08	a : 0.04	U : 0.02	C : 0.01	
A : 0.85	C : 0.04	a : 0.04	U : 0.04	G : 0.01	
A : 0.89	G : 0.05	a : 0.04	
U : 0.76	A : 0.13	G : 0.05	u : 0.04	

#score	1132.5882352941162
#seq	68
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_UTR_m2_run1.nuc.txt

#NT
UCCUUUU	chr9:33917266-33917506(+)$1	240	126	133	13.4999
UGCUUUC	chr2:224742111-224742355(-)$1	244	56	63	13.5925
UCUUUUC	chr7:29960627-29960867(-)$1	240	48	55	13.2222
CCCUUUC	chr2:216981385-216981625(+)$1	240	60	67	12.6666
UCCUUUU	chr4:25280080-25280320(+)$1	240	60	67	13.4999
UACUUUC	chr3:152554872-152555112(+)$1	240	67	74	13.0370
UCCUUAC	chr5:145667352-145667601(+)$1	249	77	84	12.2962
UUCUUUC	chr7:27221512-27221792(-)$1	280	47	54	13.3148
UCCUUUA	chr1:46016647-46016887(+)$1	240	34	41	13.2222
UCCUUUC	chr1:204525252-204525536(+)$1	284	221	228	16.8333
UCCUUUU	chr20:49576863-49577107(+)$1	244	24	31	13.4999
UCCUUUA	chr15:72877281-72877521(+)$1	240	20	27	13.2222
CCCUUUC	chr15:99501833-99502076(+)$1	243	173	180	12.6666
UCAUUUC	chr14:69708101-69708350(+)$1	249	212	219	12.8518
ACCUUUC	chr1:28527001-28527241(-)$1	240	65	72	12.3888
UCCUUUA	chr5:135517561-135517818(+)$1	257	202	209	13.2222
UGCUUUC	chr1:113667028-113667273(+)$1	245	83	90	13.5925
CCCUUUC	chr2:239360051-239360300(+)$1	249	178	185	12.6666
UCUUUUC	chr16:4931949-4932189(+)$1	240	111	118	13.2222
UCCUCUC	chr3:42577939-42578179(+)$1	240	47	54	12.3888
UGCUUUC	chr19:57869419-57869659(+)$1	240	135	142	13.5925
UCUUUUC	chr11:59342644-59342906(-)$1	262	200	207	13.2222
UCUUUUC	chr3:122144640-122144884(-)$1	244	147	154	13.2222
UCCUUUA	chr2:85545217-85545501(-)$1	284	61	68	13.2222
UCCUUUC	chr17:20902842-20903122(-)$1	280	117	124	16.8333
UCCUUUU	chr17:4173664-4174013(-)$1	349	66	73	13.4999
UUCUUUC	chr16:71883445-71883685(+)$1	240	10	17	13.3148
UGCUUUC	chr1:115259535-115259873(-)$1	338	265	272	13.5925
UCCUUCC	chr2:169628671-169628911(+)$1	240	68	75	12.2037
UCUUUUC	chr2:61024737-61024978(+)$1	241	74	81	13.2222
UGCUUUC	chr1:51702205-51702528(+)$1	323	182	189	13.5925
UGCUUUC	chrX:47305812-47306052(-)$1	240	167	174	13.5925
UCCUAUC	chr21:34823018-34823258(-)$1	240	74	81	12.2962
UCCUUUU	chr15:100254998-100255291(+)$1	293	37	44	13.4999
UCGUUUC	chr17:41180819-41181059(+)$1	240	36	43	12.7592
UUCUUUC	chr1:207218832-207219119(-)$1	287	217	224	13.3148
UCCUUUC	chr14:53244709-53245072(-)$1	363	328	335	16.8333
UCCCUUC	chr1:27480723-27480963(-)$1	240	184	191	12.0185
UCCUUUC	chr12:2912732-2913032(+)$1	300	73	80	16.8333
UCCUUUC	chr10:34690653-34690933(-)$1	280	23	30	16.8333
UCCUUUC	chr13:22277526-22277766(+)$1	240	132	139	16.8333
UCCUUUC	chr3:42265384-42265624(+)$1	240	145	152	16.8333
UCUUUUC	chr3:9495355-9495595(+)$1	240	52	59	13.2222
CCCUUUC	chr17:18112152-18112393(+)$1	241	90	97	12.6666
UUCUUUC	chr16:97101-97344(-)$1	243	174	181	13.3148
UGCUUUC	chr21:34106290-34106530(-)$1	240	204	211	13.5925
UCCUUUC	chr1:77095902-77096142(+)$1	240	194	201	16.8333
UCCUCUC	chr9:89560370-89560622(-)$1	252	156	163	12.3888
UCCUGUC	chr15:78454507-78454747(+)$1	240	55	62	12.2962
UCCUUUU	chr2:128030396-128030636(-)$1	240	22	29	13.4999
UCCUUAC	chr12:57452806-57453046(-)$1	240	204	211	12.2962
UCAUUUC	chr2:85546901-85547141(-)$1	240	96	103	12.8518
UCCUUUC	chr22:18218193-18218433(-)$1	240	60	67	16.8333

#otherMatches

#Struct PSSM
wwwwwww	chr13:114294628-114294868(+)$1	240	32	39	13.4999
ddhhhhh	chr9:33917266-33917506(+)$1	240	126	133	13.4999
dddd$$$	chr2:224742111-224742355(-)$1	244	56	63	13.5925
2ccc555	chr7:29960627-29960867(-)$1	240	48	55	13.2222
fffqqqq	chr2:216981385-216981625(+)$1	240	60	67	12.6666
dddd22b	chr4:25280080-25280320(+)$1	240	60	67	13.4999
CCCLLLC	chr3:152554872-152555112(+)$1	240	67	74	13.0370
eeeee]b	chr5:145667352-145667601(+)$1	249	77	84	12.2962
====[cc	chr7:27221512-27221792(-)$1	280	47	54	13.3148
mmmmfff	chr1:46016647-46016887(+)$1	240	34	41	13.2222
eeee22c	chr1:204525252-204525536(+)$1	284	221	228	16.8333
hhhhhnn	chr20:49576863-49577107(+)$1	244	24	31	13.4999
ff:::::	chr15:72877281-72877521(+)$1	240	20	27	13.2222
:::eeee	chr15:99501833-99502076(+)$1	243	173	180	12.6666
=======	chr14:69708101-69708350(+)$1	249	212	219	12.8518
::::::d	chr1:28527001-28527241(-)$1	240	65	72	12.3888
nnnnncc	chr5:135517561-135517818(+)$1	257	202	209	13.2222
hhhhhhm	chr1:113667028-113667273(+)$1	245	83	90	13.5925
ddd"""d	chr2:239360051-239360300(+)$1	249	178	185	12.6666
DDD}DDD	chr16:4931949-4932189(+)$1	240	111	118	13.2222
ffffffl	chr3:42577939-42578179(+)$1	240	47	54	12.3888
=======	chr19:57869419-57869659(+)$1	240	135	142	13.5925
e"""hhh	chr11:59342644-59342906(-)$1	262	200	207	13.2222
tttttbb	chr3:122144640-122144884(-)$1	244	147	154	13.2222
GOOOOOO	chr2:85545217-85545501(-)$1	284	61	68	13.2222
FFFFFFF	chr17:20902842-20903122(-)$1	280	117	124	16.8333
bb22fff	chr17:4173664-4174013(-)$1	349	66	73	13.4999
LLLDDDD	chr16:71883445-71883685(+)$1	240	10	17	13.3148
gggg$$$	chr1:115259535-115259873(-)$1	338	265	272	13.5925
'''''cc	chr2:169628671-169628911(+)$1	240	68	75	12.2037
bb66666	chr2:61024737-61024978(+)$1	241	74	81	13.2222
ddd:fff	chr1:51702205-51702528(+)$1	323	182	189	13.5925
^^^^^^^	chrX:47305812-47306052(-)$1	240	167	174	13.5925
^^^^^^^	chr21:34823018-34823258(-)$1	240	74	81	12.2962
FOOOOOO	chr15:100254998-100255291(+)$1	293	37	44	13.4999
oa]eeee	chr17:41180819-41181059(+)$1	240	36	43	12.7592
fffff33	chr1:207218832-207219119(-)$1	287	217	224	13.3148
[bboooo	chr14:53244709-53245072(-)$1	363	328	335	16.8333
qqqqqcc	chr1:27480723-27480963(-)$1	240	184	191	12.0185
ccc::::	chr12:2912732-2913032(+)$1	300	73	80	16.8333
dddd[bb	chr10:34690653-34690933(-)$1	280	23	30	16.8333
=======	chr13:22277526-22277766(+)$1	240	132	139	16.8333
H:::::f	chr3:42265384-42265624(+)$1	240	145	152	16.8333
D::::::	chr3:9495355-9495595(+)$1	240	52	59	13.2222
:::::::	chr17:18112152-18112393(+)$1	241	90	97	12.6666
f]a::::	chr16:97101-97344(-)$1	243	174	181	13.3148
66666ee	chr21:34106290-34106530(-)$1	240	204	211	13.5925
hhhhhdd	chr1:77095902-77096142(+)$1	240	194	201	16.8333
2ccc:bb	chr9:89560370-89560622(-)$1	252	156	163	12.3888
ddd[ccc	chr15:78454507-78454747(+)$1	240	55	62	12.2962
DDDJJJJ	chr2:128030396-128030636(-)$1	240	22	29	13.4999
iiii%%%	chr12:57452806-57453046(-)$1	240	204	211	12.2962
CCCLLLD	chr2:85546901-85547141(-)$1	240	96	103	12.8518
ccc[eee	chr22:18218193-18218433(-)$1	240	60	67	16.8333

#DB
.......	chr13:114294628-114294868(+)$1	1	32	39	13.4999
(((((((	chr9:33917266-33917506(+)$1	1	126	133	13.4999
((((...	chr2:224742111-224742355(-)$1	1	56	63	13.5925
.)))...	chr7:29960627-29960867(-)$1	1	48	55	13.2222
(((....	chr2:216981385-216981625(+)$1	1	60	67	12.6666
))))..)	chr4:25280080-25280320(+)$1	1	60	67	13.4999
(((...(	chr3:152554872-152555112(+)$1	1	67	74	13.0370
))))).)	chr5:145667352-145667601(+)$1	1	77	84	12.2962
((((.((	chr7:27221512-27221792(-)$1	1	47	54	13.3148
....)))	chr1:46016647-46016887(+)$1	1	34	41	13.2222
))))..)	chr1:204525252-204525536(+)$1	1	221	228	16.8333
(((((..	chr20:49576863-49577107(+)$1	1	24	31	13.4999
)).....	chr15:72877281-72877521(+)$1	1	20	27	13.2222
...((((	chr15:99501833-99502076(+)$1	1	173	180	12.6666
)))))))	chr14:69708101-69708350(+)$1	1	212	219	12.8518
......(	chr1:28527001-28527241(-)$1	1	65	72	12.3888
.....))	chr5:135517561-135517818(+)$1	1	202	209	13.2222
((((((.	chr1:113667028-113667273(+)$1	1	83	90	13.5925
(((...(	chr2:239360051-239360300(+)$1	1	178	185	12.6666
))).)))	chr16:4931949-4932189(+)$1	1	111	118	13.2222
((((((.	chr3:42577939-42578179(+)$1	1	47	54	12.3888
)))))))	chr19:57869419-57869659(+)$1	1	135	142	13.5925
(...(((	chr11:59342644-59342906(-)$1	1	200	207	13.2222
.....))	chr3:122144640-122144884(-)$1	1	147	154	13.2222
(......	chr2:85545217-85545501(-)$1	1	61	68	13.2222
(((((((	chr17:20902842-20903122(-)$1	1	117	124	16.8333
))..)))	chr17:4173664-4174013(-)$1	1	66	73	13.4999
...((((	chr16:71883445-71883685(+)$1	1	10	17	13.3148
((((...	chr1:115259535-115259873(-)$1	1	265	272	13.5925
.....((	chr2:169628671-169628911(+)$1	1	68	75	12.2037
)).....	chr2:61024737-61024978(+)$1	1	74	81	13.2222
))).(((	chr1:51702205-51702528(+)$1	1	182	189	13.5925
.......	chrX:47305812-47306052(-)$1	1	167	174	13.5925
.......	chr21:34823018-34823258(-)$1	1	74	81	12.2962
(......	chr15:100254998-100255291(+)$1	1	37	44	13.4999
.).))))	chr17:41180819-41181059(+)$1	1	36	43	12.7592
)))))..	chr1:207218832-207219119(-)$1	1	217	224	13.3148
.((....	chr14:53244709-53245072(-)$1	1	328	335	16.8333
.....))	chr1:27480723-27480963(-)$1	1	184	191	12.0185
)))....	chr12:2912732-2913032(+)$1	1	73	80	16.8333
((((.((	chr10:34690653-34690933(-)$1	1	23	30	16.8333
)))))))	chr13:22277526-22277766(+)$1	1	132	139	16.8333
).....(	chr3:42265384-42265624(+)$1	1	145	152	16.8333
(......	chr3:9495355-9495595(+)$1	1	52	59	13.2222
.......	chr17:18112152-18112393(+)$1	1	90	97	12.6666
).)....	chr16:97101-97344(-)$1	1	174	181	13.3148
.....))	chr21:34106290-34106530(-)$1	1	204	211	13.5925
)))))))	chr1:77095902-77096142(+)$1	1	194	201	16.8333
.))).((	chr9:89560370-89560622(-)$1	1	156	163	12.3888
(((.(((	chr15:78454507-78454747(+)$1	1	55	62	12.2962
(((((((	chr2:128030396-128030636(-)$1	1	22	29	13.4999
((((...	chr12:57452806-57453046(-)$1	1	204	211	12.2962
(((...(	chr2:85546901-85547141(-)$1	1	96	103	12.8518
(((.(((	chr22:18218193-18218433(-)$1	1	60	67	16.8333

#PSSM
U : 0.90	C : 0.07	A : 0.01	
C : 0.77	G : 0.12	U : 0.07	A : 0.01	
C : 0.83	U : 0.11	A : 0.03	G : 0.01	
U : 0.98	C : 0.01	
U : 0.92	C : 0.03	A : 0.01	G : 0.01	
U : 0.94	A : 0.03	C : 0.01	
C : 0.79	U : 0.12	A : 0.07	

#score	739.3703703703695
#seq	54
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR1_Ascano2012e_hg19_CDS_m3_run2.nuc.txt

#NT
GCAAAUCUUAUUCAGCAUCAGAGUAUUCAUACUGGAGAGAAACCCUUUGAAUGUAAGGAGUGUGGGAAAGCCUUUCGACUUCACAUACAAUUUACUCGACAUCAGAAAUUUCAUACUGGU	chr19:40581620-40581840(-)$1	220	23	143	225.0000
UCAAUCCUUACUACACAUAAGAGAAUUCACACUGGAGAGAAACCCUACAAAUGUGAAGAAUGUGGCAAAGCUUUUAACCGAUCCUCAAAUCUUACUAAACAUAAGAUAAUUCAUACAGGA	chr19:21366408-21366630(+)$1	222	102	222	282.5000
UCACAACUUACUACACAUAAGAUAAUUCAUACUGGAGAGAAACCCUACAAAUGUAAAGAAUGUGGCAAAGCUUUUAAGCGGUCCUCAAACCUUACUGAACAUAGGAUAAUUCAUACUGGA	chr19:23405624-23405847(-)$1	223	103	223	286.2500

#otherMatches

#Struct PSSM
&&&&&eeeeepppppppeeeee88888888eeeeeeeeee4444eeeee::::::::bb[cccbb[hhhhhhhh"""ccc[ffffff&&&&&&&ccc####bb[bbmmmmbb]bb333cc	chr7:64167673-64167899(+)$1	226	29	149	286.2500
ee"""ccc[bbnnnnnbb]ccceeeee333ggggggg55555ccc::gggggggccc[bb[ggggggg[ggggggg[bbcccdddd[ccc$$$$$bb!!ffffffssssssssssfffff	chr19:40581620-40581840(-)$1	220	23	143	225.0000
%%%%bbddddpppppppdddd]bb666666eeeee22dddd::::::::::DDDDYYBBZZZCCC}HHHHHHHH:::bb(((((((((ffffffpppppppffffff0000000000bb:	chr19:21366408-21366630(+)$1	222	102	222	282.5000
dd[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^bbdddd:::::dddd$$$$$dddd[a!!bb[bb####cccmmmmccc333bb]bb22a]dddd666666dddd:::::::::EEEEE:	chr19:23405624-23405847(-)$1	223	103	223	286.2500

#DB
.....(((((.......)))))........))))))))))....)))))........((.(((((.((((((((...(((.((((((.......(((....((.((....)).))...))	chr7:64167673-64167899(+)$1	1	29	149	286.2500
((...(((.((.....)).))))))))...))))))).....)))..((((((((((.((.(((((((.(((((((.(((((((((.(((.....((..((((((..........)))))	chr19:40581620-40581840(-)$1	1	23	143	225.0000
....((((((.......)))).))......)))))..))))..........))))..))...))).))))))))...((.........((((((.......))))))..........)).	chr19:21366408-21366630(+)$1	1	102	222	282.5000
((.((...........................)))))).....((((.....((((.(..((.((....(((....)))...)).))..).))))......)))).........))))).	chr19:23405624-23405847(-)$1	1	103	223	286.2500

#PSSM
U : 0.75	G : 0.25	
C : 1.00	
A : 1.00	
A : 0.75	C : 0.25	
A : 0.50	C : 0.25	U : 0.25	
U : 0.50	C : 0.25	A : 0.25	
C : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
C : 0.75	U : 0.25	
U : 1.00	
A : 0.75	C : 0.25	
C : 0.50	G : 0.25	A : 0.25	
A : 0.75	G : 0.25	
C : 1.00	
A : 1.00	
U : 1.00	
A : 0.75	C : 0.25	
A : 1.00	
G : 1.00	
A : 1.00	
U : 0.50	G : 0.50	
A : 0.75	U : 0.25	
A : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 0.75	C : 0.25	
A : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 0.75	U : 0.25	
C : 0.75	U : 0.25	
A : 0.75	G : 0.25	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 0.75	G : 0.25	
A : 1.00	
A : 0.75	G : 0.25	
G : 1.00	
A : 1.00	
A : 0.75	G : 0.25	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 0.75	G : 0.25	
A : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 0.75	C : 0.25	
U : 1.00	
U : 1.00	
U : 1.00	
A : 0.75	C : 0.25	
A : 0.75	G : 0.25	
C : 0.50	A : 0.25	G : 0.25	
C : 1.00	
G : 0.50	A : 0.25	U : 0.25	
A : 0.50	U : 0.25	G : 0.25	
U : 0.75	C : 0.25	
C : 0.75	A : 0.25	
C : 0.75	U : 0.25	
U : 0.75	A : 0.25	
C : 0.75	U : 0.25	
A : 1.00	
A : 0.75	C : 0.25	
A : 1.00	
C : 0.50	A : 0.25	U : 0.25	
C : 0.75	U : 0.25	
U : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
G : 0.50	C : 0.25	A : 0.25	
A : 0.75	G : 0.25	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
A : 0.75	C : 0.25	
A : 0.75	G : 0.25	
G : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
A : 1.00	
A : 0.75	U : 0.25	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
U : 0.75	A : 0.25	
G : 1.00	
G : 0.75	C : 0.25	
A : 0.75	U : 0.25	

#score	1080.0
#seq	4
#width	120
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_PUM2_Hafner2010b_hg19_UTR_m2_run1.nuc.txt

#NT
UCAGUUCCAUGGUGUUAAUUUGAAAUGCCUUAAUGGCAGGCAAAAACCAGUCAUUUCAUUUUUGUAAAUUACAGAUUUUAUCACAGAGUAACAAAUGUUGCUGUAAUUAAACUUCUGUUUuauauauauauacguauacauaucuguauauauacauauauauauauauaaauauaaauauauUCUUUACUUUUUGUAUCAGUAACCAGGCUCGCACACACAGGGUCUGCUGCCACGUCGCAAACCACUCAGUAAAGGAAAUUAAAAAUGUAUUUGUCAUGUUAAAAAGUGUUA	chr5:123973233-123973530(-)$1	297	0	294	399.5000

#otherMatches

#Struct PSSM
!!ffffffpppppppffffff22bbccc333===========:::dddd####ccc!!ccc!!eeeeemmmmeeeee]ccc]ccc4444ddddbb[eeeee!!iiiiiiiiieeeee!!ccc####eeeee[ccc!!ccc####ddddpppppppdddd22ccc22ccceeeee7777777ccc22eeeee666666iiiiiiiii22eeeee]bbggggggg$$$$$cccooooooccc55555ggggggg::::ffffff"""ffffff%%%%%%bb[cccooooooccc]b	chr1:31404967-31405328(-)$1	361	40	334	399.5000
:::CCC{CCCMMMMEEEEE{BB:::ddddnnnnndddd:ggggggg!!bbmmmmbb22ggggggg:::::eeeee[dddd####a[ffffffmmmmffffff]a333dddd22eeeee::============[eeeee[cccmmmmccc]eeeee]============:::::iiiiiiiiiiiiiiiiii[eeeee!!a[ccc!!gggggggrrrrrrrrrggggggg]ccc333a22eeeee666666iiiiiiiii999999999iiiiiiiiiBB}EEEEEZZZCCCYYC	chr5:123973233-123973530(-)$1	297	0	294	399.5000

#DB
..((((((.......))))))..)))))...)))))))))))...((((....(((..(((..(((((....))))).))).)))....))))((.(((((..((((((((((((((..(((....(((((.(((..(((....((((.......))))..)))..)))))))).......)))..)))))......)))))))))..))))).))(((((((.....(((......))).....)))))))....((((((...((((((......((.(((......))).)	chr1:31404967-31405328(-)$1	1	40	334	399.5000
...(((.(((....(((((.((...((((.....)))).(((((((..((....))..))))))).....(((((.((((....(.((((((....)))))).)...))))..)))))..((((((((((((.(((((.(((....))).))))).)))))))))))).....((((((((((((((((((.(((((..(.(((..(((((((.........))))))).)))...)..)))))......))))))))).........))))))))))).)))))...)))..)	chr5:123973233-123973530(-)$1	1	0	294	399.5000

#PSSM
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 0.50	G : 0.50	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
U : 1.00	
G : 1.00	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
A : 1.00	
A : 1.00	
C : 0.50	A : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
C : 0.50	G : 0.50	
U : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
C : 1.00	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
U : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
U : 1.00	
G : 0.50	C : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
U : 0.50	u : 0.50	
U : 0.50	a : 0.50	
U : 0.50	u : 0.50	
U : 0.50	a : 0.50	
C : 0.50	u : 0.50	
U : 0.50	a : 0.50	
U : 0.50	u : 0.50	
G : 0.50	a : 0.50	
U : 0.50	u : 0.50	
U : 0.50	a : 0.50	
U : 0.50	u : 0.50	
U : 0.50	a : 0.50	
G : 0.50	c : 0.50	
A : 0.50	g : 0.50	
U : 0.50	u : 0.50	
G : 0.50	a : 0.50	
U : 0.50	u : 0.50	
C : 0.50	a : 0.50	
U : 0.50	c : 0.50	
A : 0.50	a : 0.50	
A : 0.50	u : 0.50	
U : 0.50	a : 0.50	
C : 0.50	u : 0.50	
U : 0.50	c : 0.50	
G : 0.50	u : 0.50	
U : 0.50	g : 0.50	
A : 0.50	u : 0.50	
U : 0.50	a : 0.50	
C : 0.50	u : 0.50	
U : 0.50	a : 0.50	
A : 0.50	u : 0.50	
U : 0.50	a : 0.50	
A : 0.50	u : 0.50	
A : 0.50	a : 0.50	
U : 0.50	c : 0.50	
G : 0.50	a : 0.50	
U : 0.50	u : 0.50	
A : 0.50	a : 0.50	
C : 0.50	u : 0.50	
C : 0.50	a : 0.50	
C : 0.50	u : 0.50	
U : 0.50	a : 0.50	
A : 0.50	u : 0.50	
G : 0.50	a : 0.50	
U : 0.50	u : 0.50	
A : 0.50	a : 0.50	
G : 0.50	u : 0.50	
U : 0.50	a : 0.50	
C : 0.50	u : 0.50	
G : 0.50	a : 0.50	
A : 0.50	a : 0.50	
A : 0.50	a : 0.50	
C : 0.50	u : 0.50	
A : 0.50	a : 0.50	
U : 0.50	u : 0.50	
A : 0.50	a : 0.50	
C : 0.50	a : 0.50	
U : 0.50	a : 0.50	
U : 0.50	u : 0.50	
U : 0.50	a : 0.50	
U : 0.50	u : 0.50	
G : 0.50	a : 0.50	
A : 0.50	u : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
A : 0.50	G : 0.50	
C : 0.50	U : 0.50	
A : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
U : 1.00	
A : 1.00	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
U : 0.50	G : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
U : 0.50	C : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
A : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
U : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
G : 0.50	A : 0.50	

#score	799.0
#seq	2
#width	294
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_CDS_m3_run2.nuc.txt

#NT
UAAGAAAUU	chr3:122591304-122591544(+)$1	240	141	150	11.2187
AAAAAAAAU	chr5:134086460-134086700(+)$1	240	215	224	15.2812
AAGGAAAAA	chr4:71895044-71895284(+)$1	240	170	179	11.2187
UCAGAAAAU	chr1:214816452-214816692(+)$1	240	38	47	12.3125
aauuaaaau	chr6:108375617-108375857(-)$1	240	186	195	10.9062
AGUGAAAAU	chr7:77379176-77379416(+)$1	240	28	37	11.2968
GCAGAAAAU	chr11:10821615-10821865(-)$1	250	212	221	12.0781
CAAGAAUAU	chr17:60060310-60060550(-)$1	240	94	103	10.9062
AAUAAAAAU	chr5:132228659-132228899(-)$1	240	52	61	11.3750
AAAGAAAGU	chr11:94917483-94917723(-)$1	240	85	94	14.1093
AGAGCAAAU	chr6:99819315-99819555(-)$1	240	163	172	10.8281
UAAUAAAAU	chr1:237060821-237061071(+)$1	250	9	18	12.0000
AAAGAUAAU	chr5:43644758-43644998(+)$1	240	62	71	14.4218
ucagaaaau	chr12:102116856-102117096(+)$1	240	19	28	12.3125
AAAGACAAG	chr6:87966405-87966645(+)$1	240	6	15	10.8281
AAGGAGAAU	chr1:170004494-170004743(-)$1	249	9	18	10.7500
ACAGAAAAA	chr2:33810578-33810818(-)$1	240	60	69	12.0781
AAGGAAAAU	chr5:33461211-33461451(+)$1	240	7	16	14.2656
GAAGGAAAU	chr15:72190464-72190704(-)$1	240	33	42	11.1406
CAGGAAAAU	chr4:24556351-24556591(-)$1	240	53	62	11.0625
AAAGAAAAG	chr11:47774427-47774667(-)$1	240	223	232	14.7343
AUAGAAAAG	chr6:7585949-7586189(+)$1	240	226	235	11.2187
AGAAAAAAU	chr19:37036638-37036878(-)$1	240	177	186	12.2343
AGAGAAAAU	chr7:107221164-107221407(+)$1	243	12	21	15.2031
GAAGAAAAA	chr15:64423901-64424141(+)$1	240	88	97	12.1562
AAACUAAAU	chr10:98286905-98287145(-)$1	240	10	19	10.5937
UCAGAAAAU	chr5:102440194-102440434(-)$1	240	147	156	12.3125
AAUGACAAU	chr18:214495-214735(-)$1	240	86	95	10.4375
AAAGAAAAA	chr15:48434387-48434667(-)$1	280	265	274	15.2031
AAUGAGAAU	chr13:39585374-39585614(-)$1	240	210	219	10.8281
AAAGAAAAA	chr14:61442491-61442731(-)$1	240	45	54	15.2031
GUAGAAAAU	chr3:56682928-56683168(-)$1	240	5	14	11.6875
AAACAAAAG	chr3:125295003-125295243(-)$1	240	2	11	11.4531
AAAGAAGAA	chr11:32956745-32956985(+)$1	240	222	231	11.0625
AAAGAAACU	chr1:100174500-100174740(-)$1	240	208	217	14.1093
AGAGAAAAU	chr3:121435710-121435950(-)$1	240	82	91	15.2031
GAAGAAGAU	chr2:203071820-203072101(-)$1	281	69	78	11.0625
AAAGAGAAC	chr13:41507448-41507688(-)$1	240	2	11	10.9843
AAAAAGAAU	chr16:57282410-57282650(+)$1	240	6	15	11.7656
AAAGGUAAU	chr12:62954694-62954934(+)$1	240	195	204	10.3593
AAAAAAUAU	chr3:37032980-37033220(-)$1	240	6	15	11.1406
CAAGAAAAA	chr2:223773428-223773709(+)$1	281	206	215	12.0000
AAAGAAUAU	chr3:160155801-160156041(-)$1	240	215	224	14.1093
AAAGAAGAU	chr3:129155750-129155990(-)$1	240	146	155	14.1093
AAAAAAAAU	chr9:32542129-32542369(-)$1	240	100	109	15.2812
AAAAGAAAU	chr5:79770395-79770635(+)$1	240	145	154	11.2187
AAAGAGAAA	chr1:154524467-154524707(-)$1	240	91	100	11.6875
UGAGAAAAU	chr5:76342233-76342473(+)$1	240	141	150	12.3906
AGAGAAAAA	chr14:60585107-60585347(+)$1	240	19	28	12.1562
UAAGAAAGU	chr1:165712392-165712632(-)$1	240	27	36	11.2968
AAACAAAUU	chr13:21721358-21721608(+)$1	250	223	232	10.7500
AAACAAACU	chr14:39536342-39536582(-)$1	240	125	134	10.8281
AAAAAAACU	chr4:17825195-17825435(+)$1	240	74	83	11.1406
AAAGAUAAU	chr11:32997910-32998150(+)$1	240	170	179	14.4218
AAAGAGAGU	chr1:64038061-64038301(+)$1	240	17	26	10.5937
AAAGGAAAU	chr13:48938928-48939168(+)$1	240	187	196	14.1875
ACAGAACAU	chr1:165697120-165697363(-)$1	243	1	10	10.9062
UGAGAAAAU	chr3:15288160-15288400(+)$1	240	142	151	12.3906
AAAUGAAAU	chr15:64458167-64458416(-)$1	249	187	196	10.7500
UAAAAAAAU	chr10:32328177-32328417(-)$1	240	215	224	12.4687
ACAGAAAAA	chr5:176562801-176563041(+)$1	240	7	16	12.0781
GAACAAAAU	chr14:96779596-96779836(-)$1	240	186	195	11.9218
AAAGAGCAU	chr11:9459608-9459848(+)$1	240	146	155	10.5156

#otherMatches

#Struct PSSM
ggiiiiiii	chrX:109416570-109416810(+)$1	240	93	102	15.0468
ggggg5555	chr3:122591304-122591544(+)$1	240	141	150	11.2187
:::::::::	chr5:134086460-134086700(+)$1	240	215	224	15.2812
=======:g	chr4:71895044-71895284(+)$1	240	170	179	11.2187
fffuuuuuu	chr1:214816452-214816692(+)$1	240	38	47	12.3125
zzziiiiii	chr6:108375617-108375857(-)$1	240	186	195	10.9062
dd[a[ffff	chr7:77379176-77379416(+)$1	240	28	37	11.2968
}CCC:::::	chr11:10821615-10821865(-)$1	250	212	221	12.0781
hhhh]dddd	chr17:60060310-60060550(-)$1	240	94	103	10.9062
GGG::::::	chr5:132228659-132228899(-)$1	240	52	61	11.3750
gpppppppg	chr11:94917483-94917723(-)$1	240	85	94	14.1093
ggggggg]b	chr6:99819315-99819555(-)$1	240	163	172	10.8281
:::::::::	chr1:237060821-237061071(+)$1	250	9	18	12.0000
eeee[bb[g	chr5:43644758-43644998(+)$1	240	62	71	14.4218
ffff"""dd	chr12:102116856-102117096(+)$1	240	19	28	12.3125
:::::eeee	chr6:87966405-87966645(+)$1	240	6	15	10.8281
ggggggg""	chr1:170004494-170004743(-)$1	249	9	18	10.7500
hhhhhhh""	chr2:33810578-33810818(-)$1	240	60	69	12.0781
GGLLLEEEE	chr5:33461211-33461451(+)$1	240	7	16	14.2656
####ggggg	chr15:72190464-72190704(-)$1	240	33	42	11.1406
bdddd%%%%	chr4:24556351-24556591(-)$1	240	53	62	11.0625
ffff22ddd	chr11:47774427-47774667(-)$1	240	223	232	14.7343
fffff333d	chr6:7585949-7586189(+)$1	240	226	235	11.2187
66666dddd	chr19:37036638-37036878(-)$1	240	177	186	12.2343
[dddd####	chr7:107221164-107221407(+)$1	243	12	21	15.2031
gggggg"""	chr15:64423901-64424141(+)$1	240	88	97	12.1562
FFFFF::::	chr10:98286905-98287145(-)$1	240	10	19	10.5937
^^^^^^^^^	chr5:102440194-102440434(-)$1	240	147	156	12.3125
qqqccc:::	chr18:214495-214735(-)$1	240	86	95	10.4375
55eeeee::	chr15:48434387-48434667(-)$1	280	265	274	15.2031
:::JJJJJJ	chr13:39585374-39585614(-)$1	240	210	219	10.8281
iiiii::::	chr14:61442491-61442731(-)$1	240	45	54	15.2031
GGGGGGG::	chr3:56682928-56683168(-)$1	240	5	14	11.6875
::::JJJJJ	chr3:125295003-125295243(-)$1	240	2	11	11.4531
ppeeeee::	chr11:32956745-32956985(+)$1	240	222	231	11.0625
^^^^^^eee	chr1:100174500-100174740(-)$1	240	208	217	14.1093
:::::::::	chr3:121435710-121435950(-)$1	240	82	91	15.2031
ggghhhhhh	chr2:203071820-203072101(-)$1	281	69	78	11.0625
:::::::BB	chr13:41507448-41507688(-)$1	240	2	11	10.9843
%%%%%ccco	chr16:57282410-57282650(+)$1	240	6	15	11.7656
mmmbb]eee	chr12:62954694-62954934(+)$1	240	195	204	10.3593
HHHHHHKKE	chr3:37032980-37033220(-)$1	240	6	15	11.1406
333gggggg	chr2:223773428-223773709(+)$1	281	206	215	12.0000
22dddd::E	chr3:160155801-160156041(-)$1	240	215	224	14.1093
mccc]gggg	chr3:129155750-129155990(-)$1	240	146	155	14.1093
TTTTTTTTT	chr9:32542129-32542369(-)$1	240	100	109	15.2812
b!!bb!!ee	chr5:79770395-79770635(+)$1	240	145	154	11.2187
:cccdddd[	chr1:154524467-154524707(-)$1	240	91	100	11.6875
ee666666d	chr5:76342233-76342473(+)$1	240	141	150	12.3906
!ggggggg[	chr14:60585107-60585347(+)$1	240	19	28	12.1562
IIIIIIII:	chr1:165712392-165712632(-)$1	240	27	36	11.2968
^^^^^^^^^	chr13:21721358-21721608(+)$1	250	223	232	10.7500
:::::::::	chr14:39536342-39536582(-)$1	240	125	134	10.8281
pppppppdd	chr4:17825195-17825435(+)$1	240	74	83	11.1406
:::ddddoo	chr11:32997910-32998150(+)$1	240	170	179	14.4218
iiggggggg	chr1:64038061-64038301(+)$1	240	17	26	10.5937
IIIIHHHHH	chr13:48938928-48939168(+)$1	240	187	196	14.1875
:::::::II	chr1:165697120-165697363(-)$1	243	1	10	10.9062
ffff55555	chr3:15288160-15288400(+)$1	240	142	151	12.3906
44ggggggg	chr15:64458167-64458416(-)$1	249	187	196	10.7500
e>>>>>>>>	chr10:32328177-32328417(-)$1	240	215	224	12.4687
EEEEEPPPP	chr5:176562801-176563041(+)$1	240	7	16	12.0781
eeeee4444	chr14:96779596-96779836(-)$1	240	186	195	11.9218
cIIIIIIII	chr11:9459608-9459848(+)$1	240	146	155	10.5156

#DB
))(((((((	chrX:109416570-109416810(+)$1	1	93	102	15.0468
)))))....	chr3:122591304-122591544(+)$1	1	141	150	11.2187
.........	chr5:134086460-134086700(+)$1	1	215	224	15.2812
))))))).(	chr4:71895044-71895284(+)$1	1	170	179	11.2187
(((......	chr1:214816452-214816692(+)$1	1	38	47	12.3125
...))))))	chr6:108375617-108375857(-)$1	1	186	195	10.9062
((.(.((((	chr7:77379176-77379416(+)$1	1	28	37	11.2968
.))).....	chr11:10821615-10821865(-)$1	1	212	221	12.0781
)))).))))	chr17:60060310-60060550(-)$1	1	94	103	10.9062
(((......	chr5:132228659-132228899(-)$1	1	52	61	11.3750
(.......)	chr11:94917483-94917723(-)$1	1	85	94	14.1093
))))))).)	chr6:99819315-99819555(-)$1	1	163	172	10.8281
.........	chr1:237060821-237061071(+)$1	1	9	18	12.0000
((((.((.(	chr5:43644758-43644998(+)$1	1	62	71	14.4218
((((...((	chr12:102116856-102117096(+)$1	1	19	28	12.3125
.....((((	chr6:87966405-87966645(+)$1	1	6	15	10.8281
(((((((..	chr1:170004494-170004743(-)$1	1	9	18	10.7500
(((((((..	chr2:33810578-33810818(-)$1	1	60	69	12.0781
((...((((	chr5:33461211-33461451(+)$1	1	7	16	14.2656
....(((((	chr15:72190464-72190704(-)$1	1	33	42	11.1406
)((((....	chr4:24556351-24556591(-)$1	1	53	62	11.0625
))))..)))	chr11:47774427-47774667(-)$1	1	223	232	14.7343
)))))...)	chr6:7585949-7586189(+)$1	1	226	235	11.2187
.....))))	chr19:37036638-37036878(-)$1	1	177	186	12.2343
.((((....	chr7:107221164-107221407(+)$1	1	12	21	15.2031
((((((...	chr15:64423901-64424141(+)$1	1	88	97	12.1562
(((((....	chr10:98286905-98287145(-)$1	1	10	19	10.5937
.........	chr5:102440194-102440434(-)$1	1	147	156	12.3125
...)))...	chr18:214495-214735(-)$1	1	86	95	10.4375
..)))))..	chr15:48434387-48434667(-)$1	1	265	274	15.2031
...))))))	chr13:39585374-39585614(-)$1	1	210	219	10.8281
)))))....	chr14:61442491-61442731(-)$1	1	45	54	15.2031
(((((((..	chr3:56682928-56683168(-)$1	1	5	14	11.6875
....(((((	chr3:125295003-125295243(-)$1	1	2	11	11.4531
..)))))..	chr11:32956745-32956985(+)$1	1	222	231	11.0625
......)))	chr1:100174500-100174740(-)$1	1	208	217	14.1093
.........	chr3:121435710-121435950(-)$1	1	82	91	15.2031
)))))))))	chr2:203071820-203072101(-)$1	1	69	78	11.0625
.......((	chr13:41507448-41507688(-)$1	1	2	11	10.9843
.....(((.	chr16:57282410-57282650(+)$1	1	6	15	11.7656
...)).)))	chr12:62954694-62954934(+)$1	1	195	204	10.3593
((((((..(	chr3:37032980-37033220(-)$1	1	6	15	11.1406
...))))))	chr2:223773428-223773709(+)$1	1	206	215	12.0000
..))))..)	chr3:160155801-160156041(-)$1	1	215	224	14.1093
.))).))))	chr3:129155750-129155990(-)$1	1	146	155	14.1093
.........	chr9:32542129-32542369(-)$1	1	100	109	15.2812
(..((..((	chr5:79770395-79770635(+)$1	1	145	154	11.2187
.(((((((.	chr1:154524467-154524707(-)$1	1	91	100	11.6875
))......)	chr5:76342233-76342473(+)$1	1	141	150	12.3906
.(((((((.	chr14:60585107-60585347(+)$1	1	19	28	12.1562
((((((((.	chr1:165712392-165712632(-)$1	1	27	36	11.2968
.........	chr13:21721358-21721608(+)$1	1	223	232	10.7500
.........	chr14:39536342-39536582(-)$1	1	125	134	10.8281
.......))	chr4:17825195-17825435(+)$1	1	74	83	11.1406
...((((..	chr11:32997910-32998150(+)$1	1	170	179	14.4218
(((((((((	chr1:64038061-64038301(+)$1	1	17	26	10.5937
)))))))))	chr13:48938928-48939168(+)$1	1	187	196	14.1875
.......((	chr1:165697120-165697363(-)$1	1	1	10	10.9062
)))).....	chr3:15288160-15288400(+)$1	1	142	151	12.3906
..)))))))	chr15:64458167-64458416(-)$1	1	187	196	10.7500
)........	chr10:32328177-32328417(-)$1	1	215	224	12.4687
(((((....	chr5:176562801-176563041(+)$1	1	7	16	12.0781
)))))....	chr14:96779596-96779836(-)$1	1	186	195	11.9218
)))))))))	chr11:9459608-9459848(+)$1	1	146	155	10.5156

#PSSM
A : 0.68	U : 0.12	G : 0.09	C : 0.06	a : 0.01	u : 0.01	
A : 0.71	G : 0.12	C : 0.09	U : 0.03	a : 0.01	c : 0.01	
A : 0.84	G : 0.06	U : 0.06	u : 0.01	a : 0.01	
G : 0.71	A : 0.14	C : 0.07	U : 0.03	u : 0.01	g : 0.01	
A : 0.85	G : 0.07	a : 0.03	C : 0.01	U : 0.01	
A : 0.78	G : 0.10	U : 0.04	a : 0.03	C : 0.03	
A : 0.84	U : 0.04	G : 0.04	a : 0.03	C : 0.03	
A : 0.84	G : 0.04	C : 0.04	U : 0.03	a : 0.03	
U : 0.73	A : 0.15	G : 0.06	u : 0.03	C : 0.01	

#score	781.59375
#seq	64
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuRMNase_Kishore2011f_hg19_CDS_m2_run2.nuc.txt

#NT

#otherMatches

#Struct PSSM
gggggg22bb22bb::DDDD{FFFFFFccc[ffffff####aooooooa4444ffffff]ccc::::eeeeea####a[eeeee!!ddddoooooodddd22eeeeea333a]eeeeedddd[gggggggmmmmggggggg333dddd::::eeeee[hhhhhhhhoooooohhhhhhhh]eeeee:ffffff"""ccc!!cccooooooccc22ccc]ffffff::::::::::::::FFFFFF}DDDDCCCYYGGGGGGG:::::::::ccc[ffffffbb!!cccmmmmccc	chr19:37854206-37854567(+)$1	361	48	343	885.0000

#DB
))))))..))..))..((((.(((((((((.((((((....(......)....)))))).)))....((((((....(.(((((..((((......))))..))))))...).)))))((((.(((((((....)))))))...))))....(((((.((((((((......)))))))).))))).((((((...(((..(((......)))..))).))))))..............)))))).)))))))..))))))).........(((.((((((((..(((....)))	chr19:37854206-37854567(+)$1	1	48	343	885.0000

#PSSM
U : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	

#score	885.0
#seq	1
#width	295
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012d_hg19_CDS_m3_run2.nuc.txt

#NT
UGGA	chr3:52442442-52442664(-)$1	222	51	55	11.9999
UGGA	chr3:184060449-184060663(+)$1	214	136	140	11.9999
UGGA	chr15:90633673-90633900(-)$1	227	40	44	11.9999
UGGA	chr14:31626029-31626243(-)$1	214	100	104	11.9999
UGGA	chr7:72848626-72848849(+)$1	223	87	91	11.9999
UGGA	chr2:27354515-27354738(-)$1	223	160	164	11.9999
UGGA	chr3:150285590-150285810(+)$1	220	169	173	11.9999
UGGA	chr6:31753332-31753598(-)$1	266	116	120	11.9999
UGGA	chr16:67271853-67272068(-)$1	215	61	65	11.9999
UGGA	chr19:2120833-2121082(-)$1	249	23	27	11.9999
UGGA	chr19:41306542-41306803(+)$1	261	8	12	11.9999
UGGA	chr5:71495130-71495361(+)$1	231	2	6	11.9999
UGGA	chr19:16989307-16989551(+)$1	244	61	65	11.9999
UGGA	chr11:62414702-62414922(-)$1	220	81	85	11.9999
UGGA	chr3:127325033-127325278(+)$1	245	44	48	11.9999
UGGA	chr2:242176023-242176255(-)$1	232	221	225	11.9999
UGGA	chr17:79803480-79803693(-)$1	213	171	175	11.9999
UGGA	chr21:33060560-33060779(-)$1	219	4	8	11.9999
UGGA	chr11:64081415-64081632(+)$1	217	209	213	11.9999
UGGA	chr15:69548049-69548272(+)$1	223	177	181	11.9999
UGGA	chr19:13875278-13875503(+)$1	225	4	8	11.9999
UGGA	chr2:207011663-207011883(-)$1	220	33	37	11.9999
UGGA	chr7:156746773-156746996(+)$1	223	61	65	11.9999
UGGA	chr16:71683418-71683635(-)$1	217	187	191	11.9999
UGGA	chr19:10260157-10260392(-)$1	235	160	164	11.9999
UGGA	chr3:48474133-48474357(-)$1	224	7	11	11.9999
UGGA	chr16:84693369-84693604(+)$1	235	21	25	11.9999
UGGA	chr20:3128399-3128644(-)$1	245	30	34	11.9999
UGGA	chr3:9780858-9781081(+)$1	223	33	37	11.9999
UGGA	chr19:36109227-36109450(+)$1	223	198	202	11.9999
UGGA	chr19:13189352-13189569(+)$1	217	104	108	11.9999
UGGA	chr10:1170167-1170384(+)$1	217	201	205	11.9999
UGGA	chr9:139937748-139937965(-)$1	217	65	69	11.9999
UGGA	chr10:101464285-101464502(+)$1	217	96	100	11.9999
UGGA	chr8:141551312-141551541(-)$1	229	97	101	11.9999
UGGA	chr4:144106713-144106934(+)$1	221	38	42	11.9999
UGGA	chr13:30782616-30782839(-)$1	223	119	123	11.9999
UGGA	chr9:136910325-136910537(-)$1	212	1	5	11.9999
UGGA	chr21:46193403-46193632(-)$1	229	113	117	11.9999
UGGA	chr17:79817023-79817252(-)$1	229	88	92	11.9999
UGGA	chr9:131587175-131587404(-)$1	229	10	14	11.9999
UGGA	chr16:46960761-46961037(+)$1	276	118	122	11.9999
UGGA	chr1:36558844-36559064(+)$1	220	45	49	11.9999
UGGA	chr19:11558292-11558512(+)$1	220	161	165	11.9999
UGGA	chr6:151672263-151672492(+)$1	229	72	76	11.9999
UGGA	chr11:65389667-65389902(+)$1	235	19	23	11.9999
UGGA	chr21:33706453-33706676(-)$1	223	59	63	11.9999
UGGA	chr9:139910765-139910983(-)$1	218	75	79	11.9999
UGGA	chr16:89351758-89352038(-)$1	280	170	174	11.9999
UGGA	chr21:38308810-38309039(-)$1	229	214	218	11.9999
UGGA	chr14:104641397-104641644(+)$1	247	18	22	11.9999
UGGA	chr3:30713773-30713998(+)$1	225	112	116	11.9999
UGGA	chr22:19119707-19119938(-)$1	231	2	6	11.9999
UGGA	chr17:46136278-46136501(+)$1	223	3	7	11.9999
UGGA	chr17:73488507-73488723(+)$1	216	60	64	11.9999
UGGA	chr13:42873912-42874128(+)$1	216	142	146	11.9999
UGGA	chr3:14693222-14693447(+)$1	225	96	100	11.9999
UGGA	chr21:47671400-47671628(-)$1	228	82	86	11.9999
UGGA	chr14:23344545-23344765(+)$1	220	198	202	11.9999
UGGA	chr12:58217731-58217957(-)$1	226	110	114	11.9999
UGGA	chr10:5790595-5790816(+)$1	221	143	147	11.9999
UGGA	chr10:75295978-75296201(-)$1	223	18	22	11.9999
UGGA	chr1:155447764-155448015(-)$1	251	118	122	11.9999
UGGA	chr1:36210956-36211181(-)$1	225	84	88	11.9999
UGGA	chr12:49171140-49171363(-)$1	223	7	11	11.9999
UGGA	chr6:138751900-138752176(-)$1	276	68	72	11.9999
UGGA	chr15:44149100-44149330(+)$1	230	126	130	11.9999
UGGA	chr1:38039926-38040157(-)$1	231	102	106	11.9999
UGGA	chr1:94047937-94048163(-)$1	226	100	104	11.9999
UGGA	chr9:35750822-35751034(+)$1	212	179	183	11.9999
UGGA	chr1:28800514-28800730(+)$1	216	31	35	11.9999
UGGA	chr12:69202146-69202374(+)$1	228	10	14	11.9999
UGGA	chr3:10107007-10107224(+)$1	217	18	22	11.9999
UGGA	chr19:15281445-15281717(-)$1	272	95	99	11.9999
UGGA	chr16:67876982-67877221(+)$1	239	17	21	11.9999
UGGA	chr7:44880403-44880647(-)$1	244	86	90	11.9999
UGGA	chr14:53618928-53619142(-)$1	214	71	75	11.9999
UGGA	chr21:45540821-45541070(+)$1	249	19	23	11.9999
UGGA	chr11:71726621-71726847(-)$1	226	115	119	11.9999

#otherMatches

#Struct PSSM
ccc!	chr15:41280038-41280257(-)$1	219	106	110	11.9999
FFFL	chr3:52442442-52442664(-)$1	222	51	55	11.9999
b]ii	chr3:184060449-184060663(+)$1	214	136	140	11.9999
cccm	chr15:90633673-90633900(-)$1	227	40	44	11.9999
:eee	chr14:31626029-31626243(-)$1	214	100	104	11.9999
:ddd	chr7:72848626-72848849(+)$1	223	87	91	11.9999
!!cc	chr2:27354515-27354738(-)$1	223	160	164	11.9999
eeee	chr3:150285590-150285810(+)$1	220	169	173	11.9999
eee3	chr6:31753332-31753598(-)$1	266	116	120	11.9999
cc33	chr16:67271853-67272068(-)$1	215	61	65	11.9999
{BB:	chr19:2120833-2121082(-)$1	249	23	27	11.9999
GGG:	chr19:41306542-41306803(+)$1	261	8	12	11.9999
FFFF	chr5:71495130-71495361(+)$1	231	2	6	11.9999
b]dd	chr19:16989307-16989551(+)$1	244	61	65	11.9999
4fff	chr11:62414702-62414922(-)$1	220	81	85	11.9999
ddd:	chr3:127325033-127325278(+)$1	245	44	48	11.9999
GGGG	chr2:242176023-242176255(-)$1	232	221	225	11.9999
eee[	chr17:79803480-79803693(-)$1	213	171	175	11.9999
EGGG	chr21:33060560-33060779(-)$1	219	4	8	11.9999
YA}E	chr11:64081415-64081632(+)$1	217	209	213	11.9999
fff3	chr15:69548049-69548272(+)$1	223	177	181	11.9999
e[a[	chr19:13875278-13875503(+)$1	225	4	8	11.9999
b333	chr2:207011663-207011883(-)$1	220	33	37	11.9999
eee[	chr7:156746773-156746996(+)$1	223	61	65	11.9999
III:	chr16:71683418-71683635(-)$1	217	187	191	11.9999
2bb:	chr19:10260157-10260392(-)$1	235	160	164	11.9999
:ddd	chr3:48474133-48474357(-)$1	224	7	11	11.9999
DDDD	chr16:84693369-84693604(+)$1	235	21	25	11.9999
{EEE	chr20:3128399-3128644(-)$1	245	30	34	11.9999
{BB:	chr3:9780858-9781081(+)$1	223	33	37	11.9999
>bb5	chr19:36109227-36109450(+)$1	223	198	202	11.9999
ddd6	chr19:13189352-13189569(+)$1	217	104	108	11.9999
EEEC	chr10:1170167-1170384(+)$1	217	201	205	11.9999
rrrr	chr9:139937748-139937965(-)$1	217	65	69	11.9999
lccc	chr10:101464285-101464502(+)$1	217	96	100	11.9999
EEEE	chr8:141551312-141551541(-)$1	229	97	101	11.9999
fffm	chr4:144106713-144106934(+)$1	221	38	42	11.9999
===:	chr13:30782616-30782839(-)$1	223	119	123	11.9999
::::	chr9:136910325-136910537(-)$1	212	1	5	11.9999
gggg	chr21:46193403-46193632(-)$1	229	113	117	11.9999
cddd	chr17:79817023-79817252(-)$1	229	88	92	11.9999
FFFF	chr9:131587175-131587404(-)$1	229	10	14	11.9999
GGGG	chr16:46960761-46961037(+)$1	276	118	122	11.9999
eee:	chr1:36558844-36559064(+)$1	220	45	49	11.9999
B}BB	chr19:11558292-11558512(+)$1	220	161	165	11.9999
++++	chr6:151672263-151672492(+)$1	229	72	76	11.9999
CBB{	chr11:65389667-65389902(+)$1	235	19	23	11.9999
bb]d	chr21:33706453-33706676(-)$1	223	59	63	11.9999
A{II	chr9:139910765-139910983(-)$1	218	75	79	11.9999
ddrr	chr16:89351758-89352038(-)$1	280	170	174	11.9999
gggg	chr21:38308810-38309039(-)$1	229	214	218	11.9999
[bb!	chr14:104641397-104641644(+)$1	247	18	22	11.9999
eddd	chr3:30713773-30713998(+)$1	225	112	116	11.9999
ffff	chr22:19119707-19119938(-)$1	231	2	6	11.9999
DDKK	chr17:46136278-46136501(+)$1	223	3	7	11.9999
===:	chr17:73488507-73488723(+)$1	216	60	64	11.9999
fffm	chr13:42873912-42874128(+)$1	216	142	146	11.9999
rrrr	chr3:14693222-14693447(+)$1	225	96	100	11.9999
{BBK	chr21:47671400-47671628(-)$1	228	82	86	11.9999
DDDD	chr14:23344545-23344765(+)$1	220	198	202	11.9999
====	chr12:58217731-58217957(-)$1	226	110	114	11.9999
gggn	chr10:5790595-5790816(+)$1	221	143	147	11.9999
PCCC	chr10:75295978-75296201(-)$1	223	18	22	11.9999
====	chr1:155447764-155448015(-)$1	251	118	122	11.9999
::ee	chr1:36210956-36211181(-)$1	225	84	88	11.9999
dddd	chr12:49171140-49171363(-)$1	223	7	11	11.9999
^ggg	chr6:138751900-138752176(-)$1	276	68	72	11.9999
}EEE	chr15:44149100-44149330(+)$1	230	126	130	11.9999
deee	chr1:38039926-38040157(-)$1	231	102	106	11.9999
KBB{	chr1:94047937-94048163(-)$1	226	100	104	11.9999
hhhh	chr9:35750822-35751034(+)$1	212	179	183	11.9999
oddd	chr1:28800514-28800730(+)$1	216	31	35	11.9999
rrrr	chr12:69202146-69202374(+)$1	228	10	14	11.9999
ffff	chr3:10107007-10107224(+)$1	217	18	22	11.9999
eees	chr19:15281445-15281717(-)$1	272	95	99	11.9999
eedd	chr16:67876982-67877221(+)$1	239	17	21	11.9999
eee[	chr7:44880403-44880647(-)$1	244	86	90	11.9999
ddd2	chr14:53618928-53619142(-)$1	214	71	75	11.9999
cccd	chr21:45540821-45541070(+)$1	249	19	23	11.9999
EEE:	chr11:71726621-71726847(-)$1	226	115	119	11.9999

#DB
(((.	chr15:41280038-41280257(-)$1	1	106	110	11.9999
(((.	chr3:52442442-52442664(-)$1	1	51	55	11.9999
).))	chr3:184060449-184060663(+)$1	1	136	140	11.9999
(((.	chr15:90633673-90633900(-)$1	1	40	44	11.9999
.(((	chr14:31626029-31626243(-)$1	1	100	104	11.9999
.(((	chr7:72848626-72848849(+)$1	1	87	91	11.9999
..((	chr2:27354515-27354738(-)$1	1	160	164	11.9999
))))	chr3:150285590-150285810(+)$1	1	169	173	11.9999
))).	chr6:31753332-31753598(-)$1	1	116	120	11.9999
))..	chr16:67271853-67272068(-)$1	1	61	65	11.9999
.((.	chr19:2120833-2121082(-)$1	1	23	27	11.9999
(((.	chr19:41306542-41306803(+)$1	1	8	12	11.9999
((((	chr5:71495130-71495361(+)$1	1	2	6	11.9999
).))	chr19:16989307-16989551(+)$1	1	61	65	11.9999
.)))	chr11:62414702-62414922(-)$1	1	81	85	11.9999
))).	chr3:127325033-127325278(+)$1	1	44	48	11.9999
))))	chr2:242176023-242176255(-)$1	1	221	225	11.9999
(((.	chr17:79803480-79803693(-)$1	1	171	175	11.9999
((((	chr21:33060560-33060779(-)$1	1	4	8	11.9999
.).)	chr11:64081415-64081632(+)$1	1	209	213	11.9999
))).	chr15:69548049-69548272(+)$1	1	177	181	11.9999
(.(.	chr19:13875278-13875503(+)$1	1	4	8	11.9999
)...	chr2:207011663-207011883(-)$1	1	33	37	11.9999
(((.	chr7:156746773-156746996(+)$1	1	61	65	11.9999
))).	chr16:71683418-71683635(-)$1	1	187	191	11.9999
.)).	chr19:10260157-10260392(-)$1	1	160	164	11.9999
.(((	chr3:48474133-48474357(-)$1	1	7	11	11.9999
((((	chr16:84693369-84693604(+)$1	1	21	25	11.9999
.(((	chr20:3128399-3128644(-)$1	1	30	34	11.9999
.((.	chr3:9780858-9781081(+)$1	1	33	37	11.9999
.)).	chr19:36109227-36109450(+)$1	1	198	202	11.9999
))).	chr19:13189352-13189569(+)$1	1	104	108	11.9999
))))	chr10:1170167-1170384(+)$1	1	201	205	11.9999
....	chr9:139937748-139937965(-)$1	1	65	69	11.9999
.)))	chr10:101464285-101464502(+)$1	1	96	100	11.9999
((((	chr8:141551312-141551541(-)$1	1	97	101	11.9999
(((.	chr4:144106713-144106934(+)$1	1	38	42	11.9999
))).	chr13:30782616-30782839(-)$1	1	119	123	11.9999
....	chr9:136910325-136910537(-)$1	1	1	5	11.9999
))))	chr21:46193403-46193632(-)$1	1	113	117	11.9999
((((	chr17:79817023-79817252(-)$1	1	88	92	11.9999
((((	chr9:131587175-131587404(-)$1	1	10	14	11.9999
((((	chr16:46960761-46961037(+)$1	1	118	122	11.9999
))).	chr1:36558844-36559064(+)$1	1	45	49	11.9999
).))	chr19:11558292-11558512(+)$1	1	161	165	11.9999
....	chr6:151672263-151672492(+)$1	1	72	76	11.9999
(((.	chr11:65389667-65389902(+)$1	1	19	23	11.9999
)).)	chr21:33706453-33706676(-)$1	1	59	63	11.9999
(.((	chr9:139910765-139910983(-)$1	1	75	79	11.9999
((..	chr16:89351758-89352038(-)$1	1	170	174	11.9999
))))	chr21:38308810-38309039(-)$1	1	214	218	11.9999
.((.	chr14:104641397-104641644(+)$1	1	18	22	11.9999
((((	chr3:30713773-30713998(+)$1	1	112	116	11.9999
((((	chr22:19119707-19119938(-)$1	1	2	6	11.9999
((..	chr17:46136278-46136501(+)$1	1	3	7	11.9999
))).	chr17:73488507-73488723(+)$1	1	60	64	11.9999
(((.	chr13:42873912-42874128(+)$1	1	142	146	11.9999
....	chr3:14693222-14693447(+)$1	1	96	100	11.9999
.((.	chr21:47671400-47671628(-)$1	1	82	86	11.9999
))))	chr14:23344545-23344765(+)$1	1	198	202	11.9999
))))	chr12:58217731-58217957(-)$1	1	110	114	11.9999
(((.	chr10:5790595-5790816(+)$1	1	143	147	11.9999
.(((	chr10:75295978-75296201(-)$1	1	18	22	11.9999
))))	chr1:155447764-155448015(-)$1	1	118	122	11.9999
..((	chr1:36210956-36211181(-)$1	1	84	88	11.9999
((((	chr12:49171140-49171363(-)$1	1	7	11	11.9999
.)))	chr6:138751900-138752176(-)$1	1	68	72	11.9999
.)))	chr15:44149100-44149330(+)$1	1	126	130	11.9999
))))	chr1:38039926-38040157(-)$1	1	102	106	11.9999
.((.	chr1:94047937-94048163(-)$1	1	100	104	11.9999
))))	chr9:35750822-35751034(+)$1	1	179	183	11.9999
.)))	chr1:28800514-28800730(+)$1	1	31	35	11.9999
....	chr12:69202146-69202374(+)$1	1	10	14	11.9999
((((	chr3:10107007-10107224(+)$1	1	18	22	11.9999
(((.	chr19:15281445-15281717(-)$1	1	95	99	11.9999
((((	chr16:67876982-67877221(+)$1	1	17	21	11.9999
(((.	chr7:44880403-44880647(-)$1	1	86	90	11.9999
))).	chr14:53618928-53619142(-)$1	1	71	75	11.9999
((((	chr21:45540821-45541070(+)$1	1	19	23	11.9999
(((.	chr11:71726621-71726847(-)$1	1	115	119	11.9999

#PSSM
U : 0.99	
G : 0.99	
G : 0.99	
A : 0.99	

#score	959.9999999999995
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_CDS_m1_run2.nuc.txt

#NT
UUU	chr2:55825477-55825717(-)$1	240	71	74	9.0000
UUU	chr3:56682928-56683168(-)$1	240	97	100	9.0000
UUU	chr14:31576154-31576395(-)$1	241	8	11	9.0000
UUU	chr2:203071820-203072101(-)$1	281	11	14	9.0000
UUU	chrX:70756051-70756291(+)$1	240	46	49	9.0000
UUU	chr12:105238218-105238458(-)$1	240	25	28	9.0000
UUU	chr2:148709897-148710139(-)$1	242	11	14	9.0000
UUU	chr14:60749712-60749952(+)$1	240	20	23	9.0000
UUU	chr20:50342319-50342559(-)$1	240	0	3	9.0000
UUU	chr10:103920169-103920409(+)$1	240	2	5	9.0000
UUU	chr6:108375617-108375857(-)$1	240	46	49	9.0000
UUU	chr19:42411460-42411700(+)$1	240	91	94	9.0000
UUU	chr1:64038061-64038301(+)$1	240	32	35	9.0000
UUU	chr9:19096605-19096845(-)$1	240	13	16	9.0000
UUU	chr5:54931285-54931525(-)$1	240	21	24	9.0000
UUU	chr3:182605294-182605534(+)$1	240	66	69	9.0000
UUU	chr1:63884940-63885180(+)$1	240	4	7	9.0000
UUU	chr6:99991312-99991552(-)$1	240	26	29	9.0000
UUU	chr15:49327559-49327799(-)$1	240	11	14	9.0000
UUU	chr5:137521897-137522137(+)$1	240	77	80	9.0000
UUU	chr5:79770395-79770635(+)$1	240	3	6	9.0000
UUU	chr5:61778838-61779078(+)$1	240	43	46	9.0000
UUU	chr6:146126254-146126494(-)$1	240	98	101	9.0000
UUU	chr13:73336069-73336309(-)$1	240	21	24	9.0000
UUU	chr19:34916921-34917161(+)$1	240	3	6	9.0000
UUU	chr1:155227030-155227270(-)$1	240	75	78	9.0000
UUU	chr5:133725938-133726178(+)$1	240	32	35	9.0000
UUU	chr1:224377685-224377925(+)$1	240	15	18	9.0000
UUU	chrX:13754635-13754875(+)$1	240	34	37	9.0000
UUU	chr19:32930585-32930825(+)$1	240	2	5	9.0000
UUU	chr6:111628590-111628830(-)$1	240	8	11	9.0000
UUU	chr11:43515349-43515589(+)$1	240	30	33	9.0000
UUU	chr7:23509626-23509866(-)$1	240	15	18	9.0000
UUU	chrX:100880844-100881084(+)$1	240	1	4	9.0000
UUU	chr5:94005815-94006056(+)$1	241	18	21	9.0000
UUU	chr17:65074249-65074489(-)$1	240	101	104	9.0000
UUU	chr19:44739401-44739641(+)$1	240	111	114	9.0000
UUU	chr12:72025965-72026205(-)$1	240	112	115	9.0000
UUU	chr12:121746152-121746392(-)$1	240	149	152	9.0000
UUU	chr19:14203260-14203500(-)$1	240	36	39	9.0000
UUU	chr3:148765778-148766018(-)$1	240	51	54	9.0000
UUU	chr2:223339207-223339447(+)$1	240	8	11	9.0000
uuu	chr5:179041678-179041958(-)$1	280	151	154	9.0000
UUU	chrX:40456415-40456655(+)$1	240	8	11	9.0000
UUU	chr11:61187910-61188150(-)$1	240	38	41	9.0000
UUU	chr5:134235166-134235406(+)$1	240	0	3	9.0000
UUU	chr3:169801936-169802176(+)$1	240	2	5	9.0000
UUU	chr16:58584953-58585193(-)$1	240	3	6	9.0000
UUU	chr1:100174500-100174740(-)$1	240	32	35	9.0000
UUU	chr11:62344063-62344541(-)$1	478	43	46	9.0000
UUU	chr5:70860605-70860845(+)$1	240	64	67	9.0000
UUU	chrX:135080182-135080424(+)$1	242	5	8	9.0000
UUU	chr3:160155801-160156041(-)$1	240	45	48	9.0000
UUU	chr6:5260852-5261103(-)$1	251	35	38	9.0000
UUU	chr8:27680565-27680805(-)$1	240	0	3	9.0000
UUU	chr5:145522356-145522596(-)$1	240	4	7	9.0000
UUU	chr12:102154933-102155173(-)$1	240	9	12	9.0000
UUU	chr2:178096525-178096765(-)$1	240	115	118	9.0000
UUU	chr3:17052031-17052271(+)$1	240	112	115	9.0000
UUU	chr3:32533202-32533442(-)$1	240	2	5	9.0000
UUU	chr13:52592943-52593183(+)$1	240	2	5	9.0000
UUU	chr1:53699171-53699411(-)$1	240	8	11	9.0000
UUU	chrX:100667781-100668021(+)$1	240	40	43	9.0000
UUU	chr11:62343511-62343791(-)$1	280	49	52	9.0000
UUU	chr3:184018053-184018293(+)$1	240	113	116	9.0000
UUU	chr8:77776365-77776605(+)$1	240	137	140	9.0000
UUU	chr11:32954039-32954279(+)$1	240	87	90	9.0000
UUU	chr14:56078703-56078943(+)$1	240	0	3	9.0000
UUU	chr13:113459214-113459454(+)$1	240	36	39	9.0000
UUU	chr17:5386062-5386302(-)$1	240	20	23	9.0000
UUU	chr10:119043318-119043558(-)$1	240	113	116	9.0000
UUU	chr7:77379176-77379416(+)$1	240	10	13	9.0000
UUU	chr10:1038365-1038605(+)$1	240	26	29	9.0000
UUU	chr20:20617934-20618174(-)$1	240	8	11	9.0000
UUU	chr5:72798690-72798930(+)$1	240	26	29	9.0000
UUU	chr5:134086460-134086700(+)$1	240	120	123	9.0000
UUU	chr6:97246739-97246979(-)$1	240	1	4	9.0000
UUU	chr21:34931511-34931751(+)$1	240	0	3	9.0000
UUU	chr20:47686670-47686910(+)$1	240	33	36	9.0000
UUU	chr7:86825896-86826136(-)$1	240	23	26	9.0000
UUU	chr3:15288160-15288400(+)$1	240	24	27	9.0000
UUU	chr8:95780589-95780829(+)$1	240	4	7	9.0000
UUU	chr16:66592064-66592304(+)$1	240	14	17	9.0000
UUU	chr10:27037381-27037621(-)$1	240	13	16	9.0000
UUU	chr3:125295003-125295243(-)$1	240	17	20	9.0000
UUU	chr9:110091831-110092080(+)$1	249	7	10	9.0000
UUU	chr13:108881780-108882020(+)$1	240	12	15	9.0000
UUU	chr10:120450764-120451004(-)$1	240	7	10	9.0000
UUU	chr5:133295131-133295371(-)$1	240	72	75	9.0000
UUU	chr12:102179770-102180010(-)$1	240	4	7	9.0000
UUU	chr9:108123461-108123701(+)$1	240	121	124	9.0000
UUU	chr3:122591304-122591544(+)$1	240	16	19	9.0000
UUU	chr11:60658153-60658393(-)$1	240	67	70	9.0000
UUU	chr2:162247527-162247767(+)$1	240	22	25	9.0000
UUU	chr2:54101433-54101673(-)$1	240	11	14	9.0000
UUU	chr21:43413824-43414064(-)$1	240	22	25	9.0000
UUU	chr5:41917258-41917498(+)$1	240	13	16	9.0000
UUU	chr13:26788511-26788751(-)$1	240	53	56	9.0000
uuu	chr6:11134536-11134776(+)$1	240	8	11	9.0000

#otherMatches

#Struct PSSM
:::	chr5:133295088-133295328(-)$1	240	29	32	9.0000
cc]	chr2:55825477-55825717(-)$1	240	71	74	9.0000
NNN	chr3:56682928-56683168(-)$1	240	97	100	9.0000
::h	chr14:31576154-31576395(-)$1	241	8	11	9.0000
sss	chr2:203071820-203072101(-)$1	281	11	14	9.0000
DDD	chrX:70756051-70756291(+)$1	240	46	49	9.0000
"""	chr12:105238218-105238458(-)$1	240	25	28	9.0000
c##	chr2:148709897-148710139(-)$1	242	11	14	9.0000
eee	chr14:60749712-60749952(+)$1	240	20	23	9.0000
:::	chr20:50342319-50342559(-)$1	240	0	3	9.0000
:::	chr10:103920169-103920409(+)$1	240	2	5	9.0000
h[e	chr6:108375617-108375857(-)$1	240	46	49	9.0000
:::	chr19:42411460-42411700(+)$1	240	91	94	9.0000
ggg	chr1:64038061-64038301(+)$1	240	32	35	9.0000
qqq	chr9:19096605-19096845(-)$1	240	13	16	9.0000
mmm	chr5:54931285-54931525(-)$1	240	21	24	9.0000
d[c	chr3:182605294-182605534(+)$1	240	66	69	9.0000
MMM	chr1:63884940-63885180(+)$1	240	4	7	9.0000
fff	chr6:99991312-99991552(-)$1	240	26	29	9.0000
QQQ	chr15:49327559-49327799(-)$1	240	11	14	9.0000
ddt	chr5:137521897-137522137(+)$1	240	77	80	9.0000
:::	chr5:79770395-79770635(+)$1	240	3	6	9.0000
pff	chr5:61778838-61779078(+)$1	240	43	46	9.0000
ecc	chr6:146126254-146126494(-)$1	240	98	101	9.0000
$ee	chr13:73336069-73336309(-)$1	240	21	24	9.0000
:::	chr19:34916921-34917161(+)$1	240	3	6	9.0000
:::	chr1:155227030-155227270(-)$1	240	75	78	9.0000
FFF	chr5:133725938-133726178(+)$1	240	32	35	9.0000
GGG	chr1:224377685-224377925(+)$1	240	15	18	9.0000
ggg	chrX:13754635-13754875(+)$1	240	34	37	9.0000
BMM	chr19:32930585-32930825(+)$1	240	2	5	9.0000
KKE	chr6:111628590-111628830(-)$1	240	8	11	9.0000
ddd	chr11:43515349-43515589(+)$1	240	30	33	9.0000
DDD	chr7:23509626-23509866(-)$1	240	15	18	9.0000
ddd	chrX:100880844-100881084(+)$1	240	1	4	9.0000
###	chr5:94005815-94006056(+)$1	241	18	21	9.0000
d::	chr17:65074249-65074489(-)$1	240	101	104	9.0000
ggg	chr19:44739401-44739641(+)$1	240	111	114	9.0000
[dd	chr12:72025965-72026205(-)$1	240	112	115	9.0000
###	chr12:121746152-121746392(-)$1	240	149	152	9.0000
2cc	chr19:14203260-14203500(-)$1	240	36	39	9.0000
mmm	chr3:148765778-148766018(-)$1	240	51	54	9.0000
===	chr2:223339207-223339447(+)$1	240	8	11	9.0000
:::	chr5:179041678-179041958(-)$1	280	151	154	9.0000
hhh	chrX:40456415-40456655(+)$1	240	8	11	9.0000
fff	chr11:61187910-61188150(-)$1	240	38	41	9.0000
:::	chr5:134235166-134235406(+)$1	240	0	3	9.0000
:::	chr3:169801936-169802176(+)$1	240	2	5	9.0000
:::	chr16:58584953-58585193(-)$1	240	3	6	9.0000
fff	chr1:100174500-100174740(-)$1	240	32	35	9.0000
]bb	chr11:62344063-62344541(-)$1	478	43	46	9.0000
JJ:	chr5:70860605-70860845(+)$1	240	64	67	9.0000
:::	chrX:135080182-135080424(+)$1	242	5	8	9.0000
::f	chr3:160155801-160156041(-)$1	240	45	48	9.0000
sss	chr6:5260852-5261103(-)$1	251	35	38	9.0000
:::	chr8:27680565-27680805(-)$1	240	0	3	9.0000
EKK	chr5:145522356-145522596(-)$1	240	4	7	9.0000
fff	chr12:102154933-102155173(-)$1	240	9	12	9.0000
]dd	chr2:178096525-178096765(-)$1	240	115	118	9.0000
FFF	chr3:17052031-17052271(+)$1	240	112	115	9.0000
:::	chr3:32533202-32533442(-)$1	240	2	5	9.0000
GGG	chr13:52592943-52593183(+)$1	240	2	5	9.0000
===	chr1:53699171-53699411(-)$1	240	8	11	9.0000
JJJ	chrX:100667781-100668021(+)$1	240	40	43	9.0000
:::	chr11:62343511-62343791(-)$1	280	49	52	9.0000
^^^	chr3:184018053-184018293(+)$1	240	113	116	9.0000
:::	chr8:77776365-77776605(+)$1	240	137	140	9.0000
%ee	chr11:32954039-32954279(+)$1	240	87	90	9.0000
JJJ	chr14:56078703-56078943(+)$1	240	0	3	9.0000
cdd	chr13:113459214-113459454(+)$1	240	36	39	9.0000
:::	chr17:5386062-5386302(-)$1	240	20	23	9.0000
vee	chr10:119043318-119043558(-)$1	240	113	116	9.0000
g$$	chr7:77379176-77379416(+)$1	240	10	13	9.0000
ggg	chr10:1038365-1038605(+)$1	240	26	29	9.0000
qqq	chr20:20617934-20618174(-)$1	240	8	11	9.0000
:::	chr5:72798690-72798930(+)$1	240	26	29	9.0000
hhh	chr5:134086460-134086700(+)$1	240	120	123	9.0000
:ff	chr6:97246739-97246979(-)$1	240	1	4	9.0000
:hh	chr21:34931511-34931751(+)$1	240	0	3	9.0000
GGG	chr20:47686670-47686910(+)$1	240	33	36	9.0000
ddd	chr7:86825896-86826136(-)$1	240	23	26	9.0000
lle	chr3:15288160-15288400(+)$1	240	24	27	9.0000
:::	chr8:95780589-95780829(+)$1	240	4	7	9.0000
]cc	chr16:66592064-66592304(+)$1	240	14	17	9.0000
ggg	chr10:27037381-27037621(-)$1	240	13	16	9.0000
:::	chr3:125295003-125295243(-)$1	240	17	20	9.0000
mmm	chr9:110091831-110092080(+)$1	249	7	10	9.0000
ggg	chr13:108881780-108882020(+)$1	240	12	15	9.0000
gge	chr10:120450764-120451004(-)$1	240	7	10	9.0000
HHO	chr5:133295131-133295371(-)$1	240	72	75	9.0000
:ee	chr12:102179770-102180010(-)$1	240	4	7	9.0000
___	chr9:108123461-108123701(+)$1	240	121	124	9.0000
QQQ	chr3:122591304-122591544(+)$1	240	16	19	9.0000
hhh	chr11:60658153-60658393(-)$1	240	67	70	9.0000
FFF	chr2:162247527-162247767(+)$1	240	22	25	9.0000
LLF	chr2:54101433-54101673(-)$1	240	11	14	9.0000
dd%	chr21:43413824-43414064(-)$1	240	22	25	9.0000
mmm	chr5:41917258-41917498(+)$1	240	13	16	9.0000
mmm	chr13:26788511-26788751(-)$1	240	53	56	9.0000
dqq	chr6:11134536-11134776(+)$1	240	8	11	9.0000

#DB
...	chr5:133295088-133295328(-)$1	1	29	32	9.0000
)).	chr2:55825477-55825717(-)$1	1	71	74	9.0000
...	chr3:56682928-56683168(-)$1	1	97	100	9.0000
..(	chr14:31576154-31576395(-)$1	1	8	11	9.0000
...	chr2:203071820-203072101(-)$1	1	11	14	9.0000
(((	chrX:70756051-70756291(+)$1	1	46	49	9.0000
...	chr12:105238218-105238458(-)$1	1	25	28	9.0000
(..	chr2:148709897-148710139(-)$1	1	11	14	9.0000
)))	chr14:60749712-60749952(+)$1	1	20	23	9.0000
...	chr20:50342319-50342559(-)$1	1	0	3	9.0000
...	chr10:103920169-103920409(+)$1	1	2	5	9.0000
(.(	chr6:108375617-108375857(-)$1	1	46	49	9.0000
...	chr19:42411460-42411700(+)$1	1	91	94	9.0000
)))	chr1:64038061-64038301(+)$1	1	32	35	9.0000
...	chr9:19096605-19096845(-)$1	1	13	16	9.0000
...	chr5:54931285-54931525(-)$1	1	21	24	9.0000
(.(	chr3:182605294-182605534(+)$1	1	66	69	9.0000
...	chr1:63884940-63885180(+)$1	1	4	7	9.0000
(((	chr6:99991312-99991552(-)$1	1	26	29	9.0000
...	chr15:49327559-49327799(-)$1	1	11	14	9.0000
((.	chr5:137521897-137522137(+)$1	1	77	80	9.0000
...	chr5:79770395-79770635(+)$1	1	3	6	9.0000
.))	chr5:61778838-61779078(+)$1	1	43	46	9.0000
)))	chr6:146126254-146126494(-)$1	1	98	101	9.0000
.((	chr13:73336069-73336309(-)$1	1	21	24	9.0000
...	chr19:34916921-34917161(+)$1	1	3	6	9.0000
...	chr1:155227030-155227270(-)$1	1	75	78	9.0000
(((	chr5:133725938-133726178(+)$1	1	32	35	9.0000
(((	chr1:224377685-224377925(+)$1	1	15	18	9.0000
)))	chrX:13754635-13754875(+)$1	1	34	37	9.0000
(..	chr19:32930585-32930825(+)$1	1	2	5	9.0000
..(	chr6:111628590-111628830(-)$1	1	8	11	9.0000
(((	chr11:43515349-43515589(+)$1	1	30	33	9.0000
(((	chr7:23509626-23509866(-)$1	1	15	18	9.0000
(((	chrX:100880844-100881084(+)$1	1	1	4	9.0000
...	chr5:94005815-94006056(+)$1	1	18	21	9.0000
)..	chr17:65074249-65074489(-)$1	1	101	104	9.0000
(((	chr19:44739401-44739641(+)$1	1	111	114	9.0000
.((	chr12:72025965-72026205(-)$1	1	112	115	9.0000
...	chr12:121746152-121746392(-)$1	1	149	152	9.0000
.))	chr19:14203260-14203500(-)$1	1	36	39	9.0000
...	chr3:148765778-148766018(-)$1	1	51	54	9.0000
(((	chr2:223339207-223339447(+)$1	1	8	11	9.0000
...	chr5:179041678-179041958(-)$1	1	151	154	9.0000
(((	chrX:40456415-40456655(+)$1	1	8	11	9.0000
(((	chr11:61187910-61188150(-)$1	1	38	41	9.0000
...	chr5:134235166-134235406(+)$1	1	0	3	9.0000
...	chr3:169801936-169802176(+)$1	1	2	5	9.0000
...	chr16:58584953-58585193(-)$1	1	3	6	9.0000
(((	chr1:100174500-100174740(-)$1	1	32	35	9.0000
.))	chr11:62344063-62344541(-)$1	1	43	46	9.0000
((.	chr5:70860605-70860845(+)$1	1	64	67	9.0000
...	chrX:135080182-135080424(+)$1	1	5	8	9.0000
..(	chr3:160155801-160156041(-)$1	1	45	48	9.0000
...	chr6:5260852-5261103(-)$1	1	35	38	9.0000
...	chr8:27680565-27680805(-)$1	1	0	3	9.0000
(..	chr5:145522356-145522596(-)$1	1	4	7	9.0000
(((	chr12:102154933-102155173(-)$1	1	9	12	9.0000
.))	chr2:178096525-178096765(-)$1	1	115	118	9.0000
(((	chr3:17052031-17052271(+)$1	1	112	115	9.0000
...	chr3:32533202-32533442(-)$1	1	2	5	9.0000
(((	chr13:52592943-52593183(+)$1	1	2	5	9.0000
(((	chr1:53699171-53699411(-)$1	1	8	11	9.0000
(((	chrX:100667781-100668021(+)$1	1	40	43	9.0000
...	chr11:62343511-62343791(-)$1	1	49	52	9.0000
...	chr3:184018053-184018293(+)$1	1	113	116	9.0000
...	chr8:77776365-77776605(+)$1	1	137	140	9.0000
.((	chr11:32954039-32954279(+)$1	1	87	90	9.0000
(((	chr14:56078703-56078943(+)$1	1	0	3	9.0000
(((	chr13:113459214-113459454(+)$1	1	36	39	9.0000
...	chr17:5386062-5386302(-)$1	1	20	23	9.0000
.))	chr10:119043318-119043558(-)$1	1	113	116	9.0000
(..	chr7:77379176-77379416(+)$1	1	10	13	9.0000
)))	chr10:1038365-1038605(+)$1	1	26	29	9.0000
...	chr20:20617934-20618174(-)$1	1	8	11	9.0000
...	chr5:72798690-72798930(+)$1	1	26	29	9.0000
(((	chr5:134086460-134086700(+)$1	1	120	123	9.0000
.((	chr6:97246739-97246979(-)$1	1	1	4	9.0000
.((	chr21:34931511-34931751(+)$1	1	0	3	9.0000
(((	chr20:47686670-47686910(+)$1	1	33	36	9.0000
(((	chr7:86825896-86826136(-)$1	1	23	26	9.0000
..)	chr3:15288160-15288400(+)$1	1	24	27	9.0000
...	chr8:95780589-95780829(+)$1	1	4	7	9.0000
.))	chr16:66592064-66592304(+)$1	1	14	17	9.0000
(((	chr10:27037381-27037621(-)$1	1	13	16	9.0000
...	chr3:125295003-125295243(-)$1	1	17	20	9.0000
...	chr9:110091831-110092080(+)$1	1	7	10	9.0000
(((	chr13:108881780-108882020(+)$1	1	12	15	9.0000
(((	chr10:120450764-120451004(-)$1	1	7	10	9.0000
((.	chr5:133295131-133295371(-)$1	1	72	75	9.0000
.((	chr12:102179770-102180010(-)$1	1	4	7	9.0000
...	chr9:108123461-108123701(+)$1	1	121	124	9.0000
...	chr3:122591304-122591544(+)$1	1	16	19	9.0000
(((	chr11:60658153-60658393(-)$1	1	67	70	9.0000
(((	chr2:162247527-162247767(+)$1	1	22	25	9.0000
..(	chr2:54101433-54101673(-)$1	1	11	14	9.0000
((.	chr21:43413824-43414064(-)$1	1	22	25	9.0000
...	chr5:41917258-41917498(+)$1	1	13	16	9.0000
...	chr13:26788511-26788751(-)$1	1	53	56	9.0000
(..	chr6:11134536-11134776(+)$1	1	8	11	9.0000

#PSSM
U : 0.98	u : 0.02	
U : 0.98	u : 0.02	
U : 0.98	u : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_stringent_Lebedeva2011_hg19_UTR_m2_run2.nuc.txt

#NT
UUUUUUUAA	chr15:67485956-67486189(+)$1	233	106	115	23.5625
UUUCUUUAA	chr2:153511864-153512143(-)$1	279	113	122	19.2916
UCUUUUUAA	chr2:69551463-69551693(-)$1	230	40	49	19.8125
uuuuuuuaa	chr8:94745434-94745689(-)$1	255	135	144	23.5625
UUUAUUUAA	chr18:48701566-48701837(-)$1	271	139	148	19.2916
UUUCUUUAA	chr13:114294695-114294954(+)$1	259	144	153	19.2916
UUUUGUUAA	chr2:188331477-188331711(-)$1	234	30	39	18.9791
UUUUUUUAA	chr8:133024776-133025011(+)$1	235	54	63	23.5625
UUAUUUUAA	chr3:42687637-42687882(+)$1	245	114	123	19.2916
UUUUUUUAU	chr4:26433030-26433299(+)$1	269	28	37	18.9791
uuuauuuaa	chrX:62568351-62568628(-)$1	277	20	29	19.2916
UAUUUUUAA	chr5:83237013-83237305(-)$1	292	29	38	20.0208
UUUUUUUAA	chr17:29109812-29110068(-)$1	256	19	28	23.5625
UUGUUUUAA	chr1:11082969-11083200(+)$1	231	118	127	19.1875
uuuuuauaa	chr5:157213917-157214199(-)$1	282	17	26	19.3958
UUUUUUUAA	chr2:20451091-20451385(-)$1	294	137	146	23.5625
UUAUUUUAA	chr9:73000522-73000801(-)$1	279	106	115	19.2916
UUUUUGUAA	chr3:93773702-93773930(+)$1	228	55	64	19.5000
UAUUUUUAA	chr6:43754027-43754259(+)$1	232	111	120	20.0208
UGUUUUUAA	chr9:123521899-123522130(-)$1	231	145	154	19.6041
UUUUUUUAA	chr8:38020889-38021123(-)$1	234	104	113	23.5625
uuuuuauaa	chr18:12985529-12985821(+)$1	292	177	186	19.3958
UUUUUGUAA	chr16:16236688-16236926(+)$1	238	106	115	19.5000
UUUUUUUAA	chr15:38644588-38644816(+)$1	228	58	67	23.5625
UUCUUUUAA	chr5:90666277-90666509(-)$1	232	49	58	19.2916
uauuuuuaa	chr1:109180151-109180402(+)$1	251	48	57	20.0208
UCUUUUUAA	chr16:67133335-67133597(+)$1	262	105	114	19.8125
UCUUUUUAA	chr20:50005021-50005293(-)$1	272	207	216	19.8125
UUUUUUUAA	chr3:9848030-9848298(+)$1	268	111	120	23.5625
UUUUUUUGA	chr2:38523149-38523459(-)$1	310	59	68	18.7708
UUUUCUUAA	chr4:39780157-39780386(+)$1	229	115	124	19.0833
UAUUUUUAA	chr10:65381335-65381621(+)$1	286	65	74	20.0208
UUUUUUUAA	chr17:36923419-36923654(-)$1	235	7	16	23.5625
UUUUUUUAA	chr13:96443144-96443447(+)$1	303	166	175	23.5625
UUUGUUUAA	chr3:152882154-152882420(+)$1	266	148	157	19.1875
UAUUUUUAA	chr9:22003431-22003661(-)$1	230	44	53	20.0208
UUUUUUUAA	chr20:11905143-11905401(+)$1	258	212	221	23.5625
uuuuuUUAA	chr7:92237570-92237868(-)$1	298	1	10	23.5625
UUUUUGUAA	chr3:10192894-10193216(+)$1	322	145	154	19.5000
UUUUUUUAA	chr16:72818673-72818935(-)$1	262	242	251	23.5625
UUUUUUUAA	chr14:91924316-91924575(-)$1	259	40	49	23.5625
AUUUUUUAA	chr9:127911096-127911356(-)$1	260	50	59	18.9791
UUUUCUUAA	chr18:45362715-45362943(-)$1	228	108	117	19.0833
AUUUUUUAA	chr19:57766402-57766688(+)$1	286	139	148	18.9791
uuuuuuuau	chr15:73043653-73043888(-)$1	235	116	125	18.9791
UUUUUUUAA	chr6:170105105-170105331(+)$1	226	107	116	23.5625
UUUUUCUAA	chr8:71486708-71486934(-)$1	226	34	43	19.2916

#otherMatches

#Struct PSSM
bb"""hhhh	chr11:110041487-110041736(+)$1	249	41	50	19.2916
wwwwwwwww	chr15:67485956-67486189(+)$1	233	106	115	23.5625
ppppdddd2	chr2:153511864-153512143(-)$1	279	113	122	19.2916
gggg[bbqq	chr2:69551463-69551693(-)$1	230	40	49	19.8125
&&&&&&ddd	chr8:94745434-94745689(-)$1	255	135	144	23.5625
:::::::::	chr18:48701566-48701837(-)$1	271	139	148	19.2916
doooooodd	chr13:114294695-114294954(+)$1	259	144	153	19.2916
ffffff!!g	chr2:188331477-188331711(-)$1	234	30	39	18.9791
JJJJJJJ::	chr8:133024776-133025011(+)$1	235	54	63	23.5625
:iiiiiiii	chr3:42687637-42687882(+)$1	245	114	123	19.2916
hhhh]ccc:	chr4:26433030-26433299(+)$1	269	28	37	18.9791
iiinnnnni	chrX:62568351-62568628(-)$1	277	20	29	19.2916
JJJJJJJJJ	chr5:83237013-83237305(-)$1	292	29	38	20.0208
hhhh[eeee	chr17:29109812-29110068(-)$1	256	19	28	23.5625
zziiiiiii	chr1:11082969-11083200(+)$1	231	118	127	19.1875
ggggghhhh	chr5:157213917-157214199(-)$1	282	17	26	19.3958
HHHHHHeee	chr2:20451091-20451385(-)$1	294	137	146	23.5625
iiiiiii!!	chr9:73000522-73000801(-)$1	279	106	115	19.2916
iiiiiiii:	chr3:93773702-93773930(+)$1	228	55	64	19.5000
:::::::::	chr6:43754027-43754259(+)$1	232	111	120	20.0208
[ggggggg#	chr9:123521899-123522130(-)$1	231	145	154	19.6041
:::::::::	chr8:38020889-38021123(-)$1	234	104	113	23.5625
cc]dddd]c	chr18:12985529-12985821(+)$1	292	177	186	19.3958
ffff]gggg	chr16:16236688-16236926(+)$1	238	106	115	19.5000
JJJJJJJJ:	chr15:38644588-38644816(+)$1	228	58	67	23.5625
ggggg:ccc	chr5:90666277-90666509(-)$1	232	49	58	19.2916
cc22ggggg	chr1:109180151-109180402(+)$1	251	48	57	20.0208
bb!!fffff	chr16:67133335-67133597(+)$1	262	105	114	19.8125
ee!!dddd[	chr20:50005021-50005293(-)$1	272	207	216	19.8125
cccffffff	chr3:9848030-9848298(+)$1	268	111	120	23.5625
gggggglll	chr2:38523149-38523459(-)$1	310	59	68	18.7708
rrrrrdddd	chr4:39780157-39780386(+)$1	229	115	124	19.0833
+bb[eeeee	chr10:65381335-65381621(+)$1	286	65	74	20.0208
:::dddd[e	chr17:36923419-36923654(-)$1	235	7	16	23.5625
ggggmmmmg	chr13:96443144-96443447(+)$1	303	166	175	23.5625
:::::::::	chr3:152882154-152882420(+)$1	266	148	157	19.1875
E{FFFFFFO	chr9:22003431-22003661(-)$1	230	44	53	20.0208
iiiiiiiii	chr20:11905143-11905401(+)$1	258	212	221	23.5625
hhhhhhhll	chr7:92237570-92237868(-)$1	298	1	10	23.5625
ee::dddd[	chr3:10192894-10193216(+)$1	322	145	154	19.5000
GGGGGYYDD	chr16:72818673-72818935(-)$1	262	242	251	23.5625
::::::===	chr14:91924316-91924575(-)$1	259	40	49	23.5625
dddmmmmdd	chr9:127911096-127911356(-)$1	260	50	59	18.9791
GGGGGGG::	chr18:45362715-45362943(-)$1	228	108	117	19.0833
eeee[hhhh	chr19:57766402-57766688(+)$1	286	139	148	18.9791
fooooooff	chr15:73043653-73043888(-)$1	235	116	125	18.9791
dddd####c	chr6:170105105-170105331(+)$1	226	107	116	23.5625
iiiiiiiii	chr8:71486708-71486934(-)$1	226	34	43	19.2916

#DB
((...((((	chr11:110041487-110041736(+)$1	1	41	50	19.2916
.........	chr15:67485956-67486189(+)$1	1	106	115	23.5625
....)))).	chr2:153511864-153512143(-)$1	1	113	122	19.2916
((((.((..	chr2:69551463-69551693(-)$1	1	40	49	19.8125
......(((	chr8:94745434-94745689(-)$1	1	135	144	23.5625
.........	chr18:48701566-48701837(-)$1	1	139	148	19.2916
(......))	chr13:114294695-114294954(+)$1	1	144	153	19.2916
((((((..(	chr2:188331477-188331711(-)$1	1	30	39	18.9791
(((((((..	chr8:133024776-133025011(+)$1	1	54	63	23.5625
.((((((((	chr3:42687637-42687882(+)$1	1	114	123	19.2916
)))).))).	chr4:26433030-26433299(+)$1	1	28	37	18.9791
(((.....)	chrX:62568351-62568628(-)$1	1	20	29	19.2916
(((((((((	chr5:83237013-83237305(-)$1	1	29	38	20.0208
((((.((((	chr17:29109812-29110068(-)$1	1	19	28	23.5625
..)))))))	chr1:11082969-11083200(+)$1	1	118	127	19.1875
(((((((((	chr5:157213917-157214199(-)$1	1	17	26	19.3958
))))))(((	chr2:20451091-20451385(-)$1	1	137	146	23.5625
(((((((..	chr9:73000522-73000801(-)$1	1	106	115	19.2916
)))))))).	chr3:93773702-93773930(+)$1	1	55	64	19.5000
.........	chr6:43754027-43754259(+)$1	1	111	120	20.0208
.(((((((.	chr9:123521899-123522130(-)$1	1	145	154	19.6041
.........	chr8:38020889-38021123(-)$1	1	104	113	23.5625
)).)))).)	chr18:12985529-12985821(+)$1	1	177	186	19.3958
)))).))))	chr16:16236688-16236926(+)$1	1	106	115	19.5000
((((((((.	chr15:38644588-38644816(+)$1	1	58	67	23.5625
))))).(((	chr5:90666277-90666509(-)$1	1	49	58	19.2916
))..)))))	chr1:109180151-109180402(+)$1	1	48	57	20.0208
((..(((((	chr16:67133335-67133597(+)$1	1	105	114	19.8125
((..((((.	chr20:50005021-50005293(-)$1	1	207	216	19.8125
(((((((((	chr3:9848030-9848298(+)$1	1	111	120	23.5625
((((((...	chr2:38523149-38523459(-)$1	1	59	68	18.7708
.....))))	chr4:39780157-39780386(+)$1	1	115	124	19.0833
.((.(((((	chr10:65381335-65381621(+)$1	1	65	74	20.0208
...((((.(	chr17:36923419-36923654(-)$1	1	7	16	23.5625
((((....)	chr13:96443144-96443447(+)$1	1	166	175	23.5625
.........	chr3:152882154-152882420(+)$1	1	148	157	19.1875
(.((((((.	chr9:22003431-22003661(-)$1	1	44	53	20.0208
)))))))))	chr20:11905143-11905401(+)$1	1	212	221	23.5625
(((((((..	chr7:92237570-92237868(-)$1	1	1	10	23.5625
))..((((.	chr3:10192894-10193216(+)$1	1	145	154	19.5000
)))))..))	chr16:72818673-72818935(-)$1	1	242	251	23.5625
......(((	chr14:91924316-91924575(-)$1	1	40	49	23.5625
(((....))	chr9:127911096-127911356(-)$1	1	50	59	18.9791
(((((((..	chr18:45362715-45362943(-)$1	1	108	117	19.0833
((((.((((	chr19:57766402-57766688(+)$1	1	139	148	18.9791
(......))	chr15:73043653-73043888(-)$1	1	116	125	18.9791
((((....(	chr6:170105105-170105331(+)$1	1	107	116	23.5625
(((((((((	chr8:71486708-71486934(-)$1	1	34	43	19.2916

#PSSM
U : 0.81	u : 0.14	A : 0.04	
U : 0.68	u : 0.12	A : 0.08	C : 0.06	G : 0.02	a : 0.02	
U : 0.75	u : 0.14	C : 0.04	A : 0.04	G : 0.02	
U : 0.77	u : 0.12	C : 0.04	A : 0.02	a : 0.02	G : 0.02	
U : 0.79	u : 0.14	C : 0.04	G : 0.02	
U : 0.79	u : 0.08	G : 0.06	a : 0.04	C : 0.02	
U : 0.87	u : 0.12	
A : 0.85	a : 0.12	G : 0.02	
A : 0.85	a : 0.10	U : 0.02	u : 0.02	

#score	993.7083333333334
#seq	48
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_TAF15_Hoel2011_hg19_UTR_m3_run1.nuc.txt

#NT
UUUUA	chr5:71505121-71505349(+)$1	228	169	174	15.0000
UUUUA	chr22:42482022-42482245(-)$1	223	92	97	15.0000
UUUUA	chr12:125514856-125515087(+)$1	231	0	5	15.0000
UUUUA	chr1:229440007-229440234(+)$1	227	173	178	15.0000
UUUUA	chr18:29203341-29203570(-)$1	229	31	36	15.0000
UUUUA	chr12:46754250-46754475(-)$1	225	55	60	15.0000
UUUUA	chr6:26158693-26158914(+)$1	221	126	131	15.0000
UUUUA	chr19:37006157-37006384(-)$1	227	48	53	15.0000
UUUUA	chr9:133513114-133513342(+)$1	228	29	34	15.0000
UUUUA	chr2:178095143-178095370(-)$1	227	219	224	15.0000
UUUUA	chr12:79982765-79982987(-)$1	222	53	58	15.0000
UUUUA	chr4:140187453-140187677(-)$1	224	74	79	15.0000
UUUUA	chr2:60685958-60686182(-)$1	224	57	62	15.0000
UUUUA	chr2:206858595-206858821(-)$1	226	144	149	15.0000
UUUUA	chr14:23033770-23034001(-)$1	231	60	65	15.0000
UUUUA	chr9:135567643-135567873(+)$1	230	180	185	15.0000
UUUUA	chr7:43906174-43906396(-)$1	222	30	35	15.0000
UUUUA	chr1:204374792-204375014(-)$1	222	41	46	15.0000
UUUUA	chr10:35298917-35299141(-)$1	224	218	223	15.0000
uuuua	chr6:44416247-44416472(+)$1	225	193	198	15.0000
UUUUA	chr4:39782071-39782297(+)$1	226	19	24	15.0000
UUUUA	chr20:21369889-21370117(+)$1	228	128	133	15.0000
UUUUA	chr1:151376606-151376829(-)$1	223	109	114	15.0000
UUUUA	chr1:23636308-23636528(-)$1	220	90	95	15.0000
UUUUA	chr8:90938365-90938594(+)$1	229	5	10	15.0000
uuuua	chr12:53807151-53807373(+)$1	222	37	42	15.0000
UUUUA	chr3:88106096-88106326(-)$1	230	102	107	15.0000
UUUUA	chr8:17086869-17087088(-)$1	219	11	16	15.0000
UUUUA	chr10:75882139-75882374(-)$1	235	103	108	15.0000
UUUUA	chr5:177637637-177637861(+)$1	224	214	219	15.0000
uuuua	chr1:168214172-168214397(+)$1	225	157	162	15.0000
UUUUA	chrX:103435702-103435926(+)$1	224	153	158	15.0000
UUUUA	chr19:34306194-34306416(+)$1	222	1	6	15.0000
UUUUA	chr6:116597758-116597987(-)$1	229	58	63	15.0000
UUUUA	chr5:41918822-41919053(+)$1	231	125	130	15.0000
UUUUA	chrX:13727652-13727874(+)$1	222	181	186	15.0000
UUUUA	chr13:73283943-73284166(-)$1	223	203	208	15.0000
UUUUA	chr2:148692632-148692854(-)$1	222	14	19	15.0000
UUUUA	chr21:28209260-28209479(-)$1	219	7	12	15.0000
UUUUA	chr4:17804303-17804528(-)$1	225	196	201	15.0000
UUUUA	chr21:40714152-40714379(-)$1	227	48	53	15.0000
UUUUA	chr9:135569763-135569985(+)$1	222	147	152	15.0000
UUUUA	chr5:134194701-134194936(+)$1	235	197	202	15.0000
UUUUA	chr7:120427996-120428219(-)$1	223	1	6	15.0000
UUUUA	chr16:46990663-46990885(-)$1	222	70	75	15.0000
UUUUA	chr12:124105481-124105703(-)$1	222	70	75	15.0000
UUUUA	chr5:148731662-148731885(+)$1	223	31	36	15.0000
UUUUA	chr5:179155904-179156130(+)$1	226	11	16	15.0000
UUUUA	chr8:48890428-48890650(+)$1	222	142	147	15.0000
UUUUA	chr6:159054583-159054811(+)$1	228	108	113	15.0000
uuuua	chr11:71145366-71145591(-)$1	225	74	79	15.0000
UUUUA	chr4:103716439-103716669(-)$1	230	206	211	15.0000
UUUUA	chr2:9989415-9989653(+)$1	238	57	62	15.0000
UUUUA	chr20:61536257-61536479(-)$1	222	69	74	15.0000
UUUUA	chr2:172964319-172964541(-)$1	222	9	14	15.0000
UUUUA	chr10:102034888-102035120(-)$1	232	124	129	15.0000
UUUUA	chr13:73283215-73283444(-)$1	229	104	109	15.0000
UUUUA	chr15:52842764-52842989(-)$1	225	106	111	15.0000
UUUUA	chr6:47592515-47592744(+)$1	229	123	128	15.0000
UUUUA	chrX:106894031-106894256(+)$1	225	61	66	15.0000
UUUUA	chr8:10983908-10984129(-)$1	221	139	144	15.0000
UUUUA	chr1:21071077-21071307(-)$1	230	19	24	15.0000
UUUUA	chr10:96371193-96371423(+)$1	230	89	94	15.0000

#otherMatches

#Struct PSSM
bb!!b	chr9:73001547-73001782(-)$1	235	101	106	15.0000
iiiii	chr5:71505121-71505349(+)$1	228	169	174	15.0000
:::::	chr22:42482022-42482245(-)$1	223	92	97	15.0000
:::::	chr12:125514856-125515087(+)$1	231	0	5	15.0000
+++++	chr1:229440007-229440234(+)$1	227	173	178	15.0000
77777	chr18:29203341-29203570(-)$1	229	31	36	15.0000
c5555	chr12:46754250-46754475(-)$1	225	55	60	15.0000
fmmmm	chr6:26158693-26158914(+)$1	221	126	131	15.0000
vvvvv	chr19:37006157-37006384(-)$1	227	48	53	15.0000
fffft	chr9:133513114-133513342(+)$1	228	29	34	15.0000
FFF::	chr2:178095143-178095370(-)$1	227	219	224	15.0000
e[hhh	chr12:79982765-79982987(-)$1	222	53	58	15.0000
=====	chr4:140187453-140187677(-)$1	224	74	79	15.0000
JJKKB	chr2:60685958-60686182(-)$1	224	57	62	15.0000
ggggg	chr2:206858595-206858821(-)$1	226	144	149	15.0000
ggggq	chr14:23033770-23034001(-)$1	231	60	65	15.0000
%%%%c	chr9:135567643-135567873(+)$1	230	180	185	15.0000
####b	chr7:43906174-43906396(-)$1	222	30	35	15.0000
qqqqq	chr1:204374792-204375014(-)$1	222	41	46	15.0000
:::::	chr10:35298917-35299141(-)$1	224	218	223	15.0000
YBBZZ	chr6:44416247-44416472(+)$1	225	193	198	15.0000
e^^^^	chr4:39782071-39782297(+)$1	226	19	24	15.0000
FF:::	chr20:21369889-21370117(+)$1	228	128	133	15.0000
fffff	chr1:151376606-151376829(-)$1	223	109	114	15.0000
qqqqq	chr1:23636308-23636528(-)$1	220	90	95	15.0000
HHH::	chr8:90938365-90938594(+)$1	229	5	10	15.0000
lllgg	chr12:53807151-53807373(+)$1	222	37	42	15.0000
gggmm	chr3:88106096-88106326(-)$1	230	102	107	15.0000
cnnnn	chr8:17086869-17087088(-)$1	219	11	16	15.0000
4444b	chr10:75882139-75882374(-)$1	235	103	108	15.0000
EEEEE	chr5:177637637-177637861(+)$1	224	214	219	15.0000
ee555	chr1:168214172-168214397(+)$1	225	157	162	15.0000
ggggg	chrX:103435702-103435926(+)$1	224	153	158	15.0000
:FFFF	chr19:34306194-34306416(+)$1	222	1	6	15.0000
wwwee	chr6:116597758-116597987(-)$1	229	58	63	15.0000
ooooo	chr5:41918822-41919053(+)$1	231	125	130	15.0000
:::::	chrX:13727652-13727874(+)$1	222	181	186	15.0000
:::::	chr13:73283943-73284166(-)$1	223	203	208	15.0000
CNNNN	chr2:148692632-148692854(-)$1	222	14	19	15.0000
gggff	chr21:28209260-28209479(-)$1	219	7	12	15.0000
ggggg	chr4:17804303-17804528(-)$1	225	196	201	15.0000
EEOOO	chr21:40714152-40714379(-)$1	227	48	53	15.0000
:::::	chr9:135569763-135569985(+)$1	222	147	152	15.0000
cc22i	chr5:134194701-134194936(+)$1	235	197	202	15.0000
:::::	chr7:120427996-120428219(-)$1	223	1	6	15.0000
^^^^^	chr16:46990663-46990885(-)$1	222	70	75	15.0000
ggggg	chr12:124105481-124105703(-)$1	222	70	75	15.0000
##eee	chr5:148731662-148731885(+)$1	223	31	36	15.0000
+++++	chr5:179155904-179156130(+)$1	226	11	16	15.0000
b[ddd	chr8:48890428-48890650(+)$1	222	142	147	15.0000
c4444	chr6:159054583-159054811(+)$1	228	108	113	15.0000
%%%%%	chr11:71145366-71145591(-)$1	225	74	79	15.0000
ff22c	chr4:103716439-103716669(-)$1	230	206	211	15.0000
rrrrr	chr2:9989415-9989653(+)$1	238	57	62	15.0000
:FFFF	chr20:61536257-61536479(-)$1	222	69	74	15.0000
HHHHH	chr2:172964319-172964541(-)$1	222	9	14	15.0000
]====	chr10:102034888-102035120(-)$1	232	124	129	15.0000
::ggg	chr13:73283215-73283444(-)$1	229	104	109	15.0000
iiiii	chr15:52842764-52842989(-)$1	225	106	111	15.0000
d"""b	chr6:47592515-47592744(+)$1	229	123	128	15.0000
==22c	chrX:106894031-106894256(+)$1	225	61	66	15.0000
dddbb	chr8:10983908-10984129(-)$1	221	139	144	15.0000
WWWWW	chr1:21071077-21071307(-)$1	230	19	24	15.0000
88888	chr10:96371193-96371423(+)$1	230	89	94	15.0000

