
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m2_run1.nuc.txt

#NT
UUC	chr14:65820654-65820893(-)$1	239	77	80	8.9999
UUC	chrX:92244257-92244498(-)$1	241	66	69	8.9999
UUC	chr1:190036846-190037139(+)$1	293	46	49	8.9999
UUC	chr4:47483833-47484095(-)$1	262	56	59	8.9999
UUC	chr2:62163200-62163440(+)$1	240	0	3	8.9999
UUC	chr11:53231196-53231446(+)$1	250	11	14	8.9999
UUC	chr2:68946690-68946930(+)$1	240	1	4	8.9999
UUC	chr5:124824153-124824402(-)$1	249	61	64	8.9999
UUC	chr5:149316775-149317016(-)$1	241	69	72	8.9999
UUC	chr11:41725164-41725415(-)$1	251	54	57	8.9999
UUC	chr16:73044546-73044783(+)$1	237	14	17	8.9999
uuc	chr4:134970932-134971169(-)$1	237	22	25	8.9999
UUC	chr16:67080706-67080945(-)$1	239	35	38	8.9999
UUC	chrX:162826080-162826324(+)$1	244	31	34	8.9999
UUC	chr2:102621818-102622058(+)$1	240	86	89	8.9999
UUC	chr12:3247801-3248045(-)$1	244	46	49	8.9999
UUC	chr2:21749726-21749984(+)$1	258	5	8	8.9999
UUC	chr18:6789456-6789695(+)$1	239	68	71	8.9999
UUC	chrX:10172774-10173058(+)$1	284	46	49	8.9999
UUC	chrX:96661644-96661902(-)$1	258	35	38	8.9999
UUC	chr2:32164102-32164341(-)$1	239	16	19	8.9999
UUC	chr10:20799643-20799891(+)$1	248	2	5	8.9999
UUC	chr17:64630367-64630635(-)$1	268	3	6	8.9999
UUC	chr5:122904118-122904378(-)$1	260	29	32	8.9999
UUC	chr11:17100124-17100433(+)$1	309	12	15	8.9999
UUC	chr13:110851792-110852038(-)$1	246	88	91	8.9999
UUC	chr1:59927210-59927447(+)$1	237	31	34	8.9999
UUC	chr3:103544022-103544279(-)$1	257	17	20	8.9999
UUC	chr15:37986467-37986724(-)$1	257	56	59	8.9999
UUC	chr3:31018142-31018386(+)$1	244	21	24	8.9999
UUC	chr14:105708093-105708352(+)$1	259	13	16	8.9999
uuc	chr2:129456607-129456851(+)$1	244	38	41	8.9999
UUC	chr5:65986677-65986918(+)$1	241	5	8	8.9999
UUC	chr9:75069990-75070247(+)$1	257	38	41	8.9999
UUC	chr12:11331969-11332250(-)$1	281	83	86	8.9999
UUC	chr16:94690461-94690700(+)$1	239	20	23	8.9999
UUC	chr2:164250281-164250530(-)$1	249	22	25	8.9999
UUC	chr11:87865010-87865251(+)$1	241	1	4	8.9999
uuc	chr14:124910830-124911067(-)$1	237	111	114	8.9999
UUC	chr10:39283831-39284076(+)$1	245	1	4	8.9999
UUC	chr3:136598376-136598668(+)$1	292	50	53	8.9999
UUC	chr18:61747725-61747971(+)$1	246	13	16	8.9999
UUC	chr11:72581655-72581892(+)$1	237	38	41	8.9999
UUC	chr11:98218413-98218649(+)$1	236	16	19	8.9999
UUC	chr1:136644631-136644868(+)$1	237	5	8	8.9999
UUC	chr5:32794483-32794768(+)$1	285	20	23	8.9999
UUC	chr1:155541635-155541875(+)$1	240	19	22	8.9999
UUC	chr3:31101926-31102161(-)$1	235	6	9	8.9999
UUC	chr4:109877461-109877702(-)$1	241	12	15	8.9999
UUC	chr2:165697484-165697725(-)$1	241	21	24	8.9999
UUC	chr1:79791176-79791411(-)$1	235	136	139	8.9999
UUC	chr6:23213341-23213587(-)$1	246	164	167	8.9999
UUC	chr4:6322045-6322294(+)$1	249	33	36	8.9999
UUC	chrX:149935907-149936144(+)$1	237	15	18	8.9999
UUC	chr8:70216403-70216647(-)$1	244	54	57	8.9999
UUC	chr8:86464595-86464838(+)$1	243	14	17	8.9999
UUC	chr5:122906744-122907038(-)$1	294	20	23	8.9999
UUC	chr11:53233665-53233900(+)$1	235	65	68	8.9999
UUC	chr11:41723670-41723905(-)$1	235	138	141	8.9999
UUC	chr12:73313051-73313369(-)$1	318	83	86	8.9999
UUC	chr12:71347000-71347238(-)$1	238	32	35	8.9999
UUC	chr14:70868427-70868672(+)$1	245	82	85	8.9999
UUC	chr10:86300856-86301101(+)$1	245	9	12	8.9999
UUC	chr7:6659187-6659465(-)$1	278	74	77	8.9999
UUC	chr13:59033610-59033866(+)$1	256	49	52	8.9999
UUC	chr17:34782494-34782729(+)$1	235	95	98	8.9999
uuc	chr5:147572769-147573004(-)$1	235	17	20	8.9999
UUC	chr9:24218135-24218370(-)$1	235	7	10	8.9999
UUC	chr4:155386474-155386713(+)$1	239	45	48	8.9999
UUC	chrX:96661470-96661722(-)$1	252	39	42	8.9999
UUC	chr4:126421030-126421299(-)$1	269	52	55	8.9999
uuc	chr18:61147502-61147742(+)$1	240	12	15	8.9999
UUC	chr11:17098232-17098536(+)$1	304	109	112	8.9999
uuc	chr5:142506696-142506931(+)$1	235	103	106	8.9999
uuc	chr12:29463754-29463990(+)$1	236	24	27	8.9999
UUC	chr2:174171813-174172084(+)$1	271	16	19	8.9999
UUC	chr11:51799897-51800143(-)$1	246	55	58	8.9999
UUC	chr11:87033984-87034239(+)$1	255	38	41	8.9999
UUC	chr9:53760011-53760247(-)$1	236	18	21	8.9999
UUC	chr18:34506502-34506769(-)$1	267	91	94	8.9999
UUC	chr1:52222712-52222963(-)$1	251	33	36	8.9999
UUC	chr11:97371321-97371558(-)$1	237	218	221	8.9999
UUC	chrX:162823625-162823903(+)$1	278	41	44	8.9999
UUC	chr5:122906460-122906727(-)$1	267	19	22	8.9999
UUC	chr17:5139856-5140091(+)$1	235	21	24	8.9999
UUC	chr1:79790888-79791127(-)$1	239	80	83	8.9999
UUC	chr16:17044950-17045193(+)$1	243	6	9	8.9999
UUC	chr11:32645254-32645499(+)$1	245	90	93	8.9999
UUC	chr4:11512896-11513131(+)$1	235	49	52	8.9999
UUC	chr18:54112882-54113144(+)$1	262	29	32	8.9999
UUC	chr11:109530158-109530409(+)$1	251	5	8	8.9999
UUC	chr13:98021849-98022111(+)$1	262	58	61	8.9999
UUC	chr13:110847795-110848040(-)$1	245	80	83	8.9999
UUC	chr9:120869119-120869363(+)$1	244	39	42	8.9999
UUC	chr2:134420264-134420541(-)$1	277	16	19	8.9999

#otherMatches

#Struct PSSM
GGG	chr16:96289360-96289603(-)$1	243	29	32	8.9999
ffm	chr14:65820654-65820893(-)$1	239	77	80	8.9999
HHH	chrX:92244257-92244498(-)$1	241	66	69	8.9999
c[d	chr1:190036846-190037139(+)$1	293	46	49	8.9999
::G	chr4:47483833-47484095(-)$1	262	56	59	8.9999
FFF	chr2:62163200-62163440(+)$1	240	0	3	8.9999
###	chr11:53231196-53231446(+)$1	250	11	14	8.9999
fff	chr2:68946690-68946930(+)$1	240	1	4	8.9999
:::	chr5:124824153-124824402(-)$1	249	61	64	8.9999
:::	chr5:149316775-149317016(-)$1	241	69	72	8.9999
GGG	chr11:41725164-41725415(-)$1	251	54	57	8.9999
mmf	chr16:73044546-73044783(+)$1	237	14	17	8.9999
(((	chr4:134970932-134971169(-)$1	237	22	25	8.9999
:::	chr16:67080706-67080945(-)$1	239	35	38	8.9999
eee	chrX:162826080-162826324(+)$1	244	31	34	8.9999
ttt	chr2:102621818-102622058(+)$1	240	86	89	8.9999
ooo	chr12:3247801-3248045(-)$1	244	46	49	8.9999
WWW	chr2:21749726-21749984(+)$1	258	5	8	8.9999
c]c	chr18:6789456-6789695(+)$1	239	68	71	8.9999
:::	chrX:10172774-10173058(+)$1	284	46	49	8.9999
:::	chrX:96661644-96661902(-)$1	258	35	38	8.9999
:::	chr2:32164102-32164341(-)$1	239	16	19	8.9999
ggg	chr10:20799643-20799891(+)$1	248	2	5	8.9999
:::	chr17:64630367-64630635(-)$1	268	3	6	8.9999
:::	chr5:122904118-122904378(-)$1	260	29	32	8.9999
:::	chr11:17100124-17100433(+)$1	309	12	15	8.9999
[dd	chr13:110851792-110852038(-)$1	246	88	91	8.9999
oob	chr1:59927210-59927447(+)$1	237	31	34	8.9999
qqq	chr3:103544022-103544279(-)$1	257	17	20	8.9999
eee	chr15:37986467-37986724(-)$1	257	56	59	8.9999
hhh	chr3:31018142-31018386(+)$1	244	21	24	8.9999
GGG	chr14:105708093-105708352(+)$1	259	13	16	8.9999
+++	chr2:129456607-129456851(+)$1	244	38	41	8.9999
:::	chr5:65986677-65986918(+)$1	241	5	8	8.9999
hh)	chr9:75069990-75070247(+)$1	257	38	41	8.9999
gg+	chr12:11331969-11332250(-)$1	281	83	86	8.9999
ccc	chr16:94690461-94690700(+)$1	239	20	23	8.9999
++i	chr2:164250281-164250530(-)$1	249	22	25	8.9999
::E	chr11:87865010-87865251(+)$1	241	1	4	8.9999
fff	chr14:124910830-124911067(-)$1	237	111	114	8.9999
FFF	chr10:39283831-39284076(+)$1	245	1	4	8.9999
FFF	chr3:136598376-136598668(+)$1	292	50	53	8.9999
HH{	chr18:61747725-61747971(+)$1	246	13	16	8.9999
ff]	chr11:72581655-72581892(+)$1	237	38	41	8.9999
$$$	chr11:98218413-98218649(+)$1	236	16	19	8.9999
{CC	chr1:136644631-136644868(+)$1	237	5	8	8.9999
iii	chr5:32794483-32794768(+)$1	285	20	23	8.9999
EEE	chr1:155541635-155541875(+)$1	240	19	22	8.9999
LLL	chr3:31101926-31102161(-)$1	235	6	9	8.9999
&&&	chr4:109877461-109877702(-)$1	241	12	15	8.9999
GGG	chr2:165697484-165697725(-)$1	241	21	24	8.9999
ee"	chr1:79791176-79791411(-)$1	235	136	139	8.9999
:::	chr6:23213341-23213587(-)$1	246	164	167	8.9999
gg3	chr4:6322045-6322294(+)$1	249	33	36	8.9999
fff	chrX:149935907-149936144(+)$1	237	15	18	8.9999
===	chr8:70216403-70216647(-)$1	244	54	57	8.9999
&&&	chr8:86464595-86464838(+)$1	243	14	17	8.9999
ggg	chr5:122906744-122907038(-)$1	294	20	23	8.9999
fff	chr11:53233665-53233900(+)$1	235	65	68	8.9999
^^^	chr11:41723670-41723905(-)$1	235	138	141	8.9999
:ff	chr12:73313051-73313369(-)$1	318	83	86	8.9999
:::	chr12:71347000-71347238(-)$1	238	32	35	8.9999
%%%	chr14:70868427-70868672(+)$1	245	82	85	8.9999
E::	chr10:86300856-86301101(+)$1	245	9	12	8.9999
^^^	chr7:6659187-6659465(-)$1	278	74	77	8.9999
eee	chr13:59033610-59033866(+)$1	256	49	52	8.9999
:cc	chr17:34782494-34782729(+)$1	235	95	98	8.9999
fff	chr5:147572769-147573004(-)$1	235	17	20	8.9999
:::	chr9:24218135-24218370(-)$1	235	7	10	8.9999
nnn	chr4:155386474-155386713(+)$1	239	45	48	8.9999
fff	chrX:96661470-96661722(-)$1	252	39	42	8.9999
%%%	chr4:126421030-126421299(-)$1	269	52	55	8.9999
===	chr18:61147502-61147742(+)$1	240	12	15	8.9999
!ee	chr11:17098232-17098536(+)$1	304	109	112	8.9999
rrr	chr5:142506696-142506931(+)$1	235	103	106	8.9999
d[a	chr12:29463754-29463990(+)$1	236	24	27	8.9999
ooo	chr2:174171813-174172084(+)$1	271	16	19	8.9999
eee	chr11:51799897-51800143(-)$1	246	55	58	8.9999
g##	chr11:87033984-87034239(+)$1	255	38	41	8.9999
=tt	chr9:53760011-53760247(-)$1	236	18	21	8.9999
eee	chr18:34506502-34506769(-)$1	267	91	94	8.9999
CCC	chr1:52222712-52222963(-)$1	251	33	36	8.9999
F}C	chr11:97371321-97371558(-)$1	237	218	221	8.9999
LDD	chrX:162823625-162823903(+)$1	278	41	44	8.9999
:::	chr5:122906460-122906727(-)$1	267	19	22	8.9999
sdd	chr17:5139856-5140091(+)$1	235	21	24	8.9999
555	chr1:79790888-79791127(-)$1	239	80	83	8.9999
:::	chr16:17044950-17045193(+)$1	243	6	9	8.9999
22e	chr11:32645254-32645499(+)$1	245	90	93	8.9999
hhh	chr4:11512896-11513131(+)$1	235	49	52	8.9999
fff	chr18:54112882-54113144(+)$1	262	29	32	8.9999
ee!	chr11:109530158-109530409(+)$1	251	5	8	8.9999
BKK	chr13:98021849-98022111(+)$1	262	58	61	8.9999
HHH	chr13:110847795-110848040(-)$1	245	80	83	8.9999
EEE	chr9:120869119-120869363(+)$1	244	39	42	8.9999
^^^	chr2:134420264-134420541(-)$1	277	16	19	8.9999

#DB
(((	chr16:96289360-96289603(-)$1	1	29	32	8.9999
((.	chr14:65820654-65820893(-)$1	1	77	80	8.9999
(((	chrX:92244257-92244498(-)$1	1	66	69	8.9999
(.(	chr1:190036846-190037139(+)$1	1	46	49	8.9999
..(	chr4:47483833-47484095(-)$1	1	56	59	8.9999
(((	chr2:62163200-62163440(+)$1	1	0	3	8.9999
...	chr11:53231196-53231446(+)$1	1	11	14	8.9999
(((	chr2:68946690-68946930(+)$1	1	1	4	8.9999
...	chr5:124824153-124824402(-)$1	1	61	64	8.9999
...	chr5:149316775-149317016(-)$1	1	69	72	8.9999
(((	chr11:41725164-41725415(-)$1	1	54	57	8.9999
..)	chr16:73044546-73044783(+)$1	1	14	17	8.9999
...	chr4:134970932-134971169(-)$1	1	22	25	8.9999
...	chr16:67080706-67080945(-)$1	1	35	38	8.9999
)))	chrX:162826080-162826324(+)$1	1	31	34	8.9999
...	chr2:102621818-102622058(+)$1	1	86	89	8.9999
...	chr12:3247801-3248045(-)$1	1	46	49	8.9999
...	chr2:21749726-21749984(+)$1	1	5	8	8.9999
).)	chr18:6789456-6789695(+)$1	1	68	71	8.9999
...	chrX:10172774-10173058(+)$1	1	46	49	8.9999
...	chrX:96661644-96661902(-)$1	1	35	38	8.9999
...	chr2:32164102-32164341(-)$1	1	16	19	8.9999
(((	chr10:20799643-20799891(+)$1	1	2	5	8.9999
...	chr17:64630367-64630635(-)$1	1	3	6	8.9999
...	chr5:122904118-122904378(-)$1	1	29	32	8.9999
...	chr11:17100124-17100433(+)$1	1	12	15	8.9999
.((	chr13:110851792-110852038(-)$1	1	88	91	8.9999
..)	chr1:59927210-59927447(+)$1	1	31	34	8.9999
...	chr3:103544022-103544279(-)$1	1	17	20	8.9999
)))	chr15:37986467-37986724(-)$1	1	56	59	8.9999
(((	chr3:31018142-31018386(+)$1	1	21	24	8.9999
(((	chr14:105708093-105708352(+)$1	1	13	16	8.9999
...	chr2:129456607-129456851(+)$1	1	38	41	8.9999
...	chr5:65986677-65986918(+)$1	1	5	8	8.9999
((.	chr9:75069990-75070247(+)$1	1	38	41	8.9999
((.	chr12:11331969-11332250(-)$1	1	83	86	8.9999
(((	chr16:94690461-94690700(+)$1	1	20	23	8.9999
..(	chr2:164250281-164250530(-)$1	1	22	25	8.9999
..(	chr11:87865010-87865251(+)$1	1	1	4	8.9999
)))	chr14:124910830-124911067(-)$1	1	111	114	8.9999
(((	chr10:39283831-39284076(+)$1	1	1	4	8.9999
(((	chr3:136598376-136598668(+)$1	1	50	53	8.9999
((.	chr18:61747725-61747971(+)$1	1	13	16	8.9999
)).	chr11:72581655-72581892(+)$1	1	38	41	8.9999
...	chr11:98218413-98218649(+)$1	1	16	19	8.9999
.((	chr1:136644631-136644868(+)$1	1	5	8	8.9999
(((	chr5:32794483-32794768(+)$1	1	20	23	8.9999
(((	chr1:155541635-155541875(+)$1	1	19	22	8.9999
...	chr3:31101926-31102161(-)$1	1	6	9	8.9999
...	chr4:109877461-109877702(-)$1	1	12	15	8.9999
(((	chr2:165697484-165697725(-)$1	1	21	24	8.9999
((.	chr1:79791176-79791411(-)$1	1	136	139	8.9999
...	chr6:23213341-23213587(-)$1	1	164	167	8.9999
)).	chr4:6322045-6322294(+)$1	1	33	36	8.9999
)))	chrX:149935907-149936144(+)$1	1	15	18	8.9999
)))	chr8:70216403-70216647(-)$1	1	54	57	8.9999
...	chr8:86464595-86464838(+)$1	1	14	17	8.9999
(((	chr5:122906744-122907038(-)$1	1	20	23	8.9999
(((	chr11:53233665-53233900(+)$1	1	65	68	8.9999
...	chr11:41723670-41723905(-)$1	1	138	141	8.9999
.((	chr12:73313051-73313369(-)$1	1	83	86	8.9999
...	chr12:71347000-71347238(-)$1	1	32	35	8.9999
...	chr14:70868427-70868672(+)$1	1	82	85	8.9999
(..	chr10:86300856-86301101(+)$1	1	9	12	8.9999
...	chr7:6659187-6659465(-)$1	1	74	77	8.9999
(((	chr13:59033610-59033866(+)$1	1	49	52	8.9999
.((	chr17:34782494-34782729(+)$1	1	95	98	8.9999
(((	chr5:147572769-147573004(-)$1	1	17	20	8.9999
...	chr9:24218135-24218370(-)$1	1	7	10	8.9999
...	chr4:155386474-155386713(+)$1	1	45	48	8.9999
)))	chrX:96661470-96661722(-)$1	1	39	42	8.9999
...	chr4:126421030-126421299(-)$1	1	52	55	8.9999
(((	chr18:61147502-61147742(+)$1	1	12	15	8.9999
.((	chr11:17098232-17098536(+)$1	1	109	112	8.9999
...	chr5:142506696-142506931(+)$1	1	103	106	8.9999
(.(	chr12:29463754-29463990(+)$1	1	24	27	8.9999
...	chr2:174171813-174172084(+)$1	1	16	19	8.9999
(((	chr11:51799897-51800143(-)$1	1	55	58	8.9999
(..	chr11:87033984-87034239(+)$1	1	38	41	8.9999
(..	chr9:53760011-53760247(-)$1	1	18	21	8.9999
(((	chr18:34506502-34506769(-)$1	1	91	94	8.9999
(((	chr1:52222712-52222963(-)$1	1	33	36	8.9999
).)	chr11:97371321-97371558(-)$1	1	218	221	8.9999
.((	chrX:162823625-162823903(+)$1	1	41	44	8.9999
...	chr5:122906460-122906727(-)$1	1	19	22	8.9999
.))	chr17:5139856-5140091(+)$1	1	21	24	8.9999
...	chr1:79790888-79791127(-)$1	1	80	83	8.9999
...	chr16:17044950-17045193(+)$1	1	6	9	8.9999
..)	chr11:32645254-32645499(+)$1	1	90	93	8.9999
(((	chr4:11512896-11513131(+)$1	1	49	52	8.9999
(((	chr18:54112882-54113144(+)$1	1	29	32	8.9999
((.	chr11:109530158-109530409(+)$1	1	5	8	8.9999
(..	chr13:98021849-98022111(+)$1	1	58	61	8.9999
(((	chr13:110847795-110848040(-)$1	1	80	83	8.9999
(((	chr9:120869119-120869363(+)$1	1	39	42	8.9999
...	chr2:134420264-134420541(-)$1	1	16	19	8.9999

#PSSM
U : 0.92	u : 0.07	
U : 0.92	u : 0.07	
C : 0.92	c : 0.07	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m1_run1.nuc.txt

#NT
UGGA	chr4:122539562-122539803(-)$1	241	121	125	11.9999
UGGA	chr4:131926501-131926744(-)$1	243	186	190	11.9999
UGGA	chr3:131245409-131245644(+)$1	235	16	20	11.9999
UGGA	chr19:9091433-9091699(+)$1	266	8	12	11.9999
UGGA	chr15:59184004-59184242(-)$1	238	175	179	11.9999
UGGA	chr1:45432809-45433073(-)$1	264	6	10	11.9999
UGGA	chr2:181283312-181283550(+)$1	238	204	208	11.9999
UGGA	chrX:133606033-133606268(+)$1	235	27	31	11.9999
UGGA	chr8:64163677-64163934(-)$1	257	144	148	11.9999
UGGA	chr14:55054513-55054770(+)$1	257	2	6	11.9999
UGGA	chr10:126995506-126995759(-)$1	253	126	130	11.9999
UGGA	chr13:55583954-55584211(-)$1	257	229	233	11.9999
UGGA	chr9:21203740-21203983(+)$1	243	68	72	11.9999
UGGA	chr2:73408387-73408639(-)$1	252	7	11	11.9999
UGGA	chr12:117519811-117520046(+)$1	235	95	99	11.9999
UGGA	chr14:21385032-21385270(-)$1	238	52	56	11.9999
UGGA	chr5:124842541-124842786(-)$1	245	157	161	11.9999
UGGA	chr8:4749612-4749850(-)$1	238	36	40	11.9999
UGGA	chr15:99155618-99155861(-)$1	243	92	96	11.9999
UGGA	chrX:131341097-131341336(-)$1	239	61	65	11.9999
UGGA	chr17:23948533-23948794(+)$1	261	187	191	11.9999
UGGA	chr4:133242242-133242489(-)$1	247	27	31	11.9999
UGGA	chr17:24710965-24711227(+)$1	262	16	20	11.9999
UGGA	chr11:87863398-87863634(+)$1	236	95	99	11.9999
UGGA	chr2:109852016-109852316(+)$1	300	245	249	11.9999
UGGA	chr11:75224272-75224536(-)$1	264	240	244	11.9999
UGGA	chr2:71100663-71100944(+)$1	281	258	262	11.9999
UGGA	chr4:122541750-122542010(-)$1	260	32	36	11.9999
UGGA	chr17:56425568-56425815(-)$1	247	130	134	11.9999
UGGA	chr1:191657118-191657375(+)$1	257	68	72	11.9999
UGGA	chr1:179706529-179706766(-)$1	237	128	132	11.9999
UGGA	chr17:35282265-35282506(+)$1	241	12	16	11.9999
UGGA	chr11:48616822-48617087(+)$1	265	260	264	11.9999
UGGA	chr10:59219413-59219648(+)$1	235	93	97	11.9999
UGGA	chr11:6303764-6304047(+)$1	283	43	47	11.9999
UGGA	chr8:26677134-26677375(+)$1	241	51	55	11.9999
UGGA	chr1:75305867-75306104(-)$1	237	104	108	11.9999
UGGA	chr4:43558232-43558476(-)$1	244	27	31	11.9999
UGGA	chr15:25732960-25733220(+)$1	260	82	86	11.9999
UGGA	chr15:76735156-76735460(+)$1	304	157	161	11.9999
UGGA	chr6:71546516-71546774(-)$1	258	89	93	11.9999
UGGA	chr8:113334721-113334992(-)$1	271	22	26	11.9999
UGGA	chr1:170361466-170361729(-)$1	263	95	99	11.9999
UGGA	chr15:99469959-99470202(-)$1	243	21	25	11.9999
UGGA	chr15:99835611-99835855(+)$1	244	140	144	11.9999
UGGA	chr5:29923509-29923771(+)$1	262	8	12	11.9999
UGGA	chr18:52688587-52688828(-)$1	241	234	238	11.9999
UGGA	chr15:77603634-77603881(-)$1	247	44	48	11.9999
UGGA	chr7:29689554-29689798(-)$1	244	102	106	11.9999
UGGA	chr15:83401814-83402081(+)$1	267	167	171	11.9999
UGGA	chr8:3496892-3497146(+)$1	254	185	189	11.9999
UGGA	chr1:135611701-135611960(-)$1	259	247	251	11.9999
UGGA	chr2:30736228-30736478(+)$1	250	131	135	11.9999
UGGA	chr11:115681829-115682064(+)$1	235	97	101	11.9999
UGGA	chr18:12360010-12360247(-)$1	237	140	144	11.9999
UGGA	chr13:53438419-53438673(-)$1	254	162	166	11.9999
UGGA	chr13:94710502-94710776(+)$1	274	131	135	11.9999
UGGA	chr15:37933740-37933987(-)$1	247	134	138	11.9999
UGGA	chr2:83564822-83565099(+)$1	277	166	170	11.9999
UGGA	chr11:119970671-119970928(-)$1	257	154	158	11.9999
UGGA	chr4:122812736-122812974(-)$1	238	34	38	11.9999
UGGA	chrX:39589411-39589658(+)$1	247	79	83	11.9999
UGGA	chr4:133042624-133042874(+)$1	250	59	63	11.9999
UGGA	chr3:88290675-88290958(-)$1	283	161	165	11.9999
UGGA	chr15:101947105-101947385(-)$1	280	16	20	11.9999
UGGA	chr17:35287420-35287672(-)$1	252	99	103	11.9999
UGGA	chrX:98488708-98488943(+)$1	235	67	71	11.9999
UGGA	chr10:80640709-80640972(+)$1	263	60	64	11.9999
UGGA	chr8:46037684-46037937(+)$1	253	51	55	11.9999
UGGA	chr16:21211442-21211694(+)$1	252	72	76	11.9999
UGGA	chr1:36569600-36569861(+)$1	261	2	6	11.9999
UGGA	chr17:23957169-23957422(+)$1	253	48	52	11.9999
UGGA	chr10:59453478-59453720(-)$1	242	1	5	11.9999
UGGA	chr3:121437022-121437269(+)$1	247	213	217	11.9999
UGGA	chr7:105053172-105053421(+)$1	249	46	50	11.9999
UGGA	chr15:76079328-76079585(+)$1	257	179	183	11.9999
UGGA	chrX:163645273-163645540(-)$1	267	12	16	11.9999

#otherMatches

#Struct PSSM
!bb[	chr6:34712195-34712431(+)$1	236	108	112	11.9999
:eee	chr4:122539562-122539803(-)$1	241	121	125	11.9999
lccc	chr4:131926501-131926744(-)$1	243	186	190	11.9999
:eee	chr3:131245409-131245644(+)$1	235	16	20	11.9999
nbbF	chr19:9091433-9091699(+)$1	266	8	12	11.9999
eee>	chr15:59184004-59184242(-)$1	238	175	179	11.9999
BBLL	chr1:45432809-45433073(-)$1	264	6	10	11.9999
[a[b	chr2:181283312-181283550(+)$1	238	204	208	11.9999
ccc]	chrX:133606033-133606268(+)$1	235	27	31	11.9999
iiii	chr8:64163677-64163934(-)$1	257	144	148	11.9999
FFFF	chr14:55054513-55054770(+)$1	257	2	6	11.9999
ddd"	chr10:126995506-126995759(-)$1	253	126	130	11.9999
CCCC	chr13:55583954-55584211(-)$1	257	229	233	11.9999
hhhh	chr9:21203740-21203983(+)$1	243	68	72	11.9999
####	chr2:73408387-73408639(-)$1	252	7	11	11.9999
mmmd	chr12:117519811-117520046(+)$1	235	95	99	11.9999
3ccc	chr14:21385032-21385270(-)$1	238	52	56	11.9999
a[dd	chr5:124842541-124842786(-)$1	245	157	161	11.9999
ssss	chr8:4749612-4749850(-)$1	238	36	40	11.9999
ggcc	chr15:99155618-99155861(-)$1	243	92	96	11.9999
EEEK	chrX:131341097-131341336(-)$1	239	61	65	11.9999
2===	chr17:23948533-23948794(+)$1	261	187	191	11.9999
NNFF	chr4:133242242-133242489(-)$1	247	27	31	11.9999
EEEB	chr17:24710965-24711227(+)$1	262	16	20	11.9999
hhhh	chr11:87863398-87863634(+)$1	236	95	99	11.9999
gggg	chr2:109852016-109852316(+)$1	300	245	249	11.9999
YBB}	chr11:75224272-75224536(-)$1	264	240	244	11.9999
CC__	chr2:71100663-71100944(+)$1	281	258	262	11.9999
CCCC	chr4:122541750-122542010(-)$1	260	32	36	11.9999
FBB{	chr17:56425568-56425815(-)$1	247	130	134	11.9999
GGGG	chr1:191657118-191657375(+)$1	257	68	72	11.9999
[bb[	chr1:179706529-179706766(-)$1	237	128	132	11.9999
GGGG	chr17:35282265-35282506(+)$1	241	12	16	11.9999
3ddd	chr11:48616822-48617087(+)$1	265	260	264	11.9999
eeee	chr10:59219413-59219648(+)$1	235	93	97	11.9999
hddd	chr11:6303764-6304047(+)$1	283	43	47	11.9999
dddd	chr8:26677134-26677375(+)$1	241	51	55	11.9999
lbb:	chr1:75305867-75306104(-)$1	237	104	108	11.9999
FFFF	chr4:43558232-43558476(-)$1	244	27	31	11.9999
[ccc	chr15:25732960-25733220(+)$1	260	82	86	11.9999
YDDD	chr15:76735156-76735460(+)$1	304	157	161	11.9999
LBB:	chr6:71546516-71546774(-)$1	258	89	93	11.9999
ffff	chr8:113334721-113334992(-)$1	271	22	26	11.9999
]bb]	chr1:170361466-170361729(-)$1	263	95	99	11.9999
dddd	chr15:99469959-99470202(-)$1	243	21	25	11.9999
ddd!	chr15:99835611-99835855(+)$1	244	140	144	11.9999
fffl	chr5:29923509-29923771(+)$1	262	8	12	11.9999
ooee	chr18:52688587-52688828(-)$1	241	234	238	11.9999
cooo	chr15:77603634-77603881(-)$1	247	44	48	11.9999
ppdd	chr7:29689554-29689798(-)$1	244	102	106	11.9999
g]ac	chr15:83401814-83402081(+)$1	267	167	171	11.9999
ffff	chr8:3496892-3497146(+)$1	254	185	189	11.9999
YCCC	chr1:135611701-135611960(-)$1	259	247	251	11.9999
:EEE	chr2:30736228-30736478(+)$1	250	131	135	11.9999
:::d	chr11:115681829-115682064(+)$1	235	97	101	11.9999
hhhh	chr18:12360010-12360247(-)$1	237	140	144	11.9999
FFFF	chr13:53438419-53438673(-)$1	254	162	166	11.9999
ccc6	chr13:94710502-94710776(+)$1	274	131	135	11.9999
CCCZ	chr15:37933740-37933987(-)$1	247	134	138	11.9999
qbb]	chr2:83564822-83565099(+)$1	277	166	170	11.9999
FFFF	chr11:119970671-119970928(-)$1	257	154	158	11.9999
EEEE	chr4:122812736-122812974(-)$1	238	34	38	11.9999
mbb2	chrX:39589411-39589658(+)$1	247	79	83	11.9999
HH{A	chr4:133042624-133042874(+)$1	250	59	63	11.9999
dd!!	chr3:88290675-88290958(-)$1	283	161	165	11.9999
pggg	chr15:101947105-101947385(-)$1	280	16	20	11.9999
cc::	chr17:35287420-35287672(-)$1	252	99	103	11.9999
]fff	chrX:98488708-98488943(+)$1	235	67	71	11.9999
ffff	chr10:80640709-80640972(+)$1	263	60	64	11.9999
mddd	chr8:46037684-46037937(+)$1	253	51	55	11.9999
gggg	chr16:21211442-21211694(+)$1	252	72	76	11.9999
CCC{	chr1:36569600-36569861(+)$1	261	2	6	11.9999
NFFF	chr17:23957169-23957422(+)$1	253	48	52	11.9999
DDDB	chr10:59453478-59453720(-)$1	242	1	5	11.9999
BBFF	chr3:121437022-121437269(+)$1	247	213	217	11.9999
ccc3	chr7:105053172-105053421(+)$1	249	46	50	11.9999
ffff	chr15:76079328-76079585(+)$1	257	179	183	11.9999
fffq	chrX:163645273-163645540(-)$1	267	12	16	11.9999

#DB
.((.	chr6:34712195-34712431(+)$1	1	108	112	11.9999
.(((	chr4:122539562-122539803(-)$1	1	121	125	11.9999
.)))	chr4:131926501-131926744(-)$1	1	186	190	11.9999
.(((	chr3:131245409-131245644(+)$1	1	16	20	11.9999
.))(	chr19:9091433-9091699(+)$1	1	8	12	11.9999
))).	chr15:59184004-59184242(-)$1	1	175	179	11.9999
((..	chr1:45432809-45433073(-)$1	1	6	10	11.9999
.(.(	chr2:181283312-181283550(+)$1	1	204	208	11.9999
))).	chrX:133606033-133606268(+)$1	1	27	31	11.9999
((((	chr8:64163677-64163934(-)$1	1	144	148	11.9999
((((	chr14:55054513-55054770(+)$1	1	2	6	11.9999
(((.	chr10:126995506-126995759(-)$1	1	126	130	11.9999
))))	chr13:55583954-55584211(-)$1	1	229	233	11.9999
))))	chr9:21203740-21203983(+)$1	1	68	72	11.9999
....	chr2:73408387-73408639(-)$1	1	7	11	11.9999
...)	chr12:117519811-117520046(+)$1	1	95	99	11.9999
.)))	chr14:21385032-21385270(-)$1	1	52	56	11.9999
(.((	chr5:124842541-124842786(-)$1	1	157	161	11.9999
....	chr8:4749612-4749850(-)$1	1	36	40	11.9999
))))	chr15:99155618-99155861(-)$1	1	92	96	11.9999
(((.	chrX:131341097-131341336(-)$1	1	61	65	11.9999
.)))	chr17:23948533-23948794(+)$1	1	187	191	11.9999
..((	chr4:133242242-133242489(-)$1	1	27	31	11.9999
((((	chr17:24710965-24711227(+)$1	1	16	20	11.9999
))))	chr11:87863398-87863634(+)$1	1	95	99	11.9999
))))	chr2:109852016-109852316(+)$1	1	245	249	11.9999
.)).	chr11:75224272-75224536(-)$1	1	240	244	11.9999
))..	chr2:71100663-71100944(+)$1	1	258	262	11.9999
((((	chr4:122541750-122542010(-)$1	1	32	36	11.9999
(((.	chr17:56425568-56425815(-)$1	1	130	134	11.9999
((((	chr1:191657118-191657375(+)$1	1	68	72	11.9999
.((.	chr1:179706529-179706766(-)$1	1	128	132	11.9999
((((	chr17:35282265-35282506(+)$1	1	12	16	11.9999
.)))	chr11:48616822-48617087(+)$1	1	260	264	11.9999
((((	chr10:59219413-59219648(+)$1	1	93	97	11.9999
))))	chr11:6303764-6304047(+)$1	1	43	47	11.9999
))))	chr8:26677134-26677375(+)$1	1	51	55	11.9999
.)).	chr1:75305867-75306104(-)$1	1	104	108	11.9999
((((	chr4:43558232-43558476(-)$1	1	27	31	11.9999
.(((	chr15:25732960-25733220(+)$1	1	82	86	11.9999
.)))	chr15:76735156-76735460(+)$1	1	157	161	11.9999
.((.	chr6:71546516-71546774(-)$1	1	89	93	11.9999
((((	chr8:113334721-113334992(-)$1	1	22	26	11.9999
.)).	chr1:170361466-170361729(-)$1	1	95	99	11.9999
((((	chr15:99469959-99470202(-)$1	1	21	25	11.9999
(((.	chr15:99835611-99835855(+)$1	1	140	144	11.9999
(((.	chr5:29923509-29923771(+)$1	1	8	12	11.9999
..))	chr18:52688587-52688828(-)$1	1	234	238	11.9999
(...	chr15:77603634-77603881(-)$1	1	44	48	11.9999
..))	chr7:29689554-29689798(-)$1	1	102	106	11.9999
).))	chr15:83401814-83402081(+)$1	1	167	171	11.9999
))))	chr8:3496892-3497146(+)$1	1	185	189	11.9999
.)))	chr1:135611701-135611960(-)$1	1	247	251	11.9999
.)))	chr2:30736228-30736478(+)$1	1	131	135	11.9999
...(	chr11:115681829-115682064(+)$1	1	97	101	11.9999
((((	chr18:12360010-12360247(-)$1	1	140	144	11.9999
))))	chr13:53438419-53438673(-)$1	1	162	166	11.9999
))).	chr13:94710502-94710776(+)$1	1	131	135	11.9999
))).	chr15:37933740-37933987(-)$1	1	134	138	11.9999
.)).	chr2:83564822-83565099(+)$1	1	166	170	11.9999
))))	chr11:119970671-119970928(-)$1	1	154	158	11.9999
((((	chr4:122812736-122812974(-)$1	1	34	38	11.9999
.)).	chrX:39589411-39589658(+)$1	1	79	83	11.9999
((.(	chr4:133042624-133042874(+)$1	1	59	63	11.9999
((..	chr3:88290675-88290958(-)$1	1	161	165	11.9999
.)))	chr15:101947105-101947385(-)$1	1	16	20	11.9999
))..	chr17:35287420-35287672(-)$1	1	99	103	11.9999
.)))	chrX:98488708-98488943(+)$1	1	67	71	11.9999
((((	chr10:80640709-80640972(+)$1	1	60	64	11.9999
.)))	chr8:46037684-46037937(+)$1	1	51	55	11.9999
((((	chr16:21211442-21211694(+)$1	1	72	76	11.9999
(((.	chr1:36569600-36569861(+)$1	1	2	6	11.9999
.(((	chr17:23957169-23957422(+)$1	1	48	52	11.9999
((((	chr10:59453478-59453720(-)$1	1	1	5	11.9999
))))	chr3:121437022-121437269(+)$1	1	213	217	11.9999
))).	chr7:105053172-105053421(+)$1	1	46	50	11.9999
((((	chr15:76079328-76079585(+)$1	1	179	183	11.9999
(((.	chrX:163645273-163645540(-)$1	1	12	16	11.9999

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

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m3_run1.nuc.txt

#NT
AUUUU	chr5:122907217-122907452(-)$1	235	20	25	11.9014
AUUUU	chr5:122906038-122906273(-)$1	235	55	60	11.9014
AUUUU	chr10:117252017-117252253(-)$1	236	147	152	11.9014
AUUUG	chr11:109530163-109530414(+)$1	251	21	26	12.0422
AUUUG	chr8:109895182-109895417(+)$1	235	26	31	12.0422
AUUUU	chr5:32794739-32794979(+)$1	240	6	11	11.9014
AUUUG	chr15:4104924-4105174(+)$1	250	224	229	12.0422
AUUUU	chr1:34178373-34178608(+)$1	235	55	60	11.9014
AUUUC	chr18:31941014-31941249(+)$1	235	13	18	11.0563
AUUUG	chr14:37688389-37688631(-)$1	242	67	72	12.0422
AUUUG	chr8:71430247-71430482(+)$1	235	5	10	12.0422
AUUUC	chr12:54249529-54249776(+)$1	247	50	55	11.0563
AUUUU	chr4:80924787-80925029(-)$1	242	79	84	11.9014
AUUUU	chr17:50132649-50132887(-)$1	238	49	54	11.9014
AUUUU	chr15:12280154-12280391(+)$1	237	95	100	11.9014
AUUUG	chr9:30957848-30958085(-)$1	237	40	45	12.0422
AUUUU	chr13:12153525-12153765(-)$1	240	154	159	11.9014
AUUUG	chr11:94887931-94888172(-)$1	241	78	83	12.0422
AUUUG	chr16:58678960-58679203(+)$1	243	139	144	12.0422
AUUUG	chr17:73290105-73290353(+)$1	248	43	48	12.0422
AUUUC	chr1:89088986-89089221(+)$1	235	93	98	11.0563
AUUUC	chr1:166367681-166367925(-)$1	244	9	14	11.0563
AUUUG	chr1:123202257-123202496(-)$1	239	196	201	12.0422
auuug	chr5:33964509-33964753(-)$1	244	14	19	12.0422
AUUUU	chr9:21297934-21298171(+)$1	237	3	8	11.9014
AUUUG	chr12:112779076-112779330(+)$1	254	116	121	12.0422
AUUUG	chr18:4994934-4995169(+)$1	235	206	211	12.0422
AUUUU	chr9:30882939-30883174(+)$1	235	41	46	11.9014
AUUUC	chr13:109668888-109669124(+)$1	236	172	177	11.0563
AUUUC	chr2:72244950-72245202(+)$1	252	165	170	11.0563
AUUUG	chr9:120868786-120869057(+)$1	271	72	77	12.0422
AUUUC	chr6:13034868-13035117(+)$1	249	17	22	11.0563
AUUUU	chr12:75047502-75047738(+)$1	236	64	69	11.9014
AUUUC	chr8:124121256-124121494(+)$1	238	213	218	11.0563
AUUUC	chr11:87793883-87794158(-)$1	275	36	41	11.0563
AUUUU	chr17:13208997-13209239(+)$1	242	2	7	11.9014
AUUUU	chr11:20125159-20125400(+)$1	241	54	59	11.9014
AUUUG	chr2:155973180-155973415(-)$1	235	37	42	12.0422
AUUUG	chr5:143533280-143533519(-)$1	239	146	151	12.0422
AUUUU	chr15:76912729-76912967(-)$1	238	63	68	11.9014
AUUUG	chr9:96218373-96218629(+)$1	256	43	48	12.0422
AUUUC	chr2:72245089-72245325(+)$1	236	26	31	11.0563
AUUUG	chr7:118215763-118216008(-)$1	245	197	202	12.0422
AUUUG	chr2:155214476-155214718(+)$1	242	63	68	12.0422
AUUUC	chr10:59764595-59764836(+)$1	241	1	6	11.0563
AUUUG	chr1:196519484-196519719(+)$1	235	205	210	12.0422
AUUUU	chr2:90856710-90856961(+)$1	251	152	157	11.9014
auuug	chr13:94615440-94615675(+)$1	235	159	164	12.0422
AUUUU	chr2:155214408-155214646(+)$1	238	11	16	11.9014
AUUUG	chr16:8849473-8849708(+)$1	235	25	30	12.0422
auuuc	chr7:28481410-28481646(+)$1	236	8	13	11.0563
AUUUU	chr2:75817091-75817333(-)$1	242	11	16	11.9014
Auuug	chr17:81787502-81787752(-)$1	250	3	8	12.0422
AUUUG	chr1:191032649-191032887(-)$1	238	37	42	12.0422
AUUUG	chr3:101264456-101264692(+)$1	236	2	7	12.0422
AUUUU	chr8:107740674-107740915(+)$1	241	231	236	11.9014
AUUUC	chr5:23633758-23634000(+)$1	242	40	45	11.0563
AUUUU	chr10:18576309-18576544(+)$1	235	10	15	11.9014
AUUUU	chr4:97780330-97780591(+)$1	261	224	229	11.9014
AUUUG	chr2:163450342-163450596(-)$1	254	157	162	12.0422
AUUUU	chr14:58309449-58309699(-)$1	250	2	7	11.9014
AUUUU	chr14:35339882-35340126(-)$1	244	135	140	11.9014
auuuc	chr1:134473175-134473411(-)$1	236	16	21	11.0563
auuuu	chr6:93867622-93867857(-)$1	235	28	33	11.9014
AUUUG	chr11:109529368-109529612(+)$1	244	196	201	12.0422
AUUUC	chr16:13417071-13417306(+)$1	235	4	9	11.0563
auuuu	chr12:75046634-75046871(+)$1	237	138	143	11.9014
AUUUG	chr9:3478532-3478767(+)$1	235	166	171	12.0422
AUUUU	chr11:60370461-60370714(+)$1	253	143	148	11.9014
auuug	chr9:30957186-30957440(-)$1	254	117	122	12.0422

#otherMatches

#Struct PSSM
ee###	chr12:111819804-111820044(+)$1	240	77	82	11.9014
QQQQD	chr5:122907217-122907452(-)$1	235	20	25	11.9014
IIIII	chr5:122906038-122906273(-)$1	235	55	60	11.9014
+++++	chr10:117252017-117252253(-)$1	236	147	152	11.9014
''''f	chr11:109530163-109530414(+)$1	251	21	26	12.0422
::::E	chr8:109895182-109895417(+)$1	235	26	31	12.0422
=====	chr5:32794739-32794979(+)$1	240	6	11	11.9014
IIIII	chr15:4104924-4105174(+)$1	250	224	229	12.0422
ggggg	chr1:34178373-34178608(+)$1	235	55	60	11.9014
III::	chr18:31941014-31941249(+)$1	235	13	18	11.0563
hhhhh	chr14:37688389-37688631(-)$1	242	67	72	12.0422
%%%gg	chr8:71430247-71430482(+)$1	235	5	10	12.0422
mmccc	chr12:54249529-54249776(+)$1	247	50	55	11.0563
gg###	chr4:80924787-80925029(-)$1	242	79	84	11.9014
%%%%%	chr17:50132649-50132887(-)$1	238	49	54	11.9014
[hhhh	chr15:12280154-12280391(+)$1	237	95	100	11.9014
ooooc	chr9:30957848-30958085(-)$1	237	40	45	12.0422
ddddd	chr13:12153525-12153765(-)$1	240	154	159	11.9014
:hhhh	chr11:94887931-94888172(-)$1	241	78	83	12.0422
ooocc	chr16:58678960-58679203(+)$1	243	139	144	12.0422
:::::	chr17:73290105-73290353(+)$1	248	43	48	12.0422
ttttt	chr1:89088986-89089221(+)$1	235	93	98	11.0563
mmmcc	chr1:166367681-166367925(-)$1	244	9	14	11.0563
d]ggg	chr1:123202257-123202496(-)$1	239	196	201	12.0422
{EEEE	chr5:33964509-33964753(-)$1	244	14	19	12.0422
:::JJ	chr9:21297934-21298171(+)$1	237	3	8	11.9014
333bb	chr12:112779076-112779330(+)$1	254	116	121	12.0422
:::::	chr18:4994934-4995169(+)$1	235	206	211	12.0422
LLLHH	chr9:30882939-30883174(+)$1	235	41	46	11.9014
fssss	chr13:109668888-109669124(+)$1	236	172	177	11.0563
ffff2	chr2:72244950-72245202(+)$1	252	165	170	11.0563
555ff	chr9:120868786-120869057(+)$1	271	72	77	12.0422
D::::	chr6:13034868-13035117(+)$1	249	17	22	11.0563
:::::	chr12:75047502-75047738(+)$1	236	64	69	11.9014
nnnnn	chr8:124121256-124121494(+)$1	238	213	218	11.0563
hhh[a	chr11:87793883-87794158(-)$1	275	36	41	11.0563
:::::	chr17:13208997-13209239(+)$1	242	2	7	11.9014
HHHHH	chr11:20125159-20125400(+)$1	241	54	59	11.9014
dddd2	chr2:155973180-155973415(-)$1	235	37	42	12.0422
nnnnb	chr5:143533280-143533519(-)$1	239	146	151	12.0422
=====	chr15:76912729-76912967(-)$1	238	63	68	11.9014
:::::	chr9:96218373-96218629(+)$1	256	43	48	12.0422
wwwww	chr2:72245089-72245325(+)$1	236	26	31	11.0563
____C	chr7:118215763-118216008(-)$1	245	197	202	12.0422
hhhh]	chr2:155214476-155214718(+)$1	242	63	68	12.0422
::::f	chr10:59764595-59764836(+)$1	241	1	6	11.0563
vveee	chr1:196519484-196519719(+)$1	235	205	210	12.0422
qqqqq	chr2:90856710-90856961(+)$1	251	152	157	11.9014
ooooa	chr13:94615440-94615675(+)$1	235	159	164	12.0422
sssss	chr2:155214408-155214646(+)$1	238	11	16	11.9014
{BB{E	chr16:8849473-8849708(+)$1	235	25	30	12.0422
hhhhh	chr7:28481410-28481646(+)$1	236	8	13	11.0563
fffff	chr2:75817091-75817333(-)$1	242	11	16	11.9014
:::::	chr17:81787502-81787752(-)$1	250	3	8	12.0422
d!!cc	chr1:191032649-191032887(-)$1	238	37	42	12.0422
::::g	chr3:101264456-101264692(+)$1	236	2	7	12.0422
DYYEE	chr8:107740674-107740915(+)$1	241	231	236	11.9014
eeee:	chr5:23633758-23634000(+)$1	242	40	45	11.0563
KFFFF	chr10:18576309-18576544(+)$1	235	10	15	11.9014
::::c	chr4:97780330-97780591(+)$1	261	224	229	11.9014
=====	chr2:163450342-163450596(-)$1	254	157	162	12.0422
IIIII	chr14:58309449-58309699(-)$1	250	2	7	11.9014
lhhhh	chr14:35339882-35340126(-)$1	244	135	140	11.9014
:ffff	chr1:134473175-134473411(-)$1	236	16	21	11.0563
GGGGG	chr6:93867622-93867857(-)$1	235	28	33	11.9014
b333i	chr11:109529368-109529612(+)$1	244	196	201	12.0422
:::::	chr16:13417071-13417306(+)$1	235	4	9	11.0563
fffss	chr12:75046634-75046871(+)$1	237	138	143	11.9014
rrrrr	chr9:3478532-3478767(+)$1	235	166	171	12.0422
::::D	chr11:60370461-60370714(+)$1	253	143	148	11.9014
^^^^^	chr9:30957186-30957440(-)$1	254	117	122	12.0422

#DB
((...	chr12:111819804-111820044(+)$1	1	77	82	11.9014
....(	chr5:122907217-122907452(-)$1	1	20	25	11.9014
(((((	chr5:122906038-122906273(-)$1	1	55	60	11.9014
.....	chr10:117252017-117252253(-)$1	1	147	152	11.9014
....(	chr11:109530163-109530414(+)$1	1	21	26	12.0422
....(	chr8:109895182-109895417(+)$1	1	26	31	12.0422
(((((	chr5:32794739-32794979(+)$1	1	6	11	11.9014
)))))	chr15:4104924-4105174(+)$1	1	224	229	12.0422
)))))	chr1:34178373-34178608(+)$1	1	55	60	11.9014
(((..	chr18:31941014-31941249(+)$1	1	13	18	11.0563
(((((	chr14:37688389-37688631(-)$1	1	67	72	12.0422
...((	chr8:71430247-71430482(+)$1	1	5	10	12.0422
..)))	chr12:54249529-54249776(+)$1	1	50	55	11.0563
((...	chr4:80924787-80925029(-)$1	1	79	84	11.9014
.....	chr17:50132649-50132887(-)$1	1	49	54	11.9014
.((((	chr15:12280154-12280391(+)$1	1	95	100	11.9014
....)	chr9:30957848-30958085(-)$1	1	40	45	12.0422
)))((	chr13:12153525-12153765(-)$1	1	154	159	11.9014
.((((	chr11:94887931-94888172(-)$1	1	78	83	12.0422
...))	chr16:58678960-58679203(+)$1	1	139	144	12.0422
.....	chr17:73290105-73290353(+)$1	1	43	48	12.0422
.....	chr1:89088986-89089221(+)$1	1	93	98	11.0563
...))	chr1:166367681-166367925(-)$1	1	9	14	11.0563
).)))	chr1:123202257-123202496(-)$1	1	196	201	12.0422
.((((	chr5:33964509-33964753(-)$1	1	14	19	12.0422
...((	chr9:21297934-21298171(+)$1	1	3	8	11.9014
...))	chr12:112779076-112779330(+)$1	1	116	121	12.0422
.....	chr18:4994934-4995169(+)$1	1	206	211	12.0422
...((	chr9:30882939-30883174(+)$1	1	41	46	11.9014
(....	chr13:109668888-109669124(+)$1	1	172	177	11.0563
)))).	chr2:72244950-72245202(+)$1	1	165	170	11.0563
...))	chr9:120868786-120869057(+)$1	1	72	77	12.0422
(....	chr6:13034868-13035117(+)$1	1	17	22	11.0563
.....	chr12:75047502-75047738(+)$1	1	64	69	11.9014
.....	chr8:124121256-124121494(+)$1	1	213	218	11.0563
(((.(	chr11:87793883-87794158(-)$1	1	36	41	11.0563
.....	chr17:13208997-13209239(+)$1	1	2	7	11.9014
(((((	chr11:20125159-20125400(+)$1	1	54	59	11.9014
)))).	chr2:155973180-155973415(-)$1	1	37	42	12.0422
....)	chr5:143533280-143533519(-)$1	1	146	151	12.0422
(((((	chr15:76912729-76912967(-)$1	1	63	68	11.9014
.....	chr9:96218373-96218629(+)$1	1	43	48	12.0422
.....	chr2:72245089-72245325(+)$1	1	26	31	11.0563
....)	chr7:118215763-118216008(-)$1	1	197	202	12.0422
)))).	chr2:155214476-155214718(+)$1	1	63	68	12.0422
....(	chr10:59764595-59764836(+)$1	1	1	6	11.0563
..)))	chr1:196519484-196519719(+)$1	1	205	210	12.0422
.....	chr2:90856710-90856961(+)$1	1	152	157	11.9014
....)	chr13:94615440-94615675(+)$1	1	159	164	12.0422
.....	chr2:155214408-155214646(+)$1	1	11	16	11.9014
.((.(	chr16:8849473-8849708(+)$1	1	25	30	12.0422
(((((	chr7:28481410-28481646(+)$1	1	8	13	11.0563
(((((	chr2:75817091-75817333(-)$1	1	11	16	11.9014
.....	chr17:81787502-81787752(-)$1	1	3	8	12.0422
(..((	chr1:191032649-191032887(-)$1	1	37	42	12.0422
....(	chr3:101264456-101264692(+)$1	1	2	7	12.0422
)..))	chr8:107740674-107740915(+)$1	1	231	236	11.9014
)))).	chr5:23633758-23634000(+)$1	1	40	45	11.0563
.((((	chr10:18576309-18576544(+)$1	1	10	15	11.9014
....(	chr4:97780330-97780591(+)$1	1	224	229	11.9014
)))))	chr2:163450342-163450596(-)$1	1	157	162	12.0422
(((((	chr14:58309449-58309699(-)$1	1	2	7	11.9014
.))))	chr14:35339882-35340126(-)$1	1	135	140	11.9014
.((((	chr1:134473175-134473411(-)$1	1	16	21	11.0563
(((((	chr6:93867622-93867857(-)$1	1	28	33	11.9014
)...)	chr11:109529368-109529612(+)$1	1	196	201	12.0422
.....	chr16:13417071-13417306(+)$1	1	4	9	11.0563
(((..	chr12:75046634-75046871(+)$1	1	138	143	11.9014
.....	chr9:3478532-3478767(+)$1	1	166	171	12.0422
....)	chr11:60370461-60370714(+)$1	1	143	148	11.9014
.....	chr9:30957186-30957440(-)$1	1	117	122	12.0422

#PSSM
A : 0.90	a : 0.09	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.35	G : 0.35	C : 0.18	g : 0.05	c : 0.02	u : 0.02	

#score	836.4084507042251
#seq	71
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m1_run1.nuc.txt

#NT
GCC	chr7:27949678-27950016(-)$1	338	44	47	8.9999
GCC	chr14:58352846-58353120(-)$1	274	72	75	8.9999
GCC	chr10:25219551-25219823(+)$1	272	6	9	8.9999
GCC	chr11:69550323-69550593(-)$1	270	21	24	8.9999
GCC	chr1:164628233-164628501(-)$1	268	163	166	8.9999
gcc	chr4:41066380-41066652(-)$1	272	6	9	8.9999
GCC	chr15:94116703-94116978(-)$1	275	165	168	8.9999
GCC	chr1:89687675-89687956(+)$1	281	26	29	8.9999
GCC	chr4:117832654-117832930(-)$1	276	39	42	8.9999
GCC	chr12:81975083-81975356(+)$1	273	160	163	8.9999
GCC	chr8:34722258-34722540(+)$1	282	7	10	8.9999
GCC	chr18:12301437-12301710(+)$1	273	163	166	8.9999
GCC	chr8:82197699-82197995(+)$1	296	64	67	8.9999
GCC	chr8:87433104-87433375(+)$1	271	31	34	8.9999
GCC	chr4:98400196-98400501(+)$1	305	106	109	8.9999
GCC	chr4:41137660-41137947(+)$1	287	67	70	8.9999
GCC	chr11:55220600-55220897(-)$1	297	4	7	8.9999
GCC	chr18:50342753-50343040(+)$1	287	99	102	8.9999
GCC	chr8:119873108-119873392(+)$1	284	30	33	8.9999
GCC	chr19:46107485-46107753(-)$1	268	21	24	8.9999
GCC	chr9:43972114-43972410(-)$1	296	156	159	8.9999
GCC	chr15:10391926-10392198(-)$1	272	116	119	8.9999
GCC	chr5:124170651-124170938(-)$1	287	5	8	8.9999
GCC	chr4:41071072-41071341(-)$1	269	7	10	8.9999
GCC	chr18:78244145-78244417(-)$1	272	75	78	8.9999
GCC	chr9:7184676-7184956(+)$1	280	6	9	8.9999
GCC	chr19:44122007-44122285(-)$1	278	37	40	8.9999
GCC	chr13:35907724-35908005(+)$1	281	148	151	8.9999
gCC	chr19:42025161-42025434(-)$1	273	12	15	8.9999
GCC	chr4:10917794-10918069(-)$1	275	1	4	8.9999
GCC	chr11:62162744-62163014(-)$1	270	30	33	8.9999
GCC	chr11:103088294-103088570(-)$1	276	91	94	8.9999
GCC	chr7:66531784-66532059(+)$1	275	55	58	8.9999
GCC	chr16:13887667-13887962(-)$1	295	166	169	8.9999
GCC	chr14:55688801-55689082(-)$1	281	75	78	8.9999
GCC	chrX:20429054-20429357(+)$1	303	122	125	8.9999
GCC	chr17:34165643-34165932(-)$1	289	41	44	8.9999
GCC	chr1:134891007-134891283(-)$1	276	34	37	8.9999
gcc	chr6:52210156-52210422(-)$1	266	0	3	8.9999
GCC	chr2:117003515-117003808(+)$1	293	36	39	8.9999
GCC	chr17:23953084-23953358(+)$1	274	26	29	8.9999
GCC	chr4:149986603-149986871(+)$1	268	32	35	8.9999
GCC	chr14:51457233-51457510(-)$1	277	35	38	8.9999
GCC	chr4:42950966-42951237(+)$1	271	9	12	8.9999
GCC	chr7:4759713-4759996(-)$1	283	3	6	8.9999
GCC	chr2:59821757-59822037(-)$1	280	38	41	8.9999
GCC	chr12:111933434-111933714(-)$1	280	111	114	8.9999
GCC	chr11:97025920-97026209(-)$1	289	28	31	8.9999
GCC	chr17:33803431-33803726(-)$1	295	5	8	8.9999
GCC	chr8:11612500-11612782(-)$1	282	0	3	8.9999
GCC	chr5:135097208-135097499(-)$1	291	33	36	8.9999
GCC	chr6:122663277-122663549(+)$1	272	6	9	8.9999
GCC	chr10:80785424-80785708(+)$1	284	3	6	8.9999
GCC	chr7:52144514-52144785(-)$1	271	61	64	8.9999
GCC	chr11:99957022-99957293(-)$1	271	4	7	8.9999
GCC	chr3:55894880-55895165(-)$1	285	70	73	8.9999
GCC	chr19:4792162-4792550(-)$1	388	26	29	8.9999
GCC	chr16:94880968-94881240(+)$1	272	204	207	8.9999
GCC	chr7:104864887-104865166(+)$1	279	105	108	8.9999
GCC	chr2:29862934-29863206(+)$1	272	128	131	8.9999
GCC	chr7:20201613-20201890(-)$1	277	5	8	8.9999
GCC	chr1:187238145-187238428(+)$1	283	25	28	8.9999
GCC	chr7:29605474-29605749(+)$1	275	14	17	8.9999
GCC	chr18:76446389-76446666(+)$1	277	186	189	8.9999
GCC	chr17:47755818-47756090(+)$1	272	14	17	8.9999
GCC	chr17:28499240-28499508(-)$1	268	47	50	8.9999
GCC	chr11:97539648-97540030(+)$1	382	1	4	8.9999
GCC	chr11:18910118-18910403(-)$1	285	71	74	8.9999
GCC	chr3:95142370-95142641(-)$1	271	61	64	8.9999
GCC	chr7:27949938-27950218(-)$1	280	11	14	8.9999
GCC	chrX:98409040-98409312(-)$1	272	55	58	8.9999
GCC	chr5:21167263-21167539(+)$1	276	9	12	8.9999
gcc	chr14:122878253-122878533(+)$1	280	23	26	8.9999
GCC	chr5:104868238-104868512(+)$1	274	23	26	8.9999
GCC	chr14:12386700-12386993(+)$1	293	30	33	8.9999
gcc	chr11:69182600-69182900(-)$1	300	118	121	8.9999
GCC	chr8:110106166-110106445(-)$1	279	0	3	8.9999
GCC	chr8:125924723-125924998(+)$1	275	1	4	8.9999
GCC	chr19:16056004-16056312(-)$1	308	199	202	8.9999
GCC	chr16:18283730-18284013(-)$1	283	21	24	8.9999
GCC	chr17:27559574-27559842(-)$1	268	4	7	8.9999
GCC	chr17:35293280-35293649(-)$1	369	3	6	8.9999
GCC	chr14:32100945-32101215(-)$1	270	48	51	8.9999
GCC	chr2:32777520-32777794(+)$1	274	1	4	8.9999
GCC	chr8:41586053-41586321(-)$1	268	49	52	8.9999
GCC	chr11:58145238-58145513(+)$1	275	23	26	8.9999
GCC	chr6:86345913-86346193(-)$1	280	114	117	8.9999
GCC	chr11:86899599-86899868(-)$1	269	30	33	8.9999
GCC	chr7:88851505-88851774(-)$1	269	5	8	8.9999
GCC	chr18:56698242-56698513(-)$1	271	51	54	8.9999
GCC	chr3:35712937-35713220(+)$1	283	98	101	8.9999
GCC	chr14:55728286-55728561(-)$1	275	23	26	8.9999
GCC	chr15:79749263-79749551(-)$1	288	7	10	8.9999
GCC	chr12:80273099-80273370(-)$1	271	8	11	8.9999
GCC	chr7:4614893-4615181(-)$1	288	86	89	8.9999
GCC	chr15:89137829-89138097(-)$1	268	5	8	8.9999
GCC	chr4:98404133-98404432(+)$1	299	62	65	8.9999
GCC	chr10:12257788-12258065(-)$1	277	4	7	8.9999

#otherMatches

#Struct PSSM
ddd	chr7:5013810-5014092(+)$1	282	15	18	8.9999
2ee	chr7:27949678-27950016(-)$1	338	44	47	8.9999
bcc	chr14:58352846-58353120(-)$1	274	72	75	8.9999
GGG	chr10:25219551-25219823(+)$1	272	6	9	8.9999
CCC	chr11:69550323-69550593(-)$1	270	21	24	8.9999
fff	chr1:164628233-164628501(-)$1	268	163	166	8.9999
ppp	chr4:41066380-41066652(-)$1	272	6	9	8.9999
fff	chr15:94116703-94116978(-)$1	275	165	168	8.9999
[ac	chr1:89687675-89687956(+)$1	281	26	29	8.9999
333	chr4:117832654-117832930(-)$1	276	39	42	8.9999
]ff	chr12:81975083-81975356(+)$1	273	160	163	8.9999
EEE	chr8:34722258-34722540(+)$1	282	7	10	8.9999
c44	chr18:12301437-12301710(+)$1	273	163	166	8.9999
2bb	chr8:82197699-82197995(+)$1	296	64	67	8.9999
BB:	chr8:87433104-87433375(+)$1	271	31	34	8.9999
ggg	chr4:98400196-98400501(+)$1	305	106	109	8.9999
{FF	chr4:41137660-41137947(+)$1	287	67	70	8.9999
CCC	chr11:55220600-55220897(-)$1	297	4	7	8.9999
c::	chr18:50342753-50343040(+)$1	287	99	102	8.9999
ddd	chr8:119873108-119873392(+)$1	284	30	33	8.9999
[cc	chr19:46107485-46107753(-)$1	268	21	24	8.9999
FF:	chr9:43972114-43972410(-)$1	296	156	159	8.9999
[dd	chr15:10391926-10392198(-)$1	272	116	119	8.9999
:CC	chr5:124170651-124170938(-)$1	287	5	8	8.9999
JJJ	chr4:41071072-41071341(-)$1	269	7	10	8.9999
f::	chr18:78244145-78244417(-)$1	272	75	78	8.9999
gg'	chr9:7184676-7184956(+)$1	280	6	9	8.9999
iii	chr19:44122007-44122285(-)$1	278	37	40	8.9999
eee	chr13:35907724-35908005(+)$1	281	148	151	8.9999
qqq	chr19:42025161-42025434(-)$1	273	12	15	8.9999
fff	chr4:10917794-10918069(-)$1	275	1	4	8.9999
bbe	chr11:62162744-62163014(-)$1	270	30	33	8.9999
!al	chr11:103088294-103088570(-)$1	276	91	94	8.9999
8bb	chr7:66531784-66532059(+)$1	275	55	58	8.9999
::d	chr16:13887667-13887962(-)$1	295	166	169	8.9999
EEE	chr14:55688801-55689082(-)$1	281	75	78	8.9999
ddd	chrX:20429054-20429357(+)$1	303	122	125	8.9999
eeq	chr17:34165643-34165932(-)$1	289	41	44	8.9999
ddd	chr1:134891007-134891283(-)$1	276	34	37	8.9999
BB{	chr6:52210156-52210422(-)$1	266	0	3	8.9999
eee	chr2:117003515-117003808(+)$1	293	36	39	8.9999
b33	chr17:23953084-23953358(+)$1	274	26	29	8.9999
BB{	chr4:149986603-149986871(+)$1	268	32	35	8.9999
eee	chr14:51457233-51457510(-)$1	277	35	38	8.9999
ggg	chr4:42950966-42951237(+)$1	271	9	12	8.9999
EEc	chr7:4759713-4759996(-)$1	283	3	6	8.9999
BB{	chr2:59821757-59822037(-)$1	280	38	41	8.9999
hhh	chr12:111933434-111933714(-)$1	280	111	114	8.9999
b33	chr11:97025920-97026209(-)$1	289	28	31	8.9999
EEE	chr17:33803431-33803726(-)$1	295	5	8	8.9999
:EE	chr8:11612500-11612782(-)$1	282	0	3	8.9999
vvv	chr5:135097208-135097499(-)$1	291	33	36	8.9999
:dd	chr6:122663277-122663549(+)$1	272	6	9	8.9999
:CC	chr10:80785424-80785708(+)$1	284	3	6	8.9999
eFF	chr7:52144514-52144785(-)$1	271	61	64	8.9999
ggg	chr11:99957022-99957293(-)$1	271	4	7	8.9999
ccc	chr3:55894880-55895165(-)$1	285	70	73	8.9999
eee	chr19:4792162-4792550(-)$1	388	26	29	8.9999
ddd	chr16:94880968-94881240(+)$1	272	204	207	8.9999
ddd	chr7:104864887-104865166(+)$1	279	105	108	8.9999
iii	chr2:29862934-29863206(+)$1	272	128	131	8.9999
fff	chr7:20201613-20201890(-)$1	277	5	8	8.9999
EEE	chr1:187238145-187238428(+)$1	283	25	28	8.9999
CC:	chr7:29605474-29605749(+)$1	275	14	17	8.9999
ddp	chr18:76446389-76446666(+)$1	277	186	189	8.9999
hhh	chr17:47755818-47756090(+)$1	272	14	17	8.9999
III	chr17:28499240-28499508(-)$1	268	47	50	8.9999
bbm	chr11:97539648-97540030(+)$1	382	1	4	8.9999
ddd	chr11:18910118-18910403(-)$1	285	71	74	8.9999
ffb	chr3:95142370-95142641(-)$1	271	61	64	8.9999
fff	chr7:27949938-27950218(-)$1	280	11	14	8.9999
DDD	chrX:98409040-98409312(-)$1	272	55	58	8.9999
dd[	chr5:21167263-21167539(+)$1	276	9	12	8.9999
FFF	chr14:122878253-122878533(+)$1	280	23	26	8.9999
ddo	chr5:104868238-104868512(+)$1	274	23	26	8.9999
{AH	chr14:12386700-12386993(+)$1	293	30	33	8.9999
Ebb	chr11:69182600-69182900(-)$1	300	118	121	8.9999
BBE	chr8:110106166-110106445(-)$1	279	0	3	8.9999
III	chr8:125924723-125924998(+)$1	275	1	4	8.9999
mbb	chr19:16056004-16056312(-)$1	308	199	202	8.9999
GGG	chr16:18283730-18284013(-)$1	283	21	24	8.9999
::B	chr17:27559574-27559842(-)$1	268	4	7	8.9999
ddd	chr17:35293280-35293649(-)$1	369	3	6	8.9999
:EE	chr14:32100945-32101215(-)$1	270	48	51	8.9999
DDD	chr2:32777520-32777794(+)$1	274	1	4	8.9999
fff	chr8:41586053-41586321(-)$1	268	49	52	8.9999
MDD	chr11:58145238-58145513(+)$1	275	23	26	8.9999
aqq	chr6:86345913-86346193(-)$1	280	114	117	8.9999
"cc	chr11:86899599-86899868(-)$1	269	30	33	8.9999
{DD	chr7:88851505-88851774(-)$1	269	5	8	8.9999
HHL	chr18:56698242-56698513(-)$1	271	51	54	8.9999
ddd	chr3:35712937-35713220(+)$1	283	98	101	8.9999
{CC	chr14:55728286-55728561(-)$1	275	23	26	8.9999
cc"	chr15:79749263-79749551(-)$1	288	7	10	8.9999
ff"	chr12:80273099-80273370(-)$1	271	8	11	8.9999
ddd	chr7:4614893-4615181(-)$1	288	86	89	8.9999
:::	chr15:89137829-89138097(-)$1	268	5	8	8.9999
"bb	chr4:98404133-98404432(+)$1	299	62	65	8.9999
DDD	chr10:12257788-12258065(-)$1	277	4	7	8.9999

#DB
)))	chr7:5013810-5014092(+)$1	1	15	18	8.9999
.))	chr7:27949678-27950016(-)$1	1	44	47	8.9999
)))	chr14:58352846-58353120(-)$1	1	72	75	8.9999
(((	chr10:25219551-25219823(+)$1	1	6	9	8.9999
(((	chr11:69550323-69550593(-)$1	1	21	24	8.9999
)))	chr1:164628233-164628501(-)$1	1	163	166	8.9999
...	chr4:41066380-41066652(-)$1	1	6	9	8.9999
)))	chr15:94116703-94116978(-)$1	1	165	168	8.9999
.((	chr1:89687675-89687956(+)$1	1	26	29	8.9999
...	chr4:117832654-117832930(-)$1	1	39	42	8.9999
.))	chr12:81975083-81975356(+)$1	1	160	163	8.9999
(((	chr8:34722258-34722540(+)$1	1	7	10	8.9999
)..	chr18:12301437-12301710(+)$1	1	163	166	8.9999
.))	chr8:82197699-82197995(+)$1	1	64	67	8.9999
((.	chr8:87433104-87433375(+)$1	1	31	34	8.9999
(((	chr4:98400196-98400501(+)$1	1	106	109	8.9999
.((	chr4:41137660-41137947(+)$1	1	67	70	8.9999
(((	chr11:55220600-55220897(-)$1	1	4	7	8.9999
)..	chr18:50342753-50343040(+)$1	1	99	102	8.9999
)))	chr8:119873108-119873392(+)$1	1	30	33	8.9999
.((	chr19:46107485-46107753(-)$1	1	21	24	8.9999
((.	chr9:43972114-43972410(-)$1	1	156	159	8.9999
.((	chr15:10391926-10392198(-)$1	1	116	119	8.9999
.((	chr5:124170651-124170938(-)$1	1	5	8	8.9999
(((	chr4:41071072-41071341(-)$1	1	7	10	8.9999
)..	chr18:78244145-78244417(-)$1	1	75	78	8.9999
((.	chr9:7184676-7184956(+)$1	1	6	9	8.9999
)))	chr19:44122007-44122285(-)$1	1	37	40	8.9999
)))	chr13:35907724-35908005(+)$1	1	148	151	8.9999
...	chr19:42025161-42025434(-)$1	1	12	15	8.9999
(((	chr4:10917794-10918069(-)$1	1	1	4	8.9999
(((	chr11:62162744-62163014(-)$1	1	30	33	8.9999
.(.	chr11:103088294-103088570(-)$1	1	91	94	8.9999
.))	chr7:66531784-66532059(+)$1	1	55	58	8.9999
..(	chr16:13887667-13887962(-)$1	1	166	169	8.9999
)))	chr14:55688801-55689082(-)$1	1	75	78	8.9999
(((	chrX:20429054-20429357(+)$1	1	122	125	8.9999
((.	chr17:34165643-34165932(-)$1	1	41	44	8.9999
(((	chr1:134891007-134891283(-)$1	1	34	37	8.9999
((.	chr6:52210156-52210422(-)$1	1	0	3	8.9999
(((	chr2:117003515-117003808(+)$1	1	36	39	8.9999
)..	chr17:23953084-23953358(+)$1	1	26	29	8.9999
((.	chr4:149986603-149986871(+)$1	1	32	35	8.9999
)))	chr14:51457233-51457510(-)$1	1	35	38	8.9999
(((	chr4:42950966-42951237(+)$1	1	9	12	8.9999
(((	chr7:4759713-4759996(-)$1	1	3	6	8.9999
((.	chr2:59821757-59822037(-)$1	1	38	41	8.9999
)))	chr12:111933434-111933714(-)$1	1	111	114	8.9999
)..	chr11:97025920-97026209(-)$1	1	28	31	8.9999
(((	chr17:33803431-33803726(-)$1	1	5	8	8.9999
.((	chr8:11612500-11612782(-)$1	1	0	3	8.9999
...	chr5:135097208-135097499(-)$1	1	33	36	8.9999
.((	chr6:122663277-122663549(+)$1	1	6	9	8.9999
.((	chr10:80785424-80785708(+)$1	1	3	6	8.9999
)((	chr7:52144514-52144785(-)$1	1	61	64	8.9999
(((	chr11:99957022-99957293(-)$1	1	4	7	8.9999
)))	chr3:55894880-55895165(-)$1	1	70	73	8.9999
(((	chr19:4792162-4792550(-)$1	1	26	29	8.9999
)))	chr16:94880968-94881240(+)$1	1	204	207	8.9999
)))	chr7:104864887-104865166(+)$1	1	105	108	8.9999
)))	chr2:29862934-29863206(+)$1	1	128	131	8.9999
(((	chr7:20201613-20201890(-)$1	1	5	8	8.9999
(((	chr1:187238145-187238428(+)$1	1	25	28	8.9999
((.	chr7:29605474-29605749(+)$1	1	14	17	8.9999
((.	chr18:76446389-76446666(+)$1	1	186	189	8.9999
(((	chr17:47755818-47756090(+)$1	1	14	17	8.9999
(((	chr17:28499240-28499508(-)$1	1	47	50	8.9999
((.	chr11:97539648-97540030(+)$1	1	1	4	8.9999
)))	chr11:18910118-18910403(-)$1	1	71	74	8.9999
)))	chr3:95142370-95142641(-)$1	1	61	64	8.9999
(((	chr7:27949938-27950218(-)$1	1	11	14	8.9999
(((	chrX:98409040-98409312(-)$1	1	55	58	8.9999
((.	chr5:21167263-21167539(+)$1	1	9	12	8.9999
(((	chr14:122878253-122878533(+)$1	1	23	26	8.9999
((.	chr5:104868238-104868512(+)$1	1	23	26	8.9999
.((	chr14:12386700-12386993(+)$1	1	30	33	8.9999
(((	chr11:69182600-69182900(-)$1	1	118	121	8.9999
(((	chr8:110106166-110106445(-)$1	1	0	3	8.9999
(((	chr8:125924723-125924998(+)$1	1	1	4	8.9999
.))	chr19:16056004-16056312(-)$1	1	199	202	8.9999
(((	chr16:18283730-18284013(-)$1	1	21	24	8.9999
..(	chr17:27559574-27559842(-)$1	1	4	7	8.9999
(((	chr17:35293280-35293649(-)$1	1	3	6	8.9999
.((	chr14:32100945-32101215(-)$1	1	48	51	8.9999
(((	chr2:32777520-32777794(+)$1	1	1	4	8.9999
(((	chr8:41586053-41586321(-)$1	1	49	52	8.9999
.((	chr11:58145238-58145513(+)$1	1	23	26	8.9999
(..	chr6:86345913-86346193(-)$1	1	114	117	8.9999
.((	chr11:86899599-86899868(-)$1	1	30	33	8.9999
.((	chr7:88851505-88851774(-)$1	1	5	8	8.9999
((.	chr18:56698242-56698513(-)$1	1	51	54	8.9999
(((	chr3:35712937-35713220(+)$1	1	98	101	8.9999
.((	chr14:55728286-55728561(-)$1	1	23	26	8.9999
((.	chr15:79749263-79749551(-)$1	1	7	10	8.9999
((.	chr12:80273099-80273370(-)$1	1	8	11	8.9999
(((	chr7:4614893-4615181(-)$1	1	86	89	8.9999
...	chr15:89137829-89138097(-)$1	1	5	8	8.9999
.((	chr4:98404133-98404432(+)$1	1	62	65	8.9999
(((	chr10:12257788-12258065(-)$1	1	4	7	8.9999

#PSSM
G : 0.94	g : 0.05	
C : 0.95	c : 0.04	
C : 0.95	c : 0.04	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m1_run2.nuc.txt

#NT
AUG	chr1:136509758-136509962(+)$1	204	27	30	8.9999
AUG	chr4:133276649-133276854(-)$1	205	70	73	8.9999
AUG	chr17:23957887-23958090(+)$1	203	67	70	8.9999
AUG	chr10:17813589-17813790(+)$1	201	10	13	8.9999
AUG	chr1:33965040-33965252(+)$1	212	76	79	8.9999
AUG	chr9:113820494-113820696(+)$1	202	159	162	8.9999
AUG	chr11:86476927-86477130(-)$1	203	22	25	8.9999
AUG	chr5:122252048-122252265(+)$1	217	49	52	8.9999
AUG	chr2:130441595-130441817(-)$1	222	214	217	8.9999
AUG	chr17:85471279-85471484(-)$1	205	62	65	8.9999
AUG	chr7:25845499-25845700(-)$1	201	72	75	8.9999
AUG	chr4:53058888-53059095(-)$1	207	11	14	8.9999
AUG	chr2:91334145-91334368(+)$1	223	54	57	8.9999
AUG	chr2:163456680-163456884(-)$1	204	15	18	8.9999
AUG	chr11:109528873-109529073(+)$1	200	73	76	8.9999
AUG	chr11:69639024-69639242(-)$1	218	14	17	8.9999
AUG	chr2:35570831-35571050(+)$1	219	87	90	8.9999
AUG	chr6:22950193-22950403(+)$1	210	3	6	8.9999
AUG	chr7:31902648-31902860(-)$1	212	5	8	8.9999
AUG	chr15:76452595-76452807(-)$1	212	46	49	8.9999
AUG	chr1:175268085-175268291(-)$1	206	200	203	8.9999
AUG	chr15:76002565-76002779(-)$1	214	55	58	8.9999
AUG	chr6:83101899-83102110(+)$1	211	72	75	8.9999
AUG	chr11:6303762-6303962(+)$1	200	37	40	8.9999
AUG	chr3:125570205-125570413(-)$1	208	14	17	8.9999
AUG	chrX:96661807-96662013(-)$1	206	13	16	8.9999
AUG	chr16:17026418-17026626(+)$1	208	16	19	8.9999
AUG	chr1:75471489-75471691(-)$1	202	108	111	8.9999
AUG	chr5:143535406-143535610(-)$1	204	61	64	8.9999
AUG	chr1:157137322-157137526(-)$1	204	28	31	8.9999
AUG	chr12:86356196-86356413(+)$1	217	27	30	8.9999
AUG	chr8:72847004-72847227(+)$1	223	117	120	8.9999
AUG	chr7:3637294-3637512(-)$1	218	82	85	8.9999
AUG	chr2:80341398-80341600(-)$1	202	59	62	8.9999
AUG	chr7:63984934-63985154(-)$1	220	17	20	8.9999
AUG	chrX:132280683-132280895(+)$1	212	50	53	8.9999
AUG	chr14:55728256-55728457(-)$1	201	66	69	8.9999
AUG	chr11:6303235-6303441(+)$1	206	18	21	8.9999
AUG	chr2:157769821-157770035(+)$1	214	52	55	8.9999
AUG	chr4:137682190-137682397(+)$1	207	69	72	8.9999
AUG	chr17:32339021-32339239(-)$1	218	100	103	8.9999
AUG	chr2:91015754-91015958(-)$1	204	117	120	8.9999
AUG	chr15:102111463-102111673(+)$1	210	26	29	8.9999
AUG	chr8:41547421-41547627(+)$1	206	168	171	8.9999
AUG	chr14:55525842-55526042(-)$1	200	37	40	8.9999
AUG	chr8:114541949-114542170(+)$1	221	81	84	8.9999
AUG	chr7:17546503-17546710(+)$1	207	76	79	8.9999
AUG	chr7:25807936-25808151(-)$1	215	97	100	8.9999
AUG	chr15:82201892-82202098(-)$1	206	36	39	8.9999
AUG	chr13:69121214-69121420(-)$1	206	11	14	8.9999
AUG	chr14:120828175-120828382(+)$1	207	5	8	8.9999
AUG	chr5:3847365-3847583(+)$1	218	173	176	8.9999
AUG	chr10:93331527-93331750(-)$1	223	89	92	8.9999
AUG	chrX:133268068-133268269(-)$1	201	22	25	8.9999
AUG	chr7:31307938-31308139(-)$1	201	18	21	8.9999
AUG	chr9:61257679-61257898(+)$1	219	17	20	8.9999
AUG	chrX:55287496-55287731(+)$1	235	37	40	8.9999
AUG	chr3:129743879-129744094(-)$1	215	98	101	8.9999
aug	chr2:180821409-180821611(-)$1	202	184	187	8.9999
AUG	chr11:44368601-44368820(+)$1	219	156	159	8.9999
AUG	chr3:94970860-94971077(-)$1	217	0	3	8.9999
AUG	chr17:6037380-6037608(+)$1	228	6	9	8.9999
AUG	chr2:25172234-25172438(-)$1	204	143	146	8.9999
AUG	chr14:52529662-52529872(-)$1	210	8	11	8.9999
AUG	chr11:67063937-67064156(+)$1	219	0	3	8.9999
AUG	chr14:31844039-31844253(+)$1	214	7	10	8.9999
AUG	chr14:13176767-13177001(-)$1	234	2	5	8.9999
AUG	chr12:34051770-34051970(+)$1	200	15	18	8.9999
AUG	chr9:50564473-50564679(+)$1	206	17	20	8.9999
AUG	chr3:54703255-54703460(-)$1	205	66	69	8.9999
AUG	chr1:59872079-59872281(+)$1	202	6	9	8.9999
AUG	chr11:41725781-41725982(-)$1	201	52	55	8.9999
AUG	chr15:12763988-12764195(+)$1	207	7	10	8.9999
AUG	chr11:100437590-100437793(+)$1	203	16	19	8.9999
AUG	chr10:119475276-119475510(+)$1	234	164	167	8.9999
AUG	chr8:96491851-96492051(+)$1	200	46	49	8.9999
AUG	chr10:126723255-126723464(-)$1	209	82	85	8.9999
AUG	chr4:129689500-129689712(+)$1	212	79	82	8.9999
AUG	chr4:43682609-43682809(+)$1	200	157	160	8.9999
AUG	chr10:70021931-70022132(-)$1	201	66	69	8.9999
AUG	chrX:20224915-20225138(+)$1	223	68	71	8.9999
AUG	chr5:135857883-135858084(-)$1	201	10	13	8.9999
AUG	chr7:107647288-107647488(+)$1	200	28	31	8.9999
AUG	chr3:90155370-90155595(+)$1	225	0	3	8.9999
AUG	chr17:15091802-15092010(-)$1	208	67	70	8.9999
AUG	chr11:62143014-62143214(-)$1	200	33	36	8.9999
AUG	chr7:31220437-31220648(-)$1	211	61	64	8.9999
AUG	chr10:41916792-41917009(-)$1	217	22	25	8.9999
AUG	chr17:31983386-31983605(-)$1	219	100	103	8.9999
AUG	chr1:39416495-39416712(+)$1	217	0	3	8.9999

#otherMatches

#Struct PSSM
eee	chr5:65986055-65986257(+)$1	202	28	31	8.9999
ee]	chr1:136509758-136509962(+)$1	204	27	30	8.9999
^^^	chr4:133276649-133276854(-)$1	205	70	73	8.9999
nnn	chr17:23957887-23958090(+)$1	203	67	70	8.9999
HHH	chr10:17813589-17813790(+)$1	201	10	13	8.9999
::b	chr1:33965040-33965252(+)$1	212	76	79	8.9999
pdd	chr9:113820494-113820696(+)$1	202	159	162	8.9999
ddd	chr11:86476927-86477130(-)$1	203	22	25	8.9999
DDD	chr5:122252048-122252265(+)$1	217	49	52	8.9999
b]c	chr2:130441595-130441817(-)$1	222	214	217	8.9999
[dd	chr17:85471279-85471484(-)$1	205	62	65	8.9999
fff	chr7:25845499-25845700(-)$1	201	72	75	8.9999
{FF	chr4:53058888-53059095(-)$1	207	11	14	8.9999
KKC	chr2:91334145-91334368(+)$1	223	54	57	8.9999
JJJ	chr2:163456680-163456884(-)$1	204	15	18	8.9999
!cc	chr11:109528873-109529073(+)$1	200	73	76	8.9999
:::	chr11:69639024-69639242(-)$1	218	14	17	8.9999
22c	chr2:35570831-35571050(+)$1	219	87	90	8.9999
EEE	chr6:22950193-22950403(+)$1	210	3	6	8.9999
ccc	chr7:31902648-31902860(-)$1	212	5	8	8.9999
::e	chr15:76452595-76452807(-)$1	212	46	49	8.9999
FFF	chr1:175268085-175268291(-)$1	206	200	203	8.9999
pff	chr15:76002565-76002779(-)$1	214	55	58	8.9999
>>>	chr6:83101899-83102110(+)$1	211	72	75	8.9999
oii	chr11:6303762-6303962(+)$1	200	37	40	8.9999
""g	chr3:125570205-125570413(-)$1	208	14	17	8.9999
EEE	chrX:96661807-96662013(-)$1	206	13	16	8.9999
ndd	chr16:17026418-17026626(+)$1	208	16	19	8.9999
ppd	chr1:75471489-75471691(-)$1	202	108	111	8.9999
::d	chr5:143535406-143535610(-)$1	204	61	64	8.9999
{DD	chr1:157137322-157137526(-)$1	204	28	31	8.9999
dmm	chr12:86356196-86356413(+)$1	217	27	30	8.9999
cc!	chr8:72847004-72847227(+)$1	223	117	120	8.9999
qqb	chr7:3637294-3637512(-)$1	218	82	85	8.9999
GGG	chr2:80341398-80341600(-)$1	202	59	62	8.9999
]bb	chr7:63984934-63985154(-)$1	220	17	20	8.9999
cdd	chrX:132280683-132280895(+)$1	212	50	53	8.9999
mmm	chr14:55728256-55728457(-)$1	201	66	69	8.9999
ppa	chr11:6303235-6303441(+)$1	206	18	21	8.9999
[ee	chr2:157769821-157770035(+)$1	214	52	55	8.9999
ccc	chr4:137682190-137682397(+)$1	207	69	72	8.9999
^gg	chr17:32339021-32339239(-)$1	218	100	103	8.9999
sss	chr2:91015754-91015958(-)$1	204	117	120	8.9999
EEE	chr15:102111463-102111673(+)$1	210	26	29	8.9999
dd"	chr8:41547421-41547627(+)$1	206	168	171	8.9999
""d	chr14:55525842-55526042(-)$1	200	37	40	8.9999
mmm	chr8:114541949-114542170(+)$1	221	81	84	8.9999
"dd	chr7:17546503-17546710(+)$1	207	76	79	8.9999
eee	chr7:25807936-25808151(-)$1	215	97	100	8.9999
""d	chr15:82201892-82202098(-)$1	206	36	39	8.9999
c[a	chr13:69121214-69121420(-)$1	206	11	14	8.9999
GGG	chr14:120828175-120828382(+)$1	207	5	8	8.9999
pph	chr5:3847365-3847583(+)$1	218	173	176	8.9999
:::	chr10:93331527-93331750(-)$1	223	89	92	8.9999
nnc	chrX:133268068-133268269(-)$1	201	22	25	8.9999
lee	chr7:31307938-31308139(-)$1	201	18	21	8.9999
eee	chr9:61257679-61257898(+)$1	219	17	20	8.9999
fff	chrX:55287496-55287731(+)$1	235	37	40	8.9999
EEE	chr3:129743879-129744094(-)$1	215	98	101	8.9999
}EE	chr2:180821409-180821611(-)$1	202	184	187	8.9999
::F	chr11:44368601-44368820(+)$1	219	156	159	8.9999
:::	chr3:94970860-94971077(-)$1	217	0	3	8.9999
:::	chr17:6037380-6037608(+)$1	228	6	9	8.9999
rrc	chr2:25172234-25172438(-)$1	204	143	146	8.9999
ncc	chr14:52529662-52529872(-)$1	210	8	11	8.9999
:::	chr11:67063937-67064156(+)$1	219	0	3	8.9999
dd[	chr14:31844039-31844253(+)$1	214	7	10	8.9999
[cc	chr14:13176767-13177001(-)$1	234	2	5	8.9999
b[d	chr12:34051770-34051970(+)$1	200	15	18	8.9999
CCb	chr9:50564473-50564679(+)$1	206	17	20	8.9999
ddd	chr3:54703255-54703460(-)$1	205	66	69	8.9999
[a[	chr1:59872079-59872281(+)$1	202	6	9	8.9999
hhh	chr11:41725781-41725982(-)$1	201	52	55	8.9999
FFF	chr15:12763988-12764195(+)$1	207	7	10	8.9999
MMC	chr11:100437590-100437793(+)$1	203	16	19	8.9999
:GG	chr10:119475276-119475510(+)$1	234	164	167	8.9999
##e	chr8:96491851-96492051(+)$1	200	46	49	8.9999
2dd	chr10:126723255-126723464(-)$1	209	82	85	8.9999
===	chr4:129689500-129689712(+)$1	212	79	82	8.9999
ccc	chr4:43682609-43682809(+)$1	200	157	160	8.9999
""a	chr10:70021931-70022132(-)$1	201	66	69	8.9999
:::	chrX:20224915-20225138(+)$1	223	68	71	8.9999
ccc	chr5:135857883-135858084(-)$1	201	10	13	8.9999
dde	chr7:107647288-107647488(+)$1	200	28	31	8.9999
::G	chr3:90155370-90155595(+)$1	225	0	3	8.9999
mmb	chr17:15091802-15092010(-)$1	208	67	70	8.9999
EEE	chr11:62143014-62143214(-)$1	200	33	36	8.9999
::E	chr7:31220437-31220648(-)$1	211	61	64	8.9999
rrr	chr10:41916792-41917009(-)$1	217	22	25	8.9999
^^^	chr17:31983386-31983605(-)$1	219	100	103	8.9999
:CC	chr1:39416495-39416712(+)$1	217	0	3	8.9999

#DB
(((	chr5:65986055-65986257(+)$1	1	28	31	8.9999
)).	chr1:136509758-136509962(+)$1	1	27	30	8.9999
...	chr4:133276649-133276854(-)$1	1	70	73	8.9999
...	chr17:23957887-23958090(+)$1	1	67	70	8.9999
(((	chr10:17813589-17813790(+)$1	1	10	13	8.9999
..(	chr1:33965040-33965252(+)$1	1	76	79	8.9999
.))	chr9:113820494-113820696(+)$1	1	159	162	8.9999
(((	chr11:86476927-86477130(-)$1	1	22	25	8.9999
(((	chr5:122252048-122252265(+)$1	1	49	52	8.9999
).)	chr2:130441595-130441817(-)$1	1	214	217	8.9999
.((	chr17:85471279-85471484(-)$1	1	62	65	8.9999
)))	chr7:25845499-25845700(-)$1	1	72	75	8.9999
.((	chr4:53058888-53059095(-)$1	1	11	14	8.9999
..(	chr2:91334145-91334368(+)$1	1	54	57	8.9999
(((	chr2:163456680-163456884(-)$1	1	15	18	8.9999
.((	chr11:109528873-109529073(+)$1	1	73	76	8.9999
...	chr11:69639024-69639242(-)$1	1	14	17	8.9999
..)	chr2:35570831-35571050(+)$1	1	87	90	8.9999
(((	chr6:22950193-22950403(+)$1	1	3	6	8.9999
(((	chr7:31902648-31902860(-)$1	1	5	8	8.9999
..(	chr15:76452595-76452807(-)$1	1	46	49	8.9999
)))	chr1:175268085-175268291(-)$1	1	200	203	8.9999
.))	chr15:76002565-76002779(-)$1	1	55	58	8.9999
...	chr6:83101899-83102110(+)$1	1	72	75	8.9999
.))	chr11:6303762-6303962(+)$1	1	37	40	8.9999
..(	chr3:125570205-125570413(-)$1	1	14	17	8.9999
(((	chrX:96661807-96662013(-)$1	1	13	16	8.9999
.))	chr16:17026418-17026626(+)$1	1	16	19	8.9999
..)	chr1:75471489-75471691(-)$1	1	108	111	8.9999
..(	chr5:143535406-143535610(-)$1	1	61	64	8.9999
.((	chr1:157137322-157137526(-)$1	1	28	31	8.9999
(..	chr12:86356196-86356413(+)$1	1	27	30	8.9999
((.	chr8:72847004-72847227(+)$1	1	117	120	8.9999
..)	chr7:3637294-3637512(-)$1	1	82	85	8.9999
(((	chr2:80341398-80341600(-)$1	1	59	62	8.9999
.))	chr7:63984934-63985154(-)$1	1	17	20	8.9999
(((	chrX:132280683-132280895(+)$1	1	50	53	8.9999
...	chr14:55728256-55728457(-)$1	1	66	69	8.9999
..)	chr11:6303235-6303441(+)$1	1	18	21	8.9999
.((	chr2:157769821-157770035(+)$1	1	52	55	8.9999
(((	chr4:137682190-137682397(+)$1	1	69	72	8.9999
.))	chr17:32339021-32339239(-)$1	1	100	103	8.9999
...	chr2:91015754-91015958(-)$1	1	117	120	8.9999
(((	chr15:102111463-102111673(+)$1	1	26	29	8.9999
((.	chr8:41547421-41547627(+)$1	1	168	171	8.9999
..(	chr14:55525842-55526042(-)$1	1	37	40	8.9999
...	chr8:114541949-114542170(+)$1	1	81	84	8.9999
.((	chr7:17546503-17546710(+)$1	1	76	79	8.9999
)))	chr7:25807936-25808151(-)$1	1	97	100	8.9999
..(	chr15:82201892-82202098(-)$1	1	36	39	8.9999
(.(	chr13:69121214-69121420(-)$1	1	11	14	8.9999
(((	chr14:120828175-120828382(+)$1	1	5	8	8.9999
..)	chr5:3847365-3847583(+)$1	1	173	176	8.9999
...	chr10:93331527-93331750(-)$1	1	89	92	8.9999
..)	chrX:133268068-133268269(-)$1	1	22	25	8.9999
.))	chr7:31307938-31308139(-)$1	1	18	21	8.9999
(((	chr9:61257679-61257898(+)$1	1	17	20	8.9999
)))	chrX:55287496-55287731(+)$1	1	37	40	8.9999
)))	chr3:129743879-129744094(-)$1	1	98	101	8.9999
.))	chr2:180821409-180821611(-)$1	1	184	187	8.9999
..)	chr11:44368601-44368820(+)$1	1	156	159	8.9999
...	chr3:94970860-94971077(-)$1	1	0	3	8.9999
...	chr17:6037380-6037608(+)$1	1	6	9	8.9999
..)	chr2:25172234-25172438(-)$1	1	143	146	8.9999
.))	chr14:52529662-52529872(-)$1	1	8	11	8.9999
...	chr11:67063937-67064156(+)$1	1	0	3	8.9999
((.	chr14:31844039-31844253(+)$1	1	7	10	8.9999
.((	chr14:13176767-13177001(-)$1	1	2	5	8.9999
(.(	chr12:34051770-34051970(+)$1	1	15	18	8.9999
(((	chr9:50564473-50564679(+)$1	1	17	20	8.9999
(((	chr3:54703255-54703460(-)$1	1	66	69	8.9999
.(.	chr1:59872079-59872281(+)$1	1	6	9	8.9999
(((	chr11:41725781-41725982(-)$1	1	52	55	8.9999
(((	chr15:12763988-12764195(+)$1	1	7	10	8.9999
..(	chr11:100437590-100437793(+)$1	1	16	19	8.9999
.))	chr10:119475276-119475510(+)$1	1	164	167	8.9999
..(	chr8:96491851-96492051(+)$1	1	46	49	8.9999
.))	chr10:126723255-126723464(-)$1	1	82	85	8.9999
)))	chr4:129689500-129689712(+)$1	1	79	82	8.9999
)))	chr4:43682609-43682809(+)$1	1	157	160	8.9999
..(	chr10:70021931-70022132(-)$1	1	66	69	8.9999
...	chrX:20224915-20225138(+)$1	1	68	71	8.9999
(((	chr5:135857883-135858084(-)$1	1	10	13	8.9999
)))	chr7:107647288-107647488(+)$1	1	28	31	8.9999
..(	chr3:90155370-90155595(+)$1	1	0	3	8.9999
..)	chr17:15091802-15092010(-)$1	1	67	70	8.9999
(((	chr11:62143014-62143214(-)$1	1	33	36	8.9999
..)	chr7:31220437-31220648(-)$1	1	61	64	8.9999
...	chr10:41916792-41917009(-)$1	1	22	25	8.9999
...	chr17:31983386-31983605(-)$1	1	100	103	8.9999
.((	chr1:39416495-39416712(+)$1	1	0	3	8.9999

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

#score	818.9999999999998
#seq	91
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m2_run2.nuc.txt

#NT
UUUUUAA	chr3:135070520-135070832(-)$1	312	3	10	18.9166
UUUUUAA	chr12:66043395-66043722(-)$1	327	116	123	18.9166
uuuuuaa	chr11:88156268-88156603(-)$1	335	161	168	18.9166
UUUUUAA	chr7:16745451-16745768(+)$1	317	99	106	18.9166
uuuuuAC	chr7:151033829-151034082(+)$1	253	114	121	15.2708
UUUUUAA	chr1:38109601-38109897(-)$1	296	73	80	18.9166
UUUUUAA	chr13:89459520-89459829(+)$1	309	64	71	18.9166
UUUUUAU	chr1:145603515-145603897(-)$1	382	243	250	15.4791
UUUUUAA	chr15:100874449-100874795(+)$1	346	250	257	18.9166
UUUUUAA	chr10:87982138-87982391(-)$1	253	222	229	18.9166
UUUUUAA	chr14:31408436-31408778(-)$1	342	67	74	18.9166
UUUUUAC	chr5:67447523-67447794(+)$1	271	14	21	15.2708
UUUUUAA	chr13:94972324-94972705(-)$1	381	44	51	18.9166
UUUUUAA	chr12:36818325-36818645(-)$1	320	191	198	18.9166
UUUUUCA	chrX:140291362-140291644(-)$1	282	57	64	15.6875
UUUUUAA	chr6:62332033-62332305(+)$1	272	252	259	18.9166
uuuuuau	chr1:34364747-34365019(+)$1	272	94	101	15.4791
UUUUUAA	chr8:13255861-13256136(-)$1	275	70	77	18.9166
UUUUUCA	chr1:11289238-11289614(+)$1	376	76	83	15.6875
UUUUUCA	chrX:72779458-72779776(+)$1	318	37	44	15.6875
UUUUUAA	chr1:158609297-158609544(-)$1	247	96	103	18.9166
UUUUUUA	chr4:137798788-137799167(+)$1	379	221	228	15.2708
UUUUUAA	chrX:53915384-53915747(+)$1	363	209	216	18.9166
UUUUUAA	chr6:30402620-30402954(+)$1	334	96	103	18.9166
UUUUUAC	chr1:165842114-165842370(+)$1	256	73	80	15.2708
UUUUUAA	chr17:66316707-66317008(-)$1	301	19	26	18.9166
UUUUUAG	chr6:8547118-8547386(+)$1	268	138	145	15.1666
UUUUUAA	chr16:31251601-31251985(-)$1	384	201	208	18.9166
UUUUUCA	chr10:94874029-94874328(-)$1	299	118	125	15.6875
UUUUUAA	chr12:109150715-109151045(-)$1	330	123	130	18.9166
UUUUUCA	chr15:25902430-25902738(+)$1	308	273	280	15.6875
UUUUUAA	chr13:43498225-43498715(-)$1	490	282	289	18.9166
uuuuuaa	chr9:53425423-53425687(-)$1	264	191	198	18.9166
UUUUUUA	chr1:63097193-63097501(-)$1	308	26	33	15.2708
UUUUUAA	chr13:34994284-34994541(+)$1	257	106	113	18.9166
UUUUUAA	chr3:19126654-19126958(-)$1	304	29	36	18.9166
UUUUUAU	chr9:56466753-56467017(-)$1	264	61	68	15.4791
UUUUUAU	chr10:25213251-25213605(+)$1	354	2	9	15.4791
UUUUUAU	chr3:40593976-40594407(+)$1	431	91	98	15.4791
UUUUUAA	chr4:128788712-128789100(-)$1	388	244	251	18.9166
UUUUUCA	chrX:34338374-34338707(+)$1	333	75	82	15.6875
UUUUUAA	chr10:4514847-4515129(+)$1	282	252	259	18.9166
UUUUUUA	chr3:122243904-122244262(-)$1	358	54	61	15.2708
uuuuuaa	chr11:24072917-24073292(+)$1	375	39	46	18.9166
UUUUUCA	chr16:45382148-45382607(-)$1	459	38	45	15.6875
UUUUUAG	chr17:53645936-53646225(+)$1	289	151	158	15.1666
UUUUUAA	chr13:94204470-94204818(-)$1	348	40	47	18.9166

#otherMatches

#Struct PSSM
####ccc	chr4:4692888-4693216(-)$1	328	158	165	18.9166
:::iiii	chr3:135070520-135070832(-)$1	312	3	10	18.9166
cc]ffff	chr12:66043395-66043722(-)$1	327	116	123	18.9166
gggg333	chr11:88156268-88156603(-)$1	335	161	168	18.9166
gg"""cc	chr7:16745451-16745768(+)$1	317	99	106	18.9166
rrrrrrr	chr7:151033829-151034082(+)$1	253	114	121	15.2708
FFFHHHH	chr1:38109601-38109897(-)$1	296	73	80	18.9166
:::::::	chr13:89459520-89459829(+)$1	309	64	71	18.9166
:::::::	chr1:145603515-145603897(-)$1	382	243	250	15.4791
@@@@@@@	chr15:100874449-100874795(+)$1	346	250	257	18.9166
@@@@@@@	chr10:87982138-87982391(-)$1	253	222	229	18.9166
FFFFF::	chr14:31408436-31408778(-)$1	342	67	74	18.9166
TTTTTTT	chr5:67447523-67447794(+)$1	271	14	21	15.2708
sssssss	chr13:94972324-94972705(-)$1	381	44	51	18.9166
iiiiiii	chr12:36818325-36818645(-)$1	320	191	198	18.9166
hhhhh!!	chrX:140291362-140291644(-)$1	282	57	64	15.6875
eee22ee	chr6:62332033-62332305(+)$1	272	252	259	18.9166
dddd%%%	chr1:34364747-34365019(+)$1	272	94	101	15.4791
EWWWWWW	chr8:13255861-13256136(-)$1	275	70	77	18.9166
fffoooo	chr1:11289238-11289614(+)$1	376	76	83	15.6875
vvggggg	chrX:72779458-72779776(+)$1	318	37	44	15.6875
=======	chr1:158609297-158609544(-)$1	247	96	103	18.9166
ggggggg	chr4:137798788-137799167(+)$1	379	221	228	15.2708
=======	chrX:53915384-53915747(+)$1	363	209	216	18.9166
:::::::	chr6:30402620-30402954(+)$1	334	96	103	18.9166
fffff]b	chr1:165842114-165842370(+)$1	256	73	80	15.2708
:::ffff	chr17:66316707-66317008(-)$1	301	19	26	18.9166
:::iiii	chr6:8547118-8547386(+)$1	268	138	145	15.1666
^^^^^^^	chr16:31251601-31251985(-)$1	384	201	208	18.9166
ee:::::	chr10:94874029-94874328(-)$1	299	118	125	15.6875
oooobb]	chr12:109150715-109151045(-)$1	330	123	130	18.9166
ggggccc	chr15:25902430-25902738(+)$1	308	273	280	15.6875
ffffccc	chr13:43498225-43498715(-)$1	490	282	289	18.9166
fff[ddd	chr9:53425423-53425687(-)$1	264	191	198	18.9166
A::::::	chr1:63097193-63097501(-)$1	308	26	33	15.2708
gggggg[	chr13:34994284-34994541(+)$1	257	106	113	18.9166
dd####e	chr3:19126654-19126958(-)$1	304	29	36	18.9166
&&&&&&&	chr9:56466753-56467017(-)$1	264	61	68	15.4791
:::::::	chr10:25213251-25213605(+)$1	354	2	9	15.4791
777ffff	chr3:40593976-40594407(+)$1	431	91	98	15.4791
F@@@@@@	chr4:128788712-128789100(-)$1	388	244	251	18.9166
=======	chrX:34338374-34338707(+)$1	333	75	82	15.6875
FF@@@@@	chr10:4514847-4515129(+)$1	282	252	259	18.9166
dd$$$$$	chr3:122243904-122244262(-)$1	358	54	61	15.2708
sssssgg	chr11:24072917-24073292(+)$1	375	39	46	18.9166
EEEE{DD	chr16:45382148-45382607(-)$1	459	38	45	15.6875
$$$eeee	chr17:53645936-53646225(+)$1	289	151	158	15.1666
vvvvvvv	chr13:94204470-94204818(-)$1	348	40	47	18.9166

#DB
....(((	chr4:4692888-4693216(-)$1	1	158	165	18.9166
...((((	chr3:135070520-135070832(-)$1	1	3	10	18.9166
)).))))	chr12:66043395-66043722(-)$1	1	116	123	18.9166
))))...	chr11:88156268-88156603(-)$1	1	161	168	18.9166
((...((	chr7:16745451-16745768(+)$1	1	99	106	18.9166
.......	chr7:151033829-151034082(+)$1	1	114	121	15.2708
(((((((	chr1:38109601-38109897(-)$1	1	73	80	18.9166
.......	chr13:89459520-89459829(+)$1	1	64	71	18.9166
.......	chr1:145603515-145603897(-)$1	1	243	250	15.4791
.......	chr15:100874449-100874795(+)$1	1	250	257	18.9166
.......	chr10:87982138-87982391(-)$1	1	222	229	18.9166
(((((..	chr14:31408436-31408778(-)$1	1	67	74	18.9166
.......	chr5:67447523-67447794(+)$1	1	14	21	15.2708
.......	chr13:94972324-94972705(-)$1	1	44	51	18.9166
(((((((	chr12:36818325-36818645(-)$1	1	191	198	18.9166
(((((..	chrX:140291362-140291644(-)$1	1	57	64	15.6875
)))..))	chr6:62332033-62332305(+)$1	1	252	259	18.9166
((((...	chr1:34364747-34365019(+)$1	1	94	101	15.4791
(......	chr8:13255861-13256136(-)$1	1	70	77	18.9166
(((....	chr1:11289238-11289614(+)$1	1	76	83	15.6875
..)))))	chrX:72779458-72779776(+)$1	1	37	44	15.6875
(((((((	chr1:158609297-158609544(-)$1	1	96	103	18.9166
(((((((	chr4:137798788-137799167(+)$1	1	221	228	15.2708
(((((((	chrX:53915384-53915747(+)$1	1	209	216	18.9166
.......	chr6:30402620-30402954(+)$1	1	96	103	18.9166
))))).)	chr1:165842114-165842370(+)$1	1	73	80	15.2708
...((((	chr17:66316707-66317008(-)$1	1	19	26	18.9166
...((((	chr6:8547118-8547386(+)$1	1	138	145	15.1666
.......	chr16:31251601-31251985(-)$1	1	201	208	18.9166
)).....	chr10:94874029-94874328(-)$1	1	118	125	15.6875
....)).	chr12:109150715-109151045(-)$1	1	123	130	18.9166
)))))))	chr15:25902430-25902738(+)$1	1	273	280	15.6875
)))))))	chr13:43498225-43498715(-)$1	1	282	289	18.9166
(((.(((	chr9:53425423-53425687(-)$1	1	191	198	18.9166
(......	chr1:63097193-63097501(-)$1	1	26	33	15.2708
((((((.	chr13:34994284-34994541(+)$1	1	106	113	18.9166
((....(	chr3:19126654-19126958(-)$1	1	29	36	18.9166
.......	chr9:56466753-56467017(-)$1	1	61	68	15.4791
.......	chr10:25213251-25213605(+)$1	1	2	9	15.4791
...))))	chr3:40593976-40594407(+)$1	1	91	98	15.4791
)......	chr4:128788712-128789100(-)$1	1	244	251	18.9166
)))))))	chrX:34338374-34338707(+)$1	1	75	82	15.6875
)).....	chr10:4514847-4515129(+)$1	1	252	259	18.9166
((.....	chr3:122243904-122244262(-)$1	1	54	61	15.2708
.....))	chr11:24072917-24073292(+)$1	1	39	46	18.9166
((((.((	chr16:45382148-45382607(-)$1	1	38	45	15.6875
...((((	chr17:53645936-53646225(+)$1	1	151	158	15.1666
.......	chr13:94204470-94204818(-)$1	1	40	47	18.9166

#PSSM
U : 0.89	u : 0.10	
U : 0.89	u : 0.10	
U : 0.89	u : 0.10	
U : 0.89	u : 0.10	
U : 0.89	u : 0.10	
A : 0.70	C : 0.14	a : 0.08	U : 0.06	
A : 0.72	U : 0.08	a : 0.06	C : 0.06	G : 0.04	u : 0.02	

#score	838.8333333333331
#seq	48
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_transcript_m1_run2.nuc.txt

#NT
CAU	chr5:136386344-136386584(-)$1	240	56	59	9.0000
CAU	chr17:80863185-80863420(-)$1	235	90	93	9.0000
CAU	chr17:24313602-24313837(-)$1	235	24	27	9.0000
CAU	chr15:37297729-37297964(-)$1	235	20	23	9.0000
CAU	chr4:147247927-147248162(-)$1	235	37	40	9.0000
CAU	chr2:155214476-155214718(+)$1	242	29	32	9.0000
CAU	chr4:33108448-33108691(+)$1	243	87	90	9.0000
CAU	chr11:87793700-87793945(-)$1	245	66	69	9.0000
CAU	chr17:34406174-34406409(+)$1	235	78	81	9.0000
CAU	chr2:35151973-35152210(+)$1	237	22	25	9.0000
CAU	chr2:76561979-76562240(-)$1	261	2	5	9.0000
CAU	chr11:67062033-67062294(+)$1	261	1	4	9.0000
CAU	chr13:29999174-29999409(-)$1	235	14	17	9.0000
CAU	chr1:135554227-135554464(-)$1	237	9	12	9.0000
CAU	chr13:83802497-83802751(+)$1	254	45	48	9.0000
CAU	chr4:104704900-104705153(-)$1	253	17	20	9.0000
CAU	chr1:36879850-36880085(-)$1	235	24	27	9.0000
CAU	chr9:79818807-79819042(-)$1	235	29	32	9.0000
CAU	chr3:116445349-116445591(-)$1	242	33	36	9.0000
CAU	chr7:138588944-138589179(+)$1	235	9	12	9.0000
cau	chr2:31012711-31012946(+)$1	235	2	5	9.0000
CAU	chr4:150421354-150421589(-)$1	235	0	3	9.0000
CAU	chr16:44160309-44160547(+)$1	238	191	194	9.0000
CAU	chr9:30957625-30957860(-)$1	235	45	48	9.0000
CAU	chr11:60013257-60013493(-)$1	236	100	103	9.0000
CAU	chr17:71475852-71476088(+)$1	236	25	28	9.0000
CAU	chr8:107740674-107740909(+)$1	235	10	13	9.0000
CAU	chr16:32472416-32472656(+)$1	240	63	66	9.0000
cau	chr6:112331868-112332103(-)$1	235	78	81	9.0000
CAU	chr2:6465641-6465886(-)$1	245	59	62	9.0000
CAU	chr16:36035202-36035440(+)$1	238	24	27	9.0000
CAU	chr2:6793373-6793609(-)$1	236	133	136	9.0000
CAU	chr3:97725293-97725538(+)$1	245	78	81	9.0000
CAU	chr13:60807317-60807555(+)$1	238	31	34	9.0000
CAU	chr7:107789095-107789330(+)$1	235	135	138	9.0000
CAU	chr2:172179044-172179279(+)$1	235	15	18	9.0000
CAU	chr13:83802224-83802482(+)$1	258	7	10	9.0000
CAU	chr3:51322110-51322367(-)$1	257	19	22	9.0000
CAU	chr2:155214406-155214651(+)$1	245	12	15	9.0000
CAU	chr18:78021176-78021422(+)$1	246	7	10	9.0000
CAU	chr11:105800355-105800590(-)$1	235	80	83	9.0000
CAU	chr1:134401574-134401813(+)$1	239	99	102	9.0000
CAU	chr3:138589963-138590208(-)$1	245	167	170	9.0000
CAU	chr8:114542481-114542716(+)$1	235	73	76	9.0000
CAU	chr7:122797650-122797885(-)$1	235	17	20	9.0000
CAU	chr7:133603008-133603243(-)$1	235	119	122	9.0000
CAU	chr5:108929627-108929862(+)$1	235	25	28	9.0000
CAU	chr5:23121948-23122183(-)$1	235	57	60	9.0000
CAU	chr11:35197248-35197483(+)$1	235	43	46	9.0000
cau	chr7:17399196-17399433(-)$1	237	134	137	9.0000
CAU	chr2:76594261-76594496(-)$1	235	36	39	9.0000
CAU	chr6:71758227-71758463(+)$1	236	48	51	9.0000
CAU	chr11:29642168-29642473(+)$1	305	20	23	9.0000
CAU	chr2:72244243-72244491(+)$1	248	99	102	9.0000
CAU	chr5:136386537-136386774(-)$1	237	61	64	9.0000
CAU	chr7:52665530-52665765(+)$1	235	25	28	9.0000
CAU	chr7:133589729-133589973(-)$1	244	54	57	9.0000
CAU	chr9:107950750-107950985(+)$1	235	48	51	9.0000
CAU	chr12:3249201-3249436(-)$1	235	37	40	9.0000
cau	chr11:100782339-100782574(-)$1	235	39	42	9.0000
CAU	chr15:4104015-4104251(+)$1	236	19	22	9.0000
CAU	chr2:20885594-20885829(-)$1	235	80	83	9.0000
CAU	chr11:60370509-60370744(+)$1	235	23	26	9.0000
CAU	chr10:77670618-77670856(-)$1	238	4	7	9.0000
CAU	chr12:112776564-112776799(+)$1	235	215	218	9.0000
CAU	chr7:119254506-119254741(+)$1	235	31	34	9.0000
CAU	chr6:29411059-29411294(+)$1	235	29	32	9.0000
CAU	chr4:15845268-15845503(-)$1	235	48	51	9.0000
CAU	chr7:99792676-99792911(-)$1	235	147	150	9.0000
CAU	chr16:4480665-4480901(-)$1	236	114	117	9.0000
CAU	chr4:109126604-109126839(-)$1	235	15	18	9.0000
CAU	chr13:23831577-23831839(+)$1	262	122	125	9.0000
CAU	chr13:19684740-19684975(-)$1	235	89	92	9.0000
CAU	chr7:122615150-122615411(-)$1	261	27	30	9.0000
CAU	chr15:76845848-76846084(-)$1	236	97	100	9.0000
CAU	chr12:16992172-16992410(+)$1	238	0	3	9.0000
CAU	chr7:31339759-31340011(+)$1	252	165	168	9.0000
CAU	chr17:25969080-25969315(-)$1	235	18	21	9.0000
CAU	chr5:36944678-36944920(-)$1	242	85	88	9.0000
CAU	chr14:60248649-60248884(+)$1	235	14	17	9.0000
CAU	chr15:12114164-12114401(+)$1	237	25	28	9.0000
CAU	chr7:119254173-119254453(+)$1	280	36	39	9.0000
CAU	chr2:104266800-104267037(-)$1	237	3	6	9.0000
CAU	chr12:33660678-33660920(+)$1	242	50	53	9.0000
CAU	chr8:35233354-35233615(+)$1	261	9	12	9.0000
CAU	chr12:55960170-55960414(-)$1	244	0	3	9.0000
CAU	chr2:130101955-130102202(+)$1	247	2	5	9.0000
CAU	chr16:36035790-36036034(+)$1	244	133	136	9.0000
CAU	chr4:132851049-132851284(-)$1	235	24	27	9.0000
cau	chr6:93867623-93867858(-)$1	235	20	23	9.0000
CAU	chr2:121137360-121137598(-)$1	238	4	7	9.0000
CAU	chr2:152106642-152106889(+)$1	247	16	19	9.0000
CAU	chr7:20006559-20006808(+)$1	249	34	37	9.0000
CAU	chr2:76565493-76565731(-)$1	238	192	195	9.0000
CAU	chr6:117126337-117126573(+)$1	236	2	5	9.0000
CAU	chr14:21319545-21319780(-)$1	235	80	83	9.0000
CAU	chr7:119910450-119910685(+)$1	235	42	45	9.0000
CAU	chr12:4108975-4109237(+)$1	262	1	4	9.0000
CAU	chrX:98835693-98835928(+)$1	235	32	35	9.0000

#otherMatches

#Struct PSSM
dd:	chr5:136386488-136386735(-)$1	247	22	25	9.0000
fff	chr5:136386344-136386584(-)$1	240	56	59	9.0000
22c	chr17:80863185-80863420(-)$1	235	90	93	9.0000
DDD	chr17:24313602-24313837(-)$1	235	24	27	9.0000
ooo	chr15:37297729-37297964(-)$1	235	20	23	9.0000
www	chr4:147247927-147248162(-)$1	235	37	40	9.0000
h""	chr2:155214476-155214718(+)$1	242	29	32	9.0000
CC{	chr4:33108448-33108691(+)$1	243	87	90	9.0000
dd]	chr11:87793700-87793945(-)$1	245	66	69	9.0000
ppd	chr17:34406174-34406409(+)$1	235	78	81	9.0000
:::	chr2:35151973-35152210(+)$1	237	22	25	9.0000
::E	chr2:76561979-76562240(-)$1	261	2	5	9.0000
B{H	chr11:67062033-67062294(+)$1	261	1	4	9.0000
MMB	chr13:29999174-29999409(-)$1	235	14	17	9.0000
===	chr1:135554227-135554464(-)$1	237	9	12	9.0000
:::	chr13:83802497-83802751(+)$1	254	45	48	9.0000
iii	chr4:104704900-104705153(-)$1	253	17	20	9.0000
EEE	chr1:36879850-36880085(-)$1	235	24	27	9.0000
LLA	chr9:79818807-79819042(-)$1	235	29	32	9.0000
:::	chr3:116445349-116445591(-)$1	242	33	36	9.0000
!!d	chr7:138588944-138589179(+)$1	235	9	12	9.0000
DDD	chr2:31012711-31012946(+)$1	235	2	5	9.0000
::d	chr4:150421354-150421589(-)$1	235	0	3	9.0000
DDD	chr16:44160309-44160547(+)$1	238	191	194	9.0000
===	chr9:30957625-30957860(-)$1	235	45	48	9.0000
cll	chr11:60013257-60013493(-)$1	236	100	103	9.0000
:gg	chr17:71475852-71476088(+)$1	236	25	28	9.0000
eee	chr8:107740674-107740909(+)$1	235	10	13	9.0000
ppp	chr16:32472416-32472656(+)$1	240	63	66	9.0000
fff	chr6:112331868-112332103(-)$1	235	78	81	9.0000
HHH	chr2:6465641-6465886(-)$1	245	59	62	9.0000
www	chr16:36035202-36035440(+)$1	238	24	27	9.0000
:::	chr2:6793373-6793609(-)$1	236	133	136	9.0000
ee[	chr3:97725293-97725538(+)$1	245	78	81	9.0000
###	chr13:60807317-60807555(+)$1	238	31	34	9.0000
===	chr7:107789095-107789330(+)$1	235	135	138	9.0000
DD{	chr2:172179044-172179279(+)$1	235	15	18	9.0000
:::	chr13:83802224-83802482(+)$1	258	7	10	9.0000
ppp	chr3:51322110-51322367(-)$1	257	19	22	9.0000
gss	chr2:155214406-155214651(+)$1	245	12	15	9.0000
::f	chr18:78021176-78021422(+)$1	246	7	10	9.0000
eee	chr11:105800355-105800590(-)$1	235	80	83	9.0000
ffo	chr1:134401574-134401813(+)$1	239	99	102	9.0000
^^^	chr3:138589963-138590208(-)$1	245	167	170	9.0000
bb]	chr8:114542481-114542716(+)$1	235	73	76	9.0000
:::	chr7:122797650-122797885(-)$1	235	17	20	9.0000
:::	chr7:133603008-133603243(-)$1	235	119	122	9.0000
$$d	chr5:108929627-108929862(+)$1	235	25	28	9.0000
eee	chr5:23121948-23122183(-)$1	235	57	60	9.0000
dpp	chr11:35197248-35197483(+)$1	235	43	46	9.0000
F}C	chr7:17399196-17399433(-)$1	237	134	137	9.0000
dd]	chr2:76594261-76594496(-)$1	235	36	39	9.0000
B{D	chr6:71758227-71758463(+)$1	236	48	51	9.0000
g[c	chr11:29642168-29642473(+)$1	305	20	23	9.0000
ccc	chr2:72244243-72244491(+)$1	248	99	102	9.0000
c[g	chr5:136386537-136386774(-)$1	237	61	64	9.0000
eee	chr7:52665530-52665765(+)$1	235	25	28	9.0000
&&c	chr7:133589729-133589973(-)$1	244	54	57	9.0000
:::	chr9:107950750-107950985(+)$1	235	48	51	9.0000
D{A	chr12:3249201-3249436(-)$1	235	37	40	9.0000
eee	chr11:100782339-100782574(-)$1	235	39	42	9.0000
gg&	chr15:4104015-4104251(+)$1	236	19	22	9.0000
fff	chr2:20885594-20885829(-)$1	235	80	83	9.0000
{DD	chr11:60370509-60370744(+)$1	235	23	26	9.0000
:::	chr10:77670618-77670856(-)$1	238	4	7	9.0000
EYY	chr12:112776564-112776799(+)$1	235	215	218	9.0000
cc:	chr7:119254506-119254741(+)$1	235	31	34	9.0000
FFF	chr6:29411059-29411294(+)$1	235	29	32	9.0000
eee	chr4:15845268-15845503(-)$1	235	48	51	9.0000
:dd	chr7:99792676-99792911(-)$1	235	147	150	9.0000
tdd	chr16:4480665-4480901(-)$1	236	114	117	9.0000
iii	chr4:109126604-109126839(-)$1	235	15	18	9.0000
b:G	chr13:23831577-23831839(+)$1	262	122	125	9.0000
OOO	chr13:19684740-19684975(-)$1	235	89	92	9.0000
dd2	chr7:122615150-122615411(-)$1	261	27	30	9.0000
ffv	chr15:76845848-76846084(-)$1	236	97	100	9.0000
:::	chr12:16992172-16992410(+)$1	238	0	3	9.0000
:::	chr7:31339759-31340011(+)$1	252	165	168	9.0000
BB{	chr17:25969080-25969315(-)$1	235	18	21	9.0000
>>>	chr5:36944678-36944920(-)$1	242	85	88	9.0000
[bb	chr14:60248649-60248884(+)$1	235	14	17	9.0000
DDH	chr15:12114164-12114401(+)$1	237	25	28	9.0000
HHH	chr7:119254173-119254453(+)$1	280	36	39	9.0000
:::	chr2:104266800-104267037(-)$1	237	3	6	9.0000
eee	chr12:33660678-33660920(+)$1	242	50	53	9.0000
ddd	chr8:35233354-35233615(+)$1	261	9	12	9.0000
GGG	chr12:55960170-55960414(-)$1	244	0	3	9.0000
DDK	chr2:130101955-130102202(+)$1	247	2	5	9.0000
hh:	chr16:36035790-36036034(+)$1	244	133	136	9.0000
cnn	chr4:132851049-132851284(-)$1	235	24	27	9.0000
mmm	chr6:93867623-93867858(-)$1	235	20	23	9.0000
:::	chr2:121137360-121137598(-)$1	238	4	7	9.0000
:::	chr2:152106642-152106889(+)$1	247	16	19	9.0000
ddd	chr7:20006559-20006808(+)$1	249	34	37	9.0000
FFF	chr2:76565493-76565731(-)$1	238	192	195	9.0000
:::	chr6:117126337-117126573(+)$1	236	2	5	9.0000
xxx	chr14:21319545-21319780(-)$1	235	80	83	9.0000
bb!	chr7:119910450-119910685(+)$1	235	42	45	9.0000
:::	chr12:4108975-4109237(+)$1	262	1	4	9.0000
qqq	chrX:98835693-98835928(+)$1	235	32	35	9.0000

#DB
)).	chr5:136386488-136386735(-)$1	1	22	25	9.0000
)))	chr5:136386344-136386584(-)$1	1	56	59	9.0000
..)	chr17:80863185-80863420(-)$1	1	90	93	9.0000
(((	chr17:24313602-24313837(-)$1	1	24	27	9.0000
...	chr15:37297729-37297964(-)$1	1	20	23	9.0000
...	chr4:147247927-147248162(-)$1	1	37	40	9.0000
(..	chr2:155214476-155214718(+)$1	1	29	32	9.0000
((.	chr4:33108448-33108691(+)$1	1	87	90	9.0000
)).	chr11:87793700-87793945(-)$1	1	66	69	9.0000
..)	chr17:34406174-34406409(+)$1	1	78	81	9.0000
...	chr2:35151973-35152210(+)$1	1	22	25	9.0000
..(	chr2:76561979-76562240(-)$1	1	2	5	9.0000
(.(	chr11:67062033-67062294(+)$1	1	1	4	9.0000
..(	chr13:29999174-29999409(-)$1	1	14	17	9.0000
(((	chr1:135554227-135554464(-)$1	1	9	12	9.0000
...	chr13:83802497-83802751(+)$1	1	45	48	9.0000
(((	chr4:104704900-104705153(-)$1	1	17	20	9.0000
(((	chr1:36879850-36880085(-)$1	1	24	27	9.0000
..(	chr9:79818807-79819042(-)$1	1	29	32	9.0000
...	chr3:116445349-116445591(-)$1	1	33	36	9.0000
..(	chr7:138588944-138589179(+)$1	1	9	12	9.0000
(((	chr2:31012711-31012946(+)$1	1	2	5	9.0000
..(	chr4:150421354-150421589(-)$1	1	0	3	9.0000
)))	chr16:44160309-44160547(+)$1	1	191	194	9.0000
(((	chr9:30957625-30957860(-)$1	1	45	48	9.0000
(..	chr11:60013257-60013493(-)$1	1	100	103	9.0000
.((	chr17:71475852-71476088(+)$1	1	25	28	9.0000
)))	chr8:107740674-107740909(+)$1	1	10	13	9.0000
...	chr16:32472416-32472656(+)$1	1	63	66	9.0000
(((	chr6:112331868-112332103(-)$1	1	78	81	9.0000
(((	chr2:6465641-6465886(-)$1	1	59	62	9.0000
...	chr16:36035202-36035440(+)$1	1	24	27	9.0000
...	chr2:6793373-6793609(-)$1	1	133	136	9.0000
((.	chr3:97725293-97725538(+)$1	1	78	81	9.0000
...	chr13:60807317-60807555(+)$1	1	31	34	9.0000
)))	chr7:107789095-107789330(+)$1	1	135	138	9.0000
((.	chr2:172179044-172179279(+)$1	1	15	18	9.0000
...	chr13:83802224-83802482(+)$1	1	7	10	9.0000
...	chr3:51322110-51322367(-)$1	1	19	22	9.0000
(..	chr2:155214406-155214651(+)$1	1	12	15	9.0000
..(	chr18:78021176-78021422(+)$1	1	7	10	9.0000
)))	chr11:105800355-105800590(-)$1	1	80	83	9.0000
((.	chr1:134401574-134401813(+)$1	1	99	102	9.0000
...	chr3:138589963-138590208(-)$1	1	167	170	9.0000
)).	chr8:114542481-114542716(+)$1	1	73	76	9.0000
...	chr7:122797650-122797885(-)$1	1	17	20	9.0000
...	chr7:133603008-133603243(-)$1	1	119	122	9.0000
..(	chr5:108929627-108929862(+)$1	1	25	28	9.0000
(((	chr5:23121948-23122183(-)$1	1	57	60	9.0000
(..	chr11:35197248-35197483(+)$1	1	43	46	9.0000
).)	chr7:17399196-17399433(-)$1	1	134	137	9.0000
)).	chr2:76594261-76594496(-)$1	1	36	39	9.0000
(.(	chr6:71758227-71758463(+)$1	1	48	51	9.0000
(.(	chr11:29642168-29642473(+)$1	1	20	23	9.0000
)))	chr2:72244243-72244491(+)$1	1	99	102	9.0000
(.(	chr5:136386537-136386774(-)$1	1	61	64	9.0000
(((	chr7:52665530-52665765(+)$1	1	25	28	9.0000
..(	chr7:133589729-133589973(-)$1	1	54	57	9.0000
...	chr9:107950750-107950985(+)$1	1	48	51	9.0000
(.(	chr12:3249201-3249436(-)$1	1	37	40	9.0000
(((	chr11:100782339-100782574(-)$1	1	39	42	9.0000
((.	chr15:4104015-4104251(+)$1	1	19	22	9.0000
)))	chr2:20885594-20885829(-)$1	1	80	83	9.0000
.((	chr11:60370509-60370744(+)$1	1	23	26	9.0000
...	chr10:77670618-77670856(-)$1	1	4	7	9.0000
)..	chr12:112776564-112776799(+)$1	1	215	218	9.0000
)).	chr7:119254506-119254741(+)$1	1	31	34	9.0000
(((	chr6:29411059-29411294(+)$1	1	29	32	9.0000
(((	chr4:15845268-15845503(-)$1	1	48	51	9.0000
.((	chr7:99792676-99792911(-)$1	1	147	150	9.0000
.))	chr16:4480665-4480901(-)$1	1	114	117	9.0000
(((	chr4:109126604-109126839(-)$1	1	15	18	9.0000
).(	chr13:23831577-23831839(+)$1	1	122	125	9.0000
...	chr13:19684740-19684975(-)$1	1	89	92	9.0000
)).	chr7:122615150-122615411(-)$1	1	27	30	9.0000
((.	chr15:76845848-76846084(-)$1	1	97	100	9.0000
...	chr12:16992172-16992410(+)$1	1	0	3	9.0000
...	chr7:31339759-31340011(+)$1	1	165	168	9.0000
((.	chr17:25969080-25969315(-)$1	1	18	21	9.0000
...	chr5:36944678-36944920(-)$1	1	85	88	9.0000
.((	chr14:60248649-60248884(+)$1	1	14	17	9.0000
(((	chr15:12114164-12114401(+)$1	1	25	28	9.0000
(((	chr7:119254173-119254453(+)$1	1	36	39	9.0000
...	chr2:104266800-104267037(-)$1	1	3	6	9.0000
(((	chr12:33660678-33660920(+)$1	1	50	53	9.0000
(((	chr8:35233354-35233615(+)$1	1	9	12	9.0000
(((	chr12:55960170-55960414(-)$1	1	0	3	9.0000
((.	chr2:130101955-130102202(+)$1	1	2	5	9.0000
)).	chr16:36035790-36036034(+)$1	1	133	136	9.0000
(..	chr4:132851049-132851284(-)$1	1	24	27	9.0000
...	chr6:93867623-93867858(-)$1	1	20	23	9.0000
...	chr2:121137360-121137598(-)$1	1	4	7	9.0000
...	chr2:152106642-152106889(+)$1	1	16	19	9.0000
(((	chr7:20006559-20006808(+)$1	1	34	37	9.0000
)))	chr2:76565493-76565731(-)$1	1	192	195	9.0000
...	chr6:117126337-117126573(+)$1	1	2	5	9.0000
...	chr14:21319545-21319780(-)$1	1	80	83	9.0000
((.	chr7:119910450-119910685(+)$1	1	42	45	9.0000
...	chr12:4108975-4109237(+)$1	1	1	4	9.0000
...	chrX:98835693-98835928(+)$1	1	32	35	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m3_run2.nuc.txt

#NT
UUC	chr2:131122346-131122566(+)$1	220	8	11	9.0000
uuc	chr17:22064439-22064660(-)$1	221	20	23	9.0000
UUC	chr1:4887240-4887460(+)$1	220	121	124	9.0000
UUC	chr5:93611163-93611383(-)$1	220	86	89	9.0000
UUC	chr1:64840666-64840886(-)$1	220	4	7	9.0000
UUC	chr15:84022626-84022854(+)$1	228	77	80	9.0000
UUC	chr6:94554585-94554805(-)$1	220	97	100	9.0000
UUC	chr16:32387591-32387828(+)$1	237	7	10	9.0000
UUC	chr18:57552141-57552361(+)$1	220	24	27	9.0000
UUC	chr5:125020859-125021091(-)$1	232	15	18	9.0000
UUC	chr9:42776401-42776621(-)$1	220	53	56	9.0000
UUC	chr15:96518402-96518622(-)$1	220	22	25	9.0000
UUC	chr17:30354469-30354690(-)$1	221	79	82	9.0000
UUC	chr11:4822112-4822332(+)$1	220	17	20	9.0000
UUC	chr2:131073191-131073411(+)$1	220	19	22	9.0000
UUC	chr2:131099625-131099845(+)$1	220	6	9	9.0000
UUC	chr8:124941086-124941336(+)$1	250	2	5	9.0000
UUC	chr2:80193507-80193727(+)$1	220	26	29	9.0000
UUC	chr19:41843256-41843476(-)$1	220	26	29	9.0000
UUC	chr2:160772796-160773016(-)$1	220	53	56	9.0000
UUC	chr19:21932008-21932229(+)$1	221	14	17	9.0000
UUC	chr11:17166760-17166981(+)$1	221	29	32	9.0000
UUC	chr2:28085819-28086039(+)$1	220	90	93	9.0000
UUC	chr3:58326463-58326683(-)$1	220	17	20	9.0000
UUC	chr1:34933900-34934121(+)$1	221	5	8	9.0000
UUC	chr16:36034193-36034419(+)$1	226	136	139	9.0000
UUC	chr6:113338916-113339137(+)$1	221	76	79	9.0000
UUC	chr19:23241163-23241383(+)$1	220	11	14	9.0000
UUC	chr13:38071064-38071298(-)$1	234	20	23	9.0000
UUC	chr1:46866395-46866667(-)$1	272	15	18	9.0000
UUC	chr3:94986446-94986666(-)$1	220	0	3	9.0000
UUC	chr5:108331007-108331234(+)$1	227	1	4	9.0000
UUC	chr6:65064467-65064687(+)$1	220	10	13	9.0000
UUC	chr2:131879107-131879327(-)$1	220	9	12	9.0000
UUC	chr16:17430645-17430865(+)$1	220	119	122	9.0000
UUC	chr4:41238315-41238535(-)$1	220	16	19	9.0000
UUC	chr6:49290364-49290584(+)$1	220	23	26	9.0000
UUC	chr9:20770479-20770701(-)$1	222	24	27	9.0000
uuc	chr10:82828916-82829136(+)$1	220	31	34	9.0000
UUC	chr5:146006658-146006878(+)$1	220	13	16	9.0000
UUC	chr11:75461954-75462174(+)$1	220	0	3	9.0000
UUC	chr11:77524371-77524591(+)$1	220	5	8	9.0000
UUC	chr11:54923563-54923791(+)$1	228	100	103	9.0000
UUC	chr3:95737799-95738019(+)$1	220	15	18	9.0000
uuc	chr11:97697964-97698185(+)$1	221	23	26	9.0000
UUC	chr11:72989668-72989888(-)$1	220	107	110	9.0000
UUC	chr11:53234059-53234291(+)$1	232	7	10	9.0000
UUC	chr17:34165348-34165571(-)$1	223	101	104	9.0000
UUC	chr4:134876474-134876694(-)$1	220	23	26	9.0000
UUC	chr5:129709327-129709561(+)$1	234	34	37	9.0000
UUC	chr15:102265700-102265920(+)$1	220	42	45	9.0000
UUC	chr11:77349190-77349410(-)$1	220	3	6	9.0000
UUC	chr6:38553226-38553458(+)$1	232	41	44	9.0000
UUC	chr3:68819914-68820150(+)$1	236	37	40	9.0000
UUC	chr17:23957017-23957237(+)$1	220	59	62	9.0000
UUC	chr4:107545452-107545672(+)$1	220	25	28	9.0000
UUC	chr12:45413007-45413227(+)$1	220	4	7	9.0000
UUC	chr9:72860343-72860564(+)$1	221	18	21	9.0000
UUC	chr11:3244445-3244665(-)$1	220	115	118	9.0000
UUC	chr2:150409298-150409529(-)$1	231	75	78	9.0000
uuc	chr11:79748703-79748923(-)$1	220	3	6	9.0000
UUC	chr14:47396098-47396318(-)$1	220	75	78	9.0000
UUC	chr3:87726869-87727089(+)$1	220	34	37	9.0000
UUC	chr13:47180390-47180610(-)$1	220	55	58	9.0000
UUC	chr7:25673203-25673423(+)$1	220	41	44	9.0000
UUC	chr18:31941192-31941412(+)$1	220	21	24	9.0000
UUC	chr11:30743425-30743658(+)$1	233	3	6	9.0000
UUC	chr7:118199348-118199583(+)$1	235	21	24	9.0000
UUC	chr11:45958729-45958949(+)$1	220	1	4	9.0000
UUC	chr12:9035318-9035538(+)$1	220	40	43	9.0000
UUC	chr9:94420122-94420345(-)$1	223	22	25	9.0000
UUC	chr17:27173053-27173273(+)$1	220	121	124	9.0000
UUC	chr3:157668935-157669155(+)$1	220	11	14	9.0000
UUC	chr18:7348176-7348397(-)$1	221	85	88	9.0000
UUC	chr15:72935974-72936194(-)$1	220	20	23	9.0000
UUC	chr1:90161600-90161821(-)$1	221	31	34	9.0000
UUC	chr11:35602096-35602317(+)$1	221	74	77	9.0000
UUC	chr4:40683573-40683794(-)$1	221	13	16	9.0000
UUC	chr9:67744857-67745078(+)$1	221	4	7	9.0000
UUC	chr16:31665596-31665816(+)$1	220	42	45	9.0000
UUC	chr5:135628805-135629025(+)$1	220	59	62	9.0000
UUC	chr16:58467213-58467433(+)$1	220	35	38	9.0000
UUC	chr1:182797999-182798219(+)$1	220	12	15	9.0000
UUC	chr9:21507332-21507573(+)$1	241	29	32	9.0000
UUC	chr5:76051652-76051872(+)$1	220	54	57	9.0000
UUC	chr15:41690638-41690876(+)$1	238	60	63	9.0000
UUC	chr2:3375526-3375746(-)$1	220	21	24	9.0000
UUC	chr4:125388480-125388700(+)$1	220	143	146	9.0000
UUC	chr7:129225470-129225690(+)$1	220	3	6	9.0000
UUC	chr6:29324337-29324559(+)$1	222	4	7	9.0000
UUC	chr18:61290886-61291106(-)$1	220	116	119	9.0000
UUC	chr17:5411224-5411445(-)$1	221	11	14	9.0000
UUC	chr14:51547350-51547588(-)$1	238	11	14	9.0000
UUC	chr8:88062522-88062749(-)$1	227	37	40	9.0000

#otherMatches

#Struct PSSM
e&&	chr2:80157439-80157659(+)$1	220	30	33	9.0000
mmm	chr2:131122346-131122566(+)$1	220	8	11	9.0000
eee	chr17:22064439-22064660(-)$1	221	20	23	9.0000
ccc	chr1:4887240-4887460(+)$1	220	121	124	9.0000
]bb	chr5:93611163-93611383(-)$1	220	86	89	9.0000
fff	chr1:64840666-64840886(-)$1	220	4	7	9.0000
eee	chr15:84022626-84022854(+)$1	228	77	80	9.0000
uuc	chr6:94554585-94554805(-)$1	220	97	100	9.0000
hhh	chr16:32387591-32387828(+)$1	237	7	10	9.0000
ddd	chr18:57552141-57552361(+)$1	220	24	27	9.0000
HHH	chr5:125020859-125021091(-)$1	232	15	18	9.0000
ppp	chr9:42776401-42776621(-)$1	220	53	56	9.0000
:::	chr15:96518402-96518622(-)$1	220	22	25	9.0000
ssg	chr17:30354469-30354690(-)$1	221	79	82	9.0000
ttt	chr11:4822112-4822332(+)$1	220	17	20	9.0000
eee	chr2:131073191-131073411(+)$1	220	19	22	9.0000
JJJ	chr2:131099625-131099845(+)$1	220	6	9	9.0000
fff	chr8:124941086-124941336(+)$1	250	2	5	9.0000
QQQ	chr2:80193507-80193727(+)$1	220	26	29	9.0000
hhh	chr19:41843256-41843476(-)$1	220	26	29	9.0000
LLL	chr2:160772796-160773016(-)$1	220	53	56	9.0000
ggg	chr19:21932008-21932229(+)$1	221	14	17	9.0000
iii	chr11:17166760-17166981(+)$1	221	29	32	9.0000
fff	chr2:28085819-28086039(+)$1	220	90	93	9.0000
ggg	chr3:58326463-58326683(-)$1	220	17	20	9.0000
bb=	chr1:34933900-34934121(+)$1	221	5	8	9.0000
mee	chr16:36034193-36034419(+)$1	226	136	139	9.0000
::C	chr6:113338916-113339137(+)$1	221	76	79	9.0000
:::	chr19:23241163-23241383(+)$1	220	11	14	9.0000
KKD	chr13:38071064-38071298(-)$1	234	20	23	9.0000
Jcc	chr1:46866395-46866667(-)$1	272	15	18	9.0000
:CC	chr3:94986446-94986666(-)$1	220	0	3	9.0000
EEE	chr5:108331007-108331234(+)$1	227	1	4	9.0000
ELL	chr6:65064467-65064687(+)$1	220	10	13	9.0000
ccc	chr2:131879107-131879327(-)$1	220	9	12	9.0000
666	chr16:17430645-17430865(+)$1	220	119	122	9.0000
:::	chr4:41238315-41238535(-)$1	220	16	19	9.0000
yyd	chr6:49290364-49290584(+)$1	220	23	26	9.0000
HHH	chr9:20770479-20770701(-)$1	222	24	27	9.0000
RRR	chr10:82828916-82829136(+)$1	220	31	34	9.0000
fqq	chr5:146006658-146006878(+)$1	220	13	16	9.0000
:::	chr11:75461954-75462174(+)$1	220	0	3	9.0000
FFF	chr11:77524371-77524591(+)$1	220	5	8	9.0000
eee	chr11:54923563-54923791(+)$1	228	100	103	9.0000
eee	chr3:95737799-95738019(+)$1	220	15	18	9.0000
nnb	chr11:97697964-97698185(+)$1	221	23	26	9.0000
hh2	chr11:72989668-72989888(-)$1	220	107	110	9.0000
CLL	chr11:53234059-53234291(+)$1	232	7	10	9.0000
eee	chr17:34165348-34165571(-)$1	223	101	104	9.0000
xxx	chr4:134876474-134876694(-)$1	220	23	26	9.0000
$$g	chr5:129709327-129709561(+)$1	234	34	37	9.0000
gg!	chr15:102265700-102265920(+)$1	220	42	45	9.0000
EEE	chr11:77349190-77349410(-)$1	220	3	6	9.0000
ddd	chr6:38553226-38553458(+)$1	232	41	44	9.0000
EEE	chr3:68819914-68820150(+)$1	236	37	40	9.0000
hhh	chr17:23957017-23957237(+)$1	220	59	62	9.0000
eel	chr4:107545452-107545672(+)$1	220	25	28	9.0000
fff	chr12:45413007-45413227(+)$1	220	4	7	9.0000
ddd	chr9:72860343-72860564(+)$1	221	18	21	9.0000
:cc	chr11:3244445-3244665(-)$1	220	115	118	9.0000
===	chr2:150409298-150409529(-)$1	231	75	78	9.0000
ppp	chr11:79748703-79748923(-)$1	220	3	6	9.0000
ggg	chr14:47396098-47396318(-)$1	220	75	78	9.0000
ccc	chr3:87726869-87727089(+)$1	220	34	37	9.0000
cc[	chr13:47180390-47180610(-)$1	220	55	58	9.0000
eee	chr7:25673203-25673423(+)$1	220	41	44	9.0000
ddd	chr18:31941192-31941412(+)$1	220	21	24	9.0000
:::	chr11:30743425-30743658(+)$1	233	3	6	9.0000
ccf	chr7:118199348-118199583(+)$1	235	21	24	9.0000
:::	chr11:45958729-45958949(+)$1	220	1	4	9.0000
:==	chr12:9035318-9035538(+)$1	220	40	43	9.0000
:::	chr9:94420122-94420345(-)$1	223	22	25	9.0000
ooo	chr17:27173053-27173273(+)$1	220	121	124	9.0000
G::	chr3:157668935-157669155(+)$1	220	11	14	9.0000
FFK	chr18:7348176-7348397(-)$1	221	85	88	9.0000
:FF	chr15:72935974-72936194(-)$1	220	20	23	9.0000
:::	chr1:90161600-90161821(-)$1	221	31	34	9.0000
ccc	chr11:35602096-35602317(+)$1	221	74	77	9.0000
ggg	chr4:40683573-40683794(-)$1	221	13	16	9.0000
FFF	chr9:67744857-67745078(+)$1	221	4	7	9.0000
ddd	chr16:31665596-31665816(+)$1	220	42	45	9.0000
hhh	chr5:135628805-135629025(+)$1	220	59	62	9.0000
OOO	chr16:58467213-58467433(+)$1	220	35	38	9.0000
nnn	chr1:182797999-182798219(+)$1	220	12	15	9.0000
CCC	chr9:21507332-21507573(+)$1	241	29	32	9.0000
::b	chr5:76051652-76051872(+)$1	220	54	57	9.0000
555	chr15:41690638-41690876(+)$1	238	60	63	9.0000
=dd	chr2:3375526-3375746(-)$1	220	21	24	9.0000
dmm	chr4:125388480-125388700(+)$1	220	143	146	9.0000
FFF	chr7:129225470-129225690(+)$1	220	3	6	9.0000
:::	chr6:29324337-29324559(+)$1	222	4	7	9.0000
c]g	chr18:61290886-61291106(-)$1	220	116	119	9.0000
LLL	chr17:5411224-5411445(-)$1	221	11	14	9.0000
(((	chr14:51547350-51547588(-)$1	238	11	14	9.0000
ddd	chr8:88062522-88062749(-)$1	227	37	40	9.0000

#DB
(..	chr2:80157439-80157659(+)$1	1	30	33	9.0000
...	chr2:131122346-131122566(+)$1	1	8	11	9.0000
)))	chr17:22064439-22064660(-)$1	1	20	23	9.0000
)))	chr1:4887240-4887460(+)$1	1	121	124	9.0000
.))	chr5:93611163-93611383(-)$1	1	86	89	9.0000
(((	chr1:64840666-64840886(-)$1	1	4	7	9.0000
(((	chr15:84022626-84022854(+)$1	1	77	80	9.0000
..)	chr6:94554585-94554805(-)$1	1	97	100	9.0000
(((	chr16:32387591-32387828(+)$1	1	7	10	9.0000
(((	chr18:57552141-57552361(+)$1	1	24	27	9.0000
(((	chr5:125020859-125021091(-)$1	1	15	18	9.0000
...	chr9:42776401-42776621(-)$1	1	53	56	9.0000
...	chr15:96518402-96518622(-)$1	1	22	25	9.0000
..)	chr17:30354469-30354690(-)$1	1	79	82	9.0000
...	chr11:4822112-4822332(+)$1	1	17	20	9.0000
(((	chr2:131073191-131073411(+)$1	1	19	22	9.0000
(((	chr2:131099625-131099845(+)$1	1	6	9	9.0000
(((	chr8:124941086-124941336(+)$1	1	2	5	9.0000
...	chr2:80193507-80193727(+)$1	1	26	29	9.0000
(((	chr19:41843256-41843476(-)$1	1	26	29	9.0000
...	chr2:160772796-160773016(-)$1	1	53	56	9.0000
(((	chr19:21932008-21932229(+)$1	1	14	17	9.0000
(((	chr11:17166760-17166981(+)$1	1	29	32	9.0000
(((	chr2:28085819-28086039(+)$1	1	90	93	9.0000
(((	chr3:58326463-58326683(-)$1	1	17	20	9.0000
(((	chr1:34933900-34934121(+)$1	1	5	8	9.0000
.))	chr16:36034193-36034419(+)$1	1	136	139	9.0000
..(	chr6:113338916-113339137(+)$1	1	76	79	9.0000
...	chr19:23241163-23241383(+)$1	1	11	14	9.0000
..(	chr13:38071064-38071298(-)$1	1	20	23	9.0000
(((	chr1:46866395-46866667(-)$1	1	15	18	9.0000
.((	chr3:94986446-94986666(-)$1	1	0	3	9.0000
(((	chr5:108331007-108331234(+)$1	1	1	4	9.0000
(..	chr6:65064467-65064687(+)$1	1	10	13	9.0000
(((	chr2:131879107-131879327(-)$1	1	9	12	9.0000
...	chr16:17430645-17430865(+)$1	1	119	122	9.0000
...	chr4:41238315-41238535(-)$1	1	16	19	9.0000
..)	chr6:49290364-49290584(+)$1	1	23	26	9.0000
(((	chr9:20770479-20770701(-)$1	1	24	27	9.0000
...	chr10:82828916-82829136(+)$1	1	31	34	9.0000
(..	chr5:146006658-146006878(+)$1	1	13	16	9.0000
...	chr11:75461954-75462174(+)$1	1	0	3	9.0000
(((	chr11:77524371-77524591(+)$1	1	5	8	9.0000
)))	chr11:54923563-54923791(+)$1	1	100	103	9.0000
(((	chr3:95737799-95738019(+)$1	1	15	18	9.0000
..)	chr11:97697964-97698185(+)$1	1	23	26	9.0000
)).	chr11:72989668-72989888(-)$1	1	107	110	9.0000
(..	chr11:53234059-53234291(+)$1	1	7	10	9.0000
)))	chr17:34165348-34165571(-)$1	1	101	104	9.0000
...	chr4:134876474-134876694(-)$1	1	23	26	9.0000
..(	chr5:129709327-129709561(+)$1	1	34	37	9.0000
((.	chr15:102265700-102265920(+)$1	1	42	45	9.0000
(((	chr11:77349190-77349410(-)$1	1	3	6	9.0000
)))	chr6:38553226-38553458(+)$1	1	41	44	9.0000
(((	chr3:68819914-68820150(+)$1	1	37	40	9.0000
(((	chr17:23957017-23957237(+)$1	1	59	62	9.0000
((.	chr4:107545452-107545672(+)$1	1	25	28	9.0000
(((	chr12:45413007-45413227(+)$1	1	4	7	9.0000
)))	chr9:72860343-72860564(+)$1	1	18	21	9.0000
.((	chr11:3244445-3244665(-)$1	1	115	118	9.0000
)))	chr2:150409298-150409529(-)$1	1	75	78	9.0000
...	chr11:79748703-79748923(-)$1	1	3	6	9.0000
)))	chr14:47396098-47396318(-)$1	1	75	78	9.0000
)))	chr3:87726869-87727089(+)$1	1	34	37	9.0000
((.	chr13:47180390-47180610(-)$1	1	55	58	9.0000
(((	chr7:25673203-25673423(+)$1	1	41	44	9.0000
)((	chr18:31941192-31941412(+)$1	1	21	24	9.0000
...	chr11:30743425-30743658(+)$1	1	3	6	9.0000
(((	chr7:118199348-118199583(+)$1	1	21	24	9.0000
...	chr11:45958729-45958949(+)$1	1	1	4	9.0000
.((	chr12:9035318-9035538(+)$1	1	40	43	9.0000
...	chr9:94420122-94420345(-)$1	1	22	25	9.0000
...	chr17:27173053-27173273(+)$1	1	121	124	9.0000
(..	chr3:157668935-157669155(+)$1	1	11	14	9.0000
((.	chr18:7348176-7348397(-)$1	1	85	88	9.0000
.((	chr15:72935974-72936194(-)$1	1	20	23	9.0000
...	chr1:90161600-90161821(-)$1	1	31	34	9.0000
)))	chr11:35602096-35602317(+)$1	1	74	77	9.0000
(((	chr4:40683573-40683794(-)$1	1	13	16	9.0000
(((	chr9:67744857-67745078(+)$1	1	4	7	9.0000
)))	chr16:31665596-31665816(+)$1	1	42	45	9.0000
)))	chr5:135628805-135629025(+)$1	1	59	62	9.0000
...	chr16:58467213-58467433(+)$1	1	35	38	9.0000
...	chr1:182797999-182798219(+)$1	1	12	15	9.0000
(((	chr9:21507332-21507573(+)$1	1	29	32	9.0000
..(	chr5:76051652-76051872(+)$1	1	54	57	9.0000
...	chr15:41690638-41690876(+)$1	1	60	63	9.0000
(((	chr2:3375526-3375746(-)$1	1	21	24	9.0000
(..	chr4:125388480-125388700(+)$1	1	143	146	9.0000
(((	chr7:129225470-129225690(+)$1	1	3	6	9.0000
...	chr6:29324337-29324559(+)$1	1	4	7	9.0000
).)	chr18:61290886-61291106(-)$1	1	116	119	9.0000
...	chr17:5411224-5411445(-)$1	1	11	14	9.0000
...	chr14:51547350-51547588(-)$1	1	11	14	9.0000
)))	chr8:88062522-88062749(-)$1	1	37	40	9.0000

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

#score	855.0000000000002
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m3_run1.nuc.txt

#NT
CUUAGAAAAA	chr2:68949333-68949564(+)$1	231	39	49	14.3103
UUUAAAAAAG	chr7:81086124-81086365(-)$1	241	145	155	18.9655
AUUAAAAAUA	chr16:37886381-37886613(+)$1	232	97	107	15.8620
UUGAAAAAAA	chr2:115688886-115689153(-)$1	267	115	125	18.0172
AUUaaagaaa	chr18:43480539-43480884(-)$1	345	156	166	15.8620
AUUAAUAAAA	chr6:30698296-30698535(+)$1	239	139	149	15.0862
UUUAAAGAAA	chrX:102992857-102993108(-)$1	251	51	61	19.0517
UUUAAACAAU	chr5:92482306-92482545(-)$1	239	181	191	15.2586
UUUAAAAACA	chr9:24912987-24913310(-)$1	323	91	101	19.0517
auuaaaaaaa	chr16:42248604-42248905(-)$1	301	227	237	19.3103
AUUAAAAAAA	chr9:28732430-28732675(+)$1	245	198	208	19.3103
UUUAAAGACA	chr5:93602167-93602399(+)$1	232	50	60	15.6034
uuGAAAAAAA	chr4:53873622-53873853(+)$1	231	19	29	18.0172
UCUAAAGAAA	chr13:64001448-64001692(+)$1	244	12	22	14.3965
UUUAAAAAAA	chr16:78338888-78339143(+)$1	255	231	241	22.5000
CUUAAAAGAA	chr16:30314453-30314809(-)$1	356	205	215	15.0862
uuuaaaauau	chr13:100789354-100789592(-)$1	238	34	44	15.0000
UUUACAAAGA	chr15:79504620-79504863(-)$1	243	133	143	14.4827
UUUGAAUAAA	chr3:95751124-95751396(+)$1	272	158	168	15.1724
UUUAAAAAAC	chr1:60041406-60041691(+)$1	285	32	42	18.7931
UUUAAAGAAA	chrX:68813511-68813777(+)$1	266	143	153	19.0517
uuuaaaaaaa	chr9:86659930-86660161(-)$1	231	112	122	22.5000
UUUUAAACAA	chr3:100368641-100368872(-)$1	231	136	146	14.9137
AUUAAAAAAA	chr11:54530931-54531202(-)$1	271	196	206	19.3103
UUUAAAAAUG	chr15:7145886-7146145(+)$1	259	28	38	15.5172
UUUAAAAAAA	chr7:29959175-29959412(-)$1	237	97	107	22.5000
uuuuAAAGAA	chr19:54003512-54003767(+)$1	255	240	250	15.1724
UGUAAAACAA	chr3:148479615-148479848(-)$1	233	0	10	13.9655
UUUAUAAGAA	chr15:34071537-34071779(+)$1	242	8	18	14.3965
CUUAAAAACA	chr13:89459542-89459790(+)$1	248	184	194	15.3448
UGUAAAUAAA	chr13:55781279-55781510(+)$1	231	165	175	14.4827
UUUCAAAAAC	chr8:72618062-72618316(-)$1	254	181	191	14.7413
AUUAAAAAAA	chr4:13819938-13820172(+)$1	234	198	208	19.3103
AUUAAAAAAA	chr4:109877164-109877414(-)$1	250	164	174	19.3103
UUUAAGCAAA	chr7:17080330-17080582(-)$1	252	137	147	14.4827
UUUAAAAACA	chrX:101157386-101157664(-)$1	278	15	25	19.0517
UUUGACAAAA	chr5:143665031-143665446(-)$1	415	5	15	14.3103
UUUUAAAAAA	chr4:153532001-153532237(-)$1	236	115	125	18.8793
UUUUUAAAAA	chr9:113827403-113827647(+)$1	244	113	123	14.4827
AUUAAAaaac	chr9:109905814-109906048(-)$1	234	35	45	15.6034
UUUAAACUAA	chr18:10560844-10561075(-)$1	231	47	57	15.0000
UUUAAAAGAU	chr2:90853630-90853961(+)$1	331	258	268	15.1724
UUUAAAAAUG	chr11:45864957-45865215(-)$1	258	236	246	15.5172
UUUGAAAAGA	chrX:155936397-155936646(+)$1	249	150	160	15.0000
UUUAACAAUA	chr10:9478110-9478341(-)$1	231	9	19	14.7413
UUUAAAUAAA	chrX:91433963-91434213(-)$1	250	138	148	19.0517
UUUUAAAAAG	chr9:112136158-112136389(-)$1	231	96	106	15.3448
UUUAAAAAAA	chr2:104269645-104269915(-)$1	270	51	61	22.5000
UUUAAAUAGA	chr6:100178470-100178732(-)$1	262	107	117	15.4310
uuuuaaaaaa	chr1:52244033-52244264(-)$1	231	39	49	18.8793
UUGaaaaaaa	chr11:24068150-24068489(+)$1	339	255	265	18.0172
UUUAAAUACA	chr16:24981999-24982270(+)$1	271	173	183	15.6034
UUUAAUAAAA	chr5:75397045-75397316(-)$1	271	246	256	18.2758
uuuaaaauaa	chr10:123176692-123176924(+)$1	232	171	181	18.6206
UUUACAAAAG	chr10:22425319-22425551(-)$1	232	134	144	14.5689
uuuaauaaua	chr12:54249327-54249558(+)$1	231	6	16	14.8275
uuuaaaaaau	chr19:44378262-44378576(+)$1	314	141	151	18.8793

#otherMatches

#Struct PSSM
gglllggggg	chr8:13019845-13020081(+)$1	236	78	88	18.7931
mmmmdddd::	chr2:68949333-68949564(+)$1	231	39	49	14.3103
EE::::::::	chr7:81086124-81086365(-)$1	241	145	155	18.9655
hhhhh:::::	chr16:37886381-37886613(+)$1	232	97	107	15.8620
2eeeee6666	chr2:115688886-115689153(-)$1	267	115	125	18.0172
>>>>>>>>>>	chr18:43480539-43480884(-)$1	345	156	166	15.8620
EEE:::::::	chr6:30698296-30698535(+)$1	239	139	149	15.0862
))))))))gg	chrX:102992857-102993108(-)$1	251	51	61	19.0517
::::hhhhhh	chr5:92482306-92482545(-)$1	239	181	191	15.2586
:ggggggg[b	chr9:24912987-24913310(-)$1	323	91	101	19.0517
::::::::::	chr16:42248604-42248905(-)$1	301	227	237	19.3103
EEEEE@@@@@	chr9:28732430-28732675(+)$1	245	198	208	19.3103
uuuuuuuuuu	chr5:93602167-93602399(+)$1	232	50	60	15.6034
Dggggggg[b	chr4:53873622-53873853(+)$1	231	19	29	18.0172
"""dddd###	chr13:64001448-64001692(+)$1	244	12	22	14.3965
FFF@@@@@@@	chr16:78338888-78339143(+)$1	255	231	241	22.5000
c::GGGGGGG	chr16:30314453-30314809(-)$1	356	205	215	15.0862
::::::::::	chr13:100789354-100789592(-)$1	238	34	44	15.0000
eeee&&&&&&	chr15:79504620-79504863(-)$1	243	133	143	14.4827
EEEE:::::h	chr3:95751124-95751396(+)$1	272	158	168	15.1724
ffff22hhhh	chr1:60041406-60041691(+)$1	285	32	42	18.7931
]gggggggdd	chrX:68813511-68813777(+)$1	266	143	153	19.0517
hhhnnnnnhh	chr9:86659930-86660161(-)$1	231	112	122	22.5000
II:::::::b	chr3:100368641-100368872(-)$1	231	136	146	14.9137
:::::::iii	chr11:54530931-54531202(-)$1	271	196	206	19.3103
KCCC{HHHHH	chr15:7145886-7146145(+)$1	259	28	38	15.5172
e:::::::::	chr7:29959175-29959412(-)$1	237	97	107	22.5000
ooooffffff	chr19:54003512-54003767(+)$1	255	240	250	15.1724
::iiiiiiii	chr3:148479615-148479848(-)$1	233	0	10	13.9655
:eeeee[bbm	chr15:34071537-34071779(+)$1	242	8	18	14.3965
>>>>>>>>ff	chr13:89459542-89459790(+)$1	248	184	194	15.3448
========[g	chr13:55781279-55781510(+)$1	231	165	175	14.4827
^^^^^^^^^^	chr8:72618062-72618316(-)$1	254	181	191	14.7413
::::::::::	chr4:13819938-13820172(+)$1	234	198	208	19.3103
f:::::::::	chr4:109877164-109877414(-)$1	250	164	174	19.3103
ggggggarrr	chr7:17080330-17080582(-)$1	252	137	147	14.4827
:::::::fff	chrX:101157386-101157664(-)$1	278	15	25	19.0517
:::HHHHHHH	chr5:143665031-143665446(-)$1	415	5	15	14.3103
e$$$$$ccc[	chr4:153532001-153532237(-)$1	236	115	125	18.8793
^^^^^^^^ii	chr9:113827403-113827647(+)$1	244	113	123	14.4827
::::::::::	chr9:109905814-109906048(-)$1	234	35	45	15.6034
eee:::::::	chr18:10560844-10561075(-)$1	231	47	57	15.0000
?????GGGGG	chr2:90853630-90853961(+)$1	331	258	268	15.1724
@HHHHHHHHI	chr11:45864957-45865215(-)$1	258	236	246	15.5172
IIIII:::::	chrX:155936397-155936646(+)$1	249	150	160	15.0000
::::::::::	chr10:9478110-9478341(-)$1	231	9	19	14.7413
YYEEEEE}GG	chrX:91433963-91434213(-)$1	250	138	148	19.0517
::::::::hh	chr9:112136158-112136389(-)$1	231	96	106	15.3448
cccmmmmccc	chr2:104269645-104269915(-)$1	270	51	61	22.5000
eee]eeeee4	chr6:100178470-100178732(-)$1	262	107	117	15.4310
hhhhhhhhdd	chr1:52244033-52244264(-)$1	231	39	49	18.8793
JJJJJJJJJH	chr11:24068150-24068489(+)$1	339	255	265	18.0172
::::::::::	chr16:24981999-24982270(+)$1	271	173	183	15.6034
::::::::::	chr5:75397045-75397316(-)$1	271	246	256	18.2758
gg:FFFFFFY	chr10:123176692-123176924(+)$1	232	171	181	18.6206
%%%%%ccc[c	chr10:22425319-22425551(-)$1	232	134	144	14.5689
JJJJJJJDDD	chr12:54249327-54249558(+)$1	231	6	16	14.8275
d:::::::gg	chr19:44378262-44378576(+)$1	314	141	151	18.8793

#DB
((...)))))	chr8:13019845-13020081(+)$1	1	78	88	18.7931
....))))..	chr2:68949333-68949564(+)$1	1	39	49	14.3103
((........	chr7:81086124-81086365(-)$1	1	145	155	18.9655
))))).....	chr16:37886381-37886613(+)$1	1	97	107	15.8620
.)))))....	chr2:115688886-115689153(-)$1	1	115	125	18.0172
..........	chr18:43480539-43480884(-)$1	1	156	166	15.8620
))).......	chr6:30698296-30698535(+)$1	1	139	149	15.0862
........((	chrX:102992857-102993108(-)$1	1	51	61	19.0517
....((((((	chr5:92482306-92482545(-)$1	1	181	191	15.2586
.(((((((.(	chr9:24912987-24913310(-)$1	1	91	101	19.0517
..........	chr16:42248604-42248905(-)$1	1	227	237	19.3103
))))).....	chr9:28732430-28732675(+)$1	1	198	208	19.3103
..........	chr5:93602167-93602399(+)$1	1	50	60	15.6034
((((((((.(	chr4:53873622-53873853(+)$1	1	19	29	18.0172
...((((...	chr13:64001448-64001692(+)$1	1	12	22	14.3965
))).......	chr16:78338888-78339143(+)$1	1	231	241	22.5000
)..)))))))	chr16:30314453-30314809(-)$1	1	205	215	15.0862
..........	chr13:100789354-100789592(-)$1	1	34	44	15.0000
((((......	chr15:79504620-79504863(-)$1	1	133	143	14.4827
)))).....(	chr3:95751124-95751396(+)$1	1	158	168	15.1724
))))..))))	chr1:60041406-60041691(+)$1	1	32	42	18.7931
.)))))))))	chrX:68813511-68813777(+)$1	1	143	153	19.0517
(((.....))	chr9:86659930-86660161(-)$1	1	112	122	22.5000
)).......(	chr3:100368641-100368872(-)$1	1	136	146	14.9137
.......(((	chr11:54530931-54531202(-)$1	1	196	206	19.3103
.(((.(((((	chr15:7145886-7146145(+)$1	1	28	38	15.5172
).........	chr7:29959175-29959412(-)$1	1	97	107	22.5000
....))))))	chr19:54003512-54003767(+)$1	1	240	250	15.1724
..((((((((	chr3:148479615-148479848(-)$1	1	0	10	13.9655
.(((((.((.	chr15:34071537-34071779(+)$1	1	8	18	14.3965
........))	chr13:89459542-89459790(+)$1	1	184	194	15.3448
((((((((.(	chr13:55781279-55781510(+)$1	1	165	175	14.4827
..........	chr8:72618062-72618316(-)$1	1	181	191	14.7413
..........	chr4:13819938-13820172(+)$1	1	198	208	19.3103
).........	chr4:109877164-109877414(-)$1	1	164	174	19.3103
(((((((...	chr7:17080330-17080582(-)$1	1	137	147	14.4827
.......(((	chrX:101157386-101157664(-)$1	1	15	25	19.0517
...(((((((	chr5:143665031-143665446(-)$1	1	5	15	14.3103
(.....(((.	chr4:153532001-153532237(-)$1	1	115	125	18.8793
........))	chr9:113827403-113827647(+)$1	1	113	123	14.4827
..........	chr9:109905814-109906048(-)$1	1	35	45	15.6034
))).......	chr18:10560844-10561075(-)$1	1	47	57	15.0000
.....)))))	chr2:90853630-90853961(+)$1	1	258	268	15.1724
.)))))))))	chr11:45864957-45865215(-)$1	1	236	246	15.5172
(((((.....	chrX:155936397-155936646(+)$1	1	150	160	15.0000
..........	chr10:9478110-9478341(-)$1	1	9	19	14.7413
..))))).))	chrX:91433963-91434213(-)$1	1	138	148	19.0517
........((	chr9:112136158-112136389(-)$1	1	96	106	15.3448
(((....)))	chr2:104269645-104269915(-)$1	1	51	61	22.5000
))).))))).	chr6:100178470-100178732(-)$1	1	107	117	15.4310
))))))))((	chr1:52244033-52244264(-)$1	1	39	49	18.8793
))))))))))	chr11:24068150-24068489(+)$1	1	255	265	18.0172
..........	chr16:24981999-24982270(+)$1	1	173	183	15.6034
..........	chr5:75397045-75397316(-)$1	1	246	256	18.2758
)).)))))).	chr10:123176692-123176924(+)$1	1	171	181	18.6206
.....(((.(	chr10:22425319-22425551(-)$1	1	134	144	14.5689
((((((((((	chr12:54249327-54249558(+)$1	1	6	16	14.8275
).......((	chr19:44378262-44378576(+)$1	1	141	151	18.8793

#PSSM
U : 0.65	A : 0.13	u : 0.13	C : 0.05	a : 0.01	
U : 0.79	u : 0.15	G : 0.03	C : 0.01	
U : 0.81	u : 0.13	G : 0.05	
A : 0.68	a : 0.13	U : 0.06	G : 0.05	u : 0.03	C : 0.01	
A : 0.75	a : 0.15	C : 0.03	U : 0.03	G : 0.01	
A : 0.75	a : 0.13	U : 0.03	C : 0.03	G : 0.01	u : 0.01	
A : 0.62	a : 0.15	U : 0.08	G : 0.06	C : 0.05	g : 0.01	
A : 0.68	a : 0.13	G : 0.08	u : 0.03	C : 0.03	U : 0.01	
A : 0.62	a : 0.15	C : 0.08	U : 0.06	G : 0.05	u : 0.01	
A : 0.67	a : 0.12	G : 0.08	U : 0.03	u : 0.03	C : 0.03	c : 0.01	

#score	980.6896551724136
#seq	58
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_UTR_m1_run1.nuc.txt

#NT
UUGGGGG	chr10:126908696-126908973(+)$1	277	81	88	12.9827
GUGGUGG	chr2:152106630-152106912(+)$1	282	55	62	13.5000
UUGGGGG	chr12:66162687-66162968(+)$1	281	134	141	12.9827
GUGGGAG	chr15:82987834-82988122(-)$1	288	181	188	12.4655
GAGGGGG	chr5:93605039-93605342(+)$1	303	138	145	12.8965
GUGUGGG	chr10:90623775-90624054(-)$1	279	123	130	12.9827
GUGUGGG	chr8:90781397-90781677(+)$1	280	93	100	12.9827
GUGUGGG	chr8:123178707-123179019(-)$1	312	149	156	12.9827
GUUGGGG	chr4:155540084-155540375(-)$1	291	157	164	12.2931
GUGGGGG	chr8:109900741-109901013(+)$1	272	26	33	17.0344
GUGGUGG	chr8:81033350-81033629(+)$1	279	171	178	13.5000
GUGGGGG	chr16:17278213-17278492(+)$1	279	132	139	17.0344
GUGGAGG	chr1:158577130-158577409(+)$1	279	127	134	13.5862
GUGGGGA	chr7:114514377-114514659(+)$1	282	24	31	12.8965
GUGGAGG	chr6:146551804-146552085(-)$1	281	132	139	13.5862
GUGCGGG	chr2:172860016-172860295(+)$1	279	90	97	12.8965
GUGGGAG	chr9:106365956-106366241(+)$1	285	78	85	12.4655
GUGGGGG	chr4:117880932-117881204(-)$1	272	127	134	17.0344
GAGGGGG	chr14:55195953-55196245(-)$1	292	114	121	12.8965
GUGGGGG	chr4:132752782-132753084(+)$1	302	39	46	17.0344
GUGGGGA	chr14:54860843-54861122(-)$1	279	143	150	12.8965
GUGGUGG	chr13:54782522-54782867(-)$1	345	87	94	13.5000
UUGGGGG	chr5:124824063-124824418(-)$1	355	2	9	12.9827
GUGGGGG	chr2:14917596-14917874(-)$1	278	87	94	17.0344
GUGGGGU	chr7:52488648-52488937(+)$1	289	4	11	12.8965
GUGGCGG	chr17:27717443-27717753(-)$1	310	160	167	13.1551
GCGGGGG	chr8:109619993-109620277(-)$1	284	129	136	12.9827
gucgggg	chr10:82831346-82831638(+)$1	292	156	163	12.2931
CUGGGGG	chr8:93741930-93742207(-)$1	277	127	134	12.8965
GUGGGGG	chr7:26452796-26453085(+)$1	289	151	158	17.0344
cuggggg	chr4:118898107-118898386(-)$1	279	172	179	12.8965
GAGGGGG	chr1:62863892-62864169(+)$1	277	222	229	12.8965
GCGGGGG	chr18:31881884-31882165(+)$1	281	147	154	12.9827
GUGGUGG	chr11:102025171-102025454(-)$1	283	111	118	13.5000
GUGCGGG	chr15:80761597-80761877(+)$1	280	144	151	12.8965
GUGGAGG	chr18:37454496-37454769(+)$1	273	241	248	13.5862
GUGGGCG	chr13:55418873-55419160(+)$1	287	146	153	12.3793
GUGGGGG	chr11:97947146-97947497(-)$1	351	131	138	17.0344
GUGGUGG	chr9:53915911-53916180(-)$1	269	73	80	13.5000
GUGGAGG	chr9:86446780-86447056(-)$1	276	184	191	13.5862
gcggggg	chr12:52792436-52792714(-)$1	278	142	149	12.9827
GUGGGGG	chr16:44140093-44140361(+)$1	268	156	163	17.0344
GUGGGGC	chr7:38979927-38980199(+)$1	272	79	86	12.7241
cuggggg	chr2:73401534-73401804(-)$1	270	168	175	12.8965
GUGAGGG	chr5:136384732-136385109(-)$1	377	127	134	12.9827
GUGGAGG	chr9:59526684-59526984(+)$1	300	149	156	13.5862
GUGAGGG	chr18:10816334-10816605(+)$1	271	95	102	12.9827
GUGAGGG	chr4:128266670-128266939(-)$1	269	21	28	12.9827
GUGGAGG	chr19:32895242-32895510(+)$1	268	110	117	13.5862
GCGGGGG	chr10:79619891-79620171(+)$1	280	182	189	12.9827
GUGGGGU	chr3:87340505-87340851(+)$1	346	143	150	12.8965
GUGGGGG	chr14:68372698-68372967(-)$1	269	104	111	17.0344
GUGGGGA	chr6:122679559-122679898(-)$1	339	3	10	12.8965
UUGGGGG	chr5:114893821-114894117(-)$1	296	133	140	12.9827
GUGGGGG	chr11:118146006-118146295(-)$1	289	139	146	17.0344
GUGGGGG	chr14:55503587-55503878(+)$1	291	52	59	17.0344
GUGGGGG	chr5:135813334-135813602(-)$1	268	229	236	17.0344

#otherMatches

#Struct PSSM
gg::DDD	chr11:72893364-72893639(+)$1	275	16	23	12.8965
rr=====	chr10:126908696-126908973(+)$1	277	81	88	12.9827
iiiiggg	chr2:152106630-152106912(+)$1	282	55	62	13.5000
FFFFFee	chr12:66162687-66162968(+)$1	281	134	141	12.9827
D}FFFFF	chr15:82987834-82988122(-)$1	288	181	188	12.4655
2ddddFF	chr5:93605039-93605342(+)$1	303	138	145	12.8965
###ccc!	chr10:90623775-90624054(-)$1	279	123	130	12.9827
:ccc[bb	chr8:90781397-90781677(+)$1	280	93	100	12.9827
DD}A}CC	chr8:123178707-123179019(-)$1	312	149	156	12.9827
I::eeee	chr4:155540084-155540375(-)$1	291	157	164	12.2931
gg:DDDD	chr8:109900741-109901013(+)$1	272	26	33	17.0344
hhhhhh[	chr8:81033350-81033629(+)$1	279	171	178	13.5000
=======	chr16:17278213-17278492(+)$1	279	132	139	17.0344
=======	chr1:158577130-158577409(+)$1	279	127	134	13.5862
ee:CCCK	chr7:114514377-114514659(+)$1	282	24	31	12.8965
c]bb22h	chr6:146551804-146552085(-)$1	281	132	139	13.5862
cc]ccc]	chr2:172860016-172860295(+)$1	279	90	97	12.8965
&&&gggg	chr9:106365956-106366241(+)$1	285	78	85	12.4655
g22eeee	chr4:117880932-117881204(-)$1	272	127	134	17.0344
cccffff	chr14:55195953-55196245(-)$1	292	114	121	12.8965
g[=====	chr4:132752782-132753084(+)$1	302	39	46	17.0344
edddd44	chr14:54860843-54861122(-)$1	279	143	150	12.8965
mccc]bb	chr13:54782522-54782867(-)$1	345	87	94	13.5000
GGGGGGG	chr5:124824063-124824418(-)$1	355	2	9	12.9827
==]a::H	chr2:14917596-14917874(-)$1	278	87	94	17.0344
HHHHHHH	chr7:52488648-52488937(+)$1	289	4	11	12.8965
CYYBBYY	chr17:27717443-27717753(-)$1	310	160	167	13.1551
eeecccm	chr8:109619993-109620277(-)$1	284	129	136	12.9827
GYYCCCE	chr10:82831346-82831638(+)$1	292	156	163	12.2931
ee]eeee	chr8:93741930-93742207(-)$1	277	127	134	12.8965
EEEEiii	chr7:26452796-26453085(+)$1	289	151	158	17.0344
bffffff	chr4:118898107-118898386(-)$1	279	172	179	12.8965
gggggg2	chr1:62863892-62864169(+)$1	277	222	229	12.8965
[bb"""g	chr18:31881884-31882165(+)$1	281	147	154	12.9827
eeeeecc	chr11:102025171-102025454(-)$1	283	111	118	13.5000
g[bb[dd	chr15:80761597-80761877(+)$1	280	144	151	12.8965
nnnnndd	chr18:37454496-37454769(+)$1	273	241	248	13.5862
ffff22d	chr13:55418873-55419160(+)$1	287	146	153	12.3793
cc]ccc]	chr11:97947146-97947497(-)$1	351	131	138	17.0344
hhhhh$$	chr9:53915911-53916180(-)$1	269	73	80	13.5000
b[fffff	chr9:86446780-86447056(-)$1	276	184	191	13.5862
[======	chr12:52792436-52792714(-)$1	278	142	149	12.9827
[annnnn	chr16:44140093-44140361(+)$1	268	156	163	17.0344
hhhhhhh	chr7:38979927-38980199(+)$1	272	79	86	12.7241
dd]dddd	chr2:73401534-73401804(-)$1	270	168	175	12.8965
bb]eeee	chr5:136384732-136385109(-)$1	377	127	134	12.9827
ffff]bb	chr9:59526684-59526984(+)$1	300	149	156	13.5862
hhfffff	chr18:10816334-10816605(+)$1	271	95	102	12.9827
IIIIFFF	chr4:128266670-128266939(-)$1	269	21	28	12.9827
eeee:FF	chr19:32895242-32895510(+)$1	268	110	117	13.5862
hhhhhhh	chr10:79619891-79620171(+)$1	280	182	189	12.9827
ccc[fff	chr3:87340505-87340851(+)$1	346	143	150	12.8965
:::eeee	chr14:68372698-68372967(-)$1	269	104	111	17.0344
ffffff[	chr6:122679559-122679898(-)$1	339	3	10	12.8965
lllhhhh	chr5:114893821-114894117(-)$1	296	133	140	12.9827
eee]aff	chr11:118146006-118146295(-)$1	289	139	146	17.0344
ggggggg	chr14:55503587-55503878(+)$1	291	52	59	17.0344
hhhhhhl	chr5:135813334-135813602(-)$1	268	229	236	17.0344

#DB
))..(((	chr11:72893364-72893639(+)$1	1	16	23	12.8965
..)))))	chr10:126908696-126908973(+)$1	1	81	88	12.9827
))))(((	chr2:152106630-152106912(+)$1	1	55	62	13.5000
(((((((	chr12:66162687-66162968(+)$1	1	134	141	12.9827
).)))))	chr15:82987834-82988122(-)$1	1	181	188	12.4655
.))))))	chr5:93605039-93605342(+)$1	1	138	145	12.8965
...(((.	chr10:90623775-90624054(-)$1	1	123	130	12.9827
.(((.((	chr8:90781397-90781677(+)$1	1	93	100	12.9827
)).).))	chr8:123178707-123179019(-)$1	1	149	156	12.9827
)..((((	chr4:155540084-155540375(-)$1	1	157	164	12.2931
)).((((	chr8:109900741-109901013(+)$1	1	26	33	17.0344
((((((.	chr8:81033350-81033629(+)$1	1	171	178	13.5000
)))))))	chr16:17278213-17278492(+)$1	1	132	139	17.0344
(((((((	chr1:158577130-158577409(+)$1	1	127	134	13.5862
)).(((.	chr7:114514377-114514659(+)$1	1	24	31	12.8965
).))..)	chr6:146551804-146552085(-)$1	1	132	139	13.5862
)).))).	chr2:172860016-172860295(+)$1	1	90	97	12.8965
...((((	chr9:106365956-106366241(+)$1	1	78	85	12.4655
)..))))	chr4:117880932-117881204(-)$1	1	127	134	17.0344
)))((((	chr14:55195953-55196245(-)$1	1	114	121	12.8965
(.(((((	chr4:132752782-132753084(+)$1	1	39	46	17.0344
)))))..	chr14:54860843-54861122(-)$1	1	143	150	12.8965
.))).))	chr13:54782522-54782867(-)$1	1	87	94	13.5000
(((((((	chr5:124824063-124824418(-)$1	1	2	9	12.9827
)).)..(	chr2:14917596-14917874(-)$1	1	87	94	17.0344
(((((((	chr7:52488648-52488937(+)$1	1	4	11	12.8965
)..))..	chr17:27717443-27717753(-)$1	1	160	167	13.1551
)))(((.	chr8:109619993-109620277(-)$1	1	129	136	12.9827
)..)))(	chr10:82831346-82831638(+)$1	1	156	163	12.2931
)).))))	chr8:93741930-93742207(-)$1	1	127	134	12.8965
))))(((	chr7:26452796-26453085(+)$1	1	151	158	17.0344
(((((((	chr4:118898107-118898386(-)$1	1	172	179	12.8965
)))))).	chr1:62863892-62864169(+)$1	1	222	229	12.8965
.((...(	chr18:31881884-31882165(+)$1	1	147	154	12.9827
)))))((	chr11:102025171-102025454(-)$1	1	111	118	13.5000
(.((.((	chr15:80761597-80761877(+)$1	1	144	151	12.8965
.....))	chr18:37454496-37454769(+)$1	1	241	248	13.5862
))))..)	chr13:55418873-55419160(+)$1	1	146	153	12.3793
)).))).	chr11:97947146-97947497(-)$1	1	131	138	17.0344
(((((..	chr9:53915911-53916180(-)$1	1	73	80	13.5000
(.(((((	chr9:86446780-86447056(-)$1	1	184	191	13.5862
.((((((	chr12:52792436-52792714(-)$1	1	142	149	12.9827
.(.....	chr16:44140093-44140361(+)$1	1	156	163	17.0344
)))))))	chr7:38979927-38980199(+)$1	1	79	86	12.7241
)).))))	chr2:73401534-73401804(-)$1	1	168	175	12.8965
)).))))	chr5:136384732-136385109(-)$1	1	127	134	12.9827
)))).))	chr9:59526684-59526984(+)$1	1	149	156	13.5862
))(((((	chr18:10816334-10816605(+)$1	1	95	102	12.9827
(((((((	chr4:128266670-128266939(-)$1	1	21	28	12.9827
)))).((	chr19:32895242-32895510(+)$1	1	110	117	13.5862
(((((((	chr10:79619891-79620171(+)$1	1	182	189	12.9827
(((.(((	chr3:87340505-87340851(+)$1	1	143	150	12.8965
...((((	chr14:68372698-68372967(-)$1	1	104	111	17.0344
((((((.	chr6:122679559-122679898(-)$1	1	3	10	12.8965
...))))	chr5:114893821-114894117(-)$1	1	133	140	12.9827
))).)((	chr11:118146006-118146295(-)$1	1	139	146	17.0344
(((((((	chr14:55503587-55503878(+)$1	1	52	59	17.0344
((((((.	chr5:135813334-135813602(-)$1	1	229	236	17.0344

#PSSM
G : 0.84	U : 0.06	g : 0.03	c : 0.03	C : 0.01	
U : 0.82	A : 0.05	C : 0.05	u : 0.05	c : 0.01	
G : 0.91	g : 0.05	U : 0.01	c : 0.01	
G : 0.79	g : 0.06	U : 0.05	A : 0.05	C : 0.03	
G : 0.72	A : 0.10	U : 0.08	g : 0.06	C : 0.01	
G : 0.87	g : 0.06	A : 0.03	C : 0.01	
G : 0.81	g : 0.06	U : 0.05	A : 0.05	C : 0.01	

#score	803.5172413793107
#seq	58
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m3_run1.nuc.txt

#NT
ugugugugugugu	chr12:106854477-106854945(-)$1	468	202	215	35.7391
ugugugugugugu	chr3:151898486-151898955(+)$1	469	228	241	35.7391
UAUCUGUGUGUGU	chr17:10407877-10408240(-)$1	363	270	283	26.7173
ugugugugugugu	chr6:40196703-40197118(+)$1	415	112	125	35.7391
UGUGUGUGUGUGU	chr8:42004296-42004725(+)$1	429	208	221	35.7391
UGUGUGUGUGUGU	chr16:10530021-10530508(-)$1	487	234	247	35.7391
UGUCUGUGUGUGG	chr9:61220148-61220516(+)$1	368	83	96	26.8260
ugugugugugugu	chr11:107533108-107533526(+)$1	418	288	301	35.7391
UGUAUGUGUGUGU	chr3:81898081-81898341(-)$1	260	92	105	31.1739
ugugugugugugu	chr7:24866875-24867295(+)$1	420	90	103	35.7391
UGUGUUUGUGUUU	chr11:87032688-87032989(+)$1	301	69	82	26.3913
UGUGUGUGUGUGU	chr14:56500932-56501241(-)$1	309	100	113	35.7391
ugugugugugugu	chr11:74483263-74483592(+)$1	329	147	160	35.7391
UGAGUGUGUGUGU	chr7:116174028-116174306(+)$1	278	122	135	31.0652
ugcgugugugugu	chr9:120083248-120083588(+)$1	340	157	170	31.0652
UGUGUGUAUGUGU	chr16:35002206-35002544(+)$1	338	140	153	31.6086
UGUGCGAGUGUGU	chr9:75417696-75418175(-)$1	479	313	326	26.7173
ugugugugugugu	chr16:94631108-94631606(+)$1	498	476	489	35.7391
ugugugugugugu	chr15:3532386-3532776(-)$1	390	98	111	35.7391
UGUGUGCGUGUGU	chr2:127124290-127124753(+)$1	463	221	234	31.3913
ugugugugugugu	chr2:26875211-26875634(+)$1	423	35	48	35.7391
ugugugugugugu	chr5:30111583-30111813(+)$1	230	100	113	35.7391
ugugugugugugu	chr3:60812603-60812882(+)$1	279	143	156	35.7391
UGUGUGUGGAUGU	chr14:71064675-71065047(-)$1	372	216	229	26.3913
ugugugugugugu	chr7:128048649-128048970(+)$1	321	199	212	35.7391
UGUGUGUGUGUGG	chr11:117019229-117019697(+)$1	468	403	416	31.2826
ugugugugugugu	chr11:94150929-94151394(-)$1	465	225	238	35.7391
ugugugugugugu	chr3:22114031-22114320(+)$1	289	51	64	35.7391
ugugugcgugugu	chr3:30408431-30408709(-)$1	278	151	164	31.3913
UGUGUGUAUGUGU	chr4:48675343-48675669(+)$1	326	106	119	31.6086
uguguguguguuu	chr6:40196405-40196903(+)$1	498	414	427	31.1739
AGUGUGUGUGUGU	chrX:70904601-70905043(-)$1	442	299	312	31.1739
ugugugugugugu	chr9:121383026-121383493(+)$1	467	355	368	35.7391
ugugugugugugu	chr12:68322051-68322546(-)$1	495	215	228	35.7391
UGUGUGUAUGUGU	chr6:71763741-71763977(-)$1	236	86	99	31.6086
ugugugugugugu	chr1:132594025-132594486(-)$1	461	362	375	35.7391
ugugugugugagu	chr6:121324320-121324809(-)$1	489	231	244	30.9565
UUUGUGAGUGUGU	chr6:71340154-71340449(-)$1	295	165	178	26.9347
UGUGUGUGUGUGU	chr8:87195546-87195823(-)$1	277	152	165	35.7391
UGUGGGUGGGUGU	chr11:72017071-72017313(-)$1	242	93	106	26.4999
ugugugugugugu	chr18:34930992-34931443(+)$1	451	30	43	35.7391
uuugugugugugu	chr2:118614445-118614790(+)$1	345	90	103	31.2826
UGUGUGUGUGUGU	chr17:37210491-37210988(+)$1	497	245	258	35.7391
ugugugugugugu	chr4:57906975-57907465(+)$1	490	229	242	35.7391
AGUGUGUGUGUGC	chr16:42248663-42249106(-)$1	443	317	330	26.6086

#otherMatches

#Struct PSSM
iiiiiiiiooooo	chr9:106590818-106591076(-)$1	258	83	96	31.6086
EEEE:eeeee###	chr12:106854477-106854945(-)$1	468	202	215	35.7391
nndddd]dddd::	chr3:151898486-151898955(+)$1	469	228	241	35.7391
bb!!ccc[dddd[	chr17:10407877-10408240(-)$1	363	270	283	26.7173
ccc]a]aBB}CCC	chr6:40196703-40197118(+)$1	415	112	125	35.7391
mffffff22====	chr8:42004296-42004725(+)$1	429	208	221	35.7391
E:::A{CCC{A{F	chr16:10530021-10530508(-)$1	487	234	247	35.7391
::::::::eeeee	chr9:61220148-61220516(+)$1	368	83	96	26.8260
:::::::::::::	chr11:107533108-107533526(+)$1	418	288	301	35.7391
b[cccddddhhhh	chr3:81898081-81898341(-)$1	260	92	105	31.1739
ee22ccc::::bb	chr7:24866875-24867295(+)$1	420	90	103	35.7391
:::::::dddd!!	chr11:87032688-87032989(+)$1	301	69	82	26.3913
d[ggggggg[ccc	chr14:56500932-56501241(-)$1	309	100	113	35.7391
bmmmmbb]ccc44	chr11:74483263-74483592(+)$1	329	147	160	35.7391
fffffff[ddddm	chr7:116174028-116174306(+)$1	278	122	135	31.0652
:============	chr9:120083248-120083588(+)$1	340	157	170	31.0652
ppppppphhhhhh	chr16:35002206-35002544(+)$1	338	140	153	31.6086
333eeeee:dddd	chr9:75417696-75418175(-)$1	479	313	326	26.7173
eeeee:::CCC}E	chr16:94631108-94631606(+)$1	498	476	489	35.7391
nnnnna]======	chr15:3532386-3532776(-)$1	390	98	111	35.7391
mmmmggggggg::	chr2:127124290-127124753(+)$1	463	221	234	31.3913
II{BB::::::::	chr2:26875211-26875634(+)$1	423	35	48	35.7391
3ccc]bbbb!!==	chr5:30111583-30111813(+)$1	230	100	113	35.7391
::::::::::bb!	chr3:60812603-60812882(+)$1	279	143	156	35.7391
ZZA}BB}EEEEE}	chr14:71064675-71065047(-)$1	372	216	229	26.3913
J::::::::::::	chr7:128048649-128048970(+)$1	321	199	212	35.7391
JJJJJJ::::eee	chr11:117019229-117019697(+)$1	468	403	416	31.2826
HHHHH?????CCC	chr11:94150929-94151394(-)$1	465	225	238	35.7391
nnnnnffffff]b	chr3:22114031-22114320(+)$1	289	51	64	35.7391
::JJJJJJJJJJJ	chr3:30408431-30408709(-)$1	278	151	164	31.3913
dddd[gggggggq	chr4:48675343-48675669(+)$1	326	106	119	31.6086
:::::::::dddd	chr6:40196405-40196903(+)$1	498	414	427	31.1739
bb]bb]ggggggg	chrX:70904601-70905043(-)$1	442	299	312	31.1739
c::::::CCC~~~	chr9:121383026-121383493(+)$1	467	355	368	35.7391
EE}BBYYCCC:::	chr12:68322051-68322546(-)$1	495	215	228	35.7391
ggg[ccc[a[ccc	chr6:71763741-71763977(-)$1	236	86	99	31.6086
====qqqqqqqq=	chr1:132594025-132594486(-)$1	461	362	375	35.7391
]ccc]a]bb]a]b	chr6:121324320-121324809(-)$1	489	231	244	30.9565
===========bb	chr6:71340154-71340449(-)$1	295	165	178	26.9347
##bb[bb[a[fff	chr8:87195546-87195823(-)$1	277	152	165	35.7391
44dddd55555ff	chr11:72017071-72017313(-)$1	242	93	106	26.4999
ee4444a]=====	chr18:34930992-34931443(+)$1	451	30	43	35.7391
E{CCCOOOOOOA{	chr2:118614445-118614790(+)$1	345	90	103	31.2826
ddccc4444dddd	chr17:37210491-37210988(+)$1	497	245	258	35.7391
[a%%%%%%ggggg	chr4:57906975-57907465(+)$1	490	229	242	35.7391
oooooobb]a]cc	chr16:42248663-42249106(-)$1	443	317	330	26.6086

#DB
((((((((.....	chr9:106590818-106591076(-)$1	1	83	96	31.6086
)))).(((((...	chr12:106854477-106854945(-)$1	1	202	215	35.7391
..)))).))))..	chr3:151898486-151898955(+)$1	1	228	241	35.7391
((..(((.((((.	chr17:10407877-10408240(-)$1	1	270	283	26.7173
))).).))).)))	chr6:40196703-40197118(+)$1	1	112	125	35.7391
.))))))..))))	chr8:42004296-42004725(+)$1	1	208	221	35.7391
)...(.(((.(.(	chr16:10530021-10530508(-)$1	1	234	247	35.7391
........(((((	chr9:61220148-61220516(+)$1	1	83	96	26.8260
.............	chr11:107533108-107533526(+)$1	1	288	301	35.7391
(.(((((((((((	chr3:81898081-81898341(-)$1	1	92	105	31.1739
))..)))....((	chr7:24866875-24867295(+)$1	1	90	103	35.7391
.......((((..	chr11:87032688-87032989(+)$1	1	69	82	26.3913
(.(((((((.(((	chr14:56500932-56501241(-)$1	1	100	113	35.7391
(....)).)))..	chr11:74483263-74483592(+)$1	1	147	160	35.7391
)((((((.((((.	chr7:116174028-116174306(+)$1	1	122	135	31.0652
.((((((((((((	chr9:120083248-120083588(+)$1	1	157	170	31.0652
.......))))))	chr16:35002206-35002544(+)$1	1	140	153	31.6086
...))))).((((	chr9:75417696-75418175(-)$1	1	313	326	26.7173
)))))...))).)	chr16:94631108-94631606(+)$1	1	476	489	35.7391
.....).))))))	chr15:3532386-3532776(-)$1	1	98	111	35.7391
....)))))))..	chr2:127124290-127124753(+)$1	1	221	234	31.3913
((.((........	chr2:26875211-26875634(+)$1	1	35	48	35.7391
.))).))((..((	chr5:30111583-30111813(+)$1	1	100	113	35.7391
..........((.	chr3:60812603-60812882(+)$1	1	143	156	35.7391
..).)).))))).	chr14:71064675-71065047(-)$1	1	216	229	26.3913
)............	chr7:128048649-128048970(+)$1	1	199	212	35.7391
))))))....(((	chr11:117019229-117019697(+)$1	1	403	416	31.2826
))))).....)))	chr11:94150929-94151394(-)$1	1	225	238	35.7391
.....)))))).)	chr3:22114031-22114320(+)$1	1	51	64	35.7391
..)))))))))))	chr3:30408431-30408709(-)$1	1	151	164	31.3913
((((.(((((((.	chr4:48675343-48675669(+)$1	1	106	119	31.6086
.........((((	chr6:40196405-40196903(+)$1	1	414	427	31.1739
)).)).)))))))	chrX:70904601-70905043(-)$1	1	299	312	31.1739
)......)))...	chr9:121383026-121383493(+)$1	1	355	368	35.7391
)).))..)))...	chr12:68322051-68322546(-)$1	1	215	228	35.7391
(((.(((.(.(((	chr6:71763741-71763977(-)$1	1	86	99	31.6086
((((........)	chr1:132594025-132594486(-)$1	1	362	375	35.7391
.))).).)).).)	chr6:121324320-121324809(-)$1	1	231	244	30.9565
)))))))))))((	chr6:71340154-71340449(-)$1	1	165	178	26.9347
..((.((.(.(((	chr8:87195546-87195823(-)$1	1	152	165	35.7391
..)))).....))	chr11:72017071-72017313(-)$1	1	93	106	26.4999
))....).)))))	chr18:34930992-34931443(+)$1	1	30	43	35.7391
(.(((......(.	chr2:118614445-118614790(+)$1	1	90	103	31.2826
)))))....))))	chr17:37210491-37210988(+)$1	1	245	258	35.7391
.(......(((((	chr4:57906975-57907465(+)$1	1	229	242	35.7391
......)).).))	chr16:42248663-42249106(-)$1	1	317	330	26.6086

#PSSM
u : 0.54	U : 0.41	A : 0.04	
g : 0.52	G : 0.41	A : 0.02	U : 0.02	u : 0.02	
u : 0.52	U : 0.43	A : 0.02	c : 0.02	
g : 0.54	G : 0.39	C : 0.04	A : 0.02	
u : 0.54	U : 0.41	C : 0.02	G : 0.02	
g : 0.54	G : 0.43	U : 0.02	
u : 0.52	U : 0.39	A : 0.04	C : 0.02	c : 0.02	
g : 0.52	G : 0.39	A : 0.06	a : 0.02	
u : 0.54	U : 0.41	G : 0.04	
g : 0.54	G : 0.43	A : 0.02	
u : 0.52	U : 0.45	a : 0.02	
g : 0.52	G : 0.43	U : 0.02	u : 0.02	
u : 0.54	U : 0.39	G : 0.04	C : 0.02	

#score	1509.2173913043478
#seq	46
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m3_run2.nuc.txt

#NT
uuuuuucuuuuuuuuuuucuuu	chr15:77591165-77591489(-)$1	324	225	247	37.4130
uucuuucuuuuuuuuuuuuuuu	chr10:96081208-96081456(+)$1	248	223	245	36.8695
UUAGGGUUUUCGUUUUCUUUUU	chr14:31932296-31932535(+)$1	239	110	132	23.1739
UUUCUUGUUUGUUUUUUGCUUG	chr15:103025157-103025440(-)$1	283	68	90	21.1086
AUUUUUAACCUUUUUACUUUUU	chr17:56552167-56552433(-)$1	266	216	238	20.2391
uuuuuucuuucuuuuuuuuuuu	chr2:90856815-90857072(+)$1	257	81	103	39.1521
UUACCUUUUAUUUUUUCUUUUU	chr10:116784342-116784629(-)$1	287	94	116	26.5434
uuguuuguuuguuuguuuguuu	chr13:99612445-99612683(-)$1	238	146	168	25.6739
UUUGUUCUUUCUUUUCCUGUAC	chr1:133828186-133828459(+)$1	273	236	258	22.0869
UUUUUGUGUUUUGUUUCUGUUG	chr13:29998833-29999080(-)$1	247	96	118	22.4130
UUUUUUUUUUUGUCUGAUUUUU	chr18:69843433-69843669(+)$1	236	85	107	28.0652
UUUUUGUUUUUUGUUUGUUUUU	chr11:50108332-50108579(-)$1	247	171	193	31.7608
AUCUUACUGUUUUGUUUUUUUU	chr19:38148346-38148590(+)$1	244	48	70	22.9565
uuugguuuuuguuuuuguuuuu	chr9:42772495-42772801(-)$1	306	277	299	30.2391
uuuuuccuuuuuucuucuuucu	chr4:140669442-140669686(-)$1	244	79	101	31.4347
UUGGUCCUUUUAUUUUCAUUGU	chr11:30006803-30007081(-)$1	278	228	250	19.3695
CUUUCACUUCAUUUGUGUUUUU	chr6:67234124-67234375(+)$1	251	185	207	20.5652
UUUUUUUUUUGCUGUUGUUGUU	chr6:91222377-91222615(+)$1	238	76	98	25.0217
UUUCCUCUGUCUUUUUCUUUCU	chr1:133830289-133830548(+)$1	259	23	45	26.7608
uuuuuccuuucuuuuucuuuuu	chr10:114726961-114727229(-)$1	268	200	222	37.0869
Uuuuuuguuuuguuuuguuuug	chr7:150253177-150253420(+)$1	243	220	242	30.7826
UUUUUUCUUUUUUUUUCUUUUU	chr17:44743939-44744175(-)$1	236	71	93	41.7608
UUUCUUCAAAUGUUUUCUUUUU	chr3:51319514-51319767(-)$1	253	59	81	24.1521
uuuuuuuuuuuuuuuuuuuuuu	chr14:123290307-123290543(-)$1	236	191	213	39.3695
CUUUUUCAUUAUUUUGAUUUUA	chr15:12114096-12114352(+)$1	256	20	42	22.8478
GUUUAACUUUCUUUCUUUUUUU	chr4:151364267-151364506(-)$1	239	70	92	25.5652
UAUUAGCAUUuucuuucuuucu	chr11:78005529-78005766(+)$1	237	153	175	19.9130
Gauuuuauuuauuuuuuuuuuu	chr8:27055054-27055289(-)$1	235	190	212	28.0652
GUUGUUUUGUUUUGGGCUUUUU	chr18:6788752-6789014(+)$1	262	126	148	19.9130
UUUUUGUUUGUUUCAUCUUUUU	chr9:51894657-51894915(+)$1	258	179	201	26.5434
uuauuuauuuauuuauuuauuu	chr8:4285777-4286013(-)$1	236	207	229	25.3478
UUUUUUUUUUUAAGUUCUUUUA	chr18:56912511-56912824(+)$1	313	80	102	25.1304
uuuuuuuuuucuuuuucuuuuu	chr5:93602458-93602712(+)$1	254	212	234	39.1521
cuuucucuuuuccuuucuuucu	chr19:45130079-45130335(+)$1	256	179	201	24.0434
GUUUUUGUUUUGUUUUAUUUUU	chr6:38456626-38456882(+)$1	256	50	72	30.8913
UUUUGUCAUUUGUUUUGUAUCU	chr10:59412654-59412891(-)$1	237	75	97	23.0652
uucuuucuuucuuuuuuuuuuu	chr10:36855298-36855535(-)$1	237	170	192	35.4565
UUUGUGCUUUCUUUCUGUUUUC	chr5:135096963-135097205(-)$1	242	26	48	25.2391
UUAUUUUUGUCCUUUGCUGUUU	chr4:94609606-94609843(-)$1	237	146	168	21.5434
CUUUUGUUUGUUUUUUCUCUUC	chr4:131912454-131912731(-)$1	277	94	116	23.3913
UUUUUUCUUUUUUUGGCUCUCU	chr4:4692406-4692654(-)$1	248	87	109	28.0652
UUUUAUCUUAUUUUAUCUUAUU	chr18:64617438-64617700(-)$1	262	83	105	26.5434
uuuuauccuuuuuauuuuuauu	chrX:102280208-102280443(+)$1	235	160	182	25.0217
uuuuuucuaucuucuucuuuuu	chr5:124823143-124823396(-)$1	253	86	108	33.1739
UCUGUUCUAUGuuuuuauauuu	chr16:18222254-18222527(-)$1	273	143	165	22.9565

#otherMatches

#Struct PSSM
bb22eeeee:::::::::::::	chrX:70740604-70740891(+)$1	287	90	112	19.6956
JJJJJJJJJJJ::::::::iii	chr15:77591165-77591489(-)$1	324	225	247	37.4130
eHHHHHHHH:::::::::::::	chr10:96081208-96081456(+)$1	248	223	245	36.8695
dd####==========[iiiii	chr14:31932296-31932535(+)$1	239	110	132	23.1739
c!!a!!bbrrrrrrrrrbb22a	chr15:103025157-103025440(-)$1	283	68	90	21.1086
}GGGGGGGYYDDDD}CCCJJJJ	chr17:56552167-56552433(-)$1	266	216	238	20.2391
::::::::::::::::::::ii	chr2:90856815-90857072(+)$1	257	81	103	39.1521
::CCCJJJJJJJJJJJJJJKKC	chr10:116784342-116784629(-)$1	287	94	116	26.5434
i^^^^^^^^^^^^^^^^^^^^^	chr13:99612445-99612683(-)$1	238	146	168	25.6739
cc333gggggggccc22ccc22	chr1:133828186-133828459(+)$1	273	236	258	22.0869
JJJJJJKKHHHHHHHH{A{CCC	chr13:29998833-29999080(-)$1	247	96	118	22.4130
==========:FFFFFF?????	chr18:69843433-69843669(+)$1	236	85	107	28.0652
GGGGGGGGZZZCCCYYEEEEE_	chr11:50108332-50108579(-)$1	247	171	193	31.7608
vvveeeee]eeeee]=======	chr19:38148346-38148590(+)$1	244	48	70	22.9565
d]iiiiiiiii:::::::::::	chr9:42772495-42772801(-)$1	306	277	299	30.2391
:::::::::::::a!!ccc[bb	chr4:140669442-140669686(-)$1	244	79	101	31.4347
ZZCCC@@@@@@@@@@@@@@@EE	chr11:30006803-30007081(-)$1	278	228	250	19.3695
cceeeee333===========:	chr6:67234124-67234375(+)$1	251	185	207	20.5652
=======::ggggggggggggg	chr6:91222377-91222615(+)$1	238	76	98	25.0217
::::::::::::::::::::::	chr1:133830289-133830548(+)$1	259	23	45	26.7608
::::::::::::::::::::::	chr10:114726961-114727229(-)$1	268	200	222	37.0869
HHHHHHHZZZCCCYYCCC::::	chr7:150253177-150253420(+)$1	243	220	242	30.7826
++++++++++++++++++++++	chr17:44743939-44744175(-)$1	236	71	93	41.7608
::::::::::::JJJJJJJJJJ	chr3:51319514-51319767(-)$1	253	59	81	24.1521
::::::::::::::::::::::	chr14:123290307-123290543(-)$1	236	191	213	39.3695
:::::cccooooooccc:::::	chr15:12114096-12114352(+)$1	256	20	42	22.8478
dd"""dddd[bb!!dddd^^^^	chr4:151364267-151364506(-)$1	239	70	92	25.5652
ee22hhhhhhhh:::::::::i	chr11:78005529-78005766(+)$1	237	153	175	19.9130
II::::::::::::::::::::	chr8:27055054-27055289(-)$1	235	190	212	28.0652
wwwwwwwwwwwwwwccc22hhh	chr18:6788752-6789014(+)$1	262	126	148	19.9130
::::dddd"""dddd[bbnnnn	chr9:51894657-51894915(+)$1	258	179	201	26.5434
h####bboooooobb333hhhh	chr8:4285777-4286013(-)$1	236	207	229	25.3478
+++===========mmmm====	chr18:56912511-56912824(+)$1	313	80	102	25.1304
::::::::::::::::::::::	chr5:93602458-93602712(+)$1	254	212	234	39.1521
::::::::::::::::::::::	chr19:45130079-45130335(+)$1	256	179	201	24.0434
:::::::dddd[==========	chr6:38456626-38456882(+)$1	256	50	72	30.8913
qqqqqqdddd::::::::::::	chr10:59412654-59412891(-)$1	237	75	97	23.0652
HHHHHHHgggggggqqqqqqqq	chr10:36855298-36855535(-)$1	237	170	192	35.4565
oooa]bb:::::::::::::::	chr5:135096963-135097205(-)$1	242	26	48	25.2391
JJJJJJJJ::::ccc[ccc%%%	chr4:94609606-94609843(-)$1	237	146	168	21.5434
ffJJJJJJJJJJ==========	chr4:131912454-131912731(-)$1	277	94	116	23.3913
>>>>>ccc666666dddd::::	chr4:4692406-4692654(-)$1	248	87	109	28.0652
::::::::::::::::::::::	chr18:64617438-64617700(-)$1	262	83	105	26.5434
::::::ggggggg[========	chrX:102280208-102280443(+)$1	235	160	182	25.0217
hhhhh22eeeee::::::::::	chr5:124823143-124823396(-)$1	253	86	108	33.1739
dGGGGGGGDDDD:::eeeeeqq	chr16:18222254-18222527(-)$1	273	143	165	22.9565

#DB
))..))))).............	chrX:70740604-70740891(+)$1	1	90	112	19.6956
)))))))))))........(((	chr15:77591165-77591489(-)$1	1	225	247	37.4130
))))))))).............	chr10:96081208-96081456(+)$1	1	223	245	36.8695
((....((((((((((.(((((	chr14:31932296-31932535(+)$1	1	110	132	23.1739
(..(..((.........))..)	chr15:103025157-103025440(-)$1	1	68	90	21.1086
.)))))))..)))).)))))))	chr17:56552167-56552433(-)$1	1	216	238	20.2391
....................((	chr2:90856815-90857072(+)$1	1	81	103	39.1521
..(((((((((((((((((..(	chr10:116784342-116784629(-)$1	1	94	116	26.5434
(.....................	chr13:99612445-99612683(-)$1	1	146	168	25.6739
))...))))))))))..)))..	chr1:133828186-133828459(+)$1	1	236	258	22.0869
((((((..((((((((.(.(((	chr13:29998833-29999080(-)$1	1	96	118	22.4130
)))))))))).)))))).....	chr18:69843433-69843669(+)$1	1	85	107	28.0652
))))))))...)))..))))).	chr11:50108332-50108579(-)$1	1	171	193	31.7608
...))))).))))).)))))))	chr19:38148346-38148590(+)$1	1	48	70	22.9565
).)))))))))...........	chr9:42772495-42772801(-)$1	1	277	299	30.2391
.............(..(((.((	chr4:140669442-140669686(-)$1	1	79	101	31.4347
..)))...............))	chr11:30006803-30007081(-)$1	1	228	250	19.3695
)))))))...))))))))))).	chr6:67234124-67234375(+)$1	1	185	207	20.5652
)))))))..(((((((((((((	chr6:91222377-91222615(+)$1	1	76	98	25.0217
......................	chr1:133830289-133830548(+)$1	1	23	45	26.7608
......................	chr10:114726961-114727229(-)$1	1	200	222	37.0869
)))))))...)))..)))....	chr7:150253177-150253420(+)$1	1	220	242	30.7826
......................	chr17:44743939-44744175(-)$1	1	71	93	41.7608
............((((((((((	chr3:51319514-51319767(-)$1	1	59	81	24.1521
......................	chr14:123290307-123290543(-)$1	1	191	213	39.3695
.....(((......))).....	chr15:12114096-12114352(+)$1	1	20	42	22.8478
((...((((.((..((((....	chr4:151364267-151364506(-)$1	1	70	92	25.5652
))..)))))))).........(	chr11:78005529-78005766(+)$1	1	153	175	19.9130
))....................	chr8:27055054-27055289(-)$1	1	190	212	28.0652
..............)))..)))	chr18:6788752-6789014(+)$1	1	126	148	19.9130
....((((...((((.((....	chr9:51894657-51894915(+)$1	1	179	201	26.5434
(....((......))...))))	chr8:4285777-4286013(-)$1	1	207	229	25.3478
...(((((((((((....))))	chr18:56912511-56912824(+)$1	1	80	102	25.1304
......................	chr5:93602458-93602712(+)$1	1	212	234	39.1521
......................	chr19:45130079-45130335(+)$1	1	179	201	24.0434
.......((((.((((((((((	chr6:38456626-38456882(+)$1	1	50	72	30.8913
......))))............	chr10:59412654-59412891(-)$1	1	75	97	23.0652
)))))))(((((((........	chr10:36855298-36855535(-)$1	1	170	192	35.4565
...).))...............	chr5:135096963-135097205(-)$1	1	26	48	25.2391
))))))))....(((.(((...	chr4:94609606-94609843(-)$1	1	146	168	21.5434
))))))))))))((((((((((	chr4:131912454-131912731(-)$1	1	94	116	23.3913
.....)))......))))....	chr4:4692406-4692654(-)$1	1	87	109	28.0652
......................	chr18:64617438-64617700(-)$1	1	83	105	26.5434
......(((((((.((((((((	chrX:102280208-102280443(+)$1	1	160	182	25.0217
)))))..)))))..........	chr5:124823143-124823396(-)$1	1	86	108	33.1739
))))))))))))...(((((..	chr16:18222254-18222527(-)$1	1	143	165	22.9565

#PSSM
U : 0.47	u : 0.28	G : 0.08	A : 0.06	C : 0.06	c : 0.02	
U : 0.60	u : 0.32	A : 0.02	a : 0.02	C : 0.02	
U : 0.54	u : 0.26	A : 0.06	c : 0.04	g : 0.02	C : 0.02	G : 0.02	a : 0.02	
U : 0.41	u : 0.34	G : 0.13	C : 0.08	g : 0.02	
U : 0.45	u : 0.28	C : 0.06	A : 0.06	c : 0.04	G : 0.04	g : 0.02	a : 0.02	
U : 0.39	u : 0.32	G : 0.15	A : 0.06	c : 0.04	C : 0.02	
C : 0.32	U : 0.23	c : 0.21	u : 0.06	G : 0.04	g : 0.04	a : 0.04	A : 0.02	
U : 0.49	u : 0.32	A : 0.10	c : 0.04	G : 0.02	
U : 0.47	u : 0.32	G : 0.08	a : 0.04	A : 0.04	C : 0.02	
U : 0.47	u : 0.36	A : 0.06	C : 0.04	G : 0.04	
U : 0.36	u : 0.17	c : 0.13	C : 0.13	G : 0.06	g : 0.04	A : 0.04	a : 0.04	
U : 0.39	u : 0.36	G : 0.10	A : 0.04	C : 0.04	g : 0.02	c : 0.02	
U : 0.52	u : 0.36	G : 0.04	c : 0.04	A : 0.02	
U : 0.45	u : 0.34	G : 0.08	C : 0.04	c : 0.04	a : 0.02	
U : 0.43	u : 0.34	G : 0.06	g : 0.04	C : 0.04	A : 0.04	a : 0.02	
U : 0.43	u : 0.41	G : 0.10	A : 0.02	C : 0.02	
C : 0.34	u : 0.19	c : 0.15	G : 0.10	U : 0.06	A : 0.06	g : 0.04	a : 0.02	
U : 0.54	u : 0.41	G : 0.02	A : 0.02	
U : 0.43	u : 0.30	C : 0.06	G : 0.06	c : 0.04	a : 0.04	g : 0.02	A : 0.02	
U : 0.54	u : 0.39	G : 0.02	A : 0.02	a : 0.02	
U : 0.47	u : 0.34	c : 0.06	C : 0.06	A : 0.02	G : 0.02	
U : 0.43	u : 0.39	C : 0.06	G : 0.04	A : 0.04	g : 0.02	

#score	1255.565217391304
#seq	46
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m3_run1.nuc.txt

#NT
CUUU	chr13:97425745-97426051(-)$1	306	255	259	12.0000
CUUU	chr17:10406115-10406612(-)$1	497	209	213	12.0000
CUUU	chr18:36957489-36957940(+)$1	451	113	117	12.0000
CUUU	chr8:63401766-63402065(-)$1	299	48	52	12.0000
CUUU	chr2:167332502-167332848(+)$1	346	6	10	12.0000
CUUU	chrX:12680443-12680746(+)$1	303	1	5	12.0000
CUUU	chr2:118289699-118289938(+)$1	239	170	174	12.0000
CUUU	chr7:134628797-134629154(+)$1	357	55	59	12.0000
CUUU	chr11:115117117-115117505(-)$1	388	58	62	12.0000
CUUU	chr1:156320681-156321095(-)$1	414	285	289	12.0000
CUUU	chr4:58831798-58832237(-)$1	439	32	36	12.0000
CUUU	chr5:90651026-90651450(-)$1	424	56	60	12.0000
CUUU	chr11:87794637-87795093(-)$1	456	4	8	12.0000
CUUU	chr11:103774433-103774794(-)$1	361	2	6	12.0000
CUUU	chr12:54248764-54249104(+)$1	340	3	7	12.0000
CUUU	chr2:102588531-102588895(+)$1	364	107	111	12.0000
CUUU	chrX:12733486-12733774(+)$1	288	152	156	12.0000
CUUU	chr15:38609013-38609469(+)$1	456	52	56	12.0000
CUUU	chr1:175262058-175262332(-)$1	274	35	39	12.0000
CUUU	chr14:73768027-73768310(-)$1	283	3	7	12.0000
CUUU	chr11:88702491-88702906(-)$1	415	123	127	12.0000
CUUU	chr6:4583965-4584185(+)$1	220	28	32	12.0000
CUUU	chr17:35272358-35272734(+)$1	376	288	292	12.0000
CUUU	chr2:102862022-102862343(-)$1	321	135	139	12.0000
CUUU	chr15:95071752-95072172(-)$1	420	6	10	12.0000
CUUU	chr7:116168776-116169225(+)$1	449	13	17	12.0000
CUUU	chr10:127029065-127029552(-)$1	487	332	336	12.0000
CUUU	chr9:113771383-113771849(+)$1	466	164	168	12.0000
CUUU	chr1:58476928-58477273(-)$1	345	337	341	12.0000
CUUU	chr8:26941573-26941858(-)$1	285	7	11	12.0000
CUUU	chr8:3161067-3161546(-)$1	479	42	46	12.0000
CUUU	chr12:53617741-53617958(+)$1	217	39	43	12.0000
CUUU	chr17:33783166-33783649(-)$1	483	217	221	12.0000
CUUU	chr11:77623227-77623529(+)$1	302	23	27	12.0000
CUUU	chr1:145592322-145592775(+)$1	453	99	103	12.0000
CUUU	chrX:162782815-162783179(+)$1	364	232	236	12.0000
CUUU	chr4:148709019-148709353(-)$1	334	105	109	12.0000
CUUU	chr3:152020918-152021299(+)$1	381	57	61	12.0000
CUUU	chr14:103581576-103581789(-)$1	213	57	61	12.0000
CUUU	chr2:32279048-32279470(-)$1	422	57	61	12.0000
CUUU	chr13:108516414-108516638(-)$1	224	188	192	12.0000
CUUU	chr13:53014100-53014471(-)$1	371	137	141	12.0000
CUUU	chr2:155974743-155975153(-)$1	410	64	68	12.0000
CUUU	chr2:164824421-164824905(+)$1	484	189	193	12.0000
CUUU	chr9:67706585-67706986(+)$1	401	5	9	12.0000
CUUU	chr1:175266817-175267250(-)$1	433	242	246	12.0000
CUUU	chr19:27314087-27314511(+)$1	424	12	16	12.0000
CUUU	chr3:80605271-80605759(-)$1	488	214	218	12.0000
CUUU	chr17:47067317-47067664(-)$1	347	139	143	12.0000
CUUU	chr2:131762559-131762893(+)$1	334	308	312	12.0000
CUUU	chr14:46248392-46248717(-)$1	325	37	41	12.0000
CUUU	chr3:90058866-90059346(+)$1	480	9	13	12.0000
CUUU	chr12:79954216-79954469(-)$1	253	80	84	12.0000
CUUU	chr4:57088870-57089274(-)$1	404	123	127	12.0000
CUUU	chr16:94631108-94631606(+)$1	498	75	79	12.0000
CUUU	chr3:58392026-58392487(+)$1	461	180	184	12.0000
CUUU	chr16:85056517-85056838(-)$1	321	7	11	12.0000
CUUU	chr19:44377492-44377905(+)$1	413	398	402	12.0000
CUUU	chr11:69418680-69419127(-)$1	447	4	8	12.0000
CUUU	chr5:135097139-135097542(-)$1	403	112	116	12.0000
CUUU	chr19:60638888-60639284(-)$1	396	52	56	12.0000
CUUU	chr16:34513850-34514224(-)$1	374	17	21	12.0000
cuuu	chr16:28372732-28373173(-)$1	441	34	38	12.0000
CUUU	chr9:58491256-58491679(+)$1	423	40	44	12.0000
CUUU	chr7:133644375-133644746(-)$1	371	218	222	12.0000
CUUU	chr12:84935600-84936095(-)$1	495	5	9	12.0000
CUUU	chr1:160432378-160432585(+)$1	207	117	121	12.0000
CUUU	chr2:92453793-92454023(+)$1	230	25	29	12.0000
CUUU	chr1:182878911-182879275(+)$1	364	18	22	12.0000
CUUU	chr1:92978648-92978898(+)$1	250	176	180	12.0000
CUUU	chr5:122910047-122910436(-)$1	389	67	71	12.0000
CUUU	chr17:66321492-66321809(-)$1	317	69	73	12.0000
CUUU	chr1:184812994-184813414(+)$1	420	161	165	12.0000
CUUU	chr15:54697158-54697584(-)$1	426	10	14	12.0000
CUUU	chr10:98431342-98431688(+)$1	346	257	261	12.0000
CUUU	chr16:72935895-72936247(+)$1	352	31	35	12.0000
CUUU	chr11:101180575-101180899(+)$1	324	235	239	12.0000
CUUU	chrX:133366608-133366841(+)$1	233	92	96	12.0000
CUUU	chr10:58813201-58813560(+)$1	359	236	240	12.0000
CUUU	chr17:33806746-33807199(-)$1	453	8	12	12.0000
CUUU	chr2:90403875-90404326(-)$1	451	176	180	12.0000
CUUU	chrX:130971789-130972073(+)$1	284	5	9	12.0000

#otherMatches

#Struct PSSM
::::	chr7:135117771-135118263(+)$1	492	9	13	12.0000
eee]	chr13:97425745-97426051(-)$1	306	255	259	12.0000
EKKF	chr17:10406115-10406612(-)$1	497	209	213	12.0000
eeee	chr18:36957489-36957940(+)$1	451	113	117	12.0000
JJJJ	chr8:63401766-63402065(-)$1	299	48	52	12.0000
HHHH	chr2:167332502-167332848(+)$1	346	6	10	12.0000
CC{D	chrX:12680443-12680746(+)$1	303	1	5	12.0000
ddnn	chr2:118289699-118289938(+)$1	239	170	174	12.0000
6666	chr7:134628797-134629154(+)$1	357	55	59	12.0000
FFFL	chr11:115117117-115117505(-)$1	388	58	62	12.0000
dddd	chr1:156320681-156321095(-)$1	414	285	289	12.0000
neee	chr4:58831798-58832237(-)$1	439	32	36	12.0000
eeee	chr5:90651026-90651450(-)$1	424	56	60	12.0000
::::	chr11:87794637-87795093(-)$1	456	4	8	12.0000
ffff	chr11:103774433-103774794(-)$1	361	2	6	12.0000
::::	chr12:54248764-54249104(+)$1	340	3	7	12.0000
IIII	chr2:102588531-102588895(+)$1	364	107	111	12.0000
ffff	chrX:12733486-12733774(+)$1	288	152	156	12.0000
DDHH	chr15:38609013-38609469(+)$1	456	52	56	12.0000
eeee	chr1:175262058-175262332(-)$1	274	35	39	12.0000
::ff	chr14:73768027-73768310(-)$1	283	3	7	12.0000
EEOO	chr11:88702491-88702906(-)$1	415	123	127	12.0000
b333	chr6:4583965-4584185(+)$1	220	28	32	12.0000
e22b	chr17:35272358-35272734(+)$1	376	288	292	12.0000
#ddd	chr2:102862022-102862343(-)$1	321	135	139	12.0000
eeee	chr15:95071752-95072172(-)$1	420	6	10	12.0000
ff::	chr7:116168776-116169225(+)$1	449	13	17	12.0000
FFFF	chr10:127029065-127029552(-)$1	487	332	336	12.0000
e+++	chr9:113771383-113771849(+)$1	466	164	168	12.0000
c]dd	chr1:58476928-58477273(-)$1	345	337	341	12.0000
GGGG	chr8:26941573-26941858(-)$1	285	7	11	12.0000
EEE{	chr8:3161067-3161546(-)$1	479	42	46	12.0000
((((	chr12:53617741-53617958(+)$1	217	39	43	12.0000
KJJJ	chr17:33783166-33783649(-)$1	483	217	221	12.0000
EEEK	chr11:77623227-77623529(+)$1	302	23	27	12.0000
IIII	chr1:145592322-145592775(+)$1	453	99	103	12.0000
gggg	chrX:162782815-162783179(+)$1	364	232	236	12.0000
pppp	chr4:148709019-148709353(-)$1	334	105	109	12.0000
CKKF	chr3:152020918-152021299(+)$1	381	57	61	12.0000
oooo	chr14:103581576-103581789(-)$1	213	57	61	12.0000
eeee	chr2:32279048-32279470(-)$1	422	57	61	12.0000
hhh2	chr13:108516414-108516638(-)$1	224	188	192	12.0000
5555	chr13:53014100-53014471(-)$1	371	137	141	12.0000
oooo	chr2:155974743-155975153(-)$1	410	64	68	12.0000
c444	chr2:164824421-164824905(+)$1	484	189	193	12.0000
hhhh	chr9:67706585-67706986(+)$1	401	5	9	12.0000
dppp	chr1:175266817-175267250(-)$1	433	242	246	12.0000
TTTT	chr19:27314087-27314511(+)$1	424	12	16	12.0000
$$$$	chr3:80605271-80605759(-)$1	488	214	218	12.0000
ddd=	chr17:47067317-47067664(-)$1	347	139	143	12.0000
dd22	chr2:131762559-131762893(+)$1	334	308	312	12.0000
EEEE	chr14:46248392-46248717(-)$1	325	37	41	12.0000
CCC:	chr3:90058866-90059346(+)$1	480	9	13	12.0000
$$dd	chr12:79954216-79954469(-)$1	253	80	84	12.0000
AOOO	chr4:57088870-57089274(-)$1	404	123	127	12.0000
f666	chr16:94631108-94631606(+)$1	498	75	79	12.0000
f:::	chr3:58392026-58392487(+)$1	461	180	184	12.0000
h!!d	chr16:85056517-85056838(-)$1	321	7	11	12.0000
FFF}	chr19:44377492-44377905(+)$1	413	398	402	12.0000
GGGG	chr11:69418680-69419127(-)$1	447	4	8	12.0000
ttff	chr5:135097139-135097542(-)$1	403	112	116	12.0000
oooo	chr19:60638888-60639284(-)$1	396	52	56	12.0000
ffmm	chr16:34513850-34514224(-)$1	374	17	21	12.0000
GGGG	chr16:28372732-28373173(-)$1	441	34	38	12.0000
::::	chr9:58491256-58491679(+)$1	423	40	44	12.0000
gggg	chr7:133644375-133644746(-)$1	371	218	222	12.0000
HHHH	chr12:84935600-84936095(-)$1	495	5	9	12.0000
dddd	chr1:160432378-160432585(+)$1	207	117	121	12.0000
hhhh	chr2:92453793-92454023(+)$1	230	25	29	12.0000
::::	chr1:182878911-182879275(+)$1	364	18	22	12.0000
CCC:	chr1:92978648-92978898(+)$1	250	176	180	12.0000
cc33	chr5:122910047-122910436(-)$1	389	67	71	12.0000
bbmm	chr17:66321492-66321809(-)$1	317	69	73	12.0000
b!!i	chr1:184812994-184813414(+)$1	420	161	165	12.0000
DNNN	chr15:54697158-54697584(-)$1	426	10	14	12.0000
HHHH	chr10:98431342-98431688(+)$1	346	257	261	12.0000
nnnc	chr16:72935895-72936247(+)$1	352	31	35	12.0000
D}BB	chr11:101180575-101180899(+)$1	324	235	239	12.0000
qqqq	chrX:133366608-133366841(+)$1	233	92	96	12.0000
c###	chr10:58813201-58813560(+)$1	359	236	240	12.0000
eeee	chr17:33806746-33807199(-)$1	453	8	12	12.0000
ccc[	chr2:90403875-90404326(-)$1	451	176	180	12.0000
$$$c	chrX:130971789-130972073(+)$1	284	5	9	12.0000

#DB
....	chr7:135117771-135118263(+)$1	1	9	13	12.0000
))).	chr13:97425745-97426051(-)$1	1	255	259	12.0000
(..(	chr17:10406115-10406612(-)$1	1	209	213	12.0000
))))	chr18:36957489-36957940(+)$1	1	113	117	12.0000
((((	chr8:63401766-63402065(-)$1	1	48	52	12.0000
((((	chr2:167332502-167332848(+)$1	1	6	10	12.0000
((.(	chrX:12680443-12680746(+)$1	1	1	5	12.0000
((..	chr2:118289699-118289938(+)$1	1	170	174	12.0000
....	chr7:134628797-134629154(+)$1	1	55	59	12.0000
(((.	chr11:115117117-115117505(-)$1	1	58	62	12.0000
((((	chr1:156320681-156321095(-)$1	1	285	289	12.0000
.)))	chr4:58831798-58832237(-)$1	1	32	36	12.0000
))))	chr5:90651026-90651450(-)$1	1	56	60	12.0000
....	chr11:87794637-87795093(-)$1	1	4	8	12.0000
((((	chr11:103774433-103774794(-)$1	1	2	6	12.0000
....	chr12:54248764-54249104(+)$1	1	3	7	12.0000
((((	chr2:102588531-102588895(+)$1	1	107	111	12.0000
))))	chrX:12733486-12733774(+)$1	1	152	156	12.0000
((((	chr15:38609013-38609469(+)$1	1	52	56	12.0000
((((	chr1:175262058-175262332(-)$1	1	35	39	12.0000
..((	chr14:73768027-73768310(-)$1	1	3	7	12.0000
((..	chr11:88702491-88702906(-)$1	1	123	127	12.0000
)...	chr6:4583965-4584185(+)$1	1	28	32	12.0000
)..)	chr17:35272358-35272734(+)$1	1	288	292	12.0000
.(((	chr2:102862022-102862343(-)$1	1	135	139	12.0000
((((	chr15:95071752-95072172(-)$1	1	6	10	12.0000
))..	chr7:116168776-116169225(+)$1	1	13	17	12.0000
((((	chr10:127029065-127029552(-)$1	1	332	336	12.0000
(...	chr9:113771383-113771849(+)$1	1	164	168	12.0000
).))	chr1:58476928-58477273(-)$1	1	337	341	12.0000
((((	chr8:26941573-26941858(-)$1	1	7	11	12.0000
(((.	chr8:3161067-3161546(-)$1	1	42	46	12.0000
....	chr12:53617741-53617958(+)$1	1	39	43	12.0000
.(((	chr17:33783166-33783649(-)$1	1	217	221	12.0000
(((.	chr11:77623227-77623529(+)$1	1	23	27	12.0000
((((	chr1:145592322-145592775(+)$1	1	99	103	12.0000
((((	chrX:162782815-162783179(+)$1	1	232	236	12.0000
....	chr4:148709019-148709353(-)$1	1	105	109	12.0000
(..(	chr3:152020918-152021299(+)$1	1	57	61	12.0000
....	chr14:103581576-103581789(-)$1	1	57	61	12.0000
((((	chr2:32279048-32279470(-)$1	1	57	61	12.0000
))).	chr13:108516414-108516638(-)$1	1	188	192	12.0000
....	chr13:53014100-53014471(-)$1	1	137	141	12.0000
....	chr2:155974743-155975153(-)$1	1	64	68	12.0000
)...	chr2:164824421-164824905(+)$1	1	189	193	12.0000
((((	chr9:67706585-67706986(+)$1	1	5	9	12.0000
(...	chr1:175266817-175267250(-)$1	1	242	246	12.0000
....	chr19:27314087-27314511(+)$1	1	12	16	12.0000
....	chr3:80605271-80605759(-)$1	1	214	218	12.0000
((((	chr17:47067317-47067664(-)$1	1	139	143	12.0000
))..	chr2:131762559-131762893(+)$1	1	308	312	12.0000
((((	chr14:46248392-46248717(-)$1	1	37	41	12.0000
(((.	chr3:90058866-90059346(+)$1	1	9	13	12.0000
..((	chr12:79954216-79954469(-)$1	1	80	84	12.0000
(...	chr4:57088870-57089274(-)$1	1	123	127	12.0000
)...	chr16:94631108-94631606(+)$1	1	75	79	12.0000
)...	chr3:58392026-58392487(+)$1	1	180	184	12.0000
(..(	chr16:85056517-85056838(-)$1	1	7	11	12.0000
))).	chr19:44377492-44377905(+)$1	1	398	402	12.0000
((((	chr11:69418680-69419127(-)$1	1	4	8	12.0000
..))	chr5:135097139-135097542(-)$1	1	112	116	12.0000
....	chr19:60638888-60639284(-)$1	1	52	56	12.0000
((..	chr16:34513850-34514224(-)$1	1	17	21	12.0000
((((	chr16:28372732-28373173(-)$1	1	34	38	12.0000
....	chr9:58491256-58491679(+)$1	1	40	44	12.0000
((((	chr7:133644375-133644746(-)$1	1	218	222	12.0000
((((	chr12:84935600-84936095(-)$1	1	5	9	12.0000
))))	chr1:160432378-160432585(+)$1	1	117	121	12.0000
))))	chr2:92453793-92454023(+)$1	1	25	29	12.0000
....	chr1:182878911-182879275(+)$1	1	18	22	12.0000
(((.	chr1:92978648-92978898(+)$1	1	176	180	12.0000
))..	chr5:122910047-122910436(-)$1	1	67	71	12.0000
((..	chr17:66321492-66321809(-)$1	1	69	73	12.0000
(..(	chr1:184812994-184813414(+)$1	1	161	165	12.0000
(...	chr15:54697158-54697584(-)$1	1	10	14	12.0000
))))	chr10:98431342-98431688(+)$1	1	257	261	12.0000
...)	chr16:72935895-72936247(+)$1	1	31	35	12.0000
).))	chr11:101180575-101180899(+)$1	1	235	239	12.0000
....	chrX:133366608-133366841(+)$1	1	92	96	12.0000
(...	chr10:58813201-58813560(+)$1	1	236	240	12.0000
((((	chr17:33806746-33807199(-)$1	1	8	12	12.0000
(((.	chr2:90403875-90404326(-)$1	1	176	180	12.0000
...(	chrX:130971789-130972073(+)$1	1	5	9	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	996.0000000000005
#seq	83
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m3_run1.nuc.txt

#NT
AGCAG	chr15:27832378-27832597(-)$1	219	153	158	15.0000
AGCAG	chr2:34580914-34581138(-)$1	224	195	200	15.0000
AGCAG	chr5:139717310-139717527(+)$1	217	138	143	15.0000
AGCAG	chr9:59674843-59675077(+)$1	234	146	151	15.0000
AGCAG	chr5:140184764-140184973(-)$1	209	1	6	15.0000
AGCAG	chr10:122569959-122570169(-)$1	210	108	113	15.0000
AGCAG	chr5:34225148-34225362(+)$1	214	58	63	15.0000
AGCAG	chr15:79728082-79728300(+)$1	218	169	174	15.0000
AGCAG	chrX:39603462-39603683(+)$1	221	129	134	15.0000
AGCAG	chr10:110932308-110932520(+)$1	212	126	131	15.0000
AGCAG	chr15:25736207-25736417(+)$1	210	51	56	15.0000
AGCAG	chr11:40536927-40537154(-)$1	227	158	163	15.0000
AGCAG	chr12:66207265-66207475(+)$1	210	191	196	15.0000
AGCAG	chr10:127720063-127720298(+)$1	235	32	37	15.0000
agcag	chr10:107677760-107677984(+)$1	224	215	220	15.0000
AGCAG	chr17:10475645-10475877(-)$1	232	36	41	15.0000
AGCAG	chr14:105529366-105529601(-)$1	235	34	39	15.0000
AGCAG	chr7:90904639-90904857(+)$1	218	14	19	15.0000
AGCAG	chr15:101919343-101919551(+)$1	208	140	145	15.0000
AGCAG	chr18:79283240-79283470(-)$1	230	95	100	15.0000
AGCAG	chr5:34009239-34009460(+)$1	221	135	140	15.0000
AGCAG	chr4:122716668-122716906(+)$1	238	66	71	15.0000
AGCAG	chr18:6452264-6452471(-)$1	207	184	189	15.0000
AGCAG	chr5:124091712-124091922(-)$1	210	179	184	15.0000
AGCAG	chr2:32673856-32674077(-)$1	221	211	216	15.0000
AGCAG	chr11:93954736-93954962(+)$1	226	68	73	15.0000
AGCAG	chrX:148288007-148288216(+)$1	209	123	128	15.0000
AGCAG	chr4:46144831-46145053(-)$1	222	104	109	15.0000
AGCAG	chr1:74441178-74441403(+)$1	225	6	11	15.0000
AGCAG	chr5:134880551-134880761(-)$1	210	131	136	15.0000
AGCAG	chr8:72436928-72437152(-)$1	224	27	32	15.0000
AGCAG	chr18:35098232-35098443(-)$1	211	165	170	15.0000
AGCAG	chr6:85291459-85291679(-)$1	220	53	58	15.0000
AGCAG	chr7:135591583-135591808(-)$1	225	186	191	15.0000
AGCAG	chr19:28614723-28614940(-)$1	217	110	115	15.0000
AGCAG	chr2:181246207-181246414(+)$1	207	66	71	15.0000
AGCAG	chr8:87359598-87359805(-)$1	207	6	11	15.0000
AGCAG	chr11:79064390-79064617(-)$1	227	0	5	15.0000
AGCAG	chr13:113293918-113294129(+)$1	211	147	152	15.0000
AGCAG	chr17:35516965-35517199(+)$1	234	39	44	15.0000
AGCAG	chr6:51417167-51417381(-)$1	214	2	7	15.0000
AGCAG	chr8:125031520-125031738(-)$1	218	51	56	15.0000
AGCAG	chr17:75017725-75017953(+)$1	228	155	160	15.0000
AGCAG	chr5:108590631-108590848(+)$1	217	81	86	15.0000
AGCAG	chr6:71545407-71545615(-)$1	208	47	52	15.0000
AGCAG	chr15:96523947-96524168(-)$1	221	185	190	15.0000
AGCAG	chr1:162557329-162557541(-)$1	212	138	143	15.0000

#otherMatches

#Struct PSSM
^^^^^	chr9:100638343-100638582(+)$1	239	92	97	15.0000
ggggg	chr15:27832378-27832597(-)$1	219	153	158	15.0000
cdddd	chr2:34580914-34581138(-)$1	224	195	200	15.0000
?DDDD	chr5:139717310-139717527(+)$1	217	138	143	15.0000
qqeee	chr9:59674843-59675077(+)$1	234	146	151	15.0000
:DDDD	chr5:140184764-140184973(-)$1	209	1	6	15.0000
nnnnd	chr10:122569959-122570169(-)$1	210	108	113	15.0000
lccce	chr5:34225148-34225362(+)$1	214	58	63	15.0000
fffff	chr15:79728082-79728300(+)$1	218	169	174	15.0000
mccc]	chrX:39603462-39603683(+)$1	221	129	134	15.0000
ddddo	chr10:110932308-110932520(+)$1	212	126	131	15.0000
22bb2	chr15:25736207-25736417(+)$1	210	51	56	15.0000
dd$$$	chr11:40536927-40537154(-)$1	227	158	163	15.0000
mmmmc	chr12:66207265-66207475(+)$1	210	191	196	15.0000
!!ddd	chr10:127720063-127720298(+)$1	235	32	37	15.0000
CCCFF	chr10:107677760-107677984(+)$1	224	215	220	15.0000
::bb!	chr17:10475645-10475877(-)$1	232	36	41	15.0000
LLCCC	chr14:105529366-105529601(-)$1	235	34	39	15.0000
FFFFK	chr7:90904639-90904857(+)$1	218	14	19	15.0000
qqqqc	chr15:101919343-101919551(+)$1	208	140	145	15.0000
00000	chr18:79283240-79283470(-)$1	230	95	100	15.0000
c!!dd	chr5:34009239-34009460(+)$1	221	135	140	15.0000
FFFFb	chr4:122716668-122716906(+)$1	238	66	71	15.0000
88888	chr18:6452264-6452471(-)$1	207	184	189	15.0000
fffff	chr5:124091712-124091922(-)$1	210	179	184	15.0000
ddd:D	chr2:32673856-32674077(-)$1	221	211	216	15.0000
hhhh!	chr11:93954736-93954962(+)$1	226	68	73	15.0000
JJeee	chrX:148288007-148288216(+)$1	209	123	128	15.0000
CCIII	chr4:46144831-46145053(-)$1	222	104	109	15.0000
MMMBB	chr1:74441178-74441403(+)$1	225	6	11	15.0000
3iiii	chr5:134880551-134880761(-)$1	210	131	136	15.0000
ccc[d	chr8:72436928-72437152(-)$1	224	27	32	15.0000
ccc22	chr18:35098232-35098443(-)$1	211	165	170	15.0000
[bbnn	chr6:85291459-85291679(-)$1	220	53	58	15.0000
tbb]e	chr7:135591583-135591808(-)$1	225	186	191	15.0000
d[bbo	chr19:28614723-28614940(-)$1	217	110	115	15.0000
]bb::	chr2:181246207-181246414(+)$1	207	66	71	15.0000
dd!!f	chr8:87359598-87359805(-)$1	207	6	11	15.0000
eeeee	chr11:79064390-79064617(-)$1	227	0	5	15.0000
$$$$$	chr13:113293918-113294129(+)$1	211	147	152	15.0000
RRRRR	chr17:35516965-35517199(+)$1	234	39	44	15.0000
:eeee	chr6:51417167-51417381(-)$1	214	2	7	15.0000
eeeee	chr8:125031520-125031738(-)$1	218	51	56	15.0000
$$$$f	chr17:75017725-75017953(+)$1	228	155	160	15.0000
nnnnn	chr5:108590631-108590848(+)$1	217	81	86	15.0000
:::cc	chr6:71545407-71545615(-)$1	208	47	52	15.0000
CCC~~	chr15:96523947-96524168(-)$1	221	185	190	15.0000
ppppb	chr1:162557329-162557541(-)$1	212	138	143	15.0000

#DB
.....	chr9:100638343-100638582(+)$1	1	92	97	15.0000
)))))	chr15:27832378-27832597(-)$1	1	153	158	15.0000
)))))	chr2:34580914-34581138(-)$1	1	195	200	15.0000
.))))	chr5:139717310-139717527(+)$1	1	138	143	15.0000
..)))	chr9:59674843-59675077(+)$1	1	146	151	15.0000
.((((	chr5:140184764-140184973(-)$1	1	1	6	15.0000
....)	chr10:122569959-122570169(-)$1	1	108	113	15.0000
.))))	chr5:34225148-34225362(+)$1	1	58	63	15.0000
)))))	chr15:79728082-79728300(+)$1	1	169	174	15.0000
.))).	chrX:39603462-39603683(+)$1	1	129	134	15.0000
((((.	chr10:110932308-110932520(+)$1	1	126	131	15.0000
..)).	chr15:25736207-25736417(+)$1	1	51	56	15.0000
((...	chr11:40536927-40537154(-)$1	1	158	163	15.0000
....)	chr12:66207265-66207475(+)$1	1	191	196	15.0000
..(((	chr10:127720063-127720298(+)$1	1	32	37	15.0000
)))))	chr10:107677760-107677984(+)$1	1	215	220	15.0000
..((.	chr17:10475645-10475877(-)$1	1	36	41	15.0000
..(((	chr14:105529366-105529601(-)$1	1	34	39	15.0000
((((.	chr7:90904639-90904857(+)$1	1	14	19	15.0000
....)	chr15:101919343-101919551(+)$1	1	140	145	15.0000
.....	chr18:79283240-79283470(-)$1	1	95	100	15.0000
(..((	chr5:34009239-34009460(+)$1	1	135	140	15.0000
(((((	chr4:122716668-122716906(+)$1	1	66	71	15.0000
.....	chr18:6452264-6452471(-)$1	1	184	189	15.0000
(((((	chr5:124091712-124091922(-)$1	1	179	184	15.0000
))).)	chr2:32673856-32674077(-)$1	1	211	216	15.0000
((((.	chr11:93954736-93954962(+)$1	1	68	73	15.0000
))(((	chrX:148288007-148288216(+)$1	1	123	128	15.0000
(((((	chr4:46144831-46145053(-)$1	1	104	109	15.0000
...((	chr1:74441178-74441403(+)$1	1	6	11	15.0000
.))))	chr5:134880551-134880761(-)$1	1	131	136	15.0000
(((.(	chr8:72436928-72437152(-)$1	1	27	32	15.0000
)))..	chr18:35098232-35098443(-)$1	1	165	170	15.0000
.((..	chr6:85291459-85291679(-)$1	1	53	58	15.0000
.)).)	chr7:135591583-135591808(-)$1	1	186	191	15.0000
(.((.	chr19:28614723-28614940(-)$1	1	110	115	15.0000
.))..	chr2:181246207-181246414(+)$1	1	66	71	15.0000
((..(	chr8:87359598-87359805(-)$1	1	6	11	15.0000
(((((	chr11:79064390-79064617(-)$1	1	0	5	15.0000
.....	chr13:113293918-113294129(+)$1	1	147	152	15.0000
.....	chr17:35516965-35517199(+)$1	1	39	44	15.0000
.((((	chr6:51417167-51417381(-)$1	1	2	7	15.0000
(((((	chr8:125031520-125031738(-)$1	1	51	56	15.0000
....(	chr17:75017725-75017953(+)$1	1	155	160	15.0000
.....	chr5:108590631-108590848(+)$1	1	81	86	15.0000
...((	chr6:71545407-71545615(-)$1	1	47	52	15.0000
)))..	chr15:96523947-96524168(-)$1	1	185	190	15.0000
....)	chr1:162557329-162557541(-)$1	1	138	143	15.0000

#PSSM
A : 0.97	a : 0.02	
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	720.0000000000001
#seq	48
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m2_run1.nuc.txt

#NT
GGGAAGA	chr18:36806257-36806481(+)$1	224	132	139	14.7499
UGGAAGA	chr2:154360967-154361184(+)$1	217	114	121	15.3181
AGGAAGG	chr8:72706039-72706249(+)$1	210	0	7	10.2045
UAGAAGA	chr1:137300709-137300944(-)$1	235	79	86	11.6818
AGGAAGU	chr8:125756251-125756458(+)$1	207	75	82	10.5454
UGGAAGG	chr2:180706696-180706916(+)$1	220	20	27	11.9090
UGGAAGA	chr4:70021751-70021972(-)$1	221	112	119	15.3181
UAGAAGA	chr14:79740721-79740931(-)$1	210	42	49	11.6818
GGGAAGA	chr5:100466770-100467004(-)$1	234	115	122	14.7499
UGGAAGU	chr4:147991135-147991349(-)$1	214	126	133	12.2499
UGGAGGA	chr13:115610937-115611150(+)$1	213	189	196	10.9999
GGGAAGA	chr13:55657377-55657587(-)$1	210	68	75	14.7499
GAGAAGA	chrX:148286919-148287138(+)$1	219	167	174	11.1136
GGGAAGA	chr10:127102276-127102492(-)$1	216	21	28	14.7499
UGGAAGA	chr16:24442849-24443069(+)$1	220	48	55	15.3181
AGGAAGU	chr16:10421981-10422201(+)$1	220	203	210	10.5454
GGGAAGA	chr17:37193671-37193896(+)$1	225	82	89	14.7499
UGGAAGC	chr4:98603752-98603983(-)$1	231	124	131	11.7954
UGGAAGC	chr9:14305084-14305311(+)$1	227	16	23	11.7954
AGGAAGA	chr8:131246274-131246480(+)$1	206	154	161	13.6136
GGGGAGA	chr4:144746429-144746639(-)$1	210	79	86	10.8863
gggaaga	chr15:35002752-35003036(-)$1	284	0	7	14.7499
UGGAAGA	chr1:135543926-135544143(-)$1	217	77	84	15.3181
UGGAAAA	chr2:35034094-35034303(+)$1	209	133	140	10.7727
UGGAGGA	chr8:124175925-124176143(-)$1	218	73	80	10.9999
UGGAAGA	chr6:113579483-113579701(+)$1	218	63	70	15.3181
GGGAAGA	chr13:97256714-97256938(-)$1	224	3	10	14.7499
UGGAGGA	chr14:27352863-27353074(-)$1	211	12	19	10.9999
GGGGAGA	chr15:99451408-99451622(-)$1	214	47	54	10.8863
GAGAAGA	chr11:71988640-71988856(-)$1	216	29	36	11.1136
AGGAAGA	chr1:129869492-129869712(-)$1	220	132	139	13.6136
AGGAAGG	chr2:153075387-153075602(+)$1	215	27	34	10.2045
UGGAAGU	chr16:18823235-18823459(+)$1	224	10	17	12.2499
GGGAAGA	chrX:126477392-126477608(+)$1	216	166	173	14.7499
UGGAAGU	chrX:12193639-12193868(+)$1	229	150	157	12.2499
UAGAAGA	chr17:28736618-28736836(-)$1	218	19	26	11.6818
GGGGAGA	chr17:46305060-46305272(+)$1	212	49	56	10.8863
GGGGAGA	chr9:42913314-42913533(-)$1	219	32	39	10.8863
UGGAAAA	chr15:65649933-65650171(+)$1	238	83	90	10.7727
GAGAAGA	chr15:6366773-6367008(+)$1	235	208	215	11.1136
UGGAAGA	chr17:33785651-33785886(-)$1	235	95	102	15.3181
GGGGAGA	chr11:117641783-117642002(-)$1	219	165	172	10.8863
UGGAAGU	chr3:68826104-68826334(+)$1	230	101	108	12.2499

#otherMatches

#Struct PSSM
reeeee:	chr1:45436837-45437081(-)$1	244	66	73	13.0454
gggggg]	chr18:36806257-36806481(+)$1	224	132	139	14.7499
!ddddbb	chr2:154360967-154361184(+)$1	217	114	121	15.3181
:::gggg	chr8:72706039-72706249(+)$1	210	0	7	10.2045
g]dddd:	chr1:137300709-137300944(-)$1	235	79	86	11.6818
yyyyyyy	chr8:125756251-125756458(+)$1	207	75	82	10.5454
qqqqqa2	chr2:180706696-180706916(+)$1	220	20	27	11.9090
dlllddd	chr4:70021751-70021972(-)$1	221	112	119	15.3181
gggggg:	chr14:79740721-79740931(-)$1	210	42	49	11.6818
fff[eee	chr5:100466770-100467004(-)$1	234	115	122	14.7499
3ccc555	chr4:147991135-147991349(-)$1	214	126	133	12.2499
ccc::::	chr13:115610937-115611150(+)$1	213	189	196	10.9999
b[ddddo	chr13:55657377-55657587(-)$1	210	68	75	14.7499
/////BB	chrX:148286919-148287138(+)$1	219	167	174	11.1136
$$dddd[	chr10:127102276-127102492(-)$1	216	21	28	14.7499
dd:::FF	chr16:24442849-24443069(+)$1	220	48	55	15.3181
ggg::::	chr16:10421981-10422201(+)$1	220	203	210	10.5454
dddd]gg	chr17:37193671-37193896(+)$1	225	82	89	14.7499
eee[ddd	chr4:98603752-98603983(-)$1	231	124	131	11.7954
:ffffff	chr9:14305084-14305311(+)$1	227	16	23	11.7954
HHHHH::	chr8:131246274-131246480(+)$1	206	154	161	13.6136
ccc!!ao	chr4:144746429-144746639(-)$1	210	79	86	10.8863
BBKKDDD	chr15:35002752-35003036(-)$1	284	0	7	14.7499
fffff22	chr1:135543926-135544143(-)$1	217	77	84	15.3181
DDDDKKE	chr2:35034094-35034303(+)$1	209	133	140	10.7727
cccbb!!	chr8:124175925-124176143(-)$1	218	73	80	10.9999
fffff[f	chr6:113579483-113579701(+)$1	218	63	70	15.3181
GGGGGGG	chr13:97256714-97256938(-)$1	224	3	10	14.7499
CCC{BB{	chr14:27352863-27353074(-)$1	211	12	19	10.9999
gggggpp	chr15:99451408-99451622(-)$1	214	47	54	10.8863
JJJLLLF	chr11:71988640-71988856(-)$1	216	29	36	11.1136
5555bb]	chr1:129869492-129869712(-)$1	220	132	139	13.6136
::iiiii	chr2:153075387-153075602(+)$1	215	27	34	10.2045
ddd:GGG	chr16:18823235-18823459(+)$1	224	10	17	12.2499
eeeeccc	chrX:126477392-126477608(+)$1	216	166	173	14.7499
ffffeee	chrX:12193639-12193868(+)$1	229	150	157	12.2499
hhh!!bb	chr17:28736618-28736836(-)$1	218	19	26	11.6818
=======	chr17:46305060-46305272(+)$1	212	49	56	10.8863
bb]ccc:	chr9:42913314-42913533(-)$1	219	32	39	10.8863
ffffff3	chr15:65649933-65650171(+)$1	238	83	90	10.7727
GGYYCCC	chr15:6366773-6367008(+)$1	235	208	215	11.1136
ddd:FFF	chr17:33785651-33785886(-)$1	235	95	102	15.3181
fff[ccc	chr11:117641783-117642002(-)$1	219	165	172	10.8863
ppccc22	chr3:68826104-68826334(+)$1	230	101	108	12.2499

#DB
.))))).	chr1:45436837-45437081(-)$1	1	66	73	13.0454
)))))).	chr18:36806257-36806481(+)$1	1	132	139	14.7499
.((((((	chr2:154360967-154361184(+)$1	1	114	121	15.3181
...((((	chr8:72706039-72706249(+)$1	1	0	7	10.2045
).)))).	chr1:137300709-137300944(-)$1	1	79	86	11.6818
.......	chr8:125756251-125756458(+)$1	1	75	82	10.5454
.....).	chr2:180706696-180706916(+)$1	1	20	27	11.9090
(...)))	chr4:70021751-70021972(-)$1	1	112	119	15.3181
)))))).	chr14:79740721-79740931(-)$1	1	42	49	11.6818
(((.(((	chr5:100466770-100467004(-)$1	1	115	122	14.7499
.)))...	chr4:147991135-147991349(-)$1	1	126	133	12.2499
)))....	chr13:115610937-115611150(+)$1	1	189	196	10.9999
(.((((.	chr13:55657377-55657587(-)$1	1	68	75	14.7499
.....))	chrX:148286919-148287138(+)$1	1	167	174	11.1136
..((((.	chr10:127102276-127102492(-)$1	1	21	28	14.7499
))...((	chr16:24442849-24443069(+)$1	1	48	55	15.3181
)))....	chr16:10421981-10422201(+)$1	1	203	210	10.5454
)))).))	chr17:37193671-37193896(+)$1	1	82	89	14.7499
(((.(((	chr4:98603752-98603983(-)$1	1	124	131	11.7954
.((((((	chr9:14305084-14305311(+)$1	1	16	23	11.7954
)))))..	chr8:131246274-131246480(+)$1	1	154	161	13.6136
(((..(.	chr4:144746429-144746639(-)$1	1	79	86	10.8863
((..(((	chr15:35002752-35003036(-)$1	1	0	7	14.7499
)))))..	chr1:135543926-135544143(-)$1	1	77	84	15.3181
((((..(	chr2:35034094-35034303(+)$1	1	133	140	10.7727
(((((..	chr8:124175925-124176143(-)$1	1	73	80	10.9999
(((((.(	chr6:113579483-113579701(+)$1	1	63	70	15.3181
(((((((	chr13:97256714-97256938(-)$1	1	3	10	14.7499
(((.((.	chr14:27352863-27353074(-)$1	1	12	19	10.9999
(((((..	chr15:99451408-99451622(-)$1	1	47	54	10.8863
(((...(	chr11:71988640-71988856(-)$1	1	29	36	11.1136
....)).	chr1:129869492-129869712(-)$1	1	132	139	13.6136
..(((((	chr2:153075387-153075602(+)$1	1	27	34	10.2045
))).(((	chr16:18823235-18823459(+)$1	1	10	17	12.2499
(((((((	chrX:126477392-126477608(+)$1	1	166	173	14.7499
))))(((	chrX:12193639-12193868(+)$1	1	150	157	12.2499
(((..((	chr17:28736618-28736836(-)$1	1	19	26	11.6818
)))))))	chr17:46305060-46305272(+)$1	1	49	56	10.8863
)).))).	chr9:42913314-42913533(-)$1	1	32	39	10.8863
)))))).	chr15:65649933-65650171(+)$1	1	83	90	10.7727
))..)))	chr15:6366773-6367008(+)$1	1	208	215	11.1136
))).)))	chr17:33785651-33785886(-)$1	1	95	102	15.3181
(((.(((	chr11:117641783-117642002(-)$1	1	165	172	10.8863
..)))..	chr3:68826104-68826334(+)$1	1	101	108	12.2499

#PSSM
U : 0.47	G : 0.34	A : 0.13	C : 0.02	g : 0.02	
G : 0.84	A : 0.13	g : 0.02	
G : 0.97	g : 0.02	
A : 0.86	G : 0.11	a : 0.02	
A : 0.90	G : 0.06	a : 0.02	
G : 0.93	A : 0.04	g : 0.02	
A : 0.72	U : 0.13	G : 0.06	C : 0.04	a : 0.02	

#score	553.5454545454543
#seq	44
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m3_run1.nuc.txt

#NT
UCA	chr9:56051039-56051256(-)$1	217	52	55	8.9999
UCA	chr11:3550202-3550426(+)$1	224	6	9	8.9999
UCA	chr3:55787604-55787836(-)$1	232	19	22	8.9999
UCA	chr1:137303508-137303738(-)$1	230	86	89	8.9999
UCA	chr1:141348241-141348456(+)$1	215	82	85	8.9999
UCA	chr7:63051185-63051393(+)$1	208	5	8	8.9999
UCA	chr11:54329037-54329260(+)$1	223	25	28	8.9999
UCA	chrX:70737266-70737495(+)$1	229	204	207	8.9999
UCA	chrX:138034671-138034904(+)$1	233	0	3	8.9999
UCA	chr11:50047889-50048109(+)$1	220	98	101	8.9999
UCA	chr8:26950408-26950629(-)$1	221	73	76	8.9999
UCA	chr2:61489233-61489453(+)$1	220	33	36	8.9999
UCA	chr16:84844436-84844662(+)$1	226	116	119	8.9999
UCA	chr2:93283434-93283657(-)$1	223	18	21	8.9999
UCA	chr5:147042783-147043001(+)$1	218	161	164	8.9999
UCA	chr9:82853281-82853509(-)$1	228	80	83	8.9999
UCA	chr5:34214038-34214257(+)$1	219	4	7	8.9999
UCA	chr18:83124813-83125033(+)$1	220	8	11	8.9999
UCA	chr2:90607907-90608192(+)$1	285	206	209	8.9999
UCA	chr19:32199630-32199849(-)$1	219	12	15	8.9999
UCA	chr1:134893161-134893377(-)$1	216	68	71	8.9999
UCA	chr17:24830923-24831144(+)$1	221	4	7	8.9999
UCA	chr8:12842811-12843018(+)$1	207	109	112	8.9999
UCA	chr1:23898609-23898853(-)$1	244	63	66	8.9999
UCA	chr19:43976078-43976297(-)$1	219	98	101	8.9999
UCA	chr19:6371970-6372195(+)$1	225	98	101	8.9999
UCA	chr1:99658181-99658400(-)$1	219	44	47	8.9999
uCA	chr17:33471036-33471254(-)$1	218	2	5	8.9999
UCA	chr3:88516292-88516517(+)$1	225	95	98	8.9999
UCA	chr14:68358262-68358482(+)$1	220	7	10	8.9999
UCA	chr10:13272593-13272806(-)$1	213	111	114	8.9999
UCA	chr17:36054203-36054424(+)$1	221	41	44	8.9999
UCA	chr1:133873250-133873469(+)$1	219	13	16	8.9999
UCA	chr3:65750660-65750874(-)$1	214	41	44	8.9999
UCA	chr1:58770203-58770418(+)$1	215	18	21	8.9999
UCA	chr11:21270322-21270571(-)$1	249	182	185	8.9999
UCA	chr5:145637489-145637704(-)$1	215	188	191	8.9999
UCA	chr2:17986569-17986807(+)$1	238	116	119	8.9999
uca	chr15:35002752-35003036(-)$1	284	29	32	8.9999
uca	chr2:152720680-152720907(+)$1	227	18	21	8.9999
UCA	chr12:4233470-4233694(-)$1	224	168	171	8.9999
UCA	chr6:29522504-29522732(-)$1	228	35	38	8.9999
UCA	chr14:15561651-15561875(+)$1	224	20	23	8.9999
UCA	chr9:83287673-83287883(-)$1	210	48	51	8.9999
UCA	chr15:99239064-99239282(+)$1	218	19	22	8.9999
UCA	chr7:5019113-5019319(+)$1	206	106	109	8.9999
UCA	chr14:56300035-56300244(-)$1	209	158	161	8.9999
UCA	chr3:108969369-108969583(+)$1	214	3	6	8.9999
UCA	chr9:96652792-96653005(-)$1	213	38	41	8.9999
UCA	chr3:19118992-19119200(+)$1	208	126	129	8.9999
UCA	chr10:5217974-5218199(+)$1	225	6	9	8.9999
UCA	chr4:83108223-83108435(-)$1	212	95	98	8.9999
uCA	chr8:122480838-122481049(+)$1	211	189	192	8.9999
UCA	chr18:57551229-57551436(+)$1	207	86	89	8.9999
UCA	chrX:98752542-98752754(+)$1	212	19	22	8.9999
UCA	chr10:57720922-57721139(+)$1	217	8	11	8.9999
UCA	chr9:36533335-36533568(-)$1	233	17	20	8.9999
UCA	chr10:79321827-79322041(+)$1	214	19	22	8.9999
UCA	chr19:42030957-42031171(-)$1	214	194	197	8.9999
UCA	chr5:145638203-145638418(-)$1	215	39	42	8.9999
UCA	chrX:35774676-35774889(-)$1	213	119	122	8.9999
UCA	chr12:77197821-77198059(+)$1	238	29	32	8.9999
uca	chr11:100882312-100882542(+)$1	230	20	23	8.9999
UCA	chr12:17002193-17002417(+)$1	224	38	41	8.9999
UCA	chr14:21839709-21839933(+)$1	224	91	94	8.9999
UCA	chr2:119590415-119590633(-)$1	218	38	41	8.9999
UCA	chr2:181098988-181099205(-)$1	217	98	101	8.9999
UCA	chr2:29544557-29544771(+)$1	214	19	22	8.9999
UCA	chr7:148083425-148083650(+)$1	225	33	36	8.9999
UCA	chrX:156029937-156030160(+)$1	223	4	7	8.9999
UCA	chr6:32999251-32999460(-)$1	209	4	7	8.9999
UCA	chr1:45435127-45435348(-)$1	221	38	41	8.9999
UCA	chr1:153853678-153853902(-)$1	224	169	172	8.9999
UCA	chr13:59605507-59605727(-)$1	220	37	40	8.9999
UCA	chr5:65431939-65432149(+)$1	210	41	44	8.9999
UCa	chr2:155998565-155998799(-)$1	234	37	40	8.9999
UCA	chr6:120275276-120275496(-)$1	220	11	14	8.9999
UCA	chr6:30835494-30835707(-)$1	213	73	76	8.9999
UCA	chr5:13399563-13399791(+)$1	228	5	8	8.9999
UCA	chr9:66366097-66366318(-)$1	221	68	71	8.9999
UCA	chr4:137176918-137177135(+)$1	217	3	6	8.9999
UCA	chr11:43517991-43518204(+)$1	213	2	5	8.9999
UCA	chr13:49481494-49481710(+)$1	216	42	45	8.9999
UCA	chr11:28826606-28826818(+)$1	212	56	59	8.9999
UCA	chr3:85932166-85932379(+)$1	213	80	83	8.9999
UCA	chr16:22259040-22259266(-)$1	226	56	59	8.9999
UCA	chrX:148463747-148463955(+)$1	208	66	69	8.9999
UCA	chr7:52409714-52409933(+)$1	219	43	46	8.9999
UCA	chr6:112570670-112570879(-)$1	209	1	4	8.9999
UCA	chr8:108167353-108167563(+)$1	210	33	36	8.9999
UCA	chr5:108998821-108999046(-)$1	225	41	44	8.9999
UCA	chr13:49703372-49703589(+)$1	217	9	12	8.9999
UCA	chr17:21672618-21672843(+)$1	225	25	28	8.9999
UCA	chr18:67705273-67705485(-)$1	212	102	105	8.9999
UCA	chr18:35750215-35750421(+)$1	206	162	165	8.9999

#otherMatches

#Struct PSSM
===	chr5:31255210-31255426(+)$1	216	105	108	8.9999
:::	chr9:56051039-56051256(-)$1	217	52	55	8.9999
:::	chr11:3550202-3550426(+)$1	224	6	9	8.9999
uuu	chr3:55787604-55787836(-)$1	232	19	22	8.9999
mdd	chr1:137303508-137303738(-)$1	230	86	89	8.9999
eee	chr1:141348241-141348456(+)$1	215	82	85	8.9999
:::	chr7:63051185-63051393(+)$1	208	5	8	8.9999
GGG	chr11:54329037-54329260(+)$1	223	25	28	8.9999
DDD	chrX:70737266-70737495(+)$1	229	204	207	8.9999
:::	chrX:138034671-138034904(+)$1	233	0	3	8.9999
hhh	chr11:50047889-50048109(+)$1	220	98	101	8.9999
ddo	chr8:26950408-26950629(-)$1	221	73	76	8.9999
qqq	chr2:61489233-61489453(+)$1	220	33	36	8.9999
ccc	chr16:84844436-84844662(+)$1	226	116	119	8.9999
{JJ	chr2:93283434-93283657(-)$1	223	18	21	8.9999
:::	chr5:147042783-147043001(+)$1	218	161	164	8.9999
:::	chr9:82853281-82853509(-)$1	228	80	83	8.9999
DDH	chr5:34214038-34214257(+)$1	219	4	7	8.9999
:::	chr18:83124813-83125033(+)$1	220	8	11	8.9999
hhh	chr2:90607907-90608192(+)$1	285	206	209	8.9999
ccc	chr19:32199630-32199849(-)$1	219	12	15	8.9999
cbb	chr1:134893161-134893377(-)$1	216	68	71	8.9999
hhh	chr17:24830923-24831144(+)$1	221	4	7	8.9999
ee!	chr8:12842811-12843018(+)$1	207	109	112	8.9999
CCL	chr1:23898609-23898853(-)$1	244	63	66	8.9999
DD:	chr19:43976078-43976297(-)$1	219	98	101	8.9999
bbc	chr19:6371970-6372195(+)$1	225	98	101	8.9999
ddd	chr1:99658181-99658400(-)$1	219	44	47	8.9999
eee	chr17:33471036-33471254(-)$1	218	2	5	8.9999
FF:	chr3:88516292-88516517(+)$1	225	95	98	8.9999
III	chr14:68358262-68358482(+)$1	220	7	10	8.9999
(((	chr10:13272593-13272806(-)$1	213	111	114	8.9999
$$b	chr17:36054203-36054424(+)$1	221	41	44	8.9999
CCC	chr1:133873250-133873469(+)$1	219	13	16	8.9999
DD{	chr3:65750660-65750874(-)$1	214	41	44	8.9999
qqq	chr1:58770203-58770418(+)$1	215	18	21	8.9999
ppp	chr11:21270322-21270571(-)$1	249	182	185	8.9999
qff	chr5:145637489-145637704(-)$1	215	188	191	8.9999
cc]	chr2:17986569-17986807(+)$1	238	116	119	8.9999
GAK	chr15:35002752-35003036(-)$1	284	29	32	8.9999
iii	chr2:152720680-152720907(+)$1	227	18	21	8.9999
"dd	chr12:4233470-4233694(-)$1	224	168	171	8.9999
hhh	chr6:29522504-29522732(-)$1	228	35	38	8.9999
{BB	chr14:15561651-15561875(+)$1	224	20	23	8.9999
:::	chr9:83287673-83287883(-)$1	210	48	51	8.9999
ggg	chr15:99239064-99239282(+)$1	218	19	22	8.9999
cpp	chr7:5019113-5019319(+)$1	206	106	109	8.9999
ccc	chr14:56300035-56300244(-)$1	209	158	161	8.9999
[ee	chr3:108969369-108969583(+)$1	214	3	6	8.9999
c!!	chr9:96652792-96653005(-)$1	213	38	41	8.9999
33g	chr3:19118992-19119200(+)$1	208	126	129	8.9999
BLL	chr10:5217974-5218199(+)$1	225	6	9	8.9999
dd[	chr4:83108223-83108435(-)$1	212	95	98	8.9999
fff	chr8:122480838-122481049(+)$1	211	189	192	8.9999
dd]	chr18:57551229-57551436(+)$1	207	86	89	8.9999
EE:	chrX:98752542-98752754(+)$1	212	19	22	8.9999
eee	chr10:57720922-57721139(+)$1	217	8	11	8.9999
rrr	chr9:36533335-36533568(-)$1	233	17	20	8.9999
ppp	chr10:79321827-79322041(+)$1	214	19	22	8.9999
ddd	chr19:42030957-42031171(-)$1	214	194	197	8.9999
dd[	chr5:145638203-145638418(-)$1	215	39	42	8.9999
bbw	chrX:35774676-35774889(-)$1	213	119	122	8.9999
fff	chr12:77197821-77198059(+)$1	238	29	32	8.9999
iii	chr11:100882312-100882542(+)$1	230	20	23	8.9999
iii	chr12:17002193-17002417(+)$1	224	38	41	8.9999
:::	chr14:21839709-21839933(+)$1	224	91	94	8.9999
IIF	chr2:119590415-119590633(-)$1	218	38	41	8.9999
ddd	chr2:181098988-181099205(-)$1	217	98	101	8.9999
CCM	chr2:29544557-29544771(+)$1	214	19	22	8.9999
ee]	chr7:148083425-148083650(+)$1	225	33	36	8.9999
::G	chrX:156029937-156030160(+)$1	223	4	7	8.9999
:::	chr6:32999251-32999460(-)$1	209	4	7	8.9999
ggg	chr1:45435127-45435348(-)$1	221	38	41	8.9999
ddd	chr1:153853678-153853902(-)$1	224	169	172	8.9999
cc[	chr13:59605507-59605727(-)$1	220	37	40	8.9999
ooo	chr5:65431939-65432149(+)$1	210	41	44	8.9999
lll	chr2:155998565-155998799(-)$1	234	37	40	8.9999
KDD	chr6:120275276-120275496(-)$1	220	11	14	8.9999
ddd	chr6:30835494-30835707(-)$1	213	73	76	8.9999
CCC	chr5:13399563-13399791(+)$1	228	5	8	8.9999
nnn	chr9:66366097-66366318(-)$1	221	68	71	8.9999
GGG	chr4:137176918-137177135(+)$1	217	3	6	8.9999
:::	chr11:43517991-43518204(+)$1	213	2	5	8.9999
fff	chr13:49481494-49481710(+)$1	216	42	45	8.9999
bb5	chr11:28826606-28826818(+)$1	212	56	59	8.9999
444	chr3:85932166-85932379(+)$1	213	80	83	8.9999
EE{	chr16:22259040-22259266(-)$1	226	56	59	8.9999
ggg	chrX:148463747-148463955(+)$1	208	66	69	8.9999
]a]	chr7:52409714-52409933(+)$1	219	43	46	8.9999
:::	chr6:112570670-112570879(-)$1	209	1	4	8.9999
]ff	chr8:108167353-108167563(+)$1	210	33	36	8.9999
ccc	chr5:108998821-108999046(-)$1	225	41	44	8.9999
DCC	chr13:49703372-49703589(+)$1	217	9	12	8.9999
dd:	chr17:21672618-21672843(+)$1	225	25	28	8.9999
h!!	chr18:67705273-67705485(-)$1	212	102	105	8.9999
:::	chr18:35750215-35750421(+)$1	206	162	165	8.9999

#DB
)))	chr5:31255210-31255426(+)$1	1	105	108	8.9999
...	chr9:56051039-56051256(-)$1	1	52	55	8.9999
...	chr11:3550202-3550426(+)$1	1	6	9	8.9999
...	chr3:55787604-55787836(-)$1	1	19	22	8.9999
.))	chr1:137303508-137303738(-)$1	1	86	89	8.9999
(((	chr1:141348241-141348456(+)$1	1	82	85	8.9999
...	chr7:63051185-63051393(+)$1	1	5	8	8.9999
(((	chr11:54329037-54329260(+)$1	1	25	28	8.9999
)))	chrX:70737266-70737495(+)$1	1	204	207	8.9999
...	chrX:138034671-138034904(+)$1	1	0	3	8.9999
(((	chr11:50047889-50048109(+)$1	1	98	101	8.9999
((.	chr8:26950408-26950629(-)$1	1	73	76	8.9999
...	chr2:61489233-61489453(+)$1	1	33	36	8.9999
(((	chr16:84844436-84844662(+)$1	1	116	119	8.9999
.((	chr2:93283434-93283657(-)$1	1	18	21	8.9999
...	chr5:147042783-147043001(+)$1	1	161	164	8.9999
...	chr9:82853281-82853509(-)$1	1	80	83	8.9999
(((	chr5:34214038-34214257(+)$1	1	4	7	8.9999
...	chr18:83124813-83125033(+)$1	1	8	11	8.9999
(((	chr2:90607907-90608192(+)$1	1	206	209	8.9999
(((	chr19:32199630-32199849(-)$1	1	12	15	8.9999
(((	chr1:134893161-134893377(-)$1	1	68	71	8.9999
(((	chr17:24830923-24831144(+)$1	1	4	7	8.9999
((.	chr8:12842811-12843018(+)$1	1	109	112	8.9999
((.	chr1:23898609-23898853(-)$1	1	63	66	8.9999
((.	chr19:43976078-43976297(-)$1	1	98	101	8.9999
)))	chr19:6371970-6372195(+)$1	1	98	101	8.9999
(((	chr1:99658181-99658400(-)$1	1	44	47	8.9999
(((	chr17:33471036-33471254(-)$1	1	2	5	8.9999
((.	chr3:88516292-88516517(+)$1	1	95	98	8.9999
(((	chr14:68358262-68358482(+)$1	1	7	10	8.9999
...	chr10:13272593-13272806(-)$1	1	111	114	8.9999
..(	chr17:36054203-36054424(+)$1	1	41	44	8.9999
(((	chr1:133873250-133873469(+)$1	1	13	16	8.9999
((.	chr3:65750660-65750874(-)$1	1	41	44	8.9999
...	chr1:58770203-58770418(+)$1	1	18	21	8.9999
...	chr11:21270322-21270571(-)$1	1	182	185	8.9999
.))	chr5:145637489-145637704(-)$1	1	188	191	8.9999
)).	chr2:17986569-17986807(+)$1	1	116	119	8.9999
((.	chr15:35002752-35003036(-)$1	1	29	32	8.9999
(((	chr2:152720680-152720907(+)$1	1	18	21	8.9999
.((	chr12:4233470-4233694(-)$1	1	168	171	8.9999
(((	chr6:29522504-29522732(-)$1	1	35	38	8.9999
.((	chr14:15561651-15561875(+)$1	1	20	23	8.9999
...	chr9:83287673-83287883(-)$1	1	48	51	8.9999
(((	chr15:99239064-99239282(+)$1	1	19	22	8.9999
(..	chr7:5019113-5019319(+)$1	1	106	109	8.9999
)))	chr14:56300035-56300244(-)$1	1	158	161	8.9999
.((	chr3:108969369-108969583(+)$1	1	3	6	8.9999
(..	chr9:96652792-96653005(-)$1	1	38	41	8.9999
..)	chr3:19118992-19119200(+)$1	1	126	129	8.9999
(..	chr10:5217974-5218199(+)$1	1	6	9	8.9999
((.	chr4:83108223-83108435(-)$1	1	95	98	8.9999
)))	chr8:122480838-122481049(+)$1	1	189	192	8.9999
)).	chr18:57551229-57551436(+)$1	1	86	89	8.9999
((.	chrX:98752542-98752754(+)$1	1	19	22	8.9999
(((	chr10:57720922-57721139(+)$1	1	8	11	8.9999
...	chr9:36533335-36533568(-)$1	1	17	20	8.9999
...	chr10:79321827-79322041(+)$1	1	19	22	8.9999
(((	chr19:42030957-42031171(-)$1	1	194	197	8.9999
((.	chr5:145638203-145638418(-)$1	1	39	42	8.9999
((.	chrX:35774676-35774889(-)$1	1	119	122	8.9999
(((	chr12:77197821-77198059(+)$1	1	29	32	8.9999
(((	chr11:100882312-100882542(+)$1	1	20	23	8.9999
(((	chr12:17002193-17002417(+)$1	1	38	41	8.9999
...	chr14:21839709-21839933(+)$1	1	91	94	8.9999
(((	chr2:119590415-119590633(-)$1	1	38	41	8.9999
(((	chr2:181098988-181099205(-)$1	1	98	101	8.9999
((.	chr2:29544557-29544771(+)$1	1	19	22	8.9999
)).	chr7:148083425-148083650(+)$1	1	33	36	8.9999
..(	chrX:156029937-156030160(+)$1	1	4	7	8.9999
...	chr6:32999251-32999460(-)$1	1	4	7	8.9999
)))	chr1:45435127-45435348(-)$1	1	38	41	8.9999
(((	chr1:153853678-153853902(-)$1	1	169	172	8.9999
((.	chr13:59605507-59605727(-)$1	1	37	40	8.9999
...	chr5:65431939-65432149(+)$1	1	41	44	8.9999
...	chr2:155998565-155998799(-)$1	1	37	40	8.9999
.((	chr6:120275276-120275496(-)$1	1	11	14	8.9999
(((	chr6:30835494-30835707(-)$1	1	73	76	8.9999
(((	chr5:13399563-13399791(+)$1	1	5	8	8.9999
...	chr9:66366097-66366318(-)$1	1	68	71	8.9999
(((	chr4:137176918-137177135(+)$1	1	3	6	8.9999
...	chr11:43517991-43518204(+)$1	1	2	5	8.9999
)))	chr13:49481494-49481710(+)$1	1	42	45	8.9999
)).	chr11:28826606-28826818(+)$1	1	56	59	8.9999
...	chr3:85932166-85932379(+)$1	1	80	83	8.9999
((.	chr16:22259040-22259266(-)$1	1	56	59	8.9999
)))	chrX:148463747-148463955(+)$1	1	66	69	8.9999
.).	chr7:52409714-52409933(+)$1	1	43	46	8.9999
...	chr6:112570670-112570879(-)$1	1	1	4	8.9999
.))	chr8:108167353-108167563(+)$1	1	33	36	8.9999
)))	chr5:108998821-108999046(-)$1	1	41	44	8.9999
(((	chr13:49703372-49703589(+)$1	1	9	12	8.9999
)).	chr17:21672618-21672843(+)$1	1	25	28	8.9999
(..	chr18:67705273-67705485(-)$1	1	102	105	8.9999
...	chr18:35750215-35750421(+)$1	1	162	165	8.9999

#PSSM
U : 0.94	u : 0.05	
C : 0.96	c : 0.03	
A : 0.95	a : 0.04	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m2_run1.nuc.txt