#DB
((..(	chr9:73001547-73001782(-)$1	1	101	106	15.0000
)))))	chr5:71505121-71505349(+)$1	1	169	174	15.0000
.....	chr22:42482022-42482245(-)$1	1	92	97	15.0000
.....	chr12:125514856-125515087(+)$1	1	0	5	15.0000
.....	chr1:229440007-229440234(+)$1	1	173	178	15.0000
.....	chr18:29203341-29203570(-)$1	1	31	36	15.0000
)....	chr12:46754250-46754475(-)$1	1	55	60	15.0000
(....	chr6:26158693-26158914(+)$1	1	126	131	15.0000
.....	chr19:37006157-37006384(-)$1	1	48	53	15.0000
((((.	chr9:133513114-133513342(+)$1	1	29	34	15.0000
)))..	chr2:178095143-178095370(-)$1	1	219	224	15.0000
(.(((	chr12:79982765-79982987(-)$1	1	53	58	15.0000
)))))	chr4:140187453-140187677(-)$1	1	74	79	15.0000
((..(	chr2:60685958-60686182(-)$1	1	57	62	15.0000
(((((	chr2:206858595-206858821(-)$1	1	144	149	15.0000
((((.	chr14:23033770-23034001(-)$1	1	60	65	15.0000
....(	chr9:135567643-135567873(+)$1	1	180	185	15.0000
....(	chr7:43906174-43906396(-)$1	1	30	35	15.0000
.....	chr1:204374792-204375014(-)$1	1	41	46	15.0000
.....	chr10:35298917-35299141(-)$1	1	218	223	15.0000
.))..	chr6:44416247-44416472(+)$1	1	193	198	15.0000
(....	chr4:39782071-39782297(+)$1	1	19	24	15.0000
((...	chr20:21369889-21370117(+)$1	1	128	133	15.0000
(((((	chr1:151376606-151376829(-)$1	1	109	114	15.0000
.....	chr1:23636308-23636528(-)$1	1	90	95	15.0000
(((..	chr8:90938365-90938594(+)$1	1	5	10	15.0000
...))	chr12:53807151-53807373(+)$1	1	37	42	15.0000
(((..	chr3:88106096-88106326(-)$1	1	102	107	15.0000
(....	chr8:17086869-17087088(-)$1	1	11	16	15.0000
....)	chr10:75882139-75882374(-)$1	1	103	108	15.0000
)))))	chr5:177637637-177637861(+)$1	1	214	219	15.0000
))...	chr1:168214172-168214397(+)$1	1	157	162	15.0000
)))))	chrX:103435702-103435926(+)$1	1	153	158	15.0000
.((((	chr19:34306194-34306416(+)$1	1	1	6	15.0000
...))	chr6:116597758-116597987(-)$1	1	58	63	15.0000
.....	chr5:41918822-41919053(+)$1	1	125	130	15.0000
.....	chrX:13727652-13727874(+)$1	1	181	186	15.0000
.....	chr13:73283943-73284166(-)$1	1	203	208	15.0000
(....	chr2:148692632-148692854(-)$1	1	14	19	15.0000
(((((	chr21:28209260-28209479(-)$1	1	7	12	15.0000
)))))	chr4:17804303-17804528(-)$1	1	196	201	15.0000
((...	chr21:40714152-40714379(-)$1	1	48	53	15.0000
.....	chr9:135569763-135569985(+)$1	1	147	152	15.0000
))..)	chr5:134194701-134194936(+)$1	1	197	202	15.0000
.....	chr7:120427996-120428219(-)$1	1	1	6	15.0000
.....	chr16:46990663-46990885(-)$1	1	70	75	15.0000
(((((	chr12:124105481-124105703(-)$1	1	70	75	15.0000
..(((	chr5:148731662-148731885(+)$1	1	31	36	15.0000
.....	chr5:179155904-179156130(+)$1	1	11	16	15.0000
(.(((	chr8:48890428-48890650(+)$1	1	142	147	15.0000
)....	chr6:159054583-159054811(+)$1	1	108	113	15.0000
.....	chr11:71145366-71145591(-)$1	1	74	79	15.0000
))..)	chr4:103716439-103716669(-)$1	1	206	211	15.0000
.....	chr2:9989415-9989653(+)$1	1	57	62	15.0000
.((((	chr20:61536257-61536479(-)$1	1	69	74	15.0000
(((((	chr2:172964319-172964541(-)$1	1	9	14	15.0000
.))))	chr10:102034888-102035120(-)$1	1	124	129	15.0000
..(((	chr13:73283215-73283444(-)$1	1	104	109	15.0000
)))))	chr15:52842764-52842989(-)$1	1	106	111	15.0000
(...(	chr6:47592515-47592744(+)$1	1	123	128	15.0000
))..)	chrX:106894031-106894256(+)$1	1	61	66	15.0000
)))))	chr8:10983908-10984129(-)$1	1	139	144	15.0000
.....	chr1:21071077-21071307(-)$1	1	19	24	15.0000
.....	chr10:96371193-96371423(+)$1	1	89	94	15.0000

#PSSM
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
A : 0.93	a : 0.06	

#score	960.0
#seq	64
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012b_hg19_CDS_m3_run1.nuc.txt

#NT
CCUCAA	chr10:115610261-115610491(-)$1	230	112	118	11.1034
CCUGCA	chr11:9771331-9771561(+)$1	230	114	120	10.8448
CCUUCA	chr19:37238889-37239109(-)$1	220	49	55	11.0172
ccucca	chr12:6438983-6439213(-)$1	230	93	99	14.3793
CCUGCA	chr15:68378787-68379009(+)$1	222	45	51	10.8448
CCUCCC	chr19:11664946-11665165(-)$1	219	33	39	10.5862
CCUCAA	chr7:91752443-91752662(-)$1	219	107	113	11.1034
CCUACA	chr12:133732533-133732755(+)$1	222	8	14	11.1034
CCUCCA	chr7:90042233-90042456(+)$1	223	11	17	14.3793
CCUCCC	chr17:40267676-40267903(-)$1	227	40	46	10.5862
CCUCAA	chr5:133295089-133295313(-)$1	224	28	34	11.1034
CCUCCA	chr3:47963181-47963402(-)$1	221	82	88	14.3793
GCUCCA	chr19:10791811-10792029(+)$1	218	26	32	10.5000
CCUACA	chr11:4150241-4150463(+)$1	222	92	98	11.1034
CCUUCA	chr6:619353-619572(+)$1	219	44	50	11.0172
CCUCCC	chr19:50385248-50385473(+)$1	225	34	40	10.5862
CCUCGA	chrX:71427801-71428028(-)$1	227	89	95	10.7586
CCUACA	chr12:14613685-14613909(+)$1	224	51	57	11.1034
CCUCCC	chr12:57627929-57628151(+)$1	222	18	24	10.5862
CCUCUA	chr7:27833921-27834144(+)$1	223	108	114	10.7586
CCUUCA	chr7:86823967-86824191(+)$1	224	101	107	11.0172
GCUCCA	chr4:87968242-87968462(+)$1	220	42	48	10.5000
CCUCCC	chrX:70330647-70330872(-)$1	225	24	30	10.5862
GCUCCA	chr16:81944099-81944329(+)$1	230	57	63	10.5000
CCUCAA	chr20:37144761-37144985(+)$1	224	194	200	11.1034
CCUACA	chr4:435893-436123(-)$1	230	38	44	11.1034
CCUCCA	chr1:145595054-145595284(-)$1	230	195	201	14.3793
UCUCCA	chr7:101840019-101840245(+)$1	226	120	126	10.3275
CCUCCA	chr7:23651030-23651260(+)$1	230	171	177	14.3793
CCUCAA	chr9:104075027-104075244(+)$1	217	144	150	11.1034
CCUCUA	chr11:4128581-4128806(+)$1	225	96	102	10.7586
GCUCCA	chr6:36839472-36839693(-)$1	221	82	88	10.5000
CCUCAA	chrX:122761548-122761770(-)$1	222	101	107	11.1034
CCUCCA	chr6:30078182-30078400(-)$1	218	87	93	14.3793
CCUACA	chr4:103505773-103505992(+)$1	219	31	37	11.1034
CCUCCA	chr1:7527818-7528041(-)$1	223	20	26	14.3793
CCUCCC	chr5:67593277-67593497(+)$1	220	78	84	10.5862
CCUCCA	chr19:10220233-10220446(+)$1	213	196	202	14.3793
CCUUCA	chr13:23911913-23912139(-)$1	226	147	153	11.0172
CCUCCA	chr10:89717533-89717763(+)$1	230	118	124	14.3793
CCUCCA	chr15:57524914-57525136(+)$1	222	1	7	14.3793
CCUCCA	chr17:17924955-17925185(-)$1	230	34	40	14.3793
CCUCCC	chrM:10501-10721(+)$1	220	51	57	10.5862
UCUCCA	chr19:6362426-6362647(+)$1	221	17	23	10.3275
UCUCCA	chr9:125582684-125582904(-)$1	220	125	131	10.3275
CCUCGA	chr5:99897702-99897921(+)$1	219	182	188	10.7586
CCUCCA	chr10:103919913-103920143(+)$1	230	144	150	14.3793
CCUCCA	chr1:201058360-201058581(+)$1	221	48	54	14.3793
CCUCGA	chr2:209136213-209136438(+)$1	225	81	87	10.7586
CCUCAA	chr1:153905297-153905530(-)$1	233	116	122	11.1034
CCUCUA	chr2:211018731-211018961(-)$1	230	63	69	10.7586
CCUGCA	chr5:96111723-96111942(-)$1	219	51	57	10.8448
CCUACA	chr8:94745599-94745819(-)$1	220	73	79	11.1034
CCUCCA	chr2:74274926-74275156(+)$1	230	129	135	14.3793
CCUUCA	chr10:112724591-112724815(+)$1	224	77	83	11.0172
GCUCCA	chr10:106075668-106075889(-)$1	221	71	77	10.5000
CCUCCA	chr20:3888684-3888901(+)$1	217	17	23	14.3793

#otherMatches

#Struct PSSM
H:::::	chr16:81711844-81712067(+)$1	223	193	199	14.3793
[ccc^^	chr10:115610261-115610491(-)$1	230	112	118	11.1034
Dbb###	chr11:9771331-9771561(+)$1	230	114	120	10.8448
cnnnnn	chr19:37238889-37239109(-)$1	220	49	55	11.0172
::::cc	chr12:6438983-6439213(-)$1	230	93	99	14.3793
b!!ccc	chr15:68378787-68379009(+)$1	222	45	51	10.8448
ffff::	chr19:11664946-11665165(-)$1	219	33	39	10.5862
ee"""c	chr7:91752443-91752662(-)$1	219	107	113	11.1034
::::::	chr12:133732533-133732755(+)$1	222	8	14	11.1034
cCCCDD	chr7:90042233-90042456(+)$1	223	11	17	14.3793
tttttt	chr17:40267676-40267903(-)$1	227	40	46	10.5862
DDD:::	chr5:133295089-133295313(-)$1	224	28	34	11.1034
III{CC	chr3:47963181-47963402(-)$1	221	82	88	14.3793
ccc]dd	chr19:10791811-10792029(+)$1	218	26	32	10.5000
pppccc	chr11:4150241-4150463(+)$1	222	92	98	11.1034
mmeeee	chr6:619353-619572(+)$1	219	44	50	11.0172
FFFFFF	chr19:50385248-50385473(+)$1	225	34	40	10.5862
elllee	chrX:71427801-71428028(-)$1	227	89	95	10.7586
::JJJJ	chr12:14613685-14613909(+)$1	224	51	57	11.1034
GKKCCC	chr12:57627929-57628151(+)$1	222	18	24	10.5862
4444ee	chr7:27833921-27834144(+)$1	223	108	114	10.7586
:DDDD:	chr7:86823967-86824191(+)$1	224	101	107	11.0172
cc"""e	chr4:87968242-87968462(+)$1	220	42	48	10.5000
HHHHHH	chrX:70330647-70330872(-)$1	225	24	30	10.5862
g:::::	chr16:81944099-81944329(+)$1	230	57	63	10.5000
22ccc3	chr20:37144761-37144985(+)$1	224	194	200	11.1034
eeee44	chr4:435893-436123(-)$1	230	38	44	11.1034
yydddd	chr1:145595054-145595284(-)$1	230	195	201	14.3793
^^cccc	chr7:101840019-101840245(+)$1	226	120	126	10.3275
GGGG__	chr7:23651030-23651260(+)$1	230	171	177	14.3793
eeennn	chr9:104075027-104075244(+)$1	217	144	150	11.1034
DCCC::	chr11:4128581-4128806(+)$1	225	96	102	10.7586
ffffff	chr6:36839472-36839693(-)$1	221	82	88	10.5000
::::::	chrX:122761548-122761770(-)$1	222	101	107	11.1034
2dddd]	chr6:30078182-30078400(-)$1	218	87	93	14.3793
!eeeee	chr4:103505773-103505992(+)$1	219	31	37	11.1034
B{CCCO	chr1:7527818-7528041(-)$1	223	20	26	14.3793
dddd!!	chr5:67593277-67593497(+)$1	220	78	84	10.5862
J:::::	chr19:10220233-10220446(+)$1	213	196	202	14.3793
d:gggg	chr13:23911913-23912139(-)$1	226	147	153	11.0172
bbccco	chr10:89717533-89717763(+)$1	230	118	124	14.3793
::FFFF	chr15:57524914-57525136(+)$1	222	1	7	14.3793
qfffff	chr17:17924955-17925185(-)$1	230	34	40	14.3793
^^^^^c	chrM:10501-10721(+)$1	220	51	57	10.5862
::::FF	chr19:6362426-6362647(+)$1	221	17	23	10.3275
eeeeel	chr9:125582684-125582904(-)$1	220	125	131	10.3275
ggbbff	chr5:99897702-99897921(+)$1	219	182	188	10.7586
@@@@@@	chr10:103919913-103920143(+)$1	230	144	150	14.3793
:ggggg	chr1:201058360-201058581(+)$1	221	48	54	14.3793
oooodd	chr2:209136213-209136438(+)$1	225	81	87	10.7586
::::::	chr1:153905297-153905530(-)$1	233	116	122	11.1034
]dddd]	chr2:211018731-211018961(-)$1	230	63	69	10.7586
llleee	chr5:96111723-96111942(-)$1	219	51	57	10.8448
cccmmm	chr8:94745599-94745819(-)$1	220	73	79	11.1034
eemmmm	chr2:74274926-74275156(+)$1	230	129	135	14.3793
$$ffff	chr10:112724591-112724815(+)$1	224	77	83	11.0172
gggggg	chr10:106075668-106075889(-)$1	221	71	77	10.5000
GGGGGG	chr20:3888684-3888901(+)$1	217	17	23	14.3793

#DB
).....	chr16:81711844-81712067(+)$1	1	193	199	14.3793
.(((..	chr10:115610261-115610491(-)$1	1	112	118	11.1034
)((...	chr11:9771331-9771561(+)$1	1	114	120	10.8448
(.....	chr19:37238889-37239109(-)$1	1	49	55	11.0172
....((	chr12:6438983-6439213(-)$1	1	93	99	14.3793
(..(((	chr15:68378787-68379009(+)$1	1	45	51	10.8448
))))..	chr19:11664946-11665165(-)$1	1	33	39	10.5862
((...(	chr7:91752443-91752662(-)$1	1	107	113	11.1034
......	chr12:133732533-133732755(+)$1	1	8	14	11.1034
)(((((	chr7:90042233-90042456(+)$1	1	11	17	14.3793
......	chr17:40267676-40267903(-)$1	1	40	46	10.5862
(((...	chr5:133295089-133295313(-)$1	1	28	34	11.1034
(((.((	chr3:47963181-47963402(-)$1	1	82	88	14.3793
))).))	chr19:10791811-10792029(+)$1	1	26	32	10.5000
...)))	chr11:4150241-4150463(+)$1	1	92	98	11.1034
..))))	chr6:619353-619572(+)$1	1	44	50	11.0172
((((((	chr19:50385248-50385473(+)$1	1	34	40	10.5862
(...))	chrX:71427801-71428028(-)$1	1	89	95	10.7586
..((((	chr12:14613685-14613909(+)$1	1	51	57	11.1034
(..(((	chr12:57627929-57628151(+)$1	1	18	24	10.5862
....))	chr7:27833921-27834144(+)$1	1	108	114	10.7586
.)))).	chr7:86823967-86824191(+)$1	1	101	107	11.0172
((...(	chr4:87968242-87968462(+)$1	1	42	48	10.5000
((((((	chrX:70330647-70330872(-)$1	1	24	30	10.5862
).....	chr16:81944099-81944329(+)$1	1	57	63	10.5000
..))).	chr20:37144761-37144985(+)$1	1	194	200	11.1034
))))..	chr4:435893-436123(-)$1	1	38	44	11.1034
..))))	chr1:145595054-145595284(-)$1	1	195	201	14.3793
..)))(	chr7:101840019-101840245(+)$1	1	120	126	10.3275
))))..	chr7:23651030-23651260(+)$1	1	171	177	14.3793
(((...	chr9:104075027-104075244(+)$1	1	144	150	11.1034
((((..	chr11:4128581-4128806(+)$1	1	96	102	10.7586
))))))	chr6:36839472-36839693(-)$1	1	82	88	10.5000
......	chrX:122761548-122761770(-)$1	1	101	107	11.1034
.)))).	chr6:30078182-30078400(-)$1	1	87	93	14.3793
.(((((	chr4:103505773-103505992(+)$1	1	31	37	11.1034
(.(((.	chr1:7527818-7528041(-)$1	1	20	26	14.3793
((((..	chr5:67593277-67593497(+)$1	1	78	84	10.5862
).....	chr19:10220233-10220446(+)$1	1	196	202	14.3793
).((((	chr13:23911913-23912139(-)$1	1	147	153	11.0172
))(((.	chr10:89717533-89717763(+)$1	1	118	124	14.3793
..((((	chr15:57524914-57525136(+)$1	1	1	7	14.3793
.)))))	chr17:17924955-17925185(-)$1	1	34	40	14.3793
.....)	chrM:10501-10721(+)$1	1	51	57	10.5862
....((	chr19:6362426-6362647(+)$1	1	17	23	10.3275
(((((.	chr9:125582684-125582904(-)$1	1	125	131	10.3275
))))))	chr5:99897702-99897921(+)$1	1	182	188	10.7586
......	chr10:103919913-103920143(+)$1	1	144	150	14.3793
.(((((	chr1:201058360-201058581(+)$1	1	48	54	14.3793
....))	chr2:209136213-209136438(+)$1	1	81	87	10.7586
......	chr1:153905297-153905530(-)$1	1	116	122	11.1034
.)))).	chr2:211018731-211018961(-)$1	1	63	69	10.7586
...)))	chr5:96111723-96111942(-)$1	1	51	57	10.8448
(((...	chr8:94745599-94745819(-)$1	1	73	79	11.1034
((....	chr2:74274926-74275156(+)$1	1	129	135	14.3793
..((((	chr10:112724591-112724815(+)$1	1	77	83	11.0172
((((((	chr10:106075668-106075889(-)$1	1	71	77	10.5000
((((((	chr20:3888684-3888901(+)$1	1	17	23	14.3793

#PSSM
C : 0.84	G : 0.08	U : 0.05	c : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	
C : 0.74	A : 0.10	U : 0.08	G : 0.05	c : 0.01	
C : 0.75	A : 0.12	G : 0.05	U : 0.05	c : 0.01	
A : 0.86	C : 0.12	a : 0.01	

#score	684.1724137931039
#seq	58
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013b_hg19_UTR_m1_run1.nuc.txt

#NT
UGGA	chrX:153184276-153184477(-)$1	201	73	77	11.9999
UGGA	chr17:2321919-2322120(-)$1	201	174	178	11.9999
UGGA	chr10:96093082-96093283(-)$1	201	20	24	11.9999
UGGA	chr1:110166486-110166687(+)$1	201	3	7	11.9999
UGGA	chr1:228332014-228332215(+)$1	201	177	181	11.9999
UGGA	chr5:133486718-133486919(-)$1	201	92	96	11.9999
UGGA	chr3:146239574-146239775(-)$1	201	103	107	11.9999
ugga	chr19:36133221-36133422(+)$1	201	13	17	11.9999
UGGA	chr11:803112-803313(-)$1	201	47	51	11.9999
UGGA	chr3:98512502-98512703(+)$1	201	177	181	11.9999
UGGA	chr1:183497994-183498195(+)$1	201	176	180	11.9999
UGGA	chr9:139757121-139757322(-)$1	201	90	94	11.9999
UGGA	chr17:41151667-41151868(+)$1	201	100	104	11.9999
UGGA	chr3:185332354-185332555(+)$1	201	13	17	11.9999
UGGA	chr6:146240495-146240696(-)$1	201	84	88	11.9999
UGGA	chr17:41154634-41154835(+)$1	201	63	67	11.9999
UGGA	chr7:90014259-90014460(+)$1	201	28	32	11.9999
UGGA	chr4:39207137-39207338(+)$1	201	81	85	11.9999
UGGA	chr10:99519149-99519350(+)$1	201	58	62	11.9999
UGGA	chr9:33264275-33264476(-)$1	201	101	105	11.9999
UGGA	chr1:185093987-185094188(-)$1	201	11	15	11.9999
UGGA	chr6:168312669-168312870(+)$1	201	83	87	11.9999
UGGA	chr14:64434368-64434569(+)$1	201	13	17	11.9999
UGGA	chr5:176966143-176966344(-)$1	201	189	193	11.9999
UGGA	chr10:103347012-103347213(-)$1	201	17	21	11.9999
UGGA	chr6:56357721-56357922(-)$1	201	42	46	11.9999
UGGA	chr17:73702067-73702268(+)$1	201	142	146	11.9999
UGGA	chr10:14939289-14939490(+)$1	201	154	158	11.9999
UGGA	chr2:220043452-220043653(+)$1	201	88	92	11.9999
UGGA	chr19:9268496-9268697(+)$1	201	100	104	11.9999
UGGA	chr20:2448225-2448426(-)$1	201	182	186	11.9999
UGGA	chr7:102036411-102036612(+)$1	201	26	30	11.9999
UGGA	chr9:132397902-132398103(-)$1	201	22	26	11.9999
UGGA	chr2:69552150-69552351(-)$1	201	49	53	11.9999
UGGA	chr14:62213585-62213786(+)$1	201	96	100	11.9999
UGGA	chr19:40827030-40827231(-)$1	201	91	95	11.9999
UGGA	chr9:95077482-95077683(-)$1	201	96	100	11.9999
UGGA	chr2:182780382-182780583(+)$1	201	47	51	11.9999
UGGA	chr3:121435497-121435698(-)$1	201	2	6	11.9999
UGGA	chr11:46693817-46694018(+)$1	201	48	52	11.9999
UGGA	chr3:41280975-41281176(+)$1	201	17	21	11.9999
UGGA	chr13:49772533-49772734(+)$1	201	59	63	11.9999
UGGA	chr7:127964546-127964747(-)$1	201	16	20	11.9999
UGGA	chr7:935592-935793(+)$1	201	23	27	11.9999
UGGA	chr9:88207426-88207627(-)$1	201	182	186	11.9999
UGGA	chr18:44641488-44641689(-)$1	201	51	55	11.9999
UGGA	chr2:61577390-61577591(-)$1	201	28	32	11.9999
UGGA	chr12:42629326-42629527(-)$1	201	5	9	11.9999
UGGA	chr1:184589018-184589219(+)$1	201	132	136	11.9999
UGGA	chr14:76621213-76621414(+)$1	201	3	7	11.9999
UGGA	chr1:39776475-39776676(+)$1	201	90	94	11.9999
ugga	chr4:75049337-75049538(+)$1	201	78	82	11.9999
UGGA	chr4:129193490-129193691(-)$1	201	29	33	11.9999
UGGA	chr17:20907526-20907727(-)$1	201	101	105	11.9999
UGGA	chr11:47869379-47869580(-)$1	201	132	136	11.9999
ugga	chr12:46368535-46368736(-)$1	201	91	95	11.9999
UGGA	chr5:37206235-37206436(-)$1	201	63	67	11.9999
UGGA	chr1:150240534-150240735(-)$1	201	61	65	11.9999
UGGA	chr6:64423084-64423285(+)$1	201	125	129	11.9999
UGGA	chr2:128493494-128493695(-)$1	201	122	126	11.9999
UGGA	chr7:99169800-99170001(+)$1	201	68	72	11.9999
UGGA	chr1:205684517-205684718(-)$1	201	96	100	11.9999
UGGA	chr5:43161760-43161961(+)$1	201	125	129	11.9999
UGGA	chr16:448013-448214(+)$1	201	102	106	11.9999
UGGA	chr12:49331770-49331971(-)$1	201	4	8	11.9999
UGGA	chr7:26229946-26230147(-)$1	201	18	22	11.9999
UGGA	chr8:6357240-6357441(+)$1	201	159	163	11.9999
UGGA	chr8:27665650-27665851(+)$1	201	144	148	11.9999
UGGA	chr5:94860150-94860351(-)$1	201	110	114	11.9999
UGGA	chr13:80122401-80122602(+)$1	201	78	82	11.9999

#otherMatches

#Struct PSSM
ffff	chr5:869280-869481(-)$1	201	176	180	11.9999
rrrr	chrX:153184276-153184477(-)$1	201	73	77	11.9999
ddd4	chr17:2321919-2322120(-)$1	201	174	178	11.9999
bb22	chr10:96093082-96093283(-)$1	201	20	24	11.9999
:ddd	chr1:110166486-110166687(+)$1	201	3	7	11.9999
ccc2	chr1:228332014-228332215(+)$1	201	177	181	11.9999
hhhh	chr5:133486718-133486919(-)$1	201	92	96	11.9999
fffa	chr3:146239574-146239775(-)$1	201	103	107	11.9999
Hbbl	chr19:36133221-36133422(+)$1	201	13	17	11.9999
]bb:	chr11:803112-803313(-)$1	201	47	51	11.9999
eee]	chr3:98512502-98512703(+)$1	201	177	181	11.9999
gggg	chr1:183497994-183498195(+)$1	201	176	180	11.9999
gggg	chr9:139757121-139757322(-)$1	201	90	94	11.9999
d[dd	chr17:41151667-41151868(+)$1	201	100	104	11.9999
ccc[	chr3:185332354-185332555(+)$1	201	13	17	11.9999
ccc2	chr6:146240495-146240696(-)$1	201	84	88	11.9999
[hhh	chr17:41154634-41154835(+)$1	201	63	67	11.9999
cc]c	chr7:90014259-90014460(+)$1	201	28	32	11.9999
9999	chr4:39207137-39207338(+)$1	201	81	85	11.9999
dddd	chr10:99519149-99519350(+)$1	201	58	62	11.9999
ddd[	chr9:33264275-33264476(-)$1	201	101	105	11.9999
iiii	chr1:185093987-185094188(-)$1	201	11	15	11.9999
ccss	chr6:168312669-168312870(+)$1	201	83	87	11.9999
eeqq	chr14:64434368-64434569(+)$1	201	13	17	11.9999
lggg	chr5:176966143-176966344(-)$1	201	189	193	11.9999
ccce	chr10:103347012-103347213(-)$1	201	17	21	11.9999
cc]c	chr6:56357721-56357922(-)$1	201	42	46	11.9999
"""h	chr17:73702067-73702268(+)$1	201	142	146	11.9999
ddd:	chr10:14939289-14939490(+)$1	201	154	158	11.9999
BBhh	chr2:220043452-220043653(+)$1	201	88	92	11.9999
bb!!	chr19:9268496-9268697(+)$1	201	100	104	11.9999
JJJJ	chr20:2448225-2448426(-)$1	201	182	186	11.9999
::::	chr7:102036411-102036612(+)$1	201	26	30	11.9999
ff::	chr9:132397902-132398103(-)$1	201	22	26	11.9999
FFF:	chr2:69552150-69552351(-)$1	201	49	53	11.9999
ccc%	chr14:62213585-62213786(+)$1	201	96	100	11.9999
gggg	chr19:40827030-40827231(-)$1	201	91	95	11.9999
bbff	chr9:95077482-95077683(-)$1	201	96	100	11.9999
hhhh	chr2:182780382-182780583(+)$1	201	47	51	11.9999
EEEE	chr3:121435497-121435698(-)$1	201	2	6	11.9999
fffn	chr11:46693817-46694018(+)$1	201	48	52	11.9999
[ggg	chr3:41280975-41281176(+)$1	201	17	21	11.9999
eee!	chr13:49772533-49772734(+)$1	201	59	63	11.9999
tttt	chr7:127964546-127964747(-)$1	201	16	20	11.9999
ddd:	chr7:935592-935793(+)$1	201	23	27	11.9999
====	chr9:88207426-88207627(-)$1	201	182	186	11.9999
ccc"	chr18:44641488-44641689(-)$1	201	51	55	11.9999
KHHH	chr2:61577390-61577591(-)$1	201	28	32	11.9999
ggmm	chr12:42629326-42629527(-)$1	201	5	9	11.9999
gggg	chr1:184589018-184589219(+)$1	201	132	136	11.9999
CDDD	chr14:76621213-76621414(+)$1	201	3	7	11.9999
ccuu	chr1:39776475-39776676(+)$1	201	90	94	11.9999
ccc3	chr4:75049337-75049538(+)$1	201	78	82	11.9999
dddd	chr4:129193490-129193691(-)$1	201	29	33	11.9999
:FFF	chr17:20907526-20907727(-)$1	201	101	105	11.9999
:BB}	chr11:47869379-47869580(-)$1	201	132	136	11.9999
i!!f	chr12:46368535-46368736(-)$1	201	91	95	11.9999
eeee	chr5:37206235-37206436(-)$1	201	63	67	11.9999
dggg	chr1:150240534-150240735(-)$1	201	61	65	11.9999
ccc4	chr6:64423084-64423285(+)$1	201	125	129	11.9999
d"""	chr2:128493494-128493695(-)$1	201	122	126	11.9999
====	chr7:99169800-99170001(+)$1	201	68	72	11.9999
====	chr1:205684517-205684718(-)$1	201	96	100	11.9999
bbmm	chr5:43161760-43161961(+)$1	201	125	129	11.9999
dddl	chr16:448013-448214(+)$1	201	102	106	11.9999
ccc[	chr12:49331770-49331971(-)$1	201	4	8	11.9999
hhhh	chr7:26229946-26230147(-)$1	201	18	22	11.9999
b]bb	chr8:6357240-6357441(+)$1	201	159	163	11.9999
oddd	chr8:27665650-27665851(+)$1	201	144	148	11.9999
gggg	chr5:94860150-94860351(-)$1	201	110	114	11.9999
ee!!	chr13:80122401-80122602(+)$1	201	78	82	11.9999

#DB
))))	chr5:869280-869481(-)$1	1	176	180	11.9999
....	chrX:153184276-153184477(-)$1	1	73	77	11.9999
))).	chr17:2321919-2322120(-)$1	1	174	178	11.9999
))..	chr10:96093082-96093283(-)$1	1	20	24	11.9999
.(((	chr1:110166486-110166687(+)$1	1	3	7	11.9999
))).	chr1:228332014-228332215(+)$1	1	177	181	11.9999
))))	chr5:133486718-133486919(-)$1	1	92	96	11.9999
((((	chr3:146239574-146239775(-)$1	1	103	107	11.9999
(((.	chr19:36133221-36133422(+)$1	1	13	17	11.9999
.)).	chr11:803112-803313(-)$1	1	47	51	11.9999
))).	chr3:98512502-98512703(+)$1	1	177	181	11.9999
))))	chr1:183497994-183498195(+)$1	1	176	180	11.9999
((((	chr9:139757121-139757322(-)$1	1	90	94	11.9999
(.((	chr17:41151667-41151868(+)$1	1	100	104	11.9999
(((.	chr3:185332354-185332555(+)$1	1	13	17	11.9999
))).	chr6:146240495-146240696(-)$1	1	84	88	11.9999
.(((	chr17:41154634-41154835(+)$1	1	63	67	11.9999
)).)	chr7:90014259-90014460(+)$1	1	28	32	11.9999
....	chr4:39207137-39207338(+)$1	1	81	85	11.9999
((((	chr10:99519149-99519350(+)$1	1	58	62	11.9999
(((.	chr9:33264275-33264476(-)$1	1	101	105	11.9999
((((	chr1:185093987-185094188(-)$1	1	11	15	11.9999
((..	chr6:168312669-168312870(+)$1	1	83	87	11.9999
((..	chr14:64434368-64434569(+)$1	1	13	17	11.9999
.)))	chr5:176966143-176966344(-)$1	1	189	193	11.9999
((((	chr10:103347012-103347213(-)$1	1	17	21	11.9999
)).)	chr6:56357721-56357922(-)$1	1	42	46	11.9999
...(	chr17:73702067-73702268(+)$1	1	142	146	11.9999
))).	chr10:14939289-14939490(+)$1	1	154	158	11.9999
((((	chr2:220043452-220043653(+)$1	1	88	92	11.9999
((..	chr19:9268496-9268697(+)$1	1	100	104	11.9999
))))	chr20:2448225-2448426(-)$1	1	182	186	11.9999
....	chr7:102036411-102036612(+)$1	1	26	30	11.9999
))..	chr9:132397902-132398103(-)$1	1	22	26	11.9999
(((.	chr2:69552150-69552351(-)$1	1	49	53	11.9999
(((.	chr14:62213585-62213786(+)$1	1	96	100	11.9999
((((	chr19:40827030-40827231(-)$1	1	91	95	11.9999
))((	chr9:95077482-95077683(-)$1	1	96	100	11.9999
((((	chr2:182780382-182780583(+)$1	1	47	51	11.9999
((((	chr3:121435497-121435698(-)$1	1	2	6	11.9999
(((.	chr11:46693817-46694018(+)$1	1	48	52	11.9999
.(((	chr3:41280975-41281176(+)$1	1	17	21	11.9999
(((.	chr13:49772533-49772734(+)$1	1	59	63	11.9999
....	chr7:127964546-127964747(-)$1	1	16	20	11.9999
))).	chr7:935592-935793(+)$1	1	23	27	11.9999
))))	chr9:88207426-88207627(-)$1	1	182	186	11.9999
(((.	chr18:44641488-44641689(-)$1	1	51	55	11.9999
.(((	chr2:61577390-61577591(-)$1	1	28	32	11.9999
((..	chr12:42629326-42629527(-)$1	1	5	9	11.9999
))))	chr1:184589018-184589219(+)$1	1	132	136	11.9999
((((	chr14:76621213-76621414(+)$1	1	3	7	11.9999
((..	chr1:39776475-39776676(+)$1	1	90	94	11.9999
))).	chr4:75049337-75049538(+)$1	1	78	82	11.9999
((((	chr4:129193490-129193691(-)$1	1	29	33	11.9999
.)))	chr17:20907526-20907727(-)$1	1	101	105	11.9999
.)).	chr11:47869379-47869580(-)$1	1	132	136	11.9999
(..(	chr12:46368535-46368736(-)$1	1	91	95	11.9999
))))	chr5:37206235-37206436(-)$1	1	63	67	11.9999
((((	chr1:150240534-150240735(-)$1	1	61	65	11.9999
))).	chr6:64423084-64423285(+)$1	1	125	129	11.9999
(...	chr2:128493494-128493695(-)$1	1	122	126	11.9999
))))	chr7:99169800-99170001(+)$1	1	68	72	11.9999
((((	chr1:205684517-205684718(-)$1	1	96	100	11.9999
((..	chr5:43161760-43161961(+)$1	1	125	129	11.9999
(((.	chr16:448013-448214(+)$1	1	102	106	11.9999
(((.	chr12:49331770-49331971(-)$1	1	4	8	11.9999
))))	chr7:26229946-26230147(-)$1	1	18	22	11.9999
).))	chr8:6357240-6357441(+)$1	1	159	163	11.9999
.)))	chr8:27665650-27665851(+)$1	1	144	148	11.9999
((((	chr5:94860150-94860351(-)$1	1	110	114	11.9999
((..	chr13:80122401-80122602(+)$1	1	78	82	11.9999

#PSSM
U : 0.94	u : 0.05	
G : 0.94	g : 0.05	
G : 0.94	g : 0.05	
A : 0.94	a : 0.05	

#score	851.9999999999998
#seq	71
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_transcript_m3_run1.nuc.txt

#NT
UUUUU	chr6:142937724-142937944(-)$1	220	8	13	14.9999
uuuuu	chr16:68776280-68776516(+)$1	236	69	74	14.9999
UUUUU	chr8:6527947-6528173(+)$1	226	57	62	14.9999
UUUUU	chr3:186504389-186504608(+)$1	219	128	133	14.9999
UUUUU	chr4:119625032-119625307(-)$1	275	156	161	14.9999
uuuuu	chr13:79959990-79960211(-)$1	221	132	137	14.9999
UUUUU	chr15:41010944-41011183(+)$1	239	42	47	14.9999
uuuuu	chr17:2321568-2321795(-)$1	227	68	73	14.9999
uuuuu	chr1:155268422-155268676(-)$1	254	239	244	14.9999
UUUUU	chr3:150905838-150906074(+)$1	236	15	20	14.9999
UUUUU	chr4:119631121-119631487(+)$1	366	12	17	14.9999
uuuuu	chr12:7052895-7053123(+)$1	228	127	132	14.9999
UUUUU	chr6:28565011-28565232(-)$1	221	126	131	14.9999
uuuuu	chr20:18246293-18246517(-)$1	224	94	99	14.9999
uuuuu	chr17:75438093-75438316(+)$1	223	196	201	14.9999
UUUUU	chr15:90305779-90306003(+)$1	224	34	39	14.9999
uuuuu	chr17:59831715-59831935(-)$1	220	2	7	14.9999
uuuuu	chr4:1704633-1704869(-)$1	236	55	60	14.9999
UUUUU	chr4:2882391-2882612(-)$1	221	78	83	14.9999
UUUUU	chr9:96938535-96938756(+)$1	221	1	6	14.9999
UUUUU	chr6:28615883-28616120(-)$1	237	150	155	14.9999
uuuuu	chr16:53967816-53968083(+)$1	267	22	27	14.9999
uuuuu	chr10:103124505-103124793(-)$1	288	100	105	14.9999
UUUUU	chr1:71533263-71533485(-)$1	222	77	82	14.9999
uuuuu	chrX:91053086-91053319(+)$1	233	104	109	14.9999
uuuuu	chr12:51333630-51333849(-)$1	219	94	99	14.9999
UUUUU	chr4:71863727-71863954(+)$1	227	6	11	14.9999
UUUUU	chr1:39579840-39580069(+)$1	229	14	19	14.9999
uuuuu	chr5:311944-312189(+)$1	245	22	27	14.9999
UUUUU	chr10:128883253-128883483(+)$1	230	150	155	14.9999
UUUUU	chr9:5720083-5720302(+)$1	219	5	10	14.9999
uuuuu	chr11:93995933-93996153(+)$1	220	78	83	14.9999
UUUUU	chr17:8130211-8130441(-)$1	230	142	147	14.9999
UUUUU	chr1:16993177-16993536(-)$1	359	302	307	14.9999
UUUUU	chr1:39906650-39906885(+)$1	235	94	99	14.9999
UUUUU	chr17:61436972-61437192(+)$1	220	48	53	14.9999
UUUUU	chr22:21802675-21802896(+)$1	221	149	154	14.9999
uuuuu	chr19:47591871-47592104(-)$1	233	175	180	14.9999
UUUUU	chr1:22252081-22252309(-)$1	228	195	200	14.9999
uuuuu	chr11:40330121-40330340(-)$1	219	19	24	14.9999
uuuuu	chr9:89037756-89037989(-)$1	233	45	50	14.9999
UUUUU	chr22:28369412-28369649(+)$1	237	88	93	14.9999
uuuuu	chrY:4887095-4887344(+)$1	249	120	125	14.9999
uUUUU	chr17:19093241-19093514(-)$1	273	172	177	14.9999
UUUUU	chr10:76980463-76980684(+)$1	221	2	7	14.9999
uuuuu	chr3:73160113-73160372(+)$1	259	128	133	14.9999
uuuuu	chr2:133012544-133012787(-)$1	243	162	167	14.9999
UUUUU	chr2:43798857-43799082(-)$1	225	73	78	14.9999
UUUUU	chr5:40763781-40764001(-)$1	220	26	31	14.9999
uuuuu	chr9:89037815-89038066(-)$1	251	122	127	14.9999
uuuuu	chr15:83682425-83682651(+)$1	226	6	11	14.9999
UUUUU	chr13:79891584-79891816(-)$1	232	118	123	14.9999
UUUUU	chr10:126703859-126704090(-)$1	231	133	138	14.9999
UUUUU	chr12:6690643-6690876(-)$1	233	98	103	14.9999
uuuuu	chr19:58378578-58378818(+)$1	240	158	163	14.9999
uuuuu	chr8:141625347-141625566(-)$1	219	169	174	14.9999
uuuuu	chr14:23794523-23794760(+)$1	237	84	89	14.9999

#otherMatches

#Struct PSSM
:::ff	chr20:43516329-43516551(+)$1	222	160	165	14.9999
LLLDD	chr6:142937724-142937944(-)$1	220	8	13	14.9999
ttttt	chr16:68776280-68776516(+)$1	236	69	74	14.9999
na22c	chr8:6527947-6528173(+)$1	226	57	62	14.9999
h]hhh	chr3:186504389-186504608(+)$1	219	128	133	14.9999
=====	chr4:119625032-119625307(-)$1	275	156	161	14.9999
&&&&&	chr13:79959990-79960211(-)$1	221	132	137	14.9999
cc!!b	chr15:41010944-41011183(+)$1	239	42	47	14.9999
))))d	chr17:2321568-2321795(-)$1	227	68	73	14.9999
:::::	chr1:155268422-155268676(-)$1	254	239	244	14.9999
QQQQQ	chr3:150905838-150906074(+)$1	236	15	20	14.9999
eeee:	chr4:119631121-119631487(+)$1	366	12	17	14.9999
ppppp	chr12:7052895-7053123(+)$1	228	127	132	14.9999
[bboo	chr6:28565011-28565232(-)$1	221	126	131	14.9999
ff444	chr20:18246293-18246517(-)$1	224	94	99	14.9999
66===	chr17:75438093-75438316(+)$1	223	196	201	14.9999
ttttt	chr15:90305779-90306003(+)$1	224	34	39	14.9999
:::::	chr17:59831715-59831935(-)$1	220	2	7	14.9999
iiiii	chr4:1704633-1704869(-)$1	236	55	60	14.9999
ggggg	chr4:2882391-2882612(-)$1	221	78	83	14.9999
:::::	chr9:96938535-96938756(+)$1	221	1	6	14.9999
EEEE:	chr6:28615883-28616120(-)$1	237	150	155	14.9999
:::::	chr16:53967816-53968083(+)$1	267	22	27	14.9999
JJJJJ	chr10:103124505-103124793(-)$1	288	100	105	14.9999
GGGGG	chr1:71533263-71533485(-)$1	222	77	82	14.9999
hhhhh	chrX:91053086-91053319(+)$1	233	104	109	14.9999
dd333	chr12:51333630-51333849(-)$1	219	94	99	14.9999
:::::	chr4:71863727-71863954(+)$1	227	6	11	14.9999
!!a!!	chr1:39579840-39580069(+)$1	229	14	19	14.9999
ttttt	chr5:311944-312189(+)$1	245	22	27	14.9999
>>>>>	chr10:128883253-128883483(+)$1	230	150	155	14.9999
fffff	chr9:5720083-5720302(+)$1	219	5	10	14.9999
ttttt	chr11:93995933-93996153(+)$1	220	78	83	14.9999
ff:::	chr17:8130211-8130441(-)$1	230	142	147	14.9999
eeee2	chr1:16993177-16993536(-)$1	359	302	307	14.9999
fffff	chr1:39906650-39906885(+)$1	235	94	99	14.9999
ff&&&	chr17:61436972-61437192(+)$1	220	48	53	14.9999
gggg:	chr22:21802675-21802896(+)$1	221	149	154	14.9999
f++++	chr19:47591871-47592104(-)$1	233	175	180	14.9999
D~~~~	chr1:22252081-22252309(-)$1	228	195	200	14.9999
FFFFF	chr11:40330121-40330340(-)$1	219	19	24	14.9999
GGGGG	chr9:89037756-89037989(-)$1	233	45	50	14.9999
eeee)	chr22:28369412-28369649(+)$1	237	88	93	14.9999
hhhhh	chrY:4887095-4887344(+)$1	249	120	125	14.9999
IIIII	chr17:19093241-19093514(-)$1	273	172	177	14.9999
:::DD	chr10:76980463-76980684(+)$1	221	2	7	14.9999
EEE{F	chr3:73160113-73160372(+)$1	259	128	133	14.9999
2ffff	chr2:133012544-133012787(-)$1	243	162	167	14.9999
i!!dd	chr2:43798857-43799082(-)$1	225	73	78	14.9999
hhhh2	chr5:40763781-40764001(-)$1	220	26	31	14.9999
GGGGG	chr9:89037815-89038066(-)$1	251	122	127	14.9999
:IIII	chr15:83682425-83682651(+)$1	226	6	11	14.9999
"""ff	chr13:79891584-79891816(-)$1	232	118	123	14.9999
qqqqq	chr10:126703859-126704090(-)$1	231	133	138	14.9999
::::g	chr12:6690643-6690876(-)$1	233	98	103	14.9999
zzzzz	chr19:58378578-58378818(+)$1	240	158	163	14.9999
444hh	chr8:141625347-141625566(-)$1	219	169	174	14.9999
iiiii	chr14:23794523-23794760(+)$1	237	84	89	14.9999

#DB
...((	chr20:43516329-43516551(+)$1	1	160	165	14.9999
...((	chr6:142937724-142937944(-)$1	1	8	13	14.9999
.....	chr16:68776280-68776516(+)$1	1	69	74	14.9999
.)..)	chr8:6527947-6528173(+)$1	1	57	62	14.9999
).)))	chr3:186504389-186504608(+)$1	1	128	133	14.9999
)))))	chr4:119625032-119625307(-)$1	1	156	161	14.9999
.....	chr13:79959990-79960211(-)$1	1	132	137	14.9999
((..(	chr15:41010944-41011183(+)$1	1	42	47	14.9999
....(	chr17:2321568-2321795(-)$1	1	68	73	14.9999
.....	chr1:155268422-155268676(-)$1	1	239	244	14.9999
.....	chr3:150905838-150906074(+)$1	1	15	20	14.9999
)))).	chr4:119631121-119631487(+)$1	1	12	17	14.9999
.....	chr12:7052895-7053123(+)$1	1	127	132	14.9999
.((..	chr6:28565011-28565232(-)$1	1	126	131	14.9999
))...	chr20:18246293-18246517(-)$1	1	94	99	14.9999
..)))	chr17:75438093-75438316(+)$1	1	196	201	14.9999
.....	chr15:90305779-90306003(+)$1	1	34	39	14.9999
.....	chr17:59831715-59831935(-)$1	1	2	7	14.9999
(((((	chr4:1704633-1704869(-)$1	1	55	60	14.9999
(((((	chr4:2882391-2882612(-)$1	1	78	83	14.9999
.....	chr9:96938535-96938756(+)$1	1	1	6	14.9999
)))).	chr6:28615883-28616120(-)$1	1	150	155	14.9999
.....	chr16:53967816-53968083(+)$1	1	22	27	14.9999
(((((	chr10:103124505-103124793(-)$1	1	100	105	14.9999
(((((	chr1:71533263-71533485(-)$1	1	77	82	14.9999
)))))	chrX:91053086-91053319(+)$1	1	104	109	14.9999
))...	chr12:51333630-51333849(-)$1	1	94	99	14.9999
.....	chr4:71863727-71863954(+)$1	1	6	11	14.9999
..(..	chr1:39579840-39580069(+)$1	1	14	19	14.9999
.....	chr5:311944-312189(+)$1	1	22	27	14.9999
.....	chr10:128883253-128883483(+)$1	1	150	155	14.9999
(((((	chr9:5720083-5720302(+)$1	1	5	10	14.9999
.....	chr11:93995933-93996153(+)$1	1	78	83	14.9999
))...	chr17:8130211-8130441(-)$1	1	142	147	14.9999
)))).	chr1:16993177-16993536(-)$1	1	302	307	14.9999
(((((	chr1:39906650-39906885(+)$1	1	94	99	14.9999
((...	chr17:61436972-61437192(+)$1	1	48	53	14.9999
)))).	chr22:21802675-21802896(+)$1	1	149	154	14.9999
(....	chr19:47591871-47592104(-)$1	1	175	180	14.9999
)....	chr1:22252081-22252309(-)$1	1	195	200	14.9999
(((((	chr11:40330121-40330340(-)$1	1	19	24	14.9999
(((((	chr9:89037756-89037989(-)$1	1	45	50	14.9999
((((.	chr22:28369412-28369649(+)$1	1	88	93	14.9999
)))))	chrY:4887095-4887344(+)$1	1	120	125	14.9999
)))))	chr17:19093241-19093514(-)$1	1	172	177	14.9999
...((	chr10:76980463-76980684(+)$1	1	2	7	14.9999
(((.(	chr3:73160113-73160372(+)$1	1	128	133	14.9999
.))))	chr2:133012544-133012787(-)$1	1	162	167	14.9999
(..((	chr2:43798857-43799082(-)$1	1	73	78	14.9999
)))).	chr5:40763781-40764001(-)$1	1	26	31	14.9999
(((((	chr9:89037815-89038066(-)$1	1	122	127	14.9999
.((((	chr15:83682425-83682651(+)$1	1	6	11	14.9999
...((	chr13:79891584-79891816(-)$1	1	118	123	14.9999
.....	chr10:126703859-126704090(-)$1	1	133	138	14.9999
....(	chr12:6690643-6690876(-)$1	1	98	103	14.9999
.....	chr19:58378578-58378818(+)$1	1	158	163	14.9999
...))	chr8:141625347-141625566(-)$1	1	169	174	14.9999
(((((	chr14:23794523-23794760(+)$1	1	84	89	14.9999

#PSSM
U : 0.53	u : 0.46	
U : 0.55	u : 0.44	
U : 0.55	u : 0.44	
U : 0.55	u : 0.44	
U : 0.55	u : 0.44	

#score	869.9999999999999
#seq	58
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUUUAAA	chr2:74443575-74443811(+)$1	236	149	158	22.2500
UAUUUUCAA	chr3:185639769-185640001(-)$1	232	210	219	15.5000
uguuuuaaa	chr2:228423751-228423977(+)$1	226	145	154	19.2500
uuauuuaaa	chr13:73335698-73335943(-)$1	245	233	242	17.7500
UAUUUUAAA	chr2:152659231-152659444(-)$1	213	62	71	19.1250
UUUUUUCAA	chr17:45195667-45195893(-)$1	226	139	148	18.6250
uuuuuuaua	chr5:61683723-61683936(+)$1	213	78	87	18.1250
UUUUUUCCA	chr12:57908449-57908667(+)$1	218	18	27	14.5000
UUUUUUCAA	chr5:65375039-65375262(+)$1	223	170	179	18.6250
CUUUUUAAA	chr5:167976842-167977092(-)$1	250	85	94	18.0000
AUUUUUAAA	chr19:24309088-24309309(+)$1	221	208	217	18.0000
UUUUUUAAA	chr12:26222139-26222371(+)$1	232	220	229	22.2500
UUUUUUAAA	chr2:48033823-48034151(+)$1	328	255	264	22.2500
UUUUUUAAC	chr7:97837677-97837905(+)$1	228	35	44	17.9999
UUUCUUAAA	chr1:224347840-224348112(+)$1	272	208	217	17.5000
UUUUUCAAA	chr5:157186731-157186961(+)$1	230	184	193	17.5000
UUUUCUAAA	chr6:116901389-116901611(+)$1	222	161	170	17.7500
UGUUUUAAA	chr5:150089115-150089340(-)$1	225	48	57	19.2500
UUUUUUGUA	chr17:79476999-79477228(-)$1	229	102	111	14.2500
UUUUUUAAA	chr1:198289525-198289784(+)$1	259	217	226	22.2500
UAUUUUAAA	chr3:196311704-196311926(+)$1	222	11	20	19.1250
UUUUCUAAA	chr8:17423424-17423682(+)$1	258	180	189	17.7500
UCUUUUAAA	chr5:176724290-176724514(+)$1	224	55	64	18.8750
UGUUUUAAA	chr3:179110436-179110660(+)$1	224	177	186	19.2500
UUUUUUUCA	chr1:225675481-225675716(-)$1	235	65	74	14.1250
UGUUUUAAA	chr9:73000181-73000410(-)$1	229	37	46	19.2500
UUUUUUAAA	chr21:19162862-19163087(-)$1	225	76	85	22.2500
UUUUUUAAC	chr1:179072086-179072322(-)$1	236	201	210	17.9999
UUUUUUAAG	chr2:87004772-87004991(+)$1	219	58	67	17.9999
uuuuuuaaa	chr1:218510685-218510927(+)$1	242	81	90	22.2500
UUGUUUAAA	chr7:26708478-26708697(-)$1	219	130	139	17.7500
UGUUUUAAA	chr13:25905840-25906070(+)$1	230	193	202	19.2500
UUUUUUAAA	chr1:65300123-65300336(-)$1	213	159	168	22.2500
UCUUUUAGA	chr2:24222621-24222851(+)$1	230	89	98	14.6250
UUUUUUAAA	chr16:11964124-11964357(-)$1	233	131	140	22.2500
UUUUUUAAG	chr9:101912635-101912859(+)$1	224	60	69	17.9999
UAUUUUAAA	chr1:200828535-200828756(+)$1	221	21	30	19.1250
AUUUUUGAA	chr8:38118510-38118733(+)$1	223	103	112	14.1250
UUCuuuaaa	chr1:41477329-41477571(+)$1	242	74	83	17.7500

#otherMatches

#Struct PSSM
ddd"""ccc	chr1:224345772-224345996(+)$1	224	74	83	18.0000
:::::::::	chr2:74443575-74443811(+)$1	236	149	158	22.2500
h::::::::	chr3:185639769-185640001(-)$1	232	210	219	15.5000
ii9999999	chr2:228423751-228423977(+)$1	226	145	154	19.2500
oooooffff	chr13:73335698-73335943(-)$1	245	233	242	17.7500
ggggg333e	chr2:152659231-152659444(-)$1	213	62	71	19.1250
33hhhhhhh	chr17:45195667-45195893(-)$1	226	139	148	18.6250
FFFZZZFFF	chr5:61683723-61683936(+)$1	213	78	87	18.1250
:::::::::	chr12:57908449-57908667(+)$1	218	18	27	14.5000
:::::::ff	chr5:65375039-65375262(+)$1	223	170	179	18.6250
dd[dddd%%	chr5:167976842-167977092(-)$1	250	85	94	18.0000
:::::::::	chr19:24309088-24309309(+)$1	221	208	217	18.0000
F::::::::	chr12:26222139-26222371(+)$1	232	220	229	22.2500
gggglllgg	chr2:48033823-48034151(+)$1	328	255	264	22.2500
ii"""gggg	chr7:97837677-97837905(+)$1	228	35	44	17.9999
:::::::::	chr1:224347840-224348112(+)$1	272	208	217	17.5000
b::::::ee	chr5:157186731-157186961(+)$1	230	184	193	17.5000
FFFFFF___	chr6:116901389-116901611(+)$1	222	161	170	17.7500
gggglllgg	chr5:150089115-150089340(-)$1	225	48	57	19.2500
:::eeeee"	chr17:79476999-79477228(-)$1	229	102	111	14.2500
FF~~~~FFF	chr1:198289525-198289784(+)$1	259	217	226	22.2500
iqqqqqqqq	chr3:196311704-196311926(+)$1	222	11	20	19.1250
555eeeee4	chr8:17423424-17423682(+)$1	258	180	189	17.7500
hhhhhh:::	chr5:176724290-176724514(+)$1	224	55	64	18.8750
aqqqqqqqq	chr3:179110436-179110660(+)$1	224	177	186	19.2500
gg::::DDD	chr1:225675481-225675716(-)$1	235	65	74	14.1250
==&&&&&&&	chr9:73000181-73000410(-)$1	229	37	46	19.2500
fffmmmmff	chr21:19162862-19163087(-)$1	225	76	85	22.2500
d]ccc:::D	chr1:179072086-179072322(-)$1	236	201	210	17.9999
gggg'''''	chr2:87004772-87004991(+)$1	219	58	67	17.9999
:ggggggg!	chr1:218510685-218510927(+)$1	242	81	90	22.2500
hhhhhhsss	chr7:26708478-26708697(-)$1	219	130	139	17.7500
^^^^^^^^e	chr13:25905840-25906070(+)$1	230	193	202	19.2500
::::::::h	chr1:65300123-65300336(-)$1	213	159	168	22.2500
hhhhhhhh:	chr2:24222621-24222851(+)$1	230	89	98	14.6250
=========	chr16:11964124-11964357(-)$1	233	131	140	22.2500
##ffffff#	chr9:101912635-101912859(+)$1	224	60	69	17.9999
hhhhhhppp	chr1:200828535-200828756(+)$1	221	21	30	19.1250
::ggggggg	chr8:38118510-38118733(+)$1	223	103	112	14.1250
fffff22ff	chr1:41477329-41477571(+)$1	242	74	83	17.7500

#DB
(((...(((	chr1:224345772-224345996(+)$1	1	74	83	18.0000
.........	chr2:74443575-74443811(+)$1	1	149	158	22.2500
)........	chr3:185639769-185640001(-)$1	1	210	219	15.5000
)).......	chr2:228423751-228423977(+)$1	1	145	154	19.2500
.....))))	chr13:73335698-73335943(-)$1	1	233	242	17.7500
)))))...)	chr2:152659231-152659444(-)$1	1	62	71	19.1250
..)))))))	chr17:45195667-45195893(-)$1	1	139	148	18.6250
)))...)))	chr5:61683723-61683936(+)$1	1	78	87	18.1250
.........	chr12:57908449-57908667(+)$1	1	18	27	14.5000
.......((	chr5:65375039-65375262(+)$1	1	170	179	18.6250
((.((((..	chr5:167976842-167977092(-)$1	1	85	94	18.0000
.........	chr19:24309088-24309309(+)$1	1	208	217	18.0000
)........	chr12:26222139-26222371(+)$1	1	220	229	22.2500
((((...))	chr2:48033823-48034151(+)$1	1	255	264	22.2500
((...((((	chr7:97837677-97837905(+)$1	1	35	44	17.9999
.........	chr1:224347840-224348112(+)$1	1	208	217	17.5000
)......((	chr5:157186731-157186961(+)$1	1	184	193	17.5000
))))))...	chr6:116901389-116901611(+)$1	1	161	170	17.7500
((((...))	chr5:150089115-150089340(-)$1	1	48	57	19.2500
...(((((.	chr17:79476999-79477228(-)$1	1	102	111	14.2500
))....)))	chr1:198289525-198289784(+)$1	1	217	226	22.2500
(........	chr3:196311704-196311926(+)$1	1	11	20	19.1250
...))))).	chr8:17423424-17423682(+)$1	1	180	189	17.7500
))))))...	chr5:176724290-176724514(+)$1	1	55	64	18.8750
(........	chr3:179110436-179110660(+)$1	1	177	186	19.2500
))....(((	chr1:225675481-225675716(-)$1	1	65	74	14.1250
((.......	chr9:73000181-73000410(-)$1	1	37	46	19.2500
(((....))	chr21:19162862-19163087(-)$1	1	76	85	22.2500
).)))...)	chr1:179072086-179072322(-)$1	1	201	210	17.9999
((((.....	chr2:87004772-87004991(+)$1	1	58	67	17.9999
.(((((((.	chr1:218510685-218510927(+)$1	1	81	90	22.2500
((((((...	chr7:26708478-26708697(-)$1	1	130	139	17.7500
........)	chr13:25905840-25906070(+)$1	1	193	202	19.2500
........(	chr1:65300123-65300336(-)$1	1	159	168	22.2500
)))))))).	chr2:24222621-24222851(+)$1	1	89	98	14.6250
(((((((((	chr16:11964124-11964357(-)$1	1	131	140	22.2500
..((((((.	chr9:101912635-101912859(+)$1	1	60	69	17.9999
((((((...	chr1:200828535-200828756(+)$1	1	21	30	19.1250
..(((((((	chr8:38118510-38118733(+)$1	1	103	112	14.1250
)))))..))	chr1:41477329-41477571(+)$1	1	74	83	17.7500

#PSSM
U : 0.80	u : 0.10	C : 0.05	A : 0.05	
U : 0.65	A : 0.10	G : 0.10	u : 0.07	C : 0.05	g : 0.02	
U : 0.85	u : 0.07	a : 0.02	G : 0.02	C : 0.02	
U : 0.85	u : 0.12	C : 0.02	
U : 0.82	u : 0.12	C : 0.05	
U : 0.85	u : 0.12	C : 0.02	
A : 0.70	a : 0.12	C : 0.10	G : 0.05	U : 0.02	
A : 0.77	a : 0.10	C : 0.05	u : 0.02	U : 0.02	G : 0.02	
A : 0.77	a : 0.12	C : 0.05	G : 0.05	

#score	742.75
#seq	40
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_MOV10_Sievers2014_hg19_UTR_m2_run1.nuc.txt

#NT
UUUGAAA	chr10:103922802-103923043(+)$1	241	96	103	14.8524
UUUGAAA	chr15:68588034-68588249(+)$1	215	96	103	14.8524
UUUGAAA	chr5:167980676-167980920(-)$1	244	212	219	14.8524
UUUAAAA	chr10:99192475-99192714(+)$1	239	68	75	17.9672
UUUAAGA	chr19:39874786-39875020(+)$1	234	8	15	14.2786
UUUCAAA	chr6:64290481-64290732(+)$1	251	48	55	14.6885
GUUAAAA	chr19:10795586-10795818(+)$1	232	75	82	14.1147
UUUAAGA	chr1:110565176-110565409(+)$1	233	127	134	14.2786
UUUAAAA	chr22:40726524-40726751(+)$1	227	129	136	17.9672
UUUAAUA	chr10:119764721-119765029(-)$1	308	75	82	14.6065
GUUAAAA	chr7:158525572-158525802(-)$1	230	122	129	14.1147
UUUAAUA	chr1:97280048-97280301(+)$1	253	0	7	14.6065
UUUAAAA	chr1:213166822-213167064(-)$1	242	81	88	17.9672
UUUCAAA	chr5:179157143-179157366(+)$1	223	17	24	14.6885
UUUAAUA	chr6:150139878-150140097(-)$1	219	140	147	14.6065
UUUAAAA	chr6:109687781-109688017(-)$1	236	77	84	17.9672
UUUGAAA	chr1:166822087-166822311(+)$1	224	168	175	14.8524
UUUUAAA	chr6:105526761-105526981(+)$1	220	24	31	14.6065
UUUAAAA	chr3:178737248-178737492(-)$1	244	19	26	17.9672
UUUCAAA	chr20:4834382-4834610(-)$1	228	130	137	14.6885
uuuaaaa	chr12:10851759-10852046(-)$1	287	218	225	17.9672
CUUAAAA	chr1:245014786-245015054(-)$1	268	121	128	14.0327
UUUAAGA	chr12:31434895-31435134(-)$1	239	116	123	14.2786
UUUAAAA	chr5:151188654-151188871(+)$1	217	166	173	17.9672
UUUAAUA	chr5:151188079-151188300(+)$1	221	78	85	14.6065
uuuaaaa	chr3:176741133-176741355(-)$1	222	19	26	17.9672
UUUAAAA	chr1:93617411-93617641(-)$1	230	76	83	17.9672
CUUAAAA	chr13:77579373-77579606(-)$1	233	100	107	14.0327
GUUaaaa	chr1:92147739-92147987(-)$1	248	2	9	14.1147
GUUAAAA	chrX:100668656-100668886(+)$1	230	5	12	14.1147
UUUAAAA	chr2:74441415-74441647(+)$1	232	54	61	17.9672
UUUGAAA	chr7:112406301-112406553(-)$1	252	87	94	14.8524
UUUAAGA	chr1:93617841-93618086(-)$1	245	55	62	14.2786
UUUAAUA	chr16:90071469-90071713(-)$1	244	14	21	14.6065
UUUCAAA	chrX:41207673-41207886(+)$1	213	17	24	14.6885
UUUAAUA	chr1:169100778-169101022(+)$1	244	44	51	14.6065
UUUAAUA	chr1:153778351-153778582(-)$1	231	121	128	14.6065
uuuaaaa	chr4:1984693-1984927(-)$1	234	60	67	17.9672
UUUAAAA	chr7:6443100-6443327(+)$1	227	129	136	17.9672
UUUAAAA	chr1:223962793-223963044(+)$1	251	187	194	17.9672
UUUAAAA	chr10:112053300-112053524(-)$1	224	60	67	17.9672
uuuaaaa	chr12:27118001-27118228(+)$1	227	14	21	17.9672
UUUAAAA	chr17:5287865-5288117(+)$1	252	160	167	17.9672
UUUAAAA	chr5:10435498-10435727(+)$1	229	151	158	17.9672
UUUAAAA	chr17:17093686-17093922(+)$1	236	120	127	17.9672
UUUAAAA	chr1:230972781-230973012(-)$1	231	134	141	17.9672
UUUAAAA	chr9:99150240-99150476(-)$1	236	156	163	17.9672
CUUAAAA	chr16:56463690-56463906(-)$1	216	42	49	14.0327
UUUUAAA	chr10:22618488-22618740(+)$1	252	8	15	14.6065
UUUGAAA	chr2:198417109-198417328(+)$1	219	103	110	14.8524
UUUGAAA	chr8:77779322-77779535(+)$1	213	46	53	14.8524
UUUUAAA	chr13:115091878-115092106(+)$1	228	117	124	14.6065
UUUAAUA	chr11:130102064-130102294(-)$1	230	85	92	14.6065
UUUCAAA	chr5:55233295-55233506(-)$1	211	102	109	14.6885
UUUAAAA	chr17:6026602-6026835(+)$1	233	72	79	17.9672
UUUAAAA	chr1:93827719-93827944(+)$1	225	128	135	17.9672
CUUAAAA	chr1:245017157-245017395(-)$1	238	202	209	14.0327
UUUAAAA	chr1:31405651-31405873(-)$1	222	180	187	17.9672
GUUAAAA	chr5:82876940-82877163(+)$1	223	182	189	14.1147
UUUAAAA	chr5:153436028-153436255(+)$1	227	102	109	17.9672

#otherMatches

#Struct PSSM
::::eee	chr19:33873346-33873577(+)$1	231	184	191	14.6065
eee))))	chr10:103922802-103923043(+)$1	241	96	103	14.8524
#cccppp	chr15:68588034-68588249(+)$1	215	96	103	14.8524
EEE||||	chr5:167980676-167980920(-)$1	244	212	219	14.8524
h%%%%%%	chr10:99192475-99192714(+)$1	239	68	75	17.9672
:ffffff	chr19:39874786-39875020(+)$1	234	8	15	14.2786
ffffffl	chr6:64290481-64290732(+)$1	251	48	55	14.6885
a22dddd	chr19:10795586-10795818(+)$1	232	75	82	14.1147
dd]dddd	chr1:110565176-110565409(+)$1	233	127	134	14.2786
ppppppd	chr22:40726524-40726751(+)$1	227	129	136	17.9672
EEEE:::	chr10:119764721-119765029(-)$1	308	75	82	14.6065
[dddd!!	chr7:158525572-158525802(-)$1	230	122	129	14.1147
:::::::	chr1:97280048-97280301(+)$1	253	0	7	14.6065
ccc]fff	chr1:213166822-213167064(-)$1	242	81	88	17.9672
:::::::	chr5:179157143-179157366(+)$1	223	17	24	14.6885
::ggggg	chr6:150139878-150140097(-)$1	219	140	147	14.6065
llliiii	chr6:109687781-109688017(-)$1	236	77	84	17.9672
333dddd	chr1:166822087-166822311(+)$1	224	168	175	14.8524
ttttttd	chr6:105526761-105526981(+)$1	220	24	31	14.6065
eeeee[g	chr3:178737248-178737492(-)$1	244	19	26	17.9672
ggg::::	chr20:4834382-4834610(-)$1	228	130	137	14.6885
22eeeee	chr12:10851759-10852046(-)$1	287	218	225	17.9672
eeepppp	chr1:245014786-245015054(-)$1	268	121	128	14.0327
ellleee	chr12:31434895-31435134(-)$1	239	116	123	14.2786
eeee[cc	chr5:151188654-151188871(+)$1	217	166	173	17.9672
D:::ggg	chr5:151188079-151188300(+)$1	221	78	85	14.6065
:::::::	chr3:176741133-176741355(-)$1	222	19	26	17.9672
$ddddoo	chr1:93617411-93617641(-)$1	230	76	83	17.9672
ffff[bb	chr13:77579373-77579606(-)$1	233	100	107	14.0327
:::::::	chr1:92147739-92147987(-)$1	248	2	9	14.1147
[ccc[dd	chrX:100668656-100668886(+)$1	230	5	12	14.1147
]ffffff	chr2:74441415-74441647(+)$1	232	54	61	17.9672
ssssssc	chr7:112406301-112406553(-)$1	252	87	94	14.8524
GGGGGKK	chr1:93617841-93618086(-)$1	245	55	62	14.2786
:::::::	chr16:90071469-90071713(-)$1	244	14	21	14.6065
CCKKFFF	chrX:41207673-41207886(+)$1	213	17	24	14.6885
(((((((	chr1:169100778-169101022(+)$1	244	44	51	14.6065
eeee444	chr1:153778351-153778582(-)$1	231	121	128	14.6065
HHHHHHH	chr4:1984693-1984927(-)$1	234	60	67	17.9672
=%%%%%%	chr7:6443100-6443327(+)$1	227	129	136	17.9672
DDD____	chr1:223962793-223963044(+)$1	251	187	194	17.9672
fffff!!	chr10:112053300-112053524(-)$1	224	60	67	17.9672
::ggggg	chr12:27118001-27118228(+)$1	227	14	21	17.9672
eeeemmm	chr17:5287865-5288117(+)$1	252	160	167	17.9672
g::::::	chr5:10435498-10435727(+)$1	229	151	158	17.9672
cccmmmm	chr17:17093686-17093922(+)$1	236	120	127	17.9672
dddd22c	chr1:230972781-230973012(-)$1	231	134	141	17.9672
DDDD:::	chr9:99150240-99150476(-)$1	236	156	163	17.9672
d^^^^^^	chr16:56463690-56463906(-)$1	216	42	49	14.0327
EEEENNN	chr10:22618488-22618740(+)$1	252	8	15	14.6065
ggggggg	chr2:198417109-198417328(+)$1	219	103	110	14.8524
eeccc^^	chr8:77779322-77779535(+)$1	213	46	53	14.8524
ee&&&&&	chr13:115091878-115092106(+)$1	228	117	124	14.6065
====444	chr11:130102064-130102294(-)$1	230	85	92	14.6065
:::::::	chr5:55233295-55233506(-)$1	211	102	109	14.6885
:::::::	chr17:6026602-6026835(+)$1	233	72	79	17.9672
YYDDDD:	chr1:93827719-93827944(+)$1	225	128	135	17.9672
FF:::cc	chr1:245017157-245017395(-)$1	238	202	209	14.0327
iii^^^^	chr1:31405651-31405873(-)$1	222	180	187	17.9672
ddsssss	chr5:82876940-82877163(+)$1	223	182	189	14.1147
iii$$$$	chr5:153436028-153436255(+)$1	227	102	109	17.9672

#DB
....(((	chr19:33873346-33873577(+)$1	1	184	191	14.6065
(((....	chr10:103922802-103923043(+)$1	1	96	103	14.8524
.(((...	chr15:68588034-68588249(+)$1	1	96	103	14.8524
)))....	chr5:167980676-167980920(-)$1	1	212	219	14.8524
(......	chr10:99192475-99192714(+)$1	1	68	75	17.9672
.((((((	chr19:39874786-39875020(+)$1	1	8	15	14.2786
((((((.	chr6:64290481-64290732(+)$1	1	48	55	14.6885
)..))))	chr19:10795586-10795818(+)$1	1	75	82	14.1147
)).))))	chr1:110565176-110565409(+)$1	1	127	134	14.2786
......)	chr22:40726524-40726751(+)$1	1	129	136	17.9672
((((...	chr10:119764721-119765029(-)$1	1	75	82	14.6065
.((((..	chr7:158525572-158525802(-)$1	1	122	129	14.1147
.......	chr1:97280048-97280301(+)$1	1	0	7	14.6065
))).)))	chr1:213166822-213167064(-)$1	1	81	88	17.9672
.......	chr5:179157143-179157366(+)$1	1	17	24	14.6885
..(((((	chr6:150139878-150140097(-)$1	1	140	147	14.6065
...))))	chr6:109687781-109688017(-)$1	1	77	84	17.9672
...))))	chr1:166822087-166822311(+)$1	1	168	175	14.8524
......)	chr6:105526761-105526981(+)$1	1	24	31	14.6065
(((((.(	chr3:178737248-178737492(-)$1	1	19	26	17.9672
)))....	chr20:4834382-4834610(-)$1	1	130	137	14.6885
..)))))	chr12:10851759-10852046(-)$1	1	218	225	17.9672
(((....	chr1:245014786-245015054(-)$1	1	121	128	14.0327
(...)))	chr12:31434895-31435134(-)$1	1	116	123	14.2786
((((.((	chr5:151188654-151188871(+)$1	1	166	173	17.9672
(...(((	chr5:151188079-151188300(+)$1	1	78	85	14.6065
.......	chr3:176741133-176741355(-)$1	1	19	26	17.9672
.((((..	chr1:93617411-93617641(-)$1	1	76	83	17.9672
((((.((	chr13:77579373-77579606(-)$1	1	100	107	14.0327
.......	chr1:92147739-92147987(-)$1	1	2	9	14.1147
.(((.((	chrX:100668656-100668886(+)$1	1	5	12	14.1147
.))))))	chr2:74441415-74441647(+)$1	1	54	61	17.9672
......)	chr7:112406301-112406553(-)$1	1	87	94	14.8524
(((((..	chr1:93617841-93618086(-)$1	1	55	62	14.2786
.......	chr16:90071469-90071713(-)$1	1	14	21	14.6065
((..(((	chrX:41207673-41207886(+)$1	1	17	24	14.6885
.......	chr1:169100778-169101022(+)$1	1	44	51	14.6065
))))...	chr1:153778351-153778582(-)$1	1	121	128	14.6065
(((((((	chr4:1984693-1984927(-)$1	1	60	67	17.9672
(......	chr7:6443100-6443327(+)$1	1	129	136	17.9672
)))....	chr1:223962793-223963044(+)$1	1	187	194	17.9672
(((((..	chr10:112053300-112053524(-)$1	1	60	67	17.9672
..(((((	chr12:27118001-27118228(+)$1	1	14	21	17.9672
((((...	chr17:5287865-5288117(+)$1	1	160	167	17.9672
)......	chr5:10435498-10435727(+)$1	1	151	158	17.9672
(((....	chr17:17093686-17093922(+)$1	1	120	127	17.9672
))))..)	chr1:230972781-230973012(-)$1	1	134	141	17.9672
))))...	chr9:99150240-99150476(-)$1	1	156	163	17.9672
(......	chr16:56463690-56463906(-)$1	1	42	49	14.0327
((((...	chr10:22618488-22618740(+)$1	1	8	15	14.6065
(((((((	chr2:198417109-198417328(+)$1	1	103	110	14.8524
(((((..	chr8:77779322-77779535(+)$1	1	46	53	14.8524
((.....	chr13:115091878-115092106(+)$1	1	117	124	14.6065
))))...	chr11:130102064-130102294(-)$1	1	85	92	14.6065
.......	chr5:55233295-55233506(-)$1	1	102	109	14.6885
.......	chr17:6026602-6026835(+)$1	1	72	79	17.9672
..)))).	chr1:93827719-93827944(+)$1	1	128	135	17.9672
))...((	chr1:245017157-245017395(-)$1	1	202	209	14.0327
(((....	chr1:31405651-31405873(-)$1	1	180	187	17.9672
((.....	chr5:82876940-82877163(+)$1	1	182	189	14.1147
(((....	chr5:153436028-153436255(+)$1	1	102	109	17.9672

#PSSM
U : 0.77	u : 0.08	G : 0.08	C : 0.06	
U : 0.91	u : 0.08	
U : 0.91	u : 0.08	
A : 0.65	G : 0.11	C : 0.08	a : 0.08	U : 0.04	u : 0.01	
A : 0.90	a : 0.09	
A : 0.70	U : 0.13	a : 0.09	G : 0.06	
A : 0.90	a : 0.09	

#score	967.7213114754106
#seq	61
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m2_run1.nuc.txt

#NT
AGAG	chr16:14357170-14357395(+)$1	225	26	30	11.9999
AGAG	chr1:9648850-9649074(+)$1	224	132	136	11.9999
AGAG	chr11:62608995-62609381(-)$1	386	299	303	11.9999
AGAG	chr20:418111-418341(-)$1	230	3	7	11.9999
AGAG	chr12:42481414-42481634(-)$1	220	11	15	11.9999
agag	chr16:53843950-53844207(+)$1	257	39	43	11.9999
AGAG	chr1:209955621-209955848(-)$1	227	107	111	11.9999
AGAG	chr21:44515477-44515703(-)$1	226	95	99	11.9999
AGAG	chr15:40998302-40998551(-)$1	249	25	29	11.9999
AGAG	chr5:79946505-79946748(-)$1	243	94	98	11.9999
AGAG	chr20:56814656-56814881(-)$1	225	180	184	11.9999
AGAG	chr15:41021695-41021927(+)$1	232	157	161	11.9999
AGAG	chr1:117452663-117452888(-)$1	225	147	151	11.9999
AGAG	chr17:19770982-19771205(-)$1	223	116	120	11.9999
AGAG	chr14:21971242-21971467(+)$1	225	36	40	11.9999
AGAG	chr6:37787493-37787720(+)$1	227	162	166	11.9999
AGAG	chr6:163835768-163835995(+)$1	227	6	10	11.9999
AGAG	chr16:53967888-53968122(+)$1	234	35	39	11.9999
AGAG	chr14:21971870-21972125(+)$1	255	80	84	11.9999
AGAG	chr16:70605660-70605910(+)$1	250	82	86	11.9999
AGAG	chr1:228364043-228364269(+)$1	226	23	27	11.9999
AGAG	chr12:6875577-6875797(+)$1	220	136	140	11.9999
AGAG	chr20:62331482-62331711(+)$1	229	162	166	11.9999
AGAG	chr12:5024027-5024248(-)$1	221	111	115	11.9999
AGAG	chr17:47126803-47127032(+)$1	229	53	57	11.9999
AGAG	chr6:62283948-62284192(+)$1	244	184	188	11.9999
AGAG	chr6:43970400-43970626(+)$1	226	96	100	11.9999
AGAG	chr12:129299395-129299629(-)$1	234	198	202	11.9999
AGAG	chr16:53922645-53922882(+)$1	237	24	28	11.9999
agag	chr17:2321568-2321795(-)$1	227	76	80	11.9999
AGAG	chr5:79946296-79946532(-)$1	236	99	103	11.9999
AGAG	chr4:119606629-119606848(+)$1	219	5	9	11.9999
AGAG	chr17:48827813-48828068(+)$1	255	51	55	11.9999
AGAG	chr19:1248508-1248732(-)$1	224	24	28	11.9999
AGAG	chr1:1271123-1271342(-)$1	219	41	45	11.9999
AGAG	chr17:28444013-28444236(+)$1	223	107	111	11.9999
AGAG	chr2:242695143-242695375(+)$1	232	149	153	11.9999
AGAG	chr1:247151334-247151563(-)$1	229	40	44	11.9999
AGAG	chr14:21968957-21969221(-)$1	264	120	124	11.9999
AGAG	chr12:120972109-120972334(+)$1	225	179	183	11.9999
AGAG	chr11:64845933-64846157(-)$1	224	51	55	11.9999
AGAG	chr1:151665820-151666047(+)$1	227	104	108	11.9999
AGAG	chr22:39259522-39259743(-)$1	221	34	38	11.9999
AGAG	chr19:2271681-2271900(+)$1	219	119	123	11.9999
AGAG	chr16:53913665-53913977(+)$1	312	37	41	11.9999
AGAG	chr6:34557226-34557456(-)$1	230	221	225	11.9999
AGAG	chr12:122630549-122630780(+)$1	231	39	43	11.9999
AGAG	chr19:50534226-50534446(+)$1	220	88	92	11.9999
agag	chr16:20746669-20746888(-)$1	219	77	81	11.9999
AGAG	chr2:97475918-97476145(+)$1	227	4	8	11.9999
AGAG	chr14:21966350-21966595(-)$1	245	208	212	11.9999
AGAG	chr5:180687812-180688040(-)$1	228	30	34	11.9999
AGAG	chr3:124458825-124459068(+)$1	243	212	216	11.9999
AGAG	chr12:48138482-48138701(-)$1	219	1	5	11.9999
AGAG	chr1:154574511-154574739(-)$1	228	65	69	11.9999
AGAG	chr3:48732681-48732937(-)$1	256	84	88	11.9999
AGAG	chr12:110719031-110719257(+)$1	226	23	27	11.9999
AGAG	chr15:41021604-41021842(+)$1	238	76	80	11.9999
AGAG	chr3:195635516-195635743(-)$1	227	30	34	11.9999
AGAG	chr3:50685587-50685816(+)$1	229	89	93	11.9999
AGAG	chr19:36726650-36726881(+)$1	231	13	17	11.9999
AGAG	chr16:54145650-54145919(+)$1	269	147	151	11.9999
AGAG	chr5:126793063-126793289(+)$1	226	142	146	11.9999
AGAG	chr19:13029956-13030180(-)$1	224	75	79	11.9999
AGAG	chr11:64619989-64620223(-)$1	234	107	111	11.9999
AGAG	chr2:231931676-231931899(+)$1	223	21	25	11.9999
AGAG	chr5:176900466-176900688(-)$1	222	63	67	11.9999

#otherMatches

#Struct PSSM
ee[c	chr11:61197286-61197518(-)$1	232	73	77	11.9999
J:::	chr16:14357170-14357395(+)$1	225	26	30	11.9999
nnnb	chr1:9648850-9649074(+)$1	224	132	136	11.9999
gggg	chr11:62608995-62609381(-)$1	386	299	303	11.9999
eeee	chr20:418111-418341(-)$1	230	3	7	11.9999
fppp	chr12:42481414-42481634(-)$1	220	11	15	11.9999
====	chr16:53843950-53844207(+)$1	257	39	43	11.9999
dd]c	chr1:209955621-209955848(-)$1	227	107	111	11.9999
c>>>	chr21:44515477-44515703(-)$1	226	95	99	11.9999
ffff	chr15:40998302-40998551(-)$1	249	25	29	11.9999
:BB{	chr5:79946505-79946748(-)$1	243	94	98	11.9999
meee	chr20:56814656-56814881(-)$1	225	180	184	11.9999
||||	chr15:41021695-41021927(+)$1	232	157	161	11.9999
dddd	chr1:117452663-117452888(-)$1	225	147	151	11.9999
bb55	chr17:19770982-19771205(-)$1	223	116	120	11.9999
ffff	chr14:21971242-21971467(+)$1	225	36	40	11.9999
}CCC	chr6:37787493-37787720(+)$1	227	162	166	11.9999
KEEE	chr6:163835768-163835995(+)$1	227	6	10	11.9999
{HHH	chr16:53967888-53968122(+)$1	234	35	39	11.9999
llle	chr14:21971870-21972125(+)$1	255	80	84	11.9999
eeee	chr16:70605660-70605910(+)$1	250	82	86	11.9999
::::	chr1:228364043-228364269(+)$1	226	23	27	11.9999
dddd	chr12:6875577-6875797(+)$1	220	136	140	11.9999
4ddd	chr20:62331482-62331711(+)$1	229	162	166	11.9999
%%%%	chr12:5024027-5024248(-)$1	221	111	115	11.9999
eeee	chr17:47126803-47127032(+)$1	229	53	57	11.9999
gggg	chr6:62283948-62284192(+)$1	244	184	188	11.9999
333d	chr6:43970400-43970626(+)$1	226	96	100	11.9999
eeee	chr12:129299395-129299629(-)$1	234	198	202	11.9999
$$$c	chr16:53922645-53922882(+)$1	237	24	28	11.9999
[eee	chr17:2321568-2321795(-)$1	227	76	80	11.9999
====	chr5:79946296-79946532(-)$1	236	99	103	11.9999
:ddd	chr4:119606629-119606848(+)$1	219	5	9	11.9999
iiii	chr17:48827813-48828068(+)$1	255	51	55	11.9999
nnnd	chr19:1248508-1248732(-)$1	224	24	28	11.9999
HHHH	chr1:1271123-1271342(-)$1	219	41	45	11.9999
!!cc	chr17:28444013-28444236(+)$1	223	107	111	11.9999
eeee	chr2:242695143-242695375(+)$1	232	149	153	11.9999
bb[b	chr1:247151334-247151563(-)$1	229	40	44	11.9999
dd[e	chr14:21968957-21969221(-)$1	264	120	124	11.9999
ee[d	chr12:120972109-120972334(+)$1	225	179	183	11.9999
::::	chr11:64845933-64846157(-)$1	224	51	55	11.9999
dddd	chr1:151665820-151666047(+)$1	227	104	108	11.9999
ggg[	chr22:39259522-39259743(-)$1	221	34	38	11.9999
:eee	chr19:2271681-2271900(+)$1	219	119	123	11.9999
hhhh	chr16:53913665-53913977(+)$1	312	37	41	11.9999
a]cc	chr6:34557226-34557456(-)$1	230	221	225	11.9999
cc!!	chr12:122630549-122630780(+)$1	231	39	43	11.9999
:::e	chr19:50534226-50534446(+)$1	220	88	92	11.9999
mddd	chr16:20746669-20746888(-)$1	219	77	81	11.9999
GGGG	chr2:97475918-97476145(+)$1	227	4	8	11.9999
====	chr14:21966350-21966595(-)$1	245	208	212	11.9999
fff"	chr5:180687812-180688040(-)$1	228	30	34	11.9999
555d	chr3:124458825-124459068(+)$1	243	212	216	11.9999
::GG	chr12:48138482-48138701(-)$1	219	1	5	11.9999
==]a	chr1:154574511-154574739(-)$1	228	65	69	11.9999
fffb	chr3:48732681-48732937(-)$1	256	84	88	11.9999
nndd	chr12:110719031-110719257(+)$1	226	23	27	11.9999
eee6	chr15:41021604-41021842(+)$1	238	76	80	11.9999
:::c	chr3:195635516-195635743(-)$1	227	30	34	11.9999
pppp	chr3:50685587-50685816(+)$1	229	89	93	11.9999
ffff	chr19:36726650-36726881(+)$1	231	13	17	11.9999
]hhh	chr16:54145650-54145919(+)$1	269	147	151	11.9999
:eee	chr5:126793063-126793289(+)$1	226	142	146	11.9999
]bbe	chr19:13029956-13030180(-)$1	224	75	79	11.9999
CC::	chr11:64619989-64620223(-)$1	234	107	111	11.9999
pppf	chr2:231931676-231931899(+)$1	223	21	25	11.9999
[bbb	chr5:176900466-176900688(-)$1	222	63	67	11.9999

#DB
((.(	chr11:61197286-61197518(-)$1	1	73	77	11.9999
(...	chr16:14357170-14357395(+)$1	1	26	30	11.9999
...)	chr1:9648850-9649074(+)$1	1	132	136	11.9999
))))	chr11:62608995-62609381(-)$1	1	299	303	11.9999
((((	chr20:418111-418341(-)$1	1	3	7	11.9999
(...	chr12:42481414-42481634(-)$1	1	11	15	11.9999
))))	chr16:53843950-53844207(+)$1	1	39	43	11.9999
)).)	chr1:209955621-209955848(-)$1	1	107	111	11.9999
)...	chr21:44515477-44515703(-)$1	1	95	99	11.9999
))))	chr15:40998302-40998551(-)$1	1	25	29	11.9999
.((.	chr5:79946505-79946748(-)$1	1	94	98	11.9999
.)))	chr20:56814656-56814881(-)$1	1	180	184	11.9999
....	chr15:41021695-41021927(+)$1	1	157	161	11.9999
))))	chr1:117452663-117452888(-)$1	1	147	151	11.9999
))..	chr17:19770982-19771205(-)$1	1	116	120	11.9999
((((	chr14:21971242-21971467(+)$1	1	36	40	11.9999
.)))	chr6:37787493-37787720(+)$1	1	162	166	11.9999
.(((	chr6:163835768-163835995(+)$1	1	6	10	11.9999
.(((	chr16:53967888-53968122(+)$1	1	35	39	11.9999
...)	chr14:21971870-21972125(+)$1	1	80	84	11.9999
))))	chr16:70605660-70605910(+)$1	1	82	86	11.9999
....	chr1:228364043-228364269(+)$1	1	23	27	11.9999
))))	chr12:6875577-6875797(+)$1	1	136	140	11.9999
.)))	chr20:62331482-62331711(+)$1	1	162	166	11.9999
....	chr12:5024027-5024248(-)$1	1	111	115	11.9999
((((	chr17:47126803-47127032(+)$1	1	53	57	11.9999
))))	chr6:62283948-62284192(+)$1	1	184	188	11.9999
...)	chr6:43970400-43970626(+)$1	1	96	100	11.9999
))))	chr12:129299395-129299629(-)$1	1	198	202	11.9999
...(	chr16:53922645-53922882(+)$1	1	24	28	11.9999
.(((	chr17:2321568-2321795(-)$1	1	76	80	11.9999
((((	chr5:79946296-79946532(-)$1	1	99	103	11.9999
.(((	chr4:119606629-119606848(+)$1	1	5	9	11.9999
))))	chr17:48827813-48828068(+)$1	1	51	55	11.9999
...)	chr19:1248508-1248732(-)$1	1	24	28	11.9999
((((	chr1:1271123-1271342(-)$1	1	41	45	11.9999
..((	chr17:28444013-28444236(+)$1	1	107	111	11.9999
))))	chr2:242695143-242695375(+)$1	1	149	153	11.9999
((.(	chr1:247151334-247151563(-)$1	1	40	44	11.9999
((.(	chr14:21968957-21969221(-)$1	1	120	124	11.9999
((.(	chr12:120972109-120972334(+)$1	1	179	183	11.9999
....	chr11:64845933-64846157(-)$1	1	51	55	11.9999
((((	chr1:151665820-151666047(+)$1	1	104	108	11.9999
(((.	chr22:39259522-39259743(-)$1	1	34	38	11.9999
.(((	chr19:2271681-2271900(+)$1	1	119	123	11.9999
((((	chr16:53913665-53913977(+)$1	1	37	41	11.9999
).))	chr6:34557226-34557456(-)$1	1	221	225	11.9999
((..	chr12:122630549-122630780(+)$1	1	39	43	11.9999
...(	chr19:50534226-50534446(+)$1	1	88	92	11.9999
.)))	chr16:20746669-20746888(-)$1	1	77	81	11.9999
((((	chr2:97475918-97476145(+)$1	1	4	8	11.9999
((((	chr14:21966350-21966595(-)$1	1	208	212	11.9999
(((.	chr5:180687812-180688040(-)$1	1	30	34	11.9999
...)	chr3:124458825-124459068(+)$1	1	212	216	11.9999
..((	chr12:48138482-48138701(-)$1	1	1	5	11.9999
)).)	chr1:154574511-154574739(-)$1	1	65	69	11.9999
)))(	chr3:48732681-48732937(-)$1	1	84	88	11.9999
..))	chr12:110719031-110719257(+)$1	1	23	27	11.9999
))).	chr15:41021604-41021842(+)$1	1	76	80	11.9999
...(	chr3:195635516-195635743(-)$1	1	30	34	11.9999
....	chr3:50685587-50685816(+)$1	1	89	93	11.9999
((((	chr19:36726650-36726881(+)$1	1	13	17	11.9999
.)))	chr16:54145650-54145919(+)$1	1	147	151	11.9999
.(((	chr5:126793063-126793289(+)$1	1	142	146	11.9999
.)))	chr19:13029956-13030180(-)$1	1	75	79	11.9999
((..	chr11:64619989-64620223(-)$1	1	107	111	11.9999
...)	chr2:231931676-231931899(+)$1	1	21	25	11.9999
.(((	chr5:176900466-176900688(-)$1	1	63	67	11.9999

#PSSM
A : 0.95	a : 0.04	
G : 0.95	g : 0.04	
A : 0.95	a : 0.04	
G : 0.95	g : 0.04	

#score	815.9999999999995
#seq	68
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_HuR_Kishore2011e_hg19_UTR_m2_run1.nuc.txt

#NT
UUUGGUCUUGUUUU	chr12:14650913-14651154(+)$1	241	136	150	17.8035
UUUUAUUUUUACUU	chr5:74075130-74075370(-)$1	240	83	97	21.0178
UUUUCUUUAUUUUU	chr14:102547821-102548061(-)$1	240	83	97	20.9285
UUUUAGUUUGUUUU	chr4:71896214-71896454(+)$1	240	85	99	19.7678
UUACAUAUUUAUUU	chr7:91742161-91742401(-)$1	240	121	135	17.3571
UUUAAUUUGGUUUU	chr7:107560096-107560342(+)$1	246	12	26	19.0535
UUUUGUAUUUAUUU	chr10:97365857-97366097(-)$1	240	108	122	18.9642
UAUUAUUUUUUUCU	chr15:90623980-90624220(+)$1	240	117	131	19.1428
UUUGAUUUUUUUUU	chrX:73807096-73807336(-)$1	240	23	37	27.9821
uuuucuuuuucuuu	chr1:31732452-31732692(-)$1	240	11	25	21.5535
UGUGAuauuuuuuu	chr1:155259027-155259280(+)$1	253	25	39	21.0178
UAUGCUUUUUUGUU	chr9:14086140-14086380(-)$1	240	4	18	16.6428
UUAGAUUUUUAUUU	chr15:32930133-32930373(+)$1	240	67	81	21.3750
UUUUAUUUAUUUUU	chr1:184661614-184661854(-)$1	240	47	61	23.9642
UUGGAUUUUUUUUU	chr3:37031819-37032059(-)$1	240	11	25	24.0535
CUUUAUUAUUUUUU	chr7:116201041-116201285(+)$1	244	199	213	19.4107
UUUUCUUUUCUUUU	chr10:101465680-101465920(+)$1	240	124	138	20.6607
UUGGAUUUUUUUAU	chr6:163988311-163988551(+)$1	240	83	97	19.8571
UUAUAUUUUUUGUU	chr8:104344513-104344753(+)$1	240	102	116	20.0357
AUAGAAUUUUUUUU	chr5:151184127-151184367(+)$1	240	89	103	15.8392
uuuuuuuuuuuuuu	chr12:54627860-54628101(-)$1	241	124	138	24.7678
UCCCAUUUUUUUUU	chr2:145146351-145146631(-)$1	280	113	127	18.1607
UUUAACUUUGUUUU	chr12:59266034-59266274(-)$1	240	130	144	18.6071
uuuuauauuuuuuu	chr6:123046984-123047232(+)$1	248	199	213	25.2142
UUUAAUUUUUAAUU	chr5:130979867-130980107(-)$1	240	119	133	19.5892
UAUGAUUUUUAUAU	chr1:173902632-173902872(-)$1	240	23	37	16.5535
UUUAAUUUUAGUUU	chr11:111610428-111610668(-)$1	240	158	172	19.4107
UUUGUUUUUGUCUU	chr6:53787675-53787915(+)$1	240	182	196	17.8035
GUUGUUUUUUCUUU	chr5:173316358-173316598(+)$1	240	183	197	17.8928
UUAUAUUUUAUUUU	chr4:77956061-77956341(+)$1	280	123	137	20.1250
GUUGAUUUUUUUUA	chr5:64961246-64961499(+)$1	253	109	123	20.1250
UUUGAUGUUUCUGU	chr5:1462849-1463089(-)$1	240	150	164	17.0892
AUUCAUUUUUUUUU	chr2:30866816-30867056(+)$1	240	123	137	22.2678
UUUGCUUUCUUUUA	chr19:45684345-45684585(+)$1	240	98	112	17.0892
UUUGAUUUUGGUUU	chr1:203710865-203711105(+)$1	240	13	27	21.2857
UUUACUGUAUUUUU	chr4:76569685-76569925(-)$1	240	162	176	16.3750
UUUCAUAUUUUCUU	chr20:56937301-56937541(+)$1	240	112	126	20.2142
GUUGAUUUUUUUUC	chr9:125865734-125865974(+)$1	240	96	110	20.0357
UUUCAUUUUUUUCC	chr1:235715114-235715354(-)$1	240	109	123	18.2500
UUUGUUUUUUUCUG	chr16:21667567-21667807(+)$1	240	20	34	17.2678
UUUAGUUAUUCUUU	chr5:115165762-115166002(-)$1	240	39	53	16.1071
UUUUAUUCUUUCUU	chr5:60169861-60170101(-)$1	240	119	133	19.5892
UUUGAUUUGUUUUC	chr20:61576593-61576848(+)$1	255	201	215	20.0357
uuuguuuuuguuuu	chr6:136579478-136579718(-)$1	240	160	174	21.5535
uuuuauaauuuuuu	chr4:55606479-55606722(+)$1	243	116	130	21.1964
GUUGAUUUUUUUUA	chr21:17251406-17251648(+)$1	242	72	86	20.1250
UUCCAUUAUUUUUU	chr1:193221729-193221981(+)$1	252	124	138	18.6071
UUUAAUAUUUGUUU	chr3:124946802-124947042(-)$1	240	25	39	20.8392
uuuuuaauuuuuuu	chr18:25531103-25531343(-)$1	240	109	123	17.9821
UUCUAUAUUUGUUU	chr2:152975459-152975699(-)$1	240	83	97	18.1607
UUUUAAAUAUUUUU	chr10:21783998-21784238(-)$1	240	117	131	17.1785
UUUGUUUUCUUAUU	chr14:36340798-36341038(+)$1	240	100	114	17.0000
UUUGAUAUAUUUUG	chr4:75975169-75975409(+)$1	240	178	192	17.7142
UUUGAUCUUUAUAU	chr7:134654261-134654501(+)$1	240	81	95	17.4464
UUUUAUAUUUCUUU	chr10:31817464-31817705(+)$1	241	111	125	22.0892

#otherMatches

#Struct PSSM
qqqqggggggg:::	chr3:130720965-130721205(+)$1	240	145	159	19.8571
mmmccc55555fff	chr12:14650913-14651154(+)$1	241	136	150	17.8035
cc55555eeeee]g	chr5:74075130-74075370(-)$1	240	83	97	21.0178
qqqqqqqhhhhhhh	chr14:102547821-102548061(-)$1	240	83	97	20.9285
^^^ggggggg4444	chr4:71896214-71896454(+)$1	240	85	99	19.7678
%============n	chr7:91742161-91742401(-)$1	240	121	135	17.3571
mmgggggggggggg	chr7:107560096-107560342(+)$1	246	12	26	19.0535
eeeee:hhhhhhhh	chr10:97365857-97366097(-)$1	240	108	122	18.9642
mmhhhhhhhh6666	chr15:90623980-90624220(+)$1	240	117	131	19.1428
ww===========:	chrX:73807096-73807336(-)$1	240	23	37	27.9821
::::::::::::::	chr1:31732452-31732692(-)$1	240	11	25	21.5535
[ggggggg++++++	chr1:155259027-155259280(+)$1	253	25	39	21.0178
gggg(((((((((b	chr9:14086140-14086380(-)$1	240	4	18	16.6428
xxxxxxxxxxxhhh	chr15:32930133-32930373(+)$1	240	67	81	21.3750
IIIIIIIVVVVVVV	chr1:184661614-184661854(-)$1	240	47	61	23.9642
{BB{A:::::::::	chr3:37031819-37032059(-)$1	240	11	25	24.0535
::::::::::::::	chr7:116201041-116201285(+)$1	244	199	213	19.4107
i]cccHHHHHHHHK	chr10:101465680-101465920(+)$1	240	124	138	20.6607
HHHHHH::::::::	chr6:163988311-163988551(+)$1	240	83	97	19.8571
::ggggggg[dddd	chr8:104344513-104344753(+)$1	240	102	116	20.0357
!ggggggg[dddd[	chr5:151184127-151184367(+)$1	240	89	103	15.8392
===========::e	chr12:54627860-54628101(-)$1	241	124	138	24.7678
BBKKJJJJJJJJJJ	chr2:145146351-145146631(-)$1	280	113	127	18.1607
d]ccc]dddd]eee	chr12:59266034-59266274(-)$1	240	130	144	18.6071
:::::fffffflll	chr6:123046984-123047232(+)$1	248	199	213	25.2142
::::::::::::::	chr5:130979867-130980107(-)$1	240	119	133	19.5892
H:::::::::::::	chr1:173902632-173902872(-)$1	240	23	37	16.5535
dddd4444dddd22	chr11:111610428-111610668(-)$1	240	158	172	19.4107
:::::::CCC}BBZ	chr6:53787675-53787915(+)$1	240	182	196	17.8035
BBYYFFFFFF}HHH	chr5:173316358-173316598(+)$1	240	183	197	17.8928
^^^^^^^^^^^^^^	chr4:77956061-77956341(+)$1	280	123	137	20.1250
gggggggoooooog	chr5:64961246-64961499(+)$1	253	109	123	20.1250
$$$bbmmmmbb777	chr5:1462849-1463089(-)$1	240	150	164	17.0892
eee::::::=====	chr2:30866816-30867056(+)$1	240	123	137	22.2678
###bbttttttttt	chr19:45684345-45684585(+)$1	240	98	112	17.0892
KKFFFFFF{CCC::	chr1:203710865-203711105(+)$1	240	13	27	21.2857
hhhhhhhh::::::	chr4:76569685-76569925(-)$1	240	162	176	16.3750
:::::::=======	chr20:56937301-56937541(+)$1	240	112	126	20.2142
]hhhhhhhh22bb]	chr9:125865734-125865974(+)$1	240	96	110	20.0357
::::::::::::::	chr1:235715114-235715354(-)$1	240	109	123	18.2500
llldddd666666e	chr16:21667567-21667807(+)$1	240	20	34	17.2678
rrrreeeee333hh	chr5:115165762-115166002(-)$1	240	39	53	16.1071
iiiii:::::::::	chr5:60169861-60170101(-)$1	240	119	133	19.5892
EEHHHHHHHH:::c	chr20:61576593-61576848(+)$1	255	201	215	20.0357
::::::::::::::	chr6:136579478-136579718(-)$1	240	160	174	21.5535
5555eeeee=====	chr4:55606479-55606722(+)$1	243	116	130	21.1964
fffeeeeennnnne	chr21:17251406-17251648(+)$1	242	72	86	20.1250
::::::::::::::	chr1:193221729-193221981(+)$1	252	124	138	18.6071
NNNNNFFFFFFKKB	chr3:124946802-124947042(-)$1	240	25	39	20.8392
::::::HHHHHHHH	chr18:25531103-25531343(-)$1	240	109	123	17.9821
gggggg333bb]hh	chr2:152975459-152975699(-)$1	240	83	97	18.1607
::::::::::::::	chr10:21783998-21784238(-)$1	240	117	131	17.1785
cc22==========	chr14:36340798-36341038(+)$1	240	100	114	17.0000
vvvvvvvvvvvvcc	chr4:75975169-75975409(+)$1	240	178	192	17.7142
bbcccffffff]ee	chr7:134654261-134654501(+)$1	240	81	95	17.4464
::::::::::::::	chr10:31817464-31817705(+)$1	241	111	125	22.0892

#DB
....)))))))...	chr3:130720965-130721205(+)$1	1	145	159	19.8571
...))).....)))	chr12:14650913-14651154(+)$1	1	136	150	17.8035
)).....))))).)	chr5:74075130-74075370(-)$1	1	83	97	21.0178
.......)))))))	chr14:102547821-102548061(-)$1	1	83	97	20.9285
...)))))))....	chr4:71896214-71896454(+)$1	1	85	99	19.7678
.((((((((((((.	chr7:91742161-91742401(-)$1	1	121	135	17.3571
..)))))))(((((	chr7:107560096-107560342(+)$1	1	12	26	19.0535
))))).((((((((	chr10:97365857-97366097(-)$1	1	108	122	18.9642
..))))))))....	chr15:90623980-90624220(+)$1	1	117	131	19.1428
..))))))))))).	chrX:73807096-73807336(-)$1	1	23	37	27.9821
..............	chr1:31732452-31732692(-)$1	1	11	25	21.5535
.(((((((......	chr1:155259027-155259280(+)$1	1	25	39	21.0178
((((.........(	chr9:14086140-14086380(-)$1	1	4	18	16.6428
...........)))	chr15:32930133-32930373(+)$1	1	67	81	21.3750
(((((((.......	chr1:184661614-184661854(-)$1	1	47	61	23.9642
.((.(.........	chr3:37031819-37032059(-)$1	1	11	25	24.0535
..............	chr7:116201041-116201285(+)$1	1	199	213	19.4107
).)))((((((((.	chr10:101465680-101465920(+)$1	1	124	138	20.6607
((((((........	chr6:163988311-163988551(+)$1	1	83	97	19.8571
..(((((((.((((	chr8:104344513-104344753(+)$1	1	102	116	20.0357
.(((((((.((((.	chr5:151184127-151184367(+)$1	1	89	103	15.8392
)))))))))))..(	chr12:54627860-54628101(-)$1	1	124	138	24.7678
((..((((((((((	chr2:145146351-145146631(-)$1	1	113	127	18.1607
).))).)))).)))	chr12:59266034-59266274(-)$1	1	130	144	18.6071
.....((((((...	chr6:123046984-123047232(+)$1	1	199	213	25.2142
..............	chr5:130979867-130980107(-)$1	1	119	133	19.5892
(.............	chr1:173902632-173902872(-)$1	1	23	37	16.5535
))))....))))..	chr11:111610428-111610668(-)$1	1	158	172	19.4107
.......))).)).	chr6:53787675-53787915(+)$1	1	182	196	17.8035
))..)))))).)))	chr5:173316358-173316598(+)$1	1	183	197	17.8928
..............	chr4:77956061-77956341(+)$1	1	123	137	20.1250
(((((((......)	chr5:64961246-64961499(+)$1	1	109	123	20.1250
...((....))...	chr5:1462849-1463089(-)$1	1	150	164	17.0892
)))......(((((	chr2:30866816-30867056(+)$1	1	123	137	22.2678
...((.........	chr19:45684345-45684585(+)$1	1	98	112	17.0892
..((((((.(((..	chr1:203710865-203711105(+)$1	1	13	27	21.2857
))))))))......	chr4:76569685-76569925(-)$1	1	162	176	16.3750
.......(((((((	chr20:56937301-56937541(+)$1	1	112	126	20.2142
.))))))))..)).	chr9:125865734-125865974(+)$1	1	96	110	20.0357
..............	chr1:235715114-235715354(-)$1	1	109	123	18.2500
...))))......)	chr16:21667567-21667807(+)$1	1	20	34	17.2678
....)))))...))	chr5:115165762-115166002(-)$1	1	39	53	16.1071
))))).........	chr5:60169861-60170101(-)$1	1	119	133	19.5892
))))))))))...(	chr20:61576593-61576848(+)$1	1	201	215	20.0357
..............	chr6:136579478-136579718(-)$1	1	160	174	21.5535
....))))))))))	chr4:55606479-55606722(+)$1	1	116	130	21.1964
((((((((.....)	chr21:17251406-17251648(+)$1	1	72	86	20.1250
..............	chr1:193221729-193221981(+)$1	1	124	138	18.6071
.....((((((..(	chr3:124946802-124947042(-)$1	1	25	39	20.8392
......((((((((	chr18:25531103-25531343(-)$1	1	109	123	17.9821
))))))...)).))	chr2:152975459-152975699(-)$1	1	83	97	18.1607
..............	chr10:21783998-21784238(-)$1	1	117	131	17.1785
))..))))))))))	chr14:36340798-36341038(+)$1	1	100	114	17.0000
............))	chr4:75975169-75975409(+)$1	1	178	192	17.7142
))))))))))).))	chr7:134654261-134654501(+)$1	1	81	95	17.4464
..............	chr10:31817464-31817705(+)$1	1	111	125	22.0892

#PSSM
U : 0.76	u : 0.10	G : 0.07	A : 0.03	C : 0.01	
U : 0.80	u : 0.10	A : 0.05	G : 0.01	C : 0.01	
U : 0.71	u : 0.10	A : 0.08	C : 0.05	G : 0.03	
G : 0.39	U : 0.26	A : 0.12	C : 0.10	u : 0.08	g : 0.01	
A : 0.67	C : 0.08	U : 0.07	G : 0.05	u : 0.05	a : 0.03	c : 0.01	
U : 0.80	u : 0.10	A : 0.03	G : 0.01	C : 0.01	a : 0.01	
U : 0.66	A : 0.14	a : 0.07	u : 0.05	C : 0.03	G : 0.03	
U : 0.78	u : 0.10	A : 0.07	C : 0.01	a : 0.01	
U : 0.71	u : 0.12	A : 0.08	G : 0.03	C : 0.03	
U : 0.71	G : 0.10	u : 0.10	A : 0.03	C : 0.01	g : 0.01	
U : 0.60	A : 0.12	u : 0.10	G : 0.07	C : 0.07	c : 0.01	
U : 0.71	u : 0.12	C : 0.08	G : 0.03	A : 0.03	
U : 0.76	u : 0.12	A : 0.05	C : 0.03	G : 0.01	
U : 0.71	u : 0.12	A : 0.07	C : 0.05	G : 0.03	

#score	1100.035714285715
#seq	56
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_transcript_m3_run1.nuc.txt

#NT
acaaauau	chr18:32875302-32875534(+)$1	232	1	9	15.0000
auuaauau	chr4:2677275-2677506(+)$1	231	2	10	15.6250
AUUAAUAU	chr4:170555582-170555815(+)$1	233	103	111	15.6250
auuaauau	chr1:40339212-40339439(-)$1	227	107	115	15.6250
auaaauau	chr8:25212833-25213065(+)$1	232	7	15	19.2499
aaaaauau	chr4:186608587-186608818(-)$1	231	61	69	15.2500
AUAAAUAU	chr13:97934657-97934889(+)$1	232	103	111	19.2499
AUAAAUGU	chr10:35468458-35468692(+)$1	234	66	74	14.7500
aaaaauau	chr20:14202316-14202549(+)$1	233	201	209	15.2500
auuaauau	chr1:85138955-85139189(-)$1	234	116	124	15.6250
AUAAAAAU	chr2:88881130-88881356(-)$1	226	103	111	15.7499
AUAAAUCU	chr6:128355742-128355990(-)$1	248	233	241	14.7500
auaaauau	chr14:55766204-55766433(+)$1	229	197	205	19.2499
auaauaau	chr3:78822165-78822397(-)$1	232	53	61	12.5000
AAAAAUAU	chr6:56465263-56465495(-)$1	232	9	17	15.2500
AUAAUAAU	chr4:124061772-124062004(+)$1	232	101	109	12.5000
auauauau	chr4:68558980-68559213(-)$1	233	150	158	15.0000
AUAAUUAU	chr1:61890181-61890408(+)$1	227	214	222	15.9999
AUGAAUAU	chr6:42979527-42979759(+)$1	232	107	115	15.2500
AUAAAUAG	chr1:162482015-162482243(+)$1	228	120	128	14.7500
auaaagau	chr1:93660087-93660319(+)$1	232	41	49	15.6249
AUAACUAU	chr1:154593166-154593396(-)$1	230	52	60	15.5000
AUAAAUAU	chr5:144859683-144859915(-)$1	232	2	10	19.2499
agaaauau	chrX:73449189-73449421(-)$1	232	98	106	15.0000
auaacuau	chr4:57312341-57312573(+)$1	232	109	117	15.5000
AUAAACAU	chr8:64122966-64123196(+)$1	230	206	214	15.3749
AUCAAUAU	chr12:34402329-34402561(+)$1	232	159	167	15.3750
AUAUAUAU	chr6:71219908-71220134(+)$1	226	10	18	15.0000
AUAAAUUU	chr16:78577688-78577922(+)$1	234	140	148	14.7500
auCAAUAU	chr8:10893161-10893393(-)$1	232	220	228	15.3750
AUAAAUAU	chr13:114116613-114116847(-)$1	234	157	165	19.2499
AUAAAGAU	chr2:148831573-148831804(+)$1	231	48	56	15.6249
GUAAAUAU	chr2:213208409-213208641(-)$1	232	60	68	14.6250
CUAAAUAU	chr7:80527762-80527987(-)$1	225	100	108	14.6250
auauauau	chr12:39142649-39142881(-)$1	232	199	207	15.0000
AUAAAUAG	chr13:60585918-60586150(-)$1	232	38	46	14.7500
AUAAAUAU	chr7:26231664-26231889(-)$1	225	32	40	19.2499
auaaugau	chr13:50791297-50791529(+)$1	232	132	140	12.3750
auaauuau	chrX:34291700-34291930(-)$1	230	52	60	15.9999

#otherMatches

#Struct PSSM
EE:HHHHH	chr3:154009864-154010097(-)$1	233	47	55	12.5000
::::::::	chr18:32875302-32875534(+)$1	232	1	9	15.0000
::::::::	chr4:2677275-2677506(+)$1	231	2	10	15.6250
:::::fff	chr4:170555582-170555815(+)$1	233	103	111	15.6250
gggggg[e	chr1:40339212-40339439(-)$1	227	107	115	15.6250
cppppppp	chr8:25212833-25213065(+)$1	232	7	15	19.2499
f:::::::	chr4:186608587-186608818(-)$1	231	61	69	15.2500
::::::::	chr13:97934657-97934889(+)$1	232	103	111	19.2499
d!!ddddr	chr10:35468458-35468692(+)$1	234	66	74	14.7500
::::::::	chr20:14202316-14202549(+)$1	233	201	209	15.2500
99999999	chr1:85138955-85139189(-)$1	234	116	124	15.6250
::::::::	chr2:88881130-88881356(-)$1	226	103	111	15.7499
JJJJJJ__	chr6:128355742-128355990(-)$1	248	233	241	14.7500
:::::::e	chr14:55766204-55766433(+)$1	229	197	205	19.2499
[eeeeemm	chr3:78822165-78822397(-)$1	232	53	61	12.5000
ggggffff	chr6:56465263-56465495(-)$1	232	9	17	15.2500
cqqqqqqq	chr4:124061772-124062004(+)$1	232	101	109	12.5000
[ddddmmm	chr4:68558980-68559213(-)$1	233	150	158	15.0000
rrrrrree	chr1:61890181-61890408(+)$1	227	214	222	15.9999
[ccc"""f	chr6:42979527-42979759(+)$1	232	107	115	15.2500
gggggggp	chr1:162482015-162482243(+)$1	228	120	128	14.7500
$$$fffff	chr1:93660087-93660319(+)$1	232	41	49	15.6249
eeemmmme	chr1:154593166-154593396(-)$1	230	52	60	15.5000
::::::::	chr5:144859683-144859915(-)$1	232	2	10	19.2499
llleeeee	chrX:73449189-73449421(-)$1	232	98	106	15.0000
e!!ccc((	chr4:57312341-57312573(+)$1	232	109	117	15.5000
GGGGG}HH	chr8:64122966-64123196(+)$1	230	206	214	15.3749
hhbbbb[c	chr12:34402329-34402561(+)$1	232	159	167	15.3750
::::::::	chr6:71219908-71220134(+)$1	226	10	18	15.0000
+++hhhhh	chr16:78577688-78577922(+)$1	234	140	148	14.7500
mmeeeee]	chr8:10893161-10893393(-)$1	232	220	228	15.3750
hhhhh###	chr13:114116613-114116847(-)$1	234	157	165	19.2499
iiiiiivv	chr2:148831573-148831804(+)$1	231	48	56	15.6249
ee::::::	chr2:213208409-213208641(-)$1	232	60	68	14.6250
gggggg44	chr7:80527762-80527987(-)$1	225	100	108	14.6250
qqqqeeee	chr12:39142649-39142881(-)$1	232	199	207	15.0000
d$$$$$cc	chr13:60585918-60586150(-)$1	232	38	46	14.7500
eemmmmee	chr7:26231664-26231889(-)$1	225	32	40	19.2499
ffffff]c	chr13:50791297-50791529(+)$1	232	132	140	12.3750
ff::::::	chrX:34291700-34291930(-)$1	230	52	60	15.9999

#DB
((.(((((	chr3:154009864-154010097(-)$1	1	47	55	12.5000
........	chr18:32875302-32875534(+)$1	1	1	9	15.0000
........	chr4:2677275-2677506(+)$1	1	2	10	15.6250
.....(((	chr4:170555582-170555815(+)$1	1	103	111	15.6250
((((((.(	chr1:40339212-40339439(-)$1	1	107	115	15.6250
(.......	chr8:25212833-25213065(+)$1	1	7	15	19.2499
).......	chr4:186608587-186608818(-)$1	1	61	69	15.2500
........	chr13:97934657-97934889(+)$1	1	103	111	19.2499
(..((((.	chr10:35468458-35468692(+)$1	1	66	74	14.7500
........	chr20:14202316-14202549(+)$1	1	201	209	15.2500
........	chr1:85138955-85139189(-)$1	1	116	124	15.6250
........	chr2:88881130-88881356(-)$1	1	103	111	15.7499
))))))..	chr6:128355742-128355990(-)$1	1	233	241	14.7500
.......(	chr14:55766204-55766433(+)$1	1	197	205	19.2499
.(((((..	chr3:78822165-78822397(-)$1	1	53	61	12.5000
((((((((	chr6:56465263-56465495(-)$1	1	9	17	15.2500
(.......	chr4:124061772-124062004(+)$1	1	101	109	12.5000
.((((...	chr4:68558980-68559213(-)$1	1	150	158	15.0000
......))	chr1:61890181-61890408(+)$1	1	214	222	15.9999
.(((...(	chr6:42979527-42979759(+)$1	1	107	115	15.2500
(((((((.	chr1:162482015-162482243(+)$1	1	120	128	14.7500
...(((((	chr1:93660087-93660319(+)$1	1	41	49	15.6249
(((....)	chr1:154593166-154593396(-)$1	1	52	60	15.5000
........	chr5:144859683-144859915(-)$1	1	2	10	19.2499
...)))))	chrX:73449189-73449421(-)$1	1	98	106	15.0000
(..(((..	chr4:57312341-57312573(+)$1	1	109	117	15.5000
))))).))	chr8:64122966-64123196(+)$1	1	206	214	15.3749
((((((.(	chr12:34402329-34402561(+)$1	1	159	167	15.3750
........	chr6:71219908-71220134(+)$1	1	10	18	15.0000
...(((((	chr16:78577688-78577922(+)$1	1	140	148	14.7500
..))))).	chr8:10893161-10893393(-)$1	1	220	228	15.3750
(((((...	chr13:114116613-114116847(-)$1	1	157	165	19.2499
((((((..	chr2:148831573-148831804(+)$1	1	48	56	15.6249
))......	chr2:213208409-213208641(-)$1	1	60	68	14.6250
))))))..	chr7:80527762-80527987(-)$1	1	100	108	14.6250
....))))	chr12:39142649-39142881(-)$1	1	199	207	15.0000
(.....((	chr13:60585918-60586150(-)$1	1	38	46	14.7500
((....))	chr7:26231664-26231889(-)$1	1	32	40	19.2499
)))))).)	chr13:50791297-50791529(+)$1	1	132	140	12.3750
))......	chrX:34291700-34291930(-)$1	1	52	60	15.9999

#PSSM
A : 0.52	a : 0.42	G : 0.02	C : 0.02	
U : 0.55	u : 0.32	a : 0.05	c : 0.02	A : 0.02	g : 0.02	
A : 0.50	a : 0.32	u : 0.07	C : 0.05	U : 0.02	G : 0.02	
A : 0.57	a : 0.35	u : 0.05	U : 0.02	
A : 0.50	a : 0.30	U : 0.07	u : 0.07	C : 0.02	c : 0.02	
U : 0.47	u : 0.32	a : 0.05	A : 0.05	g : 0.05	C : 0.02	G : 0.02	
A : 0.50	a : 0.42	G : 0.02	C : 0.02	U : 0.02	
U : 0.52	u : 0.42	G : 0.05	

#score	623.0
#seq	40
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m1_run1.nuc.txt

#NT
CUGU	chr14:74180303-74180523(-)$1	220	11	15	12.0000
CUGU	chr4:183723453-183723689(+)$1	236	67	71	12.0000
CUGU	chr2:42558674-42558891(+)$1	217	131	135	12.0000
CUGU	chr4:15629415-15629634(-)$1	219	77	81	12.0000
CUGU	chr8:144696460-144696682(-)$1	222	45	49	12.0000
CUGU	chr4:53468083-53468307(-)$1	224	7	11	12.0000
CUGU	chr14:68115609-68115825(-)$1	216	112	116	12.0000
CUGU	chr17:38436075-38436298(+)$1	223	75	79	12.0000
CUGU	chr17:21433802-21434015(-)$1	213	49	53	12.0000
CUGU	chr16:28109654-28109879(-)$1	225	7	11	12.0000
CUGU	chr13:53272197-53272417(+)$1	220	179	183	12.0000
CUGU	chr14:21853394-21853614(-)$1	220	168	172	12.0000
cugu	chr9:35658856-35659080(-)$1	224	216	220	12.0000
CUGU	chr6:34840380-34840603(+)$1	223	57	61	12.0000
CUGU	chr3:113439899-113440122(-)$1	223	212	216	12.0000
cugu	chr2:183962710-183962923(+)$1	213	19	23	12.0000
CUGU	chr6:111215363-111215577(+)$1	214	148	152	12.0000
CUGU	chr11:67021734-67021972(+)$1	238	43	47	12.0000
CUGU	chr19:44740933-44741154(+)$1	221	127	131	12.0000
CUGU	chr5:167983024-167983251(-)$1	227	162	166	12.0000
CUGU	chr2:95847837-95848055(+)$1	218	75	79	12.0000
CUGU	chr5:64865387-64865604(+)$1	217	32	36	12.0000
CUGU	chr1:115248538-115248762(-)$1	224	31	35	12.0000
CUGU	chr17:61768428-61768645(+)$1	217	107	111	12.0000
CUGU	chr20:4836657-4836885(-)$1	228	43	47	12.0000
cugu	chr11:76735287-76735507(+)$1	220	22	26	12.0000
CUGU	chr16:11962186-11962407(-)$1	221	81	85	12.0000
CUGU	chr2:239357117-239357355(+)$1	238	135	139	12.0000
CUGU	chr12:133349188-133349417(-)$1	229	68	72	12.0000
CUGU	chr10:22618911-22619125(+)$1	214	42	46	12.0000
CUGU	chr22:29191125-29191345(-)$1	220	65	69	12.0000
CUGU	chr7:129472803-129473023(-)$1	220	104	108	12.0000
CUGU	chr12:69238176-69238400(+)$1	224	22	26	12.0000
CUGU	chr7:124482836-124483061(-)$1	225	167	171	12.0000
CUGU	chr10:119042138-119042361(-)$1	223	176	180	12.0000
CUGU	chr5:38479743-38479965(-)$1	222	166	170	12.0000
CUGU	chr5:179669484-179669701(-)$1	217	21	25	12.0000
CUGU	chr12:125431605-125431835(-)$1	230	35	39	12.0000
CUGU	chr17:15935479-15935705(-)$1	226	75	79	12.0000
CUGU	chr9:35738247-35738469(-)$1	222	104	108	12.0000
CUGU	chr5:75991218-75991436(+)$1	218	7	11	12.0000
CUGU	chr19:41313731-41313950(+)$1	219	9	13	12.0000
CUGU	chr7:133978734-133978950(-)$1	216	40	44	12.0000
CUGU	chr3:38524954-38525189(+)$1	235	84	88	12.0000
CUGU	chr19:56599056-56599287(-)$1	231	34	38	12.0000
CUGU	chr17:46137154-46137388(+)$1	234	91	95	12.0000
CUGU	chr1:6653525-6653745(-)$1	220	66	70	12.0000
CUGU	chr1:41445297-41445520(+)$1	223	134	138	12.0000
CUGU	chrX:20169295-20169521(-)$1	226	116	120	12.0000
CUGU	chr15:91312280-91312496(+)$1	216	84	88	12.0000
cugu	chr19:36883113-36883326(-)$1	213	38	42	12.0000
CUGU	chr19:46190726-46190943(-)$1	217	140	144	12.0000
CUGU	chr17:72199729-72199969(+)$1	240	118	122	12.0000
CUGU	chr11:86661790-86662009(-)$1	219	59	63	12.0000
CUGU	chr21:47610617-47610837(-)$1	220	12	16	12.0000
CUGU	chr3:196199447-196199663(-)$1	216	7	11	12.0000
CUGU	chr17:57725632-57725862(+)$1	230	2	6	12.0000
CUGU	chr6:16302037-16302257(-)$1	220	114	118	12.0000
CUGU	chr11:63394049-63394260(-)$1	211	76	80	12.0000
cugu	chr21:35472160-35472397(+)$1	237	130	134	12.0000
CUGU	chr20:20350754-20350968(+)$1	214	36	40	12.0000
CUGU	chr2:24253577-24253791(-)$1	214	6	10	12.0000
CUGU	chr6:7899755-7899977(-)$1	222	36	40	12.0000
CUGU	chr18:672937-673156(+)$1	219	52	56	12.0000
CUGU	chr15:41870501-41870724(+)$1	223	79	83	12.0000
CUGU	chr12:76441596-76441819(-)$1	223	11	15	12.0000
cugu	chr19:52517925-52518152(-)$1	227	11	15	12.0000
CUGU	chr9:115632391-115632610(+)$1	219	45	49	12.0000
CUGU	chr3:15481121-15481340(+)$1	219	140	144	12.0000
cugu	chr3:113436888-113437115(-)$1	227	39	43	12.0000
CUGU	chr11:63448878-63449127(+)$1	249	96	100	12.0000
CUGU	chr9:111782464-111782680(-)$1	216	2	6	12.0000
CUGU	chr16:633027-633247(+)$1	220	96	100	12.0000
CUGU	chr3:101369784-101370001(-)$1	217	62	66	12.0000
CUGU	chr5:78617560-78617776(+)$1	216	113	117	12.0000
CUGU	chr16:88927356-88927576(+)$1	220	16	20	12.0000
CUGU	chr10:98917519-98917750(-)$1	231	66	70	12.0000
CUGU	chr3:12940343-12940562(-)$1	219	32	36	12.0000
CUGU	chr16:84695644-84695862(+)$1	218	13	17	12.0000
CUGU	chr5:72206427-72206645(+)$1	218	115	119	12.0000
CUGU	chr19:49611548-49611767(+)$1	219	173	177	12.0000

#otherMatches

#Struct PSSM
E{DD	chr8:146015109-146015350(-)$1	241	4	8	12.0000
HHHH	chr14:74180303-74180523(-)$1	220	11	15	12.0000
ccff	chr4:183723453-183723689(+)$1	236	67	71	12.0000
hccc	chr2:42558674-42558891(+)$1	217	131	135	12.0000
""bb	chr4:15629415-15629634(-)$1	219	77	81	12.0000
b[cc	chr8:144696460-144696682(-)$1	222	45	49	12.0000
:JJJ	chr4:53468083-53468307(-)$1	224	7	11	12.0000
ddd[	chr14:68115609-68115825(-)$1	216	112	116	12.0000
eeee	chr17:38436075-38436298(+)$1	223	75	79	12.0000
ffff	chr17:21433802-21434015(-)$1	213	49	53	12.0000
eeee	chr16:28109654-28109879(-)$1	225	7	11	12.0000
:ddd	chr13:53272197-53272417(+)$1	220	179	183	12.0000
c:==	chr14:21853394-21853614(-)$1	220	168	172	12.0000
D:::	chr9:35658856-35659080(-)$1	224	216	220	12.0000
annn	chr6:34840380-34840603(+)$1	223	57	61	12.0000
ggg]	chr3:113439899-113440122(-)$1	223	212	216	12.0000
FFFF	chr2:183962710-183962923(+)$1	213	19	23	12.0000
oddd	chr6:111215363-111215577(+)$1	214	148	152	12.0000
dddd	chr11:67021734-67021972(+)$1	238	43	47	12.0000
hh[a	chr19:44740933-44741154(+)$1	221	127	131	12.0000
DDDD	chr5:167983024-167983251(-)$1	227	162	166	12.0000
ddd]	chr2:95847837-95848055(+)$1	218	75	79	12.0000
hhhh	chr5:64865387-64865604(+)$1	217	32	36	12.0000
::EE	chr1:115248538-115248762(-)$1	224	31	35	12.0000
ppbb	chr17:61768428-61768645(+)$1	217	107	111	12.0000
ittt	chr20:4836657-4836885(-)$1	228	43	47	12.0000
llff	chr11:76735287-76735507(+)$1	220	22	26	12.0000
ffff	chr16:11962186-11962407(-)$1	221	81	85	12.0000
ccc"	chr2:239357117-239357355(+)$1	238	135	139	12.0000
####	chr12:133349188-133349417(-)$1	229	68	72	12.0000
b333	chr10:22618911-22619125(+)$1	214	42	46	12.0000
444e	chr22:29191125-29191345(-)$1	220	65	69	12.0000
eeee	chr7:129472803-129473023(-)$1	220	104	108	12.0000
FFF:	chr12:69238176-69238400(+)$1	224	22	26	12.0000
ee::	chr7:124482836-124483061(-)$1	225	167	171	12.0000
vvvv	chr10:119042138-119042361(-)$1	223	176	180	12.0000
FFFY	chr5:38479743-38479965(-)$1	222	166	170	12.0000
qqqe	chr5:179669484-179669701(-)$1	217	21	25	12.0000
ppdd	chr12:125431605-125431835(-)$1	230	35	39	12.0000
dddb	chr17:15935479-15935705(-)$1	226	75	79	12.0000
ddd3	chr9:35738247-35738469(-)$1	222	104	108	12.0000
DDDD	chr5:75991218-75991436(+)$1	218	7	11	12.0000
ANNN	chr19:41313731-41313950(+)$1	219	9	13	12.0000
KKEE	chr7:133978734-133978950(-)$1	216	40	44	12.0000
gggg	chr3:38524954-38525189(+)$1	235	84	88	12.0000
#ggg	chr19:56599056-56599287(-)$1	231	34	38	12.0000
ccll	chr17:46137154-46137388(+)$1	234	91	95	12.0000
DDD{	chr1:6653525-6653745(-)$1	220	66	70	12.0000
c]bb	chr1:41445297-41445520(+)$1	223	134	138	12.0000
GGGG	chrX:20169295-20169521(-)$1	226	116	120	12.0000
eeee	chr15:91312280-91312496(+)$1	216	84	88	12.0000
eeee	chr19:36883113-36883326(-)$1	213	38	42	12.0000
eeee	chr19:46190726-46190943(-)$1	217	140	144	12.0000
ff##	chr17:72199729-72199969(+)$1	240	118	122	12.0000
ccdd	chr11:86661790-86662009(-)$1	219	59	63	12.0000
dddd	chr21:47610617-47610837(-)$1	220	12	16	12.0000
====	chr3:196199447-196199663(-)$1	216	7	11	12.0000
::::	chr17:57725632-57725862(+)$1	230	2	6	12.0000
gggg	chr6:16302037-16302257(-)$1	220	114	118	12.0000
ebbc	chr11:63394049-63394260(-)$1	211	76	80	12.0000
"eee	chr21:35472160-35472397(+)$1	237	130	134	12.0000
d###	chr20:20350754-20350968(+)$1	214	36	40	12.0000
[ddd	chr2:24253577-24253791(-)$1	214	6	10	12.0000
xeee	chr6:7899755-7899977(-)$1	222	36	40	12.0000
HHHK	chr18:672937-673156(+)$1	219	52	56	12.0000
blll	chr15:41870501-41870724(+)$1	223	79	83	12.0000
c:EE	chr12:76441596-76441819(-)$1	223	11	15	12.0000
{DDD	chr19:52517925-52518152(-)$1	227	11	15	12.0000
pppp	chr9:115632391-115632610(+)$1	219	45	49	12.0000
dddd	chr3:15481121-15481340(+)$1	219	140	144	12.0000
::::	chr3:113436888-113437115(-)$1	227	39	43	12.0000
f:::	chr11:63448878-63449127(+)$1	249	96	100	12.0000
::CC	chr9:111782464-111782680(-)$1	216	2	6	12.0000
eee]	chr16:633027-633247(+)$1	220	96	100	12.0000
gggg	chr3:101369784-101370001(-)$1	217	62	66	12.0000
#eee	chr5:78617560-78617776(+)$1	216	113	117	12.0000
clll	chr16:88927356-88927576(+)$1	220	16	20	12.0000
mmmm	chr10:98917519-98917750(-)$1	231	66	70	12.0000
b[cc	chr3:12940343-12940562(-)$1	219	32	36	12.0000
dBB{	chr16:84695644-84695862(+)$1	218	13	17	12.0000
d444	chr5:72206427-72206645(+)$1	218	115	119	12.0000
c]ff	chr19:49611548-49611767(+)$1	219	173	177	12.0000

#DB
(.((	chr8:146015109-146015350(-)$1	1	4	8	12.0000
((((	chr14:74180303-74180523(-)$1	1	11	15	12.0000
))))	chr4:183723453-183723689(+)$1	1	67	71	12.0000
)(((	chr2:42558674-42558891(+)$1	1	131	135	12.0000
..((	chr4:15629415-15629634(-)$1	1	77	81	12.0000
(.((	chr8:144696460-144696682(-)$1	1	45	49	12.0000
.(((	chr4:53468083-53468307(-)$1	1	7	11	12.0000
(((.	chr14:68115609-68115825(-)$1	1	112	116	12.0000
((((	chr17:38436075-38436298(+)$1	1	75	79	12.0000
((((	chr17:21433802-21434015(-)$1	1	49	53	12.0000
((((	chr16:28109654-28109879(-)$1	1	7	11	12.0000
.(((	chr13:53272197-53272417(+)$1	1	179	183	12.0000
).((	chr14:21853394-21853614(-)$1	1	168	172	12.0000
)...	chr9:35658856-35659080(-)$1	1	216	220	12.0000
(...	chr6:34840380-34840603(+)$1	1	57	61	12.0000
))).	chr3:113439899-113440122(-)$1	1	212	216	12.0000
((((	chr2:183962710-183962923(+)$1	1	19	23	12.0000
.)))	chr6:111215363-111215577(+)$1	1	148	152	12.0000
((((	chr11:67021734-67021972(+)$1	1	43	47	12.0000
((.(	chr19:44740933-44741154(+)$1	1	127	131	12.0000
))))	chr5:167983024-167983251(-)$1	1	162	166	12.0000
))).	chr2:95847837-95848055(+)$1	1	75	79	12.0000
((((	chr5:64865387-64865604(+)$1	1	32	36	12.0000
..((	chr1:115248538-115248762(-)$1	1	31	35	12.0000
..))	chr17:61768428-61768645(+)$1	1	107	111	12.0000
(...	chr20:4836657-4836885(-)$1	1	43	47	12.0000
..))	chr11:76735287-76735507(+)$1	1	22	26	12.0000
((((	chr16:11962186-11962407(-)$1	1	81	85	12.0000
(((.	chr2:239357117-239357355(+)$1	1	135	139	12.0000
....	chr12:133349188-133349417(-)$1	1	68	72	12.0000
)...	chr10:22618911-22619125(+)$1	1	42	46	12.0000
...)	chr22:29191125-29191345(-)$1	1	65	69	12.0000
))))	chr7:129472803-129473023(-)$1	1	104	108	12.0000
(((.	chr12:69238176-69238400(+)$1	1	22	26	12.0000
))..	chr7:124482836-124483061(-)$1	1	167	171	12.0000
....	chr10:119042138-119042361(-)$1	1	176	180	12.0000
))).	chr5:38479743-38479965(-)$1	1	166	170	12.0000
...)	chr5:179669484-179669701(-)$1	1	21	25	12.0000
..))	chr12:125431605-125431835(-)$1	1	35	39	12.0000
))))	chr17:15935479-15935705(-)$1	1	75	79	12.0000
))).	chr9:35738247-35738469(-)$1	1	104	108	12.0000
((((	chr5:75991218-75991436(+)$1	1	7	11	12.0000
(...	chr19:41313731-41313950(+)$1	1	9	13	12.0000
..((	chr7:133978734-133978950(-)$1	1	40	44	12.0000
((((	chr3:38524954-38525189(+)$1	1	84	88	12.0000
.(((	chr19:56599056-56599287(-)$1	1	34	38	12.0000
((..	chr17:46137154-46137388(+)$1	1	91	95	12.0000
(((.	chr1:6653525-6653745(-)$1	1	66	70	12.0000
).))	chr1:41445297-41445520(+)$1	1	134	138	12.0000
))))	chrX:20169295-20169521(-)$1	1	116	120	12.0000
((((	chr15:91312280-91312496(+)$1	1	84	88	12.0000
((((	chr19:36883113-36883326(-)$1	1	38	42	12.0000
((((	chr19:46190726-46190943(-)$1	1	140	144	12.0000
((..	chr17:72199729-72199969(+)$1	1	118	122	12.0000
((((	chr11:86661790-86662009(-)$1	1	59	63	12.0000
((((	chr21:47610617-47610837(-)$1	1	12	16	12.0000
((((	chr3:196199447-196199663(-)$1	1	7	11	12.0000
....	chr17:57725632-57725862(+)$1	1	2	6	12.0000
((((	chr6:16302037-16302257(-)$1	1	114	118	12.0000
((((	chr11:63394049-63394260(-)$1	1	76	80	12.0000
.(((	chr21:35472160-35472397(+)$1	1	130	134	12.0000
(...	chr20:20350754-20350968(+)$1	1	36	40	12.0000
.(((	chr2:24253577-24253791(-)$1	1	6	10	12.0000
.)))	chr6:7899755-7899977(-)$1	1	36	40	12.0000
(((.	chr18:672937-673156(+)$1	1	52	56	12.0000
(...	chr15:41870501-41870724(+)$1	1	79	83	12.0000
).((	chr12:76441596-76441819(-)$1	1	11	15	12.0000
.(((	chr19:52517925-52518152(-)$1	1	11	15	12.0000
....	chr9:115632391-115632610(+)$1	1	45	49	12.0000
((((	chr3:15481121-15481340(+)$1	1	140	144	12.0000
....	chr3:113436888-113437115(-)$1	1	39	43	12.0000
)...	chr11:63448878-63449127(+)$1	1	96	100	12.0000
..((	chr9:111782464-111782680(-)$1	1	2	6	12.0000
))).	chr16:633027-633247(+)$1	1	96	100	12.0000
))))	chr3:101369784-101370001(-)$1	1	62	66	12.0000
.(((	chr5:78617560-78617776(+)$1	1	113	117	12.0000
(...	chr16:88927356-88927576(+)$1	1	16	20	12.0000
....	chr10:98917519-98917750(-)$1	1	66	70	12.0000
(.((	chr3:12940343-12940562(-)$1	1	32	36	12.0000
)((.	chr16:84695644-84695862(+)$1	1	13	17	12.0000
)...	chr5:72206427-72206645(+)$1	1	115	119	12.0000
).))	chr19:49611548-49611767(+)$1	1	173	177	12.0000

#PSSM
C : 0.91	c : 0.08	
U : 0.91	u : 0.08	
G : 0.91	g : 0.08	
U : 0.91	u : 0.08	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_UTR_m3_run1.nuc.txt

#NT
CCAG	chr9:115925769-115926009(+)$1	240	200	204	11.9999
CCAG	chr16:87438189-87438429(+)$1	240	198	202	11.9999
ccag	chr6:31807388-31807628(+)$1	240	227	231	11.9999
CCAG	chr16:48396204-48396444(-)$1	240	161	165	11.9999
CCAG	chr6:32945130-32945432(+)$1	302	178	182	11.9999
CCAG	chr19:57746219-57746459(+)$1	240	69	73	11.9999
CCAG	chr17:45901149-45901389(-)$1	240	64	68	11.9999
CCAG	chr8:144898448-144898688(-)$1	240	77	81	11.9999
CCAG	chr20:42089599-42089879(+)$1	280	81	85	11.9999
CCAG	chr5:141380170-141380410(-)$1	240	32	36	11.9999
CCAG	chr17:76220574-76220871(+)$1	297	24	28	11.9999
CCAG	chr20:417745-418073(-)$1	328	0	4	11.9999
CCAG	chr9:98207800-98208040(-)$1	240	224	228	11.9999
CCAG	chr5:68473290-68473572(+)$1	282	56	60	11.9999
CCAG	chr15:69745096-69745376(+)$1	280	168	172	11.9999
CCAG	chr1:44462181-44462421(-)$1	240	2	6	11.9999
CCAG	chr2:39025262-39025502(-)$1	240	176	180	11.9999
CCAG	chr2:105709899-105710139(+)$1	240	167	171	11.9999
CCAG	chr10:114925350-114925590(+)$1	240	113	117	11.9999
CCAG	chr6:43481031-43481271(-)$1	240	7	11	11.9999
CCAG	chr16:47116507-47116747(-)$1	240	176	180	11.9999
CCAG	chr5:174953933-174954173(+)$1	240	70	74	11.9999
CCAG	chr21:34727736-34727976(+)$1	240	119	123	11.9999
CCAG	chr10:103912117-103912357(+)$1	240	81	85	11.9999
CCAG	chr19:47112579-47112819(+)$1	240	109	113	11.9999
CCAG	chr2:74699092-74699332(-)$1	240	34	38	11.9999
CCAG	chr7:158449230-158449470(-)$1	240	217	221	11.9999
CCAG	chr19:39220267-39220507(+)$1	240	19	23	11.9999
CCAG	chr2:74329244-74329484(+)$1	240	62	66	11.9999
CCAG	chr2:27664766-27665047(+)$1	281	194	198	11.9999
CCAG	chr20:36718648-36718888(+)$1	240	89	93	11.9999
CCAG	chr3:42688880-42689120(+)$1	240	193	197	11.9999
CCAG	chr6:31785357-31785637(+)$1	280	8	12	11.9999
CCAG	chr17:30666739-30666979(-)$1	240	62	66	11.9999
CCAG	chr20:33872199-33872439(-)$1	240	9	13	11.9999
CCAG	chr16:23478359-23478599(-)$1	240	117	121	11.9999
CCAG	chr17:35878572-35878812(-)$1	240	138	142	11.9999
CCAG	chr17:40993640-40993880(+)$1	240	203	207	11.9999
CCAG	chr11:62365935-62366175(-)$1	240	4	8	11.9999
CCAG	chr12:118587931-118588171(-)$1	240	126	130	11.9999
CCAG	chrX:106957532-106957772(-)$1	240	79	83	11.9999
CCAG	chr20:62375117-62375357(+)$1	240	181	185	11.9999
CCAG	chr13:107143203-107143443(-)$1	240	184	188	11.9999
CCAG	chr5:150175702-150175968(+)$1	266	26	30	11.9999
CCAG	chr12:42480310-42480550(-)$1	240	44	48	11.9999
CCAG	chr17:1641695-1641935(+)$1	240	53	57	11.9999
CCAG	chr7:100483779-100484019(+)$1	240	84	88	11.9999
CCAG	chr3:12940483-12940723(-)$1	240	25	29	11.9999
CCAG	chr11:44266473-44266713(+)$1	240	125	129	11.9999
CCAG	chr22:42998739-42998979(-)$1	240	34	38	11.9999
CCAG	chr6:138744690-138744930(-)$1	240	78	82	11.9999
ccag	chr19:37002474-37002714(-)$1	240	185	189	11.9999
CCAG	chrX:153671324-153671588(+)$1	264	73	77	11.9999
CCAG	chr9:34087138-34087378(-)$1	240	60	64	11.9999
CCAG	chr15:83205405-83205645(-)$1	240	9	13	11.9999
CCAG	chr7:75615605-75615845(+)$1	240	18	22	11.9999
CCAG	chr8:11695935-11696175(+)$1	240	143	147	11.9999
CCAG	chr5:137759838-137760078(+)$1	240	38	42	11.9999
CCAG	chr17:42112997-42113237(-)$1	240	114	118	11.9999
CCAG	chr5:76129784-76130024(+)$1	240	60	64	11.9999
CCAG	chr1:38269173-38269413(-)$1	240	198	202	11.9999
CCAG	chr14:55518288-55518528(+)$1	240	2	6	11.9999
CCAG	chr1:28824609-28824850(+)$1	241	96	100	11.9999
CCAG	chr1:226548504-226548744(-)$1	240	183	187	11.9999
CCAG	chr17:7481835-7482110(+)$1	275	162	166	11.9999
CCAG	chr17:73059484-73059724(+)$1	240	199	203	11.9999
CCAG	chr3:49764854-49765096(-)$1	242	13	17	11.9999
CCAG	chr17:2588683-2588923(+)$1	240	29	33	11.9999
CCAG	chr2:32502922-32503162(+)$1	240	39	43	11.9999
CCAG	chr1:26605058-26605298(+)$1	240	35	39	11.9999
CCAG	chr2:27917548-27917788(+)$1	240	79	83	11.9999
CCAG	chr17:18709255-18709502(+)$1	247	181	185	11.9999
CCAG	chr15:72534402-72534642(-)$1	240	13	17	11.9999
CCAG	chrX:24230350-24230590(+)$1	240	130	134	11.9999
CCAG	chr22:47085858-47086098(-)$1	240	42	46	11.9999
CCAG	chr17:34050997-34051277(+)$1	280	169	173	11.9999
CCAG	chr7:100278356-100278599(-)$1	243	111	115	11.9999

#otherMatches

#Struct PSSM
HBB:	chr6:33377352-33377592(+)$1	240	66	70	11.9999
nnne	chr9:115925769-115926009(+)$1	240	200	204	11.9999
22ff	chr16:87438189-87438429(+)$1	240	198	202	11.9999
eeee	chr6:31807388-31807628(+)$1	240	227	231	11.9999
444d	chr16:48396204-48396444(-)$1	240	161	165	11.9999
GGGG	chr6:32945130-32945432(+)$1	302	178	182	11.9999
ee##	chr19:57746219-57746459(+)$1	240	69	73	11.9999
FFFF	chr17:45901149-45901389(-)$1	240	64	68	11.9999
iiii	chr8:144898448-144898688(-)$1	240	77	81	11.9999
FFFF	chr20:42089599-42089879(+)$1	280	81	85	11.9999
eeee	chr5:141380170-141380410(-)$1	240	32	36	11.9999
JJ:b	chr17:76220574-76220871(+)$1	297	24	28	11.9999
:eee	chr20:417745-418073(-)$1	328	0	4	11.9999
nnnb	chr9:98207800-98208040(-)$1	240	224	228	11.9999
lldd	chr5:68473290-68473572(+)$1	282	56	60	11.9999
BEEE	chr15:69745096-69745376(+)$1	280	168	172	11.9999
::::	chr1:44462181-44462421(-)$1	240	2	6	11.9999
c!!d	chr2:39025262-39025502(-)$1	240	176	180	11.9999
cccd	chr2:105709899-105710139(+)$1	240	167	171	11.9999
NNNB	chr10:114925350-114925590(+)$1	240	113	117	11.9999
KFFF	chr6:43481031-43481271(-)$1	240	7	11	11.9999
!ccc	chr16:47116507-47116747(-)$1	240	176	180	11.9999
f[cc	chr5:174953933-174954173(+)$1	240	70	74	11.9999
dccc	chr21:34727736-34727976(+)$1	240	119	123	11.9999
{DDD	chr10:103912117-103912357(+)$1	240	81	85	11.9999
eeee	chr19:47112579-47112819(+)$1	240	109	113	11.9999
22cc	chr2:74699092-74699332(-)$1	240	34	38	11.9999
ee22	chr7:158449230-158449470(-)$1	240	217	221	11.9999
ffff	chr19:39220267-39220507(+)$1	240	19	23	11.9999
33dd	chr2:74329244-74329484(+)$1	240	62	66	11.9999
$$$g	chr2:27664766-27665047(+)$1	281	194	198	11.9999
&fff	chr20:36718648-36718888(+)$1	240	89	93	11.9999
ccc:	chr3:42688880-42689120(+)$1	240	193	197	11.9999
bb[c	chr6:31785357-31785637(+)$1	280	8	12	11.9999
b"""	chr17:30666739-30666979(-)$1	240	62	66	11.9999
ccpp	chr20:33872199-33872439(-)$1	240	9	13	11.9999
gggg	chr16:23478359-23478599(-)$1	240	117	121	11.9999
]ddd	chr17:35878572-35878812(-)$1	240	138	142	11.9999
ffff	chr17:40993640-40993880(+)$1	240	203	207	11.9999
FFF:	chr11:62365935-62366175(-)$1	240	4	8	11.9999
ffff	chr12:118587931-118588171(-)$1	240	126	130	11.9999
b[bb	chrX:106957532-106957772(-)$1	240	79	83	11.9999
vvvv	chr20:62375117-62375357(+)$1	240	181	185	11.9999
rrrr	chr13:107143203-107143443(-)$1	240	184	188	11.9999
:ddd	chr5:150175702-150175968(+)$1	266	26	30	11.9999
FFFF	chr12:42480310-42480550(-)$1	240	44	48	11.9999
c!!c	chr17:1641695-1641935(+)$1	240	53	57	11.9999
:fff	chr7:100483779-100484019(+)$1	240	84	88	11.9999
====	chr3:12940483-12940723(-)$1	240	25	29	11.9999
b!!e	chr11:44266473-44266713(+)$1	240	125	129	11.9999
c!!e	chr22:42998739-42998979(-)$1	240	34	38	11.9999
ccee	chr6:138744690-138744930(-)$1	240	78	82	11.9999
!!cc	chr19:37002474-37002714(-)$1	240	185	189	11.9999
gggg	chrX:153671324-153671588(+)$1	264	73	77	11.9999
>>>>	chr9:34087138-34087378(-)$1	240	60	64	11.9999
iiii	chr15:83205405-83205645(-)$1	240	9	13	11.9999
CCCE	chr7:75615605-75615845(+)$1	240	18	22	11.9999
ueee	chr8:11695935-11696175(+)$1	240	143	147	11.9999
nccc	chr5:137759838-137760078(+)$1	240	38	42	11.9999
fvvv	chr17:42112997-42113237(-)$1	240	114	118	11.9999
:ccc	chr5:76129784-76130024(+)$1	240	60	64	11.9999
cc]f	chr1:38269173-38269413(-)$1	240	198	202	11.9999
::::	chr14:55518288-55518528(+)$1	240	2	6	11.9999
iiii	chr1:28824609-28824850(+)$1	241	96	100	11.9999
$ccc	chr1:226548504-226548744(-)$1	240	183	187	11.9999
====	chr17:7481835-7482110(+)$1	275	162	166	11.9999
ddd2	chr17:73059484-73059724(+)$1	240	199	203	11.9999
"""c	chr3:49764854-49765096(-)$1	242	13	17	11.9999
bagg	chr17:2588683-2588923(+)$1	240	29	33	11.9999
dddg	chr2:32502922-32503162(+)$1	240	39	43	11.9999
eeee	chr1:26605058-26605298(+)$1	240	35	39	11.9999
ffff	chr2:27917548-27917788(+)$1	240	79	83	11.9999
EEff	chr17:18709255-18709502(+)$1	247	181	185	11.9999
BB{D	chr15:72534402-72534642(-)$1	240	13	17	11.9999
999c	chrX:24230350-24230590(+)$1	240	130	134	11.9999
eeed	chr22:47085858-47086098(-)$1	240	42	46	11.9999
22dd	chr17:34050997-34051277(+)$1	280	169	173	11.9999
f:::	chr7:100278356-100278599(-)$1	243	111	115	11.9999

#DB
(((.	chr6:33377352-33377592(+)$1	1	66	70	11.9999
...)	chr9:115925769-115926009(+)$1	1	200	204	11.9999
..))	chr16:87438189-87438429(+)$1	1	198	202	11.9999
((((	chr6:31807388-31807628(+)$1	1	227	231	11.9999
...)	chr16:48396204-48396444(-)$1	1	161	165	11.9999
))))	chr6:32945130-32945432(+)$1	1	178	182	11.9999
((..	chr19:57746219-57746459(+)$1	1	69	73	11.9999
((((	chr17:45901149-45901389(-)$1	1	64	68	11.9999
((((	chr8:144898448-144898688(-)$1	1	77	81	11.9999
((((	chr20:42089599-42089879(+)$1	1	81	85	11.9999
))))	chr5:141380170-141380410(-)$1	1	32	36	11.9999
((.(	chr17:76220574-76220871(+)$1	1	24	28	11.9999
.(((	chr20:417745-418073(-)$1	1	0	4	11.9999
...)	chr9:98207800-98208040(-)$1	1	224	228	11.9999
..))	chr5:68473290-68473572(+)$1	1	56	60	11.9999
))))	chr15:69745096-69745376(+)$1	1	168	172	11.9999
....	chr1:44462181-44462421(-)$1	1	2	6	11.9999
(..(	chr2:39025262-39025502(-)$1	1	176	180	11.9999
))))	chr2:105709899-105710139(+)$1	1	167	171	11.9999
...(	chr10:114925350-114925590(+)$1	1	113	117	11.9999
.(((	chr6:43481031-43481271(-)$1	1	7	11	11.9999
.(((	chr16:47116507-47116747(-)$1	1	176	180	11.9999
(.((	chr5:174953933-174954173(+)$1	1	70	74	11.9999
((((	chr21:34727736-34727976(+)$1	1	119	123	11.9999
.(((	chr10:103912117-103912357(+)$1	1	81	85	11.9999
((((	chr19:47112579-47112819(+)$1	1	109	113	11.9999
..))	chr2:74699092-74699332(-)$1	1	34	38	11.9999
))..	chr7:158449230-158449470(-)$1	1	217	221	11.9999
((((	chr19:39220267-39220507(+)$1	1	19	23	11.9999
..))	chr2:74329244-74329484(+)$1	1	62	66	11.9999
...(	chr2:27664766-27665047(+)$1	1	194	198	11.9999
.(((	chr20:36718648-36718888(+)$1	1	89	93	11.9999
))).	chr3:42688880-42689120(+)$1	1	193	197	11.9999
((.(	chr6:31785357-31785637(+)$1	1	8	12	11.9999
(...	chr17:30666739-30666979(-)$1	1	62	66	11.9999
((..	chr20:33872199-33872439(-)$1	1	9	13	11.9999
))))	chr16:23478359-23478599(-)$1	1	117	121	11.9999
.)))	chr17:35878572-35878812(-)$1	1	138	142	11.9999
))))	chr17:40993640-40993880(+)$1	1	203	207	11.9999
(((.	chr11:62365935-62366175(-)$1	1	4	8	11.9999
((((	chr12:118587931-118588171(-)$1	1	126	130	11.9999
(.((	chrX:106957532-106957772(-)$1	1	79	83	11.9999
....	chr20:62375117-62375357(+)$1	1	181	185	11.9999
....	chr13:107143203-107143443(-)$1	1	184	188	11.9999
.(((	chr5:150175702-150175968(+)$1	1	26	30	11.9999
((((	chr12:42480310-42480550(-)$1	1	44	48	11.9999
(..(	chr17:1641695-1641935(+)$1	1	53	57	11.9999
.(((	chr7:100483779-100484019(+)$1	1	84	88	11.9999
))))	chr3:12940483-12940723(-)$1	1	25	29	11.9999
(..(	chr11:44266473-44266713(+)$1	1	125	129	11.9999
(..(	chr22:42998739-42998979(-)$1	1	34	38	11.9999
((((	chr6:138744690-138744930(-)$1	1	78	82	11.9999
..((	chr19:37002474-37002714(-)$1	1	185	189	11.9999
))))	chrX:153671324-153671588(+)$1	1	73	77	11.9999
....	chr9:34087138-34087378(-)$1	1	60	64	11.9999
((((	chr15:83205405-83205645(-)$1	1	9	13	11.9999
((((	chr7:75615605-75615845(+)$1	1	18	22	11.9999
.)))	chr8:11695935-11696175(+)$1	1	143	147	11.9999
.)))	chr5:137759838-137760078(+)$1	1	38	42	11.9999
(...	chr17:42112997-42113237(-)$1	1	114	118	11.9999
.(((	chr5:76129784-76130024(+)$1	1	60	64	11.9999
)).)	chr1:38269173-38269413(-)$1	1	198	202	11.9999
....	chr14:55518288-55518528(+)$1	1	2	6	11.9999
((((	chr1:28824609-28824850(+)$1	1	96	100	11.9999
.(((	chr1:226548504-226548744(-)$1	1	183	187	11.9999
))))	chr17:7481835-7482110(+)$1	1	162	166	11.9999
))).	chr17:73059484-73059724(+)$1	1	199	203	11.9999
...(	chr3:49764854-49765096(-)$1	1	13	17	11.9999
))((	chr17:2588683-2588923(+)$1	1	29	33	11.9999
((((	chr2:32502922-32503162(+)$1	1	39	43	11.9999
((((	chr1:26605058-26605298(+)$1	1	35	39	11.9999
((((	chr2:27917548-27917788(+)$1	1	79	83	11.9999
((((	chr17:18709255-18709502(+)$1	1	181	185	11.9999
((.(	chr15:72534402-72534642(-)$1	1	13	17	11.9999
...)	chrX:24230350-24230590(+)$1	1	130	134	11.9999
((((	chr22:47085858-47086098(-)$1	1	42	46	11.9999
..))	chr17:34050997-34051277(+)$1	1	169	173	11.9999
)...	chr7:100278356-100278599(-)$1	1	111	115	11.9999

#PSSM
C : 0.97	c : 0.02	
C : 0.97	c : 0.02	
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011a_hg19_UTR_m2_run1.nuc.txt

#NT
UUUAA	chr1:53679585-53679809(+)$1	224	113	118	14.9999
UUUAA	chr4:90157467-90157675(-)$1	208	106	111	14.9999
UUUAA	chr5:135514109-135514358(+)$1	249	129	134	14.9999
UUUAA	chr11:9304818-9305041(-)$1	223	140	145	14.9999
UUUAA	chr11:121178962-121179185(+)$1	223	8	13	14.9999
UUUAA	chr1:203768241-203768462(+)$1	221	169	174	14.9999
UUUAA	chr11:77320470-77320697(+)$1	227	101	106	14.9999
UUUAA	chr13:41703306-41703540(-)$1	234	42	47	14.9999
UUUAA	chr7:135301348-135301570(+)$1	222	2	7	14.9999
UUUAA	chr12:123892350-123892580(+)$1	230	17	22	14.9999
UUUAA	chr1:179888694-179888916(+)$1	222	203	208	14.9999
UUUAA	chr1:36523810-36524039(+)$1	229	14	19	14.9999
UUUAA	chr1:84630353-84630572(+)$1	219	178	183	14.9999
UUUAA	chr15:101191365-101191603(+)$1	238	103	108	14.9999
UUUAA	chr3:155657844-155658070(+)$1	226	196	201	14.9999
UUUAA	chr5:129521503-129521723(-)$1	220	108	113	14.9999
UUUAA	chr20:46282743-46282964(+)$1	221	82	87	14.9999
UUUAA	chr22:41855642-41855872(-)$1	230	1	6	14.9999
UUUAA	chr6:90352452-90352670(-)$1	218	63	68	14.9999
UUUAA	chr7:138988767-138988987(+)$1	220	45	50	14.9999
UUUAA	chr1:162493911-162494137(+)$1	226	172	177	14.9999
UUUAA	chr1:184042385-184042604(+)$1	219	141	146	14.9999
UUUAA	chr1:186282902-186283132(-)$1	230	97	102	14.9999
UUUAA	chr4:89182020-89182248(-)$1	228	81	86	14.9999
UUUAA	chr6:152442890-152443113(-)$1	223	13	18	14.9999
UUUAA	chr4:125632054-125632279(-)$1	225	151	156	14.9999
UUUAA	chr10:95790397-95790620(-)$1	223	37	42	14.9999
UUUAA	chr1:28177579-28177811(+)$1	232	10	15	14.9999
UUUAA	chr17:61671307-61671543(+)$1	236	108	113	14.9999
UUUAA	chr4:123813466-123813683(+)$1	217	86	91	14.9999
UUUAA	chr6:34252098-34252325(-)$1	227	62	67	14.9999
UUUAA	chr13:33349869-33350100(+)$1	231	38	43	14.9999
UUUAA	chr12:121861706-121861936(+)$1	230	13	18	14.9999
UUUAA	chr11:71595258-71595482(-)$1	224	31	36	14.9999
UUUAA	chr2:224622813-224623047(-)$1	234	157	162	14.9999
UUUAA	chr3:69153922-69154152(+)$1	230	133	138	14.9999
UUUAA	chr4:77968932-77969165(-)$1	233	25	30	14.9999
UUUAA	chr3:167401832-167402066(-)$1	234	34	39	14.9999
uuuAA	chr1:7904109-7904337(+)$1	228	23	28	14.9999
UUUAA	chr9:135768824-135769050(-)$1	226	106	111	14.9999
UUUAA	chr11:85367445-85367675(+)$1	230	101	106	14.9999
UUUAA	chr7:156474875-156475105(-)$1	230	176	181	14.9999
UUUAA	chr14:74181762-74181993(-)$1	231	133	138	14.9999
UUUAA	chr8:133023466-133023687(+)$1	221	104	109	14.9999
UUUAA	chr17:38974280-38974500(-)$1	220	56	61	14.9999
UUUAA	chr7:39612339-39612573(+)$1	234	171	176	14.9999
UUUAA	chr8:94744021-94744251(-)$1	230	53	58	14.9999
uuuaa	chr7:63985745-63985967(-)$1	222	198	203	14.9999
UUUAA	chr7:101894555-101894785(+)$1	230	118	123	14.9999
UUUAA	chr15:83673252-83673479(-)$1	227	6	11	14.9999
UUUAA	chr8:79630538-79630768(+)$1	230	22	27	14.9999
UUUAA	chr1:165712323-165712553(-)$1	230	170	175	14.9999
UUUAA	chr7:114332328-114332537(+)$1	209	76	81	14.9999
UUUAA	chr14:60749551-60749770(+)$1	219	122	127	14.9999
UUUAA	chr1:197479476-197479701(-)$1	225	204	209	14.9999
UUUAA	chr18:48701008-48701241(-)$1	233	173	178	14.9999
UUUAA	chr8:101932305-101932527(-)$1	222	20	25	14.9999
UUUAA	chr3:120047596-120047826(-)$1	230	139	144	14.9999
UUUAA	chr14:32627140-32627357(+)$1	217	59	64	14.9999
UUUAA	chr5:148733935-148734157(+)$1	222	85	90	14.9999
UUUAA	chrX:133562574-133562811(+)$1	237	8	13	14.9999
UUUAA	chr10:225947-226169(+)$1	222	13	18	14.9999
UUUAA	chr3:123632539-123632760(-)$1	221	72	77	14.9999
UUUAA	chr3:23574051-23574284(+)$1	233	82	87	14.9999
UUUAA	chr15:78790847-78791077(+)$1	230	20	25	14.9999

#otherMatches

#Struct PSSM
::fff	chr2:10141042-10141278(+)$1	236	42	47	14.9999
iiiii	chr1:53679585-53679809(+)$1	224	113	118	14.9999
fffff	chr4:90157467-90157675(-)$1	208	106	111	14.9999
""ddd	chr5:135514109-135514358(+)$1	249	129	134	14.9999
nnddd	chr11:9304818-9305041(-)$1	223	140	145	14.9999
:::GG	chr11:121178962-121179185(+)$1	223	8	13	14.9999
DYYEE	chr1:203768241-203768462(+)$1	221	169	174	14.9999
2dddd	chr11:77320470-77320697(+)$1	227	101	106	14.9999
:::FF	chr13:41703306-41703540(-)$1	234	42	47	14.9999
::::E	chr7:135301348-135301570(+)$1	222	2	7	14.9999
MMMJJ	chr12:123892350-123892580(+)$1	230	17	22	14.9999
~~DDD	chr1:179888694-179888916(+)$1	222	203	208	14.9999
:::::	chr1:36523810-36524039(+)$1	229	14	19	14.9999
ffooo	chr1:84630353-84630572(+)$1	219	178	183	14.9999
^^^^^	chr15:101191365-101191603(+)$1	238	103	108	14.9999
@@@@@	chr3:155657844-155658070(+)$1	226	196	201	14.9999
dddpp	chr5:129521503-129521723(-)$1	220	108	113	14.9999
:::::	chr20:46282743-46282964(+)$1	221	82	87	14.9999
:::::	chr22:41855642-41855872(-)$1	230	1	6	14.9999
ooooo	chr6:90352452-90352670(-)$1	218	63	68	14.9999
ccc""	chr7:138988767-138988987(+)$1	220	45	50	14.9999
@@@@@	chr1:162493911-162494137(+)$1	226	172	177	14.9999
ppppg	chr1:184042385-184042604(+)$1	219	141	146	14.9999
$$$==	chr1:186282902-186283132(-)$1	230	97	102	14.9999
gggg]	chr4:89182020-89182248(-)$1	228	81	86	14.9999
HHH::	chr6:152442890-152443113(-)$1	223	13	18	14.9999
eeooo	chr4:125632054-125632279(-)$1	225	151	156	14.9999
ffff[	chr10:95790397-95790620(-)$1	223	37	42	14.9999
hhhhh	chr1:28177579-28177811(+)$1	232	10	15	14.9999
uuuuc	chr17:61671307-61671543(+)$1	236	108	113	14.9999
!cccc	chr4:123813466-123813683(+)$1	217	86	91	14.9999
iiii#	chr6:34252098-34252325(-)$1	227	62	67	14.9999
GGGGG	chr13:33349869-33350100(+)$1	231	38	43	14.9999
:::::	chr12:121861706-121861936(+)$1	230	13	18	14.9999
uuuuu	chr11:71595258-71595482(-)$1	224	31	36	14.9999
eee22	chr2:224622813-224623047(-)$1	234	157	162	14.9999
fmmmm	chr3:69153922-69154152(+)$1	230	133	138	14.9999
ggggm	chr4:77968932-77969165(-)$1	233	25	30	14.9999
H::::	chr3:167401832-167402066(-)$1	234	34	39	14.9999
OOODD	chr1:7904109-7904337(+)$1	228	23	28	14.9999
ff777	chr9:135768824-135769050(-)$1	226	106	111	14.9999
fff::	chr11:85367445-85367675(+)$1	230	101	106	14.9999
55eee	chr7:156474875-156475105(-)$1	230	176	181	14.9999
:::gg	chr14:74181762-74181993(-)$1	231	133	138	14.9999
:::::	chr8:133023466-133023687(+)$1	221	104	109	14.9999
eeenn	chr17:38974280-38974500(-)$1	220	56	61	14.9999
gggee	chr7:39612339-39612573(+)$1	234	171	176	14.9999
iii##	chr8:94744021-94744251(-)$1	230	53	58	14.9999
GGGGG	chr7:63985745-63985967(-)$1	222	198	203	14.9999
:::::	chr7:101894555-101894785(+)$1	230	118	123	14.9999
iiiii	chr15:83673252-83673479(-)$1	227	6	11	14.9999
fff++	chr8:79630538-79630768(+)$1	230	22	27	14.9999
II}CC	chr1:165712323-165712553(-)$1	230	170	175	14.9999
dddd:	chr7:114332328-114332537(+)$1	209	76	81	14.9999
:::::	chr14:60749551-60749770(+)$1	219	122	127	14.9999
d::::	chr1:197479476-197479701(-)$1	225	204	209	14.9999
:::::	chr18:48701008-48701241(-)$1	233	173	178	14.9999
OOOOO	chr8:101932305-101932527(-)$1	222	20	25	14.9999
eeeee	chr3:120047596-120047826(-)$1	230	139	144	14.9999
::::f	chr14:32627140-32627357(+)$1	217	59	64	14.9999
iii:G	chr5:148733935-148734157(+)$1	222	85	90	14.9999
hhlll	chrX:133562574-133562811(+)$1	237	8	13	14.9999
eeepp	chr10:225947-226169(+)$1	222	13	18	14.9999
dd22b	chr3:123632539-123632760(-)$1	221	72	77	14.9999
ggggq	chr3:23574051-23574284(+)$1	233	82	87	14.9999
bblll	chr15:78790847-78791077(+)$1	230	20	25	14.9999

#DB
..(((	chr2:10141042-10141278(+)$1	1	42	47	14.9999
(((((	chr1:53679585-53679809(+)$1	1	113	118	14.9999
)))))	chr4:90157467-90157675(-)$1	1	106	111	14.9999
..(((	chr5:135514109-135514358(+)$1	1	129	134	14.9999
..)))	chr11:9304818-9305041(-)$1	1	140	145	14.9999
...((	chr11:121178962-121179185(+)$1	1	8	13	14.9999
)..))	chr1:203768241-203768462(+)$1	1	169	174	14.9999
.))))	chr11:77320470-77320697(+)$1	1	101	106	14.9999
...((	chr13:41703306-41703540(-)$1	1	42	47	14.9999
....(	chr7:135301348-135301570(+)$1	1	2	7	14.9999
...((	chr12:123892350-123892580(+)$1	1	17	22	14.9999
..)))	chr1:179888694-179888916(+)$1	1	203	208	14.9999
.....	chr1:36523810-36524039(+)$1	1	14	19	14.9999
((...	chr1:84630353-84630572(+)$1	1	178	183	14.9999
.....	chr15:101191365-101191603(+)$1	1	103	108	14.9999
.....	chr3:155657844-155658070(+)$1	1	196	201	14.9999
(((..	chr5:129521503-129521723(-)$1	1	108	113	14.9999
.....	chr20:46282743-46282964(+)$1	1	82	87	14.9999
.....	chr22:41855642-41855872(-)$1	1	1	6	14.9999
.....	chr6:90352452-90352670(-)$1	1	63	68	14.9999
(((..	chr7:138988767-138988987(+)$1	1	45	50	14.9999
.....	chr1:162493911-162494137(+)$1	1	172	177	14.9999
....)	chr1:184042385-184042604(+)$1	1	141	146	14.9999
...((	chr1:186282902-186283132(-)$1	1	97	102	14.9999
)))).	chr4:89182020-89182248(-)$1	1	81	86	14.9999
(((..	chr6:152442890-152443113(-)$1	1	13	18	14.9999
((...	chr4:125632054-125632279(-)$1	1	151	156	14.9999
((((.	chr10:95790397-95790620(-)$1	1	37	42	14.9999
(((((	chr1:28177579-28177811(+)$1	1	10	15	14.9999
....)	chr17:61671307-61671543(+)$1	1	108	113	14.9999
.((((	chr4:123813466-123813683(+)$1	1	86	91	14.9999
((((.	chr6:34252098-34252325(-)$1	1	62	67	14.9999
(((((	chr13:33349869-33350100(+)$1	1	38	43	14.9999
.....	chr12:121861706-121861936(+)$1	1	13	18	14.9999
.....	chr11:71595258-71595482(-)$1	1	31	36	14.9999
)))..	chr2:224622813-224623047(-)$1	1	157	162	14.9999
(....	chr3:69153922-69154152(+)$1	1	133	138	14.9999
((((.	chr4:77968932-77969165(-)$1	1	25	30	14.9999
(....	chr3:167401832-167402066(-)$1	1	34	39	14.9999
...((	chr1:7904109-7904337(+)$1	1	23	28	14.9999
))...	chr9:135768824-135769050(-)$1	1	106	111	14.9999
)))..	chr11:85367445-85367675(+)$1	1	101	106	14.9999
..)))	chr7:156474875-156475105(-)$1	1	176	181	14.9999
...((	chr14:74181762-74181993(-)$1	1	133	138	14.9999
.....	chr8:133023466-133023687(+)$1	1	104	109	14.9999
(((..	chr17:38974280-38974500(-)$1	1	56	61	14.9999
)))))	chr7:39612339-39612573(+)$1	1	171	176	14.9999
(((..	chr8:94744021-94744251(-)$1	1	53	58	14.9999
)))))	chr7:63985745-63985967(-)$1	1	198	203	14.9999
.....	chr7:101894555-101894785(+)$1	1	118	123	14.9999
(((((	chr15:83673252-83673479(-)$1	1	6	11	14.9999
(((..	chr8:79630538-79630768(+)$1	1	22	27	14.9999
)).))	chr1:165712323-165712553(-)$1	1	170	175	14.9999
)))).	chr7:114332328-114332537(+)$1	1	76	81	14.9999
.....	chr14:60749551-60749770(+)$1	1	122	127	14.9999
)....	chr1:197479476-197479701(-)$1	1	204	209	14.9999
.....	chr18:48701008-48701241(-)$1	1	173	178	14.9999
.....	chr8:101932305-101932527(-)$1	1	20	25	14.9999
(((((	chr3:120047596-120047826(-)$1	1	139	144	14.9999
....(	chr14:32627140-32627357(+)$1	1	59	64	14.9999
))).(	chr5:148733935-148734157(+)$1	1	85	90	14.9999
((...	chrX:133562574-133562811(+)$1	1	8	13	14.9999
(((..	chr10:225947-226169(+)$1	1	13	18	14.9999
))..)	chr3:123632539-123632760(-)$1	1	72	77	14.9999
((((.	chr3:23574051-23574284(+)$1	1	82	87	14.9999
((...	chr15:78790847-78791077(+)$1	1	20	25	14.9999

#PSSM
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	

#score	989.9999999999999
#seq	66
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_CDS_m2_run2.nuc.txt

#NT
CCUCUG	chr8:48883895-48884128(+)$1	233	36	42	14.5000
CCCCUG	chr3:126733515-126733743(+)$1	228	14	20	11.5833
CCACUG	chr19:44111675-44111918(-)$1	243	65	71	11.1666
CCUCUG	chr1:934441-934661(-)$1	220	115	121	14.5000
CCCCUG	chr10:52066855-52067083(-)$1	228	118	124	11.5833
CCUUUG	chr17:26919555-26919775(-)$1	220	0	6	10.5833
CCUCUA	chr12:49432915-49433158(-)$1	243	132	138	11.0000
CCUCUA	chr16:3274200-3274426(-)$1	226	25	31	11.0000
CCGCUG	chr19:10799767-10799997(+)$1	230	41	47	11.0833
CCUCUG	chrM:4780-5021(+)$1	241	56	62	14.5000
CCUGUG	chr6:80201205-80201424(-)$1	219	2	8	11.0000
CCUCUG	chr1:150443845-150444065(+)$1	220	106	112	14.5000
CCACUG	chr12:22622592-22622811(-)$1	219	114	120	11.1666
CCUCUG	chr16:67267460-67267694(-)$1	234	44	50	14.5000
CCCCUG	chr8:145727149-145727370(+)$1	221	65	71	11.5833
CCUCUC	chr7:156976475-156976697(+)$1	222	3	9	11.5000
CCUCUC	chr19:1271902-1272132(+)$1	230	214	220	11.5000
CCCCUG	chr20:44578485-44578707(+)$1	222	74	80	11.5833
CCUCUU	chr11:4133105-4133325(+)$1	220	8	14	11.0000
CCUCUG	chrX:123171284-123171512(+)$1	228	80	86	14.5000
CCUCUC	chr10:60461733-60462002(-)$1	269	84	90	11.5000
ccuaug	chr8:26365360-26365582(-)$1	222	110	116	10.5833
CCUCUG	chr17:74078511-74078734(-)$1	223	178	184	14.5000
CCCCUG	chr12:1741845-1742067(+)$1	222	61	67	11.5833
CCUCUC	chr3:43122026-43122248(-)$1	222	29	35	11.5000
CCUCUG	chr1:184679514-184679734(-)$1	220	84	90	14.5000
CCUCUg	chr3:184428973-184429201(-)$1	228	42	48	14.5000
CCUCUU	chr11:62396340-62396584(-)$1	244	62	68	11.0000
CCUGUG	chr19:18391499-18391742(-)$1	243	102	108	11.0000
CCCCUG	chr19:1270846-1271110(+)$1	264	46	52	11.5833
CCUCUC	chrM:14225-14465(+)$1	240	58	64	11.5000
CCUCUG	chr8:22471812-22472032(+)$1	220	186	192	14.5000
CCUCUC	chr6:44221185-44221430(+)$1	245	102	108	11.5000
CCUUUG	chr6:136990367-136990591(-)$1	224	150	156	10.5833
CCUCUG	chr19:55815965-55816188(+)$1	223	137	143	14.5000
CCUGUG	chr19:50312386-50312614(-)$1	228	82	88	11.0000
CCCCUG	chr19:14079507-14079727(-)$1	220	70	76	11.5833
CCUCUA	chr12:66703768-66703991(+)$1	223	99	105	11.0000
CCUCUG	chr11:1784963-1785206(-)$1	243	146	152	14.5000
CCGCUG	chr1:28661204-28661426(+)$1	222	176	182	11.0833
CCUCUG	chr19:1432517-1432743(+)$1	226	81	87	14.5000
CCUCUG	chr5:68716053-68716274(+)$1	221	115	121	14.5000
CCUCUG	chr18:29848168-29848404(-)$1	236	172	178	14.5000
CCUCUU	chr14:96773027-96773248(-)$1	221	41	47	11.0000
CCUAUG	chr17:1585373-1585599(-)$1	226	61	67	10.5833
CCACUG	chr12:25362020-25362256(-)$1	236	81	87	11.1666
CCUCUC	chr6:31593151-31593378(+)$1	227	58	64	11.5000
CCUGUG	chrX:135288512-135288733(+)$1	221	17	23	11.0000
CCCCUG	chr17:17080551-17080781(+)$1	230	145	151	11.5833
CCACUG	chr2:152320251-152320475(+)$1	224	65	71	11.1666
CCUCUG	chr17:42153191-42153416(+)$1	225	132	138	14.5000
CCUGUG	chr6:155145354-155145580(+)$1	226	64	70	11.0000
CCUCUC	chr17:37565176-37565407(-)$1	231	166	172	11.5000
CCUCUG	chr1:214625118-214625344(-)$1	226	93	99	14.5000
CCUGUG	chr9:131757083-131757303(+)$1	220	67	73	11.0000
CCGCUG	chr12:113610115-113610334(-)$1	219	110	116	11.0833
CCUCUG	chr7:99123346-99123568(+)$1	222	74	80	14.5000
CCUGUG	chr2:74692010-74692234(-)$1	224	94	100	11.0000
CCUCUC	chr10:85909855-85910074(+)$1	219	46	52	11.5000

#otherMatches

#Struct PSSM
GGGG??	chr17:47117230-47117459(+)$1	229	150	156	11.5833
DD{CCC	chr8:48883895-48884128(+)$1	233	36	42	14.5000
ffff:G	chr3:126733515-126733743(+)$1	228	14	20	11.5833
HHHHHH	chr19:44111675-44111918(-)$1	243	65	71	11.1666
GGGGGG	chr1:934441-934661(-)$1	220	115	121	14.5000
ggggbb	chr10:52066855-52067083(-)$1	228	118	124	11.5833
:::BB{	chr17:26919555-26919775(-)$1	220	0	6	10.5833
ccnnnn	chr12:49432915-49433158(-)$1	243	132	138	11.0000
cnnnnn	chr16:3274200-3274426(-)$1	226	25	31	11.0000
]bb===	chr19:10799767-10799997(+)$1	230	41	47	11.0833
::::::	chrM:4780-5021(+)$1	241	56	62	14.5000
:::::D	chr6:80201205-80201424(-)$1	219	2	8	11.0000
:eeeee	chr1:150443845-150444065(+)$1	220	106	112	14.5000
3bb::g	chr12:22622592-22622811(-)$1	219	114	120	11.1666
DDDKKE	chr16:67267460-67267694(-)$1	234	44	50	14.5000
bbgggg	chr8:145727149-145727370(+)$1	221	65	71	11.5833
FFFFF{	chr7:156976475-156976697(+)$1	222	3	9	11.5000
JJJJ}B	chr19:1271902-1272132(+)$1	230	214	220	11.5000
cccccc	chr20:44578485-44578707(+)$1	222	74	80	11.5833
::ffff	chr11:4133105-4133325(+)$1	220	8	14	11.0000
::::gg	chrX:123171284-123171512(+)$1	228	80	86	14.5000
c"""bb	chr10:60461733-60462002(-)$1	269	84	90	11.5000
cccbb]	chr8:26365360-26365582(-)$1	222	110	116	10.5833
ffffdd	chr17:74078511-74078734(-)$1	223	178	184	14.5000
ggggge	chr12:1741845-1742067(+)$1	222	61	67	11.5833
eee'''	chr3:43122026-43122248(-)$1	222	29	35	11.5000
ffccc%	chr1:184679514-184679734(-)$1	220	84	90	14.5000
eeeeel	chr3:184428973-184429201(-)$1	228	42	48	14.5000
::::::	chr11:62396340-62396584(-)$1	244	62	68	11.0000
hhhhhh	chr19:18391499-18391742(-)$1	243	102	108	11.0000
bggggg	chr19:1270846-1271110(+)$1	264	46	52	11.5833
ssssss	chrM:14225-14465(+)$1	240	58	64	11.5000
BBBB}A	chr8:22471812-22472032(+)$1	220	186	192	14.5000
ddddcc	chr6:44221185-44221430(+)$1	245	102	108	11.5000
((eeee	chr6:136990367-136990591(-)$1	224	150	156	10.5833
oooooa	chr19:55815965-55816188(+)$1	223	137	143	14.5000
eeee]e	chr19:50312386-50312614(-)$1	228	82	88	11.0000
((((ff	chr19:14079507-14079727(-)$1	220	70	76	11.5833
>>>>>>	chr12:66703768-66703991(+)$1	223	99	105	11.0000
ca]ccc	chr11:1784963-1785206(-)$1	243	146	152	14.5000
dddd]c	chr1:28661204-28661426(+)$1	222	176	182	11.0833
%%%%%c	chr19:1432517-1432743(+)$1	226	81	87	14.5000
fmmmmf	chr5:68716053-68716274(+)$1	221	115	121	14.5000
pppppp	chr18:29848168-29848404(-)$1	236	172	178	14.5000
rrra22	chr14:96773027-96773248(-)$1	221	41	47	11.0000
ddddnn	chr17:1585373-1585599(-)$1	226	61	67	10.5833
FFF{DD	chr12:25362020-25362256(-)$1	236	81	87	11.1666
$$ccc^	chr6:31593151-31593378(+)$1	227	58	64	11.5000
H::JJJ	chrX:135288512-135288733(+)$1	221	17	23	11.0000
eeee33	chr17:17080551-17080781(+)$1	230	145	151	11.5833
d22eee	chr2:152320251-152320475(+)$1	224	65	71	11.1666
::IIII	chr17:42153191-42153416(+)$1	225	132	138	14.5000
rrrrrr	chr6:155145354-155145580(+)$1	226	64	70	11.0000
::::::	chr17:37565176-37565407(-)$1	231	166	172	11.5000
hh333d	chr1:214625118-214625344(-)$1	226	93	99	14.5000
CCC{DD	chr9:131757083-131757303(+)$1	220	67	73	11.0000
bboooo	chr12:113610115-113610334(-)$1	219	110	116	11.0833
eee"""	chr7:99123346-99123568(+)$1	222	74	80	14.5000
555ccc	chr2:74692010-74692234(-)$1	224	94	100	11.0000
ggg[ff	chr10:85909855-85910074(+)$1	219	46	52	11.5000

#DB
))))..	chr17:47117230-47117459(+)$1	1	150	156	11.5833
((.(((	chr8:48883895-48884128(+)$1	1	36	42	14.5000
)))).(	chr3:126733515-126733743(+)$1	1	14	20	11.5833
((((((	chr19:44111675-44111918(-)$1	1	65	71	11.1666
))))))	chr1:934441-934661(-)$1	1	115	121	14.5000
((((((	chr10:52066855-52067083(-)$1	1	118	124	11.5833
...((.	chr17:26919555-26919775(-)$1	1	0	6	10.5833
((....	chr12:49432915-49433158(-)$1	1	132	138	11.0000
(.....	chr16:3274200-3274426(-)$1	1	25	31	11.0000
.))(((	chr19:10799767-10799997(+)$1	1	41	47	11.0833
......	chrM:4780-5021(+)$1	1	56	62	14.5000
.....(	chr6:80201205-80201424(-)$1	1	2	8	11.0000
.(((((	chr1:150443845-150444065(+)$1	1	106	112	14.5000
.))..(	chr12:22622592-22622811(-)$1	1	114	120	11.1666
(((..(	chr16:67267460-67267694(-)$1	1	44	50	14.5000
))))))	chr8:145727149-145727370(+)$1	1	65	71	11.5833
(((((.	chr7:156976475-156976697(+)$1	1	3	9	11.5000
)))).)	chr19:1271902-1272132(+)$1	1	214	220	11.5000
((((((	chr20:44578485-44578707(+)$1	1	74	80	11.5833
..((((	chr11:4133105-4133325(+)$1	1	8	14	11.0000
....((	chrX:123171284-123171512(+)$1	1	80	86	14.5000
(...((	chr10:60461733-60462002(-)$1	1	84	90	11.5000
))))).	chr8:26365360-26365582(-)$1	1	110	116	10.5833
((((((	chr17:74078511-74078734(-)$1	1	178	184	14.5000
((((((	chr12:1741845-1742067(+)$1	1	61	67	11.5833
(((...	chr3:43122026-43122248(-)$1	1	29	35	11.5000
(((((.	chr1:184679514-184679734(-)$1	1	84	90	14.5000
(((((.	chr3:184428973-184429201(-)$1	1	42	48	14.5000
......	chr11:62396340-62396584(-)$1	1	62	68	11.0000
))))))	chr19:18391499-18391742(-)$1	1	102	108	11.0000
))))))	chr19:1270846-1271110(+)$1	1	46	52	11.5833
......	chrM:14225-14465(+)$1	1	58	64	11.5000
)))).)	chr8:22471812-22472032(+)$1	1	186	192	14.5000
((((((	chr6:44221185-44221430(+)$1	1	102	108	11.5000
..((((	chr6:136990367-136990591(-)$1	1	150	156	10.5833
.....)	chr19:55815965-55816188(+)$1	1	137	143	14.5000
)))).)	chr19:50312386-50312614(-)$1	1	82	88	11.0000
....((	chr19:14079507-14079727(-)$1	1	70	76	11.5833
......	chr12:66703768-66703991(+)$1	1	99	105	11.0000
)).)))	chr11:1784963-1785206(-)$1	1	146	152	14.5000
)))).)	chr1:28661204-28661426(+)$1	1	176	182	11.0833
.....(	chr19:1432517-1432743(+)$1	1	81	87	14.5000
(....)	chr5:68716053-68716274(+)$1	1	115	121	14.5000
......	chr18:29848168-29848404(-)$1	1	172	178	14.5000
...)..	chr14:96773027-96773248(-)$1	1	41	47	11.0000
((((..	chr17:1585373-1585599(-)$1	1	61	67	10.5833
(((.((	chr12:25362020-25362256(-)$1	1	81	87	11.1666
..(((.	chr6:31593151-31593378(+)$1	1	58	64	11.5000
(..(((	chrX:135288512-135288733(+)$1	1	17	23	11.0000
))))..	chr17:17080551-17080781(+)$1	1	145	151	11.5833
)..)))	chr2:152320251-152320475(+)$1	1	65	71	11.1666
..))))	chr17:42153191-42153416(+)$1	1	132	138	14.5000
......	chr6:155145354-155145580(+)$1	1	64	70	11.0000
......	chr17:37565176-37565407(-)$1	1	166	172	11.5000
))...)	chr1:214625118-214625344(-)$1	1	93	99	14.5000
(((.((	chr9:131757083-131757303(+)$1	1	67	73	11.0000
((....	chr12:113610115-113610334(-)$1	1	110	116	11.0833
(((...	chr7:99123346-99123568(+)$1	1	74	80	14.5000
...)))	chr2:74692010-74692234(-)$1	1	94	100	11.0000
(((.((	chr10:85909855-85910074(+)$1	1	46	52	11.5000

#PSSM
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
U : 0.71	C : 0.15	A : 0.06	G : 0.05	u : 0.01	
C : 0.81	G : 0.11	U : 0.03	a : 0.01	A : 0.01	
U : 0.98	u : 0.01	
G : 0.71	C : 0.15	A : 0.05	U : 0.05	g : 0.03	

#score	732.0000000000007
#seq	60
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_UTR_m1_run1.nuc.txt

#NT
UUUUAAUUUCCU	chr6:116918331-116918558(+)$1	227	101	113	18.4999
UUUUCAUUUUUU	chr10:5805114-5805352(+)$1	238	16	28	23.7631
UUAGAAUUUUUU	chr10:119038496-119038733(-)$1	237	44	56	18.4999
UUCAAAUUUUUU	chr6:82914512-82914745(-)$1	233	1	13	18.1052
UUUUAAAUUUUU	chr4:15646201-15646431(-)$1	230	82	94	23.4999
uuuuacuuuuuu	chr19:2273195-2273424(+)$1	229	124	136	23.1052
UUUAAACUUUUU	chr11:110036547-110036789(+)$1	242	106	118	19.2894
UUUUUUUUUUUU	chr13:100617351-100617573(-)$1	222	133	145	21.6578
CUAUAAUUUUUU	chr6:144150772-144150998(+)$1	226	102	114	17.9736
UUUGAAUUUUUU	chr6:89322114-89322335(-)$1	221	11	23	22.1842
UCUUAAUUUUAU	chr2:191798374-191798606(+)$1	232	115	127	18.3684
UUUUAAUCUUUU	chr7:139251140-139251372(-)$1	232	102	114	21.9210
UUUUACUUUUUG	chr19:37035224-37035457(-)$1	233	185	197	18.6315
UGUUUACUUUUU	chr1:78343076-78343300(+)$1	224	97	109	17.3157
UUUUCACUUUAU	chrX:24003172-24003414(-)$1	242	100	112	16.7894
UUUUCUUUUUUU	chr12:16056057-16056298(+)$1	241	219	231	21.2631
uuuuaauauuuu	chr3:120114982-120115215(-)$1	233	136	148	22.0526
UUUUCAUUUGUU	chr6:56357052-56357295(-)$1	243	23	35	20.0789
UUUUUAUUUUUA	chr11:117040212-117040439(+)$1	227	203	215	19.6842
UGUUAAUUUAUU	chr6:149982613-149982848(-)$1	235	143	155	18.8947
uuuuuauuuuuu	chr1:211840094-211840320(-)$1	226	166	178	24.1578
UUUUUUUUUUUU	chr3:57913464-57913701(+)$1	237	205	217	21.6578
UUUUUAUUUCUU	chr6:18225185-18225415(-)$1	230	80	92	20.6052
UUUUAUUUAUUU	chr8:90938365-90938594(+)$1	229	5	17	19.6842
UUUUAAAUUUUC	chr5:65475424-65475674(+)$1	250	20	32	19.0263
UUAUAAAUUAUU	chr11:9304520-9304748(-)$1	228	13	25	16.2631
UUUUUAUUUGUU	chr18:77897290-77897514(+)$1	224	31	43	20.4736
UUAUAACUUUUU	chr3:160119734-160119966(+)$1	232	170	182	19.8157
UUUUAGUUAUUU	chrX:131338573-131338801(-)$1	228	204	216	18.7631
uuuuaauuuuuu	chr12:120899559-120899795(-)$1	236	75	87	26.3947
UUUUAUUAUUUU	chr11:119170656-119170879(+)$1	223	18	30	19.5526
UUGUAAGUUUUU	chr6:151677487-151677717(+)$1	230	213	225	18.8947
UUUUUUUUUUUU	chr4:177249515-177249770(+)$1	255	72	84	21.6578
UAUUAAAUAUUU	chr20:34238059-34238285(-)$1	226	15	27	15.3421
UAUUAUCUUUUU	chr5:167978204-167978429(-)$1	225	85	97	17.0526
UUUUAAAUUAUU	chr16:20808613-20808833(-)$1	220	26	38	19.9473
UCUUAAUUUCUU	chr1:222840505-222840731(-)$1	226	106	118	18.8947

#otherMatches

#Struct PSSM
###hhhhhhhh"	chr20:43119152-43119380(+)$1	228	114	126	17.1842
ffff]eeeee]d	chr6:116918331-116918558(+)$1	227	101	113	18.4999
hmmmmhhhhhhh	chr10:5805114-5805352(+)$1	238	16	28	23.7631
fggggggg[ddd	chr10:119038496-119038733(-)$1	237	44	56	18.4999
:::::::::hhh	chr6:82914512-82914745(-)$1	233	1	13	18.1052
]dddd22ccc]c	chr4:15646201-15646431(-)$1	230	82	94	23.4999
fffff666666=	chr19:2273195-2273424(+)$1	229	124	136	23.1052
^^^^^^^^^^^^	chr11:110036547-110036789(+)$1	242	106	118	19.2894
ffffff[ccc[e	chr13:100617351-100617573(-)$1	222	133	145	21.6578
ccc[ccc!!ddd	chr6:144150772-144150998(+)$1	226	102	114	17.9736
::::========	chr6:89322114-89322335(-)$1	221	11	23	22.1842
[awwwwwwwwww	chr2:191798374-191798606(+)$1	232	115	127	18.3684
ssssseeeee::	chr7:139251140-139251372(-)$1	232	102	114	21.9210
gggqqqqqqqqg	chr19:37035224-37035457(-)$1	233	185	197	18.6315
dddduuuuuuuu	chr1:78343076-78343300(+)$1	224	97	109	17.3157
C:::::::::::	chrX:24003172-24003414(-)$1	242	100	112	16.7894
uuuuuuuuhhhh	chr12:16056057-16056298(+)$1	241	219	231	21.2631
qqqffffff:::	chr3:120114982-120115215(-)$1	233	136	148	22.0526
GGGGGKKBB{HH	chr6:56357052-56357295(-)$1	243	23	35	20.0789
ffffff:HHHHH	chr11:117040212-117040439(+)$1	227	203	215	19.6842
:::hhhhhhhhc	chr6:149982613-149982848(-)$1	235	143	155	18.8947
::hhhhhhhhmm	chr1:211840094-211840320(-)$1	226	166	178	24.1578
=========mmm	chr3:57913464-57913701(+)$1	237	205	217	21.6578
tttttttttddd	chr6:18225185-18225415(-)$1	230	80	92	20.6052
HHH::::::::d	chr8:90938365-90938594(+)$1	229	5	17	19.6842
::::::::::::	chr5:65475424-65475674(+)$1	250	20	32	19.0263
deeeeemmmmee	chr11:9304520-9304748(-)$1	228	13	25	16.2631
ggggggg22ddd	chr18:77897290-77897514(+)$1	224	31	43	20.4736
::::::::::::	chr3:160119734-160119966(+)$1	232	170	182	19.8157
hh::JJJJJJJJ	chrX:131338573-131338801(-)$1	228	204	216	18.7631
###bb[======	chr12:120899559-120899795(-)$1	236	75	87	26.3947
iiiiiii:::::	chr11:119170656-119170879(+)$1	223	18	30	19.5526
oooooggggggg	chr6:151677487-151677717(+)$1	230	213	225	18.8947
ggggg^^^^^^^	chr4:177249515-177249770(+)$1	255	72	84	21.6578
:::::::::::C	chr20:34238059-34238285(-)$1	226	15	27	15.3421
gggggggppppp	chr5:167978204-167978429(-)$1	225	85	97	17.0526
ggggg!!ccc[e	chr16:20808613-20808833(-)$1	220	26	38	19.9473
c]eeeee]dddd	chr1:222840505-222840731(-)$1	226	106	118	18.8947

#DB
...((((((((.	chr20:43119152-43119380(+)$1	1	114	126	17.1842
)))).))))).)	chr6:116918331-116918558(+)$1	1	101	113	18.4999
(....)))))))	chr10:5805114-5805352(+)$1	1	16	28	23.7631
((((((((.(((	chr10:119038496-119038733(-)$1	1	44	56	18.4999
.........(((	chr6:82914512-82914745(-)$1	1	1	13	18.1052
.))))..))).)	chr4:15646201-15646431(-)$1	1	82	94	23.4999
)))))......)	chr19:2273195-2273424(+)$1	1	124	136	23.1052
............	chr11:110036547-110036789(+)$1	1	106	118	19.2894
((((((.(((.(	chr13:100617351-100617573(-)$1	1	133	145	21.6578
(((.(((..(((	chr6:144150772-144150998(+)$1	1	102	114	17.9736
....((((((((	chr6:89322114-89322335(-)$1	1	11	23	22.1842
.(..........	chr2:191798374-191798606(+)$1	1	115	127	18.3684
.....)))))..	chr7:139251140-139251372(-)$1	1	102	114	21.9210
(((........)	chr19:37035224-37035457(-)$1	1	185	197	18.6315
((((........	chr1:78343076-78343300(+)$1	1	97	109	17.3157
)...........	chrX:24003172-24003414(-)$1	1	100	112	16.7894
........))))	chr12:16056057-16056298(+)$1	1	219	231	21.2631
...))))))...	chr3:120114982-120115215(-)$1	1	136	148	22.0526
(((((..((.((	chr6:56357052-56357295(-)$1	1	23	35	20.0789
)))))).)))))	chr11:117040212-117040439(+)$1	1	203	215	19.6842
...(((((((((	chr6:149982613-149982848(-)$1	1	143	155	18.8947
..((((((((..	chr1:211840094-211840320(-)$1	1	166	178	24.1578
(((((((((...	chr3:57913464-57913701(+)$1	1	205	217	21.6578
.........)))	chr6:18225185-18225415(-)$1	1	80	92	20.6052
(((........(	chr8:90938365-90938594(+)$1	1	5	17	19.6842
............	chr5:65475424-65475674(+)$1	1	20	32	19.0263
((((((....))	chr11:9304520-9304748(-)$1	1	13	25	16.2631
)))))))..)))	chr18:77897290-77897514(+)$1	1	31	43	20.4736
............	chr3:160119734-160119966(+)$1	1	170	182	19.8157
))..))))))))	chrX:131338573-131338801(-)$1	1	204	216	18.7631
...((.((((((	chr12:120899559-120899795(-)$1	1	75	87	26.3947
))))))).....	chr11:119170656-119170879(+)$1	1	18	30	19.5526
.....)))))))	chr6:151677487-151677717(+)$1	1	213	225	18.8947
(((((.......	chr4:177249515-177249770(+)$1	1	72	84	21.6578
...........(	chr20:34238059-34238285(-)$1	1	15	27	15.3421
(((((((.....	chr5:167978204-167978429(-)$1	1	85	97	17.0526
(((((..(((.(	chr16:20808613-20808833(-)$1	1	26	38	19.9473
).))))).))))	chr1:222840505-222840731(-)$1	1	106	118	18.8947

#PSSM
U : 0.86	u : 0.10	C : 0.02	
U : 0.73	u : 0.10	C : 0.05	G : 0.05	A : 0.05	
U : 0.73	A : 0.10	u : 0.10	C : 0.02	G : 0.02	
U : 0.78	u : 0.10	G : 0.05	A : 0.05	
A : 0.57	U : 0.18	C : 0.13	a : 0.07	u : 0.02	
A : 0.63	U : 0.21	a : 0.07	c : 0.02	C : 0.02	G : 0.02	
U : 0.60	A : 0.13	C : 0.13	u : 0.10	G : 0.02	
U : 0.84	u : 0.07	C : 0.02	a : 0.02	A : 0.02	
U : 0.81	u : 0.10	A : 0.07	
U : 0.68	u : 0.10	C : 0.07	A : 0.07	G : 0.05	
U : 0.78	u : 0.10	A : 0.07	C : 0.02	
U : 0.81	u : 0.10	G : 0.02	A : 0.02	C : 0.02	

#score	756.947368421052
#seq	38
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_CDS_m3_run2.nuc.txt

#NT
AAGUCACCAUCGCACAGGGUGGCGUCCUGCCCAACAUCCAGGCCGUGCUACUGCCCAAGAAGACCGAGAGCCACCACAAGGCGAAGGGCAAGUAGAAGCCUGGAUUAGUUUGCAGCAACUCAAUCCCAAAGGAACCAAAGGCUCUUUUCAGAGCCACCUACAAUUUUGUGGAAGAACUGAGCACUAUGUUUAAUGUAAUUUCUCGUCUUUGCCUACUUCUAAACCACUCCAAAGGUUACGUAGAUC	chr6:27776265-27776543(+)$1	278	20	266	315.5000

#otherMatches

#Struct PSSM
::FFFFFFQQQQQQQQCCCKKDDDDSSSSSSSSSSFFFFFF::::::fffffflllffffff:::::ccclllccc::FFFFFF{A{DDDD:bb!!dddd[ffffff####bbssssssssssbb55555ffffffdddd22bb:::::::::ccc[ccc!!dddd[ddddnnnnndddddddd22cccccc:bbqqqqqqqqbb::DDDD}A}FFFFFF?????FFFFFFDDDD}CCC\\\\\\\	chr12:112843631-112843890(-)$1	259	0	246	315.5000
!!ffffffrrrrrrrrrffffff4444ffffff::hhhhhhhh####eeeeedddd+++++++++++++cccpppppppccc333dddd]eeeee22hhhhhhhh:FFFFFF}CCC:::::::cccmmmmcccCCC:::ffffffmmmmffffff:::ddddmmmmddddEEEEE{DDDDLLLFFFFFF:::::ddddssssssssssdddd:::::::::ddddqqqqqqqqddddFFFFFF}DD	chr6:27776265-27776543(+)$1	278	20	266	315.5000

#DB
..((((((........(((..((((..........((((((......((((((...)))))).....(((...)))..((((((.(.((((.((..((((.((((((....((..........)).....))))))))))..)).........(((.(((..((((.((((.....))))))))..)))))).((........))..)))).).)))))).....)))))))))).))).......	chr12:112843631-112843890(-)$1	1	0	246	315.5000
..((((((.........))))))....))))))..((((((((....(((((((((.............(((.......)))...)))).)))))..)))))))).)))))).))).......(((....)))(((...((((((....))))))...((((....))))(((((.((((...((((((.....((((..........)))).........((((........)))))))))).))	chr6:27776265-27776543(+)$1	1	20	266	315.5000

#PSSM
A : 1.00	
U : 0.50	A : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
U : 0.50	G : 0.50	
U : 1.00	
G : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
C : 0.50	G : 0.50	
C : 1.00	
C : 1.00	
C : 0.50	G : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
G : 1.00	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 1.00	
A : 1.00	
A : 1.00	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 0.50	G : 0.50	
A : 0.50	C : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
G : 0.50	U : 0.50	
A : 1.00	
A : 0.50	G : 0.50	
A : 1.00	
U : 0.50	A : 0.50	
U : 0.50	G : 0.50	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 1.00	
C : 0.50	G : 0.50	
A : 0.50	G : 0.50	
U : 0.50	A : 0.50	
U : 1.00	
G : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
C : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
G : 0.50	U : 0.50	
A : 0.50	C : 0.50	
U : 0.50	C : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
G : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
U : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
U : 0.50	G : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
C : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	G : 0.50	
G : 0.50	A : 0.50	
A : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
C : 1.00	
U : 1.00	
G : 0.50	A : 0.50	
C : 0.50	U : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
C : 0.50	A : 0.50	
C : 0.50	U : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
A : 1.00	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 1.00	
G : 1.00	
A : 0.50	C : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
A : 1.00	
C : 0.50	A : 0.50	
A : 1.00	
C : 1.00	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
A : 1.00	
G : 0.50	C : 0.50	
U : 0.50	G : 0.50	
U : 1.00	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
A : 0.50	U : 0.50	
C : 1.00	

#score	631.0
#seq	2
#width	246
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_CAPRIN1_Baltz2012d_hg19_UTR_m1_run2.nuc.txt

#NT
UUG	chr12:27876879-27877139(+)$1	260	1	4	9.0000
UUG	chr5:133291276-133291520(-)$1	244	8	11	9.0000
UUG	chr12:51213461-51213740(+)$1	279	18	21	9.0000
UUG	chrX:119391107-119391410(+)$1	303	23	26	9.0000
UUG	chr5:10680640-10680867(-)$1	227	11	14	9.0000
UUG	chr12:118582496-118582738(+)$1	242	121	124	9.0000
UUG	chr19:33873084-33873310(+)$1	226	7	10	9.0000
UUG	chr16:81415625-81415874(+)$1	249	7	10	9.0000
UUG	chrX:135292608-135292849(+)$1	241	95	98	9.0000
UUG	chr3:107526196-107526425(+)$1	229	17	20	9.0000
UUG	chr15:77338753-77339053(-)$1	300	5	8	9.0000
UUG	chr1:229459405-229459635(-)$1	230	0	3	9.0000
UUG	chr19:1435161-1435384(+)$1	223	40	43	9.0000
UUG	chr1:1716803-1717071(-)$1	268	14	17	9.0000
UUG	chr1:155708037-155708359(+)$1	322	97	100	9.0000
UUG	chr15:90414641-90414868(-)$1	227	29	32	9.0000
UUG	chr10:59955621-59955842(-)$1	221	2	5	9.0000
UUG	chr1:67873435-67873659(-)$1	224	58	61	9.0000
UUG	chr11:43877190-43877411(+)$1	221	16	19	9.0000
UUG	chr8:22880067-22880319(-)$1	252	28	31	9.0000
UUG	chr19:10800681-10800906(+)$1	225	102	105	9.0000
UUG	chr11:118964591-118964885(-)$1	294	16	19	9.0000
UUG	chr16:2821410-2821638(-)$1	228	97	100	9.0000
UUG	chr12:121137907-121138163(+)$1	256	46	49	9.0000
UUG	chr5:132440134-132440397(+)$1	263	3	6	9.0000
UUG	chr19:47656107-47656357(+)$1	250	7	10	9.0000
UUG	chr5:112354395-112354648(+)$1	253	10	13	9.0000
UUG	chr17:40023645-40023938(-)$1	293	107	110	9.0000
UUG	chr3:196662900-196663127(-)$1	227	18	21	9.0000
UUG	chrX:123234514-123234747(+)$1	233	76	79	9.0000
UUG	chr5:162871734-162872001(+)$1	267	50	53	9.0000
UUG	chr20:25426496-25426776(+)$1	280	50	53	9.0000
UUG	chr13:98117921-98118218(+)$1	297	26	29	9.0000
UUG	chr20:34319373-34319607(-)$1	234	31	34	9.0000
UUG	chr22:19838410-19838639(-)$1	229	4	7	9.0000
UUG	chr17:45195663-45195887(-)$1	224	48	51	9.0000
UUG	chr7:138983578-138983804(+)$1	226	14	17	9.0000
UUG	chr8:22880222-22880505(-)$1	283	32	35	9.0000
UUG	chr19:16757143-16757384(-)$1	241	10	13	9.0000
UUG	chr10:73993089-73993349(+)$1	260	40	43	9.0000
UUG	chr17:76168243-76168493(+)$1	250	216	219	9.0000
UUG	chr1:205685451-205685871(-)$1	420	16	19	9.0000
UUG	chr13:41701841-41702065(-)$1	224	7	10	9.0000
UUG	chr8:42691781-42692007(-)$1	226	20	23	9.0000
UUG	chr14:78182056-78182295(+)$1	239	46	49	9.0000
UUG	chr10:121334709-121334966(-)$1	257	58	61	9.0000
UUG	chr11:16760243-16760464(+)$1	221	0	3	9.0000
UUG	chrX:106893954-106894210(+)$1	256	4	7	9.0000
UUG	chr6:91225556-91225800(-)$1	244	60	63	9.0000
UUG	chr5:64962074-64962295(-)$1	221	10	13	9.0000
uug	chr7:133978385-133978635(-)$1	250	10	13	9.0000
UUG	chr2:174773806-174774034(-)$1	228	19	22	9.0000
UUG	chr17:15931628-15931895(+)$1	267	105	108	9.0000
UUG	chr1:183596078-183596302(-)$1	224	10	13	9.0000
UUG	chr2:198416440-198416667(+)$1	227	6	9	9.0000
UUG	chr14:103807242-103807556(+)$1	314	1	4	9.0000
UUG	chr22:42078282-42078568(-)$1	286	99	102	9.0000
UUG	chr8:37611762-37612017(+)$1	255	97	100	9.0000
UUG	chr3:113439167-113439443(-)$1	276	18	21	9.0000
uuG	chr4:31147244-31147469(+)$1	225	32	35	9.0000
UUG	chr17:30327201-30327460(+)$1	259	10	13	9.0000
UUG	chr1:213167034-213167262(-)$1	228	15	18	9.0000
UUG	chr11:118888891-118889146(-)$1	255	33	36	9.0000
UUG	chr1:39330111-39330334(-)$1	223	6	9	9.0000
UUG	chr6:11136331-11136609(+)$1	278	15	18	9.0000
UUG	chr1:235295037-235295268(-)$1	231	76	79	9.0000
UUG	chr1:162494452-162494686(+)$1	234	54	57	9.0000
UUG	chr11:61732136-61732363(-)$1	227	0	3	9.0000
UUG	chrX:70795040-70795266(+)$1	226	4	7	9.0000
uug	chr7:114657046-114657269(+)$1	223	33	36	9.0000
UUG	chr6:26104348-26104610(+)$1	262	244	247	9.0000
UUG	chr17:57119101-57119324(-)$1	223	23	26	9.0000
UUG	chr1:12072780-12073009(+)$1	229	6	9	9.0000
UUG	chr7:99689626-99689897(+)$1	271	29	32	9.0000
UUG	chr16:19564602-19564826(+)$1	224	6	9	9.0000
UUG	chr1:150547251-150547496(-)$1	245	36	39	9.0000
UUG	chr7:112461613-112461852(-)$1	239	97	100	9.0000
UUG	chr3:32525319-32525580(-)$1	261	25	28	9.0000
UUG	chr16:89630254-89630544(+)$1	290	91	94	9.0000
UUG	chr19:3578912-3579164(+)$1	252	1	4	9.0000
UUG	chr9:115449061-115449292(-)$1	231	78	81	9.0000
UUG	chr10:63855803-63856044(+)$1	241	56	59	9.0000
UUG	chr14:32626551-32626775(+)$1	224	61	64	9.0000
UUG	chrX:106893452-106893692(+)$1	240	22	25	9.0000
UUG	chr5:31535811-31536046(+)$1	235	16	19	9.0000
UUG	chr15:48634337-48634596(+)$1	259	1	4	9.0000
UUG	chr14:23395241-23395493(-)$1	252	27	30	9.0000
UUG	chr9:138395992-138396278(+)$1	286	78	81	9.0000
UUG	chr4:2517184-2517407(+)$1	223	6	9	9.0000
UUG	chr19:12256618-12256896(-)$1	278	157	160	9.0000
UUG	chr3:113503496-113503742(+)$1	246	1	4	9.0000
UUG	chr11:73583884-73584190(-)$1	306	146	149	9.0000
UUG	chr1:32799894-32800123(-)$1	229	41	44	9.0000
UUG	chr20:34238535-34238804(-)$1	269	59	62	9.0000
UUG	chr16:75664256-75664506(-)$1	250	84	87	9.0000
UUG	chr16:2821095-2821341(+)$1	246	17	20	9.0000
UUG	chr4:83276373-83276622(-)$1	249	54	57	9.0000
UUG	chr15:44086672-44086900(+)$1	228	16	19	9.0000
UUG	chr15:77338334-77338607(-)$1	273	6	9	9.0000

#otherMatches

#Struct PSSM
FFF	chr6:149690959-149691191(+)$1	232	6	9	9.0000
DDD	chr12:27876879-27877139(+)$1	260	1	4	9.0000
::e	chr5:133291276-133291520(-)$1	244	8	11	9.0000
EE{	chr12:51213461-51213740(+)$1	279	18	21	9.0000
FFF	chrX:119391107-119391410(+)$1	303	23	26	9.0000
III	chr5:10680640-10680867(-)$1	227	11	14	9.0000
hhh	chr12:118582496-118582738(+)$1	242	121	124	9.0000
::f	chr19:33873084-33873310(+)$1	226	7	10	9.0000
FFF	chr16:81415625-81415874(+)$1	249	7	10	9.0000
hh:	chrX:135292608-135292849(+)$1	241	95	98	9.0000
CCd	chr3:107526196-107526425(+)$1	229	17	20	9.0000
::c	chr15:77338753-77339053(-)$1	300	5	8	9.0000
:::	chr1:229459405-229459635(-)$1	230	0	3	9.0000
qqd	chr19:1435161-1435384(+)$1	223	40	43	9.0000
:GG	chr1:1716803-1717071(-)$1	268	14	17	9.0000
eee	chr1:155708037-155708359(+)$1	322	97	100	9.0000
::g	chr15:90414641-90414868(-)$1	227	29	32	9.0000
:::	chr10:59955621-59955842(-)$1	221	2	5	9.0000
###	chr1:67873435-67873659(-)$1	224	58	61	9.0000
:dd	chr11:43877190-43877411(+)$1	221	16	19	9.0000
EEE	chr8:22880067-22880319(-)$1	252	28	31	9.0000
!dd	chr19:10800681-10800906(+)$1	225	102	105	9.0000
FFD	chr11:118964591-118964885(-)$1	294	16	19	9.0000
gg2	chr16:2821410-2821638(-)$1	228	97	100	9.0000
KKH	chr12:121137907-121138163(+)$1	256	46	49	9.0000
GGG	chr5:132440134-132440397(+)$1	263	3	6	9.0000
hhh	chr19:47656107-47656357(+)$1	250	7	10	9.0000
:::	chr5:112354395-112354648(+)$1	253	10	13	9.0000
fff	chr17:40023645-40023938(-)$1	293	107	110	9.0000
GGG	chr3:196662900-196663127(-)$1	227	18	21	9.0000
ddd	chrX:123234514-123234747(+)$1	233	76	79	9.0000
"dd	chr5:162871734-162872001(+)$1	267	50	53	9.0000
iii	chr20:25426496-25426776(+)$1	280	50	53	9.0000
PPG	chr13:98117921-98118218(+)$1	297	26	29	9.0000
ff:	chr20:34319373-34319607(-)$1	234	31	34	9.0000
ooo	chr22:19838410-19838639(-)$1	229	4	7	9.0000
ddo	chr17:45195663-45195887(-)$1	224	48	51	9.0000
ddd	chr7:138983578-138983804(+)$1	226	14	17	9.0000
EEE	chr8:22880222-22880505(-)$1	283	32	35	9.0000
DLL	chr19:16757143-16757384(-)$1	241	10	13	9.0000
hh[	chr10:73993089-73993349(+)$1	260	40	43	9.0000
ooo	chr17:76168243-76168493(+)$1	250	216	219	9.0000
::f	chr1:205685451-205685871(-)$1	420	16	19	9.0000
b[b	chr13:41701841-41702065(-)$1	224	7	10	9.0000
:::	chr8:42691781-42692007(-)$1	226	20	23	9.0000
vvv	chr14:78182056-78182295(+)$1	239	46	49	9.0000
ddd	chr10:121334709-121334966(-)$1	257	58	61	9.0000
:FF	chr11:16760243-16760464(+)$1	221	0	3	9.0000
:::	chrX:106893954-106894210(+)$1	256	4	7	9.0000
CCM	chr6:91225556-91225800(-)$1	244	60	63	9.0000
FFh	chr5:64962074-64962295(-)$1	221	10	13	9.0000
:ff	chr7:133978385-133978635(-)$1	250	10	13	9.0000
ggg	chr2:174773806-174774034(-)$1	228	19	22	9.0000
ddd	chr17:15931628-15931895(+)$1	267	105	108	9.0000
NNE	chr1:183596078-183596302(-)$1	224	10	13	9.0000
::e	chr2:198416440-198416667(+)$1	227	6	9	9.0000
:HH	chr14:103807242-103807556(+)$1	314	1	4	9.0000
GGG	chr22:42078282-42078568(-)$1	286	99	102	9.0000
3gg	chr8:37611762-37612017(+)$1	255	97	100	9.0000
!==	chr3:113439167-113439443(-)$1	276	18	21	9.0000
FFF	chr4:31147244-31147469(+)$1	225	32	35	9.0000
::e	chr17:30327201-30327460(+)$1	259	10	13	9.0000
QQQ	chr1:213167034-213167262(-)$1	228	15	18	9.0000
44b	chr11:118888891-118889146(-)$1	255	33	36	9.0000
:::	chr1:39330111-39330334(-)$1	223	6	9	9.0000
III	chr6:11136331-11136609(+)$1	278	15	18	9.0000
eee	chr1:235295037-235295268(-)$1	231	76	79	9.0000
DMM	chr1:162494452-162494686(+)$1	234	54	57	9.0000
:ee	chr11:61732136-61732363(-)$1	227	0	3	9.0000
LLL	chrX:70795040-70795266(+)$1	226	4	7	9.0000
ee[	chr7:114657046-114657269(+)$1	223	33	36	9.0000
bb4	chr6:26104348-26104610(+)$1	262	244	247	9.0000
ddd	chr17:57119101-57119324(-)$1	223	23	26	9.0000
III	chr1:12072780-12073009(+)$1	229	6	9	9.0000
HHH	chr7:99689626-99689897(+)$1	271	29	32	9.0000
::J	chr16:19564602-19564826(+)$1	224	6	9	9.0000
ooc	chr1:150547251-150547496(-)$1	245	36	39	9.0000
ggg	chr7:112461613-112461852(-)$1	239	97	100	9.0000
III	chr3:32525319-32525580(-)$1	261	25	28	9.0000
fff	chr16:89630254-89630544(+)$1	290	91	94	9.0000
HHH	chr19:3578912-3579164(+)$1	252	1	4	9.0000
fff	chr9:115449061-115449292(-)$1	231	78	81	9.0000
eee	chr10:63855803-63856044(+)$1	241	56	59	9.0000
hhh	chr14:32626551-32626775(+)$1	224	61	64	9.0000
ggg	chrX:106893452-106893692(+)$1	240	22	25	9.0000
:::	chr5:31535811-31536046(+)$1	235	16	19	9.0000
:::	chr15:48634337-48634596(+)$1	259	1	4	9.0000
odd	chr14:23395241-23395493(-)$1	252	27	30	9.0000
ddd	chr9:138395992-138396278(+)$1	286	78	81	9.0000
:::	chr4:2517184-2517407(+)$1	223	6	9	9.0000
2ff	chr19:12256618-12256896(-)$1	278	157	160	9.0000
:::	chr3:113503496-113503742(+)$1	246	1	4	9.0000
4cc	chr11:73583884-73584190(-)$1	306	146	149	9.0000
vvv	chr1:32799894-32800123(-)$1	229	41	44	9.0000
nnc	chr20:34238535-34238804(-)$1	269	59	62	9.0000
""d	chr16:75664256-75664506(-)$1	250	84	87	9.0000
JJJ	chr16:2821095-2821341(+)$1	246	17	20	9.0000
vvv	chr4:83276373-83276622(-)$1	249	54	57	9.0000
:::	chr15:44086672-44086900(+)$1	228	16	19	9.0000
hhh	chr15:77338334-77338607(-)$1	273	6	9	9.0000