#NT
CCUGCUG	chr6:22950193-22950403(+)$1	210	95	102	13.3015
CCCGCUU	chr13:110728151-110728359(+)$1	208	176	183	12.5079
CCUGCUG	chr7:31349403-31349612(+)$1	209	198	205	13.3015
GCUGCUU	chr4:142723412-142723622(-)$1	210	106	113	13.7777
CCUCCUU	chr6:124696336-124696540(-)$1	204	196	203	12.1904
CCCGCUU	chr2:118256823-118257037(+)$1	214	51	58	12.5079
CCAGCUU	chr13:106040361-106040569(-)$1	208	14	21	12.5873
UCUGCUU	chr5:135858165-135858373(-)$1	208	110	117	14.0158
UCUGCUU	chr11:49961601-49961810(+)$1	209	73	80	14.0158
CCUGCUG	chr2:166765098-166765309(+)$1	211	114	121	13.3015
CCUGCUU	chr6:92110210-92110430(+)$1	220	167	174	16.6349
ACUGCUU	chr5:65986055-65986257(+)$1	202	114	121	13.7777
CCUGCUC	chr15:98427531-98427759(-)$1	228	67	74	12.9047
UCUGCUU	chr7:30168174-30168388(-)$1	214	5	12	14.0158
CCUGCUA	chr9:44627588-44627789(-)$1	201	117	124	12.8253
CCUGCUU	chr5:118393768-118393979(+)$1	211	131	138	16.6349
CCUGCUC	chr7:52427113-52427322(+)$1	209	120	127	12.9047
GCUGCUU	chr17:64632711-64632911(-)$1	200	84	91	13.7777
CCUGCUU	chr10:41916792-41917009(-)$1	217	96	103	16.6349
GCUGCUU	chr1:176433217-176433426(+)$1	209	106	113	13.7777
CUUGCUU	chr12:74373299-74373533(+)$1	234	34	41	12.5079
ACUGCUU	chrX:132337531-132337744(+)$1	213	196	203	13.7777
CCUCCUU	chr11:119719112-119719341(+)$1	229	11	18	12.1904
CCUACUU	chr11:44365140-44365348(+)$1	208	117	124	12.0317
CCAGCUU	chr11:115940558-115940761(-)$1	203	80	87	12.5873
CCUGCUG	chrX:148315107-148315308(+)$1	201	57	64	13.3015
CCUGCUU	chr11:69639024-69639242(-)$1	218	210	217	16.6349
CCUGCAU	chr16:32680377-32680578(+)$1	201	148	155	11.9523
GCUGCUU	chr11:90125770-90125981(+)$1	211	101	108	13.7777
CCUGCUG	chr7:52381780-52381983(-)$1	203	15	22	13.3015
CCUGCUU	chr11:59999640-59999841(+)$1	201	103	110	16.6349
CCUGCUU	chr7:25845499-25845700(-)$1	201	12	19	16.6349
CCGGCUU	chr10:126723255-126723464(-)$1	209	20	27	12.3492
GCUGCUU	chr7:31220437-31220648(-)$1	211	99	106	13.7777
CUUGCUU	chr2:157769821-157770035(+)$1	214	108	115	12.5079
UCUGCUU	chr2:122520075-122520296(-)$1	221	98	105	14.0158
CCUGCUG	chrX:20224915-20225138(+)$1	223	94	101	13.3015
CCUGCUU	chr3:54703255-54703460(-)$1	205	97	104	16.6349
UCUGCUu	chr15:82686748-82686970(-)$1	222	39	46	14.0158
CCCGCUU	chr18:78018573-78018786(+)$1	213	41	48	12.5079
ccugcug	chr10:72137034-72137235(+)$1	201	95	102	13.3015
CCUGCCU	chr11:70483359-70483567(-)$1	208	118	125	12.0317
CCAGCUU	chr1:75471489-75471691(-)$1	202	98	105	12.5873
UCUGCUU	chrX:70925242-70925462(+)$1	220	118	125	14.0158
GCUGCUU	chr18:75216227-75216441(+)$1	214	100	107	13.7777
UCUGCUU	chr11:62143014-62143214(-)$1	200	135	142	14.0158
CCUGCUA	chr8:128374901-128375110(-)$1	209	97	104	12.8253
ACUGCUU	chr8:96491851-96492051(+)$1	200	80	87	13.7777
CAUGCUU	chrX:133366464-133366664(+)$1	200	31	38	12.1904
CCUGCCU	chr2:163453596-163453806(-)$1	210	104	111	12.0317
ACUGCUU	chr2:102596159-102596362(+)$1	203	127	134	13.7777
CCUGCUU	chr6:42628543-42628745(-)$1	202	71	78	16.6349
ACUGCUU	chr8:96528993-96529193(-)$1	200	80	87	13.7777
CUUGCUU	chr2:14882386-14882601(-)$1	215	199	206	12.5079
CCUGCUG	chr11:69722467-69722690(+)$1	223	103	110	13.3015
CCUGCUC	chr9:28804002-28804231(-)$1	229	94	101	12.9047
CCUCCUU	chr8:114541949-114542170(+)$1	221	24	31	12.1904
CUUGCUU	chr11:31954954-31955157(+)$1	203	91	98	12.5079
ACUGCUU	chr14:103604316-103604516(-)$1	200	38	45	13.7777
UCUGCUU	chr3:125570205-125570413(-)$1	208	96	103	14.0158
CCAGCUU	chr15:36527935-36528156(-)$1	221	154	161	12.5873
CUUGCUU	chr7:20281563-20281764(-)$1	201	118	125	12.5079

#otherMatches

#Struct PSSM
qqqqqqq	chr1:127769815-127770020(-)$1	205	88	95	14.0158
:eeeeeo	chr6:22950193-22950403(+)$1	210	95	102	13.3015
rrrrrrr	chr13:110728151-110728359(+)$1	208	176	183	12.5079
lllccc2	chr7:31349403-31349612(+)$1	209	198	205	13.3015
ccc::::	chr4:142723412-142723622(-)$1	210	106	113	13.7777
:::::::	chr6:124696336-124696540(-)$1	204	196	203	12.1904
mmmcccc	chr2:118256823-118257037(+)$1	214	51	58	12.5079
EEECCCe	chr13:106040361-106040569(-)$1	208	14	21	12.5873
!!dddd!	chr5:135858165-135858373(-)$1	208	110	117	14.0158
::ddddn	chr11:49961601-49961810(+)$1	209	73	80	14.0158
c[bb[cc	chr2:166765098-166765309(+)$1	211	114	121	13.3015
ppccc::	chr6:92110210-92110430(+)$1	220	167	174	16.6349
eeeeeee	chr5:65986055-65986257(+)$1	202	114	121	13.7777
bb[bb!!	chr15:98427531-98427759(-)$1	228	67	74	12.9047
""fffff	chr7:30168174-30168388(-)$1	214	5	12	14.0158
:dddd!!	chr9:44627588-44627789(-)$1	201	117	124	12.8253
dddd]dd	chr5:118393768-118393979(+)$1	211	131	138	16.6349
\\\BB}D	chr7:52427113-52427322(+)$1	209	120	127	12.9047
c"""app	chr17:64632711-64632911(-)$1	200	84	91	13.7777
""dddd[	chr10:41916792-41917009(-)$1	217	96	103	16.6349
dddd:::	chr1:176433217-176433426(+)$1	209	106	113	13.7777
ffbb[dd	chr12:74373299-74373533(+)$1	234	34	41	12.5079
FFFFF}B	chrX:132337531-132337744(+)$1	213	196	203	13.7777
drrrrrr	chr11:119719112-119719341(+)$1	229	11	18	12.1904
qbb5555	chr11:44365140-44365348(+)$1	208	117	124	12.0317
qqqgggg	chr11:115940558-115940761(-)$1	203	80	87	12.5873
:ccc!!c	chrX:148315107-148315308(+)$1	201	57	64	13.3015
bb]bb::	chr11:69639024-69639242(-)$1	218	210	217	16.6349
dddd::g	chr16:32680377-32680578(+)$1	201	148	155	11.9523
eeddddb	chr11:90125770-90125981(+)$1	211	101	108	13.7777
DDDD{FF	chr7:52381780-52381983(-)$1	203	15	22	13.3015
"""dddd	chr11:59999640-59999841(+)$1	201	103	110	16.6349
::DDDDL	chr7:25845499-25845700(-)$1	201	12	19	16.6349
:::ccc[	chr10:126723255-126723464(-)$1	209	20	27	12.3492
ee[bbmm	chr7:31220437-31220648(-)$1	211	99	106	13.7777
bccc$$$	chr2:157769821-157770035(+)$1	214	108	115	12.5079
dddd[cc	chr2:122520075-122520296(-)$1	221	98	105	14.0158
^eeeee:	chrX:20224915-20225138(+)$1	223	94	101	13.3015
:::gggg	chr3:54703255-54703460(-)$1	205	97	104	16.6349
333ccc]	chr15:82686748-82686970(-)$1	222	39	46	14.0158
c"""ccc	chr18:78018573-78018786(+)$1	213	41	48	12.5079
mmmbb]d	chr10:72137034-72137235(+)$1	201	95	102	13.3015
444bb22	chr11:70483359-70483567(-)$1	208	118	125	12.0317
:ddddpp	chr1:75471489-75471691(-)$1	202	98	105	12.5873
>>>>>>>	chrX:70925242-70925462(+)$1	220	118	125	14.0158
bbnnnnn	chr18:75216227-75216441(+)$1	214	100	107	13.7777
^dddd::	chr11:62143014-62143214(-)$1	200	135	142	14.0158
!!bb%%%	chr8:128374901-128375110(-)$1	209	97	104	12.8253
hhh:a!!	chr8:96491851-96492051(+)$1	200	80	87	13.7777
ffffffm	chrX:133366464-133366664(+)$1	200	31	38	12.1904
mmmbb::	chr2:163453596-163453806(-)$1	210	104	111	12.0317
nnnnnff	chr2:102596159-102596362(+)$1	203	127	134	13.7777
FFFFF::	chr6:42628543-42628745(-)$1	202	71	78	16.6349
ffff"""	chr8:96528993-96529193(-)$1	200	80	87	13.7777
:GGGGGG	chr2:14882386-14882601(-)$1	215	199	206	12.5079
HH::eee	chr11:69722467-69722690(+)$1	223	103	110	13.3015
44bb22e	chr9:28804002-28804231(-)$1	229	94	101	12.9047
GGGGKKC	chr8:114541949-114542170(+)$1	221	24	31	12.1904
eee####	chr11:31954954-31955157(+)$1	203	91	98	12.5079
[cccttt	chr14:103604316-103604516(-)$1	200	38	45	13.7777
KKEEEEE	chr3:125570205-125570413(-)$1	208	96	103	14.0158
:::::::	chr15:36527935-36528156(-)$1	221	154	161	12.5873
cccqqqq	chr7:20281563-20281764(-)$1	201	118	125	12.5079

#DB
.......	chr1:127769815-127770020(-)$1	1	88	95	14.0158
.(((((.	chr6:22950193-22950403(+)$1	1	95	102	13.3015
.......	chr13:110728151-110728359(+)$1	1	176	183	12.5079
...))).	chr7:31349403-31349612(+)$1	1	198	205	13.3015
)))....	chr4:142723412-142723622(-)$1	1	106	113	13.7777
.......	chr6:124696336-124696540(-)$1	1	196	203	12.1904
...)))(	chr2:118256823-118257037(+)$1	1	51	58	12.5079
(((((((	chr13:106040361-106040569(-)$1	1	14	21	12.5873
..((((.	chr5:135858165-135858373(-)$1	1	110	117	14.0158
..((((.	chr11:49961601-49961810(+)$1	1	73	80	14.0158
(.((.((	chr2:166765098-166765309(+)$1	1	114	121	13.3015
..)))..	chr6:92110210-92110430(+)$1	1	167	174	16.6349
)))))))	chr5:65986055-65986257(+)$1	1	114	121	13.7777
((.((..	chr15:98427531-98427759(-)$1	1	67	74	12.9047
..(((((	chr7:30168174-30168388(-)$1	1	5	12	14.0158
.((((..	chr9:44627588-44627789(-)$1	1	117	124	12.8253
)))).))	chr5:118393768-118393979(+)$1	1	131	138	16.6349
...)).)	chr7:52427113-52427322(+)$1	1	120	127	12.9047
(...(..	chr17:64632711-64632911(-)$1	1	84	91	13.7777
..((((.	chr10:41916792-41917009(-)$1	1	96	103	16.6349
))))...	chr1:176433217-176433426(+)$1	1	106	113	13.7777
((((.((	chr12:74373299-74373533(+)$1	1	34	41	12.5079
))))).)	chrX:132337531-132337744(+)$1	1	196	203	13.7777
(......	chr11:119719112-119719341(+)$1	1	11	18	12.1904
.))....	chr11:44365140-44365348(+)$1	1	117	124	12.0317
...))))	chr11:115940558-115940761(-)$1	1	80	87	12.5873
.(((..(	chrX:148315107-148315308(+)$1	1	57	64	13.3015
)).))..	chr11:69639024-69639242(-)$1	1	210	217	16.6349
))))..(	chr16:32680377-32680578(+)$1	1	148	155	11.9523
))(((((	chr11:90125770-90125981(+)$1	1	101	108	13.7777
((((.((	chr7:52381780-52381983(-)$1	1	15	22	13.3015
...((((	chr11:59999640-59999841(+)$1	1	103	110	16.6349
..((((.	chr7:25845499-25845700(-)$1	1	12	19	16.6349
...(((.	chr10:126723255-126723464(-)$1	1	20	27	12.3492
((.((..	chr7:31220437-31220648(-)$1	1	99	106	13.7777
((((...	chr2:157769821-157770035(+)$1	1	108	115	12.5079
((((.((	chr2:122520075-122520296(-)$1	1	98	105	14.0158
.))))).	chrX:20224915-20225138(+)$1	1	94	101	13.3015
...((((	chr3:54703255-54703460(-)$1	1	97	104	16.6349
...))).	chr15:82686748-82686970(-)$1	1	39	46	14.0158
(...(((	chr18:78018573-78018786(+)$1	1	41	48	12.5079
...)).)	chr10:72137034-72137235(+)$1	1	95	102	13.3015
...))..	chr11:70483359-70483567(-)$1	1	118	125	12.0317
.((((..	chr1:75471489-75471691(-)$1	1	98	105	12.5873
.......	chrX:70925242-70925462(+)$1	1	118	125	14.0158
((.....	chr18:75216227-75216441(+)$1	1	100	107	13.7777
.))))..	chr11:62143014-62143214(-)$1	1	135	142	14.0158
..((...	chr8:128374901-128375110(-)$1	1	97	104	12.8253
))).(..	chr8:96491851-96492051(+)$1	1	80	87	13.7777
((((((.	chrX:133366464-133366664(+)$1	1	31	38	12.1904
...))..	chr2:163453596-163453806(-)$1	1	104	111	12.0317
.....))	chr2:102596159-102596362(+)$1	1	127	134	13.7777
(((((..	chr6:42628543-42628745(-)$1	1	71	78	16.6349
((((...	chr8:96528993-96529193(-)$1	1	80	87	13.7777
.))))))	chr2:14882386-14882601(-)$1	1	199	206	12.5079
))..(((	chr11:69722467-69722690(+)$1	1	103	110	13.3015
..))..)	chr9:28804002-28804231(-)$1	1	94	101	12.9047
((((..(	chr8:114541949-114542170(+)$1	1	24	31	12.1904
(((....	chr11:31954954-31955157(+)$1	1	91	98	12.5079
.(((...	chr14:103604316-103604516(-)$1	1	38	45	13.7777
..(((((	chr3:125570205-125570413(-)$1	1	96	103	14.0158
.......	chr15:36527935-36528156(-)$1	1	154	161	12.5873
(((....	chr7:20281563-20281764(-)$1	1	118	125	12.5079

#PSSM
C : 0.65	U : 0.14	G : 0.09	A : 0.09	c : 0.01	
C : 0.88	U : 0.07	c : 0.01	A : 0.01	
U : 0.85	A : 0.06	C : 0.04	G : 0.01	u : 0.01	
G : 0.92	C : 0.04	A : 0.01	g : 0.01	
C : 0.98	c : 0.01	
U : 0.93	C : 0.03	A : 0.01	u : 0.01	
U : 0.77	G : 0.11	C : 0.04	A : 0.03	u : 0.01	g : 0.01	

#score	854.9047619047604
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_transcript_m1_run2.nuc.txt

#NT
UUCA	chr5:36367127-36367345(-)$1	218	25	29	11.9999
uuca	chr11:106602106-106602326(+)$1	220	90	94	11.9999
UUCA	chr2:69718737-69718952(-)$1	215	36	40	11.9999
UUCA	chr10:121007654-121007880(-)$1	226	28	32	11.9999
UUCA	chr8:107741160-107741369(+)$1	209	67	71	11.9999
UUCA	chr10:57217265-57217481(+)$1	216	39	43	11.9999
UUCA	chr2:155470599-155470812(-)$1	213	38	42	11.9999
UUCA	chr16:37041715-37041934(+)$1	219	73	77	11.9999
UUCA	chr11:106124326-106124536(+)$1	210	145	149	11.9999
UUCA	chrX:49033405-49033624(-)$1	219	166	170	11.9999
UUCA	chr5:121704112-121704337(+)$1	225	0	4	11.9999
UUCA	chr3:144253513-144253730(+)$1	217	196	200	11.9999
UUCA	chr18:77365492-77365711(+)$1	219	186	190	11.9999
UUCA	chr8:125589809-125590026(+)$1	217	59	63	11.9999
UUCA	chr5:140779476-140779735(-)$1	259	22	26	11.9999
UUCA	chr15:34442383-34442589(+)$1	206	79	83	11.9999
UUCA	chr11:69170837-69171046(-)$1	209	168	172	11.9999
UUCA	chr4:83120099-83120367(-)$1	268	74	78	11.9999
UUCA	chr5:90713977-90714194(-)$1	217	42	46	11.9999
UUCA	chr4:11510796-11511003(+)$1	207	153	157	11.9999
UUCA	chr14:87367533-87367752(-)$1	219	138	142	11.9999
UUCA	chr19:29069474-29069708(+)$1	234	18	22	11.9999
UUCA	chr1:164632226-164632486(-)$1	260	180	184	11.9999
UUCA	chr1:54835047-54835288(-)$1	241	174	178	11.9999
UUCA	chr11:70700503-70700710(+)$1	207	36	40	11.9999
UUCA	chr11:4980408-4980632(-)$1	224	88	92	11.9999
UUCA	chr14:17242263-17242489(+)$1	226	3	7	11.9999
UUCA	chr17:83843866-83844087(+)$1	221	56	60	11.9999
UUCA	chr14:19703915-19704133(-)$1	218	63	67	11.9999
UUCA	chr12:32020258-32020475(-)$1	217	51	55	11.9999
UUCA	chr18:44669762-44669972(-)$1	210	44	48	11.9999
UUCA	chr2:124907817-124908041(-)$1	224	33	37	11.9999
UUCA	chr11:54323353-54323575(+)$1	222	97	101	11.9999
UUCA	chr6:84050083-84050303(+)$1	220	16	20	11.9999
UUCA	chrX:39150750-39150968(-)$1	218	199	203	11.9999
UUCA	chr2:153581589-153581812(+)$1	223	72	76	11.9999
UUCA	chrX:72357218-72357427(-)$1	209	116	120	11.9999
UUCA	chr1:162186364-162186582(-)$1	218	139	143	11.9999
UUCA	chr9:82778350-82778568(-)$1	218	9	13	11.9999
UUCA	chr1:181318510-181318741(-)$1	231	142	146	11.9999
UUCA	chr17:47112872-47113095(-)$1	223	107	111	11.9999
UUCA	chr2:163906470-163906691(+)$1	221	152	156	11.9999
UUCA	chr15:79369653-79369888(-)$1	235	152	156	11.9999
uuca	chr13:93617890-93618105(+)$1	215	37	41	11.9999
UUCA	chr11:26398900-26399121(-)$1	221	27	31	11.9999
UUCA	chr4:147418506-147418714(+)$1	208	84	88	11.9999
UUCA	chr5:150529301-150529514(+)$1	213	51	55	11.9999
UUCA	chr2:61558433-61558660(+)$1	227	147	151	11.9999
UUCA	chr9:82848968-82849182(-)$1	214	15	19	11.9999
UUCA	chr11:106390520-106390735(-)$1	215	35	39	11.9999
UUCA	chr10:126983398-126983623(-)$1	225	56	60	11.9999
UUCA	chr1:158367761-158367972(-)$1	211	89	93	11.9999
UUCA	chrX:35917243-35917458(-)$1	215	57	61	11.9999
UUCA	chr1:187220031-187220253(+)$1	222	29	33	11.9999
UUCA	chr13:49016902-49017130(-)$1	228	87	91	11.9999
UUCA	chr12:56158135-56158353(-)$1	218	9	13	11.9999
UUCA	chr16:32898867-32899078(+)$1	211	4	8	11.9999
UUCA	chr4:132195665-132195891(+)$1	226	38	42	11.9999
UUCA	chr11:107480476-107480701(+)$1	225	23	27	11.9999
uuca	chr16:22078815-22079033(-)$1	218	30	34	11.9999
UUCA	chr13:85377670-85377926(-)$1	256	11	15	11.9999
UUCA	chr3:141250270-141250484(+)$1	214	139	143	11.9999
UUCA	chr19:8815871-8816093(+)$1	222	206	210	11.9999
UUCA	chr7:148817141-148817361(+)$1	220	44	48	11.9999
UUCA	chr17:84920990-84921211(+)$1	221	137	141	11.9999
UUCA	chr9:14350943-14351171(-)$1	228	95	99	11.9999
UUCA	chr1:34280568-34280785(+)$1	217	75	79	11.9999
UUCA	chr14:22656983-22657204(+)$1	221	75	79	11.9999
uuca	chr1:71637806-71638015(-)$1	209	67	71	11.9999
UUCA	chr13:6557321-6557538(+)$1	217	109	113	11.9999
UUCA	chr2:153177841-153178054(+)$1	213	48	52	11.9999

#otherMatches

#Struct PSSM
:CCC	chr18:31993789-31994012(+)$1	223	6	10	11.9999
[ddd	chr5:36367127-36367345(-)$1	218	25	29	11.9999
dd##	chr11:106602106-106602326(+)$1	220	90	94	11.9999
IIII	chr2:69718737-69718952(-)$1	215	36	40	11.9999
dddd	chr10:121007654-121007880(-)$1	226	28	32	11.9999
gggg	chr8:107741160-107741369(+)$1	209	67	71	11.9999
c!!e	chr10:57217265-57217481(+)$1	216	39	43	11.9999
gggu	chr2:155470599-155470812(-)$1	213	38	42	11.9999
$bbx	chr16:37041715-37041934(+)$1	219	73	77	11.9999
~~CC	chr11:106124326-106124536(+)$1	210	145	149	11.9999
ggg9	chrX:49033405-49033624(-)$1	219	166	170	11.9999
::::	chr5:121704112-121704337(+)$1	225	0	4	11.9999
???C	chr3:144253513-144253730(+)$1	217	196	200	11.9999
eeee	chr18:77365492-77365711(+)$1	219	186	190	11.9999
ddd[	chr8:125589809-125590026(+)$1	217	59	63	11.9999
LLLG	chr5:140779476-140779735(-)$1	259	22	26	11.9999
::::	chr15:34442383-34442589(+)$1	206	79	83	11.9999
eee:	chr11:69170837-69171046(-)$1	209	168	172	11.9999
HHHH	chr4:83120099-83120367(-)$1	268	74	78	11.9999
!!dd	chr5:90713977-90714194(-)$1	217	42	46	11.9999
ffff	chr4:11510796-11511003(+)$1	207	153	157	11.9999
####	chr14:87367533-87367752(-)$1	219	138	142	11.9999
:::E	chr19:29069474-29069708(+)$1	234	18	22	11.9999
cc22	chr1:164632226-164632486(-)$1	260	180	184	11.9999
rccc	chr1:54835047-54835288(-)$1	241	174	178	11.9999
hhhm	chr11:70700503-70700710(+)$1	207	36	40	11.9999
fff2	chr11:4980408-4980632(-)$1	224	88	92	11.9999
::::	chr14:17242263-17242489(+)$1	226	3	7	11.9999
DDdd	chr17:83843866-83844087(+)$1	221	56	60	11.9999
====	chr14:19703915-19704133(-)$1	218	63	67	11.9999
gggg	chr12:32020258-32020475(-)$1	217	51	55	11.9999
2bb:	chr18:44669762-44669972(-)$1	210	44	48	11.9999
%%%%	chr2:124907817-124908041(-)$1	224	33	37	11.9999
::::	chr11:54323353-54323575(+)$1	222	97	101	11.9999
qqqq	chr6:84050083-84050303(+)$1	220	16	20	11.9999
lddd	chrX:39150750-39150968(-)$1	218	199	203	11.9999
====	chr2:153581589-153581812(+)$1	223	72	76	11.9999
hhhh	chrX:72357218-72357427(-)$1	209	116	120	11.9999
7777	chr1:162186364-162186582(-)$1	218	139	143	11.9999
KCCC	chr9:82778350-82778568(-)$1	218	9	13	11.9999
eeee	chr1:181318510-181318741(-)$1	231	142	146	11.9999
ddd:	chr17:47112872-47113095(-)$1	223	107	111	11.9999
d]dd	chr2:163906470-163906691(+)$1	221	152	156	11.9999
f:::	chr15:79369653-79369888(-)$1	235	152	156	11.9999
eeee	chr13:93617890-93618105(+)$1	215	37	41	11.9999
:::d	chr11:26398900-26399121(-)$1	221	27	31	11.9999
ffff	chr4:147418506-147418714(+)$1	208	84	88	11.9999
333c	chr5:150529301-150529514(+)$1	213	51	55	11.9999
qqqq	chr2:61558433-61558660(+)$1	227	147	151	11.9999
#ddd	chr9:82848968-82849182(-)$1	214	15	19	11.9999
:ccc	chr11:106390520-106390735(-)$1	215	35	39	11.9999
GGGG	chr10:126983398-126983623(-)$1	225	56	60	11.9999
!!cc	chr1:158367761-158367972(-)$1	211	89	93	11.9999
^^^^	chrX:35917243-35917458(-)$1	215	57	61	11.9999
ddd!	chr1:187220031-187220253(+)$1	222	29	33	11.9999
hhhr	chr13:49016902-49017130(-)$1	228	87	91	11.9999
:::c	chr12:56158135-56158353(-)$1	218	9	13	11.9999
::::	chr16:32898867-32899078(+)$1	211	4	8	11.9999
IKKB	chr4:132195665-132195891(+)$1	226	38	42	11.9999
LLDD	chr11:107480476-107480701(+)$1	225	23	27	11.9999
::::	chr16:22078815-22079033(-)$1	218	30	34	11.9999
hhhh	chr13:85377670-85377926(-)$1	256	11	15	11.9999
::::	chr3:141250270-141250484(+)$1	214	139	143	11.9999
EE||	chr19:8815871-8816093(+)$1	222	206	210	11.9999
WWFF	chr7:148817141-148817361(+)$1	220	44	48	11.9999
ee33	chr17:84920990-84921211(+)$1	221	137	141	11.9999
ffff	chr9:14350943-14351171(-)$1	228	95	99	11.9999
eee3	chr1:34280568-34280785(+)$1	217	75	79	11.9999
ffff	chr14:22656983-22657204(+)$1	221	75	79	11.9999
KKEE	chr1:71637806-71638015(-)$1	209	67	71	11.9999
::CC	chr13:6557321-6557538(+)$1	217	109	113	11.9999
f$$$	chr2:153177841-153178054(+)$1	213	48	52	11.9999

#DB
.(((	chr18:31993789-31994012(+)$1	1	6	10	11.9999
.(((	chr5:36367127-36367345(-)$1	1	25	29	11.9999
((..	chr11:106602106-106602326(+)$1	1	90	94	11.9999
((((	chr2:69718737-69718952(-)$1	1	36	40	11.9999
((((	chr10:121007654-121007880(-)$1	1	28	32	11.9999
))))	chr8:107741160-107741369(+)$1	1	67	71	11.9999
(..(	chr10:57217265-57217481(+)$1	1	39	43	11.9999
(((.	chr2:155470599-155470812(-)$1	1	38	42	11.9999
.((.	chr16:37041715-37041934(+)$1	1	73	77	11.9999
..))	chr11:106124326-106124536(+)$1	1	145	149	11.9999
))).	chrX:49033405-49033624(-)$1	1	166	170	11.9999
....	chr5:121704112-121704337(+)$1	1	0	4	11.9999
...)	chr3:144253513-144253730(+)$1	1	196	200	11.9999
))))	chr18:77365492-77365711(+)$1	1	186	190	11.9999
(((.	chr8:125589809-125590026(+)$1	1	59	63	11.9999
...(	chr5:140779476-140779735(-)$1	1	22	26	11.9999
....	chr15:34442383-34442589(+)$1	1	79	83	11.9999
))).	chr11:69170837-69171046(-)$1	1	168	172	11.9999
((((	chr4:83120099-83120367(-)$1	1	74	78	11.9999
..((	chr5:90713977-90714194(-)$1	1	42	46	11.9999
))))	chr4:11510796-11511003(+)$1	1	153	157	11.9999
....	chr14:87367533-87367752(-)$1	1	138	142	11.9999
...(	chr19:29069474-29069708(+)$1	1	18	22	11.9999
))..	chr1:164632226-164632486(-)$1	1	180	184	11.9999
.)))	chr1:54835047-54835288(-)$1	1	174	178	11.9999
(((.	chr11:70700503-70700710(+)$1	1	36	40	11.9999
))).	chr11:4980408-4980632(-)$1	1	88	92	11.9999
....	chr14:17242263-17242489(+)$1	1	3	7	11.9999
((((	chr17:83843866-83844087(+)$1	1	56	60	11.9999
))))	chr14:19703915-19704133(-)$1	1	63	67	11.9999
))))	chr12:32020258-32020475(-)$1	1	51	55	11.9999
.)).	chr18:44669762-44669972(-)$1	1	44	48	11.9999
....	chr2:124907817-124908041(-)$1	1	33	37	11.9999
....	chr11:54323353-54323575(+)$1	1	97	101	11.9999
....	chr6:84050083-84050303(+)$1	1	16	20	11.9999
.)))	chrX:39150750-39150968(-)$1	1	199	203	11.9999
((((	chr2:153581589-153581812(+)$1	1	72	76	11.9999
((((	chrX:72357218-72357427(-)$1	1	116	120	11.9999
....	chr1:162186364-162186582(-)$1	1	139	143	11.9999
.(((	chr9:82778350-82778568(-)$1	1	9	13	11.9999
((((	chr1:181318510-181318741(-)$1	1	142	146	11.9999
))).	chr17:47112872-47113095(-)$1	1	107	111	11.9999
).))	chr2:163906470-163906691(+)$1	1	152	156	11.9999
)...	chr15:79369653-79369888(-)$1	1	152	156	11.9999
((((	chr13:93617890-93618105(+)$1	1	37	41	11.9999
...(	chr11:26398900-26399121(-)$1	1	27	31	11.9999
((((	chr4:147418506-147418714(+)$1	1	84	88	11.9999
...)	chr5:150529301-150529514(+)$1	1	51	55	11.9999
....	chr2:61558433-61558660(+)$1	1	147	151	11.9999
.(((	chr9:82848968-82849182(-)$1	1	15	19	11.9999
.(((	chr11:106390520-106390735(-)$1	1	35	39	11.9999
((((	chr10:126983398-126983623(-)$1	1	56	60	11.9999
..((	chr1:158367761-158367972(-)$1	1	89	93	11.9999
....	chrX:35917243-35917458(-)$1	1	57	61	11.9999
(((.	chr1:187220031-187220253(+)$1	1	29	33	11.9999
(((.	chr13:49016902-49017130(-)$1	1	87	91	11.9999
...(	chr12:56158135-56158353(-)$1	1	9	13	11.9999
....	chr16:32898867-32899078(+)$1	1	4	8	11.9999
(..(	chr4:132195665-132195891(+)$1	1	38	42	11.9999
..((	chr11:107480476-107480701(+)$1	1	23	27	11.9999
....	chr16:22078815-22079033(-)$1	1	30	34	11.9999
((((	chr13:85377670-85377926(-)$1	1	11	15	11.9999
....	chr3:141250270-141250484(+)$1	1	139	143	11.9999
))..	chr19:8815871-8816093(+)$1	1	206	210	11.9999
..((	chr7:148817141-148817361(+)$1	1	44	48	11.9999
))..	chr17:84920990-84921211(+)$1	1	137	141	11.9999
))))	chr9:14350943-14351171(-)$1	1	95	99	11.9999
))).	chr1:34280568-34280785(+)$1	1	75	79	11.9999
((((	chr14:22656983-22657204(+)$1	1	75	79	11.9999
..((	chr1:71637806-71638015(-)$1	1	67	71	11.9999
..))	chr13:6557321-6557538(+)$1	1	109	113	11.9999
(...	chr2:153177841-153178054(+)$1	1	48	52	11.9999

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

#score	863.9999999999995
#seq	72
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m2_run2.nuc.txt

#NT
GAGGA	chr9:70391649-70391926(+)$1	277	136	141	15.0000
GAGGA	chr10:66681847-66682134(+)$1	287	75	80	15.0000
GAGGA	chr17:34249703-34250005(-)$1	302	111	116	15.0000
GAGGA	chr5:73306049-73306338(+)$1	289	78	83	15.0000
GAGGA	chr5:104888829-104889109(+)$1	280	102	107	15.0000
GAGGA	chr1:173327524-173327795(+)$1	271	258	263	15.0000
GAGGA	chr18:78016158-78016514(+)$1	356	125	130	15.0000
GAGGA	chr1:52981942-52982248(-)$1	306	65	70	15.0000
GAGGA	chr6:108328137-108328405(+)$1	268	260	265	15.0000
GAGGA	chr18:65783234-65783529(+)$1	295	83	88	15.0000
GAGGA	chr16:96266053-96266338(-)$1	285	2	7	15.0000
GAGGA	chr17:27904684-27904967(-)$1	283	125	130	15.0000
GAGGA	chr1:180259915-180260189(-)$1	274	126	131	15.0000
GAGGA	chr7:29091378-29091658(-)$1	280	6	11	15.0000
GAGGA	chrX:7514933-7515222(-)$1	289	96	101	15.0000
GAGGA	chr14:46242427-46242697(-)$1	270	128	133	15.0000
GAGGA	chr12:83084419-83084692(+)$1	273	71	76	15.0000
GAGGA	chr8:73053243-73053530(+)$1	287	168	173	15.0000
GAGGA	chr16:20679552-20679845(+)$1	293	143	148	15.0000
GAGGA	chr3:88512709-88512986(+)$1	277	109	114	15.0000
GAGGA	chr10:80785424-80785708(+)$1	284	29	34	15.0000
GAGGA	chr5:146003740-146004016(+)$1	276	175	180	15.0000
GAGGA	chr10:90625453-90625815(-)$1	362	167	172	15.0000
GAGGA	chr5:125538066-125538348(-)$1	282	131	136	15.0000
GAGGA	chr15:12864682-12864990(+)$1	308	168	173	15.0000
GAGGA	chr6:67217235-67217518(+)$1	283	131	136	15.0000
gagga	chr4:142725470-142725754(-)$1	284	0	5	15.0000
GAGGA	chr5:138609190-138609465(-)$1	275	158	163	15.0000
GAGGA	chr10:74997877-74998171(+)$1	294	143	148	15.0000
GAGGA	chr15:78171935-78172205(+)$1	270	89	94	15.0000
GAGGA	chr1:36995895-36996261(-)$1	366	87	92	15.0000
GAGGA	chr12:17290648-17290935(+)$1	287	104	109	15.0000
GAGGA	chr7:52107813-52108107(+)$1	294	74	79	15.0000
GAGGA	chr4:147315056-147315344(+)$1	288	5	10	15.0000
GAGGA	chr4:130224992-130225287(+)$1	295	141	146	15.0000
GAGGA	chr9:70526857-70527145(+)$1	288	132	137	15.0000
GAGGA	chr15:101925580-101925871(+)$1	291	49	54	15.0000
GAGGA	chr9:65642328-65642605(-)$1	277	4	9	15.0000
GAGGA	chr5:124848319-124848593(-)$1	274	136	141	15.0000
GAGGA	chr10:75832597-75832879(-)$1	282	136	141	15.0000
GAGGA	chrX:154357645-154357915(-)$1	270	130	135	15.0000
gagga	chr19:41338138-41338419(-)$1	281	29	34	15.0000
GAGGA	chr7:31360148-31360426(-)$1	278	190	195	15.0000
GAGGA	chr7:87465377-87465650(-)$1	273	137	142	15.0000
GAGGA	chr13:55425560-55425838(+)$1	278	137	142	15.0000
GAGGA	chr7:52222357-52222628(-)$1	271	203	208	15.0000
GAGGA	chr18:32056431-32056723(+)$1	292	54	59	15.0000
GAGGA	chr8:72657239-72657526(+)$1	287	94	99	15.0000
GAGGA	chr15:27538324-27538597(-)$1	273	53	58	15.0000
gagga	chr1:88253406-88253721(-)$1	315	12	17	15.0000
GAGGA	chr2:155232761-155233029(-)$1	268	165	170	15.0000
GAGGA	chr13:59901155-59901456(-)$1	301	25	30	15.0000
GAGGA	chr2:92200793-92201080(+)$1	287	147	152	15.0000
GAGGA	chr11:116162457-116162726(-)$1	269	25	30	15.0000
GAGGA	chr17:29099627-29099902(+)$1	275	59	64	15.0000
GAGGA	chr16:13332679-13333019(+)$1	340	303	308	15.0000
GAGGA	chr17:35292437-35292803(-)$1	366	32	37	15.0000
GAGGA	chr1:174420447-174420727(+)$1	280	89	94	15.0000
GAGGA	chr3:122322307-122322594(-)$1	287	51	56	15.0000
GAGGA	chr2:84886715-84886987(+)$1	272	96	101	15.0000

#otherMatches

#Struct PSSM
qqqqq	chr13:55698266-55698581(+)$1	315	136	141	15.0000
44hhh	chr9:70391649-70391926(+)$1	277	136	141	15.0000
=====	chr10:66681847-66682134(+)$1	287	75	80	15.0000
FFFCC	chr17:34249703-34250005(-)$1	302	111	116	15.0000
ammmm	chr5:73306049-73306338(+)$1	289	78	83	15.0000
33fff	chr5:104888829-104889109(+)$1	280	102	107	15.0000
CC}HH	chr1:173327524-173327795(+)$1	271	258	263	15.0000
nnnnn	chr18:78016158-78016514(+)$1	356	125	130	15.0000
ccbb]	chr1:52981942-52982248(-)$1	306	65	70	15.0000
d]eee	chr6:108328137-108328405(+)$1	268	260	265	15.0000
EEEEE	chr18:65783234-65783529(+)$1	295	83	88	15.0000
dddd[	chr16:96266053-96266338(-)$1	285	2	7	15.0000
mmmcc	chr17:27904684-27904967(-)$1	283	125	130	15.0000
:bb[d	chr1:180259915-180260189(-)$1	274	126	131	15.0000
eeeel	chr7:29091378-29091658(-)$1	280	6	11	15.0000
mmbb:	chrX:7514933-7515222(-)$1	289	96	101	15.0000
iiii6	chr14:46242427-46242697(-)$1	270	128	133	15.0000
ggggg	chr12:83084419-83084692(+)$1	273	71	76	15.0000
dccc4	chr8:73053243-73053530(+)$1	287	168	173	15.0000
dddd!	chr16:20679552-20679845(+)$1	293	143	148	15.0000
ooocc	chr3:88512709-88512986(+)$1	277	109	114	15.0000
eeee[	chr10:80785424-80785708(+)$1	284	29	34	15.0000
bbmmm	chr5:146003740-146004016(+)$1	276	175	180	15.0000
fff:I	chr10:90625453-90625815(-)$1	362	167	172	15.0000
oooob	chr5:125538066-125538348(-)$1	282	131	136	15.0000
ILLLC	chr15:12864682-12864990(+)$1	308	168	173	15.0000
:::cc	chr6:67217235-67217518(+)$1	283	131	136	15.0000
:::::	chr4:142725470-142725754(-)$1	284	0	5	15.0000
mmmee	chr5:138609190-138609465(-)$1	275	158	163	15.0000
====d	chr10:74997877-74998171(+)$1	294	143	148	15.0000
cceee	chr15:78171935-78172205(+)$1	270	89	94	15.0000
b]bb4	chr1:36995895-36996261(-)$1	366	87	92	15.0000
dddd[	chr12:17290648-17290935(+)$1	287	104	109	15.0000
eeeeb	chr7:52107813-52108107(+)$1	294	74	79	15.0000
::BBK	chr4:147315056-147315344(+)$1	288	5	10	15.0000
}CCC}	chr4:130224992-130225287(+)$1	295	141	146	15.0000
eeee]	chr9:70526857-70527145(+)$1	288	132	137	15.0000
d]ccc	chr15:101925580-101925871(+)$1	291	49	54	15.0000
[bb!!	chr9:65642328-65642605(-)$1	277	4	9	15.0000
eehhh	chr5:124848319-124848593(-)$1	274	136	141	15.0000
GGGGG	chr10:75832597-75832879(-)$1	282	136	141	15.0000
aoooo	chrX:154357645-154357915(-)$1	270	130	135	15.0000
H{AKK	chr19:41338138-41338419(-)$1	281	29	34	15.0000
c[bb[	chr7:31360148-31360426(-)$1	278	190	195	15.0000
dddll	chr7:87465377-87465650(-)$1	273	137	142	15.0000
ddddd	chr13:55425560-55425838(+)$1	278	137	142	15.0000
eeeee	chr7:52222357-52222628(-)$1	271	203	208	15.0000
33eee	chr18:32056431-32056723(+)$1	292	54	59	15.0000
ccc::	chr8:72657239-72657526(+)$1	287	94	99	15.0000
:eeee	chr15:27538324-27538597(-)$1	273	53	58	15.0000
:::::	chr1:88253406-88253721(-)$1	315	12	17	15.0000
eeeee	chr2:155232761-155233029(-)$1	268	165	170	15.0000
:::::	chr13:59901155-59901456(-)$1	301	25	30	15.0000
ee[dd	chr2:92200793-92201080(+)$1	287	147	152	15.0000
JCCC:	chr11:116162457-116162726(-)$1	269	25	30	15.0000
EEEEE	chr17:29099627-29099902(+)$1	275	59	64	15.0000
ccccc	chr16:13332679-13333019(+)$1	340	303	308	15.0000
c[bbx	chr17:35292437-35292803(-)$1	366	32	37	15.0000
!!a[b	chr1:174420447-174420727(+)$1	280	89	94	15.0000
22eee	chr3:122322307-122322594(-)$1	287	51	56	15.0000
hhh]b	chr2:84886715-84886987(+)$1	272	96	101	15.0000

#DB
.....	chr13:55698266-55698581(+)$1	1	136	141	15.0000
..)))	chr9:70391649-70391926(+)$1	1	136	141	15.0000
)))))	chr10:66681847-66682134(+)$1	1	75	80	15.0000
(((((	chr17:34249703-34250005(-)$1	1	111	116	15.0000
(....	chr5:73306049-73306338(+)$1	1	78	83	15.0000
..)))	chr5:104888829-104889109(+)$1	1	102	107	15.0000
)).))	chr1:173327524-173327795(+)$1	1	258	263	15.0000
.....	chr18:78016158-78016514(+)$1	1	125	130	15.0000
)))).	chr1:52981942-52982248(-)$1	1	65	70	15.0000
).)))	chr6:108328137-108328405(+)$1	1	260	265	15.0000
(((((	chr18:65783234-65783529(+)$1	1	83	88	15.0000
((((.	chr16:96266053-96266338(-)$1	1	2	7	15.0000
...))	chr17:27904684-27904967(-)$1	1	125	130	15.0000
.((.(	chr1:180259915-180260189(-)$1	1	126	131	15.0000
((((.	chr7:29091378-29091658(-)$1	1	6	11	15.0000
..)).	chrX:7514933-7515222(-)$1	1	96	101	15.0000
)))).	chr14:46242427-46242697(-)$1	1	128	133	15.0000
)))))	chr12:83084419-83084692(+)$1	1	71	76	15.0000
)))).	chr8:73053243-73053530(+)$1	1	168	173	15.0000
((((.	chr16:20679552-20679845(+)$1	1	143	148	15.0000
...))	chr3:88512709-88512986(+)$1	1	109	114	15.0000
((((.	chr10:80785424-80785708(+)$1	1	29	34	15.0000
((...	chr5:146003740-146004016(+)$1	1	175	180	15.0000
))).)	chr10:90625453-90625815(-)$1	1	167	172	15.0000
....)	chr5:125538066-125538348(-)$1	1	131	136	15.0000
(...(	chr15:12864682-12864990(+)$1	1	168	173	15.0000
...((	chr6:67217235-67217518(+)$1	1	131	136	15.0000
.....	chr4:142725470-142725754(-)$1	1	0	5	15.0000
...))	chr5:138609190-138609465(-)$1	1	158	163	15.0000
))))(	chr10:74997877-74998171(+)$1	1	143	148	15.0000
))(((	chr15:78171935-78172205(+)$1	1	89	94	15.0000
).)).	chr1:36995895-36996261(-)$1	1	87	92	15.0000
((((.	chr12:17290648-17290935(+)$1	1	104	109	15.0000
))))(	chr7:52107813-52108107(+)$1	1	74	79	15.0000
..((.	chr4:147315056-147315344(+)$1	1	5	10	15.0000
.))).	chr4:130224992-130225287(+)$1	1	141	146	15.0000
)))).	chr9:70526857-70527145(+)$1	1	132	137	15.0000
).)))	chr15:101925580-101925871(+)$1	1	49	54	15.0000
.((..	chr9:65642328-65642605(-)$1	1	4	9	15.0000
(((((	chr5:124848319-124848593(-)$1	1	136	141	15.0000
(((((	chr10:75832597-75832879(-)$1	1	136	141	15.0000
(....	chrX:154357645-154357915(-)$1	1	130	135	15.0000
(.(..	chr19:41338138-41338419(-)$1	1	29	34	15.0000
(.((.	chr7:31360148-31360426(-)$1	1	190	195	15.0000
(((..	chr7:87465377-87465650(-)$1	1	137	142	15.0000
)))((	chr13:55425560-55425838(+)$1	1	137	142	15.0000
)))))	chr7:52222357-52222628(-)$1	1	203	208	15.0000
..)))	chr18:32056431-32056723(+)$1	1	54	59	15.0000
)))..	chr8:72657239-72657526(+)$1	1	94	99	15.0000
.((((	chr15:27538324-27538597(-)$1	1	53	58	15.0000
.....	chr1:88253406-88253721(-)$1	1	12	17	15.0000
(((((	chr2:155232761-155233029(-)$1	1	165	170	15.0000
.....	chr13:59901155-59901456(-)$1	1	25	30	15.0000
((.((	chr2:92200793-92201080(+)$1	1	147	152	15.0000
((((.	chr11:116162457-116162726(-)$1	1	25	30	15.0000
(((((	chr17:29099627-29099902(+)$1	1	59	64	15.0000
)))))	chr16:13332679-13333019(+)$1	1	303	308	15.0000
(.((.	chr17:35292437-35292803(-)$1	1	32	37	15.0000
..(.(	chr1:174420447-174420727(+)$1	1	89	94	15.0000
..)))	chr3:122322307-122322594(-)$1	1	51	56	15.0000
))).)	chr2:84886715-84886987(+)$1	1	96	101	15.0000

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

#score	915.0000000000001
#seq	61
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m1_run2.nuc.txt

#NT
UUUUCUUGUGUUU	chr5:67677275-67677509(+)$1	234	20	33	21.6000
UUUUCUUUUUAUU	chr14:34203380-34203617(-)$1	237	61	74	22.8000
UUUUGUUUUCUUA	chr12:8941399-8941635(+)$1	236	88	101	22.3000
UUUUCUAUUUUUU	chr1:182048760-182049017(+)$1	257	72	85	21.9000
UUGUGUUUUCUUU	chrX:101278403-101278643(-)$1	240	118	131	23.1000
UUUUUUUUUCUUU	chrX:163645148-163645558(-)$1	410	69	82	27.6000
uuuucuuuuuuuu	chr5:21523725-21523966(-)$1	241	185	198	26.5000
uuuuauuuuuauu	chrX:45228231-45228503(-)$1	272	14	27	20.8000
uuuuguuuuguuu	chr10:107701658-107701889(+)$1	231	24	37	24.2000
UUGUGUUUUCUUU	chrX:101278454-101278709(-)$1	255	184	197	23.1000
UUUUUUUUUCUUU	chr15:98763525-98763762(-)$1	237	107	120	27.6000
UUUUCAUUUCUUU	chr4:123074190-123074441(-)$1	251	163	176	24.5000
UUUUUUUGUUUUU	chr1:56947923-56948206(-)$1	283	214	227	21.3000
UUUUCUUUUCUGU	chr8:56132504-56132744(+)$1	240	64	77	24.1000
UAUUUUuuuguuu	chr5:122939139-122939383(-)$1	244	228	241	20.8000
UUUUCCUUUCAUU	chr6:36691299-36691531(-)$1	232	63	76	21.3000
UUUUUGCUUCUUU	chr10:48964142-48964376(-)$1	234	41	54	19.1000
UUUUUUUUUCCUU	chr2:74542547-74542790(-)$1	243	117	130	23.4000
AUUUGUUUUAUUU	chr19:45826587-45826830(-)$1	243	43	56	20.0000
UUGACUUUUCUUU	chr18:38620165-38620396(+)$1	231	10	23	20.8000
UCUUUUUGUCUUU	chr18:16791454-16791686(-)$1	232	15	28	19.0000
uuuuuuuuucuuu	chr3:102832945-102833190(+)$1	245	54	67	27.6000
UUAUCUUUUCuuu	chr13:14145804-14146066(-)$1	262	173	186	24.6000
UUUUCUUCUUUUU	chr2:124913837-124914089(-)$1	252	9	22	22.0000
UUUUCCUUAUUUU	chr6:4027820-4028056(-)$1	236	0	13	18.3000
guuucuguucuuu	chr15:76924817-76925071(-)$1	254	102	115	19.7000
UUCUCUUUUCUCU	chr9:96506457-96506710(-)$1	253	78	91	20.3000
UUUUCUUUUCUUU	chr16:31122613-31122844(-)$1	231	55	68	28.5000
AUUUUUUUUUUUU	chr3:10347101-10347333(-)$1	232	103	116	21.6000
UAUCCUUUUGUUU	chr13:9146613-9146844(+)$1	231	6	19	17.7000
uuuuauuuuaauu	chr4:123074550-123074786(-)$1	236	27	40	20.0000
AUUUCUUUUCUUU	chr10:102872212-102872443(+)$1	231	59	72	24.5000
UUUUUGUUUAUUU	chr6:13552132-13552389(-)$1	257	165	178	20.9000
UUCUCUUUUGUUU	chr10:107082475-107082711(-)$1	236	60	73	22.1000
UCUCUUUUUCUUU	chr6:4579922-4580180(+)$1	258	179	192	19.3000
AUUUCCUUUUUUU	chr15:9107967-9108201(+)$1	234	162	175	19.0000
UUUUCUUUUCUUU	chr13:113389134-113389365(-)$1	231	99	112	28.5000
UAGACUUUUCUUU	chr4:97777806-97778070(+)$1	264	78	91	16.6000
UUUUUUUUUUUUU	chr10:9531718-9531953(-)$1	235	104	117	25.6000
UUUUCCUUUCUUG	chr3:80510924-80511168(-)$1	244	120	133	20.5000
UUAUUUUUUCUUU	chr1:52766244-52766475(-)$1	231	151	164	23.7000
uuuuccuuccuuu	chrX:73061388-73061624(-)$1	236	17	30	20.3000
uucaguuuucuuu	chr2:98506640-98506872(-)$1	232	155	168	19.0000
uuuuauuuuuauu	chr15:31412452-31412690(-)$1	238	144	157	20.8000
UUUUACUUUCUUU	chr17:56585153-56585384(-)$1	231	83	96	23.0000
UUUUGUUUUCAGU	chr14:20600291-20600527(+)$1	236	9	22	18.7000
uuuccuuuucuuu	chr6:51538155-51538386(+)$1	231	14	27	24.5000
GUUUUUUUUCUUU	chr3:80511022-80511271(-)$1	249	66	79	23.4000
UUUUUUUUUCUCC	chr3:57649062-57649304(-)$1	242	220	233	18.8000

#otherMatches

#Struct PSSM
eeeerrrrrrrrr	chr1:174122601-174122832(+)$1	231	26	39	19.9000
EEhhhhhhhh$$$	chr5:67677275-67677509(+)$1	234	20	33	21.6000
e(((((((((eee	chr14:34203380-34203617(-)$1	237	61	74	22.8000
ssssdddd22===	chr12:8941399-8941635(+)$1	236	88	101	22.3000
::::::::fffff	chr1:182048760-182049017(+)$1	257	72	85	21.9000
22bb]hhhhhhhh	chrX:101278403-101278643(-)$1	240	118	131	23.1000
:::::::::::::	chrX:163645148-163645558(-)$1	410	69	82	27.6000
:::::::::::::	chr5:21523725-21523966(-)$1	241	185	198	26.5000
pppppppeeeee3	chrX:45228231-45228503(-)$1	272	14	27	20.8000
ggggggghhhhhh	chr10:107701658-107701889(+)$1	231	24	37	24.2000
22bb]hhhhhhhh	chrX:101278454-101278709(-)$1	255	184	197	23.1000
:::::::::::::	chr15:98763525-98763762(-)$1	237	107	120	27.6000
FFF}A@@@@@@@@	chr4:123074190-123074441(-)$1	251	163	176	24.5000
3hhhhhhhh::::	chr1:56947923-56948206(-)$1	283	214	227	21.3000
"""bb!!eeeeem	chr8:56132504-56132744(+)$1	240	64	77	24.1000
HHHHHHHH:::::	chr5:122939139-122939383(-)$1	244	228	241	20.8000
pppppppccc]cc	chr6:36691299-36691531(-)$1	232	63	76	21.3000
:::::EEEEE:::	chr10:48964142-48964376(-)$1	234	41	54	19.1000
JJKKBBLLLBB::	chr2:74542547-74542790(-)$1	243	117	130	23.4000
mmmmffffff:::	chr19:45826587-45826830(-)$1	243	43	56	20.0000
H{FFFFFFQQQQQ	chr18:38620165-38620396(+)$1	231	10	23	20.8000
!gggggggooooo	chr18:16791454-16791686(-)$1	232	15	28	19.0000
:::::::::::::	chr3:102832945-102833190(+)$1	245	54	67	27.6000
ff]bbeeeee:::	chr13:14145804-14146066(-)$1	262	173	186	24.6000
:::::::::::::	chr2:124913837-124914089(-)$1	252	9	22	22.0000
eeeee####iiii	chr6:4027820-4028056(-)$1	236	0	13	18.3000
g22dddd::::::	chr15:76924817-76925071(-)$1	254	102	115	19.7000
IIII:::ccc[bb	chr9:96506457-96506710(-)$1	253	78	91	20.3000
:::::::::::::	chr16:31122613-31122844(-)$1	231	55	68	28.5000
===uuuuuuuuuu	chr3:10347101-10347333(-)$1	232	103	116	21.6000
:::dddd"""hhh	chr13:9146613-9146844(+)$1	231	6	19	17.7000
eqqqqqqqqeeee	chr4:123074550-123074786(-)$1	236	27	40	20.0000
eee:::::::::c	chr10:102872212-102872443(+)$1	231	59	72	24.5000
DDYYCCC}FFFFF	chr6:13552132-13552389(-)$1	257	165	178	20.9000
KKEEEEE{BB:::	chr10:107082475-107082711(-)$1	236	60	73	22.1000
dddd22ggggggg	chr6:4579922-4580180(+)$1	258	179	192	19.3000
yyyyyyyyyyddd	chr15:9107967-9108201(+)$1	234	162	175	19.0000
!!gggggggvvvv	chr13:113389134-113389365(-)$1	231	99	112	28.5000
!cccmmmmccc22	chr4:97777806-97778070(+)$1	264	78	91	16.6000
f0000000000cc	chr10:9531718-9531953(-)$1	235	104	117	25.6000
::::::::ccc[d	chr3:80510924-80511168(-)$1	244	120	133	20.5000
HHHHHYYDDDD~~	chr1:52766244-52766475(-)$1	231	151	164	23.7000
:::::::::dddd	chrX:73061388-73061624(-)$1	236	17	30	20.3000
g::::::::::::	chr2:98506640-98506872(-)$1	232	155	168	19.0000
e"""gggggggoo	chr15:31412452-31412690(-)$1	238	144	157	20.8000
eeee!!ggggggg	chr17:56585153-56585384(-)$1	231	83	96	23.0000
mmmffffff::::	chr14:20600291-20600527(+)$1	236	9	22	18.7000
:::::::JJJJJJ	chr6:51538155-51538386(+)$1	231	14	27	24.5000
d:::::::::ggg	chr3:80511022-80511271(-)$1	249	66	79	23.4000
qqccc]hhhhhhh	chr3:57649062-57649304(-)$1	242	220	233	18.8000

#DB
((((.........	chr1:174122601-174122832(+)$1	1	26	39	19.9000
((((((((((...	chr5:67677275-67677509(+)$1	1	20	33	21.6000
(.........(((	chr14:34203380-34203617(-)$1	1	61	74	22.8000
....))))..)))	chr12:8941399-8941635(+)$1	1	88	101	22.3000
........(((((	chr1:182048760-182049017(+)$1	1	72	85	21.9000
..)).))))))))	chrX:101278403-101278643(-)$1	1	118	131	23.1000
.............	chrX:163645148-163645558(-)$1	1	69	82	27.6000
.............	chr5:21523725-21523966(-)$1	1	185	198	26.5000
.......))))).	chrX:45228231-45228503(-)$1	1	14	27	20.8000
(((((((((((((	chr10:107701658-107701889(+)$1	1	24	37	24.2000
..)).))))))))	chrX:101278454-101278709(-)$1	1	184	197	23.1000
.............	chr15:98763525-98763762(-)$1	1	107	120	27.6000
))).)........	chr4:123074190-123074441(-)$1	1	163	176	24.5000
.))))))))....	chr1:56947923-56948206(-)$1	1	214	227	21.3000
...((..(((((.	chr8:56132504-56132744(+)$1	1	64	77	24.1000
)))))))).....	chr5:122939139-122939383(-)$1	1	228	241	20.8000
.......))).))	chr6:36691299-36691531(-)$1	1	63	76	21.3000
.....(((((...	chr10:48964142-48964376(-)$1	1	41	54	19.1000
((..((...((..	chr2:74542547-74542790(-)$1	1	117	130	23.4000
....))))))...	chr19:45826587-45826830(-)$1	1	43	56	20.0000
(.((((((.....	chr18:38620165-38620396(+)$1	1	10	23	20.8000
.(((((((.....	chr18:16791454-16791686(-)$1	1	15	28	19.0000
.............	chr3:102832945-102833190(+)$1	1	54	67	27.6000
)).)))))))...	chr13:14145804-14146066(-)$1	1	173	186	24.6000
.............	chr2:124913837-124914089(-)$1	1	9	22	22.0000
(((((....((((	chr6:4027820-4028056(-)$1	1	0	13	18.3000
)..))))......	chr15:76924817-76925071(-)$1	1	102	115	19.7000
((((...(((.((	chr9:96506457-96506710(-)$1	1	78	91	20.3000
.............	chr16:31122613-31122844(-)$1	1	55	68	28.5000
(((..........	chr3:10347101-10347333(-)$1	1	103	116	21.6000
...((((...(((	chr13:9146613-9146844(+)$1	1	6	19	17.7000
(........))))	chr4:123074550-123074786(-)$1	1	27	40	20.0000
))).........(	chr10:102872212-102872443(+)$1	1	59	72	24.5000
))..))).)))))	chr6:13552132-13552389(-)$1	1	165	178	20.9000
..(((((.((...	chr10:107082475-107082711(-)$1	1	60	73	22.1000
))))..)))))))	chr6:4579922-4580180(+)$1	1	179	192	19.3000
..........)))	chr15:9107967-9108201(+)$1	1	162	175	19.0000
..(((((((....	chr13:113389134-113389365(-)$1	1	99	112	28.5000
.(((....)))..	chr4:97777806-97778070(+)$1	1	78	91	16.6000
)..........))	chr10:9531718-9531953(-)$1	1	104	117	25.6000
........(((.(	chr3:80510924-80511168(-)$1	1	120	133	20.5000
)))))..))))..	chr1:52766244-52766475(-)$1	1	151	164	23.7000
.........((((	chrX:73061388-73061624(-)$1	1	17	30	20.3000
)............	chr2:98506640-98506872(-)$1	1	155	168	19.0000
(...(((((((..	chr15:31412452-31412690(-)$1	1	144	157	20.8000
((((..(((((((	chr17:56585153-56585384(-)$1	1	83	96	23.0000
...))))))....	chr14:20600291-20600527(+)$1	1	9	22	18.7000
.......((((((	chr6:51538155-51538386(+)$1	1	14	27	24.5000
).........(((	chr3:80511022-80511271(-)$1	1	66	79	23.4000
..))).)))))))	chr3:57649062-57649304(-)$1	1	220	233	18.8000

#PSSM
U : 0.70	u : 0.18	A : 0.08	g : 0.02	G : 0.02	
U : 0.70	u : 0.19	A : 0.06	C : 0.04	
U : 0.64	u : 0.18	G : 0.08	A : 0.04	C : 0.04	c : 0.02	
U : 0.70	u : 0.16	A : 0.04	C : 0.04	G : 0.02	a : 0.02	c : 0.02	
C : 0.40	U : 0.27	G : 0.10	c : 0.08	a : 0.06	g : 0.04	u : 0.02	A : 0.02	
U : 0.64	u : 0.18	C : 0.10	G : 0.04	A : 0.02	c : 0.02	
U : 0.74	u : 0.19	A : 0.02	C : 0.02	g : 0.02	
U : 0.70	u : 0.21	G : 0.06	C : 0.02	
U : 0.76	u : 0.19	A : 0.02	c : 0.02	
C : 0.52	U : 0.16	c : 0.10	G : 0.06	u : 0.06	g : 0.04	A : 0.04	a : 0.02	
U : 0.68	u : 0.18	A : 0.06	a : 0.06	C : 0.02	
U : 0.68	u : 0.23	G : 0.04	C : 0.04	
U : 0.68	u : 0.23	C : 0.04	A : 0.02	G : 0.02	

#score	1105.200000000001
#seq	50
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m3_run2.nuc.txt

#NT
CUGU	chr9:113885607-113885863(+)$1	256	39	43	11.9999
CUGU	chr13:34166130-34166378(-)$1	248	79	83	11.9999
CUGU	chr1:46864681-46864930(-)$1	249	125	129	11.9999
CUGU	chr13:98021044-98021281(+)$1	237	14	18	11.9999
CUGU	chr15:31388225-31388481(-)$1	256	32	36	11.9999
CUGU	chr5:137509001-137509236(+)$1	235	52	56	11.9999
CUGU	chr6:86939775-86940064(+)$1	289	86	90	11.9999
CUGU	chr18:9995406-9995644(-)$1	238	7	11	11.9999
CUGU	chr1:155756600-155756860(+)$1	260	23	27	11.9999
CUGU	chr5:93600345-93600582(+)$1	237	95	99	11.9999
CUGU	chr18:35023933-35024195(+)$1	262	43	47	11.9999
CUGU	chr14:21554054-21554291(-)$1	237	208	212	11.9999
CUGU	chr19:16459820-16460081(+)$1	261	11	15	11.9999
CUGU	chrX:54486260-54486498(-)$1	238	226	230	11.9999
CUGU	chr17:24215643-24215891(-)$1	248	127	131	11.9999
CUGU	chrX:149044585-149044829(-)$1	244	140	144	11.9999
CUGU	chr5:13601966-13602201(+)$1	235	161	165	11.9999
CUGU	chr19:7501280-7501580(-)$1	300	76	80	11.9999
CUGU	chr1:166367605-166367872(-)$1	267	12	16	11.9999
cugu	chr1:74400061-74400319(+)$1	258	16	20	11.9999
CUGU	chr3:107815196-107815451(-)$1	255	112	116	11.9999
CUGU	chr1:165845958-165846194(+)$1	236	45	49	11.9999
CUGU	chr2:163844109-163844348(+)$1	239	30	34	11.9999
CUGU	chr13:74170998-74171241(+)$1	243	13	17	11.9999
CUGU	chr15:79358603-79358847(-)$1	244	5	9	11.9999
CUGU	chr15:12279560-12279814(+)$1	254	169	173	11.9999
CUGU	chr4:136878137-136878376(-)$1	239	16	20	11.9999
CUGU	chr3:28694285-28694524(+)$1	239	154	158	11.9999
CUGU	chrX:154270889-154271149(-)$1	260	7	11	11.9999
CUGU	chr6:115224509-115224776(+)$1	267	8	12	11.9999
CUGU	chr19:10523731-10523966(+)$1	235	11	15	11.9999
CUGU	chr2:102630352-102630598(+)$1	246	140	144	11.9999
CUGU	chr8:96492581-96492836(+)$1	255	198	202	11.9999
CUGU	chr5:122903450-122903749(-)$1	299	132	136	11.9999
CUGU	chr1:75143877-75144118(+)$1	241	57	61	11.9999
CUGU	chr6:13035521-13035767(+)$1	246	230	234	11.9999
CUGU	chr6:119432177-119432422(+)$1	245	6	10	11.9999
CUGU	chr16:92087388-92087630(+)$1	242	11	15	11.9999
CUGU	chr4:48674929-48675180(+)$1	251	142	146	11.9999
CUGU	chrX:162826314-162826580(+)$1	266	0	4	11.9999
CUGU	chr8:56145478-56145720(+)$1	242	115	119	11.9999
CUGU	chr19:47098395-47098640(+)$1	245	112	116	11.9999
CUGU	chr12:16992165-16992435(+)$1	270	252	256	11.9999
CUGU	chr9:58500439-58500750(+)$1	311	73	77	11.9999
CUGU	chr4:148554568-148554806(-)$1	238	24	28	11.9999
CUGU	chr19:45607587-45607826(+)$1	239	192	196	11.9999
CUGU	chr3:88883066-88883304(+)$1	238	30	34	11.9999
CUGU	chr13:58278499-58278744(-)$1	245	32	36	11.9999
CUGU	chr7:26013303-26013538(-)$1	235	108	112	11.9999
CUGU	chr4:10826042-10826302(+)$1	260	4	8	11.9999
CUGU	chr11:32645082-32645319(+)$1	237	50	54	11.9999
CUGU	chr15:41691926-41692182(+)$1	256	108	112	11.9999
CUGU	chr9:107850835-107851070(+)$1	235	1	5	11.9999
CUGU	chr4:59233332-59233585(+)$1	253	81	85	11.9999
CUGU	chr10:4514013-4514272(+)$1	259	108	112	11.9999
CUGU	chr2:164824647-164824928(+)$1	281	115	119	11.9999
CUGU	chr15:36700964-36701200(-)$1	236	88	92	11.9999
CUGU	chrX:136207239-136207481(+)$1	242	84	88	11.9999
CUGU	chr1:165847023-165847271(+)$1	248	215	219	11.9999
CUGU	chr2:48756378-48756625(+)$1	247	6	10	11.9999
CUGU	chr6:108500118-108500395(+)$1	277	71	75	11.9999
CUGU	chr13:110846562-110846822(-)$1	260	35	39	11.9999
CUGU	chr16:37884877-37885123(+)$1	246	3	7	11.9999
CUGU	chr6:4707781-4708024(+)$1	243	202	206	11.9999
CUGU	chr12:11332635-11332919(-)$1	284	249	253	11.9999
CUGU	chrX:8470920-8471173(+)$1	253	15	19	11.9999
cugu	chr2:144296789-144297027(-)$1	238	13	17	11.9999
CUGU	chr11:41725498-41725750(-)$1	252	44	48	11.9999
CUGU	chr15:90764099-90764382(-)$1	283	68	72	11.9999
CUGU	chr14:37691395-37691635(-)$1	240	117	121	11.9999
CUGU	chrX:5630176-5630455(+)$1	279	116	120	11.9999
CUGU	chr19:55698571-55698820(+)$1	249	104	108	11.9999
CUGU	chrX:96661644-96661902(-)$1	258	39	43	11.9999
CUGU	chr8:26875029-26875280(-)$1	251	61	65	11.9999
CUGU	chr4:150435600-150435837(-)$1	237	196	200	11.9999
CUGU	chr1:123202217-123202452(-)$1	235	113	117	11.9999
CUGU	chr17:9174461-9174699(+)$1	238	109	113	11.9999
CUGU	chr5:8072611-8072853(-)$1	242	1	5	11.9999
CUGU	chr5:104508298-104508584(-)$1	286	247	251	11.9999
CUGU	chr2:49627551-49627793(+)$1	242	82	86	11.9999
CUGU	chr1:23373738-23373982(-)$1	244	77	81	11.9999
CUGU	chrX:12193508-12193806(+)$1	298	27	31	11.9999
cugu	chr2:143641336-143641574(+)$1	238	70	74	11.9999
CUGU	chr4:48675631-48675876(+)$1	245	174	178	11.9999
CUGU	chr6:108772472-108772722(+)$1	250	221	225	11.9999
CUGU	chr15:103025148-103025424(-)$1	276	126	130	11.9999
CUGU	chr1:152209721-152209959(-)$1	238	112	116	11.9999

#otherMatches

#Struct PSSM
{BB{	chr10:107935999-107936272(-)$1	273	67	71	11.9999
clll	chr9:113885607-113885863(+)$1	256	39	43	11.9999
EEE:	chr13:34166130-34166378(-)$1	248	79	83	11.9999
CCCY	chr1:46864681-46864930(-)$1	249	125	129	11.9999
f$$$	chr13:98021044-98021281(+)$1	237	14	18	11.9999
eeee	chr15:31388225-31388481(-)$1	256	32	36	11.9999
KKFF	chr5:137509001-137509236(+)$1	235	52	56	11.9999
EEE:	chr6:86939775-86940064(+)$1	289	86	90	11.9999
{DDD	chr18:9995406-9995644(-)$1	238	7	11	11.9999
====	chr1:155756600-155756860(+)$1	260	23	27	11.9999
ffff	chr5:93600345-93600582(+)$1	237	95	99	11.9999
PEEE	chr18:35023933-35024195(+)$1	262	43	47	11.9999
ddd]	chr14:21554054-21554291(-)$1	237	208	212	11.9999
dddd	chr19:16459820-16460081(+)$1	261	11	15	11.9999
JJJJ	chrX:54486260-54486498(-)$1	238	226	230	11.9999
eee3	chr17:24215643-24215891(-)$1	248	127	131	11.9999
HHH@	chrX:149044585-149044829(-)$1	244	140	144	11.9999
dddd	chr5:13601966-13602201(+)$1	235	161	165	11.9999
b]dd	chr19:7501280-7501580(-)$1	300	76	80	11.9999
dd[d	chr1:166367605-166367872(-)$1	267	12	16	11.9999
LCCC	chr1:74400061-74400319(+)$1	258	16	20	11.9999
booo	chr3:107815196-107815451(-)$1	255	112	116	11.9999
[bb[	chr1:165845958-165846194(+)$1	236	45	49	11.9999
ccc[	chr2:163844109-163844348(+)$1	239	30	34	11.9999
gggg	chr13:74170998-74171241(+)$1	243	13	17	11.9999
HHHP	chr15:79358603-79358847(-)$1	244	5	9	11.9999
::::	chr15:12279560-12279814(+)$1	254	169	173	11.9999
DD{D	chr4:136878137-136878376(-)$1	239	16	20	11.9999
ccdd	chr3:28694285-28694524(+)$1	239	154	158	11.9999
:eee	chrX:154270889-154271149(-)$1	260	7	11	11.9999
::ee	chr6:115224509-115224776(+)$1	267	8	12	11.9999
!!bb	chr19:10523731-10523966(+)$1	235	11	15	11.9999
ffff	chr2:102630352-102630598(+)$1	246	140	144	11.9999
::a[	chr8:96492581-96492836(+)$1	255	198	202	11.9999
eee"	chr5:122903450-122903749(-)$1	299	132	136	11.9999
oocc	chr1:75143877-75144118(+)$1	241	57	61	11.9999
DDEE	chr6:13035521-13035767(+)$1	246	230	234	11.9999
dd[b	chr6:119432177-119432422(+)$1	245	6	10	11.9999
OEEE	chr16:92087388-92087630(+)$1	242	11	15	11.9999
c]ee	chr4:48674929-48675180(+)$1	251	142	146	11.9999
:FFF	chrX:162826314-162826580(+)$1	266	0	4	11.9999
b333	chr8:56145478-56145720(+)$1	242	115	119	11.9999
ffff	chr19:47098395-47098640(+)$1	245	112	116	11.9999
gggg	chr12:16992165-16992435(+)$1	270	252	256	11.9999
:EEE	chr9:58500439-58500750(+)$1	311	73	77	11.9999
PPDD	chr4:148554568-148554806(-)$1	238	24	28	11.9999
bbnn	chr19:45607587-45607826(+)$1	239	192	196	11.9999
mggg	chr3:88883066-88883304(+)$1	238	30	34	11.9999
HHHH	chr13:58278499-58278744(-)$1	245	32	36	11.9999
eee[	chr7:26013303-26013538(-)$1	235	108	112	11.9999
ddd[	chr4:10826042-10826302(+)$1	260	4	8	11.9999
cqqq	chr11:32645082-32645319(+)$1	237	50	54	11.9999
gggg	chr15:41691926-41692182(+)$1	256	108	112	11.9999
EEEE	chr9:107850835-107851070(+)$1	235	1	5	11.9999
aeee	chr4:59233332-59233585(+)$1	253	81	85	11.9999
b[dd	chr10:4514013-4514272(+)$1	259	108	112	11.9999
FFKK	chr2:164824647-164824928(+)$1	281	115	119	11.9999
ddmm	chr15:36700964-36701200(-)$1	236	88	92	11.9999
^^^^	chrX:136207239-136207481(+)$1	242	84	88	11.9999
CC::	chr1:165847023-165847271(+)$1	248	215	219	11.9999
cccw	chr2:48756378-48756625(+)$1	247	6	10	11.9999
ddd]	chr6:108500118-108500395(+)$1	277	71	75	11.9999
::cc	chr13:110846562-110846822(-)$1	260	35	39	11.9999
EEEE	chr16:37884877-37885123(+)$1	246	3	7	11.9999
dddf	chr6:4707781-4708024(+)$1	243	202	206	11.9999
c[cc	chr12:11332635-11332919(-)$1	284	249	253	11.9999
GGGG	chrX:8470920-8471173(+)$1	253	15	19	11.9999
CCMM	chr2:144296789-144297027(-)$1	238	13	17	11.9999
[ccc	chr11:41725498-41725750(-)$1	252	44	48	11.9999
bb55	chr15:90764099-90764382(-)$1	283	68	72	11.9999
offf	chr14:37691395-37691635(-)$1	240	117	121	11.9999
55dd	chrX:5630176-5630455(+)$1	279	116	120	11.9999
bfff	chr19:55698571-55698820(+)$1	249	104	108	11.9999
eeee	chrX:96661644-96661902(-)$1	258	39	43	11.9999
666g	chr8:26875029-26875280(-)$1	251	61	65	11.9999
EEEE	chr4:150435600-150435837(-)$1	237	196	200	11.9999
flll	chr1:123202217-123202452(-)$1	235	113	117	11.9999
gfff	chr17:9174461-9174699(+)$1	238	109	113	11.9999
::::	chr5:8072611-8072853(-)$1	242	1	5	11.9999
iiii	chr5:104508298-104508584(-)$1	286	247	251	11.9999
EEE:	chr2:49627551-49627793(+)$1	242	82	86	11.9999
gggg	chr1:23373738-23373982(-)$1	244	77	81	11.9999
))))	chrX:12193508-12193806(+)$1	298	27	31	11.9999
:eee	chr2:143641336-143641574(+)$1	238	70	74	11.9999
ffff	chr4:48675631-48675876(+)$1	245	174	178	11.9999
:GGG	chr6:108772472-108772722(+)$1	250	221	225	11.9999
eee:	chr15:103025148-103025424(-)$1	276	126	130	11.9999
ffll	chr1:152209721-152209959(-)$1	238	112	116	11.9999

#DB
.((.	chr10:107935999-107936272(-)$1	1	67	71	11.9999
(...	chr9:113885607-113885863(+)$1	1	39	43	11.9999
(((.	chr13:34166130-34166378(-)$1	1	79	83	11.9999
))).	chr1:46864681-46864930(-)$1	1	125	129	11.9999
(...	chr13:98021044-98021281(+)$1	1	14	18	11.9999
((((	chr15:31388225-31388481(-)$1	1	32	36	11.9999
..((	chr5:137509001-137509236(+)$1	1	52	56	11.9999
(((.	chr6:86939775-86940064(+)$1	1	86	90	11.9999
.(((	chr18:9995406-9995644(-)$1	1	7	11	11.9999
((((	chr1:155756600-155756860(+)$1	1	23	27	11.9999
))))	chr5:93600345-93600582(+)$1	1	95	99	11.9999
.(((	chr18:35023933-35024195(+)$1	1	43	47	11.9999
))).	chr14:21554054-21554291(-)$1	1	208	212	11.9999
))))	chr19:16459820-16460081(+)$1	1	11	15	11.9999
))))	chrX:54486260-54486498(-)$1	1	226	230	11.9999
))).	chr17:24215643-24215891(-)$1	1	127	131	11.9999
))).	chrX:149044585-149044829(-)$1	1	140	144	11.9999
))))	chr5:13601966-13602201(+)$1	1	161	165	11.9999
).))	chr19:7501280-7501580(-)$1	1	76	80	11.9999
((.(	chr1:166367605-166367872(-)$1	1	12	16	11.9999
.(((	chr1:74400061-74400319(+)$1	1	16	20	11.9999
(...	chr3:107815196-107815451(-)$1	1	112	116	11.9999
.((.	chr1:165845958-165846194(+)$1	1	45	49	11.9999
(((.	chr2:163844109-163844348(+)$1	1	30	34	11.9999
((((	chr13:74170998-74171241(+)$1	1	13	17	11.9999
(((.	chr15:79358603-79358847(-)$1	1	5	9	11.9999
....	chr15:12279560-12279814(+)$1	1	169	173	11.9999
((.(	chr4:136878137-136878376(-)$1	1	16	20	11.9999
((((	chr3:28694285-28694524(+)$1	1	154	158	11.9999
.(((	chrX:154270889-154271149(-)$1	1	7	11	11.9999
..((	chr6:115224509-115224776(+)$1	1	8	12	11.9999
..((	chr19:10523731-10523966(+)$1	1	11	15	11.9999
((((	chr2:102630352-102630598(+)$1	1	140	144	11.9999
..(.	chr8:96492581-96492836(+)$1	1	198	202	11.9999
(((.	chr5:122903450-122903749(-)$1	1	132	136	11.9999
..))	chr1:75143877-75144118(+)$1	1	57	61	11.9999
))))	chr6:13035521-13035767(+)$1	1	230	234	11.9999
((.(	chr6:119432177-119432422(+)$1	1	6	10	11.9999
.(((	chr16:92087388-92087630(+)$1	1	11	15	11.9999
).))	chr4:48674929-48675180(+)$1	1	142	146	11.9999
.(((	chrX:162826314-162826580(+)$1	1	0	4	11.9999
)...	chr8:56145478-56145720(+)$1	1	115	119	11.9999
((((	chr19:47098395-47098640(+)$1	1	112	116	11.9999
))))	chr12:16992165-16992435(+)$1	1	252	256	11.9999
.(((	chr9:58500439-58500750(+)$1	1	73	77	11.9999
..((	chr4:148554568-148554806(-)$1	1	24	28	11.9999
((..	chr19:45607587-45607826(+)$1	1	192	196	11.9999
.)))	chr3:88883066-88883304(+)$1	1	30	34	11.9999
((((	chr13:58278499-58278744(-)$1	1	32	36	11.9999
(((.	chr7:26013303-26013538(-)$1	1	108	112	11.9999
(((.	chr4:10826042-10826302(+)$1	1	4	8	11.9999
(...	chr11:32645082-32645319(+)$1	1	50	54	11.9999
((((	chr15:41691926-41692182(+)$1	1	108	112	11.9999
((((	chr9:107850835-107851070(+)$1	1	1	5	11.9999
))))	chr4:59233332-59233585(+)$1	1	81	85	11.9999
(.((	chr10:4514013-4514272(+)$1	1	108	112	11.9999
((..	chr2:164824647-164824928(+)$1	1	115	119	11.9999
((..	chr15:36700964-36701200(-)$1	1	88	92	11.9999
....	chrX:136207239-136207481(+)$1	1	84	88	11.9999
))..	chr1:165847023-165847271(+)$1	1	215	219	11.9999
(((.	chr2:48756378-48756625(+)$1	1	6	10	11.9999
))).	chr6:108500118-108500395(+)$1	1	71	75	11.9999
..((	chr13:110846562-110846822(-)$1	1	35	39	11.9999
((((	chr16:37884877-37885123(+)$1	1	3	7	11.9999
((((	chr6:4707781-4708024(+)$1	1	202	206	11.9999
(.((	chr12:11332635-11332919(-)$1	1	249	253	11.9999
((((	chrX:8470920-8471173(+)$1	1	15	19	11.9999
((..	chr2:144296789-144297027(-)$1	1	13	17	11.9999
.(((	chr11:41725498-41725750(-)$1	1	44	48	11.9999
))..	chr15:90764099-90764382(-)$1	1	68	72	11.9999
.)))	chr14:37691395-37691635(-)$1	1	117	121	11.9999
..))	chrX:5630176-5630455(+)$1	1	116	120	11.9999
((((	chr19:55698571-55698820(+)$1	1	104	108	11.9999
((((	chrX:96661644-96661902(-)$1	1	39	43	11.9999
...)	chr8:26875029-26875280(-)$1	1	61	65	11.9999
))))	chr4:150435600-150435837(-)$1	1	196	200	11.9999
(...	chr1:123202217-123202452(-)$1	1	113	117	11.9999
((((	chr17:9174461-9174699(+)$1	1	109	113	11.9999
....	chr5:8072611-8072853(-)$1	1	1	5	11.9999
((((	chr5:104508298-104508584(-)$1	1	247	251	11.9999
(((.	chr2:49627551-49627793(+)$1	1	82	86	11.9999
))))	chr1:23373738-23373982(-)$1	1	77	81	11.9999
....	chrX:12193508-12193806(+)$1	1	27	31	11.9999
.(((	chr2:143641336-143641574(+)$1	1	70	74	11.9999
((((	chr4:48675631-48675876(+)$1	1	174	178	11.9999
.)))	chr6:108772472-108772722(+)$1	1	221	225	11.9999
))).	chr15:103025148-103025424(-)$1	1	126	130	11.9999
((..	chr1:152209721-152209959(-)$1	1	112	116	11.9999

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

#score	1055.9999999999998
#seq	88
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m3_run2.nuc.txt

#NT
UAC	chr4:85034949-85035152(+)$1	203	53	56	8.9999
UAC	chr19:15979808-15980016(+)$1	208	36	39	8.9999
UAC	chr6:118412077-118412305(+)$1	228	31	34	8.9999
uac	chr4:58873308-58873522(-)$1	214	17	20	8.9999
UAC	chr2:129457820-129458026(-)$1	206	69	72	8.9999
UAC	chr7:63984934-63985154(-)$1	220	136	139	8.9999
UAC	chr16:49913322-49913525(+)$1	203	153	156	8.9999
UAC	chr12:113032636-113032842(+)$1	206	90	93	8.9999
UAC	chr7:137899280-137899488(+)$1	208	155	158	8.9999
uac	chr4:133222215-133222435(-)$1	220	18	21	8.9999
UAC	chr18:46664201-46664405(-)$1	204	3	6	8.9999
uac	chr14:18686479-18686680(+)$1	201	152	155	8.9999
UAC	chr11:87403855-87404055(+)$1	200	116	119	8.9999
UAC	chr12:11332656-11332860(-)$1	204	27	30	8.9999
UAC	chr8:96491851-96492051(+)$1	200	75	78	8.9999
UAC	chrX:96143022-96143223(-)$1	201	21	24	8.9999
UAC	chr2:174171943-174172143(+)$1	200	8	11	8.9999
UAC	chr2:148522894-148523094(-)$1	200	133	136	8.9999
UAC	chr5:135095912-135096114(-)$1	202	11	14	8.9999
uac	chr9:107726839-107727043(-)$1	204	31	34	8.9999
UAC	chr11:98629216-98629422(+)$1	206	159	162	8.9999
UAC	chr18:63829963-63830184(-)$1	221	3	6	8.9999
UAC	chr15:37856060-37856278(-)$1	218	144	147	8.9999
UAC	chr14:121649056-121649279(+)$1	223	198	201	8.9999
UAC	chr14:64741402-64741618(-)$1	216	29	32	8.9999
UAC	chr17:32339021-32339239(-)$1	218	159	162	8.9999
UAC	chr8:113579311-113579537(-)$1	226	13	16	8.9999
UAC	chr1:136097724-136097931(+)$1	207	43	46	8.9999
UAC	chr14:57309771-57309988(+)$1	217	65	68	8.9999
UAC	chr4:129687095-129687309(+)$1	214	22	25	8.9999
UAC	chr12:101149988-101150216(+)$1	228	156	159	8.9999
UAC	chr11:36493301-36493505(-)$1	204	14	17	8.9999
UAC	chr2:62855633-62855842(-)$1	209	38	41	8.9999
UAC	chr18:37346264-37346473(+)$1	209	13	16	8.9999
UAC	chr1:66487129-66487344(+)$1	215	0	3	8.9999
UAC	chr10:126435959-126436174(+)$1	215	121	124	8.9999
UAC	chr8:88062563-88062764(-)$1	201	34	37	8.9999
UAC	chr8:96528993-96529193(-)$1	200	79	82	8.9999
UAC	chr4:59741870-59742085(+)$1	215	51	54	8.9999
UAC	chr2:64849911-64850123(-)$1	212	0	3	8.9999
UAC	chr4:28891486-28891699(+)$1	213	173	176	8.9999
UAC	chr3:144351086-144351305(+)$1	219	35	38	8.9999
UAC	chr14:46079252-46079453(-)$1	201	41	44	8.9999
UAC	chr5:15878317-15878521(+)$1	204	39	42	8.9999
UAC	chrX:101479217-101479422(+)$1	205	87	90	8.9999
uac	chr15:78908587-78908818(+)$1	231	129	132	8.9999
UAC	chr2:103987436-103987655(-)$1	219	77	80	8.9999
UAC	chr14:8998560-8998766(-)$1	206	85	88	8.9999
UAC	chr18:51288694-51288905(+)$1	211	148	151	8.9999
UAC	chr5:24733941-24734157(+)$1	216	46	49	8.9999
UAC	chrX:132379016-132379223(+)$1	207	106	109	8.9999
UAC	chr1:168323268-168323488(-)$1	220	54	57	8.9999
UAC	chr14:104103182-104103390(+)$1	208	108	111	8.9999
UAC	chr7:150253639-150253843(-)$1	204	62	65	8.9999
UAC	chr2:38721140-38721368(-)$1	228	130	133	8.9999
UAC	chr8:85796471-85796681(-)$1	210	34	37	8.9999
UAC	chr11:90139629-90139830(-)$1	201	74	77	8.9999
UAC	chrX:12193711-12193918(-)$1	207	139	142	8.9999
UAC	chr13:104930740-104930942(-)$1	202	46	49	8.9999
UAC	chr15:76001862-76002062(-)$1	200	39	42	8.9999
UAC	chr9:70439871-70440080(-)$1	209	6	9	8.9999
UAC	chr1:36161595-36161804(-)$1	209	201	204	8.9999
UAC	chr11:29407929-29408148(+)$1	219	63	66	8.9999
UAC	chr1:130260250-130260473(+)$1	223	90	93	8.9999
UAC	chr15:68923422-68923649(+)$1	227	3	6	8.9999
UAC	chr11:103683423-103683624(-)$1	201	180	183	8.9999
UAC	chr15:85681711-85681927(+)$1	216	52	55	8.9999
UAC	chr9:58499777-58499977(+)$1	200	40	43	8.9999
UAC	chr9:107950677-107950879(+)$1	202	88	91	8.9999
UAC	chr16:64858258-64858466(+)$1	208	37	40	8.9999
UAC	chrX:35966483-35966703(+)$1	220	30	33	8.9999
UAC	chr6:63601476-63601680(+)$1	204	31	34	8.9999
UAC	chr12:73312673-73312876(-)$1	203	28	31	8.9999
UAC	chr3:79745524-79745746(-)$1	222	51	54	8.9999
UAC	chr7:126117223-126117423(-)$1	200	92	95	8.9999
UAC	chr12:107075231-107075450(+)$1	219	58	61	8.9999
uac	chr2:64821197-64821430(-)$1	233	163	166	8.9999
UAC	chr6:116206354-116206571(+)$1	217	33	36	8.9999
UAC	chr19:7414325-7414533(-)$1	208	25	28	8.9999
UAC	chr2:90856711-90856912(+)$1	201	64	67	8.9999
UAC	chr2:62164235-62164438(+)$1	203	102	105	8.9999
UAC	chr1:89901016-89901239(-)$1	223	143	146	8.9999
UAC	chr3:144259936-144260144(+)$1	208	1	4	8.9999
UAC	chr18:57454602-57454809(+)$1	207	10	13	8.9999
UAC	chrX:69069822-69070025(+)$1	203	126	129	8.9999
UAC	chr5:77515969-77516169(-)$1	200	38	41	8.9999
UAC	chr12:45694097-45694298(+)$1	201	88	91	8.9999
uac	chr12:79979681-79979916(+)$1	235	23	26	8.9999
UAC	chrX:97269594-97269829(+)$1	235	106	109	8.9999
uac	chrX:117442265-117442489(+)$1	224	4	7	8.9999
UAC	chr3:40505574-40505787(+)$1	213	16	19	8.9999
uac	chr12:38079352-38079579(+)$1	227	2	5	8.9999
UAC	chr6:117124816-117125035(+)$1	219	64	67	8.9999
uac	chr13:104814096-104814316(+)$1	220	19	22	8.9999
UAC	chr6:5114396-5114619(+)$1	223	38	41	8.9999

#otherMatches

#Struct PSSM
mmm	chr4:150378455-150378684(-)$1	229	60	63	8.9999
===	chr4:85034949-85035152(+)$1	203	53	56	8.9999
::e	chr19:15979808-15980016(+)$1	208	36	39	8.9999
::D	chr6:118412077-118412305(+)$1	228	31	34	8.9999
:CC	chr4:58873308-58873522(-)$1	214	17	20	8.9999
d::	chr2:129457820-129458026(-)$1	206	69	72	8.9999
ppp	chr7:63984934-63985154(-)$1	220	136	139	8.9999
CCC	chr16:49913322-49913525(+)$1	203	153	156	8.9999
ggg	chr12:113032636-113032842(+)$1	206	90	93	8.9999
ddd	chr7:137899280-137899488(+)$1	208	155	158	8.9999
::b	chr4:133222215-133222435(-)$1	220	18	21	8.9999
:::	chr18:46664201-46664405(-)$1	204	3	6	8.9999
H::	chr14:18686479-18686680(+)$1	201	152	155	8.9999
ooo	chr11:87403855-87404055(+)$1	200	116	119	8.9999
DDD	chr12:11332656-11332860(-)$1	204	27	30	8.9999
hhh	chr8:96491851-96492051(+)$1	200	75	78	8.9999
ttt	chrX:96143022-96143223(-)$1	201	21	24	8.9999
:::	chr2:174171943-174172143(+)$1	200	8	11	8.9999
4bb	chr2:148522894-148523094(-)$1	200	133	136	8.9999
qqq	chr5:135095912-135096114(-)$1	202	11	14	8.9999
###	chr9:107726839-107727043(-)$1	204	31	34	8.9999
^^^	chr11:98629216-98629422(+)$1	206	159	162	8.9999
KKD	chr18:63829963-63830184(-)$1	221	3	6	8.9999
d]g	chr15:37856060-37856278(-)$1	218	144	147	8.9999
ee!	chr14:121649056-121649279(+)$1	223	198	201	8.9999
###	chr14:64741402-64741618(-)$1	216	29	32	8.9999
:dd	chr17:32339021-32339239(-)$1	218	159	162	8.9999
:::	chr8:113579311-113579537(-)$1	226	13	16	8.9999
fff	chr1:136097724-136097931(+)$1	207	43	46	8.9999
eel	chr14:57309771-57309988(+)$1	217	65	68	8.9999
)dd	chr4:129687095-129687309(+)$1	214	22	25	8.9999
C}D	chr12:101149988-101150216(+)$1	228	156	159	8.9999
ooo	chr11:36493301-36493505(-)$1	204	14	17	8.9999
ggg	chr2:62855633-62855842(-)$1	209	38	41	8.9999
:::	chr18:37346264-37346473(+)$1	209	13	16	8.9999
:FF	chr1:66487129-66487344(+)$1	215	0	3	8.9999
ooo	chr10:126435959-126436174(+)$1	215	121	124	8.9999
22e	chr8:88062563-88062764(-)$1	201	34	37	8.9999
fff	chr8:96528993-96529193(-)$1	200	79	82	8.9999
[ff	chr4:59741870-59742085(+)$1	215	51	54	8.9999
:::	chr2:64849911-64850123(-)$1	212	0	3	8.9999
>>>	chr4:28891486-28891699(+)$1	213	173	176	8.9999
ffp	chr3:144351086-144351305(+)$1	219	35	38	8.9999
:::	chr14:46079252-46079453(-)$1	201	41	44	8.9999
fff	chr5:15878317-15878521(+)$1	204	39	42	8.9999
'''	chrX:101479217-101479422(+)$1	205	87	90	8.9999
7dd	chr15:78908587-78908818(+)$1	231	129	132	8.9999
ppp	chr2:103987436-103987655(-)$1	219	77	80	8.9999
:::	chr14:8998560-8998766(-)$1	206	85	88	8.9999
uuu	chr18:51288694-51288905(+)$1	211	148	151	8.9999
eee	chr5:24733941-24734157(+)$1	216	46	49	8.9999
sss	chrX:132379016-132379223(+)$1	207	106	109	8.9999
ggg	chr1:168323268-168323488(-)$1	220	54	57	8.9999
>>>	chr14:104103182-104103390(+)$1	208	108	111	8.9999
mmm	chr7:150253639-150253843(-)$1	204	62	65	8.9999
:::	chr2:38721140-38721368(-)$1	228	130	133	8.9999
NNN	chr8:85796471-85796681(-)$1	210	34	37	8.9999
:::	chr11:90139629-90139830(-)$1	201	74	77	8.9999
3ee	chrX:12193711-12193918(-)$1	207	139	142	8.9999
e33	chr13:104930740-104930942(-)$1	202	46	49	8.9999
uuu	chr15:76001862-76002062(-)$1	200	39	42	8.9999
EE:	chr9:70439871-70440080(-)$1	209	6	9	8.9999
~~A	chr1:36161595-36161804(-)$1	209	201	204	8.9999
eee	chr11:29407929-29408148(+)$1	219	63	66	8.9999
===	chr1:130260250-130260473(+)$1	223	90	93	8.9999
:::	chr15:68923422-68923649(+)$1	227	3	6	8.9999
444	chr11:103683423-103683624(-)$1	201	180	183	8.9999
GG{	chr15:85681711-85681927(+)$1	216	52	55	8.9999
eee	chr9:58499777-58499977(+)$1	200	40	43	8.9999
hhh	chr9:107950677-107950879(+)$1	202	88	91	8.9999
!dd	chr16:64858258-64858466(+)$1	208	37	40	8.9999
eee	chrX:35966483-35966703(+)$1	220	30	33	8.9999
E:c	chr6:63601476-63601680(+)$1	204	31	34	8.9999
ddd	chr12:73312673-73312876(-)$1	203	28	31	8.9999
fmm	chr3:79745524-79745746(-)$1	222	51	54	8.9999
333	chr7:126117223-126117423(-)$1	200	92	95	8.9999
mmm	chr12:107075231-107075450(+)$1	219	58	61	8.9999
444	chr2:64821197-64821430(-)$1	233	163	166	8.9999
cmm	chr6:116206354-116206571(+)$1	217	33	36	8.9999
ddd	chr19:7414325-7414533(-)$1	208	25	28	8.9999
ddd	chr2:90856711-90856912(+)$1	201	64	67	8.9999
E::	chr2:62164235-62164438(+)$1	203	102	105	8.9999
44d	chr1:89901016-89901239(-)$1	223	143	146	8.9999
:::	chr3:144259936-144260144(+)$1	208	1	4	8.9999
:gg	chr18:57454602-57454809(+)$1	207	10	13	8.9999
ccc	chrX:69069822-69070025(+)$1	203	126	129	8.9999
%%%	chr5:77515969-77516169(-)$1	200	38	41	8.9999
ddd	chr12:45694097-45694298(+)$1	201	88	91	8.9999
ddd	chr12:79979681-79979916(+)$1	235	23	26	8.9999
eee	chrX:97269594-97269829(+)$1	235	106	109	8.9999
coo	chrX:117442265-117442489(+)$1	224	4	7	8.9999
EE{	chr3:40505574-40505787(+)$1	213	16	19	8.9999
coo	chr12:38079352-38079579(+)$1	227	2	5	8.9999
iii	chr6:117124816-117125035(+)$1	219	64	67	8.9999
foo	chr13:104814096-104814316(+)$1	220	19	22	8.9999
{EE	chr6:5114396-5114619(+)$1	223	38	41	8.9999

#DB
...	chr4:150378455-150378684(-)$1	1	60	63	8.9999
)))	chr4:85034949-85035152(+)$1	1	53	56	8.9999
..(	chr19:15979808-15980016(+)$1	1	36	39	8.9999
..(	chr6:118412077-118412305(+)$1	1	31	34	8.9999
.((	chr4:58873308-58873522(-)$1	1	17	20	8.9999
)..	chr2:129457820-129458026(-)$1	1	69	72	8.9999
...	chr7:63984934-63985154(-)$1	1	136	139	8.9999
)))	chr16:49913322-49913525(+)$1	1	153	156	8.9999
(((	chr12:113032636-113032842(+)$1	1	90	93	8.9999
)))	chr7:137899280-137899488(+)$1	1	155	158	8.9999
..(	chr4:133222215-133222435(-)$1	1	18	21	8.9999
...	chr18:46664201-46664405(-)$1	1	3	6	8.9999
)..	chr14:18686479-18686680(+)$1	1	152	155	8.9999
...	chr11:87403855-87404055(+)$1	1	116	119	8.9999
(((	chr12:11332656-11332860(-)$1	1	27	30	8.9999
)))	chr8:96491851-96492051(+)$1	1	75	78	8.9999
...	chrX:96143022-96143223(-)$1	1	21	24	8.9999
...	chr2:174171943-174172143(+)$1	1	8	11	8.9999
.))	chr2:148522894-148523094(-)$1	1	133	136	8.9999
...	chr5:135095912-135096114(-)$1	1	11	14	8.9999
...	chr9:107726839-107727043(-)$1	1	31	34	8.9999
...	chr11:98629216-98629422(+)$1	1	159	162	8.9999
..(	chr18:63829963-63830184(-)$1	1	3	6	8.9999
).)	chr15:37856060-37856278(-)$1	1	144	147	8.9999
((.	chr14:121649056-121649279(+)$1	1	198	201	8.9999
...	chr14:64741402-64741618(-)$1	1	29	32	8.9999
.((	chr17:32339021-32339239(-)$1	1	159	162	8.9999
...	chr8:113579311-113579537(-)$1	1	13	16	8.9999
(((	chr1:136097724-136097931(+)$1	1	43	46	8.9999
((.	chr14:57309771-57309988(+)$1	1	65	68	8.9999
.((	chr4:129687095-129687309(+)$1	1	22	25	8.9999
).)	chr12:101149988-101150216(+)$1	1	156	159	8.9999
...	chr11:36493301-36493505(-)$1	1	14	17	8.9999
(((	chr2:62855633-62855842(-)$1	1	38	41	8.9999
...	chr18:37346264-37346473(+)$1	1	13	16	8.9999
.((	chr1:66487129-66487344(+)$1	1	0	3	8.9999
...	chr10:126435959-126436174(+)$1	1	121	124	8.9999
..)	chr8:88062563-88062764(-)$1	1	34	37	8.9999
(((	chr8:96528993-96529193(-)$1	1	79	82	8.9999
.((	chr4:59741870-59742085(+)$1	1	51	54	8.9999
...	chr2:64849911-64850123(-)$1	1	0	3	8.9999
...	chr4:28891486-28891699(+)$1	1	173	176	8.9999
((.	chr3:144351086-144351305(+)$1	1	35	38	8.9999
...	chr14:46079252-46079453(-)$1	1	41	44	8.9999
(((	chr5:15878317-15878521(+)$1	1	39	42	8.9999
...	chrX:101479217-101479422(+)$1	1	87	90	8.9999
.))	chr15:78908587-78908818(+)$1	1	129	132	8.9999
...	chr2:103987436-103987655(-)$1	1	77	80	8.9999
...	chr14:8998560-8998766(-)$1	1	85	88	8.9999
...	chr18:51288694-51288905(+)$1	1	148	151	8.9999
(((	chr5:24733941-24734157(+)$1	1	46	49	8.9999
...	chrX:132379016-132379223(+)$1	1	106	109	8.9999
(((	chr1:168323268-168323488(-)$1	1	54	57	8.9999
...	chr14:104103182-104103390(+)$1	1	108	111	8.9999
...	chr7:150253639-150253843(-)$1	1	62	65	8.9999
...	chr2:38721140-38721368(-)$1	1	130	133	8.9999
...	chr8:85796471-85796681(-)$1	1	34	37	8.9999
...	chr11:90139629-90139830(-)$1	1	74	77	8.9999
.))	chrX:12193711-12193918(-)$1	1	139	142	8.9999
)..	chr13:104930740-104930942(-)$1	1	46	49	8.9999
...	chr15:76001862-76002062(-)$1	1	39	42	8.9999
((.	chr9:70439871-70440080(-)$1	1	6	9	8.9999
..)	chr1:36161595-36161804(-)$1	1	201	204	8.9999
)))	chr11:29407929-29408148(+)$1	1	63	66	8.9999
)))	chr1:130260250-130260473(+)$1	1	90	93	8.9999
...	chr15:68923422-68923649(+)$1	1	3	6	8.9999
...	chr11:103683423-103683624(-)$1	1	180	183	8.9999
((.	chr15:85681711-85681927(+)$1	1	52	55	8.9999
(((	chr9:58499777-58499977(+)$1	1	40	43	8.9999
(((	chr9:107950677-107950879(+)$1	1	88	91	8.9999
.((	chr16:64858258-64858466(+)$1	1	37	40	8.9999
(((	chrX:35966483-35966703(+)$1	1	30	33	8.9999
(.(	chr6:63601476-63601680(+)$1	1	31	34	8.9999
(((	chr12:73312673-73312876(-)$1	1	28	31	8.9999
(..	chr3:79745524-79745746(-)$1	1	51	54	8.9999
...	chr7:126117223-126117423(-)$1	1	92	95	8.9999
...	chr12:107075231-107075450(+)$1	1	58	61	8.9999
...	chr2:64821197-64821430(-)$1	1	163	166	8.9999
(..	chr6:116206354-116206571(+)$1	1	33	36	8.9999
(((	chr19:7414325-7414533(-)$1	1	25	28	8.9999
(((	chr2:90856711-90856912(+)$1	1	64	67	8.9999
(..	chr2:62164235-62164438(+)$1	1	102	105	8.9999
..)	chr1:89901016-89901239(-)$1	1	143	146	8.9999
...	chr3:144259936-144260144(+)$1	1	1	4	8.9999
.((	chr18:57454602-57454809(+)$1	1	10	13	8.9999
(((	chrX:69069822-69070025(+)$1	1	126	129	8.9999
...	chr5:77515969-77516169(-)$1	1	38	41	8.9999
)))	chr12:45694097-45694298(+)$1	1	88	91	8.9999
(((	chr12:79979681-79979916(+)$1	1	23	26	8.9999
(((	chrX:97269594-97269829(+)$1	1	106	109	8.9999
(..	chrX:117442265-117442489(+)$1	1	4	7	8.9999
((.	chr3:40505574-40505787(+)$1	1	16	19	8.9999
(..	chr12:38079352-38079579(+)$1	1	2	5	8.9999
)))	chr6:117124816-117125035(+)$1	1	64	67	8.9999
(..	chr13:104814096-104814316(+)$1	1	19	22	8.9999
.((	chr6:5114396-5114619(+)$1	1	38	41	8.9999

#PSSM
U : 0.89	u : 0.10	
A : 0.89	a : 0.10	
C : 0.89	c : 0.10	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m1_run2.nuc.txt

#NT
UUUG	chr6:134396799-134397020(-)$1	221	199	203	11.9999
UUUG	chr11:77343131-77343351(-)$1	220	37	41	11.9999
UUUG	chrX:78340585-78340808(+)$1	223	67	71	11.9999
UUUG	chrX:33710348-33710568(+)$1	220	85	89	11.9999
UUUG	chr14:37891743-37891964(-)$1	221	178	182	11.9999
UUUG	chr10:120361269-120361490(-)$1	221	172	176	11.9999
UUUG	chr10:127564902-127565131(+)$1	229	6	10	11.9999
UUUG	chr1:155755960-155756192(+)$1	232	60	64	11.9999
UUUG	chr1:53404551-53404795(-)$1	244	157	161	11.9999
UUUG	chr13:8972150-8972370(-)$1	220	45	49	11.9999
UUUG	chr16:94645577-94645806(+)$1	229	2	6	11.9999
UUUG	chr6:146547140-146547365(+)$1	225	6	10	11.9999
UUUG	chr11:87556907-87557132(+)$1	225	149	153	11.9999
UUUG	chr2:29770704-29770927(+)$1	223	140	144	11.9999
UUUG	chr13:101549199-101549419(-)$1	220	118	122	11.9999
UUUG	chr7:35833586-35833822(-)$1	236	7	11	11.9999
UUUG	chr2:120333154-120333374(-)$1	220	67	71	11.9999
UUUG	chr9:47658597-47658817(+)$1	220	30	34	11.9999
UUUG	chr7:29606978-29607198(+)$1	220	10	14	11.9999
UUUG	chr10:98485871-98486111(+)$1	240	73	77	11.9999
UUUG	chr1:4835055-4835304(+)$1	249	150	154	11.9999
UUUG	chr5:116004285-116004511(+)$1	226	150	154	11.9999
UUUG	chr14:80029022-80029242(+)$1	220	39	43	11.9999
UUUG	chr11:78320486-78320707(-)$1	221	159	163	11.9999
UUUG	chr1:121442151-121442371(-)$1	220	151	155	11.9999
UUUG	chr3:108482198-108482418(-)$1	220	149	153	11.9999
UUUG	chr7:118214848-118215071(-)$1	223	207	211	11.9999
UUUG	chr6:117873637-117873857(+)$1	220	26	30	11.9999
UUUG	chr2:179816706-179816951(+)$1	245	7	11	11.9999
UUUG	chr18:32256948-32257168(+)$1	220	91	95	11.9999
UUUG	chr11:32645869-32646099(+)$1	230	192	196	11.9999
UUUG	chr18:35023889-35024109(+)$1	220	4	8	11.9999
UUUG	chr7:25867299-25867519(+)$1	220	92	96	11.9999
UUUG	chr11:98667090-98667310(+)$1	220	184	188	11.9999
UUUG	chr3:82196750-82196970(+)$1	220	70	74	11.9999
UUUG	chr1:183107763-183107983(-)$1	220	54	58	11.9999
UUUG	chr2:154519855-154520086(+)$1	231	135	139	11.9999
UUUG	chr10:59412389-59412609(-)$1	220	181	185	11.9999
uuug	chr11:43239274-43239513(-)$1	239	61	65	11.9999
UUUG	chr5:24215959-24216179(+)$1	220	68	72	11.9999
UUUG	chrX:153883517-153883762(-)$1	245	10	14	11.9999
UUUG	chr6:113102629-113102849(+)$1	220	65	69	11.9999
UUUG	chr11:76780178-76780398(+)$1	220	13	17	11.9999
UUUG	chr6:92137775-92138004(-)$1	229	36	40	11.9999
UUUG	chr10:89281855-89282075(+)$1	220	20	24	11.9999
uuug	chr9:114657451-114657678(+)$1	227	155	159	11.9999
UUUG	chr1:141071698-141071918(+)$1	220	7	11	11.9999
UUUG	chr14:121346837-121347057(+)$1	220	5	9	11.9999
UUUG	chr11:100899493-100899717(+)$1	224	11	15	11.9999
UUUG	chr16:96378287-96378509(+)$1	222	129	133	11.9999
UUUG	chr15:85293415-85293636(+)$1	221	100	104	11.9999
UUUG	chr10:95010405-95010626(-)$1	221	62	66	11.9999
UUUG	chr9:55984079-55984299(-)$1	220	204	208	11.9999
UUUG	chr10:127513857-127514077(+)$1	220	12	16	11.9999
UUUG	chr18:46747945-46748165(-)$1	220	212	216	11.9999
UUUG	chr2:26777135-26777355(-)$1	220	8	12	11.9999
UUUG	chr15:7142432-7142653(+)$1	221	55	59	11.9999
UUUG	chr17:13208005-13208225(+)$1	220	200	204	11.9999
UUUG	chr12:72316977-72317209(+)$1	232	41	45	11.9999
UUUG	chr6:100178865-100179086(-)$1	221	100	104	11.9999
UUUG	chr12:107066478-107066700(+)$1	222	188	192	11.9999
UUUG	chr15:9042075-9042295(-)$1	220	65	69	11.9999
UUUG	chr9:7793203-7793424(+)$1	221	21	25	11.9999
UUUG	chr19:7500820-7501042(-)$1	222	144	148	11.9999
UUUG	chr10:80315537-80315757(-)$1	220	119	123	11.9999
UUUG	chr2:153229269-153229491(+)$1	222	17	21	11.9999
UUUG	chr8:48270802-48271026(-)$1	224	20	24	11.9999
UUUG	chr12:82047557-82047777(+)$1	220	138	142	11.9999
UUUG	chr5:151439892-151440113(-)$1	221	74	78	11.9999
UUUG	chr17:73198496-73198716(+)$1	220	22	26	11.9999
UUUG	chr1:84718099-84718330(-)$1	231	27	31	11.9999
UUUG	chr18:24643775-24643995(-)$1	220	144	148	11.9999
UUUG	chr6:71529802-71530022(+)$1	220	101	105	11.9999
UUUG	chr17:48556120-48556341(+)$1	221	23	27	11.9999
UUUG	chr4:145728783-145729003(-)$1	220	0	4	11.9999
UUUG	chr14:61382276-61382501(+)$1	225	107	111	11.9999
UUUG	chr2:112253279-112253499(+)$1	220	6	10	11.9999
UUUG	chr1:167108536-167108757(-)$1	221	79	83	11.9999
UUUG	chr14:64111357-64111593(-)$1	236	180	184	11.9999
UUUG	chr12:16993390-16993627(+)$1	237	4	8	11.9999
uuug	chr19:47205318-47205538(+)$1	220	203	207	11.9999
uuuG	chr2:132131762-132131985(+)$1	223	27	31	11.9999
UUUG	chr6:129491450-129491716(+)$1	266	26	30	11.9999

#otherMatches

#Struct PSSM
eeee	chr8:82199188-82199408(+)$1	220	73	77	11.9999
hhhh	chr6:134396799-134397020(-)$1	221	199	203	11.9999
6666	chr11:77343131-77343351(-)$1	220	37	41	11.9999
EEEE	chrX:78340585-78340808(+)$1	223	67	71	11.9999
gggg	chrX:33710348-33710568(+)$1	220	85	89	11.9999
iiii	chr14:37891743-37891964(-)$1	221	178	182	11.9999
dd]e	chr10:120361269-120361490(-)$1	221	172	176	11.9999
::CC	chr10:127564902-127565131(+)$1	229	6	10	11.9999
qbb]	chr1:155755960-155756192(+)$1	232	60	64	11.9999
gggg	chr1:53404551-53404795(-)$1	244	157	161	11.9999
iii[	chr13:8972150-8972370(-)$1	220	45	49	11.9999
JJJJ	chr16:94645577-94645806(+)$1	229	2	6	11.9999
dd[b	chr6:146547140-146547365(+)$1	225	6	10	11.9999
iiii	chr11:87556907-87557132(+)$1	225	149	153	11.9999
ffff	chr2:29770704-29770927(+)$1	223	140	144	11.9999
::::	chr13:101549199-101549419(-)$1	220	118	122	11.9999
###f	chr7:35833586-35833822(-)$1	236	7	11	11.9999
qqqq	chr2:120333154-120333374(-)$1	220	67	71	11.9999
JJJD	chr9:47658597-47658817(+)$1	220	30	34	11.9999
DD{D	chr7:29606978-29607198(+)$1	220	10	14	11.9999
HHHb	chr10:98485871-98486111(+)$1	240	73	77	11.9999
ueee	chr1:4835055-4835304(+)$1	249	150	154	11.9999
##cc	chr5:116004285-116004511(+)$1	226	150	154	11.9999
mmcc	chr14:80029022-80029242(+)$1	220	39	43	11.9999
eeee	chr11:78320486-78320707(-)$1	221	159	163	11.9999
cc33	chr1:121442151-121442371(-)$1	220	151	155	11.9999
eee[	chr3:108482198-108482418(-)$1	220	149	153	11.9999
====	chr7:118214848-118215071(-)$1	223	207	211	11.9999
eeee	chr6:117873637-117873857(+)$1	220	26	30	11.9999
GGGb	chr2:179816706-179816951(+)$1	245	7	11	11.9999
33ee	chr18:32256948-32257168(+)$1	220	91	95	11.9999
CC}G	chr11:32645869-32646099(+)$1	230	192	196	11.9999
:::g	chr18:35023889-35024109(+)$1	220	4	8	11.9999
JJJJ	chr7:25867299-25867519(+)$1	220	92	96	11.9999
ffff	chr11:98667090-98667310(+)$1	220	184	188	11.9999
cc[d	chr3:82196750-82196970(+)$1	220	70	74	11.9999
ggg[	chr1:183107763-183107983(-)$1	220	54	58	11.9999
ffff	chr2:154519855-154520086(+)$1	231	135	139	11.9999
mmdd	chr10:59412389-59412609(-)$1	220	181	185	11.9999
###c	chr11:43239274-43239513(-)$1	239	61	65	11.9999
mmmd	chr5:24215959-24216179(+)$1	220	68	72	11.9999
IIII	chrX:153883517-153883762(-)$1	245	10	14	11.9999
:ccc	chr6:113102629-113102849(+)$1	220	65	69	11.9999
HHHH	chr11:76780178-76780398(+)$1	220	13	17	11.9999
d:::	chr6:92137775-92138004(-)$1	229	36	40	11.9999
f!!b	chr10:89281855-89282075(+)$1	220	20	24	11.9999
mmhh	chr9:114657451-114657678(+)$1	227	155	159	11.9999
Ffff	chr1:141071698-141071918(+)$1	220	7	11	11.9999
hhhh	chr14:121346837-121347057(+)$1	220	5	9	11.9999
{GGG	chr11:100899493-100899717(+)$1	224	11	15	11.9999
444i	chr16:96378287-96378509(+)$1	222	129	133	11.9999
:::g	chr15:85293415-85293636(+)$1	221	100	104	11.9999
qqdd	chr10:95010405-95010626(-)$1	221	62	66	11.9999
????	chr9:55984079-55984299(-)$1	220	204	208	11.9999
ELLL	chr10:127513857-127514077(+)$1	220	12	16	11.9999
:DDD	chr18:46747945-46748165(-)$1	220	212	216	11.9999
ffff	chr2:26777135-26777355(-)$1	220	8	12	11.9999
###d	chr15:7142432-7142653(+)$1	221	55	59	11.9999
88ff	chr17:13208005-13208225(+)$1	220	200	204	11.9999
hnnn	chr12:72316977-72317209(+)$1	232	41	45	11.9999
"""h	chr6:100178865-100179086(-)$1	221	100	104	11.9999
e555	chr12:107066478-107066700(+)$1	222	188	192	11.9999
:FFF	chr15:9042075-9042295(-)$1	220	65	69	11.9999
HHHH	chr9:7793203-7793424(+)$1	221	21	25	11.9999
::::	chr19:7500820-7501042(-)$1	222	144	148	11.9999
ddCC	chr10:80315537-80315757(-)$1	220	119	123	11.9999
::::	chr2:153229269-153229491(+)$1	222	17	21	11.9999
ffff	chr8:48270802-48271026(-)$1	224	20	24	11.9999
gggg	chr12:82047557-82047777(+)$1	220	138	142	11.9999
^^^f	chr5:151439892-151440113(-)$1	221	74	78	11.9999
[eee	chr17:73198496-73198716(+)$1	220	22	26	11.9999
Cfff	chr1:84718099-84718330(-)$1	231	27	31	11.9999
5fff	chr18:24643775-24643995(-)$1	220	144	148	11.9999
###a	chr6:71529802-71530022(+)$1	220	101	105	11.9999
dddd	chr17:48556120-48556341(+)$1	221	23	27	11.9999
::::	chr4:145728783-145729003(-)$1	220	0	4	11.9999
dlll	chr14:61382276-61382501(+)$1	225	107	111	11.9999
f[cc	chr2:112253279-112253499(+)$1	220	6	10	11.9999
tttt	chr1:167108536-167108757(-)$1	221	79	83	11.9999
hhhh	chr14:64111357-64111593(-)$1	236	180	184	11.9999
::HH	chr12:16993390-16993627(+)$1	237	4	8	11.9999
====	chr19:47205318-47205538(+)$1	220	203	207	11.9999
[ddd	chr2:132131762-132131985(+)$1	223	27	31	11.9999
JJJJ	chr6:129491450-129491716(+)$1	266	26	30	11.9999

#DB
((((	chr8:82199188-82199408(+)$1	1	73	77	11.9999
))))	chr6:134396799-134397020(-)$1	1	199	203	11.9999
....	chr11:77343131-77343351(-)$1	1	37	41	11.9999
((((	chrX:78340585-78340808(+)$1	1	67	71	11.9999
))))	chrX:33710348-33710568(+)$1	1	85	89	11.9999
))))	chr14:37891743-37891964(-)$1	1	178	182	11.9999
)).)	chr10:120361269-120361490(-)$1	1	172	176	11.9999
..((	chr10:127564902-127565131(+)$1	1	6	10	11.9999
.)).	chr1:155755960-155756192(+)$1	1	60	64	11.9999
))))	chr1:53404551-53404795(-)$1	1	157	161	11.9999
(((.	chr13:8972150-8972370(-)$1	1	45	49	11.9999
((((	chr16:94645577-94645806(+)$1	1	2	6	11.9999
((.(	chr6:146547140-146547365(+)$1	1	6	10	11.9999
((((	chr11:87556907-87557132(+)$1	1	149	153	11.9999
((((	chr2:29770704-29770927(+)$1	1	140	144	11.9999
....	chr13:101549199-101549419(-)$1	1	118	122	11.9999
...(	chr7:35833586-35833822(-)$1	1	7	11	11.9999
....	chr2:120333154-120333374(-)$1	1	67	71	11.9999
((((	chr9:47658597-47658817(+)$1	1	30	34	11.9999
((.(	chr7:29606978-29607198(+)$1	1	10	14	11.9999
((((	chr10:98485871-98486111(+)$1	1	73	77	11.9999
.)))	chr1:4835055-4835304(+)$1	1	150	154	11.9999
..((	chr5:116004285-116004511(+)$1	1	150	154	11.9999
..))	chr14:80029022-80029242(+)$1	1	39	43	11.9999
((((	chr11:78320486-78320707(-)$1	1	159	163	11.9999
))..	chr1:121442151-121442371(-)$1	1	151	155	11.9999
(((.	chr3:108482198-108482418(-)$1	1	149	153	11.9999
))))	chr7:118214848-118215071(-)$1	1	207	211	11.9999
((((	chr6:117873637-117873857(+)$1	1	26	30	11.9999
((((	chr2:179816706-179816951(+)$1	1	7	11	11.9999
..))	chr18:32256948-32257168(+)$1	1	91	95	11.9999
)).)	chr11:32645869-32646099(+)$1	1	192	196	11.9999
...(	chr18:35023889-35024109(+)$1	1	4	8	11.9999
))))	chr7:25867299-25867519(+)$1	1	92	96	11.9999
((((	chr11:98667090-98667310(+)$1	1	184	188	11.9999
((.(	chr3:82196750-82196970(+)$1	1	70	74	11.9999
(((.	chr1:183107763-183107983(-)$1	1	54	58	11.9999
))))	chr2:154519855-154520086(+)$1	1	135	139	11.9999
..))	chr10:59412389-59412609(-)$1	1	181	185	11.9999
...(	chr11:43239274-43239513(-)$1	1	61	65	11.9999
...)	chr5:24215959-24216179(+)$1	1	68	72	11.9999
((((	chrX:153883517-153883762(-)$1	1	10	14	11.9999
.(((	chr6:113102629-113102849(+)$1	1	65	69	11.9999
((((	chr11:76780178-76780398(+)$1	1	13	17	11.9999
)...	chr6:92137775-92138004(-)$1	1	36	40	11.9999
(..(	chr10:89281855-89282075(+)$1	1	20	24	11.9999
..))	chr9:114657451-114657678(+)$1	1	155	159	11.9999
((((	chr1:141071698-141071918(+)$1	1	7	11	11.9999
((((	chr14:121346837-121347057(+)$1	1	5	9	11.9999
.(((	chr11:100899493-100899717(+)$1	1	11	15	11.9999
...)	chr16:96378287-96378509(+)$1	1	129	133	11.9999
...(	chr15:85293415-85293636(+)$1	1	100	104	11.9999
..))	chr10:95010405-95010626(-)$1	1	62	66	11.9999
....	chr9:55984079-55984299(-)$1	1	204	208	11.9999
(...	chr10:127513857-127514077(+)$1	1	12	16	11.9999
.)))	chr18:46747945-46748165(-)$1	1	212	216	11.9999
((((	chr2:26777135-26777355(-)$1	1	8	12	11.9999
...(	chr15:7142432-7142653(+)$1	1	55	59	11.9999
..))	chr17:13208005-13208225(+)$1	1	200	204	11.9999
(...	chr12:72316977-72317209(+)$1	1	41	45	11.9999
...(	chr6:100178865-100179086(-)$1	1	100	104	11.9999
)...	chr12:107066478-107066700(+)$1	1	188	192	11.9999
.(((	chr15:9042075-9042295(-)$1	1	65	69	11.9999
((((	chr9:7793203-7793424(+)$1	1	21	25	11.9999
....	chr19:7500820-7501042(-)$1	1	144	148	11.9999
))))	chr10:80315537-80315757(-)$1	1	119	123	11.9999
....	chr2:153229269-153229491(+)$1	1	17	21	11.9999
((((	chr8:48270802-48271026(-)$1	1	20	24	11.9999
))))	chr12:82047557-82047777(+)$1	1	138	142	11.9999
...)	chr5:151439892-151440113(-)$1	1	74	78	11.9999
.(((	chr17:73198496-73198716(+)$1	1	22	26	11.9999
((((	chr1:84718099-84718330(-)$1	1	27	31	11.9999
.)))	chr18:24643775-24643995(-)$1	1	144	148	11.9999
...(	chr6:71529802-71530022(+)$1	1	101	105	11.9999
((((	chr17:48556120-48556341(+)$1	1	23	27	11.9999
....	chr4:145728783-145729003(-)$1	1	0	4	11.9999
(...	chr14:61382276-61382501(+)$1	1	107	111	11.9999
(.((	chr2:112253279-112253499(+)$1	1	6	10	11.9999
....	chr1:167108536-167108757(-)$1	1	79	83	11.9999
((((	chr14:64111357-64111593(-)$1	1	180	184	11.9999
..((	chr12:16993390-16993627(+)$1	1	4	8	11.9999
))))	chr19:47205318-47205538(+)$1	1	203	207	11.9999
.(((	chr2:132131762-132131985(+)$1	1	27	31	11.9999
((((	chr6:129491450-129491716(+)$1	1	26	30	11.9999

#PSSM
U : 0.95	u : 0.04	
U : 0.95	u : 0.04	
U : 0.95	u : 0.04	
G : 0.96	g : 0.03	

#score	1007.9999999999995
#seq	84
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m2_run1.nuc.txt

#NT
GCUUU	chr12:109148794-109148999(-)$1	205	39	44	15.0000
GCUUU	chr10:3457284-3457488(+)$1	204	46	51	15.0000
gcuuu	chrX:110192258-110192460(-)$1	202	109	114	15.0000
gcuuu	chr12:86683460-86683667(-)$1	207	170	175	15.0000
GCUUU	chr3:97510630-97510842(-)$1	212	111	116	15.0000
GCUUU	chr6:120948877-120949112(-)$1	235	206	211	15.0000
GCUUU	chr1:34935432-34935632(+)$1	200	56	61	15.0000
GCUUU	chr13:83803040-83803243(+)$1	203	101	106	15.0000
GCuuu	chr12:103979879-103980090(-)$1	211	203	208	15.0000
GCUUU	chr1:136096988-136097194(-)$1	206	40	45	15.0000
GCUUU	chr16:49912361-49912564(+)$1	203	97	102	15.0000
GCUUU	chr5:123318589-123318810(+)$1	221	199	204	15.0000
gcuuu	chr11:36355074-36355281(-)$1	207	97	102	15.0000
GCUUU	chr7:63422822-63423048(+)$1	226	57	62	15.0000
GCUUU	chr6:71758196-71758401(+)$1	205	106	111	15.0000
GCUUU	chr9:59526791-59527005(+)$1	214	105	110	15.0000
GCUUU	chr3:8560529-8560737(+)$1	208	96	101	15.0000
GCUUU	chr2:120562099-120562309(-)$1	210	91	96	15.0000
GCUUU	chr1:172247656-172247866(-)$1	210	136	141	15.0000
GCUUU	chr7:6659177-6659387(-)$1	210	103	108	15.0000
gcuuu	chr13:59555801-59556012(-)$1	211	112	117	15.0000
GCUUU	chr13:17972440-17972652(-)$1	212	99	104	15.0000
GCUUU	chr6:71342456-71342660(+)$1	204	150	155	15.0000
GCUUU	chr7:17501163-17501365(-)$1	202	188	193	15.0000
GCUUU	chr2:32086334-32086534(+)$1	200	100	105	15.0000
GCUUU	chr13:59037202-59037409(+)$1	207	142	147	15.0000
GCUUU	chr10:110732690-110732904(+)$1	214	100	105	15.0000
gcuuu	chr11:28467624-28467825(-)$1	201	102	107	15.0000
GCUUU	chr9:45737608-45737814(-)$1	206	27	32	15.0000
GCUUU	chr14:21275342-21275556(-)$1	214	100	105	15.0000
GCUUU	chr12:86965277-86965477(+)$1	200	93	98	15.0000
GCUUU	chrX:73031516-73031716(-)$1	200	116	121	15.0000
GCUUU	chr2:160721113-160721331(+)$1	218	0	5	15.0000
GCUUU	chr4:154449694-154449921(-)$1	227	80	85	15.0000
GCUUU	chr13:69121214-69121420(-)$1	206	164	169	15.0000
gcuuu	chr13:29634627-29634858(-)$1	231	102	107	15.0000
GCUUU	chr5:107404298-107404517(+)$1	219	128	133	15.0000
GCUUU	chr11:51935639-51935840(+)$1	201	105	110	15.0000
GCUUU	chr6:115224924-115225124(+)$1	200	99	104	15.0000
GCUUU	chr11:76177013-76177248(-)$1	235	138	143	15.0000
GCUUU	chr8:13020071-13020284(+)$1	213	105	110	15.0000
GCUUU	chr14:19573396-19573610(-)$1	214	205	210	15.0000
GCUUU	chr11:74490375-74490576(-)$1	201	102	107	15.0000
GCUUU	chr2:57220044-57220245(+)$1	201	117	122	15.0000
GCUUU	chr5:72494553-72494768(+)$1	215	11	16	15.0000
gcuuu	chr9:68550472-68550692(+)$1	220	108	113	15.0000
GCUUU	chr5:108354916-108355125(-)$1	209	111	116	15.0000

#otherMatches

#Struct PSSM
epppp	chr8:109901807-109902013(+)$1	206	97	102	15.0000
b::hh	chr12:109148794-109148999(-)$1	205	39	44	15.0000
ccc^^	chr10:3457284-3457488(+)$1	204	46	51	15.0000
eeeer	chrX:110192258-110192460(-)$1	202	109	114	15.0000
HHHYY	chr12:86683460-86683667(-)$1	207	170	175	15.0000
ffff!	chr3:97510630-97510842(-)$1	212	111	116	15.0000
b[ddd	chr6:120948877-120949112(-)$1	235	206	211	15.0000
ddddm	chr1:34935432-34935632(+)$1	200	56	61	15.0000
fffff	chr13:83803040-83803243(+)$1	203	101	106	15.0000
GG:::	chr12:103979879-103980090(-)$1	211	203	208	15.0000
bbooo	chr1:136096988-136097194(-)$1	206	40	45	15.0000
:dddd	chr16:49912361-49912564(+)$1	203	97	102	15.0000
hhhhh	chr5:123318589-123318810(+)$1	221	199	204	15.0000
b!!bb	chr11:36355074-36355281(-)$1	207	97	102	15.0000
eeeee	chr7:63422822-63423048(+)$1	226	57	62	15.0000
iiiii	chr6:71758196-71758401(+)$1	205	106	111	15.0000
ccc]a	chr9:59526791-59527005(+)$1	214	105	110	15.0000
cc###	chr3:8560529-8560737(+)$1	208	96	101	15.0000
55555	chr2:120562099-120562309(-)$1	210	91	96	15.0000
eee!!	chr1:172247656-172247866(-)$1	210	136	141	15.0000
]ccc0	chr7:6659177-6659387(-)$1	210	103	108	15.0000
dd!!b	chr13:59555801-59556012(-)$1	211	112	117	15.0000
eeeee	chr13:17972440-17972652(-)$1	212	99	104	15.0000
::::C	chr6:71342456-71342660(+)$1	204	150	155	15.0000
CCYYC	chr7:17501163-17501365(-)$1	202	188	193	15.0000
dddee	chr2:32086334-32086534(+)$1	200	100	105	15.0000
bb333	chr13:59037202-59037409(+)$1	207	142	147	15.0000
bbooo	chr10:110732690-110732904(+)$1	214	100	105	15.0000
hhhhh	chr11:28467624-28467825(-)$1	201	102	107	15.0000
{BBii	chr9:45737608-45737814(-)$1	206	27	32	15.0000
HHHHH	chr14:21275342-21275556(-)$1	214	100	105	15.0000
d::::	chr12:86965277-86965477(+)$1	200	93	98	15.0000
mmmmd	chrX:73031516-73031716(-)$1	200	116	121	15.0000
:::::	chr2:160721113-160721331(+)$1	218	0	5	15.0000
ooooo	chr4:154449694-154449921(-)$1	227	80	85	15.0000
ppppd	chr13:69121214-69121420(-)$1	206	164	169	15.0000
bblll	chr13:29634627-29634858(-)$1	231	102	107	15.0000
DDDDC	chr5:107404298-107404517(+)$1	219	128	133	15.0000
sssss	chr11:51935639-51935840(+)$1	201	105	110	15.0000
eeeee	chr6:115224924-115225124(+)$1	200	99	104	15.0000
dddqq	chr11:76177013-76177248(-)$1	235	138	143	15.0000
bb22e	chr8:13020071-13020284(+)$1	213	105	110	15.0000
:::::	chr14:19573396-19573610(-)$1	214	205	210	15.0000
fFFFF	chr11:74490375-74490576(-)$1	201	102	107	15.0000
ddzzz	chr2:57220044-57220245(+)$1	201	117	122	15.0000
[eeee	chr5:72494553-72494768(+)$1	215	11	16	15.0000
iiiii	chr9:68550472-68550692(+)$1	220	108	113	15.0000
cc:::	chr5:108354916-108355125(-)$1	209	111	116	15.0000

#DB
(....	chr8:109901807-109902013(+)$1	1	97	102	15.0000
)..((	chr12:109148794-109148999(-)$1	1	39	44	15.0000
(((..	chr10:3457284-3457488(+)$1	1	46	51	15.0000
((((.	chrX:110192258-110192460(-)$1	1	109	114	15.0000
)))..	chr12:86683460-86683667(-)$1	1	170	175	15.0000
((((.	chr3:97510630-97510842(-)$1	1	111	116	15.0000
(.(((	chr6:120948877-120949112(-)$1	1	206	211	15.0000
((((.	chr1:34935432-34935632(+)$1	1	56	61	15.0000
)))))	chr13:83803040-83803243(+)$1	1	101	106	15.0000
))...	chr12:103979879-103980090(-)$1	1	203	208	15.0000
((...	chr1:136096988-136097194(-)$1	1	40	45	15.0000
.((((	chr16:49912361-49912564(+)$1	1	97	102	15.0000
(((((	chr5:123318589-123318810(+)$1	1	199	204	15.0000
(..((	chr11:36355074-36355281(-)$1	1	97	102	15.0000
(((((	chr7:63422822-63423048(+)$1	1	57	62	15.0000
(((((	chr6:71758196-71758401(+)$1	1	106	111	15.0000
))).)	chr9:59526791-59527005(+)$1	1	105	110	15.0000
((...	chr3:8560529-8560737(+)$1	1	96	101	15.0000
.....	chr2:120562099-120562309(-)$1	1	91	96	15.0000
(((..	chr1:172247656-172247866(-)$1	1	136	141	15.0000
.))).	chr7:6659177-6659387(-)$1	1	103	108	15.0000
((..(	chr13:59555801-59556012(-)$1	1	112	117	15.0000
(((((	chr13:17972440-17972652(-)$1	1	99	104	15.0000
....)	chr6:71342456-71342660(+)$1	1	150	155	15.0000
))..)	chr7:17501163-17501365(-)$1	1	188	193	15.0000
)))))	chr2:32086334-32086534(+)$1	1	100	105	15.0000
))...	chr13:59037202-59037409(+)$1	1	142	147	15.0000
((...	chr10:110732690-110732904(+)$1	1	100	105	15.0000
)))))	chr11:28467624-28467825(-)$1	1	102	107	15.0000
.((((	chr9:45737608-45737814(-)$1	1	27	32	15.0000
(((((	chr14:21275342-21275556(-)$1	1	100	105	15.0000
)....	chr12:86965277-86965477(+)$1	1	93	98	15.0000
....)	chrX:73031516-73031716(-)$1	1	116	121	15.0000
.....	chr2:160721113-160721331(+)$1	1	0	5	15.0000
.....	chr4:154449694-154449921(-)$1	1	80	85	15.0000
....)	chr13:69121214-69121420(-)$1	1	164	169	15.0000
((...	chr13:29634627-29634858(-)$1	1	102	107	15.0000
(((((	chr5:107404298-107404517(+)$1	1	128	133	15.0000
.....	chr11:51935639-51935840(+)$1	1	105	110	15.0000
)))))	chr6:115224924-115225124(+)$1	1	99	104	15.0000
(((..	chr11:76177013-76177248(-)$1	1	138	143	15.0000
))..)	chr8:13020071-13020284(+)$1	1	105	110	15.0000
.....	chr14:19573396-19573610(-)$1	1	205	210	15.0000
)))))	chr11:74490375-74490576(-)$1	1	102	107	15.0000
((...	chr2:57220044-57220245(+)$1	1	117	122	15.0000
.((((	chr5:72494553-72494768(+)$1	1	11	16	15.0000
(((((	chr9:68550472-68550692(+)$1	1	108	113	15.0000
))...	chr5:108354916-108355125(-)$1	1	111	116	15.0000

#PSSM
G : 0.83	g : 0.16	
C : 0.83	c : 0.16	
U : 0.81	u : 0.18	
U : 0.81	u : 0.18	
U : 0.81	u : 0.18	

#score	720.0000000000001
#seq	48
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m1_run1.nuc.txt

#NT
CUUUUAUGU	chr11:87793793-87794058(-)$1	265	133	142	13.1111
UUUUUCCUU	chr8:106942833-106943068(-)$1	235	220	229	15.8888
AUUUUCUUU	chr3:95292215-95292460(+)$1	245	16	25	18.4814
UUUUUCUUU	chr2:155214476-155214718(+)$1	242	161	170	19.9629
cuuuucuuu	chr14:35339882-35340126(-)$1	244	166	175	19.9629
AUUGUCUUU	chr1:99717957-99718198(-)$1	241	14	23	13.9444
GUUUUUUUU	chr2:136607123-136607367(+)$1	244	58	67	15.6111
UUUGUCUUU	chr2:132134389-132134639(+)$1	250	56	65	15.4259
UUUUUCCUU	chr2:164824339-164824574(+)$1	235	47	56	15.8888
Uuuuucuuu	chr17:33884446-33884681(-)$1	235	84	93	19.9629
cuUUUCUGU	chr11:60371177-60371412(+)$1	235	100	109	16.0740
UUUUUCUUC	chr12:111820777-111821023(+)$1	246	24	33	15.2407
CUUUGCUGU	chr5:136384957-136385202(-)$1	245	195	204	12.2777
CUUUCCUUU	chr9:30957625-30957869(-)$1	244	69	78	15.7962
UUUUUCUUU	chr2:155214586-155214823(+)$1	237	51	60	19.9629
CUUUUCUUU	chr1:134473175-134473411(-)$1	236	205	214	19.9629
CUUUUAUGU	chr11:87793705-87793951(-)$1	246	26	35	13.1111
UUUUGCUUU	chr15:36407463-36407701(-)$1	238	66	75	16.1666
UUUUUCUUU	chr2:163842323-163842558(+)$1	235	67	76	19.9629
AUUUGCUUU	chr4:19538380-19538627(-)$1	247	114	123	14.6851
AUuuuuuuu	chr5:36943056-36943295(-)$1	239	100	109	15.7962
CUUUUCUUG	chr3:58394690-58394925(+)$1	235	176	185	15.2407
auuuuguuu	chr6:119875219-119875455(-)$1	236	99	108	15.7962
UUUUACUUU	chr11:88155614-88155849(-)$1	235	19	28	15.8888
uuuuucuuu	chr1:166367681-166367925(-)$1	244	97	106	19.9629
CUUUUAUUU	chr6:39554848-39555083(-)$1	235	39	48	16.9999
UUUUGCUUU	chr15:36407513-36407748(-)$1	235	113	122	16.1666
CUUUACUUU	chr14:21319413-21319648(-)$1	235	193	202	15.8888
CUUUGUUUU	chr17:73289277-73289513(+)$1	236	81	90	13.4814
CUUUUCAUU	chr7:118214765-118215000(-)$1	235	4	13	15.6111
CUUUUCCUU	chr7:35130774-35131009(-)$1	235	18	27	15.8888
UUUUUGUUU	chr4:114633348-114633583(-)$1	235	112	121	17.2777
UUUUUCUGU	chr6:82597858-82598093(-)$1	235	48	57	16.0740
uuuuuguuu	chr2:71190389-71190626(-)$1	237	106	115	17.2777
GUUUUCUUU	chr11:17100124-17100379(+)$1	255	105	114	18.2962
CUUUUUUGU	chr9:30882939-30883174(+)$1	235	110	119	13.3888
UAUUUCUUU	chr11:50108530-50108781(-)$1	251	103	112	15.1481
AUUUUCUUU	chr12:73090945-73091181(+)$1	236	206	215	18.4814
CUUUUGUUU	chr2:121373570-121373818(-)$1	248	24	33	17.2777
UUUAUCUUU	chr6:72561602-72561837(-)$1	235	62	71	15.3333
GUUUUGUUU	chr19:8908274-8908512(+)$1	238	62	71	15.6111
UUUUUGUUU	chr4:150421751-150421986(-)$1	235	170	179	17.2777
CUUUUCUUU	chr8:125154020-125154255(-)$1	235	85	94	19.9629
UUUUUCUUU	chr2:72240601-72240839(+)$1	238	171	180	19.9629
CUUUUAUUU	chr9:96233096-96233334(-)$1	238	189	198	16.9999
CUUUUUUUU	chr2:179769162-179769397(+)$1	235	142	151	17.2777
UUUUUCUUU	chr1:179380299-179380534(+)$1	235	38	47	19.9629
UUUUUCCUU	chr4:107904863-107905105(-)$1	242	23	32	15.8888
CUUUUCGUU	chr10:110732124-110732359(+)$1	235	104	113	15.6111
CUUUUCUUU	chr18:66142309-66142546(-)$1	237	167	176	19.9629
UUUUUGUUU	chr18:4994934-4995169(+)$1	235	32	41	17.2777
CUUUUUUUU	chr12:54249968-54250203(+)$1	235	216	225	17.2777
GUUUUCUUU	chr9:71352180-71352416(-)$1	236	93	102	18.2962

#otherMatches

#Struct PSSM
ddddwwwww	chr11:115940745-115940980(-)$1	235	50	59	17.2777
eeee333ee	chr11:87793793-87794058(-)$1	265	133	142	13.1111
ppdddd:::	chr8:106942833-106943068(-)$1	235	220	229	15.8888
JJJJJ{CCC	chr3:95292215-95292460(+)$1	245	16	25	18.4814
:::::::GG	chr2:155214476-155214718(+)$1	242	161	170	19.9629
d::::::::	chr14:35339882-35340126(-)$1	244	166	175	19.9629
D::gggggg	chr1:99717957-99718198(-)$1	241	14	23	13.9444
:::::::::	chr2:136607123-136607367(+)$1	244	58	67	15.6111
LHHHHHHHH	chr2:132134389-132134639(+)$1	250	56	65	15.4259
gggggeeee	chr2:164824339-164824574(+)$1	235	47	56	15.8888
>>>>>>>>>	chr17:33884446-33884681(-)$1	235	84	93	19.9629
JJJJJJJJJ	chr11:60371177-60371412(+)$1	235	100	109	16.0740
dssssssss	chr12:111820777-111821023(+)$1	246	24	33	15.2407
####eeeee	chr5:136384957-136385202(-)$1	245	195	204	12.2777
cc+++++++	chr9:30957625-30957869(-)$1	244	69	78	15.7962
:::::::GG	chr2:155214586-155214823(+)$1	237	51	60	19.9629
::::::::E	chr1:134473175-134473411(-)$1	236	205	214	19.9629
ee4444eee	chr11:87793705-87793951(-)$1	246	26	35	13.1111
mmmmdddd:	chr15:36407463-36407701(-)$1	238	66	75	16.1666
^^^^^^^^^	chr2:163842323-163842558(+)$1	235	67	76	19.9629
GGKKCCC{C	chr4:19538380-19538627(-)$1	247	114	123	14.6851
bpppppppb	chr5:36943056-36943295(-)$1	239	100	109	15.7962
e7777777e	chr3:58394690-58394925(+)$1	235	176	185	15.2407
333eeeee:	chr6:119875219-119875455(-)$1	236	99	108	15.7962
EEEEEKKDD	chr11:88155614-88155849(-)$1	235	19	28	15.8888
^^^^^^^^^	chr1:166367681-166367925(-)$1	244	97	106	19.9629
"ffffff[c	chr6:39554848-39555083(-)$1	235	39	48	16.9999
g::cccmmm	chr15:36407513-36407748(-)$1	235	113	122	16.1666
bb[hhhhhh	chr14:21319413-21319648(-)$1	235	193	202	15.8888
[ddddrrrr	chr17:73289277-73289513(+)$1	236	81	90	13.4814
{EEEEELLL	chr7:118214765-118215000(-)$1	235	4	13	15.6111
gggggqqqq	chr7:35130774-35131009(-)$1	235	18	27	15.8888
ddd[eeeee	chr4:114633348-114633583(-)$1	235	112	121	17.2777
=========	chr6:82597858-82598093(-)$1	235	48	57	16.0740
:::::::::	chr2:71190389-71190626(-)$1	237	106	115	17.2777
hhhhhhhh[	chr11:17100124-17100379(+)$1	255	105	114	18.2962
:::HHHHHH	chr9:30882939-30883174(+)$1	235	110	119	13.3888
fffwwwwww	chr11:50108530-50108781(-)$1	251	103	112	15.1481
&&&cccppp	chr12:73090945-73091181(+)$1	236	206	215	18.4814
:iiiiiiii	chr2:121373570-121373818(-)$1	248	24	33	17.2777
=====[eee	chr6:72561602-72561837(-)$1	235	62	71	15.3333
brrrrrrrr	chr19:8908274-8908512(+)$1	238	62	71	15.6111
3eeeee444	chr4:150421751-150421986(-)$1	235	170	179	17.2777
HHH::::ff	chr8:125154020-125154255(-)$1	235	85	94	19.9629
eeeqqqqqq	chr2:72240601-72240839(+)$1	238	171	180	19.9629
mmmmggggg	chr9:96233096-96233334(-)$1	238	189	198	16.9999
dddd:::::	chr2:179769162-179769397(+)$1	235	142	151	17.2777
++++bb!!f	chr1:179380299-179380534(+)$1	235	38	47	19.9629
55555bb::	chr4:107904863-107905105(-)$1	242	23	32	15.8888
[dddd[bb[	chr10:110732124-110732359(+)$1	235	104	113	15.6111
ffff55555	chr18:66142309-66142546(-)$1	237	167	176	19.9629
gggg[bb[h	chr18:4994934-4995169(+)$1	235	32	41	17.2777
888888===	chr12:54249968-54250203(+)$1	235	216	225	17.2777
f####bb##	chr9:71352180-71352416(-)$1	236	93	102	18.2962

#DB
((((.....	chr11:115940745-115940980(-)$1	1	50	59	17.2777
))))...))	chr11:87793793-87794058(-)$1	1	133	142	13.1111
..))))...	chr8:106942833-106943068(-)$1	1	220	229	15.8888
(((((.(((	chr3:95292215-95292460(+)$1	1	16	25	18.4814
.......((	chr2:155214476-155214718(+)$1	1	161	170	19.9629
)........	chr14:35339882-35340126(-)$1	1	166	175	19.9629
(..((((((	chr1:99717957-99718198(-)$1	1	14	23	13.9444
.........	chr2:136607123-136607367(+)$1	1	58	67	15.6111
.((((((((	chr2:132134389-132134639(+)$1	1	56	65	15.4259
(((((((((	chr2:164824339-164824574(+)$1	1	47	56	15.8888
.........	chr17:33884446-33884681(-)$1	1	84	93	19.9629
)))))))))	chr11:60371177-60371412(+)$1	1	100	109	16.0740
(........	chr12:111820777-111821023(+)$1	1	24	33	15.2407
....(((((	chr5:136384957-136385202(-)$1	1	195	204	12.2777
((.......	chr9:30957625-30957869(-)$1	1	69	78	15.7962
.......((	chr2:155214586-155214823(+)$1	1	51	60	19.9629
........)	chr1:134473175-134473411(-)$1	1	205	214	19.9629
))....)))	chr11:87793705-87793951(-)$1	1	26	35	13.1111
....)))).	chr15:36407463-36407701(-)$1	1	66	75	16.1666
.........	chr2:163842323-163842558(+)$1	1	67	76	19.9629
((..(((.(	chr4:19538380-19538627(-)$1	1	114	123	14.6851
(.......)	chr5:36943056-36943295(-)$1	1	100	109	15.7962
).......)	chr3:58394690-58394925(+)$1	1	176	185	15.2407
...))))).	chr6:119875219-119875455(-)$1	1	99	108	15.7962
(((((..((	chr11:88155614-88155849(-)$1	1	19	28	15.8888
.........	chr1:166367681-166367925(-)$1	1	97	106	19.9629
.((((((.(	chr6:39554848-39555083(-)$1	1	39	48	16.9999
)..(((...	chr15:36407513-36407748(-)$1	1	113	122	16.1666
((.((((((	chr14:21319413-21319648(-)$1	1	193	202	15.8888
.((((....	chr17:73289277-73289513(+)$1	1	81	90	13.4814
.(((((...	chr7:118214765-118215000(-)$1	1	4	13	15.6111
(((((....	chr7:35130774-35131009(-)$1	1	18	27	15.8888
(((.(((((	chr4:114633348-114633583(-)$1	1	112	121	17.2777
(((((((((	chr6:82597858-82598093(-)$1	1	48	57	16.0740
.........	chr2:71190389-71190626(-)$1	1	106	115	17.2777
((((((((.	chr11:17100124-17100379(+)$1	1	105	114	18.2962
...))))))	chr9:30882939-30883174(+)$1	1	110	119	13.3888
(((......	chr11:50108530-50108781(-)$1	1	103	112	15.1481
...(((...	chr12:73090945-73091181(+)$1	1	206	215	18.4814
.((((((((	chr2:121373570-121373818(-)$1	1	24	33	17.2777
(((((.(((	chr6:72561602-72561837(-)$1	1	62	71	15.3333
(........	chr19:8908274-8908512(+)$1	1	62	71	15.6111
.)))))...	chr4:150421751-150421986(-)$1	1	170	179	17.2777
(((....((	chr8:125154020-125154255(-)$1	1	85	94	19.9629
(((......	chr2:72240601-72240839(+)$1	1	171	180	19.9629
....)))))	chr9:96233096-96233334(-)$1	1	189	198	16.9999
)))).....	chr2:179769162-179769397(+)$1	1	142	151	17.2777
....((..(	chr1:179380299-179380534(+)$1	1	38	47	19.9629
.....))..	chr4:107904863-107905105(-)$1	1	23	32	15.8888
.((((.((.	chr10:110732124-110732359(+)$1	1	104	113	15.6111
)))).....	chr18:66142309-66142546(-)$1	1	167	176	19.9629
((((.((.(	chr18:4994934-4995169(+)$1	1	32	41	17.2777
......)))	chr12:54249968-54250203(+)$1	1	216	225	17.2777
(....((..	chr9:71352180-71352416(-)$1	1	93	102	18.2962

#PSSM
C : 0.37	U : 0.37	A : 0.09	G : 0.07	c : 0.03	u : 0.03	a : 0.01	
U : 0.87	u : 0.11	A : 0.01	
U : 0.88	u : 0.11	
U : 0.83	u : 0.11	G : 0.03	A : 0.01	
U : 0.74	u : 0.11	G : 0.09	A : 0.03	C : 0.01	
C : 0.61	U : 0.11	G : 0.09	A : 0.07	c : 0.05	g : 0.03	u : 0.01	
U : 0.77	u : 0.11	C : 0.07	A : 0.01	G : 0.01	
U : 0.77	G : 0.11	u : 0.11	
U : 0.85	u : 0.11	C : 0.01	G : 0.01	

#score	905.4074074074063
#seq	54
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m1_run2.nuc.txt

#NT
AGA	chr1:36405693-36405907(-)$1	214	48	51	9.0000
AGA	chr15:12070204-12070426(+)$1	222	164	167	9.0000
AGA	chr12:83534666-83534884(+)$1	218	17	20	9.0000
AGA	chr8:106961165-106961391(-)$1	226	48	51	9.0000
aga	chr11:5771554-5771787(+)$1	233	123	126	9.0000
AGA	chr14:28293034-28293242(+)$1	208	26	29	9.0000
AGA	chr8:113390468-113390692(+)$1	224	14	17	9.0000
AGA	chr11:79756741-79756947(-)$1	206	33	36	9.0000
AGA	chr4:41198522-41198755(-)$1	233	49	52	9.0000
AGA	chr18:33012054-33012275(+)$1	221	7	10	9.0000
AGA	chr3:152410541-152410760(+)$1	219	88	91	9.0000
AGA	chr5:13451081-13451295(+)$1	214	20	23	9.0000
AGA	chr16:8646211-8646425(+)$1	214	52	55	9.0000
aga	chr3:96418218-96418439(+)$1	221	15	18	9.0000
AGA	chr4:24424976-24425196(+)$1	220	47	50	9.0000
AGA	chrX:39209872-39210087(-)$1	215	34	37	9.0000
AGA	chr2:120203604-120203813(-)$1	209	10	13	9.0000
AGA	chr6:149357958-149358183(+)$1	225	0	3	9.0000
AGA	chr9:95898614-95898859(+)$1	245	29	32	9.0000
AGA	chr5:22979320-22979545(+)$1	225	76	79	9.0000
AGA	chr11:79809174-79809396(+)$1	222	87	90	9.0000
AGA	chr18:10106232-10106471(-)$1	239	25	28	9.0000
AGA	chr14:57578538-57578760(+)$1	222	18	21	9.0000
AGA	chr8:83403363-83403586(-)$1	223	136	139	9.0000
AGA	chr19:10607722-10607946(+)$1	224	58	61	9.0000
AGA	chr9:55707478-55707687(-)$1	209	0	3	9.0000
AGA	chr11:79053783-79053989(-)$1	206	107	110	9.0000
AGA	chr2:23041712-23041938(+)$1	226	18	21	9.0000
AGA	chr9:103236283-103236496(+)$1	213	34	37	9.0000
AGA	chr7:96658516-96658736(-)$1	220	5	8	9.0000
AGA	chr3:157684855-157685063(-)$1	208	12	15	9.0000
AGA	chr17:25379325-25379542(+)$1	217	121	124	9.0000
AGA	chr15:37958324-37958535(-)$1	211	56	59	9.0000
AGA	chr16:10627410-10627617(+)$1	207	115	118	9.0000
AGA	chr6:113067447-113067669(+)$1	222	34	37	9.0000
AGA	chr17:28552768-28552987(-)$1	219	60	63	9.0000
AGA	chr6:119723807-119724018(-)$1	211	32	35	9.0000
AGA	chr5:139818471-139818705(-)$1	234	50	53	9.0000
AGA	chr19:57770675-57770898(+)$1	223	1	4	9.0000
AGA	chr11:80497808-80498018(-)$1	210	24	27	9.0000
AGA	chr19:9078461-9078672(+)$1	211	5	8	9.0000
AGA	chr2:29781362-29781575(+)$1	213	7	10	9.0000
AGA	chr11:94318530-94318755(-)$1	225	74	77	9.0000
AGA	chr9:44626325-44626535(-)$1	210	62	65	9.0000
AGA	chr11:119315732-119315975(+)$1	243	32	35	9.0000
AGA	chr17:74979425-74979633(+)$1	208	16	19	9.0000
AGA	chr5:101225861-101226073(-)$1	212	6	9	9.0000
AGA	chr10:81038487-81038710(+)$1	223	60	63	9.0000
AGA	chr14:76141446-76141664(-)$1	218	46	49	9.0000
AGA	chr5:23030040-23030263(-)$1	223	5	8	9.0000
AGA	chr8:74014955-74015174(+)$1	219	14	17	9.0000
AGA	chrX:71479214-71479435(-)$1	221	167	170	9.0000
AGA	chr2:72816951-72817173(-)$1	222	133	136	9.0000
AGA	chr5:32033265-32033477(+)$1	212	139	142	9.0000
AGA	chr2:157116213-157116421(+)$1	208	57	60	9.0000
AGA	chr19:42012536-42012759(+)$1	223	200	203	9.0000
AGA	chr3:151498256-151498472(-)$1	216	33	36	9.0000
AGA	chr18:67962651-67962874(+)$1	223	0	3	9.0000
AGA	chr6:116158972-116159185(+)$1	213	30	33	9.0000
AGA	chr9:79541229-79541454(-)$1	225	42	45	9.0000
AGA	chr18:35091156-35091393(-)$1	237	80	83	9.0000
AGA	chr17:29128216-29128453(-)$1	237	26	29	9.0000
AGA	chr2:69704496-69704704(+)$1	208	66	69	9.0000
AGA	chr3:95959781-95959991(+)$1	210	18	21	9.0000
AGA	chr5:151464866-151465086(-)$1	220	42	45	9.0000
AGA	chr4:105989006-105989222(+)$1	216	161	164	9.0000
AGA	chr18:7920112-7920330(+)$1	218	0	3	9.0000
AGA	chr5:124020783-124021016(-)$1	233	86	89	9.0000
AGA	chr14:37944673-37944911(-)$1	238	163	166	9.0000
AGA	chr11:79826857-79827077(+)$1	220	26	29	9.0000
AGA	chr2:92070755-92070973(+)$1	218	37	40	9.0000
AGA	chr4:128999990-129000211(-)$1	221	96	99	9.0000
AGA	chr17:26394804-26395021(+)$1	217	80	83	9.0000
AGA	chr16:11088305-11088520(-)$1	215	93	96	9.0000
AGA	chr8:12832534-12832747(+)$1	213	30	33	9.0000
AGA	chr11:85014876-85015088(-)$1	212	32	35	9.0000
AGA	chr5:66006562-66006772(-)$1	210	9	12	9.0000
AGA	chr5:145579017-145579245(+)$1	228	75	78	9.0000
AGA	chr2:64937115-64937327(-)$1	212	6	9	9.0000
AGA	chr2:118247630-118247847(+)$1	217	66	69	9.0000
AGA	chr15:89107628-89107837(+)$1	209	0	3	9.0000
AGA	chr4:129334928-129335149(-)$1	221	57	60	9.0000
AGA	chr13:97256714-97256938(-)$1	224	7	10	9.0000
AGA	chr11:3588032-3588259(+)$1	227	79	82	9.0000
AGA	chr8:3202853-3203069(-)$1	216	3	6	9.0000
AGA	chr1:134330868-134331075(+)$1	207	95	98	9.0000
AGA	chr15:98669704-98669920(-)$1	216	12	15	9.0000
AGA	chr4:34554325-34554535(-)$1	210	56	59	9.0000
AGA	chrX:162890031-162890241(+)$1	210	116	119	9.0000
AGA	chr8:11506668-11506881(+)$1	213	6	9	9.0000
AGA	chr15:77596042-77596345(-)$1	303	91	94	9.0000
AGA	chr15:40605547-40605771(+)$1	224	10	13	9.0000
AGA	chr10:12363125-12363331(-)$1	206	28	31	9.0000
AGA	chr7:25865658-25865867(+)$1	209	24	27	9.0000
AGA	chr3:38894763-38894969(+)$1	206	11	14	9.0000
AGA	chr15:88559832-88560044(-)$1	212	11	14	9.0000
AGA	chr11:84729695-84729911(-)$1	216	38	41	9.0000
AGA	chr11:21212168-21212394(+)$1	226	86	89	9.0000
AGA	chr11:102723879-102724107(-)$1	228	30	33	9.0000

#otherMatches

#Struct PSSM
===	chr10:79545333-79545566(-)$1	233	32	35	9.0000
llc	chr1:36405693-36405907(-)$1	214	48	51	9.0000
:::	chr15:12070204-12070426(+)$1	222	164	167	9.0000
::d	chr12:83534666-83534884(+)$1	218	17	20	9.0000
b##	chr8:106961165-106961391(-)$1	226	48	51	9.0000
ddl	chr11:5771554-5771787(+)$1	233	123	126	9.0000
GGG	chr14:28293034-28293242(+)$1	208	26	29	9.0000
GGG	chr8:113390468-113390692(+)$1	224	14	17	9.0000
JJJ	chr11:79756741-79756947(-)$1	206	33	36	9.0000
fff	chr4:41198522-41198755(-)$1	233	49	52	9.0000
ccc	chr18:33012054-33012275(+)$1	221	7	10	9.0000
d22	chr3:152410541-152410760(+)$1	219	88	91	9.0000
KEE	chr5:13451081-13451295(+)$1	214	20	23	9.0000
[bb	chr16:8646211-8646425(+)$1	214	52	55	9.0000
PPP	chr3:96418218-96418439(+)$1	221	15	18	9.0000
fff	chr4:24424976-24425196(+)$1	220	47	50	9.0000
ddd	chrX:39209872-39210087(-)$1	215	34	37	9.0000
cc!	chr2:120203604-120203813(-)$1	209	10	13	9.0000
::G	chr6:149357958-149358183(+)$1	225	0	3	9.0000
ppp	chr9:95898614-95898859(+)$1	245	29	32	9.0000
KKE	chr5:22979320-22979545(+)$1	225	76	79	9.0000
HHH	chr11:79809174-79809396(+)$1	222	87	90	9.0000
ccc	chr18:10106232-10106471(-)$1	239	25	28	9.0000
GGG	chr14:57578538-57578760(+)$1	222	18	21	9.0000
KEE	chr8:83403363-83403586(-)$1	223	136	139	9.0000
hhh	chr19:10607722-10607946(+)$1	224	58	61	9.0000
:::	chr9:55707478-55707687(-)$1	209	0	3	9.0000
DDD	chr11:79053783-79053989(-)$1	206	107	110	9.0000
###	chr2:23041712-23041938(+)$1	226	18	21	9.0000
fff	chr9:103236283-103236496(+)$1	213	34	37	9.0000
EE:	chr7:96658516-96658736(-)$1	220	5	8	9.0000
:::	chr3:157684855-157685063(-)$1	208	12	15	9.0000
BB:	chr17:25379325-25379542(+)$1	217	121	124	9.0000
g]b	chr15:37958324-37958535(-)$1	211	56	59	9.0000
fff	chr16:10627410-10627617(+)$1	207	115	118	9.0000
qqq	chr6:113067447-113067669(+)$1	222	34	37	9.0000
FFF	chr17:28552768-28552987(-)$1	219	60	63	9.0000
[cc	chr6:119723807-119724018(-)$1	211	32	35	9.0000
>>>	chr5:139818471-139818705(-)$1	234	50	53	9.0000
CCC	chr19:57770675-57770898(+)$1	223	1	4	9.0000
hhC	chr11:80497808-80498018(-)$1	210	24	27	9.0000
:::	chr19:9078461-9078672(+)$1	211	5	8	9.0000
A{F	chr2:29781362-29781575(+)$1	213	7	10	9.0000
fff	chr11:94318530-94318755(-)$1	225	74	77	9.0000
ooo	chr9:44626325-44626535(-)$1	210	62	65	9.0000
BB{	chr11:119315732-119315975(+)$1	243	32	35	9.0000
FFF	chr17:74979425-74979633(+)$1	208	16	19	9.0000
:DD	chr5:101225861-101226073(-)$1	212	6	9	9.0000
cco	chr10:81038487-81038710(+)$1	223	60	63	9.0000
ggg	chr14:76141446-76141664(-)$1	218	46	49	9.0000
EEE	chr5:23030040-23030263(-)$1	223	5	8	9.0000
ooo	chr8:74014955-74015174(+)$1	219	14	17	9.0000
FFF	chrX:71479214-71479435(-)$1	221	167	170	9.0000
bb]	chr2:72816951-72817173(-)$1	222	133	136	9.0000
ffd	chr5:32033265-32033477(+)$1	212	139	142	9.0000
:::	chr2:157116213-157116421(+)$1	208	57	60	9.0000
d[c	chr19:42012536-42012759(+)$1	223	200	203	9.0000
ddd	chr3:151498256-151498472(-)$1	216	33	36	9.0000
:::	chr18:67962651-67962874(+)$1	223	0	3	9.0000
ddd	chr6:116158972-116159185(+)$1	213	30	33	9.0000
EEE	chr9:79541229-79541454(-)$1	225	42	45	9.0000
YYE	chr18:35091156-35091393(-)$1	237	80	83	9.0000
ma]	chr17:29128216-29128453(-)$1	237	26	29	9.0000
%bb	chr2:69704496-69704704(+)$1	208	66	69	9.0000
::d	chr3:95959781-95959991(+)$1	210	18	21	9.0000
fff	chr5:151464866-151465086(-)$1	220	42	45	9.0000
:::	chr4:105989006-105989222(+)$1	216	161	164	9.0000
:::	chr18:7920112-7920330(+)$1	218	0	3	9.0000
nnn	chr5:124020783-124021016(-)$1	233	86	89	9.0000
llf	chr14:37944673-37944911(-)$1	238	163	166	9.0000
oee	chr11:79826857-79827077(+)$1	220	26	29	9.0000
D{H	chr2:92070755-92070973(+)$1	218	37	40	9.0000
bb]	chr4:128999990-129000211(-)$1	221	96	99	9.0000
qqq	chr17:26394804-26395021(+)$1	217	80	83	9.0000
[dd	chr16:11088305-11088520(-)$1	215	93	96	9.0000
:::	chr8:12832534-12832747(+)$1	213	30	33	9.0000
hhh	chr11:85014876-85015088(-)$1	212	32	35	9.0000
:::	chr5:66006562-66006772(-)$1	210	9	12	9.0000
dd]	chr5:145579017-145579245(+)$1	228	75	78	9.0000
LLE	chr2:64937115-64937327(-)$1	212	6	9	9.0000
ee[	chr2:118247630-118247847(+)$1	217	66	69	9.0000
:::	chr15:89107628-89107837(+)$1	209	0	3	9.0000
ooo	chr4:129334928-129335149(-)$1	221	57	60	9.0000
GGG	chr13:97256714-97256938(-)$1	224	7	10	9.0000
mcc	chr11:3588032-3588259(+)$1	227	79	82	9.0000
DD{	chr8:3202853-3203069(-)$1	216	3	6	9.0000
d::	chr1:134330868-134331075(+)$1	207	95	98	9.0000
::f	chr15:98669704-98669920(-)$1	216	12	15	9.0000
iii	chr4:34554325-34554535(-)$1	210	56	59	9.0000
HHH	chrX:162890031-162890241(+)$1	210	116	119	9.0000
GGG	chr8:11506668-11506881(+)$1	213	6	9	9.0000
&&&	chr15:77596042-77596345(-)$1	303	91	94	9.0000
###	chr15:40605547-40605771(+)$1	224	10	13	9.0000
:::	chr10:12363125-12363331(-)$1	206	28	31	9.0000
eee	chr7:25865658-25865867(+)$1	209	24	27	9.0000
:::	chr3:38894763-38894969(+)$1	206	11	14	9.0000
KDD	chr15:88559832-88560044(-)$1	212	11	14	9.0000
sss	chr11:84729695-84729911(-)$1	216	38	41	9.0000
hhh	chr11:21212168-21212394(+)$1	226	86	89	9.0000
ff:	chr11:102723879-102724107(-)$1	228	30	33	9.0000

#DB
(((	chr10:79545333-79545566(-)$1	1	32	35	9.0000
..)	chr1:36405693-36405907(-)$1	1	48	51	9.0000
...	chr15:12070204-12070426(+)$1	1	164	167	9.0000
..(	chr12:83534666-83534884(+)$1	1	17	20	9.0000
(..	chr8:106961165-106961391(-)$1	1	48	51	9.0000
((.	chr11:5771554-5771787(+)$1	1	123	126	9.0000
(((	chr14:28293034-28293242(+)$1	1	26	29	9.0000
(((	chr8:113390468-113390692(+)$1	1	14	17	9.0000
(((	chr11:79756741-79756947(-)$1	1	33	36	9.0000
(((	chr4:41198522-41198755(-)$1	1	49	52	9.0000
(((	chr18:33012054-33012275(+)$1	1	7	10	9.0000
)..	chr3:152410541-152410760(+)$1	1	88	91	9.0000
.((	chr5:13451081-13451295(+)$1	1	20	23	9.0000
.((	chr16:8646211-8646425(+)$1	1	52	55	9.0000
...	chr3:96418218-96418439(+)$1	1	15	18	9.0000
(((	chr4:24424976-24425196(+)$1	1	47	50	9.0000
)))	chrX:39209872-39210087(-)$1	1	34	37	9.0000
((.	chr2:120203604-120203813(-)$1	1	10	13	9.0000
..(	chr6:149357958-149358183(+)$1	1	0	3	9.0000
...	chr9:95898614-95898859(+)$1	1	29	32	9.0000
..(	chr5:22979320-22979545(+)$1	1	76	79	9.0000
(((	chr11:79809174-79809396(+)$1	1	87	90	9.0000
(((	chr18:10106232-10106471(-)$1	1	25	28	9.0000
(((	chr14:57578538-57578760(+)$1	1	18	21	9.0000
.((	chr8:83403363-83403586(-)$1	1	136	139	9.0000
)))	chr19:10607722-10607946(+)$1	1	58	61	9.0000
...	chr9:55707478-55707687(-)$1	1	0	3	9.0000
)))	chr11:79053783-79053989(-)$1	1	107	110	9.0000
...	chr2:23041712-23041938(+)$1	1	18	21	9.0000
)))	chr9:103236283-103236496(+)$1	1	34	37	9.0000
((.	chr7:96658516-96658736(-)$1	1	5	8	9.0000
...	chr3:157684855-157685063(-)$1	1	12	15	9.0000
)).	chr17:25379325-25379542(+)$1	1	121	124	9.0000
).)	chr15:37958324-37958535(-)$1	1	56	59	9.0000
)))	chr16:10627410-10627617(+)$1	1	115	118	9.0000
...	chr6:113067447-113067669(+)$1	1	34	37	9.0000
(((	chr17:28552768-28552987(-)$1	1	60	63	9.0000
.((	chr6:119723807-119724018(-)$1	1	32	35	9.0000
...	chr5:139818471-139818705(-)$1	1	50	53	9.0000
(((	chr19:57770675-57770898(+)$1	1	1	4	9.0000
))(	chr11:80497808-80498018(-)$1	1	24	27	9.0000
...	chr19:9078461-9078672(+)$1	1	5	8	9.0000
(.(	chr2:29781362-29781575(+)$1	1	7	10	9.0000
(((	chr11:94318530-94318755(-)$1	1	74	77	9.0000
...	chr9:44626325-44626535(-)$1	1	62	65	9.0000
((.	chr11:119315732-119315975(+)$1	1	32	35	9.0000
(((	chr17:74979425-74979633(+)$1	1	16	19	9.0000
.((	chr5:101225861-101226073(-)$1	1	6	9	9.0000
((.	chr10:81038487-81038710(+)$1	1	60	63	9.0000
(((	chr14:76141446-76141664(-)$1	1	46	49	9.0000
(((	chr5:23030040-23030263(-)$1	1	5	8	9.0000
...	chr8:74014955-74015174(+)$1	1	14	17	9.0000
)))	chrX:71479214-71479435(-)$1	1	167	170	9.0000
)).	chr2:72816951-72817173(-)$1	1	133	136	9.0000
))(	chr5:32033265-32033477(+)$1	1	139	142	9.0000
...	chr2:157116213-157116421(+)$1	1	57	60	9.0000
(.(	chr19:42012536-42012759(+)$1	1	200	203	9.0000
(((	chr3:151498256-151498472(-)$1	1	33	36	9.0000
...	chr18:67962651-67962874(+)$1	1	0	3	9.0000
(((	chr6:116158972-116159185(+)$1	1	30	33	9.0000
(((	chr9:79541229-79541454(-)$1	1	42	45	9.0000
..)	chr18:35091156-35091393(-)$1	1	80	83	9.0000
.).	chr17:29128216-29128453(-)$1	1	26	29	9.0000
.((	chr2:69704496-69704704(+)$1	1	66	69	9.0000
..(	chr3:95959781-95959991(+)$1	1	18	21	9.0000
)))	chr5:151464866-151465086(-)$1	1	42	45	9.0000
...	chr4:105989006-105989222(+)$1	1	161	164	9.0000
...	chr18:7920112-7920330(+)$1	1	0	3	9.0000
...	chr5:124020783-124021016(-)$1	1	86	89	9.0000
..)	chr14:37944673-37944911(-)$1	1	163	166	9.0000
.))	chr11:79826857-79827077(+)$1	1	26	29	9.0000
(.(	chr2:92070755-92070973(+)$1	1	37	40	9.0000
)).	chr4:128999990-129000211(-)$1	1	96	99	9.0000
...	chr17:26394804-26395021(+)$1	1	80	83	9.0000
.((	chr16:11088305-11088520(-)$1	1	93	96	9.0000
...	chr8:12832534-12832747(+)$1	1	30	33	9.0000
)))	chr11:85014876-85015088(-)$1	1	32	35	9.0000
...	chr5:66006562-66006772(-)$1	1	9	12	9.0000
)).	chr5:145579017-145579245(+)$1	1	75	78	9.0000
..(	chr2:64937115-64937327(-)$1	1	6	9	9.0000
((.	chr2:118247630-118247847(+)$1	1	66	69	9.0000
...	chr15:89107628-89107837(+)$1	1	0	3	9.0000
...	chr4:129334928-129335149(-)$1	1	57	60	9.0000
(((	chr13:97256714-97256938(-)$1	1	7	10	9.0000
.))	chr11:3588032-3588259(+)$1	1	79	82	9.0000
((.	chr8:3202853-3203069(-)$1	1	3	6	9.0000
)..	chr1:134330868-134331075(+)$1	1	95	98	9.0000
..(	chr15:98669704-98669920(-)$1	1	12	15	9.0000
(((	chr4:34554325-34554535(-)$1	1	56	59	9.0000
)))	chrX:162890031-162890241(+)$1	1	116	119	9.0000
(((	chr8:11506668-11506881(+)$1	1	6	9	9.0000
...	chr15:77596042-77596345(-)$1	1	91	94	9.0000
...	chr15:40605547-40605771(+)$1	1	10	13	9.0000
...	chr10:12363125-12363331(-)$1	1	28	31	9.0000
)))	chr7:25865658-25865867(+)$1	1	24	27	9.0000
...	chr3:38894763-38894969(+)$1	1	11	14	9.0000
.((	chr15:88559832-88560044(-)$1	1	11	14	9.0000
...	chr11:84729695-84729911(-)$1	1	38	41	9.0000
(((	chr11:21212168-21212394(+)$1	1	86	89	9.0000
)).	chr11:102723879-102724107(-)$1	1	30	33	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m1_run1.nuc.txt

#NT
GUGUUUUUUU	chr2:134420525-134420770(-)$1	245	199	209	17.8688
AUGUUUUAUU	chr1:24821453-24821705(+)$1	252	125	135	14.0983
UUGUUAAUUU	chr3:152055762-152056004(+)$1	242	17	27	15.4918
UUGUUCUUUU	chr2:38922172-38922415(-)$1	243	176	186	18.1967
UUGUUUUUAU	chr18:61747725-61747971(+)$1	246	167	177	17.2131
UUGUGUGUUU	chr7:107421221-107421465(+)$1	244	115	125	15.9836
UUGUAAUUUU	chr7:129777608-129777871(+)$1	263	105	115	15.4918
UUUUUAUUUU	chr18:58105896-58106147(+)$1	251	101	111	14.7540
UUGUUUGuuu	chr2:163450342-163450603(-)$1	261	208	218	19.0163
UUGUGUUUUA	chr11:74487425-74487676(-)$1	251	106	116	14.5081
uuguuuuuug	chr18:61147502-61147742(+)$1	240	212	222	17.4590
UUUUUUUUUU	chr1:155756535-155756793(+)$1	258	41	51	17.7868
UUGUUCUGUU	chr16:94690221-94690486(+)$1	265	104	114	14.6721
uuauuuauuu	chr5:104508405-104508686(-)$1	281	66	76	14.8360
UUAUUGUUUU	chr16:38243331-38243583(+)$1	252	98	108	14.5081
CUGUUUGUUU	chr1:24820607-24820849(+)$1	242	162	172	15.0819
GUGUUUUGUU	chrX:162826471-162826720(+)$1	249	57	67	14.3442
UUGAUUGUUU	chr12:73313257-73313564(-)$1	307	122	132	14.9180
UUGUUUGUUU	chr6:115226082-115226321(+)$1	239	11	21	19.0163
uuguuuuguu	chr13:54860178-54860450(-)$1	272	30	40	18.1967
UUGUUUGUUU	chr2:103900277-103900526(+)$1	249	159	169	19.0163
UUGUGUUUUU	chr12:79785055-79785310(+)$1	255	156	166	18.6885
UUGGAUUUUU	chrX:162826314-162826580(+)$1	266	110	120	14.6721
AUGUAUUUUU	chr3:57645854-57646164(-)$1	310	33	43	14.5901
GUGUUAUUUU	chr16:92087388-92087630(+)$1	242	153	163	14.8360
uuauuauuuu	chr1:66485835-66486077(+)$1	242	9	19	15.0000
UUGUUCUUUA	chr2:104269479-104269726(-)$1	247	168	178	14.0163
UUGUUUUUUU	chr8:82198805-82199040(+)$1	235	19	29	21.7213
UUGGAUUUUU	chrX:162826387-162826669(+)$1	282	37	47	14.6721
UUGUCUUAUU	chr6:13034877-13035125(+)$1	248	1	11	14.8360
UUGCCUUUUU	chrX:162826707-162827009(+)$1	302	218	228	14.4262
UUGUUUUGUU	chr5:32793668-32793958(+)$1	290	150	160	18.1967
UUGUCUUUUC	chr7:116177609-116177851(+)$1	242	104	114	14.2622
UUGUCGUUUU	chr11:109530539-109530777(+)$1	238	108	118	15.0000
UUGUGUUUUU	chr11:103683139-103683395(-)$1	256	210	220	18.6885
GUGUUUUUUU	chr17:44223329-44223588(+)$1	259	112	122	17.8688
UUGGUUAUUU	chr4:154932290-154932578(+)$1	288	253	263	14.6721
UUGUUAGUUU	chr10:110732704-110732946(+)$1	242	112	122	15.9836
AUGUAUUUUU	chr16:44085676-44085921(-)$1	245	230	240	14.5901
UUGUGUUUGU	chr19:44381122-44381370(+)$1	248	190	200	14.1803
UUGUUUCUUA	chr15:82122812-82123058(+)$1	246	73	83	14.0163
UUGUUUUGGU	chr2:131763080-131763341(+)$1	261	121	131	13.6885
UUGUUUUCAU	chr15:31388225-31388481(-)$1	256	128	138	13.3606
CUGUCUUUUU	chr13:54782193-54782452(-)$1	259	107	117	14.5901
UUGUGUUAUU	chr2:102621705-102622016(+)$1	311	206	216	15.0000
CUAUUUUUUU	chrX:91975244-91975479(+)$1	235	186	196	14.0983
UUGUUAAUUU	chr19:29686065-29686312(-)$1	247	231	241	15.4918
UUUUUAUUUU	chr2:18607414-18607655(+)$1	241	229	239	14.7540
uuguuuuuuu	chr11:97577850-97578106(-)$1	256	3	13	21.7213
UUGUGUUUUU	chr6:115224767-115225019(+)$1	252	221	231	18.6885
UUGUUUGUUU	chr17:17664820-17665076(-)$1	256	1	11	19.0163
UUGGUUUUUC	chr4:122869382-122869663(+)$1	281	15	25	13.6065
UUGUUUUAUG	chr11:76232105-76232364(-)$1	259	15	25	13.7704
UUCCUUUUUU	chrX:48358269-48358532(-)$1	263	246	256	13.5245
uuguuuguuu	chr2:49627551-49627793(+)$1	242	204	214	19.0163
UUAUUAUUUU	chr18:31597494-31597733(-)$1	239	60	70	15.0000
UUGUUUGGUU	chr2:134421324-134421560(-)$1	236	44	54	15.4918
Uuguuugcuu	chr17:24212691-24212937(-)$1	246	15	25	15.1639
UUAAUUUUUU	chr12:101447485-101447737(+)$1	252	193	203	13.9344
UUGUUGAUUU	chr11:118162470-118162730(-)$1	260	123	133	15.0000

#otherMatches

#Struct PSSM
ddd[ffffff	chr19:45607587-45607826(+)$1	239	180	190	17.8688
ssssss====	chr2:134420525-134420770(-)$1	245	199	209	17.8688
rrffffff22	chr1:24821453-24821705(+)$1	252	125	135	14.0983
ldddd]ccc]	chr3:152055762-152056004(+)$1	242	17	27	15.4918
dddd''''''	chr2:38922172-38922415(-)$1	243	176	186	18.1967
c[ggggggg"	chr18:61747725-61747971(+)$1	246	167	177	17.2131
dd[bb[eeee	chr7:107421221-107421465(+)$1	244	115	125	15.9836
===vvvvvvv	chr7:129777608-129777871(+)$1	263	105	115	15.4918
::::::::::	chr18:58105896-58106147(+)$1	251	101	111	14.7540
c22dddd]cc	chr2:163450342-163450603(-)$1	261	208	218	19.0163
ccc22eeeee	chr11:74487425-74487676(-)$1	251	106	116	14.5081
c]ffffff]g	chr18:61147502-61147742(+)$1	240	212	222	17.4590
gggggg0000	chr1:155756535-155756793(+)$1	258	41	51	17.7868
YJJJJJJJJJ	chr16:94690221-94690486(+)$1	265	104	114	14.6721
::::::::::	chr5:104508405-104508686(-)$1	281	66	76	14.8360
ff"""dddd[	chr16:38243331-38243583(+)$1	252	98	108	14.5081
ffffoooooo	chr1:24820607-24820849(+)$1	242	162	172	15.0819
oggggggg::	chrX:162826471-162826720(+)$1	249	57	67	14.3442
$$ffffff""	chr12:73313257-73313564(-)$1	307	122	132	14.9180
qqqqqccc22	chr6:115226082-115226321(+)$1	239	11	21	19.0163
ccc22ccc22	chr13:54860178-54860450(-)$1	272	30	40	18.1967
GG{HHHHHHH	chr2:103900277-103900526(+)$1	249	159	169	19.0163
hhhhhhhhtt	chr12:79785055-79785310(+)$1	255	156	166	18.6885
JJJJJJ~~~~	chrX:162826314-162826580(+)$1	266	110	120	14.6721
hhhhh:::::	chr3:57645854-57646164(-)$1	310	33	43	14.5901
dsssssssss	chr16:92087388-92087630(+)$1	242	153	163	14.8360
::::::::::	chr1:66485835-66486077(+)$1	242	9	19	15.0000
mmdddd:eee	chr2:104269479-104269726(-)$1	247	168	178	14.0163
::::::::::	chr8:82198805-82199040(+)$1	235	19	29	21.7213
WIIIIIIIII	chrX:162826387-162826669(+)$1	282	37	47	14.6721
::::::::::	chr6:13034877-13035125(+)$1	248	1	11	14.8360
55555hhhhh	chrX:162826707-162827009(+)$1	302	218	228	14.4262
c]dddd4444	chr5:32793668-32793958(+)$1	290	150	160	18.1967
ccc[bb[ddd	chr7:116177609-116177851(+)$1	242	104	114	14.2622
>>>>>>>>>>	chr11:109530539-109530777(+)$1	238	108	118	15.0000
iidddd!!bb	chr11:103683139-103683395(-)$1	256	210	220	18.6885
ggiiiiiiii	chr17:44223329-44223588(+)$1	259	112	122	17.8688
::::::====	chr4:154932290-154932578(+)$1	288	253	263	14.6721
HHEEEEE:::	chr10:110732704-110732946(+)$1	242	112	122	15.9836
3ggggggg22	chr16:44085676-44085921(-)$1	245	230	240	14.5901
33eeeeeCCC	chr19:44381122-44381370(+)$1	248	190	200	14.1803
eeeennnnne	chr15:82122812-82123058(+)$1	246	73	83	14.0163
G?????GGGG	chr2:131763080-131763341(+)$1	261	121	131	13.6885
::::ffffff	chr15:31388225-31388481(-)$1	256	128	138	13.3606
{GGGGGGG::	chr13:54782193-54782452(-)$1	259	107	117	14.5901
eeeee]iiii	chr2:102621705-102622016(+)$1	311	206	216	15.0000
IIIIIIII::	chrX:91975244-91975479(+)$1	235	186	196	14.0983
::::::::::	chr19:29686065-29686312(-)$1	247	231	241	15.4918
ooa]gggggg	chr2:18607414-18607655(+)$1	241	229	239	14.7540
::::::::::	chr11:97577850-97578106(-)$1	256	3	13	21.7213
iiiiiiiiip	chr6:115224767-115225019(+)$1	252	221	231	18.6885
::::::::::	chr17:17664820-17665076(-)$1	256	1	11	19.0163
GGGGGLLLCC	chr4:122869382-122869663(+)$1	281	15	25	13.6065
KBBOOOOOOC	chr11:76232105-76232364(-)$1	259	15	25	13.7704
eerrrrrrrr	chrX:48358269-48358532(-)$1	263	246	256	13.5245
::::::::::	chr2:49627551-49627793(+)$1	242	204	214	19.0163
fttttttttt	chr18:31597494-31597733(-)$1	239	60	70	15.0000
GGGGGGG{DD	chr2:134421324-134421560(-)$1	236	44	54	15.4918
rra22ccc::	chr17:24212691-24212937(-)$1	246	15	25	15.1639
e&&&&&&&ff	chr12:101447485-101447737(+)$1	252	193	203	13.9344
nneeeee:::	chr11:118162470-118162730(-)$1	260	123	133	15.0000

#DB
(((.((((((	chr19:45607587-45607826(+)$1	1	180	190	17.8688
......))))	chr2:134420525-134420770(-)$1	1	199	209	17.8688
..))))))..	chr1:24821453-24821705(+)$1	1	125	135	14.0983
.)))).))).	chr3:152055762-152056004(+)$1	1	17	27	15.4918
((((......	chr2:38922172-38922415(-)$1	1	176	186	18.1967
(.(((((((.	chr18:61747725-61747971(+)$1	1	167	177	17.2131
((.((.((((	chr7:107421221-107421465(+)$1	1	115	125	15.9836
(((.......	chr7:129777608-129777871(+)$1	1	105	115	15.4918
..........	chr18:58105896-58106147(+)$1	1	101	111	14.7540
)..)))).))	chr2:163450342-163450603(-)$1	1	208	218	19.0163
)))..)))))	chr11:74487425-74487676(-)$1	1	106	116	14.5081
).)))))).)	chr18:61147502-61147742(+)$1	1	212	222	17.4590
))))))....	chr1:155756535-155756793(+)$1	1	41	51	17.7868
.)))))))))	chr16:94690221-94690486(+)$1	1	104	114	14.6721
..........	chr5:104508405-104508686(-)$1	1	66	76	14.8360
((...((((.	chr16:38243331-38243583(+)$1	1	98	108	14.5081
((((......	chr1:24820607-24820849(+)$1	1	162	172	15.0819
.)))))))..	chrX:162826471-162826720(+)$1	1	57	67	14.3442
..((((((..	chr12:73313257-73313564(-)$1	1	122	132	14.9180
.....)))..	chr6:115226082-115226321(+)$1	1	11	21	19.0163
)))..)))..	chr13:54860178-54860450(-)$1	1	30	40	18.1967
((.(((((((	chr2:103900277-103900526(+)$1	1	159	169	19.0163
((((((((..	chr12:79785055-79785310(+)$1	1	156	166	18.6885
))))))....	chrX:162826314-162826580(+)$1	1	110	120	14.6721
))))).....	chr3:57645854-57646164(-)$1	1	33	43	14.5901
(.........	chr16:92087388-92087630(+)$1	1	153	163	14.8360
..........	chr1:66485835-66486077(+)$1	1	9	19	15.0000
..)))).(((	chr2:104269479-104269726(-)$1	1	168	178	14.0163
..........	chr8:82198805-82199040(+)$1	1	19	29	21.7213
.(((((((((	chrX:162826387-162826669(+)$1	1	37	47	14.6721
..........	chr6:13034877-13035125(+)$1	1	1	11	14.8360
.....)))))	chrX:162826707-162827009(+)$1	1	218	228	14.4262
).))))....	chr5:32793668-32793958(+)$1	1	150	160	18.1967
(((.((.(((	chr7:116177609-116177851(+)$1	1	104	114	14.2622
..........	chr11:109530539-109530777(+)$1	1	108	118	15.0000
((((((..((	chr11:103683139-103683395(-)$1	1	210	220	18.6885
))((((((((	chr17:44223329-44223588(+)$1	1	112	122	17.8688
......((((	chr4:154932290-154932578(+)$1	1	253	263	14.6721
(((((((...	chr10:110732704-110732946(+)$1	1	112	122	15.9836
.)))))))..	chr16:44085676-44085921(-)$1	1	230	240	14.5901
..))))))))	chr19:44381122-44381370(+)$1	1	190	200	14.1803
((((.....)	chr15:82122812-82123058(+)$1	1	73	83	14.0163
).....))))	chr2:131763080-131763341(+)$1	1	121	131	13.6885
....((((((	chr15:31388225-31388481(-)$1	1	128	138	13.3606
.(((((((..	chr13:54782193-54782452(-)$1	1	107	117	14.5901
))))).))))	chr2:102621705-102622016(+)$1	1	206	216	15.0000
))))))))..	chrX:91975244-91975479(+)$1	1	186	196	14.0983
..........	chr19:29686065-29686312(-)$1	1	231	241	15.4918
..).))))))	chr2:18607414-18607655(+)$1	1	229	239	14.7540
..........	chr11:97577850-97578106(-)$1	1	3	13	21.7213
(((((((((.	chr6:115224767-115225019(+)$1	1	221	231	18.6885
..........	chr17:17664820-17665076(-)$1	1	1	11	19.0163
(((((...((	chr4:122869382-122869663(+)$1	1	15	25	13.6065
.((......(	chr11:76232105-76232364(-)$1	1	15	25	13.7704
((........	chrX:48358269-48358532(-)$1	1	246	256	13.5245
..........	chr2:49627551-49627793(+)$1	1	204	214	19.0163
(.........	chr18:31597494-31597733(-)$1	1	60	70	15.0000
(((((((.((	chr2:134421324-134421560(-)$1	1	44	54	15.4918
..)..)))..	chr17:24212691-24212937(-)$1	1	15	25	15.1639
(.......((	chr12:101447485-101447737(+)$1	1	193	203	13.9344
..)))))...	chr11:118162470-118162730(-)$1	1	123	133	15.0000

#PSSM
U : 0.73	u : 0.09	G : 0.06	A : 0.04	C : 0.04	
U : 0.88	u : 0.11	
G : 0.75	g : 0.08	A : 0.06	U : 0.04	a : 0.03	C : 0.01	
U : 0.73	u : 0.11	G : 0.08	A : 0.03	C : 0.03	
U : 0.60	G : 0.11	u : 0.11	A : 0.08	C : 0.08	
U : 0.65	A : 0.13	u : 0.09	C : 0.04	G : 0.04	a : 0.01	
U : 0.65	G : 0.14	A : 0.06	u : 0.06	g : 0.03	a : 0.01	C : 0.01	
U : 0.70	u : 0.09	G : 0.08	A : 0.06	g : 0.01	C : 0.01	c : 0.01	
U : 0.80	u : 0.13	A : 0.03	G : 0.03	
U : 0.77	u : 0.11	A : 0.04	C : 0.03	g : 0.01	G : 0.01	

#score	970.1639344262305
#seq	61
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m2_run2.nuc.txt

#NT
GAAGA	chr7:104784818-104785038(+)$1	220	109	114	15.0000
GAAGA	chr7:51885231-51885451(-)$1	220	165	170	15.0000
GAAGA	chr12:66157262-66157482(+)$1	220	13	18	15.0000
GAAGA	chr4:57869648-57869884(+)$1	236	122	127	15.0000
GAAGA	chrX:132335835-132336055(+)$1	220	22	27	15.0000
GAAGA	chr12:112862636-112862856(+)$1	220	176	181	15.0000
GAAGA	chr5:88984276-88984496(+)$1	220	6	11	15.0000
GAAGA	chr5:124374706-124374943(+)$1	237	36	41	15.0000
GAAGA	chr9:51893215-51893435(+)$1	220	7	12	15.0000
GAAGA	chr16:90229887-90230107(-)$1	220	128	133	15.0000
GAAGA	chr15:75900705-75900935(-)$1	230	10	15	15.0000
GAAGA	chr19:29722608-29722848(-)$1	240	143	148	15.0000
GAAGA	chr6:85410952-85411194(+)$1	242	155	160	15.0000
GAAGA	chr18:5118253-5118473(+)$1	220	152	157	15.0000
GAAGA	chr1:38090765-38090985(+)$1	220	110	115	15.0000
GAAGA	chr12:103124377-103124597(-)$1	220	183	188	15.0000
gaaga	chr13:62470204-62470424(-)$1	220	68	73	15.0000
GAAGA	chr1:152270986-152271206(+)$1	220	84	89	15.0000
GAAGA	chr13:89831866-89832086(-)$1	220	129	134	15.0000
GAAGA	chr3:134900900-134901120(+)$1	220	68	73	15.0000
GAAGA	chr15:76005439-76005659(-)$1	220	56	61	15.0000
GAAGA	chr4:57905637-57905857(+)$1	220	39	44	15.0000
GAAGA	chr16:91499611-91499831(+)$1	220	206	211	15.0000
GAAGA	chr11:7061822-7062042(+)$1	220	64	69	15.0000
GAAGA	chr16:36915039-36915259(+)$1	220	23	28	15.0000
gaaga	chr8:87633847-87634073(-)$1	226	189	194	15.0000
GAAGA	chr12:11306029-11306250(+)$1	221	35	40	15.0000
GAAGA	chr4:130063099-130063341(+)$1	242	54	59	15.0000
GAAGA	chr4:40701426-40701646(-)$1	220	124	129	15.0000
GAAGA	chr7:148637083-148637303(+)$1	220	54	59	15.0000
GAAGA	chr1:108668923-108669143(-)$1	220	83	88	15.0000
GAAGA	chr10:30254829-30255050(-)$1	221	108	113	15.0000
GAAGA	chr11:76859653-76859873(-)$1	220	49	54	15.0000
GAAGA	chr1:34248744-34248976(+)$1	232	109	114	15.0000
GAAGA	chr5:77407592-77407823(+)$1	231	78	83	15.0000
GAAGA	chr8:86455762-86455982(+)$1	220	32	37	15.0000
GAAGA	chr5:21305185-21305424(+)$1	239	61	66	15.0000
GAAGA	chr8:23175489-23175709(+)$1	220	124	129	15.0000
GAAGA	chr17:75026247-75026468(+)$1	221	167	172	15.0000
GAAGA	chr4:135895272-135895492(+)$1	220	65	70	15.0000
GAAGA	chr16:90226386-90226606(+)$1	220	47	52	15.0000
GAAGA	chr11:69177431-69177651(-)$1	220	12	17	15.0000
GAAGA	chr1:60533644-60533864(+)$1	220	18	23	15.0000
GAAGA	chr12:16977776-16978018(+)$1	242	81	86	15.0000
GAAGA	chr2:152962338-152962567(+)$1	229	126	131	15.0000
GAAGA	chr10:4532301-4532521(+)$1	220	99	104	15.0000
GAAGA	chr10:127686495-127686715(+)$1	220	196	201	15.0000
GAAGA	chr3:104605323-104605543(-)$1	220	98	103	15.0000

#otherMatches

#Struct PSSM
:::::	chr14:52906990-52907211(+)$1	221	44	49	15.0000
ddbbn	chr7:104784818-104785038(+)$1	220	109	114	15.0000
^^^^^	chr7:51885231-51885451(-)$1	220	165	170	15.0000
EEEEE	chr12:66157262-66157482(+)$1	220	13	18	15.0000
qqqqq	chr4:57869648-57869884(+)$1	236	122	127	15.0000
vvvvv	chrX:132335835-132336055(+)$1	220	22	27	15.0000
:::dd	chr12:112862636-112862856(+)$1	220	176	181	15.0000
G::::	chr5:88984276-88984496(+)$1	220	6	11	15.0000
ggggg	chr5:124374706-124374943(+)$1	237	36	41	15.0000
'''''	chr9:51893215-51893435(+)$1	220	7	12	15.0000
ooooo	chr16:90229887-90230107(-)$1	220	128	133	15.0000
[a[ee	chr15:75900705-75900935(-)$1	230	10	15	15.0000
444cc	chr19:29722608-29722848(-)$1	240	143	148	15.0000
ggggg	chr6:85410952-85411194(+)$1	242	155	160	15.0000
ddd33	chr18:5118253-5118473(+)$1	220	152	157	15.0000
333dd	chr1:38090765-38090985(+)$1	220	110	115	15.0000
:::::	chr12:103124377-103124597(-)$1	220	183	188	15.0000
eeeee	chr13:62470204-62470424(-)$1	220	68	73	15.0000
oooa]	chr1:152270986-152271206(+)$1	220	84	89	15.0000
fffff	chr13:89831866-89832086(-)$1	220	129	134	15.0000
b$$$$	chr3:134900900-134901120(+)$1	220	68	73	15.0000
""a[c	chr15:76005439-76005659(-)$1	220	56	61	15.0000
=====	chr4:57905637-57905857(+)$1	220	39	44	15.0000
mmmmc	chr16:91499611-91499831(+)$1	220	206	211	15.0000
EKKFF	chr11:7061822-7062042(+)$1	220	64	69	15.0000
hh+++	chr16:36915039-36915259(+)$1	220	23	28	15.0000
E::::	chr8:87633847-87634073(-)$1	226	189	194	15.0000
nnnee	chr12:11306029-11306250(+)$1	221	35	40	15.0000
ccc[d	chr4:130063099-130063341(+)$1	242	54	59	15.0000
GGGG:	chr4:40701426-40701646(-)$1	220	124	129	15.0000
KDDDD	chr7:148637083-148637303(+)$1	220	54	59	15.0000
nnnnn	chr1:108668923-108669143(-)$1	220	83	88	15.0000
:::::	chr10:30254829-30255050(-)$1	221	108	113	15.0000
:::::	chr11:76859653-76859873(-)$1	220	49	54	15.0000
DDDD:	chr1:34248744-34248976(+)$1	232	109	114	15.0000
22ccc	chr5:77407592-77407823(+)$1	231	78	83	15.0000
rrrrr	chr8:86455762-86455982(+)$1	220	32	37	15.0000
cc$$$	chr5:21305185-21305424(+)$1	239	61	66	15.0000
FFFF~	chr8:23175489-23175709(+)$1	220	124	129	15.0000
!!bb!	chr17:75026247-75026468(+)$1	221	167	172	15.0000
cc[cc	chr4:135895272-135895492(+)$1	220	65	70	15.0000
eeee:	chr16:90226386-90226606(+)$1	220	47	52	15.0000
)))))	chr11:69177431-69177651(-)$1	220	12	17	15.0000
qqqqq	chr1:60533644-60533864(+)$1	220	18	23	15.0000
cdddd	chr12:16977776-16978018(+)$1	242	81	86	15.0000
bb888	chr2:152962338-152962567(+)$1	229	126	131	15.0000
cnnnn	chr10:4532301-4532521(+)$1	220	99	104	15.0000
444bb	chr10:127686495-127686715(+)$1	220	196	201	15.0000
GGGGG	chr3:104605323-104605543(-)$1	220	98	103	15.0000

#DB
.....	chr14:52906990-52907211(+)$1	1	44	49	15.0000
((((.	chr7:104784818-104785038(+)$1	1	109	114	15.0000
.....	chr7:51885231-51885451(-)$1	1	165	170	15.0000
(((((	chr12:66157262-66157482(+)$1	1	13	18	15.0000
.....	chr4:57869648-57869884(+)$1	1	122	127	15.0000
.....	chrX:132335835-132336055(+)$1	1	22	27	15.0000
...((	chr12:112862636-112862856(+)$1	1	176	181	15.0000
(....	chr5:88984276-88984496(+)$1	1	6	11	15.0000
)))))	chr5:124374706-124374943(+)$1	1	36	41	15.0000
.....	chr9:51893215-51893435(+)$1	1	7	12	15.0000
.....	chr16:90229887-90230107(-)$1	1	128	133	15.0000
.(.((	chr15:75900705-75900935(-)$1	1	10	15	15.0000
...))	chr19:29722608-29722848(-)$1	1	143	148	15.0000
)))))	chr6:85410952-85411194(+)$1	1	155	160	15.0000
)))..	chr18:5118253-5118473(+)$1	1	152	157	15.0000
...))	chr1:38090765-38090985(+)$1	1	110	115	15.0000
.....	chr12:103124377-103124597(-)$1	1	183	188	15.0000
)))))	chr13:62470204-62470424(-)$1	1	68	73	15.0000
...).	chr1:152270986-152271206(+)$1	1	84	89	15.0000
)))))	chr13:89831866-89832086(-)$1	1	129	134	15.0000
(....	chr3:134900900-134901120(+)$1	1	68	73	15.0000
..(.(	chr15:76005439-76005659(-)$1	1	56	61	15.0000
(((((	chr4:57905637-57905857(+)$1	1	39	44	15.0000
....)	chr16:91499611-91499831(+)$1	1	206	211	15.0000
(..((	chr11:7061822-7062042(+)$1	1	64	69	15.0000
((...	chr16:36915039-36915259(+)$1	1	23	28	15.0000
)....	chr8:87633847-87634073(-)$1	1	189	194	15.0000
...))	chr12:11306029-11306250(+)$1	1	35	40	15.0000
(((.(	chr4:130063099-130063341(+)$1	1	54	59	15.0000
)))).	chr4:40701426-40701646(-)$1	1	124	129	15.0000
.((((	chr7:148637083-148637303(+)$1	1	54	59	15.0000
.....	chr1:108668923-108669143(-)$1	1	83	88	15.0000
.....	chr10:30254829-30255050(-)$1	1	108	113	15.0000
.....	chr11:76859653-76859873(-)$1	1	49	54	15.0000
((((.	chr1:34248744-34248976(+)$1	1	109	114	15.0000
..)))	chr5:77407592-77407823(+)$1	1	78	83	15.0000
.....	chr8:86455762-86455982(+)$1	1	32	37	15.0000
((...	chr5:21305185-21305424(+)$1	1	61	66	15.0000
)))).	chr8:23175489-23175709(+)$1	1	124	129	15.0000
..((.	chr17:75026247-75026468(+)$1	1	167	172	15.0000
((.((	chr4:135895272-135895492(+)$1	1	65	70	15.0000
)))).	chr16:90226386-90226606(+)$1	1	47	52	15.0000
.....	chr11:69177431-69177651(-)$1	1	12	17	15.0000
.....	chr1:60533644-60533864(+)$1	1	18	23	15.0000
(((((	chr12:16977776-16978018(+)$1	1	81	86	15.0000
))...	chr2:152962338-152962567(+)$1	1	126	131	15.0000
(....	chr10:4532301-4532521(+)$1	1	99	104	15.0000
...))	chr10:127686495-127686715(+)$1	1	196	201	15.0000
)))))	chr3:104605323-104605543(-)$1	1	98	103	15.0000

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

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m2_run2.nuc.txt

#NT
GGUAAUUGGUUCACCAUUGUUUGGGGGAUAUUUUAAUUCACCGUUUCUCUGUAUGUAGUGUUACAACAGCAGAAACCCAUACUUGAAAAUGUGCUUUUCUUUUUUGUUUUCUAGGAUGGGUUUGUGGAGUUCUUCCACGUACAGGACCUAGAAGGCGGCAUCAGAAAUGUGCUGCUGGCUUUUGCGGGUGUUGCUGGAGUAGGGGCUGGUCUGGCAUAUCUAAUAAGAUAGCCUUGUGAGUGCAAUAGGGGACUCUUAAAGCUCCAGCCACCAAACUACAUGCAUCUGUGAAAACAUGUGUAUUUAUGAAGGUGGACUUGAAGCUGCCCAGGAUUUUAACAGUCCAGUUCUACUGUAGCAACAUAGCAAAAAGAAAGUGGCUACAGGAUUGUGGCUAACAAGAAUAAAUACAUGGGAAAAGUGCUCCCCCUGGAAGA	chr3:95464504-95464999(+)$1	495	11	448	563.5000

#otherMatches

#Struct PSSM
FFFFLLLHHHHHHHHEEEEE{DDDD{FFFFFF:::::::::::::::hhhhhhhh[bbnnnnnbbhhhhhhhh==========[hhhhhhhhddddmmmmdddd55555hhhhhhhh]==========FFFFFF}DDDD}EEEEE:::::::BBKKDDDD{BBdddd[ffffffnnnnnffffff]ddddffffff####ffffffmmmmffffff]ffffff:DDDD{FFFFFFGGGGGGG:::iiiiiiiii%%%%%%ffffff"""ccc!!ddddoooooodddd22ccc666666ffffff55555iiiiiiiiicccqqqqqqqqccc:GGGGGGG:::hhhhhhhhoooooohhhhhhhh::cccooooooccc:::::FFFFFF}DDDDBB}DDDD}BB~~~~HHHHHHHHFFFFFF}CCC~~~~CCC}E	chr8:87579481-87579963(+)$1	482	28	465	563.5000
cccrrrrrrrrrccc4444ffffffCCC{EEEEEKKDDDD::ffffffdddd[ddddmmmmdddddddd]ffffff:bbmmmmbb:::::JJJJJJJJJJGGGGGGG:ggggggg####bb[ffffffnnnnnffffff]bb4444gggggggggggggg[bbmmmmbbggggggg:::FFFFFFKKIIIIIIIII{GGGGGGG{DDDD{CCCMMMMDDDD::eeeee"""ffffffpppppppffffff333eeeee:dddda[bbeeeee####bb[ffffff[cccmmmmccc]ffffff]bb4444eeeee]bb]a]dddd:::::DDDD?????CCC}DDDDGGGGGGG}IIIIIIIII}FFFFFF::::::hhhhhhhhmmmmhhhhhhhhGGGGGGG@@@@@@@@@@JJJJJJJJJJcccmmmmcccccc	chr3:95464504-95464999(+)$1	495	11	448	563.5000

#DB
((((...(((((((((((((.((((.((((((...............((((((((.((.....))))))))))((((((((((.((((((((((((....)))).....)))))))).)))))))))))))))).)))).))))).......((..((((.((((((.((((((.....)))))).))))((((((....((((((....)))))).)))))).((((.(((((((((((((...(((((((((......((((((...(((..((((......))))..)))......)))))).....)))))))))(((........))).)))))))...((((((((......))))))))..(((......))).....)))))).)))))).)))).))....)))))))))))))).)))....))).)	chr8:87579481-87579963(+)$1	1	28	465	563.5000
(((.........)))....))))))(((.(((((..((((..((((((((((.((((....)))))))).)))))).((....)).....(((((((((((((((((.(((((((....((.((((((.....)))))).))....)))))))(((((((.((....)))))))))...((((((..(((((((((.(((((((.((((.(((....((((..(((((...((((((.......))))))...))))).(((((.(((((((....((.((((((.(((....))).)))))).))....))))).)).).)))).....)))).....))).))))))))))).))))))))).))))))......((((((((....)))))))))))))))..........))))))))))(((....)))(((	chr3:95464504-95464999(+)$1	1	11	448	563.5000

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

#score	1127.0
#seq	2
#width	437
#escape	false
#onStep	14957
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m1_run1.nuc.txt

#NT
CUG	chr9:119147934-119148213(-)$1	279	15	18	9.0000
CUG	chr1:133921794-133922065(+)$1	271	22	25	9.0000
CUG	chr2:157383278-157383551(-)$1	273	18	21	9.0000
CUG	chr16:91227498-91227771(+)$1	273	6	9	9.0000
CUG	chr10:80611569-80611846(+)$1	277	50	53	9.0000
CUG	chr11:87794777-87795061(-)$1	284	15	18	9.0000
CUG	chr7:134911688-134911984(+)$1	296	6	9	9.0000
CUG	chr16:37882822-37883102(+)$1	280	30	33	9.0000
CUG	chr2:157382615-157382901(-)$1	286	68	71	9.0000
CUG	chr12:113887155-113887428(+)$1	273	27	30	9.0000
CUG	chr19:5456361-5456634(-)$1	273	1	4	9.0000
CUG	chr15:81678793-81679086(-)$1	293	92	95	9.0000
CUG	chr11:79507176-79507447(+)$1	271	46	49	9.0000
CUG	chr15:80761609-80761882(+)$1	273	170	173	9.0000
CUG	chr1:189057919-189058218(+)$1	299	12	15	9.0000
CUG	chr16:37882880-37883165(+)$1	285	18	21	9.0000
CUG	chr6:56728726-56729000(-)$1	274	1	4	9.0000
CUG	chr8:11834139-11834413(+)$1	274	46	49	9.0000
CUG	chr7:117008957-117009223(-)$1	266	82	85	9.0000
CUG	chr1:184398225-184398498(-)$1	273	94	97	9.0000
CUG	chr7:107985091-107985371(+)$1	280	8	11	9.0000
CUG	chr16:91227771-91228058(+)$1	287	45	48	9.0000
CUG	chr8:123178705-123178982(-)$1	277	82	85	9.0000
CUG	chr6:136757209-136757499(+)$1	290	119	122	9.0000
CUG	chr3:133126987-133127268(-)$1	281	80	83	9.0000
CUG	chr11:98015256-98015533(-)$1	277	52	55	9.0000
CUG	chr15:79655068-79655353(-)$1	285	10	13	9.0000
CUG	chr8:86621057-86621344(-)$1	287	1	4	9.0000
CUG	chr7:25670028-25670303(+)$1	275	10	13	9.0000
CUG	chr8:109599437-109599706(-)$1	269	13	16	9.0000
CUG	chr6:40353079-40353347(-)$1	268	20	23	9.0000
CUG	chr5:138223490-138223786(-)$1	296	4	7	9.0000
CUG	chr10:116510443-116510718(-)$1	275	21	24	9.0000
cug	chr5:123807810-123808084(+)$1	274	2	5	9.0000
CUG	chr15:102261444-102261729(+)$1	285	100	103	9.0000
CUG	chr19:5456434-5456714(-)$1	280	0	3	9.0000
CUG	chr12:8798856-8799128(+)$1	272	6	9	9.0000
CUG	chr15:79658142-79658416(-)$1	274	47	50	9.0000
CUG	chr4:49669033-49669321(+)$1	288	87	90	9.0000
CUG	chr11:53590397-53590671(+)$1	274	8	11	9.0000
CUG	chr4:140884838-140885115(+)$1	277	27	30	9.0000
CUG	chr15:79655896-79656195(-)$1	299	15	18	9.0000
CUG	chr3:32240090-32240398(-)$1	308	14	17	9.0000
CUG	chr15:81535417-81535702(-)$1	285	27	30	9.0000
CUG	chr11:105142915-105143222(+)$1	307	43	46	9.0000
CUG	chr8:74842841-74843113(+)$1	272	12	15	9.0000
CUG	chr12:114059359-114059639(-)$1	280	0	3	9.0000
CUG	chr16:98014687-98014959(-)$1	272	13	16	9.0000
CUG	chr2:30882339-30882614(-)$1	275	2	5	9.0000
CUG	chr5:137968786-137969068(+)$1	282	55	58	9.0000
CUG	chr7:51506862-51507143(+)$1	281	1	4	9.0000
CUG	chr5:141098323-141098602(-)$1	279	20	23	9.0000
CUG	chr5:138223116-138223399(-)$1	283	6	9	9.0000
CUG	chr8:11834072-11834348(+)$1	276	35	38	9.0000
CUG	chr10:86297866-86298144(+)$1	278	36	39	9.0000
CUG	chr8:74844691-74844960(+)$1	269	5	8	9.0000
cug	chr17:27062050-27062328(+)$1	278	20	23	9.0000
CUG	chr13:5869145-5869421(+)$1	276	49	52	9.0000
CUG	chr16:98170671-98170948(-)$1	277	44	47	9.0000
CUG	chr2:168780770-168781049(-)$1	279	39	42	9.0000
CUG	chr4:137798692-137798972(+)$1	280	37	40	9.0000
CUG	chr4:140669562-140669861(-)$1	299	2	5	9.0000
CUG	chr18:24443321-24443593(+)$1	272	32	35	9.0000
CUG	chr16:98170652-98170921(-)$1	269	17	20	9.0000
CUG	chr14:71003926-71004195(-)$1	269	42	45	9.0000
CUG	chr15:75831591-75831876(-)$1	285	11	14	9.0000
CUG	chr11:68923178-68923496(+)$1	318	13	16	9.0000
CUG	chr4:147320746-147321041(+)$1	295	31	34	9.0000
CUG	chr5:37138907-37139205(-)$1	298	31	34	9.0000
CUG	chr3:105771255-105771535(+)$1	280	35	38	9.0000
CUG	chr11:69813257-69813539(+)$1	282	125	128	9.0000
CUG	chr2:34678076-34678352(-)$1	276	24	27	9.0000
CUG	chr11:117828673-117828943(-)$1	270	26	29	9.0000
cug	chr4:133831673-133831946(-)$1	273	67	70	9.0000
cug	chr7:152050685-152050968(+)$1	283	58	61	9.0000
CUG	chr8:125096552-125096860(+)$1	308	17	20	9.0000
CUG	chr13:69138016-69138287(-)$1	271	68	71	9.0000
CUG	chr15:75900547-75900820(-)$1	273	13	16	9.0000
CUG	chr17:34791800-34792094(+)$1	294	9	12	9.0000
CUG	chr3:95464614-95464908(+)$1	294	72	75	9.0000
CUG	chr10:127827760-127828042(+)$1	282	1	4	9.0000
CUG	chr3:154259844-154260110(-)$1	266	55	58	9.0000
CUG	chr6:124863939-124864209(-)$1	270	14	17	9.0000
cug	chr3:108163838-108164128(+)$1	290	9	12	9.0000
CUG	chr3:121969333-121969624(+)$1	291	10	13	9.0000
CUG	chr2:144232685-144232977(+)$1	292	8	11	9.0000
CUG	chr5:123809705-123809984(+)$1	279	12	15	9.0000
CUG	chr7:24891391-24891687(+)$1	296	30	33	9.0000
CUG	chr18:75555294-75555568(+)$1	274	3	6	9.0000
CUG	chr4:83921329-83921604(-)$1	275	31	34	9.0000
CUG	chr2:153054827-153055101(-)$1	274	10	13	9.0000
CUG	chr11:87794725-87795014(-)$1	289	136	139	9.0000
CUG	chr1:62843167-62843435(+)$1	268	35	38	9.0000
CUG	chr19:24758574-24758848(-)$1	274	81	84	9.0000
CUG	chr7:107985018-107985335(+)$1	317	34	37	9.0000
CUG	chr19:8964904-8965185(+)$1	281	111	114	9.0000
CUG	chr17:34791868-34792151(+)$1	283	16	19	9.0000
CUG	chr11:114729900-114730186(+)$1	286	97	100	9.0000
CUG	chr11:79506359-79506633(+)$1	274	13	16	9.0000

#otherMatches

#Struct PSSM
===	chr11:29642123-29642419(+)$1	296	23	26	9.0000
EED	chr9:119147934-119148213(-)$1	279	15	18	9.0000
iii	chr1:133921794-133922065(+)$1	271	22	25	9.0000
GGG	chr2:157383278-157383551(-)$1	273	18	21	9.0000
DDD	chr16:91227498-91227771(+)$1	273	6	9	9.0000
d[d	chr10:80611569-80611846(+)$1	277	50	53	9.0000
GGG	chr11:87794777-87795061(-)$1	284	15	18	9.0000
ff[	chr7:134911688-134911984(+)$1	296	6	9	9.0000
NCC	chr16:37882822-37883102(+)$1	280	30	33	9.0000
aff	chr2:157382615-157382901(-)$1	286	68	71	9.0000
aa!	chr12:113887155-113887428(+)$1	273	27	30	9.0000
:DD	chr19:5456361-5456634(-)$1	273	1	4	9.0000
dbb	chr15:81678793-81679086(-)$1	293	92	95	9.0000
vvv	chr11:79507176-79507447(+)$1	271	46	49	9.0000
]gg	chr15:80761609-80761882(+)$1	273	170	173	9.0000
NNE	chr1:189057919-189058218(+)$1	299	12	15	9.0000
KKA	chr16:37882880-37883165(+)$1	285	18	21	9.0000
iii	chr6:56728726-56729000(-)$1	274	1	4	9.0000
GGG	chr8:11834139-11834413(+)$1	274	46	49	9.0000
b[e	chr7:117008957-117009223(-)$1	266	82	85	9.0000
ppp	chr1:184398225-184398498(-)$1	273	94	97	9.0000
eee	chr7:107985091-107985371(+)$1	280	8	11	9.0000
333	chr16:91227771-91228058(+)$1	287	45	48	9.0000
fff	chr8:123178705-123178982(-)$1	277	82	85	9.0000
bba	chr6:136757209-136757499(+)$1	290	119	122	9.0000
nbb	chr3:133126987-133127268(-)$1	281	80	83	9.0000
eee	chr11:98015256-98015533(-)$1	277	52	55	9.0000
FFF	chr15:79655068-79655353(-)$1	285	10	13	9.0000
::H	chr8:86621057-86621344(-)$1	287	1	4	9.0000
GGG	chr7:25670028-25670303(+)$1	275	10	13	9.0000
BDD	chr8:109599437-109599706(-)$1	269	13	16	9.0000
EE{	chr6:40353079-40353347(-)$1	268	20	23	9.0000
EEC	chr5:138223490-138223786(-)$1	296	4	7	9.0000
ddh	chr10:116510443-116510718(-)$1	275	21	24	9.0000
C::	chr5:123807810-123808084(+)$1	274	2	5	9.0000
bcc	chr15:102261444-102261729(+)$1	285	100	103	9.0000
eee	chr19:5456434-5456714(-)$1	280	0	3	9.0000
FFF	chr12:8798856-8799128(+)$1	272	6	9	9.0000
==e	chr15:79658142-79658416(-)$1	274	47	50	9.0000
qqd	chr4:49669033-49669321(+)$1	288	87	90	9.0000
DDD	chr11:53590397-53590671(+)$1	274	8	11	9.0000
fff	chr4:140884838-140885115(+)$1	277	27	30	9.0000
+++	chr15:79655896-79656195(-)$1	299	15	18	9.0000
###	chr3:32240090-32240398(-)$1	308	14	17	9.0000
b[c	chr15:81535417-81535702(-)$1	285	27	30	9.0000
eee	chr11:105142915-105143222(+)$1	307	43	46	9.0000
cll	chr8:74842841-74843113(+)$1	272	12	15	9.0000
::a	chr12:114059359-114059639(-)$1	280	0	3	9.0000
LLB	chr16:98014687-98014959(-)$1	272	13	16	9.0000
::c	chr2:30882339-30882614(-)$1	275	2	5	9.0000
GGG	chr5:137968786-137969068(+)$1	282	55	58	9.0000
BB{	chr7:51506862-51507143(+)$1	281	1	4	9.0000
FFF	chr5:141098323-141098602(-)$1	279	20	23	9.0000
F{G	chr5:138223116-138223399(-)$1	283	6	9	9.0000
ggg	chr8:11834072-11834348(+)$1	276	35	38	9.0000
FFF	chr10:86297866-86298144(+)$1	278	36	39	9.0000
dmm	chr8:74844691-74844960(+)$1	269	5	8	9.0000
EEE	chr17:27062050-27062328(+)$1	278	20	23	9.0000
dd=	chr13:5869145-5869421(+)$1	276	49	52	9.0000
III	chr16:98170671-98170948(-)$1	277	44	47	9.0000
hhh	chr2:168780770-168781049(-)$1	279	39	42	9.0000
2dd	chr4:137798692-137798972(+)$1	280	37	40	9.0000
EEE	chr4:140669562-140669861(-)$1	299	2	5	9.0000
eee	chr18:24443321-24443593(+)$1	272	32	35	9.0000
{HH	chr16:98170652-98170921(-)$1	269	17	20	9.0000
mmm	chr14:71003926-71004195(-)$1	269	42	45	9.0000
::c	chr15:75831591-75831876(-)$1	285	11	14	9.0000
ddd	chr11:68923178-68923496(+)$1	318	13	16	9.0000
fff	chr4:147320746-147321041(+)$1	295	31	34	9.0000
DDD	chr5:37138907-37139205(-)$1	298	31	34	9.0000
ggg	chr3:105771255-105771535(+)$1	280	35	38	9.0000
:BB	chr11:69813257-69813539(+)$1	282	125	128	9.0000
eee	chr2:34678076-34678352(-)$1	276	24	27	9.0000
BB{	chr11:117828673-117828943(-)$1	270	26	29	9.0000
ddd	chr4:133831673-133831946(-)$1	273	67	70	9.0000
fff	chr7:152050685-152050968(+)$1	283	58	61	9.0000
FFF	chr8:125096552-125096860(+)$1	308	17	20	9.0000
ddd	chr13:69138016-69138287(-)$1	271	68	71	9.0000
CKK	chr15:75900547-75900820(-)$1	273	13	16	9.0000
GG{	chr17:34791800-34792094(+)$1	294	9	12	9.0000
FFF	chr3:95464614-95464908(+)$1	294	72	75	9.0000
FFF	chr10:127827760-127828042(+)$1	282	1	4	9.0000
pcc	chr3:154259844-154260110(-)$1	266	55	58	9.0000
qdd	chr6:124863939-124864209(-)$1	270	14	17	9.0000
hhh	chr3:108163838-108164128(+)$1	290	9	12	9.0000
:::	chr3:121969333-121969624(+)$1	291	10	13	9.0000
mdd	chr2:144232685-144232977(+)$1	292	8	11	9.0000
GG:	chr5:123809705-123809984(+)$1	279	12	15	9.0000
III	chr7:24891391-24891687(+)$1	296	30	33	9.0000
CKK	chr18:75555294-75555568(+)$1	274	3	6	9.0000
ooo	chr4:83921329-83921604(-)$1	275	31	34	9.0000
DDD	chr2:153054827-153055101(-)$1	274	10	13	9.0000
f]b	chr11:87794725-87795014(-)$1	289	136	139	9.0000
MEE	chr1:62843167-62843435(+)$1	268	35	38	9.0000
a]g	chr19:24758574-24758848(-)$1	274	81	84	9.0000
wee	chr7:107985018-107985335(+)$1	317	34	37	9.0000
ddd	chr19:8964904-8965185(+)$1	281	111	114	9.0000
sss	chr17:34791868-34792151(+)$1	283	16	19	9.0000
cc[	chr11:114729900-114730186(+)$1	286	97	100	9.0000
ddd	chr11:79506359-79506633(+)$1	274	13	16	9.0000

#DB
(((	chr11:29642123-29642419(+)$1	1	23	26	9.0000
(((	chr9:119147934-119148213(-)$1	1	15	18	9.0000
(((	chr1:133921794-133922065(+)$1	1	22	25	9.0000
(((	chr2:157383278-157383551(-)$1	1	18	21	9.0000
(((	chr16:91227498-91227771(+)$1	1	6	9	9.0000
(.(	chr10:80611569-80611846(+)$1	1	50	53	9.0000
(((	chr11:87794777-87795061(-)$1	1	15	18	9.0000
((.	chr7:134911688-134911984(+)$1	1	6	9	9.0000
.((	chr16:37882822-37883102(+)$1	1	30	33	9.0000
(((	chr2:157382615-157382901(-)$1	1	68	71	9.0000
((.	chr12:113887155-113887428(+)$1	1	27	30	9.0000
.((	chr19:5456361-5456634(-)$1	1	1	4	9.0000
(((	chr15:81678793-81679086(-)$1	1	92	95	9.0000
...	chr11:79507176-79507447(+)$1	1	46	49	9.0000
.))	chr15:80761609-80761882(+)$1	1	170	173	9.0000
..(	chr1:189057919-189058218(+)$1	1	12	15	9.0000
..(	chr16:37882880-37883165(+)$1	1	18	21	9.0000
(((	chr6:56728726-56729000(-)$1	1	1	4	9.0000
(((	chr8:11834139-11834413(+)$1	1	46	49	9.0000
(.(	chr7:117008957-117009223(-)$1	1	82	85	9.0000
...	chr1:184398225-184398498(-)$1	1	94	97	9.0000
)))	chr7:107985091-107985371(+)$1	1	8	11	9.0000
...	chr16:91227771-91228058(+)$1	1	45	48	9.0000
)))	chr8:123178705-123178982(-)$1	1	82	85	9.0000
)))	chr6:136757209-136757499(+)$1	1	119	122	9.0000
.))	chr3:133126987-133127268(-)$1	1	80	83	9.0000
(((	chr11:98015256-98015533(-)$1	1	52	55	9.0000
(((	chr15:79655068-79655353(-)$1	1	10	13	9.0000
..(	chr8:86621057-86621344(-)$1	1	1	4	9.0000
(((	chr7:25670028-25670303(+)$1	1	10	13	9.0000
(((	chr8:109599437-109599706(-)$1	1	13	16	9.0000
((.	chr6:40353079-40353347(-)$1	1	20	23	9.0000
(((	chr5:138223490-138223786(-)$1	1	4	7	9.0000
(((	chr10:116510443-116510718(-)$1	1	21	24	9.0000
(..	chr5:123807810-123808084(+)$1	1	2	5	9.0000
)))	chr15:102261444-102261729(+)$1	1	100	103	9.0000
(((	chr19:5456434-5456714(-)$1	1	0	3	9.0000
(((	chr12:8798856-8799128(+)$1	1	6	9	9.0000
))(	chr15:79658142-79658416(-)$1	1	47	50	9.0000
..)	chr4:49669033-49669321(+)$1	1	87	90	9.0000
(((	chr11:53590397-53590671(+)$1	1	8	11	9.0000
(((	chr4:140884838-140885115(+)$1	1	27	30	9.0000
...	chr15:79655896-79656195(-)$1	1	15	18	9.0000
...	chr3:32240090-32240398(-)$1	1	14	17	9.0000
(.(	chr15:81535417-81535702(-)$1	1	27	30	9.0000
(((	chr11:105142915-105143222(+)$1	1	43	46	9.0000
(..	chr8:74842841-74843113(+)$1	1	12	15	9.0000
..(	chr12:114059359-114059639(-)$1	1	0	3	9.0000
..(	chr16:98014687-98014959(-)$1	1	13	16	9.0000
..(	chr2:30882339-30882614(-)$1	1	2	5	9.0000
(((	chr5:137968786-137969068(+)$1	1	55	58	9.0000
((.	chr7:51506862-51507143(+)$1	1	1	4	9.0000
(((	chr5:141098323-141098602(-)$1	1	20	23	9.0000
(.(	chr5:138223116-138223399(-)$1	1	6	9	9.0000
)))	chr8:11834072-11834348(+)$1	1	35	38	9.0000
(((	chr10:86297866-86298144(+)$1	1	36	39	9.0000
(..	chr8:74844691-74844960(+)$1	1	5	8	9.0000
(((	chr17:27062050-27062328(+)$1	1	20	23	9.0000
)))	chr13:5869145-5869421(+)$1	1	49	52	9.0000
(((	chr16:98170671-98170948(-)$1	1	44	47	9.0000
(((	chr2:168780770-168781049(-)$1	1	39	42	9.0000
.))	chr4:137798692-137798972(+)$1	1	37	40	9.0000
(((	chr4:140669562-140669861(-)$1	1	2	5	9.0000
)))	chr18:24443321-24443593(+)$1	1	32	35	9.0000
.((	chr16:98170652-98170921(-)$1	1	17	20	9.0000
...	chr14:71003926-71004195(-)$1	1	42	45	9.0000
..(	chr15:75831591-75831876(-)$1	1	11	14	9.0000
)))	chr11:68923178-68923496(+)$1	1	13	16	9.0000
(((	chr4:147320746-147321041(+)$1	1	31	34	9.0000
(((	chr5:37138907-37139205(-)$1	1	31	34	9.0000
(((	chr3:105771255-105771535(+)$1	1	35	38	9.0000
.))	chr11:69813257-69813539(+)$1	1	125	128	9.0000
(((	chr2:34678076-34678352(-)$1	1	24	27	9.0000
((.	chr11:117828673-117828943(-)$1	1	26	29	9.0000
)))	chr4:133831673-133831946(-)$1	1	67	70	9.0000
(((	chr7:152050685-152050968(+)$1	1	58	61	9.0000
(((	chr8:125096552-125096860(+)$1	1	17	20	9.0000
(((	chr13:69138016-69138287(-)$1	1	68	71	9.0000
(..	chr15:75900547-75900820(-)$1	1	13	16	9.0000
((.	chr17:34791800-34792094(+)$1	1	9	12	9.0000
(((	chr3:95464614-95464908(+)$1	1	72	75	9.0000
(((	chr10:127827760-127828042(+)$1	1	1	4	9.0000
.))	chr3:154259844-154260110(-)$1	1	55	58	9.0000
.))	chr6:124863939-124864209(-)$1	1	14	17	9.0000
(((	chr3:108163838-108164128(+)$1	1	9	12	9.0000
...	chr3:121969333-121969624(+)$1	1	10	13	9.0000
.))	chr2:144232685-144232977(+)$1	1	8	11	9.0000
((.	chr5:123809705-123809984(+)$1	1	12	15	9.0000
(((	chr7:24891391-24891687(+)$1	1	30	33	9.0000
(..	chr18:75555294-75555568(+)$1	1	3	6	9.0000
...	chr4:83921329-83921604(-)$1	1	31	34	9.0000
(((	chr2:153054827-153055101(-)$1	1	10	13	9.0000
).)	chr11:87794725-87795014(-)$1	1	136	139	9.0000
.((	chr1:62843167-62843435(+)$1	1	35	38	9.0000
).)	chr19:24758574-24758848(-)$1	1	81	84	9.0000
.))	chr7:107985018-107985335(+)$1	1	34	37	9.0000
)))	chr19:8964904-8965185(+)$1	1	111	114	9.0000
...	chr17:34791868-34792151(+)$1	1	16	19	9.0000
((.	chr11:114729900-114730186(+)$1	1	97	100	9.0000
(((	chr11:79506359-79506633(+)$1	1	13	16	9.0000

#PSSM
C : 0.95	c : 0.05	
U : 0.95	u : 0.05	
G : 0.95	g : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m2_run2.nuc.txt

#NT
UGG	chr9:21200398-21200618(+)$1	220	88	91	9.0000
UGG	chr7:150256596-150256817(+)$1	221	11	14	9.0000
UGG	chr17:69587667-69587899(+)$1	232	88	91	9.0000
UGG	chr17:71979483-71979703(+)$1	220	21	24	9.0000
UGG	chr4:155276152-155276372(+)$1	220	53	56	9.0000
UGG	chr7:30970214-30970434(+)$1	220	11	14	9.0000
UGG	chr6:88415432-88415652(+)$1	220	16	19	9.0000
UGG	chr2:112173484-112173709(+)$1	225	2	5	9.0000
UGG	chr2:3239832-3240052(+)$1	220	38	41	9.0000
UGG	chr19:9023335-9023555(+)$1	220	35	38	9.0000
UGG	chr6:21917520-21917740(+)$1	220	8	11	9.0000
UGG	chr14:62058480-62058700(-)$1	220	73	76	9.0000
UGG	chr4:122971969-122972189(+)$1	220	29	32	9.0000
UGG	chr5:139710582-139710802(+)$1	220	15	18	9.0000
UGG	chr17:24570047-24570268(+)$1	221	78	81	9.0000
UGG	chrX:130846451-130846671(+)$1	220	20	23	9.0000
UGG	chr2:154998207-154998427(+)$1	220	22	25	9.0000
UGG	chr17:68171594-68171818(+)$1	224	127	130	9.0000
UGG	chr3:144382875-144383106(-)$1	231	99	102	9.0000
UGG	chr12:107300749-107300969(+)$1	220	6	9	9.0000
UGG	chr1:179178697-179178919(-)$1	222	43	46	9.0000
UGG	chr15:81195833-81196053(-)$1	220	58	61	9.0000
UGG	chr14:61406096-61406316(+)$1	220	43	46	9.0000
UGG	chr9:114421640-114421870(-)$1	230	8	11	9.0000
UGG	chr7:117194744-117194981(+)$1	237	118	121	9.0000
UGG	chr3:82872114-82872334(+)$1	220	5	8	9.0000
UGG	chrX:109477673-109477894(+)$1	221	1	4	9.0000
UGG	chr4:40673063-40673298(+)$1	235	43	46	9.0000
UGG	chr17:25296474-25296694(+)$1	220	15	18	9.0000
UGG	chr2:25077843-25078063(-)$1	220	1	4	9.0000
UGG	chr5:150547904-150548124(+)$1	220	19	22	9.0000
UGG	chr10:80266131-80266351(+)$1	220	97	100	9.0000
UGG	chr3:157654553-157654774(+)$1	221	101	104	9.0000
UGG	chr4:118293988-118294234(+)$1	246	17	20	9.0000
UGG	chr18:85129355-85129591(+)$1	236	52	55	9.0000
UGG	chr3:88437332-88437552(+)$1	220	0	3	9.0000
UGG	chr5:108998820-108999040(-)$1	220	12	15	9.0000
UGG	chr7:26408720-26408940(+)$1	220	46	49	9.0000
UGG	chr17:75024353-75024573(+)$1	220	113	116	9.0000
UGG	chr9:122761642-122761876(-)$1	234	52	55	9.0000
UGG	chr13:34010048-34010268(-)$1	220	3	6	9.0000
UGG	chr11:79924933-79925153(+)$1	220	47	50	9.0000
UGG	chr13:34978461-34978681(+)$1	220	39	42	9.0000
UGG	chr19:9085301-9085524(+)$1	223	71	74	9.0000
UGG	chr11:83822825-83823045(+)$1	220	11	14	9.0000
UGG	chr9:114421886-114422106(-)$1	220	18	21	9.0000
UGG	chr3:88972595-88972817(+)$1	222	0	3	9.0000
UGG	chr16:18223188-18223414(-)$1	226	0	3	9.0000
UGG	chr8:47618853-47619073(+)$1	220	30	33	9.0000
UGG	chr8:124948867-124949087(-)$1	220	42	45	9.0000
UGG	chr11:72635308-72635534(+)$1	226	41	44	9.0000
UGG	chr10:67559766-67560007(-)$1	241	136	139	9.0000
UGG	chr1:120565193-120565413(+)$1	220	55	58	9.0000
UGG	chr11:30753214-30753434(+)$1	220	81	84	9.0000
UGG	chr7:51989230-51989450(-)$1	220	16	19	9.0000
UGG	chr9:43944804-43945037(+)$1	233	78	81	9.0000
UGG	chr4:118295859-118296079(+)$1	220	77	80	9.0000
UGG	chr2:127042360-127042596(+)$1	236	6	9	9.0000
UGG	chr5:76043704-76043924(+)$1	220	1	4	9.0000
UGG	chr2:20728095-20728324(+)$1	229	15	18	9.0000
UGG	chr6:13533108-13533328(-)$1	220	29	32	9.0000
UGG	chr16:20680997-20681217(+)$1	220	6	9	9.0000
UGG	chr15:100011663-100011883(+)$1	220	43	46	9.0000
UGG	chr11:72795148-72795368(+)$1	220	23	26	9.0000
UGG	chr1:187239623-187239843(+)$1	220	114	117	9.0000
UGG	chr19:35031831-35032051(+)$1	220	78	81	9.0000
UGG	chr6:122680030-122680266(-)$1	236	47	50	9.0000
UGG	chr2:179909825-179910046(+)$1	221	1	4	9.0000
UGG	chr8:13373746-13373976(+)$1	230	101	104	9.0000
UGG	chr17:66319420-66319641(-)$1	221	27	30	9.0000
UGG	chr9:120032740-120032988(+)$1	248	24	27	9.0000
UGG	chr5:137464113-137464333(+)$1	220	16	19	9.0000
UGG	chr16:31743089-31743309(+)$1	220	26	29	9.0000
ugg	chr11:51596180-51596433(+)$1	253	46	49	9.0000
UGG	chr8:74143527-74143749(+)$1	222	131	134	9.0000
UGG	chr7:148815870-148816092(+)$1	222	1	4	9.0000
UGG	chr1:153201656-153201877(+)$1	221	66	69	9.0000
UGG	chrX:148493223-148493443(+)$1	220	44	47	9.0000
UGG	chr10:80644022-80644257(+)$1	235	36	39	9.0000
UGG	chr6:120706674-120706894(+)$1	220	31	34	9.0000
UGG	chr7:53338519-53338740(+)$1	221	2	5	9.0000
UGG	chr3:153573013-153573233(-)$1	220	5	8	9.0000
UGG	chr9:103118030-103118259(-)$1	229	53	56	9.0000
UGG	chr7:152118418-152118638(-)$1	220	2	5	9.0000
UGG	chr17:88379477-88379697(+)$1	220	3	6	9.0000
UGG	chr13:84361899-84362130(+)$1	231	84	87	9.0000
UGG	chr2:104493068-104493288(+)$1	220	12	15	9.0000
UGG	chr5:143722070-143722290(+)$1	220	192	195	9.0000
UGG	chr5:120122268-120122489(+)$1	221	33	36	9.0000
UGG	chr15:99138178-99138399(+)$1	221	1	4	9.0000
UGG	chr19:4151603-4151823(+)$1	220	70	73	9.0000
UGG	chr13:108516409-108516648(-)$1	239	27	30	9.0000
UGG	chr12:60173500-60173741(+)$1	241	94	97	9.0000
UGG	chr1:34332529-34332749(+)$1	220	34	37	9.0000
UGG	chr12:72274016-72274236(+)$1	220	57	60	9.0000
UGG	chr3:59122618-59122838(-)$1	220	18	21	9.0000
UGG	chr18:54055483-54055703(+)$1	220	3	6	9.0000
UGG	chr12:66068134-66068369(+)$1	235	4	7	9.0000
UGG	chr17:23947927-23948150(+)$1	223	132	135	9.0000

#otherMatches

#Struct PSSM
ggg	chr4:108079089-108079309(-)$1	220	28	31	9.0000
GGG	chr9:21200398-21200618(+)$1	220	88	91	9.0000
dd!	chr7:150256596-150256817(+)$1	221	11	14	9.0000
fff	chr17:69587667-69587899(+)$1	232	88	91	9.0000
iii	chr17:71979483-71979703(+)$1	220	21	24	9.0000
fff	chr4:155276152-155276372(+)$1	220	53	56	9.0000
JJJ	chr7:30970214-30970434(+)$1	220	11	14	9.0000
ccc	chr6:88415432-88415652(+)$1	220	16	19	9.0000
::C	chr2:112173484-112173709(+)$1	225	2	5	9.0000
a]e	chr2:3239832-3240052(+)$1	220	38	41	9.0000
MDD	chr19:9023335-9023555(+)$1	220	35	38	9.0000
{DD	chr6:21917520-21917740(+)$1	220	8	11	9.0000
[ee	chr14:62058480-62058700(-)$1	220	73	76	9.0000
ehh	chr4:122971969-122972189(+)$1	220	29	32	9.0000
::D	chr5:139710582-139710802(+)$1	220	15	18	9.0000
qee	chr17:24570047-24570268(+)$1	221	78	81	9.0000
gg[	chrX:130846451-130846671(+)$1	220	20	23	9.0000
Bbb	chr2:154998207-154998427(+)$1	220	22	25	9.0000
hh3	chr17:68171594-68171818(+)$1	224	127	130	9.0000
eeq	chr3:144382875-144383106(-)$1	231	99	102	9.0000
NNN	chr12:107300749-107300969(+)$1	220	6	9	9.0000
eee	chr1:179178697-179178919(-)$1	222	43	46	9.0000
4cc	chr15:81195833-81196053(-)$1	220	58	61	9.0000
hhh	chr14:61406096-61406316(+)$1	220	43	46	9.0000
{BB	chr9:114421640-114421870(-)$1	230	8	11	9.0000
ffb	chr7:117194744-117194981(+)$1	237	118	121	9.0000
[ee	chr3:82872114-82872334(+)$1	220	5	8	9.0000
:::	chrX:109477673-109477894(+)$1	221	1	4	9.0000
Idd	chr4:40673063-40673298(+)$1	235	43	46	9.0000
EEE	chr17:25296474-25296694(+)$1	220	15	18	9.0000
:::	chr2:25077843-25078063(-)$1	220	1	4	9.0000
FF{	chr5:150547904-150548124(+)$1	220	19	22	9.0000
fff	chr10:80266131-80266351(+)$1	220	97	100	9.0000
iii	chr3:157654553-157654774(+)$1	221	101	104	9.0000
fff	chr4:118293988-118294234(+)$1	246	17	20	9.0000
fff	chr18:85129355-85129591(+)$1	236	52	55	9.0000
BB{	chr3:88437332-88437552(+)$1	220	0	3	9.0000
:gg	chr5:108998820-108999040(-)$1	220	12	15	9.0000
DDD	chr7:26408720-26408940(+)$1	220	46	49	9.0000
ggq	chr17:75024353-75024573(+)$1	220	113	116	9.0000
:cc	chr9:122761642-122761876(-)$1	234	52	55	9.0000
BB{	chr13:34010048-34010268(-)$1	220	3	6	9.0000
ee"	chr11:79924933-79925153(+)$1	220	47	50	9.0000
EEE	chr13:34978461-34978681(+)$1	220	39	42	9.0000
dgg	chr19:9085301-9085524(+)$1	223	71	74	9.0000
EEE	chr11:83822825-83823045(+)$1	220	11	14	9.0000
DDD	chr9:114421886-114422106(-)$1	220	18	21	9.0000
fff	chr3:88972595-88972817(+)$1	222	0	3	9.0000
:ee	chr16:18223188-18223414(-)$1	226	0	3	9.0000
caf	chr8:47618853-47619073(+)$1	220	30	33	9.0000
ddd	chr8:124948867-124949087(-)$1	220	42	45	9.0000
fff	chr11:72635308-72635534(+)$1	226	41	44	9.0000
eee	chr10:67559766-67560007(-)$1	241	136	139	9.0000
cc!	chr1:120565193-120565413(+)$1	220	55	58	9.0000
ddd	chr11:30753214-30753434(+)$1	220	81	84	9.0000
hhx	chr7:51989230-51989450(-)$1	220	16	19	9.0000
:dd	chr9:43944804-43945037(+)$1	233	78	81	9.0000
$cc	chr4:118295859-118296079(+)$1	220	77	80	9.0000
GGG	chr2:127042360-127042596(+)$1	236	6	9	9.0000
:cc	chr5:76043704-76043924(+)$1	220	1	4	9.0000
EE:	chr2:20728095-20728324(+)$1	229	15	18	9.0000
ggg	chr6:13533108-13533328(-)$1	220	29	32	9.0000
:::	chr16:20680997-20681217(+)$1	220	6	9	9.0000
ttt	chr15:100011663-100011883(+)$1	220	43	46	9.0000
fff	chr11:72795148-72795368(+)$1	220	23	26	9.0000
ddd	chr1:187239623-187239843(+)$1	220	114	117	9.0000
===	chr19:35031831-35032051(+)$1	220	78	81	9.0000
ddd	chr6:122680030-122680266(-)$1	236	47	50	9.0000
fff	chr2:179909825-179910046(+)$1	221	1	4	9.0000
!dd	chr8:13373746-13373976(+)$1	230	101	104	9.0000
:EE	chr17:66319420-66319641(-)$1	221	27	30	9.0000
::c	chr9:120032740-120032988(+)$1	248	24	27	9.0000
mmm	chr5:137464113-137464333(+)$1	220	16	19	9.0000
!!d	chr16:31743089-31743309(+)$1	220	26	29	9.0000
ggb	chr11:51596180-51596433(+)$1	253	46	49	9.0000
ddg	chr8:74143527-74143749(+)$1	222	131	134	9.0000
ccc	chr7:148815870-148816092(+)$1	222	1	4	9.0000
iii	chr1:153201656-153201877(+)$1	221	66	69	9.0000
eee	chrX:148493223-148493443(+)$1	220	44	47	9.0000
CCC	chr10:80644022-80644257(+)$1	235	36	39	9.0000
eee	chr6:120706674-120706894(+)$1	220	31	34	9.0000
b!!	chr7:53338519-53338740(+)$1	221	2	5	9.0000
fff	chr3:153573013-153573233(-)$1	220	5	8	9.0000
ddd	chr9:103118030-103118259(-)$1	229	53	56	9.0000
:AK	chr7:152118418-152118638(-)$1	220	2	5	9.0000
ddd	chr17:88379477-88379697(+)$1	220	3	6	9.0000
fff	chr13:84361899-84362130(+)$1	231	84	87	9.0000
GGG	chr2:104493068-104493288(+)$1	220	12	15	9.0000
ff]	chr5:143722070-143722290(+)$1	220	192	195	9.0000
bb"	chr5:120122268-120122489(+)$1	221	33	36	9.0000
:::	chr15:99138178-99138399(+)$1	221	1	4	9.0000
fff	chr19:4151603-4151823(+)$1	220	70	73	9.0000
a[b	chr13:108516409-108516648(-)$1	239	27	30	9.0000
cc2	chr12:60173500-60173741(+)$1	241	94	97	9.0000
cc$	chr1:34332529-34332749(+)$1	220	34	37	9.0000
aee	chr12:72274016-72274236(+)$1	220	57	60	9.0000
{CC	chr3:59122618-59122838(-)$1	220	18	21	9.0000
cc[	chr18:54055483-54055703(+)$1	220	3	6	9.0000
fff	chr12:66068134-66068369(+)$1	235	4	7	9.0000
hhi	chr17:23947927-23948150(+)$1	223	132	135	9.0000

#DB
(((	chr4:108079089-108079309(-)$1	1	28	31	9.0000
(((	chr9:21200398-21200618(+)$1	1	88	91	9.0000
((.	chr7:150256596-150256817(+)$1	1	11	14	9.0000
)))	chr17:69587667-69587899(+)$1	1	88	91	9.0000
)))	chr17:71979483-71979703(+)$1	1	21	24	9.0000
(((	chr4:155276152-155276372(+)$1	1	53	56	9.0000
(((	chr7:30970214-30970434(+)$1	1	11	14	9.0000
(((	chr6:88415432-88415652(+)$1	1	16	19	9.0000
..(	chr2:112173484-112173709(+)$1	1	2	5	9.0000
).)	chr2:3239832-3240052(+)$1	1	38	41	9.0000
.((	chr19:9023335-9023555(+)$1	1	35	38	9.0000
.((	chr6:21917520-21917740(+)$1	1	8	11	9.0000
.((	chr14:62058480-62058700(-)$1	1	73	76	9.0000
)((	chr4:122971969-122972189(+)$1	1	29	32	9.0000
..(	chr5:139710582-139710802(+)$1	1	15	18	9.0000
.))	chr17:24570047-24570268(+)$1	1	78	81	9.0000
((.	chrX:130846451-130846671(+)$1	1	20	23	9.0000
(((	chr2:154998207-154998427(+)$1	1	22	25	9.0000
)).	chr17:68171594-68171818(+)$1	1	127	130	9.0000
((.	chr3:144382875-144383106(-)$1	1	99	102	9.0000
...	chr12:107300749-107300969(+)$1	1	6	9	9.0000
)))	chr1:179178697-179178919(-)$1	1	43	46	9.0000
.))	chr15:81195833-81196053(-)$1	1	58	61	9.0000
(((	chr14:61406096-61406316(+)$1	1	43	46	9.0000
.((	chr9:114421640-114421870(-)$1	1	8	11	9.0000
))(	chr7:117194744-117194981(+)$1	1	118	121	9.0000
.((	chr3:82872114-82872334(+)$1	1	5	8	9.0000
...	chrX:109477673-109477894(+)$1	1	1	4	9.0000
(((	chr4:40673063-40673298(+)$1	1	43	46	9.0000
(((	chr17:25296474-25296694(+)$1	1	15	18	9.0000
...	chr2:25077843-25078063(-)$1	1	1	4	9.0000
((.	chr5:150547904-150548124(+)$1	1	19	22	9.0000
)))	chr10:80266131-80266351(+)$1	1	97	100	9.0000
(((	chr3:157654553-157654774(+)$1	1	101	104	9.0000
)))	chr4:118293988-118294234(+)$1	1	17	20	9.0000
(((	chr18:85129355-85129591(+)$1	1	52	55	9.0000
((.	chr3:88437332-88437552(+)$1	1	0	3	9.0000
.((	chr5:108998820-108999040(-)$1	1	12	15	9.0000
(((	chr7:26408720-26408940(+)$1	1	46	49	9.0000
((.	chr17:75024353-75024573(+)$1	1	113	116	9.0000
.((	chr9:122761642-122761876(-)$1	1	52	55	9.0000
((.	chr13:34010048-34010268(-)$1	1	3	6	9.0000
((.	chr11:79924933-79925153(+)$1	1	47	50	9.0000
(((	chr13:34978461-34978681(+)$1	1	39	42	9.0000
(((	chr19:9085301-9085524(+)$1	1	71	74	9.0000
(((	chr11:83822825-83823045(+)$1	1	11	14	9.0000
(((	chr9:114421886-114422106(-)$1	1	18	21	9.0000
(((	chr3:88972595-88972817(+)$1	1	0	3	9.0000
.((	chr16:18223188-18223414(-)$1	1	0	3	9.0000
)))	chr8:47618853-47619073(+)$1	1	30	33	9.0000
(((	chr8:124948867-124949087(-)$1	1	42	45	9.0000
(((	chr11:72635308-72635534(+)$1	1	41	44	9.0000
(((	chr10:67559766-67560007(-)$1	1	136	139	9.0000
((.	chr1:120565193-120565413(+)$1	1	55	58	9.0000
)))	chr11:30753214-30753434(+)$1	1	81	84	9.0000
((.	chr7:51989230-51989450(-)$1	1	16	19	9.0000
.((	chr9:43944804-43945037(+)$1	1	78	81	9.0000
.((	chr4:118295859-118296079(+)$1	1	77	80	9.0000
(((	chr2:127042360-127042596(+)$1	1	6	9	9.0000
.((	chr5:76043704-76043924(+)$1	1	1	4	9.0000
((.	chr2:20728095-20728324(+)$1	1	15	18	9.0000
(((	chr6:13533108-13533328(-)$1	1	29	32	9.0000
...	chr16:20680997-20681217(+)$1	1	6	9	9.0000
...	chr15:100011663-100011883(+)$1	1	43	46	9.0000
)))	chr11:72795148-72795368(+)$1	1	23	26	9.0000
)))	chr1:187239623-187239843(+)$1	1	114	117	9.0000
)))	chr19:35031831-35032051(+)$1	1	78	81	9.0000
(((	chr6:122680030-122680266(-)$1	1	47	50	9.0000
(((	chr2:179909825-179910046(+)$1	1	1	4	9.0000
.((	chr8:13373746-13373976(+)$1	1	101	104	9.0000
.((	chr17:66319420-66319641(-)$1	1	27	30	9.0000
..(	chr9:120032740-120032988(+)$1	1	24	27	9.0000
...	chr5:137464113-137464333(+)$1	1	16	19	9.0000
..(	chr16:31743089-31743309(+)$1	1	26	29	9.0000
))(	chr11:51596180-51596433(+)$1	1	46	49	9.0000
))(	chr8:74143527-74143749(+)$1	1	131	134	9.0000
(((	chr7:148815870-148816092(+)$1	1	1	4	9.0000
(((	chr1:153201656-153201877(+)$1	1	66	69	9.0000
))(	chrX:148493223-148493443(+)$1	1	44	47	9.0000
(((	chr10:80644022-80644257(+)$1	1	36	39	9.0000
(((	chr6:120706674-120706894(+)$1	1	31	34	9.0000
(..	chr7:53338519-53338740(+)$1	1	2	5	9.0000
(((	chr3:153573013-153573233(-)$1	1	5	8	9.0000
(((	chr9:103118030-103118259(-)$1	1	53	56	9.0000
.(.	chr7:152118418-152118638(-)$1	1	2	5	9.0000
(((	chr17:88379477-88379697(+)$1	1	3	6	9.0000
(((	chr13:84361899-84362130(+)$1	1	84	87	9.0000
(((	chr2:104493068-104493288(+)$1	1	12	15	9.0000
)).	chr5:143722070-143722290(+)$1	1	192	195	9.0000
((.	chr5:120122268-120122489(+)$1	1	33	36	9.0000
...	chr15:99138178-99138399(+)$1	1	1	4	9.0000
(((	chr19:4151603-4151823(+)$1	1	70	73	9.0000
(.(	chr13:108516409-108516648(-)$1	1	27	30	9.0000
)).	chr12:60173500-60173741(+)$1	1	94	97	9.0000
((.	chr1:34332529-34332749(+)$1	1	34	37	9.0000
(((	chr12:72274016-72274236(+)$1	1	57	60	9.0000
.((	chr3:59122618-59122838(-)$1	1	18	21	9.0000
((.	chr18:54055483-54055703(+)$1	1	3	6	9.0000
(((	chr12:66068134-66068369(+)$1	1	4	7	9.0000
))(	chr17:23947927-23948150(+)$1	1	132	135	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
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m1_run1.nuc.txt

#NT
GUGCUGCCC	chr8:88078987-88079206(-)$1	219	40	49	11.0740
CAUCUCCCC	chr13:98669615-98669836(-)$1	221	98	107	10.7037
CAGCUGCAG	chr5:44076499-44076714(+)$1	215	111	120	12.0925
AAGCUGUCC	chr17:24401174-24401391(-)$1	217	40	49	10.7962
UCGCUGCCC	chr7:64668990-64669210(-)$1	220	93	102	10.7962
CAGGAGCCC	chr17:36124609-36124832(+)$1	223	93	102	11.3518
CAGGUGCAC	chr3:89041442-89041667(+)$1	225	115	124	11.5370
CAGCUGCCA	chr4:132618550-132618775(-)$1	225	141	150	15.2407
CAGCAGCAC	chr9:108041481-108041720(-)$1	239	64	73	12.1851
CAACUGCCU	chr9:72439480-72439711(+)$1	231	125	134	11.0740
CAGCUGCCC	chr18:34476611-34476846(+)$1	235	124	133	18.4814
CAGCUGAAC	chr12:113016138-113016367(+)$1	229	60	69	11.1666
CUGCUGCUC	chr14:28307237-28307459(+)$1	222	110	119	11.5370
CAGCUGCAC	chr9:108110056-108110280(-)$1	224	188	197	15.4259
CUGCUGCCC	chr11:3622002-3622227(+)$1	225	199	208	14.7777
CAGAUGCCA	chr9:53779243-53779470(-)$1	227	18	27	11.2592
GAGCUGCCC	chr11:94854106-94854333(+)$1	227	151	160	14.7777
AAGCUGCAC	chr15:73435813-73436030(+)$1	217	14	23	11.9074
CAGCUACCU	chr6:113698463-113698690(-)$1	227	104	113	11.4444
CAGCUCCCG	chr17:85471293-85471517(-)$1	224	65	74	11.4444
AGGCUGCCC	chr7:19720714-19720933(-)$1	219	110	119	10.9814
UAGCUGCCC	chr11:70028875-70029096(+)$1	221	183	192	14.7777
CACCUGUCC	chrX:147059592-147059810(+)$1	218	108	117	10.1481
CUGCUGCUC	chr8:23789177-23789400(+)$1	223	185	194	11.5370
UAGCAGCCC	chr6:101101631-101101854(-)$1	223	157	166	11.5370
CAGCACCCC	chr10:80186222-80186442(-)$1	220	71	80	11.5370
CAGCUUCCC	chr17:32513881-32514101(+)$1	220	127	136	14.6851
CAGCUGUUC	chr5:119188894-119189116(-)$1	222	148	157	11.0740
AAGCUGGCC	chr8:86736199-86736425(-)$1	226	77	86	10.6111
CAGCUGACG	chr8:113160233-113160455(+)$1	222	12	21	10.8888
CAGCUUCCC	chr8:108632674-108632901(+)$1	227	22	31	14.6851
CAGCUGCUC	chr11:54740150-54740372(+)$1	222	93	102	15.2407
CAGCGACCC	chr11:3995123-3995344(-)$1	221	148	157	11.2592
CAGGUGCCA	chr19:41121971-41122190(-)$1	219	40	49	11.3518
CACCUCCCC	chr19:4263568-4263805(+)$1	237	128	137	10.6111
CAUCAGCCC	chr5:30080045-30080268(-)$1	223	26	35	11.1666
CAGAUGCCU	chr11:6249051-6249294(+)$1	243	6	15	11.2592
GUGCUGCCC	chr10:75683630-75683855(-)$1	225	56	65	11.0740
CAGCUGCAA	chr15:31537764-31537993(+)$1	229	93	102	12.1851
CAGCUGCCC	chr6:94557999-94558227(-)$1	228	214	223	18.4814
CAGAUGCCG	chr3:5401333-5401553(+)$1	220	21	30	11.1666
AAGCUGCCC	chr11:117887876-117888097(+)$1	221	14	23	14.9629
CCACUGCCC	chr11:119954101-119954324(+)$1	223	52	61	10.3333
CAGCCACCC	chr7:26148617-26148837(-)$1	220	127	136	11.1666
CAGCUGCCU	chr2:164647007-164647231(+)$1	224	59	68	15.2407
CAGCGGCGC	chr18:37604347-37604573(+)$1	226	93	102	11.5370
CAGCGGCCA	chr11:116273914-116274149(-)$1	235	43	52	11.8148
CAGCCUCCC	chr7:3109128-3109357(-)$1	229	30	39	11.1666
CAGGUGCUC	chr13:99998661-99998884(-)$1	223	171	180	11.3518
CAGCAGCCC	chrX:40010729-40010950(-)$1	221	108	117	15.2407
CAGCCGCCU	chr6:148811933-148812174(-)$1	241	128	137	11.7222
CGGCUGCCC	chr12:99921650-99921876(-)$1	226	129	138	14.4999
CAGUGGCCC	chr7:13511011-13511228(+)$1	217	109	118	10.8888

#otherMatches

#Struct PSSM
::EEEEEDD	chr1:90131847-90132063(-)$1	216	2	11	10.8888
FFFFFbbdd	chr8:88078987-88079206(-)$1	219	40	49	11.0740
cccccCCCF	chr13:98669615-98669836(-)$1	221	98	107	10.7037
eccc[====	chr5:44076499-44076714(+)$1	215	111	120	12.0925
D{EEEEE{A	chr17:24401174-24401391(-)$1	217	40	49	10.7962
!!eeeeenn	chr7:64668990-64669210(-)$1	220	93	102	10.7962
eeeeeeeee	chr17:36124609-36124832(+)$1	223	93	102	11.3518
ggggggg]b	chr3:89041442-89041667(+)$1	225	115	124	11.5370
eqqqqqqqq	chr4:132618550-132618775(-)$1	225	141	150	15.2407
::DDDD{CC	chr9:108041481-108041720(-)$1	239	64	73	12.1851
ggggg22cc	chr9:72439480-72439711(+)$1	231	125	134	11.0740
HHHHHHhhh	chr18:34476611-34476846(+)$1	235	124	133	18.4814
c!!ffffff	chr12:113016138-113016367(+)$1	229	60	69	11.1666
ffbb[bb[b	chr14:28307237-28307459(+)$1	222	110	119	11.5370
c[ddddlll	chr9:108110056-108110280(-)$1	224	188	197	15.4259
33cccgggg	chr11:3622002-3622227(+)$1	225	199	208	14.7777
bmmmmbbdd	chr9:53779243-53779470(-)$1	227	18	27	11.2592
fff666666	chr11:94854106-94854333(+)$1	227	151	160	14.7777
qffffff::	chr15:73435813-73436030(+)$1	217	14	23	11.9074
gggggg)))	chr6:113698463-113698690(-)$1	227	104	113	11.4444
ccc!!cccn	chr17:85471293-85471517(-)$1	224	65	74	11.4444
mmmffffff	chr7:19720714-19720933(-)$1	219	110	119	10.9814
FFFFFEEEE	chr11:70028875-70029096(+)$1	221	183	192	14.7777
III:ccchh	chrX:147059592-147059810(+)$1	218	108	117	10.1481
eee!!bb[e	chr8:23789177-23789400(+)$1	223	185	194	11.5370
hhhhhhhbb	chr6:101101631-101101854(-)$1	223	157	166	11.5370
ffffff===	chr10:80186222-80186442(-)$1	220	71	80	11.5370
hhhh[bboo	chr17:32513881-32514101(+)$1	220	127	136	14.6851
g####eeee	chr5:119188894-119189116(-)$1	222	148	157	11.0740
::ffffffl	chr8:86736199-86736425(-)$1	226	77	86	10.6111
::ccc!!ee	chr8:113160233-113160455(+)$1	222	12	21	10.8888
KKFFFFFF:	chr8:108632674-108632901(+)$1	227	22	31	14.6851
::cccqqqq	chr11:54740150-54740372(+)$1	222	93	102	15.2407
c22a]bba]	chr11:3995123-3995344(-)$1	221	148	157	11.2592
c]ccc:CCC	chr19:41121971-41122190(-)$1	219	40	49	11.3518
e[a[ccccc	chr19:4263568-4263805(+)$1	237	128	137	10.6111
pppppccc:	chr5:30080045-30080268(-)$1	223	26	35	11.1666
""dddd[cc	chr11:6249051-6249294(+)$1	243	6	15	11.2592
ee:eeeeeo	chr10:75683630-75683855(-)$1	225	56	65	11.0740
bb]cccbb]	chr15:31537764-31537993(+)$1	229	93	102	12.1851
YYFFFFFF:	chr6:94557999-94558227(-)$1	228	214	223	18.4814
::::DDDDF	chr3:5401333-5401553(+)$1	220	21	30	11.1666
eebb[dddd	chr11:117887876-117888097(+)$1	221	14	23	14.9629
$$$$$dddd	chr11:119954101-119954324(+)$1	223	52	61	10.3333
d!!bb!!a[	chr7:26148617-26148837(-)$1	220	127	136	11.1666
qqaffffff	chr2:164647007-164647231(+)$1	224	59	68	15.2407
bb]ccc]gg	chr18:37604347-37604573(+)$1	226	93	102	11.5370
ccc[ddddn	chr11:116273914-116274149(-)$1	235	43	52	11.8148
mmeeeee55	chr7:3109128-3109357(-)$1	229	30	39	11.1666
c]a]=====	chr13:99998661-99998884(-)$1	223	171	180	11.3518
gg4444bbb	chrX:40010729-40010950(-)$1	221	108	117	15.2407
[cccqqqqq	chr6:148811933-148812174(-)$1	241	128	137	11.7222
6ggggggg:	chr12:99921650-99921876(-)$1	226	129	138	14.4999
:::ffffff	chr7:13511011-13511228(+)$1	217	109	118	10.8888

#DB
..(((((((	chr1:90131847-90132063(-)$1	1	2	11	10.8888
(((((((((	chr8:88078987-88079206(-)$1	1	40	49	11.0740
)))))))))	chr13:98669615-98669836(-)$1	1	98	107	10.7037
)(((.((((	chr5:44076499-44076714(+)$1	1	111	120	12.0925
(.(((((.(	chr17:24401174-24401391(-)$1	1	40	49	10.7962
..(((((..	chr7:64668990-64669210(-)$1	1	93	102	10.7962
(((((((((	chr17:36124609-36124832(+)$1	1	93	102	11.3518
))))))).)	chr3:89041442-89041667(+)$1	1	115	124	11.5370
(........	chr4:132618550-132618775(-)$1	1	141	150	15.2407
..((((.((	chr9:108041481-108041720(-)$1	1	64	73	12.1851
)))))..))	chr9:72439480-72439711(+)$1	1	125	134	11.0740
(((((((((	chr18:34476611-34476846(+)$1	1	124	133	18.4814
(..((((((	chr12:113016138-113016367(+)$1	1	60	69	11.1666
((((.((.(	chr14:28307237-28307459(+)$1	1	110	119	11.5370
(.((((...	chr9:108110056-108110280(-)$1	1	188	197	15.4259
..)))))))	chr11:3622002-3622227(+)$1	1	199	208	14.7777
(....))((	chr9:53779243-53779470(-)$1	1	18	27	11.2592
)))......	chr11:94854106-94854333(+)$1	1	151	160	14.7777
.))))))..	chr15:73435813-73436030(+)$1	1	14	23	11.9074
((((((...	chr6:113698463-113698690(-)$1	1	104	113	11.4444
(((..(((.	chr17:85471293-85471517(-)$1	1	65	74	11.4444
...))))))	chr7:19720714-19720933(-)$1	1	110	119	10.9814
)))))))))	chr11:70028875-70029096(+)$1	1	183	192	14.7777
))).(((((	chrX:147059592-147059810(+)$1	1	108	117	10.1481
(((..((.(	chr8:23789177-23789400(+)$1	1	185	194	11.5370
(((((((((	chr6:101101631-101101854(-)$1	1	157	166	11.5370
)))))))))	chr10:80186222-80186442(-)$1	1	71	80	11.5370
((((.((..	chr17:32513881-32514101(+)$1	1	127	136	14.6851
(....((((	chr5:119188894-119189116(-)$1	1	148	157	11.0740
..((((((.	chr8:86736199-86736425(-)$1	1	77	86	10.6111
..(((..((	chr8:113160233-113160455(+)$1	1	12	21	10.8888
..((((((.	chr8:108632674-108632901(+)$1	1	22	31	14.6851
..(((....	chr11:54740150-54740372(+)$1	1	93	102	15.2407
)..).))).	chr11:3995123-3995344(-)$1	1	148	157	11.2592
).))).(((	chr19:41121971-41122190(-)$1	1	40	49	11.3518
(.(.(((((	chr19:4263568-4263805(+)$1	1	128	137	10.6111
.....))).	chr5:30080045-30080268(-)$1	1	26	35	11.1666
..((((.((	chr11:6249051-6249294(+)$1	1	6	15	11.2592
)).(((((.	chr10:75683630-75683855(-)$1	1	56	65	11.0740
)).))))).	chr15:31537764-31537993(+)$1	1	93	102	12.1851
..)))))).	chr6:94557999-94558227(-)$1	1	214	223	18.4814
....(((((	chr3:5401333-5401553(+)$1	1	21	30	11.1666
((((.((((	chr11:117887876-117888097(+)$1	1	14	23	14.9629
.....((((	chr11:119954101-119954324(+)$1	1	52	61	10.3333
(..((..(.	chr7:26148617-26148837(-)$1	1	127	136	11.1666
..)))))))	chr2:164647007-164647231(+)$1	1	59	68	15.2407
)).))).))	chr18:37604347-37604573(+)$1	1	93	102	11.5370
(((.((((.	chr11:116273914-116274149(-)$1	1	43	52	11.8148
..)))))..	chr7:3109128-3109357(-)$1	1	30	39	11.1666
).).)))))	chr13:99998661-99998884(-)$1	1	171	180	11.3518
))....)))	chrX:40010729-40010950(-)$1	1	108	117	15.2407
.(((.....	chr6:148811933-148812174(-)$1	1	128	137	11.7222
.))))))).	chr12:99921650-99921876(-)$1	1	129	138	14.4999
...((((((	chr7:13511011-13511228(+)$1	1	109	118	10.8888

#PSSM
C : 0.79	A : 0.09	G : 0.05	U : 0.05	
A : 0.83	U : 0.09	C : 0.03	G : 0.03	
G : 0.87	U : 0.05	A : 0.03	C : 0.03	
C : 0.85	G : 0.07	A : 0.05	U : 0.01	
U : 0.75	A : 0.11	G : 0.07	C : 0.05	
G : 0.81	C : 0.07	A : 0.05	U : 0.05	
C : 0.88	U : 0.05	A : 0.03	G : 0.01	
C : 0.74	A : 0.12	U : 0.09	G : 0.03	
C : 0.74	A : 0.09	U : 0.09	G : 0.07	

#score	666.1481481481474
#seq	54
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m1_run1.nuc.txt

#NT
UUUAUGUUU	chr14:21319606-21319809(-)$1	203	113	122	15.2608
UUUCUUUGU	chr19:7500515-7500715(-)$1	200	90	99	16.3478
UUUCUUUUU	chr1:75143894-75144101(+)$1	207	68	77	20.6956
UUUCUUCUU	chr17:87397601-87397814(+)$1	213	122	131	16.5652
UUUCUUCUU	chr16:43630023-43630239(+)$1	216	47	56	16.5652
UUUCUUUCU	chr5:102339864-102340067(-)$1	203	165	174	16.5652
UUGCUUUUU	chr7:126117223-126117423(-)$1	200	110	119	15.9130
UUUUUUUUU	chr8:70220505-70220726(-)$1	221	173	182	19.2826
UUUGAUUUU	chr7:149189740-149189954(-)$1	214	25	34	15.5869
UUUUUUUUU	chr11:118941454-118941657(+)$1	203	132	141	19.2826
UUUAUUUUU	chr16:17045195-17045401(+)$1	206	56	65	19.6086
UUUCUUUAU	chrX:33709698-33709910(+)$1	212	42	51	16.3478
UGUCUUUUU	chr9:28728504-28728712(+)$1	208	188	197	16.0217
UUUUUUUUU	chr19:26852481-26852681(+)$1	200	73	82	19.2826
UUUCUUUUU	chr1:179380315-179380515(+)$1	200	24	33	20.6956
auuauuuuu	chr11:97067172-97067372(+)$1	200	24	33	15.3695
UUUUUUUUU	chr10:74645946-74646147(+)$1	201	175	184	19.2826
UUUCAUUUU	chr17:44233265-44233473(-)$1	208	3	12	16.7826
UUUCGUUUU	chr4:85034949-85035152(+)$1	203	118	127	16.7826
UUUAUUGUU	chr2:59683637-59683848(+)$1	211	30	39	15.5869
UUUUUUAUU	chr6:47249321-47249521(+)$1	200	0	9	15.0434
UUUAUUGUU	chr10:67349566-67349767(-)$1	201	50	59	15.5869
UUUGGUUUU	chr11:87794730-87794931(+)$1	201	38	47	15.5869
UUUAUUUUG	chr4:126421241-126421441(-)$1	200	72	81	15.0434
Guuuuuuuu	chr17:85463812-85464013(-)$1	201	109	118	14.8260
UUUAUUUUC	chr5:65558809-65559012(-)$1	203	105	114	15.1521
UUUCUUUCU	chr1:136656272-136656493(-)$1	221	133	142	16.5652
UUUAUUUUU	chr12:30605780-30605983(+)$1	203	96	105	19.6086
UUUCAUUUU	chr7:118214891-118215096(-)$1	205	102	111	16.7826
UUUCGUUUU	chrX:10173410-10173629(+)$1	219	106	115	16.7826
UUUCUCUUU	chr18:58106140-58106356(+)$1	216	54	63	16.3478
AUUGUUUUU	chr8:82208584-82208794(-)$1	210	188	197	15.2608
UUUAUCUUU	chr8:109896390-109896592(+)$1	202	32	41	15.2608
AUUGUUUUU	chr6:126051468-126051695(-)$1	227	24	33	15.2608
uUUCUUUUU	chr3:94304586-94304788(-)$1	202	66	75	20.6956
UUUGUUUUU	chrX:35549956-35550167(-)$1	211	182	191	19.4999
UUUAUUUUC	chr3:54939668-54939881(+)$1	213	138	147	15.1521
UUUCCUUUU	chr4:138013733-138013934(+)$1	201	10	19	16.5652
UUUCUUGUU	chr5:38660572-38660774(+)$1	202	160	169	16.6739
UUUGUUUUU	chr1:82748422-82748625(+)$1	203	114	123	19.4999
UUUGUUUUU	chr5:148375612-148375821(-)$1	209	138	147	19.4999
UUUGUUUUU	chr9:62641535-62641753(-)$1	218	129	138	19.4999
UUUCUUUCU	chr15:63762241-63762444(-)$1	203	27	36	16.5652
UUUGUGUUU	chr1:23373777-23373977(-)$1	200	76	85	15.1521
UCUCUUUUU	chr2:52991044-52991247(+)$1	203	57	66	16.0217

#otherMatches

#Struct PSSM
:::::::::	chr5:136384722-136384923(-)$1	201	183	192	19.2826
xxxxxxxxx	chr14:21319606-21319809(-)$1	203	113	122	15.2608
yyyyyyyyy	chr19:7500515-7500715(-)$1	200	90	99	16.3478
:::::::::	chr1:75143894-75144101(+)$1	207	68	77	20.6956
ff22hhhhh	chr17:87397601-87397814(+)$1	213	122	131	16.5652
+++++++++	chr16:43630023-43630239(+)$1	216	47	56	16.5652
nccc]bb22	chr5:102339864-102340067(-)$1	203	165	174	16.5652
oobb333cc	chr7:126117223-126117423(-)$1	200	110	119	15.9130
dddd%%%%%	chr8:70220505-70220726(-)$1	221	173	182	19.2826
FFFKKFFFF	chr7:149189740-149189954(-)$1	214	25	34	15.5869
:::::::::	chr11:118941454-118941657(+)$1	203	132	141	19.2826
=========	chr16:17045195-17045401(+)$1	206	56	65	19.6086
[ccc%%%%%	chrX:33709698-33709910(+)$1	212	42	51	16.3478
:::::::::	chr9:28728504-28728712(+)$1	208	188	197	16.0217
=========	chr19:26852481-26852681(+)$1	200	73	82	19.2826
++bb!!fff	chr1:179380315-179380515(+)$1	200	24	33	20.6956
ammmma22f	chr11:97067172-97067372(+)$1	200	24	33	15.3695
:::::::::	chr10:74645946-74646147(+)$1	201	175	184	19.2826
:::::::::	chr17:44233265-44233473(-)$1	208	3	12	16.7826
gggggg[cc	chr4:85034949-85035152(+)$1	203	118	127	16.7826
:::::::::	chr2:59683637-59683848(+)$1	211	30	39	15.5869
:::::::::	chr6:47249321-47249521(+)$1	200	0	9	15.0434
!ccc!!eee	chr10:67349566-67349767(-)$1	201	50	59	15.5869
hhhhhhh::	chr11:87794730-87794931(+)$1	201	38	47	15.5869
'''''''dd	chr4:126421241-126421441(-)$1	200	72	81	15.0434
bb$$$$$ff	chr17:85463812-85464013(-)$1	201	109	118	14.8260
JJJJJJJJJ	chr5:65558809-65559012(-)$1	203	105	114	15.1521
dddd$$$$$	chr1:136656272-136656493(-)$1	221	133	142	16.5652
rrrrfffff	chr12:30605780-30605983(+)$1	203	96	105	19.6086
FFFFFYYGG	chr7:118214891-118215096(-)$1	205	102	111	16.7826
=========	chrX:10173410-10173629(+)$1	219	106	115	16.7826
$$$$$a!!d	chr18:58106140-58106356(+)$1	216	54	63	16.3478
eeeemmmme	chr8:82208584-82208794(-)$1	210	188	197	15.2608
^^^^^^^^^	chr8:109896390-109896592(+)$1	202	32	41	15.2608
eeee!!===	chr6:126051468-126051695(-)$1	227	24	33	15.2608
JJJJJJJJJ	chr3:94304586-94304788(-)$1	202	66	75	20.6956
DYYEEEEEZ	chrX:35549956-35550167(-)$1	211	182	191	19.4999
hhhccc###	chr3:54939668-54939881(+)$1	213	138	147	15.1521
e!!dddd##	chr4:138013733-138013934(+)$1	201	10	19	16.5652
deeeee]cc	chr5:38660572-38660774(+)$1	202	160	169	16.6739
ggg[bbmmm	chr1:82748422-82748625(+)$1	203	114	123	19.4999
5eeeee444	chr5:148375612-148375821(-)$1	209	138	147	19.4999
>>>>>>>>e	chr9:62641535-62641753(-)$1	218	129	138	19.4999
:HHHHHHHH	chr15:63762241-63762444(-)$1	203	27	36	16.5652
gg:dddd[c	chr1:23373777-23373977(-)$1	200	76	85	15.1521
eqqqqqqqq	chr2:52991044-52991247(+)$1	203	57	66	16.0217

#DB
.........	chr5:136384722-136384923(-)$1	1	183	192	19.2826
.........	chr14:21319606-21319809(-)$1	1	113	122	15.2608
.........	chr19:7500515-7500715(-)$1	1	90	99	16.3478
.........	chr1:75143894-75144101(+)$1	1	68	77	20.6956
))..)))))	chr17:87397601-87397814(+)$1	1	122	131	16.5652
.........	chr16:43630023-43630239(+)$1	1	47	56	16.5652
.))).))..	chr5:102339864-102340067(-)$1	1	165	174	16.5652
..))...))	chr7:126117223-126117423(-)$1	1	110	119	15.9130
((((.....	chr8:70220505-70220726(-)$1	1	173	182	19.2826
(((..((((	chr7:149189740-149189954(-)$1	1	25	34	15.5869
.........	chr11:118941454-118941657(+)$1	1	132	141	19.2826
(((((((((	chr16:17045195-17045401(+)$1	1	56	65	19.6086
.(((.....	chrX:33709698-33709910(+)$1	1	42	51	16.3478
.........	chr9:28728504-28728712(+)$1	1	188	197	16.0217
)))))))))	chr19:26852481-26852681(+)$1	1	73	82	19.2826
..((..(((	chr1:179380315-179380515(+)$1	1	24	33	20.6956
(....)..)	chr11:97067172-97067372(+)$1	1	24	33	15.3695
.........	chr10:74645946-74646147(+)$1	1	175	184	19.2826
.........	chr17:44233265-44233473(-)$1	1	3	12	16.7826
((((((.((	chr4:85034949-85035152(+)$1	1	118	127	16.7826
.........	chr2:59683637-59683848(+)$1	1	30	39	15.5869
.........	chr6:47249321-47249521(+)$1	1	0	9	15.0434
.(((..(((	chr10:67349566-67349767(-)$1	1	50	59	15.5869
)))))))..	chr11:87794730-87794931(+)$1	1	38	47	15.5869
.......((	chr4:126421241-126421441(-)$1	1	72	81	15.0434
((.....((	chr17:85463812-85464013(-)$1	1	109	118	14.8260
)))))))))	chr5:65558809-65559012(-)$1	1	105	114	15.1521
((((.....	chr1:136656272-136656493(-)$1	1	133	142	16.5652
....)))))	chr12:30605780-30605983(+)$1	1	96	105	19.6086
)))))..))	chr7:118214891-118215096(-)$1	1	102	111	16.7826
(((((((((	chrX:10173410-10173629(+)$1	1	106	115	16.7826
.....(..(	chr18:58106140-58106356(+)$1	1	54	63	16.3478
((((....)	chr8:82208584-82208794(-)$1	1	188	197	15.2608
.........	chr8:109896390-109896592(+)$1	1	32	41	15.2608
((((..(((	chr6:126051468-126051695(-)$1	1	24	33	15.2608
(((((((((	chr3:94304586-94304788(-)$1	1	66	75	20.6956
)..))))).	chrX:35549956-35550167(-)$1	1	182	191	19.4999
((((((...	chr3:54939668-54939881(+)$1	1	138	147	15.1521
(..((((..	chr4:138013733-138013934(+)$1	1	10	19	16.5652
)))))).))	chr5:38660572-38660774(+)$1	1	160	169	16.6739
(((.((...	chr1:82748422-82748625(+)$1	1	114	123	19.4999
.)))))...	chr5:148375612-148375821(-)$1	1	138	147	19.4999
........)	chr9:62641535-62641753(-)$1	1	129	138	19.4999
.((((((((	chr15:63762241-63762444(-)$1	1	27	36	16.5652
)).((((.(	chr1:23373777-23373977(-)$1	1	76	85	15.1521
(........	chr2:52991044-52991247(+)$1	1	57	66	16.0217

#PSSM
U : 0.86	u : 0.04	A : 0.04	a : 0.02	G : 0.02	
U : 0.89	u : 0.06	G : 0.02	C : 0.02	
U : 0.91	u : 0.06	G : 0.02	
C : 0.43	A : 0.19	G : 0.19	U : 0.10	u : 0.04	a : 0.02	
U : 0.78	u : 0.06	A : 0.06	G : 0.06	C : 0.02	
U : 0.84	u : 0.06	G : 0.04	C : 0.04	
U : 0.80	u : 0.06	G : 0.06	C : 0.04	A : 0.02	
U : 0.82	u : 0.06	C : 0.06	G : 0.02	A : 0.02	
U : 0.86	u : 0.06	C : 0.04	G : 0.02	

#score	785.0434782608693
#seq	46
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_transcript_m3_run2.nuc.txt

#NT
UCuuucuuu	chr16:8849515-8849755(+)$1	240	66	75	14.7083
UGUUUGUUU	chr11:87033468-87033727(+)$1	259	111	120	18.2500
uuuuugguu	chr17:24212691-24212937(-)$1	246	224	233	17.3125
UUUUUUUUU	chr11:4382365-4382603(-)$1	238	59	68	18.9791
UUUGUGUUU	chr3:31017468-31017706(+)$1	238	105	114	18.2500
GUUUUGUUU	chr6:17237501-17237740(+)$1	239	105	114	19.1875
UUUUUUUUU	chr5:69968056-69968291(-)$1	235	153	162	18.9791
AUUUUUUUU	chr16:84954883-84955167(-)$1	284	247	256	15.9583
UUUUUGUUG	chr14:63761672-63761934(+)$1	262	221	230	17.8333
AUUUUCUUU	chr2:37225966-37226213(-)$1	247	101	110	15.4375
UUUUUAUUU	chr3:80647668-80647903(-)$1	235	14	23	18.4583
uuuuuguuu	chr11:97577850-97578106(-)$1	256	8	17	22.1041
GUUUUGUUU	chr6:23213209-23213446(-)$1	237	153	162	19.1875
UUUUUGUUU	chr5:144266769-144267004(-)$1	235	179	188	22.1041
UUUUUGUUU	chr15:58772862-58773120(-)$1	258	227	236	22.1041
AUUUUGUUU	chr8:41532325-41532562(+)$1	237	58	67	19.0833
uuguuguuu	chr11:41724655-41724934(-)$1	279	70	79	17.6250
UUUGUGUUU	chr1:23373790-23374025(-)$1	235	124	133	18.2500
UCUUUGUUU	chr7:52085518-52085779(+)$1	261	73	82	18.3541
AAUUUGUUU	chr4:154931883-154932126(+)$1	243	143	152	15.0208
GUUUUUUUU	chr7:11073285-11073520(-)$1	235	183	192	16.0625
Uuuuuguuu	chr7:66561836-66562082(+)$1	246	57	66	22.1041
UUUUUUUUU	chr6:108772299-108772537(+)$1	238	17	26	18.9791
UUUCUGUUU	chr19:29686065-29686312(-)$1	247	124	133	18.1458
UCUGUGUUU	chr2:180837845-180838086(-)$1	241	120	129	14.5000
UGUUUGUUu	chr19:47697376-47697611(+)$1	235	160	169	18.2500
UUUUUGUUU	chr7:105060692-105060952(+)$1	260	228	237	22.1041
UUUUUGUUG	chr9:25115060-25115324(+)$1	264	208	217	17.8333
AUUUUAUUU	chr5:122906185-122906440(-)$1	255	222	231	15.4375
UUUUUGUUU	chr19:59373408-59373647(-)$1	239	171	180	22.1041
UUUCUGUUU	chr17:57219415-57219652(-)$1	237	169	178	18.1458
UUUUUGUUU	chr5:44136205-44136448(-)$1	243	98	107	22.1041
guuuuguuu	chr1:179379112-179379354(+)$1	242	42	51	19.1875
GUUUUGUUU	chr4:15210855-15211098(+)$1	243	71	80	19.1875
UUUUUGUUG	chr11:74488130-74488365(-)$1	235	210	219	17.8333
UUUGUGUUU	chr6:77223749-77223987(-)$1	238	133	142	18.2500
GCUUUGUUU	chr1:58584832-58585086(-)$1	254	14	23	15.4375
UUUUUGUUC	chr2:44843181-44843416(-)$1	235	208	217	17.6250
UUCUUGUUU	chr8:75700736-75700985(-)$1	249	105	114	17.5208
GUUUUGUUU	chr19:29678975-29679216(+)$1	241	52	61	19.1875
UUUUUUUUU	chr5:77515979-77516221(-)$1	242	220	229	18.9791
UUUUUGUUU	chr9:75067472-75067746(+)$1	274	123	132	22.1041
UUUUUGUUU	chr4:138847504-138847739(+)$1	235	88	97	22.1041
AGUUUGUUU	chrX:8886941-8887183(+)$1	242	100	109	15.2291
UUUUUUUUU	chr6:11850322-11850557(-)$1	235	133	142	18.9791
uuuuuguuu	chr4:47483833-47484095(-)$1	262	197	206	22.1041
UUGUUGUUU	chr4:47482667-47482910(-)$1	243	114	123	17.6250

#otherMatches

#Struct PSSM
DDD::::::	chr5:125935504-125935739(+)$1	235	196	205	18.1458
]bb]fffff	chr16:8849515-8849755(+)$1	240	66	75	14.7083
a]=======	chr11:87033468-87033727(+)$1	259	111	120	18.2500
5555bbfff	chr17:24212691-24212937(-)$1	246	224	233	17.3125
=========	chr11:4382365-4382603(-)$1	238	59	68	18.9791
44ggggggg	chr3:31017468-31017706(+)$1	238	105	114	18.2500
mmffffff:	chr6:17237501-17237740(+)$1	239	105	114	19.1875
++++++++d	chr5:69968056-69968291(-)$1	235	153	162	18.9791
:::::::::	chr16:84954883-84955167(-)$1	284	247	256	15.9583
eeeee]bb]	chr14:63761672-63761934(+)$1	262	221	230	17.8333
DDddddfff	chr2:37225966-37226213(-)$1	247	101	110	15.4375
:::eeeee!	chr3:80647668-80647903(-)$1	235	14	23	18.4583
:::::::::	chr11:97577850-97578106(-)$1	256	8	17	22.1041
ggggfffff	chr6:23213209-23213446(-)$1	237	153	162	19.1875
333ffffff	chr5:144266769-144267004(-)$1	235	179	188	22.1041
eeeennnnn	chr15:58772862-58773120(-)$1	258	227	236	22.1041
fffff6666	chr8:41532325-41532562(+)$1	237	58	67	19.0833
"eeeeezzz	chr11:41724655-41724934(-)$1	279	70	79	17.6250
gg:dddd[c	chr1:23373790-23374025(-)$1	235	124	133	18.2500
[ffffffff	chr7:52085518-52085779(+)$1	261	73	82	18.3541
iiiiiiiii	chr4:154931883-154932126(+)$1	243	143	152	15.0208
dqqqqqqqq	chr7:11073285-11073520(-)$1	235	183	192	16.0625
>>>>>>>>>	chr7:66561836-66562082(+)$1	246	57	66	22.1041
iiiiiuuuu	chr6:108772299-108772537(+)$1	238	17	26	18.9791
e]ccc6666	chr19:29686065-29686312(-)$1	247	124	133	18.1458
}CCC}CCCF	chr2:180837845-180838086(-)$1	241	120	129	14.5000
JJJJJJJJ:	chr19:47697376-47697611(+)$1	235	160	169	18.2500
:::::::::	chr7:105060692-105060952(+)$1	260	228	237	22.1041
=========	chr9:25115060-25115324(+)$1	264	208	217	17.8333
iiiii::::	chr5:122906185-122906440(-)$1	255	222	231	15.4375
22eeeee>>	chr19:59373408-59373647(-)$1	239	171	180	22.1041
c::::::::	chr17:57219415-57219652(-)$1	237	169	178	18.1458
fffffqqqq	chr5:44136205-44136448(-)$1	243	98	107	22.1041
EEEEECCCF	chr1:179379112-179379354(+)$1	242	42	51	19.1875
cccoooooo	chr4:15210855-15211098(+)$1	243	71	80	19.1875
:::::::::	chr11:74488130-74488365(-)$1	235	210	219	17.8333
eeeee[eee	chr6:77223749-77223987(-)$1	238	133	142	18.2500
fflllffff	chr1:58584832-58585086(-)$1	254	14	23	15.4375
c22eeeee3	chr2:44843181-44843416(-)$1	235	208	217	17.6250
nndddd::C	chr8:75700736-75700985(-)$1	249	105	114	17.5208
i333ccc22	chr19:29678975-29679216(+)$1	241	52	61	19.1875
c========	chr5:77515979-77516221(-)$1	242	220	229	18.9791
pppppeeee	chr9:75067472-75067746(+)$1	274	123	132	22.1041
HHHHHKKHH	chr4:138847504-138847739(+)$1	235	88	97	22.1041
ccc22eeee	chrX:8886941-8887183(+)$1	242	100	109	15.2291
gggg:::::	chr6:11850322-11850557(-)$1	235	133	142	18.9791
IIIIIIII}	chr4:47483833-47484095(-)$1	262	197	206	22.1041
qqffffff3	chr4:47482667-47482910(-)$1	243	114	123	17.6250

#DB
)))......	chr5:125935504-125935739(+)$1	1	196	205	18.1458
.)).)))))	chr16:8849515-8849755(+)$1	1	66	75	14.7083
).)))))))	chr11:87033468-87033727(+)$1	1	111	120	18.2500
....)))))	chr17:24212691-24212937(-)$1	1	224	233	17.3125
)))))))))	chr11:4382365-4382603(-)$1	1	59	68	18.9791
..)))))))	chr3:31017468-31017706(+)$1	1	105	114	18.2500
..)))))).	chr6:17237501-17237740(+)$1	1	105	114	19.1875
........(	chr5:69968056-69968291(-)$1	1	153	162	18.9791
.........	chr16:84954883-84955167(-)$1	1	247	256	15.9583
))))).)).	chr14:63761672-63761934(+)$1	1	221	230	17.8333
(((((((((	chr2:37225966-37226213(-)$1	1	101	110	15.4375
...(((((.	chr3:80647668-80647903(-)$1	1	14	23	18.4583
.........	chr11:97577850-97578106(-)$1	1	8	17	22.1041
)))))))))	chr6:23213209-23213446(-)$1	1	153	162	19.1875
...))))))	chr5:144266769-144267004(-)$1	1	179	188	22.1041
((((.....	chr15:58772862-58773120(-)$1	1	227	236	22.1041
)))))....	chr8:41532325-41532562(+)$1	1	58	67	19.0833
.(((((...	chr11:41724655-41724934(-)$1	1	70	79	17.6250
)).((((.(	chr1:23373790-23374025(-)$1	1	124	133	18.2500
.((((((((	chr7:52085518-52085779(+)$1	1	73	82	18.3541
)))))))))	chr4:154931883-154932126(+)$1	1	143	152	15.0208
(........	chr7:11073285-11073520(-)$1	1	183	192	16.0625
.........	chr7:66561836-66562082(+)$1	1	57	66	22.1041
(((((....	chr6:108772299-108772537(+)$1	1	17	26	18.9791
).)))....	chr19:29686065-29686312(-)$1	1	124	133	18.1458
.))).))))	chr2:180837845-180838086(-)$1	1	120	129	14.5000
)))))))).	chr19:47697376-47697611(+)$1	1	160	169	18.2500
.........	chr7:105060692-105060952(+)$1	1	228	237	22.1041
)))))))))	chr9:25115060-25115324(+)$1	1	208	217	17.8333
)))))....	chr5:122906185-122906440(-)$1	1	222	231	15.4375
..)))))..	chr19:59373408-59373647(-)$1	1	171	180	22.1041
)........	chr17:57219415-57219652(-)$1	1	169	178	18.1458
(((((....	chr5:44136205-44136448(-)$1	1	98	107	22.1041
(((((((((	chr1:179379112-179379354(+)$1	1	42	51	19.1875
(((......	chr4:15210855-15211098(+)$1	1	71	80	19.1875
.........	chr11:74488130-74488365(-)$1	1	210	219	17.8333
(((((.(((	chr6:77223749-77223987(-)$1	1	133	142	18.2500
((...))))	chr1:58584832-58585086(-)$1	1	14	23	15.4375
)..))))).	chr2:44843181-44843416(-)$1	1	208	217	17.6250
..))))..)	chr8:75700736-75700985(-)$1	1	105	114	17.5208
)...)))..	chr19:29678975-29679216(+)$1	1	52	61	19.1875
)))))))))	chr5:77515979-77516221(-)$1	1	220	229	18.9791
.....))))	chr9:75067472-75067746(+)$1	1	123	132	22.1041
(((((..((	chr4:138847504-138847739(+)$1	1	88	97	22.1041
)))..))))	chrX:8886941-8887183(+)$1	1	100	109	15.2291
)))).....	chr6:11850322-11850557(-)$1	1	133	142	18.9791
)))))))).	chr4:47483833-47484095(-)$1	1	197	206	22.1041
..)))))).	chr4:47482667-47482910(-)$1	1	114	123	17.6250

#PSSM
U : 0.64	G : 0.12	A : 0.12	u : 0.08	g : 0.02	
U : 0.70	u : 0.12	C : 0.08	G : 0.06	A : 0.02	
U : 0.81	u : 0.12	g : 0.02	C : 0.02	G : 0.02	
U : 0.70	u : 0.14	G : 0.08	C : 0.06	
U : 0.85	u : 0.14	
G : 0.64	U : 0.14	g : 0.12	A : 0.04	c : 0.02	C : 0.02	
U : 0.85	u : 0.12	g : 0.02	
U : 0.85	u : 0.14	
U : 0.75	u : 0.16	G : 0.06	C : 0.02	

#score	892.4583333333333
#seq	48
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m3_run1.nuc.txt

#NT
GGAGAAC	chr6:67227651-67228037(+)$1	386	103	110	12.6666
ggugaag	chr6:22952048-22952316(+)$1	268	133	140	13.1428
GUAGAAG	chr3:106342304-106342578(-)$1	274	112	119	13.0634
GGACAAG	chr17:33958657-33958940(+)$1	283	127	134	12.2698
GAAGAAG	chr5:100821866-100822144(-)$1	278	214	221	13.6190
CGAGAAG	chr7:3655828-3656103(+)$1	275	184	191	13.1428
GGAGGAG	chr13:51740714-51740990(+)$1	276	141	148	13.4603
GGAGAAG	chr19:41330559-41330831(-)$1	272	139	146	17.1111
GAAGAAG	chr12:110698424-110698692(+)$1	268	28	35	13.6190
ggagaaa	chr13:67926463-67926737(+)$1	274	46	53	12.9047
GGAGAAA	chr4:33333324-33333602(-)$1	278	146	153	12.9047
GGAGAAG	chr8:107858490-107858759(-)$1	269	93	100	17.1111
GGGGAAG	chr19:6454986-6455255(+)$1	269	131	138	13.1428
GGAGGAG	chr5:136265477-136265767(+)$1	290	224	231	13.4603
GGAGGAG	chr3:104585431-104585713(+)$1	282	158	165	13.4603
UGAGAAG	chr15:84770080-84770413(+)$1	333	95	102	13.2222
GGGGAAG	chr10:127525950-127526220(+)$1	270	208	215	13.1428
GGAGAAG	chr15:79749263-79749566(-)$1	303	163	170	17.1111
GGAGCAG	chr1:137326799-137327084(-)$1	285	208	215	13.1428
GGCGAAG	chr12:85015957-85016241(+)$1	284	170	177	12.9047
GGAGAAG	chr4:116283706-116283999(-)$1	293	138	145	17.1111
GGAGAAG	chr12:16586551-16586820(-)$1	269	94	101	17.1111
GAAGAAG	chr7:29108662-29108941(-)$1	279	146	153	13.6190
GAAGAAG	chr2:53009572-53009852(-)$1	280	106	113	13.6190
AGAGAAG	chr2:151369514-151369795(+)$1	281	232	239	13.1428
UGAGAAG	chr7:19628752-19629027(+)$1	275	138	145	13.2222
GGGGAAG	chr5:72915766-72916034(-)$1	268	136	143	13.1428
GGAGAAG	chr15:77597848-77598177(-)$1	329	95	102	17.1111
GGAGAAG	chr16:20688738-20689030(+)$1	292	83	90	17.1111
AGAGAAG	chr8:87366519-87366802(-)$1	283	64	71	13.1428
GGAGAAG	chr9:111116607-111116895(+)$1	288	154	161	17.1111
GGAGGAG	chr2:119635065-119635355(+)$1	290	276	283	13.4603
GGAGAAG	chr8:33028504-33028779(-)$1	275	240	247	17.1111
GAAGAAG	chr11:68598637-68598922(+)$1	285	144	151	13.6190
AGAGAAG	chr2:125082482-125082762(+)$1	280	163	170	13.1428
GGAGAAG	chr16:90931165-90931435(-)$1	270	129	136	17.1111
GGAGAAG	chr7:34931135-34931405(-)$1	270	223	230	17.1111
CGAGAAG	chr4:40163246-40163522(-)$1	276	83	90	13.1428
GGGGAAG	chr8:97349000-97349279(-)$1	279	129	136	13.1428
GAAGAAG	chr5:30690889-30691157(-)$1	268	93	100	13.6190
GGAGGAG	chr12:109924500-109924773(+)$1	273	125	132	13.4603
UGAGAAG	chr17:88386043-88386321(+)$1	278	138	145	13.2222
GCAGAAG	chr17:88384478-88384828(+)$1	350	98	105	13.1428
GAAGAAG	chr4:125911254-125911534(-)$1	280	10	17	13.6190
GGAGAAA	chr8:96703593-96703882(+)$1	289	5	12	12.9047
ggagacg	chr10:45138737-45139017(-)$1	280	5	12	12.3492
GGAGAAU	chr11:6197028-6197301(+)$1	273	149	156	12.6666
GGUGAAG	chr9:107560193-107560461(-)$1	268	175	182	13.1428
GGUGAAG	chr3:41408435-41408711(+)$1	276	109	116	13.1428
GGAGAAG	chr9:44656894-44657162(-)$1	268	99	106	17.1111
GGAGAAG	chr15:76499574-76499865(-)$1	291	7	14	17.1111
CGAGAAG	chr5:123805890-123806164(+)$1	274	88	95	13.1428
GGAGGAG	chr11:106063360-106063635(-)$1	275	61	68	13.4603
GAAGAAG	chr8:87200184-87200473(-)$1	289	137	144	13.6190
GCAGAAG	chr12:8348644-8348917(+)$1	273	149	156	13.1428
GGAGGAG	chr9:21222610-21222887(+)$1	277	164	171	13.4603
GGUGAAG	chr5:135906001-135906277(-)$1	276	98	105	13.1428
GGAGAAA	chrX:7508483-7508760(-)$1	277	31	38	12.9047
GGAGAGG	chr5:147023261-147023539(-)$1	278	237	244	12.3492
GGAGCAG	chr5:138610483-138610753(-)$1	270	102	109	13.1428
GGAGCAG	chr10:126976587-126976856(-)$1	269	102	109	13.1428
ggagaag	chr4:148335399-148335672(-)$1	273	42	49	17.1111

#otherMatches

#Struct PSSM
3ffffff	chr16:11235370-11235639(-)$1	269	136	143	13.2222
eeeee22	chr6:67227651-67228037(+)$1	386	103	110	12.6666
CCC}BBY	chr6:22952048-22952316(+)$1	268	133	140	13.1428
:::::::	chr3:106342304-106342578(-)$1	274	112	119	13.0634
FF::III	chr17:33958657-33958940(+)$1	283	127	134	12.2698
c:::::f	chr5:100821866-100822144(-)$1	278	214	221	13.6190
dHHHHHH	chr7:3655828-3656103(+)$1	275	184	191	13.1428
eeeeeee	chr13:51740714-51740990(+)$1	276	141	148	13.4603
FFFFFLL	chr19:41330559-41330831(-)$1	272	139	146	17.1111
dddd:bb	chr12:110698424-110698692(+)$1	268	28	35	13.6190
gggggg[	chr13:67926463-67926737(+)$1	274	46	53	12.9047
bb[cccq	chr4:33333324-33333602(-)$1	278	146	153	12.9047
uuuuuub	chr8:107858490-107858759(-)$1	269	93	100	17.1111
a]dddde	chr19:6454986-6455255(+)$1	269	131	138	13.1428
EEEEYYF	chr5:136265477-136265767(+)$1	290	224	231	13.4603
c]bbddd	chr3:104585431-104585713(+)$1	282	158	165	13.4603
gggg:::	chr15:84770080-84770413(+)$1	333	95	102	13.2222
aoooooo	chr10:127525950-127526220(+)$1	270	208	215	13.1428
ee::::d	chr15:79749263-79749566(-)$1	303	163	170	17.1111
:::::::	chr1:137326799-137327084(-)$1	285	208	215	13.1428
DDD}A}C	chr12:85015957-85016241(+)$1	284	170	177	12.9047
55555cc	chr4:116283706-116283999(-)$1	293	138	145	17.1111
dddd]ee	chr12:16586551-16586820(-)$1	269	94	101	17.1111
}CCC::b	chr7:29108662-29108941(-)$1	279	146	153	13.6190
:::::::	chr2:53009572-53009852(-)$1	280	106	113	13.6190
ddbbccc	chr2:151369514-151369795(+)$1	281	232	239	13.1428
JJ:::dd	chr7:19628752-19629027(+)$1	275	138	145	13.2222
iiiiiii	chr5:72915766-72916034(-)$1	268	136	143	13.1428
gg[annn	chr15:77597848-77598177(-)$1	329	95	102	17.1111
cccoooo	chr16:20688738-20689030(+)$1	292	83	90	17.1111
ooooood	chr8:87366519-87366802(-)$1	283	64	71	13.1428
f::::::	chr9:111116607-111116895(+)$1	288	154	161	17.1111
BB}IIII	chr2:119635065-119635355(+)$1	290	276	283	13.4603
ggEEEEE	chr8:33028504-33028779(-)$1	275	240	247	17.1111
hhhhhhh	chr11:68598637-68598922(+)$1	285	144	151	13.6190
dddd[ee	chr2:125082482-125082762(+)$1	280	163	170	13.1428
EECCC:E	chr16:90931165-90931435(-)$1	270	129	136	17.1111
gg::::e	chr7:34931135-34931405(-)$1	270	223	230	17.1111
ffffddd	chr4:40163246-40163522(-)$1	276	83	90	13.1428
=======	chr8:97349000-97349279(-)$1	279	129	136	13.1428
ee4444c	chr5:30690889-30691157(-)$1	268	93	100	13.6190
d333a]c	chr12:109924500-109924773(+)$1	273	125	132	13.4603
eee[ddd	chr17:88386043-88386321(+)$1	278	138	145	13.2222
[ammmma	chr17:88384478-88384828(+)$1	350	98	105	13.1428
ppppppp	chr4:125911254-125911534(-)$1	280	10	17	13.6190
dddd"""	chr8:96703593-96703882(+)$1	289	5	12	12.9047
DDDCCC:	chr10:45138737-45139017(-)$1	280	5	12	12.3492
]ccc22d	chr11:6197028-6197301(+)$1	273	149	156	12.6666
cccpppp	chr9:107560193-107560461(-)$1	268	175	182	13.1428
&&&&&&b	chr3:41408435-41408711(+)$1	276	109	116	13.1428
DDDD{FF	chr9:44656894-44657162(-)$1	268	99	106	17.1111
IIIIIII	chr15:76499574-76499865(-)$1	291	7	14	17.1111
gggg"""	chr5:123805890-123806164(+)$1	274	88	95	13.1428
a[eeeee	chr11:106063360-106063635(-)$1	275	61	68	13.4603
CKKDDDD	chr8:87200184-87200473(-)$1	289	137	144	13.6190
:EEEEE}	chr12:8348644-8348917(+)$1	273	149	156	13.1428
cc22bb3	chr9:21222610-21222887(+)$1	277	164	171	13.4603
iiiii]b	chr5:135906001-135906277(-)$1	276	98	105	13.1428
dtttttt	chrX:7508483-7508760(-)$1	277	31	38	12.9047
::::::E	chr5:147023261-147023539(-)$1	278	237	244	12.3492
dddd22d	chr5:138610483-138610753(-)$1	270	102	109	13.1428
effffff	chr10:126976587-126976856(-)$1	269	102	109	13.1428
A::::::	chr4:148335399-148335672(-)$1	273	42	49	17.1111

#DB
.))))))	chr16:11235370-11235639(-)$1	1	136	143	13.2222
)))))..	chr6:67227651-67228037(+)$1	1	103	110	12.6666
))).)).	chr6:22952048-22952316(+)$1	1	133	140	13.1428
.......	chr3:106342304-106342578(-)$1	1	112	119	13.0634
))..(((	chr17:33958657-33958940(+)$1	1	127	134	12.2698
).....(	chr5:100821866-100822144(-)$1	1	214	221	13.6190
)))))))	chr7:3655828-3656103(+)$1	1	184	191	13.1428
(((((((	chr13:51740714-51740990(+)$1	1	141	148	13.4603
(((((..	chr19:41330559-41330831(-)$1	1	139	146	17.1111
)))).((	chr12:110698424-110698692(+)$1	1	28	35	13.6190
((((((.	chr13:67926463-67926737(+)$1	1	46	53	12.9047
((.(((.	chr4:33333324-33333602(-)$1	1	146	153	12.9047
......)	chr8:107858490-107858759(-)$1	1	93	100	17.1111
).)))))	chr19:6454986-6455255(+)$1	1	131	138	13.1428
))))..)	chr5:136265477-136265767(+)$1	1	224	231	13.4603
).)))))	chr3:104585431-104585713(+)$1	1	158	165	13.4603
))))...	chr15:84770080-84770413(+)$1	1	95	102	13.2222
(......	chr10:127525950-127526220(+)$1	1	208	215	13.1428
))....(	chr15:79749263-79749566(-)$1	1	163	170	17.1111
.......	chr1:137326799-137327084(-)$1	1	208	215	13.1428
))).).)	chr12:85015957-85016241(+)$1	1	170	177	12.9047
.....))	chr4:116283706-116283999(-)$1	1	138	145	17.1111
)))).))	chr12:16586551-16586820(-)$1	1	94	101	17.1111
.)))..(	chr7:29108662-29108941(-)$1	1	146	153	13.6190
.......	chr2:53009572-53009852(-)$1	1	106	113	13.6190
)))))))	chr2:151369514-151369795(+)$1	1	232	239	13.1428
((...((	chr7:19628752-19629027(+)$1	1	138	145	13.2222
)))))))	chr5:72915766-72916034(-)$1	1	136	143	13.1428
((.(...	chr15:77597848-77598177(-)$1	1	95	102	17.1111
(((....	chr16:20688738-20689030(+)$1	1	83	90	17.1111
......)	chr8:87366519-87366802(-)$1	1	64	71	13.1428
)......	chr9:111116607-111116895(+)$1	1	154	161	17.1111
)).))))	chr2:119635065-119635355(+)$1	1	276	283	13.4603
)))))))	chr8:33028504-33028779(-)$1	1	240	247	17.1111
(((((((	chr11:68598637-68598922(+)$1	1	144	151	13.6190
((((.((	chr2:125082482-125082762(+)$1	1	163	170	13.1428
))))).(	chr16:90931165-90931435(-)$1	1	129	136	17.1111
))....(	chr7:34931135-34931405(-)$1	1	223	230	17.1111
(((((((	chr4:40163246-40163522(-)$1	1	83	90	13.1428
(((((((	chr8:97349000-97349279(-)$1	1	129	136	13.1428
))....)	chr5:30690889-30691157(-)$1	1	93	100	13.6190
)...).)	chr12:109924500-109924773(+)$1	1	125	132	13.4603
(((.(((	chr17:88386043-88386321(+)$1	1	138	145	13.2222
.(....)	chr17:88384478-88384828(+)$1	1	98	105	13.1428
.......	chr4:125911254-125911534(-)$1	1	10	17	13.6190
((((...	chr8:96703593-96703882(+)$1	1	5	12	12.9047
((((((.	chr10:45138737-45139017(-)$1	1	5	12	12.3492
.)))..)	chr11:6197028-6197301(+)$1	1	149	156	12.6666
(((....	chr9:107560193-107560461(-)$1	1	175	182	13.1428
......(	chr3:41408435-41408711(+)$1	1	109	116	13.1428
((((.((	chr9:44656894-44657162(-)$1	1	99	106	17.1111
(((((((	chr15:76499574-76499865(-)$1	1	7	14	17.1111
((((...	chr5:123805890-123806164(+)$1	1	88	95	13.1428
(.(((((	chr11:106063360-106063635(-)$1	1	61	68	13.4603
(..((((	chr8:87200184-87200473(-)$1	1	137	144	13.6190
.))))).	chr12:8348644-8348917(+)$1	1	149	156	13.1428
))..)).	chr9:21222610-21222887(+)$1	1	164	171	13.4603
))))).)	chr5:135906001-135906277(-)$1	1	98	105	13.1428
(......	chrX:7508483-7508760(-)$1	1	31	38	12.9047
......)	chr5:147023261-147023539(-)$1	1	237	244	12.3492
))))..)	chr5:138610483-138610753(-)$1	1	102	109	13.1428
)))))))	chr10:126976587-126976856(-)$1	1	102	109	13.1428
(......	chr4:148335399-148335672(-)$1	1	42	49	17.1111

#PSSM
G : 0.77	U : 0.06	g : 0.06	C : 0.04	A : 0.04	
G : 0.76	A : 0.12	g : 0.06	C : 0.03	U : 0.01	
A : 0.80	G : 0.06	a : 0.04	U : 0.04	u : 0.01	C : 0.01	
G : 0.92	g : 0.06	C : 0.01	
A : 0.77	G : 0.11	a : 0.06	C : 0.04	
A : 0.92	a : 0.04	c : 0.01	G : 0.01	
G : 0.85	g : 0.04	A : 0.04	C : 0.01	a : 0.01	U : 0.01	

#score	885.222222222221
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m1_run2.nuc.txt

#NT
UGCAUGG	chr10:90614806-90615058(-)$1	252	94	101	14.2500
UACAUGC	chrX:92246405-92246796(-)$1	391	195	202	12.5833
ugcaugc	chr9:107693131-107693440(-)$1	309	180	187	16.9166
UGCAUGU	chr7:98598168-98598510(+)$1	342	177	184	14.9166
UGCAUGG	chr9:4478746-4479135(-)$1	389	159	166	14.2500
UGCAUGU	chr19:7530548-7530891(-)$1	343	125	132	14.9166
AGCAUGC	chr2:14896709-14896969(+)$1	260	115	122	13.3333
UGCAUGC	chr11:86518292-86518554(-)$1	262	124	131	16.9166
UGCAUGU	chr9:123494051-123494375(+)$1	324	166	173	14.9166
UCCAUGc	chr8:69413297-69413557(+)$1	260	27	34	12.6666
UGCAUGG	chr17:46785081-46785378(+)$1	297	116	123	14.2500
UGCAUGU	chr15:82180470-82180848(-)$1	378	197	204	14.9166
CGCAUGC	chr16:29629646-29629916(+)$1	270	104	111	13.0000
UGCAUGU	chr11:29607727-29608022(+)$1	295	144	151	14.9166
AGCAUGC	chrX:20485053-20485337(-)$1	284	136	143	13.3333
AGCAUGC	chr1:79791459-79791719(-)$1	260	27	34	13.3333
UGCAUGC	chr15:9037851-9038169(+)$1	318	280	287	16.9166
AGCAUGC	chr1:22401989-22402427(-)$1	438	111	118	13.3333
UUCAUGC	chrX:12733343-12733818(+)$1	475	436	443	12.8333
UGCAUGC	chr3:154749694-154749931(-)$1	237	123	130	16.9166
UGCCUGC	chr17:73589351-73589753(+)$1	402	44	51	12.5000
UUCAUGC	chr3:157687543-157687853(-)$1	310	119	126	12.8333
UGCAUGU	chr14:73768027-73768338(-)$1	311	152	159	14.9166
UGCAUGU	chr11:77787622-77787931(+)$1	309	166	173	14.9166
UGGAUGC	chr5:123250250-123250582(-)$1	332	14	21	12.4166
UGCAUGU	chr1:153655322-153655595(+)$1	273	113	120	14.9166
UGCAUGC	chr7:129744104-129744477(+)$1	373	301	308	16.9166
AGCAUGC	chr4:58812684-58813169(-)$1	485	221	228	13.3333
UGCAUGG	chr14:103572901-103573226(-)$1	325	107	114	14.2500
UGCAUGU	chrX:53914448-53914936(+)$1	488	256	263	14.9166
AGCAUGC	chrX:92326253-92326546(-)$1	293	40	47	13.3333
UGCAUGC	chr19:45871282-45871622(-)$1	340	184	191	16.9166
CGCAUGC	chr17:35299100-35299393(-)$1	293	119	126	13.0000
CGCAUGC	chr15:79314774-79315091(-)$1	317	159	166	13.0000
UGCUUGC	chr4:98120889-98121222(+)$1	333	21	28	12.3333
UGCCUGC	chr4:40114023-40114280(+)$1	257	68	75	12.5000
UGCAUGC	chrX:98838265-98838546(+)$1	281	141	148	16.9166
UUCAUGC	chr15:58770818-58771147(+)$1	329	160	167	12.8333
UGUAUGC	chr14:76906126-76906424(+)$1	298	119	126	12.3333
AGCAUGC	chr11:53185685-53186017(+)$1	332	130	137	13.3333
UGCCUGC	chr13:6592229-6592664(-)$1	435	238	245	12.5000
UGCAUGC	chr18:50024609-50024904(+)$1	295	149	156	16.9166
UGCAUGU	chr8:82214097-82214348(-)$1	251	104	111	14.9166
UGGAUGC	chr4:149008796-149009120(+)$1	324	168	175	12.4166
UGCAUGA	chr13:94212470-94212741(-)$1	271	118	125	14.5833
UGCAUGU	chr1:152229292-152229680(-)$1	388	85	92	14.9166
UGCAUGA	chr11:62140505-62140815(-)$1	310	144	151	14.5833
UGCAUGA	chr10:89267524-89267859(+)$1	335	191	198	14.5833
UGCAUGC	chr4:120655610-120655904(-)$1	294	107	114	16.9166
UUCAUGC	chr4:48224435-48224683(-)$1	248	10	17	12.8333
UGAAUGC	chrX:103216986-103217344(+)$1	358	227	234	12.3333
UGCAUGA	chr2:178003820-178004123(+)$1	303	141	148	14.5833
UGCAUGC	chr6:108382514-108382783(+)$1	269	114	121	16.9166
UCCAUGC	chr6:108306282-108306584(+)$1	302	121	128	12.6666
UGCAUGA	chr2:91516444-91516712(-)$1	268	117	124	14.5833
UGCAUGA	chr2:29589618-29589882(+)$1	264	112	119	14.5833
ugcauga	chr7:48905562-48905813(+)$1	251	108	115	14.5833
UGCAUGA	chr14:52792012-52792263(-)$1	251	109	116	14.5833
UGCAUGU	chrX:71026902-71027234(-)$1	332	138	145	14.9166

#otherMatches

#Struct PSSM
qqqqeee	chr17:78780867-78781117(-)$1	250	107	114	16.9166
ndddd:e	chr10:90614806-90615058(-)$1	252	94	101	14.2500
eeeeddd	chrX:92246405-92246796(-)$1	391	195	202	12.5833
J}BBccc	chr9:107693131-107693440(-)$1	309	180	187	16.9166
ddbb]dd	chr7:98598168-98598510(+)$1	342	177	184	14.9166
cccHHHH	chr9:4478746-4479135(-)$1	389	159	166	14.2500
EEE::dd	chr19:7530548-7530891(-)$1	343	125	132	14.9166
EEDDDD:	chr2:14896709-14896969(+)$1	260	115	122	13.3333
c]fffff	chr11:86518292-86518554(-)$1	262	124	131	16.9166
0ccc]ee	chr9:123494051-123494375(+)$1	324	166	173	14.9166
:::::DD	chr8:69413297-69413557(+)$1	260	27	34	12.6666
ddd22cc	chr17:46785081-46785378(+)$1	297	116	123	14.2500
ffff!!b	chr15:82180470-82180848(-)$1	378	197	204	14.9166
ddooooo	chr16:29629646-29629916(+)$1	270	104	111	13.0000
{BBKKEE	chr11:29607727-29608022(+)$1	295	144	151	14.9166
CCC{DDD	chrX:20485053-20485337(-)$1	284	136	143	13.3333
:bbnnnn	chr1:79791459-79791719(-)$1	260	27	34	13.3333
EEEE}BB	chr15:9037851-9038169(+)$1	318	280	287	16.9166
:::::::	chr1:22401989-22402427(-)$1	438	111	118	13.3333
ddd]ccc	chrX:12733343-12733818(+)$1	475	436	443	12.8333
[cccttt	chr3:154749694-154749931(-)$1	237	123	130	16.9166
]eeeee>	chr17:73589351-73589753(+)$1	402	44	51	12.5000
+eeeeeq	chr3:157687543-157687853(-)$1	310	119	126	12.8333
dddd]a]	chr14:73768027-73768338(-)$1	311	152	159	14.9166
CCLLLDD	chr11:77787622-77787931(+)$1	309	166	173	14.9166
DDD{DDD	chr5:123250250-123250582(-)$1	332	14	21	12.4166
ddddmmm	chr1:153655322-153655595(+)$1	273	113	120	14.9166
gIIIIII	chr7:129744104-129744477(+)$1	373	301	308	16.9166
eee]ccc	chr4:58812684-58813169(-)$1	485	221	228	13.3333
c55555e	chr14:103572901-103573226(-)$1	325	107	114	14.2500
=======	chrX:53914448-53914936(+)$1	488	256	263	14.9166
''''eee	chrX:92326253-92326546(-)$1	293	40	47	13.3333
hhhhhhh	chr19:45871282-45871622(-)$1	340	184	191	16.9166
cmmmmcc	chr17:35299100-35299393(-)$1	293	119	126	13.0000
[bboooo	chr15:79314774-79315091(-)$1	317	159	166	13.0000
cc!!ccc	chr4:98120889-98121222(+)$1	333	21	28	12.3333
ooddddC	chr4:40114023-40114280(+)$1	257	68	75	12.5000
ee!!bbc	chrX:98838265-98838546(+)$1	281	141	148	16.9166
KKEEEEE	chr15:58770818-58771147(+)$1	329	160	167	12.8333
}FFFFFF	chr14:76906126-76906424(+)$1	298	119	126	12.3333
QCCC{FF	chr11:53185685-53186017(+)$1	332	130	137	13.3333
gg333cc	chr13:6592229-6592664(-)$1	435	238	245	12.5000
ddddnnn	chr18:50024609-50024904(+)$1	295	149	156	16.9166
cc]ffff	chr8:82214097-82214348(-)$1	251	104	111	14.9166
b[bb[ee	chr4:149008796-149009120(+)$1	324	168	175	12.4166
hhhhh]c	chr13:94212470-94212741(-)$1	271	118	125	14.5833
ee333dd	chr1:152229292-152229680(-)$1	388	85	92	14.9166
eebb[cc	chr11:62140505-62140815(-)$1	310	144	151	14.5833
:::::cc	chr10:89267524-89267859(+)$1	335	191	198	14.5833
]bbccc]	chr4:120655610-120655904(-)$1	294	107	114	16.9166
hh!!ccc	chr4:48224435-48224683(-)$1	248	10	17	12.8333
c::::::	chrX:103216986-103217344(+)$1	358	227	234	12.3333
g[ddddr	chr2:178003820-178004123(+)$1	303	141	148	14.5833
####eee	chr6:108382514-108382783(+)$1	269	114	121	16.9166
dda[ccc	chr6:108306282-108306584(+)$1	302	121	128	12.6666
ccc]a]e	chr2:91516444-91516712(-)$1	268	117	124	14.5833
oooooa2	chr2:29589618-29589882(+)$1	264	112	119	14.5833
%dddd''	chr7:48905562-48905813(+)$1	251	108	115	14.5833
cc55555	chr14:52792012-52792263(-)$1	251	109	116	14.5833
hhheeee	chrX:71026902-71027234(-)$1	332	138	145	14.9166

#DB
....)))	chr17:78780867-78781117(-)$1	1	107	114	16.9166
.)))).(	chr10:90614806-90615058(-)$1	1	94	101	14.2500
)))))))	chrX:92246405-92246796(-)$1	1	195	202	12.5833
).))(((	chr9:107693131-107693440(-)$1	1	180	187	16.9166
)))).))	chr7:98598168-98598510(+)$1	1	177	184	14.9166
)))((((	chr9:4478746-4479135(-)$1	1	159	166	14.2500
(((..((	chr19:7530548-7530891(-)$1	1	125	132	14.9166
((((((.	chr2:14896709-14896969(+)$1	1	115	122	13.3333
).)))))	chr11:86518292-86518554(-)$1	1	124	131	16.9166
.))).))	chr9:123494051-123494375(+)$1	1	166	173	14.9166
.....((	chr8:69413297-69413557(+)$1	1	27	34	12.6666
)))..))	chr17:46785081-46785378(+)$1	1	116	123	14.2500
((((..(	chr15:82180470-82180848(-)$1	1	197	204	14.9166
((.....	chr16:29629646-29629916(+)$1	1	104	111	13.0000
.((..((	chr11:29607727-29608022(+)$1	1	144	151	14.9166
(((.(((	chrX:20485053-20485337(-)$1	1	136	143	13.3333
.((....	chr1:79791459-79791719(-)$1	1	27	34	13.3333
)))).))	chr15:9037851-9038169(+)$1	1	280	287	16.9166
.......	chr1:22401989-22402427(-)$1	1	111	118	13.3333
))).)))	chrX:12733343-12733818(+)$1	1	436	443	12.8333
.(((...	chr3:154749694-154749931(-)$1	1	123	130	16.9166
.))))).	chr17:73589351-73589753(+)$1	1	44	51	12.5000
.(((((.	chr3:157687543-157687853(-)$1	1	119	126	12.8333
)))).).	chr14:73768027-73768338(-)$1	1	152	159	14.9166
((...((	chr11:77787622-77787931(+)$1	1	166	173	14.9166
(((.(((	chr5:123250250-123250582(-)$1	1	14	21	12.4166
((((...	chr1:153655322-153655595(+)$1	1	113	120	14.9166
)))))))	chr7:129744104-129744477(+)$1	1	301	308	16.9166
))).)))	chr4:58812684-58813169(-)$1	1	221	228	13.3333
).....)	chr14:103572901-103573226(-)$1	1	107	114	14.2500
)))))))	chrX:53914448-53914936(+)$1	1	256	263	14.9166
....(((	chrX:92326253-92326546(-)$1	1	40	47	13.3333
(((((((	chr19:45871282-45871622(-)$1	1	184	191	16.9166
(....))	chr17:35299100-35299393(-)$1	1	119	126	13.0000
.((....	chr15:79314774-79315091(-)$1	1	159	166	13.0000
((..(((	chr4:98120889-98121222(+)$1	1	21	28	12.3333
..))))(	chr4:40114023-40114280(+)$1	1	68	75	12.5000
((..(((	chrX:98838265-98838546(+)$1	1	141	148	16.9166
..(((((	chr15:58770818-58771147(+)$1	1	160	167	12.8333
.))))))	chr14:76906126-76906424(+)$1	1	119	126	12.3333
.(((.((	chr11:53185685-53186017(+)$1	1	130	137	13.3333
))...))	chr13:6592229-6592664(-)$1	1	238	245	12.5000
((((...	chr18:50024609-50024904(+)$1	1	149	156	16.9166
)).))))	chr8:82214097-82214348(-)$1	1	104	111	14.9166
(.((.((	chr4:149008796-149009120(+)$1	1	168	175	12.4166
))))).)	chr13:94212470-94212741(-)$1	1	118	125	14.5833
))...))	chr1:152229292-152229680(-)$1	1	85	92	14.9166
((((.((	chr11:62140505-62140815(-)$1	1	144	151	14.5833
.....((	chr10:89267524-89267859(+)$1	1	191	198	14.5833
.))))).	chr4:120655610-120655904(-)$1	1	107	114	16.9166
((..(((	chr4:48224435-48224683(-)$1	1	10	17	12.8333
)......	chrX:103216986-103217344(+)$1	1	227	234	12.3333
(.((((.	chr2:178003820-178004123(+)$1	1	141	148	14.5833
....(((	chr6:108382514-108382783(+)$1	1	114	121	16.9166
(((.(((	chr6:108306282-108306584(+)$1	1	121	128	12.6666
))).).)	chr2:91516444-91516712(-)$1	1	117	124	14.5833
.....).	chr2:29589618-29589882(+)$1	1	112	119	14.5833
.((((..	chr7:48905562-48905813(+)$1	1	108	115	14.5833
)).....	chr14:52792012-52792263(-)$1	1	109	116	14.5833
)))((((	chrX:71026902-71027234(-)$1	1	138	145	14.9166

#PSSM
U : 0.80	A : 0.11	C : 0.05	u : 0.03	
G : 0.85	U : 0.06	g : 0.03	C : 0.03	A : 0.01	
C : 0.90	c : 0.03	G : 0.03	U : 0.01	A : 0.01	
A : 0.90	C : 0.05	a : 0.03	U : 0.01	
U : 0.96	u : 0.03	
G : 0.96	g : 0.03	
C : 0.56	U : 0.19	A : 0.11	G : 0.06	c : 0.03	a : 0.01	

#score	859.666666666668
#seq	60
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_CDS_m3_run2.nuc.txt

#NT

#otherMatches

#Struct PSSM
FFFFFFAFFFFFFddddnnnnndddd:GGGGGGG::eeeeemmmmeeeee:::::::dddd!!gggggggggggggg[bb[==========+++++++++++++++ccc[ffffff[bb"""bbmmmmbb333bb]ffffff]ccc==========333bbggggggg22ggggggg22ddddGGGGGGG@@@@@@@@@@@FFFFFF}A?????FFFFFF?????EEEE	chr2:76723096-76723358(-)$1	262	29	258	687.0000

#DB
(((((((((((((((((.....)))).(((((((..(((((....))))).......((((..((((((((((((((.((.((((((((((...............(((.((((((.((...((....))...)).)))))).)))))))))))))...)))))))))..)))))))..)))))))))))...........)))))).).....)))))).....))))	chr2:76723096-76723358(-)$1	1	29	258	687.0000

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

#score	687.0
#seq	1
#width	229
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m1_run2.nuc.txt

#NT
CCUCUC	chr11:117828171-117828444(-)$1	273	175	181	14.3559
CUUCUC	chr4:63211331-63211605(+)$1	274	155	161	10.7966
CCUCUA	chr2:144232685-144232982(+)$1	297	132	138	11.5593
CCUCUU	chr6:30079454-30079738(+)$1	284	8	14	12.0677
CCUCUC	chr8:109599382-109599653(-)$1	271	1	7	14.3559
CCUCUU	chr2:152654216-152654493(-)$1	277	37	43	12.0677
CCUCUC	chr17:34791783-34792075(+)$1	292	16	22	14.3559
CCUCUC	chr15:75831594-75831869(-)$1	275	25	31	14.3559
CCUCUU	chr5:75006662-75006928(-)$1	266	80	86	12.0677
CCUCUG	chr4:137798696-137798973(+)$1	277	102	108	12.5762
CCUCUG	chr15:80761852-80762143(+)$1	291	12	18	12.5762
CCUCUG	chr16:92084365-92084642(+)$1	277	114	120	12.5762
ccuguc	chr17:27062059-27062328(+)$1	269	10	16	10.5423
CAUCUC	chr1:184398226-184398498(-)$1	272	39	45	10.9661
CCUCUG	chr8:74842835-74843118(+)$1	283	77	83	12.5762
CCUGUC	chr6:56728722-56729000(-)$1	278	22	28	10.5423
CCUGUC	chr1:189057862-189058135(+)$1	273	75	81	10.5423
CCUCUA	chr7:24891396-24891687(+)$1	291	131	137	11.5593
CUUCUC	chr11:68635138-68635416(-)$1	278	2	8	10.7966
CCUCUC	chr13:69138020-69138287(-)$1	267	258	264	14.3559
CCUCUG	chr17:37114860-37115128(-)$1	268	9	15	12.5762
CCUGUC	chr16:91227775-91228057(+)$1	282	192	198	10.5423
CCUCUC	chr5:67078040-67078310(+)$1	270	26	32	14.3559
CAUCUC	chr2:173526976-173527254(+)$1	278	3	9	10.9661
CUUCUC	chr5:138223097-138223399(-)$1	302	73	79	10.7966
CAUCUC	chr9:119147937-119148232(-)$1	295	28	34	10.9661
CAUCUC	chr11:32327052-32327325(+)$1	273	24	30	10.9661
CAUCUC	chr3:96066811-96067101(-)$1	290	11	17	10.9661
CCUCUG	chr5:31924774-31925053(+)$1	279	18	24	12.5762
CCUCUG	chr16:92085376-92085654(+)$1	278	31	37	12.5762
CCUGUC	chr3:87340637-87340930(+)$1	293	174	180	10.5423
CCUCUG	chr19:3808352-3808623(+)$1	271	55	61	12.5762
CCUCUU	chr19:8907647-8907942(+)$1	295	46	52	12.0677
CCUCUC	chr2:152607454-152607733(-)$1	279	186	192	14.3559
ccucuu	chr4:133831673-133831946(-)$1	273	252	258	12.0677
CCUCUG	chr4:83921320-83921603(-)$1	283	27	33	12.5762
CCUCUG	chr3:105771255-105771551(+)$1	296	78	84	12.5762
CCUCUU	chr1:62843122-62843399(+)$1	277	62	68	12.0677
CAUCUC	chr9:60586481-60586749(+)$1	268	4	10	10.9661
CCUCUG	chr10:116510428-116510732(-)$1	304	260	266	12.5762
CCUCUU	chr18:24443319-24443593(+)$1	274	137	143	12.0677
CCUCUU	chr8:11834059-11834348(+)$1	289	163	169	12.0677
CCUCUG	chr2:79512562-79512842(+)$1	280	4	10	12.5762
CCUCUC	chr11:87794728-87795014(-)$1	286	171	177	14.3559
CUUCUC	chr2:14999759-15000046(+)$1	287	233	239	10.7966
CCUCUG	chr15:98734275-98734547(-)$1	272	59	65	12.5762
CAUCUC	chr10:127827825-127828099(+)$1	274	236	242	10.9661
CCUCUC	chr17:47760163-47760455(+)$1	292	236	242	14.3559
CCUCUC	chr15:75900547-75900820(-)$1	273	50	56	14.3559
CCUCUC	chr11:117828673-117828941(-)$1	268	115	121	14.3559
CCUCUC	chr6:54767279-54767565(+)$1	286	164	170	14.3559
CCUCUC	chr4:140884838-140885115(+)$1	277	119	125	14.3559
CCUCUG	chr5:138223461-138223741(-)$1	280	11	17	12.5762
CUUCUC	chr2:32162879-32163158(+)$1	279	87	93	10.7966
CCUCUC	chr6:124863939-124864222(-)$1	283	161	167	14.3559
CCUGUC	chr1:64840465-64840739(-)$1	274	31	37	10.5423
CCUCUC	chr3:154259844-154260111(-)$1	267	27	33	14.3559
CCUCUC	chr11:117828728-117829006(-)$1	278	2	8	14.3559

#otherMatches

#Struct PSSM
oooccc	chr5:123807806-123808084(+)$1	278	31	37	10.5423
]dddd]	chr11:117828171-117828444(-)$1	273	175	181	14.3559
hhhhff	chr4:63211331-63211605(+)$1	274	155	161	10.7966
:ccc[e	chr2:144232685-144232982(+)$1	297	132	138	11.5593
EE:eee	chr6:30079454-30079738(+)$1	284	8	14	12.0677
::::::	chr8:109599382-109599653(-)$1	271	1	7	14.3559
dd]bb2	chr2:152654216-152654493(-)$1	277	37	43	12.0677
BBCCCG	chr17:34791783-34792075(+)$1	292	16	22	14.3559
ubb]ee	chr15:75831594-75831869(-)$1	275	25	31	14.3559
FFFFFF	chr5:75006662-75006928(-)$1	266	80	86	12.0677
iiiiii	chr4:137798696-137798973(+)$1	277	102	108	12.5762
CCCBBF	chr15:80761852-80762143(+)$1	291	12	18	12.5762
ffffff	chr16:92084365-92084642(+)$1	277	114	120	12.5762
EKKDDD	chr17:27062059-27062328(+)$1	269	10	16	10.5423
::GGGG	chr1:184398226-184398498(-)$1	272	39	45	10.9661
CCCccc	chr8:74842835-74843118(+)$1	283	77	83	12.5762
uuuuuu	chr6:56728722-56729000(-)$1	278	22	28	10.5423
ccdddd	chr1:189057862-189058135(+)$1	273	75	81	10.5423
::CCCF	chr7:24891396-24891687(+)$1	291	131	137	11.5593
ggggg!	chr11:68635138-68635416(-)$1	278	2	8	10.7966
eeee::	chr13:69138020-69138287(-)$1	267	258	264	14.3559
:JJJJJ	chr17:37114860-37115128(-)$1	268	9	15	12.5762
b::ddd	chr16:91227775-91228057(+)$1	282	192	198	10.5423
::::dd	chr5:67078040-67078310(+)$1	270	26	32	14.3559
fff[dd	chr2:173526976-173527254(+)$1	278	3	9	10.9661
======	chr5:138223097-138223399(-)$1	302	73	79	10.7966
GGGGG:	chr9:119147937-119148232(-)$1	295	28	34	10.9661
dnnnnn	chr11:32327052-32327325(+)$1	273	24	30	10.9661
MMMEEE	chr3:96066811-96067101(-)$1	290	11	17	10.9661
GGccc[	chr5:31924774-31925053(+)$1	279	18	24	12.5762
FFFBB{	chr16:92085376-92085654(+)$1	278	31	37	12.5762
eee]ee	chr3:87340637-87340930(+)$1	293	174	180	10.5423
{HHHHH	chr19:3808352-3808623(+)$1	271	55	61	12.5762
eiiiii	chr19:8907647-8907942(+)$1	295	46	52	12.0677
lllfff	chr2:152607454-152607733(-)$1	279	186	192	14.3559
ddd:::	chr4:133831673-133831946(-)$1	273	252	258	12.0677
booooo	chr4:83921320-83921603(-)$1	283	27	33	12.5762
ccc[bb	chr3:105771255-105771551(+)$1	296	78	84	12.5762
hhhhhh	chr1:62843122-62843399(+)$1	277	62	68	12.0677
LLLFFF	chr9:60586481-60586749(+)$1	268	4	10	10.9661
dcccoo	chr10:116510428-116510732(-)$1	304	260	266	12.5762
e]bbdd	chr18:24443319-24443593(+)$1	274	137	143	12.0677
cccqqq	chr8:11834059-11834348(+)$1	289	163	169	12.0677
::CCC:	chr2:79512562-79512842(+)$1	280	4	10	12.5762
ppppcc	chr11:87794728-87795014(-)$1	286	171	177	14.3559
FFFF}C	chr2:14999759-15000046(+)$1	287	233	239	10.7966
======	chr15:98734275-98734547(-)$1	272	59	65	12.5762
GGGGCC	chr10:127827825-127828099(+)$1	274	236	242	10.9661
eedddd	chr17:47760163-47760455(+)$1	292	236	242	14.3559
pppppp	chr15:75900547-75900820(-)$1	273	50	56	14.3559
eeeeoo	chr11:117828673-117828941(-)$1	268	115	121	14.3559
BBKKBB	chr6:54767279-54767565(+)$1	286	164	170	14.3559
FFFeee	chr4:140884838-140885115(+)$1	277	119	125	14.3559
FFFFFK	chr5:138223461-138223741(-)$1	280	11	17	12.5762
55555f	chr2:32162879-32163158(+)$1	279	87	93	10.7966
!!cccx	chr6:124863939-124864222(-)$1	283	161	167	14.3559
""dddd	chr1:64840465-64840739(-)$1	274	31	37	10.5423
C{CCCF	chr3:154259844-154260111(-)$1	267	27	33	14.3559
::::::	chr11:117828728-117829006(-)$1	278	2	8	14.3559

#DB
...)))	chr5:123807806-123808084(+)$1	1	31	37	10.5423
.)))).	chr11:117828171-117828444(-)$1	1	175	181	14.3559
))))))	chr4:63211331-63211605(+)$1	1	155	161	10.7966
.(((.(	chr2:144232685-144232982(+)$1	1	132	138	11.5593
((.(((	chr6:30079454-30079738(+)$1	1	8	14	12.0677
......	chr8:109599382-109599653(-)$1	1	1	7	14.3559
)).)).	chr2:152654216-152654493(-)$1	1	37	43	12.0677
((((((	chr17:34791783-34792075(+)$1	1	16	22	14.3559
.)).))	chr15:75831594-75831869(-)$1	1	25	31	14.3559
((((((	chr5:75006662-75006928(-)$1	1	80	86	12.0677
((((((	chr4:137798696-137798973(+)$1	1	102	108	12.5762
((((((	chr15:80761852-80762143(+)$1	1	12	18	12.5762
((((((	chr16:92084365-92084642(+)$1	1	114	120	12.5762
(..(((	chr17:27062059-27062328(+)$1	1	10	16	10.5423
..((((	chr1:184398226-184398498(-)$1	1	39	45	10.9661
((((((	chr8:74842835-74843118(+)$1	1	77	83	12.5762
......	chr6:56728722-56729000(-)$1	1	22	28	10.5423
))))))	chr1:189057862-189058135(+)$1	1	75	81	10.5423
..))))	chr7:24891396-24891687(+)$1	1	131	137	11.5593
(((((.	chr11:68635138-68635416(-)$1	1	2	8	10.7966
))))..	chr13:69138020-69138287(-)$1	1	258	264	14.3559
.(((((	chr17:37114860-37115128(-)$1	1	9	15	12.5762
)..(((	chr16:91227775-91228057(+)$1	1	192	198	10.5423
....((	chr5:67078040-67078310(+)$1	1	26	32	14.3559
(((.((	chr2:173526976-173527254(+)$1	1	3	9	10.9661
((((((	chr5:138223097-138223399(-)$1	1	73	79	10.7966
(((((.	chr9:119147937-119148232(-)$1	1	28	34	10.9661
(.....	chr11:32327052-32327325(+)$1	1	24	30	10.9661
...(((	chr3:96066811-96067101(-)$1	1	11	17	10.9661
(((((.	chr5:31924774-31925053(+)$1	1	18	24	12.5762
(((((.	chr16:92085376-92085654(+)$1	1	31	37	12.5762
))).))	chr3:87340637-87340930(+)$1	1	174	180	10.5423
.(((((	chr19:3808352-3808623(+)$1	1	55	61	12.5762
)(((((	chr19:8907647-8907942(+)$1	1	46	52	12.0677
...)))	chr2:152607454-152607733(-)$1	1	186	192	14.3559
)))...	chr4:133831673-133831946(-)$1	1	252	258	12.0677
(.....	chr4:83921320-83921603(-)$1	1	27	33	12.5762
(((.((	chr3:105771255-105771551(+)$1	1	78	84	12.5762
))))))	chr1:62843122-62843399(+)$1	1	62	68	12.0677
...(((	chr9:60586481-60586749(+)$1	1	4	10	10.9661
((((..	chr10:116510428-116510732(-)$1	1	260	266	12.5762
).))))	chr18:24443319-24443593(+)$1	1	137	143	12.0677
(((...	chr8:11834059-11834348(+)$1	1	163	169	12.0677
..(((.	chr2:79512562-79512842(+)$1	1	4	10	12.5762
....))	chr11:87794728-87795014(-)$1	1	171	177	14.3559
)))).)	chr2:14999759-15000046(+)$1	1	233	239	10.7966
))))))	chr15:98734275-98734547(-)$1	1	59	65	12.5762
))))))	chr10:127827825-127828099(+)$1	1	236	242	10.9661
((((((	chr17:47760163-47760455(+)$1	1	236	242	14.3559
......	chr15:75900547-75900820(-)$1	1	50	56	14.3559
((((..	chr11:117828673-117828941(-)$1	1	115	121	14.3559
((..((	chr6:54767279-54767565(+)$1	1	164	170	14.3559
((((((	chr4:140884838-140885115(+)$1	1	119	125	14.3559
(((((.	chr5:138223461-138223741(-)$1	1	11	17	12.5762
.....)	chr2:32162879-32163158(+)$1	1	87	93	10.7966
..(((.	chr6:124863939-124864222(-)$1	1	161	167	14.3559
..((((	chr1:64840465-64840739(-)$1	1	31	37	10.5423
(.((((	chr3:154259844-154260111(-)$1	1	27	33	14.3559
......	chr11:117828728-117829006(-)$1	1	2	8	14.3559

#PSSM
C : 0.94	c : 0.05	
C : 0.74	A : 0.11	U : 0.08	c : 0.05	
U : 0.94	u : 0.05	
C : 0.86	G : 0.08	g : 0.03	c : 0.01	
U : 0.94	u : 0.05	
C : 0.55	G : 0.23	U : 0.11	c : 0.03	A : 0.03	u : 0.01	

#score	729.9661016949144
#seq	59
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m3_run2.nuc.txt

#NT
AUU	chr2:136607904-136608169(+)$1	265	203	206	9.0000
AUU	chr9:58500334-58500635(+)$1	301	25	28	9.0000
AUU	chr3:89238790-89239031(+)$1	241	27	30	9.0000
AUU	chr15:30958474-30958715(+)$1	241	174	177	9.0000
AUU	chr1:52220705-52220953(-)$1	248	16	19	9.0000
AUU	chr2:102629044-102629314(+)$1	270	122	125	9.0000
AUU	chr4:150436197-150436479(-)$1	282	235	238	9.0000
AUU	chr16:37888154-37888398(+)$1	244	129	132	9.0000
AUU	chr10:70020236-70020476(+)$1	240	17	20	9.0000
AUU	chr19:59373408-59373647(-)$1	239	2	5	9.0000
AUU	chr6:92324993-92325229(-)$1	236	34	37	9.0000
AUU	chr5:89664881-89665126(+)$1	245	59	62	9.0000
AUU	chr9:107950602-107950848(+)$1	246	3	6	9.0000
AUU	chr2:131762909-131763211(+)$1	302	48	51	9.0000
AUU	chr2:158211402-158211658(+)$1	256	13	16	9.0000
AUU	chr6:114197708-114197947(+)$1	239	39	42	9.0000
AUU	chr10:40657864-40658102(+)$1	238	22	25	9.0000
AUU	chr8:122686328-122686564(+)$1	236	26	29	9.0000
AUU	chr11:109529284-109529537(+)$1	253	20	23	9.0000
AUU	chr3:120907317-120907565(-)$1	248	3	6	9.0000
AUU	chr18:63156896-63157151(+)$1	255	33	36	9.0000
AUU	chr18:35966507-35966742(+)$1	235	30	33	9.0000
AUU	chr5:122906322-122906560(-)$1	238	45	48	9.0000
AUU	chr18:65373136-65373394(+)$1	258	9	12	9.0000
AUU	chrX:96661226-96661469(-)$1	243	31	34	9.0000
AUU	chr6:72561784-72562025(-)$1	241	100	103	9.0000
AUU	chr16:7412006-7412266(+)$1	260	56	59	9.0000
AUU	chr13:110844350-110844643(-)$1	293	52	55	9.0000
AUU	chr10:9476906-9477142(-)$1	236	43	46	9.0000
AUU	chr2:138110336-138110575(+)$1	239	32	35	9.0000
AUU	chr7:91394776-91395045(-)$1	269	140	143	9.0000
AUU	chr10:34018422-34018682(+)$1	260	216	219	9.0000
AUU	chr13:98021788-98022044(+)$1	256	5	8	9.0000
AUU	chr16:31095308-31095565(-)$1	257	30	33	9.0000
AUU	chr5:143040156-143040391(-)$1	235	1	4	9.0000
AUU	chr2:163450342-163450603(-)$1	261	71	74	9.0000
AUU	chr2:102621705-102622016(+)$1	311	4	7	9.0000
AUU	chr10:13869999-13870248(+)$1	249	12	15	9.0000
AUU	chr1:23373438-23373695(-)$1	257	4	7	9.0000
AUU	chr5:4803753-4803991(-)$1	238	65	68	9.0000
AUU	chr3:107815196-107815451(-)$1	255	30	33	9.0000
AUU	chr5:77515979-77516221(-)$1	242	47	50	9.0000
AUU	chr4:122871556-122871807(+)$1	251	0	3	9.0000
AUU	chr10:57236816-57237127(-)$1	311	22	25	9.0000
AUU	chr3:80647535-80647791(-)$1	256	13	16	9.0000
AUU	chr1:52222521-52222773(-)$1	252	73	76	9.0000
AUU	chr18:59235342-59235577(+)$1	235	7	10	9.0000
AUU	chr17:65929526-65929778(-)$1	252	12	15	9.0000
AUU	chr11:86508092-86508333(-)$1	241	9	12	9.0000
AUU	chr4:59234115-59234356(+)$1	241	17	20	9.0000
AUU	chr2:117107126-117107376(-)$1	250	35	38	9.0000
AUU	chr1:38852135-38852371(-)$1	236	160	163	9.0000
AUU	chr4:55402861-55403112(+)$1	251	12	15	9.0000
AUU	chr14:14446837-14447080(+)$1	243	34	37	9.0000
AUU	chr9:86660070-86660332(-)$1	262	22	25	9.0000
AUU	chr9:79618792-79619037(-)$1	245	36	39	9.0000
AUU	chr11:20724828-20725065(-)$1	237	43	46	9.0000
AUU	chr1:153210412-153210653(+)$1	241	68	71	9.0000
AUU	chr1:33855577-33855826(-)$1	249	14	17	9.0000
AUU	chrX:162823430-162823735(+)$1	305	12	15	9.0000
AUU	chr8:42418143-42418382(+)$1	239	19	22	9.0000
AUU	chr10:82212054-82212289(-)$1	235	81	84	9.0000
AUU	chr4:107904064-107904301(-)$1	237	99	102	9.0000
auu	chr14:46078490-46078735(-)$1	245	1	4	9.0000
AUU	chr9:58499727-58500004(+)$1	277	56	59	9.0000
AUU	chr12:11331969-11332250(-)$1	281	24	27	9.0000
AUU	chr7:58926109-58926392(+)$1	283	19	22	9.0000
AUU	chrX:149046577-149046823(-)$1	246	99	102	9.0000
AUU	chr11:90139470-90139714(+)$1	244	24	27	9.0000
AUU	chr2:171862234-171862477(-)$1	243	39	42	9.0000
AUU	chr17:57219415-57219652(-)$1	237	154	157	9.0000
AUU	chr11:40492988-40493232(-)$1	244	46	49	9.0000
AUU	chr12:17798571-17798809(+)$1	238	15	18	9.0000
AUU	chr5:67681792-67682039(+)$1	247	9	12	9.0000
AUU	chr19:7500373-7500616(-)$1	243	21	24	9.0000
AUU	chr4:120640967-120641207(-)$1	240	151	154	9.0000
AUU	chr6:5111178-5111446(+)$1	268	11	14	9.0000
AUU	chr7:149836734-149836969(-)$1	235	216	219	9.0000
AUU	chr2:62162808-62163047(+)$1	239	51	54	9.0000
AUU	chr1:94911959-94912233(-)$1	274	164	167	9.0000
AUU	chr8:91275365-91275606(+)$1	241	44	47	9.0000
AUU	chr9:55984075-55984323(-)$1	248	10	13	9.0000
AUU	chr11:42442929-42443173(+)$1	244	29	32	9.0000
AUU	chr15:98000145-98000402(+)$1	257	41	44	9.0000
AUU	chr11:41945539-41945852(-)$1	313	44	47	9.0000
auu	chr12:86682950-86683192(-)$1	242	2	5	9.0000
AUU	chr16:7411239-7411495(+)$1	256	99	102	9.0000
AUU	chr8:56145814-56146102(+)$1	288	15	18	9.0000
AUU	chr4:6322045-6322294(+)$1	249	37	40	9.0000
AUU	chr13:98021044-98021281(+)$1	237	3	6	9.0000
AUU	chr1:186720782-186721020(-)$1	238	27	30	9.0000
AUU	chr1:58584643-58584879(-)$1	236	8	11	9.0000
AUU	chr11:66027299-66027554(-)$1	255	25	28	9.0000
AUU	chr8:67071732-67072013(-)$1	281	48	51	9.0000

#otherMatches

#Struct PSSM
hhh	chr12:36741081-36741318(-)$1	237	39	42	9.0000
hhh	chr2:136607904-136608169(+)$1	265	203	206	9.0000
ftt	chr9:58500334-58500635(+)$1	301	25	28	9.0000
::C	chr3:89238790-89239031(+)$1	241	27	30	9.0000
ff3	chr15:30958474-30958715(+)$1	241	174	177	9.0000
{DD	chr1:52220705-52220953(-)$1	248	16	19	9.0000
===	chr2:102629044-102629314(+)$1	270	122	125	9.0000
===	chr4:150436197-150436479(-)$1	282	235	238	9.0000
GGG	chr16:37888154-37888398(+)$1	244	129	132	9.0000
:::	chr10:70020236-70020476(+)$1	240	17	20	9.0000
:::	chr19:59373408-59373647(-)$1	239	2	5	9.0000
III	chr6:92324993-92325229(-)$1	236	34	37	9.0000
:::	chr5:89664881-89665126(+)$1	245	59	62	9.0000
:::	chr9:107950602-107950848(+)$1	246	3	6	9.0000
ooo	chr2:131762909-131763211(+)$1	302	48	51	9.0000
fff	chr2:158211402-158211658(+)$1	256	13	16	9.0000
mmd	chr6:114197708-114197947(+)$1	239	39	42	9.0000
:::	chr10:40657864-40658102(+)$1	238	22	25	9.0000
ddd	chr8:122686328-122686564(+)$1	236	26	29	9.0000
cco	chr11:109529284-109529537(+)$1	253	20	23	9.0000
:==	chr3:120907317-120907565(-)$1	248	3	6	9.0000
e""	chr18:63156896-63157151(+)$1	255	33	36	9.0000
LFF	chr18:35966507-35966742(+)$1	235	30	33	9.0000
DKK	chr5:122906322-122906560(-)$1	238	45	48	9.0000
:::	chr18:65373136-65373394(+)$1	258	9	12	9.0000
dff	chrX:96661226-96661469(-)$1	243	31	34	9.0000
qqd	chr6:72561784-72562025(-)$1	241	100	103	9.0000
fff	chr16:7412006-7412266(+)$1	260	56	59	9.0000
d!!	chr13:110844350-110844643(-)$1	293	52	55	9.0000
mmm	chr10:9476906-9477142(-)$1	236	43	46	9.0000
:::	chr2:138110336-138110575(+)$1	239	32	35	9.0000
FFF	chr7:91394776-91395045(-)$1	269	140	143	9.0000
CCC	chr10:34018422-34018682(+)$1	260	216	219	9.0000
D::	chr13:98021788-98022044(+)$1	256	5	8	9.0000
CCC	chr16:31095308-31095565(-)$1	257	30	33	9.0000
:::	chr5:143040156-143040391(-)$1	235	1	4	9.0000
^^^	chr2:163450342-163450603(-)$1	261	71	74	9.0000
:::	chr2:102621705-102622016(+)$1	311	4	7	9.0000
c%%	chr10:13869999-13870248(+)$1	249	12	15	9.0000
ggg	chr1:23373438-23373695(-)$1	257	4	7	9.0000
qqq	chr5:4803753-4803991(-)$1	238	65	68	9.0000
:::	chr3:107815196-107815451(-)$1	255	30	33	9.0000
2hh	chr5:77515979-77516221(-)$1	242	47	50	9.0000
:::	chr4:122871556-122871807(+)$1	251	0	3	9.0000
$$$	chr10:57236816-57237127(-)$1	311	22	25	9.0000
""g	chr3:80647535-80647791(-)$1	256	13	16	9.0000
xxx	chr1:52222521-52222773(-)$1	252	73	76	9.0000
qqq	chr18:59235342-59235577(+)$1	235	7	10	9.0000
OOO	chr17:65929526-65929778(-)$1	252	12	15	9.0000
b!!	chr11:86508092-86508333(-)$1	241	9	12	9.0000
:::	chr4:59234115-59234356(+)$1	241	17	20	9.0000
III	chr2:117107126-117107376(-)$1	250	35	38	9.0000
hhh	chr1:38852135-38852371(-)$1	236	160	163	9.0000
:::	chr4:55402861-55403112(+)$1	251	12	15	9.0000
:::	chr14:14446837-14447080(+)$1	243	34	37	9.0000
QQQ	chr9:86660070-86660332(-)$1	262	22	25	9.0000
c==	chr9:79618792-79619037(-)$1	245	36	39	9.0000
hhh	chr11:20724828-20725065(-)$1	237	43	46	9.0000
ggg	chr1:153210412-153210653(+)$1	241	68	71	9.0000
ggv	chr1:33855577-33855826(-)$1	249	14	17	9.0000
CKK	chrX:162823430-162823735(+)$1	305	12	15	9.0000
LCC	chr8:42418143-42418382(+)$1	239	19	22	9.0000
hhh	chr10:82212054-82212289(-)$1	235	81	84	9.0000
e::	chr4:107904064-107904301(-)$1	237	99	102	9.0000
:::	chr14:46078490-46078735(-)$1	245	1	4	9.0000
GGG	chr9:58499727-58500004(+)$1	277	56	59	9.0000
SSS	chr12:11331969-11332250(-)$1	281	24	27	9.0000
FFF	chr7:58926109-58926392(+)$1	283	19	22	9.0000
ttt	chrX:149046577-149046823(-)$1	246	99	102	9.0000
###	chr11:90139470-90139714(+)$1	244	24	27	9.0000
KDD	chr2:171862234-171862477(-)$1	243	39	42	9.0000
ddd	chr17:57219415-57219652(-)$1	237	154	157	9.0000
ggg	chr11:40492988-40493232(-)$1	244	46	49	9.0000
JJO	chr12:17798571-17798809(+)$1	238	15	18	9.0000
GGG	chr5:67681792-67682039(+)$1	247	9	12	9.0000
TTT	chr19:7500373-7500616(-)$1	243	21	24	9.0000
FDD	chr4:120640967-120641207(-)$1	240	151	154	9.0000
::E	chr6:5111178-5111446(+)$1	268	11	14	9.0000
^^^	chr7:149836734-149836969(-)$1	235	216	219	9.0000
d::	chr2:62162808-62163047(+)$1	239	51	54	9.0000
^^^	chr1:94911959-94912233(-)$1	274	164	167	9.0000
c]d	chr8:91275365-91275606(+)$1	241	44	47	9.0000
^^^	chr9:55984075-55984323(-)$1	248	10	13	9.0000
llg	chr11:42442929-42443173(+)$1	244	29	32	9.0000
:::	chr15:98000145-98000402(+)$1	257	41	44	9.0000
ggg	chr11:41945539-41945852(-)$1	313	44	47	9.0000
:::	chr12:86682950-86683192(-)$1	242	2	5	9.0000
[ee	chr16:7411239-7411495(+)$1	256	99	102	9.0000
EKK	chr8:56145814-56146102(+)$1	288	15	18	9.0000
3dd	chr4:6322045-6322294(+)$1	249	37	40	9.0000
ddd	chr13:98021044-98021281(+)$1	237	3	6	9.0000
eee	chr1:186720782-186721020(-)$1	238	27	30	9.0000
EOO	chr1:58584643-58584879(-)$1	236	8	11	9.0000
III	chr11:66027299-66027554(-)$1	255	25	28	9.0000
MMM	chr8:67071732-67072013(-)$1	281	48	51	9.0000

#DB
(((	chr12:36741081-36741318(-)$1	1	39	42	9.0000
(((	chr2:136607904-136608169(+)$1	1	203	206	9.0000
(..	chr9:58500334-58500635(+)$1	1	25	28	9.0000
..(	chr3:89238790-89239031(+)$1	1	27	30	9.0000
)).	chr15:30958474-30958715(+)$1	1	174	177	9.0000
.((	chr1:52220705-52220953(-)$1	1	16	19	9.0000
(((	chr2:102629044-102629314(+)$1	1	122	125	9.0000
)))	chr4:150436197-150436479(-)$1	1	235	238	9.0000
)))	chr16:37888154-37888398(+)$1	1	129	132	9.0000
...	chr10:70020236-70020476(+)$1	1	17	20	9.0000
...	chr19:59373408-59373647(-)$1	1	2	5	9.0000
(((	chr6:92324993-92325229(-)$1	1	34	37	9.0000
...	chr5:89664881-89665126(+)$1	1	59	62	9.0000
...	chr9:107950602-107950848(+)$1	1	3	6	9.0000
...	chr2:131762909-131763211(+)$1	1	48	51	9.0000
(((	chr2:158211402-158211658(+)$1	1	13	16	9.0000
..)	chr6:114197708-114197947(+)$1	1	39	42	9.0000
...	chr10:40657864-40658102(+)$1	1	22	25	9.0000
)))	chr8:122686328-122686564(+)$1	1	26	29	9.0000
((.	chr11:109529284-109529537(+)$1	1	20	23	9.0000
.((	chr3:120907317-120907565(-)$1	1	3	6	9.0000
(..	chr18:63156896-63157151(+)$1	1	33	36	9.0000
.((	chr18:35966507-35966742(+)$1	1	30	33	9.0000
(..	chr5:122906322-122906560(-)$1	1	45	48	9.0000
...	chr18:65373136-65373394(+)$1	1	9	12	9.0000
(((	chrX:96661226-96661469(-)$1	1	31	34	9.0000
..)	chr6:72561784-72562025(-)$1	1	100	103	9.0000
)))	chr16:7412006-7412266(+)$1	1	56	59	9.0000
(..	chr13:110844350-110844643(-)$1	1	52	55	9.0000
...	chr10:9476906-9477142(-)$1	1	43	46	9.0000
...	chr2:138110336-138110575(+)$1	1	32	35	9.0000
(((	chr7:91394776-91395045(-)$1	1	140	143	9.0000
)))	chr10:34018422-34018682(+)$1	1	216	219	9.0000
(..	chr13:98021788-98022044(+)$1	1	5	8	9.0000
(((	chr16:31095308-31095565(-)$1	1	30	33	9.0000
...	chr5:143040156-143040391(-)$1	1	1	4	9.0000
...	chr2:163450342-163450603(-)$1	1	71	74	9.0000
...	chr2:102621705-102622016(+)$1	1	4	7	9.0000
(..	chr10:13869999-13870248(+)$1	1	12	15	9.0000
(((	chr1:23373438-23373695(-)$1	1	4	7	9.0000
...	chr5:4803753-4803991(-)$1	1	65	68	9.0000
...	chr3:107815196-107815451(-)$1	1	30	33	9.0000
.))	chr5:77515979-77516221(-)$1	1	47	50	9.0000
...	chr4:122871556-122871807(+)$1	1	0	3	9.0000
...	chr10:57236816-57237127(-)$1	1	22	25	9.0000
..(	chr3:80647535-80647791(-)$1	1	13	16	9.0000
...	chr1:52222521-52222773(-)$1	1	73	76	9.0000
...	chr18:59235342-59235577(+)$1	1	7	10	9.0000
...	chr17:65929526-65929778(-)$1	1	12	15	9.0000
(..	chr11:86508092-86508333(-)$1	1	9	12	9.0000
...	chr4:59234115-59234356(+)$1	1	17	20	9.0000
(((	chr2:117107126-117107376(-)$1	1	35	38	9.0000
)))	chr1:38852135-38852371(-)$1	1	160	163	9.0000
...	chr4:55402861-55403112(+)$1	1	12	15	9.0000
...	chr14:14446837-14447080(+)$1	1	34	37	9.0000
...	chr9:86660070-86660332(-)$1	1	22	25	9.0000
)((	chr9:79618792-79619037(-)$1	1	36	39	9.0000
(((	chr11:20724828-20725065(-)$1	1	43	46	9.0000
(((	chr1:153210412-153210653(+)$1	1	68	71	9.0000
((.	chr1:33855577-33855826(-)$1	1	14	17	9.0000
(..	chrX:162823430-162823735(+)$1	1	12	15	9.0000
.((	chr8:42418143-42418382(+)$1	1	19	22	9.0000
(((	chr10:82212054-82212289(-)$1	1	81	84	9.0000
)..	chr4:107904064-107904301(-)$1	1	99	102	9.0000
...	chr14:46078490-46078735(-)$1	1	1	4	9.0000
(((	chr9:58499727-58500004(+)$1	1	56	59	9.0000
...	chr12:11331969-11332250(-)$1	1	24	27	9.0000
(((	chr7:58926109-58926392(+)$1	1	19	22	9.0000
...	chrX:149046577-149046823(-)$1	1	99	102	9.0000
...	chr11:90139470-90139714(+)$1	1	24	27	9.0000
.((	chr2:171862234-171862477(-)$1	1	39	42	9.0000
)))	chr17:57219415-57219652(-)$1	1	154	157	9.0000
(((	chr11:40492988-40493232(-)$1	1	46	49	9.0000
((.	chr12:17798571-17798809(+)$1	1	15	18	9.0000
(((	chr5:67681792-67682039(+)$1	1	9	12	9.0000
...	chr19:7500373-7500616(-)$1	1	21	24	9.0000
(((	chr4:120640967-120641207(-)$1	1	151	154	9.0000
..(	chr6:5111178-5111446(+)$1	1	11	14	9.0000
...	chr7:149836734-149836969(-)$1	1	216	219	9.0000
)..	chr2:62162808-62163047(+)$1	1	51	54	9.0000
...	chr1:94911959-94912233(-)$1	1	164	167	9.0000
).)	chr8:91275365-91275606(+)$1	1	44	47	9.0000
...	chr9:55984075-55984323(-)$1	1	10	13	9.0000
..)	chr11:42442929-42443173(+)$1	1	29	32	9.0000
...	chr15:98000145-98000402(+)$1	1	41	44	9.0000
(((	chr11:41945539-41945852(-)$1	1	44	47	9.0000
...	chr12:86682950-86683192(-)$1	1	2	5	9.0000
.((	chr16:7411239-7411495(+)$1	1	99	102	9.0000
(..	chr8:56145814-56146102(+)$1	1	15	18	9.0000
.))	chr4:6322045-6322294(+)$1	1	37	40	9.0000
(((	chr13:98021044-98021281(+)$1	1	3	6	9.0000
)))	chr1:186720782-186721020(-)$1	1	27	30	9.0000
(..	chr1:58584643-58584879(-)$1	1	8	11	9.0000
(((	chr11:66027299-66027554(-)$1	1	25	28	9.0000
...	chr8:67071732-67072013(-)$1	1	48	51	9.0000

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

#score	855.0000000000002
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m2_run2.nuc.txt

#NT
UUC	chr2:179932920-179933136(-)$1	216	155	158	9.0000
UUC	chr1:36236305-36236538(-)$1	233	5	8	9.0000
UUC	chr1:55084090-55084336(-)$1	246	61	64	9.0000
UUC	chr17:34027357-34027564(-)$1	207	37	40	9.0000
UUC	chr13:46772391-46772607(+)$1	216	6	9	9.0000
UUC	chr19:46966026-46966254(-)$1	228	46	49	9.0000
UUC	chr8:124328860-124329072(-)$1	212	24	27	9.0000
UUC	chr6:28657017-28657237(+)$1	220	91	94	9.0000
uuc	chr17:3412541-3412759(+)$1	218	42	45	9.0000
UUC	chr2:168008017-168008230(-)$1	213	61	64	9.0000
UUC	chr2:69218549-69218776(+)$1	227	47	50	9.0000
UUC	chr10:66620689-66620900(+)$1	211	30	33	9.0000
UUC	chr4:117549418-117549644(-)$1	226	6	9	9.0000
UUC	chr3:68877613-68877821(-)$1	208	88	91	9.0000
UUC	chr15:55394446-55394662(+)$1	216	36	39	9.0000
UUC	chr5:89102648-89102868(-)$1	220	91	94	9.0000
UUC	chr9:30977996-30978215(-)$1	219	63	66	9.0000
UUC	chr11:94149535-94149755(-)$1	220	11	14	9.0000
UUC	chr8:109889984-109890214(+)$1	230	57	60	9.0000
UUC	chr13:102527698-102527904(-)$1	206	82	85	9.0000
UUC	chr16:57153363-57153569(+)$1	206	32	35	9.0000
UUC	chr15:77241282-77241498(-)$1	216	57	60	9.0000
UUC	chr15:76520551-76520771(+)$1	220	25	28	9.0000
UUC	chrX:71558425-71558636(+)$1	211	104	107	9.0000
UUC	chr9:7155081-7155306(-)$1	225	42	45	9.0000
UUC	chr12:21337907-21338125(-)$1	218	146	149	9.0000
UUC	chr16:57156628-57156854(+)$1	226	13	16	9.0000
UUC	chr2:125083064-125083276(+)$1	212	0	3	9.0000
UUC	chr10:39536974-39537202(+)$1	228	6	9	9.0000
UUC	chr9:64882603-64882831(+)$1	228	25	28	9.0000
UUC	chr19:15995361-15995582(-)$1	221	78	81	9.0000
UUC	chr1:66445887-66446117(+)$1	230	12	15	9.0000
UUC	chr1:52244437-52244668(-)$1	231	32	35	9.0000
UUC	chr9:44615270-44615483(-)$1	213	11	14	9.0000
UUC	chr1:137303435-137303653(-)$1	218	26	29	9.0000
UUC	chr10:5191915-5192132(+)$1	217	67	70	9.0000
UUC	chr14:35490049-35490271(+)$1	222	69	72	9.0000
UUC	chr2:25784563-25784795(-)$1	232	7	10	9.0000
UUC	chr6:32842229-32842453(-)$1	224	3	6	9.0000
UUC	chr11:29924962-29925186(-)$1	224	30	33	9.0000
UUC	chr12:8716911-8717141(+)$1	230	6	9	9.0000
UUC	chr5:28744758-28744981(+)$1	223	17	20	9.0000
UUC	chr9:56934293-56934516(+)$1	223	28	31	9.0000
UUC	chr17:35258016-35258230(-)$1	214	11	14	9.0000
UUC	chr4:114672711-114672941(+)$1	230	25	28	9.0000
UUC	chr9:98993440-98993646(-)$1	206	18	21	9.0000
UUC	chr9:107517261-107517472(-)$1	211	102	105	9.0000
UUC	chr14:21843333-21843545(+)$1	212	87	90	9.0000
UUC	chrX:130758952-130759175(-)$1	223	11	14	9.0000
UUC	chr9:96240619-96240845(-)$1	226	2	5	9.0000
UUC	chr1:189049426-189049646(+)$1	220	57	60	9.0000
UUC	chr16:24442770-24442996(+)$1	226	17	20	9.0000
UUC	chr2:60800748-60800960(-)$1	212	124	127	9.0000
UUC	chr19:41289426-41289664(-)$1	238	0	3	9.0000
UUC	chr2:29541555-29541769(+)$1	214	3	6	9.0000
UUC	chr16:17651565-17651774(-)$1	209	71	74	9.0000
UUC	chr2:113682100-113682310(-)$1	210	33	36	9.0000
UUC	chr11:51417842-51418050(-)$1	208	33	36	9.0000
UUC	chr2:23366720-23366931(-)$1	211	27	30	9.0000
UUC	chr11:86998318-86998525(+)$1	207	52	55	9.0000
UUC	chr9:67741802-67742010(+)$1	208	34	37	9.0000
UUC	chr6:35461567-35461773(-)$1	206	6	9	9.0000
UUC	chr5:143145343-143145562(+)$1	219	76	79	9.0000
UUC	chr6:86363759-86363974(+)$1	215	23	26	9.0000
UUC	chr2:164838410-164838632(-)$1	222	23	26	9.0000
UUC	chr10:57786281-57786502(+)$1	221	9	12	9.0000
UUC	chr10:75386245-75386466(-)$1	221	0	3	9.0000
UUC	chrX:23333817-23334035(+)$1	218	53	56	9.0000
UUC	chr7:30972318-30972537(-)$1	219	5	8	9.0000
UUC	chr1:34213550-34213757(+)$1	207	4	7	9.0000
UUC	chr8:109893216-109893424(+)$1	208	71	74	9.0000
UUC	chr16:36874726-36874936(-)$1	210	12	15	9.0000
UUC	chr17:14041401-14041614(+)$1	213	81	84	9.0000
UUC	chr1:164504366-164504575(+)$1	209	20	23	9.0000
UUC	chr1:34248997-34249217(+)$1	220	146	149	9.0000
UUC	chr6:125312307-125312530(+)$1	223	20	23	9.0000
UUC	chr17:33801435-33801652(-)$1	217	142	145	9.0000
UUC	chr12:105960509-105960721(-)$1	212	49	52	9.0000
UUC	chr2:34627676-34627882(+)$1	206	31	34	9.0000
UUC	chrX:97818633-97818863(-)$1	230	81	84	9.0000
UUC	chr8:131237039-131237245(+)$1	206	10	13	9.0000
UUC	chr17:71793128-71793349(-)$1	221	0	3	9.0000
UUC	chr6:121202247-121202461(+)$1	214	78	81	9.0000
UUC	chr1:34269234-34269477(+)$1	243	70	73	9.0000
UUC	chr5:142927299-142927508(+)$1	209	129	132	9.0000
UUC	chr2:70926325-70926531(+)$1	206	30	33	9.0000
UUC	chr16:55890766-55890988(-)$1	222	1	4	9.0000
UUC	chr8:122032720-122032927(-)$1	207	102	105	9.0000
UUC	chr5:130007121-130007335(+)$1	214	89	92	9.0000
UUC	chr15:78605659-78605869(-)$1	210	35	38	9.0000
UUC	chr1:93284902-93285114(-)$1	212	45	48	9.0000
UUC	chr14:32004515-32004743(-)$1	228	18	21	9.0000
UUC	chr10:75723287-75723502(-)$1	215	1	4	9.0000
UUC	chr10:126986322-126986540(-)$1	218	77	80	9.0000
uuc	chr7:109309055-109309280(-)$1	225	2	5	9.0000
UUC	chr11:75314188-75314397(+)$1	209	6	9	9.0000
uuc	chr17:32914318-32914539(-)$1	221	18	21	9.0000

#otherMatches

#Struct PSSM
:::	chr11:62134556-62134775(-)$1	219	0	3	9.0000
c!!	chr2:179932920-179933136(-)$1	216	155	158	9.0000
:::	chr1:36236305-36236538(-)$1	233	5	8	9.0000
rrr	chr1:55084090-55084336(-)$1	246	61	64	9.0000
eeb	chr17:34027357-34027564(-)$1	207	37	40	9.0000
:::	chr13:46772391-46772607(+)$1	216	6	9	9.0000
ggg	chr19:46966026-46966254(-)$1	228	46	49	9.0000
KCC	chr8:124328860-124329072(-)$1	212	24	27	9.0000
]cc	chr6:28657017-28657237(+)$1	220	91	94	9.0000
eee	chr17:3412541-3412759(+)$1	218	42	45	9.0000
:::	chr2:168008017-168008230(-)$1	213	61	64	9.0000
#cc	chr2:69218549-69218776(+)$1	227	47	50	9.0000
gBB	chr10:66620689-66620900(+)$1	211	30	33	9.0000
fff	chr4:117549418-117549644(-)$1	226	6	9	9.0000
eee	chr3:68877613-68877821(-)$1	208	88	91	9.0000
h::	chr15:55394446-55394662(+)$1	216	36	39	9.0000
ccc	chr5:89102648-89102868(-)$1	220	91	94	9.0000
d]g	chr9:30977996-30978215(-)$1	219	63	66	9.0000
DDK	chr11:94149535-94149755(-)$1	220	11	14	9.0000
ee]	chr8:109889984-109890214(+)$1	230	57	60	9.0000
hhh	chr13:102527698-102527904(-)$1	206	82	85	9.0000
ggg	chr16:57153363-57153569(+)$1	206	32	35	9.0000
fff	chr15:77241282-77241498(-)$1	216	57	60	9.0000
yyy	chr15:76520551-76520771(+)$1	220	25	28	9.0000
f[d	chrX:71558425-71558636(+)$1	211	104	107	9.0000
III	chr9:7155081-7155306(-)$1	225	42	45	9.0000
ggn	chr12:21337907-21338125(-)$1	218	146	149	9.0000
hhh	chr16:57156628-57156854(+)$1	226	13	16	9.0000
:::	chr2:125083064-125083276(+)$1	212	0	3	9.0000
JJJ	chr10:39536974-39537202(+)$1	228	6	9	9.0000
HHH	chr9:64882603-64882831(+)$1	228	25	28	9.0000
fff	chr19:15995361-15995582(-)$1	221	78	81	9.0000
FFF	chr1:66445887-66446117(+)$1	230	12	15	9.0000
ccc	chr1:52244437-52244668(-)$1	231	32	35	9.0000
cc#	chr9:44615270-44615483(-)$1	213	11	14	9.0000
D::	chr1:137303435-137303653(-)$1	218	26	29	9.0000
d00	chr10:5191915-5192132(+)$1	217	67	70	9.0000
===	chr14:35490049-35490271(+)$1	222	69	72	9.0000
:II	chr2:25784563-25784795(-)$1	232	7	10	9.0000
:CC	chr6:32842229-32842453(-)$1	224	3	6	9.0000
:::	chr11:29924962-29925186(-)$1	224	30	33	9.0000
:JJ	chr12:8716911-8717141(+)$1	230	6	9	9.0000
nnn	chr5:28744758-28744981(+)$1	223	17	20	9.0000
ELL	chr9:56934293-56934516(+)$1	223	28	31	9.0000
LLF	chr17:35258016-35258230(-)$1	214	11	14	9.0000
ooo	chr4:114672711-114672941(+)$1	230	25	28	9.0000
+ff	chr9:98993440-98993646(-)$1	206	18	21	9.0000
+++	chr9:107517261-107517472(-)$1	211	102	105	9.0000
GGG	chr14:21843333-21843545(+)$1	212	87	90	9.0000
ooo	chrX:130758952-130759175(-)$1	223	11	14	9.0000
:::	chr9:96240619-96240845(-)$1	226	2	5	9.0000
gg"	chr1:189049426-189049646(+)$1	220	57	60	9.0000
b!!	chr16:24442770-24442996(+)$1	226	17	20	9.0000
:::	chr2:60800748-60800960(-)$1	212	124	127	9.0000
:::	chr19:41289426-41289664(-)$1	238	0	3	9.0000
:::	chr2:29541555-29541769(+)$1	214	3	6	9.0000
:::	chr16:17651565-17651774(-)$1	209	71	74	9.0000
B{D	chr2:113682100-113682310(-)$1	210	33	36	9.0000
GGG	chr11:51417842-51418050(-)$1	208	33	36	9.0000
vvv	chr2:23366720-23366931(-)$1	211	27	30	9.0000
eee	chr11:86998318-86998525(+)$1	207	52	55	9.0000
ll=	chr9:67741802-67742010(+)$1	208	34	37	9.0000
###	chr6:35461567-35461773(-)$1	206	6	9	9.0000
ddd	chr5:143145343-143145562(+)$1	219	76	79	9.0000
dd]	chr6:86363759-86363974(+)$1	215	23	26	9.0000
MCC	chr2:164838410-164838632(-)$1	222	23	26	9.0000
rrr	chr10:57786281-57786502(+)$1	221	9	12	9.0000
:DD	chr10:75386245-75386466(-)$1	221	0	3	9.0000
cff	chrX:23333817-23334035(+)$1	218	53	56	9.0000
KKB	chr7:30972318-30972537(-)$1	219	5	8	9.0000
:::	chr1:34213550-34213757(+)$1	207	4	7	9.0000
:::	chr8:109893216-109893424(+)$1	208	71	74	9.0000
GGG	chr16:36874726-36874936(-)$1	210	12	15	9.0000
:::	chr17:14041401-14041614(+)$1	213	81	84	9.0000
CC{	chr1:164504366-164504575(+)$1	209	20	23	9.0000
D||	chr1:34248997-34249217(+)$1	220	146	149	9.0000
c##	chr6:125312307-125312530(+)$1	223	20	23	9.0000
odd	chr17:33801435-33801652(-)$1	217	142	145	9.0000
]dd	chr12:105960509-105960721(-)$1	212	49	52	9.0000
GGG	chr2:34627676-34627882(+)$1	206	31	34	9.0000
ddd	chrX:97818633-97818863(-)$1	230	81	84	9.0000
eee	chr8:131237039-131237245(+)$1	206	10	13	9.0000
eee	chr17:71793128-71793349(-)$1	221	0	3	9.0000
mmm	chr6:121202247-121202461(+)$1	214	78	81	9.0000
EE:	chr1:34269234-34269477(+)$1	243	70	73	9.0000
ddd	chr5:142927299-142927508(+)$1	209	129	132	9.0000
eee	chr2:70926325-70926531(+)$1	206	30	33	9.0000
:::	chr16:55890766-55890988(-)$1	222	1	4	9.0000
dbb	chr8:122032720-122032927(-)$1	207	102	105	9.0000
fff	chr5:130007121-130007335(+)$1	214	89	92	9.0000
:::	chr15:78605659-78605869(-)$1	210	35	38	9.0000
d:g	chr1:93284902-93285114(-)$1	212	45	48	9.0000
eee	chr14:32004515-32004743(-)$1	228	18	21	9.0000
:ee	chr10:75723287-75723502(-)$1	215	1	4	9.0000
dll	chr10:126986322-126986540(-)$1	218	77	80	9.0000
:::	chr7:109309055-109309280(-)$1	225	2	5	9.0000
:ee	chr11:75314188-75314397(+)$1	209	6	9	9.0000
mmm	chr17:32914318-32914539(-)$1	221	18	21	9.0000

#DB
...	chr11:62134556-62134775(-)$1	1	0	3	9.0000
(..	chr2:179932920-179933136(-)$1	1	155	158	9.0000
...	chr1:36236305-36236538(-)$1	1	5	8	9.0000
...	chr1:55084090-55084336(-)$1	1	61	64	9.0000
(((	chr17:34027357-34027564(-)$1	1	37	40	9.0000
...	chr13:46772391-46772607(+)$1	1	6	9	9.0000
(((	chr19:46966026-46966254(-)$1	1	46	49	9.0000
.((	chr8:124328860-124329072(-)$1	1	24	27	9.0000
.))	chr6:28657017-28657237(+)$1	1	91	94	9.0000
)))	chr17:3412541-3412759(+)$1	1	42	45	9.0000
...	chr2:168008017-168008230(-)$1	1	61	64	9.0000
.((	chr2:69218549-69218776(+)$1	1	47	50	9.0000
)((	chr10:66620689-66620900(+)$1	1	30	33	9.0000
(((	chr4:117549418-117549644(-)$1	1	6	9	9.0000
)))	chr3:68877613-68877821(-)$1	1	88	91	9.0000
)..	chr15:55394446-55394662(+)$1	1	36	39	9.0000
)))	chr5:89102648-89102868(-)$1	1	91	94	9.0000
).)	chr9:30977996-30978215(-)$1	1	63	66	9.0000
((.	chr11:94149535-94149755(-)$1	1	11	14	9.0000
)).	chr8:109889984-109890214(+)$1	1	57	60	9.0000
(((	chr13:102527698-102527904(-)$1	1	82	85	9.0000
(((	chr16:57153363-57153569(+)$1	1	32	35	9.0000
)))	chr15:77241282-77241498(-)$1	1	57	60	9.0000
...	chr15:76520551-76520771(+)$1	1	25	28	9.0000
(.(	chrX:71558425-71558636(+)$1	1	104	107	9.0000
(((	chr9:7155081-7155306(-)$1	1	42	45	9.0000
((.	chr12:21337907-21338125(-)$1	1	146	149	9.0000
(((	chr16:57156628-57156854(+)$1	1	13	16	9.0000
...	chr2:125083064-125083276(+)$1	1	0	3	9.0000
(((	chr10:39536974-39537202(+)$1	1	6	9	9.0000
(((	chr9:64882603-64882831(+)$1	1	25	28	9.0000
(((	chr19:15995361-15995582(-)$1	1	78	81	9.0000
(((	chr1:66445887-66446117(+)$1	1	12	15	9.0000
(((	chr1:52244437-52244668(-)$1	1	32	35	9.0000
((.	chr9:44615270-44615483(-)$1	1	11	14	9.0000
(..	chr1:137303435-137303653(-)$1	1	26	29	9.0000
)..	chr10:5191915-5192132(+)$1	1	67	70	9.0000
(((	chr14:35490049-35490271(+)$1	1	69	72	9.0000
.((	chr2:25784563-25784795(-)$1	1	7	10	9.0000
.((	chr6:32842229-32842453(-)$1	1	3	6	9.0000
...	chr11:29924962-29925186(-)$1	1	30	33	9.0000
.((	chr12:8716911-8717141(+)$1	1	6	9	9.0000
...	chr5:28744758-28744981(+)$1	1	17	20	9.0000
(..	chr9:56934293-56934516(+)$1	1	28	31	9.0000
..(	chr17:35258016-35258230(-)$1	1	11	14	9.0000
...	chr4:114672711-114672941(+)$1	1	25	28	9.0000
.((	chr9:98993440-98993646(-)$1	1	18	21	9.0000
...	chr9:107517261-107517472(-)$1	1	102	105	9.0000
(((	chr14:21843333-21843545(+)$1	1	87	90	9.0000
...	chrX:130758952-130759175(-)$1	1	11	14	9.0000
...	chr9:96240619-96240845(-)$1	1	2	5	9.0000
((.	chr1:189049426-189049646(+)$1	1	57	60	9.0000
(..	chr16:24442770-24442996(+)$1	1	17	20	9.0000
...	chr2:60800748-60800960(-)$1	1	124	127	9.0000
...	chr19:41289426-41289664(-)$1	1	0	3	9.0000
...	chr2:29541555-29541769(+)$1	1	3	6	9.0000
...	chr16:17651565-17651774(-)$1	1	71	74	9.0000
(.(	chr2:113682100-113682310(-)$1	1	33	36	9.0000
(((	chr11:51417842-51418050(-)$1	1	33	36	9.0000
...	chr2:23366720-23366931(-)$1	1	27	30	9.0000
(((	chr11:86998318-86998525(+)$1	1	52	55	9.0000
..)	chr9:67741802-67742010(+)$1	1	34	37	9.0000
...	chr6:35461567-35461773(-)$1	1	6	9	9.0000
(((	chr5:143145343-143145562(+)$1	1	76	79	9.0000
)).	chr6:86363759-86363974(+)$1	1	23	26	9.0000
.((	chr2:164838410-164838632(-)$1	1	23	26	9.0000
...	chr10:57786281-57786502(+)$1	1	9	12	9.0000
.((	chr10:75386245-75386466(-)$1	1	0	3	9.0000
)((	chrX:23333817-23334035(+)$1	1	53	56	9.0000
..(	chr7:30972318-30972537(-)$1	1	5	8	9.0000
...	chr1:34213550-34213757(+)$1	1	4	7	9.0000
...	chr8:109893216-109893424(+)$1	1	71	74	9.0000
(((	chr16:36874726-36874936(-)$1	1	12	15	9.0000
...	chr17:14041401-14041614(+)$1	1	81	84	9.0000
((.	chr1:164504366-164504575(+)$1	1	20	23	9.0000
)..	chr1:34248997-34249217(+)$1	1	146	149	9.0000
(..	chr6:125312307-125312530(+)$1	1	20	23	9.0000
.))	chr17:33801435-33801652(-)$1	1	142	145	9.0000
.))	chr12:105960509-105960721(-)$1	1	49	52	9.0000
(((	chr2:34627676-34627882(+)$1	1	31	34	9.0000
(((	chrX:97818633-97818863(-)$1	1	81	84	9.0000
(((	chr8:131237039-131237245(+)$1	1	10	13	9.0000
(((	chr17:71793128-71793349(-)$1	1	0	3	9.0000
...	chr6:121202247-121202461(+)$1	1	78	81	9.0000
)).	chr1:34269234-34269477(+)$1	1	70	73	9.0000
(((	chr5:142927299-142927508(+)$1	1	129	132	9.0000
(((	chr2:70926325-70926531(+)$1	1	30	33	9.0000
...	chr16:55890766-55890988(-)$1	1	1	4	9.0000
)))	chr8:122032720-122032927(-)$1	1	102	105	9.0000
)))	chr5:130007121-130007335(+)$1	1	89	92	9.0000
...	chr15:78605659-78605869(-)$1	1	35	38	9.0000
).(	chr1:93284902-93285114(-)$1	1	45	48	9.0000
)))	chr14:32004515-32004743(-)$1	1	18	21	9.0000
.((	chr10:75723287-75723502(-)$1	1	1	4	9.0000
(..	chr10:126986322-126986540(-)$1	1	77	80	9.0000
...	chr7:109309055-109309280(-)$1	1	2	5	9.0000
.((	chr11:75314188-75314397(+)$1	1	6	9	9.0000
...	chr17:32914318-32914539(-)$1	1	18	21	9.0000

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

#score	882.0000000000002
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_CDS_m2_run1.nuc.txt

#NT
UUUCU	chr9:79481417-79481642(-)$1	225	74	79	15.0000
UUUCU	chr5:124736303-124736511(-)$1	208	67	72	15.0000
UUUCU	chr10:117218357-117218584(-)$1	227	213	218	15.0000
UUUCU	chr15:8124675-8124900(+)$1	225	40	45	15.0000
UUUCU	chrX:126494499-126494718(+)$1	219	64	69	15.0000
UUUCU	chr16:17522663-17522883(+)$1	220	116	121	15.0000
UUUCU	chr11:98857121-98857363(-)$1	242	116	121	15.0000
UUUCU	chr11:62224278-62224488(-)$1	210	37	42	15.0000
UUUCU	chr2:156321565-156321789(+)$1	224	18	23	15.0000
UUUCU	chr5:130663219-130663434(+)$1	215	156	161	15.0000
UUUCU	chr3:159586309-159586527(+)$1	218	18	23	15.0000
UUUCU	chr1:182080175-182080398(+)$1	223	76	81	15.0000
UUUCU	chr9:115176360-115176566(-)$1	206	129	134	15.0000
UUUCU	chr9:58491246-58491465(+)$1	219	93	98	15.0000
UUUCU	chr8:81054905-81055125(+)$1	220	59	64	15.0000
UUUCU	chr1:60196062-60196287(+)$1	225	151	156	15.0000
UUUCU	chrX:65948091-65948343(+)$1	252	203	208	15.0000
UUUCU	chrX:20252921-20253132(+)$1	211	35	40	15.0000
UUUCU	chr7:77499703-77499923(-)$1	220	96	101	15.0000
UUUCU	chr9:7936429-7936646(-)$1	217	176	181	15.0000
UUUCU	chrX:90708567-90708781(-)$1	214	167	172	15.0000
UUUCU	chr15:38978146-38978365(+)$1	219	7	12	15.0000
UUUCU	chr2:120772304-120772524(-)$1	220	172	177	15.0000
UUUCU	chr5:121864750-121864959(+)$1	209	151	156	15.0000
UUUCU	chr2:119456006-119456225(+)$1	219	52	57	15.0000
UUUCU	chr1:10150704-10150933(-)$1	229	27	32	15.0000
UUUCU	chr2:104286625-104286844(-)$1	219	12	17	15.0000
UUUCU	chr5:4101179-4101404(-)$1	225	39	44	15.0000
UUUCU	chr1:89882605-89882820(-)$1	215	70	75	15.0000
UUUCU	chr17:15093661-15093875(-)$1	214	205	210	15.0000
UUUCU	chr18:36749102-36749327(+)$1	225	137	142	15.0000
UUUCU	chr18:32572718-32572936(+)$1	218	16	21	15.0000
UUUCU	chr15:99534122-99534337(+)$1	215	32	37	15.0000
uuucu	chr13:55401178-55401410(+)$1	232	225	230	15.0000
UUUCU	chr8:34872457-34872680(+)$1	223	103	108	15.0000
UUUCU	chr1:164637833-164638039(-)$1	206	46	51	15.0000
UUUCU	chr5:123164345-123164571(+)$1	226	54	59	15.0000
UUUCU	chr14:8973908-8974125(+)$1	217	39	44	15.0000
UUUCU	chr2:14059666-14059885(+)$1	219	46	51	15.0000
UUUCU	chr11:78042394-78042613(-)$1	219	31	36	15.0000
UUUCU	chr4:106019149-106019374(+)$1	225	197	202	15.0000
UUUCU	chr1:95524135-95524368(-)$1	233	66	71	15.0000
UUUCU	chr15:36535168-36535398(-)$1	230	25	30	15.0000
UUUCU	chr4:123059798-123060013(-)$1	215	24	29	15.0000
UUUCU	chr4:123045118-123045354(-)$1	236	160	165	15.0000
UUUCU	chr18:34988006-34988216(+)$1	210	204	209	15.0000
UUUCU	chr8:108627872-108628088(+)$1	216	208	213	15.0000
UUUCU	chr12:88709932-88710159(-)$1	227	218	223	15.0000
UUUCU	chr18:5095107-5095327(+)$1	220	26	31	15.0000
UUUCU	chr8:75572241-75572459(-)$1	218	42	47	15.0000
UUUCU	chr19:41330667-41330904(-)$1	237	61	66	15.0000
UUUCU	chr3:38876090-38876308(+)$1	218	3	8	15.0000
UUUCU	chr1:34247269-34247476(+)$1	207	33	38	15.0000
UUUCU	chr14:69974696-69974914(+)$1	218	47	52	15.0000
UUUCU	chr17:29815900-29816119(+)$1	219	175	180	15.0000
UUUCU	chr11:119294685-119294910(+)$1	225	181	186	15.0000
UUUCU	chr10:44817172-44817391(+)$1	219	199	204	15.0000
UUUCU	chr5:144662571-144662816(+)$1	245	71	76	15.0000
UUUCU	chr11:4718432-4718662(-)$1	230	145	150	15.0000

#otherMatches

#Struct PSSM
nnnne	chr19:42040603-42040852(-)$1	249	26	31	15.0000
cc555	chr9:79481417-79481642(-)$1	225	74	79	15.0000
{HHHH	chr5:124736303-124736511(-)$1	208	67	72	15.0000
oofff	chr10:117218357-117218584(-)$1	227	213	218	15.0000
ggggg	chr15:8124675-8124900(+)$1	225	40	45	15.0000
hhh]c	chrX:126494499-126494718(+)$1	219	64	69	15.0000
""ddd	chr16:17522663-17522883(+)$1	220	116	121	15.0000
ggggg	chr11:98857121-98857363(-)$1	242	116	121	15.0000
hhhhh	chr11:62224278-62224488(-)$1	210	37	42	15.0000
EKKBB	chr2:156321565-156321789(+)$1	224	18	23	15.0000
cdddd	chr5:130663219-130663434(+)$1	215	156	161	15.0000
d[fff	chr3:159586309-159586527(+)$1	218	18	23	15.0000
iiiii	chr1:182080175-182080398(+)$1	223	76	81	15.0000
e"""i	chr9:115176360-115176566(-)$1	206	129	134	15.0000
EEEEE	chr9:58491246-58491465(+)$1	219	93	98	15.0000
fffff	chr8:81054905-81055125(+)$1	220	59	64	15.0000
2eeee	chr1:60196062-60196287(+)$1	225	151	156	15.0000
hhhhh	chrX:65948091-65948343(+)$1	252	203	208	15.0000
KDDDD	chrX:20252921-20253132(+)$1	211	35	40	15.0000
:====	chr7:77499703-77499923(-)$1	220	96	101	15.0000
a333c	chr9:7936429-7936646(-)$1	217	176	181	15.0000
d####	chrX:90708567-90708781(-)$1	214	167	172	15.0000
eeeeq	chr15:38978146-38978365(+)$1	219	7	12	15.0000
fffff	chr2:120772304-120772524(-)$1	220	172	177	15.0000
iiiii	chr5:121864750-121864959(+)$1	209	151	156	15.0000
JJJJJ	chr2:119456006-119456225(+)$1	219	52	57	15.0000
iiiii	chr1:10150704-10150933(-)$1	229	27	32	15.0000
FFFFF	chr2:104286625-104286844(-)$1	219	12	17	15.0000
:HHHH	chr5:4101179-4101404(-)$1	225	39	44	15.0000
mmddd	chr1:89882605-89882820(-)$1	215	70	75	15.0000
:::::	chr17:15093661-15093875(-)$1	214	205	210	15.0000
iiiii	chr18:36749102-36749327(+)$1	225	137	142	15.0000
::ddd	chr18:32572718-32572936(+)$1	218	16	21	15.0000
LLLEE	chr15:99534122-99534337(+)$1	215	32	37	15.0000
:::::	chr13:55401178-55401410(+)$1	232	225	230	15.0000
""fff	chr8:34872457-34872680(+)$1	223	103	108	15.0000
::eee	chr1:164637833-164638039(-)$1	206	46	51	15.0000
ggggg	chr5:123164345-123164571(+)$1	226	54	59	15.0000
eelll	chr14:8973908-8974125(+)$1	217	39	44	15.0000
fqqqq	chr2:14059666-14059885(+)$1	219	46	51	15.0000
eeccc	chr11:78042394-78042613(-)$1	219	31	36	15.0000
ZZZFF	chr4:106019149-106019374(+)$1	225	197	202	15.0000
mmmmd	chr1:95524135-95524368(-)$1	233	66	71	15.0000
ggggg	chr15:36535168-36535398(-)$1	230	25	30	15.0000
JJJJJ	chr4:123059798-123060013(-)$1	215	24	29	15.0000
eee22	chr4:123045118-123045354(-)$1	236	160	165	15.0000
}CCC:	chr18:34988006-34988216(+)$1	210	204	209	15.0000
:::::	chr8:108627872-108628088(+)$1	216	208	213	15.0000
?????	chr12:88709932-88710159(-)$1	227	218	223	15.0000
fqqqq	chr18:5095107-5095327(+)$1	220	26	31	15.0000
:::::	chr8:75572241-75572459(-)$1	218	42	47	15.0000
hhhhh	chr19:41330667-41330904(-)$1	237	61	66	15.0000
:::::	chr3:38876090-38876308(+)$1	218	3	8	15.0000
qqqqc	chr1:34247269-34247476(+)$1	207	33	38	15.0000
g]bb2	chr14:69974696-69974914(+)$1	218	47	52	15.0000
DZZZF	chr17:29815900-29816119(+)$1	219	175	180	15.0000
F}CCC	chr11:119294685-119294910(+)$1	225	181	186	15.0000
|||BB	chr10:44817172-44817391(+)$1	219	199	204	15.0000
hhhhh	chr5:144662571-144662816(+)$1	245	71	76	15.0000
fffff	chr11:4718432-4718662(-)$1	230	145	150	15.0000

#DB
....)	chr19:42040603-42040852(-)$1	1	26	31	15.0000
))...	chr9:79481417-79481642(-)$1	1	74	79	15.0000
.((((	chr5:124736303-124736511(-)$1	1	67	72	15.0000
..)))	chr10:117218357-117218584(-)$1	1	213	218	15.0000
(((((	chr15:8124675-8124900(+)$1	1	40	45	15.0000
))).)	chrX:126494499-126494718(+)$1	1	64	69	15.0000
..(((	chr16:17522663-17522883(+)$1	1	116	121	15.0000
(((((	chr11:98857121-98857363(-)$1	1	116	121	15.0000
(((((	chr11:62224278-62224488(-)$1	1	37	42	15.0000
(..((	chr2:156321565-156321789(+)$1	1	18	23	15.0000
(((((	chr5:130663219-130663434(+)$1	1	156	161	15.0000
(.(((	chr3:159586309-159586527(+)$1	1	18	23	15.0000
(((((	chr1:182080175-182080398(+)$1	1	76	81	15.0000
(...(	chr9:115176360-115176566(-)$1	1	129	134	15.0000
(((((	chr9:58491246-58491465(+)$1	1	93	98	15.0000
)))))	chr8:81054905-81055125(+)$1	1	59	64	15.0000
.))))	chr1:60196062-60196287(+)$1	1	151	156	15.0000
)))))	chrX:65948091-65948343(+)$1	1	203	208	15.0000
.((((	chrX:20252921-20253132(+)$1	1	35	40	15.0000
.((((	chr7:77499703-77499923(-)$1	1	96	101	15.0000
)...)	chr9:7936429-7936646(-)$1	1	176	181	15.0000
(....	chrX:90708567-90708781(-)$1	1	167	172	15.0000
((((.	chr15:38978146-38978365(+)$1	1	7	12	15.0000
(((((	chr2:120772304-120772524(-)$1	1	172	177	15.0000
)))))	chr5:121864750-121864959(+)$1	1	151	156	15.0000
(((((	chr2:119456006-119456225(+)$1	1	52	57	15.0000
(((((	chr1:10150704-10150933(-)$1	1	27	32	15.0000
(((((	chr2:104286625-104286844(-)$1	1	12	17	15.0000
.((((	chr5:4101179-4101404(-)$1	1	39	44	15.0000
..)))	chr1:89882605-89882820(-)$1	1	70	75	15.0000
.....	chr17:15093661-15093875(-)$1	1	205	210	15.0000
)))))	chr18:36749102-36749327(+)$1	1	137	142	15.0000
..(((	chr18:32572718-32572936(+)$1	1	16	21	15.0000
...((	chr15:99534122-99534337(+)$1	1	32	37	15.0000
.....	chr13:55401178-55401410(+)$1	1	225	230	15.0000
..(((	chr8:34872457-34872680(+)$1	1	103	108	15.0000
..(((	chr1:164637833-164638039(-)$1	1	46	51	15.0000
(((((	chr5:123164345-123164571(+)$1	1	54	59	15.0000
((...	chr14:8973908-8974125(+)$1	1	39	44	15.0000
(....	chr2:14059666-14059885(+)$1	1	46	51	15.0000
)))))	chr11:78042394-78042613(-)$1	1	31	36	15.0000
...))	chr4:106019149-106019374(+)$1	1	197	202	15.0000
....)	chr1:95524135-95524368(-)$1	1	66	71	15.0000
(((((	chr15:36535168-36535398(-)$1	1	25	30	15.0000
(((((	chr4:123059798-123060013(-)$1	1	24	29	15.0000
)))..	chr4:123045118-123045354(-)$1	1	160	165	15.0000
.))).	chr18:34988006-34988216(+)$1	1	204	209	15.0000
.....	chr8:108627872-108628088(+)$1	1	208	213	15.0000
.....	chr12:88709932-88710159(-)$1	1	218	223	15.0000
(....	chr18:5095107-5095327(+)$1	1	26	31	15.0000
.....	chr8:75572241-75572459(-)$1	1	42	47	15.0000
(((((	chr19:41330667-41330904(-)$1	1	61	66	15.0000
.....	chr3:38876090-38876308(+)$1	1	3	8	15.0000
....)	chr1:34247269-34247476(+)$1	1	33	38	15.0000
).)).	chr14:69974696-69974914(+)$1	1	47	52	15.0000
)...)	chr17:29815900-29816119(+)$1	1	175	180	15.0000
).)))	chr11:119294685-119294910(+)$1	1	181	186	15.0000
...))	chr10:44817172-44817391(+)$1	1	199	204	15.0000
(((((	chr5:144662571-144662816(+)$1	1	71	76	15.0000
)))))	chr11:4718432-4718662(-)$1	1	145	150	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
HITSCLIP_AGO2_Chi2009_mm9_UTR_m2_run1.nuc.txt

#NT
UUUCU	chr3:57260634-57260968(-)$1	334	128	133	14.9999
UUUCU	chr12:91570971-91571236(+)$1	265	184	189	14.9999
UUUCU	chr2:140484064-140484338(-)$1	274	0	5	14.9999
UUUCU	chr9:72595712-72596015(+)$1	303	69	74	14.9999
UUUCU	chr4:138013090-138013373(+)$1	283	15	20	14.9999
UUUCU	chr19:57111263-57111516(-)$1	253	7	12	14.9999
UUUCU	chr2:156365974-156366237(+)$1	263	233	238	14.9999
UUUCU	chr12:101444912-101445265(+)$1	353	38	43	14.9999
UUUCU	chr11:117020309-117020630(+)$1	321	112	117	14.9999
UUUCU	chr12:8349497-8349753(+)$1	256	117	122	14.9999
UUUCU	chr18:75555264-75555519(+)$1	255	242	247	14.9999
UUUCU	chrX:71109394-71109630(-)$1	236	170	175	14.9999
UUUCU	chr6:71760197-71760473(+)$1	276	42	47	14.9999
UUUCU	chr13:31652027-31652265(+)$1	238	84	89	14.9999
UUUCU	chr12:81208710-81208975(-)$1	265	131	136	14.9999
UUUCU	chr11:8893389-8893654(-)$1	265	32	37	14.9999
UUUCU	chr16:44087395-44087719(-)$1	324	54	59	14.9999
UUUCU	chr11:77694141-77694400(-)$1	259	54	59	14.9999
UUUCU	chr16:37881799-37882046(+)$1	247	208	213	14.9999
UUUCU	chr1:65320326-65320577(+)$1	251	82	87	14.9999
UUUCU	chr19:23241191-23241457(+)$1	266	90	95	14.9999
UUUCU	chr7:135036515-135036792(-)$1	277	200	205	14.9999
UUUCU	chr3:107271962-107272212(-)$1	250	48	53	14.9999
UUUCU	chr13:38593051-38593316(-)$1	265	12	17	14.9999
UUUCU	chr1:175264517-175264768(-)$1	251	96	101	14.9999
UUUCU	chr5:122906964-122907239(-)$1	275	150	155	14.9999
UUUCU	chr16:43862569-43862848(-)$1	279	33	38	14.9999
uuucu	chr1:174202457-174202896(-)$1	439	246	251	14.9999
UUUCU	chr11:68628417-68628672(+)$1	255	31	36	14.9999
UUUCU	chr1:37496161-37496448(-)$1	287	5	10	14.9999
UUUCU	chr11:55208585-55208857(-)$1	272	111	116	14.9999
UUUCU	chr8:131256395-131256729(+)$1	334	218	223	14.9999
UUUCU	chr2:28085569-28085809(+)$1	240	141	146	14.9999
UUUCU	chr3:146394178-146394436(-)$1	258	103	108	14.9999
UUUCU	chr17:31982873-31983129(-)$1	256	32	37	14.9999
UUUCU	chr13:110741513-110741807(+)$1	294	61	66	14.9999
UUUCU	chr6:13036253-13036510(+)$1	257	78	83	14.9999
UUUCU	chr15:32964077-32964354(+)$1	277	146	151	14.9999
UUUCU	chr4:123054309-123054559(-)$1	250	71	76	14.9999
UUUCU	chr11:94200910-94201176(+)$1	266	25	30	14.9999
UUUCU	chr7:74385108-74385409(-)$1	301	253	258	14.9999
UUUCU	chr6:38456332-38456624(+)$1	292	67	72	14.9999
UUUCU	chr2:84442701-84442997(-)$1	296	30	35	14.9999
uuucu	chr6:48386615-48386850(-)$1	235	172	177	14.9999
UUUCU	chr1:13129457-13129710(-)$1	253	84	89	14.9999
UUUCU	chr17:17665317-17665599(-)$1	282	188	193	14.9999
UUUCU	chr3:108596393-108596653(-)$1	260	111	116	14.9999
UUUCU	chr5:124943052-124943292(-)$1	240	223	228	14.9999
UUUCU	chr18:31597435-31597719(-)$1	284	272	277	14.9999
UUUCU	chr11:101052353-101052593(-)$1	240	103	108	14.9999
UUUCU	chr6:38769134-38769402(-)$1	268	75	80	14.9999
UUUCU	chr12:109151877-109152142(-)$1	265	114	119	14.9999
UUUCU	chr4:100823016-100823307(+)$1	291	149	154	14.9999
UUUCU	chr16:89787282-89787538(-)$1	256	85	90	14.9999
UUUCU	chr6:131315179-131315517(-)$1	338	84	89	14.9999
UUUCU	chrX:23382308-23382547(+)$1	239	73	78	14.9999
UUUCU	chr3:89072066-89072343(-)$1	277	111	116	14.9999
uUUCU	chr2:121136302-121136570(-)$1	268	64	69	14.9999

#otherMatches

#Struct PSSM
DDDKK	chr8:113265122-113265376(+)$1	254	45	50	14.9999
ggg::	chr3:57260634-57260968(-)$1	334	128	133	14.9999
mmmdd	chr12:91570971-91571236(+)$1	265	184	189	14.9999
::::g	chr2:140484064-140484338(-)$1	274	0	5	14.9999
ffff:	chr9:72595712-72596015(+)$1	303	69	74	14.9999
IIIII	chr4:138013090-138013373(+)$1	283	15	20	14.9999
lleee	chr19:57111263-57111516(-)$1	253	7	12	14.9999
edddd	chr2:156365974-156366237(+)$1	263	233	238	14.9999
::::c	chr12:101444912-101445265(+)$1	353	38	43	14.9999
GGGGG	chr11:117020309-117020630(+)$1	321	112	117	14.9999
d22bb	chr12:8349497-8349753(+)$1	256	117	122	14.9999
IIIII	chr18:75555264-75555519(+)$1	255	242	247	14.9999
eeeee	chrX:71109394-71109630(-)$1	236	170	175	14.9999
RRRRD	chr6:71760197-71760473(+)$1	276	42	47	14.9999
nnccc	chr13:31652027-31652265(+)$1	238	84	89	14.9999
:::::	chr12:81208710-81208975(-)$1	265	131	136	14.9999
:::ff	chr11:8893389-8893654(-)$1	265	32	37	14.9999
''''e	chr16:44087395-44087719(-)$1	324	54	59	14.9999
ooooo	chr11:77694141-77694400(-)$1	259	54	59	14.9999
c!!cc	chr16:37881799-37882046(+)$1	247	208	213	14.9999
hhhhh	chr1:65320326-65320577(+)$1	251	82	87	14.9999
444ee	chr19:23241191-23241457(+)$1	266	90	95	14.9999
:::::	chr7:135036515-135036792(-)$1	277	200	205	14.9999
h####	chr3:107271962-107272212(-)$1	250	48	53	14.9999
:::::	chr13:38593051-38593316(-)$1	265	12	17	14.9999
=====	chr1:175264517-175264768(-)$1	251	96	101	14.9999
:cccm	chr5:122906964-122907239(-)$1	275	150	155	14.9999
MMMMG	chr16:43862569-43862848(-)$1	279	33	38	14.9999
ggggg	chr1:174202457-174202896(-)$1	439	246	251	14.9999
doooo	chr11:68628417-68628672(+)$1	255	31	36	14.9999
:::::	chr1:37496161-37496448(-)$1	287	5	10	14.9999
KFFFF	chr11:55208585-55208857(-)$1	272	111	116	14.9999
C}EEE	chr8:131256395-131256729(+)$1	334	218	223	14.9999
##eee	chr2:28085569-28085809(+)$1	240	141	146	14.9999
:::::	chr3:146394178-146394436(-)$1	258	103	108	14.9999
"""ii	chr17:31982873-31983129(-)$1	256	32	37	14.9999
GGGGG	chr13:110741513-110741807(+)$1	294	61	66	14.9999
:::::	chr6:13036253-13036510(+)$1	257	78	83	14.9999
eeeab	chr15:32964077-32964354(+)$1	277	146	151	14.9999
fffff	chr4:123054309-123054559(-)$1	250	71	76	14.9999
qqqqq	chr11:94200910-94201176(+)$1	266	25	30	14.9999
/////	chr7:74385108-74385409(-)$1	301	253	258	14.9999
ddddo	chr6:38456332-38456624(+)$1	292	67	72	14.9999
sssss	chr2:84442701-84442997(-)$1	296	30	35	14.9999
iiiii	chr6:48386615-48386850(-)$1	235	172	177	14.9999
:::::	chr1:13129457-13129710(-)$1	253	84	89	14.9999
wwwww	chr17:17665317-17665599(-)$1	282	188	193	14.9999
d22a2	chr3:108596393-108596653(-)$1	260	111	116	14.9999
FFFFF	chr5:124943052-124943292(-)$1	240	223	228	14.9999
iiiii	chr18:31597435-31597719(-)$1	284	272	277	14.9999
%%eee	chr11:101052353-101052593(-)$1	240	103	108	14.9999
ffff]	chr6:38769134-38769402(-)$1	268	75	80	14.9999
doooo	chr12:109151877-109152142(-)$1	265	114	119	14.9999
rrrrr	chr4:100823016-100823307(+)$1	291	149	154	14.9999
iiiii	chr16:89787282-89787538(-)$1	256	85	90	14.9999
:eeee	chr6:131315179-131315517(-)$1	338	84	89	14.9999
qqqqf	chrX:23382308-23382547(+)$1	239	73	78	14.9999
IIIII	chr3:89072066-89072343(-)$1	277	111	116	14.9999
iifff	chr2:121136302-121136570(-)$1	268	64	69	14.9999

#DB
(((..	chr8:113265122-113265376(+)$1	1	45	50	14.9999
)))..	chr3:57260634-57260968(-)$1	1	128	133	14.9999
...))	chr12:91570971-91571236(+)$1	1	184	189	14.9999
....(	chr2:140484064-140484338(-)$1	1	0	5	14.9999
)))).	chr9:72595712-72596015(+)$1	1	69	74	14.9999
(((((	chr4:138013090-138013373(+)$1	1	15	20	14.9999
..)))	chr19:57111263-57111516(-)$1	1	7	12	14.9999
)))))	chr2:156365974-156366237(+)$1	1	233	238	14.9999
....(	chr12:101444912-101445265(+)$1	1	38	43	14.9999
(((((	chr11:117020309-117020630(+)$1	1	112	117	14.9999
)..))	chr12:8349497-8349753(+)$1	1	117	122	14.9999
)))))	chr18:75555264-75555519(+)$1	1	242	247	14.9999
)))))	chrX:71109394-71109630(-)$1	1	170	175	14.9999
....(	chr6:71760197-71760473(+)$1	1	42	47	14.9999
..)))	chr13:31652027-31652265(+)$1	1	84	89	14.9999
.....	chr12:81208710-81208975(-)$1	1	131	136	14.9999
...((	chr11:8893389-8893654(-)$1	1	32	37	14.9999
....(	chr16:44087395-44087719(-)$1	1	54	59	14.9999
.....	chr11:77694141-77694400(-)$1	1	54	59	14.9999
(..((	chr16:37881799-37882046(+)$1	1	208	213	14.9999
)))))	chr1:65320326-65320577(+)$1	1	82	87	14.9999
...))	chr19:23241191-23241457(+)$1	1	90	95	14.9999
.....	chr7:135036515-135036792(-)$1	1	200	205	14.9999
(....	chr3:107271962-107272212(-)$1	1	48	53	14.9999
.....	chr13:38593051-38593316(-)$1	1	12	17	14.9999
)))))	chr1:175264517-175264768(-)$1	1	96	101	14.9999
.(((.	chr5:122906964-122907239(-)$1	1	150	155	14.9999
....(	chr16:43862569-43862848(-)$1	1	33	38	14.9999
(((((	chr1:174202457-174202896(-)$1	1	246	251	14.9999
(....	chr11:68628417-68628672(+)$1	1	31	36	14.9999
.....	chr1:37496161-37496448(-)$1	1	5	10	14.9999
.((((	chr11:55208585-55208857(-)$1	1	111	116	14.9999
).)))	chr8:131256395-131256729(+)$1	1	218	223	14.9999
..(((	chr2:28085569-28085809(+)$1	1	141	146	14.9999
.....	chr3:146394178-146394436(-)$1	1	103	108	14.9999
...((	chr17:31982873-31983129(-)$1	1	32	37	14.9999
(((((	chr13:110741513-110741807(+)$1	1	61	66	14.9999
.....	chr6:13036253-13036510(+)$1	1	78	83	14.9999
(((((	chr15:32964077-32964354(+)$1	1	146	151	14.9999
(((((	chr4:123054309-123054559(-)$1	1	71	76	14.9999
.....	chr11:94200910-94201176(+)$1	1	25	30	14.9999
.....	chr7:74385108-74385409(-)$1	1	253	258	14.9999
((((.	chr6:38456332-38456624(+)$1	1	67	72	14.9999
.....	chr2:84442701-84442997(-)$1	1	30	35	14.9999
(((((	chr6:48386615-48386850(-)$1	1	172	177	14.9999
.....	chr1:13129457-13129710(-)$1	1	84	89	14.9999
.....	chr17:17665317-17665599(-)$1	1	188	193	14.9999
)..).	chr3:108596393-108596653(-)$1	1	111	116	14.9999
)))))	chr5:124943052-124943292(-)$1	1	223	228	14.9999
)))))	chr18:31597435-31597719(-)$1	1	272	277	14.9999
..(((	chr11:101052353-101052593(-)$1	1	103	108	14.9999
)))).	chr6:38769134-38769402(-)$1	1	75	80	14.9999
(....	chr12:109151877-109152142(-)$1	1	114	119	14.9999
.....	chr4:100823016-100823307(+)$1	1	149	154	14.9999
(((((	chr16:89787282-89787538(-)$1	1	85	90	14.9999
.((((	chr6:131315179-131315517(-)$1	1	84	89	14.9999
....)	chrX:23382308-23382547(+)$1	1	73	78	14.9999
)))))	chr3:89072066-89072343(-)$1	1	111	116	14.9999
)))))	chr2:121136302-121136570(-)$1	1	64	69	14.9999

#PSSM
U : 0.94	u : 0.05	
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	884.9999999999995
#seq	59
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m1_run1.nuc.txt

#NT
CAU	chr18:54055277-54055478(+)$1	201	51	54	9.0000
CAU	chr11:46007286-46007487(-)$1	201	91	94	9.0000
CAU	chr6:143155565-143155766(+)$1	201	81	84	9.0000
CAU	chr15:18943803-18944004(+)$1	201	20	23	9.0000
CAU	chr16:43628386-43628587(+)$1	201	48	51	9.0000
CAU	chr14:120829469-120829670(+)$1	201	94	97	9.0000
CAU	chr7:86508771-86508972(+)$1	201	85	88	9.0000
CAU	chr4:128896326-128896527(+)$1	201	89	92	9.0000
CAU	chr15:82122055-82122256(+)$1	201	93	96	9.0000
CAU	chr9:44611697-44611898(-)$1	201	58	61	9.0000
CAU	chr9:74905527-74905728(+)$1	201	12	15	9.0000
CAU	chr11:68904057-68904258(+)$1	201	181	184	9.0000
CAU	chr9:49310235-49310436(-)$1	201	0	3	9.0000
CAU	chr2:132355960-132356161(-)$1	201	0	3	9.0000
CAU	chr18:61747364-61747565(+)$1	201	28	31	9.0000
CAU	chrX:70600818-70601019(+)$1	201	30	33	9.0000
CAU	chr17:17664683-17664884(-)$1	201	27	30	9.0000
CAU	chr16:16313640-16313841(-)$1	201	30	33	9.0000
CAU	chr9:75418041-75418242(-)$1	201	85	88	9.0000
CAU	chr11:16182139-16182340(+)$1	201	42	45	9.0000
CAU	chr9:62643691-62643892(-)$1	201	107	110	9.0000
CAU	chrX:8887943-8888144(+)$1	201	7	10	9.0000
CAU	chr13:104992045-104992246(+)$1	201	29	32	9.0000
CAU	chr6:72560389-72560590(-)$1	201	7	10	9.0000
CAU	chr2:164316278-164316479(+)$1	201	4	7	9.0000
CAU	chr13:58228193-58228394(-)$1	201	43	46	9.0000
CAU	chr8:93577017-93577218(+)$1	201	61	64	9.0000
CAU	chr14:122557881-122558082(+)$1	201	7	10	9.0000
CAU	chr18:44577490-44577691(+)$1	201	1	4	9.0000
CAU	chr4:15212233-15212434(+)$1	201	21	24	9.0000
CAU	chr8:63389593-63389794(-)$1	201	28	31	9.0000
CAU	chr2:5150849-5151050(+)$1	201	33	36	9.0000
CAU	chr4:116660759-116660960(+)$1	201	21	24	9.0000
CAU	chr1:72906418-72906619(-)$1	201	8	11	9.0000
CAU	chr3:146392654-146392855(-)$1	201	50	53	9.0000
CAU	chr19:8990474-8990675(+)$1	201	66	69	9.0000
CAU	chr3:16116618-16116819(+)$1	201	21	24	9.0000
CAU	chr15:82124051-82124252(+)$1	201	30	33	9.0000
CAU	chr6:58855987-58856188(-)$1	201	24	27	9.0000
CAU	chr11:54723340-54723541(+)$1	201	11	14	9.0000
CAU	chr7:151610056-151610257(+)$1	201	65	68	9.0000
CAU	chr19:12541312-12541513(-)$1	201	98	101	9.0000
CAU	chr7:6659697-6659898(-)$1	201	44	47	9.0000
CAU	chr11:62129523-62129724(+)$1	201	102	105	9.0000
CAU	chr9:111179134-111179335(+)$1	201	20	23	9.0000
CAU	chr13:59037288-59037489(+)$1	201	65	68	9.0000
CAU	chr13:24999429-24999630(-)$1	201	25	28	9.0000
CAU	chr15:50489326-50489527(-)$1	201	14	17	9.0000
CAU	chr1:108620034-108620235(-)$1	201	14	17	9.0000
CAU	chr11:30006715-30006916(-)$1	201	2	5	9.0000
CAU	chr19:47098685-47098886(+)$1	201	4	7	9.0000
CAU	chr19:47717433-47717634(+)$1	201	9	12	9.0000
CAU	chr17:87232533-87232734(+)$1	201	18	21	9.0000
CAU	chr1:66485749-66485950(+)$1	201	13	16	9.0000
CAU	chr17:80599773-80599974(-)$1	201	11	14	9.0000
CAU	chr7:120714646-120714847(+)$1	201	34	37	9.0000
CAU	chr11:67498037-67498238(+)$1	201	84	87	9.0000
CAU	chr15:10376553-10376754(-)$1	201	34	37	9.0000
CAU	chr9:44444937-44445138(+)$1	201	2	5	9.0000
CAU	chr19:26852261-26852462(+)$1	201	40	43	9.0000
CAU	chr5:84494815-84495016(-)$1	201	1	4	9.0000
CAU	chr16:52205187-52205388(+)$1	201	1	4	9.0000
CAU	chr14:67422553-67422754(-)$1	201	28	31	9.0000
CAU	chr2:83722904-83723105(+)$1	201	61	64	9.0000
CAU	chr2:126584600-126584801(+)$1	201	16	19	9.0000
CAU	chr12:101444854-101445055(+)$1	201	58	61	9.0000
CAU	chr18:75591413-75591614(-)$1	201	62	65	9.0000
cau	chr1:23375396-23375597(-)$1	201	0	3	9.0000
CAU	chr17:57184029-57184230(-)$1	201	27	30	9.0000
CAU	chrX:154259924-154260125(-)$1	201	96	99	9.0000
CAU	chr7:86505210-86505411(+)$1	201	27	30	9.0000
cau	chr13:24824404-24824605(+)$1	201	6	9	9.0000
CAU	chrX:101479197-101479398(-)$1	201	27	30	9.0000
CAU	chr7:6659696-6659897(-)$1	201	43	46	9.0000
CAU	chr13:41368429-41368630(+)$1	201	13	16	9.0000
CAU	chr9:116482691-116482892(-)$1	201	29	32	9.0000
CAU	chr10:90579472-90579673(-)$1	201	125	128	9.0000
CAU	chrX:67598615-67598816(-)$1	201	104	107	9.0000
CAU	chr6:122837665-122837866(+)$1	201	42	45	9.0000
CAU	chr13:54481988-54482189(+)$1	201	54	57	9.0000
CAU	chr3:31105483-31105684(-)$1	201	26	29	9.0000
CAU	chr13:94174421-94174622(+)$1	201	25	28	9.0000
CAU	chrX:8887243-8887444(+)$1	201	1	4	9.0000
CAU	chrX:162824641-162824842(+)$1	201	21	24	9.0000
CAU	chr6:122838202-122838403(+)$1	201	40	43	9.0000
CAU	chr12:101445398-101445599(+)$1	201	24	27	9.0000
CAU	chr6:8377212-8377413(+)$1	201	30	33	9.0000
CAU	chr5:29558503-29558704(-)$1	201	70	73	9.0000
CAU	chr9:111176341-111176542(+)$1	201	2	5	9.0000
CAU	chr17:37210898-37211099(+)$1	201	11	14	9.0000
CAU	chr10:52830289-52830490(+)$1	201	13	16	9.0000
CAU	chr6:100180693-100180894(-)$1	201	10	13	9.0000
CAU	chr10:94254880-94255081(-)$1	201	13	16	9.0000
CAU	chr2:136606991-136607192(+)$1	201	47	50	9.0000
CAU	chr8:56144529-56144730(+)$1	201	26	29	9.0000
CAU	chr8:46911521-46911722(+)$1	201	14	17	9.0000
CAU	chr6:113696667-113696868(-)$1	201	57	60	9.0000
CAU	chr2:146903563-146903764(+)$1	201	21	24	9.0000
CAU	chr12:39593845-39594046(+)$1	201	40	43	9.0000

#otherMatches

#Struct PSSM
777	chr18:32394822-32395023(+)$1	201	95	98	9.0000
ddd	chr18:54055277-54055478(+)$1	201	51	54	9.0000
sss	chr11:46007286-46007487(-)$1	201	91	94	9.0000
xxx	chr6:143155565-143155766(+)$1	201	81	84	9.0000
ggg	chr15:18943803-18944004(+)$1	201	20	23	9.0000
mee	chr16:43628386-43628587(+)$1	201	48	51	9.0000
eee	chr14:120829469-120829670(+)$1	201	94	97	9.0000
:::	chr7:86508771-86508972(+)$1	201	85	88	9.0000
ooo	chr4:128896326-128896527(+)$1	201	89	92	9.0000
:::	chr15:82122055-82122256(+)$1	201	93	96	9.0000
444	chr9:44611697-44611898(-)$1	201	58	61	9.0000
ddd	chr9:74905527-74905728(+)$1	201	12	15	9.0000
///	chr11:68904057-68904258(+)$1	201	181	184	9.0000
:::	chr9:49310235-49310436(-)$1	201	0	3	9.0000
:::	chr2:132355960-132356161(-)$1	201	0	3	9.0000
bmm	chr18:61747364-61747565(+)$1	201	28	31	9.0000
:::	chrX:70600818-70601019(+)$1	201	30	33	9.0000
bb"	chr17:17664683-17664884(-)$1	201	27	30	9.0000
ff2	chr16:16313640-16313841(-)$1	201	30	33	9.0000
:::	chr9:75418041-75418242(-)$1	201	85	88	9.0000
^^^	chr11:16182139-16182340(+)$1	201	42	45	9.0000
DDD	chr9:62643691-62643892(-)$1	201	107	110	9.0000
iii	chrX:8887943-8888144(+)$1	201	7	10	9.0000
bmm	chr13:104992045-104992246(+)$1	201	29	32	9.0000
dd[	chr6:72560389-72560590(-)$1	201	7	10	9.0000
FFF	chr2:164316278-164316479(+)$1	201	4	7	9.0000
&&&	chr13:58228193-58228394(-)$1	201	43	46	9.0000
555	chr8:93577017-93577218(+)$1	201	61	64	9.0000
[cc	chr14:122557881-122558082(+)$1	201	7	10	9.0000
:::	chr18:44577490-44577691(+)$1	201	1	4	9.0000
:::	chr4:15212233-15212434(+)$1	201	21	24	9.0000
[dd	chr8:63389593-63389794(-)$1	201	28	31	9.0000
fff	chr2:5150849-5151050(+)$1	201	33	36	9.0000
$$d	chr4:116660759-116660960(+)$1	201	21	24	9.0000
:::	chr1:72906418-72906619(-)$1	201	8	11	9.0000
eee	chr3:146392654-146392855(-)$1	201	50	53	9.0000
ddd	chr19:8990474-8990675(+)$1	201	66	69	9.0000
::F	chr3:16116618-16116819(+)$1	201	21	24	9.0000
d!!	chr15:82124051-82124252(+)$1	201	30	33	9.0000
nnd	chr6:58855987-58856188(-)$1	201	24	27	9.0000
d[e	chr11:54723340-54723541(+)$1	201	11	14	9.0000
+++	chr7:151610056-151610257(+)$1	201	65	68	9.0000
nnn	chr19:12541312-12541513(-)$1	201	98	101	9.0000
ddd	chr7:6659697-6659898(-)$1	201	44	47	9.0000
^^^	chr11:62129523-62129724(+)$1	201	102	105	9.0000
^^^	chr9:111179134-111179335(+)$1	201	20	23	9.0000
nnn	chr13:59037288-59037489(+)$1	201	65	68	9.0000
PPP	chr13:24999429-24999630(-)$1	201	25	28	9.0000
iii	chr15:50489326-50489527(-)$1	201	14	17	9.0000
CLL	chr1:108620034-108620235(-)$1	201	14	17	9.0000
:::	chr11:30006715-30006916(-)$1	201	2	5	9.0000
:::	chr19:47098685-47098886(+)$1	201	4	7	9.0000
sss	chr19:47717433-47717634(+)$1	201	9	12	9.0000
HHH	chr17:87232533-87232734(+)$1	201	18	21	9.0000
:::	chr1:66485749-66485950(+)$1	201	13	16	9.0000
JJJ	chr17:80599773-80599974(-)$1	201	11	14	9.0000
ddd	chr7:120714646-120714847(+)$1	201	34	37	9.0000
mmm	chr11:67498037-67498238(+)$1	201	84	87	9.0000
EEK	chr15:10376553-10376754(-)$1	201	34	37	9.0000
:HH	chr9:44444937-44445138(+)$1	201	2	5	9.0000
&&&	chr19:26852261-26852462(+)$1	201	40	43	9.0000
:::	chr5:84494815-84495016(-)$1	201	1	4	9.0000
ddd	chr16:52205187-52205388(+)$1	201	1	4	9.0000
LLL	chr14:67422553-67422754(-)$1	201	28	31	9.0000
"dd	chr2:83722904-83723105(+)$1	201	61	64	9.0000
BB{	chr2:126584600-126584801(+)$1	201	16	19	9.0000
hhh	chr12:101444854-101445055(+)$1	201	58	61	9.0000
:ii	chr18:75591413-75591614(-)$1	201	62	65	9.0000
::B	chr1:23375396-23375597(-)$1	201	0	3	9.0000
ccq	chr17:57184029-57184230(-)$1	201	27	30	9.0000
:::	chrX:154259924-154260125(-)$1	201	96	99	9.0000
D{D	chr7:86505210-86505411(+)$1	201	27	30	9.0000
cmm	chr13:24824404-24824605(+)$1	201	6	9	9.0000
FFF	chrX:101479197-101479398(-)$1	201	27	30	9.0000
ddd	chr7:6659696-6659897(-)$1	201	43	46	9.0000
hhh	chr13:41368429-41368630(+)$1	201	13	16	9.0000
ccm	chr9:116482691-116482892(-)$1	201	29	32	9.0000
ddd	chr10:90579472-90579673(-)$1	201	125	128	9.0000
bb!	chrX:67598615-67598816(-)$1	201	104	107	9.0000
:::	chr6:122837665-122837866(+)$1	201	42	45	9.0000
NNN	chr13:54481988-54482189(+)$1	201	54	57	9.0000
=ll	chr3:31105483-31105684(-)$1	201	26	29	9.0000
ggg	chr13:94174421-94174622(+)$1	201	25	28	9.0000
:::	chrX:8887243-8887444(+)$1	201	1	4	9.0000
ttt	chrX:162824641-162824842(+)$1	201	21	24	9.0000
:::	chr6:122838202-122838403(+)$1	201	40	43	9.0000
bbp	chr12:101445398-101445599(+)$1	201	24	27	9.0000
cqq	chr6:8377212-8377413(+)$1	201	30	33	9.0000
IIg	chr5:29558503-29558704(-)$1	201	70	73	9.0000
:::	chr9:111176341-111176542(+)$1	201	2	5	9.0000
ccx	chr17:37210898-37211099(+)$1	201	11	14	9.0000
bqq	chr10:52830289-52830490(+)$1	201	13	16	9.0000
BKK	chr6:100180693-100180894(-)$1	201	10	13	9.0000
CPP	chr10:94254880-94255081(-)$1	201	13	16	9.0000
ppp	chr2:136606991-136607192(+)$1	201	47	50	9.0000
&&d	chr8:56144529-56144730(+)$1	201	26	29	9.0000
b[c	chr8:46911521-46911722(+)$1	201	14	17	9.0000
ooo	chr6:113696667-113696868(-)$1	201	57	60	9.0000
mee	chr2:146903563-146903764(+)$1	201	21	24	9.0000
HHH	chr12:39593845-39594046(+)$1	201	40	43	9.0000

#DB
...	chr18:32394822-32395023(+)$1	1	95	98	9.0000
(((	chr18:54055277-54055478(+)$1	1	51	54	9.0000
...	chr11:46007286-46007487(-)$1	1	91	94	9.0000
...	chr6:143155565-143155766(+)$1	1	81	84	9.0000
)))	chr15:18943803-18944004(+)$1	1	20	23	9.0000
.))	chr16:43628386-43628587(+)$1	1	48	51	9.0000
(((	chr14:120829469-120829670(+)$1	1	94	97	9.0000
...	chr7:86508771-86508972(+)$1	1	85	88	9.0000
...	chr4:128896326-128896527(+)$1	1	89	92	9.0000
...	chr15:82122055-82122256(+)$1	1	93	96	9.0000
...	chr9:44611697-44611898(-)$1	1	58	61	9.0000
(((	chr9:74905527-74905728(+)$1	1	12	15	9.0000
...	chr11:68904057-68904258(+)$1	1	181	184	9.0000
...	chr9:49310235-49310436(-)$1	1	0	3	9.0000
...	chr2:132355960-132356161(-)$1	1	0	3	9.0000
(..	chr18:61747364-61747565(+)$1	1	28	31	9.0000
...	chrX:70600818-70601019(+)$1	1	30	33	9.0000
((.	chr17:17664683-17664884(-)$1	1	27	30	9.0000
)).	chr16:16313640-16313841(-)$1	1	30	33	9.0000
...	chr9:75418041-75418242(-)$1	1	85	88	9.0000
...	chr11:16182139-16182340(+)$1	1	42	45	9.0000
(((	chr9:62643691-62643892(-)$1	1	107	110	9.0000
(((	chrX:8887943-8888144(+)$1	1	7	10	9.0000
(..	chr13:104992045-104992246(+)$1	1	29	32	9.0000
((.	chr6:72560389-72560590(-)$1	1	7	10	9.0000
(((	chr2:164316278-164316479(+)$1	1	4	7	9.0000
...	chr13:58228193-58228394(-)$1	1	43	46	9.0000
...	chr8:93577017-93577218(+)$1	1	61	64	9.0000
.((	chr14:122557881-122558082(+)$1	1	7	10	9.0000
...	chr18:44577490-44577691(+)$1	1	1	4	9.0000
...	chr4:15212233-15212434(+)$1	1	21	24	9.0000
.((	chr8:63389593-63389794(-)$1	1	28	31	9.0000
(((	chr2:5150849-5151050(+)$1	1	33	36	9.0000
..(	chr4:116660759-116660960(+)$1	1	21	24	9.0000
...	chr1:72906418-72906619(-)$1	1	8	11	9.0000
(((	chr3:146392654-146392855(-)$1	1	50	53	9.0000
(((	chr19:8990474-8990675(+)$1	1	66	69	9.0000
..(	chr3:16116618-16116819(+)$1	1	21	24	9.0000
(..	chr15:82124051-82124252(+)$1	1	30	33	9.0000
..)	chr6:58855987-58856188(-)$1	1	24	27	9.0000
(.(	chr11:54723340-54723541(+)$1	1	11	14	9.0000
...	chr7:151610056-151610257(+)$1	1	65	68	9.0000
...	chr19:12541312-12541513(-)$1	1	98	101	9.0000
)))	chr7:6659697-6659898(-)$1	1	44	47	9.0000
...	chr11:62129523-62129724(+)$1	1	102	105	9.0000
...	chr9:111179134-111179335(+)$1	1	20	23	9.0000
...	chr13:59037288-59037489(+)$1	1	65	68	9.0000
...	chr13:24999429-24999630(-)$1	1	25	28	9.0000
(((	chr15:50489326-50489527(-)$1	1	14	17	9.0000
(..	chr1:108620034-108620235(-)$1	1	14	17	9.0000
...	chr11:30006715-30006916(-)$1	1	2	5	9.0000
...	chr19:47098685-47098886(+)$1	1	4	7	9.0000
...	chr19:47717433-47717634(+)$1	1	9	12	9.0000
(((	chr17:87232533-87232734(+)$1	1	18	21	9.0000
...	chr1:66485749-66485950(+)$1	1	13	16	9.0000
(((	chr17:80599773-80599974(-)$1	1	11	14	9.0000
)))	chr7:120714646-120714847(+)$1	1	34	37	9.0000
...	chr11:67498037-67498238(+)$1	1	84	87	9.0000
((.	chr15:10376553-10376754(-)$1	1	34	37	9.0000
.((	chr9:44444937-44445138(+)$1	1	2	5	9.0000
...	chr19:26852261-26852462(+)$1	1	40	43	9.0000
...	chr5:84494815-84495016(-)$1	1	1	4	9.0000
(((	chr16:52205187-52205388(+)$1	1	1	4	9.0000
...	chr14:67422553-67422754(-)$1	1	28	31	9.0000
.((	chr2:83722904-83723105(+)$1	1	61	64	9.0000
((.	chr2:126584600-126584801(+)$1	1	16	19	9.0000
(((	chr12:101444854-101445055(+)$1	1	58	61	9.0000
.((	chr18:75591413-75591614(-)$1	1	62	65	9.0000
..(	chr1:23375396-23375597(-)$1	1	0	3	9.0000
((.	chr17:57184029-57184230(-)$1	1	27	30	9.0000
...	chrX:154259924-154260125(-)$1	1	96	99	9.0000
(.(	chr7:86505210-86505411(+)$1	1	27	30	9.0000
(..	chr13:24824404-24824605(+)$1	1	6	9	9.0000
(((	chrX:101479197-101479398(-)$1	1	27	30	9.0000
)))	chr7:6659696-6659897(-)$1	1	43	46	9.0000
(((	chr13:41368429-41368630(+)$1	1	13	16	9.0000
((.	chr9:116482691-116482892(-)$1	1	29	32	9.0000
(((	chr10:90579472-90579673(-)$1	1	125	128	9.0000
((.	chrX:67598615-67598816(-)$1	1	104	107	9.0000
...	chr6:122837665-122837866(+)$1	1	42	45	9.0000
...	chr13:54481988-54482189(+)$1	1	54	57	9.0000
(..	chr3:31105483-31105684(-)$1	1	26	29	9.0000
(((	chr13:94174421-94174622(+)$1	1	25	28	9.0000
...	chrX:8887243-8887444(+)$1	1	1	4	9.0000
...	chrX:162824641-162824842(+)$1	1	21	24	9.0000
...	chr6:122838202-122838403(+)$1	1	40	43	9.0000
((.	chr12:101445398-101445599(+)$1	1	24	27	9.0000
(..	chr6:8377212-8377413(+)$1	1	30	33	9.0000
(((	chr5:29558503-29558704(-)$1	1	70	73	9.0000
...	chr9:111176341-111176542(+)$1	1	2	5	9.0000
((.	chr17:37210898-37211099(+)$1	1	11	14	9.0000
(..	chr10:52830289-52830490(+)$1	1	13	16	9.0000
(..	chr6:100180693-100180894(-)$1	1	10	13	9.0000
(..	chr10:94254880-94255081(-)$1	1	13	16	9.0000
...	chr2:136606991-136607192(+)$1	1	47	50	9.0000
..(	chr8:56144529-56144730(+)$1	1	26	29	9.0000
(.(	chr8:46911521-46911722(+)$1	1	14	17	9.0000
...	chr6:113696667-113696868(-)$1	1	57	60	9.0000
.))	chr2:146903563-146903764(+)$1	1	21	24	9.0000
(((	chr12:39593845-39594046(+)$1	1	40	43	9.0000

#PSSM
C : 0.98	c : 0.02	
A : 0.98	a : 0.02	
U : 0.98	u : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_transcript_m3_run2.nuc.txt

#NT
GCUG	chr15:98570598-98570878(-)$1	280	0	4	12.0000
GCUG	chr13:73950579-73950847(+)$1	268	116	120	12.0000
GCUG	chr10:5632787-5633024(-)$1	237	3	7	12.0000
GCUG	chr14:121743408-121743645(-)$1	237	128	132	12.0000
GCUG	chr4:59783696-59783933(-)$1	237	55	59	12.0000
GCUG	chr4:129524964-129525201(+)$1	237	23	27	12.0000
gcug	chr2:26875304-26875539(+)$1	235	5	9	12.0000
gcug	chr9:71835047-71835286(-)$1	239	165	169	12.0000
GCUG	chr15:88561319-88561556(-)$1	237	7	11	12.0000
GCUG	chr3:153571978-153572222(-)$1	244	68	72	12.0000
GCUG	chr1:71689489-71689739(-)$1	250	135	139	12.0000
GCUG	chr11:6303202-6303447(+)$1	245	19	23	12.0000
GCUG	chr5:30445993-30446272(-)$1	279	199	203	12.0000
GCUG	chr7:4973135-4973385(+)$1	250	0	4	12.0000
GCUG	chr1:183745618-183745906(-)$1	288	156	160	12.0000
gcug	chr5:3440233-3440476(+)$1	243	1	5	12.0000
gcug	chrX:93352176-93352430(+)$1	254	75	79	12.0000
GCUG	chr15:9017071-9017314(+)$1	243	67	71	12.0000
GCUG	chr4:116826624-116826867(-)$1	243	44	48	12.0000
GCUG	chr1:88248495-88248750(-)$1	255	54	58	12.0000
GCUG	chr2:32643895-32644134(-)$1	239	64	68	12.0000
GCUG	chr15:64056232-64056467(-)$1	235	103	107	12.0000
GCUG	chr2:73747265-73747522(-)$1	257	129	133	12.0000
gcug	chr17:5847864-5848131(+)$1	267	154	158	12.0000
GCUG	chr8:90839982-90840220(+)$1	238	124	128	12.0000
GCUG	chr2:80391162-80391410(-)$1	248	25	29	12.0000
GCUG	chr11:77345163-77345456(-)$1	293	59	63	12.0000
GCUG	chr5:115722389-115722641(-)$1	252	73	77	12.0000
GCUG	chr14:55194460-55194697(-)$1	237	184	188	12.0000
GCUG	chr4:155120616-155120860(-)$1	244	7	11	12.0000
GCUG	chr10:126424717-126424953(+)$1	236	174	178	12.0000
GCUG	chr13:89838815-89839050(-)$1	235	121	125	12.0000
GCUG	chr14:121506037-121506290(+)$1	253	12	16	12.0000
GCUG	chr11:105916007-105916247(+)$1	240	66	70	12.0000
GCUG	chr2:71112870-71113124(-)$1	254	240	244	12.0000
GCUG	chr8:3515072-3515314(+)$1	242	16	20	12.0000
GCUG	chr7:5044504-5044757(+)$1	253	26	30	12.0000
GCUG	chr15:36722183-36722418(-)$1	235	129	133	12.0000
GCUG	chr7:73419626-73419868(-)$1	242	16	20	12.0000
GCUG	chr11:116672280-116672515(-)$1	235	92	96	12.0000
GCUG	chr7:116760480-116760728(-)$1	248	127	131	12.0000
GCUG	chr11:97642144-97642395(-)$1	251	16	20	12.0000
GCUG	chr4:149100954-149101205(-)$1	251	21	25	12.0000
GCUG	chr3:144240489-144240746(+)$1	257	193	197	12.0000
GCUG	chr13:45652017-45652255(-)$1	238	26	30	12.0000
gcug	chr15:54884308-54884555(-)$1	247	26	30	12.0000
GCUG	chr8:74146824-74147068(+)$1	244	41	45	12.0000
GCUG	chr8:87296063-87296308(-)$1	245	1	5	12.0000
GCUG	chr1:63223614-63223869(+)$1	255	105	109	12.0000
GCUG	chr10:80255099-80255409(+)$1	310	65	69	12.0000
GCUG	chr16:49906324-49906580(+)$1	256	109	113	12.0000
GCUG	chr11:77342664-77342938(-)$1	274	141	145	12.0000
GCUG	chr11:108112731-108112966(-)$1	235	23	27	12.0000
GCUG	chr15:57878927-57879178(-)$1	251	57	61	12.0000
GCUG	chr4:53475497-53475763(+)$1	266	50	54	12.0000
gcug	chr6:91212739-91212999(+)$1	260	151	155	12.0000
GCUG	chrX:101152914-101153152(-)$1	238	31	35	12.0000
GCUG	chr15:7147304-7147539(+)$1	235	68	72	12.0000
gcug	chr9:70333446-70333685(-)$1	239	76	80	12.0000
GCUG	chr19:7612039-7612313(+)$1	274	138	142	12.0000
GCUG	chr17:80291304-80291546(-)$1	242	45	49	12.0000
GCUG	chr2:35151954-35152199(+)$1	245	72	76	12.0000
GCUG	chr4:137633481-137633728(+)$1	247	43	47	12.0000
GCUG	chr1:178705506-178705773(-)$1	267	60	64	12.0000
GCUG	chr15:90058901-90059140(+)$1	239	125	129	12.0000
GCUG	chr10:7350802-7351051(-)$1	249	118	122	12.0000
GCUG	chr14:65695916-65696154(-)$1	238	17	21	12.0000
GCUG	chr15:77657812-77658085(-)$1	273	91	95	12.0000
GCUG	chr15:32876303-32876551(+)$1	248	114	118	12.0000
gcug	chr3:141961437-141961683(-)$1	246	117	121	12.0000
GCUG	chrX:101153016-101153271(-)$1	255	29	33	12.0000
GCUG	chr1:130228110-130228379(-)$1	269	120	124	12.0000
GCUG	chr15:99424477-99424765(+)$1	288	124	128	12.0000
GCUG	chr19:44470964-44471223(-)$1	259	148	152	12.0000
GCUG	chr7:97356539-97356790(+)$1	251	220	224	12.0000
GCUG	chr10:59764509-59764777(+)$1	268	107	111	12.0000
GCUG	chr11:62654446-62654681(+)$1	235	1	5	12.0000
gcug	chr16:32058164-32058404(-)$1	240	35	39	12.0000
GCUG	chr4:149943902-149944148(+)$1	246	119	123	12.0000
gcug	chr7:144424255-144424495(-)$1	240	74	78	12.0000