#DB
(((	chr6:149690959-149691191(+)$1	1	6	9	9.0000
(((	chr12:27876879-27877139(+)$1	1	1	4	9.0000
..(	chr5:133291276-133291520(-)$1	1	8	11	9.0000
((.	chr12:51213461-51213740(+)$1	1	18	21	9.0000
(((	chrX:119391107-119391410(+)$1	1	23	26	9.0000
(((	chr5:10680640-10680867(-)$1	1	11	14	9.0000
(((	chr12:118582496-118582738(+)$1	1	121	124	9.0000
..(	chr19:33873084-33873310(+)$1	1	7	10	9.0000
(((	chr16:81415625-81415874(+)$1	1	7	10	9.0000
)).	chrX:135292608-135292849(+)$1	1	95	98	9.0000
(((	chr3:107526196-107526425(+)$1	1	17	20	9.0000
..(	chr15:77338753-77339053(-)$1	1	5	8	9.0000
...	chr1:229459405-229459635(-)$1	1	0	3	9.0000
..)	chr19:1435161-1435384(+)$1	1	40	43	9.0000
.((	chr1:1716803-1717071(-)$1	1	14	17	9.0000
(((	chr1:155708037-155708359(+)$1	1	97	100	9.0000
..(	chr15:90414641-90414868(-)$1	1	29	32	9.0000
...	chr10:59955621-59955842(-)$1	1	2	5	9.0000
...	chr1:67873435-67873659(-)$1	1	58	61	9.0000
.((	chr11:43877190-43877411(+)$1	1	16	19	9.0000
(((	chr8:22880067-22880319(-)$1	1	28	31	9.0000
.((	chr19:10800681-10800906(+)$1	1	102	105	9.0000
(((	chr11:118964591-118964885(-)$1	1	16	19	9.0000
)).	chr16:2821410-2821638(-)$1	1	97	100	9.0000
..(	chr12:121137907-121138163(+)$1	1	46	49	9.0000
(((	chr5:132440134-132440397(+)$1	1	3	6	9.0000
(((	chr19:47656107-47656357(+)$1	1	7	10	9.0000
...	chr5:112354395-112354648(+)$1	1	10	13	9.0000
)))	chr17:40023645-40023938(-)$1	1	107	110	9.0000
(((	chr3:196662900-196663127(-)$1	1	18	21	9.0000
)))	chrX:123234514-123234747(+)$1	1	76	79	9.0000
.((	chr5:162871734-162872001(+)$1	1	50	53	9.0000
(((	chr20:25426496-25426776(+)$1	1	50	53	9.0000
..(	chr13:98117921-98118218(+)$1	1	26	29	9.0000
)).	chr20:34319373-34319607(-)$1	1	31	34	9.0000
...	chr22:19838410-19838639(-)$1	1	4	7	9.0000
((.	chr17:45195663-45195887(-)$1	1	48	51	9.0000
(((	chr7:138983578-138983804(+)$1	1	14	17	9.0000
(((	chr8:22880222-22880505(-)$1	1	32	35	9.0000
(..	chr19:16757143-16757384(-)$1	1	10	13	9.0000
((.	chr10:73993089-73993349(+)$1	1	40	43	9.0000
...	chr17:76168243-76168493(+)$1	1	216	219	9.0000
..(	chr1:205685451-205685871(-)$1	1	16	19	9.0000
(.(	chr13:41701841-41702065(-)$1	1	7	10	9.0000
...	chr8:42691781-42692007(-)$1	1	20	23	9.0000
...	chr14:78182056-78182295(+)$1	1	46	49	9.0000
(((	chr10:121334709-121334966(-)$1	1	58	61	9.0000
.((	chr11:16760243-16760464(+)$1	1	0	3	9.0000
...	chrX:106893954-106894210(+)$1	1	4	7	9.0000
((.	chr6:91225556-91225800(-)$1	1	60	63	9.0000
(((	chr5:64962074-64962295(-)$1	1	10	13	9.0000
.((	chr7:133978385-133978635(-)$1	1	10	13	9.0000
(((	chr2:174773806-174774034(-)$1	1	19	22	9.0000
(((	chr17:15931628-15931895(+)$1	1	105	108	9.0000
..(	chr1:183596078-183596302(-)$1	1	10	13	9.0000
..(	chr2:198416440-198416667(+)$1	1	6	9	9.0000
.((	chr14:103807242-103807556(+)$1	1	1	4	9.0000
)))	chr22:42078282-42078568(-)$1	1	99	102	9.0000
.))	chr8:37611762-37612017(+)$1	1	97	100	9.0000
.((	chr3:113439167-113439443(-)$1	1	18	21	9.0000
(((	chr4:31147244-31147469(+)$1	1	32	35	9.0000
..(	chr17:30327201-30327460(+)$1	1	10	13	9.0000
...	chr1:213167034-213167262(-)$1	1	15	18	9.0000
..)	chr11:118888891-118889146(-)$1	1	33	36	9.0000
...	chr1:39330111-39330334(-)$1	1	6	9	9.0000
(((	chr6:11136331-11136609(+)$1	1	15	18	9.0000
)))	chr1:235295037-235295268(-)$1	1	76	79	9.0000
(..	chr1:162494452-162494686(+)$1	1	54	57	9.0000
.((	chr11:61732136-61732363(-)$1	1	0	3	9.0000
...	chrX:70795040-70795266(+)$1	1	4	7	9.0000
((.	chr7:114657046-114657269(+)$1	1	33	36	9.0000
)).	chr6:26104348-26104610(+)$1	1	244	247	9.0000
)))	chr17:57119101-57119324(-)$1	1	23	26	9.0000
(((	chr1:12072780-12073009(+)$1	1	6	9	9.0000
(((	chr7:99689626-99689897(+)$1	1	29	32	9.0000
..(	chr16:19564602-19564826(+)$1	1	6	9	9.0000
..)	chr1:150547251-150547496(-)$1	1	36	39	9.0000
(((	chr7:112461613-112461852(-)$1	1	97	100	9.0000
(((	chr3:32525319-32525580(-)$1	1	25	28	9.0000
(((	chr16:89630254-89630544(+)$1	1	91	94	9.0000
(((	chr19:3578912-3579164(+)$1	1	1	4	9.0000
)))	chr9:115449061-115449292(-)$1	1	78	81	9.0000
(((	chr10:63855803-63856044(+)$1	1	56	59	9.0000
(((	chr14:32626551-32626775(+)$1	1	61	64	9.0000
(((	chrX:106893452-106893692(+)$1	1	22	25	9.0000
...	chr5:31535811-31536046(+)$1	1	16	19	9.0000
...	chr15:48634337-48634596(+)$1	1	1	4	9.0000
.))	chr14:23395241-23395493(-)$1	1	27	30	9.0000
(((	chr9:138395992-138396278(+)$1	1	78	81	9.0000
...	chr4:2517184-2517407(+)$1	1	6	9	9.0000
.))	chr19:12256618-12256896(-)$1	1	157	160	9.0000
...	chr3:113503496-113503742(+)$1	1	1	4	9.0000
.))	chr11:73583884-73584190(-)$1	1	146	149	9.0000
...	chr1:32799894-32800123(-)$1	1	41	44	9.0000
..)	chr20:34238535-34238804(-)$1	1	59	62	9.0000
..(	chr16:75664256-75664506(-)$1	1	84	87	9.0000
(((	chr16:2821095-2821341(+)$1	1	17	20	9.0000
...	chr4:83276373-83276622(-)$1	1	54	57	9.0000
...	chr15:44086672-44086900(+)$1	1	16	19	9.0000
(((	chr15:77338334-77338607(-)$1	1	6	9	9.0000

#PSSM
U : 0.97	u : 0.03	
U : 0.97	u : 0.03	
G : 0.98	g : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Gottwein2011b_hg19_UTR_m2_run2.nuc.txt

#NT
UAAA	chr12:110972797-110973022(-)$1	225	68	72	11.9999
UAAA	chr6:111215211-111215433(+)$1	222	29	33	11.9999
UAAA	chr2:178094991-178095232(-)$1	241	43	47	11.9999
UAAA	chr6:145173794-145174018(+)$1	224	48	52	11.9999
UAAA	chr1:90059155-90059378(+)$1	223	34	38	11.9999
UAAA	chr7:99091104-99091328(-)$1	224	29	33	11.9999
UAAA	chr17:63007038-63007260(-)$1	222	91	95	11.9999
UAAA	chr4:39123082-39123299(+)$1	217	7	11	11.9999
UAAA	chr2:190331052-190331278(+)$1	226	15	19	11.9999
UAAA	chr9:95381344-95381562(+)$1	218	20	24	11.9999
UAAA	chr17:27870575-27870793(+)$1	218	0	4	11.9999
UAAA	chr5:134190660-134190881(+)$1	221	105	109	11.9999
UAAA	chr13:47345324-47345545(-)$1	221	29	33	11.9999
UAAA	chr8:66630079-66630309(-)$1	230	107	111	11.9999
UAAA	chr9:100362769-100362991(+)$1	222	88	92	11.9999
UAAA	chr5:6756977-6757200(+)$1	223	115	119	11.9999
UAAA	chr15:40686125-40686365(+)$1	240	8	12	11.9999
UAAA	chr19:47291251-47291478(-)$1	227	69	73	11.9999
UAAA	chr12:104743278-104743502(+)$1	224	14	18	11.9999
UAAA	chr5:64961773-64962003(-)$1	230	51	55	11.9999
UAAA	chr6:122764514-122764734(-)$1	220	86	90	11.9999
uaaa	chr11:46111912-46112142(-)$1	230	3	7	11.9999
UAAA	chr13:21548669-21548899(-)$1	230	113	117	11.9999
uaaa	chr19:21987743-21987969(-)$1	226	57	61	11.9999
UAAA	chr3:48674367-48674596(-)$1	229	58	62	11.9999
uaaa	chr1:19953762-19953980(+)$1	218	90	94	11.9999
UAAA	chr1:213164781-213165014(+)$1	233	16	20	11.9999
UAAA	chr8:126450154-126450380(+)$1	226	207	211	11.9999
UAAA	chr1:78030435-78030663(-)$1	228	18	22	11.9999
UAAA	chr2:231041099-231041320(-)$1	221	104	108	11.9999
UAAA	chr13:53261973-53262203(+)$1	230	196	200	11.9999
UAAA	chr4:165998466-165998690(-)$1	224	155	159	11.9999
UAAA	chr14:31171446-31171676(+)$1	230	18	22	11.9999
UAAA	chr6:108365584-108365826(-)$1	242	165	169	11.9999
UAAA	chr6:408516-408740(+)$1	224	65	69	11.9999
UAAA	chr10:115668534-115668764(+)$1	230	74	78	11.9999
UAAA	chr12:120899205-120899427(+)$1	222	68	72	11.9999
UAAA	chr4:106198286-106198516(+)$1	230	15	19	11.9999
UAAA	chr4:17826951-17827170(+)$1	219	63	67	11.9999
UAAA	chr14:57115329-57115559(+)$1	230	107	111	11.9999
UAAA	chr12:50871407-50871640(+)$1	233	126	130	11.9999
UAAA	chr14:103807327-103807547(+)$1	220	15	19	11.9999
uaaa	chr8:101165603-101165820(+)$1	217	145	149	11.9999
UAAA	chr8:72110998-72111232(-)$1	234	77	81	11.9999
UAAA	chr7:135046513-135046751(-)$1	238	122	126	11.9999
UAAA	chr8:126445484-126445706(+)$1	222	48	52	11.9999
UAAA	chr9:134133467-134133697(-)$1	230	203	207	11.9999
UAAA	chr4:83847097-83847323(-)$1	226	99	103	11.9999
UAAA	chr15:68482707-68482937(+)$1	230	82	86	11.9999
UAAA	chr8:91029311-91029530(+)$1	219	18	22	11.9999
UAAA	chr12:4409966-4410196(+)$1	230	64	68	11.9999
UAAA	chr3:150301772-150301992(+)$1	220	69	73	11.9999
UAAA	chr13:28003927-28004157(+)$1	230	0	4	11.9999
UAAA	chr10:89730309-89730527(+)$1	218	59	63	11.9999
UAAA	chr12:44180574-44180802(+)$1	228	16	20	11.9999
UAAA	chr3:14239697-14239926(+)$1	229	91	95	11.9999
UAAA	chr2:220084305-220084536(-)$1	231	10	14	11.9999
UAAA	chr4:26434575-26434828(+)$1	253	6	10	11.9999
UAAA	chr12:111160236-111160454(-)$1	218	60	64	11.9999
UAAA	chr9:111780773-111781000(-)$1	227	32	36	11.9999
UAAA	chr2:165542314-165542544(-)$1	230	86	90	11.9999
UAAA	chr3:169810691-169810917(-)$1	226	215	219	11.9999
UAAA	chr11:110038364-110038572(+)$1	208	17	21	11.9999
uaaa	chr7:150070921-150071145(+)$1	224	146	150	11.9999
UAAA	chr12:65109948-65110178(-)$1	230	64	68	11.9999
UAAA	chr8:42873742-42873961(+)$1	219	135	139	11.9999
UAAA	chr8:74705125-74705351(-)$1	226	69	73	11.9999
UAAA	chr9:25677189-25677411(-)$1	222	24	28	11.9999
uaaa	chr13:73332016-73332241(-)$1	225	14	18	11.9999
UAAA	chr10:74127569-74127796(-)$1	227	76	80	11.9999
UAAA	chr9:132589788-132590036(-)$1	248	81	85	11.9999
UAAA	chr8:17088051-17088274(-)$1	223	217	221	11.9999
UAAA	chr3:133305939-133306170(+)$1	231	32	36	11.9999
UAAA	chr8:92099086-92099317(+)$1	231	112	116	11.9999
UAAA	chr10:70743085-70743304(+)$1	219	165	169	11.9999
UAAA	chr12:109072036-109072257(-)$1	221	5	9	11.9999
UAAA	chr7:103008422-103008653(+)$1	231	14	18	11.9999
UAAA	chr12:104743147-104743370(+)$1	223	74	78	11.9999
UAAA	chr3:119211306-119211527(+)$1	221	143	147	11.9999
UAAA	chr5:32604033-32604255(+)$1	222	123	127	11.9999
uaaa	chr12:46367956-46368189(-)$1	233	224	228	11.9999
UAAA	chr3:88205892-88206106(+)$1	214	155	159	11.9999
UAAA	chr17:4175091-4175333(-)$1	242	7	11	11.9999
UAAA	chr6:80413056-80413286(+)$1	230	25	29	11.9999
UAAA	chr20:16032280-16032498(+)$1	218	20	24	11.9999
UAAA	chr12:4410751-4410976(+)$1	225	129	133	11.9999

#otherMatches

#Struct PSSM
d22f	chr19:2813401-2813619(+)$1	218	176	180	11.9999
qqqq	chr12:110972797-110973022(-)$1	225	68	72	11.9999
::hh	chr6:111215211-111215433(+)$1	222	29	33	11.9999
qqqq	chr2:178094991-178095232(-)$1	241	43	47	11.9999
gggg	chr6:145173794-145174018(+)$1	224	48	52	11.9999
))))	chr1:90059155-90059378(+)$1	223	34	38	11.9999
::::	chr7:99091104-99091328(-)$1	224	29	33	11.9999
ddnn	chr17:63007038-63007260(-)$1	222	91	95	11.9999
====	chr4:39123082-39123299(+)$1	217	7	11	11.9999
FFFQ	chr2:190331052-190331278(+)$1	226	15	19	11.9999
ii##	chr9:95381344-95381562(+)$1	218	20	24	11.9999
::FF	chr17:27870575-27870793(+)$1	218	0	4	11.9999
^^^^	chr5:134190660-134190881(+)$1	221	105	109	11.9999
c"""	chr13:47345324-47345545(-)$1	221	29	33	11.9999
[ddd	chr8:66630079-66630309(-)$1	230	107	111	11.9999
nnnn	chr9:100362769-100362991(+)$1	222	88	92	11.9999
"fff	chr5:6756977-6757200(+)$1	223	115	119	11.9999
h!!d	chr15:40686125-40686365(+)$1	240	8	12	11.9999
::::	chr19:47291251-47291478(-)$1	227	69	73	11.9999
::ff	chr12:104743278-104743502(+)$1	224	14	18	11.9999
::::	chr5:64961773-64962003(-)$1	230	51	55	11.9999
gggg	chr6:122764514-122764734(-)$1	220	86	90	11.9999
d"""	chr11:46111912-46112142(-)$1	230	3	7	11.9999
ffff	chr13:21548669-21548899(-)$1	230	113	117	11.9999
hhhh	chr19:21987743-21987969(-)$1	226	57	61	11.9999
[ccc	chr3:48674367-48674596(-)$1	229	58	62	11.9999
::::	chr1:19953762-19953980(+)$1	218	90	94	11.9999
e"""	chr1:213164781-213165014(+)$1	233	16	20	11.9999
qqqq	chr8:126450154-126450380(+)$1	226	207	211	11.9999
ee[c	chr1:78030435-78030663(-)$1	228	18	22	11.9999
::::	chr2:231041099-231041320(-)$1	221	104	108	11.9999
lllc	chr13:53261973-53262203(+)$1	230	196	200	11.9999
qqqq	chr4:165998466-165998690(-)$1	224	155	159	11.9999
JJJJ	chr14:31171446-31171676(+)$1	230	18	22	11.9999
yyye	chr6:108365584-108365826(-)$1	242	165	169	11.9999
::::	chr6:408516-408740(+)$1	224	65	69	11.9999
^^^^	chr10:115668534-115668764(+)$1	230	74	78	11.9999
::::	chr12:120899205-120899427(+)$1	222	68	72	11.9999
uuuu	chr4:106198286-106198516(+)$1	230	15	19	11.9999
eeee	chr4:17826951-17827170(+)$1	219	63	67	11.9999
eepp	chr14:57115329-57115559(+)$1	230	107	111	11.9999
>>>>	chr12:50871407-50871640(+)$1	233	126	130	11.9999
mmmd	chr14:103807327-103807547(+)$1	220	15	19	11.9999
ssss	chr8:101165603-101165820(+)$1	217	145	149	11.9999
ll==	chr8:72110998-72111232(-)$1	234	77	81	11.9999
::dd	chr7:135046513-135046751(-)$1	238	122	126	11.9999
6666	chr8:126445484-126445706(+)$1	222	48	52	11.9999
FF::	chr9:134133467-134133697(-)$1	230	203	207	11.9999
fff]	chr4:83847097-83847323(-)$1	226	99	103	11.9999
::hh	chr15:68482707-68482937(+)$1	230	82	86	11.9999
%%%%	chr8:91029311-91029530(+)$1	219	18	22	11.9999
::::	chr12:4409966-4410196(+)$1	230	64	68	11.9999
iiii	chr3:150301772-150301992(+)$1	220	69	73	11.9999
::::	chr13:28003927-28004157(+)$1	230	0	4	11.9999
tttt	chr10:89730309-89730527(+)$1	218	59	63	11.9999
DDD:	chr12:44180574-44180802(+)$1	228	16	20	11.9999
dfff	chr3:14239697-14239926(+)$1	229	91	95	11.9999
::::	chr2:220084305-220084536(-)$1	231	10	14	11.9999
eeee	chr4:26434575-26434828(+)$1	253	6	10	11.9999
""cc	chr12:111160236-111160454(-)$1	218	60	64	11.9999
&&&c	chr9:111780773-111781000(-)$1	227	32	36	11.9999
22dd	chr2:165542314-165542544(-)$1	230	86	90	11.9999
::::	chr3:169810691-169810917(-)$1	226	215	219	11.9999
ccgg	chr11:110038364-110038572(+)$1	208	17	21	11.9999
tthh	chr7:150070921-150071145(+)$1	224	146	150	11.9999
^^^^	chr12:65109948-65110178(-)$1	230	64	68	11.9999
qqqq	chr8:42873742-42873961(+)$1	219	135	139	11.9999
fff2	chr8:74705125-74705351(-)$1	226	69	73	11.9999
))))	chr9:25677189-25677411(-)$1	222	24	28	11.9999
::::	chr13:73332016-73332241(-)$1	225	14	18	11.9999
pppp	chr10:74127569-74127796(-)$1	227	76	80	11.9999
::::	chr9:132589788-132590036(-)$1	248	81	85	11.9999
::::	chr8:17088051-17088274(-)$1	223	217	221	11.9999
mmcc	chr3:133305939-133306170(+)$1	231	32	36	11.9999
qqqq	chr8:92099086-92099317(+)$1	231	112	116	11.9999
ff33	chr10:70743085-70743304(+)$1	219	165	169	11.9999
::::	chr12:109072036-109072257(-)$1	221	5	9	11.9999
::::	chr7:103008422-103008653(+)$1	231	14	18	11.9999
mmmm	chr12:104743147-104743370(+)$1	223	74	78	11.9999
::::	chr3:119211306-119211527(+)$1	221	143	147	11.9999
hhhl	chr5:32604033-32604255(+)$1	222	123	127	11.9999
::::	chr12:46367956-46368189(-)$1	233	224	228	11.9999
:::c	chr3:88205892-88206106(+)$1	214	155	159	11.9999
::::	chr17:4175091-4175333(-)$1	242	7	11	11.9999
mmmm	chr6:80413056-80413286(+)$1	230	25	29	11.9999
ffff	chr20:16032280-16032498(+)$1	218	20	24	11.9999
====	chr12:4410751-4410976(+)$1	225	129	133	11.9999

#DB
)..)	chr19:2813401-2813619(+)$1	1	176	180	11.9999
....	chr12:110972797-110973022(-)$1	1	68	72	11.9999
..((	chr6:111215211-111215433(+)$1	1	29	33	11.9999
....	chr2:178094991-178095232(-)$1	1	43	47	11.9999
((((	chr6:145173794-145174018(+)$1	1	48	52	11.9999
....	chr1:90059155-90059378(+)$1	1	34	38	11.9999
....	chr7:99091104-99091328(-)$1	1	29	33	11.9999
((..	chr17:63007038-63007260(-)$1	1	91	95	11.9999
((((	chr4:39123082-39123299(+)$1	1	7	11	11.9999
(((.	chr2:190331052-190331278(+)$1	1	15	19	11.9999
((..	chr9:95381344-95381562(+)$1	1	20	24	11.9999
..((	chr17:27870575-27870793(+)$1	1	0	4	11.9999
....	chr5:134190660-134190881(+)$1	1	105	109	11.9999
(...	chr13:47345324-47345545(-)$1	1	29	33	11.9999
.(((	chr8:66630079-66630309(-)$1	1	107	111	11.9999
....	chr9:100362769-100362991(+)$1	1	88	92	11.9999
.(((	chr5:6756977-6757200(+)$1	1	115	119	11.9999
(..(	chr15:40686125-40686365(+)$1	1	8	12	11.9999
....	chr19:47291251-47291478(-)$1	1	69	73	11.9999
..((	chr12:104743278-104743502(+)$1	1	14	18	11.9999
....	chr5:64961773-64962003(-)$1	1	51	55	11.9999
((((	chr6:122764514-122764734(-)$1	1	86	90	11.9999
(...	chr11:46111912-46112142(-)$1	1	3	7	11.9999
((((	chr13:21548669-21548899(-)$1	1	113	117	11.9999
((((	chr19:21987743-21987969(-)$1	1	57	61	11.9999
.(((	chr3:48674367-48674596(-)$1	1	58	62	11.9999
....	chr1:19953762-19953980(+)$1	1	90	94	11.9999
(...	chr1:213164781-213165014(+)$1	1	16	20	11.9999
....	chr8:126450154-126450380(+)$1	1	207	211	11.9999
((.(	chr1:78030435-78030663(-)$1	1	18	22	11.9999
....	chr2:231041099-231041320(-)$1	1	104	108	11.9999
...)	chr13:53261973-53262203(+)$1	1	196	200	11.9999
....	chr4:165998466-165998690(-)$1	1	155	159	11.9999
((((	chr14:31171446-31171676(+)$1	1	18	22	11.9999
...)	chr6:108365584-108365826(-)$1	1	165	169	11.9999
....	chr6:408516-408740(+)$1	1	65	69	11.9999
....	chr10:115668534-115668764(+)$1	1	74	78	11.9999
....	chr12:120899205-120899427(+)$1	1	68	72	11.9999
....	chr4:106198286-106198516(+)$1	1	15	19	11.9999
((((	chr4:17826951-17827170(+)$1	1	63	67	11.9999
((..	chr14:57115329-57115559(+)$1	1	107	111	11.9999
....	chr12:50871407-50871640(+)$1	1	126	130	11.9999
...)	chr14:103807327-103807547(+)$1	1	15	19	11.9999
....	chr8:101165603-101165820(+)$1	1	145	149	11.9999
..))	chr8:72110998-72111232(-)$1	1	77	81	11.9999
..((	chr7:135046513-135046751(-)$1	1	122	126	11.9999
....	chr8:126445484-126445706(+)$1	1	48	52	11.9999
))..	chr9:134133467-134133697(-)$1	1	203	207	11.9999
))).	chr4:83847097-83847323(-)$1	1	99	103	11.9999
..((	chr15:68482707-68482937(+)$1	1	82	86	11.9999
....	chr8:91029311-91029530(+)$1	1	18	22	11.9999
....	chr12:4409966-4410196(+)$1	1	64	68	11.9999
))))	chr3:150301772-150301992(+)$1	1	69	73	11.9999
....	chr13:28003927-28004157(+)$1	1	0	4	11.9999
....	chr10:89730309-89730527(+)$1	1	59	63	11.9999
(((.	chr12:44180574-44180802(+)$1	1	16	20	11.9999
((((	chr3:14239697-14239926(+)$1	1	91	95	11.9999
....	chr2:220084305-220084536(-)$1	1	10	14	11.9999
((((	chr4:26434575-26434828(+)$1	1	6	10	11.9999
..((	chr12:111160236-111160454(-)$1	1	60	64	11.9999
...(	chr9:111780773-111781000(-)$1	1	32	36	11.9999
..))	chr2:165542314-165542544(-)$1	1	86	90	11.9999
....	chr3:169810691-169810917(-)$1	1	215	219	11.9999
((((	chr11:110038364-110038572(+)$1	1	17	21	11.9999
..))	chr7:150070921-150071145(+)$1	1	146	150	11.9999
....	chr12:65109948-65110178(-)$1	1	64	68	11.9999
....	chr8:42873742-42873961(+)$1	1	135	139	11.9999
))).	chr8:74705125-74705351(-)$1	1	69	73	11.9999
....	chr9:25677189-25677411(-)$1	1	24	28	11.9999
....	chr13:73332016-73332241(-)$1	1	14	18	11.9999
....	chr10:74127569-74127796(-)$1	1	76	80	11.9999
....	chr9:132589788-132590036(-)$1	1	81	85	11.9999
....	chr8:17088051-17088274(-)$1	1	217	221	11.9999
..))	chr3:133305939-133306170(+)$1	1	32	36	11.9999
....	chr8:92099086-92099317(+)$1	1	112	116	11.9999
))..	chr10:70743085-70743304(+)$1	1	165	169	11.9999
....	chr12:109072036-109072257(-)$1	1	5	9	11.9999
....	chr7:103008422-103008653(+)$1	1	14	18	11.9999
....	chr12:104743147-104743370(+)$1	1	74	78	11.9999
....	chr3:119211306-119211527(+)$1	1	143	147	11.9999
(((.	chr5:32604033-32604255(+)$1	1	123	127	11.9999
....	chr12:46367956-46368189(-)$1	1	224	228	11.9999
...(	chr3:88205892-88206106(+)$1	1	155	159	11.9999
....	chr17:4175091-4175333(-)$1	1	7	11	11.9999
....	chr6:80413056-80413286(+)$1	1	25	29	11.9999
((((	chr20:16032280-16032498(+)$1	1	20	24	11.9999
))))	chr12:4410751-4410976(+)$1	1	129	133	11.9999

#PSSM
U : 0.91	u : 0.08	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	
A : 0.91	a : 0.08	

#score	1043.9999999999998
#seq	87
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_CDS_m3_run1.nuc.txt

#NT
AGAA	chr16:29822233-29822466(+)$1	233	135	139	11.9999
AGAA	chr17:1563938-1564159(-)$1	221	40	44	11.9999
AGAA	chr10:112590798-112591021(-)$1	223	146	150	11.9999
AGAA	chr9:129154268-129154495(+)$1	227	16	20	11.9999
AGAA	chr6:107827385-107827606(+)$1	221	58	62	11.9999
AGAA	chr17:61465989-61466218(+)$1	229	71	75	11.9999
AGAA	chr2:179407143-179407366(+)$1	223	156	160	11.9999
AGAA	chr2:61722569-61722788(-)$1	219	98	102	11.9999
AGAA	chr1:169345921-169346143(+)$1	222	65	69	11.9999
AGAA	chr7:64864642-64864871(+)$1	229	4	8	11.9999
AGAA	chr19:8601122-8601343(-)$1	221	2	6	11.9999
AGAA	chr16:31895759-31895980(+)$1	221	9	13	11.9999
AGAA	chr1:1562195-1562427(+)$1	232	175	179	11.9999
AGAA	chr16:88875808-88876032(-)$1	224	129	133	11.9999
AGAA	chr8:48887402-48887621(+)$1	219	140	144	11.9999
AGAA	chr3:182988407-182988627(+)$1	220	156	160	11.9999
AGAA	chr1:212792687-212792907(+)$1	220	19	23	11.9999
AGAA	chr15:65954112-65954335(+)$1	223	217	221	11.9999
AGAA	chr4:113539007-113539226(-)$1	219	36	40	11.9999
AGAA	chr5:6604255-6604474(-)$1	219	118	122	11.9999
AGAA	chrX:107978246-107978466(-)$1	220	8	12	11.9999
AGAA	chr14:32315624-32315846(+)$1	222	198	202	11.9999
AGAA	chr14:55510106-55510334(+)$1	228	187	191	11.9999
AGAA	chr10:871065-871287(-)$1	222	94	98	11.9999
AGAA	chr19:39423232-39423462(+)$1	230	97	101	11.9999
AGAA	chr1:215792155-215792377(+)$1	222	70	74	11.9999
AGAA	chr19:40542170-40542402(-)$1	232	2	6	11.9999
AGAA	chr8:116427176-116427403(-)$1	227	148	152	11.9999
AGAA	chr5:140056546-140056768(-)$1	222	1	5	11.9999
AGAA	chr11:32975354-32975574(+)$1	220	46	50	11.9999
AGAA	chr12:57965888-57966107(-)$1	219	82	86	11.9999
AGAA	chr7:91714833-91715061(+)$1	228	73	77	11.9999
AGAA	chr6:11134553-11134776(+)$1	223	194	198	11.9999
AGAA	chr13:42874044-42874263(+)$1	219	74	78	11.9999
AGAA	chrX:123224487-123224707(+)$1	220	174	178	11.9999
AGAA	chr7:97946544-97946767(-)$1	223	122	126	11.9999
AGAA	chr16:74660288-74660529(+)$1	241	175	179	11.9999
AGAA	chr13:31835020-31835240(+)$1	220	94	98	11.9999
AGAA	chr11:82570945-82571176(-)$1	231	87	91	11.9999
AGAA	chr1:36383143-36383369(+)$1	226	138	142	11.9999
AGAA	chr10:63851575-63851794(+)$1	219	58	62	11.9999
AGAA	chr14:105170155-105170384(+)$1	229	32	36	11.9999
AGAA	chr2:190647048-190647274(-)$1	226	130	134	11.9999
AGAA	chr7:156619267-156619489(-)$1	222	149	153	11.9999
AGAA	chr12:123006622-123006849(-)$1	227	35	39	11.9999
AGAA	chr19:9676704-9676924(-)$1	220	61	65	11.9999
AGAA	chr10:60549339-60549787(-)$1	448	351	355	11.9999
AGAA	chr19:8381367-8381586(-)$1	219	55	59	11.9999
AGAA	chr4:166238950-166239170(+)$1	220	97	101	11.9999
AGAA	chr20:43135457-43135681(-)$1	224	135	139	11.9999
agaa	chr17:37421569-37421795(-)$1	226	22	26	11.9999
AGAA	chr1:2520323-2520550(+)$1	227	67	71	11.9999
AGAA	chr10:60558082-60558313(-)$1	231	51	55	11.9999
AGAA	chr6:33288224-33288455(+)$1	231	191	195	11.9999
AGAA	chrM:11649-12083(+)$1	434	241	245	11.9999
AGAA	chr9:106900325-106900546(+)$1	221	124	128	11.9999
AGAA	chrX:54185820-54186055(-)$1	235	160	164	11.9999
AGAA	chr5:36181838-36182057(+)$1	219	90	94	11.9999
AGAA	chr10:99132711-99132930(-)$1	219	6	10	11.9999
AGAA	chr20:35219551-35219785(+)$1	234	212	216	11.9999
AGAA	chr16:2034772-2035003(+)$1	231	85	89	11.9999
AGAA	chr5:150484709-150484928(-)$1	219	76	80	11.9999
AGAA	chr22:30730533-30730781(-)$1	248	191	195	11.9999
AGAA	chr1:161200719-161200938(+)$1	219	100	104	11.9999
AGAA	chr14:95570230-95570455(-)$1	225	137	141	11.9999
AGAA	chr1:153634802-153635036(-)$1	234	53	57	11.9999
AGAA	chr10:104620171-104620399(+)$1	228	160	164	11.9999
AGAA	chr3:107799056-107799280(-)$1	224	126	130	11.9999
AGAA	chr16:31200926-31201147(+)$1	221	66	70	11.9999

#otherMatches

#Struct PSSM
::::	chr12:112371596-112371824(-)$1	228	21	25	11.9999
pppp	chr16:29822233-29822466(+)$1	233	135	139	11.9999
hhhh	chr17:1563938-1564159(-)$1	221	40	44	11.9999
[aoo	chr10:112590798-112591021(-)$1	223	146	150	11.9999
####	chr9:129154268-129154495(+)$1	227	16	20	11.9999
ffff	chr6:107827385-107827606(+)$1	221	58	62	11.9999
KKBB	chr17:61465989-61466218(+)$1	229	71	75	11.9999
c]cc	chr2:179407143-179407366(+)$1	223	156	160	11.9999
cc::	chr2:61722569-61722788(-)$1	219	98	102	11.9999
bb88	chr1:169345921-169346143(+)$1	222	65	69	11.9999
FFF{	chr7:64864642-64864871(+)$1	229	4	8	11.9999
:FFF	chr19:8601122-8601343(-)$1	221	2	6	11.9999
iiib	chr16:31895759-31895980(+)$1	221	9	13	11.9999
EE::	chr1:1562195-1562427(+)$1	232	175	179	11.9999
fff!	chr16:88875808-88876032(-)$1	224	129	133	11.9999
ddd3	chr8:48887402-48887621(+)$1	219	140	144	11.9999
::::	chr3:182988407-182988627(+)$1	220	156	160	11.9999
[ddd	chr1:212792687-212792907(+)$1	220	19	23	11.9999
::::	chr15:65954112-65954335(+)$1	223	217	221	11.9999
hhhh	chr4:113539007-113539226(-)$1	219	36	40	11.9999
^^^^	chr5:6604255-6604474(-)$1	219	118	122	11.9999
:DDD	chrX:107978246-107978466(-)$1	220	8	12	11.9999
ssss	chr14:32315624-32315846(+)$1	222	198	202	11.9999
::::	chr14:55510106-55510334(+)$1	228	187	191	11.9999
dd33	chr10:871065-871287(-)$1	222	94	98	11.9999
==44	chr19:39423232-39423462(+)$1	230	97	101	11.9999
ffff	chr1:215792155-215792377(+)$1	222	70	74	11.9999
::::	chr19:40542170-40542402(-)$1	232	2	6	11.9999
ffff	chr8:116427176-116427403(-)$1	227	148	152	11.9999
hhhh	chr5:140056546-140056768(-)$1	222	1	5	11.9999
$$$$	chr11:32975354-32975574(+)$1	220	46	50	11.9999
ffff	chr12:57965888-57966107(-)$1	219	82	86	11.9999
NNNI	chr7:91714833-91715061(+)$1	228	73	77	11.9999
ff88	chr6:11134553-11134776(+)$1	223	194	198	11.9999
}AZZ	chr13:42874044-42874263(+)$1	219	74	78	11.9999
::::	chrX:123224487-123224707(+)$1	220	174	178	11.9999
^^^^	chr7:97946544-97946767(-)$1	223	122	126	11.9999
tttt	chr16:74660288-74660529(+)$1	241	175	179	11.9999
dvvv	chr13:31835020-31835240(+)$1	220	94	98	11.9999
eeee	chr11:82570945-82571176(-)$1	231	87	91	11.9999
====	chr1:36383143-36383369(+)$1	226	138	142	11.9999
qqqq	chr10:63851575-63851794(+)$1	219	58	62	11.9999
EE{B	chr14:105170155-105170384(+)$1	229	32	36	11.9999
h%%%	chr2:190647048-190647274(-)$1	226	130	134	11.9999
dddd	chr7:156619267-156619489(-)$1	222	149	153	11.9999
MMMM	chr12:123006622-123006849(-)$1	227	35	39	11.9999
((((	chr19:9676704-9676924(-)$1	220	61	65	11.9999
qqqq	chr10:60549339-60549787(-)$1	448	351	355	11.9999
::::	chr19:8381367-8381586(-)$1	219	55	59	11.9999
2ccc	chr4:166238950-166239170(+)$1	220	97	101	11.9999
dd::	chr20:43135457-43135681(-)$1	224	135	139	11.9999
::::	chr17:37421569-37421795(-)$1	226	22	26	11.9999
neee	chr1:2520323-2520550(+)$1	227	67	71	11.9999
dd22	chr10:60558082-60558313(-)$1	231	51	55	11.9999
4444	chr6:33288224-33288455(+)$1	231	191	195	11.9999
ee%%	chrM:11649-12083(+)$1	434	241	245	11.9999
mmmc	chr9:106900325-106900546(+)$1	221	124	128	11.9999
ff!!	chrX:54185820-54186055(-)$1	235	160	164	11.9999
DD{D	chr5:36181838-36182057(+)$1	219	90	94	11.9999
::::	chr10:99132711-99132930(-)$1	219	6	10	11.9999
ZZZC	chr20:35219551-35219785(+)$1	234	212	216	11.9999
::::	chr16:2034772-2035003(+)$1	231	85	89	11.9999
eeee	chr5:150484709-150484928(-)$1	219	76	80	11.9999
!bb#	chr22:30730533-30730781(-)$1	248	191	195	11.9999
mmmm	chr1:161200719-161200938(+)$1	219	100	104	11.9999
GGG:	chr14:95570230-95570455(-)$1	225	137	141	11.9999
::::	chr1:153634802-153635036(-)$1	234	53	57	11.9999
bbHH	chr10:104620171-104620399(+)$1	228	160	164	11.9999
pppp	chr3:107799056-107799280(-)$1	224	126	130	11.9999
((((	chr16:31200926-31201147(+)$1	221	66	70	11.9999

#DB
....	chr12:112371596-112371824(-)$1	1	21	25	11.9999
....	chr16:29822233-29822466(+)$1	1	135	139	11.9999
))))	chr17:1563938-1564159(-)$1	1	40	44	11.9999
.(..	chr10:112590798-112591021(-)$1	1	146	150	11.9999
....	chr9:129154268-129154495(+)$1	1	16	20	11.9999
))))	chr6:107827385-107827606(+)$1	1	58	62	11.9999
..((	chr17:61465989-61466218(+)$1	1	71	75	11.9999
).))	chr2:179407143-179407366(+)$1	1	156	160	11.9999
))..	chr2:61722569-61722788(-)$1	1	98	102	11.9999
))..	chr1:169345921-169346143(+)$1	1	65	69	11.9999
(((.	chr7:64864642-64864871(+)$1	1	4	8	11.9999
.(((	chr19:8601122-8601343(-)$1	1	2	6	11.9999
((((	chr16:31895759-31895980(+)$1	1	9	13	11.9999
))..	chr1:1562195-1562427(+)$1	1	175	179	11.9999
(((.	chr16:88875808-88876032(-)$1	1	129	133	11.9999
))).	chr8:48887402-48887621(+)$1	1	140	144	11.9999
....	chr3:182988407-182988627(+)$1	1	156	160	11.9999
.(((	chr1:212792687-212792907(+)$1	1	19	23	11.9999
....	chr15:65954112-65954335(+)$1	1	217	221	11.9999
((((	chr4:113539007-113539226(-)$1	1	36	40	11.9999
....	chr5:6604255-6604474(-)$1	1	118	122	11.9999
.(((	chrX:107978246-107978466(-)$1	1	8	12	11.9999
....	chr14:32315624-32315846(+)$1	1	198	202	11.9999
....	chr14:55510106-55510334(+)$1	1	187	191	11.9999
))..	chr10:871065-871287(-)$1	1	94	98	11.9999
))..	chr19:39423232-39423462(+)$1	1	97	101	11.9999
))))	chr1:215792155-215792377(+)$1	1	70	74	11.9999
....	chr19:40542170-40542402(-)$1	1	2	6	11.9999
))))	chr8:116427176-116427403(-)$1	1	148	152	11.9999
((((	chr5:140056546-140056768(-)$1	1	1	5	11.9999
....	chr11:32975354-32975574(+)$1	1	46	50	11.9999
))))	chr12:57965888-57966107(-)$1	1	82	86	11.9999
...(	chr7:91714833-91715061(+)$1	1	73	77	11.9999
))..	chr6:11134553-11134776(+)$1	1	194	198	11.9999
.)..	chr13:42874044-42874263(+)$1	1	74	78	11.9999
....	chrX:123224487-123224707(+)$1	1	174	178	11.9999
....	chr7:97946544-97946767(-)$1	1	122	126	11.9999
....	chr16:74660288-74660529(+)$1	1	175	179	11.9999
(...	chr13:31835020-31835240(+)$1	1	94	98	11.9999
((((	chr11:82570945-82571176(-)$1	1	87	91	11.9999
((((	chr1:36383143-36383369(+)$1	1	138	142	11.9999
....	chr10:63851575-63851794(+)$1	1	58	62	11.9999
((.(	chr14:105170155-105170384(+)$1	1	32	36	11.9999
(...	chr2:190647048-190647274(-)$1	1	130	134	11.9999
))))	chr7:156619267-156619489(-)$1	1	149	153	11.9999
....	chr12:123006622-123006849(-)$1	1	35	39	11.9999
....	chr19:9676704-9676924(-)$1	1	61	65	11.9999
....	chr10:60549339-60549787(-)$1	1	351	355	11.9999
....	chr19:8381367-8381586(-)$1	1	55	59	11.9999
.)))	chr4:166238950-166239170(+)$1	1	97	101	11.9999
))..	chr20:43135457-43135681(-)$1	1	135	139	11.9999
....	chr17:37421569-37421795(-)$1	1	22	26	11.9999
.)))	chr1:2520323-2520550(+)$1	1	67	71	11.9999
))..	chr10:60558082-60558313(-)$1	1	51	55	11.9999
....	chr6:33288224-33288455(+)$1	1	191	195	11.9999
((..	chrM:11649-12083(+)$1	1	241	245	11.9999
...)	chr9:106900325-106900546(+)$1	1	124	128	11.9999
((..	chrX:54185820-54186055(-)$1	1	160	164	11.9999
((.(	chr5:36181838-36182057(+)$1	1	90	94	11.9999
....	chr10:99132711-99132930(-)$1	1	6	10	11.9999
...)	chr20:35219551-35219785(+)$1	1	212	216	11.9999
....	chr16:2034772-2035003(+)$1	1	85	89	11.9999
((((	chr5:150484709-150484928(-)$1	1	76	80	11.9999
.((.	chr22:30730533-30730781(-)$1	1	191	195	11.9999
....	chr1:161200719-161200938(+)$1	1	100	104	11.9999
))).	chr14:95570230-95570455(-)$1	1	137	141	11.9999
....	chr1:153634802-153635036(-)$1	1	53	57	11.9999
))))	chr10:104620171-104620399(+)$1	1	160	164	11.9999
....	chr3:107799056-107799280(-)$1	1	126	130	11.9999
....	chr16:31200926-31201147(+)$1	1	66	70	11.9999

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	
A : 0.98	a : 0.01	

#score	839.9999999999994
#seq	70
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1MNASE_hg19_CDS_m2_run1.nuc.txt

#NT
AGGA	chr19:13218476-13218716(-)$1	240	2	6	12.0000
AGGA	chr12:4722705-4722945(+)$1	240	50	54	12.0000
AGGA	chr1:91180169-91180409(-)$1	240	31	35	12.0000
AGGA	chr5:78533154-78533394(+)$1	240	25	29	12.0000
AGGA	chr1:214793947-214794187(+)$1	240	188	192	12.0000
AGGA	chr1:166815788-166816028(+)$1	240	103	107	12.0000
AGGA	chr9:33354017-33354257(+)$1	240	10	14	12.0000
AGGA	chr14:78021674-78021914(-)$1	240	198	202	12.0000
AGGA	chr17:61511664-61511931(-)$1	267	233	237	12.0000
AGGA	chr6:149983080-149983320(-)$1	240	32	36	12.0000
AGGA	chr19:39214778-39215018(+)$1	240	100	104	12.0000
AGGA	chr9:131514990-131515230(-)$1	240	29	33	12.0000
AGGA	chr15:59350609-59350849(+)$1	240	135	139	12.0000
AGGA	chr16:3639909-3640149(-)$1	240	112	116	12.0000
AGGA	chr1:10464182-10464422(+)$1	240	99	103	12.0000
AGGA	chr12:113624450-113624690(+)$1	240	188	192	12.0000
AGGA	chr10:119805558-119805841(-)$1	283	80	84	12.0000
AGGA	chr14:75387882-75388122(-)$1	240	77	81	12.0000
AGGA	chr9:35075555-35075795(-)$1	240	153	157	12.0000
AGGA	chr11:65826576-65826816(+)$1	240	41	45	12.0000
AGGA	chr11:13443214-13443454(-)$1	240	90	94	12.0000
AGGA	chr1:85718136-85718416(-)$1	280	77	81	12.0000
AGGA	chr14:55453779-55454019(-)$1	240	13	17	12.0000
AGGA	chr6:4032837-4033077(+)$1	240	129	133	12.0000
AGGA	chr17:47119522-47119842(+)$1	320	54	58	12.0000
AGGA	chr19:33588564-33588804(+)$1	240	121	125	12.0000
AGGA	chr2:96964971-96965251(-)$1	280	42	46	12.0000
AGGA	chr14:31575819-31576059(-)$1	240	147	151	12.0000
AGGA	chr4:106640409-106640655(+)$1	246	51	55	12.0000
AGGA	chr6:44216310-44216554(+)$1	244	63	67	12.0000
AGGA	chr1:23395479-23395719(+)$1	240	136	140	12.0000
AGGA	chr1:153932947-153933187(-)$1	240	39	43	12.0000
AGGA	chr17:59667797-59668037(-)$1	240	176	180	12.0000
AGGA	chr8:6590031-6590271(+)$1	240	55	59	12.0000
AGGA	chr1:78041662-78041942(-)$1	280	240	244	12.0000
AGGA	chr10:103912052-103912376(+)$1	324	112	116	12.0000
AGGA	chr15:81041808-81042048(+)$1	240	193	197	12.0000
AGGA	chr19:39219822-39220231(+)$1	409	107	111	12.0000
AGGA	chr22:20109760-20110040(+)$1	280	76	80	12.0000
AGGA	chr11:85956169-85956409(+)$1	240	76	80	12.0000
AGGA	chr1:217784232-217784487(-)$1	255	107	111	12.0000
AGGA	chr6:26388166-26388410(+)$1	244	113	117	12.0000
AGGA	chr2:54147336-54147576(-)$1	240	87	91	12.0000
AGGA	chr12:22199216-22199456(+)$1	240	15	19	12.0000
AGGA	chr6:28057056-28057296(+)$1	240	191	195	12.0000
AGGA	chr9:100364678-100364972(-)$1	294	14	18	12.0000
AGGA	chr20:36630959-36631256(-)$1	297	78	82	12.0000
AGGA	chr16:68266048-68266288(-)$1	240	116	120	12.0000
AGGA	chr17:27958109-27958362(-)$1	253	139	143	12.0000
AGGA	chr10:15290611-15290851(-)$1	240	35	39	12.0000
AGGA	chr3:49005943-49006188(+)$1	245	21	25	12.0000
AGGA	chr17:1756320-1756566(+)$1	246	72	76	12.0000
agga	chr19:10662470-10662710(+)$1	240	35	39	12.0000
AGGA	chr1:153736206-153736446(+)$1	240	130	134	12.0000
AGGA	chr20:47860252-47860492(+)$1	240	107	111	12.0000
AGGA	chr11:47446089-47446329(-)$1	240	1	5	12.0000
AGGA	chr14:89083072-89083312(-)$1	240	95	99	12.0000
AGGA	chr2:26357734-26358054(+)$1	320	119	123	12.0000
AGGA	chr14:75264778-75265021(+)$1	243	122	126	12.0000
AGGA	chr16:88643536-88643777(+)$1	241	38	42	12.0000
AGGA	chr14:31816935-31817175(-)$1	240	95	99	12.0000
AGGA	chr7:92083799-92084079(+)$1	280	104	108	12.0000
AGGA	chr2:149402488-149402728(+)$1	240	5	9	12.0000
AGGA	chr11:32956565-32956845(+)$1	280	41	45	12.0000
AGGA	chr3:40353367-40353607(+)$1	240	106	110	12.0000
AGGA	chr19:37853632-37854067(+)$1	435	25	29	12.0000
AGGA	chr6:150386501-150386752(-)$1	251	114	118	12.0000
AGGA	chr22:32874902-32875182(+)$1	280	100	104	12.0000
AGGA	chr5:52096174-52096414(+)$1	240	5	9	12.0000
AGGA	chr12:52369095-52369339(+)$1	244	124	128	12.0000
AGGA	chr10:33545226-33545466(-)$1	240	22	26	12.0000
AGGA	chr6:168348954-168349195(+)$1	241	16	20	12.0000
AGGA	chr19:35757491-35757735(+)$1	244	17	21	12.0000
AGGA	chr11:77335924-77336204(-)$1	280	143	147	12.0000
AGGA	chr13:39262033-39262273(+)$1	240	88	92	12.0000
AGGA	chr1:180044070-180044350(+)$1	280	136	140	12.0000
AGGA	chr7:114582284-114582524(+)$1	240	43	47	12.0000
AGGA	chr19:579424-579702(+)$1	278	195	199	12.0000
AGGA	chr16:11935706-11935946(-)$1	240	158	162	12.0000
AGGA	chr19:37619729-37619969(+)$1	240	100	104	12.0000
AGGA	chr17:73231600-73231840(+)$1	240	70	74	12.0000

#otherMatches

#Struct PSSM
eeem	chr16:8952936-8953176(-)$1	240	135	139	12.0000
CCC{	chr19:13218476-13218716(-)$1	240	2	6	12.0000
HHHH	chr12:4722705-4722945(+)$1	240	50	54	12.0000
mmmm	chr1:91180169-91180409(-)$1	240	31	35	12.0000
dddd	chr5:78533154-78533394(+)$1	240	25	29	12.0000
ffgg	chr1:214793947-214794187(+)$1	240	188	192	12.0000
nnnn	chr1:166815788-166816028(+)$1	240	103	107	12.0000
hhhh	chr9:33354017-33354257(+)$1	240	10	14	12.0000
::::	chr14:78021674-78021914(-)$1	240	198	202	12.0000
ddd3	chr17:61511664-61511931(-)$1	267	233	237	12.0000
cc66	chr6:149983080-149983320(-)$1	240	32	36	12.0000
mccc	chr19:39214778-39215018(+)$1	240	100	104	12.0000
====	chr9:131514990-131515230(-)$1	240	29	33	12.0000
!ggg	chr15:59350609-59350849(+)$1	240	135	139	12.0000
eeee	chr16:3639909-3640149(-)$1	240	112	116	12.0000
ccbb	chr1:10464182-10464422(+)$1	240	99	103	12.0000
dccc	chr12:113624450-113624690(+)$1	240	188	192	12.0000
GG{B	chr10:119805558-119805841(-)$1	283	80	84	12.0000
CCC:	chr14:75387882-75388122(-)$1	240	77	81	12.0000
offf	chr9:35075555-35075795(-)$1	240	153	157	12.0000
::::	chr11:65826576-65826816(+)$1	240	41	45	12.0000
ffff	chr11:13443214-13443454(-)$1	240	90	94	12.0000
BEEE	chr1:85718136-85718416(-)$1	280	77	81	12.0000
oacc	chr14:55453779-55454019(-)$1	240	13	17	12.0000
}FFF	chr6:4032837-4033077(+)$1	240	129	133	12.0000
eeee	chr17:47119522-47119842(+)$1	320	54	58	12.0000
dd$$	chr19:33588564-33588804(+)$1	240	121	125	12.0000
''''	chr2:96964971-96965251(-)$1	280	42	46	12.0000
cc[a	chr14:31575819-31576059(-)$1	240	147	151	12.0000
pccc	chr4:106640409-106640655(+)$1	246	51	55	12.0000
fff7	chr6:44216310-44216554(+)$1	244	63	67	12.0000
d:ff	chr1:23395479-23395719(+)$1	240	136	140	12.0000
dddd	chr1:153932947-153933187(-)$1	240	39	43	12.0000
hhhh	chr17:59667797-59668037(-)$1	240	176	180	12.0000
gmmm	chr8:6590031-6590271(+)$1	240	55	59	12.0000
[ccc	chr1:78041662-78041942(-)$1	280	240	244	12.0000
Geee	chr10:103912052-103912376(+)$1	324	112	116	12.0000
ddd:	chr15:81041808-81042048(+)$1	240	193	197	12.0000
mmme	chr19:39219822-39220231(+)$1	409	107	111	12.0000
KBB{	chr22:20109760-20110040(+)$1	280	76	80	12.0000
eee"	chr11:85956169-85956409(+)$1	240	76	80	12.0000
phhh	chr1:217784232-217784487(-)$1	255	107	111	12.0000
BFFF	chr6:26388166-26388410(+)$1	244	113	117	12.0000
CCC{	chr2:54147336-54147576(-)$1	240	87	91	12.0000
[ccc	chr12:22199216-22199456(+)$1	240	15	19	12.0000
::::	chr6:28057056-28057296(+)$1	240	191	195	12.0000
lldd	chr9:100364678-100364972(-)$1	294	14	18	12.0000
ddd[	chr20:36630959-36631256(-)$1	297	78	82	12.0000
ggg#	chr16:68266048-68266288(-)$1	240	116	120	12.0000
eee]	chr17:27958109-27958362(-)$1	253	139	143	12.0000
eeee	chr10:15290611-15290851(-)$1	240	35	39	12.0000
::ee	chr3:49005943-49006188(+)$1	245	21	25	12.0000
eee]	chr17:1756320-1756566(+)$1	246	72	76	12.0000
gggg	chr19:10662470-10662710(+)$1	240	35	39	12.0000
ddmm	chr1:153736206-153736446(+)$1	240	130	134	12.0000
eeee	chr20:47860252-47860492(+)$1	240	107	111	12.0000
CCLL	chr11:47446089-47446329(-)$1	240	1	5	12.0000
c]cc	chr14:89083072-89083312(-)$1	240	95	99	12.0000
BB{D	chr2:26357734-26358054(+)$1	320	119	123	12.0000
CCYY	chr14:75264778-75265021(+)$1	243	122	126	12.0000
h%%%	chr16:88643536-88643777(+)$1	241	38	42	12.0000
:ddd	chr14:31816935-31817175(-)$1	240	95	99	12.0000
ffff	chr7:92083799-92084079(+)$1	280	104	108	12.0000
:GGG	chr2:149402488-149402728(+)$1	240	5	9	12.0000
dd[b	chr11:32956565-32956845(+)$1	280	41	45	12.0000
22ff	chr3:40353367-40353607(+)$1	240	106	110	12.0000
::::	chr19:37853632-37854067(+)$1	435	25	29	12.0000
hhh"	chr6:150386501-150386752(-)$1	251	114	118	12.0000
:::c	chr22:32874902-32875182(+)$1	280	100	104	12.0000
:FFF	chr5:52096174-52096414(+)$1	240	5	9	12.0000
]eee	chr12:52369095-52369339(+)$1	244	124	128	12.0000
KKFF	chr10:33545226-33545466(-)$1	240	22	26	12.0000
eeee	chr6:168348954-168349195(+)$1	241	16	20	12.0000
!ccc	chr19:35757491-35757735(+)$1	244	17	21	12.0000
pppp	chr11:77335924-77336204(-)$1	280	143	147	12.0000
[a!!	chr13:39262033-39262273(+)$1	240	88	92	12.0000
da!!	chr1:180044070-180044350(+)$1	280	136	140	12.0000
dd$$	chr7:114582284-114582524(+)$1	240	43	47	12.0000
}FFF	chr19:579424-579702(+)$1	278	195	199	12.0000
"bb[	chr16:11935706-11935946(-)$1	240	158	162	12.0000
qqa]	chr19:37619729-37619969(+)$1	240	100	104	12.0000
gggg	chr17:73231600-73231840(+)$1	240	70	74	12.0000

#DB
(((.	chr16:8952936-8953176(-)$1	1	135	139	12.0000
(((.	chr19:13218476-13218716(-)$1	1	2	6	12.0000
((((	chr12:4722705-4722945(+)$1	1	50	54	12.0000
....	chr1:91180169-91180409(-)$1	1	31	35	12.0000
))))	chr5:78533154-78533394(+)$1	1	25	29	12.0000
))))	chr1:214793947-214794187(+)$1	1	188	192	12.0000
....	chr1:166815788-166816028(+)$1	1	103	107	12.0000
((((	chr9:33354017-33354257(+)$1	1	10	14	12.0000
....	chr14:78021674-78021914(-)$1	1	198	202	12.0000
))).	chr17:61511664-61511931(-)$1	1	233	237	12.0000
))..	chr6:149983080-149983320(-)$1	1	32	36	12.0000
.)))	chr19:39214778-39215018(+)$1	1	100	104	12.0000
((((	chr9:131514990-131515230(-)$1	1	29	33	12.0000
.(((	chr15:59350609-59350849(+)$1	1	135	139	12.0000
))))	chr16:3639909-3640149(-)$1	1	112	116	12.0000
((((	chr1:10464182-10464422(+)$1	1	99	103	12.0000
((((	chr12:113624450-113624690(+)$1	1	188	192	12.0000
((.(	chr10:119805558-119805841(-)$1	1	80	84	12.0000
))).	chr14:75387882-75388122(-)$1	1	77	81	12.0000
.)))	chr9:35075555-35075795(-)$1	1	153	157	12.0000
....	chr11:65826576-65826816(+)$1	1	41	45	12.0000
))))	chr11:13443214-13443454(-)$1	1	90	94	12.0000
((((	chr1:85718136-85718416(-)$1	1	77	81	12.0000
.)))	chr14:55453779-55454019(-)$1	1	13	17	12.0000
.)))	chr6:4032837-4033077(+)$1	1	129	133	12.0000
))))	chr17:47119522-47119842(+)$1	1	54	58	12.0000
((..	chr19:33588564-33588804(+)$1	1	121	125	12.0000
....	chr2:96964971-96965251(-)$1	1	42	46	12.0000
((.(	chr14:31575819-31576059(-)$1	1	147	151	12.0000
.)))	chr4:106640409-106640655(+)$1	1	51	55	12.0000
))).	chr6:44216310-44216554(+)$1	1	63	67	12.0000
).((	chr1:23395479-23395719(+)$1	1	136	140	12.0000
))))	chr1:153932947-153933187(-)$1	1	39	43	12.0000
))))	chr17:59667797-59668037(-)$1	1	176	180	12.0000
(...	chr8:6590031-6590271(+)$1	1	55	59	12.0000
.(((	chr1:78041662-78041942(-)$1	1	240	244	12.0000
((((	chr10:103912052-103912376(+)$1	1	112	116	12.0000
))).	chr15:81041808-81042048(+)$1	1	193	197	12.0000
...)	chr19:39219822-39220231(+)$1	1	107	111	12.0000
.((.	chr22:20109760-20110040(+)$1	1	76	80	12.0000
(((.	chr11:85956169-85956409(+)$1	1	76	80	12.0000
.)))	chr1:217784232-217784487(-)$1	1	107	111	12.0000
))))	chr6:26388166-26388410(+)$1	1	113	117	12.0000
(((.	chr2:54147336-54147576(-)$1	1	87	91	12.0000
.(((	chr12:22199216-22199456(+)$1	1	15	19	12.0000
....	chr6:28057056-28057296(+)$1	1	191	195	12.0000
..))	chr9:100364678-100364972(-)$1	1	14	18	12.0000
(((.	chr20:36630959-36631256(-)$1	1	78	82	12.0000
(((.	chr16:68266048-68266288(-)$1	1	116	120	12.0000
))).	chr17:27958109-27958362(-)$1	1	139	143	12.0000
))))	chr10:15290611-15290851(-)$1	1	35	39	12.0000
..((	chr3:49005943-49006188(+)$1	1	21	25	12.0000
))).	chr17:1756320-1756566(+)$1	1	72	76	12.0000
((((	chr19:10662470-10662710(+)$1	1	35	39	12.0000
((..	chr1:153736206-153736446(+)$1	1	130	134	12.0000
))))	chr20:47860252-47860492(+)$1	1	107	111	12.0000
((..	chr11:47446089-47446329(-)$1	1	1	5	12.0000
).))	chr14:89083072-89083312(-)$1	1	95	99	12.0000
((.(	chr2:26357734-26358054(+)$1	1	119	123	12.0000
))..	chr14:75264778-75265021(+)$1	1	122	126	12.0000
(...	chr16:88643536-88643777(+)$1	1	38	42	12.0000
.(((	chr14:31816935-31817175(-)$1	1	95	99	12.0000
))))	chr7:92083799-92084079(+)$1	1	104	108	12.0000
.(((	chr2:149402488-149402728(+)$1	1	5	9	12.0000
((.(	chr11:32956565-32956845(+)$1	1	41	45	12.0000
..))	chr3:40353367-40353607(+)$1	1	106	110	12.0000
....	chr19:37853632-37854067(+)$1	1	25	29	12.0000
(((.	chr6:150386501-150386752(-)$1	1	114	118	12.0000
...(	chr22:32874902-32875182(+)$1	1	100	104	12.0000
.(((	chr5:52096174-52096414(+)$1	1	5	9	12.0000
.)))	chr12:52369095-52369339(+)$1	1	124	128	12.0000
..((	chr10:33545226-33545466(-)$1	1	22	26	12.0000
((((	chr6:168348954-168349195(+)$1	1	16	20	12.0000
.(((	chr19:35757491-35757735(+)$1	1	17	21	12.0000
....	chr11:77335924-77336204(-)$1	1	143	147	12.0000
.(..	chr13:39262033-39262273(+)$1	1	88	92	12.0000
)(..	chr1:180044070-180044350(+)$1	1	136	140	12.0000
((..	chr7:114582284-114582524(+)$1	1	43	47	12.0000
.)))	chr19:579424-579702(+)$1	1	195	199	12.0000
.((.	chr16:11935706-11935946(-)$1	1	158	162	12.0000
..).	chr19:37619729-37619969(+)$1	1	100	104	12.0000
((((	chr17:73231600-73231840(+)$1	1	70	74	12.0000

#PSSM
A : 0.98	a : 0.01	
G : 0.98	g : 0.01	
G : 0.98	g : 0.01	
A : 0.98	a : 0.01	

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28A_Hafner2013_hg19_UTR_m1_run1.nuc.txt

#NT
CUUU	chr11:82535292-82535514(-)$1	222	44	48	11.9999
CUUU	chr14:90446825-90447066(+)$1	241	31	35	11.9999
CUUU	chr16:23583298-23583525(+)$1	227	191	195	11.9999
CUUU	chr1:193056683-193056907(+)$1	224	7	11	11.9999
CUUU	chr1:213071730-213071952(+)$1	222	126	130	11.9999
CUUU	chr5:114461422-114461645(-)$1	223	186	190	11.9999
CUUU	chr19:11172755-11172982(+)$1	227	6	10	11.9999
CUUU	chr20:11904755-11904980(+)$1	225	76	80	11.9999
CUUU	chr3:129033550-129033801(-)$1	251	58	62	11.9999
CUUU	chr19:30498303-30498524(+)$1	221	23	27	11.9999
CUUU	chr15:101812748-101812967(-)$1	219	9	13	11.9999
cuuu	chr12:70214026-70214248(+)$1	222	24	28	11.9999
CUUU	chr1:19231387-19231611(-)$1	224	170	174	11.9999
CUUU	chr2:32534938-32535164(+)$1	226	120	124	11.9999
CUUU	chr2:171819281-171819508(+)$1	227	39	43	11.9999
CUUU	chr7:139247481-139247701(-)$1	220	29	33	11.9999
CUUU	chr19:33204540-33204764(+)$1	224	48	52	11.9999
CUUU	chr3:10192988-10193213(+)$1	225	80	84	11.9999
CUUU	chr1:33328764-33328994(-)$1	230	3	7	11.9999
CUUU	chr11:111744760-111744981(-)$1	221	20	24	11.9999
cuuu	chr2:191370483-191370702(-)$1	219	159	163	11.9999
CUUU	chr1:193054622-193054845(+)$1	223	158	162	11.9999
CUUU	chr8:56923192-56923412(+)$1	220	4	8	11.9999
CUUU	chr13:28536923-28537146(-)$1	223	95	99	11.9999
CUUU	chr12:110787119-110787350(+)$1	231	38	42	11.9999
CUUU	chr17:40176390-40176620(+)$1	230	40	44	11.9999
CUUU	chr20:50215352-50215575(-)$1	223	112	116	11.9999
CUUU	chr1:6285061-6285284(-)$1	223	60	64	11.9999
CUUU	chr1:224605911-224606161(-)$1	250	17	21	11.9999
CUUU	chr4:39207133-39207359(+)$1	226	38	42	11.9999
CUUU	chr5:112354680-112354912(+)$1	232	51	55	11.9999
CUUU	chr6:79911161-79911388(-)$1	227	30	34	11.9999
CUUU	chr1:167758301-167758526(+)$1	225	10	14	11.9999
CUUU	chr1:109855836-109856058(-)$1	222	0	4	11.9999
CUUU	chr17:37360834-37361076(+)$1	242	35	39	11.9999
cuuu	chr9:96208734-96208966(-)$1	232	53	57	11.9999
CUUU	chr11:58386132-58386354(+)$1	222	10	14	11.9999
cuuu	chr10:14950097-14950329(+)$1	232	66	70	11.9999
CUUU	chr16:66648712-66648936(-)$1	224	5	9	11.9999
CUUU	chr2:170938779-170939001(+)$1	222	101	105	11.9999
CUUU	chr14:89627017-89627237(-)$1	220	210	214	11.9999
CUUU	chr1:114516653-114516876(+)$1	223	14	18	11.9999
cuuu	chr3:56654924-56655151(-)$1	227	121	125	11.9999
CUUU	chr19:49378890-49379122(+)$1	232	182	186	11.9999
CUUU	chr6:64290197-64290429(+)$1	232	134	138	11.9999
CUUU	chr22:38881115-38881339(-)$1	224	104	108	11.9999
CUUU	chr3:101486434-101486654(+)$1	220	53	57	11.9999
CUUU	chr1:114308222-114308452(-)$1	230	77	81	11.9999
CUUU	chr21:46934533-46934766(-)$1	233	2	6	11.9999
CUUU	chr1:243667542-243667775(-)$1	233	13	17	11.9999
CUUU	chr12:2912913-2913142(+)$1	229	213	217	11.9999
CUUU	chr11:14300027-14300249(-)$1	222	63	67	11.9999
CUUU	chr6:30152897-30153128(-)$1	231	173	177	11.9999
CUUU	chr2:70315981-70316202(+)$1	221	82	86	11.9999
CUUU	chrX:41376710-41376941(-)$1	231	0	4	11.9999
CUUU	chr19:6458181-6458401(-)$1	220	51	55	11.9999
CUUU	chr22:39900130-39900365(+)$1	235	24	28	11.9999
CUUU	chr19:44741004-44741227(+)$1	223	0	4	11.9999
CUUU	chr17:27582853-27583094(-)$1	241	71	75	11.9999
CUUU	chr1:6206766-6207004(-)$1	238	222	226	11.9999
CUUU	chr3:12624863-12625085(+)$1	222	37	41	11.9999
CUUU	chr15:73044034-73044260(-)$1	226	120	124	11.9999
CUUU	chr7:111982706-111982930(+)$1	224	37	41	11.9999
CUUU	chr14:96559722-96559955(+)$1	233	24	28	11.9999
CUUU	chr8:33370018-33370240(-)$1	222	14	18	11.9999
CUUU	chr7:98993993-98994215(-)$1	222	112	116	11.9999
CUUU	chr7:90016780-90017005(+)$1	225	137	141	11.9999
CUUU	chr4:108832001-108832225(+)$1	224	3	7	11.9999
cuuu	chr19:58104280-58104504(+)$1	224	13	17	11.9999
CUUU	chr14:51443399-51443621(-)$1	222	4	8	11.9999
CUUU	chr1:164528927-164529156(+)$1	229	124	128	11.9999
CUUU	chr8:80950072-80950295(-)$1	223	43	47	11.9999
CUUU	chr19:39369291-39369518(-)$1	227	32	36	11.9999
CUUU	chr2:69549114-69549346(-)$1	232	80	84	11.9999
CUUU	chr19:18642902-18643125(-)$1	223	46	50	11.9999
CUUU	chr10:71267255-71267481(+)$1	226	176	180	11.9999
CUUU	chr8:64125176-64125398(+)$1	222	129	133	11.9999
CUUU	chr16:107299-107518(+)$1	219	36	40	11.9999
CUUU	chr12:49086999-49087229(-)$1	230	99	103	11.9999
CUUU	chr12:3920686-3920913(-)$1	227	24	28	11.9999
CUUU	chr1:229458231-229458453(-)$1	222	25	29	11.9999
CUUU	chrX:154467592-154467821(+)$1	229	142	146	11.9999
CUUU	chr1:231136097-231136326(+)$1	229	138	142	11.9999
CUUU	chr12:12629327-12629553(-)$1	226	85	89	11.9999
CUUU	chr1:226333730-226333964(-)$1	234	87	91	11.9999
CUUU	chr1:236380174-236380408(-)$1	234	122	126	11.9999

#otherMatches

#Struct PSSM
:::C	chr3:196077529-196077748(-)$1	219	0	4	11.9999
hhhb	chr11:82535292-82535514(-)$1	222	44	48	11.9999
gggg	chr14:90446825-90447066(+)$1	241	31	35	11.9999
c!!b	chr16:23583298-23583525(+)$1	227	191	195	11.9999
nnne	chr1:193056683-193056907(+)$1	224	7	11	11.9999
qqqq	chr1:213071730-213071952(+)$1	222	126	130	11.9999
::::	chr5:114461422-114461645(-)$1	223	186	190	11.9999
::::	chr19:11172755-11172982(+)$1	227	6	10	11.9999
diii	chr20:11904755-11904980(+)$1	225	76	80	11.9999
DDD{	chr3:129033550-129033801(-)$1	251	58	62	11.9999
::::	chr19:30498303-30498524(+)$1	221	23	27	11.9999
mmmm	chr15:101812748-101812967(-)$1	219	9	13	11.9999
h:::	chr12:70214026-70214248(+)$1	222	24	28	11.9999
eeee	chr1:19231387-19231611(-)$1	224	170	174	11.9999
====	chr2:32534938-32535164(+)$1	226	120	124	11.9999
::::	chr2:171819281-171819508(+)$1	227	39	43	11.9999
:III	chr7:139247481-139247701(-)$1	220	29	33	11.9999
d:::	chr19:33204540-33204764(+)$1	224	48	52	11.9999
!ccc	chr3:10192988-10193213(+)$1	225	80	84	11.9999
::::	chr1:33328764-33328994(-)$1	230	3	7	11.9999
'ddd	chr11:111744760-111744981(-)$1	221	20	24	11.9999
dd44	chr2:191370483-191370702(-)$1	219	159	163	11.9999
]ddd	chr1:193054622-193054845(+)$1	223	158	162	11.9999
FFFF	chr8:56923192-56923412(+)$1	220	4	8	11.9999
>>>>	chr13:28536923-28537146(-)$1	223	95	99	11.9999
::::	chr12:110787119-110787350(+)$1	231	38	42	11.9999
IIIB	chr17:40176390-40176620(+)$1	230	40	44	11.9999
====	chr20:50215352-50215575(-)$1	223	112	116	11.9999
ffff	chr1:6285061-6285284(-)$1	223	60	64	11.9999
::::	chr1:224605911-224606161(-)$1	250	17	21	11.9999
pppp	chr4:39207133-39207359(+)$1	226	38	42	11.9999
cc22	chr5:112354680-112354912(+)$1	232	51	55	11.9999
%%%%	chr6:79911161-79911388(-)$1	227	30	34	11.9999
::::	chr1:167758301-167758526(+)$1	225	10	14	11.9999
::::	chr1:109855836-109856058(-)$1	222	0	4	11.9999
HHHK	chr17:37360834-37361076(+)$1	242	35	39	11.9999
LLHH	chr9:96208734-96208966(-)$1	232	53	57	11.9999
::::	chr11:58386132-58386354(+)$1	222	10	14	11.9999
hh++	chr10:14950097-14950329(+)$1	232	66	70	11.9999
::::	chr16:66648712-66648936(-)$1	224	5	9	11.9999
gggg	chr2:170938779-170939001(+)$1	222	101	105	11.9999
::::	chr14:89627017-89627237(-)$1	220	210	214	11.9999
::::	chr1:114516653-114516876(+)$1	223	14	18	11.9999
bnnn	chr3:56654924-56655151(-)$1	227	121	125	11.9999
cc33	chr19:49378890-49379122(+)$1	232	182	186	11.9999
::::	chr6:64290197-64290429(+)$1	232	134	138	11.9999
!ddd	chr22:38881115-38881339(-)$1	224	104	108	11.9999
cc::	chr3:101486434-101486654(+)$1	220	53	57	11.9999
c333	chr1:114308222-114308452(-)$1	230	77	81	11.9999
ddpp	chr21:46934533-46934766(-)$1	233	2	6	11.9999
nncc	chr1:243667542-243667775(-)$1	233	13	17	11.9999
d:::	chr12:2912913-2913142(+)$1	229	213	217	11.9999
b555	chr11:14300027-14300249(-)$1	222	63	67	11.9999
hhh[	chr6:30152897-30153128(-)$1	231	173	177	11.9999
::::	chr2:70315981-70316202(+)$1	221	82	86	11.9999
::::	chrX:41376710-41376941(-)$1	231	0	4	11.9999
LLDD	chr19:6458181-6458401(-)$1	220	51	55	11.9999
cc!!	chr22:39900130-39900365(+)$1	235	24	28	11.9999
:DDD	chr19:44741004-44741227(+)$1	223	0	4	11.9999
ff::	chr17:27582853-27583094(-)$1	241	71	75	11.9999
dddd	chr1:6206766-6207004(-)$1	238	222	226	11.9999
nnnn	chr3:12624863-12625085(+)$1	222	37	41	11.9999
bb22	chr15:73044034-73044260(-)$1	226	120	124	11.9999
gggg	chr7:111982706-111982930(+)$1	224	37	41	11.9999
oooo	chr14:96559722-96559955(+)$1	233	24	28	11.9999
EEEE	chr8:33370018-33370240(-)$1	222	14	18	11.9999
ffff	chr7:98993993-98994215(-)$1	222	112	116	11.9999
::::	chr7:90016780-90017005(+)$1	225	137	141	11.9999
::::	chr4:108832001-108832225(+)$1	224	3	7	11.9999
::::	chr19:58104280-58104504(+)$1	224	13	17	11.9999
:::g	chr14:51443399-51443621(-)$1	222	4	8	11.9999
brrr	chr1:164528927-164529156(+)$1	229	124	128	11.9999
!ddd	chr8:80950072-80950295(-)$1	223	43	47	11.9999
EEEE	chr19:39369291-39369518(-)$1	227	32	36	11.9999
ffff	chr2:69549114-69549346(-)$1	232	80	84	11.9999
::::	chr19:18642902-18643125(-)$1	223	46	50	11.9999
^^^^	chr10:71267255-71267481(+)$1	226	176	180	11.9999
dsss	chr8:64125176-64125398(+)$1	222	129	133	11.9999
7777	chr16:107299-107518(+)$1	219	36	40	11.9999
F:::	chr12:49086999-49087229(-)$1	230	99	103	11.9999
JJJJ	chr12:3920686-3920913(-)$1	227	24	28	11.9999
eee:	chr1:229458231-229458453(-)$1	222	25	29	11.9999
:eee	chrX:154467592-154467821(+)$1	229	142	146	11.9999
cc55	chr1:231136097-231136326(+)$1	229	138	142	11.9999
###e	chr12:12629327-12629553(-)$1	226	85	89	11.9999
####	chr1:226333730-226333964(-)$1	234	87	91	11.9999
fffr	chr1:236380174-236380408(-)$1	234	122	126	11.9999

#DB
...(	chr3:196077529-196077748(-)$1	1	0	4	11.9999
))))	chr11:82535292-82535514(-)$1	1	44	48	11.9999
))))	chr14:90446825-90447066(+)$1	1	31	35	11.9999
(..(	chr16:23583298-23583525(+)$1	1	191	195	11.9999
...)	chr1:193056683-193056907(+)$1	1	7	11	11.9999
....	chr1:213071730-213071952(+)$1	1	126	130	11.9999
....	chr5:114461422-114461645(-)$1	1	186	190	11.9999
....	chr19:11172755-11172982(+)$1	1	6	10	11.9999
((((	chr20:11904755-11904980(+)$1	1	76	80	11.9999
(((.	chr3:129033550-129033801(-)$1	1	58	62	11.9999
....	chr19:30498303-30498524(+)$1	1	23	27	11.9999
....	chr15:101812748-101812967(-)$1	1	9	13	11.9999
)...	chr12:70214026-70214248(+)$1	1	24	28	11.9999
))))	chr1:19231387-19231611(-)$1	1	170	174	11.9999
))))	chr2:32534938-32535164(+)$1	1	120	124	11.9999
....	chr2:171819281-171819508(+)$1	1	39	43	11.9999
.(((	chr7:139247481-139247701(-)$1	1	29	33	11.9999
)...	chr19:33204540-33204764(+)$1	1	48	52	11.9999
.(((	chr3:10192988-10193213(+)$1	1	80	84	11.9999
....	chr1:33328764-33328994(-)$1	1	3	7	11.9999
.(((	chr11:111744760-111744981(-)$1	1	20	24	11.9999
))..	chr2:191370483-191370702(-)$1	1	159	163	11.9999
.)))	chr1:193054622-193054845(+)$1	1	158	162	11.9999
((((	chr8:56923192-56923412(+)$1	1	4	8	11.9999
....	chr13:28536923-28537146(-)$1	1	95	99	11.9999
....	chr12:110787119-110787350(+)$1	1	38	42	11.9999
((((	chr17:40176390-40176620(+)$1	1	40	44	11.9999
((((	chr20:50215352-50215575(-)$1	1	112	116	11.9999
((((	chr1:6285061-6285284(-)$1	1	60	64	11.9999
....	chr1:224605911-224606161(-)$1	1	17	21	11.9999
....	chr4:39207133-39207359(+)$1	1	38	42	11.9999
))..	chr5:112354680-112354912(+)$1	1	51	55	11.9999
....	chr6:79911161-79911388(-)$1	1	30	34	11.9999
....	chr1:167758301-167758526(+)$1	1	10	14	11.9999
....	chr1:109855836-109856058(-)$1	1	0	4	11.9999
(((.	chr17:37360834-37361076(+)$1	1	35	39	11.9999
..((	chr9:96208734-96208966(-)$1	1	53	57	11.9999
....	chr11:58386132-58386354(+)$1	1	10	14	11.9999
((..	chr10:14950097-14950329(+)$1	1	66	70	11.9999
....	chr16:66648712-66648936(-)$1	1	5	9	11.9999
((((	chr2:170938779-170939001(+)$1	1	101	105	11.9999
....	chr14:89627017-89627237(-)$1	1	210	214	11.9999
....	chr1:114516653-114516876(+)$1	1	14	18	11.9999
(...	chr3:56654924-56655151(-)$1	1	121	125	11.9999
))..	chr19:49378890-49379122(+)$1	1	182	186	11.9999
....	chr6:64290197-64290429(+)$1	1	134	138	11.9999
.(((	chr22:38881115-38881339(-)$1	1	104	108	11.9999
))..	chr3:101486434-101486654(+)$1	1	53	57	11.9999
)...	chr1:114308222-114308452(-)$1	1	77	81	11.9999
((..	chr21:46934533-46934766(-)$1	1	2	6	11.9999
..))	chr1:243667542-243667775(-)$1	1	13	17	11.9999
)...	chr12:2912913-2913142(+)$1	1	213	217	11.9999
)...	chr11:14300027-14300249(-)$1	1	63	67	11.9999
(((.	chr6:30152897-30153128(-)$1	1	173	177	11.9999
....	chr2:70315981-70316202(+)$1	1	82	86	11.9999
....	chrX:41376710-41376941(-)$1	1	0	4	11.9999
..((	chr19:6458181-6458401(-)$1	1	51	55	11.9999
((..	chr22:39900130-39900365(+)$1	1	24	28	11.9999
.(((	chr19:44741004-44741227(+)$1	1	0	4	11.9999
))..	chr17:27582853-27583094(-)$1	1	71	75	11.9999
))))	chr1:6206766-6207004(-)$1	1	222	226	11.9999
....	chr3:12624863-12625085(+)$1	1	37	41	11.9999
))..	chr15:73044034-73044260(-)$1	1	120	124	11.9999
((((	chr7:111982706-111982930(+)$1	1	37	41	11.9999
....	chr14:96559722-96559955(+)$1	1	24	28	11.9999
((((	chr8:33370018-33370240(-)$1	1	14	18	11.9999
((((	chr7:98993993-98994215(-)$1	1	112	116	11.9999
....	chr7:90016780-90017005(+)$1	1	137	141	11.9999
....	chr4:108832001-108832225(+)$1	1	3	7	11.9999
....	chr19:58104280-58104504(+)$1	1	13	17	11.9999
...(	chr14:51443399-51443621(-)$1	1	4	8	11.9999
(...	chr1:164528927-164529156(+)$1	1	124	128	11.9999
.(((	chr8:80950072-80950295(-)$1	1	43	47	11.9999
((((	chr19:39369291-39369518(-)$1	1	32	36	11.9999
))))	chr2:69549114-69549346(-)$1	1	80	84	11.9999
....	chr19:18642902-18643125(-)$1	1	46	50	11.9999
....	chr10:71267255-71267481(+)$1	1	176	180	11.9999
(...	chr8:64125176-64125398(+)$1	1	129	133	11.9999
....	chr16:107299-107518(+)$1	1	36	40	11.9999
(...	chr12:49086999-49087229(-)$1	1	99	103	11.9999
((((	chr12:3920686-3920913(-)$1	1	24	28	11.9999
))).	chr1:229458231-229458453(-)$1	1	25	29	11.9999
.(((	chrX:154467592-154467821(+)$1	1	142	146	11.9999
))..	chr1:231136097-231136326(+)$1	1	138	142	11.9999
...(	chr12:12629327-12629553(-)$1	1	85	89	11.9999
....	chr1:226333730-226333964(-)$1	1	87	91	11.9999
(((.	chr1:236380174-236380408(-)$1	1	122	126	11.9999

#PSSM
C : 0.93	c : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	
U : 0.93	u : 0.06	

#score	1043.9999999999998
#seq	87
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_CDS_m1_run2.nuc.txt

#NT
UGGUGAA	chr20:30898241-30898481(+)$1	240	31	38	10.9999
UUCUGAC	chr6:57012060-57012300(+)$1	240	58	65	8.9999
UUGGGAG	chr10:35324040-35324280(-)$1	240	20	27	8.3076
UUGUGAG	chr6:142525018-142525301(+)$1	283	202	209	12.5384
UUGUGAU	chr6:44220684-44220924(+)$1	240	81	88	13.2307
UGGUGAG	chr2:55518727-55518967(-)$1	240	154	161	9.4615
UGGUGAC	chr9:125652551-125652791(-)$1	240	18	25	9.1538
UGGUGAU	chr2:86371487-86371734(-)$1	247	166	173	10.1538
UUCUGAU	chr11:111931701-111931941(+)$1	240	8	15	9.9999
UUGUGAU	chr9:95077992-95078232(-)$1	240	99	106	13.2307
UUAUGAG	chr2:175742525-175742765(-)$1	240	74	81	9.3076
UUCUGAA	chr11:34145760-34146000(+)$1	240	40	47	10.8461
CUGUGAA	chr16:2817366-2817606(+)$1	240	4	11	10.3846
UUGUGAA	chr9:72879124-72879364(+)$1	240	107	114	14.0769
CUGUGAA	chr6:64395239-64395491(+)$1	252	83	90	10.3846
UUGGGAG	chr12:120578629-120578869(-)$1	240	57	64	8.3076
UUUUGAA	chr16:2812928-2813168(+)$1	240	216	223	10.7692
UUAUGAC	chr6:116747770-116748010(+)$1	240	32	39	8.9999
UUAUGAA	chr19:36940129-36940369(-)$1	240	79	86	10.8461
UUCUGAG	chr8:53599344-53599584(-)$1	240	59	66	9.3076
UUUUGAU	chr6:97339016-97339256(-)$1	240	48	55	9.9230
UCGUGAA	chr1:19923426-19923666(+)$1	240	165	172	10.3846
AUGUGAA	chr16:14738178-14738434(+)$1	256	47	54	10.0769
CUGUGAU	chr11:58893310-58893550(+)$1	240	31	38	9.5384
UAGUGAU	chr3:37067066-37067306(+)$1	240	144	151	9.6153
UUGUAAU	chr10:22015079-22015359(+)$1	280	73	80	8.6923
UUGUGGU	chr3:57545497-57545737(+)$1	240	32	39	8.5384
UUGUCAU	chr1:118039368-118039608(+)$1	240	210	217	8.6923
UUGUGAU	chr6:83829422-83829662(+)$1	240	23	30	13.2307
UAGUGAA	chr8:12943821-12944061(-)$1	240	11	18	10.4615
UUGGGAA	chr17:76073172-76073412(+)$1	240	22	29	9.8461
UGGUGAU	chr5:77334948-77335188(-)$1	240	197	204	10.1538
UUGGGAA	chr8:61734523-61734763(+)$1	240	20	27	9.8461
UGGUGAA	chr5:147793716-147793956(+)$1	240	3	10	10.9999
UUGUGUG	chr16:15163946-15164186(-)$1	240	5	12	7.9230
UUGGGAA	chr3:182987973-182988213(+)$1	240	53	60	9.8461
GUGUGAU	chr12:50146191-50146431(+)$1	240	7	14	9.3076
UUGUGAA	chr2:65466897-65467137(+)$1	240	89	96	14.0769
UGGUGAA	chr19:37733602-37733842(+)$1	240	114	121	10.9999
UUGUCAA	chr6:7240594-7240834(+)$1	240	92	99	9.5384
CUGUGAA	chr21:33057793-33058033(-)$1	240	167	174	10.3846
UGGUGAC	chr3:52558482-52558722(-)$1	240	212	219	9.1538
AUGUGAA	chr5:138260187-138260427(+)$1	240	29	36	10.0769
UUGUGUU	chr3:49005941-49006181(+)$1	240	73	80	8.6153
UUGUGAU	chr10:120820163-120820403(-)$1	240	172	179	13.2307
UUAUGAU	chr15:30010891-30011131(-)$1	240	64	71	9.9999
CUGUGAA	chr5:66462011-66462251(+)$1	240	8	15	10.3846
UUCUGAU	chr21:35183352-35183592(+)$1	240	193	200	9.9999
UUGUGAA	chr15:101109392-101109636(-)$1	244	1	8	14.0769
UCGUGAA	chr4:142053797-142054037(-)$1	240	202	209	10.3846
UUGUAAA	chr8:25341569-25341809(+)$1	240	54	61	9.5384
GUGUGAG	chr3:194790343-194790583(-)$1	240	79	86	8.6153
UUUUGAG	chr2:182765492-182765732(+)$1	240	82	89	9.2307
CUGUGAA	chr10:104233230-104233470(+)$1	240	23	30	10.3846
UUGUGAA	chrX:62569830-62570070(-)$1	240	186	193	14.0769
UUGUGAA	chr14:32560324-32560564(+)$1	240	86	93	14.0769
UGGUGAG	chr1:44446933-44447173(+)$1	240	210	217	9.4615
GUGUGAC	chr1:55223616-55223856(-)$1	240	49	56	8.3076
UAGUGAU	chr19:8922427-8922667(-)$1	240	152	159	9.6153
UUAUGAA	chr1:220287561-220287801(+)$1	240	77	84	10.8461
UGGUGAA	chr16:58031628-58031868(-)$1	240	168	175	10.9999
UUUUGAC	chr18:8638119-8638359(+)$1	240	214	221	8.9230
UUCUGAU	chr16:48337004-48337244(+)$1	240	189	196	9.9999
UUAUGAA	chr12:50152093-50152333(+)$1	240	1	8	10.8461

#otherMatches

#Struct PSSM
iiiiiil	chr8:67576690-67576930(-)$1	240	127	134	10.7692
ddddmmm	chr20:30898241-30898481(+)$1	240	31	38	10.9999
e]ccc::	chr6:57012060-57012300(+)$1	240	58	65	8.9999
iiiiiqq	chr10:35324040-35324280(-)$1	240	20	27	8.3076
::::fff	chr6:142525018-142525301(+)$1	283	202	209	12.5384
JJJJJJJ	chr6:44220684-44220924(+)$1	240	81	88	13.2307
eeeGGGG	chr2:55518727-55518967(-)$1	240	154	161	9.4615
JJJJ::d	chr9:125652551-125652791(-)$1	240	18	25	9.1538
777777e	chr2:86371487-86371734(-)$1	247	166	173	10.1538
xxxxxxx	chr11:111931701-111931941(+)$1	240	8	15	9.9999
eeeee::	chr9:95077992-95078232(-)$1	240	99	106	13.2307
c!!bb[b	chr2:175742525-175742765(-)$1	240	74	81	9.3076
EEEEEff	chr11:34145760-34146000(+)$1	240	40	47	10.8461
fff$$$$	chr16:2817366-2817606(+)$1	240	4	11	10.3846
HHHHH}C	chr9:72879124-72879364(+)$1	240	107	114	14.0769
[dddd++	chr6:64395239-64395491(+)$1	252	83	90	10.3846
IIIIIII	chr12:120578629-120578869(-)$1	240	57	64	8.3076
ZZZCCC/	chr16:2812928-2813168(+)$1	240	216	223	10.7692
(((((bb	chr6:116747770-116748010(+)$1	240	32	39	8.9999
d22eeee	chr19:36940129-36940369(-)$1	240	79	86	10.8461
fffff]c	chr8:53599344-53599584(-)$1	240	59	66	9.3076
iiiiiii	chr6:97339016-97339256(-)$1	240	48	55	9.9230
ccnnnnn	chr1:19923426-19923666(+)$1	240	165	172	10.3846
pa]ccc:	chr16:14738178-14738434(+)$1	256	47	54	10.0769
CCC{A::	chr11:58893310-58893550(+)$1	240	31	38	9.5384
fff]ccc	chr3:37067066-37067306(+)$1	240	144	151	9.6153
ddd''''	chr10:22015079-22015359(+)$1	280	73	80	8.6923
eeebbdd	chr3:57545497-57545737(+)$1	240	32	39	8.5384
b[fffff	chr1:118039368-118039608(+)$1	240	210	217	8.6923
##ccc""	chr6:83829422-83829662(+)$1	240	23	30	13.2307
eeeee::	chr8:12943821-12944061(-)$1	240	11	18	10.4615
lllffff	chr17:76073172-76073412(+)$1	240	22	29	9.8461
?BB}BB}	chr5:77334948-77335188(-)$1	240	197	204	10.1538
mmmbb22	chr8:61734523-61734763(+)$1	240	20	27	9.8461
:::::::	chr5:147793716-147793956(+)$1	240	3	10	10.9999
CCC{CCC	chr16:15163946-15164186(-)$1	240	5	12	7.9230
:hhhhhh	chr3:182987973-182988213(+)$1	240	53	60	9.8461
a[bb[cc	chr12:50146191-50146431(+)$1	240	7	14	9.3076
4444fff	chr2:65466897-65467137(+)$1	240	89	96	14.0769
mmeeeee	chr19:37733602-37733842(+)$1	240	114	121	10.9999
eeeee::	chr6:7240594-7240834(+)$1	240	92	99	9.5384
bb[dddd	chr21:33057793-33058033(-)$1	240	167	174	10.3846
fffff]b	chr3:52558482-52558722(-)$1	240	212	219	9.1538
!!ddddb	chr5:138260187-138260427(+)$1	240	29	36	10.0769
:hhhhhh	chr3:49005941-49006181(+)$1	240	73	80	8.6153
=======	chr10:120820163-120820403(-)$1	240	172	179	13.2307
:::dddd	chr15:30010891-30011131(-)$1	240	64	71	9.9999
:::::::	chr5:66462011-66462251(+)$1	240	8	15	10.3846
''''ggg	chr21:35183352-35183592(+)$1	240	193	200	9.9999
CCC{GGG	chr15:101109392-101109636(-)$1	244	1	8	14.0769
eeddddl	chr4:142053797-142054037(-)$1	240	202	209	10.3846
ddppppp	chr8:25341569-25341809(+)$1	240	54	61	9.5384
mmmccce	chr3:194790343-194790583(-)$1	240	79	86	8.6153
dd:::::	chr2:182765492-182765732(+)$1	240	82	89	9.2307
ggmmmmg	chr10:104233230-104233470(+)$1	240	23	30	10.3846
mbb]iii	chrX:62569830-62570070(-)$1	240	186	193	14.0769
""bbnnn	chr14:32560324-32560564(+)$1	240	86	93	14.0769
ggggggg	chr1:44446933-44447173(+)$1	240	210	217	9.4615
CCC{GGG	chr1:55223616-55223856(-)$1	240	49	56	8.3076
nnbb22d	chr19:8922427-8922667(-)$1	240	152	159	9.6153
cccnnnn	chr1:220287561-220287801(+)$1	240	77	84	10.8461
====ddd	chr16:58031628-58031868(-)$1	240	168	175	10.9999
GGGGZZZ	chr18:8638119-8638359(+)$1	240	214	221	8.9230
:::HHHH	chr16:48337004-48337244(+)$1	240	189	196	9.9999
:::::::	chr12:50152093-50152333(+)$1	240	1	8	10.8461

#DB
((((((.	chr8:67576690-67576930(-)$1	1	127	134	10.7692
((((...	chr20:30898241-30898481(+)$1	1	31	38	10.9999
).)))..	chr6:57012060-57012300(+)$1	1	58	65	8.9999
(((((..	chr10:35324040-35324280(-)$1	1	20	27	8.3076
....(((	chr6:142525018-142525301(+)$1	1	202	209	12.5384
(((((((	chr6:44220684-44220924(+)$1	1	81	88	13.2307
)))))))	chr2:55518727-55518967(-)$1	1	154	161	9.4615
((((..(	chr9:125652551-125652791(-)$1	1	18	25	9.1538
......)	chr2:86371487-86371734(-)$1	1	166	173	10.1538
.......	chr11:111931701-111931941(+)$1	1	8	15	9.9999
)))))..	chr9:95077992-95078232(-)$1	1	99	106	13.2307
(..((.(	chr2:175742525-175742765(-)$1	1	74	81	9.3076
(((((((	chr11:34145760-34146000(+)$1	1	40	47	10.8461
(((....	chr16:2817366-2817606(+)$1	1	4	11	10.3846
))))).)	chr9:72879124-72879364(+)$1	1	107	114	14.0769
.((((..	chr6:64395239-64395491(+)$1	1	83	90	10.3846
(((((((	chr12:120578629-120578869(-)$1	1	57	64	8.3076
...))).	chr16:2812928-2813168(+)$1	1	216	223	10.7692
.....((	chr6:116747770-116748010(+)$1	1	32	39	8.9999
)..))))	chr19:36940129-36940369(-)$1	1	79	86	10.8461
))))).)	chr8:53599344-53599584(-)$1	1	59	66	9.3076
(((((((	chr6:97339016-97339256(-)$1	1	48	55	9.9230
((.....	chr1:19923426-19923666(+)$1	1	165	172	10.3846
.).))).	chr16:14738178-14738434(+)$1	1	47	54	10.0769
(((.(..	chr11:58893310-58893550(+)$1	1	31	38	9.5384
))).)))	chr3:37067066-37067306(+)$1	1	144	151	9.6153
(((....	chr10:22015079-22015359(+)$1	1	73	80	8.6923
)))((((	chr3:57545497-57545737(+)$1	1	32	39	8.5384
(.(((((	chr1:118039368-118039608(+)$1	1	210	217	8.6923
..(((..	chr6:83829422-83829662(+)$1	1	23	30	13.2307
)))))..	chr8:12943821-12944061(-)$1	1	11	18	10.4615
...))))	chr17:76073172-76073412(+)$1	1	22	29	9.8461
.)).)).	chr5:77334948-77335188(-)$1	1	197	204	10.1538
...))..	chr8:61734523-61734763(+)$1	1	20	27	9.8461
.......	chr5:147793716-147793956(+)$1	1	3	10	10.9999
(((.(((	chr16:15163946-15164186(-)$1	1	5	12	7.9230
.((((((	chr3:182987973-182988213(+)$1	1	53	60	9.8461
(.((.((	chr12:50146191-50146431(+)$1	1	7	14	9.3076
....)))	chr2:65466897-65467137(+)$1	1	89	96	14.0769
..)))))	chr19:37733602-37733842(+)$1	1	114	121	10.9999
)))))..	chr6:7240594-7240834(+)$1	1	92	99	9.5384
((.((((	chr21:33057793-33058033(-)$1	1	167	174	10.3846
))))).)	chr3:52558482-52558722(-)$1	1	212	219	9.1538
..(((((	chr5:138260187-138260427(+)$1	1	29	36	10.0769
.((((((	chr3:49005941-49006181(+)$1	1	73	80	8.6153
(((((((	chr10:120820163-120820403(-)$1	1	172	179	13.2307
...((((	chr15:30010891-30011131(-)$1	1	64	71	9.9999
.......	chr5:66462011-66462251(+)$1	1	8	15	10.3846
....(((	chr21:35183352-35183592(+)$1	1	193	200	9.9999
(((.(((	chr15:101109392-101109636(-)$1	1	1	8	14.0769
))((((.	chr4:142053797-142054037(-)$1	1	202	209	10.3846
((.....	chr8:25341569-25341809(+)$1	1	54	61	9.5384
...))))	chr3:194790343-194790583(-)$1	1	79	86	8.6153
)).....	chr2:182765492-182765732(+)$1	1	82	89	9.2307
((....)	chr10:104233230-104233470(+)$1	1	23	30	10.3846
.)).)))	chrX:62569830-62570070(-)$1	1	186	193	14.0769
..((...	chr14:32560324-32560564(+)$1	1	86	93	14.0769
)))))))	chr1:44446933-44447173(+)$1	1	210	217	9.4615
(((.(((	chr1:55223616-55223856(-)$1	1	49	56	8.3076
..))..)	chr19:8922427-8922667(-)$1	1	152	159	9.6153
(((....	chr1:220287561-220287801(+)$1	1	77	84	10.8461
)))))))	chr16:58031628-58031868(-)$1	1	168	175	10.9999
))))...	chr18:8638119-8638359(+)$1	1	214	221	8.9230
...))))	chr16:48337004-48337244(+)$1	1	189	196	9.9999
.......	chr12:50152093-50152333(+)$1	1	1	8	10.8461

#PSSM
U : 0.83	C : 0.09	G : 0.04	A : 0.03	
U : 0.76	G : 0.15	A : 0.04	C : 0.03	
G : 0.73	C : 0.09	A : 0.09	U : 0.07	
U : 0.92	G : 0.07	
G : 0.93	A : 0.03	C : 0.03	
A : 0.95	U : 0.03	G : 0.01	
A : 0.46	U : 0.29	G : 0.15	C : 0.09	

#score	672.999999999999
#seq	65
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m2_run2.nuc.txt

#NT
UUCA	chr2:114195409-114195610(+)$1	201	3	7	12.0000
UUCA	chr1:114225710-114225911(+)$1	201	172	176	12.0000
UUCA	chr10:79752944-79753145(-)$1	201	101	105	12.0000
UUCA	chr18:18566832-18567033(-)$1	201	22	26	12.0000
UUCA	chr11:46569285-46569486(-)$1	201	106	110	12.0000
UUCA	chr17:27001479-27001680(+)$1	201	70	74	12.0000
UUCA	chr1:165651286-165651487(-)$1	201	102	106	12.0000
UUCA	chr10:126631644-126631845(+)$1	201	106	110	12.0000
UUCA	chr1:31426590-31426791(-)$1	201	52	56	12.0000
UUCA	chr1:115275284-115275485(-)$1	201	170	174	12.0000
UUCA	chr3:49083877-49084078(-)$1	201	37	41	12.0000
UUCA	chr1:150917357-150917558(+)$1	201	80	84	12.0000
UUCA	chr14:92609444-92609645(+)$1	201	64	68	12.0000
UUCA	chr3:16344838-16345039(+)$1	201	113	117	12.0000
UUCA	chr1:46034057-46034258(+)$1	201	69	73	12.0000
UUCA	chr3:51297567-51297768(+)$1	201	14	18	12.0000
UUCA	chr2:43520178-43520379(-)$1	201	107	111	12.0000
UUCA	chr1:70877041-70877242(+)$1	201	51	55	12.0000
UUCA	chr3:49153490-49153691(-)$1	201	78	82	12.0000
UUCA	chr9:79864944-79865145(+)$1	201	151	155	12.0000
UUCA	chr1:100353440-100353641(+)$1	201	15	19	12.0000
UUCA	chr12:62715187-62715388(+)$1	201	86	90	12.0000
UUCA	chr4:57860862-57861063(+)$1	201	12	16	12.0000
UUCA	chrX:118724415-118724616(-)$1	201	87	91	12.0000
uuCA	chr6:126667273-126667474(+)$1	201	23	27	12.0000
UUCA	chr12:76453915-76454116(-)$1	201	52	56	12.0000
UUCA	chr9:72933347-72933548(+)$1	201	153	157	12.0000
UUCA	chr10:35854968-35855169(+)$1	201	19	23	12.0000
UUCA	chr20:422525-422726(-)$1	201	10	14	12.0000
UUCA	chr5:92920981-92921182(+)$1	201	48	52	12.0000
UUCA	chr1:237886361-237886562(+)$1	201	187	191	12.0000
UUCA	chrX:135312585-135312786(-)$1	201	79	83	12.0000
UUCA	chr7:148524185-148524386(-)$1	201	9	13	12.0000
UUCA	chr20:61527828-61528029(-)$1	201	93	97	12.0000
UUCA	chr13:111353737-111353938(-)$1	201	31	35	12.0000
UUCA	chr2:179411847-179412048(+)$1	201	34	38	12.0000
UUCA	chr5:34922280-34922481(+)$1	201	12	16	12.0000
UUCA	chr12:123106358-123106559(+)$1	201	149	153	12.0000
uuca	chr3:184048958-184049159(+)$1	201	2	6	12.0000
UUCA	chr15:51829801-51830002(-)$1	201	41	45	12.0000
UUCA	chr22:41619972-41620173(+)$1	201	46	50	12.0000
UUCA	chr1:45923182-45923383(-)$1	201	100	104	12.0000
UUCA	chr4:2940493-2940694(-)$1	201	125	129	12.0000
UUCA	chr12:66707744-66707945(+)$1	201	38	42	12.0000
UUCA	chr7:26236970-26237171(-)$1	201	34	38	12.0000
UUCA	chr1:235335940-235336141(-)$1	201	104	108	12.0000
UUCA	chr4:146041130-146041331(+)$1	201	0	4	12.0000
UUCA	chr16:1500516-1500717(-)$1	201	79	83	12.0000
UUCA	chr14:88935972-88936173(-)$1	201	20	24	12.0000
UUCA	chr1:167823561-167823762(-)$1	201	0	4	12.0000
UUCA	chr11:134018443-134018644(+)$1	201	99	103	12.0000
UUCA	chr9:134349923-134350124(+)$1	201	102	106	12.0000
UUCA	chr19:38871514-38871715(+)$1	201	96	100	12.0000
UUCA	chr17:29653127-29653328(+)$1	201	172	176	12.0000
UUCA	chr4:88979056-88979257(+)$1	201	79	83	12.0000
UUCA	chr4:20533532-20533733(+)$1	201	69	73	12.0000
UUCA	chr12:133446138-133446339(-)$1	201	182	186	12.0000
uuca	chr12:27109388-27109589(+)$1	201	57	61	12.0000
UUCA	chr3:40557755-40557956(+)$1	201	26	30	12.0000
UUCA	chr16:23430011-23430212(-)$1	201	17	21	12.0000
UUCA	chr12:58163297-58163498(-)$1	201	73	77	12.0000
UUCA	chr1:180034169-180034370(+)$1	201	30	34	12.0000
uuca	chr8:56637688-56637889(-)$1	201	93	97	12.0000
UUCA	chr17:60140541-60140742(-)$1	201	75	79	12.0000
UUCA	chr1:114254301-114254502(-)$1	201	86	90	12.0000
UUCA	chr2:32725013-32725214(+)$1	201	49	53	12.0000
UUCA	chr21:27269818-27270019(-)$1	201	118	122	12.0000
UUCA	chr8:28019454-28019655(+)$1	201	161	165	12.0000
UUCA	chr7:56082718-56082919(-)$1	201	139	143	12.0000
UUCA	chr5:179994086-179994287(+)$1	201	70	74	12.0000
UUCA	chr2:37349638-37349839(-)$1	201	85	89	12.0000
UUCA	chr3:52726862-52727063(+)$1	201	20	24	12.0000
UUCA	chr1:223988339-223988540(-)$1	201	65	69	12.0000
UUCA	chr5:151179380-151179581(+)$1	201	6	10	12.0000
UUCA	chr15:75684941-75685142(-)$1	201	119	123	12.0000