#otherMatches

#Struct PSSM
~~~D	chr19:37053185-37053421(+)$1	236	187	191	12.0000
::dd	chr15:98570598-98570878(-)$1	280	0	4	12.0000
JJJJ	chr13:73950579-73950847(+)$1	268	116	120	12.0000
dddd	chr10:5632787-5633024(-)$1	237	3	7	12.0000
]bb]	chr14:121743408-121743645(-)$1	237	128	132	12.0000
eeeD	chr4:59783696-59783933(-)$1	237	55	59	12.0000
DDFF	chr4:129524964-129525201(+)$1	237	23	27	12.0000
BBBK	chr2:26875304-26875539(+)$1	235	5	9	12.0000
ffff	chr9:71835047-71835286(-)$1	239	165	169	12.0000
FFFF	chr15:88561319-88561556(-)$1	237	7	11	12.0000
FF::	chr3:153571978-153572222(-)$1	244	68	72	12.0000
====	chr1:71689489-71689739(-)$1	250	135	139	12.0000
ffmm	chr11:6303202-6303447(+)$1	245	19	23	12.0000
c]cc	chr5:30445993-30446272(-)$1	279	199	203	12.0000
::::	chr7:4973135-4973385(+)$1	250	0	4	12.0000
eebb	chr1:183745618-183745906(-)$1	288	156	160	12.0000
gggg	chr5:3440233-3440476(+)$1	243	1	5	12.0000
beee	chrX:93352176-93352430(+)$1	254	75	79	12.0000
[ddd	chr15:9017071-9017314(+)$1	243	67	71	12.0000
dddu	chr4:116826624-116826867(-)$1	243	44	48	12.0000
ee[c	chr1:88248495-88248750(-)$1	255	54	58	12.0000
rfff	chr2:32643895-32644134(-)$1	239	64	68	12.0000
bb[h	chr15:64056232-64056467(-)$1	235	103	107	12.0000
99cc	chr2:73747265-73747522(-)$1	257	129	133	12.0000
bbcc	chr17:5847864-5848131(+)$1	267	154	158	12.0000
e"""	chr8:90839982-90840220(+)$1	238	124	128	12.0000
gggg	chr2:80391162-80391410(-)$1	248	25	29	12.0000
bbcc	chr11:77345163-77345456(-)$1	293	59	63	12.0000
gg]d	chr5:115722389-115722641(-)$1	252	73	77	12.0000
[hhh	chr14:55194460-55194697(-)$1	237	184	188	12.0000
BBFF	chr4:155120616-155120860(-)$1	244	7	11	12.0000
]ddd	chr10:126424717-126424953(+)$1	236	174	178	12.0000
"ccc	chr13:89838815-89839050(-)$1	235	121	125	12.0000
LCCC	chr14:121506037-121506290(+)$1	253	12	16	12.0000
ceee	chr11:105916007-105916247(+)$1	240	66	70	12.0000
dddo	chr2:71112870-71113124(-)$1	254	240	244	12.0000
eeee	chr8:3515072-3515314(+)$1	242	16	20	12.0000
dddo	chr7:5044504-5044757(+)$1	253	26	30	12.0000
ggg%	chr15:36722183-36722418(-)$1	235	129	133	12.0000
qfff	chr7:73419626-73419868(-)$1	242	16	20	12.0000
gggg	chr11:116672280-116672515(-)$1	235	92	96	12.0000
dddd	chr7:116760480-116760728(-)$1	248	127	131	12.0000
gggq	chr11:97642144-97642395(-)$1	251	16	20	12.0000
dddd	chr4:149100954-149101205(-)$1	251	21	25	12.0000
eeee	chr3:144240489-144240746(+)$1	257	193	197	12.0000
ccc[	chr13:45652017-45652255(-)$1	238	26	30	12.0000
eeed	chr15:54884308-54884555(-)$1	247	26	30	12.0000
###c	chr8:74146824-74147068(+)$1	244	41	45	12.0000
HHHH	chr8:87296063-87296308(-)$1	245	1	5	12.0000
dddd	chr1:63223614-63223869(+)$1	255	105	109	12.0000
c!!c	chr10:80255099-80255409(+)$1	310	65	69	12.0000
cc[d	chr16:49906324-49906580(+)$1	256	109	113	12.0000
dddp	chr11:77342664-77342938(-)$1	274	141	145	12.0000
ffff	chr11:108112731-108112966(-)$1	235	23	27	12.0000
B{CC	chr15:57878927-57879178(-)$1	251	57	61	12.0000
ffff	chr4:53475497-53475763(+)$1	266	50	54	12.0000
pppd	chr6:91212739-91212999(+)$1	260	151	155	12.0000
eeee	chrX:101152914-101153152(-)$1	238	31	35	12.0000
gggg	chr15:7147304-7147539(+)$1	235	68	72	12.0000
cccb	chr9:70333446-70333685(-)$1	239	76	80	12.0000
]a55	chr19:7612039-7612313(+)$1	274	138	142	12.0000
gggg	chr17:80291304-80291546(-)$1	242	45	49	12.0000
ddd]	chr2:35151954-35152199(+)$1	245	72	76	12.0000
ffff	chr4:137633481-137633728(+)$1	247	43	47	12.0000
ffll	chr1:178705506-178705773(-)$1	267	60	64	12.0000
gggg	chr15:90058901-90059140(+)$1	239	125	129	12.0000
mmmd	chr10:7350802-7351051(-)$1	249	118	122	12.0000
e::e	chr14:65695916-65696154(-)$1	238	17	21	12.0000
===[	chr15:77657812-77658085(-)$1	273	91	95	12.0000
eeee	chr15:32876303-32876551(+)$1	248	114	118	12.0000
gggg	chr3:141961437-141961683(-)$1	246	117	121	12.0000
fffF	chrX:101153016-101153271(-)$1	255	29	33	12.0000
nnnb	chr1:130228110-130228379(-)$1	269	120	124	12.0000
]bb:	chr15:99424477-99424765(+)$1	288	124	128	12.0000
ccbb	chr19:44470964-44471223(-)$1	259	148	152	12.0000
cc:G	chr7:97356539-97356790(+)$1	251	220	224	12.0000
iii]	chr10:59764509-59764777(+)$1	268	107	111	12.0000
::gg	chr11:62654446-62654681(+)$1	235	1	5	12.0000
cccp	chr16:32058164-32058404(-)$1	240	35	39	12.0000
hhhh	chr4:149943902-149944148(+)$1	246	119	123	12.0000
gbbm	chr7:144424255-144424495(-)$1	240	74	78	12.0000

#DB
...)	chr19:37053185-37053421(+)$1	1	187	191	12.0000
..((	chr15:98570598-98570878(-)$1	1	0	4	12.0000
))))	chr13:73950579-73950847(+)$1	1	116	120	12.0000
((((	chr10:5632787-5633024(-)$1	1	3	7	12.0000
.)).	chr14:121743408-121743645(-)$1	1	128	132	12.0000
)))(	chr4:59783696-59783933(-)$1	1	55	59	12.0000
((((	chr4:129524964-129525201(+)$1	1	23	27	12.0000
(((.	chr2:26875304-26875539(+)$1	1	5	9	12.0000
((((	chr9:71835047-71835286(-)$1	1	165	169	12.0000
((((	chr15:88561319-88561556(-)$1	1	7	11	12.0000
((..	chr3:153571978-153572222(-)$1	1	68	72	12.0000
))))	chr1:71689489-71689739(-)$1	1	135	139	12.0000
((..	chr11:6303202-6303447(+)$1	1	19	23	12.0000
).))	chr5:30445993-30446272(-)$1	1	199	203	12.0000
....	chr7:4973135-4973385(+)$1	1	0	4	12.0000
((((	chr1:183745618-183745906(-)$1	1	156	160	12.0000
((((	chr5:3440233-3440476(+)$1	1	1	5	12.0000
((((	chrX:93352176-93352430(+)$1	1	75	79	12.0000
.(((	chr15:9017071-9017314(+)$1	1	67	71	12.0000
(((.	chr4:116826624-116826867(-)$1	1	44	48	12.0000
((.(	chr1:88248495-88248750(-)$1	1	54	58	12.0000
.)))	chr2:32643895-32644134(-)$1	1	64	68	12.0000
((.(	chr15:64056232-64056467(-)$1	1	103	107	12.0000
..))	chr2:73747265-73747522(-)$1	1	129	133	12.0000
))))	chr17:5847864-5848131(+)$1	1	154	158	12.0000
(...	chr8:90839982-90840220(+)$1	1	124	128	12.0000
((((	chr2:80391162-80391410(-)$1	1	25	29	12.0000
))))	chr11:77345163-77345456(-)$1	1	59	63	12.0000
)).)	chr5:115722389-115722641(-)$1	1	73	77	12.0000
.(((	chr14:55194460-55194697(-)$1	1	184	188	12.0000
((((	chr4:155120616-155120860(-)$1	1	7	11	12.0000
.)))	chr10:126424717-126424953(+)$1	1	174	178	12.0000
.(((	chr13:89838815-89839050(-)$1	1	121	125	12.0000
.(((	chr14:121506037-121506290(+)$1	1	12	16	12.0000
((((	chr11:105916007-105916247(+)$1	1	66	70	12.0000
(((.	chr2:71112870-71113124(-)$1	1	240	244	12.0000
((((	chr8:3515072-3515314(+)$1	1	16	20	12.0000
(((.	chr7:5044504-5044757(+)$1	1	26	30	12.0000
(((.	chr15:36722183-36722418(-)$1	1	129	133	12.0000
.)))	chr7:73419626-73419868(-)$1	1	16	20	12.0000
((((	chr11:116672280-116672515(-)$1	1	92	96	12.0000
((((	chr7:116760480-116760728(-)$1	1	127	131	12.0000
(((.	chr11:97642144-97642395(-)$1	1	16	20	12.0000
((((	chr4:149100954-149101205(-)$1	1	21	25	12.0000
))))	chr3:144240489-144240746(+)$1	1	193	197	12.0000
(((.	chr13:45652017-45652255(-)$1	1	26	30	12.0000
((((	chr15:54884308-54884555(-)$1	1	26	30	12.0000
...(	chr8:74146824-74147068(+)$1	1	41	45	12.0000
((((	chr8:87296063-87296308(-)$1	1	1	5	12.0000
))))	chr1:63223614-63223869(+)$1	1	105	109	12.0000
(..(	chr10:80255099-80255409(+)$1	1	65	69	12.0000
((.(	chr16:49906324-49906580(+)$1	1	109	113	12.0000
(((.	chr11:77342664-77342938(-)$1	1	141	145	12.0000
))))	chr11:108112731-108112966(-)$1	1	23	27	12.0000
(.((	chr15:57878927-57879178(-)$1	1	57	61	12.0000
((((	chr4:53475497-53475763(+)$1	1	50	54	12.0000
...)	chr6:91212739-91212999(+)$1	1	151	155	12.0000
((((	chrX:101152914-101153152(-)$1	1	31	35	12.0000
))))	chr15:7147304-7147539(+)$1	1	68	72	12.0000
((((	chr9:70333446-70333685(-)$1	1	76	80	12.0000
.)..	chr19:7612039-7612313(+)$1	1	138	142	12.0000
((((	chr17:80291304-80291546(-)$1	1	45	49	12.0000
))).	chr2:35151954-35152199(+)$1	1	72	76	12.0000
))))	chr4:137633481-137633728(+)$1	1	43	47	12.0000
((..	chr1:178705506-178705773(-)$1	1	60	64	12.0000
))))	chr15:90058901-90059140(+)$1	1	125	129	12.0000
...)	chr10:7350802-7351051(-)$1	1	118	122	12.0000
)..(	chr14:65695916-65696154(-)$1	1	17	21	12.0000
(((.	chr15:77657812-77658085(-)$1	1	91	95	12.0000
((((	chr15:32876303-32876551(+)$1	1	114	118	12.0000
))))	chr3:141961437-141961683(-)$1	1	117	121	12.0000
)))(	chrX:101153016-101153271(-)$1	1	29	33	12.0000
...)	chr1:130228110-130228379(-)$1	1	120	124	12.0000
.)).	chr15:99424477-99424765(+)$1	1	124	128	12.0000
((((	chr19:44470964-44471223(-)$1	1	148	152	12.0000
)).)	chr7:97356539-97356790(+)$1	1	220	224	12.0000
))).	chr10:59764509-59764777(+)$1	1	107	111	12.0000
..((	chr11:62654446-62654681(+)$1	1	1	5	12.0000
(((.	chr16:32058164-32058404(-)$1	1	35	39	12.0000
))))	chr4:149943902-149944148(+)$1	1	119	123	12.0000
(((.	chr7:144424255-144424495(-)$1	1	74	78	12.0000

#PSSM
G : 0.85	g : 0.14	
C : 0.85	c : 0.14	
U : 0.85	u : 0.14	
G : 0.85	g : 0.14	

#score	972.0000000000006
#seq	81
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m2_run2.nuc.txt

#NT
CUGGA	chr13:23849052-23849332(+)$1	280	23	28	15.0000
CUGGA	chr8:82163810-82164082(+)$1	272	48	53	15.0000
CUGGA	chr5:36828835-36829107(+)$1	272	124	129	15.0000
CUGGA	chr7:4448993-4449265(-)$1	272	135	140	15.0000
CUGGA	chr1:95197961-95198238(-)$1	277	260	265	15.0000
CUGGA	chr6:86345862-86346153(-)$1	291	51	56	15.0000
CUGGA	chr16:91625564-91625845(-)$1	281	90	95	15.0000
CUGGA	chr1:156945530-156945807(-)$1	277	146	151	15.0000
CUGGA	chr6:128386513-128386854(-)$1	341	227	232	15.0000
CUGGA	chr1:88248648-88248940(-)$1	292	137	142	15.0000
CUGGA	chr12:8716032-8716314(+)$1	282	134	139	15.0000
CUGGA	chr7:16863698-16863970(-)$1	272	53	58	15.0000
CUGGA	chr9:108241671-108241992(+)$1	321	299	304	15.0000
CUGGA	chr19:6059029-6059313(+)$1	284	141	146	15.0000
CUGGA	chr11:78342578-78342853(-)$1	275	57	62	15.0000
CUGGA	chr2:69735756-69736043(+)$1	287	58	63	15.0000
CUGGA	chr18:34963154-34963432(+)$1	278	137	142	15.0000
CUGGA	chr1:183835874-183836144(-)$1	270	89	94	15.0000
CUGGA	chr2:34666441-34666729(-)$1	288	119	124	15.0000
CUGGA	chr6:129401596-129401865(-)$1	269	199	204	15.0000
CUGGA	chr15:76028312-76028680(-)$1	368	192	197	15.0000
CUGGA	chr8:8660420-8660697(-)$1	277	193	198	15.0000
CUGGA	chr17:15905584-15905852(+)$1	268	161	166	15.0000
CUGGA	chr11:75314748-75315025(+)$1	277	95	100	15.0000
CUGGA	chr11:22898941-22899231(+)$1	290	256	261	15.0000
CUGGA	chr3:82873510-82873838(+)$1	328	143	148	15.0000
CUGGA	chr4:47003946-47004214(-)$1	268	208	213	15.0000
CUGGA	chr10:12378282-12378553(-)$1	271	87	92	15.0000
CUGGA	chr7:134177308-134177592(-)$1	284	82	87	15.0000
CUGGA	chr13:97876913-97877181(+)$1	268	99	104	15.0000
CUGGA	chrX:71487046-71487326(-)$1	280	131	136	15.0000
CUGGA	chr19:6105704-6105984(+)$1	280	225	230	15.0000
CUGGA	chr4:137759216-137759493(+)$1	277	225	230	15.0000
CUGGA	chr15:84685987-84686258(-)$1	271	181	186	15.0000
CUGGA	chr15:76424499-76424773(+)$1	274	44	49	15.0000
CUGGA	chr3:107559455-107559724(-)$1	269	37	42	15.0000
CUGGA	chr2:128510222-128510498(-)$1	276	188	193	15.0000
CUGGA	chr11:74722469-74722752(+)$1	283	104	109	15.0000
CUGGA	chr3:83739840-83740115(-)$1	275	244	249	15.0000
CUGGA	chr1:92981438-92981709(+)$1	271	5	10	15.0000
CUGGA	chr14:104865907-104866176(-)$1	269	112	117	15.0000
CUGGA	chr9:62658969-62659258(-)$1	289	13	18	15.0000
CUGGA	chr4:44038238-44038520(+)$1	282	135	140	15.0000
CUGGA	chr14:76168566-76168836(-)$1	270	45	50	15.0000
CUGGA	chr11:80276001-80276290(+)$1	289	41	46	15.0000
CUGGA	chr19:11860073-11860357(-)$1	284	2	7	15.0000
CUGGA	chr18:36916082-36916350(+)$1	268	44	49	15.0000
cugga	chr7:28962035-28962317(+)$1	282	83	88	15.0000
CUGGA	chr9:58097336-58097613(-)$1	277	159	164	15.0000
CUGGA	chr17:7160247-7160519(-)$1	272	212	217	15.0000
CUGGA	chr17:27259618-27259908(-)$1	290	217	222	15.0000
CUGGA	chr16:87493860-87494130(-)$1	270	125	130	15.0000
CUGGA	chr11:101387441-101387710(-)$1	269	171	176	15.0000
CUGGA	chr8:87391660-87391928(+)$1	268	45	50	15.0000
CUGGA	chr12:79984215-79984496(+)$1	281	74	79	15.0000
CUGGA	chr3:108187863-108188142(+)$1	279	166	171	15.0000
CUGGA	chr17:25241928-25242196(-)$1	268	30	35	15.0000

#otherMatches

#Struct PSSM
cc444	chr18:74376730-74376998(+)$1	268	108	113	15.0000
!dddd	chr13:23849052-23849332(+)$1	280	23	28	15.0000
ffff]	chr8:82163810-82164082(+)$1	272	48	53	15.0000
ffff%	chr5:36828835-36829107(+)$1	272	124	129	15.0000
c[fff	chr7:4448993-4449265(-)$1	272	135	140	15.0000
cc333	chr1:95197961-95198238(-)$1	277	260	265	15.0000
eee44	chr6:86345862-86346153(-)$1	291	51	56	15.0000
ddddf	chr16:91625564-91625845(-)$1	281	90	95	15.0000
b::::	chr1:156945530-156945807(-)$1	277	146	151	15.0000
cccc:	chr6:128386513-128386854(-)$1	341	227	232	15.0000
bb[ff	chr1:88248648-88248940(-)$1	292	137	142	15.0000
fffDD	chr12:8716032-8716314(+)$1	282	134	139	15.0000
DDD{D	chr7:16863698-16863970(-)$1	272	53	58	15.0000
22ccc	chr9:108241671-108241992(+)$1	321	299	304	15.0000
eeebb	chr19:6059029-6059313(+)$1	284	141	146	15.0000
dddmm	chr11:78342578-78342853(-)$1	275	57	62	15.0000
DDDD{	chr2:69735756-69736043(+)$1	287	58	63	15.0000
hhhh%	chr18:34963154-34963432(+)$1	278	137	142	15.0000
[bb##	chr1:183835874-183836144(-)$1	270	89	94	15.0000
%%a!!	chr2:34666441-34666729(-)$1	288	119	124	15.0000
JJJJ~	chr6:129401596-129401865(-)$1	269	199	204	15.0000
ddd22	chr15:76028312-76028680(-)$1	368	192	197	15.0000
::bbm	chr8:8660420-8660697(-)$1	277	193	198	15.0000
!!ddd	chr17:15905584-15905852(+)$1	268	161	166	15.0000
2hhhh	chr11:75314748-75315025(+)$1	277	95	100	15.0000
cc[ff	chr11:22898941-22899231(+)$1	290	256	261	15.0000
]====	chr3:82873510-82873838(+)$1	328	143	148	15.0000
!!bb"	chr4:47003946-47004214(-)$1	268	208	213	15.0000
cc333	chr10:12378282-12378553(-)$1	271	87	92	15.0000
:::::	chr7:134177308-134177592(-)$1	284	82	87	15.0000
EEEE:	chr13:97876913-97877181(+)$1	268	99	104	15.0000
BB:::	chrX:71487046-71487326(-)$1	280	131	136	15.0000
ddd""	chr19:6105704-6105984(+)$1	280	225	230	15.0000
3gggg	chr4:137759216-137759493(+)$1	277	225	230	15.0000
qqqqq	chr15:84685987-84686258(-)$1	271	181	186	15.0000
i4444	chr15:76424499-76424773(+)$1	274	44	49	15.0000
bbmmm	chr3:107559455-107559724(-)$1	269	37	42	15.0000
]ffff	chr2:128510222-128510498(-)$1	276	188	193	15.0000
mccc]	chr11:74722469-74722752(+)$1	283	104	109	15.0000
fff]a	chr3:83739840-83740115(-)$1	275	244	249	15.0000
:CCC{	chr1:92981438-92981709(+)$1	271	5	10	15.0000
lccc]	chr14:104865907-104866176(-)$1	269	112	117	15.0000
=[amm	chr9:62658969-62659258(-)$1	289	13	18	15.0000
fdddd	chr4:44038238-44038520(+)$1	282	135	140	15.0000
dddd[	chr14:76168566-76168836(-)$1	270	45	50	15.0000
mmmme	chr11:80276001-80276290(+)$1	289	41	46	15.0000
ccc!!	chr19:11860073-11860357(-)$1	284	2	7	15.0000
BB{BB	chr18:36916082-36916350(+)$1	268	44	49	15.0000
hhddd	chr7:28962035-28962317(+)$1	282	83	88	15.0000
:CCC}	chr9:58097336-58097613(-)$1	277	159	164	15.0000
bffff	chr17:7160247-7160519(-)$1	272	212	217	15.0000
hhhh:	chr17:27259618-27259908(-)$1	290	217	222	15.0000
FFDDD	chr16:87493860-87494130(-)$1	270	125	130	15.0000
b]bb]	chr11:101387441-101387710(-)$1	269	171	176	15.0000
!ccce	chr8:87391660-87391928(+)$1	268	45	50	15.0000
eeee:	chr12:79984215-79984496(+)$1	281	74	79	15.0000
dddd2	chr3:108187863-108188142(+)$1	279	166	171	15.0000
EEEii	chr17:25241928-25242196(-)$1	268	30	35	15.0000

#DB
))...	chr18:74376730-74376998(+)$1	1	108	113	15.0000
.((((	chr13:23849052-23849332(+)$1	1	23	28	15.0000
)))).	chr8:82163810-82164082(+)$1	1	48	53	15.0000
((((.	chr5:36828835-36829107(+)$1	1	124	129	15.0000
(.(((	chr7:4448993-4449265(-)$1	1	135	140	15.0000
))...	chr1:95197961-95198238(-)$1	1	260	265	15.0000
)))..	chr6:86345862-86346153(-)$1	1	51	56	15.0000
)))))	chr16:91625564-91625845(-)$1	1	90	95	15.0000
)....	chr1:156945530-156945807(-)$1	1	146	151	15.0000
)))).	chr6:128386513-128386854(-)$1	1	227	232	15.0000
((.((	chr1:88248648-88248940(-)$1	1	137	142	15.0000
)))))	chr12:8716032-8716314(+)$1	1	134	139	15.0000
(((.(	chr7:16863698-16863970(-)$1	1	53	58	15.0000
..)))	chr9:108241671-108241992(+)$1	1	299	304	15.0000
(((((	chr19:6059029-6059313(+)$1	1	141	146	15.0000
(((..	chr11:78342578-78342853(-)$1	1	57	62	15.0000
((((.	chr2:69735756-69736043(+)$1	1	58	63	15.0000
((((.	chr18:34963154-34963432(+)$1	1	137	142	15.0000
.((..	chr1:183835874-183836144(-)$1	1	89	94	15.0000
..(..	chr2:34666441-34666729(-)$1	1	119	124	15.0000
)))).	chr6:129401596-129401865(-)$1	1	199	204	15.0000
)))..	chr15:76028312-76028680(-)$1	1	192	197	15.0000
..((.	chr8:8660420-8660697(-)$1	1	193	198	15.0000
..(((	chr17:15905584-15905852(+)$1	1	161	166	15.0000
.))))	chr11:75314748-75315025(+)$1	1	95	100	15.0000
((.((	chr11:22898941-22899231(+)$1	1	256	261	15.0000
.))))	chr3:82873510-82873838(+)$1	1	143	148	15.0000
..((.	chr4:47003946-47004214(-)$1	1	208	213	15.0000
))...	chr10:12378282-12378553(-)$1	1	87	92	15.0000
.....	chr7:134177308-134177592(-)$1	1	82	87	15.0000
((((.	chr13:97876913-97877181(+)$1	1	99	104	15.0000
))...	chrX:71487046-71487326(-)$1	1	131	136	15.0000
(((..	chr19:6105704-6105984(+)$1	1	225	230	15.0000
.))))	chr4:137759216-137759493(+)$1	1	225	230	15.0000
.....	chr15:84685987-84686258(-)$1	1	181	186	15.0000
)....	chr15:76424499-76424773(+)$1	1	44	49	15.0000
((...	chr3:107559455-107559724(-)$1	1	37	42	15.0000
.))))	chr2:128510222-128510498(-)$1	1	188	193	15.0000
.))).	chr11:74722469-74722752(+)$1	1	104	109	15.0000
))).)	chr3:83739840-83740115(-)$1	1	244	249	15.0000
.(((.	chr1:92981438-92981709(+)$1	1	5	10	15.0000
.))).	chr14:104865907-104866176(-)$1	1	112	117	15.0000
(.(..	chr9:62658969-62659258(-)$1	1	13	18	15.0000
(((((	chr4:44038238-44038520(+)$1	1	135	140	15.0000
((((.	chr14:76168566-76168836(-)$1	1	45	50	15.0000
....)	chr11:80276001-80276290(+)$1	1	41	46	15.0000
(((..	chr19:11860073-11860357(-)$1	1	2	7	15.0000
((.((	chr18:36916082-36916350(+)$1	1	44	49	15.0000
))(((	chr7:28962035-28962317(+)$1	1	83	88	15.0000
.))).	chr9:58097336-58097613(-)$1	1	159	164	15.0000
(((((	chr17:7160247-7160519(-)$1	1	212	217	15.0000
)))).	chr17:27259618-27259908(-)$1	1	217	222	15.0000
(((((	chr16:87493860-87494130(-)$1	1	125	130	15.0000
).)).	chr11:101387441-101387710(-)$1	1	171	176	15.0000
.((((	chr8:87391660-87391928(+)$1	1	45	50	15.0000
)))).	chr12:79984215-79984496(+)$1	1	74	79	15.0000
)))).	chr3:108187863-108188142(+)$1	1	166	171	15.0000
(((((	chr17:25241928-25242196(-)$1	1	30	35	15.0000

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

#score	870.0000000000001
#seq	58
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_UTR_m3_run2.nuc.txt

#NT
AGG	chr11:76543454-76543677(-)$1	223	15	18	8.9999
AGG	chr7:87370617-87370839(+)$1	222	24	27	8.9999
AGG	chr7:135348928-135349152(+)$1	224	81	84	8.9999
AGG	chr12:81857070-81857325(-)$1	255	4	7	8.9999
AGG	chr8:35199339-35199566(-)$1	227	57	60	8.9999
AGG	chr9:86475746-86475965(-)$1	219	96	99	8.9999
AGG	chr7:25867952-25868173(-)$1	221	37	40	8.9999
AGG	chr14:59967466-59967687(-)$1	221	152	155	8.9999
AGG	chr9:90099673-90099930(-)$1	257	29	32	8.9999
AGG	chr3:95480390-95480613(-)$1	223	75	78	8.9999
AGG	chr9:64929091-64929311(+)$1	220	96	99	8.9999
AGG	chr12:102985927-102986149(+)$1	222	74	77	8.9999
agg	chr4:11907584-11907802(-)$1	218	44	47	8.9999
AGG	chr7:74376479-74376700(-)$1	221	3	6	8.9999
AGG	chr11:116192077-116192299(+)$1	222	1	4	8.9999
AGG	chr2:144298180-144298399(-)$1	219	14	17	8.9999
AGG	chr4:62052635-62052854(-)$1	219	184	187	8.9999
AGG	chr19:6134426-6134660(-)$1	234	41	44	8.9999
AGG	chr15:36701157-36701382(-)$1	225	172	175	8.9999
AGG	chr1:74399277-74399498(+)$1	221	1	4	8.9999
AGG	chr3:88951057-88951283(-)$1	226	34	37	8.9999
AGG	chr5:141140838-141141085(-)$1	247	11	14	8.9999
AGG	chr10:127565165-127565401(+)$1	236	26	29	8.9999
AGG	chr17:13166635-13166866(-)$1	231	47	50	8.9999
AGG	chr5:123822737-123822969(+)$1	232	18	21	8.9999
AGG	chr19:7378464-7378695(-)$1	231	89	92	8.9999
AGG	chr7:109334286-109334532(-)$1	246	12	15	8.9999
AGG	chr13:73757554-73757786(+)$1	232	23	26	8.9999
AGG	chr2:174171651-174171898(+)$1	247	41	44	8.9999
AGG	chr19:21931430-21931659(+)$1	229	6	9	8.9999
AGG	chr11:96629448-96629671(-)$1	223	28	31	8.9999
AGG	chr2:136907148-136907369(-)$1	221	15	18	8.9999
AGG	chr16:92081459-92081680(+)$1	221	79	82	8.9999
AGG	chr4:149354712-149354965(-)$1	253	2	5	8.9999
AGG	chr17:25409718-25409933(-)$1	215	42	45	8.9999
AGG	chr8:72345043-72345265(+)$1	222	13	16	8.9999
AGG	chr11:70458039-70458260(-)$1	221	65	68	8.9999
AGG	chr9:66871333-66871552(-)$1	219	130	133	8.9999
AGG	chr17:25236044-25236267(+)$1	223	96	99	8.9999
AGG	chr7:134655720-134655943(+)$1	223	37	40	8.9999
AGG	chr9:103084406-103084630(+)$1	224	5	8	8.9999
AGG	chr9:69230774-69230995(-)$1	221	2	5	8.9999
AGG	chr9:44199828-44200049(+)$1	221	3	6	8.9999
AGG	chr10:82286290-82286515(+)$1	225	154	157	8.9999
AGG	chr7:28536307-28536524(-)$1	217	15	18	8.9999
AGG	chr7:86955713-86955936(-)$1	223	13	16	8.9999
AGG	chr2:155641694-155641922(+)$1	228	34	37	8.9999
AGG	chr18:35006186-35006408(+)$1	222	53	56	8.9999
AGG	chr11:106648155-106648370(+)$1	215	88	91	8.9999
AGG	chr7:28137603-28137824(-)$1	221	101	104	8.9999
AGG	chr6:92484569-92484798(-)$1	229	40	43	8.9999
AGG	chr6:85893648-85893872(-)$1	224	20	23	8.9999
AGG	chr2:25374202-25374427(-)$1	225	79	82	8.9999
AGG	chr19:59982514-59982738(-)$1	224	30	33	8.9999
AGG	chr6:71758527-71758760(+)$1	233	4	7	8.9999
AGG	chr10:74971485-74971703(-)$1	218	19	22	8.9999
AGG	chr8:96591240-96591472(+)$1	232	79	82	8.9999
AGG	chr4:147527247-147527499(-)$1	252	73	76	8.9999
agg	chr6:128309423-128309638(-)$1	215	1	4	8.9999
AGG	chr2:11711743-11711973(+)$1	230	87	90	8.9999
AGG	chr12:12943260-12943477(+)$1	217	46	49	8.9999
AGG	chr6:148127927-148128165(-)$1	238	22	25	8.9999
AGG	chr6:120391468-120391701(+)$1	233	147	150	8.9999
AGG	chr1:133071183-133071404(+)$1	221	11	14	8.9999
AGG	chr2:122105983-122106201(+)$1	218	84	87	8.9999
AGG	chr4:138299608-138299829(-)$1	221	33	36	8.9999
AGG	chr6:122679194-122679415(-)$1	221	4	7	8.9999
AGG	chr14:66929341-66929562(+)$1	221	79	82	8.9999
AGG	chr8:23898728-23898966(-)$1	238	52	55	8.9999
AGG	chr5:151298900-151299131(+)$1	231	31	34	8.9999
AGG	chr4:61958859-61959078(+)$1	219	24	27	8.9999
AGG	chr3:122242835-122243073(-)$1	238	3	6	8.9999
AGG	chr8:125009117-125009340(+)$1	223	6	9	8.9999
AGG	chr13:53024938-53025160(+)$1	222	16	19	8.9999
AGG	chr10:67007968-67008191(-)$1	223	175	178	8.9999
AGG	chr2:84441715-84441936(-)$1	221	91	94	8.9999
AGG	chr19:7012469-7012706(-)$1	237	28	31	8.9999
AGG	chr19:46576120-46576338(+)$1	218	75	78	8.9999
AGG	chr8:72619474-72619695(-)$1	221	95	98	8.9999
AGG	chr16:32392742-32392969(+)$1	227	32	35	8.9999
AGG	chr5:34239355-34239578(+)$1	223	24	27	8.9999
AGG	chr17:34165419-34165643(-)$1	224	16	19	8.9999
AGG	chr16:37887813-37888049(+)$1	236	27	30	8.9999
AGG	chr8:122223823-122224038(-)$1	215	54	57	8.9999
AGG	chr9:46030869-46031091(+)$1	222	2	5	8.9999
AGG	chr7:138055638-138055866(+)$1	228	68	71	8.9999
AGG	chr6:57459650-57459871(+)$1	221	10	13	8.9999
AGG	chrX:153987288-153987504(-)$1	216	134	137	8.9999
AGG	chr6:67237002-67237232(+)$1	230	52	55	8.9999
agg	chr3:65859955-65860170(-)$1	215	2	5	8.9999

#otherMatches

#Struct PSSM
FFF	chr18:25624474-25624707(+)$1	233	56	59	8.9999
ggg	chr11:76543454-76543677(-)$1	223	15	18	8.9999
III	chr7:87370617-87370839(+)$1	222	24	27	8.9999
CGG	chr7:135348928-135349152(+)$1	224	81	84	8.9999
emm	chr12:81857070-81857325(-)$1	255	4	7	8.9999
lll	chr8:35199339-35199566(-)$1	227	57	60	8.9999
ddd	chr9:86475746-86475965(-)$1	219	96	99	8.9999
eee	chr7:25867952-25868173(-)$1	221	37	40	8.9999
ccc	chr14:59967466-59967687(-)$1	221	152	155	8.9999
DDB	chr9:90099673-90099930(-)$1	257	29	32	8.9999
^hh	chr3:95480390-95480613(-)$1	223	75	78	8.9999
ddd	chr9:64929091-64929311(+)$1	220	96	99	8.9999
fff	chr12:102985927-102986149(+)$1	222	74	77	8.9999
[dd	chr4:11907584-11907802(-)$1	218	44	47	8.9999
ccc	chr7:74376479-74376700(-)$1	221	3	6	8.9999
:FF	chr11:116192077-116192299(+)$1	222	1	4	8.9999
qqq	chr2:144298180-144298399(-)$1	219	14	17	8.9999
tcc	chr4:62052635-62052854(-)$1	219	184	187	8.9999
[cc	chr19:6134426-6134660(-)$1	234	41	44	8.9999
e""	chr15:36701157-36701382(-)$1	225	172	175	8.9999
FFF	chr1:74399277-74399498(+)$1	221	1	4	8.9999
fff	chr3:88951057-88951283(-)$1	226	34	37	8.9999
EEE	chr5:141140838-141141085(-)$1	247	11	14	8.9999
"bb	chr10:127565165-127565401(+)$1	236	26	29	8.9999
www	chr17:13166635-13166866(-)$1	231	47	50	8.9999
EEE	chr5:123822737-123822969(+)$1	232	18	21	8.9999
ggg	chr19:7378464-7378695(-)$1	231	89	92	8.9999
HHH	chr7:109334286-109334532(-)$1	246	12	15	8.9999
===	chr13:73757554-73757786(+)$1	232	23	26	8.9999
iii	chr2:174171651-174171898(+)$1	247	41	44	8.9999
CCE	chr19:21931430-21931659(+)$1	229	6	9	8.9999
]gg	chr11:96629448-96629671(-)$1	223	28	31	8.9999
JJJ	chr2:136907148-136907369(-)$1	221	15	18	8.9999
fff	chr16:92081459-92081680(+)$1	221	79	82	8.9999
HHH	chr4:149354712-149354965(-)$1	253	2	5	8.9999
rgg	chr17:25409718-25409933(-)$1	215	42	45	8.9999
]ff	chr8:72345043-72345265(+)$1	222	13	16	8.9999
fff	chr11:70458039-70458260(-)$1	221	65	68	8.9999
ggg	chr9:66871333-66871552(-)$1	219	130	133	8.9999
===	chr17:25236044-25236267(+)$1	223	96	99	8.9999
eee	chr7:134655720-134655943(+)$1	223	37	40	8.9999
DDD	chr9:103084406-103084630(+)$1	224	5	8	8.9999
HHH	chr9:69230774-69230995(-)$1	221	2	5	8.9999
iii	chr9:44199828-44200049(+)$1	221	3	6	8.9999
hhh	chr10:82286290-82286515(+)$1	225	154	157	8.9999
ccp	chr7:28536307-28536524(-)$1	217	15	18	8.9999
KKC	chr7:86955713-86955936(-)$1	223	13	16	8.9999
:gg	chr2:155641694-155641922(+)$1	228	34	37	8.9999
ttd	chr18:35006186-35006408(+)$1	222	53	56	8.9999
hhh	chr11:106648155-106648370(+)$1	215	88	91	8.9999
qdd	chr7:28137603-28137824(-)$1	221	101	104	8.9999
ohh	chr6:92484569-92484798(-)$1	229	40	43	8.9999
c##	chr6:85893648-85893872(-)$1	224	20	23	8.9999
ddd	chr2:25374202-25374427(-)$1	225	79	82	8.9999
CEE	chr19:59982514-59982738(-)$1	224	30	33	8.9999
:::	chr6:71758527-71758760(+)$1	233	4	7	8.9999
EEK	chr10:74971485-74971703(-)$1	218	19	22	8.9999
eee	chr8:96591240-96591472(+)$1	232	79	82	8.9999
ddd	chr4:147527247-147527499(-)$1	252	73	76	8.9999
ddd	chr6:128309423-128309638(-)$1	215	1	4	8.9999
fff	chr2:11711743-11711973(+)$1	230	87	90	8.9999
ggg	chr12:12943260-12943477(+)$1	217	46	49	8.9999
HHH	chr6:148127927-148128165(-)$1	238	22	25	8.9999
33c	chr6:120391468-120391701(+)$1	233	147	150	8.9999
hhh	chr1:133071183-133071404(+)$1	221	11	14	8.9999
'a!	chr2:122105983-122106201(+)$1	218	84	87	8.9999
ff[	chr4:138299608-138299829(-)$1	221	33	36	8.9999
CKK	chr6:122679194-122679415(-)$1	221	4	7	8.9999
[cc	chr14:66929341-66929562(+)$1	221	79	82	8.9999
bb"	chr8:23898728-23898966(-)$1	238	52	55	8.9999
ggg	chr5:151298900-151299131(+)$1	231	31	34	8.9999
ddd	chr4:61958859-61959078(+)$1	219	24	27	8.9999
bb"	chr3:122242835-122243073(-)$1	238	3	6	8.9999
KKD	chr8:125009117-125009340(+)$1	223	6	9	8.9999
HHH	chr13:53024938-53025160(+)$1	222	16	19	8.9999
ddd	chr10:67007968-67008191(-)$1	223	175	178	8.9999
iii	chr2:84441715-84441936(-)$1	221	91	94	8.9999
ee:	chr19:7012469-7012706(-)$1	237	28	31	8.9999
fff	chr19:46576120-46576338(+)$1	218	75	78	8.9999
ggg	chr8:72619474-72619695(-)$1	221	95	98	8.9999
HH:	chr16:32392742-32392969(+)$1	227	32	35	8.9999
FFF	chr5:34239355-34239578(+)$1	223	24	27	8.9999
c!!	chr17:34165419-34165643(-)$1	224	16	19	8.9999
===	chr16:37887813-37888049(+)$1	236	27	30	8.9999
fff	chr8:122223823-122224038(-)$1	215	54	57	8.9999
:DD	chr9:46030869-46031091(+)$1	222	2	5	8.9999
ggg	chr7:138055638-138055866(+)$1	228	68	71	8.9999
:::	chr6:57459650-57459871(+)$1	221	10	13	8.9999
]bb	chrX:153987288-153987504(-)$1	216	134	137	8.9999
===	chr6:67237002-67237232(+)$1	230	52	55	8.9999
DDD	chr3:65859955-65860170(-)$1	215	2	5	8.9999

#DB
(((	chr18:25624474-25624707(+)$1	1	56	59	8.9999
(((	chr11:76543454-76543677(-)$1	1	15	18	8.9999
(((	chr7:87370617-87370839(+)$1	1	24	27	8.9999
(((	chr7:135348928-135349152(+)$1	1	81	84	8.9999
(..	chr12:81857070-81857325(-)$1	1	4	7	8.9999
...	chr8:35199339-35199566(-)$1	1	57	60	8.9999
)))	chr9:86475746-86475965(-)$1	1	96	99	8.9999
(((	chr7:25867952-25868173(-)$1	1	37	40	8.9999
(((	chr14:59967466-59967687(-)$1	1	152	155	8.9999
(((	chr9:90099673-90099930(-)$1	1	29	32	8.9999
.))	chr3:95480390-95480613(-)$1	1	75	78	8.9999
(((	chr9:64929091-64929311(+)$1	1	96	99	8.9999
)))	chr12:102985927-102986149(+)$1	1	74	77	8.9999
.((	chr4:11907584-11907802(-)$1	1	44	47	8.9999
(((	chr7:74376479-74376700(-)$1	1	3	6	8.9999
.((	chr11:116192077-116192299(+)$1	1	1	4	8.9999
...	chr2:144298180-144298399(-)$1	1	14	17	8.9999
.))	chr4:62052635-62052854(-)$1	1	184	187	8.9999
.((	chr19:6134426-6134660(-)$1	1	41	44	8.9999
(..	chr15:36701157-36701382(-)$1	1	172	175	8.9999
(((	chr1:74399277-74399498(+)$1	1	1	4	8.9999
)))	chr3:88951057-88951283(-)$1	1	34	37	8.9999
(((	chr5:141140838-141141085(-)$1	1	11	14	8.9999
.((	chr10:127565165-127565401(+)$1	1	26	29	8.9999
...	chr17:13166635-13166866(-)$1	1	47	50	8.9999
(((	chr5:123822737-123822969(+)$1	1	18	21	8.9999
(((	chr19:7378464-7378695(-)$1	1	89	92	8.9999
(((	chr7:109334286-109334532(-)$1	1	12	15	8.9999
(((	chr13:73757554-73757786(+)$1	1	23	26	8.9999
(((	chr2:174171651-174171898(+)$1	1	41	44	8.9999
(((	chr19:21931430-21931659(+)$1	1	6	9	8.9999
.))	chr11:96629448-96629671(-)$1	1	28	31	8.9999
(((	chr2:136907148-136907369(-)$1	1	15	18	8.9999
(((	chr16:92081459-92081680(+)$1	1	79	82	8.9999
(((	chr4:149354712-149354965(-)$1	1	2	5	8.9999
.))	chr17:25409718-25409933(-)$1	1	42	45	8.9999
.))	chr8:72345043-72345265(+)$1	1	13	16	8.9999
)))	chr11:70458039-70458260(-)$1	1	65	68	8.9999
)))	chr9:66871333-66871552(-)$1	1	130	133	8.9999
)))	chr17:25236044-25236267(+)$1	1	96	99	8.9999
(((	chr7:134655720-134655943(+)$1	1	37	40	8.9999
(((	chr9:103084406-103084630(+)$1	1	5	8	8.9999
(((	chr9:69230774-69230995(-)$1	1	2	5	8.9999
(((	chr9:44199828-44200049(+)$1	1	3	6	8.9999
)))	chr10:82286290-82286515(+)$1	1	154	157	8.9999
((.	chr7:28536307-28536524(-)$1	1	15	18	8.9999
..(	chr7:86955713-86955936(-)$1	1	13	16	8.9999
.((	chr2:155641694-155641922(+)$1	1	34	37	8.9999
..)	chr18:35006186-35006408(+)$1	1	53	56	8.9999
)))	chr11:106648155-106648370(+)$1	1	88	91	8.9999
.))	chr7:28137603-28137824(-)$1	1	101	104	8.9999
.))	chr6:92484569-92484798(-)$1	1	40	43	8.9999
(..	chr6:85893648-85893872(-)$1	1	20	23	8.9999
)))	chr2:25374202-25374427(-)$1	1	79	82	8.9999
(((	chr19:59982514-59982738(-)$1	1	30	33	8.9999
...	chr6:71758527-71758760(+)$1	1	4	7	8.9999
((.	chr10:74971485-74971703(-)$1	1	19	22	8.9999
)))	chr8:96591240-96591472(+)$1	1	79	82	8.9999
)))	chr4:147527247-147527499(-)$1	1	73	76	8.9999
(((	chr6:128309423-128309638(-)$1	1	1	4	8.9999
)))	chr2:11711743-11711973(+)$1	1	87	90	8.9999
(((	chr12:12943260-12943477(+)$1	1	46	49	8.9999
(((	chr6:148127927-148128165(-)$1	1	22	25	8.9999
..)	chr6:120391468-120391701(+)$1	1	147	150	8.9999
(((	chr1:133071183-133071404(+)$1	1	11	14	8.9999
.(.	chr2:122105983-122106201(+)$1	1	84	87	8.9999
((.	chr4:138299608-138299829(-)$1	1	33	36	8.9999
(..	chr6:122679194-122679415(-)$1	1	4	7	8.9999
.((	chr14:66929341-66929562(+)$1	1	79	82	8.9999
((.	chr8:23898728-23898966(-)$1	1	52	55	8.9999
(((	chr5:151298900-151299131(+)$1	1	31	34	8.9999
)))	chr4:61958859-61959078(+)$1	1	24	27	8.9999
((.	chr3:122242835-122243073(-)$1	1	3	6	8.9999
..(	chr8:125009117-125009340(+)$1	1	6	9	8.9999
(((	chr13:53024938-53025160(+)$1	1	16	19	8.9999
(((	chr10:67007968-67008191(-)$1	1	175	178	8.9999
)))	chr2:84441715-84441936(-)$1	1	91	94	8.9999
)).	chr19:7012469-7012706(-)$1	1	28	31	8.9999
)))	chr19:46576120-46576338(+)$1	1	75	78	8.9999
(((	chr8:72619474-72619695(-)$1	1	95	98	8.9999
((.	chr16:32392742-32392969(+)$1	1	32	35	8.9999
(((	chr5:34239355-34239578(+)$1	1	24	27	8.9999
(..	chr17:34165419-34165643(-)$1	1	16	19	8.9999
)))	chr16:37887813-37888049(+)$1	1	27	30	8.9999
(((	chr8:122223823-122224038(-)$1	1	54	57	8.9999
.((	chr9:46030869-46031091(+)$1	1	2	5	8.9999
(((	chr7:138055638-138055866(+)$1	1	68	71	8.9999
...	chr6:57459650-57459871(+)$1	1	10	13	8.9999
.))	chrX:153987288-153987504(-)$1	1	134	137	8.9999
(((	chr6:67237002-67237232(+)$1	1	52	55	8.9999
(((	chr3:65859955-65860170(-)$1	1	2	5	8.9999

#PSSM
A : 0.96	a : 0.03	
G : 0.96	g : 0.03	
G : 0.96	g : 0.03	

#score	818.9999999999998
#seq	91
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_transcript_m3_run2.nuc.txt

#NT
ucuu	chr4:76891967-76892168(-)$1	201	36	40	11.9999
UCUU	chr2:28069648-28069849(+)$1	201	76	80	11.9999
UCUU	chr1:153193910-153194111(+)$1	201	182	186	11.9999
ucuu	chr17:55634165-55634366(+)$1	201	5	9	11.9999
UCUU	chr3:108195041-108195242(-)$1	201	93	97	11.9999
UCUU	chr17:65957903-65958104(-)$1	201	8	12	11.9999
UCUU	chr19:5798199-5798400(-)$1	201	42	46	11.9999
UCUU	chr2:62074796-62074997(+)$1	201	18	22	11.9999
UCUU	chr6:71341763-71341964(-)$1	201	104	108	11.9999
UCUU	chr6:45231009-45231210(+)$1	201	1	5	11.9999
UCUU	chr17:10404448-10404649(-)$1	201	87	91	11.9999
ucuu	chr16:65052298-65052499(-)$1	201	164	168	11.9999
UCUU	chr2:96191331-96191532(+)$1	201	61	65	11.9999
UCUU	chr9:75417223-75417424(-)$1	201	40	44	11.9999
UCUU	chr1:134894694-134894895(-)$1	201	6	10	11.9999
ucuu	chrX:138783066-138783267(-)$1	201	30	34	11.9999
UCUU	chr11:36628898-36629099(-)$1	201	58	62	11.9999
UCUU	chr18:33346932-33347133(+)$1	201	12	16	11.9999
ucuu	chr5:120934789-120934990(-)$1	201	28	32	11.9999
UCUU	chr1:108256434-108256635(+)$1	201	1	5	11.9999
UCUU	chr7:98758622-98758823(+)$1	201	114	118	11.9999
UCUU	chr5:82215432-82215633(+)$1	201	142	146	11.9999
UCUU	chr5:136386079-136386280(-)$1	201	153	157	11.9999
UCUU	chr17:91178421-91178622(-)$1	201	121	125	11.9999
UCUU	chr14:14857588-14857789(+)$1	201	5	9	11.9999
UCUU	chrX:162824279-162824480(+)$1	201	147	151	11.9999
ucuu	chr9:72554844-72555045(+)$1	201	35	39	11.9999
UCUU	chr8:39524566-39524767(-)$1	201	131	135	11.9999
ucuu	chr3:60339911-60340112(+)$1	201	67	71	11.9999
UCUU	chr10:20799627-20799828(+)$1	201	10	14	11.9999
ucuu	chr5:46224067-46224268(-)$1	201	21	25	11.9999
UCUU	chr18:55140216-55140417(-)$1	201	117	121	11.9999
UCUU	chr18:39000010-39000211(-)$1	201	58	62	11.9999
UCUU	chr5:110595870-110596071(+)$1	201	5	9	11.9999
UCUU	chrX:69678526-69678727(-)$1	201	61	65	11.9999
UCUU	chr1:192847530-192847731(-)$1	201	54	58	11.9999
UCUU	chr16:3917464-3917665(+)$1	201	9	13	11.9999
UCUU	chr1:25880256-25880457(-)$1	201	46	50	11.9999
UCUU	chrX:100662180-100662381(-)$1	201	1	5	11.9999
UCUU	chr10:21719317-21719518(+)$1	201	164	168	11.9999
UCUU	chr16:67263231-67263432(-)$1	201	3	7	11.9999
ucuu	chr2:141127342-141127543(+)$1	201	28	32	11.9999
UCUU	chr18:39136682-39136883(+)$1	201	1	5	11.9999
UCUU	chr10:106369350-106369551(+)$1	201	51	55	11.9999
UCUU	chr12:117558291-117558492(+)$1	201	148	152	11.9999
UCUU	chr11:85407139-85407340(+)$1	201	69	73	11.9999
UCUU	chr7:85499691-85499892(-)$1	201	10	14	11.9999
UCUU	chr2:180763790-180763991(-)$1	201	121	125	11.9999
UCUU	chr6:29859580-29859781(+)$1	201	50	54	11.9999
UCUU	chr9:28236740-28236941(+)$1	201	66	70	11.9999
UCUU	chr1:52261682-52261883(-)$1	201	115	119	11.9999
ucuu	chr11:57119341-57119542(+)$1	201	154	158	11.9999
UCUU	chr4:36511812-36512013(-)$1	201	21	25	11.9999
UCUU	chr12:110803102-110803303(+)$1	201	88	92	11.9999
UCUU	chr8:26787657-26787858(+)$1	201	13	17	11.9999
UCUU	chr6:9070690-9070891(+)$1	201	59	63	11.9999
ucuu	chr5:49690139-49690340(-)$1	201	45	49	11.9999
ucuu	chr5:49666785-49666986(-)$1	201	162	166	11.9999
ucuu	chr8:60594080-60594281(-)$1	201	2	6	11.9999
UCUU	chr12:56704738-56704939(-)$1	201	147	151	11.9999
UCUU	chr3:25761718-25761919(-)$1	201	77	81	11.9999
UCUU	chr4:115725186-115725387(-)$1	201	107	111	11.9999
UCUU	chr15:48452125-48452326(-)$1	201	28	32	11.9999
UCUU	chr1:54235030-54235231(-)$1	201	43	47	11.9999
UCUU	chr1:121698259-121698460(-)$1	201	26	30	11.9999
UCUU	chr4:132203238-132203439(+)$1	201	41	45	11.9999
ucuu	chr2:102226588-102226789(-)$1	201	152	156	11.9999
ucuu	chr2:48776120-48776321(-)$1	201	176	180	11.9999
ucuu	chr14:125064363-125064564(-)$1	201	183	187	11.9999
UCUU	chrX:143919403-143919604(-)$1	201	16	20	11.9999
UCUU	chr15:25903137-25903338(+)$1	201	155	159	11.9999
UCUU	chrM:581-782(+)$1	201	80	84	11.9999
UCUU	chr6:8677494-8677695(-)$1	201	1	5	11.9999
UCUU	chr6:142776442-142776643(-)$1	201	21	25	11.9999
UCUU	chr3:127028200-127028401(-)$1	201	183	187	11.9999
ucuu	chr7:98396271-98396472(+)$1	201	129	133	11.9999
UCUU	chr4:101313554-101313755(+)$1	201	148	152	11.9999
UCUU	chr11:74489830-74490031(-)$1	201	18	22	11.9999
UCUU	chr14:50083962-50084163(-)$1	201	109	113	11.9999
UCUU	chr14:35558896-35559097(+)$1	201	123	127	11.9999
UCUU	chr10:20787551-20787752(+)$1	201	106	110	11.9999
ucuu	chr17:37210877-37211078(+)$1	201	6	10	11.9999
UCUU	chr1:63639841-63640042(+)$1	201	73	77	11.9999
UCUU	chr16:17011066-17011267(+)$1	201	20	24	11.9999

#otherMatches

#Struct PSSM
::::	chr1:63790263-63790464(+)$1	201	115	119	11.9999
[a[d	chr4:76891967-76892168(-)$1	201	36	40	11.9999
DEEE	chr2:28069648-28069849(+)$1	201	76	80	11.9999
::::	chr1:153193910-153194111(+)$1	201	182	186	11.9999
::::	chr17:55634165-55634366(+)$1	201	5	9	11.9999
d[ee	chr3:108195041-108195242(-)$1	201	93	97	11.9999
ffff	chr17:65957903-65958104(-)$1	201	8	12	11.9999
EEEE	chr19:5798199-5798400(-)$1	201	42	46	11.9999
vfff	chr2:62074796-62074997(+)$1	201	18	22	11.9999
e22a	chr6:71341763-71341964(-)$1	201	104	108	11.9999
::::	chr6:45231009-45231210(+)$1	201	1	5	11.9999
^^^^	chr17:10404448-10404649(-)$1	201	87	91	11.9999
ee::	chr16:65052298-65052499(-)$1	201	164	168	11.9999
F:::	chr2:96191331-96191532(+)$1	201	61	65	11.9999
::gg	chr9:75417223-75417424(-)$1	201	40	44	11.9999
EEEE	chr1:134894694-134894895(-)$1	201	6	10	11.9999
cc]b	chrX:138783066-138783267(-)$1	201	30	34	11.9999
:::G	chr11:36628898-36629099(-)$1	201	58	62	11.9999
GGGG	chr18:33346932-33347133(+)$1	201	12	16	11.9999
::::	chr5:120934789-120934990(-)$1	201	28	32	11.9999
::gg	chr1:108256434-108256635(+)$1	201	1	5	11.9999
dddd	chr7:98758622-98758823(+)$1	201	114	118	11.9999
g]bb	chr5:82215432-82215633(+)$1	201	142	146	11.9999
====	chr5:136386079-136386280(-)$1	201	153	157	11.9999
dddd	chr17:91178421-91178622(-)$1	201	121	125	11.9999
::::	chr14:14857588-14857789(+)$1	201	5	9	11.9999
gggg	chrX:162824279-162824480(+)$1	201	147	151	11.9999
::::	chr9:72554844-72555045(+)$1	201	35	39	11.9999
::::	chr8:39524566-39524767(-)$1	201	131	135	11.9999
^^^^	chr3:60339911-60340112(+)$1	201	67	71	11.9999
E{CC	chr10:20799627-20799828(+)$1	201	10	14	11.9999
::::	chr5:46224067-46224268(-)$1	201	21	25	11.9999
^^^c	chr18:55140216-55140417(-)$1	201	117	121	11.9999
iiii	chr18:39000010-39000211(-)$1	201	58	62	11.9999
::::	chr5:110595870-110596071(+)$1	201	5	9	11.9999
eee:	chrX:69678526-69678727(-)$1	201	61	65	11.9999
333c	chr1:192847530-192847731(-)$1	201	54	58	11.9999
:fff	chr16:3917464-3917665(+)$1	201	9	13	11.9999
####	chr1:25880256-25880457(-)$1	201	46	50	11.9999
:ddd	chrX:100662180-100662381(-)$1	201	1	5	11.9999
EEEE	chr10:21719317-21719518(+)$1	201	164	168	11.9999
::FF	chr16:67263231-67263432(-)$1	201	3	7	11.9999
::::	chr2:141127342-141127543(+)$1	201	28	32	11.9999
::::	chr18:39136682-39136883(+)$1	201	1	5	11.9999
E:::	chr10:106369350-106369551(+)$1	201	51	55	11.9999
::::	chr12:117558291-117558492(+)$1	201	148	152	11.9999
bb!!	chr11:85407139-85407340(+)$1	201	69	73	11.9999
qqdd	chr7:85499691-85499892(-)$1	201	10	14	11.9999
cnnn	chr2:180763790-180763991(-)$1	201	121	125	11.9999
nnnd	chr6:29859580-29859781(+)$1	201	50	54	11.9999
&&&&	chr9:28236740-28236941(+)$1	201	66	70	11.9999
eee[	chr1:52261682-52261883(-)$1	201	115	119	11.9999
dddd	chr11:57119341-57119542(+)$1	201	154	158	11.9999
::cc	chr4:36511812-36512013(-)$1	201	21	25	11.9999
KKDD	chr12:110803102-110803303(+)$1	201	88	92	11.9999
::::	chr8:26787657-26787858(+)$1	201	13	17	11.9999
GGGG	chr6:9070690-9070891(+)$1	201	59	63	11.9999
::::	chr5:49690139-49690340(-)$1	201	45	49	11.9999
^^^^	chr5:49666785-49666986(-)$1	201	162	166	11.9999
::::	chr8:60594080-60594281(-)$1	201	2	6	11.9999
ddd=	chr12:56704738-56704939(-)$1	201	147	151	11.9999
4fff	chr3:25761718-25761919(-)$1	201	77	81	11.9999
^^^^	chr4:115725186-115725387(-)$1	201	107	111	11.9999
::::	chr15:48452125-48452326(-)$1	201	28	32	11.9999
OOOF	chr1:54235030-54235231(-)$1	201	43	47	11.9999
::::	chr1:121698259-121698460(-)$1	201	26	30	11.9999
eeee	chr4:132203238-132203439(+)$1	201	41	45	11.9999
:fff	chr2:102226588-102226789(-)$1	201	152	156	11.9999
iiii	chr2:48776120-48776321(-)$1	201	176	180	11.9999
]ccc	chr14:125064363-125064564(-)$1	201	183	187	11.9999
FFFF	chrX:143919403-143919604(-)$1	201	16	20	11.9999
IIII	chr15:25903137-25903338(+)$1	201	155	159	11.9999
DDDD	chrM:581-782(+)$1	201	80	84	11.9999
::::	chr6:8677494-8677695(-)$1	201	1	5	11.9999
:ddd	chr6:142776442-142776643(-)$1	201	21	25	11.9999
JJJ~	chr3:127028200-127028401(-)$1	201	183	187	11.9999
tbb]	chr7:98396271-98396472(+)$1	201	129	133	11.9999
shhh	chr4:101313554-101313755(+)$1	201	148	152	11.9999
:::h	chr11:74489830-74490031(-)$1	201	18	22	11.9999
4444	chr14:50083962-50084163(-)$1	201	109	113	11.9999
HHHH	chr14:35558896-35559097(+)$1	201	123	127	11.9999
ssss	chr10:20787551-20787752(+)$1	201	106	110	11.9999
ee^^	chr17:37210877-37211078(+)$1	201	6	10	11.9999
GGGG	chr1:63639841-63640042(+)$1	201	73	77	11.9999
::::	chr16:17011066-17011267(+)$1	201	20	24	11.9999

#DB
....	chr1:63790263-63790464(+)$1	1	115	119	11.9999
.(.(	chr4:76891967-76892168(-)$1	1	36	40	11.9999
))))	chr2:28069648-28069849(+)$1	1	76	80	11.9999
....	chr1:153193910-153194111(+)$1	1	182	186	11.9999
....	chr17:55634165-55634366(+)$1	1	5	9	11.9999
(.((	chr3:108195041-108195242(-)$1	1	93	97	11.9999
((((	chr17:65957903-65958104(-)$1	1	8	12	11.9999
((((	chr19:5798199-5798400(-)$1	1	42	46	11.9999
.)))	chr2:62074796-62074997(+)$1	1	18	22	11.9999
)..)	chr6:71341763-71341964(-)$1	1	104	108	11.9999
....	chr6:45231009-45231210(+)$1	1	1	5	11.9999
....	chr17:10404448-10404649(-)$1	1	87	91	11.9999
))..	chr16:65052298-65052499(-)$1	1	164	168	11.9999
(...	chr2:96191331-96191532(+)$1	1	61	65	11.9999
..((	chr9:75417223-75417424(-)$1	1	40	44	11.9999
((((	chr1:134894694-134894895(-)$1	1	6	10	11.9999
)).)	chrX:138783066-138783267(-)$1	1	30	34	11.9999
...(	chr11:36628898-36629099(-)$1	1	58	62	11.9999
((((	chr18:33346932-33347133(+)$1	1	12	16	11.9999
....	chr5:120934789-120934990(-)$1	1	28	32	11.9999
..((	chr1:108256434-108256635(+)$1	1	1	5	11.9999
))))	chr7:98758622-98758823(+)$1	1	114	118	11.9999
).))	chr5:82215432-82215633(+)$1	1	142	146	11.9999
((((	chr5:136386079-136386280(-)$1	1	153	157	11.9999
((((	chr17:91178421-91178622(-)$1	1	121	125	11.9999
....	chr14:14857588-14857789(+)$1	1	5	9	11.9999
))))	chrX:162824279-162824480(+)$1	1	147	151	11.9999
....	chr9:72554844-72555045(+)$1	1	35	39	11.9999
....	chr8:39524566-39524767(-)$1	1	131	135	11.9999
....	chr3:60339911-60340112(+)$1	1	67	71	11.9999
(.((	chr10:20799627-20799828(+)$1	1	10	14	11.9999
....	chr5:46224067-46224268(-)$1	1	21	25	11.9999
...)	chr18:55140216-55140417(-)$1	1	117	121	11.9999
))))	chr18:39000010-39000211(-)$1	1	58	62	11.9999
....	chr5:110595870-110596071(+)$1	1	5	9	11.9999
))).	chrX:69678526-69678727(-)$1	1	61	65	11.9999
...)	chr1:192847530-192847731(-)$1	1	54	58	11.9999
.(((	chr16:3917464-3917665(+)$1	1	9	13	11.9999
....	chr1:25880256-25880457(-)$1	1	46	50	11.9999
.(((	chrX:100662180-100662381(-)$1	1	1	5	11.9999
))))	chr10:21719317-21719518(+)$1	1	164	168	11.9999
..((	chr16:67263231-67263432(-)$1	1	3	7	11.9999
....	chr2:141127342-141127543(+)$1	1	28	32	11.9999
....	chr18:39136682-39136883(+)$1	1	1	5	11.9999
(...	chr10:106369350-106369551(+)$1	1	51	55	11.9999
....	chr12:117558291-117558492(+)$1	1	148	152	11.9999
((..	chr11:85407139-85407340(+)$1	1	69	73	11.9999
..))	chr7:85499691-85499892(-)$1	1	10	14	11.9999
(...	chr2:180763790-180763991(-)$1	1	121	125	11.9999
...)	chr6:29859580-29859781(+)$1	1	50	54	11.9999
....	chr9:28236740-28236941(+)$1	1	66	70	11.9999
(((.	chr1:52261682-52261883(-)$1	1	115	119	11.9999
))))	chr11:57119341-57119542(+)$1	1	154	158	11.9999
..((	chr4:36511812-36512013(-)$1	1	21	25	11.9999
..((	chr12:110803102-110803303(+)$1	1	88	92	11.9999
....	chr8:26787657-26787858(+)$1	1	13	17	11.9999
((((	chr6:9070690-9070891(+)$1	1	59	63	11.9999
....	chr5:49690139-49690340(-)$1	1	45	49	11.9999
....	chr5:49666785-49666986(-)$1	1	162	166	11.9999
....	chr8:60594080-60594281(-)$1	1	2	6	11.9999
)))(	chr12:56704738-56704939(-)$1	1	147	151	11.9999
.)))	chr3:25761718-25761919(-)$1	1	77	81	11.9999
....	chr4:115725186-115725387(-)$1	1	107	111	11.9999
....	chr15:48452125-48452326(-)$1	1	28	32	11.9999
...(	chr1:54235030-54235231(-)$1	1	43	47	11.9999
....	chr1:121698259-121698460(-)$1	1	26	30	11.9999
))))	chr4:132203238-132203439(+)$1	1	41	45	11.9999
.(((	chr2:102226588-102226789(-)$1	1	152	156	11.9999
))))	chr2:48776120-48776321(-)$1	1	176	180	11.9999
.)))	chr14:125064363-125064564(-)$1	1	183	187	11.9999
((((	chrX:143919403-143919604(-)$1	1	16	20	11.9999
))))	chr15:25903137-25903338(+)$1	1	155	159	11.9999
((((	chrM:581-782(+)$1	1	80	84	11.9999
....	chr6:8677494-8677695(-)$1	1	1	5	11.9999
.(((	chr6:142776442-142776643(-)$1	1	21	25	11.9999
))).	chr3:127028200-127028401(-)$1	1	183	187	11.9999
.)).	chr7:98396271-98396472(+)$1	1	129	133	11.9999
.)))	chr4:101313554-101313755(+)$1	1	148	152	11.9999
...(	chr11:74489830-74490031(-)$1	1	18	22	11.9999
....	chr14:50083962-50084163(-)$1	1	109	113	11.9999
))))	chr14:35558896-35559097(+)$1	1	123	127	11.9999
....	chr10:20787551-20787752(+)$1	1	106	110	11.9999
((..	chr17:37210877-37211078(+)$1	1	6	10	11.9999
((((	chr1:63639841-63640042(+)$1	1	73	77	11.9999
....	chr16:17011066-17011267(+)$1	1	20	24	11.9999

#PSSM
U : 0.77	u : 0.22	
C : 0.77	c : 0.22	
U : 0.77	u : 0.22	
U : 0.77	u : 0.22	

#score	1019.9999999999999
#seq	85
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m2_run1.nuc.txt

#NT
UGCUU	chr1:87975215-87975425(+)$1	210	97	102	14.9999
UGCUU	chr1:66487129-66487344(+)$1	215	103	108	14.9999
UGCUU	chr3:89038209-89038430(-)$1	221	131	136	14.9999
UGCUU	chr6:33922206-33922424(+)$1	218	87	92	14.9999
UGCUU	chr4:65277068-65277268(-)$1	200	29	34	14.9999
UGCUU	chrX:12193257-12193458(+)$1	201	93	98	14.9999
UGCUU	chr15:10265251-10265457(+)$1	206	194	199	14.9999
UGCUU	chr2:29952767-29952973(-)$1	206	4	9	14.9999
UGCUU	chr11:62143014-62143214(-)$1	200	137	142	14.9999
UGCUU	chr16:20234149-20234359(-)$1	210	34	39	14.9999
UGCUU	chr5:44566847-44567059(-)$1	212	198	203	14.9999
UGCUU	chr3:14900116-14900316(+)$1	200	103	108	14.9999
UGCUU	chr4:14882269-14882472(-)$1	203	40	45	14.9999
UGCUU	chr11:60043149-60043352(+)$1	203	32	37	14.9999
UGCUU	chr14:13073401-13073602(+)$1	201	183	188	14.9999
UGCUU	chr5:37815918-37816128(-)$1	210	199	204	14.9999
UGCUU	chr18:38999943-39000164(-)$1	221	20	25	14.9999
UGCUU	chr8:26684771-26684986(+)$1	215	103	108	14.9999
UGCUU	chr9:74905111-74905316(+)$1	205	90	95	14.9999
UGCUU	chr16:33502279-33502486(+)$1	207	97	102	14.9999
UGCUU	chr2:22549046-22549253(-)$1	207	139	144	14.9999
UGCUU	chr4:122536694-122536916(+)$1	222	166	171	14.9999
UGCUU	chr16:35108033-35108239(-)$1	206	25	30	14.9999
UGCUU	chr14:34194961-34195166(+)$1	205	61	66	14.9999
UGCUU	chr3:81758404-81758610(-)$1	206	116	121	14.9999
UGCUU	chr19:21468772-21468976(-)$1	204	119	124	14.9999
UGCUU	chr14:13205875-13206088(+)$1	213	50	55	14.9999
UGCUU	chr13:120246100-120246319(+)$1	219	116	121	14.9999
UGCUU	chr14:70186070-70186305(-)$1	235	178	183	14.9999
UGCUU	chr11:41945074-41945278(-)$1	204	164	169	14.9999
UGCUU	chr5:15878317-15878521(+)$1	204	91	96	14.9999
UGCUU	chrX:50598634-50598852(-)$1	218	103	108	14.9999
UGCUU	chr16:92081790-92082003(+)$1	213	117	122	14.9999
UGCUU	chr9:58499777-58499977(+)$1	200	54	59	14.9999
UGCUU	chr7:135036657-135036875(+)$1	218	149	154	14.9999
UGCUU	chr4:119299136-119299339(+)$1	203	20	25	14.9999
UGCUU	chr10:113837079-113837299(-)$1	220	97	102	14.9999
UGCUU	chr9:55984173-55984394(-)$1	221	211	216	14.9999
UGCUU	chr12:77432416-77432621(+)$1	205	40	45	14.9999
UGCUU	chr1:84720002-84720223(-)$1	221	176	181	14.9999
UGCUU	chr6:148181016-148181223(-)$1	207	164	169	14.9999
ugcuu	chr9:120078367-120078576(+)$1	209	85	90	14.9999
UGCUU	chr5:113339432-113339635(-)$1	203	46	51	14.9999
UGCUU	chr15:82121954-82122155(+)$1	201	95	100	14.9999
UGCUU	chr19:8907358-8907565(+)$1	207	89	94	14.9999
UGCUU	chr19:59371892-59372092(-)$1	200	152	157	14.9999
UGCUU	chr6:117124148-117124349(+)$1	201	86	91	14.9999
UGCUU	chr4:28891486-28891699(+)$1	213	103	108	14.9999
UGCuu	chr14:46078679-46078887(-)$1	208	132	137	14.9999
UGCUU	chr13:58493035-58493239(-)$1	204	145	150	14.9999
UGCUU	chr7:52155832-52156045(+)$1	213	45	50	14.9999
UGCUU	chr19:14522874-14523078(-)$1	204	57	62	14.9999
UGCUU	chr2:52283910-52284117(-)$1	207	60	65	14.9999

#otherMatches

#Struct PSSM
:iiii	chr14:64741402-64741618(-)$1	216	104	109	14.9999
:::ee	chr1:87975215-87975425(+)$1	210	97	102	14.9999
gg!!c	chr1:66487129-66487344(+)$1	215	103	108	14.9999
dddds	chr3:89038209-89038430(-)$1	221	131	136	14.9999
vvvvv	chr6:33922206-33922424(+)$1	218	87	92	14.9999
##bbm	chr4:65277068-65277268(-)$1	200	29	34	14.9999
ccc::	chrX:12193257-12193458(+)$1	201	93	98	14.9999
~~EEE	chr15:10265251-10265457(+)$1	206	194	199	14.9999
eeerr	chr2:29952767-29952973(-)$1	206	4	9	14.9999
ddd::	chr11:62143014-62143214(-)$1	200	137	142	14.9999
Dbb""	chr16:20234149-20234359(-)$1	210	34	39	14.9999
fffDD	chr5:44566847-44567059(-)$1	212	198	203	14.9999
eeeee	chr3:14900116-14900316(+)$1	200	103	108	14.9999
GGGLL	chr4:14882269-14882472(-)$1	203	40	45	14.9999
eeee!	chr11:60043149-60043352(+)$1	203	32	37	14.9999
sssss	chr14:13073401-13073602(+)$1	201	183	188	14.9999
FF}CC	chr5:37815918-37816128(-)$1	210	199	204	14.9999
eeeee	chr18:38999943-39000164(-)$1	221	20	25	14.9999
oa22c	chr8:26684771-26684986(+)$1	215	103	108	14.9999
FFFFF	chr9:74905111-74905316(+)$1	205	90	95	14.9999
>>>>>	chr16:33502279-33502486(+)$1	207	97	102	14.9999
BB}DD	chr2:22549046-22549253(-)$1	207	139	144	14.9999
a[bbl	chr4:122536694-122536916(+)$1	222	166	171	14.9999
sdddd	chr16:35108033-35108239(-)$1	206	25	30	14.9999
ffff!	chr14:34194961-34195166(+)$1	205	61	66	14.9999
bcccb	chr3:81758404-81758610(-)$1	206	116	121	14.9999
cc[dd	chr19:21468772-21468976(-)$1	204	119	124	14.9999
c[bbc	chr14:13205875-13206088(+)$1	213	50	55	14.9999
d5555	chr13:120246100-120246319(+)$1	219	116	121	14.9999
fff]e	chr14:70186070-70186305(-)$1	235	178	183	14.9999
}A}CC	chr11:41945074-41945278(-)$1	204	164	169	14.9999
reeee	chr5:15878317-15878521(+)$1	204	91	96	14.9999
c]eee	chrX:50598634-50598852(-)$1	218	103	108	14.9999
ffnnn	chr16:92081790-92082003(+)$1	213	117	122	14.9999
ccc[c	chr9:58499777-58499977(+)$1	200	54	59	14.9999
[cccm	chr7:135036657-135036875(+)$1	218	149	154	14.9999
^^^^^	chr4:119299136-119299339(+)$1	203	20	25	14.9999
2bb:D	chr10:113837079-113837299(-)$1	220	97	102	14.9999
IIIII	chr9:55984173-55984394(-)$1	221	211	216	14.9999
ccc55	chr12:77432416-77432621(+)$1	205	40	45	14.9999
bbooo	chr1:84720002-84720223(-)$1	221	176	181	14.9999
:gggg	chr6:148181016-148181223(-)$1	207	164	169	14.9999
ccc22	chr9:120078367-120078576(+)$1	209	85	90	14.9999
[bbnn	chr5:113339432-113339635(-)$1	203	46	51	14.9999
qqqqq	chr15:82121954-82122155(+)$1	201	95	100	14.9999
JJJJJ	chr19:8907358-8907565(+)$1	207	89	94	14.9999
ddd>>	chr19:59371892-59372092(-)$1	200	152	157	14.9999
00000	chr6:117124148-117124349(+)$1	201	86	91	14.9999
555gg	chr4:28891486-28891699(+)$1	213	103	108	14.9999
f22dd	chr14:46078679-46078887(-)$1	208	132	137	14.9999
[eeee	chr13:58493035-58493239(-)$1	204	145	150	14.9999
a::::	chr7:52155832-52156045(+)$1	213	45	50	14.9999
:dddd	chr19:14522874-14523078(-)$1	204	57	62	14.9999
ff333	chr2:52283910-52284117(-)$1	207	60	65	14.9999

#DB
.((((	chr14:64741402-64741618(-)$1	1	104	109	14.9999
...((	chr1:87975215-87975425(+)$1	1	97	102	14.9999
((..(	chr1:66487129-66487344(+)$1	1	103	108	14.9999
((((.	chr3:89038209-89038430(-)$1	1	131	136	14.9999
.....	chr6:33922206-33922424(+)$1	1	87	92	14.9999
..((.	chr4:65277068-65277268(-)$1	1	29	34	14.9999
)))..	chrX:12193257-12193458(+)$1	1	93	98	14.9999
..)))	chr15:10265251-10265457(+)$1	1	194	199	14.9999
(((..	chr2:29952767-29952973(-)$1	1	4	9	14.9999
)))..	chr11:62143014-62143214(-)$1	1	137	142	14.9999
(((..	chr16:20234149-20234359(-)$1	1	34	39	14.9999
)))))	chr5:44566847-44567059(-)$1	1	198	203	14.9999
(((((	chr3:14900116-14900316(+)$1	1	103	108	14.9999
(((..	chr4:14882269-14882472(-)$1	1	40	45	14.9999
((((.	chr11:60043149-60043352(+)$1	1	32	37	14.9999
.....	chr14:13073401-13073602(+)$1	1	183	188	14.9999
)).))	chr5:37815918-37816128(-)$1	1	199	204	14.9999
(((((	chr18:38999943-39000164(-)$1	1	20	25	14.9999
.)..)	chr8:26684771-26684986(+)$1	1	103	108	14.9999
)))))	chr9:74905111-74905316(+)$1	1	90	95	14.9999
.....	chr16:33502279-33502486(+)$1	1	97	102	14.9999
)).))	chr2:22549046-22549253(-)$1	1	139	144	14.9999
(.((.	chr4:122536694-122536916(+)$1	1	166	171	14.9999
.))))	chr16:35108033-35108239(-)$1	1	25	30	14.9999
((((.	chr14:34194961-34195166(+)$1	1	61	66	14.9999
)))))	chr3:81758404-81758610(-)$1	1	116	121	14.9999
((.((	chr19:21468772-21468976(-)$1	1	119	124	14.9999
(.(((	chr14:13205875-13206088(+)$1	1	50	55	14.9999
)....	chr13:120246100-120246319(+)$1	1	116	121	14.9999
))).)	chr14:70186070-70186305(-)$1	1	178	183	14.9999
.).))	chr11:41945074-41945278(-)$1	1	164	169	14.9999
.))))	chr5:15878317-15878521(+)$1	1	91	96	14.9999
).)))	chrX:50598634-50598852(-)$1	1	103	108	14.9999
((...	chr16:92081790-92082003(+)$1	1	117	122	14.9999
(((.(	chr9:58499777-58499977(+)$1	1	54	59	14.9999
.(((.	chr7:135036657-135036875(+)$1	1	149	154	14.9999
.....	chr4:119299136-119299339(+)$1	1	20	25	14.9999
.)).(	chr10:113837079-113837299(-)$1	1	97	102	14.9999
)))))	chr9:55984173-55984394(-)$1	1	211	216	14.9999
)))..	chr12:77432416-77432621(+)$1	1	40	45	14.9999
((...	chr1:84720002-84720223(-)$1	1	176	181	14.9999
.((((	chr6:148181016-148181223(-)$1	1	164	169	14.9999
)))..	chr9:120078367-120078576(+)$1	1	85	90	14.9999
.((..	chr5:113339432-113339635(-)$1	1	46	51	14.9999
.....	chr15:82121954-82122155(+)$1	1	95	100	14.9999
)))))	chr19:8907358-8907565(+)$1	1	89	94	14.9999
)))..	chr19:59371892-59372092(-)$1	1	152	157	14.9999
.....	chr6:117124148-117124349(+)$1	1	86	91	14.9999
...))	chr4:28891486-28891699(+)$1	1	103	108	14.9999
)..))	chr14:46078679-46078887(-)$1	1	132	137	14.9999
.((((	chr13:58493035-58493239(-)$1	1	145	150	14.9999
)....	chr7:52155832-52156045(+)$1	1	45	50	14.9999
.((((	chr19:14522874-14523078(-)$1	1	57	62	14.9999
))...	chr2:52283910-52284117(-)$1	1	60	65	14.9999

#PSSM
U : 0.98	u : 0.01	
G : 0.98	g : 0.01	
C : 0.98	c : 0.01	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	

#score	809.9999999999995
#seq	54
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m3_run1.nuc.txt

#NT
UGGCUG	chr1:155067946-155068163(-)$1	217	78	84	10.1093
GGUCUG	chr15:59205746-59206013(+)$1	267	110	116	8.6250
UGUCUG	chr5:139724429-139724639(+)$1	210	75	81	13.4687
UGGCUG	chr10:74773434-74773650(+)$1	216	25	31	10.1093
UGGCUG	chr5:32033257-32033485(+)$1	228	212	218	10.1093
UGACUG	chr12:117700247-117700453(+)$1	206	74	80	10.1875
UAUCUG	chr5:17187785-17188011(+)$1	226	9	15	9.7187
UGUUUG	chr11:106109791-106110005(+)$1	214	127	133	10.5781
UGUCUG	chr2:50986694-50986937(-)$1	243	144	150	13.4687
UGUCAG	chr10:39543764-39543996(+)$1	232	30	36	9.4843
UGUCGG	chr11:119684217-119684432(+)$1	215	11	17	9.2500
UGUAUG	chr3:105764840-105765061(+)$1	221	28	34	10.2656
UAUCUG	chr12:85022621-85022827(+)$1	206	182	188	9.7187
UGACUG	chr6:72544765-72544973(-)$1	208	62	68	10.1875
UGUCAG	chr3:16083377-16083616(+)$1	239	120	126	9.4843
UGUUUG	chr10:115938239-115938461(-)$1	222	46	52	10.5781
UCUCUG	chr11:59561991-59562214(+)$1	223	48	54	9.8750
UCUCUG	chr10:5892365-5892577(-)$1	212	134	140	9.8750
UCUCUG	chr12:3500305-3500513(+)$1	208	100	106	9.8750
UCUCUG	chr17:29834808-29835044(+)$1	236	72	78	9.8750
UGCCUG	chr2:181304105-181304334(-)$1	229	15	21	9.7968
UGUCUC	chr5:9119853-9120072(-)$1	219	88	94	9.0937
UGGCUG	chr11:106644993-106645247(-)$1	254	165	171	10.1093
UGUAUG	chr7:135587239-135587458(-)$1	219	32	38	10.2656
UAUCUG	chrX:72779480-72779703(+)$1	223	59	65	9.7187
UGACUG	chr13:85355241-85355447(-)$1	206	24	30	10.1875
UGUUUG	chr5:106339128-106339354(+)$1	226	52	58	10.5781
UGGCUG	chr9:96240619-96240845(-)$1	226	6	12	10.1093
UCUCUG	chr5:111094212-111094435(-)$1	223	18	24	9.8750
UGUCUG	chr5:34211391-34211615(+)$1	224	23	29	13.4687
UGGCUG	chr2:112106308-112106527(+)$1	219	169	175	10.1093
UCUCUG	chr15:40486815-40487035(+)$1	220	53	59	9.8750
UGUUUG	chr10:43621682-43621901(+)$1	219	16	22	10.5781
UGUCCG	chr15:27955467-27955691(-)$1	224	167	173	9.1718
UGUCUC	chr7:52229959-52230179(-)$1	220	47	53	9.0937
UGUCAG	chr13:39024418-39024641(-)$1	223	108	114	9.4843
UGUCAG	chr7:51788654-51788880(-)$1	226	102	108	9.4843
UGUCUG	chr14:67634534-67634757(-)$1	223	186	192	13.4687
UGUCUU	chr1:140938431-140938654(+)$1	223	60	66	9.0156
UGUUUG	chr5:46061101-46061342(+)$1	241	30	36	10.5781
UGUUUG	chr3:104301329-104301551(-)$1	222	11	17	10.5781
UGUUUG	chr2:37482905-37483130(-)$1	225	52	58	10.5781
UGACUG	chr4:122531541-122531756(+)$1	215	59	65	10.1875
UGUCUG	chr5:116458080-116458291(+)$1	211	24	30	13.4687
UGUCUU	chr16:87458815-87459035(+)$1	220	27	33	9.0156
UGUUUG	chr1:134360672-134360890(+)$1	218	21	27	10.5781
UAUCUG	chr1:36218955-36219178(-)$1	223	6	12	9.7187
UGACUG	chr17:8389052-8389263(+)$1	211	36	42	10.1875
UGACUG	chr13:54753446-54753665(+)$1	219	23	29	10.1875
ugucug	chr5:138592189-138592412(-)$1	223	104	110	13.4687
UGACUG	chr8:108008178-108008387(-)$1	209	23	29	10.1875
UGUAUG	chr10:66680784-66681007(+)$1	223	148	154	10.2656
UGUCGG	chrX:7172017-7172225(-)$1	208	48	54	9.2500
UUUCUG	chr5:72950759-72950980(-)$1	221	164	170	9.5625
UGUGUG	chr1:33834015-33834232(-)$1	217	5	11	9.8750
UGUUUG	chr7:38746240-38746447(-)$1	207	46	52	10.5781
UGCCUG	chr9:119149240-119149451(-)$1	211	103	109	9.7968
UUUCUG	chr9:7157564-7157785(-)$1	221	133	139	9.5625
UGUAUG	chr17:24215306-24215521(-)$1	215	53	59	10.2656
UGUAUG	chr14:30787675-30787893(+)$1	218	81	87	10.2656
UGUCAG	chr2:71101086-71101309(+)$1	223	114	120	9.4843
UGUUUG	chr10:90615297-90615561(-)$1	264	27	33	10.5781
UGUAUG	chrX:98773662-98773876(+)$1	214	14	20	10.2656

#otherMatches

#Struct PSSM
cclllc	chr1:178804700-178804916(+)$1	216	4	10	9.0937
ddd]cc	chr1:155067946-155068163(-)$1	217	78	84	10.1093
JJJJJJ	chr15:59205746-59206013(+)$1	267	110	116	8.6250
eeeees	chr5:139724429-139724639(+)$1	210	75	81	13.4687
:::::d	chr10:74773434-74773650(+)$1	216	25	31	10.1093
::ccco	chr5:32033257-32033485(+)$1	228	212	218	10.1093
oooddd	chr12:117700247-117700453(+)$1	206	74	80	10.1875
oooogg	chr5:17187785-17188011(+)$1	226	9	15	9.7187
!eeeee	chr11:106109791-106110005(+)$1	214	127	133	10.5781
ee]ccc	chr2:50986694-50986937(-)$1	243	144	150	13.4687
ee!!cc	chr10:39543764-39543996(+)$1	232	30	36	9.4843
EEEEFF	chr11:119684217-119684432(+)$1	215	11	17	9.2500
ff[bb!	chr3:105764840-105765061(+)$1	221	28	34	10.2656
000000	chr12:85022621-85022827(+)$1	206	182	188	9.7187
fffff!	chr6:72544765-72544973(-)$1	208	62	68	10.1875
dddd]c	chr3:16083377-16083616(+)$1	239	120	126	9.4843
iiiiii	chr10:115938239-115938461(-)$1	222	46	52	10.5781
HHHHHH	chr11:59561991-59562214(+)$1	223	48	54	9.8750
"""fff	chr10:5892365-5892577(-)$1	212	134	140	9.8750
EEEEE}	chr12:3500305-3500513(+)$1	208	100	106	9.8750
::dddd	chr17:29834808-29835044(+)$1	236	72	78	9.8750
GGGGGG	chr2:181304105-181304334(-)$1	229	15	21	9.7968
bb[ddd	chr5:9119853-9120072(-)$1	219	88	94	9.0937
===ooo	chr11:106644993-106645247(-)$1	254	165	171	10.1093
ccc[cc	chr7:135587239-135587458(-)$1	219	32	38	10.2656
ssssss	chrX:72779480-72779703(+)$1	223	59	65	9.7187
GGGGGG	chr13:85355241-85355447(-)$1	206	24	30	10.1875
======	chr5:106339128-106339354(+)$1	226	52	58	10.5781
::eeee	chr9:96240619-96240845(-)$1	226	6	12	10.1093
d"""cc	chr5:111094212-111094435(-)$1	223	18	24	9.8750
eee::f	chr5:34211391-34211615(+)$1	224	23	29	13.4687
ffffff	chr2:112106308-112106527(+)$1	219	169	175	10.1093
e"""cc	chr15:40486815-40487035(+)$1	220	53	59	9.8750
{CCC{B	chr10:43621682-43621901(+)$1	219	16	22	10.5781
cc[ccc	chr15:27955467-27955691(-)$1	224	167	173	9.1718
iiiiii	chr7:52229959-52230179(-)$1	220	47	53	9.0937
ff"""d	chr13:39024418-39024641(-)$1	223	108	114	9.4843
fffnnn	chr7:51788654-51788880(-)$1	226	102	108	9.4843
mmmmee	chr14:67634534-67634757(-)$1	223	186	192	13.4687
]dddd4	chr1:140938431-140938654(+)$1	223	60	66	9.0156
[ccc[b	chr5:46061101-46061342(+)$1	241	30	36	10.5781
oa333c	chr3:104301329-104301551(-)$1	222	11	17	10.5781
nnnnnd	chr2:37482905-37483130(-)$1	225	52	58	10.5781
ffffff	chr4:122531541-122531756(+)$1	215	59	65	10.1875
dd[eee	chr5:116458080-116458291(+)$1	211	24	30	13.4687
SSSSSS	chr16:87458815-87459035(+)$1	220	27	33	9.0156
nnnnne	chr1:134360672-134360890(+)$1	218	21	27	10.5781
cmmmmc	chr1:36218955-36219178(-)$1	223	6	12	9.7187
[dddd[	chr17:8389052-8389263(+)$1	211	36	42	10.1875
{BBDDD	chr13:54753446-54753665(+)$1	219	23	29	10.1875
ddd22e	chr5:138592189-138592412(-)$1	223	104	110	13.4687
nnneee	chr8:108008178-108008387(-)$1	209	23	29	10.1875
:dddd[	chr10:66680784-66681007(+)$1	223	148	154	10.2656
gggggg	chrX:7172017-7172225(-)$1	208	48	54	9.2500
hhhhh=	chr5:72950759-72950980(-)$1	221	164	170	9.5625
iiiii!	chr1:33834015-33834232(-)$1	217	5	11	9.8750
]bb22b	chr7:38746240-38746447(-)$1	207	46	52	10.5781
:bb[dd	chr9:119149240-119149451(-)$1	211	103	109	9.7968
iiiiii	chr9:7157564-7157785(-)$1	221	133	139	9.5625
GGGGOO	chr17:24215306-24215521(-)$1	215	53	59	10.2656
Fccc[d	chr14:30787675-30787893(+)$1	218	81	87	10.2656
ddd333	chr2:71101086-71101309(+)$1	223	114	120	9.4843
DDD{DD	chr10:90615297-90615561(-)$1	264	27	33	10.5781
{CCC{F	chrX:98773662-98773876(+)$1	214	14	20	10.2656

#DB
((...)	chr1:178804700-178804916(+)$1	1	4	10	9.0937
))).))	chr1:155067946-155068163(-)$1	1	78	84	10.1093
))))))	chr15:59205746-59206013(+)$1	1	110	116	8.6250
(((((.	chr5:139724429-139724639(+)$1	1	75	81	13.4687
.....(	chr10:74773434-74773650(+)$1	1	25	31	10.1093
..(((.	chr5:32033257-32033485(+)$1	1	212	218	10.1093
...)))	chr12:117700247-117700453(+)$1	1	74	80	10.1875
....))	chr5:17187785-17188011(+)$1	1	9	15	9.7187
.(((((	chr11:106109791-106110005(+)$1	1	127	133	10.5781
)).)))	chr2:50986694-50986937(-)$1	1	144	150	13.4687
((..((	chr10:39543764-39543996(+)$1	1	30	36	9.4843
((((((	chr11:119684217-119684432(+)$1	1	11	17	9.2500
((.((.	chr3:105764840-105765061(+)$1	1	28	34	10.2656
......	chr12:85022621-85022827(+)$1	1	182	188	9.7187
(((((.	chr6:72544765-72544973(-)$1	1	62	68	10.1875
)))).)	chr3:16083377-16083616(+)$1	1	120	126	9.4843
((((((	chr10:115938239-115938461(-)$1	1	46	52	10.5781
((((((	chr11:59561991-59562214(+)$1	1	48	54	9.8750
...(((	chr10:5892365-5892577(-)$1	1	134	140	9.8750
))))).	chr12:3500305-3500513(+)$1	1	100	106	9.8750
..((((	chr17:29834808-29835044(+)$1	1	72	78	9.8750
((((((	chr2:181304105-181304334(-)$1	1	15	21	9.7968
((.(((	chr5:9119853-9120072(-)$1	1	88	94	9.0937
(((...	chr11:106644993-106645247(-)$1	1	165	171	10.1093
(((.((	chr7:135587239-135587458(-)$1	1	32	38	10.2656
......	chrX:72779480-72779703(+)$1	1	59	65	9.7187
((((((	chr13:85355241-85355447(-)$1	1	24	30	10.1875
((((((	chr5:106339128-106339354(+)$1	1	52	58	10.5781
..((((	chr9:96240619-96240845(-)$1	1	6	12	10.1093
(...((	chr5:111094212-111094435(-)$1	1	18	24	9.8750
)))..(	chr5:34211391-34211615(+)$1	1	23	29	13.4687
))))))	chr2:112106308-112106527(+)$1	1	169	175	10.1093
(...((	chr15:40486815-40487035(+)$1	1	53	59	9.8750
.(((.(	chr10:43621682-43621901(+)$1	1	16	22	10.5781
((.(((	chr15:27955467-27955691(-)$1	1	167	173	9.1718
))))))	chr7:52229959-52230179(-)$1	1	47	53	9.0937
((...(	chr13:39024418-39024641(-)$1	1	108	114	9.4843
(((...	chr7:51788654-51788880(-)$1	1	102	108	9.4843
....))	chr14:67634534-67634757(-)$1	1	186	192	13.4687
.)))).	chr1:140938431-140938654(+)$1	1	60	66	9.0156
.(((.(	chr5:46061101-46061342(+)$1	1	30	36	10.5781
.)...)	chr3:104301329-104301551(-)$1	1	11	17	10.5781
.....)	chr2:37482905-37483130(-)$1	1	52	58	10.5781
))))))	chr4:122531541-122531756(+)$1	1	59	65	10.1875
((.(((	chr5:116458080-116458291(+)$1	1	24	30	13.4687
......	chr16:87458815-87459035(+)$1	1	27	33	9.0156
.....)	chr1:134360672-134360890(+)$1	1	21	27	10.5781
(....)	chr1:36218955-36219178(-)$1	1	6	12	9.7187
.((((.	chr17:8389052-8389263(+)$1	1	36	42	10.1875
.(((((	chr13:54753446-54753665(+)$1	1	23	29	10.1875
)))..)	chr5:138592189-138592412(-)$1	1	104	110	13.4687
...)))	chr8:108008178-108008387(-)$1	1	23	29	10.1875
.((((.	chr10:66680784-66681007(+)$1	1	148	154	10.2656
))))))	chrX:7172017-7172225(-)$1	1	48	54	9.2500
))))))	chr5:72950759-72950980(-)$1	1	164	170	9.5625
(((((.	chr1:33834015-33834232(-)$1	1	5	11	9.8750
.))..)	chr7:38746240-38746447(-)$1	1	46	52	10.5781
.((.((	chr9:119149240-119149451(-)$1	1	103	109	9.7968
((((((	chr9:7157564-7157785(-)$1	1	133	139	9.5625
((((..	chr17:24215306-24215521(-)$1	1	53	59	10.2656
)(((.(	chr14:30787675-30787893(+)$1	1	81	87	10.2656
)))...	chr2:71101086-71101309(+)$1	1	114	120	9.4843
(((.((	chr10:90615297-90615561(-)$1	1	27	33	10.5781
.(((.(	chrX:98773662-98773876(+)$1	1	14	20	10.2656

#PSSM
U : 0.96	G : 0.01	u : 0.01	
G : 0.79	C : 0.09	A : 0.06	U : 0.03	g : 0.01	
U : 0.75	A : 0.10	G : 0.09	C : 0.03	u : 0.01	
C : 0.71	U : 0.15	A : 0.09	c : 0.01	G : 0.01	
U : 0.85	A : 0.07	G : 0.03	C : 0.01	u : 0.01	
G : 0.90	C : 0.04	U : 0.03	g : 0.01	

#score	655.90625
#seq	64
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m3_run2.nuc.txt

#NT
ACAGAAAGA	chr13:29042774-29043067(-)$1	293	167	176	12.2777
GCAGAAGAU	chr7:118221914-118222150(-)$1	236	149	158	10.7037
GCAGAAGAG	chr14:55514612-55514858(+)$1	246	59	68	10.6111
GCAGAACAA	chr3:103581357-103581598(-)$1	241	217	226	14.1296
CUAGAAAAA	chr7:89028055-89028298(-)$1	243	110	119	11.2592
UCAGUAAAA	chr12:25725294-25725525(+)$1	231	98	107	11.9074
GAAGGAAAA	chr18:34580579-34580812(-)$1	233	114	123	11.7222
UCAGAAAGA	chr1:180260808-180261039(-)$1	231	120	129	12.4629
GGAAAAAAA	chr6:136557348-136557611(+)$1	263	218	227	11.1666
GCAGAAGAA	chr2:124913659-124913937(-)$1	278	240	249	14.6851
GCAGCAAGA	chr10:104680597-104680859(-)$1	262	194	203	11.6296
GCAGACACA	chr9:47658277-47658508(+)$1	231	124	133	10.5185
AAAGAAAAA	chr16:32367355-32367592(+)$1	237	194	203	12.3703
GCACAAGAA	chr12:109227809-109228085(-)$1	276	211	220	10.6111
GAAGAAGAA	chr9:36668323-36668558(+)$1	235	85	94	11.8148
GCAGCAAAA	chr3:122261849-122262109(-)$1	260	145	154	14.5925
GGAGCAAAA	chr3:126645098-126645333(-)$1	235	145	154	11.5370
UCAGAAAUA	chr11:29636286-29636545(+)$1	259	115	124	12.1851
UCAGAAAAU	chr19:32761673-32761904(-)$1	231	36	45	11.4444
GAAGAGAAA	chr9:75440293-75440525(-)$1	232	77	86	10.8888
GCAGUAACA	chr13:110744580-110744824(+)$1	244	11	20	11.1666
GCAGACAAA	chr19:45850594-45850830(-)$1	236	187	196	13.7592
UCAGCAAAA	chr5:71353043-71353276(-)$1	233	120	129	12.0925
CCAGAAAGA	chr7:66542111-66542342(-)$1	231	112	121	11.8148
GGAGAGAAA	chr11:96680455-96680687(-)$1	232	167	176	10.7037
GCAACAAAA	chr8:80120490-80120730(-)$1	240	48	57	10.8888
ACAGGAAAA	chrM:12153-12430(+)$1	277	248	257	11.9074
GCAGAAUGA	chr4:129192241-129192501(+)$1	260	222	231	11.0740
ACAGAAAUA	chrX:73061388-73061624(-)$1	236	158	167	11.9999
GGAGAAGAA	chr8:10475967-10476198(-)$1	231	190	199	11.6296
GCAAUAAAA	chr12:56712941-56713205(-)$1	264	30	39	10.7037
UCAGAAAAC	chr6:36691170-36691441(-)$1	271	105	114	11.4444
GCAGAAACA	chr5:42190935-42191166(-)$1	231	16	25	14.6851
GCAGAAAGA	chr13:103526978-103527209(-)$1	231	18	27	14.9629
GCAGAACAA	chr17:35972083-35972314(-)$1	231	51	60	14.1296
GCUGAGAAA	chr12:28025958-28026198(-)$1	240	209	218	9.3148
ACAGAAAGA	chr1:178685945-178686186(-)$1	241	61	70	12.2777
UCAGAAAAC	chr5:73506347-73506607(-)$1	260	87	96	11.4444
GCAGAAACA	chr9:106787578-106787817(-)$1	239	185	194	14.6851
UCAGAAAAC	chr1:71676248-71676499(-)$1	251	78	87	11.4444
GCUGAAGAA	chr3:144259781-144260068(+)$1	287	59	68	10.2407
GCAGGAAAU	chr3:96364370-96364610(+)$1	240	86	95	10.6111
GCAAAAAUA	chr15:97875724-97875956(-)$1	232	95	104	10.9814
GGAGGAAAA	chr3:20037801-20038044(-)$1	243	215	224	11.5370
GAAGAAAAG	chr17:35253079-35253311(-)$1	232	156	165	10.9814
ACAGAAAUA	chr2:124913837-124914089(-)$1	252	213	222	11.9999
gaggaaaaa	chr7:48905611-48905847(+)$1	236	163	172	10.6111
GAAGACAAA	chr16:3866379-3866610(-)$1	231	20	29	10.8888
GCAAGAAAA	chr13:29042875-29043140(-)$1	265	32	41	10.8888
GGGGAAAAA	chr1:54532600-54532853(-)$1	253	235	244	10.4259
ACAGAAGAA	chr8:29777174-29777405(-)$1	231	147	156	11.9999
GCAGAAAAA	chr11:51418917-51419153(-)$1	236	18	27	17.9259
GAACAAAAA	chr9:101114119-101114350(-)$1	231	182	191	10.9814

#otherMatches

#Struct PSSM
^^^^^^^^^	chr5:3673082-3673316(-)$1	234	97	106	11.7222
e]eeeee99	chr13:29042774-29043067(-)$1	293	167	176	12.2777
ggggggg::	chr7:118221914-118222150(-)$1	236	149	158	10.7037
ddooooood	chr14:55514612-55514858(+)$1	246	59	68	10.6111
wwwa]hhhh	chr3:103581357-103581598(-)$1	241	217	226	14.1296
IIIIII:::	chr7:89028055-89028298(-)$1	243	110	119	11.2592
bb[bbmmmm	chr12:25725294-25725525(+)$1	231	98	107	11.9074
=========	chr18:34580579-34580812(-)$1	233	114	123	11.7222
eee&&&&&&	chr1:180260808-180261039(-)$1	231	120	129	12.4629
uuuuuuggg	chr6:136557348-136557611(+)$1	263	218	227	11.1666
DD:::::::	chr2:124913659-124913937(-)$1	278	240	249	14.6851
bcccnnnnn	chr10:104680597-104680859(-)$1	262	194	203	11.6296
BB:EEEEE:	chr9:47658277-47658508(+)$1	231	124	133	10.5185
ttttttfff	chr16:32367355-32367592(+)$1	237	194	203	12.3703
auuuuuuuu	chr12:109227809-109228085(-)$1	276	211	220	10.6111
f::cccooo	chr9:36668323-36668558(+)$1	235	85	94	11.8148
dd:::::::	chr3:122261849-122262109(-)$1	260	145	154	14.5925
dddd+++++	chr3:126645098-126645333(-)$1	235	145	154	11.5370
eeeee5555	chr11:29636286-29636545(+)$1	259	115	124	12.1851
HHHHHH:::	chr19:32761673-32761904(-)$1	231	36	45	11.4444
gggggeeee	chr9:75440293-75440525(-)$1	232	77	86	10.8888
ffffffddd	chr13:110744580-110744824(+)$1	244	11	20	11.1666
cc55555ff	chr19:45850594-45850830(-)$1	236	187	196	13.7592
eeeee::::	chr5:71353043-71353276(-)$1	233	120	129	12.0925
zdddd:EEE	chr7:66542111-66542342(-)$1	231	112	121	11.8148
vvvvvvvvv	chr11:96680455-96680687(-)$1	232	167	176	10.7037
ttttttttt	chr8:80120490-80120730(-)$1	240	48	57	10.8888
yyyyyyyyy	chrM:12153-12430(+)$1	277	248	257	11.9074
ccc333bb]	chr4:129192241-129192501(+)$1	260	222	231	11.0740
A}HHHHHHH	chrX:73061388-73061624(-)$1	236	158	167	11.9999
dddoooooo	chr8:10475967-10476198(-)$1	231	190	199	11.6296
:::::::::	chr12:56712941-56713205(-)$1	264	30	39	10.7037
dddd:::::	chr6:36691170-36691441(-)$1	271	105	114	11.4444
ccdddd!!c	chr5:42190935-42191166(-)$1	231	16	25	14.6851
qqqqqqqdd	chr13:103526978-103527209(-)$1	231	18	27	14.9629
ccuuuuuuu	chr17:35972083-35972314(-)$1	231	51	60	14.1296
22dddd:::	chr12:28025958-28026198(-)$1	240	209	218	9.3148
ffbb"""dd	chr1:178685945-178686186(-)$1	241	61	70	12.2777
###iiiiii	chr5:73506347-73506607(-)$1	260	87	96	11.4444
CCCC::::e	chr9:106787578-106787817(-)$1	239	185	194	14.6851
yyggggggg	chr1:71676248-71676499(-)$1	251	78	87	11.4444
CCLLLIIII	chr3:144259781-144260068(+)$1	287	59	68	10.2407
ddddfffff	chr3:96364370-96364610(+)$1	240	86	95	10.6111
dddd[dddd	chr15:97875724-97875956(-)$1	232	95	104	10.9814
FFFFFF///	chr3:20037801-20038044(-)$1	243	215	224	11.5370
ccc22====	chr17:35253079-35253311(-)$1	232	156	165	10.9814
dd:::::::	chr2:124913837-124914089(-)$1	252	213	222	11.9999
iddddmmmm	chr7:48905611-48905847(+)$1	236	163	172	10.6111
ggsssssss	chr16:3866379-3866610(-)$1	231	20	29	10.8888
IIIIIIIIf	chr13:29042875-29043140(-)$1	265	32	41	10.8888
fffff333f	chr1:54532600-54532853(-)$1	253	235	244	10.4259
]dddd::::	chr8:29777174-29777405(-)$1	231	147	156	11.9999
!!bb[ffff	chr11:51418917-51419153(-)$1	236	18	27	17.9259
4ccc55555	chr9:101114119-101114350(-)$1	231	182	191	10.9814

#DB
.........	chr5:3673082-3673316(-)$1	1	97	106	11.7222
).)))))..	chr13:29042774-29043067(-)$1	1	167	176	12.2777
)))))))..	chr7:118221914-118222150(-)$1	1	149	158	10.7037
((......)	chr14:55514612-55514858(+)$1	1	59	68	10.6111
...).))))	chr3:103581357-103581598(-)$1	1	217	226	14.1296
((((((...	chr7:89028055-89028298(-)$1	1	110	119	11.2592
((.((....	chr12:25725294-25725525(+)$1	1	98	107	11.9074
)))))))))	chr18:34580579-34580812(-)$1	1	114	123	11.7222
(((......	chr1:180260808-180261039(-)$1	1	120	129	12.4629
......)))	chr6:136557348-136557611(+)$1	1	218	227	11.1666
)).......	chr2:124913659-124913937(-)$1	1	240	249	14.6851
((((.....	chr10:104680597-104680859(-)$1	1	194	203	11.6296
)).(((((.	chr9:47658277-47658508(+)$1	1	124	133	10.5185
......)))	chr16:32367355-32367592(+)$1	1	194	203	12.3703
(........	chr12:109227809-109228085(-)$1	1	211	220	10.6111
)..(((...	chr9:36668323-36668558(+)$1	1	85	94	11.8148
)).......	chr3:122261849-122262109(-)$1	1	145	154	14.5925
((((.....	chr3:126645098-126645333(-)$1	1	145	154	11.5370
)))))....	chr11:29636286-29636545(+)$1	1	115	124	12.1851
((((((...	chr19:32761673-32761904(-)$1	1	36	45	11.4444
)))))))))	chr9:75440293-75440525(-)$1	1	77	86	10.8888
(((((((((	chr13:110744580-110744824(+)$1	1	11	20	11.1666
)).....))	chr19:45850594-45850830(-)$1	1	187	196	13.7592
)))))....	chr5:71353043-71353276(-)$1	1	120	129	12.0925
.)))).(((	chr7:66542111-66542342(-)$1	1	112	121	11.8148
.........	chr11:96680455-96680687(-)$1	1	167	176	10.7037
.........	chr8:80120490-80120730(-)$1	1	48	57	10.8888
.........	chrM:12153-12430(+)$1	1	248	257	11.9074
)))...)).	chr4:129192241-129192501(+)$1	1	222	231	11.0740
).)))))))	chrX:73061388-73061624(-)$1	1	158	167	11.9999
(((......	chr8:10475967-10476198(-)$1	1	190	199	11.6296
.........	chr12:56712941-56713205(-)$1	1	30	39	10.7037
)))).....	chr6:36691170-36691441(-)$1	1	105	114	11.4444
))((((..(	chr5:42190935-42191166(-)$1	1	16	25	14.6851
.......))	chr13:103526978-103527209(-)$1	1	18	27	14.9629
((.......	chr17:35972083-35972314(-)$1	1	51	60	14.1296
..))))...	chr12:28025958-28026198(-)$1	1	209	218	9.3148
((((...((	chr1:178685945-178686186(-)$1	1	61	70	12.2777
...((((((	chr5:73506347-73506607(-)$1	1	87	96	11.4444
))))....(	chr9:106787578-106787817(-)$1	1	185	194	14.6851
..)))))))	chr1:71676248-71676499(-)$1	1	78	87	11.4444
((...((((	chr3:144259781-144260068(+)$1	1	59	68	10.2407
(((((((((	chr3:96364370-96364610(+)$1	1	86	95	10.6111
((((.((((	chr15:97875724-97875956(-)$1	1	95	104	10.9814
))))))...	chr3:20037801-20038044(-)$1	1	215	224	11.5370
)))..))))	chr17:35253079-35253311(-)$1	1	156	165	10.9814
)).......	chr2:124913837-124914089(-)$1	1	213	222	11.9999
(((((....	chr7:48905611-48905847(+)$1	1	163	172	10.6111
((.......	chr16:3866379-3866610(-)$1	1	20	29	10.8888
(((((((((	chr13:29042875-29043140(-)$1	1	32	41	10.8888
)))))...)	chr1:54532600-54532853(-)$1	1	235	244	10.4259
.))))....	chr8:29777174-29777405(-)$1	1	147	156	11.9999
..((.((((	chr11:51418917-51419153(-)$1	1	18	27	17.9259
.))).....	chr9:101114119-101114350(-)$1	1	182	191	10.9814

#PSSM
G : 0.64	U : 0.14	A : 0.12	C : 0.03	u : 0.01	g : 0.01	
C : 0.70	A : 0.12	G : 0.11	c : 0.01	U : 0.01	a : 0.01	
A : 0.90	U : 0.03	a : 0.01	g : 0.01	G : 0.01	
G : 0.83	A : 0.09	C : 0.03	a : 0.01	g : 0.01	
A : 0.72	G : 0.09	C : 0.09	U : 0.05	a : 0.03	
A : 0.85	C : 0.05	G : 0.05	a : 0.03	
A : 0.77	G : 0.14	C : 0.03	U : 0.01	a : 0.01	
A : 0.70	G : 0.12	C : 0.07	U : 0.07	a : 0.01	
A : 0.83	U : 0.05	C : 0.05	G : 0.03	a : 0.01	

#score	642.4444444444437
#seq	54
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_UTR_m3_run1.nuc.txt

#NT
UGCACUAAA	chr2:136607277-136607477(+)$1	200	157	166	11.1525
AGCAAAAAA	chr1:30860179-30860399(-)$1	220	160	169	13.8644
UGGAAAAAA	chr1:137056774-137056974(-)$1	200	119	128	15.8983
UUCAAACAA	chr4:120640883-120641083(-)$1	200	48	57	11.5762
UGCAAAAAA	chr15:41691844-41692053(+)$1	209	171	180	18.1016
UACAUAAAA	chr8:116897781-116897989(+)$1	208	155	164	11.9999
UUCAAAGAA	chr7:38746269-38746487(-)$1	218	179	188	11.7457
UGCAAAAAA	chr4:138013733-138013934(+)$1	201	122	131	18.1016
UUCAACAAA	chr16:91272027-91272229(-)$1	202	23	32	11.4067
UGAAUAAAA	chr3:105476334-105476562(-)$1	228	142	151	13.1016
UGGAAAUAA	chr11:77346438-77346639(-)$1	201	155	164	12.2542
UGUAAAUAA	chr14:58308579-58308787(+)$1	208	45	54	12.1694
UCCAGAAAA	chr18:82754721-82754921(+)$1	200	141	150	11.7457
UGAAAUAAA	chr11:50107925-50108127(-)$1	202	129	138	12.8474
UGCAAAGAA	chrX:106356132-106356339(+)$1	207	171	180	14.3728
UGUCAAAAA	chr3:7551724-7551937(+)$1	213	64	73	11.9152
UGAAAAAAA	chrX:119508454-119508659(-)$1	205	192	201	16.4067
UGCAGAAAA	chr14:60999348-60999563(+)$1	215	117	126	14.8813
UACAAAAUA	chr10:117252320-117252533(-)$1	213	167	176	10.4745
UUCAUAAAA	chr6:112672198-112672410(+)$1	212	67	76	12.1694
UUCAAGAAA	chr3:138588882-138589089(-)$1	207	14	23	11.4915
UGCAAUAAG	chr18:31742173-31742373(+)$1	200	19	28	10.6440
AGUAAAAAA	chr14:34194961-34195166(+)$1	205	91	100	11.5762
UUAAAAAAA	chr10:101944455-101944658(-)$1	203	74	83	13.7796
ggaaaaaaa	chr14:68373324-68373544(+)$1	220	0	9	11.9152
UGCAAACAC	chrX:17134588-17134793(+)$1	205	24	33	10.0508
UGCUAAUAA	chr10:79373614-79373821(-)$1	207	83	92	10.4745
UACAAAAAG	chr5:107535985-107536203(+)$1	218	7	16	11.4067
UGCAGAAAU	chr5:122904191-122904391(-)$1	200	109	118	10.9830
UGAGAAAAA	chrX:8843715-8843941(-)$1	226	211	220	12.3389
UGUAAUAAA	chrX:155936192-155936399(+)$1	207	118	127	12.2542
UGUAAUAAA	chr15:27661208-27661410(-)$1	202	140	149	12.2542
UACAAGAAA	chr13:47181238-47181441(+)$1	203	43	52	11.3220
uggaauaaa	chr7:28536522-28536732(+)$1	210	158	167	12.3389
UGCACAAAU	chr10:107937261-107937461(-)$1	200	8	17	10.8135
UGACAAAAA	chr14:49706117-49706336(-)$1	219	136	145	12.5084
UCCCAAAAA	chr1:92509601-92509819(-)$1	218	4	13	11.0677
UGAAGAAAA	chr7:17500680-17500880(-)$1	200	105	114	13.1864
AGAAAAAAA	chr11:90200294-90200495(-)$1	201	31	40	12.1694
UGCAGAAAU	chrX:159216528-159216745(+)$1	217	174	183	10.9830
UGCUAAAAA	chr11:120824653-120824861(-)$1	208	90	99	14.1186
UGCACAAAG	chr15:100223226-100223439(+)$1	213	58	67	10.8135
UGCAAAGAA	chr12:11332656-11332860(-)$1	204	61	70	14.3728
UGCCAAUAA	chr12:60059707-60059920(-)$1	213	118	127	10.5593
UUCUAAAAA	chr2:29037770-29037973(+)$1	203	61	70	11.4915
UGGAUAAAA	chr12:75047403-75047610(+)$1	207	13	22	12.5932
UGGAAAUAA	chr17:85463812-85464013(-)$1	201	62	71	12.2542
UUCAGAAAA	chr12:33660882-33661093(+)$1	211	10	19	12.2542
UAAAAAAAA	chr5:24777970-24778175(-)$1	205	72	81	13.6101
UUaaaaaaa	chr6:67233903-67234105(+)$1	202	136	145	13.7796
UGAGAAAAA	chr12:54249411-54249626(+)$1	215	33	42	12.3389
UCCAAAAAG	chr7:138486835-138487035(-)$1	200	8	17	11.0677
UGUAAAAAU	chr18:6789724-6789931(-)$1	207	35	44	11.9152
UGCAUUAAA	chr7:107994941-107995175(+)$1	234	129	138	11.2372
UGCAAAAAA	chr13:120246100-120246319(+)$1	219	178	187	18.1016
UACACAAAA	chr15:78967196-78967407(-)$1	211	30	39	11.9152
AGGAAAAAA	chr11:49918089-49918294(+)$1	205	13	22	11.6610
UGGAAAGAA	chr6:119875390-119875592(-)$1	202	149	158	12.1694

#otherMatches

#Struct PSSM
:::::::::	chr9:105314888-105315106(+)$1	218	139	148	13.6101
!!ddddlll	chr2:136607277-136607477(+)$1	200	157	166	11.1525
[bboooooo	chr1:30860179-30860399(-)$1	220	160	169	13.8644
eee4444ff	chr1:137056774-137056974(-)$1	200	119	128	15.8983
mddddccc[	chr4:120640883-120641083(-)$1	200	48	57	11.5762
ZZCCC::::	chr15:41691844-41692053(+)$1	209	171	180	18.1016
mmeeeee:c	chr8:116897781-116897989(+)$1	208	155	164	11.9999
g55555bb]	chr7:38746269-38746487(-)$1	218	179	188	11.7457
goooooogg	chr4:138013733-138013934(+)$1	201	122	131	18.1016
:::::::ee	chr16:91272027-91272229(-)$1	202	23	32	11.4067
@@@@@@@@@	chr3:105476334-105476562(-)$1	228	142	151	13.1016
33ffffffc	chr11:77346438-77346639(-)$1	201	155	164	12.2542
eeepppppp	chr14:58308579-58308787(+)$1	208	45	54	12.1694
eee]a6666	chr18:82754721-82754921(+)$1	200	141	150	11.7457
]eeeee555	chr11:50107925-50108127(-)$1	202	129	138	12.8474
:DDDDDDDD	chrX:106356132-106356339(+)$1	207	171	180	14.3728
hhhhhhqqq	chr3:7551724-7551937(+)$1	213	64	73	11.9152
FF|||||||	chrX:119508454-119508659(-)$1	205	192	201	16.4067
meeeee:::	chr14:60999348-60999563(+)$1	215	117	126	14.8813
eeeee]ddd	chr10:117252320-117252533(-)$1	213	167	176	10.4745
dddpppppp	chr6:112672198-112672410(+)$1	212	67	76	12.1694
qqqqqeeee	chr3:138588882-138589089(-)$1	207	14	23	11.4915
eee::::GG	chr18:31742173-31742373(+)$1	200	19	28	10.6440
pffffff22	chr14:34194961-34195166(+)$1	205	91	100	11.5762
sssssssdd	chr10:101944455-101944658(-)$1	203	74	83	13.7796
:::::::::	chr14:68373324-68373544(+)$1	220	0	9	11.9152
[bb^^^^^^	chrX:17134588-17134793(+)$1	205	24	33	10.0508
ee:::::::	chr10:79373614-79373821(-)$1	207	83	92	10.4745
G::::::::	chr5:107535985-107536203(+)$1	218	7	16	11.4067
ffffff&&&	chr5:122904191-122904391(-)$1	200	109	118	10.9830
HHHHHHHH:	chrX:8843715-8843941(-)$1	226	211	220	12.3389
bvvvvvvvv	chrX:155936192-155936399(+)$1	207	118	127	12.2542
666666eee	chr15:27661208-27661410(-)$1	202	140	149	12.2542
zzzzzzzzz	chr13:47181238-47181441(+)$1	203	43	52	11.3220
=====pppp	chr7:28536522-28536732(+)$1	210	158	167	12.3389
gggggqqqq	chr10:107937261-107937461(-)$1	200	8	17	10.8135
eeee:::dd	chr14:49706117-49706336(-)$1	219	136	145	12.5084
cc[iiiiii	chr1:92509601-92509819(-)$1	218	4	13	11.0677
cccvvvvvv	chr7:17500680-17500880(-)$1	200	105	114	13.1864
::dddd"""	chr11:90200294-90200495(-)$1	201	31	40	12.1694
3ccc55555	chrX:159216528-159216745(+)$1	217	174	183	10.9830
"ddddqqqq	chr11:120824653-120824861(-)$1	208	90	99	14.1186
EEEEE::::	chr15:100223226-100223439(+)$1	213	58	67	10.8135
eeeee[ccc	chr12:11332656-11332860(-)$1	204	61	70	14.3728
occc:::::	chr12:60059707-60059920(-)$1	213	118	127	10.5593
iiiiiiiiu	chr2:29037770-29037973(+)$1	203	61	70	11.4915
DDeeeee!!	chr12:75047403-75047610(+)$1	207	13	22	12.5932
iiiiiiiii	chr17:85463812-85464013(-)$1	201	62	71	12.2542
JJJJJJJJJ	chr12:33660882-33661093(+)$1	211	10	19	12.2542
77777gggg	chr5:24777970-24778175(-)$1	205	72	81	13.6101
:::::::::	chr6:67233903-67234105(+)$1	202	136	145	13.7796
c]eeeee::	chr12:54249411-54249626(+)$1	215	33	42	12.3389
uuuuuuuud	chr7:138486835-138487035(-)$1	200	8	17	11.0677
ffff^^^^^	chr18:6789724-6789931(-)$1	207	35	44	11.9152
mbb666666	chr7:107994941-107995175(+)$1	234	129	138	11.2372
eeeennnnn	chr13:120246100-120246319(+)$1	219	178	187	18.1016
E::::::::	chr15:78967196-78967407(-)$1	211	30	39	11.9152
[a[aeeeee	chr11:49918089-49918294(+)$1	205	13	22	11.6610
ggggcccmm	chr6:119875390-119875592(-)$1	202	149	158	12.1694

#DB
.........	chr9:105314888-105315106(+)$1	1	139	148	13.6101
..((((...	chr2:136607277-136607477(+)$1	1	157	166	11.1525
.((......	chr1:30860179-30860399(-)$1	1	160	169	13.8644
)))....))	chr1:137056774-137056974(-)$1	1	119	128	15.8983
.))))(((.	chr4:120640883-120641083(-)$1	1	48	57	11.5762
..)))....	chr15:41691844-41692053(+)$1	1	171	180	18.1016
..))))).(	chr8:116897781-116897989(+)$1	1	155	164	11.9999
).....)).	chr7:38746269-38746487(-)$1	1	179	188	11.7457
(......))	chr4:138013733-138013934(+)$1	1	122	131	18.1016
.......((	chr16:91272027-91272229(-)$1	1	23	32	11.4067
.........	chr3:105476334-105476562(-)$1	1	142	151	13.1016
..)))))))	chr11:77346438-77346639(-)$1	1	155	164	12.2542
(((......	chr14:58308579-58308787(+)$1	1	45	54	12.1694
))).)....	chr18:82754721-82754921(+)$1	1	141	150	11.7457
.)))))...	chr11:50107925-50108127(-)$1	1	129	138	12.8474
.))))))))	chrX:106356132-106356339(+)$1	1	171	180	14.3728
((((((...	chr3:7551724-7551937(+)$1	1	64	73	11.9152
)).......	chrX:119508454-119508659(-)$1	1	192	201	16.4067
.)))))...	chr14:60999348-60999563(+)$1	1	117	126	14.8813
))))).)))	chr10:117252320-117252533(-)$1	1	167	176	10.4745
(((......	chr6:112672198-112672410(+)$1	1	67	76	12.1694
.....))))	chr3:138588882-138589089(-)$1	1	14	23	11.4915
)))....((	chr18:31742173-31742373(+)$1	1	19	28	10.6440
.))))))..	chr14:34194961-34195166(+)$1	1	91	100	11.5762
.......))	chr10:101944455-101944658(-)$1	1	74	83	13.7796
.........	chr14:68373324-68373544(+)$1	1	0	9	11.9152
.((......	chrX:17134588-17134793(+)$1	1	24	33	10.0508
)).......	chr10:79373614-79373821(-)$1	1	83	92	10.4745
(........	chr5:107535985-107536203(+)$1	1	7	16	11.4067
((((((...	chr5:122904191-122904391(-)$1	1	109	118	10.9830
)))))))).	chrX:8843715-8843941(-)$1	1	211	220	12.3389
(........	chrX:155936192-155936399(+)$1	1	118	127	12.2542
......)))	chr15:27661208-27661410(-)$1	1	140	149	12.2542
.........	chr13:47181238-47181441(+)$1	1	43	52	11.3220
(((((....	chr7:28536522-28536732(+)$1	1	158	167	12.3389
(((((....	chr10:107937261-107937461(-)$1	1	8	17	10.8135
))))...((	chr14:49706117-49706336(-)$1	1	136	145	12.5084
((.((((((	chr1:92509601-92509819(-)$1	1	4	13	11.0677
(((......	chr7:17500680-17500880(-)$1	1	105	114	13.1864
..((((...	chr11:90200294-90200495(-)$1	1	31	40	12.1694
.))).....	chrX:159216528-159216745(+)$1	1	174	183	10.9830
.((((....	chr11:120824653-120824861(-)$1	1	90	99	14.1186
)))))....	chr15:100223226-100223439(+)$1	1	58	67	10.8135
(((((.(((	chr12:11332656-11332860(-)$1	1	61	70	14.3728
.))).....	chr12:60059707-60059920(-)$1	1	118	127	10.5593
((((((((.	chr2:29037770-29037973(+)$1	1	61	70	11.4915
(((((((..	chr12:75047403-75047610(+)$1	1	13	22	12.5932
(((((((((	chr17:85463812-85464013(-)$1	1	62	71	12.2542
(((((((((	chr12:33660882-33661093(+)$1	1	10	19	12.2542
.....))))	chr5:24777970-24778175(-)$1	1	72	81	13.6101
.........	chr6:67233903-67234105(+)$1	1	136	145	13.7796
).)))))..	chr12:54249411-54249626(+)$1	1	33	42	12.3389
........)	chr7:138486835-138487035(-)$1	1	8	17	11.0677
((((.....	chr18:6789724-6789931(-)$1	1	35	44	11.9152
.))......	chr7:107994941-107995175(+)$1	1	129	138	11.2372
((((.....	chr13:120246100-120246319(+)$1	1	178	187	18.1016
(........	chr15:78967196-78967407(-)$1	1	30	39	11.9152
.(.((((((	chr11:49918089-49918294(+)$1	1	13	22	11.6610
(((((((..	chr6:119875390-119875592(-)$1	1	149	158	12.1694

#PSSM
U : 0.88	A : 0.06	u : 0.03	g : 0.01	
G : 0.64	U : 0.15	A : 0.10	C : 0.05	g : 0.03	a : 0.01	
C : 0.55	A : 0.16	G : 0.10	U : 0.10	a : 0.05	g : 0.01	
A : 0.77	a : 0.06	C : 0.06	U : 0.05	G : 0.03	
A : 0.67	G : 0.10	U : 0.08	a : 0.06	C : 0.06	
A : 0.77	U : 0.10	a : 0.05	G : 0.03	C : 0.01	u : 0.01	
A : 0.74	U : 0.08	a : 0.06	G : 0.06	C : 0.03	
A : 0.91	a : 0.06	U : 0.01	
A : 0.77	a : 0.06	G : 0.06	U : 0.06	C : 0.01	

#score	739.6101694915251
#seq	59
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m1_run2.nuc.txt

#NT
CCUCUUCAU	chr4:134392212-134392413(-)$1	201	102	111	16.6491
CAUCUACAU	chr3:124024517-124024718(+)$1	201	180	189	15.4210
CAUCGUCAC	chr1:75182270-75182471(-)$1	201	81	90	13.0526
CAACAUCAU	chr2:37373021-37373222(+)$1	201	76	85	12.7894
CGUCUUCAU	chrX:58437195-58437396(+)$1	201	97	106	16.1228
CACCUUCAU	chr5:23006227-23006428(+)$1	201	89	98	16.8245
CAUUUUCAG	chr5:14680503-14680704(+)$1	201	95	104	13.1403
UAUCUUCAU	chr7:149541800-149542001(-)$1	201	92	101	15.7719
CACCUUCAC	chr6:124694676-124694877(-)$1	201	103	112	13.8421
CCUCUUCCU	chr10:102856505-102856706(+)$1	201	107	116	12.7017
CAUUUUCAG	chr5:105910521-105910722(+)$1	201	95	104	13.1403
GAACUUCAU	chr4:53034117-53034318(+)$1	201	6	15	12.3508
CAUCCUCAU	chr7:52302548-52302749(-)$1	201	92	101	16.3859
CAUCUUCAA	chr6:113709150-113709351(-)$1	201	96	105	17.2631
UCUCUUCAU	chr8:46881630-46881831(+)$1	201	95	104	12.3508
CCUCUUCAU	chr15:88898600-88898801(+)$1	201	96	105	16.6491
CAUCAUCAA	chr9:75001562-75001763(+)$1	201	101	110	13.4912
CCUUUUCAU	chr3:108430248-108430449(+)$1	201	95	104	12.9649
CAUCUUCAU	chr6:30700485-30700686(+)$1	201	72	81	20.0701
CAUCUUCAU	chr2:91052014-91052215(+)$1	201	85	94	20.0701
CUGCUUCAU	chr1:138189398-138189599(-)$1	201	126	135	12.9649
CACCUUCAA	chr4:144750454-144750655(-)$1	201	103	112	14.0175
CCUCUUCAA	chr6:118601923-118602124(-)$1	201	65	74	13.8421
CAUCUUCAA	chr2:132130873-132131074(+)$1	201	78	87	17.2631
GAGCUUCAU	chr8:9987414-9987615(+)$1	201	13	22	12.5263
CAUGUUCAU	chr1:156292617-156292818(-)$1	201	96	105	15.8596
CAGCUUCAC	chr17:12888077-12888278(-)$1	201	144	153	13.7543
CAUCUUCAU	chr6:30700462-30700663(+)$1	201	95	104	20.0701
CAUCUUCUU	chr8:9987572-9987773(+)$1	201	43	52	16.2982
CAUCCUCAA	chr12:97017065-97017266(+)$1	201	75	84	13.5789
CCUCUUCAU	chr8:3512703-3512904(+)$1	201	95	104	16.6491
CAUUUUCAU	chr2:44852590-44852791(-)$1	201	98	107	16.3859
CAUCUCCAU	chr18:37344642-37344843(+)$1	201	102	111	15.5087
CAUCUUCUC	chr15:81441771-81441972(+)$1	201	80	89	13.3157
CAUCUUAAU	chrM:13347-13548(+)$1	201	178	187	15.2456
CAUCUUCAU	chr12:91560353-91560554(+)$1	201	101	110	20.0701
CACCUUCUU	chrX:152008144-152008345(-)$1	201	93	102	13.0526
CAUCCUCAC	chr2:127058878-127059079(+)$1	201	177	186	13.4035
CACCUUCAC	chr6:124694677-124694878(-)$1	201	104	113	13.8421
CAUUUUCAA	chr1:82727604-82727805(+)$1	201	101	110	13.5789
GUUCUUCAU	chr18:35731770-35731971(+)$1	201	88	97	12.0877
CAUCCUCUU	chr14:68739303-68739504(-)$1	201	39	48	12.6140
CAUUUUCAU	chr1:165745867-165746068(+)$1	201	95	104	16.3859
CUUCCUCAU	chr9:122989423-122989624(-)$1	201	92	101	12.6140
CAUCUCCAU	chr9:116731881-116732082(-)$1	201	112	121	15.5087
CAGCUUCAG	chr1:36749228-36749429(+)$1	201	95	104	13.4912
CAUCAUCAU	chr4:70094272-70094473(-)$1	201	92	101	16.2982
CAUCUUCCU	chr14:21538638-21538839(+)$1	201	109	118	16.1228
CAUCUUCAU	chr15:76079389-76079590(+)$1	201	95	104	20.0701
CAUCUUCUU	chr11:66188605-66188806(-)$1	201	37	46	16.2982
AAGCUUCAU	chr9:54294249-54294450(-)$1	201	56	65	12.3508
CAUCUUCCU	chr7:66531915-66532116(-)$1	201	160	169	16.1228
CAUCUUCAU	chr15:76079443-76079644(+)$1	201	41	50	20.0701
CAACUUCAU	chr11:94323115-94323316(-)$1	201	79	88	16.5614
CAUUUUCAA	chr6:38695590-38695791(-)$1	201	98	107	13.5789
CAUCUUCGU	chr7:25763890-25764091(-)$1	201	106	115	15.9473

#otherMatches

#Struct PSSM
DDD::::::	chr4:86637289-86637490(-)$1	201	17	26	13.0526
)))))))))	chr4:134392212-134392413(-)$1	201	102	111	16.6491
ZZCCC}BBY	chr3:124024517-124024718(+)$1	201	180	189	15.4210
c:BB{HHHH	chr1:75182270-75182471(-)$1	201	81	90	13.0526
dd####ccc	chr2:37373021-37373222(+)$1	201	76	85	12.7894
^^^^^^ddd	chrX:58437195-58437396(+)$1	201	97	106	16.1228
e]dddd:::	chr5:23006227-23006428(+)$1	201	89	98	16.8245
qqqqqqqcc	chr5:14680503-14680704(+)$1	201	95	104	13.1403
66666ffff	chr7:149541800-149542001(-)$1	201	92	101	15.7719
::::::::e	chr6:124694676-124694877(-)$1	201	103	112	13.8421
))))))bb!	chr10:102856505-102856706(+)$1	201	107	116	12.7017
eeggggggg	chr5:105910521-105910722(+)$1	201	95	104	13.1403
ccc"""ccc	chr4:53034117-53034318(+)$1	201	6	15	12.3508
::::eeeee	chr7:52302548-52302749(-)$1	201	92	101	16.3859
:::::::::	chr6:113709150-113709351(-)$1	201	96	105	17.2631
ppdddd:::	chr8:46881630-46881831(+)$1	201	95	104	12.3508
hhh))))))	chr15:88898600-88898801(+)$1	201	96	105	16.6491
!!ccc[ddd	chr9:75001562-75001763(+)$1	201	101	110	13.4912
d666666dd	chr3:108430248-108430449(+)$1	201	95	104	12.9649
c!!dddd[c	chr6:30700485-30700686(+)$1	201	72	81	20.0701
::eeeee[c	chr2:91052014-91052215(+)$1	201	85	94	20.0701
b4444bb]d	chr1:138189398-138189599(-)$1	201	126	135	12.9649
ffff:::::	chr4:144750454-144750655(-)$1	201	103	112	14.0175
OOOOOCCC:	chr6:118601923-118602124(-)$1	201	65	74	13.8421
BB{EEEEE{	chr2:132130873-132131074(+)$1	201	78	87	17.2631
GGGG:::::	chr8:9987414-9987615(+)$1	201	13	22	12.5263
eeeeebb[f	chr1:156292617-156292818(-)$1	201	96	105	15.8596
eeee!!eee	chr17:12888077-12888278(-)$1	201	144	153	13.7543
C::::::::	chr6:30700462-30700663(+)$1	201	95	104	20.0701
gggggg[cc	chr8:9987572-9987773(+)$1	201	43	52	16.2982
pppeeeee5	chr12:97017065-97017266(+)$1	201	75	84	13.5789
d::::DDDD	chr8:3512703-3512904(+)$1	201	95	104	16.6491
RRRRGGGGG	chr2:44852590-44852791(-)$1	201	98	107	16.3859
xxxxxxxxx	chr18:37344642-37344843(+)$1	201	102	111	15.5087
dd]ccc22c	chr15:81441771-81441972(+)$1	201	80	89	13.3157
ppppggggg	chrM:13347-13548(+)$1	201	178	187	15.2456
:::::::::	chr12:91560353-91560554(+)$1	201	101	110	20.0701
:::EEEEE:	chrX:152008144-152008345(-)$1	201	93	102	13.0526
E::::::::	chr2:127058878-127059079(+)$1	201	177	186	13.4035
::::::::e	chr6:124694677-124694878(-)$1	201	104	113	13.8421
ffff:ffff	chr1:82727604-82727805(+)$1	201	101	110	13.5789
======!!c	chr18:35731770-35731971(+)$1	201	88	97	12.0877
!!dddd[ff	chr14:68739303-68739504(-)$1	201	39	48	12.6140
eee!!ccc!	chr1:165745867-165746068(+)$1	201	95	104	16.3859
ssseeeee4	chr9:122989423-122989624(-)$1	201	92	101	12.6140
cc[dddd[b	chr9:116731881-116732082(-)$1	201	112	121	15.5087
]ccc4444b	chr1:36749228-36749429(+)$1	201	95	104	13.4912
cc"""eeee	chr4:70094272-70094473(-)$1	201	92	101	16.2982
^^^^^^^^^	chr14:21538638-21538839(+)$1	201	109	118	16.1228
=========	chr15:76079389-76079590(+)$1	201	95	104	20.0701
eee$$$$$c	chr11:66188605-66188806(-)$1	201	37	46	16.2982
^^^^^^^^^	chr9:54294249-54294450(-)$1	201	56	65	12.3508
eeessssss	chr7:66531915-66532116(-)$1	201	160	169	16.1228
=========	chr15:76079443-76079644(+)$1	201	41	50	20.0701
:::::::::	chr11:94323115-94323316(-)$1	201	79	88	16.5614
ooodddd33	chr6:38695590-38695791(-)$1	201	98	107	13.5789
ffffrrrrr	chr7:25763890-25764091(-)$1	201	106	115	15.9473

#DB
(((......	chr4:86637289-86637490(-)$1	1	17	26	13.0526
.........	chr4:134392212-134392413(-)$1	1	102	111	16.6491
..))).)).	chr3:124024517-124024718(+)$1	1	180	189	15.4210
).((.((((	chr1:75182270-75182471(-)$1	1	81	90	13.0526
((....(((	chr2:37373021-37373222(+)$1	1	76	85	12.7894
......)))	chrX:58437195-58437396(+)$1	1	97	106	16.1228
).))))...	chr5:23006227-23006428(+)$1	1	89	98	16.8245
.......))	chr5:14680503-14680704(+)$1	1	95	104	13.1403
.....))))	chr7:149541800-149542001(-)$1	1	92	101	15.7719
........(	chr6:124694676-124694877(-)$1	1	103	112	13.8421
......((.	chr10:102856505-102856706(+)$1	1	107	116	12.7017
)))))))))	chr5:105910521-105910722(+)$1	1	95	104	13.1403
(((...(((	chr4:53034117-53034318(+)$1	1	6	15	12.3508
....(((((	chr7:52302548-52302749(-)$1	1	92	101	16.3859
.........	chr6:113709150-113709351(-)$1	1	96	105	17.2631
..))))...	chr8:46881630-46881831(+)$1	1	95	104	12.3508
(((......	chr15:88898600-88898801(+)$1	1	96	105	16.6491
..(((.(((	chr9:75001562-75001763(+)$1	1	101	110	13.4912
)......))	chr3:108430248-108430449(+)$1	1	95	104	12.9649
(..((((.(	chr6:30700485-30700686(+)$1	1	72	81	20.0701
..(((((.(	chr2:91052014-91052215(+)$1	1	85	94	20.0701
)....)).)	chr1:138189398-138189599(-)$1	1	126	135	12.9649
)))).....	chr4:144750454-144750655(-)$1	1	103	112	14.0175
.....(((.	chr6:118601923-118602124(-)$1	1	65	74	13.8421
((.(((((.	chr2:132130873-132131074(+)$1	1	78	87	17.2631
((((.....	chr8:9987414-9987615(+)$1	1	13	22	12.5263
(((((((.(	chr1:156292617-156292818(-)$1	1	96	105	15.8596
((((..(((	chr17:12888077-12888278(-)$1	1	144	153	13.7543
(........	chr6:30700462-30700663(+)$1	1	95	104	20.0701
((((((.((	chr8:9987572-9987773(+)$1	1	43	52	16.2982
...))))).	chr12:97017065-97017266(+)$1	1	75	84	13.5789
)....))))	chr8:3512703-3512904(+)$1	1	95	104	16.6491
....(((((	chr2:44852590-44852791(-)$1	1	98	107	16.3859
.........	chr18:37344642-37344843(+)$1	1	102	111	15.5087
)).)))..)	chr15:81441771-81441972(+)$1	1	80	89	13.3157
....)))))	chrM:13347-13548(+)$1	1	178	187	15.2456
.........	chr12:91560353-91560554(+)$1	1	101	110	20.0701
...(((((.	chrX:152008144-152008345(-)$1	1	93	102	13.0526
)........	chr2:127058878-127059079(+)$1	1	177	186	13.4035
........(	chr6:124694677-124694878(-)$1	1	104	113	13.8421
)))).((((	chr1:82727604-82727805(+)$1	1	101	110	13.5789
((((((..(	chr18:35731770-35731971(+)$1	1	88	97	12.0877
..((((.((	chr14:68739303-68739504(-)$1	1	39	48	12.6140
(((..(((.	chr1:165745867-165746068(+)$1	1	95	104	16.3859
...))))).	chr9:122989423-122989624(-)$1	1	92	101	12.6140
((.((((.(	chr9:116731881-116732082(-)$1	1	112	121	15.5087
.)))....)	chr1:36749228-36749429(+)$1	1	95	104	13.4912
((...((((	chr4:70094272-70094473(-)$1	1	92	101	16.2982
.........	chr14:21538638-21538839(+)$1	1	109	118	16.1228
(((((((((	chr15:76079389-76079590(+)$1	1	95	104	20.0701
(((.....(	chr11:66188605-66188806(-)$1	1	37	46	16.2982
.........	chr9:54294249-54294450(-)$1	1	56	65	12.3508
(((......	chr7:66531915-66532116(-)$1	1	160	169	16.1228
(((((((((	chr15:76079443-76079644(+)$1	1	41	50	20.0701
.........	chr11:94323115-94323316(-)$1	1	79	88	16.5614
...))))..	chr6:38695590-38695791(-)$1	1	98	107	13.5789
((((.....	chr7:25763890-25764091(-)$1	1	106	115	15.9473

#PSSM
C : 0.89	G : 0.05	U : 0.03	A : 0.01	
A : 0.80	C : 0.12	U : 0.05	G : 0.01	
U : 0.75	C : 0.10	G : 0.08	A : 0.05	
C : 0.85	U : 0.12	G : 0.01	
U : 0.82	C : 0.08	A : 0.07	G : 0.01	
U : 0.94	C : 0.03	A : 0.01	
C : 0.98	A : 0.01	
A : 0.84	U : 0.08	C : 0.05	G : 0.01	
U : 0.70	A : 0.14	C : 0.10	G : 0.05	

#score	861.4561403508785
#seq	57
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m2_run1.nuc.txt

#NT
AUUUUUUU	chr9:45775431-45775738(-)$1	307	100	108	19.9090
AUUUUUUU	chr15:96180386-96180640(+)$1	254	6	14	19.9090
AUUUUUAU	chr1:184062369-184062600(+)$1	231	85	93	16.2727
AUUUUUCU	chr6:8544197-8544463(+)$1	266	60	68	15.9696
AUCUUUUU	chr9:42222547-42222807(-)$1	260	243	251	16.0454
AUUUUGUU	chr10:59765130-59765371(+)$1	241	163	171	15.7424
AUUUUUUU	chr12:41572357-41572601(+)$1	244	100	108	19.9090
AUUUAUUU	chr6:115568400-115568631(+)$1	231	75	83	15.5151
AUUAUUUU	chr6:127078340-127078575(-)$1	235	40	48	15.9696
AUUUAUUU	chr2:72095341-72095589(+)$1	248	1	9	15.5151
AUUUUUGU	chr13:57530314-57530563(-)$1	249	100	108	16.1212
AUUUCUUU	chr14:120905450-120905692(+)$1	242	47	55	15.4393
AUUGUUUU	chr5:100389567-100389800(-)$1	233	143	151	15.8181
AUUUUUAU	chr2:131878455-131878713(-)$1	258	242	250	16.2727
AUUUUGUU	chr2:33265370-33265604(-)$1	234	139	147	15.7424
AUUGUUUU	chr17:24315706-24315963(-)$1	257	28	36	15.8181
AUUUUUAU	chr19:41288816-41289089(-)$1	273	13	21	16.2727
AUUUUUGU	chr11:120242027-120242297(-)$1	270	171	179	16.1212
AUUUUUAU	chr4:59486902-59487138(-)$1	236	15	23	16.2727
auuuuuuu	chr11:88898536-88898768(-)$1	232	98	106	19.9090
aauuuuuu	chr3:83967070-83967333(-)$1	263	47	55	15.1363
GUUUUUUU	chr16:91673934-91674185(+)$1	251	185	193	15.2121
AUCUUUUU	chr14:78894154-78894396(-)$1	242	82	90	16.0454
AUUUUUAU	chr12:87166749-87166980(+)$1	231	162	170	16.2727
AUUAUUUU	chr8:68993494-68993746(+)$1	252	236	244	15.9696
AUUUUUUG	chrX:53840888-53841119(-)$1	231	110	118	15.3636
AUGUUUUU	chr5:76051392-76051672(+)$1	280	28	36	15.7424
AUUUUUUA	chr12:72420761-72421005(+)$1	244	50	58	15.4393
AUUUUUUC	chr3:31106729-31106960(-)$1	231	105	113	15.4393
AUUAUUUU	chr3:78867807-78868080(-)$1	273	196	204	15.9696
AUUUUUUU	chr3:108194354-108194610(-)$1	256	81	89	19.9090
AUUAUUUU	chr9:75418149-75418395(-)$1	246	111	119	15.9696
AUUUUUGU	chr9:25115690-25115953(+)$1	263	100	108	16.1212
AUAUUUUU	chr5:76641269-76641503(-)$1	234	90	98	15.9696
AUUGUUUU	chr2:14068476-14068709(+)$1	233	41	49	15.8181
AUUUUAUU	chr15:12280746-12281020(+)$1	274	14	22	15.8939
AUUUUUGU	chrX:132569265-132569502(+)$1	237	105	113	16.1212
AUUUUAUU	chr10:116781636-116781906(-)$1	270	4	12	15.8939
AUUUUUCU	chr6:55627780-55628011(-)$1	231	110	118	15.9696
AUUCUUUU	chr10:79619474-79619736(+)$1	262	46	54	15.6666
AUUUUCUU	chr9:44445175-44445411(+)$1	236	113	121	15.8181
AUCUUUUU	chr5:124823475-124823733(-)$1	258	91	99	16.0454
AUUUUCUU	chr15:96233521-96233755(+)$1	234	186	194	15.8181
GUUUUUUU	chr4:83107413-83107695(+)$1	282	5	13	15.2121
AUUUUUUU	chr14:62153379-62153666(-)$1	287	0	8	19.9090
AUUUUUAU	chr4:19449624-19449881(-)$1	257	130	138	16.2727
AUUUUCUU	chr11:75518860-75519127(+)$1	267	119	127	15.8181
AUUUUAUU	chr1:95404571-95404819(+)$1	248	33	41	15.8939
AUUAUUUU	chr9:41774874-41775105(-)$1	231	91	99	15.9696
AUUUUUUA	chr5:67681749-67681980(+)$1	231	4	12	15.4393
AUUUUUUU	chr10:100035691-100035938(-)$1	247	71	79	19.9090
AUUUUUUU	chr18:73751567-73751814(+)$1	247	173	181	19.9090
AUUUCUUU	chr15:103028647-103028939(-)$1	292	191	199	15.4393
ACUUUUUU	chr5:92377880-92378122(-)$1	242	112	120	15.1363
AUCUUUUU	chr3:126624990-126625258(-)$1	268	213	221	16.0454
AUCUUUUU	chr14:27476099-27476331(+)$1	232	34	42	16.0454
AUUUUAUU	chr4:150435635-150435906(-)$1	271	100	108	15.8939
AUUUUUUC	chr2:23052975-23053222(+)$1	247	175	183	15.4393
AUUUUUUU	chr9:62641868-62642107(-)$1	239	92	100	19.9090
AUAUUUUU	chr11:75519527-75519758(+)$1	231	83	91	15.9696
AUAUUUUU	chr16:66659441-66659691(-)$1	250	229	237	15.9696
AUAUUUUU	chr17:66316781-66317020(-)$1	239	168	176	15.9696
AUUUUUUU	chr2:102621782-102622041(+)$1	259	229	237	19.9090
AUUUUUUU	chr10:57508065-57508332(+)$1	267	91	99	19.9090
AUUUUUUU	chr2:101539383-101539614(+)$1	231	178	186	19.9090

#otherMatches

#Struct PSSM
&&&&&&&e	chr5:138172412-138172665(-)$1	253	100	108	15.5151
::::::::	chr9:45775431-45775738(-)$1	307	100	108	19.9090
::::::::	chr15:96180386-96180640(+)$1	254	6	14	19.9090
========	chr1:184062369-184062600(+)$1	231	85	93	16.2727
gmmmmggg	chr6:8544197-8544463(+)$1	266	60	68	15.9696
dmmmmddd	chr9:42222547-42222807(-)$1	260	243	251	16.0454
dddd4444	chr10:59765130-59765371(+)$1	241	163	171	15.7424
ff999999	chr12:41572357-41572601(+)$1	244	100	108	19.9090
dooooood	chr6:115568400-115568631(+)$1	231	75	83	15.5151
::::::::	chr6:127078340-127078575(-)$1	235	40	48	15.9696
::::::::	chr2:72095341-72095589(+)$1	248	1	9	15.5151
uuuuuuuu	chr13:57530314-57530563(-)$1	249	100	108	16.1212
4ggggggg	chr14:120905450-120905692(+)$1	242	47	55	15.4393
3iiiiiii	chr5:100389567-100389800(-)$1	233	143	151	15.8181
JJJ:::::	chr2:131878455-131878713(-)$1	258	242	250	16.2727
GGGG}BB:	chr2:33265370-33265604(-)$1	234	139	147	15.7424
e!!ammmm	chr17:24315706-24315963(-)$1	257	28	36	15.8181
::::::::	chr19:41288816-41289089(-)$1	273	13	21	16.2727
55555eee	chr11:120242027-120242297(-)$1	270	171	179	16.1212
c"""ccc[	chr4:59486902-59487138(-)$1	236	15	23	16.2727
========	chr11:88898536-88898768(-)$1	232	98	106	19.9090
iiiiiiil	chr3:83967070-83967333(-)$1	263	47	55	15.1363
JJJJJJJJ	chr16:91673934-91674185(+)$1	251	185	193	15.2121
dddooooo	chr14:78894154-78894396(-)$1	242	82	90	16.0454
eeeqqqqq	chr12:87166749-87166980(+)$1	231	162	170	16.2727
////GGGG	chr8:68993494-68993746(+)$1	252	236	244	15.9696
ggggggnn	chrX:53840888-53841119(-)$1	231	110	118	15.3636
ohhhhhhh	chr5:76051392-76051672(+)$1	280	28	36	15.7424
::::::::	chr12:72420761-72421005(+)$1	244	50	58	15.4393
=====xxx	chr3:31106729-31106960(-)$1	231	105	113	15.4393
ddd]hhhh	chr3:78867807-78868080(-)$1	273	196	204	15.9696
ttttttti	chr3:108194354-108194610(-)$1	256	81	89	19.9090
fnnnnnff	chr9:75418149-75418395(-)$1	246	111	119	15.9696
uuuuuuee	chr9:25115690-25115953(+)$1	263	100	108	16.1212
xxxxxxxx	chr5:76641269-76641503(-)$1	234	90	98	15.9696
hh]ccc::	chr2:14068476-14068709(+)$1	233	41	49	15.8181
::::::DD	chr15:12280746-12281020(+)$1	274	14	22	15.8939
rrrrrddd	chrX:132569265-132569502(+)$1	237	105	113	16.1212
E:::::::	chr10:116781636-116781906(-)$1	270	4	12	15.8939
ellleeee	chr6:55627780-55628011(-)$1	231	110	118	15.9696
::::::::	chr10:79619474-79619736(+)$1	262	46	54	15.6666
::::::dd	chr9:44445175-44445411(+)$1	236	113	121	15.8181
:ccc!!ee	chr5:124823475-124823733(-)$1	258	91	99	16.0454
ii:dddd[	chr15:96233521-96233755(+)$1	234	186	194	15.8181
:::::iii	chr4:83107413-83107695(+)$1	282	5	13	15.2121
::::::::	chr14:62153379-62153666(-)$1	287	0	8	19.9090
iiiiittt	chr4:19449624-19449881(-)$1	257	130	138	16.2727
ggggggg2	chr11:75518860-75519127(+)$1	267	119	127	15.8181
xxxxxxee	chr1:95404571-95404819(+)$1	248	33	41	15.8939
^^^^^^^^	chr9:41774874-41775105(-)$1	231	91	99	15.9696
xxxxxxxx	chr5:67681749-67681980(+)$1	231	4	12	15.4393
hhhhhhhh	chr10:100035691-100035938(-)$1	247	71	79	19.9090
dooooood	chr18:73751567-73751814(+)$1	247	173	181	19.9090
"ffffff[	chr15:103028647-103028939(-)$1	292	191	199	15.4393
22dddd::	chr5:92377880-92378122(-)$1	242	112	120	15.1363
IIIIIIGG	chr3:126624990-126625258(-)$1	268	213	221	16.0454
(((((((c	chr14:27476099-27476331(+)$1	232	34	42	16.0454
iiiii]cc	chr4:150435635-150435906(-)$1	271	100	108	15.8939
gggggg55	chr2:23052975-23053222(+)$1	247	175	183	15.4393
::::::::	chr9:62641868-62642107(-)$1	239	92	100	19.9090
%%%ccc!!	chr11:75519527-75519758(+)$1	231	83	91	15.9696
:::fffff	chr16:66659441-66659691(-)$1	250	229	237	15.9696
ccdddd::	chr17:66316781-66317020(-)$1	239	168	176	15.9696
uuuuuuuu	chr2:102621782-102622041(+)$1	259	229	237	19.9090
======!!	chr10:57508065-57508332(+)$1	267	91	99	19.9090
::::::gg	chr2:101539383-101539614(+)$1	231	178	186	19.9090

#DB
.......(	chr5:138172412-138172665(-)$1	1	100	108	15.5151
........	chr9:45775431-45775738(-)$1	1	100	108	19.9090
........	chr15:96180386-96180640(+)$1	1	6	14	19.9090
((((((((	chr1:184062369-184062600(+)$1	1	85	93	16.2727
(....)))	chr6:8544197-8544463(+)$1	1	60	68	15.9696
(....)))	chr9:42222547-42222807(-)$1	1	243	251	16.0454
))))....	chr10:59765130-59765371(+)$1	1	163	171	15.7424
))......	chr12:41572357-41572601(+)$1	1	100	108	19.9090
(......)	chr6:115568400-115568631(+)$1	1	75	83	15.5151
........	chr6:127078340-127078575(-)$1	1	40	48	15.9696
........	chr2:72095341-72095589(+)$1	1	1	9	15.5151
........	chr13:57530314-57530563(-)$1	1	100	108	16.1212
.)))))))	chr14:120905450-120905692(+)$1	1	47	55	15.4393
.)))))))	chr5:100389567-100389800(-)$1	1	143	151	15.8181
))).....	chr2:131878455-131878713(-)$1	1	242	250	16.2727
)))).)).	chr2:33265370-33265604(-)$1	1	139	147	15.7424
(..(....	chr17:24315706-24315963(-)$1	1	28	36	15.8181
........	chr19:41288816-41289089(-)$1	1	13	21	16.2727
.....)))	chr11:120242027-120242297(-)$1	1	171	179	16.1212
(...(((.	chr4:59486902-59487138(-)$1	1	15	23	16.2727
((((((((	chr11:88898536-88898768(-)$1	1	98	106	19.9090
(((((((.	chr3:83967070-83967333(-)$1	1	47	55	15.1363
))))))))	chr16:91673934-91674185(+)$1	1	185	193	15.2121
(((.....	chr14:78894154-78894396(-)$1	1	82	90	16.0454
(((.....	chr12:87166749-87166980(+)$1	1	162	170	16.2727
....))))	chr8:68993494-68993746(+)$1	1	236	244	15.9696
((((((..	chrX:53840888-53841119(-)$1	1	110	118	15.3636
.)))))))	chr5:76051392-76051672(+)$1	1	28	36	15.7424
........	chr12:72420761-72421005(+)$1	1	50	58	15.4393
(((((...	chr3:31106729-31106960(-)$1	1	105	113	15.4393
))).))))	chr3:78867807-78868080(-)$1	1	196	204	15.9696
.......)	chr3:108194354-108194610(-)$1	1	81	89	19.9090
(.....))	chr9:75418149-75418395(-)$1	1	111	119	15.9696
......))	chr9:25115690-25115953(+)$1	1	100	108	16.1212
........	chr5:76641269-76641503(-)$1	1	90	98	15.9696
)).)))..	chr2:14068476-14068709(+)$1	1	41	49	15.8181
......((	chr15:12280746-12281020(+)$1	1	14	22	15.8939
.....)))	chrX:132569265-132569502(+)$1	1	105	113	16.1212
(.......	chr10:116781636-116781906(-)$1	1	4	12	15.8939
(...))))	chr6:55627780-55628011(-)$1	1	110	118	15.9696
........	chr10:79619474-79619736(+)$1	1	46	54	15.6666
......((	chr9:44445175-44445411(+)$1	1	113	121	15.8181
.(((..((	chr5:124823475-124823733(-)$1	1	91	99	16.0454
)).((((.	chr15:96233521-96233755(+)$1	1	186	194	15.8181
.....(((	chr4:83107413-83107695(+)$1	1	5	13	15.2121
........	chr14:62153379-62153666(-)$1	1	0	8	19.9090
(((((...	chr4:19449624-19449881(-)$1	1	130	138	16.2727
))))))).	chr11:75518860-75519127(+)$1	1	119	127	15.8181
......))	chr1:95404571-95404819(+)$1	1	33	41	15.8939
........	chr9:41774874-41775105(-)$1	1	91	99	15.9696
........	chr5:67681749-67681980(+)$1	1	4	12	15.4393
((((((((	chr10:100035691-100035938(-)$1	1	71	79	19.9090
(......)	chr18:73751567-73751814(+)$1	1	173	181	19.9090
.((((((.	chr15:103028647-103028939(-)$1	1	191	199	15.4393
..))))..	chr5:92377880-92378122(-)$1	1	112	120	15.1363
))))))))	chr3:126624990-126625258(-)$1	1	213	221	16.0454
.......(	chr14:27476099-27476331(+)$1	1	34	42	16.0454
))))).))	chr4:150435635-150435906(-)$1	1	100	108	15.8939
))))))..	chr2:23052975-23053222(+)$1	1	175	183	15.4393
........	chr9:62641868-62642107(-)$1	1	92	100	19.9090
...(((..	chr11:75519527-75519758(+)$1	1	83	91	15.9696
...(((((	chr16:66659441-66659691(-)$1	1	229	237	15.9696
))))))..	chr17:66316781-66317020(-)$1	1	168	176	15.9696
........	chr2:102621782-102622041(+)$1	1	229	237	19.9090
((((((..	chr10:57508065-57508332(+)$1	1	91	99	19.9090
......((	chr2:101539383-101539614(+)$1	1	178	186	19.9090

#PSSM
A : 0.93	a : 0.03	G : 0.03	
U : 0.95	u : 0.01	a : 0.01	C : 0.01	
U : 0.81	C : 0.07	A : 0.06	u : 0.03	G : 0.01	
U : 0.83	A : 0.07	G : 0.04	u : 0.03	C : 0.01	
U : 0.89	A : 0.04	C : 0.03	u : 0.03	
U : 0.83	A : 0.06	C : 0.04	G : 0.03	u : 0.03	
U : 0.78	A : 0.09	G : 0.06	C : 0.03	u : 0.03	
U : 0.89	u : 0.03	A : 0.03	C : 0.03	G : 0.01	

#score	1093.5454545454536
#seq	66
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m1_run1.nuc.txt

#NT
UGA	chr12:71568417-71568671(+)$1	254	10	13	8.9999
UGA	chr11:60884496-60884731(+)$1	235	55	58	8.9999
UGA	chr15:4104066-4104302(+)$1	236	34	37	8.9999
UGA	chr8:71430485-71430793(+)$1	308	75	78	8.9999
UGA	chr8:11834228-11834463(+)$1	235	11	14	8.9999
UGA	chr12:85716749-85716991(-)$1	242	15	18	8.9999
UGA	chr14:21319413-21319648(-)$1	235	96	99	8.9999
UGA	chr2:109739556-109739796(+)$1	240	12	15	8.9999
UGA	chr13:102451321-102451579(-)$1	258	7	10	8.9999
UGA	chr9:55906171-55906406(+)$1	235	36	39	8.9999
UGA	chrX:70604132-70604375(+)$1	243	5	8	8.9999
UGA	chr10:18576309-18576544(+)$1	235	156	159	8.9999
UGA	chr13:21605280-21605515(-)$1	235	88	91	8.9999
UGA	chr4:134772377-134772627(-)$1	250	122	125	8.9999
UGA	chr3:141965381-141965616(-)$1	235	120	123	8.9999
UGA	chr8:35233273-35233512(+)$1	239	50	53	8.9999
UGA	chr13:74460049-74460289(-)$1	240	48	51	8.9999
UGA	chr17:13208221-13208456(+)$1	235	8	11	8.9999
UGA	chr13:19684290-19684525(-)$1	235	26	29	8.9999
UGA	chr5:122903658-122903893(-)$1	235	0	3	8.9999
UGA	chr15:4104168-4104412(+)$1	244	12	15	8.9999
UGA	chr1:190035104-190035339(+)$1	235	1	4	8.9999
UGA	chr2:72245204-72245439(+)$1	235	2	5	8.9999
UGA	chr5:136384853-136385106(-)$1	253	12	15	8.9999
UGA	chr12:52710630-52710865(-)$1	235	12	15	8.9999
UGA	chr19:43574327-43574562(-)$1	235	19	22	8.9999
UGA	chr3:103545044-103545290(-)$1	246	53	56	8.9999
uga	chr8:125154020-125154255(-)$1	235	14	17	8.9999
UGA	chr2:72244950-72245202(+)$1	252	55	58	8.9999
UGA	chr11:50108323-50108564(-)$1	241	5	8	8.9999
UGA	chrX:102993034-102993276(-)$1	242	10	13	8.9999
UGA	chr16:96289023-96289273(-)$1	250	111	114	8.9999
UGA	chr11:50108261-50108515(-)$1	254	213	216	8.9999
UGA	chrX:39150455-39150694(-)$1	239	37	40	8.9999
UGA	chr1:34869058-34869293(+)$1	235	44	47	8.9999
UGA	chr7:104497391-104497626(+)$1	235	9	12	8.9999
UGA	chr15:79657552-79657796(-)$1	244	18	21	8.9999
UGA	chr1:123202257-123202496(-)$1	239	11	14	8.9999
UGA	chr10:81028331-81028570(+)$1	239	85	88	8.9999
UGA	chr1:166367593-166367844(-)$1	251	81	84	8.9999
UGA	chr9:58499729-58499990(+)$1	261	18	21	8.9999
UGA	chr6:108808308-108808543(+)$1	235	44	47	8.9999
UGA	chr16:57152881-57153132(+)$1	251	27	30	8.9999
UGA	chr5:33590727-33590969(-)$1	242	146	149	8.9999
UGA	chr8:71429898-71430160(+)$1	262	18	21	8.9999
UGA	chr3:22113353-22113588(+)$1	235	4	7	8.9999
UGA	chr7:146764317-146764554(+)$1	237	121	124	8.9999
UGA	chr17:80249097-80249332(-)$1	235	26	29	8.9999
UGA	chr7:120043232-120043478(+)$1	246	149	152	8.9999
UGA	chr6:124885829-124886072(+)$1	243	8	11	8.9999
UGA	chr6:119524930-119525172(-)$1	242	34	37	8.9999
UGA	chr19:57111016-57111251(-)$1	235	93	96	8.9999
UGA	chr2:103900277-103900539(+)$1	262	61	64	8.9999
UGA	chr6:30404433-30404668(+)$1	235	43	46	8.9999
UGA	chr11:74490419-74490654(-)$1	235	19	22	8.9999
UGA	chr7:135583316-135583554(-)$1	238	85	88	8.9999
UGA	chr10:110732785-110733047(+)$1	262	135	138	8.9999
UGA	chr11:62215867-62216106(-)$1	239	10	13	8.9999
UGA	chr3:7444770-7445008(+)$1	238	29	32	8.9999
UGA	chr14:35340832-35341082(-)$1	250	38	41	8.9999
UGA	chr2:73157791-73158026(+)$1	235	33	36	8.9999
UGA	chr7:35130774-35131009(-)$1	235	5	8	8.9999
UGA	chr1:191032649-191032887(-)$1	238	40	43	8.9999
UGA	chr3:104459972-104460212(+)$1	240	29	32	8.9999
UGA	chr4:6321962-6322226(+)$1	264	8	11	8.9999
UGA	chr2:155214408-155214646(+)$1	238	23	26	8.9999
UGA	chr9:30957253-30957494(-)$1	241	3	6	8.9999
UGA	chr7:120042256-120042492(+)$1	236	49	52	8.9999
UGA	chr4:15844545-15844787(-)$1	242	34	37	8.9999
UGA	chr2:6462887-6463179(-)$1	292	138	141	8.9999
UGA	chr18:4994934-4995169(+)$1	235	9	12	8.9999
UGA	chr9:42772398-42772633(-)$1	235	40	43	8.9999
UGA	chr7:134861138-134861380(+)$1	242	41	44	8.9999
UGA	chr11:53074190-53074441(-)$1	251	59	62	8.9999
UGA	chr1:153210533-153210769(+)$1	236	26	29	8.9999
UGA	chr1:167106634-167106870(-)$1	236	57	60	8.9999
UGA	chr5:108708170-108708410(+)$1	240	92	95	8.9999
UGA	chr5:111093814-111094054(-)$1	240	21	24	8.9999
UGA	chr4:154933049-154933289(+)$1	240	112	115	8.9999
UGA	chr6:39554848-39555083(-)$1	235	10	13	8.9999
UGA	chr11:74488085-74488320(-)$1	235	49	52	8.9999
UGA	chr2:179769162-179769397(+)$1	235	24	27	8.9999
UGA	chr5:136384420-136384663(-)$1	243	8	11	8.9999
UGA	chr6:29324651-29324896(+)$1	245	11	14	8.9999
UGA	chr3:7443032-7443267(+)$1	235	47	50	8.9999
UGA	chr2:104269417-104269656(-)$1	239	30	33	8.9999
UGA	chr1:123201220-123201461(-)$1	241	33	36	8.9999
UGA	chr6:35458992-35459232(-)$1	240	22	25	8.9999
UGA	chr17:87398130-87398365(+)$1	235	149	152	8.9999
UGA	chr18:35750845-35751081(+)$1	236	77	80	8.9999
UGA	chr19:54003973-54004208(+)$1	235	9	12	8.9999
UGA	chr11:68635611-68635852(-)$1	241	8	11	8.9999
UGA	chr17:44174023-44174259(+)$1	236	56	59	8.9999
UGA	chr2:164824339-164824574(+)$1	235	32	35	8.9999
UGA	chr9:48463289-48463524(-)$1	235	94	97	8.9999
UGA	chrX:35773906-35774202(-)$1	296	21	24	8.9999
UGA	chr13:114384120-114384358(-)$1	238	57	60	8.9999
UGA	chr15:103029637-103029873(-)$1	236	57	60	8.9999

#otherMatches

#Struct PSSM
:dd	chr5:36943056-36943295(-)$1	239	21	24	8.9999
lff	chr12:71568417-71568671(+)$1	254	10	13	8.9999
:ee	chr11:60884496-60884731(+)$1	235	55	58	8.9999
bb]	chr15:4104066-4104302(+)$1	236	34	37	8.9999
ccc	chr8:71430485-71430793(+)$1	308	75	78	8.9999
{CC	chr8:11834228-11834463(+)$1	235	11	14	8.9999
GGG	chr12:85716749-85716991(-)$1	242	15	18	8.9999
ggg	chr14:21319413-21319648(-)$1	235	96	99	8.9999
dbb	chr2:109739556-109739796(+)$1	240	12	15	8.9999
:::	chr13:102451321-102451579(-)$1	258	7	10	8.9999
eee	chr9:55906171-55906406(+)$1	235	36	39	8.9999
ddd	chrX:70604132-70604375(+)$1	243	5	8	8.9999
ccc	chr10:18576309-18576544(+)$1	235	156	159	8.9999
rrr	chr13:21605280-21605515(-)$1	235	88	91	8.9999
GG:	chr4:134772377-134772627(-)$1	250	122	125	8.9999
hqq	chr3:141965381-141965616(-)$1	235	120	123	8.9999
cpp	chr8:35233273-35233512(+)$1	239	50	53	8.9999
:cc	chr13:74460049-74460289(-)$1	240	48	51	8.9999
ddd	chr17:13208221-13208456(+)$1	235	8	11	8.9999
:::	chr13:19684290-19684525(-)$1	235	26	29	8.9999
:::	chr5:122903658-122903893(-)$1	235	0	3	8.9999
ood	chr15:4104168-4104412(+)$1	244	12	15	8.9999
:::	chr1:190035104-190035339(+)$1	235	1	4	8.9999
:::	chr2:72245204-72245439(+)$1	235	2	5	8.9999
EKK	chr5:136384853-136385106(-)$1	253	12	15	8.9999
FFF	chr12:52710630-52710865(-)$1	235	12	15	8.9999
ccc	chr19:43574327-43574562(-)$1	235	19	22	8.9999
ehh	chr3:103545044-103545290(-)$1	246	53	56	8.9999
G{D	chr8:125154020-125154255(-)$1	235	14	17	8.9999
h""	chr2:72244950-72245202(+)$1	252	55	58	8.9999
[ee	chr11:50108323-50108564(-)$1	241	5	8	8.9999
[dd	chrX:102993034-102993276(-)$1	242	10	13	8.9999
DDD	chr16:96289023-96289273(-)$1	250	111	114	8.9999
D}A	chr11:50108261-50108515(-)$1	254	213	216	8.9999
EMM	chrX:39150455-39150694(-)$1	239	37	40	8.9999
eee	chr1:34869058-34869293(+)$1	235	44	47	8.9999
fff	chr7:104497391-104497626(+)$1	235	9	12	8.9999
gff	chr15:79657552-79657796(-)$1	244	18	21	8.9999
:::	chr1:123202257-123202496(-)$1	239	11	14	8.9999
ddd	chr10:81028331-81028570(+)$1	239	85	88	8.9999
ccm	chr1:166367593-166367844(-)$1	251	81	84	8.9999
]cc	chr9:58499729-58499990(+)$1	261	18	21	8.9999
fff	chr6:108808308-108808543(+)$1	235	44	47	8.9999
fff	chr16:57152881-57153132(+)$1	251	27	30	8.9999
ccc	chr5:33590727-33590969(-)$1	242	146	149	8.9999
ggg	chr8:71429898-71430160(+)$1	262	18	21	8.9999
LLL	chr3:22113353-22113588(+)$1	235	4	7	8.9999
b%%	chr7:146764317-146764554(+)$1	237	121	124	8.9999
FFF	chr17:80249097-80249332(-)$1	235	26	29	8.9999
!cc	chr7:120043232-120043478(+)$1	246	149	152	8.9999
ccc	chr6:124885829-124886072(+)$1	243	8	11	8.9999
bb!	chr6:119524930-119525172(-)$1	242	34	37	8.9999
ccg	chr19:57111016-57111251(-)$1	235	93	96	8.9999
dll	chr2:103900277-103900539(+)$1	262	61	64	8.9999
==l	chr6:30404433-30404668(+)$1	235	43	46	8.9999
c!!	chr11:74490419-74490654(-)$1	235	19	22	8.9999
&&&	chr7:135583316-135583554(-)$1	238	85	88	8.9999
nbb	chr10:110732785-110733047(+)$1	262	135	138	8.9999
FFM	chr11:62215867-62216106(-)$1	239	10	13	8.9999
hhh	chr3:7444770-7445008(+)$1	238	29	32	8.9999
mcc	chr14:35340832-35341082(-)$1	250	38	41	8.9999
:::	chr2:73157791-73158026(+)$1	235	33	36	8.9999
:::	chr7:35130774-35131009(-)$1	235	5	8	8.9999
ccc	chr1:191032649-191032887(-)$1	238	40	43	8.9999
d!!	chr3:104459972-104460212(+)$1	240	29	32	8.9999
JJJ	chr4:6321962-6322226(+)$1	264	8	11	8.9999
ggg	chr2:155214408-155214646(+)$1	238	23	26	8.9999
eee	chr9:30957253-30957494(-)$1	241	3	6	8.9999
gg:	chr7:120042256-120042492(+)$1	236	49	52	8.9999
DDD	chr4:15844545-15844787(-)$1	242	34	37	8.9999
fff	chr2:6462887-6463179(-)$1	292	138	141	8.9999
eee	chr18:4994934-4995169(+)$1	235	9	12	8.9999
[dd	chr9:42772398-42772633(-)$1	235	40	43	8.9999
4cc	chr7:134861138-134861380(+)$1	242	41	44	8.9999
e%%	chr11:53074190-53074441(-)$1	251	59	62	8.9999
:EE	chr1:153210533-153210769(+)$1	236	26	29	8.9999
d[e	chr1:167106634-167106870(-)$1	236	57	60	8.9999
hhh	chr5:108708170-108708410(+)$1	240	92	95	8.9999
C::	chr5:111093814-111094054(-)$1	240	21	24	8.9999
]cc	chr4:154933049-154933289(+)$1	240	112	115	8.9999
:FF	chr6:39554848-39555083(-)$1	235	10	13	8.9999
ddd	chr11:74488085-74488320(-)$1	235	49	52	8.9999
gee	chr2:179769162-179769397(+)$1	235	24	27	8.9999
DEE	chr5:136384420-136384663(-)$1	243	8	11	8.9999
mmm	chr6:29324651-29324896(+)$1	245	11	14	8.9999
ppp	chr3:7443032-7443267(+)$1	235	47	50	8.9999
DDD	chr2:104269417-104269656(-)$1	239	30	33	8.9999
EEE	chr1:123201220-123201461(-)$1	241	33	36	8.9999
ddd	chr6:35458992-35459232(-)$1	240	22	25	8.9999
ooe	chr17:87398130-87398365(+)$1	235	149	152	8.9999
:::	chr18:35750845-35751081(+)$1	236	77	80	8.9999
HHH	chr19:54003973-54004208(+)$1	235	9	12	8.9999
JJJ	chr11:68635611-68635852(-)$1	241	8	11	8.9999
qqq	chr17:44174023-44174259(+)$1	236	56	59	8.9999
C{A	chr2:164824339-164824574(+)$1	235	32	35	8.9999
ggg	chr9:48463289-48463524(-)$1	235	94	97	8.9999
ppp	chrX:35773906-35774202(-)$1	296	21	24	8.9999
bb2	chr13:114384120-114384358(-)$1	238	57	60	8.9999
fff	chr15:103029637-103029873(-)$1	236	57	60	8.9999

#DB
.((	chr5:36943056-36943295(-)$1	1	21	24	8.9999
.))	chr12:71568417-71568671(+)$1	1	10	13	8.9999
.((	chr11:60884496-60884731(+)$1	1	55	58	8.9999
)).	chr15:4104066-4104302(+)$1	1	34	37	8.9999
(((	chr8:71430485-71430793(+)$1	1	75	78	8.9999
.((	chr8:11834228-11834463(+)$1	1	11	14	8.9999
(((	chr12:85716749-85716991(-)$1	1	15	18	8.9999
)))	chr14:21319413-21319648(-)$1	1	96	99	8.9999
(((	chr2:109739556-109739796(+)$1	1	12	15	8.9999
...	chr13:102451321-102451579(-)$1	1	7	10	8.9999
)))	chr9:55906171-55906406(+)$1	1	36	39	8.9999
(((	chrX:70604132-70604375(+)$1	1	5	8	8.9999
(((	chr10:18576309-18576544(+)$1	1	156	159	8.9999
...	chr13:21605280-21605515(-)$1	1	88	91	8.9999
((.	chr4:134772377-134772627(-)$1	1	122	125	8.9999
(..	chr3:141965381-141965616(-)$1	1	120	123	8.9999
(..	chr8:35233273-35233512(+)$1	1	50	53	8.9999
.((	chr13:74460049-74460289(-)$1	1	48	51	8.9999
(((	chr17:13208221-13208456(+)$1	1	8	11	8.9999
...	chr13:19684290-19684525(-)$1	1	26	29	8.9999
...	chr5:122903658-122903893(-)$1	1	0	3	8.9999
..)	chr15:4104168-4104412(+)$1	1	12	15	8.9999
...	chr1:190035104-190035339(+)$1	1	1	4	8.9999
...	chr2:72245204-72245439(+)$1	1	2	5	8.9999
(..	chr5:136384853-136385106(-)$1	1	12	15	8.9999
(((	chr12:52710630-52710865(-)$1	1	12	15	8.9999
(((	chr19:43574327-43574562(-)$1	1	19	22	8.9999
)))	chr3:103545044-103545290(-)$1	1	53	56	8.9999
(.(	chr8:125154020-125154255(-)$1	1	14	17	8.9999
(..	chr2:72244950-72245202(+)$1	1	55	58	8.9999
.((	chr11:50108323-50108564(-)$1	1	5	8	8.9999
.((	chrX:102993034-102993276(-)$1	1	10	13	8.9999
(((	chr16:96289023-96289273(-)$1	1	111	114	8.9999
).)	chr11:50108261-50108515(-)$1	1	213	216	8.9999
(..	chrX:39150455-39150694(-)$1	1	37	40	8.9999
(((	chr1:34869058-34869293(+)$1	1	44	47	8.9999
(((	chr7:104497391-104497626(+)$1	1	9	12	8.9999
(((	chr15:79657552-79657796(-)$1	1	18	21	8.9999
...	chr1:123202257-123202496(-)$1	1	11	14	8.9999
(((	chr10:81028331-81028570(+)$1	1	85	88	8.9999
((.	chr1:166367593-166367844(-)$1	1	81	84	8.9999
.))	chr9:58499729-58499990(+)$1	1	18	21	8.9999
)))	chr6:108808308-108808543(+)$1	1	44	47	8.9999
)))	chr16:57152881-57153132(+)$1	1	27	30	8.9999
)))	chr5:33590727-33590969(-)$1	1	146	149	8.9999
(((	chr8:71429898-71430160(+)$1	1	18	21	8.9999
...	chr3:22113353-22113588(+)$1	1	4	7	8.9999
(..	chr7:146764317-146764554(+)$1	1	121	124	8.9999
(((	chr17:80249097-80249332(-)$1	1	26	29	8.9999
.((	chr7:120043232-120043478(+)$1	1	149	152	8.9999
(((	chr6:124885829-124886072(+)$1	1	8	11	8.9999
((.	chr6:119524930-119525172(-)$1	1	34	37	8.9999
)))	chr19:57111016-57111251(-)$1	1	93	96	8.9999
(..	chr2:103900277-103900539(+)$1	1	61	64	8.9999
((.	chr6:30404433-30404668(+)$1	1	43	46	8.9999
(..	chr11:74490419-74490654(-)$1	1	19	22	8.9999
...	chr7:135583316-135583554(-)$1	1	85	88	8.9999
.))	chr10:110732785-110733047(+)$1	1	135	138	8.9999
((.	chr11:62215867-62216106(-)$1	1	10	13	8.9999
)))	chr3:7444770-7445008(+)$1	1	29	32	8.9999
.))	chr14:35340832-35341082(-)$1	1	38	41	8.9999
...	chr2:73157791-73158026(+)$1	1	33	36	8.9999
...	chr7:35130774-35131009(-)$1	1	5	8	8.9999
(((	chr1:191032649-191032887(-)$1	1	40	43	8.9999
(..	chr3:104459972-104460212(+)$1	1	29	32	8.9999
(((	chr4:6321962-6322226(+)$1	1	8	11	8.9999
)))	chr2:155214408-155214646(+)$1	1	23	26	8.9999
(((	chr9:30957253-30957494(-)$1	1	3	6	8.9999
)).	chr7:120042256-120042492(+)$1	1	49	52	8.9999
(((	chr4:15844545-15844787(-)$1	1	34	37	8.9999
(((	chr2:6462887-6463179(-)$1	1	138	141	8.9999
(((	chr18:4994934-4995169(+)$1	1	9	12	8.9999
.((	chr9:42772398-42772633(-)$1	1	40	43	8.9999
.))	chr7:134861138-134861380(+)$1	1	41	44	8.9999
(..	chr11:53074190-53074441(-)$1	1	59	62	8.9999
.((	chr1:153210533-153210769(+)$1	1	26	29	8.9999
(.(	chr1:167106634-167106870(-)$1	1	57	60	8.9999
)))	chr5:108708170-108708410(+)$1	1	92	95	8.9999
(..	chr5:111093814-111094054(-)$1	1	21	24	8.9999
.))	chr4:154933049-154933289(+)$1	1	112	115	8.9999
.((	chr6:39554848-39555083(-)$1	1	10	13	8.9999
(((	chr11:74488085-74488320(-)$1	1	49	52	8.9999
(((	chr2:179769162-179769397(+)$1	1	24	27	8.9999
(((	chr5:136384420-136384663(-)$1	1	8	11	8.9999
...	chr6:29324651-29324896(+)$1	1	11	14	8.9999
...	chr3:7443032-7443267(+)$1	1	47	50	8.9999
(((	chr2:104269417-104269656(-)$1	1	30	33	8.9999
(((	chr1:123201220-123201461(-)$1	1	33	36	8.9999
(((	chr6:35458992-35459232(-)$1	1	22	25	8.9999
..)	chr17:87398130-87398365(+)$1	1	149	152	8.9999
...	chr18:35750845-35751081(+)$1	1	77	80	8.9999
(((	chr19:54003973-54004208(+)$1	1	9	12	8.9999
(((	chr11:68635611-68635852(-)$1	1	8	11	8.9999
...	chr17:44174023-44174259(+)$1	1	56	59	8.9999
(.(	chr2:164824339-164824574(+)$1	1	32	35	8.9999
)))	chr9:48463289-48463524(-)$1	1	94	97	8.9999
...	chrX:35773906-35774202(-)$1	1	21	24	8.9999
)).	chr13:114384120-114384358(-)$1	1	57	60	8.9999
)))	chr15:103029637-103029873(-)$1	1	57	60	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m2_run1.nuc.txt

#NT
UGCAG	chr2:37417357-37417577(+)$1	220	9	14	15.0000
UGCAG	chr8:13171225-13171446(+)$1	221	204	209	15.0000
UGCAG	chr6:86975413-86975636(+)$1	223	74	79	15.0000
UGCAG	chr3:54500775-54500996(+)$1	221	29	34	15.0000
UGCAG	chr11:119756125-119756345(+)$1	220	33	38	15.0000
UGCAG	chr6:83007275-83007499(+)$1	224	73	78	15.0000
UGCAG	chr14:20587472-20587692(+)$1	220	100	105	15.0000
UGCAG	chr8:77645347-77645588(+)$1	241	133	138	15.0000
UGCAG	chr17:35261393-35261613(+)$1	220	71	76	15.0000
UGCAG	chr4:63240905-63241128(+)$1	223	95	100	15.0000
UGCAG	chr12:71565289-71565509(+)$1	220	92	97	15.0000
UGCAG	chr8:74670246-74670468(+)$1	222	99	104	15.0000
UGCAG	chr1:169280317-169280537(+)$1	220	60	65	15.0000
UGCAG	chr7:25704615-25704839(+)$1	224	205	210	15.0000
Ugcag	chrX:74891666-74891886(+)$1	220	2	7	15.0000
UGCAG	chrX:99338507-99338744(-)$1	237	169	174	15.0000
UGCAG	chr2:148509683-148509911(+)$1	228	39	44	15.0000
UGCAG	chr5:124261292-124261521(+)$1	229	197	202	15.0000
UGCAG	chr11:4821839-4822070(+)$1	231	2	7	15.0000
UGCAG	chr4:44376581-44376809(+)$1	228	47	52	15.0000
UGCAG	chr13:23844519-23844739(+)$1	220	6	11	15.0000
UGCAG	chr5:87249080-87249300(+)$1	220	115	120	15.0000
UGCAG	chr7:63471116-63471336(+)$1	220	95	100	15.0000
UGCAG	chr9:55071153-55071373(+)$1	220	15	20	15.0000
UGCAG	chr9:103238305-103238531(+)$1	226	42	47	15.0000
UGCAG	chr7:142885042-142885262(-)$1	220	142	147	15.0000
UGCAG	chr17:36117966-36118187(+)$1	221	114	119	15.0000
UGCAG	chr13:12524018-12524238(+)$1	220	101	106	15.0000
UGCAG	chr18:67564897-67565117(-)$1	220	195	200	15.0000
UGCAG	chr11:95906480-95906720(+)$1	240	122	127	15.0000
UGCAG	chr5:31807265-31807518(+)$1	253	125	130	15.0000
UGCAG	chr19:35004146-35004366(+)$1	220	76	81	15.0000
UGCAG	chr12:34122587-34122807(+)$1	220	114	119	15.0000
UGCAG	chr1:39601923-39602143(+)$1	220	54	59	15.0000
UGCAG	chr3:134909866-134910088(+)$1	222	32	37	15.0000
UGCAG	chr17:13115461-13115681(+)$1	220	168	173	15.0000
UGCAG	chr14:48305839-48306074(+)$1	235	195	200	15.0000
UGCAG	chr8:23320756-23320977(+)$1	221	204	209	15.0000
UGCAG	chr9:67746404-67746662(+)$1	258	86	91	15.0000
UGCAG	chr12:70397943-70398164(+)$1	221	26	31	15.0000
UGCAG	chr11:75305430-75305650(+)$1	220	104	109	15.0000
UGCAG	chr15:82000147-82000371(+)$1	224	168	173	15.0000
UGCAG	chr19:8837157-8837379(+)$1	222	105	110	15.0000
UGCAG	chr8:86439302-86439549(+)$1	247	109	114	15.0000
UGCAG	chr1:152271694-152271914(+)$1	220	208	213	15.0000
UGCAG	chr2:120229586-120229806(-)$1	220	105	110	15.0000
UGCAG	chr7:13610548-13610768(+)$1	220	36	41	15.0000
UGCAG	chr2:104598571-104598796(-)$1	225	44	49	15.0000
UGCAG	chr8:13796466-13796698(+)$1	232	142	147	15.0000

#otherMatches

#Struct PSSM
ee22c	chr11:102770274-102770494(-)$1	220	135	140	15.0000
[gggg	chr2:37417357-37417577(+)$1	220	9	14	15.0000
2ffff	chr8:13171225-13171446(+)$1	221	204	209	15.0000
cc!!d	chr6:86975413-86975636(+)$1	223	74	79	15.0000
hhh""	chr3:54500775-54500996(+)$1	221	29	34	15.0000
fffff	chr11:119756125-119756345(+)$1	220	33	38	15.0000
fff!!	chr6:83007275-83007499(+)$1	224	73	78	15.0000
EEKKC	chr14:20587472-20587692(+)$1	220	100	105	15.0000
mmmmd	chr8:77645347-77645588(+)$1	241	133	138	15.0000
bb22b	chr17:35261393-35261613(+)$1	220	71	76	15.0000
mmeee	chr4:63240905-63241128(+)$1	223	95	100	15.0000
pdddd	chr12:71565289-71565509(+)$1	220	92	97	15.0000
bbEEE	chr8:74670246-74670468(+)$1	222	99	104	15.0000
ddd::	chr1:169280317-169280537(+)$1	220	60	65	15.0000
ldddd	chr7:25704615-25704839(+)$1	224	205	210	15.0000
:JJJJ	chrX:74891666-74891886(+)$1	220	2	7	15.0000
fff::	chrX:99338507-99338744(-)$1	237	169	174	15.0000
d]ccc	chr2:148509683-148509911(+)$1	228	39	44	15.0000
]dddd	chr5:124261292-124261521(+)$1	229	197	202	15.0000
FFFFF	chr11:4821839-4822070(+)$1	231	2	7	15.0000
oobb]	chr4:44376581-44376809(+)$1	228	47	52	15.0000
HH:::	chr13:23844519-23844739(+)$1	220	6	11	15.0000
ggggg	chr5:87249080-87249300(+)$1	220	115	120	15.0000
:bb[b	chr7:63471116-63471336(+)$1	220	95	100	15.0000
mmmcc	chr9:55071153-55071373(+)$1	220	15	20	15.0000
hhhhh	chr9:103238305-103238531(+)$1	226	42	47	15.0000
ee]ee	chr7:142885042-142885262(-)$1	220	142	147	15.0000
c333d	chr17:36117966-36118187(+)$1	221	114	119	15.0000
fffff	chr13:12524018-12524238(+)$1	220	101	106	15.0000
c]a44	chr18:67564897-67565117(-)$1	220	195	200	15.0000
cdddd	chr11:95906480-95906720(+)$1	240	122	127	15.0000
e[all	chr5:31807265-31807518(+)$1	253	125	130	15.0000
ggggg	chr19:35004146-35004366(+)$1	220	76	81	15.0000
:::::	chr12:34122587-34122807(+)$1	220	114	119	15.0000
hhhhh	chr1:39601923-39602143(+)$1	220	54	59	15.0000
2dddd	chr3:134909866-134910088(+)$1	222	32	37	15.0000
hhhhl	chr17:13115461-13115681(+)$1	220	168	173	15.0000
ccc44	chr14:48305839-48306074(+)$1	235	195	200	15.0000
EEE::	chr8:23320756-23320977(+)$1	221	204	209	15.0000
''ddd	chr9:67746404-67746662(+)$1	258	86	91	15.0000
b[eee	chr12:70397943-70398164(+)$1	221	26	31	15.0000
[cccm	chr11:75305430-75305650(+)$1	220	104	109	15.0000
ccnnn	chr15:82000147-82000371(+)$1	224	168	173	15.0000
g[app	chr19:8837157-8837379(+)$1	222	105	110	15.0000
5555d	chr8:86439302-86439549(+)$1	247	109	114	15.0000
}GGGG	chr1:152271694-152271914(+)$1	220	208	213	15.0000
eeeee	chr2:120229586-120229806(-)$1	220	105	110	15.0000
b]ddd	chr7:13610548-13610768(+)$1	220	36	41	15.0000
DDDNN	chr2:104598571-104598796(-)$1	225	44	49	15.0000
44ddd	chr8:13796466-13796698(+)$1	232	142	147	15.0000

#DB
))..)	chr11:102770274-102770494(-)$1	1	135	140	15.0000
.((((	chr2:37417357-37417577(+)$1	1	9	14	15.0000
.))))	chr8:13171225-13171446(+)$1	1	204	209	15.0000
((..(	chr6:86975413-86975636(+)$1	1	74	79	15.0000
(((..	chr3:54500775-54500996(+)$1	1	29	34	15.0000
(((((	chr11:119756125-119756345(+)$1	1	33	38	15.0000
(((..	chr6:83007275-83007499(+)$1	1	73	78	15.0000
((..(	chr14:20587472-20587692(+)$1	1	100	105	15.0000
....)	chr8:77645347-77645588(+)$1	1	133	138	15.0000
))..)	chr17:35261393-35261613(+)$1	1	71	76	15.0000
..)))	chr4:63240905-63241128(+)$1	1	95	100	15.0000
.))))	chr12:71565289-71565509(+)$1	1	92	97	15.0000
))(((	chr8:74670246-74670468(+)$1	1	99	104	15.0000
)))..	chr1:169280317-169280537(+)$1	1	60	65	15.0000
.))))	chr7:25704615-25704839(+)$1	1	205	210	15.0000
.((((	chrX:74891666-74891886(+)$1	1	2	7	15.0000
)))..	chrX:99338507-99338744(-)$1	1	169	174	15.0000
).)))	chr2:148509683-148509911(+)$1	1	39	44	15.0000
.))))	chr5:124261292-124261521(+)$1	1	197	202	15.0000
(((((	chr11:4821839-4822070(+)$1	1	2	7	15.0000
..)).	chr4:44376581-44376809(+)$1	1	47	52	15.0000
((...	chr13:23844519-23844739(+)$1	1	6	11	15.0000
)))))	chr5:87249080-87249300(+)$1	1	115	120	15.0000
.((.(	chr7:63471116-63471336(+)$1	1	95	100	15.0000
...))	chr9:55071153-55071373(+)$1	1	15	20	15.0000
)))))	chr9:103238305-103238531(+)$1	1	42	47	15.0000
)).))	chr7:142885042-142885262(-)$1	1	142	147	15.0000
)...)	chr17:36117966-36118187(+)$1	1	114	119	15.0000
)))))	chr13:12524018-12524238(+)$1	1	101	106	15.0000
).)..	chr18:67564897-67565117(-)$1	1	195	200	15.0000
)))))	chr11:95906480-95906720(+)$1	1	122	127	15.0000
(.(..	chr5:31807265-31807518(+)$1	1	125	130	15.0000
)))))	chr19:35004146-35004366(+)$1	1	76	81	15.0000
.....	chr12:34122587-34122807(+)$1	1	114	119	15.0000
(((((	chr1:39601923-39602143(+)$1	1	54	59	15.0000
.))))	chr3:134909866-134910088(+)$1	1	32	37	15.0000
((((.	chr17:13115461-13115681(+)$1	1	168	173	15.0000
)))..	chr14:48305839-48306074(+)$1	1	195	200	15.0000
)))..	chr8:23320756-23320977(+)$1	1	204	209	15.0000
..(((	chr9:67746404-67746662(+)$1	1	86	91	15.0000
(.(((	chr12:70397943-70398164(+)$1	1	26	31	15.0000
.(((.	chr11:75305430-75305650(+)$1	1	104	109	15.0000
((...	chr15:82000147-82000371(+)$1	1	168	173	15.0000
(.(..	chr19:8837157-8837379(+)$1	1	105	110	15.0000
....)	chr8:86439302-86439549(+)$1	1	109	114	15.0000
.))))	chr1:152271694-152271914(+)$1	1	208	213	15.0000
(((((	chr2:120229586-120229806(-)$1	1	105	110	15.0000
).)))	chr7:13610548-13610768(+)$1	1	36	41	15.0000
(((..	chr2:104598571-104598796(-)$1	1	44	49	15.0000
..)))	chr8:13796466-13796698(+)$1	1	142	147	15.0000

#PSSM
U : 1.00	
G : 0.98	g : 0.02	
C : 0.98	c : 0.02	
A : 0.98	a : 0.02	
G : 0.98	g : 0.02	

#score	750.0000000000001
#seq	50
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m3_run1.nuc.txt

#NT
CCGCAGG	chr7:117008957-117009223(-)$1	266	88	95	12.8548
CCCCAGU	chr11:53590397-53590671(+)$1	274	196	203	13.4193
CCCGAGG	chr3:121969333-121969624(+)$1	291	103	110	12.5322
CCUCAGG	chr11:117828673-117828943(-)$1	270	205	212	13.1774
CCCCAGG	chr15:79655896-79656195(-)$1	299	30	37	17.2096
CCUCAGG	chr15:75831591-75831876(-)$1	285	238	245	13.1774
CUCCAGG	chr8:74844691-74844960(+)$1	269	81	88	13.1774
ACCCAGG	chr17:46305889-46306171(+)$1	282	240	247	13.4999
CCCUAGG	chr19:24758574-24758848(-)$1	274	157	164	12.5322
CUCCAGG	chr1:62843167-62843435(+)$1	268	155	162	13.1774
CCCCAGC	chr2:153054827-153055101(-)$1	274	46	53	13.7419
UCCCAGG	chr4:147320746-147321041(+)$1	295	249	256	13.4193
CCCCAGU	chr11:79507176-79507447(+)$1	271	88	95	13.4193
CCCCAAG	chr11:68923178-68923496(+)$1	318	57	64	12.6935
CCCCAUG	chr8:125096552-125096860(+)$1	308	281	288	12.6935
ACCCAGG	chr15:79658142-79658416(-)$1	274	132	139	13.4999
CCCCAGC	chr7:72016753-72017039(-)$1	286	55	62	13.7419
UCCCAGG	chr18:24443321-24443593(+)$1	272	217	224	13.4193
CCUCAGG	chr14:55505758-55506035(+)$1	277	107	114	13.1774
CUCCAGG	chr8:74842841-74843113(+)$1	272	198	205	13.1774
GCCCAGG	chr3:95464614-95464908(+)$1	294	226	233	13.2580
CCCCAGG	chr9:90098144-90098412(-)$1	268	145	152	17.2096
CCCCAGG	chr19:8964904-8965185(+)$1	281	64	71	17.2096
ucccagg	chr4:133831673-133831946(-)$1	273	235	242	13.4193
CCUCAGG	chr6:124863939-124864209(-)$1	270	42	49	13.1774
CCCCAGG	chr15:79656085-79656364(-)$1	279	199	206	17.2096
CCCAAGG	chr11:32327052-32327325(+)$1	273	170	177	12.5322
ACCCAGG	chr9:119147934-119148213(-)$1	279	142	149	13.4999
CCCCAGG	chr2:152654266-152654557(-)$1	291	15	22	17.2096
ACCCAGG	chr4:140884838-140885115(+)$1	277	66	73	13.4999
CCUCAGG	chr8:11834072-11834348(+)$1	276	21	28	13.1774
CCCCAGC	chr3:154259844-154260110(-)$1	266	99	106	13.7419
CACCAGG	chr19:5456434-5456714(-)$1	280	21	28	13.1774
CCCCAGC	chr16:98014687-98014959(-)$1	272	187	194	13.7419
CCCCAGU	chr15:81535368-81535654(-)$1	286	70	77	13.4193
CUCCAGG	chr5:138223116-138223399(-)$1	283	36	43	13.1774
CCCCAGA	chr11:29642123-29642419(+)$1	296	121	128	13.3387
CACCAGG	chr11:114729900-114730186(+)$1	286	17	24	13.1774
CCCCAGC	chr5:137968786-137969068(+)$1	282	40	47	13.7419
CCCCAGG	chr17:34791868-34792151(+)$1	283	44	51	17.2096
CCACAGG	chr2:32134292-32134577(-)$1	285	20	27	12.8548
ACCCAGG	chr15:81678793-81679086(-)$1	293	46	53	13.4999
CCCCagg	chr10:86297866-86298144(+)$1	278	109	116	17.2096
CCCCAGG	chr7:107985018-107985335(+)$1	317	66	73	17.2096
CCCCAGG	chr16:91227771-91228058(+)$1	287	149	156	17.2096
CCCCAGG	chr18:34930961-34931234(+)$1	273	202	209	17.2096
CCCCUGG	chr17:57032824-57033135(-)$1	311	234	241	12.4516
CCCCAGG	chr10:127827760-127828042(+)$1	282	232	239	17.2096
CCCCAGC	chr16:37882822-37883102(+)$1	280	159	166	13.7419
CCCCAGG	chr17:34791800-34792094(+)$1	294	112	119	17.2096
CCCCAGG	chr2:30882339-30882614(-)$1	275	181	188	17.2096
CCCCAGC	chr16:37882880-37883165(+)$1	285	101	108	13.7419
UCCCAGG	chr1:133921794-133922065(+)$1	271	69	76	13.4193
CACCAGG	chr3:32240090-32240398(-)$1	308	161	168	13.1774
CCCCCGG	chr5:108863240-108863508(-)$1	268	134	141	12.4516
CCCCAAG	chr15:101926286-101926567(+)$1	281	39	46	12.6935
CCCCAUG	chr8:109599437-109599706(-)$1	269	75	82	12.6935
CACCAGG	chr2:31615419-31615714(+)$1	295	242	249	13.1774
GCCCAGG	chr7:152050685-152050968(+)$1	283	225	232	13.2580
CCCCAGG	chr7:51506862-51507143(+)$1	281	66	73	17.2096
CCCCAGA	chr11:117828172-117828460(-)$1	288	234	241	13.3387

#otherMatches

#Struct PSSM
cc]bbbb	chr15:89012665-89012935(-)$1	270	156	163	17.2096
eeeeeec	chr7:117008957-117009223(-)$1	266	88	95	12.8548
EEEEE||	chr11:53590397-53590671(+)$1	274	196	203	13.4193
nnnnnee	chr3:121969333-121969624(+)$1	291	103	110	12.5322
=======	chr11:117828673-117828943(-)$1	270	205	212	13.1774
nnnnnhh	chr15:79655896-79656195(-)$1	299	30	37	17.2096
ddd]ccc	chr15:75831591-75831876(-)$1	285	238	245	13.1774
nnnnggg	chr8:74844691-74844960(+)$1	269	81	88	13.1774
CCC:ddd	chr17:46305889-46306171(+)$1	282	240	247	13.4999
bblllbb	chr19:24758574-24758848(-)$1	274	157	164	12.5322
[ddddcc	chr1:62843167-62843435(+)$1	268	155	162	13.1774
ee:::bb	chr2:153054827-153055101(-)$1	274	46	53	13.7419
%%%%ddd	chr4:147320746-147321041(+)$1	295	249	256	13.4193
DDDD:::	chr11:79507176-79507447(+)$1	271	88	95	13.4193
!ddddll	chr11:68923178-68923496(+)$1	318	57	64	12.6935
ffbb]bb	chr8:125096552-125096860(+)$1	308	281	288	12.6935
e]adddd	chr15:79658142-79658416(-)$1	274	132	139	13.4999
dd22ddd	chr7:72016753-72017039(-)$1	286	55	62	13.7419
llleeee	chr18:24443321-24443593(+)$1	272	217	224	13.4193
:ffffff	chr14:55505758-55506035(+)$1	277	107	114	13.1774
eeellle	chr8:74842841-74843113(+)$1	272	198	205	13.1774
:::::DD	chr3:95464614-95464908(+)$1	294	226	233	13.2580
=======	chr9:90098144-90098412(-)$1	268	145	152	17.2096
:::dddd	chr19:8964904-8965185(+)$1	281	64	71	17.2096
JJJ:ddd	chr4:133831673-133831946(-)$1	273	235	242	13.4193
"""dddd	chr6:124863939-124864209(-)$1	270	42	49	13.1774
nnnnngg	chr15:79656085-79656364(-)$1	279	199	206	17.2096
d!!dddd	chr11:32327052-32327325(+)$1	273	170	177	12.5322
]ccc]ee	chr9:119147934-119148213(-)$1	279	142	149	13.4999
KKIIIII	chr2:152654266-152654557(-)$1	291	15	22	17.2096
22ggggg	chr4:140884838-140885115(+)$1	277	66	73	13.4999
bblllbb	chr8:11834072-11834348(+)$1	276	21	28	13.1774
ppppppp	chr3:154259844-154260110(-)$1	266	99	106	13.7419
]eeeeeC	chr19:5456434-5456714(-)$1	280	21	28	13.1774
f::::BB	chr16:98014687-98014959(-)$1	272	187	194	13.7419
dddcccl	chr15:81535368-81535654(-)$1	286	70	77	13.4193
gggg:::	chr5:138223116-138223399(-)$1	283	36	43	13.1774
hhh&&&&	chr11:29642123-29642419(+)$1	296	121	128	13.3387
c!!a[ff	chr11:114729900-114730186(+)$1	286	17	24	13.1774
iii22bb	chr5:137968786-137969068(+)$1	282	40	47	13.7419
eeea:BB	chr17:34791868-34792151(+)$1	283	44	51	17.2096
:::DDDD	chr2:32134292-32134577(-)$1	285	20	27	12.8548
dddyyyy	chr15:81678793-81679086(-)$1	293	46	53	13.4999
ZZFFFFF	chr10:86297866-86298144(+)$1	278	109	116	17.2096
=======	chr7:107985018-107985335(+)$1	317	66	73	17.2096
sssgggg	chr16:91227771-91228058(+)$1	287	149	156	17.2096
bmmmmbb	chr18:34930961-34931234(+)$1	273	202	209	17.2096
dd:::EE	chr17:57032824-57033135(-)$1	311	234	241	12.4516
mbb]eee	chr10:127827760-127828042(+)$1	282	232	239	17.2096
d!!dddd	chr16:37882822-37883102(+)$1	280	159	166	13.7419
}CCCYYA	chr17:34791800-34792094(+)$1	294	112	119	17.2096
cc]eeee	chr2:30882339-30882614(-)$1	275	181	188	17.2096
qa]ccc]	chr16:37882880-37883165(+)$1	285	101	108	13.7419
iiiii""	chr1:133921794-133922065(+)$1	271	69	76	13.4193
:::::GG	chr3:32240090-32240398(-)$1	308	161	168	13.1774
d"""ccc	chr5:108863240-108863508(-)$1	268	134	141	12.4516
hhhlllh	chr15:101926286-101926567(+)$1	281	39	46	12.6935
c55555d	chr8:109599437-109599706(-)$1	269	75	82	12.6935
GGGGGZZ	chr2:31615419-31615714(+)$1	295	242	249	13.1774
4444bb]	chr7:152050685-152050968(+)$1	283	225	232	13.2580
ccmmmmc	chr7:51506862-51507143(+)$1	281	66	73	17.2096
FFFFFFY	chr11:117828172-117828460(-)$1	288	234	241	13.3387

#DB
)).))((	chr15:89012665-89012935(-)$1	1	156	163	17.2096
(((((((	chr7:117008957-117009223(-)$1	1	88	95	12.8548
)))))..	chr11:53590397-53590671(+)$1	1	196	203	13.4193
.....))	chr3:121969333-121969624(+)$1	1	103	110	12.5322
(((((((	chr11:117828673-117828943(-)$1	1	205	212	13.1774
.....))	chr15:79655896-79656195(-)$1	1	30	37	17.2096
))).)))	chr15:75831591-75831876(-)$1	1	238	245	13.1774
....)))	chr8:74844691-74844960(+)$1	1	81	88	13.1774
))).(((	chr17:46305889-46306171(+)$1	1	240	247	13.4999
((...))	chr19:24758574-24758848(-)$1	1	157	164	12.5322
.((((((	chr1:62843167-62843435(+)$1	1	155	162	13.1774
))...((	chr2:153054827-153055101(-)$1	1	46	53	13.7419
....(((	chr4:147320746-147321041(+)$1	1	249	256	13.4193
((((...	chr11:79507176-79507447(+)$1	1	88	95	13.4193
.((((..	chr11:68923178-68923496(+)$1	1	57	64	12.6935
)))).))	chr8:125096552-125096860(+)$1	1	281	288	12.6935
).)))))	chr15:79658142-79658416(-)$1	1	132	139	13.4999
))..)))	chr7:72016753-72017039(-)$1	1	55	62	13.7419
...))))	chr18:24443321-24443593(+)$1	1	217	224	13.4193
.((((((	chr14:55505758-55506035(+)$1	1	107	114	13.1774
(((...)	chr8:74842841-74843113(+)$1	1	198	205	13.1774
.....))	chr3:95464614-95464908(+)$1	1	226	233	13.2580
)))))))	chr9:90098144-90098412(-)$1	1	145	152	17.2096
...((((	chr19:8964904-8965185(+)$1	1	64	71	17.2096
))).(((	chr4:133831673-133831946(-)$1	1	235	242	13.4193
...((((	chr6:124863939-124864209(-)$1	1	42	49	13.1774
.....))	chr15:79656085-79656364(-)$1	1	199	206	17.2096
(..((((	chr11:32327052-32327325(+)$1	1	170	177	12.5322
.))).))	chr9:119147934-119148213(-)$1	1	142	149	13.4999
..(((((	chr2:152654266-152654557(-)$1	1	15	22	17.2096
..)))))	chr4:140884838-140885115(+)$1	1	66	73	13.4999
((...))	chr8:11834072-11834348(+)$1	1	21	28	13.1774
.......	chr3:154259844-154260110(-)$1	1	99	106	13.7419
.)))))(	chr19:5456434-5456714(-)$1	1	21	28	13.1774
)....))	chr16:98014687-98014959(-)$1	1	187	194	13.7419
((((((.	chr15:81535368-81535654(-)$1	1	70	77	13.4193
))))...	chr5:138223116-138223399(-)$1	1	36	43	13.1774
(((....	chr11:29642123-29642419(+)$1	1	121	128	13.3387
(..(.((	chr11:114729900-114730186(+)$1	1	17	24	13.1774
)))..))	chr5:137968786-137969068(+)$1	1	40	47	13.7419
)))).((	chr17:34791868-34792151(+)$1	1	44	51	17.2096
...((((	chr2:32134292-32134577(-)$1	1	20	27	12.8548
(((....	chr15:81678793-81679086(-)$1	1	46	53	13.4999
..)))))	chr10:86297866-86298144(+)$1	1	109	116	17.2096
(((((((	chr7:107985018-107985335(+)$1	1	66	73	17.2096
...))))	chr16:91227771-91228058(+)$1	1	149	156	17.2096
(....))	chr18:34930961-34931234(+)$1	1	202	209	17.2096
))...))	chr17:57032824-57033135(-)$1	1	234	241	12.4516
.)).)))	chr10:127827760-127828042(+)$1	1	232	239	17.2096
(..((((	chr16:37882822-37883102(+)$1	1	159	166	13.7419
.)))..)	chr17:34791800-34792094(+)$1	1	112	119	17.2096
)).))))	chr2:30882339-30882614(-)$1	1	181	188	17.2096
.).))).	chr16:37882880-37883165(+)$1	1	101	108	13.7419
(((((..	chr1:133921794-133922065(+)$1	1	69	76	13.4193
.....((	chr3:32240090-32240398(-)$1	1	161	168	13.1774
(...(((	chr5:108863240-108863508(-)$1	1	134	141	12.4516
(((...)	chr15:101926286-101926567(+)$1	1	39	46	12.6935
).....)	chr8:109599437-109599706(-)$1	1	75	82	12.6935
)))))..	chr2:31615419-31615714(+)$1	1	242	249	13.1774
....)).	chr7:152050685-152050968(+)$1	1	225	232	13.2580
((....)	chr7:51506862-51507143(+)$1	1	66	73	17.2096
)))))).	chr11:117828172-117828460(-)$1	1	234	241	13.3387

#PSSM
C : 0.82	A : 0.08	U : 0.04	G : 0.03	u : 0.01	
C : 0.85	U : 0.06	A : 0.06	c : 0.01	
C : 0.87	U : 0.08	G : 0.01	c : 0.01	A : 0.01	
C : 0.93	G : 0.01	U : 0.01	c : 0.01	A : 0.01	
A : 0.93	a : 0.03	U : 0.01	C : 0.01	
G : 0.90	A : 0.03	U : 0.03	g : 0.03	
G : 0.77	C : 0.11	U : 0.04	g : 0.03	A : 0.03	

#score	879.2580645161289
#seq	62
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_transcript_m3_run2.nuc.txt

#NT
UGA	chr10:118654799-118655025(-)$1	226	14	17	8.9999
UGA	chr14:70879957-70880178(-)$1	221	97	100	8.9999
UGA	chr2:30180704-30180926(+)$1	222	86	89	8.9999
UGA	chr14:22656983-22657204(+)$1	221	70	73	8.9999
uga	chr6:30375599-30375818(+)$1	219	7	10	8.9999
UGA	chr2:121976531-121976763(+)$1	232	38	41	8.9999
UGA	chr15:100219465-100219679(-)$1	214	48	51	8.9999
UGA	chr8:87811511-87811744(-)$1	233	39	42	8.9999
UGA	chr8:12834571-12834799(+)$1	228	20	23	8.9999
UGA	chr3:95486120-95486340(-)$1	220	90	93	8.9999
UGA	chr2:160585350-160585568(+)$1	218	125	128	8.9999
UGA	chr1:33537253-33537466(-)$1	213	30	33	8.9999
UGA	chr10:59459122-59459329(-)$1	207	135	138	8.9999
UGA	chr11:22001063-22001286(-)$1	223	150	153	8.9999
UGA	chr5:65814695-65814924(-)$1	229	36	39	8.9999
UGA	chr1:7138187-7138412(+)$1	225	107	110	8.9999
UGA	chr9:54805401-54805636(+)$1	235	0	3	8.9999
UGA	chr11:61717363-61717569(-)$1	206	46	49	8.9999
UGA	chr5:123193823-123194037(-)$1	214	6	9	8.9999
UGA	chr7:112898037-112898248(-)$1	211	6	9	8.9999
UGA	chr1:93008752-93008961(+)$1	209	42	45	8.9999
UGA	chr4:132925713-132925937(+)$1	224	30	33	8.9999
UGA	chr11:115648692-115648901(+)$1	209	97	100	8.9999
UGA	chr19:4834164-4834374(-)$1	210	38	41	8.9999
UGA	chr3:63151948-63152168(+)$1	220	84	87	8.9999
UGA	chr17:57162898-57163116(-)$1	218	61	64	8.9999
UGA	chr18:67978440-67978673(+)$1	233	8	11	8.9999
UGA	chr1:71644888-71645107(-)$1	219	12	15	8.9999
UGA	chrX:148457477-148457700(+)$1	223	1	4	8.9999
UGA	chr13:74476920-74477151(-)$1	231	47	50	8.9999
UGA	chr2:153571912-153572131(+)$1	219	5	8	8.9999
UGA	chr16:85080070-85080293(-)$1	223	158	161	8.9999
UGA	chrX:101500556-101500789(-)$1	233	16	19	8.9999
UGA	chr7:148083504-148083712(+)$1	208	15	18	8.9999
UGA	chr1:181540619-181540827(+)$1	208	8	11	8.9999
UGA	chr3:68811088-68811294(+)$1	206	32	35	8.9999
UGA	chr5:123973984-123974212(-)$1	228	93	96	8.9999
UGA	chr15:12772009-12772217(+)$1	208	12	15	8.9999
UGA	chr9:95877864-95878109(+)$1	245	29	32	8.9999
UGA	chr1:62807320-62807535(+)$1	215	0	3	8.9999
UGA	chr4:135883239-135883466(+)$1	227	2	5	8.9999
UGA	chr19:57731575-57731799(+)$1	224	42	45	8.9999
UGA	chr9:30969254-30969475(-)$1	221	17	20	8.9999
UGA	chr11:21996013-21996239(-)$1	226	32	35	8.9999
UGA	chr4:94639509-94639728(-)$1	219	75	78	8.9999
UGA	chr2:80187798-80188017(+)$1	219	51	54	8.9999
UGA	chr17:35975014-35975244(-)$1	230	142	145	8.9999
UGA	chr9:45759998-45760215(-)$1	217	48	51	8.9999
uga	chr10:104675450-104675686(+)$1	236	93	96	8.9999
UGA	chr16:18808757-18808975(-)$1	218	75	78	8.9999
UGA	chr6:86885478-86885700(+)$1	222	62	65	8.9999
UGA	chr6:84037734-84037960(+)$1	226	69	72	8.9999
UGA	chr3:123085594-123085820(-)$1	226	34	37	8.9999
UGA	chr17:33519133-33519341(-)$1	208	11	14	8.9999
UGA	chr9:35284438-35284651(+)$1	213	146	149	8.9999
UGA	chr11:60055225-60055484(-)$1	259	10	13	8.9999
UGA	chr14:57578538-57578760(+)$1	222	166	169	8.9999
UGA	chr4:43592149-43592365(+)$1	216	69	72	8.9999
UGA	chr8:109862130-109862352(+)$1	222	74	77	8.9999
UGA	chr5:65632105-65632327(+)$1	222	124	127	8.9999
UGA	chr19:38060386-38060612(-)$1	226	46	49	8.9999
UGA	chrX:72766625-72766858(+)$1	233	78	81	8.9999
UGA	chr1:30887543-30887766(-)$1	223	20	23	8.9999
UGA	chr1:54719445-54719654(-)$1	209	47	50	8.9999
UGA	chr15:99946215-99946432(+)$1	217	6	9	8.9999
UGA	chr4:154889650-154889870(+)$1	220	1	4	8.9999
UGA	chr3:152113455-152113673(+)$1	218	28	31	8.9999
UGA	chr2:24680404-24680617(-)$1	213	44	47	8.9999
UGA	chr14:31676298-31676526(+)$1	228	41	44	8.9999
UGA	chr13:55642934-55643169(-)$1	235	13	16	8.9999
UGA	chr18:83174009-83174223(+)$1	214	28	31	8.9999
UGA	chr9:20884114-20884337(-)$1	223	58	61	8.9999
UGA	chr10:122450858-122451074(-)$1	216	2	5	8.9999
UGA	chr10:13852381-13852597(+)$1	216	89	92	8.9999
UGA	chr5:124186278-124186496(-)$1	218	72	75	8.9999
UGA	chr9:122906806-122907027(+)$1	221	65	68	8.9999
UGA	chr11:96663988-96664227(+)$1	239	4	7	8.9999
UGA	chr5:110846789-110847018(-)$1	229	26	29	8.9999
UGA	chr4:151204526-151204747(-)$1	221	37	40	8.9999
UGA	chr2:157116213-157116421(+)$1	208	73	76	8.9999
uga	chr2:128478838-128479062(-)$1	224	28	31	8.9999
uga	chrX:150175518-150175747(+)$1	229	3	6	8.9999
UGA	chr3:151895333-151895551(+)$1	218	111	114	8.9999
UGA	chr5:73472108-73472344(-)$1	236	34	37	8.9999
UGA	chr6:55213686-55213907(+)$1	221	1	4	8.9999
UGA	chr16:34385335-34385553(-)$1	218	20	23	8.9999
UGA	chr9:107994219-107994427(-)$1	208	10	13	8.9999
UGA	chr12:87184656-87184882(+)$1	226	50	53	8.9999
UGA	chr4:122535885-122536096(+)$1	211	44	47	8.9999
UGA	chr19:42225252-42225473(+)$1	221	2	5	8.9999
UGA	chr3:33702390-33702604(+)$1	214	20	23	8.9999
UGA	chr11:30042282-30042514(-)$1	232	47	50	8.9999
UGA	chr9:108912435-108912658(+)$1	223	105	108	8.9999
UGA	chr15:73099160-73099383(-)$1	223	1	4	8.9999
UGA	chr11:77835581-77835791(+)$1	210	46	49	8.9999

#otherMatches

#Struct PSSM
fqq	chr12:77039561-77039795(+)$1	234	10	13	8.9999
fff	chr10:118654799-118655025(-)$1	226	14	17	8.9999
eee	chr14:70879957-70880178(-)$1	221	97	100	8.9999
B}D	chr2:30180704-30180926(+)$1	222	86	89	8.9999
f::	chr14:22656983-22657204(+)$1	221	70	73	8.9999
ggg	chr6:30375599-30375818(+)$1	219	7	10	8.9999
dd]	chr2:121976531-121976763(+)$1	232	38	41	8.9999
]bb	chr15:100219465-100219679(-)$1	214	48	51	8.9999
ff[	chr8:87811511-87811744(-)$1	233	39	42	8.9999
c]b	chr8:12834571-12834799(+)$1	228	20	23	8.9999
iii	chr3:95486120-95486340(-)$1	220	90	93	8.9999
DDD	chr2:160585350-160585568(+)$1	218	125	128	8.9999
:::	chr1:33537253-33537466(-)$1	213	30	33	8.9999
===	chr10:59459122-59459329(-)$1	207	135	138	8.9999
ddd	chr11:22001063-22001286(-)$1	223	150	153	8.9999
ddm	chr5:65814695-65814924(-)$1	229	36	39	8.9999
eee	chr1:7138187-7138412(+)$1	225	107	110	8.9999
:::	chr9:54805401-54805636(+)$1	235	0	3	8.9999
mdd	chr11:61717363-61717569(-)$1	206	46	49	8.9999
:::	chr5:123193823-123194037(-)$1	214	6	9	8.9999
:::	chr7:112898037-112898248(-)$1	211	6	9	8.9999
:cc	chr1:93008752-93008961(+)$1	209	42	45	8.9999
eee	chr4:132925713-132925937(+)$1	224	30	33	8.9999
F{A	chr11:115648692-115648901(+)$1	209	97	100	8.9999
FF{	chr19:4834164-4834374(-)$1	210	38	41	8.9999
II{	chr3:63151948-63152168(+)$1	220	84	87	8.9999
sgg	chr17:57162898-57163116(-)$1	218	61	64	8.9999
FFF	chr18:67978440-67978673(+)$1	233	8	11	8.9999
{DD	chr1:71644888-71645107(-)$1	219	12	15	8.9999
CCC	chrX:148457477-148457700(+)$1	223	1	4	8.9999
hh3	chr13:74476920-74477151(-)$1	231	47	50	8.9999
:::	chr2:153571912-153572131(+)$1	219	5	8	8.9999
:::	chr16:85080070-85080293(-)$1	223	158	161	8.9999
EEE	chrX:101500556-101500789(-)$1	233	16	19	8.9999
rrr	chr7:148083504-148083712(+)$1	208	15	18	8.9999
dd[	chr1:181540619-181540827(+)$1	208	8	11	8.9999
:FF	chr3:68811088-68811294(+)$1	206	32	35	8.9999
hhh	chr5:123973984-123974212(-)$1	228	93	96	8.9999
eee	chr15:12772009-12772217(+)$1	208	12	15	8.9999
===	chr9:95877864-95878109(+)$1	245	29	32	8.9999
:::	chr1:62807320-62807535(+)$1	215	0	3	8.9999
:gg	chr4:135883239-135883466(+)$1	227	2	5	8.9999
ppb	chr19:57731575-57731799(+)$1	224	42	45	8.9999
ccc	chr9:30969254-30969475(-)$1	221	17	20	8.9999
qee	chr11:21996013-21996239(-)$1	226	32	35	8.9999
iii	chr4:94639509-94639728(-)$1	219	75	78	8.9999
ppp	chr2:80187798-80188017(+)$1	219	51	54	8.9999
GGG	chr17:35975014-35975244(-)$1	230	142	145	8.9999
]cc	chr9:45759998-45760215(-)$1	217	48	51	8.9999
ooo	chr10:104675450-104675686(+)$1	236	93	96	8.9999
ooo	chr16:18808757-18808975(-)$1	218	75	78	8.9999
bdd	chr6:86885478-86885700(+)$1	222	62	65	8.9999
ccc	chr6:84037734-84037960(+)$1	226	69	72	8.9999
a))	chr3:123085594-123085820(-)$1	226	34	37	8.9999
DDD	chr17:33519133-33519341(-)$1	208	11	14	8.9999
:DD	chr9:35284438-35284651(+)$1	213	146	149	8.9999
EEE	chr11:60055225-60055484(-)$1	259	10	13	8.9999
ggg	chr14:57578538-57578760(+)$1	222	166	169	8.9999
eee	chr4:43592149-43592365(+)$1	216	69	72	8.9999
===	chr8:109862130-109862352(+)$1	222	74	77	8.9999
b[d	chr5:65632105-65632327(+)$1	222	124	127	8.9999
BB:	chr19:38060386-38060612(-)$1	226	46	49	8.9999
2gg	chrX:72766625-72766858(+)$1	233	78	81	8.9999
:::	chr1:30887543-30887766(-)$1	223	20	23	8.9999
!!c	chr1:54719445-54719654(-)$1	209	47	50	8.9999
KDD	chr15:99946215-99946432(+)$1	217	6	9	8.9999
eee	chr4:154889650-154889870(+)$1	220	1	4	8.9999
===	chr3:152113455-152113673(+)$1	218	28	31	8.9999
bb]	chr2:24680404-24680617(-)$1	213	44	47	8.9999
"bb	chr14:31676298-31676526(+)$1	228	41	44	8.9999
fff	chr13:55642934-55643169(-)$1	235	13	16	8.9999
ddq	chr18:83174009-83174223(+)$1	214	28	31	8.9999
ddd	chr9:20884114-20884337(-)$1	223	58	61	8.9999
:::	chr10:122450858-122451074(-)$1	216	2	5	8.9999
eee	chr10:13852381-13852597(+)$1	216	89	92	8.9999
bb]	chr5:124186278-124186496(-)$1	218	72	75	8.9999
CCC	chr9:122906806-122907027(+)$1	221	65	68	8.9999
::H	chr11:96663988-96664227(+)$1	239	4	7	8.9999
hh[	chr5:110846789-110847018(-)$1	229	26	29	8.9999
d""	chr4:151204526-151204747(-)$1	221	37	40	8.9999
mee	chr2:157116213-157116421(+)$1	208	73	76	8.9999
cc:	chr2:128478838-128479062(-)$1	224	28	31	8.9999
::F	chrX:150175518-150175747(+)$1	229	3	6	8.9999
%cc	chr3:151895333-151895551(+)$1	218	111	114	8.9999
CCC	chr5:73472108-73472344(-)$1	236	34	37	8.9999
:::	chr6:55213686-55213907(+)$1	221	1	4	8.9999
f^^	chr16:34385335-34385553(-)$1	218	20	23	8.9999
EEE	chr9:107994219-107994427(-)$1	208	10	13	8.9999
qqq	chr12:87184656-87184882(+)$1	226	50	53	8.9999
ccc	chr4:122535885-122536096(+)$1	211	44	47	8.9999
:::	chr19:42225252-42225473(+)$1	221	2	5	8.9999
eee	chr3:33702390-33702604(+)$1	214	20	23	8.9999
MDD	chr11:30042282-30042514(-)$1	232	47	50	8.9999
iii	chr9:108912435-108912658(+)$1	223	105	108	8.9999
:::	chr15:73099160-73099383(-)$1	223	1	4	8.9999
g[d	chr11:77835581-77835791(+)$1	210	46	49	8.9999

#DB
(..	chr12:77039561-77039795(+)$1	1	10	13	8.9999
(((	chr10:118654799-118655025(-)$1	1	14	17	8.9999
)))	chr14:70879957-70880178(-)$1	1	97	100	8.9999
).)	chr2:30180704-30180926(+)$1	1	86	89	8.9999
)..	chr14:22656983-22657204(+)$1	1	70	73	8.9999
(((	chr6:30375599-30375818(+)$1	1	7	10	8.9999
)).	chr2:121976531-121976763(+)$1	1	38	41	8.9999
.))	chr15:100219465-100219679(-)$1	1	48	51	8.9999
((.	chr8:87811511-87811744(-)$1	1	39	42	8.9999
).)	chr8:12834571-12834799(+)$1	1	20	23	8.9999
)))	chr3:95486120-95486340(-)$1	1	90	93	8.9999
)))	chr2:160585350-160585568(+)$1	1	125	128	8.9999
...	chr1:33537253-33537466(-)$1	1	30	33	8.9999
)))	chr10:59459122-59459329(-)$1	1	135	138	8.9999
(((	chr11:22001063-22001286(-)$1	1	150	153	8.9999
((.	chr5:65814695-65814924(-)$1	1	36	39	8.9999
(((	chr1:7138187-7138412(+)$1	1	107	110	8.9999
...	chr9:54805401-54805636(+)$1	1	0	3	8.9999
.))	chr11:61717363-61717569(-)$1	1	46	49	8.9999
...	chr5:123193823-123194037(-)$1	1	6	9	8.9999
...	chr7:112898037-112898248(-)$1	1	6	9	8.9999
.((	chr1:93008752-93008961(+)$1	1	42	45	8.9999
)))	chr4:132925713-132925937(+)$1	1	30	33	8.9999
(.(	chr11:115648692-115648901(+)$1	1	97	100	8.9999
((.	chr19:4834164-4834374(-)$1	1	38	41	8.9999
((.	chr3:63151948-63152168(+)$1	1	84	87	8.9999
.))	chr17:57162898-57163116(-)$1	1	61	64	8.9999
(((	chr18:67978440-67978673(+)$1	1	8	11	8.9999
.((	chr1:71644888-71645107(-)$1	1	12	15	8.9999
(((	chrX:148457477-148457700(+)$1	1	1	4	8.9999
)).	chr13:74476920-74477151(-)$1	1	47	50	8.9999
...	chr2:153571912-153572131(+)$1	1	5	8	8.9999
...	chr16:85080070-85080293(-)$1	1	158	161	8.9999
(((	chrX:101500556-101500789(-)$1	1	16	19	8.9999
...	chr7:148083504-148083712(+)$1	1	15	18	8.9999
((.	chr1:181540619-181540827(+)$1	1	8	11	8.9999
.((	chr3:68811088-68811294(+)$1	1	32	35	8.9999
(((	chr5:123973984-123974212(-)$1	1	93	96	8.9999
)))	chr15:12772009-12772217(+)$1	1	12	15	8.9999
(((	chr9:95877864-95878109(+)$1	1	29	32	8.9999
...	chr1:62807320-62807535(+)$1	1	0	3	8.9999
.((	chr4:135883239-135883466(+)$1	1	2	5	8.9999
..)	chr19:57731575-57731799(+)$1	1	42	45	8.9999
(((	chr9:30969254-30969475(-)$1	1	17	20	8.9999
.))	chr11:21996013-21996239(-)$1	1	32	35	8.9999
(((	chr4:94639509-94639728(-)$1	1	75	78	8.9999
...	chr2:80187798-80188017(+)$1	1	51	54	8.9999
)))	chr17:35975014-35975244(-)$1	1	142	145	8.9999
.))	chr9:45759998-45760215(-)$1	1	48	51	8.9999
...	chr10:104675450-104675686(+)$1	1	93	96	8.9999
...	chr16:18808757-18808975(-)$1	1	75	78	8.9999
(((	chr6:86885478-86885700(+)$1	1	62	65	8.9999
)))	chr6:84037734-84037960(+)$1	1	69	72	8.9999
(..	chr3:123085594-123085820(-)$1	1	34	37	8.9999
(((	chr17:33519133-33519341(-)$1	1	11	14	8.9999
.))	chr9:35284438-35284651(+)$1	1	146	149	8.9999
(((	chr11:60055225-60055484(-)$1	1	10	13	8.9999
(((	chr14:57578538-57578760(+)$1	1	166	169	8.9999
(((	chr4:43592149-43592365(+)$1	1	69	72	8.9999
(((	chr8:109862130-109862352(+)$1	1	74	77	8.9999
(.(	chr5:65632105-65632327(+)$1	1	124	127	8.9999
((.	chr19:38060386-38060612(-)$1	1	46	49	8.9999
.))	chrX:72766625-72766858(+)$1	1	78	81	8.9999
...	chr1:30887543-30887766(-)$1	1	20	23	8.9999
..(	chr1:54719445-54719654(-)$1	1	47	50	8.9999
.((	chr15:99946215-99946432(+)$1	1	6	9	8.9999
(((	chr4:154889650-154889870(+)$1	1	1	4	8.9999
(((	chr3:152113455-152113673(+)$1	1	28	31	8.9999
)).	chr2:24680404-24680617(-)$1	1	44	47	8.9999
.((	chr14:31676298-31676526(+)$1	1	41	44	8.9999
(((	chr13:55642934-55643169(-)$1	1	13	16	8.9999
((.	chr18:83174009-83174223(+)$1	1	28	31	8.9999
(((	chr9:20884114-20884337(-)$1	1	58	61	8.9999
...	chr10:122450858-122451074(-)$1	1	2	5	8.9999
)))	chr10:13852381-13852597(+)$1	1	89	92	8.9999
)).	chr5:124186278-124186496(-)$1	1	72	75	8.9999
(((	chr9:122906806-122907027(+)$1	1	65	68	8.9999
..(	chr11:96663988-96664227(+)$1	1	4	7	8.9999
((.	chr5:110846789-110847018(-)$1	1	26	29	8.9999
(..	chr4:151204526-151204747(-)$1	1	37	40	8.9999
.))	chr2:157116213-157116421(+)$1	1	73	76	8.9999
)).	chr2:128478838-128479062(-)$1	1	28	31	8.9999
..(	chrX:150175518-150175747(+)$1	1	3	6	8.9999
.((	chr3:151895333-151895551(+)$1	1	111	114	8.9999
(((	chr5:73472108-73472344(-)$1	1	34	37	8.9999
...	chr6:55213686-55213907(+)$1	1	1	4	8.9999
(..	chr16:34385335-34385553(-)$1	1	20	23	8.9999
(((	chr9:107994219-107994427(-)$1	1	10	13	8.9999
...	chr12:87184656-87184882(+)$1	1	50	53	8.9999
(((	chr4:122535885-122536096(+)$1	1	44	47	8.9999
...	chr19:42225252-42225473(+)$1	1	2	5	8.9999
(((	chr3:33702390-33702604(+)$1	1	20	23	8.9999
.((	chr11:30042282-30042514(-)$1	1	47	50	8.9999
(((	chr9:108912435-108912658(+)$1	1	105	108	8.9999
...	chr15:73099160-73099383(-)$1	1	1	4	8.9999
(.(	chr11:77835581-77835791(+)$1	1	46	49	8.9999

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

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m3_run2.nuc.txt

#NT
UGCU	chr15:38419438-38419673(-)$1	235	18	22	11.9999
UGCU	chr12:4108975-4109237(+)$1	262	107	111	11.9999
UGCU	chr2:75764693-75764928(+)$1	235	111	115	11.9999
UGCU	chr15:31385712-31385954(-)$1	242	224	228	11.9999
UGCU	chr18:34504828-34505089(-)$1	261	2	6	11.9999
UGCU	chr13:23831577-23831839(+)$1	262	65	69	11.9999
UGCU	chr11:50014066-50014324(-)$1	258	36	40	11.9999
UGCU	chr3:141965425-141965660(-)$1	235	107	111	11.9999
UGCU	chr13:59037387-59037622(+)$1	235	152	156	11.9999
UGCU	chr17:87398130-87398377(+)$1	247	67	71	11.9999
UGCU	chrX:99709798-99710042(-)$1	244	117	121	11.9999
UGCU	chr2:153594688-153594923(+)$1	235	33	37	11.9999
UGCU	chr3:126546663-126546898(+)$1	235	103	107	11.9999
UGCU	chr15:76845848-76846084(-)$1	236	59	63	11.9999
UGCU	chr11:29642168-29642473(+)$1	305	39	43	11.9999
UGCU	chr2:180882414-180882658(-)$1	244	144	148	11.9999
UGCU	chr11:29642759-29642996(+)$1	237	10	14	11.9999
UGCU	chr7:20006710-20007002(+)$1	292	150	154	11.9999
UGCU	chr14:37688389-37688624(-)$1	235	82	86	11.9999
UGCU	chr15:103023875-103024111(-)$1	236	41	45	11.9999
UGCU	chr10:59764804-59765062(+)$1	258	120	124	11.9999
UGCU	chr4:150421354-150421589(-)$1	235	44	48	11.9999
UGCU	chr7:138588944-138589179(+)$1	235	66	70	11.9999
UGCU	chr11:94202029-94202276(+)$1	247	117	121	11.9999
UGCU	chr3:60332760-60332997(+)$1	237	107	111	11.9999
UGCU	chr17:10401591-10401830(-)$1	239	195	199	11.9999
UGCU	chr3:51323609-51323852(-)$1	243	25	29	11.9999
UGCU	chr5:15878929-15879164(+)$1	235	10	14	11.9999
UGCU	chr7:99792676-99792911(-)$1	235	26	30	11.9999
UGCU	chr10:39679454-39679689(-)$1	235	175	179	11.9999
UGCU	chr15:12114164-12114401(+)$1	237	67	71	11.9999
UGCU	chr7:139905158-139905393(-)$1	235	65	69	11.9999
UGCU	chr5:36944678-36944920(-)$1	242	66	70	11.9999
UGCU	chr2:174155522-174155762(+)$1	240	115	119	11.9999
UGCU	chr9:102445317-102445562(+)$1	245	40	44	11.9999
UGCU	chr11:51799963-51800205(-)$1	242	35	39	11.9999
UGCU	chr8:114542481-114542716(+)$1	235	10	14	11.9999
UGCU	chr11:29642590-29642878(+)$1	288	7	11	11.9999
UGCU	chr2:6465641-6465886(-)$1	245	40	44	11.9999
UGCU	chr2:152106383-152106623(+)$1	240	22	26	11.9999
UGCU	chr4:153531615-153531858(-)$1	243	10	14	11.9999
UGCU	chr10:127514114-127514349(+)$1	235	74	78	11.9999
UGCU	chr13:21608338-21608573(-)$1	235	24	28	11.9999
UGCU	chr13:97408636-97408876(+)$1	240	77	81	11.9999
UGCU	chr15:4105022-4105266(+)$1	244	18	22	11.9999
UGCU	chr2:152106642-152106889(+)$1	247	81	85	11.9999
UGCU	chr16:94690321-94690556(+)$1	235	209	213	11.9999
UGCU	chr11:50014137-50014377(-)$1	240	40	44	11.9999
UGCU	chr16:4480665-4480901(-)$1	236	12	16	11.9999
UGCU	chr4:6322128-6322363(+)$1	235	164	168	11.9999
UGCU	chr6:71342636-71342873(-)$1	237	75	79	11.9999
UGCU	chr8:88062522-88062769(-)$1	247	36	40	11.9999
UGCU	chr6:5434848-5435110(-)$1	262	17	21	11.9999
UGCU	chr18:32391957-32392192(+)$1	235	7	11	11.9999
UGCU	chr3:138589963-138590208(-)$1	245	122	126	11.9999
UGCU	chr3:120905483-120905743(-)$1	260	68	72	11.9999
UGCU	chr2:180639581-180639817(-)$1	236	17	21	11.9999
UGCU	chr3:69357854-69358091(+)$1	237	100	104	11.9999
UGCU	chr7:122617910-122618153(-)$1	243	155	159	11.9999
UGCU	chr19:44646605-44646848(+)$1	243	143	147	11.9999
UGCU	chr1:54702798-54703044(-)$1	246	0	4	11.9999
UGCU	chr19:47333693-47333940(+)$1	247	10	14	11.9999
UGCU	chr2:155214476-155214718(+)$1	242	37	41	11.9999
UGCU	chr18:34505052-34505293(-)$1	241	143	147	11.9999
UGCU	chr16:36035202-36035440(+)$1	238	37	41	11.9999
UGCU	chr1:36587649-36587884(-)$1	235	71	75	11.9999
UGCU	chr2:72240598-72240836(+)$1	238	49	53	11.9999
UGCU	chr1:180181907-180182144(+)$1	237	54	58	11.9999
UGCU	chr13:29999174-29999409(-)$1	235	20	24	11.9999
UGCU	chr9:14348715-14348958(-)$1	243	231	235	11.9999
UGCU	chr14:21319545-21319780(-)$1	235	38	42	11.9999
UGCU	chr3:144352137-144352377(-)$1	240	54	58	11.9999
UGCU	chr3:51322110-51322367(-)$1	257	30	34	11.9999
UGCU	chr11:75578686-75578922(+)$1	236	29	33	11.9999
UGCU	chr19:12843558-12843801(-)$1	243	117	121	11.9999
UGCU	chr2:118301678-118301913(-)$1	235	9	13	11.9999
UGCU	chr5:136384359-136384619(-)$1	260	143	147	11.9999
UGCU	chr19:47809707-47809942(+)$1	235	56	60	11.9999
UGCU	chr3:89253899-89254141(+)$1	242	121	125	11.9999
UGCU	chr5:67446814-67447060(+)$1	246	221	225	11.9999
UGCU	chr4:147247927-147248162(-)$1	235	4	8	11.9999
Ugcu	chr15:27396439-27396677(+)$1	238	30	34	11.9999
UGCU	chr1:165175599-165175844(-)$1	245	53	57	11.9999
UGCU	chr16:32472416-32472656(+)$1	240	56	60	11.9999

#otherMatches

#Struct PSSM
pccc	chr4:33107838-33108088(+)$1	250	33	37	11.9999
!ddd	chr15:38419438-38419673(-)$1	235	18	22	11.9999
""a!	chr12:4108975-4109237(+)$1	262	107	111	11.9999
22bb	chr2:75764693-75764928(+)$1	235	111	115	11.9999
6eee	chr15:31385712-31385954(-)$1	242	224	228	11.9999
IIII	chr18:34504828-34505089(-)$1	261	2	6	11.9999
JJJJ	chr13:23831577-23831839(+)$1	262	65	69	11.9999
:ccc	chr11:50014066-50014324(-)$1	258	36	40	11.9999
oooo	chr3:141965425-141965660(-)$1	235	107	111	11.9999
ffff	chr13:59037387-59037622(+)$1	235	152	156	11.9999
ffff	chr17:87398130-87398377(+)$1	247	67	71	11.9999
ffff	chrX:99709798-99710042(-)$1	244	117	121	11.9999
dd::	chr2:153594688-153594923(+)$1	235	33	37	11.9999
rrgg	chr3:126546663-126546898(+)$1	235	103	107	11.9999
ddd"	chr15:76845848-76846084(-)$1	236	59	63	11.9999
eeee	chr11:29642168-29642473(+)$1	305	39	43	11.9999
ddnn	chr2:180882414-180882658(-)$1	244	144	148	11.9999
ccc$	chr11:29642759-29642996(+)$1	237	10	14	11.9999
yyyy	chr7:20006710-20007002(+)$1	292	150	154	11.9999
))))	chr14:37688389-37688624(-)$1	235	82	86	11.9999
cccc	chr15:103023875-103024111(-)$1	236	41	45	11.9999
[ddd	chr10:59764804-59765062(+)$1	258	120	124	11.9999
qqqq	chr4:150421354-150421589(-)$1	235	44	48	11.9999
ffff	chr7:138588944-138589179(+)$1	235	66	70	11.9999
eebb	chr11:94202029-94202276(+)$1	247	117	121	11.9999
eeee	chr3:60332760-60332997(+)$1	237	107	111	11.9999
c]dd	chr17:10401591-10401830(-)$1	239	195	199	11.9999
EE{E	chr3:51323609-51323852(-)$1	243	25	29	11.9999
:CCC	chr5:15878929-15879164(+)$1	235	10	14	11.9999
MMFF	chr7:99792676-99792911(-)$1	235	26	30	11.9999
ffff	chr10:39679454-39679689(-)$1	235	175	179	11.9999
ddd!	chr15:12114164-12114401(+)$1	237	67	71	11.9999
2abb	chr7:139905158-139905393(-)$1	235	65	69	11.9999
eeee	chr5:36944678-36944920(-)$1	242	66	70	11.9999
gggg	chr2:174155522-174155762(+)$1	240	115	119	11.9999
dd[e	chr9:102445317-102445562(+)$1	245	40	44	11.9999
ee]c	chr11:51799963-51800205(-)$1	242	35	39	11.9999
BB{D	chr8:114542481-114542716(+)$1	235	10	14	11.9999
gggg	chr11:29642590-29642878(+)$1	288	7	11	11.9999
nddd	chr2:6465641-6465886(-)$1	245	40	44	11.9999
FFFF	chr2:152106383-152106623(+)$1	240	22	26	11.9999
{CCC	chr4:153531615-153531858(-)$1	243	10	14	11.9999
{EEE	chr10:127514114-127514349(+)$1	235	74	78	11.9999
^^^^	chr13:21608338-21608573(-)$1	235	24	28	11.9999
::::	chr13:97408636-97408876(+)$1	240	77	81	11.9999
eeee	chr15:4105022-4105266(+)$1	244	18	22	11.9999
[ccc	chr2:152106642-152106889(+)$1	247	81	85	11.9999
HHHH	chr16:94690321-94690556(+)$1	235	209	213	11.9999
::::	chr11:50014137-50014377(-)$1	240	40	44	11.9999
MFFF	chr16:4480665-4480901(-)$1	236	12	16	11.9999
ffff	chr4:6322128-6322363(+)$1	235	164	168	11.9999
iiii	chr6:71342636-71342873(-)$1	237	75	79	11.9999
GGGG	chr8:88062522-88062769(-)$1	247	36	40	11.9999
mggg	chr6:5434848-5435110(-)$1	262	17	21	11.9999
D:::	chr18:32391957-32392192(+)$1	235	7	11	11.9999
EEEH	chr3:138589963-138590208(-)$1	245	122	126	11.9999
CDDD	chr3:120905483-120905743(-)$1	260	68	72	11.9999
ee!!	chr2:180639581-180639817(-)$1	236	17	21	11.9999
c[ff	chr3:69357854-69358091(+)$1	237	100	104	11.9999
gggg	chr7:122617910-122618153(-)$1	243	155	159	11.9999
$$a!	chr19:44646605-44646848(+)$1	243	143	147	11.9999
:ddd	chr1:54702798-54703044(-)$1	246	0	4	11.9999
[ccc	chr19:47333693-47333940(+)$1	247	10	14	11.9999
!ccc	chr2:155214476-155214718(+)$1	242	37	41	11.9999
ffff	chr18:34505052-34505293(-)$1	241	143	147	11.9999
d::e	chr16:36035202-36035440(+)$1	238	37	41	11.9999
:ggg	chr1:36587649-36587884(-)$1	235	71	75	11.9999
qqqq	chr2:72240598-72240836(+)$1	238	49	53	11.9999
dddd	chr1:180181907-180182144(+)$1	237	54	58	11.9999
LCCC	chr13:29999174-29999409(-)$1	235	20	24	11.9999
2eee	chr9:14348715-14348958(-)$1	243	231	235	11.9999
[bb&	chr14:21319545-21319780(-)$1	235	38	42	11.9999
====	chr3:144352137-144352377(-)$1	240	54	58	11.9999
heee	chr3:51322110-51322367(-)$1	257	30	34	11.9999
oooo	chr11:75578686-75578922(+)$1	236	29	33	11.9999
(fff	chr19:12843558-12843801(-)$1	243	117	121	11.9999
eeee	chr2:118301678-118301913(-)$1	235	9	13	11.9999
gggg	chr5:136384359-136384619(-)$1	260	143	147	11.9999
fqqq	chr19:47809707-47809942(+)$1	235	56	60	11.9999
ooee	chr3:89253899-89254141(+)$1	242	121	125	11.9999
=]dd	chr5:67446814-67447060(+)$1	246	221	225	11.9999
JJJJ	chr4:147247927-147248162(-)$1	235	4	8	11.9999
gggg	chr15:27396439-27396677(+)$1	238	30	34	11.9999
bb!!	chr1:165175599-165175844(-)$1	245	53	57	11.9999
cccp	chr16:32472416-32472656(+)$1	240	56	60	11.9999

#DB
.)))	chr4:33107838-33108088(+)$1	1	33	37	11.9999
.(((	chr15:38419438-38419673(-)$1	1	18	22	11.9999
..(.	chr12:4108975-4109237(+)$1	1	107	111	11.9999
..))	chr2:75764693-75764928(+)$1	1	111	115	11.9999
.)))	chr15:31385712-31385954(-)$1	1	224	228	11.9999
((((	chr18:34504828-34505089(-)$1	1	2	6	11.9999
((((	chr13:23831577-23831839(+)$1	1	65	69	11.9999
.(((	chr11:50014066-50014324(-)$1	1	36	40	11.9999
....	chr3:141965425-141965660(-)$1	1	107	111	11.9999
((((	chr13:59037387-59037622(+)$1	1	152	156	11.9999
))))	chr17:87398130-87398377(+)$1	1	67	71	11.9999
))))	chrX:99709798-99710042(-)$1	1	117	121	11.9999
))..	chr2:153594688-153594923(+)$1	1	33	37	11.9999
..))	chr3:126546663-126546898(+)$1	1	103	107	11.9999
(((.	chr15:76845848-76846084(-)$1	1	59	63	11.9999
((((	chr11:29642168-29642473(+)$1	1	39	43	11.9999
((..	chr2:180882414-180882658(-)$1	1	144	148	11.9999
(((.	chr11:29642759-29642996(+)$1	1	10	14	11.9999
....	chr7:20006710-20007002(+)$1	1	150	154	11.9999
....	chr14:37688389-37688624(-)$1	1	82	86	11.9999
))))	chr15:103023875-103024111(-)$1	1	41	45	11.9999
.(((	chr10:59764804-59765062(+)$1	1	120	124	11.9999
....	chr4:150421354-150421589(-)$1	1	44	48	11.9999
((((	chr7:138588944-138589179(+)$1	1	66	70	11.9999
((((	chr11:94202029-94202276(+)$1	1	117	121	11.9999
))))	chr3:60332760-60332997(+)$1	1	107	111	11.9999
).))	chr17:10401591-10401830(-)$1	1	195	199	11.9999
((.(	chr3:51323609-51323852(-)$1	1	25	29	11.9999
.(((	chr5:15878929-15879164(+)$1	1	10	14	11.9999
..((	chr7:99792676-99792911(-)$1	1	26	30	11.9999
((((	chr10:39679454-39679689(-)$1	1	175	179	11.9999
(((.	chr15:12114164-12114401(+)$1	1	67	71	11.9999
.)))	chr7:139905158-139905393(-)$1	1	65	69	11.9999
))))	chr5:36944678-36944920(-)$1	1	66	70	11.9999
((((	chr2:174155522-174155762(+)$1	1	115	119	11.9999
((.(	chr9:102445317-102445562(+)$1	1	40	44	11.9999
)).)	chr11:51799963-51800205(-)$1	1	35	39	11.9999
((.(	chr8:114542481-114542716(+)$1	1	10	14	11.9999
((((	chr11:29642590-29642878(+)$1	1	7	11	11.9999
.)))	chr2:6465641-6465886(-)$1	1	40	44	11.9999
((((	chr2:152106383-152106623(+)$1	1	22	26	11.9999
.(((	chr4:153531615-153531858(-)$1	1	10	14	11.9999
.(((	chr10:127514114-127514349(+)$1	1	74	78	11.9999
....	chr13:21608338-21608573(-)$1	1	24	28	11.9999
....	chr13:97408636-97408876(+)$1	1	77	81	11.9999
((((	chr15:4105022-4105266(+)$1	1	18	22	11.9999
.(((	chr2:152106642-152106889(+)$1	1	81	85	11.9999
))))	chr16:94690321-94690556(+)$1	1	209	213	11.9999
....	chr11:50014137-50014377(-)$1	1	40	44	11.9999
.(((	chr16:4480665-4480901(-)$1	1	12	16	11.9999
((((	chr4:6322128-6322363(+)$1	1	164	168	11.9999
))))	chr6:71342636-71342873(-)$1	1	75	79	11.9999
((((	chr8:88062522-88062769(-)$1	1	36	40	11.9999
.)))	chr6:5434848-5435110(-)$1	1	17	21	11.9999
(...	chr18:32391957-32392192(+)$1	1	7	11	11.9999
)))(	chr3:138589963-138590208(-)$1	1	122	126	11.9999
((((	chr3:120905483-120905743(-)$1	1	68	72	11.9999
((..	chr2:180639581-180639817(-)$1	1	17	21	11.9999
(.((	chr3:69357854-69358091(+)$1	1	100	104	11.9999
((((	chr7:122617910-122618153(-)$1	1	155	159	11.9999
..(.	chr19:44646605-44646848(+)$1	1	143	147	11.9999
.(((	chr1:54702798-54703044(-)$1	1	0	4	11.9999
.(((	chr19:47333693-47333940(+)$1	1	10	14	11.9999
.(((	chr2:155214476-155214718(+)$1	1	37	41	11.9999
))))	chr18:34505052-34505293(-)$1	1	143	147	11.9999
)..(	chr16:36035202-36035440(+)$1	1	37	41	11.9999
.(((	chr1:36587649-36587884(-)$1	1	71	75	11.9999
....	chr2:72240598-72240836(+)$1	1	49	53	11.9999
))))	chr1:180181907-180182144(+)$1	1	54	58	11.9999
.(((	chr13:29999174-29999409(-)$1	1	20	24	11.9999
.)))	chr9:14348715-14348958(-)$1	1	231	235	11.9999
.((.	chr14:21319545-21319780(-)$1	1	38	42	11.9999
((((	chr3:144352137-144352377(-)$1	1	54	58	11.9999
)(((	chr3:51322110-51322367(-)$1	1	30	34	11.9999
....	chr11:75578686-75578922(+)$1	1	29	33	11.9999
.(((	chr19:12843558-12843801(-)$1	1	117	121	11.9999
((((	chr2:118301678-118301913(-)$1	1	9	13	11.9999
))))	chr5:136384359-136384619(-)$1	1	143	147	11.9999
(...	chr19:47809707-47809942(+)$1	1	56	60	11.9999
..))	chr3:89253899-89254141(+)$1	1	121	125	11.9999
).))	chr5:67446814-67447060(+)$1	1	221	225	11.9999
((((	chr4:147247927-147248162(-)$1	1	4	8	11.9999
))))	chr15:27396439-27396677(+)$1	1	30	34	11.9999
((..	chr1:165175599-165175844(-)$1	1	53	57	11.9999
(((.	chr16:32472416-32472656(+)$1	1	56	60	11.9999

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

#score	1019.9999999999998
#seq	85
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m3_run1.nuc.txt

#NT
UUUUUCA	chr4:81940723-81940924(-)$1	201	32	39	13.1428
uuuuuaa	chr1:66485749-66485950(+)$1	201	102	109	17.0317
UUUUUGA	chr8:56040511-56040712(+)$1	201	55	62	12.9841
UUUUGAA	chr12:88221595-88221796(-)$1	201	14	21	12.9841
CUUUUAA	chr17:66687051-66687252(-)$1	201	82	89	13.6190
UUUUUAA	chr10:107936044-107936245(-)$1	201	16	23	17.0317
UUUUUAA	chr11:115884158-115884359(-)$1	201	164	171	17.0317
UUUGUAA	chr13:97419982-97420183(-)$1	201	81	88	13.0634
GUUUUAA	chr7:110974999-110975200(-)$1	201	159	166	13.5396
UUUUUAA	chr14:26531790-26531991(-)$1	201	124	131	17.0317
UUUUGAA	chr4:11091492-11091693(+)$1	201	57	64	12.9841
UUUUCAA	chr10:112364597-112364798(-)$1	201	77	84	13.3809
UUUAUaa	chrX:133613776-133613977(+)$1	201	66	73	13.1428
uuuuuaa	chr11:53291016-53291217(-)$1	201	179	186	17.0317
UUUUUCA	chr3:36943623-36943824(+)$1	201	68	75	13.1428
UUUUUAC	chr10:80861742-80861943(-)$1	201	100	107	12.2698
UUAUUAA	chr10:80295505-80295706(-)$1	201	10	17	12.7460
GUUUUAA	chr11:117623892-117624093(+)$1	201	167	174	13.5396
UUUUUGA	chr19:53320252-53320453(+)$1	201	129	136	12.9841
UUUGUAA	chr11:117020398-117020599(+)$1	201	88	95	13.0634
GUUUUAA	chr7:110974998-110975199(-)$1	201	158	165	13.5396
UUUUUUA	chr2:31148285-31148486(+)$1	201	50	57	12.8253
UUUUCAA	chr10:112364596-112364797(-)$1	201	76	83	13.3809
UUUGUAA	chr3:102868618-102868819(+)$1	201	131	138	13.0634
UUUUAAA	chr15:9126782-9126983(+)$1	201	0	7	12.9047
UUUAUAA	chr11:74489934-74490135(-)$1	201	42	49	13.1428
AUUUUAA	chr11:54532782-54532983(-)$1	201	69	76	13.3809
UCUUUAA	chr4:11130394-11130595(+)$1	201	188	195	12.1904
UUUUUAA	chr5:73369041-73369242(+)$1	201	66	73	17.0317
UUUUUGA	chr7:73317372-73317573(+)$1	201	4	11	12.9841
AUUUUAA	chr13:43232308-43232509(+)$1	201	43	50	13.3809
UUUUCAA	chr5:68013051-68013252(-)$1	201	26	33	13.3809
UUUUUaa	chrX:39885523-39885724(-)$1	201	123	130	17.0317
UUUUUCA	chr19:43570256-43570457(+)$1	201	140	147	13.1428
UUUUUAA	chr8:93576348-93576549(+)$1	201	165	172	17.0317
UUUAUAA	chr2:102621774-102621975(+)$1	201	113	120	13.1428
UUUUUAA	chr10:107936045-107936246(-)$1	201	17	24	17.0317
UUUAUAA	chr11:74489933-74490134(-)$1	201	41	48	13.1428
guuuuAA	chr12:99672769-99672970(-)$1	201	22	29	13.5396
GUUUUAA	chr7:118215758-118215959(-)$1	201	68	75	13.5396
UUUUUAA	chr5:73369040-73369241(+)$1	201	67	74	17.0317
UUUUUAU	chr6:90332759-90332960(+)$1	201	193	200	12.2698
UUAUUAA	chr3:80491784-80491985(-)$1	201	171	178	12.7460
AUUUUAA	chr18:34478807-34479008(+)$1	201	80	87	13.3809
UUUUUAA	chr7:72441306-72441507(-)$1	201	182	189	17.0317
CUUUUAA	chr17:66687050-66687251(-)$1	201	81	88	13.6190
UUUUCAA	chr3:55791875-55792076(-)$1	201	71	78	13.3809
CUUUUAA	chr2:3144475-3144676(+)$1	201	18	25	13.6190
UUUGUAA	chr11:117020397-117020598(+)$1	201	89	96	13.0634
UUUAUAA	chr8:88242641-88242842(-)$1	201	167	174	13.1428
CUUUUAA	chr14:56500767-56500968(-)$1	201	108	115	13.6190
uuuuuaa	chr11:117622645-117622846(+)$1	201	59	66	17.0317
UUUUCAA	chr8:11448449-11448650(+)$1	201	136	143	13.3809
UUUUCAA	chr8:11448450-11448651(+)$1	201	135	142	13.3809
UUUUUAA	chr18:33598196-33598397(-)$1	201	23	30	17.0317
UUUUUCA	chr2:165609674-165609875(-)$1	201	168	175	13.1428
CUUUUAA	chr4:126115682-126115883(-)$1	201	53	60	13.6190
UUCUUAA	chr3:120908767-120908968(-)$1	201	66	73	12.5079
UUUUCAA	chr1:171673408-171673609(-)$1	201	63	70	13.3809
UUAUUAA	chr6:119875446-119875647(-)$1	201	6	13	12.7460
CUUUUAA	chr2:103988355-103988556(-)$1	201	170	177	13.6190
UUUUUCA	chr1:157899928-157900129(+)$1	201	66	73	13.1428

#otherMatches

#Struct PSSM
seeeee]	chr9:103083662-103083863(+)$1	201	146	153	12.7460
)))))))	chr4:81940723-81940924(-)$1	201	32	39	13.1428
:::::::	chr1:66485749-66485950(+)$1	201	102	109	17.0317
d!!cccn	chr8:56040511-56040712(+)$1	201	55	62	12.9841
eeeqqqq	chr12:88221595-88221796(-)$1	201	14	21	12.9841
cc:::::	chr17:66687051-66687252(-)$1	201	82	89	13.6190
iiiiiii	chr10:107936044-107936245(-)$1	201	16	23	17.0317
gggpppp	chr11:115884158-115884359(-)$1	201	164	171	17.0317
nnngggg	chr13:97419982-97420183(-)$1	201	81	88	13.0634
hhhhh33	chr7:110974999-110975200(-)$1	201	159	166	13.5396
f"""ccc	chr14:26531790-26531991(-)$1	201	124	131	17.0317
dd!!bb[	chr4:11091492-11091693(+)$1	201	57	64	12.9841
hhhhhho	chr10:112364597-112364798(-)$1	201	77	84	13.3809
hhhh:::	chrX:133613776-133613977(+)$1	201	66	73	13.1428
HHH~~~~	chr11:53291016-53291217(-)$1	201	179	186	17.0317
$$$dddd	chr3:36943623-36943824(+)$1	201	68	75	13.1428
:::::::	chr10:80861742-80861943(-)$1	201	100	107	12.2698
ccppppp	chr10:80295505-80295706(-)$1	201	10	17	12.7460
fff:::=	chr11:117623892-117624093(+)$1	201	167	174	13.5396
ffffff2	chr19:53320252-53320453(+)$1	201	129	136	12.9841
SFFFFFF	chr11:117020398-117020599(+)$1	201	88	95	13.0634
hhhhh33	chr7:110974998-110975199(-)$1	201	158	165	13.5396
h"""eee	chr2:31148285-31148486(+)$1	201	50	57	12.8253
hhhhhho	chr10:112364596-112364797(-)$1	201	76	83	13.3809
lleeeee	chr3:102868618-102868819(+)$1	201	131	138	13.0634
::::::E	chr15:9126782-9126983(+)$1	201	0	7	12.9047
c[dddd[	chr11:74489934-74490135(-)$1	201	42	49	13.1428
SEEEEE{	chr11:54532782-54532983(-)$1	201	69	76	13.3809
:::::::	chr4:11130394-11130595(+)$1	201	188	195	12.1904
hhhhhhh	chr5:73369041-73369242(+)$1	201	66	73	17.0317
JJJJJJJ	chr7:73317372-73317573(+)$1	201	4	11	12.9841
JJJJJ{B	chr13:43232308-43232509(+)$1	201	43	50	13.3809
mmmdddd	chr5:68013051-68013252(-)$1	201	26	33	13.3809
ffffooo	chrX:39885523-39885724(-)$1	201	123	130	17.0317
:::::::	chr19:43570256-43570457(+)$1	201	140	147	13.1428
vvvvvvv	chr8:93576348-93576549(+)$1	201	165	172	17.0317
""eeeee	chr2:102621774-102621975(+)$1	201	113	120	13.1428
iiiiiii	chr10:107936045-107936246(-)$1	201	17	24	17.0317
c[dddd[	chr11:74489933-74490134(-)$1	201	41	48	13.1428
ggggggs	chr12:99672769-99672970(-)$1	201	22	29	13.5396
=====22	chr7:118215758-118215959(-)$1	201	68	75	13.5396
hhhhhhh	chr5:73369040-73369241(+)$1	201	67	74	17.0317
:::::::	chr6:90332759-90332960(+)$1	201	193	200	12.2698
mgggggg	chr3:80491784-80491985(-)$1	201	171	178	12.7460
ggggggg	chr18:34478807-34479008(+)$1	201	80	87	13.3809
99999ii	chr7:72441306-72441507(-)$1	201	182	189	17.0317
cc:::::	chr17:66687050-66687251(-)$1	201	81	88	13.6190
fffffcc	chr3:55791875-55792076(-)$1	201	71	78	13.3809
'''''''	chr2:3144475-3144676(+)$1	201	18	25	13.6190
SFFFFFF	chr11:117020397-117020598(+)$1	201	89	96	13.0634
:::::::	chr8:88242641-88242842(-)$1	201	167	174	13.1428
:::::::	chr14:56500767-56500968(-)$1	201	108	115	13.6190
eeeee66	chr11:117622645-117622846(+)$1	201	59	66	17.0317
qqqqqqq	chr8:11448449-11448650(+)$1	201	136	143	13.3809
qqqqqqq	chr8:11448450-11448651(+)$1	201	135	142	13.3809
++++++d	chr18:33598196-33598397(-)$1	201	23	30	17.0317
GGGGGGZ	chr2:165609674-165609875(-)$1	201	168	175	13.1428
eeeeell	chr4:126115682-126115883(-)$1	201	53	60	13.6190
"""eeee	chr3:120908767-120908968(-)$1	201	66	73	12.5079
sssssss	chr1:171673408-171673609(-)$1	201	63	70	13.3809
:::::::	chr6:119875446-119875647(-)$1	201	6	13	12.7460
ddd::::	chr2:103988355-103988556(-)$1	201	170	177	13.6190
zzzzz==	chr1:157899928-157900129(+)$1	201	66	73	13.1428

#DB
.))))).	chr9:103083662-103083863(+)$1	1	146	153	12.7460
.......	chr4:81940723-81940924(-)$1	1	32	39	13.1428
.......	chr1:66485749-66485950(+)$1	1	102	109	17.0317
(..(((.	chr8:56040511-56040712(+)$1	1	55	62	12.9841
(((....	chr12:88221595-88221796(-)$1	1	14	21	12.9841
)).....	chr17:66687051-66687252(-)$1	1	82	89	13.6190
(((((((	chr10:107936044-107936245(-)$1	1	16	23	17.0317
(((....	chr11:115884158-115884359(-)$1	1	164	171	17.0317
...))))	chr13:97419982-97420183(-)$1	1	81	88	13.0634
)))))..	chr7:110974999-110975200(-)$1	1	159	166	13.5396
(...(((	chr14:26531790-26531991(-)$1	1	124	131	17.0317
((..((.	chr4:11091492-11091693(+)$1	1	57	64	12.9841
((((((.	chr10:112364597-112364798(-)$1	1	77	84	13.3809
))))...	chrX:133613776-133613977(+)$1	1	66	73	13.1428
)))....	chr11:53291016-53291217(-)$1	1	179	186	17.0317
...((((	chr3:36943623-36943824(+)$1	1	68	75	13.1428
.......	chr10:80861742-80861943(-)$1	1	100	107	12.2698
((.....	chr10:80295505-80295706(-)$1	1	10	17	12.7460
)))...(	chr11:117623892-117624093(+)$1	1	167	174	13.5396
)))))).	chr19:53320252-53320453(+)$1	1	129	136	12.9841
.((((((	chr11:117020398-117020599(+)$1	1	88	95	13.0634
)))))..	chr7:110974998-110975199(-)$1	1	158	165	13.5396
(...(((	chr2:31148285-31148486(+)$1	1	50	57	12.8253
((((((.	chr10:112364596-112364797(-)$1	1	76	83	13.3809
..)))))	chr3:102868618-102868819(+)$1	1	131	138	13.0634
......(	chr15:9126782-9126983(+)$1	1	0	7	12.9047
(.((((.	chr11:74489934-74490135(-)$1	1	42	49	13.1428
.(((((.	chr11:54532782-54532983(-)$1	1	69	76	13.3809
.......	chr4:11130394-11130595(+)$1	1	188	195	12.1904
)))))))	chr5:73369041-73369242(+)$1	1	66	73	17.0317
(((((((	chr7:73317372-73317573(+)$1	1	4	11	12.9841
(((((.(	chr13:43232308-43232509(+)$1	1	43	50	13.3809
...))))	chr5:68013051-68013252(-)$1	1	26	33	13.3809
((((...	chrX:39885523-39885724(-)$1	1	123	130	17.0317
.......	chr19:43570256-43570457(+)$1	1	140	147	13.1428
.......	chr8:93576348-93576549(+)$1	1	165	172	17.0317
..(((((	chr2:102621774-102621975(+)$1	1	113	120	13.1428
(((((((	chr10:107936045-107936246(-)$1	1	17	24	17.0317
(.((((.	chr11:74489933-74490134(-)$1	1	41	48	13.1428
((((((.	chr12:99672769-99672970(-)$1	1	22	29	13.5396
)))))..	chr7:118215758-118215959(-)$1	1	68	75	13.5396
)))))))	chr5:73369040-73369241(+)$1	1	67	74	17.0317
.......	chr6:90332759-90332960(+)$1	1	193	200	12.2698
.))))))	chr3:80491784-80491985(-)$1	1	171	178	12.7460
(((((((	chr18:34478807-34479008(+)$1	1	80	87	13.3809
.....))	chr7:72441306-72441507(-)$1	1	182	189	17.0317
)).....	chr17:66687050-66687251(-)$1	1	81	88	13.6190
(((((((	chr3:55791875-55792076(-)$1	1	71	78	13.3809
.......	chr2:3144475-3144676(+)$1	1	18	25	13.6190
.((((((	chr11:117020397-117020598(+)$1	1	89	96	13.0634
.......	chr8:88242641-88242842(-)$1	1	167	174	13.1428
.......	chr14:56500767-56500968(-)$1	1	108	115	13.6190
)))))..	chr11:117622645-117622846(+)$1	1	59	66	17.0317
.......	chr8:11448449-11448650(+)$1	1	136	143	13.3809
.......	chr8:11448450-11448651(+)$1	1	135	142	13.3809
......(	chr18:33598196-33598397(-)$1	1	23	30	17.0317
)))))).	chr2:165609674-165609875(-)$1	1	168	175	13.1428
(((((..	chr4:126115682-126115883(-)$1	1	53	60	13.6190
...((((	chr3:120908767-120908968(-)$1	1	66	73	12.5079
.......	chr1:171673408-171673609(-)$1	1	63	70	13.3809
.......	chr6:119875446-119875647(-)$1	1	6	13	12.7460
)))....	chr2:103988355-103988556(-)$1	1	170	177	13.6190
.....))	chr1:157899928-157900129(+)$1	1	66	73	13.1428

#PSSM
U : 0.73	C : 0.09	G : 0.06	u : 0.04	A : 0.04	g : 0.01	
U : 0.92	u : 0.06	C : 0.01	
U : 0.85	A : 0.06	u : 0.06	C : 0.01	
U : 0.79	A : 0.07	u : 0.06	G : 0.06	
U : 0.77	C : 0.11	u : 0.06	G : 0.03	A : 0.01	
A : 0.77	C : 0.07	a : 0.07	G : 0.04	U : 0.01	
A : 0.88	a : 0.07	C : 0.01	U : 0.01	

#score	879.1904761904751
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_CDS_m2_run1.nuc.txt

#NT
UGCCUGA	chr2:76723068-76723305(-)$1	237	66	73	13.3076
UGCCUGG	chr13:55422845-55423080(-)$1	235	18	25	13.6923
UGUCUGU	chr2:163842323-163842558(+)$1	235	138	145	12.3461
UGCCUGC	chr2:113875924-113876162(-)$1	238	75	82	13.1153
UGCUUGU	chr10:128243637-128243873(+)$1	236	9	16	12.3461
CGCCUGU	chr19:57229539-57229774(-)$1	235	115	122	12.7307
UGCCUGA	chr13:11843033-11843270(-)$1	237	218	225	13.3076
UGCCUGG	chr8:23678687-23678922(+)$1	235	108	115	13.6923
UGGCUGU	chr10:81028331-81028570(+)$1	239	226	233	12.5384
UGCUUGU	chr14:37935173-37935433(-)$1	260	142	149	12.3461
UCCCUGU	chr11:109528792-109529029(+)$1	237	109	116	12.9230
UGCCUGU	chr5:122907217-122907452(-)$1	235	78	85	16.5769
GGCCUGU	chr6:113678312-113678549(-)$1	237	12	19	12.5384
UCCCUGU	chr1:43180304-43180550(-)$1	246	114	121	12.9230
UGCCGGU	chr15:100228029-100228266(-)$1	237	30	37	12.5384
UGCCUGU	chr16:58732621-58732862(+)$1	241	148	155	16.5769
UGCCGGU	chr1:89088986-89089221(+)$1	235	21	28	12.5384
UGGCUGU	chr3:95292215-95292460(+)$1	245	124	131	12.5384
UUCCUGU	chr16:31104864-31105099(-)$1	235	80	87	12.5384
UGCCUGU	chr5:143533280-143533519(-)$1	239	149	156	16.5769
AGCCUGU	chr1:172771744-172771979(-)$1	235	133	140	12.5384
UGCCUGG	chr4:126425743-126425995(-)$1	252	88	95	13.6923
UGCCUGG	chr8:23678766-23679001(+)$1	235	29	36	13.6923
CGCCUGU	chr2:156795708-156795945(-)$1	237	177	184	12.7307
UGCCCGU	chr1:34178373-34178608(+)$1	235	88	95	12.3461

#otherMatches

#Struct PSSM
ooooocc	chr10:127478579-127478814(+)$1	235	121	128	12.9230
=++++++	chr2:76723068-76723305(-)$1	237	66	73	13.3076
!!=====	chr13:55422845-55423080(-)$1	235	18	25	13.6923
qqqqqcc	chr2:163842323-163842558(+)$1	235	138	145	12.3461
(bbeeee	chr2:113875924-113876162(-)$1	238	75	82	13.1153
C{CCC{E	chr10:128243637-128243873(+)$1	236	9	16	12.3461
fffff]c	chr19:57229539-57229774(-)$1	235	115	122	12.7307
b666666	chr13:11843033-11843270(-)$1	237	218	225	13.3076
dCCC}FF	chr8:23678687-23678922(+)$1	235	108	115	13.6923
44fffff	chr10:81028331-81028570(+)$1	239	226	233	12.5384
[dddd[a	chr14:37935173-37935433(-)$1	260	142	149	12.3461
cccbb44	chr11:109528792-109529029(+)$1	237	109	116	12.9230
ddddGGG	chr5:122907217-122907452(-)$1	235	78	85	16.5769
HHHHH{D	chr6:113678312-113678549(-)$1	237	12	19	12.5384
e:::fff	chr1:43180304-43180550(-)$1	246	114	121	12.9230
[ccclll	chr15:100228029-100228266(-)$1	237	30	37	12.5384
3bb333d	chr16:58732621-58732862(+)$1	241	148	155	16.5769
IIIIIII	chr1:89088986-89089221(+)$1	235	21	28	12.5384
ccc333d	chr3:95292215-95292460(+)$1	245	124	131	12.5384
fff]bb2	chr16:31104864-31105099(-)$1	235	80	87	12.5384
nbb22cc	chr5:143533280-143533519(-)$1	239	149	156	16.5769
[bb!!bb	chr1:172771744-172771979(-)$1	235	133	140	12.5384
EEA{DDD	chr4:126425743-126425995(-)$1	252	88	95	13.6923
d]bb::b	chr8:23678766-23679001(+)$1	235	29	36	13.6923
ldddd33	chr2:156795708-156795945(-)$1	237	177	184	12.7307
]bbgggg	chr1:34178373-34178608(+)$1	235	88	95	12.3461

#DB
.....))	chr10:127478579-127478814(+)$1	1	121	128	12.9230
(......	chr2:76723068-76723305(-)$1	1	66	73	13.3076
..(((((	chr13:55422845-55423080(-)$1	1	18	25	13.6923
.....))	chr2:163842323-163842558(+)$1	1	138	145	12.3461
.((((((	chr2:113875924-113876162(-)$1	1	75	82	13.1153
(.(((.(	chr10:128243637-128243873(+)$1	1	9	16	12.3461
))))).)	chr19:57229539-57229774(-)$1	1	115	122	12.7307
)......	chr13:11843033-11843270(-)$1	1	218	225	13.3076
)))).))	chr8:23678687-23678922(+)$1	1	108	115	13.6923
..)))))	chr10:81028331-81028570(+)$1	1	226	233	12.5384
.((((.(	chr14:37935173-37935433(-)$1	1	142	149	12.3461
)))))..	chr11:109528792-109529029(+)$1	1	109	116	12.9230
)))))))	chr5:122907217-122907452(-)$1	1	78	85	16.5769
(((((.(	chr6:113678312-113678549(-)$1	1	12	19	12.5384
)...(((	chr1:43180304-43180550(-)$1	1	114	121	12.9230
.(((...	chr15:100228029-100228266(-)$1	1	30	37	12.5384
.))...)	chr16:58732621-58732862(+)$1	1	148	155	16.5769
(((((((	chr1:89088986-89089221(+)$1	1	21	28	12.5384
)))...)	chr3:95292215-95292460(+)$1	1	124	131	12.5384
))).)).	chr16:31104864-31105099(-)$1	1	80	87	12.5384
.))..))	chr5:143533280-143533519(-)$1	1	149	156	16.5769
.((..((	chr1:172771744-172771979(-)$1	1	133	140	12.5384
(((.(((	chr4:126425743-126425995(-)$1	1	88	95	13.6923
).))..(	chr8:23678766-23679001(+)$1	1	29	36	13.6923
.))))..	chr2:156795708-156795945(-)$1	1	177	184	12.7307
.))))))	chr1:34178373-34178608(+)$1	1	88	95	12.3461

#PSSM
U : 0.84	C : 0.07	G : 0.03	A : 0.03	
G : 0.84	C : 0.11	U : 0.03	
C : 0.88	G : 0.07	U : 0.03	
C : 0.92	U : 0.07	
U : 0.88	G : 0.07	C : 0.03	
G : 0.99	
U : 0.73	G : 0.15	A : 0.07	C : 0.03	

#score	345.6153846153845
#seq	26
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_UTR_m1_run2.nuc.txt

#NT
UUUUCUUUUUu	chr14:31932253-31932485(+)$1	232	165	176	22.8936
UGUUGUUUUUU	chr1:157124418-157124678(-)$1	260	113	124	20.1276
UUUUGUUGUUU	chr19:5308243-5308482(+)$1	239	128	139	20.3404
UUUUAUUUUUU	chr10:116784368-116784604(-)$1	236	74	85	24.0638
UUUUGCUUUUU	chr12:60060749-60061007(-)$1	258	71	82	20.7659
uuuuauuuuuu	chr9:106786177-106786432(-)$1	255	50	61	24.0638
GUGUGUUUUUU	chr2:134420424-134420689(-)$1	265	116	127	18.7446
AUUUAUUUUUU	chr9:20299985-20300396(-)$1	411	105	116	23.0000
GUUUUUUUUUU	chr11:79508243-79508481(+)$1	238	146	157	22.2553
GUUUGCUUUUU	chr17:74790159-74790496(+)$1	337	138	149	19.1702
Cuuuuuuuuuu	chr7:73966970-73967206(+)$1	236	101	112	23.0000
CUUUUUUUUUU	chr9:82763122-82763379(-)$1	257	127	138	23.0000
uuuuguuuugu	chr14:124378148-124378454(-)$1	306	142	153	20.3404
CUUUAUUUUUU	chr1:157851729-157851978(-)$1	249	68	79	23.2127
UUUUGUUUUUU	chr4:130382013-130382245(+)$1	232	152	163	24.9148
uuuuaauuuuu	chr5:137969253-137969514(-)$1	261	103	114	19.7021
CUUUuuuuuuu	chr19:3799435-3799670(-)$1	235	105	116	23.0000
UUUUGUUUUGU	chr1:56851655-56851974(-)$1	319	117	128	20.3404
UUUUAGUUUUU	chr5:134833457-134833696(-)$1	239	87	98	19.7021
Cuuuuuuuuuu	chr12:101175463-101175694(-)$1	231	103	114	23.0000
GUUUGUUUAUU	chrX:75008548-75008812(-)$1	264	128	139	19.3829
CUUUGUAUUUU	chr4:132411095-132411344(-)$1	249	192	203	19.4893
Uuuuacuuuuu	chr7:135127794-135128052(+)$1	258	220	231	19.9148
AUUUGUGUUUU	chr2:53076854-53077102(+)$1	248	160	171	19.3829
cuuuuuuuuuu	chr11:88156196-88156454(-)$1	258	24	35	23.0000
AUUUGUUUUUG	chr19:3816606-3816842(+)$1	236	194	205	19.0638
CUUUGUUAUUU	chr5:84495947-84496206(-)$1	259	10	21	19.4893
CUUUGUUCUUU	chr3:53254428-53254692(-)$1	264	61	72	19.4893
UUUUGUUUUUU	chr10:62782967-62783209(-)$1	242	85	96	24.9148
AUUUUUUUUUU	chr9:115152809-115153040(-)$1	231	186	197	22.7872
UUUUCUUUAUU	chrX:72779630-72779897(+)$1	267	2	13	18.9574
AUUUUUUUUUU	chr3:115645160-115645391(-)$1	231	76	87	22.7872
auuuuuuuuuu	chr4:137212954-137213215(+)$1	261	58	69	22.7872
uuuuguuuuuu	chr7:95279725-95279994(+)$1	269	139	150	24.9148
UUUUGUUUUUU	chr16:44160333-44160598(+)$1	265	122	133	24.9148
CUUUGUGUUUU	chr1:133829371-133829608(+)$1	237	15	26	19.5957
AUUUUUUUUUU	chr8:83224211-83224447(-)$1	236	222	233	22.7872
uuuuauuuauu	chr4:147197837-147198068(-)$1	231	73	84	20.1276
UUUUAUUUAUU	chr9:71693892-71694149(-)$1	257	128	139	20.1276
GUUUAUUUUUU	chr16:42178147-42178420(+)$1	273	67	78	22.4680
UUUUGUUUGUU	chr5:37186801-37187048(-)$1	247	96	107	20.7659
UUUUGUUUGUU	chr10:90611018-90611317(-)$1	299	18	29	20.7659
AUUUGUUUUUU	chr13:120246520-120246776(+)$1	256	30	41	23.8510
AUUUAUUUUUU	chr16:33499143-33499389(+)$1	246	38	49	23.0000
AUGUAUUUUUU	chr1:63358869-63359100(+)$1	231	70	81	18.4255
CUUUAUUUUUU	chr11:77342617-77342856(-)$1	239	203	214	23.2127

#otherMatches

#Struct PSSM
:::::::::::	chr2:109739069-109739431(+)$1	362	338	349	23.0000
iiii[iiiiii	chr14:31932253-31932485(+)$1	232	165	176	22.8936
JJJJJJJJJJ@	chr1:157124418-157124678(-)$1	260	113	124	20.1276
f::::::::::	chr19:5308243-5308482(+)$1	239	128	139	20.3404
eeeeetttttt	chr10:116784368-116784604(-)$1	236	74	85	24.0638
fffff"""ggg	chr12:60060749-60061007(-)$1	258	71	82	20.7659
%%cccoooooo	chr9:106786177-106786432(-)$1	255	50	61	24.0638
ssssssss===	chr2:134420424-134420689(-)$1	265	116	127	18.7446
f:::::::::G	chr9:20299985-20300396(-)$1	411	105	116	23.0000
cc>>>>>>>>>	chr11:79508243-79508481(+)$1	238	146	157	22.2553
b"""bbnnnnn	chr17:74790159-74790496(+)$1	337	138	149	19.1702
d::::::::::	chr7:73966970-73967206(+)$1	236	101	112	23.0000
eettttttttt	chr9:82763122-82763379(-)$1	257	127	138	23.0000
:::GGGGGGGM	chr14:124378148-124378454(-)$1	306	142	153	20.3404
OOOOOOJJJJJ	chr1:157851729-157851978(-)$1	249	68	79	23.2127
+++++++++++	chr4:130382013-130382245(+)$1	232	152	163	24.9148
c!!ccclllcc	chr5:137969253-137969514(-)$1	261	103	114	19.7021
^^^^^^^^^^^	chr19:3799435-3799670(-)$1	235	105	116	23.0000
&&dddd"""hh	chr1:56851655-56851974(-)$1	319	117	128	20.3404
JJJJJJJJJJJ	chr5:134833457-134833696(-)$1	239	87	98	19.7021
:::::::::::	chr12:101175463-101175694(-)$1	231	103	114	23.0000
:::::::::::	chrX:75008548-75008812(-)$1	264	128	139	19.3829
:::::::::::	chr4:132411095-132411344(-)$1	249	192	203	19.4893
tttccc22ggg	chr7:135127794-135128052(+)$1	258	220	231	19.9148
B}FFFFFF:ee	chr2:53076854-53077102(+)$1	248	160	171	19.3829
vvvvvvvvvvv	chr11:88156196-88156454(-)$1	258	24	35	23.0000
gggg[eeeee!	chr19:3816606-3816842(+)$1	236	194	205	19.0638
HHHHHHHH:::	chr5:84495947-84496206(-)$1	259	10	21	19.4893
++++++++++i	chr3:53254428-53254692(-)$1	264	61	72	19.4893
ggggg>>>>>>	chr10:62782967-62783209(-)$1	242	85	96	24.9148
EEE::::::::	chr9:115152809-115153040(-)$1	231	186	197	22.7872
:::::::::::	chrX:72779630-72779897(+)$1	267	2	13	18.9574
b!!========	chr3:115645160-115645391(-)$1	231	76	87	22.7872
""ccc####ff	chr4:137212954-137213215(+)$1	261	58	69	22.7872
^^^^^^^^^^^	chr7:95279725-95279994(+)$1	269	139	150	24.9148
8888dddd]ff	chr16:44160333-44160598(+)$1	265	122	133	24.9148
CKKCCC:::::	chr1:133829371-133829608(+)$1	237	15	26	19.5957
:::::::::::	chr8:83224211-83224447(-)$1	236	222	233	22.7872
&&&ggggggg!	chr4:147197837-147198068(-)$1	231	73	84	20.1276
ffffffqqqqq	chr9:71693892-71694149(-)$1	257	128	139	20.1276
I:::=======	chr16:42178147-42178420(+)$1	273	67	78	22.4680
:::::::::::	chr5:37186801-37187048(-)$1	247	96	107	20.7659
NNNEEEEEHHH	chr10:90611018-90611317(-)$1	299	18	29	20.7659
b:::ccc!!cc	chr13:120246520-120246776(+)$1	256	30	41	23.8510
DDDKKEEEEEM	chr16:33499143-33499389(+)$1	246	38	49	23.0000
:ffffffoooo	chr1:63358869-63359100(+)$1	231	70	81	18.4255
dd::JJJJJJJ	chr11:77342617-77342856(-)$1	239	203	214	23.2127

#DB
...........	chr2:109739069-109739431(+)$1	1	338	349	23.0000
((((.((((((	chr14:31932253-31932485(+)$1	1	165	176	22.8936
)))))))))).	chr1:157124418-157124678(-)$1	1	113	124	20.1276
)..........	chr19:5308243-5308482(+)$1	1	128	139	20.3404
(((((......	chr10:116784368-116784604(-)$1	1	74	85	24.0638
(((((...(((	chr12:60060749-60061007(-)$1	1	71	82	20.7659
..(((......	chr9:106786177-106786432(-)$1	1	50	61	24.0638
........)))	chr2:134420424-134420689(-)$1	1	116	127	18.7446
).........)	chr9:20299985-20300396(-)$1	1	105	116	23.0000
)).........	chr11:79508243-79508481(+)$1	1	146	157	22.2553
(...((.....	chr17:74790159-74790496(+)$1	1	138	149	19.1702
)..........	chr7:73966970-73967206(+)$1	1	101	112	23.0000
((.........	chr9:82763122-82763379(-)$1	1	127	138	23.0000
...(((((((.	chr14:124378148-124378454(-)$1	1	142	153	20.3404
......(((((	chr1:157851729-157851978(-)$1	1	68	79	23.2127
...........	chr4:130382013-130382245(+)$1	1	152	163	24.9148
(..(((...))	chr5:137969253-137969514(-)$1	1	103	114	19.7021
...........	chr19:3799435-3799670(-)$1	1	105	116	23.0000
..((((...((	chr1:56851655-56851974(-)$1	1	117	128	20.3404
)))))))))))	chr5:134833457-134833696(-)$1	1	87	98	19.7021
...........	chr12:101175463-101175694(-)$1	1	103	114	23.0000
...........	chrX:75008548-75008812(-)$1	1	128	139	19.3829
...........	chr4:132411095-132411344(-)$1	1	192	203	19.4893
...)))..)))	chr7:135127794-135128052(+)$1	1	220	231	19.9148
).)))))).((	chr2:53076854-53077102(+)$1	1	160	171	19.3829
...........	chr11:88156196-88156454(-)$1	1	24	35	23.0000
((((.(((((.	chr19:3816606-3816842(+)$1	1	194	205	19.0638
((((((((...	chr5:84495947-84496206(-)$1	1	10	21	19.4893
..........(	chr3:53254428-53254692(-)$1	1	61	72	19.4893
)))))......	chr10:62782967-62783209(-)$1	1	85	96	24.9148
)))........	chr9:115152809-115153040(-)$1	1	186	197	22.7872
...........	chrX:72779630-72779897(+)$1	1	2	13	18.9574
(..((((((((	chr3:115645160-115645391(-)$1	1	76	87	22.7872
..(((....((	chr4:137212954-137213215(+)$1	1	58	69	22.7872
...........	chr7:95279725-95279994(+)$1	1	139	150	24.9148
....)))).))	chr16:44160333-44160598(+)$1	1	122	133	24.9148
(..(((.....	chr1:133829371-133829608(+)$1	1	15	26	19.5957
...........	chr8:83224211-83224447(-)$1	1	222	233	22.7872
...(((((((.	chr4:147197837-147198068(-)$1	1	73	84	20.1276
((((((.....	chr9:71693892-71694149(-)$1	1	128	139	20.1276
(...(((((((	chr16:42178147-42178420(+)$1	1	67	78	22.4680
...........	chr5:37186801-37187048(-)$1	1	96	107	20.7659
...((((((((	chr10:90611018-90611317(-)$1	1	18	29	20.7659
)...(((..((	chr13:120246520-120246776(+)$1	1	30	41	23.8510
(((..(((((.	chr16:33499143-33499389(+)$1	1	38	49	23.0000
.((((((....	chr1:63358869-63359100(+)$1	1	70	81	18.4255
))..)))))))	chr11:77342617-77342856(-)$1	1	203	214	23.2127

#PSSM
U : 0.31	C : 0.23	A : 0.19	u : 0.10	G : 0.10	c : 0.02	a : 0.02	
U : 0.76	u : 0.21	G : 0.02	
U : 0.74	u : 0.21	G : 0.04	
U : 0.78	u : 0.21	
G : 0.40	A : 0.19	U : 0.12	u : 0.10	a : 0.08	C : 0.04	g : 0.04	
U : 0.70	u : 0.19	C : 0.04	a : 0.02	G : 0.02	c : 0.02	
U : 0.70	u : 0.23	G : 0.04	A : 0.02	
U : 0.70	u : 0.23	G : 0.02	A : 0.02	C : 0.02	
U : 0.65	u : 0.21	A : 0.06	G : 0.04	a : 0.02	
U : 0.74	u : 0.21	g : 0.02	G : 0.02	
U : 0.72	u : 0.25	G : 0.02	

#score	1015.0425531914901
#seq	47
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m3_run2.nuc.txt

#NT
CUU	chr1:37863791-37864008(+)$1	217	7	10	8.9999
CUU	chr10:96942291-96942523(+)$1	232	32	35	8.9999
CUU	chr18:35776074-35776304(+)$1	230	50	53	8.9999
CUU	chr5:150099398-150099621(-)$1	223	16	19	8.9999
CUU	chr11:11830525-11830758(-)$1	233	105	108	8.9999
CUU	chr8:19696096-19696322(+)$1	226	66	69	8.9999
CUU	chr18:24119613-24119834(+)$1	221	39	42	8.9999
CUU	chr9:65542518-65542750(-)$1	232	11	14	8.9999
CUU	chr19:3389554-3389775(-)$1	221	54	57	8.9999
CUU	chr2:173924680-173924912(+)$1	232	18	21	8.9999
CUU	chr8:79768213-79768435(+)$1	222	100	103	8.9999
CUU	chr2:165200817-165201039(-)$1	222	177	180	8.9999
CUU	chr11:107073656-107073897(-)$1	241	36	39	8.9999
CUU	chr12:74374701-74374921(-)$1	220	49	52	8.9999
CUU	chr14:6915604-6915828(+)$1	224	46	49	8.9999
CUU	chr7:26082519-26082740(+)$1	221	116	119	8.9999
CUU	chr15:102262283-102262499(+)$1	216	10	13	8.9999
CUU	chr6:129781215-129781437(-)$1	222	5	8	8.9999
CUU	chr14:52636427-52636649(-)$1	222	22	25	8.9999
CUU	chr1:99603045-99603270(-)$1	225	51	54	8.9999
CUU	chr8:4284801-4285018(-)$1	217	57	60	8.9999
CUU	chr7:3612125-3612346(+)$1	221	24	27	8.9999
CUU	chr19:9001493-9001714(-)$1	221	2	5	8.9999
CUU	chr4:143040094-143040316(+)$1	222	39	42	8.9999
CUU	chr11:116715102-116715326(+)$1	224	16	19	8.9999
CUU	chr13:110851764-110851998(-)$1	234	47	50	8.9999
CUU	chrX:135770055-135770278(+)$1	223	60	63	8.9999
cuu	chr6:124280355-124280578(+)$1	223	5	8	8.9999
CUU	chr3:89252882-89253103(-)$1	221	77	80	8.9999
CUU	chr6:85892628-85892851(-)$1	223	14	17	8.9999
CUU	chr2:31149500-31149743(+)$1	243	33	36	8.9999
CUU	chr17:34324596-34324817(+)$1	221	45	48	8.9999
CUU	chr5:20265828-20266080(-)$1	252	16	19	8.9999
CUU	chr5:130459766-130459986(+)$1	220	64	67	8.9999
CUU	chr12:36741947-36742172(-)$1	225	26	29	8.9999
CUU	chr10:79326713-79326936(+)$1	223	19	22	8.9999
CUU	chr1:64647846-64648074(+)$1	228	9	12	8.9999
CUU	chr1:184397301-184397533(-)$1	232	33	36	8.9999
CUU	chr7:134950203-134950433(-)$1	230	132	135	8.9999
CUU	chrX:152008193-152008412(-)$1	219	95	98	8.9999
CUU	chr17:90436007-90436253(-)$1	246	142	145	8.9999
CUU	chr14:55725746-55725966(-)$1	220	35	38	8.9999
CUU	chrX:150268683-150268905(+)$1	222	13	16	8.9999
CUU	chr2:180330369-180330588(+)$1	219	19	22	8.9999
CUU	chr11:118026917-118027152(-)$1	235	123	126	8.9999
CUU	chr2:158322641-158322861(+)$1	220	2	5	8.9999
CUU	chr1:24018989-24019210(-)$1	221	17	20	8.9999
CUU	chr10:80614600-80614835(+)$1	235	23	26	8.9999
CUU	chr17:15661242-15661462(+)$1	220	21	24	8.9999
CUU	chr1:64080785-64081005(-)$1	220	31	34	8.9999
CUU	chr7:53079879-53080100(+)$1	221	32	35	8.9999
CUU	chr11:74713906-74714155(+)$1	249	4	7	8.9999
CUU	chrX:119508859-119509079(-)$1	220	13	16	8.9999
CUU	chr15:75449582-75449800(-)$1	218	105	108	8.9999
CUU	chr3:156224803-156225030(-)$1	227	13	16	8.9999
CUU	chr17:56542071-56542310(+)$1	239	24	27	8.9999
CUU	chr19:7169093-7169328(-)$1	235	107	110	8.9999
CUU	chr6:136558481-136558707(+)$1	226	0	3	8.9999
CUU	chr11:3617035-3617256(+)$1	221	59	62	8.9999
CUU	chr2:69591480-69591714(+)$1	234	189	192	8.9999
CUU	chr11:11167244-11167472(+)$1	228	36	39	8.9999
CUU	chr15:103023875-103024093(+)$1	218	27	30	8.9999
CUU	chr4:117507847-117508065(-)$1	218	40	43	8.9999
CUU	chr17:13165983-13166206(+)$1	223	0	3	8.9999
CUU	chr4:147991977-147992211(-)$1	234	11	14	8.9999
CUU	chr9:107458906-107459128(+)$1	222	13	16	8.9999
CUU	chr5:35422509-35422733(-)$1	224	11	14	8.9999
CUU	chr4:137817135-137817356(-)$1	221	43	46	8.9999
CUU	chr10:76017202-76017444(+)$1	242	8	11	8.9999
CUU	chr15:38448828-38449052(-)$1	224	28	31	8.9999
CUU	chr16:35305543-35305771(+)$1	228	47	50	8.9999
CUU	chr12:56239891-56240118(+)$1	227	111	114	8.9999
CUU	chr15:84213639-84213861(-)$1	222	90	93	8.9999
CUU	chr16:58466696-58466917(+)$1	221	15	18	8.9999
CUU	chr1:135198769-135198990(+)$1	221	33	36	8.9999
CUU	chr10:44083904-44084128(+)$1	224	59	62	8.9999
CUU	chr19:5885314-5885529(+)$1	215	29	32	8.9999
CUU	chr12:17291347-17291567(-)$1	220	42	45	8.9999
CUU	chr4:129055171-129055392(-)$1	221	5	8	8.9999
CUU	chr17:35796480-35796698(-)$1	218	24	27	8.9999
CUU	chr17:27846909-27847139(+)$1	230	14	17	8.9999
CUU	chr1:62687123-62687344(-)$1	221	21	24	8.9999
CUU	chr2:155212738-155212959(+)$1	221	13	16	8.9999
CUU	chr13:76007992-76008212(+)$1	220	54	57	8.9999
CUU	chr5:130475650-130475870(-)$1	220	26	29	8.9999
CUU	chr5:33135759-33135984(-)$1	225	13	16	8.9999
CUU	chr10:82696068-82696287(-)$1	219	51	54	8.9999
CUU	chr2:37226367-37226592(-)$1	225	19	22	8.9999
CUU	chr15:76913176-76913416(-)$1	240	108	111	8.9999
cuu	chrX:50622328-50622556(-)$1	228	17	20	8.9999
CUU	chr1:173145019-173145242(-)$1	223	40	43	8.9999
CUU	chr5:136210766-136211006(+)$1	240	101	104	8.9999
CUU	chr1:65205131-65205367(-)$1	236	62	65	8.9999

#otherMatches

#Struct PSSM
%%%	chr18:36124676-36124897(+)$1	221	33	36	8.9999
:::	chr1:37863791-37864008(+)$1	217	7	10	8.9999
EEE	chr10:96942291-96942523(+)$1	232	32	35	8.9999
c::	chr18:35776074-35776304(+)$1	230	50	53	8.9999
ccp	chr5:150099398-150099621(-)$1	223	16	19	8.9999
eee	chr11:11830525-11830758(-)$1	233	105	108	8.9999
:::	chr8:19696096-19696322(+)$1	226	66	69	8.9999
eee	chr18:24119613-24119834(+)$1	221	39	42	8.9999
GGG	chr9:65542518-65542750(-)$1	232	11	14	8.9999
eee	chr19:3389554-3389775(-)$1	221	54	57	8.9999
b!!	chr2:173924680-173924912(+)$1	232	18	21	8.9999
+++	chr8:79768213-79768435(+)$1	222	100	103	8.9999
::J	chr2:165200817-165201039(-)$1	222	177	180	8.9999
:::	chr11:107073656-107073897(-)$1	241	36	39	8.9999
eee	chr12:74374701-74374921(-)$1	220	49	52	8.9999
:::	chr14:6915604-6915828(+)$1	224	46	49	8.9999
FKK	chr7:26082519-26082740(+)$1	221	116	119	8.9999
ggg	chr15:102262283-102262499(+)$1	216	10	13	8.9999
:dd	chr6:129781215-129781437(-)$1	222	5	8	8.9999
BHH	chr14:52636427-52636649(-)$1	222	22	25	8.9999
eee	chr1:99603045-99603270(-)$1	225	51	54	8.9999
:::	chr8:4284801-4285018(-)$1	217	57	60	8.9999
H::	chr7:3612125-3612346(+)$1	221	24	27	8.9999
:::	chr19:9001493-9001714(-)$1	221	2	5	8.9999
bmm	chr4:143040094-143040316(+)$1	222	39	42	8.9999
cdd	chr11:116715102-116715326(+)$1	224	16	19	8.9999
c[d	chr13:110851764-110851998(-)$1	234	47	50	8.9999
mmm	chrX:135770055-135770278(+)$1	223	60	63	8.9999
eee	chr6:124280355-124280578(+)$1	223	5	8	8.9999
mmm	chr3:89252882-89253103(-)$1	221	77	80	8.9999
:::	chr6:85892628-85892851(-)$1	223	14	17	8.9999
%%%	chr2:31149500-31149743(+)$1	243	33	36	8.9999
ccc	chr17:34324596-34324817(+)$1	221	45	48	8.9999
ccc	chr5:20265828-20266080(-)$1	252	16	19	8.9999
ddd	chr5:130459766-130459986(+)$1	220	64	67	8.9999
cc!	chr12:36741947-36742172(-)$1	225	26	29	8.9999
[cc	chr10:79326713-79326936(+)$1	223	19	22	8.9999
BKK	chr1:64647846-64648074(+)$1	228	9	12	8.9999
mdd	chr1:184397301-184397533(-)$1	232	33	36	8.9999
$$$	chr7:134950203-134950433(-)$1	230	132	135	8.9999
:::	chrX:152008193-152008412(-)$1	219	95	98	8.9999
!cc	chr17:90436007-90436253(-)$1	246	142	145	8.9999
:ee	chr14:55725746-55725966(-)$1	220	35	38	8.9999
ooe	chrX:150268683-150268905(+)$1	222	13	16	8.9999
LLC	chr2:180330369-180330588(+)$1	219	19	22	8.9999
EE:	chr11:118026917-118027152(-)$1	235	123	126	8.9999
:::	chr2:158322641-158322861(+)$1	220	2	5	8.9999
:::	chr1:24018989-24019210(-)$1	221	17	20	8.9999
ccm	chr10:80614600-80614835(+)$1	235	23	26	8.9999
TEE	chr17:15661242-15661462(+)$1	220	21	24	8.9999
)))	chr1:64080785-64081005(-)$1	220	31	34	8.9999
b]e	chr7:53079879-53080100(+)$1	221	32	35	8.9999
:::	chr11:74713906-74714155(+)$1	249	4	7	8.9999
ddd	chrX:119508859-119509079(-)$1	220	13	16	8.9999
eee	chr15:75449582-75449800(-)$1	218	105	108	8.9999
uuu	chr3:156224803-156225030(-)$1	227	13	16	8.9999
BKK	chr17:56542071-56542310(+)$1	239	24	27	8.9999
EEE	chr19:7169093-7169328(-)$1	235	107	110	8.9999
:::	chr6:136558481-136558707(+)$1	226	0	3	8.9999
cc#	chr11:3617035-3617256(+)$1	221	59	62	8.9999
bb4	chr2:69591480-69591714(+)$1	234	189	192	8.9999
c""	chr11:11167244-11167472(+)$1	228	36	39	8.9999
::D	chr15:103023875-103024093(+)$1	218	27	30	8.9999
===	chr4:117507847-117508065(-)$1	218	40	43	8.9999
:::	chr17:13165983-13166206(+)$1	223	0	3	8.9999
fmm	chr4:147991977-147992211(-)$1	234	11	14	8.9999
ccc	chr9:107458906-107459128(+)$1	222	13	16	8.9999
FF:	chr5:35422509-35422733(-)$1	224	11	14	8.9999
ell	chr4:137817135-137817356(-)$1	221	43	46	8.9999
$$$	chr10:76017202-76017444(+)$1	242	8	11	8.9999
C::	chr15:38448828-38449052(-)$1	224	28	31	8.9999
hhh	chr16:35305543-35305771(+)$1	228	47	50	8.9999
ddd	chr12:56239891-56240118(+)$1	227	111	114	8.9999
ii!	chr15:84213639-84213861(-)$1	222	90	93	8.9999
HHH	chr16:58466696-58466917(+)$1	221	15	18	8.9999
CCC	chr1:135198769-135198990(+)$1	221	33	36	8.9999
b!!	chr10:44083904-44084128(+)$1	224	59	62	8.9999
cmm	chr19:5885314-5885529(+)$1	215	29	32	8.9999
EEK	chr12:17291347-17291567(-)$1	220	42	45	8.9999
DKK	chr4:129055171-129055392(-)$1	221	5	8	8.9999
ee:	chr17:35796480-35796698(-)$1	218	24	27	8.9999
qqq	chr17:27846909-27847139(+)$1	230	14	17	8.9999
:ii	chr1:62687123-62687344(-)$1	221	21	24	8.9999
:::	chr2:155212738-155212959(+)$1	221	13	16	8.9999
dDD	chr13:76007992-76008212(+)$1	220	54	57	8.9999
:::	chr5:130475650-130475870(-)$1	220	26	29	8.9999
[cc	chr5:33135759-33135984(-)$1	225	13	16	8.9999
MMM	chr10:82696068-82696287(-)$1	219	51	54	8.9999
^^^	chr2:37226367-37226592(-)$1	225	19	22	8.9999
::e	chr15:76913176-76913416(-)$1	240	108	111	8.9999
:::	chrX:50622328-50622556(-)$1	228	17	20	8.9999
333	chr1:173145019-173145242(-)$1	223	40	43	8.9999
f::	chr5:136210766-136211006(+)$1	240	101	104	8.9999
:::	chr1:65205131-65205367(-)$1	236	62	65	8.9999

#DB
...	chr18:36124676-36124897(+)$1	1	33	36	8.9999
...	chr1:37863791-37864008(+)$1	1	7	10	8.9999
(((	chr10:96942291-96942523(+)$1	1	32	35	8.9999
)..	chr18:35776074-35776304(+)$1	1	50	53	8.9999
((.	chr5:150099398-150099621(-)$1	1	16	19	8.9999
)))	chr11:11830525-11830758(-)$1	1	105	108	8.9999
...	chr8:19696096-19696322(+)$1	1	66	69	8.9999
)))	chr18:24119613-24119834(+)$1	1	39	42	8.9999
(((	chr9:65542518-65542750(-)$1	1	11	14	8.9999
(((	chr19:3389554-3389775(-)$1	1	54	57	8.9999
(..	chr2:173924680-173924912(+)$1	1	18	21	8.9999
...	chr8:79768213-79768435(+)$1	1	100	103	8.9999
..)	chr2:165200817-165201039(-)$1	1	177	180	8.9999
...	chr11:107073656-107073897(-)$1	1	36	39	8.9999
(((	chr12:74374701-74374921(-)$1	1	49	52	8.9999
...	chr14:6915604-6915828(+)$1	1	46	49	8.9999
(..	chr7:26082519-26082740(+)$1	1	116	119	8.9999
(((	chr15:102262283-102262499(+)$1	1	10	13	8.9999
.((	chr6:129781215-129781437(-)$1	1	5	8	8.9999
(((	chr14:52636427-52636649(-)$1	1	22	25	8.9999
)))	chr1:99603045-99603270(-)$1	1	51	54	8.9999
...	chr8:4284801-4285018(-)$1	1	57	60	8.9999
(..	chr7:3612125-3612346(+)$1	1	24	27	8.9999
...	chr19:9001493-9001714(-)$1	1	2	5	8.9999
(..	chr4:143040094-143040316(+)$1	1	39	42	8.9999
(((	chr11:116715102-116715326(+)$1	1	16	19	8.9999
(.(	chr13:110851764-110851998(-)$1	1	47	50	8.9999
...	chrX:135770055-135770278(+)$1	1	60	63	8.9999
(((	chr6:124280355-124280578(+)$1	1	5	8	8.9999
...	chr3:89252882-89253103(-)$1	1	77	80	8.9999
...	chr6:85892628-85892851(-)$1	1	14	17	8.9999
...	chr2:31149500-31149743(+)$1	1	33	36	8.9999
(((	chr17:34324596-34324817(+)$1	1	45	48	8.9999
(((	chr5:20265828-20266080(-)$1	1	16	19	8.9999
(((	chr5:130459766-130459986(+)$1	1	64	67	8.9999
((.	chr12:36741947-36742172(-)$1	1	26	29	8.9999
.((	chr10:79326713-79326936(+)$1	1	19	22	8.9999
(..	chr1:64647846-64648074(+)$1	1	9	12	8.9999
.))	chr1:184397301-184397533(-)$1	1	33	36	8.9999
...	chr7:134950203-134950433(-)$1	1	132	135	8.9999
...	chrX:152008193-152008412(-)$1	1	95	98	8.9999
.((	chr17:90436007-90436253(-)$1	1	142	145	8.9999
.((	chr14:55725746-55725966(-)$1	1	35	38	8.9999
..)	chrX:150268683-150268905(+)$1	1	13	16	8.9999
..(	chr2:180330369-180330588(+)$1	1	19	22	8.9999
)).	chr11:118026917-118027152(-)$1	1	123	126	8.9999
...	chr2:158322641-158322861(+)$1	1	2	5	8.9999
...	chr1:24018989-24019210(-)$1	1	17	20	8.9999
((.	chr10:80614600-80614835(+)$1	1	23	26	8.9999
.((	chr17:15661242-15661462(+)$1	1	21	24	8.9999
...	chr1:64080785-64081005(-)$1	1	31	34	8.9999
).)	chr7:53079879-53080100(+)$1	1	32	35	8.9999
...	chr11:74713906-74714155(+)$1	1	4	7	8.9999
(((	chrX:119508859-119509079(-)$1	1	13	16	8.9999
)))	chr15:75449582-75449800(-)$1	1	105	108	8.9999
...	chr3:156224803-156225030(-)$1	1	13	16	8.9999
(..	chr17:56542071-56542310(+)$1	1	24	27	8.9999
)))	chr19:7169093-7169328(-)$1	1	107	110	8.9999
...	chr6:136558481-136558707(+)$1	1	0	3	8.9999
((.	chr11:3617035-3617256(+)$1	1	59	62	8.9999
)).	chr2:69591480-69591714(+)$1	1	189	192	8.9999
(..	chr11:11167244-11167472(+)$1	1	36	39	8.9999
..(	chr15:103023875-103024093(+)$1	1	27	30	8.9999
(((	chr4:117507847-117508065(-)$1	1	40	43	8.9999
...	chr17:13165983-13166206(+)$1	1	0	3	8.9999
(..	chr4:147991977-147992211(-)$1	1	11	14	8.9999
(((	chr9:107458906-107459128(+)$1	1	13	16	8.9999
((.	chr5:35422509-35422733(-)$1	1	11	14	8.9999
(..	chr4:137817135-137817356(-)$1	1	43	46	8.9999
...	chr10:76017202-76017444(+)$1	1	8	11	8.9999
(..	chr15:38448828-38449052(-)$1	1	28	31	8.9999
(((	chr16:35305543-35305771(+)$1	1	47	50	8.9999
)))	chr12:56239891-56240118(+)$1	1	111	114	8.9999
((.	chr15:84213639-84213861(-)$1	1	90	93	8.9999
(((	chr16:58466696-58466917(+)$1	1	15	18	8.9999
(((	chr1:135198769-135198990(+)$1	1	33	36	8.9999
(..	chr10:44083904-44084128(+)$1	1	59	62	8.9999
(..	chr19:5885314-5885529(+)$1	1	29	32	8.9999
((.	chr12:17291347-17291567(-)$1	1	42	45	8.9999
(..	chr4:129055171-129055392(-)$1	1	5	8	8.9999
)).	chr17:35796480-35796698(-)$1	1	24	27	8.9999
...	chr17:27846909-27847139(+)$1	1	14	17	8.9999
.((	chr1:62687123-62687344(-)$1	1	21	24	8.9999
...	chr2:155212738-155212959(+)$1	1	13	16	8.9999
)((	chr13:76007992-76008212(+)$1	1	54	57	8.9999
...	chr5:130475650-130475870(-)$1	1	26	29	8.9999
.((	chr5:33135759-33135984(-)$1	1	13	16	8.9999
...	chr10:82696068-82696287(-)$1	1	51	54	8.9999
...	chr2:37226367-37226592(-)$1	1	19	22	8.9999
..(	chr15:76913176-76913416(-)$1	1	108	111	8.9999
...	chrX:50622328-50622556(-)$1	1	17	20	8.9999
...	chr1:173145019-173145242(-)$1	1	40	43	8.9999
)..	chr5:136210766-136211006(+)$1	1	101	104	8.9999
...	chr1:65205131-65205367(-)$1	1	62	65	8.9999

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

#score	845.9999999999998
#seq	94
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_CDS_m3_run1.nuc.txt

#NT
CAGCA	chr11:104199387-104199649(-)$1	262	85	90	15.0000
CAGCA	chr1:39427713-39428004(+)$1	291	276	281	15.0000
CAGCA	chr3:9447208-9447476(-)$1	268	261	266	15.0000
CAGCA	chr7:26531266-26531497(-)$1	231	210	215	15.0000
CAGCA	chrX:56320479-56320739(-)$1	260	44	49	15.0000
CAGCA	chr11:86520450-86520700(-)$1	250	77	82	15.0000
CAGCA	chr4:43702963-43703209(+)$1	246	81	86	15.0000
CAGCA	chr14:103488512-103488792(-)$1	280	268	273	15.0000
CAGCA	chr14:122034277-122034507(-)$1	230	122	127	15.0000
CAGCA	chr7:6661077-6661351(-)$1	274	106	111	15.0000
CAGCA	chr16:13986792-13987027(+)$1	235	40	45	15.0000
CAGCA	chr13:105756979-105757214(-)$1	235	40	45	15.0000
CAGCA	chr11:69416162-69416465(-)$1	303	224	229	15.0000
CAGCA	chr10:93432987-93433233(-)$1	246	32	37	15.0000
CAGCA	chr5:90673282-90673555(-)$1	273	146	151	15.0000
CAGCA	chr6:85878677-85878920(+)$1	243	60	65	15.0000
CAGCA	chr5:21402554-21402850(-)$1	296	85	90	15.0000
CAGCA	chr9:102097404-102097698(-)$1	294	77	82	15.0000
CAGCA	chr1:55053895-55054130(-)$1	235	204	209	15.0000
CAGCA	chr4:59232994-59233260(+)$1	266	25	30	15.0000
CAGCA	chr1:37501594-37501853(-)$1	259	219	224	15.0000
CAGCA	chr8:112200528-112200784(-)$1	256	101	106	15.0000
CAGCA	chr9:88371860-88372111(-)$1	251	176	181	15.0000
CAGCA	chr5:115180137-115180404(-)$1	267	130	135	15.0000
CAGCA	chr4:148631884-148632148(-)$1	264	33	38	15.0000
CAGCA	chr14:118512159-118512410(-)$1	251	245	250	15.0000
CAGCA	chr15:57885024-57885275(-)$1	251	100	105	15.0000
CAGCA	chr13:104652282-104652523(-)$1	241	195	200	15.0000
CAGCA	chr5:21501073-21501332(-)$1	259	41	46	15.0000
CAGCA	chr3:107926394-107926653(-)$1	259	112	117	15.0000
CAGCA	chr8:124408831-124409096(-)$1	265	19	24	15.0000
cAGCA	chr7:119247385-119247681(+)$1	296	4	9	15.0000
CAGCA	chr11:30036947-30037232(-)$1	285	101	106	15.0000
CAGCA	chr3:67262057-67262298(-)$1	241	175	180	15.0000
CAGCA	chr9:65544794-65545034(-)$1	240	166	171	15.0000
CAGCA	chr5:119200775-119201057(+)$1	282	237	242	15.0000
CAGCA	chr12:77043126-77043366(+)$1	240	58	63	15.0000
CAGCA	chr5:21157506-21157769(+)$1	263	2	7	15.0000
CAGCA	chr5:21248586-21248855(+)$1	269	20	25	15.0000
CAGCA	chr7:28442982-28443235(-)$1	253	195	200	15.0000
CAGCA	chr12:118139342-118139601(+)$1	259	109	114	15.0000
CAGCA	chr1:154691276-154691527(-)$1	251	140	145	15.0000
CAGCA	chr5:151603346-151603611(+)$1	265	214	219	15.0000
CAGCA	chr2:52290025-52290282(-)$1	257	30	35	15.0000
CAGCA	chr9:42252387-42252639(-)$1	252	99	104	15.0000
CAGCA	chr18:89590308-89590543(-)$1	235	135	140	15.0000
CAGCA	chr1:50984781-50985056(+)$1	275	39	44	15.0000

#otherMatches

#Struct PSSM
apppp	chr19:8912577-8912863(-)$1	286	112	117	15.0000
DDDDD	chr11:104199387-104199649(-)$1	262	85	90	15.0000
BZZZG	chr1:39427713-39428004(+)$1	291	276	281	15.0000
2dddd	chr3:9447208-9447476(-)$1	268	261	266	15.0000
llbb2	chr7:26531266-26531497(-)$1	231	210	215	15.0000
b[bbr	chrX:56320479-56320739(-)$1	260	44	49	15.0000
ddddn	chr11:86520450-86520700(-)$1	250	77	82	15.0000
CCCKK	chr4:43702963-43703209(+)$1	246	81	86	15.0000
bmmmm	chr14:103488512-103488792(-)$1	280	268	273	15.0000
IIII:	chr14:122034277-122034507(-)$1	230	122	127	15.0000
5bb22	chr7:6661077-6661351(-)$1	274	106	111	15.0000
E{BB:	chr16:13986792-13987027(+)$1	235	40	45	15.0000
ERRRR	chr13:105756979-105757214(-)$1	235	40	45	15.0000
::ddd	chr11:69416162-69416465(-)$1	303	224	229	15.0000
eeeee	chr10:93432987-93433233(-)$1	246	32	37	15.0000
555cc	chr5:90673282-90673555(-)$1	273	146	151	15.0000
:hhhh	chr6:85878677-85878920(+)$1	243	60	65	15.0000
eeee:	chr5:21402554-21402850(-)$1	296	85	90	15.0000
5gggg	chr9:102097404-102097698(-)$1	294	77	82	15.0000
::BB}	chr1:55053895-55054130(-)$1	235	204	209	15.0000
fffmm	chr4:59232994-59233260(+)$1	266	25	30	15.0000
!ccc[	chr1:37501594-37501853(-)$1	259	219	224	15.0000
MEEEE	chr8:112200528-112200784(-)$1	256	101	106	15.0000
hhhhh	chr9:88371860-88372111(-)$1	251	176	181	15.0000
::FFF	chr5:115180137-115180404(-)$1	267	130	135	15.0000
&eeee	chr4:148631884-148632148(-)$1	264	33	38	15.0000
f::::	chr14:118512159-118512410(-)$1	251	245	250	15.0000
bbccc	chr15:57885024-57885275(-)$1	251	100	105	15.0000
dd[dd	chr13:104652282-104652523(-)$1	241	195	200	15.0000
55bb]	chr5:21501073-21501332(-)$1	259	41	46	15.0000
d4444	chr3:107926394-107926653(-)$1	259	112	117	15.0000
HHHH:	chr8:124408831-124409096(-)$1	265	19	24	15.0000
:::::	chr7:119247385-119247681(+)$1	296	4	9	15.0000
&&&&&	chr11:30036947-30037232(-)$1	285	101	106	15.0000
c]bb:	chr3:67262057-67262298(-)$1	241	175	180	15.0000
a::::	chr9:65544794-65545034(-)$1	240	166	171	15.0000
FFFFF	chr5:119200775-119201057(+)$1	282	237	242	15.0000
qqqqq	chr12:77043126-77043366(+)$1	240	58	63	15.0000
::ccc	chr5:21157506-21157769(+)$1	263	2	7	15.0000
eeeee	chr5:21248586-21248855(+)$1	269	20	25	15.0000
eeee[	chr7:28442982-28443235(-)$1	253	195	200	15.0000
##ccc	chr12:118139342-118139601(+)$1	259	109	114	15.0000
b]bb:	chr1:154691276-154691527(-)$1	251	140	145	15.0000
:eeee	chr5:151603346-151603611(+)$1	265	214	219	15.0000
uuuuu	chr2:52290025-52290282(-)$1	257	30	35	15.0000
:::::	chr9:42252387-42252639(-)$1	252	99	104	15.0000
ccbbc	chr18:89590308-89590543(-)$1	235	135	140	15.0000
=====	chr1:50984781-50985056(+)$1	275	39	44	15.0000

#DB
(....	chr19:8912577-8912863(-)$1	1	112	117	15.0000
)))))	chr11:104199387-104199649(-)$1	1	85	90	15.0000
)...)	chr1:39427713-39428004(+)$1	1	276	281	15.0000
.))))	chr3:9447208-9447476(-)$1	1	261	266	15.0000
..)).	chr7:26531266-26531497(-)$1	1	210	215	15.0000
(.((.	chrX:56320479-56320739(-)$1	1	44	49	15.0000
((((.	chr11:86520450-86520700(-)$1	1	77	82	15.0000
(((..	chr4:43702963-43703209(+)$1	1	81	86	15.0000
(....	chr14:103488512-103488792(-)$1	1	268	273	15.0000
)))).	chr14:122034277-122034507(-)$1	1	122	127	15.0000
.))..	chr7:6661077-6661351(-)$1	1	106	111	15.0000
(.((.	chr16:13986792-13987027(+)$1	1	40	45	15.0000
(....	chr13:105756979-105757214(-)$1	1	40	45	15.0000
..(((	chr11:69416162-69416465(-)$1	1	224	229	15.0000
(((((	chr10:93432987-93433233(-)$1	1	32	37	15.0000
...))	chr5:90673282-90673555(-)$1	1	146	151	15.0000
.((((	chr6:85878677-85878920(+)$1	1	60	65	15.0000
)))).	chr5:21402554-21402850(-)$1	1	85	90	15.0000
.))))	chr9:102097404-102097698(-)$1	1	77	82	15.0000
..)).	chr1:55053895-55054130(-)$1	1	204	209	15.0000
(((..	chr4:59232994-59233260(+)$1	1	25	30	15.0000
.(((.	chr1:37501594-37501853(-)$1	1	219	224	15.0000
.((((	chr8:112200528-112200784(-)$1	1	101	106	15.0000
(((((	chr9:88371860-88372111(-)$1	1	176	181	15.0000
..(((	chr5:115180137-115180404(-)$1	1	130	135	15.0000
.((((	chr4:148631884-148632148(-)$1	1	33	38	15.0000
)....	chr14:118512159-118512410(-)$1	1	245	250	15.0000
(((((	chr15:57885024-57885275(-)$1	1	100	105	15.0000
((.((	chr13:104652282-104652523(-)$1	1	195	200	15.0000
..)).	chr5:21501073-21501332(-)$1	1	41	46	15.0000
)....	chr3:107926394-107926653(-)$1	1	112	117	15.0000
((((.	chr8:124408831-124409096(-)$1	1	19	24	15.0000
.....	chr7:119247385-119247681(+)$1	1	4	9	15.0000
.....	chr11:30036947-30037232(-)$1	1	101	106	15.0000
).)).	chr3:67262057-67262298(-)$1	1	175	180	15.0000
)....	chr9:65544794-65545034(-)$1	1	166	171	15.0000
)))))	chr5:119200775-119201057(+)$1	1	237	242	15.0000
.....	chr12:77043126-77043366(+)$1	1	58	63	15.0000
..(((	chr5:21157506-21157769(+)$1	1	2	7	15.0000
)))))	chr5:21248586-21248855(+)$1	1	20	25	15.0000
((((.	chr7:28442982-28443235(-)$1	1	195	200	15.0000
..(((	chr12:118139342-118139601(+)$1	1	109	114	15.0000
).)).	chr1:154691276-154691527(-)$1	1	140	145	15.0000
.((((	chr5:151603346-151603611(+)$1	1	214	219	15.0000
.....	chr2:52290025-52290282(-)$1	1	30	35	15.0000
.....	chr9:42252387-42252639(-)$1	1	99	104	15.0000
(((((	chr18:89590308-89590543(-)$1	1	135	140	15.0000
(((((	chr1:50984781-50985056(+)$1	1	39	44	15.0000

#PSSM
C : 0.97	c : 0.02	
A : 1.00	
G : 1.00	
C : 1.00	
A : 1.00	

#score	720.0000000000001
#seq	48
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m1_run1.nuc.txt

#NT
GGAAGAC	chr5:150005897-150006119(+)$1	222	5	12	13.8048
UGAAGAU	chr1:187218177-187218397(+)$1	220	46	53	11.8536
GGAAAAA	chr17:15867679-15867899(+)$1	220	50	57	11.0000
GGAUGAA	chr14:27906484-27906705(+)$1	221	35	42	11.1219
GGAAUAA	chr2:20728354-20728574(+)$1	220	101	108	11.0000
UGAAGAA	chr1:136251103-136251346(-)$1	243	95	102	13.4390
GGAUGAA	chr13:51234864-51235084(+)$1	220	71	78	11.1219
GGAAGCA	chr9:64025994-64026214(+)$1	220	58	65	10.6341
AGAAGAU	chr12:112871792-112872012(+)$1	220	108	115	11.2439
UGAAGAG	chr11:88023587-88023807(+)$1	220	63	70	11.8536
GGAAGAG	chr18:65972333-65972557(+)$1	224	88	95	13.8048
GGAAGAC	chr11:117828919-117829141(-)$1	222	177	184	13.8048
UGAAGAA	chr1:182682269-182682489(+)$1	220	33	40	13.4390
AGAAGAU	chr10:57861766-57861986(+)$1	220	67	74	11.2439
GGAAGAU	chr2:162858911-162859147(+)$1	236	151	158	13.8048
GGAAGAU	chr17:88389427-88389667(+)$1	240	7	14	13.8048
AGAAGAA	chr8:97385511-97385731(+)$1	220	24	31	12.8292
GGCAGAA	chr14:63757798-63758018(+)$1	220	80	87	10.6341
AGAAGAA	chr1:141368109-141368329(+)$1	220	70	77	12.8292
GGAAGAA	chr5:64702279-64702499(+)$1	220	97	104	15.3902
UGAAGAC	chr1:59920624-59920863(+)$1	239	26	33	11.8536
UGAAGAA	chr17:57142771-57142992(-)$1	221	9	16	13.4390
GGAAGAG	chr1:65302428-65302648(+)$1	220	86	93	13.8048
GGAAGAG	chr10:90558585-90558823(+)$1	238	121	128	13.8048
UGAAGAA	chr9:75019464-75019684(+)$1	220	17	24	13.4390
GGAAGAU	chr19:46836149-46836369(+)$1	220	186	193	13.8048
UGAAGAC	chr11:99071447-99071667(-)$1	220	89	96	11.8536
GGAACAA	chr18:77178235-77178457(+)$1	222	14	21	11.1219
GGAAGAG	chr11:70519450-70519671(+)$1	221	49	56	13.8048
GGAGGAA	chr13:35964365-35964603(+)$1	238	20	27	11.1219
UGAAGAA	chr1:127290452-127290676(-)$1	224	47	54	13.4390
GGAAGAC	chr10:25161521-25161764(+)$1	243	188	195	13.8048
GGAACAA	chr4:146987914-146988150(-)$1	236	36	43	11.1219
GGAAGAA	chr14:51436630-51436850(+)$1	220	118	125	15.3902
GGAAGAC	chr3:101949141-101949361(+)$1	220	37	44	13.8048
GGAAGAA	chr2:127109731-127109969(+)$1	238	123	130	15.3902
UGAAGAC	chr2:118894076-118894307(+)$1	231	77	84	11.8536
GGAGGAA	chr10:75967024-75967244(+)$1	220	5	12	11.1219
ggaagAG	chr19:47201372-47201592(+)$1	220	157	164	13.8048
AGAAGAG	chr4:102834967-102835194(+)$1	227	0	7	11.2439

#otherMatches

#Struct PSSM
cc]dddd	chr12:111864075-111864295(+)$1	220	144	151	13.8048
GGGGGGK	chr5:150005897-150006119(+)$1	222	5	12	13.8048
bb]ffff	chr1:187218177-187218397(+)$1	220	46	53	11.8536
ggggg::	chr17:15867679-15867899(+)$1	220	50	57	11.0000
ddd:ggg	chr14:27906484-27906705(+)$1	221	35	42	11.1219
ccc:ddd	chr2:20728354-20728574(+)$1	220	101	108	11.0000
cc:::::	chr1:136251103-136251346(-)$1	243	95	102	13.4390
+dddd""	chr13:51234864-51235084(+)$1	220	71	78	11.1219
dmmmmdd	chr9:64025994-64026214(+)$1	220	58	65	10.6341
:JJJJJJ	chr12:112871792-112872012(+)$1	220	108	115	11.2439
hhhpppp	chr11:88023587-88023807(+)$1	220	63	70	11.8536
$$bb[bb	chr18:65972333-65972557(+)$1	224	88	95	13.8048
meeeeec	chr11:117828919-117829141(-)$1	222	177	184	13.8048
ee]ccc:	chr1:182682269-182682489(+)$1	220	33	40	13.4390
[dddd!!	chr10:57861766-57861986(+)$1	220	67	74	11.2439
fffff[c	chr2:162858911-162859147(+)$1	236	151	158	13.8048
GGGGGG{	chr17:88389427-88389667(+)$1	240	7	14	13.8048
cccmmmm	chr8:97385511-97385731(+)$1	220	24	31	12.8292
ccc::::	chr14:63757798-63758018(+)$1	220	80	87	10.6341
rrrrrrf	chr1:141368109-141368329(+)$1	220	70	77	12.8292
bb4444c	chr5:64702279-64702499(+)$1	220	97	104	15.3902
ddd]ddd	chr1:59920624-59920863(+)$1	239	26	33	11.8536
DKKBBKK	chr17:57142771-57142992(-)$1	221	9	16	13.4390
a]ccc22	chr1:65302428-65302648(+)$1	220	86	93	13.8048
hhhh:::	chr10:90558585-90558823(+)$1	238	121	128	13.8048
FFF:bb!	chr9:75019464-75019684(+)$1	220	17	24	13.4390
||||||J	chr19:46836149-46836369(+)$1	220	186	193	13.8048
eee::::	chr11:99071447-99071667(-)$1	220	89	96	11.8536
F:::iii	chr18:77178235-77178457(+)$1	222	14	21	11.1219
sssssss	chr11:70519450-70519671(+)$1	221	49	56	13.8048
dddmmmm	chr13:35964365-35964603(+)$1	238	20	27	11.1219
ccc[bb"	chr1:127290452-127290676(-)$1	224	47	54	13.4390
b22eeee	chr10:25161521-25161764(+)$1	243	188	195	13.8048
flllfff	chr4:146987914-146988150(-)$1	236	36	43	11.1219
ddd5555	chr14:51436630-51436850(+)$1	220	118	125	15.3902
FFF:::e	chr3:101949141-101949361(+)$1	220	37	44	13.8048
HHHHggg	chr2:127109731-127109969(+)$1	238	123	130	15.3902
:ffffff	chr2:118894076-118894307(+)$1	231	77	84	11.8536
gg$$$$$	chr10:75967024-75967244(+)$1	220	5	12	11.1219
::::::e	chr19:47201372-47201592(+)$1	220	157	164	13.8048
:======	chr4:102834967-102835194(+)$1	227	0	7	11.2439

#DB
)).))))	chr12:111864075-111864295(+)$1	1	144	151	13.8048
((((((.	chr5:150005897-150006119(+)$1	1	5	12	13.8048
)).))))	chr1:187218177-187218397(+)$1	1	46	53	11.8536
)))))..	chr17:15867679-15867899(+)$1	1	50	57	11.0000
))).(((	chr14:27906484-27906705(+)$1	1	35	42	11.1219
))).(((	chr2:20728354-20728574(+)$1	1	101	108	11.0000
)).....	chr1:136251103-136251346(-)$1	1	95	102	13.4390
.((((..	chr13:51234864-51235084(+)$1	1	71	78	11.1219
(....))	chr9:64025994-64026214(+)$1	1	58	65	10.6341
.))))))	chr12:112871792-112872012(+)$1	1	108	115	11.2439
(((....	chr11:88023587-88023807(+)$1	1	63	70	11.8536
..((.((	chr18:65972333-65972557(+)$1	1	88	95	13.8048
.))))))	chr11:117828919-117829141(-)$1	1	177	184	13.8048
)).))).	chr1:182682269-182682489(+)$1	1	33	40	13.4390
.((((..	chr10:57861766-57861986(+)$1	1	67	74	11.2439
(((((.(	chr2:162858911-162859147(+)$1	1	151	158	13.8048
((((((.	chr17:88389427-88389667(+)$1	1	7	14	13.8048
(((....	chr8:97385511-97385731(+)$1	1	24	31	12.8292
)))....	chr14:63757798-63758018(+)$1	1	80	87	10.6341
......)	chr1:141368109-141368329(+)$1	1	70	77	12.8292
))....)	chr5:64702279-64702499(+)$1	1	97	104	15.3902
))).)))	chr1:59920624-59920863(+)$1	1	26	33	11.8536
(..((..	chr17:57142771-57142992(-)$1	1	9	16	13.4390
).)))..	chr1:65302428-65302648(+)$1	1	86	93	13.8048
))))...	chr10:90558585-90558823(+)$1	1	121	128	13.8048
(((.((.	chr9:75019464-75019684(+)$1	1	17	24	13.4390
......)	chr19:46836149-46836369(+)$1	1	186	193	13.8048
)))....	chr11:99071447-99071667(-)$1	1	89	96	11.8536
(...(((	chr18:77178235-77178457(+)$1	1	14	21	11.1219
.......	chr11:70519450-70519671(+)$1	1	49	56	13.8048
(((....	chr13:35964365-35964603(+)$1	1	20	27	11.1219
(((.((.	chr1:127290452-127290676(-)$1	1	47	54	13.4390
)..))))	chr10:25161521-25161764(+)$1	1	188	195	13.8048
(...)))	chr4:146987914-146988150(-)$1	1	36	43	11.1219
)))....	chr14:51436630-51436850(+)$1	1	118	125	15.3902
(((...(	chr3:101949141-101949361(+)$1	1	37	44	13.8048
))))(((	chr2:127109731-127109969(+)$1	1	123	130	15.3902
.((((((	chr2:118894076-118894307(+)$1	1	77	84	11.8536
((.....	chr10:75967024-75967244(+)$1	1	5	12	11.1219
......(	chr19:47201372-47201592(+)$1	1	157	164	13.8048
.((((((	chr4:102834967-102835194(+)$1	1	0	7	11.2439

#PSSM
G : 0.60	U : 0.24	A : 0.12	g : 0.02	
G : 0.97	g : 0.02	
A : 0.95	C : 0.02	a : 0.02	
A : 0.87	U : 0.04	G : 0.04	a : 0.02	
G : 0.87	C : 0.04	A : 0.02	U : 0.02	g : 0.02	
A : 0.97	C : 0.02	
A : 0.48	U : 0.17	C : 0.17	G : 0.17	

#score	521.4878048780489
#seq	41
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m3_run1.nuc.txt

#NT
CAAGAACCAG	chr4:11091480-11091706(+)$1	226	178	188	12.0454
CAGAAGACUG	chr11:106020181-106020405(-)$1	224	62	72	12.3863
CAGGAACCUG	chr13:52706347-52706566(+)$1	219	136	146	16.8181
GAGGAGCCAG	chr16:4875432-4875653(+)$1	221	139	149	13.1818
CAGGUGACUG	chr19:21922389-21922604(-)$1	215	120	130	13.4090
CAAGACCCUG	chr17:24318118-24318341(-)$1	223	135	145	13.7499
CUGGGGACUG	chr11:57034533-57034750(+)$1	217	83	93	9.3181
CAGGUACCUG	chr8:97529087-97529318(+)$1	231	99	109	14.0909
CAGGUGGGUG	chr6:124795514-124795729(+)$1	215	33	43	10.1136
GAAGGGCCUG	chr3:19574150-19574365(-)$1	215	53	63	10.3409
CAGGAACUUG	chr4:88802259-88802483(+)$1	224	5	15	13.1818
GAAGAGCCUG	chr3:88694641-88694878(+)$1	237	2	12	12.9545
CAGGUACGUG	chr6:86647348-86647572(-)$1	224	127	137	10.4545
CAAGAGGCUG	chr6:41166206-41166428(-)$1	222	27	37	13.9772
caggagcuag	chr14:119279892-119280117(-)$1	225	213	223	13.1818
CAGAACCCUG	chr18:78388790-78389015(-)$1	225	211	221	12.4999
GAGGAGCCGG	chr17:23956311-23956535(+)$1	224	24	34	12.4999
CAGGCACCAG	chr3:125416143-125416363(-)$1	220	24	34	11.2499
GUGGAGCCUG	chr6:100523425-100523650(+)$1	225	193	203	11.2499
CAGGGACGUG	chr16:32143573-32143795(-)$1	222	149	159	10.5681
GAAGAGCCUG	chr14:60027983-60028204(-)$1	221	31	41	12.9545
CAGGAGCCAG	chr3:126632627-126632855(-)$1	228	129	139	16.8181
CAAGAGCCUC	chr14:33473815-33474031(-)$1	216	88	98	12.3863
CAGAGGCCAG	chr15:12196360-12196585(+)$1	225	132	142	10.4545
CUGGAGCCAG	chr9:107440126-107440360(-)$1	234	165	175	12.6136
CAGGGGCCAG	chr12:88626073-88626299(+)$1	226	182	192	14.2045
CAGGAGGUUG	chr3:138209186-138209415(+)$1	229	155	165	12.8409
CAGGAGCCUG	chr7:133251858-133252084(-)$1	226	35	45	19.0909
CAGCAGCUUG	chr15:98604612-98604832(+)$1	220	167	177	11.2499
CAGAGGCCGG	chr7:30114040-30114259(+)$1	219	54	64	9.7727
CAAGAGGCAG	chr5:23006469-23006698(+)$1	229	20	30	11.7045
CAGGAGACUC	chr2:121731624-121731850(+)$1	226	38	48	11.9318
CAGGAGGCUG	chr7:26531264-26531480(+)$1	216	153	163	16.4772
CAGGAGACAG	chr8:47209387-47209605(-)$1	218	126	136	13.8636
CAAGAAGCUG	chr11:120148383-120148626(+)$1	243	53	63	11.7045
CAGGUUCCUG	chr15:79538096-79538332(+)$1	236	9	19	13.2954
CACAAGCCUG	chr11:119070378-119070604(-)$1	226	88	98	11.8181
CAGGUGGCGG	chr2:132695832-132696055(-)$1	223	17	27	10.7954
CAGGACCCUC	chr9:65127519-65127741(+)$1	222	155	165	12.0454
CAAGGACCUG	chr5:34844001-34844226(-)$1	225	89	99	11.7045
CCGGACCCUG	chr13:39052372-39052593(+)$1	221	10	20	11.8181
CAGGAGCGUA	chr8:108210058-108210280(-)$1	222	152	162	11.0227
CAGGAUGCUG	chr17:53810073-53810295(-)$1	222	153	163	13.4090

#otherMatches

#Struct PSSM
]ccc::CCCF	chr2:88705117-88705338(+)$1	221	44	54	12.6136
ffffffccc#	chr4:11091480-11091706(+)$1	226	178	188	12.0454
]bb22ggggg	chr11:106020181-106020405(-)$1	224	62	72	12.3863
f[bb!!bbcc	chr13:52706347-52706566(+)$1	219	136	146	16.8181
22========	chr16:4875432-4875653(+)$1	221	139	149	13.1818
dddmmmmddd	chr19:21922389-21922604(-)$1	215	120	130	13.4090
LLLA{CCCA{	chr17:24318118-24318341(-)$1	223	135	145	13.7499
gggggg22dd	chr11:57034533-57034750(+)$1	217	83	93	9.3181
ldddd22fff	chr8:97529087-97529318(+)$1	231	99	109	14.0909
b=========	chr6:124795514-124795729(+)$1	215	33	43	10.1136
:::bbdddd"	chr3:19574150-19574365(-)$1	215	53	63	10.3409
[eeeee"""c	chr4:88802259-88802483(+)$1	224	5	15	13.1818
::a[cccbbn	chr3:88694641-88694878(+)$1	237	2	12	12.9545
hhhhhhhhqq	chr6:86647348-86647572(-)$1	224	127	137	10.4545
JJJJJ:ffff	chr6:41166206-41166428(-)$1	222	27	37	13.9772
JJJJJ}A:::	chr14:119279892-119280117(-)$1	225	213	223	13.1818
D}BBYYAEEE	chr18:78388790-78389015(-)$1	225	211	221	12.4999
GGGGGGG{BB	chr17:23956311-23956535(+)$1	224	24	34	12.4999
MHHHHHHHHe	chr3:125416143-125416363(-)$1	220	24	34	11.2499
A}HHHHHHHH	chr6:100523425-100523650(+)$1	225	193	203	11.2499
llffffff]f	chr16:32143573-32143795(-)$1	222	149	159	10.5681
444dddd:::	chr14:60027983-60028204(-)$1	221	31	41	12.9545
bbbbdddd:c	chr3:126632627-126632855(-)$1	228	129	139	16.8181
ddDDDD::::	chr14:33473815-33474031(-)$1	216	88	98	12.3863
777777ccc2	chr15:12196360-12196585(+)$1	225	132	142	10.4545
ffff:::::f	chr9:107440126-107440360(-)$1	234	165	175	12.6136
dddIIIIIII	chr12:88626073-88626299(+)$1	226	182	192	14.2045
ddd[ccc!!c	chr3:138209186-138209415(+)$1	229	155	165	12.8409
iiiiiiiDDD	chr7:133251858-133252084(-)$1	226	35	45	19.0909
lllffffffc	chr15:98604612-98604832(+)$1	220	167	177	11.2499
EEEKKCCCKK	chr7:30114040-30114259(+)$1	219	54	64	9.7727
c:EEEEEDDD	chr5:23006469-23006698(+)$1	229	20	30	11.7045
IIIIIII:dd	chr2:121731624-121731850(+)$1	226	38	48	11.9318
innnnniiii	chr7:26531264-26531480(+)$1	216	153	163	16.4772
llccc22bb3	chr8:47209387-47209605(-)$1	218	126	136	13.8636
EEELLLBB{E	chr11:120148383-120148626(+)$1	243	53	63	11.7045
ggggggg!!c	chr15:79538096-79538332(+)$1	236	9	19	13.2954
4444cccbb]	chr11:119070378-119070604(-)$1	226	88	98	11.8181
IIIIHHHHHH	chr2:132695832-132696055(-)$1	223	17	27	10.7954
HHHHZZZEEE	chr9:65127519-65127741(+)$1	222	155	165	12.0454
ooccc]dddd	chr5:34844001-34844226(-)$1	225	89	99	11.7045
JJGGGGGGGf	chr13:39052372-39052593(+)$1	221	10	20	11.8181
ccc::CCC??	chr8:108210058-108210280(-)$1	222	152	162	11.0227
ccceeeeemm	chr17:53810073-53810295(-)$1	222	153	163	13.4090

#DB
.)))..((((	chr2:88705117-88705338(+)$1	1	44	54	12.6136
(((((((((.	chr4:11091480-11091706(+)$1	1	178	188	12.0454
.))..)))))	chr11:106020181-106020405(-)$1	1	62	72	12.3863
(.((..((((	chr13:52706347-52706566(+)$1	1	136	146	16.8181
..))))))))	chr16:4875432-4875653(+)$1	1	139	149	13.1818
(((....)))	chr19:21922389-21922604(-)$1	1	120	130	13.4090
...(.((((.	chr17:24318118-24318341(-)$1	1	135	145	13.7499
))))))..))	chr11:57034533-57034750(+)$1	1	83	93	9.3181
.))))..)))	chr8:97529087-97529318(+)$1	1	99	109	14.0909
)(((((((((	chr6:124795514-124795729(+)$1	1	33	43	10.1136
...((((((.	chr3:19574150-19574365(-)$1	1	53	63	10.3409
.(((((...(	chr4:88802259-88802483(+)$1	1	5	15	13.1818
..(.(((((.	chr3:88694641-88694878(+)$1	1	2	12	12.9545
((((((((..	chr6:86647348-86647572(-)$1	1	127	137	10.4545
(((((.((((	chr6:41166206-41166428(-)$1	1	27	37	13.9772
))))).)...	chr14:119279892-119280117(-)$1	1	213	223	13.1818
).))..))))	chr18:78388790-78389015(-)$1	1	211	221	12.4999
(((((((.((	chr17:23956311-23956535(+)$1	1	24	34	12.4999
.(((((((((	chr3:125416143-125416363(-)$1	1	24	34	11.2499
).))))))))	chr6:100523425-100523650(+)$1	1	193	203	11.2499
..)))))).)	chr16:32143573-32143795(-)$1	1	149	159	10.5681
...))))...	chr14:60027983-60028204(-)$1	1	31	41	12.9545
)))))))).(	chr3:126632627-126632855(-)$1	1	129	139	16.8181
))))))....	chr14:33473815-33474031(-)$1	1	88	98	12.3863
......))).	chr15:12196360-12196585(+)$1	1	132	142	10.4545
)))).....(	chr9:107440126-107440360(-)$1	1	165	175	12.6136
))))))))))	chr12:88626073-88626299(+)$1	1	182	192	14.2045
(((.(((..(	chr3:138209186-138209415(+)$1	1	155	165	12.8409
)))))))(((	chr7:133251858-133252084(-)$1	1	35	45	19.0909
...)))))))	chr15:98604612-98604832(+)$1	1	167	177	11.2499
(((..(((..	chr7:30114040-30114259(+)$1	1	54	64	9.7727
).((((((((	chr5:23006469-23006698(+)$1	1	20	30	11.7045
(((((((.((	chr2:121731624-121731850(+)$1	1	38	48	11.9318
(.....))))	chr7:26531264-26531480(+)$1	1	153	163	16.4772
..)))..)).	chr8:47209387-47209605(-)$1	1	126	136	13.8636
(((...((.(	chr11:120148383-120148626(+)$1	1	53	63	11.7045
(((((((..(	chr15:79538096-79538332(+)$1	1	9	19	13.2954
....))))).	chr11:119070378-119070604(-)$1	1	88	98	11.8181
((((((((((	chr2:132695832-132696055(-)$1	1	17	27	10.7954
))))...)))	chr9:65127519-65127741(+)$1	1	155	165	12.0454
..))).))))	chr5:34844001-34844226(-)$1	1	89	99	11.7045
((((((((((	chr13:39052372-39052593(+)$1	1	10	20	11.8181
)))..)))..	chr8:108210058-108210280(-)$1	1	152	162	11.0227
)))(((((..	chr17:53810073-53810295(-)$1	1	153	163	13.4090

#PSSM
C : 0.84	G : 0.13	c : 0.02	
A : 0.88	U : 0.06	a : 0.02	C : 0.02	
G : 0.70	A : 0.22	U : 0.02	g : 0.02	C : 0.02	
G : 0.84	A : 0.11	g : 0.02	C : 0.02	
A : 0.65	G : 0.15	U : 0.13	a : 0.02	C : 0.02	
G : 0.63	A : 0.20	C : 0.09	U : 0.04	g : 0.02	
C : 0.68	G : 0.18	A : 0.11	c : 0.02	
C : 0.81	G : 0.09	U : 0.06	u : 0.02	
U : 0.68	A : 0.20	G : 0.09	a : 0.02	
G : 0.88	C : 0.06	g : 0.02	A : 0.02	

#score	553.863636363636
#seq	44
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_UTR_m2_run2.nuc.txt

#NT
UUUGG	chr15:81535368-81535654(-)$1	286	192	197	15.0000
UUUGG	chr7:72016753-72017039(-)$1	286	11	16	15.0000
UUUGG	chr5:37138907-37139205(-)$1	298	161	166	15.0000
UUUGG	chr15:81678793-81679086(-)$1	293	265	270	15.0000
UUUGG	chr17:57032824-57033135(-)$1	311	44	49	15.0000
UUUGG	chr2:34678076-34678352(-)$1	276	96	101	15.0000
UUUGG	chr4:140669562-140669861(-)$1	299	64	69	15.0000
UUUGG	chr7:152050685-152050968(+)$1	283	246	251	15.0000
UUUGG	chr14:55505758-55506035(+)$1	277	129	134	15.0000
UUUGG	chr11:69813257-69813539(+)$1	282	74	79	15.0000
UUUGG	chr11:98015256-98015533(-)$1	277	204	209	15.0000
UUUGG	chr4:49669033-49669321(+)$1	288	127	132	15.0000
UUUGG	chr13:5869145-5869421(+)$1	276	17	22	15.0000
UUUGG	chr3:108163838-108164128(+)$1	290	159	164	15.0000
UUUGG	chr19:24758574-24758848(-)$1	274	68	73	15.0000
UUUGG	chr11:87794777-87795061(-)$1	284	40	45	15.0000
UUUGG	chr2:157383364-157383639(-)$1	275	135	140	15.0000
UUUGG	chr1:133921794-133922065(+)$1	271	174	179	15.0000
UUUGG	chr7:107985091-107985371(+)$1	280	24	29	15.0000
UUUGG	chr8:109599437-109599706(-)$1	269	175	180	15.0000
UUUGG	chr12:114059359-114059639(-)$1	280	261	266	15.0000
UUUGG	chr5:138223116-138223399(-)$1	283	144	149	15.0000
UUUGG	chr11:29642123-29642419(+)$1	296	199	204	15.0000
UUUGG	chr11:105142915-105143222(+)$1	307	276	281	15.0000
UUUGG	chr15:79658142-79658416(-)$1	274	30	35	15.0000
UUUGG	chr15:44595248-44595531(-)$1	283	50	55	15.0000
UUUGG	chr7:25670028-25670303(+)$1	275	28	33	15.0000
UUUGG	chr2:32134292-32134577(-)$1	285	116	121	15.0000
UUUGG	chr17:34791800-34792094(+)$1	294	87	92	15.0000
uuugg	chr2:152654266-152654557(-)$1	291	171	176	15.0000
UUUGG	chr9:90098144-90098412(-)$1	268	203	208	15.0000
UUUGG	chr2:168780770-168781049(-)$1	279	1	6	15.0000
UUUGG	chr16:98170652-98170921(-)$1	269	0	5	15.0000
UUUGG	chr4:147320746-147321041(+)$1	295	64	69	15.0000
UUUGG	chr2:157383278-157383551(-)$1	273	47	52	15.0000
UUUGG	chr16:91227771-91228058(+)$1	287	56	61	15.0000
UUUGG	chr12:8798856-8799128(+)$1	272	82	87	15.0000
UUUGG	chr3:32240090-32240398(-)$1	308	155	160	15.0000
UUUGG	chr11:68923178-68923496(+)$1	318	26	31	15.0000
UUUGG	chr2:31071139-31071424(+)$1	285	258	263	15.0000
UUUGG	chr3:154259844-154260110(-)$1	266	20	25	15.0000
UUUGG	chr7:107985018-107985335(+)$1	317	97	102	15.0000
UUUGG	chr15:75900547-75900820(-)$1	273	64	69	15.0000
UUUGG	chr2:157382615-157382901(-)$1	286	130	135	15.0000
UUUGG	chr11:114729900-114730186(+)$1	286	147	152	15.0000
UUUGG	chr8:125096552-125096860(+)$1	308	130	135	15.0000
UUUGG	chr9:119147934-119148213(-)$1	279	115	120	15.0000
uuugg	chr10:86297866-86298144(+)$1	278	127	132	15.0000
UUUGG	chr15:81535417-81535702(-)$1	285	240	245	15.0000
UUUGG	chr19:8964904-8965185(+)$1	281	153	158	15.0000
UUUGG	chr16:98170671-98170948(-)$1	277	27	32	15.0000

#otherMatches

#Struct PSSM
:::DD	chr8:11834072-11834348(+)$1	276	0	5	15.0000
ZZFFF	chr15:81535368-81535654(-)$1	286	192	197	15.0000
d!!dd	chr7:72016753-72017039(-)$1	286	11	16	15.0000
9999=	chr5:37138907-37139205(-)$1	298	161	166	15.0000
::DDD	chr15:81678793-81679086(-)$1	293	265	270	15.0000
:dddd	chr17:57032824-57033135(-)$1	311	44	49	15.0000
:::::	chr2:34678076-34678352(-)$1	276	96	101	15.0000
eee!!	chr4:140669562-140669861(-)$1	299	64	69	15.0000
555==	chr7:152050685-152050968(+)$1	283	246	251	15.0000
c22cc	chr14:55505758-55506035(+)$1	277	129	134	15.0000
eeeee	chr11:69813257-69813539(+)$1	282	74	79	15.0000
cccmm	chr11:98015256-98015533(-)$1	277	204	209	15.0000
eeeff	chr4:49669033-49669321(+)$1	288	127	132	15.0000
JJJJ:	chr13:5869145-5869421(+)$1	276	17	22	15.0000
"""ee	chr3:108163838-108164128(+)$1	290	159	164	15.0000
ggggg	chr19:24758574-24758848(-)$1	274	68	73	15.0000
meeee	chr11:87794777-87795061(-)$1	284	40	45	15.0000
mmmcc	chr2:157383364-157383639(-)$1	275	135	140	15.0000
ee'''	chr1:133921794-133922065(+)$1	271	174	179	15.0000
GGGGG	chr7:107985091-107985371(+)$1	280	24	29	15.0000
c]ggg	chr8:109599437-109599706(-)$1	269	175	180	15.0000
JJJJJ	chr12:114059359-114059639(-)$1	280	261	266	15.0000
=22bb	chr5:138223116-138223399(-)$1	283	144	149	15.0000
gggg>	chr11:29642123-29642419(+)$1	296	199	204	15.0000
EEE}C	chr11:105142915-105143222(+)$1	307	276	281	15.0000
==mmm	chr15:79658142-79658416(-)$1	274	30	35	15.0000
FFFDD	chr15:44595248-44595531(-)$1	283	50	55	15.0000
{GGGG	chr7:25670028-25670303(+)$1	275	28	33	15.0000
lffff	chr2:32134292-32134577(-)$1	285	116	121	15.0000
nnnnc	chr17:34791800-34792094(+)$1	294	87	92	15.0000
ddddm	chr2:152654266-152654557(-)$1	291	171	176	15.0000
eeeee	chr9:90098144-90098412(-)$1	268	203	208	15.0000
::FFF	chr2:168780770-168781049(-)$1	279	1	6	15.0000
EEEEE	chr16:98170652-98170921(-)$1	269	0	5	15.0000
"dddd	chr4:147320746-147321041(+)$1	295	64	69	15.0000
mmmcc	chr2:157383278-157383551(-)$1	273	47	52	15.0000
d]a]c	chr16:91227771-91228058(+)$1	287	56	61	15.0000
!!ccc	chr12:8798856-8799128(+)$1	272	82	87	15.0000
iiii:	chr3:32240090-32240398(-)$1	308	155	160	15.0000
::hhh	chr11:68923178-68923496(+)$1	318	26	31	15.0000
hhlll	chr2:31071139-31071424(+)$1	285	258	263	15.0000
EEEEC	chr3:154259844-154260110(-)$1	266	20	25	15.0000
=====	chr7:107985018-107985335(+)$1	317	97	102	15.0000
qqqqq	chr15:75900547-75900820(-)$1	273	64	69	15.0000
3ccc]	chr2:157382615-157382901(-)$1	286	130	135	15.0000
fffpp	chr11:114729900-114730186(+)$1	286	147	152	15.0000
ceeee	chr8:125096552-125096860(+)$1	308	130	135	15.0000
nnnee	chr9:119147934-119148213(-)$1	279	115	120	15.0000
JJJdd	chr10:86297866-86298144(+)$1	278	127	132	15.0000
ZZFFF	chr15:81535417-81535702(-)$1	285	240	245	15.0000
JJJJJ	chr19:8964904-8965185(+)$1	281	153	158	15.0000
JJJJJ	chr16:98170671-98170948(-)$1	277	27	32	15.0000

#DB
...((	chr8:11834072-11834348(+)$1	1	0	5	15.0000
..)))	chr15:81535368-81535654(-)$1	1	192	197	15.0000
(..((	chr7:72016753-72017039(-)$1	1	11	16	15.0000
....)	chr5:37138907-37139205(-)$1	1	161	166	15.0000
..)))	chr15:81678793-81679086(-)$1	1	265	270	15.0000
.((((	chr17:57032824-57033135(-)$1	1	44	49	15.0000
.....	chr2:34678076-34678352(-)$1	1	96	101	15.0000
(((..	chr4:140669562-140669861(-)$1	1	64	69	15.0000
...))	chr7:152050685-152050968(+)$1	1	246	251	15.0000
)..))	chr14:55505758-55506035(+)$1	1	129	134	15.0000
(((((	chr11:69813257-69813539(+)$1	1	74	79	15.0000
(((..	chr11:98015256-98015533(-)$1	1	204	209	15.0000
)))))	chr4:49669033-49669321(+)$1	1	127	132	15.0000
((((.	chr13:5869145-5869421(+)$1	1	17	22	15.0000
...((	chr3:108163838-108164128(+)$1	1	159	164	15.0000
(((((	chr19:24758574-24758848(-)$1	1	68	73	15.0000
.))))	chr11:87794777-87795061(-)$1	1	40	45	15.0000
...))	chr2:157383364-157383639(-)$1	1	135	140	15.0000
((...	chr1:133921794-133922065(+)$1	1	174	179	15.0000
(((((	chr7:107985091-107985371(+)$1	1	24	29	15.0000
).)))	chr8:109599437-109599706(-)$1	1	175	180	15.0000
)))))	chr12:114059359-114059639(-)$1	1	261	266	15.0000
)..))	chr5:138223116-138223399(-)$1	1	144	149	15.0000
)))).	chr11:29642123-29642419(+)$1	1	199	204	15.0000
))).)	chr11:105142915-105143222(+)$1	1	276	281	15.0000
((...	chr15:79658142-79658416(-)$1	1	30	35	15.0000
(((((	chr15:44595248-44595531(-)$1	1	50	55	15.0000
.((((	chr7:25670028-25670303(+)$1	1	28	33	15.0000
.))))	chr2:32134292-32134577(-)$1	1	116	121	15.0000
....)	chr17:34791800-34792094(+)$1	1	87	92	15.0000
((((.	chr2:152654266-152654557(-)$1	1	171	176	15.0000
)))))	chr9:90098144-90098412(-)$1	1	203	208	15.0000
..(((	chr2:168780770-168781049(-)$1	1	1	6	15.0000
(((((	chr16:98170652-98170921(-)$1	1	0	5	15.0000
.((((	chr4:147320746-147321041(+)$1	1	64	69	15.0000
...))	chr2:157383278-157383551(-)$1	1	47	52	15.0000
).).)	chr16:91227771-91228058(+)$1	1	56	61	15.0000
..(((	chr12:8798856-8799128(+)$1	1	82	87	15.0000
)))).	chr3:32240090-32240398(-)$1	1	155	160	15.0000
..(((	chr11:68923178-68923496(+)$1	1	26	31	15.0000
((...	chr2:31071139-31071424(+)$1	1	258	263	15.0000
(((((	chr3:154259844-154260110(-)$1	1	20	25	15.0000
)))))	chr7:107985018-107985335(+)$1	1	97	102	15.0000
.....	chr15:75900547-75900820(-)$1	1	64	69	15.0000
.))).	chr2:157382615-157382901(-)$1	1	130	135	15.0000
(((..	chr11:114729900-114730186(+)$1	1	147	152	15.0000
(((((	chr8:125096552-125096860(+)$1	1	130	135	15.0000
...))	chr9:119147934-119148213(-)$1	1	115	120	15.0000
(((((	chr10:86297866-86298144(+)$1	1	127	132	15.0000
..)))	chr15:81535417-81535702(-)$1	1	240	245	15.0000
)))))	chr19:8964904-8965185(+)$1	1	153	158	15.0000
(((((	chr16:98170671-98170948(-)$1	1	27	32	15.0000

#PSSM
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
G : 0.96	g : 0.03	
G : 0.96	g : 0.03	

#score	780.0000000000001
#seq	52
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m3_run2.nuc.txt

#NT
AAAAGGAAA	chr11:85002255-85002456(-)$1	201	26	35	15.3962
CAAAUAAAA	chr15:6748703-6748904(+)$1	201	124	133	17.7547
caaagaaaa	chr3:28572801-28573002(+)$1	201	17	26	16.2452
AAAAUAAAA	chr11:41944982-41945183(-)$1	201	173	182	21.5283
AAAAGAAGA	chrX:35551366-35551567(-)$1	201	156	165	15.3962
aaaagaaaa	chr7:129772025-129772226(+)$1	201	143	152	20.0188
aaaaaaaaa	chr16:66656841-66657042(-)$1	201	139	148	20.2075
AAAAUAAAA	chr11:104189605-104189806(+)$1	201	128	137	21.5283
AAAAUAAAA	chr10:76016601-76016802(+)$1	201	57	66	21.5283
GAAAUAAAA	chr5:67679831-67680032(+)$1	201	181	190	17.5660
AAAACAAAU	chr17:79049614-79049815(-)$1	201	133	142	15.6792
GAAAUAAAA	chr11:75519292-75519493(+)$1	201	142	151	17.5660
AAAAUAAAG	chr19:32899915-32900116(+)$1	201	14	23	16.9056
aaaaaaaaa	chr9:47660574-47660775(+)$1	201	186	195	20.2075
AAAAUAAAA	chr4:25537130-25537331(-)$1	201	141	150	21.5283
AAAAUAAAA	chr4:82448920-82449121(-)$1	201	132	141	21.5283
AAAACAAAA	chr19:5493851-5494052(+)$1	201	136	145	20.3018
AAACUAAAA	chr18:61747761-61747962(+)$1	201	177	186	16.8113
AAAAUAAAA	chr16:16309595-16309796(+)$1	201	102	111	21.5283
AAAAAAAAA	chr11:42444170-42444371(+)$1	201	40	49	20.2075
CAAAUAAAA	chr11:16182140-16182341(+)$1	201	83	92	17.7547
CAAAUAAAA	chr11:16182139-16182340(+)$1	201	84	93	17.7547
AAAAUAGAA	chr9:25115655-25115856(+)$1	201	185	194	17.2830
AAAAGAAAC	chr6:13576994-13577195(-)$1	201	86	95	15.3962
AAAAAAGAA	chr9:45671721-45671922(+)$1	201	75	84	15.9622
aaaauaaaa	chr15:25293072-25293273(-)$1	201	26	35	21.5283
AGAAUAAAA	chr12:3249376-3249577(-)$1	201	124	133	17.2830
AAAACAAAA	chr11:106641832-106642033(-)$1	201	30	39	20.3018
AAAGCAAAA	chr3:90161869-90162070(+)$1	201	161	170	15.5849
AAAACAAAA	chr18:10813335-10813536(+)$1	201	117	126	20.3018
AAAAGAAAA	chr12:101444639-101444840(+)$1	201	70	79	20.0188
UAAAAAAAA	chr10:107934710-107934911(-)$1	201	145	154	16.3396
AAAAUAUAA	chrX:9231378-9231579(-)$1	201	154	163	17.0943
AAAAAAAAA	chr2:102630350-102630551(+)$1	201	165	174	20.2075
UAAAUAAAA	chr5:54048436-54048637(+)$1	201	140	149	17.6603
AGAAUAAAA	chr12:3249377-3249578(-)$1	201	125	134	17.2830
aaaaaaaaa	chr5:29558503-29558704(-)$1	201	46	55	20.2075
aaaagaaaa	chr16:66659411-66659612(-)$1	201	73	82	20.0188
AAAAUACAA	chr3:96594610-96594811(+)$1	201	149	158	17.0943
AGAACAAAA	chr13:100195082-100195283(-)$1	201	159	168	16.0566
AAAACAACA	chr3:60430504-60430705(+)$1	201	22	31	15.6792
AAAAAAAAA	chr2:102630497-102630698(+)$1	201	18	27	20.2075
AAAAAAAAA	chr18:80323798-80323999(-)$1	201	106	115	20.2075
aacauaaaa	chr16:8620148-8620349(+)$1	201	164	173	16.7169
AAAAUGAAA	chr3:83968280-83968481(-)$1	201	121	130	16.9056
AAAACAAUA	chr6:21721840-21722041(-)$1	201	44	53	15.6792
AAAACAGAA	chr13:24999507-24999708(-)$1	201	62	71	16.0566
AAAAAAAAA	chr4:34034128-34034329(+)$1	201	83	92	20.2075
UAAAUAAAA	chr11:103683663-103683864(-)$1	201	129	138	17.6603
AAAACAAAA	chrX:130117551-130117752(-)$1	201	125	134	20.3018
AGAAGAAAA	chr14:26485749-26485950(+)$1	201	52	61	15.7735
AAAACAAAA	chr5:116456286-116456487(+)$1	201	62	71	20.3018

#otherMatches

#Struct PSSM
hdddd!!cc	chr13:94972780-94972981(-)$1	201	121	130	21.5283
MMMMBB:::	chr11:85002255-85002456(-)$1	201	26	35	15.3962
bssssssss	chr15:6748703-6748904(+)$1	201	124	133	17.7547
GGGGGG:::	chr3:28572801-28573002(+)$1	201	17	26	16.2452
ddd::::::	chr11:41944982-41945183(-)$1	201	173	182	21.5283
JJJ~~~~EE	chrX:35551366-35551567(-)$1	201	156	165	15.3962
c333bb444	chr7:129772025-129772226(+)$1	201	143	152	20.0188
:::::::::	chr16:66656841-66657042(-)$1	201	139	148	20.2075
ii:::::::	chr11:104189605-104189806(+)$1	201	128	137	21.5283
:::::::::	chr10:76016601-76016802(+)$1	201	57	66	21.5283
ffffflllf	chr5:67679831-67680032(+)$1	201	181	190	17.5660
ooodddd33	chr17:79049614-79049815(-)$1	201	133	142	15.6792
]dddd22dd	chr11:75519292-75519493(+)$1	201	142	151	17.5660
hhhhvvvvv	chr19:32899915-32900116(+)$1	201	14	23	16.9056
:::::::::	chr9:47660574-47660775(+)$1	201	186	195	20.2075
::::EEEEE	chr4:25537130-25537331(-)$1	201	141	150	21.5283
iiiiiiiii	chr4:82448920-82449121(-)$1	201	132	141	21.5283
EYYCCC}CC	chr19:5493851-5494052(+)$1	201	136	145	20.3018
gggg]ccc2	chr18:61747761-61747962(+)$1	201	177	186	16.8113
f:::::eee	chr16:16309595-16309796(+)$1	201	102	111	21.5283
g::::::::	chr11:42444170-42444371(+)$1	201	40	49	20.2075
mhhhhhhhh	chr11:16182140-16182341(+)$1	201	83	92	17.7547
mhhhhhhhh	chr11:16182139-16182340(+)$1	201	84	93	17.7547
eeeffffff	chr9:25115655-25115856(+)$1	201	185	194	17.2830
:::FFFFFF	chr6:13576994-13577195(-)$1	201	86	95	15.3962
$$$$$ccc[	chr9:45671721-45671922(+)$1	201	75	84	15.9622
:::::::::	chr15:25293072-25293273(-)$1	201	26	35	21.5283
===[eeeee	chr12:3249376-3249577(-)$1	201	124	133	17.2830
FFFFMMMMB	chr11:106641832-106642033(-)$1	201	30	39	20.3018
:::::::::	chr3:90161869-90162070(+)$1	201	161	170	15.5849
rrrrrrrre	chr18:10813335-10813536(+)$1	201	117	126	20.3018
qqdddd:::	chr12:101444639-101444840(+)$1	201	70	79	20.0188
ff22hhhhh	chr10:107934710-107934911(-)$1	201	145	154	16.3396
wwwwwwwww	chrX:9231378-9231579(-)$1	201	154	163	17.0943
>>>>>>>>>	chr2:102630350-102630551(+)$1	201	165	174	20.2075
xxxxxxxxx	chr5:54048436-54048637(+)$1	201	140	149	17.6603
===[eeeee	chr12:3249377-3249578(-)$1	201	125	134	17.2830
f::::::::	chr5:29558503-29558704(-)$1	201	46	55	20.2075
::::ggggg	chr16:66659411-66659612(-)$1	201	73	82	20.0188
^^^^^^^^^	chr3:96594610-96594811(+)$1	201	149	158	17.0943
zzzzzzzzz	chr13:100195082-100195283(-)$1	201	159	168	16.0566
&&&&&&ccc	chr3:60430504-60430705(+)$1	201	22	31	15.6792
:::::::::	chr2:102630497-102630698(+)$1	201	18	27	20.2075
hhhhhffff	chr18:80323798-80323999(-)$1	201	106	115	20.2075
hhhhhhhh:	chr16:8620148-8620349(+)$1	201	164	173	16.7169
cc+++++++	chr3:83968280-83968481(-)$1	201	121	130	16.9056
444bb::::	chr6:21721840-21722041(-)$1	201	44	53	15.6792
wwwdddd66	chr13:24999507-24999708(-)$1	201	62	71	16.0566
ooooooddd	chr4:34034128-34034329(+)$1	201	83	92	20.2075
^^^^^^^^g	chr11:103683663-103683864(-)$1	201	129	138	17.6603
:::::dddd	chrX:130117551-130117752(-)$1	201	125	134	20.3018
mmmmdddd:	chr14:26485749-26485950(+)$1	201	52	61	15.7735
:::::::::	chr5:116456286-116456487(+)$1	201	62	71	20.3018

#DB
(((((..((	chr13:94972780-94972981(-)$1	1	121	130	21.5283
....((...	chr11:85002255-85002456(-)$1	1	26	35	15.3962
(........	chr15:6748703-6748904(+)$1	1	124	133	17.7547
((((((...	chr3:28572801-28573002(+)$1	1	17	26	16.2452
)))......	chr11:41944982-41945183(-)$1	1	173	182	21.5283
)))....))	chrX:35551366-35551567(-)$1	1	156	165	15.3962
)...))...	chr7:129772025-129772226(+)$1	1	143	152	20.0188
.........	chr16:66656841-66657042(-)$1	1	139	148	20.2075
)).......	chr11:104189605-104189806(+)$1	1	128	137	21.5283
.........	chr10:76016601-76016802(+)$1	1	57	66	21.5283
(((((...)	chr5:67679831-67680032(+)$1	1	181	190	17.5660
...))))..	chr17:79049614-79049815(-)$1	1	133	142	15.6792
.))))..))	chr11:75519292-75519493(+)$1	1	142	151	17.5660
((((.....	chr19:32899915-32900116(+)$1	1	14	23	16.9056
.........	chr9:47660574-47660775(+)$1	1	186	195	20.2075
....)))))	chr4:25537130-25537331(-)$1	1	141	150	21.5283
(((((((((	chr4:82448920-82449121(-)$1	1	132	141	21.5283
)..))).))	chr19:5493851-5494052(+)$1	1	136	145	20.3018
)))).))).	chr18:61747761-61747962(+)$1	1	177	186	16.8113
).....(((	chr16:16309595-16309796(+)$1	1	102	111	21.5283
)........	chr11:42444170-42444371(+)$1	1	40	49	20.2075
.))))))))	chr11:16182140-16182341(+)$1	1	83	92	17.7547
.))))))))	chr11:16182139-16182340(+)$1	1	84	93	17.7547
)))))))))	chr9:25115655-25115856(+)$1	1	185	194	17.2830
...((((((	chr6:13576994-13577195(-)$1	1	86	95	15.3962
.....(((.	chr9:45671721-45671922(+)$1	1	75	84	15.9622
.........	chr15:25293072-25293273(-)$1	1	26	35	21.5283
(((.(((((	chr12:3249376-3249577(-)$1	1	124	133	17.2830
((((....(	chr11:106641832-106642033(-)$1	1	30	39	20.3018
.........	chr3:90161869-90162070(+)$1	1	161	170	15.5849
........)	chr18:10813335-10813536(+)$1	1	117	126	20.3018
..))))...	chr12:101444639-101444840(+)$1	1	70	79	20.0188
))..)))))	chr10:107934710-107934911(-)$1	1	145	154	16.3396
.........	chrX:9231378-9231579(-)$1	1	154	163	17.0943
.........	chr2:102630350-102630551(+)$1	1	165	174	20.2075
.........	chr5:54048436-54048637(+)$1	1	140	149	17.6603
(((.(((((	chr12:3249377-3249578(-)$1	1	125	134	17.2830
)........	chr5:29558503-29558704(-)$1	1	46	55	20.2075
....(((((	chr16:66659411-66659612(-)$1	1	73	82	20.0188
.........	chr3:96594610-96594811(+)$1	1	149	158	17.0943
.........	chr13:100195082-100195283(-)$1	1	159	168	16.0566
......(((	chr3:60430504-60430705(+)$1	1	22	31	15.6792
.........	chr2:102630497-102630698(+)$1	1	18	27	20.2075
)))))((((	chr18:80323798-80323999(-)$1	1	106	115	20.2075
)))))))).	chr16:8620148-8620349(+)$1	1	164	173	16.7169
((.......	chr3:83968280-83968481(-)$1	1	121	130	16.9056
...))....	chr6:21721840-21722041(-)$1	1	44	53	15.6792
...))))..	chr13:24999507-24999708(-)$1	1	62	71	16.0566
......)))	chr4:34034128-34034329(+)$1	1	83	92	20.2075
........)	chr11:103683663-103683864(-)$1	1	129	138	17.6603
.....((((	chrX:130117551-130117752(-)$1	1	125	134	20.3018
....)))).	chr14:26485749-26485950(+)$1	1	52	61	15.7735
.........	chr5:116456286-116456487(+)$1	1	62	71	20.3018

#PSSM
A : 0.69	a : 0.13	C : 0.05	U : 0.05	G : 0.03	c : 0.01	
A : 0.77	a : 0.15	G : 0.07	
A : 0.84	a : 0.13	c : 0.01	
A : 0.81	a : 0.15	C : 0.01	G : 0.01	
U : 0.41	C : 0.20	A : 0.13	G : 0.09	g : 0.05	a : 0.05	u : 0.03	
A : 0.81	a : 0.15	G : 0.03	
A : 0.75	a : 0.15	G : 0.05	U : 0.01	C : 0.01	
A : 0.79	a : 0.15	G : 0.01	C : 0.01	U : 0.01	
A : 0.79	a : 0.15	U : 0.01	G : 0.01	C : 0.01	

#score	977.7924528301886
#seq	53
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m3_run2.nuc.txt

#NT
CCAG	chr17:34782494-34782729(+)$1	235	115	119	11.9999
CCAG	chr8:63391717-63391957(-)$1	240	33	37	11.9999
CCAG	chr7:129777075-129777383(+)$1	308	7	11	11.9999
CCAG	chr10:126675733-126675988(-)$1	255	79	83	11.9999
CCAG	chr4:148761180-148761417(-)$1	237	108	112	11.9999
CCAG	chr12:111865180-111865415(+)$1	235	148	152	11.9999
CCAG	chr1:175262352-175262595(-)$1	243	54	58	11.9999
CCAG	chr4:126425761-126425997(-)$1	236	40	44	11.9999
CCAG	chr6:36693305-36693540(-)$1	235	97	101	11.9999
CCAG	chr13:100195648-100195890(-)$1	242	21	25	11.9999
CCAG	chr13:104623795-104624032(-)$1	237	38	42	11.9999
CCAG	chr17:82047059-82047320(-)$1	261	154	158	11.9999
CCAG	chr14:76818619-76818854(+)$1	235	22	26	11.9999
CCAG	chr11:50014060-50014371(-)$1	311	49	53	11.9999
CCAG	chr14:60997232-60997490(+)$1	258	77	81	11.9999
CCAG	chr9:95945897-95946132(+)$1	235	78	82	11.9999
CCAG	chr11:41960533-41960768(-)$1	235	69	73	11.9999
CCAG	chr14:31989531-31989766(-)$1	235	38	42	11.9999
CCAG	chr2:6468061-6468303(-)$1	242	40	44	11.9999
CCAG	chr19:10058581-10058825(+)$1	244	199	203	11.9999
CCAG	chr11:90202099-90202341(-)$1	242	133	137	11.9999
CCAG	chr2:181041364-181041632(-)$1	268	176	180	11.9999
CCAG	chr7:104877404-104877644(-)$1	240	76	80	11.9999
CCAG	chr13:6602544-6602805(-)$1	261	18	22	11.9999
CCAG	chr7:148337524-148337759(+)$1	235	29	33	11.9999
CCAG	chr3:95023988-95024224(-)$1	236	83	87	11.9999
CCAG	chrX:162824810-162825047(+)$1	237	69	73	11.9999
CCAG	chrX:143628695-143628930(+)$1	235	230	234	11.9999
CCAG	chr9:66883791-66884029(-)$1	238	28	32	11.9999
CCAG	chr11:55208949-55209192(-)$1	243	12	16	11.9999
CCAG	chr3:87798024-87798262(-)$1	238	45	49	11.9999
CCAG	chr2:181283313-181283550(+)$1	237	38	42	11.9999
CCAG	chr11:78335201-78335436(+)$1	235	210	214	11.9999
CCAG	chr11:72025341-72025578(-)$1	237	32	36	11.9999
CCAG	chr18:34506673-34506910(-)$1	237	28	32	11.9999
CCAG	chr10:126699751-126699986(-)$1	235	8	12	11.9999
CCAG	chrX:148317008-148317269(+)$1	261	212	216	11.9999
CCAG	chr6:97128843-97129081(-)$1	238	92	96	11.9999
CCAG	chr18:67778820-67779055(-)$1	235	68	72	11.9999
CCAG	chr15:3987046-3987281(+)$1	235	64	68	11.9999
CCAG	chr6:117123446-117123681(+)$1	235	176	180	11.9999
CCAG	chr14:65673532-65673769(-)$1	237	7	11	11.9999
CCAG	chr7:137872027-137872262(+)$1	235	132	136	11.9999
CCAG	chr5:34186114-34186353(+)$1	239	38	42	11.9999
CCAG	chr7:118217767-118218002(-)$1	235	145	149	11.9999
CCAG	chr10:106256389-106256638(+)$1	249	39	43	11.9999
CCAG	chr16:90229856-90230093(-)$1	237	29	33	11.9999
CCAG	chr10:34018422-34018682(+)$1	260	76	80	11.9999
CCAG	chr15:58767736-58767981(+)$1	245	167	171	11.9999
CCAG	chr11:4964001-4964239(-)$1	238	38	42	11.9999
CCAG	chr10:98477548-98477791(+)$1	243	207	211	11.9999
CCAG	chr8:96491846-96492107(+)$1	261	194	198	11.9999
CCAG	chr19:4726530-4726776(+)$1	246	52	56	11.9999
CCAG	chr2:71114420-71114661(-)$1	241	42	46	11.9999
CCAG	chr11:49502571-49502808(-)$1	237	100	104	11.9999
CCAG	chr10:57236816-57237127(-)$1	311	88	92	11.9999
CCAG	chr11:109528789-109529095(+)$1	306	90	94	11.9999
CCAG	chr18:46664687-46664922(-)$1	235	25	29	11.9999
CCAG	chr19:10058659-10058899(+)$1	240	121	125	11.9999
CCAG	chr13:74476965-74477204(-)$1	239	37	41	11.9999
CCAG	chr16:35283532-35283777(+)$1	245	29	33	11.9999
CCAG	chr5:137736972-137737209(-)$1	237	12	16	11.9999
CCAG	chr4:126707100-126707361(+)$1	261	45	49	11.9999
CCAG	chr10:29067362-29067599(-)$1	237	178	182	11.9999
CCAG	chr5:29619320-29619555(-)$1	235	172	176	11.9999
CCAG	chr11:87794612-87794923(-)$1	311	65	69	11.9999
CCAG	chr11:60530652-60530893(-)$1	241	31	35	11.9999
CCAG	chr10:76784989-76785224(-)$1	235	13	17	11.9999
CCAG	chrX:162824888-162825125(+)$1	237	63	67	11.9999
CCAG	chr15:31412540-31412775(-)$1	235	142	146	11.9999
CCAG	chr7:31226612-31226851(-)$1	239	178	182	11.9999
CCAG	chr12:106028213-106028448(-)$1	235	109	113	11.9999
CCAG	chr2:25077838-25078075(-)$1	237	175	179	11.9999
CCAG	chrX:162824700-162824996(+)$1	296	49	53	11.9999

#otherMatches

#Struct PSSM
fccc	chr7:17501488-17501778(-)$1	290	8	12	11.9999
eeee	chr17:34782494-34782729(+)$1	235	115	119	11.9999
EEEE	chr8:63391717-63391957(-)$1	240	33	37	11.9999
IIII	chr7:129777075-129777383(+)$1	308	7	11	11.9999
gggg	chr10:126675733-126675988(-)$1	255	79	83	11.9999
ee]c	chr4:148761180-148761417(-)$1	237	108	112	11.9999
dooo	chr12:111865180-111865415(+)$1	235	148	152	11.9999
hhhd	chr1:175262352-175262595(-)$1	243	54	58	11.9999
]eee	chr4:126425761-126425997(-)$1	236	40	44	11.9999
bb!!	chr6:36693305-36693540(-)$1	235	97	101	11.9999
B::b	chr13:100195648-100195890(-)$1	242	21	25	11.9999
oobb	chr13:104623795-104624032(-)$1	237	38	42	11.9999
GGGG	chr17:82047059-82047320(-)$1	261	154	158	11.9999
DDbb	chr14:76818619-76818854(+)$1	235	22	26	11.9999
eeee	chr11:50014060-50014371(-)$1	311	49	53	11.9999
cc##	chr14:60997232-60997490(+)$1	258	77	81	11.9999
dlll	chr9:95945897-95946132(+)$1	235	78	82	11.9999
eee!	chr11:41960533-41960768(-)$1	235	69	73	11.9999
ffpp	chr14:31989531-31989766(-)$1	235	38	42	11.9999
:FFF	chr2:6468061-6468303(-)$1	242	40	44	11.9999
ZBB}	chr19:10058581-10058825(+)$1	244	199	203	11.9999
rccc	chr11:90202099-90202341(-)$1	242	133	137	11.9999
$$$$	chr2:181041364-181041632(-)$1	268	176	180	11.9999
DDDD	chr7:104877404-104877644(-)$1	240	76	80	11.9999
offf	chr13:6602544-6602805(-)$1	261	18	22	11.9999
KKFF	chr7:148337524-148337759(+)$1	235	29	33	11.9999
ccdd	chr3:95023988-95024224(-)$1	236	83	87	11.9999
NNNN	chrX:162824810-162825047(+)$1	237	69	73	11.9999
EEEE	chrX:143628695-143628930(+)$1	235	230	234	11.9999
!!bb	chr9:66883791-66884029(-)$1	238	28	32	11.9999
eeee	chr11:55208949-55209192(-)$1	243	12	16	11.9999
:::g	chr3:87798024-87798262(-)$1	238	45	49	11.9999
ddd2	chr2:181283313-181283550(+)$1	237	38	42	11.9999
BBEE	chr11:78335201-78335436(+)$1	235	210	214	11.9999
eooo	chr11:72025341-72025578(-)$1	237	32	36	11.9999
FFFF	chr18:34506673-34506910(-)$1	237	28	32	11.9999
DDKK	chr10:126699751-126699986(-)$1	235	8	12	11.9999
IIII	chrX:148317008-148317269(+)$1	261	212	216	11.9999
gggg	chr6:97128843-97129081(-)$1	238	92	96	11.9999
dddd	chr18:67778820-67779055(-)$1	235	68	72	11.9999
hhhh	chr15:3987046-3987281(+)$1	235	64	68	11.9999
GGGG	chr6:117123446-117123681(+)$1	235	176	180	11.9999
d[cc	chr14:65673532-65673769(-)$1	237	7	11	11.9999
DDD~	chr7:137872027-137872262(+)$1	235	132	136	11.9999
CCC{	chr5:34186114-34186353(+)$1	239	38	42	11.9999
qqdd	chr7:118217767-118218002(-)$1	235	145	149	11.9999
uuuu	chr10:106256389-106256638(+)$1	249	39	43	11.9999
b[cc	chr16:90229856-90230093(-)$1	237	29	33	11.9999
JJJJ	chr10:34018422-34018682(+)$1	260	76	80	11.9999
mmcc	chr15:58767736-58767981(+)$1	245	167	171	11.9999
GEEE	chr11:4964001-4964239(-)$1	238	38	42	11.9999
dddd	chr10:98477548-98477791(+)$1	243	207	211	11.9999
::cc	chr8:96491846-96492107(+)$1	261	194	198	11.9999
iiii	chr19:4726530-4726776(+)$1	246	52	56	11.9999
:BB{	chr2:71114420-71114661(-)$1	241	42	46	11.9999
ffff	chr11:49502571-49502808(-)$1	237	100	104	11.9999
eeee	chr10:57236816-57237127(-)$1	311	88	92	11.9999
!!cc	chr11:109528789-109529095(+)$1	306	90	94	11.9999
eeee	chr18:46664687-46664922(-)$1	235	25	29	11.9999
:ccc	chr19:10058659-10058899(+)$1	240	121	125	11.9999
iiii	chr13:74476965-74477204(-)$1	239	37	41	11.9999
((dd	chr16:35283532-35283777(+)$1	245	29	33	11.9999
dd[b	chr5:137736972-137737209(-)$1	237	12	16	11.9999
bb]g	chr4:126707100-126707361(+)$1	261	45	49	11.9999
CDDD	chr10:29067362-29067599(-)$1	237	178	182	11.9999
eee[	chr5:29619320-29619555(-)$1	235	172	176	11.9999
c!!c	chr11:87794612-87794923(-)$1	311	65	69	11.9999
qccc	chr11:60530652-60530893(-)$1	241	31	35	11.9999
eee]	chr10:76784989-76785224(-)$1	235	13	17	11.9999
:::D	chrX:162824888-162825125(+)$1	237	63	67	11.9999
}DDD	chr15:31412540-31412775(-)$1	235	142	146	11.9999
CCC:	chr7:31226612-31226851(-)$1	239	178	182	11.9999
gggg	chr12:106028213-106028448(-)$1	235	109	113	11.9999
dnnn	chr2:25077838-25078075(-)$1	237	175	179	11.9999
e!!b	chrX:162824700-162824996(+)$1	296	49	53	11.9999

#DB
((((	chr7:17501488-17501778(-)$1	1	8	12	11.9999
))))	chr17:34782494-34782729(+)$1	1	115	119	11.9999
((((	chr8:63391717-63391957(-)$1	1	33	37	11.9999
((((	chr7:129777075-129777383(+)$1	1	7	11	11.9999
))))	chr10:126675733-126675988(-)$1	1	79	83	11.9999
)).)	chr4:148761180-148761417(-)$1	1	108	112	11.9999
(...	chr12:111865180-111865415(+)$1	1	148	152	11.9999
((((	chr1:175262352-175262595(-)$1	1	54	58	11.9999
.)))	chr4:126425761-126425997(-)$1	1	40	44	11.9999
((..	chr6:36693305-36693540(-)$1	1	97	101	11.9999
(..(	chr13:100195648-100195890(-)$1	1	21	25	11.9999
..))	chr13:104623795-104624032(-)$1	1	38	42	11.9999
))))	chr17:82047059-82047320(-)$1	1	154	158	11.9999
((((	chr14:76818619-76818854(+)$1	1	22	26	11.9999
))))	chr11:50014060-50014371(-)$1	1	49	53	11.9999
((..	chr14:60997232-60997490(+)$1	1	77	81	11.9999
(...	chr9:95945897-95946132(+)$1	1	78	82	11.9999
(((.	chr11:41960533-41960768(-)$1	1	69	73	11.9999
((..	chr14:31989531-31989766(-)$1	1	38	42	11.9999
.(((	chr2:6468061-6468303(-)$1	1	40	44	11.9999
.)).	chr19:10058581-10058825(+)$1	1	199	203	11.9999
.)))	chr11:90202099-90202341(-)$1	1	133	137	11.9999
....	chr2:181041364-181041632(-)$1	1	176	180	11.9999
((((	chr7:104877404-104877644(-)$1	1	76	80	11.9999
.)))	chr13:6602544-6602805(-)$1	1	18	22	11.9999
..((	chr7:148337524-148337759(+)$1	1	29	33	11.9999
((((	chr3:95023988-95024224(-)$1	1	83	87	11.9999
....	chrX:162824810-162825047(+)$1	1	69	73	11.9999
))))	chrX:143628695-143628930(+)$1	1	230	234	11.9999
..((	chr9:66883791-66884029(-)$1	1	28	32	11.9999
((((	chr11:55208949-55209192(-)$1	1	12	16	11.9999
...(	chr3:87798024-87798262(-)$1	1	45	49	11.9999
))).	chr2:181283313-181283550(+)$1	1	38	42	11.9999
))))	chr11:78335201-78335436(+)$1	1	210	214	11.9999
(...	chr11:72025341-72025578(-)$1	1	32	36	11.9999
((((	chr18:34506673-34506910(-)$1	1	28	32	11.9999
((..	chr10:126699751-126699986(-)$1	1	8	12	11.9999
))))	chrX:148317008-148317269(+)$1	1	212	216	11.9999
))))	chr6:97128843-97129081(-)$1	1	92	96	11.9999
((((	chr18:67778820-67779055(-)$1	1	68	72	11.9999
((((	chr15:3987046-3987281(+)$1	1	64	68	11.9999
))))	chr6:117123446-117123681(+)$1	1	176	180	11.9999
(.((	chr14:65673532-65673769(-)$1	1	7	11	11.9999
))).	chr7:137872027-137872262(+)$1	1	132	136	11.9999
(((.	chr5:34186114-34186353(+)$1	1	38	42	11.9999
..))	chr7:118217767-118218002(-)$1	1	145	149	11.9999
....	chr10:106256389-106256638(+)$1	1	39	43	11.9999
(.((	chr16:90229856-90230093(-)$1	1	29	33	11.9999
((((	chr10:34018422-34018682(+)$1	1	76	80	11.9999
..))	chr15:58767736-58767981(+)$1	1	167	171	11.9999
((((	chr11:4964001-4964239(-)$1	1	38	42	11.9999
)(((	chr10:98477548-98477791(+)$1	1	207	211	11.9999
..((	chr8:96491846-96492107(+)$1	1	194	198	11.9999
((((	chr19:4726530-4726776(+)$1	1	52	56	11.9999
.((.	chr2:71114420-71114661(-)$1	1	42	46	11.9999
))))	chr11:49502571-49502808(-)$1	1	100	104	11.9999
))))	chr10:57236816-57237127(-)$1	1	88	92	11.9999
..((	chr11:109528789-109529095(+)$1	1	90	94	11.9999
((((	chr18:46664687-46664922(-)$1	1	25	29	11.9999
.(((	chr19:10058659-10058899(+)$1	1	121	125	11.9999
((((	chr13:74476965-74477204(-)$1	1	37	41	11.9999
..((	chr16:35283532-35283777(+)$1	1	29	33	11.9999
((.(	chr5:137736972-137737209(-)$1	1	12	16	11.9999
)).)	chr4:126707100-126707361(+)$1	1	45	49	11.9999
))))	chr10:29067362-29067599(-)$1	1	178	182	11.9999
(((.	chr5:29619320-29619555(-)$1	1	172	176	11.9999
(..(	chr11:87794612-87794923(-)$1	1	65	69	11.9999
.)))	chr11:60530652-60530893(-)$1	1	31	35	11.9999
))).	chr10:76784989-76785224(-)$1	1	13	17	11.9999
...(	chrX:162824888-162825125(+)$1	1	63	67	11.9999
.)))	chr15:31412540-31412775(-)$1	1	142	146	11.9999
))).	chr7:31226612-31226851(-)$1	1	178	182	11.9999
((((	chr12:106028213-106028448(-)$1	1	109	113	11.9999
(...	chr2:25077838-25078075(-)$1	1	175	179	11.9999
(..(	chrX:162824700-162824996(+)$1	1	49	53	11.9999

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

#score	899.9999999999995
#seq	75
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_UTR_m2_run1.nuc.txt

#NT
UGCUUUA	chr10:42254574-42254823(+)$1	249	162	169	12.5909
UGUUUUG	chr11:109529284-109529537(+)$1	253	141	148	13.8030
UGCUUAG	chr11:87793999-87794305(-)$1	306	114	121	12.3636
UGCUCUG	chr17:9177497-9177766(+)$1	269	41	48	13.1212
UGCUUGG	chr3:143851878-143852120(-)$1	242	120	127	12.3636
UGGUUUG	chr11:77345323-77345558(-)$1	235	98	105	13.8030
UGCUUUG	chr8:70220576-70220839(-)$1	263	146	153	16.8333
UGCUUuc	chr11:68904067-68904326(+)$1	259	3	10	12.5909
UGCUUUG	chr11:105920089-105920387(+)$1	298	17	24	16.8333
UGCUGUG	chr11:4667755-4668009(-)$1	254	118	125	13.2727
UGCCUUG	chr6:113696064-113696351(-)$1	287	90	97	12.2121
UGCAUUG	chr9:44446194-44446429(+)$1	235	44	51	12.1363
UGUUUUG	chr9:25115578-25115832(+)$1	254	136	143	13.8030
UGCUUUU	chr9:79618583-79618902(-)$1	319	63	70	12.7424
UUCUUUG	chr6:108772299-108772537(+)$1	238	117	124	12.7424
UGUUUUG	chr1:166367304-166367599(-)$1	295	62	69	13.8030
UGCCUUG	chrX:132748537-132748775(-)$1	238	82	89	12.2121
UGCUGUG	chr19:37097573-37097808(-)$1	235	221	228	13.2727
UGCUUUG	chr2:70439387-70439627(+)$1	240	21	28	16.8333
UACUUUG	chr8:26875029-26875280(-)$1	251	210	217	12.5909
UUCUUUG	chr13:98021788-98022044(+)$1	256	151	158	12.7424
UGGUUUG	chr2:32643400-32643705(-)$1	305	253	260	13.8030
UGCUUUG	chr10:75722802-75723082(+)$1	280	157	164	16.8333
UGCUUUC	chr18:36957772-36958009(+)$1	237	167	174	12.5909
UGCUUUG	chr3:116446164-116446403(-)$1	239	5	12	16.8333
UGCUUUU	chr15:98568053-98568311(-)$1	258	6	13	12.7424
UGAUUUG	chr1:34933799-34934049(+)$1	250	145	152	13.6515
UGUUUUG	chr5:65986736-65986975(+)$1	239	117	124	13.8030
UGCUGUG	chr6:47974257-47974517(-)$1	260	18	25	13.2727
UACUUUG	chr3:32849173-32849408(-)$1	235	107	114	12.5909
UGGUUUG	chr11:97578064-97578315(-)$1	251	189	196	13.8030
UGCUUUU	chr1:163917627-163917873(-)$1	246	115	122	12.7424
UGGUUUG	chr19:3456222-3456457(-)$1	235	153	160	13.8030
UGCUCUG	chr10:98487879-98488126(+)$1	247	120	127	13.1212
UGUUUUG	chr10:36854607-36854858(-)$1	251	82	89	13.8030
UGGUUUG	chr18:6788940-6789181(+)$1	241	10	17	13.8030
UGCUUUA	chr17:85463522-85463778(-)$1	256	209	216	12.5909
UUCUUUG	chr2:120562923-120563158(-)$1	235	114	121	12.7424
UGCUUUG	chr1:129700194-129700448(+)$1	254	50	57	16.8333
UGCUUUG	chr8:56145814-56146102(+)$1	288	278	285	16.8333
UGCUUUG	chr1:134401910-134402146(+)$1	236	101	108	16.8333
UGCUUAG	chr9:75067565-75067816(+)$1	251	38	45	12.3636
UGUUUUG	chr14:72938319-72938574(-)$1	255	125	132	13.8030
UGCUGUG	chr9:45773557-45773802(-)$1	245	106	113	13.2727
UGCUUCG	chr2:69861428-69861670(+)$1	242	23	30	12.2878
UGCUCUG	chrX:92244257-92244498(-)$1	241	45	52	13.1212
UGCUCUG	chr19:21468794-21469035(-)$1	241	220	227	13.1212
UGGUUUG	chr7:107421549-107421790(+)$1	241	115	122	13.8030
UGAUUUG	chrX:10173441-10173689(+)$1	248	43	50	13.6515
UGCUGUG	chr8:56145478-56145720(+)$1	242	113	120	13.2727
UGAUUUG	chr12:30605470-30605720(+)$1	250	87	94	13.6515
UGGUUUG	chr19:5370342-5370578(+)$1	236	3	10	13.8030
ugauuug	chr2:73448726-73449004(-)$1	278	186	193	13.6515
UGCUGUG	chr16:17044950-17045193(+)$1	243	19	26	13.2727
UCCUUUG	chr4:148554398-148554636(-)$1	238	73	80	12.5909
UGCUGUG	chrX:143630390-143630635(+)$1	245	72	79	13.2727
UGCUUUG	chr6:113696548-113696811(-)$1	263	32	39	16.8333
UUCUUUG	chr15:31385917-31386158(-)$1	241	41	48	12.7424
UGCUUUU	chr9:75491098-75491335(-)$1	237	179	186	12.7424
UGCUCUG	chr1:194332962-194333199(+)$1	237	136	143	13.1212
UGCUUGG	chr9:58499600-58499858(+)$1	258	113	120	12.3636
UGAUUUG	chr15:92171549-92171784(+)$1	235	187	194	13.6515
UGCUUUG	chr17:51876264-51876527(-)$1	263	75	82	16.8333
UCCUUUG	chr16:58465881-58466129(+)$1	248	13	20	12.5909
UGCUUUG	chr11:35602994-35603236(+)$1	242	90	97	16.8333

#otherMatches

#Struct PSSM
GGGGeee	chr16:17046878-17047138(+)$1	260	18	25	13.8030
:ccc!!e	chr10:42254574-42254823(+)$1	249	162	169	12.5909
iiiii]d	chr11:109529284-109529537(+)$1	253	141	148	13.8030
fff::FF	chr11:87793999-87794305(-)$1	306	114	121	12.3636
mccc888	chr17:9177497-9177766(+)$1	269	41	48	13.1212
ddddfff	chr3:143851878-143852120(-)$1	242	120	127	12.3636
iiiiiii	chr11:77345323-77345558(-)$1	235	98	105	13.8030
odddd]b	chr8:70220576-70220839(-)$1	263	146	153	16.8333
:::::::	chr11:68904067-68904326(+)$1	259	3	10	12.5909
ndddd]c	chr11:105920089-105920387(+)$1	298	17	24	16.8333
mmfffff	chr11:4667755-4668009(-)$1	254	118	125	13.2727
b]ggggg	chr6:113696064-113696351(-)$1	287	90	97	12.2121
eeellle	chr9:44446194-44446429(+)$1	235	44	51	12.1363
5gggggg	chr9:25115578-25115832(+)$1	254	136	143	13.8030
::::fff	chr9:79618583-79618902(-)$1	319	63	70	12.7424
JJJJJJJ	chr6:108772299-108772537(+)$1	238	117	124	12.7424
!!dddd[	chr1:166367304-166367599(-)$1	295	62	69	13.8030
+++++++	chrX:132748537-132748775(-)$1	238	82	89	12.2121
ccc]ccc	chr19:37097573-37097808(-)$1	235	221	228	13.2727
cca333e	chr2:70439387-70439627(+)$1	240	21	28	16.8333
ffffffg	chr8:26875029-26875280(-)$1	251	210	217	12.5909
ZZAEEEE	chr13:98021788-98022044(+)$1	256	151	158	12.7424
hhh22bb	chr2:32643400-32643705(-)$1	305	253	260	13.8030
=]ddddd	chr10:75722802-75723082(+)$1	280	157	164	16.8333
FFFZZZA	chr18:36957772-36958009(+)$1	237	167	174	12.5909
E{DDDD{	chr3:116446164-116446403(-)$1	239	5	12	16.8333
:::::::	chr15:98568053-98568311(-)$1	258	6	13	12.7424
ddd::bb	chr1:34933799-34934049(+)$1	250	145	152	13.6515
ff22ccc	chr5:65986736-65986975(+)$1	239	117	124	13.8030
EEBB{CC	chr6:47974257-47974517(-)$1	260	18	25	13.2727
e666666	chr3:32849173-32849408(-)$1	235	107	114	12.5909
!eeeeel	chr11:97578064-97578315(-)$1	251	189	196	13.8030
[dddd[b	chr1:163917627-163917873(-)$1	246	115	122	12.7424
ccceeee	chr19:3456222-3456457(-)$1	235	153	160	13.8030
dd"""ff	chr10:98487879-98488126(+)$1	247	120	127	13.1212
ffffff6	chr10:36854607-36854858(-)$1	251	82	89	13.8030
eeeeqqq	chr18:6788940-6789181(+)$1	241	10	17	13.8030
ffff:::	chr17:85463522-85463778(-)$1	256	209	216	12.5909
:::iiii	chr2:120562923-120563158(-)$1	235	114	121	12.7424
eeaccc[	chr1:129700194-129700448(+)$1	254	50	57	16.8333
:::::::	chr8:56145814-56146102(+)$1	288	278	285	16.8333
CCZZZEE	chr1:134401910-134402146(+)$1	236	101	108	16.8333
LJJJJJJ	chr9:75067565-75067816(+)$1	251	38	45	12.3636
""ggggg	chr14:72938319-72938574(-)$1	255	125	132	13.8030
neeeee3	chr9:45773557-45773802(-)$1	245	106	113	13.2727
JJJJJJJ	chr2:69861428-69861670(+)$1	242	23	30	12.2878
EBB{CCC	chrX:92244257-92244498(-)$1	241	45	52	13.1212
EEEEEEE	chr19:21468794-21469035(-)$1	241	220	227	13.1212
g:::::f	chr7:107421549-107421790(+)$1	241	115	122	13.8030
:::::::	chrX:10173441-10173689(+)$1	248	43	50	13.6515
rbb333c	chr8:56145478-56145720(+)$1	242	113	120	13.2727
ggg6666	chr12:30605470-30605720(+)$1	250	87	94	13.6515
:FFFFFF	chr19:5370342-5370578(+)$1	236	3	10	13.8030
eeeee[c	chr2:73448726-73449004(-)$1	278	186	193	13.6515
!dddd[c	chr16:17044950-17045193(+)$1	243	19	26	13.2727
bb]ffff	chr4:148554398-148554636(-)$1	238	73	80	12.5909
hhh]ccc	chrX:143630390-143630635(+)$1	245	72	79	13.2727
goooooo	chr6:113696548-113696811(-)$1	263	32	39	16.8333
rrrrrrr	chr15:31385917-31386158(-)$1	241	41	48	12.7424
D:a!!gg	chr9:75491098-75491335(-)$1	237	179	186	12.7424
nnncccc	chr1:194332962-194333199(+)$1	237	136	143	13.1212
eeeeedd	chr9:58499600-58499858(+)$1	258	113	120	12.3636
ddd::::	chr15:92171549-92171784(+)$1	235	187	194	13.6515
hh66666	chr17:51876264-51876527(-)$1	263	75	82	16.8333
IIIIIII	chr16:58465881-58466129(+)$1	248	13	20	12.5909
:ccc[dd	chr11:35602994-35603236(+)$1	242	90	97	16.8333

#DB
(((((((	chr16:17046878-17047138(+)$1	1	18	25	13.8030
.(((..(	chr10:42254574-42254823(+)$1	1	162	169	12.5909
))))).)	chr11:109529284-109529537(+)$1	1	141	148	13.8030
)))..))	chr11:87793999-87794305(-)$1	1	114	121	12.3636
.)))...	chr17:9177497-9177766(+)$1	1	41	48	13.1212
(((((((	chr3:143851878-143852120(-)$1	1	120	127	12.3636
)))))))	chr11:77345323-77345558(-)$1	1	98	105	13.8030
.)))).)	chr8:70220576-70220839(-)$1	1	146	153	16.8333
.......	chr11:68904067-68904326(+)$1	1	3	10	12.5909
.)))).)	chr11:105920089-105920387(+)$1	1	17	24	16.8333
..)))))	chr11:4667755-4668009(-)$1	1	118	125	13.2727
).)))))	chr6:113696064-113696351(-)$1	1	90	97	12.2121
(((...)	chr9:44446194-44446429(+)$1	1	44	51	12.1363
.))))))	chr9:25115578-25115832(+)$1	1	136	143	13.8030
....(((	chr9:79618583-79618902(-)$1	1	63	70	12.7424
(((((((	chr6:108772299-108772537(+)$1	1	117	124	12.7424
..((((.	chr1:166367304-166367599(-)$1	1	62	69	13.8030
.......	chrX:132748537-132748775(-)$1	1	82	89	12.2121
))).)))	chr19:37097573-37097808(-)$1	1	221	228	13.2727
)))...)	chr2:70439387-70439627(+)$1	1	21	28	16.8333
)))))))	chr8:26875029-26875280(-)$1	1	210	217	12.5909
..)))))	chr13:98021788-98022044(+)$1	1	151	158	12.7424
)))..))	chr2:32643400-32643705(-)$1	1	253	260	13.8030
).))))(	chr10:75722802-75723082(+)$1	1	157	164	16.8333
)))...)	chr18:36957772-36958009(+)$1	1	167	174	12.5909
(.((((.	chr3:116446164-116446403(-)$1	1	5	12	16.8333
.......	chr15:98568053-98568311(-)$1	1	6	13	12.7424
)))..((	chr1:34933799-34934049(+)$1	1	145	152	13.6515
))..)))	chr5:65986736-65986975(+)$1	1	117	124	13.8030
((((.((	chr6:47974257-47974517(-)$1	1	18	25	13.2727
)......	chr3:32849173-32849408(-)$1	1	107	114	12.5909
.(((((.	chr11:97578064-97578315(-)$1	1	189	196	13.8030
.((((.(	chr1:163917627-163917873(-)$1	1	115	122	12.7424
)))))))	chr19:3456222-3456457(-)$1	1	153	160	13.8030
((...((	chr10:98487879-98488126(+)$1	1	120	127	13.1212
)))))).	chr10:36854607-36854858(-)$1	1	82	89	13.8030
((((...	chr18:6788940-6789181(+)$1	1	10	17	13.8030
))))...	chr17:85463522-85463778(-)$1	1	209	216	12.5909
...((((	chr2:120562923-120563158(-)$1	1	114	121	12.7424
((((((.	chr1:129700194-129700448(+)$1	1	50	57	16.8333
.......	chr8:56145814-56146102(+)$1	1	278	285	16.8333
))...))	chr1:134401910-134402146(+)$1	1	101	108	16.8333
.((((((	chr9:75067565-75067816(+)$1	1	38	45	12.3636
..(((((	chr14:72938319-72938574(-)$1	1	125	132	13.8030
.))))).	chr9:45773557-45773802(-)$1	1	106	113	13.2727
(((((((	chr2:69861428-69861670(+)$1	1	23	30	12.2878
)((.(((	chrX:92244257-92244498(-)$1	1	45	52	13.1212
)))))))	chr19:21468794-21469035(-)$1	1	220	227	13.1212
).....(	chr7:107421549-107421790(+)$1	1	115	122	13.8030
.......	chrX:10173441-10173689(+)$1	1	43	50	13.6515
.))...)	chr8:56145478-56145720(+)$1	1	113	120	13.2727
)))....	chr12:30605470-30605720(+)$1	1	87	94	13.6515
.((((((	chr19:5370342-5370578(+)$1	1	3	10	13.8030
(((((.(	chr2:73448726-73449004(-)$1	1	186	193	13.6515
.((((.(	chr16:17044950-17045193(+)$1	1	19	26	13.2727
)).))))	chr4:148554398-148554636(-)$1	1	73	80	12.5909
))).)))	chrX:143630390-143630635(+)$1	1	72	79	13.2727
(......	chr6:113696548-113696811(-)$1	1	32	39	16.8333
.......	chr15:31385917-31386158(-)$1	1	41	48	12.7424
).(..((	chr9:75491098-75491335(-)$1	1	179	186	12.7424
...))))	chr1:194332962-194333199(+)$1	1	136	143	13.1212
(((((((	chr9:58499600-58499858(+)$1	1	113	120	12.3636
)))....	chr15:92171549-92171784(+)$1	1	187	194	13.6515
)).....	chr17:51876264-51876527(-)$1	1	75	82	16.8333
(((((((	chr16:58465881-58466129(+)$1	1	13	20	12.5909
.(((.((	chr11:35602994-35603236(+)$1	1	90	97	16.8333

#PSSM
U : 0.98	u : 0.01	
G : 0.86	U : 0.06	A : 0.03	C : 0.03	g : 0.01	
C : 0.71	U : 0.10	G : 0.10	A : 0.06	a : 0.01	
U : 0.93	C : 0.03	A : 0.01	u : 0.01	
U : 0.80	G : 0.10	C : 0.07	u : 0.01	
U : 0.89	A : 0.03	G : 0.03	u : 0.03	C : 0.01	
G : 0.86	U : 0.06	A : 0.03	c : 0.01	C : 0.01	g : 0.01	

#score	906.1515151515143
#seq	66
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m2_run1.nuc.txt

#NT
UGUGUGUUUGUG	chr5:33135591-33136001(-)$1	410	293	305	29.4042
UGUGUGUAUGUA	chr7:116174028-116174306(+)$1	278	128	140	26.2127
UGUGUGUGUGUC	chr1:155542091-155542513(+)$1	422	203	215	27.5957
ugugugugugug	chr8:67071266-67071761(-)$1	495	475	487	31.9574
UGUGUGUAUGUA	chr14:60919273-60919696(+)$1	423	308	320	26.2127
UGUGUGACUGUG	chr7:148725025-148725497(-)$1	472	353	365	24.8297
UGUGUGUAUGUG	chr11:95275607-95276083(+)$1	476	116	128	30.2553
UGUGAGUGUGUG	chr6:71340154-71340449(-)$1	295	167	179	27.2765
ugugugugugug	chr7:116176248-116176645(+)$1	397	100	112	31.9574
ugugugugugug	chr8:75217242-75217565(+)$1	323	141	153	31.9574
UGUGUGUGUGUG	chrX:61521744-61522050(-)$1	306	96	108	31.9574
UGUGUGUGCGUG	chr15:37387931-37388429(-)$1	498	71	83	27.5957
UGUGUGUGUGUG	chr8:74152108-74152509(-)$1	401	204	216	31.9574
ugugugugugug	chr6:135680527-135681010(-)$1	483	404	416	31.9574
UGUGUGUUUGUG	chr7:16860755-16861091(-)$1	336	109	121	29.4042
UGUGUGUGUGUG	chr5:53498262-53498632(-)$1	370	141	153	31.9574
UGUGUGUGCGUG	chr4:57704361-57704721(+)$1	360	204	216	27.5957
UGGGUGUUUGUG	chr18:36957489-36957940(+)$1	451	318	330	24.6170
UGUGUGUACGUG	chr10:82093410-82093868(+)$1	458	288	300	25.8936
UGUGUGAGUGUG	chr16:20400683-20401002(-)$1	319	203	215	27.4893
uguguguaugua	chr13:55756328-55756766(+)$1	438	419	431	26.2127
UGUGCGUGUGUG	chr2:132131050-132131491(+)$1	441	101	113	27.2765
ugugugugugug	chr4:6147340-6147568(+)$1	228	100	112	31.9574
ugugugugugug	chr11:97699743-97700054(+)$1	311	113	125	31.9574
uguguguaugug	chr10:85511866-85512260(+)$1	394	124	136	30.2553
ugugugugugug	chr15:6748161-6748618(+)$1	457	126	138	31.9574
UGUGUGUCUGGG	chr15:89331599-89331819(+)$1	220	96	108	24.5106
UGUGUGCaugug	chr17:78774662-78775121(+)$1	459	12	24	25.6808
ugucuguaugug	chr11:77347650-77347897(-)$1	247	92	104	25.4680
UGUGUGUGUGUG	chr16:10530021-10530508(-)$1	487	234	246	31.9574
UGUGUGUUUGUG	chr2:173606494-173606785(+)$1	291	160	172	29.4042
UGUGUGUAUCUG	chr5:89666056-89666390(+)$1	334	135	147	25.4680
ugugugugugug	chr15:98568430-98568905(-)$1	475	2	14	31.9574
ugugugugugug	chr5:48779882-48780136(+)$1	254	135	147	31.9574
ugugugugugug	chr3:97476488-97476846(+)$1	358	193	205	31.9574
ugugugugugug	chr2:24646250-24646670(-)$1	420	205	217	31.9574
uguguguaugug	chr6:113120390-113120886(-)$1	496	136	148	30.2553
UGUGUGUAUGUA	chr18:84909276-84909773(+)$1	497	188	200	26.2127
ugugugugugug	chr15:97575335-97575752(-)$1	417	182	194	31.9574
ugugugugugug	chr17:80247701-80248179(-)$1	478	20	32	31.9574
ugugugugugug	chr8:86135415-86135823(+)$1	408	1	13	31.9574
UAUGUGUCUGUG	chr13:64392320-64392611(-)$1	291	173	185	24.5106
ugugugugugug	chr13:63610542-63610846(-)$1	304	103	115	31.9574
Ggugugugugug	chr11:60527288-60527664(+)$1	376	232	244	27.1702
UGUGUGUAUGUG	chr13:91840351-91840645(+)$1	294	180	192	30.2553
UGUGUGUGUGUG	chr18:60934819-60935217(+)$1	398	276	288	31.9574

#otherMatches

#Struct PSSM
^^^^^^^^^^^^	chr10:79372975-79373388(-)$1	413	202	214	31.9574
?CCCFFFFFF}A	chr5:33135591-33136001(-)$1	410	293	305	29.4042
f[ddddmmmmdd	chr7:116174028-116174306(+)$1	278	128	140	26.2127
uuuuuuuudddd	chr1:155542091-155542513(+)$1	422	203	215	27.5957
@@@@@@DDDD}H	chr8:67071266-67071761(-)$1	495	475	487	31.9574
f[ffffff####	chr14:60919273-60919696(+)$1	423	308	320	26.2127
a]a]a]ccc]a:	chr7:148725025-148725497(-)$1	472	353	365	24.8297
bFFFFFF{EEEE	chr11:95275607-95276083(+)$1	476	116	128	30.2553
=========bb[	chr6:71340154-71340449(-)$1	295	167	179	27.2765
dd[eeeee####	chr7:116176248-116176645(+)$1	397	100	112	31.9574
============	chr8:75217242-75217565(+)$1	323	141	153	31.9574
:dddd[hhhhhh	chrX:61521744-61522050(-)$1	306	96	108	31.9574
eeemmmmeeeee	chr15:37387931-37388429(-)$1	498	71	83	27.5957
emmmmeeeeeII	chr8:74152108-74152509(-)$1	401	204	216	31.9574
==qqqqqqqq==	chr6:135680527-135681010(-)$1	483	404	416	31.9574
::eeeeeooooo	chr7:16860755-16861091(-)$1	336	109	121	29.4042
hh333a]ggggg	chr5:53498262-53498632(-)$1	370	141	153	31.9574
a[ddddqqqqqq	chr4:57704361-57704721(+)$1	360	204	216	27.5957
MMMCCC{BB{DD	chr18:36957489-36957940(+)$1	451	318	330	24.6170
hhmmmmhhhhhh	chr10:82093410-82093868(+)$1	458	288	300	25.8936
333ccccccggg	chr16:20400683-20401002(-)$1	319	203	215	27.4893
?????GGGGGGG	chr13:55756328-55756766(+)$1	438	419	431	26.2127
^cccbb333eee	chr2:132131050-132131491(+)$1	441	101	113	27.2765
::ccc[a[bb[a	chr4:6147340-6147568(+)$1	228	100	112	31.9574
]dddd=======	chr11:97699743-97700054(+)$1	311	113	125	31.9574
gggeeeeemmmm	chr10:85511866-85512260(+)$1	394	124	136	30.2553
FFFF}A}CCC}E	chr15:6748161-6748618(+)$1	457	126	138	31.9574
eee!!ccclllc	chr15:89331599-89331819(+)$1	220	96	108	24.5106
gggggggmmmmg	chr17:78774662-78775121(+)$1	459	12	24	25.6808
==]ffffffiii	chr11:77347650-77347897(-)$1	247	92	104	25.4680
E:::A{CCC{A{	chr16:10530021-10530508(-)$1	487	234	246	31.9574
c::::=======	chr2:173606494-173606785(+)$1	291	160	172	29.4042
dd]bb]bbffff	chr5:89666056-89666390(+)$1	334	135	147	25.4680
FFFFF{BB:ccc	chr15:98568430-98568905(-)$1	475	2	14	31.9574
dd[dddd[iiii	chr5:48779882-48780136(+)$1	254	135	147	31.9574
22bbgggggggf	chr3:97476488-97476846(+)$1	358	193	205	31.9574
:::::::ccc!!	chr2:24646250-24646670(-)$1	420	205	217	31.9574
=========ooo	chr6:113120390-113120886(-)$1	496	136	148	30.2553
hhhhhhhhuuuu	chr18:84909276-84909773(+)$1	497	188	200	26.2127
nnffffff]eee	chr15:97575335-97575752(-)$1	417	182	194	31.9574
nnnccc]a]ccc	chr17:80247701-80248179(-)$1	478	20	32	31.9574
::BB{BB{A{EE	chr8:86135415-86135823(+)$1	408	1	13	31.9574
============	chr13:64392320-64392611(-)$1	291	173	185	24.5106
obb4444a]ccc	chr13:63610542-63610846(-)$1	304	103	115	31.9574
:::::::::::f	chr11:60527288-60527664(+)$1	376	232	244	27.1702
EEEdddd[a[ff	chr13:91840351-91840645(+)$1	294	180	192	30.2553
}FFFFFF}A}CC	chr18:60934819-60935217(+)$1	398	276	288	31.9574

#DB
............	chr10:79372975-79373388(-)$1	1	202	214	31.9574
.))))))))).)	chr5:33135591-33136001(-)$1	1	293	305	29.4042
(.((((....))	chr7:116174028-116174306(+)$1	1	128	140	26.2127
........))))	chr1:155542091-155542513(+)$1	1	203	215	27.5957
......)))).)	chr8:67071266-67071761(-)$1	1	475	487	31.9574
(.((((((....	chr14:60919273-60919696(+)$1	1	308	320	26.2127
).).).))).).	chr7:148725025-148725497(-)$1	1	353	365	24.8297
)((((((.((((	chr11:95275607-95276083(+)$1	1	116	128	30.2553
)))))))))((.	chr6:71340154-71340449(-)$1	1	167	179	27.2765
((.(((((....	chr7:116176248-116176645(+)$1	1	100	112	31.9574
((((((((((((	chr8:75217242-75217565(+)$1	1	141	153	31.9574
.((((.((((((	chrX:61521744-61522050(-)$1	1	96	108	31.9574
(((....)))))	chr15:37387931-37388429(-)$1	1	71	83	27.5957
(....)))))))	chr8:74152108-74152509(-)$1	1	204	216	31.9574
((........))	chr6:135680527-135681010(-)$1	1	404	416	31.9574
..(((((.....	chr7:16860755-16861091(-)$1	1	109	121	29.4042
))...).)))))	chr5:53498262-53498632(-)$1	1	141	153	31.9574
(.((((......	chr4:57704361-57704721(+)$1	1	204	216	27.5957
...(((.((.((	chr18:36957489-36957940(+)$1	1	318	330	24.6170
((....))))))	chr10:82093410-82093868(+)$1	1	288	300	25.8936
...)))))))))	chr16:20400683-20401002(-)$1	1	203	215	27.4893
.....)))))))	chr13:55756328-55756766(+)$1	1	419	431	26.2127
.)))))...)))	chr2:132131050-132131491(+)$1	1	101	113	27.2765
..(((.(.((.(	chr4:6147340-6147568(+)$1	1	100	112	31.9574
.))))(((((((	chr11:97699743-97700054(+)$1	1	113	125	31.9574
)))(((((....	chr10:85511866-85512260(+)$1	1	124	136	30.2553
)))).).))).)	chr15:6748161-6748618(+)$1	1	126	138	31.9574
(((..(((...)	chr15:89331599-89331819(+)$1	1	96	108	24.5106
(((((((....)	chr17:78774662-78775121(+)$1	1	12	24	25.6808
)).)))))))))	chr11:77347650-77347897(-)$1	1	92	104	25.4680
)...(.(((.(.	chr16:10530021-10530508(-)$1	1	234	246	31.9574
)....(((((((	chr2:173606494-173606785(+)$1	1	160	172	29.4042
)).)).))))))	chr5:89666056-89666390(+)$1	1	135	147	25.4680
(((((.((.(((	chr15:98568430-98568905(-)$1	1	2	14	31.9574
((.((((.((((	chr5:48779882-48780136(+)$1	1	135	147	31.9574
..)))))))))(	chr3:97476488-97476846(+)$1	1	193	205	31.9574
.......(((..	chr2:24646250-24646670(-)$1	1	205	217	31.9574
(((((((((...	chr6:113120390-113120886(-)$1	1	136	148	30.2553
((((((((....	chr18:84909276-84909773(+)$1	1	188	200	26.2127
..)))))).)))	chr15:97575335-97575752(-)$1	1	182	194	31.9574
...))).).)))	chr17:80247701-80248179(-)$1	1	20	32	31.9574
..((.((.(.((	chr8:86135415-86135823(+)$1	1	1	13	31.9574
))))))))))))	chr13:64392320-64392611(-)$1	1	173	185	24.5106
.))....).)))	chr13:63610542-63610846(-)$1	1	103	115	31.9574
...........(	chr11:60527288-60527664(+)$1	1	232	244	27.1702
)))((((.(.((	chr13:91840351-91840645(+)$1	1	180	192	30.2553
.)))))).).))	chr18:60934819-60935217(+)$1	1	276	288	31.9574

#PSSM
U : 0.55	u : 0.42	G : 0.02	
G : 0.53	g : 0.44	A : 0.02	
U : 0.53	u : 0.44	G : 0.02	
G : 0.55	g : 0.42	c : 0.02	
U : 0.51	u : 0.44	A : 0.02	C : 0.02	
G : 0.55	g : 0.44	
U : 0.48	u : 0.44	A : 0.04	C : 0.02	
g : 0.36	G : 0.23	A : 0.14	a : 0.10	U : 0.08	C : 0.06	
u : 0.46	U : 0.46	C : 0.06	
G : 0.51	g : 0.46	C : 0.02	
U : 0.51	u : 0.46	G : 0.02	
g : 0.44	G : 0.44	A : 0.06	C : 0.02	a : 0.02	

#score	1378.170212765957
#seq	47
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_CDS_m2_run2.nuc.txt

#NT
CAGCCAACUA	chr18:36908130-36908409(+)$1	279	205	215	10.4878
CGGCCUGCAG	chr16:36049850-36050132(-)$1	282	230	240	11.8292
AGGCCAGCGC	chr2:174125804-174126076(+)$1	272	172	182	12.4390
CGUCCAUCUC	chr5:75006662-75006928(-)$1	266	106	116	10.3658
CGGCCGGCGA	chrX:98514856-98515126(+)$1	270	208	218	10.2439
CGGCCCGCCC	chr5:67078040-67078309(+)$1	269	177	187	11.5853
CCCCCAGCUG	chr17:32498275-32498549(-)$1	274	61	71	10.8536
CUGACAGCUC	chr14:70066965-70067244(+)$1	279	49	59	11.9512
CAGCCAGCGC	chr18:24743678-24743948(-)$1	270	212	222	13.9024
CGGCAAGCCA	chr2:153142650-153142935(+)$1	285	116	126	9.8780
CUGCCAGGUG	chr8:95850590-95850858(-)$1	268	85	95	11.8292
CGGGCAGCCG	chr13:69138016-69138287(-)$1	271	7	17	11.8292
CUGCCAACUU	chr8:87359374-87359661(-)$1	287	161	171	10.7317
CUGACAGCUC	chr9:3411328-3411617(+)$1	289	109	119	11.9512
CGGCCAGGCA	chr17:35292431-35292717(-)$1	286	252	262	10.4878
CUGCCAGCCA	chr8:28383689-28383967(+)$1	278	182	192	12.6829
UGGCCAGCAC	chr3:146444016-146444284(-)$1	268	13	23	12.6829
CGGCCAGCUC	chr5:93697524-93697808(+)$1	284	48	58	17.8048
GGGCCAGCAU	chr11:87794777-87795061(-)$1	284	200	210	11.5853
CUGCCAGGUC	chr13:73773754-73774025(+)$1	271	6	16	11.9512
AGGCCAGCGC	chr2:174125832-174126111(+)$1	279	144	154	12.4390
CGGCCCUCUG	chr8:74842841-74843113(+)$1	272	67	77	9.7560
UAGCCAGCUG	chr11:70466238-70466523(-)$1	285	39	49	11.9512
CAGCCAUCUC	chr1:184398226-184398498(-)$1	272	35	45	12.0731
CGUCCAGCGG	chr2:91803312-91803591(-)$1	279	49	59	12.0731
CAGCCAGCAG	chr10:79879360-79879636(-)$1	276	117	127	14.1463
GGCCCAGCUG	chr7:28151313-28151603(-)$1	290	97	107	10.2439
GGUCCAGCUU	chr11:120481895-120482204(-)$1	309	230	240	9.2682
CUGCCAGCGU	chr13:24843895-24844177(-)$1	282	253	263	12.8048
CAGCCAGCAU	chr19:46681119-46681390(+)$1	271	241	251	12.9268
GGGCCAGCUC	chr2:156359444-156359715(+)$1	271	170	180	14.3902
CUGCCAGCUG	chr1:93275013-93275289(-)$1	276	223	233	15.8536
CGGCCACCUG	chr11:117828707-117828977(-)$1	270	26	36	13.6585
CGUGCAGCUG	chr18:60859085-60859370(-)$1	285	148	158	10.0000
CAGCCAGGUC	chr11:102978351-102978633(+)$1	282	232	242	11.7073
CGGCCAUCAG	chr7:135038927-135039193(-)$1	266	237	247	12.5609
CGGCCAGCAC	chr9:97269861-97270130(-)$1	269	108	118	16.3414
CGGGGAGCUG	chr1:181447940-181448228(-)$1	288	223	233	9.1463
CUGCCAGCAG	chr19:7273741-7274022(-)$1	281	151	161	14.3902
CGGUCAGCAC	chr5:123244330-123244627(-)$1	297	231	241	12.1951

#otherMatches

#Struct PSSM
rrrrrrrccc	chr17:6084525-6084804(+)$1	279	176	186	14.2682
hhhhhqqqqq	chr18:36908130-36908409(+)$1	279	205	215	10.4878
pffffffddd	chr16:36049850-36050132(-)$1	282	230	240	11.8292
::ccc!!ddd	chr2:174125804-174126076(+)$1	272	172	182	12.4390
ff[aoooooo	chr5:75006662-75006928(-)$1	266	106	116	10.3658
EEEEAdddd[	chrX:98514856-98515126(+)$1	270	208	218	10.2439
nnbbbbdddd	chr5:67078040-67078309(+)$1	269	177	187	11.5853
CGGGGGGGA{	chr17:32498275-32498549(-)$1	274	61	71	10.8536
ccssssssss	chr14:70066965-70067244(+)$1	279	49	59	11.9512
:cccmmmmcc	chr18:24743678-24743948(-)$1	270	212	222	13.9024
gggggggccc	chr2:153142650-153142935(+)$1	285	116	126	9.8780
eee!!dddd$	chr8:95850590-95850858(-)$1	268	85	95	11.8292
FFF:::dddd	chr13:69138016-69138287(-)$1	271	7	17	11.8292
llldddd]bb	chr8:87359374-87359661(-)$1	287	161	171	10.7317
ffffffbb[d	chr9:3411328-3411617(+)$1	289	109	119	11.9512
3ccca]ccc]	chr17:35292431-35292717(-)$1	286	252	262	10.4878
uuuuuuuuuu	chr8:28383689-28383967(+)$1	278	182	192	12.6829
:CCC{CCC::	chr3:146444016-146444284(-)$1	268	13	23	12.6829
bnnnnnbbgg	chr5:93697524-93697808(+)$1	284	48	58	17.8048
[ccc!!ccc[	chr11:87794777-87795061(-)$1	284	200	210	11.5853
JJJJJJJJJJ	chr13:73773754-73774025(+)$1	271	6	16	11.9512
ldddd::ddd	chr2:174125832-174126111(+)$1	279	144	154	12.4390
{BB{CCCccc	chr8:74842841-74843113(+)$1	272	67	77	9.7560
::cccooooo	chr11:70466238-70466523(-)$1	285	39	49	11.9512
HHH:::GGGG	chr1:184398226-184398498(-)$1	272	35	45	12.0731
III{BB{Agg	chr2:91803312-91803591(-)$1	279	49	59	12.0731
annnnna]bb	chr10:79879360-79879636(-)$1	276	117	127	14.1463
cccffffffn	chr7:28151313-28151603(-)$1	290	97	107	10.2439
foooooofff	chr11:120481895-120482204(-)$1	309	230	240	9.2682
bb22eeeee]	chr13:24843895-24844177(-)$1	282	253	263	12.8048
DDYYDDDD::	chr19:46681119-46681390(+)$1	271	241	251	12.9268
FFFF::::::	chr2:156359444-156359715(+)$1	271	170	180	14.3902
dd:EEEEEYY	chr1:93275013-93275289(-)$1	276	223	233	15.8536
A{CCC{EEEE	chr11:117828707-117828977(-)$1	270	26	36	13.6585
b[cccccc[b	chr18:60859085-60859370(-)$1	285	148	158	10.0000
AYYEEEEE~~	chr11:102978351-102978633(+)$1	282	232	242	11.7073
eeeennnnne	chr7:135038927-135039193(-)$1	266	237	247	12.5609
diiiiiiiii	chr9:97269861-97270130(-)$1	269	108	118	16.3414
CCCeeeeerr	chr1:181447940-181448228(-)$1	288	223	233	9.1463
~~JJJJJJJJ	chr19:7273741-7274022(-)$1	281	151	161	14.3902
na22dddd:d	chr5:123244330-123244627(-)$1	297	231	241	12.1951

#DB
.......)))	chr17:6084525-6084804(+)$1	1	176	186	14.2682
(((((.....	chr18:36908130-36908409(+)$1	1	205	215	10.4878
.)))))))))	chr16:36049850-36050132(-)$1	1	230	240	11.8292
..(((..(((	chr2:174125804-174126076(+)$1	1	172	182	12.4390
((.(......	chr5:75006662-75006928(-)$1	1	106	116	10.3658
)))))((((.	chrX:98514856-98515126(+)$1	1	208	218	10.2439
..))))))))	chr5:67078040-67078309(+)$1	1	177	187	11.5853
(((((((((.	chr17:32498275-32498549(-)$1	1	61	71	10.8536
((........	chr14:70066965-70067244(+)$1	1	49	59	11.9512
.(((....))	chr18:24743678-24743948(-)$1	1	212	222	13.9024
)))))))(((	chr2:153142650-153142935(+)$1	1	116	126	9.8780
(((..((((.	chr8:95850590-95850858(-)$1	1	85	95	11.8292
(((...((((	chr13:69138016-69138287(-)$1	1	7	17	11.8292
...)))).))	chr8:87359374-87359661(-)$1	1	161	171	10.7317
))))))((.(	chr9:3411328-3411617(+)$1	1	109	119	11.9512
.)))).))).	chr17:35292431-35292717(-)$1	1	252	262	10.4878
..........	chr8:28383689-28383967(+)$1	1	182	192	12.6829
.(((.(((..	chr3:146444016-146444284(-)$1	1	13	23	12.6829
(.....))))	chr5:93697524-93697808(+)$1	1	48	58	17.8048
.(((..(((.	chr11:87794777-87795061(-)$1	1	200	210	11.5853
((((((((((	chr13:73773754-73774025(+)$1	1	6	16	11.9512
.))))..(((	chr2:174125832-174126111(+)$1	1	144	154	12.4390
.((.((((((	chr8:74842841-74843113(+)$1	1	67	77	9.7560
..(((.....	chr11:70466238-70466523(-)$1	1	39	49	11.9512
(((...((((	chr1:184398226-184398498(-)$1	1	35	45	12.0731
(((.((.(((	chr2:91803312-91803591(-)$1	1	49	59	12.0731
(.....).))	chr10:79879360-79879636(-)$1	1	117	127	14.1463
(((((((((.	chr7:28151313-28151603(-)$1	1	97	107	10.2439
(......)))	chr11:120481895-120482204(-)$1	1	230	240	9.2682
))..))))).	chr13:24843895-24844177(-)$1	1	253	263	12.8048
))..))))..	chr19:46681119-46681390(+)$1	1	241	251	12.9268
))))......	chr2:156359444-156359715(+)$1	1	170	180	14.3902
)).)))))..	chr1:93275013-93275289(-)$1	1	223	233	15.8536
(.(((.((((	chr11:117828707-117828977(-)$1	1	26	36	13.6585
(.((((((.(	chr18:60859085-60859370(-)$1	1	148	158	10.0000
)..)))))..	chr11:102978351-102978633(+)$1	1	232	242	11.7073
((((.....)	chr7:135038927-135039193(-)$1	1	237	247	12.5609
)(((((((((	chr9:97269861-97270130(-)$1	1	108	118	16.3414
((((((((..	chr1:181447940-181448228(-)$1	1	223	233	9.1463
..))))))))	chr19:7273741-7274022(-)$1	1	151	161	14.3902
.)..)))).(	chr5:123244330-123244627(-)$1	1	231	241	12.1951

#PSSM
C : 0.78	G : 0.09	A : 0.07	U : 0.04	
G : 0.58	U : 0.21	A : 0.17	C : 0.02	
G : 0.85	U : 0.09	C : 0.04	
C : 0.85	G : 0.07	A : 0.04	U : 0.02	
C : 0.95	A : 0.02	G : 0.02	
A : 0.90	C : 0.04	U : 0.02	G : 0.02	
G : 0.82	U : 0.09	A : 0.04	C : 0.02	
C : 0.90	G : 0.09	
U : 0.51	A : 0.21	G : 0.14	C : 0.12	
C : 0.39	G : 0.36	A : 0.12	U : 0.12	

#score	499.2682926829269
#seq	41
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_UTR_m3_run2.nuc.txt

#NT
UUUGUGUUU	chr19:12542405-12542640(-)$1	235	131	140	12.7894
UUUUUAUUU	chr9:113886880-113887137(-)$1	257	6	15	19.3684
UUUUUAUUU	chr11:102150504-102150793(-)$1	289	65	74	19.3684
UUUUUUUUU	chr13:99016718-99016963(-)$1	245	229	238	16.2982
UUGUCAUUU	chr3:127510155-127510416(-)$1	261	188	197	11.6491
UUCUUGUUU	chr11:65501747-65502005(-)$1	258	42	51	12.2631
GUUUUAUUU	chr15:76348093-76348358(-)$1	265	119	128	15.7719
UUUUUUUUU	chr11:100881708-100881974(+)$1	266	64	73	16.2982
ucuugauuu	chr9:123370925-123371405(+)$1	480	55	64	12.0000
AUUUUGUUU	chr3:94295586-94295853(+)$1	267	253	262	12.7894
UGUGUAUUU	chr19:46731696-46731955(+)$1	259	40	49	11.8245
UUUAUACUU	chr7:152116984-152117266(-)$1	282	10	19	11.5614
uuuuuguuu	chr11:88156413-88156673(-)$1	260	49	58	16.5614
UUUUUGUUU	chr17:45704777-45705164(-)$1	387	375	384	16.5614
UUUUUAUCA	chr9:108108769-108109094(-)$1	325	117	126	10.9473
GUAUUAUUU	chr3:33711103-33711341(+)$1	238	30	39	11.5614
UUUUUAUUU	chr8:92771784-92772044(-)$1	260	99	108	19.3684
UUAUUGUUU	chr2:91769900-91770289(-)$1	389	3	12	12.3508
UUUGGAUUU	chr18:64431217-64431608(+)$1	391	59	68	12.0000
UGUUCAUUU	chr3:50171387-50171643(-)$1	256	20	29	11.9122
UUUGUAUAU	chr13:43233546-43233804(+)$1	258	239	248	11.7368
UUUUUUUUU	chr9:72970295-72970537(+)$1	242	232	241	16.2982
CUUUUAUUU	chr2:124491904-124492178(+)$1	274	199	208	15.5964
UUUUUAGAU	chr19:21931384-21931689(+)$1	305	66	75	11.4736
UUUUUAUUA	chr9:48207295-48207538(+)$1	243	67	76	15.0701
CUUUUAUUU	chr10:7343574-7343863(+)$1	289	255	264	15.5964
UUGUUAUAU	chr12:109776589-109776860(+)$1	271	14	23	11.4736
GUUUuauau	chr18:55048334-55048569(-)$1	235	19	28	11.9122
UUUUGAUUU	chr6:122266366-122266615(+)$1	249	220	229	15.7719
UUUUUAUAC	chr17:66436674-66436932(-)$1	258	71	80	11.1228
UUUCCAUUU	chr16:10282768-10283023(-)$1	255	194	203	11.5614
CUUUUGUUU	chr5:121583285-121583524(-)$1	239	144	153	12.7894
UUUUUUUUU	chr5:33133326-33133609(-)$1	283	210	219	16.2982
UUGUAAUUU	chr3:80491748-80492009(-)$1	261	179	188	11.8245
UUUUUUUUU	chr11:119400049-119400348(-)$1	299	239	248	16.2982
GUUUUAUUU	chr3:103768434-103768706(+)$1	272	33	42	15.7719
UAUUUAUUU	chr2:37894578-37894820(-)$1	242	178	187	15.4210
AUUUUUUUU	chr5:150026683-150026922(+)$1	239	65	74	12.5263
UCUUUAAUU	chr5:137966978-137967225(+)$1	247	173	182	11.6491
UUUUAAUCU	chr17:10405389-10405685(-)$1	296	34	43	11.7368
UUUUUAUUU	chr6:17614961-17615213(+)$1	252	220	229	19.3684
UAUUUAUUC	chr7:48629208-48629473(-)$1	265	48	57	11.0350
UUUUAAUUU	chr7:66561196-66561438(-)$1	242	2	11	15.8596
UUUUAAUUU	chr9:61905537-61905798(-)$1	261	175	184	15.8596
UUUUUGUUU	chr1:88015040-88015305(+)$1	265	22	31	16.5614
AUGUUAUUU	chr3:103546366-103546692(-)$1	326	35	44	11.5614
UUUGUCUUU	chr5:9479667-9479912(-)$1	245	167	176	12.0877
UUUAUACUU	chr13:99494533-99494843(-)$1	310	60	69	11.5614
UGUUAAUUU	chr18:86887442-86887699(+)$1	257	145	154	12.0877
GUUUUAUUA	chr2:148263681-148263944(-)$1	263	234	243	11.4736
UUUUUAUUU	chr4:75590200-75590460(-)$1	260	243	252	19.3684
UUUUUGCUU	chr2:14997887-14998161(+)$1	274	46	55	12.7017
UCUUUAUGU	chr13:118062595-118062846(+)$1	251	157	166	11.3859
UUUUGAAUU	chr11:97022799-97023067(-)$1	268	157	166	11.8245
UUUAUAAUU	chr5:104508026-104508368(-)$1	342	86	95	11.4736
UCUUUAGUU	chr12:34123776-34124055(+)$1	279	136	145	11.5614

#otherMatches

#Struct PSSM
ccc!!bbqq	chr3:100844603-100844915(-)$1	312	94	103	11.7368
)))hhhhhh	chr19:12542405-12542640(-)$1	235	131	140	12.7894
:::::::::	chr9:113886880-113887137(-)$1	257	6	15	19.3684
dd!!cccqq	chr11:102150504-102150793(-)$1	289	65	74	19.3684
:::::::::	chr13:99016718-99016963(-)$1	245	229	238	16.2982
sggggggg:	chr3:127510155-127510416(-)$1	261	188	197	11.6491
gggg::GGG	chr11:65501747-65502005(-)$1	258	42	51	12.2631
eeeeppppp	chr15:76348093-76348358(-)$1	265	119	128	15.7719
bb=======	chr11:100881708-100881974(+)$1	266	64	73	16.2982
:::ccclll	chr9:123370925-123371405(+)$1	480	55	64	12.0000
:::::::::	chr3:94295586-94295853(+)$1	267	253	262	12.7894
mmmmeeeee	chr19:46731696-46731955(+)$1	259	40	49	11.8245
:::::::::	chr7:152116984-152117266(-)$1	282	10	19	11.5614
====[iiii	chr11:88156413-88156673(-)$1	260	49	58	16.5614
JJJJJJJ::	chr17:45704777-45705164(-)$1	387	375	384	16.5614
gggg333ee	chr9:108108769-108109094(-)$1	325	117	126	10.9473
ggggqqqqq	chr3:33711103-33711341(+)$1	238	30	39	11.5614
hhhhhhh!!	chr8:92771784-92772044(-)$1	260	99	108	19.3684
C{DDDDOOO	chr2:91769900-91770289(-)$1	389	3	12	12.3508
$$$ffffff	chr18:64431217-64431608(+)$1	391	59	68	12.0000
occc22ggg	chr3:50171387-50171643(-)$1	256	20	29	11.9122
fffffmmmm	chr13:43233546-43233804(+)$1	258	239	248	11.7368
:::::::::	chr9:72970295-72970537(+)$1	242	232	241	16.2982
::::fffff	chr2:124491904-124492178(+)$1	274	199	208	15.5964
E{EEEEE{E	chr19:21931384-21931689(+)$1	305	66	75	11.4736
wwwwwwwww	chr9:48207295-48207538(+)$1	243	67	76	15.0701
FFF::::::	chr10:7343574-7343863(+)$1	289	255	264	15.5964
eee%%%%%%	chr12:109776589-109776860(+)$1	271	14	23	11.4736
dddd=====	chr18:55048334-55048569(-)$1	235	19	28	11.9122
:DDDDYYCC	chr6:122266366-122266615(+)$1	249	220	229	15.7719
eee]eeeee	chr17:66436674-66436932(-)$1	258	71	80	11.1228
ffffff!!e	chr16:10282768-10283023(-)$1	255	194	203	11.5614
=========	chr5:121583285-121583524(-)$1	239	144	153	12.7894
eeee:::::	chr5:33133326-33133609(-)$1	283	210	219	16.2982
ee]a::ggg	chr3:80491748-80492009(-)$1	261	179	188	11.8245
JJJJJJJJJ	chr11:119400049-119400348(-)$1	299	239	248	16.2982
ccc888888	chr3:103768434-103768706(+)$1	272	33	42	15.7719
:::::iiii	chr2:37894578-37894820(-)$1	242	178	187	15.4210
:::::::::	chr5:150026683-150026922(+)$1	239	65	74	12.5263
eeeewwwww	chr5:137966978-137967225(+)$1	247	173	182	11.6491
::::::FFF	chr17:10405389-10405685(-)$1	296	34	43	11.7368
E:::=====	chr6:17614961-17615213(+)$1	252	220	229	19.3684
::ggggggg	chr7:48629208-48629473(-)$1	265	48	57	11.0350
HHHHHHH:i	chr7:66561196-66561438(-)$1	242	2	11	15.8596
uuuuuuuuu	chr9:61905537-61905798(-)$1	261	175	184	15.8596
EEEeeeee[	chr1:88015040-88015305(+)$1	265	22	31	16.5614
:::::::::	chr3:103546366-103546692(-)$1	326	35	44	11.5614
ppppppfff	chr5:9479667-9479912(-)$1	245	167	176	12.0877
dddd:::::	chr13:99494533-99494843(-)$1	310	60	69	11.5614
eeooooooe	chr18:86887442-86887699(+)$1	257	145	154	12.0877
e88888888	chr2:148263681-148263944(-)$1	263	234	243	11.4736
:::::::::	chr4:75590200-75590460(-)$1	260	243	252	19.3684
gggggnnnn	chr2:14997887-14998161(+)$1	274	46	55	12.7017
:::::::::	chr13:118062595-118062846(+)$1	251	157	166	11.3859
b[ggggggg	chr11:97022799-97023067(-)$1	268	157	166	11.8245
=========	chr5:104508026-104508368(-)$1	342	86	95	11.4736
nnnnhhhhh	chr12:34123776-34124055(+)$1	279	136	145	11.5614

#DB
(((..((..	chr3:100844603-100844915(-)$1	1	94	103	11.7368
...((((((	chr19:12542405-12542640(-)$1	1	131	140	12.7894
.........	chr9:113886880-113887137(-)$1	1	6	15	19.3684
((..(((..	chr11:102150504-102150793(-)$1	1	65	74	19.3684
.........	chr13:99016718-99016963(-)$1	1	229	238	16.2982
.))))))).	chr3:127510155-127510416(-)$1	1	188	197	11.6491
))))..(((	chr11:65501747-65502005(-)$1	1	42	51	12.2631
((((.....	chr15:76348093-76348358(-)$1	1	119	128	15.7719
(((((((((	chr11:100881708-100881974(+)$1	1	64	73	16.2982
...(((...	chr9:123370925-123371405(+)$1	1	55	64	12.0000
.........	chr3:94295586-94295853(+)$1	1	253	262	12.7894
....)))))	chr19:46731696-46731955(+)$1	1	40	49	11.8245
.........	chr7:152116984-152117266(-)$1	1	10	19	11.5614
((((.((((	chr11:88156413-88156673(-)$1	1	49	58	16.5614
)))))))..	chr17:45704777-45705164(-)$1	1	375	384	16.5614
))))...))	chr9:108108769-108109094(-)$1	1	117	126	10.9473
((((.....	chr3:33711103-33711341(+)$1	1	30	39	11.5614
(((((((..	chr8:92771784-92772044(-)$1	1	99	108	19.3684
(.((((...	chr2:91769900-91770289(-)$1	1	3	12	12.3508
...((((((	chr18:64431217-64431608(+)$1	1	59	68	12.0000
.)))..)))	chr3:50171387-50171643(-)$1	1	20	29	11.9122
(((((....	chr13:43233546-43233804(+)$1	1	239	248	11.7368
.........	chr9:72970295-72970537(+)$1	1	232	241	16.2982
....(((((	chr2:124491904-124492178(+)$1	1	199	208	15.5964
(.(((((.(	chr19:21931384-21931689(+)$1	1	66	75	11.4736
.........	chr9:48207295-48207538(+)$1	1	67	76	15.0701
)))......	chr10:7343574-7343863(+)$1	1	255	264	15.5964
(((......	chr12:109776589-109776860(+)$1	1	14	23	11.4736
))))(((((	chr18:55048334-55048569(-)$1	1	19	28	11.9122
.))))..))	chr6:122266366-122266615(+)$1	1	220	229	15.7719
))).)))))	chr17:66436674-66436932(-)$1	1	71	80	11.1228
((((((..(	chr16:10282768-10283023(-)$1	1	194	203	11.5614
(((((((((	chr5:121583285-121583524(-)$1	1	144	153	12.7894
)))).....	chr5:33133326-33133609(-)$1	1	210	219	16.2982
)).)..(((	chr3:80491748-80492009(-)$1	1	179	188	11.8245
)))))))))	chr11:119400049-119400348(-)$1	1	239	248	16.2982
)))......	chr3:103768434-103768706(+)$1	1	33	42	15.7719
.....((((	chr2:37894578-37894820(-)$1	1	178	187	15.4210
.........	chr5:150026683-150026922(+)$1	1	65	74	12.5263
((((.....	chr5:137966978-137967225(+)$1	1	173	182	11.6491
......(((	chr17:10405389-10405685(-)$1	1	34	43	11.7368
)...(((((	chr6:17614961-17615213(+)$1	1	220	229	19.3684
..(((((((	chr7:48629208-48629473(-)$1	1	48	57	11.0350
(((((((.(	chr7:66561196-66561438(-)$1	1	2	11	15.8596
.........	chr9:61905537-61905798(-)$1	1	175	184	15.8596
((((((((.	chr1:88015040-88015305(+)$1	1	22	31	16.5614
.........	chr3:103546366-103546692(-)$1	1	35	44	11.5614
......)))	chr5:9479667-9479912(-)$1	1	167	176	12.0877
)))).....	chr13:99494533-99494843(-)$1	1	60	69	11.5614
((......)	chr18:86887442-86887699(+)$1	1	145	154	12.0877
)........	chr2:148263681-148263944(-)$1	1	234	243	11.4736
.........	chr4:75590200-75590460(-)$1	1	243	252	19.3684
(((((....	chr2:14997887-14998161(+)$1	1	46	55	12.7017
.........	chr13:118062595-118062846(+)$1	1	157	166	11.3859
(.(((((((	chr11:97022799-97023067(-)$1	1	157	166	11.8245
(((((((((	chr5:104508026-104508368(-)$1	1	86	95	11.4736
....)))))	chr12:34123776-34124055(+)$1	1	136	145	11.5614

#PSSM
U : 0.77	G : 0.08	A : 0.05	C : 0.05	u : 0.03	
U : 0.80	G : 0.07	C : 0.05	A : 0.03	c : 0.01	u : 0.01	
U : 0.84	G : 0.07	u : 0.03	A : 0.03	C : 0.01	
U : 0.80	G : 0.08	A : 0.05	u : 0.03	C : 0.01	
U : 0.75	A : 0.08	C : 0.05	G : 0.05	u : 0.03	g : 0.01	
A : 0.68	G : 0.14	U : 0.10	a : 0.03	g : 0.01	C : 0.01	
U : 0.78	C : 0.07	u : 0.05	A : 0.05	G : 0.03	
U : 0.82	A : 0.07	u : 0.03	C : 0.03	a : 0.01	G : 0.01	
U : 0.85	u : 0.05	A : 0.05	C : 0.03	

#score	782.6842105263166
#seq	57
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m1_run2.nuc.txt

#NT
AUUU	chr3:72852070-72852271(-)$1	201	46	50	11.9999
AUUU	chr10:112364597-112364798(-)$1	201	94	98	11.9999
AUUU	chr5:104542378-104542579(-)$1	201	0	4	11.9999
AUUU	chr4:81940723-81940924(-)$1	201	0	4	11.9999
AUUU	chr13:97419982-97420183(-)$1	201	36	40	11.9999
AUUU	chr8:113659249-113659450(+)$1	201	49	53	11.9999
AUUU	chr1:78702938-78703139(+)$1	201	181	185	11.9999
AUUU	chr15:9126781-9126982(+)$1	201	0	4	11.9999
AUUU	chr4:148550625-148550826(-)$1	201	175	179	11.9999
AUUU	chr18:77700887-77701088(-)$1	201	109	113	11.9999
AUUU	chr14:65430470-65430671(-)$1	201	182	186	11.9999
AUUU	chrX:133371564-133371765(+)$1	201	160	164	11.9999
AUUU	chr10:112364596-112364797(-)$1	201	93	97	11.9999
AUUU	chr2:33263737-33263938(-)$1	201	30	34	11.9999
AUUU	chr10:66718543-66718744(+)$1	201	79	83	11.9999
AUUU	chr10:66718544-66718745(+)$1	201	78	82	11.9999
AUUU	chr18:61145078-61145279(+)$1	201	97	101	11.9999
AUUU	chrX:39029573-39029774(+)$1	201	16	20	11.9999
AUUU	chr6:113697619-113697820(-)$1	201	68	72	11.9999
AUUU	chr2:30885422-30885623(-)$1	201	169	173	11.9999
AUUU	chr12:100027590-100027791(-)$1	201	63	67	11.9999
AUUU	chr11:119400102-119400303(-)$1	201	78	82	11.9999
AUUU	chr17:66687050-66687251(-)$1	201	164	168	11.9999
AUUU	chr5:15876961-15877162(+)$1	201	82	86	11.9999
AUUU	chr2:102629438-102629639(+)$1	201	94	98	11.9999
AUUU	chr7:73317372-73317573(+)$1	201	28	32	11.9999
AUUU	chr14:120724245-120724446(+)$1	201	168	172	11.9999
AUUU	chr1:157899928-157900129(+)$1	201	10	14	11.9999
AUUU	chr11:49985400-49985601(+)$1	201	68	72	11.9999
AUUU	chr6:35461665-35461866(-)$1	201	19	23	11.9999
AUUU	chr17:25957999-25958200(+)$1	201	23	27	11.9999
AUUU	chr18:85049068-85049269(+)$1	201	136	140	11.9999
AUUU	chr2:117952173-117952374(+)$1	201	10	14	11.9999
AUUU	chr1:196641293-196641494(+)$1	201	74	78	11.9999
AUUU	chr8:13019494-13019695(+)$1	201	21	25	11.9999
AUUU	chr18:77700888-77701089(-)$1	201	110	114	11.9999
AUUU	chr14:26531790-26531991(-)$1	201	3	7	11.9999
AUUU	chr9:94419771-94419972(-)$1	201	178	182	11.9999
AUUU	chr1:174308133-174308334(+)$1	201	26	30	11.9999
AUUU	chr15:3935411-3935612(-)$1	201	99	103	11.9999
AUUU	chr13:21536448-21536649(-)$1	201	3	7	11.9999
AUUU	chr1:166368245-166368446(-)$1	201	68	72	11.9999
AUUU	chr2:102622374-102622575(+)$1	201	63	67	11.9999
AUUU	chr13:43232300-43232501(+)$1	201	9	13	11.9999
AUUU	chr14:80166980-80167181(-)$1	201	129	133	11.9999
AUUU	chr11:119400218-119400419(-)$1	201	29	33	11.9999
AUUU	chr6:83315234-83315435(-)$1	201	148	152	11.9999
AUUU	chr1:166367299-166367500(-)$1	201	14	18	11.9999
AUUU	chr1:155067172-155067373(-)$1	201	99	103	11.9999
AUUU	chr11:109528870-109529071(+)$1	201	180	184	11.9999
AUUU	chrX:71104631-71104832(-)$1	201	99	103	11.9999
AUUU	chr2:146050380-146050581(+)$1	201	97	101	11.9999
AUUU	chr1:172123560-172123761(-)$1	201	17	21	11.9999
AUUU	chr15:9126782-9126983(+)$1	201	42	46	11.9999
AUUU	chr8:34527694-34527895(+)$1	201	23	27	11.9999
AUUU	chr17:66687052-66687253(-)$1	201	166	170	11.9999
AUUU	chr1:166368246-166368447(-)$1	201	69	73	11.9999
AUUU	chr1:157692647-157692848(-)$1	201	57	61	11.9999
AUUU	chr1:121555656-121555857(-)$1	201	12	16	11.9999
AUUU	chr10:107937284-107937485(-)$1	201	29	33	11.9999
AUUU	chr19:43570256-43570457(+)$1	201	28	32	11.9999
AUUU	chr2:102624838-102625039(+)$1	201	42	46	11.9999
AUUU	chr17:6138514-6138715(+)$1	201	160	164	11.9999
AUUU	chr1:196641294-196641495(+)$1	201	73	77	11.9999
AUUU	chr16:94690242-94690443(+)$1	201	179	183	11.9999
AUUU	chr1:194330836-194331037(+)$1	201	144	148	11.9999
AUUU	chr2:30119122-30119323(+)$1	201	47	51	11.9999
AUUU	chr10:80861742-80861943(-)$1	201	80	84	11.9999
AUUU	chr18:33598196-33598397(-)$1	201	43	47	11.9999
AUUU	chr6:83315235-83315436(-)$1	201	149	153	11.9999
AUUU	chr1:157692648-157692849(-)$1	201	58	62	11.9999
AUUU	chr3:117022304-117022505(-)$1	201	39	43	11.9999
AUUU	chr12:99672769-99672970(-)$1	201	99	103	11.9999
AUUU	chr18:56691301-56691502(-)$1	201	110	114	11.9999
AUUU	chr2:60590326-60590527(-)$1	201	99	103	11.9999
AUUU	chr2:124491255-124491456(+)$1	201	7	11	11.9999
AUUU	chr7:99595199-99595400(+)$1	201	97	101	11.9999
AUUU	chr3:55791875-55792076(-)$1	201	32	36	11.9999
AUUU	chr8:125153259-125153460(-)$1	201	87	91	11.9999

#otherMatches

#Struct PSSM
mmme	chrX:133613777-133613978(+)$1	201	38	42	11.9999
ooff	chr3:72852070-72852271(-)$1	201	46	50	11.9999
hhh:	chr10:112364597-112364798(-)$1	201	94	98	11.9999
::::	chr5:104542378-104542579(-)$1	201	0	4	11.9999
::::	chr4:81940723-81940924(-)$1	201	0	4	11.9999
::::	chr13:97419982-97420183(-)$1	201	36	40	11.9999
{BBK	chr8:113659249-113659450(+)$1	201	49	53	11.9999
::::	chr1:78702938-78703139(+)$1	201	181	185	11.9999
::::	chr15:9126781-9126982(+)$1	201	0	4	11.9999
::::	chr4:148550625-148550826(-)$1	201	175	179	11.9999
qqqq	chr18:77700887-77701088(-)$1	201	109	113	11.9999
::::	chr14:65430470-65430671(-)$1	201	182	186	11.9999
vvvb	chrX:133371564-133371765(+)$1	201	160	164	11.9999
hhh:	chr10:112364596-112364797(-)$1	201	93	97	11.9999
####	chr2:33263737-33263938(-)$1	201	30	34	11.9999
$$$e	chr10:66718543-66718744(+)$1	201	79	83	11.9999
$$$e	chr10:66718544-66718745(+)$1	201	78	82	11.9999
:EEE	chr18:61145078-61145279(+)$1	201	97	101	11.9999
HHHH	chrX:39029573-39029774(+)$1	201	16	20	11.9999
[eee	chr6:113697619-113697820(-)$1	201	68	72	11.9999
:::d	chr2:30885422-30885623(-)$1	201	169	173	11.9999
ffff	chr12:100027590-100027791(-)$1	201	63	67	11.9999
2eee	chr11:119400102-119400303(-)$1	201	78	82	11.9999
:::e	chr17:66687050-66687251(-)$1	201	164	168	11.9999
ffff	chr5:15876961-15877162(+)$1	201	82	86	11.9999
d[dd	chr2:102629438-102629639(+)$1	201	94	98	11.9999
pppp	chr7:73317372-73317573(+)$1	201	28	32	11.9999
iiii	chr14:120724245-120724446(+)$1	201	168	172	11.9999
++++	chr1:157899928-157900129(+)$1	201	10	14	11.9999
::::	chr11:49985400-49985601(+)$1	201	68	72	11.9999
::::	chr6:35461665-35461866(-)$1	201	19	23	11.9999
dddd	chr17:25957999-25958200(+)$1	201	23	27	11.9999
:eee	chr18:85049068-85049269(+)$1	201	136	140	11.9999
oooo	chr2:117952173-117952374(+)$1	201	10	14	11.9999
qqqc	chr1:196641293-196641494(+)$1	201	74	78	11.9999
[ccc	chr8:13019494-13019695(+)$1	201	21	25	11.9999
qqqq	chr18:77700888-77701089(-)$1	201	110	114	11.9999
:::H	chr14:26531790-26531991(-)$1	201	3	7	11.9999
::::	chr9:94419771-94419972(-)$1	201	178	182	11.9999
pppp	chr1:174308133-174308334(+)$1	201	26	30	11.9999
::::	chr15:3935411-3935612(-)$1	201	99	103	11.9999
FFFF	chr13:21536448-21536649(-)$1	201	3	7	11.9999
((((	chr1:166368245-166368446(-)$1	201	68	72	11.9999
:::c	chr2:102622374-102622575(+)$1	201	63	67	11.9999
GGGG	chr13:43232300-43232501(+)$1	201	9	13	11.9999
nngg	chr14:80166980-80167181(-)$1	201	129	133	11.9999
::::	chr11:119400218-119400419(-)$1	201	29	33	11.9999
g:::	chr6:83315234-83315435(-)$1	201	148	152	11.9999
::::	chr1:166367299-166367500(-)$1	201	14	18	11.9999
peee	chr1:155067172-155067373(-)$1	201	99	103	11.9999
7777	chr11:109528870-109529071(+)$1	201	180	184	11.9999
cc""	chrX:71104631-71104832(-)$1	201	99	103	11.9999
mmmc	chr2:146050380-146050581(+)$1	201	97	101	11.9999
uuuu	chr1:172123560-172123761(-)$1	201	17	21	11.9999
[bbm	chr15:9126782-9126983(+)$1	201	42	46	11.9999
QQQE	chr8:34527694-34527895(+)$1	201	23	27	11.9999
:::e	chr17:66687052-66687253(-)$1	201	166	170	11.9999
((((	chr1:166368246-166368447(-)$1	201	69	73	11.9999
mggg	chr1:157692647-157692848(-)$1	201	57	61	11.9999
EEEE	chr1:121555656-121555857(-)$1	201	12	16	11.9999
:ggg	chr10:107937284-107937485(-)$1	201	29	33	11.9999
::::	chr19:43570256-43570457(+)$1	201	28	32	11.9999
====	chr2:102624838-102625039(+)$1	201	42	46	11.9999
c555	chr17:6138514-6138715(+)$1	201	160	164	11.9999
qqqc	chr1:196641294-196641495(+)$1	201	73	77	11.9999
mmmf	chr16:94690242-94690443(+)$1	201	179	183	11.9999
ddmm	chr1:194330836-194331037(+)$1	201	144	148	11.9999
B{GG	chr2:30119122-30119323(+)$1	201	47	51	11.9999
::::	chr10:80861742-80861943(-)$1	201	80	84	11.9999
dd[c	chr18:33598196-33598397(-)$1	201	43	47	11.9999
g:::	chr6:83315235-83315436(-)$1	201	149	153	11.9999
mggg	chr1:157692648-157692849(-)$1	201	58	62	11.9999
''''	chr3:117022304-117022505(-)$1	201	39	43	11.9999
eeee	chr12:99672769-99672970(-)$1	201	99	103	11.9999
gggg	chr18:56691301-56691502(-)$1	201	110	114	11.9999
))cc	chr2:60590326-60590527(-)$1	201	99	103	11.9999
[eee	chr2:124491255-124491456(+)$1	201	7	11	11.9999
((((	chr7:99595199-99595400(+)$1	201	97	101	11.9999
mmdd	chr3:55791875-55792076(-)$1	201	32	36	11.9999
pppp	chr8:125153259-125153460(-)$1	201	87	91	11.9999

#DB
...)	chrX:133613777-133613978(+)$1	1	38	42	11.9999
..))	chr3:72852070-72852271(-)$1	1	46	50	11.9999
))).	chr10:112364597-112364798(-)$1	1	94	98	11.9999
....	chr5:104542378-104542579(-)$1	1	0	4	11.9999
....	chr4:81940723-81940924(-)$1	1	0	4	11.9999
....	chr13:97419982-97420183(-)$1	1	36	40	11.9999
.((.	chr8:113659249-113659450(+)$1	1	49	53	11.9999
....	chr1:78702938-78703139(+)$1	1	181	185	11.9999
....	chr15:9126781-9126982(+)$1	1	0	4	11.9999
....	chr4:148550625-148550826(-)$1	1	175	179	11.9999
....	chr18:77700887-77701088(-)$1	1	109	113	11.9999
....	chr14:65430470-65430671(-)$1	1	182	186	11.9999
...)	chrX:133371564-133371765(+)$1	1	160	164	11.9999
))).	chr10:112364596-112364797(-)$1	1	93	97	11.9999
....	chr2:33263737-33263938(-)$1	1	30	34	11.9999
...(	chr10:66718543-66718744(+)$1	1	79	83	11.9999
...(	chr10:66718544-66718745(+)$1	1	78	82	11.9999
.(((	chr18:61145078-61145279(+)$1	1	97	101	11.9999
((((	chrX:39029573-39029774(+)$1	1	16	20	11.9999
.(((	chr6:113697619-113697820(-)$1	1	68	72	11.9999
...(	chr2:30885422-30885623(-)$1	1	169	173	11.9999
((((	chr12:100027590-100027791(-)$1	1	63	67	11.9999
.)))	chr11:119400102-119400303(-)$1	1	78	82	11.9999
...(	chr17:66687050-66687251(-)$1	1	164	168	11.9999
((((	chr5:15876961-15877162(+)$1	1	82	86	11.9999
(.((	chr2:102629438-102629639(+)$1	1	94	98	11.9999
....	chr7:73317372-73317573(+)$1	1	28	32	11.9999
))))	chr14:120724245-120724446(+)$1	1	168	172	11.9999
....	chr1:157899928-157900129(+)$1	1	10	14	11.9999
....	chr11:49985400-49985601(+)$1	1	68	72	11.9999
....	chr6:35461665-35461866(-)$1	1	19	23	11.9999
((((	chr17:25957999-25958200(+)$1	1	23	27	11.9999
.(((	chr18:85049068-85049269(+)$1	1	136	140	11.9999
....	chr2:117952173-117952374(+)$1	1	10	14	11.9999
...)	chr1:196641293-196641494(+)$1	1	74	78	11.9999
.(((	chr8:13019494-13019695(+)$1	1	21	25	11.9999
....	chr18:77700888-77701089(-)$1	1	110	114	11.9999
...(	chr14:26531790-26531991(-)$1	1	3	7	11.9999
....	chr9:94419771-94419972(-)$1	1	178	182	11.9999
....	chr1:174308133-174308334(+)$1	1	26	30	11.9999
....	chr15:3935411-3935612(-)$1	1	99	103	11.9999
((((	chr13:21536448-21536649(-)$1	1	3	7	11.9999
....	chr1:166368245-166368446(-)$1	1	68	72	11.9999
...(	chr2:102622374-102622575(+)$1	1	63	67	11.9999
((((	chr13:43232300-43232501(+)$1	1	9	13	11.9999
..))	chr14:80166980-80167181(-)$1	1	129	133	11.9999
....	chr11:119400218-119400419(-)$1	1	29	33	11.9999
)...	chr6:83315234-83315435(-)$1	1	148	152	11.9999
....	chr1:166367299-166367500(-)$1	1	14	18	11.9999
.)))	chr1:155067172-155067373(-)$1	1	99	103	11.9999
....	chr11:109528870-109529071(+)$1	1	180	184	11.9999
((..	chrX:71104631-71104832(-)$1	1	99	103	11.9999
...)	chr2:146050380-146050581(+)$1	1	97	101	11.9999
....	chr1:172123560-172123761(-)$1	1	17	21	11.9999
.((.	chr15:9126782-9126983(+)$1	1	42	46	11.9999
...(	chr8:34527694-34527895(+)$1	1	23	27	11.9999
...(	chr17:66687052-66687253(-)$1	1	166	170	11.9999
....	chr1:166368246-166368447(-)$1	1	69	73	11.9999
.)))	chr1:157692647-157692848(-)$1	1	57	61	11.9999
((((	chr1:121555656-121555857(-)$1	1	12	16	11.9999
.(((	chr10:107937284-107937485(-)$1	1	29	33	11.9999
....	chr19:43570256-43570457(+)$1	1	28	32	11.9999
((((	chr2:102624838-102625039(+)$1	1	42	46	11.9999
)...	chr17:6138514-6138715(+)$1	1	160	164	11.9999
...)	chr1:196641294-196641495(+)$1	1	73	77	11.9999
...)	chr16:94690242-94690443(+)$1	1	179	183	11.9999
((..	chr1:194330836-194331037(+)$1	1	144	148	11.9999
(.((	chr2:30119122-30119323(+)$1	1	47	51	11.9999
....	chr10:80861742-80861943(-)$1	1	80	84	11.9999
((.(	chr18:33598196-33598397(-)$1	1	43	47	11.9999
)...	chr6:83315235-83315436(-)$1	1	149	153	11.9999
.)))	chr1:157692648-157692849(-)$1	1	58	62	11.9999
....	chr3:117022304-117022505(-)$1	1	39	43	11.9999
))))	chr12:99672769-99672970(-)$1	1	99	103	11.9999
((((	chr18:56691301-56691502(-)$1	1	110	114	11.9999
..((	chr2:60590326-60590527(-)$1	1	99	103	11.9999
.(((	chr2:124491255-124491456(+)$1	1	7	11	11.9999
....	chr7:99595199-99595400(+)$1	1	97	101	11.9999
..))	chr3:55791875-55792076(-)$1	1	32	36	11.9999
....	chr8:125153259-125153460(-)$1	1	87	91	11.9999

#PSSM
A : 0.99	
U : 0.99	
U : 0.99	
U : 0.99	

#score	959.9999999999995
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m2_run1.nuc.txt

#NT
UCCU	chr7:146027964-146028187(-)$1	223	8	12	11.9999
UCCU	chr19:36992841-36993062(-)$1	221	182	186	11.9999
UCCU	chr11:60367692-60367909(+)$1	217	3	7	11.9999
UCCU	chr3:94292349-94292592(+)$1	243	159	163	11.9999
UCCU	chr10:80172539-80172780(-)$1	241	7	11	11.9999
UCCU	chr19:6066437-6066662(-)$1	225	53	57	11.9999
UCCU	chr7:126127572-126127793(-)$1	221	14	18	11.9999
UCCU	chr12:112107151-112107374(+)$1	223	54	58	11.9999
UCCU	chr9:57434815-57435059(+)$1	244	13	17	11.9999
UCCU	chr8:23780056-23780284(-)$1	228	105	109	11.9999
UCCU	chrX:132806085-132806334(+)$1	249	57	61	11.9999
UCCU	chrX:71555333-71555555(+)$1	222	56	60	11.9999
UCCU	chr7:50692565-50692787(+)$1	222	206	210	11.9999
UCCU	chr19:46577159-46577380(+)$1	221	171	175	11.9999
UCCU	chr9:83676714-83676949(-)$1	235	49	53	11.9999
UCCU	chr18:14583411-14583639(+)$1	228	25	29	11.9999
UCCU	chr5:136758625-136758846(-)$1	221	191	195	11.9999
UCCU	chr16:91628280-91628520(-)$1	240	219	223	11.9999
UCCU	chr14:65425006-65425228(-)$1	222	65	69	11.9999
UCCU	chr1:66485552-66485801(+)$1	249	36	40	11.9999
UCCU	chr8:108703143-108703360(+)$1	217	29	33	11.9999
UCCU	chr13:69877482-69877710(-)$1	228	75	79	11.9999
UCCU	chrX:71485492-71485712(-)$1	220	30	34	11.9999
UCCU	chr16:90944505-90944740(-)$1	235	123	127	11.9999
UCCU	chr2:60165776-60165999(-)$1	223	6	10	11.9999
UCCU	chr12:84878812-84879033(-)$1	221	80	84	11.9999
UCCU	chr4:120657734-120657955(-)$1	221	2	6	11.9999
UCCU	chr4:114696272-114696497(+)$1	225	134	138	11.9999
UCCU	chr2:27388759-27388983(+)$1	224	197	201	11.9999
UCCU	chr12:110829891-110830108(+)$1	217	81	85	11.9999
UCCU	chr11:75078159-75078381(+)$1	222	55	59	11.9999
UCCU	chrX:148362774-148363001(+)$1	227	33	37	11.9999
UCCU	chr10:116798113-116798367(-)$1	254	9	13	11.9999
UCCU	chrX:71106905-71107129(-)$1	224	74	78	11.9999
UCCU	chr11:115662078-115662300(-)$1	222	116	120	11.9999
uccu	chrX:10062217-10062471(+)$1	254	5	9	11.9999
UCCU	chr6:106694137-106694358(-)$1	221	170	174	11.9999
UCCU	chr10:93107347-93107568(+)$1	221	104	108	11.9999
UCCU	chr15:80710246-80710466(+)$1	220	39	43	11.9999
UCCU	chr19:7273885-7274104(-)$1	219	14	18	11.9999
UCCU	chr19:44413352-44413579(+)$1	227	26	30	11.9999
UCCU	chr10:127790046-127790285(+)$1	239	19	23	11.9999
UCCU	chr3:94970819-94971046(+)$1	227	122	126	11.9999
UCCU	chr5:128131053-128131268(-)$1	215	116	120	11.9999
UCCU	chr9:39859267-39859490(+)$1	223	16	20	11.9999
UCCU	chr8:11443542-11443766(+)$1	224	17	21	11.9999
UCCU	chr18:77098348-77098572(+)$1	224	192	196	11.9999
UCCU	chr18:75389612-75389838(+)$1	226	16	20	11.9999
UCCU	chr8:111380601-111380820(+)$1	219	4	8	11.9999
UCCU	chr10:126723340-126723560(-)$1	220	5	9	11.9999
UCCU	chr10:127042778-127043001(-)$1	223	6	10	11.9999
UCCU	chr3:144368356-144368579(+)$1	223	68	72	11.9999
UCCU	chr5:116101109-116101327(-)$1	218	39	43	11.9999
UCCU	chr17:24757977-24758206(-)$1	229	87	91	11.9999
UCCU	chr4:8679355-8679583(+)$1	228	114	118	11.9999
UCCU	chr9:21752219-21752453(+)$1	234	1	5	11.9999
UCCU	chr11:57343375-57343593(-)$1	218	157	161	11.9999
UCCU	chr10:95012351-95012578(-)$1	227	181	185	11.9999
UCCU	chr9:110290848-110291081(-)$1	233	84	88	11.9999
UCCU	chr6:86932436-86932655(+)$1	219	29	33	11.9999
UCCU	chr7:116696451-116696694(-)$1	243	73	77	11.9999
UCCU	chr7:19878460-19878684(+)$1	224	42	46	11.9999
UCCU	chr7:134010390-134010612(+)$1	222	64	68	11.9999
UCCU	chr14:55685718-55685954(-)$1	236	168	172	11.9999
UCCU	chr7:26518207-26518438(-)$1	231	39	43	11.9999
UCCU	chr7:147185070-147185311(-)$1	241	6	10	11.9999
UCCU	chr5:143640266-143640498(-)$1	232	152	156	11.9999
UCCU	chr8:125008651-125008877(-)$1	226	3	7	11.9999
UCCU	chrX:12264104-12264341(-)$1	237	156	160	11.9999
UCCU	chr11:105263226-105263445(-)$1	219	33	37	11.9999
UCCU	chr5:121823045-121823269(-)$1	224	90	94	11.9999
UCCU	chr10:57955535-57955777(+)$1	242	2	6	11.9999
UCCU	chr7:108812319-108812542(+)$1	223	54	58	11.9999
UCCU	chr14:78912251-78912474(-)$1	223	100	104	11.9999
UCCU	chr10:85172307-85172528(-)$1	221	123	127	11.9999
UCCU	chr17:15944311-15944535(-)$1	224	28	32	11.9999
UCCU	chr17:35985855-35986108(+)$1	253	240	244	11.9999
UCCU	chr8:35911715-35911944(-)$1	229	188	192	11.9999

#otherMatches

#Struct PSSM
bbnn	chr13:65284167-65284387(-)$1	220	56	60	11.9999
EOOO	chr7:146027964-146028187(-)$1	223	8	12	11.9999
DDDD	chr19:36992841-36993062(-)$1	221	182	186	11.9999
DDBB	chr11:60367692-60367909(+)$1	217	3	7	11.9999
i:::	chr3:94292349-94292592(+)$1	243	159	163	11.9999
[bbq	chr10:80172539-80172780(-)$1	241	7	11	11.9999
hhhh	chr19:6066437-6066662(-)$1	225	53	57	11.9999
hhmm	chr7:126127572-126127793(-)$1	221	14	18	11.9999
iiii	chr12:112107151-112107374(+)$1	223	54	58	11.9999
dddm	chr9:57434815-57435059(+)$1	244	13	17	11.9999
!!bb	chr8:23780056-23780284(-)$1	228	105	109	11.9999
cc[c	chrX:132806085-132806334(+)$1	249	57	61	11.9999
d[bb	chrX:71555333-71555555(+)$1	222	56	60	11.9999
b22c	chr7:50692565-50692787(+)$1	222	206	210	11.9999
eeem	chr19:46577159-46577380(+)$1	221	171	175	11.9999
qqqe	chr9:83676714-83676949(-)$1	235	49	53	11.9999
:::h	chr18:14583411-14583639(+)$1	228	25	29	11.9999
eee2	chr5:136758625-136758846(-)$1	221	191	195	11.9999
3ccc	chr16:91628280-91628520(-)$1	240	219	223	11.9999
gggg	chr14:65425006-65425228(-)$1	222	65	69	11.9999
eeee	chr1:66485552-66485801(+)$1	249	36	40	11.9999
eeee	chr8:108703143-108703360(+)$1	217	29	33	11.9999
gggg	chr13:69877482-69877710(-)$1	228	75	79	11.9999
==!!	chrX:71485492-71485712(-)$1	220	30	34	11.9999
::::	chr16:90944505-90944740(-)$1	235	123	127	11.9999
::bb	chr2:60165776-60165999(-)$1	223	6	10	11.9999
d:::	chr12:84878812-84879033(-)$1	221	80	84	11.9999
gggg	chr4:120657734-120657955(-)$1	221	2	6	11.9999
GGGG	chr4:114696272-114696497(+)$1	225	134	138	11.9999
oooo	chr2:27388759-27388983(+)$1	224	197	201	11.9999
oeee	chr12:110829891-110830108(+)$1	217	81	85	11.9999
oooo	chr11:75078159-75078381(+)$1	222	55	59	11.9999
vvvv	chrX:148362774-148363001(+)$1	227	33	37	11.9999
ssss	chr10:116798113-116798367(-)$1	254	9	13	11.9999
MMCC	chrX:71106905-71107129(-)$1	224	74	78	11.9999
!!cc	chr11:115662078-115662300(-)$1	222	116	120	11.9999
FUUU	chrX:10062217-10062471(+)$1	254	5	9	11.9999
ff!!	chr6:106694137-106694358(-)$1	221	170	174	11.9999
"bb[	chr10:93107347-93107568(+)$1	221	104	108	11.9999
CCCb	chr15:80710246-80710466(+)$1	220	39	43	11.9999
[hhh	chr19:7273885-7274104(-)$1	219	14	18	11.9999
eeee	chr19:44413352-44413579(+)$1	227	26	30	11.9999
GGGG	chr10:127790046-127790285(+)$1	239	19	23	11.9999
oooc	chr3:94970819-94971046(+)$1	227	122	126	11.9999
oooo	chr5:128131053-128131268(-)$1	215	116	120	11.9999
KKCC	chr9:39859267-39859490(+)$1	223	16	20	11.9999
%%%%	chr8:11443542-11443766(+)$1	224	17	21	11.9999
::::	chr18:77098348-77098572(+)$1	224	192	196	11.9999
HH{C	chr18:75389612-75389838(+)$1	226	16	20	11.9999
{CCC	chr8:111380601-111380820(+)$1	219	4	8	11.9999
::::	chr10:126723340-126723560(-)$1	220	5	9	11.9999
::::	chr10:127042778-127043001(-)$1	223	6	10	11.9999
::::	chr3:144368356-144368579(+)$1	223	68	72	11.9999
[ddd	chr5:116101109-116101327(-)$1	218	39	43	11.9999
eeee	chr17:24757977-24758206(-)$1	229	87	91	11.9999
::CC	chr4:8679355-8679583(+)$1	228	114	118	11.9999
ccco	chr9:21752219-21752453(+)$1	234	1	5	11.9999
::::	chr11:57343375-57343593(-)$1	218	157	161	11.9999
333e	chr10:95012351-95012578(-)$1	227	181	185	11.9999
bbdd	chr9:110290848-110291081(-)$1	233	84	88	11.9999
::II	chr6:86932436-86932655(+)$1	219	29	33	11.9999
ffff	chr7:116696451-116696694(-)$1	243	73	77	11.9999
ffff	chr7:19878460-19878684(+)$1	224	42	46	11.9999
KKEE	chr7:134010390-134010612(+)$1	222	64	68	11.9999
b[dd	chr14:55685718-55685954(-)$1	236	168	172	11.9999
ENNN	chr7:26518207-26518438(-)$1	231	39	43	11.9999
::::	chr7:147185070-147185311(-)$1	241	6	10	11.9999
cccl	chr5:143640266-143640498(-)$1	232	152	156	11.9999
::::	chr8:125008651-125008877(-)$1	226	3	7	11.9999
[a[c	chrX:12264104-12264341(-)$1	237	156	160	11.9999
::::	chr11:105263226-105263445(-)$1	219	33	37	11.9999
iiii	chr5:121823045-121823269(-)$1	224	90	94	11.9999
dddt	chr10:57955535-57955777(+)$1	242	2	6	11.9999
mmmm	chr7:108812319-108812542(+)$1	223	54	58	11.9999
pppp	chr14:78912251-78912474(-)$1	223	100	104	11.9999
neee	chr10:85172307-85172528(-)$1	221	123	127	11.9999
dddd	chr17:15944311-15944535(-)$1	224	28	32	11.9999
::::	chr17:35985855-35986108(+)$1	253	240	244	11.9999
::::	chr8:35911715-35911944(-)$1	229	188	192	11.9999

#DB
((..	chr13:65284167-65284387(-)$1	1	56	60	11.9999
(...	chr7:146027964-146028187(-)$1	1	8	12	11.9999
))))	chr19:36992841-36993062(-)$1	1	182	186	11.9999
((((	chr11:60367692-60367909(+)$1	1	3	7	11.9999
)...	chr3:94292349-94292592(+)$1	1	159	163	11.9999
.((.	chr10:80172539-80172780(-)$1	1	7	11	11.9999
))))	chr19:6066437-6066662(-)$1	1	53	57	11.9999
((..	chr7:126127572-126127793(-)$1	1	14	18	11.9999
))))	chr12:112107151-112107374(+)$1	1	54	58	11.9999
(((.	chr9:57434815-57435059(+)$1	1	13	17	11.9999
..((	chr8:23780056-23780284(-)$1	1	105	109	11.9999
((.(	chrX:132806085-132806334(+)$1	1	57	61	11.9999
(.((	chrX:71555333-71555555(+)$1	1	56	60	11.9999
)..)	chr7:50692565-50692787(+)$1	1	206	210	11.9999
(((.	chr19:46577159-46577380(+)$1	1	171	175	11.9999
...)	chr9:83676714-83676949(-)$1	1	49	53	11.9999
...(	chr18:14583411-14583639(+)$1	1	25	29	11.9999
))).	chr5:136758625-136758846(-)$1	1	191	195	11.9999
.)))	chr16:91628280-91628520(-)$1	1	219	223	11.9999
((((	chr14:65425006-65425228(-)$1	1	65	69	11.9999
((((	chr1:66485552-66485801(+)$1	1	36	40	11.9999
))))	chr8:108703143-108703360(+)$1	1	29	33	11.9999
))))	chr13:69877482-69877710(-)$1	1	75	79	11.9999
((..	chrX:71485492-71485712(-)$1	1	30	34	11.9999
....	chr16:90944505-90944740(-)$1	1	123	127	11.9999
..((	chr2:60165776-60165999(-)$1	1	6	10	11.9999
)...	chr12:84878812-84879033(-)$1	1	80	84	11.9999
((((	chr4:120657734-120657955(-)$1	1	2	6	11.9999
))))	chr4:114696272-114696497(+)$1	1	134	138	11.9999
....	chr2:27388759-27388983(+)$1	1	197	201	11.9999
.)))	chr12:110829891-110830108(+)$1	1	81	85	11.9999
....	chr11:75078159-75078381(+)$1	1	55	59	11.9999
....	chrX:148362774-148363001(+)$1	1	33	37	11.9999
....	chr10:116798113-116798367(-)$1	1	9	13	11.9999
..((	chrX:71106905-71107129(-)$1	1	74	78	11.9999
..((	chr11:115662078-115662300(-)$1	1	116	120	11.9999
(...	chrX:10062217-10062471(+)$1	1	5	9	11.9999
((..	chr6:106694137-106694358(-)$1	1	170	174	11.9999
.((.	chr10:93107347-93107568(+)$1	1	104	108	11.9999
((((	chr15:80710246-80710466(+)$1	1	39	43	11.9999
.(((	chr19:7273885-7274104(-)$1	1	14	18	11.9999
))))	chr19:44413352-44413579(+)$1	1	26	30	11.9999
((((	chr10:127790046-127790285(+)$1	1	19	23	11.9999
...)	chr3:94970819-94971046(+)$1	1	122	126	11.9999
....	chr5:128131053-128131268(-)$1	1	116	120	11.9999
..((	chr9:39859267-39859490(+)$1	1	16	20	11.9999
....	chr8:11443542-11443766(+)$1	1	17	21	11.9999
....	chr18:77098348-77098572(+)$1	1	192	196	11.9999
((.(	chr18:75389612-75389838(+)$1	1	16	20	11.9999
.(((	chr8:111380601-111380820(+)$1	1	4	8	11.9999
....	chr10:126723340-126723560(-)$1	1	5	9	11.9999
....	chr10:127042778-127043001(-)$1	1	6	10	11.9999
....	chr3:144368356-144368579(+)$1	1	68	72	11.9999
.(((	chr5:116101109-116101327(-)$1	1	39	43	11.9999
((((	chr17:24757977-24758206(-)$1	1	87	91	11.9999
..))	chr4:8679355-8679583(+)$1	1	114	118	11.9999
(((.	chr9:21752219-21752453(+)$1	1	1	5	11.9999
....	chr11:57343375-57343593(-)$1	1	157	161	11.9999
...)	chr10:95012351-95012578(-)$1	1	181	185	11.9999
))))	chr9:110290848-110291081(-)$1	1	84	88	11.9999
..((	chr6:86932436-86932655(+)$1	1	29	33	11.9999
((((	chr7:116696451-116696694(-)$1	1	73	77	11.9999
))))	chr7:19878460-19878684(+)$1	1	42	46	11.9999
..((	chr7:134010390-134010612(+)$1	1	64	68	11.9999
(.((	chr14:55685718-55685954(-)$1	1	168	172	11.9999
(...	chr7:26518207-26518438(-)$1	1	39	43	11.9999
....	chr7:147185070-147185311(-)$1	1	6	10	11.9999
(((.	chr5:143640266-143640498(-)$1	1	152	156	11.9999
....	chr8:125008651-125008877(-)$1	1	3	7	11.9999
.(.(	chrX:12264104-12264341(-)$1	1	156	160	11.9999
....	chr11:105263226-105263445(-)$1	1	33	37	11.9999
((((	chr5:121823045-121823269(-)$1	1	90	94	11.9999
(((.	chr10:57955535-57955777(+)$1	1	2	6	11.9999
....	chr7:108812319-108812542(+)$1	1	54	58	11.9999
....	chr14:78912251-78912474(-)$1	1	100	104	11.9999
.)))	chr10:85172307-85172528(-)$1	1	123	127	11.9999
((((	chr17:15944311-15944535(-)$1	1	28	32	11.9999
....	chr17:35985855-35986108(+)$1	1	240	244	11.9999
....	chr8:35911715-35911944(-)$1	1	188	192	11.9999

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

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_UTR_m2_run1.nuc.txt

#NT
AUUUCUAUUU	chr2:37230208-37230409(-)$1	201	64	74	15.8823
AUUUUAAUUU	chr10:56110034-56110235(+)$1	201	169	179	17.0588
guuuuuguuu	chr6:146598946-146599147(+)$1	201	182	192	18.2352
GUUUUUUUUU	chr11:74489945-74490146(-)$1	201	17	27	18.6274
GUUUUUCUGU	chr12:75396233-75396434(+)$1	201	61	71	13.8235
GGUUUAAUUU	chr2:134420597-134420798(-)$1	201	132	142	13.8235
AUUUUAAUUU	chr11:75519292-75519493(+)$1	201	75	85	17.0588
UUUUUUAUUA	chr14:35560023-35560224(+)$1	201	35	45	15.0980
GUAUUGAUUU	chr10:29065187-29065388(+)$1	201	63	73	14.3137
GUUUUCAUUC	chr10:85810228-85810429(+)$1	201	96	106	13.5294
CUUUUUAUAU	chr3:10314484-10314685(-)$1	201	73	83	14.9019
AUUUUUAUUU	chr13:94130050-94130251(+)$1	201	34	44	19.9019
guuuucauuu	chr11:3799832-3800033(+)$1	201	91	101	17.8431
AUGUUUAUUU	chr1:66742443-66742644(+)$1	201	108	118	16.2745
CUAUUUAUUU	chr14:78892413-78892614(-)$1	201	68	78	15.6862
UUUUUUAUAU	chr7:117980639-117980840(-)$1	201	12	22	14.9019
GUCUUUUUUU	chr7:25320608-25320809(+)$1	201	187	197	14.7058
GUUUUUAUUA	chr4:86630687-86630888(-)$1	201	1	11	17.0588
UUUUUUCUUU	chr14:67421676-67421877(-)$1	201	25	35	16.3725
GUUUGUAUUU	chr1:13129358-13129559(-)$1	201	167	177	17.2549
AUUUUAAUUU	chr5:68010708-68010909(-)$1	201	27	37	17.0588
CUUUUUUUUU	chr15:54432543-54432744(+)$1	201	34	44	16.6666
Cuuuuuuuuu	chr12:25779246-25779447(-)$1	201	17	27	16.6666
GGUUUUAUUU	chr9:51753384-51753585(-)$1	201	36	46	16.6666
AUUUUUAUUU	chr2:131878287-131878488(-)$1	201	17	27	19.9019
guauuuauug	chr5:125367560-125367761(+)$1	201	117	127	13.4313
GUUUUAAUUA	chr9:75413407-75413608(-)$1	201	56	66	14.2156
GUUUUUGUUU	chr6:128359788-128359989(-)$1	201	180	190	18.2352
GUUUGUGUUU	chr6:57456850-57457051(-)$1	201	1	11	14.3137
GUGUUGAUUU	chr2:39051738-39051939(-)$1	201	16	26	14.2156
uuuuuucuuu	chr15:98634277-98634478(-)$1	201	20	30	16.3725
GUUUUUUUUU	chr2:92794469-92794670(+)$1	201	158	168	18.6274
GUUUUAAUUG	chrX:61522261-61522462(-)$1	201	29	39	14.1176
GUUUUAAUUU	chr6:108772823-108773024(+)$1	201	157	167	18.3333
GUUUAAAUUU	chr11:17100238-17100439(+)$1	201	46	56	14.4117
AUUUUUCUUU	chr1:68080482-68080683(-)$1	201	168	178	17.0588
UUUUUUAAUU	chr6:67234309-67234510(+)$1	201	17	27	14.6078
guuuuuauuu	chr16:45962929-45963130(-)$1	201	158	168	21.1764
UUUUUUCUUU	chr7:129771256-129771457(+)$1	201	135	145	16.3725
CUUUUUAUAU	chr11:68628733-68628934(+)$1	201	25	35	14.9019
AUUUUUUUUU	chr4:41464719-41464920(-)$1	201	100	110	17.3529
GUAUCUAUUU	chr4:56975652-56975853(-)$1	201	37	47	13.6274
guguauauuu	chr1:23375396-23375597(-)$1	201	45	55	13.6274
AUUUUUAGUU	chr3:106852712-106852913(+)$1	201	4	14	15.2941
GUGUUUGUUU	chr9:30957340-30957541(-)$1	201	88	98	14.6078
AUAUUUUUUU	chr11:54723340-54723541(+)$1	201	91	101	13.8235
GAUUUUUUUU	chr10:36855688-36855889(-)$1	201	86	96	14.0196
GUUUUGACuu	chr2:102623321-102623522(+)$1	201	173	183	13.2352
AUUUGUAUUU	chr13:21605812-21606013(-)$1	201	35	45	15.9803
AUUUAUAUUU	chr2:73450367-73450568(-)$1	201	113	123	15.9803

#otherMatches

#Struct PSSM
B?????EEEE	chr2:132355960-132356161(-)$1	201	188	198	15.8823
dddd]dddd2	chr2:37230208-37230409(-)$1	201	64	74	15.8823
ddmmmmdddd	chr10:56110034-56110235(+)$1	201	169	179	17.0588
FFFFFF}FFF	chr6:146598946-146599147(+)$1	201	182	192	18.2352
dsssssssss	chr11:74489945-74490146(-)$1	201	17	27	18.6274
cccsssssss	chr12:75396233-75396434(+)$1	201	61	71	13.8235
eeeee"""dd	chr2:134420597-134420798(-)$1	201	132	142	13.8235
777777ffff	chr11:75519292-75519493(+)$1	201	75	85	17.0588
::::::::::	chr14:35560023-35560224(+)$1	201	35	45	15.0980
ffffff[hhh	chr10:29065187-29065388(+)$1	201	63	73	14.3137
[eeeee[ccc	chr10:85810228-85810429(+)$1	201	96	106	13.5294
2ffffff:::	chr3:10314484-10314685(-)$1	201	73	83	14.9019
ggggggg:::	chr13:94130050-94130251(+)$1	201	34	44	19.9019
ccc:::::::	chr11:3799832-3800033(+)$1	201	91	101	17.8431
eeee:::::H	chr1:66742443-66742644(+)$1	201	108	118	16.2745
:::::::::E	chr14:78892413-78892614(-)$1	201	68	78	15.6862
DD::::dddd	chr7:117980639-117980840(-)$1	201	12	22	14.9019
EEcccnnnnn	chr7:25320608-25320809(+)$1	201	187	197	14.7058
HHHHHHH:::	chr4:86630687-86630888(-)$1	201	1	11	17.0588
nggggggg::	chr14:67421676-67421877(-)$1	201	25	35	16.3725
ggg:GGGGGG	chr1:13129358-13129559(-)$1	201	167	177	17.2549
EEEEMMMMEE	chr5:68010708-68010909(-)$1	201	27	37	17.0588
DD{DDDD:::	chr15:54432543-54432744(+)$1	201	34	44	16.6666
CEEEEE{JJJ	chr12:25779246-25779447(-)$1	201	17	27	16.6666
D:::::::::	chr9:51753384-51753585(-)$1	201	36	46	16.6666
NNNEEEEELL	chr2:131878287-131878488(-)$1	201	17	27	19.9019
eeee"""bb!	chr5:125367560-125367761(+)$1	201	117	127	13.4313
ffff333eee	chr9:75413407-75413608(-)$1	201	56	66	14.2156
DDDYYBBZZZ	chr6:128359788-128359989(-)$1	201	180	190	18.2352
EEEEE{EEEE	chr6:57456850-57457051(-)$1	201	1	11	14.3137
ffffff:FFF	chr2:39051738-39051939(-)$1	201	16	26	14.2156
::::::::::	chr15:98634277-98634478(-)$1	201	20	30	16.3725
BB@@@@@@@@	chr2:92794469-92794670(+)$1	201	158	168	18.6274
eeeffffffv	chrX:61522261-61522462(-)$1	201	29	39	14.1176
ddddqqqqqq	chr6:108772823-108773024(+)$1	201	157	167	18.3333
JJJJKKHHHH	chr11:17100238-17100439(+)$1	201	46	56	14.4117
::::::::::	chr1:68080482-68080683(-)$1	201	168	178	17.0588
:::::eeeee	chr6:67234309-67234510(+)$1	201	17	27	14.6078
ggggg:::::	chr16:45962929-45963130(-)$1	201	158	168	21.1764
::::::::::	chr7:129771256-129771457(+)$1	201	135	145	16.3725
::::::::::	chr11:68628733-68628934(+)$1	201	25	35	14.9019
>>>>>>>>>>	chr4:41464719-41464920(-)$1	201	100	110	17.3529
c####ddddm	chr4:56975652-56975853(-)$1	201	37	47	13.6274
f[cccmmmmc	chr1:23375396-23375597(-)$1	201	45	55	13.6274
::::::dddd	chr3:106852712-106852913(+)$1	201	4	14	15.2941
hhhhhhh22c	chr9:30957340-30957541(-)$1	201	88	98	14.6078
^^^^^^^^^^	chr11:54723340-54723541(+)$1	201	91	101	13.8235
hhmmmmhhhh	chr10:36855688-36855889(-)$1	201	86	96	14.0196
iqqqqqqqqi	chr2:102623321-102623522(+)$1	201	173	183	13.2352
d!!bbnnnnn	chr13:21605812-21606013(-)$1	201	35	45	15.9803
hhhhh[ccc!	chr2:73450367-73450568(-)$1	201	113	123	15.9803

#DB
).....))))	chr2:132355960-132356161(-)$1	1	188	198	15.8823
)))).)))).	chr2:37230208-37230409(-)$1	1	64	74	15.8823
((....))))	chr10:56110034-56110235(+)$1	1	169	179	17.0588
)))))).)))	chr6:146598946-146599147(+)$1	1	182	192	18.2352
(.........	chr11:74489945-74490146(-)$1	1	17	27	18.6274
(((.......	chr12:75396233-75396434(+)$1	1	61	71	13.8235
(((((...((	chr2:134420597-134420798(-)$1	1	132	142	13.8235
......))))	chr11:75519292-75519493(+)$1	1	75	85	17.0588
..........	chr14:35560023-35560224(+)$1	1	35	45	15.0980
((((((.(((	chr10:29065187-29065388(+)$1	1	63	73	14.3137
.(((((.(((	chr10:85810228-85810429(+)$1	1	96	106	13.5294
.))))))...	chr3:10314484-10314685(-)$1	1	73	83	14.9019
)))))))...	chr13:94130050-94130251(+)$1	1	34	44	19.9019
))).......	chr11:3799832-3800033(+)$1	1	91	101	17.8431
)))).....)	chr1:66742443-66742644(+)$1	1	108	118	16.2745
.........(	chr14:78892413-78892614(-)$1	1	68	78	15.6862
((....((((	chr7:117980639-117980840(-)$1	1	12	22	14.9019
))(((.....	chr7:25320608-25320809(+)$1	1	187	197	14.7058
(((((((...	chr4:86630687-86630888(-)$1	1	1	11	17.0588
.)))))))..	chr14:67421676-67421877(-)$1	1	25	35	16.3725
))).))))))	chr1:13129358-13129559(-)$1	1	167	177	17.2549
((((....((	chr5:68010708-68010909(-)$1	1	27	37	17.0588
((.((((...	chr15:54432543-54432744(+)$1	1	34	44	16.6666
((((((.(((	chr12:25779246-25779447(-)$1	1	17	27	16.6666
(.........	chr9:51753384-51753585(-)$1	1	36	46	16.6666
...(((((..	chr2:131878287-131878488(-)$1	1	17	27	19.9019
((((...((.	chr5:125367560-125367761(+)$1	1	117	127	13.4313
))))...)))	chr9:75413407-75413608(-)$1	1	56	66	14.2156
)))..))...	chr6:128359788-128359989(-)$1	1	180	190	18.2352
(((((.((((	chr6:57456850-57457051(-)$1	1	1	11	14.3137
)))))).(((	chr2:39051738-39051939(-)$1	1	16	26	14.2156
..........	chr15:98634277-98634478(-)$1	1	20	30	16.3725
))........	chr2:92794469-92794670(+)$1	1	158	168	18.6274
(((((((((.	chrX:61522261-61522462(-)$1	1	29	39	14.1176
((((......	chr6:108772823-108773024(+)$1	1	157	167	18.3333
((((..((((	chr11:17100238-17100439(+)$1	1	46	56	14.4117
..........	chr1:68080482-68080683(-)$1	1	168	178	17.0588
.....(((((	chr6:67234309-67234510(+)$1	1	17	27	14.6078
))))).....	chr16:45962929-45963130(-)$1	1	158	168	21.1764
..........	chr7:129771256-129771457(+)$1	1	135	145	16.3725
..........	chr11:68628733-68628934(+)$1	1	25	35	14.9019
..........	chr4:41464719-41464920(-)$1	1	100	110	17.3529
(....((((.	chr4:56975652-56975853(-)$1	1	37	47	13.6274
(.(((....)	chr1:23375396-23375597(-)$1	1	45	55	13.6274
......((((	chr3:106852712-106852913(+)$1	1	4	14	15.2941
)))))))..)	chr9:30957340-30957541(-)$1	1	88	98	14.6078
..........	chr11:54723340-54723541(+)$1	1	91	101	13.8235
((....))))	chr10:36855688-36855889(-)$1	1	86	96	14.0196
(........)	chr2:102623321-102623522(+)$1	1	173	183	13.2352
(..((.....	chr13:21605812-21606013(-)$1	1	35	45	15.9803
(((((.(((.	chr2:73450367-73450568(-)$1	1	113	123	15.9803

#PSSM
G : 0.41	A : 0.25	C : 0.11	g : 0.09	U : 0.09	u : 0.01	
U : 0.80	u : 0.13	G : 0.03	A : 0.01	
U : 0.70	u : 0.09	A : 0.07	G : 0.05	C : 0.01	a : 0.01	g : 0.01	
U : 0.86	u : 0.13	
U : 0.72	u : 0.11	G : 0.05	C : 0.03	A : 0.03	a : 0.01	
U : 0.60	A : 0.15	u : 0.11	G : 0.05	C : 0.03	c : 0.01	
A : 0.58	U : 0.13	C : 0.07	a : 0.07	G : 0.05	g : 0.01	u : 0.01	c : 0.01	
U : 0.80	u : 0.13	A : 0.01	G : 0.01	C : 0.01	
U : 0.76	u : 0.15	A : 0.05	G : 0.01	
U : 0.74	u : 0.13	A : 0.05	C : 0.01	g : 0.01	G : 0.01	

#score	813.1372549019612
#seq	51
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m3_run1.nuc.txt

#NT
CCUG	chr13:5869145-5869421(+)$1	276	77	81	11.9999
ccug	chr5:123807810-123808084(+)$1	274	27	31	11.9999
ccug	chr8:123178705-123178986(-)$1	281	1	5	11.9999
CCUG	chr2:157383278-157383553(-)$1	275	19	23	11.9999
CCUG	chr19:8907655-8907942(+)$1	287	3	7	11.9999
CCUG	chr7:25670028-25670303(+)$1	275	65	69	11.9999
CCUG	chrX:11614220-11614489(-)$1	269	220	224	11.9999
CCUG	chr1:36501838-36502111(-)$1	273	55	59	11.9999
CCUG	chr5:31924703-31924994(+)$1	291	266	270	11.9999
CCUG	chr14:99472877-99473151(+)$1	274	104	108	11.9999
CCUG	chr5:67078040-67078309(+)$1	269	161	165	11.9999
CCUG	chr2:152607437-152607723(-)$1	286	141	145	11.9999
CCUG	chr5:138223116-138223429(-)$1	313	35	39	11.9999
CCUG	chr2:32162847-32163126(+)$1	279	45	49	11.9999
CCUG	chr2:30882339-30882614(-)$1	275	1	5	11.9999
CCUG	chr1:184398226-184398498(-)$1	272	93	97	11.9999
CCUG	chr5:137966809-137967086(+)$1	277	13	17	11.9999
CCUG	chr13:69138016-69138287(-)$1	271	146	150	11.9999
CCUG	chr15:80761843-80762129(+)$1	286	6	10	11.9999
CCUG	chr4:33125089-33125364(+)$1	275	59	63	11.9999
CCUG	chr11:117828707-117828977(-)$1	270	32	36	11.9999
CCUG	chr15:80766809-80767079(+)$1	270	8	12	11.9999
CCUG	chr18:24443321-24443593(+)$1	272	213	217	11.9999
ccug	chr7:152050685-152050968(+)$1	283	117	121	11.9999
CCUG	chr11:69813257-69813538(+)$1	281	124	128	11.9999
CCUG	chr11:87794777-87795061(-)$1	284	14	18	11.9999
CCUG	chr11:53590397-53590671(+)$1	274	7	11	11.9999
CCUG	chr5:137968786-137969068(+)$1	282	76	80	11.9999
CCUG	chr11:117828673-117828945(-)$1	272	0	4	11.9999
CCUG	chr16:37882822-37883102(+)$1	280	87	91	11.9999
CCUG	chr4:140669561-140669856(-)$1	295	27	31	11.9999
CCUG	chr9:90098144-90098412(-)$1	268	50	54	11.9999
CCUG	chr15:81535366-81535658(-)$1	292	70	74	11.9999
CCUG	chr11:114729900-114730186(+)$1	286	142	146	11.9999
CCUG	chr1:133921794-133922065(+)$1	271	29	33	11.9999
CCUG	chr2:30302693-30302995(+)$1	302	71	75	11.9999
CCUG	chr15:80761601-80761877(+)$1	276	232	236	11.9999
CCUG	chr11:68635132-68635416(-)$1	284	144	148	11.9999
CCUG	chr16:92084361-92084635(+)$1	274	25	29	11.9999
CCUG	chr16:37882880-37883165(+)$1	285	29	33	11.9999
CCUG	chr9:119147934-119148232(-)$1	298	33	37	11.9999
CCUG	chr7:24891391-24891687(+)$1	296	29	33	11.9999
CCUG	chr16:91227830-91228116(+)$1	286	69	73	11.9999
CCUG	chr14:65431215-65431492(-)$1	277	2	6	11.9999
CCUG	chr13:73773790-73774082(+)$1	292	4	8	11.9999
CCUG	chr3:122242260-122242557(-)$1	297	9	13	11.9999
CCUG	chr7:30106085-30106361(-)$1	276	178	182	11.9999
CCUG	chr14:119377448-119377719(+)$1	271	128	132	11.9999
CCUG	chr16:91227771-91228065(+)$1	294	44	48	11.9999
CCUG	chr15:98734299-98734578(-)$1	279	124	128	11.9999
CCUG	chr11:98015256-98015533(-)$1	277	142	146	11.9999
CCUG	chr2:168780769-168781049(-)$1	280	38	42	11.9999
CCUG	chr4:138012732-138013003(+)$1	271	96	100	11.9999
CCUG	chr4:137798692-137798972(+)$1	280	174	178	11.9999
CCUG	chr8:11834069-11834348(+)$1	279	196	200	11.9999
CCUG	chr1:64840465-64840748(-)$1	283	40	44	11.9999
CCUG	chr5:93697524-93697808(+)$1	284	194	198	11.9999
CCUG	chr4:99324900-99325179(+)$1	279	111	115	11.9999
CCUG	chr14:121941982-121942255(-)$1	273	13	17	11.9999
CCUG	chr9:30881655-30881942(+)$1	287	33	37	11.9999
ccug	chr2:144232685-144232977(+)$1	292	160	164	11.9999
CCUG	chr17:37114860-37115135(-)$1	275	74	78	11.9999
CCUG	chr11:79506341-79506633(+)$1	292	30	34	11.9999
ccug	chr3:90057072-90057343(+)$1	271	2	6	11.9999
CCUG	chr17:57032824-57033135(-)$1	311	17	21	11.9999
CCUG	chr17:37209972-37210240(+)$1	268	217	221	11.9999
CCUG	chr14:71003925-71004195(-)$1	270	49	53	11.9999
CCUG	chr5:114588885-114589158(+)$1	273	2	6	11.9999
CCUG	chr2:31615419-31615714(+)$1	295	55	59	11.9999
CCUG	chr7:151775188-151775455(-)$1	267	53	57	11.9999
CCUG	chr19:5456361-5456634(-)$1	273	97	101	11.9999
CCUG	chr15:89012664-89012935(-)$1	271	26	30	11.9999
CCUG	chr15:79655049-79655353(-)$1	304	141	145	11.9999
CCUG	chr2:34678076-34678352(-)$1	276	27	31	11.9999
CCUG	chr15:79656085-79656364(-)$1	279	8	12	11.9999
CCUG	chr5:37138907-37139205(-)$1	298	30	34	11.9999
CCUG	chr5:137966884-137967196(+)$1	312	2	6	11.9999
CCUG	chr1:181447940-181448228(-)$1	288	7	11	11.9999

#otherMatches

#Struct PSSM
eeee	chr7:72016753-72017039(-)$1	286	39	43	11.9999
""gg	chr13:5869145-5869421(+)$1	276	77	81	11.9999
oooc	chr5:123807810-123808084(+)$1	274	27	31	11.9999
gggg	chr8:123178705-123178986(-)$1	281	1	5	11.9999
mmff	chr2:157383278-157383553(-)$1	275	19	23	11.9999
ffff	chr19:8907655-8907942(+)$1	287	3	7	11.9999
eee[	chr7:25670028-25670303(+)$1	275	65	69	11.9999
CCCY	chrX:11614220-11614489(-)$1	269	220	224	11.9999
ccc!	chr1:36501838-36502111(-)$1	273	55	59	11.9999
22dd	chr5:31924703-31924994(+)$1	291	266	270	11.9999
ff::	chr14:99472877-99473151(+)$1	274	104	108	11.9999
b!!d	chr5:67078040-67078309(+)$1	269	161	165	11.9999
]ccc	chr2:152607437-152607723(-)$1	286	141	145	11.9999
FF{G	chr5:138223116-138223429(-)$1	313	35	39	11.9999
[ggg	chr2:32162847-32163126(+)$1	279	45	49	11.9999
:::c	chr2:30882339-30882614(-)$1	275	1	5	11.9999
pppp	chr1:184398226-184398498(-)$1	272	93	97	11.9999
CCC:	chr5:137966809-137967086(+)$1	277	13	17	11.9999
eeee	chr13:69138016-69138287(-)$1	271	146	150	11.9999
FFF{	chr15:80761843-80762129(+)$1	286	6	10	11.9999
::GG	chr4:33125089-33125364(+)$1	275	59	63	11.9999
EEEE	chr11:117828707-117828977(-)$1	270	32	36	11.9999
bb[b	chr15:80766809-80767079(+)$1	270	8	12	11.9999
eeee	chr18:24443321-24443593(+)$1	272	213	217	11.9999
[a[d	chr7:152050685-152050968(+)$1	283	117	121	11.9999
::BB	chr11:69813257-69813538(+)$1	281	124	128	11.9999
GGGG	chr11:87794777-87795061(-)$1	284	14	18	11.9999
DDDD	chr11:53590397-53590671(+)$1	274	7	11	11.9999
CC:=	chr5:137968786-137969068(+)$1	282	76	80	11.9999
:EEE	chr11:117828673-117828945(-)$1	272	0	4	11.9999
::::	chr16:37882822-37883102(+)$1	280	87	91	11.9999
eeee	chr4:140669561-140669856(-)$1	295	27	31	11.9999
ENNN	chr9:90098144-90098412(-)$1	268	50	54	11.9999
$$$d	chr15:81535366-81535658(-)$1	292	70	74	11.9999
##ff	chr11:114729900-114730186(+)$1	286	142	146	11.9999
ddpp	chr1:133921794-133922065(+)$1	271	29	33	11.9999
gggg	chr2:30302693-30302995(+)$1	302	71	75	11.9999
GGGG	chr15:80761601-80761877(+)$1	276	232	236	11.9999
hhhh	chr11:68635132-68635416(-)$1	284	144	148	11.9999
444b	chr16:92084361-92084635(+)$1	274	25	29	11.9999
JJJ:	chr16:37882880-37883165(+)$1	285	29	33	11.9999
:::e	chr9:119147934-119148232(-)$1	298	33	37	11.9999
IIII	chr7:24891391-24891687(+)$1	296	29	33	11.9999
EEEE	chr16:91227830-91228116(+)$1	286	69	73	11.9999
::::	chr14:65431215-65431492(-)$1	277	2	6	11.9999
EEKK	chr13:73773790-73774082(+)$1	292	4	8	11.9999
eee[	chr3:122242260-122242557(-)$1	297	9	13	11.9999
ddd[	chr7:30106085-30106361(-)$1	276	178	182	11.9999
eeec	chr14:119377448-119377719(+)$1	271	128	132	11.9999
d333	chr16:91227771-91228065(+)$1	294	44	48	11.9999
oooc	chr15:98734299-98734578(-)$1	279	124	128	11.9999
b]ff	chr11:98015256-98015533(-)$1	277	142	146	11.9999
hhhh	chr2:168780769-168781049(-)$1	280	38	42	11.9999
=bb[	chr4:138012732-138013003(+)$1	271	96	100	11.9999
a22d	chr4:137798692-137798972(+)$1	280	174	178	11.9999
dddm	chr8:11834069-11834348(+)$1	279	196	200	11.9999
""dd	chr1:64840465-64840748(-)$1	283	40	44	11.9999
ccc#	chr5:93697524-93697808(+)$1	284	194	198	11.9999
b[bb	chr4:99324900-99325179(+)$1	279	111	115	11.9999
:ddd	chr14:121941982-121942255(-)$1	273	13	17	11.9999
D{DD	chr9:30881655-30881942(+)$1	287	33	37	11.9999
IIII	chr2:144232685-144232977(+)$1	292	160	164	11.9999
::ii	chr17:37114860-37115135(-)$1	275	74	78	11.9999
eeee	chr11:79506341-79506633(+)$1	292	30	34	11.9999
DDD{	chr3:90057072-90057343(+)$1	271	2	6	11.9999
cc[c	chr17:57032824-57033135(-)$1	311	17	21	11.9999
GGGG	chr17:37209972-37210240(+)$1	268	217	221	11.9999
cccG	chr14:71003925-71004195(-)$1	270	49	53	11.9999
cccq	chr5:114588885-114589158(+)$1	273	2	6	11.9999
iiii	chr2:31615419-31615714(+)$1	295	55	59	11.9999
d::b	chr7:151775188-151775455(-)$1	267	53	57	11.9999
iiii	chr19:5456361-5456634(-)$1	273	97	101	11.9999
meee	chr15:89012664-89012935(-)$1	271	26	30	11.9999
ZZZF	chr15:79655049-79655353(-)$1	304	141	145	11.9999
e[cc	chr2:34678076-34678352(-)$1	276	27	31	11.9999
BFFF	chr15:79656085-79656364(-)$1	279	8	12	11.9999
{DDD	chr5:37138907-37139205(-)$1	298	30	34	11.9999
::::	chr5:137966884-137967196(+)$1	312	2	6	11.9999
"""b	chr1:181447940-181448228(-)$1	288	7	11	11.9999

#DB
))))	chr7:72016753-72017039(-)$1	1	39	43	11.9999
..((	chr13:5869145-5869421(+)$1	1	77	81	11.9999
...)	chr5:123807810-123808084(+)$1	1	27	31	11.9999
((((	chr8:123178705-123178986(-)$1	1	1	5	11.9999
..))	chr2:157383278-157383553(-)$1	1	19	23	11.9999
((((	chr19:8907655-8907942(+)$1	1	3	7	11.9999
(((.	chr7:25670028-25670303(+)$1	1	65	69	11.9999
))).	chrX:11614220-11614489(-)$1	1	220	224	11.9999
(((.	chr1:36501838-36502111(-)$1	1	55	59	11.9999
..))	chr5:31924703-31924994(+)$1	1	266	270	11.9999
))..	chr14:99472877-99473151(+)$1	1	104	108	11.9999
(..(	chr5:67078040-67078309(+)$1	1	161	165	11.9999
.)))	chr2:152607437-152607723(-)$1	1	141	145	11.9999
((.(	chr5:138223116-138223429(-)$1	1	35	39	11.9999
.(((	chr2:32162847-32163126(+)$1	1	45	49	11.9999
...(	chr2:30882339-30882614(-)$1	1	1	5	11.9999
....	chr1:184398226-184398498(-)$1	1	93	97	11.9999
(((.	chr5:137966809-137967086(+)$1	1	13	17	11.9999
((((	chr13:69138016-69138287(-)$1	1	146	150	11.9999
(((.	chr15:80761843-80762129(+)$1	1	6	10	11.9999
..((	chr4:33125089-33125364(+)$1	1	59	63	11.9999
((((	chr11:117828707-117828977(-)$1	1	32	36	11.9999
((.(	chr15:80766809-80767079(+)$1	1	8	12	11.9999
((((	chr18:24443321-24443593(+)$1	1	213	217	11.9999
.(.(	chr7:152050685-152050968(+)$1	1	117	121	11.9999
..))	chr11:69813257-69813538(+)$1	1	124	128	11.9999
((((	chr11:87794777-87795061(-)$1	1	14	18	11.9999
((((	chr11:53590397-53590671(+)$1	1	7	11	11.9999
((.(	chr5:137968786-137969068(+)$1	1	76	80	11.9999
.(((	chr11:117828673-117828945(-)$1	1	0	4	11.9999
....	chr16:37882822-37883102(+)$1	1	87	91	11.9999
((((	chr4:140669561-140669856(-)$1	1	27	31	11.9999
(...	chr9:90098144-90098412(-)$1	1	50	54	11.9999
...(	chr15:81535366-81535658(-)$1	1	70	74	11.9999
..((	chr11:114729900-114730186(+)$1	1	142	146	11.9999
((..	chr1:133921794-133922065(+)$1	1	29	33	11.9999
))))	chr2:30302693-30302995(+)$1	1	71	75	11.9999
))))	chr15:80761601-80761877(+)$1	1	232	236	11.9999
))))	chr11:68635132-68635416(-)$1	1	144	148	11.9999
...)	chr16:92084361-92084635(+)$1	1	25	29	11.9999
(((.	chr16:37882880-37883165(+)$1	1	29	33	11.9999
...(	chr9:119147934-119148232(-)$1	1	33	37	11.9999
((((	chr7:24891391-24891687(+)$1	1	29	33	11.9999
((((	chr16:91227830-91228116(+)$1	1	69	73	11.9999
....	chr14:65431215-65431492(-)$1	1	2	6	11.9999
((..	chr13:73773790-73774082(+)$1	1	4	8	11.9999
(((.	chr3:122242260-122242557(-)$1	1	9	13	11.9999
(((.	chr7:30106085-30106361(-)$1	1	178	182	11.9999
))))	chr14:119377448-119377719(+)$1	1	128	132	11.9999
)...	chr16:91227771-91228065(+)$1	1	44	48	11.9999
...)	chr15:98734299-98734578(-)$1	1	124	128	11.9999
).))	chr11:98015256-98015533(-)$1	1	142	146	11.9999
((((	chr2:168780769-168781049(-)$1	1	38	42	11.9999
)((.	chr4:138012732-138013003(+)$1	1	96	100	11.9999
)..)	chr4:137798692-137798972(+)$1	1	174	178	11.9999
(((.	chr8:11834069-11834348(+)$1	1	196	200	11.9999
..((	chr1:64840465-64840748(-)$1	1	40	44	11.9999
(((.	chr5:93697524-93697808(+)$1	1	194	198	11.9999
(.((	chr4:99324900-99325179(+)$1	1	111	115	11.9999
.(((	chr14:121941982-121942255(-)$1	1	13	17	11.9999
(.((	chr9:30881655-30881942(+)$1	1	33	37	11.9999
))))	chr2:144232685-144232977(+)$1	1	160	164	11.9999
..((	chr17:37114860-37115135(-)$1	1	74	78	11.9999
))))	chr11:79506341-79506633(+)$1	1	30	34	11.9999
(((.	chr3:90057072-90057343(+)$1	1	2	6	11.9999
((.(	chr17:57032824-57033135(-)$1	1	17	21	11.9999
))))	chr17:37209972-37210240(+)$1	1	217	221	11.9999
)))(	chr14:71003925-71004195(-)$1	1	49	53	11.9999
(((.	chr5:114588885-114589158(+)$1	1	2	6	11.9999
((((	chr2:31615419-31615714(+)$1	1	55	59	11.9999
)..(	chr7:151775188-151775455(-)$1	1	53	57	11.9999
))))	chr19:5456361-5456634(-)$1	1	97	101	11.9999
.)))	chr15:89012664-89012935(-)$1	1	26	30	11.9999
...)	chr15:79655049-79655353(-)$1	1	141	145	11.9999
(.((	chr2:34678076-34678352(-)$1	1	27	31	11.9999
((((	chr15:79656085-79656364(-)$1	1	8	12	11.9999
.(((	chr5:37138907-37139205(-)$1	1	30	34	11.9999
....	chr5:137966884-137967196(+)$1	1	2	6	11.9999
...(	chr1:181447940-181448228(-)$1	1	7	11	11.9999

#PSSM
C : 0.93	c : 0.06	
C : 0.93	c : 0.06	
U : 0.93	u : 0.06	
G : 0.93	g : 0.06	

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_transcript_m2_run2.nuc.txt

#NT
cucu	chr10:120890005-120890241(-)$1	236	76	80	12.0000
cucu	chr1:183126633-183126874(-)$1	241	3	7	12.0000
CUCU	chr7:141074972-141075235(-)$1	263	127	131	12.0000
CUCU	chr4:138638346-138638585(-)$1	239	131	135	12.0000
cucu	chr15:93321410-93321658(+)$1	248	61	65	12.0000
CUCU	chr15:3932198-3932474(-)$1	276	228	232	12.0000
CUCU	chr7:52067739-52067994(-)$1	255	91	95	12.0000
CUCU	chr11:30066654-30066898(-)$1	244	140	144	12.0000
CUCU	chr1:167118279-167118535(-)$1	256	131	135	12.0000
CUCU	chr3:19140947-19141182(-)$1	235	103	107	12.0000
CUCU	chr5:74915467-74915705(-)$1	238	225	229	12.0000
CUCU	chr17:31667988-31668229(+)$1	241	152	156	12.0000
cucu	chr1:75056032-75056280(-)$1	248	118	122	12.0000
CUCU	chr5:90673029-90673271(-)$1	242	63	67	12.0000
CUCU	chr6:91707045-91707294(+)$1	249	71	75	12.0000
CUCU	chr10:126995215-126995466(-)$1	251	135	139	12.0000
CUCU	chr15:102821563-102821828(+)$1	265	97	101	12.0000
CUCU	chr6:83687669-83687924(+)$1	255	2	6	12.0000
CUCU	chr11:119581465-119581712(+)$1	247	1	5	12.0000
cucu	chr10:24613731-24613971(+)$1	240	233	237	12.0000
CUCU	chr18:6788662-6788897(+)$1	235	7	11	12.0000
CUCU	chr9:71862175-71862424(-)$1	249	12	16	12.0000
CUCU	chr11:106060960-106061197(-)$1	237	13	17	12.0000
CUCU	chr1:174436214-174436458(+)$1	244	173	177	12.0000
CUCU	chr15:58774097-58774332(-)$1	235	125	129	12.0000
CUCU	chr5:36655638-36655890(-)$1	252	2	6	12.0000
CUCU	chr15:76921027-76921280(-)$1	253	57	61	12.0000
CUCU	chr2:4410567-4410809(+)$1	242	5	9	12.0000
CUCU	chr1:34125584-34125843(+)$1	259	137	141	12.0000
CUCU	chr5:90722126-90722367(-)$1	241	121	125	12.0000
CUCU	chr4:40752180-40752420(-)$1	240	10	14	12.0000
CUCU	chr15:27544075-27544334(-)$1	259	100	104	12.0000
CUCU	chr6:101291304-101291559(-)$1	255	11	15	12.0000
cucu	chr4:131957814-131958049(-)$1	235	56	60	12.0000
cucu	chr11:115545212-115545461(-)$1	249	174	178	12.0000
CUCU	chr9:113672019-113672259(+)$1	240	104	108	12.0000
CUCU	chr15:25714889-25715129(+)$1	240	49	53	12.0000
cucu	chr2:130481860-130482114(-)$1	254	175	179	12.0000
CUCU	chr3:60419570-60419862(+)$1	292	14	18	12.0000
CUCU	chr10:61746180-61746426(-)$1	246	160	164	12.0000
CUCU	chr11:118164134-118164380(-)$1	246	56	60	12.0000
CUCU	chr19:5100106-5100389(-)$1	283	77	81	12.0000
cucu	chr17:42943163-42943414(-)$1	251	147	151	12.0000
CUCU	chr18:69718052-69718301(+)$1	249	32	36	12.0000
CUCU	chr8:96502763-96503003(-)$1	240	1	5	12.0000
CUCU	chr2:115889281-115889520(-)$1	239	0	4	12.0000
CUCU	chr15:96213872-96214122(+)$1	250	114	118	12.0000
CUCU	chr9:72572863-72573106(+)$1	243	38	42	12.0000
CUCU	chr6:72560325-72560570(-)$1	245	7	11	12.0000
cucu	chr12:3278617-3278858(-)$1	241	12	16	12.0000
cucu	chr1:37473986-37474248(-)$1	262	98	102	12.0000
CUCU	chrX:35774670-35774906(-)$1	236	10	14	12.0000
CUCU	chr10:60561445-60561737(-)$1	292	239	243	12.0000
CUCU	chr7:71054892-71055145(-)$1	253	135	139	12.0000
CUCU	chr11:102916416-102916654(+)$1	238	81	85	12.0000
cucu	chr19:7409972-7410207(-)$1	235	85	89	12.0000
CUCU	chr15:76912720-76912966(-)$1	246	127	131	12.0000
cucu	chr13:56182501-56182736(-)$1	235	6	10	12.0000
CUCU	chrX:101153016-101153271(-)$1	255	44	48	12.0000
cucu	chr3:119435807-119436066(-)$1	259	47	51	12.0000
CUCU	chr4:9553820-9554062(-)$1	242	66	70	12.0000
CUCU	chr8:24050350-24050589(+)$1	239	102	106	12.0000
CUCU	chr6:136494924-136495175(+)$1	251	50	54	12.0000
CUCU	chr8:93866095-93866338(+)$1	243	231	235	12.0000
CUCU	chr9:48276535-48276845(-)$1	310	74	78	12.0000
CUCU	chr1:92958144-92958379(+)$1	235	73	77	12.0000
CUCU	chr5:143664700-143665007(-)$1	307	222	226	12.0000
CUCU	chr11:50191212-50191458(+)$1	246	126	130	12.0000
CUCU	chr2:90806118-90806355(+)$1	237	132	136	12.0000
CUCU	chr11:4811504-4811767(+)$1	263	75	79	12.0000
CUCU	chr12:99930984-99931223(-)$1	239	30	34	12.0000
CUCU	chr19:32867894-32868144(+)$1	250	117	121	12.0000
CUCU	chr3:95749299-95749573(+)$1	274	99	103	12.0000
CUCU	chr4:153531602-153531847(-)$1	245	121	125	12.0000
CUCU	chr12:81290530-81290787(-)$1	257	76	80	12.0000
CUCU	chr11:75441653-75441907(+)$1	254	89	93	12.0000
CUCU	chr5:29923509-29923771(+)$1	262	90	94	12.0000
CUCU	chr9:44211905-44212176(-)$1	271	27	31	12.0000
CUCU	chr1:36408387-36408624(-)$1	237	28	32	12.0000
CUCU	chr4:147430207-147430445(+)$1	238	33	37	12.0000
CUCU	chr11:105785200-105785453(+)$1	253	0	4	12.0000
CUCU	chr3:86897600-86897862(-)$1	262	38	42	12.0000
CUCU	chr8:87825911-87826164(+)$1	253	17	21	12.0000
CUCU	chr9:69854582-69854833(+)$1	251	16	20	12.0000
CUCU	chr17:56578093-56578345(-)$1	252	23	27	12.0000

#otherMatches

#Struct PSSM
IIII	chr7:54015922-54016157(-)$1	235	25	29	12.0000
!!a[	chr10:120890005-120890241(-)$1	236	76	80	12.0000
C{BB	chr1:183126633-183126874(-)$1	241	3	7	12.0000
fffI	chr7:141074972-141075235(-)$1	263	127	131	12.0000
oooo	chr4:138638346-138638585(-)$1	239	131	135	12.0000
[bbd	chr15:93321410-93321658(+)$1	248	61	65	12.0000
dd[e	chr15:3932198-3932474(-)$1	276	228	232	12.0000
dddd	chr7:52067739-52067994(-)$1	255	91	95	12.0000
cc33	chr11:30066654-30066898(-)$1	244	140	144	12.0000
cc!!	chr1:167118279-167118535(-)$1	256	131	135	12.0000
::::	chr3:19140947-19141182(-)$1	235	103	107	12.0000
EEEE	chr5:74915467-74915705(-)$1	238	225	229	12.0000
mmmd	chr17:31667988-31668229(+)$1	241	152	156	12.0000
d]a]	chr1:75056032-75056280(-)$1	248	118	122	12.0000
ddd3	chr5:90673029-90673271(-)$1	242	63	67	12.0000
^^^^	chr6:91707045-91707294(+)$1	249	71	75	12.0000
555e	chr10:126995215-126995466(-)$1	251	135	139	12.0000
eee3	chr15:102821563-102821828(+)$1	265	97	101	12.0000
DDDN	chr6:83687669-83687924(+)$1	255	2	6	12.0000
::dd	chr11:119581465-119581712(+)$1	247	1	5	12.0000
gggg	chr10:24613731-24613971(+)$1	240	233	237	12.0000
:GGG	chr18:6788662-6788897(+)$1	235	7	11	12.0000
eeee	chr9:71862175-71862424(-)$1	249	12	16	12.0000
DDDD	chr11:106060960-106061197(-)$1	237	13	17	12.0000
[eee	chr1:174436214-174436458(+)$1	244	173	177	12.0000
dd33	chr15:58774097-58774332(-)$1	235	125	129	12.0000
::::	chr5:36655638-36655890(-)$1	252	2	6	12.0000
pfff	chr15:76921027-76921280(-)$1	253	57	61	12.0000
::::	chr2:4410567-4410809(+)$1	242	5	9	12.0000
====	chr1:34125584-34125843(+)$1	259	137	141	12.0000
deee	chr5:90722126-90722367(-)$1	241	121	125	12.0000
oooo	chr4:40752180-40752420(-)$1	240	10	14	12.0000
iiii	chr15:27544075-27544334(-)$1	259	100	104	12.0000
ooog	chr6:101291304-101291559(-)$1	255	11	15	12.0000
iii$	chr4:131957814-131958049(-)$1	235	56	60	12.0000
bmmm	chr11:115545212-115545461(-)$1	249	174	178	12.0000
ff::	chr9:113672019-113672259(+)$1	240	104	108	12.0000
!!cc	chr15:25714889-25715129(+)$1	240	49	53	12.0000
d333	chr2:130481860-130482114(-)$1	254	175	179	12.0000
G{BB	chr3:60419570-60419862(+)$1	292	14	18	12.0000
c:::	chr10:61746180-61746426(-)$1	246	160	164	12.0000
::::	chr11:118164134-118164380(-)$1	246	56	60	12.0000
c]dd	chr19:5100106-5100389(-)$1	283	77	81	12.0000
ffff	chr17:42943163-42943414(-)$1	251	147	151	12.0000
:ddd	chr18:69718052-69718301(+)$1	249	32	36	12.0000
b###	chr8:96502763-96503003(-)$1	240	1	5	12.0000
::::	chr2:115889281-115889520(-)$1	239	0	4	12.0000
eeee	chr15:96213872-96214122(+)$1	250	114	118	12.0000
eee:	chr9:72572863-72573106(+)$1	243	38	42	12.0000
::::	chr6:72560325-72560570(-)$1	245	7	11	12.0000
d$$$	chr12:3278617-3278858(-)$1	241	12	16	12.0000
BKKC	chr1:37473986-37474248(-)$1	262	98	102	12.0000
LLGG	chrX:35774670-35774906(-)$1	236	10	14	12.0000
::::	chr10:60561445-60561737(-)$1	292	239	243	12.0000
dd44	chr7:71054892-71055145(-)$1	253	135	139	12.0000
::::	chr11:102916416-102916654(+)$1	238	81	85	12.0000
::::	chr19:7409972-7410207(-)$1	235	85	89	12.0000
22a]	chr15:76912720-76912966(-)$1	246	127	131	12.0000
b!!b	chr13:56182501-56182736(-)$1	235	6	10	12.0000
CGGG	chrX:101153016-101153271(-)$1	255	44	48	12.0000
H:::	chr3:119435807-119436066(-)$1	259	47	51	12.0000
:bbm	chr4:9553820-9554062(-)$1	242	66	70	12.0000
rrrr	chr8:24050350-24050589(+)$1	239	102	106	12.0000
NFFF	chr6:136494924-136495175(+)$1	251	50	54	12.0000
||||	chr8:93866095-93866338(+)$1	243	231	235	12.0000
cc::	chr9:48276535-48276845(-)$1	310	74	78	12.0000
hhll	chr1:92958144-92958379(+)$1	235	73	77	12.0000
ddmm	chr5:143664700-143665007(-)$1	307	222	226	12.0000
cJJJ	chr11:50191212-50191458(+)$1	246	126	130	12.0000
!ddd	chr2:90806118-90806355(+)$1	237	132	136	12.0000
ffff	chr11:4811504-4811767(+)$1	263	75	79	12.0000
b]a2	chr12:99930984-99931223(-)$1	239	30	34	12.0000
++bb	chr19:32867894-32868144(+)$1	250	117	121	12.0000
33ff	chr3:95749299-95749573(+)$1	274	99	103	12.0000
eeee	chr4:153531602-153531847(-)$1	245	121	125	12.0000
b]a]	chr12:81290530-81290787(-)$1	257	76	80	12.0000
flll	chr11:75441653-75441907(+)$1	254	89	93	12.0000
mmmm	chr5:29923509-29923771(+)$1	262	90	94	12.0000
dd:F	chr9:44211905-44212176(-)$1	271	27	31	12.0000
B{BB	chr1:36408387-36408624(-)$1	237	28	32	12.0000
dddd	chr4:147430207-147430445(+)$1	238	33	37	12.0000
::dd	chr11:105785200-105785453(+)$1	253	0	4	12.0000
DDDD	chr3:86897600-86897862(-)$1	262	38	42	12.0000
::::	chr8:87825911-87826164(+)$1	253	17	21	12.0000
crrr	chr9:69854582-69854833(+)$1	251	16	20	12.0000
pddd	chr17:56578093-56578345(-)$1	252	23	27	12.0000

#DB
((((	chr7:54015922-54016157(-)$1	1	25	29	12.0000
..(.	chr10:120890005-120890241(-)$1	1	76	80	12.0000
(.((	chr1:183126633-183126874(-)$1	1	3	7	12.0000
))))	chr7:141074972-141075235(-)$1	1	127	131	12.0000
....	chr4:138638346-138638585(-)$1	1	131	135	12.0000
.(((	chr15:93321410-93321658(+)$1	1	61	65	12.0000
((.(	chr15:3932198-3932474(-)$1	1	228	232	12.0000
((((	chr7:52067739-52067994(-)$1	1	91	95	12.0000
))..	chr11:30066654-30066898(-)$1	1	140	144	12.0000
((..	chr1:167118279-167118535(-)$1	1	131	135	12.0000
....	chr3:19140947-19141182(-)$1	1	103	107	12.0000
))))	chr5:74915467-74915705(-)$1	1	225	229	12.0000
...)	chr17:31667988-31668229(+)$1	1	152	156	12.0000
).).	chr1:75056032-75056280(-)$1	1	118	122	12.0000
))).	chr5:90673029-90673271(-)$1	1	63	67	12.0000
....	chr6:91707045-91707294(+)$1	1	71	75	12.0000
...)	chr10:126995215-126995466(-)$1	1	135	139	12.0000
))).	chr15:102821563-102821828(+)$1	1	97	101	12.0000
(((.	chr6:83687669-83687924(+)$1	1	2	6	12.0000
..((	chr11:119581465-119581712(+)$1	1	1	5	12.0000
))))	chr10:24613731-24613971(+)$1	1	233	237	12.0000
.(((	chr18:6788662-6788897(+)$1	1	7	11	12.0000
((((	chr9:71862175-71862424(-)$1	1	12	16	12.0000
((((	chr11:106060960-106061197(-)$1	1	13	17	12.0000
.(((	chr1:174436214-174436458(+)$1	1	173	177	12.0000
))..	chr15:58774097-58774332(-)$1	1	125	129	12.0000
....	chr5:36655638-36655890(-)$1	1	2	6	12.0000
.)))	chr15:76921027-76921280(-)$1	1	57	61	12.0000
....	chr2:4410567-4410809(+)$1	1	5	9	12.0000
))))	chr1:34125584-34125843(+)$1	1	137	141	12.0000
))))	chr5:90722126-90722367(-)$1	1	121	125	12.0000
....	chr4:40752180-40752420(-)$1	1	10	14	12.0000
))))	chr15:27544075-27544334(-)$1	1	100	104	12.0000
...)	chr6:101291304-101291559(-)$1	1	11	15	12.0000
(((.	chr4:131957814-131958049(-)$1	1	56	60	12.0000
(...	chr11:115545212-115545461(-)$1	1	174	178	12.0000
))..	chr9:113672019-113672259(+)$1	1	104	108	12.0000
..((	chr15:25714889-25715129(+)$1	1	49	53	12.0000
)...	chr2:130481860-130482114(-)$1	1	175	179	12.0000
(.((	chr3:60419570-60419862(+)$1	1	14	18	12.0000
)...	chr10:61746180-61746426(-)$1	1	160	164	12.0000
....	chr11:118164134-118164380(-)$1	1	56	60	12.0000
).))	chr19:5100106-5100389(-)$1	1	77	81	12.0000
))))	chr17:42943163-42943414(-)$1	1	147	151	12.0000
.(((	chr18:69718052-69718301(+)$1	1	32	36	12.0000
(...	chr8:96502763-96503003(-)$1	1	1	5	12.0000
....	chr2:115889281-115889520(-)$1	1	0	4	12.0000
))))	chr15:96213872-96214122(+)$1	1	114	118	12.0000
))).	chr9:72572863-72573106(+)$1	1	38	42	12.0000
....	chr6:72560325-72560570(-)$1	1	7	11	12.0000
(...	chr12:3278617-3278858(-)$1	1	12	16	12.0000
(..(	chr1:37473986-37474248(-)$1	1	98	102	12.0000
..((	chrX:35774670-35774906(-)$1	1	10	14	12.0000
....	chr10:60561445-60561737(-)$1	1	239	243	12.0000
))..	chr7:71054892-71055145(-)$1	1	135	139	12.0000
....	chr11:102916416-102916654(+)$1	1	81	85	12.0000
....	chr19:7409972-7410207(-)$1	1	85	89	12.0000
..).	chr15:76912720-76912966(-)$1	1	127	131	12.0000
(..(	chr13:56182501-56182736(-)$1	1	6	10	12.0000
((((	chrX:101153016-101153271(-)$1	1	44	48	12.0000
(...	chr3:119435807-119436066(-)$1	1	47	51	12.0000
.((.	chr4:9553820-9554062(-)$1	1	66	70	12.0000
....	chr8:24050350-24050589(+)$1	1	102	106	12.0000
.(((	chr6:136494924-136495175(+)$1	1	50	54	12.0000
....	chr8:93866095-93866338(+)$1	1	231	235	12.0000
))..	chr9:48276535-48276845(-)$1	1	74	78	12.0000
((..	chr1:92958144-92958379(+)$1	1	73	77	12.0000
((..	chr5:143664700-143665007(-)$1	1	222	226	12.0000
))))	chr11:50191212-50191458(+)$1	1	126	130	12.0000
.(((	chr2:90806118-90806355(+)$1	1	132	136	12.0000
((((	chr11:4811504-4811767(+)$1	1	75	79	12.0000
).).	chr12:99930984-99931223(-)$1	1	30	34	12.0000
..((	chr19:32867894-32868144(+)$1	1	117	121	12.0000
..))	chr3:95749299-95749573(+)$1	1	99	103	12.0000
((((	chr4:153531602-153531847(-)$1	1	121	125	12.0000
).).	chr12:81290530-81290787(-)$1	1	76	80	12.0000
(...	chr11:75441653-75441907(+)$1	1	89	93	12.0000
....	chr5:29923509-29923771(+)$1	1	90	94	12.0000
)).(	chr9:44211905-44212176(-)$1	1	27	31	12.0000
(.((	chr1:36408387-36408624(-)$1	1	28	32	12.0000
))))	chr4:147430207-147430445(+)$1	1	33	37	12.0000
..((	chr11:105785200-105785453(+)$1	1	0	4	12.0000
((((	chr3:86897600-86897862(-)$1	1	38	42	12.0000
....	chr8:87825911-87826164(+)$1	1	17	21	12.0000
(...	chr9:69854582-69854833(+)$1	1	16	20	12.0000
.)))	chr17:56578093-56578345(-)$1	1	23	27	12.0000

#PSSM
C : 0.82	c : 0.17	
U : 0.82	u : 0.17	
C : 0.82	c : 0.17	
U : 0.82	u : 0.17	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m2_run1.nuc.txt

#NT
UGUGUG	chr2:167332502-167332848(+)$1	346	27	33	15.1212
AGUGUG	chr15:100225326-100225762(-)$1	436	163	169	13.9848
UGUGUG	chr7:135117771-135118263(+)$1	492	331	337	15.1212
UGUGUG	chr8:56140035-56140294(+)$1	259	149	155	15.1212
Cgugug	chr5:145653792-145654141(-)$1	349	181	187	13.4545
GGUGUG	chr18:35024331-35024698(+)$1	367	265	271	14.4393
Ggugug	chr12:71373350-71373847(-)$1	497	203	209	14.4393
AGUGUG	chr1:9714311-9714703(-)$1	392	285	291	13.9848
AGUGUG	chr19:45871213-45871631(-)$1	418	117	123	13.9848
ugugug	chr9:67731244-67731576(+)$1	332	169	175	15.1212
GGUGUG	chr13:120167362-120167857(-)$1	495	208	214	14.4393
CGUGUG	chr17:33783451-33783775(-)$1	324	140	146	13.4545
GGUGUG	chr3:89812042-89812351(-)$1	309	95	101	14.4393
UGUGUG	chr16:52305522-52305824(-)$1	302	91	97	15.1212
UGUGUG	chr11:109522564-109522950(+)$1	386	120	126	15.1212
UGUGUG	chr10:31670723-31670965(-)$1	242	104	110	15.1212
UGUGUG	chr9:53400103-53400486(-)$1	383	95	101	15.1212
AGUGUG	chr6:113441918-113442267(+)$1	349	208	214	13.9848
UGUGUG	chr11:79329730-79330113(+)$1	383	94	100	15.1212
UGUGUG	chr11:5889986-5890273(-)$1	287	116	122	15.1212
UGUGUG	chr17:86568130-86568477(+)$1	347	17	23	15.1212
GGUGUG	chr7:71879400-71879781(+)$1	381	175	181	14.4393
ugugug	chr8:75216954-75217272(+)$1	318	89	95	15.1212
UGUGUG	chr9:57376755-57377089(+)$1	334	210	216	15.1212
GGUGUG	chr1:162125525-162125777(+)$1	252	94	100	14.4393
AGUGUG	chr18:61086262-61086760(+)$1	498	111	117	13.9848
UGUGUG	chr13:55756328-55756766(+)$1	438	130	136	15.1212
GGUGUG	chr8:3161067-3161546(-)$1	479	207	213	14.4393
ggugug	chr7:38781417-38781808(-)$1	391	186	192	14.4393
UGUGUG	chr2:5812064-5812507(-)$1	443	0	6	15.1212
UGUGUG	chr12:81689361-81689577(+)$1	216	105	111	15.1212
GGUGUG	chr4:46481519-46481867(+)$1	348	112	118	14.4393
GGUGUG	chr10:79736946-79737326(+)$1	380	85	91	14.4393
UGUGUG	chr10:59761746-59761997(+)$1	251	114	120	15.1212
GGUGUG	chr16:17506242-17506613(+)$1	371	194	200	14.4393
UGUGUG	chr5:148354363-148354769(+)$1	406	234	240	15.1212
Cgugug	chr10:83073831-83074266(-)$1	435	148	154	13.4545
UGUGUG	chr4:117225471-117225810(+)$1	339	84	90	15.1212
UGUGUG	chr4:58831798-58832237(-)$1	439	104	110	15.1212
ugugug	chr2:28309249-28309670(+)$1	421	172	178	15.1212
UGUGUG	chr3:152020918-152021299(+)$1	381	137	143	15.1212
GGUGUG	chr2:164824421-164824905(+)$1	484	20	26	14.4393
GGUGUG	chr18:40367294-40367581(-)$1	287	149	155	14.4393
ugugug	chr15:100787913-100788347(+)$1	434	138	144	15.1212
UGUGUG	chr8:47292623-47293054(-)$1	431	267	273	15.1212
AGUGUG	chr12:118493955-118494365(+)$1	410	249	255	13.9848
AGUGUG	chr15:84533464-84533838(+)$1	374	105	111	13.9848
AGUGUG	chr8:73055485-73055837(+)$1	352	63	69	13.9848
CGUGUG	chr18:65363477-65363768(+)$1	291	163	169	13.4545
UGUGUG	chr8:74779973-74780331(+)$1	358	197	203	15.1212
GGUGUG	chr4:126289475-126289913(+)$1	438	143	149	14.4393
GGUGUG	chr8:96703944-96704318(+)$1	374	296	302	14.4393
GGUGUG	chr17:23960569-23960868(+)$1	299	30	36	14.4393
UGUGUG	chr8:13370985-13371453(+)$1	468	353	359	15.1212
CGUGUG	chr13:9694301-9694673(-)$1	372	126	132	13.4545
CGUGUG	chr3:33708169-33708451(+)$1	282	159	165	13.4545
AGUGUG	chr8:123196822-123197272(+)$1	450	3	9	13.9848
AGUGUG	chr8:96677724-96678057(+)$1	333	109	115	13.9848
UGUGUG	chr6:135681870-135682222(-)$1	352	14	20	15.1212
AGUGUG	chr19:32748514-32748902(-)$1	388	320	326	13.9848
AGUGUG	chr19:16760908-16761154(-)$1	246	136	142	13.9848
UGUGUG	chr18:10811902-10812391(+)$1	489	91	97	15.1212
GGUGUG	chr5:122910047-122910436(-)$1	389	240	246	14.4393
GGUGUG	chr11:30004540-30004907(-)$1	367	102	108	14.4393
GGUGUG	chr11:101178939-101179261(+)$1	322	99	105	14.4393

#otherMatches

#Struct PSSM
[bb[cc	chr2:90978134-90978606(-)$1	472	11	17	13.9848
a]ffff	chr2:167332502-167332848(+)$1	346	27	33	15.1212
ggggg6	chr15:100225326-100225762(-)$1	436	163	169	13.9848
!bbbb[	chr7:135117771-135118263(+)$1	492	331	337	15.1212
FFFFFF	chr8:56140035-56140294(+)$1	259	149	155	15.1212
iiimmm	chr5:145653792-145654141(-)$1	349	181	187	13.4545
gggggg	chr18:35024331-35024698(+)$1	367	265	271	14.4393
g"""gg	chr12:71373350-71373847(-)$1	497	203	209	14.4393
[fffff	chr1:9714311-9714703(-)$1	392	285	291	13.9848
gggggh	chr19:45871213-45871631(-)$1	418	117	123	13.9848
HHHHHH	chr9:67731244-67731576(+)$1	332	169	175	15.1212
DDDD}B	chr13:120167362-120167857(-)$1	495	208	214	14.4393
IIIIII	chr17:33783451-33783775(-)$1	324	140	146	13.4545
FFFFLL	chr3:89812042-89812351(-)$1	309	95	101	14.4393
e4444d	chr16:52305522-52305824(-)$1	302	91	97	15.1212
ddddoo	chr11:109522564-109522950(+)$1	386	120	126	15.1212
f333cc	chr10:31670723-31670965(-)$1	242	104	110	15.1212
hhh[bb	chr9:53400103-53400486(-)$1	383	95	101	15.1212
cccnnn	chr6:113441918-113442267(+)$1	349	208	214	13.9848
e:dddd	chr11:79329730-79330113(+)$1	383	94	100	15.1212
dd]ddd	chr11:5889986-5890273(-)$1	287	116	122	15.1212
d[eeee	chr17:86568130-86568477(+)$1	347	17	23	15.1212
fff]aH	chr7:71879400-71879781(+)$1	381	175	181	14.4393
====::	chr8:75216954-75217272(+)$1	318	89	95	15.1212
eeeeef	chr9:57376755-57377089(+)$1	334	210	216	15.1212
2eeeee	chr1:162125525-162125777(+)$1	252	94	100	14.4393
EEEEE{	chr18:61086262-61086760(+)$1	498	111	117	13.9848
ZFFFFF	chr13:55756328-55756766(+)$1	438	130	136	15.1212
EEEEE:	chr8:3161067-3161546(-)$1	479	207	213	14.4393
JJJJJJ	chr7:38781417-38781808(-)$1	391	186	192	14.4393
:::A{D	chr2:5812064-5812507(-)$1	443	0	6	15.1212
bb]a]b	chr12:81689361-81689577(+)$1	216	105	111	15.1212
bb[eee	chr4:46481519-46481867(+)$1	348	112	118	14.4393
dddbb3	chr10:79736946-79737326(+)$1	380	85	91	14.4393
bb[eee	chr10:59761746-59761997(+)$1	251	114	120	15.1212
CCC}BB	chr16:17506242-17506613(+)$1	371	194	200	14.4393
GGGG}B	chr5:148354363-148354769(+)$1	406	234	240	15.1212
cc]ccc	chr10:83073831-83074266(-)$1	435	148	154	13.4545
ddddqq	chr4:117225471-117225810(+)$1	339	84	90	15.1212
H{FFFF	chr4:58831798-58832237(-)$1	439	104	110	15.1212
55dddd	chr2:28309249-28309670(+)$1	421	172	178	15.1212
:fffff	chr3:152020918-152021299(+)$1	381	137	143	15.1212
DD{BBe	chr2:164824421-164824905(+)$1	484	20	26	14.4393
FF}III	chr18:40367294-40367581(-)$1	287	149	155	14.4393
88888c	chr15:100787913-100788347(+)$1	434	138	144	15.1212
B{JJJJ	chr8:47292623-47293054(-)$1	431	267	273	15.1212
bb]fff	chr12:118493955-118494365(+)$1	410	249	255	13.9848
oooccc	chr15:84533464-84533838(+)$1	374	105	111	13.9848
dddd[c	chr8:73055485-73055837(+)$1	352	63	69	13.9848
iiiii2	chr18:65363477-65363768(+)$1	291	163	169	13.4545
HHHHHH	chr8:74779973-74780331(+)$1	358	197	203	15.1212
:iiiii	chr4:126289475-126289913(+)$1	438	143	149	14.4393
cc]a]g	chr8:96703944-96704318(+)$1	374	296	302	14.4393
==]ddd	chr17:23960569-23960868(+)$1	299	30	36	14.4393
b[ccc[	chr8:13370985-13371453(+)$1	468	353	359	15.1212
fmmmmf	chr13:9694301-9694673(-)$1	372	126	132	13.4545
]hhhhh	chr3:33708169-33708451(+)$1	282	159	165	13.4545
iiiiii	chr8:123196822-123197272(+)$1	450	3	9	13.9848
]eeeee	chr8:96677724-96678057(+)$1	333	109	115	13.9848
eecccq	chr6:135681870-135682222(-)$1	352	14	20	15.1212
hhh]ee	chr19:32748514-32748902(-)$1	388	320	326	13.9848
gggggg	chr19:16760908-16761154(-)$1	246	136	142	13.9848
"dddd[	chr18:10811902-10812391(+)$1	489	91	97	15.1212
ffffff	chr5:122910047-122910436(-)$1	389	240	246	14.4393
ccceee	chr11:30004540-30004907(-)$1	367	102	108	14.4393
eeeegg	chr11:101178939-101179261(+)$1	322	99	105	14.4393

#DB
.((.((	chr2:90978134-90978606(-)$1	1	11	17	13.9848
).))))	chr2:167332502-167332848(+)$1	1	27	33	15.1212
))))).	chr15:100225326-100225762(-)$1	1	163	169	13.9848
.((((.	chr7:135117771-135118263(+)$1	1	331	337	15.1212
((((((	chr8:56140035-56140294(+)$1	1	149	155	15.1212
(((...	chr5:145653792-145654141(-)$1	1	181	187	13.4545
))))))	chr18:35024331-35024698(+)$1	1	265	271	14.4393
(...((	chr12:71373350-71373847(-)$1	1	203	209	14.4393
.(((((	chr1:9714311-9714703(-)$1	1	285	291	13.9848
))))))	chr19:45871213-45871631(-)$1	1	117	123	13.9848
))))))	chr9:67731244-67731576(+)$1	1	169	175	15.1212
)))).)	chr13:120167362-120167857(-)$1	1	208	214	14.4393
))))))	chr17:33783451-33783775(-)$1	1	140	146	13.4545
((((..	chr3:89812042-89812351(-)$1	1	95	101	14.4393
)....)	chr16:52305522-52305824(-)$1	1	91	97	15.1212
((((..	chr11:109522564-109522950(+)$1	1	120	126	15.1212
)...))	chr10:31670723-31670965(-)$1	1	104	110	15.1212
(((.((	chr9:53400103-53400486(-)$1	1	95	101	15.1212
(((...	chr6:113441918-113442267(+)$1	1	208	214	13.9848
).((((	chr11:79329730-79330113(+)$1	1	94	100	15.1212
)).)))	chr11:5889986-5890273(-)$1	1	116	122	15.1212
(.((((	chr17:86568130-86568477(+)$1	1	17	23	15.1212
))).)(	chr7:71879400-71879781(+)$1	1	175	181	14.4393
))))..	chr8:75216954-75217272(+)$1	1	89	95	15.1212
)))))(	chr9:57376755-57377089(+)$1	1	210	216	15.1212
.)))))	chr1:162125525-162125777(+)$1	1	94	100	14.4393
(((((.	chr18:61086262-61086760(+)$1	1	111	117	13.9848
.)))))	chr13:55756328-55756766(+)$1	1	130	136	15.1212
))))).	chr8:3161067-3161546(-)$1	1	207	213	14.4393
((((((	chr7:38781417-38781808(-)$1	1	186	192	14.4393
...(.(	chr2:5812064-5812507(-)$1	1	0	6	15.1212
)).).)	chr12:81689361-81689577(+)$1	1	105	111	15.1212
((.(((	chr4:46481519-46481867(+)$1	1	112	118	14.4393
))))).	chr10:79736946-79737326(+)$1	1	85	91	14.4393
((.(((	chr10:59761746-59761997(+)$1	1	114	120	15.1212
))).))	chr16:17506242-17506613(+)$1	1	194	200	14.4393
)))).)	chr5:148354363-148354769(+)$1	1	234	240	15.1212
)).)))	chr10:83073831-83074266(-)$1	1	148	154	13.4545
((((..	chr4:117225471-117225810(+)$1	1	84	90	15.1212
(.((((	chr4:58831798-58832237(-)$1	1	104	110	15.1212
..))))	chr2:28309249-28309670(+)$1	1	172	178	15.1212
.(((((	chr3:152020918-152021299(+)$1	1	137	143	15.1212
((.(((	chr2:164824421-164824905(+)$1	1	20	26	14.4393
)).)))	chr18:40367294-40367581(-)$1	1	149	155	14.4393
.....)	chr15:100787913-100788347(+)$1	1	138	144	15.1212
(.((((	chr8:47292623-47293054(-)$1	1	267	273	15.1212
)).)))	chr12:118493955-118494365(+)$1	1	249	255	13.9848
...)))	chr15:84533464-84533838(+)$1	1	105	111	13.9848
((((.(	chr8:73055485-73055837(+)$1	1	63	69	13.9848
))))).	chr18:65363477-65363768(+)$1	1	163	169	13.4545
))))))	chr8:74779973-74780331(+)$1	1	197	203	15.1212
.(((((	chr4:126289475-126289913(+)$1	1	143	149	14.4393
)).).)	chr8:96703944-96704318(+)$1	1	296	302	14.4393
)).)))	chr17:23960569-23960868(+)$1	1	30	36	14.4393
(.(((.	chr8:13370985-13371453(+)$1	1	353	359	15.1212
(....)	chr13:9694301-9694673(-)$1	1	126	132	13.4545
.)))))	chr3:33708169-33708451(+)$1	1	159	165	13.4545
((((((	chr8:123196822-123197272(+)$1	1	3	9	13.9848
.)))))	chr8:96677724-96678057(+)$1	1	109	115	13.9848
(((((.	chr6:135681870-135682222(-)$1	1	14	20	15.1212
))).))	chr19:32748514-32748902(-)$1	1	320	326	13.9848
))))))	chr19:16760908-16761154(-)$1	1	136	142	13.9848
.((((.	chr18:10811902-10812391(+)$1	1	91	97	15.1212
))))))	chr5:122910047-122910436(-)$1	1	240	246	14.4393
((((((	chr11:30004540-30004907(-)$1	1	102	108	14.4393
))))((	chr11:101178939-101179261(+)$1	1	99	105	14.4393

#PSSM
U : 0.36	G : 0.27	A : 0.19	C : 0.09	u : 0.06	g : 0.01	
G : 0.87	g : 0.12	
U : 0.87	u : 0.12	
G : 0.87	g : 0.12	
U : 0.87	u : 0.12	
G : 0.87	g : 0.12	

#score	960.2727272727269
#seq	66
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_CDS_m3_run1.nuc.txt

#NT
CAGCCAU	chr5:102339864-102340067(-)$1	203	10	17	12.6949
CAGCCCC	chr10:126921121-126921322(+)$1	201	57	64	13.1186
CAGGCCU	chr9:40610849-40611059(+)$1	210	175	182	12.4406
CAGGCCU	chr17:34870516-34870738(-)$1	222	201	208	12.4406
CAGGCCU	chr11:70483359-70483567(-)$1	208	11	18	12.4406
CACCCCU	chr2:121131153-121131362(+)$1	209	90	97	12.4406
CAGCCCA	chr4:64816856-64817077(+)$1	221	62	69	13.3728
CAGCCCU	chr2:102601103-102601303(+)$1	200	178	185	16.7627
CAGCCCC	chr12:86356196-86356413(+)$1	217	43	50	13.1186
CAGCCUU	chr4:133276649-133276854(-)$1	205	75	82	13.1186
CAGCCCA	chr7:29616141-29616368(+)$1	227	193	200	13.3728
CAGCCCU	chr3:129743879-129744094(-)$1	215	43	50	16.7627
CAGCCCU	chr5:131950837-131951042(-)$1	205	95	102	16.7627
UAGCCCU	chr11:31954954-31955157(+)$1	203	192	199	12.1864
CAGCCCA	chr17:32339021-32339239(-)$1	218	12	19	13.3728
CACCCCU	chr7:119480349-119480554(+)$1	205	167	174	12.4406
CAGCCCA	chr11:102085966-102086169(+)$1	203	23	30	13.3728
CAGCCUU	chr4:129689500-129689712(+)$1	212	110	117	13.1186
CUGCCCU	chr7:25807936-25808151(-)$1	215	207	214	12.2711
CAGCCCA	chr17:32339100-32339301(-)$1	201	74	81	13.3728
CAGCCUU	chr12:34051911-34052114(+)$1	203	4	11	13.1186
CAGUCCU	chr2:118256823-118257037(+)$1	214	125	132	12.3559
CCGCCCU	chr11:69639024-69639242(-)$1	218	113	120	12.3559
GAGCCCU	chr11:102266105-102266314(-)$1	209	41	48	12.1016
CAGCUCU	chr13:8885112-8885332(+)$1	220	86	93	13.2033
CAGCCAU	chr5:135857883-135858084(-)$1	201	173	180	12.6949
CAGCCCA	chr19:41676515-41676726(-)$1	211	52	59	13.3728
CAGCCCU	chr2:80346278-80346487(-)$1	209	25	32	16.7627
CAGCGCU	chr15:82201892-82202098(-)$1	206	11	18	12.7796
CAUCCCU	chr17:43592153-43592357(+)$1	204	87	94	12.3559
CACCCCU	chr2:25172234-25172438(-)$1	204	82	89	12.4406
CAGCCUU	chr4:80959340-80959557(-)$1	217	81	88	13.1186
CAGCUCU	chr18:37980591-37980793(+)$1	202	105	112	13.2033
CAGCCCU	chr8:97301891-97302101(+)$1	210	197	204	16.7627
CAGCCCC	chr4:133276481-133276682(-)$1	201	56	63	13.1186
CCGCCCU	chr8:123196549-123196758(+)$1	209	15	22	12.3559
CAGCUCU	chr11:76021501-76021704(+)$1	203	102	109	13.2033
CAGCACU	chr9:28804002-28804231(-)$1	229	167	174	13.0338
CAUCCCU	chr2:37656033-37656246(-)$1	213	87	94	12.3559
CAGCACU	chr15:82686748-82686970(-)$1	222	24	31	13.0338
CAGCACU	chr2:14882386-14882601(-)$1	215	94	101	13.0338
CAGCUCU	chr12:25562983-25563188(+)$1	205	90	97	13.2033
CAGCUCU	chr15:12763988-12764195(+)$1	207	138	145	13.2033
CAGCCUU	chr11:62142965-62143175(-)$1	210	63	70	13.1186
CAGCCCU	chrX:148315107-148315308(+)$1	201	79	86	16.7627
CAGCCCU	chr5:136111810-136112026(+)$1	216	20	27	16.7627
CAGCCCU	chr5:122252048-122252265(+)$1	217	165	172	16.7627
CAGCCCA	chr18:36807011-36807229(+)$1	218	11	18	13.3728
CAGCCCU	chr12:86337893-86338096(+)$1	203	89	96	16.7627
CAGCUCU	chr1:127769815-127770020(-)$1	205	26	33	13.2033
UAGCCCU	chr7:31307938-31308139(-)$1	201	186	193	12.1864
CAGCCUU	chr15:102111463-102111673(+)$1	210	34	41	13.1186
CGGCCCU	chr8:96528993-96529193(-)$1	200	133	140	12.3559
CAGCCUU	chr11:62143014-62143214(-)$1	200	102	109	13.1186
CAGUCCU	chr7:5049131-5049335(+)$1	204	124	131	12.3559
CAGCACU	chr1:148598850-148599084(+)$1	234	82	89	13.0338
CGGCCCU	chr9:61257679-61257898(+)$1	219	66	73	12.3559
CAGCCCG	chr12:106009939-106010149(-)$1	210	58	65	12.8644

#otherMatches

#Struct PSSM
ODDDDKK	chr12:88029108-88029339(+)$1	231	29	36	13.1186
""eeeee	chr5:102339864-102340067(-)$1	203	10	17	12.6949
22bb:::	chr10:126921121-126921322(+)$1	201	57	64	13.1186
eeeEEEE	chr9:40610849-40611059(+)$1	210	175	182	12.4406
DDDCCC}	chr17:34870516-34870738(-)$1	222	201	208	12.4406
eeeee$$	chr11:70483359-70483567(-)$1	208	11	18	12.4406
ggg:ggg	chr2:121131153-121131362(+)$1	209	90	97	12.4406
fff!!ee	chr4:64816856-64817077(+)$1	221	62	69	13.3728
gggggqq	chr2:102601103-102601303(+)$1	200	178	185	16.7627
4ccc]cc	chr12:86356196-86356413(+)$1	217	43	50	13.1186
^^bb333	chr4:133276649-133276854(-)$1	205	75	82	13.1186
mmmccc2	chr7:29616141-29616368(+)$1	227	193	200	13.3728
fffvvvv	chr3:129743879-129744094(-)$1	215	43	50	16.7627
ccc::::	chr5:131950837-131951042(-)$1	205	95	102	16.7627
rriiiii	chr11:31954954-31955157(+)$1	203	192	199	12.1864
ttccc::	chr17:32339021-32339239(-)$1	218	12	19	13.3728
wwwwwww	chr7:119480349-119480554(+)$1	205	167	174	12.4406
cccmmmm	chr11:102085966-102086169(+)$1	203	23	30	13.3728
c!!bbmm	chr4:129689500-129689712(+)$1	212	110	117	13.1186
GGGGG::	chr7:25807936-25808151(-)$1	215	207	214	12.2711
ttcccbb	chr17:32339100-32339301(-)$1	201	74	81	13.3728
HHHHHNN	chr12:34051911-34052114(+)$1	203	4	11	13.1186
22eeeee	chr2:118256823-118257037(+)$1	214	125	132	12.3559
dddccc[	chr11:69639024-69639242(-)$1	218	113	120	12.3559
eee!!ao	chr11:102266105-102266314(-)$1	209	41	48	12.1016
vvviiii	chr13:8885112-8885332(+)$1	220	86	93	13.2033
:::::::	chr5:135857883-135858084(-)$1	201	173	180	12.6949
dd:dddd	chr19:41676515-41676726(-)$1	211	52	59	13.3728
ccmmmmc	chr2:80346278-80346487(-)$1	209	25	32	16.7627
ddd:FFF	chr15:82201892-82202098(-)$1	206	11	18	12.7796
pppppdd	chr17:43592153-43592357(+)$1	204	87	94	12.3559
:::::dd	chr2:25172234-25172438(-)$1	204	82	89	12.4406
fff"""c	chr4:80959340-80959557(-)$1	217	81	88	13.1186
FFFFFF:	chr18:37980591-37980793(+)$1	202	105	112	13.2033
cbb]ddd	chr8:97301891-97302101(+)$1	210	197	204	16.7627
::ccc^^	chr4:133276481-133276682(-)$1	201	56	63	13.1186
NNNNFFF	chr8:123196549-123196758(+)$1	209	15	22	12.3559
ddddyyy	chr11:76021501-76021704(+)$1	203	102	109	13.2033
::::::c	chr9:28804002-28804231(-)$1	229	167	174	13.0338
:::::::	chr2:37656033-37656246(-)$1	213	87	94	12.3559
dssssss	chr15:82686748-82686970(-)$1	222	24	31	13.0338
c22eeee	chr2:14882386-14882601(-)$1	215	94	101	13.0338
>>>>>>>	chr12:25562983-25563188(+)$1	205	90	97	13.2033
:::::::	chr15:12763988-12764195(+)$1	207	138	145	13.2033
:::::::	chr11:62142965-62143175(-)$1	210	63	70	13.1186
ccc::::	chrX:148315107-148315308(+)$1	201	79	86	16.7627
fffff22	chr5:136111810-136112026(+)$1	216	20	27	16.7627
::bbnnn	chr5:122252048-122252265(+)$1	217	165	172	16.7627
E:::::e	chr18:36807011-36807229(+)$1	218	11	18	13.3728
[cccwww	chr12:86337893-86338096(+)$1	203	89	96	16.7627
HHHH:::	chr1:127769815-127770020(-)$1	205	26	33	13.2033
::cccmm	chr7:31307938-31308139(-)$1	201	186	193	12.1864
dddmmmm	chr15:102111463-102111673(+)$1	210	34	41	13.1186
:CCC:cc	chr8:96528993-96529193(-)$1	200	133	140	12.3559
ddd^^^^	chr11:62143014-62143214(-)$1	200	102	109	13.1186
EEEEZZZ	chr7:5049131-5049335(+)$1	204	124	131	12.3559
C:ccc""	chr1:148598850-148599084(+)$1	234	82	89	13.0338
DDDDLLL	chr9:61257679-61257898(+)$1	219	66	73	12.3559
[dddd[b	chr12:106009939-106010149(-)$1	210	58	65	12.8644

#DB
.((((..	chr12:88029108-88029339(+)$1	1	29	36	13.1186
..(((((	chr5:102339864-102340067(-)$1	1	10	17	12.6949
..))...	chr10:126921121-126921322(+)$1	1	57	64	13.1186
)))))))	chr9:40610849-40611059(+)$1	1	175	182	12.4406
)))))).	chr17:34870516-34870738(-)$1	1	201	208	12.4406
(((((..	chr11:70483359-70483567(-)$1	1	11	18	12.4406
))).(((	chr2:121131153-121131362(+)$1	1	90	97	12.4406
(((..((	chr4:64816856-64817077(+)$1	1	62	69	13.3728
(((((..	chr2:102601103-102601303(+)$1	1	178	185	16.7627
.))).))	chr12:86356196-86356413(+)$1	1	43	50	13.1186
..))...	chr4:133276649-133276854(-)$1	1	75	82	13.1186
...))).	chr7:29616141-29616368(+)$1	1	193	200	13.3728
(((....	chr3:129743879-129744094(-)$1	1	43	50	16.7627
)))....	chr5:131950837-131951042(-)$1	1	95	102	16.7627
..)))))	chr11:31954954-31955157(+)$1	1	192	199	12.1864
..)))..	chr17:32339021-32339239(-)$1	1	12	19	13.3728
.......	chr7:119480349-119480554(+)$1	1	167	174	12.4406
(((....	chr11:102085966-102086169(+)$1	1	23	30	13.3728
(..((..	chr4:129689500-129689712(+)$1	1	110	117	13.1186
)))))..	chr7:25807936-25808151(-)$1	1	207	214	12.2711
..)))))	chr17:32339100-32339301(-)$1	1	74	81	13.3728
(((((..	chr12:34051911-34052114(+)$1	1	4	11	13.1186
..)))))	chr2:118256823-118257037(+)$1	1	125	132	12.3559
((((((.	chr11:69639024-69639242(-)$1	1	113	120	12.3559
(((..(.	chr11:102266105-102266314(-)$1	1	41	48	12.1016
...))))	chr13:8885112-8885332(+)$1	1	86	93	13.2033
.......	chr5:135857883-135858084(-)$1	1	173	180	12.6949
)).((((	chr19:41676515-41676726(-)$1	1	52	59	13.3728
((....)	chr2:80346278-80346487(-)$1	1	25	32	16.7627
))).(((	chr15:82201892-82202098(-)$1	1	11	18	12.7796
.....))	chr17:43592153-43592357(+)$1	1	87	94	12.3559
.....((	chr2:25172234-25172438(-)$1	1	82	89	12.4406
(((...(	chr4:80959340-80959557(-)$1	1	81	88	13.1186
)))))).	chr18:37980591-37980793(+)$1	1	105	112	13.2033
))).)))	chr8:97301891-97302101(+)$1	1	197	204	16.7627
..(((..	chr4:133276481-133276682(-)$1	1	56	63	13.1186
....(((	chr8:123196549-123196758(+)$1	1	15	22	12.3559
((((...	chr11:76021501-76021704(+)$1	1	102	109	13.2033
......(	chr9:28804002-28804231(-)$1	1	167	174	13.0338
.......	chr2:37656033-37656246(-)$1	1	87	94	12.3559
(......	chr15:82686748-82686970(-)$1	1	24	31	13.0338
)..))))	chr2:14882386-14882601(-)$1	1	94	101	13.0338
.......	chr12:25562983-25563188(+)$1	1	90	97	13.2033
.......	chr15:12763988-12764195(+)$1	1	138	145	13.2033
.......	chr11:62142965-62143175(-)$1	1	63	70	13.1186
)))....	chrX:148315107-148315308(+)$1	1	79	86	16.7627
)))))..	chr5:136111810-136112026(+)$1	1	20	27	16.7627
..((...	chr5:122252048-122252265(+)$1	1	165	172	16.7627
(.....(	chr18:36807011-36807229(+)$1	1	11	18	13.3728
.(((...	chr12:86337893-86338096(+)$1	1	89	96	16.7627
((((...	chr1:127769815-127770020(-)$1	1	26	33	13.2033
..(((..	chr7:31307938-31308139(-)$1	1	186	193	12.1864
(((....	chr15:102111463-102111673(+)$1	1	34	41	13.1186
.))).((	chr8:96528993-96529193(-)$1	1	133	140	12.3559
(((....	chr11:62143014-62143214(-)$1	1	102	109	13.1186
))))...	chr7:5049131-5049335(+)$1	1	124	131	12.3559
).(((..	chr1:148598850-148599084(+)$1	1	82	89	13.0338
((((...	chr9:61257679-61257898(+)$1	1	66	73	12.3559
.((((.(	chr12:106009939-106010149(-)$1	1	58	65	12.8644

#PSSM
C : 0.94	U : 0.03	G : 0.01	
A : 0.91	C : 0.03	G : 0.03	U : 0.01	
G : 0.91	C : 0.05	U : 0.03	
C : 0.91	G : 0.05	U : 0.03	
C : 0.81	U : 0.10	A : 0.06	G : 0.01	
C : 0.84	U : 0.11	A : 0.03	
U : 0.79	A : 0.11	C : 0.06	G : 0.01	

#score	793.4067796610166
#seq	59
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_transcript_m3_run1.nuc.txt

#NT
aaaaaaa	chr13:94615440-94615675(+)$1	235	70	77	18.0000
AAAUAAA	chr7:20006710-20007002(+)$1	292	199	206	13.7272
GAAAAAA	chr17:10401024-10401259(-)$1	235	127	134	13.4545
AAAAAAA	chr17:10400882-10401122(-)$1	240	116	123	18.0000
aaaaaaa	chr17:55844360-55844595(-)$1	235	96	103	18.0000
AAAAAAA	chr13:83802224-83802482(+)$1	258	115	122	18.0000
AAAUAAA	chr15:93115081-93115316(-)$1	235	14	21	13.7272
AAAAAAA	chr16:31695327-31695562(+)$1	235	12	19	18.0000
aaaaaaa	chr9:50307974-50308209(+)$1	235	97	104	18.0000
AAAAUAA	chr2:76689541-76689776(-)$1	235	225	232	14.2727
AAAAAAA	chr5:51847943-51848179(-)$1	236	64	71	18.0000
AAGAAAA	chr19:6389709-6389944(+)$1	235	216	223	14.6363
GAAAAAA	chr1:196519479-196519714(+)$1	235	118	125	13.4545
aaaaaaa	chr1:134473175-134473411(-)$1	236	101	108	18.0000
AAAUAAA	chr18:34504828-34505089(-)$1	261	102	109	13.7272
AAAAGAA	chr7:91764019-91764255(-)$1	236	125	132	14.0909
AAAAAAA	chr4:33107028-33107268(+)$1	240	58	65	18.0000
AAGAAAA	chr9:102445317-102445562(+)$1	245	30	37	14.6363
AAAAAAA	chr5:68012977-68013215(-)$1	238	228	235	18.0000
AAACAAA	chr6:108772482-108772722(+)$1	240	38	45	13.6363
aaaaaaa	chr11:109530395-109530652(+)$1	257	65	72	18.0000
aaaaaaa	chr13:110214685-110214921(+)$1	236	102	109	18.0000
AAAAGAA	chr3:51321794-51322050(-)$1	256	211	218	14.0909
AAGAAAA	chr2:76594261-76594496(-)$1	235	14	21	14.6363
ACAAAAA	chr9:42772489-42772729(-)$1	240	142	149	13.2727
AAAACAA	chr2:152106383-152106623(+)$1	240	123	130	14.2727
AAAAAUA	chr5:108929627-108929862(+)$1	235	136	143	13.2727
AAAAAAA	chr2:6465641-6465886(-)$1	245	5	12	18.0000
AAAAAAA	chr7:107789095-107789330(+)$1	235	100	107	18.0000
UAAAAAA	chr5:20264762-20265003(-)$1	241	25	32	13.3636
AAAAUAA	chr9:120869215-120869478(+)$1	263	196	203	14.2727
AAAAAAA	chr15:7145780-7146022(+)$1	242	144	151	18.0000
AAACAAA	chr1:51084510-51084745(+)$1	235	20	27	13.6363
AAAAUAA	chr13:19684740-19684975(-)$1	235	40	47	14.2727
AAUAAAA	chr18:78021176-78021422(+)$1	246	55	62	14.2727
agaaaaa	chr11:40499480-40499715(-)$1	235	68	75	13.2727
aaaaaaa	chr2:38638133-38638370(-)$1	237	104	111	18.0000
aaaaaaa	chr8:74722366-74722601(+)$1	235	103	110	18.0000
AAAAAAA	chr15:37297729-37297964(-)$1	235	47	54	18.0000
AAAAAAA	chrX:39460266-39460511(+)$1	245	215	222	18.0000
AAAAAAA	chr6:30404407-30404667(+)$1	260	146	153	18.0000
AAAAUAA	chr3:116445886-116446121(-)$1	235	130	137	14.2727
AAUAAAA	chr15:38419438-38419673(-)$1	235	102	109	14.2727
AAAACAA	chr5:89088503-89088749(-)$1	246	8	15	14.2727
AAGAAAA	chr11:100643827-100644078(-)$1	251	23	30	14.6363
AAUAAAA	chr15:76001368-76001603(-)$1	235	177	184	14.2727
AAAACAA	chr16:94690321-94690556(+)$1	235	59	66	14.2727
AAAAAAA	chr16:7412188-7412449(+)$1	261	209	216	18.0000
AACAAAA	chr1:82892197-82892444(+)$1	247	28	35	14.0909
AAGAAAA	chr5:136386344-136386584(-)$1	240	30	37	14.6363
AAGAAAA	chr5:136386537-136386774(-)$1	237	220	227	14.6363
AAAAACA	chr10:77670618-77670856(-)$1	238	195	202	13.2727
AAGAAAA	chr5:29761756-29761991(+)$1	235	191	198	14.6363
aaaaaaa	chr11:35197248-35197483(+)$1	235	103	110	18.0000

#otherMatches

#Struct PSSM
f22ccc]	chr6:5435274-5435523(-)$1	249	160	167	14.2727
:::::::	chr13:94615440-94615675(+)$1	235	70	77	18.0000
^^^^^^^	chr7:20006710-20007002(+)$1	292	199	206	13.7272
ee:::::	chr17:10401024-10401259(-)$1	235	127	134	13.4545
gyyyyyy	chr17:10400882-10401122(-)$1	240	116	123	18.0000
:::::::	chr17:55844360-55844595(-)$1	235	96	103	18.0000
=======	chr13:83802224-83802482(+)$1	258	115	122	18.0000
ffffff!	chr15:93115081-93115316(-)$1	235	14	21	13.7272
:::::::	chr16:31695327-31695562(+)$1	235	12	19	18.0000
:::::::	chr9:50307974-50308209(+)$1	235	97	104	18.0000
:::::::	chr2:76689541-76689776(-)$1	235	225	232	14.2727
:::::::	chr5:51847943-51848179(-)$1	236	64	71	18.0000
HHHYYEE	chr19:6389709-6389944(+)$1	235	216	223	14.6363
eeee!!c	chr1:196519479-196519714(+)$1	235	118	125	13.4545
d::::::	chr1:134473175-134473411(-)$1	236	101	108	18.0000
c::::dd	chr18:34504828-34505089(-)$1	261	102	109	13.7272
hhhgggg	chr7:91764019-91764255(-)$1	236	125	132	14.0909
BB:::::	chr4:33107028-33107268(+)$1	240	58	65	18.0000
lccc:::	chr9:102445317-102445562(+)$1	245	30	37	14.6363
==:::::	chr5:68012977-68013215(-)$1	238	228	235	18.0000
GGGGG::	chr6:108772482-108772722(+)$1	240	38	45	13.6363
eeeeggg	chr11:109530395-109530652(+)$1	257	65	72	18.0000
^^^^^^^	chr13:110214685-110214921(+)$1	236	102	109	18.0000
:::::::	chr3:51321794-51322050(-)$1	256	211	218	14.0909
^^^^^^^	chr2:76594261-76594496(-)$1	235	14	21	14.6363
ccc!!cc	chr9:42772489-42772729(-)$1	240	142	149	13.2727
f&&&&&&	chr2:152106383-152106623(+)$1	240	123	130	14.2727
b[iiiii	chr5:108929627-108929862(+)$1	235	136	143	13.2727
:::::::	chr2:6465641-6465886(-)$1	245	5	12	18.0000
ggggggg	chr7:107789095-107789330(+)$1	235	100	107	18.0000
ff66666	chr5:20264762-20265003(-)$1	241	25	32	13.3636
flllfff	chr9:120869215-120869478(+)$1	263	196	203	14.2727
ppppppp	chr15:7145780-7146022(+)$1	242	144	151	18.0000
ttttttt	chr1:51084510-51084745(+)$1	235	20	27	13.6363
fff[bbm	chr13:19684740-19684975(-)$1	235	40	47	14.2727
==="""c	chr18:78021176-78021422(+)$1	246	55	62	14.2727
eccc"""	chr11:40499480-40499715(-)$1	235	68	75	13.2727
c::::::	chr2:38638133-38638370(-)$1	237	104	111	18.0000
oooooob	chr8:74722366-74722601(+)$1	235	103	110	18.0000
:::::::	chr15:37297729-37297964(-)$1	235	47	54	18.0000
:::::::	chrX:39460266-39460511(+)$1	245	215	222	18.0000
ftttttt	chr6:30404407-30404667(+)$1	260	146	153	18.0000
eeeeemm	chr3:116445886-116446121(-)$1	235	130	137	14.2727
fff333b	chr15:38419438-38419673(-)$1	235	102	109	14.2727
ooooa]d	chr5:89088503-89088749(-)$1	246	8	15	14.2727
:::::::	chr11:100643827-100644078(-)$1	251	23	30	14.6363
:::::::	chr15:76001368-76001603(-)$1	235	177	184	14.2727
dd%%%%%	chr16:94690321-94690556(+)$1	235	59	66	14.2727
:::::::	chr16:7412188-7412449(+)$1	261	209	216	18.0000
eeee###	chr1:82892197-82892444(+)$1	247	28	35	14.0909
GGGGG::	chr5:136386344-136386584(-)$1	240	30	37	14.6363
:::::::	chr5:136386537-136386774(-)$1	237	220	227	14.6363
CZZZDDD	chr10:77670618-77670856(-)$1	238	195	202	13.2727
'''''''	chr5:29761756-29761991(+)$1	235	191	198	14.6363
^^^^^^^	chr11:35197248-35197483(+)$1	235	103	110	18.0000

#DB
)..))).	chr6:5435274-5435523(-)$1	1	160	167	14.2727
.......	chr13:94615440-94615675(+)$1	1	70	77	18.0000
.......	chr7:20006710-20007002(+)$1	1	199	206	13.7272
)).....	chr17:10401024-10401259(-)$1	1	127	134	13.4545
(......	chr17:10400882-10401122(-)$1	1	116	123	18.0000
.......	chr17:55844360-55844595(-)$1	1	96	103	18.0000
)))))))	chr13:83802224-83802482(+)$1	1	115	122	18.0000
((((((.	chr15:93115081-93115316(-)$1	1	14	21	13.7272
.......	chr16:31695327-31695562(+)$1	1	12	19	18.0000
.......	chr9:50307974-50308209(+)$1	1	97	104	18.0000
.......	chr2:76689541-76689776(-)$1	1	225	232	14.2727
.......	chr5:51847943-51848179(-)$1	1	64	71	18.0000
)))..))	chr19:6389709-6389944(+)$1	1	216	223	14.6363
((((..(	chr1:196519479-196519714(+)$1	1	118	125	13.4545
)......	chr1:134473175-134473411(-)$1	1	101	108	18.0000
)....((	chr18:34504828-34505089(-)$1	1	102	109	13.7272
(((((((	chr7:91764019-91764255(-)$1	1	125	132	14.0909
)).....	chr4:33107028-33107268(+)$1	1	58	65	18.0000
.)))...	chr9:102445317-102445562(+)$1	1	30	37	14.6363
)).....	chr5:68012977-68013215(-)$1	1	228	235	18.0000
(((((..	chr6:108772482-108772722(+)$1	1	38	45	13.6363
))))(((	chr11:109530395-109530652(+)$1	1	65	72	18.0000
.......	chr13:110214685-110214921(+)$1	1	102	109	18.0000
.......	chr3:51321794-51322050(-)$1	1	211	218	14.0909
.......	chr2:76594261-76594496(-)$1	1	14	21	14.6363
(((..((	chr9:42772489-42772729(-)$1	1	142	149	13.2727
(......	chr2:152106383-152106623(+)$1	1	123	130	14.2727
(.(((((	chr5:108929627-108929862(+)$1	1	136	143	13.2727
.......	chr2:6465641-6465886(-)$1	1	5	12	18.0000
)))))))	chr7:107789095-107789330(+)$1	1	100	107	18.0000
)).....	chr5:20264762-20265003(-)$1	1	25	32	13.3636
(...)))	chr9:120869215-120869478(+)$1	1	196	203	14.2727
.......	chr15:7145780-7146022(+)$1	1	144	151	18.0000
.......	chr1:51084510-51084745(+)$1	1	20	27	13.6363
(((.((.	chr13:19684740-19684975(-)$1	1	40	47	14.2727
(((...(	chr18:78021176-78021422(+)$1	1	55	62	14.2727
((((...	chr11:40499480-40499715(-)$1	1	68	75	13.2727
)......	chr2:38638133-38638370(-)$1	1	104	111	18.0000
......)	chr8:74722366-74722601(+)$1	1	103	110	18.0000
.......	chr15:37297729-37297964(-)$1	1	47	54	18.0000
.......	chrX:39460266-39460511(+)$1	1	215	222	18.0000
(......	chr6:30404407-30404667(+)$1	1	146	153	18.0000
(((((..	chr3:116445886-116446121(-)$1	1	130	137	14.2727
)))...)	chr15:38419438-38419673(-)$1	1	102	109	14.2727
....).)	chr5:89088503-89088749(-)$1	1	8	15	14.2727
.......	chr11:100643827-100644078(-)$1	1	23	30	14.6363
.......	chr15:76001368-76001603(-)$1	1	177	184	14.2727
((.....	chr16:94690321-94690556(+)$1	1	59	66	14.2727
.......	chr16:7412188-7412449(+)$1	1	209	216	18.0000
((((...	chr1:82892197-82892444(+)$1	1	28	35	14.0909
(((((..	chr5:136386344-136386584(-)$1	1	30	37	14.6363
.......	chr5:136386537-136386774(-)$1	1	220	227	14.6363
)...)))	chr10:77670618-77670856(-)$1	1	195	202	13.2727
.......	chr5:29761756-29761991(+)$1	1	191	198	14.6363
.......	chr11:35197248-35197483(+)$1	1	103	110	18.0000

#PSSM
A : 0.76	a : 0.18	G : 0.03	U : 0.01	
A : 0.80	a : 0.16	C : 0.01	g : 0.01	
A : 0.61	a : 0.18	G : 0.12	U : 0.05	C : 0.01	
A : 0.72	a : 0.18	U : 0.05	C : 0.03	
A : 0.63	a : 0.18	C : 0.07	U : 0.07	G : 0.03	
A : 0.78	a : 0.18	U : 0.01	C : 0.01	
A : 0.81	a : 0.18	

#score	859.5454545454543
#seq	55
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_transcript_m1_run2.nuc.txt

#NT
CUUUU	chr11:104189542-104189789(+)$1	247	106	111	14.9999
cuUUU	chr15:36701296-36701535(-)$1	239	77	82	14.9999
CUUUU	chr14:125076015-125076258(-)$1	243	71	76	14.9999
CUUUU	chr8:26877734-26877997(-)$1	263	184	189	14.9999
CUUUU	chr2:71114420-71114661(-)$1	241	73	78	14.9999
CUUUU	chr18:38001076-38001388(+)$1	312	171	176	14.9999
CUUUU	chr12:36741632-36741870(-)$1	238	50	55	14.9999
CUUUU	chr7:129777608-129777871(+)$1	263	23	28	14.9999
CUUUU	chr18:25834619-25834855(-)$1	236	54	59	14.9999
CUUUU	chr2:138110216-138110475(+)$1	259	11	16	14.9999
CUUUU	chr6:119875376-119875652(-)$1	276	28	33	14.9999
CUUUU	chr1:33855577-33855826(-)$1	249	76	81	14.9999
CUUUU	chr1:137056758-137056993(-)$1	235	44	49	14.9999
CUUUU	chrX:10173074-10173327(+)$1	253	135	140	14.9999
CUUUU	chr5:108174394-108174647(-)$1	253	241	246	14.9999
CUUUU	chr5:72015103-72015349(-)$1	246	104	109	14.9999
CUUUU	chr14:105707647-105707891(+)$1	244	21	26	14.9999
CUUUU	chr4:101315261-101315505(+)$1	244	143	148	14.9999
CUUUU	chr18:35966507-35966742(+)$1	235	72	77	14.9999
CUUUU	chr13:110844350-110844643(-)$1	293	271	276	14.9999
CUUUU	chrX:72281005-72281242(-)$1	237	229	234	14.9999
CUUUU	chr2:49629814-49630108(+)$1	294	101	106	14.9999
CUUUU	chr11:90200168-90200404(-)$1	236	26	31	14.9999
CUUUU	chr18:63156896-63157151(+)$1	255	12	17	14.9999
CUUUU	chr16:11073439-11073687(+)$1	248	217	222	14.9999
CUUUU	chr6:86938092-86938327(+)$1	235	34	39	14.9999
CUUUU	chr5:122906744-122907038(-)$1	294	16	21	14.9999
CUUUU	chr2:136607325-136607639(+)$1	314	159	164	14.9999
CUUUU	chr14:21554054-21554291(-)$1	237	38	43	14.9999
CUUUU	chr15:31385705-31385946(-)$1	241	222	227	14.9999
CUUUU	chr12:83098107-83098365(+)$1	258	67	72	14.9999
CUUUU	chr19:56006994-56007230(+)$1	236	102	107	14.9999
CUUUU	chr7:95282990-95283248(+)$1	258	169	174	14.9999
CUUUU	chr12:75047608-75047865(+)$1	257	78	83	14.9999
CUUUU	chr11:17098232-17098536(+)$1	304	101	106	14.9999
CUUUU	chr1:138166113-138166350(-)$1	237	114	119	14.9999
CUUUU	chr2:6463507-6463747(-)$1	240	72	77	14.9999
CUUUU	chr1:59927431-59927675(+)$1	244	101	106	14.9999
CUUUU	chr2:73448726-73449004(-)$1	278	34	39	14.9999
CUUUU	chrX:132337691-132337929(+)$1	238	5	10	14.9999
CUUUU	chr2:60590243-60590486(-)$1	243	41	46	14.9999
CUUUU	chr10:82212054-82212289(-)$1	235	128	133	14.9999
CUUUU	chr14:120905707-120905981(+)$1	274	200	205	14.9999
CUUUU	chr17:66778884-66779119(-)$1	235	51	56	14.9999
CUUUU	chr2:66109220-66109464(-)$1	244	47	52	14.9999
CUUUU	chr18:37640171-37640406(+)$1	235	14	19	14.9999
CUUUU	chr4:59235119-59235379(+)$1	260	209	214	14.9999
CUUUU	chr5:108293699-108293934(-)$1	235	30	35	14.9999
CUUUU	chr16:84955258-84955558(-)$1	300	112	117	14.9999
CUUUU	chr4:136877878-136878142(-)$1	264	179	184	14.9999
CUUUU	chr3:130298173-130298419(+)$1	246	122	127	14.9999
CUUUU	chr3:146392708-146392999(-)$1	291	222	227	14.9999
CUUUU	chr11:87033311-87033548(+)$1	237	200	205	14.9999
CUUUU	chr18:77392919-77393155(+)$1	236	57	62	14.9999
CUUUU	chr2:70438993-70439272(+)$1	279	40	45	14.9999
CUUUU	chr14:63761175-63761477(+)$1	302	24	29	14.9999
CUUUU	chr3:146393690-146393925(-)$1	235	193	198	14.9999
CUUUU	chr4:138013083-138013383(+)$1	300	25	30	14.9999
CUUUU	chr7:17500915-17501177(-)$1	262	163	168	14.9999
CUUUU	chr2:136607209-136607513(+)$1	304	275	280	14.9999
CUUUU	chr19:7609581-7609819(+)$1	238	24	29	14.9999
CUUUU	chr3:7442427-7442692(+)$1	265	254	259	14.9999
CUUUU	chr2:157387822-157388057(+)$1	235	107	112	14.9999
cuuuu	chr15:31412540-31412775(-)$1	235	2	7	14.9999
CUUUU	chr2:38922172-38922415(-)$1	243	173	178	14.9999
CUUUU	chr11:6305792-6306046(+)$1	254	97	102	14.9999
CUUUU	chr16:64858493-64858732(+)$1	239	93	98	14.9999

#otherMatches

#Struct PSSM
cc::E	chr3:116446164-116446403(-)$1	239	79	84	14.9999
$$$$d	chr11:104189542-104189789(+)$1	247	106	111	14.9999
HHHH{	chr15:36701296-36701535(-)$1	239	77	82	14.9999
g4444	chr14:125076015-125076258(-)$1	243	71	76	14.9999
+++++	chr8:26877734-26877997(-)$1	263	184	189	14.9999
&&&&&	chr2:71114420-71114661(-)$1	241	73	78	14.9999
ggggg	chr18:38001076-38001388(+)$1	312	171	176	14.9999
JJJJJ	chr12:36741632-36741870(-)$1	238	50	55	14.9999
MMMCC	chr7:129777608-129777871(+)$1	263	23	28	14.9999
:::::	chr18:25834619-25834855(-)$1	236	54	59	14.9999
:::::	chr2:138110216-138110475(+)$1	259	11	16	14.9999
LJJJJ	chr6:119875376-119875652(-)$1	276	28	33	14.9999
:::::	chr1:33855577-33855826(-)$1	249	76	81	14.9999
:::::	chr1:137056758-137056993(-)$1	235	44	49	14.9999
oobb]	chrX:10173074-10173327(+)$1	253	135	140	14.9999
c::::	chr5:108174394-108174647(-)$1	253	241	246	14.9999
eeee[	chr5:72015103-72015349(-)$1	246	104	109	14.9999
JJJJJ	chr14:105707647-105707891(+)$1	244	21	26	14.9999
eeeee	chr4:101315261-101315505(+)$1	244	143	148	14.9999
cc%%%	chr18:35966507-35966742(+)$1	235	72	77	14.9999
::::C	chr13:110844350-110844643(-)$1	293	271	276	14.9999
:::::	chrX:72281005-72281242(-)$1	237	229	234	14.9999
eee22	chr2:49629814-49630108(+)$1	294	101	106	14.9999
##hhh	chr11:90200168-90200404(-)$1	236	26	31	14.9999
%%%%%	chr18:63156896-63157151(+)$1	255	12	17	14.9999
BBEEE	chr16:11073439-11073687(+)$1	248	217	222	14.9999
=====	chr6:86938092-86938327(+)$1	235	34	39	14.9999
FFggg	chr5:122906744-122907038(-)$1	294	16	21	14.9999
ooeee	chr2:136607325-136607639(+)$1	314	159	164	14.9999
ggggg	chr14:21554054-21554291(-)$1	237	38	43	14.9999
eee77	chr15:31385705-31385946(-)$1	241	222	227	14.9999
:::::	chr12:83098107-83098365(+)$1	258	67	72	14.9999
yyyyy	chr19:56006994-56007230(+)$1	236	102	107	14.9999
[dddd	chr7:95282990-95283248(+)$1	258	169	174	14.9999
333ff	chr12:75047608-75047865(+)$1	257	78	83	14.9999
ccc!!	chr11:17098232-17098536(+)$1	304	101	106	14.9999
ee:==	chr1:138166113-138166350(-)$1	237	114	119	14.9999
ggggg	chr2:6463507-6463747(-)$1	240	72	77	14.9999
HHHHH	chr1:59927431-59927675(+)$1	244	101	106	14.9999
b$$$$	chr2:73448726-73449004(-)$1	278	34	39	14.9999
:::::	chrX:132337691-132337929(+)$1	238	5	10	14.9999
dddd]	chr2:60590243-60590486(-)$1	243	41	46	14.9999
HH::=	chr10:82212054-82212289(-)$1	235	128	133	14.9999
YYGGG	chr14:120905707-120905981(+)$1	274	200	205	14.9999
nnnee	chr17:66778884-66779119(-)$1	235	51	56	14.9999
FFFFF	chr2:66109220-66109464(-)$1	244	47	52	14.9999
fffff	chr18:37640171-37640406(+)$1	235	14	19	14.9999
e7777	chr4:59235119-59235379(+)$1	260	209	214	14.9999
ggggg	chr5:108293699-108293934(-)$1	235	30	35	14.9999
]a22c	chr16:84955258-84955558(-)$1	300	112	117	14.9999
EEEEE	chr4:136877878-136878142(-)$1	264	179	184	14.9999
eeee#	chr3:130298173-130298419(+)$1	246	122	127	14.9999
FFFFF	chr3:146392708-146392999(-)$1	291	222	227	14.9999
dyyyy	chr11:87033311-87033548(+)$1	237	200	205	14.9999
ooooo	chr18:77392919-77393155(+)$1	236	57	62	14.9999
a!!cc	chr2:70438993-70439272(+)$1	279	40	45	14.9999
ee:::	chr14:63761175-63761477(+)$1	302	24	29	14.9999
88888	chr3:146393690-146393925(-)$1	235	193	198	14.9999
sssss	chr4:138013083-138013383(+)$1	300	25	30	14.9999
ff555	chr7:17500915-17501177(-)$1	262	163	168	14.9999
B}CCC	chr2:136607209-136607513(+)$1	304	275	280	14.9999
ttttt	chr19:7609581-7609819(+)$1	238	24	29	14.9999
JJJJJ	chr3:7442427-7442692(+)$1	265	254	259	14.9999
IIIII	chr2:157387822-157388057(+)$1	235	107	112	14.9999
BKKHH	chr15:31412540-31412775(-)$1	235	2	7	14.9999
[bbdd	chr2:38922172-38922415(-)$1	243	173	178	14.9999
aoooo	chr11:6305792-6306046(+)$1	254	97	102	14.9999
fffff	chr16:64858493-64858732(+)$1	239	93	98	14.9999

#DB
))..)	chr3:116446164-116446403(-)$1	1	79	84	14.9999
....(	chr11:104189542-104189789(+)$1	1	106	111	14.9999
((((.	chr15:36701296-36701535(-)$1	1	77	82	14.9999
)....	chr14:125076015-125076258(-)$1	1	71	76	14.9999
.....	chr8:26877734-26877997(-)$1	1	184	189	14.9999
.....	chr2:71114420-71114661(-)$1	1	73	78	14.9999
)))))	chr18:38001076-38001388(+)$1	1	171	176	14.9999
(((((	chr12:36741632-36741870(-)$1	1	50	55	14.9999
...((	chr7:129777608-129777871(+)$1	1	23	28	14.9999
.....	chr18:25834619-25834855(-)$1	1	54	59	14.9999
.....	chr2:138110216-138110475(+)$1	1	11	16	14.9999
.((((	chr6:119875376-119875652(-)$1	1	28	33	14.9999
.....	chr1:33855577-33855826(-)$1	1	76	81	14.9999
.....	chr1:137056758-137056993(-)$1	1	44	49	14.9999
..)).	chrX:10173074-10173327(+)$1	1	135	140	14.9999
)....	chr5:108174394-108174647(-)$1	1	241	246	14.9999
((((.	chr5:72015103-72015349(-)$1	1	104	109	14.9999
(((((	chr14:105707647-105707891(+)$1	1	21	26	14.9999
)))))	chr4:101315261-101315505(+)$1	1	143	148	14.9999
((...	chr18:35966507-35966742(+)$1	1	72	77	14.9999
....)	chr13:110844350-110844643(-)$1	1	271	276	14.9999
.....	chrX:72281005-72281242(-)$1	1	229	234	14.9999
)))..	chr2:49629814-49630108(+)$1	1	101	106	14.9999
..(((	chr11:90200168-90200404(-)$1	1	26	31	14.9999
.....	chr18:63156896-63157151(+)$1	1	12	17	14.9999
)))))	chr16:11073439-11073687(+)$1	1	217	222	14.9999
(((((	chr6:86938092-86938327(+)$1	1	34	39	14.9999
(((((	chr5:122906744-122907038(-)$1	1	16	21	14.9999
..)))	chr2:136607325-136607639(+)$1	1	159	164	14.9999
(((((	chr14:21554054-21554291(-)$1	1	38	43	14.9999
)))..	chr15:31385705-31385946(-)$1	1	222	227	14.9999
.....	chr12:83098107-83098365(+)$1	1	67	72	14.9999
.....	chr19:56006994-56007230(+)$1	1	102	107	14.9999
.((((	chr7:95282990-95283248(+)$1	1	169	174	14.9999
...))	chr12:75047608-75047865(+)$1	1	78	83	14.9999
(((..	chr11:17098232-17098536(+)$1	1	101	106	14.9999
)).((	chr1:138166113-138166350(-)$1	1	114	119	14.9999
)))))	chr2:6463507-6463747(-)$1	1	72	77	14.9999
(((((	chr1:59927431-59927675(+)$1	1	101	106	14.9999
(....	chr2:73448726-73449004(-)$1	1	34	39	14.9999
.....	chrX:132337691-132337929(+)$1	1	5	10	14.9999
)))).	chr2:60590243-60590486(-)$1	1	41	46	14.9999
))..(	chr10:82212054-82212289(-)$1	1	128	133	14.9999
..)))	chr14:120905707-120905981(+)$1	1	200	205	14.9999
...))	chr17:66778884-66779119(-)$1	1	51	56	14.9999
(((((	chr2:66109220-66109464(-)$1	1	47	52	14.9999
)))))	chr18:37640171-37640406(+)$1	1	14	19	14.9999
)....	chr4:59235119-59235379(+)$1	1	209	214	14.9999
)))))	chr5:108293699-108293934(-)$1	1	30	35	14.9999
.)..)	chr16:84955258-84955558(-)$1	1	112	117	14.9999
)))))	chr4:136877878-136878142(-)$1	1	179	184	14.9999
((((.	chr3:130298173-130298419(+)$1	1	122	127	14.9999
)))))	chr3:146392708-146392999(-)$1	1	222	227	14.9999
(....	chr11:87033311-87033548(+)$1	1	200	205	14.9999
.....	chr18:77392919-77393155(+)$1	1	57	62	14.9999
(..((	chr2:70438993-70439272(+)$1	1	40	45	14.9999
))...	chr14:63761175-63761477(+)$1	1	24	29	14.9999
.....	chr3:146393690-146393925(-)$1	1	193	198	14.9999
.....	chr4:138013083-138013383(+)$1	1	25	30	14.9999
))...	chr7:17500915-17501177(-)$1	1	163	168	14.9999
).)))	chr2:136607209-136607513(+)$1	1	275	280	14.9999
.....	chr19:7609581-7609819(+)$1	1	24	29	14.9999
)))))	chr3:7442427-7442692(+)$1	1	254	259	14.9999
)))))	chr2:157387822-157388057(+)$1	1	107	112	14.9999
(..((	chr15:31412540-31412775(-)$1	1	2	7	14.9999
.((((	chr2:38922172-38922415(-)$1	1	173	178	14.9999
(....	chr11:6305792-6306046(+)$1	1	97	102	14.9999
)))))	chr16:64858493-64858732(+)$1	1	93	98	14.9999

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

#score	1019.9999999999995
#seq	68
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m1_run2.nuc.txt

#NT
CUGC	chr19:46139755-46139986(+)$1	231	116	120	11.9999
CUGC	chr2:172828979-172829202(+)$1	223	152	156	11.9999
CUGC	chr1:196620542-196620804(+)$1	262	43	47	11.9999
CUGC	chr7:26507831-26508080(-)$1	249	146	150	11.9999
CUGC	chr18:38777197-38777419(+)$1	222	160	164	11.9999
CUGC	chr10:104807433-104807661(-)$1	228	27	31	11.9999
CUGC	chr8:41393468-41393685(+)$1	217	27	31	11.9999
CUGC	chr10:86267582-86267809(+)$1	227	96	100	11.9999
CUGC	chr16:16923995-16924224(+)$1	229	6	10	11.9999
CUGC	chr2:127056188-127056412(+)$1	224	17	21	11.9999
CUGC	chr6:120324877-120325105(+)$1	228	35	39	11.9999
CUGC	chr8:24048538-24048762(+)$1	224	111	115	11.9999
CUGC	chr14:60665397-60665625(-)$1	228	90	94	11.9999
CUGC	chr11:78161261-78161485(+)$1	224	106	110	11.9999
CUGC	chr16:4875744-4875968(-)$1	224	121	125	11.9999
CUGC	chrX:7850863-7851088(+)$1	225	42	46	11.9999
CUGC	chr5:140828076-140828304(-)$1	228	79	83	11.9999
CUGC	chr10:36860533-36860760(-)$1	227	54	58	11.9999
CUGC	chr9:108199468-108199694(+)$1	226	68	72	11.9999
CUGC	chr19:10551982-10552205(+)$1	223	0	4	11.9999
CUGC	chr15:98674635-98674874(-)$1	239	0	4	11.9999
CUGC	chr8:87568530-87568751(+)$1	221	69	73	11.9999
CUGC	chr17:36068053-36068277(+)$1	224	22	26	11.9999
CUGC	chr18:43493482-43493709(-)$1	227	45	49	11.9999
CUGC	chr2:49134074-49134305(+)$1	231	146	150	11.9999
CUGC	chr11:69591514-69591735(-)$1	221	211	215	11.9999
CUGC	chr17:25965278-25965500(+)$1	222	111	115	11.9999
CUGC	chr4:98884719-98884942(+)$1	223	105	109	11.9999
CUGC	chr3:87779971-87780192(-)$1	221	52	56	11.9999
CUGC	chr4:41137602-41137838(+)$1	236	107	111	11.9999
CUGC	chr4:41662148-41662373(+)$1	225	18	22	11.9999
CUGC	chr3:55051173-55051407(+)$1	234	12	16	11.9999
CUGC	chr8:93933031-93933261(+)$1	230	147	151	11.9999
CUGC	chr6:38768162-38768388(-)$1	226	127	131	11.9999
CUGC	chr4:115765467-115765698(+)$1	231	86	90	11.9999
CUGC	chr1:132835414-132835635(-)$1	221	9	13	11.9999
CUGC	chr9:40845515-40845763(-)$1	248	175	179	11.9999
CUGC	chr4:107300112-107300330(-)$1	218	6	10	11.9999
CUGC	chr16:93690806-93691028(+)$1	222	32	36	11.9999
CUGC	chr1:54549989-54550208(-)$1	219	83	87	11.9999
CUGC	chr3:95702698-95702915(+)$1	217	179	183	11.9999
CUGC	chr7:86502908-86503125(+)$1	217	36	40	11.9999
CUGC	chr15:81208089-81208320(-)$1	231	121	125	11.9999
CUGC	chr7:148250287-148250510(+)$1	223	89	93	11.9999
CUGC	chr5:92838223-92838438(-)$1	215	19	23	11.9999
CUGC	chr4:88366402-88366636(-)$1	234	182	186	11.9999
CUGC	chr10:9531995-9532218(-)$1	223	108	112	11.9999
CUGC	chr15:76286112-76286332(+)$1	220	62	66	11.9999
CUGC	chr2:120360178-120360423(-)$1	245	15	19	11.9999
CUGC	chr19:4324522-4324764(-)$1	242	117	121	11.9999
CUGC	chr17:56740543-56740765(+)$1	222	16	20	11.9999
CUGC	chr2:124489699-124489922(+)$1	223	121	125	11.9999
CUGC	chr8:4191233-4191455(+)$1	222	105	109	11.9999
CUGC	chr8:13122713-13122936(+)$1	223	72	76	11.9999
CUGC	chr5:20277925-20278161(-)$1	236	33	37	11.9999
CUGC	chr11:105870232-105870451(+)$1	219	27	31	11.9999
CUGC	chr10:93046109-93046348(+)$1	239	193	197	11.9999
CUGC	chr12:86381786-86382010(+)$1	224	13	17	11.9999
CUGC	chr8:111480246-111480481(+)$1	235	53	57	11.9999
CUGC	chr15:98867677-98867908(+)$1	231	128	132	11.9999
CUGC	chr9:48640306-48640527(+)$1	221	31	35	11.9999
CUGC	chr7:135285319-135285534(+)$1	215	41	45	11.9999
CUGC	chr7:105789977-105790213(-)$1	236	118	122	11.9999
CUGC	chr3:96363554-96363778(+)$1	224	180	184	11.9999
CUGC	chr12:8282568-8282790(+)$1	222	51	55	11.9999
CUGC	chr17:10405369-10405589(-)$1	220	30	34	11.9999
CUGC	chr13:109461453-109461674(-)$1	221	21	25	11.9999
CUGC	chr11:77790939-77791165(+)$1	226	111	115	11.9999
CUGC	chr3:5403867-5404115(+)$1	248	74	78	11.9999
CUGC	chr19:34050928-34051150(-)$1	222	144	148	11.9999
CUGC	chr15:7870472-7870698(-)$1	226	20	24	11.9999
CUGC	chr1:176539179-176539405(+)$1	226	30	34	11.9999
CUGC	chr8:72639069-72639295(-)$1	226	78	82	11.9999
CUGC	chr10:127751206-127751430(+)$1	224	35	39	11.9999
CUGC	chr1:24619147-24619370(-)$1	223	34	38	11.9999
CUGC	chr6:122402601-122402828(-)$1	227	124	128	11.9999
CUGC	chr19:60011772-60011992(-)$1	220	141	145	11.9999
CUGC	chr18:38417583-38417805(+)$1	222	62	66	11.9999
CUGC	chr4:114696272-114696497(+)$1	225	34	38	11.9999
CUGC	chr13:85366447-85366672(+)$1	225	5	9	11.9999
CUGC	chr19:40683656-40683882(-)$1	226	120	124	11.9999
CUGC	chr11:59188971-59189187(-)$1	216	21	25	11.9999
CUGC	chr2:158201896-158202129(+)$1	233	90	94	11.9999

#otherMatches

#Struct PSSM
::A{	chr8:4206066-4206288(-)$1	222	6	10	11.9999
eeee	chr19:46139755-46139986(+)$1	231	116	120	11.9999
"eee	chr2:172828979-172829202(+)$1	223	152	156	11.9999
fppp	chr1:196620542-196620804(+)$1	262	43	47	11.9999
bb[b	chr7:26507831-26508080(-)$1	249	146	150	11.9999
ccCC	chr18:38777197-38777419(+)$1	222	160	164	11.9999
EEEE	chr10:104807433-104807661(-)$1	228	27	31	11.9999
CCC{	chr8:41393468-41393685(+)$1	217	27	31	11.9999
ccc2	chr10:86267582-86267809(+)$1	227	96	100	11.9999
KKBB	chr16:16923995-16924224(+)$1	229	6	10	11.9999
""bb	chr2:127056188-127056412(+)$1	224	17	21	11.9999
BBDD	chr6:120324877-120325105(+)$1	228	35	39	11.9999
cccc	chr8:24048538-24048762(+)$1	224	111	115	11.9999
]bb]	chr14:60665397-60665625(-)$1	228	90	94	11.9999
{JJJ	chr11:78161261-78161485(+)$1	224	106	110	11.9999
ggg#	chr16:4875744-4875968(-)$1	224	121	125	11.9999
eee]	chrX:7850863-7851088(+)$1	225	42	46	11.9999
mmdd	chr5:140828076-140828304(-)$1	228	79	83	11.9999
cc((	chr10:36860533-36860760(-)$1	227	54	58	11.9999
d[bb	chr9:108199468-108199694(+)$1	226	68	72	11.9999
DDDD	chr19:10551982-10552205(+)$1	223	0	4	11.9999
eeee	chr15:98674635-98674874(-)$1	239	0	4	11.9999
gggg	chr8:87568530-87568751(+)$1	221	69	73	11.9999
::BB	chr17:36068053-36068277(+)$1	224	22	26	11.9999
###b	chr18:43493482-43493709(-)$1	227	45	49	11.9999
HHHH	chr2:49134074-49134305(+)$1	231	146	150	11.9999
YYBB	chr11:69591514-69591735(-)$1	221	211	215	11.9999
33bb	chr17:25965278-25965500(+)$1	222	111	115	11.9999
eeee	chr4:98884719-98884942(+)$1	223	105	109	11.9999
''cc	chr3:87779971-87780192(-)$1	221	52	56	11.9999
cccE	chr4:41137602-41137838(+)$1	236	107	111	11.9999
cc$$	chr4:41662148-41662373(+)$1	225	18	22	11.9999
nnbb	chr3:55051173-55051407(+)$1	234	12	16	11.9999
eeee	chr8:93933031-93933261(+)$1	230	147	151	11.9999
ccdd	chr6:38768162-38768388(-)$1	226	127	131	11.9999
lldd	chr4:115765467-115765698(+)$1	231	86	90	11.9999
oddd	chr1:132835414-132835635(-)$1	221	9	13	11.9999
ccc:	chr9:40845515-40845763(-)$1	248	175	179	11.9999
""dd	chr4:107300112-107300330(-)$1	218	6	10	11.9999
ffff	chr16:93690806-93691028(+)$1	222	32	36	11.9999
==55	chr1:54549989-54550208(-)$1	219	83	87	11.9999
[ggg	chr3:95702698-95702915(+)$1	217	179	183	11.9999
ddd]	chr7:86502908-86503125(+)$1	217	36	40	11.9999
cc44	chr15:81208089-81208320(-)$1	231	121	125	11.9999
fff[	chr7:148250287-148250510(+)$1	223	89	93	11.9999
HHHH	chr5:92838223-92838438(-)$1	215	19	23	11.9999
dd[b	chr4:88366402-88366636(-)$1	234	182	186	11.9999
c[cc	chr10:9531995-9532218(-)$1	223	108	112	11.9999
dddd	chr15:76286112-76286332(+)$1	220	62	66	11.9999
:DDD	chr2:120360178-120360423(-)$1	245	15	19	11.9999
EEEE	chr19:4324522-4324764(-)$1	242	117	121	11.9999
%eee	chr17:56740543-56740765(+)$1	222	16	20	11.9999
ffff	chr2:124489699-124489922(+)$1	223	121	125	11.9999
::ee	chr8:4191233-4191455(+)$1	222	105	109	11.9999
lldd	chr8:13122713-13122936(+)$1	223	72	76	11.9999
bddd	chr5:20277925-20278161(-)$1	236	33	37	11.9999
d"""	chr11:105870232-105870451(+)$1	219	27	31	11.9999
CCee	chr10:93046109-93046348(+)$1	239	193	197	11.9999
====	chr12:86381786-86382010(+)$1	224	13	17	11.9999
Feee	chr8:111480246-111480481(+)$1	235	53	57	11.9999
cccp	chr15:98867677-98867908(+)$1	231	128	132	11.9999
::ee	chr9:48640306-48640527(+)$1	221	31	35	11.9999
mmmm	chr7:135285319-135285534(+)$1	215	41	45	11.9999
fccc	chr7:105789977-105790213(-)$1	236	118	122	11.9999
eeee	chr3:96363554-96363778(+)$1	224	180	184	11.9999
a]cc	chr12:8282568-8282790(+)$1	222	51	55	11.9999
eeeq	chr17:10405369-10405589(-)$1	220	30	34	11.9999
ppgg	chr13:109461453-109461674(-)$1	221	21	25	11.9999
::bb	chr11:77790939-77791165(+)$1	226	111	115	11.9999
tddd	chr3:5403867-5404115(+)$1	248	74	78	11.9999
rrrr	chr19:34050928-34051150(-)$1	222	144	148	11.9999
EEEE	chr15:7870472-7870698(-)$1	226	20	24	11.9999
ddd"	chr1:176539179-176539405(+)$1	226	30	34	11.9999
cccg	chr8:72639069-72639295(-)$1	226	78	82	11.9999
eeee	chr10:127751206-127751430(+)$1	224	35	39	11.9999
leee	chr1:24619147-24619370(-)$1	223	34	38	11.9999
>>>>	chr6:122402601-122402828(-)$1	227	124	128	11.9999
eeee	chr19:60011772-60011992(-)$1	220	141	145	11.9999
ddd#	chr18:38417583-38417805(+)$1	222	62	66	11.9999
Cfff	chr4:114696272-114696497(+)$1	225	34	38	11.9999
EIII	chr13:85366447-85366672(+)$1	225	5	9	11.9999
fff2	chr19:40683656-40683882(-)$1	226	120	124	11.9999
deee	chr11:59188971-59189187(-)$1	216	21	25	11.9999
BHHH	chr2:158201896-158202129(+)$1	233	90	94	11.9999

#DB
..(.	chr8:4206066-4206288(-)$1	1	6	10	11.9999
))))	chr19:46139755-46139986(+)$1	1	116	120	11.9999
.(((	chr2:172828979-172829202(+)$1	1	152	156	11.9999
(...	chr1:196620542-196620804(+)$1	1	43	47	11.9999
((.(	chr7:26507831-26508080(-)$1	1	146	150	11.9999
))))	chr18:38777197-38777419(+)$1	1	160	164	11.9999
((((	chr10:104807433-104807661(-)$1	1	27	31	11.9999
(((.	chr8:41393468-41393685(+)$1	1	27	31	11.9999
))).	chr10:86267582-86267809(+)$1	1	96	100	11.9999
..((	chr16:16923995-16924224(+)$1	1	6	10	11.9999
..((	chr2:127056188-127056412(+)$1	1	17	21	11.9999
((((	chr6:120324877-120325105(+)$1	1	35	39	11.9999
((((	chr8:24048538-24048762(+)$1	1	111	115	11.9999
.)).	chr14:60665397-60665625(-)$1	1	90	94	11.9999
.(((	chr11:78161261-78161485(+)$1	1	106	110	11.9999
(((.	chr16:4875744-4875968(-)$1	1	121	125	11.9999
))).	chrX:7850863-7851088(+)$1	1	42	46	11.9999
..))	chr5:140828076-140828304(-)$1	1	79	83	11.9999
((..	chr10:36860533-36860760(-)$1	1	54	58	11.9999
(.((	chr9:108199468-108199694(+)$1	1	68	72	11.9999
((((	chr19:10551982-10552205(+)$1	1	0	4	11.9999
((((	chr15:98674635-98674874(-)$1	1	0	4	11.9999
((((	chr8:87568530-87568751(+)$1	1	69	73	11.9999
..((	chr17:36068053-36068277(+)$1	1	22	26	11.9999
...(	chr18:43493482-43493709(-)$1	1	45	49	11.9999
))))	chr2:49134074-49134305(+)$1	1	146	150	11.9999
..))	chr11:69591514-69591735(-)$1	1	211	215	11.9999
..))	chr17:25965278-25965500(+)$1	1	111	115	11.9999
((((	chr4:98884719-98884942(+)$1	1	105	109	11.9999
..((	chr3:87779971-87780192(-)$1	1	52	56	11.9999
)))(	chr4:41137602-41137838(+)$1	1	107	111	11.9999
((..	chr4:41662148-41662373(+)$1	1	18	22	11.9999
..))	chr3:55051173-55051407(+)$1	1	12	16	11.9999
))))	chr8:93933031-93933261(+)$1	1	147	151	11.9999
))))	chr6:38768162-38768388(-)$1	1	127	131	11.9999
..))	chr4:115765467-115765698(+)$1	1	86	90	11.9999
.)))	chr1:132835414-132835635(-)$1	1	9	13	11.9999
))).	chr9:40845515-40845763(-)$1	1	175	179	11.9999
..((	chr4:107300112-107300330(-)$1	1	6	10	11.9999
))))	chr16:93690806-93691028(+)$1	1	32	36	11.9999
))..	chr1:54549989-54550208(-)$1	1	83	87	11.9999
.(((	chr3:95702698-95702915(+)$1	1	179	183	11.9999
))).	chr7:86502908-86503125(+)$1	1	36	40	11.9999
))..	chr15:81208089-81208320(-)$1	1	121	125	11.9999
(((.	chr7:148250287-148250510(+)$1	1	89	93	11.9999
((((	chr5:92838223-92838438(-)$1	1	19	23	11.9999
((.(	chr4:88366402-88366636(-)$1	1	182	186	11.9999
(.((	chr10:9531995-9532218(-)$1	1	108	112	11.9999
((((	chr15:76286112-76286332(+)$1	1	62	66	11.9999
.(((	chr2:120360178-120360423(-)$1	1	15	19	11.9999
))))	chr19:4324522-4324764(-)$1	1	117	121	11.9999
.(((	chr17:56740543-56740765(+)$1	1	16	20	11.9999
((((	chr2:124489699-124489922(+)$1	1	121	125	11.9999
..((	chr8:4191233-4191455(+)$1	1	105	109	11.9999
..))	chr8:13122713-13122936(+)$1	1	72	76	11.9999
))))	chr5:20277925-20278161(-)$1	1	33	37	11.9999
(...	chr11:105870232-105870451(+)$1	1	27	31	11.9999
))((	chr10:93046109-93046348(+)$1	1	193	197	11.9999
((((	chr12:86381786-86382010(+)$1	1	13	17	11.9999
((((	chr8:111480246-111480481(+)$1	1	53	57	11.9999
(((.	chr15:98867677-98867908(+)$1	1	128	132	11.9999
..((	chr9:48640306-48640527(+)$1	1	31	35	11.9999
....	chr7:135285319-135285534(+)$1	1	41	45	11.9999
))))	chr7:105789977-105790213(-)$1	1	118	122	11.9999
))))	chr3:96363554-96363778(+)$1	1	180	184	11.9999
).))	chr12:8282568-8282790(+)$1	1	51	55	11.9999
(((.	chr17:10405369-10405589(-)$1	1	30	34	11.9999
..))	chr13:109461453-109461674(-)$1	1	21	25	11.9999
..((	chr11:77790939-77791165(+)$1	1	111	115	11.9999
.)))	chr3:5403867-5404115(+)$1	1	74	78	11.9999
....	chr19:34050928-34051150(-)$1	1	144	148	11.9999
((((	chr15:7870472-7870698(-)$1	1	20	24	11.9999
(((.	chr1:176539179-176539405(+)$1	1	30	34	11.9999
))))	chr8:72639069-72639295(-)$1	1	78	82	11.9999
))))	chr10:127751206-127751430(+)$1	1	35	39	11.9999
.)))	chr1:24619147-24619370(-)$1	1	34	38	11.9999
....	chr6:122402601-122402828(-)$1	1	124	128	11.9999
))))	chr19:60011772-60011992(-)$1	1	141	145	11.9999
(((.	chr18:38417583-38417805(+)$1	1	62	66	11.9999
((((	chr4:114696272-114696497(+)$1	1	34	38	11.9999
((((	chr13:85366447-85366672(+)$1	1	5	9	11.9999
))).	chr19:40683656-40683882(-)$1	1	120	124	11.9999
)(((	chr11:59188971-59189187(-)$1	1	21	25	11.9999
))))	chr2:158201896-158202129(+)$1	1	90	94	11.9999

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

#score	1007.9999999999995
#seq	84
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m3_run2.nuc.txt

#NT
GAU	chr2:181041975-181042222(-)$1	247	71	74	9.0000
GAU	chr19:7289793-7290030(-)$1	237	29	32	9.0000
GAU	chr10:53063680-53063917(+)$1	237	105	108	9.0000
GAU	chr11:59220569-59220827(-)$1	258	110	113	9.0000
GAU	chr5:34186114-34186353(+)$1	239	122	125	9.0000
GAU	chr1:174210640-174210877(-)$1	237	43	46	9.0000
GAU	chr9:66883791-66884029(-)$1	238	151	154	9.0000
GAU	chr11:115667985-115668222(-)$1	237	4	7	9.0000
GAU	chr14:31989531-31989766(-)$1	235	60	63	9.0000
GAU	chr18:46664687-46664922(-)$1	235	50	53	9.0000
GAU	chr2:25077838-25078075(-)$1	237	119	122	9.0000
GAU	chr10:106256389-106256638(+)$1	249	23	26	9.0000
GAU	chr4:148761180-148761417(-)$1	237	199	202	9.0000
GAU	chr12:106028213-106028448(-)$1	235	45	48	9.0000
GAU	chr11:118355369-118355606(-)$1	237	89	92	9.0000
GAU	chrX:39458041-39458277(+)$1	236	164	167	9.0000
GAU	chr7:20150502-20150751(-)$1	249	19	22	9.0000
GAU	chr14:60997232-60997490(+)$1	258	21	24	9.0000
GAU	chr15:31412540-31412775(-)$1	235	44	47	9.0000
GAU	chr12:111865180-111865415(+)$1	235	49	52	9.0000
GAU	chr16:14153931-14154176(-)$1	245	74	77	9.0000
GAU	chr9:58430182-58430417(+)$1	235	59	62	9.0000
GAU	chr9:95945897-95946132(+)$1	235	86	89	9.0000
GAU	chr15:83666718-83666956(+)$1	238	6	9	9.0000
GAU	chr14:37939004-37939242(-)$1	238	200	203	9.0000
GAU	chr2:181283313-181283550(+)$1	237	223	226	9.0000
GAU	chr10:126675733-126675988(-)$1	255	109	112	9.0000
GAU	chr3:95023988-95024224(-)$1	236	124	127	9.0000
GAU	chr11:78335201-78335436(+)$1	235	119	122	9.0000
GAU	chr4:126707015-126707250(+)$1	235	137	140	9.0000
GAU	chr5:131921174-131921409(-)$1	235	154	157	9.0000
GAU	chr2:32452594-32452855(+)$1	261	2	5	9.0000
GAU	chr2:129444097-129444360(+)$1	263	94	97	9.0000
GAU	chr8:67071868-67072108(-)$1	240	0	3	9.0000
GAU	chr11:49502571-49502808(-)$1	237	149	152	9.0000
GAU	chr5:137736972-137737209(-)$1	237	7	10	9.0000
GAU	chr12:21315974-21316209(+)$1	235	20	23	9.0000
GAU	chr9:30959798-30960060(-)$1	262	106	109	9.0000
GAU	chr11:46055717-46055965(-)$1	248	52	55	9.0000
GAU	chr19:10058659-10058899(+)$1	240	29	32	9.0000
GAU	chr9:36557080-36557315(-)$1	235	50	53	9.0000
GAU	chr4:126425761-126425997(-)$1	236	81	84	9.0000
GAU	chr5:90646461-90646698(-)$1	237	6	9	9.0000
GAU	chr1:193602238-193602475(+)$1	237	69	72	9.0000
GAU	chrX:148326258-148326496(+)$1	238	23	26	9.0000
GAU	chr11:86602657-86602898(-)$1	241	107	110	9.0000
GAU	chr10:76784989-76785224(-)$1	235	116	119	9.0000
GAU	chr4:126707100-126707361(+)$1	261	52	55	9.0000
GAU	chr8:107803318-107803553(+)$1	235	188	191	9.0000
GAU	chr8:47292820-47293064(-)$1	244	92	95	9.0000
GAU	chr3:19968893-19969128(+)$1	235	2	5	9.0000
GAU	chr5:104508405-104508686(-)$1	281	92	95	9.0000
GAU	chr1:83273913-83274169(-)$1	256	21	24	9.0000
GAU	chr1:175262352-175262595(-)$1	243	72	75	9.0000
GAU	chrX:10172306-10172551(+)$1	245	45	48	9.0000
GAU	chr16:90229856-90230093(-)$1	237	68	71	9.0000
GAU	chr13:74168748-74168984(+)$1	236	43	46	9.0000
GAU	chrX:162824810-162825047(+)$1	237	72	75	9.0000
GAU	chr2:5950315-5950550(+)$1	235	152	155	9.0000
GAU	chr3:107416213-107416450(-)$1	237	65	68	9.0000
GAU	chr19:10058581-10058825(+)$1	244	10	13	9.0000
GAU	chr17:82047059-82047320(-)$1	261	161	164	9.0000
GAU	chr2:34631511-34631748(+)$1	237	95	98	9.0000
GAU	chr2:9985644-9985896(-)$1	252	29	32	9.0000
GAU	chr11:90202099-90202341(-)$1	242	53	56	9.0000
GAU	chr6:4591853-4592090(+)$1	237	123	126	9.0000
GAU	chrX:133369561-133369797(+)$1	236	19	22	9.0000
GAU	chrX:141894531-141894792(-)$1	261	37	40	9.0000
GAU	chr11:100888528-100888792(+)$1	264	67	70	9.0000
GAU	chr3:146395453-146395688(-)$1	235	3	6	9.0000
GAU	chr15:58767736-58767981(+)$1	245	25	28	9.0000
GAU	chr14:104242207-104242444(-)$1	237	1	4	9.0000
GAU	chr11:68620525-68620761(+)$1	236	73	76	9.0000
GAU	chr2:156002938-156003173(-)$1	235	26	29	9.0000
GAU	chrX:148317008-148317269(+)$1	261	76	79	9.0000
GAU	chr11:31917577-31917812(+)$1	235	75	78	9.0000
GAU	chr16:11134462-11134700(-)$1	238	226	229	9.0000
GAU	chr11:94853901-94854141(+)$1	240	97	100	9.0000
GAU	chr11:50014060-50014371(-)$1	311	46	49	9.0000
GAU	chr15:31418450-31418687(-)$1	237	29	32	9.0000
GAU	chr13:78336959-78337194(-)$1	235	58	61	9.0000
GAU	chr12:4637380-4637615(+)$1	235	142	145	9.0000
GAU	chrX:12738488-12738723(+)$1	235	88	91	9.0000
GAU	chr7:137872027-137872262(+)$1	235	9	12	9.0000
GAU	chrX:69679876-69680119(-)$1	243	116	119	9.0000
GAU	chr11:87863329-87863588(+)$1	259	27	30	9.0000
GAU	chr3:87798024-87798262(-)$1	238	54	57	9.0000
GAU	chr1:59927210-59927447(+)$1	237	95	98	9.0000
GAU	chr11:41960533-41960768(-)$1	235	32	35	9.0000
GAU	chr16:17499962-17500197(+)$1	235	89	92	9.0000
GAU	chr13:104623795-104624032(-)$1	237	131	134	9.0000

#otherMatches

#Struct PSSM
C{C	chr17:34782494-34782729(+)$1	235	4	7	9.0000
mmc	chr2:181041975-181042222(-)$1	247	71	74	9.0000
bbd	chr19:7289793-7290030(-)$1	237	29	32	9.0000
ddd	chr10:53063680-53063917(+)$1	237	105	108	9.0000
ddl	chr11:59220569-59220827(-)$1	258	110	113	9.0000
:::	chr5:34186114-34186353(+)$1	239	122	125	9.0000
DDD	chr1:174210640-174210877(-)$1	237	43	46	9.0000
eee	chr9:66883791-66884029(-)$1	238	151	154	9.0000
:FF	chr11:115667985-115668222(-)$1	237	4	7	9.0000
FFF	chr14:31989531-31989766(-)$1	235	60	63	9.0000
fff	chr18:46664687-46664922(-)$1	235	50	53	9.0000
333	chr2:25077838-25078075(-)$1	237	119	122	9.0000
E::	chr10:106256389-106256638(+)$1	249	23	26	9.0000
ddd	chr4:148761180-148761417(-)$1	237	199	202	9.0000
ppp	chr12:106028213-106028448(-)$1	235	45	48	9.0000
ccc	chr11:118355369-118355606(-)$1	237	89	92	9.0000
ggg	chrX:39458041-39458277(+)$1	236	164	167	9.0000
DD:	chr7:20150502-20150751(-)$1	249	19	22	9.0000
MMB	chr14:60997232-60997490(+)$1	258	21	24	9.0000
HH{	chr15:31412540-31412775(-)$1	235	44	47	9.0000
:::	chr12:111865180-111865415(+)$1	235	49	52	9.0000
hhh	chr16:14153931-14154176(-)$1	245	74	77	9.0000
e::	chr9:58430182-58430417(+)$1	235	59	62	9.0000
]dd	chr9:95945897-95946132(+)$1	235	86	89	9.0000
:::	chr15:83666718-83666956(+)$1	238	6	9	9.0000
rre	chr14:37939004-37939242(-)$1	238	200	203	9.0000
666	chr2:181283313-181283550(+)$1	237	223	226	9.0000
ppf	chr10:126675733-126675988(-)$1	255	109	112	9.0000
666	chr3:95023988-95024224(-)$1	236	124	127	9.0000
fff	chr11:78335201-78335436(+)$1	235	119	122	9.0000
ggg	chr4:126707015-126707250(+)$1	235	137	140	9.0000
ddn	chr5:131921174-131921409(-)$1	235	154	157	9.0000
:::	chr2:32452594-32452855(+)$1	261	2	5	9.0000
qqq	chr2:129444097-129444360(+)$1	263	94	97	9.0000
:dd	chr8:67071868-67072108(-)$1	240	0	3	9.0000
d[d	chr11:49502571-49502808(-)$1	237	149	152	9.0000
D::	chr5:137736972-137737209(-)$1	237	7	10	9.0000
:::	chr12:21315974-21316209(+)$1	235	20	23	9.0000
ee]	chr9:30959798-30960060(-)$1	262	106	109	9.0000
KKD	chr11:46055717-46055965(-)$1	248	52	55	9.0000
:::	chr19:10058659-10058899(+)$1	240	29	32	9.0000
cc]	chr9:36557080-36557315(-)$1	235	50	53	9.0000
C{D	chr4:126425761-126425997(-)$1	236	81	84	9.0000
C::	chr5:90646461-90646698(-)$1	237	6	9	9.0000
LLC	chr1:193602238-193602475(+)$1	237	69	72	9.0000
:::	chrX:148326258-148326496(+)$1	238	23	26	9.0000
===	chr11:86602657-86602898(-)$1	241	107	110	9.0000
f]b	chr10:76784989-76785224(-)$1	235	116	119	9.0000
ggg	chr4:126707100-126707361(+)$1	261	52	55	9.0000
~~~	chr8:107803318-107803553(+)$1	235	188	191	9.0000
+++	chr8:47292820-47293064(-)$1	244	92	95	9.0000
:::	chr3:19968893-19969128(+)$1	235	2	5	9.0000
bb#	chr5:104508405-104508686(-)$1	281	92	95	9.0000
d[b	chr1:83273913-83274169(-)$1	256	21	24	9.0000
ffb	chr1:175262352-175262595(-)$1	243	72	75	9.0000
eee	chrX:10172306-10172551(+)$1	245	45	48	9.0000
cc!	chr16:90229856-90230093(-)$1	237	68	71	9.0000
KKE	chr13:74168748-74168984(+)$1	236	43	46	9.0000
NDD	chrX:162824810-162825047(+)$1	237	72	75	9.0000
bbf	chr2:5950315-5950550(+)$1	235	152	155	9.0000
FFF	chr3:107416213-107416450(-)$1	237	65	68	9.0000
FF:	chr19:10058581-10058825(+)$1	244	10	13	9.0000
c$$	chr17:82047059-82047320(-)$1	261	161	164	9.0000
d::	chr2:34631511-34631748(+)$1	237	95	98	9.0000
nnn	chr2:9985644-9985896(-)$1	252	29	32	9.0000
:::	chr11:90202099-90202341(-)$1	242	53	56	9.0000
dmm	chr6:4591853-4592090(+)$1	237	123	126	9.0000
hhh	chrX:133369561-133369797(+)$1	236	19	22	9.0000
gg:	chrX:141894531-141894792(-)$1	261	37	40	9.0000
bb:	chr11:100888528-100888792(+)$1	264	67	70	9.0000
:::	chr3:146395453-146395688(-)$1	235	3	6	9.0000
mmm	chr15:58767736-58767981(+)$1	245	25	28	9.0000
:::	chr14:104242207-104242444(-)$1	237	1	4	9.0000
ddd	chr11:68620525-68620761(+)$1	236	73	76	9.0000
ddd	chr2:156002938-156003173(-)$1	235	26	29	9.0000
ddd	chrX:148317008-148317269(+)$1	261	76	79	9.0000
===	chr11:31917577-31917812(+)$1	235	75	78	9.0000
AYY	chr16:11134462-11134700(-)$1	238	226	229	9.0000
:::	chr11:94853901-94854141(+)$1	240	97	100	9.0000
nne	chr11:50014060-50014371(-)$1	311	46	49	9.0000
ee[	chr15:31418450-31418687(-)$1	237	29	32	9.0000
ddd	chr13:78336959-78337194(-)$1	235	58	61	9.0000
fff	chr12:4637380-4637615(+)$1	235	142	145	9.0000
GGG	chrX:12738488-12738723(+)$1	235	88	91	9.0000
ccJ	chr7:137872027-137872262(+)$1	235	9	12	9.0000
ccc	chrX:69679876-69680119(-)$1	243	116	119	9.0000
fff	chr11:87863329-87863588(+)$1	259	27	30	9.0000
goo	chr3:87798024-87798262(-)$1	238	54	57	9.0000
eee	chr1:59927210-59927447(+)$1	237	95	98	9.0000
::e	chr11:41960533-41960768(-)$1	235	32	35	9.0000
bbo	chr16:17499962-17500197(+)$1	235	89	92	9.0000
EE}	chr13:104623795-104624032(-)$1	237	131	134	9.0000