#otherMatches

#Struct PSSM
c333	chr1:111986413-111986614(-)$1	201	138	142	12.0000
DNNN	chr2:114195409-114195610(+)$1	201	3	7	12.0000
gggg	chr1:114225710-114225911(+)$1	201	172	176	12.0000
::::	chr10:79752944-79753145(-)$1	201	101	105	12.0000
hhhh	chr18:18566832-18567033(-)$1	201	22	26	12.0000
&&&&	chr11:46569285-46569486(-)$1	201	106	110	12.0000
c22f	chr17:27001479-27001680(+)$1	201	70	74	12.0000
gggg	chr1:165651286-165651487(-)$1	201	102	106	12.0000
hhhh	chr10:126631644-126631845(+)$1	201	106	110	12.0000
EEE{	chr1:31426590-31426791(-)$1	201	52	56	12.0000
tttt	chr1:115275284-115275485(-)$1	201	170	174	12.0000
fff[	chr3:49083877-49084078(-)$1	201	37	41	12.0000
mmcc	chr1:150917357-150917558(+)$1	201	80	84	12.0000
[ddd	chr14:92609444-92609645(+)$1	201	64	68	12.0000
ddd8	chr3:16344838-16345039(+)$1	201	113	117	12.0000
ff""	chr1:46034057-46034258(+)$1	201	69	73	12.0000
GGGG	chr3:51297567-51297768(+)$1	201	14	18	12.0000
$$$$	chr2:43520178-43520379(-)$1	201	107	111	12.0000
qqqq	chr1:70877041-70877242(+)$1	201	51	55	12.0000
eddd	chr3:49153490-49153691(-)$1	201	78	82	12.0000
eeee	chr9:79864944-79865145(+)$1	201	151	155	12.0000
CCCK	chr1:100353440-100353641(+)$1	201	15	19	12.0000
ffff	chr12:62715187-62715388(+)$1	201	86	90	12.0000
eeee	chr4:57860862-57861063(+)$1	201	12	16	12.0000
iiii	chrX:118724415-118724616(-)$1	201	87	91	12.0000
FFLL	chr6:126667273-126667474(+)$1	201	23	27	12.0000
dd[c	chr12:76453915-76454116(-)$1	201	52	56	12.0000
]bb:	chr9:72933347-72933548(+)$1	201	153	157	12.0000
hhhh	chr10:35854968-35855169(+)$1	201	19	23	12.0000
EEMM	chr20:422525-422726(-)$1	201	10	14	12.0000
::::	chr5:92920981-92921182(+)$1	201	48	52	12.0000
===D	chr1:237886361-237886562(+)$1	201	187	191	12.0000
::::	chrX:135312585-135312786(-)$1	201	79	83	12.0000
ii##	chr7:148524185-148524386(-)$1	201	9	13	12.0000
::cc	chr20:61527828-61528029(-)$1	201	93	97	12.0000
BB{A	chr13:111353737-111353938(-)$1	201	31	35	12.0000
++++	chr2:179411847-179412048(+)$1	201	34	38	12.0000
iiii	chr5:34922280-34922481(+)$1	201	12	16	12.0000
gggg	chr12:123106358-123106559(+)$1	201	149	153	12.0000
ffff	chr3:184048958-184049159(+)$1	201	2	6	12.0000
eeee	chr15:51829801-51830002(-)$1	201	41	45	12.0000
oooo	chr22:41619972-41620173(+)$1	201	46	50	12.0000
!ccc	chr1:45923182-45923383(-)$1	201	100	104	12.0000
::::	chr4:2940493-2940694(-)$1	201	125	129	12.0000
d555	chr12:66707744-66707945(+)$1	201	38	42	12.0000
eeee	chr7:26236970-26237171(-)$1	201	34	38	12.0000
dlll	chr1:235335940-235336141(-)$1	201	104	108	12.0000
::::	chr4:146041130-146041331(+)$1	201	0	4	12.0000
eeee	chr16:1500516-1500717(-)$1	201	79	83	12.0000
e!!e	chr14:88935972-88936173(-)$1	201	20	24	12.0000
::::	chr1:167823561-167823762(-)$1	201	0	4	12.0000
gggg	chr11:134018443-134018644(+)$1	201	99	103	12.0000
4444	chr9:134349923-134350124(+)$1	201	102	106	12.0000
oooo	chr19:38871514-38871715(+)$1	201	96	100	12.0000
tttt	chr17:29653127-29653328(+)$1	201	172	176	12.0000
GGG{	chr4:88979056-88979257(+)$1	201	79	83	12.0000
ee!!	chr4:20533532-20533733(+)$1	201	69	73	12.0000
::::	chr12:133446138-133446339(-)$1	201	182	186	12.0000
EEEQ	chr12:27109388-27109589(+)$1	201	57	61	12.0000
((((	chr3:40557755-40557956(+)$1	201	26	30	12.0000
:ggg	chr16:23430011-23430212(-)$1	201	17	21	12.0000
CCC{	chr12:58163297-58163498(-)$1	201	73	77	12.0000
c"""	chr1:180034169-180034370(+)$1	201	30	34	12.0000
^^^^	chr8:56637688-56637889(-)$1	201	93	97	12.0000
eeee	chr17:60140541-60140742(-)$1	201	75	79	12.0000
E:dd	chr1:114254301-114254502(-)$1	201	86	90	12.0000
KCCC	chr2:32725013-32725214(+)$1	201	49	53	12.0000
:::d	chr21:27269818-27270019(-)$1	201	118	122	12.0000
vvvv	chr8:28019454-28019655(+)$1	201	161	165	12.0000
JJJJ	chr7:56082718-56082919(-)$1	201	139	143	12.0000
mmme	chr5:179994086-179994287(+)$1	201	70	74	12.0000
fnnn	chr2:37349638-37349839(-)$1	201	85	89	12.0000
nnnf	chr3:52726862-52727063(+)$1	201	20	24	12.0000
c22g	chr1:223988339-223988540(-)$1	201	65	69	12.0000
DD::	chr5:151179380-151179581(+)$1	201	6	10	12.0000
dddd	chr15:75684941-75685142(-)$1	201	119	123	12.0000

#DB
)...	chr1:111986413-111986614(-)$1	1	138	142	12.0000
(...	chr2:114195409-114195610(+)$1	1	3	7	12.0000
((((	chr1:114225710-114225911(+)$1	1	172	176	12.0000
....	chr10:79752944-79753145(-)$1	1	101	105	12.0000
((((	chr18:18566832-18567033(-)$1	1	22	26	12.0000
....	chr11:46569285-46569486(-)$1	1	106	110	12.0000
)..)	chr17:27001479-27001680(+)$1	1	70	74	12.0000
((((	chr1:165651286-165651487(-)$1	1	102	106	12.0000
))))	chr10:126631644-126631845(+)$1	1	106	110	12.0000
(((.	chr1:31426590-31426791(-)$1	1	52	56	12.0000
....	chr1:115275284-115275485(-)$1	1	170	174	12.0000
(((.	chr3:49083877-49084078(-)$1	1	37	41	12.0000
..))	chr1:150917357-150917558(+)$1	1	80	84	12.0000
.(((	chr14:92609444-92609645(+)$1	1	64	68	12.0000
))).	chr3:16344838-16345039(+)$1	1	113	117	12.0000
((..	chr1:46034057-46034258(+)$1	1	69	73	12.0000
((((	chr3:51297567-51297768(+)$1	1	14	18	12.0000
....	chr2:43520178-43520379(-)$1	1	107	111	12.0000
....	chr1:70877041-70877242(+)$1	1	51	55	12.0000
))))	chr3:49153490-49153691(-)$1	1	78	82	12.0000
))))	chr9:79864944-79865145(+)$1	1	151	155	12.0000
(((.	chr1:100353440-100353641(+)$1	1	15	19	12.0000
))))	chr12:62715187-62715388(+)$1	1	86	90	12.0000
))))	chr4:57860862-57861063(+)$1	1	12	16	12.0000
((((	chrX:118724415-118724616(-)$1	1	87	91	12.0000
((..	chr6:126667273-126667474(+)$1	1	23	27	12.0000
((.(	chr12:76453915-76454116(-)$1	1	52	56	12.0000
.)).	chr9:72933347-72933548(+)$1	1	153	157	12.0000
))))	chr10:35854968-35855169(+)$1	1	19	23	12.0000
((..	chr20:422525-422726(-)$1	1	10	14	12.0000
....	chr5:92920981-92921182(+)$1	1	48	52	12.0000
))))	chr1:237886361-237886562(+)$1	1	187	191	12.0000
....	chrX:135312585-135312786(-)$1	1	79	83	12.0000
((..	chr7:148524185-148524386(-)$1	1	9	13	12.0000
..((	chr20:61527828-61528029(-)$1	1	93	97	12.0000
((.(	chr13:111353737-111353938(-)$1	1	31	35	12.0000
....	chr2:179411847-179412048(+)$1	1	34	38	12.0000
((((	chr5:34922280-34922481(+)$1	1	12	16	12.0000
((((	chr12:123106358-123106559(+)$1	1	149	153	12.0000
((((	chr3:184048958-184049159(+)$1	1	2	6	12.0000
((((	chr15:51829801-51830002(-)$1	1	41	45	12.0000
....	chr22:41619972-41620173(+)$1	1	46	50	12.0000
.(((	chr1:45923182-45923383(-)$1	1	100	104	12.0000
....	chr4:2940493-2940694(-)$1	1	125	129	12.0000
)...	chr12:66707744-66707945(+)$1	1	38	42	12.0000
((((	chr7:26236970-26237171(-)$1	1	34	38	12.0000
(...	chr1:235335940-235336141(-)$1	1	104	108	12.0000
....	chr4:146041130-146041331(+)$1	1	0	4	12.0000
((((	chr16:1500516-1500717(-)$1	1	79	83	12.0000
(..(	chr14:88935972-88936173(-)$1	1	20	24	12.0000
....	chr1:167823561-167823762(-)$1	1	0	4	12.0000
((((	chr11:134018443-134018644(+)$1	1	99	103	12.0000
....	chr9:134349923-134350124(+)$1	1	102	106	12.0000
....	chr19:38871514-38871715(+)$1	1	96	100	12.0000
....	chr17:29653127-29653328(+)$1	1	172	176	12.0000
(((.	chr4:88979056-88979257(+)$1	1	79	83	12.0000
((..	chr4:20533532-20533733(+)$1	1	69	73	12.0000
....	chr12:133446138-133446339(-)$1	1	182	186	12.0000
(((.	chr12:27109388-27109589(+)$1	1	57	61	12.0000
....	chr3:40557755-40557956(+)$1	1	26	30	12.0000
.(((	chr16:23430011-23430212(-)$1	1	17	21	12.0000
(((.	chr12:58163297-58163498(-)$1	1	73	77	12.0000
(...	chr1:180034169-180034370(+)$1	1	30	34	12.0000
....	chr8:56637688-56637889(-)$1	1	93	97	12.0000
((((	chr17:60140541-60140742(-)$1	1	75	79	12.0000
(.((	chr1:114254301-114254502(-)$1	1	86	90	12.0000
.(((	chr2:32725013-32725214(+)$1	1	49	53	12.0000
...(	chr21:27269818-27270019(-)$1	1	118	122	12.0000
....	chr8:28019454-28019655(+)$1	1	161	165	12.0000
))))	chr7:56082718-56082919(-)$1	1	139	143	12.0000
...)	chr5:179994086-179994287(+)$1	1	70	74	12.0000
(...	chr2:37349638-37349839(-)$1	1	85	89	12.0000
...)	chr3:52726862-52727063(+)$1	1	20	24	12.0000
)..)	chr1:223988339-223988540(-)$1	1	65	69	12.0000
((..	chr5:151179380-151179581(+)$1	1	6	10	12.0000
))))	chr15:75684941-75685142(-)$1	1	119	123	12.0000

#PSSM
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
C : 0.96	c : 0.03	
A : 0.96	a : 0.03	

#score	912.0000000000002
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_AGO2_Skalsky2012d_hg19_UTR_m3_run2.nuc.txt

#NT

#otherMatches

#Struct PSSM
:::::::FFFFFFggggggg[a[ccc!!ccc[bbmmmmbb]ccc333ccc]a]ggggggg:::::bbrrrrrrrrrbbeeeee[ffffffdddd))))))))))bb####ccc[dddd[bbqqqqqqqqbb]dddd]ccc4444bb>>>>>>>>>>>dddd22ffffff]eeeee:::FFFFFF::ccc"""ffffff[cccqqqqqqqqccc]ffffff]ccc::::	chr20:35221404-35221634(+)$1	230	1	229	684.0000

#DB
.......(((((((((((((.(.(((..(((.((....)).)))...))).).))))))).....((.........))(((((.((((((((((..........((....(((.((((.((........)).)))).)))....))...........))))..)))))).)))))...))))))..(((...((((((.(((........))).)))))).)))....	chr20:35221404-35221634(+)$1	1	1	229	684.0000

#PSSM
c : 1.00	
a : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 1.00	
u : 1.00	
g : 1.00	
g : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
g : 1.00	
g : 1.00	
c : 1.00	
u : 1.00	
g : 1.00	
g : 1.00	
u : 1.00	
c : 1.00	
u : 1.00	
u : 1.00	
g : 1.00	
g : 1.00	
a : 1.00	
a : 1.00	
c : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
u : 1.00	
g : 1.00	
a : 1.00	
c : 1.00	
c : 1.00	
u : 1.00	
c : 1.00	
g : 1.00	
u : 1.00	
g : 1.00	
a : 1.00	
g : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 1.00	
g : 1.00	
c : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
g : 1.00	
c : 1.00	
c : 1.00	
u : 1.00	
c : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	

#score	684.0
#seq	1
#width	228
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_CDS_m1_run2.nuc.txt

#NT
CUUUCCU	chr12:6666366-6666618(-)$1	252	155	162	13.0175
CUUCCUU	chr12:53664064-53664346(+)$1	282	84	91	12.5789
GUUUCUU	chr3:183962288-183962581(-)$1	293	123	130	13.2807
CAUUCUU	chr10:102120332-102120630(+)$1	298	239	246	12.2280
AUUUCUU	chr19:19606760-19607023(+)$1	263	69	76	13.0175
CUUUCUC	chr10:114900866-114901160(+)$1	294	52	59	12.5789
CUUUCCU	chr1:150065529-150065838(+)$1	309	124	131	13.0175
CUUUGUU	chr1:11147413-11147748(-)$1	335	60	67	12.4912
CUCUCUU	chr1:179310094-179310463(+)$1	369	229	236	13.1052
CUCUCUU	chrX:71425271-71425538(-)$1	267	67	74	13.1052
CUUGCUU	chr13:42877125-42877447(+)$1	322	216	223	12.4035
CUUUCCU	chr1:84955920-84956237(+)$1	317	0	7	13.0175
CUUUCUG	chr1:87208809-87209111(+)$1	302	240	247	12.5789
CUUUUUU	chr1:198261978-198262269(+)$1	291	269	276	12.4035
CUUUAUU	chr10:32304394-32304687(-)$1	293	64	71	12.4912
CUUUCUU	chr10:27403350-27403629(-)$1	279	72	79	16.8771
UUUUCUU	chr3:52439037-52439380(-)$1	343	18	25	13.1929
CUUCCUU	chr16:69153998-69154295(-)$1	297	113	120	12.5789
CUUUCAU	chr11:9609984-9610351(+)$1	367	338	345	12.5789
CUUUCUU	chr3:39435800-39436168(+)$1	368	2	9	16.8771
CUUUCUU	chr10:75277266-75277548(-)$1	282	126	133	16.8771
CUUUCUA	chr16:30093971-30094270(+)$1	299	77	84	12.5789
CUUUAUU	chr16:70562676-70563067(+)$1	391	78	85	12.4912
UUUUCUU	chr9:108123398-108123712(+)$1	314	25	32	13.1929
CCUUCUU	chrM:13125-13413(+)$1	288	209	216	12.2280
CUUUCUU	chr10:72636182-72636510(+)$1	328	74	81	16.8771
CUUUCUU	chr16:56976989-56977294(+)$1	305	163	170	16.8771
CGUUCUU	chr5:162944442-162944723(+)$1	281	115	122	12.2280
CUGUCUU	chr22:41996855-41997248(-)$1	393	371	378	13.1929
CUUACUU	chr6:101098333-101098677(-)$1	344	188	195	12.4035
CUUUCCU	chr1:54509041-54509286(-)$1	245	120	127	13.0175
GUUUCUU	chr7:112407090-112407373(-)$1	283	67	74	13.2807
CUUUCUG	chr19:58806102-58806465(+)$1	363	33	40	12.5789
CUUUCCU	chr9:116022517-116022767(+)$1	250	49	56	13.0175
CUGUCUU	chr9:131387284-131387624(-)$1	340	216	223	13.1929
CUUUCUC	chr4:83740084-83740506(-)$1	422	73	80	12.5789
CUUUCUA	chr19:4676454-4676729(-)$1	275	132	139	12.5789
CUAUCUU	chr1:32696601-32696968(+)$1	367	100	107	12.8421
AUUUCUU	chr13:37422662-37423025(-)$1	363	195	202	13.0175
CUCUCUU	chr3:119155534-119155898(-)$1	364	52	59	13.1052
CUCUCUU	chr1:151400714-151400989(-)$1	275	87	94	13.1052
CUGUCUU	chr1:29040619-29041014(+)$1	395	109	116	13.1929
UUUUCUU	chr22:24807455-24807752(+)$1	297	81	88	13.1929
GUUUCUU	chr12:120637128-120637388(-)$1	260	33	40	13.2807
CUUUGUU	chr20:4837562-4837880(-)$1	318	2	9	12.4912
CUUUCUU	chr1:44121204-44121517(+)$1	313	246	253	16.8771
GUUUCUU	chr6:99930453-99930777(-)$1	324	74	81	13.2807
CUUUCCU	chr1:38058245-38058506(-)$1	261	84	91	13.0175
CUUUCUU	chr20:61491376-61491755(-)$1	379	76	83	16.8771
GUUUCUU	chr8:25364036-25364372(+)$1	336	279	286	13.2807
CUGUCUU	chr14:23946379-23946656(+)$1	277	12	19	13.1929
CUGUCUU	chr5:137767050-137767369(+)$1	319	225	232	13.1929
CUUCCUU	chr1:155629797-155630049(-)$1	252	141	148	12.5789
CUUUCUU	chr18:19087985-19088300(+)$1	315	72	79	16.8771
UUUUCUU	chr8:90965622-90965971(-)$1	349	26	33	13.1929
CUUUCUU	chr6:1394881-1395251(+)$1	370	35	42	16.8771

#otherMatches

#Struct PSSM
eeeccc[	chr9:36651713-36651974(+)$1	261	107	114	16.8771
hhhh555	chr12:6666366-6666618(-)$1	252	155	162	13.0175
d++++++	chr12:53664064-53664346(+)$1	282	84	91	12.5789
66ccc]c	chr3:183962288-183962581(-)$1	293	123	130	13.2807
bb[bboo	chr10:102120332-102120630(+)$1	298	239	246	12.2280
eeee[ee	chr19:19606760-19607023(+)$1	263	69	76	13.0175
%%%%%%d	chr10:114900866-114901160(+)$1	294	52	59	12.5789
FFFDDDD	chr1:150065529-150065838(+)$1	309	124	131	13.0175
bb22ccc	chr1:11147413-11147748(-)$1	335	60	67	12.4912
77eeeee	chr1:179310094-179310463(+)$1	369	229	236	13.1052
c22eeee	chrX:71425271-71425538(-)$1	267	67	74	13.1052
qqqqqqq	chr13:42877125-42877447(+)$1	322	216	223	12.4035
:IIIIII	chr1:84955920-84956237(+)$1	317	0	7	13.0175
FFFFFF}	chr1:87208809-87209111(+)$1	302	240	247	12.5789
dd77777	chr1:198261978-198262269(+)$1	291	269	276	12.4035
fffffll	chr10:32304394-32304687(-)$1	293	64	71	12.4912
ddd!!ff	chr10:27403350-27403629(-)$1	279	72	79	16.8771
HHHHHKK	chr3:52439037-52439380(-)$1	343	18	25	13.1929
nnccc::	chr16:69153998-69154295(-)$1	297	113	120	12.5789
c22eeee	chr11:9609984-9610351(+)$1	367	338	345	12.5789
b"""===	chr3:39435800-39436168(+)$1	368	2	9	16.8771
tttttee	chr10:75277266-75277548(-)$1	282	126	133	16.8771
ccceeee	chr16:30093971-30094270(+)$1	299	77	84	12.5789
d[cccnn	chr16:70562676-70563067(+)$1	391	78	85	12.4912
d]fffff	chr9:108123398-108123712(+)$1	314	25	32	13.1929
EEE____	chrM:13125-13413(+)$1	288	209	216	12.2280
:::::::	chr10:72636182-72636510(+)$1	328	74	81	16.8771
bb:::::	chr16:56976989-56977294(+)$1	305	163	170	16.8771
fdddd""	chr5:162944442-162944723(+)$1	281	115	122	12.2280
c4444cc	chr22:41996855-41997248(-)$1	393	371	378	13.1929
:::::::	chr6:101098333-101098677(-)$1	344	188	195	12.4035
FF}DDDD	chr1:54509041-54509286(-)$1	245	120	127	13.0175
gggg]cc	chr7:112407090-112407373(-)$1	283	67	74	13.2807
qqqqqa]	chr19:58806102-58806465(+)$1	363	33	40	12.5789
nnnnndd	chr9:116022517-116022767(+)$1	250	49	56	13.0175
=======	chr9:131387284-131387624(-)$1	340	216	223	13.1929
gggggg!	chr4:83740084-83740506(-)$1	422	73	80	12.5789
!!ccc""	chr19:4676454-4676729(-)$1	275	132	139	12.5789
B::::::	chr1:32696601-32696968(+)$1	367	100	107	12.8421
E:::GGG	chr13:37422662-37423025(-)$1	363	195	202	13.0175
vvvvvvv	chr3:119155534-119155898(-)$1	364	52	59	13.1052
rrrrrrr	chr1:151400714-151400989(-)$1	275	87	94	13.1052
ccc4444	chr1:29040619-29041014(+)$1	395	109	116	13.1929
h55555f	chr22:24807455-24807752(+)$1	297	81	88	13.1929
ssssssc	chr12:120637128-120637388(-)$1	260	33	40	13.2807
ffff[dd	chr20:4837562-4837880(-)$1	318	2	9	12.4912
ccc]ddd	chr1:44121204-44121517(+)$1	313	246	253	16.8771
eeeee]d	chr6:99930453-99930777(-)$1	324	74	81	13.2807
hhhssss	chr1:38058245-38058506(-)$1	261	84	91	13.0175
dqqqqqq	chr20:61491376-61491755(-)$1	379	76	83	16.8771
ddd[a[c	chr8:25364036-25364372(+)$1	336	279	286	13.2807
ttttttt	chr14:23946379-23946656(+)$1	277	12	19	13.1929
ZZGGGGG	chr5:137767050-137767369(+)$1	319	225	232	13.1929
btttttt	chr1:155629797-155630049(-)$1	252	141	148	12.5789
eeeee::	chr18:19087985-19088300(+)$1	315	72	79	16.8771
eeeee==	chr8:90965622-90965971(-)$1	349	26	33	13.1929
vvvvddd	chr6:1394881-1395251(+)$1	370	35	42	16.8771

#DB
((((((.	chr9:36651713-36651974(+)$1	1	107	114	16.8771
))))...	chr12:6666366-6666618(-)$1	1	155	162	13.0175
(......	chr12:53664064-53664346(+)$1	1	84	91	12.5789
..))).)	chr3:183962288-183962581(-)$1	1	123	130	13.2807
((.((..	chr10:102120332-102120630(+)$1	1	239	246	12.2280
((((.((	chr19:19606760-19607023(+)$1	1	69	76	13.0175
......(	chr10:114900866-114901160(+)$1	1	52	59	12.5789
(((((((	chr1:150065529-150065838(+)$1	1	124	131	13.0175
))..)))	chr1:11147413-11147748(-)$1	1	60	67	12.4912
..)))))	chr1:179310094-179310463(+)$1	1	229	236	13.1052
)..))))	chrX:71425271-71425538(-)$1	1	67	74	13.1052
.......	chr13:42877125-42877447(+)$1	1	216	223	12.4035
.((((((	chr1:84955920-84956237(+)$1	1	0	7	13.0175
)))))).	chr1:87208809-87209111(+)$1	1	240	247	12.5789
)).....	chr1:198261978-198262269(+)$1	1	269	276	12.4035
(((((..	chr10:32304394-32304687(-)$1	1	64	71	12.4912
(((..((	chr10:27403350-27403629(-)$1	1	72	79	16.8771
(((((..	chr3:52439037-52439380(-)$1	1	18	25	13.1929
..)))..	chr16:69153998-69154295(-)$1	1	113	120	12.5789
)..))))	chr11:9609984-9610351(+)$1	1	338	345	12.5789
(...(((	chr3:39435800-39436168(+)$1	1	2	9	16.8771
.....))	chr10:75277266-75277548(-)$1	1	126	133	16.8771
)))((((	chr16:30093971-30094270(+)$1	1	77	84	12.5789
(.(((..	chr16:70562676-70563067(+)$1	1	78	85	12.4912
).)))))	chr9:108123398-108123712(+)$1	1	25	32	13.1929
)))....	chrM:13125-13413(+)$1	1	209	216	12.2280
.......	chr10:72636182-72636510(+)$1	1	74	81	16.8771
)).....	chr16:56976989-56977294(+)$1	1	163	170	16.8771
(((((..	chr5:162944442-162944723(+)$1	1	115	122	12.2280
)....))	chr22:41996855-41997248(-)$1	1	371	378	13.1929
.......	chr6:101098333-101098677(-)$1	1	188	195	12.4035
)).))))	chr1:54509041-54509286(-)$1	1	120	127	13.0175
)))).))	chr7:112407090-112407373(-)$1	1	67	74	13.2807
.....).	chr19:58806102-58806465(+)$1	1	33	40	12.5789
.....))	chr9:116022517-116022767(+)$1	1	49	56	13.0175
)))))))	chr9:131387284-131387624(-)$1	1	216	223	13.1929
((((((.	chr4:83740084-83740506(-)$1	1	73	80	12.5789
..(((..	chr19:4676454-4676729(-)$1	1	132	139	12.5789
)......	chr1:32696601-32696968(+)$1	1	100	107	12.8421
)...(((	chr13:37422662-37423025(-)$1	1	195	202	13.0175
.......	chr3:119155534-119155898(-)$1	1	52	59	13.1052
.......	chr1:151400714-151400989(-)$1	1	87	94	13.1052
)))....	chr1:29040619-29041014(+)$1	1	109	116	13.1929
).....)	chr22:24807455-24807752(+)$1	1	81	88	13.1929
......)	chr12:120637128-120637388(-)$1	1	33	40	13.2807
((((.((	chr20:4837562-4837880(-)$1	1	2	9	12.4912
))).)))	chr1:44121204-44121517(+)$1	1	246	253	16.8771
))))).)	chr6:99930453-99930777(-)$1	1	74	81	13.2807
(((....	chr1:38058245-38058506(-)$1	1	84	91	13.0175
(......	chr20:61491376-61491755(-)$1	1	76	83	16.8771
(((.(.(	chr8:25364036-25364372(+)$1	1	279	286	13.2807
.......	chr14:23946379-23946656(+)$1	1	12	19	13.1929
..)))))	chr5:137767050-137767369(+)$1	1	225	232	13.1929
(......	chr1:155629797-155630049(-)$1	1	141	148	12.5789
)))))..	chr18:19087985-19088300(+)$1	1	72	79	16.8771
(((((((	chr8:90965622-90965971(-)$1	1	26	33	13.1929
....)))	chr6:1394881-1395251(+)$1	1	35	42	16.8771

#PSSM
C : 0.80	G : 0.08	U : 0.07	A : 0.03	
U : 0.94	A : 0.01	C : 0.01	G : 0.01	
U : 0.82	G : 0.08	C : 0.07	A : 0.01	
U : 0.91	C : 0.05	G : 0.01	A : 0.01	
C : 0.91	G : 0.03	A : 0.03	U : 0.01	
U : 0.87	C : 0.10	A : 0.01	
U : 0.89	C : 0.03	G : 0.03	A : 0.03	

#score	772.9649122807033
#seq	57
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_RBM10_Wang2013a_hg19_CDS_m3_run1.nuc.txt

#NT
UUUUCUU	chr9:4705984-4706185(+)$1	201	10	17	16.8928
uuuccuu	chr1:156908199-156908400(-)$1	201	43	50	12.8750
UUUUCGU	chr2:136536475-136536676(+)$1	201	66	73	12.3392
UUUUCUA	chr5:115336210-115336411(+)$1	201	63	70	13.0535
UUUUCUU	chr12:46243752-46243953(+)$1	201	48	55	16.8928
UUGUCUU	chr9:139353842-139354043(-)$1	201	123	130	12.5178
UUUUCUC	chr7:127013447-127013648(-)$1	201	101	108	13.3214
UAUUCUU	chr4:20482281-20482482(+)$1	201	34	41	12.5178
UUGUCUU	chr6:158353128-158353329(+)$1	201	87	94	12.5178
UUUGCUU	chr2:38570535-38570736(-)$1	201	3	10	12.9642
UUUUCUU	chr2:32726697-32726898(+)$1	201	73	80	16.8928
UUUUCCU	chr7:23387229-23387430(-)$1	201	48	55	12.5178
CUUUCUU	chr10:79764527-79764728(-)$1	201	54	61	12.1607
UUUUCUU	chr7:42018224-42018425(-)$1	201	7	14	16.8928
UUUUCUG	chr5:108691563-108691764(-)$1	201	10	17	13.2321
UUUUAUU	chr6:131915167-131915368(-)$1	201	137	144	13.4107
UUUUCCU	chr5:61789756-61789957(+)$1	201	55	62	12.5178
UCUUCUU	chr5:102490520-102490721(+)$1	201	171	178	12.5178
UUUUUUU	chr2:153550992-153551193(-)$1	201	37	44	13.1428
UUUUCUC	chr9:131370363-131370564(+)$1	201	16	23	13.3214
UGUUCUU	chr12:29509232-29509433(-)$1	201	122	129	12.7857
UUUUCUU	chr6:170846274-170846475(-)$1	201	33	40	16.8928
UUAUCUU	chr7:107052880-107053081(-)$1	201	5	12	12.3392
UUUUCUU	chr6:49416460-49416661(-)$1	201	9	16	16.8928
UUUUCUC	chr14:31416330-31416531(-)$1	201	49	56	13.3214
UUGUCUU	chr2:27424197-27424398(-)$1	201	105	112	12.5178
UUUUUUU	chr17:28505014-28505215(+)$1	201	62	69	13.1428
UUUUGUU	chr14:76186841-76187042(+)$1	201	85	92	13.0535
UGUUCUU	chr2:73680884-73681085(+)$1	201	92	99	12.7857
UUUUCUU	chr3:69104943-69105144(-)$1	201	172	179	16.8928
uuuuauu	chr15:83486635-83486836(+)$1	201	14	21	13.4107
UUUUCUU	chr13:99555215-99555416(-)$1	201	37	44	16.8928
UUUCCUU	chr10:74912010-74912211(-)$1	201	185	192	12.8750
UUUUAUU	chr12:46215127-46215328(+)$1	201	38	45	13.4107
UUUUCUG	chr19:1388480-1388681(+)$1	201	171	178	13.2321
UUUUCUU	chr2:203142590-203142791(+)$1	201	192	199	16.8928
UUUUCUG	chr22:29747201-29747402(-)$1	201	128	135	13.2321
UUUGCUU	chr1:52943332-52943533(-)$1	201	60	67	12.9642
UUUUCUG	chr6:43534940-43535141(-)$1	201	39	46	13.2321
UUUUAUU	chr5:70930891-70931092(+)$1	201	2	9	13.4107
AUUUCUU	chr1:66075817-66076018(+)$1	201	40	47	12.1607
uuuucuc	chr15:52646078-52646279(-)$1	201	4	11	13.3214
UUUUAUU	chr11:63667409-63667610(+)$1	201	192	199	13.4107
UUUGCUU	chr1:93580493-93580694(+)$1	201	23	30	12.9642
UUUGCUU	chr2:32640795-32640996(+)$1	201	143	150	12.9642
UUUACUU	chr8:18725421-18725622(-)$1	201	31	38	12.6964
UUUUAUU	chr12:118823878-118824079(+)$1	201	13	20	13.4107
UUUUCUA	chrX:20181028-20181229(-)$1	201	63	70	13.0535
UGUUCUU	chr15:59185083-59185284(-)$1	201	1	8	12.7857
UUUCCUU	chr15:43017664-43017865(-)$1	201	81	88	12.8750
UUUUCCU	chr1:155448406-155448607(-)$1	201	56	63	12.5178
UUUUUUU	chr17:7480573-7480774(+)$1	201	74	81	13.1428
UUUUGUU	chr17:38552591-38552792(-)$1	201	32	39	13.0535
UGUUCUU	chr5:140021495-140021696(+)$1	201	166	173	12.7857
UUUUCUC	chr2:170666720-170666921(+)$1	201	157	164	13.3214