#DB
(.(	chr17:34782494-34782729(+)$1	1	4	7	9.0000
..)	chr2:181041975-181042222(-)$1	1	71	74	9.0000
(((	chr19:7289793-7290030(-)$1	1	29	32	9.0000
)))	chr10:53063680-53063917(+)$1	1	105	108	9.0000
((.	chr11:59220569-59220827(-)$1	1	110	113	9.0000
...	chr5:34186114-34186353(+)$1	1	122	125	9.0000
(((	chr1:174210640-174210877(-)$1	1	43	46	9.0000
)))	chr9:66883791-66884029(-)$1	1	151	154	9.0000
.((	chr11:115667985-115668222(-)$1	1	4	7	9.0000
(((	chr14:31989531-31989766(-)$1	1	60	63	9.0000
(((	chr18:46664687-46664922(-)$1	1	50	53	9.0000
...	chr2:25077838-25078075(-)$1	1	119	122	9.0000
(..	chr10:106256389-106256638(+)$1	1	23	26	9.0000
)))	chr4:148761180-148761417(-)$1	1	199	202	9.0000
...	chr12:106028213-106028448(-)$1	1	45	48	9.0000
)))	chr11:118355369-118355606(-)$1	1	89	92	9.0000
)))	chrX:39458041-39458277(+)$1	1	164	167	9.0000
((.	chr7:20150502-20150751(-)$1	1	19	22	9.0000
..(	chr14:60997232-60997490(+)$1	1	21	24	9.0000
((.	chr15:31412540-31412775(-)$1	1	44	47	9.0000
...	chr12:111865180-111865415(+)$1	1	49	52	9.0000
)))	chr16:14153931-14154176(-)$1	1	74	77	9.0000
)..	chr9:58430182-58430417(+)$1	1	59	62	9.0000
.))	chr9:95945897-95946132(+)$1	1	86	89	9.0000
...	chr15:83666718-83666956(+)$1	1	6	9	9.0000
..)	chr14:37939004-37939242(-)$1	1	200	203	9.0000
...	chr2:181283313-181283550(+)$1	1	223	226	9.0000
..)	chr10:126675733-126675988(-)$1	1	109	112	9.0000
...	chr3:95023988-95024224(-)$1	1	124	127	9.0000
(((	chr11:78335201-78335436(+)$1	1	119	122	9.0000
)))	chr4:126707015-126707250(+)$1	1	137	140	9.0000
((.	chr5:131921174-131921409(-)$1	1	154	157	9.0000
...	chr2:32452594-32452855(+)$1	1	2	5	9.0000
...	chr2:129444097-129444360(+)$1	1	94	97	9.0000
.((	chr8:67071868-67072108(-)$1	1	0	3	9.0000
(.(	chr11:49502571-49502808(-)$1	1	149	152	9.0000
(..	chr5:137736972-137737209(-)$1	1	7	10	9.0000
...	chr12:21315974-21316209(+)$1	1	20	23	9.0000
)).	chr9:30959798-30960060(-)$1	1	106	109	9.0000
..(	chr11:46055717-46055965(-)$1	1	52	55	9.0000
...	chr19:10058659-10058899(+)$1	1	29	32	9.0000
)).	chr9:36557080-36557315(-)$1	1	50	53	9.0000
(.(	chr4:126425761-126425997(-)$1	1	81	84	9.0000
(..	chr5:90646461-90646698(-)$1	1	6	9	9.0000
..(	chr1:193602238-193602475(+)$1	1	69	72	9.0000
...	chrX:148326258-148326496(+)$1	1	23	26	9.0000
(((	chr11:86602657-86602898(-)$1	1	107	110	9.0000
).)	chr10:76784989-76785224(-)$1	1	116	119	9.0000
)))	chr4:126707100-126707361(+)$1	1	52	55	9.0000
...	chr8:107803318-107803553(+)$1	1	188	191	9.0000
...	chr8:47292820-47293064(-)$1	1	92	95	9.0000
...	chr3:19968893-19969128(+)$1	1	2	5	9.0000
((.	chr5:104508405-104508686(-)$1	1	92	95	9.0000
(.(	chr1:83273913-83274169(-)$1	1	21	24	9.0000
(((	chr1:175262352-175262595(-)$1	1	72	75	9.0000
)))	chrX:10172306-10172551(+)$1	1	45	48	9.0000
((.	chr16:90229856-90230093(-)$1	1	68	71	9.0000
..(	chr13:74168748-74168984(+)$1	1	43	46	9.0000
.((	chrX:162824810-162825047(+)$1	1	72	75	9.0000
(((	chr2:5950315-5950550(+)$1	1	152	155	9.0000
(((	chr3:107416213-107416450(-)$1	1	65	68	9.0000
((.	chr19:10058581-10058825(+)$1	1	10	13	9.0000
(..	chr17:82047059-82047320(-)$1	1	161	164	9.0000
)..	chr2:34631511-34631748(+)$1	1	95	98	9.0000
...	chr2:9985644-9985896(-)$1	1	29	32	9.0000
...	chr11:90202099-90202341(-)$1	1	53	56	9.0000
(..	chr6:4591853-4592090(+)$1	1	123	126	9.0000
)))	chrX:133369561-133369797(+)$1	1	19	22	9.0000
)).	chrX:141894531-141894792(-)$1	1	37	40	9.0000
)).	chr11:100888528-100888792(+)$1	1	67	70	9.0000
...	chr3:146395453-146395688(-)$1	1	3	6	9.0000
...	chr15:58767736-58767981(+)$1	1	25	28	9.0000
...	chr14:104242207-104242444(-)$1	1	1	4	9.0000
(((	chr11:68620525-68620761(+)$1	1	73	76	9.0000
(((	chr2:156002938-156003173(-)$1	1	26	29	9.0000
(((	chrX:148317008-148317269(+)$1	1	76	79	9.0000
(((	chr11:31917577-31917812(+)$1	1	75	78	9.0000
)..	chr16:11134462-11134700(-)$1	1	226	229	9.0000
...	chr11:94853901-94854141(+)$1	1	97	100	9.0000
..)	chr11:50014060-50014371(-)$1	1	46	49	9.0000
((.	chr15:31418450-31418687(-)$1	1	29	32	9.0000
(((	chr13:78336959-78337194(-)$1	1	58	61	9.0000
(((	chr12:4637380-4637615(+)$1	1	142	145	9.0000
(((	chrX:12738488-12738723(+)$1	1	88	91	9.0000
))(	chr7:137872027-137872262(+)$1	1	9	12	9.0000
)))	chrX:69679876-69680119(-)$1	1	116	119	9.0000
(((	chr11:87863329-87863588(+)$1	1	27	30	9.0000
(..	chr3:87798024-87798262(-)$1	1	54	57	9.0000
(((	chr1:59927210-59927447(+)$1	1	95	98	9.0000
..(	chr11:41960533-41960768(-)$1	1	32	35	9.0000
((.	chr16:17499962-17500197(+)$1	1	89	92	9.0000
)).	chr13:104623795-104624032(-)$1	1	131	134	9.0000

#PSSM
G : 1.00	
A : 1.00	
U : 1.00	

#score	828.0000000000007
#seq	92
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m2_run1.nuc.txt

#NT
UGCUCUC	chr15:99147942-99148179(-)$1	237	2	9	12.4754
UGUUCUG	chr18:77393739-77393974(+)$1	235	202	209	12.4754
UGCUCUG	chr6:39347804-39348096(-)$1	292	148	155	16.6557
UGCCCUG	chr4:115448025-115448261(+)$1	236	48	55	12.3114
UCCUCUG	chr9:65542904-65543146(-)$1	242	179	186	12.3934
UGUUCUG	chr6:72577182-72577447(-)$1	265	208	215	12.4754
UGCUCAG	chr15:103129770-103130020(+)$1	250	138	145	12.4754
UGCUUUG	chr2:90856348-90856585(+)$1	237	109	116	13.5409
UGCUGUG	chr13:38070865-38071173(-)$1	308	88	95	13.5409
UGCUCAG	chr8:108205918-108206175(+)$1	257	42	49	12.4754
UGCUCUG	chr3:126482716-126482968(+)$1	252	126	133	16.6557
UGCGCUG	chr6:72576823-72577107(-)$1	284	68	75	12.4754
UGCUGUG	chr15:65703381-65703629(+)$1	248	158	165	13.5409
UGCUUUG	chr18:39571526-39571786(-)$1	260	176	183	13.5409
UGAUCUG	chr19:37494814-37495103(+)$1	289	67	74	12.4754
UACUCUG	chr19:7610867-7611112(+)$1	245	108	115	12.3114
UGCGCUG	chr15:58286341-58286626(+)$1	285	29	36	12.4754
UCCUCUG	chrX:93362076-93362372(+)$1	296	232	239	12.3934
GGCUCUG	chr8:11615224-11615461(-)$1	237	36	43	12.3934
UACUCUG	chr2:6463493-6463768(-)$1	275	5	12	12.3114
UGCUGUG	chr5:34828426-34828680(+)$1	254	86	93	13.5409
UGCUCUG	chr2:153593869-153594115(+)$1	246	173	180	16.6557
ugcuuug	chr1:165176872-165177110(-)$1	238	118	125	13.5409
ugcgcug	chr8:26269903-26270210(-)$1	307	146	153	12.4754
UGCUCUA	chr2:153593215-153593465(+)$1	250	79	86	12.3114
UGUUCUG	chr17:28466122-28466381(+)$1	259	167	174	12.4754
CGCUCUG	chr9:113563726-113563993(-)$1	267	8	15	12.2295
GGCUCUG	chr12:86125061-86125299(-)$1	238	223	230	12.3934
UGCUCUC	chr16:27446340-27446585(+)$1	245	150	157	12.4754
UGCUGUG	chr3:88986482-88986735(+)$1	253	144	151	13.5409
UGCUCUG	chr2:29037708-29037946(+)$1	238	177	184	16.6557
UGCUUUG	chr15:76001321-76001628(-)$1	307	241	248	13.5409
UGCUGUG	chrX:99261810-99262047(-)$1	237	91	98	13.5409
UCCUCUG	chr18:9995648-9995931(-)$1	283	172	179	12.3934
UGCUGUG	chr11:113522552-113522801(-)$1	249	15	22	13.5409
UGCUCCG	chr13:38085816-38086053(-)$1	237	159	166	12.3114
UGGUCUG	chr7:38744954-38745227(-)$1	273	257	264	12.3114
UGCUCUG	chr10:126434481-126434790(+)$1	309	204	211	16.6557
UGCUCUC	chr7:56827552-56827787(+)$1	235	115	122	12.4754
UGCUUUG	chr13:96372347-96372607(-)$1	260	106	113	13.5409
UGCUCUG	chr6:42308093-42308405(+)$1	312	244	251	16.6557
AGCUCUG	chr5:150419653-150419926(-)$1	273	66	73	12.3114
UGCUUUG	chr3:157711287-157711527(+)$1	240	118	125	13.5409
UGCUCUA	chr8:106942389-106942627(-)$1	238	82	89	12.3114
UGCGCUG	chr10:116509830-116510151(-)$1	321	292	299	12.4754
UGCCCUG	chr10:42254599-42254917(+)$1	318	65	72	12.3114
UGCUCAG	chr1:133830153-133830426(+)$1	273	64	71	12.4754
UGAUCUG	chr5:149142983-149143225(-)$1	242	76	83	12.4754
UGCUCCG	chr5:120934883-120935181(-)$1	298	40	47	12.3114
UUCUCUG	chr4:107479847-107480086(+)$1	239	34	41	12.2295
UGAUCUG	chr7:137537003-137537241(-)$1	238	114	121	12.4754
UGCUCUG	chr11:53868330-53868646(-)$1	316	207	214	16.6557
UGCUUUG	chr18:77393445-77393680(+)$1	235	112	119	13.5409
UGCUCUG	chr11:119861803-119862046(+)$1	243	42	49	16.6557
UGCUAUG	chr7:148155453-148155739(+)$1	286	129	136	13.1311
UGCUCUC	chr15:81513450-81513685(+)$1	235	93	100	12.4754
ugcuaug	chr7:148657187-148657425(+)$1	238	146	153	13.1311
UGCUGUG	chr2:6465322-6465567(-)$1	245	184	191	13.5409
AGCUCUG	chr6:30404447-30404698(+)$1	251	5	12	12.3114
UGCUCAG	chr4:43439766-43440003(+)$1	237	180	187	12.4754

#otherMatches

#Struct PSSM
gggggg:	chr13:100192842-100193104(-)$1	262	140	147	12.3934
EEEEECC	chr15:99147942-99148179(-)$1	237	2	9	12.4754
Gcccmmm	chr18:77393739-77393974(+)$1	235	202	209	12.4754
doooooo	chr6:39347804-39348096(-)$1	292	148	155	16.6557
2hhhhhh	chr4:115448025-115448261(+)$1	236	48	55	12.3114
ffff:::	chr9:65542904-65543146(-)$1	242	179	186	12.3934
b]dddd5	chr6:72577182-72577447(-)$1	265	208	215	12.4754
::ddddm	chr15:103129770-103130020(+)$1	250	138	145	12.4754
]bb333e	chr2:90856348-90856585(+)$1	237	109	116	13.5409
hhhhhhh	chr13:38070865-38071173(-)$1	308	88	95	13.5409
ssssssg	chr8:108205918-108206175(+)$1	257	42	49	12.4754
ddd[a!!	chr3:126482716-126482968(+)$1	252	126	133	16.6557
{FFFFFF	chr6:72576823-72577107(-)$1	284	68	75	12.4754
qffffff	chr15:65703381-65703629(+)$1	248	158	165	13.5409
>hhhhhh	chr18:39571526-39571786(-)$1	260	176	183	13.5409
ebbdddd	chr19:37494814-37495103(+)$1	289	67	74	12.4754
eeeee]c	chr19:7610867-7611112(+)$1	245	108	115	12.3114
lcccccc	chr15:58286341-58286626(+)$1	285	29	36	12.4754
FFFZZZC	chrX:93362076-93362372(+)$1	296	232	239	12.3934
]bb:ccc	chr8:11615224-11615461(-)$1	237	36	43	12.3934
EEEEECC	chr2:6463493-6463768(-)$1	275	5	12	12.3114
eeeee]c	chr5:34828426-34828680(+)$1	254	86	93	13.5409
bbeeeee	chr2:153593869-153594115(+)$1	246	173	180	16.6557
dbb!!gg	chr1:165176872-165177110(-)$1	238	118	125	13.5409
!bb"""e	chr8:26269903-26270210(-)$1	307	146	153	12.4754
FFFFF::	chr2:153593215-153593465(+)$1	250	79	86	12.3114
3ffffff	chr17:28466122-28466381(+)$1	259	167	174	12.4754
!ccc[gg	chr9:113563726-113563993(-)$1	267	8	15	12.2295
ebb:ccc	chr12:86125061-86125299(-)$1	238	223	230	12.3934
llfffff	chr16:27446340-27446585(+)$1	245	150	157	12.4754
!bblllb	chr3:88986482-88986735(+)$1	253	144	151	13.5409
iiiiiiC	chr2:29037708-29037946(+)$1	238	177	184	16.6557
ffffff:	chr15:76001321-76001628(-)$1	307	241	248	13.5409
bbb]iii	chrX:99261810-99262047(-)$1	237	91	98	13.5409
:::hhhh	chr18:9995648-9995931(-)$1	283	172	179	12.3934
:ffffff	chr11:113522552-113522801(-)$1	249	15	22	13.5409
ooooobb	chr13:38085816-38086053(-)$1	237	159	166	12.3114
GGGGGGG	chr7:38744954-38745227(-)$1	273	257	264	12.3114
:HHHHHH	chr10:126434481-126434790(+)$1	309	204	211	16.6557
FFDDDD\	chr7:56827552-56827787(+)$1	235	115	122	12.4754
wgggggg	chr13:96372347-96372607(-)$1	260	106	113	13.5409
qqqqqqc	chr6:42308093-42308405(+)$1	312	244	251	16.6557
[bblllb	chr5:150419653-150419926(-)$1	273	66	73	12.3114
fffff:c	chr3:157711287-157711527(+)$1	240	118	125	13.5409
beeeee[	chr8:106942389-106942627(-)$1	238	82	89	12.3114
ffftttt	chr10:116509830-116510151(-)$1	321	292	299	12.4754
hhh::::	chr10:42254599-42254917(+)$1	318	65	72	12.3114
e55555c	chr1:133830153-133830426(+)$1	273	64	71	12.4754
cc:eeee	chr5:149142983-149143225(-)$1	242	76	83	12.4754
CCLLLDD	chr5:120934883-120935181(-)$1	298	40	47	12.3114
ENNNNND	chr4:107479847-107480086(+)$1	239	34	41	12.2295
doooooo	chr7:137537003-137537241(-)$1	238	114	121	12.4754
EECCCcc	chr11:53868330-53868646(-)$1	316	207	214	16.6557
KJJJJJJ	chr18:77393445-77393680(+)$1	235	112	119	13.5409
ee"""ff	chr11:119861803-119862046(+)$1	243	42	49	16.6557
:CCCYYF	chr7:148155453-148155739(+)$1	286	129	136	13.1311
hhhpppp	chr15:81513450-81513685(+)$1	235	93	100	12.4754
ddqqqqq	chr7:148657187-148657425(+)$1	238	146	153	13.1311
7777eee	chr2:6465322-6465567(-)$1	245	184	191	13.5409
[dddd##	chr6:30404447-30404698(+)$1	251	5	12	12.3114
dnnnnnd	chr4:43439766-43440003(+)$1	237	180	187	12.4754

#DB
)))))).	chr13:100192842-100193104(-)$1	1	140	147	12.3934
(((((((	chr15:99147942-99148179(-)$1	1	2	9	12.4754
)(((...	chr18:77393739-77393974(+)$1	1	202	209	12.4754
(......	chr6:39347804-39348096(-)$1	1	148	155	16.6557
.))))))	chr4:115448025-115448261(+)$1	1	48	55	12.3114
))))...	chr9:65542904-65543146(-)$1	1	179	186	12.3934
).)))).	chr6:72577182-72577447(-)$1	1	208	215	12.4754
..((((.	chr15:103129770-103130020(+)$1	1	138	145	12.4754
.))...)	chr2:90856348-90856585(+)$1	1	109	116	13.5409
)))))))	chr13:38070865-38071173(-)$1	1	88	95	13.5409
......)	chr8:108205918-108206175(+)$1	1	42	49	12.4754
(((.(..	chr3:126482716-126482968(+)$1	1	126	133	16.6557
.((((((	chr6:72576823-72577107(-)$1	1	68	75	12.4754
.))))))	chr15:65703381-65703629(+)$1	1	158	165	13.5409
.))))))	chr18:39571526-39571786(-)$1	1	176	183	13.5409
(((((((	chr19:37494814-37495103(+)$1	1	67	74	12.4754
))))).)	chr19:7610867-7611112(+)$1	1	108	115	12.3114
.))))))	chr15:58286341-58286626(+)$1	1	29	36	12.4754
)))...)	chrX:93362076-93362372(+)$1	1	232	239	12.3934
.)).(((	chr8:11615224-11615461(-)$1	1	36	43	12.3934
(((((((	chr2:6463493-6463768(-)$1	1	5	12	12.3114
))))).)	chr5:34828426-34828680(+)$1	1	86	93	13.5409
))(((((	chr2:153593869-153594115(+)$1	1	173	180	16.6557
)((..((	chr1:165176872-165177110(-)$1	1	118	125	13.5409
.((...(	chr8:26269903-26270210(-)$1	1	146	153	12.4754
(((((..	chr2:153593215-153593465(+)$1	1	79	86	12.3114
.))))))	chr17:28466122-28466381(+)$1	1	167	174	12.4754
.(((.((	chr9:113563726-113563993(-)$1	1	8	15	12.2295
))).(((	chr12:86125061-86125299(-)$1	1	223	230	12.3934
..)))))	chr16:27446340-27446585(+)$1	1	150	157	12.4754
.((...)	chr3:88986482-88986735(+)$1	1	144	151	13.5409
)))))))	chr2:29037708-29037946(+)$1	1	177	184	16.6557
)))))).	chr15:76001321-76001628(-)$1	1	241	248	13.5409
))).)))	chrX:99261810-99262047(-)$1	1	91	98	13.5409
...((((	chr18:9995648-9995931(-)$1	1	172	179	12.3934
.((((((	chr11:113522552-113522801(-)$1	1	15	22	13.5409
.....))	chr13:38085816-38086053(-)$1	1	159	166	12.3114
)))))))	chr7:38744954-38745227(-)$1	1	257	264	12.3114
.))))))	chr10:126434481-126434790(+)$1	1	204	211	16.6557
)))))).	chr7:56827552-56827787(+)$1	1	115	122	12.4754
.))))))	chr13:96372347-96372607(-)$1	1	106	113	13.5409
......)	chr6:42308093-42308405(+)$1	1	244	251	16.6557
.((...)	chr5:150419653-150419926(-)$1	1	66	73	12.3114
))))).(	chr3:157711287-157711527(+)$1	1	118	125	13.5409
)(((((.	chr8:106942389-106942627(-)$1	1	82	89	12.3114
(((....	chr10:116509830-116510151(-)$1	1	292	299	12.4754
)))....	chr10:42254599-42254917(+)$1	1	65	72	12.3114
).....)	chr1:133830153-133830426(+)$1	1	64	71	12.4754
)).((((	chr5:149142983-149143225(-)$1	1	76	83	12.4754
((...((	chr5:120934883-120935181(-)$1	1	40	47	12.3114
(.....(	chr4:107479847-107480086(+)$1	1	34	41	12.2295
(......	chr7:137537003-137537241(-)$1	1	114	121	12.4754
)))))((	chr11:53868330-53868646(-)$1	1	207	214	16.6557
.((((((	chr18:77393445-77393680(+)$1	1	112	119	13.5409
((...((	chr11:119861803-119862046(+)$1	1	42	49	16.6557
.)))..)	chr7:148155453-148155739(+)$1	1	129	136	13.1311
(((....	chr15:81513450-81513685(+)$1	1	93	100	12.4754
((.....	chr7:148657187-148657425(+)$1	1	146	153	13.1311
....)))	chr2:6465322-6465567(-)$1	1	184	191	13.5409
.((((..	chr6:30404447-30404698(+)$1	1	5	12	12.3114
(.....)	chr4:43439766-43440003(+)$1	1	180	187	12.4754

#PSSM
U : 0.85	G : 0.04	u : 0.04	A : 0.03	C : 0.01	
G : 0.85	C : 0.04	g : 0.04	A : 0.03	U : 0.01	
C : 0.83	U : 0.04	A : 0.04	c : 0.04	G : 0.01	
U : 0.86	G : 0.04	C : 0.03	u : 0.03	g : 0.01	
C : 0.72	G : 0.11	U : 0.09	u : 0.01	c : 0.01	A : 0.01	a : 0.01	
U : 0.85	A : 0.06	u : 0.04	C : 0.03	
G : 0.85	C : 0.06	g : 0.04	A : 0.03	

#score	807.8852459016402
#seq	61
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m3_run2.nuc.txt

#NT
UUGCUU	chr9:22172750-22172969(-)$1	219	0	6	10.6086
UUGUUU	chr11:106074467-106074691(-)$1	224	17	23	14.3768
UUGUUC	chr2:29877908-29878120(+)$1	212	174	180	9.7391
uuguuu	chr10:6367736-6367957(-)$1	221	167	173	14.3768
UUGUGU	chr6:86632779-86633017(-)$1	238	34	40	10.4637
UUGUUU	chr13:99547252-99547479(-)$1	227	216	222	14.3768
UUUUUU	chr11:80497867-80498082(-)$1	215	55	61	10.8985
UUAUUU	chr4:106035199-106035407(+)$1	208	55	61	10.5362
UUGUCU	chr3:8947389-8947610(-)$1	221	182	188	10.3188
UUGGUU	chr2:25130092-25130314(+)$1	222	109	115	10.3188
UUCUUU	chr12:51529001-51529227(-)$1	226	143	149	10.7536
UUCUUU	chr6:119570235-119570444(-)$1	209	7	13	10.7536
CUGUUU	chrX:33508598-33508815(+)$1	217	74	80	10.8985
uuguuu	chr16:45802706-45802936(-)$1	230	197	203	14.3768
UUGUUU	chr16:30582048-30582263(-)$1	215	26	32	14.3768
GUGUUU	chr2:174252461-174252670(+)$1	209	56	62	10.3913
UUGUAU	chr11:119270634-119270853(+)$1	219	40	46	10.2463
UUGCUU	chr5:65704142-65704356(-)$1	214	1	7	10.6086
UUGCUU	chr5:136961569-136961775(-)$1	206	25	31	10.6086
UUUUUU	chr6:47447212-47447418(+)$1	206	181	187	10.8985
UUGUCU	chr16:91817028-91817270(+)$1	242	40	46	10.3188
uuguuu	chr2:72240280-72240490(+)$1	210	185	191	14.3768
CUGUUU	chr6:52174241-52174449(-)$1	208	63	69	10.8985
UUGUUU	chr5:33734660-33734891(+)$1	231	33	39	14.3768
UUGUUU	chr3:54516998-54517213(+)$1	215	148	154	14.3768
CUGUUU	chr11:50191700-50191934(+)$1	234	48	54	10.8985
UUGUUU	chr11:49884661-49884890(+)$1	229	176	182	14.3768
CUGUUU	chr19:57781463-57781677(+)$1	214	202	208	10.8985
UUGUUC	chr10:57236895-57237118(-)$1	223	127	133	9.7391
UUUUUU	chr8:40134406-40134632(+)$1	226	8	14	10.8985
AUGUUU	chr11:79197634-79197847(+)$1	213	12	18	10.6086
UUGUGU	chr18:68010005-68010239(+)$1	234	43	49	10.4637
UUGGUU	chr9:64574423-64574629(-)$1	206	33	39	10.3188
uuguuu	chr2:120747013-120747243(-)$1	230	213	219	14.3768
UUGUGU	chr7:63377718-63377924(+)$1	206	12	18	10.4637
augUUU	chr18:6214483-6214719(-)$1	236	6	12	10.6086
CUGUUU	chr2:167480075-167480304(-)$1	229	111	117	10.8985
UUGUUA	chr5:107397827-107398047(+)$1	220	157	163	9.6666
UUGUUU	chr5:44156462-44156668(-)$1	206	143	149	14.3768
UUGCUU	chr3:55808649-55808874(-)$1	225	113	119	10.6086
UUGUUU	chr16:34696831-34697048(+)$1	217	56	62	14.3768
UUGUUU	chr9:64901517-64901723(+)$1	206	46	52	14.3768
uuguuu	chr8:54690978-54691208(-)$1	230	31	37	14.3768
UUCUUU	chr11:100380323-100380544(-)$1	221	41	47	10.7536
AUGUUU	chr10:110404663-110404882(-)$1	219	12	18	10.6086
AUGUUU	chr15:57941427-57941657(-)$1	230	121	127	10.6086
UUGUGU	chr1:182041347-182041566(+)$1	219	20	26	10.4637
CUGUUU	chr12:25671677-25671884(+)$1	207	76	82	10.8985
UUUUUU	chr10:70412693-70412919(-)$1	226	17	23	10.8985
UUGUUU	chr10:58655393-58655601(-)$1	208	19	25	14.3768
CUGUUU	chr5:100959012-100959221(+)$1	209	22	28	10.8985
UUCUUU	chr9:21451785-21452008(+)$1	223	0	6	10.7536
uugucu	chr16:22041325-22041544(+)$1	219	2	8	10.3188
UUUUUU	chr3:30505932-30506149(+)$1	217	9	15	10.8985
UUGUUU	chrX:35964874-35965103(+)$1	229	10	16	14.3768
UUCUUU	chr11:59566436-59566651(+)$1	215	182	188	10.7536
UUUUUU	chr2:181084773-181085001(+)$1	228	43	49	10.8985
UUGCUU	chrX:98770655-98770867(+)$1	212	33	39	10.6086
UUGUUU	chr3:7516359-7516591(+)$1	232	75	81	14.3768
CUGUUU	chr13:97161495-97161702(+)$1	207	36	42	10.8985
UUAUUU	chr19:37458668-37458922(+)$1	254	8	14	10.5362
UUGCUU	chr15:96221449-96221669(+)$1	220	16	22	10.6086
uuguuu	chr4:109383308-109383570(+)$1	262	197	203	14.3768
UUGUGU	chr18:44572146-44572357(+)$1	211	141	147	10.4637
UUGCUU	chr6:56731693-56731913(-)$1	220	106	112	10.6086
UUGGUU	chr17:75010368-75010591(+)$1	223	100	106	10.3188
UUGUUU	chr8:82167594-82167802(+)$1	208	49	55	14.3768
UUGUAU	chr3:97910917-97911128(+)$1	211	95	101	10.2463

#otherMatches

#Struct PSSM
$$$$==	chr3:100460051-100460261(-)$1	210	34	40	10.8985
::::::	chr9:22172750-22172969(-)$1	219	0	6	10.6086
EEEEEC	chr11:106074467-106074691(-)$1	224	17	23	14.3768
llffff	chr2:29877908-29878120(+)$1	212	174	180	9.7391
nnccc:	chr10:6367736-6367957(-)$1	221	167	173	14.3768
HHHHdd	chr6:86632779-86633017(-)$1	238	34	40	10.4637
YYHHHH	chr13:99547252-99547479(-)$1	227	216	222	14.3768
iiiiii	chr11:80497867-80498082(-)$1	215	55	61	10.8985
yyyyyy	chr4:106035199-106035407(+)$1	208	55	61	10.5362
]eeeee	chr3:8947389-8947610(-)$1	221	182	188	10.3188
gggggc	chr2:25130092-25130314(+)$1	222	109	115	10.3188
bqqqqq	chr12:51529001-51529227(-)$1	226	143	149	10.7536
LJJJJJ	chr6:119570235-119570444(-)$1	209	7	13	10.7536
eeeemm	chrX:33508598-33508815(+)$1	217	74	80	10.8985
YYDDDD	chr16:45802706-45802936(-)$1	230	197	203	14.3768
iiiiii	chr16:30582048-30582263(-)$1	215	26	32	14.3768
ccc555	chr2:174252461-174252670(+)$1	209	56	62	10.3913
!cccpp	chr11:119270634-119270853(+)$1	219	40	46	10.2463
::::::	chr5:65704142-65704356(-)$1	214	1	7	10.6086
IIIIII	chr5:136961569-136961775(-)$1	206	25	31	10.6086
DDDD}I	chr6:47447212-47447418(+)$1	206	181	187	10.8985
"""eee	chr16:91817028-91817270(+)$1	242	40	46	10.3188
fff333	chr2:72240280-72240490(+)$1	210	185	191	14.3768
GGGGGG	chr6:52174241-52174449(-)$1	208	63	69	10.8985
nbb]gg	chr5:33734660-33734891(+)$1	231	33	39	14.3768
hhhhhh	chr3:54516998-54517213(+)$1	215	148	154	14.3768
cccooo	chr11:50191700-50191934(+)$1	234	48	54	10.8985
dddd33	chr11:49884661-49884890(+)$1	229	176	182	14.3768
JJJ}GG	chr19:57781463-57781677(+)$1	214	202	208	10.8985
ddddmm	chr10:57236895-57237118(-)$1	223	127	133	9.7391
:::iii	chr8:40134406-40134632(+)$1	226	8	14	10.8985
EEEEKK	chr11:79197634-79197847(+)$1	213	12	18	10.6086
::ccc#	chr18:68010005-68010239(+)$1	234	43	49	10.4637
ggg]gg	chr9:64574423-64574629(-)$1	206	33	39	10.3188
fffmmm	chr2:120747013-120747243(-)$1	230	213	219	14.3768
pppggg	chr7:63377718-63377924(+)$1	206	12	18	10.4637
{BBKKD	chr18:6214483-6214719(-)$1	236	6	12	10.6086
ccclll	chr2:167480075-167480304(-)$1	229	111	117	10.8985
hhh444	chr5:107397827-107398047(+)$1	220	157	163	9.6666
======	chr5:44156462-44156668(-)$1	206	143	149	14.3768
eeeeeG	chr3:55808649-55808874(-)$1	225	113	119	10.6086
pfffff	chr16:34696831-34697048(+)$1	217	56	62	14.3768
pppppp	chr9:64901517-64901723(+)$1	206	46	52	14.3768
]dddd>	chr8:54690978-54691208(-)$1	230	31	37	14.3768
''''''	chr11:100380323-100380544(-)$1	221	41	47	10.7536
KKBBKK	chr10:110404663-110404882(-)$1	219	12	18	10.6086
hhhhhh	chr15:57941427-57941657(-)$1	230	121	127	10.6086
vvdddd	chr1:182041347-182041566(+)$1	219	20	26	10.4637
======	chr12:25671677-25671884(+)$1	207	76	82	10.8985
::::::	chr10:70412693-70412919(-)$1	226	17	23	10.8985
ssssss	chr10:58655393-58655601(-)$1	208	19	25	14.3768
IIIIII	chr5:100959012-100959221(+)$1	209	22	28	10.8985
::HHHH	chr9:21451785-21452008(+)$1	223	0	6	10.7536
:::::B	chr16:22041325-22041544(+)$1	219	2	8	10.3188
FFSSSS	chr3:30505932-30506149(+)$1	217	9	15	10.8985
======	chrX:35964874-35965103(+)$1	229	10	16	14.3768
iiiii!	chr11:59566436-59566651(+)$1	215	182	188	10.7536
c$$$$$	chr2:181084773-181085001(+)$1	228	43	49	10.8985
FFF{EE	chrX:98770655-98770867(+)$1	212	33	39	10.6086
gggxxx	chr3:7516359-7516591(+)$1	232	75	81	14.3768
JJJJJ{	chr13:97161495-97161702(+)$1	207	36	42	10.8985
DDDD{I	chr19:37458668-37458922(+)$1	254	8	14	10.5362
WCCCGG	chr15:96221449-96221669(+)$1	220	16	22	10.6086
======	chr4:109383308-109383570(+)$1	262	197	203	14.3768
333a]g	chr18:44572146-44572357(+)$1	211	141	147	10.4637
]ccc]c	chr6:56731693-56731913(-)$1	220	106	112	10.6086
c[hhhh	chr17:75010368-75010591(+)$1	223	100	106	10.3188
tddddi	chr8:82167594-82167802(+)$1	208	49	55	14.3768
dddd22	chr3:97910917-97911128(+)$1	211	95	101	10.2463

#DB
....((	chr3:100460051-100460261(-)$1	1	34	40	10.8985
......	chr9:22172750-22172969(-)$1	1	0	6	10.6086
((((((	chr11:106074467-106074691(-)$1	1	17	23	14.3768
..))))	chr2:29877908-29878120(+)$1	1	174	180	9.7391
..))).	chr10:6367736-6367957(-)$1	1	167	173	14.3768
((((((	chr6:86632779-86633017(-)$1	1	34	40	10.4637
..))))	chr13:99547252-99547479(-)$1	1	216	222	14.3768
((((((	chr11:80497867-80498082(-)$1	1	55	61	10.8985
......	chr4:106035199-106035407(+)$1	1	55	61	10.5362
.)))))	chr3:8947389-8947610(-)$1	1	182	188	10.3188
((((((	chr2:25130092-25130314(+)$1	1	109	115	10.3188
(.....	chr12:51529001-51529227(-)$1	1	143	149	10.7536
.(((((	chr6:119570235-119570444(-)$1	1	7	13	10.7536
((((..	chrX:33508598-33508815(+)$1	1	74	80	10.8985
..))))	chr16:45802706-45802936(-)$1	1	197	203	14.3768
((((((	chr16:30582048-30582263(-)$1	1	26	32	14.3768
)))...	chr2:174252461-174252670(+)$1	1	56	62	10.3913
.(((..	chr11:119270634-119270853(+)$1	1	40	46	10.2463
......	chr5:65704142-65704356(-)$1	1	1	7	10.6086
((((((	chr5:136961569-136961775(-)$1	1	25	31	10.6086
)))).)	chr6:47447212-47447418(+)$1	1	181	187	10.8985
...(((	chr16:91817028-91817270(+)$1	1	40	46	10.3188
)))...	chr2:72240280-72240490(+)$1	1	185	191	14.3768
((((((	chr6:52174241-52174449(-)$1	1	63	69	10.8985
.)).))	chr5:33734660-33734891(+)$1	1	33	39	14.3768
))))))	chr3:54516998-54517213(+)$1	1	148	154	14.3768
(((...	chr11:50191700-50191934(+)$1	1	48	54	10.8985
))))..	chr11:49884661-49884890(+)$1	1	176	182	14.3768
))).))	chr19:57781463-57781677(+)$1	1	202	208	10.8985
((((..	chr10:57236895-57237118(-)$1	1	127	133	9.7391
...(((	chr8:40134406-40134632(+)$1	1	8	14	10.8985
((((..	chr11:79197634-79197847(+)$1	1	12	18	10.6086
..(((.	chr18:68010005-68010239(+)$1	1	43	49	10.4637
))).))	chr9:64574423-64574629(-)$1	1	33	39	10.3188
(((...	chr2:120747013-120747243(-)$1	1	213	219	14.3768
...)))	chr7:63377718-63377924(+)$1	1	12	18	10.4637
.((..(	chr18:6214483-6214719(-)$1	1	6	12	10.6086
(((...	chr2:167480075-167480304(-)$1	1	111	117	10.8985
)))...	chr5:107397827-107398047(+)$1	1	157	163	9.6666
((((((	chr5:44156462-44156668(-)$1	1	143	149	14.3768
)))))(	chr3:55808649-55808874(-)$1	1	113	119	10.6086
.)))))	chr16:34696831-34697048(+)$1	1	56	62	14.3768
......	chr9:64901517-64901723(+)$1	1	46	52	14.3768
.)))).	chr8:54690978-54691208(-)$1	1	31	37	14.3768
......	chr11:100380323-100380544(-)$1	1	41	47	10.7536
..((..	chr10:110404663-110404882(-)$1	1	12	18	10.6086
((((((	chr15:57941427-57941657(-)$1	1	121	127	10.6086
..))))	chr1:182041347-182041566(+)$1	1	20	26	10.4637
((((((	chr12:25671677-25671884(+)$1	1	76	82	10.8985
......	chr10:70412693-70412919(-)$1	1	17	23	10.8985
......	chr10:58655393-58655601(-)$1	1	19	25	14.3768
((((((	chr5:100959012-100959221(+)$1	1	22	28	10.8985
..((((	chr9:21451785-21452008(+)$1	1	0	6	10.7536
.....(	chr16:22041325-22041544(+)$1	1	2	8	10.3188
((....	chr3:30505932-30506149(+)$1	1	9	15	10.8985
((((((	chrX:35964874-35965103(+)$1	1	10	16	14.3768
(((((.	chr11:59566436-59566651(+)$1	1	182	188	10.7536
(.....	chr2:181084773-181085001(+)$1	1	43	49	10.8985
(((.((	chrX:98770655-98770867(+)$1	1	33	39	10.6086
(((...	chr3:7516359-7516591(+)$1	1	75	81	14.3768
(((((.	chr13:97161495-97161702(+)$1	1	36	42	10.8985
((((.(	chr19:37458668-37458922(+)$1	1	8	14	10.5362
.(((((	chr15:96221449-96221669(+)$1	1	16	22	10.6086
))))))	chr4:109383308-109383570(+)$1	1	197	203	14.3768
...).)	chr18:44572146-44572357(+)$1	1	141	147	10.4637
.))).)	chr6:56731693-56731913(-)$1	1	106	112	10.6086
(.((((	chr17:75010368-75010591(+)$1	1	100	106	10.3188
.)))))	chr8:82167594-82167802(+)$1	1	49	55	14.3768
))))..	chr3:97910917-97911128(+)$1	1	95	101	10.2463

#PSSM
U : 0.69	u : 0.11	C : 0.11	A : 0.04	G : 0.01	a : 0.01	
U : 0.86	u : 0.13	
G : 0.68	g : 0.11	U : 0.08	C : 0.07	A : 0.02	u : 0.01	
U : 0.73	u : 0.11	C : 0.10	G : 0.04	
U : 0.75	u : 0.10	G : 0.07	C : 0.02	A : 0.02	c : 0.01	
U : 0.84	u : 0.11	C : 0.02	A : 0.01	

#score	802.4347826086943
#seq	69
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m2_run2.nuc.txt

#NT
CUGG	chr5:138223490-138223786(-)$1	296	4	8	12.0000
CUGG	chr8:74842841-74843113(+)$1	272	98	102	12.0000
CUGG	chr4:155331129-155331405(+)$1	276	199	203	12.0000
CUGG	chr2:174125804-174126079(+)$1	275	69	73	12.0000
CUGG	chr19:29086354-29086641(+)$1	287	148	152	12.0000
CUGG	chr3:96066825-96067098(-)$1	273	57	61	12.0000
CUGG	chr13:69138016-69138287(-)$1	271	218	222	12.0000
CUGG	chr5:123244330-123244627(-)$1	297	62	66	12.0000
CUGG	chr9:98390942-98391210(+)$1	268	109	113	12.0000
CUGG	chr11:97574608-97574878(+)$1	270	155	159	12.0000
CUGG	chr1:184398225-184398498(-)$1	273	166	170	12.0000
CUGG	chr5:122096593-122096864(-)$1	271	24	28	12.0000
CUGG	chr6:56728726-56729000(-)$1	274	93	97	12.0000
CUGG	chr14:64225930-64226213(+)$1	283	146	150	12.0000
CUGG	chr14:45912564-45912838(-)$1	274	169	173	12.0000
CUGG	chr14:103482193-103482469(-)$1	276	107	111	12.0000
CUGG	chr7:135038924-135039193(-)$1	269	80	84	12.0000
CUGG	chr9:64825927-64826205(+)$1	278	34	38	12.0000
CUGG	chr18:60859085-60859370(-)$1	285	17	21	12.0000
CUGG	chr7:27949815-27950085(-)$1	270	132	136	12.0000
CUGG	chr2:156606172-156606446(+)$1	274	68	72	12.0000
CUGG	chr2:121205209-121205478(-)$1	269	31	35	12.0000
cugG	chr7:117008957-117009223(-)$1	266	198	202	12.0000
CUGG	chr6:51413975-51414275(-)$1	300	42	46	12.0000
CUGG	chr16:36049850-36050132(-)$1	282	217	221	12.0000
CUGG	chr7:52631892-52632163(-)$1	271	89	93	12.0000
CUGG	chr2:32092890-32093158(+)$1	268	3	7	12.0000
CUGG	chr18:24743679-24743949(-)$1	270	121	125	12.0000
CUGG	chr8:23489736-23490016(-)$1	280	52	56	12.0000
CUGG	chr7:28151313-28151603(-)$1	290	53	57	12.0000
CUGG	chr6:22240953-22241221(+)$1	268	8	12	12.0000
CUGG	chr17:35292433-35292717(-)$1	284	148	152	12.0000
CUGG	chr1:93275013-93275289(-)$1	276	149	153	12.0000
CUGG	chr9:65194529-65194809(+)$1	280	27	31	12.0000
CUGG	chr2:34678076-34678352(-)$1	276	28	32	12.0000
CUGG	chr13:73773754-73774025(+)$1	271	41	45	12.0000
CUGG	chr8:74844691-74844960(+)$1	269	97	101	12.0000
CUGG	chr19:8964904-8965185(+)$1	281	230	234	12.0000
CUGG	chr9:97269861-97270130(-)$1	269	58	62	12.0000
CUGG	chr4:45372561-45372833(+)$1	272	179	183	12.0000
CUGG	chr5:108863240-108863508(-)$1	268	54	58	12.0000
CUGG	chr3:95464614-95464908(+)$1	294	75	79	12.0000
CUGG	chr4:135883045-135883347(+)$1	302	49	53	12.0000
CUGG	chr11:87794777-87795061(-)$1	284	15	19	12.0000
CUGG	chr19:5384494-5384771(-)$1	277	2	6	12.0000
CUGG	chr9:107159265-107159531(-)$1	266	123	127	12.0000
CUGG	chr8:86770433-86770706(-)$1	273	117	121	12.0000
CUGG	chr11:102978337-102978633(+)$1	296	150	154	12.0000
CUGG	chr9:66220026-66220300(+)$1	274	4	8	12.0000
CUGG	chrX:98514856-98515126(+)$1	270	76	80	12.0000
CUGG	chr2:31615419-31615714(+)$1	295	5	9	12.0000
CUGG	chr19:7273742-7274025(-)$1	283	20	24	12.0000

#otherMatches

#Struct PSSM
GGGG	chr7:25670028-25670303(+)$1	275	10	14	12.0000
EECC	chr5:138223490-138223786(-)$1	296	4	8	12.0000
333g	chr8:74842841-74843113(+)$1	272	98	102	12.0000
hhhh	chr4:155331129-155331405(+)$1	276	199	203	12.0000
HHHH	chr2:174125804-174126079(+)$1	275	69	73	12.0000
FFFF	chr19:29086354-29086641(+)$1	287	148	152	12.0000
$$$b	chr3:96066825-96067098(-)$1	273	57	61	12.0000
ff[a	chr13:69138016-69138287(-)$1	271	218	222	12.0000
GGGG	chr5:123244330-123244627(-)$1	297	62	66	12.0000
dddd	chr9:98390942-98391210(+)$1	268	109	113	12.0000
eeee	chr11:97574608-97574878(+)$1	270	155	159	12.0000
GGGG	chr1:184398225-184398498(-)$1	273	166	170	12.0000
''hh	chr5:122096593-122096864(-)$1	271	24	28	12.0000
dddd	chr6:56728726-56729000(-)$1	274	93	97	12.0000
cc[b	chr14:64225930-64226213(+)$1	283	146	150	12.0000
oocc	chr14:45912564-45912838(-)$1	274	169	173	12.0000
ffff	chr14:103482193-103482469(-)$1	276	107	111	12.0000
::ii	chr7:135038924-135039193(-)$1	269	80	84	12.0000
gggg	chr9:64825927-64826205(+)$1	278	34	38	12.0000
FFFF	chr18:60859085-60859370(-)$1	285	17	21	12.0000
dd]c	chr7:27949815-27950085(-)$1	270	132	136	12.0000
ddd2	chr2:156606172-156606446(+)$1	274	68	72	12.0000
EEEE	chr2:121205209-121205478(-)$1	269	31	35	12.0000
FFFF	chr7:117008957-117009223(-)$1	266	198	202	12.0000
FFFF	chr6:51413975-51414275(-)$1	300	42	46	12.0000
"fff	chr16:36049850-36050132(-)$1	282	217	221	12.0000
GGGG	chr7:52631892-52632163(-)$1	271	89	93	12.0000
fff[	chr2:32092890-32093158(+)$1	268	3	7	12.0000
beee	chr18:24743679-24743949(-)$1	270	121	125	12.0000
:ccc	chr8:23489736-23490016(-)$1	280	52	56	12.0000
CCCC	chr7:28151313-28151603(-)$1	290	53	57	12.0000
HHHH	chr6:22240953-22241221(+)$1	268	8	12	12.0000
ee::	chr17:35292433-35292717(-)$1	284	148	152	12.0000
EEEE	chr1:93275013-93275289(-)$1	276	149	153	12.0000
dd]f	chr9:65194529-65194809(+)$1	280	27	31	12.0000
[ccc	chr2:34678076-34678352(-)$1	276	28	32	12.0000
dddl	chr13:73773754-73774025(+)$1	271	41	45	12.0000
:fff	chr8:74844691-74844960(+)$1	269	97	101	12.0000
llff	chr19:8964904-8965185(+)$1	281	230	234	12.0000
gggg	chr9:97269861-97270130(-)$1	269	58	62	12.0000
FFFF	chr4:45372561-45372833(+)$1	272	179	183	12.0000
$$ee	chr5:108863240-108863508(-)$1	268	54	58	12.0000
FFKK	chr3:95464614-95464908(+)$1	294	75	79	12.0000
ee""	chr4:135883045-135883347(+)$1	302	49	53	12.0000
GGGG	chr11:87794777-87795061(-)$1	284	15	19	12.0000
cc[c	chr19:5384494-5384771(-)$1	277	2	6	12.0000
""ff	chr9:107159265-107159531(-)$1	266	123	127	12.0000
eeee	chr8:86770433-86770706(-)$1	273	117	121	12.0000
ggg%	chr11:102978337-102978633(+)$1	296	150	154	12.0000
FFFK	chr9:66220026-66220300(+)$1	274	4	8	12.0000
:DDD	chrX:98514856-98515126(+)$1	270	76	80	12.0000
nnnn	chr2:31615419-31615714(+)$1	295	5	9	12.0000
ddbb	chr19:7273742-7274025(-)$1	283	20	24	12.0000

#DB
((((	chr7:25670028-25670303(+)$1	1	10	14	12.0000
((((	chr5:138223490-138223786(-)$1	1	4	8	12.0000
...)	chr8:74842841-74843113(+)$1	1	98	102	12.0000
))))	chr4:155331129-155331405(+)$1	1	199	203	12.0000
((((	chr2:174125804-174126079(+)$1	1	69	73	12.0000
((((	chr19:29086354-29086641(+)$1	1	148	152	12.0000
...(	chr3:96066825-96067098(-)$1	1	57	61	12.0000
((.(	chr13:69138016-69138287(-)$1	1	218	222	12.0000
((((	chr5:123244330-123244627(-)$1	1	62	66	12.0000
))))	chr9:98390942-98391210(+)$1	1	109	113	12.0000
))))	chr11:97574608-97574878(+)$1	1	155	159	12.0000
))))	chr1:184398225-184398498(-)$1	1	166	170	12.0000
..((	chr5:122096593-122096864(-)$1	1	24	28	12.0000
))))	chr6:56728726-56729000(-)$1	1	93	97	12.0000
((.(	chr14:64225930-64226213(+)$1	1	146	150	12.0000
..))	chr14:45912564-45912838(-)$1	1	169	173	12.0000
))))	chr14:103482193-103482469(-)$1	1	107	111	12.0000
..((	chr7:135038924-135039193(-)$1	1	80	84	12.0000
((((	chr9:64825927-64826205(+)$1	1	34	38	12.0000
((((	chr18:60859085-60859370(-)$1	1	17	21	12.0000
)).)	chr7:27949815-27950085(-)$1	1	132	136	12.0000
))).	chr2:156606172-156606446(+)$1	1	68	72	12.0000
((((	chr2:121205209-121205478(-)$1	1	31	35	12.0000
))))	chr7:117008957-117009223(-)$1	1	198	202	12.0000
((((	chr6:51413975-51414275(-)$1	1	42	46	12.0000
.(((	chr16:36049850-36050132(-)$1	1	217	221	12.0000
((((	chr7:52631892-52632163(-)$1	1	89	93	12.0000
(((.	chr2:32092890-32093158(+)$1	1	3	7	12.0000
))))	chr18:24743679-24743949(-)$1	1	121	125	12.0000
.(((	chr8:23489736-23490016(-)$1	1	52	56	12.0000
((((	chr7:28151313-28151603(-)$1	1	53	57	12.0000
((((	chr6:22240953-22241221(+)$1	1	8	12	12.0000
))..	chr17:35292433-35292717(-)$1	1	148	152	12.0000
((((	chr1:93275013-93275289(-)$1	1	149	153	12.0000
)).)	chr9:65194529-65194809(+)$1	1	27	31	12.0000
.(((	chr2:34678076-34678352(-)$1	1	28	32	12.0000
(((.	chr13:73773754-73774025(+)$1	1	41	45	12.0000
.(((	chr8:74844691-74844960(+)$1	1	97	101	12.0000
..))	chr19:8964904-8965185(+)$1	1	230	234	12.0000
))))	chr9:97269861-97270130(-)$1	1	58	62	12.0000
))))	chr4:45372561-45372833(+)$1	1	179	183	12.0000
..((	chr5:108863240-108863508(-)$1	1	54	58	12.0000
((..	chr3:95464614-95464908(+)$1	1	75	79	12.0000
((..	chr4:135883045-135883347(+)$1	1	49	53	12.0000
((((	chr11:87794777-87795061(-)$1	1	15	19	12.0000
((.(	chr19:5384494-5384771(-)$1	1	2	6	12.0000
..((	chr9:107159265-107159531(-)$1	1	123	127	12.0000
((((	chr8:86770433-86770706(-)$1	1	117	121	12.0000
(((.	chr11:102978337-102978633(+)$1	1	150	154	12.0000
(((.	chr9:66220026-66220300(+)$1	1	4	8	12.0000
.(((	chrX:98514856-98515126(+)$1	1	76	80	12.0000
....	chr2:31615419-31615714(+)$1	1	5	9	12.0000
((((	chr19:7273742-7274025(-)$1	1	20	24	12.0000

#PSSM
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	
G : 0.98	g : 0.01	
G : 0.99	

#score	636.0
#seq	53
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_CDS_m1_run1.nuc.txt

#NT
GCUUGAGGAA	chr13:81930934-81931204(+)$1	270	107	117	11.1627
CCUGGCGGGC	chr13:73773790-73774082(+)$1	292	129	139	10.9302
CCUGGAGGUG	chr19:8964904-8965185(+)$1	281	229	239	16.0465
GAUGGAGGAG	chr4:33125089-33125364(+)$1	275	138	148	12.7906
CCGGAAGGAG	chr7:28151313-28151603(-)$1	290	121	131	12.9069
CCUGGAACAG	chr18:60859085-60859370(-)$1	285	16	26	11.3953
CCUGGCGGGC	chr13:73773754-73774025(+)$1	271	165	175	10.9302
CCUGCGGGAC	chr13:69138016-69138287(-)$1	271	146	156	11.1627
CCUGGAGAAG	chr11:102978351-102978633(+)$1	282	135	145	15.4651
CCUGCCGGAG	chr19:46681119-46681390(+)$1	271	148	158	13.6046
ACUGGAAGAC	chr13:24843895-24844177(-)$1	282	164	174	10.3488
CCUUGAGGAG	chr9:98390942-98391210(+)$1	268	214	224	15.6976
GCUGGAGGGG	chr3:146444016-146444284(-)$1	268	49	59	13.9534
CCUGAAGGUG	chr9:64825922-64826205(+)$1	283	127	137	13.4883
CCUGAAUGAG	chr1:184398226-184398498(-)$1	272	93	103	12.9069
CCUCCAGGAG	chr17:6084525-6084804(+)$1	279	66	76	12.5581
CCUCCAGGAG	chr8:74842841-74843113(+)$1	272	197	207	12.5581
GCGGGAGGAG	chr2:174125804-174126076(+)$1	272	8	18	13.2558
GCUGAAGGAC	chr18:24743678-24743948(-)$1	270	236	246	12.5581
CCUGGGGAAG	chr5:137966809-137967086(+)$1	277	33	43	12.2093
ACUGGAGGAC	chr2:34678076-34678352(-)$1	276	180	190	14.5348
CUUGGAGGUG	chr12:85733283-85733552(-)$1	269	76	86	11.6279
CCUGGAGCAC	chrX:98514856-98515126(+)$1	270	194	204	13.3720
CCUGGAGGAG	chr7:135038927-135039193(-)$1	266	108	118	19.5348
GCUGGAGGUA	chr1:93275013-93275289(-)$1	276	148	158	11.5116
CCUGGGGGAG	chr19:7273741-7274022(-)$1	281	245	255	16.2790
CCUGGAUCAG	chr11:117828707-117828977(-)$1	270	83	93	11.5116
CCUUAAGGAG	chr8:95850590-95850858(-)$1	268	26	36	13.1395
CCUUGAGGAG	chr4:151560200-151560489(+)$1	289	16	26	15.6976
CCUGGAGGAU	chr9:107159263-107159531(-)$1	268	215	225	16.5116
CUUGAAGGAC	chr5:123244330-123244627(-)$1	297	162	172	10.3488
GCUGGAGGGA	chr5:93697524-93697808(+)$1	284	35	45	11.6279
ACCGGAGGAG	chr11:70466238-70466523(-)$1	285	186	196	12.5581
GCUGGGGGAA	chr5:92391562-92391834(-)$1	272	30	40	11.7441
UCUGAAGGAA	chr2:163884354-163884637(-)$1	283	122	132	11.6279
UCAGGAGGAG	chr14:52760735-52761006(+)$1	271	58	68	12.5581
CCAGGCGGAG	chr19:29086354-29086641(+)$1	287	20	30	12.5581
CCUGGCUGAA	chr8:87359374-87359661(-)$1	287	16	26	10.1162
ACUGAAGGAG	chr14:45912564-45912838(-)$1	274	54	64	14.1860
CCUGGUGGAA	chr1:77503123-77503392(-)$1	269	121	131	13.6046
CCAGCAGGAG	chr7:25670028-25670303(+)$1	275	155	165	12.6744
CCUGGCGGGG	chr2:31615419-31615714(+)$1	295	83	93	13.1395

#otherMatches

#Struct PSSM
IIII{GGGGG	chr3:95464619-95464908(+)$1	289	88	98	13.1395
FFFFFKKA::	chr13:81930934-81931204(+)$1	270	107	117	11.1627
DDDDBBEEEE	chr13:73773790-73774082(+)$1	292	129	139	10.9302
lllffffff7	chr19:8964904-8965185(+)$1	281	229	239	16.0465
uuuuuugggg	chr4:33125089-33125364(+)$1	275	138	148	12.7906
ccccc::::b	chr7:28151313-28151603(-)$1	290	121	131	12.9069
FFFFFF::dd	chr18:60859085-60859370(-)$1	285	16	26	11.3953
JJJJJJJJJJ	chr13:73773754-73774025(+)$1	271	165	175	10.9302
eeeee[a!!d	chr13:69138016-69138287(-)$1	271	146	156	11.1627
EEEEEMMMMA	chr11:102978351-102978633(+)$1	282	135	145	15.4651
rrrrrrdddd	chr19:46681119-46681390(+)$1	271	148	158	13.6046
mmdddd22ff	chr13:24843895-24844177(-)$1	282	164	174	10.3488
ddddlllddd	chr9:98390942-98391210(+)$1	268	214	224	15.6976
lhhhhhhhh:	chr3:146444016-146444284(-)$1	268	49	59	13.9534
LLLEEEEE{E	chr9:64825922-64826205(+)$1	283	127	137	13.4883
pppppppfff	chr1:184398226-184398498(-)$1	272	93	103	12.9069
b::EEEEEMM	chr17:6084525-6084804(+)$1	279	66	76	12.5581
eeeellleee	chr8:74842841-74843113(+)$1	272	197	207	12.5581
CC:dddd!!h	chr2:174125804-174126076(+)$1	272	8	18	13.2558
DDDD}CCC~~	chr18:24743678-24743948(-)$1	270	236	246	12.5581
:::hhhhhhh	chr5:137966809-137967086(+)$1	277	33	43	12.2093
sbb]dddd77	chr2:34678076-34678352(-)$1	276	180	190	14.5348
ee]eeeee]c	chr12:85733283-85733552(-)$1	269	76	86	11.6279
888eeeee::	chrX:98514856-98515126(+)$1	270	194	204	13.3720
ppppppbb]d	chr7:135038927-135039193(-)$1	266	108	118	19.5348
EEEEE::ddd	chr1:93275013-93275289(-)$1	276	148	158	11.5116
4444gggggg	chr19:7273741-7274022(-)$1	281	245	255	16.2790
ggggggg:::	chr11:117828707-117828977(-)$1	270	83	93	11.5116
LLLFFFFFFK	chr8:95850590-95850858(-)$1	268	26	36	13.1395
:=========	chr4:151560200-151560489(+)$1	289	16	26	15.6976
ABB}A}BB}C	chr9:107159263-107159531(-)$1	268	215	225	16.5116
ddd]a:ccco	chr5:123244330-123244627(-)$1	297	162	172	10.3488
cc[ggggggg	chr5:93697524-93697808(+)$1	284	35	45	11.6279
YEEEEEZZZG	chr11:70466238-70466523(-)$1	285	186	196	12.5581
ccc]eeeee:	chr5:92391562-92391834(-)$1	272	30	40	11.7441
eee::JJJJJ	chr2:163884354-163884637(-)$1	283	122	132	11.6279
bb:BB{AKKD	chr14:52760735-52761006(+)$1	271	58	68	12.5581
{EEEEEeeee	chr19:29086354-29086641(+)$1	287	20	30	12.5581
::eeeeemmm	chr8:87359374-87359661(-)$1	287	16	26	10.1162
22ccc:eeee	chr14:45912564-45912838(-)$1	274	54	64	14.1860
qqqdddd22e	chr1:77503123-77503392(-)$1	269	121	131	13.6046
d::bb[gggg	chr7:25670028-25670303(+)$1	275	155	165	12.6744
fffmmmmfff	chr2:31615419-31615714(+)$1	295	83	93	13.1395

#DB
((((.(((((	chr3:95464619-95464908(+)$1	1	88	98	13.1395
(((((..(..	chr13:81930934-81931204(+)$1	1	107	117	11.1627
))))))))))	chr13:73773790-73774082(+)$1	1	129	139	10.9302
...)))))).	chr19:8964904-8965185(+)$1	1	229	239	16.0465
......))))	chr4:33125089-33125364(+)$1	1	138	148	12.7906
)))))....(	chr7:28151313-28151603(-)$1	1	121	131	12.9069
((((((..((	chr18:60859085-60859370(-)$1	1	16	26	11.3953
))))))))))	chr13:73773754-73774025(+)$1	1	165	175	10.9302
(((((.(..(	chr13:69138016-69138287(-)$1	1	146	156	11.1627
(((((....(	chr11:102978351-102978633(+)$1	1	135	145	15.4651
......))))	chr19:46681119-46681390(+)$1	1	148	158	13.6046
..))))..))	chr13:24843895-24844177(-)$1	1	164	174	10.3488
((((...)))	chr9:98390942-98391210(+)$1	1	214	224	15.6976
.)))))))).	chr3:146444016-146444284(-)$1	1	49	59	13.9534
...(((((.(	chr9:64825922-64826205(+)$1	1	127	137	13.4883
.......)))	chr1:184398226-184398498(-)$1	1	93	103	12.9069
)..(((((..	chr17:6084525-6084804(+)$1	1	66	76	12.5581
((((...)))	chr8:74842841-74843113(+)$1	1	197	207	12.5581
((.((((..(	chr2:174125804-174126076(+)$1	1	8	18	13.2558
)))).)))..	chr18:24743678-24743948(-)$1	1	236	246	12.5581
...(((((((	chr5:137966809-137967086(+)$1	1	33	43	12.2093
.)).))))..	chr2:34678076-34678352(-)$1	1	180	190	14.5348
)).))))).)	chr12:85733283-85733552(-)$1	1	76	86	11.6279
...)))))..	chrX:98514856-98515126(+)$1	1	194	204	13.3720
......)).)	chr7:135038927-135039193(-)$1	1	108	118	19.5348
(((((..(((	chr1:93275013-93275289(-)$1	1	148	158	11.5116
....))))))	chr19:7273741-7274022(-)$1	1	245	255	16.2790
)))))))...	chr11:117828707-117828977(-)$1	1	83	93	11.5116
...((((((.	chr8:95850590-95850858(-)$1	1	26	36	13.1395
.(((((((((	chr4:151560200-151560489(+)$1	1	16	26	15.6976
))).).)).)	chr9:107159263-107159531(-)$1	1	215	225	16.5116
))).).(((.	chr5:123244330-123244627(-)$1	1	162	172	10.3488
((.(((((((	chr5:93697524-93697808(+)$1	1	35	45	11.6279
.)))))...)	chr11:70466238-70466523(-)$1	1	186	196	12.5581
))).))))).	chr5:92391562-92391834(-)$1	1	30	40	11.7441
)))..(((((	chr2:163884354-163884637(-)$1	1	122	132	11.6279
)).((.(..(	chr14:52760735-52761006(+)$1	1	58	68	12.5581
.(((((((((	chr19:29086354-29086641(+)$1	1	20	30	12.5581
..(((((...	chr8:87359374-87359661(-)$1	1	16	26	10.1162
..))).((((	chr14:45912564-45912838(-)$1	1	54	64	14.1860
...))))..)	chr1:77503123-77503392(-)$1	1	121	131	13.6046
)..((.((((	chr7:25670028-25670303(+)$1	1	155	165	12.6744
(((....)))	chr2:31615419-31615714(+)$1	1	83	93	13.1395

#PSSM
C : 0.65	G : 0.20	A : 0.09	U : 0.04	
C : 0.93	U : 0.04	A : 0.02	
U : 0.86	A : 0.06	G : 0.04	C : 0.02	
G : 0.86	U : 0.09	C : 0.04	
G : 0.69	A : 0.18	C : 0.11	
A : 0.74	C : 0.13	G : 0.09	U : 0.02	
G : 0.88	U : 0.06	A : 0.04	
G : 0.86	C : 0.06	A : 0.04	U : 0.02	
A : 0.79	G : 0.11	U : 0.09	
G : 0.62	C : 0.18	A : 0.16	U : 0.02	

#score	559.5348837209301
#seq	43
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m1_run2.nuc.txt

#NT
UGCUGCC	chr8:82208560-82208780(-)$1	220	50	57	11.1000
UGCUGUU	chr13:53429042-53429265(-)$1	223	2	9	11.6000
ggcuggU	chrX:147083983-147084203(-)$1	220	148	155	11.8000
UGCUGGC	chr18:60973682-60973902(-)$1	220	172	179	13.9000
UGCUGUG	chr18:32258876-32259105(+)$1	229	96	103	11.5000
ggcuggg	chr2:32162234-32162464(+)$1	230	23	30	11.7000
UGCUGGC	chr1:87805077-87805299(+)$1	222	22	29	13.9000
UGCUGGA	chr2:84877852-84878072(+)$1	220	108	115	13.6000
GGCUGGG	chr8:74148516-74148736(+)$1	220	2	9	11.7000
AGCUGGU	chr1:72633535-72633755(+)$1	220	183	190	11.3000
UGCUGGC	chr7:52822220-52822441(+)$1	221	165	172	13.9000
AGCUGGC	chr11:97067756-97067981(-)$1	225	3	10	11.2000
UGCUGGU	chr5:114292774-114292994(-)$1	220	0	7	14.0000
UGCUGGC	chr4:138933826-138934054(+)$1	228	25	32	13.9000
GGCUGGC	chr16:17528168-17528388(-)$1	220	177	184	11.7000
UGCUGAU	chr14:118562343-118562563(+)$1	220	21	28	11.0000
UGCUGUG	chr17:44223390-44223610(+)$1	220	47	54	11.5000
UGCUGCC	chr19:4318081-4318301(-)$1	220	12	19	11.1000
GGCUGGG	chr4:40752955-40753175(-)$1	220	61	68	11.7000
UGCUGAC	chr2:120334152-120334372(-)$1	220	133	140	10.9000
AGCUGGU	chr9:120860730-120860965(+)$1	235	63	70	11.3000
UGCUGGG	chr8:109709356-109709576(+)$1	220	166	173	13.9000
UGCUGCU	chr17:34728485-34728705(+)$1	220	157	164	11.2000
GGCUGGC	chr5:124567957-124568196(+)$1	239	55	62	11.7000
UGCUGGA	chr15:100224124-100224344(-)$1	220	89	96	13.6000
UGCUGGA	chr15:102262359-102262585(+)$1	226	35	42	13.6000
UGCUGGA	chr5:37808539-37808759(+)$1	220	133	140	13.6000
UGCUGGU	chr6:82676922-82677142(-)$1	220	37	44	14.0000
UGCUGAA	chr7:127874159-127874384(+)$1	225	139	146	10.6000
UGCUGUG	chr19:29090878-29091099(+)$1	221	135	142	11.5000
UGCUGUG	chr2:155216512-155216732(-)$1	220	136	143	11.5000
AGCUGGA	chr12:82819894-82820114(-)$1	220	63	70	10.9000
AGCUGGA	chr1:173218735-173218957(-)$1	222	41	48	10.9000
UGCUGUU	chr5:74992455-74992675(+)$1	220	208	215	11.6000
UGCUGGU	chr1:60041740-60041960(+)$1	220	71	78	14.0000
UGCUGGU	chr5:9119452-9119672(-)$1	220	122	129	14.0000
UGCUGGA	chr17:46786821-46787041(+)$1	220	12	19	13.6000
UGCUGCC	chr19:6985871-6986091(-)$1	220	74	81	11.1000
UGCUGGC	chr11:118891646-118891866(+)$1	220	67	74	13.9000
GGCUGGG	chr7:26452839-26453059(+)$1	220	101	108	11.7000
AGCUGGA	chr16:18240061-18240284(-)$1	223	37	44	10.9000
GGCUGGG	chr11:6305551-6305771(+)$1	220	101	108	11.7000
UGCUGUG	chr7:53339429-53339649(+)$1	220	12	19	11.5000
UGCUGUU	chr17:71596874-71597095(+)$1	221	46	53	11.6000
UGCUGUU	chr15:72936358-72936578(-)$1	220	116	123	11.6000
GGCUGGG	chr8:122333973-122334193(-)$1	220	12	19	11.7000
UGCUGGU	chr17:44236041-44236261(-)$1	220	196	203	14.0000
GGCUGGG	chr10:58911391-58911613(-)$1	222	164	171	11.7000
UGCUGCC	chr19:6262098-6262344(+)$1	246	16	23	11.1000