#otherMatches

#Struct PSSM
:::::::	chr5:16762580-16762781(-)$1	201	15	22	16.8928
:::::::	chr9:4705984-4706185(+)$1	201	10	17	16.8928
ddd))))	chr1:156908199-156908400(-)$1	201	43	50	12.8750
pppdddd	chr2:136536475-136536676(+)$1	201	66	73	12.3392
:::::::	chr5:115336210-115336411(+)$1	201	63	70	13.0535
mmmma]c	chr12:46243752-46243953(+)$1	201	48	55	16.8928
eeedddd	chr9:139353842-139354043(-)$1	201	123	130	12.5178
ffff22e	chr7:127013447-127013648(-)$1	201	101	108	13.3214
:::::::	chr4:20482281-20482482(+)$1	201	34	41	12.5178
!cccooo	chr6:158353128-158353329(+)$1	201	87	94	12.5178
:::EEEE	chr2:38570535-38570736(-)$1	201	3	10	12.9642
ee333ee	chr2:32726697-32726898(+)$1	201	73	80	16.8928
OEEEEEN	chr7:23387229-23387430(-)$1	201	48	55	12.5178
a666666	chr10:79764527-79764728(-)$1	201	54	61	12.1607
:::FFFF	chr7:42018224-42018425(-)$1	201	7	14	16.8928
::::::H	chr5:108691563-108691764(-)$1	201	10	17	13.2321
G::ffff	chr6:131915167-131915368(-)$1	201	137	144	13.4107
GG::eee	chr5:61789756-61789957(+)$1	201	55	62	12.5178
wwwwwww	chr5:102490520-102490721(+)$1	201	171	178	12.5178
:::::::	chr2:153550992-153551193(-)$1	201	37	44	13.1428
I:fffff	chr9:131370363-131370564(+)$1	201	16	23	13.3214
DYYGGGG	chr12:29509232-29509433(-)$1	201	122	129	12.7857
ssssscc	chr6:170846274-170846475(-)$1	201	33	40	16.8928
!!ddddd	chr7:107052880-107053081(-)$1	201	5	12	12.3392
KJJJJJJ	chr6:49416460-49416661(-)$1	201	9	16	16.8928
======x	chr14:31416330-31416531(-)$1	201	49	56	13.3214
HHH@@@@	chr2:27424197-27424398(-)$1	201	105	112	12.5178
gggggg!	chr17:28505014-28505215(+)$1	201	62	69	13.1428
:::::ff	chr14:76186841-76187042(+)$1	201	85	92	13.0535
ii[ffff	chr2:73680884-73681085(+)$1	201	92	99	12.7857
>>>>>>>	chr3:69104943-69105144(-)$1	201	172	179	16.8928
gggg:::	chr15:83486635-83486836(+)$1	201	14	21	13.4107
GGeeeee	chr13:99555215-99555416(-)$1	201	37	44	16.8928
E::::::	chr10:74912010-74912211(-)$1	201	185	192	12.8750
gggmmmm	chr12:46215127-46215328(+)$1	201	38	45	13.4107
####ddd	chr19:1388480-1388681(+)$1	201	171	178	13.2321
gggg]dd	chr2:203142590-203142791(+)$1	201	192	199	16.8928
uuuuuuc	chr22:29747201-29747402(-)$1	201	128	135	13.2321
[bb[bbm	chr1:52943332-52943533(-)$1	201	60	67	12.9642
qqqqqqe	chr6:43534940-43535141(-)$1	201	39	46	13.2321
JJJJJJJ	chr5:70930891-70931092(+)$1	201	2	9	13.4107
rrrrrdd	chr1:66075817-66076018(+)$1	201	40	47	12.1607
$$$$fff	chr15:52646078-52646279(-)$1	201	4	11	13.3214
:::::::	chr11:63667409-63667610(+)$1	201	192	199	13.4107
$$$ffff	chr1:93580493-93580694(+)$1	201	23	30	12.9642
~~~CCC:	chr2:32640795-32640996(+)$1	201	143	150	12.9642
:::::HH	chr8:18725421-18725622(-)$1	201	31	38	12.6964
:::gggg	chr12:118823878-118824079(+)$1	201	13	20	13.4107
oooooob	chrX:20181028-20181229(-)$1	201	63	70	13.0535
:ffffff	chr15:59185083-59185284(-)$1	201	1	8	12.7857
:ddddmm	chr15:43017664-43017865(-)$1	201	81	88	12.8750
iiiiiii	chr1:155448406-155448607(-)$1	201	56	63	12.5178
3hhhhhh	chr17:7480573-7480774(+)$1	201	74	81	13.1428
dduuuuu	chr17:38552591-38552792(-)$1	201	32	39	13.0535
3a]ccc]	chr5:140021495-140021696(+)$1	201	166	173	12.7857
Dddddcc	chr2:170666720-170666921(+)$1	201	157	164	13.3214

#DB
.......	chr5:16762580-16762781(-)$1	1	15	22	16.8928
.......	chr9:4705984-4706185(+)$1	1	10	17	16.8928
(((....	chr1:156908199-156908400(-)$1	1	43	50	12.8750
...))))	chr2:136536475-136536676(+)$1	1	66	73	12.3392
.......	chr5:115336210-115336411(+)$1	1	63	70	13.0535
....).)	chr12:46243752-46243953(+)$1	1	48	55	16.8928
(((((((	chr9:139353842-139354043(-)$1	1	123	130	12.5178
))))..)	chr7:127013447-127013648(-)$1	1	101	108	13.3214
.......	chr4:20482281-20482482(+)$1	1	34	41	12.5178
.(((...	chr6:158353128-158353329(+)$1	1	87	94	12.5178
...((((	chr2:38570535-38570736(-)$1	1	3	10	12.9642
))...))	chr2:32726697-32726898(+)$1	1	73	80	16.8928
.(((((.	chr7:23387229-23387430(-)$1	1	48	55	12.5178
)......	chr10:79764527-79764728(-)$1	1	54	61	12.1607
...((((	chr7:42018224-42018425(-)$1	1	7	14	16.8928
......(	chr5:108691563-108691764(-)$1	1	10	17	13.2321
)..((((	chr6:131915167-131915368(-)$1	1	137	144	13.4107
((..(((	chr5:61789756-61789957(+)$1	1	55	62	12.5178
.......	chr5:102490520-102490721(+)$1	1	171	178	12.5178
.......	chr2:153550992-153551193(-)$1	1	37	44	13.1428
(.(((((	chr9:131370363-131370564(+)$1	1	16	23	13.3214
)..))))	chr12:29509232-29509433(-)$1	1	122	129	12.7857
.....))	chr6:170846274-170846475(-)$1	1	33	40	16.8928
..(((((	chr7:107052880-107053081(-)$1	1	5	12	12.3392
.((((((	chr6:49416460-49416661(-)$1	1	9	16	16.8928
((((((.	chr14:31416330-31416531(-)$1	1	49	56	13.3214
)))....	chr2:27424197-27424398(-)$1	1	105	112	12.5178
((((((.	chr17:28505014-28505215(+)$1	1	62	69	13.1428
.....((	chr14:76186841-76187042(+)$1	1	85	92	13.0535
((.((((	chr2:73680884-73681085(+)$1	1	92	99	12.7857
.......	chr3:69104943-69105144(-)$1	1	172	179	16.8928
))))...	chr15:83486635-83486836(+)$1	1	14	21	13.4107
(((((((	chr13:99555215-99555416(-)$1	1	37	44	16.8928
)......	chr10:74912010-74912211(-)$1	1	185	192	12.8750
(((....	chr12:46215127-46215328(+)$1	1	38	45	13.4107
....(((	chr19:1388480-1388681(+)$1	1	171	178	13.2321
)))).))	chr2:203142590-203142791(+)$1	1	192	199	16.8928
......)	chr22:29747201-29747402(-)$1	1	128	135	13.2321
.((.((.	chr1:52943332-52943533(-)$1	1	60	67	12.9642
......)	chr6:43534940-43535141(-)$1	1	39	46	13.2321
(((((((	chr5:70930891-70931092(+)$1	1	2	9	13.4107
.....))	chr1:66075817-66076018(+)$1	1	40	47	12.1607
....(((	chr15:52646078-52646279(-)$1	1	4	11	13.3214
.......	chr11:63667409-63667610(+)$1	1	192	199	13.4107
...((((	chr1:93580493-93580694(+)$1	1	23	30	12.9642
...))).	chr2:32640795-32640996(+)$1	1	143	150	12.9642
.....((	chr8:18725421-18725622(-)$1	1	31	38	12.6964
...((((	chr12:118823878-118824079(+)$1	1	13	20	13.4107
......)	chrX:20181028-20181229(-)$1	1	63	70	13.0535
.((((((	chr15:59185083-59185284(-)$1	1	1	8	12.7857
.((((..	chr15:43017664-43017865(-)$1	1	81	88	12.8750
)))))))	chr1:155448406-155448607(-)$1	1	56	63	12.5178
.))))))	chr17:7480573-7480774(+)$1	1	74	81	13.1428
((.....	chr17:38552591-38552792(-)$1	1	32	39	13.0535
.).))).	chr5:140021495-140021696(+)$1	1	166	173	12.7857
)((((((	chr2:170666720-170666921(+)$1	1	157	164	13.3214

#PSSM
U : 0.91	u : 0.05	C : 0.01	A : 0.01	
U : 0.83	G : 0.07	u : 0.05	A : 0.01	C : 0.01	
U : 0.87	u : 0.05	G : 0.05	A : 0.01	
U : 0.82	G : 0.07	u : 0.03	C : 0.03	c : 0.01	A : 0.01	
C : 0.76	A : 0.08	U : 0.05	c : 0.03	G : 0.03	a : 0.01	
U : 0.87	u : 0.05	C : 0.05	G : 0.01	
U : 0.76	C : 0.07	G : 0.07	u : 0.03	A : 0.03	c : 0.01	

#score	764.0357142857152
#seq	56
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_QKI_Hafner2010c_hg19_transcript_m2_run2.nuc.txt

#NT
uaaaaacauuua	chr6:142541043-142541274(+)$1	231	35	47	16.7627
UAUAAAAUUUUC	chr8:91611251-91611481(-)$1	230	206	218	16.0847
UUUAAAAUUUUA	chr2:213318293-213318527(-)$1	234	102	114	16.0847
aauaaaauuuuu	chr7:126673357-126673596(-)$1	239	10	22	12.5254
gaaauaauuuua	chr10:94629486-94629710(+)$1	224	48	60	17.2711
uaggaaauuuaa	chr10:21922643-21922875(+)$1	232	95	107	12.5254
UGAAAGGUUUUA	chr12:42949077-42949316(-)$1	239	1	13	12.2711
uaaauaCUUUUC	chr10:65082554-65082786(-)$1	232	45	57	14.1355
UCAAAAGUUUUA	chr13:52038382-52038614(+)$1	232	102	114	15.8305
UAAACAGCUUUA	chr16:50264283-50264522(+)$1	239	100	112	13.3728
ugauuaauuuua	chr17:59800348-59800580(-)$1	232	179	191	14.2203
UAAUUGAUUUUA	chr10:76225653-76225900(+)$1	247	49	61	14.1355
UAUUAAAGUUUA	chrM:14239-14517(+)$1	278	77	89	13.3728
uaaagaacuuua	chr3:153911940-153912173(+)$1	233	95	107	15.9152
GAUAAACUUUUA	chr7:156548246-156548479(-)$1	233	71	83	14.1355
AAAACACUUUUA	chr13:37403087-37403322(+)$1	235	103	115	14.3050
aaaaaaauucua	chr11:3374445-3374677(-)$1	232	12	24	15.8305
CAAAAAAUUUAA	chr10:18970077-18970310(+)$1	233	115	127	15.5762
UAUAAAAUAUGA	chr2:669144-669376(-)$1	232	127	139	12.2711
UCUUAAAUUUUA	chr8:59494746-59494978(+)$1	232	102	114	13.3728
UAUACUAUUUUA	chr1:182819862-182820093(+)$1	231	17	29	14.2203
UAACCAAUUUUC	chr3:105151675-105151907(+)$1	232	104	116	13.2881
UAAAAACUAUUA	chr2:131906339-131906565(+)$1	226	110	122	16.4237
UAAAAAACAUUA	chr15:42035589-42035817(+)$1	228	111	123	15.1525
UAUCAAAUAUUA	chr1:235367957-235368189(-)$1	232	124	136	13.2033
UAUUAAAUAUUA	chr8:17077825-17078061(+)$1	236	120	132	13.5423
uaauauauuuaa	chr9:114209901-114210144(-)$1	243	104	116	13.4576
GAAAAUGUUUUA	chr12:121339468-121339707(-)$1	239	11	23	13.3728
uaauuuauuuua	chr1:53343037-53343267(+)$1	230	158	170	14.8135
UAAACAAUUCUC	chr11:102955088-102955330(-)$1	242	23	35	12.6101
UAACAACUUUUA	chr1:117948742-117948981(+)$1	239	116	128	17.2711
UAAAAAAUUUUA	chr18:9126839-9127061(+)$1	222	134	146	22.7796
uagauaauuuaa	chr7:76998008-76998240(-)$1	232	219	231	13.6271
UAAUCAAAUUUA	chr3:152119062-152119294(+)$1	232	110	122	14.0508
GAAAAAGUAUUA	chr8:101269671-101269903(-)$1	232	58	70	12.6949
caaaaaaauaua	chr13:103275956-103276201(+)$1	245	118	130	12.1864
UAAAAACUUGGA	chr3:37348584-37348817(+)$1	233	89	101	12.5254
GAAAAUAUUUGA	chr1:77402960-77403192(+)$1	232	187	199	12.4406
uaaguaauuuua	chr2:208446140-208446372(+)$1	232	198	210	17.2711
uaACAAAUUAUA	chr10:95801711-95801944(+)$1	233	105	117	16.3389
uaaacauauuua	chr2:213384566-213384797(-)$1	231	199	211	13.2881
aauuaaauuuua	chr7:12377407-12377645(-)$1	238	8	20	14.0508
uuaaauauuaua	chr6:100011786-100012014(-)$1	228	0	12	12.2711
UAAUAACUUAUA	chr8:47504094-47504326(-)$1	232	35	47	14.1355
ugaaaacuuuug	chr2:171857020-171857251(-)$1	231	146	158	12.2711
UAAAUAAUUUAC	chr17:57228407-57228632(-)$1	225	185	197	13.1186
GAGAAAAUUUAA	chr2:39247485-39247716(-)$1	231	170	182	12.5254
UAAAAUAAAUUA	chr22:28376606-28376841(+)$1	235	168	180	12.3559
UGAAAAAUUCUA	chr1:186302774-186303004(-)$1	230	177	189	15.4067
uaaaaucuuaua	chr7:155485388-155485620(+)$1	232	38	50	13.6271
uaaauaguuuua	chrX:128676208-128676443(+)$1	235	175	187	17.6101
uaaauaauuaua	chr6:93964118-93964350(-)$1	232	79	91	17.1016
uaaaaaauuGuu	chr1:114316094-114316333(-)$1	239	176	188	14.8135
UAACUACUUUUA	chr3:52715318-52715550(-)$1	232	104	116	15.0677
UAACAUAUUUUA	chr6:124681591-124681823(+)$1	232	120	132	16.6779
AUAAUAAUUUUA	chr2:102330871-102331101(+)$1	230	113	125	13.3728
ugaaauaauuua	chr4:2962844-2963115(-)$1	271	36	48	12.4406
AAGAGAAUUUUA	chr8:119604907-119605139(-)$1	232	53	65	13.0338

#otherMatches

#Struct PSSM
drrrrrrrrrdd	chr15:41028461-41028716(-)$1	255	212	224	12.1016
E{BBLLLEEEEE	chr6:142541043-142541274(+)$1	231	35	47	16.7627
:::::HHHHHHH	chr8:91611251-91611481(-)$1	230	206	218	16.0847
gggggmmmmggg	chr2:213318293-213318527(-)$1	234	102	114	16.0847
::::::::::GG	chr7:126673357-126673596(-)$1	239	10	22	12.5254
GGGGGG::::::	chr10:94629486-94629710(+)$1	224	48	60	17.2711
d[bb))))))))	chr10:21922643-21922875(+)$1	232	95	107	12.5254
hhhhhhh"""cc	chr12:42949077-42949316(-)$1	239	1	13	12.2711
::::::::::::	chr10:65082554-65082786(-)$1	232	45	57	14.1355
+++++dddd^^^	chr13:52038382-52038614(+)$1	232	102	114	15.8305
ffffdddd!!bb	chr16:50264283-50264522(+)$1	239	100	112	13.3728
cmmmmccc22gg	chr17:59800348-59800580(-)$1	232	179	191	14.2203
::::::::::::	chr10:76225653-76225900(+)$1	247	49	61	14.1355
::::::EEEEE:	chrM:14239-14517(+)$1	278	77	89	13.3728
22dddd333ddd	chr3:153911940-153912173(+)$1	233	95	107	15.9152
ggggdddd6666	chr7:156548246-156548479(-)$1	233	71	83	14.1355
cccmmmmccc]d	chr13:37403087-37403322(+)$1	235	103	115	14.3050
::::::::::::	chr11:3374445-3374677(-)$1	232	12	24	15.8305
:eeeee[iiiii	chr10:18970077-18970310(+)$1	233	115	127	15.5762
:::::::FFFFF	chr2:669144-669376(-)$1	232	127	139	12.2711
dddd99999999	chr8:59494746-59494978(+)$1	232	102	114	13.3728
eeee]hhhhhhh	chr1:182819862-182820093(+)$1	231	17	29	14.2203
ee[bbffffff^	chr3:105151675-105151907(+)$1	232	104	116	13.2881
:gggggggoooo	chr2:131906339-131906565(+)$1	226	110	122	16.4237
:::::::fffff	chr15:42035589-42035817(+)$1	228	111	123	15.1525
::::::::::::	chr1:235367957-235368189(-)$1	232	124	136	13.2033
::::::EEEEEY	chr8:17077825-17078061(+)$1	236	120	132	13.5423
JJJJJJJJ::::	chr9:114209901-114210144(-)$1	243	104	116	13.4576
ooooooeeeee:	chr12:121339468-121339707(-)$1	239	11	23	13.3728
i[iiiiiiiiiq	chr1:53343037-53343267(+)$1	230	158	170	14.8135
::::::::::::	chr11:102955088-102955330(-)$1	242	23	35	12.6101
gggggg[ddddc	chr1:117948742-117948981(+)$1	239	116	128	17.2711
hh::::::::::	chr18:9126839-9127061(+)$1	222	134	146	22.7796
GGGGGG::::::	chr7:76998008-76998240(-)$1	232	219	231	13.6271
444ffffff333	chr3:152119062-152119294(+)$1	232	110	122	14.0508
EE:::::::::e	chr8:101269671-101269903(-)$1	232	58	70	12.6949
:::eeeeennnn	chr13:103275956-103276201(+)$1	245	118	130	12.1864
UUUUUUUGGGGG	chr3:37348584-37348817(+)$1	233	89	101	12.5254
d7777777gggg	chr1:77402960-77403192(+)$1	232	187	199	12.4406
::EEEEE~~~~E	chr2:208446140-208446372(+)$1	232	198	210	17.2711
xxxiiiiiiiii	chr10:95801711-95801944(+)$1	233	105	117	16.3389
:EEEEE::::::	chr2:213384566-213384797(-)$1	231	199	211	13.2881
::::::::::HH	chr7:12377407-12377645(-)$1	238	8	20	14.0508
:::::eeeee!!	chr6:100011786-100012014(-)$1	228	0	12	12.2711
pppffffff:::	chr8:47504094-47504326(-)$1	232	35	47	14.1355
::::FFFFFF}A	chr2:171857020-171857251(-)$1	231	146	158	12.2711
ggg[cccvvvvv	chr17:57228407-57228632(-)$1	225	185	197	13.1186
xxxxxxhhhhhh	chr2:39247485-39247716(-)$1	231	170	182	12.5254
:::::::eeeee	chr22:28376606-28376841(+)$1	235	168	180	12.3559
[a[eeeeemmmm	chr1:186302774-186303004(-)$1	230	177	189	15.4067
ffqqqqqqqqff	chr7:155485388-155485620(+)$1	232	38	50	13.6271
mmmggggggg::	chrX:128676208-128676443(+)$1	235	175	187	17.6101
ff>>>>>>>>>>	chr6:93964118-93964350(-)$1	232	79	91	17.1016
ggggg333dddd	chr1:114316094-114316333(-)$1	239	176	188	14.8135
f:::::::::::	chr3:52715318-52715550(-)$1	232	104	116	15.0677
uuuuuuhhhhhh	chr6:124681591-124681823(+)$1	232	120	132	16.6779
::::::::::::	chr2:102330871-102331101(+)$1	230	113	125	13.3728
ddd:iiiiiiii	chr4:2962844-2963115(-)$1	271	36	48	12.4406
ddddqqqqqqqq	chr8:119604907-119605139(-)$1	232	53	65	13.0338

#DB
(.........))	chr15:41028461-41028716(-)$1	1	212	224	12.1016
(.((...(((((	chr6:142541043-142541274(+)$1	1	35	47	16.7627
.....)))))))	chr8:91611251-91611481(-)$1	1	206	218	16.0847
(((((....)))	chr2:213318293-213318527(-)$1	1	102	114	16.0847
..........((	chr7:126673357-126673596(-)$1	1	10	22	12.5254
((((((......	chr10:94629486-94629710(+)$1	1	48	60	17.2711
(.((........	chr10:21922643-21922875(+)$1	1	95	107	12.5254
(((((((...((	chr12:42949077-42949316(-)$1	1	1	13	12.2711
............	chr10:65082554-65082786(-)$1	1	45	57	14.1355
.....((((...	chr13:52038382-52038614(+)$1	1	102	114	15.8305
((((((((..((	chr16:50264283-50264522(+)$1	1	100	112	13.3728
(....)))..))	chr17:59800348-59800580(-)$1	1	179	191	14.2203
............	chr10:76225653-76225900(+)$1	1	49	61	14.1355
......(((((.	chrM:14239-14517(+)$1	1	77	89	13.3728
..))))...)))	chr3:153911940-153912173(+)$1	1	95	107	15.9152
))))))))....	chr7:156548246-156548479(-)$1	1	71	83	14.1355
(((....))).)	chr13:37403087-37403322(+)$1	1	103	115	14.3050
............	chr11:3374445-3374677(-)$1	1	12	24	15.8305
.(((((.(((((	chr10:18970077-18970310(+)$1	1	115	127	15.5762
.......)))))	chr2:669144-669376(-)$1	1	127	139	12.2711
))))........	chr8:59494746-59494978(+)$1	1	102	114	13.3728
)))).)))))))	chr1:182819862-182820093(+)$1	1	17	29	14.2203
((.((((((((.	chr3:105151675-105151907(+)$1	1	104	116	13.2881
.(((((((....	chr2:131906339-131906565(+)$1	1	110	122	16.4237
.......(((((	chr15:42035589-42035817(+)$1	1	111	123	15.1525
............	chr1:235367957-235368189(-)$1	1	124	136	13.2033
......))))).	chr8:17077825-17078061(+)$1	1	120	132	13.5423
((((((((....	chr9:114209901-114210144(-)$1	1	104	116	13.4576
......))))).	chr12:121339468-121339707(-)$1	1	11	23	13.3728
(.(((((((((.	chr1:53343037-53343267(+)$1	1	158	170	14.8135
............	chr11:102955088-102955330(-)$1	1	23	35	12.6101
((((((.(((((	chr1:117948742-117948981(+)$1	1	116	128	17.2711
))..........	chr18:9126839-9127061(+)$1	1	134	146	22.7796
))))))......	chr7:76998008-76998240(-)$1	1	219	231	13.6271
...))))))...	chr3:152119062-152119294(+)$1	1	110	122	14.0508
((.........(	chr8:101269671-101269903(-)$1	1	58	70	12.6949
...(((((....	chr13:103275956-103276201(+)$1	1	118	130	12.1864
.......(((((	chr3:37348584-37348817(+)$1	1	89	101	12.5254
).......))))	chr1:77402960-77403192(+)$1	1	187	199	12.4406
..)))))....)	chr2:208446140-208446372(+)$1	1	198	210	17.2711
...)))))))))	chr10:95801711-95801944(+)$1	1	105	117	16.3389
.)))))......	chr2:213384566-213384797(-)$1	1	199	211	13.2881
..........((	chr7:12377407-12377645(-)$1	1	8	20	14.0508
.....(((((..	chr6:100011786-100012014(-)$1	1	0	12	12.2711
...))))))...	chr8:47504094-47504326(-)$1	1	35	47	14.1355
....)))))).)	chr2:171857020-171857251(-)$1	1	146	158	12.2711
(((.(((.....	chr17:57228407-57228632(-)$1	1	185	197	13.1186
......))))))	chr2:39247485-39247716(-)$1	1	170	182	12.5254
.......(((((	chr22:28376606-28376841(+)$1	1	168	180	12.3559
.(.(((((....	chr1:186302774-186303004(-)$1	1	177	189	15.4067
((........))	chr7:155485388-155485620(+)$1	1	38	50	13.6271
...)))))))..	chrX:128676208-128676443(+)$1	1	175	187	17.6101
))..........	chr6:93964118-93964350(-)$1	1	79	91	17.1016
)))))...))))	chr1:114316094-114316333(-)$1	1	176	188	14.8135
)...........	chr3:52715318-52715550(-)$1	1	104	116	15.0677
......))))))	chr6:124681591-124681823(+)$1	1	120	132	16.6779
............	chr2:102330871-102331101(+)$1	1	113	125	13.3728
))).((((((((	chr4:2962844-2963115(-)$1	1	36	48	12.4406
((((........	chr8:119604907-119605139(-)$1	1	53	65	13.0338

#PSSM
U : 0.45	u : 0.30	G : 0.08	a : 0.05	A : 0.05	g : 0.01	C : 0.01	c : 0.01	
A : 0.50	a : 0.32	g : 0.05	U : 0.03	G : 0.03	C : 0.03	u : 0.01	
A : 0.44	a : 0.30	U : 0.15	u : 0.03	g : 0.03	G : 0.03	
A : 0.42	a : 0.27	U : 0.10	C : 0.10	u : 0.06	g : 0.03	
A : 0.44	a : 0.20	u : 0.13	C : 0.10	U : 0.06	g : 0.01	c : 0.01	G : 0.01	
A : 0.50	a : 0.28	U : 0.08	u : 0.08	G : 0.03	
A : 0.42	a : 0.27	C : 0.13	G : 0.08	c : 0.05	u : 0.01	g : 0.01	
U : 0.54	u : 0.27	a : 0.06	A : 0.05	C : 0.03	G : 0.01	c : 0.01	
U : 0.52	u : 0.35	A : 0.11	
U : 0.54	u : 0.25	a : 0.06	C : 0.05	G : 0.03	A : 0.03	c : 0.01	
U : 0.52	u : 0.30	A : 0.06	a : 0.05	G : 0.05	
A : 0.55	a : 0.30	C : 0.08	u : 0.03	g : 0.01	

#score	846.5423728813565
#seq	59
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_CDS_m1_run1.nuc.txt

#NT
CCA	chr6:64421738-64421955(+)$1	217	9	12	9.0000
CCA	chr19:36215815-36216038(+)$1	223	33	36	9.0000
CCA	chr13:23906307-23906538(-)$1	231	31	34	9.0000
CCA	chr1:198233155-198233373(+)$1	218	107	110	9.0000
CCA	chr1:6285061-6285284(-)$1	223	101	104	9.0000
CCA	chr2:61709462-61709684(-)$1	222	96	99	9.0000
CCA	chr20:49509610-49509849(-)$1	239	21	24	9.0000
CCA	chr10:93723737-93723957(+)$1	220	29	32	9.0000
CCA	chr22:50893867-50894092(-)$1	225	28	31	9.0000
CCA	chr4:125592933-125593160(-)$1	227	59	62	9.0000
CCA	chr14:103988613-103988839(-)$1	226	7	10	9.0000
CCA	chr13:23905603-23905829(-)$1	226	12	15	9.0000
CCA	chr3:184040235-184040455(+)$1	220	34	37	9.0000
CCA	chr1:54238005-54238224(-)$1	219	96	99	9.0000
CCA	chr7:135322682-135322901(+)$1	219	132	135	9.0000
CCA	chr2:61558339-61558556(-)$1	217	14	17	9.0000
CCA	chr3:128984429-128984647(+)$1	218	92	95	9.0000
CCA	chr1:153789871-153790096(-)$1	225	74	77	9.0000
CCA	chr13:37427486-37427708(-)$1	222	0	3	9.0000
CCA	chr5:79747225-79747442(+)$1	217	197	200	9.0000
CCA	chr6:111345390-111345609(+)$1	219	26	29	9.0000
CCA	chr16:29818894-29819116(+)$1	222	11	14	9.0000
CCA	chr16:30723982-30724204(+)$1	222	30	33	9.0000
CCA	chr6:79680417-79680639(-)$1	222	2	5	9.0000
CCA	chr22:29383025-29383246(+)$1	221	22	25	9.0000
CCA	chr16:72991730-72991952(-)$1	222	34	37	9.0000
CCA	chr6:87967119-87967346(+)$1	227	59	62	9.0000
CCA	chr1:8927172-8927391(-)$1	219	58	61	9.0000
CCA	chr11:57581726-57581945(+)$1	219	212	215	9.0000
CCA	chr20:18506397-18506615(+)$1	218	101	104	9.0000
CCA	chr19:37203642-37203868(+)$1	226	7	10	9.0000
CCA	chr16:70562749-70562971(+)$1	222	29	32	9.0000
CCA	chr10:22618182-22618402(+)$1	220	21	24	9.0000
CCA	chr8:17814787-17815003(+)$1	216	2	5	9.0000
CCA	chr17:76433755-76433974(-)$1	219	1	4	9.0000
CCA	chr18:13072686-13072907(+)$1	221	25	28	9.0000
CCA	chr12:49666622-49666874(+)$1	252	11	14	9.0000
cca	chr17:38563039-38563261(-)$1	222	16	19	9.0000
CCA	chr8:48885369-48885595(+)$1	226	110	113	9.0000
CCA	chr19:8550442-8550660(+)$1	218	16	19	9.0000
CCA	chr13:42876078-42876301(+)$1	223	107	110	9.0000
CCA	chr1:19564485-19564700(-)$1	215	98	101	9.0000
CCA	chrX:54037455-54037673(-)$1	218	57	60	9.0000
CCA	chr14:62212343-62212561(+)$1	218	83	86	9.0000
CCA	chr1:23418167-23418389(-)$1	222	32	35	9.0000
CCA	chr5:73985169-73985389(+)$1	220	37	40	9.0000
CCA	chr19:19135624-19135848(-)$1	224	103	106	9.0000
CCA	chr17:38452895-38453110(+)$1	215	95	98	9.0000
CCA	chr11:3744494-3744719(-)$1	225	70	73	9.0000
CCA	chr6:7571987-7572212(+)$1	225	90	93	9.0000
CCA	chrX:153228606-153228830(-)$1	224	11	14	9.0000
CCA	chr16:70531822-70532040(-)$1	218	86	89	9.0000
CCA	chr12:29920865-29921083(-)$1	218	103	106	9.0000
CCA	chr9:5763482-5763705(+)$1	223	28	31	9.0000
CCA	chr6:56918710-56918931(+)$1	221	30	33	9.0000
CCA	chr18:55268771-55268989(-)$1	218	87	90	9.0000
CCA	chr5:14507973-14508196(+)$1	223	11	14	9.0000
CCA	chr12:64827252-64827474(+)$1	222	13	16	9.0000
CCA	chr19:11891832-11892051(+)$1	219	58	61	9.0000
CCA	chr7:72873848-72874079(-)$1	231	86	89	9.0000
CCA	chr16:31927403-31927622(+)$1	219	50	53	9.0000
CCA	chr16:29808121-29808334(+)$1	213	11	14	9.0000
CCA	chr2:178096173-178096396(-)$1	223	12	15	9.0000
CCA	chr5:37006436-37006656(+)$1	220	136	139	9.0000
CCA	chr7:128851959-128852177(+)$1	218	61	64	9.0000
CCA	chr3:9483728-9483949(+)$1	221	84	87	9.0000
CCA	chr8:61769323-61769541(+)$1	218	38	41	9.0000
CCA	chr16:89347484-89347705(-)$1	221	1	4	9.0000
CCA	chr17:45678937-45679156(+)$1	219	1	4	9.0000
CCA	chr7:64388254-64388474(+)$1	220	183	186	9.0000
CCA	chr3:133306772-133306991(+)$1	219	39	42	9.0000
CCA	chr1:220379170-220379391(-)$1	221	67	70	9.0000
CCA	chr19:9763803-9764025(-)$1	222	62	65	9.0000
CCA	chr1:229738284-229738501(-)$1	217	12	15	9.0000
CCA	chr18:72997994-72998217(+)$1	223	26	29	9.0000
CCA	chr5:64959997-64960217(+)$1	220	59	62	9.0000
CCA	chr12:109907220-109907440(-)$1	220	37	40	9.0000
CCA	chr4:71891475-71891699(+)$1	224	33	36	9.0000
CCA	chr18:60232189-60232404(+)$1	215	104	107	9.0000
CCA	chr8:30655014-30655231(-)$1	217	20	23	9.0000
CCA	chr19:58640284-58640508(-)$1	224	27	30	9.0000
CCA	chr16:30721072-30721292(+)$1	220	29	32	9.0000
CCA	chr10:71160663-71160883(+)$1	220	31	34	9.0000
CCA	chr1:200376756-200376975(-)$1	219	1	4	9.0000
CCA	chr17:28712047-28712266(+)$1	219	23	26	9.0000
CCA	chr13:30098187-30098409(-)$1	222	132	135	9.0000
CCA	chr17:4585710-4585926(-)$1	216	154	157	9.0000
CCA	chr13:31725740-31725963(-)$1	223	52	55	9.0000
CCA	chr2:85276436-85276656(+)$1	220	42	45	9.0000
CCA	chr1:38265191-38265411(+)$1	220	13	16	9.0000
CCA	chr19:38126809-38127032(-)$1	223	115	118	9.0000
CCA	chr2:211018162-211018379(-)$1	217	35	38	9.0000
CCA	chr3:128526321-128526543(+)$1	222	68	71	9.0000
CCA	chr1:32841948-32842172(-)$1	224	22	25	9.0000
CCA	chr22:35802481-35802706(+)$1	225	34	37	9.0000
CCA	chr15:22999334-22999554(+)$1	220	11	14	9.0000
CCA	chr3:180669060-180669283(+)$1	223	117	120	9.0000

#otherMatches

#Struct PSSM
nnn	chr15:22954198-22954417(+)$1	219	18	21	9.0000
:dd	chr6:64421738-64421955(+)$1	217	9	12	9.0000
dll	chr19:36215815-36216038(+)$1	223	33	36	9.0000
GG:	chr13:23906307-23906538(-)$1	231	31	34	9.0000
%%%	chr1:198233155-198233373(+)$1	218	107	110	9.0000
ccc	chr1:6285061-6285284(-)$1	223	101	104	9.0000
ddd	chr2:61709462-61709684(-)$1	222	96	99	9.0000
]dd	chr20:49509610-49509849(-)$1	239	21	24	9.0000
MMM	chr10:93723737-93723957(+)$1	220	29	32	9.0000
ggg	chr22:50893867-50894092(-)$1	225	28	31	9.0000
fff	chr4:125592933-125593160(-)$1	227	59	62	9.0000
FFF	chr14:103988613-103988839(-)$1	226	7	10	9.0000
:::	chr13:23905603-23905829(-)$1	226	12	15	9.0000
ccc	chr3:184040235-184040455(+)$1	220	34	37	9.0000
ccv	chr1:54238005-54238224(-)$1	219	96	99	9.0000
ddd	chr7:135322682-135322901(+)$1	219	132	135	9.0000
eee	chr2:61558339-61558556(-)$1	217	14	17	9.0000
d22	chr3:128984429-128984647(+)$1	218	92	95	9.0000
mmm	chr1:153789871-153790096(-)$1	225	74	77	9.0000
:CC	chr13:37427486-37427708(-)$1	222	0	3	9.0000
FFF	chr5:79747225-79747442(+)$1	217	197	200	9.0000
III	chr6:111345390-111345609(+)$1	219	26	29	9.0000
ppp	chr16:29818894-29819116(+)$1	222	11	14	9.0000
bb[	chr16:30723982-30724204(+)$1	222	30	33	9.0000
ccc	chr6:79680417-79680639(-)$1	222	2	5	9.0000
[dd	chr22:29383025-29383246(+)$1	221	22	25	9.0000
ff:	chr16:72991730-72991952(-)$1	222	34	37	9.0000
uub	chr6:87967119-87967346(+)$1	227	59	62	9.0000
666	chr1:8927172-8927391(-)$1	219	58	61	9.0000
CCC	chr11:57581726-57581945(+)$1	219	212	215	9.0000
ccc	chr20:18506397-18506615(+)$1	218	101	104	9.0000
DDN	chr19:37203642-37203868(+)$1	226	7	10	9.0000
ccc	chr16:70562749-70562971(+)$1	222	29	32	9.0000
ccc	chr10:22618182-22618402(+)$1	220	21	24	9.0000
ddm	chr8:17814787-17815003(+)$1	216	2	5	9.0000
:ee	chr17:76433755-76433974(-)$1	219	1	4	9.0000
ddd	chr18:13072686-13072907(+)$1	221	25	28	9.0000
&&&	chr12:49666622-49666874(+)$1	252	11	14	9.0000
DD:	chr17:38563039-38563261(-)$1	222	16	19	9.0000
!a[	chr8:48885369-48885595(+)$1	226	110	113	9.0000
ggg	chr19:8550442-8550660(+)$1	218	16	19	9.0000
44c	chr13:42876078-42876301(+)$1	223	107	110	9.0000
:::	chr1:19564485-19564700(-)$1	215	98	101	9.0000
CCC	chrX:54037455-54037673(-)$1	218	57	60	9.0000
JJJ	chr14:62212343-62212561(+)$1	218	83	86	9.0000
DDD	chr1:23418167-23418389(-)$1	222	32	35	9.0000
"""	chr5:73985169-73985389(+)$1	220	37	40	9.0000
:::	chr19:19135624-19135848(-)$1	224	103	106	9.0000
ggg	chr17:38452895-38453110(+)$1	215	95	98	9.0000
]gg	chr11:3744494-3744719(-)$1	225	70	73	9.0000
fff	chr6:7571987-7572212(+)$1	225	90	93	9.0000
eee	chrX:153228606-153228830(-)$1	224	11	14	9.0000
eee	chr16:70531822-70532040(-)$1	218	86	89	9.0000
ttt	chr12:29920865-29921083(-)$1	218	103	106	9.0000
dd[	chr9:5763482-5763705(+)$1	223	28	31	9.0000
ccc	chr6:56918710-56918931(+)$1	221	30	33	9.0000
eee	chr18:55268771-55268989(-)$1	218	87	90	9.0000
ncc	chr5:14507973-14508196(+)$1	223	11	14	9.0000
c[f	chr12:64827252-64827474(+)$1	222	13	16	9.0000
(((	chr19:11891832-11892051(+)$1	219	58	61	9.0000
eee	chr7:72873848-72874079(-)$1	231	86	89	9.0000
ddd	chr16:31927403-31927622(+)$1	219	50	53	9.0000
rrr	chr16:29808121-29808334(+)$1	213	11	14	9.0000
GGG	chr2:178096173-178096396(-)$1	223	12	15	9.0000
bnn	chr5:37006436-37006656(+)$1	220	136	139	9.0000
ggg	chr7:128851959-128852177(+)$1	218	61	64	9.0000
[dd	chr3:9483728-9483949(+)$1	221	84	87	9.0000
ddd	chr8:61769323-61769541(+)$1	218	38	41	9.0000
:::	chr16:89347484-89347705(-)$1	221	1	4	9.0000
::D	chr17:45678937-45679156(+)$1	219	1	4	9.0000
:EE	chr7:64388254-64388474(+)$1	220	183	186	9.0000
ee:	chr3:133306772-133306991(+)$1	219	39	42	9.0000
eee	chr1:220379170-220379391(-)$1	221	67	70	9.0000
ccc	chr19:9763803-9764025(-)$1	222	62	65	9.0000
:::	chr1:229738284-229738501(-)$1	217	12	15	9.0000
fff	chr18:72997994-72998217(+)$1	223	26	29	9.0000
pcc	chr5:64959997-64960217(+)$1	220	59	62	9.0000
EEE	chr12:109907220-109907440(-)$1	220	37	40	9.0000
f''	chr4:71891475-71891699(+)$1	224	33	36	9.0000
EE}	chr18:60232189-60232404(+)$1	215	104	107	9.0000
mmm	chr8:30655014-30655231(-)$1	217	20	23	9.0000
$$$	chr19:58640284-58640508(-)$1	224	27	30	9.0000
"""	chr16:30721072-30721292(+)$1	220	29	32	9.0000
EEW	chr10:71160663-71160883(+)$1	220	31	34	9.0000
:::	chr1:200376756-200376975(-)$1	219	1	4	9.0000
EE{	chr17:28712047-28712266(+)$1	219	23	26	9.0000
22c	chr13:30098187-30098409(-)$1	222	132	135	9.0000
uuu	chr17:4585710-4585926(-)$1	216	154	157	9.0000
#cc	chr13:31725740-31725963(-)$1	223	52	55	9.0000
:::	chr2:85276436-85276656(+)$1	220	42	45	9.0000
RRR	chr1:38265191-38265411(+)$1	220	13	16	9.0000
ddd	chr19:38126809-38127032(-)$1	223	115	118	9.0000
ccc	chr2:211018162-211018379(-)$1	217	35	38	9.0000
c55	chr3:128526321-128526543(+)$1	222	68	71	9.0000
ccn	chr1:32841948-32842172(-)$1	224	22	25	9.0000
:::	chr22:35802481-35802706(+)$1	225	34	37	9.0000
dmm	chr15:22999334-22999554(+)$1	220	11	14	9.0000
eee	chr3:180669060-180669283(+)$1	223	117	120	9.0000

#DB
...	chr15:22954198-22954417(+)$1	1	18	21	9.0000
.((	chr6:64421738-64421955(+)$1	1	9	12	9.0000
(..	chr19:36215815-36216038(+)$1	1	33	36	9.0000
((.	chr13:23906307-23906538(-)$1	1	31	34	9.0000
...	chr1:198233155-198233373(+)$1	1	107	110	9.0000
)))	chr1:6285061-6285284(-)$1	1	101	104	9.0000
)))	chr2:61709462-61709684(-)$1	1	96	99	9.0000
.))	chr20:49509610-49509849(-)$1	1	21	24	9.0000
...	chr10:93723737-93723957(+)$1	1	29	32	9.0000
)))	chr22:50893867-50894092(-)$1	1	28	31	9.0000
)))	chr4:125592933-125593160(-)$1	1	59	62	9.0000
(((	chr14:103988613-103988839(-)$1	1	7	10	9.0000
...	chr13:23905603-23905829(-)$1	1	12	15	9.0000
(((	chr3:184040235-184040455(+)$1	1	34	37	9.0000
((.	chr1:54238005-54238224(-)$1	1	96	99	9.0000
)))	chr7:135322682-135322901(+)$1	1	132	135	9.0000
(((	chr2:61558339-61558556(-)$1	1	14	17	9.0000
)..	chr3:128984429-128984647(+)$1	1	92	95	9.0000
...	chr1:153789871-153790096(-)$1	1	74	77	9.0000
.((	chr13:37427486-37427708(-)$1	1	0	3	9.0000
)))	chr5:79747225-79747442(+)$1	1	197	200	9.0000
(((	chr6:111345390-111345609(+)$1	1	26	29	9.0000
...	chr16:29818894-29819116(+)$1	1	11	14	9.0000
((.	chr16:30723982-30724204(+)$1	1	30	33	9.0000
(((	chr6:79680417-79680639(-)$1	1	2	5	9.0000
.((	chr22:29383025-29383246(+)$1	1	22	25	9.0000
)).	chr16:72991730-72991952(-)$1	1	34	37	9.0000
..)	chr6:87967119-87967346(+)$1	1	59	62	9.0000
...	chr1:8927172-8927391(-)$1	1	58	61	9.0000
)))	chr11:57581726-57581945(+)$1	1	212	215	9.0000
(((	chr20:18506397-18506615(+)$1	1	101	104	9.0000
((.	chr19:37203642-37203868(+)$1	1	7	10	9.0000
(((	chr16:70562749-70562971(+)$1	1	29	32	9.0000
(((	chr10:22618182-22618402(+)$1	1	21	24	9.0000
((.	chr8:17814787-17815003(+)$1	1	2	5	9.0000
.((	chr17:76433755-76433974(-)$1	1	1	4	9.0000
)))	chr18:13072686-13072907(+)$1	1	25	28	9.0000
...	chr12:49666622-49666874(+)$1	1	11	14	9.0000
((.	chr17:38563039-38563261(-)$1	1	16	19	9.0000
.(.	chr8:48885369-48885595(+)$1	1	110	113	9.0000
(((	chr19:8550442-8550660(+)$1	1	16	19	9.0000
..)	chr13:42876078-42876301(+)$1	1	107	110	9.0000
...	chr1:19564485-19564700(-)$1	1	98	101	9.0000
(((	chrX:54037455-54037673(-)$1	1	57	60	9.0000
)))	chr14:62212343-62212561(+)$1	1	83	86	9.0000
(((	chr1:23418167-23418389(-)$1	1	32	35	9.0000
...	chr5:73985169-73985389(+)$1	1	37	40	9.0000
...	chr19:19135624-19135848(-)$1	1	103	106	9.0000
)))	chr17:38452895-38453110(+)$1	1	95	98	9.0000
.))	chr11:3744494-3744719(-)$1	1	70	73	9.0000
)))	chr6:7571987-7572212(+)$1	1	90	93	9.0000
)))	chrX:153228606-153228830(-)$1	1	11	14	9.0000
(((	chr16:70531822-70532040(-)$1	1	86	89	9.0000
...	chr12:29920865-29921083(-)$1	1	103	106	9.0000
((.	chr9:5763482-5763705(+)$1	1	28	31	9.0000
(((	chr6:56918710-56918931(+)$1	1	30	33	9.0000
)))	chr18:55268771-55268989(-)$1	1	87	90	9.0000
.))	chr5:14507973-14508196(+)$1	1	11	14	9.0000
(.(	chr12:64827252-64827474(+)$1	1	13	16	9.0000
...	chr19:11891832-11892051(+)$1	1	58	61	9.0000
)))	chr7:72873848-72874079(-)$1	1	86	89	9.0000
(((	chr16:31927403-31927622(+)$1	1	50	53	9.0000
...	chr16:29808121-29808334(+)$1	1	11	14	9.0000
(((	chr2:178096173-178096396(-)$1	1	12	15	9.0000
(..	chr5:37006436-37006656(+)$1	1	136	139	9.0000
(((	chr7:128851959-128852177(+)$1	1	61	64	9.0000
.((	chr3:9483728-9483949(+)$1	1	84	87	9.0000
)))	chr8:61769323-61769541(+)$1	1	38	41	9.0000
...	chr16:89347484-89347705(-)$1	1	1	4	9.0000
..(	chr17:45678937-45679156(+)$1	1	1	4	9.0000
.))	chr7:64388254-64388474(+)$1	1	183	186	9.0000
)).	chr3:133306772-133306991(+)$1	1	39	42	9.0000
(((	chr1:220379170-220379391(-)$1	1	67	70	9.0000
)))	chr19:9763803-9764025(-)$1	1	62	65	9.0000
...	chr1:229738284-229738501(-)$1	1	12	15	9.0000
)))	chr18:72997994-72998217(+)$1	1	26	29	9.0000
.))	chr5:64959997-64960217(+)$1	1	59	62	9.0000
(((	chr12:109907220-109907440(-)$1	1	37	40	9.0000
(..	chr4:71891475-71891699(+)$1	1	33	36	9.0000
)).	chr18:60232189-60232404(+)$1	1	104	107	9.0000
...	chr8:30655014-30655231(-)$1	1	20	23	9.0000
...	chr19:58640284-58640508(-)$1	1	27	30	9.0000
...	chr16:30721072-30721292(+)$1	1	29	32	9.0000
((.	chr10:71160663-71160883(+)$1	1	31	34	9.0000
...	chr1:200376756-200376975(-)$1	1	1	4	9.0000
((.	chr17:28712047-28712266(+)$1	1	23	26	9.0000
..)	chr13:30098187-30098409(-)$1	1	132	135	9.0000
...	chr17:4585710-4585926(-)$1	1	154	157	9.0000
.((	chr13:31725740-31725963(-)$1	1	52	55	9.0000
...	chr2:85276436-85276656(+)$1	1	42	45	9.0000
...	chr1:38265191-38265411(+)$1	1	13	16	9.0000
(((	chr19:38126809-38127032(-)$1	1	115	118	9.0000
)))	chr2:211018162-211018379(-)$1	1	35	38	9.0000
)..	chr3:128526321-128526543(+)$1	1	68	71	9.0000
((.	chr1:32841948-32842172(-)$1	1	22	25	9.0000
...	chr22:35802481-35802706(+)$1	1	34	37	9.0000
(..	chr15:22999334-22999554(+)$1	1	11	14	9.0000
(((	chr3:180669060-180669283(+)$1	1	117	120	9.0000

#PSSM
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
A : 0.98	a : 0.01	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2MNase_Kishore2011c_hg19_CDS_m2_run2.nuc.txt

#NT
CAG	chr22:36624003-36624243(-)$1	240	2	5	9.0000
CAG	chr3:25637984-25638224(+)$1	240	46	49	9.0000
CAG	chr1:26798929-26799209(+)$1	280	31	34	9.0000
CAG	chr12:58142863-58143103(-)$1	240	0	3	9.0000
CAG	chr8:61777599-61777839(+)$1	240	43	46	9.0000
CAG	chr1:23857165-23857405(-)$1	240	52	55	9.0000
CAG	chr8:90784855-90785095(+)$1	240	36	39	9.0000
CAG	chr1:223177225-223177465(+)$1	240	37	40	9.0000
CAG	chr22:32112964-32113204(-)$1	240	53	56	9.0000
CAG	chr11:66113415-66113655(-)$1	240	58	61	9.0000
CAG	chr11:122928893-122929133(-)$1	240	12	15	9.0000
CAG	chr15:32929927-32930167(+)$1	240	7	10	9.0000
CAG	chr4:88343952-88344192(+)$1	240	7	10	9.0000
CAG	chr14:23371119-23371359(-)$1	240	104	107	9.0000
CAG	chr16:88874513-88874801(+)$1	288	6	9	9.0000
CAG	chr11:62361225-62361465(-)$1	240	42	45	9.0000
CAG	chr1:89318787-89319027(-)$1	240	35	38	9.0000
CAG	chr8:26484053-26484293(+)$1	240	123	126	9.0000
CAG	chr5:132232681-132232925(-)$1	244	75	78	9.0000
CAG	chr1:214830423-214830663(+)$1	240	37	40	9.0000
CAG	chr5:172750119-172750359(-)$1	240	15	18	9.0000
CAG	chr20:34309650-34309890(-)$1	240	92	95	9.0000
CAG	chr5:71494009-71494249(+)$1	240	37	40	9.0000
CAG	chr19:41777993-41778233(+)$1	240	2	5	9.0000
CAG	chrX:119388995-119389235(+)$1	240	41	44	9.0000
CAG	chr3:49765517-49765757(-)$1	240	43	46	9.0000
CAG	chr17:27493012-27493252(-)$1	240	35	38	9.0000
CAG	chr1:32495868-32496108(+)$1	240	27	30	9.0000
CAG	chr19:47422487-47422727(+)$1	240	3	6	9.0000
CAG	chr20:60575608-60575848(-)$1	240	11	14	9.0000
CAG	chr8:101534795-101535035(-)$1	240	33	36	9.0000
CAG	chr10:120488761-120489006(-)$1	245	3	6	9.0000
CAG	chr21:33043703-33043943(-)$1	240	38	41	9.0000
CAG	chr9:71869457-71869697(+)$1	240	55	58	9.0000
CAG	chr1:54293702-54293942(-)$1	240	74	77	9.0000
CAG	chr17:26652521-26652761(+)$1	240	4	7	9.0000
CAG	chr6:106740814-106741054(-)$1	240	117	120	9.0000
CAG	chr18:9337117-9337357(+)$1	240	171	174	9.0000
CAG	chr2:96942585-96942825(-)$1	240	4	7	9.0000
CAG	chr11:62416668-62416908(-)$1	240	8	11	9.0000
CAG	chrX:47001669-47001909(-)$1	240	25	28	9.0000
CAG	chr12:53703283-53703524(-)$1	241	16	19	9.0000
CAG	chr2:9581962-9582202(+)$1	240	13	16	9.0000
CAG	chr10:43292031-43292271(+)$1	240	54	57	9.0000
CAG	chr9:36357764-36358004(-)$1	240	29	32	9.0000
CAG	chr19:16664387-16664627(-)$1	240	30	33	9.0000
CAG	chr19:36573875-36574115(+)$1	240	37	40	9.0000
CAG	chr12:89917890-89918146(-)$1	256	25	28	9.0000
CAG	chr7:42966052-42966292(-)$1	240	60	63	9.0000
CAG	chr20:60879470-60879710(+)$1	240	43	46	9.0000
CAG	chr1:44435782-44436022(+)$1	240	5	8	9.0000
CAG	chr9:94172570-94172810(-)$1	240	188	191	9.0000
CAG	chr4:84188651-84188891(-)$1	240	38	41	9.0000
CAG	chr2:25043143-25043383(+)$1	240	3	6	9.0000
CAG	chr19:33089041-33089281(-)$1	240	24	27	9.0000
CAG	chr8:81399854-81400103(+)$1	249	29	32	9.0000
cag	chr7:141401813-141402053(-)$1	240	32	35	9.0000
CAG	chr1:46501109-46501349(+)$1	240	10	13	9.0000
CAG	chr7:5413962-5414202(-)$1	240	16	19	9.0000
CAG	chr3:127774439-127774679(+)$1	240	38	41	9.0000
CAG	chr17:43226438-43226718(+)$1	280	138	141	9.0000
CAG	chr8:67970219-67970460(-)$1	241	98	101	9.0000
CAG	chr2:20974598-20974838(-)$1	240	50	53	9.0000
CAG	chr7:143001947-143002187(+)$1	240	53	56	9.0000
CAG	chr3:43344680-43344920(+)$1	240	11	14	9.0000
CAG	chr4:48901763-48902003(-)$1	240	30	33	9.0000
CAG	chr12:56384416-56384656(+)$1	240	9	12	9.0000
CAG	chr9:71395154-71395394(+)$1	240	0	3	9.0000
CAG	chr17:30815317-30815557(+)$1	240	140	143	9.0000
CAG	chr2:71576351-71576591(+)$1	240	12	15	9.0000
CAG	chr19:46206185-46206425(+)$1	240	168	171	9.0000
CAG	chr7:2302763-2303003(-)$1	240	3	6	9.0000
CAG	chr9:114341001-114341241(-)$1	240	29	32	9.0000
CAG	chr19:11486243-11486483(+)$1	240	21	24	9.0000
CAG	chr5:314471-314711(+)$1	240	2	5	9.0000
CAG	chr4:20706177-20706417(+)$1	240	39	42	9.0000
CAG	chr1:150479335-150479575(+)$1	240	53	56	9.0000
CAG	chr16:71701066-71701317(-)$1	251	0	3	9.0000
CAG	chr12:110826245-110826485(-)$1	240	54	57	9.0000
CAG	chr19:44418031-44418271(-)$1	240	42	45	9.0000
CAG	chr6:44221136-44221454(+)$1	318	86	89	9.0000
CAG	chr4:83349390-83349633(-)$1	243	84	87	9.0000
CAG	chr9:33944364-33944606(-)$1	242	7	10	9.0000
CAG	chr1:43851755-43851995(-)$1	240	0	3	9.0000
CAG	chr3:25832764-25833004(+)$1	240	4	7	9.0000
CAG	chr12:56619120-56619360(+)$1	240	33	36	9.0000
CAG	chr16:31049750-31049990(+)$1	240	4	7	9.0000
CAG	chr2:85768662-85768902(+)$1	240	8	11	9.0000
CAG	chr6:7895238-7895528(-)$1	290	2	5	9.0000
CAG	chr14:102452610-102452850(+)$1	240	1	4	9.0000
CAG	chr3:49064154-49064394(-)$1	240	72	75	9.0000
CAG	chr3:149470076-149470316(-)$1	240	77	80	9.0000
CAG	chr7:148921401-148921641(+)$1	240	14	17	9.0000
CAG	chr3:88104579-88104819(-)$1	240	5	8	9.0000
CAG	chr19:57930908-57931148(+)$1	240	24	27	9.0000
CAG	chr19:55912835-55913076(-)$1	241	58	61	9.0000
CAG	chr14:62187077-62187317(+)$1	240	60	63	9.0000
CAG	chr19:11038244-11038484(-)$1	240	36	39	9.0000
CAG	chr9:19063410-19063650(-)$1	240	91	94	9.0000

#otherMatches

#Struct PSSM
ldd	chr19:10870332-10870572(+)$1	240	78	81	9.0000
DDD	chr22:36624003-36624243(-)$1	240	2	5	9.0000
%%a	chr3:25637984-25638224(+)$1	240	46	49	9.0000
###	chr1:26798929-26799209(+)$1	280	31	34	9.0000
fff	chr12:58142863-58143103(-)$1	240	0	3	9.0000
AMM	chr8:61777599-61777839(+)$1	240	43	46	9.0000
!!e	chr1:23857165-23857405(-)$1	240	52	55	9.0000
dmm	chr8:90784855-90785095(+)$1	240	36	39	9.0000
ccc	chr1:223177225-223177465(+)$1	240	37	40	9.0000
""e	chr22:32112964-32113204(-)$1	240	53	56	9.0000
eee	chr11:66113415-66113655(-)$1	240	58	61	9.0000
G::	chr11:122928893-122929133(-)$1	240	12	15	9.0000
FFF	chr15:32929927-32930167(+)$1	240	7	10	9.0000
:::	chr4:88343952-88344192(+)$1	240	7	10	9.0000
HHH	chr14:23371119-23371359(-)$1	240	104	107	9.0000
FFF	chr16:88874513-88874801(+)$1	288	6	9	9.0000
eee	chr11:62361225-62361465(-)$1	240	42	45	9.0000
eee	chr1:89318787-89319027(-)$1	240	35	38	9.0000
ddd	chr8:26484053-26484293(+)$1	240	123	126	9.0000
fff	chr5:132232681-132232925(-)$1	244	75	78	9.0000
3cc	chr1:214830423-214830663(+)$1	240	37	40	9.0000
eeo	chr5:172750119-172750359(-)$1	240	15	18	9.0000
eee	chr20:34309650-34309890(-)$1	240	92	95	9.0000
bb2	chr5:71494009-71494249(+)$1	240	37	40	9.0000
:::	chr19:41777993-41778233(+)$1	240	2	5	9.0000
fff	chrX:119388995-119389235(+)$1	240	41	44	9.0000
e:D	chr3:49765517-49765757(-)$1	240	43	46	9.0000
III	chr17:27493012-27493252(-)$1	240	35	38	9.0000
cc#	chr1:32495868-32496108(+)$1	240	27	30	9.0000
:EE	chr19:47422487-47422727(+)$1	240	3	6	9.0000
::G	chr20:60575608-60575848(-)$1	240	11	14	9.0000
FGG	chr8:101534795-101535035(-)$1	240	33	36	9.0000
:HH	chr10:120488761-120489006(-)$1	245	3	6	9.0000
##c	chr21:33043703-33043943(-)$1	240	38	41	9.0000
qqq	chr9:71869457-71869697(+)$1	240	55	58	9.0000
fff	chr1:54293702-54293942(-)$1	240	74	77	9.0000
ggg	chr17:26652521-26652761(+)$1	240	4	7	9.0000
2cc	chr6:106740814-106741054(-)$1	240	117	120	9.0000
JJJ	chr18:9337117-9337357(+)$1	240	171	174	9.0000
fff	chr2:96942585-96942825(-)$1	240	4	7	9.0000
MMC	chr11:62416668-62416908(-)$1	240	8	11	9.0000
FFF	chrX:47001669-47001909(-)$1	240	25	28	9.0000
eee	chr12:53703283-53703524(-)$1	241	16	19	9.0000
EEE	chr2:9581962-9582202(+)$1	240	13	16	9.0000
ddw	chr10:43292031-43292271(+)$1	240	54	57	9.0000
mbb	chr9:36357764-36358004(-)$1	240	29	32	9.0000
ooo	chr19:16664387-16664627(-)$1	240	30	33	9.0000
ggg	chr19:36573875-36574115(+)$1	240	37	40	9.0000
g""	chr12:89917890-89918146(-)$1	256	25	28	9.0000
EEE	chr7:42966052-42966292(-)$1	240	60	63	9.0000
eee	chr20:60879470-60879710(+)$1	240	43	46	9.0000
::D	chr1:44435782-44436022(+)$1	240	5	8	9.0000
ccc	chr9:94172570-94172810(-)$1	240	188	191	9.0000
ggg	chr4:84188651-84188891(-)$1	240	38	41	9.0000
FFF	chr2:25043143-25043383(+)$1	240	3	6	9.0000
ccc	chr19:33089041-33089281(-)$1	240	24	27	9.0000
:::	chr8:81399854-81400103(+)$1	249	29	32	9.0000
!!c	chr7:141401813-141402053(-)$1	240	32	35	9.0000
qqq	chr1:46501109-46501349(+)$1	240	10	13	9.0000
eee	chr7:5413962-5414202(-)$1	240	16	19	9.0000
ggg	chr3:127774439-127774679(+)$1	240	38	41	9.0000
mee	chr17:43226438-43226718(+)$1	280	138	141	9.0000
ooo	chr8:67970219-67970460(-)$1	241	98	101	9.0000
ffd	chr2:20974598-20974838(-)$1	240	50	53	9.0000
rrr	chr7:143001947-143002187(+)$1	240	53	56	9.0000
KKB	chr3:43344680-43344920(+)$1	240	11	14	9.0000
FFF	chr4:48901763-48902003(-)$1	240	30	33	9.0000
:::	chr12:56384416-56384656(+)$1	240	9	12	9.0000
:FF	chr9:71395154-71395394(+)$1	240	0	3	9.0000
cco	chr17:30815317-30815557(+)$1	240	140	143	9.0000
:::	chr2:71576351-71576591(+)$1	240	12	15	9.0000
ccc	chr19:46206185-46206425(+)$1	240	168	171	9.0000
KKE	chr7:2302763-2303003(-)$1	240	3	6	9.0000
!!e	chr9:114341001-114341241(-)$1	240	29	32	9.0000
nnn	chr19:11486243-11486483(+)$1	240	21	24	9.0000
::D	chr5:314471-314711(+)$1	240	2	5	9.0000
22g	chr4:20706177-20706417(+)$1	240	39	42	9.0000
EEE	chr1:150479335-150479575(+)$1	240	53	56	9.0000
:::	chr16:71701066-71701317(-)$1	251	0	3	9.0000
ggg	chr12:110826245-110826485(-)$1	240	54	57	9.0000
KKD	chr19:44418031-44418271(-)$1	240	42	45	9.0000
eeq	chr6:44221136-44221454(+)$1	318	86	89	9.0000
###	chr4:83349390-83349633(-)$1	243	84	87	9.0000
{DD	chr9:33944364-33944606(-)$1	242	7	10	9.0000
CCC	chr1:43851755-43851995(-)$1	240	0	3	9.0000
eee	chr3:25832764-25833004(+)$1	240	4	7	9.0000
MEE	chr12:56619120-56619360(+)$1	240	33	36	9.0000
iii	chr16:31049750-31049990(+)$1	240	4	7	9.0000
HHH	chr2:85768662-85768902(+)$1	240	8	11	9.0000
C:I	chr6:7895238-7895528(-)$1	290	2	5	9.0000
B{B	chr14:102452610-102452850(+)$1	240	1	4	9.0000
ddd	chr3:49064154-49064394(-)$1	240	72	75	9.0000
DDD	chr3:149470076-149470316(-)$1	240	77	80	9.0000
qqe	chr7:148921401-148921641(+)$1	240	14	17	9.0000
fff	chr3:88104579-88104819(-)$1	240	5	8	9.0000
eee	chr19:57930908-57931148(+)$1	240	24	27	9.0000
www	chr19:55912835-55913076(-)$1	241	58	61	9.0000
qqq	chr14:62187077-62187317(+)$1	240	60	63	9.0000
EEE	chr19:11038244-11038484(-)$1	240	36	39	9.0000
ddd	chr9:19063410-19063650(-)$1	240	91	94	9.0000

#DB
.))	chr19:10870332-10870572(+)$1	1	78	81	9.0000
(((	chr22:36624003-36624243(-)$1	1	2	5	9.0000
..(	chr3:25637984-25638224(+)$1	1	46	49	9.0000
...	chr1:26798929-26799209(+)$1	1	31	34	9.0000
(((	chr12:58142863-58143103(-)$1	1	0	3	9.0000
(..	chr8:61777599-61777839(+)$1	1	43	46	9.0000
..(	chr1:23857165-23857405(-)$1	1	52	55	9.0000
(..	chr8:90784855-90785095(+)$1	1	36	39	9.0000
(((	chr1:223177225-223177465(+)$1	1	37	40	9.0000
..(	chr22:32112964-32113204(-)$1	1	53	56	9.0000
)))	chr11:66113415-66113655(-)$1	1	58	61	9.0000
(..	chr11:122928893-122929133(-)$1	1	12	15	9.0000
(((	chr15:32929927-32930167(+)$1	1	7	10	9.0000
...	chr4:88343952-88344192(+)$1	1	7	10	9.0000
(((	chr14:23371119-23371359(-)$1	1	104	107	9.0000
(((	chr16:88874513-88874801(+)$1	1	6	9	9.0000
)))	chr11:62361225-62361465(-)$1	1	42	45	9.0000
)))	chr1:89318787-89319027(-)$1	1	35	38	9.0000
)))	chr8:26484053-26484293(+)$1	1	123	126	9.0000
(((	chr5:132232681-132232925(-)$1	1	75	78	9.0000
.))	chr1:214830423-214830663(+)$1	1	37	40	9.0000
((.	chr5:172750119-172750359(-)$1	1	15	18	9.0000
)))	chr20:34309650-34309890(-)$1	1	92	95	9.0000
)).	chr5:71494009-71494249(+)$1	1	37	40	9.0000
...	chr19:41777993-41778233(+)$1	1	2	5	9.0000
(((	chrX:119388995-119389235(+)$1	1	41	44	9.0000
).(	chr3:49765517-49765757(-)$1	1	43	46	9.0000
(((	chr17:27493012-27493252(-)$1	1	35	38	9.0000
((.	chr1:32495868-32496108(+)$1	1	27	30	9.0000
.((	chr19:47422487-47422727(+)$1	1	3	6	9.0000
..(	chr20:60575608-60575848(-)$1	1	11	14	9.0000
(((	chr8:101534795-101535035(-)$1	1	33	36	9.0000
.((	chr10:120488761-120489006(-)$1	1	3	6	9.0000
..(	chr21:33043703-33043943(-)$1	1	38	41	9.0000
...	chr9:71869457-71869697(+)$1	1	55	58	9.0000
)))	chr1:54293702-54293942(-)$1	1	74	77	9.0000
(((	chr17:26652521-26652761(+)$1	1	4	7	9.0000
.))	chr6:106740814-106741054(-)$1	1	117	120	9.0000
)))	chr18:9337117-9337357(+)$1	1	171	174	9.0000
(((	chr2:96942585-96942825(-)$1	1	4	7	9.0000
..(	chr11:62416668-62416908(-)$1	1	8	11	9.0000
(((	chrX:47001669-47001909(-)$1	1	25	28	9.0000
(((	chr12:53703283-53703524(-)$1	1	16	19	9.0000
(((	chr2:9581962-9582202(+)$1	1	13	16	9.0000
((.	chr10:43292031-43292271(+)$1	1	54	57	9.0000
.))	chr9:36357764-36358004(-)$1	1	29	32	9.0000
...	chr19:16664387-16664627(-)$1	1	30	33	9.0000
(((	chr19:36573875-36574115(+)$1	1	37	40	9.0000
(..	chr12:89917890-89918146(-)$1	1	25	28	9.0000
(((	chr7:42966052-42966292(-)$1	1	60	63	9.0000
)))	chr20:60879470-60879710(+)$1	1	43	46	9.0000
..(	chr1:44435782-44436022(+)$1	1	5	8	9.0000
)))	chr9:94172570-94172810(-)$1	1	188	191	9.0000
(((	chr4:84188651-84188891(-)$1	1	38	41	9.0000
(((	chr2:25043143-25043383(+)$1	1	3	6	9.0000
(((	chr19:33089041-33089281(-)$1	1	24	27	9.0000
...	chr8:81399854-81400103(+)$1	1	29	32	9.0000
..(	chr7:141401813-141402053(-)$1	1	32	35	9.0000
...	chr1:46501109-46501349(+)$1	1	10	13	9.0000
(((	chr7:5413962-5414202(-)$1	1	16	19	9.0000
(((	chr3:127774439-127774679(+)$1	1	38	41	9.0000
.))	chr17:43226438-43226718(+)$1	1	138	141	9.0000
...	chr8:67970219-67970460(-)$1	1	98	101	9.0000
(((	chr2:20974598-20974838(-)$1	1	50	53	9.0000
...	chr7:143001947-143002187(+)$1	1	53	56	9.0000
..(	chr3:43344680-43344920(+)$1	1	11	14	9.0000
(((	chr4:48901763-48902003(-)$1	1	30	33	9.0000
...	chr12:56384416-56384656(+)$1	1	9	12	9.0000
.((	chr9:71395154-71395394(+)$1	1	0	3	9.0000
((.	chr17:30815317-30815557(+)$1	1	140	143	9.0000
...	chr2:71576351-71576591(+)$1	1	12	15	9.0000
)))	chr19:46206185-46206425(+)$1	1	168	171	9.0000
..(	chr7:2302763-2303003(-)$1	1	3	6	9.0000
..(	chr9:114341001-114341241(-)$1	1	29	32	9.0000
...	chr19:11486243-11486483(+)$1	1	21	24	9.0000
..(	chr5:314471-314711(+)$1	1	2	5	9.0000
..)	chr4:20706177-20706417(+)$1	1	39	42	9.0000
(((	chr1:150479335-150479575(+)$1	1	53	56	9.0000
...	chr16:71701066-71701317(-)$1	1	0	3	9.0000
)))	chr12:110826245-110826485(-)$1	1	54	57	9.0000
..(	chr19:44418031-44418271(-)$1	1	42	45	9.0000
((.	chr6:44221136-44221454(+)$1	1	86	89	9.0000
...	chr4:83349390-83349633(-)$1	1	84	87	9.0000
.((	chr9:33944364-33944606(-)$1	1	7	10	9.0000
(((	chr1:43851755-43851995(-)$1	1	0	3	9.0000
(((	chr3:25832764-25833004(+)$1	1	4	7	9.0000
.((	chr12:56619120-56619360(+)$1	1	33	36	9.0000
(((	chr16:31049750-31049990(+)$1	1	4	7	9.0000
(((	chr2:85768662-85768902(+)$1	1	8	11	9.0000
(.(	chr6:7895238-7895528(-)$1	1	2	5	9.0000
(.(	chr14:102452610-102452850(+)$1	1	1	4	9.0000
)))	chr3:49064154-49064394(-)$1	1	72	75	9.0000
(((	chr3:149470076-149470316(-)$1	1	77	80	9.0000
..)	chr7:148921401-148921641(+)$1	1	14	17	9.0000
(((	chr3:88104579-88104819(-)$1	1	5	8	9.0000
(((	chr19:57930908-57931148(+)$1	1	24	27	9.0000
...	chr19:55912835-55913076(-)$1	1	58	61	9.0000
...	chr14:62187077-62187317(+)$1	1	60	63	9.0000
(((	chr19:11038244-11038484(-)$1	1	36	39	9.0000
)))	chr9:19063410-19063650(-)$1	1	91	94	9.0000

#PSSM
C : 0.99	c : 0.01	
A : 0.99	a : 0.01	
G : 0.99	g : 0.01	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012a_hg19_CDS_m3_run1.nuc.txt

#NT

#otherMatches

#Struct PSSM
"""eeeeeqqqqqqqqeeeee]dddd333ffffffccc[a!!bbammmma]bb22a]cccDDDDKKCCCKKCCCBBKKBB:::::cccbb"""ccc[ffffffmmmmffffff]ccc]bb]ccc:::::::::cccqqqqqqqqccc::::eeeeennnnneeeee::::::::BBYYBBYYCCCYYCCCDDDD}DDDD}CCC~~~~FFFFFF:a[bb[ddddbbddddpppppppdddd]bb]dddd]bb]a:bb[eeeee[bb[adddd"""cccoooooocccdddd]a]bb]eee	chr10:120801788-120802154(-)$1	366	53	352	897.0000

#DB
...(((((........))))).))))...))))))(((.(..(((....).))..).)))((((..(((..(((((..((.....(((((...(((.((((((....)))))).))).)).))).........(((........)))....(((((.....)))))........))..))..)))..))))))).)))).)))....)))))).(.((.((((((((((.......)))).)).)))).)).).((.(((((.((.(((((...(((......))))))).).)).)))	chr10:120801788-120802154(-)$1	1	53	352	897.0000

#PSSM
C : 1.00	
U : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	

#score	897.0
#seq	1
#width	299
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m2_run1.nuc.txt

#NT
UGGUGGA	chr15:64447953-64448175(-)$1	222	46	53	12.7857
AGGAGGA	chr1:205684898-205685145(-)$1	247	97	104	13.2321
UGUAGGA	chr15:77338450-77338671(-)$1	221	16	23	12.6964
UGGAGAA	chr11:57100873-57101095(-)$1	222	133	140	12.8750
UGGAAGA	chr19:54656189-54656424(+)$1	235	119	126	13.3214
UGGAGGA	chr12:110780936-110781159(+)$1	223	13	20	17.0714
UCGAGGA	chr7:931931-932154(+)$1	223	54	61	12.6071
GGGAGGA	chrX:118370199-118370421(+)$1	222	63	70	13.3214
UGGAGGA	chrX:153581061-153581290(-)$1	229	61	68	17.0714
UGGAGGA	chr14:100746968-100747209(+)$1	241	174	181	17.0714
UGGAGUA	chr19:30101417-30101639(+)$1	222	10	17	12.8750
UGGCGGA	chr19:3976338-3976625(-)$1	287	0	7	12.6071
UGUAGGA	chr16:74655400-74655624(-)$1	224	66	73	12.6964
UGGAGGG	chr16:89353870-89354091(-)$1	221	162	169	12.8750
AGGAGGA	chr16:30996433-30996653(+)$1	220	84	91	13.2321
UGGAUGA	chr1:171766182-171766410(+)$1	228	214	221	13.2321
UGGAAGA	chr5:60455469-60455710(-)$1	241	63	70	13.3214
UUGAGGA	chr5:71505120-71505341(+)$1	221	205	212	12.5178
UGGAUGA	chrX:23804162-23804421(+)$1	259	251	258	13.2321
UGGUGGA	chr5:179041765-179042007(-)$1	242	147	154	12.7857
UGGAGGA	chrX:10414402-10414629(-)$1	227	147	154	17.0714
UGGUGGA	chr4:6643366-6643613(+)$1	247	117	124	12.7857
UGGAGGA	chr11:6423242-6423475(-)$1	233	58	65	17.0714
UGGAGGG	chr19:40316065-40316288(-)$1	223	190	197	12.8750
UGGAGGC	chr6:7883314-7883544(-)$1	230	104	111	12.7857
UGGAGGA	chr14:93694684-93694922(+)$1	238	0	7	17.0714
UGGAGGA	chr3:9518883-9519120(+)$1	237	80	87	17.0714
UGGAGAA	chr15:72499078-72499300(-)$1	222	177	184	12.8750
UGGAGGA	chr20:2448176-2448406(-)$1	230	183	190	17.0714
UGAAGGA	chr10:70101832-70102075(+)$1	243	79	86	12.7857
UGAAGGA	chr9:34635423-34635651(-)$1	228	34	41	12.7857
UGGAAGA	chr1:6281389-6281619(-)$1	230	181	188	13.3214
UGGAAGA	chr17:74266619-74266881(+)$1	262	82	89	13.3214
UGGAGGA	chr1:68151041-68151269(+)$1	228	143	150	17.0714
UCGAGGA	chr4:109546247-109546494(+)$1	247	56	63	12.6071
UGGAGGA	chr7:5270489-5270720(+)$1	231	15	22	17.0714
UGGAAGA	chr18:57570186-57570428(+)$1	242	40	47	13.3214
UGGAGGA	chr5:10258231-10258482(+)$1	251	116	123	17.0714
GGGAGGA	chr16:28855194-28855414(-)$1	220	70	77	13.3214
UGGAGAA	chr16:69154371-69154610(-)$1	239	113	120	12.8750
UGGAUGA	chr11:64535072-64535297(-)$1	225	14	21	13.2321
GGGAGGA	chr18:47018585-47018819(-)$1	234	81	88	13.3214
UGGGGGA	chr11:18428654-18428913(+)$1	259	144	151	12.6071
UGGAGGU	chr16:2821207-2821431(+)$1	224	19	26	12.6964
GGGAGGA	chr1:32799503-32799747(-)$1	244	14	21	13.3214
UGGAGGA	chr10:81111997-81112240(+)$1	243	199	206	17.0714
UGAAGGA	chr12:54059042-54059294(-)$1	252	194	201	12.7857
UAGAGGA	chr12:74934568-74934798(+)$1	230	34	41	12.5178
AGGAGGA	chr19:47341538-47341774(-)$1	236	174	181	13.2321
UGGAGUA	chr14:104378772-104379035(-)$1	263	44	51	12.8750
UGGAGGC	chr12:27950555-27950791(+)$1	236	55	62	12.7857
UGGAUGA	chr12:46299509-46299738(+)$1	229	113	120	13.2321
UGGAGUA	chr19:33872344-33872579(+)$1	235	59	66	12.8750
AGGAGGA	chr16:29822167-29822393(+)$1	226	19	26	13.2321
UGGAGGG	chr12:51636836-51637068(+)$1	232	104	111	12.8750

#otherMatches

#Struct PSSM
FFFLLLH	chr11:64846048-64846292(-)$1	244	6	13	13.3214
:bb[ddd	chr15:64447953-64448175(-)$1	222	46	53	12.7857
CCEEEEE	chr1:205684898-205685145(-)$1	247	97	104	13.2321
dmmmmdd	chr15:77338450-77338671(-)$1	221	16	23	12.6964
[bbpppp	chr11:57100873-57101095(-)$1	222	133	140	12.8750
#bb!!ee	chr19:54656189-54656424(+)$1	235	119	126	13.3214
FFFFKKD	chr12:110780936-110781159(+)$1	223	13	20	17.0714
Jbb[fff	chr7:931931-932154(+)$1	223	54	61	12.6071
hhhhhhh	chrX:118370199-118370421(+)$1	222	63	70	13.3214
ddnnnnn	chrX:153581061-153581290(-)$1	229	61	68	17.0714
%%%%ddd	chr14:100746968-100747209(+)$1	241	174	181	17.0714
{BBMMMM	chr19:30101417-30101639(+)$1	222	10	17	12.8750
::ddddm	chr19:3976338-3976625(-)$1	287	0	7	12.6071
qqqqddd	chr16:74655400-74655624(-)$1	224	66	73	12.6964
}DDDDYY	chr16:89353870-89354091(-)$1	221	162	169	12.8750
:::::::	chr16:30996433-30996653(+)$1	220	84	91	13.2321
eee::::	chr1:171766182-171766410(+)$1	228	214	221	13.2321
:bb[eee	chr5:60455469-60455710(-)$1	241	63	70	13.3214
ppdddd:	chr5:71505120-71505341(+)$1	221	205	212	12.5178
mmdddd:	chrX:23804162-23804421(+)$1	259	251	258	13.2321
[ccc[cc	chr5:179041765-179042007(-)$1	242	147	154	12.7857
eeeeeee	chrX:10414402-10414629(-)$1	227	147	154	17.0714
eeeeeee	chr4:6643366-6643613(+)$1	247	117	124	12.7857
cc]eeee	chr11:6423242-6423475(-)$1	233	58	65	17.0714
6ffffff	chr19:40316065-40316288(-)$1	223	190	197	12.8750
fff:EEE	chr6:7883314-7883544(-)$1	230	104	111	12.7857
:gggggg	chr14:93694684-93694922(+)$1	238	0	7	17.0714
6iiiiii	chr3:9518883-9519120(+)$1	237	80	87	17.0714
FFFF:::	chr15:72499078-72499300(-)$1	222	177	184	12.8750
ffffff]	chr20:2448176-2448406(-)$1	230	183	190	17.0714
eeeeeCC	chr10:70101832-70102075(+)$1	243	79	86	12.7857
boooooo	chr9:34635423-34635651(-)$1	228	34	41	12.7857
flllfff	chr1:6281389-6281619(-)$1	230	181	188	13.3214
!!iiiii	chr17:74266619-74266881(+)$1	262	82	89	13.3214
bb]ccc4	chr1:68151041-68151269(+)$1	228	143	150	17.0714
!ccc[bb	chr4:109546247-109546494(+)$1	247	56	63	12.6071
c[a####	chr7:5270489-5270720(+)$1	231	15	22	17.0714
hddddbb	chr18:57570186-57570428(+)$1	242	40	47	13.3214
hhhhh!!	chr5:10258231-10258482(+)$1	251	116	123	17.0714
eeemmmm	chr16:28855194-28855414(-)$1	220	70	77	13.3214
[dddd%%	chr16:69154371-69154610(-)$1	239	113	120	12.8750
ccc]bb2	chr11:64535072-64535297(-)$1	225	14	21	13.2321
eeeeenn	chr18:47018585-47018819(-)$1	234	81	88	13.3214
2gggggg	chr11:18428654-18428913(+)$1	259	144	151	12.6071
"eeeee"	chr16:2821207-2821431(+)$1	224	19	26	12.6964
cc[bbmm	chr1:32799503-32799747(-)$1	244	14	21	13.3214
qbb:EEE	chr10:81111997-81112240(+)$1	243	199	206	17.0714
]eeeee]	chr12:54059042-54059294(-)$1	252	194	201	12.7857
KGGGGGG	chr12:74934568-74934798(+)$1	230	34	41	12.5178
ssdddd]	chr19:47341538-47341774(-)$1	236	174	181	13.2321
JJJJJJJ	chr14:104378772-104379035(-)$1	263	44	51	12.8750
cbb[ggg	chr12:27950555-27950791(+)$1	236	55	62	12.7857
GGccc[a	chr12:46299509-46299738(+)$1	229	113	120	13.2321
ccc[ccc	chr19:33872344-33872579(+)$1	235	59	66	12.8750
qqqqqqq	chr16:29822167-29822393(+)$1	226	19	26	13.2321
dgggggg	chr12:51636836-51637068(+)$1	232	104	111	12.8750

#DB
(((...(	chr11:64846048-64846292(-)$1	1	6	13	13.3214
.((.(((	chr15:64447953-64448175(-)$1	1	46	53	12.7857
(((((((	chr1:205684898-205685145(-)$1	1	97	104	13.2321
(....))	chr15:77338450-77338671(-)$1	1	16	23	12.6964
.((....	chr11:57100873-57101095(-)$1	1	133	140	12.8750
.((..((	chr19:54656189-54656424(+)$1	1	119	126	13.3214
((((..(	chr12:110780936-110781159(+)$1	1	13	20	17.0714
(((.(((	chr7:931931-932154(+)$1	1	54	61	12.6071
)))))))	chrX:118370199-118370421(+)$1	1	63	70	13.3214
((.....	chrX:153581061-153581290(-)$1	1	61	68	17.0714
....(((	chr14:100746968-100747209(+)$1	1	174	181	17.0714
.((....	chr19:30101417-30101639(+)$1	1	10	17	12.8750
..((((.	chr19:3976338-3976625(-)$1	1	0	7	12.6071
....)))	chr16:74655400-74655624(-)$1	1	66	73	12.6964
.))))..	chr16:89353870-89354091(-)$1	1	162	169	12.8750
.......	chr16:30996433-30996653(+)$1	1	84	91	13.2321
)))....	chr1:171766182-171766410(+)$1	1	214	221	13.2321
.((.(((	chr5:60455469-60455710(-)$1	1	63	70	13.3214
..)))).	chr5:71505120-71505341(+)$1	1	205	212	12.5178
..)))).	chrX:23804162-23804421(+)$1	1	251	258	13.2321
.(((.((	chr5:179041765-179042007(-)$1	1	147	154	12.7857
)))))))	chrX:10414402-10414629(-)$1	1	147	154	17.0714
(((((((	chr4:6643366-6643613(+)$1	1	117	124	12.7857
)).))))	chr11:6423242-6423475(-)$1	1	58	65	17.0714
.))))))	chr19:40316065-40316288(-)$1	1	190	197	12.8750
))).(((	chr6:7883314-7883544(-)$1	1	104	111	12.7857
.((((((	chr14:93694684-93694922(+)$1	1	0	7	17.0714
.))))))	chr3:9518883-9519120(+)$1	1	80	87	17.0714
))))...	chr15:72499078-72499300(-)$1	1	177	184	12.8750
)))))).	chr20:2448176-2448406(-)$1	1	183	190	17.0714
)))))((	chr10:70101832-70102075(+)$1	1	79	86	12.7857
(......	chr9:34635423-34635651(-)$1	1	34	41	12.7857
(...)))	chr1:6281389-6281619(-)$1	1	181	188	13.3214
..(((((	chr17:74266619-74266881(+)$1	1	82	89	13.3214
)).))).	chr1:68151041-68151269(+)$1	1	143	150	17.0714
.(((.((	chr4:109546247-109546494(+)$1	1	56	63	12.6071
(.(....	chr7:5270489-5270720(+)$1	1	15	22	17.0714
(((((((	chr18:57570186-57570428(+)$1	1	40	47	13.3214
(((((..	chr5:10258231-10258482(+)$1	1	116	123	17.0714
(((....	chr16:28855194-28855414(-)$1	1	70	77	13.3214
.((((..	chr16:69154371-69154610(-)$1	1	113	120	12.8750
))).)).	chr11:64535072-64535297(-)$1	1	14	21	13.2321
(((((..	chr18:47018585-47018819(-)$1	1	81	88	13.3214
.))))))	chr11:18428654-18428913(+)$1	1	144	151	12.6071
.(((((.	chr16:2821207-2821431(+)$1	1	19	26	12.6964
((.((..	chr1:32799503-32799747(-)$1	1	14	21	13.3214
.)).)))	chr10:81111997-81112240(+)$1	1	199	206	17.0714
.))))).	chr12:54059042-54059294(-)$1	1	194	201	12.7857
.((((((	chr12:74934568-74934798(+)$1	1	34	41	12.5178
..)))).	chr19:47341538-47341774(-)$1	1	174	181	13.2321
(((((((	chr14:104378772-104379035(-)$1	1	44	51	12.8750
)((.(((	chr12:27950555-27950791(+)$1	1	55	62	12.7857
))(((.(	chr12:46299509-46299738(+)$1	1	113	120	13.2321
(((.(((	chr19:33872344-33872579(+)$1	1	59	66	12.8750
.......	chr16:29822167-29822393(+)$1	1	19	26	13.2321
)((((((	chr12:51636836-51637068(+)$1	1	104	111	12.8750

#PSSM
U : 0.83	G : 0.08	A : 0.07	
G : 0.92	C : 0.03	U : 0.01	A : 0.01	
G : 0.91	A : 0.05	U : 0.03	
A : 0.91	U : 0.05	C : 0.01	G : 0.01	
G : 0.83	A : 0.08	U : 0.07	
G : 0.89	A : 0.05	U : 0.05	
A : 0.89	G : 0.05	C : 0.03	U : 0.01	

#score	775.6428571428577
#seq	56
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FXR2_Ascano2012f_hg19_UTR_m1_run2.nuc.txt

#NT
UUUUA	chr1:50907063-50907282(-)$1	219	81	86	14.9999
UUUUA	chr7:92239353-92239573(-)$1	220	143	148	14.9999
UUUUA	chr8:81433122-81433344(+)$1	222	81	86	14.9999
UUUUA	chr13:30779088-30779310(-)$1	222	92	97	14.9999
UUUUA	chr2:160176494-160176715(-)$1	221	91	96	14.9999
UUUUA	chr4:76569192-76569407(-)$1	215	41	46	14.9999
UUUUA	chr17:65070186-65070406(-)$1	220	70	75	14.9999
UUUUA	chr5:167983532-167983749(-)$1	217	3	8	14.9999
UUUUA	chr8:42932569-42932786(+)$1	217	197	202	14.9999
UUUUA	chr13:41506325-41506548(-)$1	223	61	66	14.9999
UUUUA	chr18:43669537-43669755(-)$1	218	41	46	14.9999
UUUUA	chr1:120162589-120162815(-)$1	226	190	195	14.9999
UUUUA	chr4:25279772-25279992(+)$1	220	184	189	14.9999
UUUUA	chr3:8940583-8940804(-)$1	221	40	45	14.9999
UUUUA	chr6:18225784-18226002(-)$1	218	185	190	14.9999
uuuua	chr3:158317758-158317982(+)$1	224	36	41	14.9999
UUUUA	chr1:100660615-100660836(-)$1	221	78	83	14.9999
UUUUA	chr16:2647890-2648109(+)$1	219	10	15	14.9999
UUUUA	chr19:37039062-37039279(-)$1	217	10	15	14.9999
UUUUA	chr2:29169933-29170151(+)$1	218	144	149	14.9999
UUUUA	chr1:193058735-193058954(+)$1	219	140	145	14.9999
UUUUA	chr5:154255109-154255330(+)$1	221	27	32	14.9999
UUUUA	chr6:41066541-41066761(+)$1	220	57	62	14.9999
UUUUA	chr1:211746923-211747141(-)$1	218	74	79	14.9999
uuuua	chr5:132216273-132216496(-)$1	223	43	48	14.9999
uuuua	chr1:227847360-227847581(+)$1	221	77	82	14.9999
UUUUA	chr1:89299177-89299400(+)$1	223	66	71	14.9999
UUUUA	chr1:204522764-204522987(+)$1	223	149	154	14.9999
UUUUA	chr12:120881903-120882126(-)$1	223	5	10	14.9999
UUUUA	chr1:151090997-151091215(+)$1	218	27	32	14.9999
UUUUA	chr2:8910815-8911034(-)$1	219	11	16	14.9999
UUUUA	chr6:149981603-149981821(-)$1	218	128	133	14.9999
UUUUA	chr5:14508621-14508842(+)$1	221	147	152	14.9999
UUUUA	chr4:53461461-53461679(-)$1	218	136	141	14.9999
UUUUA	chr18:32915740-32915959(-)$1	219	92	97	14.9999
UUUUA	chr2:191556977-191557197(+)$1	220	34	39	14.9999
UUUUA	chr17:29553548-29553767(+)$1	219	175	180	14.9999
UUUUA	chr12:12673978-12674200(-)$1	222	70	75	14.9999
UUUUA	chr13:73284138-73284356(-)$1	218	7	12	14.9999
UUUUA	chr5:135514744-135514969(+)$1	225	78	83	14.9999
UUUUA	chr1:192984346-192984566(-)$1	220	88	93	14.9999
UUUUA	chr1:169434980-169435199(-)$1	219	180	185	14.9999
UUUUA	chr7:141360496-141360721(-)$1	225	107	112	14.9999
UUUUA	chr1:225681256-225681478(-)$1	222	184	189	14.9999
UUUUA	chr5:114950181-114950403(-)$1	222	78	83	14.9999
UUUUA	chr10:32298421-32298647(-)$1	226	136	141	14.9999
UUUUA	chr4:1983561-1983782(+)$1	221	165	170	14.9999
UUUUA	chr3:10143481-10143703(+)$1	222	105	110	14.9999
UUUUA	chr14:55514368-55514593(+)$1	225	117	122	14.9999
UUUUA	chr10:116736940-116737155(+)$1	215	52	57	14.9999
UUUUA	chr1:168212233-168212453(+)$1	220	206	211	14.9999
UUUUA	chrX:118722984-118723202(-)$1	218	120	125	14.9999
UUUUA	chr13:75859729-75859952(-)$1	223	117	122	14.9999
UUUUA	chr12:1017958-1018180(+)$1	222	134	139	14.9999
UUUUA	chr5:167978815-167979038(-)$1	223	0	5	14.9999
UUUUA	chr1:156446874-156447092(-)$1	218	70	75	14.9999
UUUUA	chr6:170103446-170103670(+)$1	224	30	35	14.9999
UUUUA	chr20:57025287-57025509(+)$1	222	5	10	14.9999

#otherMatches

#Struct PSSM
:::::	chr5:61681742-61681964(+)$1	222	34	39	14.9999
d"""c	chr1:50907063-50907282(-)$1	219	81	86	14.9999
f''''	chr7:92239353-92239573(-)$1	220	143	148	14.9999
:::::	chr8:81433122-81433344(+)$1	222	81	86	14.9999
''''c	chr13:30779088-30779310(-)$1	222	92	97	14.9999
eeee:	chr2:160176494-160176715(-)$1	221	91	96	14.9999
ee[cc	chr4:76569192-76569407(-)$1	215	41	46	14.9999
(((dd	chr17:65070186-65070406(-)$1	220	70	75	14.9999
:::::	chr5:167983532-167983749(-)$1	217	3	8	14.9999
FFFF~	chr8:42932569-42932786(+)$1	217	197	202	14.9999
:::HH	chr13:41506325-41506548(-)$1	223	61	66	14.9999
:::::	chr18:43669537-43669755(-)$1	218	41	46	14.9999
cc!!d	chr1:120162589-120162815(-)$1	226	190	195	14.9999
e]bb]	chr4:25279772-25279992(+)$1	220	184	189	14.9999
hhh[c	chr3:8940583-8940804(-)$1	221	40	45	14.9999
:JJJJ	chr6:18225784-18226002(-)$1	218	185	190	14.9999
==mmm	chr3:158317758-158317982(+)$1	224	36	41	14.9999
>>>>>	chr1:100660615-100660836(-)$1	221	78	83	14.9999
:::::	chr16:2647890-2648109(+)$1	219	10	15	14.9999
FFFFK	chr19:37039062-37039279(-)$1	217	10	15	14.9999
GG:::	chr2:29169933-29170151(+)$1	218	144	149	14.9999
EEEE:	chr1:193058735-193058954(+)$1	219	140	145	14.9999
====m	chr5:154255109-154255330(+)$1	221	27	32	14.9999
ggggg	chr6:41066541-41066761(+)$1	220	57	62	14.9999
HHHHf	chr1:211746923-211747141(-)$1	218	74	79	14.9999
dd666	chr5:132216273-132216496(-)$1	223	43	48	14.9999
iiiii	chr1:227847360-227847581(+)$1	221	77	82	14.9999
====:	chr1:89299177-89299400(+)$1	223	66	71	14.9999
ccc[f	chr1:204522764-204522987(+)$1	223	149	154	14.9999
PPPPP	chr12:120881903-120882126(-)$1	223	5	10	14.9999
JJJJJ	chr1:151090997-151091215(+)$1	218	27	32	14.9999
FF:::	chr2:8910815-8911034(-)$1	219	11	16	14.9999
%%%%=	chr6:149981603-149981821(-)$1	218	128	133	14.9999
=====	chr5:14508621-14508842(+)$1	221	147	152	14.9999
fffff	chr4:53461461-53461679(-)$1	218	136	141	14.9999
dmmmm	chr18:32915740-32915959(-)$1	219	92	97	14.9999
:::::	chr2:191556977-191557197(+)$1	220	34	39	14.9999
:::DD	chr17:29553548-29553767(+)$1	219	175	180	14.9999
fffrr	chr12:12673978-12674200(-)$1	222	70	75	14.9999
:::ii	chr13:73284138-73284356(-)$1	218	7	12	14.9999
xxxxx	chr5:135514744-135514969(+)$1	225	78	83	14.9999
"""ii	chr1:192984346-192984566(-)$1	220	88	93	14.9999
vvvvv	chr1:169434980-169435199(-)$1	219	180	185	14.9999
:::::	chr7:141360496-141360721(-)$1	225	107	112	14.9999
HHHHH	chr1:225681256-225681478(-)$1	222	184	189	14.9999
333gg	chr5:114950181-114950403(-)$1	222	78	83	14.9999
8888=	chr10:32298421-32298647(-)$1	226	136	141	14.9999
flllf	chr4:1983561-1983782(+)$1	221	165	170	14.9999
pppee	chr3:10143481-10143703(+)$1	222	105	110	14.9999
fnnnn	chr14:55514368-55514593(+)$1	225	117	122	14.9999
eeeee	chr10:116736940-116737155(+)$1	215	52	57	14.9999
qqqqq	chr1:168212233-168212453(+)$1	220	206	211	14.9999
c22gg	chrX:118722984-118723202(-)$1	218	120	125	14.9999
eeeen	chr13:75859729-75859952(-)$1	223	117	122	14.9999
sssss	chr12:1017958-1018180(+)$1	222	134	139	14.9999
::::E	chr5:167978815-167979038(-)$1	223	0	5	14.9999
fff22	chr1:156446874-156447092(-)$1	218	70	75	14.9999
::::e	chr6:170103446-170103670(+)$1	224	30	35	14.9999
E::::	chr20:57025287-57025509(+)$1	222	5	10	14.9999

#DB
.....	chr5:61681742-61681964(+)$1	1	34	39	14.9999
(...(	chr1:50907063-50907282(-)$1	1	81	86	14.9999
(....	chr7:92239353-92239573(-)$1	1	143	148	14.9999
.....	chr8:81433122-81433344(+)$1	1	81	86	14.9999
....(	chr13:30779088-30779310(-)$1	1	92	97	14.9999
)))).	chr2:160176494-160176715(-)$1	1	91	96	14.9999
((.((	chr4:76569192-76569407(-)$1	1	41	46	14.9999
...((	chr17:65070186-65070406(-)$1	1	70	75	14.9999
.....	chr5:167983532-167983749(-)$1	1	3	8	14.9999
)))).	chr8:42932569-42932786(+)$1	1	197	202	14.9999
...((	chr13:41506325-41506548(-)$1	1	61	66	14.9999
.....	chr18:43669537-43669755(-)$1	1	41	46	14.9999
((..(	chr1:120162589-120162815(-)$1	1	190	195	14.9999
).)).	chr4:25279772-25279992(+)$1	1	184	189	14.9999
(((.(	chr3:8940583-8940804(-)$1	1	40	45	14.9999
.))))	chr6:18225784-18226002(-)$1	1	185	190	14.9999
((...	chr3:158317758-158317982(+)$1	1	36	41	14.9999
.....	chr1:100660615-100660836(-)$1	1	78	83	14.9999
.....	chr16:2647890-2648109(+)$1	1	10	15	14.9999
((((.	chr19:37039062-37039279(-)$1	1	10	15	14.9999
))...	chr2:29169933-29170151(+)$1	1	144	149	14.9999
)))).	chr1:193058735-193058954(+)$1	1	140	145	14.9999
((((.	chr5:154255109-154255330(+)$1	1	27	32	14.9999
(((((	chr6:41066541-41066761(+)$1	1	57	62	14.9999
(((((	chr1:211746923-211747141(-)$1	1	74	79	14.9999
))...	chr5:132216273-132216496(-)$1	1	43	48	14.9999
)))))	chr1:227847360-227847581(+)$1	1	77	82	14.9999
)))).	chr1:89299177-89299400(+)$1	1	66	71	14.9999
(((.(	chr1:204522764-204522987(+)$1	1	149	154	14.9999
.....	chr12:120881903-120882126(-)$1	1	5	10	14.9999
(((((	chr1:151090997-151091215(+)$1	1	27	32	14.9999
((...	chr2:8910815-8911034(-)$1	1	11	16	14.9999
....(	chr6:149981603-149981821(-)$1	1	128	133	14.9999
(((((	chr5:14508621-14508842(+)$1	1	147	152	14.9999
)))))	chr4:53461461-53461679(-)$1	1	136	141	14.9999
(....	chr18:32915740-32915959(-)$1	1	92	97	14.9999
.....	chr2:191556977-191557197(+)$1	1	34	39	14.9999
...))	chr17:29553548-29553767(+)$1	1	175	180	14.9999
(((..	chr12:12673978-12674200(-)$1	1	70	75	14.9999
...((	chr13:73284138-73284356(-)$1	1	7	12	14.9999
.....	chr5:135514744-135514969(+)$1	1	78	83	14.9999
...((	chr1:192984346-192984566(-)$1	1	88	93	14.9999
.....	chr1:169434980-169435199(-)$1	1	180	185	14.9999
.....	chr7:141360496-141360721(-)$1	1	107	112	14.9999
)))))	chr1:225681256-225681478(-)$1	1	184	189	14.9999
...))	chr5:114950181-114950403(-)$1	1	78	83	14.9999
....)	chr10:32298421-32298647(-)$1	1	136	141	14.9999
(...)	chr4:1983561-1983782(+)$1	1	165	170	14.9999
...))	chr3:10143481-10143703(+)$1	1	105	110	14.9999
(....	chr14:55514368-55514593(+)$1	1	117	122	14.9999
)))))	chr10:116736940-116737155(+)$1	1	52	57	14.9999
.....	chr1:168212233-168212453(+)$1	1	206	211	14.9999
)..))	chrX:118722984-118723202(-)$1	1	120	125	14.9999
((((.	chr13:75859729-75859952(-)$1	1	117	122	14.9999
.....	chr12:1017958-1018180(+)$1	1	134	139	14.9999
....(	chr5:167978815-167979038(-)$1	1	0	5	14.9999
)))..	chr1:156446874-156447092(-)$1	1	70	75	14.9999
....(	chr6:170103446-170103670(+)$1	1	30	35	14.9999
(....	chr20:57025287-57025509(+)$1	1	5	10	14.9999

#PSSM
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
A : 0.94	a : 0.05	

#score	884.9999999999999
#seq	59
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012b_hg19_CDS_m3_run1.nuc.txt

#NT
CCAG	chr12:970228-970458(+)$1	230	116	120	12.0000
CCAG	chr19:38609933-38610173(+)$1	240	62	66	12.0000
CCAG	chr14:77493597-77493836(-)$1	239	101	105	12.0000
CCAG	chr20:62192465-62192699(-)$1	234	11	15	12.0000
CCAG	chr12:50834199-50834415(+)$1	216	108	112	12.0000
CCAG	chr11:770892-771123(-)$1	231	15	19	12.0000
CCAG	chr22:29745167-29745441(-)$1	274	65	69	12.0000
CCAG	chr12:57007729-57007960(-)$1	231	220	224	12.0000
CCAG	chr21:40570766-40570990(-)$1	224	31	35	12.0000
CCAG	chr3:3195564-3195784(-)$1	220	104	108	12.0000
CCAG	chr20:34241328-34241544(-)$1	216	1	5	12.0000
CCAG	chr17:48212849-48213094(-)$1	245	33	37	12.0000
CCAG	chr7:4861989-4862209(-)$1	220	24	28	12.0000
CCAG	chr15:85147438-85147660(+)$1	222	106	110	12.0000
CCAG	chr17:7507043-7507275(-)$1	232	48	52	12.0000
CCAG	chr14:74205220-74205438(-)$1	218	79	83	12.0000
CCAG	chr18:12366947-12367183(-)$1	236	63	67	12.0000
CCAG	chr1:155932814-155933031(-)$1	217	20	24	12.0000
CCAG	chr7:129394792-129395002(+)$1	210	3	7	12.0000
CCAG	chr6:32139108-32139332(-)$1	224	9	13	12.0000
CCAG	chr9:134073977-134074189(+)$1	212	34	38	12.0000
CCAG	chr17:80040799-80041055(-)$1	256	10	14	12.0000
CCAG	chr20:2640251-2640481(-)$1	230	12	16	12.0000
CCAG	chr19:581247-581484(+)$1	237	165	169	12.0000
CCAG	chr12:121789912-121790141(-)$1	229	2	6	12.0000
CCAG	chr1:118477037-118477288(+)$1	251	109	113	12.0000
CCAG	chr12:117426534-117426763(+)$1	229	30	34	12.0000
CCAG	chr8:144885938-144886170(-)$1	232	6	10	12.0000
CCAG	chr8:116631281-116631502(-)$1	221	53	57	12.0000
CCAG	chr14:50065719-50065939(+)$1	220	128	132	12.0000
CCAG	chr11:14515139-14515352(-)$1	213	85	89	12.0000
CCAG	chr21:33057346-33057613(-)$1	267	232	236	12.0000
CCAG	chr5:179195768-179195986(+)$1	218	95	99	12.0000
CCAG	chr1:36751939-36752157(+)$1	218	25	29	12.0000
CCAG	chr7:100275745-100275983(+)$1	238	199	203	12.0000
CCAG	chr8:61773419-61773650(+)$1	231	127	131	12.0000
CCAG	chr19:49303366-49303585(-)$1	219	66	70	12.0000
CCAG	chr19:47878673-47878908(+)$1	235	84	88	12.0000
CCAG	chr5:127668578-127668796(-)$1	218	132	136	12.0000
CCAG	chr12:57011163-57011387(-)$1	224	9	13	12.0000
CCAG	chr15:90169086-90169313(+)$1	227	95	99	12.0000
CCAG	chr19:10220562-10220780(+)$1	218	77	81	12.0000
CCAG	chr3:58106942-58107163(+)$1	221	21	25	12.0000
CCAG	chr16:4410181-4410426(-)$1	245	68	72	12.0000
CCAG	chr17:7139341-7139562(-)$1	221	30	34	12.0000
CCAG	chr8:17820538-17820757(+)$1	219	191	195	12.0000
CCAG	chr1:2518535-2518752(+)$1	217	83	87	12.0000
CCAG	chr15:85326467-85326735(+)$1	268	12	16	12.0000
CCAG	chr19:48248852-48249073(+)$1	221	57	61	12.0000
CCAG	chr7:142991669-142991903(+)$1	234	184	188	12.0000
CCAG	chr7:140386702-140386930(+)$1	228	83	87	12.0000
CCAG	chr8:6590044-6590270(+)$1	226	124	128	12.0000
CCAG	chr6:158924931-158925158(+)$1	227	26	30	12.0000
CCAG	chr1:226109158-226109385(-)$1	227	121	125	12.0000
CCAG	chr22:19365385-19365606(-)$1	221	118	122	12.0000
CCAG	chr12:56648366-56648585(-)$1	219	174	178	12.0000
CCAG	chr5:112920017-112920243(+)$1	226	3	7	12.0000
CCAG	chr19:4547959-4548184(-)$1	225	122	126	12.0000
CCAG	chr14:77272955-77273191(-)$1	236	68	72	12.0000
CCAG	chr5:145631195-145631473(+)$1	278	48	52	12.0000
CCAG	chr10:8019109-8019340(+)$1	231	106	110	12.0000
CCAG	chr22:36913282-36913570(-)$1	288	204	208	12.0000
CCAG	chr22:42609363-42609670(-)$1	307	64	68	12.0000
CCAG	chr18:43842838-43843060(+)$1	222	130	134	12.0000
CCAG	chr5:60455835-60456086(-)$1	251	56	60	12.0000
CCAG	chr14:102552016-102552263(-)$1	247	35	39	12.0000
CCAG	chr9:131395107-131395328(+)$1	221	47	51	12.0000
CCAG	chr11:68700771-68700996(+)$1	225	94	98	12.0000
CCAG	chr19:57722654-57722907(+)$1	253	111	115	12.0000
CCAG	chr11:58893402-58893630(+)$1	228	17	21	12.0000
CCAg	chr20:32273847-32274109(-)$1	262	163	167	12.0000
CCAG	chr17:5280354-5280576(+)$1	222	52	56	12.0000
CCAG	chr17:40271478-40271710(-)$1	232	96	100	12.0000
CCAG	chr19:11015596-11015823(+)$1	227	9	13	12.0000
ccag	chr16:30748851-30749135(+)$1	284	34	38	12.0000

#otherMatches

#Struct PSSM
IIII	chr17:4916876-4917099(+)$1	223	147	151	12.0000
bb[e	chr12:970228-970458(+)$1	230	116	120	12.0000
:::f	chr19:38609933-38610173(+)$1	240	62	66	12.0000
fff[	chr14:77493597-77493836(-)$1	239	101	105	12.0000
KDDD	chr20:62192465-62192699(-)$1	234	11	15	12.0000
]ddd	chr12:50834199-50834415(+)$1	216	108	112	12.0000
eeee	chr11:770892-771123(-)$1	231	15	19	12.0000
eeee	chr22:29745167-29745441(-)$1	274	65	69	12.0000
eeee	chr12:57007729-57007960(-)$1	231	220	224	12.0000
eeee	chr21:40570766-40570990(-)$1	224	31	35	12.0000
beee	chr3:3195564-3195784(-)$1	220	104	108	12.0000
:eee	chr20:34241328-34241544(-)$1	216	1	5	12.0000
c:::	chr17:48212849-48213094(-)$1	245	33	37	12.0000
gggg	chr7:4861989-4862209(-)$1	220	24	28	12.0000
ccc"	chr15:85147438-85147660(+)$1	222	106	110	12.0000
[ddd	chr17:7507043-7507275(-)$1	232	48	52	12.0000
qqqq	chr14:74205220-74205438(-)$1	218	79	83	12.0000
dddc	chr18:12366947-12367183(-)$1	236	63	67	12.0000
B{DD	chr1:155932814-155933031(-)$1	217	20	24	12.0000
DDDK	chr7:129394792-129395002(+)$1	210	3	7	12.0000
ccc[	chr6:32139108-32139332(-)$1	224	9	13	12.0000
eedd	chr9:134073977-134074189(+)$1	212	34	38	12.0000
HHH{	chr17:80040799-80041055(-)$1	256	10	14	12.0000
EEEE	chr20:2640251-2640481(-)$1	230	12	16	12.0000
ddbb	chr19:581247-581484(+)$1	237	165	169	12.0000
GGGG	chr12:121789912-121790141(-)$1	229	2	6	12.0000
eeee	chr1:118477037-118477288(+)$1	251	109	113	12.0000
b:::	chr12:117426534-117426763(+)$1	229	30	34	12.0000
::ee	chr8:144885938-144886170(-)$1	232	6	10	12.0000
"eee	chr8:116631281-116631502(-)$1	221	53	57	12.0000
eccc	chr14:50065719-50065939(+)$1	220	128	132	12.0000
:CCC	chr11:14515139-14515352(-)$1	213	85	89	12.0000
cc::	chr21:33057346-33057613(-)$1	267	232	236	12.0000
uuuu	chr5:179195768-179195986(+)$1	218	95	99	12.0000
::::	chr1:36751939-36752157(+)$1	218	25	29	12.0000
oooc	chr7:100275745-100275983(+)$1	238	199	203	12.0000
bbqq	chr8:61773419-61773650(+)$1	231	127	131	12.0000
ccmm	chr19:49303366-49303585(-)$1	219	66	70	12.0000
22cc	chr19:47878673-47878908(+)$1	235	84	88	12.0000
ccc:	chr5:127668578-127668796(-)$1	218	132	136	12.0000
:::c	chr12:57011163-57011387(-)$1	224	9	13	12.0000
9ddd	chr15:90169086-90169313(+)$1	227	95	99	12.0000
clll	chr19:10220562-10220780(+)$1	218	77	81	12.0000
====	chr3:58106942-58107163(+)$1	221	21	25	12.0000
dlll	chr16:4410181-4410426(-)$1	245	68	72	12.0000
BB::	chr17:7139341-7139562(-)$1	221	30	34	12.0000
bggg	chr8:17820538-17820757(+)$1	219	191	195	12.0000
ffff	chr1:2518535-2518752(+)$1	217	83	87	12.0000
KKCC	chr15:85326467-85326735(+)$1	268	12	16	12.0000
pppp	chr19:48248852-48249073(+)$1	221	57	61	12.0000
c666	chr7:142991669-142991903(+)$1	234	184	188	12.0000
2ddd	chr7:140386702-140386930(+)$1	228	83	87	12.0000
##ii	chr8:6590044-6590270(+)$1	226	124	128	12.0000
ba[e	chr6:158924931-158925158(+)$1	227	26	30	12.0000
ffff	chr1:226109158-226109385(-)$1	227	121	125	12.0000
eeee	chr22:19365385-19365606(-)$1	221	118	122	12.0000
====	chr12:56648366-56648585(-)$1	219	174	178	12.0000
BBBB	chr5:112920017-112920243(+)$1	226	3	7	12.0000
ddd]	chr19:4547959-4548184(-)$1	225	122	126	12.0000
h"""	chr14:77272955-77273191(-)$1	236	68	72	12.0000
JJJJ	chr5:145631195-145631473(+)$1	278	48	52	12.0000
::::	chr10:8019109-8019340(+)$1	231	106	110	12.0000
!!cc	chr22:36913282-36913570(-)$1	288	204	208	12.0000
:::D	chr22:42609363-42609670(-)$1	307	64	68	12.0000
cccc	chr18:43842838-43843060(+)$1	222	130	134	12.0000
[fff	chr5:60455835-60456086(-)$1	251	56	60	12.0000
"""a	chr14:102552016-102552263(-)$1	247	35	39	12.0000
333c	chr9:131395107-131395328(+)$1	221	47	51	12.0000
tttt	chr11:68700771-68700996(+)$1	225	94	98	12.0000
b!!a	chr19:57722654-57722907(+)$1	253	111	115	12.0000
:eee	chr11:58893402-58893630(+)$1	228	17	21	12.0000
cc[c	chr20:32273847-32274109(-)$1	262	163	167	12.0000
555b	chr17:5280354-5280576(+)$1	222	52	56	12.0000
eppp	chr17:40271478-40271710(-)$1	232	96	100	12.0000
e%%%	chr19:11015596-11015823(+)$1	227	9	13	12.0000
F{CC	chr16:30748851-30749135(+)$1	284	34	38	12.0000

#DB
))))	chr17:4916876-4917099(+)$1	1	147	151	12.0000
((.(	chr12:970228-970458(+)$1	1	116	120	12.0000
...(	chr19:38609933-38610173(+)$1	1	62	66	12.0000
(((.	chr14:77493597-77493836(-)$1	1	101	105	12.0000
.(((	chr20:62192465-62192699(-)$1	1	11	15	12.0000
.)))	chr12:50834199-50834415(+)$1	1	108	112	12.0000
((((	chr11:770892-771123(-)$1	1	15	19	12.0000
((((	chr22:29745167-29745441(-)$1	1	65	69	12.0000
))))	chr12:57007729-57007960(-)$1	1	220	224	12.0000
((((	chr21:40570766-40570990(-)$1	1	31	35	12.0000
((((	chr3:3195564-3195784(-)$1	1	104	108	12.0000
.(((	chr20:34241328-34241544(-)$1	1	1	5	12.0000
)...	chr17:48212849-48213094(-)$1	1	33	37	12.0000
((((	chr7:4861989-4862209(-)$1	1	24	28	12.0000
(((.	chr15:85147438-85147660(+)$1	1	106	110	12.0000
.(((	chr17:7507043-7507275(-)$1	1	48	52	12.0000
....	chr14:74205220-74205438(-)$1	1	79	83	12.0000
((((	chr18:12366947-12367183(-)$1	1	63	67	12.0000
(.((	chr1:155932814-155933031(-)$1	1	20	24	12.0000
(((.	chr7:129394792-129395002(+)$1	1	3	7	12.0000
(((.	chr6:32139108-32139332(-)$1	1	9	13	12.0000
))))	chr9:134073977-134074189(+)$1	1	34	38	12.0000
(((.	chr17:80040799-80041055(-)$1	1	10	14	12.0000
((((	chr20:2640251-2640481(-)$1	1	12	16	12.0000
))))	chr19:581247-581484(+)$1	1	165	169	12.0000
((((	chr12:121789912-121790141(-)$1	1	2	6	12.0000
((((	chr1:118477037-118477288(+)$1	1	109	113	12.0000
)...	chr12:117426534-117426763(+)$1	1	30	34	12.0000
..((	chr8:144885938-144886170(-)$1	1	6	10	12.0000
.(((	chr8:116631281-116631502(-)$1	1	53	57	12.0000
))))	chr14:50065719-50065939(+)$1	1	128	132	12.0000
.(((	chr11:14515139-14515352(-)$1	1	85	89	12.0000
))..	chr21:33057346-33057613(-)$1	1	232	236	12.0000
....	chr5:179195768-179195986(+)$1	1	95	99	12.0000
....	chr1:36751939-36752157(+)$1	1	25	29	12.0000
...)	chr7:100275745-100275983(+)$1	1	199	203	12.0000
((..	chr8:61773419-61773650(+)$1	1	127	131	12.0000
((..	chr19:49303366-49303585(-)$1	1	66	70	12.0000
..))	chr19:47878673-47878908(+)$1	1	84	88	12.0000
))).	chr5:127668578-127668796(-)$1	1	132	136	12.0000
...(	chr12:57011163-57011387(-)$1	1	9	13	12.0000
.)))	chr15:90169086-90169313(+)$1	1	95	99	12.0000
(...	chr19:10220562-10220780(+)$1	1	77	81	12.0000
((((	chr3:58106942-58107163(+)$1	1	21	25	12.0000
(...	chr16:4410181-4410426(-)$1	1	68	72	12.0000
((..	chr17:7139341-7139562(-)$1	1	30	34	12.0000
((((	chr8:17820538-17820757(+)$1	1	191	195	12.0000
((((	chr1:2518535-2518752(+)$1	1	83	87	12.0000
..((	chr15:85326467-85326735(+)$1	1	12	16	12.0000
....	chr19:48248852-48249073(+)$1	1	57	61	12.0000
)...	chr7:142991669-142991903(+)$1	1	184	188	12.0000
.)))	chr7:140386702-140386930(+)$1	1	83	87	12.0000
..((	chr8:6590044-6590270(+)$1	1	124	128	12.0000
((.(	chr6:158924931-158925158(+)$1	1	26	30	12.0000
))))	chr1:226109158-226109385(-)$1	1	121	125	12.0000
))))	chr22:19365385-19365606(-)$1	1	118	122	12.0000
))))	chr12:56648366-56648585(-)$1	1	174	178	12.0000
((((	chr5:112920017-112920243(+)$1	1	3	7	12.0000
))).	chr19:4547959-4548184(-)$1	1	122	126	12.0000
(...	chr14:77272955-77273191(-)$1	1	68	72	12.0000
((((	chr5:145631195-145631473(+)$1	1	48	52	12.0000
....	chr10:8019109-8019340(+)$1	1	106	110	12.0000
..((	chr22:36913282-36913570(-)$1	1	204	208	12.0000
...(	chr22:42609363-42609670(-)$1	1	64	68	12.0000
((((	chr18:43842838-43843060(+)$1	1	130	134	12.0000
.(((	chr5:60455835-60456086(-)$1	1	56	60	12.0000
...(	chr14:102552016-102552263(-)$1	1	35	39	12.0000
...)	chr9:131395107-131395328(+)$1	1	47	51	12.0000
....	chr11:68700771-68700996(+)$1	1	94	98	12.0000
(..(	chr19:57722654-57722907(+)$1	1	111	115	12.0000
.(((	chr11:58893402-58893630(+)$1	1	17	21	12.0000
((.(	chr20:32273847-32274109(-)$1	1	163	167	12.0000
...)	chr17:5280354-5280576(+)$1	1	52	56	12.0000
(...	chr17:40271478-40271710(-)$1	1	96	100	12.0000
(...	chr19:11015596-11015823(+)$1	1	9	13	12.0000
(.((	chr16:30748851-30749135(+)$1	1	34	38	12.0000

#PSSM
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
A : 0.98	a : 0.01	
G : 0.97	g : 0.02	

#score	912.0000000000002
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Graf2013_hg19_UTR_m3_run2.nuc.txt

#NT
AGGCGCAGAAGAAAGACGGCAAGAAGCGCAAGCGCAGCCGCAAGGAGAGCUAUUCCAUCUAUGUGUACAAGGUUCUGAAGCAGGUCCACCCUGACACCGGCAUUUCGUCCAAGGCCAUGGGCAUCAUGAAUUCGUUUGUGAACGACAUUUUCGAGCGCAUCGCAGGUGAGGCUUCCCGCCUGGCGCAUUACAACAAGCGCUCGACCAUCACCUCCAGGGAGAUCCAGACGGCCGUGCGCCUGCUGCUGCCUGGGGAGUUGGCCAAGCACGCCGUGUCCGAGGGUACUAAGGCCGUCACCAAGUACACCAGCGCUAAGUAAACAGUGAGUUGGUUGCAAACUCUCAACCCUAACGGCUCUUUUAAGAGCCACCCAUGUUCUCAAAGAAAGAGCUGGUGCUUGUAUUCCUCCUCUGCUGGCCACUGACAAACCCUUGUAACUUGCUACUGUGUUUUUUGGUCUGAAGUAGAGCA	chr6:27099996-27100468(-)$1	472	0	472	1056.0000

#otherMatches

#Struct PSSM
mmbbdddd:::::dddd[bb####eeeee####ccc&&&&&&&ddddnnnnndddd7777777ccc55555eeeee333bb22dddd::EEEEENNNNNEEEEE{CCCMMMMHHHHHHHHKKBBNNNNNGGGGGGGccc"""cccnnnnnccc]ccc::HHHHHHHH:eeeeellleeeeeeeeeesssssssssseeeee:::::::::::HHHHHHHHDDDD:::::ddddbb[dddd[bbmmmmbb22dddd]bb]dddd:::::ddddeeeeemmmmeeeee333ddddccc[bb!!ffffffa[ccclllccc22a]ffffff22bbccc::::::DDDD::::DDDD{CCC:::::ffffffmmmmffffff::::::::::::::::::::ffffffdddd[cccmmmmccc]dddd]ffffff:::CCC}DDDDGGGGGGGBBYYHHHHHHHHCCCEEEEEYYE	chr1:149783335-149783833(-)$1	498	16	488	1056.0000
::BBRRRRRRRRRDDDDKKJJJJJJJJJJJDDDD{BBKKFFFFFFffffff####cccmmmmccc55555ffffff::::ddddnnnnndddd:GGGGGGG{DDDDNNNNNCCC{FFFFFF::gggggggmmmmggggggg::EEEEE::hhhhhhhhbbccceeeee[bblllbbeeeee]ccc]bb88888888hhhhhhhh:::::bbggggggg[bb"""ccc!!cccnnnnnccc22cccbb]ggggggg]bb:cccpppppppcccEEEEE:::bbeeeee!!bboooooobb]eeeee]bb::ddddqqqqqqqqdddd:ccceeeeeqqqqqqqqeeeee22cccffffffmmmmffffff:FFFFFF}CCC~~~~DDDDYYGGGGGGG:dddd%%%%%%bboooooobb666666dddd::FFFFFFYYBBDDDDYYJJJJJJJJJJJDDDD////////BB:	chr6:27099996-27100468(-)$1	472	0	472	1056.0000

#DB
..)))))).....((((.((....(((((....(((.......((((.....)))).......))).....)))))...))..))))..(((((.....(((((.(((....((((((((..((.....((((((((((...(((.....))).)))..((((((((.(((((...)))))(((((..........)))))...........))))))))((((.....((((((.((((.((....))..)))).)).)))).....(((((((((....)))))...))))(((.((..(((((((.(((...)))..).))))))..)))))......))))....((((.(((.....((((((....))))))....................((((((((((.(((....))).)))).))))))...))).)))))))))))))..))))))))))))))))..)	chr1:149783335-149783833(-)$1	1	16	488	1056.0000
..((.........((((..(((((((((((((((.((..((((((((((((....(((....))).....))))))....((((.....)))).(((((((.((((.....(((.((((((..(((((((....)))))))..(((((..((((((((((((((((((.((...))))))).))).))........)))))))).....(((((((((.((...(((..(((.....)))..))))).))))))).)).(((.......))))))))...(((((((..((......)).))))).))..((((........)))).((((((((........)))))..)))((((((....)))))).)))))).)))....))))..))))))).((((......((......))......))))..))))))..))))))..)))))))))))))))........)).	chr6:27099996-27100468(-)$1	1	0	472	1056.0000

#PSSM
A : 1.00	
A : 0.50	G : 0.50	
G : 1.00	
U : 0.50	C : 0.50	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
C : 1.00	
G : 0.50	A : 0.50	
U : 1.00	
U : 0.50	C : 0.50	
U : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
G : 0.50	U : 0.50	
C : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
G : 1.00	
A : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
C : 0.50	G : 0.50	
U : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
G : 1.00	
U : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
G : 0.50	A : 0.50	
G : 1.00	
G : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 0.50	U : 0.50	
U : 1.00	
C : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
C : 1.00	
C : 0.50	G : 0.50	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
A : 0.50	C : 0.50	
U : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	A : 0.50	
G : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
U : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
C : 0.50	G : 0.50	
G : 1.00	
A : 1.00	
G : 1.00	
C : 0.50	U : 0.50	
U : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
G : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
C : 1.00	
C : 1.00	
G : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
G : 1.00	
C : 0.50	U : 0.50	
A : 1.00	
C : 1.00	
C : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
G : 1.00	
G : 1.00	
C : 1.00	
G : 0.50	C : 0.50	
G : 1.00	
U : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
C : 1.00	
A : 1.00	
C : 1.00	
C : 1.00	
A : 1.00	
G : 1.00	
C : 1.00	
U : 0.50	G : 0.50	
C : 1.00	
G : 0.50	U : 0.50	
A : 1.00	
A : 1.00	
G : 1.00	
U : 1.00	
A : 1.00	
A : 1.00	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
U : 0.50	G : 0.50	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
A : 0.50	U : 0.50	
C : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
U : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
A : 0.50	C : 0.50	
C : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
C : 0.50	A : 0.50	
C : 0.50	A : 0.50	
U : 0.50	C : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
C : 1.00	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
A : 0.50	U : 0.50	
G : 0.50	A : 0.50	
G : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	A : 0.50	
C : 0.50	G : 0.50	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
U : 0.50	C : 0.50	
C : 1.00	
A : 0.50	C : 0.50	
G : 0.50	A : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 1.00	
G : 1.00	
U : 0.50	A : 0.50	
A : 1.00	
A : 1.00	
U : 0.50	G : 0.50	
C : 0.50	A : 0.50	
G : 1.00	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
A : 0.50	G : 0.50	
A : 0.50	G : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
C : 1.00	
A : 0.50	U : 0.50	
G : 0.50	U : 0.50	
C : 0.50	G : 0.50	
U : 1.00	
G : 0.50	A : 0.50	
U : 1.00	
A : 0.50	U : 0.50	
A : 0.50	C : 0.50	
A : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	C : 0.50	
C : 1.00	
U : 1.00	
U : 0.50	C : 0.50	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
C : 1.00	
A : 0.50	U : 0.50	
G : 1.00	
A : 0.50	G : 0.50	
G : 0.50	C : 0.50	
C : 1.00	
G : 0.50	A : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
U : 0.50	G : 0.50	
G : 0.50	A : 0.50	
A : 0.50	C : 0.50	
U : 0.50	A : 0.50	
A : 1.00	
G : 0.50	A : 0.50	
C : 1.00	
U : 0.50	C : 0.50	
U : 0.50	C : 0.50	
U : 1.00	
U : 1.00	
G : 1.00	
G : 0.50	U : 0.50	
U : 0.50	A : 0.50	
C : 0.50	A : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	U : 0.50	
U : 0.50	G : 0.50	
A : 0.50	C : 0.50	
G : 0.50	U : 0.50	
G : 0.50	A : 0.50	
G : 0.50	C : 0.50	
A : 0.50	U : 0.50	
G : 1.00	
U : 1.00	
G : 1.00	
U : 1.00	
U : 1.00	
A : 0.50	U : 0.50	
C : 0.50	U : 0.50	
C : 0.50	U : 0.50	
A : 0.50	U : 0.50	
U : 0.50	G : 0.50	
G : 1.00	
G : 0.50	U : 0.50	
U : 0.50	C : 0.50	
C : 0.50	U : 0.50	
A : 0.50	G : 0.50	
C : 0.50	A : 0.50	
G : 0.50	A : 0.50	
G : 1.00	
A : 0.50	U : 0.50	
U : 0.50	A : 0.50	
G : 1.00	
C : 0.50	A : 0.50	
A : 0.50	G : 0.50	
U : 0.50	C : 0.50	
U : 0.50	A : 0.50	

#score	2112.0
#seq	2
#width	472
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_C22ORF28_Baltz2012c_hg19_UTR_m3_run1.nuc.txt

#NT
UUG	chr16:28855194-28855414(-)$1	220	63	66	8.9999
UUG	chr2:241070156-241070415(-)$1	259	51	54	8.9999
UUG	chrX:154005585-154005829(+)$1	244	26	29	8.9999
UUG	chr6:18225743-18225989(-)$1	246	36	39	8.9999
UUG	chr5:150070954-150071175(-)$1	221	21	24	8.9999
UUG	chr2:27015560-27015799(+)$1	239	4	7	8.9999
UUG	chr11:122931797-122932055(-)$1	258	42	45	8.9999
UUG	chr10:129897182-129897428(-)$1	246	14	17	8.9999
UUG	chr5:167980572-167980795(-)$1	223	8	11	8.9999
UUG	chr22:38879463-38879729(-)$1	266	43	46	8.9999
UUG	chr11:108388950-108389196(-)$1	246	13	16	8.9999
UUG	chr5:148732488-148732732(+)$1	244	21	24	8.9999
UUG	chr7:116437049-116437297(+)$1	248	61	64	8.9999
UUG	chr20:33866834-33867054(-)$1	220	68	71	8.9999
UUG	chr6:18224641-18224892(-)$1	251	77	80	8.9999
UUG	chr12:12976704-12976947(+)$1	243	77	80	8.9999
UUG	chr15:91509445-91509693(-)$1	248	3	6	8.9999
UUG	chrX:17772038-17772275(+)$1	237	132	135	8.9999
UUG	chr20:47729830-47730082(-)$1	252	28	31	8.9999
UUG	chr17:73058187-73058431(+)$1	244	15	18	8.9999
UUG	chr6:160169898-160170121(+)$1	223	6	9	8.9999
UUG	chr12:54635121-54635344(-)$1	223	55	58	8.9999
UUG	chr11:108345335-108345562(-)$1	227	5	8	8.9999
UUG	chr10:81111997-81112240(+)$1	243	69	72	8.9999
UUG	chr6:27775866-27776090(+)$1	224	92	95	8.9999
UUG	chr6:11136517-11136740(+)$1	223	77	80	8.9999
UUG	chr12:120634434-120634666(-)$1	232	29	32	8.9999
UUG	chr16:31104573-31104794(-)$1	221	7	10	8.9999
UUG	chr1:10490774-10491004(+)$1	230	127	130	8.9999
UUG	chr8:37611997-37612252(+)$1	255	92	95	8.9999
UUG	chr1:229736092-229736322(-)$1	230	96	99	8.9999
UUG	chr19:8551089-8551327(+)$1	238	33	36	8.9999
UUG	chr3:49924653-49924881(-)$1	228	25	28	8.9999
UUG	chr1:33138291-33138518(+)$1	227	3	6	8.9999
UUG	chr6:24425023-24425257(+)$1	234	5	8	8.9999
UUG	chr19:3976160-3976428(-)$1	268	35	38	8.9999
UUG	chr6:42994863-42995089(+)$1	226	11	14	8.9999
UUG	chr12:120899629-120899870(-)$1	241	98	101	8.9999
UUG	chr1:205683571-205683851(-)$1	280	15	18	8.9999
UUG	chr17:76220261-76220492(+)$1	231	52	55	8.9999
UUG	chr8:117657143-117657380(-)$1	237	174	177	8.9999
UUG	chr14:75367702-75367935(+)$1	233	30	33	8.9999
UUG	chr6:86322459-86322704(-)$1	245	48	51	8.9999
UUG	chr19:10370382-10370619(+)$1	237	103	106	8.9999
UUG	chr19:17342811-17343040(-)$1	229	23	26	8.9999
UUG	chr12:54062945-54063175(-)$1	230	62	65	8.9999
UUG	chr1:174973733-174973972(+)$1	239	2	5	8.9999
UUG	chr3:128889117-128889339(-)$1	222	9	12	8.9999
UUG	chr8:41368247-41368468(+)$1	221	42	45	8.9999
UUG	chr16:74655400-74655624(-)$1	224	139	142	8.9999
UUG	chr8:27667603-27667839(-)$1	236	42	45	8.9999
UUG	chr12:54449625-54449872(+)$1	247	74	77	8.9999
UUG	chr7:148979841-148980070(+)$1	229	3	6	8.9999
UUG	chr2:39107686-39107912(+)$1	226	129	132	8.9999
UUG	chr14:21956845-21957072(+)$1	227	5	8	8.9999
UUG	chr7:26231460-26231745(-)$1	285	10	13	8.9999
UUG	chr20:35869864-35870097(+)$1	233	99	102	8.9999
UUG	chr16:87885298-87885532(-)$1	234	137	140	8.9999
UUG	chr1:226548483-226548704(-)$1	221	21	24	8.9999
UUG	chr4:109543012-109543267(+)$1	255	35	38	8.9999
UUG	chr16:30096158-30096388(+)$1	230	117	120	8.9999
UUG	chr13:30338611-30338856(-)$1	245	22	25	8.9999
UUG	chr6:1613719-1613949(+)$1	230	6	9	8.9999
UUG	chr15:67483541-67483765(+)$1	224	33	36	8.9999
UUG	chrX:16862992-16863214(-)$1	222	82	85	8.9999
UUG	chr12:50152122-50152359(+)$1	237	225	228	8.9999
UUG	chr1:156304407-156304639(-)$1	232	58	61	8.9999
UUG	chr1:26227002-26227240(-)$1	238	26	29	8.9999
UUG	chr12:21788359-21788654(-)$1	295	24	27	8.9999
UUG	chr22:38880990-38881225(-)$1	235	17	20	8.9999
UUG	chr19:19617653-19617872(+)$1	219	10	13	8.9999
UUG	chr2:62106022-62106244(-)$1	222	1	4	8.9999
UUG	chr5:134181728-134181957(+)$1	229	53	56	8.9999
UUG	chr3:127336125-127336348(+)$1	223	102	105	8.9999
UUG	chr1:236648027-236648257(+)$1	230	35	38	8.9999
UUG	chr8:146279456-146279687(+)$1	231	119	122	8.9999
UUG	chr4:41263672-41263911(+)$1	239	15	18	8.9999
UUG	chr18:43674922-43675145(-)$1	223	9	12	8.9999
UUG	chr18:47018585-47018819(-)$1	234	10	13	8.9999
UUG	chr3:133524584-133524824(+)$1	240	78	81	8.9999
UUG	chr1:51702168-51702397(+)$1	229	71	74	8.9999
UUG	chr4:174253067-174253309(-)$1	242	134	137	8.9999
UUG	chr18:47803367-47803615(-)$1	248	70	73	8.9999
UUG	chr6:56967751-56967975(+)$1	224	85	88	8.9999
UUG	chr20:48808932-48809155(+)$1	223	111	114	8.9999
UUG	chr3:140660663-140660899(+)$1	236	87	90	8.9999
UUG	chr3:48643111-48643344(-)$1	233	20	23	8.9999
UUG	chr10:112771582-112771809(+)$1	227	79	82	8.9999
UUG	chr8:21995555-21995791(-)$1	236	13	16	8.9999
UUG	chr16:68293502-68293733(+)$1	231	47	50	8.9999
UUG	chr4:83345363-83345615(-)$1	252	55	58	8.9999
UUG	chr5:140026779-140027007(-)$1	228	8	11	8.9999
UUG	chr16:30093987-30094209(+)$1	222	125	128	8.9999
UUG	chr12:118582584-118582837(+)$1	253	33	36	8.9999
UUG	chr1:3805752-3805982(-)$1	230	43	46	8.9999
UUG	chr1:46782268-46782514(+)$1	246	50	53	8.9999

#otherMatches

#Struct PSSM
2cc	chr17:80011782-80012019(+)$1	237	22	25	8.9999
GGG	chr16:28855194-28855414(-)$1	220	63	66	8.9999
cpp	chr2:241070156-241070415(-)$1	259	51	54	8.9999
i::	chrX:154005585-154005829(+)$1	244	26	29	8.9999
JJJ	chr6:18225743-18225989(-)$1	246	36	39	8.9999
fff	chr5:150070954-150071175(-)$1	221	21	24	8.9999
:::	chr2:27015560-27015799(+)$1	239	4	7	8.9999
GGG	chr11:122931797-122932055(-)$1	258	42	45	8.9999
===	chr10:129897182-129897428(-)$1	246	14	17	8.9999
CC{	chr5:167980572-167980795(-)$1	223	8	11	8.9999
::B	chr22:38879463-38879729(-)$1	266	43	46	8.9999
DDF	chr11:108388950-108389196(-)$1	246	13	16	8.9999
hhh	chr5:148732488-148732732(+)$1	244	21	24	8.9999
ddn	chr7:116437049-116437297(+)$1	248	61	64	8.9999
:::	chr20:33866834-33867054(-)$1	220	68	71	8.9999
emm	chr6:18224641-18224892(-)$1	251	77	80	8.9999
ndd	chr12:12976704-12976947(+)$1	243	77	80	8.9999
:::	chr15:91509445-91509693(-)$1	248	3	6	8.9999
eee	chrX:17772038-17772275(+)$1	237	132	135	8.9999
qqq	chr20:47729830-47730082(-)$1	252	28	31	8.9999
::e	chr17:73058187-73058431(+)$1	244	15	18	8.9999
hhh	chr6:160169898-160170121(+)$1	223	6	9	8.9999
""g	chr12:54635121-54635344(-)$1	223	55	58	8.9999
LLL	chr11:108345335-108345562(-)$1	227	5	8	8.9999
ggg	chr10:81111997-81112240(+)$1	243	69	72	8.9999
ooc	chr6:27775866-27776090(+)$1	224	92	95	8.9999
iii	chr6:11136517-11136740(+)$1	223	77	80	8.9999
CLL	chr12:120634434-120634666(-)$1	232	29	32	8.9999
iii	chr16:31104573-31104794(-)$1	221	7	10	8.9999
ggc	chr1:10490774-10491004(+)$1	230	127	130	8.9999
KFF	chr8:37611997-37612252(+)$1	255	92	95	8.9999
==[	chr1:229736092-229736322(-)$1	230	96	99	8.9999
ppp	chr19:8551089-8551327(+)$1	238	33	36	8.9999
EFF	chr3:49924653-49924881(-)$1	228	25	28	8.9999
[cc	chr1:33138291-33138518(+)$1	227	3	6	8.9999
hhh	chr6:24425023-24425257(+)$1	234	5	8	8.9999
HHH	chr19:3976160-3976428(-)$1	268	35	38	8.9999
'''	chr6:42994863-42995089(+)$1	226	11	14	8.9999
qqq	chr12:120899629-120899870(-)$1	241	98	101	8.9999
JJJ	chr1:205683571-205683851(-)$1	280	15	18	8.9999
GGE	chr17:76220261-76220492(+)$1	231	52	55	8.9999
hhh	chr8:117657143-117657380(-)$1	237	174	177	8.9999
ff$	chr14:75367702-75367935(+)$1	233	30	33	8.9999
:::	chr6:86322459-86322704(-)$1	245	48	51	8.9999
}HH	chr19:10370382-10370619(+)$1	237	103	106	8.9999
:a[	chr19:17342811-17343040(-)$1	229	23	26	8.9999
dde	chr12:54062945-54063175(-)$1	230	62	65	8.9999
JJJ	chr1:174973733-174973972(+)$1	239	2	5	8.9999
$$c	chr3:128889117-128889339(-)$1	222	9	12	8.9999
JJJ	chr8:41368247-41368468(+)$1	221	42	45	8.9999
:::	chr16:74655400-74655624(-)$1	224	139	142	8.9999
f""	chr8:27667603-27667839(-)$1	236	42	45	8.9999
ggg	chr12:54449625-54449872(+)$1	247	74	77	8.9999
{JJ	chr7:148979841-148980070(+)$1	229	3	6	8.9999
HHH	chr2:39107686-39107912(+)$1	226	129	132	8.9999
ddd	chr14:21956845-21957072(+)$1	227	5	8	8.9999
FFF	chr7:26231460-26231745(-)$1	285	10	13	8.9999
===	chr20:35869864-35870097(+)$1	233	99	102	8.9999
b[b	chr16:87885298-87885532(-)$1	234	137	140	8.9999
dd"	chr1:226548483-226548704(-)$1	221	21	24	8.9999
666	chr4:109543012-109543267(+)$1	255	35	38	8.9999
HHH	chr16:30096158-30096388(+)$1	230	117	120	8.9999
#ee	chr13:30338611-30338856(-)$1	245	22	25	8.9999
fff	chr6:1613719-1613949(+)$1	230	6	9	8.9999
ddh	chr15:67483541-67483765(+)$1	224	33	36	8.9999
$$$	chrX:16862992-16863214(-)$1	222	82	85	8.9999
:::	chr12:50152122-50152359(+)$1	237	225	228	8.9999
ddd	chr1:156304407-156304639(-)$1	232	58	61	8.9999
::I	chr1:26227002-26227240(-)$1	238	26	29	8.9999
iii	chr12:21788359-21788654(-)$1	295	24	27	8.9999
FFF	chr22:38880990-38881225(-)$1	235	17	20	8.9999
nnd	chr19:19617653-19617872(+)$1	219	10	13	8.9999
:::	chr2:62106022-62106244(-)$1	222	1	4	8.9999
dd[	chr5:134181728-134181957(+)$1	229	53	56	8.9999
:ff	chr3:127336125-127336348(+)$1	223	102	105	8.9999
mmb	chr1:236648027-236648257(+)$1	230	35	38	8.9999
ood	chr8:146279456-146279687(+)$1	231	119	122	8.9999
EEE	chr4:41263672-41263911(+)$1	239	15	18	8.9999
bb[	chr18:43674922-43675145(-)$1	223	9	12	8.9999
B{A	chr18:47018585-47018819(-)$1	234	10	13	8.9999
fff	chr3:133524584-133524824(+)$1	240	78	81	8.9999
ee:	chr1:51702168-51702397(+)$1	229	71	74	8.9999
eee	chr4:174253067-174253309(-)$1	242	134	137	8.9999
fff	chr18:47803367-47803615(-)$1	248	70	73	8.9999
""a	chr6:56967751-56967975(+)$1	224	85	88	8.9999
ggg	chr20:48808932-48809155(+)$1	223	111	114	8.9999
fff	chr3:140660663-140660899(+)$1	236	87	90	8.9999
dpp	chr3:48643111-48643344(-)$1	233	20	23	8.9999
h]f	chr10:112771582-112771809(+)$1	227	79	82	8.9999
+++	chr8:21995555-21995791(-)$1	236	13	16	8.9999
PPE	chr16:68293502-68293733(+)$1	231	47	50	8.9999
:::	chr4:83345363-83345615(-)$1	252	55	58	8.9999
ppp	chr5:140026779-140027007(-)$1	228	8	11	8.9999
44e	chr16:30093987-30094209(+)$1	222	125	128	8.9999
hhh	chr12:118582584-118582837(+)$1	253	33	36	8.9999
:ff	chr1:3805752-3805982(-)$1	230	43	46	8.9999
rrr	chr1:46782268-46782514(+)$1	246	50	53	8.9999

#DB
.))	chr17:80011782-80012019(+)$1	1	22	25	8.9999
(((	chr16:28855194-28855414(-)$1	1	63	66	8.9999
(..	chr2:241070156-241070415(-)$1	1	51	54	8.9999
)..	chrX:154005585-154005829(+)$1	1	26	29	8.9999
(((	chr6:18225743-18225989(-)$1	1	36	39	8.9999
(((	chr5:150070954-150071175(-)$1	1	21	24	8.9999
...	chr2:27015560-27015799(+)$1	1	4	7	8.9999
(((	chr11:122931797-122932055(-)$1	1	42	45	8.9999
(((	chr10:129897182-129897428(-)$1	1	14	17	8.9999
((.	chr5:167980572-167980795(-)$1	1	8	11	8.9999
..(	chr22:38879463-38879729(-)$1	1	43	46	8.9999
(((	chr11:108388950-108389196(-)$1	1	13	16	8.9999
)))	chr5:148732488-148732732(+)$1	1	21	24	8.9999
((.	chr7:116437049-116437297(+)$1	1	61	64	8.9999
...	chr20:33866834-33867054(-)$1	1	68	71	8.9999
(..	chr6:18224641-18224892(-)$1	1	77	80	8.9999
.))	chr12:12976704-12976947(+)$1	1	77	80	8.9999
...	chr15:91509445-91509693(-)$1	1	3	6	8.9999
)))	chrX:17772038-17772275(+)$1	1	132	135	8.9999
...	chr20:47729830-47730082(-)$1	1	28	31	8.9999
..(	chr17:73058187-73058431(+)$1	1	15	18	8.9999
(((	chr6:160169898-160170121(+)$1	1	6	9	8.9999
..(	chr12:54635121-54635344(-)$1	1	55	58	8.9999
...	chr11:108345335-108345562(-)$1	1	5	8	8.9999
)))	chr10:81111997-81112240(+)$1	1	69	72	8.9999
..)	chr6:27775866-27776090(+)$1	1	92	95	8.9999
(((	chr6:11136517-11136740(+)$1	1	77	80	8.9999
(..	chr12:120634434-120634666(-)$1	1	29	32	8.9999
(((	chr16:31104573-31104794(-)$1	1	7	10	8.9999
))(	chr1:10490774-10491004(+)$1	1	127	130	8.9999
.((	chr8:37611997-37612252(+)$1	1	92	95	8.9999
((.	chr1:229736092-229736322(-)$1	1	96	99	8.9999
...	chr19:8551089-8551327(+)$1	1	33	36	8.9999
(((	chr3:49924653-49924881(-)$1	1	25	28	8.9999
.((	chr1:33138291-33138518(+)$1	1	3	6	8.9999
(((	chr6:24425023-24425257(+)$1	1	5	8	8.9999
(((	chr19:3976160-3976428(-)$1	1	35	38	8.9999
...	chr6:42994863-42995089(+)$1	1	11	14	8.9999
...	chr12:120899629-120899870(-)$1	1	98	101	8.9999
(((	chr1:205683571-205683851(-)$1	1	15	18	8.9999
(((	chr17:76220261-76220492(+)$1	1	52	55	8.9999
)))	chr8:117657143-117657380(-)$1	1	174	177	8.9999
((.	chr14:75367702-75367935(+)$1	1	30	33	8.9999
...	chr6:86322459-86322704(-)$1	1	48	51	8.9999
.))	chr19:10370382-10370619(+)$1	1	103	106	8.9999
.(.	chr19:17342811-17343040(-)$1	1	23	26	8.9999
)))	chr12:54062945-54063175(-)$1	1	62	65	8.9999
(((	chr1:174973733-174973972(+)$1	1	2	5	8.9999
..(	chr3:128889117-128889339(-)$1	1	9	12	8.9999
(((	chr8:41368247-41368468(+)$1	1	42	45	8.9999
...	chr16:74655400-74655624(-)$1	1	139	142	8.9999
(..	chr8:27667603-27667839(-)$1	1	42	45	8.9999
(((	chr12:54449625-54449872(+)$1	1	74	77	8.9999
.((	chr7:148979841-148980070(+)$1	1	3	6	8.9999
(((	chr2:39107686-39107912(+)$1	1	129	132	8.9999
(((	chr14:21956845-21957072(+)$1	1	5	8	8.9999
(((	chr7:26231460-26231745(-)$1	1	10	13	8.9999
(((	chr20:35869864-35870097(+)$1	1	99	102	8.9999
(.(	chr16:87885298-87885532(-)$1	1	137	140	8.9999
((.	chr1:226548483-226548704(-)$1	1	21	24	8.9999
...	chr4:109543012-109543267(+)$1	1	35	38	8.9999
(((	chr16:30096158-30096388(+)$1	1	117	120	8.9999
.((	chr13:30338611-30338856(-)$1	1	22	25	8.9999
(((	chr6:1613719-1613949(+)$1	1	6	9	8.9999
))(	chr15:67483541-67483765(+)$1	1	33	36	8.9999
...	chrX:16862992-16863214(-)$1	1	82	85	8.9999
...	chr12:50152122-50152359(+)$1	1	225	228	8.9999
)))	chr1:156304407-156304639(-)$1	1	58	61	8.9999
..(	chr1:26227002-26227240(-)$1	1	26	29	8.9999
(((	chr12:21788359-21788654(-)$1	1	24	27	8.9999
(((	chr22:38880990-38881225(-)$1	1	17	20	8.9999
..)	chr19:19617653-19617872(+)$1	1	10	13	8.9999
...	chr2:62106022-62106244(-)$1	1	1	4	8.9999
((.	chr5:134181728-134181957(+)$1	1	53	56	8.9999
.((	chr3:127336125-127336348(+)$1	1	102	105	8.9999
..)	chr1:236648027-236648257(+)$1	1	35	38	8.9999
..)	chr8:146279456-146279687(+)$1	1	119	122	8.9999
(((	chr4:41263672-41263911(+)$1	1	15	18	8.9999
((.	chr18:43674922-43675145(-)$1	1	9	12	8.9999
(.(	chr18:47018585-47018819(-)$1	1	10	13	8.9999
(((	chr3:133524584-133524824(+)$1	1	78	81	8.9999
)).	chr1:51702168-51702397(+)$1	1	71	74	8.9999
)))	chr4:174253067-174253309(-)$1	1	134	137	8.9999
(((	chr18:47803367-47803615(-)$1	1	70	73	8.9999
..(	chr6:56967751-56967975(+)$1	1	85	88	8.9999
)))	chr20:48808932-48809155(+)$1	1	111	114	8.9999
(((	chr3:140660663-140660899(+)$1	1	87	90	8.9999
(..	chr3:48643111-48643344(-)$1	1	20	23	8.9999
).)	chr10:112771582-112771809(+)$1	1	79	82	8.9999
...	chr8:21995555-21995791(-)$1	1	13	16	8.9999
..(	chr16:68293502-68293733(+)$1	1	47	50	8.9999
...	chr4:83345363-83345615(-)$1	1	55	58	8.9999
...	chr5:140026779-140027007(-)$1	1	8	11	8.9999
..)	chr16:30093987-30094209(+)$1	1	125	128	8.9999
(((	chr12:118582584-118582837(+)$1	1	33	36	8.9999
.((	chr1:3805752-3805982(-)$1	1	43	46	8.9999
...	chr1:46782268-46782514(+)$1	1	50	53	8.9999

#PSSM
U : 0.99	
U : 0.99	
G : 0.99	

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_METTL3_Ping2014_hg19_UTR_m3_run2.nuc.txt

#NT
CCCA	chr22:22116049-22116284(-)$1	235	146	150	12.0000
CCCA	chr15:64463548-64463784(-)$1	236	12	16	12.0000
CCCA	chr20:30157078-30157324(+)$1	246	135	139	12.0000
CCCA	chr22:42981784-42982026(-)$1	242	67	71	12.0000
CCCA	chr16:30435342-30435566(-)$1	224	143	147	12.0000
CCCA	chr8:98740802-98741062(+)$1	260	23	27	12.0000
CCCA	chr3:131221646-131221874(-)$1	228	108	112	12.0000
ccca	chr12:123261480-123261709(+)$1	229	106	110	12.0000
CCCA	chr6:31765217-31765447(-)$1	230	135	139	12.0000
CCCA	chr2:241407135-241407372(+)$1	237	6	10	12.0000
CCCA	chr1:36358052-36358271(-)$1	219	198	202	12.0000
ccca	chr7:2270173-2270399(-)$1	226	78	82	12.0000
CCCA	chr7:102066265-102066493(+)$1	228	30	34	12.0000
CCCA	chr5:175935768-175935990(+)$1	222	90	94	12.0000
CCCA	chr11:34073789-34074011(+)$1	222	54	58	12.0000
ccca	chr19:55901743-55901976(+)$1	233	35	39	12.0000
ccca	chr19:38125153-38125393(-)$1	240	112	116	12.0000
CCCA	chr3:183960140-183960366(-)$1	226	29	33	12.0000
CCCA	chr19:37825771-37825999(+)$1	228	51	55	12.0000
CCCA	chr3:39425096-39425318(+)$1	222	63	67	12.0000
CCCA	chr17:22023101-22023330(+)$1	229	30	34	12.0000
CCCA	chr1:156713040-156713292(-)$1	252	75	79	12.0000
ccca	chr1:19585363-19585585(+)$1	222	140	144	12.0000
CCCA	chr6:143097189-143097408(-)$1	219	100	104	12.0000
CCCA	chr15:65868845-65869088(+)$1	243	3	7	12.0000
CCCA	chr3:9834683-9834906(+)$1	223	105	109	12.0000
CCCA	chr19:47855949-47856182(+)$1	233	22	26	12.0000
ccca	chr22:36883960-36884208(-)$1	248	92	96	12.0000
CCCA	chr10:103370784-103371007(-)$1	223	53	57	12.0000
CCCA	chr17:78185191-78185446(-)$1	255	17	21	12.0000
CCCA	chr3:196311447-196311667(+)$1	220	101	105	12.0000
CCCA	chr7:128411076-128411304(+)$1	228	39	43	12.0000
CCCA	chr12:56078747-56078970(-)$1	223	60	64	12.0000
CCCA	chr11:1297152-1297380(-)$1	228	23	27	12.0000
CCCA	chr22:39913418-39913649(+)$1	231	121	125	12.0000
CCCA	chr19:19617056-19617290(+)$1	234	19	23	12.0000
CCCA	chr12:49666247-49666478(+)$1	231	75	79	12.0000
ccca	chr2:217394079-217394306(+)$1	227	47	51	12.0000
CCCA	chr7:140178928-140179154(-)$1	226	91	95	12.0000
CCCA	chr15:75194952-75195185(-)$1	233	154	158	12.0000
ccca	chr4:177250345-177250575(+)$1	230	123	127	12.0000
CCCA	chr17:7478364-7478590(+)$1	226	22	26	12.0000
CCCA	chr2:74381402-74381659(-)$1	257	148	152	12.0000
CCCA	chr4:140430245-140430473(-)$1	228	64	68	12.0000
CCCA	chr2:232597445-232597672(-)$1	227	189	193	12.0000
CCCA	chr11:57080039-57080274(-)$1	235	88	92	12.0000
CCCA	chr2:219460666-219460891(+)$1	225	136	140	12.0000
CCCA	chr17:17746837-17747059(-)$1	222	150	154	12.0000
ccca	chr4:177250419-177250642(+)$1	223	49	53	12.0000
ccca	chrX:123041710-123041934(+)$1	224	119	123	12.0000
CCCA	chr8:144687614-144687836(-)$1	222	166	170	12.0000
CCCA	chr3:63985556-63985776(+)$1	220	171	175	12.0000
CCCA	chr17:73124814-73125039(+)$1	225	21	25	12.0000
CCCA	chr14:75601423-75601650(-)$1	227	83	87	12.0000
CCCA	chr11:117157344-117157570(-)$1	226	101	105	12.0000
ccca	chr12:112944441-112944665(+)$1	224	12	16	12.0000
CCCA	chr19:19293337-19293568(-)$1	231	174	178	12.0000
CCCA	chr19:51302470-51302699(-)$1	229	43	47	12.0000
CCCA	chr17:1548877-1549105(+)$1	228	8	12	12.0000
CCCA	chr17:74078872-74079100(-)$1	228	25	29	12.0000
CCCA	chr19:2101882-2102107(-)$1	225	30	34	12.0000
CCCA	chr19:10791642-10791863(+)$1	221	124	128	12.0000
ccca	chr20:60756017-60756242(+)$1	225	81	85	12.0000
CCCA	chr1:153924383-153924615(-)$1	232	56	60	12.0000
ccca	chr3:155541469-155541737(-)$1	268	101	105	12.0000
CCCA	chr1:180471492-180471715(-)$1	223	134	138	12.0000
CCCA	chr11:64532525-64532751(-)$1	226	166	170	12.0000
CCCA	chr7:133975702-133975925(-)$1	223	113	117	12.0000
CCCA	chr18:12325194-12325446(+)$1	252	110	114	12.0000
CCCA	chr11:118415367-118415589(-)$1	222	4	8	12.0000
CCCA	chr20:43380561-43380788(-)$1	227	40	44	12.0000
CCCA	chr1:109235303-109235523(+)$1	220	87	91	12.0000
CCCA	chr1:165796760-165796987(+)$1	227	144	148	12.0000
CCCA	chr4:113108218-113108440(+)$1	222	140	144	12.0000
CCCA	chr17:47126856-47127112(+)$1	256	76	80	12.0000

#otherMatches

#Struct PSSM
::ff	chr11:118473090-118473328(+)$1	238	106	110	12.0000
c]bb	chr22:22116049-22116284(-)$1	235	146	150	12.0000
eeee	chr15:64463548-64463784(-)$1	236	12	16	12.0000
eeee	chr20:30157078-30157324(+)$1	246	135	139	12.0000
eea>	chr22:42981784-42982026(-)$1	242	67	71	12.0000
gggg	chr16:30435342-30435566(-)$1	224	143	147	12.0000
qqqq	chr8:98740802-98741062(+)$1	260	23	27	12.0000
hhhh	chr3:131221646-131221874(-)$1	228	108	112	12.0000
c[cc	chr12:123261480-123261709(+)$1	229	106	110	12.0000
iiii	chr6:31765217-31765447(-)$1	230	135	139	12.0000
GGG:	chr2:241407135-241407372(+)$1	237	6	10	12.0000
EEEE	chr1:36358052-36358271(-)$1	219	198	202	12.0000
FFFF	chr7:2270173-2270399(-)$1	226	78	82	12.0000
hhhq	chr7:102066265-102066493(+)$1	228	30	34	12.0000
ffff	chr5:175935768-175935990(+)$1	222	90	94	12.0000
::::	chr11:34073789-34074011(+)$1	222	54	58	12.0000
bmmm	chr19:55901743-55901976(+)$1	233	35	39	12.0000
^^^^	chr19:38125153-38125393(-)$1	240	112	116	12.0000
MCCC	chr3:183960140-183960366(-)$1	226	29	33	12.0000
F{BB	chr19:37825771-37825999(+)$1	228	51	55	12.0000
hhhh	chr3:39425096-39425318(+)$1	222	63	67	12.0000
++++	chr17:22023101-22023330(+)$1	229	30	34	12.0000
rrrr	chr1:156713040-156713292(-)$1	252	75	79	12.0000
cccc	chr1:19585363-19585585(+)$1	222	140	144	12.0000
dd$$	chr6:143097189-143097408(-)$1	219	100	104	12.0000
::cc	chr15:65868845-65869088(+)$1	243	3	7	12.0000
cc[a	chr3:9834683-9834906(+)$1	223	105	109	12.0000
DD::	chr19:47855949-47856182(+)$1	233	22	26	12.0000
dddd	chr22:36883960-36884208(-)$1	248	92	96	12.0000
ccc:	chr10:103370784-103371007(-)$1	223	53	57	12.0000
CCLL	chr17:78185191-78185446(-)$1	255	17	21	12.0000
mmbb	chr3:196311447-196311667(+)$1	220	101	105	12.0000
dddd	chr7:128411076-128411304(+)$1	228	39	43	12.0000
bboo	chr12:56078747-56078970(-)$1	223	60	64	12.0000
ffff	chr11:1297152-1297380(-)$1	228	23	27	12.0000
JJJJ	chr22:39913418-39913649(+)$1	231	121	125	12.0000
:BBK	chr19:19617056-19617290(+)$1	234	19	23	12.0000
::::	chr12:49666247-49666478(+)$1	231	75	79	12.0000
]eee	chr2:217394079-217394306(+)$1	227	47	51	12.0000
]ccc	chr7:140178928-140179154(-)$1	226	91	95	12.0000
D:dd	chr15:75194952-75195185(-)$1	233	154	158	12.0000
nncc	chr4:177250345-177250575(+)$1	230	123	127	12.0000
ffmm	chr17:7478364-7478590(+)$1	226	22	26	12.0000
"""f	chr2:74381402-74381659(-)$1	257	148	152	12.0000
::::	chr4:140430245-140430473(-)$1	228	64	68	12.0000
oooc	chr2:232597445-232597672(-)$1	227	189	193	12.0000
++++	chr11:57080039-57080274(-)$1	235	88	92	12.0000
aggg	chr2:219460666-219460891(+)$1	225	136	140	12.0000
55ii	chr17:17746837-17747059(-)$1	222	150	154	12.0000
nncc	chr4:177250419-177250642(+)$1	223	49	53	12.0000
===w	chrX:123041710-123041934(+)$1	224	119	123	12.0000
ffff	chr8:144687614-144687836(-)$1	222	166	170	12.0000
ffff	chr3:63985556-63985776(+)$1	220	171	175	12.0000
ssss	chr17:73124814-73125039(+)$1	225	21	25	12.0000
IIII	chr14:75601423-75601650(-)$1	227	83	87	12.0000
FFFF	chr11:117157344-117157570(-)$1	226	101	105	12.0000
dddd	chr12:112944441-112944665(+)$1	224	12	16	12.0000
FBB}	chr19:19293337-19293568(-)$1	231	174	178	12.0000
bb55	chr19:51302470-51302699(-)$1	229	43	47	12.0000
!bb!	chr17:1548877-1549105(+)$1	228	8	12	12.0000
eeee	chr17:74078872-74079100(-)$1	228	25	29	12.0000
D:cc	chr19:2101882-2102107(-)$1	225	30	34	12.0000
dd::	chr19:10791642-10791863(+)$1	221	124	128	12.0000
f[ee	chr20:60756017-60756242(+)$1	225	81	85	12.0000
CCCL	chr1:153924383-153924615(-)$1	232	56	60	12.0000
F{EE	chr3:155541469-155541737(-)$1	268	101	105	12.0000
eeee	chr1:180471492-180471715(-)$1	223	134	138	12.0000
eeee	chr11:64532525-64532751(-)$1	226	166	170	12.0000
ffff	chr7:133975702-133975925(-)$1	223	113	117	12.0000
FFFF	chr18:12325194-12325446(+)$1	252	110	114	12.0000
GGGf	chr11:118415367-118415589(-)$1	222	4	8	12.0000
++++	chr20:43380561-43380788(-)$1	227	40	44	12.0000
eeee	chr1:109235303-109235523(+)$1	220	87	91	12.0000
ccce	chr1:165796760-165796987(+)$1	227	144	148	12.0000
dd((	chr4:113108218-113108440(+)$1	222	140	144	12.0000
bbdd	chr17:47126856-47127112(+)$1	256	76	80	12.0000

#DB
..((	chr11:118473090-118473328(+)$1	1	106	110	12.0000
).))	chr22:22116049-22116284(-)$1	1	146	150	12.0000
((((	chr15:64463548-64463784(-)$1	1	12	16	12.0000
)(((	chr20:30157078-30157324(+)$1	1	135	139	12.0000
))).	chr22:42981784-42982026(-)$1	1	67	71	12.0000
))))	chr16:30435342-30435566(-)$1	1	143	147	12.0000
....	chr8:98740802-98741062(+)$1	1	23	27	12.0000
((((	chr3:131221646-131221874(-)$1	1	108	112	12.0000
(.((	chr12:123261480-123261709(+)$1	1	106	110	12.0000
))))	chr6:31765217-31765447(-)$1	1	135	139	12.0000
(((.	chr2:241407135-241407372(+)$1	1	6	10	12.0000
))))	chr1:36358052-36358271(-)$1	1	198	202	12.0000
((((	chr7:2270173-2270399(-)$1	1	78	82	12.0000
(((.	chr7:102066265-102066493(+)$1	1	30	34	12.0000
((((	chr5:175935768-175935990(+)$1	1	90	94	12.0000
....	chr11:34073789-34074011(+)$1	1	54	58	12.0000
(...	chr19:55901743-55901976(+)$1	1	35	39	12.0000
....	chr19:38125153-38125393(-)$1	1	112	116	12.0000
.(((	chr3:183960140-183960366(-)$1	1	29	33	12.0000
(.((	chr19:37825771-37825999(+)$1	1	51	55	12.0000
((((	chr3:39425096-39425318(+)$1	1	63	67	12.0000
....	chr17:22023101-22023330(+)$1	1	30	34	12.0000
....	chr1:156713040-156713292(-)$1	1	75	79	12.0000
))))	chr1:19585363-19585585(+)$1	1	140	144	12.0000
((..	chr6:143097189-143097408(-)$1	1	100	104	12.0000
..((	chr15:65868845-65869088(+)$1	1	3	7	12.0000
((.(	chr3:9834683-9834906(+)$1	1	105	109	12.0000
((..	chr19:47855949-47856182(+)$1	1	22	26	12.0000
((((	chr22:36883960-36884208(-)$1	1	92	96	12.0000
))).	chr10:103370784-103371007(-)$1	1	53	57	12.0000
((..	chr17:78185191-78185446(-)$1	1	17	21	12.0000
..))	chr3:196311447-196311667(+)$1	1	101	105	12.0000
))))	chr7:128411076-128411304(+)$1	1	39	43	12.0000
((..	chr12:56078747-56078970(-)$1	1	60	64	12.0000
))))	chr11:1297152-1297380(-)$1	1	23	27	12.0000
))))	chr22:39913418-39913649(+)$1	1	121	125	12.0000
.((.	chr19:19617056-19617290(+)$1	1	19	23	12.0000
....	chr12:49666247-49666478(+)$1	1	75	79	12.0000
.)))	chr2:217394079-217394306(+)$1	1	47	51	12.0000
.)))	chr7:140178928-140179154(-)$1	1	91	95	12.0000
).((	chr15:75194952-75195185(-)$1	1	154	158	12.0000
..))	chr4:177250345-177250575(+)$1	1	123	127	12.0000
((..	chr17:7478364-7478590(+)$1	1	22	26	12.0000
...(	chr2:74381402-74381659(-)$1	1	148	152	12.0000
....	chr4:140430245-140430473(-)$1	1	64	68	12.0000
...)	chr2:232597445-232597672(-)$1	1	189	193	12.0000
....	chr11:57080039-57080274(-)$1	1	88	92	12.0000
))))	chr2:219460666-219460891(+)$1	1	136	140	12.0000
..))	chr17:17746837-17747059(-)$1	1	150	154	12.0000
..))	chr4:177250419-177250642(+)$1	1	49	53	12.0000
(((.	chrX:123041710-123041934(+)$1	1	119	123	12.0000
))))	chr8:144687614-144687836(-)$1	1	166	170	12.0000
((((	chr3:63985556-63985776(+)$1	1	171	175	12.0000
....	chr17:73124814-73125039(+)$1	1	21	25	12.0000
((((	chr14:75601423-75601650(-)$1	1	83	87	12.0000
((((	chr11:117157344-117157570(-)$1	1	101	105	12.0000
((((	chr12:112944441-112944665(+)$1	1	12	16	12.0000
))).	chr19:19293337-19293568(-)$1	1	174	178	12.0000
))..	chr19:51302470-51302699(-)$1	1	43	47	12.0000
.((.	chr17:1548877-1549105(+)$1	1	8	12	12.0000
((((	chr17:74078872-74079100(-)$1	1	25	29	12.0000
(.((	chr19:2101882-2102107(-)$1	1	30	34	12.0000
))..	chr19:10791642-10791863(+)$1	1	124	128	12.0000
(.((	chr20:60756017-60756242(+)$1	1	81	85	12.0000
(((.	chr1:153924383-153924615(-)$1	1	56	60	12.0000
(.((	chr3:155541469-155541737(-)$1	1	101	105	12.0000
((((	chr1:180471492-180471715(-)$1	1	134	138	12.0000
((((	chr11:64532525-64532751(-)$1	1	166	170	12.0000
))))	chr7:133975702-133975925(-)$1	1	113	117	12.0000
))))	chr18:12325194-12325446(+)$1	1	110	114	12.0000
((((	chr11:118415367-118415589(-)$1	1	4	8	12.0000
....	chr20:43380561-43380788(-)$1	1	40	44	12.0000
))))	chr1:109235303-109235523(+)$1	1	87	91	12.0000
)))(	chr1:165796760-165796987(+)$1	1	144	148	12.0000
((..	chr4:113108218-113108440(+)$1	1	140	144	12.0000
((((	chr17:47126856-47127112(+)$1	1	76	80	12.0000

#PSSM
C : 0.82	c : 0.17	
C : 0.82	c : 0.17	
C : 0.82	c : 0.17	
A : 0.82	a : 0.17	

#score	912.0000000000001
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_IGF2BP123_Hafner2010d_hg19_UTR_m2_run2.nuc.txt

#NT
GUCAUUUGUUUUU	chr9:80331863-80332177(-)$1	314	290	303	18.6739
UUAUCUUUCUUUU	chr11:85669403-85669713(-)$1	310	54	67	18.3478
UUCUUUUUUGUUU	chr4:170641743-170642026(+)$1	283	258	271	23.8913
UUAUUUUUAUUUU	chr5:32355387-32355654(-)$1	267	27	40	22.6956
UUAUUAUUUUUUU	chr13:37586241-37586511(-)$1	270	58	71	22.4782
AUAUUUUGUUUUU	chr10:70742201-70742678(+)$1	477	21	34	20.7391
uucuuucuuuuuu	chr10:72185801-72186196(+)$1	395	218	231	24.1086
UUUUUUUUUUUUU	chr1:61921119-61921365(+)$1	246	66	79	26.2826
AUGUUUUUUUUUU	chr1:185069917-185070302(+)$1	385	114	127	23.2391
AUCUGUUAUUUUU	chr4:39779883-39780320(+)$1	437	225	238	17.0434
GUCUUUGUUUUGU	chr8:99963915-99964238(+)$1	323	285	298	17.4782
AGCUUUUUUAUUU	chr2:206866782-206867067(-)$1	285	56	69	17.1521
UUCUUGUUUUUUA	chr7:155256784-155257080(+)$1	296	61	74	19.1086
UUCAUUUUUUUUU	chr4:99801826-99802085(-)$1	259	78	91	24.1086
GUCUUAUUUUAUU	chr15:73595163-73595559(+)$1	396	262	275	17.2608
uucauuacuuuuu	chr6:27820176-27820453(+)$1	277	159	172	16.6086
UUGUUUUUUGUUG	chr18:13762729-13763179(+)$1	450	208	221	17.3695
UGCUUUUGUUUUU	chr9:132995381-132995672(+)$1	291	195	208	21.1739
UUUUUUUUUUCUU	chr8:17425197-17425604(+)$1	407	332	345	22.1521
GUUUUUUUCUUUU	chr7:139256684-139257014(-)$1	330	140	153	20.0869
UUUUUUUGUUGUU	chr2:170668116-170668449(+)$1	333	269	282	19.2173
uuuuuuguguuuu	chr3:158263093-158263359(+)$1	266	64	77	18.9999
UUGUUUUUUUUUU	chr11:118964481-118964936(-)$1	455	337	350	26.1739
GUCAUUUUUUUUU	chrX:103435203-103435678(+)$1	475	168	181	21.6086
UUAUUCUUAUUUU	chrX:108787285-108787776(+)$1	491	324	337	18.6739
uuguuuuguuuuU	chr5:10436092-10436530(+)$1	438	74	87	23.2391
UUUUUUGUCUUUU	chr4:139978486-139978807(-)$1	321	275	288	19.2173
UGCUUUUGUUUUU	chr9:110093292-110093612(+)$1	320	43	56	21.1739
UUGUUUGUUUGUU	chr6:82456992-82457330(-)$1	338	19	32	18.6739
AUCUUUUAUUAUU	chr1:183521180-183521602(+)$1	422	342	355	17.3695
uuguuuuguuuuu	chr1:204519877-204520267(+)$1	390	297	310	23.2391
GUAUUUGUUUUUU	chr10:11375319-11375631(+)$1	312	290	303	20.7391
UUCUUCAGUUUUU	chr5:64019475-64019775(-)$1	300	51	64	17.2608
UUCUUUGUUUUCU	chr7:133976468-133976742(-)$1	274	194	207	19.9782
UUCUUUUUGUCUU	chr7:27565618-27565919(-)$1	301	240	253	19.9782
GUAUUUUUUAUUU	chr1:3697645-3697979(-)$1	334	62	75	20.0869
UUUUUUUUUCUUU	chr17:56050620-56050934(-)$1	314	253	266	22.0434
UACUUCUUUUUUU	chr12:40153027-40153369(-)$1	342	221	234	19.7608
uuauuuuuuauuu	chr20:47790616-47790906(-)$1	290	82	95	22.5869
GUAUUUUUUUUUU	chr12:28459574-28459836(+)$1	262	75	88	24.1086
UUCUGUUUCUUUU	chr1:167393921-167394385(+)$1	464	234	247	19.8695
UGAUUUUUUUUUU	chr11:58385662-58386090(+)$1	428	384	397	22.6956
UUCUUUUUUUUUU	chr1:155869351-155869802(-)$1	451	353	366	28.0217
uucuuuuuuuuuu	chr1:26796530-26796923(+)$1	393	273	286	28.0217
uucuuuuuuuuuu	chr17:78108919-78109322(-)$1	403	359	372	28.0217

#otherMatches

#Struct PSSM
JJGGGGGGG::::	chr1:214522937-214523325(-)$1	388	147	160	17.3695
EEEEeeeeepppp	chr9:80331863-80332177(-)$1	314	290	303	18.6739
^^^^^^^^^^^ff	chr11:85669403-85669713(-)$1	310	54	67	18.3478
:::::::::::::	chr4:170641743-170642026(+)$1	283	258	271	23.8913
:::::::::::::	chr5:32355387-32355654(-)$1	267	27	40	22.6956
:::::::::::::	chr13:37586241-37586511(-)$1	270	58	71	22.4782
:::==========	chr10:70742201-70742678(+)$1	477	21	34	20.7391
:::::::::::::	chr10:72185801-72186196(+)$1	395	218	231	24.1086
ddddrrrrrrrrr	chr1:61921119-61921365(+)$1	246	66	79	26.2826
fff::::::::::	chr1:185069917-185070302(+)$1	385	114	127	23.2391
6ffffff:ggggg	chr4:39779883-39780320(+)$1	437	225	238	17.0434
EEEYYBB@@@@@@	chr8:99963915-99964238(+)$1	323	285	298	17.4782
:GGGGGGG::::G	chr2:206866782-206867067(-)$1	285	56	69	17.1521
fffffGGGGGGGM	chr7:155256784-155257080(+)$1	296	61	74	19.1086
::::::::::::e	chr4:99801826-99802085(-)$1	259	78	91	24.1086
eee999999999e	chr15:73595163-73595559(+)$1	396	262	275	17.2608
eedddd[ccclll	chr6:27820176-27820453(+)$1	277	159	172	16.6086
fff::::::EEEE	chr18:13762729-13763179(+)$1	450	208	221	17.3695
E::::iiiiiiii	chr9:132995381-132995672(+)$1	291	195	208	21.1739
:::HHHHHHHH}C	chr8:17425197-17425604(+)$1	407	332	345	22.1521
E:::eeeeeoooo	chr7:139256684-139257014(-)$1	330	140	153	20.0869
GGGGGGG}FFFFF	chr2:170668116-170668449(+)$1	333	269	282	19.2173
:::::::::::::	chr3:158263093-158263359(+)$1	266	64	77	18.9999
dd[dddd%%%%%%	chr11:118964481-118964936(-)$1	455	337	350	26.1739
gggbb####ffff	chrX:103435203-103435678(+)$1	475	168	181	21.6086
:::::::::gggg	chrX:108787285-108787776(+)$1	491	324	337	18.6739
""ccc!!a[====	chr5:10436092-10436530(+)$1	438	74	87	23.2391
[ffffff[ccc^^	chr4:139978486-139978807(-)$1	321	275	288	19.2173
===========::	chr9:110093292-110093612(+)$1	320	43	56	21.1739
nnnnddddeeeee	chr6:82456992-82457330(-)$1	338	19	32	18.6739
IIIIIII::::hh	chr1:183521180-183521602(+)$1	422	342	355	17.3695
ddd22ccc4444h	chr1:204519877-204520267(+)$1	390	297	310	23.2391
EEEEYYJJJJJJJ	chr10:11375319-11375631(+)$1	312	290	303	20.7391
+++++++++++++	chr5:64019475-64019775(-)$1	300	51	64	17.2608
:::::ffffffxx	chr7:133976468-133976742(-)$1	274	194	207	19.9782
::::::ddddppp	chr7:27565618-27565919(-)$1	301	240	253	19.9782
iiiiiiiii[eee	chr1:3697645-3697979(-)$1	334	62	75	20.0869
@@@@@@@@@FFFF	chr17:56050620-56050934(-)$1	314	253	266	22.0434
[ggggggg&&&&&	chr12:40153027-40153369(-)$1	342	221	234	19.7608
LHHHHHHHHLLLF	chr20:47790616-47790906(-)$1	290	82	95	22.5869
LLGGGGGGG::::	chr12:28459574-28459836(+)$1	262	75	88	24.1086
=====qqqqqqqq	chr1:167393921-167394385(+)$1	464	234	247	19.8695
cc]bb00000000	chr11:58385662-58386090(+)$1	428	384	397	22.6956
:::::::::::gg	chr1:155869351-155869802(-)$1	451	353	366	28.0217
^^^^^^^^^^^^^	chr1:26796530-26796923(+)$1	393	273	286	28.0217
@@@@@@@@@@@@@	chr17:78108919-78109322(-)$1	403	359	372	28.0217

#DB
)))))))))....	chr1:214522937-214523325(-)$1	1	147	160	17.3695
))))(((((....	chr9:80331863-80332177(-)$1	1	290	303	18.6739
...........))	chr11:85669403-85669713(-)$1	1	54	67	18.3478
.............	chr4:170641743-170642026(+)$1	1	258	271	23.8913
.............	chr5:32355387-32355654(-)$1	1	27	40	22.6956
.............	chr13:37586241-37586511(-)$1	1	58	71	22.4782
...((((((((((	chr10:70742201-70742678(+)$1	1	21	34	20.7391
.............	chr10:72185801-72186196(+)$1	1	218	231	24.1086
((((.........	chr1:61921119-61921365(+)$1	1	66	79	26.2826
)))..........	chr1:185069917-185070302(+)$1	1	114	127	23.2391
.)))))).(((((	chr4:39779883-39780320(+)$1	1	225	238	17.0434
)))..))......	chr8:99963915-99964238(+)$1	1	285	298	17.4782
.(((((((....(	chr2:206866782-206867067(-)$1	1	56	69	17.1521
)))))(((((((.	chr7:155256784-155257080(+)$1	1	61	74	19.1086
............(	chr4:99801826-99802085(-)$1	1	78	91	24.1086
))).........)	chr15:73595163-73595559(+)$1	1	262	275	17.2608
((((((.(((...	chr6:27820176-27820453(+)$1	1	159	172	16.6086
)))......))))	chr18:13762729-13763179(+)$1	1	208	221	17.3695
)....((((((((	chr9:132995381-132995672(+)$1	1	195	208	21.1739
...)))))))).)	chr8:17425197-17425604(+)$1	1	332	345	22.1521
(...(((((....	chr7:139256684-139257014(-)$1	1	140	153	20.0869
))))))).)))))	chr2:170668116-170668449(+)$1	1	269	282	19.2173
.............	chr3:158263093-158263359(+)$1	1	64	77	18.9999
((.((((......	chr11:118964481-118964936(-)$1	1	337	350	26.1739
(((((....((((	chrX:103435203-103435678(+)$1	1	168	181	21.6086
.........((((	chrX:108787285-108787776(+)$1	1	324	337	18.6739
..(((..(.((((	chr5:10436092-10436530(+)$1	1	74	87	23.2391
.((((((.(((..	chr4:139978486-139978807(-)$1	1	275	288	19.2173
)))))))))))..	chr9:110093292-110093612(+)$1	1	43	56	21.1739
....)))))))))	chr6:82456992-82457330(-)$1	1	19	32	18.6739
)))))))....((	chr1:183521180-183521602(+)$1	1	342	355	17.3695
)))..)))....)	chr1:204519877-204520267(+)$1	1	297	310	23.2391
))))..)))))))	chr10:11375319-11375631(+)$1	1	290	303	20.7391
.............	chr5:64019475-64019775(-)$1	1	51	64	17.2608
.....((((((..	chr7:133976468-133976742(-)$1	1	194	207	19.9782
......((((...	chr7:27565618-27565919(-)$1	1	240	253	19.9782
(((((((((.(((	chr1:3697645-3697979(-)$1	1	62	75	20.0869
.........))))	chr17:56050620-56050934(-)$1	1	253	266	22.0434
.(((((((.....	chr12:40153027-40153369(-)$1	1	221	234	19.7608
.((((((((...(	chr20:47790616-47790906(-)$1	1	82	95	22.5869
..(((((((....	chr12:28459574-28459836(+)$1	1	75	88	24.1086
(((((........	chr1:167393921-167394385(+)$1	1	234	247	19.8695
)).))........	chr11:58385662-58386090(+)$1	1	384	397	22.6956
...........((	chr1:155869351-155869802(-)$1	1	353	366	28.0217
.............	chr1:26796530-26796923(+)$1	1	273	286	28.0217
.............	chr17:78108919-78109322(-)$1	1	359	372	28.0217

#PSSM
U : 0.52	G : 0.19	u : 0.17	A : 0.10	
U : 0.69	u : 0.17	G : 0.08	C : 0.02	A : 0.02	
C : 0.41	A : 0.19	U : 0.13	c : 0.08	G : 0.08	g : 0.04	u : 0.02	a : 0.02	
U : 0.73	u : 0.15	A : 0.08	a : 0.02	
U : 0.76	u : 0.17	G : 0.04	C : 0.02	
U : 0.69	u : 0.17	C : 0.06	A : 0.04	G : 0.02	
U : 0.69	G : 0.10	u : 0.10	c : 0.02	a : 0.02	g : 0.02	A : 0.02	
U : 0.65	G : 0.13	u : 0.10	A : 0.04	g : 0.04	c : 0.02	
U : 0.67	u : 0.15	C : 0.08	A : 0.04	g : 0.02	G : 0.02	
U : 0.71	u : 0.15	G : 0.04	A : 0.04	C : 0.02	a : 0.02	
U : 0.69	u : 0.17	A : 0.04	C : 0.04	G : 0.04	
U : 0.78	u : 0.17	G : 0.02	C : 0.02	
U : 0.80	u : 0.15	A : 0.02	G : 0.02	

#score	968.130434782608
#seq	46
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1_Lebedeva2011_hg19_CDS_m2_run1.nuc.txt

#NT
UUAUAUUU	chr1:62907804-62908027(+)$1	223	64	72	15.6379
UUGUUUUU	chr10:30630304-30630556(-)$1	252	224	232	16.2413
UUAUUUUC	chr13:108882142-108882368(+)$1	226	108	116	15.3793
UUCUUUUU	chr17:34892967-34893208(+)$1	241	123	131	16.2413
UUAUUCUU	chr4:39512212-39512443(-)$1	231	191	199	15.4655
UUAUUUUC	chr19:3594739-3594971(-)$1	232	191	199	15.3793
UUGUUUUU	chr5:36116507-36116735(-)$1	228	20	28	16.2413
UUAUUUUU	chr1:186302307-186302540(-)$1	233	3	11	19.8620
UUAUUAUU	chr5:134231912-134232136(+)$1	224	111	119	15.4655
UGAUUUUU	chr1:63884952-63885186(+)$1	234	4	12	15.3793
UUAUUUAU	chr1:213037081-213037305(+)$1	224	108	116	15.5517
UUAUUUUU	chr9:123367816-123368090(-)$1	274	28	36	19.8620
UUGUUUUU	chr15:42823584-42823827(+)$1	243	15	23	16.2413
UUAUUUUU	chr6:57188935-57189158(+)$1	223	52	60	19.8620
UUCUUUUU	chr9:86584191-86584441(-)$1	250	133	141	16.2413
UUAUUUUU	chr2:196544704-196544931(+)$1	227	111	119	19.8620
UGAUUUUU	chr8:38961084-38961386(+)$1	302	132	140	15.3793
CUAUUUUU	chr2:178362337-178362563(+)$1	226	106	114	15.7241
CUAUUUUU	chr11:121174108-121174340(+)$1	232	5	13	15.7241
uuacuuuu	chr19:18390706-18390940(-)$1	234	53	61	15.8103
UUCUUUUU	chr20:52835585-52835870(+)$1	285	197	205	16.2413
UUGUUUUU	chr9:88592141-88592388(+)$1	247	124	132	16.2413
UUAUGUUU	chr3:148767926-148768151(-)$1	225	33	41	15.3793
AUAUUUUU	chr8:17921910-17922135(-)$1	225	113	121	15.7241
UUGUUUUU	chr5:108672956-108673183(-)$1	227	7	15	16.2413
UUAUAUUU	chr21:34715766-34715992(+)$1	226	57	65	15.6379
UUAAUUUU	chr5:134079620-134079869(+)$1	249	31	39	15.8965
UUAUAUUU	chr5:133292569-133292858(-)$1	289	75	83	15.6379
GUAUUUUU	chr9:103109491-103109713(-)$1	222	9	17	15.5517
UUAUUGUU	chr1:205683552-205683821(-)$1	269	58	66	15.3793
UUAUUUUU	chr4:54915322-54915549(-)$1	227	61	69	19.8620
UUAUUUAU	chr11:71149995-71150217(-)$1	222	71	79	15.5517
AUAUUUUU	chr1:246707772-246707996(-)$1	224	109	117	15.7241
AUAUUUUU	chr12:46591649-46591879(-)$1	230	160	168	15.7241
UUAUUCUU	chr5:134235167-134235401(+)$1	234	112	120	15.4655
UUAUUAUU	chr12:57066491-57066722(-)$1	231	70	78	15.4655
UUUUUUUU	chr1:100588690-100588914(-)$1	224	105	113	15.8965
uuauauuu	chr14:35222740-35222995(-)$1	255	25	33	15.6379
UUACUUUU	chr8:124267821-124268087(-)$1	266	154	162	15.8103
UUAAUUUU	chrM:9999-10227(+)$1	228	72	80	15.8965
UUAUUUUU	chr12:102154932-102155163(-)$1	231	111	119	19.8620
UUCUUUUU	chr19:32930597-32930825(+)$1	228	72	80	16.2413
CUAUUUUU	chr4:139093069-139093330(-)$1	261	100	108	15.7241
UUAUUUUU	chr1:40756456-40756679(+)$1	223	190	198	19.8620
UUAUUUAU	chr3:194168493-194168716(-)$1	223	174	182	15.5517
UUACUUUU	chr2:223489393-223489629(-)$1	236	108	116	15.8103
UUAUUUUU	chr6:136564008-136564242(-)$1	234	25	33	19.8620
uuaauuuu	chr2:183821157-183821385(-)$1	228	3	11	15.8965
UUCUUUUU	chr1:40735617-40735850(+)$1	233	17	25	16.2413
UCAUUUUU	chr7:888005-888229(+)$1	224	114	122	15.3793
UUAUUUAU	chr4:85730961-85731195(-)$1	234	116	124	15.5517
UUAUUUUA	chr10:70721763-70721989(+)$1	226	188	196	15.3793
uuauuuua	chr3:31641768-31641999(+)$1	231	31	39	15.3793
UCAUUUUU	chr2:86344122-86344355(+)$1	233	58	66	15.3793
UUAGUUUU	chr2:38973761-38974010(-)$1	249	14	22	15.6379
UUAUUUUU	chr4:38691226-38691455(+)$1	229	112	120	19.8620
UUAAUUUU	chr13:96443144-96443447(+)$1	303	162	170	15.8965

#otherMatches

#Struct PSSM
:::HHHHH	chr4:159636389-159636611(-)$1	222	183	191	19.8620
ggg[bb""	chr1:62907804-62908027(+)$1	223	64	72	15.6379
iiiiiiii	chr10:30630304-30630556(-)$1	252	224	232	16.2413
[bb^^^^^	chr13:108882142-108882368(+)$1	226	108	116	15.3793
EEEE::::	chr17:34892967-34893208(+)$1	241	123	131	16.2413
ooeeeee]	chr4:39512212-39512443(-)$1	231	191	199	15.4655
:EEEEEFF	chr19:3594739-3594971(-)$1	232	191	199	15.3793
ggggggHH	chr5:36116507-36116735(-)$1	228	20	28	16.2413
::::::::	chr1:186302307-186302540(-)$1	233	3	11	19.8620
oooodddd	chr5:134231912-134232136(+)$1	224	111	119	15.4655
EE{JJJJJ	chr1:63884952-63885186(+)$1	234	4	12	15.3793
^^^^^^^^	chr1:213037081-213037305(+)$1	224	108	116	15.5517
GGGGGG{D	chr9:123367816-123368090(-)$1	274	28	36	19.8620
ccc####c	chr15:42823584-42823827(+)$1	243	15	23	16.2413
C:::gggg	chr6:57188935-57189158(+)$1	223	52	60	19.8620
pdddd:ee	chr9:86584191-86584441(-)$1	250	133	141	16.2413
DDD{DDDD	chr2:196544704-196544931(+)$1	227	111	119	19.8620
$ccc[ccc	chr8:38961084-38961386(+)$1	302	132	140	15.3793
dddxxxxx	chr2:178362337-178362563(+)$1	226	106	114	15.7241
EE::::::	chr11:121174108-121174340(+)$1	232	5	13	15.7241
::::::::	chr19:18390706-18390940(-)$1	234	53	61	15.8103
ffff::::	chr20:52835585-52835870(+)$1	285	197	205	16.2413
::::::::	chr9:88592141-88592388(+)$1	247	124	132	16.2413
]ffffff:	chr3:148767926-148768151(-)$1	225	33	41	15.3793
[bbnnnnn	chr8:17921910-17922135(-)$1	225	113	121	15.7241
::::::::	chr5:108672956-108673183(-)$1	227	7	15	16.2413
eeeeehhh	chr21:34715766-34715992(+)$1	226	57	65	15.6379
fffff333	chr5:134079620-134079869(+)$1	249	31	39	15.8965
QQQQFFFF	chr5:133292569-133292858(-)$1	289	75	83	15.6379
::::::::	chr9:103109491-103109713(-)$1	222	9	17	15.5517
ff!!eeee	chr1:205683552-205683821(-)$1	269	58	66	15.3793
::::::::	chr4:54915322-54915549(-)$1	227	61	69	19.8620
rrrrrggg	chr11:71149995-71150217(-)$1	222	71	79	15.5517
qqqqa22d	chr1:246707772-246707996(-)$1	224	109	117	15.7241
nnnccc]e	chr12:46591649-46591879(-)$1	230	160	168	15.7241
LLLGGGGG	chr5:134235167-134235401(+)$1	234	112	120	15.4655
iiiii:::	chr12:57066491-57066722(-)$1	231	70	78	15.4655
::::::::	chr1:100588690-100588914(-)$1	224	105	113	15.8965
hhhhhnnn	chr14:35222740-35222995(-)$1	255	25	33	15.6379
rrrrrrrr	chr8:124267821-124268087(-)$1	266	154	162	15.8103
^^^^^^^^	chrM:9999-10227(+)$1	228	72	80	15.8965
eeeeuuuu	chr12:102154932-102155163(-)$1	231	111	119	19.8620
JJJJJ~~~	chr19:32930597-32930825(+)$1	228	72	80	16.2413
ggggggg4	chr4:139093069-139093330(-)$1	261	100	108	15.7241
::::::::	chr1:40756456-40756679(+)$1	223	190	198	19.8620
g^^^^^^^	chr3:194168493-194168716(-)$1	223	174	182	15.5517
dddnnnnn	chr2:223489393-223489629(-)$1	236	108	116	15.8103
:::::FFF	chr6:136564008-136564242(-)$1	234	25	33	19.8620
::::::::	chr2:183821157-183821385(-)$1	228	3	11	15.8965
!ffffffb	chr1:40735617-40735850(+)$1	233	17	25	16.2413
e:::::::	chr7:888005-888229(+)$1	224	114	122	15.3793
vvvvvvvv	chr4:85730961-85731195(-)$1	234	116	124	15.5517
::======	chr10:70721763-70721989(+)$1	226	188	196	15.3793
::::::::	chr3:31641768-31641999(+)$1	231	31	39	15.3793
eeeeeeee	chr2:86344122-86344355(+)$1	233	58	66	15.3793
::::::ff	chr2:38973761-38974010(-)$1	249	14	22	15.6379
gggg!!ff	chr4:38691226-38691455(+)$1	229	112	120	19.8620
Eggggggg	chr13:96443144-96443447(+)$1	303	162	170	15.8965

#DB
...)))))	chr4:159636389-159636611(-)$1	1	183	191	19.8620
(((.((..	chr1:62907804-62908027(+)$1	1	64	72	15.6379
))))))))	chr10:30630304-30630556(-)$1	1	224	232	16.2413
.((.....	chr13:108882142-108882368(+)$1	1	108	116	15.3793
))))....	chr17:34892967-34893208(+)$1	1	123	131	16.2413
..))))).	chr4:39512212-39512443(-)$1	1	191	199	15.4655
.)))))))	chr19:3594739-3594971(-)$1	1	191	199	15.3793
))))))((	chr5:36116507-36116735(-)$1	1	20	28	16.2413
........	chr1:186302307-186302540(-)$1	1	3	11	19.8620
....))))	chr5:134231912-134232136(+)$1	1	111	119	15.4655
((.(((((	chr1:63884952-63885186(+)$1	1	4	12	15.3793
........	chr1:213037081-213037305(+)$1	1	108	116	15.5517
((((((.(	chr9:123367816-123368090(-)$1	1	28	36	19.8620
(((....(	chr15:42823584-42823827(+)$1	1	15	23	16.2413
(...((((	chr6:57188935-57189158(+)$1	1	52	60	19.8620
.)))).((	chr9:86584191-86584441(-)$1	1	133	141	16.2413
(((.((((	chr2:196544704-196544931(+)$1	1	111	119	19.8620
.(((.(((	chr8:38961084-38961386(+)$1	1	132	140	15.3793
(((.....	chr2:178362337-178362563(+)$1	1	106	114	15.7241
((......	chr11:121174108-121174340(+)$1	1	5	13	15.7241
........	chr19:18390706-18390940(-)$1	1	53	61	15.8103
))))....	chr20:52835585-52835870(+)$1	1	197	205	16.2413
........	chr9:88592141-88592388(+)$1	1	124	132	16.2413
.)))))).	chr3:148767926-148768151(-)$1	1	33	41	15.3793
.((.....	chr8:17921910-17922135(-)$1	1	113	121	15.7241
........	chr5:108672956-108673183(-)$1	1	7	15	16.2413
((((((((	chr21:34715766-34715992(+)$1	1	57	65	15.6379
)))))...	chr5:134079620-134079869(+)$1	1	31	39	15.8965
....((((	chr5:133292569-133292858(-)$1	1	75	83	15.6379
........	chr9:103109491-103109713(-)$1	1	9	17	15.5517
((..((((	chr1:205683552-205683821(-)$1	1	58	66	15.3793
........	chr4:54915322-54915549(-)$1	1	61	69	19.8620
.....)))	chr11:71149995-71150217(-)$1	1	71	79	15.5517
....)..)	chr1:246707772-246707996(-)$1	1	109	117	15.7241
...))).)	chr12:46591649-46591879(-)$1	1	160	168	15.7241
...(((((	chr5:134235167-134235401(+)$1	1	112	120	15.4655
)))))...	chr12:57066491-57066722(-)$1	1	70	78	15.4655
........	chr1:100588690-100588914(-)$1	1	105	113	15.8965
(((((...	chr14:35222740-35222995(-)$1	1	25	33	15.6379
........	chr8:124267821-124268087(-)$1	1	154	162	15.8103
........	chrM:9999-10227(+)$1	1	72	80	15.8965
((((....	chr12:102154932-102155163(-)$1	1	111	119	19.8620
)))))...	chr19:32930597-32930825(+)$1	1	72	80	16.2413
))))))).	chr4:139093069-139093330(-)$1	1	100	108	15.7241
........	chr1:40756456-40756679(+)$1	1	190	198	19.8620
(.......	chr3:194168493-194168716(-)$1	1	174	182	15.5517
(((.....	chr2:223489393-223489629(-)$1	1	108	116	15.8103
.....(((	chr6:136564008-136564242(-)$1	1	25	33	19.8620
........	chr2:183821157-183821385(-)$1	1	3	11	15.8965
.(((((((	chr1:40735617-40735850(+)$1	1	17	25	16.2413
).......	chr7:888005-888229(+)$1	1	114	122	15.3793
........	chr4:85730961-85731195(-)$1	1	116	124	15.5517
..((((((	chr10:70721763-70721989(+)$1	1	188	196	15.3793
........	chr3:31641768-31641999(+)$1	1	31	39	15.3793
((((((((	chr2:86344122-86344355(+)$1	1	58	66	15.3793
......((	chr2:38973761-38974010(-)$1	1	14	22	15.6379
((((..((	chr4:38691226-38691455(+)$1	1	112	120	19.8620
)(((((((	chr13:96443144-96443447(+)$1	1	162	170	15.8965

#PSSM
U : 0.79	u : 0.08	C : 0.05	A : 0.05	G : 0.01	
U : 0.84	u : 0.08	G : 0.03	C : 0.03	
A : 0.72	a : 0.08	G : 0.08	C : 0.08	U : 0.01	
U : 0.81	u : 0.05	A : 0.05	C : 0.03	c : 0.01	a : 0.01	G : 0.01	
U : 0.84	u : 0.06	A : 0.05	G : 0.01	a : 0.01	
U : 0.82	u : 0.08	C : 0.03	A : 0.03	G : 0.01	
U : 0.84	u : 0.08	A : 0.06	
U : 0.86	u : 0.06	C : 0.03	A : 0.01	a : 0.01	

#score	953.8965517241381
#seq	58
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m2_run2.nuc.txt

#NT
GAGGAGGAAG	chr1:1413986-1414216(+)$1	230	96	106	17.0588
gaagaggagg	chr9:131456076-131456317(+)$1	241	152	162	15.8823
gcgggggcgg	chr16:447128-447352(+)$1	224	18	28	13.1372
GGGGAGUCGG	chr17:7788242-7788471(-)$1	229	47	57	13.0392
gaggaggcag	chr9:131260677-131260912(+)$1	235	167	177	18.0392
GAGGAGAAGG	chr1:85725193-85725418(-)$1	225	111	121	15.5882
AAGAAGGCGG	chr6:26273091-26273314(+)$1	223	157	167	13.6274
gaggaggagg	chr14:100705602-100705847(+)$1	245	105	115	20.0000
AAGGAGGCAG	chr22:37966302-37966522(+)$1	220	137	147	14.7058
GAGGAGCGGG	chr17:43226582-43226816(+)$1	234	83	93	14.1176
GACGAGGAGG	chr5:180687234-180687468(-)$1	234	17	27	15.6862
GCGGAGCCGG	chr16:29818819-29819047(+)$1	228	11	21	13.0392
GUGGAGGCUG	chr3:12458207-12458441(+)$1	234	127	137	13.9215
CAGGAGGCAG	chr1:155110377-155110597(-)$1	220	63	73	14.3137
GAUGAGGAGG	chr17:7245259-7245484(+)$1	225	166	176	15.7843
GAGACGGCGG	chr21:44515477-44515703(-)$1	226	170	180	13.0392
gaggaagcug	chr16:53843950-53844207(+)$1	257	243	253	13.6274
GAGGAUGGGG	chr20:30136768-30136995(+)$1	227	177	187	14.5098
GAGGAUGCGG	chr3:183882576-183882806(+)$1	230	203	213	17.1568
AAGAAGGCGG	chr17:79846989-79847219(-)$1	230	41	51	13.6274
GAGGAGCCCG	chr20:61510849-61511088(-)$1	239	81	91	13.8235
GAGGAGGCCU	chr17:7157921-7158148(+)$1	227	29	39	13.6274
AAGGAGGAGG	chr20:51871854-51872081(+)$1	227	96	106	16.6666
GAGGCGGCGG	chr6:2765967-2766190(+)$1	223	98	108	17.0588
gaggaggcgg	chrX:114468370-114468590(-)$1	220	2	12	20.9803
gaGGAGGAGG	chr2:232325325-232325600(-)$1	275	193	203	20.0000
AAGGAGGCCG	chr17:54990973-54991194(-)$1	221	178	188	14.7058
gaggaggaug	chr2:232326151-232326395(-)$1	244	0	10	16.7647
GAGGGGGCGG	chr11:130297598-130297819(+)$1	221	100	110	16.8627
GAGGUGGCGG	chr10:120863559-120863805(+)$1	246	107	117	16.7647
ggggcggcgg	chr7:74489428-74489651(-)$1	223	113	123	13.5294
GAGGAGGAGC	chr15:89173403-89173626(+)$1	223	84	94	15.5882
GGUGAGGCGG	chr10:135085262-135085481(-)$1	219	171	181	13.2352
CUGGAGGCGG	chr20:17608061-17608284(-)$1	223	97	107	13.4313
gcggcggcgg	chr16:29818521-29818746(+)$1	225	56	66	13.3333
GAGGAGGCGG	chr4:119606601-119606855(-)$1	254	38	48	20.9803
gaggaggagg	chr4:142154889-142155118(+)$1	229	98	108	20.0000
AAGGAGGCAG	chrX:153581584-153581807(-)$1	223	175	185	14.7058
GAGGAUGCGA	chr16:53859850-53860080(-)$1	230	134	144	12.9411
GGGGAGGCAG	chr5:180670212-180670478(-)$1	266	187	197	14.5098
AAGGAAGAGG	chr12:109530294-109530521(-)$1	227	40	50	12.5490
GAGGAGGAGA	chr22:50716464-50716708(-)$1	244	22	32	15.7843
GAGGAGGCCA	chrX:129139083-129139310(+)$1	227	212	222	13.8235
GAAGAGGACG	chr6:3089763-3089986(+)$1	223	104	114	12.9411
GAGAAGGAGG	chr4:1820976-1821205(-)$1	229	90	100	15.9803
GAGgaugacg	chr17:42284588-42284826(-)$1	238	97	107	13.2352
gaggaggagg	chr2:55277167-55277440(-)$1	273	115	125	20.0000
CAGGAUGAGG	chr17:74077955-74078176(-)$1	221	52	62	12.4509
GGGGAGGAGG	chr19:46002632-46002851(+)$1	219	103	113	16.4705
GAAGAGGUGG	chr9:86586885-86587109(-)$1	224	129	139	14.1176

#otherMatches

#Struct PSSM
dd]eeeee]d	chr1:28845051-28845283(+)$1	232	167	177	16.9607
vvvvvvvvvv	chr1:1413986-1414216(+)$1	230	96	106	17.0588
::::::::::	chr9:131456076-131456317(+)$1	241	152	162	15.8823
a[hhhhhhhh	chr16:447128-447352(+)$1	224	18	28	13.1372
chhhhhhhhe	chr17:7788242-7788471(-)$1	229	47	57	13.0392
]ccc333bb]	chr9:131260677-131260912(+)$1	235	167	177	18.0392
ffffqqqqqq	chr1:85725193-85725418(-)$1	225	111	121	15.5882
88888bb]a]	chr6:26273091-26273314(+)$1	223	157	167	13.6274
E{BB{BB{BB	chr14:100705602-100705847(+)$1	245	105	115	20.0000
DDDD}CCC}B	chr22:37966302-37966522(+)$1	220	137	147	14.7058
""ccc[ccc[	chr17:43226582-43226816(+)$1	234	83	93	14.1176
{BBKKBB:EE	chr5:180687234-180687468(-)$1	234	17	27	15.6862
CCCKKEEEEE	chr16:29818819-29819047(+)$1	228	11	21	13.0392
]bb]ccceee	chr3:12458207-12458441(+)$1	234	127	137	13.9215
:FFFFFFLLL	chr1:155110377-155110597(-)$1	220	63	73	14.3137
YYA}EEEEE}	chr17:7245259-7245484(+)$1	225	166	176	15.7843
boooooobb]	chr21:44515477-44515703(-)$1	226	170	180	13.0392
ffff:FFFFF	chr16:53843950-53844207(+)$1	257	243	253	13.6274
GGGG}A}DDD	chr20:30136768-30136995(+)$1	227	177	187	14.5098
eooooooeee	chr3:183882576-183882806(+)$1	230	203	213	17.1568
oooooddddf	chr17:79846989-79847219(-)$1	230	41	51	13.6274
FFF::::BB{	chr20:61510849-61511088(-)$1	239	81	91	13.8235
CCEEEEEbbo	chr17:7157921-7158148(+)$1	227	29	39	13.6274
nnnnccc]cc	chr20:51871854-51872081(+)$1	227	96	106	16.6666
a22cccffff	chr6:2765967-2766190(+)$1	223	98	108	17.0588
DDDDKKBBCC	chrX:114468370-114468590(-)$1	220	2	12	20.9803
[dddd'''''	chr2:232325325-232325600(-)$1	275	193	203	20.0000
22a]hhhhhh	chr17:54990973-54991194(-)$1	221	178	188	14.7058
:EEEEE{CCC	chr2:232326151-232326395(-)$1	244	0	10	16.7647
=======ddd	chr11:130297598-130297819(+)$1	221	100	110	16.8627
ggggggg[bb	chr10:120863559-120863805(+)$1	246	107	117	16.7647
iooooooiii	chr7:74489428-74489651(-)$1	223	113	123	13.5294
!!eeeee===	chr15:89173403-89173626(+)$1	223	84	94	15.5882
dddd]ggggg	chr10:135085262-135085481(-)$1	219	171	181	13.2352
b[ffffff[d	chr20:17608061-17608284(-)$1	223	97	107	13.4313
ggggggg]cc	chr16:29818521-29818746(+)$1	225	56	66	13.3333
A{CCCFFFFF	chr4:119606601-119606855(-)$1	254	38	48	20.9803
oooa]bb]bb	chr4:142154889-142155118(+)$1	229	98	108	20.0000
""eeeee!!b	chrX:153581584-153581807(-)$1	223	175	185	14.7058
beeeee[ddd	chr16:53859850-53860080(-)$1	230	134	144	12.9411
iieeeee[dd	chr5:180670212-180670478(-)$1	266	187	197	14.5098
:::::bb[dd	chr12:109530294-109530521(-)$1	227	40	50	12.5490
G{BB{DDDDN	chr22:50716464-50716708(-)$1	244	22	32	15.7843
EEEEEYYGGG	chrX:129139083-129139310(+)$1	227	212	222	13.8235
666666iiii	chr6:3089763-3089986(+)$1	223	104	114	12.9411
++++++++++	chr4:1820976-1821205(-)$1	229	90	100	15.9803
hhhhhhh22c	chr17:42284588-42284826(-)$1	238	97	107	13.2352
::BB}BB}BB	chr2:55277167-55277440(-)$1	273	115	125	20.0000
nccc]bb]cc	chr17:74077955-74078176(-)$1	221	52	62	12.4509
>>>>>>>iii	chr19:46002632-46002851(+)$1	219	103	113	16.4705
::::ccc[cc	chr9:86586885-86587109(-)$1	224	129	139	14.1176

#DB
)).))))).)	chr1:28845051-28845283(+)$1	1	167	177	16.9607
..........	chr1:1413986-1414216(+)$1	1	96	106	17.0588
..........	chr9:131456076-131456317(+)$1	1	152	162	15.8823
(.((((((((	chr16:447128-447352(+)$1	1	18	28	13.1372
))))))))))	chr17:7788242-7788471(-)$1	1	47	57	13.0392
.)))...)).	chr9:131260677-131260912(+)$1	1	167	177	18.0392
((((......	chr1:85725193-85725418(-)$1	1	111	121	15.5882
.....)).).	chr6:26273091-26273314(+)$1	1	157	167	13.6274
(.((.((.((	chr14:100705602-100705847(+)$1	1	105	115	20.0000
)))).))).)	chr22:37966302-37966522(+)$1	1	137	147	14.7058
..(((.(((.	chr17:43226582-43226816(+)$1	1	83	93	14.1176
.((..((.((	chr5:180687234-180687468(-)$1	1	17	27	15.6862
(((..(((((	chr16:29818819-29819047(+)$1	1	11	21	13.0392
.)).)))(((	chr3:12458207-12458441(+)$1	1	127	137	13.9215
.((((((...	chr1:155110377-155110597(-)$1	1	63	73	14.3137
..).))))).	chr17:7245259-7245484(+)$1	1	166	176	15.7843
(......)).	chr21:44515477-44515703(-)$1	1	170	180	13.0392
)))).)))))	chr16:53843950-53844207(+)$1	1	243	253	13.6274
)))).).)))	chr20:30136768-30136995(+)$1	1	177	187	14.5098
(......)))	chr3:183882576-183882806(+)$1	1	203	213	17.1568
.....))))(	chr17:79846989-79847219(-)$1	1	41	51	13.6274
(((....((.	chr20:61510849-61511088(-)$1	1	81	91	13.8235
(((((((((.	chr17:7157921-7158148(+)$1	1	29	39	13.6274
....))).))	chr20:51871854-51872081(+)$1	1	96	106	16.6666
)..)))((((	chr6:2765967-2766190(+)$1	1	98	108	17.0588
((((..((((	chrX:114468370-114468590(-)$1	1	2	12	20.9803
.((((.....	chr2:232325325-232325600(-)$1	1	193	203	20.0000
..).))))))	chr17:54990973-54991194(-)$1	1	178	188	14.7058
.(((((.(((	chr2:232326151-232326395(-)$1	1	0	10	16.7647
))))))))))	chr11:130297598-130297819(+)$1	1	100	110	16.8627
(((((((.((	chr10:120863559-120863805(+)$1	1	107	117	16.7647
(......)))	chr7:74489428-74489651(-)$1	1	113	123	13.5294
..((((((((	chr15:89173403-89173626(+)$1	1	84	94	15.5882
)))).)))))	chr10:135085262-135085481(-)$1	1	171	181	13.2352
(.((((((.(	chr20:17608061-17608284(-)$1	1	97	107	13.4313
))))))).))	chr16:29818521-29818746(+)$1	1	56	66	13.3333
(.((((((((	chr4:119606601-119606855(-)$1	1	38	48	20.9803
...).)).))	chr4:142154889-142155118(+)$1	1	98	108	20.0000
..(((((..(	chrX:153581584-153581807(-)$1	1	175	185	14.7058
)(((((.(((	chr16:53859850-53860080(-)$1	1	134	144	12.9411
))(((((.((	chr5:180670212-180670478(-)$1	1	187	197	14.5098
.....((.((	chr12:109530294-109530521(-)$1	1	40	50	12.5490
(.((.((((.	chr22:50716464-50716708(-)$1	1	22	32	15.7843
)))))..)))	chrX:129139083-129139310(+)$1	1	212	222	13.8235
......))))	chr6:3089763-3089986(+)$1	1	104	114	12.9411
..........	chr4:1820976-1821205(-)$1	1	90	100	15.9803
)))))))..)	chr17:42284588-42284826(-)$1	1	97	107	13.2352
..)).)).))	chr2:55277167-55277440(-)$1	1	115	125	20.0000
.))).)).))	chr17:74077955-74078176(-)$1	1	52	62	12.4509
.......)))	chr19:46002632-46002851(+)$1	1	103	113	16.4705
....(((.((	chr9:86586885-86587109(-)$1	1	129	139	14.1176

#PSSM
G : 0.56	g : 0.23	A : 0.13	C : 0.05	
A : 0.62	a : 0.17	G : 0.07	c : 0.03	U : 0.03	C : 0.01	g : 0.01	
G : 0.68	g : 0.19	U : 0.03	A : 0.03	a : 0.01	C : 0.01	
G : 0.66	g : 0.23	A : 0.09	
A : 0.68	a : 0.17	C : 0.03	c : 0.03	g : 0.01	G : 0.01	U : 0.01	
G : 0.66	g : 0.19	U : 0.07	a : 0.01	A : 0.01	u : 0.01	
G : 0.66	g : 0.23	C : 0.05	U : 0.01	A : 0.01	
C : 0.45	A : 0.25	a : 0.11	c : 0.11	G : 0.03	U : 0.01	
G : 0.54	g : 0.15	A : 0.09	C : 0.09	u : 0.03	a : 0.01	U : 0.01	c : 0.01	
G : 0.66	g : 0.23	A : 0.05	U : 0.01	C : 0.01	

#score	783.7254901960788
#seq	51
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_EWSR1_hg19_CDS_m1_run1.nuc.txt

#NT
GAAA	chr3:156877111-156877332(-)$1	221	180	184	12.0000
GAAA	chr19:40542170-40542402(-)$1	232	78	82	12.0000
GAAA	chr2:183888494-183888725(-)$1	231	143	147	12.0000
GAAA	chr10:129903295-129903514(-)$1	219	1	5	12.0000
GAAA	chr10:129900758-129901019(-)$1	261	125	129	12.0000
GAAA	chr19:39329456-39329685(-)$1	229	32	36	12.0000
GAAA	chr16:19554122-19554354(+)$1	232	89	93	12.0000
GAAA	chr3:98309402-98309626(-)$1	224	172	176	12.0000
GAAA	chr7:127013434-127013658(-)$1	224	139	143	12.0000
GAAA	chr18:9257118-9257347(+)$1	229	212	216	12.0000
GAAA	chr4:187539797-187540021(-)$1	224	5	9	12.0000
GAAA	chr17:38290019-38290253(+)$1	234	62	66	12.0000
GAAA	chr20:17956387-17956627(+)$1	240	19	23	12.0000
GAAA	chr4:187584353-187584578(-)$1	225	87	91	12.0000
GAAA	chr6:87967638-87967862(+)$1	224	83	87	12.0000
GAAA	chr22:32111595-32111817(-)$1	222	217	221	12.0000
GAAA	chr10:129905124-129905371(-)$1	247	5	9	12.0000
GAAA	chr19:37239765-37239987(-)$1	222	55	59	12.0000
GAAA	chrM:9931-10243(-)$1	312	31	35	12.0000
GAAA	chr7:97821839-97822059(+)$1	220	98	102	12.0000
GAAA	chr19:21300581-21300815(+)$1	234	67	71	12.0000
GAAA	chr17:27016997-27017230(+)$1	233	225	229	12.0000
GAAA	chr14:21894242-21894465(-)$1	223	36	40	12.0000
GAAA	chr12:67700067-67700287(+)$1	220	72	76	12.0000
GAAA	chr4:128726197-128726423(+)$1	226	59	63	12.0000
GAAA	chr4:39457937-39458172(-)$1	235	92	96	12.0000
GAAA	chr19:53884324-53884546(+)$1	222	141	145	12.0000
GAAA	chrX:14883061-14883287(-)$1	226	9	13	12.0000
GAAA	chr16:19548049-19548277(+)$1	228	149	153	12.0000
GAAA	chr8:71126081-71126321(-)$1	240	27	31	12.0000
GAAA	chr5:112177077-112177298(+)$1	221	58	62	12.0000
GAAA	chr9:95078238-95078465(-)$1	227	170	174	12.0000
GAAA	chr17:60088110-60088341(-)$1	231	39	43	12.0000
GAAA	chr11:32954685-32954920(+)$1	235	144	148	12.0000
GAAA	chr11:10823564-10823789(-)$1	225	184	188	12.0000
GAAA	chrM:14820-15059(+)$1	239	18	22	12.0000
GAAA	chr8:29921240-29921459(-)$1	219	60	64	12.0000
GAAA	chr1:222806448-222806672(+)$1	224	92	96	12.0000
GAAA	chr10:120830369-120830611(-)$1	242	163	167	12.0000
GAAA	chr5:122713969-122714196(-)$1	227	99	103	12.0000
GAAA	chr11:121177977-121178202(+)$1	225	167	171	12.0000
GAAA	chr1:203818983-203819211(+)$1	228	13	17	12.0000
GAAA	chr9:74344871-74345096(-)$1	225	99	103	12.0000
GAAA	chr6:87968235-87968464(+)$1	229	3	7	12.0000
GAAA	chr2:26461702-26461923(-)$1	221	183	187	12.0000
GAAA	chr3:169496604-169496830(+)$1	226	85	89	12.0000
GAAA	chr16:14041708-14041943(+)$1	235	192	196	12.0000
GAAA	chr4:48569286-48569509(-)$1	223	94	98	12.0000
GAAA	chr10:7866283-7866515(+)$1	232	185	189	12.0000
GAAA	chr19:9721425-9721659(-)$1	234	68	72	12.0000
GAAA	chr1:59131120-59131344(-)$1	224	10	14	12.0000
GAAA	chr10:22617508-22617727(+)$1	219	75	79	12.0000
GAAA	chr14:102550167-102550399(-)$1	232	158	162	12.0000
GAAA	chr17:1582235-1582480(-)$1	245	151	155	12.0000
GAAA	chr3:160151361-160151585(+)$1	224	123	127	12.0000
GAAA	chr9:103108293-103108515(-)$1	222	125	129	12.0000
GAAA	chr14:91947843-91948079(-)$1	236	15	19	12.0000
GAAA	chr11:68305049-68305272(+)$1	223	7	11	12.0000
GAAA	chr12:12653369-12653601(-)$1	232	30	34	12.0000
GAAA	chr1:91406135-91406363(-)$1	228	151	155	12.0000
GAAA	chr2:30785014-30785240(+)$1	226	37	41	12.0000
gaaa	chr12:80189379-80189603(-)$1	224	69	73	12.0000
GAAA	chr8:42977352-42977581(+)$1	229	98	102	12.0000
GAAA	chr10:98287069-98287301(-)$1	232	165	169	12.0000
GAAA	chr13:23908523-23908744(-)$1	221	162	166	12.0000
GAAA	chr14:96779597-96779831(-)$1	234	7	11	12.0000
GAAA	chr6:57012354-57012578(+)$1	224	39	43	12.0000
GAAA	chr19:48830735-48830963(+)$1	228	62	66	12.0000
GAAA	chr7:64168345-64168578(+)$1	233	93	97	12.0000
GAAA	chr2:200803558-200803780(-)$1	222	3	7	12.0000
Gaaa	chr11:4130805-4131033(+)$1	228	15	19	12.0000
GAAA	chr5:74077160-74077388(+)$1	228	13	17	12.0000
GAAA	chr2:183831897-183832123(-)$1	226	89	93	12.0000
GAAA	chr1:78045177-78045398(-)$1	221	2	6	12.0000
GAAA	chr17:49052103-49052328(-)$1	225	44	48	12.0000
GAAA	chr14:55510780-55511037(+)$1	257	223	227	12.0000
GAAA	chr7:17838567-17838790(-)$1	223	76	80	12.0000
GAAA	chr10:5772998-5773229(+)$1	231	154	158	12.0000
GAAA	chr5:112175984-112176210(+)$1	226	23	27	12.0000
GAAA	chr5:82876055-82876279(+)$1	224	98	102	12.0000
GAAA	chr11:62291706-62291929(-)$1	223	84	88	12.0000
GAAA	chr2:183866835-183867057(-)$1	222	20	24	12.0000
GAAA	chr12:46245471-46245695(+)$1	224	3	7	12.0000
GAAA	chr12:42503355-42503581(-)$1	226	42	46	12.0000
GAAA	chr10:119043222-119043450(-)$1	228	187	191	12.0000

#otherMatches

#Struct PSSM
CCC:	chr11:64851093-64851327(-)$1	234	178	182	12.0000
CCFF	chr3:156877111-156877332(-)$1	221	180	184	12.0000
bb22	chr19:40542170-40542402(-)$1	232	78	82	12.0000
ffll	chr2:183888494-183888725(-)$1	231	143	147	12.0000
::::	chr10:129903295-129903514(-)$1	219	1	5	12.0000
ee22	chr10:129900758-129901019(-)$1	261	125	129	12.0000
ddll	chr19:39329456-39329685(-)$1	229	32	36	12.0000
JJJJ	chr16:19554122-19554354(+)$1	232	89	93	12.0000
b:::	chr3:98309402-98309626(-)$1	224	172	176	12.0000
dd!!	chr7:127013434-127013658(-)$1	224	139	143	12.0000
ffff	chr18:9257118-9257347(+)$1	229	212	216	12.0000
C:::	chr4:187539797-187540021(-)$1	224	5	9	12.0000
gggg	chr17:38290019-38290253(+)$1	234	62	66	12.0000
mmmm	chr20:17956387-17956627(+)$1	240	19	23	12.0000
dmmm	chr4:187584353-187584578(-)$1	225	87	91	12.0000
DD::	chr6:87967638-87967862(+)$1	224	83	87	12.0000
::::	chr22:32111595-32111817(-)$1	222	217	221	12.0000
e###	chr10:129905124-129905371(-)$1	247	5	9	12.0000
f333	chr19:37239765-37239987(-)$1	222	55	59	12.0000
bb!!	chrM:9931-10243(-)$1	312	31	35	12.0000
ggg:	chr7:97821839-97822059(+)$1	220	98	102	12.0000
cmmm	chr19:21300581-21300815(+)$1	234	67	71	12.0000
b:::	chr17:27016997-27017230(+)$1	233	225	229	12.0000
DD::	chr14:21894242-21894465(-)$1	223	36	40	12.0000
booo	chr12:67700067-67700287(+)$1	220	72	76	12.0000
:::=	chr4:128726197-128726423(+)$1	226	59	63	12.0000
'''g	chr4:39457937-39458172(-)$1	235	92	96	12.0000
ffmm	chr19:53884324-53884546(+)$1	222	141	145	12.0000
DD{D	chrX:14883061-14883287(-)$1	226	9	13	12.0000
b666	chr16:19548049-19548277(+)$1	228	149	153	12.0000
::::	chr8:71126081-71126321(-)$1	240	27	31	12.0000
ccmm	chr5:112177077-112177298(+)$1	221	58	62	12.0000
E:::	chr9:95078238-95078465(-)$1	227	170	174	12.0000
bb::	chr17:60088110-60088341(-)$1	231	39	43	12.0000
pppp	chr11:32954685-32954920(+)$1	235	144	148	12.0000
nnnd	chr11:10823564-10823789(-)$1	225	184	188	12.0000
hhhh	chrM:14820-15059(+)$1	239	18	22	12.0000
gggg	chr8:29921240-29921459(-)$1	219	60	64	12.0000
ccqq	chr1:222806448-222806672(+)$1	224	92	96	12.0000
clll	chr10:120830369-120830611(-)$1	242	163	167	12.0000
nnnn	chr5:122713969-122714196(-)$1	227	99	103	12.0000
::::	chr11:121177977-121178202(+)$1	225	167	171	12.0000
b###	chr1:203818983-203819211(+)$1	228	13	17	12.0000
c:::	chr9:74344871-74345096(-)$1	225	99	103	12.0000
::::	chr6:87968235-87968464(+)$1	229	3	7	12.0000
ee::	chr2:26461702-26461923(-)$1	221	183	187	12.0000
ff::	chr3:169496604-169496830(+)$1	226	85	89	12.0000
IIII	chr16:14041708-14041943(+)$1	235	192	196	12.0000
dnnn	chr4:48569286-48569509(-)$1	223	94	98	12.0000
eeev	chr10:7866283-7866515(+)$1	232	185	189	12.0000
ccoo	chr19:9721425-9721659(-)$1	234	68	72	12.0000
immm	chr1:59131120-59131344(-)$1	224	10	14	12.0000
a]dd	chr10:22617508-22617727(+)$1	219	75	79	12.0000
::::	chr14:102550167-102550399(-)$1	232	158	162	12.0000
BB::	chr17:1582235-1582480(-)$1	245	151	155	12.0000
c444	chr3:160151361-160151585(+)$1	224	123	127	12.0000
b:::	chr9:103108293-103108515(-)$1	222	125	129	12.0000
C:::	chr14:91947843-91948079(-)$1	236	15	19	12.0000
eeee	chr11:68305049-68305272(+)$1	223	7	11	12.0000
hh++	chr12:12653369-12653601(-)$1	232	30	34	12.0000
::::	chr1:91406135-91406363(-)$1	228	151	155	12.0000
GGGG	chr2:30785014-30785240(+)$1	226	37	41	12.0000
^^^^	chr12:80189379-80189603(-)$1	224	69	73	12.0000
dddd	chr8:42977352-42977581(+)$1	229	98	102	12.0000
mmmm	chr10:98287069-98287301(-)$1	232	165	169	12.0000
e666	chr13:23908523-23908744(-)$1	221	162	166	12.0000
::::	chr14:96779597-96779831(-)$1	234	7	11	12.0000
hh!!	chr6:57012354-57012578(+)$1	224	39	43	12.0000
ddnn	chr19:48830735-48830963(+)$1	228	62	66	12.0000
:::H	chr7:64168345-64168578(+)$1	233	93	97	12.0000
gggg	chr2:200803558-200803780(-)$1	222	3	7	12.0000
F:::	chr11:4130805-4131033(+)$1	228	15	19	12.0000
EEEE	chr5:74077160-74077388(+)$1	228	13	17	12.0000
EEEE	chr2:183831897-183832123(-)$1	226	89	93	12.0000
dddd	chr1:78045177-78045398(-)$1	221	2	6	12.0000
gggg	chr17:49052103-49052328(-)$1	225	44	48	12.0000
dmmm	chr14:55510780-55511037(+)$1	257	223	227	12.0000
C{DD	chr7:17838567-17838790(-)$1	223	76	80	12.0000
uuuu	chr10:5772998-5773229(+)$1	231	154	158	12.0000
c)))	chr5:112175984-112176210(+)$1	226	23	27	12.0000
g:::	chr5:82876055-82876279(+)$1	224	98	102	12.0000
^^^^	chr11:62291706-62291929(-)$1	223	84	88	12.0000
:::E	chr2:183866835-183867057(-)$1	222	20	24	12.0000
cqqq	chr12:46245471-46245695(+)$1	224	3	7	12.0000
eeee	chr12:42503355-42503581(-)$1	226	42	46	12.0000
JJ::	chr10:119043222-119043450(-)$1	228	187	191	12.0000

#DB
))).	chr11:64851093-64851327(-)$1	1	178	182	12.0000
))))	chr3:156877111-156877332(-)$1	1	180	184	12.0000
))..	chr19:40542170-40542402(-)$1	1	78	82	12.0000
((..	chr2:183888494-183888725(-)$1	1	143	147	12.0000
....	chr10:129903295-129903514(-)$1	1	1	5	12.0000
))..	chr10:129900758-129901019(-)$1	1	125	129	12.0000
((..	chr19:39329456-39329685(-)$1	1	32	36	12.0000
((((	chr16:19554122-19554354(+)$1	1	89	93	12.0000
)...	chr3:98309402-98309626(-)$1	1	172	176	12.0000
((..	chr7:127013434-127013658(-)$1	1	139	143	12.0000
((((	chr18:9257118-9257347(+)$1	1	212	216	12.0000
(...	chr4:187539797-187540021(-)$1	1	5	9	12.0000
))))	chr17:38290019-38290253(+)$1	1	62	66	12.0000
....	chr20:17956387-17956627(+)$1	1	19	23	12.0000
(...	chr4:187584353-187584578(-)$1	1	87	91	12.0000
((..	chr6:87967638-87967862(+)$1	1	83	87	12.0000
....	chr22:32111595-32111817(-)$1	1	217	221	12.0000
(...	chr10:129905124-129905371(-)$1	1	5	9	12.0000
)...	chr19:37239765-37239987(-)$1	1	55	59	12.0000
((..	chrM:9931-10243(-)$1	1	31	35	12.0000
))).	chr7:97821839-97822059(+)$1	1	98	102	12.0000
(...	chr19:21300581-21300815(+)$1	1	67	71	12.0000
)...	chr17:27016997-27017230(+)$1	1	225	229	12.0000
((..	chr14:21894242-21894465(-)$1	1	36	40	12.0000
(...	chr12:67700067-67700287(+)$1	1	72	76	12.0000
...(	chr4:128726197-128726423(+)$1	1	59	63	12.0000
...(	chr4:39457937-39458172(-)$1	1	92	96	12.0000
((..	chr19:53884324-53884546(+)$1	1	141	145	12.0000
((.(	chrX:14883061-14883287(-)$1	1	9	13	12.0000
)...	chr16:19548049-19548277(+)$1	1	149	153	12.0000
....	chr8:71126081-71126321(-)$1	1	27	31	12.0000
((..	chr5:112177077-112177298(+)$1	1	58	62	12.0000
)...	chr9:95078238-95078465(-)$1	1	170	174	12.0000
))..	chr17:60088110-60088341(-)$1	1	39	43	12.0000
....	chr11:32954685-32954920(+)$1	1	144	148	12.0000
...)	chr11:10823564-10823789(-)$1	1	184	188	12.0000
((((	chrM:14820-15059(+)$1	1	18	22	12.0000
((((	chr8:29921240-29921459(-)$1	1	60	64	12.0000
((..	chr1:222806448-222806672(+)$1	1	92	96	12.0000
(...	chr10:120830369-120830611(-)$1	1	163	167	12.0000
....	chr5:122713969-122714196(-)$1	1	99	103	12.0000
....	chr11:121177977-121178202(+)$1	1	167	171	12.0000
(...	chr1:203818983-203819211(+)$1	1	13	17	12.0000
)...	chr9:74344871-74345096(-)$1	1	99	103	12.0000
....	chr6:87968235-87968464(+)$1	1	3	7	12.0000
))..	chr2:26461702-26461923(-)$1	1	183	187	12.0000
))..	chr3:169496604-169496830(+)$1	1	85	89	12.0000
))))	chr16:14041708-14041943(+)$1	1	192	196	12.0000
(...	chr4:48569286-48569509(-)$1	1	94	98	12.0000
(((.	chr10:7866283-7866515(+)$1	1	185	189	12.0000
((..	chr19:9721425-9721659(-)$1	1	68	72	12.0000
(...	chr1:59131120-59131344(-)$1	1	10	14	12.0000
).))	chr10:22617508-22617727(+)$1	1	75	79	12.0000
....	chr14:102550167-102550399(-)$1	1	158	162	12.0000
((..	chr17:1582235-1582480(-)$1	1	151	155	12.0000
)...	chr3:160151361-160151585(+)$1	1	123	127	12.0000
)...	chr9:103108293-103108515(-)$1	1	125	129	12.0000
(...	chr14:91947843-91948079(-)$1	1	15	19	12.0000
((((	chr11:68305049-68305272(+)$1	1	7	11	12.0000
((..	chr12:12653369-12653601(-)$1	1	30	34	12.0000
....	chr1:91406135-91406363(-)$1	1	151	155	12.0000
((((	chr2:30785014-30785240(+)$1	1	37	41	12.0000
....	chr12:80189379-80189603(-)$1	1	69	73	12.0000
((((	chr8:42977352-42977581(+)$1	1	98	102	12.0000
....	chr10:98287069-98287301(-)$1	1	165	169	12.0000
)...	chr13:23908523-23908744(-)$1	1	162	166	12.0000
....	chr14:96779597-96779831(-)$1	1	7	11	12.0000
((..	chr6:57012354-57012578(+)$1	1	39	43	12.0000
((..	chr19:48830735-48830963(+)$1	1	62	66	12.0000
...(	chr7:64168345-64168578(+)$1	1	93	97	12.0000
((((	chr2:200803558-200803780(-)$1	1	3	7	12.0000
(...	chr11:4130805-4131033(+)$1	1	15	19	12.0000
((((	chr5:74077160-74077388(+)$1	1	13	17	12.0000
((((	chr2:183831897-183832123(-)$1	1	89	93	12.0000
((((	chr1:78045177-78045398(-)$1	1	2	6	12.0000
))))	chr17:49052103-49052328(-)$1	1	44	48	12.0000
(...	chr14:55510780-55511037(+)$1	1	223	227	12.0000
(.((	chr7:17838567-17838790(-)$1	1	76	80	12.0000
....	chr10:5772998-5773229(+)$1	1	154	158	12.0000
(...	chr5:112175984-112176210(+)$1	1	23	27	12.0000
)...	chr5:82876055-82876279(+)$1	1	98	102	12.0000
....	chr11:62291706-62291929(-)$1	1	84	88	12.0000
...(	chr2:183866835-183867057(-)$1	1	20	24	12.0000
(...	chr12:46245471-46245695(+)$1	1	3	7	12.0000
((((	chr12:42503355-42503581(-)$1	1	42	46	12.0000
))..	chr10:119043222-119043450(-)$1	1	187	191	12.0000

#PSSM
G : 0.98	g : 0.01	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FMR1_Ascano2012c_hg19_UTR_m2_run2.nuc.txt

#NT
UGG	chr16:77232128-77232347(+)$1	219	55	58	9.0000
UGG	chr1:204190531-204190750(-)$1	219	1	4	9.0000
UGG	chr1:20238330-20238550(+)$1	220	22	25	9.0000
UGG	chr19:16662145-16662372(-)$1	227	13	16	9.0000
UGG	chr5:156765990-156766217(+)$1	227	54	57	9.0000
UGG	chr12:2975508-2975751(-)$1	243	123	126	9.0000
UGG	chr3:49049617-49049840(+)$1	223	2	5	9.0000
UGG	chr16:70605583-70605850(+)$1	267	3	6	9.0000
UGG	chr6:16761493-16761711(+)$1	218	48	51	9.0000
UGG	chr16:2050096-2050334(-)$1	238	4	7	9.0000
UGG	chr1:15994623-15994841(+)$1	218	13	16	9.0000
UGG	chr2:230630464-230630684(-)$1	220	1	4	9.0000
UGG	chr16:69362886-69363111(-)$1	225	32	35	9.0000
UGG	chr14:103376683-103376901(+)$1	218	150	153	9.0000
UGG	chr12:72181512-72181727(+)$1	215	4	7	9.0000
UGG	chr2:87001075-87001299(+)$1	224	101	104	9.0000
UGG	chr3:5259472-5259697(+)$1	225	58	61	9.0000
UGG	chr19:18561422-18561644(-)$1	222	55	58	9.0000
UGG	chr3:108288254-108288483(-)$1	229	112	115	9.0000
UGG	chr17:74084795-74085020(-)$1	225	23	26	9.0000
UGG	chr1:70716770-70716989(+)$1	219	10	13	9.0000
UGG	chr12:53584264-53584484(+)$1	220	61	64	9.0000
UGG	chr5:122758774-122758991(-)$1	217	26	29	9.0000
UGG	chr5:137033945-137034158(-)$1	213	106	109	9.0000
UGG	chr9:125752264-125752478(+)$1	214	61	64	9.0000
UGG	chr17:48770846-48771057(-)$1	211	4	7	9.0000
ugg	chr13:21752084-21752305(+)$1	221	14	17	9.0000
UGG	chr19:50544894-50545111(+)$1	217	40	43	9.0000
UGG	chr11:46695369-46695597(+)$1	228	0	3	9.0000
UGG	chr11:119173290-119173517(+)$1	227	33	36	9.0000
UGG	chr8:109260790-109261013(-)$1	223	75	78	9.0000
UGG	chr22:24813360-24813582(+)$1	222	9	12	9.0000
UGG	chr10:5807499-5807715(-)$1	216	5	8	9.0000
UGG	chr6:139695496-139695723(-)$1	227	120	123	9.0000
UGG	chr3:193853880-193854092(+)$1	212	72	75	9.0000
UGG	chr20:3847472-3847691(+)$1	219	8	11	9.0000
UGG	chr20:35237976-35238190(+)$1	214	2	5	9.0000
UGG	chr17:4848946-4849177(-)$1	231	66	69	9.0000
UGG	chr4:39460075-39460288(-)$1	213	7	10	9.0000
UGG	chr1:46827764-46827988(+)$1	224	73	76	9.0000
UGG	chr2:182784008-182784233(+)$1	225	58	61	9.0000
UGG	chr3:47103574-47103790(-)$1	216	143	146	9.0000
UGG	chr7:22984671-22984893(-)$1	222	19	22	9.0000
UGG	chr15:73994650-73994880(+)$1	230	33	36	9.0000
ugg	chr6:150070877-150071096(+)$1	219	3	6	9.0000
UGG	chr19:41800387-41800617(+)$1	230	79	82	9.0000
UGg	chr19:53301383-53301601(-)$1	218	47	50	9.0000
UGG	chr1:62905402-62905624(+)$1	222	74	77	9.0000
UGG	chr10:72638889-72639107(+)$1	218	78	81	9.0000
UGG	chr1:32637942-32638161(+)$1	219	78	81	9.0000
UGG	chr13:77456513-77456733(-)$1	220	5	8	9.0000
UGG	chr17:20905243-20905469(-)$1	226	42	45	9.0000
UGG	chr6:163984572-163984790(+)$1	218	87	90	9.0000
UGG	chr12:54058950-54059173(-)$1	223	2	5	9.0000
UGG	chr1:204373472-204373714(-)$1	242	43	46	9.0000
UGG	chr14:64675510-64675731(+)$1	221	2	5	9.0000
UGG	chr11:3022188-3022409(-)$1	221	40	43	9.0000
UGG	chr22:20109816-20110034(+)$1	218	16	19	9.0000
UGG	chr10:75009241-75009464(-)$1	223	2	5	9.0000
UGG	chr21:44451496-44451727(+)$1	231	59	62	9.0000
UGG	chr12:56214808-56215021(-)$1	213	21	24	9.0000
UGG	chr2:54895955-54896174(+)$1	219	42	45	9.0000
UGG	chr13:52603356-52603576(+)$1	220	10	13	9.0000
UGG	chr7:32627175-32627392(+)$1	217	12	15	9.0000
UGG	chr5:178509606-178509832(-)$1	226	19	22	9.0000
UGG	chr5:71504898-71505143(+)$1	245	83	86	9.0000
UGG	chr1:153779816-153780038(-)$1	222	112	115	9.0000
UGG	chr1:71529133-71529348(-)$1	215	136	139	9.0000
UGG	chr7:44916279-44916503(-)$1	224	103	106	9.0000
UGG	chr12:53805514-53805725(+)$1	211	15	18	9.0000
UGG	chr12:9101999-9102231(-)$1	232	24	27	9.0000
UGG	chr8:1951250-1951469(+)$1	219	37	40	9.0000
ugg	chr18:48610093-48610318(+)$1	225	15	18	9.0000
UGG	chr1:19653660-19653871(+)$1	211	106	109	9.0000
UGG	chr2:118675951-118676174(-)$1	223	23	26	9.0000
UGG	chr12:49415327-49415573(-)$1	246	114	117	9.0000
UGG	chr11:9609946-9610167(+)$1	221	69	72	9.0000
UGG	chr22:18369866-18370086(-)$1	220	3	6	9.0000
UGG	chr1:167391762-167391980(+)$1	218	18	21	9.0000
UGG	chr12:112485378-112485596(-)$1	218	66	69	9.0000
UGG	chr18:9550022-9550253(-)$1	231	30	33	9.0000
UGG	chr17:18205586-18205803(-)$1	217	1	4	9.0000
UGG	chr1:114517744-114517955(+)$1	211	35	38	9.0000
UGG	chr20:34526848-34527077(+)$1	229	21	24	9.0000
ugg	chr5:80711024-80711235(-)$1	211	22	25	9.0000
UGG	chr7:4804126-4804345(+)$1	219	15	18	9.0000
UGG	chr19:19606463-19606688(+)$1	225	52	55	9.0000
UGG	chr16:4930575-4930799(+)$1	224	58	61	9.0000
UGG	chr17:44143946-44144172(-)$1	226	88	91	9.0000
UGG	chr22:24236860-24237098(+)$1	238	23	26	9.0000
UGG	chr12:121000718-121000943(+)$1	225	5	8	9.0000
UGG	chr6:16302369-16302595(-)$1	226	9	12	9.0000
UGG	chr3:50107827-50108048(+)$1	221	24	27	9.0000
UGG	chr1:233344174-233344391(-)$1	217	9	12	9.0000
UGG	chr5:149769411-149769632(+)$1	221	53	56	9.0000
UGG	chr2:129025389-129025607(-)$1	218	24	27	9.0000
UGG	chr10:129894984-129895209(-)$1	225	74	77	9.0000
UGG	chr12:53806467-53806692(+)$1	225	36	39	9.0000
UGG	chr12:46766275-46766502(-)$1	227	60	63	9.0000

#otherMatches

#Struct PSSM
g[a	chr19:58101862-58102083(+)$1	221	18	21	9.0000
rff	chr16:77232128-77232347(+)$1	219	55	58	9.0000
:::	chr1:204190531-204190750(-)$1	219	1	4	9.0000
ddd	chr1:20238330-20238550(+)$1	220	22	25	9.0000
eee	chr19:16662145-16662372(-)$1	227	13	16	9.0000
###	chr5:156765990-156766217(+)$1	227	54	57	9.0000
ldd	chr12:2975508-2975751(-)$1	243	123	126	9.0000
EEE	chr3:49049617-49049840(+)$1	223	2	5	9.0000
BBK	chr16:70605583-70605850(+)$1	267	3	6	9.0000
:hh	chr6:16761493-16761711(+)$1	218	48	51	9.0000
fff	chr16:2050096-2050334(-)$1	238	4	7	9.0000
:ff	chr1:15994623-15994841(+)$1	218	13	16	9.0000
::b	chr2:230630464-230630684(-)$1	220	1	4	9.0000
ddd	chr16:69362886-69363111(-)$1	225	32	35	9.0000
dd]	chr14:103376683-103376901(+)$1	218	150	153	9.0000
{GG	chr12:72181512-72181727(+)$1	215	4	7	9.0000
66b	chr2:87001075-87001299(+)$1	224	101	104	9.0000
mmf	chr3:5259472-5259697(+)$1	225	58	61	9.0000
hhh	chr19:18561422-18561644(-)$1	222	55	58	9.0000
ccE	chr3:108288254-108288483(-)$1	229	112	115	9.0000
BNN	chr17:74084795-74085020(-)$1	225	23	26	9.0000
hhh	chr1:70716770-70716989(+)$1	219	10	13	9.0000
eee	chr12:53584264-53584484(+)$1	220	61	64	9.0000
nna	chr5:122758774-122758991(-)$1	217	26	29	9.0000
===	chr5:137033945-137034158(-)$1	213	106	109	9.0000
ee[	chr9:125752264-125752478(+)$1	214	61	64	9.0000
fff	chr17:48770846-48771057(-)$1	211	4	7	9.0000
FFF	chr13:21752084-21752305(+)$1	221	14	17	9.0000
dd:	chr19:50544894-50545111(+)$1	217	40	43	9.0000
:::	chr11:46695369-46695597(+)$1	228	0	3	9.0000
ccc	chr11:119173290-119173517(+)$1	227	33	36	9.0000
e!!	chr8:109260790-109261013(-)$1	223	75	78	9.0000
EEE	chr22:24813360-24813582(+)$1	222	9	12	9.0000
Fbb	chr10:5807499-5807715(-)$1	216	5	8	9.0000
cc2	chr6:139695496-139695723(-)$1	227	120	123	9.0000
KCC	chr3:193853880-193854092(+)$1	212	72	75	9.0000
ccc	chr20:3847472-3847691(+)$1	219	8	11	9.0000
:II	chr20:35237976-35238190(+)$1	214	2	5	9.0000
ddd	chr17:4848946-4849177(-)$1	231	66	69	9.0000
{GG	chr4:39460075-39460288(-)$1	213	7	10	9.0000
nnb	chr1:46827764-46827988(+)$1	224	73	76	9.0000
ddd	chr2:182784008-182784233(+)$1	225	58	61	9.0000
fff	chr3:47103574-47103790(-)$1	216	143	146	9.0000
CCK	chr7:22984671-22984893(-)$1	222	19	22	9.0000
ggg	chr15:73994650-73994880(+)$1	230	33	36	9.0000
eee	chr6:150070877-150071096(+)$1	219	3	6	9.0000
]cc	chr19:41800387-41800617(+)$1	230	79	82	9.0000
III	chr19:53301383-53301601(-)$1	218	47	50	9.0000
EEE	chr1:62905402-62905624(+)$1	222	74	77	9.0000
ffG	chr10:72638889-72639107(+)$1	218	78	81	9.0000
:ff	chr1:32637942-32638161(+)$1	219	78	81	9.0000
EEE	chr13:77456513-77456733(-)$1	220	5	8	9.0000
{CC	chr17:20905243-20905469(-)$1	226	42	45	9.0000
ggg	chr6:163984572-163984790(+)$1	218	87	90	9.0000
:dd	chr12:54058950-54059173(-)$1	223	2	5	9.0000
c""	chr1:204373472-204373714(-)$1	242	43	46	9.0000
cff	chr14:64675510-64675731(+)$1	221	2	5	9.0000
bbd	chr11:3022188-3022409(-)$1	221	40	43	9.0000
:::	chr22:20109816-20110034(+)$1	218	16	19	9.0000
iii	chr10:75009241-75009464(-)$1	223	2	5	9.0000
4cc	chr21:44451496-44451727(+)$1	231	59	62	9.0000
GGG	chr12:56214808-56215021(-)$1	213	21	24	9.0000
ggg	chr2:54895955-54896174(+)$1	219	42	45	9.0000
EEE	chr13:52603356-52603576(+)$1	220	10	13	9.0000
c[a	chr7:32627175-32627392(+)$1	217	12	15	9.0000
GGG	chr5:178509606-178509832(-)$1	226	19	22	9.0000
gbb	chr5:71504898-71505143(+)$1	245	83	86	9.0000
[gg	chr1:153779816-153780038(-)$1	222	112	115	9.0000
lcc	chr1:71529133-71529348(-)$1	215	136	139	9.0000
::f	chr7:44916279-44916503(-)$1	224	103	106	9.0000
hhh	chr12:53805514-53805725(+)$1	211	15	18	9.0000
[dd	chr12:9101999-9102231(-)$1	232	24	27	9.0000
mee	chr8:1951250-1951469(+)$1	219	37	40	9.0000
===	chr18:48610093-48610318(+)$1	225	15	18	9.0000
ddd	chr1:19653660-19653871(+)$1	211	106	109	9.0000
C::	chr2:118675951-118676174(-)$1	223	23	26	9.0000
dff	chr12:49415327-49415573(-)$1	246	114	117	9.0000
CCO	chr11:9609946-9610167(+)$1	221	69	72	9.0000
HHH	chr22:18369866-18370086(-)$1	220	3	6	9.0000
E:E	chr1:167391762-167391980(+)$1	218	18	21	9.0000
lld	chr12:112485378-112485596(-)$1	218	66	69	9.0000
2a3	chr18:9550022-9550253(-)$1	231	30	33	9.0000
ddd	chr17:18205586-18205803(-)$1	217	1	4	9.0000
]cc	chr1:114517744-114517955(+)$1	211	35	38	9.0000
eee	chr20:34526848-34527077(+)$1	229	21	24	9.0000
:::	chr5:80711024-80711235(-)$1	211	22	25	9.0000
fff	chr7:4804126-4804345(+)$1	219	15	18	9.0000
===	chr19:19606463-19606688(+)$1	225	52	55	9.0000
eee	chr16:4930575-4930799(+)$1	224	58	61	9.0000
[cc	chr17:44143946-44144172(-)$1	226	88	91	9.0000
ggg	chr22:24236860-24237098(+)$1	238	23	26	9.0000
DDD	chr12:121000718-121000943(+)$1	225	5	8	9.0000
JJJ	chr6:16302369-16302595(-)$1	226	9	12	9.0000
FFF	chr3:50107827-50108048(+)$1	221	24	27	9.0000
#dd	chr1:233344174-233344391(-)$1	217	9	12	9.0000
ddd	chr5:149769411-149769632(+)$1	221	53	56	9.0000
bb:	chr2:129025389-129025607(-)$1	218	24	27	9.0000
eee	chr10:129894984-129895209(-)$1	225	74	77	9.0000
doo	chr12:53806467-53806692(+)$1	225	36	39	9.0000
2bb	chr12:46766275-46766502(-)$1	227	60	63	9.0000

#DB
(.(	chr19:58101862-58102083(+)$1	1	18	21	9.0000
.))	chr16:77232128-77232347(+)$1	1	55	58	9.0000
...	chr1:204190531-204190750(-)$1	1	1	4	9.0000
(((	chr1:20238330-20238550(+)$1	1	22	25	9.0000
)))	chr19:16662145-16662372(-)$1	1	13	16	9.0000
...	chr5:156765990-156766217(+)$1	1	54	57	9.0000
.))	chr12:2975508-2975751(-)$1	1	123	126	9.0000
(((	chr3:49049617-49049840(+)$1	1	2	5	9.0000
((.	chr16:70605583-70605850(+)$1	1	3	6	9.0000
.((	chr6:16761493-16761711(+)$1	1	48	51	9.0000
(((	chr16:2050096-2050334(-)$1	1	4	7	9.0000
.((	chr1:15994623-15994841(+)$1	1	13	16	9.0000
..(	chr2:230630464-230630684(-)$1	1	1	4	9.0000
)))	chr16:69362886-69363111(-)$1	1	32	35	9.0000
)).	chr14:103376683-103376901(+)$1	1	150	153	9.0000
.((	chr12:72181512-72181727(+)$1	1	4	7	9.0000
..)	chr2:87001075-87001299(+)$1	1	101	104	9.0000
..)	chr3:5259472-5259697(+)$1	1	58	61	9.0000
)))	chr19:18561422-18561644(-)$1	1	55	58	9.0000
)))	chr3:108288254-108288483(-)$1	1	112	115	9.0000
(..	chr17:74084795-74085020(-)$1	1	23	26	9.0000
(((	chr1:70716770-70716989(+)$1	1	10	13	9.0000
)))	chr12:53584264-53584484(+)$1	1	61	64	9.0000
..)	chr5:122758774-122758991(-)$1	1	26	29	9.0000
)))	chr5:137033945-137034158(-)$1	1	106	109	9.0000
((.	chr9:125752264-125752478(+)$1	1	61	64	9.0000
(((	chr17:48770846-48771057(-)$1	1	4	7	9.0000
(((	chr13:21752084-21752305(+)$1	1	14	17	9.0000
)).	chr19:50544894-50545111(+)$1	1	40	43	9.0000
...	chr11:46695369-46695597(+)$1	1	0	3	9.0000
(((	chr11:119173290-119173517(+)$1	1	33	36	9.0000
(..	chr8:109260790-109261013(-)$1	1	75	78	9.0000
(((	chr22:24813360-24813582(+)$1	1	9	12	9.0000
(((	chr10:5807499-5807715(-)$1	1	5	8	9.0000
)).	chr6:139695496-139695723(-)$1	1	120	123	9.0000
.((	chr3:193853880-193854092(+)$1	1	72	75	9.0000
(((	chr20:3847472-3847691(+)$1	1	8	11	9.0000
.((	chr20:35237976-35238190(+)$1	1	2	5	9.0000
(((	chr17:4848946-4849177(-)$1	1	66	69	9.0000
.((	chr4:39460075-39460288(-)$1	1	7	10	9.0000
..)	chr1:46827764-46827988(+)$1	1	73	76	9.0000
)))	chr2:182784008-182784233(+)$1	1	58	61	9.0000
)))	chr3:47103574-47103790(-)$1	1	143	146	9.0000
((.	chr7:22984671-22984893(-)$1	1	19	22	9.0000
(((	chr15:73994650-73994880(+)$1	1	33	36	9.0000
(((	chr6:150070877-150071096(+)$1	1	3	6	9.0000
.))	chr19:41800387-41800617(+)$1	1	79	82	9.0000
(((	chr19:53301383-53301601(-)$1	1	47	50	9.0000
)))	chr1:62905402-62905624(+)$1	1	74	77	9.0000
)))	chr10:72638889-72639107(+)$1	1	78	81	9.0000
.((	chr1:32637942-32638161(+)$1	1	78	81	9.0000
(((	chr13:77456513-77456733(-)$1	1	5	8	9.0000
.((	chr17:20905243-20905469(-)$1	1	42	45	9.0000
(((	chr6:163984572-163984790(+)$1	1	87	90	9.0000
.((	chr12:54058950-54059173(-)$1	1	2	5	9.0000
(..	chr1:204373472-204373714(-)$1	1	43	46	9.0000
(((	chr14:64675510-64675731(+)$1	1	2	5	9.0000
(((	chr11:3022188-3022409(-)$1	1	40	43	9.0000
...	chr22:20109816-20110034(+)$1	1	16	19	9.0000
(((	chr10:75009241-75009464(-)$1	1	2	5	9.0000
.))	chr21:44451496-44451727(+)$1	1	59	62	9.0000
(((	chr12:56214808-56215021(-)$1	1	21	24	9.0000
(((	chr2:54895955-54896174(+)$1	1	42	45	9.0000
(((	chr13:52603356-52603576(+)$1	1	10	13	9.0000
(.(	chr7:32627175-32627392(+)$1	1	12	15	9.0000
(((	chr5:178509606-178509832(-)$1	1	19	22	9.0000
(((	chr5:71504898-71505143(+)$1	1	83	86	9.0000
.((	chr1:153779816-153780038(-)$1	1	112	115	9.0000
.))	chr1:71529133-71529348(-)$1	1	136	139	9.0000
..(	chr7:44916279-44916503(-)$1	1	103	106	9.0000
)))	chr12:53805514-53805725(+)$1	1	15	18	9.0000
.((	chr12:9101999-9102231(-)$1	1	24	27	9.0000
.))	chr8:1951250-1951469(+)$1	1	37	40	9.0000
(((	chr18:48610093-48610318(+)$1	1	15	18	9.0000
)))	chr1:19653660-19653871(+)$1	1	106	109	9.0000
(..	chr2:118675951-118676174(-)$1	1	23	26	9.0000
)((	chr12:49415327-49415573(-)$1	1	114	117	9.0000
((.	chr11:9609946-9610167(+)$1	1	69	72	9.0000
(((	chr22:18369866-18370086(-)$1	1	3	6	9.0000
(.(	chr1:167391762-167391980(+)$1	1	18	21	9.0000
..)	chr12:112485378-112485596(-)$1	1	66	69	9.0000
.).	chr18:9550022-9550253(-)$1	1	30	33	9.0000
(((	chr17:18205586-18205803(-)$1	1	1	4	9.0000
.))	chr1:114517744-114517955(+)$1	1	35	38	9.0000
)))	chr20:34526848-34527077(+)$1	1	21	24	9.0000
...	chr5:80711024-80711235(-)$1	1	22	25	9.0000
)))	chr7:4804126-4804345(+)$1	1	15	18	9.0000
(((	chr19:19606463-19606688(+)$1	1	52	55	9.0000
)))	chr16:4930575-4930799(+)$1	1	58	61	9.0000
.((	chr17:44143946-44144172(-)$1	1	88	91	9.0000
(((	chr22:24236860-24237098(+)$1	1	23	26	9.0000
(((	chr12:121000718-121000943(+)$1	1	5	8	9.0000
(((	chr6:16302369-16302595(-)$1	1	9	12	9.0000
(((	chr3:50107827-50108048(+)$1	1	24	27	9.0000
.((	chr1:233344174-233344391(-)$1	1	9	12	9.0000
)))	chr5:149769411-149769632(+)$1	1	53	56	9.0000
)).	chr2:129025389-129025607(-)$1	1	24	27	9.0000
)))	chr10:129894984-129895209(-)$1	1	74	77	9.0000
(..	chr12:53806467-53806692(+)$1	1	36	39	9.0000
.))	chr12:46766275-46766502(-)$1	1	60	63	9.0000

#PSSM
U : 0.96	u : 0.04	
G : 0.96	g : 0.04	
G : 0.95	g : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_LIN28B_Hafner2013_hg19_UTR_m3_run2.nuc.txt

#NT
AUGUGUUUG	chr19:41713067-41713287(-)$1	220	160	169	12.0000
AUUUAUGUU	chr12:72080343-72080563(+)$1	220	14	23	11.3269
AUUUGACUU	chr1:53290633-53290857(+)$1	224	83	92	11.1346
GUUGGUUUU	chr1:184588913-184589135(+)$1	222	83	92	11.4230
AUUUGGUGU	chr21:30716216-30716437(+)$1	221	81	90	11.2307
AUUUAUUUU	chr19:21907180-21907403(-)$1	223	157	166	15.7500
AUCUGUUUG	chr1:29446428-29446651(+)$1	223	67	76	12.2884
AUAUUUUUU	chr11:75718539-75718760(+)$1	221	0	9	12.9615
AUCUGUUUA	chr11:134022571-134022792(-)$1	221	184	193	12.0961
AUUUGCUUU	chr10:27036714-27036947(-)$1	233	166	175	15.4615
AAUUAUUUU	chr6:64290739-64290967(+)$1	228	116	125	11.0384
AUUUGAUUC	chr5:133726464-133726685(+)$1	221	132	141	11.2307
AUGUGUUUU	chr12:72181340-72181566(+)$1	226	158	167	16.1346
auauguuau	chr3:111711008-111711232(+)$1	224	82	91	11.9038
AUUCCUUUU	chr4:73922103-73922327(-)$1	224	103	112	11.5192
AUUUGUUUU	chr13:100615894-100616134(-)$1	240	0	9	18.7307
CUUUGCUUU	chr6:139498222-139498447(+)$1	225	26	35	12.0000
CUCUGUUUU	chrX:21890053-21890281(+)$1	228	43	52	12.9615
UUUUGUUUU	chr3:72427117-72427343(-)$1	226	130	139	15.2692
AUUCCUUUU	chr1:167393851-167394070(+)$1	219	108	117	11.5192
AUUAGGUUU	chr8:21863856-21864079(+)$1	223	51	60	11.9038
AUUAAUUUU	chr18:12794164-12794384(-)$1	220	111	120	12.0000
CUUUGUUUU	chr15:98516850-98517075(+)$1	225	29	38	15.2692
uuuuguuuu	chr1:183596330-183596554(-)$1	224	214	223	15.2692
AUUUCAUUU	chr10:70153508-70153728(-)$1	220	19	28	12.1923
AUUUAUUUU	chr8:77895093-77895322(-)$1	229	177	186	15.7500
AUAUGAUUU	chr1:101444225-101444461(+)$1	236	12	21	13.0576
AUGUGUAUU	chr8:42692950-42693172(-)$1	222	77	86	11.8076
AUAUGUCUU	chr2:131809054-131809274(-)$1	220	73	82	12.0000
AUAUGGUUU	chr10:120442753-120442975(-)$1	222	93	102	13.2500
GUCUGUUUU	chr7:28861697-28861920(+)$1	223	13	22	12.9615
UCUUGUUUU	chr14:36340176-36340399(+)$1	223	35	44	10.5576
GUUUCUUUU	chr1:160186944-160187167(-)$1	223	99	108	12.0000
AUAUGUUUU	chr10:69677947-69678166(+)$1	219	70	79	16.3269
AUGUGGUUU	chr6:26027028-26027256(-)$1	228	32	41	13.0576
AUUUGGAUU	chr4:113108521-113108740(+)$1	219	46	55	11.3269
GUUUGUUUU	chr20:57601619-57601845(-)$1	226	42	51	15.2692
AUGUGUUUU	chr11:35642304-35642527(+)$1	223	196	205	16.1346
AUCUAUUUU	chr5:137727146-137727378(+)$1	232	33	42	13.4423
AUUUGUUAU	chr4:153832800-153833032(+)$1	232	13	22	14.3076
AUUGUUUUU	chr12:48362557-48362780(+)$1	223	0	9	11.5192
CUUUGUUUU	chr2:32248989-32249210(-)$1	221	193	202	15.2692
AUCUAUUUU	chr8:17086869-17087088(-)$1	219	6	15	13.4423
UUUUGUUUU	chr5:147821927-147822150(+)$1	223	52	61	15.2692
AUUUGUUUC	chr16:75478594-75478820(-)$1	226	67	76	14.5000
AUCUGUUUG	chr18:13651749-13651976(+)$1	227	217	226	12.2884
AUUGGGUUU	chr17:53014790-53015011(+)$1	221	117	126	11.8076
AUUAUUUUU	chr10:3820707-3820934(-)$1	227	170	179	11.6153
AUAUGUUGU	chr19:10243994-10244219(-)$1	225	155	164	11.9038
AUUUGCUUU	chr10:49646974-49647194(+)$1	220	173	182	15.4615
AUUUGCUUU	chr20:34237828-34238051(-)$1	223	180	189	15.4615

#otherMatches

#Struct PSSM
5ggggggg2	chr15:52105995-52106233(+)$1	238	52	61	12.6730
hhhhmmmmh	chr19:41713067-41713287(-)$1	220	160	169	12.0000
e"""fffff	chr12:72080343-72080563(+)$1	220	14	23	11.3269
gggg!!ccc	chr1:53290633-53290857(+)$1	224	83	92	11.1346
eeeeexxxx	chr1:184588913-184589135(+)$1	222	83	92	11.4230
::::HHHHH	chr21:30716216-30716437(+)$1	221	81	90	11.2307
========:	chr19:21907180-21907403(-)$1	223	157	166	15.7500
MMMMDDDDF	chr1:29446428-29446651(+)$1	223	67	76	12.2884
ffffffooo	chr11:75718539-75718760(+)$1	221	0	9	12.9615
fffff::::	chr11:134022571-134022792(-)$1	221	184	193	12.0961
::::::::G	chr10:27036714-27036947(-)$1	233	166	175	15.4615
^^^^^^^^^	chr6:64290739-64290967(+)$1	228	116	125	11.0384
!!dddd!!d	chr5:133726464-133726685(+)$1	221	132	141	11.2307
2bb]dddd]	chr12:72181340-72181566(+)$1	226	158	167	16.1346
n========	chr3:111711008-111711232(+)$1	224	82	91	11.9038
]ccc:GGGG	chr4:73922103-73922327(-)$1	224	103	112	11.5192
::::dddd!	chr13:100615894-100616134(-)$1	240	0	9	18.7307
hhhhh::::	chr6:139498222-139498447(+)$1	225	26	35	12.0000
^^^^^^^^^	chrX:21890053-21890281(+)$1	228	43	52	12.9615
hhhh77777	chr3:72427117-72427343(-)$1	226	130	139	15.2692
xxxxxxxxx	chr1:167393851-167394070(+)$1	219	108	117	11.5192
####dddd+	chr8:21863856-21864079(+)$1	223	51	60	11.9038
::::::eee	chr18:12794164-12794384(-)$1	220	111	120	12.0000
:gggggggg	chr15:98516850-98517075(+)$1	225	29	38	15.2692
F::::::::	chr1:183596330-183596554(-)$1	224	214	223	15.2692
QIIIIIIII	chr10:70153508-70153728(-)$1	220	19	28	12.1923
eeeee]===	chr8:77895093-77895322(-)$1	229	177	186	15.7500
FFFFFF:::	chr1:101444225-101444461(+)$1	236	12	21	13.0576
::::fffff	chr8:42692950-42693172(-)$1	222	77	86	11.8076
iiiii[ddd	chr2:131809054-131809274(-)$1	220	73	82	12.0000
c!!cccsss	chr10:120442753-120442975(-)$1	222	93	102	13.2500
^^^^^^^^^	chr7:28861697-28861920(+)$1	223	13	22	12.9615
GG:::::::	chr14:36340176-36340399(+)$1	223	35	44	10.5576
]========	chr1:160186944-160187167(-)$1	223	99	108	12.0000
ELLLFFFFF	chr10:69677947-69678166(+)$1	219	70	79	16.3269
e[cccdddd	chr6:26027028-26027256(-)$1	228	32	41	13.0576
gggggg:::	chr4:113108521-113108740(+)$1	219	46	55	11.3269
dddd]eeee	chr20:57601619-57601845(-)$1	226	42	51	15.2692
=========	chr11:35642304-35642527(+)$1	223	196	205	16.1346
C{EEEEE::	chr5:137727146-137727378(+)$1	232	33	42	13.4423
eeeeetttt	chr4:153832800-153833032(+)$1	232	13	22	14.3076
:::::::::	chr12:48362557-48362780(+)$1	223	0	9	11.5192
////GGGGG	chr2:32248989-32249210(-)$1	221	193	202	15.2692
dd[cccnnn	chr8:17086869-17087088(-)$1	219	6	15	13.4423
mmmmggggg	chr5:147821927-147822150(+)$1	223	52	61	15.2692
4444dddd5	chr16:75478594-75478820(-)$1	226	67	76	14.5000
ffffff:::	chr18:13651749-13651976(+)$1	227	217	226	12.2884
::=======	chr17:53014790-53015011(+)$1	221	117	126	11.8076
======mmm	chr10:3820707-3820934(-)$1	227	170	179	11.6153
:::::EEEE	chr19:10243994-10244219(-)$1	225	155	164	11.9038
fff[bbuuu	chr10:49646974-49647194(+)$1	220	173	182	15.4615
ffffff777	chr20:34237828-34238051(-)$1	223	180	189	15.4615

#DB
.))))))).	chr15:52105995-52106233(+)$1	1	52	61	12.6730
((((....)	chr19:41713067-41713287(-)$1	1	160	169	12.0000
(...(((((	chr12:72080343-72080563(+)$1	1	14	23	11.3269
((((..(((	chr1:53290633-53290857(+)$1	1	83	92	11.1346
(((((....	chr1:184588913-184589135(+)$1	1	83	92	11.4230
....(((((	chr21:30716216-30716437(+)$1	1	81	90	11.2307
)))))))).	chr19:21907180-21907403(-)$1	1	157	166	15.7500
....(((((	chr1:29446428-29446651(+)$1	1	67	76	12.2884
((((((...	chr11:75718539-75718760(+)$1	1	0	9	12.9615
)))))....	chr11:134022571-134022792(-)$1	1	184	193	12.0961
........)	chr10:27036714-27036947(-)$1	1	166	175	15.4615
.........	chr6:64290739-64290967(+)$1	1	116	125	11.0384
..((((..(	chr5:133726464-133726685(+)$1	1	132	141	11.2307
.)).)))).	chr12:72181340-72181566(+)$1	1	158	167	16.1346
.))))))))	chr3:111711008-111711232(+)$1	1	82	91	11.9038
.))).((((	chr4:73922103-73922327(-)$1	1	103	112	11.5192
....((((.	chr13:100615894-100616134(-)$1	1	0	9	18.7307
)))))....	chr6:139498222-139498447(+)$1	1	26	35	12.0000
.........	chrX:21890053-21890281(+)$1	1	43	52	12.9615
)))).....	chr3:72427117-72427343(-)$1	1	130	139	15.2692
.........	chr1:167393851-167394070(+)$1	1	108	117	11.5192
....((((.	chr8:21863856-21864079(+)$1	1	51	60	11.9038
......(((	chr18:12794164-12794384(-)$1	1	111	120	12.0000
.((((((((	chr15:98516850-98517075(+)$1	1	29	38	15.2692
)........	chr1:183596330-183596554(-)$1	1	214	223	15.2692
.((((((((	chr10:70153508-70153728(-)$1	1	19	28	12.1923
))))).)))	chr8:77895093-77895322(-)$1	1	177	186	15.7500