#otherMatches

#Struct PSSM
ggggggg	chr9:46081537-46081764(+)$1	227	101	108	11.4000
gpppppp	chr8:82208560-82208780(-)$1	220	50	57	11.1000
CCCMMMM	chr13:53429042-53429265(-)$1	223	2	9	11.6000
44=====	chrX:147083983-147084203(-)$1	220	148	155	11.8000
YYBB}EE	chr18:60973682-60973902(-)$1	220	172	179	13.9000
EEEEEEE	chr18:32258876-32259105(+)$1	229	96	103	11.5000
dd]eeee	chr2:32162234-32162464(+)$1	230	23	30	11.7000
eeea[ff	chr1:87805077-87805299(+)$1	222	22	29	13.9000
oooccc2	chr2:84877852-84878072(+)$1	220	108	115	13.6000
ddd[ccc	chr8:74148516-74148736(+)$1	220	2	9	11.7000
:DDDDBB	chr1:72633535-72633755(+)$1	220	183	190	11.3000
EEEEeee	chr7:52822220-52822441(+)$1	221	165	172	13.9000
::::BB{	chr11:97067756-97067981(-)$1	225	3	10	11.2000
ggggggg	chr5:114292774-114292994(-)$1	220	0	7	14.0000
nna]ccc	chr4:138933826-138934054(+)$1	228	25	32	13.9000
###bbtt	chr16:17528168-17528388(-)$1	220	177	184	11.7000
=======	chr14:118562343-118562563(+)$1	220	21	28	11.0000
hhhh:==	chr17:44223390-44223610(+)$1	220	47	54	11.5000
{EEEEEB	chr19:4318081-4318301(-)$1	220	12	19	11.1000
===GGGG	chr4:40752955-40753175(-)$1	220	61	68	11.7000
=======	chr2:120334152-120334372(-)$1	220	133	140	10.9000
nnnnddd	chr9:120860730-120860965(+)$1	235	63	70	11.3000
gggg!!c	chr8:109709356-109709576(+)$1	220	166	173	13.9000
CCCEEEE	chr17:34728485-34728705(+)$1	220	157	164	11.2000
eeeeeff	chr5:124567957-124568196(+)$1	239	55	62	11.7000
QQQQHHH	chr15:100224124-100224344(-)$1	220	89	96	13.6000
eeeeeee	chr15:102262359-102262585(+)$1	226	35	42	13.6000
d333ddd	chr5:37808539-37808759(+)$1	220	133	140	13.6000
fcccbbo	chr6:82676922-82677142(-)$1	220	37	44	14.0000
sssssss	chr7:127874159-127874384(+)$1	225	139	146	10.6000
####a[c	chr19:29090878-29091099(+)$1	221	135	142	11.5000
ff[ccc"	chr2:155216512-155216732(-)$1	220	136	143	11.5000
:::::DD	chr12:82819894-82820114(-)$1	220	63	70	10.9000
=======	chr1:173218735-173218957(-)$1	222	41	48	10.9000
JJJJJJJ	chr5:74992455-74992675(+)$1	220	208	215	11.6000
bmmmmbb	chr1:60041740-60041960(+)$1	220	71	78	14.0000
=======	chr5:9119452-9119672(-)$1	220	122	129	14.0000
cbbdddd	chr17:46786821-46787041(+)$1	220	12	19	13.6000
EEEEEEE	chr19:6985871-6986091(-)$1	220	74	81	11.1000
#ccc[dd	chr11:118891646-118891866(+)$1	220	67	74	13.9000
eeeCCCE	chr7:26452839-26453059(+)$1	220	101	108	11.7000
%%dddd"	chr16:18240061-18240284(-)$1	223	37	44	10.9000
d22hhhh	chr11:6305551-6305771(+)$1	220	101	108	11.7000
ggggggg	chr7:53339429-53339649(+)$1	220	12	19	11.5000
eee]bbe	chr17:71596874-71597095(+)$1	221	46	53	11.6000
bIIIIII	chr15:72936358-72936578(-)$1	220	116	123	11.6000
eeeee!!	chr8:122333973-122334193(-)$1	220	12	19	11.7000
ddd6666	chr17:44236041-44236261(-)$1	220	196	203	14.0000
ZCCCZZZ	chr10:58911391-58911613(-)$1	222	164	171	11.7000
E:::eee	chr19:6262098-6262344(+)$1	246	16	23	11.1000

#DB
(((((((	chr9:46081537-46081764(+)$1	1	101	108	11.4000
(......	chr8:82208560-82208780(-)$1	1	50	57	11.1000
(((....	chr13:53429042-53429265(-)$1	1	2	9	11.6000
..)))))	chrX:147083983-147084203(-)$1	1	148	155	11.8000
..)).))	chr18:60973682-60973902(-)$1	1	172	179	13.9000
)))))((	chr18:32258876-32259105(+)$1	1	96	103	11.5000
)).))))	chr2:32162234-32162464(+)$1	1	23	30	11.7000
)))(.((	chr1:87805077-87805299(+)$1	1	22	29	13.9000
...))).	chr2:84877852-84878072(+)$1	1	108	115	13.6000
(((.(((	chr8:74148516-74148736(+)$1	1	2	9	11.7000
.))))))	chr1:72633535-72633755(+)$1	1	183	190	11.3000
))))(((	chr7:52822220-52822441(+)$1	1	165	172	13.9000
....((.	chr11:97067756-97067981(-)$1	1	3	10	11.2000
(((((((	chr5:114292774-114292994(-)$1	1	0	7	14.0000
..).)))	chr4:138933826-138934054(+)$1	1	25	32	13.9000
...((..	chr16:17528168-17528388(-)$1	1	177	184	11.7000
)))))))	chr14:118562343-118562563(+)$1	1	21	28	11.0000
)))).((	chr17:44223390-44223610(+)$1	1	47	54	11.5000
.((((((	chr19:4318081-4318301(-)$1	1	12	19	11.1000
)))((((	chr4:40752955-40753175(-)$1	1	61	68	11.7000
(((((((	chr2:120334152-120334372(-)$1	1	133	140	10.9000
....)))	chr9:120860730-120860965(+)$1	1	63	70	11.3000
((((..(	chr8:109709356-109709576(+)$1	1	166	173	13.9000
)))))))	chr17:34728485-34728705(+)$1	1	157	164	11.2000
(((((((	chr5:124567957-124568196(+)$1	1	55	62	11.7000
....(((	chr15:100224124-100224344(-)$1	1	89	96	13.6000
))))(((	chr15:102262359-102262585(+)$1	1	35	42	13.6000
)...)))	chr5:37808539-37808759(+)$1	1	133	140	13.6000
)(((((.	chr6:82676922-82677142(-)$1	1	37	44	14.0000
.......	chr7:127874159-127874384(+)$1	1	139	146	10.6000
....(.(	chr19:29090878-29091099(+)$1	1	135	142	11.5000
((.(((.	chr2:155216512-155216732(-)$1	1	136	143	11.5000
.....((	chr12:82819894-82820114(-)$1	1	63	70	10.9000
)))))))	chr1:173218735-173218957(-)$1	1	41	48	10.9000
)))))))	chr5:74992455-74992675(+)$1	1	208	215	11.6000
(....))	chr1:60041740-60041960(+)$1	1	71	78	14.0000
)))))))	chr5:9119452-9119672(-)$1	1	122	129	14.0000
(((((((	chr17:46786821-46787041(+)$1	1	12	19	13.6000
(((((((	chr19:6985871-6986091(-)$1	1	74	81	11.1000
.(((.((	chr11:118891646-118891866(+)$1	1	67	74	13.9000
)))))))	chr7:26452839-26453059(+)$1	1	101	108	11.7000
..((((.	chr16:18240061-18240284(-)$1	1	37	44	10.9000
)..))))	chr11:6305551-6305771(+)$1	1	101	108	11.7000
(((((((	chr7:53339429-53339649(+)$1	1	12	19	11.5000
))).))(	chr17:71596874-71597095(+)$1	1	46	53	11.6000
)((((((	chr15:72936358-72936578(-)$1	1	116	123	11.6000
(((((..	chr8:122333973-122334193(-)$1	1	12	19	11.7000
)))....	chr17:44236041-44236261(-)$1	1	196	203	14.0000
.)))...	chr10:58911391-58911613(-)$1	1	164	171	11.7000
(...(((	chr19:6262098-6262344(+)$1	1	16	23	11.1000

#PSSM
U : 0.66	G : 0.18	A : 0.12	g : 0.04	
G : 0.96	g : 0.04	
C : 0.96	c : 0.04	
U : 0.96	u : 0.04	
G : 0.96	g : 0.04	
G : 0.62	U : 0.18	C : 0.10	A : 0.06	g : 0.04	
U : 0.27	C : 0.25	G : 0.23	A : 0.19	g : 0.02	

#score	608.4000000000007
#seq	50
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m2_run1.nuc.txt

#NT
CAUUUCC	chr13:67034485-67034686(+)$1	201	15	22	13.2131
CAUUUCA	chr11:62166663-62166864(-)$1	201	98	105	17.6393
CCUUUCA	chr1:196615842-196616043(+)$1	201	12	19	13.7868
CAUUACA	chr17:44217689-44217890(+)$1	201	166	173	12.8852
CCUUUCA	chr17:32335839-32336040(-)$1	201	124	131	13.7868
CAUCUCA	chr9:45509811-45510012(+)$1	201	95	102	14.5245
CAUGUCA	chr2:35570821-35571022(+)$1	201	96	103	13.8688
CUUUUCA	chr9:42063723-42063924(-)$1	201	99	106	13.9508
CACUUCA	chr16:45187743-45187944(+)$1	201	96	103	13.2950
CACUUCA	chr1:94933358-94933559(-)$1	201	6	13	13.2950
CAUCUCA	chr8:96524225-96524426(-)$1	201	57	64	14.5245
UAUUUCA	chr8:128912997-128913198(+)$1	201	96	103	12.8852
CAUUUCA	chr19:10496237-10496438(+)$1	201	96	103	17.6393
CAUUUCU	chr12:32393814-32394015(-)$1	201	98	105	13.2950
CAUUUAA	chr6:30700485-30700686(+)$1	201	14	21	13.2131
CAUCUCA	chr8:11817576-11817777(+)$1	201	45	52	14.5245
CAUUUCA	chr17:71764892-71765093(-)$1	201	97	104	17.6393
CAUCUCA	chr15:85223778-85223979(+)$1	201	101	108	14.5245
CAUUUCA	chr2:155899066-155899267(-)$1	201	98	105	17.6393
CAUCUCA	chr9:44627180-44627381(-)$1	201	97	104	14.5245
CAUUUCA	chr7:64434912-64435113(-)$1	201	98	105	17.6393
CAUUUCA	chr2:69661781-69661982(+)$1	201	96	103	17.6393
CCUUUCA	chr3:101383673-101383874(-)$1	201	98	105	13.7868
CAUUUCA	chrX:154264291-154264492(-)$1	201	98	105	17.6393
CAUCUCA	chr5:130716145-130716346(+)$1	201	96	103	14.5245
CAUUUCA	chr13:51942901-51943102(+)$1	201	96	103	17.6393
CAUCUCA	chrX:67093634-67093835(+)$1	201	96	103	14.5245
cauuuca	chr2:98502463-98502664(+)$1	201	175	182	17.6393
CCUUUCA	chr14:120268426-120268627(+)$1	201	96	103	13.7868
CUUUUCA	chr10:4929568-4929769(-)$1	201	99	106	13.9508
CAUUUCA	chr16:94664224-94664425(+)$1	201	96	103	17.6393
CAUAUCA	chr8:67098096-67098297(-)$1	201	99	106	13.7868
CACUUCA	chr13:55392502-55392703(+)$1	201	96	103	13.2950
CAUCUCA	chr2:23015634-23015835(+)$1	201	95	102	14.5245
CAUUUCU	chr14:69972405-69972606(+)$1	201	0	7	13.2950
CAUUUCA	chr14:122372763-122372964(+)$1	201	96	103	17.6393
CAUUUCU	chr17:47100560-47100761(-)$1	201	98	105	13.2950
CAUUUCA	chr8:60906507-60906708(-)$1	201	98	105	17.6393
CAUUUCA	chr13:49027586-49027787(-)$1	201	98	105	17.6393
CAUCUCA	chr3:107480569-107480770(-)$1	201	98	105	14.5245
CAUUUCA	chr16:87483259-87483460(-)$1	201	98	105	17.6393
CAUUCCA	chr11:62142973-62143174(-)$1	201	78	85	12.8852
CAUUUCA	chr2:29001845-29002046(+)$1	201	96	103	17.6393
CAUUUCC	chr2:104096172-104096373(-)$1	201	34	41	13.2131
CAGUUCA	chr3:136566059-136566260(+)$1	201	48	55	13.2131
CAUUUAA	chr18:35023025-35023226(+)$1	201	40	47	13.2131
CAUUUCA	chr18:21013389-21013590(-)$1	201	98	105	17.6393
CAUUUCA	chr17:80819632-80819833(-)$1	201	98	105	17.6393
CAUUUGA	chr17:87423061-87423262(-)$1	201	147	154	13.0491
CUUUUCA	chr5:114491780-114491981(-)$1	201	99	106	13.9508
CAUCUCA	chr5:121778058-121778259(+)$1	201	96	103	14.5245
CUUUUCA	chr6:83149618-83149819(+)$1	201	96	103	13.9508
CAUGUCA	chr1:154703577-154703778(-)$1	201	79	86	13.8688
GAUUUCA	chr6:135993862-135994063(-)$1	201	80	87	12.8852
CAGUUCA	chr9:16181020-16181221(-)$1	201	103	110	13.2131
CUUUUCA	chr3:125618256-125618457(-)$1	201	70	77	13.9508
CUUUUCA	chr5:23988007-23988208(+)$1	201	96	103	13.9508
CAUUUAA	chr11:6196949-6197150(+)$1	201	37	44	13.2131
CAUUUCA	chr2:91045917-91046118(+)$1	201	96	103	17.6393
CAUUUCA	chr12:53618466-53618667(+)$1	201	96	103	17.6393

#otherMatches

#Struct PSSM
d::::::	chr11:78842481-78842682(-)$1	201	98	105	17.6393
doooooo	chr13:67034485-67034686(+)$1	201	15	22	13.2131
b####bb	chr11:62166663-62166864(-)$1	201	98	105	17.6393
MMMCCC{	chr1:196615842-196616043(+)$1	201	12	19	13.7868
ddqqqqq	chr17:44217689-44217890(+)$1	201	166	173	12.8852
EEEEPPP	chr17:32335839-32336040(-)$1	201	124	131	13.7868
^^^^^^^	chr9:45509811-45510012(+)$1	201	95	102	14.5245
:::::::	chr2:35570821-35571022(+)$1	201	96	103	13.8688
zzzzzzz	chr9:42063723-42063924(-)$1	201	99	106	13.9508
::fffff	chr16:45187743-45187944(+)$1	201	96	103	13.2950
:::::::	chr1:94933358-94933559(-)$1	201	6	13	13.2950
hhh[ggg	chr8:96524225-96524426(-)$1	201	57	64	14.5245
hhhhhhh	chr8:128912997-128913198(+)$1	201	96	103	12.8852
ffffff:	chr19:10496237-10496438(+)$1	201	96	103	17.6393
666eeee	chr12:32393814-32394015(-)$1	201	98	105	13.2950
b[ccc!!	chr6:30700485-30700686(+)$1	201	14	21	13.2131
:::::::	chr8:11817576-11817777(+)$1	201	45	52	14.5245
uufffff	chr17:71764892-71765093(-)$1	201	97	104	17.6393
22ccc22	chr15:85223778-85223979(+)$1	201	101	108	14.5245
))))ccc	chr2:155899066-155899267(-)$1	201	98	105	17.6393
cqqqqqq	chr9:44627180-44627381(-)$1	201	97	104	14.5245
[a!!bbo	chr7:64434912-64435113(-)$1	201	98	105	17.6393
e::::::	chr2:69661781-69661982(+)$1	201	96	103	17.6393
EENNNNN	chr3:101383673-101383874(-)$1	201	98	105	13.7868
qqqccc2	chrX:154264291-154264492(-)$1	201	98	105	17.6393
eeellle	chr5:130716145-130716346(+)$1	201	96	103	14.5245
6666hhh	chr13:51942901-51943102(+)$1	201	96	103	17.6393
e[dddd#	chrX:67093634-67093835(+)$1	201	96	103	14.5245
nnnnnff	chr2:98502463-98502664(+)$1	201	175	182	17.6393
:::::::	chr14:120268426-120268627(+)$1	201	96	103	13.7868
eeeCCC}	chr10:4929568-4929769(-)$1	201	99	106	13.9508
"eeeee$	chr16:94664224-94664425(+)$1	201	96	103	17.6393
:::::::	chr8:67098096-67098297(-)$1	201	99	106	13.7868
HHHHH::	chr13:55392502-55392703(+)$1	201	96	103	13.2950
e::::::	chr2:23015634-23015835(+)$1	201	95	102	14.5245
:::::::	chr14:69972405-69972606(+)$1	201	0	7	13.2950
:::::::	chr14:122372763-122372964(+)$1	201	96	103	17.6393
+++++++	chr17:47100560-47100761(-)$1	201	98	105	13.2950
::ddddn	chr8:60906507-60906708(-)$1	201	98	105	17.6393
:::::::	chr13:49027586-49027787(-)$1	201	98	105	17.6393
^^^^^^^	chr3:107480569-107480770(-)$1	201	98	105	14.5245
88ggggg	chr16:87483259-87483460(-)$1	201	98	105	17.6393
:::::::	chr11:62142973-62143174(-)$1	201	78	85	12.8852
b"""ccc	chr2:29001845-29002046(+)$1	201	96	103	17.6393
EEEEE::	chr2:104096172-104096373(-)$1	201	34	41	13.2131
fffflll	chr3:136566059-136566260(+)$1	201	48	55	13.2131
:::::::	chr18:35023025-35023226(+)$1	201	40	47	13.2131
ppdddd3	chr18:21013389-21013590(-)$1	201	98	105	17.6393
:::::::	chr17:80819632-80819833(-)$1	201	98	105	17.6393
:::::::	chr17:87423061-87423262(-)$1	201	147	154	13.0491
6666bb3	chr5:114491780-114491981(-)$1	201	99	106	13.9508
:::::::	chr5:121778058-121778259(+)$1	201	96	103	14.5245
nnnnddd	chr6:83149618-83149819(+)$1	201	96	103	13.9508
eeccc[e	chr1:154703577-154703778(-)$1	201	79	86	13.8688
>>>>>>>	chr6:135993862-135994063(-)$1	201	80	87	12.8852
::eeeee	chr9:16181020-16181221(-)$1	201	103	110	13.2131
oooooff	chr3:125618256-125618457(-)$1	201	70	77	13.9508
:::::::	chr5:23988007-23988208(+)$1	201	96	103	13.9508
eeeee::	chr11:6196949-6197150(+)$1	201	37	44	13.2131
:::::::	chr2:91045917-91046118(+)$1	201	96	103	17.6393
hhhhhh:	chr12:53618466-53618667(+)$1	201	96	103	17.6393

#DB
)......	chr11:78842481-78842682(-)$1	1	98	105	17.6393
(......	chr13:67034485-67034686(+)$1	1	15	22	13.2131
(....((	chr11:62166663-62166864(-)$1	1	98	105	17.6393
...(((.	chr1:196615842-196616043(+)$1	1	12	19	13.7868
((.....	chr17:44217689-44217890(+)$1	1	166	173	12.8852
((((...	chr17:32335839-32336040(-)$1	1	124	131	13.7868
.......	chr9:45509811-45510012(+)$1	1	95	102	14.5245
.......	chr2:35570821-35571022(+)$1	1	96	103	13.8688
.......	chr9:42063723-42063924(-)$1	1	99	106	13.9508
..(((((	chr16:45187743-45187944(+)$1	1	96	103	13.2950
.......	chr1:94933358-94933559(-)$1	1	6	13	13.2950
(((.(((	chr8:96524225-96524426(-)$1	1	57	64	14.5245
(((((((	chr8:128912997-128913198(+)$1	1	96	103	12.8852
)))))).	chr19:10496237-10496438(+)$1	1	96	103	17.6393
...))))	chr12:32393814-32394015(-)$1	1	98	105	13.2950
(.(((..	chr6:30700485-30700686(+)$1	1	14	21	13.2131
.......	chr8:11817576-11817777(+)$1	1	45	52	14.5245
..)))))	chr17:71764892-71765093(-)$1	1	97	104	17.6393
..)))..	chr15:85223778-85223979(+)$1	1	101	108	14.5245
....(((	chr2:155899066-155899267(-)$1	1	98	105	17.6393
(......	chr9:44627180-44627381(-)$1	1	97	104	14.5245
.(..((.	chr7:64434912-64435113(-)$1	1	98	105	17.6393
)......	chr2:69661781-69661982(+)$1	1	96	103	17.6393
((.....	chr3:101383673-101383874(-)$1	1	98	105	13.7868
...))).	chrX:154264291-154264492(-)$1	1	98	105	17.6393
(((...)	chr5:130716145-130716346(+)$1	1	96	103	14.5245
....)))	chr13:51942901-51943102(+)$1	1	96	103	17.6393
(.((((.	chrX:67093634-67093835(+)$1	1	96	103	14.5245
.....))	chr2:98502463-98502664(+)$1	1	175	182	17.6393
.......	chr14:120268426-120268627(+)$1	1	96	103	13.7868
)))))).	chr10:4929568-4929769(-)$1	1	99	106	13.9508
.(((((.	chr16:94664224-94664425(+)$1	1	96	103	17.6393
.......	chr8:67098096-67098297(-)$1	1	99	106	13.7868
(((((..	chr13:55392502-55392703(+)$1	1	96	103	13.2950
)......	chr2:23015634-23015835(+)$1	1	95	102	14.5245
.......	chr14:69972405-69972606(+)$1	1	0	7	13.2950
.......	chr14:122372763-122372964(+)$1	1	96	103	17.6393
.......	chr17:47100560-47100761(-)$1	1	98	105	13.2950
..((((.	chr8:60906507-60906708(-)$1	1	98	105	17.6393
.......	chr13:49027586-49027787(-)$1	1	98	105	17.6393
.......	chr3:107480569-107480770(-)$1	1	98	105	14.5245
..)))))	chr16:87483259-87483460(-)$1	1	98	105	17.6393
.......	chr11:62142973-62143174(-)$1	1	78	85	12.8852
(...(((	chr2:29001845-29002046(+)$1	1	96	103	17.6393
(((((..	chr2:104096172-104096373(-)$1	1	34	41	13.2131
((((...	chr3:136566059-136566260(+)$1	1	48	55	13.2131
.......	chr18:35023025-35023226(+)$1	1	40	47	13.2131
..)))).	chr18:21013389-21013590(-)$1	1	98	105	17.6393
.......	chr17:80819632-80819833(-)$1	1	98	105	17.6393
.......	chr17:87423061-87423262(-)$1	1	147	154	13.0491
....)).	chr5:114491780-114491981(-)$1	1	99	106	13.9508
.......	chr5:121778058-121778259(+)$1	1	96	103	14.5245
....)))	chr6:83149618-83149819(+)$1	1	96	103	13.9508
(((((.(	chr1:154703577-154703778(-)$1	1	79	86	13.8688
.......	chr6:135993862-135994063(-)$1	1	80	87	12.8852
..(((((	chr9:16181020-16181221(-)$1	1	103	110	13.2131
.....))	chr3:125618256-125618457(-)$1	1	70	77	13.9508
.......	chr5:23988007-23988208(+)$1	1	96	103	13.9508
)))))..	chr11:6196949-6197150(+)$1	1	37	44	13.2131
.......	chr2:91045917-91046118(+)$1	1	96	103	17.6393
)))))).	chr12:53618466-53618667(+)$1	1	96	103	17.6393

#PSSM
C : 0.95	U : 0.01	c : 0.01	G : 0.01	
A : 0.81	U : 0.09	C : 0.06	a : 0.01	
U : 0.90	C : 0.04	G : 0.03	u : 0.01	
U : 0.77	C : 0.16	G : 0.03	u : 0.01	A : 0.01	
U : 0.95	A : 0.01	u : 0.01	C : 0.01	
C : 0.91	A : 0.04	c : 0.01	G : 0.01	
A : 0.90	U : 0.04	C : 0.03	a : 0.01	

#score	915.2622950819682
#seq	61
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_UTR_m1_run2.nuc.txt

#NT
gugugugugugugugugugugugugugugugugugugugugugugugu	chr9:45670977-45671454(+)$1	477	37	85	129.3278
AAgugugugugugugugugugugugugugugugugugugugugugugu	chr4:115506994-115507363(+)$1	369	149	197	125.0655
guguguguguguguguguguguguguguguguguguguguauguaugu	chr3:152482178-152482665(-)$1	487	108	156	120.5573
Augugugugugugugugugugugugugugugugugugugugugugugu	chr11:119399829-119400277(-)$1	448	269	317	128.6721
uguggggugugugugugugugugugugugugugugugugugugugugA	chr9:57443737-57444087(+)$1	350	99	147	108.4262
guguguauguguguguguguguguguguaugugugugugugugugugu	chr11:95275315-95275802(+)$1	487	140	188	120.4754
UCCugugugugugugugugugugugugugugugugugugugGUCGUAU	chr6:149505888-149506364(+)$1	476	173	221	102.5245
UUGGUUCCgugugugugugugugugugugugugugugugugugugugu	chr7:117773040-117773346(+)$1	306	125	173	111.9508
augugugugugugugugugugugugugugugugugugugugugugugu	chr12:45956225-45956703(-)$1	478	237	285	128.6721
gugugugugugugugugugugugugugugugugugugugugugugugu	chr9:50571208-50571422(-)$1	214	41	89	129.3278
CCgugugugugugugugugugugugugugugugugugugugugugugu	chr14:61381193-61381550(+)$1	357	143	191	124.9836
cuuugugugugugugugugugugugugugugugugugugugugCGCGU	chr6:148123717-148124042(+)$1	325	144	192	116.0491
GGGUUCAUUugugugugugugugugugugugugugugugugugugugu	chrX:140296440-140296758(-)$1	318	251	299	108.7540
gugugugugugugugugugugugugugugugugugugugugugugcgu	chr6:55448913-55449385(+)$1	472	199	247	124.9836
guguguguguguguguguguguguguguguguguguguguaugugugu	chr16:15552519-15552908(-)$1	389	196	244	125.0655
gugugugugugugugugugugugugugugugugugugugugugugugu	chr4:107544779-107545255(+)$1	476	266	314	129.3278
augugugugugugugugugugugugugugugugugugugugugugugu	chr10:60225758-60226069(-)$1	311	155	203	128.6721
Uugugugugugugugugugugugugugugugugugugugugugugugu	chr8:113973776-113974090(-)$1	314	38	86	128.2622
cugugugugugcgugugcguguguguaugugugugcgugugugugugu	chr4:41466222-41466709(-)$1	487	423	471	109.9836
cuguguguguaugagugugugugugagugugugugugugugugugugu	chr4:149090042-149090309(-)$1	267	156	204	114.4918
ACGGgugugugugugugugugugugugugugugugugugugagggaga	chr11:43233849-43234332(-)$1	483	86	134	103.1803
augugugugugugugugugugugugugugugcucaugugugugugugc	chr17:34746396-34746753(+)$1	357	44	92	105.8852
cucucucugugugugugugugugugugugugugugugugugugugugu	chr7:134949923-134950414(-)$1	491	309	357	116.5409
UGgugugugugugugugugugugugugugugugugugugugugugugu	chr1:136308026-136308379(+)$1	353	124	172	124.6557
UAGAguguguguguguguguguguguguguguguaugugaguguguau	chr1:77365578-77366011(-)$1	433	324	372	106.8688
AGgugugugugugugugugugugugugugugugugugugugugugugu	chr2:153083062-153083543(+)$1	481	267	315	125.0655
gugugugugugugugugugugugugugugugugugugugugugugugu	chr9:48462119-48462543(-)$1	424	185	233	129.3278
ACgugugugugugugugugugugugugugugucugucugucugucugu	chr5:89187329-89187653(+)$1	324	133	181	106.7868
UUCAUUCUGAGGgugugugugugugugugugugugugugugugugugu	chr6:127639117-127639616(-)$1	499	307	355	103.2622
gugcgcgcgcgcgugugugugugugugugugugugugugugugugugu	chr6:48387239-48387619(-)$1	380	211	259	107.9344
UUUugcgugucugugugugugugugugugugugugugugugugugugc	chr16:91014890-91015267(-)$1	377	262	310	111.4590
Uuguguguguguguguguguguguguguguguguguguguguguguau	chr17:46154369-46154651(-)$1	282	129	177	123.8360
augugugugugugugugugugugugugugugugugugugugugugugu	chr15:84533464-84533838(+)$1	374	216	264	128.6721
Auguguguguguguguguguguguguguguguguguguguaugugugu	chr9:86717496-86717981(-)$1	485	318	366	124.4098
AAgugugugugugugugugugugugugugugugugugugugugcgcgc	chr15:3532386-3532776(-)$1	390	43	91	112.1147
Cugugugugugugugugugugugugugugugugugugugugugugugu	chr8:109898652-109899117(+)$1	465	41	89	128.5081
CUCCUAAugugugugugugugugugugugugugugugugugugugugu	chr19:5371119-5371411(+)$1	292	56	104	108.4262
CugugugugugugugugugugugugugugugugugugugugugugGUU	chr5:52928173-52928629(-)$1	456	205	253	119.4098
gugugugugugugugugugugugugugugugugugugugugugugugu	chr17:44413014-44413291(+)$1	277	115	163	129.3278
augugugugugugugugugugcgugugugugugugugugugugugugu	chr2:30881776-30882273(-)$1	497	306	354	123.8360
AAguguguguguguguguguguguguguauguauguauguauguaugu	chr2:120445080-120445387(+)$1	307	126	174	102.5245
gugugugugugugugugugugugugugugugugugugugugugugugu	chr11:70477287-70477608(-)$1	321	169	217	129.3278
gugugugugugugugugugugugugugugugugugugugugugugugu	chr3:105520491-105520933(+)$1	442	220	268	129.3278
Cugugugugugugugugugugugugugugugugugugugugugugugu	chr17:56315347-56315779(-)$1	432	174	222	128.5081
GCAugugugugugugugugugugagaguguguaugugugugugugugu	chr11:97362677-97363137(+)$1	460	192	240	108.1803
cuuugugugugcgcaugugugugugugugugugugugugugugugugu	chr13:110851193-110851682(-)$1	489	51	99	110.9672
gugugugugugugugugugugugugugugugugugugugcgugugugu	chr8:66494142-66494513(-)$1	371	166	214	124.5737
gugugugugugugugugugugugugugugugugugugugugugugugA	chr1:173393965-173394215(+)$1	250	1	49	125.2295
guguguguguguguguaugugugcgugcgugcgugcgugugugugugu	chr1:34872008-34872507(-)$1	499	76	124	105.7213
Cugugugugugugugugugugugugugugugugugugugugugugugu	chr9:40153367-40153855(-)$1	488	386	434	128.5081
CuguaugagugugugugagugugugaguguguguaugugugugugugA	chr3:32832500-32832863(+)$1	363	150	198	102.1967
gugcguguguguguguguguguguguguguguguguguguguguuugu	chr12:103807813-103808219(-)$1	406	167	215	120.8032
UUGUUUUGGGgugugugugugugugugugugugugugugugugugugu	chr8:96838755-96839159(+)$1	404	51	99	110.9672
gugcgugcgugcgugcgugcgugcgugugugugugugugugugugugu	chr9:108000430-108000921(-)$1	491	145	193	102.5245
gugugugugugugugugugugugugugugugugugugugugugugugu	chr9:112134775-112135263(-)$1	488	132	180	129.3278
CUUUCugugugugugugugugugugugugugugugugugugugugugu	chr2:102622148-102622631(+)$1	483	174	222	120.8032
guauacgugugugugugugugugugugugugugugugugugugugugu	chr10:59595545-59595902(+)$1	357	251	299	117.2786
Augugugugugugugugugugugugugugugugugugugugugugugu	chr1:174428714-174429055(+)$1	341	137	185	128.6721
auguauguguguguguguguguguguguguguguguaugugugugugu	chr4:106418853-106419345(-)$1	492	220	268	120.1475
gugugugugugugugugugugugugugugcgugugugugugugugugu	chr6:120432437-120432771(+)$1	334	119	167	124.4918

#otherMatches

#Struct PSSM
DD{DDDD{DDDDQQQQQQQQBBKKA{BBMMMMCCC{AKKDDDD:::::	chr17:24213376-24213837(-)$1	461	158	206	129.3278
CCC{EEEEE{A{DDDD{EEEEEKKCCC{CCCLLLBB{DDDDLLLCCC{	chr9:45670977-45671454(+)$1	477	37	85	129.3278
c::CCCYYCCC}CCC}A}EEEEE}A}BB~~~~DDDD:ggggggg[bb[	chr4:115506994-115507363(+)$1	369	149	197	125.0655
hhh:::JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ	chr3:152482178-152482665(-)$1	487	108	156	120.5573
ccc]a:::::ggggggg%%%%%%ccc[bb[ffffff"""ddddooooo	chr11:119399829-119400277(-)$1	448	269	317	128.6721
{GGGGGGG::::::::::::::::::::::::GGGGGGG{EEEEE{DD	chr9:57443737-57444087(+)$1	350	99	147	108.4262
4444ffffff]bbdddd]ccc]hhhhhhhh:a[ccc[a[a[eeeee[c	chr11:95275315-95275802(+)$1	487	140	188	120.4754
CCCCLLLJJJJJJJJJJJJJJJLLLEEEEELLLDDDDiiiiiiiii!!	chr6:149505888-149506364(+)$1	476	173	221	102.5245
FFFFFF::::::::::::::::::::::::::::::::::::::::::	chr7:117773040-117773346(+)$1	306	125	173	111.9508
EE{BB{BB{CCCLLLBB{BB{BB{BB{EEEEE::::::::::::::==	chr12:45956225-45956703(-)$1	478	237	285	128.6721
oobb]ffffffccc]a::::::::::::::::::::::::::::::::	chr9:50571208-50571422(-)$1	214	41	89	129.3278
gg]dddd]a]a]ccc::::::CCC}DDDD}CCCYYEEEEE~~~~EEEE	chr14:61381193-61381550(+)$1	357	143	191	124.9836
66dddd]a22a]a]dddd]bb]aDDDD{A{CCC{CCC{DDDD======	chr6:148123717-148124042(+)$1	325	144	192	116.0491
ddd22bb]hhhhhhhh:BB}IIIIIIIII}BB===============m	chrX:140296440-140296758(-)$1	318	251	299	108.7540
ffff::::::::::::::::::::::::::hhhhhhhhoooooohhhh	chr6:55448913-55449385(+)$1	472	199	247	124.9836
gggg666666ggggggg]dddd:::::::::::eeeee[bb[bb####	chr16:15552519-15552908(-)$1	389	196	244	125.0655
E}EEEEE}CCC}CCC:EEEEELLLBBKKGGGGGGGOOOOOOJJJJJJJ	chr4:107544779-107545255(+)$1	476	266	314	129.3278
##==========[a[bb[a[a[a[dddd[a!!ffffff####bb%%%%	chr10:60225758-60226069(-)$1	311	155	203	128.6721
dd]ccc22bb:::::::::::::a[a[a[a[a[a[a[a[a[a[a[a[a	chr8:113973776-113974090(-)$1	314	38	86	128.2622
=:::::CCC}CCC}A}CCC}EEEEEeeeeemmmmeeeee:::CCCZZZ	chr4:41466222-41466709(-)$1	487	423	471	109.9836
ee]aFFFFFF}A}GGGGGGGYYFFFFFF}DDDD}DDDD}A::::eeee	chr4:149090042-149090309(-)$1	267	156	204	114.4918
IIIIIII{BB::::::DDDDKKDDDDKKEEEEE{CCC{BB{FFFFFFB	chr11:43233849-43234332(-)$1	483	86	134	103.1803
dddBB{DDDD{BB{CCCLLLDDDDccc[dddd[cccmmmmccc]dddd	chr17:34746396-34746753(+)$1	357	44	92	105.8852
::::::::::::::::::::::::::::GGGGGGG}EEEEE}BB}JJJ	chr7:134949923-134950414(-)$1	491	309	357	116.5409
ddd]bb:::::::::::::::::::::::::::EEEEE}DDDD}EEEE	chr1:136308026-136308379(+)$1	353	124	172	124.6557
f4444bb]ccc]dddd88888888dddd]ggggggg22ccc]bbbb]b	chr1:77365578-77366011(-)$1	433	324	372	106.8688
hhh55555dddd55555ffffff]bb]ccc::::::::::::::::::	chr2:153083062-153083543(+)$1	481	267	315	125.0655
ooooooccc]a4444ccc]ccc22ccc]bb22ccc:::::::::::::	chr9:48462119-48462543(-)$1	424	185	233	129.3278
ff]ccc::::::::::::::::CCC}CCC}EEEEE}EEEEEffffff[	chr5:89187329-89187653(+)$1	324	133	181	106.7868
iiiiii55555ccc]==================333dddd]bb]ccc]	chr6:127639117-127639616(-)$1	499	307	355	103.2622
""==========mmmm==========333ddddIIIIIIIII}A}CCC	chr6:48387239-48387619(-)$1	380	211	259	107.9344
fff:eeeee"""bb[dddd[ccc[eeeee[==========oooooo==	chr16:91014890-91015267(-)$1	377	262	310	111.4590
ooooooccc333ccc]a]a]a]ccc:::::::bb!!ccc!!ccc"""c	chr17:46154369-46154651(-)$1	282	129	177	123.8360
::CCC{CCC{CCC{BBeeeee[ccc####bb[a[ccc[cccbb[a[a!	chr15:84533464-84533838(+)$1	374	216	264	128.6721
ff[ccc[ggggggg^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr9:86717496-86717981(-)$1	485	318	366	124.4098
::::::::::::::::::::::::::::::::::::::::::======	chr15:3532386-3532776(-)$1	390	43	91	112.1147
annnnna]a]iiiiiiiii]ccc:::::::::::ggggggg[dddd[a	chr8:109898652-109899117(+)$1	465	41	89	128.5081
5ccc333dddd]a]ccc]a]ccc]ccc:::EEEEEKKDDDDMMMMEEE	chr19:5371119-5371411(+)$1	292	56	104	108.4262
EEEE:::::::::::::::::::::::::bb[bb[ccc[ccc!!dddd	chr5:52928173-52928629(-)$1	456	205	253	119.4098
^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee]bb]a]bb]ccc]af	chr17:44413014-44413291(+)$1	277	115	163	129.3278
ddDDDD}BB}DDDDYYA}BBDDDDYYCCC}BB}A}A}GGGGGGG}CCC	chr2:30881776-30882273(-)$1	497	306	354	123.8360
uuuccc333ggggggg====================mmmm========	chr2:120445080-120445387(+)$1	307	126	174	102.5245
fff"""a[a[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr11:70477287-70477608(-)$1	321	169	217	129.3278
oooooccc]cccdddd[ffffff"""ffffff[ccc"""a[a[ccc[b	chr3:105520491-105520933(+)$1	442	220	268	129.3278
eeBB}DDDD}A}AZZZCCC}BB}AZZZA}DDDD}BB}AYYCCCDDDD{	chr17:56315347-56315779(-)$1	432	174	222	128.5081
ddddoooooodddd::::CCC{FFFFFF:eeeee[dddduuuuuuuuu	chr11:97362677-97363137(+)$1	460	192	240	108.1803
GGG{DDDDEEEEE{JJJJJJJJJJJJJJJJJJdddd[gggggggmmmm	chr13:110851193-110851682(-)$1	489	51	99	110.9672
ooooo==========::::::::::::::::FFFFFF{CCC{BBKKBB	chr8:66494142-66494513(-)$1	371	166	214	124.5737
EEEE{ALLLCCC{DDDDLLLCCC{BBKKBB{A{BB{DDDD{EEEEEKK	chr1:173393965-173394215(+)$1	250	1	49	125.2295
G{BB{GGGGGGG:::::ggggggg[a[bb[ccc[ffffff[ccc[a[e	chr1:34872008-34872507(-)$1	499	76	124	105.7213
EEEEZZZBB}FFFFFF}EEEEE}EEEEE}EEEEE}A}A}A}A}A}A}A	chr9:40153367-40153855(-)$1	488	386	434	128.5081
eennnnneeeeeggggggg]bb]ccc]dddd22bb:DDDD{CCC{BB{	chr3:32832500-32832863(+)$1	363	150	198	102.1967
JJJ{A{BB{BB{EEEEE{CCC{EEEEE:::::::::::::dddd"""d	chr12:103807813-103808219(-)$1	406	167	215	120.8032
c]iiiiiiiii:::::::::::::::::::::::::::::::cccooo	chr8:96838755-96839159(+)$1	404	51	99	110.9672
IIII::==========[==============yyyyyyyyyyyyyyyy=	chr9:108000430-108000921(-)$1	491	145	193	102.5245
hhh[bb"""bb[a[a!!bb[bb!!ggggggg[bb[bbyyyyyyyyyyy	chr9:112134775-112135263(-)$1	488	132	180	129.3278
ffffff[a[a[a[a[a[a[a[a[a[a[a[a[a[a[avvvvvvvvvvvv	chr2:102622148-102622631(+)$1	483	174	222	120.8032
======mmmm==========7777777==========55555a]dddd	chr10:59595545-59595902(+)$1	357	251	299	117.2786
========[===============^^^^^^^^^^^^^^^^^^^^^^^^	chr1:174428714-174429055(+)$1	341	137	185	128.6721
======]bb]ddddCCC{BB{BB{CCCSSSSSSSSSSFFFFFFNNNNN	chr4:106418853-106419345(-)$1	492	220	268	120.1475
NNNA{A{BB{A{BB{ALLLEEEEEggggggg####eeeee''''''''	chr6:120432437-120432771(+)$1	334	119	167	124.4918

#DB
((.((((.((((........((..(.((....(((.(..((((.....	chr17:24213376-24213837(-)$1	1	158	206	129.3278
(((.(((((.(.((((.(((((..(((.(((...((.((((...(((.	chr9:45670977-45671454(+)$1	1	37	85	129.3278
)..)))..))).))).).))))).).))....)))).(((((((.((.	chr4:115506994-115507363(+)$1	1	149	197	125.0655
)))...((((((((((((((((((((((((((((((((((((((((((	chr3:152482178-152482665(-)$1	1	108	156	120.5573
))).).....(((((((......(((.((.((((((...((((.....	chr11:119399829-119400277(-)$1	1	269	317	128.6721
.(((((((........................(((((((.(((((.((	chr9:57443737-57444087(+)$1	1	99	147	108.4262
....)))))).)))))).))).)))))))).(.(((.(.(.(((((.(	chr11:95275315-95275802(+)$1	1	140	188	120.4754
((((...(((((((((((((((...(((((...(((((((((((((..	chr6:149505888-149506364(+)$1	1	173	221	102.5245
((((((..........................................	chr7:117773040-117773346(+)$1	1	125	173	111.9508
((.((.((.(((...((.((.((.((.(((((..............((	chr12:45956225-45956703(-)$1	1	237	285	128.6721
..)).))))))))).)................................	chr9:50571208-50571422(-)$1	1	41	89	129.3278
)).)))).).).)))......))).)))).)))..)))))....))))	chr14:61381193-61381550(+)$1	1	143	191	124.9836
..)))).)..).).)))).)).)((((.(.(((.(((.((((((((((	chr6:148123717-148124042(+)$1	1	144	192	116.0491
)))..)).)))))))).)).))))))))).))(((((((((((((((.	chrX:140296440-140296758(-)$1	1	251	299	108.7540
))))..........................((((((((......))))	chr6:55448913-55449385(+)$1	1	199	247	124.9836
))))......))))))).))))...........(((((.((.((....	chr16:15552519-15552908(-)$1	1	196	244	125.0655
).))))).))).))).(((((...((..(((((((......(((((((	chr4:107544779-107545255(+)$1	1	266	314	129.3278
..((((((((((.(.((.(.(.(.((((.(..((((((....((....	chr10:60225758-60226069(-)$1	1	155	203	128.6721
)).)))..)).............(.(.(.(.(.(.(.(.(.(.(.(.(	chr8:113973776-113974090(-)$1	1	38	86	128.2622
).....))).))).).))).)))))(((((....)))))...)))...	chr4:41466222-41466709(-)$1	1	423	471	109.9836
)).))))))).).)))))))..)))))).)))).)))).)....((((	chr4:149090042-149090309(-)$1	1	156	204	114.4918
(((((((.((......((((..((((..(((((.(((.((.(((((((	chr11:43233849-43234332(-)$1	1	86	134	103.1803
)))((.((((.((.(((...(((((((.((((.(((....))).))))	chr17:34746396-34746753(+)$1	1	44	92	105.8852
............................))))))).))))).)).)))	chr7:134949923-134950414(-)$1	1	309	357	116.5409
))).))...........................))))).)))).))))	chr1:136308026-136308379(+)$1	1	124	172	124.6557
)....)).))).))))........)))).)))))))..))).)))).)	chr1:77365578-77366011(-)$1	1	324	372	106.8688
))).....)))).....)))))).)).)))..................	chr2:153083062-153083543(+)$1	1	267	315	125.0655
......))).)....))).)))..))).))..))).............	chr9:48462119-48462543(-)$1	1	185	233	129.3278
)).)))................))).))).))))).)))))((((((.	chr5:89187329-89187653(+)$1	1	133	181	106.7868
)))))).....))).))))))))))))))))))...)))).)).))).	chr6:127639117-127639616(-)$1	1	307	355	103.2622
..((((((((((....))))))))))...))))))))))))).).)))	chr6:48387239-48387619(-)$1	1	211	259	107.9344
))).(((((...((.((((.(((.(((((.((((((((((......))	chr16:91014890-91015267(-)$1	1	262	310	111.4590
......)))...))).).).).))).......((..(((..(((...(	chr17:46154369-46154651(-)$1	1	129	177	123.8360
..(((.(((.(((.(((((((.(((....((.(.(((.(((((.(.(.	chr15:84533464-84533838(+)$1	1	216	264	128.6721
((.(((.(((((((..................................	chr9:86717496-86717981(-)$1	1	318	366	124.4098
..........................................((((((	chr15:3532386-3532776(-)$1	1	43	91	112.1147
(.....).).))))))))).)))...........(((((((.((((.(	chr8:109898652-109899117(+)$1	1	41	89	128.5081
.)))...)))).).))).).))).)))...(((((..((((....(((	chr19:5371119-5371411(+)$1	1	56	104	108.4262
((((.........................((.((.(((.(((..((((	chr5:52928173-52928629(-)$1	1	205	253	119.4098
............................))))).)).).)).))).))	chr17:44413014-44413291(+)$1	1	115	163	129.3278
)))))).)).))))..).))))))..))).)).).).))))))).)))	chr2:30881776-30882273(-)$1	1	306	354	123.8360
...)))...)))))))((((((((((((((((((((....))))))))	chr2:120445080-120445387(+)$1	1	126	174	102.5245
(((...(.(.(((...................................	chr11:70477287-70477608(-)$1	1	169	217	129.3278
.....))).)))((((.((((((...((((((.(((...(.(.(((.(	chr3:105520491-105520933(+)$1	1	220	268	129.3278
)))).)))).).)...))).)).)...).)))).)).)..)))((((.	chr17:56315347-56315779(-)$1	1	174	222	128.5081
((((......))))....(((.((((((.(((((.((((.........	chr11:97362677-97363137(+)$1	1	192	240	108.1803
(((.(((((((((.((((((((((((((((((((((.(((((((....	chr13:110851193-110851682(-)$1	1	51	99	110.9672
.....))))))))))................((((((.(((.((..((	chr8:66494142-66494513(-)$1	1	166	214	124.5737
((((.(...(((.((((...(((.((..((.(.((.((((.(((((..	chr1:173393965-173394215(+)$1	1	1	49	125.2295
(.((.(((((((.....(((((((.(.((.(((.((((((.(((.(.(	chr1:34872008-34872507(-)$1	1	76	124	105.7213
))))...)).)))))).))))).))))).))))).).).).).).).)	chr9:40153367-40153855(-)$1	1	386	434	128.5081
((.....)))))))))))).)).))).))))..)).((((.(((.((.	chr3:32832500-32832863(+)$1	1	150	198	102.1967
(((.(.((.((.(((((.(((.(((((.............((((...(	chr12:103807813-103808219(-)$1	1	167	215	120.8032
).)))))))))...............................(((...	chr8:96838755-96839159(+)$1	1	51	99	110.9672
((((..((((((((((.((((((((((((((................)	chr9:108000430-108000921(-)$1	1	145	193	102.5245
(((.((...((.(.(..((.((..(((((((.((.((...........	chr9:112134775-112135263(-)$1	1	132	180	129.3278
((((((.(.(.(.(.(.(.(.(.(.(.(.(.(.(.(............	chr2:102622148-102622631(+)$1	1	174	222	120.8032
((((((....)))))))))).......)))))))))).....).))))	chr10:59595545-59595902(+)$1	1	251	299	117.2786
((((((((.(((((((((((((((........................	chr1:174428714-174429055(+)$1	1	137	185	128.6721
)))))).)).))))(((.((.((.(((..........((((((.....	chr4:106418853-106419345(-)$1	1	220	268	120.1475
...(.(.((.(.((.(...((((((((((((....(((((........	chr6:120432437-120432771(+)$1	1	119	167	124.4918

#PSSM
g : 0.34	A : 0.14	U : 0.14	C : 0.13	a : 0.09	c : 0.08	G : 0.03	u : 0.01	
u : 0.68	U : 0.09	C : 0.08	A : 0.06	G : 0.04	g : 0.01	
g : 0.73	G : 0.08	u : 0.04	C : 0.04	U : 0.03	c : 0.01	A : 0.01	a : 0.01	
u : 0.80	U : 0.04	c : 0.04	G : 0.03	A : 0.03	g : 0.01	C : 0.01	
g : 0.83	U : 0.08	a : 0.04	c : 0.01	C : 0.01	
u : 0.85	U : 0.04	c : 0.04	g : 0.01	C : 0.01	A : 0.01	
g : 0.88	C : 0.03	A : 0.03	a : 0.01	c : 0.01	U : 0.01	
u : 0.88	U : 0.03	c : 0.03	C : 0.01	a : 0.01	G : 0.01	
g : 0.95	G : 0.03	U : 0.01	
u : 0.95	A : 0.01	c : 0.01	G : 0.01	
g : 0.95	a : 0.01	G : 0.01	c : 0.01	
u : 0.91	c : 0.06	G : 0.01	
g : 1.00	
u : 0.96	a : 0.01	c : 0.01	
g : 0.98	a : 0.01	
u : 0.98	c : 0.01	
g : 0.98	a : 0.01	
u : 0.96	c : 0.01	a : 0.01	
g : 1.00	
u : 0.98	c : 0.01	
g : 1.00	
u : 0.98	c : 0.01	
g : 1.00	
u : 0.95	c : 0.03	a : 0.01	
g : 1.00	
u : 0.95	a : 0.04	
g : 0.98	a : 0.01	
u : 0.98	c : 0.01	
g : 0.96	a : 0.03	
u : 0.98	c : 0.01	
g : 1.00	
u : 0.96	c : 0.03	
g : 0.93	a : 0.03	u : 0.01	c : 0.01	
u : 0.98	c : 0.01	
g : 0.95	a : 0.04	
u : 0.96	c : 0.03	
g : 0.95	a : 0.03	c : 0.01	
u : 1.00	
g : 1.00	
u : 0.96	a : 0.01	c : 0.01	
g : 0.91	a : 0.06	c : 0.01	
u : 0.96	G : 0.01	a : 0.01	
g : 0.98	U : 0.01	
u : 0.93	C : 0.03	g : 0.01	c : 0.01	
g : 0.90	a : 0.03	G : 0.03	c : 0.01	u : 0.01	
u : 0.90	c : 0.03	U : 0.01	C : 0.01	a : 0.01	G : 0.01	
g : 0.91	a : 0.03	A : 0.01	G : 0.01	U : 0.01	
u : 0.83	A : 0.04	U : 0.04	c : 0.04	a : 0.01	

#score	7254.491803278695
#seq	61
#width	48
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m1_run2.nuc.txt

#NT
UAUUCUU	chr5:93697524-93697808(+)$1	284	90	97	12.4179
UUUUCUG	chr14:65431215-65431492(-)$1	277	94	101	13.0895
AUUUCUU	chr3:122242260-122242557(-)$1	297	54	61	13.0149
UUUUCAU	chr14:55505758-55506041(+)$1	283	155	162	12.2686
UUUUGUU	chr5:76641535-76641823(-)$1	288	121	128	13.8358
uuuuguu	chr16:98170671-98170948(-)$1	277	176	183	13.8358
UUUUAUU	chr6:56728726-56729000(-)$1	274	230	237	13.6865
UUUUCUU	chr17:46305889-46306172(+)$1	283	188	195	16.9701
UUUUGUU	chr7:72016753-72017039(-)$1	286	202	209	13.8358
UUUUUUU	chr3:145309905-145310179(-)$1	274	99	106	13.7611
UUUUCUC	chr17:6084525-6084804(+)$1	279	106	113	13.0149
GUUUCUU	chr5:114588885-114589158(+)$1	273	237	244	13.0149
UUUUCUC	chr14:121941982-121942255(-)$1	273	168	175	13.0149
UUCUCUU	chr2:144232685-144232977(+)$1	292	98	105	12.4179
UCUUCUU	chr5:67078040-67078309(+)$1	269	222	229	12.5671
UUUUGUU	chr13:5869145-5869421(+)$1	276	12	19	13.8358
UUCUCUU	chr11:98015256-98015533(-)$1	277	7	14	12.4179
GUUUCUU	chr7:152050685-152050968(+)$1	283	194	201	13.0149
GUUUCUU	chr8:125096545-125096859(+)$1	314	26	33	13.0149
UUUUUUU	chr18:34930930-34931222(+)$1	292	250	257	13.7611
UUUUUUU	chr7:30106085-30106361(-)$1	276	56	63	13.7611
UUUUGUU	chr5:123807810-123808084(+)$1	274	65	72	13.8358
uuuuuuu	chr14:99472877-99473151(+)$1	274	199	206	13.7611
UGUUCUU	chr4:33125089-33125364(+)$1	275	49	56	12.4179
UCUUCUU	chr3:108163839-108164128(+)$1	289	170	177	12.5671
uuuuauu	chr10:20845089-20845386(-)$1	297	19	26	13.6865
UUUUCUG	chr5:37138907-37139205(-)$1	298	78	85	13.0895
UUUUCUC	chr17:6084557-6084835(+)$1	278	74	81	13.0149
UUUUCUU	chr4:49669033-49669321(+)$1	288	61	68	16.9701
UUUUCUU	chr3:108706698-108706973(-)$1	275	253	260	16.9701
UUUUCUU	chr6:30079454-30079729(+)$1	275	177	184	16.9701
UUUUCUG	chr9:30881655-30881942(+)$1	287	12	19	13.0895
CUUUCUU	chr4:126924673-126924951(+)$1	278	182	189	12.8656
UUUUCCU	chr17:37114860-37115135(-)$1	275	38	45	12.3432
UUUGCUU	chr18:75555293-75555568(+)$1	275	143	150	12.4925
UUUUCUU	chrX:11614220-11614489(-)$1	269	11	18	16.9701
auuucuu	chr9:60586481-60586749(+)$1	268	155	162	13.0149
UUUUUUU	chr6:140543072-140543349(+)$1	277	191	198	13.7611
CUUUCUU	chr15:75831591-75831877(-)$1	286	104	111	12.8656
UUUUCUU	chr6:140599382-140599676(+)$1	294	239	246	16.9701
UUUUCUU	chr15:98734299-98734578(-)$1	279	210	217	16.9701
UUUGCUU	chr2:173526976-173527252(+)$1	276	148	155	12.4925
UUUUAUU	chr15:101926263-101926530(+)$1	267	47	54	13.6865
UUUUCUG	chr19:45079711-45079992(-)$1	281	44	51	13.0895
UUUUCCU	chr2:32162847-32163126(+)$1	279	52	59	12.3432
GUUUCUU	chr11:69813257-69813538(+)$1	281	25	32	13.0149
UUUUCUU	chr5:31924703-31924994(+)$1	291	30	37	16.9701
UUUUCUU	chr10:29066280-29066564(-)$1	284	171	178	16.9701
uuuuuuu	chr5:145942303-145942575(+)$1	272	24	31	13.7611
UUGUCUU	chr8:11834139-11834413(+)$1	274	33	40	12.4179
UUUUCUA	chr19:8907655-8907942(+)$1	287	94	101	12.7910
UUUUCUU	chr17:37209972-37210240(+)$1	268	164	171	16.9701
AUUUCUU	chr15:80761601-80761877(+)$1	276	37	44	13.0149
UUUUCUU	chr3:87340651-87340919(+)$1	268	104	111	16.9701
UUUCCUU	chr16:98014687-98014959(-)$1	272	5	12	12.3432
uuuucuu	chr4:140669561-140669856(-)$1	295	258	265	16.9701
UUUUCUU	chr15:80766809-80767079(+)$1	270	43	50	16.9701
UUGUCUU	chr8:11834069-11834348(+)$1	279	103	110	12.4179
UUUUCUG	chr2:31071139-31071426(+)$1	287	177	184	13.0895
UCUUCUU	chr4:63211330-63211606(+)$1	276	10	17	12.5671
UUUUCUC	chr15:79655049-79655353(-)$1	304	44	51	13.0149
UUUUAUU	chr15:101926280-101926567(+)$1	287	30	37	13.6865
UUUUGUU	chr14:119377448-119377719(+)$1	271	13	20	13.8358
AUUUCUU	chr16:30067668-30067940(+)$1	272	109	116	13.0149
uuuuauu	chr4:140884838-140885115(+)$1	277	148	155	13.6865
UUUUGUU	chr2:32134292-32134590(-)$1	298	229	236	13.8358

#otherMatches

#Struct PSSM
[eeeeen	chr9:119147934-119148232(-)$1	298	126	133	12.4925
ooooooc	chr5:93697524-93697808(+)$1	284	90	97	12.4179
:::eeee	chr14:65431215-65431492(-)$1	277	94	101	13.0895
nnfffff	chr3:122242260-122242557(-)$1	297	54	61	13.0149
eee:eee	chr14:55505758-55506041(+)$1	283	155	162	12.2686
gggxxxx	chr5:76641535-76641823(-)$1	288	121	128	13.8358
}CCC@@@	chr16:98170671-98170948(-)$1	277	176	183	13.8358
ffffff]	chr6:56728726-56729000(-)$1	274	230	237	13.6865
qqqqqqq	chr17:46305889-46306172(+)$1	283	188	195	16.9701
dddd]ii	chr7:72016753-72017039(-)$1	286	202	209	13.8358
JJJJJJJ	chr3:145309905-145310179(-)$1	274	99	106	13.7611
IIIIIIe	chr17:6084525-6084804(+)$1	279	106	113	13.0149
FFYYGGG	chr5:114588885-114589158(+)$1	273	237	244	13.0149
hhhhhh:	chr14:121941982-121942255(-)$1	273	168	175	13.0149
eeewwww	chr2:144232685-144232977(+)$1	292	98	105	12.4179
evvvvvv	chr5:67078040-67078309(+)$1	269	222	229	12.5671
JJJJJJJ	chr13:5869145-5869421(+)$1	276	12	19	13.8358
II:eeee	chr11:98015256-98015533(-)$1	277	7	14	12.4179
coooooo	chr7:152050685-152050968(+)$1	283	194	201	13.0149
cssssss	chr8:125096545-125096859(+)$1	314	26	33	13.0149
eeee]ee	chr18:34930930-34931222(+)$1	292	250	257	13.7611
^^^^fff	chr7:30106085-30106361(-)$1	276	56	63	13.7611
2dddd::	chr5:123807810-123808084(+)$1	274	65	72	13.8358
mma22ee	chr14:99472877-99473151(+)$1	274	199	206	13.7611
gggg:::	chr4:33125089-33125364(+)$1	275	49	56	12.4179
(((((((	chr3:108163839-108164128(+)$1	289	170	177	12.5671
hhhhooo	chr10:20845089-20845386(-)$1	297	19	26	13.6865
NNFFFFF	chr5:37138907-37139205(-)$1	298	78	85	13.0895
####ggg	chr17:6084557-6084835(+)$1	278	74	81	13.0149
!gggggg	chr4:49669033-49669321(+)$1	288	61	68	16.9701
JJJJJJJ	chr3:108706698-108706973(-)$1	275	253	260	16.9701
5555fff	chr6:30079454-30079729(+)$1	275	177	184	16.9701
OEEEEE{	chr9:30881655-30881942(+)$1	287	12	19	13.0895
nnnnfff	chr4:126924673-126924951(+)$1	278	182	189	12.8656
:::::::	chr17:37114860-37115135(-)$1	275	38	45	12.3432
]dddd::	chr18:75555293-75555568(+)$1	275	143	150	12.4925
eeccc$$	chrX:11614220-11614489(-)$1	269	11	18	16.9701
dnnnnnd	chr9:60586481-60586749(+)$1	268	155	162	13.0149
:::::::	chr6:140543072-140543349(+)$1	277	191	198	13.7611
""dddd[	chr15:75831591-75831877(-)$1	286	104	111	12.8656
"bb[bbq	chr6:140599382-140599676(+)$1	294	239	246	16.9701
&&&&&&&	chr15:98734299-98734578(-)$1	279	210	217	16.9701
e$$$$$f	chr2:173526976-173527252(+)$1	276	148	155	12.4925
:::::::	chr15:101926263-101926530(+)$1	267	47	54	13.6865
gggmmmm	chr19:45079711-45079992(-)$1	281	44	51	13.0895
g"""fff	chr2:32162847-32163126(+)$1	279	52	59	12.3432
:GGGGGG	chr11:69813257-69813538(+)$1	281	25	32	13.0149
EEEEEDD	chr5:31924703-31924994(+)$1	291	30	37	16.9701
iiiiiii	chr10:29066280-29066564(-)$1	284	171	178	16.9701
hhhhhhh	chr5:145942303-145942575(+)$1	272	24	31	13.7611
eee]ccc	chr8:11834139-11834413(+)$1	274	33	40	12.4179
!ammmma	chr19:8907655-8907942(+)$1	287	94	101	12.7910
::::JJJ	chr17:37209972-37210240(+)$1	268	164	171	16.9701
!ffffff	chr15:80761601-80761877(+)$1	276	37	44	13.0149
NNNBBKK	chr3:87340651-87340919(+)$1	268	104	111	16.9701
JJJJJJJ	chr16:98014687-98014959(-)$1	272	5	12	12.3432
:::::::	chr4:140669561-140669856(-)$1	295	258	265	16.9701
HHH{BB{	chr15:80766809-80767079(+)$1	270	43	50	16.9701
eee]ccc	chr8:11834069-11834348(+)$1	279	103	110	12.4179
cnnnnnc	chr2:31071139-31071426(+)$1	287	177	184	13.0895
odddd::	chr4:63211330-63211606(+)$1	276	10	17	12.5671
^^^^^^^	chr15:79655049-79655353(-)$1	304	44	51	13.0149
:::::::	chr15:101926280-101926567(+)$1	287	30	37	13.6865
llfffff	chr14:119377448-119377719(+)$1	271	13	20	13.8358
ggGGGGG	chr16:30067668-30067940(+)$1	272	109	116	13.0149
:::::::	chr4:140884838-140885115(+)$1	277	148	155	13.6865
EEEE\\\	chr2:32134292-32134590(-)$1	298	229	236	13.8358

#DB
.(((((.	chr9:119147934-119148232(-)$1	1	126	133	12.4925
......)	chr5:93697524-93697808(+)$1	1	90	97	12.4179
...((((	chr14:65431215-65431492(-)$1	1	94	101	13.0895
..)))))	chr3:122242260-122242557(-)$1	1	54	61	13.0149
))).(((	chr14:55505758-55506041(+)$1	1	155	162	12.2686
(((....	chr5:76641535-76641823(-)$1	1	121	128	13.8358
.)))...	chr16:98170671-98170948(-)$1	1	176	183	13.8358
)))))).	chr6:56728726-56729000(-)$1	1	230	237	13.6865
.......	chr17:46305889-46306172(+)$1	1	188	195	16.9701
)))).))	chr7:72016753-72017039(-)$1	1	202	209	13.8358
(((((((	chr3:145309905-145310179(-)$1	1	99	106	13.7611
(((((((	chr17:6084525-6084804(+)$1	1	106	113	13.0149
))..)))	chr5:114588885-114589158(+)$1	1	237	244	13.0149
)))))).	chr14:121941982-121942255(-)$1	1	168	175	13.0149
(((....	chr2:144232685-144232977(+)$1	1	98	105	12.4179
(......	chr5:67078040-67078309(+)$1	1	222	229	12.5671
(((((((	chr13:5869145-5869421(+)$1	1	12	19	13.8358
((.((((	chr11:98015256-98015533(-)$1	1	7	14	12.4179
(......	chr7:152050685-152050968(+)$1	1	194	201	13.0149
(......	chr8:125096545-125096859(+)$1	1	26	33	13.0149
)))).))	chr18:34930930-34931222(+)$1	1	250	257	13.7611
....)))	chr7:30106085-30106361(-)$1	1	56	63	13.7611
.))))..	chr5:123807810-123808084(+)$1	1	65	72	13.8358
..)..))	chr14:99472877-99473151(+)$1	1	199	206	13.7611
))))...	chr4:33125089-33125364(+)$1	1	49	56	12.4179
.......	chr3:108163839-108164128(+)$1	1	170	177	12.5671
((((...	chr10:20845089-20845386(-)$1	1	19	26	13.6865
..(((((	chr5:37138907-37139205(-)$1	1	78	85	13.0895
....(((	chr17:6084557-6084835(+)$1	1	74	81	13.0149
.((((((	chr4:49669033-49669321(+)$1	1	61	68	16.9701
)))))))	chr3:108706698-108706973(-)$1	1	253	260	16.9701
....)))	chr6:30079454-30079729(+)$1	1	177	184	16.9701
.(((((.	chr9:30881655-30881942(+)$1	1	12	19	13.0895
....)))	chr4:126924673-126924951(+)$1	1	182	189	12.8656
.......	chr17:37114860-37115135(-)$1	1	38	45	12.3432
.))))..	chr18:75555293-75555568(+)$1	1	143	150	12.4925
(((((..	chrX:11614220-11614489(-)$1	1	11	18	16.9701
(.....)	chr9:60586481-60586749(+)$1	1	155	162	13.0149
.......	chr6:140543072-140543349(+)$1	1	191	198	13.7611
..((((.	chr15:75831591-75831877(-)$1	1	104	111	12.8656
.((.((.	chr6:140599382-140599676(+)$1	1	239	246	16.9701
.......	chr15:98734299-98734578(-)$1	1	210	217	16.9701
(.....(	chr2:173526976-173527252(+)$1	1	148	155	12.4925
.......	chr15:101926263-101926530(+)$1	1	47	54	13.6865
(((....	chr19:45079711-45079992(-)$1	1	44	51	13.0895
(...(((	chr2:32162847-32163126(+)$1	1	52	59	12.3432
.((((((	chr11:69813257-69813538(+)$1	1	25	32	13.0149
(((((((	chr5:31924703-31924994(+)$1	1	30	37	16.9701
)))))))	chr10:29066280-29066564(-)$1	1	171	178	16.9701
(((((((	chr5:145942303-145942575(+)$1	1	24	31	13.7611
))).)))	chr8:11834139-11834413(+)$1	1	33	40	12.4179
.(....)	chr19:8907655-8907942(+)$1	1	94	101	12.7910
....)))	chr17:37209972-37210240(+)$1	1	164	171	16.9701
.((((((	chr15:80761601-80761877(+)$1	1	37	44	13.0149
...((..	chr3:87340651-87340919(+)$1	1	104	111	16.9701
(((((((	chr16:98014687-98014959(-)$1	1	5	12	12.3432
.......	chr4:140669561-140669856(-)$1	1	258	265	16.9701
(((.((.	chr15:80766809-80767079(+)$1	1	43	50	16.9701
))).)))	chr8:11834069-11834348(+)$1	1	103	110	12.4179
(.....)	chr2:31071139-31071426(+)$1	1	177	184	13.0895
.))))..	chr4:63211330-63211606(+)$1	1	10	17	12.5671
.......	chr15:79655049-79655353(-)$1	1	44	51	13.0149
.......	chr15:101926280-101926567(+)$1	1	30	37	13.6865
..)))))	chr14:119377448-119377719(+)$1	1	13	20	13.8358
))(((((	chr16:30067668-30067940(+)$1	1	109	116	13.0149
.......	chr4:140884838-140885115(+)$1	1	148	155	13.6865
))))...	chr2:32134292-32134590(-)$1	1	229	236	13.8358

#PSSM
U : 0.76	u : 0.08	G : 0.05	A : 0.04	C : 0.02	a : 0.01	
U : 0.82	u : 0.10	C : 0.04	A : 0.01	G : 0.01	
U : 0.83	u : 0.10	C : 0.02	G : 0.02	
U : 0.83	u : 0.10	G : 0.04	C : 0.01	
C : 0.70	G : 0.08	U : 0.05	A : 0.04	u : 0.02	a : 0.02	c : 0.02	g : 0.01	
U : 0.85	u : 0.10	C : 0.02	A : 0.01	
U : 0.74	u : 0.10	G : 0.07	C : 0.05	A : 0.01	

#score	927.5970149253741
#seq	67
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_UTR_m2_run2.nuc.txt

#NT
AUUGAUUUG	chr5:150021153-150021373(+)$1	220	35	44	11.0000
UGUGUUUAG	chr11:69470135-69470365(-)$1	230	168	177	10.5454
CUGGUUUUG	chr2:104430624-104430844(+)$1	220	119	128	10.7272
CUUGGUUUG	chr16:20678623-20678857(+)$1	234	149	158	11.0000
uuuguuuug	chr10:127514039-127514289(+)$1	250	93	102	18.9090
UUUGUUUUG	chr11:23196280-23196501(+)$1	221	12	21	18.9090
UUUGACUUG	chr2:109739753-109739991(+)$1	238	0	9	10.9090
UUUGUUGUG	chr18:36754406-36754626(+)$1	220	33	42	14.4545
UUUGUUUUU	chrX:148285164-148285384(+)$1	220	14	23	17.0000
UUUGGGUUG	chr8:131256538-131256758(+)$1	220	193	202	11.0909
UUUCUUUUU	chr1:127289733-127289953(-)$1	220	125	134	14.5454
UUUUUAUUG	chr7:30629671-30629893(-)$1	222	141	150	12.9090
UAUUUUUUG	chr15:96520011-96520231(-)$1	220	123	132	12.6363
UUUGGCUUG	chr11:105795636-105795856(-)$1	220	175	184	11.0909
uuuguuuug	chr8:82207925-82208145(-)$1	220	19	28	18.9090
UUUUUUUUU	chr6:51413125-51413346(-)$1	221	61	70	14.9090
UUUUUUUUG	chrX:101157553-101157773(-)$1	220	15	24	16.8181
uuuguuuug	chr6:72559456-72559676(-)$1	220	165	174	18.9090
UUUGUGUUG	chr5:24810382-24810602(-)$1	220	162	171	15.0000
UGUGUUUUU	chr4:132455557-132455777(-)$1	220	117	126	13.0000
UUUUUUUUU	chr19:60939934-60940178(-)$1	244	57	66	14.9090
UUUGUGGUG	chr5:48640964-48641185(+)$1	221	31	40	10.5454
UUUAUUUUG	chr18:38746033-38746254(-)$1	221	191	200	16.0909
uuuguauuu	chr10:20845519-20845741(-)$1	222	70	79	13.0909
UUUUUUUUu	chr7:87857064-87857302(-)$1	238	203	212	14.9090
UCUCUUUUG	chr19:27843050-27843270(-)$1	220	52	61	12.5454
UUUGUUUUU	chr11:70465378-70465598(-)$1	220	169	178	17.0000
uuuuuuuuc	chr9:121855804-121856024(+)$1	220	86	95	13.9090
GUUAUUUUG	chr13:8972184-8972404(-)$1	220	74	83	12.1818
GUUGUUUUA	chr5:8454540-8454770(+)$1	230	201	210	12.0909
UUUCUUUUG	chr11:75517201-75517421(+)$1	220	72	81	16.4545
UUUGUUUUG	chr4:10915887-10916111(-)$1	224	85	94	18.9090
AUUGUUUAG	chr19:10525551-10525775(+)$1	224	88	97	10.7272
UUAGUUUUU	chr9:88344877-88345097(-)$1	220	206	215	12.8181
UCUGUUCUG	chr14:58426213-58426434(-)$1	221	14	23	10.5454
GUUGUUUUA	chr2:168008426-168008646(-)$1	220	17	26	12.0909
UUUUUUUUU	chr9:67068387-67068607(-)$1	220	49	58	14.9090
AUUUUUUUG	chr6:30431986-30432207(-)$1	221	109	118	13.0000
UUUGCUUUG	chr7:72442123-72442343(-)$1	220	131	140	14.8181
UUUCUUUAG	chr13:89796385-89796605(-)$1	220	4	13	12.0909
UUGGUUUuu	chr12:74204024-74204244(-)$1	220	204	213	12.8181
UUUGCCUUG	chr17:32334008-32334231(-)$1	223	61	70	10.9090
UUUCUUUGG	chr11:21219953-21220173(+)$1	220	159	168	11.9090
UGUGUUUUU	chr15:99239383-99239603(+)$1	220	177	186	13.0000
UUUGUUUUA	chr4:4694302-4694522(-)$1	220	90	99	16.0000
UUGGUUUUG	chr18:65239596-65239816(+)$1	220	137	146	14.7272
UUUUUUUUC	chr13:46844829-46845049(-)$1	220	192	201	13.9090
UUUAuuuuu	chr2:181236508-181236729(+)$1	221	4	13	14.1818
UUAGUUUUG	chr7:152086032-152086252(+)$1	220	70	79	14.7272
UCUCUUUUG	chr4:24829578-24829798(+)$1	220	58	67	12.5454
UUAGUUUUC	chr5:67678085-67678307(+)$1	222	142	151	11.8181
AUUUUUUUG	chr5:17771806-17772028(-)$1	222	179	188	13.0000
UUUGGAUUG	chr19:9187058-9187278(-)$1	220	69	78	11.0909
UCUGUUUUU	chr17:79349002-79349222(-)$1	220	191	200	13.0909

#otherMatches

#Struct PSSM
22dddd:::	chrX:101155828-101156048(-)$1	220	102	111	12.0000
:::CCC{GG	chr5:150021153-150021373(+)$1	220	35	44	11.0000
=======:A	chr11:69470135-69470365(-)$1	230	168	177	10.5454
b[ccc!!dd	chr2:104430624-104430844(+)$1	220	119	128	10.7272
ee]ccc]dd	chr16:20678623-20678857(+)$1	234	149	158	11.0000
^^^^^^^^^	chr10:127514039-127514289(+)$1	250	93	102	18.9090
FFFFF{DDD	chr11:23196280-23196501(+)$1	221	12	21	18.9090
::::::eee	chr2:109739753-109739991(+)$1	238	0	9	10.9090
eeeeeffff	chr18:36754406-36754626(+)$1	220	33	42	14.4545
GGeeeeepp	chrX:148285164-148285384(+)$1	220	14	23	17.0000
fffffFFFF	chr8:131256538-131256758(+)$1	220	193	202	11.0909
mmmmeeeee	chr1:127289733-127289953(-)$1	220	125	134	14.5454
JJJJJJ:::	chr7:30629671-30629893(-)$1	222	141	150	12.9090
iiiiiiiii	chr15:96520011-96520231(-)$1	220	123	132	12.6363
nnffffff:	chr11:105795636-105795856(-)$1	220	175	184	11.0909
:::::ffff	chr8:82207925-82208145(-)$1	220	19	28	18.9090
:::::::::	chr6:51413125-51413346(-)$1	221	61	70	14.9090
qqqqqqqqf	chrX:101157553-101157773(-)$1	220	15	24	16.8181
2ggggggg]	chr6:72559456-72559676(-)$1	220	165	174	18.9090
gggGGGGGG	chr5:24810382-24810602(-)$1	220	162	171	15.0000
deeeeennn	chr4:132455557-132455777(-)$1	220	117	126	13.0000
dd+++++++	chr19:60939934-60940178(-)$1	244	57	66	14.9090
KBB{CCC{G	chr5:48640964-48641185(+)$1	221	31	40	10.5454
eeeee333f	chr18:38746033-38746254(-)$1	221	191	200	16.0909
ggg333===	chr10:20845519-20845741(-)$1	222	70	79	13.0909
JJJJJJJJJ	chr7:87857064-87857302(-)$1	238	203	212	14.9090
==[ffffff	chr19:27843050-27843270(-)$1	220	52	61	12.5454
@@@@@@@@@	chr11:70465378-70465598(-)$1	220	169	178	17.0000
>>>>>eeee	chr9:121855804-121856024(+)$1	220	86	95	13.9090
iiiiiiii[	chr13:8972184-8972404(-)$1	220	74	83	12.1818
ddooooood	chr5:8454540-8454770(+)$1	230	201	210	12.0909
dddd333ff	chr11:75517201-75517421(+)$1	220	72	81	16.4545
gggggg]ee	chr4:10915887-10916111(-)$1	224	85	94	18.9090
333gggggg	chr19:10525551-10525775(+)$1	224	88	97	10.7272
eeee]dddd	chr9:88344877-88345097(-)$1	220	206	215	12.8181
EEEgggggg	chr14:58426213-58426434(-)$1	221	14	23	10.5454
"""a!!ccc	chr2:168008426-168008646(-)$1	220	17	26	12.0909
rrrrrreee	chr9:67068387-67068607(-)$1	220	49	58	14.9090
>>>>>>>>e	chr6:30431986-30432207(-)$1	221	109	118	13.0000
#ddddllld	chr7:72442123-72442343(-)$1	220	131	140	14.8181
nnnnndddd	chr13:89796385-89796605(-)$1	220	4	13	12.0909
DDD}CCC::	chr12:74204024-74204244(-)$1	220	204	213	12.8181
ppdddd::A	chr17:32334008-32334231(-)$1	223	61	70	10.9090
ddd[fffff	chr11:21219953-21220173(+)$1	220	159	168	11.9090
}BB::::::	chr15:99239383-99239603(+)$1	220	177	186	13.0000
========e	chr4:4694302-4694522(-)$1	220	90	99	16.0000
%ffffffa[	chr18:65239596-65239816(+)$1	220	137	146	14.7272
b]ccc22ff	chr13:46844829-46845049(-)$1	220	192	201	13.9090
:::::::::	chr2:181236508-181236729(+)$1	221	4	13	14.1818
:::EEEEEE	chr7:152086032-152086252(+)$1	220	70	79	14.7272
FFFF:dddd	chr4:24829578-24829798(+)$1	220	58	67	12.5454
::::EEEEE	chr5:67678085-67678307(+)$1	222	142	151	11.8181
rrrrrrrrr	chr5:17771806-17772028(-)$1	222	179	188	13.0000
===rrrrrr	chr19:9187058-9187278(-)$1	220	69	78	11.0909
qqqccc22e	chr17:79349002-79349222(-)$1	220	191	200	13.0909

#DB
..))))...	chrX:101155828-101156048(-)$1	1	102	111	12.0000
...(((.((	chr5:150021153-150021373(+)$1	1	35	44	11.0000
))))))).)	chr11:69470135-69470365(-)$1	1	168	177	10.5454
(.(((..((	chr2:104430624-104430844(+)$1	1	119	128	10.7272
)).))).))	chr16:20678623-20678857(+)$1	1	149	158	11.0000
.........	chr10:127514039-127514289(+)$1	1	93	102	18.9090
(((((.(((	chr11:23196280-23196501(+)$1	1	12	21	18.9090
......(((	chr2:109739753-109739991(+)$1	1	0	9	10.9090
(((((((((	chr18:36754406-36754626(+)$1	1	33	42	14.4545
(((((((..	chrX:148285164-148285384(+)$1	1	14	23	17.0000
)))))))))	chr8:131256538-131256758(+)$1	1	193	202	11.0909
....)))))	chr1:127289733-127289953(-)$1	1	125	134	14.5454
))))))...	chr7:30629671-30629893(-)$1	1	141	150	12.9090
(((((((((	chr15:96520011-96520231(-)$1	1	123	132	12.6363
..)))))).	chr11:105795636-105795856(-)$1	1	175	184	11.0909
.....((((	chr8:82207925-82208145(-)$1	1	19	28	18.9090
.........	chr6:51413125-51413346(-)$1	1	61	70	14.9090
........)	chrX:101157553-101157773(-)$1	1	15	24	16.8181
.))))))).	chr6:72559456-72559676(-)$1	1	165	174	18.9090
)))))))))	chr5:24810382-24810602(-)$1	1	162	171	15.0000
((((((...	chr4:132455557-132455777(-)$1	1	117	126	13.0000
((.......	chr19:60939934-60940178(-)$1	1	57	66	14.9090
.((.(((.(	chr5:48640964-48641185(+)$1	1	31	40	10.5454
)))))...)	chr18:38746033-38746254(-)$1	1	191	200	16.0909
)))...)))	chr10:20845519-20845741(-)$1	1	70	79	13.0909
)))))))))	chr7:87857064-87857302(-)$1	1	203	212	14.9090
((.((((((	chr19:27843050-27843270(-)$1	1	52	61	12.5454
.........	chr11:70465378-70465598(-)$1	1	169	178	17.0000
.....))))	chr9:121855804-121856024(+)$1	1	86	95	13.9090
((((((((.	chr13:8972184-8972404(-)$1	1	74	83	12.1818
((......)	chr5:8454540-8454770(+)$1	1	201	210	12.0909
))))...))	chr11:75517201-75517421(+)$1	1	72	81	16.4545
)))))).))	chr4:10915887-10916111(-)$1	1	85	94	18.9090
...))))))	chr19:10525551-10525775(+)$1	1	88	97	10.7272
)))).))))	chr9:88344877-88345097(-)$1	1	206	215	12.8181
(((((((((	chr14:58426213-58426434(-)$1	1	14	23	10.5454
...(..(((	chr2:168008426-168008646(-)$1	1	17	26	12.0909
......)))	chr9:67068387-67068607(-)$1	1	49	58	14.9090
........)	chr6:30431986-30432207(-)$1	1	109	118	13.0000
.((((...)	chr7:72442123-72442343(-)$1	1	131	140	14.8181
.....))))	chr13:89796385-89796605(-)$1	1	4	13	12.0909
))).)))..	chr12:74204024-74204244(-)$1	1	204	213	12.8181
..))))..(	chr17:32334008-32334231(-)$1	1	61	70	10.9090
(((.(((((	chr11:21219953-21220173(+)$1	1	159	168	11.9090
.))......	chr15:99239383-99239603(+)$1	1	177	186	13.0000
(((((((((	chr4:4694302-4694522(-)$1	1	90	99	16.0000
.(((((((.	chr18:65239596-65239816(+)$1	1	137	146	14.7272
).)))..))	chr13:46844829-46845049(-)$1	1	192	201	13.9090
.........	chr2:181236508-181236729(+)$1	1	4	13	14.1818
...((((((	chr7:152086032-152086252(+)$1	1	70	79	14.7272
((((.((((	chr4:24829578-24829798(+)$1	1	58	67	12.5454
....(((((	chr5:67678085-67678307(+)$1	1	142	151	11.8181
.........	chr5:17771806-17772028(-)$1	1	179	188	13.0000
(((......	chr19:9187058-9187278(-)$1	1	69	78	11.0909
...)))..)	chr17:79349002-79349222(-)$1	1	191	200	13.0909

#PSSM
U : 0.74	u : 0.09	A : 0.07	G : 0.05	C : 0.03	
U : 0.76	u : 0.09	C : 0.07	G : 0.05	A : 0.01	
U : 0.80	u : 0.09	G : 0.05	A : 0.05	
G : 0.54	U : 0.18	C : 0.12	g : 0.07	A : 0.05	u : 0.01	
U : 0.74	u : 0.10	G : 0.07	A : 0.03	C : 0.03	
U : 0.74	u : 0.09	C : 0.05	G : 0.05	A : 0.03	a : 0.01	
U : 0.81	u : 0.10	C : 0.03	G : 0.03	
U : 0.80	u : 0.12	A : 0.05	G : 0.01	
G : 0.58	U : 0.18	u : 0.07	g : 0.05	A : 0.05	C : 0.03	c : 0.01	

#score	752.636363636364
#seq	55
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_UTR_m1_run2.nuc.txt

#NT
UUUCUGGA	chr2:32991731-32991977(-)$1	246	184	192	9.7031
CUGCUGCC	chr9:62268369-62268608(-)$1	239	28	36	11.1093
CUGCUGAU	chr12:118994792-118995046(+)$1	254	112	120	11.6562
CUGCUGAC	chr3:31103380-31103604(-)$1	224	186	194	11.1093
CUGCUGGA	chr8:108238959-108239183(-)$1	224	19	27	13.8437
CUGCUGGA	chr4:69883179-69883400(-)$1	221	56	64	13.8437
CUUCUGGG	chr9:44627364-44627596(-)$1	232	68	76	12.1250
CUGCUUGC	chr9:45677163-45677396(-)$1	233	179	187	9.6250
UUUCUGGU	chr15:102368395-102368619(-)$1	224	84	92	10.7968
UUACUGGU	chr9:111178578-111178803(+)$1	225	47	55	10.4062
CUGCUGGG	chr11:70427166-70427404(+)$1	238	172	180	14.7031
UUUCUGGU	chr10:112363051-112363279(-)$1	228	161	169	10.7968
CUACUGGU	chr10:85765523-85765739(-)$1	216	71	79	11.9687
CUGCUGAA	chr11:80079968-80080189(+)$1	221	117	125	10.5625
CUGCAGGC	chr2:35584693-35584916(+)$1	223	136	144	9.5468
CUGCUGUC	chr6:122795037-122795252(-)$1	215	102	110	10.9531
CUUCUGGU	chr19:60965561-60965781(+)$1	220	29	37	12.3593
GUGCUGUC	chr7:19577946-19578170(+)$1	224	142	150	9.3906
GUGCUGGC	chr11:58160079-58160324(+)$1	245	49	57	12.8281
AUGCUGGU	chr5:138545057-138545287(+)$1	230	23	31	13.0625
UUUCUGGU	chr15:79748209-79748430(-)$1	221	15	23	10.7968
AUGCUGCU	chr19:29040486-29040730(+)$1	244	135	143	9.7812
CUACUGGG	chr7:36558481-36558701(-)$1	220	1	9	11.7343
CUGCUGGG	chr6:124653856-124654075(-)$1	219	190	198	14.7031
CUGCUGGA	chr2:131003608-131003830(-)$1	222	19	27	13.8437
CUGCUGCU	chr15:100046434-100046657(+)$1	223	3	11	11.6562
GUGCUGUG	chr18:78254005-78254227(+)$1	222	67	75	9.7031
CUGCUGGU	chr8:131248056-131248281(+)$1	225	201	209	14.9375
UUGCUGCC	chr9:65033500-65033750(+)$1	250	147	155	9.5468
UUGCUGGC	chr1:16094432-16094654(+)$1	222	163	171	12.8281
AUCCUGGG	chr17:28725563-28725786(-)$1	223	25	33	10.2500
CUGCUGGA	chr4:102874695-102874919(-)$1	224	73	81	13.8437
CUCCUGGG	chr2:27303503-27303783(-)$1	280	39	47	12.1250
CUGCUGCC	chr3:60807142-60807362(+)$1	220	161	169	11.1093
GUGCUGAA	chr17:57219553-57219781(-)$1	228	172	180	9.0000
CUGCUGGG	chr11:68635755-68635994(-)$1	239	64	72	14.7031
UUGCUGUG	chr10:93435088-93435336(-)$1	248	17	25	9.7031
GUGCUGGU	chr5:114813646-114813865(-)$1	219	96	104	13.3750
GUGCUGGG	chr12:70782478-70782707(-)$1	229	210	218	13.1406
CUGCUGCC	chr5:100790829-100791057(-)$1	228	108	116	11.1093
UUGCUGAU	chr16:11192968-11193201(-)$1	233	75	83	10.0937
GUCCUGGG	chr8:13176712-13176938(+)$1	226	127	135	10.5625
AUCCUGGC	chr2:33308924-33309157(-)$1	233	127	135	9.9375
CUGCUGGG	chr4:114696272-114696497(+)$1	225	166	174	14.7031
CUGGUGGU	chr3:95566362-95566590(-)$1	228	125	133	10.0937
CUGCUGGU	chr9:107458906-107459128(+)$1	222	72	80	14.9375
GUGCUGGC	chr2:146070430-146070651(+)$1	221	210	218	12.8281
AUUCUGGG	chr19:43570959-43571187(+)$1	228	46	54	10.2500
GUGCUGGU	chr2:152163389-152163645(-)$1	256	9	17	13.3750
GUCCUGGU	chr4:120731783-120732020(-)$1	237	180	188	10.7968
GUGCUGGG	chr9:64985575-64985796(+)$1	221	44	52	13.1406
GUGCUGGG	chr4:123078943-123079168(-)$1	225	200	208	13.1406
CUUCUGGC	chr3:106909450-106909678(+)$1	228	154	162	11.8125
UUGCUGAG	chr6:38242772-38242995(-)$1	223	39	47	9.8593
CUCCUGGU	chr1:94912346-94912581(-)$1	235	112	120	12.3593
UUGCUGGC	chr11:119401221-119401455(-)$1	234	139	147	12.8281
CUGCUGGU	chr5:38529554-38529780(-)$1	226	198	206	14.9375
AUGCUGGU	chr9:121663762-121663986(+)$1	224	96	104	13.0625
AUCCUGGU	chr5:141235071-141235306(-)$1	235	100	108	10.4843
CUCCUGGA	chr17:45704757-45704984(-)$1	227	24	32	11.2656
AUACUGGG	chrX:63556510-63556733(+)$1	223	97	105	9.8593
CUGCUAGG	chrX:98614942-98615158(-)$1	216	35	43	9.9375
CUUCUGGU	chr8:112466926-112467155(+)$1	229	70	78	12.3593

#otherMatches

#Struct PSSM
fff]ccc3	chr7:126686468-126686690(+)$1	222	116	124	10.5625
gggggDDD	chr2:32991731-32991977(-)$1	246	184	192	9.7031
qqqqqqqq	chr9:62268369-62268608(-)$1	239	28	36	11.1093
"dddd$$$	chr12:118994792-118995046(+)$1	254	112	120	11.6562
dddcccnn	chr3:31103380-31103604(-)$1	224	186	194	11.1093
LDDDDCCC	chr8:108238959-108239183(-)$1	224	19	27	13.8437
dmmmmddd	chr4:69883179-69883400(-)$1	221	56	64	13.8437
ffffffmm	chr9:44627364-44627596(-)$1	232	68	76	12.1250
fffff]bb	chr9:45677163-45677396(-)$1	233	179	187	9.6250
eee[bb[b	chr15:102368395-102368619(-)$1	224	84	92	10.7968
gg!!bb[a	chr9:111178578-111178803(+)$1	225	47	55	10.4062
ZZCCCbb!	chr11:70427166-70427404(+)$1	238	172	180	14.7031
oooooccc	chr10:112363051-112363279(-)$1	228	161	169	10.7968
fmmmmfff	chr10:85765523-85765739(-)$1	216	71	79	11.9687
{CCC{DDD	chr11:80079968-80080189(+)$1	221	117	125	10.5625
fffff]bb	chr2:35584693-35584916(+)$1	223	136	144	9.5468
fffff333	chr6:122795037-122795252(-)$1	215	102	110	10.9531
CCLLLFFF	chr19:60965561-60965781(+)$1	220	29	37	12.3593
GGGGGGG}	chr7:19577946-19578170(+)$1	224	142	150	9.3906
a]bb]ccc	chr11:58160079-58160324(+)$1	245	49	57	12.8281
::eeeeeo	chr5:138545057-138545287(+)$1	230	23	31	13.0625
gg!!bb[d	chr15:79748209-79748430(-)$1	221	15	23	10.7968
hhhhhhhh	chr19:29040486-29040730(+)$1	244	135	143	9.7812
cc[ccccc	chr7:36558481-36558701(-)$1	220	1	9	11.7343
hhhh::::	chr6:124653856-124654075(-)$1	219	190	198	14.7031
DGGGGGGG	chr2:131003608-131003830(-)$1	222	19	27	13.8437
::ffffff	chr15:100046434-100046657(+)$1	223	3	11	11.6562
ddd22eee	chr18:78254005-78254227(+)$1	222	67	75	9.7031
eeeee22h	chr8:131248056-131248281(+)$1	225	201	209	14.9375
eeeeeooo	chr9:65033500-65033750(+)$1	250	147	155	9.5468
nnnnnbb]	chr1:16094432-16094654(+)$1	222	163	171	12.8281
:ddddnnn	chr17:28725563-28725786(-)$1	223	25	33	10.2500
e::hhhhh	chr4:102874695-102874919(-)$1	224	73	81	13.8437
{GGGGGGG	chr2:27303503-27303783(-)$1	280	39	47	12.1250
33eeeeec	chr3:60807142-60807362(+)$1	220	161	169	11.1093
FFFFFFDD	chr17:57219553-57219781(-)$1	228	172	180	9.0000
!!gggggg	chr11:68635755-68635994(-)$1	239	64	72	14.7031
ggggg[dd	chr10:93435088-93435336(-)$1	248	17	25	9.7031
qqbb]ddd	chr5:114813646-114813865(-)$1	219	96	104	13.3750
:DDDD}FF	chr12:70782478-70782707(-)$1	229	210	218	13.1406
KCCC::::	chr5:100790829-100791057(-)$1	228	108	116	11.1093
eeee[bb[	chr16:11192968-11193201(-)$1	233	75	83	10.0937
fffmmmmf	chr8:13176712-13176938(+)$1	226	127	135	10.5625
cc::GGGG	chr2:33308924-33309157(-)$1	233	127	135	9.9375
eeeee]dd	chr4:114696272-114696497(+)$1	225	166	174	14.7031
iiiiiiii	chr3:95566362-95566590(-)$1	228	125	133	10.0937
ggggggg[	chr9:107458906-107459128(+)$1	222	72	80	14.9375
ddd]ccc]	chr2:146070430-146070651(+)$1	221	210	218	12.8281
55bb]ccc	chr19:43570959-43571187(+)$1	228	46	54	10.2500
iiiiiiii	chr2:152163389-152163645(-)$1	256	9	17	13.3750
:::::HHH	chr4:120731783-120732020(-)$1	237	180	188	10.7968
mmgggggg	chr9:64985575-64985796(+)$1	221	44	52	13.1406
:::GGGGG	chr4:123078943-123079168(-)$1	225	200	208	13.1406
:::::fff	chr3:106909450-106909678(+)$1	228	154	162	11.8125
eeeee:::	chr6:38242772-38242995(-)$1	223	39	47	9.8593
eeeeqqqq	chr1:94912346-94912581(-)$1	235	112	120	12.3593
eeee[ccc	chr11:119401221-119401455(-)$1	234	139	147	12.8281
ddd:DDDD	chr5:38529554-38529780(-)$1	226	198	206	14.9375
dddfffff	chr9:121663762-121663986(+)$1	224	96	104	13.0625
ee[eeeee	chr5:141235071-141235306(-)$1	235	100	108	10.4843
"""dddd!	chr17:45704757-45704984(-)$1	227	24	32	11.2656
:::ddddc	chrX:63556510-63556733(+)$1	223	97	105	9.8593
JJJJJ{A{	chrX:98614942-98615158(-)$1	216	35	43	9.9375
bmmmmbb2	chr8:112466926-112467155(+)$1	229	70	78	12.3593

#DB
))).))).	chr7:126686468-126686690(+)$1	1	116	124	10.5625
))))))))	chr2:32991731-32991977(-)$1	1	184	192	9.7031
........	chr9:62268369-62268608(-)$1	1	28	36	11.1093
.((((...	chr12:118994792-118995046(+)$1	1	112	120	11.6562
((((((..	chr3:31103380-31103604(-)$1	1	186	194	11.1093
.(((((((	chr8:108238959-108239183(-)$1	1	19	27	13.8437
(....)))	chr4:69883179-69883400(-)$1	1	56	64	13.8437
((((((..	chr9:44627364-44627596(-)$1	1	68	76	12.1250
))))).))	chr9:45677163-45677396(-)$1	1	179	187	9.6250
(((.((.(	chr15:102368395-102368619(-)$1	1	84	92	10.7968
((..((.(	chr9:111178578-111178803(+)$1	1	47	55	10.4062
..)))((.	chr11:70427166-70427404(+)$1	1	172	180	14.7031
.....)))	chr10:112363051-112363279(-)$1	1	161	169	10.7968
(....)))	chr10:85765523-85765739(-)$1	1	71	79	11.9687
.(((.(((	chr11:80079968-80080189(+)$1	1	117	125	10.5625
))))).))	chr2:35584693-35584916(+)$1	1	136	144	9.5468
)))))...	chr6:122795037-122795252(-)$1	1	102	110	10.9531
((...(((	chr19:60965561-60965781(+)$1	1	29	37	12.3593
))))))).	chr7:19577946-19578170(+)$1	1	142	150	9.3906
).)).)))	chr11:58160079-58160324(+)$1	1	49	57	12.8281
..(((((.	chr5:138545057-138545287(+)$1	1	23	31	13.0625
((..((.(	chr15:79748209-79748430(-)$1	1	15	23	10.7968
((((((((	chr19:29040486-29040730(+)$1	1	135	143	9.7812
((.(((((	chr7:36558481-36558701(-)$1	1	1	9	11.7343
))))....	chr6:124653856-124654075(-)$1	1	190	198	14.7031
((((((((	chr2:131003608-131003830(-)$1	1	19	27	13.8437
..((((((	chr15:100046434-100046657(+)$1	1	3	11	11.6562
)))..)))	chr18:78254005-78254227(+)$1	1	67	75	9.7031
)))))..)	chr8:131248056-131248281(+)$1	1	201	209	14.9375
(((((...	chr9:65033500-65033750(+)$1	1	147	155	9.5468
.....)).	chr1:16094432-16094654(+)$1	1	163	171	12.8281
.((((...	chr17:28725563-28725786(-)$1	1	25	33	10.2500
)..(((((	chr4:102874695-102874919(-)$1	1	73	81	13.8437
.(((((((	chr2:27303503-27303783(-)$1	1	39	47	12.1250
..))))))	chr3:60807142-60807362(+)$1	1	161	169	11.1093
))))))))	chr17:57219553-57219781(-)$1	1	172	180	9.0000
..((((((	chr11:68635755-68635994(-)$1	1	64	72	14.7031
(((((.((	chr10:93435088-93435336(-)$1	1	17	25	9.7031
..)).)))	chr5:114813646-114813865(-)$1	1	96	104	13.3750
.)))).))	chr12:70782478-70782707(-)$1	1	210	218	13.1406
.(((....	chr5:100790829-100791057(-)$1	1	108	116	11.1093
((((.((.	chr16:11192968-11193201(-)$1	1	75	83	10.0937
(((....)	chr8:13176712-13176938(+)$1	1	127	135	10.5625
))..))))	chr2:33308924-33309157(-)$1	1	127	135	9.9375
))))).))	chr4:114696272-114696497(+)$1	1	166	174	14.7031
((((((((	chr3:95566362-95566590(-)$1	1	125	133	10.0937
(((((((.	chr9:107458906-107459128(+)$1	1	72	80	14.9375
))).))).	chr2:146070430-146070651(+)$1	1	210	218	12.8281
..)).)))	chr19:43570959-43571187(+)$1	1	46	54	10.2500
((((((((	chr2:152163389-152163645(-)$1	1	9	17	13.3750
.....)))	chr4:120731783-120732020(-)$1	1	180	188	10.7968
..))))))	chr9:64985575-64985796(+)$1	1	44	52	13.1406
...)))))	chr4:123078943-123079168(-)$1	1	200	208	13.1406
.....(((	chr3:106909450-106909678(+)$1	1	154	162	11.8125
)))))...	chr6:38242772-38242995(-)$1	1	39	47	9.8593
((((....	chr1:94912346-94912581(-)$1	1	112	120	12.3593
((((.(((	chr11:119401221-119401455(-)$1	1	139	147	12.8281
))).))))	chr5:38529554-38529780(-)$1	1	198	206	14.9375
)))(((((	chr9:121663762-121663986(+)$1	1	96	104	13.0625
((.(((((	chr5:141235071-141235306(-)$1	1	100	108	10.4843
...((((.	chr17:45704757-45704984(-)$1	1	24	32	11.2656
...(((((	chrX:63556510-63556733(+)$1	1	97	105	9.8593
(((((.(.	chrX:98614942-98615158(-)$1	1	35	43	9.9375
(....)).	chr8:112466926-112467155(+)$1	1	70	78	12.3593

#PSSM
C : 0.50	U : 0.18	G : 0.18	A : 0.12	
U : 1.00	
G : 0.65	C : 0.14	U : 0.14	A : 0.06	
C : 0.98	G : 0.01	
U : 0.98	A : 0.01	
G : 0.96	U : 0.01	A : 0.01	
G : 0.75	C : 0.09	A : 0.09	U : 0.06	
U : 0.34	G : 0.29	C : 0.23	A : 0.12	

#score	751.46875
#seq	64
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m2_run1.nuc.txt

#NT
CUUUUU	chr15:100090258-100090478(+)$1	220	189	195	15.1818
CUUUUU	chr7:30811710-30811930(+)$1	220	83	89	15.1818
CUGUUU	chrX:130426113-130426333(-)$1	220	61	67	11.8181
CUUCUU	chr12:88447928-88448148(-)$1	220	23	29	11.3636
CUUUUU	chr12:25346457-25346677(+)$1	220	42	48	15.1818
CUUUUU	chr5:20392347-20392567(+)$1	220	92	98	15.1818
CUUUGU	chr6:87768673-87768926(-)$1	253	71	77	11.5454
cuuucu	chr5:114293714-114293936(-)$1	222	2	8	11.6363
CUGUUU	chr8:13147142-13147362(+)$1	220	149	155	11.8181
cuuuuu	chr9:22052268-22052498(-)$1	230	31	37	15.1818
CUUUCU	chr1:60041684-60041906(+)$1	222	25	31	11.6363
CUUUCU	chrX:17740429-17740651(+)$1	222	68	74	11.6363
CUUUUU	chr10:82112452-82112690(+)$1	238	216	222	15.1818
CUAUUU	chr7:133929508-133929728(-)$1	220	40	46	11.6363
CUUUGU	chr2:130103487-130103707(+)$1	220	69	75	11.5454
CUUUUU	chr14:121858763-121858983(-)$1	220	63	69	15.1818
CUUUUU	chr6:24564560-24564781(-)$1	221	166	172	15.1818
CUUUUU	chr1:63641785-63642005(+)$1	220	1	7	15.1818
CUUGUU	chr3:36461972-36462192(+)$1	220	12	18	10.9090
CUAUUU	chr3:88980632-88980853(+)$1	221	69	75	11.6363
CUCUUU	chr10:110730288-110730508(+)$1	220	63	69	11.8181
CUUUUU	chr2:118301669-118301900(-)$1	231	195	201	15.1818
CUUCUU	chrX:106355685-106355905(+)$1	220	91	97	11.3636
CUAUUU	chr11:77523181-77523401(+)$1	220	69	75	11.6363
CUUUUU	chr2:72931140-72931360(-)$1	220	29	35	15.1818
CUUUAU	chr11:80208526-80208746(+)$1	220	40	46	11.3636
CUCUUU	chr13:56839838-56840058(+)$1	220	103	109	11.8181
CUUUUU	chr16:98183505-98183728(-)$1	223	162	168	15.1818
CUUCUU	chr2:117107821-117108045(-)$1	224	6	12	11.3636
CUUUUU	chr19:32899330-32899568(+)$1	238	34	40	15.1818
CUUUGU	chr6:100180705-100180925(-)$1	220	99	105	11.5454
CUUCUU	chr3:57450250-57450471(-)$1	221	15	21	11.3636
CUGUUU	chr1:137198277-137198497(-)$1	220	75	81	11.8181
Cuuuuu	chr11:72949106-72949326(-)$1	220	25	31	15.1818
CUUUUU	chr9:118490945-118491165(+)$1	220	3	9	15.1818
CUUUUU	chr1:180259176-180259396(-)$1	220	28	34	15.1818
CUCUUU	chr4:147284211-147284432(-)$1	221	42	48	11.8181
CUCUUU	chr6:34836793-34837013(-)$1	220	199	205	11.8181
CUUUUU	chr1:63777892-63778124(+)$1	232	101	107	15.1818
CUUCUU	chr15:12280190-12280410(+)$1	220	36	42	11.3636
CUUUUU	chr7:135029135-135029355(+)$1	220	51	57	15.1818
CUGUUU	chr3:90303420-90303640(-)$1	220	70	76	11.8181
CUUUCU	chr2:139996180-139996406(-)$1	226	219	225	11.6363
CUUUUU	chr12:100025197-100025419(+)$1	222	53	59	15.1818
CUUUUU	chr14:19037315-19037535(-)$1	220	121	127	15.1818
CUUUUU	chr3:137529424-137529644(+)$1	220	91	97	15.1818
CUGUUU	chr4:11097903-11098150(+)$1	247	143	149	11.8181
CUUUUU	chr2:126718149-126718369(-)$1	220	152	158	15.1818
CUUUAU	chr5:150021153-150021373(+)$1	220	150	156	11.3636
CUUCUU	chr4:32108672-32108892(+)$1	220	124	130	11.3636
CUUUGU	chr4:107905429-107905649(-)$1	220	98	104	11.5454
CUUUUU	chr7:106987519-106987740(-)$1	221	144	150	15.1818
CUUUUU	chr2:37439223-37439456(-)$1	233	42	48	15.1818
CUUUCU	chr11:23632242-23632462(+)$1	220	23	29	11.6363

#otherMatches

#Struct PSSM
lccc22	chr5:30002166-30002388(+)$1	222	55	61	11.8181
GGGGGY	chr15:100090258-100090478(+)$1	220	189	195	15.1818
JJJJJ:	chr7:30811710-30811930(+)$1	220	83	89	15.1818
offfff	chrX:130426113-130426333(-)$1	220	61	67	11.8181
HHGGGG	chr12:88447928-88448148(-)$1	220	23	29	11.3636
ff:ddd	chr12:25346457-25346677(+)$1	220	42	48	15.1818
gggggm	chr5:20392347-20392567(+)$1	220	92	98	15.1818
:::fff	chr6:87768673-87768926(-)$1	253	71	77	11.5454
::::::	chr5:114293714-114293936(-)$1	222	2	8	11.6363
eeee!!	chr8:13147142-13147362(+)$1	220	149	155	11.8181
bb++++	chr9:22052268-22052498(-)$1	230	31	37	15.1818
mmmggg	chr1:60041684-60041906(+)$1	222	25	31	11.6363
qqqqqq	chrX:17740429-17740651(+)$1	222	68	74	11.6363
\\\\\\	chr10:82112452-82112690(+)$1	238	216	222	15.1818
$$$$$b	chr7:133929508-133929728(-)$1	220	40	46	11.6363
ccc]dd	chr2:130103487-130103707(+)$1	220	69	75	11.5454
wwwwww	chr14:121858763-121858983(-)$1	220	63	69	15.1818
C}CCCY	chr6:24564560-24564781(-)$1	221	166	172	15.1818
::::::	chr1:63641785-63642005(+)$1	220	1	7	15.1818
dd::::	chr3:36461972-36462192(+)$1	220	12	18	10.9090
333fff	chr3:88980632-88980853(+)$1	221	69	75	11.6363
ddrrrr	chr10:110730288-110730508(+)$1	220	63	69	11.8181
\\\\\\	chr2:118301669-118301900(-)$1	231	195	201	15.1818
[ggggg	chrX:106355685-106355905(+)$1	220	91	97	11.3636
hhhhhh	chr11:77523181-77523401(+)$1	220	69	75	11.6363
ddddqq	chr2:72931140-72931360(-)$1	220	29	35	15.1818
"""eee	chr11:80208526-80208746(+)$1	220	40	46	11.3636
]fffff	chr13:56839838-56840058(+)$1	220	103	109	11.8181
::::::	chr16:98183505-98183728(-)$1	223	162	168	15.1818
::::dd	chr2:117107821-117108045(-)$1	224	6	12	11.3636
bb]hhh	chr19:32899330-32899568(+)$1	238	34	40	15.1818
dsssss	chr6:100180705-100180925(-)$1	220	99	105	11.5454
e:dddd	chr3:57450250-57450471(-)$1	221	15	21	11.3636
dd[ddd	chr1:137198277-137198497(-)$1	220	75	81	11.8181
:fffff	chr11:72949106-72949326(-)$1	220	25	31	15.1818
::::::	chr9:118490945-118491165(+)$1	220	3	9	15.1818
gggggg	chr1:180259176-180259396(-)$1	220	28	34	15.1818
JJJJJ{	chr4:147284211-147284432(-)$1	221	42	48	11.8181
dddd]c	chr6:34836793-34837013(-)$1	220	199	205	11.8181
eeeeel	chr1:63777892-63778124(+)$1	232	101	107	15.1818
rrrrrr	chr15:12280190-12280410(+)$1	220	36	42	11.3636
JJJJ::	chr7:135029135-135029355(+)$1	220	51	57	15.1818
ffffff	chr3:90303420-90303640(-)$1	220	70	76	11.8181
FYYDDD	chr2:139996180-139996406(-)$1	226	219	225	11.6363
FFFFNN	chr12:100025197-100025419(+)$1	222	53	59	15.1818
hh::::	chr14:19037315-19037535(-)$1	220	121	127	15.1818
:::::d	chr3:137529424-137529644(+)$1	220	91	97	15.1818
ooooob	chr4:11097903-11098150(+)$1	247	143	149	11.8181
======	chr2:126718149-126718369(-)$1	220	152	158	15.1818
ff::::	chr5:150021153-150021373(+)$1	220	150	156	11.3636
qqq===	chr4:32108672-32108892(+)$1	220	124	130	11.3636
ffffqq	chr4:107905429-107905649(-)$1	220	98	104	11.5454
^^^^^^	chr7:106987519-106987740(-)$1	221	144	150	15.1818
wwwwwb	chr2:37439223-37439456(-)$1	233	42	48	15.1818
JEEEEE	chr11:23632242-23632462(+)$1	220	23	29	11.6363

#DB
.)))..	chr5:30002166-30002388(+)$1	1	55	61	11.8181
))))).	chr15:100090258-100090478(+)$1	1	189	195	15.1818
(((((.	chr7:30811710-30811930(+)$1	1	83	89	15.1818
.)))))	chrX:130426113-130426333(-)$1	1	61	67	11.8181
((((((	chr12:88447928-88448148(-)$1	1	23	29	11.3636
)).(((	chr12:25346457-25346677(+)$1	1	42	48	15.1818
(((((.	chr5:20392347-20392567(+)$1	1	92	98	15.1818
...(((	chr6:87768673-87768926(-)$1	1	71	77	11.5454
......	chr5:114293714-114293936(-)$1	1	2	8	11.6363
((((..	chr8:13147142-13147362(+)$1	1	149	155	11.8181
((....	chr9:22052268-22052498(-)$1	1	31	37	15.1818
...)))	chr1:60041684-60041906(+)$1	1	25	31	11.6363
......	chrX:17740429-17740651(+)$1	1	68	74	11.6363
......	chr10:82112452-82112690(+)$1	1	216	222	15.1818
.....(	chr7:133929508-133929728(-)$1	1	40	46	11.6363
))).))	chr2:130103487-130103707(+)$1	1	69	75	11.5454
......	chr14:121858763-121858983(-)$1	1	63	69	15.1818
).))).	chr6:24564560-24564781(-)$1	1	166	172	15.1818
......	chr1:63641785-63642005(+)$1	1	1	7	15.1818
))....	chr3:36461972-36462192(+)$1	1	12	18	10.9090
...)))	chr3:88980632-88980853(+)$1	1	69	75	11.6363
((....	chr10:110730288-110730508(+)$1	1	63	69	11.8181
......	chr2:118301669-118301900(-)$1	1	195	201	15.1818
.(((((	chrX:106355685-106355905(+)$1	1	91	97	11.3636
((((((	chr11:77523181-77523401(+)$1	1	69	75	11.6363
((((..	chr2:72931140-72931360(-)$1	1	29	35	15.1818
...(((	chr11:80208526-80208746(+)$1	1	40	46	11.3636
.)))))	chr13:56839838-56840058(+)$1	1	103	109	11.8181
......	chr16:98183505-98183728(-)$1	1	162	168	15.1818
....((	chr2:117107821-117108045(-)$1	1	6	12	11.3636
)).)))	chr19:32899330-32899568(+)$1	1	34	40	15.1818
(.....	chr6:100180705-100180925(-)$1	1	99	105	11.5454
).((((	chr3:57450250-57450471(-)$1	1	15	21	11.3636
((.(((	chr1:137198277-137198497(-)$1	1	75	81	11.8181
.(((((	chr11:72949106-72949326(-)$1	1	25	31	15.1818
......	chr9:118490945-118491165(+)$1	1	3	9	15.1818
))))))	chr1:180259176-180259396(-)$1	1	28	34	15.1818
(((((.	chr4:147284211-147284432(-)$1	1	42	48	11.8181
)))).)	chr6:34836793-34837013(-)$1	1	199	205	11.8181
(((((.	chr1:63777892-63778124(+)$1	1	101	107	15.1818
......	chr15:12280190-12280410(+)$1	1	36	42	11.3636
((((..	chr7:135029135-135029355(+)$1	1	51	57	15.1818
((((((	chr3:90303420-90303640(-)$1	1	70	76	11.8181
)..)))	chr2:139996180-139996406(-)$1	1	219	225	11.6363
((((..	chr12:100025197-100025419(+)$1	1	53	59	15.1818
))....	chr14:19037315-19037535(-)$1	1	121	127	15.1818
.....(	chr3:137529424-137529644(+)$1	1	91	97	15.1818
.....)	chr4:11097903-11098150(+)$1	1	143	149	11.8181
((((((	chr2:126718149-126718369(-)$1	1	152	158	15.1818
))....	chr5:150021153-150021373(+)$1	1	150	156	11.3636
...)))	chr4:32108672-32108892(+)$1	1	124	130	11.3636
((((..	chr4:107905429-107905649(-)$1	1	98	104	11.5454
......	chr7:106987519-106987740(-)$1	1	144	150	15.1818
.....)	chr2:37439223-37439456(-)$1	1	42	48	15.1818
((((((	chr11:23632242-23632462(+)$1	1	23	29	11.6363

#PSSM
C : 0.96	c : 0.03	
U : 0.94	u : 0.05	
U : 0.70	C : 0.09	G : 0.09	u : 0.05	A : 0.05	
U : 0.81	C : 0.10	u : 0.05	G : 0.01	
U : 0.76	G : 0.07	C : 0.07	u : 0.03	A : 0.03	c : 0.01	
U : 0.94	u : 0.05	

#score	723.6363636363641
#seq	55
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m3_run1.nuc.txt

#NT
GUGAUGU	chr2:136607209-136607513(+)$1	304	235	242	16.5882
GUGAGGU	chr6:115224509-115224776(+)$1	267	170	177	12.1764
GUGGUGU	chr14:73762429-73762698(-)$1	269	30	37	12.9607
GUGUUGU	chr11:106641590-106641828(-)$1	238	106	113	13.0588
GUGAUGG	chr11:19963965-19964203(-)$1	238	88	95	12.2745
GUCAUGU	chr13:98022755-98023004(+)$1	249	123	130	12.2745
GUGCUGU	chr11:41945539-41945852(-)$1	313	260	267	13.4509
AUGAUGU	chr11:66027299-66027554(-)$1	255	198	205	12.6666
AUGAUGU	chr11:46007295-46007544(-)$1	249	57	64	12.6666
GUGCUGU	chr6:15389612-15389854(+)$1	242	178	185	13.4509
AUGAUGU	chr7:52085518-52085779(+)$1	261	116	123	12.6666
CUGAUGU	chr10:98461312-98461549(+)$1	237	86	93	12.6666
GUGUUGU	chr18:31599397-31599640(-)$1	243	114	121	13.0588
GUGAUAU	chr6:17237501-17237740(+)$1	239	69	76	12.2745
GUGAUGU	chr2:32644496-32644814(-)$1	318	184	191	16.5882
GUGAUGG	chr9:58499600-58499858(+)$1	258	10	17	12.2745
GUGACGU	chr17:9174461-9174699(+)$1	238	67	74	12.1764
CUGAUGU	chr15:80922580-80922815(-)$1	235	43	50	12.6666
GUGAUCU	chr9:62643229-62643464(-)$1	235	173	180	12.4705
GUAAUGU	chr5:17771193-17771449(-)$1	256	200	207	12.3725
GUGCUGU	chr13:98022059-98022344(+)$1	285	10	17	13.4509
CUGAUGU	chr16:94690221-94690486(+)$1	265	84	91	12.6666
GUGAUUU	chr18:6788815-6789066(+)$1	251	126	133	12.3725
UUGAUGU	chr15:41691983-41692247(+)$1	264	121	128	12.5686
GUGAUUU	chr5:8348086-8348321(-)$1	235	31	38	12.3725
GUGAGGU	chr11:97370730-97370976(-)$1	246	42	49	12.1764
GUGAUGU	chrX:132337691-132337929(+)$1	238	196	203	16.5882
GUGACGU	chr13:57527441-57527677(-)$1	236	74	81	12.1764
GUGUUGU	chr19:7289793-7290030(-)$1	237	88	95	13.0588
GUGAUGA	chr13:99018363-99018601(-)$1	238	49	56	12.3725
GGGAUGU	chr4:97780058-97780298(+)$1	240	178	185	12.1764
guggugu	chr1:123202217-123202452(-)$1	235	74	81	12.9607
GAGAUGU	chr11:29642157-29642440(+)$1	283	269	276	12.4705
GUGAUCU	chr7:129238340-129238575(-)$1	235	10	17	12.4705
GUAAUGU	chr18:34478629-34478872(+)$1	243	65	72	12.3725
GUGCUGU	chrX:17134633-17134893(-)$1	260	23	30	13.4509
GUGCUGU	chr1:66457514-66457760(+)$1	246	40	47	13.4509
GUGCUGU	chr19:29678975-29679216(+)$1	241	110	117	13.4509
GUAAUGU	chr5:65986677-65986918(+)$1	241	207	214	12.3725
GUGCUGU	chr1:172254180-172254466(-)$1	286	139	146	13.4509
GAGAUGU	chr16:44085816-44086071(-)$1	255	136	143	12.4705
gagaugu	chr12:86682880-86683115(-)$1	235	57	64	12.4705
GUCAUGU	chr19:31520266-31520511(-)$1	245	169	176	12.2745
GAGAUGU	chr15:12280217-12280463(+)$1	246	123	130	12.4705
GUGAUGU	chr12:16992165-16992435(+)$1	270	241	248	16.5882
GUGAUGA	chr17:44223329-44223588(+)$1	259	20	27	12.3725
UUGAUGU	chr17:9177335-9177581(+)$1	246	22	29	12.5686
gugaUGU	chr8:26875511-26875792(-)$1	281	128	135	16.5882
GUGAUCU	chr1:176765957-176766192(-)$1	235	171	178	12.4705
GUGAUGA	chr6:129491118-129491362(+)$1	244	41	48	12.3725

#otherMatches

#Struct PSSM
eeee]ff	chr5:20939889-20940126(+)$1	237	98	105	16.5882
ggggggg	chr2:136607209-136607513(+)$1	304	235	242	16.5882
hhhhhhh	chr6:115224509-115224776(+)$1	267	170	177	12.1764
FFFFF{J	chr14:73762429-73762698(-)$1	269	30	37	12.9607
nnnneee	chr11:106641590-106641828(-)$1	238	106	113	13.0588
vvvvccc	chr11:19963965-19964203(-)$1	238	88	95	12.2745
coooooo	chr13:98022755-98023004(+)$1	249	123	130	12.2745
fffffff	chr11:41945539-41945852(-)$1	313	260	267	13.4509
IIII}A~	chr11:66027299-66027554(-)$1	255	198	205	12.6666
d]dddd]	chr11:46007295-46007544(-)$1	249	57	64	12.6666
]bbffff	chr6:15389612-15389854(+)$1	242	178	185	13.4509
ddbb[bb	chr7:52085518-52085779(+)$1	261	116	123	12.6666
::eeeee	chr10:98461312-98461549(+)$1	237	86	93	12.6666
ddd4444	chr18:31599397-31599640(-)$1	243	114	121	13.0588
EEEEE{G	chr6:17237501-17237740(+)$1	239	69	76	12.2745
hhhh&&&	chr2:32644496-32644814(-)$1	318	184	191	16.5882
hhhh[dd	chr9:58499600-58499858(+)$1	258	10	17	12.2745
CCC::::	chr17:9174461-9174699(+)$1	238	67	74	12.1764
ammmma2	chr15:80922580-80922815(-)$1	235	43	50	12.6666
eeee444	chr9:62643229-62643464(-)$1	235	173	180	12.4705
ggggggg	chr5:17771193-17771449(-)$1	256	200	207	12.3725
IIIdddd	chr13:98022059-98022344(+)$1	285	10	17	13.4509
:::::GG	chr16:94690221-94690486(+)$1	265	84	91	12.6666
]======	chr18:6788815-6789066(+)$1	251	126	133	12.3725
rreeeee	chr15:41691983-41692247(+)$1	264	121	128	12.5686
iii::::	chr5:8348086-8348321(-)$1	235	31	38	12.3725
a[a[fff	chr11:97370730-97370976(-)$1	246	42	49	12.1764
ccc::::	chrX:132337691-132337929(+)$1	238	196	203	16.5882
e]dddd]	chr13:57527441-57527677(-)$1	236	74	81	12.1764
CCCCC{C	chr19:7289793-7290030(-)$1	237	88	95	13.0588
ccc!!dd	chr13:99018363-99018601(-)$1	238	49	56	12.3725
iiiiii]	chr4:97780058-97780298(+)$1	240	178	185	12.1764
E{EEEEE	chr1:123202217-123202452(-)$1	235	74	81	12.9607
]bb333d	chr11:29642157-29642440(+)$1	283	269	276	12.4705
E:::HHH	chr7:129238340-129238575(-)$1	235	10	17	12.4705
gg]hhhh	chr18:34478629-34478872(+)$1	243	65	72	12.3725
edddd!!	chrX:17134633-17134893(-)$1	260	23	30	13.4509
2dddd]a	chr1:66457514-66457760(+)$1	246	40	47	13.4509
e[bb[hh	chr19:29678975-29679216(+)$1	241	110	117	13.4509
:::::ff	chr5:65986677-65986918(+)$1	241	207	214	12.3725
dddd333	chr1:172254180-172254466(-)$1	286	139	146	13.4509
dddvvvv	chr16:44085816-44086071(-)$1	255	136	143	12.4705
HHKKBB{	chr12:86682880-86683115(-)$1	235	57	64	12.4705
C}DDDD}	chr19:31520266-31520511(-)$1	245	169	176	12.2745
2ccc]cc	chr15:12280217-12280463(+)$1	246	123	130	12.4705
]eeeee4	chr12:16992165-16992435(+)$1	270	241	248	16.5882
:::::::	chr17:44223329-44223588(+)$1	259	20	27	12.3725
qqqqqqb	chr17:9177335-9177581(+)$1	246	22	29	12.5686
eeddddl	chr8:26875511-26875792(-)$1	281	128	135	16.5882
FFFFiii	chr1:176765957-176766192(-)$1	235	171	178	12.4705
HHHHHHH	chr6:129491118-129491362(+)$1	244	41	48	12.3725

#DB
)))).))	chr5:20939889-20940126(+)$1	1	98	105	16.5882
)))))))	chr2:136607209-136607513(+)$1	1	235	242	16.5882
(((((((	chr6:115224509-115224776(+)$1	1	170	177	12.1764
(((((.(	chr14:73762429-73762698(-)$1	1	30	37	12.9607
....)))	chr11:106641590-106641828(-)$1	1	106	113	13.0588
....)))	chr11:19963965-19964203(-)$1	1	88	95	12.2745
(......	chr13:98022755-98023004(+)$1	1	123	130	12.2745
)))((((	chr11:41945539-41945852(-)$1	1	260	267	13.4509
)))).).	chr11:66027299-66027554(-)$1	1	198	205	12.6666
).)))).	chr11:46007295-46007544(-)$1	1	57	64	12.6666
.))))))	chr6:15389612-15389854(+)$1	1	178	185	13.4509
))((.((	chr7:52085518-52085779(+)$1	1	116	123	12.6666
..(((((	chr10:98461312-98461549(+)$1	1	86	93	12.6666
)))....	chr18:31599397-31599640(-)$1	1	114	121	13.0588
(((((.(	chr6:17237501-17237740(+)$1	1	69	76	12.2745
((((...	chr2:32644496-32644814(-)$1	1	184	191	16.5882
((((.((	chr9:58499600-58499858(+)$1	1	10	17	12.2745
(((....	chr17:9174461-9174699(+)$1	1	67	74	12.1764
(....).	chr15:80922580-80922815(-)$1	1	43	50	12.6666
))))...	chr9:62643229-62643464(-)$1	1	173	180	12.4705
(((((((	chr5:17771193-17771449(-)$1	1	200	207	12.3725
(((((((	chr13:98022059-98022344(+)$1	1	10	17	13.4509
.....))	chr16:94690221-94690486(+)$1	1	84	91	12.6666
.))))))	chr18:6788815-6789066(+)$1	1	126	133	12.3725
..)))))	chr15:41691983-41692247(+)$1	1	121	128	12.5686
)))....	chr5:8348086-8348321(-)$1	1	31	38	12.3725
(.(.(((	chr11:97370730-97370976(-)$1	1	42	49	12.1764
)))....	chrX:132337691-132337929(+)$1	1	196	203	16.5882
).)))).	chr13:57527441-57527677(-)$1	1	74	81	12.1764
(((((.(	chr19:7289793-7290030(-)$1	1	88	95	13.0588
(((..((	chr13:99018363-99018601(-)$1	1	49	56	12.3725
)))))).	chr4:97780058-97780298(+)$1	1	178	185	12.1764
(.(((((	chr1:123202217-123202452(-)$1	1	74	81	12.9607
.))...)	chr11:29642157-29642440(+)$1	1	269	276	12.4705
(...(((	chr7:129238340-129238575(-)$1	1	10	17	12.4705
)).))))	chr18:34478629-34478872(+)$1	1	65	72	12.3725
(((((..	chrX:17134633-17134893(-)$1	1	23	30	13.4509
.)))).)	chr1:66457514-66457760(+)$1	1	40	47	13.4509
(.((.((	chr19:29678975-29679216(+)$1	1	110	117	13.4509
.....((	chr5:65986677-65986918(+)$1	1	207	214	12.3725
))))...	chr1:172254180-172254466(-)$1	1	139	146	13.4509
(((....	chr16:44085816-44086071(-)$1	1	136	143	12.4705
((..((.	chr12:86682880-86683115(-)$1	1	57	64	12.4705
).)))).	chr19:31520266-31520511(-)$1	1	169	176	12.2745
.))).))	chr15:12280217-12280463(+)$1	1	123	130	12.4705
.))))).	chr12:16992165-16992435(+)$1	1	241	248	16.5882
.......	chr17:44223329-44223588(+)$1	1	20	27	12.3725
......)	chr17:9177335-9177581(+)$1	1	22	29	12.5686
((((((.	chr8:26875511-26875792(-)$1	1	128	135	16.5882
(((((((	chr1:176765957-176766192(-)$1	1	171	178	12.4705
(((((((	chr6:129491118-129491362(+)$1	1	41	48	12.3725

#PSSM
G : 0.76	g : 0.07	A : 0.05	C : 0.05	U : 0.03	
U : 0.84	u : 0.05	A : 0.05	G : 0.01	a : 0.01	
G : 0.82	g : 0.07	A : 0.05	C : 0.03	
A : 0.70	C : 0.13	a : 0.05	U : 0.05	G : 0.01	g : 0.01	
U : 0.86	u : 0.05	G : 0.03	C : 0.03	
G : 0.82	g : 0.05	C : 0.05	U : 0.03	A : 0.01	
U : 0.84	u : 0.05	A : 0.05	G : 0.03	

#score	668.4509803921575
#seq	51
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m3_run2.nuc.txt

#NT
UUUU	chr1:194333782-194334064(+)$1	282	20	24	12.0000
UUUU	chr4:118809414-118809683(+)$1	269	146	150	12.0000
UUUU	chr11:68505849-68506142(+)$1	293	259	263	12.0000
UUUU	chr7:97592865-97593156(+)$1	291	114	118	12.0000
UUUU	chr11:33374020-33374299(-)$1	279	93	97	12.0000
UUUU	chr4:90919170-90919443(-)$1	273	18	22	12.0000
UUUU	chr11:120824490-120824813(-)$1	323	29	33	12.0000
UUUU	chr1:84720777-84721053(-)$1	276	95	99	12.0000
uuuu	chr7:88035570-88035856(-)$1	286	218	222	12.0000
UUUU	chr17:13209269-13209542(+)$1	273	53	57	12.0000
UUUU	chr2:30301871-30302315(+)$1	444	6	10	12.0000
UUUU	chr5:128080706-128080984(-)$1	278	26	30	12.0000
UUUU	chr9:57100769-57101038(-)$1	269	58	62	12.0000
UUUU	chr2:51976940-51977259(+)$1	319	33	37	12.0000
UUUU	chr7:87858011-87858279(-)$1	268	96	100	12.0000
UUUU	chr2:172181818-172182096(-)$1	278	161	165	12.0000
UUUU	chr15:89012664-89012935(-)$1	271	189	193	12.0000
UUUU	chr16:17046093-17046370(+)$1	277	25	29	12.0000
UUUU	chrX:91436027-91436306(-)$1	279	31	35	12.0000
UUUU	chr14:56281245-56281532(-)$1	287	33	37	12.0000
UUUU	chr10:60563118-60563403(-)$1	285	37	41	12.0000
UUUU	chr11:62158623-62158898(-)$1	275	69	73	12.0000
UUUU	chr4:116299856-116300129(-)$1	273	40	44	12.0000
UUUU	chr1:173148123-173148402(-)$1	279	198	202	12.0000
UUUU	chr3:103159647-103159931(+)$1	284	16	20	12.0000
UUUU	chr4:59488345-59488652(-)$1	307	18	22	12.0000
UUUU	chr5:92482533-92482844(-)$1	311	194	198	12.0000
UUUU	chr2:27303312-27303590(-)$1	278	209	213	12.0000
UUUU	chr8:88062766-88063041(-)$1	275	196	200	12.0000
UUUU	chr13:21874707-21874984(-)$1	277	185	189	12.0000
UUUU	chr8:131256790-131257059(+)$1	269	12	16	12.0000
UUUU	chr8:90657749-90658031(+)$1	282	14	18	12.0000
UUUU	chr15:101926928-101927212(+)$1	284	27	31	12.0000
UUUU	chr2:172383566-172383872(+)$1	306	9	13	12.0000
UUUU	chr18:56912487-56912879(+)$1	392	62	66	12.0000
UUUU	chr4:53034363-53034636(+)$1	273	58	62	12.0000
UUUU	chr14:72938071-72938342(-)$1	271	79	83	12.0000
UUUU	chr17:57032948-57033232(-)$1	284	53	57	12.0000
UUUU	chr7:144577614-144577888(-)$1	274	187	191	12.0000
UUUU	chr3:121461854-121462140(-)$1	286	242	246	12.0000
UUUU	chr3:142472673-142472949(-)$1	276	4	8	12.0000
UUUU	chr17:31981968-31982326(-)$1	358	10	14	12.0000
UUUU	chr3:95465577-95465916(+)$1	339	1	5	12.0000
UUUU	chr18:54113913-54114204(+)$1	291	248	252	12.0000
UUUU	chr12:8798840-8799138(+)$1	298	245	249	12.0000
UUUU	chr5:21168178-21168456(+)$1	278	62	66	12.0000
UUUU	chr10:126502125-126502455(+)$1	330	20	24	12.0000
UUUU	chr10:127514018-127514294(+)$1	276	42	46	12.0000
UUUU	chr6:146551280-146551550(-)$1	270	37	41	12.0000
UUUU	chr9:14347928-14348203(-)$1	275	0	4	12.0000
UUUU	chr11:117884677-117885047(+)$1	370	258	262	12.0000
UUUU	chr17:56715168-56715444(-)$1	276	30	34	12.0000
UUUU	chr11:77523204-77523477(+)$1	273	100	104	12.0000
UUUU	chr6:122679565-122679908(-)$1	343	131	135	12.0000
UUUU	chr12:25640036-25640310(+)$1	274	8	12	12.0000
UUUU	chr6:66985312-66985671(-)$1	359	60	64	12.0000
UUUU	chr12:112351000-112351292(+)$1	292	19	23	12.0000
UUUU	chr12:3501412-3501693(+)$1	281	117	121	12.0000
UUUU	chr4:83921508-83921780(-)$1	272	239	243	12.0000
UUUU	chr17:17666510-17666804(-)$1	294	214	218	12.0000
UUUU	chr12:84888325-84888599(-)$1	274	174	178	12.0000
UUUU	chr2:131878295-131878578(-)$1	283	46	50	12.0000
UUUU	chr4:21802405-21802683(+)$1	278	12	16	12.0000
UUUU	chr11:77345802-77346117(-)$1	315	18	22	12.0000
UUUU	chr18:15057490-15057761(+)$1	271	0	4	12.0000
UUUU	chr13:49829190-49829463(+)$1	273	108	112	12.0000
UUUU	chr9:45776418-45776852(-)$1	434	238	242	12.0000
UUUU	chr6:91705152-91705425(+)$1	273	0	4	12.0000
UUUU	chr11:95136249-95136551(-)$1	302	198	202	12.0000
UUUU	chr13:113294718-113295013(+)$1	295	268	272	12.0000
UUUU	chr2:117004401-117004676(+)$1	275	42	46	12.0000
UUUU	chr7:107070040-107070346(-)$1	306	193	197	12.0000
UUUU	chr2:146069065-146069341(-)$1	276	89	93	12.0000
UUUU	chr18:38004349-38004712(-)$1	363	90	94	12.0000
UUUU	chr8:125924985-125925284(+)$1	299	257	261	12.0000
UUUU	chr7:133700766-133701049(-)$1	283	126	130	12.0000
UUUU	chr1:43171750-43172039(+)$1	289	209	213	12.0000
UUUU	chr12:111933368-111933732(-)$1	364	75	79	12.0000
UUUU	chr16:16272293-16272564(+)$1	271	141	145	12.0000
UUUU	chr9:44614474-44614750(-)$1	276	55	59	12.0000
UUUU	chr19:29090505-29090925(+)$1	420	148	152	12.0000

#otherMatches

#Struct PSSM
::::	chr15:6749299-6749570(+)$1	271	1	5	12.0000
ccc"	chr1:194333782-194334064(+)$1	282	20	24	12.0000
oooo	chr4:118809414-118809683(+)$1	269	146	150	12.0000
flll	chr11:68505849-68506142(+)$1	293	259	263	12.0000
qqqq	chr7:97592865-97593156(+)$1	291	114	118	12.0000
gggg	chr11:33374020-33374299(-)$1	279	93	97	12.0000
ffff	chr4:90919170-90919443(-)$1	273	18	22	12.0000
dddd	chr11:120824490-120824813(-)$1	323	29	33	12.0000
eee2	chr1:84720777-84721053(-)$1	276	95	99	12.0000
====	chr7:88035570-88035856(-)$1	286	218	222	12.0000
d!!b	chr17:13209269-13209542(+)$1	273	53	57	12.0000
c%%%	chr2:30301871-30302315(+)$1	444	6	10	12.0000
QQQQ	chr5:128080706-128080984(-)$1	278	26	30	12.0000
hhhh	chr9:57100769-57101038(-)$1	269	58	62	12.0000
gggg	chr2:51976940-51977259(+)$1	319	33	37	12.0000
eeee	chr7:87858011-87858279(-)$1	268	96	100	12.0000
$fff	chr2:172181818-172182096(-)$1	278	161	165	12.0000
uuuu	chr15:89012664-89012935(-)$1	271	189	193	12.0000
::::	chr16:17046093-17046370(+)$1	277	25	29	12.0000
cc[f	chrX:91436027-91436306(-)$1	279	31	35	12.0000
9999	chr14:56281245-56281532(-)$1	287	33	37	12.0000
::::	chr10:60563118-60563403(-)$1	285	37	41	12.0000
oooo	chr11:62158623-62158898(-)$1	275	69	73	12.0000
LLEE	chr4:116299856-116300129(-)$1	273	40	44	12.0000
eeee	chr1:173148123-173148402(-)$1	279	198	202	12.0000
H:::	chr3:103159647-103159931(+)$1	284	16	20	12.0000
GGG{	chr4:59488345-59488652(-)$1	307	18	22	12.0000
====	chr5:92482533-92482844(-)$1	311	194	198	12.0000
bb]c	chr2:27303312-27303590(-)$1	278	209	213	12.0000
dmmm	chr8:88062766-88063041(-)$1	275	196	200	12.0000
fmmm	chr13:21874707-21874984(-)$1	277	185	189	12.0000
::::	chr8:131256790-131257059(+)$1	269	12	16	12.0000
:bb[	chr8:90657749-90658031(+)$1	282	14	18	12.0000
###e	chr15:101926928-101927212(+)$1	284	27	31	12.0000
$$$$	chr2:172383566-172383872(+)$1	306	9	13	12.0000
tttt	chr18:56912487-56912879(+)$1	392	62	66	12.0000
gggg	chr4:53034363-53034636(+)$1	273	58	62	12.0000
:::f	chr14:72938071-72938342(-)$1	271	79	83	12.0000
mmmm	chr17:57032948-57033232(-)$1	284	53	57	12.0000
ccc]	chr7:144577614-144577888(-)$1	274	187	191	12.0000
::::	chr3:121461854-121462140(-)$1	286	242	246	12.0000
eeee	chr3:142472673-142472949(-)$1	276	4	8	12.0000
eeee	chr17:31981968-31982326(-)$1	358	10	14	12.0000
::::	chr3:95465577-95465916(+)$1	339	1	5	12.0000
DD::	chr18:54113913-54114204(+)$1	291	248	252	12.0000
qqqq	chr12:8798840-8799138(+)$1	298	245	249	12.0000
::::	chr5:21168178-21168456(+)$1	278	62	66	12.0000
::::	chr10:126502125-126502455(+)$1	330	20	24	12.0000
MMJJ	chr10:127514018-127514294(+)$1	276	42	46	12.0000
::::	chr6:146551280-146551550(-)$1	270	37	41	12.0000
:EEE	chr9:14347928-14348203(-)$1	275	0	4	12.0000
FFFF	chr11:117884677-117885047(+)$1	370	258	262	12.0000
eeee	chr17:56715168-56715444(-)$1	276	30	34	12.0000
fff]	chr11:77523204-77523477(+)$1	273	100	104	12.0000
KKEE	chr6:122679565-122679908(-)$1	343	131	135	12.0000
B{BB	chr12:25640036-25640310(+)$1	274	8	12	12.0000
JJJJ	chr6:66985312-66985671(-)$1	359	60	64	12.0000
DKKF	chr12:112351000-112351292(+)$1	292	19	23	12.0000
HHHH	chr12:3501412-3501693(+)$1	281	117	121	12.0000
##bb	chr4:83921508-83921780(-)$1	272	239	243	12.0000
:FFF	chr17:17666510-17666804(-)$1	294	214	218	12.0000
qqqq	chr12:84888325-84888599(-)$1	274	174	178	12.0000
e:::	chr2:131878295-131878578(-)$1	283	46	50	12.0000
""cc	chr4:21802405-21802683(+)$1	278	12	16	12.0000
H:::	chr11:77345802-77346117(-)$1	315	18	22	12.0000
::::	chr18:15057490-15057761(+)$1	271	0	4	12.0000
::::	chr13:49829190-49829463(+)$1	273	108	112	12.0000
FFFF	chr9:45776418-45776852(-)$1	434	238	242	12.0000
::EE	chr6:91705152-91705425(+)$1	273	0	4	12.0000
hhhh	chr11:95136249-95136551(-)$1	302	198	202	12.0000
ZZZB	chr13:113294718-113295013(+)$1	295	268	272	12.0000
FFFF	chr2:117004401-117004676(+)$1	275	42	46	12.0000
f+++	chr7:107070040-107070346(-)$1	306	193	197	12.0000
eeee	chr2:146069065-146069341(-)$1	276	89	93	12.0000
xxxx	chr18:38004349-38004712(-)$1	363	90	94	12.0000
''''	chr8:125924985-125925284(+)$1	299	257	261	12.0000
8888	chr7:133700766-133701049(-)$1	283	126	130	12.0000
d333	chr1:43171750-43172039(+)$1	289	209	213	12.0000
qqqq	chr12:111933368-111933732(-)$1	364	75	79	12.0000
pfff	chr16:16272293-16272564(+)$1	271	141	145	12.0000
::::	chr9:44614474-44614750(-)$1	276	55	59	12.0000
gggg	chr19:29090505-29090925(+)$1	420	148	152	12.0000

#DB
....	chr15:6749299-6749570(+)$1	1	1	5	12.0000
(((.	chr1:194333782-194334064(+)$1	1	20	24	12.0000
....	chr4:118809414-118809683(+)$1	1	146	150	12.0000
(...	chr11:68505849-68506142(+)$1	1	259	263	12.0000
....	chr7:97592865-97593156(+)$1	1	114	118	12.0000
((((	chr11:33374020-33374299(-)$1	1	93	97	12.0000
))))	chr4:90919170-90919443(-)$1	1	18	22	12.0000
((((	chr11:120824490-120824813(-)$1	1	29	33	12.0000
))).	chr1:84720777-84721053(-)$1	1	95	99	12.0000
))))	chr7:88035570-88035856(-)$1	1	218	222	12.0000
(..(	chr17:13209269-13209542(+)$1	1	53	57	12.0000
(...	chr2:30301871-30302315(+)$1	1	6	10	12.0000
....	chr5:128080706-128080984(-)$1	1	26	30	12.0000
((((	chr9:57100769-57101038(-)$1	1	58	62	12.0000
))))	chr2:51976940-51977259(+)$1	1	33	37	12.0000
))))	chr7:87858011-87858279(-)$1	1	96	100	12.0000
.(((	chr2:172181818-172182096(-)$1	1	161	165	12.0000
....	chr15:89012664-89012935(-)$1	1	189	193	12.0000
....	chr16:17046093-17046370(+)$1	1	25	29	12.0000
((.(	chrX:91436027-91436306(-)$1	1	31	35	12.0000
....	chr14:56281245-56281532(-)$1	1	33	37	12.0000
....	chr10:60563118-60563403(-)$1	1	37	41	12.0000
....	chr11:62158623-62158898(-)$1	1	69	73	12.0000
..((	chr4:116299856-116300129(-)$1	1	40	44	12.0000
))))	chr1:173148123-173148402(-)$1	1	198	202	12.0000
(...	chr3:103159647-103159931(+)$1	1	16	20	12.0000
(((.	chr4:59488345-59488652(-)$1	1	18	22	12.0000
((((	chr5:92482533-92482844(-)$1	1	194	198	12.0000
)).)	chr2:27303312-27303590(-)$1	1	209	213	12.0000
(...	chr8:88062766-88063041(-)$1	1	196	200	12.0000
(...	chr13:21874707-21874984(-)$1	1	185	189	12.0000
....	chr8:131256790-131257059(+)$1	1	12	16	12.0000
.((.	chr8:90657749-90658031(+)$1	1	14	18	12.0000
...(	chr15:101926928-101927212(+)$1	1	27	31	12.0000
....	chr2:172383566-172383872(+)$1	1	9	13	12.0000
....	chr18:56912487-56912879(+)$1	1	62	66	12.0000
))))	chr4:53034363-53034636(+)$1	1	58	62	12.0000
...(	chr14:72938071-72938342(-)$1	1	79	83	12.0000
....	chr17:57032948-57033232(-)$1	1	53	57	12.0000
))).	chr7:144577614-144577888(-)$1	1	187	191	12.0000
....	chr3:121461854-121462140(-)$1	1	242	246	12.0000
((((	chr3:142472673-142472949(-)$1	1	4	8	12.0000
((((	chr17:31981968-31982326(-)$1	1	10	14	12.0000
....	chr3:95465577-95465916(+)$1	1	1	5	12.0000
))..	chr18:54113913-54114204(+)$1	1	248	252	12.0000
....	chr12:8798840-8799138(+)$1	1	245	249	12.0000
....	chr5:21168178-21168456(+)$1	1	62	66	12.0000
....	chr10:126502125-126502455(+)$1	1	20	24	12.0000
..((	chr10:127514018-127514294(+)$1	1	42	46	12.0000
....	chr6:146551280-146551550(-)$1	1	37	41	12.0000
.(((	chr9:14347928-14348203(-)$1	1	0	4	12.0000
))))	chr11:117884677-117885047(+)$1	1	258	262	12.0000
))))	chr17:56715168-56715444(-)$1	1	30	34	12.0000
))).	chr11:77523204-77523477(+)$1	1	100	104	12.0000
..((	chr6:122679565-122679908(-)$1	1	131	135	12.0000
(.((	chr12:25640036-25640310(+)$1	1	8	12	12.0000
((((	chr6:66985312-66985671(-)$1	1	60	64	12.0000
(..(	chr12:112351000-112351292(+)$1	1	19	23	12.0000
((((	chr12:3501412-3501693(+)$1	1	117	121	12.0000
..((	chr4:83921508-83921780(-)$1	1	239	243	12.0000
.)))	chr17:17666510-17666804(-)$1	1	214	218	12.0000
....	chr12:84888325-84888599(-)$1	1	174	178	12.0000
)...	chr2:131878295-131878578(-)$1	1	46	50	12.0000
..((	chr4:21802405-21802683(+)$1	1	12	16	12.0000
(...	chr11:77345802-77346117(-)$1	1	18	22	12.0000
....	chr18:15057490-15057761(+)$1	1	0	4	12.0000
....	chr13:49829190-49829463(+)$1	1	108	112	12.0000
))))	chr9:45776418-45776852(-)$1	1	238	242	12.0000
..((	chr6:91705152-91705425(+)$1	1	0	4	12.0000
))))	chr11:95136249-95136551(-)$1	1	198	202	12.0000
...)	chr13:113294718-113295013(+)$1	1	268	272	12.0000
((((	chr2:117004401-117004676(+)$1	1	42	46	12.0000
(...	chr7:107070040-107070346(-)$1	1	193	197	12.0000
))))	chr2:146069065-146069341(-)$1	1	89	93	12.0000
....	chr18:38004349-38004712(-)$1	1	90	94	12.0000
....	chr8:125924985-125925284(+)$1	1	257	261	12.0000
....	chr7:133700766-133701049(-)$1	1	126	130	12.0000
)...	chr1:43171750-43172039(+)$1	1	209	213	12.0000
....	chr12:111933368-111933732(-)$1	1	75	79	12.0000
.)))	chr16:16272293-16272564(+)$1	1	141	145	12.0000
....	chr9:44614474-44614750(-)$1	1	55	59	12.0000
))))	chr19:29090505-29090925(+)$1	1	148	152	12.0000

#PSSM
U : 0.98	u : 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
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m3_run2.nuc.txt

#NT
GAAAGU	chr17:24214616-24214836(-)$1	220	103	109	11.0000
GAAAGA	chr4:106113391-106113611(+)$1	220	34	40	14.9090
gaaaga	chrX:98281076-98281297(-)$1	221	6	12	14.9090
CAAAGA	chr15:90059146-90059366(+)$1	220	156	162	11.8181
GAAAGA	chr17:23947321-23947553(+)$1	232	14	20	14.9090
GAAAGG	chr5:147829637-147829857(-)$1	220	206	212	11.0909
GAAAGA	chr13:38041447-38041670(+)$1	223	157	163	14.9090
GAAAGA	chr10:94874985-94875225(-)$1	240	21	27	14.9090
CAAAGA	chr8:106878650-106878870(-)$1	220	23	29	11.8181
AAAAGA	chr2:69709255-69709475(-)$1	220	60	66	11.8181
AAAAGA	chr9:21572138-21572358(-)$1	220	46	52	11.8181
GAAAGG	chr11:106896343-106896563(-)$1	220	7	13	11.0909
UAAAGA	chr12:73884584-73884804(+)$1	220	18	24	11.9090
GAAAGC	chr6:119875923-119876143(-)$1	220	62	68	11.2727
GAAAGC	chr15:101926317-101926542(+)$1	225	100	106	11.2727
GAAAGA	chr2:4828225-4828452(+)$1	227	34	40	14.9090
GAAAGG	chr4:98404811-98405032(+)$1	221	105	111	11.0909
GAAAGA	chr14:121346380-121346600(+)$1	220	59	65	14.9090
GAAAGU	chr6:140600351-140600571(+)$1	220	87	93	11.0000
GAAAGA	chr15:34213793-34214028(+)$1	235	99	105	14.9090
aaaaga	chr13:62274635-62274855(+)$1	220	71	77	11.8181
UAAAGA	chr10:95009629-95009863(-)$1	234	11	17	11.9090
GAAAUA	chr9:70615583-70615827(+)$1	244	7	13	10.9090
CAAAGA	chr6:73213796-73214016(+)$1	220	7	13	11.8181
GAAAGA	chr16:44086015-44086248(-)$1	233	202	208	14.9090
GAAAGA	chr7:30946438-30946664(-)$1	226	55	61	14.9090
GAAAAA	chr10:120361056-120361284(-)$1	228	87	93	11.0909
AAAAGA	chr3:84301466-84301686(-)$1	220	39	45	11.8181
GAAAGC	chr11:3878790-3879018(+)$1	228	62	68	11.2727
GAAAGA	chr10:61918681-61918901(-)$1	220	1	7	14.9090
GAAAGA	chr6:91705635-91705855(+)$1	220	60	66	14.9090
GAAAGA	chrX:162939720-162939944(-)$1	224	11	17	14.9090
CAAAGA	chr5:31505173-31505393(-)$1	220	74	80	11.8181
GAAAGA	chr14:122558053-122558273(+)$1	220	208	214	14.9090
CAAAGA	chr8:125414408-125414628(-)$1	220	84	90	11.8181
GAAAAA	chr12:101444878-101445098(+)$1	220	127	133	11.0909
UAAAGA	chr1:53366813-53367053(+)$1	240	14	20	11.9090
GAAAGA	chr17:24551995-24552217(+)$1	222	40	46	14.9090
GAAAAA	chr17:36002210-36002437(+)$1	227	109	115	11.0909
UAAAGA	chr11:8334165-8334385(-)$1	220	64	70	11.9090
GAAAUA	chr15:36170324-36170555(-)$1	231	17	23	10.9090
GAAAGC	chr19:59371694-59371916(-)$1	222	14	20	11.2727
AAAAGA	chr10:20059540-20059761(+)$1	221	10	16	11.8181
GAAAAA	chr11:113524323-113524562(-)$1	239	33	39	11.0909
GAAAGA	chr11:102297815-102298035(+)$1	220	141	147	14.9090
GAAAGC	chr3:65185664-65185922(-)$1	258	87	93	11.2727
GAAAGA	chr7:134165938-134166158(-)$1	220	70	76	14.9090
GAAAAA	chr2:119435725-119435945(-)$1	220	9	15	11.0909
GAAAGA	chr5:117829275-117829512(-)$1	237	214	220	14.9090
GAAAUA	chrX:159217281-159217506(-)$1	225	3	9	10.9090
UAAAGA	chr5:23468838-23469058(-)$1	220	117	123	11.9090
GAAAGA	chr3:144353134-144353375(-)$1	241	117	123	14.9090
UAAAGA	chr11:23388816-23389036(+)$1	220	74	80	11.9090
GAAAGA	chr4:118805947-118806173(+)$1	226	61	67	14.9090

#otherMatches

#Struct PSSM
bqqqqq	chr11:6170513-6170733(-)$1	220	79	85	14.9090
qqqqqq	chr17:24214616-24214836(-)$1	220	103	109	11.0000
77777=	chr4:106113391-106113611(+)$1	220	34	40	14.9090
qqqqqc	chrX:98281076-98281297(-)$1	221	6	12	14.9090
ttttt=	chr15:90059146-90059366(+)$1	220	156	162	11.8181
DDKKAK	chr17:23947321-23947553(+)$1	232	14	20	14.9090
:eeeee	chr5:147829637-147829857(-)$1	220	206	212	11.0909
777bb]	chr13:38041447-38041670(+)$1	223	157	163	14.9090
HHHHHH	chr10:94874985-94875225(-)$1	240	21	27	14.9090
::::a!	chr8:106878650-106878870(-)$1	220	23	29	11.8181
:::CCC	chr2:69709255-69709475(-)$1	220	60	66	11.8181
"""bbb	chr9:21572138-21572358(-)$1	220	46	52	11.8181
:CCC{C	chr11:106896343-106896563(-)$1	220	7	13	11.0909
oooeee	chr12:73884584-73884804(+)$1	220	18	24	11.9090
::::::	chr6:119875923-119876143(-)$1	220	62	68	11.2727
::::::	chr15:101926317-101926542(+)$1	225	100	106	11.2727
::::cc	chr2:4828225-4828452(+)$1	227	34	40	14.9090
FNNNNN	chr4:98404811-98405032(+)$1	221	105	111	11.0909
tttttt	chr14:121346380-121346600(+)$1	220	59	65	14.9090
oooocc	chr6:140600351-140600571(+)$1	220	87	93	11.0000
eeee33	chr15:34213793-34214028(+)$1	235	99	105	14.9090
hhhhhh	chr13:62274635-62274855(+)$1	220	71	77	11.8181
ccc###	chr10:95009629-95009863(-)$1	234	11	17	11.9090
WWWWWW	chr9:70615583-70615827(+)$1	244	7	13	10.9090
:::::c	chr6:73213796-73214016(+)$1	220	7	13	11.8181
eemmmm	chr16:44086015-44086248(-)$1	233	202	208	14.9090
NNNNNC	chr7:30946438-30946664(-)$1	226	55	61	14.9090
EEEE??	chr10:120361056-120361284(-)$1	228	87	93	11.0909
qqqqqq	chr3:84301466-84301686(-)$1	220	39	45	11.8181
ggggg7	chr11:3878790-3879018(+)$1	228	62	68	11.2727
::dddd	chr10:61918681-61918901(-)$1	220	1	7	14.9090
::::::	chr6:91705635-91705855(+)$1	220	60	66	14.9090
ddoooo	chrX:162939720-162939944(-)$1	224	11	17	14.9090
yyyygg	chr5:31505173-31505393(-)$1	220	74	80	11.8181
CCC}GG	chr14:122558053-122558273(+)$1	220	208	214	14.9090
QQQQQQ	chr8:125414408-125414628(-)$1	220	84	90	11.8181
777hhh	chr12:101444878-101445098(+)$1	220	127	133	11.0909
EEHHHH	chr1:53366813-53367053(+)$1	240	14	20	11.9090
GG{CCC	chr17:24551995-24552217(+)$1	222	40	46	14.9090
"ddddp	chr17:36002210-36002437(+)$1	227	109	115	11.0909
ggggg!	chr11:8334165-8334385(-)$1	220	64	70	11.9090
mmmmee	chr15:36170324-36170555(-)$1	231	17	23	10.9090
DDLLLF	chr19:59371694-59371916(-)$1	222	14	20	11.2727
oooooo	chr10:20059540-20059761(+)$1	221	10	16	11.8181
DD::::	chr11:113524323-113524562(-)$1	239	33	39	11.0909
iiiiii	chr11:102297815-102298035(+)$1	220	141	147	14.9090
c77777	chr3:65185664-65185922(-)$1	258	87	93	11.2727
fffff:	chr7:134165938-134166158(-)$1	220	70	76	14.9090
::::::	chr2:119435725-119435945(-)$1	220	9	15	11.0909
gg::::	chr5:117829275-117829512(-)$1	237	214	220	14.9090
::::::	chrX:159217281-159217506(-)$1	225	3	9	10.9090
eee]bb	chr5:23468838-23469058(-)$1	220	117	123	11.9090
^^^^dd	chr3:144353134-144353375(-)$1	241	117	123	14.9090
oooood	chr11:23388816-23389036(+)$1	220	74	80	11.9090
EEKKBB	chr4:118805947-118806173(+)$1	226	61	67	14.9090

#DB
(.....	chr11:6170513-6170733(-)$1	1	79	85	14.9090
......	chr17:24214616-24214836(-)$1	1	103	109	11.0000
.....)	chr4:106113391-106113611(+)$1	1	34	40	14.9090
.....)	chrX:98281076-98281297(-)$1	1	6	12	14.9090
.....)	chr15:90059146-90059366(+)$1	1	156	162	11.8181
((..(.	chr17:23947321-23947553(+)$1	1	14	20	14.9090
.(((((	chr5:147829637-147829857(-)$1	1	206	212	11.0909
...)).	chr13:38041447-38041670(+)$1	1	157	163	14.9090
((((((	chr10:94874985-94875225(-)$1	1	21	27	14.9090
....(.	chr8:106878650-106878870(-)$1	1	23	29	11.8181
...(((	chr2:69709255-69709475(-)$1	1	60	66	11.8181
...(((	chr9:21572138-21572358(-)$1	1	46	52	11.8181
.(((.(	chr11:106896343-106896563(-)$1	1	7	13	11.0909
...)))	chr12:73884584-73884804(+)$1	1	18	24	11.9090
......	chr6:119875923-119876143(-)$1	1	62	68	11.2727
......	chr15:101926317-101926542(+)$1	1	100	106	11.2727
....((	chr2:4828225-4828452(+)$1	1	34	40	14.9090
(.....	chr4:98404811-98405032(+)$1	1	105	111	11.0909
......	chr14:121346380-121346600(+)$1	1	59	65	14.9090
....))	chr6:140600351-140600571(+)$1	1	87	93	11.0000
))))..	chr15:34213793-34214028(+)$1	1	99	105	14.9090
((((((	chr13:62274635-62274855(+)$1	1	71	77	11.8181
(((...	chr10:95009629-95009863(-)$1	1	11	17	11.9090
......	chr9:70615583-70615827(+)$1	1	7	13	10.9090
.....(	chr6:73213796-73214016(+)$1	1	7	13	11.8181
((....	chr16:44086015-44086248(-)$1	1	202	208	14.9090
.....(	chr7:30946438-30946664(-)$1	1	55	61	14.9090
))))..	chr10:120361056-120361284(-)$1	1	87	93	11.0909
......	chr3:84301466-84301686(-)$1	1	39	45	11.8181
))))).	chr11:3878790-3879018(+)$1	1	62	68	11.2727
..((((	chr10:61918681-61918901(-)$1	1	1	7	14.9090
......	chr6:91705635-91705855(+)$1	1	60	66	14.9090
((....	chrX:162939720-162939944(-)$1	1	11	17	14.9090
....))	chr5:31505173-31505393(-)$1	1	74	80	11.8181
))).))	chr14:122558053-122558273(+)$1	1	208	214	14.9090
......	chr8:125414408-125414628(-)$1	1	84	90	11.8181
...)))	chr12:101444878-101445098(+)$1	1	127	133	11.0909
((((((	chr1:53366813-53367053(+)$1	1	14	20	11.9090
((.(((	chr17:24551995-24552217(+)$1	1	40	46	14.9090
.((((.	chr17:36002210-36002437(+)$1	1	109	115	11.0909
(((((.	chr11:8334165-8334385(-)$1	1	64	70	11.9090
....))	chr15:36170324-36170555(-)$1	1	17	23	10.9090
((...(	chr19:59371694-59371916(-)$1	1	14	20	11.2727
......	chr10:20059540-20059761(+)$1	1	10	16	11.8181
((....	chr11:113524323-113524562(-)$1	1	33	39	11.0909
))))))	chr11:102297815-102298035(+)$1	1	141	147	14.9090
).....	chr3:65185664-65185922(-)$1	1	87	93	11.2727
))))).	chr7:134165938-134166158(-)$1	1	70	76	14.9090
......	chr2:119435725-119435945(-)$1	1	9	15	11.0909
))....	chr5:117829275-117829512(-)$1	1	214	220	14.9090
......	chrX:159217281-159217506(-)$1	1	3	9	10.9090
))).))	chr5:23468838-23469058(-)$1	1	117	123	11.9090
....))	chr3:144353134-144353375(-)$1	1	117	123	14.9090
.....)	chr11:23388816-23389036(+)$1	1	74	80	11.9090
((..((	chr4:118805947-118806173(+)$1	1	61	67	14.9090

#PSSM
G : 0.69	U : 0.10	C : 0.09	A : 0.07	g : 0.01	a : 0.01	
A : 0.96	a : 0.03	
A : 0.96	a : 0.03	
A : 0.96	a : 0.03	
G : 0.81	A : 0.09	U : 0.05	g : 0.03	
A : 0.78	C : 0.09	G : 0.05	U : 0.03	a : 0.03	

#score	702.5454545454546
#seq	55
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m1_run2.nuc.txt

#NT
CUGUGAC	chr19:29086354-29086641(+)$1	287	118	125	13.3214
CUGGGAC	chr2:32092890-32093158(+)$1	268	91	98	13.8571
CUGAGAA	chr4:45372561-45372833(+)$1	272	132	139	12.4285
CUCAGAC	chr19:7273742-7274025(-)$1	283	46	53	12.4285
CUGAGAC	chr8:23489736-23490016(-)$1	280	10	17	16.1785
CUGAGGC	chr9:65194529-65194809(+)$1	280	8	15	12.7857
CUGGGGC	chr16:91227498-91227771(+)$1	273	6	13	10.4642
CUGAGAG	chr2:121205209-121205478(-)$1	269	193	200	12.0714
CUGACAC	chr3:96066825-96067098(-)$1	273	259	266	11.7142
CUCAGAC	chr17:35292433-35292717(-)$1	284	26	33	12.4285
CUGGGAC	chr8:86770433-86770706(-)$1	273	260	267	13.8571
CUGAGCC	chr8:74842841-74843113(+)$1	272	12	19	12.2499
CUGGGAC	chr9:53773691-53773960(-)$1	269	168	175	13.8571
CUGAGGC	chr11:97574608-97574878(+)$1	270	29	36	12.7857
CUGAGAA	chr5:138223490-138223786(-)$1	296	135	142	12.4285
CCGAGAC	chr14:103482193-103482469(-)$1	276	92	99	12.0714
CUGGGAC	chr11:87794777-87795061(-)$1	284	183	190	13.8571
CUGAGGC	chr7:25670028-25670303(+)$1	275	21	28	12.7857
CUCAGAC	chr2:34678076-34678352(-)$1	276	5	12	12.4285
CUGAAAC	chrX:98514856-98515126(+)$1	270	19	26	11.7142
CUGGGAC	chr18:60859085-60859370(-)$1	285	71	78	13.8571
CUGUGAC	chr7:27949815-27950085(-)$1	270	20	27	13.3214
CCGAGAC	chr5:122096593-122096864(-)$1	271	4	11	12.0714
CUGAGAC	chr9:66220026-66220300(+)$1	274	108	115	16.1785
CUGUGAC	chr6:22240953-22241221(+)$1	268	61	68	13.3214
CAGAGAC	chr16:36049850-36050132(-)$1	282	192	199	11.8928
CUAAGAC	chr1:184398225-184398498(-)$1	273	8	15	12.0714

#otherMatches

#Struct PSSM
CCC}AZZ	chr19:8964904-8965185(+)$1	281	143	150	12.4285
EEE}DDD	chr19:29086354-29086641(+)$1	287	118	125	13.3214
ddd!!dd	chr2:32092890-32093158(+)$1	268	91	98	13.8571
ba]ccc:	chr4:45372561-45372833(+)$1	272	132	139	12.4285
2dddd]d	chr19:7273742-7274025(-)$1	283	46	53	12.4285
===lll=	chr8:23489736-23490016(-)$1	280	10	17	16.1785
ff[dddd	chr9:65194529-65194809(+)$1	280	8	15	12.7857
DDDDhhh	chr16:91227498-91227771(+)$1	273	6	13	10.4642
::GGGGG	chr2:121205209-121205478(-)$1	269	193	200	12.0714
BDDDD::	chr3:96066825-96067098(-)$1	273	259	266	11.7142
2dddd:c	chr17:35292433-35292717(-)$1	284	26	33	12.4285
HHHGGGG	chr8:86770433-86770706(-)$1	273	260	267	13.8571
clllccc	chr8:74842841-74843113(+)$1	272	12	19	12.2499
bCCCCCC	chr9:53773691-53773960(-)$1	269	168	175	13.8571
dddDDDD	chr11:97574608-97574878(+)$1	270	29	36	12.7857
DDDDDDD	chr5:138223490-138223786(-)$1	296	135	142	12.4285
fff::ff	chr14:103482193-103482469(-)$1	276	92	99	12.0714
GGGGG::	chr11:87794777-87795061(-)$1	284	183	190	13.8571
KCCC{BB	chr7:25670028-25670303(+)$1	275	21	28	12.7857
:::::ff	chr2:34678076-34678352(-)$1	276	5	12	12.4285
ee"""cc	chrX:98514856-98515126(+)$1	270	19	26	11.7142
C:cccqq	chr18:60859085-60859370(-)$1	285	71	78	13.8571
eeee!!a	chr7:27949815-27950085(-)$1	270	20	27	13.3214
ggggg""	chr5:122096593-122096864(-)$1	271	4	11	12.0714
DDDDYYF	chr9:66220026-66220300(+)$1	274	108	115	16.1785
HHHHH::	chr6:22240953-22241221(+)$1	268	61	68	13.3214
::ddddl	chr16:36049850-36050132(-)$1	282	192	199	11.8928
MMCCC{C	chr1:184398225-184398498(-)$1	273	8	15	12.0714

#DB
))).)..	chr19:8964904-8965185(+)$1	1	143	150	12.4285
))).)))	chr19:29086354-29086641(+)$1	1	118	125	13.3214
(((..((	chr2:32092890-32093158(+)$1	1	91	98	13.8571
)).))).	chr4:45372561-45372833(+)$1	1	132	139	12.4285
.)))).)	chr19:7273742-7274025(-)$1	1	46	53	12.4285
(((...)	chr8:23489736-23490016(-)$1	1	10	17	16.1785
((.((((	chr9:65194529-65194809(+)$1	1	8	15	12.7857
(((((((	chr16:91227498-91227771(+)$1	1	6	13	10.4642
..)))))	chr2:121205209-121205478(-)$1	1	193	200	12.0714
)))))..	chr3:96066825-96067098(-)$1	1	259	266	11.7142
.)))).(	chr17:35292433-35292717(-)$1	1	26	33	12.4285
)))))))	chr8:86770433-86770706(-)$1	1	260	267	13.8571
(...)))	chr8:74842841-74843113(+)$1	1	12	19	12.2499
)))))))	chr9:53773691-53773960(-)$1	1	168	175	13.8571
)))((((	chr11:97574608-97574878(+)$1	1	29	36	12.7857
)))))))	chr5:138223490-138223786(-)$1	1	135	142	12.4285
)))..((	chr14:103482193-103482469(-)$1	1	92	99	12.0714
)))))..	chr11:87794777-87795061(-)$1	1	183	190	13.8571
.(((.((	chr7:25670028-25670303(+)$1	1	21	28	12.7857
.....((	chr2:34678076-34678352(-)$1	1	5	12	12.4285
((...((	chrX:98514856-98515126(+)$1	1	19	26	11.7142
(.(((..	chr18:60859085-60859370(-)$1	1	71	78	13.8571
((((..(	chr7:27949815-27950085(-)$1	1	20	27	13.3214
(((((..	chr5:122096593-122096864(-)$1	1	4	11	12.0714
))))..)	chr9:66220026-66220300(+)$1	1	108	115	16.1785
(((((..	chr6:22240953-22241221(+)$1	1	61	68	13.3214
..((((.	chr16:36049850-36050132(-)$1	1	192	199	11.8928
..(((.(	chr1:184398225-184398498(-)$1	1	8	15	12.0714

#PSSM
C : 0.99	
U : 0.89	C : 0.07	A : 0.03	
G : 0.85	C : 0.10	A : 0.03	
A : 0.67	G : 0.21	U : 0.10	
G : 0.92	C : 0.03	A : 0.03	
A : 0.82	G : 0.14	C : 0.03	
C : 0.85	A : 0.10	G : 0.03	

#score	360.8571428571427
#seq	28
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m1_run1.nuc.txt

#NT
CUG	chr9:107522655-107522882(-)$1	227	27	30	8.9999
CUG	chr19:42055391-42055615(-)$1	224	0	3	8.9999
CUG	chr6:112997521-112997741(+)$1	220	52	55	8.9999
CUG	chr4:155571264-155571493(-)$1	229	0	3	8.9999
CUG	chr7:147191201-147191415(-)$1	214	20	23	8.9999
CUG	chr5:151595058-151595279(+)$1	221	32	35	8.9999
CUG	chr9:22180655-22180873(-)$1	218	23	26	8.9999
CUG	chr16:11087812-11088023(-)$1	211	42	45	8.9999
CUG	chr15:91556498-91556721(+)$1	223	5	8	8.9999
cug	chr11:69457289-69457509(+)$1	220	4	7	8.9999
CUG	chr1:140977660-140977881(+)$1	221	21	24	8.9999
CUG	chr15:98781572-98781785(-)$1	213	57	60	8.9999
CUG	chr15:37932054-37932266(-)$1	212	46	49	8.9999
CUG	chr16:31131294-31131512(-)$1	218	101	104	8.9999
CUG	chr13:15640310-15640528(+)$1	218	50	53	8.9999
CUG	chr16:90247822-90248053(-)$1	231	20	23	8.9999
CUG	chr2:84790226-84790445(+)$1	219	34	37	8.9999
CUG	chr8:11267500-11267728(-)$1	228	40	43	8.9999
CUG	chr2:119602371-119602592(-)$1	221	80	83	8.9999
CUG	chr4:100826055-100826266(-)$1	211	31	34	8.9999
CUG	chr18:34657085-34657303(-)$1	218	108	111	8.9999
CUG	chrX:147520635-147520845(+)$1	210	39	42	8.9999
CUG	chr9:77827552-77827772(+)$1	220	27	30	8.9999
CUG	chr10:77867599-77867827(-)$1	228	124	127	8.9999
CUG	chr1:95319772-95319991(-)$1	219	13	16	8.9999
CUG	chr13:95160682-95160912(+)$1	230	55	58	8.9999
CUG	chr12:77011954-77012184(+)$1	230	26	29	8.9999
CUG	chr13:14285540-14285787(+)$1	247	69	72	8.9999
CUG	chr14:35490290-35490496(+)$1	206	76	79	8.9999
CUG	chr14:47909810-47910026(+)$1	216	22	25	8.9999
CUG	chr7:137362486-137362703(-)$1	217	15	18	8.9999
CUG	chr10:75896323-75896546(-)$1	223	23	26	8.9999
CUG	chr16:87415722-87415946(-)$1	224	33	36	8.9999
CUG	chr19:4290750-4290958(-)$1	208	1	4	8.9999
CUG	chr4:130328474-130328698(+)$1	224	4	7	8.9999
CUG	chr19:18668259-18668473(-)$1	214	40	43	8.9999
CUG	chr16:13326383-13326617(+)$1	234	10	13	8.9999
CUG	chr12:112865987-112866204(+)$1	217	12	15	8.9999
CUG	chr7:141973938-141974157(+)$1	219	41	44	8.9999
CUG	chr17:26279649-26279863(+)$1	214	70	73	8.9999
CUG	chr5:77379919-77380128(-)$1	209	25	28	8.9999
CUG	chr9:110463536-110463754(+)$1	218	51	54	8.9999
CUG	chr12:77072720-77072940(+)$1	220	23	26	8.9999
CUG	chr8:12637669-12637891(-)$1	222	151	154	8.9999
CUG	chr14:21532532-21532748(+)$1	216	27	30	8.9999
CUG	chr18:36827152-36827358(-)$1	206	9	12	8.9999
CUG	chr1:40046844-40047059(+)$1	215	13	16	8.9999
CUG	chr8:74774485-74774696(+)$1	211	119	122	8.9999
CUG	chr11:93963325-93963546(+)$1	221	3	6	8.9999
CUG	chr11:30019329-30019557(-)$1	228	63	66	8.9999
CUG	chr11:85017682-85017891(-)$1	209	28	31	8.9999
CUG	chr9:82781068-82781294(-)$1	226	7	10	8.9999
CUG	chr6:146334358-146334572(-)$1	214	75	78	8.9999
CUG	chr11:84853479-84853692(-)$1	213	25	28	8.9999
CUG	chr17:32338163-32338374(-)$1	211	11	14	8.9999
CUG	chr12:74268984-74269190(+)$1	206	24	27	8.9999
CUG	chr11:106936103-106936312(-)$1	209	29	32	8.9999
CUG	chr12:70925471-70925698(-)$1	227	79	82	8.9999
CUG	chr8:125136923-125137149(+)$1	226	14	17	8.9999
CUG	chr11:84819231-84819467(-)$1	236	14	17	8.9999
CUG	chr10:39526628-39526844(+)$1	216	26	29	8.9999
CUG	chr14:55054507-55054725(+)$1	218	28	31	8.9999
CUG	chr6:98953121-98953329(-)$1	208	26	29	8.9999
CUG	chr1:40018936-40019179(+)$1	243	3	6	8.9999
CUG	chr5:121713829-121714039(+)$1	210	13	16	8.9999
CUG	chr10:62455854-62456077(+)$1	223	32	35	8.9999
CUG	chrM:5797-6013(+)$1	216	84	87	8.9999
CUG	chr5:116375373-116375604(+)$1	231	31	34	8.9999
CUG	chr14:32558399-32558622(-)$1	223	112	115	8.9999
CUG	chr2:143779625-143779840(-)$1	215	0	3	8.9999
CUG	chr12:87365165-87365383(+)$1	218	61	64	8.9999
CUG	chr5:123689489-123689704(+)$1	215	6	9	8.9999
CUG	chr16:4669803-4670010(-)$1	207	12	15	8.9999
CUG	chr18:63880365-63880585(+)$1	220	60	63	8.9999
CUG	chrX:98871508-98871729(+)$1	221	74	77	8.9999
CUG	chr15:102314523-102314737(+)$1	214	14	17	8.9999
CUG	chr1:169291488-169291717(+)$1	229	47	50	8.9999
CUG	chr2:126934144-126934352(-)$1	208	28	31	8.9999
CUG	chr4:148450022-148450249(-)$1	227	5	8	8.9999
CUG	chr3:104301329-104301551(-)$1	222	5	8	8.9999
CUG	chr18:42458768-42458977(+)$1	209	15	18	8.9999
CUG	chr12:8750498-8750716(+)$1	218	16	19	8.9999
cug	chr2:109880725-109880958(+)$1	233	132	135	8.9999
CUG	chr8:97984497-97984706(-)$1	209	24	27	8.9999
CUG	chr18:32239902-32240123(+)$1	221	47	50	8.9999
CUG	chr2:75503185-75503409(+)$1	224	85	88	8.9999
CUG	chr14:32534996-32535217(-)$1	221	5	8	8.9999
CUG	chr17:66336328-66336538(-)$1	210	22	25	8.9999
CUG	chr10:87902155-87902380(+)$1	225	163	166	8.9999
CUG	chr5:65665524-65665739(-)$1	215	39	42	8.9999
CUG	chr8:73883141-73883359(+)$1	218	44	47	8.9999
CUG	chr11:87797316-87797552(-)$1	236	12	15	8.9999
CUG	chr5:23940655-23940877(+)$1	222	49	52	8.9999
CUG	chr11:70764688-70764908(-)$1	220	73	76	8.9999
CUG	chr19:47610710-47610917(-)$1	207	66	69	8.9999
CUG	chr2:35145890-35146100(+)$1	210	59	62	8.9999
CUG	chr7:134985832-134986053(-)$1	221	29	32	8.9999
CUG	chr14:68446363-68446593(-)$1	230	20	23	8.9999

#otherMatches

#Struct PSSM
::G	chr18:83124961-83125192(+)$1	231	18	21	8.9999
fff	chr9:107522655-107522882(-)$1	227	27	30	8.9999
BBK	chr19:42055391-42055615(-)$1	224	0	3	8.9999
bb:	chr6:112997521-112997741(+)$1	220	52	55	8.9999
:bb	chr4:155571264-155571493(-)$1	229	0	3	8.9999
d##	chr7:147191201-147191415(-)$1	214	20	23	8.9999
::H	chr5:151595058-151595279(+)$1	221	32	35	8.9999
mmd	chr9:22180655-22180873(-)$1	218	23	26	8.9999
bb[	chr16:11087812-11088023(-)$1	211	42	45	8.9999
cc[	chr15:91556498-91556721(+)$1	223	5	8	8.9999
:::	chr11:69457289-69457509(+)$1	220	4	7	8.9999
:::	chr1:140977660-140977881(+)$1	221	21	24	8.9999
ddd	chr15:98781572-98781785(-)$1	213	57	60	8.9999
hhh	chr15:37932054-37932266(-)$1	212	46	49	8.9999
bnn	chr16:31131294-31131512(-)$1	218	101	104	8.9999
iii	chr13:15640310-15640528(+)$1	218	50	53	8.9999
eef	chr16:90247822-90248053(-)$1	231	20	23	8.9999
ppp	chr2:84790226-84790445(+)$1	219	34	37	8.9999
:::	chr8:11267500-11267728(-)$1	228	40	43	8.9999
!bb	chr2:119602371-119602592(-)$1	221	80	83	8.9999
:cc	chr4:100826055-100826266(-)$1	211	31	34	8.9999
b]b	chr18:34657085-34657303(-)$1	218	108	111	8.9999
2ee	chrX:147520635-147520845(+)$1	210	39	42	8.9999
:cc	chr9:77827552-77827772(+)$1	220	27	30	8.9999
ddd	chr10:77867599-77867827(-)$1	228	124	127	8.9999
{CC	chr1:95319772-95319991(-)$1	219	13	16	8.9999
fff	chr13:95160682-95160912(+)$1	230	55	58	8.9999
::b	chr12:77011954-77012184(+)$1	230	26	29	8.9999
ddd	chr13:14285540-14285787(+)$1	247	69	72	8.9999
dd2	chr14:35490290-35490496(+)$1	206	76	79	8.9999
ddd	chr14:47909810-47910026(+)$1	216	22	25	8.9999
ooo	chr7:137362486-137362703(-)$1	217	15	18	8.9999
cuu	chr10:75896323-75896546(-)$1	223	23	26	8.9999
fff	chr16:87415722-87415946(-)$1	224	33	36	8.9999
:EE	chr19:4290750-4290958(-)$1	208	1	4	8.9999
FFF	chr4:130328474-130328698(+)$1	224	4	7	8.9999
ddd	chr19:18668259-18668473(-)$1	214	40	43	8.9999
{FF	chr16:13326383-13326617(+)$1	234	10	13	8.9999
ddd	chr12:112865987-112866204(+)$1	217	12	15	8.9999
ffg	chr7:141973938-141974157(+)$1	219	41	44	8.9999
!!e	chr17:26279649-26279863(+)$1	214	70	73	8.9999
bb[	chr5:77379919-77380128(-)$1	209	25	28	8.9999
ood	chr9:110463536-110463754(+)$1	218	51	54	8.9999
!!b	chr12:77072720-77072940(+)$1	220	23	26	8.9999
%%e	chr8:12637669-12637891(-)$1	222	151	154	8.9999
ddd	chr14:21532532-21532748(+)$1	216	27	30	8.9999
DDD	chr18:36827152-36827358(-)$1	206	9	12	8.9999
fnn	chr1:40046844-40047059(+)$1	215	13	16	8.9999
ddd	chr8:74774485-74774696(+)$1	211	119	122	8.9999
fff	chr11:93963325-93963546(+)$1	221	3	6	8.9999
ddd	chr11:30019329-30019557(-)$1	228	63	66	8.9999
ggg	chr11:85017682-85017891(-)$1	209	28	31	8.9999
FFF	chr9:82781068-82781294(-)$1	226	7	10	8.9999
eea	chr6:146334358-146334572(-)$1	214	75	78	8.9999
eee	chr11:84853479-84853692(-)$1	213	25	28	8.9999
ddd	chr17:32338163-32338374(-)$1	211	11	14	8.9999
enn	chr12:74268984-74269190(+)$1	206	24	27	8.9999
FFF	chr11:106936103-106936312(-)$1	209	29	32	8.9999
gg:	chr12:70925471-70925698(-)$1	227	79	82	8.9999
BB{	chr8:125136923-125137149(+)$1	226	14	17	8.9999
GGG	chr11:84819231-84819467(-)$1	236	14	17	8.9999
hhh	chr10:39526628-39526844(+)$1	216	26	29	8.9999
===	chr14:55054507-55054725(+)$1	218	28	31	8.9999
!!c	chr6:98953121-98953329(-)$1	208	26	29	8.9999
fff	chr1:40018936-40019179(+)$1	243	3	6	8.9999
GGG	chr5:121713829-121714039(+)$1	210	13	16	8.9999
hhh	chr10:62455854-62456077(+)$1	223	32	35	8.9999
EEE	chrM:5797-6013(+)$1	216	84	87	8.9999
:DD	chr5:116375373-116375604(+)$1	231	31	34	8.9999
===	chr14:32558399-32558622(-)$1	223	112	115	8.9999
::G	chr2:143779625-143779840(-)$1	215	0	3	8.9999
DDD	chr12:87365165-87365383(+)$1	218	61	64	8.9999
DDF	chr5:123689489-123689704(+)$1	215	6	9	8.9999
ddo	chr16:4669803-4670010(-)$1	207	12	15	8.9999
a[c	chr18:63880365-63880585(+)$1	220	60	63	8.9999
ccc	chrX:98871508-98871729(+)$1	221	74	77	8.9999
eee	chr15:102314523-102314737(+)$1	214	14	17	8.9999
GGG	chr1:169291488-169291717(+)$1	229	47	50	8.9999
ddp	chr2:126934144-126934352(-)$1	208	28	31	8.9999
a[d	chr4:148450022-148450249(-)$1	227	5	8	8.9999
aoo	chr3:104301329-104301551(-)$1	222	5	8	8.9999
CCd	chr18:42458768-42458977(+)$1	209	15	18	8.9999
ddd	chr12:8750498-8750716(+)$1	218	16	19	8.9999
ccm	chr2:109880725-109880958(+)$1	233	132	135	8.9999
ann	chr8:97984497-97984706(-)$1	209	24	27	8.9999
app	chr18:32239902-32240123(+)$1	221	47	50	8.9999
NFF	chr2:75503185-75503409(+)$1	224	85	88	8.9999
DDD	chr14:32534996-32535217(-)$1	221	5	8	8.9999
fff	chr17:66336328-66336538(-)$1	210	22	25	8.9999
!!f	chr10:87902155-87902380(+)$1	225	163	166	8.9999
nnn	chr5:65665524-65665739(-)$1	215	39	42	8.9999
Fee	chr8:73883141-73883359(+)$1	218	44	47	8.9999
CC{	chr11:87797316-87797552(-)$1	236	12	15	8.9999
::F	chr5:23940655-23940877(+)$1	222	49	52	8.9999
ddc	chr11:70764688-70764908(-)$1	220	73	76	8.9999
NNG	chr19:47610710-47610917(-)$1	207	66	69	8.9999
e33	chr2:35145890-35146100(+)$1	210	59	62	8.9999
22c	chr7:134985832-134986053(-)$1	221	29	32	8.9999
MA{	chr14:68446363-68446593(-)$1	230	20	23	8.9999

#DB
..(	chr18:83124961-83125192(+)$1	1	18	21	8.9999
)))	chr9:107522655-107522882(-)$1	1	27	30	8.9999
((.	chr19:42055391-42055615(-)$1	1	0	3	8.9999
)).	chr6:112997521-112997741(+)$1	1	52	55	8.9999
.((	chr4:155571264-155571493(-)$1	1	0	3	8.9999
(..	chr7:147191201-147191415(-)$1	1	20	23	8.9999
..(	chr5:151595058-151595279(+)$1	1	32	35	8.9999
..)	chr9:22180655-22180873(-)$1	1	23	26	8.9999
((.	chr16:11087812-11088023(-)$1	1	42	45	8.9999
((.	chr15:91556498-91556721(+)$1	1	5	8	8.9999
...	chr11:69457289-69457509(+)$1	1	4	7	8.9999
...	chr1:140977660-140977881(+)$1	1	21	24	8.9999
(((	chr15:98781572-98781785(-)$1	1	57	60	8.9999
(((	chr15:37932054-37932266(-)$1	1	46	49	8.9999
(..	chr16:31131294-31131512(-)$1	1	101	104	8.9999
)))	chr13:15640310-15640528(+)$1	1	50	53	8.9999
(((	chr16:90247822-90248053(-)$1	1	20	23	8.9999
...	chr2:84790226-84790445(+)$1	1	34	37	8.9999
...	chr8:11267500-11267728(-)$1	1	40	43	8.9999
.((	chr2:119602371-119602592(-)$1	1	80	83	8.9999
.((	chr4:100826055-100826266(-)$1	1	31	34	8.9999
).)	chr18:34657085-34657303(-)$1	1	108	111	8.9999
.))	chrX:147520635-147520845(+)$1	1	39	42	8.9999
.((	chr9:77827552-77827772(+)$1	1	27	30	8.9999
)))	chr10:77867599-77867827(-)$1	1	124	127	8.9999
.((	chr1:95319772-95319991(-)$1	1	13	16	8.9999
(((	chr13:95160682-95160912(+)$1	1	55	58	8.9999
..(	chr12:77011954-77012184(+)$1	1	26	29	8.9999
(((	chr13:14285540-14285787(+)$1	1	69	72	8.9999
)).	chr14:35490290-35490496(+)$1	1	76	79	8.9999
)))	chr14:47909810-47910026(+)$1	1	22	25	8.9999
...	chr7:137362486-137362703(-)$1	1	15	18	8.9999
(..	chr10:75896323-75896546(-)$1	1	23	26	8.9999
(((	chr16:87415722-87415946(-)$1	1	33	36	8.9999
.((	chr19:4290750-4290958(-)$1	1	1	4	8.9999
(((	chr4:130328474-130328698(+)$1	1	4	7	8.9999
)))	chr19:18668259-18668473(-)$1	1	40	43	8.9999
.((	chr16:13326383-13326617(+)$1	1	10	13	8.9999
(((	chr12:112865987-112866204(+)$1	1	12	15	8.9999
))(	chr7:141973938-141974157(+)$1	1	41	44	8.9999
..(	chr17:26279649-26279863(+)$1	1	70	73	8.9999
((.	chr5:77379919-77380128(-)$1	1	25	28	8.9999
..)	chr9:110463536-110463754(+)$1	1	51	54	8.9999
..(	chr12:77072720-77072940(+)$1	1	23	26	8.9999
..(	chr8:12637669-12637891(-)$1	1	151	154	8.9999
)))	chr14:21532532-21532748(+)$1	1	27	30	8.9999
(((	chr18:36827152-36827358(-)$1	1	9	12	8.9999
(..	chr1:40046844-40047059(+)$1	1	13	16	8.9999
(((	chr8:74774485-74774696(+)$1	1	119	122	8.9999
(((	chr11:93963325-93963546(+)$1	1	3	6	8.9999
(((	chr11:30019329-30019557(-)$1	1	63	66	8.9999
)))	chr11:85017682-85017891(-)$1	1	28	31	8.9999
(((	chr9:82781068-82781294(-)$1	1	7	10	8.9999
(((	chr6:146334358-146334572(-)$1	1	75	78	8.9999
(((	chr11:84853479-84853692(-)$1	1	25	28	8.9999
(((	chr17:32338163-32338374(-)$1	1	11	14	8.9999
(..	chr12:74268984-74269190(+)$1	1	24	27	8.9999
(((	chr11:106936103-106936312(-)$1	1	29	32	8.9999
)).	chr12:70925471-70925698(-)$1	1	79	82	8.9999
((.	chr8:125136923-125137149(+)$1	1	14	17	8.9999
(((	chr11:84819231-84819467(-)$1	1	14	17	8.9999
(((	chr10:39526628-39526844(+)$1	1	26	29	8.9999
(((	chr14:55054507-55054725(+)$1	1	28	31	8.9999
..(	chr6:98953121-98953329(-)$1	1	26	29	8.9999
(((	chr1:40018936-40019179(+)$1	1	3	6	8.9999
(((	chr5:121713829-121714039(+)$1	1	13	16	8.9999
(((	chr10:62455854-62456077(+)$1	1	32	35	8.9999
(((	chrM:5797-6013(+)$1	1	84	87	8.9999
.((	chr5:116375373-116375604(+)$1	1	31	34	8.9999
)))	chr14:32558399-32558622(-)$1	1	112	115	8.9999
..(	chr2:143779625-143779840(-)$1	1	0	3	8.9999
(((	chr12:87365165-87365383(+)$1	1	61	64	8.9999
(((	chr5:123689489-123689704(+)$1	1	6	9	8.9999
((.	chr16:4669803-4670010(-)$1	1	12	15	8.9999
(.(	chr18:63880365-63880585(+)$1	1	60	63	8.9999
(((	chrX:98871508-98871729(+)$1	1	74	77	8.9999
(((	chr15:102314523-102314737(+)$1	1	14	17	8.9999
(((	chr1:169291488-169291717(+)$1	1	47	50	8.9999
((.	chr2:126934144-126934352(-)$1	1	28	31	8.9999
(.(	chr4:148450022-148450249(-)$1	1	5	8	8.9999
(..	chr3:104301329-104301551(-)$1	1	5	8	8.9999
(((	chr18:42458768-42458977(+)$1	1	15	18	8.9999
(((	chr12:8750498-8750716(+)$1	1	16	19	8.9999
((.	chr2:109880725-109880958(+)$1	1	132	135	8.9999
(..	chr8:97984497-97984706(-)$1	1	24	27	8.9999
(..	chr18:32239902-32240123(+)$1	1	47	50	8.9999
.((	chr2:75503185-75503409(+)$1	1	85	88	8.9999
(((	chr14:32534996-32535217(-)$1	1	5	8	8.9999
)))	chr17:66336328-66336538(-)$1	1	22	25	8.9999
..(	chr10:87902155-87902380(+)$1	1	163	166	8.9999
...	chr5:65665524-65665739(-)$1	1	39	42	8.9999
(((	chr8:73883141-73883359(+)$1	1	44	47	8.9999
((.	chr11:87797316-87797552(-)$1	1	12	15	8.9999
..(	chr5:23940655-23940877(+)$1	1	49	52	8.9999
(((	chr11:70764688-70764908(-)$1	1	73	76	8.9999
..(	chr19:47610710-47610917(-)$1	1	66	69	8.9999
)..	chr2:35145890-35146100(+)$1	1	59	62	8.9999
..)	chr7:134985832-134986053(-)$1	1	29	32	8.9999
.(.	chr14:68446363-68446593(-)$1	1	20	23	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m3_run2.nuc.txt

#NT
AAAGUGUGCUUCUGAGAGGGGAAUAACAACAGCAAUAGCCAGGACGUUUCCUUCUCUAAAGACCCAAGAAGUACAUUUGUAAAAAGAAGAUUUUCCAAAACAUGUAGUUGGCUGCUCUCCAAUGAGUAUGUUGUAGGACAUUGUGUGUUCAUCUGCUGGCUCAUGGCUAGCCACAUCCGAGUAUUGGAAUUUGUAUUGCAGCCUGCUUAUUUUGUG	chr2:29037153-29037394(+)$1	241	24	240	290.5000

#otherMatches

#Struct PSSM
"ffffff+++++++++++ccc[ccc!!bb[cccnnnnnccc]bb22ccc]ccc22ffffff55555ffffff:CCC::::::::::===========!!cccrrrrrrrrrccc22===========ddddqqqqqqqqdddd:::::::::ffffff[bb!!eeeee"""ffffffqqqqqqqqffffff4444eeeee]bbffffff::::CCC	chr4:59915984-59916211(+)$1	227	8	224	290.5000
:=======================!!a####bbmmmmbb333a22===========0000000000============:::::::::a[a!!ffffff[bb[bb####eeeeeccc$$$$$ffffff!!bb####fffffflllffffff4444bb22ffffffccc]eeeee4444bb]bb]ffffff22a]aDDDD}CCCBB}EEEEE::::::	chr2:29037153-29037394(+)$1	241	24	240	290.5000

#DB
.((((((...........(((.(((..((.(((.....))).))..))).)))..)))))).....)))))).(((..........(((((((((((..(((.........)))..)))))))))))((((........)))).........((((((.((..(((((...((((((........))))))....))))).))))))))....)))	chr4:59915984-59916211(+)$1	1	8	224	290.5000
.(((((((((((((((((((((((..(....((....))...)..)))))))))))..........)))))))))))).........(.(..((((((.((.((....((((((((.....((((((..((....((((((...))))))....))..))))))))).)))))....)).)).))))))..).))))).))))).)))))......	chr2:29037153-29037394(+)$1	1	24	240	290.5000

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

#score	581.0
#seq	2
#width	216
#escape	false
#onStep	13028
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_CDS_m1_run1.nuc.txt

#NT
CUG	chr11:30008996-30009231(-)$1	235	123	126	8.9999
CUG	chr11:30014728-30014963(-)$1	235	15	18	8.9999
CUG	chr9:72510245-72510480(+)$1	235	88	91	8.9999
CUG	chr2:76689541-76689776(-)$1	235	6	9	8.9999
CUG	chr10:19329021-19329256(+)$1	235	22	25	8.9999
CUG	chr4:129523617-129523873(+)$1	256	45	48	8.9999
CUG	chr2:76565493-76565731(-)$1	238	27	30	8.9999
CUG	chr1:36879850-36880085(-)$1	235	52	55	8.9999
CUG	chr2:76561979-76562240(-)$1	261	41	44	8.9999
CUG	chr4:43535508-43535762(-)$1	254	43	46	8.9999
CUG	chr11:67067428-67067680(+)$1	252	4	7	8.9999
CUG	chr7:52399799-52400034(-)$1	235	3	6	8.9999
CUG	chr2:76723096-76723358(-)$1	262	1	4	8.9999
CUG	chr7:133592024-133592270(-)$1	246	24	27	8.9999
CUG	chr14:60898841-60899085(+)$1	244	55	58	8.9999
CUG	chr7:74904121-74904374(-)$1	253	15	18	8.9999
CUG	chr10:77670618-77670856(-)$1	238	24	27	8.9999
CUG	chr19:6389709-6389944(+)$1	235	4	7	8.9999
CUG	chr2:76594261-76594496(-)$1	235	7	10	8.9999
CUG	chr15:97962359-97962622(+)$1	263	14	17	8.9999
CUG	chr9:59525865-59526101(+)$1	236	53	56	8.9999
CUG	chr4:43527519-43527758(-)$1	239	6	9	8.9999
CUG	chr2:35151973-35152210(+)$1	237	2	5	8.9999
CUG	chr5:29761756-29761991(+)$1	235	37	40	8.9999
CUG	chr9:109934542-109934779(+)$1	237	16	19	8.9999
CUG	chr2:121137360-121137598(-)$1	238	19	22	8.9999
CUG	chr2:67350602-67350837(+)$1	235	35	38	8.9999
cug	chr13:12380759-12380997(-)$1	238	4	7	8.9999
CUG	chr17:25969080-25969315(-)$1	235	33	36	8.9999
CUG	chr7:133603008-133603243(-)$1	235	42	45	8.9999
CUG	chr14:60248649-60248884(+)$1	235	38	41	8.9999
CUG	chr7:20006559-20006808(+)$1	249	12	15	8.9999
CUG	chr11:67062033-67062294(+)$1	261	53	56	8.9999
CUG	chr4:132851049-132851284(-)$1	235	5	8	8.9999
CUG	chr6:29411059-29411294(+)$1	235	5	8	8.9999
CUG	chr11:50014137-50014377(-)$1	240	39	42	8.9999
CUG	chr7:134356893-134357130(+)$1	237	107	110	8.9999
CUG	chr4:129522281-129522528(+)$1	247	84	87	8.9999
CUG	chr15:102797233-102797477(+)$1	244	18	21	8.9999
CUG	chr2:76544419-76544660(-)$1	241	80	83	8.9999
CUG	chr17:34406174-34406409(+)$1	235	23	26	8.9999
CUG	chr11:6523715-6523950(-)$1	235	3	6	8.9999
CUG	chr2:76606134-76606371(-)$1	237	77	80	8.9999
CUG	chr11:67065960-67066209(+)$1	249	26	29	8.9999
CUG	chr19:9078779-9079016(+)$1	237	39	42	8.9999

#otherMatches

#Struct PSSM
!!b	chr1:174215791-174216027(-)$1	236	11	14	8.9999
EEE	chr11:30008996-30009231(-)$1	235	123	126	8.9999
:::	chr11:30014728-30014963(-)$1	235	15	18	8.9999
ddd	chr9:72510245-72510480(+)$1	235	88	91	8.9999
ddd	chr2:76689541-76689776(-)$1	235	6	9	8.9999
ddd	chr10:19329021-19329256(+)$1	235	22	25	8.9999
3ee	chr4:129523617-129523873(+)$1	256	45	48	8.9999
LLL	chr2:76565493-76565731(-)$1	238	27	30	8.9999
ccc	chr1:36879850-36880085(-)$1	235	52	55	8.9999
g[b	chr2:76561979-76562240(-)$1	261	41	44	8.9999
JJJ	chr4:43535508-43535762(-)$1	254	43	46	8.9999
nnn	chr11:67067428-67067680(+)$1	252	4	7	8.9999
DDB	chr7:52399799-52400034(-)$1	235	3	6	8.9999
::E	chr2:76723096-76723358(-)$1	262	1	4	8.9999
:ff	chr7:133592024-133592270(-)$1	246	24	27	8.9999
###	chr14:60898841-60899085(+)$1	244	55	58	8.9999
ccf	chr7:74904121-74904374(-)$1	253	15	18	8.9999
EEE	chr10:77670618-77670856(-)$1	238	24	27	8.9999
fff	chr19:6389709-6389944(+)$1	235	4	7	8.9999
[dd	chr2:76594261-76594496(-)$1	235	7	10	8.9999
eee	chr15:97962359-97962622(+)$1	263	14	17	8.9999
a%%	chr9:59525865-59526101(+)$1	236	53	56	8.9999
HHH	chr4:43527519-43527758(-)$1	239	6	9	8.9999
HHH	chr2:35151973-35152210(+)$1	237	2	5	8.9999
sss	chr5:29761756-29761991(+)$1	235	37	40	8.9999
eee	chr9:109934542-109934779(+)$1	237	16	19	8.9999
{BB	chr2:121137360-121137598(-)$1	238	19	22	8.9999
eee	chr2:67350602-67350837(+)$1	235	35	38	8.9999
hhh	chr13:12380759-12380997(-)$1	238	4	7	8.9999
hhh	chr17:25969080-25969315(-)$1	235	33	36	8.9999
ccc	chr7:133603008-133603243(-)$1	235	42	45	8.9999
FFF	chr14:60248649-60248884(+)$1	235	38	41	8.9999
i[b	chr7:20006559-20006808(+)$1	249	12	15	8.9999
!!d	chr11:67062033-67062294(+)$1	261	53	56	8.9999
d[e	chr4:132851049-132851284(-)$1	235	5	8	8.9999
:CC	chr6:29411059-29411294(+)$1	235	5	8	8.9999
:::	chr11:50014137-50014377(-)$1	240	39	42	8.9999
ggg	chr7:134356893-134357130(+)$1	237	107	110	8.9999
ddd	chr4:129522281-129522528(+)$1	247	84	87	8.9999
GGG	chr15:102797233-102797477(+)$1	244	18	21	8.9999
eee	chr2:76544419-76544660(-)$1	241	80	83	8.9999
F{F	chr17:34406174-34406409(+)$1	235	23	26	8.9999
CCB	chr11:6523715-6523950(-)$1	235	3	6	8.9999
GGG	chr2:76606134-76606371(-)$1	237	77	80	8.9999
EE{	chr11:67065960-67066209(+)$1	249	26	29	8.9999
ddd	chr19:9078779-9079016(+)$1	237	39	42	8.9999

#DB
..(	chr1:174215791-174216027(-)$1	1	11	14	8.9999
(((	chr11:30008996-30009231(-)$1	1	123	126	8.9999
...	chr11:30014728-30014963(-)$1	1	15	18	8.9999
(((	chr9:72510245-72510480(+)$1	1	88	91	8.9999
(((	chr2:76689541-76689776(-)$1	1	6	9	8.9999
(((	chr10:19329021-19329256(+)$1	1	22	25	8.9999
.))	chr4:129523617-129523873(+)$1	1	45	48	8.9999
...	chr2:76565493-76565731(-)$1	1	27	30	8.9999
)))	chr1:36879850-36880085(-)$1	1	52	55	8.9999
(.(	chr2:76561979-76562240(-)$1	1	41	44	8.9999
(((	chr4:43535508-43535762(-)$1	1	43	46	8.9999
...	chr11:67067428-67067680(+)$1	1	4	7	8.9999
(((	chr7:52399799-52400034(-)$1	1	3	6	8.9999
..(	chr2:76723096-76723358(-)$1	1	1	4	8.9999
.((	chr7:133592024-133592270(-)$1	1	24	27	8.9999
...	chr14:60898841-60899085(+)$1	1	55	58	8.9999
))(	chr7:74904121-74904374(-)$1	1	15	18	8.9999
(((	chr10:77670618-77670856(-)$1	1	24	27	8.9999
(((	chr19:6389709-6389944(+)$1	1	4	7	8.9999
.((	chr2:76594261-76594496(-)$1	1	7	10	8.9999
(((	chr15:97962359-97962622(+)$1	1	14	17	8.9999
(..	chr9:59525865-59526101(+)$1	1	53	56	8.9999
(((	chr4:43527519-43527758(-)$1	1	6	9	8.9999
(((	chr2:35151973-35152210(+)$1	1	2	5	8.9999
...	chr5:29761756-29761991(+)$1	1	37	40	8.9999
(((	chr9:109934542-109934779(+)$1	1	16	19	8.9999
.((	chr2:121137360-121137598(-)$1	1	19	22	8.9999
(((	chr2:67350602-67350837(+)$1	1	35	38	8.9999
(((	chr13:12380759-12380997(-)$1	1	4	7	8.9999
(((	chr17:25969080-25969315(-)$1	1	33	36	8.9999
)))	chr7:133603008-133603243(-)$1	1	42	45	8.9999
(((	chr14:60248649-60248884(+)$1	1	38	41	8.9999
(.(	chr7:20006559-20006808(+)$1	1	12	15	8.9999
..(	chr11:67062033-67062294(+)$1	1	53	56	8.9999
(.(	chr4:132851049-132851284(-)$1	1	5	8	8.9999
.((	chr6:29411059-29411294(+)$1	1	5	8	8.9999
...	chr11:50014137-50014377(-)$1	1	39	42	8.9999
)))	chr7:134356893-134357130(+)$1	1	107	110	8.9999
(((	chr4:129522281-129522528(+)$1	1	84	87	8.9999
(((	chr15:102797233-102797477(+)$1	1	18	21	8.9999
(((	chr2:76544419-76544660(-)$1	1	80	83	8.9999
(.(	chr17:34406174-34406409(+)$1	1	23	26	8.9999
(((	chr11:6523715-6523950(-)$1	1	3	6	8.9999
(((	chr2:76606134-76606371(-)$1	1	77	80	8.9999
((.	chr11:67065960-67066209(+)$1	1	26	29	8.9999
(((	chr19:9078779-9079016(+)$1	1	39	42	8.9999

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

#score	413.99999999999994
#seq	46
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_CDS_m3_run1.nuc.txt

#NT
GGA	chr11:19964579-19964869(-)$1	290	41	44	9.0000
GGA	chr4:41062245-41062526(-)$1	281	2	5	9.0000
GGA	chr11:70209789-70210061(-)$1	272	129	132	9.0000
GGA	chr11:45758044-45758314(-)$1	270	70	73	9.0000
GGA	chr2:70587178-70587448(-)$1	270	120	123	9.0000
GGA	chrX:71069462-71069747(-)$1	285	70	73	9.0000
GGA	chr4:143984693-143984965(-)$1	272	7	10	9.0000
GGA	chr18:32048624-32048901(+)$1	277	17	20	9.0000
GGA	chr17:25027665-25027932(-)$1	267	3	6	9.0000
GGA	chr10:62788735-62789006(-)$1	271	15	18	9.0000
GGA	chr7:28160317-28160587(-)$1	270	45	48	9.0000
GGA	chr7:111376629-111376907(+)$1	278	38	41	9.0000
GGA	chr17:35119183-35119472(+)$1	289	0	3	9.0000
GGA	chr6:124654828-124655118(-)$1	290	195	198	9.0000
GGA	chr10:98481379-98481648(+)$1	269	23	26	9.0000
GGA	chr15:78171935-78172205(+)$1	270	12	15	9.0000
GGA	chr11:68717859-68718152(+)$1	293	30	33	9.0000
GGA	chr15:72886045-72886320(-)$1	275	27	30	9.0000
GGA	chr4:126703038-126703314(+)$1	276	3	6	9.0000
GGA	chr4:98660275-98660547(-)$1	272	33	36	9.0000
GGA	chr8:11785699-11785980(+)$1	281	12	15	9.0000
GGA	chr9:65194667-65194955(+)$1	288	39	42	9.0000
GGA	chr13:23853651-23853951(-)$1	300	10	13	9.0000
GGA	chr3:86595629-86595905(-)$1	276	15	18	9.0000
GGA	chr4:133091598-133091866(-)$1	268	129	132	9.0000
GGA	chr2:25107184-25107453(-)$1	269	56	59	9.0000
GGA	chr4:154360176-154360452(-)$1	276	25	28	9.0000
GGA	chr11:102264823-102265097(-)$1	274	12	15	9.0000
GGA	chrX:101279664-101279934(-)$1	270	1	4	9.0000
GGA	chr15:55428761-55429037(+)$1	276	72	75	9.0000
GGA	chr13:14046930-14047198(+)$1	268	4	7	9.0000
GGA	chr5:108336819-108337087(+)$1	268	98	101	9.0000
GGA	chr16:30561597-30561881(-)$1	284	36	39	9.0000
GGA	chr4:9786731-9786999(+)$1	268	20	23	9.0000
GGA	chr7:20309959-20310238(-)$1	279	73	76	9.0000
GGA	chr13:30077344-30077625(-)$1	281	5	8	9.0000
GGA	chr13:100109744-100110012(-)$1	268	46	49	9.0000
GGA	chr10:128349669-128349945(+)$1	276	11	14	9.0000
GGA	chr5:30107795-30108142(+)$1	347	130	133	9.0000
GGA	chr9:103962459-103962733(-)$1	274	30	33	9.0000
GGA	chr6:128384677-128384952(-)$1	275	31	34	9.0000
GGA	chr15:82958160-82958444(-)$1	284	6	9	9.0000
GGA	chr3:9438721-9439004(-)$1	283	105	108	9.0000
GGA	chr1:43124233-43124511(-)$1	278	37	40	9.0000
GGA	chr8:87888567-87888840(-)$1	273	57	60	9.0000
GGA	chr4:98404133-98404432(+)$1	299	28	31	9.0000
GGA	chr16:96303329-96303607(-)$1	278	4	7	9.0000
gga	chr15:81305401-81305694(+)$1	293	0	3	9.0000
GGA	chr17:34047461-34047731(+)$1	270	32	35	9.0000
GGA	chr17:32453054-32453327(-)$1	273	11	14	9.0000
GGA	chr11:117584189-117584532(+)$1	343	38	41	9.0000
GGA	chr17:29312983-29313252(-)$1	269	44	47	9.0000
GGA	chr2:32115393-32115661(-)$1	268	44	47	9.0000
GGA	chr11:35860665-35860933(-)$1	268	35	38	9.0000
GGA	chr13:34219142-34219509(-)$1	367	40	43	9.0000
GGA	chr12:66163586-66163866(+)$1	280	135	138	9.0000
GGA	chr11:95911569-95911844(-)$1	275	7	10	9.0000
GGA	chr2:156700077-156700345(-)$1	268	35	38	9.0000
GGA	chr19:10671709-10672001(-)$1	292	3	6	9.0000
GGA	chr18:36898542-36898814(+)$1	272	24	27	9.0000
GGA	chr1:10130472-10130740(-)$1	268	84	87	9.0000
GGA	chr4:126584247-126584530(-)$1	283	132	135	9.0000
GGA	chr13:120238609-120238883(+)$1	274	107	110	9.0000
GGA	chr5:25197802-25198082(-)$1	280	40	43	9.0000
GGA	chr5:33994504-33994786(-)$1	282	78	81	9.0000
GGA	chr1:5125844-5126129(+)$1	285	25	28	9.0000
GGA	chr11:117583822-117584093(+)$1	271	6	9	9.0000
GGA	chr6:39350302-39350587(-)$1	285	44	47	9.0000
GGA	chr4:126384704-126384975(+)$1	271	48	51	9.0000
GGA	chr17:34164515-34164787(-)$1	272	78	81	9.0000
GGA	chr10:77679811-77680083(-)$1	272	49	52	9.0000
GGA	chr5:66217769-66218055(+)$1	286	133	136	9.0000
GGA	chr16:37881243-37881521(+)$1	278	30	33	9.0000
GGA	chr4:117586801-117587099(-)$1	298	114	117	9.0000
GGA	chr4:129276074-129276352(-)$1	278	32	35	9.0000
GGA	chr9:114422631-114422920(-)$1	289	21	24	9.0000
GGA	chr10:77079187-77079523(+)$1	336	65	68	9.0000
GGA	chr15:100236569-100236841(-)$1	272	31	34	9.0000
GGA	chr15:32107537-32107805(+)$1	268	105	108	9.0000
GGA	chr3:101383350-101383632(-)$1	282	20	23	9.0000
GGA	chr5:145944560-145944832(-)$1	272	6	9	9.0000
GGA	chr6:85417983-85418257(+)$1	274	6	9	9.0000
GGA	chr5:101197253-101197530(-)$1	277	33	36	9.0000
GGA	chr9:45668025-45668294(+)$1	269	12	15	9.0000
GGA	chr11:53079310-53079583(-)$1	273	49	52	9.0000
GGA	chr19:39018198-39018527(+)$1	329	4	7	9.0000
GGA	chr7:19846096-19846366(-)$1	270	68	71	9.0000
GGA	chr4:132383952-132384240(-)$1	288	6	9	9.0000
GGA	chr5:115798474-115798755(-)$1	281	2	5	9.0000
GGA	chr5:105397168-105397439(-)$1	271	7	10	9.0000
GGA	chr4:155553548-155553816(-)$1	268	37	40	9.0000
GGA	chr19:7532199-7532469(-)$1	270	112	115	9.0000
GGA	chr10:110375623-110375895(+)$1	272	26	29	9.0000
GGA	chr11:80199289-80199566(+)$1	277	72	75	9.0000
GGA	chr12:114426842-114427109(+)$1	267	5	8	9.0000
GGA	chr7:28130169-28130452(-)$1	283	13	16	9.0000
GGA	chr12:16959174-16959453(+)$1	279	127	130	9.0000
GGA	chr11:98857077-98857387(-)$1	310	119	122	9.0000
GGA	chr18:67637448-67637726(+)$1	278	76	79	9.0000

#otherMatches

#Struct PSSM
DDD	chr6:86345913-86346193(-)$1	280	31	34	9.0000
eee	chr11:19964579-19964869(-)$1	290	41	44	9.0000
DDD	chr4:41062245-41062526(-)$1	281	2	5	9.0000
]cc	chr11:70209789-70210061(-)$1	272	129	132	9.0000
ee]	chr11:45758044-45758314(-)$1	270	70	73	9.0000
qqq	chr2:70587178-70587448(-)$1	270	120	123	9.0000
###	chrX:71069462-71069747(-)$1	285	70	73	9.0000
DD:	chr4:143984693-143984965(-)$1	272	7	10	9.0000
[a#	chr18:32048624-32048901(+)$1	277	17	20	9.0000
dd[	chr17:25027665-25027932(-)$1	267	3	6	9.0000
BB{	chr10:62788735-62789006(-)$1	271	15	18	9.0000
DDD	chr7:28160317-28160587(-)$1	270	45	48	9.0000
lll	chr7:111376629-111376907(+)$1	278	38	41	9.0000
:::	chr17:35119183-35119472(+)$1	289	0	3	9.0000
===	chr6:124654828-124655118(-)$1	290	195	198	9.0000
CCO	chr10:98481379-98481648(+)$1	269	23	26	9.0000
Cbb	chr15:78171935-78172205(+)$1	270	12	15	9.0000
dd2	chr11:68717859-68718152(+)$1	293	30	33	9.0000
GGG	chr15:72886045-72886320(-)$1	275	27	30	9.0000
b[d	chr4:126703038-126703314(+)$1	276	3	6	9.0000
iii	chr4:98660275-98660547(-)$1	272	33	36	9.0000
eee	chr8:11785699-11785980(+)$1	281	12	15	9.0000
uuu	chr9:65194667-65194955(+)$1	288	39	42	9.0000
ccf	chr13:23853651-23853951(-)$1	300	10	13	9.0000
a[d	chr3:86595629-86595905(-)$1	276	15	18	9.0000
e))	chr4:133091598-133091866(-)$1	268	129	132	9.0000
===	chr2:25107184-25107453(-)$1	269	56	59	9.0000
acc	chr4:154360176-154360452(-)$1	276	25	28	9.0000
FFF	chr11:102264823-102265097(-)$1	274	12	15	9.0000
:::	chrX:101279664-101279934(-)$1	270	1	4	9.0000
ccc	chr15:55428761-55429037(+)$1	276	72	75	9.0000
B::	chr13:14046930-14047198(+)$1	268	4	7	9.0000
eee	chr5:108336819-108337087(+)$1	268	98	101	9.0000
ccl	chr16:30561597-30561881(-)$1	284	36	39	9.0000
ff"	chr4:9786731-9786999(+)$1	268	20	23	9.0000
gg:	chr7:20309959-20310238(-)$1	279	73	76	9.0000
EEE	chr13:30077344-30077625(-)$1	281	5	8	9.0000
eee	chr13:100109744-100110012(-)$1	268	46	49	9.0000
FFF	chr10:128349669-128349945(+)$1	276	11	14	9.0000
bb:	chr5:30107795-30108142(+)$1	347	130	133	9.0000
fff	chr9:103962459-103962733(-)$1	274	30	33	9.0000
GGG	chr6:128384677-128384952(-)$1	275	31	34	9.0000
iii	chr15:82958160-82958444(-)$1	284	6	9	9.0000
ggg	chr3:9438721-9439004(-)$1	283	105	108	9.0000
fff	chr1:43124233-43124511(-)$1	278	37	40	9.0000
FF{	chr8:87888567-87888840(-)$1	273	57	60	9.0000
Hgg	chr4:98404133-98404432(+)$1	299	28	31	9.0000
:bb	chr16:96303329-96303607(-)$1	278	4	7	9.0000
BBL	chr15:81305401-81305694(+)$1	293	0	3	9.0000
eee	chr17:34047461-34047731(+)$1	270	32	35	9.0000
eee	chr17:32453054-32453327(-)$1	273	11	14	9.0000
ddd	chr11:117584189-117584532(+)$1	343	38	41	9.0000
===	chr17:29312983-29313252(-)$1	269	44	47	9.0000
eee	chr2:32115393-32115661(-)$1	268	44	47	9.0000
cc!	chr11:35860665-35860933(-)$1	268	35	38	9.0000
:::	chr13:34219142-34219509(-)$1	367	40	43	9.0000
ddd	chr12:66163586-66163866(+)$1	280	135	138	9.0000
DDD	chr11:95911569-95911844(-)$1	275	7	10	9.0000
cdd	chr2:156700077-156700345(-)$1	268	35	38	9.0000
DDD	chr19:10671709-10672001(-)$1	292	3	6	9.0000
sss	chr18:36898542-36898814(+)$1	272	24	27	9.0000
HHH	chr1:10130472-10130740(-)$1	268	84	87	9.0000
EEE	chr4:126584247-126584530(-)$1	283	132	135	9.0000
ggg	chr13:120238609-120238883(+)$1	274	107	110	9.0000
eCC	chr5:25197802-25198082(-)$1	280	40	43	9.0000
lll	chr5:33994504-33994786(-)$1	282	78	81	9.0000
ggg	chr1:5125844-5126129(+)$1	285	25	28	9.0000
:::	chr11:117583822-117584093(+)$1	271	6	9	9.0000
eee	chr6:39350302-39350587(-)$1	285	44	47	9.0000
nnn	chr4:126384704-126384975(+)$1	271	48	51	9.0000
oa2	chr17:34164515-34164787(-)$1	272	78	81	9.0000
dpp	chr10:77679811-77680083(-)$1	272	49	52	9.0000
gg]	chr5:66217769-66218055(+)$1	286	133	136	9.0000
ddd	chr16:37881243-37881521(+)$1	278	30	33	9.0000
hhh	chr4:117586801-117587099(-)$1	298	114	117	9.0000
ggg	chr4:129276074-129276352(-)$1	278	32	35	9.0000
DMM	chr9:114422631-114422920(-)$1	289	21	24	9.0000
ddd	chr10:77079187-77079523(+)$1	336	65	68	9.0000
ffo	chr15:100236569-100236841(-)$1	272	31	34	9.0000
ggg	chr15:32107537-32107805(+)$1	268	105	108	9.0000
EEE	chr3:101383350-101383632(-)$1	282	20	23	9.0000
CC{	chr5:145944560-145944832(-)$1	272	6	9	9.0000
g##	chr6:85417983-85418257(+)$1	274	6	9	9.0000
EEE	chr5:101197253-101197530(-)$1	277	33	36	9.0000
nnn	chr9:45668025-45668294(+)$1	269	12	15	9.0000
:::	chr11:53079310-53079583(-)$1	273	49	52	9.0000
ccc	chr19:39018198-39018527(+)$1	329	4	7	9.0000
bb:	chr7:19846096-19846366(-)$1	270	68	71	9.0000
GGB	chr4:132383952-132384240(-)$1	288	6	9	9.0000
DDD	chr5:115798474-115798755(-)$1	281	2	5	9.0000
DDD	chr5:105397168-105397439(-)$1	271	7	10	9.0000
ooh	chr4:155553548-155553816(-)$1	268	37	40	9.0000
bb:	chr19:7532199-7532469(-)$1	270	112	115	9.0000
ccc	chr10:110375623-110375895(+)$1	272	26	29	9.0000
hhh	chr11:80199289-80199566(+)$1	277	72	75	9.0000
cc[	chr12:114426842-114427109(+)$1	267	5	8	9.0000
FFF	chr7:28130169-28130452(-)$1	283	13	16	9.0000
f!!	chr12:16959174-16959453(+)$1	279	127	130	9.0000
EEE	chr11:98857077-98857387(-)$1	310	119	122	9.0000
fff	chr18:67637448-67637726(+)$1	278	76	79	9.0000

#DB
(((	chr6:86345913-86346193(-)$1	1	31	34	9.0000
(((	chr11:19964579-19964869(-)$1	1	41	44	9.0000
(((	chr4:41062245-41062526(-)$1	1	2	5	9.0000
.))	chr11:70209789-70210061(-)$1	1	129	132	9.0000
)).	chr11:45758044-45758314(-)$1	1	70	73	9.0000
...	chr2:70587178-70587448(-)$1	1	120	123	9.0000
...	chrX:71069462-71069747(-)$1	1	70	73	9.0000
((.	chr4:143984693-143984965(-)$1	1	7	10	9.0000
.(.	chr18:32048624-32048901(+)$1	1	17	20	9.0000
((.	chr17:25027665-25027932(-)$1	1	3	6	9.0000
((.	chr10:62788735-62789006(-)$1	1	15	18	9.0000
(((	chr7:28160317-28160587(-)$1	1	45	48	9.0000
...	chr7:111376629-111376907(+)$1	1	38	41	9.0000
...	chr17:35119183-35119472(+)$1	1	0	3	9.0000
(((	chr6:124654828-124655118(-)$1	1	195	198	9.0000
((.	chr10:98481379-98481648(+)$1	1	23	26	9.0000
(((	chr15:78171935-78172205(+)$1	1	12	15	9.0000
)).	chr11:68717859-68718152(+)$1	1	30	33	9.0000
(((	chr15:72886045-72886320(-)$1	1	27	30	9.0000
(.(	chr4:126703038-126703314(+)$1	1	3	6	9.0000
(((	chr4:98660275-98660547(-)$1	1	33	36	9.0000
)))	chr8:11785699-11785980(+)$1	1	12	15	9.0000
...	chr9:65194667-65194955(+)$1	1	39	42	9.0000
(((	chr13:23853651-23853951(-)$1	1	10	13	9.0000
(.(	chr3:86595629-86595905(-)$1	1	15	18	9.0000
(..	chr4:133091598-133091866(-)$1	1	129	132	9.0000
(((	chr2:25107184-25107453(-)$1	1	56	59	9.0000
(((	chr4:154360176-154360452(-)$1	1	25	28	9.0000
(((	chr11:102264823-102265097(-)$1	1	12	15	9.0000
...	chrX:101279664-101279934(-)$1	1	1	4	9.0000
(((	chr15:55428761-55429037(+)$1	1	72	75	9.0000
(..	chr13:14046930-14047198(+)$1	1	4	7	9.0000
)))	chr5:108336819-108337087(+)$1	1	98	101	9.0000
((.	chr16:30561597-30561881(-)$1	1	36	39	9.0000
((.	chr4:9786731-9786999(+)$1	1	20	23	9.0000
)).	chr7:20309959-20310238(-)$1	1	73	76	9.0000
(((	chr13:30077344-30077625(-)$1	1	5	8	9.0000
)))	chr13:100109744-100110012(-)$1	1	46	49	9.0000
(((	chr10:128349669-128349945(+)$1	1	11	14	9.0000
)).	chr5:30107795-30108142(+)$1	1	130	133	9.0000
(((	chr9:103962459-103962733(-)$1	1	30	33	9.0000
(((	chr6:128384677-128384952(-)$1	1	31	34	9.0000
(((	chr15:82958160-82958444(-)$1	1	6	9	9.0000
)))	chr3:9438721-9439004(-)$1	1	105	108	9.0000
)))	chr1:43124233-43124511(-)$1	1	37	40	9.0000
((.	chr8:87888567-87888840(-)$1	1	57	60	9.0000
(((	chr4:98404133-98404432(+)$1	1	28	31	9.0000
.((	chr16:96303329-96303607(-)$1	1	4	7	9.0000
((.	chr15:81305401-81305694(+)$1	1	0	3	9.0000
)))	chr17:34047461-34047731(+)$1	1	32	35	9.0000
)))	chr17:32453054-32453327(-)$1	1	11	14	9.0000
)))	chr11:117584189-117584532(+)$1	1	38	41	9.0000
(((	chr17:29312983-29313252(-)$1	1	44	47	9.0000
(((	chr2:32115393-32115661(-)$1	1	44	47	9.0000
((.	chr11:35860665-35860933(-)$1	1	35	38	9.0000
...	chr13:34219142-34219509(-)$1	1	40	43	9.0000
)))	chr12:66163586-66163866(+)$1	1	135	138	9.0000
(((	chr11:95911569-95911844(-)$1	1	7	10	9.0000
(((	chr2:156700077-156700345(-)$1	1	35	38	9.0000
(((	chr19:10671709-10672001(-)$1	1	3	6	9.0000
...	chr18:36898542-36898814(+)$1	1	24	27	9.0000
(((	chr1:10130472-10130740(-)$1	1	84	87	9.0000
(((	chr4:126584247-126584530(-)$1	1	132	135	9.0000
)))	chr13:120238609-120238883(+)$1	1	107	110	9.0000
)((	chr5:25197802-25198082(-)$1	1	40	43	9.0000
...	chr5:33994504-33994786(-)$1	1	78	81	9.0000
)))	chr1:5125844-5126129(+)$1	1	25	28	9.0000
...	chr11:117583822-117584093(+)$1	1	6	9	9.0000
(((	chr6:39350302-39350587(-)$1	1	44	47	9.0000
...	chr4:126384704-126384975(+)$1	1	48	51	9.0000
.).	chr17:34164515-34164787(-)$1	1	78	81	9.0000
(..	chr10:77679811-77680083(-)$1	1	49	52	9.0000
)).	chr5:66217769-66218055(+)$1	1	133	136	9.0000
)))	chr16:37881243-37881521(+)$1	1	30	33	9.0000
)))	chr4:117586801-117587099(-)$1	1	114	117	9.0000
(((	chr4:129276074-129276352(-)$1	1	32	35	9.0000
(..	chr9:114422631-114422920(-)$1	1	21	24	9.0000
(((	chr10:77079187-77079523(+)$1	1	65	68	9.0000
((.	chr15:100236569-100236841(-)$1	1	31	34	9.0000
)))	chr15:32107537-32107805(+)$1	1	105	108	9.0000
(((	chr3:101383350-101383632(-)$1	1	20	23	9.0000
((.	chr5:145944560-145944832(-)$1	1	6	9	9.0000
(..	chr6:85417983-85418257(+)$1	1	6	9	9.0000
(((	chr5:101197253-101197530(-)$1	1	33	36	9.0000
...	chr9:45668025-45668294(+)$1	1	12	15	9.0000
...	chr11:53079310-53079583(-)$1	1	49	52	9.0000
(((	chr19:39018198-39018527(+)$1	1	4	7	9.0000
)).	chr7:19846096-19846366(-)$1	1	68	71	9.0000
(((	chr4:132383952-132384240(-)$1	1	6	9	9.0000
(((	chr5:115798474-115798755(-)$1	1	2	5	9.0000
(((	chr5:105397168-105397439(-)$1	1	7	10	9.0000
..)	chr4:155553548-155553816(-)$1	1	37	40	9.0000
)).	chr19:7532199-7532469(-)$1	1	112	115	9.0000
)))	chr10:110375623-110375895(+)$1	1	26	29	9.0000
)))	chr11:80199289-80199566(+)$1	1	72	75	9.0000
((.	chr12:114426842-114427109(+)$1	1	5	8	9.0000
(((	chr7:28130169-28130452(-)$1	1	13	16	9.0000
(..	chr12:16959174-16959453(+)$1	1	127	130	9.0000
(((	chr11:98857077-98857387(-)$1	1	119	122	9.0000
)))	chr18:67637448-67637726(+)$1	1	76	79	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_UTR_m1_run1.nuc.txt

#NT
GGAAAAG	chr17:8387352-8387586(+)$1	234	111	118	12.4655
AGAGAAG	chr16:31743111-31743318(+)$1	207	175	182	13.0689
GCAGAAG	chr1:64968731-64968943(-)$1	212	176	183	13.5862
GGAAAAG	chr1:165243619-165243881(-)$1	262	102	109	12.4655
AGAGAAG	chr1:192769889-192770097(+)$1	208	86	93	13.0689
GGAGAGG	chr10:127057894-127058108(-)$1	214	107	114	12.2931
GGAGAUG	chr14:46276808-46277014(-)$1	206	17	24	12.2068
GGAGGAG	chr2:34987735-34987946(+)$1	211	180	187	13.1551
GGAGAAG	chr8:131248039-131248262(+)$1	223	152	159	16.6034
AGAGAAG	chr2:4544498-4544716(-)$1	218	118	125	13.0689
UGAGAAG	chr7:17150438-17150656(-)$1	218	2	9	12.7241
GCAGAAG	chr2:166775189-166775400(-)$1	211	171	178	13.5862
GGAAAAG	chr1:162897919-162898138(+)$1	219	116	123	12.4655
GAAGAAG	chr14:46249268-46249480(-)$1	212	114	121	13.3275
GCAGAAG	chr18:69504424-69504640(+)$1	216	182	189	13.5862
GGAGAAG	chr10:99959347-99959561(+)$1	214	55	62	16.6034
GCAGAAG	chr8:125432561-125432769(-)$1	208	182	189	13.5862
GGAGAGG	chr1:191610466-191610672(+)$1	206	153	160	12.2931
AGAGAAG	chr6:32999275-32999514(-)$1	239	226	233	13.0689
GCAGAAG	chr5:110861917-110862143(-)$1	226	19	26	13.5862
GAAGAAG	chr5:34211325-34211545(+)$1	220	111	118	13.3275
GUAGAAG	chr4:144721558-144721785(-)$1	227	68	75	13.0689
AGAGAAG	chr10:39550643-39550855(+)$1	212	17	24	13.0689
GGCGAAG	chr10:75902897-75903103(-)$1	206	62	69	11.7758
GGAGAAU	chr4:48465724-48465944(-)$1	220	208	215	12.1206
GGAGAAU	chr8:42502300-42502510(-)$1	210	58	65	12.1206
GGAGCAG	chr17:56742862-56743080(+)$1	218	113	120	12.8965
GGAGAAG	chr2:158321751-158321960(+)$1	209	58	65	16.6034
GAAGAAG	chr4:134483278-134483503(+)$1	225	43	50	13.3275
GGAGAAA	chr11:116167898-116168105(-)$1	207	188	195	12.1206
GGAAAAG	chr17:35134000-35134232(-)$1	232	98	105	12.4655
GGAGAGG	chr10:126983820-126984027(-)$1	207	86	93	12.2931
GGAGGAG	chr10:114822141-114822354(+)$1	213	29	36	13.1551
GCAGAAG	chr16:14470557-14470764(+)$1	207	77	84	13.5862
GGAGCAG	chr4:69927421-69927636(-)$1	215	32	39	12.8965
GAAGAAG	chr5:134765107-134765331(-)$1	224	45	52	13.3275
GCAGAAG	chr7:82870875-82871097(+)$1	222	90	97	13.5862
GCAGAAG	chr11:119780522-119780740(+)$1	218	46	53	13.5862
GGAGAAG	chr3:88712091-88712299(+)$1	208	158	165	16.6034
UGAGAAG	chr2:152680611-152680844(+)$1	233	53	60	12.7241
GGAGGAG	chr5:107393910-107394148(+)$1	238	128	135	13.1551
GGAGAAG	chr17:37206019-37206229(+)$1	210	132	139	16.6034
GGAGCAG	chr2:60800748-60800960(-)$1	212	8	15	12.8965
GGAAAAG	chr11:21457347-21457563(-)$1	216	78	85	12.4655
GGAGAAG	chr1:173341365-173341579(+)$1	214	160	167	16.6034
GGAGGAG	chr8:87493518-87493747(+)$1	229	171	178	13.1551
GGAGGAG	chr16:3991923-3992144(-)$1	221	82	89	13.1551
GGAGGAG	chr5:31505348-31505555(-)$1	207	29	36	13.1551
GGAGAUG	chr5:115354787-115355005(+)$1	218	130	137	12.2068
UGAGAAG	chrX:70737277-70737492(+)$1	215	47	54	12.7241
AGAGAAG	chr11:23517043-23517268(-)$1	225	17	24	13.0689
AGAGAAG	chr2:105842076-105842303(-)$1	227	77	84	13.0689
GGAGAAA	chr18:61744948-61745159(+)$1	211	76	83	12.1206
GUAGAAG	chr16:14457897-14458103(+)$1	206	0	7	13.0689
GGAGCAG	chr12:86642046-86642253(-)$1	207	126	133	12.8965
GAAGAAG	chr2:102144530-102144747(-)$1	217	96	103	13.3275
GGAGGAG	chr8:89385881-89386099(-)$1	218	122	129	13.1551

#otherMatches

#Struct PSSM
cc[a!!h	chr7:87857298-87857504(-)$1	206	36	43	16.6034
cbb"""a	chr17:8387352-8387586(+)$1	234	111	118	12.4655
[bb[aoo	chr16:31743111-31743318(+)$1	207	175	182	13.0689
HHHHYYE	chr1:64968731-64968943(-)$1	212	176	183	13.5862
C}BB}FF	chr1:165243619-165243881(-)$1	262	102	109	12.4655
eeeeggg	chr1:192769889-192770097(+)$1	208	86	93	13.0689
dd]dddd	chr10:127057894-127058108(-)$1	214	107	114	12.2931
ee[eeee	chr14:46276808-46277014(-)$1	206	17	24	12.2068
iiiiiii	chr2:34987735-34987946(+)$1	211	180	187	13.1551
ff[bb!!	chr8:131248039-131248262(+)$1	223	152	159	16.6034
[ffffff	chr2:4544498-4544716(-)$1	218	118	125	13.0689
dd"""ee	chr7:17150438-17150656(-)$1	218	2	9	12.7241
[bb[a!!	chr2:166775189-166775400(-)$1	211	171	178	13.5862
bbppppp	chr1:162897919-162898138(+)$1	219	116	123	12.4655
===++++	chr14:46249268-46249480(-)$1	212	114	121	13.3275
]gggggg	chr18:69504424-69504640(+)$1	216	182	189	13.5862
EE:::::	chr10:99959347-99959561(+)$1	214	55	62	16.6034
HHH:::b	chr8:125432561-125432769(-)$1	208	182	189	13.5862
EEEE}GG	chr1:191610466-191610672(+)$1	206	153	160	12.2931
cccHHHH	chr6:32999275-32999514(-)$1	239	226	233	13.0689
iiiii[e	chr5:110861917-110862143(-)$1	226	19	26	13.5862
)))eeee	chr5:34211325-34211545(+)$1	220	111	118	13.3275
66eeeee	chr4:144721558-144721785(-)$1	227	68	75	13.0689
qqqiiii	chr10:39550643-39550855(+)$1	212	17	24	13.0689
22dddd2	chr10:75902897-75903103(-)$1	206	62	69	11.7758
FFFF:::	chr4:48465724-48465944(-)$1	220	208	215	12.1206
EEEEKKF	chr8:42502300-42502510(-)$1	210	58	65	12.1206
dddgggg	chr17:56742862-56743080(+)$1	218	113	120	12.8965
HHHHHdd	chr2:158321751-158321960(+)$1	209	58	65	16.6034
IIIIIII	chr4:134483278-134483503(+)$1	225	43	50	13.3275
@@@@@@@	chr11:116167898-116168105(-)$1	207	188	195	12.1206
DDDgggg	chr17:35134000-35134232(-)$1	232	98	105	12.4655
[a(((((	chr10:126983820-126984027(-)$1	207	86	93	12.2931
BKKEEEE	chr10:114822141-114822354(+)$1	213	29	36	13.1551
[aooooo	chr16:14470557-14470764(+)$1	207	77	84	13.5862
KDDDDEE	chr4:69927421-69927636(-)$1	215	32	39	12.8965
b]ccc22	chr5:134765107-134765331(-)$1	224	45	52	13.3275
bb:::cc	chr7:82870875-82871097(+)$1	222	90	97	13.5862
FKKBB{D	chr11:119780522-119780740(+)$1	218	46	53	13.5862
eeee:::	chr3:88712091-88712299(+)$1	208	158	165	16.6034
mmmdddd	chr2:152680611-152680844(+)$1	233	53	60	12.7241
dgggggg	chr5:107393910-107394148(+)$1	238	128	135	13.1551
eeeee22	chr17:37206019-37206229(+)$1	210	132	139	16.6034
EE:bb[e	chr2:60800748-60800960(-)$1	212	8	15	12.8965
eee"""f	chr11:21457347-21457563(-)$1	216	78	85	12.4655
ff::::b	chr1:173341365-173341579(+)$1	214	160	167	16.6034
DDD}FFF	chr8:87493518-87493747(+)$1	229	171	178	13.1551
HHHHHHH	chr16:3991923-3992144(-)$1	221	82	89	13.1551
CCC{EEE	chr5:31505348-31505555(-)$1	207	29	36	13.1551
fffff]c	chr5:115354787-115355005(+)$1	218	130	137	12.2068
DDDD{A{	chrX:70737277-70737492(+)$1	215	47	54	12.7241
=======	chr11:23517043-23517268(-)$1	225	17	24	13.0689
HHfffff	chr2:105842076-105842303(-)$1	227	77	84	13.0689
mmmmeee	chr18:61744948-61745159(+)$1	211	76	83	12.1206
cccccc%	chr16:14457897-14458103(+)$1	206	0	7	13.0689
eeeee:E	chr12:86642046-86642253(-)$1	207	126	133	12.8965
ee333cc	chr2:102144530-102144747(-)$1	217	96	103	13.3275
$$$$$hh	chr8:89385881-89386099(-)$1	218	122	129	13.1551

#DB
((.(..(	chr7:87857298-87857504(-)$1	1	36	43	16.6034
(((...(	chr17:8387352-8387586(+)$1	1	111	118	12.4655
.((.(..	chr16:31743111-31743318(+)$1	1	175	182	13.0689
))))..)	chr1:64968731-64968943(-)$1	1	176	183	13.5862
).)).))	chr1:165243619-165243881(-)$1	1	102	109	12.4655
(((((((	chr1:192769889-192770097(+)$1	1	86	93	13.0689
)).))))	chr10:127057894-127058108(-)$1	1	107	114	12.2931
((.((((	chr14:46276808-46277014(-)$1	1	17	24	12.2068
)))))))	chr2:34987735-34987946(+)$1	1	180	187	13.1551
((.((..	chr8:131248039-131248262(+)$1	1	152	159	16.6034
.((((((	chr2:4544498-4544716(-)$1	1	118	125	13.0689
((...((	chr7:17150438-17150656(-)$1	1	2	9	12.7241
.((.(..	chr2:166775189-166775400(-)$1	1	171	178	13.5862
((.....	chr1:162897919-162898138(+)$1	1	116	123	12.4655
(((....	chr14:46249268-46249480(-)$1	1	114	121	13.3275
.))))))	chr18:69504424-69504640(+)$1	1	182	189	13.5862
((.....	chr10:99959347-99959561(+)$1	1	55	62	16.6034
)))...(	chr8:125432561-125432769(-)$1	1	182	189	13.5862
)))).))	chr1:191610466-191610672(+)$1	1	153	160	12.2931
)))))))	chr6:32999275-32999514(-)$1	1	226	233	13.0689
(((((.(	chr5:110861917-110862143(-)$1	1	19	26	13.5862
...((((	chr5:34211325-34211545(+)$1	1	111	118	13.3275
..)))))	chr4:144721558-144721785(-)$1	1	68	75	13.0689
...))))	chr10:39550643-39550855(+)$1	1	17	24	13.0689
..)))).	chr10:75902897-75903103(-)$1	1	62	69	11.7758
))))...	chr4:48465724-48465944(-)$1	1	208	215	12.1206
((((..(	chr8:42502300-42502510(-)$1	1	58	65	12.1206
)))))))	chr17:56742862-56743080(+)$1	1	113	120	12.8965
(((((((	chr2:158321751-158321960(+)$1	1	58	65	16.6034
(((((((	chr4:134483278-134483503(+)$1	1	43	50	13.3275
.......	chr11:116167898-116168105(-)$1	1	188	195	12.1206
)))((((	chr17:35134000-35134232(-)$1	1	98	105	12.4655
.(.....	chr10:126983820-126984027(-)$1	1	86	93	12.2931
(..((((	chr10:114822141-114822354(+)$1	1	29	36	13.1551
.(.....	chr16:14470557-14470764(+)$1	1	77	84	13.5862
.((((((	chr4:69927421-69927636(-)$1	1	32	39	12.8965
).)))..	chr5:134765107-134765331(-)$1	1	45	52	13.3275
))...((	chr7:82870875-82871097(+)$1	1	90	97	13.5862
(..((.(	chr11:119780522-119780740(+)$1	1	46	53	13.5862
))))...	chr3:88712091-88712299(+)$1	1	158	165	16.6034
...))))	chr2:152680611-152680844(+)$1	1	53	60	12.7241
)))))))	chr5:107393910-107394148(+)$1	1	128	135	13.1551
)))))..	chr17:37206019-37206229(+)$1	1	132	139	16.6034
((.((.(	chr2:60800748-60800960(-)$1	1	8	15	12.8965
(((...(	chr11:21457347-21457563(-)$1	1	78	85	12.4655
))....(	chr1:173341365-173341579(+)$1	1	160	167	16.6034
))).)))	chr8:87493518-87493747(+)$1	1	171	178	13.1551
)))))))	chr16:3991923-3992144(-)$1	1	82	89	13.1551
(((.(((	chr5:31505348-31505555(-)$1	1	29	36	13.1551
))))).)	chr5:115354787-115355005(+)$1	1	130	137	12.2068
((((.(.	chrX:70737277-70737492(+)$1	1	47	54	12.7241
(((((((	chr11:23517043-23517268(-)$1	1	17	24	13.0689
(((((((	chr2:105842076-105842303(-)$1	1	77	84	13.0689
....)))	chr18:61744948-61745159(+)$1	1	76	83	12.1206
((((((.	chr16:14457897-14458103(+)$1	1	0	7	13.0689
))))).)	chr12:86642046-86642253(-)$1	1	126	133	12.8965
))...))	chr2:102144530-102144747(-)$1	1	96	103	13.3275
.....((	chr8:89385881-89386099(-)$1	1	122	129	13.1551

#PSSM
G : 0.82	A : 0.12	U : 0.05	
G : 0.74	C : 0.13	A : 0.08	U : 0.03	
A : 0.98	C : 0.01	
G : 0.91	A : 0.08	
A : 0.81	G : 0.12	C : 0.06	
A : 0.91	G : 0.05	U : 0.03	
G : 0.93	U : 0.03	A : 0.03	

#score	774.8965517241389
#seq	58
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_UTR_m2_run1.nuc.txt

#NT
UUCUU	chr7:105053121-105053341(+)$1	220	7	12	14.9999
UUCUU	chr10:40007738-40007981(-)$1	243	195	200	14.9999
UUCUU	chr10:76515523-76515780(-)$1	257	75	80	14.9999
UUCUU	chr2:91511436-91511656(+)$1	220	104	109	14.9999
UUCUU	chr11:59269768-59269988(+)$1	220	43	48	14.9999
UUCUU	chr1:120574434-120574654(+)$1	220	35	40	14.9999
UUCUU	chr13:13603928-13604165(+)$1	237	165	170	14.9999
UUCUU	chrX:133267413-133267638(-)$1	225	167	172	14.9999
UUCUU	chr11:104364216-104364436(-)$1	220	170	175	14.9999
UUCUU	chr2:150408909-150409129(-)$1	220	79	84	14.9999
UUCUU	chr12:76816388-76816608(-)$1	220	126	131	14.9999
UUCUU	chr15:55084581-55084801(+)$1	220	27	32	14.9999
UUCUU	chr17:36026305-36026530(+)$1	225	206	211	14.9999
UUCUU	chr18:75169144-75169427(+)$1	283	46	51	14.9999
UUCUU	chr16:18912078-18912298(+)$1	220	1	6	14.9999
UUCUU	chr1:108620491-108620711(-)$1	220	31	36	14.9999
UUCUU	chr7:87410036-87410258(+)$1	222	167	172	14.9999
UUCUU	chr11:95820058-95820278(-)$1	220	114	119	14.9999
UUCUU	chr4:146951101-146951321(+)$1	220	69	74	14.9999
UUCUU	chr5:104280078-104280320(+)$1	242	201	206	14.9999
UUCUU	chr8:26827842-26828068(+)$1	226	143	148	14.9999
UUCUU	chr11:4080562-4080782(+)$1	220	57	62	14.9999
UUCUU	chr11:98557014-98557237(+)$1	223	53	58	14.9999
UUCUU	chr5:30582755-30582975(+)$1	220	21	26	14.9999
UUCUU	chr6:13532315-13532535(-)$1	220	168	173	14.9999
UUCUU	chr16:15889596-15889816(-)$1	220	158	163	14.9999
UUCUU	chr11:77349591-77349812(-)$1	221	115	120	14.9999
UUCUU	chr11:57598451-57598671(+)$1	220	130	135	14.9999
UUCUU	chr6:39286877-39287110(-)$1	233	222	227	14.9999
UUCUU	chr2:131880021-131880241(-)$1	220	74	79	14.9999
UUCUU	chrX:137910102-137910322(+)$1	220	211	216	14.9999
UUCUU	chr1:60346693-60346913(+)$1	220	116	121	14.9999
UUCUU	chr6:30441071-30441293(-)$1	222	15	20	14.9999
UUCUU	chr5:28403303-28403533(+)$1	230	6	11	14.9999
UUCUU	chr10:7344640-7344860(+)$1	220	138	143	14.9999
UUCUU	chr15:7142375-7142595(+)$1	220	71	76	14.9999
UUCUU	chr4:129304570-129304802(-)$1	232	47	52	14.9999
UUCUU	chr5:39059811-39060033(-)$1	222	68	73	14.9999
UUCUU	chr6:58628182-58628413(+)$1	231	58	63	14.9999
UUCUU	chrX:12193146-12193367(+)$1	221	4	9	14.9999
UUCUU	chr16:94609777-94609997(+)$1	220	202	207	14.9999
UUCUU	chr2:156005629-156005849(-)$1	220	63	68	14.9999
UUCUU	chr16:10742553-10742773(+)$1	220	117	122	14.9999
UUCUU	chr1:63641908-63642132(+)$1	224	122	127	14.9999
UUCUU	chr14:27233266-27233490(-)$1	224	105	110	14.9999
UUCUU	chr4:62051935-62052155(+)$1	220	35	40	14.9999
UUCUU	chr1:141346191-141346411(+)$1	220	129	134	14.9999
UUCUU	chr1:58520725-58520945(-)$1	220	139	144	14.9999
UUCUU	chr18:34478245-34478468(+)$1	223	100	105	14.9999
UUCUU	chrX:153988589-153988809(-)$1	220	14	19	14.9999
UUCUU	chr13:63949953-63950173(+)$1	220	80	85	14.9999
UUCUU	chr2:144076634-144076854(-)$1	220	127	132	14.9999

#otherMatches

#Struct PSSM
c5555	chr4:117561439-117561673(-)$1	234	117	122	14.9999
LLDDD	chr7:105053121-105053341(+)$1	220	7	12	14.9999
DDD}D	chr10:40007738-40007981(-)$1	243	195	200	14.9999
QQQQD	chr10:76515523-76515780(-)$1	257	75	80	14.9999
2bb]d	chr2:91511436-91511656(+)$1	220	104	109	14.9999
eeeee	chr11:59269768-59269988(+)$1	220	43	48	14.9999
ppppp	chr1:120574434-120574654(+)$1	220	35	40	14.9999
:::::	chr13:13603928-13604165(+)$1	237	165	170	14.9999
EE___	chrX:133267413-133267638(-)$1	225	167	172	14.9999
iiiii	chr11:104364216-104364436(-)$1	220	170	175	14.9999
=++++	chr2:150408909-150409129(-)$1	220	79	84	14.9999
::::h	chr12:76816388-76816608(-)$1	220	126	131	14.9999
:::::	chr15:55084581-55084801(+)$1	220	27	32	14.9999
B}FFF	chr17:36026305-36026530(+)$1	225	206	211	14.9999
e[ddd	chr18:75169144-75169427(+)$1	283	46	51	14.9999
::eee	chr16:18912078-18912298(+)$1	220	1	6	14.9999
GGGGG	chr1:108620491-108620711(-)$1	220	31	36	14.9999
ppppp	chr7:87410036-87410258(+)$1	222	167	172	14.9999
ggggg	chr11:95820058-95820278(-)$1	220	114	119	14.9999
hhhhh	chr4:146951101-146951321(+)$1	220	69	74	14.9999
fffff	chr5:104280078-104280320(+)$1	242	201	206	14.9999
:::::	chr8:26827842-26828068(+)$1	226	143	148	14.9999
eeee!	chr11:4080562-4080782(+)$1	220	57	62	14.9999
I{III	chr11:98557014-98557237(+)$1	223	53	58	14.9999
DDLLL	chr5:30582755-30582975(+)$1	220	21	26	14.9999
F::::	chr6:13532315-13532535(-)$1	220	168	173	14.9999
bhhhh	chr16:15889596-15889816(-)$1	220	158	163	14.9999
ttttt	chr11:77349591-77349812(-)$1	221	115	120	14.9999
eeeee	chr11:57598451-57598671(+)$1	220	130	135	14.9999
EEEEE	chr6:39286877-39287110(-)$1	233	222	227	14.9999
22a22	chr2:131880021-131880241(-)$1	220	74	79	14.9999
FZZZD	chrX:137910102-137910322(+)$1	220	211	216	14.9999
:::::	chr1:60346693-60346913(+)$1	220	116	121	14.9999
:ffff	chr6:30441071-30441293(-)$1	222	15	20	14.9999
:::::	chr5:28403303-28403533(+)$1	230	6	11	14.9999
cccqq	chr10:7344640-7344860(+)$1	220	138	143	14.9999
$$$$c	chr15:7142375-7142595(+)$1	220	71	76	14.9999
''fff	chr4:129304570-129304802(-)$1	232	47	52	14.9999
wwddd	chr5:39059811-39060033(-)$1	222	68	73	14.9999
DD:::	chr6:58628182-58628413(+)$1	231	58	63	14.9999
:::::	chrX:12193146-12193367(+)$1	221	4	9	14.9999
GGGGZ	chr16:94609777-94609997(+)$1	220	202	207	14.9999
!cccl	chr2:156005629-156005849(-)$1	220	63	68	14.9999
ccc))	chr16:10742553-10742773(+)$1	220	117	122	14.9999
:::::	chr1:63641908-63642132(+)$1	224	122	127	14.9999
EEEEE	chr14:27233266-27233490(-)$1	224	105	110	14.9999
[dddd	chr4:62051935-62052155(+)$1	220	35	40	14.9999
i:::D	chr1:141346191-141346411(+)$1	220	129	134	14.9999
$$$$$	chr1:58520725-58520945(-)$1	220	139	144	14.9999
:::hh	chr18:34478245-34478468(+)$1	223	100	105	14.9999
:::::	chrX:153988589-153988809(-)$1	220	14	19	14.9999
d!!ff	chr13:63949953-63950173(+)$1	220	80	85	14.9999
FFFFF	chr2:144076634-144076854(-)$1	220	127	132	14.9999

#DB
)....	chr4:117561439-117561673(-)$1	1	117	122	14.9999
..(((	chr7:105053121-105053341(+)$1	1	7	12	14.9999
))).)	chr10:40007738-40007981(-)$1	1	195	200	14.9999
....(	chr10:76515523-76515780(-)$1	1	75	80	14.9999
.)).)	chr2:91511436-91511656(+)$1	1	104	109	14.9999
)))))	chr11:59269768-59269988(+)$1	1	43	48	14.9999
.....	chr1:120574434-120574654(+)$1	1	35	40	14.9999
.....	chr13:13603928-13604165(+)$1	1	165	170	14.9999
))...	chrX:133267413-133267638(-)$1	1	167	172	14.9999
(((((	chr11:104364216-104364436(-)$1	1	170	175	14.9999
(....	chr2:150408909-150409129(-)$1	1	79	84	14.9999
....(	chr12:76816388-76816608(-)$1	1	126	131	14.9999
.....	chr15:55084581-55084801(+)$1	1	27	32	14.9999
).)))	chr17:36026305-36026530(+)$1	1	206	211	14.9999
(.(((	chr18:75169144-75169427(+)$1	1	46	51	14.9999
..(((	chr16:18912078-18912298(+)$1	1	1	6	14.9999
(((((	chr1:108620491-108620711(-)$1	1	31	36	14.9999
.....	chr7:87410036-87410258(+)$1	1	167	172	14.9999
)))))	chr11:95820058-95820278(-)$1	1	114	119	14.9999
(((((	chr4:146951101-146951321(+)$1	1	69	74	14.9999
(((((	chr5:104280078-104280320(+)$1	1	201	206	14.9999
.....	chr8:26827842-26828068(+)$1	1	143	148	14.9999
((((.	chr11:4080562-4080782(+)$1	1	57	62	14.9999
(.(((	chr11:98557014-98557237(+)$1	1	53	58	14.9999
((...	chr5:30582755-30582975(+)$1	1	21	26	14.9999
)....	chr6:13532315-13532535(-)$1	1	168	173	14.9999
)))))	chr16:15889596-15889816(-)$1	1	158	163	14.9999
.....	chr11:77349591-77349812(-)$1	1	115	120	14.9999
)))))	chr11:57598451-57598671(+)$1	1	130	135	14.9999
)))))	chr6:39286877-39287110(-)$1	1	222	227	14.9999
..)..	chr2:131880021-131880241(-)$1	1	74	79	14.9999
)...)	chrX:137910102-137910322(+)$1	1	211	216	14.9999
.....	chr1:60346693-60346913(+)$1	1	116	121	14.9999
.((((	chr6:30441071-30441293(-)$1	1	15	20	14.9999
.....	chr5:28403303-28403533(+)$1	1	6	11	14.9999
(((..	chr10:7344640-7344860(+)$1	1	138	143	14.9999
....(	chr15:7142375-7142595(+)$1	1	71	76	14.9999
..(((	chr4:129304570-129304802(-)$1	1	47	52	14.9999
..)))	chr5:39059811-39060033(-)$1	1	68	73	14.9999
((...	chr6:58628182-58628413(+)$1	1	58	63	14.9999
.....	chrX:12193146-12193367(+)$1	1	4	9	14.9999
)))).	chr16:94609777-94609997(+)$1	1	202	207	14.9999
.(((.	chr2:156005629-156005849(-)$1	1	63	68	14.9999
(((..	chr16:10742553-10742773(+)$1	1	117	122	14.9999
.....	chr1:63641908-63642132(+)$1	1	122	127	14.9999
)))))	chr14:27233266-27233490(-)$1	1	105	110	14.9999
.((((	chr4:62051935-62052155(+)$1	1	35	40	14.9999
)...)	chr1:141346191-141346411(+)$1	1	129	134	14.9999
.....	chr1:58520725-58520945(-)$1	1	139	144	14.9999
...((	chr18:34478245-34478468(+)$1	1	100	105	14.9999
.....	chrX:153988589-153988809(-)$1	1	14	19	14.9999
(..((	chr13:63949953-63950173(+)$1	1	80	85	14.9999
)))))	chr2:144076634-144076854(-)$1	1	127	132	14.9999

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

#score	794.9999999999999
#seq	53
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m1_run1.nuc.txt

#NT
GCU	chr5:76005461-76005681(+)$1	220	38	41	9.0000
GCU	chr3:84707675-84707898(+)$1	223	63	66	9.0000
GCU	chr6:115739365-115739585(+)$1	220	29	32	9.0000
GCU	chr14:62223672-62223900(+)$1	228	32	35	9.0000
GCU	chr9:108474453-108474688(+)$1	235	26	29	9.0000
GCU	chr7:148429678-148429898(+)$1	220	19	22	9.0000
GCU	chr2:48760822-48761051(-)$1	229	9	12	9.0000
GCU	chr11:68599324-68599565(+)$1	241	61	64	9.0000
GCU	chr3:153585826-153586047(-)$1	221	16	19	9.0000
GCU	chr3:65750497-65750720(-)$1	223	125	128	9.0000
GCU	chr1:59924517-59924737(+)$1	220	39	42	9.0000
GCU	chr17:71194219-71194440(-)$1	221	86	89	9.0000
GCU	chr4:140879277-140879522(+)$1	245	17	20	9.0000
GCU	chr11:79261618-79261838(+)$1	220	8	11	9.0000
GCU	chr9:26811151-26811372(+)$1	221	15	18	9.0000
GCU	chr6:65048720-65048940(+)$1	220	77	80	9.0000
GCU	chr2:109158045-109158265(+)$1	220	1	4	9.0000
GCU	chr13:3537471-3537691(+)$1	220	20	23	9.0000
GCU	chr13:67444439-67444659(-)$1	220	75	78	9.0000
GCU	chr17:80434656-80434876(-)$1	220	12	15	9.0000
GCU	chrX:131139837-131140075(+)$1	238	71	74	9.0000
GCU	chr10:105282390-105282610(+)$1	220	100	103	9.0000
GCU	chr10:93506471-93506691(+)$1	220	25	28	9.0000
GCU	chr4:132977986-132978206(+)$1	220	33	36	9.0000
GCU	chr10:98478127-98478362(+)$1	235	37	40	9.0000
GCU	chr13:12502753-12502973(+)$1	220	2	5	9.0000
GCU	chrX:148291976-148292197(+)$1	221	77	80	9.0000
GCU	chr7:86047136-86047356(+)$1	220	10	13	9.0000
GCU	chr17:33114110-33114330(+)$1	220	96	99	9.0000
GCU	chr6:137697189-137697409(+)$1	220	160	163	9.0000
GCU	chr2:30811228-30811448(+)$1	220	41	44	9.0000
GCU	chr3:102935458-102935680(+)$1	222	30	33	9.0000
GCU	chr18:50082219-50082452(+)$1	233	65	68	9.0000
GCU	chr19:8983099-8983333(+)$1	234	51	54	9.0000
GCU	chr3:37363401-37363625(+)$1	224	89	92	9.0000
GCU	chr1:130162837-130163079(+)$1	242	44	47	9.0000
GCU	chr7:109302247-109302467(-)$1	220	44	47	9.0000
GCU	chr5:4029909-4030143(+)$1	234	48	51	9.0000
GCU	chr7:87365596-87365834(+)$1	238	15	18	9.0000
GCU	chr16:93807384-93807604(+)$1	220	130	133	9.0000
GCU	chr8:3536445-3536665(+)$1	220	102	105	9.0000
gcu	chr2:162759380-162759656(+)$1	276	48	51	9.0000
GCU	chr4:138905516-138905737(-)$1	221	65	68	9.0000
GCU	chr11:69462326-69462546(+)$1	220	79	82	9.0000
GCU	chr3:152090844-152091065(+)$1	221	14	17	9.0000
GCU	chr1:34244911-34245131(+)$1	220	12	15	9.0000
GCU	chr10:5991971-5992191(-)$1	220	32	35	9.0000
GCU	chr8:122464938-122465158(+)$1	220	132	135	9.0000
gcu	chr11:52188348-52188570(+)$1	222	4	7	9.0000
GCU	chr11:50071252-50071472(-)$1	220	29	32	9.0000
GCU	chr2:130104545-130104766(+)$1	221	8	11	9.0000
GCU	chr5:114837150-114837370(+)$1	220	44	47	9.0000
GCU	chr16:43956892-43957112(+)$1	220	19	22	9.0000
GCU	chr4:106244824-106245044(+)$1	220	84	87	9.0000
GCU	chr4:137101413-137101640(+)$1	227	121	124	9.0000
GCU	chr1:174043357-174043577(+)$1	220	75	78	9.0000
GCU	chr19:8988933-8989161(+)$1	228	12	15	9.0000
GCU	chr15:100005586-100005806(+)$1	220	38	41	9.0000
GCU	chr8:11808723-11808962(+)$1	239	49	52	9.0000
GCU	chr13:95178634-95178860(+)$1	226	0	3	9.0000
GCU	chr19:17469723-17469943(+)$1	220	132	135	9.0000
GCU	chr7:135036800-135037021(-)$1	221	19	22	9.0000
GCU	chr9:110453451-110453706(+)$1	255	3	6	9.0000
GCU	chr9:120860361-120860581(+)$1	220	38	41	9.0000
GCU	chr5:121874491-121874711(+)$1	220	15	18	9.0000
GCU	chr11:102340739-102340963(-)$1	224	6	9	9.0000
GCU	chr9:31019196-31019417(-)$1	221	12	15	9.0000
GCU	chr2:91780046-91780275(-)$1	229	43	46	9.0000
GCU	chr9:64022598-64022818(+)$1	220	32	35	9.0000
GCU	chr8:120107296-120107517(+)$1	221	54	57	9.0000
GCU	chr6:8172591-8172825(+)$1	234	45	48	9.0000
GCU	chr2:179887918-179888138(+)$1	220	26	29	9.0000
GCU	chr11:102979112-102979345(+)$1	233	34	37	9.0000
GCU	chr1:129833946-129834173(+)$1	227	78	81	9.0000
GCU	chr1:62862021-62862241(+)$1	220	11	14	9.0000
GCU	chr6:128307556-128307776(-)$1	220	74	77	9.0000
GCU	chr13:120283933-120284153(+)$1	220	11	14	9.0000
GCU	chr9:54745300-54745520(+)$1	220	1	4	9.0000
GCU	chr11:60249776-60250005(+)$1	229	13	16	9.0000
GCU	chr11:70700515-70700735(+)$1	220	34	37	9.0000
GCU	chr4:49657276-49657496(+)$1	220	27	30	9.0000
GCU	chr4:34757799-34758019(-)$1	220	10	13	9.0000
GCU	chr19:55154755-55154975(-)$1	220	67	70	9.0000
GCU	chr2:154336182-154336402(+)$1	220	14	17	9.0000
GCU	chr8:73054745-73054980(+)$1	235	29	32	9.0000
GCU	chr1:59540726-59540968(+)$1	242	23	26	9.0000
GCU	chr12:86609294-86609518(-)$1	224	8	11	9.0000
GCU	chr4:149017343-149017571(+)$1	228	1	4	9.0000
GCU	chr7:53327759-53327979(+)$1	220	36	39	9.0000
GCU	chr4:43937934-43938171(+)$1	237	62	65	9.0000
GCU	chr7:135920766-135920990(+)$1	224	15	18	9.0000
GCU	chr5:138574485-138574705(+)$1	220	69	72	9.0000
GCU	chr3:36460837-36461057(+)$1	220	122	125	9.0000
GCU	chr17:26391882-26392102(+)$1	220	159	162	9.0000
GCU	chr16:36722251-36722471(+)$1	220	4	7	9.0000
GCU	chr6:108491812-108492033(+)$1	221	161	164	9.0000
GCU	chr6:7625327-7625562(-)$1	235	105	108	9.0000

#otherMatches

#Struct PSSM
e!!	chr2:128948881-128949101(+)$1	220	79	82	9.0000
cc:	chr5:76005461-76005681(+)$1	220	38	41	9.0000
fff	chr3:84707675-84707898(+)$1	223	63	66	9.0000
ggg	chr6:115739365-115739585(+)$1	220	29	32	9.0000
g22	chr14:62223672-62223900(+)$1	228	32	35	9.0000
d""	chr9:108474453-108474688(+)$1	235	26	29	9.0000
JJJ	chr7:148429678-148429898(+)$1	220	19	22	9.0000
FFF	chr2:48760822-48761051(-)$1	229	9	12	9.0000
:ee	chr11:68599324-68599565(+)$1	241	61	64	9.0000
gbb	chr3:153585826-153586047(-)$1	221	16	19	9.0000
ddd	chr3:65750497-65750720(-)$1	223	125	128	9.0000
ccc	chr1:59924517-59924737(+)$1	220	39	42	9.0000
fff	chr17:71194219-71194440(-)$1	221	86	89	9.0000
ccc	chr4:140879277-140879522(+)$1	245	17	20	9.0000
DDD	chr11:79261618-79261838(+)$1	220	8	11	9.0000
fff	chr9:26811151-26811372(+)$1	221	15	18	9.0000
HHH	chr6:65048720-65048940(+)$1	220	77	80	9.0000
::=	chr2:109158045-109158265(+)$1	220	1	4	9.0000
^^^	chr13:3537471-3537691(+)$1	220	20	23	9.0000
:::	chr13:67444439-67444659(-)$1	220	75	78	9.0000
Gee	chr17:80434656-80434876(-)$1	220	12	15	9.0000
GGG	chrX:131139837-131140075(+)$1	238	71	74	9.0000
qqd	chr10:105282390-105282610(+)$1	220	100	103	9.0000
ddd	chr10:93506471-93506691(+)$1	220	25	28	9.0000
ddd	chr4:132977986-132978206(+)$1	220	33	36	9.0000
b]c	chr10:98478127-98478362(+)$1	235	37	40	9.0000
:::	chr13:12502753-12502973(+)$1	220	2	5	9.0000
===	chrX:148291976-148292197(+)$1	221	77	80	9.0000
a[b	chr7:86047136-86047356(+)$1	220	10	13	9.0000
bb:	chr17:33114110-33114330(+)$1	220	96	99	9.0000
22f	chr6:137697189-137697409(+)$1	220	160	163	9.0000
DDD	chr2:30811228-30811448(+)$1	220	41	44	9.0000
ggg	chr3:102935458-102935680(+)$1	222	30	33	9.0000
b]e	chr18:50082219-50082452(+)$1	233	65	68	9.0000
mbb	chr19:8983099-8983333(+)$1	234	51	54	9.0000
"dd	chr3:37363401-37363625(+)$1	224	89	92	9.0000
cll	chr1:130162837-130163079(+)$1	242	44	47	9.0000
EEE	chr7:109302247-109302467(-)$1	220	44	47	9.0000
ddd	chr5:4029909-4030143(+)$1	234	48	51	9.0000
DD{	chr7:87365596-87365834(+)$1	238	15	18	9.0000
cc[	chr16:93807384-93807604(+)$1	220	130	133	9.0000
!cc	chr8:3536445-3536665(+)$1	220	102	105	9.0000
{CC	chr2:162759380-162759656(+)$1	276	48	51	9.0000
ddd	chr4:138905516-138905737(-)$1	221	65	68	9.0000
d:=	chr11:69462326-69462546(+)$1	220	79	82	9.0000
{HH	chr3:152090844-152091065(+)$1	221	14	17	9.0000
FA:	chr1:34244911-34245131(+)$1	220	12	15	9.0000
llg	chr10:5991971-5992191(-)$1	220	32	35	9.0000
ccm	chr8:122464938-122465158(+)$1	220	132	135	9.0000
EEE	chr11:52188348-52188570(+)$1	222	4	7	9.0000
ooo	chr11:50071252-50071472(-)$1	220	29	32	9.0000
HHH	chr2:130104545-130104766(+)$1	221	8	11	9.0000
EEE	chr5:114837150-114837370(+)$1	220	44	47	9.0000
!!i	chr16:43956892-43957112(+)$1	220	19	22	9.0000
C{B	chr4:106244824-106245044(+)$1	220	84	87	9.0000
ccc	chr4:137101413-137101640(+)$1	227	121	124	9.0000
[ap	chr1:174043357-174043577(+)$1	220	75	78	9.0000
HHH	chr19:8988933-8989161(+)$1	228	12	15	9.0000
dd[	chr15:100005586-100005806(+)$1	220	38	41	9.0000
eec	chr8:11808723-11808962(+)$1	239	49	52	9.0000
EEE	chr13:95178634-95178860(+)$1	226	0	3	9.0000
ggg	chr19:17469723-17469943(+)$1	220	132	135	9.0000
KDD	chr7:135036800-135037021(-)$1	221	19	22	9.0000
bee	chr9:110453451-110453706(+)$1	255	3	6	9.0000
ddd	chr9:120860361-120860581(+)$1	220	38	41	9.0000
GG:	chr5:121874491-121874711(+)$1	220	15	18	9.0000
ooo	chr11:102340739-102340963(-)$1	224	6	9	9.0000
nnc	chr9:31019196-31019417(-)$1	221	12	15	9.0000
bdd	chr2:91780046-91780275(-)$1	229	43	46	9.0000
:::	chr9:64022598-64022818(+)$1	220	32	35	9.0000
hbb	chr8:120107296-120107517(+)$1	221	54	57	9.0000
hhh	chr6:8172591-8172825(+)$1	234	45	48	9.0000
EEE	chr2:179887918-179888138(+)$1	220	26	29	9.0000
hhh	chr11:102979112-102979345(+)$1	233	34	37	9.0000
[bb	chr1:129833946-129834173(+)$1	227	78	81	9.0000
GGG	chr1:62862021-62862241(+)$1	220	11	14	9.0000
[dd	chr6:128307556-128307776(-)$1	220	74	77	9.0000
GLL	chr13:120283933-120284153(+)$1	220	11	14	9.0000
ddd	chr9:54745300-54745520(+)$1	220	1	4	9.0000
cee	chr11:60249776-60250005(+)$1	229	13	16	9.0000
hhh	chr11:70700515-70700735(+)$1	220	34	37	9.0000
ddd	chr4:49657276-49657496(+)$1	220	27	30	9.0000
!!b	chr4:34757799-34758019(-)$1	220	10	13	9.0000
ggg	chr19:55154755-55154975(-)$1	220	67	70	9.0000
:::	chr2:154336182-154336402(+)$1	220	14	17	9.0000
ggg	chr8:73054745-73054980(+)$1	235	29	32	9.0000
[a[	chr1:59540726-59540968(+)$1	242	23	26	9.0000
G::	chr12:86609294-86609518(-)$1	224	8	11	9.0000
JJJ	chr4:149017343-149017571(+)$1	228	1	4	9.0000
$ee	chr7:53327759-53327979(+)$1	220	36	39	9.0000
fff	chr4:43937934-43938171(+)$1	237	62	65	9.0000
MMM	chr7:135920766-135920990(+)$1	224	15	18	9.0000
ccc	chr5:138574485-138574705(+)$1	220	69	72	9.0000
e[e	chr3:36460837-36461057(+)$1	220	122	125	9.0000
fff	chr17:26391882-26392102(+)$1	220	159	162	9.0000
FFF	chr16:36722251-36722471(+)$1	220	4	7	9.0000
CFF	chr6:108491812-108492033(+)$1	221	161	164	9.0000
e22	chr6:7625327-7625562(-)$1	235	105	108	9.0000

#DB
(..	chr2:128948881-128949101(+)$1	1	79	82	9.0000
)).	chr5:76005461-76005681(+)$1	1	38	41	9.0000
)))	chr3:84707675-84707898(+)$1	1	63	66	9.0000
)))	chr6:115739365-115739585(+)$1	1	29	32	9.0000
)..	chr14:62223672-62223900(+)$1	1	32	35	9.0000
(..	chr9:108474453-108474688(+)$1	1	26	29	9.0000
(((	chr7:148429678-148429898(+)$1	1	19	22	9.0000
(((	chr2:48760822-48761051(-)$1	1	9	12	9.0000
.((	chr11:68599324-68599565(+)$1	1	61	64	9.0000
(((	chr3:153585826-153586047(-)$1	1	16	19	9.0000
)))	chr3:65750497-65750720(-)$1	1	125	128	9.0000
(((	chr1:59924517-59924737(+)$1	1	39	42	9.0000
(((	chr17:71194219-71194440(-)$1	1	86	89	9.0000
(((	chr4:140879277-140879522(+)$1	1	17	20	9.0000
(((	chr11:79261618-79261838(+)$1	1	8	11	9.0000
(((	chr9:26811151-26811372(+)$1	1	15	18	9.0000
(((	chr6:65048720-65048940(+)$1	1	77	80	9.0000
..(	chr2:109158045-109158265(+)$1	1	1	4	9.0000
...	chr13:3537471-3537691(+)$1	1	20	23	9.0000
...	chr13:67444439-67444659(-)$1	1	75	78	9.0000
(((	chr17:80434656-80434876(-)$1	1	12	15	9.0000
(((	chrX:131139837-131140075(+)$1	1	71	74	9.0000
..)	chr10:105282390-105282610(+)$1	1	100	103	9.0000
(((	chr10:93506471-93506691(+)$1	1	25	28	9.0000
)))	chr4:132977986-132978206(+)$1	1	33	36	9.0000
).)	chr10:98478127-98478362(+)$1	1	37	40	9.0000
...	chr13:12502753-12502973(+)$1	1	2	5	9.0000
(((	chrX:148291976-148292197(+)$1	1	77	80	9.0000
(.(	chr7:86047136-86047356(+)$1	1	10	13	9.0000
)).	chr17:33114110-33114330(+)$1	1	96	99	9.0000
..)	chr6:137697189-137697409(+)$1	1	160	163	9.0000
(((	chr2:30811228-30811448(+)$1	1	41	44	9.0000
(((	chr3:102935458-102935680(+)$1	1	30	33	9.0000
).)	chr18:50082219-50082452(+)$1	1	65	68	9.0000
.))	chr19:8983099-8983333(+)$1	1	51	54	9.0000
.((	chr3:37363401-37363625(+)$1	1	89	92	9.0000
(..	chr1:130162837-130163079(+)$1	1	44	47	9.0000
(((	chr7:109302247-109302467(-)$1	1	44	47	9.0000
(((	chr5:4029909-4030143(+)$1	1	48	51	9.0000
((.	chr7:87365596-87365834(+)$1	1	15	18	9.0000
((.	chr16:93807384-93807604(+)$1	1	130	133	9.0000
.((	chr8:3536445-3536665(+)$1	1	102	105	9.0000
.((	chr2:162759380-162759656(+)$1	1	48	51	9.0000
)))	chr4:138905516-138905737(-)$1	1	65	68	9.0000
).(	chr11:69462326-69462546(+)$1	1	79	82	9.0000
.((	chr3:152090844-152091065(+)$1	1	14	17	9.0000
((.	chr1:34244911-34245131(+)$1	1	12	15	9.0000
..)	chr10:5991971-5992191(-)$1	1	32	35	9.0000
((.	chr8:122464938-122465158(+)$1	1	132	135	9.0000
(((	chr11:52188348-52188570(+)$1	1	4	7	9.0000
...	chr11:50071252-50071472(-)$1	1	29	32	9.0000
(((	chr2:130104545-130104766(+)$1	1	8	11	9.0000
(((	chr5:114837150-114837370(+)$1	1	44	47	9.0000
..(	chr16:43956892-43957112(+)$1	1	19	22	9.0000
(.(	chr4:106244824-106245044(+)$1	1	84	87	9.0000
(((	chr4:137101413-137101640(+)$1	1	121	124	9.0000
.(.	chr1:174043357-174043577(+)$1	1	75	78	9.0000
(((	chr19:8988933-8989161(+)$1	1	12	15	9.0000
((.	chr15:100005586-100005806(+)$1	1	38	41	9.0000
(((	chr8:11808723-11808962(+)$1	1	49	52	9.0000
(((	chr13:95178634-95178860(+)$1	1	0	3	9.0000
)))	chr19:17469723-17469943(+)$1	1	132	135	9.0000
.((	chr7:135036800-135037021(-)$1	1	19	22	9.0000
(((	chr9:110453451-110453706(+)$1	1	3	6	9.0000
)))	chr9:120860361-120860581(+)$1	1	38	41	9.0000
((.	chr5:121874491-121874711(+)$1	1	15	18	9.0000
...	chr11:102340739-102340963(-)$1	1	6	9	9.0000
..)	chr9:31019196-31019417(-)$1	1	12	15	9.0000
)))	chr2:91780046-91780275(-)$1	1	43	46	9.0000
...	chr9:64022598-64022818(+)$1	1	32	35	9.0000
(((	chr8:120107296-120107517(+)$1	1	54	57	9.0000
(((	chr6:8172591-8172825(+)$1	1	45	48	9.0000
(((	chr2:179887918-179888138(+)$1	1	26	29	9.0000
(((	chr11:102979112-102979345(+)$1	1	34	37	9.0000
.((	chr1:129833946-129834173(+)$1	1	78	81	9.0000
(((	chr1:62862021-62862241(+)$1	1	11	14	9.0000
.((	chr6:128307556-128307776(-)$1	1	74	77	9.0000
(..	chr13:120283933-120284153(+)$1	1	11	14	9.0000
(((	chr9:54745300-54745520(+)$1	1	1	4	9.0000
(((	chr11:60249776-60250005(+)$1	1	13	16	9.0000
)))	chr11:70700515-70700735(+)$1	1	34	37	9.0000
(((	chr4:49657276-49657496(+)$1	1	27	30	9.0000
..(	chr4:34757799-34758019(-)$1	1	10	13	9.0000
)))	chr19:55154755-55154975(-)$1	1	67	70	9.0000
...	chr2:154336182-154336402(+)$1	1	14	17	9.0000
)))	chr8:73054745-73054980(+)$1	1	29	32	9.0000
.(.	chr1:59540726-59540968(+)$1	1	23	26	9.0000
(..	chr12:86609294-86609518(-)$1	1	8	11	9.0000
(((	chr4:149017343-149017571(+)$1	1	1	4	9.0000
.((	chr7:53327759-53327979(+)$1	1	36	39	9.0000
(((	chr4:43937934-43938171(+)$1	1	62	65	9.0000
...	chr7:135920766-135920990(+)$1	1	15	18	9.0000
)))	chr5:138574485-138574705(+)$1	1	69	72	9.0000
(.(	chr3:36460837-36461057(+)$1	1	122	125	9.0000
(((	chr17:26391882-26392102(+)$1	1	159	162	9.0000
(((	chr16:36722251-36722471(+)$1	1	4	7	9.0000
)))	chr6:108491812-108492033(+)$1	1	161	164	9.0000
)..	chr6:7625327-7625562(-)$1	1	105	108	9.0000

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

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m3_run2.nuc.txt

#NT
GUUUUCU	chr3:68827994-68828214(+)$1	220	27	34	12.6666
UCUUUCU	chr18:33001525-33001746(+)$1	221	152	159	13.0454
UUUUUUU	chr18:4386143-4386402(+)$1	259	36	43	13.4242
AUUUUCU	chr13:74493805-74494043(+)$1	238	24	31	12.4393
UGUUUCU	chr10:60896449-60896669(-)$1	220	49	56	12.8939
UUUUUAU	chr13:17788594-17788849(+)$1	255	47	54	12.8939
UUUGUCU	chr4:44055047-44055267(-)$1	220	76	83	12.5909
UUUUUCU	chr1:166192719-166192964(+)$1	245	16	23	16.7575
UUUUUCU	chr4:108214562-108214798(+)$1	236	104	111	16.7575
UUAUUCU	chr19:8900443-8900679(+)$1	236	133	140	12.4393
UUUUUCU	chr2:132126231-132126451(+)$1	220	116	123	16.7575
UUUUUUU	chr15:77794451-77794683(-)$1	232	75	82	13.4242
UUUUACU	chr14:47910099-47910319(+)$1	220	98	105	12.5151
GUUUUCU	chr11:75570407-75570627(+)$1	220	182	189	12.6666
UUUUGCU	chr12:17556766-17556991(+)$1	225	131	138	12.3636
UUAUUCU	chr3:67405164-67405384(+)$1	220	92	99	12.4393
UUUCUCU	chr7:107645204-107645437(+)$1	233	87	94	12.5909
GUUUUCU	chr16:16880599-16880819(+)$1	220	193	200	12.6666
UUGUUCU	chr19:10689265-10689485(+)$1	220	55	62	12.4393
CUUUUCU	chr11:101420726-101420959(+)$1	233	212	219	12.5909
UGUUUCU	chr9:103235219-103235441(+)$1	222	31	38	12.8939
UUUUUCU	chr3:121987205-121987425(+)$1	220	96	103	16.7575
UAUUUCU	chr12:112861383-112861603(+)$1	220	54	61	12.6666
cuuuucu	chr7:141936634-141936854(+)$1	220	193	200	12.5909
UCUUUCU	chr9:44434450-44434670(+)$1	220	206	213	13.0454
UUUUUGU	chr5:122112027-122112267(+)$1	240	195	202	12.8939
UUUUUCU	chr9:94420900-94421137(-)$1	237	58	65	16.7575
UUUUUUU	chr5:67654948-67655170(+)$1	222	0	7	13.4242
UUUUUGU	chr12:11289833-11290080(+)$1	247	22	29	12.8939
GUUUUCU	chr15:79725811-79726036(+)$1	225	7	14	12.6666
UUUCUCU	chr6:125059713-125059934(+)$1	221	151	158	12.5909
UUUUUCU	chr11:26368584-26368804(+)$1	220	62	69	16.7575
UUUUUUU	chr6:120368557-120368777(+)$1	220	6	13	13.4242
UUUAUCU	chr7:5027176-5027398(+)$1	222	155	162	12.5151
UUUUUUU	chr1:169255977-169256197(+)$1	220	7	14	13.4242
UUGUUCU	chr2:170342021-170342241(+)$1	220	9	16	12.4393
uuuuucu	chr14:56298593-56298817(-)$1	224	213	220	16.7575
UGUUUCU	chr9:67737421-67737668(+)$1	247	33	40	12.8939
UGUUUCu	chr11:107531267-107531487(+)$1	220	36	43	12.8939
UUUUUUU	chrX:96138726-96138947(+)$1	221	93	100	13.4242
UUUUUUU	chr14:121342824-121343044(+)$1	220	28	35	13.4242
UUCUUCU	chr17:23955610-23955830(+)$1	220	176	183	12.5151
UUCUUCU	chr8:42410227-42410447(+)$1	220	56	63	12.5151
UCUUUCU	chr9:72943010-72943230(+)$1	220	11	18	13.0454
UUUGUCU	chr14:35537923-35538155(+)$1	232	182	189	12.5909
UUUUCCU	chr10:59757180-59757408(+)$1	228	87	94	12.5151
UUCUUCU	chr4:154984180-154984400(+)$1	220	172	179	12.5151
UUUUCCU	chr6:92110252-92110472(+)$1	220	130	137	12.5151
UUUUUCU	chr18:53868601-53868821(-)$1	220	2	9	16.7575
UUUGUCU	chr3:85920647-85920870(+)$1	223	79	86	12.5909
UUUCUCU	chr17:24733585-24733806(-)$1	221	80	87	12.5909
UCUUUCU	chr8:81615683-81615907(+)$1	224	10	17	13.0454
UUUUUCU	chr15:12279423-12279643(+)$1	220	145	152	16.7575
UUUUACU	chr7:127001457-127001677(-)$1	220	69	76	12.5151
ucuuucu	chr5:29964110-29964330(+)$1	220	19	26	13.0454
UUUUCCU	chr6:85416556-85416776(+)$1	220	44	51	12.5151
UUUAUCU	chr5:76037093-76037313(+)$1	220	188	195	12.5151
UUUUUUU	chr12:73052097-73052333(+)$1	236	6	13	13.4242
UUUUACU	chr1:44039828-44040049(+)$1	221	43	50	12.5151
CUUUUCU	chr1:37954518-37954738(+)$1	220	5	12	12.5909
UUUUUCA	chr15:25916528-25916748(+)$1	220	1	8	11.9848
UCUUUCU	chr10:39524656-39524876(+)$1	220	88	95	13.0454
UUUUUCC	chr14:22200624-22200844(+)$1	220	79	86	11.9848
uuuuucu	chr2:37358280-37358528(+)$1	248	17	24	16.7575
UUUUUAU	chr19:5425880-5426101(+)$1	221	24	31	12.8939