((((((...	chr1:101444225-101444461(+)$1	1	12	21	13.0576
....(((((	chr8:42692950-42693172(-)$1	1	77	86	11.8076
(((((.(((	chr2:131809054-131809274(-)$1	1	73	82	12.0000
(..(((...	chr10:120442753-120442975(-)$1	1	93	102	13.2500
.........	chr7:28861697-28861920(+)$1	1	13	22	12.9615
((.......	chr14:36340176-36340399(+)$1	1	35	44	10.5576
.))))))))	chr1:160186944-160187167(-)$1	1	99	108	12.0000
(...(((((	chr10:69677947-69678166(+)$1	1	70	79	16.3269
(.(((((((	chr6:26027028-26027256(-)$1	1	32	41	13.0576
))))))...	chr4:113108521-113108740(+)$1	1	46	55	11.3269
)))).))))	chr20:57601619-57601845(-)$1	1	42	51	15.2692
(((((((((	chr11:35642304-35642527(+)$1	1	196	205	16.1346
(.(((((..	chr5:137727146-137727378(+)$1	1	33	42	13.4423
(((((....	chr4:153832800-153833032(+)$1	1	13	22	14.3076
.........	chr12:48362557-48362780(+)$1	1	0	9	11.5192
....)))))	chr2:32248989-32249210(-)$1	1	193	202	15.2692
((.(((...	chr8:17086869-17087088(-)$1	1	6	15	13.4423
....)))))	chr5:147821927-147822150(+)$1	1	52	61	15.2692
....)))).	chr16:75478594-75478820(-)$1	1	67	76	14.5000
))))))...	chr18:13651749-13651976(+)$1	1	217	226	12.2884
..(((((((	chr17:53014790-53015011(+)$1	1	117	126	11.8076
((((((...	chr10:3820707-3820934(-)$1	1	170	179	11.6153
.....))))	chr19:10243994-10244219(-)$1	1	155	164	11.9038
(((.((...	chr10:49646974-49647194(+)$1	1	173	182	15.4615
))))))...	chr20:34237828-34238051(-)$1	1	180	189	15.4615

#PSSM
A : 0.73	G : 0.07	C : 0.07	U : 0.05	a : 0.03	u : 0.01	
U : 0.90	u : 0.05	A : 0.01	C : 0.01	
U : 0.59	C : 0.13	A : 0.11	G : 0.09	c : 0.01	a : 0.01	u : 0.01	
U : 0.78	G : 0.05	A : 0.05	u : 0.03	C : 0.03	a : 0.01	
G : 0.67	A : 0.13	C : 0.07	g : 0.05	U : 0.05	
U : 0.67	G : 0.11	A : 0.07	C : 0.07	u : 0.05	
U : 0.84	u : 0.05	C : 0.03	A : 0.03	G : 0.01	
U : 0.88	u : 0.03	G : 0.03	a : 0.01	A : 0.01	
U : 0.82	u : 0.05	G : 0.05	C : 0.03	A : 0.01	

#score	687.0769230769238
#seq	52
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_Ago2_Kishore2011b_hg19_UTR_m1_run1.nuc.txt

#NT
AUUU	chr4:122737830-122738206(-)$1	376	48	52	12.0000
AUUU	chr17:42880981-42881221(-)$1	240	136	140	12.0000
AUUU	chr14:69255243-69255483(-)$1	240	17	21	12.0000
AUUU	chr9:123942367-123942607(-)$1	240	27	31	12.0000
AUUU	chr8:8642851-8643131(-)$1	280	56	60	12.0000
auuu	chr12:112330828-112331068(+)$1	240	66	70	12.0000
AUUU	chr3:172349796-172350036(-)$1	240	8	12	12.0000
AUUU	chr19:57840638-57840878(+)$1	240	81	85	12.0000
AUUU	chr6:117869913-117870153(+)$1	240	9	13	12.0000
AUUU	chr7:116199397-116199637(+)$1	240	4	8	12.0000
AUUU	chr6:1395560-1395920(+)$1	360	5	9	12.0000
AUUU	chr6:158619777-158620017(+)$1	240	99	103	12.0000
AUUU	chr14:74167681-74167921(+)$1	240	36	40	12.0000
AUUU	chr12:46753391-46753631(-)$1	240	81	85	12.0000
AUUU	chr3:172538876-172539116(+)$1	240	97	101	12.0000
AUUU	chr19:14072093-14072333(+)$1	240	2	6	12.0000
AUUU	chr3:66293577-66293817(+)$1	240	42	46	12.0000
AUUU	chr12:88592587-88592827(+)$1	240	33	37	12.0000
AUUU	chr20:49369477-49369721(+)$1	244	16	20	12.0000
AUUU	chr4:185616188-185616428(-)$1	240	107	111	12.0000
AUUU	chr22:18211460-18211706(+)$1	246	33	37	12.0000
AUUU	chr1:100757097-100757337(+)$1	240	5	9	12.0000
AUUU	chr8:104081995-104082235(+)$1	240	36	40	12.0000
AUUU	chr13:95058110-95058350(+)$1	240	15	19	12.0000
AUUU	chr3:191111612-191111852(+)$1	240	4	8	12.0000
AUUU	chr7:44919509-44919749(-)$1	240	14	18	12.0000
AUUU	chr17:27582852-27583092(-)$1	240	6	10	12.0000
AUUU	chr8:87573262-87573504(+)$1	242	12	16	12.0000
AUUU	chr6:97338331-97338571(-)$1	240	19	23	12.0000
AUUU	chr7:19155561-19155804(-)$1	243	134	138	12.0000
AUUU	chr2:32530796-32531036(+)$1	240	43	47	12.0000
AUUU	chr16:46989443-46989683(-)$1	240	8	12	12.0000
AUUU	chr8:90939005-90939245(+)$1	240	33	37	12.0000
AUUU	chr8:101533808-101534088(-)$1	280	2	6	12.0000
AUUU	chr16:46731402-46731642(+)$1	240	50	54	12.0000
AUUU	chr2:131805633-131805873(-)$1	240	130	134	12.0000
AUUU	chr1:36389515-36389759(+)$1	244	202	206	12.0000
AUUU	chr16:4307501-4307741(-)$1	240	41	45	12.0000
AUUU	chr9:745959-746199(+)$1	240	31	35	12.0000
AUUU	chr1:231696785-231697025(+)$1	240	66	70	12.0000
AUUU	chr7:158524928-158525168(-)$1	240	46	50	12.0000
AUUU	chrX:37589139-37589379(+)$1	240	17	21	12.0000
AUUU	chr8:28573165-28573405(+)$1	240	25	29	12.0000
AUUU	chr6:16301066-16301306(-)$1	240	32	36	12.0000
AUUU	chr1:225684995-225685275(-)$1	280	38	42	12.0000
AUUU	chr3:133307018-133307260(+)$1	242	48	52	12.0000
AUUU	chr1:90059486-90059726(+)$1	240	34	38	12.0000
AUUU	chr5:162868002-162868247(+)$1	245	72	76	12.0000
AUUU	chr2:74089854-74090094(+)$1	240	42	46	12.0000
AUUU	chr3:52728405-52728645(-)$1	240	92	96	12.0000
AUUU	chr3:183398301-183398541(+)$1	240	45	49	12.0000
AUUU	chr5:179662690-179662930(-)$1	240	16	20	12.0000
AUUU	chr6:64290727-64290973(+)$1	246	59	63	12.0000
AUUU	chr17:46684770-46685109(-)$1	339	48	52	12.0000
AUUU	chr3:122880781-122881021(+)$1	240	88	92	12.0000
AUUU	chr2:187545002-187545242(+)$1	240	112	116	12.0000
AUUU	chr19:14831261-14831501(+)$1	240	36	40	12.0000
AUUU	chr16:24835364-24835705(+)$1	341	121	125	12.0000
AUUU	chr22:40729812-40730052(+)$1	240	23	27	12.0000
AUUU	chr1:78030267-78030551(-)$1	284	38	42	12.0000
AUUU	chr2:32842964-32843204(+)$1	240	68	72	12.0000
AUUU	chr11:9304977-9305217(-)$1	240	15	19	12.0000
AUUU	chr1:33475786-33476026(-)$1	240	87	91	12.0000
AUUU	chr18:72912865-72913105(-)$1	240	77	81	12.0000
AUUU	chrX:69256316-69256556(+)$1	240	74	78	12.0000
auuu	chr3:30734282-30734602(+)$1	320	21	25	12.0000
AUUU	chr17:4442132-4442372(-)$1	240	44	48	12.0000
AUUU	chr8:27986985-27987225(+)$1	240	13	17	12.0000
AUUU	chr3:142027353-142027593(-)$1	240	16	20	12.0000
AUUU	chr16:66836727-66836967(-)$1	240	11	15	12.0000
AUUU	chr5:139622953-139623233(+)$1	280	242	246	12.0000
AUUU	chr7:79848358-79848598(+)$1	240	46	50	12.0000
AUUU	chr19:32875062-32875302(+)$1	240	31	35	12.0000
auuu	chr10:70506867-70507107(+)$1	240	1	5	12.0000
AUUU	chr15:65159263-65159503(+)$1	240	119	123	12.0000
AUUU	chr19:34929520-34929760(+)$1	240	3	7	12.0000
AUUU	chr12:75893765-75894005(+)$1	240	4	8	12.0000
AUUU	chr11:111921866-111922106(+)$1	240	112	116	12.0000
AUUU	chr19:1272383-1272623(+)$1	240	175	179	12.0000
AUUU	chr3:196663165-196663405(-)$1	240	161	165	12.0000
AUUU	chr8:104341825-104342065(+)$1	240	22	26	12.0000
AUUU	chr4:20255182-20255422(+)$1	240	119	123	12.0000
AUUU	chr17:45197959-45198244(-)$1	285	119	123	12.0000
AUUU	chr17:34945764-34946004(+)$1	240	38	42	12.0000
AUUU	chr10:16553436-16553676(+)$1	240	25	29	12.0000
AUUU	chr7:90043035-90043275(+)$1	240	37	41	12.0000
AUUU	chr17:41144490-41144749(+)$1	259	193	197	12.0000
AUUU	chr12:89983554-89983794(-)$1	240	69	73	12.0000
AUUU	chrX:103434655-103434895(+)$1	240	194	198	12.0000
AUUU	chr10:70672890-70673130(+)$1	240	180	184	12.0000
AUUU	chr7:87514299-87514539(+)$1	240	5	9	12.0000

#otherMatches

#Struct PSSM
WWWW	chr15:99502368-99502629(+)$1	261	65	69	12.0000
VVVG	chr4:122737830-122738206(-)$1	376	48	52	12.0000
cc22	chr17:42880981-42881221(-)$1	240	136	140	12.0000
:ddd	chr14:69255243-69255483(-)$1	240	17	21	12.0000
F{FF	chr9:123942367-123942607(-)$1	240	27	31	12.0000
pppp	chr8:8642851-8643131(-)$1	280	56	60	12.0000
eeee	chr12:112330828-112331068(+)$1	240	66	70	12.0000
eemm	chr3:172349796-172350036(-)$1	240	8	12	12.0000
nnnn	chr19:57840638-57840878(+)$1	240	81	85	12.0000
nnnn	chr6:117869913-117870153(+)$1	240	9	13	12.0000
EFFF	chr7:116199397-116199637(+)$1	240	4	8	12.0000
::::	chr6:1395560-1395920(+)$1	360	5	9	12.0000
++++	chr6:158619777-158620017(+)$1	240	99	103	12.0000
:ggg	chr14:74167681-74167921(+)$1	240	36	40	12.0000
::::	chr12:46753391-46753631(-)$1	240	81	85	12.0000
))))	chr3:172538876-172539116(+)$1	240	97	101	12.0000
::::	chr19:14072093-14072333(+)$1	240	2	6	12.0000
::::	chr3:66293577-66293817(+)$1	240	42	46	12.0000
hhhh	chr12:88592587-88592827(+)$1	240	33	37	12.0000
ssss	chr20:49369477-49369721(+)$1	244	16	20	12.0000
ffff	chr4:185616188-185616428(-)$1	240	107	111	12.0000
llle	chr22:18211460-18211706(+)$1	246	33	37	12.0000
GGGG	chr1:100757097-100757337(+)$1	240	5	9	12.0000
((((	chr8:104081995-104082235(+)$1	240	36	40	12.0000
HHHK	chr13:95058110-95058350(+)$1	240	15	19	12.0000
::::	chr3:191111612-191111852(+)$1	240	4	8	12.0000
HHHH	chr7:44919509-44919749(-)$1	240	14	18	12.0000
ccnn	chr17:27582852-27583092(-)$1	240	6	10	12.0000
G:cc	chr8:87573262-87573504(+)$1	242	12	16	12.0000
IIII	chr6:97338331-97338571(-)$1	240	19	23	12.0000
%fff	chr7:19155561-19155804(-)$1	243	134	138	12.0000
EELL	chr2:32530796-32531036(+)$1	240	43	47	12.0000
LLLF	chr16:46989443-46989683(-)$1	240	8	12	12.0000
hh$$	chr8:90939005-90939245(+)$1	240	33	37	12.0000
:::c	chr8:101533808-101534088(-)$1	280	2	6	12.0000
eeee	chr16:46731402-46731642(+)$1	240	50	54	12.0000
b999	chr2:131805633-131805873(-)$1	240	130	134	12.0000
dd!!	chr1:36389515-36389759(+)$1	244	202	206	12.0000
ssss	chr16:4307501-4307741(-)$1	240	41	45	12.0000
"""e	chr9:745959-746199(+)$1	240	31	35	12.0000
IIII	chr1:231696785-231697025(+)$1	240	66	70	12.0000
777b	chr7:158524928-158525168(-)$1	240	46	50	12.0000
eeep	chrX:37589139-37589379(+)$1	240	17	21	12.0000
:ccc	chr8:28573165-28573405(+)$1	240	25	29	12.0000
gggg	chr6:16301066-16301306(-)$1	240	32	36	12.0000
DDDD	chr1:225684995-225685275(-)$1	280	38	42	12.0000
[ccc	chr3:133307018-133307260(+)$1	242	48	52	12.0000
eeee	chr1:90059486-90059726(+)$1	240	34	38	12.0000
gggg	chr5:162868002-162868247(+)$1	245	72	76	12.0000
i::d	chr2:74089854-74090094(+)$1	240	42	46	12.0000
ccff	chr3:52728405-52728645(-)$1	240	92	96	12.0000
HHHH	chr3:183398301-183398541(+)$1	240	45	49	12.0000
gggs	chr5:179662690-179662930(-)$1	240	16	20	12.0000
lllf	chr6:64290727-64290973(+)$1	246	59	63	12.0000
[bbn	chr17:46684770-46685109(-)$1	339	48	52	12.0000
ddqq	chr3:122880781-122881021(+)$1	240	88	92	12.0000
hhhh	chr2:187545002-187545242(+)$1	240	112	116	12.0000
nfff	chr19:14831261-14831501(+)$1	240	36	40	12.0000
cnnn	chr16:24835364-24835705(+)$1	341	121	125	12.0000
JJJc	chr22:40729812-40730052(+)$1	240	23	27	12.0000
&&&&	chr1:78030267-78030551(-)$1	284	38	42	12.0000
gggg	chr2:32842964-32843204(+)$1	240	68	72	12.0000
:fff	chr11:9304977-9305217(-)$1	240	15	19	12.0000
ffff	chr1:33475786-33476026(-)$1	240	87	91	12.0000
====	chr18:72912865-72913105(-)$1	240	77	81	12.0000
iiii	chrX:69256316-69256556(+)$1	240	74	78	12.0000
JJJJ	chr3:30734282-30734602(+)$1	320	21	25	12.0000
::::	chr17:4442132-4442372(-)$1	240	44	48	12.0000
::::	chr8:27986985-27987225(+)$1	240	13	17	12.0000
eeez	chr3:142027353-142027593(-)$1	240	16	20	12.0000
B{GG	chr16:66836727-66836967(-)$1	240	11	15	12.0000
eeee	chr5:139622953-139623233(+)$1	280	242	246	12.0000
gggg	chr7:79848358-79848598(+)$1	240	46	50	12.0000
vvvv	chr19:32875062-32875302(+)$1	240	31	35	12.0000
::::	chr10:70506867-70507107(+)$1	240	1	5	12.0000
#eee	chr15:65159263-65159503(+)$1	240	119	123	12.0000
::::	chr19:34929520-34929760(+)$1	240	3	7	12.0000
:fff	chr12:75893765-75894005(+)$1	240	4	8	12.0000
((((	chr11:111921866-111922106(+)$1	240	112	116	12.0000
====	chr19:1272383-1272623(+)$1	240	175	179	12.0000
ffff	chr3:196663165-196663405(-)$1	240	161	165	12.0000
::::	chr8:104341825-104342065(+)$1	240	22	26	12.0000
pppc	chr4:20255182-20255422(+)$1	240	119	123	12.0000
ssss	chr17:45197959-45198244(-)$1	285	119	123	12.0000
dddb	chr17:34945764-34946004(+)$1	240	38	42	12.0000
gggg	chr10:16553436-16553676(+)$1	240	25	29	12.0000
e"""	chr7:90043035-90043275(+)$1	240	37	41	12.0000
b]bb	chr17:41144490-41144749(+)$1	259	193	197	12.0000
dddn	chr12:89983554-89983794(-)$1	240	69	73	12.0000
ffdd	chrX:103434655-103434895(+)$1	240	194	198	12.0000
]ddd	chr10:70672890-70673130(+)$1	240	180	184	12.0000
KEEE	chr7:87514299-87514539(+)$1	240	5	9	12.0000

#DB
....	chr15:99502368-99502629(+)$1	1	65	69	12.0000
...(	chr4:122737830-122738206(-)$1	1	48	52	12.0000
))..	chr17:42880981-42881221(-)$1	1	136	140	12.0000
.(((	chr14:69255243-69255483(-)$1	1	17	21	12.0000
(.((	chr9:123942367-123942607(-)$1	1	27	31	12.0000
....	chr8:8642851-8643131(-)$1	1	56	60	12.0000
))))	chr12:112330828-112331068(+)$1	1	66	70	12.0000
((..	chr3:172349796-172350036(-)$1	1	8	12	12.0000
....	chr19:57840638-57840878(+)$1	1	81	85	12.0000
....	chr6:117869913-117870153(+)$1	1	9	13	12.0000
((((	chr7:116199397-116199637(+)$1	1	4	8	12.0000
....	chr6:1395560-1395920(+)$1	1	5	9	12.0000
....	chr6:158619777-158620017(+)$1	1	99	103	12.0000
.(((	chr14:74167681-74167921(+)$1	1	36	40	12.0000
....	chr12:46753391-46753631(-)$1	1	81	85	12.0000
....	chr3:172538876-172539116(+)$1	1	97	101	12.0000
....	chr19:14072093-14072333(+)$1	1	2	6	12.0000
....	chr3:66293577-66293817(+)$1	1	42	46	12.0000
((((	chr12:88592587-88592827(+)$1	1	33	37	12.0000
....	chr20:49369477-49369721(+)$1	1	16	20	12.0000
((((	chr4:185616188-185616428(-)$1	1	107	111	12.0000
...)	chr22:18211460-18211706(+)$1	1	33	37	12.0000
((((	chr1:100757097-100757337(+)$1	1	5	9	12.0000
....	chr8:104081995-104082235(+)$1	1	36	40	12.0000
(((.	chr13:95058110-95058350(+)$1	1	15	19	12.0000
....	chr3:191111612-191111852(+)$1	1	4	8	12.0000
((((	chr7:44919509-44919749(-)$1	1	14	18	12.0000
((..	chr17:27582852-27583092(-)$1	1	6	10	12.0000
(.((	chr8:87573262-87573504(+)$1	1	12	16	12.0000
((((	chr6:97338331-97338571(-)$1	1	19	23	12.0000
.(((	chr7:19155561-19155804(-)$1	1	134	138	12.0000
((..	chr2:32530796-32531036(+)$1	1	43	47	12.0000
...(	chr16:46989443-46989683(-)$1	1	8	12	12.0000
((..	chr8:90939005-90939245(+)$1	1	33	37	12.0000
...(	chr8:101533808-101534088(-)$1	1	2	6	12.0000
))))	chr16:46731402-46731642(+)$1	1	50	54	12.0000
)...	chr2:131805633-131805873(-)$1	1	130	134	12.0000
((..	chr1:36389515-36389759(+)$1	1	202	206	12.0000
....	chr16:4307501-4307741(-)$1	1	41	45	12.0000
...(	chr9:745959-746199(+)$1	1	31	35	12.0000
((((	chr1:231696785-231697025(+)$1	1	66	70	12.0000
...)	chr7:158524928-158525168(-)$1	1	46	50	12.0000
(((.	chrX:37589139-37589379(+)$1	1	17	21	12.0000
.(((	chr8:28573165-28573405(+)$1	1	25	29	12.0000
((((	chr6:16301066-16301306(-)$1	1	32	36	12.0000
((((	chr1:225684995-225685275(-)$1	1	38	42	12.0000
.(((	chr3:133307018-133307260(+)$1	1	48	52	12.0000
))))	chr1:90059486-90059726(+)$1	1	34	38	12.0000
((((	chr5:162868002-162868247(+)$1	1	72	76	12.0000
)..(	chr2:74089854-74090094(+)$1	1	42	46	12.0000
))))	chr3:52728405-52728645(-)$1	1	92	96	12.0000
((((	chr3:183398301-183398541(+)$1	1	45	49	12.0000
(((.	chr5:179662690-179662930(-)$1	1	16	20	12.0000
...)	chr6:64290727-64290973(+)$1	1	59	63	12.0000
.((.	chr17:46684770-46685109(-)$1	1	48	52	12.0000
((..	chr3:122880781-122881021(+)$1	1	88	92	12.0000
))))	chr2:187545002-187545242(+)$1	1	112	116	12.0000
.)))	chr19:14831261-14831501(+)$1	1	36	40	12.0000
(...	chr16:24835364-24835705(+)$1	1	121	125	12.0000
((((	chr22:40729812-40730052(+)$1	1	23	27	12.0000
....	chr1:78030267-78030551(-)$1	1	38	42	12.0000
((((	chr2:32842964-32843204(+)$1	1	68	72	12.0000
.(((	chr11:9304977-9305217(-)$1	1	15	19	12.0000
((((	chr1:33475786-33476026(-)$1	1	87	91	12.0000
))))	chr18:72912865-72913105(-)$1	1	77	81	12.0000
((((	chrX:69256316-69256556(+)$1	1	74	78	12.0000
((((	chr3:30734282-30734602(+)$1	1	21	25	12.0000
....	chr17:4442132-4442372(-)$1	1	44	48	12.0000
....	chr8:27986985-27987225(+)$1	1	13	17	12.0000
(((.	chr3:142027353-142027593(-)$1	1	16	20	12.0000
(.((	chr16:66836727-66836967(-)$1	1	11	15	12.0000
((((	chr5:139622953-139623233(+)$1	1	242	246	12.0000
((((	chr7:79848358-79848598(+)$1	1	46	50	12.0000
....	chr19:32875062-32875302(+)$1	1	31	35	12.0000
....	chr10:70506867-70507107(+)$1	1	1	5	12.0000
.(((	chr15:65159263-65159503(+)$1	1	119	123	12.0000
....	chr19:34929520-34929760(+)$1	1	3	7	12.0000
.(((	chr12:75893765-75894005(+)$1	1	4	8	12.0000
....	chr11:111921866-111922106(+)$1	1	112	116	12.0000
((((	chr19:1272383-1272623(+)$1	1	175	179	12.0000
((((	chr3:196663165-196663405(-)$1	1	161	165	12.0000
....	chr8:104341825-104342065(+)$1	1	22	26	12.0000
...)	chr4:20255182-20255422(+)$1	1	119	123	12.0000
....	chr17:45197959-45198244(-)$1	1	119	123	12.0000
((((	chr17:34945764-34946004(+)$1	1	38	42	12.0000
((((	chr10:16553436-16553676(+)$1	1	25	29	12.0000
(...	chr7:90043035-90043275(+)$1	1	37	41	12.0000
).))	chr17:41144490-41144749(+)$1	1	193	197	12.0000
(((.	chr12:89983554-89983794(-)$1	1	69	73	12.0000
))))	chrX:103434655-103434895(+)$1	1	194	198	12.0000
.)))	chr10:70672890-70673130(+)$1	1	180	184	12.0000
.(((	chr7:87514299-87514539(+)$1	1	5	9	12.0000

#PSSM
A : 0.95	a : 0.04	
U : 0.95	u : 0.04	
U : 0.95	u : 0.04	
U : 0.95	u : 0.04	

#score	1104.0000000000007
#seq	92
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_CDS_m3_run2.nuc.txt

#NT
AAA	chr12:50529681-50529904(-)$1	223	183	186	8.9999
AAA	chr7:32590868-32591091(+)$1	223	100	103	8.9999
AAA	chr6:26156812-26157045(+)$1	233	121	124	8.9999
AAA	chr5:138994237-138994459(+)$1	222	110	113	8.9999
AAA	chr6:105474125-105474351(+)$1	226	50	53	8.9999
AAA	chr12:72092737-72092968(+)$1	231	192	195	8.9999
AAA	chr1:226564754-226564976(-)$1	222	24	27	8.9999
AAA	chr1:217793392-217793613(-)$1	221	46	49	8.9999
AAA	chr3:41266884-41267103(+)$1	219	59	62	8.9999
AAA	chr2:152311395-152311615(+)$1	220	39	42	8.9999
AAA	chr5:64931045-64931269(+)$1	224	138	141	8.9999
AAA	chr1:115269504-115269731(-)$1	227	62	65	8.9999
AAA	chr12:123813309-123813530(-)$1	221	45	48	8.9999
AAA	chr10:16806344-16806568(-)$1	224	119	122	8.9999
AAA	chr7:107224286-107224511(+)$1	225	74	77	8.9999
AAA	chr1:151640871-151641094(+)$1	223	81	84	8.9999
AAA	chr2:169727830-169728051(-)$1	221	81	84	8.9999
AAA	chr1:68948053-68948271(-)$1	218	29	32	8.9999
AAA	chr19:57802774-57803003(+)$1	229	50	53	8.9999
AAA	chrX:71495412-71495631(-)$1	219	158	161	8.9999
AAA	chr2:183817784-183818008(-)$1	224	56	59	8.9999
AAA	chr10:7841916-7842142(+)$1	226	19	22	8.9999
AAA	chr17:40764938-40765164(+)$1	226	212	215	8.9999
AAA	chr1:220206831-220207054(-)$1	223	12	15	8.9999
AAA	chr1:193044864-193045086(+)$1	222	21	24	8.9999
AAA	chr17:27869920-27870151(+)$1	231	85	88	8.9999
AAA	chr3:180666126-180666350(+)$1	224	51	54	8.9999
AAA	chr8:53540531-53540756(-)$1	225	6	9	8.9999
AAA	chr19:37240018-37240238(-)$1	220	55	58	8.9999
AAA	chr8:71486424-71486651(-)$1	227	63	66	8.9999
AAA	chr7:888006-888229(+)$1	223	18	21	8.9999
AAA	chr1:54237971-54238191(-)$1	220	0	3	8.9999
AAA	chr2:183790311-183790534(-)$1	223	56	59	8.9999
AAA	chr10:98286904-98287137(-)$1	233	2	5	8.9999
AAA	chr7:34989373-34989596(-)$1	223	2	5	8.9999
AAA	chr10:112768907-112769135(+)$1	228	3	6	8.9999
AAA	chr5:96506817-96507037(-)$1	220	0	3	8.9999
AAA	chr17:65941919-65942143(+)$1	224	109	112	8.9999
AAA	chr1:51439817-51440045(+)$1	228	91	94	8.9999
AAA	chr12:29498308-29498538(-)$1	230	42	45	8.9999
AAA	chr3:183585558-183585783(-)$1	225	63	66	8.9999
AAA	chr16:15138090-15138318(-)$1	228	104	107	8.9999
AAA	chr5:153432557-153432779(+)$1	222	209	212	8.9999
AAA	chr3:127774290-127774513(+)$1	223	28	31	8.9999
AAA	chr15:68582624-68582845(+)$1	221	195	198	8.9999
AAA	chr18:9588641-9588867(-)$1	226	76	79	8.9999
AAA	chr14:97000808-97001037(+)$1	229	13	16	8.9999
AAA	chr12:49521614-49521848(-)$1	234	180	183	8.9999
AAA	chr15:73854183-73854410(-)$1	227	15	18	8.9999
AAA	chr6:71571259-71571485(+)$1	226	7	10	8.9999
AAA	chr3:184082705-184082928(+)$1	223	103	106	8.9999
AAA	chr13:23909497-23909719(-)$1	222	6	9	8.9999
AAA	chr4:166254629-166254856(+)$1	227	128	131	8.9999
AAA	chr20:47704479-47704712(+)$1	233	29	32	8.9999
AAA	chr5:43486920-43487140(-)$1	220	1	4	8.9999
AAA	chr1:85112986-85113226(-)$1	240	2	5	8.9999
AAA	chr16:71807031-71807253(-)$1	222	100	103	8.9999
AAA	chr16:24801366-24801586(+)$1	220	132	135	8.9999
AAA	chr2:190719485-190719705(+)$1	220	15	18	8.9999
AAA	chr2:29164320-29164541(+)$1	221	52	55	8.9999
AAA	chr1:111490745-111490965(-)$1	220	6	9	8.9999
AAA	chr1:155883849-155884074(-)$1	225	61	64	8.9999
AAA	chr17:28749840-28750058(+)$1	218	37	40	8.9999
aaa	chr6:108544129-108544351(-)$1	222	0	3	8.9999
AAA	chr12:50571680-50571909(-)$1	229	121	124	8.9999
AAA	chr20:54974212-54974443(+)$1	231	23	26	8.9999
AAA	chr21:34901113-34901332(-)$1	219	109	112	8.9999
AAA	chr3:160151366-160151585(+)$1	219	0	3	8.9999
AAA	chr10:28884805-28885024(+)$1	219	73	76	8.9999
AAA	chr1:197112528-197112753(-)$1	225	18	21	8.9999
AAA	chr10:98287069-98287301(-)$1	232	11	14	8.9999
aaa	chrX:123185117-123185345(+)$1	228	19	22	8.9999
AAA	chr4:164061288-164061511(-)$1	223	51	54	8.9999
aaa	chr1:225155083-225155308(+)$1	225	8	11	8.9999
AAA	chr4:159601607-159601836(+)$1	229	33	36	8.9999
AAA	chr1:155449498-155449718(-)$1	220	10	13	8.9999
AAA	chrX:123020157-123020385(+)$1	228	107	110	8.9999
AAA	chr4:57883276-57883496(+)$1	220	29	32	8.9999
AAA	chr10:70243158-70243379(-)$1	221	82	85	8.9999
AAA	chr6:82925835-82926065(-)$1	230	60	63	8.9999
AAA	chr17:1582281-1582500(-)$1	219	19	22	8.9999
AAA	chr13:23909318-23909547(-)$1	229	23	26	8.9999
AAA	chr1:75229548-75229774(+)$1	226	58	61	8.9999
AAA	chr2:231657844-231658068(+)$1	224	53	56	8.9999
AAA	chr16:82184819-82185041(-)$1	222	18	21	8.9999
AAA	chr7:102944784-102945013(+)$1	229	48	51	8.9999
AAA	chrX:99890568-99890789(-)$1	221	117	120	8.9999
AAA	chr11:92086433-92086652(+)$1	219	38	41	8.9999
AAA	chr12:42481535-42481761(-)$1	226	47	50	8.9999
AAA	chr6:122741181-122741402(+)$1	221	47	50	8.9999
AAA	chr17:16068273-16068499(-)$1	226	20	23	8.9999
AAA	chr6:149982876-149983093(-)$1	217	0	3	8.9999
AAA	chr19:39329457-39329685(-)$1	228	33	36	8.9999
AAA	chr2:42936011-42936246(+)$1	235	58	61	8.9999
AAA	chr6:56919248-56919474(+)$1	226	3	6	8.9999

#otherMatches

#Struct PSSM
:::	chr12:48468055-48468286(-)$1	231	89	92	8.9999
HHZ	chr12:50529681-50529904(-)$1	223	183	186	8.9999
c^^	chr7:32590868-32591091(+)$1	223	100	103	8.9999
ttt	chr6:26156812-26157045(+)$1	233	121	124	8.9999
yyy	chr5:138994237-138994459(+)$1	222	110	113	8.9999
f99	chr6:105474125-105474351(+)$1	226	50	53	8.9999
2ee	chr12:72092737-72092968(+)$1	231	192	195	8.9999
MMM	chr1:226564754-226564976(-)$1	222	24	27	8.9999
WWW	chr1:217793392-217793613(-)$1	221	46	49	8.9999
:::	chr3:41266884-41267103(+)$1	219	59	62	8.9999
::g	chr2:152311395-152311615(+)$1	220	39	42	8.9999
FFF	chr5:64931045-64931269(+)$1	224	138	141	8.9999
III	chr1:115269504-115269731(-)$1	227	62	65	8.9999
hhh	chr12:123813309-123813530(-)$1	221	45	48	8.9999
ccc	chr10:16806344-16806568(-)$1	224	119	122	8.9999
eee	chr7:107224286-107224511(+)$1	225	74	77	8.9999
::e	chr1:151640871-151641094(+)$1	223	81	84	8.9999
hhh	chr2:169727830-169728051(-)$1	221	81	84	8.9999
fqq	chr1:68948053-68948271(-)$1	218	29	32	8.9999
nnn	chr19:57802774-57803003(+)$1	229	50	53	8.9999
eee	chrX:71495412-71495631(-)$1	219	158	161	8.9999
!bb	chr2:183817784-183818008(-)$1	224	56	59	8.9999
]ee	chr10:7841916-7842142(+)$1	226	19	22	8.9999
:::	chr17:40764938-40765164(+)$1	226	212	215	8.9999
ggg	chr1:220206831-220207054(-)$1	223	12	15	8.9999
===	chr1:193044864-193045086(+)$1	222	21	24	8.9999
:::	chr17:27869920-27870151(+)$1	231	85	88	8.9999
KFF	chr3:180666126-180666350(+)$1	224	51	54	8.9999
ggg	chr8:53540531-53540756(-)$1	225	6	9	8.9999
gg:	chr19:37240018-37240238(-)$1	220	55	58	8.9999
)))	chr8:71486424-71486651(-)$1	227	63	66	8.9999
eee	chr7:888006-888229(+)$1	223	18	21	8.9999
:::	chr1:54237971-54238191(-)$1	220	0	3	8.9999
FFF	chr2:183790311-183790534(-)$1	223	56	59	8.9999
C:d	chr10:98286904-98287137(-)$1	233	2	5	8.9999
fff	chr7:34989373-34989596(-)$1	223	2	5	8.9999
:::	chr10:112768907-112769135(+)$1	228	3	6	8.9999
:CC	chr5:96506817-96507037(-)$1	220	0	3	8.9999
:::	chr17:65941919-65942143(+)$1	224	109	112	8.9999
]cc	chr1:51439817-51440045(+)$1	228	91	94	8.9999
ggg	chr12:29498308-29498538(-)$1	230	42	45	8.9999
h""	chr3:183585558-183585783(-)$1	225	63	66	8.9999
]bb	chr16:15138090-15138318(-)$1	228	104	107	8.9999
CC?	chr5:153432557-153432779(+)$1	222	209	212	8.9999
mff	chr3:127774290-127774513(+)$1	223	28	31	8.9999
rrr	chr15:68582624-68582845(+)$1	221	195	198	8.9999
:::	chr18:9588641-9588867(-)$1	226	76	79	8.9999
:::	chr14:97000808-97001037(+)$1	229	13	16	8.9999
YYH	chr12:49521614-49521848(-)$1	234	180	183	8.9999
::E	chr15:73854183-73854410(-)$1	227	15	18	8.9999
:::	chr6:71571259-71571485(+)$1	226	7	10	8.9999
:::	chr3:184082705-184082928(+)$1	223	103	106	8.9999
:::	chr13:23909497-23909719(-)$1	222	6	9	8.9999
f]e	chr4:166254629-166254856(+)$1	227	128	131	8.9999
eee	chr20:47704479-47704712(+)$1	233	29	32	8.9999
:::	chr5:43486920-43487140(-)$1	220	1	4	8.9999
DDD	chr1:85112986-85113226(-)$1	240	2	5	8.9999
:::	chr16:71807031-71807253(-)$1	222	100	103	8.9999
sss	chr16:24801366-24801586(+)$1	220	132	135	8.9999
:::	chr2:190719485-190719705(+)$1	220	15	18	8.9999
22c	chr2:29164320-29164541(+)$1	221	52	55	8.9999
:::	chr1:111490745-111490965(-)$1	220	6	9	8.9999
BBL	chr1:155883849-155884074(-)$1	225	61	64	8.9999
LLL	chr17:28749840-28750058(+)$1	218	37	40	8.9999
:::	chr6:108544129-108544351(-)$1	222	0	3	8.9999
ppp	chr12:50571680-50571909(-)$1	229	121	124	8.9999
eee	chr20:54974212-54974443(+)$1	231	23	26	8.9999
:::	chr21:34901113-34901332(-)$1	219	109	112	8.9999
:::	chr3:160151366-160151585(+)$1	219	0	3	8.9999
ddd	chr10:28884805-28885024(+)$1	219	73	76	8.9999
hh:	chr1:197112528-197112753(-)$1	225	18	21	8.9999
:::	chr10:98287069-98287301(-)$1	232	11	14	8.9999
fff	chrX:123185117-123185345(+)$1	228	19	22	8.9999
hhh	chr4:164061288-164061511(-)$1	223	51	54	8.9999
fff	chr1:225155083-225155308(+)$1	225	8	11	8.9999
eel	chr4:159601607-159601836(+)$1	229	33	36	8.9999
:::	chr1:155449498-155449718(-)$1	220	10	13	8.9999
:::	chrX:123020157-123020385(+)$1	228	107	110	8.9999
QQQ	chr4:57883276-57883496(+)$1	220	29	32	8.9999
nnn	chr10:70243158-70243379(-)$1	221	82	85	8.9999
fff	chr6:82925835-82926065(-)$1	230	60	63	8.9999
OOO	chr17:1582281-1582500(-)$1	219	19	22	8.9999
f::	chr13:23909318-23909547(-)$1	229	23	26	8.9999
"""	chr1:75229548-75229774(+)$1	226	58	61	8.9999
ee[	chr2:231657844-231658068(+)$1	224	53	56	8.9999
ttt	chr16:82184819-82185041(-)$1	222	18	21	8.9999
ggg	chr7:102944784-102945013(+)$1	229	48	51	8.9999
>>>	chrX:99890568-99890789(-)$1	221	117	120	8.9999
dd$	chr11:92086433-92086652(+)$1	219	38	41	8.9999
eee	chr12:42481535-42481761(-)$1	226	47	50	8.9999
mmd	chr6:122741181-122741402(+)$1	221	47	50	8.9999
D{A	chr17:16068273-16068499(-)$1	226	20	23	8.9999
:::	chr6:149982876-149983093(-)$1	217	0	3	8.9999
dll	chr19:39329457-39329685(-)$1	228	33	36	8.9999
ppp	chr2:42936011-42936246(+)$1	235	58	61	8.9999
:::	chr6:56919248-56919474(+)$1	226	3	6	8.9999

#DB
...	chr12:48468055-48468286(-)$1	1	89	92	8.9999
)).	chr12:50529681-50529904(-)$1	1	183	186	8.9999
(..	chr7:32590868-32591091(+)$1	1	100	103	8.9999
...	chr6:26156812-26157045(+)$1	1	121	124	8.9999
...	chr5:138994237-138994459(+)$1	1	110	113	8.9999
)..	chr6:105474125-105474351(+)$1	1	50	53	8.9999
.))	chr12:72092737-72092968(+)$1	1	192	195	8.9999
...	chr1:226564754-226564976(-)$1	1	24	27	8.9999
...	chr1:217793392-217793613(-)$1	1	46	49	8.9999
...	chr3:41266884-41267103(+)$1	1	59	62	8.9999
..(	chr2:152311395-152311615(+)$1	1	39	42	8.9999
)))	chr5:64931045-64931269(+)$1	1	138	141	8.9999
(((	chr1:115269504-115269731(-)$1	1	62	65	8.9999
(((	chr12:123813309-123813530(-)$1	1	45	48	8.9999
)))	chr10:16806344-16806568(-)$1	1	119	122	8.9999
)))	chr7:107224286-107224511(+)$1	1	74	77	8.9999
..(	chr1:151640871-151641094(+)$1	1	81	84	8.9999
)))	chr2:169727830-169728051(-)$1	1	81	84	8.9999
(..	chr1:68948053-68948271(-)$1	1	29	32	8.9999
...	chr19:57802774-57803003(+)$1	1	50	53	8.9999
(((	chrX:71495412-71495631(-)$1	1	158	161	8.9999
.((	chr2:183817784-183818008(-)$1	1	56	59	8.9999
.))	chr10:7841916-7842142(+)$1	1	19	22	8.9999
...	chr17:40764938-40765164(+)$1	1	212	215	8.9999
(((	chr1:220206831-220207054(-)$1	1	12	15	8.9999
(((	chr1:193044864-193045086(+)$1	1	21	24	8.9999
...	chr17:27869920-27870151(+)$1	1	85	88	8.9999
.((	chr3:180666126-180666350(+)$1	1	51	54	8.9999
(((	chr8:53540531-53540756(-)$1	1	6	9	8.9999
)).	chr19:37240018-37240238(-)$1	1	55	58	8.9999
...	chr8:71486424-71486651(-)$1	1	63	66	8.9999
(((	chr7:888006-888229(+)$1	1	18	21	8.9999
...	chr1:54237971-54238191(-)$1	1	0	3	8.9999
(((	chr2:183790311-183790534(-)$1	1	56	59	8.9999
(.(	chr10:98286904-98287137(-)$1	1	2	5	8.9999
(((	chr7:34989373-34989596(-)$1	1	2	5	8.9999
...	chr10:112768907-112769135(+)$1	1	3	6	8.9999
.((	chr5:96506817-96507037(-)$1	1	0	3	8.9999
...	chr17:65941919-65942143(+)$1	1	109	112	8.9999
.))	chr1:51439817-51440045(+)$1	1	91	94	8.9999
(((	chr12:29498308-29498538(-)$1	1	42	45	8.9999
(..	chr3:183585558-183585783(-)$1	1	63	66	8.9999
.))	chr16:15138090-15138318(-)$1	1	104	107	8.9999
)).	chr5:153432557-153432779(+)$1	1	209	212	8.9999
.))	chr3:127774290-127774513(+)$1	1	28	31	8.9999
...	chr15:68582624-68582845(+)$1	1	195	198	8.9999
...	chr18:9588641-9588867(-)$1	1	76	79	8.9999
...	chr14:97000808-97001037(+)$1	1	13	16	8.9999
..)	chr12:49521614-49521848(-)$1	1	180	183	8.9999
..(	chr15:73854183-73854410(-)$1	1	15	18	8.9999
...	chr6:71571259-71571485(+)$1	1	7	10	8.9999
...	chr3:184082705-184082928(+)$1	1	103	106	8.9999
...	chr13:23909497-23909719(-)$1	1	6	9	8.9999
).)	chr4:166254629-166254856(+)$1	1	128	131	8.9999
)))	chr20:47704479-47704712(+)$1	1	29	32	8.9999
...	chr5:43486920-43487140(-)$1	1	1	4	8.9999
(((	chr1:85112986-85113226(-)$1	1	2	5	8.9999
...	chr16:71807031-71807253(-)$1	1	100	103	8.9999
...	chr16:24801366-24801586(+)$1	1	132	135	8.9999
...	chr2:190719485-190719705(+)$1	1	15	18	8.9999
..)	chr2:29164320-29164541(+)$1	1	52	55	8.9999
...	chr1:111490745-111490965(-)$1	1	6	9	8.9999
((.	chr1:155883849-155884074(-)$1	1	61	64	8.9999
...	chr17:28749840-28750058(+)$1	1	37	40	8.9999
...	chr6:108544129-108544351(-)$1	1	0	3	8.9999
...	chr12:50571680-50571909(-)$1	1	121	124	8.9999
(((	chr20:54974212-54974443(+)$1	1	23	26	8.9999
...	chr21:34901113-34901332(-)$1	1	109	112	8.9999
...	chr3:160151366-160151585(+)$1	1	0	3	8.9999
(((	chr10:28884805-28885024(+)$1	1	73	76	8.9999
)).	chr1:197112528-197112753(-)$1	1	18	21	8.9999
...	chr10:98287069-98287301(-)$1	1	11	14	8.9999
(((	chrX:123185117-123185345(+)$1	1	19	22	8.9999
(((	chr4:164061288-164061511(-)$1	1	51	54	8.9999
(((	chr1:225155083-225155308(+)$1	1	8	11	8.9999
((.	chr4:159601607-159601836(+)$1	1	33	36	8.9999
...	chr1:155449498-155449718(-)$1	1	10	13	8.9999
...	chrX:123020157-123020385(+)$1	1	107	110	8.9999
...	chr4:57883276-57883496(+)$1	1	29	32	8.9999
...	chr10:70243158-70243379(-)$1	1	82	85	8.9999
)))	chr6:82925835-82926065(-)$1	1	60	63	8.9999
...	chr17:1582281-1582500(-)$1	1	19	22	8.9999
)..	chr13:23909318-23909547(-)$1	1	23	26	8.9999
...	chr1:75229548-75229774(+)$1	1	58	61	8.9999
((.	chr2:231657844-231658068(+)$1	1	53	56	8.9999
...	chr16:82184819-82185041(-)$1	1	18	21	8.9999
)))	chr7:102944784-102945013(+)$1	1	48	51	8.9999
...	chrX:99890568-99890789(-)$1	1	117	120	8.9999
((.	chr11:92086433-92086652(+)$1	1	38	41	8.9999
(((	chr12:42481535-42481761(-)$1	1	47	50	8.9999
..)	chr6:122741181-122741402(+)$1	1	47	50	8.9999
(.(	chr17:16068273-16068499(-)$1	1	20	23	8.9999
...	chr6:149982876-149983093(-)$1	1	0	3	8.9999
(..	chr19:39329457-39329685(-)$1	1	33	36	8.9999
...	chr2:42936011-42936246(+)$1	1	58	61	8.9999
...	chr6:56919248-56919474(+)$1	1	3	6	8.9999

#PSSM
A : 0.96	a : 0.03	
A : 0.96	a : 0.03	
A : 0.96	a : 0.03	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_UTR_m3_run1.nuc.txt

#NT
CUGGCC	chr16:771086-771305(-)$1	219	96	102	14.0975
CGGGCC	chr5:180670212-180670478(-)$1	266	89	95	13.4878
CAGGCC	chr4:2252835-2253070(-)$1	235	13	19	15.4390
CAGGCC	chr12:133201210-133201439(-)$1	229	192	198	15.4390
CUGGCC	chr11:506515-506755(-)$1	240	14	20	14.0975
CUGGCC	chr15:45493245-45493520(+)$1	275	262	268	14.0975
CGGGCC	chr16:68298426-68298646(+)$1	220	39	45	13.4878
CAGGCC	chr19:14589036-14589268(-)$1	232	179	185	15.4390
CCGGCC	chrX:153672445-153672675(-)$1	230	58	64	13.9756
CAGGCC	chr3:155588460-155588686(+)$1	226	95	101	15.4390
CAGGCC	chr9:127269583-127269808(+)$1	225	183	189	15.4390
CAGGCC	chr7:75686629-75686854(+)$1	225	43	49	15.4390
CAGGCC	chr2:128615341-128615579(-)$1	238	28	34	15.4390
CCGGCC	chr12:110719031-110719257(+)$1	226	200	206	13.9756
CCGGCC	chr20:443045-443268(-)$1	223	25	31	13.9756
CAGGCC	chr21:45179555-45179777(+)$1	222	123	129	15.4390
CCGGCC	chr21:46237849-46238071(-)$1	222	45	51	13.9756
CAGGCC	chr1:149813705-149814020(-)$1	315	91	97	15.4390
cgggcc	chr9:127631410-127631631(+)$1	221	115	121	13.4878
CAGGCC	chr16:10912359-10912578(+)$1	219	18	24	15.4390
CUGGCC	chr16:28074419-28074647(+)$1	228	188	194	14.0975
CAGGCC	chr7:98972297-98972526(+)$1	229	2	8	15.4390
CAGGCC	chr14:21979166-21979466(-)$1	300	125	131	15.4390
CUGGCC	chr22:50656824-50657056(-)$1	232	12	18	14.0975
CAGGCC	chr2:220403279-220403515(+)$1	236	23	29	15.4390
CAGGCC	chr1:1413986-1414216(+)$1	230	133	139	15.4390
CUGGCC	chr15:89173403-89173626(+)$1	223	55	61	14.0975
CGGGCC	chr7:129592296-129592515(-)$1	219	70	76	13.4878
CAGGcc	chr19:35634046-35634270(-)$1	224	186	192	15.4390
ccggcc	chr5:176900466-176900688(-)$1	222	12	18	13.9756
CCGGCC	chr3:98451680-98451911(+)$1	231	3	9	13.9756
CUGGCC	chr3:50685587-50685816(+)$1	229	69	75	14.0975
CUGGCC	chr17:80861200-80861427(+)$1	227	117	123	14.0975
CCGGCC	chr15:75940264-75940489(-)$1	225	138	144	13.9756
CAGGCC	chr22:22893289-22893520(-)$1	231	207	213	15.4390
caggcc	chr11:129733717-129733937(-)$1	220	209	215	15.4390
CCGGCC	chr14:24027917-24028148(+)$1	231	41	47	13.9756
CAGGCC	chr19:50001103-50001340(+)$1	237	227	233	15.4390
CAGGCC	chr19:1383456-1383687(+)$1	231	55	61	15.4390
CUggcc	chr19:4065525-4065745(+)$1	220	6	12	14.0975

#otherMatches

#Struct PSSM
22ccc:	chr1:61553773-61553992(+)$1	219	119	125	15.4390
""ccc!	chr16:771086-771305(-)$1	219	96	102	14.0975
iiiiii	chr5:180670212-180670478(-)$1	266	89	95	13.4878
mmmggg	chr4:2252835-2253070(-)$1	235	13	19	15.4390
YFFFFF	chr12:133201210-133201439(-)$1	229	192	198	15.4390
:CCCCC	chr11:506515-506755(-)$1	240	14	20	14.0975
BB}FFF	chr15:45493245-45493520(+)$1	275	262	268	14.0975
d[a[cc	chr16:68298426-68298646(+)$1	220	39	45	13.4878
[cccll	chr19:14589036-14589268(-)$1	232	179	185	15.4390
b[cccl	chrX:153672445-153672675(-)$1	230	58	64	13.9756
!cccll	chr3:155588460-155588686(+)$1	226	95	101	15.4390
D}HHHH	chr9:127269583-127269808(+)$1	225	183	189	15.4390
c]eeee	chr7:75686629-75686854(+)$1	225	43	49	15.4390
EEEEE:	chr2:128615341-128615579(-)$1	238	28	34	15.4390
rrcccb	chr12:110719031-110719257(+)$1	226	200	206	13.9756
ccceee	chr20:443045-443268(-)$1	223	25	31	13.9756
[bb[af	chr21:45179555-45179777(+)$1	222	123	129	15.4390
eeeeeb	chr21:46237849-46238071(-)$1	222	45	51	13.9756
c!!ccc	chr1:149813705-149814020(-)$1	315	91	97	15.4390
hhhhhh	chr9:127631410-127631631(+)$1	221	115	121	13.4878
{FFFFF	chr16:10912359-10912578(+)$1	219	18	24	15.4390
gg]eee	chr16:28074419-28074647(+)$1	228	188	194	14.0975
CCKKDD	chr7:98972297-98972526(+)$1	229	2	8	15.4390
::DDDD	chr14:21979166-21979466(-)$1	300	125	131	15.4390
KKCCC:	chr22:50656824-50657056(-)$1	232	12	18	14.0975
nnnnnd	chr2:220403279-220403515(+)$1	236	23	29	15.4390
iiiiii	chr1:1413986-1414216(+)$1	230	133	139	15.4390
fff22b	chr15:89173403-89173626(+)$1	223	55	61	14.0975
!!gggg	chr7:129592296-129592515(-)$1	219	70	76	13.4878
hhhhhh	chr19:35634046-35634270(-)$1	224	186	192	15.4390
HHHHH{	chr5:176900466-176900688(-)$1	222	12	18	13.9756
DDD{BB	chr3:98451680-98451911(+)$1	231	3	9	13.9756
d[a[cc	chr3:50685587-50685816(+)$1	229	69	75	14.0975
%%%ccc	chr17:80861200-80861427(+)$1	227	117	123	14.0975
dddd$$	chr15:75940264-75940489(-)$1	225	138	144	13.9756
ZZEEEE	chr22:22893289-22893520(-)$1	231	207	213	15.4390
CC}GGG	chr11:129733717-129733937(-)$1	220	209	215	15.4390
""bbqq	chr14:24027917-24028148(+)$1	231	41	47	13.9756
GGGG}B	chr19:50001103-50001340(+)$1	237	227	233	15.4390
beeeee	chr19:1383456-1383687(+)$1	231	55	61	15.4390
CCKKHH	chr19:4065525-4065745(+)$1	220	6	12	14.0975

#DB
..))).	chr1:61553773-61553992(+)$1	1	119	125	15.4390
..(((.	chr16:771086-771305(-)$1	1	96	102	14.0975
((((((	chr5:180670212-180670478(-)$1	1	89	95	13.4878
...)))	chr4:2252835-2253070(-)$1	1	13	19	15.4390
.)))))	chr12:133201210-133201439(-)$1	1	192	198	15.4390
.(((((	chr11:506515-506755(-)$1	1	14	20	14.0975
)).)))	chr15:45493245-45493520(+)$1	1	262	268	14.0975
(.(.((	chr16:68298426-68298646(+)$1	1	39	45	13.4878
.(((..	chr19:14589036-14589268(-)$1	1	179	185	15.4390
(.(((.	chrX:153672445-153672675(-)$1	1	58	64	13.9756
.(((..	chr3:155588460-155588686(+)$1	1	95	101	15.4390
).))))	chr9:127269583-127269808(+)$1	1	183	189	15.4390
).))))	chr7:75686629-75686854(+)$1	1	43	49	15.4390
(((((.	chr2:128615341-128615579(-)$1	1	28	34	15.4390
..))))	chr12:110719031-110719257(+)$1	1	200	206	13.9756
((((((	chr20:443045-443268(-)$1	1	25	31	13.9756
.((.((	chr21:45179555-45179777(+)$1	1	123	129	15.4390
((((((	chr21:46237849-46238071(-)$1	1	45	51	13.9756
(..(((	chr1:149813705-149814020(-)$1	1	91	97	15.4390
((((((	chr9:127631410-127631631(+)$1	1	115	121	13.4878
.(((((	chr16:10912359-10912578(+)$1	1	18	24	15.4390
)).)))	chr16:28074419-28074647(+)$1	1	188	194	14.0975
((..((	chr7:98972297-98972526(+)$1	1	2	8	15.4390
..((((	chr14:21979166-21979466(-)$1	1	125	131	15.4390
..(((.	chr22:50656824-50657056(-)$1	1	12	18	14.0975
.....)	chr2:220403279-220403515(+)$1	1	23	29	15.4390
((((((	chr1:1413986-1414216(+)$1	1	133	139	15.4390
)))..)	chr15:89173403-89173626(+)$1	1	55	61	14.0975
..((((	chr7:129592296-129592515(-)$1	1	70	76	13.4878
))))))	chr19:35634046-35634270(-)$1	1	186	192	15.4390
(((((.	chr5:176900466-176900688(-)$1	1	12	18	13.9756
(((.((	chr3:98451680-98451911(+)$1	1	3	9	13.9756
(.(.((	chr3:50685587-50685816(+)$1	1	69	75	14.0975
...(((	chr17:80861200-80861427(+)$1	1	117	123	14.0975
((((..	chr15:75940264-75940489(-)$1	1	138	144	13.9756
..))))	chr22:22893289-22893520(-)$1	1	207	213	15.4390
)).)))	chr11:129733717-129733937(-)$1	1	209	215	15.4390
..((..	chr14:24027917-24028148(+)$1	1	41	47	13.9756
)))).)	chr19:50001103-50001340(+)$1	1	227	233	15.4390
)(((((	chr19:1383456-1383687(+)$1	1	55	61	15.4390
((..((	chr19:4065525-4065745(+)$1	1	6	12	14.0975

#PSSM
C : 0.92	c : 0.07	
A : 0.46	U : 0.21	C : 0.17	G : 0.07	g : 0.02	c : 0.02	a : 0.02	
G : 0.90	g : 0.09	
G : 0.90	g : 0.09	
C : 0.87	c : 0.12	
C : 0.87	c : 0.12	

#score	601.414634146342
#seq	41
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_WTAP_Ping2014_hg19_CDS_m3_run1.nuc.txt

#NT
CAUGCUG	chr7:151329101-151329320(-)$1	219	63	70	12.3333
CAUGCUG	chr17:7157921-7158148(+)$1	227	170	177	12.3333
CCUGCGG	chr17:80861200-80861427(+)$1	227	175	182	13.3333
GCUGCUG	chr12:69633310-69633542(+)$1	232	47	54	13.5833
CCUGGUG	chr4:119606629-119606848(+)$1	219	135	142	12.5833
CCUGCUG	chr7:2627357-2627584(+)$1	227	44	51	16.7500
CCUGCUG	chr3:119886218-119886438(+)$1	220	203	210	16.7500
CCAGCUG	chr16:29998948-29999181(+)$1	233	186	193	12.1666
GCUGCUG	chr2:217364575-217364834(+)$1	259	241	248	13.5833
UCUGCUG	chr12:54930699-54930926(+)$1	227	75	82	13.0833
CCUGCUC	chr1:19557250-19557489(+)$1	239	116	123	12.3333
CCUGCUG	chr2:24149337-24149565(-)$1	228	185	192	16.7500
CCUGCUG	chr19:39949543-39949772(+)$1	229	50	57	16.7500
CCUGCAG	chr20:44441240-44441459(+)$1	219	39	46	13.2500
CCUGCUG	chr9:139694877-139695115(+)$1	238	31	38	16.7500
ACUGCUG	chr19:10671789-10672015(-)$1	226	193	200	13.2500
CCUGCUG	chr3:48682932-48683169(-)$1	237	176	183	16.7500
CCCGCUG	chr4:2252835-2253070(-)$1	235	63	70	12.1666
CCUGGUG	chr20:62701072-62701294(+)$1	222	161	168	12.5833
ACUGCUG	chr2:220088777-220088997(-)$1	220	26	33	13.2500
GCUGCUG	chr16:53922722-53922952(+)$1	230	175	182	13.5833
CCUGCGG	chr6:42072652-42072886(+)$1	234	201	208	13.3333
CUUGCUG	chr10:76980463-76980684(+)$1	221	161	168	12.3333
CCUGCGG	chr19:56599745-56599975(-)$1	230	22	29	13.3333
CCUCCUG	chr16:18800311-18800533(-)$1	222	67	74	12.0833
CCUGCUU	chr1:38435232-38435462(-)$1	230	45	52	12.5000
CCUGGUG	chr19:18423338-18423562(-)$1	224	88	95	12.5833
ACUGCUG	chr16:70713600-70713845(-)$1	245	68	75	13.2500
CUUGCUG	chr11:66206049-66206278(-)$1	229	9	16	12.3333
CGUGCUG	chr7:138602911-138603141(-)$1	230	131	138	12.2500
CCUGCUG	chr9:34611046-34611276(-)$1	230	96	103	16.7500
CCUGCCG	chr19:3982166-3982395(-)$1	229	96	103	13.3333
CCUGCCG	chr19:36111000-36111222(+)$1	222	110	117	13.3333
CCUCCUG	chr2:232319848-232320080(-)$1	232	92	99	12.0833
CCUGCCG	chr14:99976950-99977172(+)$1	222	42	49	13.3333
GCUGCUG	chr18:48723033-48723252(-)$1	219	56	63	13.5833
CCUGCGG	chr16:67575904-67576149(-)$1	245	206	213	13.3333
GCUGCUG	chr17:17067875-17068105(+)$1	230	98	105	13.5833
CCUGCAG	chr5:865513-865755(-)$1	242	123	130	13.2500
ACUGCUG	chr9:21333684-21333907(-)$1	223	138	145	13.2500
GCUGCUG	chr17:3436046-3436272(-)$1	226	93	100	13.5833
ccggcug	chr17:40273183-40273403(-)$1	220	114	121	12.2500
CCUGGUG	chr1:24861620-24861843(+)$1	223	176	183	12.5833
CCUGCUG	chr5:139928531-139928761(+)$1	230	28	35	16.7500
CCUGCGG	chr19:56126993-56127235(+)$1	242	92	99	13.3333
CCUGCCG	chrX:118774561-118774791(-)$1	230	45	52	13.3333
CCUGCUU	chr10:112057349-112057578(-)$1	229	64	71	12.5000
CCUGUUG	chr1:8921321-8921570(-)$1	249	179	186	12.4166
CCUGCUU	chr19:50001103-50001340(+)$1	237	190	197	12.5000
GCUGCUG	chr9:140695286-140695513(+)$1	227	107	114	13.5833
UCUGCUG	chr1:183520115-183520345(+)$1	230	183	190	13.0833
CCUGCCG	chr16:30456857-30457078(-)$1	221	13	20	13.3333
CCUGCAG	chr12:133201210-133201439(-)$1	229	36	43	13.2500
CCUGUUG	chr11:497893-498113(+)$1	220	148	155	12.4166
CCUGCUA	chr15:41001160-41001400(+)$1	240	203	210	12.4166
CCUGCAG	chr3:183882576-183882806(+)$1	230	0	7	13.2500
CCUGCUA	chr19:45150444-45150664(+)$1	220	113	120	12.4166
GCUGCUG	chr19:39340382-39340603(-)$1	221	8	15	13.5833
CCUGCUG	chr22:50656824-50657056(-)$1	232	75	82	16.7500

#otherMatches

#Struct PSSM
tttbb]e	chr17:46136750-46136973(+)$1	223	15	22	12.2500
cclllcc	chr7:151329101-151329320(-)$1	219	63	70	12.3333
b::cccl	chr17:7157921-7158148(+)$1	227	170	177	12.3333
"ffffff	chr17:80861200-80861427(+)$1	227	175	182	13.3333
=======	chr12:69633310-69633542(+)$1	232	47	54	13.5833
dddd]cc	chr4:119606629-119606848(+)$1	219	135	142	12.5833
EEEE{GG	chr7:2627357-2627584(+)$1	227	44	51	16.7500
GGG____	chr3:119886218-119886438(+)$1	220	203	210	16.7500
ee]bb]e	chr16:29998948-29999181(+)$1	233	186	193	12.1666
ppppeee	chr2:217364575-217364834(+)$1	259	241	248	13.5833
ddd!!cc	chr12:54930699-54930926(+)$1	227	75	82	13.0833
fff####	chr1:19557250-19557489(+)$1	239	116	123	12.3333
ooooooe	chr2:24149337-24149565(-)$1	228	185	192	16.7500
e:::iii	chr19:39949543-39949772(+)$1	229	50	57	16.7500
###dddd	chr20:44441240-44441459(+)$1	219	39	46	13.2500
ffffff[	chr9:139694877-139695115(+)$1	238	31	38	16.7500
3eeeee2	chr19:10671789-10672015(-)$1	226	193	200	13.2500
ndddd22	chr3:48682932-48683169(-)$1	237	176	183	16.7500
gggffff	chr4:2252835-2253070(-)$1	235	63	70	12.1666
}EEEEE}	chr20:62701072-62701294(+)$1	222	161	168	12.5833
e:HHHHH	chr2:220088777-220088997(-)$1	220	26	33	13.2500
gccc]bb	chr16:53922722-53922952(+)$1	230	175	182	13.5833
GGGGG}D	chr6:42072652-42072886(+)$1	234	201	208	13.3333
eemmmme	chr10:76980463-76980684(+)$1	221	161	168	12.3333
KDDDD{E	chr19:56599745-56599975(-)$1	230	22	29	13.3333
DDDKKEE	chr16:18800311-18800533(-)$1	222	67	74	12.0833
ddddlll	chr1:38435232-38435462(-)$1	230	45	52	12.5000
EEEEE}A	chr19:18423338-18423562(-)$1	224	88	95	12.5833
mdddd]d	chr16:70713600-70713845(-)$1	245	68	75	13.2500
mmmbb:C	chr11:66206049-66206278(-)$1	229	9	16	12.3333
:ffffff	chr7:138602911-138603141(-)$1	230	131	138	12.2500
llcccEE	chr9:34611046-34611276(-)$1	230	96	103	16.7500
gggggll	chr19:3982166-3982395(-)$1	229	96	103	13.3333
dd::::f	chr19:36111000-36111222(+)$1	222	110	117	13.3333
ddddbbm	chr2:232319848-232320080(-)$1	232	92	99	12.0833
GGGGGG{	chr14:99976950-99977172(+)$1	222	42	49	13.3333
:hhhhhh	chr18:48723033-48723252(-)$1	219	56	63	13.5833
eee]ccc	chr16:67575904-67576149(-)$1	245	206	213	13.3333
iiiiiii	chr17:17067875-17068105(+)$1	230	98	105	13.5833
a[eeeee	chr5:865513-865755(-)$1	242	123	130	13.2500
ccccddd	chr9:21333684-21333907(-)$1	223	138	145	13.2500
ffffff3	chr17:3436046-3436272(-)$1	226	93	100	13.5833
!!ddddm	chr17:40273183-40273403(-)$1	220	114	121	12.2500
ddmmmmd	chr1:24861620-24861843(+)$1	223	176	183	12.5833
ffffff[	chr5:139928531-139928761(+)$1	230	28	35	16.7500
nnfffff	chr19:56126993-56127235(+)$1	242	92	99	13.3333
dddd:::	chrX:118774561-118774791(-)$1	230	45	52	13.3333
eeeee::	chr10:112057349-112057578(-)$1	229	64	71	12.5000
dddd!!d	chr1:8921321-8921570(-)$1	249	179	186	12.4166
ttttttt	chr19:50001103-50001340(+)$1	237	190	197	12.5000
ccmmmmc	chr9:140695286-140695513(+)$1	227	107	114	13.5833
rrrrrrf	chr1:183520115-183520345(+)$1	230	183	190	13.0833
b[dddd!	chr16:30456857-30457078(-)$1	221	13	20	13.3333
LLLA{FF	chr12:133201210-133201439(-)$1	229	36	43	13.2500
dddd!!e	chr11:497893-498113(+)$1	220	148	155	12.4166
yycccff	chr15:41001160-41001400(+)$1	240	203	210	12.4166
ccc"""c	chr3:183882576-183882806(+)$1	230	0	7	13.2500
GGGGG::	chr19:45150444-45150664(+)$1	220	113	120	12.4166
IIIIIII	chr19:39340382-39340603(-)$1	221	8	15	13.5833
affffff	chr22:50656824-50657056(-)$1	232	75	82	16.7500

#DB
...)).)	chr17:46136750-46136973(+)$1	1	15	22	12.2500
((...))	chr7:151329101-151329320(-)$1	1	63	70	12.3333
)..(((.	chr17:7157921-7158148(+)$1	1	170	177	12.3333
.((((((	chr17:80861200-80861427(+)$1	1	175	182	13.3333
(((((((	chr12:69633310-69633542(+)$1	1	47	54	13.5833
)))).))	chr4:119606629-119606848(+)$1	1	135	142	12.5833
((((.((	chr7:2627357-2627584(+)$1	1	44	51	16.7500
)))....	chr3:119886218-119886438(+)$1	1	203	210	16.7500
)).)).)	chr16:29998948-29999181(+)$1	1	186	193	12.1666
....)))	chr2:217364575-217364834(+)$1	1	241	248	13.5833
(((..((	chr12:54930699-54930926(+)$1	1	75	82	13.0833
(((....	chr1:19557250-19557489(+)$1	1	116	123	12.3333
......)	chr2:24149337-24149565(-)$1	1	185	192	16.7500
)...(((	chr19:39949543-39949772(+)$1	1	50	57	16.7500
...((((	chr20:44441240-44441459(+)$1	1	39	46	13.2500
((((((.	chr9:139694877-139695115(+)$1	1	31	38	16.7500
.))))).	chr19:10671789-10672015(-)$1	1	193	200	13.2500
.))))..	chr3:48682932-48683169(-)$1	1	176	183	16.7500
)))((((	chr4:2252835-2253070(-)$1	1	63	70	12.1666
.))))).	chr20:62701072-62701294(+)$1	1	161	168	12.5833
).(((((	chr2:220088777-220088997(-)$1	1	26	33	13.2500
)))).))	chr16:53922722-53922952(+)$1	1	175	182	13.5833
))))).)	chr6:42072652-42072886(+)$1	1	201	208	13.3333
((....)	chr10:76980463-76980684(+)$1	1	161	168	12.3333
.((((.(	chr19:56599745-56599975(-)$1	1	22	29	13.3333
(((..((	chr16:18800311-18800533(-)$1	1	67	74	12.0833
((((...	chr1:38435232-38435462(-)$1	1	45	52	12.5000
))))).)	chr19:18423338-18423562(-)$1	1	88	95	12.5833
.)))).)	chr16:70713600-70713845(-)$1	1	68	75	13.2500
...)).(	chr11:66206049-66206278(-)$1	1	9	16	12.3333
.((((((	chr7:138602911-138603141(-)$1	1	131	138	12.2500
..)))))	chr9:34611046-34611276(-)$1	1	96	103	16.7500
(((((..	chr19:3982166-3982395(-)$1	1	96	103	13.3333
))....(	chr19:36111000-36111222(+)$1	1	110	117	13.3333
((((((.	chr2:232319848-232320080(-)$1	1	92	99	12.0833
((((((.	chr14:99976950-99977172(+)$1	1	42	49	13.3333
.((((((	chr18:48723033-48723252(-)$1	1	56	63	13.5833
))).)))	chr16:67575904-67576149(-)$1	1	206	213	13.3333
)))))))	chr17:17067875-17068105(+)$1	1	98	105	13.5833
(.(((((	chr5:865513-865755(-)$1	1	123	130	13.2500
(((((((	chr9:21333684-21333907(-)$1	1	138	145	13.2500
)))))).	chr17:3436046-3436272(-)$1	1	93	100	13.5833
..((((.	chr17:40273183-40273403(-)$1	1	114	121	12.2500
((....)	chr1:24861620-24861843(+)$1	1	176	183	12.5833
((((((.	chr5:139928531-139928761(+)$1	1	28	35	16.7500
..)))))	chr19:56126993-56127235(+)$1	1	92	99	13.3333
))))...	chrX:118774561-118774791(-)$1	1	45	52	13.3333
)))))..	chr10:112057349-112057578(-)$1	1	64	71	12.5000
((((..(	chr1:8921321-8921570(-)$1	1	179	186	12.4166
.......	chr19:50001103-50001340(+)$1	1	190	197	12.5000
((....)	chr9:140695286-140695513(+)$1	1	107	114	13.5833
......)	chr1:183520115-183520345(+)$1	1	183	190	13.0833
(.((((.	chr16:30456857-30457078(-)$1	1	13	20	13.3333
...(.((	chr12:133201210-133201439(-)$1	1	36	43	13.2500
((((..(	chr11:497893-498113(+)$1	1	148	155	12.4166
..)))))	chr15:41001160-41001400(+)$1	1	203	210	12.4166
(((...(	chr3:183882576-183882806(+)$1	1	0	7	13.2500
(((((..	chr19:45150444-45150664(+)$1	1	113	120	12.4166
(((((((	chr19:39340382-39340603(-)$1	1	8	15	13.5833
)))))))	chr22:50656824-50657056(-)$1	1	75	82	16.7500

#PSSM
C : 0.75	G : 0.13	A : 0.06	U : 0.03	c : 0.01	
C : 0.90	A : 0.03	U : 0.03	G : 0.01	c : 0.01	
U : 0.93	G : 0.01	A : 0.01	C : 0.01	g : 0.01	
G : 0.95	C : 0.03	g : 0.01	
C : 0.88	G : 0.06	U : 0.03	c : 0.01	
U : 0.75	G : 0.08	C : 0.08	A : 0.06	u : 0.01	
G : 0.88	U : 0.05	A : 0.03	C : 0.01	g : 0.01	

#score	809.333333333335
#seq	60
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011a_hg19_UTR_m2_run1.nuc.txt

#NT
UUUCUAAA	chr2:207177906-207178131(+)$1	225	28	36	15.8548
UUUUUAAU	chr13:107142453-107142684(-)$1	231	111	119	15.8548
UAUUUAAA	chr5:122950531-122950750(+)$1	219	11	19	16.4193
UUUUUAAA	chr14:92529761-92529988(-)$1	227	54	62	20.2903
UUUUGAAA	chr13:110407836-110408059(-)$1	223	141	149	15.7741
uuauuaaa	chr12:66737290-66737514(+)$1	224	107	115	16.1774
UUUUUCAA	chr2:233208812-233209036(+)$1	224	90	98	15.6935
AUUUUAAA	chrX:118968513-118968736(-)$1	223	115	123	16.3387
UUAUUAAA	chr2:114471781-114472003(-)$1	222	46	54	16.1774
UUUAUAAA	chr9:123526129-123526354(-)$1	225	20	28	15.9354
UUUUCAAA	chr1:225590642-225590861(-)$1	219	189	197	15.7741
UUCUUAAA	chr10:18964903-18965128(+)$1	225	208	216	16.0967
UUUUUUAA	chr1:47142152-47142379(-)$1	227	73	81	15.7741
UUUUUAUA	chr16:19564603-19564826(+)$1	223	55	63	15.6935
UCUUUAAA	chr10:119766090-119766309(-)$1	219	11	19	16.0161
UUUUUAAA	chr1:213166665-213166892(-)$1	227	109	117	20.2903
UUUAUAAA	chr15:42858861-42859085(+)$1	224	76	84	15.9354
UAUUUAAA	chr7:26412155-26412382(+)$1	227	147	155	16.4193
UAUUUAAA	chr17:76849230-76849462(-)$1	232	110	118	16.4193
UUUUUAAA	chr10:98724051-98724283(+)$1	232	145	153	20.2903
cuuuuaaa	chr21:28208580-28208800(-)$1	220	105	113	16.1774
UUUUUAAC	chr10:102896826-102897054(+)$1	228	119	127	15.8548
UUUUUAAG	chr15:66841376-66841595(+)$1	219	36	44	15.7741
auuuuaaa	chr1:228288335-228288567(-)$1	232	123	131	16.3387
UUGUUaaa	chr19:44126603-44126833(-)$1	230	193	201	16.1774
UUUUGAAA	chr3:122128638-122128858(+)$1	220	63	71	15.7741
UUUUUAAA	chr2:198284872-198285094(-)$1	222	44	52	20.2903
UUCUUAAA	chrX:135127078-135127300(+)$1	222	108	116	16.0967
AUUUUAAA	chr11:20530195-20530422(+)$1	227	112	120	16.3387
UUUUUAAA	chr1:25169226-25169456(+)$1	230	119	127	20.2903
UUUUUAAA	chr2:32248989-32249210(-)$1	221	198	206	20.2903
UUAUUAAA	chr13:21751371-21751594(+)$1	223	102	110	16.1774
UAUUUAAA	chr17:53470395-53470614(-)$1	219	13	21	16.4193
UUUUUGAA	chr1:68153811-68154032(+)$1	221	158	166	15.6935
UUUUUUAA	chr20:43128238-43128463(-)$1	225	100	108	15.7741
UUUUUAAC	chr18:21061743-21061969(+)$1	226	169	177	15.8548
UUUUCAAA	chr3:170077933-170078165(+)$1	232	120	128	15.7741
UUGUUAAA	chr8:17081250-17081475(+)$1	225	69	77	16.1774
UAUUUAAA	chr17:61671254-61671484(+)$1	230	15	23	16.4193
UGUUUAAA	chr9:72330003-72330231(-)$1	228	127	135	16.0161
AUUUUAAA	chr5:115249302-115249526(+)$1	224	69	77	16.3387
UUUUUAAA	chr3:101369179-101369411(-)$1	232	69	77	20.2903
UUUUUAAA	chr10:69828855-69829077(-)$1	222	28	36	20.2903
UUUUUAAA	chr12:21670608-21670844(+)$1	236	154	162	20.2903
UUUAUAAA	chr14:96853012-96853234(+)$1	222	102	110	15.9354
UUGUUAAA	chr6:99847629-99847852(-)$1	223	5	13	16.1774
UUUUUAAA	chr20:60711719-60711945(-)$1	226	57	65	20.2903
UUUUUAAA	chr16:50140168-50140394(+)$1	226	101	109	20.2903
CUUUUAAA	chr14:61111324-61111546(-)$1	222	73	81	16.1774
uuuuuaaa	chr8:94742950-94743171(-)$1	221	78	86	20.2903
UUUCUAAA	chr19:23404893-23405126(-)$1	233	114	122	15.8548
UUUUUAAA	chr14:95553560-95553792(-)$1	232	85	93	20.2903
uuuuuaaa	chr11:30359295-30359523(+)$1	228	153	161	20.2903
uuuuuaga	chr5:81569763-81569985(-)$1	222	200	208	15.7741
uuuuuaaa	chr19:36729222-36729479(+)$1	257	241	249	20.2903
UAUUUAaa	chr14:21966196-21966423(-)$1	227	110	118	16.4193
CUUUUAAA	chr14:32626405-32626629(+)$1	224	69	77	16.1774
AUUUUAAA	chr1:229458035-229458258(-)$1	223	36	44	16.3387
UUUUUAAU	chr17:38458362-38458597(+)$1	235	103	111	15.8548
UUUUUAGA	chr14:51721661-51721897(+)$1	236	54	62	15.7741
UUUUUAAA	chr5:54921798-54922022(-)$1	224	183	191	20.2903

#otherMatches

#Struct PSSM
^^^^^^^^	chr14:51371944-51372165(-)$1	221	104	112	15.6935
C:::ffff	chr2:207177906-207178131(+)$1	225	28	36	15.8548
ffffffvv	chr13:107142453-107142684(-)$1	231	111	119	15.8548
WWWWWWWW	chr5:122950531-122950750(+)$1	219	11	19	16.4193
ffmmmmff	chr14:92529761-92529988(-)$1	227	54	62	20.2903
iiii[a""	chr13:110407836-110408059(-)$1	223	141	149	15.7741
::::hhhh	chr12:66737290-66737514(+)$1	224	107	115	16.1774
mffffff]	chr2:233208812-233209036(+)$1	224	90	98	15.6935
mmmmccc2	chrX:118968513-118968736(-)$1	223	115	123	16.3387
eennnnne	chr2:114471781-114472003(-)$1	222	46	54	16.1774
::::::::	chr9:123526129-123526354(-)$1	225	20	28	15.9354
"""ddddl	chr1:225590642-225590861(-)$1	219	189	197	15.7741
FF||||||	chr10:18964903-18965128(+)$1	225	208	216	16.0967
GGGWWWWW	chr1:47142152-47142379(-)$1	227	73	81	15.7741
qqqqqddd	chr16:19564603-19564826(+)$1	223	55	63	15.6935
::::::::	chr10:119766090-119766309(-)$1	219	11	19	16.0161
::::::::	chr1:213166665-213166892(-)$1	227	109	117	20.2903
ffff6666	chr15:42858861-42859085(+)$1	224	76	84	15.9354
ff:::::F	chr7:26412155-26412382(+)$1	227	147	155	16.4193
##ffffff	chr17:76849230-76849462(-)$1	232	110	118	16.4193
b!!fffff	chr10:98724051-98724283(+)$1	232	145	153	20.2903
>>>>>>>>	chr21:28208580-28208800(-)$1	220	105	113	16.1774
hhhhhhhh	chr10:102896826-102897054(+)$1	228	119	127	15.8548
b333eeee	chr15:66841376-66841595(+)$1	219	36	44	15.7741
iiiiiooo	chr1:228288335-228288567(-)$1	232	123	131	16.3387
eeeeemmm	chr19:44126603-44126833(-)$1	230	193	201	16.1774
hhhlllhh	chr3:122128638-122128858(+)$1	220	63	71	15.7741
hhhhhh''	chr2:198284872-198285094(-)$1	222	44	52	20.2903
iiiii!!d	chrX:135127078-135127300(+)$1	222	108	116	16.0967
eeeennnn	chr11:20530195-20530422(+)$1	227	112	120	16.3387
=::::::E	chr1:25169226-25169456(+)$1	230	119	127	20.2903
GGGGGG??	chr2:32248989-32249210(-)$1	221	198	206	20.2903
::::::::	chr13:21751371-21751594(+)$1	223	102	110	16.1774
eee"""cc	chr17:53470395-53470614(-)$1	219	13	21	16.4193
5555ffff	chr1:68153811-68154032(+)$1	221	158	166	15.6935
hffffff[	chr20:43128238-43128463(-)$1	225	100	108	15.7741
fffff::G	chr18:21061743-21061969(+)$1	226	169	177	15.8548
hhhhhhhh	chr3:170077933-170078165(+)$1	232	120	128	15.7741
eeeeqqqq	chr8:17081250-17081475(+)$1	225	69	77	16.1774
:::::::F	chr17:61671254-61671484(+)$1	230	15	23	16.4193
}EEEEEZZ	chr9:72330003-72330231(-)$1	228	127	135	16.0161
hhhhhhhh	chr5:115249302-115249526(+)$1	224	69	77	16.3387
GGGGGOOO	chr3:101369179-101369411(-)$1	232	69	77	20.2903
::::::::	chr10:69828855-69829077(-)$1	222	28	36	20.2903
vvvvvvvv	chr12:21670608-21670844(+)$1	236	154	162	20.2903
eee:::::	chr14:96853012-96853234(+)$1	222	102	110	15.9354
::::::::	chr6:99847629-99847852(-)$1	223	5	13	16.1774
:::::::f	chr20:60711719-60711945(-)$1	226	57	65	20.2903
::::::::	chr16:50140168-50140394(+)$1	226	101	109	20.2903
bbrrrrrr	chr14:61111324-61111546(-)$1	222	73	81	16.1774
!!eeeee+	chr8:94742950-94743171(-)$1	221	78	86	20.2903
^^^^^^^^	chr19:23404893-23405126(-)$1	233	114	122	15.8548
qqqdddd3	chr14:95553560-95553792(-)$1	232	85	93	20.2903
mmdddd::	chr11:30359295-30359523(+)$1	228	153	161	20.2903
IIIII???	chr5:81569763-81569985(-)$1	222	200	208	15.7741
JJJJJYYE	chr19:36729222-36729479(+)$1	257	241	249	20.2903
::::::::	chr14:21966196-21966423(-)$1	227	110	118	16.4193
qqqqqqqe	chr14:32626405-32626629(+)$1	224	69	77	16.1774
====::::	chr1:229458035-229458258(-)$1	223	36	44	16.3387
666666dd	chr17:38458362-38458597(+)$1	235	103	111	15.8548
cccdddd!	chr14:51721661-51721897(+)$1	236	54	62	15.7741
::::::::	chr5:54921798-54922022(-)$1	224	183	191	20.2903

#DB
........	chr14:51371944-51372165(-)$1	1	104	112	15.6935
(...((((	chr2:207177906-207178131(+)$1	1	28	36	15.8548
((((((..	chr13:107142453-107142684(-)$1	1	111	119	15.8548
........	chr5:122950531-122950750(+)$1	1	11	19	16.4193
((....))	chr14:92529761-92529988(-)$1	1	54	62	20.2903
((((.(..	chr13:110407836-110408059(-)$1	1	141	149	15.7741
....((((	chr12:66737290-66737514(+)$1	1	107	115	16.1774
.)))))).	chr2:233208812-233209036(+)$1	1	90	98	15.6935
....))).	chrX:118968513-118968736(-)$1	1	115	123	16.3387
((.....)	chr2:114471781-114472003(-)$1	1	46	54	16.1774
........	chr9:123526129-123526354(-)$1	1	20	28	15.9354
...((((.	chr1:225590642-225590861(-)$1	1	189	197	15.7741
))......	chr10:18964903-18965128(+)$1	1	208	216	16.0967
(((.....	chr1:47142152-47142379(-)$1	1	73	81	15.7741
.....)))	chr16:19564603-19564826(+)$1	1	55	63	15.6935
........	chr10:119766090-119766309(-)$1	1	11	19	16.0161
........	chr1:213166665-213166892(-)$1	1	109	117	20.2903
))))....	chr15:42858861-42859085(+)$1	1	76	84	15.9354
)).....)	chr7:26412155-26412382(+)$1	1	147	155	16.4193
..((((((	chr17:76849230-76849462(-)$1	1	110	118	16.4193
(..(((((	chr10:98724051-98724283(+)$1	1	145	153	20.2903
........	chr21:28208580-28208800(-)$1	1	105	113	16.1774
))))))))	chr10:102896826-102897054(+)$1	1	119	127	15.8548
)...))))	chr15:66841376-66841595(+)$1	1	36	44	15.7741
(((((...	chr1:228288335-228288567(-)$1	1	123	131	16.3387
(((((...	chr19:44126603-44126833(-)$1	1	193	201	16.1774
(((...))	chr3:122128638-122128858(+)$1	1	63	71	15.7741
((((((..	chr2:198284872-198285094(-)$1	1	44	52	20.2903
(((((..(	chrX:135127078-135127300(+)$1	1	108	116	16.0967
((((....	chr11:20530195-20530422(+)$1	1	112	120	16.3387
)......)	chr1:25169226-25169456(+)$1	1	119	127	20.2903
))))))..	chr2:32248989-32249210(-)$1	1	198	206	20.2903
........	chr13:21751371-21751594(+)$1	1	102	110	16.1774
(((...((	chr17:53470395-53470614(-)$1	1	13	21	16.4193
....))))	chr1:68153811-68154032(+)$1	1	158	166	15.6935
(((((((.	chr20:43128238-43128463(-)$1	1	100	108	15.7741
)))))..)	chr18:21061743-21061969(+)$1	1	169	177	15.8548
))))))))	chr3:170077933-170078165(+)$1	1	120	128	15.7741
((((....	chr8:17081250-17081475(+)$1	1	69	77	16.1774
.......(	chr17:61671254-61671484(+)$1	1	15	23	16.4193
.)))))..	chr9:72330003-72330231(-)$1	1	127	135	16.0161
))))))((	chr5:115249302-115249526(+)$1	1	69	77	16.3387
(((((...	chr3:101369179-101369411(-)$1	1	69	77	20.2903
........	chr10:69828855-69829077(-)$1	1	28	36	20.2903
........	chr12:21670608-21670844(+)$1	1	154	162	20.2903
))).....	chr14:96853012-96853234(+)$1	1	102	110	15.9354
........	chr6:99847629-99847852(-)$1	1	5	13	16.1774
.......(	chr20:60711719-60711945(-)$1	1	57	65	20.2903
........	chr16:50140168-50140394(+)$1	1	101	109	20.2903
((......	chr14:61111324-61111546(-)$1	1	73	81	16.1774
..(((((.	chr8:94742950-94743171(-)$1	1	78	86	20.2903
........	chr19:23404893-23405126(-)$1	1	114	122	15.8548
...)))).	chr14:95553560-95553792(-)$1	1	85	93	20.2903
..))))..	chr11:30359295-30359523(+)$1	1	153	161	20.2903
)))))...	chr5:81569763-81569985(-)$1	1	200	208	15.7741
)))))..)	chr19:36729222-36729479(+)$1	1	241	249	20.2903
........	chr14:21966196-21966423(-)$1	1	110	118	16.4193
.......)	chr14:32626405-32626629(+)$1	1	69	77	16.1774
))))....	chr1:229458035-229458258(-)$1	1	36	44	16.3387
......))	chr17:38458362-38458597(+)$1	1	103	111	15.8548
(((((((.	chr14:51721661-51721897(+)$1	1	54	62	15.7741
........	chr5:54921798-54922022(-)$1	1	183	191	20.2903

#PSSM
U : 0.79	u : 0.08	A : 0.06	C : 0.03	c : 0.01	a : 0.01	
U : 0.75	u : 0.11	A : 0.09	C : 0.01	G : 0.01	
U : 0.77	u : 0.09	G : 0.04	A : 0.03	C : 0.03	a : 0.01	
U : 0.80	u : 0.11	A : 0.04	C : 0.03	
U : 0.82	u : 0.11	G : 0.03	C : 0.03	
A : 0.80	a : 0.12	U : 0.03	C : 0.01	G : 0.01	
A : 0.80	a : 0.12	C : 0.01	U : 0.01	g : 0.01	G : 0.01	
A : 0.77	a : 0.14	U : 0.03	C : 0.03	G : 0.01	

#score	1062.354838709676
#seq	62
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ELAVL1A_hg19_UTR_m3_run2.nuc.txt

#NT
GUUUUUU	chr15:58888487-58888727(-)$1	240	21	28	13.2131
AUUUUUG	chr6:158932089-158932329(+)$1	240	66	73	13.2950
GUUUUUU	chr11:9467782-9468024(+)$1	242	12	19	13.2131
GUAUUUG	chr2:207657039-207657280(+)$1	241	1	8	12.3934
GAUUUUG	chr17:48828235-48828487(+)$1	252	102	109	12.8852
GUUUUUU	chr19:1555161-1555401(-)$1	240	208	215	13.2131
AUUUUUG	chr18:66342916-66343156(-)$1	240	215	222	13.2950
GGUUUUG	chr1:21069104-21069344(-)$1	240	197	204	12.8032
CUUUUUG	chr9:131852491-131852731(+)$1	240	127	134	13.2950
GUUUUUC	chr2:171847379-171847637(-)$1	258	83	90	12.8852
GUUUUUG	chr16:84812972-84813212(+)$1	240	140	147	16.8196
GUAUUUG	chr13:42893446-42893686(+)$1	240	167	174	12.3934
AUUUUUG	chr12:42553002-42553242(-)$1	240	7	14	13.2950
GUUUAUG	chr9:107522163-107522403(+)$1	240	83	90	13.0491
GUUAUUG	chr4:38701311-38701551(+)$1	240	189	196	11.9836
UUUUUUG	chr16:1727650-1727891(+)$1	241	92	99	13.1311
AUUUUUG	chr6:26285262-26285507(-)$1	245	201	208	13.2950
uuuuuuG	chr8:42692791-42693031(-)$1	240	88	95	13.1311
GUUUUUG	chr5:135514777-135515017(+)$1	240	139	146	16.8196
GAUUUUG	chr10:112271021-112271261(+)$1	240	103	110	12.8852
GUUUUUU	chr8:27143670-27143910(-)$1	240	163	170	13.2131
GUUUUUA	chr6:53788292-53788532(+)$1	240	23	30	12.9672
GUUUAUG	chr7:63980279-63980519(-)$1	240	7	14	13.0491
GUUUUUG	chr17:27588807-27589047(-)$1	240	79	86	16.8196
GUUUUUG	chr8:42709504-42709744(-)$1	240	212	219	16.8196
CUUUUUG	chr6:138743142-138743382(-)$1	240	217	224	13.2950
GCUUUUG	chr1:224573933-224574173(-)$1	240	92	99	12.7213
GCUUUUG	chr19:38125493-38125735(-)$1	242	97	104	12.7213
GAUUUUG	chr2:231684588-231684828(+)$1	240	185	192	12.8852
GGUUUUG	chr1:231469790-231470035(-)$1	245	8	15	12.8032
GUUUUGG	chr9:74480272-74480512(-)$1	240	45	52	12.2295
GUUUAUG	chr7:12693074-12693314(+)$1	240	11	18	13.0491
GUUUAUG	chr17:29701544-29701784(+)$1	240	70	77	13.0491
GUUUUUG	chr2:230899611-230899851(-)$1	240	166	173	16.8196
GUUUUUA	chr8:26267952-26268225(+)$1	273	84	91	12.9672
UUUUUUG	chr3:101543716-101543956(+)$1	240	49	56	13.1311
GUUUGUG	chr12:30782684-30782924(-)$1	240	206	213	12.6393
CUUUUUG	chr11:61567091-61567334(-)$1	243	166	173	13.2950
GGUUUUG	chr11:9304386-9304626(-)$1	240	45	52	12.8032
CUUUUUG	chr2:37334175-37334415(-)$1	240	160	167	13.2950
GUUUUUA	chr4:122738597-122738837(-)$1	240	103	110	12.9672
GUUUCUG	chr5:142603550-142603790(+)$1	240	44	51	12.7213
GUCUUUG	chr15:42859072-42859312(+)$1	240	20	27	12.4754
GUUUAUG	chr10:1063483-1063723(+)$1	240	21	28	13.0491
GUUUUUG	chr17:26654717-26654957(+)$1	240	53	60	16.8196
GUUUUUG	chr18:57570088-57570328(+)$1	240	207	214	16.8196
CUUUUUG	chr2:26359653-26359893(+)$1	240	153	160	13.2950
GUUUUUG	chr2:42936176-42936419(+)$1	243	206	213	16.8196
GUUUUGG	chr7:91742031-91742281(-)$1	250	93	100	12.2295
GUCUUUG	chr2:113287082-113287323(+)$1	241	27	34	12.4754
GUUUCUG	chr13:45968757-45969007(-)$1	250	93	100	12.7213
GUUUUUU	chr2:207176890-207177132(+)$1	242	43	50	13.2131
GUUUUUU	chr6:96056411-96056651(+)$1	240	106	113	13.2131
GUUUUUG	chr5:64014517-64014757(-)$1	240	4	11	16.8196
GUUUUUC	chr5:60453785-60454025(-)$1	240	49	56	12.8852
GUUUAUG	chr7:148116077-148116331(+)$1	254	183	190	13.0491
GUUUUAG	chr3:195777149-195777389(-)$1	240	139	146	12.1475
AUUUUUG	chr14:95553556-95553796(-)$1	240	18	25	13.2950
GUCUUUG	chr18:61057743-61057990(-)$1	247	94	101	12.4754
GUUUUUG	chr3:15483841-15484081(+)$1	240	75	82	16.8196

#otherMatches

#Struct PSSM
22ccc]c	chr7:108214901-108215141(+)$1	240	78	85	12.8852
HHHHHHH	chr15:58888487-58888727(-)$1	240	21	28	13.2131
d!!ccc!	chr6:158932089-158932329(+)$1	240	66	73	13.2950
dddpppp	chr11:9467782-9468024(+)$1	242	12	19	13.2131
:hhhhhh	chr2:207657039-207657280(+)$1	241	1	8	12.3934
fff]eee	chr17:48828235-48828487(+)$1	252	102	109	12.8852
dgggggg	chr19:1555161-1555401(-)$1	240	208	215	13.2131
:::::::	chr18:66342916-66343156(-)$1	240	215	222	13.2950
a[ggggg	chr1:21069104-21069344(-)$1	240	197	204	12.8032
::::FFF	chr9:131852491-131852731(+)$1	240	127	134	13.2950
======:	chr2:171847379-171847637(-)$1	258	83	90	12.8852
+++hhhh	chr16:84812972-84813212(+)$1	240	140	147	16.8196
ccc22ff	chr13:42893446-42893686(+)$1	240	167	174	12.3934
F{HHHHH	chr12:42553002-42553242(-)$1	240	7	14	13.2950
CC{FFFF	chr9:107522163-107522403(+)$1	240	83	90	13.0491
=====]f	chr4:38701311-38701551(+)$1	240	189	196	11.9836
sssssss	chr16:1727650-1727891(+)$1	241	92	99	13.1311
####eee	chr6:26285262-26285507(-)$1	245	201	208	13.2950
oooooo=	chr8:42692791-42693031(-)$1	240	88	95	13.1311
GGG:::f	chr5:135514777-135515017(+)$1	240	139	146	16.8196
ee4444c	chr10:112271021-112271261(+)$1	240	103	110	12.8852
b++++++	chr8:27143670-27143910(-)$1	240	163	170	13.2131
iiiiii"	chr6:53788292-53788532(+)$1	240	23	30	12.9672
IIIIIII	chr7:63980279-63980519(-)$1	240	7	14	13.0491
dd22eee	chr17:27588807-27589047(-)$1	240	79	86	16.8196
ffff]dd	chr8:42709504-42709744(-)$1	240	212	219	16.8196
ccc::HH	chr6:138743142-138743382(-)$1	240	217	224	13.2950
:::::HH	chr1:224573933-224574173(-)$1	240	92	99	12.7213
^^^^^^^	chr19:38125493-38125735(-)$1	242	97	104	12.7213
fffffff	chr2:231684588-231684828(+)$1	240	185	192	12.8852
DD:::ff	chr1:231469790-231470035(-)$1	245	8	15	12.8032
IIIIIdd	chr9:74480272-74480512(-)$1	240	45	52	12.2295
cc"""hh	chr7:12693074-12693314(+)$1	240	11	18	13.0491
dddd]gg	chr17:29701544-29701784(+)$1	240	70	77	13.0491
+++++++	chr2:230899611-230899851(-)$1	240	166	173	16.8196
bb>>>>>	chr8:26267952-26268225(+)$1	273	84	91	12.9672
PPPPPCC	chr3:101543716-101543956(+)$1	240	49	56	13.1311
iiiii]f	chr12:30782684-30782924(-)$1	240	206	213	12.6393
fffff[b	chr11:61567091-61567334(-)$1	243	166	173	13.2950
ee)))))	chr11:9304386-9304626(-)$1	240	45	52	12.8032
:ffffff	chr2:37334175-37334415(-)$1	240	160	167	13.2950
]ccc22c	chr4:122738597-122738837(-)$1	240	103	110	12.9672
ppppppd	chr5:142603550-142603790(+)$1	240	44	51	12.7213
C{CCCKK	chr15:42859072-42859312(+)$1	240	20	27	12.4754
eeeee[h	chr10:1063483-1063723(+)$1	240	21	28	13.0491
ccc]eee	chr17:26654717-26654957(+)$1	240	53	60	16.8196
IIIIIA}	chr18:57570088-57570328(+)$1	240	207	214	16.8196
ddddmmm	chr2:26359653-26359893(+)$1	240	153	160	13.2950
:::::CC	chr2:42936176-42936419(+)$1	243	206	213	16.8196
bbmmmmb	chr7:91742031-91742281(-)$1	250	93	100	12.2295
F:::::f	chr2:113287082-113287323(+)$1	241	27	34	12.4754
qqqqqqa	chr13:45968757-45969007(-)$1	250	93	100	12.7213
gg55555	chr2:207176890-207177132(+)$1	242	43	50	13.2131
:::::::	chr6:96056411-96056651(+)$1	240	106	113	13.2131
nnnnndd	chr5:64014517-64014757(-)$1	240	4	11	16.8196
::IIIII	chr5:60453785-60454025(-)$1	240	49	56	12.8852
fffff::	chr7:148116077-148116331(+)$1	254	183	190	13.0491
eeeeepp	chr3:195777149-195777389(-)$1	240	139	146	12.1475
=====$$	chr14:95553556-95553796(-)$1	240	18	25	13.2950
[ddddmm	chr18:61057743-61057990(-)$1	247	94	101	12.4754
ppppppp	chr3:15483841-15484081(+)$1	240	75	82	16.8196

#DB
..))).)	chr7:108214901-108215141(+)$1	1	78	85	12.8852
(((((((	chr15:58888487-58888727(-)$1	1	21	28	13.2131
(..(((.	chr6:158932089-158932329(+)$1	1	66	73	13.2950
(((....	chr11:9467782-9468024(+)$1	1	12	19	13.2131
.((((((	chr2:207657039-207657280(+)$1	1	1	8	12.3934
))).)))	chr17:48828235-48828487(+)$1	1	102	109	12.8852
)))))))	chr19:1555161-1555401(-)$1	1	208	215	13.2131
.......	chr18:66342916-66343156(-)$1	1	215	222	13.2950
(.(((((	chr1:21069104-21069344(-)$1	1	197	204	12.8032
....)))	chr9:131852491-131852731(+)$1	1	127	134	13.2950
)))))).	chr2:171847379-171847637(-)$1	1	83	90	12.8852
...((((	chr16:84812972-84813212(+)$1	1	140	147	16.8196
)))..))	chr13:42893446-42893686(+)$1	1	167	174	12.3934
(.(((((	chr12:42553002-42553242(-)$1	1	7	14	13.2950
((.((((	chr9:107522163-107522403(+)$1	1	83	90	13.0491
))))).)	chr4:38701311-38701551(+)$1	1	189	196	11.9836
.......	chr16:1727650-1727891(+)$1	1	92	99	13.1311
....(((	chr6:26285262-26285507(-)$1	1	201	208	13.2950
......)	chr8:42692791-42693031(-)$1	1	88	95	13.1311
(((...(	chr5:135514777-135515017(+)$1	1	139	146	16.8196
))....)	chr10:112271021-112271261(+)$1	1	103	110	12.8852
(......	chr8:27143670-27143910(-)$1	1	163	170	13.2131
((((((.	chr6:53788292-53788532(+)$1	1	23	30	12.9672
(((((((	chr7:63980279-63980519(-)$1	1	7	14	13.0491
))..)))	chr17:27588807-27589047(-)$1	1	79	86	16.8196
)))).))	chr8:42709504-42709744(-)$1	1	212	219	16.8196
)))..))	chr6:138743142-138743382(-)$1	1	217	224	13.2950
.....((	chr1:224573933-224574173(-)$1	1	92	99	12.7213
.......	chr19:38125493-38125735(-)$1	1	97	104	12.7213
)))))))	chr2:231684588-231684828(+)$1	1	185	192	12.8852
((...((	chr1:231469790-231470035(-)$1	1	8	15	12.8032
(((((((	chr9:74480272-74480512(-)$1	1	45	52	12.2295
((...((	chr7:12693074-12693314(+)$1	1	11	18	13.0491
)))).))	chr17:29701544-29701784(+)$1	1	70	77	13.0491
.......	chr2:230899611-230899851(-)$1	1	166	173	16.8196
)).....	chr8:26267952-26268225(+)$1	1	84	91	12.9672
.....((	chr3:101543716-101543956(+)$1	1	49	56	13.1311
))))).)	chr12:30782684-30782924(-)$1	1	206	213	12.6393
(((((.(	chr11:61567091-61567334(-)$1	1	166	173	13.2950
((.....	chr11:9304386-9304626(-)$1	1	45	52	12.8032
.((((((	chr2:37334175-37334415(-)$1	1	160	167	13.2950
.)))..)	chr4:122738597-122738837(-)$1	1	103	110	12.9672
......)	chr5:142603550-142603790(+)$1	1	44	51	12.7213
(.(((..	chr15:42859072-42859312(+)$1	1	20	27	12.4754
(((((.(	chr10:1063483-1063723(+)$1	1	21	28	13.0491
))).)))	chr17:26654717-26654957(+)$1	1	53	60	16.8196
)))))).	chr18:57570088-57570328(+)$1	1	207	214	16.8196
((((...	chr2:26359653-26359893(+)$1	1	153	160	13.2950
.....))	chr2:42936176-42936419(+)$1	1	206	213	16.8196
((....)	chr7:91742031-91742281(-)$1	1	93	100	12.2295
(.....(	chr2:113287082-113287323(+)$1	1	27	34	12.4754
......)	chr13:45968757-45969007(-)$1	1	93	100	12.7213
)).....	chr2:207176890-207177132(+)$1	1	43	50	13.2131
.......	chr6:96056411-96056651(+)$1	1	106	113	13.2131
.....))	chr5:64014517-64014757(-)$1	1	4	11	16.8196
..(((((	chr5:60453785-60454025(-)$1	1	49	56	12.8852
)))))..	chr7:148116077-148116331(+)$1	1	183	190	13.0491
(((((..	chr3:195777149-195777389(-)$1	1	139	146	12.1475
(((((..	chr14:95553556-95553796(-)$1	1	18	25	13.2950
.((((..	chr18:61057743-61057990(-)$1	1	94	101	12.4754
.......	chr3:15483841-15484081(+)$1	1	75	82	16.8196

#PSSM
G : 0.78	A : 0.08	C : 0.08	U : 0.03	u : 0.01	
U : 0.83	A : 0.06	G : 0.04	C : 0.03	u : 0.01	
U : 0.90	C : 0.04	A : 0.03	u : 0.01	
U : 0.96	A : 0.01	u : 0.01	
U : 0.83	A : 0.09	C : 0.03	u : 0.01	G : 0.01	
U : 0.93	G : 0.03	u : 0.01	A : 0.01	
G : 0.81	U : 0.09	A : 0.04	C : 0.03	

#score	827.0655737704924
#seq	61
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_ZC3H7B_Baltz2012e_hg19_UTR_m1_run2.nuc.txt

#NT
UUUGUCUUCUG	chr7:99690822-99691082(-)$1	260	202	213	14.5178
UUUUUUUUUUU	chr6:149912580-149912870(+)$1	290	277	288	20.5892
AUCUUUUUCUU	chr14:100748851-100749125(+)$1	274	62	73	15.1428
UUUGUUUUCUC	chr5:172742134-172742555(-)$1	421	151	162	17.5535
UUUUGUUUUUA	chr3:107762314-107762538(-)$1	224	2	13	14.8750
UUUUUUUUUUU	chr12:88589837-88590200(+)$1	363	340	351	20.5892
UUUAAUUUCUC	chr12:51636277-51636538(+)$1	261	228	239	13.7142
AUUAUUUUCUU	chr6:119499194-119499479(-)$1	285	47	58	15.5892
UUAUUUUUAUG	chr3:197509030-197509283(+)$1	253	51	62	15.2321
UUUUUUUUUUG	chr4:110736638-110736886(+)$1	248	175	186	19.6071
UUUGUUUUCUA	chr18:9103332-9103592(+)$1	260	234	245	17.8214
UCUUUUUUCUU	chr4:122737873-122738107(-)$1	234	113	124	19.0714
UUAUUCUUCUG	chr6:17609526-17609848(+)$1	322	273	284	14.0714
UUUUUGUUCUG	chr22:42070722-42070949(-)$1	227	157	168	18.2678
uuuuuuuuguu	chr2:232319562-232319823(-)$1	261	232	243	19.8750
UAUUAUUUCUU	chr10:102120811-102121119(+)$1	308	66	77	15.6785
UUUUUUUCCUU	chr5:134194827-134195216(+)$1	389	124	135	18.5357
CUUUUUUGCUU	chr5:137842212-137842447(-)$1	235	180	191	14.6071
UGUUUUUUCUU	chr5:126172158-126172395(+)$1	237	77	88	19.0714
UUUUAUUUUUA	chr1:25169689-25169969(+)$1	280	205	216	15.2321
uuuuuuuuuuu	chr3:9848158-9848381(+)$1	223	42	53	20.5892
UUUCUUAUCUU	chr4:53462114-53462365(-)$1	251	72	83	14.8750
uuuuuuuuccu	chr22:38881792-38882020(-)$1	228	144	155	18.5357
GUUGUUUUCUC	chr16:68059284-68059508(+)$1	224	182	193	13.4464
AUUUUUUUCUA	chr19:7086212-7086454(+)$1	242	60	71	17.6428
UAGUUUUUCUU	chr17:27870673-27870942(+)$1	269	56	67	15.0535
UUAUUGUUCUU	chr9:101912006-101912389(+)$1	383	162	173	15.2321
UUUUUGUUCUG	chr22:42070607-42070868(-)$1	261	76	87	18.2678
UUUUUGUUAUG	chr16:3776704-3776977(-)$1	273	214	225	15.4107
UUUAUUUUAUA	chr5:171304927-171305233(-)$1	306	7	18	14.7857
CAUUUUUUCUU	chr6:1613692-1613981(+)$1	289	113	124	15.4107
uauuuuuucua	chr8:30643030-30643348(-)$1	318	253	264	17.6428
UUUCUUUUCUU	chr20:11904754-11905096(+)$1	342	219	230	19.3392
CUCUUUUUCUG	chr13:95281396-95281621(+)$1	225	44	55	13.9821
UUUUUGGUCUG	chr12:46355482-46355739(-)$1	257	49	60	13.7142
UUUUAUUUGUA	chr16:1413933-1414179(-)$1	246	83	94	14.5178
UUUUUUUUCUC	chr3:32523670-32523943(-)$1	273	73	84	21.1250
UUUUUUUUAAg	chr5:112203890-112204122(+)$1	232	192	203	14.6071
UUUUAUUUCUG	chr3:47129548-47129774(-)$1	226	193	204	18.4464
UAUUUCUUCUG	chr14:96997989-96998228(+)$1	239	128	139	14.3392
AUUUUUUUCUU	chr1:31404829-31405120(-)$1	291	197	208	19.3392
UUUUGUUUCUG	chr11:62480309-62480551(-)$1	242	76	87	18.0892
UUUCCUUUCUU	chr7:151819184-151819481(+)$1	297	26	37	15.2321
UUUUUUUUUUA	chr6:53133473-53133902(-)$1	429	311	322	18.8928
UUUUUUAUUUG	chr3:52873623-52873855(-)$1	232	88	99	15.1428
UCUUUUUUCUG	chr7:141450092-141450356(+)$1	264	179	190	18.0892
UUUUUUUAAUU	chr7:90044281-90044536(+)$1	255	229	240	15.7678
UUUUUUUUUUU	chr4:17625892-17626131(+)$1	239	190	201	20.5892
UUAUUUUUAUU	chr12:121136889-121137198(+)$1	309	45	56	16.2142
UUUUUUUUCCU	chr20:34237467-34237726(-)$1	259	13	24	18.5357
UUUUUUCUCUU	chr6:11137457-11137728(+)$1	271	61	72	18.5357
AUUUUUUACUU	chr16:31927691-31927978(+)$1	287	131	142	14.8750
UGUUAUUUCUU	chr1:53517118-53517350(+)$1	232	76	87	15.4107
UUUGUUUUCUG	chrX:154005774-154006047(+)$1	273	200	211	18.5357
UUUUUUUUUUU	chr1:78414156-78414403(-)$1	247	75	86	20.5892

#otherMatches

#Struct PSSM
IIIIIIIZZZC	chr10:32298510-32298745(-)$1	235	150	161	21.1250
iiiiiiii::g	chr7:99690822-99691082(-)$1	260	202	213	14.5178
:::::::::::	chr6:149912580-149912870(+)$1	290	277	288	20.5892
:::GGGGGGGL	chr14:100748851-100749125(+)$1	274	62	73	15.1428
JJJJJJddddm	chr5:172742134-172742555(-)$1	421	151	162	17.5535
::::ffffff!	chr3:107762314-107762538(-)$1	224	2	13	14.8750
III}DDDD___	chr12:88589837-88590200(+)$1	363	340	351	20.5892
ee::::::::F	chr12:51636277-51636538(+)$1	261	228	239	13.7142
ddd[ccc$$$$	chr6:119499194-119499479(-)$1	285	47	58	15.5892
nnhhhhhhhhh	chr3:197509030-197509283(+)$1	253	51	62	15.2321
::::hhhhhhh	chr4:110736638-110736886(+)$1	248	175	186	19.6071
ddd]eeeee::	chr18:9103332-9103592(+)$1	260	234	245	17.8214
''''''eeeee	chr4:122737873-122738107(-)$1	234	113	124	19.0714
===rrrrrrrr	chr6:17609526-17609848(+)$1	322	273	284	14.0714
::::::::ddd	chr22:42070722-42070949(-)$1	227	157	168	18.2678
ccggggggg44	chr2:232319562-232319823(-)$1	261	232	243	19.8750
ddvvvvvvvvv	chr10:102120811-102121119(+)$1	308	66	77	15.6785
ff]dddd::::	chr5:134194827-134195216(+)$1	389	124	135	18.5357
::::hhhhhhh	chr5:137842212-137842447(-)$1	235	180	191	14.6071
===========	chr5:126172158-126172395(+)$1	237	77	88	19.0714
GGGFFFFFF~~	chr1:25169689-25169969(+)$1	280	205	216	15.2321
iiii+++++++	chr3:9848158-9848381(+)$1	223	42	53	20.5892
eeeeqqqqqqq	chr4:53462114-53462365(-)$1	251	72	83	14.8750
f::::::::::	chr22:38881792-38882020(-)$1	228	144	155	18.5357
eeeee"""ddd	chr16:68059284-68059508(+)$1	224	182	193	13.4464
fff++++++++	chr19:7086212-7086454(+)$1	242	60	71	17.6428
ooa]ffffff]	chr17:27870673-27870942(+)$1	269	56	67	15.0535
ddd]eeeee]f	chr9:101912006-101912389(+)$1	383	162	173	15.2321
fffff!!hhhh	chr22:42070607-42070868(-)$1	261	76	87	18.2678
ffffoooooof	chr16:3776704-3776977(-)$1	273	214	225	15.4107
hhhcccmmmmc	chr5:171304927-171305233(-)$1	306	7	18	14.7857
b]=========	chr6:1613692-1613981(+)$1	289	113	124	15.4107
:::::::eeee	chr8:30643030-30643348(-)$1	318	253	264	17.6428
JJJJJJJJ:JJ	chr20:11904754-11905096(+)$1	342	219	230	19.3392
dd!!ggggggg	chr13:95281396-95281621(+)$1	225	44	55	13.9821
eeeeeoooooo	chr12:46355482-46355739(-)$1	257	49	60	13.7142
tttttttta22	chr16:1413933-1414179(-)$1	246	83	94	14.5178
::::::::a[c	chr3:32523670-32523943(-)$1	273	73	84	21.1250
dddnnnnnddd	chr5:112203890-112204122(+)$1	232	192	203	14.6071
eeeee]hhhhh	chr3:47129548-47129774(-)$1	226	193	204	18.4464
::::::::::d	chr14:96997989-96998228(+)$1	239	128	139	14.3392
::gggggggmm	chr1:31404829-31405120(-)$1	291	197	208	19.3392
pppppppdddd	chr11:62480309-62480551(-)$1	242	76	87	18.0892
ggg[ccc%%%%	chr7:151819184-151819481(+)$1	297	26	37	15.2321
JJJJJJJJJ::	chr6:53133473-53133902(-)$1	429	311	322	18.8928
gggggg]dddd	chr3:52873623-52873855(-)$1	232	88	99	15.1428
dddd22ddddF	chr7:141450092-141450356(+)$1	264	179	190	18.0892
GGG}DDDDZZZ	chr7:90044281-90044536(+)$1	255	229	240	15.7678
e%%%%%%dddd	chr4:17625892-17626131(+)$1	239	190	201	20.5892
++++++++ggg	chr12:121136889-121137198(+)$1	309	45	56	16.2142
G{BB{DDDD::	chr20:34237467-34237726(-)$1	259	13	24	18.5357
9999999eeee	chr6:11137457-11137728(+)$1	271	61	72	18.5357
rrrrrrrrree	chr16:31927691-31927978(+)$1	287	131	142	14.8750
c[cccnnnnnc	chr1:53517118-53517350(+)$1	232	76	87	15.4107
hhh::::::::	chrX:154005774-154006047(+)$1	273	200	211	18.5357
:::::::::::	chr1:78414156-78414403(-)$1	247	75	86	20.5892

#DB
)))))))...)	chr10:32298510-32298745(-)$1	1	150	161	21.1250
))))))))..(	chr7:99690822-99691082(-)$1	1	202	213	14.5178
...........	chr6:149912580-149912870(+)$1	1	277	288	20.5892
...(((((((.	chr14:100748851-100749125(+)$1	1	62	73	15.1428
((((((((((.	chr5:172742134-172742555(-)$1	1	151	162	17.5535
....((((((.	chr3:107762314-107762538(-)$1	1	2	13	14.8750
))).))))...	chr12:88589837-88590200(+)$1	1	340	351	20.5892
))........)	chr12:51636277-51636538(+)$1	1	228	239	13.7142
(((.(((....	chr6:119499194-119499479(-)$1	1	47	58	15.5892
..))))))))(	chr3:197509030-197509283(+)$1	1	51	62	15.2321
....(((((((	chr4:110736638-110736886(+)$1	1	175	186	19.6071
))).)))))..	chr18:9103332-9103592(+)$1	1	234	245	17.8214
......(((((	chr4:122737873-122738107(-)$1	1	113	124	19.0714
(((........	chr6:17609526-17609848(+)$1	1	273	284	14.0714
........(((	chr22:42070722-42070949(-)$1	1	157	168	18.2678
)))))))))..	chr2:232319562-232319823(-)$1	1	232	243	19.8750
((.........	chr10:102120811-102121119(+)$1	1	66	77	15.6785
)).))))....	chr5:134194827-134195216(+)$1	1	124	135	18.5357
....(((((((	chr5:137842212-137842447(-)$1	1	180	191	14.6071
(((((((((((	chr5:126172158-126172395(+)$1	1	77	88	19.0714
)))))))))..	chr1:25169689-25169969(+)$1	1	205	216	15.2321
((((.......	chr3:9848158-9848381(+)$1	1	42	53	20.5892
((((.......	chr4:53462114-53462365(-)$1	1	72	83	14.8750
)..........	chr22:38881792-38882020(-)$1	1	144	155	18.5357
(((((...(((	chr16:68059284-68059508(+)$1	1	182	193	13.4464
(((........	chr19:7086212-7086454(+)$1	1	60	71	17.6428
..).)))))).	chr17:27870673-27870942(+)$1	1	56	67	15.0535
))).))))).)	chr9:101912006-101912389(+)$1	1	162	173	15.2321
(((((..((((	chr22:42070607-42070868(-)$1	1	76	87	18.2678
((((......)	chr16:3776704-3776977(-)$1	1	214	225	15.4107
((((((....)	chr5:171304927-171305233(-)$1	1	7	18	14.7857
).)))))))))	chr6:1613692-1613981(+)$1	1	113	124	15.4107
.......((((	chr8:30643030-30643348(-)$1	1	253	264	17.6428
)))))))).((	chr20:11904754-11905096(+)$1	1	219	230	19.3392
((..(((((((	chr13:95281396-95281621(+)$1	1	44	55	13.9821
(((((......	chr12:46355482-46355739(-)$1	1	49	60	13.7142
........)..	chr16:1413933-1414179(-)$1	1	83	94	14.5178
........(.(	chr3:32523670-32523943(-)$1	1	73	84	21.1250
(((.....)))	chr5:112203890-112204122(+)$1	1	192	203	14.6071
))))).)))))	chr3:47129548-47129774(-)$1	1	193	204	18.4464
..........(	chr14:96997989-96998228(+)$1	1	128	139	14.3392
..(((((((..	chr1:31404829-31405120(-)$1	1	197	208	19.3392
.......))))	chr11:62480309-62480551(-)$1	1	76	87	18.0892
(((.(((....	chr7:151819184-151819481(+)$1	1	26	37	15.2321
)))))))))..	chr6:53133473-53133902(-)$1	1	311	322	18.8928
)))))).))))	chr3:52873623-52873855(-)$1	1	88	99	15.1428
))))..)))))	chr7:141450092-141450356(+)$1	1	179	190	18.0892
))).))))...	chr7:90044281-90044536(+)$1	1	229	240	15.7678
(......((((	chr4:17625892-17626131(+)$1	1	190	201	20.5892
........(((	chr12:121136889-121137198(+)$1	1	45	56	16.2142
(.((.((((..	chr20:34237467-34237726(-)$1	1	13	24	18.5357
.......))))	chr6:11137457-11137728(+)$1	1	61	72	18.5357
.........))	chr16:31927691-31927978(+)$1	1	131	142	14.8750
(.(((.....)	chr1:53517118-53517350(+)$1	1	76	87	15.4107
)))........	chrX:154005774-154006047(+)$1	1	200	211	18.5357
...........	chr1:78414156-78414403(-)$1	1	75	86	20.5892

#PSSM
U : 0.76	A : 0.08	u : 0.07	C : 0.05	G : 0.01	
U : 0.78	A : 0.07	u : 0.05	C : 0.03	G : 0.03	a : 0.01	
U : 0.80	A : 0.07	u : 0.07	C : 0.03	G : 0.01	
U : 0.73	G : 0.08	u : 0.07	A : 0.05	C : 0.05	
U : 0.76	A : 0.10	u : 0.07	G : 0.03	C : 0.01	
U : 0.78	G : 0.08	u : 0.07	C : 0.05	
U : 0.85	u : 0.07	A : 0.03	G : 0.01	C : 0.01	
U : 0.85	u : 0.07	A : 0.03	C : 0.01	G : 0.01	
C : 0.64	U : 0.16	A : 0.10	c : 0.03	g : 0.01	u : 0.01	G : 0.01	
U : 0.89	u : 0.05	c : 0.01	A : 0.01	C : 0.01	
U : 0.42	G : 0.26	A : 0.12	C : 0.08	u : 0.05	a : 0.01	g : 0.01	

#score	951.571428571429
#seq	56
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
PARCLIP_FUS_Hoell2011c_hg19_CDS_m3_run1.nuc.txt

#NT
AUUUUUAAA	chr2:162036057-162036306(+)$1	249	6	15	19.6041
AUUUUUAAA	chr2:162036030-162036251(+)$1	221	33	42	19.6041
ACUUUUAAA	chr12:1299106-1299332(-)$1	226	60	69	15.8541
AUUUUUAGA	chr1:55643642-55643865(-)$1	223	0	9	14.9166
AUAUUUUAA	chr12:66715679-66715899(+)$1	220	144	153	15.0208
AUGUUUGAA	chr3:150281225-150281446(+)$1	221	137	146	14.3958
AUAUUUAAC	chr10:116879882-116880111(+)$1	229	84	93	13.8750
AUUUUUAAA	chr8:48875479-48875700(+)$1	221	45	54	19.6041
AGCUUUUAA	chr7:64168345-64168579(+)$1	234	97	106	11.4791
AUGUCUAAA	chr14:78161111-78161337(-)$1	226	204	213	13.8750
AUGUUUAAC	chr1:85331500-85331727(-)$1	227	182	191	13.8750
AUAUAUAAA	chr11:9516172-9516405(+)$1	233	142	151	13.8750
AUUUUUAAU	chr10:105883413-105883638(+)$1	225	31	40	15.1250
AUCUUUUAA	chr19:19906104-19906333(-)$1	229	150	159	15.2291
AUUUAUAAA	chr8:67478255-67478490(-)$1	235	198	207	15.3333
ACCUUUAAA	chr4:128743880-128744109(-)$1	229	15	24	14.6041
AUUUGUAAA	chr14:53217362-53217587(+)$1	225	154	163	15.2291
AUGUUUUAA	chr10:70722958-70723179(+)$1	221	40	49	15.0208
AUGUUUGAA	chr6:82924136-82924362(-)$1	226	93	102	14.3958
AUCUUCAAA	chr4:88015976-88016207(+)$1	231	103	112	14.2916
AACUUUUAA	chr10:115639269-115639490(+)$1	221	103	112	11.4791
AUUUUAAAA	chr12:98927401-98927621(+)$1	220	125	134	15.7500
AUGUUUUAA	chr5:141364350-141364573(+)$1	223	136	145	15.0208
ACUUUUAAA	chr21:34931503-34931751(+)$1	248	22	31	15.8541
AAUUUUAAA	chr16:29822350-29822585(+)$1	235	116	125	15.8541
auauugaaa	chr15:56985291-56985511(-)$1	220	37	46	14.3958
GUCUUUAAA	chr8:145948278-145948500(-)$1	222	77	86	13.9791
AUUUCUAAA	chr5:61875490-61875730(+)$1	240	113	122	15.3333
AUAAUUAAA	chrX:41446060-41446284(-)$1	224	132	141	13.4583
AUUUUAAAA	chr7:129498639-129498873(-)$1	234	142	151	15.7500
UUCUUUAAA	chr6:56338595-56338814(-)$1	219	160	169	14.0833
AUUUUUAAC	chr19:10781598-10781822(+)$1	224	23	32	15.3333
AGCUUUUAA	chr1:247150268-247150489(-)$1	221	1	10	11.4791
AUAUUUAAA	chrX:84519207-84519434(+)$1	227	192	201	18.1458
AUUUUGAAA	chr17:57289044-57289271(+)$1	227	147	156	15.8541
AUGUUUAAA	chr12:88436560-88436783(+)$1	223	159	168	18.1458
AUUUUAAAA	chr1:165860378-165860601(+)$1	223	41	50	15.7500
CUUUUUAAA	chr1:86167783-86168008(-)$1	225	9	18	15.3333
AUUUUUAUA	chr16:58614531-58614764(-)$1	233	46	55	14.9166
UUUUUUAAA	chr4:85687327-85687551(-)$1	224	158	167	15.3333
AUCUUUAAA	chr21:37418037-37418258(-)$1	221	111	120	18.3541
AUUUUGAAA	chr1:89206806-89207035(+)$1	229	68	77	15.8541
CUUUUUAAA	chr1:115282378-115282601(-)$1	223	77	86	15.3333
AGGUUUAAA	chr12:44124217-44124438(-)$1	221	32	41	14.3958
AUACUUAAA	chr11:108004914-108005136(+)$1	222	154	163	13.4583
AAAUUUAAA	chr4:68511555-68511776(-)$1	221	102	111	14.3958
AUUUUUAAA	chr18:20948579-20948801(-)$1	222	139	148	19.6041

#otherMatches

#Struct PSSM
f::::::ff	chr5:64925870-64926092(+)$1	222	137	146	11.4791
JJJJJJJJJ	chr2:162036057-162036306(+)$1	249	6	15	19.6041
33eeeee33	chr2:162036030-162036251(+)$1	221	33	42	19.6041
======:::	chr12:1299106-1299332(-)$1	226	60	69	15.8541
::::::ccc	chr1:55643642-55643865(-)$1	223	0	9	14.9166
ttttttthh	chr12:66715679-66715899(+)$1	220	144	153	15.0208
:bb!!dddd	chr3:150281225-150281446(+)$1	221	137	146	14.3958
fffff$$$$	chr10:116879882-116880111(+)$1	229	84	93	13.8750
::::::::e	chr8:48875479-48875700(+)$1	221	45	54	19.6041
HHHHHHHKK	chr7:64168345-64168579(+)$1	234	97	106	11.4791
::ddddppp	chr14:78161111-78161337(-)$1	226	204	213	13.8750
EEEEHHHHH	chr1:85331500-85331727(-)$1	227	182	191	13.8750
dd]dddd33	chr11:9516172-9516405(+)$1	233	142	151	13.8750
#ggggggg[	chr10:105883413-105883638(+)$1	225	31	40	15.1250
hhhhhhhh:	chr19:19906104-19906333(-)$1	229	150	159	15.2291
JJJJJJJ//	chr8:67478255-67478490(-)$1	235	198	207	15.3333
"""gggggg	chr4:128743880-128744109(-)$1	229	15	24	14.6041
bdddd8888	chr14:53217362-53217587(+)$1	225	154	163	15.2291
ggggggg::	chr10:70722958-70723179(+)$1	221	40	49	15.0208
b:ggggggg	chr6:82924136-82924362(-)$1	226	93	102	14.3958
HHSSSSSSS	chr4:88015976-88016207(+)$1	231	103	112	14.2916
rrrrrrrre	chr10:115639269-115639490(+)$1	221	103	112	11.4791
======:::	chr12:98927401-98927621(+)$1	220	125	134	15.7500
tttttttff	chr5:141364350-141364573(+)$1	223	136	145	15.0208
ee[cccmmm	chr21:34931503-34931751(+)$1	248	22	31	15.8541
:::::::::	chr16:29822350-29822585(+)$1	235	116	125	15.8541
====]bb:F	chr15:56985291-56985511(-)$1	220	37	46	14.3958
ff[ccc"""	chr8:145948278-145948500(-)$1	222	77	86	13.9791
YDDDD::::	chr5:61875490-61875730(+)$1	240	113	122	15.3333
rrrrrrrrd	chrX:41446060-41446284(-)$1	224	132	141	13.4583
yyyyyyyyh	chr7:129498639-129498873(-)$1	234	142	151	15.7500
ddd]ccc33	chr6:56338595-56338814(-)$1	219	160	169	14.0833
ff+++++++	chr19:10781598-10781822(+)$1	224	23	32	15.3333
CCCdddd!!	chr1:247150268-247150489(-)$1	221	1	10	11.4791
d22dddd]c	chrX:84519207-84519434(+)$1	227	192	201	18.1458
dd:::::::	chr17:57289044-57289271(+)$1	227	147	156	15.8541
}FFFFFFZZ	chr12:88436560-88436783(+)$1	223	159	168	18.1458
ee:gggggg	chr1:165860378-165860601(+)$1	223	41	50	15.7500
:========	chr1:86167783-86168008(-)$1	225	9	18	15.3333
]ggggggg]	chr16:58614531-58614764(-)$1	233	46	55	14.9166
gggggIIII	chr4:85687327-85687551(-)$1	224	158	167	15.3333
:::::::::	chr21:37418037-37418258(-)$1	221	111	120	18.3541
%ffffffzz	chr1:89206806-89207035(+)$1	229	68	77	15.8541
:::::::::	chr1:115282378-115282601(-)$1	223	77	86	15.3333
ffffppppp	chr12:44124217-44124438(-)$1	221	32	41	14.3958
iiiippppp	chr11:108004914-108005136(+)$1	222	154	163	13.4583
e::::::ee	chr4:68511555-68511776(-)$1	221	102	111	14.3958
eee$$$$$e	chr18:20948579-20948801(-)$1	222	139	148	19.6041

#DB
)......((	chr5:64925870-64926092(+)$1	1	137	146	11.4791
(((((((((	chr2:162036057-162036306(+)$1	1	6	15	19.6041
..)))))..	chr2:162036030-162036251(+)$1	1	33	42	19.6041
))))))...	chr12:1299106-1299332(-)$1	1	60	69	15.8541
......(((	chr1:55643642-55643865(-)$1	1	0	9	14.9166
.......))	chr12:66715679-66715899(+)$1	1	144	153	15.0208
.((..((((	chr3:150281225-150281446(+)$1	1	137	146	14.3958
(((((....	chr10:116879882-116880111(+)$1	1	84	93	13.8750
........(	chr8:48875479-48875700(+)$1	1	45	54	19.6041
(((((((..	chr7:64168345-64168579(+)$1	1	97	106	11.4791
..((((...	chr14:78161111-78161337(-)$1	1	204	213	13.8750
)))))))))	chr1:85331500-85331727(-)$1	1	182	191	13.8750
)).))))..	chr11:9516172-9516405(+)$1	1	142	151	13.8750
.(((((((.	chr10:105883413-105883638(+)$1	1	31	40	15.1250
)))))))).	chr19:19906104-19906333(-)$1	1	150	159	15.2291
)))))))..	chr8:67478255-67478490(-)$1	1	198	207	15.3333
...((((((	chr4:128743880-128744109(-)$1	1	15	24	14.6041
)))))....	chr14:53217362-53217587(+)$1	1	154	163	15.2291
)))))))..	chr10:70722958-70723179(+)$1	1	40	49	15.0208
).(((((((	chr6:82924136-82924362(-)$1	1	93	102	14.3958
((.......	chr4:88015976-88016207(+)$1	1	103	112	14.2916
........)	chr10:115639269-115639490(+)$1	1	103	112	11.4791
))))))...	chr12:98927401-98927621(+)$1	1	125	134	15.7500
.......))	chr5:141364350-141364573(+)$1	1	136	145	15.0208
((.(((...	chr21:34931503-34931751(+)$1	1	22	31	15.8541
.........	chr16:29822350-29822585(+)$1	1	116	125	15.8541
)))).)).(	chr15:56985291-56985511(-)$1	1	37	46	14.3958
((.(((...	chr8:145948278-145948500(-)$1	1	77	86	13.9791
.))))....	chr5:61875490-61875730(+)$1	1	113	122	15.3333
........)	chrX:41446060-41446284(-)$1	1	132	141	13.4583
........)	chr7:129498639-129498873(-)$1	1	142	151	15.7500
))).)))..	chr6:56338595-56338814(-)$1	1	160	169	14.0833
((.......	chr19:10781598-10781822(+)$1	1	23	32	15.3333
(((((((..	chr1:247150268-247150489(-)$1	1	1	10	11.4791
)..)))).)	chrX:84519207-84519434(+)$1	1	192	201	18.1458
)).......	chr17:57289044-57289271(+)$1	1	147	156	15.8541
.))))))..	chr12:88436560-88436783(+)$1	1	159	168	18.1458
)).((((((	chr1:165860378-165860601(+)$1	1	41	50	15.7500
.((((((((	chr1:86167783-86168008(-)$1	1	9	18	15.3333
.))))))).	chr16:58614531-58614764(-)$1	1	46	55	14.9166
)))))))))	chr4:85687327-85687551(-)$1	1	158	167	15.3333
.........	chr21:37418037-37418258(-)$1	1	111	120	18.3541
.((((((..	chr1:89206806-89207035(+)$1	1	68	77	15.8541
.........	chr1:115282378-115282601(-)$1	1	77	86	15.3333
((((.....	chr12:44124217-44124438(-)$1	1	32	41	14.3958
((((.....	chr11:108004914-108005136(+)$1	1	154	163	13.4583
)......((	chr4:68511555-68511776(-)$1	1	102	111	14.3958
(((.....(	chr18:20948579-20948801(-)$1	1	139	148	19.6041

#PSSM
A : 0.87	U : 0.04	C : 0.04	a : 0.02	G : 0.02	
U : 0.79	C : 0.06	G : 0.06	A : 0.06	u : 0.02	
U : 0.45	C : 0.20	G : 0.16	A : 0.14	a : 0.02	
U : 0.93	u : 0.02	A : 0.02	C : 0.02	
U : 0.87	C : 0.04	A : 0.04	G : 0.02	u : 0.02	
U : 0.83	G : 0.06	A : 0.06	C : 0.02	g : 0.02	
A : 0.77	U : 0.16	G : 0.04	a : 0.02	
A : 0.93	G : 0.02	a : 0.02	U : 0.02	
A : 0.89	C : 0.06	U : 0.02	a : 0.02	

#score	729.3333333333338
#seq	48
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000