#otherMatches

#Struct PSSM
eeee22h	chr3:35711081-35711301(+)$1	220	43	50	13.4242
ddddccc	chr3:68827994-68828214(+)$1	220	27	34	12.6666
ppppbb]	chr18:33001525-33001746(+)$1	221	152	159	13.0454
fhhhhhh	chr18:4386143-4386402(+)$1	259	36	43	13.4242
vvvvvvv	chr13:74493805-74494043(+)$1	238	24	31	12.4393
eee]eee	chr10:60896449-60896669(-)$1	220	49	56	12.8939
FFF:::i	chr13:17788594-17788849(+)$1	255	47	54	12.8939
ggggggg	chr4:44055047-44055267(-)$1	220	76	83	12.5909
:eeeeem	chr1:166192719-166192964(+)$1	245	16	23	16.7575
333gggg	chr4:108214562-108214798(+)$1	236	104	111	16.7575
qqqcccf	chr19:8900443-8900679(+)$1	236	133	140	12.4393
hqqqqqq	chr2:132126231-132126451(+)$1	220	116	123	16.7575
iiiiiii	chr15:77794451-77794683(-)$1	232	75	82	13.4242
>>>>>>>	chr14:47910099-47910319(+)$1	220	98	105	12.5151
GGGZZZF	chr11:75570407-75570627(+)$1	220	182	189	12.6666
8888888	chr12:17556766-17556991(+)$1	225	131	138	12.3636
cc]dddd	chr3:67405164-67405384(+)$1	220	92	99	12.4393
eedddd[	chr7:107645204-107645437(+)$1	233	87	94	12.5909
hhhhhh:	chr16:16880599-16880819(+)$1	220	193	200	12.6666
WWWWWWW	chr19:10689265-10689485(+)$1	220	55	62	12.4393
::HHHHH	chr11:101420726-101420959(+)$1	233	212	219	12.5909
d[eeeee	chr9:103235219-103235441(+)$1	222	31	38	12.8939
(((((ee	chr3:121987205-121987425(+)$1	220	96	103	16.7575
:eeeee[	chr12:112861383-112861603(+)$1	220	54	61	12.6666
GGGGG:d	chr7:141936634-141936854(+)$1	220	193	200	12.5909
IIIIIII	chr9:44434450-44434670(+)$1	220	206	213	13.0454
FFFFFYY	chr5:122112027-122112267(+)$1	240	195	202	12.8939
h::::::	chr9:94420900-94421137(-)$1	237	58	65	16.7575
:::::::	chr5:67654948-67655170(+)$1	222	0	7	13.4242
eeeee[h	chr12:11289833-11290080(+)$1	247	22	29	12.8939
HHHHHHH	chr15:79725811-79726036(+)$1	225	7	14	12.6666
dddpppp	chr6:125059713-125059934(+)$1	221	151	158	12.5909
c]bb]cc	chr11:26368584-26368804(+)$1	220	62	69	16.7575
:::iiii	chr6:120368557-120368777(+)$1	220	6	13	13.4242
)))))))	chr7:5027176-5027398(+)$1	222	155	162	12.5151
"""gggg	chr1:169255977-169256197(+)$1	220	7	14	13.4242
[hhhhhh	chr2:170342021-170342241(+)$1	220	9	16	12.4393
:::::::	chr14:56298593-56298817(-)$1	224	213	220	16.7575
oooccc2	chr9:67737421-67737668(+)$1	247	33	40	12.8939
TTTTTTG	chr11:107531267-107531487(+)$1	220	36	43	12.8939
c55555e	chrX:96138726-96138947(+)$1	221	93	100	13.4242
ccc]bb]	chr14:121342824-121343044(+)$1	220	28	35	13.4242
$$$cccm	chr17:23955610-23955830(+)$1	220	176	183	12.5151
ggggg::	chr8:42410227-42410447(+)$1	220	56	63	12.5151
KKDDDD:	chr9:72943010-72943230(+)$1	220	11	18	13.0454
IIIIIII	chr14:35537923-35538155(+)$1	232	182	189	12.5909
888ccc4	chr10:59757180-59757408(+)$1	228	87	94	12.5151
nnnnnbb	chr4:154984180-154984400(+)$1	220	172	179	12.5151
:::::DD	chr6:92110252-92110472(+)$1	220	130	137	12.5151
::::::c	chr18:53868601-53868821(-)$1	220	2	9	16.7575
ddd]ddd	chr3:85920647-85920870(+)$1	223	79	86	12.5909
22eeeee	chr17:24733585-24733806(-)$1	221	80	87	12.5909
hdddd!!	chr8:81615683-81615907(+)$1	224	10	17	13.0454
+++++++	chr15:12279423-12279643(+)$1	220	145	152	16.7575
+eeeee%	chr7:127001457-127001677(-)$1	220	69	76	12.5151
^^^^^^^	chr5:29964110-29964330(+)$1	220	19	26	13.0454
ffffffc	chr6:85416556-85416776(+)$1	220	44	51	12.5151
HH:::::	chr5:76037093-76037313(+)$1	220	188	195	12.5151
JJJJJJJ	chr12:73052097-73052333(+)$1	236	6	13	13.4242
::::::d	chr1:44039828-44040049(+)$1	221	43	50	12.5151
:eeeee[	chr1:37954518-37954738(+)$1	220	5	12	12.5909
gggggg[	chr15:25916528-25916748(+)$1	220	1	8	11.9848
[eeeee"	chr10:39524656-39524876(+)$1	220	88	95	13.0454
ggggg##	chr14:22200624-22200844(+)$1	220	79	86	11.9848
JJMMMMF	chr2:37358280-37358528(+)$1	248	17	24	16.7575
QQQQDDD	chr19:5425880-5426101(+)$1	221	24	31	12.8939

#DB
))))..)	chr3:35711081-35711301(+)$1	1	43	50	13.4242
(((((((	chr3:68827994-68828214(+)$1	1	27	34	12.6666
....)).	chr18:33001525-33001746(+)$1	1	152	159	13.0454
(((((((	chr18:4386143-4386402(+)$1	1	36	43	13.4242
.......	chr13:74493805-74494043(+)$1	1	24	31	12.4393
))).)))	chr10:60896449-60896669(-)$1	1	49	56	12.8939
(((...(	chr13:17788594-17788849(+)$1	1	47	54	12.8939
)))))))	chr4:44055047-44055267(-)$1	1	76	83	12.5909
.(((((.	chr1:166192719-166192964(+)$1	1	16	23	16.7575
...))))	chr4:108214562-108214798(+)$1	1	104	111	16.7575
...))))	chr19:8900443-8900679(+)$1	1	133	140	12.4393
(......	chr2:132126231-132126451(+)$1	1	116	123	16.7575
)))))))	chr15:77794451-77794683(-)$1	1	75	82	13.4242
.......	chr14:47910099-47910319(+)$1	1	98	105	12.5151
)))...)	chr11:75570407-75570627(+)$1	1	182	189	12.6666
.......	chr12:17556766-17556991(+)$1	1	131	138	12.3636
)).))))	chr3:67405164-67405384(+)$1	1	92	99	12.4393
))((((.	chr7:107645204-107645437(+)$1	1	87	94	12.5909
)))))).	chr16:16880599-16880819(+)$1	1	193	200	12.6666
.......	chr19:10689265-10689485(+)$1	1	55	62	12.4393
..)))))	chr11:101420726-101420959(+)$1	1	212	219	12.5909
(.(((((	chr9:103235219-103235441(+)$1	1	31	38	12.8939
.....((	chr3:121987205-121987425(+)$1	1	96	103	16.7575
.(((((.	chr12:112861383-112861603(+)$1	1	54	61	12.6666
))))).(	chr7:141936634-141936854(+)$1	1	193	200	12.5909
)))))))	chr9:44434450-44434670(+)$1	1	206	213	13.0454
)))))..	chr5:122112027-122112267(+)$1	1	195	202	12.8939
)......	chr9:94420900-94421137(-)$1	1	58	65	16.7575
.......	chr5:67654948-67655170(+)$1	1	0	7	13.4242
(((((.(	chr12:11289833-11290080(+)$1	1	22	29	12.8939
(((((((	chr15:79725811-79726036(+)$1	1	7	14	12.6666
(((....	chr6:125059713-125059934(+)$1	1	151	158	12.5909
).)).))	chr11:26368584-26368804(+)$1	1	62	69	16.7575
...((((	chr6:120368557-120368777(+)$1	1	6	13	13.4242
.......	chr7:5027176-5027398(+)$1	1	155	162	12.5151
...((((	chr1:169255977-169256197(+)$1	1	7	14	13.4242
.((((((	chr2:170342021-170342241(+)$1	1	9	16	12.4393
.......	chr14:56298593-56298817(-)$1	1	213	220	16.7575
...))).	chr9:67737421-67737668(+)$1	1	33	40	12.8939
......(	chr11:107531267-107531487(+)$1	1	36	43	12.8939
).....)	chrX:96138726-96138947(+)$1	1	93	100	13.4242
))).)).	chr14:121342824-121343044(+)$1	1	28	35	13.4242
...(((.	chr17:23955610-23955830(+)$1	1	176	183	12.5151
)))))..	chr8:42410227-42410447(+)$1	1	56	63	12.5151
..((((.	chr9:72943010-72943230(+)$1	1	11	18	13.0454
)))))))	chr14:35537923-35538155(+)$1	1	182	189	12.5909
...))).	chr10:59757180-59757408(+)$1	1	87	94	12.5151
.....))	chr4:154984180-154984400(+)$1	1	172	179	12.5151
.....))	chr6:92110252-92110472(+)$1	1	130	137	12.5151
......(	chr18:53868601-53868821(-)$1	1	2	9	16.7575
))).)))	chr3:85920647-85920870(+)$1	1	79	86	12.5909
..)))))	chr17:24733585-24733806(-)$1	1	80	87	12.5909
(((((..	chr8:81615683-81615907(+)$1	1	10	17	13.0454
.......	chr15:12279423-12279643(+)$1	1	145	152	16.7575
.(((((.	chr7:127001457-127001677(-)$1	1	69	76	12.5151
.......	chr5:29964110-29964330(+)$1	1	19	26	13.0454
(((((((	chr6:85416556-85416776(+)$1	1	44	51	12.5151
)).....	chr5:76037093-76037313(+)$1	1	188	195	12.5151
(((((((	chr12:73052097-73052333(+)$1	1	6	13	13.4242
......(	chr1:44039828-44040049(+)$1	1	43	50	12.5151
.(((((.	chr1:37954518-37954738(+)$1	1	5	12	12.5909
((((((.	chr15:25916528-25916748(+)$1	1	1	8	11.9848
.(((((.	chr10:39524656-39524876(+)$1	1	88	95	13.0454
(((((..	chr14:22200624-22200844(+)$1	1	79	86	11.9848
((....(	chr2:37358280-37358528(+)$1	1	17	24	16.7575
....(((	chr19:5425880-5426101(+)$1	1	24	31	12.8939

#PSSM
U : 0.83	G : 0.06	u : 0.04	C : 0.03	A : 0.01	c : 0.01	
U : 0.78	C : 0.07	G : 0.06	u : 0.04	A : 0.01	c : 0.01	
U : 0.83	u : 0.06	C : 0.04	A : 0.03	G : 0.03	
U : 0.81	u : 0.06	G : 0.04	C : 0.04	A : 0.03	
U : 0.83	u : 0.06	A : 0.04	C : 0.04	G : 0.01	
C : 0.74	U : 0.13	c : 0.06	A : 0.03	G : 0.03	
U : 0.89	u : 0.07	A : 0.01	C : 0.01	

#score	882.6666666666656
#seq	66
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_transcript_m1_run2.nuc.txt

#NT
UGUUUU	chr11:50108757-50109006(-)$1	249	127	133	15.1641
UGUUUU	chr11:74490738-74490973(-)$1	235	144	150	15.1641
UGUUUC	chr6:4592556-4592792(+)$1	236	94	100	13.7462
UGUUUU	chr2:90856174-90856425(+)$1	251	12	18	15.1641
UGUUUU	chr11:87033782-87034017(+)$1	235	227	233	15.1641
UGUUUA	chr4:90918261-90918497(-)$1	236	75	81	13.8955
UGUUUU	chr15:58774435-58774677(-)$1	242	81	87	15.1641
UGUUUU	chr3:146393690-146393925(-)$1	235	5	11	15.1641
UGUUUA	chr3:35793621-35793856(-)$1	235	12	18	13.8955
UGUUUC	chr4:15831933-15832170(+)$1	237	127	133	13.7462
uguuug	chr11:90201687-90201928(-)$1	241	12	18	14.1940
UGUUUC	chr2:131763569-131763819(+)$1	250	101	107	13.7462
UGUUUG	chr1:5152350-5152598(+)$1	248	46	52	14.1940
uguuuu	chr4:47483833-47484095(-)$1	262	189	195	15.1641
UGUUUG	chr16:17046968-17047233(+)$1	265	49	55	14.1940
UGUUUG	chr18:33596851-33597130(-)$1	279	155	161	14.1940
UGUUUU	chr14:37934879-37935169(-)$1	290	120	126	15.1641
UGUUUG	chr11:75402769-75403004(+)$1	235	72	78	14.1940
uGUUUG	chr2:68946690-68946930(+)$1	240	220	226	14.1940
UGUUUU	chr2:135300443-135300683(+)$1	240	163	169	15.1641
ugUUUU	chr16:96378321-96378556(+)$1	235	91	97	15.1641
UGUUUG	chr2:5950315-5950550(+)$1	235	97	103	14.1940
UGUUUG	chr3:57646419-57646662(-)$1	243	92	98	14.1940
UGUUUU	chr8:56144782-56145092(+)$1	310	45	51	15.1641
UGUUUG	chr2:104268029-104268282(-)$1	253	38	44	14.1940
UGUUUU	chr2:52284533-52284772(-)$1	239	10	16	15.1641
UGUUUU	chr11:87032333-87032652(+)$1	319	71	77	15.1641
UGUUUA	chr10:116785268-116785504(-)$1	236	27	33	13.8955
UGUUUC	chr4:138013018-138013274(+)$1	256	85	91	13.7462
UGUUUU	chr16:84954768-84955080(-)$1	312	122	128	15.1641
UGUUUA	chr4:154931883-154932126(+)$1	243	147	153	13.8955
UGUUUU	chr6:13035521-13035767(+)$1	246	57	63	15.1641
uguuuu	chr5:67004034-67004269(-)$1	235	114	120	15.1641
UGUUUU	chr4:59234017-59234272(+)$1	255	212	218	15.1641
UGUUUA	chr4:48674929-48675180(+)$1	251	186	192	13.8955
UGUUUG	chr17:44174391-44174642(+)$1	251	12	18	14.1940
UGUUUC	chr10:70718207-70718465(-)$1	258	19	25	13.7462
UGUUUC	chr2:102622083-102622372(+)$1	289	174	180	13.7462
UGUUUU	chr12:8504653-8504905(-)$1	252	73	79	15.1641
UGUUUG	chr13:110846027-110846281(-)$1	254	195	201	14.1940
UGUUUG	chr11:77342666-77342908(-)$1	242	166	172	14.1940
UGUUUC	chr10:66476157-66476404(-)$1	247	69	75	13.7462
UGUUUU	chr9:115152025-115152263(-)$1	238	141	147	15.1641
UGUUUG	chr10:110731923-110732162(+)$1	239	113	119	14.1940
UGUUUG	chr5:136384869-136385127(-)$1	258	59	65	14.1940
UGUUUG	chr7:107421221-107421465(+)$1	244	112	118	14.1940
UGUUUU	chr5:73949546-73949811(+)$1	265	20	26	15.1641
UGUUUU	chr1:66487173-66487420(+)$1	247	118	124	15.1641
UGUUUA	chr16:37886917-37887183(+)$1	266	38	44	13.8955
UGUUUA	chr13:98022059-98022344(+)$1	285	65	71	13.8955
UGUUUA	chr15:36408785-36409036(-)$1	251	111	117	13.8955
UGUUUU	chr2:35037265-35037508(-)$1	243	196	202	15.1641
UGUUUC	chrX:50374586-50374849(+)$1	263	160	166	13.7462
UGUUUA	chr1:75143877-75144118(+)$1	241	144	150	13.8955
UGUUUA	chr11:97317285-97317524(+)$1	239	144	150	13.8955
UGUUUA	chr11:87794732-87794987(-)$1	255	227	233	13.8955
UGUUUG	chr6:108772587-108772833(+)$1	246	66	72	14.1940
UGUUUC	chrX:162826314-162826580(+)$1	266	1	7	13.7462
UGUUUU	chr16:17045015-17045265(+)$1	250	223	229	15.1641
UGUUUU	chr19:31520266-31520511(-)$1	245	25	31	15.1641
UGUUUA	chr11:53232359-53232595(+)$1	236	153	159	13.8955
UGUUUU	chr2:6466641-6466893(-)$1	252	158	164	15.1641
UGUUUU	chr2:52283795-52284044(-)$1	249	120	126	15.1641
UGUUUU	chr10:48819694-48819932(-)$1	238	92	98	15.1641
UGUUUU	chr11:35602994-35603236(+)$1	242	102	108	15.1641
uguuuc	chr9:111179225-111179470(+)$1	245	146	152	13.7462

#otherMatches

#Struct PSSM
bb[ggg	chr1:9713368-9713606(-)$1	238	139	145	15.1641
eeeee]	chr11:50108757-50109006(-)$1	249	127	133	15.1641
eeeee2	chr11:74490738-74490973(-)$1	235	144	150	15.1641
B/////	chr6:4592556-4592792(+)$1	236	94	100	13.7462
gppppp	chr2:90856174-90856425(+)$1	251	12	18	15.1641
::::::	chr11:87033782-87034017(+)$1	235	227	233	15.1641
:IIIII	chr4:90918261-90918497(-)$1	236	75	81	13.8955
ccc22g	chr15:58774435-58774677(-)$1	242	81	87	15.1641
F{FFFF	chr3:146393690-146393925(-)$1	235	5	11	15.1641
:fffff	chr3:35793621-35793856(-)$1	235	12	18	13.8955
JJJJJJ	chr4:15831933-15832170(+)$1	237	127	133	13.7462
==qqqq	chr11:90201687-90201928(-)$1	241	12	18	14.1940
ccc:ee	chr2:131763569-131763819(+)$1	250	101	107	13.7462
hhhhhh	chr1:5152350-5152598(+)$1	248	46	52	14.1940
ee::::	chr4:47483833-47484095(-)$1	262	189	195	15.1641
gggggg	chr16:17046968-17047233(+)$1	265	49	55	14.1940
ffffff	chr18:33596851-33597130(-)$1	279	155	161	14.1940
eeee!!	chr14:37934879-37935169(-)$1	290	120	126	15.1641
eeeee>	chr11:75402769-75403004(+)$1	235	72	78	14.1940
0000gg	chr2:68946690-68946930(+)$1	240	220	226	14.1940
ddddmm	chr2:135300443-135300683(+)$1	240	163	169	15.1641
fff(((	chr16:96378321-96378556(+)$1	235	91	97	15.1641
FF::GG	chr2:5950315-5950550(+)$1	235	97	103	14.1940
[a!!cc	chr3:57646419-57646662(-)$1	243	92	98	14.1940
FFFFFF	chr8:56144782-56145092(+)$1	310	45	51	15.1641
''''ee	chr2:104268029-104268282(-)$1	253	38	44	14.1940
SSSSSS	chr2:52284533-52284772(-)$1	239	10	16	15.1641
iiiiii	chr11:87032333-87032652(+)$1	319	71	77	15.1641
h!!eee	chr10:116785268-116785504(-)$1	236	27	33	13.8955
33gggg	chr4:138013018-138013274(+)$1	256	85	91	13.7462
gg####	chr16:84954768-84955080(-)$1	312	122	128	15.1641
iiiii]	chr4:154931883-154932126(+)$1	243	147	153	13.8955
cc::dd	chr6:13035521-13035767(+)$1	246	57	63	15.1641
^^^^^^	chr5:67004034-67004269(-)$1	235	114	120	15.1641
::::cc	chr4:59234017-59234272(+)$1	255	212	218	15.1641
gggg22	chr4:48674929-48675180(+)$1	251	186	192	13.8955
FFFF::	chr17:44174391-44174642(+)$1	251	12	18	14.1940
ddddcc	chr10:70718207-70718465(-)$1	258	19	25	13.7462
:=====	chr2:102622083-102622372(+)$1	289	174	180	13.7462
eee22e	chr12:8504653-8504905(-)$1	252	73	79	15.1641
$$$$$b	chr13:110846027-110846281(-)$1	254	195	201	14.1940
h[eeee	chr11:77342666-77342908(-)$1	242	166	172	14.1940
eee:::	chr10:66476157-66476404(-)$1	247	69	75	13.7462
"bbooo	chr9:115152025-115152263(-)$1	238	141	147	15.1641
eee!!a	chr10:110731923-110732162(+)$1	239	113	119	14.1940
eee::b	chr5:136384869-136385127(-)$1	258	59	65	14.1940
[dddd[	chr7:107421221-107421465(+)$1	244	112	118	14.1940
))))))	chr5:73949546-73949811(+)$1	265	20	26	15.1641
c]ffff	chr1:66487173-66487420(+)$1	247	118	124	15.1641
IIIIII	chr16:37886917-37887183(+)$1	266	38	44	13.8955
::::::	chr13:98022059-98022344(+)$1	285	65	71	13.8955
eeeeed	chr15:36408785-36409036(-)$1	251	111	117	13.8955
YDDDD:	chr2:35037265-35037508(-)$1	243	196	202	15.1641
ffffff	chrX:50374586-50374849(+)$1	263	160	166	13.7462
YFFFFF	chr1:75143877-75144118(+)$1	241	144	150	13.8955
55555c	chr11:97317285-97317524(+)$1	239	144	150	13.8955
qdddd]	chr11:87794732-87794987(-)$1	255	227	233	13.8955
gggg]c	chr6:108772587-108772833(+)$1	246	66	72	14.1940
FFFFFF	chrX:162826314-162826580(+)$1	266	1	7	13.7462
@@@@@@	chr16:17045015-17045265(+)$1	250	223	229	15.1641
cnnnnn	chr19:31520266-31520511(-)$1	245	25	31	15.1641
III}BB	chr11:53232359-53232595(+)$1	236	153	159	13.8955
eeeeep	chr2:6466641-6466893(-)$1	252	158	164	15.1641
mmmiii	chr2:52283795-52284044(-)$1	249	120	126	15.1641
oooooo	chr10:48819694-48819932(-)$1	238	92	98	15.1641
oooddd	chr11:35602994-35603236(+)$1	242	102	108	15.1641
ccc000	chr9:111179225-111179470(+)$1	245	146	152	13.7462

#DB
((.(((	chr1:9713368-9713606(-)$1	1	139	145	15.1641
))))).	chr11:50108757-50109006(-)$1	1	127	133	15.1641
))))).	chr11:74490738-74490973(-)$1	1	144	150	15.1641
).....	chr6:4592556-4592792(+)$1	1	94	100	13.7462
(.....	chr2:90856174-90856425(+)$1	1	12	18	15.1641
......	chr11:87033782-87034017(+)$1	1	227	233	15.1641
.(((((	chr4:90918261-90918497(-)$1	1	75	81	13.8955
)))..)	chr15:58774435-58774677(-)$1	1	81	87	15.1641
(.((((	chr3:146393690-146393925(-)$1	1	5	11	15.1641
.(((((	chr3:35793621-35793856(-)$1	1	12	18	13.8955
))))))	chr4:15831933-15832170(+)$1	1	127	133	13.7462
((....	chr11:90201687-90201928(-)$1	1	12	18	14.1940
))).((	chr2:131763569-131763819(+)$1	1	101	107	13.7462
((((((	chr1:5152350-5152598(+)$1	1	46	52	14.1940
))....	chr4:47483833-47484095(-)$1	1	189	195	15.1641
((((((	chr16:17046968-17047233(+)$1	1	49	55	14.1940
((((((	chr18:33596851-33597130(-)$1	1	155	161	14.1940
((((..	chr14:37934879-37935169(-)$1	1	120	126	15.1641
))))).	chr11:75402769-75403004(+)$1	1	72	78	14.1940
....))	chr2:68946690-68946930(+)$1	1	220	226	14.1940
((((..	chr2:135300443-135300683(+)$1	1	163	169	15.1641
(((...	chr16:96378321-96378556(+)$1	1	91	97	15.1641
))..((	chr2:5950315-5950550(+)$1	1	97	103	14.1940
.(..((	chr3:57646419-57646662(-)$1	1	92	98	14.1940
((((((	chr8:56144782-56145092(+)$1	1	45	51	15.1641
....((	chr2:104268029-104268282(-)$1	1	38	44	14.1940
......	chr2:52284533-52284772(-)$1	1	10	16	15.1641
))))))	chr11:87032333-87032652(+)$1	1	71	77	15.1641
(..(((	chr10:116785268-116785504(-)$1	1	27	33	13.8955
..))))	chr4:138013018-138013274(+)$1	1	85	91	13.7462
((....	chr16:84954768-84955080(-)$1	1	122	128	15.1641
))))).	chr4:154931883-154932126(+)$1	1	147	153	13.8955
))..((	chr6:13035521-13035767(+)$1	1	57	63	15.1641
......	chr5:67004034-67004269(-)$1	1	114	120	15.1641
....((	chr4:59234017-59234272(+)$1	1	212	218	15.1641
))))..	chr4:48674929-48675180(+)$1	1	186	192	13.8955
((((..	chr17:44174391-44174642(+)$1	1	12	18	14.1940
((((((	chr10:70718207-70718465(-)$1	1	19	25	13.7462
.(((((	chr2:102622083-102622372(+)$1	1	174	180	13.7462
)))..)	chr12:8504653-8504905(-)$1	1	73	79	15.1641
.....(	chr13:110846027-110846281(-)$1	1	195	201	14.1940
(.((((	chr11:77342666-77342908(-)$1	1	166	172	14.1940
)))...	chr10:66476157-66476404(-)$1	1	69	75	13.7462
.((...	chr9:115152025-115152263(-)$1	1	141	147	15.1641
(((..(	chr10:110731923-110732162(+)$1	1	113	119	14.1940
)))..(	chr5:136384869-136385127(-)$1	1	59	65	14.1940
.((((.	chr7:107421221-107421465(+)$1	1	112	118	14.1940
......	chr5:73949546-73949811(+)$1	1	20	26	15.1641
).))))	chr1:66487173-66487420(+)$1	1	118	124	15.1641
((((((	chr16:37886917-37887183(+)$1	1	38	44	13.8955
......	chr13:98022059-98022344(+)$1	1	65	71	13.8955
))))))	chr15:36408785-36409036(-)$1	1	111	117	13.8955
.)))).	chr2:35037265-35037508(-)$1	1	196	202	15.1641
))))))	chrX:50374586-50374849(+)$1	1	160	166	13.7462
.)))))	chr1:75143877-75144118(+)$1	1	144	150	13.8955
.....)	chr11:97317285-97317524(+)$1	1	144	150	13.8955
.)))).	chr11:87794732-87794987(-)$1	1	227	233	13.8955
)))).)	chr6:108772587-108772833(+)$1	1	66	72	14.1940
((((((	chrX:162826314-162826580(+)$1	1	1	7	13.7462
......	chr16:17045015-17045265(+)$1	1	223	229	15.1641
(.....	chr19:31520266-31520511(-)$1	1	25	31	15.1641
))).))	chr11:53232359-53232595(+)$1	1	153	159	13.8955
(((((.	chr2:6466641-6466893(-)$1	1	158	164	15.1641
...)))	chr2:52283795-52284044(-)$1	1	120	126	15.1641
......	chr10:48819694-48819932(-)$1	1	92	98	15.1641
...)))	chr11:35602994-35603236(+)$1	1	102	108	15.1641
)))...	chr9:111179225-111179470(+)$1	1	146	152	13.7462

#PSSM
U : 0.91	u : 0.08	
G : 0.92	g : 0.07	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	
U : 0.40	G : 0.22	A : 0.17	C : 0.13	u : 0.02	g : 0.01	c : 0.01	

#score	971.0746268656723
#seq	67
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011a_mm9_UTR_m3_run2.nuc.txt

#NT
UUUCUUUU	chr7:13393997-13394269(-)$1	272	88	96	19.8333
UUUGUUUU	chr18:38000457-38000731(+)$1	274	27	35	17.0000
UUUCCUUU	chr3:87973067-87973400(+)$1	333	249	257	15.0000
UUUAUUUU	chr10:93432273-93432550(-)$1	277	52	60	16.6666
UUUUUUUU	chr15:96245044-96245315(-)$1	271	211	219	16.8333
uuuuuuuu	chr3:129338274-129338552(+)$1	278	9	17	16.8333
UUCCUUUU	chrX:35886358-35886636(-)$1	278	91	99	15.6666
UUACUUUU	chr2:138112183-138112454(+)$1	271	112	120	15.5000
UUUCUUUU	chr2:153596149-153596431(+)$1	282	166	174	19.8333
UUUCUUGU	chr16:8688742-8689018(-)$1	276	218	226	15.7500
UUGCUUUU	chr17:64306424-64306719(+)$1	295	34	42	15.6666
UUUCUGUU	chr8:109897859-109898147(+)$1	288	76	84	15.5000
uuuuuuuu	chr11:33373097-33373373(-)$1	276	153	161	16.8333
UGUCUUUU	chr2:130851818-130852094(+)$1	276	267	275	15.0833
UUUCUUUU	chr3:94992308-94992580(-)$1	272	246	254	19.8333
UUUGUUUU	chr5:115691748-115692023(-)$1	275	75	83	17.0000
UUUCUUUU	chr4:59488510-59488796(-)$1	286	212	220	19.8333
CUUCUUUU	chr6:112670502-112670783(-)$1	281	252	260	15.2500
UUUUUUUU	chr6:72560301-72560572(-)$1	271	126	134	16.8333
UUUAUUUU	chr1:129700613-129700886(+)$1	273	41	49	16.6666
UUUCUUUU	chr1:95303823-95304118(-)$1	295	171	179	19.8333
UUUAUUUU	chr2:109738100-109738373(+)$1	273	17	25	16.6666
uuucuuug	chr13:67440205-67440482(-)$1	277	79	87	15.6666
UUUGUUUU	chr2:91758798-91759071(+)$1	273	66	74	17.0000
UUUCUUUU	chr10:127569456-127569736(-)$1	280	49	57	19.8333
UUUGUUUU	chr1:183746754-183747041(-)$1	287	143	151	17.0000
UUUCUUGU	chr14:65672501-65672779(-)$1	278	119	127	15.7500
cuucuuuu	chr8:72285561-72285837(-)$1	276	100	108	15.2500
UAUCUUUU	chr2:37228044-37228335(-)$1	291	86	94	15.0833
UUUAUUUU	chr5:28742590-28742864(+)$1	274	175	183	16.6666
UUUGUUUU	chr3:105771857-105772168(+)$1	311	51	59	17.0000
UUUCUUUA	chr5:65987813-65988093(+)$1	280	21	29	15.5000
uuucuuuu	chr6:147060392-147060664(+)$1	272	68	76	19.8333
UUUCUUUG	chr5:104282980-104283280(+)$1	300	281	289	15.6666
UUCCUUUU	chr10:67008898-67009172(-)$1	274	117	125	15.6666
uuuguuuu	chr1:163020065-163020341(-)$1	276	27	35	17.0000
GUUCUUUU	chr17:29179708-29180012(+)$1	304	6	14	15.1666
UUCCUUUU	chr16:44159818-44160109(+)$1	291	34	42	15.6666
UUUCUCUU	chrX:55294575-55294853(+)$1	278	36	44	15.3333
UUUCUAUU	chr9:82763208-82763480(-)$1	272	209	217	15.3333
UUUCUGUU	chr2:84550426-84550714(-)$1	288	19	27	15.5000
UUUCUUGU	chr2:154363886-154364181(+)$1	295	108	116	15.7500
UUUCUUCU	chrX:35916950-35917237(-)$1	287	278	286	15.9166
UUUCUUUA	chr15:81195420-81195708(-)$1	288	101	109	15.5000
UUUCUUCU	chr1:34873976-34874265(-)$1	289	93	101	15.9166
UUUCUUCU	chr15:103025644-103025939(-)$1	295	173	181	15.9166
UUUCUUCU	chr11:77679022-77679301(+)$1	279	202	210	15.9166
UUUCUGUU	chr6:86376515-86376834(+)$1	319	80	88	15.5000
UUUCUUUG	chr3:32236611-32236886(-)$1	275	72	80	15.6666
uuuuuuuu	chr13:45015540-45015819(+)$1	279	55	63	16.8333
UUGCUUUU	chr17:37185909-37186253(+)$1	344	262	270	15.6666
UUUCUUUG	chr3:33708723-33709001(+)$1	278	171	179	15.6666
uuuguuuu	chr11:68800501-68800769(-)$1	268	34	42	17.0000
uuucuuuu	chr5:93602489-93602760(+)$1	271	188	196	19.8333
UUUCUUCU	chr9:106594464-106594808(-)$1	344	25	33	15.9166
UUUCUUUU	chr11:101149590-101149881(-)$1	291	9	17	19.8333
UUuuuuuu	chr2:168574889-168575185(-)$1	296	216	224	16.8333
UUUCUUUU	chr16:17259583-17259910(+)$1	327	287	295	19.8333
UUGCUUUU	chr5:97811604-97811888(-)$1	284	39	47	15.6666

#otherMatches

#Struct PSSM
qqqdddd:	chr13:99614299-99614600(-)$1	301	10	18	17.0000
mdddd333	chr7:13393997-13394269(-)$1	272	88	96	19.8333
JJJJJ:::	chr18:38000457-38000731(+)$1	274	27	35	17.0000
ddddmmmm	chr3:87973067-87973400(+)$1	333	249	257	15.0000
::::iiii	chr10:93432273-93432550(-)$1	277	52	60	16.6666
ffffrrrr	chr15:96245044-96245315(-)$1	271	211	219	16.8333
eeeooooo	chr3:129338274-129338552(+)$1	278	9	17	16.8333
ddddmmmm	chrX:35886358-35886636(-)$1	278	91	99	15.6666
ff[ccc""	chr2:138112183-138112454(+)$1	271	112	120	15.5000
ppppppdd	chr2:153596149-153596431(+)$1	282	166	174	19.8333
b]ccc]bb	chr16:8688742-8689018(-)$1	276	218	226	15.7500
HH::gggg	chr17:64306424-64306719(+)$1	295	34	42	15.6666
%=======	chr8:109897859-109898147(+)$1	288	76	84	15.5000
eeee::::	chr11:33373097-33373373(-)$1	276	153	161	16.8333
ee]a::::	chr2:130851818-130852094(+)$1	276	267	275	15.0833
::::::::	chr3:94992308-94992580(-)$1	272	246	254	19.8333
f$$$$$dd	chr5:115691748-115692023(-)$1	275	75	83	17.0000
22ccc999	chr4:59488510-59488796(-)$1	286	212	220	19.8333
ooooooff	chr6:112670502-112670783(-)$1	281	252	260	15.2500
:::::::c	chr6:72560301-72560572(-)$1	271	126	134	16.8333
3ggggggg	chr1:129700613-129700886(+)$1	273	41	49	16.6666
''''''''	chr1:95303823-95304118(-)$1	295	171	179	19.8333
::EEEEEK	chr2:109738100-109738373(+)$1	273	17	25	16.6666
44dddd]h	chr13:67440205-67440482(-)$1	277	79	87	15.6666
!!hhhhhh	chr2:91758798-91759071(+)$1	273	66	74	17.0000
>>>>>>>>	chr10:127569456-127569736(-)$1	280	49	57	19.8333
iiiiiii8	chr1:183746754-183747041(-)$1	287	143	151	17.0000
=======m	chr14:65672501-65672779(-)$1	278	119	127	15.7500
pppppppd	chr8:72285561-72285837(-)$1	276	100	108	15.2500
::::::::	chr2:37228044-37228335(-)$1	291	86	94	15.0833
:::::::E	chr5:28742590-28742864(+)$1	274	175	183	16.6666
""gggggg	chr3:105771857-105772168(+)$1	311	51	59	17.0000
ee"""ggg	chr5:65987813-65988093(+)$1	280	21	29	15.5000
EEEEJJJJ	chr6:147060392-147060664(+)$1	272	68	76	19.8333
GGGGGZZZ	chr5:104282980-104283280(+)$1	300	281	289	15.6666
ddd!!bb"	chr10:67008898-67009172(-)$1	274	117	125	15.6666
JJJJJJJJ	chr1:163020065-163020341(-)$1	276	27	35	17.0000
LLLEEEEE	chr17:29179708-29180012(+)$1	304	6	14	15.1666
::::::::	chr16:44159818-44160109(+)$1	291	34	42	15.6666
odddd:::	chrX:55294575-55294853(+)$1	278	36	44	15.3333
f:::::::	chr9:82763208-82763480(-)$1	272	209	217	15.3333
uuuuuccc	chr2:84550426-84550714(-)$1	288	19	27	15.5000
eeeee[a!	chr2:154363886-154364181(+)$1	295	108	116	15.7500
YYFFFFFF	chrX:35916950-35917237(-)$1	287	278	286	15.9166
g[eeeee[	chr15:81195420-81195708(-)$1	288	101	109	15.5000
hhhhhh[c	chr1:34873976-34874265(-)$1	289	93	101	15.9166
33dddd22	chr15:103025644-103025939(-)$1	295	173	181	15.9166
e]hhhhhh	chr11:77679022-77679301(+)$1	279	202	210	15.9166
&&ccc[hh	chr6:86376515-86376834(+)$1	319	80	88	15.5000
pppppppc	chr3:32236611-32236886(-)$1	275	72	80	15.6666
JJJJJJJJ	chr13:45015540-45015819(+)$1	279	55	63	16.8333
eee55555	chr17:37185909-37186253(+)$1	344	262	270	15.6666
^^^^^^^^	chr3:33708723-33709001(+)$1	278	171	179	15.6666
QQQQQQQQ	chr11:68800501-68800769(-)$1	268	34	42	17.0000
yyyccc33	chr5:93602489-93602760(+)$1	271	188	196	19.8333
EEEE{CCC	chr9:106594464-106594808(-)$1	344	25	33	15.9166
GPPPPPPP	chr11:101149590-101149881(-)$1	291	9	17	19.8333
========	chr2:168574889-168575185(-)$1	296	216	224	16.8333
::::::::	chr16:17259583-17259910(+)$1	327	287	295	19.8333
dddd$$$$	chr5:97811604-97811888(-)$1	284	39	47	15.6666

#DB
...)))).	chr13:99614299-99614600(-)$1	1	10	18	17.0000
.))))...	chr7:13393997-13394269(-)$1	1	88	96	19.8333
(((((...	chr18:38000457-38000731(+)$1	1	27	35	17.0000
((((....	chr3:87973067-87973400(+)$1	1	249	257	15.0000
....((((	chr10:93432273-93432550(-)$1	1	52	60	16.6666
((((....	chr15:96245044-96245315(-)$1	1	211	219	16.8333
(((.....	chr3:129338274-129338552(+)$1	1	9	17	16.8333
((((....	chrX:35886358-35886636(-)$1	1	91	99	15.6666
((.(((..	chr2:138112183-138112454(+)$1	1	112	120	15.5000
......))	chr2:153596149-153596431(+)$1	1	166	174	19.8333
).))).))	chr16:8688742-8689018(-)$1	1	218	226	15.7500
((..((((	chr17:64306424-64306719(+)$1	1	34	42	15.6666
.(((((((	chr8:109897859-109898147(+)$1	1	76	84	15.5000
))))....	chr11:33373097-33373373(-)$1	1	153	161	16.8333
)).)....	chr2:130851818-130852094(+)$1	1	267	275	15.0833
........	chr3:94992308-94992580(-)$1	1	246	254	19.8333
(.....((	chr5:115691748-115692023(-)$1	1	75	83	17.0000
..)))...	chr4:59488510-59488796(-)$1	1	212	220	19.8333
......))	chr6:112670502-112670783(-)$1	1	252	260	15.2500
.......(	chr6:72560301-72560572(-)$1	1	126	134	16.8333
.)))))))	chr1:129700613-129700886(+)$1	1	41	49	16.6666
........	chr1:95303823-95304118(-)$1	1	171	179	19.8333
..(((((.	chr2:109738100-109738373(+)$1	1	17	25	16.6666
..)))).)	chr13:67440205-67440482(-)$1	1	79	87	15.6666
..((((((	chr2:91758798-91759071(+)$1	1	66	74	17.0000
........	chr10:127569456-127569736(-)$1	1	49	57	19.8333
))))))).	chr1:183746754-183747041(-)$1	1	143	151	17.0000
(((((((.	chr14:65672501-65672779(-)$1	1	119	127	15.7500
.......)	chr8:72285561-72285837(-)$1	1	100	108	15.2500
........	chr2:37228044-37228335(-)$1	1	86	94	15.0833
.......)	chr5:28742590-28742864(+)$1	1	175	183	16.6666
..((((((	chr3:105771857-105772168(+)$1	1	51	59	17.0000
((...(((	chr5:65987813-65988093(+)$1	1	21	29	15.5000
((((((((	chr6:147060392-147060664(+)$1	1	68	76	19.8333
)))))...	chr5:104282980-104283280(+)$1	1	281	289	15.6666
(((..((.	chr10:67008898-67009172(-)$1	1	117	125	15.6666
((((((((	chr1:163020065-163020341(-)$1	1	27	35	17.0000
...(((((	chr17:29179708-29180012(+)$1	1	6	14	15.1666
........	chr16:44159818-44160109(+)$1	1	34	42	15.6666
.))))...	chrX:55294575-55294853(+)$1	1	36	44	15.3333
).......	chr9:82763208-82763480(-)$1	1	209	217	15.3333
.....)))	chr2:84550426-84550714(-)$1	1	19	27	15.5000
(((((.(.	chr2:154363886-154364181(+)$1	1	108	116	15.7500
..))))))	chrX:35916950-35917237(-)$1	1	278	286	15.9166
(.(((((.	chr15:81195420-81195708(-)$1	1	101	109	15.5000
((((((.(	chr1:34873976-34874265(-)$1	1	93	101	15.9166
..))))..	chr15:103025644-103025939(-)$1	1	173	181	15.9166
).))))))	chr11:77679022-77679301(+)$1	1	202	210	15.9166
..(((.((	chr6:86376515-86376834(+)$1	1	80	88	15.5000
.......)	chr3:32236611-32236886(-)$1	1	72	80	15.6666
((((((((	chr13:45015540-45015819(+)$1	1	55	63	16.8333
))).....	chr17:37185909-37186253(+)$1	1	262	270	15.6666
........	chr3:33708723-33709001(+)$1	1	171	179	15.6666
........	chr11:68800501-68800769(-)$1	1	34	42	17.0000
...)))..	chr5:93602489-93602760(+)$1	1	188	196	19.8333
((((.(((	chr9:106594464-106594808(-)$1	1	25	33	15.9166
(.......	chr11:101149590-101149881(-)$1	1	9	17	19.8333
((((((((	chr2:168574889-168575185(-)$1	1	216	224	16.8333
........	chr16:17259583-17259910(+)$1	1	287	295	19.8333
((((....	chr5:97811604-97811888(-)$1	1	39	47	15.6666

#PSSM
U : 0.81	u : 0.13	C : 0.01	c : 0.01	G : 0.01	
U : 0.81	u : 0.15	G : 0.01	A : 0.01	
U : 0.71	u : 0.16	C : 0.05	G : 0.05	A : 0.01	
C : 0.63	G : 0.09	A : 0.06	u : 0.06	c : 0.06	U : 0.03	g : 0.03	
U : 0.81	u : 0.16	C : 0.01	
U : 0.75	u : 0.16	G : 0.05	C : 0.01	A : 0.01	
U : 0.70	u : 0.16	C : 0.08	G : 0.05	
U : 0.75	u : 0.15	G : 0.05	A : 0.03	g : 0.01	

#score	1000.0000000000003
#seq	60
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m3_run2.nuc.txt

#NT
GAGAA	chrX:10172302-10172582(+)$1	280	172	177	14.9999
gagaa	chr13:67141249-67141522(-)$1	273	17	22	14.9999
GAGAA	chr9:58498977-58499242(+)$1	265	132	137	14.9999
GAGAA	chr18:35005964-35006344(+)$1	380	11	16	14.9999
GAGAA	chrX:71475908-71476194(-)$1	286	236	241	14.9999
GAGAA	chr3:107880421-107880731(-)$1	310	194	199	14.9999
GAGAA	chr9:58337971-58338304(+)$1	333	193	198	14.9999
GAGAA	chr13:118764021-118764296(+)$1	275	105	110	14.9999
GAGAA	chr10:98485405-98485751(+)$1	346	81	86	14.9999
GAGAA	chr8:86519204-86519653(+)$1	449	79	84	14.9999
GAGAA	chrX:100380902-100381191(-)$1	289	227	232	14.9999
GAGAA	chr7:95223031-95223340(+)$1	309	158	163	14.9999
GAGAA	chr9:64928507-64928834(+)$1	327	73	78	14.9999
GAGAA	chr4:98891026-98891313(+)$1	287	177	182	14.9999
GAGAA	chr9:14114588-14114874(+)$1	286	13	18	14.9999
GAGAA	chr4:34716189-34716451(-)$1	262	133	138	14.9999
GAGAA	chr8:69413297-69413557(+)$1	260	138	143	14.9999
GAGAA	chr9:115161643-115161907(-)$1	264	136	141	14.9999
GAGAA	chr1:108235955-108236223(+)$1	268	185	190	14.9999
GAGAA	chr17:88396808-88397079(-)$1	271	131	136	14.9999
GAGAA	chr2:164620989-164621258(-)$1	269	242	247	14.9999
GAGAA	chr15:57885239-57885501(-)$1	262	150	155	14.9999
GAGAA	chr19:58527548-58527830(-)$1	282	128	133	14.9999
GAGAA	chr5:58112926-58113264(+)$1	338	321	326	14.9999
GAGAA	chr4:147519130-147519402(+)$1	272	193	198	14.9999
GAGAA	chr7:151638273-151638714(-)$1	441	240	245	14.9999
GAGAA	chr13:100205010-100205321(-)$1	311	21	26	14.9999
GAGAA	chr11:20124692-20125098(+)$1	406	93	98	14.9999
GAGAA	chr3:94305986-94306251(-)$1	265	150	155	14.9999
GAGAA	chr10:5098125-5098429(+)$1	304	61	66	14.9999
GAGAA	chr12:45671092-45671407(+)$1	315	238	243	14.9999
GAGAA	chr6:17615205-17615637(+)$1	432	101	106	14.9999
GAGAA	chrX:92246405-92246796(-)$1	391	75	80	14.9999
GAGAA	chr11:104189388-104189713(+)$1	325	144	149	14.9999
GAGAA	chr6:85570052-85570366(+)$1	314	166	171	14.9999
GAGAA	chr5:123250250-123250582(-)$1	332	173	178	14.9999
GAGAA	chr7:52631857-52632197(-)$1	340	195	200	14.9999
GAGAA	chr15:34044433-34044706(+)$1	273	149	154	14.9999
GAGAA	chr17:78780867-78781117(-)$1	250	130	135	14.9999
GAGAA	chr18:12878431-12878736(+)$1	305	129	134	14.9999
GAGAA	chr11:52216633-52216899(+)$1	266	36	41	14.9999
GAGAA	chr11:118164785-118165132(-)$1	347	41	46	14.9999
GAGAA	chr8:83224772-83225065(-)$1	293	12	17	14.9999
GAGAA	chr2:180816909-180817230(-)$1	321	184	189	14.9999
GAGAA	chr2:132123267-132123531(+)$1	264	57	62	14.9999
GAGAA	chr5:115795560-115796010(-)$1	450	160	165	14.9999
GAGAA	chr7:67131423-67131866(-)$1	443	164	169	14.9999
GAGAA	chr7:67132193-67132552(-)$1	359	171	176	14.9999
GAGAA	chr6:52715947-52716237(+)$1	290	233	238	14.9999
GAGAA	chr11:29606801-29607146(+)$1	345	312	317	14.9999
GAGAA	chr1:133253163-133253460(-)$1	297	44	49	14.9999
GAGAA	chr18:82723822-82724244(+)$1	422	337	342	14.9999
GAGAA	chr1:181718324-181718615(-)$1	291	275	280	14.9999

#otherMatches

#Struct PSSM
gg]ae	chr5:99426312-99426563(-)$1	251	33	38	14.9999
iiiii	chrX:10172302-10172582(+)$1	280	172	177	14.9999
d[fff	chr13:67141249-67141522(-)$1	273	17	22	14.9999
ddd##	chr9:58498977-58499242(+)$1	265	132	137	14.9999
KKCCC	chr18:35005964-35006344(+)$1	380	11	16	14.9999
eeee!	chrX:71475908-71476194(-)$1	286	236	241	14.9999
:::ee	chr3:107880421-107880731(-)$1	310	194	199	14.9999
/////	chr9:58337971-58338304(+)$1	333	193	198	14.9999
77777	chr13:118764021-118764296(+)$1	275	105	110	14.9999
CCCKK	chr10:98485405-98485751(+)$1	346	81	86	14.9999
A{DDD	chr8:86519204-86519653(+)$1	449	79	84	14.9999
::ddd	chrX:100380902-100381191(-)$1	289	227	232	14.9999
:::ee	chr7:95223031-95223340(+)$1	309	158	163	14.9999
EEE{B	chr9:64928507-64928834(+)$1	327	73	78	14.9999
fffff	chr4:98891026-98891313(+)$1	287	177	182	14.9999
OOOOO	chr9:14114588-14114874(+)$1	286	13	18	14.9999
zzzzz	chr4:34716189-34716451(-)$1	262	133	138	14.9999
CCC::	chr8:69413297-69413557(+)$1	260	138	143	14.9999
ibb::	chr9:115161643-115161907(-)$1	264	136	141	14.9999
hhhGG	chr1:108235955-108236223(+)$1	268	185	190	14.9999
c::::	chr17:88396808-88397079(-)$1	271	131	136	14.9999
ccc::	chr2:164620989-164621258(-)$1	269	242	247	14.9999
::ccc	chr15:57885239-57885501(-)$1	262	150	155	14.9999
ddd]c	chr19:58527548-58527830(-)$1	282	128	133	14.9999
dd333	chr5:58112926-58113264(+)$1	338	321	326	14.9999
ccccc	chr4:147519130-147519402(+)$1	272	193	198	14.9999
b[fff	chr7:151638273-151638714(-)$1	441	240	245	14.9999
EEE{D	chr13:100205010-100205321(-)$1	311	21	26	14.9999
!!bbx	chr11:20124692-20125098(+)$1	406	93	98	14.9999
ee[bb	chr3:94305986-94306251(-)$1	265	150	155	14.9999
cpppp	chr10:5098125-5098429(+)$1	304	61	66	14.9999
ccc44	chr12:45671092-45671407(+)$1	315	238	243	14.9999
eeeee	chr6:17615205-17615637(+)$1	432	101	106	14.9999
cc]a]	chrX:92246405-92246796(-)$1	391	75	80	14.9999
DBBKK	chr11:104189388-104189713(+)$1	325	144	149	14.9999
EEEEE	chr6:85570052-85570366(+)$1	314	166	171	14.9999
\\\\\	chr5:123250250-123250582(-)$1	332	173	178	14.9999
ddrrr	chr7:52631857-52632197(-)$1	340	195	200	14.9999
&&&&&	chr15:34044433-34044706(+)$1	273	149	154	14.9999
ii]bb	chr17:78780867-78781117(-)$1	250	130	135	14.9999
eeeee	chr18:12878431-12878736(+)$1	305	129	134	14.9999
gg'''	chr11:52216633-52216899(+)$1	266	36	41	14.9999
ppppp	chr11:118164785-118165132(-)$1	347	41	46	14.9999
ddddd	chr8:83224772-83225065(-)$1	293	12	17	14.9999
wwwww	chr2:180816909-180817230(-)$1	321	184	189	14.9999
hhhhh	chr2:132123267-132123531(+)$1	264	57	62	14.9999
:::::	chr5:115795560-115796010(-)$1	450	160	165	14.9999
OOOOO	chr7:67131423-67131866(-)$1	443	164	169	14.9999
::::f	chr7:67132193-67132552(-)$1	359	171	176	14.9999
FFFFF	chr6:52715947-52716237(+)$1	290	233	238	14.9999
b5555	chr11:29606801-29607146(+)$1	345	312	317	14.9999
c::::	chr1:133253163-133253460(-)$1	297	44	49	14.9999
"""ee	chr18:82723822-82724244(+)$1	422	337	342	14.9999
dddd:	chr1:181718324-181718615(-)$1	291	275	280	14.9999

#DB
)).))	chr5:99426312-99426563(-)$1	1	33	38	14.9999
)))))	chrX:10172302-10172582(+)$1	1	172	177	14.9999
(.(((	chr13:67141249-67141522(-)$1	1	17	22	14.9999
(((..	chr9:58498977-58499242(+)$1	1	132	137	14.9999
..(((	chr18:35005964-35006344(+)$1	1	11	16	14.9999
((((.	chrX:71475908-71476194(-)$1	1	236	241	14.9999
...((	chr3:107880421-107880731(-)$1	1	194	199	14.9999
.....	chr9:58337971-58338304(+)$1	1	193	198	14.9999
.....	chr13:118764021-118764296(+)$1	1	105	110	14.9999
(((..	chr10:98485405-98485751(+)$1	1	81	86	14.9999
(.(((	chr8:86519204-86519653(+)$1	1	79	84	14.9999
..(((	chrX:100380902-100381191(-)$1	1	227	232	14.9999
...((	chr7:95223031-95223340(+)$1	1	158	163	14.9999
(((.(	chr9:64928507-64928834(+)$1	1	73	78	14.9999
(((((	chr4:98891026-98891313(+)$1	1	177	182	14.9999
.....	chr9:14114588-14114874(+)$1	1	13	18	14.9999
.....	chr4:34716189-34716451(-)$1	1	133	138	14.9999
(((..	chr8:69413297-69413557(+)$1	1	138	143	14.9999
)))..	chr9:115161643-115161907(-)$1	1	136	141	14.9999
)))))	chr1:108235955-108236223(+)$1	1	185	190	14.9999
)....	chr17:88396808-88397079(-)$1	1	131	136	14.9999
)))..	chr2:164620989-164621258(-)$1	1	242	247	14.9999
..(((	chr15:57885239-57885501(-)$1	1	150	155	14.9999
))).)	chr19:58527548-58527830(-)$1	1	128	133	14.9999
))...	chr5:58112926-58113264(+)$1	1	321	326	14.9999
)))((	chr4:147519130-147519402(+)$1	1	193	198	14.9999
(.(((	chr7:151638273-151638714(-)$1	1	240	245	14.9999
(((.(	chr13:100205010-100205321(-)$1	1	21	26	14.9999
..((.	chr11:20124692-20125098(+)$1	1	93	98	14.9999
((.((	chr3:94305986-94306251(-)$1	1	150	155	14.9999
(....	chr10:5098125-5098429(+)$1	1	61	66	14.9999
)))..	chr12:45671092-45671407(+)$1	1	238	243	14.9999
)))))	chr6:17615205-17615637(+)$1	1	101	106	14.9999
)).).	chrX:92246405-92246796(-)$1	1	75	80	14.9999
(((..	chr11:104189388-104189713(+)$1	1	144	149	14.9999
(((((	chr6:85570052-85570366(+)$1	1	166	171	14.9999
.....	chr5:123250250-123250582(-)$1	1	173	178	14.9999
((...	chr7:52631857-52632197(-)$1	1	195	200	14.9999
.....	chr15:34044433-34044706(+)$1	1	149	154	14.9999
)).))	chr17:78780867-78781117(-)$1	1	130	135	14.9999
)))))	chr18:12878431-12878736(+)$1	1	129	134	14.9999
((...	chr11:52216633-52216899(+)$1	1	36	41	14.9999
.....	chr11:118164785-118165132(-)$1	1	41	46	14.9999
(((((	chr8:83224772-83225065(-)$1	1	12	17	14.9999
.....	chr2:180816909-180817230(-)$1	1	184	189	14.9999
(((((	chr2:132123267-132123531(+)$1	1	57	62	14.9999
.....	chr5:115795560-115796010(-)$1	1	160	165	14.9999
.....	chr7:67131423-67131866(-)$1	1	164	169	14.9999
....(	chr7:67132193-67132552(-)$1	1	171	176	14.9999
)))))	chr6:52715947-52716237(+)$1	1	233	238	14.9999
)....	chr11:29606801-29607146(+)$1	1	312	317	14.9999
)....	chr1:133253163-133253460(-)$1	1	44	49	14.9999
...((	chr18:82723822-82724244(+)$1	1	337	342	14.9999
)))).	chr1:181718324-181718615(-)$1	1	275	280	14.9999

#PSSM
G : 0.98	g : 0.01	
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	809.9999999999995
#seq	54
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m2_run2.nuc.txt

#NT
UUUGG	chr13:5869145-5869418(+)$1	273	17	22	15.0000
UUUGG	chr11:68923114-68923385(+)$1	271	90	95	15.0000
UUUGG	chr19:8964904-8965185(+)$1	281	153	158	15.0000
UUUGG	chr4:140669579-140669861(-)$1	282	64	69	15.0000
UUUGG	chr15:44595258-44595531(-)$1	273	50	55	15.0000
UUUGG	chr17:47760163-47760455(+)$1	292	4	9	15.0000
UUUGG	chr17:34791783-34792075(+)$1	292	104	109	15.0000
UUUGG	chr11:69813266-69813543(+)$1	277	65	70	15.0000
UUUGG	chr13:73773815-73774087(+)$1	272	176	181	15.0000
UUUGG	chr7:25670028-25670303(+)$1	275	28	33	15.0000
UUUGG	chr3:145309908-145310184(-)$1	276	129	134	15.0000
UUUGG	chrX:11614171-11614458(-)$1	287	118	123	15.0000
uuugg	chr2:152654216-152654493(-)$1	277	107	112	15.0000
UUUGG	chr12:8798840-8799138(+)$1	298	98	103	15.0000
UUUGG	chr3:154259844-154260111(-)$1	267	21	26	15.0000
UUUGG	chr4:83921320-83921603(-)$1	283	127	132	15.0000
UUUGG	chr4:140884838-140885115(+)$1	277	16	21	15.0000
UUUGG	chr6:30079454-30079738(+)$1	284	107	112	15.0000
UUUGG	chr15:101926291-101926563(+)$1	272	122	127	15.0000
UUUGG	chr14:65431215-65431492(-)$1	277	144	149	15.0000
UUUGG	chr15:75900547-75900820(-)$1	273	64	69	15.0000
uuugg	chr10:86297943-86298211(+)$1	268	50	55	15.0000
UUUGG	chr16:92085376-92085654(+)$1	278	73	78	15.0000
UUUGG	chr2:34678076-34678352(-)$1	276	96	101	15.0000
UUUGG	chr3:32240109-32240398(-)$1	289	155	160	15.0000
UUUGG	chr10:76508552-76508827(+)$1	275	18	23	15.0000
UUUGG	chr15:81535366-81535645(-)$1	279	183	188	15.0000
UUUGG	chr3:105771255-105771551(+)$1	296	283	288	15.0000
UUUGG	chr10:20845086-20845380(-)$1	294	255	260	15.0000
UUUGG	chr17:35119051-35119331(+)$1	280	157	162	15.0000
UUUGG	chr5:138223097-138223399(-)$1	302	144	149	15.0000
UUUGG	chr5:37138897-37139188(-)$1	291	144	149	15.0000
UUUGG	chr9:90098128-90098412(-)$1	284	203	208	15.0000
UUUGG	chr2:31071139-31071424(+)$1	285	258	263	15.0000
UUUGG	chr5:116859149-116859423(-)$1	274	21	26	15.0000
UUUGG	chr5:137967090-137967377(+)$1	287	130	135	15.0000
UUUGG	chr11:52221422-52221709(+)$1	287	139	144	15.0000
UUUGG	chr16:91227775-91228057(+)$1	282	52	57	15.0000
UUUGG	chr7:107985088-107985371(+)$1	283	27	32	15.0000
UUUGG	chr15:98734275-98734547(-)$1	272	105	110	15.0000
UUUGG	chr8:125096582-125096860(+)$1	278	100	105	15.0000
UUUGG	chr3:87340637-87340930(+)$1	293	154	159	15.0000
UUUGG	chr4:49669033-49669317(+)$1	284	127	132	15.0000
UUUGG	chr2:32134292-32134583(-)$1	291	122	127	15.0000
UUUGG	chr11:52221498-52221774(+)$1	276	63	68	15.0000
UUUGG	chr19:46147231-46147502(+)$1	271	76	81	15.0000
UUUGG	chr2:32162879-32163158(+)$1	279	178	183	15.0000
UUUGG	chr11:114729900-114730186(+)$1	286	147	152	15.0000
UUUGG	chr1:64840465-64840739(-)$1	274	135	140	15.0000
UUUGG	chr15:81678793-81679067(-)$1	274	246	251	15.0000

#otherMatches

#Struct PSSM
c]ggg	chr8:109599382-109599653(-)$1	271	122	127	15.0000
JJJJ:	chr13:5869145-5869418(+)$1	273	17	22	15.0000
::hhh	chr11:68923114-68923385(+)$1	271	90	95	15.0000
JJJJJ	chr19:8964904-8965185(+)$1	281	153	158	15.0000
eee!!	chr4:140669579-140669861(-)$1	282	64	69	15.0000
:::CC	chr15:44595258-44595531(-)$1	273	50	55	15.0000
ff[cc	chr17:47760163-47760455(+)$1	292	4	9	15.0000
nnnnc	chr17:34791783-34792075(+)$1	292	104	109	15.0000
eeeee	chr11:69813266-69813543(+)$1	277	65	70	15.0000
fffff	chr13:73773815-73774087(+)$1	272	176	181	15.0000
{GGGG	chr7:25670028-25670303(+)$1	275	28	33	15.0000
ddduu	chr3:145309908-145310184(-)$1	276	129	134	15.0000
FFFFF	chrX:11614171-11614458(-)$1	287	118	123	15.0000
:::hh	chr2:152654216-152654493(-)$1	277	107	112	15.0000
!!ccc	chr12:8798840-8799138(+)$1	298	98	103	15.0000
EEEEC	chr3:154259844-154260111(-)$1	267	21	26	15.0000
tttii	chr4:83921320-83921603(-)$1	283	127	132	15.0000
ggggg	chr4:140884838-140885115(+)$1	277	16	21	15.0000
:::EE	chr6:30079454-30079738(+)$1	284	107	112	15.0000
ee:::	chr15:101926291-101926563(+)$1	272	122	127	15.0000
!!ccc	chr14:65431215-65431492(-)$1	277	144	149	15.0000
qqqqq	chr15:75900547-75900820(-)$1	273	64	69	15.0000
JJJdd	chr10:86297943-86298211(+)$1	268	50	55	15.0000
vvvvv	chr16:92085376-92085654(+)$1	278	73	78	15.0000
:::::	chr2:34678076-34678352(-)$1	276	96	101	15.0000
iiii:	chr3:32240109-32240398(-)$1	289	155	160	15.0000
d[fff	chr10:76508552-76508827(+)$1	275	18	23	15.0000
ZZFFF	chr15:81535366-81535645(-)$1	279	183	188	15.0000
eeeeC	chr3:105771255-105771551(+)$1	296	283	288	15.0000
GGGGG	chr10:20845086-20845380(-)$1	294	255	260	15.0000
eee""	chr17:35119051-35119331(+)$1	280	157	162	15.0000
=22bb	chr5:138223097-138223399(-)$1	302	144	149	15.0000
9999=	chr5:37138897-37139188(-)$1	291	144	149	15.0000
eeeee	chr9:90098128-90098412(-)$1	284	203	208	15.0000
hhlll	chr2:31071139-31071424(+)$1	285	258	263	15.0000
G{HHH	chr5:116859149-116859423(-)$1	274	21	26	15.0000
!cccm	chr5:137967090-137967377(+)$1	287	130	135	15.0000
ccc''	chr11:52221422-52221709(+)$1	287	139	144	15.0000
d]a]c	chr16:91227775-91228057(+)$1	282	52	57	15.0000
GGGGG	chr7:107985088-107985371(+)$1	283	27	32	15.0000
ggggg	chr15:98734275-98734547(-)$1	272	105	110	15.0000
ceeee	chr8:125096582-125096860(+)$1	278	100	105	15.0000
:::ee	chr3:87340637-87340930(+)$1	293	154	159	15.0000
eeeff	chr4:49669033-49669317(+)$1	284	127	132	15.0000
lffff	chr2:32134292-32134583(-)$1	291	122	127	15.0000
ddccc	chr11:52221498-52221774(+)$1	276	63	68	15.0000
ddd]a	chr19:46147231-46147502(+)$1	271	76	81	15.0000
ooocc	chr2:32162879-32163158(+)$1	279	178	183	15.0000
fffpp	chr11:114729900-114730186(+)$1	286	147	152	15.0000
d22==	chr1:64840465-64840739(-)$1	274	135	140	15.0000
ggggg	chr15:81678793-81679067(-)$1	274	246	251	15.0000

#DB
).)))	chr8:109599382-109599653(-)$1	1	122	127	15.0000
((((.	chr13:5869145-5869418(+)$1	1	17	22	15.0000
..(((	chr11:68923114-68923385(+)$1	1	90	95	15.0000
)))))	chr19:8964904-8965185(+)$1	1	153	158	15.0000
(((..	chr4:140669579-140669861(-)$1	1	64	69	15.0000
...((	chr15:44595258-44595531(-)$1	1	50	55	15.0000
((.((	chr17:47760163-47760455(+)$1	1	4	9	15.0000
....)	chr17:34791783-34792075(+)$1	1	104	109	15.0000
(((((	chr11:69813266-69813543(+)$1	1	65	70	15.0000
(((((	chr13:73773815-73774087(+)$1	1	176	181	15.0000
.((((	chr7:25670028-25670303(+)$1	1	28	33	15.0000
(((..	chr3:145309908-145310184(-)$1	1	129	134	15.0000
(((((	chrX:11614171-11614458(-)$1	1	118	123	15.0000
...((	chr2:152654216-152654493(-)$1	1	107	112	15.0000
..(((	chr12:8798840-8799138(+)$1	1	98	103	15.0000
(((((	chr3:154259844-154260111(-)$1	1	21	26	15.0000
...))	chr4:83921320-83921603(-)$1	1	127	132	15.0000
(((((	chr4:140884838-140885115(+)$1	1	16	21	15.0000
...))	chr6:30079454-30079738(+)$1	1	107	112	15.0000
))...	chr15:101926291-101926563(+)$1	1	122	127	15.0000
..(((	chr14:65431215-65431492(-)$1	1	144	149	15.0000
.....	chr15:75900547-75900820(-)$1	1	64	69	15.0000
(((((	chr10:86297943-86298211(+)$1	1	50	55	15.0000
.....	chr16:92085376-92085654(+)$1	1	73	78	15.0000
.....	chr2:34678076-34678352(-)$1	1	96	101	15.0000
)))).	chr3:32240109-32240398(-)$1	1	155	160	15.0000
(.(((	chr10:76508552-76508827(+)$1	1	18	23	15.0000
..)))	chr15:81535366-81535645(-)$1	1	183	188	15.0000
)))))	chr3:105771255-105771551(+)$1	1	283	288	15.0000
)))))	chr10:20845086-20845380(-)$1	1	255	260	15.0000
(((..	chr17:35119051-35119331(+)$1	1	157	162	15.0000
)..))	chr5:138223097-138223399(-)$1	1	144	149	15.0000
....)	chr5:37138897-37139188(-)$1	1	144	149	15.0000
)))))	chr9:90098128-90098412(-)$1	1	203	208	15.0000
((...	chr2:31071139-31071424(+)$1	1	258	263	15.0000
(.(((	chr5:116859149-116859423(-)$1	1	21	26	15.0000
.(((.	chr5:137967090-137967377(+)$1	1	130	135	15.0000
(((..	chr11:52221422-52221709(+)$1	1	139	144	15.0000
).).)	chr16:91227775-91228057(+)$1	1	52	57	15.0000
(((((	chr7:107985088-107985371(+)$1	1	27	32	15.0000
)))))	chr15:98734275-98734547(-)$1	1	105	110	15.0000
(((((	chr8:125096582-125096860(+)$1	1	100	105	15.0000
...((	chr3:87340637-87340930(+)$1	1	154	159	15.0000
)))))	chr4:49669033-49669317(+)$1	1	127	132	15.0000
.))))	chr2:32134292-32134583(-)$1	1	122	127	15.0000
(((((	chr11:52221498-52221774(+)$1	1	63	68	15.0000
))).)	chr19:46147231-46147502(+)$1	1	76	81	15.0000
...))	chr2:32162879-32163158(+)$1	1	178	183	15.0000
(((..	chr11:114729900-114730186(+)$1	1	147	152	15.0000
)..))	chr1:64840465-64840739(-)$1	1	135	140	15.0000
)))))	chr15:81678793-81679067(-)$1	1	246	251	15.0000

#PSSM
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
G : 0.96	g : 0.03	
G : 0.96	g : 0.03	

#score	765.0000000000001
#seq	51
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m3_run1.nuc.txt

#NT
UUGUGUU	chrX:160367336-160367628(+)$1	292	35	42	17.1594
UUGUGUC	chr2:83644051-83644353(+)$1	302	141	148	13.1014
UUGUUUU	chr14:104876649-104876914(-)$1	265	99	106	13.1739
UUGUGUG	chr5:34215053-34215420(+)$1	367	218	225	13.2463
UUCUGUU	chr8:82200817-82201112(+)$1	295	101	108	13.3913
UUGUCUU	chr19:58871633-58872043(-)$1	410	200	207	13.3188
UUGUAUU	chr18:37563065-37563470(+)$1	405	16	23	13.4637
UUGUGUU	chr6:86939916-86940263(+)$1	347	15	22	17.1594
GUGUGUU	chr1:75243512-75243973(-)$1	461	335	342	13.3913
UUGUAUU	chr3:81897166-81897433(-)$1	267	198	205	13.4637
UUUUGUU	chr2:29814502-29814829(+)$1	327	182	189	13.6811
CUGUGUU	chr12:45953487-45953946(-)$1	459	59	66	13.3188
UGGUGUU	chr16:31093832-31094214(-)$1	382	235	242	12.8115
UUGUAUU	chr4:136104701-136105067(+)$1	366	168	175	13.4637
ucguguu	chr5:115625295-115625602(-)$1	307	274	281	12.8115
UCGUGUU	chr12:79785219-79785511(+)$1	292	145	152	12.8115
UUUUGUU	chr2:122420955-122421209(-)$1	254	115	122	13.6811
UUGUGUU	chr8:70217427-70217785(-)$1	358	125	132	17.1594
UUCUGUU	chr6:124909123-124909517(-)$1	394	83	90	13.3913
UUGUGUC	chrX:68673139-68673432(-)$1	293	127	134	13.1014
uuuuguu	chr4:140671143-140671420(-)$1	277	222	229	13.6811
AUGUGUU	chr9:110164694-110165173(+)$1	479	155	162	13.2463
UUGUCUU	chr7:107989523-107989858(+)$1	335	93	100	13.3188
UUAUGUU	chr6:29909446-29909769(+)$1	323	165	172	13.1739
UUGUGUG	chr14:27233631-27233959(-)$1	328	102	109	13.2463
UUUUGUU	chr13:85354692-85355082(-)$1	390	21	28	13.6811
UUGUGUU	chr13:48975469-48975868(-)$1	399	9	16	17.1594
UUUUGUU	chr11:98218932-98219209(+)$1	277	8	15	13.6811
UUGUGUU	chr18:82724548-82724797(+)$1	249	187	194	17.1594
UGGUGUU	chr8:13174580-13174880(+)$1	300	268	275	12.8115
UUGUGUG	chr1:138166148-138166425(-)$1	277	179	186	13.2463
UUCUGUU	chr2:32645531-32645936(-)$1	405	129	136	13.3913
GUGUGUU	chr12:45664862-45665220(+)$1	358	49	56	13.3913
UUGUAUU	chr10:79634192-79634505(+)$1	313	127	134	13.4637
UUGUGUU	chr8:107740524-107740778(+)$1	254	203	210	17.1594
UUGUGUU	chr11:96679246-96679591(-)$1	345	196	203	17.1594
UUGUGUU	chr2:92455224-92455508(+)$1	284	149	156	17.1594
UUGUCUU	chr4:108534338-108534793(+)$1	455	104	111	13.3188
CUGUGUU	chr10:110378828-110379191(-)$1	363	18	25	13.3188
UUUUGUU	chr2:155214476-155214835(+)$1	359	213	220	13.6811
UUGUGUU	chrX:16262375-16262750(+)$1	375	341	348	17.1594
UUUUGUU	chrX:72779458-72779776(+)$1	318	68	75	13.6811
UUGUUUU	chr1:138165918-138166214(-)$1	296	50	57	13.1739
UUGUGUA	chr1:141982738-141982993(-)$1	255	81	88	13.0289
GUGUGUU	chr3:137820632-137820894(+)$1	262	232	239	13.3913
GUGUGUU	chr6:39554716-39555175(-)$1	459	195	202	13.3913
UCGUGUU	chr5:13599906-13600159(+)$1	253	127	134	12.8115
auguguu	chr17:28883385-28883842(+)$1	457	24	31	13.2463
GUGUGUU	chr3:7552752-7553077(+)$1	325	146	153	13.3913
UUGUGUA	chr3:156975933-156976306(+)$1	373	84	91	13.0289
UGGUGUU	chr4:101139408-101139689(+)$1	281	29	36	12.8115
UUGUGUU	chr6:143156874-143157143(+)$1	269	5	12	17.1594
UUGUAUU	chr5:71144677-71144978(-)$1	301	151	158	13.4637
CUGUGUU	chr10:106861139-106861551(+)$1	412	362	369	13.3188
UUGUGUU	chr7:104839471-104839820(+)$1	349	172	179	17.1594
UUGUGUG	chr18:65373663-65373972(+)$1	309	140	147	13.2463
UUGUGUG	chr5:129529993-129530255(+)$1	262	47	54	13.2463
UUUUGUU	chr4:18044418-18044762(+)$1	344	194	201	13.6811
UUGUGUU	chr7:116177152-116177437(+)$1	285	187	194	17.1594
UUGUGUU	chr19:10525749-10526017(+)$1	268	107	114	17.1594
UUGUGUU	chr6:129491349-129491732(+)$1	383	39	46	17.1594
UUGUCUU	chr2:121133985-121134349(+)$1	364	353	360	13.3188
CUGUGUU	chr12:88430821-88431115(+)$1	294	76	83	13.3188
UUGUAUU	chr5:34218839-34219098(+)$1	259	101	108	13.4637
UUGUGUU	chr2:131878131-131878480(-)$1	349	0	7	17.1594
UUCUGUU	chr18:61746921-61747305(+)$1	384	136	143	13.3913
UUGUGUC	chr5:135096351-135096667(-)$1	316	173	180	13.1014
AUGUGUU	chr16:32107957-32108239(+)$1	282	91	98	13.2463

#otherMatches

#Struct PSSM
::ddddh	chr2:167125071-167125342(-)$1	271	192	199	17.1594
JJJJLLL	chrX:160367336-160367628(+)$1	292	35	42	17.1594
iiii!!d	chr2:83644051-83644353(+)$1	302	141	148	13.1014
[ddddpp	chr14:104876649-104876914(-)$1	265	99	106	13.1739
dnnnnnd	chr5:34215053-34215420(+)$1	367	218	225	13.2463
:::::::	chr8:82200817-82201112(+)$1	295	101	108	13.3913
:EEEEEC	chr19:58871633-58872043(-)$1	410	200	207	13.3188
ggggg::	chr18:37563065-37563470(+)$1	405	16	23	13.4637
MMEEEEE	chr6:86939916-86940263(+)$1	347	15	22	17.1594
::ggggg	chr1:75243512-75243973(-)$1	461	335	342	13.3913
[dddd$$	chr3:81897166-81897433(-)$1	267	198	205	13.4637
iiiiiii	chr2:29814502-29814829(+)$1	327	182	189	13.6811
DDD{CCC	chr12:45953487-45953946(-)$1	459	59	66	13.3188
eee]bbb	chr16:31093832-31094214(-)$1	382	235	242	12.8115
fffnnnn	chr4:136104701-136105067(+)$1	366	168	175	13.4637
]bb]ddd	chr5:115625295-115625602(-)$1	307	274	281	12.8115
cc[a[cc	chr12:79785219-79785511(+)$1	292	145	152	12.8115
4hhhhhh	chr2:122420955-122421209(-)$1	254	115	122	13.6811
eeFFFFF	chr8:70217427-70217785(-)$1	358	125	132	17.1594
oeeeeed	chr6:124909123-124909517(-)$1	394	83	90	13.3913
::::eee	chrX:68673139-68673432(-)$1	293	127	134	13.1014
:::gggg	chr4:140671143-140671420(-)$1	277	222	229	13.6811
dddd666	chr9:110164694-110165173(+)$1	479	155	162	13.2463
ff:::::	chr7:107989523-107989858(+)$1	335	93	100	13.3188
G:fffff	chr6:29909446-29909769(+)$1	323	165	172	13.1739
ddddddd	chr14:27233631-27233959(-)$1	328	102	109	13.2463
DDBBKKF	chr13:85354692-85355082(-)$1	390	21	28	13.6811
ff"""ff	chr13:48975469-48975868(-)$1	399	9	16	17.1594
hhhh###	chr11:98218932-98219209(+)$1	277	8	15	13.6811
EEEE}BB	chr18:82724548-82724797(+)$1	249	187	194	17.1594
fffff55	chr8:13174580-13174880(+)$1	300	268	275	12.8115
44dddd]	chr1:138166148-138166425(-)$1	277	179	186	13.2463
:GGGGGG	chr2:32645531-32645936(-)$1	405	129	136	13.3913
D{JJJJJ	chr12:45664862-45665220(+)$1	358	49	56	13.3913
FFFF:::	chr10:79634192-79634505(+)$1	313	127	134	13.4637
ffffff>	chr8:107740524-107740778(+)$1	254	203	210	17.1594
DDFFFFF	chr11:96679246-96679591(-)$1	345	196	203	17.1594
eeee]dd	chr2:92455224-92455508(+)$1	284	149	156	17.1594
ggg22hh	chr4:108534338-108534793(+)$1	455	104	111	13.3188
eee]eee	chr10:110378828-110379191(-)$1	363	18	25	13.3188
mmmffff	chr2:155214476-155214835(+)$1	359	213	220	13.6811
::DDDD}	chrX:16262375-16262750(+)$1	375	341	348	17.1594
::iiiii	chrX:72779458-72779776(+)$1	318	68	75	13.6811
DDDhhhh	chr1:138165918-138166214(-)$1	296	50	57	13.1739
''fffff	chr1:141982738-141982993(-)$1	255	81	88	13.0289
fffff::	chr3:137820632-137820894(+)$1	262	232	239	13.3913
iiiiiii	chr6:39554716-39555175(-)$1	459	195	202	13.3913
eeeeeee	chr5:13599906-13600159(+)$1	253	127	134	12.8115
iiissss	chr17:28883385-28883842(+)$1	457	24	31	13.2463
qqqbb]d	chr3:7552752-7553077(+)$1	325	146	153	13.3913
JJJJJJJ	chr3:156975933-156976306(+)$1	373	84	91	13.0289
iiiiii]	chr4:101139408-101139689(+)$1	281	29	36	12.8115
:DDDDDD	chr6:143156874-143157143(+)$1	269	5	12	17.1594
8888888	chr5:71144677-71144978(-)$1	301	151	158	13.4637
|HHHHHH	chr10:106861139-106861551(+)$1	412	362	369	13.3188
bb]eeee	chr7:104839471-104839820(+)$1	349	172	179	17.1594
]ffffff	chr18:65373663-65373972(+)$1	309	140	147	13.2463
ff[dddd	chr5:129529993-129530255(+)$1	262	47	54	13.2463
ffqqqqq	chr4:18044418-18044762(+)$1	344	194	201	13.6811
eee$$$$	chr7:116177152-116177437(+)$1	285	187	194	17.1594
=======	chr19:10525749-10526017(+)$1	268	107	114	17.1594
mmmmccc	chr6:129491349-129491732(+)$1	383	39	46	17.1594
:::::::	chr2:121133985-121134349(+)$1	364	353	360	13.3188
MMMGGGG	chr12:88430821-88431115(+)$1	294	76	83	13.3188
22ggggg	chr5:34218839-34219098(+)$1	259	101	108	13.4637
:eeeee!	chr2:131878131-131878480(-)$1	349	0	7	17.1594
::ggggg	chr18:61746921-61747305(+)$1	384	136	143	13.3913
EEE{A{D	chr5:135096351-135096667(-)$1	316	173	180	13.1014
22ccc::	chr16:32107957-32108239(+)$1	282	91	98	13.2463

#DB
..(((((	chr2:167125071-167125342(-)$1	1	192	199	17.1594
((((...	chrX:160367336-160367628(+)$1	1	35	42	17.1594
((((..(	chr2:83644051-83644353(+)$1	1	141	148	13.1014
.((((..	chr14:104876649-104876914(-)$1	1	99	106	13.1739
(.....)	chr5:34215053-34215420(+)$1	1	218	225	13.2463
.......	chr8:82200817-82201112(+)$1	1	101	108	13.3913
.))))))	chr19:58871633-58872043(-)$1	1	200	207	13.3188
)))))..	chr18:37563065-37563470(+)$1	1	16	23	13.4637
..(((((	chr6:86939916-86940263(+)$1	1	15	22	17.1594
..(((((	chr1:75243512-75243973(-)$1	1	335	342	13.3913
.((((..	chr3:81897166-81897433(-)$1	1	198	205	13.4637
(((((((	chr2:29814502-29814829(+)$1	1	182	189	13.6811
(((.(((	chr12:45953487-45953946(-)$1	1	59	66	13.3188
))).)))	chr16:31093832-31094214(-)$1	1	235	242	12.8115
(((....	chr4:136104701-136105067(+)$1	1	168	175	13.4637
.)).)))	chr5:115625295-115625602(-)$1	1	274	281	12.8115
((.(.((	chr12:79785219-79785511(+)$1	1	145	152	12.8115
.))))))	chr2:122420955-122421209(-)$1	1	115	122	13.6811
))(((((	chr8:70217427-70217785(-)$1	1	125	132	17.1594
.))))))	chr6:124909123-124909517(-)$1	1	83	90	13.3913
....(((	chrX:68673139-68673432(-)$1	1	127	134	13.1014
...((((	chr4:140671143-140671420(-)$1	1	222	229	13.6811
))))...	chr9:110164694-110165173(+)$1	1	155	162	13.2463
)).....	chr7:107989523-107989858(+)$1	1	93	100	13.3188
).(((((	chr6:29909446-29909769(+)$1	1	165	172	13.1739
))))(((	chr14:27233631-27233959(-)$1	1	102	109	13.2463
((((..(	chr13:85354692-85355082(-)$1	1	21	28	13.6811
((...((	chr13:48975469-48975868(-)$1	1	9	16	17.1594
((((...	chr11:98218932-98219209(+)$1	1	8	15	13.6811
)))).))	chr18:82724548-82724797(+)$1	1	187	194	17.1594
)))))..	chr8:13174580-13174880(+)$1	1	268	275	12.8115
..)))).	chr1:138166148-138166425(-)$1	1	179	186	13.2463
.))))))	chr2:32645531-32645936(-)$1	1	129	136	13.3913
(.(((((	chr12:45664862-45665220(+)$1	1	49	56	13.3913
((((...	chr10:79634192-79634505(+)$1	1	127	134	13.4637
)))))).	chr8:107740524-107740778(+)$1	1	203	210	17.1594
)))))))	chr11:96679246-96679591(-)$1	1	196	203	17.1594
)))).))	chr2:92455224-92455508(+)$1	1	149	156	17.1594
)))..))	chr4:108534338-108534793(+)$1	1	104	111	13.3188
))).)))	chr10:110378828-110379191(-)$1	1	18	25	13.3188
...))))	chr2:155214476-155214835(+)$1	1	213	220	13.6811
..)))).	chrX:16262375-16262750(+)$1	1	341	348	17.1594
..(((((	chrX:72779458-72779776(+)$1	1	68	75	13.6811
(((((((	chr1:138165918-138166214(-)$1	1	50	57	13.1739
..(((((	chr1:141982738-141982993(-)$1	1	81	88	13.0289
)))))..	chr3:137820632-137820894(+)$1	1	232	239	13.3913
(((((((	chr6:39554716-39555175(-)$1	1	195	202	13.3913
(((((((	chr5:13599906-13600159(+)$1	1	127	134	12.8115
(((....	chr17:28883385-28883842(+)$1	1	24	31	13.2463
...)).)	chr3:7552752-7553077(+)$1	1	146	153	13.3913
(((((((	chr3:156975933-156976306(+)$1	1	84	91	13.0289
)))))).	chr4:101139408-101139689(+)$1	1	29	36	12.8115
.((((((	chr6:143156874-143157143(+)$1	1	5	12	17.1594
.......	chr5:71144677-71144978(-)$1	1	151	158	13.4637
.))))))	chr10:106861139-106861551(+)$1	1	362	369	13.3188
)).))))	chr7:104839471-104839820(+)$1	1	172	179	17.1594
.))))))	chr18:65373663-65373972(+)$1	1	140	147	13.2463
((.((((	chr5:129529993-129530255(+)$1	1	47	54	13.2463
((.....	chr4:18044418-18044762(+)$1	1	194	201	13.6811
(((....	chr7:116177152-116177437(+)$1	1	187	194	17.1594
(((((((	chr19:10525749-10526017(+)$1	1	107	114	17.1594
....)))	chr6:129491349-129491732(+)$1	1	39	46	17.1594
.......	chr2:121133985-121134349(+)$1	1	353	360	13.3188
...((((	chr12:88430821-88431115(+)$1	1	76	83	13.3188
..)))))	chr5:34218839-34219098(+)$1	1	101	108	13.4637
.(((((.	chr2:131878131-131878480(-)$1	1	0	7	17.1594
..(((((	chr18:61746921-61747305(+)$1	1	136	143	13.3913
(((.(.(	chr5:135096351-135096667(-)$1	1	173	180	13.1014
..)))..	chr16:32107957-32108239(+)$1	1	91	98	13.2463

#PSSM
U : 0.79	G : 0.07	C : 0.05	u : 0.02	A : 0.02	a : 0.01	
U : 0.88	G : 0.04	C : 0.02	u : 0.02	c : 0.01	
G : 0.78	U : 0.10	C : 0.05	g : 0.02	u : 0.01	A : 0.01	
U : 0.95	u : 0.04	
G : 0.78	A : 0.08	C : 0.05	g : 0.04	U : 0.02	
U : 0.95	u : 0.04	
U : 0.81	G : 0.07	C : 0.04	u : 0.04	A : 0.02	

#score	979.5797101449258
#seq	69
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m3_run2.nuc.txt

#NT
UGU	chr2:179769162-179769397(+)$1	235	18	21	8.9999
UGU	chr5:111093814-111094054(-)$1	240	5	8	8.9999
UGU	chr1:37476051-37476286(-)$1	235	17	20	8.9999
UGU	chr1:34869058-34869293(+)$1	235	12	15	8.9999
UGU	chr15:7146700-7146935(+)$1	235	10	13	8.9999
UGU	chr11:51414746-51414984(-)$1	238	114	117	8.9999
UGU	chr2:72241350-72241601(+)$1	251	37	40	8.9999
UGU	chr15:103029637-103029873(-)$1	236	26	29	8.9999
UGU	chr1:140382339-140382583(-)$1	244	53	56	8.9999
UGU	chr10:53064061-53064302(+)$1	241	173	176	8.9999
UGU	chr5:122903477-122903761(-)$1	284	7	10	8.9999
UGU	chr4:154530416-154530651(-)$1	235	130	133	8.9999
UGU	chr6:13034868-13035117(+)$1	249	103	106	8.9999
UGU	chr8:34893345-34893581(-)$1	236	32	35	8.9999
UGU	chr7:50553444-50553683(-)$1	239	19	22	8.9999
UGU	chr17:73288914-73289154(+)$1	240	57	60	8.9999
UGU	chr11:74488085-74488320(-)$1	235	106	109	8.9999
UGU	chr15:36407513-36407748(-)$1	235	18	21	8.9999
UGU	chr11:62708123-62708360(+)$1	237	74	77	8.9999
UGU	chr3:58394690-58394925(+)$1	235	9	12	8.9999
UGU	chr6:124885829-124886072(+)$1	243	18	21	8.9999
UGU	chr3:141965426-141965661(-)$1	235	17	20	8.9999
UGU	chr5:122904016-122904283(-)$1	267	17	20	8.9999
UGU	chr18:68421494-68421736(-)$1	242	105	108	8.9999
UGU	chr12:3248633-3248880(-)$1	247	37	40	8.9999
UGU	chr13:55445114-55445362(-)$1	248	49	52	8.9999
UGU	chr11:115940745-115940980(-)$1	235	37	40	8.9999
UGU	chr7:118215763-118216008(-)$1	245	15	18	8.9999
UGU	chr10:53626981-53627220(-)$1	239	107	110	8.9999
UGU	chr8:46912753-46912988(+)$1	235	73	76	8.9999
UGU	chrX:71674370-71674605(-)$1	235	162	165	8.9999
UGU	chr17:73290703-73290990(+)$1	287	13	16	8.9999
UGU	chr7:120042256-120042492(+)$1	236	0	3	8.9999
UGU	chr1:120194993-120195256(-)$1	263	53	56	8.9999
UGU	chr11:87793883-87794158(-)$1	275	19	22	8.9999
UGU	chr10:42254674-42254918(+)$1	244	34	37	8.9999
UGU	chr3:146394948-146395183(-)$1	235	114	117	8.9999
UGU	chr15:38419139-38419374(-)$1	235	50	53	8.9999
UGU	chr11:50108806-50109049(-)$1	243	39	42	8.9999
UGU	chr11:87794209-87794479(-)$1	270	117	120	8.9999
UGU	chr9:30882939-30883174(+)$1	235	11	14	8.9999
UGU	chr16:29651894-29652129(+)$1	235	5	8	8.9999
UGU	chr5:92481829-92482064(-)$1	235	4	7	8.9999
UGU	chr8:94192073-94192320(+)$1	247	59	62	8.9999
UGU	chr9:96218373-96218629(+)$1	256	34	37	8.9999
UGU	chr18:34505052-34505287(-)$1	235	45	48	8.9999
UGU	chr10:110732124-110732359(+)$1	235	6	9	8.9999
UGU	chr8:46912001-46912256(+)$1	255	39	42	8.9999
UGU	chr18:70742113-70742348(+)$1	235	0	3	8.9999
UGU	chr2:172859604-172859839(+)$1	235	14	17	8.9999
ugu	chr12:75046634-75046871(+)$1	237	83	86	8.9999
UGU	chr6:90595941-90596179(+)$1	238	48	51	8.9999
UGU	chr8:23678766-23679001(+)$1	235	26	29	8.9999
UGU	chr16:37885612-37885856(+)$1	244	13	16	8.9999
UGU	chr2:163450342-163450596(-)$1	254	17	20	8.9999
UGU	chrX:149935155-149935402(+)$1	247	61	64	8.9999
UGU	chr19:43574327-43574562(-)$1	235	31	34	8.9999
UGU	chr5:136384853-136385106(-)$1	253	3	6	8.9999
UGU	chr2:114019151-114019395(-)$1	244	6	9	8.9999
UGU	chr16:28827388-28827623(-)$1	235	2	5	8.9999
UGU	chr18:34506258-34506494(-)$1	236	1	4	8.9999
UGU	chrX:35772881-35773116(-)$1	235	6	9	8.9999
UGU	chr16:37834384-37834622(+)$1	238	11	14	8.9999
UGU	chr11:74490419-74490654(-)$1	235	1	4	8.9999
UGU	chr2:160587973-160588208(+)$1	235	59	62	8.9999
UGU	chr17:27716510-27716773(-)$1	263	33	36	8.9999
UGU	chr2:164824339-164824574(+)$1	235	104	107	8.9999
UGU	chr2:31923305-31923540(-)$1	235	5	8	8.9999
UGU	chr11:87793705-87793951(-)$1	246	32	35	8.9999
UGU	chr13:105627753-105627988(+)$1	235	30	33	8.9999
UGU	chr8:98238288-98238548(+)$1	260	10	13	8.9999
UGU	chr6:148181130-148181368(-)$1	238	9	12	8.9999
UGU	chr2:72244950-72245202(+)$1	252	33	36	8.9999
UGU	chr2:90856710-90856961(+)$1	251	24	27	8.9999
UGU	chr1:174127269-174127504(-)$1	235	14	17	8.9999
UGU	chr2:155214089-155214332(+)$1	243	108	111	8.9999
UGU	chr11:50108261-50108515(-)$1	254	5	8	8.9999
UGU	chr4:15844545-15844787(-)$1	242	22	25	8.9999
UGU	chr18:68426825-68427060(-)$1	235	110	113	8.9999
UGU	chr13:19684787-19685040(-)$1	253	15	18	8.9999
UGU	chr3:90310302-90310537(-)$1	235	18	21	8.9999
UGU	chr13:38071254-38071491(-)$1	237	17	20	8.9999
UGU	chr18:68427442-68427680(-)$1	238	16	19	8.9999
UGU	chr4:107904863-107905105(-)$1	242	147	150	8.9999
UGU	chr9:7933945-7934190(-)$1	245	60	63	8.9999
UGU	chr3:51319169-51319404(-)$1	235	0	3	8.9999
UGU	chr14:63761304-63761556(+)$1	252	44	47	8.9999
UGU	chr9:42772398-42772633(-)$1	235	8	11	8.9999
UGU	chr11:53232401-53232636(+)$1	235	36	39	8.9999
UGU	chr6:30404218-30404458(+)$1	240	8	11	8.9999
UGU	chr9:71352180-71352416(-)$1	236	33	36	8.9999
ugu	chr9:95461440-95461678(+)$1	238	118	121	8.9999
UGU	chr18:6789734-6789969(+)$1	235	23	26	8.9999

#otherMatches

#Struct PSSM
ccc	chr15:76910055-76910291(-)$1	236	99	102	8.9999
ggg	chr2:179769162-179769397(+)$1	235	18	21	8.9999
HHH	chr5:111093814-111094054(-)$1	240	5	8	8.9999
qqa	chr1:37476051-37476286(-)$1	235	17	20	8.9999
ppp	chr1:34869058-34869293(+)$1	235	12	15	8.9999
:::	chr15:7146700-7146935(+)$1	235	10	13	8.9999
hhh	chr11:51414746-51414984(-)$1	238	114	117	8.9999
]cc	chr2:72241350-72241601(+)$1	251	37	40	8.9999
lff	chr15:103029637-103029873(-)$1	236	26	29	8.9999
ddd	chr1:140382339-140382583(-)$1	244	53	56	8.9999
mmm	chr10:53064061-53064302(+)$1	241	173	176	8.9999
ddd	chr5:122903477-122903761(-)$1	284	7	10	8.9999
GGG	chr4:154530416-154530651(-)$1	235	130	133	8.9999
ee:	chr6:13034868-13035117(+)$1	249	103	106	8.9999
eee	chr8:34893345-34893581(-)$1	236	32	35	8.9999
eee	chr7:50553444-50553683(-)$1	239	19	22	8.9999
eee	chr17:73288914-73289154(+)$1	240	57	60	8.9999
:::	chr11:74488085-74488320(-)$1	235	106	109	8.9999
qcc	chr15:36407513-36407748(-)$1	235	18	21	8.9999
cc]	chr11:62708123-62708360(+)$1	237	74	77	8.9999
mmm	chr3:58394690-58394925(+)$1	235	9	12	8.9999
]dd	chr6:124885829-124886072(+)$1	243	18	21	8.9999
:::	chr3:141965426-141965661(-)$1	235	17	20	8.9999
DDD	chr5:122904016-122904283(-)$1	267	17	20	8.9999
3hh	chr18:68421494-68421736(-)$1	242	105	108	8.9999
[ff	chr12:3248633-3248880(-)$1	247	37	40	8.9999
EEE	chr13:55445114-55445362(-)$1	248	49	52	8.9999
{FF	chr11:115940745-115940980(-)$1	235	37	40	8.9999
iii	chr7:118215763-118216008(-)$1	245	15	18	8.9999
'a!	chr10:53626981-53627220(-)$1	239	107	110	8.9999
ddd	chr8:46912753-46912988(+)$1	235	73	76	8.9999
ggg	chrX:71674370-71674605(-)$1	235	162	165	8.9999
DDD	chr17:73290703-73290990(+)$1	287	13	16	8.9999
:::	chr7:120042256-120042492(+)$1	236	0	3	8.9999
PPP	chr1:120194993-120195256(-)$1	263	53	56	8.9999
:::	chr11:87793883-87794158(-)$1	275	19	22	8.9999
KCC	chr10:42254674-42254918(+)$1	244	34	37	8.9999
nee	chr3:146394948-146395183(-)$1	235	114	117	8.9999
c""	chr15:38419139-38419374(-)$1	235	50	53	8.9999
ooo	chr11:50108806-50109049(-)$1	243	39	42	8.9999
ccc	chr11:87794209-87794479(-)$1	270	117	120	8.9999
FFQ	chr9:30882939-30883174(+)$1	235	11	14	8.9999
:::	chr16:29651894-29652129(+)$1	235	5	8	8.9999
:::	chr5:92481829-92482064(-)$1	235	4	7	8.9999
vvv	chr8:94192073-94192320(+)$1	247	59	62	8.9999
HHH	chr9:96218373-96218629(+)$1	256	34	37	8.9999
ggg	chr18:34505052-34505287(-)$1	235	45	48	8.9999
:cc	chr10:110732124-110732359(+)$1	235	6	9	8.9999
DDN	chr8:46912001-46912256(+)$1	255	39	42	8.9999
FFF	chr18:70742113-70742348(+)$1	235	0	3	8.9999
FF:	chr2:172859604-172859839(+)$1	235	14	17	8.9999
ggg	chr12:75046634-75046871(+)$1	237	83	86	8.9999
mmc	chr6:90595941-90596179(+)$1	238	48	51	8.9999
ddd	chr8:23678766-23679001(+)$1	235	26	29	8.9999
ggg	chr16:37885612-37885856(+)$1	244	13	16	8.9999
GG{	chr2:163450342-163450596(-)$1	254	17	20	8.9999
:::	chrX:149935155-149935402(+)$1	247	61	64	8.9999
ee[	chr19:43574327-43574562(-)$1	235	31	34	8.9999
:::	chr5:136384853-136385106(-)$1	253	3	6	8.9999
EE:	chr2:114019151-114019395(-)$1	244	6	9	8.9999
:::	chr16:28827388-28827623(-)$1	235	2	5	8.9999
:bb	chr18:34506258-34506494(-)$1	236	1	4	8.9999
III	chrX:35772881-35773116(-)$1	235	6	9	8.9999
:::	chr16:37834384-37834622(+)$1	238	11	14	8.9999
DDD	chr11:74490419-74490654(-)$1	235	1	4	8.9999
:dd	chr2:160587973-160588208(+)$1	235	59	62	8.9999
BB{	chr17:27716510-27716773(-)$1	263	33	36	8.9999
ccc	chr2:164824339-164824574(+)$1	235	104	107	8.9999
===	chr2:31923305-31923540(-)$1	235	5	8	8.9999
eee	chr11:87793705-87793951(-)$1	246	32	35	8.9999
ddd	chr13:105627753-105627988(+)$1	235	30	33	8.9999
ndd	chr8:98238288-98238548(+)$1	260	10	13	8.9999
ccn	chr6:148181130-148181368(-)$1	238	9	12	8.9999
eee	chr2:72244950-72245202(+)$1	252	33	36	8.9999
%%%	chr2:90856710-90856961(+)$1	251	24	27	8.9999
hhh	chr1:174127269-174127504(-)$1	235	14	17	8.9999
nbb	chr2:155214089-155214332(+)$1	243	108	111	8.9999
DD{	chr11:50108261-50108515(-)$1	254	5	8	8.9999
EEE	chr4:15844545-15844787(-)$1	242	22	25	8.9999
CCC	chr18:68426825-68427060(-)$1	235	110	113	8.9999
DMM	chr13:19684787-19685040(-)$1	253	15	18	8.9999
dd2	chr3:90310302-90310537(-)$1	235	18	21	8.9999
LEE	chr13:38071254-38071491(-)$1	237	17	20	8.9999
eee	chr18:68427442-68427680(-)$1	238	16	19	8.9999
HHH	chr4:107904863-107905105(-)$1	242	147	150	8.9999
fff	chr9:7933945-7934190(-)$1	245	60	63	8.9999
:::	chr3:51319169-51319404(-)$1	235	0	3	8.9999
ggg	chr14:63761304-63761556(+)$1	252	44	47	8.9999
nnn	chr9:42772398-42772633(-)$1	235	8	11	8.9999
BB{	chr11:53232401-53232636(+)$1	235	36	39	8.9999
KDD	chr6:30404218-30404458(+)$1	240	8	11	8.9999
PFF	chr9:71352180-71352416(-)$1	236	33	36	8.9999
GGG	chr9:95461440-95461678(+)$1	238	118	121	8.9999
FFF	chr18:6789734-6789969(+)$1	235	23	26	8.9999

#DB
(((	chr15:76910055-76910291(-)$1	1	99	102	8.9999
(((	chr2:179769162-179769397(+)$1	1	18	21	8.9999
(((	chr5:111093814-111094054(-)$1	1	5	8	8.9999
..)	chr1:37476051-37476286(-)$1	1	17	20	8.9999
...	chr1:34869058-34869293(+)$1	1	12	15	8.9999
...	chr15:7146700-7146935(+)$1	1	10	13	8.9999
(((	chr11:51414746-51414984(-)$1	1	114	117	8.9999
.))	chr2:72241350-72241601(+)$1	1	37	40	8.9999
.))	chr15:103029637-103029873(-)$1	1	26	29	8.9999
)))	chr1:140382339-140382583(-)$1	1	53	56	8.9999
...	chr10:53064061-53064302(+)$1	1	173	176	8.9999
(((	chr5:122903477-122903761(-)$1	1	7	10	8.9999
)))	chr4:154530416-154530651(-)$1	1	130	133	8.9999
)).	chr6:13034868-13035117(+)$1	1	103	106	8.9999
(((	chr8:34893345-34893581(-)$1	1	32	35	8.9999
)))	chr7:50553444-50553683(-)$1	1	19	22	8.9999
(((	chr17:73288914-73289154(+)$1	1	57	60	8.9999
...	chr11:74488085-74488320(-)$1	1	106	109	8.9999
.))	chr15:36407513-36407748(-)$1	1	18	21	8.9999
)).	chr11:62708123-62708360(+)$1	1	74	77	8.9999
...	chr3:58394690-58394925(+)$1	1	9	12	8.9999
.))	chr6:124885829-124886072(+)$1	1	18	21	8.9999
...	chr3:141965426-141965661(-)$1	1	17	20	8.9999
(((	chr5:122904016-122904283(-)$1	1	17	20	8.9999
.))	chr18:68421494-68421736(-)$1	1	105	108	8.9999
.((	chr12:3248633-3248880(-)$1	1	37	40	8.9999
(((	chr13:55445114-55445362(-)$1	1	49	52	8.9999
.((	chr11:115940745-115940980(-)$1	1	37	40	8.9999
(((	chr7:118215763-118216008(-)$1	1	15	18	8.9999
.(.	chr10:53626981-53627220(-)$1	1	107	110	8.9999
)))	chr8:46912753-46912988(+)$1	1	73	76	8.9999
)))	chrX:71674370-71674605(-)$1	1	162	165	8.9999
(((	chr17:73290703-73290990(+)$1	1	13	16	8.9999
...	chr7:120042256-120042492(+)$1	1	0	3	8.9999
...	chr1:120194993-120195256(-)$1	1	53	56	8.9999
...	chr11:87793883-87794158(-)$1	1	19	22	8.9999
.((	chr10:42254674-42254918(+)$1	1	34	37	8.9999
.))	chr3:146394948-146395183(-)$1	1	114	117	8.9999
(..	chr15:38419139-38419374(-)$1	1	50	53	8.9999
...	chr11:50108806-50109049(-)$1	1	39	42	8.9999
)))	chr11:87794209-87794479(-)$1	1	117	120	8.9999
((.	chr9:30882939-30883174(+)$1	1	11	14	8.9999
...	chr16:29651894-29652129(+)$1	1	5	8	8.9999
...	chr5:92481829-92482064(-)$1	1	4	7	8.9999
...	chr8:94192073-94192320(+)$1	1	59	62	8.9999
(((	chr9:96218373-96218629(+)$1	1	34	37	8.9999
(((	chr18:34505052-34505287(-)$1	1	45	48	8.9999
.((	chr10:110732124-110732359(+)$1	1	6	9	8.9999
((.	chr8:46912001-46912256(+)$1	1	39	42	8.9999
(((	chr18:70742113-70742348(+)$1	1	0	3	8.9999
((.	chr2:172859604-172859839(+)$1	1	14	17	8.9999
(((	chr12:75046634-75046871(+)$1	1	83	86	8.9999
..)	chr6:90595941-90596179(+)$1	1	48	51	8.9999
)))	chr8:23678766-23679001(+)$1	1	26	29	8.9999
(((	chr16:37885612-37885856(+)$1	1	13	16	8.9999
((.	chr2:163450342-163450596(-)$1	1	17	20	8.9999
...	chrX:149935155-149935402(+)$1	1	61	64	8.9999
((.	chr19:43574327-43574562(-)$1	1	31	34	8.9999
...	chr5:136384853-136385106(-)$1	1	3	6	8.9999
((.	chr2:114019151-114019395(-)$1	1	6	9	8.9999
...	chr16:28827388-28827623(-)$1	1	2	5	8.9999
.((	chr18:34506258-34506494(-)$1	1	1	4	8.9999
(((	chrX:35772881-35773116(-)$1	1	6	9	8.9999
...	chr16:37834384-37834622(+)$1	1	11	14	8.9999
(((	chr11:74490419-74490654(-)$1	1	1	4	8.9999
.((	chr2:160587973-160588208(+)$1	1	59	62	8.9999
((.	chr17:27716510-27716773(-)$1	1	33	36	8.9999
)))	chr2:164824339-164824574(+)$1	1	104	107	8.9999
(((	chr2:31923305-31923540(-)$1	1	5	8	8.9999
)))	chr11:87793705-87793951(-)$1	1	32	35	8.9999
(((	chr13:105627753-105627988(+)$1	1	30	33	8.9999
.))	chr8:98238288-98238548(+)$1	1	10	13	8.9999
((.	chr6:148181130-148181368(-)$1	1	9	12	8.9999
(((	chr2:72244950-72245202(+)$1	1	33	36	8.9999
...	chr2:90856710-90856961(+)$1	1	24	27	8.9999
(((	chr1:174127269-174127504(-)$1	1	14	17	8.9999
.))	chr2:155214089-155214332(+)$1	1	108	111	8.9999
((.	chr11:50108261-50108515(-)$1	1	5	8	8.9999
(((	chr4:15844545-15844787(-)$1	1	22	25	8.9999
(((	chr18:68426825-68427060(-)$1	1	110	113	8.9999
(..	chr13:19684787-19685040(-)$1	1	15	18	8.9999
)).	chr3:90310302-90310537(-)$1	1	18	21	8.9999
.((	chr13:38071254-38071491(-)$1	1	17	20	8.9999
(((	chr18:68427442-68427680(-)$1	1	16	19	8.9999
)))	chr4:107904863-107905105(-)$1	1	147	150	8.9999
)))	chr9:7933945-7934190(-)$1	1	60	63	8.9999
...	chr3:51319169-51319404(-)$1	1	0	3	8.9999
(((	chr14:63761304-63761556(+)$1	1	44	47	8.9999
...	chr9:42772398-42772633(-)$1	1	8	11	8.9999
((.	chr11:53232401-53232636(+)$1	1	36	39	8.9999
.((	chr6:30404218-30404458(+)$1	1	8	11	8.9999
.((	chr9:71352180-71352416(-)$1	1	33	36	8.9999
)))	chr9:95461440-95461678(+)$1	1	118	121	8.9999
(((	chr18:6789734-6789969(+)$1	1	23	26	8.9999

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

#score	845.9999999999998
#seq	94
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_UTR_m2_run2.nuc.txt

#NT
aaaaaacaaaa	chr19:16460315-16460516(+)$1	201	154	165	18.1162
AAAAAAAAAAC	chr5:15876961-15877162(+)$1	201	62	73	22.1860
AAAAAAAAAAU	chr10:66718543-66718744(+)$1	201	7	18	25.7906
AAACAAACAAU	chr2:32992339-32992540(-)$1	201	32	43	18.2325
AAAAAAAAAAA	chr11:115884158-115884359(-)$1	201	81	92	22.3023
UGAAAAAAAAU	chr18:31598961-31599162(-)$1	201	147	158	19.5116
UUAAAAAAAAU	chr8:88242641-88242842(-)$1	201	141	152	19.0465
AAAAAAAAAAU	chr1:194330836-194331037(+)$1	201	91	102	25.7906
AAAAAAAAAAU	chr2:103988340-103988541(-)$1	201	86	97	25.7906
AAGAAAAUAAU	chr1:78702938-78703139(+)$1	201	42	53	17.6511
AAAAAAAAAAU	chr2:103988354-103988555(-)$1	201	100	111	25.7906
aaaaaaaaaau	chr5:138200860-138201061(+)$1	201	91	102	25.7906
AAAAAAAAAAU	chr10:66718544-66718745(+)$1	201	6	17	25.7906
AAAGAAAUAAU	chr5:73369041-73369242(+)$1	201	3	14	18.1162
aaaaaaaaaaU	chrX:133613776-133613977(+)$1	201	83	94	25.7906
AAAGAUAAAAU	chr15:8658642-8658843(-)$1	201	90	101	17.6511
uaaaaaaaaau	chr16:84954677-84954878(-)$1	201	2	13	23.1162
aaaaaaacaaU	chr2:165609674-165609875(-)$1	201	102	113	22.1860
AAAGAUAAAAU	chr15:8658643-8658844(-)$1	201	91	102	17.6511
AAGAAAAAUAU	chr14:67487155-67487356(-)$1	201	166	177	16.9534
AGAAAAAGAAU	chr7:72441306-72441507(-)$1	201	155	166	18.2325
AAAAAAAAAAU	chr2:103988339-103988540(-)$1	201	85	96	25.7906
AAAAAAAAAAU	chr10:80861742-80861943(-)$1	201	64	75	25.7906
AAAAAGACAAU	chr15:72936490-72936691(-)$1	201	40	51	17.8837
AAAAAAAUAGU	chr6:71760519-71760720(+)$1	201	178	189	17.7674
aaaaaaacaaU	chr2:165609651-165609852(-)$1	201	79	90	22.1860
UGAAAAAAAAU	chrX:39029573-39029774(+)$1	201	173	184	19.5116
AAAAGAAACAU	chr7:118215630-118215831(-)$1	201	175	186	16.7209
AAAAAACAAAC	chr2:102624532-102624733(+)$1	201	104	115	18.0000
AAAAAAAAAAA	chr2:27301084-27301285(-)$1	201	83	94	22.3023
UAAAAAAAGAU	chr1:166368304-166368505(-)$1	201	138	149	18.8139
UGAAAACAAAU	chr13:100193753-100193954(-)$1	201	47	58	15.3255
AAACUAAAAAU	chr5:43677473-43677674(+)$1	201	186	197	17.1860
agaaaaaaaaa	chr11:117623892-117624093(+)$1	201	12	23	18.6976
AAAAAAGAAAU	chr4:81940723-81940924(-)$1	201	161	172	21.3720
AACAAAAAAGU	chr17:10401531-10401732(-)$1	201	163	174	16.9534
AAACACAAAAU	chr2:121136297-121136498(-)$1	201	183	194	17.6511
UAAAAAAAAAG	chr1:145604335-145604536(-)$1	201	152	163	19.3953
UAAAAAAAGAU	chr1:166368303-166368504(-)$1	201	137	148	18.8139
GAAAAAAAAGU	chr1:157692648-157692849(-)$1	201	80	91	17.8837
CAAAACAAAAU	chr4:61958517-61958718(+)$1	201	182	193	18.0000
ACAAAAAAAAC	chr17:6138514-6138715(+)$1	201	9	20	18.1162

#otherMatches

#Struct PSSM
hh:::::::::	chr1:145604336-145604537(-)$1	201	153	164	19.3953
:::::::::::	chr19:16460315-16460516(+)$1	201	154	165	18.1162
:::::::::::	chr5:15876961-15877162(+)$1	201	62	73	22.1860
:::::::::::	chr10:66718543-66718744(+)$1	201	7	18	25.7906
DD{BBKKBB{E	chr2:32992339-32992540(-)$1	201	32	43	18.2325
rrrrrrrrrdd	chr11:115884158-115884359(-)$1	201	81	92	22.3023
e^^^^^^^^^^	chr18:31598961-31599162(-)$1	201	147	158	19.5116
ddnnnnndddd	chr8:88242641-88242842(-)$1	201	141	152	19.0465
ttttttttttc	chr1:194330836-194331037(+)$1	201	91	102	25.7906
hhh!!ccceee	chr2:103988340-103988541(-)$1	201	86	97	25.7906
DDD::::::::	chr1:78702938-78703139(+)$1	201	42	53	17.6511
mmmccc22eee	chr2:103988354-103988555(-)$1	201	100	111	25.7906
>>>>>>>>>>>	chr5:138200860-138201061(+)$1	201	91	102	25.7906
:::::::::::	chr10:66718544-66718745(+)$1	201	6	17	25.7906
JJJJJJJJJ::	chr5:73369041-73369242(+)$1	201	3	14	18.1162
:::::::::::	chrX:133613776-133613977(+)$1	201	83	94	25.7906
JJJJ:::::::	chr15:8658642-8658843(-)$1	201	90	101	17.6511
:::::::::::	chr16:84954677-84954878(-)$1	201	2	13	23.1162
:::::::::::	chr2:165609674-165609875(-)$1	201	102	113	22.1860
JJJJ:::::::	chr15:8658643-8658844(-)$1	201	91	102	17.6511
ddqqqqqqqqd	chr14:67487155-67487356(-)$1	201	166	177	16.9534
qqqqqgggggg	chr7:72441306-72441507(-)$1	201	155	166	18.2325
hhh!!ccceee	chr2:103988339-103988540(-)$1	201	85	96	25.7906
:::::::::::	chr10:80861742-80861943(-)$1	201	64	75	25.7906
e####bb[ddd	chr15:72936490-72936691(-)$1	201	40	51	17.8837
ttttttttbb3	chr6:71760519-71760720(+)$1	201	178	189	17.7674
:::::::::::	chr2:165609651-165609852(-)$1	201	79	90	22.1860
C::::::::::	chrX:39029573-39029774(+)$1	201	173	184	19.5116
leeeee66666	chr7:118215630-118215831(-)$1	201	175	186	16.7209
>>>>>ffffff	chr2:102624532-102624733(+)$1	201	104	115	18.0000
:::::::::::	chr2:27301084-27301285(-)$1	201	83	94	22.3023
d$$$$$eeeee	chr1:166368304-166368505(-)$1	201	138	149	18.8139
))))))))))i	chr13:100193753-100193954(-)$1	201	47	58	15.3255
:::::::::::	chr5:43677473-43677674(+)$1	201	186	197	17.1860
e^^^^^^^^^^	chr11:117623892-117624093(+)$1	201	12	23	18.6976
ggggggguuuu	chr4:81940723-81940924(-)$1	201	161	172	21.3720
:::::ffffff	chr17:10401531-10401732(-)$1	201	163	174	16.9534
DDDD:::::::	chr2:121136297-121136498(-)$1	201	183	194	17.6511
hh::::::JJJ	chr1:145604335-145604536(-)$1	201	152	163	19.3953
d$$$$$eeeee	chr1:166368303-166368504(-)$1	201	137	148	18.8139
qqqbb]eeeee	chr1:157692648-157692849(-)$1	201	80	91	17.8837
ffffff:::::	chr4:61958517-61958718(+)$1	201	182	193	18.0000
:::::::::::	chr17:6138514-6138715(+)$1	201	9	20	18.1162

#DB
)).........	chr1:145604336-145604537(-)$1	1	153	164	19.3953
...........	chr19:16460315-16460516(+)$1	1	154	165	18.1162
...........	chr5:15876961-15877162(+)$1	1	62	73	22.1860
...........	chr10:66718543-66718744(+)$1	1	7	18	25.7906
((.((..((.(	chr2:32992339-32992540(-)$1	1	32	43	18.2325
.........))	chr11:115884158-115884359(-)$1	1	81	92	22.3023
(..........	chr18:31598961-31599162(-)$1	1	147	158	19.5116
((.....))))	chr8:88242641-88242842(-)$1	1	141	152	19.0465
..........)	chr1:194330836-194331037(+)$1	1	91	102	25.7906
(((..((((((	chr2:103988340-103988541(-)$1	1	86	97	25.7906
(((........	chr1:78702938-78703139(+)$1	1	42	53	17.6511
...)))..)))	chr2:103988354-103988555(-)$1	1	100	111	25.7906
...........	chr5:138200860-138201061(+)$1	1	91	102	25.7906
...........	chr10:66718544-66718745(+)$1	1	6	17	25.7906
(((((((((..	chr5:73369041-73369242(+)$1	1	3	14	18.1162
...........	chrX:133613776-133613977(+)$1	1	83	94	25.7906
)))).......	chr15:8658642-8658843(-)$1	1	90	101	17.6511
...........	chr16:84954677-84954878(-)$1	1	2	13	23.1162
...........	chr2:165609674-165609875(-)$1	1	102	113	22.1860
)))).......	chr15:8658643-8658844(-)$1	1	91	102	17.6511
((........)	chr14:67487155-67487356(-)$1	1	166	177	16.9534
.....))))))	chr7:72441306-72441507(-)$1	1	155	166	18.2325
(((..((((((	chr2:103988339-103988540(-)$1	1	85	96	25.7906
...........	chr10:80861742-80861943(-)$1	1	64	75	25.7906
(....((.(((	chr15:72936490-72936691(-)$1	1	40	51	17.8837
........)).	chr6:71760519-71760720(+)$1	1	178	189	17.7674
...........	chr2:165609651-165609852(-)$1	1	79	90	22.1860
)..........	chrX:39029573-39029774(+)$1	1	173	184	19.5116
.))))).....	chr7:118215630-118215831(-)$1	1	175	186	16.7209
.....))))))	chr2:102624532-102624733(+)$1	1	104	115	18.0000
...........	chr2:27301084-27301285(-)$1	1	83	94	22.3023
(.....(((((	chr1:166368304-166368505(-)$1	1	138	149	18.8139
..........(	chr13:100193753-100193954(-)$1	1	47	58	15.3255
...........	chr5:43677473-43677674(+)$1	1	186	197	17.1860
(..........	chr11:117623892-117624093(+)$1	1	12	23	18.6976
(((((((....	chr4:81940723-81940924(-)$1	1	161	172	21.3720
.....((((((	chr17:10401531-10401732(-)$1	1	163	174	16.9534
)))).......	chr2:121136297-121136498(-)$1	1	183	194	17.6511
))......)))	chr1:145604335-145604536(-)$1	1	152	163	19.3953
(.....(((((	chr1:166368303-166368504(-)$1	1	137	148	18.8139
...)).)))))	chr1:157692648-157692849(-)$1	1	80	91	17.8837
)))))).....	chr4:61958517-61958718(+)$1	1	182	193	18.0000
...........	chr17:6138514-6138715(+)$1	1	9	20	18.1162

#PSSM
A : 0.60	U : 0.18	a : 0.13	u : 0.02	G : 0.02	C : 0.02	
A : 0.69	a : 0.13	G : 0.09	U : 0.02	g : 0.02	C : 0.02	
A : 0.76	a : 0.16	G : 0.04	C : 0.02	
A : 0.69	a : 0.16	C : 0.06	G : 0.06	
A : 0.79	a : 0.16	G : 0.02	U : 0.02	
A : 0.72	a : 0.16	U : 0.04	C : 0.04	G : 0.02	
A : 0.76	a : 0.13	C : 0.04	c : 0.02	G : 0.02	
A : 0.69	a : 0.11	U : 0.06	C : 0.04	c : 0.04	G : 0.02	
A : 0.74	a : 0.16	G : 0.04	U : 0.02	C : 0.02	
A : 0.76	a : 0.16	G : 0.06	
U : 0.74	C : 0.06	G : 0.04	a : 0.04	A : 0.04	u : 0.04	

#score	875.0465116279071
#seq	43
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m3_run1.nuc.txt

#NT
CUUCCA	chr15:71292706-71292907(-)$1	201	144	150	11.0158
CUCUCA	chr5:88984553-88984754(+)$1	201	178	184	9.9047
CUUUUA	chr11:21228861-21229062(-)$1	201	178	184	9.5079
CUUCCA	chr16:41955271-41955472(+)$1	201	55	61	11.0158
CUUCCA	chr13:9623109-9623310(+)$1	201	133	139	11.0158
CUUCCA	chr17:85464973-85465174(-)$1	201	72	78	11.0158
UUUUCA	chr3:55791875-55792076(-)$1	201	71	77	10.4603
CUCUCA	chr11:97317730-97317931(+)$1	201	104	110	9.9047
CUUUCA	chr12:45309095-45309296(-)$1	201	140	146	14.0317
CUUCCA	chr2:109836630-109836831(+)$1	201	34	40	11.0158
UUUUCA	chr5:34263098-34263299(-)$1	201	100	106	10.4603
CUUUCA	chr12:112782664-112782865(+)$1	201	17	23	14.0317
CUGUCA	chr13:44997710-44997911(+)$1	201	14	20	10.0634
GUUUCA	chr12:105940975-105941176(-)$1	201	16	22	10.3015
AUUUCA	chr17:24196151-24196352(-)$1	201	65	71	10.4603
CUUUCA	chr2:60071964-60072165(+)$1	201	144	150	14.0317
CUUUUA	chrX:12731145-12731346(+)$1	201	89	95	9.5079
CUUUCA	chr14:58728298-58728499(+)$1	201	166	172	14.0317
CUUUCC	chr8:67073670-67073871(-)$1	201	18	24	10.7777
CUUUCA	chr12:45309094-45309295(-)$1	201	139	145	14.0317
CUUUCC	chr1:174209728-174209929(-)$1	201	186	192	10.7777
CUUCCA	chr11:29607512-29607713(+)$1	201	138	144	11.0158
CUUUCC	chr2:29866446-29866647(+)$1	201	17	23	10.7777
CUGUCA	chr6:113712737-113712938(-)$1	201	127	133	10.0634
CUUCCA	chr11:23333141-23333342(+)$1	201	142	148	11.0158
CUUUCC	chrX:20291657-20291858(+)$1	201	36	42	10.7777
AUUUCA	chr10:66682856-66683057(+)$1	201	17	23	10.4603
CUUUCA	chr2:44851530-44851731(-)$1	201	22	28	14.0317
GUUUCA	chr5:77405372-77405573(+)$1	201	119	125	10.3015
CUUUCA	chr15:96528559-96528760(-)$1	201	10	16	14.0317
CUUUCA	chr15:96528558-96528759(-)$1	201	9	15	14.0317
UUUUCA	chr9:120483173-120483374(+)$1	201	31	37	10.4603
CUUCCA	chr13:114384775-114384976(-)$1	201	33	39	11.0158
CUGUCA	chr9:54263914-54264115(-)$1	201	42	48	10.0634
CUUCCA	chr11:104285759-104285960(-)$1	201	63	69	11.0158
AUUUCA	chr14:60898835-60899036(+)$1	201	178	184	10.4603
CUUUCA	chr7:17147927-17148128(-)$1	201	152	158	14.0317
CUUUCA	chr8:67087886-67088087(-)$1	201	129	135	14.0317
UUUUCA	chr9:120483174-120483375(+)$1	201	30	36	10.4603
CUUCCA	chr17:85464974-85465175(-)$1	201	73	79	11.0158
CUUUCC	chr9:62221226-62221427(+)$1	201	18	24	10.7777
CUUCCA	chr2:109836629-109836830(+)$1	201	35	41	11.0158
CUUUCC	chr12:88029810-88030011(+)$1	201	15	21	10.7777
CUUUCU	chr11:109528870-109529071(+)$1	201	97	103	10.3809
CUUUCC	chr12:76823578-76823779(-)$1	201	29	35	10.7777
CUUUUA	chr16:37536060-37536261(-)$1	201	78	84	9.5079
CUGUCA	chr10:59763439-59763640(+)$1	201	0	6	10.0634
AUUUCA	chr1:196633638-196633839(+)$1	201	23	29	10.4603
UUUUCA	chr11:42300679-42300880(+)$1	201	38	44	10.4603
CUUUCA	chr1:63206272-63206473(-)$1	201	185	191	14.0317
CUUCCA	chr15:31432414-31432615(-)$1	201	157	163	11.0158
AUUUCA	chr10:59569169-59569370(+)$1	201	155	161	10.4603
CUCUCA	chr1:39599188-39599389(+)$1	201	35	41	9.9047
CUUUCC	chrX:71104631-71104832(-)$1	201	71	77	10.7777
CUUUCA	chr7:17147928-17148129(-)$1	201	153	159	14.0317
CUUUCU	chr2:121128803-121129004(+)$1	201	177	183	10.3809
CUGUCA	chr9:58471460-58471661(+)$1	201	8	14	10.0634
CUUUCA	chr8:67087887-67088088(-)$1	201	130	136	14.0317
CUUUCU	chr14:24133423-24133624(-)$1	201	75	81	10.3809
CUUUCC	chr8:67073669-67073870(-)$1	201	17	23	10.7777
CUUUCU	chr4:95669064-95669265(+)$1	201	55	61	10.3809
GUUUCA	chr12:105941118-105941319(-)$1	201	159	165	10.3015

#otherMatches

#Struct PSSM
qqqa]c	chr11:104189200-104189401(+)$1	201	78	84	10.1428
dddd33	chr15:71292706-71292907(-)$1	201	144	150	11.0158
2bb:::	chr5:88984553-88984754(+)$1	201	178	184	9.9047
efffff	chr11:21228861-21229062(-)$1	201	178	184	9.5079
eeee!!	chr16:41955271-41955472(+)$1	201	55	61	11.0158
::::::	chr13:9623109-9623310(+)$1	201	133	139	11.0158
HHHKKC	chr17:85464973-85465174(-)$1	201	72	78	11.0158
fffffc	chr3:55791875-55792076(-)$1	201	71	77	10.4603
mmmeee	chr11:97317730-97317931(+)$1	201	104	110	9.9047
vvvvvv	chr12:45309095-45309296(-)$1	201	140	146	14.0317
FFFFMM	chr2:109836630-109836831(+)$1	201	34	40	11.0158
fffddd	chr5:34263098-34263299(-)$1	201	100	106	10.4603
:ddddm	chr12:112782664-112782865(+)$1	201	17	23	14.0317
::::::	chr13:44997710-44997911(+)$1	201	14	20	10.0634
iiiimm	chr12:105940975-105941176(-)$1	201	16	22	10.3015
oooooo	chr17:24196151-24196352(-)$1	201	65	71	10.4603
ddd!!c	chr2:60071964-60072165(+)$1	201	144	150	14.0317
:HHHHH	chrX:12731145-12731346(+)$1	201	89	95	9.5079
booooo	chr14:58728298-58728499(+)$1	201	166	172	14.0317
"""ddd	chr8:67073670-67073871(-)$1	201	18	24	10.7777
vvvvvv	chr12:45309094-45309295(-)$1	201	139	145	14.0317
444ddd	chr1:174209728-174209929(-)$1	201	186	192	10.7777
^^^^^^	chr11:29607512-29607713(+)$1	201	138	144	11.0158
%%%%%%	chr2:29866446-29866647(+)$1	201	17	23	10.7777
((((((	chr6:113712737-113712938(-)$1	201	127	133	10.0634
eeeee:	chr11:23333141-23333342(+)$1	201	142	148	11.0158
%%%ggg	chrX:20291657-20291858(+)$1	201	36	42	10.7777
::::::	chr10:66682856-66683057(+)$1	201	17	23	10.4603
:::DDD	chr2:44851530-44851731(-)$1	201	22	28	14.0317
eeeeel	chr5:77405372-77405573(+)$1	201	119	125	10.3015
bb$$$$	chr15:96528559-96528760(-)$1	201	10	16	14.0317
bb$$$$	chr15:96528558-96528759(-)$1	201	9	15	14.0317
qqqqgg	chr9:120483173-120483374(+)$1	201	31	37	10.4603
FFFFFF	chr13:114384775-114384976(-)$1	201	33	39	11.0158
++++++	chr9:54263914-54264115(-)$1	201	42	48	10.0634
ffff::	chr11:104285759-104285960(-)$1	201	63	69	11.0158
FF????	chr14:60898835-60899036(+)$1	201	178	184	10.4603
hhh]bb	chr7:17147927-17148128(-)$1	201	152	158	14.0317
::::::	chr8:67087886-67088087(-)$1	201	129	135	14.0317
qqqqgg	chr9:120483174-120483375(+)$1	201	30	36	10.4603
HHHKKC	chr17:85464974-85465175(-)$1	201	73	79	11.0158
DD{BB:	chr9:62221226-62221427(+)$1	201	18	24	10.7777
FFFFMM	chr2:109836629-109836830(+)$1	201	35	41	11.0158
DDTTTT	chr12:88029810-88030011(+)$1	201	15	21	10.7777
::::::	chr11:109528870-109529071(+)$1	201	97	103	10.3809
::::::	chr12:76823578-76823779(-)$1	201	29	35	10.7777
ii!!dd	chr16:37536060-37536261(-)$1	201	78	84	9.5079
::::::	chr10:59763439-59763640(+)$1	201	0	6	10.0634
^^^^^^	chr1:196633638-196633839(+)$1	201	23	29	10.4603
gggggg	chr11:42300679-42300880(+)$1	201	38	44	10.4603
ppppdd	chr1:63206272-63206473(-)$1	201	185	191	14.0317
::::::	chr15:31432414-31432615(-)$1	201	157	163	11.0158
:::::e	chr10:59569169-59569370(+)$1	201	155	161	10.4603
ssssss	chr1:39599188-39599389(+)$1	201	35	41	9.9047
eee:::	chrX:71104631-71104832(-)$1	201	71	77	10.7777
hhh]bb	chr7:17147928-17148129(-)$1	201	153	159	14.0317
GGGGGG	chr2:121128803-121129004(+)$1	201	177	183	10.3809
lfffff	chr9:58471460-58471661(+)$1	201	8	14	10.0634
::::::	chr8:67087887-67088088(-)$1	201	130	136	14.0317
FF{BB{	chr14:24133423-24133624(-)$1	201	75	81	10.3809
"""ddd	chr8:67073669-67073870(-)$1	201	17	23	10.7777
[ggggg	chr4:95669064-95669265(+)$1	201	55	61	10.3809
dddddd	chr12:105941118-105941319(-)$1	201	159	165	10.3015

#DB
...).)	chr11:104189200-104189401(+)$1	1	78	84	10.1428
))))..	chr15:71292706-71292907(-)$1	1	144	150	11.0158
.))...	chr5:88984553-88984754(+)$1	1	178	184	9.9047
))))))	chr11:21228861-21229062(-)$1	1	178	184	9.5079
((((..	chr16:41955271-41955472(+)$1	1	55	61	11.0158
......	chr13:9623109-9623310(+)$1	1	133	139	11.0158
(((..(	chr17:85464973-85465174(-)$1	1	72	78	11.0158
((((((	chr3:55791875-55792076(-)$1	1	71	77	10.4603
...)))	chr11:97317730-97317931(+)$1	1	104	110	9.9047
......	chr12:45309095-45309296(-)$1	1	140	146	14.0317
((((..	chr2:109836630-109836831(+)$1	1	34	40	11.0158
))))))	chr5:34263098-34263299(-)$1	1	100	106	10.4603
.((((.	chr12:112782664-112782865(+)$1	1	17	23	14.0317
......	chr13:44997710-44997911(+)$1	1	14	20	10.0634
((((..	chr12:105940975-105941176(-)$1	1	16	22	10.3015
......	chr17:24196151-24196352(-)$1	1	65	71	10.4603
(((..(	chr2:60071964-60072165(+)$1	1	144	150	14.0317
.(((((	chrX:12731145-12731346(+)$1	1	89	95	9.5079
(.....	chr14:58728298-58728499(+)$1	1	166	172	14.0317
...(((	chr8:67073670-67073871(-)$1	1	18	24	10.7777
......	chr12:45309094-45309295(-)$1	1	139	145	14.0317
...)))	chr1:174209728-174209929(-)$1	1	186	192	10.7777
......	chr11:29607512-29607713(+)$1	1	138	144	11.0158
......	chr2:29866446-29866647(+)$1	1	17	23	10.7777
......	chr6:113712737-113712938(-)$1	1	127	133	10.0634
))))).	chr11:23333141-23333342(+)$1	1	142	148	11.0158
...(((	chrX:20291657-20291858(+)$1	1	36	42	10.7777
......	chr10:66682856-66683057(+)$1	1	17	23	10.4603
...(((	chr2:44851530-44851731(-)$1	1	22	28	14.0317
(((((.	chr5:77405372-77405573(+)$1	1	119	125	10.3015
((....	chr15:96528559-96528760(-)$1	1	10	16	14.0317
((....	chr15:96528558-96528759(-)$1	1	9	15	14.0317
....))	chr9:120483173-120483374(+)$1	1	31	37	10.4603
((((((	chr13:114384775-114384976(-)$1	1	33	39	11.0158
......	chr9:54263914-54264115(-)$1	1	42	48	10.0634
))))..	chr11:104285759-104285960(-)$1	1	63	69	11.0158
))....	chr14:60898835-60899036(+)$1	1	178	184	10.4603
))).))	chr7:17147927-17148128(-)$1	1	152	158	14.0317
......	chr8:67087886-67088087(-)$1	1	129	135	14.0317
....))	chr9:120483174-120483375(+)$1	1	30	36	10.4603
(((..(	chr17:85464974-85465175(-)$1	1	73	79	11.0158
((.((.	chr9:62221226-62221427(+)$1	1	18	24	10.7777
((((..	chr2:109836629-109836830(+)$1	1	35	41	11.0158
((....	chr12:88029810-88030011(+)$1	1	15	21	10.7777
......	chr11:109528870-109529071(+)$1	1	97	103	10.3809
......	chr12:76823578-76823779(-)$1	1	29	35	10.7777
((..((	chr16:37536060-37536261(-)$1	1	78	84	9.5079
......	chr10:59763439-59763640(+)$1	1	0	6	10.0634
......	chr1:196633638-196633839(+)$1	1	23	29	10.4603
((((((	chr11:42300679-42300880(+)$1	1	38	44	10.4603
....))	chr1:63206272-63206473(-)$1	1	185	191	14.0317
......	chr15:31432414-31432615(-)$1	1	157	163	11.0158
.....(	chr10:59569169-59569370(+)$1	1	155	161	10.4603
......	chr1:39599188-39599389(+)$1	1	35	41	9.9047
)))...	chrX:71104631-71104832(-)$1	1	71	77	10.7777
))).))	chr7:17147928-17148129(-)$1	1	153	159	14.0317
))))))	chr2:121128803-121129004(+)$1	1	177	183	10.3809
.)))))	chr9:58471460-58471661(+)$1	1	8	14	10.0634
......	chr8:67087887-67088088(-)$1	1	130	136	14.0317
((.((.	chr14:24133423-24133624(-)$1	1	75	81	10.3809
...(((	chr8:67073669-67073870(-)$1	1	17	23	10.7777
.(((((	chr4:95669064-95669265(+)$1	1	55	61	10.3809
))))))	chr12:105941118-105941319(-)$1	1	159	165	10.3015

#PSSM
C : 0.79	U : 0.07	A : 0.07	G : 0.04	
U : 0.99	
U : 0.87	G : 0.07	C : 0.04	
U : 0.79	C : 0.19	G : 0.01	
C : 0.95	U : 0.04	
A : 0.79	C : 0.14	U : 0.06	

#score	707.3333333333327
#seq	63
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_transcript_m1_run2.nuc.txt

#NT
uucug	chr15:25558099-25558345(+)$1	246	29	34	15.0000
UUCUG	chr10:80829813-80830060(-)$1	247	240	245	15.0000
UUCUG	chr11:101528971-101529234(+)$1	263	10	15	15.0000
UUCUG	chr10:59412654-59412891(-)$1	237	50	55	15.0000
UUCUG	chrX:71468736-71469034(-)$1	298	145	150	15.0000
UUCUG	chr15:63920090-63920359(-)$1	269	166	171	15.0000
uucug	chr18:76424333-76424581(+)$1	248	167	172	15.0000
UUCUG	chr13:43261722-43261960(-)$1	238	201	206	15.0000
UUCUG	chr8:49709686-49709934(-)$1	248	130	135	15.0000
uucug	chr5:5117644-5117887(-)$1	243	54	59	15.0000
UUCUG	chr6:17055222-17055520(+)$1	298	43	48	15.0000
UUCUG	chr17:5280345-5280597(+)$1	252	135	140	15.0000
UUCUG	chr9:100544673-100544910(+)$1	237	17	22	15.0000
uucug	chr2:59017989-59018235(+)$1	246	127	132	15.0000
UUCUG	chr15:32964173-32964436(+)$1	263	51	56	15.0000
UUCUG	chr11:120668453-120668688(-)$1	235	185	190	15.0000
UUCUG	chr2:52324308-52324544(-)$1	236	120	125	15.0000
UUCUG	chr17:63066991-63067226(-)$1	235	36	41	15.0000
UUCUG	chr2:102689864-102690113(-)$1	249	93	98	15.0000
UUCUG	chr2:109851520-109851772(+)$1	252	47	52	15.0000
UUCUG	chr2:6746203-6746448(-)$1	245	223	228	15.0000
UUCUG	chr2:142510301-142510538(-)$1	237	104	109	15.0000
UUCUG	chr5:36621407-36621653(-)$1	246	186	191	15.0000
UUCUG	chr15:31191022-31191260(+)$1	238	78	83	15.0000
UUCUG	chr2:5798958-5799193(-)$1	235	109	114	15.0000
uucug	chr19:44170109-44170361(-)$1	252	129	134	15.0000
uucug	chr15:86137227-86137483(+)$1	256	23	28	15.0000
uucug	chr11:20618682-20618919(-)$1	237	4	9	15.0000
UUCUG	chr16:22255764-22256009(-)$1	245	109	114	15.0000
UUCUG	chr11:120668301-120668548(-)$1	247	45	50	15.0000
UUCUG	chr7:118875583-118875821(-)$1	238	124	129	15.0000
uucug	chr7:87922487-87922728(-)$1	241	13	18	15.0000
UUCUG	chr19:45824779-45825016(-)$1	237	67	72	15.0000
uucug	chr15:77020174-77020424(-)$1	250	128	133	15.0000
uucug	chr11:68636631-68636877(-)$1	246	150	155	15.0000
UUCUG	chr10:127828650-127828926(+)$1	276	146	151	15.0000
UUCUG	chr2:103869140-103869375(+)$1	235	34	39	15.0000
UUCUG	chr4:147968536-147968792(+)$1	256	238	243	15.0000
UUCUG	chr15:77043388-77043632(-)$1	244	173	178	15.0000
UUCUG	chr8:41585985-41586237(-)$1	252	230	235	15.0000
UUCUG	chr15:36176827-36177090(-)$1	263	2	7	15.0000
UUCUG	chr5:36721972-36722213(-)$1	241	155	160	15.0000
UUCUG	chr10:126501833-126502077(+)$1	244	31	36	15.0000
UUCUG	chr9:48276680-48276921(-)$1	241	176	181	15.0000
uucug	chr13:110626474-110626774(+)$1	300	149	154	15.0000
UUCUG	chr16:94595005-94595268(+)$1	263	11	16	15.0000
UUCUG	chr1:78703063-78703324(+)$1	261	134	139	15.0000
UUCUG	chr17:57164622-57164877(-)$1	255	182	187	15.0000
UUCUG	chr3:51568257-51568505(-)$1	248	191	196	15.0000
UUCUG	chr4:63640821-63641080(-)$1	259	98	103	15.0000

#otherMatches

#Struct PSSM
FFFFF	chr11:98834684-98834947(+)$1	263	9	14	15.0000
qqqqq	chr15:25558099-25558345(+)$1	246	29	34	15.0000
IIIII	chr10:80829813-80830060(-)$1	247	240	245	15.0000
qqqqq	chr11:101528971-101529234(+)$1	263	10	15	15.0000
HHHHe	chr10:59412654-59412891(-)$1	237	50	55	15.0000
dd===	chrX:71468736-71469034(-)$1	298	145	150	15.0000
fffff	chr15:63920090-63920359(-)$1	269	166	171	15.0000
[bb!!	chr18:76424333-76424581(+)$1	248	167	172	15.0000
yyyyy	chr13:43261722-43261960(-)$1	238	201	206	15.0000
ellle	chr8:49709686-49709934(-)$1	248	130	135	15.0000
mmmmb	chr5:5117644-5117887(-)$1	243	54	59	15.0000
dd::C	chr6:17055222-17055520(+)$1	298	43	48	15.0000
HHA}A	chr17:5280345-5280597(+)$1	252	135	140	15.0000
GGGA{	chr9:100544673-100544910(+)$1	237	17	22	15.0000
:eeee	chr2:59017989-59018235(+)$1	246	127	132	15.0000
eeabb	chr15:32964173-32964436(+)$1	263	51	56	15.0000
9gggg	chr11:120668453-120668688(-)$1	235	185	190	15.0000
33ccc	chr2:52324308-52324544(-)$1	236	120	125	15.0000
hhhhh	chr17:63066991-63067226(-)$1	235	36	41	15.0000
wwwwe	chr2:102689864-102690113(-)$1	249	93	98	15.0000
::::b	chr2:109851520-109851772(+)$1	252	47	52	15.0000
ggggg	chr2:6746203-6746448(-)$1	245	223	228	15.0000
5555b	chr2:142510301-142510538(-)$1	237	104	109	15.0000
ppppe	chr5:36621407-36621653(-)$1	246	186	191	15.0000
:::ee	chr15:31191022-31191260(+)$1	238	78	83	15.0000
eeddd	chr2:5798958-5799193(-)$1	235	109	114	15.0000
:::::	chr19:44170109-44170361(-)$1	252	129	134	15.0000
!!a""	chr15:86137227-86137483(+)$1	256	23	28	15.0000
:::::	chr11:20618682-20618919(-)$1	237	4	9	15.0000
pffff	chr16:22255764-22256009(-)$1	245	109	114	15.0000
>>>>d	chr11:120668301-120668548(-)$1	247	45	50	15.0000
yyyyy	chr7:118875583-118875821(-)$1	238	124	129	15.0000
ppppf	chr7:87922487-87922728(-)$1	241	13	18	15.0000
::hhh	chr19:45824779-45825016(-)$1	237	67	72	15.0000
fffff	chr15:77020174-77020424(-)$1	250	128	133	15.0000
JJJJJ	chr11:68636631-68636877(-)$1	246	150	155	15.0000
[ccc[	chr10:127828650-127828926(+)$1	276	146	151	15.0000
ggggg	chr2:103869140-103869375(+)$1	235	34	39	15.0000
dddll	chr4:147968536-147968792(+)$1	256	238	243	15.0000
5555d	chr15:77043388-77043632(-)$1	244	173	178	15.0000
EEEE}	chr8:41585985-41586237(-)$1	252	230	235	15.0000
:IIII	chr15:36176827-36177090(-)$1	263	2	7	15.0000
33a22	chr5:36721972-36722213(-)$1	241	155	160	15.0000
HHHH{	chr10:126501833-126502077(+)$1	244	31	36	15.0000
fqqqq	chr9:48276680-48276921(-)$1	241	176	181	15.0000
22ddd	chr13:110626474-110626774(+)$1	300	149	154	15.0000
HHHHf	chr16:94595005-94595268(+)$1	263	11	16	15.0000
fffff	chr1:78703063-78703324(+)$1	261	134	139	15.0000
]eeee	chr17:57164622-57164877(-)$1	255	182	187	15.0000
=!!bb	chr3:51568257-51568505(-)$1	248	191	196	15.0000
KKCCC	chr4:63640821-63641080(-)$1	259	98	103	15.0000

#DB
(((((	chr11:98834684-98834947(+)$1	1	9	14	15.0000
.....	chr15:25558099-25558345(+)$1	1	29	34	15.0000
)))))	chr10:80829813-80830060(-)$1	1	240	245	15.0000
.....	chr11:101528971-101529234(+)$1	1	10	15	15.0000
(((((	chr10:59412654-59412891(-)$1	1	50	55	15.0000
(((((	chrX:71468736-71469034(-)$1	1	145	150	15.0000
(((((	chr15:63920090-63920359(-)$1	1	166	171	15.0000
.((..	chr18:76424333-76424581(+)$1	1	167	172	15.0000
.....	chr13:43261722-43261960(-)$1	1	201	206	15.0000
(...)	chr8:49709686-49709934(-)$1	1	130	135	15.0000
....)	chr5:5117644-5117887(-)$1	1	54	59	15.0000
))..)	chr6:17055222-17055520(+)$1	1	43	48	15.0000
))).)	chr17:5280345-5280597(+)$1	1	135	140	15.0000
((((.	chr9:100544673-100544910(+)$1	1	17	22	15.0000
.((((	chr2:59017989-59018235(+)$1	1	127	132	15.0000
(((((	chr15:32964173-32964436(+)$1	1	51	56	15.0000
.))))	chr11:120668453-120668688(-)$1	1	185	190	15.0000
..)))	chr2:52324308-52324544(-)$1	1	120	125	15.0000
(((((	chr17:63066991-63067226(-)$1	1	36	41	15.0000
....)	chr2:102689864-102690113(-)$1	1	93	98	15.0000
....(	chr2:109851520-109851772(+)$1	1	47	52	15.0000
)))))	chr2:6746203-6746448(-)$1	1	223	228	15.0000
....)	chr2:142510301-142510538(-)$1	1	104	109	15.0000
....)	chr5:36621407-36621653(-)$1	1	186	191	15.0000
...((	chr15:31191022-31191260(+)$1	1	78	83	15.0000
)))))	chr2:5798958-5799193(-)$1	1	109	114	15.0000
.....	chr19:44170109-44170361(-)$1	1	129	134	15.0000
..(..	chr15:86137227-86137483(+)$1	1	23	28	15.0000
.....	chr11:20618682-20618919(-)$1	1	4	9	15.0000
.))))	chr16:22255764-22256009(-)$1	1	109	114	15.0000
....)	chr11:120668301-120668548(-)$1	1	45	50	15.0000
.....	chr7:118875583-118875821(-)$1	1	124	129	15.0000
....)	chr7:87922487-87922728(-)$1	1	13	18	15.0000
..(((	chr19:45824779-45825016(-)$1	1	67	72	15.0000
)))))	chr15:77020174-77020424(-)$1	1	128	133	15.0000
)))))	chr11:68636631-68636877(-)$1	1	150	155	15.0000
.(((.	chr10:127828650-127828926(+)$1	1	146	151	15.0000
)))))	chr2:103869140-103869375(+)$1	1	34	39	15.0000
(((..	chr4:147968536-147968792(+)$1	1	238	243	15.0000
....)	chr15:77043388-77043632(-)$1	1	173	178	15.0000
)))).	chr8:41585985-41586237(-)$1	1	230	235	15.0000
.((((	chr15:36176827-36177090(-)$1	1	2	7	15.0000
..)..	chr5:36721972-36722213(-)$1	1	155	160	15.0000
((((.	chr10:126501833-126502077(+)$1	1	31	36	15.0000
(....	chr9:48276680-48276921(-)$1	1	176	181	15.0000
..)))	chr13:110626474-110626774(+)$1	1	149	154	15.0000
(((((	chr16:94595005-94595268(+)$1	1	11	16	15.0000
(((((	chr1:78703063-78703324(+)$1	1	134	139	15.0000
.))))	chr17:57164622-57164877(-)$1	1	182	187	15.0000
(..((	chr3:51568257-51568505(-)$1	1	191	196	15.0000
..(((	chr4:63640821-63641080(-)$1	1	98	103	15.0000

#PSSM
U : 0.78	u : 0.21	
U : 0.78	u : 0.21	
C : 0.78	c : 0.21	
U : 0.78	u : 0.21	
G : 0.78	g : 0.21	

#score	765.0000000000001
#seq	51
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_CDS_m1_run2.nuc.txt

#NT
UGGUGGA	chr14:55565114-55565368(-)$1	254	133	140	17.1111
UGGUGGA	chr1:34178373-34178608(+)$1	235	27	34	17.1111
UGGUGGA	chr8:71425001-71425238(+)$1	237	163	170	17.1111
UGGUGGA	chr5:122915945-122916192(-)$1	247	157	164	17.1111
UGGCGGA	chr11:54792867-54793114(-)$1	247	135	142	13.7777
CGGUGGA	chr6:113678312-113678549(-)$1	237	111	118	12.8518
UGGCGGA	chr4:126425743-126425995(-)$1	252	96	103	13.7777
UGAUGGA	chr3:95292215-95292460(+)$1	245	39	46	13.0370
UGCUGGA	chr5:122950679-122950926(-)$1	247	113	120	13.4074
UGGAGGA	chr15:100228029-100228266(-)$1	237	22	29	13.9629
UGGUCGA	chr6:29402139-29402374(+)$1	235	122	129	13.0370
UGGUGGU	chr8:121868357-121868592(+)$1	235	158	165	12.8518
UGCUGGA	chr2:163842323-163842558(+)$1	235	116	123	13.4074
uggugga	chr7:50553444-50553683(-)$1	239	87	94	17.1111
CGGUGGA	chr14:21598358-21598594(-)$1	236	178	185	12.8518
UGCUGGA	chr5:52575932-52576167(-)$1	235	166	173	13.4074
UGGUAGA	chr5:143533280-143533519(-)$1	239	5	12	13.2222
UGGUUGA	chr14:55570985-55571225(-)$1	240	161	168	13.0370
UGGUAGA	chrX:12738490-12738727(+)$1	237	21	28	13.2222
UGGUGGG	chr1:43180304-43180550(-)$1	246	124	131	12.8518
UGGUGGC	chr2:154519610-154519845(+)$1	235	167	174	12.8518
UGGGGGA	chr10:128243637-128243873(+)$1	236	113	120	13.7777
UGGGGGA	chr14:55566891-55567130(-)$1	239	12	19	13.7777
UGGAGGA	chr13:11843033-11843270(-)$1	237	155	162	13.9629
UCGUGGA	chr19:57229539-57229774(-)$1	235	60	67	12.4814
UGGUGGA	chr15:100233580-100233815(-)$1	235	12	19	17.1111

#otherMatches

#Struct PSSM
eeeee::	chr1:137742034-137742281(+)$1	247	112	119	13.9629
doooooo	chr14:55565114-55565368(-)$1	254	133	140	17.1111
hhooooo	chr1:34178373-34178608(+)$1	235	27	34	17.1111
ZGGGGGG	chr8:71425001-71425238(+)$1	237	163	170	17.1111
FFFFJJJ	chr5:122915945-122916192(-)$1	247	157	164	17.1111
b======	chr11:54792867-54793114(-)$1	247	135	142	13.7777
]dddd]e	chr6:113678312-113678549(-)$1	237	111	118	12.8518
::dddd[	chr4:126425743-126425995(-)$1	252	96	103	13.7777
mmmeeee	chr3:95292215-95292460(+)$1	245	39	46	13.0370
eeee[bb	chr5:122950679-122950926(-)$1	247	113	120	13.4074
:::eeee	chr15:100228029-100228266(-)$1	237	22	29	13.9629
$$fffff	chr6:29402139-29402374(+)$1	235	122	129	13.0370
22eeeee	chr8:121868357-121868592(+)$1	235	158	165	12.8518
eeedddd	chr2:163842323-163842558(+)$1	235	116	123	13.4074
:cccooo	chr7:50553444-50553683(-)$1	239	87	94	17.1111
hhh::::	chr14:21598358-21598594(-)$1	236	178	185	12.8518
e]bbbbm	chr5:52575932-52576167(-)$1	235	166	173	13.4074
HHHHHH{	chr5:143533280-143533519(-)$1	239	5	12	13.2222
GGGGGGG	chr14:55570985-55571225(-)$1	240	161	168	13.0370
gnnnnng	chrX:12738490-12738727(+)$1	237	21	28	13.2222
mmmmfff	chr1:43180304-43180550(-)$1	246	124	131	12.8518
ee]ccch	chr2:154519610-154519845(+)$1	235	167	174	12.8518
hhhhh22	chr10:128243637-128243873(+)$1	236	113	120	13.7777
DD{BBKK	chr14:55566891-55567130(-)$1	239	12	19	13.7777
~HHHHHH	chr13:11843033-11843270(-)$1	237	155	162	13.9629
##ccc!!	chr19:57229539-57229774(-)$1	235	60	67	12.4814
CCCCCCL	chr15:100233580-100233815(-)$1	235	12	19	17.1111

#DB
)))))..	chr1:137742034-137742281(+)$1	1	112	119	13.9629
(......	chr14:55565114-55565368(-)$1	1	133	140	17.1111
((.....	chr1:34178373-34178608(+)$1	1	27	34	17.1111
.))))))	chr8:71425001-71425238(+)$1	1	163	170	17.1111
)))))))	chr5:122915945-122916192(-)$1	1	157	164	17.1111
)))))))	chr11:54792867-54793114(-)$1	1	135	142	13.7777
.)))).)	chr6:113678312-113678549(-)$1	1	111	118	12.8518
..((((.	chr4:126425743-126425995(-)$1	1	96	103	13.7777
...))))	chr3:95292215-95292460(+)$1	1	39	46	13.0370
((((.((	chr5:122950679-122950926(-)$1	1	113	120	13.4074
...((((	chr15:100228029-100228266(-)$1	1	22	29	13.9629
..(((((	chr6:29402139-29402374(+)$1	1	122	129	13.0370
..)))))	chr8:121868357-121868592(+)$1	1	158	165	12.8518
(((((((	chr2:163842323-163842558(+)$1	1	116	123	13.4074
.(((...	chr7:50553444-50553683(-)$1	1	87	94	17.1111
)))....	chr14:21598358-21598594(-)$1	1	178	185	12.8518
).))((.	chr5:52575932-52576167(-)$1	1	166	173	13.4074
((((((.	chr5:143533280-143533519(-)$1	1	5	12	13.2222
)))))))	chr14:55570985-55571225(-)$1	1	161	168	13.0370
(.....)	chrX:12738490-12738727(+)$1	1	21	28	13.2222
....)))	chr1:43180304-43180550(-)$1	1	124	131	12.8518
)).)))(	chr2:154519610-154519845(+)$1	1	167	174	12.8518
)))))..	chr10:128243637-128243873(+)$1	1	113	120	13.7777
((.((..	chr14:55566891-55567130(-)$1	1	12	19	13.7777
.))))))	chr13:11843033-11843270(-)$1	1	155	162	13.9629
..(((..	chr19:57229539-57229774(-)$1	1	60	67	12.4814
((((((.	chr15:100233580-100233815(-)$1	1	12	19	17.1111

#PSSM
U : 0.88	C : 0.07	u : 0.03	
G : 0.92	g : 0.03	C : 0.03	
G : 0.81	C : 0.11	A : 0.03	g : 0.03	
U : 0.70	A : 0.11	C : 0.07	G : 0.07	u : 0.03	
G : 0.81	A : 0.07	C : 0.03	g : 0.03	U : 0.03	
G : 0.96	g : 0.03	
A : 0.85	U : 0.03	a : 0.03	G : 0.03	C : 0.03	

#score	382.18518518518493
#seq	27
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m2_run2.nuc.txt

#NT
AGC	chr17:8535087-8535334(+)$1	247	101	104	8.9999
AGC	chr8:75228813-75229031(-)$1	218	81	84	8.9999
AGC	chr5:122231321-122231543(+)$1	222	108	111	8.9999
AGC	chr5:30926720-30926944(+)$1	224	12	15	8.9999
AGC	chr14:22559305-22559530(-)$1	225	2	5	8.9999
AGC	chr2:180717009-180717240(+)$1	231	32	35	8.9999
AGC	chr11:96902791-96903012(-)$1	221	4	7	8.9999
AGC	chr8:28089368-28089585(-)$1	217	18	21	8.9999
AGC	chr6:70715616-70715838(-)$1	222	70	73	8.9999
AGC	chr5:141228329-141228549(-)$1	220	62	65	8.9999
AGC	chr6:119874389-119874608(+)$1	219	35	38	8.9999
AGC	chr5:35251760-35251990(+)$1	230	30	33	8.9999
AGC	chr5:8072573-8072793(-)$1	220	41	44	8.9999
AGC	chr3:95997789-95998029(+)$1	240	15	18	8.9999
AGC	chr11:7073225-7073446(+)$1	221	34	37	8.9999
AGC	chr2:132133342-132133565(+)$1	223	64	67	8.9999
AGC	chr16:91671695-91671915(+)$1	220	38	41	8.9999
AGC	chr7:4097119-4097348(+)$1	229	23	26	8.9999
AGC	chr11:20549586-20549809(+)$1	223	3	6	8.9999
AGC	chr9:34843262-34843478(+)$1	216	6	9	8.9999
AGC	chr8:108403306-108403528(-)$1	222	25	28	8.9999
AGC	chr2:124491263-124491491(+)$1	228	14	17	8.9999
AGC	chr7:140177463-140177685(-)$1	222	155	158	8.9999
AGC	chr7:133635965-133636190(-)$1	225	85	88	8.9999
AGC	chr8:73901988-73902221(-)$1	233	26	29	8.9999
AGC	chr12:92795384-92795610(-)$1	226	28	31	8.9999
AGC	chr5:112807075-112807292(+)$1	217	18	21	8.9999
AGC	chr3:9430873-9431096(-)$1	223	23	26	8.9999
AGC	chr17:24213887-24214109(-)$1	222	12	15	8.9999
AGC	chr18:65375284-65375507(+)$1	223	18	21	8.9999
AGC	chr12:25345259-25345480(+)$1	221	1	4	8.9999
AGC	chr17:24551862-24552089(+)$1	227	67	70	8.9999
AGC	chr5:43677809-43678032(+)$1	223	61	64	8.9999
AGC	chr7:71032924-71033177(-)$1	253	48	51	8.9999
agc	chr7:134335357-134335578(+)$1	221	64	67	8.9999
AGC	chr2:119643208-119643436(+)$1	228	89	92	8.9999
AGC	chr17:30354437-30354665(-)$1	228	6	9	8.9999
AGC	chr19:55173768-55173988(+)$1	220	8	11	8.9999
AGC	chr11:106021689-106021909(+)$1	220	54	57	8.9999
AGC	chr3:152450137-152450359(+)$1	222	26	29	8.9999
AGC	chr11:3603732-3603964(+)$1	232	73	76	8.9999
AGC	chr1:175265188-175265420(-)$1	232	4	7	8.9999
AGC	chr5:150025230-150025462(+)$1	232	19	22	8.9999
AGC	chr2:104268869-104269104(-)$1	235	168	171	8.9999
agc	chr8:72618418-72618658(-)$1	240	3	6	8.9999
AGC	chr16:20736915-20737130(+)$1	215	17	20	8.9999
AGC	chr8:127418908-127419133(-)$1	225	62	65	8.9999
AGC	chr17:10406313-10406538(-)$1	225	133	136	8.9999
AGC	chr3:94305992-94306207(+)$1	215	115	118	8.9999
AGC	chr14:28294827-28295054(+)$1	227	125	128	8.9999
AGC	chr10:95007672-95007901(+)$1	229	55	58	8.9999
AGC	chr2:29953778-29954003(-)$1	225	45	48	8.9999
AGC	chr14:118512108-118512330(-)$1	222	5	8	8.9999
agc	chr6:113340151-113340369(-)$1	218	10	13	8.9999
AGC	chr4:122868190-122868411(+)$1	221	6	9	8.9999
AGC	chr1:173318312-173318528(+)$1	216	206	209	8.9999
AGC	chr14:47941339-47941565(+)$1	226	38	41	8.9999
AGC	chr4:53800486-53800711(-)$1	225	69	72	8.9999
AGC	chr4:123059781-123060015(-)$1	234	92	95	8.9999
AGC	chr1:33795050-33795265(-)$1	215	116	119	8.9999
AGC	chr4:133236051-133236277(-)$1	226	33	36	8.9999
AGC	chr12:88033157-88033386(+)$1	229	66	69	8.9999
AGC	chr8:72411585-72411807(-)$1	222	1	4	8.9999
AGC	chrX:153597507-153597732(+)$1	225	41	44	8.9999
AGC	chr17:54413357-54413580(-)$1	223	115	118	8.9999
AGC	chr2:17947183-17947400(-)$1	217	25	28	8.9999
AGC	chr5:134618189-134618436(+)$1	247	7	10	8.9999
AGC	chr14:26483359-26483580(+)$1	221	3	6	8.9999
AGC	chr2:3423198-3423417(-)$1	219	13	16	8.9999
AGC	chr2:127282394-127282617(+)$1	223	6	9	8.9999
AGC	chr18:73750734-73750962(+)$1	228	5	8	8.9999
AGC	chr7:134336188-134336433(-)$1	245	25	28	8.9999
AGC	chr6:52127422-52127650(-)$1	228	39	42	8.9999
Agc	chr1:74902964-74903184(+)$1	220	201	204	8.9999
AGC	chr4:14881402-14881623(-)$1	221	1	4	8.9999
AGC	chr5:108537545-108537770(+)$1	225	31	34	8.9999
AGC	chr2:32089542-32089771(+)$1	229	9	12	8.9999
AGC	chr4:107478976-107479196(+)$1	220	5	8	8.9999
AGC	chr13:34273450-34273678(-)$1	228	6	9	8.9999
AGC	chr4:130379027-130379249(+)$1	222	97	100	8.9999
AGC	chr9:21767773-21767994(+)$1	221	42	45	8.9999
AGC	chr14:67605882-67606109(-)$1	227	3	6	8.9999
AGC	chr13:54781525-54781751(-)$1	226	15	18	8.9999
AGC	chr5:36834561-36834779(-)$1	218	41	44	8.9999
AGC	chr8:32270484-32270717(-)$1	233	10	13	8.9999
AGC	chr3:146393868-146394092(-)$1	224	37	40	8.9999
AGC	chr6:122678061-122678279(-)$1	218	195	198	8.9999
AGC	chr2:104596996-104597219(-)$1	223	58	61	8.9999
AGC	chr11:45958303-45958533(+)$1	230	54	57	8.9999
AGC	chr14:9091360-9091577(-)$1	217	22	25	8.9999
AGC	chr1:178953114-178953349(-)$1	235	0	3	8.9999
AGC	chr6:115970354-115970574(-)$1	220	3	6	8.9999
AGC	chr16:64857833-64858059(+)$1	226	58	61	8.9999
AGC	chr1:36323046-36323267(-)$1	221	191	194	8.9999
AGC	chr7:69494185-69494417(+)$1	232	15	18	8.9999

#otherMatches

#Struct PSSM
ggg	chr9:119836699-119836958(-)$1	259	21	24	8.9999
mmm	chr17:8535087-8535334(+)$1	247	101	104	8.9999
hh]	chr8:75228813-75229031(-)$1	218	81	84	8.9999
[cc	chr5:122231321-122231543(+)$1	222	108	111	8.9999
off	chr5:30926720-30926944(+)$1	224	12	15	8.9999
[cc	chr14:22559305-22559530(-)$1	225	2	5	8.9999
GG{	chr2:180717009-180717240(+)$1	231	32	35	8.9999
bb[	chr11:96902791-96903012(-)$1	221	4	7	8.9999
GGG	chr8:28089368-28089585(-)$1	217	18	21	8.9999
EE:	chr6:70715616-70715838(-)$1	222	70	73	8.9999
eem	chr5:141228329-141228549(-)$1	220	62	65	8.9999
ggg	chr6:119874389-119874608(+)$1	219	35	38	8.9999
dd[	chr5:35251760-35251990(+)$1	230	30	33	8.9999
ggg	chr5:8072573-8072793(-)$1	220	41	44	8.9999
#bb	chr3:95997789-95998029(+)$1	240	15	18	8.9999
GGG	chr11:7073225-7073446(+)$1	221	34	37	8.9999
[ee	chr2:132133342-132133565(+)$1	223	64	67	8.9999
iia	chr16:91671695-91671915(+)$1	220	38	41	8.9999
$$$	chr7:4097119-4097348(+)$1	229	23	26	8.9999
DEE	chr11:20549586-20549809(+)$1	223	3	6	8.9999
E{H	chr9:34843262-34843478(+)$1	216	6	9	8.9999
GGG	chr8:108403306-108403528(-)$1	222	25	28	8.9999
{CC	chr2:124491263-124491491(+)$1	228	14	17	8.9999
ggg	chr7:140177463-140177685(-)$1	222	155	158	8.9999
[dd	chr7:133635965-133636190(-)$1	225	85	88	8.9999
FFF	chr8:73901988-73902221(-)$1	233	26	29	8.9999
cbb	chr12:92795384-92795610(-)$1	226	28	31	8.9999
HBB	chr5:112807075-112807292(+)$1	217	18	21	8.9999
CC{	chr3:9430873-9431096(-)$1	223	23	26	8.9999
nnn	chr17:24213887-24214109(-)$1	222	12	15	8.9999
[ii	chr18:65375284-65375507(+)$1	223	18	21	8.9999
:::	chr12:25345259-25345480(+)$1	221	1	4	8.9999
iii	chr17:24551862-24552089(+)$1	227	67	70	8.9999
dd:	chr5:43677809-43678032(+)$1	223	61	64	8.9999
D{C	chr7:71032924-71033177(-)$1	253	48	51	8.9999
ttt	chr7:134335357-134335578(+)$1	221	64	67	8.9999
DDD	chr2:119643208-119643436(+)$1	228	89	92	8.9999
:FF	chr17:30354437-30354665(-)$1	228	6	9	8.9999
!cc	chr19:55173768-55173988(+)$1	220	8	11	8.9999
eee	chr11:106021689-106021909(+)$1	220	54	57	8.9999
!!b	chr3:152450137-152450359(+)$1	222	26	29	8.9999
22f	chr11:3603732-3603964(+)$1	232	73	76	8.9999
ffd	chr1:175265188-175265420(-)$1	232	4	7	8.9999
MCC	chr5:150025230-150025462(+)$1	232	19	22	8.9999
fff	chr2:104268869-104269104(-)$1	235	168	171	8.9999
BB{	chr8:72618418-72618658(-)$1	240	3	6	8.9999
GG{	chr16:20736915-20737130(+)$1	215	17	20	8.9999
FFF	chr8:127418908-127419133(-)$1	225	62	65	8.9999
fdd	chr17:10406313-10406538(-)$1	225	133	136	8.9999
C}A	chr3:94305992-94306207(+)$1	215	115	118	8.9999
00h	chr14:28294827-28295054(+)$1	227	125	128	8.9999
:dd	chr10:95007672-95007901(+)$1	229	55	58	8.9999
:ee	chr2:29953778-29954003(-)$1	225	45	48	8.9999
DDL	chr14:118512108-118512330(-)$1	222	5	8	8.9999
fff	chr6:113340151-113340369(-)$1	218	10	13	8.9999
FFF	chr4:122868190-122868411(+)$1	221	6	9	8.9999
cc]	chr1:173318312-173318528(+)$1	216	206	209	8.9999
===	chr14:47941339-47941565(+)$1	226	38	41	8.9999
:DD	chr4:53800486-53800711(-)$1	225	69	72	8.9999
fff	chr4:123059781-123060015(-)$1	234	92	95	8.9999
bbx	chr1:33795050-33795265(-)$1	215	116	119	8.9999
:::	chr4:133236051-133236277(-)$1	226	33	36	8.9999
iii	chr12:88033157-88033386(+)$1	229	66	69	8.9999
:::	chr8:72411585-72411807(-)$1	222	1	4	8.9999
ggg	chrX:153597507-153597732(+)$1	225	41	44	8.9999
+++	chr17:54413357-54413580(-)$1	223	115	118	8.9999
+==	chr2:17947183-17947400(-)$1	217	25	28	8.9999
KKB	chr5:134618189-134618436(+)$1	247	7	10	8.9999
FFF	chr14:26483359-26483580(+)$1	221	3	6	8.9999
CKK	chr2:3423198-3423417(-)$1	219	13	16	8.9999
ddd	chr2:127282394-127282617(+)$1	223	6	9	8.9999
NNN	chr18:73750734-73750962(+)$1	228	5	8	8.9999
eee	chr7:134336188-134336433(-)$1	245	25	28	8.9999
ddd	chr6:52127422-52127650(-)$1	228	39	42	8.9999
JJJ	chr1:74902964-74903184(+)$1	220	201	204	8.9999
CC{	chr4:14881402-14881623(-)$1	221	1	4	8.9999
cc#	chr5:108537545-108537770(+)$1	225	31	34	8.9999
CC{	chr2:32089542-32089771(+)$1	229	9	12	8.9999
:ee	chr4:107478976-107479196(+)$1	220	5	8	8.9999
:EE	chr13:34273450-34273678(-)$1	228	6	9	8.9999
ee>	chr4:130379027-130379249(+)$1	222	97	100	8.9999
ddd	chr9:21767773-21767994(+)$1	221	42	45	8.9999
ggg	chr14:67605882-67606109(-)$1	227	3	6	8.9999
ggg	chr13:54781525-54781751(-)$1	226	15	18	8.9999
FFF	chr5:36834561-36834779(-)$1	218	41	44	8.9999
eee	chr8:32270484-32270717(-)$1	233	10	13	8.9999
b$$	chr3:146393868-146394092(-)$1	224	37	40	8.9999
ddd	chr6:122678061-122678279(-)$1	218	195	198	8.9999
ccc	chr2:104596996-104597219(-)$1	223	58	61	8.9999
]bb	chr11:45958303-45958533(+)$1	230	54	57	8.9999
cc[	chr14:9091360-9091577(-)$1	217	22	25	8.9999
bb[	chr1:178953114-178953349(-)$1	235	0	3	8.9999
[cc	chr6:115970354-115970574(-)$1	220	3	6	8.9999
FFF	chr16:64857833-64858059(+)$1	226	58	61	8.9999
EEE	chr1:36323046-36323267(-)$1	221	191	194	8.9999
ooo	chr7:69494185-69494417(+)$1	232	15	18	8.9999

#DB
(((	chr9:119836699-119836958(-)$1	1	21	24	8.9999
...	chr17:8535087-8535334(+)$1	1	101	104	8.9999
)).	chr8:75228813-75229031(-)$1	1	81	84	8.9999
.((	chr5:122231321-122231543(+)$1	1	108	111	8.9999
.))	chr5:30926720-30926944(+)$1	1	12	15	8.9999
.((	chr14:22559305-22559530(-)$1	1	2	5	8.9999
((.	chr2:180717009-180717240(+)$1	1	32	35	8.9999
((.	chr11:96902791-96903012(-)$1	1	4	7	8.9999
(((	chr8:28089368-28089585(-)$1	1	18	21	8.9999
((.	chr6:70715616-70715838(-)$1	1	70	73	8.9999
((.	chr5:141228329-141228549(-)$1	1	62	65	8.9999
(((	chr6:119874389-119874608(+)$1	1	35	38	8.9999
((.	chr5:35251760-35251990(+)$1	1	30	33	8.9999
)))	chr5:8072573-8072793(-)$1	1	41	44	8.9999
.((	chr3:95997789-95998029(+)$1	1	15	18	8.9999
(((	chr11:7073225-7073446(+)$1	1	34	37	8.9999
.((	chr2:132133342-132133565(+)$1	1	64	67	8.9999
(((	chr16:91671695-91671915(+)$1	1	38	41	8.9999
...	chr7:4097119-4097348(+)$1	1	23	26	8.9999
(((	chr11:20549586-20549809(+)$1	1	3	6	8.9999
(.(	chr9:34843262-34843478(+)$1	1	6	9	8.9999
(((	chr8:108403306-108403528(-)$1	1	25	28	8.9999
.((	chr2:124491263-124491491(+)$1	1	14	17	8.9999
)))	chr7:140177463-140177685(-)$1	1	155	158	8.9999
.((	chr7:133635965-133636190(-)$1	1	85	88	8.9999
(((	chr8:73901988-73902221(-)$1	1	26	29	8.9999
)((	chr12:92795384-92795610(-)$1	1	28	31	8.9999
(((	chr5:112807075-112807292(+)$1	1	18	21	8.9999
((.	chr3:9430873-9431096(-)$1	1	23	26	8.9999
...	chr17:24213887-24214109(-)$1	1	12	15	8.9999
.((	chr18:65375284-65375507(+)$1	1	18	21	8.9999
...	chr12:25345259-25345480(+)$1	1	1	4	8.9999
(((	chr17:24551862-24552089(+)$1	1	67	70	8.9999
)).	chr5:43677809-43678032(+)$1	1	61	64	8.9999
(.(	chr7:71032924-71033177(-)$1	1	48	51	8.9999
...	chr7:134335357-134335578(+)$1	1	64	67	8.9999
(((	chr2:119643208-119643436(+)$1	1	89	92	8.9999
.((	chr17:30354437-30354665(-)$1	1	6	9	8.9999
.((	chr19:55173768-55173988(+)$1	1	8	11	8.9999
(((	chr11:106021689-106021909(+)$1	1	54	57	8.9999
..(	chr3:152450137-152450359(+)$1	1	26	29	8.9999
..)	chr11:3603732-3603964(+)$1	1	73	76	8.9999
(((	chr1:175265188-175265420(-)$1	1	4	7	8.9999
.((	chr5:150025230-150025462(+)$1	1	19	22	8.9999
(((	chr2:104268869-104269104(-)$1	1	168	171	8.9999
((.	chr8:72618418-72618658(-)$1	1	3	6	8.9999
((.	chr16:20736915-20737130(+)$1	1	17	20	8.9999
(((	chr8:127418908-127419133(-)$1	1	62	65	8.9999
(((	chr17:10406313-10406538(-)$1	1	133	136	8.9999
).)	chr3:94305992-94306207(+)$1	1	115	118	8.9999
..)	chr14:28294827-28295054(+)$1	1	125	128	8.9999
.((	chr10:95007672-95007901(+)$1	1	55	58	8.9999
.((	chr2:29953778-29954003(-)$1	1	45	48	8.9999
((.	chr14:118512108-118512330(-)$1	1	5	8	8.9999
(((	chr6:113340151-113340369(-)$1	1	10	13	8.9999
(((	chr4:122868190-122868411(+)$1	1	6	9	8.9999
)).	chr1:173318312-173318528(+)$1	1	206	209	8.9999
)))	chr14:47941339-47941565(+)$1	1	38	41	8.9999
.((	chr4:53800486-53800711(-)$1	1	69	72	8.9999
)))	chr4:123059781-123060015(-)$1	1	92	95	8.9999
((.	chr1:33795050-33795265(-)$1	1	116	119	8.9999
...	chr4:133236051-133236277(-)$1	1	33	36	8.9999
(((	chr12:88033157-88033386(+)$1	1	66	69	8.9999
...	chr8:72411585-72411807(-)$1	1	1	4	8.9999
(((	chrX:153597507-153597732(+)$1	1	41	44	8.9999
...	chr17:54413357-54413580(-)$1	1	115	118	8.9999
.((	chr2:17947183-17947400(-)$1	1	25	28	8.9999
..(	chr5:134618189-134618436(+)$1	1	7	10	8.9999
(((	chr14:26483359-26483580(+)$1	1	3	6	8.9999
(..	chr2:3423198-3423417(-)$1	1	13	16	8.9999
(((	chr2:127282394-127282617(+)$1	1	6	9	8.9999
...	chr18:73750734-73750962(+)$1	1	5	8	8.9999
(((	chr7:134336188-134336433(-)$1	1	25	28	8.9999
)))	chr6:52127422-52127650(-)$1	1	39	42	8.9999
)))	chr1:74902964-74903184(+)$1	1	201	204	8.9999
((.	chr4:14881402-14881623(-)$1	1	1	4	8.9999
((.	chr5:108537545-108537770(+)$1	1	31	34	8.9999
((.	chr2:32089542-32089771(+)$1	1	9	12	8.9999
.((	chr4:107478976-107479196(+)$1	1	5	8	8.9999
.((	chr13:34273450-34273678(-)$1	1	6	9	8.9999
)).	chr4:130379027-130379249(+)$1	1	97	100	8.9999
)))	chr9:21767773-21767994(+)$1	1	42	45	8.9999
(((	chr14:67605882-67606109(-)$1	1	3	6	8.9999
(((	chr13:54781525-54781751(-)$1	1	15	18	8.9999
(((	chr5:36834561-36834779(-)$1	1	41	44	8.9999
(((	chr8:32270484-32270717(-)$1	1	10	13	8.9999
(..	chr3:146393868-146394092(-)$1	1	37	40	8.9999
(((	chr6:122678061-122678279(-)$1	1	195	198	8.9999
(((	chr2:104596996-104597219(-)$1	1	58	61	8.9999
.))	chr11:45958303-45958533(+)$1	1	54	57	8.9999
((.	chr14:9091360-9091577(-)$1	1	22	25	8.9999
((.	chr1:178953114-178953349(-)$1	1	0	3	8.9999
.((	chr6:115970354-115970574(-)$1	1	3	6	8.9999
(((	chr16:64857833-64858059(+)$1	1	58	61	8.9999
)))	chr1:36323046-36323267(-)$1	1	191	194	8.9999
...	chr7:69494185-69494417(+)$1	1	15	18	8.9999

#PSSM
A : 0.96	a : 0.03	
G : 0.95	g : 0.04	
C : 0.95	c : 0.04	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m2_run2.nuc.txt

#NT
AUUUCAA	chr11:29642590-29642878(+)$1	288	130	137	13.0161
GUUUUAA	chr5:107538225-107538463(-)$1	238	159	166	13.2580
AUUUUUA	chr5:115595369-115595620(-)$1	251	102	109	12.8548
AUCUUAA	chr11:29642168-29642473(+)$1	305	21	28	12.3709
AUUUUAA	chr9:74906055-74906290(+)$1	235	79	86	16.8870
UUUUUAA	chr4:109126112-109126352(-)$1	240	29	36	13.1774
AUUUUAC	chr6:5435274-5435523(-)$1	249	92	99	12.5322
AGUUUAA	chr11:20126227-20126468(+)$1	241	83	90	12.5322
AUUUGAA	chr13:23831577-23831839(+)$1	262	48	55	12.8548
UUUUUAA	chr6:30404407-30404667(+)$1	260	241	248	13.1774
GUUUUAA	chr11:51799963-51800205(-)$1	242	91	98	13.2580
AAUUUAA	chr4:104704900-104705153(-)$1	253	186	193	12.6129
AUUUUGA	chr3:89253899-89254141(+)$1	242	132	139	12.8548
aauuuaa	chr2:76542175-76542425(-)$1	250	205	212	12.6129
AUGUUAA	chr14:35374752-35374991(-)$1	239	7	14	12.3709
AUUUUAA	chr6:67235597-67235832(+)$1	235	74	81	16.8870
auuuaaa	chr3:126546663-126546898(+)$1	235	33	40	13.0161
AUUUUAA	chr3:141965425-141965660(-)$1	235	3	10	16.8870
AUUUUAG	chr13:29999174-29999409(-)$1	235	37	44	12.6129
AUUUUUA	chr4:107908261-107908497(-)$1	236	72	79	12.8548
AUUUUAA	chr7:91764019-91764255(-)$1	236	151	158	16.8870
UUUUUAA	chr1:82892197-82892444(+)$1	247	162	169	13.1774
AUUUAAA	chr19:27327567-27327806(+)$1	239	77	84	13.0161
GUUUUAA	chr17:71475852-71476088(+)$1	236	45	52	13.2580
AAUUUAA	chr11:29642759-29642996(+)$1	237	3	10	12.6129
AUUGUAA	chr6:71342636-71342873(-)$1	237	106	113	12.4516
AUUUCAA	chr3:116445886-116446121(-)$1	235	39	46	13.0161
AUUUUAC	chr19:12841729-12841976(-)$1	247	99	106	12.5322
GUUUUAA	chr14:21479143-21479380(-)$1	237	9	16	13.2580
AGUUUAA	chr5:136386537-136386774(-)$1	237	186	193	12.5322
AUUUAAA	chr5:89088503-89088749(-)$1	246	193	200	13.0161
GUUUUAA	chr16:44160392-44160638(+)$1	246	144	151	13.2580
AUAUUAA	chr8:35233354-35233615(+)$1	261	191	198	12.5322
AUUUCAA	chr15:97962359-97962622(+)$1	263	95	102	13.0161
AUUUUAA	chr7:119254506-119254741(+)$1	235	95	102	16.8870
AUUUUCA	chr6:5434848-5435110(-)$1	262	51	58	12.8548
AUUUUUA	chr11:87896599-87896838(+)$1	239	178	185	12.8548
AUAUUAA	chr11:109530395-109530652(+)$1	257	8	15	12.5322
AUUUUAA	chr11:40562394-40562629(-)$1	235	135	142	16.8870
AUUUAAA	chr12:55960170-55960414(-)$1	244	1	8	13.0161
AUUUUAA	chr17:10406395-10406643(-)$1	248	204	211	16.8870
AUUUUCA	chr7:99792676-99792911(-)$1	235	98	105	12.8548
AUUUUAA	chr5:15878929-15879164(+)$1	235	175	182	16.8870
AUUUUAA	chr17:10400882-10401122(-)$1	240	28	35	16.8870
AUUUUCA	chr10:127514114-127514349(+)$1	235	199	206	12.8548
AUUUCAA	chr2:6465641-6465886(-)$1	245	19	26	13.0161
AUUUUAA	chr19:53447618-53447853(+)$1	235	64	71	16.8870
AUAUUAA	chr8:107740674-107740909(+)$1	235	11	18	12.5322
AUUGUAA	chr5:15878304-15878555(+)$1	251	37	44	12.4516
AUUUUAG	chr16:36035790-36036034(+)$1	244	179	186	12.6129
AUUUUGA	chr5:68012977-68013215(-)$1	238	14	21	12.8548
UUUUUAA	chr2:172179044-172179279(+)$1	235	221	228	13.1774
AUUAUAA	chr19:47809707-47809942(+)$1	235	22	29	12.2903
AUUUUAU	chr15:31385712-31385954(-)$1	242	200	207	12.4516
GUUUUAA	chr3:116445349-116445591(-)$1	242	37	44	13.2580
AUUUUAG	chr14:21319545-21319780(-)$1	235	11	18	12.6129
AUUUUAA	chr11:109529223-109529470(+)$1	247	101	108	16.8870
AUUUUGA	chr15:12114164-12114401(+)$1	237	86	93	12.8548
AUUGUAA	chr3:104260867-104261102(-)$1	235	12	19	12.4516
uuuuuaa	chr3:60430627-60430891(+)$1	264	57	64	13.1774
AUUUGAA	chrX:136207501-136207737(+)$1	236	96	103	12.8548

#otherMatches

#Struct PSSM
::::::c	chr2:127124410-127124658(+)$1	248	46	53	12.4516
]dddd:f	chr11:29642590-29642878(+)$1	288	130	137	13.0161
e4444ff	chr5:107538225-107538463(-)$1	238	159	166	13.2580
e]ccc]e	chr5:115595369-115595620(-)$1	251	102	109	12.8548
[cccggg	chr11:29642168-29642473(+)$1	305	21	28	12.3709
iiiiiii	chr9:74906055-74906290(+)$1	235	79	86	16.8870
FF:::::	chr4:109126112-109126352(-)$1	240	29	36	13.1774
qqqqqqd	chr6:5435274-5435523(-)$1	249	92	99	12.5322
gg22ccc	chr11:20126227-20126468(+)$1	241	83	90	12.5322
mdddd22	chr13:23831577-23831839(+)$1	262	48	55	12.8548
hhhhhhh	chr6:30404407-30404667(+)$1	260	241	248	13.1774
###eeee	chr11:51799963-51800205(-)$1	242	91	98	13.2580
c[ddddo	chr4:104704900-104705153(-)$1	253	186	193	12.6129
:::::::	chr3:89253899-89254141(+)$1	242	132	139	12.8548
^^^^^^^	chr2:76542175-76542425(-)$1	250	205	212	12.6129
$$bb###	chr14:35374752-35374991(-)$1	239	7	14	12.3709
gggggg:	chr6:67235597-67235832(+)$1	235	74	81	16.8870
hhhhhhh	chr3:126546663-126546898(+)$1	235	33	40	13.0161
:::::::	chr3:141965425-141965660(-)$1	235	3	10	16.8870
JJJJJJJ	chr13:29999174-29999409(-)$1	235	37	44	12.6129
:::::::	chr4:107908261-107908497(-)$1	236	72	79	12.8548
>>>>>>>	chr7:91764019-91764255(-)$1	236	151	158	16.8870
]bb]bb]	chr1:82892197-82892444(+)$1	247	162	169	13.1774
ffffffi	chr19:27327567-27327806(+)$1	239	77	84	13.0161
2gggggg	chr17:71475852-71476088(+)$1	236	45	52	13.2580
c[ccc!!	chr11:29642759-29642996(+)$1	237	3	10	12.6129
rrra]dd	chr6:71342636-71342873(-)$1	237	106	113	12.4516
+++++ee	chr3:116445886-116446121(-)$1	235	39	46	13.0161
uuuuuuu	chr19:12841729-12841976(-)$1	247	99	106	12.5322
DDDDLLL	chr14:21479143-21479380(-)$1	237	9	16	13.2580
fffssss	chr5:136386537-136386774(-)$1	237	186	193	12.5322
fffff::	chr5:89088503-89088749(-)$1	246	193	200	13.0161
nnneeee	chr16:44160392-44160638(+)$1	246	144	151	13.2580
dd:::::	chr8:35233354-35233615(+)$1	261	191	198	12.5322
COOOOOO	chr15:97962359-97962622(+)$1	263	95	102	13.0161
55555dd	chr7:119254506-119254741(+)$1	235	95	102	16.8870
ffff[bb	chr6:5434848-5435110(-)$1	262	51	58	12.8548
>>>>>>>	chr11:87896599-87896838(+)$1	239	178	185	12.8548
:::::::	chr11:109530395-109530652(+)$1	257	8	15	12.5322
=====mm	chr11:40562394-40562629(-)$1	235	135	142	16.8870
GGGGGG:	chr12:55960170-55960414(-)$1	244	1	8	13.0161
]dddd44	chr17:10406395-10406643(-)$1	248	204	211	16.8870
=====33	chr7:99792676-99792911(-)$1	235	98	105	12.8548
b[ggggg	chr5:15878929-15879164(+)$1	235	175	182	16.8870
ddddeee	chr17:10400882-10401122(-)$1	240	28	35	16.8870
dd]ffff	chr10:127514114-127514349(+)$1	235	199	206	12.8548
:::::::	chr2:6465641-6465886(-)$1	245	19	26	13.0161
i''''''	chr19:53447618-53447853(+)$1	235	64	71	16.8870
eee::::	chr8:107740674-107740909(+)$1	235	11	18	12.5322
{DDDD::	chr5:15878304-15878555(+)$1	251	37	44	12.4516
DYYGGGG	chr16:36035790-36036034(+)$1	244	179	186	12.6129
mmmeeee	chr5:68012977-68013215(-)$1	238	14	21	12.8548
DDD????	chr2:172179044-172179279(+)$1	235	221	228	13.1774
ff!!ddd	chr19:47809707-47809942(+)$1	235	22	29	12.2903
333ccc]	chr15:31385712-31385954(-)$1	242	200	207	12.4516
cc(((((	chr3:116445349-116445591(-)$1	242	37	44	13.2580
KIIIIII	chr14:21319545-21319780(-)$1	235	11	18	12.6129
:ffffff	chr11:109529223-109529470(+)$1	247	101	108	16.8870
dd:::bb	chr15:12114164-12114401(+)$1	237	86	93	12.8548
f!!ccc!	chr3:104260867-104261102(-)$1	235	12	19	12.4516
cccqqqq	chr3:60430627-60430891(+)$1	264	57	64	13.1774
FFFFF::	chrX:136207501-136207737(+)$1	236	96	103	12.8548

#DB
......(	chr2:127124410-127124658(+)$1	1	46	53	12.4516
.)))).(	chr11:29642590-29642878(+)$1	1	130	137	13.0161
)....))	chr5:107538225-107538463(-)$1	1	159	166	13.2580
).))).)	chr5:115595369-115595620(-)$1	1	102	109	12.8548
.((((((	chr11:29642168-29642473(+)$1	1	21	28	12.3709
)))))))	chr9:74906055-74906290(+)$1	1	79	86	16.8870
((.....	chr4:109126112-109126352(-)$1	1	29	36	13.1774
......)	chr6:5435274-5435523(-)$1	1	92	99	12.5322
))..)))	chr11:20126227-20126468(+)$1	1	83	90	12.5322
.))))..	chr13:23831577-23831839(+)$1	1	48	55	12.8548
(((((((	chr6:30404407-30404667(+)$1	1	241	248	13.1774
...((((	chr11:51799963-51800205(-)$1	1	91	98	13.2580
(.((((.	chr4:104704900-104705153(-)$1	1	186	193	12.6129
.......	chr3:89253899-89254141(+)$1	1	132	139	12.8548
.......	chr2:76542175-76542425(-)$1	1	205	212	12.6129
..((...	chr14:35374752-35374991(-)$1	1	7	14	12.3709
)))))).	chr6:67235597-67235832(+)$1	1	74	81	16.8870
(((((((	chr3:126546663-126546898(+)$1	1	33	40	13.0161
.......	chr3:141965425-141965660(-)$1	1	3	10	16.8870
(((((((	chr13:29999174-29999409(-)$1	1	37	44	12.6129
.......	chr4:107908261-107908497(-)$1	1	72	79	12.8548
.......	chr7:91764019-91764255(-)$1	1	151	158	16.8870
.)).)).	chr1:82892197-82892444(+)$1	1	162	169	13.1774
(((((((	chr19:27327567-27327806(+)$1	1	77	84	13.0161
.))))))	chr17:71475852-71476088(+)$1	1	45	52	13.2580
(.(((..	chr11:29642759-29642996(+)$1	1	3	10	12.6129
...).))	chr6:71342636-71342873(-)$1	1	106	113	12.4516
.....((	chr3:116445886-116446121(-)$1	1	39	46	13.0161
.......	chr19:12841729-12841976(-)$1	1	99	106	12.5322
((((...	chr14:21479143-21479380(-)$1	1	9	16	13.2580
(((....	chr5:136386537-136386774(-)$1	1	186	193	12.5322
)))))..	chr5:89088503-89088749(-)$1	1	193	200	13.0161
...))))	chr16:44160392-44160638(+)$1	1	144	151	13.2580
)).....	chr8:35233354-35233615(+)$1	1	191	198	12.5322
(......	chr15:97962359-97962622(+)$1	1	95	102	13.0161
.....))	chr7:119254506-119254741(+)$1	1	95	102	16.8870
((((.((	chr6:5434848-5435110(-)$1	1	51	58	12.8548
.......	chr11:87896599-87896838(+)$1	1	178	185	12.8548
.......	chr11:109530395-109530652(+)$1	1	8	15	12.5322
(((((..	chr11:40562394-40562629(-)$1	1	135	142	16.8870
((((((.	chr12:55960170-55960414(-)$1	1	1	8	13.0161
.))))..	chr17:10406395-10406643(-)$1	1	204	211	16.8870
)))))..	chr7:99792676-99792911(-)$1	1	98	105	12.8548
(.(((((	chr5:15878929-15879164(+)$1	1	175	182	16.8870
(((((((	chr17:10400882-10401122(-)$1	1	28	35	16.8870
)).))))	chr10:127514114-127514349(+)$1	1	199	206	12.8548
.......	chr2:6465641-6465886(-)$1	1	19	26	13.0161
(......	chr19:53447618-53447853(+)$1	1	64	71	16.8870
)))....	chr8:107740674-107740909(+)$1	1	11	18	12.5322
.((((..	chr5:15878304-15878555(+)$1	1	37	44	12.4516
)..))))	chr16:36035790-36036034(+)$1	1	179	186	12.6129
...))))	chr5:68012977-68013215(-)$1	1	14	21	12.8548
)))....	chr2:172179044-172179279(+)$1	1	221	228	13.1774
((..(((	chr19:47809707-47809942(+)$1	1	22	29	12.2903
...))).	chr15:31385712-31385954(-)$1	1	200	207	12.4516
((.....	chr3:116445349-116445591(-)$1	1	37	44	13.2580
.((((((	chr14:21319545-21319780(-)$1	1	11	18	12.6129
.((((((	chr11:109529223-109529470(+)$1	1	101	108	16.8870
))...((	chr15:12114164-12114401(+)$1	1	86	93	12.8548
(..(((.	chr3:104260867-104261102(-)$1	1	12	19	12.4516
(((....	chr3:60430627-60430891(+)$1	1	57	64	13.1774
)))))..	chrX:136207501-136207737(+)$1	1	96	103	12.8548

#PSSM
A : 0.79	G : 0.09	U : 0.06	a : 0.03	u : 0.01	
U : 0.87	G : 0.03	A : 0.03	u : 0.03	C : 0.01	a : 0.01	
U : 0.87	u : 0.04	A : 0.04	C : 0.01	G : 0.01	
U : 0.88	u : 0.04	G : 0.04	A : 0.01	
U : 0.80	C : 0.06	A : 0.04	G : 0.03	u : 0.03	a : 0.01	
A : 0.80	U : 0.04	G : 0.04	a : 0.04	C : 0.04	
A : 0.85	a : 0.04	G : 0.04	C : 0.03	U : 0.01	

#score	839.4193548387088
#seq	62
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_UTR_m1_run2.nuc.txt

#NT
UUUUUAUUUU	chr15:100873138-100873523(+)$1	385	292	302	23.1914
UUUUUUUUUU	chr3:97725620-97725920(+)$1	300	199	209	27.4468
UUUUUUUUUU	chr6:56727601-56727951(-)$1	350	166	176	27.4468
uuuuuuuuuu	chr1:167805481-167805724(+)$1	243	105	115	27.4468
UUUUUUUUUU	chr18:58104449-58104808(+)$1	359	12	22	27.4468
UUUUUUUCUU	chr11:97373463-97373752(-)$1	289	117	127	22.9787
UUUUUUUUUU	chr11:79990831-79991061(+)$1	230	32	42	27.4468
uuuuuuguuu	chr8:46137129-46137569(+)$1	440	2	12	23.0851
uuuuuuuuuu	chr4:140671143-140671420(-)$1	277	200	210	27.4468
UUUUUUUUUU	chr19:9001214-9001495(+)$1	281	189	199	27.4468
UUUUUUGUUU	chr18:69844375-69844838(+)$1	463	411	421	23.0851
UUUUUUUUUU	chr13:74172761-74173096(+)$1	335	62	72	27.4468
UUUUUUUUUU	chr5:8072909-8073216(-)$1	307	141	151	27.4468
UUUUUUUUUU	chr10:56109090-56109527(+)$1	437	169	179	27.4468
uuuuuuuuuu	chr4:123168874-123169159(-)$1	285	237	247	27.4468
UUUUUUUUGU	chr5:125315218-125315588(-)$1	370	178	188	22.8723
UUUUUUCUUU	chr12:83552352-83552635(+)$1	283	96	106	23.0851
UUUUUUUUCU	chr7:53138843-53139102(+)$1	259	35	45	22.9787
uuuuuuuuuu	chr7:66560922-66561237(+)$1	315	113	123	27.4468
UUUUUUUUUU	chr2:51976935-51977342(+)$1	407	38	48	27.4468
UUUUUUUUUU	chr6:17237863-17238217(+)$1	354	184	194	27.4468
UUUUAUUUUU	chr6:82042772-82043026(+)$1	254	79	89	22.7659
UUUUUCUUUU	chr5:100464266-100464543(-)$1	277	131	141	23.1914
UUUUUUUUUU	chr5:130689346-130689611(+)$1	265	251	261	27.4468
UUuuuuuguu	chr9:70274158-70274444(-)$1	286	11	21	23.1914
UUUUUUUUUU	chr4:24935639-24936027(+)$1	388	115	125	27.4468
UUUUUUUUUU	chr7:96557492-96557760(+)$1	268	109	119	27.4468
UUUUGUUUUU	chr12:55961672-55962140(-)$1	468	106	116	22.7659
UUUUUUUUUU	chr9:57379987-57380289(+)$1	302	74	84	27.4468
UUUAUUUUUU	chr10:98485752-98486130(+)$1	378	137	147	22.9787
uuuuuuuuuu	chr1:36750071-36750319(+)$1	248	187	197	27.4468
UUUUUAUUUU	chr6:140601142-140601442(+)$1	300	104	114	23.1914
uuuuuuuuuu	chr17:31251349-31251600(+)$1	251	94	104	27.4468
UUUAUUUUUU	chrX:48247514-48247760(-)$1	246	83	93	22.9787
UUUUUUUUCU	chr3:22109707-22109974(+)$1	267	162	172	22.9787
CUUUUUUUUU	chr3:102575648-102575932(+)$1	284	202	212	22.7659
UUUUUUUUUU	chr15:82122988-82123399(+)$1	411	103	113	27.4468
UUAUUUUUUU	chr13:98022609-98023090(+)$1	481	326	336	22.6595
UUUUUUUGUU	chr15:21518904-21519330(+)$1	426	20	30	23.1914
uuuuuuuuuu	chr12:106852383-106852624(-)$1	241	96	106	27.4468
UUUUUUUUUU	chr11:51094975-51095250(+)$1	275	257	267	27.4468
UUUUUUUGUU	chr1:120197141-120197396(-)$1	255	222	232	23.1914
AUUUUUUUUU	chr2:104267947-104268387(-)$1	440	21	31	22.7659
UUUUUGUUUU	chr12:52709532-52710004(-)$1	472	278	288	23.0851
UUUCUUUUUU	chr16:31253115-31253394(-)$1	279	114	124	22.8723
uuuuucuuuu	chr9:69938162-69938472(-)$1	310	236	246	23.1914

#otherMatches

#Struct PSSM
^^^^^^^^^^	chr2:126584557-126584920(+)$1	363	285	295	23.0851
iiiiiiiii2	chr15:100873138-100873523(+)$1	385	292	302	23.1914
qqqqffffff	chr3:97725620-97725920(+)$1	300	199	209	27.4468
::::::::::	chr6:56727601-56727951(-)$1	350	166	176	27.4468
++++++++++	chr1:167805481-167805724(+)$1	243	105	115	27.4468
JJJJJJJJJJ	chr18:58104449-58104808(+)$1	359	12	22	27.4468
fffffrrrrr	chr11:97373463-97373752(-)$1	289	117	127	22.9787
yyyyyyyyyy	chr11:79990831-79991061(+)$1	230	32	42	27.4468
::::::::::	chr8:46137129-46137569(+)$1	440	2	12	23.0851
GGYYFFFFFF	chr4:140671143-140671420(-)$1	277	200	210	27.4468
fffffnnnnn	chr19:9001214-9001495(+)$1	281	189	199	27.4468
B}GGGGGGG/	chr18:69844375-69844838(+)$1	463	411	421	23.0851
c4444=====	chr13:74172761-74173096(+)$1	335	62	72	27.4468
::::::::::	chr5:8072909-8073216(-)$1	307	141	151	27.4468
::::::::::	chr10:56109090-56109527(+)$1	437	169	179	27.4468
JJJJJJJJJJ	chr4:123168874-123169159(-)$1	285	237	247	27.4468
gg4444ccc3	chr5:125315218-125315588(-)$1	370	178	188	22.8723
uuuuuuuuuu	chr12:83552352-83552635(+)$1	283	96	106	23.0851
::::::::bb	chr7:53138843-53139102(+)$1	259	35	45	22.9787
hrrrrrrrrr	chr7:66560922-66561237(+)$1	315	113	123	27.4468
ggggggffff	chr2:51976935-51977342(+)$1	407	38	48	27.4468
::::::::::	chr6:17237863-17238217(+)$1	354	184	194	27.4468
ffffffffff	chr6:82042772-82043026(+)$1	254	79	89	22.7659
dddd"""fff	chr5:100464266-100464543(-)$1	277	131	141	23.1914
::::::::::	chr5:130689346-130689611(+)$1	265	251	261	27.4468
FFPPPPPPPG	chr9:70274158-70274444(-)$1	286	11	21	23.1914
eeyyyyyyyy	chr4:24935639-24936027(+)$1	388	115	125	27.4468
==========	chr7:96557492-96557760(+)$1	268	109	119	27.4468
hhhh((((((	chr12:55961672-55962140(-)$1	468	106	116	22.7659
IIQQQQQQQQ	chr9:57379987-57380289(+)$1	302	74	84	27.4468
ddddoooooo	chr10:98485752-98486130(+)$1	378	137	147	22.9787
555hhhhhhh	chr1:36750071-36750319(+)$1	248	187	197	27.4468
hhhh55555c	chr6:140601142-140601442(+)$1	300	104	114	23.1914
gggg$$$$$c	chr17:31251349-31251600(+)$1	251	94	104	27.4468
]ccc4444ff	chrX:48247514-48247760(-)$1	246	83	93	22.9787
yyyyccc]cc	chr3:22109707-22109974(+)$1	267	162	172	22.9787
:::::hhhhh	chr3:102575648-102575932(+)$1	284	202	212	22.7659
GGGGGG::hh	chr15:82122988-82123399(+)$1	411	103	113	27.4468
fff&&&&&&&	chr13:98022609-98023090(+)$1	481	326	336	22.6595
KKFFFFFFNN	chr15:21518904-21519330(+)$1	426	20	30	23.1914
==========	chr12:106852383-106852624(-)$1	241	96	106	27.4468
::::::::::	chr11:51094975-51095250(+)$1	275	257	267	27.4468
=======:::	chr1:120197141-120197396(-)$1	255	222	232	23.1914
bmmmmbb333	chr2:104267947-104268387(-)$1	440	21	31	22.7659
======6666	chr12:52709532-52710004(-)$1	472	278	288	23.0851
eetttttttt	chr16:31253115-31253394(-)$1	279	114	124	22.8723
::========	chr9:69938162-69938472(-)$1	310	236	246	23.1914

#DB
..........	chr2:126584557-126584920(+)$1	1	285	295	23.0851
))))))))).	chr15:100873138-100873523(+)$1	1	292	302	23.1914
....))))))	chr3:97725620-97725920(+)$1	1	199	209	27.4468
..........	chr6:56727601-56727951(-)$1	1	166	176	27.4468
..........	chr1:167805481-167805724(+)$1	1	105	115	27.4468
((((((((((	chr18:58104449-58104808(+)$1	1	12	22	27.4468
(((((.....	chr11:97373463-97373752(-)$1	1	117	127	22.9787
..........	chr11:79990831-79991061(+)$1	1	32	42	27.4468
..........	chr8:46137129-46137569(+)$1	1	2	12	23.0851
))..))))))	chr4:140671143-140671420(-)$1	1	200	210	27.4468
(((((.....	chr19:9001214-9001495(+)$1	1	189	199	27.4468
).))))))).	chr18:69844375-69844838(+)$1	1	411	421	23.0851
)....)))))	chr13:74172761-74173096(+)$1	1	62	72	27.4468
..........	chr5:8072909-8073216(-)$1	1	141	151	27.4468
..........	chr10:56109090-56109527(+)$1	1	169	179	27.4468
))))))))))	chr4:123168874-123169159(-)$1	1	237	247	27.4468
))....))).	chr5:125315218-125315588(-)$1	1	178	188	22.8723
..........	chr12:83552352-83552635(+)$1	1	96	106	23.0851
........((	chr7:53138843-53139102(+)$1	1	35	45	22.9787
(.........	chr7:66560922-66561237(+)$1	1	113	123	27.4468
))))))))))	chr2:51976935-51977342(+)$1	1	38	48	27.4468
..........	chr6:17237863-17238217(+)$1	1	184	194	27.4468
((((((((((	chr6:82042772-82043026(+)$1	1	79	89	22.7659
((((...(((	chr5:100464266-100464543(-)$1	1	131	141	23.1914
..........	chr5:130689346-130689611(+)$1	1	251	261	27.4468
((.......(	chr9:70274158-70274444(-)$1	1	11	21	23.1914
((........	chr4:24935639-24936027(+)$1	1	115	125	27.4468
))))))))))	chr7:96557492-96557760(+)$1	1	109	119	27.4468
((((......	chr12:55961672-55962140(-)$1	1	106	116	22.7659
((........	chr9:57379987-57380289(+)$1	1	74	84	27.4468
((((......	chr10:98485752-98486130(+)$1	1	137	147	22.9787
...)))))))	chr1:36750071-36750319(+)$1	1	187	197	27.4468
)))).....)	chr6:140601142-140601442(+)$1	1	104	114	23.1914
((((.....(	chr17:31251349-31251600(+)$1	1	94	104	27.4468
.)))....))	chrX:48247514-48247760(-)$1	1	83	93	22.9787
....))).))	chr3:22109707-22109974(+)$1	1	162	172	22.9787
.....(((((	chr3:102575648-102575932(+)$1	1	202	212	22.7659
((((((..((	chr15:82122988-82123399(+)$1	1	103	113	27.4468
(((.......	chr13:98022609-98023090(+)$1	1	326	336	22.6595
..((((((..	chr15:21518904-21519330(+)$1	1	20	30	23.1914
))))))))))	chr12:106852383-106852624(-)$1	1	96	106	27.4468
..........	chr11:51094975-51095250(+)$1	1	257	267	27.4468
)))))))...	chr1:120197141-120197396(-)$1	1	222	232	23.1914
(....))...	chr2:104267947-104268387(-)$1	1	21	31	22.7659
))))))....	chr12:52709532-52710004(-)$1	1	278	288	23.0851
((........	chr16:31253115-31253394(-)$1	1	114	124	22.8723
..((((((((	chr9:69938162-69938472(-)$1	1	236	246	23.1914

#PSSM
U : 0.76	u : 0.19	C : 0.02	A : 0.02	
U : 0.80	u : 0.19	
U : 0.76	u : 0.21	A : 0.02	
U : 0.72	u : 0.21	A : 0.04	C : 0.02	
U : 0.74	u : 0.21	A : 0.02	G : 0.02	
U : 0.70	u : 0.19	A : 0.04	C : 0.02	G : 0.02	c : 0.02	
U : 0.72	u : 0.19	C : 0.04	g : 0.02	G : 0.02	
U : 0.72	u : 0.19	G : 0.04	C : 0.02	g : 0.02	
U : 0.72	u : 0.21	C : 0.04	G : 0.02	
U : 0.78	u : 0.21	

#score	1183.4042553191498
#seq	47
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m2_run2.nuc.txt

#NT
CCUGCU	chr16:20681274-20681531(+)$1	257	33	39	13.7142
CCUGCU	chr5:138048561-138048825(-)$1	264	24	30	13.7142
UCUGCU	chr15:76015678-76015951(-)$1	273	80	86	14.2857
GCUGCU	chr17:25057295-25057563(-)$1	268	83	89	16.0000
GCUGCU	chr9:21439876-21440114(+)$1	238	66	72	16.0000
GCUGCU	chr2:163456661-163456904(-)$1	243	125	131	16.0000
CCUGCU	chr11:120569877-120570129(+)$1	252	31	37	13.7142
UCUGCU	chr4:133242074-133242320(-)$1	246	197	203	14.2857
GCUGCU	chr7:13615003-13615253(+)$1	250	36	42	16.0000
UCUGCU	chr7:29600059-29600312(+)$1	253	35	41	14.2857
UCUGCU	chr11:120208653-120208926(-)$1	273	136	142	14.2857
GCUGCU	chr1:45879684-45879924(+)$1	240	108	114	16.0000
GCUGCU	chr2:181099261-181099497(-)$1	236	103	109	16.0000
GCUGCU	chr9:120860318-120860573(+)$1	255	81	87	16.0000
GCUGCU	chr9:45749863-45750116(-)$1	253	123	129	16.0000
GCUGCU	chr1:75471457-75471692(-)$1	235	111	117	16.0000
UCUGCU	chr15:81743556-81743797(+)$1	241	9	15	14.2857
GCUGCU	chr15:5068464-5068723(+)$1	259	63	69	16.0000
GCUGCU	chr4:43527521-43527764(-)$1	243	14	20	16.0000
GCUGCU	chr15:81539856-81540110(-)$1	254	148	154	16.0000
GCUGCU	chr3:79426665-79426903(-)$1	238	109	115	16.0000
UCUGCU	chr13:6559180-6559416(+)$1	236	83	89	14.2857
GCUGCU	chr18:43517830-43518101(-)$1	271	127	133	16.0000
UCUGCU	chr10:90579607-90579857(-)$1	250	174	180	14.2857
GCUGCU	chr18:35107476-35107735(-)$1	259	127	133	16.0000
UCUGCU	chr1:174436214-174436458(+)$1	244	70	76	14.2857
GCUGCU	chr1:95314012-95314251(-)$1	239	108	114	16.0000
GCUGCU	chr8:131249853-131250116(+)$1	263	142	148	16.0000
gcugcu	chr7:52381770-52382037(-)$1	267	151	157	16.0000
UCUGCU	chr15:99984490-99984738(+)$1	248	105	111	14.2857
GCUGCU	chr11:117217860-117218115(+)$1	255	169	175	16.0000
GCUGCU	chr1:141351545-141351804(+)$1	259	178	184	16.0000
CCUGCU	chr6:71546516-71546774(-)$1	258	52	58	13.7142
gcugcu	chr11:108204816-108205075(-)$1	259	51	57	16.0000

#otherMatches

#Struct PSSM
bbb:::	chr17:45722552-45722794(-)$1	242	202	208	13.7142
%%%eee	chr16:20681274-20681531(+)$1	257	33	39	13.7142
CDDDDL	chr5:138048561-138048825(-)$1	264	24	30	13.7142
dddd[g	chr15:76015678-76015951(-)$1	273	80	86	14.2857
bdddd$	chr17:25057295-25057563(-)$1	268	83	89	16.0000
pdddd:	chr9:21439876-21440114(+)$1	238	66	72	16.0000
ooobb:	chr2:163456661-163456904(-)$1	243	125	131	16.0000
:::bbq	chr11:120569877-120570129(+)$1	252	31	37	13.7142
]ggggg	chr4:133242074-133242320(-)$1	246	197	203	14.2857
ddd[am	chr7:13615003-13615253(+)$1	250	36	42	16.0000
tttddd	chr7:29600059-29600312(+)$1	253	35	41	14.2857
qqqqqq	chr11:120208653-120208926(-)$1	273	136	142	14.2857
bbmmmm	chr1:45879684-45879924(+)$1	240	108	114	16.0000
&&&&ee	chr2:181099261-181099497(-)$1	236	103	109	16.0000
gggggg	chr9:120860318-120860573(+)$1	255	81	87	16.0000
!!dddd	chr9:45749863-45750116(-)$1	253	123	129	16.0000
dddd::	chr1:75471457-75471692(-)$1	235	111	117	16.0000
HHHHHH	chr15:81743556-81743797(+)$1	241	9	15	14.2857
hhh]bb	chr15:5068464-5068723(+)$1	259	63	69	16.0000
HHHHHH	chr4:43527521-43527764(-)$1	243	14	20	16.0000
bbmmmm	chr15:81539856-81540110(-)$1	254	148	154	16.0000
Hbb[bb	chr3:79426665-79426903(-)$1	238	109	115	16.0000
ggggbb	chr13:6559180-6559416(+)$1	236	83	89	14.2857
:eeeee	chr18:43517830-43518101(-)$1	271	127	133	16.0000
hhhhhh	chr10:90579607-90579857(-)$1	250	174	180	14.2857
::eeee	chr18:35107476-35107735(-)$1	259	127	133	16.0000
rrccc]	chr1:174436214-174436458(+)$1	244	70	76	14.2857
ddd]a:	chr1:95314012-95314251(-)$1	239	108	114	16.0000
fffff]	chr8:131249853-131250116(+)$1	263	142	148	16.0000
2eeeee	chr7:52381770-52382037(-)$1	267	151	157	16.0000
EEEEE}	chr15:99984490-99984738(+)$1	248	105	111	14.2857
c]dddd	chr11:117217860-117218115(+)$1	255	169	175	16.0000
EEYYDD	chr1:141351545-141351804(+)$1	259	178	184	16.0000
CC{BB{	chr6:71546516-71546774(-)$1	258	52	58	13.7142
dsssss	chr11:108204816-108205075(-)$1	259	51	57	16.0000

#DB
)))...	chr17:45722552-45722794(-)$1	1	202	208	13.7142
...(((	chr16:20681274-20681531(+)$1	1	33	39	13.7142
(((((.	chr5:138048561-138048825(-)$1	1	24	30	13.7142
((((.(	chr15:76015678-76015951(-)$1	1	80	86	14.2857
(((((.	chr17:25057295-25057563(-)$1	1	83	89	16.0000
.)))).	chr9:21439876-21440114(+)$1	1	66	72	16.0000
...)).	chr2:163456661-163456904(-)$1	1	125	131	16.0000
...((.	chr11:120569877-120570129(+)$1	1	31	37	13.7142
.)))))	chr4:133242074-133242320(-)$1	1	197	203	14.2857
(((.(.	chr7:13615003-13615253(+)$1	1	36	42	16.0000
...)))	chr7:29600059-29600312(+)$1	1	35	41	14.2857
......	chr11:120208653-120208926(-)$1	1	136	142	14.2857
((....	chr1:45879684-45879924(+)$1	1	108	114	16.0000
....((	chr2:181099261-181099497(-)$1	1	103	109	16.0000
))))))	chr9:120860318-120860573(+)$1	1	81	87	16.0000
..((((	chr9:45749863-45750116(-)$1	1	123	129	16.0000
))))..	chr1:75471457-75471692(-)$1	1	111	117	16.0000
((((((	chr15:81743556-81743797(+)$1	1	9	15	14.2857
))).))	chr15:5068464-5068723(+)$1	1	63	69	16.0000
((((((	chr4:43527521-43527764(-)$1	1	14	20	16.0000
((....	chr15:81539856-81540110(-)$1	1	148	154	16.0000
(((.((	chr3:79426665-79426903(-)$1	1	109	115	16.0000
((((((	chr13:6559180-6559416(+)$1	1	83	89	14.2857
.(((((	chr18:43517830-43518101(-)$1	1	127	133	16.0000
))))))	chr10:90579607-90579857(-)$1	1	174	180	14.2857
..((((	chr18:35107476-35107735(-)$1	1	127	133	16.0000
..))).	chr1:174436214-174436458(+)$1	1	70	76	14.2857
))).).	chr1:95314012-95314251(-)$1	1	108	114	16.0000
))))).	chr8:131249853-131250116(+)$1	1	142	148	16.0000
.)))))	chr7:52381770-52382037(-)$1	1	151	157	16.0000
))))).	chr15:99984490-99984738(+)$1	1	105	111	14.2857
).))))	chr11:117217860-117218115(+)$1	1	169	175	16.0000
))..))	chr1:141351545-141351804(+)$1	1	178	184	16.0000
((.((.	chr6:71546516-71546774(-)$1	1	52	58	13.7142
(.....	chr11:108204816-108205075(-)$1	1	51	57	16.0000

#PSSM
G : 0.54	U : 0.25	C : 0.14	g : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	
G : 0.94	g : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	

#score	533.1428571428571
#seq	35
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_CDS_m3_run2.nuc.txt

#NT
CUCUGCU	chr10:22829636-22829893(-)$1	257	121	128	12.8627
CUUUGUU	chr6:146978007-146978249(+)$1	242	29	36	12.8627
CUUUGCU	chr10:82339948-82340190(+)$1	242	122	129	17.0784
CUUUGCC	chr15:58770767-58771010(+)$1	243	111	118	13.9411
GUUUGCU	chr8:123193110-123193347(+)$1	237	50	57	13.1568
CUUUACU	chr4:43565831-43566075(-)$1	244	208	215	12.2745
CUUUGCU	chr17:85105173-85105433(-)$1	260	148	155	17.0784
CUUUGCU	chr11:8418169-8418414(-)$1	245	79	86	17.0784
CGUUGCU	chr11:87794631-87794898(-)$1	267	15	22	12.4705
CUUUGCU	chr9:96240480-96240729(-)$1	249	175	182	17.0784
CUUUGCU	chr11:120433986-120434243(-)$1	257	135	142	17.0784
GUUUGCU	chr3:87783226-87783467(+)$1	241	104	111	13.1568
CAUUGCU	chr2:148532746-148533005(-)$1	259	122	129	12.4705
CUUUGCG	chr10:82353062-82353297(+)$1	235	122	129	13.4509
CUUUGCG	chr19:45153029-45153284(+)$1	255	73	80	13.4509
UUUUGCU	chr6:140595263-140595498(+)$1	235	107	114	13.2549
CUUUGCC	chr1:94749866-94750107(+)$1	241	41	48	13.9411
CUUUGCC	chr6:38441238-38441519(+)$1	281	175	182	13.9411
CUUUGCC	chr19:5426586-5426839(+)$1	253	25	32	13.9411
CUUUGCC	chr4:43046268-43046512(-)$1	244	95	102	13.9411
CUUUGCU	chr12:25397656-25397915(+)$1	259	52	59	17.0784
CUUUGCU	chr8:125945476-125945722(+)$1	246	206	213	17.0784
UUUUGCU	chr15:38420025-38420277(-)$1	252	24	31	13.2549
GUUUGCU	chr1:71674897-71675187(-)$1	290	38	45	13.1568
CUUUGCU	chr2:163456661-163456904(-)$1	243	116	123	17.0784
CUUUGCA	chrX:67599667-67599910(-)$1	243	172	179	13.5490
UUUUGCU	chr19:60843452-60843690(-)$1	238	107	114	13.2549
CUUCGCU	chr15:76014027-76014270(-)$1	243	186	193	12.7647
CUUUGCA	chr2:162760239-162760539(+)$1	300	270	277	13.5490
CUUUGCC	chr13:54625836-54626088(+)$1	252	134	141	13.9411
CCUUGCU	chr6:145811434-145811730(-)$1	296	161	168	12.4705
AUUUGCU	chr3:53281764-53282025(+)$1	261	25	32	12.9607
CUCUGCU	chr11:115216577-115216830(-)$1	253	63	70	12.8627
CUUUGCU	chr15:10505191-10505450(-)$1	259	139	146	17.0784
CUUUGGU	chr14:52799743-52799989(-)$1	246	28	35	12.6666
CUUUGCC	chr1:154433522-154433769(-)$1	247	191	198	13.9411
CUUUGCA	chr7:52140643-52140892(-)$1	249	112	119	13.5490
CUUGGCU	chr6:72582822-72583087(-)$1	265	40	47	13.1568
CUUGGCU	chr11:100272966-100273210(-)$1	244	234	241	13.1568
CUUGGCU	chr1:63196462-63196714(-)$1	252	57	64	13.1568
CUUUGUU	chr17:66003629-66003883(-)$1	254	184	191	12.8627
CUUGGCU	chr11:96716478-96716719(+)$1	241	50	57	13.1568
CUUUGCU	chr14:52636631-52636868(-)$1	237	18	25	17.0784
CUGUGCU	chr7:19956760-19956995(+)$1	235	58	65	12.7647
UUUUGCU	chr19:4150416-4150704(+)$1	288	139	146	13.2549
CUGUGCU	chr13:60277390-60277626(-)$1	236	158	165	12.7647
CUCUGCU	chr19:5674807-5675045(-)$1	238	152	159	12.8627
CUUUGAU	chr9:72569009-72569244(+)$1	235	36	43	12.6666
CUUUGCU	chr6:131326063-131326326(-)$1	263	114	121	17.0784
CUUUGUU	chr14:35156695-35156944(+)$1	249	83	90	12.8627

#otherMatches

#Struct PSSM
bb22fff	chr4:43596910-43597159(+)$1	249	194	201	13.1568
ddddDDD	chr10:22829636-22829893(-)$1	257	121	128	12.8627
fffoooo	chr6:146978007-146978249(+)$1	242	29	36	12.8627
hhhhddd	chr10:82339948-82340190(+)$1	242	122	129	17.0784
HHfffff	chr15:58770767-58771010(+)$1	243	111	118	13.9411
e22cccF	chr8:123193110-123193347(+)$1	237	50	57	13.1568
nnnnndd	chr4:43565831-43566075(-)$1	244	208	215	12.2745
dddffff	chr17:85105173-85105433(-)$1	260	148	155	17.0784
d"""ccc	chr11:8418169-8418414(-)$1	245	79	86	17.0784
[ccc!!c	chr11:87794631-87794898(-)$1	267	15	22	12.4705
EEEELLL	chr9:96240480-96240729(-)$1	249	175	182	17.0784
b333bb:	chr11:120433986-120434243(-)$1	257	135	142	17.0784
eccc[bb	chr3:87783226-87783467(+)$1	241	104	111	13.1568
[bb[ddd	chr2:148532746-148533005(-)$1	259	122	129	12.4705
mmeeeee	chr10:82353062-82353297(+)$1	235	122	129	13.4509
blllbbD	chr19:45153029-45153284(+)$1	255	73	80	13.4509
hhhhhhh	chr6:140595263-140595498(+)$1	235	107	114	13.2549
CIIIIII	chr1:94749866-94750107(+)$1	241	41	48	13.9411
D}CCC~~	chr6:38441238-38441519(+)$1	281	175	182	13.9411
mmmdddd	chr19:5426586-5426839(+)$1	253	25	32	13.9411
8888ccc	chr4:43046268-43046512(-)$1	244	95	102	13.9411
g777777	chr12:25397656-25397915(+)$1	259	52	59	17.0784
EEEE}FF	chr8:125945476-125945722(+)$1	246	206	213	17.0784
::::::J	chr15:38420025-38420277(-)$1	252	24	31	13.2549
]a]hhhh	chr1:71674897-71675187(-)$1	290	38	45	13.1568
::::bbo	chr2:163456661-163456904(-)$1	243	116	123	17.0784
ee!!eee	chrX:67599667-67599910(-)$1	243	172	179	13.5490
iii!!gg	chr19:60843452-60843690(-)$1	238	107	114	13.2549
gcccccc	chr15:76014027-76014270(-)$1	243	186	193	12.7647
DDDD}BB	chr2:162760239-162760539(+)$1	300	270	277	13.5490
HHHHH::	chr13:54625836-54626088(+)$1	252	134	141	13.9411
|||HHHH	chr6:145811434-145811730(-)$1	296	161	168	12.4705
qqqqqqq	chr3:53281764-53282025(+)$1	261	25	32	12.9607
rrrrrrr	chr11:115216577-115216830(-)$1	253	63	70	12.8627
FFWWWWW	chr15:10505191-10505450(-)$1	259	139	146	17.0784
eee!!cc	chr14:52799743-52799989(-)$1	246	28	35	12.6666
ellleee	chr1:154433522-154433769(-)$1	247	191	198	13.9411
feeeeeq	chr7:52140643-52140892(-)$1	249	112	119	13.5490
LLLDDDD	chr6:72582822-72583087(-)$1	265	40	47	13.1568
:::CCC:	chr11:100272966-100273210(-)$1	244	234	241	13.1568
FFFFLLL	chr1:63196462-63196714(-)$1	252	57	64	13.1568
####bb[	chr17:66003629-66003883(-)$1	254	184	191	12.8627
===]bb:	chr11:96716478-96716719(+)$1	241	50	57	13.1568
cc]dddd	chr14:52636631-52636868(-)$1	237	18	25	17.0784
!!fffff	chr7:19956760-19956995(+)$1	235	58	65	12.7647
iiiiiiE	chr19:4150416-4150704(+)$1	288	139	146	13.2549
ff22bb:	chr13:60277390-60277626(-)$1	236	158	165	12.7647
c======	chr19:5674807-5675045(-)$1	238	152	159	12.8627
d::::::	chr9:72569009-72569244(+)$1	235	36	43	12.6666
e::dddd	chr6:131326063-131326326(-)$1	263	114	121	17.0784
ccccc44	chr14:35156695-35156944(+)$1	249	83	90	12.8627

#DB
))..)))	chr4:43596910-43597159(+)$1	1	194	201	13.1568
)))))))	chr10:22829636-22829893(-)$1	1	121	128	12.8627
(((....	chr6:146978007-146978249(+)$1	1	29	36	12.8627
(((((((	chr10:82339948-82340190(+)$1	1	122	129	17.0784
(((((((	chr15:58770767-58771010(+)$1	1	111	118	13.9411
)..)))(	chr8:123193110-123193347(+)$1	1	50	57	13.1568
.....))	chr4:43565831-43566075(-)$1	1	208	215	12.2745
)))((((	chr17:85105173-85105433(-)$1	1	148	155	17.0784
(...(((	chr11:8418169-8418414(-)$1	1	79	86	17.0784
.(((..(	chr11:87794631-87794898(-)$1	1	15	22	12.4705
((((...	chr9:96240480-96240729(-)$1	1	175	182	17.0784
)...)).	chr11:120433986-120434243(-)$1	1	135	142	17.0784
)(((.((	chr3:87783226-87783467(+)$1	1	104	111	13.1568
.((.(((	chr2:148532746-148533005(-)$1	1	122	129	12.4705
..)))))	chr10:82353062-82353297(+)$1	1	122	129	13.4509
(...))(	chr19:45153029-45153284(+)$1	1	73	80	13.4509
(((((((	chr6:140595263-140595498(+)$1	1	107	114	13.2549
(((((((	chr1:94749866-94750107(+)$1	1	41	48	13.9411
).)))..	chr6:38441238-38441519(+)$1	1	175	182	13.9411
...))))	chr19:5426586-5426839(+)$1	1	25	32	13.9411
....)))	chr4:43046268-43046512(-)$1	1	95	102	13.9411
)......	chr12:25397656-25397915(+)$1	1	52	59	17.0784
)))).))	chr8:125945476-125945722(+)$1	1	206	213	17.0784
......(	chr15:38420025-38420277(-)$1	1	24	31	13.2549
.).))))	chr1:71674897-71675187(-)$1	1	38	45	13.1568
....((.	chr2:163456661-163456904(-)$1	1	116	123	17.0784
((..(((	chrX:67599667-67599910(-)$1	1	172	179	13.5490
(((..((	chr19:60843452-60843690(-)$1	1	107	114	13.2549
)))))))	chr15:76014027-76014270(-)$1	1	186	193	12.7647
)))).))	chr2:162760239-162760539(+)$1	1	270	277	13.5490
(((((..	chr13:54625836-54626088(+)$1	1	134	141	13.9411
...))))	chr6:145811434-145811730(-)$1	1	161	168	12.4705
.......	chr3:53281764-53282025(+)$1	1	25	32	12.9607
.......	chr11:115216577-115216830(-)$1	1	63	70	12.8627
((.....	chr15:10505191-10505450(-)$1	1	139	146	17.0784
(((..((	chr14:52799743-52799989(-)$1	1	28	35	12.6666
(...)))	chr1:154433522-154433769(-)$1	1	191	198	13.9411
)(((((.	chr7:52140643-52140892(-)$1	1	112	119	13.5490
...((((	chr6:72582822-72583087(-)$1	1	40	47	13.1568
...))).	chr11:100272966-100273210(-)$1	1	234	241	13.1568
((((...	chr1:63196462-63196714(-)$1	1	57	64	13.1568
....((.	chr17:66003629-66003883(-)$1	1	184	191	12.8627
))).)).	chr11:96716478-96716719(+)$1	1	50	57	13.1568
)).))))	chr14:52636631-52636868(-)$1	1	18	25	17.0784
..(((((	chr7:19956760-19956995(+)$1	1	58	65	12.7647
)))))))	chr19:4150416-4150704(+)$1	1	139	146	13.2549
))..)).	chr13:60277390-60277626(-)$1	1	158	165	12.7647
)((((((	chr19:5674807-5675045(-)$1	1	152	159	12.8627
)......	chr9:72569009-72569244(+)$1	1	36	43	12.6666
)..((((	chr6:131326063-131326326(-)$1	1	114	121	17.0784
)))))..	chr14:35156695-35156944(+)$1	1	83	90	12.8627

#PSSM
C : 0.84	U : 0.07	G : 0.05	A : 0.01	
U : 0.94	G : 0.01	A : 0.01	C : 0.01	
U : 0.90	C : 0.05	G : 0.03	
U : 0.88	G : 0.09	C : 0.01	
G : 0.98	A : 0.01	
C : 0.90	U : 0.05	G : 0.01	A : 0.01	
U : 0.76	C : 0.13	A : 0.05	G : 0.03	

#score	714.7254901960787
#seq	51
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Rbfox_Weynvanhentenryck2014_mm9_CDS_m2_run2.nuc.txt

#NT
CUG	chr14:47928115-47928357(+)$1	242	200	203	9.0000
CUG	chr4:151685709-151685981(-)$1	272	105	108	9.0000
CUG	chr3:107277121-107277397(-)$1	276	0	3	9.0000
CUG	chr14:29718239-29718572(-)$1	333	14	17	9.0000
CUG	chrX:162782779-162783141(+)$1	362	27	30	9.0000
CUG	chr6:71460120-71460510(+)$1	390	52	55	9.0000
CUG	chr13:100201290-100201619(-)$1	329	14	17	9.0000
CUG	chr10:69444796-69445050(+)$1	254	68	71	9.0000
CUG	chr8:124313255-124313549(+)$1	294	4	7	9.0000
CUG	chr7:67128149-67128449(-)$1	300	6	9	9.0000
CUG	chr10:79591081-79591341(+)$1	260	17	20	9.0000
CUG	chr2:32191013-32191416(-)$1	403	19	22	9.0000
CUG	chr2:121923784-121924088(-)$1	304	18	21	9.0000
CUG	chrX:132600997-132601485(-)$1	488	41	44	9.0000
CUG	chr9:89897113-89897404(+)$1	291	2	5	9.0000
CUG	chr10:126666697-126666962(-)$1	265	2	5	9.0000
CUG	chr2:174163017-174163351(+)$1	334	20	23	9.0000
CUG	chr1:155308094-155308374(-)$1	280	157	160	9.0000
CUG	chr1:51188951-51189204(+)$1	253	0	3	9.0000
CUG	chr16:14049378-14049650(+)$1	272	27	30	9.0000
CUG	chr4:148637675-148638101(-)$1	426	64	67	9.0000
CUG	chr11:30014570-30014994(-)$1	424	46	49	9.0000
cug	chr13:41369228-41369669(+)$1	441	93	96	9.0000
CUG	chr12:111904443-111904695(+)$1	252	0	3	9.0000
CUG	chr15:98570701-98571029(-)$1	328	28	31	9.0000
CUG	chr3:123255192-123255528(-)$1	336	28	31	9.0000
CUG	chr7:20281514-20281862(-)$1	348	16	19	9.0000
CUG	chr9:55993191-55993451(-)$1	260	16	19	9.0000
CUG	chr5:23345492-23345749(-)$1	257	30	33	9.0000
CUG	chr7:106464093-106464345(+)$1	252	30	33	9.0000
CUG	chr1:156259295-156259711(-)$1	416	5	8	9.0000
CUG	chr5:4888807-4889075(-)$1	268	5	8	9.0000
CUG	chr11:104169077-104169352(+)$1	275	1	4	9.0000
CUG	chr12:11332935-11333407(-)$1	472	46	49	9.0000
CUG	chr15:65829159-65829450(-)$1	291	141	144	9.0000
CUG	chr12:104655844-104656108(-)$1	264	31	34	9.0000
CUG	chr6:35461973-35462352(-)$1	379	39	42	9.0000
CUG	chr19:37365157-37365419(-)$1	262	40	43	9.0000
CUG	chr2:14896709-14896969(+)$1	260	4	7	9.0000
CUG	chr19:46387004-46387304(-)$1	300	26	29	9.0000
CUG	chr2:118226942-118227251(+)$1	309	68	71	9.0000
CUG	chr2:92453733-92454008(+)$1	275	10	13	9.0000
CUG	chr3:126650701-126651048(-)$1	347	105	108	9.0000
CUG	chr5:67070800-67071054(+)$1	254	17	20	9.0000
CUG	chr4:3477317-3477744(-)$1	427	28	31	9.0000
CUG	chr11:6224787-6225145(+)$1	358	43	46	9.0000
CUG	chr9:44686629-44686935(-)$1	306	35	38	9.0000
CUG	chr13:34166037-34166484(-)$1	447	61	64	9.0000
CUG	chr17:46862116-46862387(+)$1	271	28	31	9.0000
CUG	chr11:103042894-103043137(+)$1	243	40	43	9.0000
CUG	chr11:20124692-20125098(+)$1	406	46	49	9.0000
CUG	chr15:75900599-75900878(-)$1	279	45	48	9.0000
CUG	chr18:31603601-31603928(-)$1	327	60	63	9.0000
CUG	chr15:88988249-88988531(-)$1	282	57	60	9.0000
CUG	chr5:122950635-122950928(-)$1	293	34	37	9.0000
CUG	chr13:100205010-100205321(-)$1	311	36	39	9.0000
CUG	chr5:125866235-125866562(-)$1	327	4	7	9.0000
CUG	chr1:174049519-174049782(+)$1	263	14	17	9.0000
CUG	chr10:70027834-70028124(-)$1	290	14	17	9.0000
CUG	chr4:147519130-147519402(+)$1	272	18	21	9.0000
CUG	chr7:71556756-71557009(+)$1	253	18	21	9.0000
CUG	chr1:89379141-89379389(-)$1	248	9	12	9.0000
CUG	chr10:118648173-118648436(-)$1	263	8	11	9.0000
CUG	chr11:87403161-87403427(+)$1	266	12	15	9.0000
cug	chrX:70310247-70310520(+)$1	273	27	30	9.0000
CUG	chr19:4289567-4289829(-)$1	262	36	39	9.0000
CUG	chr16:85015371-85015692(-)$1	321	108	111	9.0000
CUG	chr3:55340453-55340846(+)$1	393	50	53	9.0000
CUG	chrX:148288604-148288898(+)$1	294	83	86	9.0000
CUG	chr17:43748781-43749119(+)$1	338	42	45	9.0000
CUG	chr4:137797433-137797725(+)$1	292	13	16	9.0000
CUG	chr1:163921908-163922307(-)$1	399	24	27	9.0000
CUG	chr2:121263320-121263617(+)$1	297	196	199	9.0000
CUG	chrX:138779869-138780176(-)$1	307	43	46	9.0000
CUG	chr11:98614797-98615072(+)$1	275	1	4	9.0000
CUG	chr13:97420957-97421214(-)$1	257	14	17	9.0000
CUG	chr6:124864052-124864342(-)$1	290	147	150	9.0000
CUG	chr2:49112374-49112673(+)$1	299	93	96	9.0000
CUG	chr2:25099504-25099868(+)$1	364	14	17	9.0000
CUG	chr15:39283640-39284024(+)$1	384	44	47	9.0000
CUG	chr9:72587159-72587432(+)$1	273	36	39	9.0000
CUG	chr5:28052113-28052428(+)$1	315	82	85	9.0000
CUG	chr7:120709825-120710091(+)$1	266	167	170	9.0000
CUG	chr3:108194593-108195072(-)$1	479	38	41	9.0000
CUG	chr5:145945330-145945611(-)$1	281	54	57	9.0000
CUG	chr5:139494407-139494767(-)$1	360	21	24	9.0000
CUG	chr5:9132294-9132601(-)$1	307	75	78	9.0000
CUG	chr14:123999020-123999285(-)$1	265	75	78	9.0000
CUG	chr7:134088350-134088611(+)$1	261	6	9	9.0000
CUG	chr11:50199174-50199481(+)$1	307	56	59	9.0000
CUG	chr14:21531450-21531802(+)$1	352	0	3	9.0000
CUG	chr5:76363661-76363938(-)$1	277	21	24	9.0000
CUG	chr3:108194380-108194630(-)$1	250	8	11	9.0000
CUG	chr7:34987256-34987566(-)$1	310	5	8	9.0000
CUG	chr12:111857316-111857643(+)$1	327	31	34	9.0000
CUG	chr11:104189388-104189713(+)$1	325	84	87	9.0000
CUG	chr2:24555226-24555550(-)$1	324	21	24	9.0000

#otherMatches

#Struct PSSM
SSS	chr14:55525707-55526020(-)$1	313	23	26	9.0000
DDD	chr14:47928115-47928357(+)$1	242	200	203	9.0000
ddd	chr4:151685709-151685981(-)$1	272	105	108	9.0000
:::	chr3:107277121-107277397(-)$1	276	0	3	9.0000
dgg	chr14:29718239-29718572(-)$1	333	14	17	9.0000
ddd	chrX:162782779-162783141(+)$1	362	27	30	9.0000
ccc	chr6:71460120-71460510(+)$1	390	52	55	9.0000
GGG	chr13:100201290-100201619(-)$1	329	14	17	9.0000
rrf	chr10:69444796-69445050(+)$1	254	68	71	9.0000
ggg	chr8:124313255-124313549(+)$1	294	4	7	9.0000
EEE	chr7:67128149-67128449(-)$1	300	6	9	9.0000
ee[	chr10:79591081-79591341(+)$1	260	17	20	9.0000
bb#	chr2:32191013-32191416(-)$1	403	19	22	9.0000
C{C	chr2:121923784-121924088(-)$1	304	18	21	9.0000
CC{	chrX:132600997-132601485(-)$1	488	41	44	9.0000
EEE	chr9:89897113-89897404(+)$1	291	2	5	9.0000
C{C	chr10:126666697-126666962(-)$1	265	2	5	9.0000
JJJ	chr2:174163017-174163351(+)$1	334	20	23	9.0000
iii	chr1:155308094-155308374(-)$1	280	157	160	9.0000
:::	chr1:51188951-51189204(+)$1	253	0	3	9.0000
FOO	chr16:14049378-14049650(+)$1	272	27	30	9.0000
oof	chr4:148637675-148638101(-)$1	426	64	67	9.0000
]gg	chr11:30014570-30014994(-)$1	424	46	49	9.0000
ggg	chr13:41369228-41369669(+)$1	441	93	96	9.0000
:DD	chr12:111904443-111904695(+)$1	252	0	3	9.0000
cqq	chr15:98570701-98571029(-)$1	328	28	31	9.0000
22b	chr3:123255192-123255528(-)$1	336	28	31	9.0000
Edd	chr7:20281514-20281862(-)$1	348	16	19	9.0000
e::	chr9:55993191-55993451(-)$1	260	16	19	9.0000
OOH	chr5:23345492-23345749(-)$1	257	30	33	9.0000
FFF	chr7:106464093-106464345(+)$1	252	30	33	9.0000
:::	chr1:156259295-156259711(-)$1	416	5	8	9.0000
FFF	chr5:4888807-4889075(-)$1	268	5	8	9.0000
ggg	chr11:104169077-104169352(+)$1	275	1	4	9.0000
c[b	chr12:11332935-11333407(-)$1	472	46	49	9.0000
ee$	chr15:65829159-65829450(-)$1	291	141	144	9.0000
bll	chr12:104655844-104656108(-)$1	264	31	34	9.0000
bbm	chr6:35461973-35462352(-)$1	379	39	42	9.0000
fDD	chr19:37365157-37365419(-)$1	262	40	43	9.0000
:::	chr2:14896709-14896969(+)$1	260	4	7	9.0000
TBB	chr19:46387004-46387304(-)$1	300	26	29	9.0000
cc]	chr2:118226942-118227251(+)$1	309	68	71	9.0000
nff	chr2:92453733-92454008(+)$1	275	10	13	9.0000
^^^	chr3:126650701-126651048(-)$1	347	105	108	9.0000
DDD	chr5:67070800-67071054(+)$1	254	17	20	9.0000
dd!	chr4:3477317-3477744(-)$1	427	28	31	9.0000
d:c	chr11:6224787-6225145(+)$1	358	43	46	9.0000
eee	chr9:44686629-44686935(-)$1	306	35	38	9.0000
ggg	chr13:34166037-34166484(-)$1	447	61	64	9.0000
d[d	chr17:46862116-46862387(+)$1	271	28	31	9.0000
ddd	chr11:103042894-103043137(+)$1	243	40	43	9.0000
FFF	chr11:20124692-20125098(+)$1	406	46	49	9.0000
ddd	chr15:75900599-75900878(-)$1	279	45	48	9.0000
ccc	chr18:31603601-31603928(-)$1	327	60	63	9.0000
ooo	chr15:88988249-88988531(-)$1	282	57	60	9.0000
:::	chr5:122950635-122950928(-)$1	293	34	37	9.0000
GGB	chr13:100205010-100205321(-)$1	311	36	39	9.0000
EEE	chr5:125866235-125866562(-)$1	327	4	7	9.0000
DD:	chr1:174049519-174049782(+)$1	263	14	17	9.0000
DDD	chr10:70027834-70028124(-)$1	290	14	17	9.0000
bb]	chr4:147519130-147519402(+)$1	272	18	21	9.0000
ii!	chr7:71556756-71557009(+)$1	253	18	21	9.0000
CDD	chr1:89379141-89379389(-)$1	248	9	12	9.0000
JJJ	chr10:118648173-118648436(-)$1	263	8	11	9.0000
DDD	chr11:87403161-87403427(+)$1	266	12	15	9.0000
f:B	chrX:70310247-70310520(+)$1	273	27	30	9.0000
ccc	chr19:4289567-4289829(-)$1	262	36	39	9.0000
EEE	chr16:85015371-85015692(-)$1	321	108	111	9.0000
{CC	chr3:55340453-55340846(+)$1	393	50	53	9.0000
fff	chrX:148288604-148288898(+)$1	294	83	86	9.0000
eee	chr17:43748781-43749119(+)$1	338	42	45	9.0000
EEE	chr4:137797433-137797725(+)$1	292	13	16	9.0000
ddd	chr1:163921908-163922307(-)$1	399	24	27	9.0000
ddd	chr2:121263320-121263617(+)$1	297	196	199	9.0000
GGG	chrX:138779869-138780176(-)$1	307	43	46	9.0000
BBB	chr11:98614797-98615072(+)$1	275	1	4	9.0000
eee	chr13:97420957-97421214(-)$1	257	14	17	9.0000
eee	chr6:124864052-124864342(-)$1	290	147	150	9.0000
55b	chr2:49112374-49112673(+)$1	299	93	96	9.0000
:ff	chr2:25099504-25099868(+)$1	364	14	17	9.0000
fff	chr15:39283640-39284024(+)$1	384	44	47	9.0000
ggg	chr9:72587159-72587432(+)$1	273	36	39	9.0000
&&d	chr5:28052113-28052428(+)$1	315	82	85	9.0000
ccc	chr7:120709825-120710091(+)$1	266	167	170	9.0000
ff4	chr3:108194593-108195072(-)$1	479	38	41	9.0000
FFF	chr5:145945330-145945611(-)$1	281	54	57	9.0000
!!d	chr5:139494407-139494767(-)$1	360	21	24	9.0000
fff	chr5:9132294-9132601(-)$1	307	75	78	9.0000
CCC	chr14:123999020-123999285(-)$1	265	75	78	9.0000
HHH	chr7:134088350-134088611(+)$1	261	6	9	9.0000
nnc	chr11:50199174-50199481(+)$1	307	56	59	9.0000
:::	chr14:21531450-21531802(+)$1	352	0	3	9.0000
!!d	chr5:76363661-76363938(-)$1	277	21	24	9.0000
ccc	chr3:108194380-108194630(-)$1	250	8	11	9.0000
GGD	chr7:34987256-34987566(-)$1	310	5	8	9.0000
eec	chr12:111857316-111857643(+)$1	327	31	34	9.0000
mme	chr11:104189388-104189713(+)$1	325	84	87	9.0000
g!!	chr2:24555226-24555550(-)$1	324	21	24	9.0000

#DB
...	chr14:55525707-55526020(-)$1	1	23	26	9.0000
)))	chr14:47928115-47928357(+)$1	1	200	203	9.0000
)))	chr4:151685709-151685981(-)$1	1	105	108	9.0000
...	chr3:107277121-107277397(-)$1	1	0	3	9.0000
(((	chr14:29718239-29718572(-)$1	1	14	17	9.0000
(((	chrX:162782779-162783141(+)$1	1	27	30	9.0000
(((	chr6:71460120-71460510(+)$1	1	52	55	9.0000
(((	chr13:100201290-100201619(-)$1	1	14	17	9.0000
..)	chr10:69444796-69445050(+)$1	1	68	71	9.0000
(((	chr8:124313255-124313549(+)$1	1	4	7	9.0000
(((	chr7:67128149-67128449(-)$1	1	6	9	9.0000
((.	chr10:79591081-79591341(+)$1	1	17	20	9.0000
((.	chr2:32191013-32191416(-)$1	1	19	22	9.0000
(.(	chr2:121923784-121924088(-)$1	1	18	21	9.0000
((.	chrX:132600997-132601485(-)$1	1	41	44	9.0000
(((	chr9:89897113-89897404(+)$1	1	2	5	9.0000
(.(	chr10:126666697-126666962(-)$1	1	2	5	9.0000
(((	chr2:174163017-174163351(+)$1	1	20	23	9.0000
)))	chr1:155308094-155308374(-)$1	1	157	160	9.0000
...	chr1:51188951-51189204(+)$1	1	0	3	9.0000
(..	chr16:14049378-14049650(+)$1	1	27	30	9.0000
..)	chr4:148637675-148638101(-)$1	1	64	67	9.0000
.))	chr11:30014570-30014994(-)$1	1	46	49	9.0000
(((	chr13:41369228-41369669(+)$1	1	93	96	9.0000
.((	chr12:111904443-111904695(+)$1	1	0	3	9.0000
(..	chr15:98570701-98571029(-)$1	1	28	31	9.0000
..)	chr3:123255192-123255528(-)$1	1	28	31	9.0000
(((	chr7:20281514-20281862(-)$1	1	16	19	9.0000
)..	chr9:55993191-55993451(-)$1	1	16	19	9.0000
..(	chr5:23345492-23345749(-)$1	1	30	33	9.0000
(((	chr7:106464093-106464345(+)$1	1	30	33	9.0000
...	chr1:156259295-156259711(-)$1	1	5	8	9.0000
(((	chr5:4888807-4889075(-)$1	1	5	8	9.0000
(((	chr11:104169077-104169352(+)$1	1	1	4	9.0000
(.(	chr12:11332935-11333407(-)$1	1	46	49	9.0000
((.	chr15:65829159-65829450(-)$1	1	141	144	9.0000
(..	chr12:104655844-104656108(-)$1	1	31	34	9.0000
((.	chr6:35461973-35462352(-)$1	1	39	42	9.0000
)((	chr19:37365157-37365419(-)$1	1	40	43	9.0000
...	chr2:14896709-14896969(+)$1	1	4	7	9.0000
.((	chr19:46387004-46387304(-)$1	1	26	29	9.0000
)).	chr2:118226942-118227251(+)$1	1	68	71	9.0000
.))	chr2:92453733-92454008(+)$1	1	10	13	9.0000
...	chr3:126650701-126651048(-)$1	1	105	108	9.0000
(((	chr5:67070800-67071054(+)$1	1	17	20	9.0000
((.	chr4:3477317-3477744(-)$1	1	28	31	9.0000
).(	chr11:6224787-6225145(+)$1	1	43	46	9.0000
(((	chr9:44686629-44686935(-)$1	1	35	38	9.0000
(((	chr13:34166037-34166484(-)$1	1	61	64	9.0000
(.(	chr17:46862116-46862387(+)$1	1	28	31	9.0000
)))	chr11:103042894-103043137(+)$1	1	40	43	9.0000
(((	chr11:20124692-20125098(+)$1	1	46	49	9.0000
)))	chr15:75900599-75900878(-)$1	1	45	48	9.0000
(((	chr18:31603601-31603928(-)$1	1	60	63	9.0000
...	chr15:88988249-88988531(-)$1	1	57	60	9.0000
...	chr5:122950635-122950928(-)$1	1	34	37	9.0000
(((	chr13:100205010-100205321(-)$1	1	36	39	9.0000
(((	chr5:125866235-125866562(-)$1	1	4	7	9.0000
((.	chr1:174049519-174049782(+)$1	1	14	17	9.0000
(((	chr10:70027834-70028124(-)$1	1	14	17	9.0000
)).	chr4:147519130-147519402(+)$1	1	18	21	9.0000
((.	chr7:71556756-71557009(+)$1	1	18	21	9.0000
(((	chr1:89379141-89379389(-)$1	1	9	12	9.0000
(((	chr10:118648173-118648436(-)$1	1	8	11	9.0000
(((	chr11:87403161-87403427(+)$1	1	12	15	9.0000
).(	chrX:70310247-70310520(+)$1	1	27	30	9.0000
)))	chr19:4289567-4289829(-)$1	1	36	39	9.0000
(((	chr16:85015371-85015692(-)$1	1	108	111	9.0000
.((	chr3:55340453-55340846(+)$1	1	50	53	9.0000
)))	chrX:148288604-148288898(+)$1	1	83	86	9.0000
)))	chr17:43748781-43749119(+)$1	1	42	45	9.0000
(((	chr4:137797433-137797725(+)$1	1	13	16	9.0000
)))	chr1:163921908-163922307(-)$1	1	24	27	9.0000
)))	chr2:121263320-121263617(+)$1	1	196	199	9.0000
(((	chrX:138779869-138780176(-)$1	1	43	46	9.0000
(((	chr11:98614797-98615072(+)$1	1	1	4	9.0000
(((	chr13:97420957-97421214(-)$1	1	14	17	9.0000
)))	chr6:124864052-124864342(-)$1	1	147	150	9.0000
..)	chr2:49112374-49112673(+)$1	1	93	96	9.0000
.((	chr2:25099504-25099868(+)$1	1	14	17	9.0000
(((	chr15:39283640-39284024(+)$1	1	44	47	9.0000
)))	chr9:72587159-72587432(+)$1	1	36	39	9.0000
..(	chr5:28052113-28052428(+)$1	1	82	85	9.0000
(((	chr7:120709825-120710091(+)$1	1	167	170	9.0000
)).	chr3:108194593-108195072(-)$1	1	38	41	9.0000
(((	chr5:145945330-145945611(-)$1	1	54	57	9.0000
..(	chr5:139494407-139494767(-)$1	1	21	24	9.0000
(((	chr5:9132294-9132601(-)$1	1	75	78	9.0000
(((	chr14:123999020-123999285(-)$1	1	75	78	9.0000
(((	chr7:134088350-134088611(+)$1	1	6	9	9.0000
..)	chr11:50199174-50199481(+)$1	1	56	59	9.0000
...	chr14:21531450-21531802(+)$1	1	0	3	9.0000
..(	chr5:76363661-76363938(-)$1	1	21	24	9.0000
(((	chr3:108194380-108194630(-)$1	1	8	11	9.0000
(((	chr7:34987256-34987566(-)$1	1	5	8	9.0000
))(	chr12:111857316-111857643(+)$1	1	31	34	9.0000
..)	chr11:104189388-104189713(+)$1	1	84	87	9.0000
(..	chr2:24555226-24555550(-)$1	1	21	24	9.0000

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

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m1_run2.nuc.txt

#NT
UGCCU	chr7:25774838-25775039(-)$1	201	74	79	15.0000
UGCCU	chr10:80769016-80769217(+)$1	201	102	107	15.0000
UGCCU	chr6:72386159-72386360(-)$1	201	69	74	15.0000
UGCCU	chr11:21228861-21229062(-)$1	201	52	57	15.0000
UGCCU	chr2:107136218-107136419(+)$1	201	101	106	15.0000
UGCCU	chr18:20823884-20824085(+)$1	201	82	87	15.0000
UGCCU	chr3:25335266-25335467(-)$1	201	40	45	15.0000
UGCCU	chrX:71200356-71200557(-)$1	201	19	24	15.0000
UGCCU	chr2:109836629-109836830(+)$1	201	182	187	15.0000
UGCCU	chr1:155067172-155067373(-)$1	201	83	88	15.0000
UGCCU	chr4:141024757-141024958(-)$1	201	8	13	15.0000
UGCCU	chr3:25335265-25335466(-)$1	201	39	44	15.0000
UGCCU	chr5:34263098-34263299(-)$1	201	164	169	15.0000
UGCCU	chr10:80769017-80769218(+)$1	201	101	106	15.0000
UGCCU	chr5:93699943-93700144(+)$1	201	70	75	15.0000
UGCCU	chr11:3615058-3615259(-)$1	201	4	9	15.0000
UGCCU	chr19:46339198-46339399(+)$1	201	119	124	15.0000
UGCCU	chr14:60898835-60899036(+)$1	201	101	106	15.0000
UGCCU	chr11:21228862-21229063(-)$1	201	53	58	15.0000
UGCCU	chr15:31405400-31405601(-)$1	201	85	90	15.0000
UGCCU	chr10:59763439-59763640(+)$1	201	102	107	15.0000
UGCCU	chr17:21088240-21088441(+)$1	201	101	106	15.0000
UGCCU	chr5:93699942-93700143(+)$1	201	71	76	15.0000
UGCCU	chr3:126637378-126637579(-)$1	201	23	28	15.0000
UGCCU	chr17:24196151-24196352(-)$1	201	183	188	15.0000
UGCCU	chr15:31432413-31432614(-)$1	201	11	16	15.0000
UGCCU	chr17:21088241-21088442(+)$1	201	100	105	15.0000
UGCCU	chr5:4083122-4083323(-)$1	201	48	53	15.0000
UGCCU	chr15:71292706-71292907(-)$1	201	43	48	15.0000
UGCCU	chr15:31432414-31432615(-)$1	201	12	17	15.0000
UGCCU	chr10:66682856-66683057(+)$1	201	100	105	15.0000
UGCCU	chr14:65871755-65871956(-)$1	201	102	107	15.0000
UGCCU	chr6:124412063-124412264(-)$1	201	102	107	15.0000
UGCCU	chrY:494799-495000(-)$1	201	23	28	15.0000
UGCCU	chr3:126657842-126658043(-)$1	201	105	110	15.0000
UGCCU	chr2:29866446-29866647(+)$1	201	166	171	15.0000
UGCCU	chr12:76823578-76823779(-)$1	201	102	107	15.0000
UGCCU	chr2:60071964-60072165(+)$1	201	93	98	15.0000
UGCCU	chr19:10163413-10163614(-)$1	201	138	143	15.0000
UGCCU	chr18:20823886-20824087(+)$1	201	80	85	15.0000
UGCCU	chr10:59763433-59763634(+)$1	201	108	113	15.0000
UGCCU	chr1:180262330-180262531(-)$1	201	103	108	15.0000
UGCCU	chr14:122875524-122875725(+)$1	201	92	97	15.0000
UGCCU	chr3:108436009-108436210(+)$1	201	100	105	15.0000
UGCCU	chr2:60071962-60072163(+)$1	201	95	100	15.0000
UGCCU	chr6:87854782-87854983(+)$1	201	114	119	15.0000

#otherMatches

#Struct PSSM
ccc]b	chr9:58491415-58491616(+)$1	201	51	56	15.0000
\DDDD	chr7:25774838-25775039(-)$1	201	74	79	15.0000
CCCLL	chr10:80769016-80769217(+)$1	201	102	107	15.0000
mbbee	chr6:72386159-72386360(-)$1	201	69	74	15.0000
GGGGG	chr11:21228861-21229062(-)$1	201	52	57	15.0000
eeeee	chr2:107136218-107136419(+)$1	201	101	106	15.0000
qqqqq	chr18:20823884-20824085(+)$1	201	82	87	15.0000
nnndd	chr3:25335266-25335467(-)$1	201	40	45	15.0000
ccc!!	chrX:71200356-71200557(-)$1	201	19	24	15.0000
B}DDD	chr2:109836629-109836830(+)$1	201	182	187	15.0000
:::::	chr1:155067172-155067373(-)$1	201	83	88	15.0000
:::::	chr4:141024757-141024958(-)$1	201	8	13	15.0000
bb333	chr3:25335265-25335466(-)$1	201	39	44	15.0000
dddae	chr5:34263098-34263299(-)$1	201	164	169	15.0000
CCCLL	chr10:80769017-80769218(+)$1	201	101	106	15.0000
EEEEE	chr5:93699943-93700144(+)$1	201	70	75	15.0000
iiiii	chr11:3615058-3615259(-)$1	201	4	9	15.0000
cccc3	chr19:46339198-46339399(+)$1	201	119	124	15.0000
:::cc	chr14:60898835-60899036(+)$1	201	101	106	15.0000
GGGGG	chr11:21228862-21229063(-)$1	201	53	58	15.0000
!dddd	chr15:31405400-31405601(-)$1	201	85	90	15.0000
dddd:	chr10:59763439-59763640(+)$1	201	102	107	15.0000
::bbg	chr17:21088240-21088441(+)$1	201	101	106	15.0000
EEEEE	chr5:93699942-93700143(+)$1	201	71	76	15.0000
ff[dd	chr3:126637378-126637579(-)$1	201	23	28	15.0000
]ffff	chr17:24196151-24196352(-)$1	201	183	188	15.0000
GGKKF	chr15:31432413-31432614(-)$1	201	11	16	15.0000
::bbg	chr17:21088241-21088442(+)$1	201	100	105	15.0000
g::::	chr5:4083122-4083323(-)$1	201	48	53	15.0000
{FFFF	chr15:71292706-71292907(-)$1	201	43	48	15.0000
GGKKF	chr15:31432414-31432615(-)$1	201	12	17	15.0000
ddaoo	chr10:66682856-66683057(+)$1	201	100	105	15.0000
=====	chr14:65871755-65871956(-)$1	201	102	107	15.0000
a[ddd	chr6:124412063-124412264(-)$1	201	102	107	15.0000
dd22b	chrY:494799-495000(-)$1	201	23	28	15.0000
ggggg	chr3:126657842-126658043(-)$1	201	105	110	15.0000
3dddd	chr2:29866446-29866647(+)$1	201	166	171	15.0000
]dddd	chr12:76823578-76823779(-)$1	201	102	107	15.0000
ff:::	chr2:60071964-60072165(+)$1	201	93	98	15.0000
4bb22	chr19:10163413-10163614(-)$1	201	138	143	15.0000
qqqqq	chr18:20823886-20824087(+)$1	201	80	85	15.0000
dddd:	chr10:59763433-59763634(+)$1	201	108	113	15.0000
ccbb:	chr1:180262330-180262531(-)$1	201	103	108	15.0000
ee>>>	chr14:122875524-122875725(+)$1	201	92	97	15.0000
dd:::	chr3:108436009-108436210(+)$1	201	100	105	15.0000
ff:::	chr2:60071962-60072163(+)$1	201	95	100	15.0000
ccc[d	chr6:87854782-87854983(+)$1	201	114	119	15.0000

#DB
))).)	chr9:58491415-58491616(+)$1	1	51	56	15.0000
.))))	chr7:25774838-25775039(-)$1	1	74	79	15.0000
(((..	chr10:80769016-80769217(+)$1	1	102	107	15.0000
.))))	chr6:72386159-72386360(-)$1	1	69	74	15.0000
(((((	chr11:21228861-21229062(-)$1	1	52	57	15.0000
(((((	chr2:107136218-107136419(+)$1	1	101	106	15.0000
.....	chr18:20823884-20824085(+)$1	1	82	87	15.0000
...))	chr3:25335266-25335467(-)$1	1	40	45	15.0000
(((..	chrX:71200356-71200557(-)$1	1	19	24	15.0000
).)))	chr2:109836629-109836830(+)$1	1	182	187	15.0000
.....	chr1:155067172-155067373(-)$1	1	83	88	15.0000
.....	chr4:141024757-141024958(-)$1	1	8	13	15.0000
))...	chr3:25335265-25335466(-)$1	1	39	44	15.0000
)))))	chr5:34263098-34263299(-)$1	1	164	169	15.0000
(((..	chr10:80769017-80769218(+)$1	1	101	106	15.0000
(((((	chr5:93699943-93700144(+)$1	1	70	75	15.0000
(((((	chr11:3615058-3615259(-)$1	1	4	9	15.0000
)))).	chr19:46339198-46339399(+)$1	1	119	124	15.0000
...((	chr14:60898835-60899036(+)$1	1	101	106	15.0000
(((((	chr11:21228862-21229063(-)$1	1	53	58	15.0000
.((((	chr15:31405400-31405601(-)$1	1	85	90	15.0000
)))).	chr10:59763439-59763640(+)$1	1	102	107	15.0000
..(((	chr17:21088240-21088441(+)$1	1	101	106	15.0000
(((((	chr5:93699942-93700143(+)$1	1	71	76	15.0000
((.((	chr3:126637378-126637579(-)$1	1	23	28	15.0000
.))))	chr17:24196151-24196352(-)$1	1	183	188	15.0000
((..(	chr15:31432413-31432614(-)$1	1	11	16	15.0000
..(((	chr17:21088241-21088442(+)$1	1	100	105	15.0000
)....	chr5:4083122-4083323(-)$1	1	48	53	15.0000
.((((	chr15:71292706-71292907(-)$1	1	43	48	15.0000
((..(	chr15:31432414-31432615(-)$1	1	12	17	15.0000
(((..	chr10:66682856-66683057(+)$1	1	100	105	15.0000
)))))	chr14:65871755-65871956(-)$1	1	102	107	15.0000
(.(((	chr6:124412063-124412264(-)$1	1	102	107	15.0000
))..)	chrY:494799-495000(-)$1	1	23	28	15.0000
(((((	chr3:126657842-126658043(-)$1	1	105	110	15.0000
.))))	chr2:29866446-29866647(+)$1	1	166	171	15.0000
.))))	chr12:76823578-76823779(-)$1	1	102	107	15.0000
))...	chr2:60071964-60072165(+)$1	1	93	98	15.0000
.))..	chr19:10163413-10163614(-)$1	1	138	143	15.0000
.....	chr18:20823886-20824087(+)$1	1	80	85	15.0000
)))).	chr10:59763433-59763634(+)$1	1	108	113	15.0000
)))).	chr1:180262330-180262531(-)$1	1	103	108	15.0000
))...	chr14:122875524-122875725(+)$1	1	92	97	15.0000
))...	chr3:108436009-108436210(+)$1	1	100	105	15.0000
))...	chr2:60071962-60072163(+)$1	1	95	100	15.0000
(((.(	chr6:87854782-87854983(+)$1	1	114	119	15.0000

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

#score	705.0000000000001
#seq	47
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_UTR_m3_run1.nuc.txt

#NT
GAA	chr4:33125089-33125363(+)$1	274	96	99	8.9999
GAA	chr3:133126987-133127277(-)$1	290	64	67	8.9999
GAA	chr3:122242267-122242549(-)$1	282	40	43	8.9999
GAA	chr5:116859149-116859423(-)$1	274	66	69	8.9999
GAA	chr5:138223461-138223741(-)$1	280	94	97	8.9999
GAA	chr17:57032818-57033129(-)$1	311	159	162	8.9999
GAA	chr6:40353079-40353347(-)$1	268	13	16	8.9999
GAA	chr12:113887155-113887427(+)$1	272	53	56	8.9999
GAA	chr1:36501804-36502071(-)$1	267	142	145	8.9999
GAA	chr9:30881664-30881966(+)$1	302	74	77	8.9999
GAA	chr4:63211331-63211605(+)$1	274	0	3	8.9999
GAA	chr3:121969343-121969622(+)$1	279	13	16	8.9999
GAA	chr14:99472889-99473185(+)$1	296	4	7	8.9999
GAA	chr1:181447930-181448215(-)$1	285	72	75	8.9999
GAA	chr17:34791783-34792075(+)$1	292	3	6	8.9999
GAA	chr19:46147231-46147502(+)$1	271	1	4	8.9999
GAA	chr8:86620998-86621281(-)$1	283	118	121	8.9999
GAA	chr14:71003925-71004204(-)$1	279	6	9	8.9999
GAA	chr3:95464619-95464902(+)$1	283	46	49	8.9999
GAA	chr5:31924774-31925053(+)$1	279	3	6	8.9999
GAA	chr4:135560383-135560657(-)$1	274	7	10	8.9999
GAA	chr15:75831594-75831869(-)$1	275	48	51	8.9999
GAA	chr7:117008949-117009223(-)$1	274	153	156	8.9999
GAA	chr18:24443319-24443593(+)$1	274	9	12	8.9999
GAA	chr5:108863239-108863508(-)$1	269	112	115	8.9999
GAA	chr15:79655890-79656177(-)$1	287	18	21	8.9999
gaa	chr5:123807806-123808084(+)$1	278	18	21	8.9999
gaa	chr4:133831673-133831946(-)$1	273	176	179	8.9999
GAA	chr16:91227775-91228057(+)$1	282	9	12	8.9999
GAA	chr2:31071139-31071424(+)$1	285	46	49	8.9999
GAA	chr11:52221422-52221709(+)$1	287	117	120	8.9999
GAA	chr2:173526976-173527254(+)$1	278	54	57	8.9999
GAA	chr11:98015255-98015545(-)$1	290	34	37	8.9999
GAA	chr17:47760163-47760455(+)$1	292	77	80	8.9999
GAA	chr10:116510428-116510732(-)$1	304	55	58	8.9999
GAA	chr4:140669579-140669861(-)$1	282	11	14	8.9999
GAA	chr10:76508552-76508827(+)$1	275	11	14	8.9999
GAA	chr5:137967090-137967377(+)$1	287	89	92	8.9999
GAA	chr15:81678793-81679067(-)$1	274	43	46	8.9999
GAA	chr15:89012665-89012935(-)$1	270	38	41	8.9999
GAA	chr4:137798696-137798973(+)$1	277	21	24	8.9999
GAA	chr10:116509561-116509829(-)$1	268	110	113	8.9999
GAA	chr5:141098323-141098600(-)$1	277	134	137	8.9999
GAA	chr7:25670028-25670303(+)$1	275	211	214	8.9999
GAA	chr3:96066811-96067101(-)$1	290	50	53	8.9999
GAA	chr9:90098128-90098412(-)$1	284	1	4	8.9999
GAA	chr7:72016758-72017030(-)$1	272	64	67	8.9999
GAA	chr5:93697524-93697801(+)$1	277	125	128	8.9999
GAA	chr15:80761597-80761877(+)$1	280	24	27	8.9999
GAA	chr6:124863939-124864222(-)$1	283	2	5	8.9999
GAA	chr19:5456362-5456644(-)$1	282	28	31	8.9999
GAA	chr10:20845086-20845380(-)$1	294	6	9	8.9999
GAA	chr11:29642127-29642419(+)$1	292	28	31	8.9999
GAA	chr4:140884838-140885115(+)$1	277	177	180	8.9999
GAA	chr19:29090645-29090925(+)$1	280	64	67	8.9999
GAA	chr5:114588885-114589158(+)$1	273	87	90	8.9999
gaa	chr17:27062059-27062328(+)$1	269	96	99	8.9999
GAA	chr4:49669033-49669317(+)$1	284	108	111	8.9999
GAA	chr15:79655086-79655360(-)$1	274	140	143	8.9999
GAA	chr6:40353055-40353326(-)$1	271	8	11	8.9999
GAA	chr1:64840465-64840739(-)$1	274	41	44	8.9999
GAA	chr4:99324902-99325179(+)$1	277	48	51	8.9999
GAA	chr15:75900547-75900820(-)$1	273	15	18	8.9999
GAA	chr3:32240109-32240398(-)$1	289	9	12	8.9999
GAA	chr17:6084525-6084794(+)$1	269	0	3	8.9999
GAA	chr7:24891396-24891687(+)$1	291	13	16	8.9999
GAA	chr6:124998851-124999134(+)$1	283	87	90	8.9999
GAA	chr12:8798840-8799138(+)$1	298	80	83	8.9999
GAA	chr13:69138020-69138287(-)$1	267	26	29	8.9999
GAA	chr2:14999759-15000046(+)$1	287	0	3	8.9999
GAA	chr3:108163830-108164132(+)$1	302	56	59	8.9999
GAA	chr10:127827825-127828099(+)$1	274	7	10	8.9999
GAA	chr8:125096582-125096860(+)$1	278	129	132	8.9999
GAA	chr17:37209978-37210255(+)$1	277	4	7	8.9999
GAA	chr4:147320759-147321044(+)$1	285	39	42	8.9999
GAA	chr3:87340637-87340930(+)$1	293	150	153	8.9999
GAA	chr19:8964904-8965185(+)$1	281	51	54	8.9999
GAA	chr2:152607454-152607733(-)$1	279	34	37	8.9999
GAA	chr17:46305894-46306170(+)$1	276	244	247	8.9999
GAA	chr7:151775188-151775456(-)$1	268	11	14	8.9999
GAA	chr9:119147937-119148232(-)$1	295	13	16	8.9999
gaa	chr18:75555296-75555568(+)$1	272	16	19	8.9999
GAA	chr11:87794728-87795014(-)$1	286	91	94	8.9999
GAA	chr11:117828673-117828941(-)$1	268	11	14	8.9999
GAA	chr12:114059366-114059639(-)$1	273	232	235	8.9999
GAA	chr2:157383309-157383584(-)$1	275	111	114	8.9999
GAA	chr17:32498259-32498531(-)$1	272	25	28	8.9999
GAA	chr11:69813266-69813543(+)$1	277	128	131	8.9999
GAA	chr11:114729900-114730186(+)$1	286	66	69	8.9999
GAA	chr15:81535366-81535645(-)$1	279	129	132	8.9999
GAA	chr10:29066348-29066634(-)$1	286	125	128	8.9999
Gaa	chrX:11614171-11614458(-)$1	287	6	9	8.9999
GAA	chr18:34930992-34931266(+)$1	274	98	101	8.9999
GAA	chr4:151560213-151560493(+)$1	280	41	44	8.9999
GAA	chr6:140599401-140599683(+)$1	282	73	76	8.9999
GAA	chr2:32134292-32134583(-)$1	291	108	111	8.9999
GAA	chr19:3808352-3808623(+)$1	271	3	6	8.9999
GAA	chr16:36750514-36750783(-)$1	269	17	20	8.9999

#otherMatches

#Struct PSSM
:::	chr5:123809705-123809975(+)$1	270	65	68	8.9999
hhh	chr4:33125089-33125363(+)$1	274	96	99	8.9999
NNI	chr3:133126987-133127277(-)$1	290	64	67	8.9999
DDD	chr3:122242267-122242549(-)$1	282	40	43	8.9999
ggg	chr5:116859149-116859423(-)$1	274	66	69	8.9999
DDD	chr5:138223461-138223741(-)$1	280	94	97	8.9999
%%%	chr17:57032818-57033129(-)$1	311	159	162	8.9999
:::	chr6:40353079-40353347(-)$1	268	13	16	8.9999
:::	chr12:113887155-113887427(+)$1	272	53	56	8.9999
ee2	chr1:36501804-36502071(-)$1	267	142	145	8.9999
ffc	chr9:30881664-30881966(+)$1	302	74	77	8.9999
ddd	chr4:63211331-63211605(+)$1	274	0	3	8.9999
ccc	chr3:121969343-121969622(+)$1	279	13	16	8.9999
err	chr14:99472889-99473185(+)$1	296	4	7	8.9999
:::	chr1:181447930-181448215(-)$1	285	72	75	8.9999
:::	chr17:34791783-34792075(+)$1	292	3	6	8.9999
:::	chr19:46147231-46147502(+)$1	271	1	4	8.9999
f!!	chr8:86620998-86621281(-)$1	283	118	121	8.9999
:::	chr14:71003925-71004204(-)$1	279	6	9	8.9999
===	chr3:95464619-95464902(+)$1	283	46	49	8.9999
FFF	chr5:31924774-31925053(+)$1	279	3	6	8.9999
H::	chr4:135560383-135560657(-)$1	274	7	10	8.9999
III	chr15:75831594-75831869(-)$1	275	48	51	8.9999
fll	chr7:117008949-117009223(-)$1	274	153	156	8.9999
KHH	chr18:24443319-24443593(+)$1	274	9	12	8.9999
::I	chr5:108863239-108863508(-)$1	269	112	115	8.9999
hhh	chr15:79655890-79656177(-)$1	287	18	21	8.9999
F::	chr5:123807806-123808084(+)$1	278	18	21	8.9999
fff	chr4:133831673-133831946(-)$1	273	176	179	8.9999
!!c	chr16:91227775-91228057(+)$1	282	9	12	8.9999
ddd	chr2:31071139-31071424(+)$1	285	46	49	8.9999
:::	chr11:52221422-52221709(+)$1	287	117	120	8.9999
dd]	chr2:173526976-173527254(+)$1	278	54	57	8.9999
eee	chr11:98015255-98015545(-)$1	290	34	37	8.9999
+++	chr17:47760163-47760455(+)$1	292	77	80	8.9999
b!!	chr10:116510428-116510732(-)$1	304	55	58	8.9999
GGG	chr4:140669579-140669861(-)$1	282	11	14	8.9999
i""	chr10:76508552-76508827(+)$1	275	11	14	8.9999
hhh	chr5:137967090-137967377(+)$1	287	89	92	8.9999
yyy	chr15:81678793-81679067(-)$1	274	43	46	8.9999
e:d	chr15:89012665-89012935(-)$1	270	38	41	8.9999
dd5	chr4:137798696-137798973(+)$1	277	21	24	8.9999
e22	chr10:116509561-116509829(-)$1	268	110	113	8.9999
aqq	chr5:141098323-141098600(-)$1	277	134	137	8.9999
cc4	chr7:25670028-25670303(+)$1	275	211	214	8.9999
"""	chr3:96066811-96067101(-)$1	290	50	53	8.9999
:::	chr9:90098128-90098412(-)$1	284	1	4	8.9999
g""	chr7:72016758-72017030(-)$1	272	64	67	8.9999
nnn	chr5:93697524-93697801(+)$1	277	125	128	8.9999
f::	chr15:80761597-80761877(+)$1	280	24	27	8.9999
DDD	chr6:124863939-124864222(-)$1	283	2	5	8.9999
i44	chr19:5456362-5456644(-)$1	282	28	31	8.9999
hhh	chr10:20845086-20845380(-)$1	294	6	9	8.9999
d''	chr11:29642127-29642419(+)$1	292	28	31	8.9999
ppp	chr4:140884838-140885115(+)$1	277	177	180	8.9999
22c	chr19:29090645-29090925(+)$1	280	64	67	8.9999
ppp	chr5:114588885-114589158(+)$1	273	87	90	8.9999
ee[	chr17:27062059-27062328(+)$1	269	96	99	8.9999
ggg	chr4:49669033-49669317(+)$1	284	108	111	8.9999
iii	chr15:79655086-79655360(-)$1	274	140	143	8.9999
eee	chr6:40353055-40353326(-)$1	271	8	11	8.9999
fff	chr1:64840465-64840739(-)$1	274	41	44	8.9999
ddd	chr4:99324902-99325179(+)$1	277	48	51	8.9999
KGG	chr15:75900547-75900820(-)$1	273	15	18	8.9999
iii	chr3:32240109-32240398(-)$1	289	9	12	8.9999
:::	chr17:6084525-6084794(+)$1	269	0	3	8.9999
DDD	chr7:24891396-24891687(+)$1	291	13	16	8.9999
ppp	chr6:124998851-124999134(+)$1	283	87	90	8.9999
:::	chr12:8798840-8799138(+)$1	298	80	83	8.9999
a!!	chr13:69138020-69138287(-)$1	267	26	29	8.9999
:::	chr2:14999759-15000046(+)$1	287	0	3	8.9999
:::	chr3:108163830-108164132(+)$1	302	56	59	8.9999
ffp	chr10:127827825-127828099(+)$1	274	7	10	8.9999
hhh	chr8:125096582-125096860(+)$1	278	129	132	8.9999
::E	chr17:37209978-37210255(+)$1	277	4	7	8.9999
ff!	chr4:147320759-147321044(+)$1	285	39	42	8.9999
e::	chr3:87340637-87340930(+)$1	293	150	153	8.9999
:::	chr19:8964904-8965185(+)$1	281	51	54	8.9999
{GG	chr2:152607454-152607733(-)$1	279	34	37	8.9999
d]f	chr17:46305894-46306170(+)$1	276	244	247	8.9999
D{B	chr7:151775188-151775456(-)$1	268	11	14	8.9999
BNN	chr9:119147937-119148232(-)$1	295	13	16	8.9999
JJJ	chr18:75555296-75555568(+)$1	272	16	19	8.9999
dd[	chr11:87794728-87795014(-)$1	286	91	94	8.9999
:::	chr11:117828673-117828941(-)$1	268	11	14	8.9999
DD}	chr12:114059366-114059639(-)$1	273	232	235	8.9999
Edd	chr2:157383309-157383584(-)$1	275	111	114	8.9999
:::	chr17:32498259-32498531(-)$1	272	25	28	8.9999
GGG	chr11:69813266-69813543(+)$1	277	128	131	8.9999
c""	chr11:114729900-114730186(+)$1	286	66	69	8.9999
cc:	chr15:81535366-81535645(-)$1	279	129	132	8.9999
EEE	chr10:29066348-29066634(-)$1	286	125	128	8.9999
:::	chrX:11614171-11614458(-)$1	287	6	9	8.9999
GGe	chr18:34930992-34931266(+)$1	274	98	101	8.9999
ddd	chr4:151560213-151560493(+)$1	280	41	44	8.9999
===	chr6:140599401-140599683(+)$1	282	73	76	8.9999
fff	chr2:32134292-32134583(-)$1	291	108	111	8.9999
EEE	chr19:3808352-3808623(+)$1	271	3	6	8.9999
:::	chr16:36750514-36750783(-)$1	269	17	20	8.9999

#DB
...	chr5:123809705-123809975(+)$1	1	65	68	8.9999
)))	chr4:33125089-33125363(+)$1	1	96	99	8.9999
..(	chr3:133126987-133127277(-)$1	1	64	67	8.9999
(((	chr3:122242267-122242549(-)$1	1	40	43	8.9999
)))	chr5:116859149-116859423(-)$1	1	66	69	8.9999
)))	chr5:138223461-138223741(-)$1	1	94	97	8.9999
...	chr17:57032818-57033129(-)$1	1	159	162	8.9999
...	chr6:40353079-40353347(-)$1	1	13	16	8.9999
...	chr12:113887155-113887427(+)$1	1	53	56	8.9999
)).	chr1:36501804-36502071(-)$1	1	142	145	8.9999
)))	chr9:30881664-30881966(+)$1	1	74	77	8.9999
(((	chr4:63211331-63211605(+)$1	1	0	3	8.9999
(((	chr3:121969343-121969622(+)$1	1	13	16	8.9999
(..	chr14:99472889-99473185(+)$1	1	4	7	8.9999
...	chr1:181447930-181448215(-)$1	1	72	75	8.9999
...	chr17:34791783-34792075(+)$1	1	3	6	8.9999
...	chr19:46147231-46147502(+)$1	1	1	4	8.9999
(..	chr8:86620998-86621281(-)$1	1	118	121	8.9999
...	chr14:71003925-71004204(-)$1	1	6	9	8.9999
)))	chr3:95464619-95464902(+)$1	1	46	49	8.9999
(((	chr5:31924774-31925053(+)$1	1	3	6	8.9999
(..	chr4:135560383-135560657(-)$1	1	7	10	8.9999
(((	chr15:75831594-75831869(-)$1	1	48	51	8.9999
(..	chr7:117008949-117009223(-)$1	1	153	156	8.9999
.((	chr18:24443319-24443593(+)$1	1	9	12	8.9999
..(	chr5:108863239-108863508(-)$1	1	112	115	8.9999
)))	chr15:79655890-79656177(-)$1	1	18	21	8.9999
(..	chr5:123807806-123808084(+)$1	1	18	21	8.9999
(((	chr4:133831673-133831946(-)$1	1	176	179	8.9999
..(	chr16:91227775-91228057(+)$1	1	9	12	8.9999
(((	chr2:31071139-31071424(+)$1	1	46	49	8.9999
...	chr11:52221422-52221709(+)$1	1	117	120	8.9999
)).	chr2:173526976-173527254(+)$1	1	54	57	8.9999
)))	chr11:98015255-98015545(-)$1	1	34	37	8.9999
...	chr17:47760163-47760455(+)$1	1	77	80	8.9999
(..	chr10:116510428-116510732(-)$1	1	55	58	8.9999
(((	chr4:140669579-140669861(-)$1	1	11	14	8.9999
(..	chr10:76508552-76508827(+)$1	1	11	14	8.9999
(((	chr5:137967090-137967377(+)$1	1	89	92	8.9999
...	chr15:81678793-81679067(-)$1	1	43	46	8.9999
).(	chr15:89012665-89012935(-)$1	1	38	41	8.9999
)).	chr4:137798696-137798973(+)$1	1	21	24	8.9999
)..	chr10:116509561-116509829(-)$1	1	110	113	8.9999
(..	chr5:141098323-141098600(-)$1	1	134	137	8.9999
)).	chr7:25670028-25670303(+)$1	1	211	214	8.9999
...	chr3:96066811-96067101(-)$1	1	50	53	8.9999
...	chr9:90098128-90098412(-)$1	1	1	4	8.9999
(..	chr7:72016758-72017030(-)$1	1	64	67	8.9999
...	chr5:93697524-93697801(+)$1	1	125	128	8.9999
)..	chr15:80761597-80761877(+)$1	1	24	27	8.9999
(((	chr6:124863939-124864222(-)$1	1	2	5	8.9999
)..	chr19:5456362-5456644(-)$1	1	28	31	8.9999
(((	chr10:20845086-20845380(-)$1	1	6	9	8.9999
(..	chr11:29642127-29642419(+)$1	1	28	31	8.9999
...	chr4:140884838-140885115(+)$1	1	177	180	8.9999
..)	chr19:29090645-29090925(+)$1	1	64	67	8.9999
...	chr5:114588885-114589158(+)$1	1	87	90	8.9999
((.	chr17:27062059-27062328(+)$1	1	96	99	8.9999
)))	chr4:49669033-49669317(+)$1	1	108	111	8.9999
(((	chr15:79655086-79655360(-)$1	1	140	143	8.9999
(((	chr6:40353055-40353326(-)$1	1	8	11	8.9999
(((	chr1:64840465-64840739(-)$1	1	41	44	8.9999
(((	chr4:99324902-99325179(+)$1	1	48	51	8.9999
.((	chr15:75900547-75900820(-)$1	1	15	18	8.9999
(((	chr3:32240109-32240398(-)$1	1	9	12	8.9999
...	chr17:6084525-6084794(+)$1	1	0	3	8.9999
(((	chr7:24891396-24891687(+)$1	1	13	16	8.9999
...	chr6:124998851-124999134(+)$1	1	87	90	8.9999
...	chr12:8798840-8799138(+)$1	1	80	83	8.9999
(..	chr13:69138020-69138287(-)$1	1	26	29	8.9999
...	chr2:14999759-15000046(+)$1	1	0	3	8.9999
...	chr3:108163830-108164132(+)$1	1	56	59	8.9999
((.	chr10:127827825-127828099(+)$1	1	7	10	8.9999
)))	chr8:125096582-125096860(+)$1	1	129	132	8.9999
..(	chr17:37209978-37210255(+)$1	1	4	7	8.9999
((.	chr4:147320759-147321044(+)$1	1	39	42	8.9999
)..	chr3:87340637-87340930(+)$1	1	150	153	8.9999
...	chr19:8964904-8965185(+)$1	1	51	54	8.9999
.((	chr2:152607454-152607733(-)$1	1	34	37	8.9999
).)	chr17:46305894-46306170(+)$1	1	244	247	8.9999
(.(	chr7:151775188-151775456(-)$1	1	11	14	8.9999
(..	chr9:119147937-119148232(-)$1	1	13	16	8.9999
(((	chr18:75555296-75555568(+)$1	1	16	19	8.9999
((.	chr11:87794728-87795014(-)$1	1	91	94	8.9999
...	chr11:117828673-117828941(-)$1	1	11	14	8.9999
)).	chr12:114059366-114059639(-)$1	1	232	235	8.9999
)((	chr2:157383309-157383584(-)$1	1	111	114	8.9999
...	chr17:32498259-32498531(-)$1	1	25	28	8.9999
)))	chr11:69813266-69813543(+)$1	1	128	131	8.9999
(..	chr11:114729900-114730186(+)$1	1	66	69	8.9999
)).	chr15:81535366-81535645(-)$1	1	129	132	8.9999
)))	chr10:29066348-29066634(-)$1	1	125	128	8.9999
...	chrX:11614171-11614458(-)$1	1	6	9	8.9999
(((	chr18:34930992-34931266(+)$1	1	98	101	8.9999
)))	chr4:151560213-151560493(+)$1	1	41	44	8.9999
)))	chr6:140599401-140599683(+)$1	1	73	76	8.9999
(((	chr2:32134292-32134583(-)$1	1	108	111	8.9999
(((	chr19:3808352-3808623(+)$1	1	3	6	8.9999
...	chr16:36750514-36750783(-)$1	1	17	20	8.9999

#PSSM
G : 0.95	g : 0.04	
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
HITSCLIP_Nova_Zhang2011b_mm9_CDS_m3_run2.nuc.txt

#NT
AGUGCAGGUGGUGCGGAGCAGGCAGACGACAAGUACUUCAAAUGUGAUGUGUGCGGGCAACUCUUCAACGACCGCCUCUCCCUUGCCAGACACCAGAAUUCUCACACUGGUUGAGUAACCAGGCUGAAGAAAAGAAGAGCAAAGCCAAACCUUCUUCCCAGAACCAGACCCUUAAUAAAUCACAAAGAGAGCCUAAACC	chr7:6660130-6660331(-)$1	201	1	200	597.0000

#otherMatches

#Struct PSSM
eeeee!!bb[bbbbpppppppbb22bb]bb22eeeee:::::FFFFFF{CCCKKCCCA:::ffffff%%%%%%dddd$$$$$ddddbb"""eeeeesssssssssseeeeebb]dddd22ddddffffff:ffffffvvvvvvvvvvvvvffffff::::::::::A}CCCZZZCCC}FFFFFF:::::::::::::::	chr7:6660129-6660330(-)$1	201	0	199	597.0000
eeeee!!bb[bbbbpppppppbb22bb]bb22eeeee:::::FFFFFF{CCCKKCCCA:::ffffff%%%%%%dddd$$$$$ddddbb"""eeeeesssssssssseeeeebb]dddd22ddddffffff:ffffffvvvvvvvvvvvvvffffff::::::::::A}CCCZZZCCC}FFFFFF:::::::::::::::	chr7:6660130-6660331(-)$1	201	1	200	597.0000

#DB
(((((..((.((((.......))..)).))..))))).....((((((.(((..((((...((((((......((((.....((((((...(((((..........))))))).))))..)))))))))).((((((.............))))))..........).)))...))).))))))...............	chr7:6660129-6660330(-)$1	1	0	199	597.0000
(((((..((.((((.......))..)).))..))))).....((((((.(((..((((...((((((......((((.....((((((...(((((..........))))))).))))..)))))))))).((((((.............))))))..........).)))...))).))))))...............	chr7:6660130-6660331(-)$1	1	1	200	597.0000

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

#score	1194.0
#seq	2
#width	199
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_CDS_m3_run1.nuc.txt

#NT
GGAGA	chrX:20197127-20197347(+)$1	220	178	183	15.0000
GGAGA	chrX:23336228-23336449(+)$1	221	156	161	15.0000
GGAGA	chr12:77129005-77129225(+)$1	220	71	76	15.0000
GGAGA	chr9:64025433-64025673(+)$1	240	5	10	15.0000
GGAGA	chr11:101489208-101489440(+)$1	232	184	189	15.0000
GGAGA	chr2:31649957-31650178(+)$1	221	123	128	15.0000
GGAGA	chr4:126876854-126877074(+)$1	220	109	114	15.0000
GGAGA	chr7:151766410-151766630(-)$1	220	4	9	15.0000
GGAGA	chr2:20727778-20727998(+)$1	220	115	120	15.0000
GGAGA	chr17:27251684-27251904(+)$1	220	139	144	15.0000
GGAGA	chr3:108143442-108143665(+)$1	223	138	143	15.0000
GGAGA	chr2:144229765-144229985(+)$1	220	116	121	15.0000
GGAGA	chr13:67064243-67064463(+)$1	220	37	42	15.0000
GGAGA	chr8:75276994-75277220(+)$1	226	187	192	15.0000
GGAGA	chr1:138423985-138424241(+)$1	256	22	27	15.0000
GGAGA	chr9:92483369-92483600(+)$1	231	217	222	15.0000
GGAGA	chr11:60611981-60612218(-)$1	237	82	87	15.0000
GGAGA	chr4:43458130-43458350(+)$1	220	95	100	15.0000
GGAGA	chrX:98877535-98877770(+)$1	235	150	155	15.0000
GGAGA	chr15:25914822-25915042(+)$1	220	0	5	15.0000
GGAGA	chr18:35021140-35021363(+)$1	223	109	114	15.0000
GGAGA	chr11:95536443-95536663(+)$1	220	196	201	15.0000
GGAGA	chr16:72933450-72933670(+)$1	220	96	101	15.0000
GGAGA	chr2:166685220-166685440(+)$1	220	86	91	15.0000
GGAGA	chr16:32381250-32381477(+)$1	227	96	101	15.0000
GGAGA	chr2:69587760-69588000(+)$1	240	212	217	15.0000
GGAGA	chr19:41633568-41633789(+)$1	221	60	65	15.0000
GGAGA	chr9:118570366-118570586(+)$1	220	189	194	15.0000
GGAGA	chr4:128685171-128685404(+)$1	233	34	39	15.0000
GGAGA	chr10:83053694-83053930(+)$1	236	125	130	15.0000
GGAGA	chr4:139035296-139035529(+)$1	233	92	97	15.0000
GGAGA	chr19:21872668-21872888(+)$1	220	158	163	15.0000
GGAGA	chr1:72371541-72371763(+)$1	222	41	46	15.0000
GGAGA	chr8:46109898-46110121(+)$1	223	109	114	15.0000
GGAGA	chr12:28027098-28027318(-)$1	220	14	19	15.0000
GGAGA	chr2:128933639-128933859(+)$1	220	144	149	15.0000
GGAGA	chr9:108109607-108109846(-)$1	239	110	115	15.0000
GGAGA	chr3:145606721-145606960(+)$1	239	86	91	15.0000
GGAGA	chr17:74787507-74787745(+)$1	238	127	132	15.0000
GGAGA	chr19:21886264-21886485(+)$1	221	91	96	15.0000
GGAGA	chr19:10274727-10274952(-)$1	225	154	159	15.0000
GGAGA	chr2:121282744-121282964(+)$1	220	133	138	15.0000
GGAGA	chr11:70539513-70539733(+)$1	220	124	129	15.0000
GGAGA	chr6:4705043-4705263(+)$1	220	187	192	15.0000
GGAGA	chr5:31768550-31768775(+)$1	225	73	78	15.0000
GGAGA	chr16:11253639-11253859(-)$1	220	196	201	15.0000
GGAGA	chr15:99237650-99237870(+)$1	220	0	5	15.0000
GGAGA	chr9:45198617-45198838(+)$1	221	109	114	15.0000
GGAGA	chr1:134390299-134390519(+)$1	220	168	173	15.0000
GGAGA	chrX:7459220-7459441(+)$1	221	108	113	15.0000
GGAGA	chr9:72590368-72590588(+)$1	220	17	22	15.0000
GGAGA	chr7:107564904-107565134(+)$1	230	23	28	15.0000
GGAGA	chr3:35980650-35980870(+)$1	220	183	188	15.0000
GGAGA	chr4:32807663-32807883(+)$1	220	73	78	15.0000
GGAGA	chr1:10117406-10117626(+)$1	220	161	166	15.0000

#otherMatches

#Struct PSSM
FFF::	chr14:55640823-55641043(+)$1	220	85	90	15.0000
dddd:	chrX:20197127-20197347(+)$1	220	178	183	15.0000
ff]cc	chrX:23336228-23336449(+)$1	221	156	161	15.0000
qqqbb	chr12:77129005-77129225(+)$1	220	71	76	15.0000
KCCC{	chr9:64025433-64025673(+)$1	240	5	10	15.0000
dddFF	chr11:101489208-101489440(+)$1	232	184	189	15.0000
e[bb%	chr2:31649957-31650178(+)$1	221	123	128	15.0000
ccmmm	chr4:126876854-126877074(+)$1	220	109	114	15.0000
a[bb[	chr7:151766410-151766630(-)$1	220	4	9	15.0000
eeeeo	chr2:20727778-20727998(+)$1	220	115	120	15.0000
c22cc	chr17:27251684-27251904(+)$1	220	139	144	15.0000
a!!a[	chr3:108143442-108143665(+)$1	223	138	143	15.0000
i::ii	chr2:144229765-144229985(+)$1	220	116	121	15.0000
EKKBB	chr13:67064243-67064463(+)$1	220	37	42	15.0000
}EEEE	chr8:75276994-75277220(+)$1	226	187	192	15.0000
#dddd	chr1:138423985-138424241(+)$1	256	22	27	15.0000
FF:::	chr9:92483369-92483600(+)$1	231	217	222	15.0000
ggggr	chr11:60611981-60612218(-)$1	237	82	87	15.0000
iiii:	chr4:43458130-43458350(+)$1	220	95	100	15.0000
ee:::	chrX:98877535-98877770(+)$1	235	150	155	15.0000
DDDDK	chr15:25914822-25915042(+)$1	220	0	5	15.0000
BBLLL	chr18:35021140-35021363(+)$1	223	109	114	15.0000
ZZZA}	chr11:95536443-95536663(+)$1	220	196	201	15.0000
]bbFF	chr16:72933450-72933670(+)$1	220	96	101	15.0000
ff]bb	chr2:166685220-166685440(+)$1	220	86	91	15.0000
ccmmm	chr16:32381250-32381477(+)$1	227	96	101	15.0000
:::::	chr2:69587760-69588000(+)$1	240	212	217	15.0000
eeeee	chr19:41633568-41633789(+)$1	221	60	65	15.0000
JJJJJ	chr9:118570366-118570586(+)$1	220	189	194	15.0000
g[eee	chr4:128685171-128685404(+)$1	233	34	39	15.0000
b]ddd	chr10:83053694-83053930(+)$1	236	125	130	15.0000
ddddd	chr4:139035296-139035529(+)$1	233	92	97	15.0000
hhmmm	chr19:21872668-21872888(+)$1	220	158	163	15.0000
=====	chr1:72371541-72371763(+)$1	222	41	46	15.0000
BB:cc	chr8:46109898-46110121(+)$1	223	109	114	15.0000
bblll	chr12:28027098-28027318(-)$1	220	14	19	15.0000
nnnnn	chr2:128933639-128933859(+)$1	220	144	149	15.0000
fffdd	chr9:108109607-108109846(-)$1	239	110	115	15.0000
ffff!	chr3:145606721-145606960(+)$1	239	86	91	15.0000
ee]cc	chr17:74787507-74787745(+)$1	238	127	132	15.0000
dddd[	chr19:21886264-21886485(+)$1	221	91	96	15.0000
annnn	chr19:10274727-10274952(-)$1	225	154	159	15.0000
EEEE:	chr2:121282744-121282964(+)$1	220	133	138	15.0000
CCCDD	chr11:70539513-70539733(+)$1	220	124	129	15.0000
::hhh	chr6:4705043-4705263(+)$1	220	187	192	15.0000
DDD{C	chr5:31768550-31768775(+)$1	225	73	78	15.0000
ee]a]	chr16:11253639-11253859(-)$1	220	196	201	15.0000
:dddd	chr15:99237650-99237870(+)$1	220	0	5	15.0000
::fff	chr9:45198617-45198838(+)$1	221	109	114	15.0000
EDDDD	chr1:134390299-134390519(+)$1	220	168	173	15.0000
DDDD:	chrX:7459220-7459441(+)$1	221	108	113	15.0000
b[bbe	chr9:72590368-72590588(+)$1	220	17	22	15.0000
lliii	chr7:107564904-107565134(+)$1	230	23	28	15.0000
gg]gg	chr3:35980650-35980870(+)$1	220	183	188	15.0000
=====	chr4:32807663-32807883(+)$1	220	73	78	15.0000
gggg$	chr1:10117406-10117626(+)$1	220	161	166	15.0000

#DB
(((..	chr14:55640823-55641043(+)$1	1	85	90	15.0000
)))).	chrX:20197127-20197347(+)$1	1	178	183	15.0000
)).))	chrX:23336228-23336449(+)$1	1	156	161	15.0000
...))	chr12:77129005-77129225(+)$1	1	71	76	15.0000
.(((.	chr9:64025433-64025673(+)$1	1	5	10	15.0000
)))))	chr11:101489208-101489440(+)$1	1	184	189	15.0000
(.((.	chr2:31649957-31650178(+)$1	1	123	128	15.0000
((...	chr4:126876854-126877074(+)$1	1	109	114	15.0000
(.((.	chr7:151766410-151766630(-)$1	1	4	9	15.0000
((((.	chr2:20727778-20727998(+)$1	1	115	120	15.0000
)..))	chr17:27251684-27251904(+)$1	1	139	144	15.0000
(..(.	chr3:108143442-108143665(+)$1	1	138	143	15.0000
)..((	chr2:144229765-144229985(+)$1	1	116	121	15.0000
(..((	chr13:67064243-67064463(+)$1	1	37	42	15.0000
.))))	chr8:75276994-75277220(+)$1	1	187	192	15.0000
.((((	chr1:138423985-138424241(+)$1	1	22	27	15.0000
))...	chr9:92483369-92483600(+)$1	1	217	222	15.0000
((((.	chr11:60611981-60612218(-)$1	1	82	87	15.0000
)))).	chr4:43458130-43458350(+)$1	1	95	100	15.0000
))...	chrX:98877535-98877770(+)$1	1	150	155	15.0000
((((.	chr15:25914822-25915042(+)$1	1	0	5	15.0000
((...	chr18:35021140-35021363(+)$1	1	109	114	15.0000
...).	chr11:95536443-95536663(+)$1	1	196	201	15.0000
.))))	chr16:72933450-72933670(+)$1	1	96	101	15.0000
)).))	chr2:166685220-166685440(+)$1	1	86	91	15.0000
((...	chr16:32381250-32381477(+)$1	1	96	101	15.0000
.....	chr2:69587760-69588000(+)$1	1	212	217	15.0000
)))))	chr19:41633568-41633789(+)$1	1	60	65	15.0000
)))))	chr9:118570366-118570586(+)$1	1	189	194	15.0000
(.(((	chr4:128685171-128685404(+)$1	1	34	39	15.0000
).)))	chr10:83053694-83053930(+)$1	1	125	130	15.0000
)))))	chr4:139035296-139035529(+)$1	1	92	97	15.0000
((...	chr19:21872668-21872888(+)$1	1	158	163	15.0000
(((((	chr1:72371541-72371763(+)$1	1	41	46	15.0000
)).((	chr8:46109898-46110121(+)$1	1	109	114	15.0000
((...	chr12:28027098-28027318(-)$1	1	14	19	15.0000
.....	chr2:128933639-128933859(+)$1	1	144	149	15.0000
)))))	chr9:108109607-108109846(-)$1	1	110	115	15.0000
((((.	chr3:145606721-145606960(+)$1	1	86	91	15.0000
)).))	chr17:74787507-74787745(+)$1	1	127	132	15.0000
((((.	chr19:21886264-21886485(+)$1	1	91	96	15.0000
(....	chr19:10274727-10274952(-)$1	1	154	159	15.0000
((((.	chr2:121282744-121282964(+)$1	1	133	138	15.0000
)))))	chr11:70539513-70539733(+)$1	1	124	129	15.0000
..(((	chr6:4705043-4705263(+)$1	1	187	192	15.0000
(((.(	chr5:31768550-31768775(+)$1	1	73	78	15.0000
)).).	chr16:11253639-11253859(-)$1	1	196	201	15.0000
.((((	chr15:99237650-99237870(+)$1	1	0	5	15.0000
..(((	chr9:45198617-45198838(+)$1	1	109	114	15.0000
)))))	chr1:134390299-134390519(+)$1	1	168	173	15.0000
((((.	chrX:7459220-7459441(+)$1	1	108	113	15.0000
(.(((	chr9:72590368-72590588(+)$1	1	17	22	15.0000
..)))	chr7:107564904-107565134(+)$1	1	23	28	15.0000
)).))	chr3:35980650-35980870(+)$1	1	183	188	15.0000
)))))	chr4:32807663-32807883(+)$1	1	73	78	15.0000
((((.	chr1:10117406-10117626(+)$1	1	161	166	15.0000

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

#score	840.0000000000005
#seq	56
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_UTR_m1_run1.nuc.txt

#NT
UGCUAU	chr5:114391619-114391847(-)$1	228	178	184	10.7692
UGCUUU	chr2:106708377-106708598(-)$1	221	162	168	10.9230
UGCUGU	chr6:72299111-72299333(+)$1	222	123	129	14.2307
UGCUGU	chr8:46912951-46913172(+)$1	221	165	171	14.2307
UGCUUU	chr11:19923087-19923308(+)$1	221	17	23	10.9230
UGAUGU	chr11:102023707-102023937(-)$1	230	128	134	10.1538
AGCUGU	chr5:121893337-121893563(-)$1	226	8	14	10.3076
UGAUGU	chr10:66730014-66730237(+)$1	223	35	41	10.1538
UACUGU	chr10:62271297-62271522(-)$1	225	20	26	9.9999
UGAUGU	chr11:78199882-78200104(-)$1	222	2	8	10.1538
UGCUGC	chr5:66687988-66688209(-)$1	221	54	60	10.8461
UGCUUU	chr11:41945938-41946176(-)$1	238	62	68	10.9230
UGCUGU	chr11:65502249-65502471(-)$1	222	97	103	14.2307
UGCUGU	chr6:120745374-120745594(-)$1	220	168	174	14.2307
UGCUGU	chr8:77593216-77593437(+)$1	221	70	76	14.2307
UGCUAU	chr7:98239286-98239505(+)$1	219	16	22	10.7692
UGCUCU	chr14:68706609-68706827(+)$1	218	0	6	10.9230
UGCUCU	chr2:25147056-25147302(-)$1	246	130	136	10.9230
AGCUGU	chr15:82123571-82123831(+)$1	260	9	15	10.3076
UGCUGA	chr1:172248388-172248607(+)$1	219	6	12	10.5384
UACUGU	chr19:29686841-29687065(-)$1	224	210	216	9.9999
UGCUGU	chr9:44211924-44212155(-)$1	231	104	110	14.2307
UGCUGU	chr16:45963558-45963779(-)$1	221	23	29	14.2307
UGAUGU	chr8:26060359-26060588(-)$1	229	141	147	10.1538
UGCUGU	chr11:50071538-50071761(+)$1	223	134	140	14.2307
AGCUGU	chr7:134944485-134944714(-)$1	229	124	130	10.3076
UGCUUU	chr6:127912556-127912781(+)$1	225	101	107	10.9230
UGCUCU	chr7:51722173-51722399(+)$1	226	169	175	10.9230
UGCUCU	chr2:181454966-181455188(+)$1	222	11	17	10.9230
UGCUGG	chr9:54452998-54453220(-)$1	222	46	52	10.9230
UACUGU	chr16:56015612-56015827(-)$1	215	72	78	9.9999
UGCUGU	chr3:95997789-95998029(+)$1	240	130	136	14.2307
UGCUGU	chr10:69486907-69487137(+)$1	230	212	218	14.2307
AGCUGU	chr13:49557429-49557658(+)$1	229	127	133	10.3076
UGCUGG	chr15:88901209-88901441(+)$1	232	155	161	10.9230
UGCUAU	chr7:19667881-19668128(+)$1	247	145	151	10.7692
UACUGU	chr13:90249296-90249519(+)$1	223	10	16	9.9999
AGCUGU	chr5:108536776-108536997(+)$1	221	68	74	10.3076
UGCUGC	chr13:54851132-54851347(+)$1	215	88	94	10.8461
UGCUGU	chr18:77801997-77802219(-)$1	222	51	57	14.2307
AGCUGU	chr5:138200513-138200735(-)$1	222	25	31	10.3076
UGAUGU	chr14:67389807-67390028(-)$1	221	78	84	10.1538
UGCUGU	chr1:36582793-36583014(+)$1	221	35	41	14.2307
UGCUGU	chr10:80936620-80936847(-)$1	227	38	44	14.2307
UGCUUU	chr2:84528347-84528565(+)$1	218	188	194	10.9230
UGCUGC	chr1:183746889-183747109(-)$1	220	125	131	10.8461
UGCUGG	chr1:175267005-175267270(-)$1	265	163	169	10.9230
UGCUAU	chr13:100194947-100195176(-)$1	229	116	122	10.7692
UGCUGU	chr2:35606805-35607024(-)$1	219	142	148	14.2307
UGAUGU	chr6:38455581-38455808(+)$1	227	165	171	10.1538
UGCUCU	chr11:97373433-97373654(-)$1	221	137	143	10.9230
UGCUGG	chr11:55065180-55065404(+)$1	224	181	187	10.9230
UGCUUU	chr6:128324399-128324622(-)$1	223	0	6	10.9230
UACUGU	chr16:44734535-44734756(+)$1	221	207	213	9.9999
UGCUCU	chr11:88899783-88900016(-)$1	233	172	178	10.9230
UGCUGU	chr1:167799804-167800031(-)$1	227	40	46	14.2307
UGCUGC	chr3:116285615-116285834(-)$1	219	24	30	10.8461
agcugu	chr11:85874175-85874396(+)$1	221	174	180	10.3076
ugcugc	chr16:67620858-67621086(-)$1	228	32	38	10.8461
UGCUGU	chr3:116209649-116209871(+)$1	222	105	111	14.2307
UGCUGG	chr18:10544763-10544987(-)$1	224	9	15	10.9230
UGCUGG	chr11:77851379-77851596(+)$1	217	165	171	10.9230
UGCUGC	chr2:37426142-37426368(-)$1	226	77	83	10.8461
UGCUGG	chr15:80764300-80764519(+)$1	219	55	61	10.9230

#otherMatches

#Struct PSSM
BBdddd	chr14:61930264-61930485(+)$1	221	52	58	10.5384
ddd22b	chr5:114391619-114391847(-)$1	228	178	184	10.7692
gggggg	chr2:106708377-106708598(-)$1	221	162	168	10.9230
ggggg(	chr6:72299111-72299333(+)$1	222	123	129	14.2307
cccwww	chr8:46912951-46913172(+)$1	221	165	171	14.2307
[ccc[d	chr11:19923087-19923308(+)$1	221	17	23	10.9230
dddmmm	chr11:102023707-102023937(-)$1	230	128	134	10.1538
GGGGGG	chr5:121893337-121893563(-)$1	226	8	14	10.3076
cc[ccc	chr10:66730014-66730237(+)$1	223	35	41	10.1538
cc[ddd	chr10:62271297-62271522(-)$1	225	20	26	9.9999
dd!!cc	chr11:78199882-78200104(-)$1	222	2	8	10.1538
fyyyyy	chr5:66687988-66688209(-)$1	221	54	60	10.8461
3ccc]b	chr11:41945938-41946176(-)$1	238	62	68	10.9230
g:::ee	chr11:65502249-65502471(-)$1	222	97	103	14.2307
ggg%%%	chr6:120745374-120745594(-)$1	220	168	174	14.2307
"a[ddd	chr8:77593216-77593437(+)$1	221	70	76	14.2307
DDDDPP	chr7:98239286-98239505(+)$1	219	16	22	10.7692
:CCCKK	chr14:68706609-68706827(+)$1	218	0	6	10.9230
cccnnn	chr2:25147056-25147302(-)$1	246	130	136	10.9230
oooodd	chr15:82123571-82123831(+)$1	260	9	15	10.3076
FFF:::	chr1:172248388-172248607(+)$1	219	6	12	10.5384
EEEEBB	chr19:29686841-29687065(-)$1	224	210	216	9.9999
a]eeee	chr9:44211924-44212155(-)$1	231	104	110	14.2307
{BB:dd	chr16:45963558-45963779(-)$1	221	23	29	14.2307
bbb22f	chr8:26060359-26060588(-)$1	229	141	147	10.1538
ggga]f	chr11:50071538-50071761(+)$1	223	134	140	14.2307
eee22c	chr7:134944485-134944714(-)$1	229	124	130	10.3076
gggg:E	chr6:127912556-127912781(+)$1	225	101	107	10.9230
[eeeee	chr7:51722173-51722399(+)$1	226	169	175	10.9230
oooddd	chr2:181454966-181455188(+)$1	222	11	17	10.9230
==hhhh	chr9:54452998-54453220(-)$1	222	46	52	10.9230
xbb]ff	chr16:56015612-56015827(-)$1	215	72	78	9.9999
ebb]ee	chr3:95997789-95998029(+)$1	240	130	136	14.2307
leeeee	chr10:69486907-69487137(+)$1	230	212	218	14.2307
dddddd	chr13:49557429-49557658(+)$1	229	127	133	10.3076
''''dd	chr15:88901209-88901441(+)$1	232	155	161	10.9230
dddd]c	chr7:19667881-19668128(+)$1	247	145	151	10.7692
CCBB{B	chr13:90249296-90249519(+)$1	223	10	16	9.9999
dggggg	chr5:108536776-108536997(+)$1	221	68	74	10.3076
]fffff	chr13:54851132-54851347(+)$1	215	88	94	10.8461
qqqqqq	chr18:77801997-77802219(-)$1	222	51	57	14.2307
CKKEEE	chr5:138200513-138200735(-)$1	222	25	31	10.3076
fooooo	chr14:67389807-67390028(-)$1	221	78	84	10.1538
iiiiii	chr1:36582793-36583014(+)$1	221	35	41	14.2307
ncccee	chr10:80936620-80936847(-)$1	227	38	44	14.2307
fff:::	chr2:84528347-84528565(+)$1	218	188	194	10.9230
[fffff	chr1:183746889-183747109(-)$1	220	125	131	10.8461
dddd""	chr1:175267005-175267270(-)$1	265	163	169	10.9230
ggoooo	chr13:100194947-100195176(-)$1	229	116	122	10.7692
66====	chr2:35606805-35607024(-)$1	219	142	148	14.2307
2cccFF	chr6:38455581-38455808(+)$1	227	165	171	10.1538
HHHHHH	chr11:97373433-97373654(-)$1	221	137	143	10.9230
[eeeee	chr11:55065180-55065404(+)$1	224	181	187	10.9230
DDDDFF	chr6:128324399-128324622(-)$1	223	0	6	10.9230
FFFF::	chr16:44734535-44734756(+)$1	221	207	213	9.9999
gg::FF	chr11:88899783-88900016(-)$1	233	172	178	10.9230
bb[bb[	chr1:167799804-167800031(-)$1	227	40	46	14.2307
:::DDD	chr3:116285615-116285834(-)$1	219	24	30	10.8461
DD}FFF	chr11:85874175-85874396(+)$1	221	174	180	10.3076
[eeeee	chr16:67620858-67621086(-)$1	228	32	38	10.8461
bb]eee	chr3:116209649-116209871(+)$1	222	105	111	14.2307
dddda[	chr18:10544763-10544987(-)$1	224	9	15	10.9230
mmmmee	chr11:77851379-77851596(+)$1	217	165	171	10.9230
]cccbb	chr2:37426142-37426368(-)$1	226	77	83	10.8461
Dcccll	chr15:80764300-80764519(+)$1	219	55	61	10.9230

#DB
((((((	chr14:61930264-61930485(+)$1	1	52	58	10.5384
)))..)	chr5:114391619-114391847(-)$1	1	178	184	10.7692
((((((	chr2:106708377-106708598(-)$1	1	162	168	10.9230
(((((.	chr6:72299111-72299333(+)$1	1	123	129	14.2307
(((...	chr8:46912951-46913172(+)$1	1	165	171	14.2307
.(((.(	chr11:19923087-19923308(+)$1	1	17	23	10.9230
(((...	chr11:102023707-102023937(-)$1	1	128	134	10.1538
((((((	chr5:121893337-121893563(-)$1	1	8	14	10.3076
((.(((	chr10:66730014-66730237(+)$1	1	35	41	10.1538
((.(((	chr10:62271297-62271522(-)$1	1	20	26	9.9999
((..((	chr11:78199882-78200104(-)$1	1	2	8	10.1538
(.....	chr5:66687988-66688209(-)$1	1	54	60	10.8461
.))).)	chr11:41945938-41946176(-)$1	1	62	68	10.9230
)...((	chr11:65502249-65502471(-)$1	1	97	103	14.2307
(((...	chr6:120745374-120745594(-)$1	1	168	174	14.2307
.(.(((	chr8:77593216-77593437(+)$1	1	70	76	14.2307
((((..	chr7:98239286-98239505(+)$1	1	16	22	10.7692
.(((..	chr14:68706609-68706827(+)$1	1	0	6	10.9230
(((...	chr2:25147056-25147302(-)$1	1	130	136	10.9230
....))	chr15:82123571-82123831(+)$1	1	9	15	10.3076
(((...	chr1:172248388-172248607(+)$1	1	6	12	10.5384
))))))	chr19:29686841-29687065(-)$1	1	210	216	9.9999
).))))	chr9:44211924-44212155(-)$1	1	104	110	14.2307
.((.((	chr16:45963558-45963779(-)$1	1	23	29	14.2307
)))..)	chr8:26060359-26060588(-)$1	1	141	147	10.1538
)))).)	chr11:50071538-50071761(+)$1	1	134	140	14.2307
)))..)	chr7:134944485-134944714(-)$1	1	124	130	10.3076
)))).)	chr6:127912556-127912781(+)$1	1	101	107	10.9230
.(((((	chr7:51722173-51722399(+)$1	1	169	175	10.9230
...)))	chr2:181454966-181455188(+)$1	1	11	17	10.9230
))((((	chr9:54452998-54453220(-)$1	1	46	52	10.9230
.)).))	chr16:56015612-56015827(-)$1	1	72	78	9.9999
))).))	chr3:95997789-95998029(+)$1	1	130	136	14.2307
.)))))	chr10:69486907-69487137(+)$1	1	212	218	14.2307
))((((	chr13:49557429-49557658(+)$1	1	127	133	10.3076
....((	chr15:88901209-88901441(+)$1	1	155	161	10.9230
)))).)	chr7:19667881-19668128(+)$1	1	145	151	10.7692
((((.(	chr13:90249296-90249519(+)$1	1	10	16	9.9999
))))))	chr5:108536776-108536997(+)$1	1	68	74	10.3076
.)))))	chr13:54851132-54851347(+)$1	1	88	94	10.8461
......	chr18:77801997-77802219(-)$1	1	51	57	14.2307
(..(((	chr5:138200513-138200735(-)$1	1	25	31	10.3076
(.....	chr14:67389807-67390028(-)$1	1	78	84	10.1538
((((((	chr1:36582793-36583014(+)$1	1	35	41	14.2307
.)))))	chr10:80936620-80936847(-)$1	1	38	44	14.2307
)))...	chr2:84528347-84528565(+)$1	1	188	194	10.9230
.(((((	chr1:183746889-183747109(-)$1	1	125	131	10.8461
((((..	chr1:175267005-175267270(-)$1	1	163	169	10.9230
((....	chr13:100194947-100195176(-)$1	1	116	122	10.7692
..))))	chr2:35606805-35607024(-)$1	1	142	148	14.2307
.)))))	chr6:38455581-38455808(+)$1	1	165	171	10.1538
))))))	chr11:97373433-97373654(-)$1	1	137	143	10.9230
.(((((	chr11:55065180-55065404(+)$1	1	181	187	10.9230
((((((	chr6:128324399-128324622(-)$1	1	0	6	10.9230
))))..	chr16:44734535-44734756(+)$1	1	207	213	9.9999
))..))	chr11:88899783-88900016(-)$1	1	172	178	10.9230
((.((.	chr1:167799804-167800031(-)$1	1	40	46	14.2307
...(((	chr3:116285615-116285834(-)$1	1	24	30	10.8461
)).)))	chr11:85874175-85874396(+)$1	1	174	180	10.3076
.(((((	chr16:67620858-67621086(-)$1	1	32	38	10.8461
)).)))	chr3:116209649-116209871(+)$1	1	105	111	14.2307
(((((.	chr18:10544763-10544987(-)$1	1	9	15	10.9230
....))	chr11:77851379-77851596(+)$1	1	165	171	10.9230
.)))))	chr2:37426142-37426368(-)$1	1	77	83	10.8461
((((..	chr15:80764300-80764519(+)$1	1	55	61	10.9230

#PSSM
U : 0.87	A : 0.09	a : 0.01	u : 0.01	
G : 0.89	A : 0.07	g : 0.03	
C : 0.87	A : 0.09	c : 0.03	
U : 0.96	u : 0.03	
G : 0.72	U : 0.09	C : 0.09	A : 0.06	g : 0.03	
U : 0.75	G : 0.10	C : 0.07	A : 0.03	u : 0.01	c : 0.01	

#score	747.5384615384604
#seq	65
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m1_run1.nuc.txt

#NT
UGUUU	chr13:94204257-94204515(-)$1	258	107	112	15.0000
uguuu	chr10:59594819-59595075(+)$1	256	114	119	15.0000
UGUUU	chr4:154932525-154932816(+)$1	291	53	58	15.0000
UGUUU	chr10:9476906-9477142(-)$1	236	8	13	15.0000
UGUUU	chr10:86297791-86298060(+)$1	269	30	35	15.0000
UGUUU	chr8:82198805-82199040(+)$1	235	15	20	15.0000
UGUUU	chr2:143641045-143641295(+)$1	250	186	191	15.0000
UGUUU	chr14:21554054-21554291(-)$1	237	109	114	15.0000
UGUUU	chr11:70483254-70483493(-)$1	239	186	191	15.0000
UGUUU	chr17:37210257-37210532(+)$1	275	240	245	15.0000
UGUUU	chr14:73762119-73762423(-)$1	304	79	84	15.0000
UGUUU	chr10:79073819-79074054(-)$1	235	56	61	15.0000
UGUUU	chr1:153210412-153210653(+)$1	241	126	131	15.0000
UGUUU	chr1:136645546-136645781(+)$1	235	49	54	15.0000
UGUUU	chr11:55208949-55209192(-)$1	243	25	30	15.0000
UGUUU	chrX:102993175-102993427(-)$1	252	21	26	15.0000
UGUUU	chr3:30995673-30995908(+)$1	235	162	167	15.0000
UGUUU	chr12:73312811-73313100(-)$1	289	50	55	15.0000
uguuu	chr13:8802337-8802585(-)$1	248	202	207	15.0000
UGUUU	chr9:58499896-58500148(+)$1	252	229	234	15.0000
UGUUU	chr14:14446730-14446975(+)$1	245	123	128	15.0000
UGUUU	chr18:20845873-20846128(-)$1	255	36	41	15.0000
UGUUU	chr6:108500277-108500549(+)$1	272	115	120	15.0000
UGUUU	chr17:15943753-15943992(-)$1	239	22	27	15.0000
UGUUU	chr9:52484402-52484646(-)$1	244	4	9	15.0000
UGUUU	chr2:102630558-102630808(+)$1	250	26	31	15.0000
UGUUU	chr14:14446931-14447175(+)$1	244	28	33	15.0000
UGUUU	chr2:109738790-109739039(+)$1	249	120	125	15.0000
UGUUU	chr15:37295936-37296191(-)$1	255	158	163	15.0000
UGUUU	chr15:98570061-98570299(-)$1	238	160	165	15.0000
UGUUU	chr11:6305792-6306046(+)$1	254	130	135	15.0000
UGUUU	chr2:131763080-131763341(+)$1	261	122	127	15.0000
UGUUU	chr3:80647535-80647791(-)$1	256	108	113	15.0000
UGUUU	chr5:4803320-4803600(-)$1	280	165	170	15.0000
UGUUU	chr2:132133244-132133523(+)$1	279	120	125	15.0000
UGUUU	chr11:51799897-51800143(-)$1	246	181	186	15.0000
uguuu	chr10:67558393-67558628(-)$1	235	4	9	15.0000
UGUUU	chr2:21749871-21750111(+)$1	240	219	224	15.0000
UGUUU	chr11:74488989-74489247(-)$1	258	92	97	15.0000
uguuu	chr3:88549792-88550071(-)$1	279	117	122	15.0000
UGUUU	chr11:87033468-87033727(+)$1	259	111	116	15.0000
UGUUU	chr1:52222197-52222455(-)$1	258	46	51	15.0000
UGUUU	chr7:58924688-58924934(+)$1	246	70	75	15.0000
UGUUU	chr1:179378755-179379016(+)$1	261	143	148	15.0000
uguuu	chr1:154684470-154684708(-)$1	238	16	21	15.0000
UGUUU	chr17:87832784-87833026(-)$1	242	82	87	15.0000
UGUUU	chr14:37934193-37934437(-)$1	244	13	18	15.0000
UGUUU	chr1:163917524-163917767(-)$1	243	15	20	15.0000
UGUUU	chr9:64034167-64034410(-)$1	243	211	216	15.0000
UGUUU	chr5:136384940-136385210(-)$1	270	142	147	15.0000
UGUUU	chrX:71273356-71273615(-)$1	259	105	110	15.0000
UGUUU	chr9:72595592-72595860(+)$1	268	187	192	15.0000
UGUUU	chr17:29294824-29295061(-)$1	237	119	124	15.0000
UGUUU	chrX:8886941-8887183(+)$1	242	104	109	15.0000
UGUUU	chr2:181286536-181286781(+)$1	245	126	131	15.0000
UGUUU	chr4:59235202-59235460(+)$1	258	1	6	15.0000
UGUUU	chr11:118163739-118163979(-)$1	240	79	84	15.0000
UGUUU	chr1:58580120-58580368(-)$1	248	76	81	15.0000
UGUUU	chr1:133831883-133832118(+)$1	235	78	83	15.0000
UGUUU	chr3:10314052-10314299(-)$1	247	108	113	15.0000
UGUUU	chr6:115226082-115226321(+)$1	239	12	17	15.0000
UGUUU	chr11:40493258-40493506(-)$1	248	159	164	15.0000
UGUUU	chr11:87033367-87033638(+)$1	271	212	217	15.0000
UGUUU	chr2:70439256-70439565(+)$1	309	162	167	15.0000
uguuu	chr17:32909630-32909869(-)$1	239	193	198	15.0000
UGUUU	chr2:102621818-102622058(+)$1	240	102	107	15.0000
uguuu	chr1:64837217-64837454(-)$1	237	112	117	15.0000
uguuu	chr1:87746789-87747024(+)$1	235	108	113	15.0000
UGUUU	chr1:52846191-52846426(-)$1	235	4	9	15.0000
UGUUU	chr18:33596934-33597172(-)$1	238	197	202	15.0000
UGUUU	chr3:146395078-146395338(-)$1	260	85	90	15.0000
UGUUU	chr9:106091894-106092134(+)$1	240	113	118	15.0000
UGUUU	chr8:42418143-42418382(+)$1	239	106	111	15.0000
UGUUU	chr11:41946465-41946709(-)$1	244	122	127	15.0000
UGUUU	chr13:94130245-94130488(+)$1	243	109	114	15.0000

#otherMatches

#Struct PSSM
FFFF:	chr12:3247801-3248045(-)$1	244	4	9	15.0000
)))))	chr13:94204257-94204515(-)$1	258	107	112	15.0000
c]bbf	chr10:59594819-59595075(+)$1	256	114	119	15.0000
ggggg	chr4:154932525-154932816(+)$1	291	53	58	15.0000
LEEEE	chr10:9476906-9477142(-)$1	236	8	13	15.0000
hh:::	chr10:86297791-86298060(+)$1	269	30	35	15.0000
:::::	chr8:82198805-82199040(+)$1	235	15	20	15.0000
!bbmm	chr2:143641045-143641295(+)$1	250	186	191	15.0000
}GGGG	chr14:21554054-21554291(-)$1	237	109	114	15.0000
dd::E	chr11:70483254-70483493(-)$1	239	186	191	15.0000
gg444	chr17:37210257-37210532(+)$1	275	240	245	15.0000
eeemm	chr14:73762119-73762423(-)$1	304	79	84	15.0000
FFFFF	chr10:79073819-79074054(-)$1	235	56	61	15.0000
bb]ee	chr1:153210412-153210653(+)$1	241	126	131	15.0000
dddee	chr1:136645546-136645781(+)$1	235	49	54	15.0000
ccc%%	chr11:55208949-55209192(-)$1	243	25	30	15.0000
gglll	chrX:102993175-102993427(-)$1	252	21	26	15.0000
coooo	chr3:30995673-30995908(+)$1	235	162	167	15.0000
444gg	chr12:73312811-73313100(-)$1	289	50	55	15.0000
a]ddd	chr13:8802337-8802585(-)$1	248	202	207	15.0000
d:III	chr9:58499896-58500148(+)$1	252	229	234	15.0000
$$$dd	chr14:14446730-14446975(+)$1	245	123	128	15.0000
eeee]	chr18:20845873-20846128(-)$1	255	36	41	15.0000
DDOOO	chr6:108500277-108500549(+)$1	272	115	120	15.0000
HHHHH	chr17:15943753-15943992(-)$1	239	22	27	15.0000
ggg!!	chr9:52484402-52484646(-)$1	244	4	9	15.0000
==^^^	chr2:102630558-102630808(+)$1	250	26	31	15.0000
ccc!!	chr14:14446931-14447175(+)$1	244	28	33	15.0000
c]hhh	chr2:109738790-109739039(+)$1	249	120	125	15.0000
[hhhh	chr15:37295936-37296191(-)$1	255	158	163	15.0000
hhh!!	chr15:98570061-98570299(-)$1	238	160	165	15.0000
]hhhh	chr11:6305792-6306046(+)$1	254	130	135	15.0000
?????	chr2:131763080-131763341(+)$1	261	122	127	15.0000
#ccc$	chr3:80647535-80647791(-)$1	256	108	113	15.0000
c"""g	chr5:4803320-4803600(-)$1	280	165	170	15.0000
ccnnn	chr2:132133244-132133523(+)$1	279	120	125	15.0000
6dddd	chr11:51799897-51800143(-)$1	246	181	186	15.0000
:::::	chr10:67558393-67558628(-)$1	235	4	9	15.0000
occc]	chr2:21749871-21750111(+)$1	240	219	224	15.0000
FFFFF	chr11:74488989-74489247(-)$1	258	92	97	15.0000
bb333	chr3:88549792-88550071(-)$1	279	117	122	15.0000
a]===	chr11:87033468-87033727(+)$1	259	111	116	15.0000
:EEEE	chr1:52222197-52222455(-)$1	258	46	51	15.0000
EEEEE	chr7:58924688-58924934(+)$1	246	70	75	15.0000
g:::d	chr1:179378755-179379016(+)$1	261	143	148	15.0000
:::::	chr1:154684470-154684708(-)$1	238	16	21	15.0000
iiiii	chr17:87832784-87833026(-)$1	242	82	87	15.0000
:::::	chr14:37934193-37934437(-)$1	244	13	18	15.0000
IIIII	chr1:163917524-163917767(-)$1	243	15	20	15.0000
2dddd	chr9:64034167-64034410(-)$1	243	211	216	15.0000
:dddd	chr5:136384940-136385210(-)$1	270	142	147	15.0000
fffff	chrX:71273356-71273615(-)$1	259	105	110	15.0000
HHHHH	chr9:72595592-72595860(+)$1	268	187	192	15.0000
nnnnn	chr17:29294824-29295061(-)$1	237	119	124	15.0000
2eeee	chrX:8886941-8887183(+)$1	242	104	109	15.0000
99999	chr2:181286536-181286781(+)$1	245	126	131	15.0000
:::::	chr4:59235202-59235460(+)$1	258	1	6	15.0000
dccc:	chr11:118163739-118163979(-)$1	240	79	84	15.0000
fffff	chr1:58580120-58580368(-)$1	248	76	81	15.0000
:::::	chr1:133831883-133832118(+)$1	235	78	83	15.0000
[bbll	chr3:10314052-10314299(-)$1	247	108	113	15.0000
qqqqc	chr6:115226082-115226321(+)$1	239	12	17	15.0000
:::==	chr11:40493258-40493506(-)$1	248	159	164	15.0000
C}HHH	chr11:87033367-87033638(+)$1	271	212	217	15.0000
:dddd	chr2:70439256-70439565(+)$1	309	162	167	15.0000
grrrr	chr17:32909630-32909869(-)$1	239	193	198	15.0000
iiiii	chr2:102621818-102622058(+)$1	240	102	107	15.0000
cbb[c	chr1:64837217-64837454(-)$1	237	112	117	15.0000
eee::	chr1:87746789-87747024(+)$1	235	108	113	15.0000
eoooo	chr1:52846191-52846426(-)$1	235	4	9	15.0000
fffff	chr18:33596934-33597172(-)$1	238	197	202	15.0000
4444e	chr3:146395078-146395338(-)$1	260	85	90	15.0000
GGGGf	chr9:106091894-106092134(+)$1	240	113	118	15.0000
ggggC	chr8:42418143-42418382(+)$1	239	106	111	15.0000
=====	chr11:41946465-41946709(-)$1	244	122	127	15.0000
:::::	chr13:94130245-94130488(+)$1	243	109	114	15.0000

#DB
((((.	chr12:3247801-3248045(-)$1	1	4	9	15.0000
.....	chr13:94204257-94204515(-)$1	1	107	112	15.0000
).)))	chr10:59594819-59595075(+)$1	1	114	119	15.0000
)))))	chr4:154932525-154932816(+)$1	1	53	58	15.0000
.((((	chr10:9476906-9477142(-)$1	1	8	13	15.0000
))...	chr10:86297791-86298060(+)$1	1	30	35	15.0000
.....	chr8:82198805-82199040(+)$1	1	15	20	15.0000
.((..	chr2:143641045-143641295(+)$1	1	186	191	15.0000
.))))	chr14:21554054-21554291(-)$1	1	109	114	15.0000
))..)	chr11:70483254-70483493(-)$1	1	186	191	15.0000
))...	chr17:37210257-37210532(+)$1	1	240	245	15.0000
(((..	chr14:73762119-73762423(-)$1	1	79	84	15.0000
(((((	chr10:79073819-79074054(-)$1	1	56	61	15.0000
)).))	chr1:153210412-153210653(+)$1	1	126	131	15.0000
)))))	chr1:136645546-136645781(+)$1	1	49	54	15.0000
(((..	chr11:55208949-55209192(-)$1	1	25	30	15.0000
((...	chrX:102993175-102993427(-)$1	1	21	26	15.0000
(....	chr3:30995673-30995908(+)$1	1	162	167	15.0000
...))	chr12:73312811-73313100(-)$1	1	50	55	15.0000
).)))	chr13:8802337-8802585(-)$1	1	202	207	15.0000
).)))	chr9:58499896-58500148(+)$1	1	229	234	15.0000
...((	chr14:14446730-14446975(+)$1	1	123	128	15.0000
)))).	chr18:20845873-20846128(-)$1	1	36	41	15.0000
((...	chr6:108500277-108500549(+)$1	1	115	120	15.0000
(((((	chr17:15943753-15943992(-)$1	1	22	27	15.0000
(((..	chr9:52484402-52484646(-)$1	1	4	9	15.0000
((...	chr2:102630558-102630808(+)$1	1	26	31	15.0000
(((..	chr14:14446931-14447175(+)$1	1	28	33	15.0000
).)))	chr2:109738790-109739039(+)$1	1	120	125	15.0000
.((((	chr15:37295936-37296191(-)$1	1	158	163	15.0000
(((..	chr15:98570061-98570299(-)$1	1	160	165	15.0000
.))))	chr11:6305792-6306046(+)$1	1	130	135	15.0000
.....	chr2:131763080-131763341(+)$1	1	122	127	15.0000
.(((.	chr3:80647535-80647791(-)$1	1	108	113	15.0000
(...(	chr5:4803320-4803600(-)$1	1	165	170	15.0000
((...	chr2:132133244-132133523(+)$1	1	120	125	15.0000
.))))	chr11:51799897-51800143(-)$1	1	181	186	15.0000
.....	chr10:67558393-67558628(-)$1	1	4	9	15.0000
.))).	chr2:21749871-21750111(+)$1	1	219	224	15.0000
(((((	chr11:74488989-74489247(-)$1	1	92	97	15.0000
))...	chr3:88549792-88550071(-)$1	1	117	122	15.0000
).)))	chr11:87033468-87033727(+)$1	1	111	116	15.0000
.((((	chr1:52222197-52222455(-)$1	1	46	51	15.0000
(((((	chr7:58924688-58924934(+)$1	1	70	75	15.0000
)...(	chr1:179378755-179379016(+)$1	1	143	148	15.0000
.....	chr1:154684470-154684708(-)$1	1	16	21	15.0000
(((((	chr17:87832784-87833026(-)$1	1	82	87	15.0000
.....	chr14:37934193-37934437(-)$1	1	13	18	15.0000
(((((	chr1:163917524-163917767(-)$1	1	15	20	15.0000
.))))	chr9:64034167-64034410(-)$1	1	211	216	15.0000
.((((	chr5:136384940-136385210(-)$1	1	142	147	15.0000
(((((	chrX:71273356-71273615(-)$1	1	105	110	15.0000
)))))	chr9:72595592-72595860(+)$1	1	187	192	15.0000
.....	chr17:29294824-29295061(-)$1	1	119	124	15.0000
.))))	chrX:8886941-8887183(+)$1	1	104	109	15.0000
.....	chr2:181286536-181286781(+)$1	1	126	131	15.0000
.....	chr4:59235202-59235460(+)$1	1	1	6	15.0000
)))).	chr11:118163739-118163979(-)$1	1	79	84	15.0000
(((((	chr1:58580120-58580368(-)$1	1	76	81	15.0000
.....	chr1:133831883-133832118(+)$1	1	78	83	15.0000
.((..	chr3:10314052-10314299(-)$1	1	108	113	15.0000
....)	chr6:115226082-115226321(+)$1	1	12	17	15.0000
...((	chr11:40493258-40493506(-)$1	1	159	164	15.0000
).)))	chr11:87033367-87033638(+)$1	1	212	217	15.0000
.((((	chr2:70439256-70439565(+)$1	1	162	167	15.0000
(....	chr17:32909630-32909869(-)$1	1	193	198	15.0000
)))))	chr2:102621818-102622058(+)$1	1	102	107	15.0000
)((.(	chr1:64837217-64837454(-)$1	1	112	117	15.0000
)))..	chr1:87746789-87747024(+)$1	1	108	113	15.0000
(....	chr1:52846191-52846426(-)$1	1	4	9	15.0000
(((((	chr18:33596934-33597172(-)$1	1	197	202	15.0000
....)	chr3:146395078-146395338(-)$1	1	85	90	15.0000
))))(	chr9:106091894-106092134(+)$1	1	113	118	15.0000
)))))	chr8:42418143-42418382(+)$1	1	106	111	15.0000
)))))	chr11:41946465-41946709(-)$1	1	122	127	15.0000
.....	chr13:94130245-94130488(+)$1	1	109	114	15.0000

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

#score	1140.0000000000005
#seq	76
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m1_run1.nuc.txt

#NT
GAAG	chr12:111865180-111865415(+)$1	235	4	8	12.0000
GAAG	chr1:83273913-83274169(-)$1	256	80	84	12.0000
GAAG	chr2:6468061-6468303(-)$1	242	126	130	12.0000
GAAG	chr8:41532325-41532562(+)$1	237	171	175	12.0000
GAAG	chr11:41946818-41947090(-)$1	272	216	220	12.0000
GAAG	chr2:181283313-181283550(+)$1	237	196	200	12.0000
GAAG	chr7:129771219-129771472(+)$1	253	22	26	12.0000
GAAG	chr1:135533828-135534091(-)$1	263	54	58	12.0000
GAAG	chr4:126707100-126707361(+)$1	261	69	73	12.0000
GAAG	chr1:174210640-174210877(-)$1	237	128	132	12.0000
GAAG	chr1:175262352-175262595(-)$1	243	117	121	12.0000
GAAG	chr16:14153931-14154176(-)$1	245	19	23	12.0000
GAAG	chr16:35283532-35283777(+)$1	245	159	163	12.0000
GAAG	chr16:90229856-90230093(-)$1	237	114	118	12.0000
GAAG	chr15:31412540-31412775(-)$1	235	197	201	12.0000
GAAG	chr14:76818619-76818854(+)$1	235	4	8	12.0000
GAAG	chr13:74476965-74477204(-)$1	239	71	75	12.0000
GAAG	chr19:47331845-47332080(+)$1	235	4	8	12.0000
GAAG	chr8:107803318-107803553(+)$1	235	47	51	12.0000
GAAG	chr10:76784989-76785224(-)$1	235	20	24	12.0000
GAAG	chr1:59927210-59927447(+)$1	237	173	177	12.0000
GAAG	chr4:126425761-126425997(-)$1	236	45	49	12.0000
GAAG	chrX:12738488-12738723(+)$1	235	57	61	12.0000
GAAG	chr6:36693305-36693540(-)$1	235	164	168	12.0000
GAAG	chr3:87798024-87798262(-)$1	238	114	118	12.0000
GAAG	chr15:58767736-58767981(+)$1	245	129	133	12.0000
GAAG	chr2:32452594-32452855(+)$1	261	56	60	12.0000
GAAG	chr17:82047059-82047320(-)$1	261	37	41	12.0000
GAAG	chr19:7289793-7290030(-)$1	237	139	143	12.0000
GAAG	chr19:4726530-4726776(+)$1	246	78	82	12.0000
GAAG	chr11:86602657-86602898(-)$1	241	46	50	12.0000
GAAG	chr12:113025641-113025876(+)$1	235	111	115	12.0000
GAAG	chr10:98477548-98477791(+)$1	243	76	80	12.0000
GAAG	chr11:31917577-31917812(+)$1	235	81	85	12.0000
GAAG	chr6:117123446-117123681(+)$1	235	72	76	12.0000
GAAG	chr11:50014060-50014371(-)$1	311	58	62	12.0000
GAAG	chr11:87863329-87863588(+)$1	259	106	110	12.0000
GAAG	chr11:90202099-90202341(-)$1	242	124	128	12.0000
GAAG	chr2:102588545-102588794(+)$1	249	29	33	12.0000
GAAG	chr7:118217767-118218002(-)$1	235	26	30	12.0000
GAAG	chr8:46095312-46095551(+)$1	239	71	75	12.0000
GAAG	chr2:156002938-156003173(-)$1	235	85	89	12.0000
GAAG	chr2:181041975-181042222(-)$1	247	130	134	12.0000
GAAG	chr6:97128843-97129081(-)$1	238	126	130	12.0000
GAAG	chr2:25077838-25078075(-)$1	237	110	114	12.0000
GAAG	chr4:57722929-57723172(+)$1	243	46	50	12.0000
GAAG	chr6:4591853-4592090(+)$1	237	188	192	12.0000
GAAG	chr16:35293974-35294230(+)$1	256	1	5	12.0000
GAAG	chr11:72025341-72025578(-)$1	237	77	81	12.0000
GAAG	chr18:46664687-46664922(-)$1	235	44	48	12.0000
GAAG	chr1:75212189-75212442(-)$1	253	54	58	12.0000
GAAG	chr19:10058581-10058825(+)$1	244	121	125	12.0000
GAAG	chr5:34186114-34186353(+)$1	239	137	141	12.0000
GAAG	chr7:17501488-17501778(-)$1	290	72	76	12.0000
GAAG	chr7:148337524-148337759(+)$1	235	50	54	12.0000
GAAG	chrX:141894531-141894792(-)$1	261	131	135	12.0000
GAAG	chrX:10172306-10172551(+)$1	245	170	174	12.0000
GAAG	chr14:65673532-65673769(-)$1	237	42	46	12.0000
GAAG	chr11:4964001-4964239(-)$1	238	129	133	12.0000
GAAG	chr10:12125570-12125808(-)$1	238	40	44	12.0000
GAAG	chr8:47292820-47293064(-)$1	244	30	34	12.0000
GAAG	chr18:34506673-34506910(-)$1	237	122	126	12.0000
GAAG	chr3:146395453-146395688(-)$1	235	74	78	12.0000
GAAG	chr11:46055717-46055965(-)$1	248	67	71	12.0000
GAAG	chr8:63391717-63391957(-)$1	240	105	109	12.0000
GAAG	chr15:3987046-3987281(+)$1	235	90	94	12.0000
GAAG	chr1:193602238-193602475(+)$1	237	48	52	12.0000
GAAG	chr12:106028213-106028448(-)$1	235	209	213	12.0000
GAAG	chrX:162824700-162824996(+)$1	296	17	21	12.0000
GAAG	chr2:181041364-181041632(-)$1	268	13	17	12.0000
GAAG	chrX:162824888-162825125(+)$1	237	82	86	12.0000
GAAG	chr13:6602544-6602805(-)$1	261	34	38	12.0000
GAAG	chr10:41239320-41239558(+)$1	238	11	15	12.0000
GAAG	chr5:104513928-104514170(-)$1	242	107	111	12.0000
GAAG	chr5:104508405-104508686(-)$1	281	239	243	12.0000

#otherMatches

#Struct PSSM
DDEE	chr10:126674771-126675012(-)$1	241	19	23	12.0000
ffnn	chr12:111865180-111865415(+)$1	235	4	8	12.0000
:::e	chr1:83273913-83274169(-)$1	256	80	84	12.0000
e444	chr2:6468061-6468303(-)$1	242	126	130	12.0000
::::	chr8:41532325-41532562(+)$1	237	171	175	12.0000
JJJJ	chr11:41946818-41947090(-)$1	272	216	220	12.0000
!!ee	chr2:181283313-181283550(+)$1	237	196	200	12.0000
D::d	chr7:129771219-129771472(+)$1	253	22	26	12.0000
dddd	chr1:135533828-135534091(-)$1	263	54	58	12.0000
iiii	chr4:126707100-126707361(+)$1	261	69	73	12.0000
FFFF	chr1:174210640-174210877(-)$1	237	128	132	12.0000
dd66	chr1:175262352-175262595(-)$1	243	117	121	12.0000
]eee	chr16:14153931-14154176(-)$1	245	19	23	12.0000
b[dd	chr16:35283532-35283777(+)$1	245	159	163	12.0000
oooo	chr16:90229856-90230093(-)$1	237	114	118	12.0000
mmdd	chr15:31412540-31412775(-)$1	235	197	201	12.0000
dlll	chr14:76818619-76818854(+)$1	235	4	8	12.0000
8888	chr13:74476965-74477204(-)$1	239	71	75	12.0000
"""e	chr19:47331845-47332080(+)$1	235	4	8	12.0000
nnnb	chr8:107803318-107803553(+)$1	235	47	51	12.0000
:::D	chr10:76784989-76785224(-)$1	235	20	24	12.0000
====	chr1:59927210-59927447(+)$1	237	173	177	12.0000
eeee	chr4:126425761-126425997(-)$1	236	45	49	12.0000
FFFF	chrX:12738488-12738723(+)$1	235	57	61	12.0000
22ee	chr6:36693305-36693540(-)$1	235	164	168	12.0000
GGGG	chr3:87798024-87798262(-)$1	238	114	118	12.0000
VVVV	chr15:58767736-58767981(+)$1	245	129	133	12.0000
b!!b	chr2:32452594-32452855(+)$1	261	56	60	12.0000
:::e	chr17:82047059-82047320(-)$1	261	37	41	12.0000
HHHH	chr19:7289793-7290030(-)$1	237	139	143	12.0000
c[cc	chr19:4726530-4726776(+)$1	246	78	82	12.0000
ccii	chr11:86602657-86602898(-)$1	241	46	50	12.0000
c999	chr12:113025641-113025876(+)$1	235	111	115	12.0000
gggg	chr10:98477548-98477791(+)$1	243	76	80	12.0000
===#	chr11:31917577-31917812(+)$1	235	81	85	12.0000
^^^^	chr6:117123446-117123681(+)$1	235	72	76	12.0000
::ee	chr11:50014060-50014371(-)$1	311	58	62	12.0000
d!!g	chr11:87863329-87863588(+)$1	259	106	110	12.0000
crrr	chr11:90202099-90202341(-)$1	242	124	128	12.0000
ffff	chr2:102588545-102588794(+)$1	249	29	33	12.0000
d22d	chr7:118217767-118218002(-)$1	235	26	30	12.0000
dd77	chr8:46095312-46095551(+)$1	239	71	75	12.0000
iiii	chr2:156002938-156003173(-)$1	235	85	89	12.0000
YYCC	chr2:181041975-181042222(-)$1	247	130	134	12.0000
oooc	chr6:97128843-97129081(-)$1	238	126	130	12.0000
ffff	chr2:25077838-25078075(-)$1	237	110	114	12.0000
::EE	chr4:57722929-57723172(+)$1	243	46	50	12.0000
gggg	chr6:4591853-4592090(+)$1	237	188	192	12.0000
::::	chr16:35293974-35294230(+)$1	256	1	5	12.0000
cccd	chr11:72025341-72025578(-)$1	237	77	81	12.0000
e[bb	chr18:46664687-46664922(-)$1	235	44	48	12.0000
LLLC	chr1:75212189-75212442(-)$1	253	54	58	12.0000
dddd	chr19:10058581-10058825(+)$1	244	121	125	12.0000
ffyy	chr5:34186114-34186353(+)$1	239	137	141	12.0000
CC{G	chr7:17501488-17501778(-)$1	290	72	76	12.0000
B{EE	chr7:148337524-148337759(+)$1	235	50	54	12.0000
a!!d	chrX:141894531-141894792(-)$1	261	131	135	12.0000
iiii	chrX:10172306-10172551(+)$1	245	170	174	12.0000
ffff	chr14:65673532-65673769(-)$1	237	42	46	12.0000
eeee	chr11:4964001-4964239(-)$1	238	129	133	12.0000
mmmd	chr10:12125570-12125808(-)$1	238	40	44	12.0000
rrrr	chr8:47292820-47293064(-)$1	244	30	34	12.0000
====	chr18:34506673-34506910(-)$1	237	122	126	12.0000
uuud	chr3:146395453-146395688(-)$1	235	74	78	12.0000
eeee	chr11:46055717-46055965(-)$1	248	67	71	12.0000
6666	chr8:63391717-63391957(-)$1	240	105	109	12.0000
cddd	chr15:3987046-3987281(+)$1	235	90	94	12.0000
hhhh	chr1:193602238-193602475(+)$1	237	48	52	12.0000
B~~~	chr12:106028213-106028448(-)$1	235	209	213	12.0000
eeee	chrX:162824700-162824996(+)$1	296	17	21	12.0000
dddd	chr2:181041364-181041632(-)$1	268	13	17	12.0000
:::d	chrX:162824888-162825125(+)$1	237	82	86	12.0000
:DDD	chr13:6602544-6602805(-)$1	261	34	38	12.0000
"""d	chr10:41239320-41239558(+)$1	238	11	15	12.0000
====	chr5:104513928-104514170(-)$1	242	107	111	12.0000
9999	chr5:104508405-104508686(-)$1	281	239	243	12.0000

#DB
((((	chr10:126674771-126675012(-)$1	1	19	23	12.0000
((..	chr12:111865180-111865415(+)$1	1	4	8	12.0000
...(	chr1:83273913-83274169(-)$1	1	80	84	12.0000
)...	chr2:6468061-6468303(-)$1	1	126	130	12.0000
....	chr8:41532325-41532562(+)$1	1	171	175	12.0000
))))	chr11:41946818-41947090(-)$1	1	216	220	12.0000
..((	chr2:181283313-181283550(+)$1	1	196	200	12.0000
(..(	chr7:129771219-129771472(+)$1	1	22	26	12.0000
((((	chr1:135533828-135534091(-)$1	1	54	58	12.0000
((((	chr4:126707100-126707361(+)$1	1	69	73	12.0000
))))	chr1:174210640-174210877(-)$1	1	128	132	12.0000
))..	chr1:175262352-175262595(-)$1	1	117	121	12.0000
.)))	chr16:14153931-14154176(-)$1	1	19	23	12.0000
(.((	chr16:35283532-35283777(+)$1	1	159	163	12.0000
....	chr16:90229856-90230093(-)$1	1	114	118	12.0000
..))	chr15:31412540-31412775(-)$1	1	197	201	12.0000
(...	chr14:76818619-76818854(+)$1	1	4	8	12.0000
....	chr13:74476965-74477204(-)$1	1	71	75	12.0000
...(	chr19:47331845-47332080(+)$1	1	4	8	12.0000
...)	chr8:107803318-107803553(+)$1	1	47	51	12.0000
...(	chr10:76784989-76785224(-)$1	1	20	24	12.0000
))))	chr1:59927210-59927447(+)$1	1	173	177	12.0000
)(((	chr4:126425761-126425997(-)$1	1	45	49	12.0000
((((	chrX:12738488-12738723(+)$1	1	57	61	12.0000
..))	chr6:36693305-36693540(-)$1	1	164	168	12.0000
))))	chr3:87798024-87798262(-)$1	1	114	118	12.0000
....	chr15:58767736-58767981(+)$1	1	129	133	12.0000
(..(	chr2:32452594-32452855(+)$1	1	56	60	12.0000
...(	chr17:82047059-82047320(-)$1	1	37	41	12.0000
))))	chr19:7289793-7290030(-)$1	1	139	143	12.0000
(.((	chr19:4726530-4726776(+)$1	1	78	82	12.0000
))))	chr11:86602657-86602898(-)$1	1	46	50	12.0000
)...	chr12:113025641-113025876(+)$1	1	111	115	12.0000
))))	chr10:98477548-98477791(+)$1	1	76	80	12.0000
(((.	chr11:31917577-31917812(+)$1	1	81	85	12.0000
....	chr6:117123446-117123681(+)$1	1	72	76	12.0000
..((	chr11:50014060-50014371(-)$1	1	58	62	12.0000
(..(	chr11:87863329-87863588(+)$1	1	106	110	12.0000
(...	chr11:90202099-90202341(-)$1	1	124	128	12.0000
((((	chr2:102588545-102588794(+)$1	1	29	33	12.0000
)..)	chr7:118217767-118218002(-)$1	1	26	30	12.0000
))..	chr8:46095312-46095551(+)$1	1	71	75	12.0000
((((	chr2:156002938-156003173(-)$1	1	85	89	12.0000
..))	chr2:181041975-181042222(-)$1	1	130	134	12.0000
...)	chr6:97128843-97129081(-)$1	1	126	130	12.0000
))))	chr2:25077838-25078075(-)$1	1	110	114	12.0000
..((	chr4:57722929-57723172(+)$1	1	46	50	12.0000
((((	chr6:4591853-4592090(+)$1	1	188	192	12.0000
....	chr16:35293974-35294230(+)$1	1	1	5	12.0000
((((	chr11:72025341-72025578(-)$1	1	77	81	12.0000
(.((	chr18:46664687-46664922(-)$1	1	44	48	12.0000
...(	chr1:75212189-75212442(-)$1	1	54	58	12.0000
((((	chr19:10058581-10058825(+)$1	1	121	125	12.0000
((..	chr5:34186114-34186353(+)$1	1	137	141	12.0000
((.(	chr7:17501488-17501778(-)$1	1	72	76	12.0000
(.((	chr7:148337524-148337759(+)$1	1	50	54	12.0000
(..(	chrX:141894531-141894792(-)$1	1	131	135	12.0000
))))	chrX:10172306-10172551(+)$1	1	170	174	12.0000
((((	chr14:65673532-65673769(-)$1	1	42	46	12.0000
))))	chr11:4964001-4964239(-)$1	1	129	133	12.0000
...)	chr10:12125570-12125808(-)$1	1	40	44	12.0000
....	chr8:47292820-47293064(-)$1	1	30	34	12.0000
))))	chr18:34506673-34506910(-)$1	1	122	126	12.0000
...)	chr3:146395453-146395688(-)$1	1	74	78	12.0000
((((	chr11:46055717-46055965(-)$1	1	67	71	12.0000
....	chr8:63391717-63391957(-)$1	1	105	109	12.0000
))))	chr15:3987046-3987281(+)$1	1	90	94	12.0000
))))	chr1:193602238-193602475(+)$1	1	48	52	12.0000
)...	chr12:106028213-106028448(-)$1	1	209	213	12.0000
))))	chrX:162824700-162824996(+)$1	1	17	21	12.0000
((((	chr2:181041364-181041632(-)$1	1	13	17	12.0000
...(	chrX:162824888-162825125(+)$1	1	82	86	12.0000
.(((	chr13:6602544-6602805(-)$1	1	34	38	12.0000
...(	chr10:41239320-41239558(+)$1	1	11	15	12.0000
))))	chr5:104513928-104514170(-)$1	1	107	111	12.0000
....	chr5:104508405-104508686(-)$1	1	239	243	12.0000

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

#score	912.0000000000002
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_transcript_m1_run2.nuc.txt

#NT
uuucau	chr8:17235845-17236046(-)$1	201	83	89	18.0000
uuucau	chr5:35182390-35182591(+)$1	201	98	104	18.0000
UUUCAU	chr16:35163642-35163843(+)$1	201	93	99	18.0000
UUUCAU	chrX:69068343-69068544(+)$1	201	114	120	18.0000
UUUCAU	chrX:84491219-84491420(-)$1	201	162	168	18.0000
UUUCAU	chr13:75243177-75243378(+)$1	201	98	104	18.0000
UUUCAU	chr12:11332742-11332943(-)$1	201	99	105	18.0000
uuucau	chr18:33145977-33146178(+)$1	201	98	104	18.0000
UUUCAU	chr7:134705287-134705488(+)$1	201	76	82	18.0000
uuucau	chr1:193556659-193556860(+)$1	201	98	104	18.0000
uuucau	chr1:125451896-125452097(-)$1	201	27	33	18.0000
uuucau	chr1:3261973-3262174(-)$1	201	100	106	18.0000
UUUCAU	chr2:37492325-37492526(-)$1	201	115	121	18.0000
UUUCAU	chr9:65936069-65936270(-)$1	201	100	106	18.0000
UUUCAU	chrX:105936511-105936712(-)$1	201	100	106	18.0000
uuucau	chr5:37464743-37464944(+)$1	201	98	104	18.0000
UUUCAU	chr12:56777748-56777949(-)$1	201	100	106	18.0000
UUUCAU	chr16:63766283-63766484(-)$1	201	100	106	18.0000
uuucau	chr2:49082967-49083168(+)$1	201	98	104	18.0000
UUUCAU	chr9:65881604-65881805(+)$1	201	93	99	18.0000
UUUCAU	chr17:70803571-70803772(+)$1	201	176	182	18.0000
UUUCAU	chr2:20774819-20775020(-)$1	201	138	144	18.0000
UUUCAU	chr3:129313232-129313433(+)$1	201	98	104	18.0000
UUUCAU	chr14:50103189-50103390(-)$1	201	49	55	18.0000
UUUCAU	chr7:82604364-82604565(+)$1	201	19	25	18.0000
uuucau	chrX:154439668-154439869(-)$1	201	172	178	18.0000
uuucau	chr2:59088014-59088215(+)$1	201	130	136	18.0000
UUUCAU	chr6:21383549-21383750(+)$1	201	92	98	18.0000
UUUCAU	chr13:67098752-67098953(+)$1	201	98	104	18.0000
UUUCAU	chr1:133926752-133926953(+)$1	201	98	104	18.0000
UUUCAU	chr6:13035906-13036107(+)$1	201	47	53	18.0000
UUUCAU	chr14:24281914-24282115(-)$1	201	95	101	18.0000
UUUCAU	chr18:35750468-35750669(+)$1	201	5	11	18.0000
UUUCAU	chr16:66729091-66729292(-)$1	201	95	101	18.0000
UUUCAU	chr1:170235993-170236194(-)$1	201	101	107	18.0000
UUUCAU	chr16:32822843-32823044(-)$1	201	100	106	18.0000
UUUCAU	chr7:129224172-129224373(+)$1	201	98	104	18.0000
UUUCAU	chr1:58583972-58584173(-)$1	201	104	110	18.0000
UUUCAU	chrX:53915760-53915961(+)$1	201	93	99	18.0000
uuucau	chr15:68886414-68886615(+)$1	201	64	70	18.0000
UUUCAU	chr8:4285323-4285524(-)$1	201	68	74	18.0000

#otherMatches

#Struct PSSM
eeee:C	chr12:73865270-73865471(+)$1	201	179	185	18.0000
ooccc]	chr8:17235845-17236046(-)$1	201	83	89	18.0000
::FFFF	chr5:35182390-35182591(+)$1	201	98	104	18.0000
::::::	chr16:35163642-35163843(+)$1	201	93	99	18.0000
rrrrbb	chrX:69068343-69068544(+)$1	201	114	120	18.0000
5555gg	chrX:84491219-84491420(-)$1	201	162	168	18.0000
eeeeeu	chr13:75243177-75243378(+)$1	201	98	104	18.0000
8ggggg	chr12:11332742-11332943(-)$1	201	99	105	18.0000
++++++	chr18:33145977-33146178(+)$1	201	98	104	18.0000
::::::	chr7:134705287-134705488(+)$1	201	76	82	18.0000
eeeeem	chr1:193556659-193556860(+)$1	201	98	104	18.0000
"""fff	chr1:125451896-125452097(-)$1	201	27	33	18.0000
ttdddd	chr1:3261973-3262174(-)$1	201	100	106	18.0000
b22ddd	chr2:37492325-37492526(-)$1	201	115	121	18.0000
::::EE	chr9:65936069-65936270(-)$1	201	100	106	18.0000
eeeeeo	chrX:105936511-105936712(-)$1	201	100	106	18.0000
fuuuuu	chr5:37464743-37464944(+)$1	201	98	104	18.0000
ggg!!d	chr12:56777748-56777949(-)$1	201	100	106	18.0000
dllldd	chr16:63766283-63766484(-)$1	201	100	106	18.0000
:dddd[	chr2:49082967-49083168(+)$1	201	98	104	18.0000
gg"""=	chr9:65881604-65881805(+)$1	201	93	99	18.0000
qqqccc	chr17:70803571-70803772(+)$1	201	176	182	18.0000
::::::	chr2:20774819-20775020(-)$1	201	138	144	18.0000
5555dd	chr3:129313232-129313433(+)$1	201	98	104	18.0000
(((ccc	chr14:50103189-50103390(-)$1	201	49	55	18.0000
PPPCCC	chr7:82604364-82604565(+)$1	201	19	25	18.0000
ZFFFFF	chrX:154439668-154439869(-)$1	201	172	178	18.0000
::::::	chr2:59088014-59088215(+)$1	201	130	136	18.0000
chhhhh	chr6:21383549-21383750(+)$1	201	92	98	18.0000
>>>ddd	chr13:67098752-67098953(+)$1	201	98	104	18.0000
::ccc!	chr1:133926752-133926953(+)$1	201	98	104	18.0000
::::::	chr6:13035906-13036107(+)$1	201	47	53	18.0000
JJJJ::	chr14:24281914-24282115(-)$1	201	95	101	18.0000
C{IIII	chr18:35750468-35750669(+)$1	201	5	11	18.0000
ffffcc	chr16:66729091-66729292(-)$1	201	95	101	18.0000
::::cc	chr1:170235993-170236194(-)$1	201	101	107	18.0000
dllldd	chr16:32822843-32823044(-)$1	201	100	106	18.0000
oodddd	chr7:129224172-129224373(+)$1	201	98	104	18.0000
ggg22g	chr1:58583972-58584173(-)$1	201	104	110	18.0000
:::::i	chrX:53915760-53915961(+)$1	201	93	99	18.0000
++++++	chr15:68886414-68886615(+)$1	201	64	70	18.0000
::HHHH	chr8:4285323-4285524(-)$1	201	68	74	18.0000

#DB
)))).)	chr12:73865270-73865471(+)$1	1	179	185	18.0000
..))).	chr8:17235845-17236046(-)$1	1	83	89	18.0000
..))))	chr5:35182390-35182591(+)$1	1	98	104	18.0000
......	chr16:35163642-35163843(+)$1	1	93	99	18.0000
....))	chrX:69068343-69068544(+)$1	1	114	120	18.0000
....))	chrX:84491219-84491420(-)$1	1	162	168	18.0000
(((((.	chr13:75243177-75243378(+)$1	1	98	104	18.0000
.)))))	chr12:11332742-11332943(-)$1	1	99	105	18.0000
......	chr18:33145977-33146178(+)$1	1	98	104	18.0000
......	chr7:134705287-134705488(+)$1	1	76	82	18.0000
(((((.	chr1:193556659-193556860(+)$1	1	98	104	18.0000
...(((	chr1:125451896-125452097(-)$1	1	27	33	18.0000
..))))	chr1:3261973-3262174(-)$1	1	100	106	18.0000
)..)))	chr2:37492325-37492526(-)$1	1	115	121	18.0000
....((	chr9:65936069-65936270(-)$1	1	100	106	18.0000
(((((.	chrX:105936511-105936712(-)$1	1	100	106	18.0000
(.....	chr5:37464743-37464944(+)$1	1	98	104	18.0000
(((..(	chr12:56777748-56777949(-)$1	1	100	106	18.0000
(...))	chr16:63766283-63766484(-)$1	1	100	106	18.0000
.((((.	chr2:49082967-49083168(+)$1	1	98	104	18.0000
((...(	chr9:65881604-65881805(+)$1	1	93	99	18.0000
...)))	chr17:70803571-70803772(+)$1	1	176	182	18.0000
......	chr2:20774819-20775020(-)$1	1	138	144	18.0000
....))	chr3:129313232-129313433(+)$1	1	98	104	18.0000
...(((	chr14:50103189-50103390(-)$1	1	49	55	18.0000
...(((	chr7:82604364-82604565(+)$1	1	19	25	18.0000
.)))))	chrX:154439668-154439869(-)$1	1	172	178	18.0000
......	chr2:59088014-59088215(+)$1	1	130	136	18.0000
))))))	chr6:21383549-21383750(+)$1	1	92	98	18.0000
...)))	chr13:67098752-67098953(+)$1	1	98	104	18.0000
..(((.	chr1:133926752-133926953(+)$1	1	98	104	18.0000
......	chr6:13035906-13036107(+)$1	1	47	53	18.0000
((((..	chr14:24281914-24282115(-)$1	1	95	101	18.0000
(.((((	chr18:35750468-35750669(+)$1	1	5	11	18.0000
))))((	chr16:66729091-66729292(-)$1	1	95	101	18.0000
....((	chr1:170235993-170236194(-)$1	1	101	107	18.0000
(...))	chr16:32822843-32823044(-)$1	1	100	106	18.0000
..))))	chr7:129224172-129224373(+)$1	1	98	104	18.0000
)))..)	chr1:58583972-58584173(-)$1	1	104	110	18.0000
.....(	chrX:53915760-53915961(+)$1	1	93	99	18.0000
......	chr15:68886414-68886615(+)$1	1	64	70	18.0000
..((((	chr8:4285323-4285524(-)$1	1	68	74	18.0000

#PSSM
U : 0.73	u : 0.26	
U : 0.73	u : 0.26	
U : 0.73	u : 0.26	
C : 0.73	c : 0.26	
A : 0.73	a : 0.26	
U : 0.73	u : 0.26	

#score	756.0000000000001
#seq	42
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m2_run1.nuc.txt

#NT
UUUCCU	chr11:100888528-100888792(+)$1	264	242	248	14.0655
GUUCCU	chr11:118355369-118355606(-)$1	237	13	19	11.5245
UUUCCC	chr9:30959798-30960060(-)$1	262	42	48	10.8688
CUUCCU	chr14:31989531-31989766(-)$1	235	137	143	11.5245
UUUCCC	chr5:131921174-131921409(-)$1	235	37	43	10.8688
UUUCCA	chr6:117123446-117123681(+)$1	235	173	179	10.9508
UUUCCA	chr15:96414691-96414926(-)$1	235	77	83	10.9508
CUUCCU	chr13:78336959-78337194(-)$1	235	102	108	11.5245
UUCCCU	chr7:129777075-129777383(+)$1	308	93	99	10.2131
UUUCCU	chr15:9104843-9105086(+)$1	243	4	10	14.0655
UUUCCU	chr15:27701031-27701272(-)$1	241	136	142	14.0655
UUUCCU	chr11:41946818-41947090(-)$1	272	221	227	14.0655
UUUCCU	chr13:94994830-94995082(-)$1	252	5	11	14.0655
CUUCCU	chr19:10058659-10058899(+)$1	240	139	145	11.5245
GUUCCU	chr2:181041364-181041632(-)$1	268	82	88	11.5245
UGUCCU	chr11:68620525-68620761(+)$1	236	91	97	9.6393
UUUCCA	chr2:6468061-6468303(-)$1	242	37	43	10.9508
GUUCCU	chr5:29619320-29619555(-)$1	235	216	222	11.5245
UUUCCU	chr12:4637380-4637615(+)$1	235	51	57	14.0655
UUGCCU	chr16:35293974-35294230(+)$1	256	56	62	9.8852
CUUCCU	chr1:135533828-135534091(-)$1	263	14	20	11.5245
CUUCCU	chr2:25077838-25078075(-)$1	237	88	94	11.5245
UCUCCU	chr8:46095312-46095551(+)$1	239	54	60	9.7213
UUUCCA	chr11:87863329-87863588(+)$1	259	6	12	10.9508
UUUCCA	chr7:148337524-148337759(+)$1	235	143	149	10.9508
UUCCCU	chr14:104242207-104242444(-)$1	237	6	12	10.2131
UUUCCA	chr1:175262352-175262595(-)$1	243	96	102	10.9508
CUUCCU	chr11:115667985-115668222(-)$1	237	27	33	11.5245
uuuccc	chr9:58430182-58430417(+)$1	235	7	13	10.8688
UUUCCU	chr18:67778820-67779055(-)$1	235	176	182	14.0655
GUUCCU	chr10:29067362-29067599(-)$1	237	7	13	11.5245
CUUCCU	chr12:106028213-106028448(-)$1	235	148	154	11.5245
UCUCCU	chr14:37939004-37939242(-)$1	238	15	21	9.7213
UCUCCU	chr1:174215791-174216026(-)$1	235	58	64	9.7213
UUUCCC	chr15:79555743-79555980(-)$1	237	150	156	10.8688
UUCCCU	chr17:82047059-82047320(-)$1	261	78	84	10.2131
UGUCCU	chr2:9985644-9985896(-)$1	252	21	27	9.6393
GUUCCU	chr11:70483294-70483530(-)$1	236	107	113	11.5245
UUCCCU	chr5:104513928-104514170(-)$1	242	29	35	10.2131
UUUCCU	chr5:137736972-137737209(-)$1	237	58	64	14.0655
UUUCCC	chrX:10172306-10172551(+)$1	245	208	214	10.8688
UUUCCU	chr11:59220569-59220827(-)$1	258	104	110	14.0655
UUUCCU	chr7:31226612-31226851(-)$1	239	136	142	14.0655
UUCCCU	chr11:49502571-49502808(-)$1	237	25	31	10.2131
GUUCCU	chrX:148317008-148317269(+)$1	261	60	66	11.5245
UUUCCU	chr11:90202099-90202341(-)$1	242	29	35	14.0655
CUUCCU	chr16:35283532-35283777(+)$1	245	22	28	11.5245
GUUCCU	chr7:65047791-65048042(+)$1	251	46	52	11.5245
UUGCCU	chr4:126425761-126425997(-)$1	236	68	74	9.8852
UUUCCU	chr1:193602238-193602475(+)$1	237	28	34	14.0655
GUUCCU	chr11:70483254-70483493(-)$1	239	70	76	11.5245
UUUCCC	chr15:99351509-99351763(-)$1	254	85	91	10.8688
UUCCCU	chr10:98477548-98477791(+)$1	243	28	34	10.2131
UUUCCA	chr13:74476965-74477204(-)$1	239	34	40	10.9508
GUUCCU	chr15:31418450-31418687(-)$1	237	15	21	11.5245
UUUCCA	chr5:104508405-104508686(-)$1	281	143	149	10.9508
UUUCCU	chrX:45721941-45722176(+)$1	235	72	78	14.0655
UUUCCC	chr19:57229539-57229775(-)$1	236	147	153	10.8688
CUUCCU	chr1:174210640-174210877(-)$1	237	30	36	11.5245
CUUCCU	chrX:162824888-162825125(+)$1	237	0	6	11.5245

#otherMatches

#Struct PSSM
cc[bbm	chrX:39458041-39458277(+)$1	236	12	18	11.5245
eee]==	chr11:100888528-100888792(+)$1	264	242	248	14.0655
GGGLLL	chr11:118355369-118355606(-)$1	237	13	19	11.5245
dddd==	chr9:30959798-30960060(-)$1	262	42	48	10.8688
!!ffff	chr14:31989531-31989766(-)$1	235	137	143	11.5245
::::::	chr5:131921174-131921409(-)$1	235	37	43	10.8688
GGGGGG	chr6:117123446-117123681(+)$1	235	173	179	10.9508
qqqqqq	chr15:96414691-96414926(-)$1	235	77	83	10.9508
i####b	chr13:78336959-78337194(-)$1	235	102	108	11.5245
33dddd	chr7:129777075-129777383(+)$1	308	93	99	10.2131
[fffff	chr15:9104843-9105086(+)$1	243	4	10	14.0655
::::::	chr15:27701031-27701272(-)$1	241	136	142	14.0655
JJJJ::	chr11:41946818-41947090(-)$1	272	221	227	14.0655
:::::F	chr13:94994830-94995082(-)$1	252	5	11	14.0655
eee]cc	chr19:10058659-10058899(+)$1	240	139	145	11.5245
iddddd	chr2:181041364-181041632(-)$1	268	82	88	11.5245
:JJJJJ	chr11:68620525-68620761(+)$1	236	91	97	9.6393
::::FF	chr2:6468061-6468303(-)$1	242	37	43	10.9508
GDDDD}	chr5:29619320-29619555(-)$1	235	216	222	11.5245
::::::	chr12:4637380-4637615(+)$1	235	51	57	14.0655
DD:BB{	chr16:35293974-35294230(+)$1	256	56	62	9.8852
FFFFCC	chr1:135533828-135534091(-)$1	263	14	20	11.5245
ffff!!	chr2:25077838-25078075(-)$1	237	88	94	11.5245
dddddd	chr8:46095312-46095551(+)$1	239	54	60	9.7213
DDDKKB	chr11:87863329-87863588(+)$1	259	6	12	10.9508
wwwwww	chr7:148337524-148337759(+)$1	235	143	149	10.9508
::::EE	chr14:104242207-104242444(-)$1	237	6	12	10.2131
ddd%%%	chr1:175262352-175262595(-)$1	243	96	102	10.9508
EEEEE:	chr11:115667985-115668222(-)$1	237	27	33	11.5245
HHHHLL	chr9:58430182-58430417(+)$1	235	7	13	10.8688
"cccmm	chr18:67778820-67779055(-)$1	235	176	182	14.0655
:::CCC	chr10:29067362-29067599(-)$1	237	7	13	11.5245
GGG:::	chr12:106028213-106028448(-)$1	235	148	154	11.5245
iiiiii	chr14:37939004-37939242(-)$1	238	15	21	9.7213
ggggg'	chr1:174215791-174216026(-)$1	235	58	64	9.7213
ffffff	chr15:79555743-79555980(-)$1	237	150	156	10.8688
dd:ccc	chr17:82047059-82047320(-)$1	261	78	84	10.2131
)fffff	chr2:9985644-9985896(-)$1	252	21	27	9.6393
^^^^^c	chr11:70483294-70483530(-)$1	236	107	113	11.5245
:ccc[c	chr5:104513928-104514170(-)$1	242	29	35	10.2131
b]eeee	chr5:137736972-137737209(-)$1	237	58	64	14.0655
mmdddd	chrX:10172306-10172551(+)$1	245	208	214	10.8688
dd!!dd	chr11:59220569-59220827(-)$1	258	104	110	14.0655
hhhhhh	chr7:31226612-31226851(-)$1	239	136	142	14.0655
:::::d	chr11:49502571-49502808(-)$1	237	25	31	10.2131
"ggggg	chrX:148317008-148317269(+)$1	261	60	66	11.5245
JJJJJJ	chr11:90202099-90202341(-)$1	242	29	35	14.0655
((((((	chr16:35283532-35283777(+)$1	245	22	28	11.5245
axxxxx	chr7:65047791-65048042(+)$1	251	46	52	11.5245
eeEEEE	chr4:126425761-126425997(-)$1	236	68	74	9.8852
ooooee	chr1:193602238-193602475(+)$1	237	28	34	14.0655
^^^^^c	chr11:70483254-70483493(-)$1	239	70	76	11.5245
i%%%%%	chr15:99351509-99351763(-)$1	254	85	91	10.8688
gggg!!	chr10:98477548-98477791(+)$1	243	28	34	10.2131
iiiiii	chr13:74476965-74477204(-)$1	239	34	40	10.9508
ddd$$$	chr15:31418450-31418687(-)$1	237	15	21	11.5245
ccc]dd	chr5:104508405-104508686(-)$1	281	143	149	10.9508
777777	chrX:45721941-45722176(+)$1	235	72	78	14.0655
44eeee	chr19:57229539-57229775(-)$1	236	147	153	10.8688
{BB{BB	chr1:174210640-174210877(-)$1	237	30	36	11.5245
::dddd	chrX:162824888-162825125(+)$1	237	0	6	11.5245

#DB
((.((.	chrX:39458041-39458277(+)$1	1	12	18	11.5245
))).))	chr11:100888528-100888792(+)$1	1	242	248	14.0655
(((...	chr11:118355369-118355606(-)$1	1	13	19	11.5245
((((((	chr9:30959798-30960060(-)$1	1	42	48	10.8688
..((((	chr14:31989531-31989766(-)$1	1	137	143	11.5245
......	chr5:131921174-131921409(-)$1	1	37	43	10.8688
))))))	chr6:117123446-117123681(+)$1	1	173	179	10.9508
......	chr15:96414691-96414926(-)$1	1	77	83	10.9508
(....(	chr13:78336959-78337194(-)$1	1	102	108	11.5245
..))))	chr7:129777075-129777383(+)$1	1	93	99	10.2131
.(((((	chr15:9104843-9105086(+)$1	1	4	10	14.0655
......	chr15:27701031-27701272(-)$1	1	136	142	14.0655
))))..	chr11:41946818-41947090(-)$1	1	221	227	14.0655
.....(	chr13:94994830-94995082(-)$1	1	5	11	14.0655
))).))	chr19:10058659-10058899(+)$1	1	139	145	11.5245
))))))	chr2:181041364-181041632(-)$1	1	82	88	11.5245
.(((((	chr11:68620525-68620761(+)$1	1	91	97	9.6393
....((	chr2:6468061-6468303(-)$1	1	37	43	10.9508
))))).	chr5:29619320-29619555(-)$1	1	216	222	11.5245
......	chr12:4637380-4637615(+)$1	1	51	57	14.0655
((.((.	chr16:35293974-35294230(+)$1	1	56	62	9.8852
((((((	chr1:135533828-135534091(-)$1	1	14	20	11.5245
((((..	chr2:25077838-25078075(-)$1	1	88	94	11.5245
((((((	chr8:46095312-46095551(+)$1	1	54	60	9.7213
(((..(	chr11:87863329-87863588(+)$1	1	6	12	10.9508
......	chr7:148337524-148337759(+)$1	1	143	149	10.9508
....((	chr14:104242207-104242444(-)$1	1	6	12	10.2131
(((...	chr1:175262352-175262595(-)$1	1	96	102	10.9508
(((((.	chr11:115667985-115668222(-)$1	1	27	33	11.5245
((((..	chr9:58430182-58430417(+)$1	1	7	13	10.8688
.(((..	chr18:67778820-67779055(-)$1	1	176	182	14.0655
...(((	chr10:29067362-29067599(-)$1	1	7	13	11.5245
)))...	chr12:106028213-106028448(-)$1	1	148	154	11.5245
))))))	chr14:37939004-37939242(-)$1	1	15	21	9.7213
(((((.	chr1:174215791-174216026(-)$1	1	58	64	9.7213
))))))	chr15:79555743-79555980(-)$1	1	150	156	10.8688
)).(((	chr17:82047059-82047320(-)$1	1	78	84	10.2131
.(((((	chr2:9985644-9985896(-)$1	1	21	27	9.6393
.....)	chr11:70483294-70483530(-)$1	1	107	113	11.5245
.(((.(	chr5:104513928-104514170(-)$1	1	29	35	10.2131
).))))	chr5:137736972-137737209(-)$1	1	58	64	14.0655
..))))	chrX:10172306-10172551(+)$1	1	208	214	10.8688
((..((	chr11:59220569-59220827(-)$1	1	104	110	14.0655
))))))	chr7:31226612-31226851(-)$1	1	136	142	14.0655
.....(	chr11:49502571-49502808(-)$1	1	25	31	10.2131
.(((((	chrX:148317008-148317269(+)$1	1	60	66	11.5245
((((((	chr11:90202099-90202341(-)$1	1	29	35	14.0655
......	chr16:35283532-35283777(+)$1	1	22	28	11.5245
(.....	chr7:65047791-65048042(+)$1	1	46	52	11.5245
))((((	chr4:126425761-126425997(-)$1	1	68	74	9.8852
....))	chr1:193602238-193602475(+)$1	1	28	34	14.0655
.....)	chr11:70483254-70483493(-)$1	1	70	76	11.5245
(.....	chr15:99351509-99351763(-)$1	1	85	91	10.8688
((((..	chr10:98477548-98477791(+)$1	1	28	34	10.2131
((((((	chr13:74476965-74477204(-)$1	1	34	40	10.9508
(((...	chr15:31418450-31418687(-)$1	1	15	21	11.5245
))).))	chr5:104508405-104508686(-)$1	1	143	149	10.9508
......	chrX:45721941-45722176(+)$1	1	72	78	14.0655
..))))	chr19:57229539-57229775(-)$1	1	147	153	10.8688
.((.((	chr1:174210640-174210877(-)$1	1	30	36	11.5245
..((((	chrX:162824888-162825125(+)$1	1	0	6	11.5245

#PSSM
U : 0.65	G : 0.16	C : 0.16	u : 0.01	
U : 0.90	C : 0.04	G : 0.03	u : 0.01	
U : 0.85	C : 0.09	G : 0.03	u : 0.01	
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
U : 0.75	A : 0.13	C : 0.09	c : 0.01	

#score	706.5245901639352
#seq	61
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_CDS_m2_run2.nuc.txt

#NT
CUUC	chr8:125757055-125757293(-)$1	238	39	43	11.9999
CUUC	chrX:148333052-148333297(+)$1	245	53	57	11.9999
CUUC	chr17:82047184-82047434(-)$1	250	21	25	11.9999
CUUC	chr7:148080279-148080538(+)$1	259	127	131	11.9999
cuuc	chr5:139048103-139048423(-)$1	320	51	55	11.9999
CUUC	chr2:126618448-126618711(-)$1	263	87	91	11.9999
CUUC	chr4:129011641-129011895(-)$1	254	138	142	11.9999
CUUC	chr3:45196621-45196884(+)$1	263	68	72	11.9999
CUUC	chr4:155550963-155551237(-)$1	274	197	201	11.9999
CUUC	chr19:38852300-38852566(+)$1	266	69	73	11.9999
CUUC	chr6:120460181-120460422(-)$1	241	52	56	11.9999
CUUC	chr5:23051234-23051474(-)$1	240	105	109	11.9999
CUUC	chr17:43222352-43222613(+)$1	261	66	70	11.9999
CUUC	chr1:180259353-180259653(-)$1	300	209	213	11.9999
CUUC	chr9:122762298-122762539(-)$1	241	229	233	11.9999
CUUC	chr11:42133838-42134097(-)$1	259	87	91	11.9999
CUUC	chr16:89897755-89898006(-)$1	251	58	62	11.9999
CUUC	chr19:53079175-53079414(-)$1	239	52	56	11.9999
CUUC	chr17:35297301-35297557(-)$1	256	89	93	11.9999
CUUC	chr2:6585061-6585323(-)$1	262	39	43	11.9999
CUUC	chr11:42410946-42411197(+)$1	251	205	209	11.9999
CUUC	chr4:129338498-129338757(-)$1	259	67	71	11.9999
CUUC	chr10:33731792-33732036(-)$1	244	115	119	11.9999
CUUC	chr4:63653992-63654251(-)$1	259	3	7	11.9999
CUUC	chr9:49315367-49315637(-)$1	270	82	86	11.9999
CUUC	chr11:53225385-53225649(+)$1	264	17	21	11.9999
CUUC	chr11:115041531-115041796(+)$1	265	31	35	11.9999
CUUC	chr11:96680937-96681183(-)$1	246	50	54	11.9999
CUUC	chr12:117557237-117557501(+)$1	264	32	36	11.9999
CUUC	chr10:10452870-10453111(-)$1	241	13	17	11.9999
CUUC	chr10:57239062-57239324(-)$1	262	90	94	11.9999
CUUC	chr9:57299061-57299316(-)$1	255	38	42	11.9999
CUUC	chr14:118560686-118560948(+)$1	262	51	55	11.9999
CUUC	chr11:35881918-35882180(-)$1	262	96	100	11.9999
CUUC	chr9:58764663-58764898(-)$1	235	10	14	11.9999
CUUC	chr2:59143341-59143589(+)$1	248	176	180	11.9999
CUUC	chr11:96683370-96683605(-)$1	235	175	179	11.9999
CUUC	chr11:117602881-117603144(+)$1	263	129	133	11.9999
CUUC	chr4:57963613-57963856(-)$1	243	59	63	11.9999
CUUC	chr13:84422833-84423070(+)$1	237	181	185	11.9999
CUUC	chr3:80514596-80514872(-)$1	276	110	114	11.9999
CUUC	chr10:57239438-57239750(-)$1	312	139	143	11.9999
CUUC	chr2:121290412-121290680(-)$1	268	73	77	11.9999
CUUC	chr12:87160372-87160616(-)$1	244	5	9	11.9999
CUUC	chr14:31989487-31989758(-)$1	271	45	49	11.9999
CUUC	chr8:98268379-98268634(-)$1	255	85	89	11.9999
CUUC	chr11:79197578-79197839(+)$1	261	98	102	11.9999
CUUC	chr14:60665412-60665683(-)$1	271	79	83	11.9999
CUUC	chr18:38362452-38362707(-)$1	255	202	206	11.9999
CUUC	chr3:105770052-105770310(+)$1	258	92	96	11.9999
CUUC	chr6:86933720-86933986(+)$1	266	147	151	11.9999
CUUC	chr11:106646139-106646395(-)$1	256	12	16	11.9999
CUUC	chr6:11855101-11855351(-)$1	250	9	13	11.9999
CUUC	chr2:138109432-138109845(+)$1	413	19	23	11.9999
CUUC	chr11:102754731-102754996(-)$1	265	63	67	11.9999
CUUC	chr12:66169910-66170175(-)$1	265	210	214	11.9999
CUUC	chr4:123058388-123058673(-)$1	285	165	169	11.9999
CUUC	chrX:12684788-12685084(+)$1	296	32	36	11.9999
CUUC	chr12:53617664-53617994(+)$1	330	233	237	11.9999
CUUC	chr14:17255055-17255299(+)$1	244	72	76	11.9999
CUUC	chr1:182529011-182529289(+)$1	278	54	58	11.9999
CUUC	chr3:148617469-148617727(-)$1	258	135	139	11.9999
CUUC	chr4:100829470-100829776(-)$1	306	14	18	11.9999
CUUC	chrX:138768131-138768389(-)$1	258	8	12	11.9999
CUUC	chr15:96525361-96525618(-)$1	257	1	5	11.9999
CUUC	chr6:113712686-113712996(-)$1	310	105	109	11.9999
CUUC	chr15:81458658-81458908(+)$1	250	161	165	11.9999
CUUC	chr3:59013944-59014249(-)$1	305	7	11	11.9999
CUUC	chr10:57942242-57942530(+)$1	288	209	213	11.9999
CUUC	chr1:160176732-160176991(-)$1	259	137	141	11.9999
CUUC	chr5:104518517-104518816(-)$1	299	92	96	11.9999
CUUC	chr2:80410176-80410468(-)$1	292	21	25	11.9999
CUUC	chr15:51795434-51795706(-)$1	272	233	237	11.9999
CUUC	chr2:72808702-72808948(-)$1	246	101	105	11.9999
CUUC	chr2:49566211-49566473(+)$1	262	211	215	11.9999
CUUC	chr8:108719161-108719402(+)$1	241	73	77	11.9999
CUUC	chr15:95265586-95265852(-)$1	266	123	127	11.9999

#otherMatches

#Struct PSSM
eeee	chr8:119147765-119148000(-)$1	235	14	18	11.9999
ddd!	chr8:125757055-125757293(-)$1	238	39	43	11.9999
ccc[	chrX:148333052-148333297(+)$1	245	53	57	11.9999
{HHH	chr17:82047184-82047434(-)$1	250	21	25	11.9999
eeee	chr7:148080279-148080538(+)$1	259	127	131	11.9999
[ccc	chr5:139048103-139048423(-)$1	320	51	55	11.9999
mmdd	chr2:126618448-126618711(-)$1	263	87	91	11.9999
c:cc	chr4:129011641-129011895(-)$1	254	138	142	11.9999
HHHH	chr3:45196621-45196884(+)$1	263	68	72	11.9999
ggCC	chr4:155550963-155551237(-)$1	274	197	201	11.9999
cooo	chr19:38852300-38852566(+)$1	266	69	73	11.9999
dddd	chr6:120460181-120460422(-)$1	241	52	56	11.9999
rrrr	chr5:23051234-23051474(-)$1	240	105	109	11.9999
TCCC	chr17:43222352-43222613(+)$1	261	66	70	11.9999
::::	chr1:180259353-180259653(-)$1	300	209	213	11.9999
ffff	chr9:122762298-122762539(-)$1	241	229	233	11.9999
eeee	chr11:42133838-42134097(-)$1	259	87	91	11.9999
^^^^	chr16:89897755-89898006(-)$1	251	58	62	11.9999
aooo	chr19:53079175-53079414(-)$1	239	52	56	11.9999
c:::	chr17:35297301-35297557(-)$1	256	89	93	11.9999
ee[b	chr2:6585061-6585323(-)$1	262	39	43	11.9999
YYDD	chr11:42410946-42411197(+)$1	251	205	209	11.9999
eell	chr4:129338498-129338757(-)$1	259	67	71	11.9999
ddd:	chr10:33731792-33732036(-)$1	244	115	119	11.9999
EEEE	chr4:63653992-63654251(-)$1	259	3	7	11.9999
::::	chr9:49315367-49315637(-)$1	270	82	86	11.9999
##ff	chr11:53225385-53225649(+)$1	264	17	21	11.9999
[ddd	chr11:115041531-115041796(+)$1	265	31	35	11.9999
OOOO	chr11:96680937-96681183(-)$1	246	50	54	11.9999
SSSS	chr12:117557237-117557501(+)$1	264	32	36	11.9999
E::e	chr10:10452870-10453111(-)$1	241	13	17	11.9999
e]ff	chr10:57239062-57239324(-)$1	262	90	94	11.9999
OFFF	chr9:57299061-57299316(-)$1	255	38	42	11.9999
HHHH	chr14:118560686-118560948(+)$1	262	51	55	11.9999
dd""	chr11:35881918-35882180(-)$1	262	96	100	11.9999
EEEE	chr9:58764663-58764898(-)$1	235	10	14	11.9999
eeee	chr2:59143341-59143589(+)$1	248	176	180	11.9999
iiii	chr11:96683370-96683605(-)$1	235	175	179	11.9999
22bb	chr11:117602881-117603144(+)$1	263	129	133	11.9999
ff[a	chr4:57963613-57963856(-)$1	243	59	63	11.9999
::::	chr13:84422833-84423070(+)$1	237	181	185	11.9999
f:::	chr3:80514596-80514872(-)$1	276	110	114	11.9999
qqqq	chr10:57239438-57239750(-)$1	312	139	143	11.9999
GGGG	chr2:121290412-121290680(-)$1	268	73	77	11.9999
eell	chr12:87160372-87160616(-)$1	244	5	9	11.9999
::BB	chr14:31989487-31989758(-)$1	271	45	49	11.9999
[bb[	chr8:98268379-98268634(-)$1	255	85	89	11.9999
cccc	chr11:79197578-79197839(+)$1	261	98	102	11.9999
ggll	chr14:60665412-60665683(-)$1	271	79	83	11.9999
GGGG	chr18:38362452-38362707(-)$1	255	202	206	11.9999
::::	chr3:105770052-105770310(+)$1	258	92	96	11.9999
b"""	chr6:86933720-86933986(+)$1	266	147	151	11.9999
FFEE	chr11:106646139-106646395(-)$1	256	12	16	11.9999
eeee	chr6:11855101-11855351(-)$1	250	9	13	11.9999
GGGG	chr2:138109432-138109845(+)$1	413	19	23	11.9999
zzzz	chr11:102754731-102754996(-)$1	265	63	67	11.9999
d]bb	chr12:66169910-66170175(-)$1	265	210	214	11.9999
nnee	chr4:123058388-123058673(-)$1	285	165	169	11.9999
deee	chrX:12684788-12685084(+)$1	296	32	36	11.9999
eeee	chr12:53617664-53617994(+)$1	330	233	237	11.9999
====	chr14:17255055-17255299(+)$1	244	72	76	11.9999
ffff	chr1:182529011-182529289(+)$1	278	54	58	11.9999
%%%%	chr3:148617469-148617727(-)$1	258	135	139	11.9999
GOOO	chr4:100829470-100829776(-)$1	306	14	18	11.9999
{HHH	chrX:138768131-138768389(-)$1	258	8	12	11.9999
::::	chr15:96525361-96525618(-)$1	257	1	5	11.9999
ssss	chr6:113712686-113712996(-)$1	310	105	109	11.9999
:eee	chr15:81458658-81458908(+)$1	250	161	165	11.9999
EKKC	chr3:59013944-59014249(-)$1	305	7	11	11.9999
CEEE	chr10:57942242-57942530(+)$1	288	209	213	11.9999
:fff	chr1:160176732-160176991(-)$1	259	137	141	11.9999
fff]	chr5:104518517-104518816(-)$1	299	92	96	11.9999
::gg	chr2:80410176-80410468(-)$1	292	21	25	11.9999
::::	chr15:51795434-51795706(-)$1	272	233	237	11.9999
::::	chr2:72808702-72808948(-)$1	246	101	105	11.9999
g22d	chr2:49566211-49566473(+)$1	262	211	215	11.9999
cc22	chr8:108719161-108719402(+)$1	241	73	77	11.9999
5555	chr15:95265586-95265852(-)$1	266	123	127	11.9999

#DB
))))	chr8:119147765-119148000(-)$1	1	14	18	11.9999
(((.	chr8:125757055-125757293(-)$1	1	39	43	11.9999
(((.	chrX:148333052-148333297(+)$1	1	53	57	11.9999
.(((	chr17:82047184-82047434(-)$1	1	21	25	11.9999
))))	chr7:148080279-148080538(+)$1	1	127	131	11.9999
.(((	chr5:139048103-139048423(-)$1	1	51	55	11.9999
..))	chr2:126618448-126618711(-)$1	1	87	91	11.9999
).((	chr4:129011641-129011895(-)$1	1	138	142	11.9999
((((	chr3:45196621-45196884(+)$1	1	68	72	11.9999
))))	chr4:155550963-155551237(-)$1	1	197	201	11.9999
(...	chr19:38852300-38852566(+)$1	1	69	73	11.9999
))))	chr6:120460181-120460422(-)$1	1	52	56	11.9999
....	chr5:23051234-23051474(-)$1	1	105	109	11.9999
.(((	chr17:43222352-43222613(+)$1	1	66	70	11.9999
....	chr1:180259353-180259653(-)$1	1	209	213	11.9999
))))	chr9:122762298-122762539(-)$1	1	229	233	11.9999
))((	chr11:42133838-42134097(-)$1	1	87	91	11.9999
....	chr16:89897755-89898006(-)$1	1	58	62	11.9999
(...	chr19:53079175-53079414(-)$1	1	52	56	11.9999
)...	chr17:35297301-35297557(-)$1	1	89	93	11.9999
((.(	chr2:6585061-6585323(-)$1	1	39	43	11.9999
..))	chr11:42410946-42411197(+)$1	1	205	209	11.9999
((..	chr4:129338498-129338757(-)$1	1	67	71	11.9999
))).	chr10:33731792-33732036(-)$1	1	115	119	11.9999
((((	chr4:63653992-63654251(-)$1	1	3	7	11.9999
....	chr9:49315367-49315637(-)$1	1	82	86	11.9999
..((	chr11:53225385-53225649(+)$1	1	17	21	11.9999
.(((	chr11:115041531-115041796(+)$1	1	31	35	11.9999
....	chr11:96680937-96681183(-)$1	1	50	54	11.9999
....	chr12:117557237-117557501(+)$1	1	32	36	11.9999
(..(	chr10:10452870-10453111(-)$1	1	13	17	11.9999
).))	chr10:57239062-57239324(-)$1	1	90	94	11.9999
.(((	chr9:57299061-57299316(-)$1	1	38	42	11.9999
((((	chr14:118560686-118560948(+)$1	1	51	55	11.9999
((..	chr11:35881918-35882180(-)$1	1	96	100	11.9999
((((	chr9:58764663-58764898(-)$1	1	10	14	11.9999
((((	chr2:59143341-59143589(+)$1	1	176	180	11.9999
))))	chr11:96683370-96683605(-)$1	1	175	179	11.9999
..))	chr11:117602881-117603144(+)$1	1	129	133	11.9999
((.(	chr4:57963613-57963856(-)$1	1	59	63	11.9999
....	chr13:84422833-84423070(+)$1	1	181	185	11.9999
)...	chr3:80514596-80514872(-)$1	1	110	114	11.9999
....	chr10:57239438-57239750(-)$1	1	139	143	11.9999
((((	chr2:121290412-121290680(-)$1	1	73	77	11.9999
((..	chr12:87160372-87160616(-)$1	1	5	9	11.9999
..((	chr14:31989487-31989758(-)$1	1	45	49	11.9999
.((.	chr8:98268379-98268634(-)$1	1	85	89	11.9999
((((	chr11:79197578-79197839(+)$1	1	98	102	11.9999
((..	chr14:60665412-60665683(-)$1	1	79	83	11.9999
))))	chr18:38362452-38362707(-)$1	1	202	206	11.9999
....	chr3:105770052-105770310(+)$1	1	92	96	11.9999
(...	chr6:86933720-86933986(+)$1	1	147	151	11.9999
((((	chr11:106646139-106646395(-)$1	1	12	16	11.9999
((((	chr6:11855101-11855351(-)$1	1	9	13	11.9999
((((	chr2:138109432-138109845(+)$1	1	19	23	11.9999
....	chr11:102754731-102754996(-)$1	1	63	67	11.9999
).))	chr12:66169910-66170175(-)$1	1	210	214	11.9999
..))	chr4:123058388-123058673(-)$1	1	165	169	11.9999
)(((	chrX:12684788-12685084(+)$1	1	32	36	11.9999
))))	chr12:53617664-53617994(+)$1	1	233	237	11.9999
((((	chr14:17255055-17255299(+)$1	1	72	76	11.9999
))))	chr1:182529011-182529289(+)$1	1	54	58	11.9999
....	chr3:148617469-148617727(-)$1	1	135	139	11.9999
(...	chr4:100829470-100829776(-)$1	1	14	18	11.9999
.(((	chrX:138768131-138768389(-)$1	1	8	12	11.9999
....	chr15:96525361-96525618(-)$1	1	1	5	11.9999
....	chr6:113712686-113712996(-)$1	1	105	109	11.9999
.(((	chr15:81458658-81458908(+)$1	1	161	165	11.9999
(..(	chr3:59013944-59014249(-)$1	1	7	11	11.9999
))))	chr10:57942242-57942530(+)$1	1	209	213	11.9999
.(((	chr1:160176732-160176991(-)$1	1	137	141	11.9999
))).	chr5:104518517-104518816(-)$1	1	92	96	11.9999
..((	chr2:80410176-80410468(-)$1	1	21	25	11.9999
....	chr15:51795434-51795706(-)$1	1	233	237	11.9999
....	chr2:72808702-72808948(-)$1	1	101	105	11.9999
)..)	chr2:49566211-49566473(+)$1	1	211	215	11.9999
))..	chr8:108719161-108719402(+)$1	1	73	77	11.9999
....	chr15:95265586-95265852(-)$1	1	123	127	11.9999

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

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_CDS_m1_run1.nuc.txt

#NT
CUCUGAG	chr1:182503801-182504079(+)$1	278	82	89	16.8163
CUCUGAG	chr8:26107145-26107416(-)$1	271	198	205	16.8163
CUCUGAC	chr11:75125734-75126033(-)$1	299	139	146	13.1428
CUCUGAG	chr11:88826334-88826601(-)$1	267	218	225	16.8163
CUCUUAG	chr4:122729700-122729971(+)$1	271	19	26	12.2244
AUCUGAG	chr14:22803805-22804073(-)$1	268	252	259	12.4285
CUAUGAG	chr8:126025782-126026058(+)$1	276	54	61	12.9387
CUCGGAG	chr15:90057860-90058150(+)$1	290	208	215	12.3265
CUGUGAG	chr8:107860182-107860450(-)$1	268	148	155	13.0408
CUCAGAG	chr17:23890646-23890918(-)$1	272	257	264	12.4285
CUUUGAG	chrY:439119-439399(-)$1	280	100	107	13.1428
CUCUGAC	chr4:149018020-149018286(+)$1	266	51	58	13.1428
CUCCGAG	chr19:24758872-24759140(-)$1	268	184	191	12.3265
CUUUGAG	chr4:115772165-115772446(-)$1	281	137	144	13.1428
CUCUGCG	chr11:97030334-97030603(-)$1	269	24	31	12.7346
CUCUGGG	chr7:148599791-148600059(-)$1	268	206	213	13.2448
CUCUGAG	chrX:147431623-147431893(-)$1	270	49	56	16.8163
CUCUGGG	chr17:35152719-35152995(+)$1	276	228	235	13.2448
CUCUGAA	chr12:106199620-106199892(-)$1	272	43	50	13.2448
CUCUGAU	chr11:95911393-95911684(-)$1	291	69	76	13.1428
CUCUGGG	chr3:88447584-88447871(+)$1	287	49	56	13.2448
GUCUGAG	chr6:142594277-142594544(-)$1	267	226	233	12.5306
CUGUGAG	chr7:52677721-52678007(-)$1	286	123	130	13.0408
CUCUCAG	chr11:106122087-106122356(+)$1	269	231	238	12.2244
CUCUGGG	chr6:28462794-28463073(+)$1	279	45	52	13.2448
CUUUGAG	chr4:57964567-57964851(-)$1	284	203	210	13.1428
CUCUGAG	chr4:116853100-116853368(-)$1	268	199	206	16.8163
CUCUGAG	chr1:19224039-19224310(+)$1	271	50	57	16.8163
CACUGAG	chr8:87391660-87391928(+)$1	268	210	217	12.2244
CUCAGAG	chr11:8448793-8449061(-)$1	268	179	186	12.4285
CUUUGAG	chr2:120361046-120361326(-)$1	280	111	118	13.1428
CUCUGAA	chrX:103026194-103026472(-)$1	278	268	275	13.2448
CUCUGUG	chr11:120458860-120459150(-)$1	290	45	52	12.7346
CUCUGAU	chr4:129233042-129233310(-)$1	268	65	72	13.1428
CUAUGAG	chr11:8896763-8897031(-)$1	268	219	226	12.9387
UUCUGAG	chr17:85075412-85075680(-)$1	268	231	238	12.5306
CUCUGAC	chr12:17556230-17556502(+)$1	272	154	161	13.1428
CACUGAG	chr8:74704396-74704674(+)$1	278	4	11	12.2244
CUCUGGG	chrX:98613547-98613822(-)$1	275	136	143	13.2448
GUCUGAG	chr17:64283581-64283858(+)$1	277	174	181	12.5306
UUCUGAG	chr8:87185944-87186217(-)$1	273	227	234	12.5306
CUCUGAA	chr17:29109349-29109678(-)$1	329	309	316	13.2448
CUCUGAA	chr6:131330786-131331064(-)$1	278	237	244	13.2448
CUGUGAG	chr8:33028504-33028779(-)$1	275	68	75	13.0408
CUCUGAG	chr11:80291634-80291902(+)$1	268	14	21	16.8163
CUCUGAG	chrX:132674633-132674929(+)$1	296	135	142	16.8163
CUCUGAU	chr11:62366242-62366513(+)$1	271	28	35	13.1428
CUCUGGG	chr3:89236521-89236791(+)$1	270	205	212	13.2448

#otherMatches

#Struct PSSM
dddd555	chr11:69947583-69947851(+)$1	268	176	183	12.2244
dd[ccc[	chr1:182503801-182504079(+)$1	278	82	89	16.8163
cccchhh	chr8:26107145-26107416(-)$1	271	198	205	16.8163
E::dddd	chr11:75125734-75126033(-)$1	299	139	146	13.1428
::::::c	chr11:88826334-88826601(-)$1	267	218	225	16.8163
:BB{CCC	chr4:122729700-122729971(+)$1	271	19	26	12.2244
mmmmccc	chr14:22803805-22804073(-)$1	268	252	259	12.4285
qqqqqqc	chr8:126025782-126026058(+)$1	276	54	61	12.9387
ffaqqqq	chr15:90057860-90058150(+)$1	290	208	215	12.3265
fffff[c	chr8:107860182-107860450(-)$1	268	148	155	13.0408
~~GGGGG	chr17:23890646-23890918(-)$1	272	257	264	12.4285
FF::eee	chrY:439119-439399(-)$1	280	100	107	13.1428
IIIIILL	chr4:149018020-149018286(+)$1	266	51	58	13.1428
ccclllc	chr19:24758872-24759140(-)$1	268	184	191	12.3265
bb!!ccc	chr4:115772165-115772446(-)$1	281	137	144	13.1428
CC:dddd	chr11:97030334-97030603(-)$1	269	24	31	12.7346
gggg!!f	chr7:148599791-148600059(-)$1	268	206	213	13.2448
cccdddd	chrX:147431623-147431893(-)$1	270	49	56	16.8163
:hhhhhh	chr17:35152719-35152995(+)$1	276	228	235	13.2448
ggggggn	chr12:106199620-106199892(-)$1	272	43	50	13.2448
]ccc22e	chr11:95911393-95911684(-)$1	291	69	76	13.1428
:ffffff	chr3:88447584-88447871(+)$1	287	49	56	13.2448
e22gggg	chr6:142594277-142594544(-)$1	267	226	233	12.5306
::FFFFF	chr7:52677721-52678007(-)$1	286	123	130	13.0408
ffffccc	chr11:106122087-106122356(+)$1	269	231	238	12.2244
{EEEEEC	chr6:28462794-28463073(+)$1	279	45	52	13.2448
JJJJ::d	chr4:57964567-57964851(-)$1	284	203	210	13.1428
eeee555	chr4:116853100-116853368(-)$1	268	199	206	16.8163
:::ffff	chr1:19224039-19224310(+)$1	271	50	57	16.8163
##ddddn	chr8:87391660-87391928(+)$1	268	210	217	12.2244
oooooof	chr11:8448793-8449061(-)$1	268	179	186	12.4285
eemmmme	chr2:120361046-120361326(-)$1	280	111	118	13.1428
nnfffff	chrX:103026194-103026472(-)$1	278	268	275	13.2448
ddddddm	chr11:120458860-120459150(-)$1	290	45	52	12.7346
ddnnnnn	chr4:129233042-129233310(-)$1	268	65	72	13.1428
444eeee	chr11:8896763-8897031(-)$1	268	219	226	12.9387
=!!bb[d	chr17:85075412-85075680(-)$1	268	231	238	12.5306
eeee]ee	chr12:17556230-17556502(+)$1	272	154	161	13.1428
IIIIIII	chr8:74704396-74704674(+)$1	278	4	11	12.2244
77ggggg	chrX:98613547-98613822(-)$1	275	136	143	13.2448
:dddd[g	chr17:64283581-64283858(+)$1	277	174	181	12.5306
::::DDD	chr8:87185944-87186217(-)$1	273	227	234	12.5306
FFFFYYB	chr17:29109349-29109678(-)$1	329	309	316	13.2448
dddd22c	chr6:131330786-131331064(-)$1	278	237	244	13.2448
BBLLLBB	chr8:33028504-33028779(-)$1	275	68	75	13.0408
mmmmeee	chr11:80291634-80291902(+)$1	268	14	21	16.8163
nccceee	chrX:132674633-132674929(+)$1	296	135	142	16.8163
[ddddtt	chr11:62366242-62366513(+)$1	271	28	35	13.1428
DDGGGGG	chr3:89236521-89236791(+)$1	270	205	212	13.2448

#DB
))))...	chr11:69947583-69947851(+)$1	1	176	183	12.2244
((.(((.	chr1:182503801-182504079(+)$1	1	82	89	16.8163
)))))))	chr8:26107145-26107416(-)$1	1	198	205	16.8163
)..((((	chr11:75125734-75126033(-)$1	1	139	146	13.1428
......(	chr11:88826334-88826601(-)$1	1	218	225	16.8163
.((.(((	chr4:122729700-122729971(+)$1	1	19	26	12.2244
....)))	chr14:22803805-22804073(-)$1	1	252	259	12.4285
......)	chr8:126025782-126026058(+)$1	1	54	61	12.9387
(((....	chr15:90057860-90058150(+)$1	1	208	215	12.3265
(((((.(	chr8:107860182-107860450(-)$1	1	148	155	13.0408
..)))))	chr17:23890646-23890918(-)$1	1	257	264	12.4285
((..(((	chrY:439119-439399(-)$1	1	100	107	13.1428
(((((..	chr4:149018020-149018286(+)$1	1	51	58	13.1428
(((...)	chr19:24758872-24759140(-)$1	1	184	191	12.3265
((..(((	chr4:115772165-115772446(-)$1	1	137	144	13.1428
((.((((	chr11:97030334-97030603(-)$1	1	24	31	12.7346
((((..(	chr7:148599791-148600059(-)$1	1	206	213	13.2448
(((((((	chrX:147431623-147431893(-)$1	1	49	56	16.8163
.((((((	chr17:35152719-35152995(+)$1	1	228	235	13.2448
((((((.	chr12:106199620-106199892(-)$1	1	43	50	13.2448
.)))..)	chr11:95911393-95911684(-)$1	1	69	76	13.1428
.((((((	chr3:88447584-88447871(+)$1	1	49	56	13.2448
)..))))	chr6:142594277-142594544(-)$1	1	226	233	12.5306
..)))))	chr7:52677721-52678007(-)$1	1	123	130	13.0408
))))(((	chr11:106122087-106122356(+)$1	1	231	238	12.2244
.((((((	chr6:28462794-28463073(+)$1	1	45	52	13.2448
((((..(	chr4:57964567-57964851(-)$1	1	203	210	13.1428
))))...	chr4:116853100-116853368(-)$1	1	199	206	16.8163
...((((	chr1:19224039-19224310(+)$1	1	50	57	16.8163
..((((.	chr8:87391660-87391928(+)$1	1	210	217	12.2244
......)	chr11:8448793-8449061(-)$1	1	179	186	12.4285
((....)	chr2:120361046-120361326(-)$1	1	111	118	13.1428
..)))))	chrX:103026194-103026472(-)$1	1	268	275	13.2448
))((((.	chr11:120458860-120459150(-)$1	1	45	52	12.7346
((.....	chr4:129233042-129233310(-)$1	1	65	72	13.1428
...))))	chr11:8896763-8897031(-)$1	1	219	226	12.9387
(..((.(	chr17:85075412-85075680(-)$1	1	231	238	12.5306
)))).))	chr12:17556230-17556502(+)$1	1	154	161	13.1428
(((((((	chr8:74704396-74704674(+)$1	1	4	11	12.2244
..)))))	chrX:98613547-98613822(-)$1	1	136	143	13.2448
.((((.(	chr17:64283581-64283858(+)$1	1	174	181	12.5306
....)))	chr8:87185944-87186217(-)$1	1	227	234	12.5306
))))..)	chr17:29109349-29109678(-)$1	1	309	316	13.2448
))))..)	chr6:131330786-131331064(-)$1	1	237	244	13.2448
((...((	chr8:33028504-33028779(-)$1	1	68	75	13.0408
....)))	chr11:80291634-80291902(+)$1	1	14	21	16.8163
.)))(((	chrX:132674633-132674929(+)$1	1	135	142	16.8163
.((((..	chr11:62366242-62366513(+)$1	1	28	35	13.1428
(((((((	chr3:89236521-89236791(+)$1	1	205	212	13.2448

#PSSM
C : 0.89	G : 0.04	U : 0.04	A : 0.02	
U : 0.95	A : 0.04	
C : 0.81	U : 0.08	G : 0.06	A : 0.04	
U : 0.91	A : 0.04	G : 0.02	C : 0.02	
G : 0.93	A : 0.02	U : 0.02	C : 0.02	
A : 0.83	G : 0.12	C : 0.02	U : 0.02	
G : 0.79	A : 0.08	C : 0.06	U : 0.06	

#score	662.0612244897967
#seq	49
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_UTR_m2_run2.nuc.txt

#NT
UCCGUGU	chr5:89210569-89210827(+)$1	258	126	133	12.5151
UCUGUCU	chr18:46664348-46664588(-)$1	240	220	227	12.8181
UCUGAGU	chr19:45606642-45606896(+)$1	254	87	94	12.2878
UUUGUGU	chr12:41572831-41573069(+)$1	238	220	227	13.8787
ACUGUGU	chr14:17263064-17263321(+)$1	257	231	238	13.3484
UCUGUGU	chr9:44445620-44445857(+)$1	237	130	137	17.1363
UUUGUGU	chr16:37888154-37888398(+)$1	244	1	8	13.8787
UCUCUGU	chr2:5219485-5219720(-)$1	235	130	137	13.3484
UCUGUGU	chr11:107798927-107799187(-)$1	260	210	217	17.1363
UUUGUGU	chr14:73762322-73762614(-)$1	292	63	70	13.8787
UCUGUCU	chr12:3248258-3248494(-)$1	236	109	116	12.8181
UCUGUGA	chr2:32164226-32164522(-)$1	296	55	62	12.8181
UCUGUGU	chr15:12114167-12114425(+)$1	258	76	83	17.1363
UCUGUGU	chr6:125171712-125171970(+)$1	258	181	188	17.1363
GCUGUGU	chr1:176765957-176766192(-)$1	235	11	18	13.3484
UUUGUGU	chr2:49628239-49628493(+)$1	254	89	96	13.8787
UUUGUGU	chr3:145554818-145555053(+)$1	235	0	7	13.8787
UCUCUGU	chr4:155386474-155386713(+)$1	239	24	31	13.3484
UGUGUGU	chr2:102624306-102624550(+)$1	244	54	61	13.4999
UGUGUGU	chr9:18117323-18117558(+)$1	235	66	73	13.4999
UGUGUGU	chr11:106641590-106641828(-)$1	238	103	110	13.4999
ACUGUGU	chr2:155216374-155216611(-)$1	237	27	34	13.3484
UUUGUGU	chr4:126421271-126421553(-)$1	282	139	146	13.8787
CCUGUGU	chr7:138056465-138056711(+)$1	246	222	229	13.3484
UCAGUGU	chr13:34994014-34994249(+)$1	235	196	203	12.6666
ACUGUGU	chr5:122904118-122904378(-)$1	260	209	216	13.3484
ucugUGU	chr12:86682950-86683192(-)$1	242	198	205	17.1363
UCUUUGU	chr3:32849173-32849408(-)$1	235	208	215	13.1969
CCUGUGU	chr13:110851792-110852038(-)$1	246	170	177	13.3484
UCUGUGU	chr4:6322126-6322363(+)$1	237	39	46	17.1363
UUUGUGU	chr2:62164323-62164568(+)$1	245	18	25	13.8787
UCUGUGG	chr19:7501384-7501627(-)$1	243	214	221	12.5909
UCUCUGU	chr15:98569475-98569735(-)$1	260	88	95	13.3484
GCUGUGU	chrX:149046529-149046767(-)$1	238	62	69	13.3484
ucugugu	chr11:77524382-77524622(+)$1	240	203	210	17.1363
UCUGUGU	chr10:107937088-107937398(-)$1	310	137	144	17.1363
UCUGUGA	chr9:115152025-115152263(-)$1	238	39	46	12.8181
UCUGUGA	chr11:4382365-4382603(-)$1	238	128	135	12.8181
GCUGUGU	chr8:98238544-98238790(+)$1	246	20	27	13.3484
ucugugu	chr4:57907111-57907347(+)$1	236	115	122	17.1363
GCUGUGU	chr2:102621818-102622058(+)$1	240	16	23	13.3484
UCUGUCU	chr13:110845916-110846208(-)$1	292	56	63	12.8181
ucugucu	chr8:26875471-26875707(-)$1	236	19	26	12.8181
UCUGUGU	chr5:136384869-136385127(-)$1	258	41	48	17.1363
UUUGUGU	chr5:17771193-17771449(-)$1	256	121	128	13.8787
UUUGUGU	chr2:32644013-32644306(-)$1	293	116	123	13.8787
ACUGUGU	chr11:118164722-118164957(-)$1	235	174	181	13.3484
UCUGUGU	chr10:79372729-79372968(-)$1	239	112	119	17.1363
UGUGUGU	chr3:120905623-120905868(-)$1	245	176	183	13.4999
UCUGUUU	chr15:12279560-12279814(+)$1	254	168	175	12.5909
CCUGUGU	chr13:98021044-98021281(+)$1	237	156	163	13.3484
UCUCUGU	chr8:107741475-107741715(+)$1	240	47	54	13.3484
UCUCUGU	chr9:75417347-75417608(-)$1	261	42	49	13.3484
UCUUUGU	chr2:138110729-138110976(+)$1	247	55	62	13.1969
UAUGUGU	chr12:16992165-16992435(+)$1	270	140	147	13.2727
UCAGUGU	chr13:110846323-110846597(-)$1	274	24	31	12.6666
UCUGUGU	chr15:82123950-82124187(+)$1	237	20	27	17.1363
UCUGUGU	chr2:181284221-181284484(+)$1	263	124	131	17.1363
CCUGUGU	chr16:96289023-96289283(-)$1	260	89	96	13.3484
UCAGUGU	chr12:11331969-11332250(-)$1	281	179	186	12.6666
UCUGUGU	chr9:58500334-58500635(+)$1	301	271	278	17.1363
UCUCUGU	chr11:97578064-97578315(-)$1	251	140	147	13.3484
UCUUUGU	chr2:136607209-136607513(+)$1	304	172	179	13.1969
UCUGUGU	chr14:60920576-60920816(+)$1	240	66	73	17.1363
UCUGUGA	chr16:45382357-45382593(-)$1	236	12	19	12.8181

#otherMatches

#Struct PSSM
qqqqqdd	chr3:31017665-31017904(+)$1	239	58	65	13.1969
cccpppp	chr5:89210569-89210827(+)$1	258	126	133	12.5151
dqqqqqq	chr18:46664348-46664588(-)$1	240	220	227	12.8181
JJJJJJJ	chr19:45606642-45606896(+)$1	254	87	94	12.2878
llleeee	chr12:41572831-41573069(+)$1	238	220	227	13.8787
]eeeee]	chr14:17263064-17263321(+)$1	257	231	238	13.3484
eeeee22	chr9:44445620-44445857(+)$1	237	130	137	17.1363
:::::::	chr16:37888154-37888398(+)$1	244	1	8	13.8787
d####dd	chr2:5219485-5219720(-)$1	235	130	137	13.3484
::bb[dd	chr11:107798927-107799187(-)$1	260	210	217	17.1363
:::dddd	chr14:73762322-73762614(-)$1	292	63	70	13.8787
d!!eeee	chr12:3248258-3248494(-)$1	236	109	116	12.8181
"ddddoo	chr2:32164226-32164522(-)$1	296	55	62	12.8181
nccc]dd	chr15:12114167-12114425(+)$1	258	76	83	17.1363
:ddddoo	chr6:125171712-125171970(+)$1	258	181	188	17.1363
eeeee[f	chr1:176765957-176766192(-)$1	235	11	18	13.3484
^^^^^^^	chr2:49628239-49628493(+)$1	254	89	96	13.8787
::::::d	chr3:145554818-145555053(+)$1	235	0	7	13.8787
ccnnnnn	chr4:155386474-155386713(+)$1	239	24	31	13.3484
=======	chr2:102624306-102624550(+)$1	244	54	61	13.4999
:::bb!!	chr9:18117323-18117558(+)$1	235	66	73	13.4999
eennnnn	chr11:106641590-106641828(-)$1	238	103	110	13.4999
fffffrr	chr2:155216374-155216611(-)$1	237	27	34	13.3484
ggggg[b	chr4:126421271-126421553(-)$1	282	139	146	13.8787
IIIIIII	chr7:138056465-138056711(+)$1	246	222	229	13.3484
dd:::::	chr13:34994014-34994249(+)$1	235	196	203	12.6666
d4444bb	chr5:122904118-122904378(-)$1	260	209	216	13.3484
:::IIII	chr12:86682950-86683192(-)$1	242	198	205	17.1363
c4444a]	chr3:32849173-32849408(-)$1	235	208	215	13.1969
ddd$$$$	chr13:110851792-110852038(-)$1	246	170	177	13.3484
::dddd[	chr4:6322126-6322363(+)$1	237	39	46	17.1363
NNNDDDD	chr2:62164323-62164568(+)$1	245	18	25	13.8787
qqqqqqd	chr19:7501384-7501627(-)$1	243	214	221	12.5909
mmmccc8	chr15:98569475-98569735(-)$1	260	88	95	13.3484
FFFFFF}	chrX:149046529-149046767(-)$1	238	62	69	13.3484
[attttt	chr11:77524382-77524622(+)$1	240	203	210	17.1363
ddd!!bb	chr10:107937088-107937398(-)$1	310	137	144	17.1363
cccbb[c	chr9:115152025-115152263(-)$1	238	39	46	12.8181
HHHHddd	chr11:4382365-4382603(-)$1	238	128	135	12.8181
::DDDD{	chr8:98238544-98238790(+)$1	246	20	27	13.3484
ggg[a""	chr4:57907111-57907347(+)$1	236	115	122	17.1363
dddd[bb	chr2:102621818-102622058(+)$1	240	16	23	13.3484
ffff:::	chr13:110845916-110846208(-)$1	292	56	63	12.8181
:::GGGG	chr8:26875471-26875707(-)$1	236	19	26	12.8181
qqqqqqq	chr5:136384869-136385127(-)$1	258	41	48	17.1363
hhhhh%%	chr5:17771193-17771449(-)$1	256	121	128	13.8787
:ffffff	chr2:32644013-32644306(-)$1	293	116	123	13.8787
cclllcc	chr11:118164722-118164957(-)$1	235	174	181	13.3484
"""bb!!	chr10:79372729-79372968(-)$1	239	112	119	17.1363
ee:::::	chr3:120905623-120905868(-)$1	245	176	183	13.4999
:::::::	chr15:12279560-12279814(+)$1	254	168	175	12.5909
lgggggg	chr13:98021044-98021281(+)$1	237	156	163	13.3484
LLLEEEE	chr8:107741475-107741715(+)$1	240	47	54	13.3484
ELLLEEE	chr9:75417347-75417608(-)$1	261	42	49	13.3484
ffffff#	chr2:138110729-138110976(+)$1	247	55	62	13.1969
oofffff	chr12:16992165-16992435(+)$1	270	140	147	13.2727
ff"""ff	chr13:110846323-110846597(-)$1	274	24	31	12.6666
BB{CCC:	chr15:82123950-82124187(+)$1	237	20	27	17.1363
]a]ccc2	chr2:181284221-181284484(+)$1	263	124	131	17.1363
xccc22f	chr16:96289023-96289283(-)$1	260	89	96	13.3484
ee22ccc	chr12:11331969-11332250(-)$1	281	179	186	12.6666
EEEEE//	chr9:58500334-58500635(+)$1	301	271	278	17.1363
cc]eeee	chr11:97578064-97578315(-)$1	251	140	147	13.3484
cc[ffff	chr2:136607209-136607513(+)$1	304	172	179	13.1969
ppppddd	chr14:60920576-60920816(+)$1	240	66	73	17.1363
&&&dddd	chr16:45382357-45382593(-)$1	236	12	19	12.8181

#DB
.....))	chr3:31017665-31017904(+)$1	1	58	65	13.1969
(((....	chr5:89210569-89210827(+)$1	1	126	133	12.5151
(......	chr18:46664348-46664588(-)$1	1	220	227	12.8181
(((((((	chr19:45606642-45606896(+)$1	1	87	94	12.2878
...))))	chr12:41572831-41573069(+)$1	1	220	227	13.8787
.))))).	chr14:17263064-17263321(+)$1	1	231	238	13.3484
)))))..	chr9:44445620-44445857(+)$1	1	130	137	17.1363
.......	chr16:37888154-37888398(+)$1	1	1	8	13.8787
(....((	chr2:5219485-5219720(-)$1	1	130	137	13.3484
..((.((	chr11:107798927-107799187(-)$1	1	210	217	17.1363
...((((	chr14:73762322-73762614(-)$1	1	63	70	13.8787
(..((((	chr12:3248258-3248494(-)$1	1	109	116	12.8181
.((((..	chr2:32164226-32164522(-)$1	1	55	62	12.8181
.))).))	chr15:12114167-12114425(+)$1	1	76	83	17.1363
.((((..	chr6:125171712-125171970(+)$1	1	181	188	17.1363
(((((.(	chr1:176765957-176766192(-)$1	1	11	18	13.3484
.......	chr2:49628239-49628493(+)$1	1	89	96	13.8787
......(	chr3:145554818-145555053(+)$1	1	0	7	13.8787
((.....	chr4:155386474-155386713(+)$1	1	24	31	13.3484
(((((((	chr2:102624306-102624550(+)$1	1	54	61	13.4999
...((..	chr9:18117323-18117558(+)$1	1	66	73	13.4999
((.....	chr11:106641590-106641828(-)$1	1	103	110	13.4999
(((((..	chr2:155216374-155216611(-)$1	1	27	34	13.3484
(((((.(	chr4:126421271-126421553(-)$1	1	139	146	13.8787
)))))))	chr7:138056465-138056711(+)$1	1	222	229	13.3484
)).....	chr13:34994014-34994249(+)$1	1	196	203	12.6666
)....))	chr5:122904118-122904378(-)$1	1	209	216	13.3484
...))))	chr12:86682950-86683192(-)$1	1	198	205	17.1363
)....).	chr3:32849173-32849408(-)$1	1	208	215	13.1969
(((....	chr13:110851792-110852038(-)$1	1	170	177	13.3484
..((((.	chr4:6322126-6322363(+)$1	1	39	46	17.1363
...((((	chr2:62164323-62164568(+)$1	1	18	25	13.8787
......)	chr19:7501384-7501627(-)$1	1	214	221	12.5909
...))).	chr15:98569475-98569735(-)$1	1	88	95	13.3484
)))))).	chrX:149046529-149046767(-)$1	1	62	69	13.3484
.(.....	chr11:77524382-77524622(+)$1	1	203	210	17.1363
(((..((	chr10:107937088-107937398(-)$1	1	137	144	17.1363
(((((.(	chr9:115152025-115152263(-)$1	1	39	46	12.8181
(((((((	chr11:4382365-4382603(-)$1	1	128	135	12.8181
..((((.	chr8:98238544-98238790(+)$1	1	20	27	13.3484
(((.(..	chr4:57907111-57907347(+)$1	1	115	122	17.1363
((((.((	chr2:102621818-102622058(+)$1	1	16	23	13.3484
))))...	chr13:110845916-110846208(-)$1	1	56	63	12.8181
...((((	chr8:26875471-26875707(-)$1	1	19	26	12.8181
.......	chr5:136384869-136385127(-)$1	1	41	48	17.1363
(((((..	chr5:17771193-17771449(-)$1	1	121	128	13.8787
.((((((	chr2:32644013-32644306(-)$1	1	116	123	13.8787
((...))	chr11:118164722-118164957(-)$1	1	174	181	13.3484
...((..	chr10:79372729-79372968(-)$1	1	112	119	17.1363
)).....	chr3:120905623-120905868(-)$1	1	176	183	13.4999
.......	chr15:12279560-12279814(+)$1	1	168	175	12.5909
.))))))	chr13:98021044-98021281(+)$1	1	156	163	13.3484
...((((	chr8:107741475-107741715(+)$1	1	47	54	13.3484
(...(((	chr9:75417347-75417608(-)$1	1	42	49	13.3484
((((((.	chr2:138110729-138110976(+)$1	1	55	62	13.1969
..)))))	chr12:16992165-16992435(+)$1	1	140	147	13.2727
((...((	chr13:110846323-110846597(-)$1	1	24	31	12.6666
((.(((.	chr15:82123950-82124187(+)$1	1	20	27	17.1363
.).))).	chr2:181284221-181284484(+)$1	1	124	131	17.1363
.)))..)	chr16:96289023-96289283(-)$1	1	89	96	13.3484
))..)))	chr12:11331969-11332250(-)$1	1	179	186	12.6666
)))))..	chr9:58500334-58500635(+)$1	1	271	278	17.1363
)).))))	chr11:97578064-97578315(-)$1	1	140	147	13.3484
((.((((	chr2:136607209-136607513(+)$1	1	172	179	13.1969
....)))	chr14:60920576-60920816(+)$1	1	66	73	17.1363
...((((	chr16:45382357-45382593(-)$1	1	12	19	12.8181

#PSSM
U : 0.75	A : 0.06	G : 0.06	C : 0.06	u : 0.06	
C : 0.72	U : 0.13	G : 0.06	c : 0.06	A : 0.01	
U : 0.87	u : 0.06	A : 0.04	C : 0.01	
G : 0.78	C : 0.09	U : 0.06	g : 0.06	
U : 0.93	u : 0.04	A : 0.01	
G : 0.89	C : 0.04	g : 0.03	c : 0.01	U : 0.01	
U : 0.87	A : 0.06	u : 0.04	G : 0.01	

#score	932.8181818181808
#seq	66
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012a_mm9_CDS_m3_run2.nuc.txt

#NT
GGCUGA	chr19:55154797-55155024(-)$1	227	7	13	11.7931
GGCUGA	chr11:98018319-98018539(-)$1	220	31	37	11.7931
GGCUGA	chr1:95402059-95402279(+)$1	220	112	118	11.7931
GGCUGG	chr8:47296077-47296297(-)$1	220	140	146	14.9827
GUCUGG	chr8:67197818-67198038(-)$1	220	26	32	11.0172
GGCUGG	chr6:116576382-116576602(-)$1	220	204	210	14.9827
GGCUGG	chr9:21193005-21193225(+)$1	220	186	192	14.9827
UGCUGG	chr12:45396901-45397130(+)$1	229	1	7	11.6206
GGCUGU	chr19:45826554-45826774(-)$1	220	72	78	11.4482
UGCUGG	chr19:38695094-38695314(+)$1	220	205	211	11.6206
GGCUGU	chr13:113294364-113294600(+)$1	236	128	134	11.4482
GACUGG	chr6:56686669-56686889(+)$1	220	73	79	11.0172
GACUGG	chr19:53444628-53444851(+)$1	223	12	18	11.0172
GGCUGG	chr8:63384378-63384599(+)$1	221	98	104	14.9827
AGCUGG	chr10:70826151-70826371(+)$1	220	112	118	11.3620
GGCUGG	chr4:147310620-147310845(-)$1	225	205	211	14.9827
GCCUGG	chr9:26889987-26890207(+)$1	220	17	23	11.0172
AGCUGG	chr1:34285636-34285859(+)$1	223	57	63	11.3620
GUCUGG	chr11:105638018-105638238(+)$1	220	167	173	11.0172
GGCUGG	chr8:3542298-3542519(+)$1	221	35	41	14.9827
GGCUGG	chr6:88839796-88840036(-)$1	240	176	182	14.9827
GUCUGG	chr9:75003881-75004101(+)$1	220	20	26	11.0172
CGCUGG	chr18:5049179-5049428(+)$1	249	81	87	11.1034
GGCUGG	chr15:80077097-80077317(+)$1	220	158	164	14.9827
UGCUGG	chr1:84743660-84743887(-)$1	227	35	41	11.6206
GGCUGG	chr19:57781363-57781583(+)$1	220	97	103	14.9827
GACUGG	chr1:190796168-190796394(-)$1	226	119	125	11.0172
GGCUGG	chr12:109427204-109427424(+)$1	220	96	102	14.9827
GGCUGC	chr2:139996497-139996720(-)$1	223	85	91	11.5344
GCCUGG	chr8:13294839-13295059(+)$1	220	97	103	11.0172
UGCUGG	chr18:12853663-12853883(+)$1	220	42	48	11.6206
AGCUGG	chr1:24788488-24788712(+)$1	224	214	220	11.3620
GGCUGG	chr4:116662940-116663160(-)$1	220	120	126	14.9827
GGCUGG	chr17:24558653-24558873(+)$1	220	180	186	14.9827
GGCUGG	chr6:85417496-85417716(+)$1	220	90	96	14.9827
AGCUGG	chr7:124692374-124692594(+)$1	220	186	192	11.3620
GGCUGU	chr1:120229254-120229487(+)$1	233	14	20	11.4482
GGCUGG	chr5:104909126-104909346(+)$1	220	188	194	14.9827
GGCUGA	chr7:150252049-150252271(+)$1	222	29	35	11.7931
GGCUGA	chr9:70616698-70616918(+)$1	220	62	68	11.7931
GCCUGG	chr11:117583305-117583525(+)$1	220	64	70	11.0172
UGCUGG	chr17:37147059-37147306(+)$1	247	123	129	11.6206
GGCUGG	chr11:115799217-115799440(+)$1	223	179	185	14.9827
GGCUGG	chr11:71602361-71602581(+)$1	220	128	134	14.9827
GGCUGC	chr4:46511899-46512120(+)$1	221	168	174	11.5344
UGCUGG	chr13:32908202-32908422(+)$1	220	14	20	11.6206
GGCUGG	chr2:148509896-148510118(+)$1	222	123	129	14.9827
GGCUGG	chrX:148705878-148706098(+)$1	220	157	163	14.9827
GGCUGA	chr15:103071488-103071708(+)$1	220	65	71	11.7931
UGCUGG	chr5:145564968-145565188(+)$1	220	39	45	11.6206
GGCUGG	chr15:102151039-102151259(+)$1	220	132	138	14.9827
GGCUGG	chr2:127421520-127421740(+)$1	220	49	55	14.9827
GGCUGC	chr3:68422510-68422730(+)$1	220	179	185	11.5344
GGCUGG	chr9:72565993-72566213(+)$1	220	34	40	14.9827
GGCUGC	chr8:86246473-86246711(+)$1	238	20	26	11.5344
ggcuGA	chr3:51245746-51245966(+)$1	220	25	31	11.7931
GGCUGG	chr2:70803588-70803825(-)$1	237	114	120	14.9827

#otherMatches

#Struct PSSM
=hhhhh	chr9:51629301-51629521(+)$1	220	81	87	14.9827
DDD{EE	chr19:55154797-55155024(-)$1	227	7	13	11.7931
dccc[b	chr11:98018319-98018539(-)$1	220	31	37	11.7931
####dd	chr1:95402059-95402279(+)$1	220	112	118	11.7931
nncccF	chr8:47296077-47296297(-)$1	220	140	146	14.9827
eee[dd	chr8:67197818-67198038(-)$1	220	26	32	11.0172
ssssss	chr6:116576382-116576602(-)$1	220	204	210	14.9827
ggggnn	chr9:21193005-21193225(+)$1	220	186	192	14.9827
::::GG	chr12:45396901-45397130(+)$1	229	1	7	11.6206
ffff""	chr19:45826554-45826774(-)$1	220	72	78	11.4482
mbb:FF	chr19:38695094-38695314(+)$1	220	205	211	11.6206
%eeeee	chr13:113294364-113294600(+)$1	236	128	134	11.4482
!ggggg	chr6:56686669-56686889(+)$1	220	73	79	11.0172
D{DDDD	chr19:53444628-53444851(+)$1	223	12	18	11.0172
gdddd#	chr8:63384378-63384599(+)$1	221	98	104	14.9827
:FFFFF	chr10:70826151-70826371(+)$1	220	112	118	11.3620
EEEECC	chr4:147310620-147310845(-)$1	225	205	211	14.9827
KGGGGG	chr9:26889987-26890207(+)$1	220	17	23	11.0172
YYEEEE	chr1:34285636-34285859(+)$1	223	57	63	11.3620
!a[ccc	chr11:105638018-105638238(+)$1	220	167	173	11.0172
CCDDDD	chr8:3542298-3542519(+)$1	221	35	41	14.9827
nnnnnc	chr6:88839796-88840036(-)$1	240	176	182	14.9827
####ff	chr9:75003881-75004101(+)$1	220	20	26	11.0172
2eeeee	chr18:5049179-5049428(+)$1	249	81	87	11.1034
gggmmm	chr15:80077097-80077317(+)$1	220	158	164	14.9827
cccddd	chr1:84743660-84743887(-)$1	227	35	41	11.6206
HHHHHH	chr19:57781363-57781583(+)$1	220	97	103	14.9827
HHHHZZ	chr1:190796168-190796394(-)$1	226	119	125	11.0172
3eeeee	chr12:109427204-109427424(+)$1	220	96	102	14.9827
gggggg	chr2:139996497-139996720(-)$1	223	85	91	11.5344
!!eeee	chr8:13294839-13295059(+)$1	220	97	103	11.0172
HHKKDD	chr18:12853663-12853883(+)$1	220	42	48	11.6206
:EEEEE	chr1:24788488-24788712(+)$1	224	214	220	11.3620
ee!!dd	chr4:116662940-116663160(-)$1	220	120	126	14.9827
f[ccc%	chr17:24558653-24558873(+)$1	220	180	186	14.9827
hhhhqq	chr6:85417496-85417716(+)$1	220	90	96	14.9827
dbbccc	chr7:124692374-124692594(+)$1	220	186	192	11.3620
ffccc#	chr1:120229254-120229487(+)$1	233	14	20	11.4482
gg22bb	chr5:104909126-104909346(+)$1	220	188	194	14.9827
eeeee[	chr7:150252049-150252271(+)$1	222	29	35	11.7931
eeeee5	chr9:70616698-70616918(+)$1	220	62	68	11.7931
nccc44	chr11:117583305-117583525(+)$1	220	64	70	11.0172
iiiiii	chr17:37147059-37147306(+)$1	247	123	129	11.6206
GGGGGG	chr11:115799217-115799440(+)$1	223	179	185	14.9827
fffooo	chr11:71602361-71602581(+)$1	220	128	134	14.9827
fffff]	chr4:46511899-46512120(+)$1	221	168	174	11.5344
pppppe	chr13:32908202-32908422(+)$1	220	14	20	11.6206
gggeee	chr2:148509896-148510118(+)$1	222	123	129	14.9827
dddd:b	chrX:148705878-148706098(+)$1	220	157	163	14.9827
FFYYCC	chr15:103071488-103071708(+)$1	220	65	71	11.7931
""bboo	chr5:145564968-145565188(+)$1	220	39	45	11.6206
eeee!!	chr15:102151039-102151259(+)$1	220	132	138	14.9827
fffff"	chr2:127421520-127421740(+)$1	220	49	55	14.9827
::::::	chr3:68422510-68422730(+)$1	220	179	185	11.5344
DD{BBe	chr9:72565993-72566213(+)$1	220	34	40	14.9827
DDD{FF	chr8:86246473-86246711(+)$1	238	20	26	11.5344
EEEEPP	chr3:51245746-51245966(+)$1	220	25	31	11.7931
ff]ccc	chr2:70803588-70803825(-)$1	237	114	120	14.9827

#DB
((((((	chr9:51629301-51629521(+)$1	1	81	87	14.9827
(((.((	chr19:55154797-55155024(-)$1	1	7	13	11.7931
((((.(	chr11:98018319-98018539(-)$1	1	31	37	11.7931
....((	chr1:95402059-95402279(+)$1	1	112	118	11.7931
..))))	chr8:47296077-47296297(-)$1	1	140	146	14.9827
(((.((	chr8:67197818-67198038(-)$1	1	26	32	11.0172
......	chr6:116576382-116576602(-)$1	1	204	210	14.9827
((((..	chr9:21193005-21193225(+)$1	1	186	192	14.9827
....((	chr12:45396901-45397130(+)$1	1	1	7	11.6206
((((..	chr19:45826554-45826774(-)$1	1	72	78	11.4482
.)).))	chr19:38695094-38695314(+)$1	1	205	211	11.6206
.(((((	chr13:113294364-113294600(+)$1	1	128	134	11.4482
.(((((	chr6:56686669-56686889(+)$1	1	73	79	11.0172
(.((((	chr19:53444628-53444851(+)$1	1	12	18	11.0172
(((((.	chr8:63384378-63384599(+)$1	1	98	104	14.9827
.)))))	chr10:70826151-70826371(+)$1	1	112	118	11.3620
))))))	chr4:147310620-147310845(-)$1	1	205	211	14.9827
.(((((	chr9:26889987-26890207(+)$1	1	17	23	11.0172
..))))	chr1:34285636-34285859(+)$1	1	57	63	11.3620
.(.(((	chr11:105638018-105638238(+)$1	1	167	173	11.0172
((((((	chr8:3542298-3542519(+)$1	1	35	41	14.9827
.....)	chr6:88839796-88840036(-)$1	1	176	182	14.9827
....((	chr9:75003881-75004101(+)$1	1	20	26	11.0172
.)))))	chr18:5049179-5049428(+)$1	1	81	87	11.1034
(((...	chr15:80077097-80077317(+)$1	1	158	164	14.9827
))))))	chr1:84743660-84743887(-)$1	1	35	41	11.6206
((((((	chr19:57781363-57781583(+)$1	1	97	103	14.9827
))))..	chr1:190796168-190796394(-)$1	1	119	125	11.0172
.)))))	chr12:109427204-109427424(+)$1	1	96	102	14.9827
((((((	chr2:139996497-139996720(-)$1	1	85	91	11.5344
..((((	chr8:13294839-13295059(+)$1	1	97	103	11.0172
((..((	chr18:12853663-12853883(+)$1	1	42	48	11.6206
.)))))	chr1:24788488-24788712(+)$1	1	214	220	11.3620
((..((	chr4:116662940-116663160(-)$1	1	120	126	14.9827
(.(((.	chr17:24558653-24558873(+)$1	1	180	186	14.9827
((((..	chr6:85417496-85417716(+)$1	1	90	96	14.9827
))))))	chr7:124692374-124692594(+)$1	1	186	192	11.3620
(((((.	chr1:120229254-120229487(+)$1	1	14	20	11.4482
))..))	chr5:104909126-104909346(+)$1	1	188	194	14.9827
(((((.	chr7:150252049-150252271(+)$1	1	29	35	11.7931
))))).	chr9:70616698-70616918(+)$1	1	62	68	11.7931
.)))..	chr11:117583305-117583525(+)$1	1	64	70	11.0172
((((((	chr17:37147059-37147306(+)$1	1	123	129	11.6206
))))))	chr11:115799217-115799440(+)$1	1	179	185	14.9827
(((...	chr11:71602361-71602581(+)$1	1	128	134	14.9827
))))).	chr4:46511899-46512120(+)$1	1	168	174	11.5344
.....)	chr13:32908202-32908422(+)$1	1	14	20	11.6206
))))))	chr2:148509896-148510118(+)$1	1	123	129	14.9827
)))).(	chrX:148705878-148706098(+)$1	1	157	163	14.9827
))..))	chr15:103071488-103071708(+)$1	1	65	71	11.7931
..((..	chr5:145564968-145565188(+)$1	1	39	45	11.6206
((((..	chr15:102151039-102151259(+)$1	1	132	138	14.9827
(((((.	chr2:127421520-127421740(+)$1	1	49	55	14.9827
......	chr3:68422510-68422730(+)$1	1	179	185	11.5344
((.(((	chr9:72565993-72566213(+)$1	1	34	40	14.9827
(((.((	chr8:86246473-86246711(+)$1	1	20	26	11.5344
((((..	chr3:51245746-51245966(+)$1	1	25	31	11.7931
)).)))	chr2:70803588-70803825(-)$1	1	114	120	14.9827

#PSSM
G : 0.77	U : 0.12	A : 0.06	C : 0.01	g : 0.01	
G : 0.82	U : 0.05	A : 0.05	C : 0.05	g : 0.01	
C : 0.98	c : 0.01	
U : 0.98	u : 0.01	
G : 1.00	
G : 0.75	A : 0.12	C : 0.06	U : 0.05	

#score	744.689655172414
#seq	58
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Chi2009_mm9_UTR_m1_run2.nuc.txt

#NT
CUGUG	chr19:46731696-46731955(+)$1	259	1	6	15.0000
CUGUG	chr7:104561636-104561919(-)$1	283	11	16	15.0000
CUGUG	chr17:37210286-37210545(+)$1	259	90	95	15.0000
CUGUG	chr11:86313577-86313829(-)$1	252	105	110	15.0000
CUGUG	chr5:137735518-137735767(+)$1	249	178	183	15.0000
CUGUG	chr1:20927273-20927601(+)$1	328	52	57	15.0000
CUGUG	chr11:3242132-3242377(+)$1	245	143	148	15.0000
CUGUG	chr12:88448165-88448425(-)$1	260	49	54	15.0000
CUGUG	chr1:174203794-174204064(-)$1	270	22	27	15.0000
CUGUG	chr10:128107392-128107673(-)$1	281	224	229	15.0000
cugug	chr9:4417847-4418136(-)$1	289	100	105	15.0000
cugug	chr2:103294240-103294498(-)$1	258	187	192	15.0000
CUGUG	chr11:119863635-119863893(+)$1	258	71	76	15.0000
CUGUG	chr6:114197718-114197982(+)$1	264	154	159	15.0000
CUGUG	chr2:73746449-73746750(-)$1	301	152	157	15.0000
CUGUG	chr11:106642296-106642571(-)$1	275	158	163	15.0000
CUGUG	chr12:91965509-91965787(-)$1	278	247	252	15.0000
CUGUG	chr9:52485465-52485761(-)$1	296	141	146	15.0000
CUGUG	chr5:24369223-24369464(-)$1	241	46	51	15.0000
CUGUG	chr2:164250091-164250342(-)$1	251	46	51	15.0000
CUGUG	chr15:77590914-77591338(-)$1	424	40	45	15.0000
CUGUG	chr17:17665147-17665425(-)$1	278	89	94	15.0000
CUGUG	chr9:34843313-34843569(+)$1	256	234	239	15.0000
CUGUG	chr8:73999479-73999766(+)$1	287	39	44	15.0000
CUGUG	chr5:33135689-33135952(-)$1	263	52	57	15.0000
CUGUG	chr8:9989548-9989806(+)$1	258	91	96	15.0000
cugug	chr7:53352452-53352738(-)$1	286	78	83	15.0000
CUGUG	chrX:131338933-131339184(-)$1	251	123	128	15.0000
CUGUG	chr11:58997333-58997585(-)$1	252	30	35	15.0000
CUGUG	chr4:59765826-59766065(+)$1	239	12	17	15.0000
CUGUG	chr13:112536730-112537187(-)$1	457	29	34	15.0000
CUGUG	chr15:79191174-79191419(-)$1	245	171	176	15.0000
CUGUG	chr19:53321174-53321427(+)$1	253	1	6	15.0000
CUGUG	chr7:125262558-125262910(-)$1	352	80	85	15.0000
CUGUG	chr10:114727549-114727812(-)$1	263	19	24	15.0000
CUGUG	chr18:84264637-84264886(+)$1	249	83	88	15.0000
CUGUG	chr12:4840108-4840348(-)$1	240	35	40	15.0000
CUGUG	chr6:129491827-129492080(+)$1	253	128	133	15.0000
CUGUG	chr7:28317025-28317395(-)$1	370	245	250	15.0000
CUGUG	chr13:9171588-9171965(+)$1	377	160	165	15.0000
CUGUG	chrY:364893-365128(+)$1	235	57	62	15.0000
CUGUG	chr2:6463516-6463776(-)$1	260	143	148	15.0000
CUGUG	chr1:156242916-156243177(-)$1	261	194	199	15.0000
CUGUG	chr3:85464723-85464973(-)$1	250	42	47	15.0000
CUGUG	chr4:106261540-106261795(+)$1	255	7	12	15.0000
cugug	chrX:160391097-160391350(-)$1	253	161	166	15.0000
CUGUG	chr3:8930862-8931121(-)$1	259	79	84	15.0000
CUGUG	chr17:87232476-87232792(+)$1	316	49	54	15.0000
CUGUG	chr3:89903728-89903979(+)$1	251	242	247	15.0000
CUGUG	chr1:191694874-191695119(+)$1	245	68	73	15.0000
CUGUG	chr3:138588884-138589120(-)$1	236	115	120	15.0000
CUGUG	chr18:20832128-20832457(+)$1	329	258	263	15.0000
CUGUG	chr1:174126834-174127098(-)$1	264	150	155	15.0000
CUGUG	chr6:115224974-115225238(+)$1	264	230	235	15.0000

#otherMatches

#Struct PSSM
LLEEE	chr2:33588522-33588782(-)$1	260	67	72	15.0000
:CCC{	chr19:46731696-46731955(+)$1	259	1	6	15.0000
B{A{B	chr7:104561636-104561919(-)$1	283	11	16	15.0000
"eeee	chr17:37210286-37210545(+)$1	259	90	95	15.0000
]dddd	chr11:86313577-86313829(-)$1	252	105	110	15.0000
33ccc	chr5:137735518-137735767(+)$1	249	178	183	15.0000
BB{EE	chr1:20927273-20927601(+)$1	328	52	57	15.0000
EEE}F	chr11:3242132-3242377(+)$1	245	143	148	15.0000
eeeee	chr12:88448165-88448425(-)$1	260	49	54	15.0000
FFFFF	chr1:174203794-174204064(-)$1	270	22	27	15.0000
C}FFF	chr10:128107392-128107673(-)$1	281	224	229	15.0000
4444d	chr9:4417847-4418136(-)$1	289	100	105	15.0000
ZDDDD	chr2:103294240-103294498(-)$1	258	187	192	15.0000
fffff	chr11:119863635-119863893(+)$1	258	71	76	15.0000
dddd!	chr6:114197718-114197982(+)$1	264	154	159	15.0000
fffff	chr2:73746449-73746750(-)$1	301	152	157	15.0000
fffff	chr11:106642296-106642571(-)$1	275	158	163	15.0000
ddddn	chr12:91965509-91965787(-)$1	278	247	252	15.0000
]bb]a	chr9:52485465-52485761(-)$1	296	141	146	15.0000
eeeeq	chr5:24369223-24369464(-)$1	241	46	51	15.0000
LLFFF	chr2:164250091-164250342(-)$1	251	46	51	15.0000
dddd[	chr15:77590914-77591338(-)$1	424	40	45	15.0000
cc[as	chr17:17665147-17665425(-)$1	278	89	94	15.0000
ldddd	chr9:34843313-34843569(+)$1	256	234	239	15.0000
=====	chr8:73999479-73999766(+)$1	287	39	44	15.0000
dd22a	chr5:33135689-33135952(-)$1	263	52	57	15.0000
eee[e	chr8:9989548-9989806(+)$1	258	91	96	15.0000
b]ccc	chr7:53352452-53352738(-)$1	286	78	83	15.0000
##ddd	chrX:131338933-131339184(-)$1	251	123	128	15.0000
KKA{D	chr11:58997333-58997585(-)$1	252	30	35	15.0000
B{EEE	chr4:59765826-59766065(+)$1	239	12	17	15.0000
6666g	chr13:112536730-112537187(-)$1	457	29	34	15.0000
:::::	chr15:79191174-79191419(-)$1	245	171	176	15.0000
DDDDg	chr19:53321174-53321427(+)$1	253	1	6	15.0000
6666e	chr7:125262558-125262910(-)$1	352	80	85	15.0000
AKKCC	chr10:114727549-114727812(-)$1	263	19	24	15.0000
ddddn	chr18:84264637-84264886(+)$1	249	83	88	15.0000
HHHHH	chr12:4840108-4840348(-)$1	240	35	40	15.0000
ddddc	chr6:129491827-129492080(+)$1	253	128	133	15.0000
a]eee	chr7:28317025-28317395(-)$1	370	245	250	15.0000
ggg]c	chr13:9171588-9171965(+)$1	377	160	165	15.0000
333dd	chrY:364893-365128(+)$1	235	57	62	15.0000
::ddd	chr2:6463516-6463776(-)$1	260	143	148	15.0000
fffff	chr1:156242916-156243177(-)$1	261	194	199	15.0000
qqeee	chr3:85464723-85464973(-)$1	250	42	47	15.0000
GGGGG	chr4:106261540-106261795(+)$1	255	7	12	15.0000
qeeee	chrX:160391097-160391350(-)$1	253	161	166	15.0000
mmmmc	chr3:8930862-8931121(-)$1	259	79	84	15.0000
cc[ee	chr17:87232476-87232792(+)$1	316	49	54	15.0000
FFFFF	chr3:89903728-89903979(+)$1	251	242	247	15.0000
""ccc	chr1:191694874-191695119(+)$1	245	68	73	15.0000
====h	chr3:138588884-138589120(-)$1	236	115	120	15.0000
ccc""	chr18:20832128-20832457(+)$1	329	258	263	15.0000
ffffd	chr1:174126834-174127098(-)$1	264	150	155	15.0000
B????	chr6:115224974-115225238(+)$1	264	230	235	15.0000

#DB
..(((	chr2:33588522-33588782(-)$1	1	67	72	15.0000
.(((.	chr19:46731696-46731955(+)$1	1	1	6	15.0000
(.(.(	chr7:104561636-104561919(-)$1	1	11	16	15.0000
.((((	chr17:37210286-37210545(+)$1	1	90	95	15.0000
.))))	chr11:86313577-86313829(-)$1	1	105	110	15.0000
..)))	chr5:137735518-137735767(+)$1	1	178	183	15.0000
((.((	chr1:20927273-20927601(+)$1	1	52	57	15.0000
))).)	chr11:3242132-3242377(+)$1	1	143	148	15.0000
)))))	chr12:88448165-88448425(-)$1	1	49	54	15.0000
(((((	chr1:174203794-174204064(-)$1	1	22	27	15.0000
).)))	chr10:128107392-128107673(-)$1	1	224	229	15.0000
....)	chr9:4417847-4418136(-)$1	1	100	105	15.0000
.))))	chr2:103294240-103294498(-)$1	1	187	192	15.0000
)))))	chr11:119863635-119863893(+)$1	1	71	76	15.0000
((((.	chr6:114197718-114197982(+)$1	1	154	159	15.0000
)))))	chr2:73746449-73746750(-)$1	1	152	157	15.0000
(((((	chr11:106642296-106642571(-)$1	1	158	163	15.0000
((((.	chr12:91965509-91965787(-)$1	1	247	252	15.0000
.)).)	chr9:52485465-52485761(-)$1	1	141	146	15.0000
((((.	chr5:24369223-24369464(-)$1	1	46	51	15.0000
..(((	chr2:164250091-164250342(-)$1	1	46	51	15.0000
((((.	chr15:77590914-77591338(-)$1	1	40	45	15.0000
((.(.	chr17:17665147-17665425(-)$1	1	89	94	15.0000
.))))	chr9:34843313-34843569(+)$1	1	234	239	15.0000
(((((	chr8:73999479-73999766(+)$1	1	39	44	15.0000
))..)	chr5:33135689-33135952(-)$1	1	52	57	15.0000
(((.(	chr8:9989548-9989806(+)$1	1	91	96	15.0000
).)))	chr7:53352452-53352738(-)$1	1	78	83	15.0000
..(((	chrX:131338933-131339184(-)$1	1	123	128	15.0000
..(.(	chr11:58997333-58997585(-)$1	1	30	35	15.0000
(.(((	chr4:59765826-59766065(+)$1	1	12	17	15.0000
....)	chr13:112536730-112537187(-)$1	1	29	34	15.0000
.....	chr15:79191174-79191419(-)$1	1	171	176	15.0000
(((((	chr19:53321174-53321427(+)$1	1	1	6	15.0000
....)	chr7:125262558-125262910(-)$1	1	80	85	15.0000
(..((	chr10:114727549-114727812(-)$1	1	19	24	15.0000
((((.	chr18:84264637-84264886(+)$1	1	83	88	15.0000
(((((	chr12:4840108-4840348(-)$1	1	35	40	15.0000
(((((	chr6:129491827-129492080(+)$1	1	128	133	15.0000
).)))	chr7:28317025-28317395(-)$1	1	245	250	15.0000
))).)	chr13:9171588-9171965(+)$1	1	160	165	15.0000
...))	chrY:364893-365128(+)$1	1	57	62	15.0000
..(((	chr2:6463516-6463776(-)$1	1	143	148	15.0000
)))))	chr1:156242916-156243177(-)$1	1	194	199	15.0000
..)))	chr3:85464723-85464973(-)$1	1	42	47	15.0000
(((((	chr4:106261540-106261795(+)$1	1	7	12	15.0000
.))))	chrX:160391097-160391350(-)$1	1	161	166	15.0000
....)	chr3:8930862-8931121(-)$1	1	79	84	15.0000
((.((	chr17:87232476-87232792(+)$1	1	49	54	15.0000
)))))	chr3:89903728-89903979(+)$1	1	242	247	15.0000
..(((	chr1:191694874-191695119(+)$1	1	68	73	15.0000
))))(	chr3:138588884-138589120(-)$1	1	115	120	15.0000
(((..	chr18:20832128-20832457(+)$1	1	258	263	15.0000
(((((	chr1:174126834-174127098(-)$1	1	150	155	15.0000
)....	chr6:115224974-115225238(+)$1	1	230	235	15.0000

#PSSM
C : 0.92	c : 0.07	
U : 0.92	u : 0.07	
G : 0.92	g : 0.07	
U : 0.92	u : 0.07	
G : 0.92	g : 0.07	

#score	825.0000000000001
#seq	55
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013b_mm9_UTR_m2_run1.nuc.txt

#NT
CCA	chr1:19202226-19202451(+)$1	225	3	6	8.9999
CCA	chr1:133904805-133905029(+)$1	224	89	92	8.9999
CCA	chr8:86463572-86463817(+)$1	245	26	29	8.9999
CCA	chr4:151766852-151767094(-)$1	242	29	32	8.9999
cca	chr13:99406042-99406263(-)$1	221	160	163	8.9999
CCA	chr13:54753398-54753628(+)$1	230	9	12	8.9999
CCA	chr9:8900652-8900876(-)$1	224	140	143	8.9999
CCA	chr9:45203112-45203342(+)$1	230	28	31	8.9999
CCA	chr7:134165987-134166209(+)$1	222	8	11	8.9999
CCA	chr1:145449236-145449464(-)$1	228	49	52	8.9999
CCA	chr8:3682304-3682525(-)$1	221	3	6	8.9999
CCA	chr7:51502399-51502622(+)$1	223	14	17	8.9999
CCA	chr5:138547581-138547810(+)$1	229	31	34	8.9999
CCA	chr8:90781292-90781519(+)$1	227	8	11	8.9999
CCA	chr7:53686509-53686728(+)$1	219	26	29	8.9999
CCA	chr11:87793715-87793945(-)$1	230	65	68	8.9999
CCA	chr12:29422015-29422236(-)$1	221	29	32	8.9999
CCA	chr8:74439394-74439616(+)$1	222	23	26	8.9999
CCA	chr9:119149567-119149800(-)$1	233	15	18	8.9999
CCA	chr16:37882013-37882237(+)$1	224	1	4	8.9999
CCA	chr15:94409095-94409323(-)$1	228	12	15	8.9999
CCA	chr10:69486907-69487137(+)$1	230	3	6	8.9999
CCA	chr17:30353021-30353260(-)$1	239	8	11	8.9999
CCA	chr1:63640845-63641075(+)$1	230	2	5	8.9999
CCA	chr14:46214114-46214341(-)$1	227	25	28	8.9999
CCA	chr5:115254524-115254759(+)$1	235	36	39	8.9999
CCA	chr11:71967418-71967635(+)$1	217	106	109	8.9999
CCA	chr15:79657881-79658100(-)$1	219	54	57	8.9999
CCA	chr5:145942167-145942395(+)$1	228	28	31	8.9999
CCA	chr1:155067188-155067416(-)$1	228	13	16	8.9999
CCA	chr4:6322164-6322403(+)$1	239	22	25	8.9999
CCA	chr7:149837571-149837793(-)$1	222	48	51	8.9999
CCA	chr14:98300488-98300718(-)$1	230	15	18	8.9999
CCA	chr19:58873666-58873906(-)$1	240	9	12	8.9999
CCA	chr11:3549462-3549681(+)$1	219	10	13	8.9999
cca	chr6:136279878-136280099(-)$1	221	0	3	8.9999
CCA	chr2:92244499-92244733(-)$1	234	193	196	8.9999
CCA	chr15:90371592-90371816(-)$1	224	85	88	8.9999
CCA	chr1:74342969-74343194(+)$1	225	17	20	8.9999
CCA	chr8:48913078-48913294(-)$1	216	23	26	8.9999
CCA	chr5:110583848-110584086(+)$1	238	11	14	8.9999
CCA	chr15:31388032-31388286(-)$1	254	126	129	8.9999
CCA	chr11:43518120-43518364(+)$1	244	5	8	8.9999
CCA	chr14:30853966-30854186(-)$1	220	42	45	8.9999
CCA	chr11:97372739-97372957(-)$1	218	12	15	8.9999
CCA	chr7:19546672-19546898(+)$1	226	39	42	8.9999
CCA	chr12:60174427-60174653(+)$1	226	206	209	8.9999
CCA	chrX:90995114-90995341(+)$1	227	27	30	8.9999
CCA	chr1:194332321-194332549(+)$1	228	33	36	8.9999
CCA	chr8:71636389-71636618(+)$1	229	5	8	8.9999
CCA	chr14:27917239-27917461(+)$1	222	78	81	8.9999
CCA	chr1:136489856-136490075(-)$1	219	19	22	8.9999
CCA	chr6:140600647-140600877(+)$1	230	142	145	8.9999
CCA	chr11:103540352-103540569(-)$1	217	21	24	8.9999
CCA	chr5:81941254-81941480(+)$1	226	106	109	8.9999
CCA	chr8:72619782-72620004(-)$1	222	22	25	8.9999
CCA	chr15:100219323-100219558(-)$1	235	36	39	8.9999
CCA	chr1:135601526-135601749(-)$1	223	39	42	8.9999
CCA	chr2:164948928-164949151(-)$1	223	23	26	8.9999
CCA	chr7:29703894-29704115(-)$1	221	169	172	8.9999
CCA	chr11:107595142-107595370(-)$1	228	51	54	8.9999
CCA	chr5:143734233-143734454(+)$1	221	0	3	8.9999
CCA	chr18:36460010-36460233(+)$1	223	5	8	8.9999
CCA	chr3:88342097-88342346(+)$1	249	41	44	8.9999
CCA	chr18:37662686-37662912(+)$1	226	12	15	8.9999
CCA	chr10:110935089-110935311(+)$1	222	38	41	8.9999
CCA	chr11:49075500-49075750(+)$1	250	111	114	8.9999
CCA	chr11:69610875-69611110(-)$1	235	17	20	8.9999
CCA	chr11:93985207-93985425(+)$1	218	18	21	8.9999
CCA	chr7:3366823-3367046(+)$1	223	14	17	8.9999
CCA	chr1:157124282-157124501(-)$1	219	74	77	8.9999
CCA	chr13:41371598-41371830(+)$1	232	11	14	8.9999
CCA	chr11:118940886-118941106(+)$1	220	0	3	8.9999
CCA	chr4:104400557-104400783(+)$1	226	7	10	8.9999
CCA	chr10:93426148-93426372(-)$1	224	44	47	8.9999
cca	chr17:56780852-56781069(+)$1	217	2	5	8.9999
CCA	chr13:14284149-14284371(+)$1	222	71	74	8.9999
CCA	chr2:37430162-37430399(-)$1	237	10	13	8.9999
CCA	chr12:91214693-91214938(+)$1	245	146	149	8.9999
CCA	chr2:49407176-49407402(+)$1	226	32	35	8.9999
CCA	chr10:80255979-80256197(+)$1	218	21	24	8.9999
CCA	chr9:43613500-43613735(+)$1	235	29	32	8.9999
CCA	chr9:107984505-107984723(-)$1	218	7	10	8.9999
CCA	chr16:91870735-91870952(+)$1	217	112	115	8.9999
CCA	chr19:47089372-47089591(-)$1	219	160	163	8.9999
CCA	chr18:75590934-75591204(-)$1	270	45	48	8.9999
CCA	chr6:91714665-91714887(+)$1	222	55	58	8.9999
CCA	chr7:106002228-106002450(-)$1	222	38	41	8.9999
CCA	chr19:55698440-55698670(+)$1	230	171	174	8.9999
CCA	chr19:44379437-44379676(+)$1	239	11	14	8.9999
CCA	chr12:3909101-3909330(+)$1	229	110	113	8.9999
CCA	chr1:164462880-164463101(-)$1	221	53	56	8.9999
CCA	chr12:70782478-70782707(-)$1	229	76	79	8.9999

#otherMatches

#Struct PSSM
:EE	chr4:43438171-43438399(+)$1	228	4	7	8.9999
DDO	chr1:19202226-19202451(+)$1	225	3	6	8.9999
mmm	chr1:133904805-133905029(+)$1	224	89	92	8.9999
444	chr8:86463572-86463817(+)$1	245	26	29	8.9999
ppp	chr4:151766852-151767094(-)$1	242	29	32	8.9999
ggg	chr13:99406042-99406263(-)$1	221	160	163	8.9999
GGG	chr13:54753398-54753628(+)$1	230	9	12	8.9999
fff	chr9:8900652-8900876(-)$1	224	140	143	8.9999
LEE	chr9:45203112-45203342(+)$1	230	28	31	8.9999
ood	chr7:134165987-134166209(+)$1	222	8	11	8.9999
DDO	chr1:145449236-145449464(-)$1	228	49	52	8.9999
:::	chr8:3682304-3682525(-)$1	221	3	6	8.9999
ood	chr7:51502399-51502622(+)$1	223	14	17	8.9999
:::	chr5:138547581-138547810(+)$1	229	31	34	8.9999
HEE	chr8:90781292-90781519(+)$1	227	8	11	8.9999
bb2	chr7:53686509-53686728(+)$1	219	26	29	8.9999
ddd	chr11:87793715-87793945(-)$1	230	65	68	8.9999
eee	chr12:29422015-29422236(-)$1	221	29	32	8.9999
nnn	chr8:74439394-74439616(+)$1	222	23	26	8.9999
:gg	chr9:119149567-119149800(-)$1	233	15	18	8.9999
:GG	chr16:37882013-37882237(+)$1	224	1	4	8.9999
EEE	chr15:94409095-94409323(-)$1	228	12	15	8.9999
:::	chr10:69486907-69487137(+)$1	230	3	6	8.9999
:::	chr17:30353021-30353260(-)$1	239	8	11	8.9999
:::	chr1:63640845-63641075(+)$1	230	2	5	8.9999
ooo	chr14:46214114-46214341(-)$1	227	25	28	8.9999
22c	chr5:115254524-115254759(+)$1	235	36	39	8.9999
999	chr11:71967418-71967635(+)$1	217	106	109	8.9999
ddd	chr15:79657881-79658100(-)$1	219	54	57	8.9999
:cc	chr5:145942167-145942395(+)$1	228	28	31	8.9999
MMC	chr1:155067188-155067416(-)$1	228	13	16	8.9999
zzz	chr4:6322164-6322403(+)$1	239	22	25	8.9999
cc[	chr7:149837571-149837793(-)$1	222	48	51	8.9999
hhc	chr14:98300488-98300718(-)$1	230	15	18	8.9999
:::	chr19:58873666-58873906(-)$1	240	9	12	8.9999
HHH	chr11:3549462-3549681(+)$1	219	10	13	8.9999
::D	chr6:136279878-136280099(-)$1	221	0	3	8.9999
ddd	chr2:92244499-92244733(-)$1	234	193	196	8.9999
css	chr15:90371592-90371816(-)$1	224	85	88	8.9999
ccc	chr1:74342969-74343194(+)$1	225	17	20	8.9999
nnn	chr8:48913078-48913294(-)$1	216	23	26	8.9999
CC:	chr5:110583848-110584086(+)$1	238	11	14	8.9999
bbb	chr15:31388032-31388286(-)$1	254	126	129	8.9999
:::	chr11:43518120-43518364(+)$1	244	5	8	8.9999
a]i	chr14:30853966-30854186(-)$1	220	42	45	8.9999
EE{	chr11:97372739-97372957(-)$1	218	12	15	8.9999
:ii	chr7:19546672-19546898(+)$1	226	39	42	8.9999
fff	chr12:60174427-60174653(+)$1	226	206	209	8.9999
ccc	chrX:90995114-90995341(+)$1	227	27	30	8.9999
eee	chr1:194332321-194332549(+)$1	228	33	36	8.9999
!bb	chr8:71636389-71636618(+)$1	229	5	8	8.9999
ee"	chr14:27917239-27917461(+)$1	222	78	81	8.9999
FFF	chr1:136489856-136490075(-)$1	219	19	22	8.9999
BDD	chr6:140600647-140600877(+)$1	230	142	145	8.9999
333	chr11:103540352-103540569(-)$1	217	21	24	8.9999
bb]	chr5:81941254-81941480(+)$1	226	106	109	8.9999
ccm	chr8:72619782-72620004(-)$1	222	22	25	8.9999
]dd	chr15:100219323-100219558(-)$1	235	36	39	8.9999
bb"	chr1:135601526-135601749(-)$1	223	39	42	8.9999
%%%	chr2:164948928-164949151(-)$1	223	23	26	8.9999
+++	chr7:29703894-29704115(-)$1	221	169	172	8.9999
g66	chr11:107595142-107595370(-)$1	228	51	54	8.9999
::c	chr5:143734233-143734454(+)$1	221	0	3	8.9999
coo	chr18:36460010-36460233(+)$1	223	5	8	8.9999
ee:	chr3:88342097-88342346(+)$1	249	41	44	8.9999
rrr	chr18:37662686-37662912(+)$1	226	12	15	8.9999
:::	chr10:110935089-110935311(+)$1	222	38	41	8.9999
ccc	chr11:49075500-49075750(+)$1	250	111	114	8.9999
c::	chr11:69610875-69611110(-)$1	235	17	20	8.9999
vvv	chr11:93985207-93985425(+)$1	218	18	21	8.9999
ggg	chr7:3366823-3367046(+)$1	223	14	17	8.9999
fff	chr1:157124282-157124501(-)$1	219	74	77	8.9999
{CC	chr13:41371598-41371830(+)$1	232	11	14	8.9999
:::	chr11:118940886-118941106(+)$1	220	0	3	8.9999
:::	chr4:104400557-104400783(+)$1	226	7	10	8.9999
"""	chr10:93426148-93426372(-)$1	224	44	47	8.9999
:cc	chr17:56780852-56781069(+)$1	217	2	5	8.9999
lcc	chr13:14284149-14284371(+)$1	222	71	74	8.9999
EEE	chr2:37430162-37430399(-)$1	237	10	13	8.9999
eee	chr12:91214693-91214938(+)$1	245	146	149	8.9999
:CC	chr2:49407176-49407402(+)$1	226	32	35	8.9999
DDD	chr10:80255979-80256197(+)$1	218	21	24	8.9999
WWW	chr9:43613500-43613735(+)$1	235	29	32	8.9999
FFF	chr9:107984505-107984723(-)$1	218	7	10	8.9999
bbq	chr16:91870735-91870952(+)$1	217	112	115	8.9999
ppp	chr19:47089372-47089591(-)$1	219	160	163	8.9999
ccc	chr18:75590934-75591204(-)$1	270	45	48	8.9999
gg$	chr6:91714665-91714887(+)$1	222	55	58	8.9999
ee!	chr7:106002228-106002450(-)$1	222	38	41	8.9999
cdd	chr19:55698440-55698670(+)$1	230	171	174	8.9999
FFF	chr19:44379437-44379676(+)$1	239	11	14	8.9999
c""	chr12:3909101-3909330(+)$1	229	110	113	8.9999
!dd	chr1:164462880-164463101(-)$1	221	53	56	8.9999
cc]	chr12:70782478-70782707(-)$1	229	76	79	8.9999

#DB
.((	chr4:43438171-43438399(+)$1	1	4	7	8.9999
((.	chr1:19202226-19202451(+)$1	1	3	6	8.9999
...	chr1:133904805-133905029(+)$1	1	89	92	8.9999
...	chr8:86463572-86463817(+)$1	1	26	29	8.9999
...	chr4:151766852-151767094(-)$1	1	29	32	8.9999
(((	chr13:99406042-99406263(-)$1	1	160	163	8.9999
(((	chr13:54753398-54753628(+)$1	1	9	12	8.9999
)))	chr9:8900652-8900876(-)$1	1	140	143	8.9999
.((	chr9:45203112-45203342(+)$1	1	28	31	8.9999
..)	chr7:134165987-134166209(+)$1	1	8	11	8.9999
((.	chr1:145449236-145449464(-)$1	1	49	52	8.9999
...	chr8:3682304-3682525(-)$1	1	3	6	8.9999
..)	chr7:51502399-51502622(+)$1	1	14	17	8.9999
...	chr5:138547581-138547810(+)$1	1	31	34	8.9999
(((	chr8:90781292-90781519(+)$1	1	8	11	8.9999
)).	chr7:53686509-53686728(+)$1	1	26	29	8.9999
)))	chr11:87793715-87793945(-)$1	1	65	68	8.9999
(((	chr12:29422015-29422236(-)$1	1	29	32	8.9999
...	chr8:74439394-74439616(+)$1	1	23	26	8.9999
.((	chr9:119149567-119149800(-)$1	1	15	18	8.9999
.((	chr16:37882013-37882237(+)$1	1	1	4	8.9999
(((	chr15:94409095-94409323(-)$1	1	12	15	8.9999
...	chr10:69486907-69487137(+)$1	1	3	6	8.9999
...	chr17:30353021-30353260(-)$1	1	8	11	8.9999
...	chr1:63640845-63641075(+)$1	1	2	5	8.9999
...	chr14:46214114-46214341(-)$1	1	25	28	8.9999
..)	chr5:115254524-115254759(+)$1	1	36	39	8.9999
...	chr11:71967418-71967635(+)$1	1	106	109	8.9999
))(	chr15:79657881-79658100(-)$1	1	54	57	8.9999
.((	chr5:145942167-145942395(+)$1	1	28	31	8.9999
..(	chr1:155067188-155067416(-)$1	1	13	16	8.9999
...	chr4:6322164-6322403(+)$1	1	22	25	8.9999
((.	chr7:149837571-149837793(-)$1	1	48	51	8.9999
(((	chr14:98300488-98300718(-)$1	1	15	18	8.9999
...	chr19:58873666-58873906(-)$1	1	9	12	8.9999
(((	chr11:3549462-3549681(+)$1	1	10	13	8.9999
..(	chr6:136279878-136280099(-)$1	1	0	3	8.9999
)))	chr2:92244499-92244733(-)$1	1	193	196	8.9999
(..	chr15:90371592-90371816(-)$1	1	85	88	8.9999
(((	chr1:74342969-74343194(+)$1	1	17	20	8.9999
...	chr8:48913078-48913294(-)$1	1	23	26	8.9999
((.	chr5:110583848-110584086(+)$1	1	11	14	8.9999
(((	chr15:31388032-31388286(-)$1	1	126	129	8.9999
...	chr11:43518120-43518364(+)$1	1	5	8	8.9999
).)	chr14:30853966-30854186(-)$1	1	42	45	8.9999
((.	chr11:97372739-97372957(-)$1	1	12	15	8.9999
.((	chr7:19546672-19546898(+)$1	1	39	42	8.9999
)))	chr12:60174427-60174653(+)$1	1	206	209	8.9999
(((	chrX:90995114-90995341(+)$1	1	27	30	8.9999
)))	chr1:194332321-194332549(+)$1	1	33	36	8.9999
.((	chr8:71636389-71636618(+)$1	1	5	8	8.9999
((.	chr14:27917239-27917461(+)$1	1	78	81	8.9999
(((	chr1:136489856-136490075(-)$1	1	19	22	8.9999
)))	chr6:140600647-140600877(+)$1	1	142	145	8.9999
...	chr11:103540352-103540569(-)$1	1	21	24	8.9999
)).	chr5:81941254-81941480(+)$1	1	106	109	8.9999
((.	chr8:72619782-72620004(-)$1	1	22	25	8.9999
.))	chr15:100219323-100219558(-)$1	1	36	39	8.9999
((.	chr1:135601526-135601749(-)$1	1	39	42	8.9999
...	chr2:164948928-164949151(-)$1	1	23	26	8.9999
...	chr7:29703894-29704115(-)$1	1	169	172	8.9999
)..	chr11:107595142-107595370(-)$1	1	51	54	8.9999
..(	chr5:143734233-143734454(+)$1	1	0	3	8.9999
(..	chr18:36460010-36460233(+)$1	1	5	8	8.9999
)).	chr3:88342097-88342346(+)$1	1	41	44	8.9999
...	chr18:37662686-37662912(+)$1	1	12	15	8.9999
...	chr10:110935089-110935311(+)$1	1	38	41	8.9999
)))	chr11:49075500-49075750(+)$1	1	111	114	8.9999
)..	chr11:69610875-69611110(-)$1	1	17	20	8.9999
...	chr11:93985207-93985425(+)$1	1	18	21	8.9999
(((	chr7:3366823-3367046(+)$1	1	14	17	8.9999
)))	chr1:157124282-157124501(-)$1	1	74	77	8.9999
.((	chr13:41371598-41371830(+)$1	1	11	14	8.9999
...	chr11:118940886-118941106(+)$1	1	0	3	8.9999
...	chr4:104400557-104400783(+)$1	1	7	10	8.9999
...	chr10:93426148-93426372(-)$1	1	44	47	8.9999
.((	chr17:56780852-56781069(+)$1	1	2	5	8.9999
.))	chr13:14284149-14284371(+)$1	1	71	74	8.9999
(((	chr2:37430162-37430399(-)$1	1	10	13	8.9999
)))	chr12:91214693-91214938(+)$1	1	146	149	8.9999
.((	chr2:49407176-49407402(+)$1	1	32	35	8.9999
(((	chr10:80255979-80256197(+)$1	1	21	24	8.9999
...	chr9:43613500-43613735(+)$1	1	29	32	8.9999
(((	chr9:107984505-107984723(-)$1	1	7	10	8.9999
((.	chr16:91870735-91870952(+)$1	1	112	115	8.9999
...	chr19:47089372-47089591(-)$1	1	160	163	8.9999
(((	chr18:75590934-75591204(-)$1	1	45	48	8.9999
((.	chr6:91714665-91714887(+)$1	1	55	58	8.9999
((.	chr7:106002228-106002450(-)$1	1	38	41	8.9999
)))	chr19:55698440-55698670(+)$1	1	171	174	8.9999
(((	chr19:44379437-44379676(+)$1	1	11	14	8.9999
(..	chr12:3909101-3909330(+)$1	1	110	113	8.9999
.((	chr1:164462880-164463101(-)$1	1	53	56	8.9999
)).	chr12:70782478-70782707(-)$1	1	76	79	8.9999

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

#score	845.9999999999998
#seq	94
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF2_Pandit2013_mm9_CDS_m2_run1.nuc.txt

#NT
AGCA	chr5:45916325-45916537(+)$1	212	118	122	11.9999
AGCA	chr9:101114037-101114245(-)$1	208	85	89	11.9999
AGCA	chr19:38117686-38117937(-)$1	251	76	80	11.9999
AGCA	chr17:42953381-42953609(-)$1	228	177	181	11.9999
AGCA	chr9:119361255-119361478(+)$1	223	57	61	11.9999
AGCA	chr2:154518185-154518395(+)$1	210	37	41	11.9999
AGCA	chr16:96275352-96275567(-)$1	215	48	52	11.9999
AGCA	chr8:89155384-89155606(+)$1	222	40	44	11.9999
AGCA	chr7:31360821-31361028(-)$1	207	39	43	11.9999
AGCA	chr13:97436055-97436281(-)$1	226	111	115	11.9999
AGCA	chr11:65635373-65635590(+)$1	217	8	12	11.9999
AGCA	chr7:128191289-128191501(+)$1	212	158	162	11.9999
AGCA	chr1:172779178-172779397(-)$1	219	139	143	11.9999
AGCA	chr4:56787782-56788036(-)$1	254	210	214	11.9999
AGCA	chr5:122917663-122917882(-)$1	219	129	133	11.9999
AGCA	chr1:137315720-137315947(-)$1	227	185	189	11.9999
AGCA	chr5:145593279-145593491(+)$1	212	149	153	11.9999
AGCA	chr1:187191333-187191563(+)$1	230	114	118	11.9999
AGCA	chr6:92102281-92102487(+)$1	206	163	167	11.9999
AGCA	chr1:14160937-14161148(-)$1	211	69	73	11.9999
AGCA	chr11:70757936-70758147(-)$1	211	178	182	11.9999
AGCA	chr2:163470651-163470871(-)$1	220	51	55	11.9999
AGCA	chr7:63370044-63370268(+)$1	224	47	51	11.9999
AGCA	chr3:78770517-78770735(-)$1	218	67	71	11.9999
AGCA	chr12:52762532-52762755(-)$1	223	190	194	11.9999
AGCA	chr1:178680091-178680306(-)$1	215	157	161	11.9999
AGCA	chr2:174167228-174167444(+)$1	216	11	15	11.9999
AGCA	chr1:84740325-84740552(-)$1	227	108	112	11.9999
AGCA	chr11:35642149-35642367(-)$1	218	188	192	11.9999
AGCA	chr12:99994314-99994537(+)$1	223	195	199	11.9999
AGCA	chr17:56556617-56556844(-)$1	227	164	168	11.9999
AGCA	chrX:159347871-159348093(+)$1	222	186	190	11.9999
AGCA	chr12:13247573-13247799(-)$1	226	57	61	11.9999
AGCA	chr18:67978442-67978665(+)$1	223	56	60	11.9999
AGCA	chr18:34621680-34621919(-)$1	239	66	70	11.9999
AGCA	chr1:141328429-141328645(+)$1	216	200	204	11.9999
AGCA	chr2:24836156-24836376(+)$1	220	6	10	11.9999
AGCA	chr10:24625588-24625798(+)$1	210	192	196	11.9999
AGCA	chr12:82633610-82633847(-)$1	237	70	74	11.9999
AGCA	chr12:100125189-100125436(-)$1	247	18	22	11.9999
AGCA	chr10:127714662-127714875(+)$1	213	60	64	11.9999
AGCA	chr12:77188745-77188952(+)$1	207	27	31	11.9999
AGCA	chr15:12812849-12813059(+)$1	210	116	120	11.9999
AGCA	chr1:67080624-67080835(-)$1	211	72	76	11.9999
AGCA	chr4:126236435-126236642(+)$1	207	57	61	11.9999
AGCA	chr11:97042965-97043188(-)$1	223	190	194	11.9999
AGCA	chr7:86470224-86470459(+)$1	235	143	147	11.9999
AGCA	chr19:6372483-6372696(+)$1	213	68	72	11.9999
AGCA	chr6:118339228-118339454(-)$1	226	15	19	11.9999
AGCA	chr2:104279377-104279590(-)$1	213	173	177	11.9999
AGCA	chr15:103119446-103119699(+)$1	253	182	186	11.9999
AGCA	chr3:103855053-103855261(-)$1	208	181	185	11.9999
AGCA	chr10:76003528-76003752(+)$1	224	91	95	11.9999
AGCA	chr10:57245165-57245401(-)$1	236	29	33	11.9999
AGCA	chr5:3961386-3961610(+)$1	224	19	23	11.9999
AGCA	chr3:35888874-35889092(-)$1	218	60	64	11.9999
AGCA	chr2:34287541-34287766(+)$1	225	218	222	11.9999
AGCA	chr2:90603577-90603793(+)$1	216	91	95	11.9999
AGCA	chr12:71067044-71067265(-)$1	221	23	27	11.9999
AGCA	chr9:14637008-14637214(+)$1	206	95	99	11.9999
AGCA	chr4:122716680-122716888(+)$1	208	54	58	11.9999
AGCA	chr10:128243949-128244158(+)$1	209	66	70	11.9999
AGCA	chr1:180261872-180262100(-)$1	228	181	185	11.9999
AGCA	chr14:14783641-14783858(-)$1	217	108	112	11.9999
AGCA	chr6:55019334-55019542(+)$1	208	171	175	11.9999
AGCA	chr3:83764594-83764816(-)$1	222	33	37	11.9999
AGCA	chr9:20999136-20999354(+)$1	218	65	69	11.9999
AGCA	chr1:164635342-164635576(-)$1	234	163	167	11.9999
AGCA	chr15:35855862-35856082(+)$1	220	10	14	11.9999
AGCA	chr8:42496570-42496777(-)$1	207	13	17	11.9999
AGCA	chr13:107669685-107669891(-)$1	206	162	166	11.9999
AGCA	chr3:36882324-36882532(+)$1	208	85	89	11.9999
AGCA	chr10:120362770-120362977(-)$1	207	129	133	11.9999
AGCA	chr5:111184506-111184724(-)$1	218	70	74	11.9999
AGCA	chr2:118896604-118896818(+)$1	214	145	149	11.9999
AGCA	chr15:81208292-81208511(-)$1	219	179	183	11.9999
AGCA	chr5:141305949-141306174(-)$1	225	141	145	11.9999
AGCA	chr1:34320020-34320229(+)$1	209	129	133	11.9999

#otherMatches

#Struct PSSM
:ddd	chr9:70595941-70596168(+)$1	227	36	40	11.9999
hhhh	chr5:45916325-45916537(+)$1	212	118	122	11.9999
:CCC	chr9:101114037-101114245(-)$1	208	85	89	11.9999
mbb:	chr19:38117686-38117937(-)$1	251	76	80	11.9999
hhhh	chr17:42953381-42953609(-)$1	228	177	181	11.9999
EE::	chr9:119361255-119361478(+)$1	223	57	61	11.9999
]ddd	chr2:154518185-154518395(+)$1	210	37	41	11.9999
mmbb	chr16:96275352-96275567(-)$1	215	48	52	11.9999
::EE	chr8:89155384-89155606(+)$1	222	40	44	11.9999
2a]e	chr7:31360821-31361028(-)$1	207	39	43	11.9999
====	chr13:97436055-97436281(-)$1	226	111	115	11.9999
oooo	chr11:65635373-65635590(+)$1	217	8	12	11.9999
Gccc	chr7:128191289-128191501(+)$1	212	158	162	11.9999
ffff	chr1:172779178-172779397(-)$1	219	139	143	11.9999
GGGG	chr4:56787782-56788036(-)$1	254	210	214	11.9999
""dd	chr5:122917663-122917882(-)$1	219	129	133	11.9999
cccq	chr1:137315720-137315947(-)$1	227	185	189	11.9999
cooo	chr5:145593279-145593491(+)$1	212	149	153	11.9999
gggg	chr1:187191333-187191563(+)$1	230	114	118	11.9999
::dd	chr6:92102281-92102487(+)$1	206	163	167	11.9999
dd]c	chr1:14160937-14161148(-)$1	211	69	73	11.9999
}CCC	chr11:70757936-70758147(-)$1	211	178	182	11.9999
eeee	chr2:163470651-163470871(-)$1	220	51	55	11.9999
====	chr7:63370044-63370268(+)$1	224	47	51	11.9999
ccc]	chr3:78770517-78770735(-)$1	218	67	71	11.9999
dddd	chr12:52762532-52762755(-)$1	223	190	194	11.9999
dddd	chr1:178680091-178680306(-)$1	215	157	161	11.9999
iiii	chr2:174167228-174167444(+)$1	216	11	15	11.9999
ddnn	chr1:84740325-84740552(-)$1	227	108	112	11.9999
dGGG	chr11:35642149-35642367(-)$1	218	188	192	11.9999
oobb	chr12:99994314-99994537(+)$1	223	195	199	11.9999
gggg	chr17:56556617-56556844(-)$1	227	164	168	11.9999
dd::	chrX:159347871-159348093(+)$1	222	186	190	11.9999
ee]c	chr12:13247573-13247799(-)$1	226	57	61	11.9999
hhhh	chr18:67978442-67978665(+)$1	223	56	60	11.9999
4ddd	chr18:34621680-34621919(-)$1	239	66	70	11.9999
FFF}	chr1:141328429-141328645(+)$1	216	200	204	11.9999
G{CC	chr2:24836156-24836376(+)$1	220	6	10	11.9999
:EEE	chr10:24625588-24625798(+)$1	210	192	196	11.9999
!!bb	chr12:82633610-82633847(-)$1	237	70	74	11.9999
fffm	chr12:100125189-100125436(-)$1	247	18	22	11.9999
pbbe	chr10:127714662-127714875(+)$1	213	60	64	11.9999
fff:	chr12:77188745-77188952(+)$1	207	27	31	11.9999
ccc"	chr15:12812849-12813059(+)$1	210	116	120	11.9999
ennn	chr1:67080624-67080835(-)$1	211	72	76	11.9999
::::	chr4:126236435-126236642(+)$1	207	57	61	11.9999
YYA}	chr11:97042965-97043188(-)$1	223	190	194	11.9999
FF::	chr7:86470224-86470459(+)$1	235	143	147	11.9999
hhww	chr19:6372483-6372696(+)$1	213	68	72	11.9999
ccc:	chr6:118339228-118339454(-)$1	226	15	19	11.9999
e888	chr2:104279377-104279590(-)$1	213	173	177	11.9999
g]ee	chr15:103119446-103119699(+)$1	253	182	186	11.9999
::::	chr3:103855053-103855261(-)$1	208	181	185	11.9999
::FF	chr10:76003528-76003752(+)$1	224	91	95	11.9999
JJJJ	chr10:57245165-57245401(-)$1	236	29	33	11.9999
ccc[	chr5:3961386-3961610(+)$1	224	19	23	11.9999
EE:e	chr3:35888874-35889092(-)$1	218	60	64	11.9999
DBB:	chr2:34287541-34287766(+)$1	225	218	222	11.9999
GGGG	chr2:90603577-90603793(+)$1	216	91	95	11.9999
KDDD	chr12:71067044-71067265(-)$1	221	23	27	11.9999
pppp	chr9:14637008-14637214(+)$1	206	95	99	11.9999
oeee	chr4:122716680-122716888(+)$1	208	54	58	11.9999
22==	chr10:128243949-128244158(+)$1	209	66	70	11.9999
fff!	chr1:180261872-180262100(-)$1	228	181	185	11.9999
b333	chr14:14783641-14783858(-)$1	217	108	112	11.9999
fbb2	chr6:55019334-55019542(+)$1	208	171	175	11.9999
FFFF	chr3:83764594-83764816(-)$1	222	33	37	11.9999
::ff	chr9:20999136-20999354(+)$1	218	65	69	11.9999
4ccc	chr1:164635342-164635576(-)$1	234	163	167	11.9999
dddd	chr15:35855862-35856082(+)$1	220	10	14	11.9999
fffo	chr8:42496570-42496777(-)$1	207	13	17	11.9999
hhhh	chr13:107669685-107669891(-)$1	206	162	166	11.9999
bccc	chr3:36882324-36882532(+)$1	208	85	89	11.9999
2ddd	chr10:120362770-120362977(-)$1	207	129	133	11.9999
f[dd	chr5:111184506-111184724(-)$1	218	70	74	11.9999
::::	chr2:118896604-118896818(+)$1	214	145	149	11.9999
GGG~	chr15:81208292-81208511(-)$1	219	179	183	11.9999
2bb4	chr5:141305949-141306174(-)$1	225	141	145	11.9999
ccc[	chr1:34320020-34320229(+)$1	209	129	133	11.9999

#DB
.(((	chr9:70595941-70596168(+)$1	1	36	40	11.9999
((((	chr5:45916325-45916537(+)$1	1	118	122	11.9999
.(((	chr9:101114037-101114245(-)$1	1	85	89	11.9999
.)).	chr19:38117686-38117937(-)$1	1	76	80	11.9999
))))	chr17:42953381-42953609(-)$1	1	177	181	11.9999
((..	chr9:119361255-119361478(+)$1	1	57	61	11.9999
.)))	chr2:154518185-154518395(+)$1	1	37	41	11.9999
..))	chr16:96275352-96275567(-)$1	1	48	52	11.9999
..((	chr8:89155384-89155606(+)$1	1	40	44	11.9999
.).)	chr7:31360821-31361028(-)$1	1	39	43	11.9999
))))	chr13:97436055-97436281(-)$1	1	111	115	11.9999
....	chr11:65635373-65635590(+)$1	1	8	12	11.9999
)(((	chr7:128191289-128191501(+)$1	1	158	162	11.9999
))))	chr1:172779178-172779397(-)$1	1	139	143	11.9999
))))	chr4:56787782-56788036(-)$1	1	210	214	11.9999
..((	chr5:122917663-122917882(-)$1	1	129	133	11.9999
(((.	chr1:137315720-137315947(-)$1	1	185	189	11.9999
(...	chr5:145593279-145593491(+)$1	1	149	153	11.9999
((((	chr1:187191333-187191563(+)$1	1	114	118	11.9999
..((	chr6:92102281-92102487(+)$1	1	163	167	11.9999
)).)	chr1:14160937-14161148(-)$1	1	69	73	11.9999
.)))	chr11:70757936-70758147(-)$1	1	178	182	11.9999
))))	chr2:163470651-163470871(-)$1	1	51	55	11.9999
))))	chr7:63370044-63370268(+)$1	1	47	51	11.9999
))).	chr3:78770517-78770735(-)$1	1	67	71	11.9999
((((	chr12:52762532-52762755(-)$1	1	190	194	11.9999
((((	chr1:178680091-178680306(-)$1	1	157	161	11.9999
((((	chr2:174167228-174167444(+)$1	1	11	15	11.9999
((..	chr1:84740325-84740552(-)$1	1	108	112	11.9999
))))	chr11:35642149-35642367(-)$1	1	188	192	11.9999
..))	chr12:99994314-99994537(+)$1	1	195	199	11.9999
))))	chr17:56556617-56556844(-)$1	1	164	168	11.9999
))..	chrX:159347871-159348093(+)$1	1	186	190	11.9999
)).)	chr12:13247573-13247799(-)$1	1	57	61	11.9999
))))	chr18:67978442-67978665(+)$1	1	56	60	11.9999
.)))	chr18:34621680-34621919(-)$1	1	66	70	11.9999
))).	chr1:141328429-141328645(+)$1	1	200	204	11.9999
(.((	chr2:24836156-24836376(+)$1	1	6	10	11.9999
.)))	chr10:24625588-24625798(+)$1	1	192	196	11.9999
..((	chr12:82633610-82633847(-)$1	1	70	74	11.9999
(((.	chr12:100125189-100125436(-)$1	1	18	22	11.9999
.))(	chr10:127714662-127714875(+)$1	1	60	64	11.9999
))).	chr12:77188745-77188952(+)$1	1	27	31	11.9999
(((.	chr15:12812849-12813059(+)$1	1	116	120	11.9999
(...	chr1:67080624-67080835(-)$1	1	72	76	11.9999
....	chr4:126236435-126236642(+)$1	1	57	61	11.9999
..).	chr11:97042965-97043188(-)$1	1	190	194	11.9999
))..	chr7:86470224-86470459(+)$1	1	143	147	11.9999
((..	chr19:6372483-6372696(+)$1	1	68	72	11.9999
))).	chr6:118339228-118339454(-)$1	1	15	19	11.9999
)...	chr2:104279377-104279590(-)$1	1	173	177	11.9999
).))	chr15:103119446-103119699(+)$1	1	182	186	11.9999
....	chr3:103855053-103855261(-)$1	1	181	185	11.9999
..((	chr10:76003528-76003752(+)$1	1	91	95	11.9999
((((	chr10:57245165-57245401(-)$1	1	29	33	11.9999
(((.	chr5:3961386-3961610(+)$1	1	19	23	11.9999
((.(	chr3:35888874-35889092(-)$1	1	60	64	11.9999
))).	chr2:34287541-34287766(+)$1	1	218	222	11.9999
))))	chr2:90603577-90603793(+)$1	1	91	95	11.9999
.(((	chr12:71067044-71067265(-)$1	1	23	27	11.9999
....	chr9:14637008-14637214(+)$1	1	95	99	11.9999
.)))	chr4:122716680-122716888(+)$1	1	54	58	11.9999
..))	chr10:128243949-128244158(+)$1	1	66	70	11.9999
(((.	chr1:180261872-180262100(-)$1	1	181	185	11.9999
)...	chr14:14783641-14783858(-)$1	1	108	112	11.9999
))).	chr6:55019334-55019542(+)$1	1	171	175	11.9999
((((	chr3:83764594-83764816(-)$1	1	33	37	11.9999
..((	chr9:20999136-20999354(+)$1	1	65	69	11.9999
.)))	chr1:164635342-164635576(-)$1	1	163	167	11.9999
((((	chr15:35855862-35856082(+)$1	1	10	14	11.9999
(((.	chr8:42496570-42496777(-)$1	1	13	17	11.9999
((((	chr13:107669685-107669891(-)$1	1	162	166	11.9999
((((	chr3:36882324-36882532(+)$1	1	85	89	11.9999
.)))	chr10:120362770-120362977(-)$1	1	129	133	11.9999
(.((	chr5:111184506-111184724(-)$1	1	70	74	11.9999
....	chr2:118896604-118896818(+)$1	1	145	149	11.9999
))).	chr15:81208292-81208511(-)$1	1	179	183	11.9999
.)).	chr5:141305949-141306174(-)$1	1	141	145	11.9999
(((.	chr1:34320020-34320229(+)$1	1	129	133	11.9999

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

#score	947.9999999999995
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Leung2011b_mm9_UTR_m1_run1.nuc.txt

#NT
AGAA	chr12:73751332-73751613(-)$1	281	43	47	12.0000
AGAA	chr6:129401596-129401865(-)$1	269	30	34	12.0000
AGAA	chr1:154684637-154684906(-)$1	269	125	129	12.0000
AGAA	chr19:43577331-43577605(-)$1	274	131	135	12.0000
AGAA	chr2:3422841-3423129(-)$1	288	69	73	12.0000
AGAA	chr16:33962082-33962368(-)$1	286	23	27	12.0000
AGAA	chr9:101004503-101004783(+)$1	280	197	201	12.0000
AGAA	chr5:140919140-140919421(+)$1	281	82	86	12.0000
AGAA	chr15:101647916-101648185(-)$1	269	230	234	12.0000
AGAA	chr15:84384623-84384908(-)$1	285	77	81	12.0000
AGAA	chr4:140572736-140573007(-)$1	271	39	43	12.0000
AGAA	chr5:109000300-109000571(-)$1	271	37	41	12.0000
AGAA	chr1:173348443-173348722(+)$1	279	187	191	12.0000
AGAA	chr8:81255455-81255749(+)$1	294	197	201	12.0000
AGAA	chr10:28315928-28316196(+)$1	268	121	125	12.0000
AGAA	chr1:193656204-193656480(+)$1	276	94	98	12.0000
AGAA	chr1:89614193-89614466(+)$1	273	142	146	12.0000
AGAA	chrX:71188544-71188825(-)$1	281	4	8	12.0000
AGAA	chr4:118108753-118109021(-)$1	268	34	38	12.0000
AGAA	chr17:26793257-26793543(+)$1	286	49	53	12.0000
AGAA	chr1:74640229-74640505(-)$1	276	156	160	12.0000
AGAA	chr7:150988960-150989232(-)$1	272	172	176	12.0000
AGAA	chr2:152107387-152107670(+)$1	283	65	69	12.0000
AGAA	chr3:32239001-32239269(-)$1	268	241	245	12.0000
AGAA	chrX:101276556-101276844(-)$1	288	143	147	12.0000
AGAA	chr18:38747350-38747659(-)$1	309	57	61	12.0000
AGAA	chr4:148326684-148326962(+)$1	278	21	25	12.0000
AGAA	chr1:51527196-51527479(-)$1	283	3	7	12.0000
AGAA	chr4:137798547-137798822(+)$1	275	12	16	12.0000
AGAA	chr15:12199782-12200052(+)$1	270	10	14	12.0000
AGAA	chr4:11100785-11101059(+)$1	274	17	21	12.0000
AGAA	chr17:31982791-31983068(-)$1	277	97	101	12.0000
AGAA	chr3:14610988-14611278(-)$1	290	72	76	12.0000
AGAA	chr11:120562719-120562990(+)$1	271	87	91	12.0000
AGAA	chr3:22109443-22109762(+)$1	319	28	32	12.0000
AGAA	chr5:45917119-45917393(+)$1	274	80	84	12.0000
AGAA	chr3:52151319-52151596(+)$1	277	59	63	12.0000
AGAA	chr5:138223461-138223786(-)$1	325	31	35	12.0000
AGAA	chr4:56892914-56893197(-)$1	283	182	186	12.0000
AGAA	chr2:144076758-144077032(-)$1	274	7	11	12.0000
AGAA	chr19:4195148-4195433(+)$1	285	73	77	12.0000
AGAA	chr6:122268257-122268558(-)$1	301	77	81	12.0000
AGAA	chr10:38869280-38869567(+)$1	287	147	151	12.0000
AGAA	chr11:102165946-102166251(-)$1	305	4	8	12.0000
AGAA	chr11:32126366-32126634(-)$1	268	165	169	12.0000
AGAA	chr9:114655620-114655960(+)$1	340	17	21	12.0000
AGAA	chr18:36923393-36923672(-)$1	279	235	239	12.0000
AGAA	chr4:33332490-33332762(-)$1	272	64	68	12.0000
AGAA	chr11:116299546-116299823(+)$1	277	38	42	12.0000
AGAA	chr11:75314748-75315025(+)$1	277	18	22	12.0000
AGAA	chr18:9315907-9316198(-)$1	291	100	104	12.0000
AGAA	chr17:33795699-33795974(-)$1	275	163	167	12.0000
AGAA	chr3:95435913-95436188(+)$1	275	27	31	12.0000
AGAA	chr4:133309233-133309641(-)$1	408	65	69	12.0000
AGAA	chr10:86153668-86153961(-)$1	293	6	10	12.0000
AGAA	chr3:41485531-41485822(-)$1	291	28	32	12.0000
AGAA	chrX:98012219-98012498(+)$1	279	32	36	12.0000
AGAA	chr9:121664319-121664595(+)$1	276	168	172	12.0000
agaa	chr4:56880165-56880436(-)$1	271	169	173	12.0000
AGAA	chr2:26250990-26251284(+)$1	294	76	80	12.0000
AGAA	chr2:153085316-153085595(+)$1	279	102	106	12.0000
AGAA	chr4:116273624-116273900(-)$1	276	63	67	12.0000
agaa	chr3:102869314-102869665(+)$1	351	78	82	12.0000
AGAA	chr5:123809496-123809781(+)$1	285	104	108	12.0000
AGAA	chr5:3520920-3521188(+)$1	268	107	111	12.0000
AGAA	chrX:70601913-70602185(+)$1	272	56	60	12.0000
AGAA	chr17:26421012-26421354(+)$1	342	157	161	12.0000
aGAA	chr9:21553771-21554047(+)$1	276	111	115	12.0000
agaa	chr6:118412224-118412491(-)$1	267	112	116	12.0000
AGAA	chr10:79620924-79621199(+)$1	275	70	74	12.0000
AGAA	chr4:11098156-11098443(+)$1	287	140	144	12.0000
AGAA	chr6:125079948-125080224(+)$1	276	34	38	12.0000
agaa	chr17:13209269-13209542(+)$1	273	125	129	12.0000
AGAA	chr7:56130318-56130597(-)$1	279	139	143	12.0000
AGAA	chr8:112254861-112255133(-)$1	272	28	32	12.0000
AGAA	chr17:36093772-36094054(-)$1	282	69	73	12.0000

#otherMatches

#Struct PSSM
ccc:	chr10:75503832-75504122(+)$1	290	246	250	12.0000
::ii	chr12:73751332-73751613(-)$1	281	43	47	12.0000
OBB{	chr6:129401596-129401865(-)$1	269	30	34	12.0000
CC::	chr1:154684637-154684906(-)$1	269	125	129	12.0000
f!!b	chr19:43577331-43577605(-)$1	274	131	135	12.0000
^^^^	chr2:3422841-3423129(-)$1	288	69	73	12.0000
dd::	chr16:33962082-33962368(-)$1	286	23	27	12.0000
::::	chr9:101004503-101004783(+)$1	280	197	201	12.0000
eeel	chr5:140919140-140919421(+)$1	281	82	86	12.0000
bnnn	chr15:101647916-101648185(-)$1	269	230	234	12.0000
bmmm	chr15:84384623-84384908(-)$1	285	77	81	12.0000
%%%%	chr4:140572736-140573007(-)$1	271	39	43	12.0000
eeee	chr5:109000300-109000571(-)$1	271	37	41	12.0000
c:::	chr1:173348443-173348722(+)$1	279	187	191	12.0000
mmii	chr8:81255455-81255749(+)$1	294	197	201	12.0000
::::	chr10:28315928-28316196(+)$1	268	121	125	12.0000
ff!!	chr1:193656204-193656480(+)$1	276	94	98	12.0000
EEEK	chr1:89614193-89614466(+)$1	273	142	146	12.0000
::::	chrX:71188544-71188825(-)$1	281	4	8	12.0000
))))	chr4:118108753-118109021(-)$1	268	34	38	12.0000
JJJJ	chr17:26793257-26793543(+)$1	286	49	53	12.0000
pppd	chr1:74640229-74640505(-)$1	276	156	160	12.0000
[ggg	chr7:150988960-150989232(-)$1	272	172	176	12.0000
eee:	chr2:152107387-152107670(+)$1	283	65	69	12.0000
deee	chr3:32239001-32239269(-)$1	268	241	245	12.0000
FFF:	chrX:101276556-101276844(-)$1	288	143	147	12.0000
EEEL	chr18:38747350-38747659(-)$1	309	57	61	12.0000
A{A{	chr4:148326684-148326962(+)$1	278	21	25	12.0000
::::	chr1:51527196-51527479(-)$1	283	3	7	12.0000
eeee	chr4:137798547-137798822(+)$1	275	12	16	12.0000
ssss	chr15:12199782-12200052(+)$1	270	10	14	12.0000
b!!b	chr4:11100785-11101059(+)$1	274	17	21	12.0000
8===	chr17:31982791-31983068(-)$1	277	97	101	12.0000
hhhh	chr3:14610988-14611278(-)$1	290	72	76	12.0000
$$$d	chr11:120562719-120562990(+)$1	271	87	91	12.0000
::::	chr3:22109443-22109762(+)$1	319	28	32	12.0000
:::b	chr5:45917119-45917393(+)$1	274	80	84	12.0000
c[ee	chr3:52151319-52151596(+)$1	277	59	63	12.0000
nnnn	chr5:138223461-138223786(-)$1	325	31	35	12.0000
GGGG	chr4:56892914-56893197(-)$1	283	182	186	12.0000
{BBF	chr2:144076758-144077032(-)$1	274	7	11	12.0000
ee::	chr19:4195148-4195433(+)$1	285	73	77	12.0000
hhhh	chr6:122268257-122268558(-)$1	301	77	81	12.0000
IIII	chr10:38869280-38869567(+)$1	287	147	151	12.0000
dddo	chr11:102165946-102166251(-)$1	305	4	8	12.0000
nnnn	chr11:32126366-32126634(-)$1	268	165	169	12.0000
B{EE	chr9:114655620-114655960(+)$1	340	17	21	12.0000
dd##	chr18:36923393-36923672(-)$1	279	235	239	12.0000
))))	chr4:33332490-33332762(-)$1	272	64	68	12.0000
EE::	chr11:116299546-116299823(+)$1	277	38	42	12.0000
ddd3	chr11:75314748-75315025(+)$1	277	18	22	12.0000
:ccc	chr18:9315907-9316198(-)$1	291	100	104	12.0000
eeee	chr17:33795699-33795974(-)$1	275	163	167	12.0000
:::e	chr3:95435913-95436188(+)$1	275	27	31	12.0000
####	chr4:133309233-133309641(-)$1	408	65	69	12.0000
::::	chr10:86153668-86153961(-)$1	293	6	10	12.0000
gg:D	chr3:41485531-41485822(-)$1	291	28	32	12.0000
qqqq	chrX:98012219-98012498(+)$1	279	32	36	12.0000
dd##	chr9:121664319-121664595(+)$1	276	168	172	12.0000
cfff	chr4:56880165-56880436(-)$1	271	169	173	12.0000
pppp	chr2:26250990-26251284(+)$1	294	76	80	12.0000
cqqq	chr2:153085316-153085595(+)$1	279	102	106	12.0000
wwww	chr4:116273624-116273900(-)$1	276	63	67	12.0000
^^^^	chr3:102869314-102869665(+)$1	351	78	82	12.0000
ssss	chr5:123809496-123809781(+)$1	285	104	108	12.0000
FF::	chr5:3520920-3521188(+)$1	268	107	111	12.0000
::::	chrX:70601913-70602185(+)$1	272	56	60	12.0000
::::	chr17:26421012-26421354(+)$1	342	157	161	12.0000
^^^^	chr9:21553771-21554047(+)$1	276	111	115	12.0000
]ddd	chr6:118412224-118412491(-)$1	267	112	116	12.0000
mmmm	chr10:79620924-79621199(+)$1	275	70	74	12.0000
dddd	chr4:11098156-11098443(+)$1	287	140	144	12.0000
I:::	chr6:125079948-125080224(+)$1	276	34	38	12.0000
GGGG	chr17:13209269-13209542(+)$1	273	125	129	12.0000
iiii	chr7:56130318-56130597(-)$1	279	139	143	12.0000
====	chr8:112254861-112255133(-)$1	272	28	32	12.0000
cc!!	chr17:36093772-36094054(-)$1	282	69	73	12.0000

#DB
))).	chr10:75503832-75504122(+)$1	1	246	250	12.0000
..((	chr12:73751332-73751613(-)$1	1	43	47	12.0000
.((.	chr6:129401596-129401865(-)$1	1	30	34	12.0000
))..	chr1:154684637-154684906(-)$1	1	125	129	12.0000
(..(	chr19:43577331-43577605(-)$1	1	131	135	12.0000
....	chr2:3422841-3423129(-)$1	1	69	73	12.0000
))..	chr16:33962082-33962368(-)$1	1	23	27	12.0000
....	chr9:101004503-101004783(+)$1	1	197	201	12.0000
(((.	chr5:140919140-140919421(+)$1	1	82	86	12.0000
(...	chr15:101647916-101648185(-)$1	1	230	234	12.0000
(...	chr15:84384623-84384908(-)$1	1	77	81	12.0000
....	chr4:140572736-140573007(-)$1	1	39	43	12.0000
((((	chr5:109000300-109000571(-)$1	1	37	41	12.0000
)...	chr1:173348443-173348722(+)$1	1	187	191	12.0000
..))	chr8:81255455-81255749(+)$1	1	197	201	12.0000
....	chr10:28315928-28316196(+)$1	1	121	125	12.0000
((..	chr1:193656204-193656480(+)$1	1	94	98	12.0000
(((.	chr1:89614193-89614466(+)$1	1	142	146	12.0000
....	chrX:71188544-71188825(-)$1	1	4	8	12.0000
....	chr4:118108753-118109021(-)$1	1	34	38	12.0000
((((	chr17:26793257-26793543(+)$1	1	49	53	12.0000
...)	chr1:74640229-74640505(-)$1	1	156	160	12.0000
.(((	chr7:150988960-150989232(-)$1	1	172	176	12.0000
))).	chr2:152107387-152107670(+)$1	1	65	69	12.0000
))))	chr3:32239001-32239269(-)$1	1	241	245	12.0000
(((.	chrX:101276556-101276844(-)$1	1	143	147	12.0000
(((.	chr18:38747350-38747659(-)$1	1	57	61	12.0000
(.(.	chr4:148326684-148326962(+)$1	1	21	25	12.0000
....	chr1:51527196-51527479(-)$1	1	3	7	12.0000
))))	chr4:137798547-137798822(+)$1	1	12	16	12.0000
....	chr15:12199782-12200052(+)$1	1	10	14	12.0000
(..(	chr4:11100785-11101059(+)$1	1	17	21	12.0000
.)))	chr17:31982791-31983068(-)$1	1	97	101	12.0000
((((	chr3:14610988-14611278(-)$1	1	72	76	12.0000
...(	chr11:120562719-120562990(+)$1	1	87	91	12.0000
....	chr3:22109443-22109762(+)$1	1	28	32	12.0000
...(	chr5:45917119-45917393(+)$1	1	80	84	12.0000
(.((	chr3:52151319-52151596(+)$1	1	59	63	12.0000
....	chr5:138223461-138223786(-)$1	1	31	35	12.0000
))))	chr4:56892914-56893197(-)$1	1	182	186	12.0000
.(((	chr2:144076758-144077032(-)$1	1	7	11	12.0000
))..	chr19:4195148-4195433(+)$1	1	73	77	12.0000
((((	chr6:122268257-122268558(-)$1	1	77	81	12.0000
((((	chr10:38869280-38869567(+)$1	1	147	151	12.0000
(((.	chr11:102165946-102166251(-)$1	1	4	8	12.0000
....	chr11:32126366-32126634(-)$1	1	165	169	12.0000
(.((	chr9:114655620-114655960(+)$1	1	17	21	12.0000
((..	chr18:36923393-36923672(-)$1	1	235	239	12.0000
....	chr4:33332490-33332762(-)$1	1	64	68	12.0000
((..	chr11:116299546-116299823(+)$1	1	38	42	12.0000
))).	chr11:75314748-75315025(+)$1	1	18	22	12.0000
.(((	chr18:9315907-9316198(-)$1	1	100	104	12.0000
((((	chr17:33795699-33795974(-)$1	1	163	167	12.0000
...(	chr3:95435913-95436188(+)$1	1	27	31	12.0000
....	chr4:133309233-133309641(-)$1	1	65	69	12.0000
....	chr10:86153668-86153961(-)$1	1	6	10	12.0000
)).(	chr3:41485531-41485822(-)$1	1	28	32	12.0000
....	chrX:98012219-98012498(+)$1	1	32	36	12.0000
((..	chr9:121664319-121664595(+)$1	1	168	172	12.0000
((((	chr4:56880165-56880436(-)$1	1	169	173	12.0000
....	chr2:26250990-26251284(+)$1	1	76	80	12.0000
(...	chr2:153085316-153085595(+)$1	1	102	106	12.0000
....	chr4:116273624-116273900(-)$1	1	63	67	12.0000
....	chr3:102869314-102869665(+)$1	1	78	82	12.0000
....	chr5:123809496-123809781(+)$1	1	104	108	12.0000
((..	chr5:3520920-3521188(+)$1	1	107	111	12.0000
....	chrX:70601913-70602185(+)$1	1	56	60	12.0000
....	chr17:26421012-26421354(+)$1	1	157	161	12.0000
....	chr9:21553771-21554047(+)$1	1	111	115	12.0000
.)))	chr6:118412224-118412491(-)$1	1	112	116	12.0000
....	chr10:79620924-79621199(+)$1	1	70	74	12.0000
((((	chr4:11098156-11098443(+)$1	1	140	144	12.0000
(...	chr6:125079948-125080224(+)$1	1	34	38	12.0000
((((	chr17:13209269-13209542(+)$1	1	125	129	12.0000
))))	chr7:56130318-56130597(-)$1	1	139	143	12.0000
((((	chr8:112254861-112255133(-)$1	1	28	32	12.0000
((..	chr17:36093772-36094054(-)$1	1	69	73	12.0000

#PSSM
A : 0.93	a : 0.06	
G : 0.94	g : 0.05	
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	

#score	924.0
#seq	77
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012b_mm9_UTR_m1_run2.nuc.txt

#NT
GUG	chr12:55746422-55746642(-)$1	220	72	75	8.9999
GUG	chr6:127078835-127079055(-)$1	220	25	28	8.9999
GUG	chr11:57931442-57931662(+)$1	220	16	19	8.9999
GUG	chr9:35024444-35024684(+)$1	240	8	11	8.9999
gug	chr1:155252220-155252440(-)$1	220	27	30	8.9999
GUG	chr16:37884184-37884404(+)$1	220	18	21	8.9999
GUG	chr8:119983540-119983760(+)$1	220	26	29	8.9999
GUG	chr4:57909597-57909817(+)$1	220	13	16	8.9999
GUG	chr2:59192501-59192728(+)$1	227	84	87	8.9999
GUG	chr16:13699040-13699266(+)$1	226	66	69	8.9999
GUG	chr10:62782342-62782562(-)$1	220	22	25	8.9999
GUG	chr6:83253357-83253577(+)$1	220	35	38	8.9999
GUG	chr17:13136366-13136587(-)$1	221	64	67	8.9999
gug	chr12:103980675-103980911(-)$1	236	7	10	8.9999
gug	chr19:10525379-10525601(+)$1	222	34	37	8.9999
GUG	chr18:5118253-5118473(+)$1	220	0	3	8.9999
gug	chr16:13948120-13948340(+)$1	220	112	115	8.9999
GUG	chr11:72499024-72499244(+)$1	220	28	31	8.9999
GUG	chr11:62326771-62326991(+)$1	220	40	43	8.9999
GUG	chr9:114640249-114640469(+)$1	220	0	3	8.9999
GUG	chr18:67478317-67478537(+)$1	220	7	10	8.9999
GUG	chr11:77678749-77678969(+)$1	220	11	14	8.9999
GUG	chr1:108620279-108620499(-)$1	220	76	79	8.9999
GUG	chr14:27732194-27732414(-)$1	220	3	6	8.9999
GUG	chr2:4829848-4830075(+)$1	227	33	36	8.9999
GUG	chr13:38064445-38064669(-)$1	224	34	37	8.9999
gug	chr17:35521154-35521374(+)$1	220	1	4	8.9999
GUG	chr5:130112749-130112989(+)$1	240	37	40	8.9999
gug	chrX:7245279-7245500(-)$1	221	1	4	8.9999
GUG	chr12:29365855-29366093(+)$1	238	14	17	8.9999
GUG	chrX:101154346-101154566(-)$1	220	110	113	8.9999
GUG	chr18:9316099-9316319(-)$1	220	69	72	8.9999
gug	chr3:33945870-33946091(+)$1	221	17	20	8.9999
GUG	chr1:184246117-184246337(-)$1	220	28	31	8.9999
GUG	chr10:117127390-117127610(-)$1	220	43	46	8.9999
GUG	chr4:118920605-118920825(+)$1	220	67	70	8.9999
GUG	chr3:9438353-9438573(-)$1	220	212	215	8.9999
gug	chr1:9930642-9930883(+)$1	241	23	26	8.9999
GUG	chr3:104260360-104260580(-)$1	220	3	6	8.9999
GUG	chr9:40613135-40613369(+)$1	234	3	6	8.9999
gug	chr1:192769630-192769850(+)$1	220	113	116	8.9999
GUG	chr3:58344908-58345128(+)$1	220	171	174	8.9999
GUG	chr5:149317100-149317320(-)$1	220	4	7	8.9999
GUG	chr7:36560575-36560795(-)$1	220	54	57	8.9999
GUG	chr7:36365401-36365666(-)$1	265	170	173	8.9999
GUG	chr2:35575395-35575615(+)$1	220	143	146	8.9999
GUG	chr1:123400156-123400391(+)$1	235	84	87	8.9999
GUG	chr5:102264712-102264932(-)$1	220	18	21	8.9999
GUG	chr4:155205452-155205675(+)$1	223	82	85	8.9999
GUG	chr7:71035934-71036164(-)$1	230	48	51	8.9999
GUG	chr3:69535429-69535649(+)$1	220	148	151	8.9999
GUG	chr3:84782394-84782614(+)$1	220	35	38	8.9999
GUG	chr4:59233709-59233929(+)$1	220	16	19	8.9999
GUG	chr12:33535866-33536086(+)$1	220	106	109	8.9999
GUG	chr8:63391311-63391531(-)$1	220	113	116	8.9999
GUG	chr4:115747493-115747713(-)$1	220	58	61	8.9999
gug	chr17:26064173-26064417(-)$1	244	71	74	8.9999
GUG	chr4:151432615-151432835(+)$1	220	31	34	8.9999
GUG	chr1:136307900-136308139(+)$1	239	27	30	8.9999
GUG	chr3:88451388-88451608(+)$1	220	109	112	8.9999
gug	chr4:116476853-116477073(-)$1	220	103	106	8.9999
GUG	chr11:57345029-57345249(+)$1	220	10	13	8.9999
GUG	chr8:86781716-86781944(-)$1	228	22	25	8.9999
GUG	chr1:137931228-137931448(+)$1	220	21	24	8.9999
GUG	chr2:109853586-109853806(+)$1	220	116	119	8.9999
gug	chr16:8635519-8635743(-)$1	224	19	22	8.9999
GUG	chrX:71516213-71516433(+)$1	220	0	3	8.9999
GUG	chr8:32270727-32270956(-)$1	229	39	42	8.9999
GUG	chr4:146986072-146986292(-)$1	220	48	51	8.9999
GUG	chr2:14999674-14999894(+)$1	220	12	15	8.9999
GUG	chr4:11098903-11099124(+)$1	221	74	77	8.9999
GUG	chr7:133908685-133908905(+)$1	220	109	112	8.9999
GUG	chr9:62641643-62641863(-)$1	220	45	48	8.9999
GUG	chr5:140918807-140919027(+)$1	220	2	5	8.9999
GUG	chr9:118809640-118809860(+)$1	220	77	80	8.9999
GUG	chr11:79948500-79948720(+)$1	220	62	65	8.9999
GUG	chr15:81512900-81513120(+)$1	220	109	112	8.9999
GUG	chr14:55515707-55515927(+)$1	220	115	118	8.9999
GUG	chr7:19791531-19791752(+)$1	221	5	8	8.9999
GUG	chr9:88376841-88377084(-)$1	243	38	41	8.9999
GUG	chr5:76051594-76051832(+)$1	238	21	24	8.9999
GUG	chr1:34225942-34226162(+)$1	220	3	6	8.9999
GUG	chr3:116373714-116373934(-)$1	220	38	41	8.9999
GUG	chr2:119411106-119411326(+)$1	220	50	53	8.9999
GUG	chr4:62050225-62050481(+)$1	256	92	95	8.9999
GUG	chr12:93046532-93046752(-)$1	220	159	162	8.9999
GUG	chr19:46952554-46952775(+)$1	221	144	147	8.9999
gug	chr5:87264777-87265009(+)$1	232	79	82	8.9999
GUG	chr19:45825991-45826212(-)$1	221	10	13	8.9999
GUG	chr11:82617035-82617255(+)$1	220	7	10	8.9999
GUG	chr8:119505978-119506199(-)$1	221	108	111	8.9999
GUG	chr6:124720003-124720231(-)$1	228	90	93	8.9999
GUG	chrX:133611085-133611308(+)$1	223	26	29	8.9999
GUG	chr6:120717576-120717799(+)$1	223	55	58	8.9999
GUG	chr9:65749993-65750218(+)$1	225	2	5	8.9999
GUG	chr4:116224502-116224722(-)$1	220	71	74	8.9999
gug	chr3:115595535-115595756(+)$1	221	0	3	8.9999
GUG	chr17:28536322-28536542(-)$1	220	6	9	8.9999

#otherMatches

#Struct PSSM
hhh	chr4:63211156-63211376(+)$1	220	16	19	8.9999
fff	chr12:55746422-55746642(-)$1	220	72	75	8.9999
###	chr6:127078835-127079055(-)$1	220	25	28	8.9999
DDD	chr11:57931442-57931662(+)$1	220	16	19	8.9999
BBK	chr9:35024444-35024684(+)$1	240	8	11	8.9999
eee	chr1:155252220-155252440(-)$1	220	27	30	8.9999
fff	chr16:37884184-37884404(+)$1	220	18	21	8.9999
ggg	chr8:119983540-119983760(+)$1	220	26	29	8.9999
::E	chr4:57909597-57909817(+)$1	220	13	16	8.9999
e::	chr2:59192501-59192728(+)$1	227	84	87	8.9999
EE{	chr16:13699040-13699266(+)$1	226	66	69	8.9999
dd[	chr10:62782342-62782562(-)$1	220	22	25	8.9999
bb!	chr6:83253357-83253577(+)$1	220	35	38	8.9999
ggg	chr17:13136366-13136587(-)$1	221	64	67	8.9999
ggg	chr12:103980675-103980911(-)$1	236	7	10	8.9999
ddd	chr19:10525379-10525601(+)$1	222	34	37	8.9999
iii	chr18:5118253-5118473(+)$1	220	0	3	8.9999
ggg	chr16:13948120-13948340(+)$1	220	112	115	8.9999
B{H	chr11:72499024-72499244(+)$1	220	28	31	8.9999
ccc	chr11:62326771-62326991(+)$1	220	40	43	8.9999
BBB	chr9:114640249-114640469(+)$1	220	0	3	8.9999
:::	chr18:67478317-67478537(+)$1	220	7	10	8.9999
gcc	chr11:77678749-77678969(+)$1	220	11	14	8.9999
ggg	chr1:108620279-108620499(-)$1	220	76	79	8.9999
D{H	chr14:27732194-27732414(-)$1	220	3	6	8.9999
]cc	chr2:4829848-4830075(+)$1	227	33	36	8.9999
llf	chr13:38064445-38064669(-)$1	224	34	37	8.9999
fff	chr17:35521154-35521374(+)$1	220	1	4	8.9999
MMM	chr5:130112749-130112989(+)$1	240	37	40	8.9999
CCe	chrX:7245279-7245500(-)$1	221	1	4	8.9999
ggg	chr12:29365855-29366093(+)$1	238	14	17	8.9999
]a]	chrX:101154346-101154566(-)$1	220	110	113	8.9999
:::	chr18:9316099-9316319(-)$1	220	69	72	8.9999
ccc	chr3:33945870-33946091(+)$1	221	17	20	8.9999
:::	chr1:184246117-184246337(-)$1	220	28	31	8.9999
ccm	chr10:117127390-117127610(-)$1	220	43	46	8.9999
2dd	chr4:118920605-118920825(+)$1	220	67	70	8.9999
:::	chr3:9438353-9438573(-)$1	220	212	215	8.9999
ccc	chr1:9930642-9930883(+)$1	241	23	26	8.9999
:gg	chr3:104260360-104260580(-)$1	220	3	6	8.9999
ggg	chr9:40613135-40613369(+)$1	234	3	6	8.9999
ddd	chr1:192769630-192769850(+)$1	220	113	116	8.9999
iil	chr3:58344908-58345128(+)$1	220	171	174	8.9999
eee	chr5:149317100-149317320(-)$1	220	4	7	8.9999
{A{	chr7:36560575-36560795(-)$1	220	54	57	8.9999
b[d	chr7:36365401-36365666(-)$1	265	170	173	8.9999
cpp	chr2:35575395-35575615(+)$1	220	143	146	8.9999
!bb	chr1:123400156-123400391(+)$1	235	84	87	8.9999
bbq	chr5:102264712-102264932(-)$1	220	18	21	8.9999
ddd	chr4:155205452-155205675(+)$1	223	82	85	8.9999
KBB	chr7:71035934-71036164(-)$1	230	48	51	8.9999
eee	chr3:69535429-69535649(+)$1	220	148	151	8.9999
!!e	chr3:84782394-84782614(+)$1	220	35	38	8.9999
fff	chr4:59233709-59233929(+)$1	220	16	19	8.9999
bb]	chr12:33535866-33536086(+)$1	220	106	109	8.9999
eee	chr8:63391311-63391531(-)$1	220	113	116	8.9999
bb]	chr4:115747493-115747713(-)$1	220	58	61	8.9999
fff	chr17:26064173-26064417(-)$1	244	71	74	8.9999
]dd	chr4:151432615-151432835(+)$1	220	31	34	8.9999
cc[	chr1:136307900-136308139(+)$1	239	27	30	8.9999
fff	chr3:88451388-88451608(+)$1	220	109	112	8.9999
fff	chr4:116476853-116477073(-)$1	220	103	106	8.9999
F:b	chr11:57345029-57345249(+)$1	220	10	13	8.9999
F:b	chr8:86781716-86781944(-)$1	228	22	25	8.9999
fff	chr1:137931228-137931448(+)$1	220	21	24	8.9999
ddd	chr2:109853586-109853806(+)$1	220	116	119	8.9999
bbd	chr16:8635519-8635743(-)$1	224	19	22	8.9999
ddd	chrX:71516213-71516433(+)$1	220	0	3	8.9999
::J	chr8:32270727-32270956(-)$1	229	39	42	8.9999
9ee	chr4:146986072-146986292(-)$1	220	48	51	8.9999
BB{	chr2:14999674-14999894(+)$1	220	12	15	8.9999
fff	chr4:11098903-11099124(+)$1	221	74	77	8.9999
dmm	chr7:133908685-133908905(+)$1	220	109	112	8.9999
GGG	chr9:62641643-62641863(-)$1	220	45	48	8.9999
DDD	chr5:140918807-140919027(+)$1	220	2	5	8.9999
ccc	chr9:118809640-118809860(+)$1	220	77	80	8.9999
dmm	chr11:79948500-79948720(+)$1	220	62	65	8.9999
d]b	chr15:81512900-81513120(+)$1	220	109	112	8.9999
f[a	chr14:55515707-55515927(+)$1	220	115	118	8.9999
[hh	chr7:19791531-19791752(+)$1	221	5	8	8.9999
C{C	chr9:88376841-88377084(-)$1	243	38	41	8.9999
ddd	chr5:76051594-76051832(+)$1	238	21	24	8.9999
b[g	chr1:34225942-34226162(+)$1	220	3	6	8.9999
:ff	chr3:116373714-116373934(-)$1	220	38	41	8.9999
ddd	chr2:119411106-119411326(+)$1	220	50	53	8.9999
0bb	chr4:62050225-62050481(+)$1	256	92	95	8.9999
EEE	chr12:93046532-93046752(-)$1	220	159	162	8.9999
bb2	chr19:46952554-46952775(+)$1	221	144	147	8.9999
dd2	chr5:87264777-87265009(+)$1	232	79	82	8.9999
::E	chr19:45825991-45826212(-)$1	221	10	13	8.9999
BBE	chr11:82617035-82617255(+)$1	220	7	10	8.9999
mmm	chr8:119505978-119506199(-)$1	221	108	111	8.9999
ff!	chr6:124720003-124720231(-)$1	228	90	93	8.9999
BBd	chrX:133611085-133611308(+)$1	223	26	29	8.9999
ee[	chr6:120717576-120717799(+)$1	223	55	58	8.9999
:::	chr9:65749993-65750218(+)$1	225	2	5	8.9999
::c	chr4:116224502-116224722(-)$1	220	71	74	8.9999
::D	chr3:115595535-115595756(+)$1	221	0	3	8.9999
[ff	chr17:28536322-28536542(-)$1	220	6	9	8.9999

#DB
(((	chr4:63211156-63211376(+)$1	1	16	19	8.9999
(((	chr12:55746422-55746642(-)$1	1	72	75	8.9999
...	chr6:127078835-127079055(-)$1	1	25	28	8.9999
(((	chr11:57931442-57931662(+)$1	1	16	19	8.9999
((.	chr9:35024444-35024684(+)$1	1	8	11	8.9999
)))	chr1:155252220-155252440(-)$1	1	27	30	8.9999
(((	chr16:37884184-37884404(+)$1	1	18	21	8.9999
(((	chr8:119983540-119983760(+)$1	1	26	29	8.9999
..(	chr4:57909597-57909817(+)$1	1	13	16	8.9999
)..	chr2:59192501-59192728(+)$1	1	84	87	8.9999
((.	chr16:13699040-13699266(+)$1	1	66	69	8.9999
((.	chr10:62782342-62782562(-)$1	1	22	25	8.9999
((.	chr6:83253357-83253577(+)$1	1	35	38	8.9999
(((	chr17:13136366-13136587(-)$1	1	64	67	8.9999
(((	chr12:103980675-103980911(-)$1	1	7	10	8.9999
(((	chr19:10525379-10525601(+)$1	1	34	37	8.9999
(((	chr18:5118253-5118473(+)$1	1	0	3	8.9999
)))	chr16:13948120-13948340(+)$1	1	112	115	8.9999
(.(	chr11:72499024-72499244(+)$1	1	28	31	8.9999
)))	chr11:62326771-62326991(+)$1	1	40	43	8.9999
(((	chr9:114640249-114640469(+)$1	1	0	3	8.9999
...	chr18:67478317-67478537(+)$1	1	7	10	8.9999
(((	chr11:77678749-77678969(+)$1	1	11	14	8.9999
)))	chr1:108620279-108620499(-)$1	1	76	79	8.9999
(.(	chr14:27732194-27732414(-)$1	1	3	6	8.9999
.))	chr2:4829848-4830075(+)$1	1	33	36	8.9999
..)	chr13:38064445-38064669(-)$1	1	34	37	8.9999
(((	chr17:35521154-35521374(+)$1	1	1	4	8.9999
...	chr5:130112749-130112989(+)$1	1	37	40	8.9999
(((	chrX:7245279-7245500(-)$1	1	1	4	8.9999
(((	chr12:29365855-29366093(+)$1	1	14	17	8.9999
.).	chrX:101154346-101154566(-)$1	1	110	113	8.9999
...	chr18:9316099-9316319(-)$1	1	69	72	8.9999
(((	chr3:33945870-33946091(+)$1	1	17	20	8.9999
...	chr1:184246117-184246337(-)$1	1	28	31	8.9999
((.	chr10:117127390-117127610(-)$1	1	43	46	8.9999
.))	chr4:118920605-118920825(+)$1	1	67	70	8.9999
...	chr3:9438353-9438573(-)$1	1	212	215	8.9999
)))	chr1:9930642-9930883(+)$1	1	23	26	8.9999
.((	chr3:104260360-104260580(-)$1	1	3	6	8.9999
(((	chr9:40613135-40613369(+)$1	1	3	6	8.9999
(((	chr1:192769630-192769850(+)$1	1	113	116	8.9999
((.	chr3:58344908-58345128(+)$1	1	171	174	8.9999
(((	chr5:149317100-149317320(-)$1	1	4	7	8.9999
.(.	chr7:36560575-36560795(-)$1	1	54	57	8.9999
(.(	chr7:36365401-36365666(-)$1	1	170	173	8.9999
(..	chr2:35575395-35575615(+)$1	1	143	146	8.9999
.((	chr1:123400156-123400391(+)$1	1	84	87	8.9999
((.	chr5:102264712-102264932(-)$1	1	18	21	8.9999
(((	chr4:155205452-155205675(+)$1	1	82	85	8.9999
.((	chr7:71035934-71036164(-)$1	1	48	51	8.9999
(((	chr3:69535429-69535649(+)$1	1	148	151	8.9999
..(	chr3:84782394-84782614(+)$1	1	35	38	8.9999
(((	chr4:59233709-59233929(+)$1	1	16	19	8.9999
)).	chr12:33535866-33536086(+)$1	1	106	109	8.9999
(((	chr8:63391311-63391531(-)$1	1	113	116	8.9999
)).	chr4:115747493-115747713(-)$1	1	58	61	8.9999
)))	chr17:26064173-26064417(-)$1	1	71	74	8.9999
.))	chr4:151432615-151432835(+)$1	1	31	34	8.9999
((.	chr1:136307900-136308139(+)$1	1	27	30	8.9999
(((	chr3:88451388-88451608(+)$1	1	109	112	8.9999
(((	chr4:116476853-116477073(-)$1	1	103	106	8.9999
(.(	chr11:57345029-57345249(+)$1	1	10	13	8.9999
(.(	chr8:86781716-86781944(-)$1	1	22	25	8.9999
(((	chr1:137931228-137931448(+)$1	1	21	24	8.9999
)))	chr2:109853586-109853806(+)$1	1	116	119	8.9999
(((	chr16:8635519-8635743(-)$1	1	19	22	8.9999
(((	chrX:71516213-71516433(+)$1	1	0	3	8.9999
..(	chr8:32270727-32270956(-)$1	1	39	42	8.9999
.))	chr4:146986072-146986292(-)$1	1	48	51	8.9999
((.	chr2:14999674-14999894(+)$1	1	12	15	8.9999
(((	chr4:11098903-11099124(+)$1	1	74	77	8.9999
(..	chr7:133908685-133908905(+)$1	1	109	112	8.9999
(((	chr9:62641643-62641863(-)$1	1	45	48	8.9999
(((	chr5:140918807-140919027(+)$1	1	2	5	8.9999
)))	chr9:118809640-118809860(+)$1	1	77	80	8.9999
(..	chr11:79948500-79948720(+)$1	1	62	65	8.9999
).)	chr15:81512900-81513120(+)$1	1	109	112	8.9999
(.(	chr14:55515707-55515927(+)$1	1	115	118	8.9999
.((	chr7:19791531-19791752(+)$1	1	5	8	8.9999
(.(	chr9:88376841-88377084(-)$1	1	38	41	8.9999
(((	chr5:76051594-76051832(+)$1	1	21	24	8.9999
(.(	chr1:34225942-34226162(+)$1	1	3	6	8.9999
.((	chr3:116373714-116373934(-)$1	1	38	41	8.9999
(((	chr2:119411106-119411326(+)$1	1	50	53	8.9999
.))	chr4:62050225-62050481(+)$1	1	92	95	8.9999
)))	chr12:93046532-93046752(-)$1	1	159	162	8.9999
)).	chr19:46952554-46952775(+)$1	1	144	147	8.9999
)).	chr5:87264777-87265009(+)$1	1	79	82	8.9999
..(	chr19:45825991-45826212(-)$1	1	10	13	8.9999
(((	chr11:82617035-82617255(+)$1	1	7	10	8.9999
...	chr8:119505978-119506199(-)$1	1	108	111	8.9999
((.	chr6:124720003-124720231(-)$1	1	90	93	8.9999
(((	chrX:133611085-133611308(+)$1	1	26	29	8.9999
((.	chr6:120717576-120717799(+)$1	1	55	58	8.9999
...	chr9:65749993-65750218(+)$1	1	2	5	8.9999
..(	chr4:116224502-116224722(-)$1	1	71	74	8.9999
..(	chr3:115595535-115595756(+)$1	1	0	3	8.9999
.((	chr17:28536322-28536542(-)$1	1	6	9	8.9999

#PSSM
G : 0.85	g : 0.14	
U : 0.85	u : 0.14	
G : 0.85	g : 0.14	

#score	890.9999999999998
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_TDP-43_Polymenidou2011_mm9_CDS_m1_run2.nuc.txt

#NT
ugugugugugugugugugugugugugugugug	chr3:28493786-28494175(+)$1	389	226	258	87.8518
ugugugugugugugugugugugugugugugug	chr12:68322051-68322546(-)$1	495	263	295	87.8518
UUGGUUGgugugugugugugugugugugugAG	chr2:163841584-163841971(+)$1	387	96	128	65.4444
ugugugugugugugugugugugugugugugug	chr1:175274896-175275273(-)$1	377	291	323	87.8518
ugugugugugugugugugugugugugugugug	chr7:71879400-71879781(+)$1	381	197	229	87.8518
ugcgagugugugugugugugugugugugugGG	chr17:17976503-17976850(+)$1	347	110	142	74.8888
ugugugugugugugugugugugugugugugug	chr3:80605271-80605759(-)$1	488	280	312	87.8518
uguguguuugugugugugugcgugugAGAGAG	chr8:40130698-40131025(+)$1	327	146	178	64.8888
uguguguguguguguguauguguguaugugGG	chr5:145653792-145654141(-)$1	349	189	221	74.0555
ugugugugugugugugugugugugugugugug	chr17:47067317-47067664(-)$1	347	0	32	87.8518
uguguguguaugugugugugugugugugugua	chr3:126928443-126928923(-)$1	480	276	308	78.8703
ugugugugugugugugugugugugugugugug	chr6:108306397-108306781(+)$1	384	195	227	87.8518
cgcgugugugugugucugcguguguguguguc	chr5:96590505-96590911(-)$1	406	363	395	66.0925
ugugugugugugugugugugugugugugugug	chr18:10811902-10812391(+)$1	489	425	457	87.8518
UGUGUGUGAGUGUGUGUGAGUGCGUGUGCUUG	chr2:115888705-115889133(-)$1	428	237	269	65.6296
ugugugugugugugugugugugugugugugug	chr11:75451604-75452086(+)$1	482	175	207	87.8518
ugugugugugugugugugugugugugugugug	chr17:66729661-66730135(-)$1	474	178	210	87.8518
UCUCUGUGUGUGUGCGUGCGAGUGUGUGUUUG	chr19:45852839-45853210(-)$1	371	138	170	60.8148
uguguguguguaugugugugugugugugugug	chr11:121323012-121323332(+)$1	320	186	218	83.2222
ugugugugugugugugugugugugugugugug	chr10:62025647-62025966(-)$1	319	65	97	87.8518
ugugugugugugugugugugugugugugugug	chr15:99059780-99060159(+)$1	379	225	257	87.8518
ACCCugugcguguguguguguguguguguguA	chr4:148709019-148709353(-)$1	334	250	282	61.8333
ugugugugugugugugugugugugugugugug	chr15:100787913-100788347(+)$1	434	159	191	87.8518
ugugugugugugugugugugugugugugugug	chr5:144312077-144312381(+)$1	304	99	131	87.8518
ugugugugugugugugugugugugugugugug	chr12:70425028-70425384(-)$1	356	184	216	87.8518
ugugugugugugugugugugugugugugugug	chr12:15816293-15816638(-)$1	345	170	202	87.8518
ugagugugugugugugugugugugugugugug	chr5:68238185-68238514(-)$1	329	189	221	83.6851
ugugugugugugugugugugugugugugugug	chr3:136594609-136595092(+)$1	483	134	166	87.8518
ugcgugcgugcgugugcgugugcgugugugug	chr17:24777491-24777817(-)$1	326	122	154	65.7222
ugugugugugugugugugugugugugugugug	chr4:109958841-109959327(-)$1	486	289	321	87.8518
ugugcguguguguguguguaugugugugugug	chr10:57245114-57245537(-)$1	423	110	142	78.6851
ugugugugugugugugugugugugugugugug	chr9:40153367-40153855(-)$1	488	387	419	87.8518
ugugugugugugugugugugugugugugugug	chr15:84533464-84533838(+)$1	374	217	249	87.8518
ugugugugugugugugugugugugugugugug	chr4:24825713-24826196(+)$1	483	199	231	87.8518
uguguguguguguguguguaugugugugugug	chr17:34070794-34071291(+)$1	497	284	316	83.4074
uguguguguguguguguaugugugugugugug	chr2:90403875-90404326(-)$1	451	256	288	83.2222
ugugugugugugugugugugugugugugugug	chr19:6066586-6066878(-)$1	292	99	131	87.8518
ugucugucugucugucuguguguGUUUGUGUG	chr17:75040679-75041079(+)$1	400	80	112	65.1666
UGUGUGUGUGUGUGUAAGUGUGCGugcgcuug	chr4:101296290-101296695(+)$1	405	181	213	60.8148
ugugugugugugugugugugugugugugugug	chrX:130971789-130972073(+)$1	284	62	94	87.8518
Ggugugugcacguguuugugugugugugugug	chr16:94631108-94631606(+)$1	498	460	492	65.5370
ugugugugugugugugugugugugugugugug	chr16:28372732-28373173(-)$1	441	188	220	87.8518
ugugugugugugugugugugugugugugugug	chr2:90978134-90978606(-)$1	472	399	431	87.8518
uuugugugugugugugugugugugugugugug	chr2:155974743-155975153(-)$1	410	370	402	83.4074
ugugugugugugugugugugugugugugugug	chr8:13370985-13371453(+)$1	468	150	182	87.8518
ugcgugagccucugugugugugugugugugug	chr2:28309249-28309670(+)$1	421	224	256	66.1851
ugugugugucugugugugugugagcgugugug	chr5:45190627-45190944(-)$1	317	84	116	74.0555
ugugugugugugugugugugugugugugugug	chr1:74337628-74337922(+)$1	294	48	80	87.8518
uguguguguguguguguguguauaugugugug	chr15:100225326-100225762(-)$1	436	259	291	78.4074
ugugugugagugugugugcacgugugcgugug	chr16:33005723-33006053(+)$1	330	116	148	65.6296
ugugugugugugugugugugugugugugugug	chr18:61086560-61086783(+)$1	223	145	177	87.8518
ugugugugugugugugugugugugugugugug	chr6:110653200-110653642(+)$1	442	20	52	87.8518
UGGUuguguguggguuuguguaugugugugug	chr10:79736946-79737326(+)$1	380	132	164	65.4444

#otherMatches

#Struct PSSM
BB}FFFFFFYYBB}EEEEEhhhhhhhhmmmmh	chr6:73213895-73214266(+)$1	371	173	205	87.8518
==========eeeee"""bb[ccc[a[dddd!	chr3:28493786-28494175(+)$1	389	226	258	87.8518
bb[a[a[bb[ccc[ccc[ccc[a[a[a[bb[c	chr12:68322051-68322546(-)$1	495	263	295	87.8518
hhh[a"""ccc####gggggggeeeeennnnn	chr2:163841584-163841971(+)$1	387	96	128	65.4444
DDDD?????CCCYYDDDD}A}BB}A}DDDD}A	chr1:175274896-175275273(-)$1	377	291	323	87.8518
H{DDDD{DDDD::bb[a[hhhhhhhh======	chr7:71879400-71879781(+)$1	381	197	229	87.8518
nbb]bb22bb]ccc]ccc]bb333ggggggg2	chr17:17976503-17976850(+)$1	347	110	142	74.8888
ggggg]a]ffffff]bb]bb55555eeeee]d	chr3:80605271-80605759(-)$1	488	280	312	87.8518
lllgggggggdddd]ccc]eeeee:ccc!!bb	chr8:40130698-40131025(+)$1	327	146	178	64.8888
iiiiiiiiDDDD}CCC~~~~DDDD}BB}BBgg	chr5:145653792-145654141(-)$1	349	189	221	74.0555
:BB{BB{BBKKBB{A{IIIIIIIII{BBMMMM	chr17:47067317-47067664(-)$1	347	0	32	87.8518
mmffffffdddd[===========oooooo==	chr3:126928443-126928923(-)$1	480	276	308	78.8703
BB}EEEEEYYBBYYCCC}CCCYYCCC}BBddd	chr6:108306397-108306781(+)$1	384	195	227	87.8518
eeeee::::::::eeeeebbqqqqqqqqbb]e	chr5:96590505-96590911(-)$1	406	363	395	66.0925
ggggggg333ccc]dddd]ccc]ccc]bb]hh	chr18:10811902-10812391(+)$1	489	425	457	87.8518
CC}FFFFFF}BB}EEEEE}A}HHHHHHHHYYC	chr2:115888705-115889133(-)$1	428	237	269	65.6296
c[a[a[a[bb^^^^^^^^^^^^^^^^^^^^^^	chr11:75451604-75452086(+)$1	482	175	207	87.8518
ccc22dddd333bb]bb]dddd]a333a]a]a	chr17:66729661-66730135(-)$1	474	178	210	87.8518
fffff::::::::JJJJJJJJJJJJJJJJJJJ	chr19:45852839-45853210(-)$1	371	138	170	60.8148
qqqqqggggggg:::::::::::::::dddd!	chr11:121323012-121323332(+)$1	320	186	218	83.2222
5555dddd]bbDDDDKKA{DDDD:a[======	chr10:62025647-62025966(-)$1	319	65	97	87.8518
a[a[bb[a[ccc[bb####a!!ccc[a[a[bb	chr15:99059780-99060159(+)$1	379	225	257	87.8518
cca]ffffff]a]bb]ccc]dddd333eeeee	chr4:148709019-148709353(-)$1	334	250	282	61.8333
::::::::::::::::::::::::::::::::	chr15:100787913-100788347(+)$1	434	159	191	87.8518
^^^^^^^^^^^^^^^^^^^^^^^dddd]a]bb	chr5:144312077-144312381(+)$1	304	99	131	87.8518
c]ccc22ccc]bb55555ffffff]bb]ccc2	chr12:70425028-70425384(-)$1	356	184	216	87.8518
gggggg[bb^^^^^^^^^^^^^^^^^^^^^^^	chr12:15816293-15816638(-)$1	345	170	202	87.8518
[ccc[a[eeeee[ccc[a[ccc[a[dddd[a[	chr5:68238185-68238514(-)$1	329	189	221	83.6851
[eeeee[a+++++++++++++dddd[ccc[bb	chr3:136594609-136595092(+)$1	483	134	166	87.8518
===mmmm================GGGGGGG{D	chr17:24777491-24777817(-)$1	326	122	154	65.7222
f::::::::::::::::::::::HHHHHHHH{	chr4:109958841-109959327(-)$1	486	289	321	87.8518
iiiiii333eeeee:DDDD}DDDDZZZCCCDD	chr10:57245114-57245537(-)$1	423	110	142	78.6851
EEEZZZBB}FFFFFF}EEEEE}EEEEE}EEEE	chr9:40153367-40153855(-)$1	488	387	419	87.8518
:CCC{CCC{CCC{BBeeeee[ccc####bb[a	chr15:84533464-84533838(+)$1	374	217	249	87.8518
b[ccc[eeeee[bb!!ccc[eeeee&&&&&&&	chr4:24825713-24826196(+)$1	483	199	231	87.8518
f[a[a[dddd"""a[bb+++++++++++ccc[	chr17:34070794-34071291(+)$1	497	284	316	83.4074
JJJJJJJJJJJJJJJJJ}JJJJJJJJJJJJJJ	chr2:90403875-90404326(-)$1	451	256	288	83.2222
ooooobb::::::::::::::::::::::::G	chr19:6066586-6066878(-)$1	292	99	131	87.8518
cc22cccffffff::::::::::=========	chr17:75040679-75041079(+)$1	400	80	112	65.1666
ff[bb[bb[dddd$$$$$hhhhhhhhccc"""	chr4:101296290-101296695(+)$1	405	181	213	60.8148
GG:::::::::::::::ggggggg[bb[bb[b	chrX:130971789-130972073(+)$1	284	62	94	87.8518
GGGGG::eeeeemmmmeeeee:::CCC}EEEE	chr16:94631108-94631606(+)$1	498	460	492	65.5370
a$$$$$bb####bb####dddd[a[cccccc[	chr16:28372732-28373173(-)$1	441	188	220	87.8518
]bb22bb]ccc>>>>>>>>>>>>>>>>>>>>>	chr2:90978134-90978606(-)$1	472	399	431	87.8518
==:::::::CCCYYBB}FFFFFF}JJJJJJJJ	chr2:155974743-155975153(-)$1	410	370	402	83.4074
ccc]a]dddd:::::::::::::EEEEE}BB/	chr8:13370985-13371453(+)$1	468	150	182	87.8518
ddd::::::dddd[a[a[a[a[a[a[a[a[an	chr2:28309249-28309670(+)$1	421	224	256	66.1851
cc]bb666666dddd]dddd]ddddGGGGGGG	chr5:45190627-45190944(-)$1	317	84	116	74.0555
IIIIIIIISSSSSSSSSSCCC:::::::::::	chr1:74337628-74337922(+)$1	294	48	80	87.8518
ggggggwwwwwwwwwwwwwwggggggg22ddd	chr15:100225326-100225762(-)$1	436	259	291	78.4074
EEEKKBB{DDDD{BBhhhhhhhhqqqqqqqqh	chr16:33005723-33006053(+)$1	330	116	148	65.6296
bb]a]dddd]ccc]a]bba]ccc::=======	chr18:61086560-61086783(+)$1	223	145	177	87.8518
]a]bb]dddd:::::::::::CCC{BBKKA{C	chr6:110653200-110653642(+)$1	442	20	52	87.8518
mmmm===========::::::::::::JJJJJ	chr10:79736946-79737326(+)$1	380	132	164	65.4444

#DB
)).))))))..)).)))))((((((((....)	chr6:73213895-73214266(+)$1	1	173	205	87.8518
))))))))))(((((...((.(((.(.((((.	chr3:28493786-28494175(+)$1	1	226	258	87.8518
((.(.(.((.(((.(((.(((.(.(.(.((.(	chr12:68322051-68322546(-)$1	1	263	295	87.8518
(((.(...(((....((((((((((((.....	chr2:163841584-163841971(+)$1	1	96	128	65.4444
)))).....)))..)))).).)).).)))).)	chr1:175274896-175275273(-)$1	1	291	323	87.8518
(.((((.((((..((.(.((((((((((((((	chr7:71879400-71879781(+)$1	1	197	229	87.8518
.)).))..)).))).))).))...))))))).	chr17:17976503-17976850(+)$1	1	110	142	74.8888
))))).).)))))).)).)).....))))).)	chr3:80605271-80605759(-)$1	1	280	312	87.8518
...))))))))))).))).))))).(((..((	chr8:40130698-40131025(+)$1	1	146	178	64.8888
)))))))))))).)))....)))).)).))((	chr5:145653792-145654141(-)$1	1	189	221	74.0555
.((.((.((..((.(.(((((((((.((....	chr17:47067317-47067664(-)$1	1	0	32	87.8518
..))))))((((.(((((((((((......))	chr3:126928443-126928923(-)$1	1	276	308	78.8703
)).)))))..))..))).)))..))).))(((	chr6:108306397-108306781(+)$1	1	195	227	87.8518
)))))........(((((((........)).)	chr5:96590505-96590911(-)$1	1	363	395	66.0925
)))))))...))).)))).))).))).)).))	chr18:10811902-10812391(+)$1	1	425	457	87.8518
)).)))))).)).))))).).))))))))..)	chr2:115888705-115889133(-)$1	1	237	269	65.6296
(.(.(.(.((......................	chr11:75451604-75452086(+)$1	1	175	207	87.8518
)))..))))...)).)).)))).)...).).)	chr17:66729661-66730135(-)$1	1	178	210	87.8518
)))))........)))))))))))))))))))	chr19:45852839-45853210(-)$1	1	138	170	60.8148
.....)))))))...............((((.	chr11:121323012-121323332(+)$1	1	186	218	83.2222
....)))).))((((..(.((((.(.((((((	chr10:62025647-62025966(-)$1	1	65	97	87.8518
(.(.((.(.(((.((....(..(((.(.(.((	chr15:99059780-99060159(+)$1	1	225	257	87.8518
))).)))))).).)).))).))))...)))))	chr4:148709019-148709353(-)$1	1	250	282	61.8333
................................	chr15:100787913-100788347(+)$1	1	159	191	87.8518
.......................)))).).))	chr5:144312077-144312381(+)$1	1	99	131	87.8518
).)))..))).)).....)))))).)).))).	chr12:70425028-70425384(-)$1	1	184	216	87.8518
((((((.((.......................	chr12:15816293-15816638(-)$1	1	170	202	87.8518
.(((.(.(((((.(((.(.(((.(.((((.(.	chr5:68238185-68238514(-)$1	1	189	221	83.6851
.(((((.(.............((((.(((.((	chr3:136594609-136595092(+)$1	1	134	166	87.8518
(((....))))))))))))))))(((((((.(	chr17:24777491-24777817(-)$1	1	122	154	65.7222
)......................((((((((.	chr4:109958841-109959327(-)$1	1	289	321	87.8518
))))))...))))).)))).))))...)))((	chr10:57245114-57245537(-)$1	1	110	142	78.6851
)))...)).)))))).))))).))))).))))	chr9:40153367-40153855(-)$1	1	387	419	87.8518
.(((.(((.(((.(((((((.(((....((.(	chr15:84533464-84533838(+)$1	1	217	249	87.8518
(.(((.(((((.((..(((.(((((.......	chr4:24825713-24826196(+)$1	1	199	231	87.8518
(.(.(.((((...(.((...........(((.	chr17:34070794-34071291(+)$1	1	284	316	83.4074
))))))))))))))))).))))))))))))))	chr2:90403875-90404326(-)$1	1	256	288	83.2222
.....))........................)	chr19:6066586-6066878(-)$1	1	99	131	87.8518
))..)))))))))..........(((((((((	chr17:75040679-75041079(+)$1	1	80	112	65.1666
((.((.((.((((.....(((((((((((...	chr4:101296290-101296695(+)$1	1	181	213	60.8148
((...............(((((((.((.((.(	chrX:130971789-130972073(+)$1	1	62	94	87.8518
)))))..(((((....)))))...))).))))	chr16:94631108-94631606(+)$1	1	460	492	65.5370
(.....((....((....((((.(.((((((.	chr16:28372732-28373173(-)$1	1	188	220	87.8518
.))..)).))).....................	chr2:90978134-90978606(-)$1	1	399	431	87.8518
)).......)))..)).)))))).))))))))	chr2:155974743-155975153(-)$1	1	370	402	83.4074
))).).)))).............))))).)).	chr8:13370985-13371453(+)$1	1	150	182	87.8518
)))......((((.(.(.(.(.(.(.(.(.(.	chr2:28309249-28309670(+)$1	1	224	256	66.1851
)).))......)))).)))).))))(((((((	chr5:45190627-45190944(-)$1	1	84	116	74.0555
((((((((..........(((...........	chr1:74337628-74337922(+)$1	1	48	80	87.8518
((((((..............)))))))..)))	chr15:100225326-100225762(-)$1	1	259	291	78.4074
(((..((.((((.((((((((((........)	chr16:33005723-33006053(+)$1	1	116	148	65.6296
)).).)))).))).).))).)))..(((((((	chr18:61086560-61086783(+)$1	1	145	177	87.8518
.).)).))))...........(((.((..(.(	chr6:110653200-110653642(+)$1	1	20	52	87.8518
....)))))))))))............)))))	chr10:79736946-79737326(+)$1	1	132	164	65.4444

#PSSM
u : 0.85	U : 0.09	c : 0.01	A : 0.01	G : 0.01	
g : 0.87	G : 0.05	C : 0.03	U : 0.01	u : 0.01	
u : 0.79	c : 0.07	U : 0.05	G : 0.03	C : 0.01	a : 0.01	
g : 0.87	G : 0.05	C : 0.03	c : 0.01	U : 0.01	
u : 0.88	U : 0.07	a : 0.01	c : 0.01	
g : 0.92	G : 0.05	U : 0.01	
u : 0.88	U : 0.05	G : 0.01	c : 0.01	a : 0.01	
g : 0.90	G : 0.05	u : 0.01	c : 0.01	
u : 0.87	c : 0.05	U : 0.03	A : 0.01	a : 0.01	
g : 0.87	G : 0.05	a : 0.03	c : 0.03	
u : 0.90	U : 0.05	c : 0.03	
g : 0.88	G : 0.05	c : 0.03	a : 0.01	
u : 0.92	U : 0.05	g : 0.01	
g : 0.94	G : 0.05	
u : 0.94	U : 0.03	C : 0.01	
g : 0.87	c : 0.03	G : 0.03	u : 0.03	A : 0.01	
u : 0.92	U : 0.03	c : 0.01	A : 0.01	
g : 0.90	G : 0.05	a : 0.03	
u : 0.90	c : 0.03	A : 0.01	C : 0.01	U : 0.01	
g : 0.88	G : 0.05	a : 0.05	
u : 0.90	c : 0.03	U : 0.03	A : 0.01	
g : 0.90	G : 0.05	a : 0.03	
u : 0.90	C : 0.03	U : 0.01	c : 0.01	a : 0.01	
g : 0.90	G : 0.07	a : 0.01	
u : 0.92	U : 0.05	c : 0.01	
g : 0.92	G : 0.03	a : 0.01	U : 0.01	
u : 0.88	U : 0.05	c : 0.03	A : 0.01	
g : 0.92	G : 0.07	
u : 0.90	U : 0.03	A : 0.01	C : 0.01	c : 0.01	
g : 0.90	G : 0.03	U : 0.03	u : 0.01	
u : 0.87	U : 0.05	A : 0.03	G : 0.03	
g : 0.81	G : 0.12	a : 0.01	c : 0.01	A : 0.01	

#score	4350.6666666666615
#seq	54
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_SRSF1_Pandit2013_mm9_UTR_m1_run1.nuc.txt

#NT
CUUUUCUUC	chr14:27353252-27353463(-)$1	211	174	183	15.4090
CUUUGUUUU	chr4:106722034-106722242(+)$1	208	28	37	15.2954
CUUCUUUUU	chr5:100464543-100464767(-)$1	224	177	186	15.6363
CUUUCCUUA	chr11:118181342-118181573(-)$1	231	17	26	10.9772
CUUUUAUUU	chr5:24881686-24881922(-)$1	236	48	57	16.0909
GUUUUUUUC	chr4:132732273-132732496(+)$1	223	82	91	14.0454
CUUUUUCUU	chr11:72563554-72563770(+)$1	216	4	13	14.7272
CUUAUUUUU	chr4:86253706-86253933(-)$1	227	83	92	15.2954
CUUCUUUUU	chr4:144721575-144721783(-)$1	208	45	54	15.6363
CUGUUUUUC	chr8:108167353-108167563(+)$1	210	47	56	13.9318
AUUUUUUUC	chr11:106643914-106644131(-)$1	217	4	13	13.9318
CUUUUUUCA	chr2:121977288-121977499(+)$1	211	82	91	13.5909
CUUUUUUUU	chr2:52997075-52997281(-)$1	206	123	132	19.2727
CUUUUAUUA	chr10:5274245-5274472(+)$1	227	78	87	14.5000
CUUUUUUUA	chr7:126930850-126931077(-)$1	227	60	69	17.6818
CUUCUUUUU	chr12:66143392-66143606(+)$1	214	12	21	15.6363
CUUGUUUUG	chr6:28481304-28481530(+)$1	226	88	97	13.8181
CAUUUAUUU	chr18:25503294-25503508(+)$1	214	55	64	11.8863
CUUUUUUCU	chr11:94813362-94813604(+)$1	242	183	192	15.1818
GUUUUUUUU	chr5:125605186-125605402(-)$1	216	27	36	14.8409
cuguuuuug	chr5:147104153-147104372(+)$1	219	6	15	13.0227
CUUUUUUGG	chr2:119915992-119916220(-)$1	228	51	60	13.2499
CUUUUGUUU	chr12:88779261-88779492(-)$1	231	204	213	15.9772
CUUUCUUUC	chr1:74719386-74719594(+)$1	208	18	27	14.8409
CUUGUUUUU	chr11:86546028-86546260(-)$1	232	75	84	15.5227
CAUUUUUUU	chr18:42213325-42213548(+)$1	223	14	23	15.0681
CUUUUUUCC	chr10:58833723-58833947(+)$1	224	10	19	14.3863
CUUUUUUUC	chr11:68936919-68937143(-)$1	224	19	28	18.4772
CUUGUCUUU	chr9:55068747-55068961(+)$1	214	113	122	12.4545
CUUUUGUUU	chr9:53466602-53466812(-)$1	210	13	22	15.9772
CUUCUCUUC	chr4:132099876-132100092(+)$1	216	78	87	11.7727
CUUUUUUAA	chr11:80211814-80212024(+)$1	210	46	55	13.3636
CUUUCUUUG	chr5:123889978-123890204(+)$1	226	44	53	13.9318
CCUUUUUUA	chr3:55796308-55796523(-)$1	215	75	84	13.2500
CUUUCUUUC	chr10:127466898-127467123(+)$1	225	49	58	14.8409
CUUUUUAUU	chr11:62194828-62195063(-)$1	235	78	87	14.7272
CUUUUGUUU	chr11:101079877-101080097(-)$1	220	16	25	15.9772
CUUUUUUUC	chr10:10905078-10905284(+)$1	206	27	36	18.4772
CUUUCAUUC	chr9:20448960-20449189(-)$1	229	213	222	11.6590
CAUUUUUUU	chr17:66479119-66479340(+)$1	221	58	67	15.0681
cuuugcuuc	chr17:36177089-36177311(-)$1	222	24	33	11.4318
CUUUUUUUU	chr5:124845894-124846132(-)$1	238	58	67	19.2727
CUUUUUGUC	chr15:40702058-40702264(+)$1	206	178	187	13.9318

#otherMatches

#Struct PSSM
ff%%%%%%b	chr11:77839300-77839532(+)$1	232	56	65	17.5681
b"""fffff	chr14:27353252-27353463(-)$1	211	174	183	15.4090
gggg!!ddd	chr4:106722034-106722242(+)$1	208	28	37	15.2954
2dddd]===	chr5:100464543-100464767(-)$1	224	177	186	15.6363
lllffffff	chr11:118181342-118181573(-)$1	231	17	26	10.9772
ddd::::::	chr5:24881686-24881922(-)$1	236	48	57	16.0909
hh!!fffff	chr4:132732273-132732496(+)$1	223	82	91	14.0454
:::::::::	chr11:72563554-72563770(+)$1	216	4	13	14.7272
:ffffff!!	chr4:86253706-86253933(-)$1	227	83	92	15.2954
eeeee"""c	chr4:144721575-144721783(-)$1	208	45	54	15.6363
bggggggg[	chr8:108167353-108167563(+)$1	210	47	56	13.9318
C{IIIIIII	chr11:106643914-106644131(-)$1	217	4	13	13.9318
ttttttttt	chr2:121977288-121977499(+)$1	211	82	91	13.5909
:::::::::	chr2:52997075-52997281(-)$1	206	123	132	19.2727
HHHHHHHH{	chr10:5274245-5274472(+)$1	227	78	87	14.5000
:iiiiiiii	chr7:126930850-126931077(-)$1	227	60	69	17.6818
DDDDHHHHH	chr12:66143392-66143606(+)$1	214	12	21	15.6363
4dddddddd	chr6:28481304-28481530(+)$1	226	88	97	13.8181
ggggggg[d	chr18:25503294-25503508(+)$1	214	55	64	11.8863
:::::::gg	chr11:94813362-94813604(+)$1	242	183	192	15.1818
:::::::::	chr5:125605186-125605402(-)$1	216	27	36	14.8409
:::::::::	chr5:147104153-147104372(+)$1	219	6	15	13.0227
333eeeee]	chr2:119915992-119916220(-)$1	228	51	60	13.2499
FFFF}CCC:	chr12:88779261-88779492(-)$1	231	204	213	15.9772
)))))))ff	chr1:74719386-74719594(+)$1	208	18	27	14.8409
GGGKKEEEE	chr11:86546028-86546260(-)$1	232	75	84	15.5227
BB:::::::	chr18:42213325-42213548(+)$1	223	14	23	15.0681
:::::::::	chr10:58833723-58833947(+)$1	224	10	19	14.3863
::::::eee	chr11:68936919-68937143(-)$1	224	19	28	18.4772
33eeeee22	chr9:55068747-55068961(+)$1	214	113	122	12.4545
d[=======	chr9:53466602-53466812(-)$1	210	13	22	15.9772
:::::::::	chr4:132099876-132100092(+)$1	216	78	87	11.7727
eee55555e	chr11:80211814-80212024(+)$1	210	46	55	13.3636
::::::::=	chr5:123889978-123890204(+)$1	226	44	53	13.9318
]ccc]ffff	chr3:55796308-55796523(-)$1	215	75	84	13.2500
'eeeeemmm	chr10:127466898-127467123(+)$1	225	49	58	14.8409
ff[gggggg	chr11:62194828-62195063(-)$1	235	78	87	14.7272
qqqqqgggg	chr11:101079877-101080097(-)$1	220	16	25	15.9772
EEEFFFFFF	chr10:10905078-10905284(+)$1	206	27	36	18.4772
f:GGGGGGG	chr9:20448960-20449189(-)$1	229	213	222	11.6590
b[hhhhhhh	chr17:66479119-66479340(+)$1	221	58	67	15.0681
EEE::FFFF	chr17:36177089-36177311(-)$1	222	24	33	11.4318
DDDDDDDDE	chr5:124845894-124846132(-)$1	238	58	67	19.2727
ggggg::DD	chr15:40702058-40702264(+)$1	206	178	187	13.9318

#DB
((......(	chr11:77839300-77839532(+)$1	1	56	65	17.5681
(...(((((	chr14:27353252-27353463(-)$1	1	174	183	15.4090
((((..(((	chr4:106722034-106722242(+)$1	1	28	37	15.2954
.)))).)))	chr5:100464543-100464767(-)$1	1	177	186	15.6363
...))))))	chr11:118181342-118181573(-)$1	1	17	26	10.9772
)))......	chr5:24881686-24881922(-)$1	1	48	57	16.0909
((..(((((	chr4:132732273-132732496(+)$1	1	82	91	14.0454
.........	chr11:72563554-72563770(+)$1	1	4	13	14.7272
.((((((..	chr4:86253706-86253933(-)$1	1	83	92	15.2954
(((((...(	chr4:144721575-144721783(-)$1	1	45	54	15.6363
((((((((.	chr8:108167353-108167563(+)$1	1	47	56	13.9318
(.(((((((	chr11:106643914-106644131(-)$1	1	4	13	13.9318
.........	chr2:121977288-121977499(+)$1	1	82	91	13.5909
.........	chr2:52997075-52997281(-)$1	1	123	132	19.2727
((((((((.	chr10:5274245-5274472(+)$1	1	78	87	14.5000
.((((((((	chr7:126930850-126931077(-)$1	1	60	69	17.6818
(((((((((	chr12:66143392-66143606(+)$1	1	12	21	15.6363
.))))))))	chr6:28481304-28481530(+)$1	1	88	97	13.8181
(((((((.(	chr18:25503294-25503508(+)$1	1	55	64	11.8863
.......((	chr11:94813362-94813604(+)$1	1	183	192	15.1818
.........	chr5:125605186-125605402(-)$1	1	27	36	14.8409
.........	chr5:147104153-147104372(+)$1	1	6	15	13.0227
...))))).	chr2:119915992-119916220(-)$1	1	51	60	13.2499
)))).))).	chr12:88779261-88779492(-)$1	1	204	213	15.9772
.......((	chr1:74719386-74719594(+)$1	1	18	27	14.8409
(((..((((	chr11:86546028-86546260(-)$1	1	75	84	15.5227
((.......	chr18:42213325-42213548(+)$1	1	14	23	15.0681
.........	chr10:58833723-58833947(+)$1	1	10	19	14.3863
......(((	chr11:68936919-68937143(-)$1	1	19	28	18.4772
..)))))..	chr9:55068747-55068961(+)$1	1	113	122	12.4545
(.(((((((	chr9:53466602-53466812(-)$1	1	13	22	15.9772
.........	chr4:132099876-132100092(+)$1	1	78	87	11.7727
))).....)	chr11:80211814-80212024(+)$1	1	46	55	13.3636
........(	chr5:123889978-123890204(+)$1	1	44	53	13.9318
.))).))))	chr3:55796308-55796523(-)$1	1	75	84	13.2500
.(((((...	chr10:127466898-127467123(+)$1	1	49	58	14.8409
((.((((((	chr11:62194828-62195063(-)$1	1	78	87	14.7272
.....))))	chr11:101079877-101080097(-)$1	1	16	25	15.9772
(((((((((	chr10:10905078-10905284(+)$1	1	27	36	18.4772
).)))))))	chr9:20448960-20449189(-)$1	1	213	222	11.6590
(.(((((((	chr17:66479119-66479340(+)$1	1	58	67	15.0681
(((..((((	chr17:36177089-36177311(-)$1	1	24	33	11.4318
(((((((((	chr5:124845894-124846132(-)$1	1	58	67	19.2727
)))))..))	chr15:40702058-40702264(+)$1	1	178	187	13.9318

#PSSM
C : 0.88	G : 0.04	c : 0.04	A : 0.02	
U : 0.86	A : 0.06	u : 0.04	C : 0.02	
U : 0.93	G : 0.02	g : 0.02	u : 0.02	
U : 0.77	C : 0.09	G : 0.06	u : 0.04	A : 0.02	
U : 0.81	C : 0.11	G : 0.02	u : 0.02	g : 0.02	
U : 0.70	C : 0.09	A : 0.09	G : 0.06	u : 0.02	c : 0.02	
U : 0.88	u : 0.04	C : 0.02	A : 0.02	G : 0.02	
U : 0.84	C : 0.06	u : 0.04	G : 0.02	A : 0.02	
U : 0.45	C : 0.27	A : 0.13	G : 0.09	g : 0.02	c : 0.02	

#score	651.6363636363634
#seq	44
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012a_mm9_CDS_m2_run2.nuc.txt

#NT
UCUGUCU	chr16:35299447-35299697(+)$1	250	82	89	16.7142
GCUGUCU	chr9:30959798-30960060(-)$1	262	189	196	12.4285
UCUGCCU	chr6:4706066-4706310(+)$1	244	3	10	12.7460
UCUGGCU	chr7:17501488-17501778(-)$1	290	183	190	13.2222
UCUCUCU	chr14:76818619-76818854(+)$1	235	135	142	12.9047
UCUGUCU	chr2:71114420-71114661(-)$1	241	68	75	16.7142
UGUGUCU	chr11:100888528-100888792(+)$1	264	194	201	13.1428
UCUGCCU	chr4:148761180-148761417(-)$1	237	25	32	12.7460
UCUGUCG	chr3:95023988-95024224(-)$1	236	94	101	12.1904
UCUGUCU	chr13:94994830-94995082(-)$1	252	49	56	16.7142
UCUGUUU	chr11:87794612-87794923(-)$1	311	161	168	12.4285
UCUUUCU	chr3:19968893-19969128(+)$1	235	43	50	12.9047
UCUGGCU	chr9:58430182-58430417(+)$1	235	111	118	13.2222
UCUGGCU	chr7:106603330-106603565(+)$1	235	20	27	13.2222
GCUGUCU	chrX:10172306-10172551(+)$1	245	120	127	12.4285
UCUUUCU	chr12:111865180-111865415(+)$1	235	171	178	12.9047
UCUGGCU	chr7:149573591-149573839(-)$1	248	91	98	13.2222
UCCGUCU	chr11:109528789-109529095(+)$1	306	118	125	12.1904
UUUGUCU	chr5:104508405-104508686(-)$1	281	30	37	13.3809
UCUGUCU	chr1:174215791-174216026(-)$1	235	41	48	16.7142
UCUUUCU	chr8:67071868-67072108(-)$1	240	108	115	12.9047
UUUGUCU	chr10:29067362-29067599(-)$1	237	23	30	13.3809
UCUGGCU	chr11:59220569-59220827(-)$1	258	34	41	13.2222
UGUGUCU	chr3:146395453-146395688(-)$1	235	91	98	13.1428
UCUGUCG	chr14:65673532-65673769(-)$1	237	48	55	12.1904
UCUGACU	chr5:137736972-137737209(-)$1	237	32	39	12.6666
UUUGUCU	chr4:126707100-126707361(+)$1	261	135	142	13.3809
UCUCUCU	chrX:133369561-133369797(+)$1	236	52	59	12.9047
UCUGUUU	chrX:148326258-148326496(+)$1	238	204	211	12.4285
CCUGUCU	chr5:125546130-125546365(-)$1	235	77	84	12.4285
UCUGUUU	chr6:108491854-108492100(+)$1	246	18	25	12.4285
UCUGGCU	chr11:4964001-4964239(-)$1	238	2	9	13.2222
CCUGUCU	chr11:78138010-78138267(+)$1	257	69	76	12.4285
UGUGUCU	chr11:87863329-87863588(+)$1	259	134	141	13.1428
UCUGUCU	chr16:35293974-35294230(+)$1	256	125	132	16.7142
CCUGUCU	chr1:83273913-83274169(-)$1	256	243	250	12.4285
UCUGUGU	chr2:131762809-131763094(+)$1	285	224	231	12.4285
UCUGUCU	chr8:56140641-56140894(+)$1	253	73	80	16.7142
UCUGUGU	chr19:4726530-4726776(+)$1	246	26	33	12.4285
UCugugu	chr5:104513928-104514170(-)$1	242	210	217	12.4285
UUUGUCU	chrX:148317008-148317269(+)$1	261	6	13	13.3809
UCUUUCU	chr19:7289793-7290030(-)$1	237	35	42	12.9047
UUUGUCU	chr15:9104843-9105086(+)$1	243	91	98	13.3809
UCAGUCU	chr2:129444097-129444360(+)$1	263	46	53	12.1904
UCUGUCU	chr10:34018422-34018682(+)$1	260	191	198	16.7142
UCUGUCU	chr1:193602238-193602475(+)$1	237	6	13	16.7142
UUUGUCU	chr1:135533828-135534091(-)$1	263	36	43	13.3809
GCUGUCU	chr17:24642176-24642411(+)$1	235	40	47	12.4285
UCAGUCU	chr19:10058581-10058825(+)$1	244	85	92	12.1904
UCUCUCU	chr7:65047791-65048042(+)$1	251	55	62	12.9047
UCUGUCA	chr9:36557080-36557315(-)$1	235	43	50	12.1904
UCCGUCU	chrX:162824700-162824996(+)$1	296	107	114	12.1904
UCUUUCU	chr1:174210640-174210877(-)$1	237	15	22	12.9047
UUUGUCU	chr11:50014060-50014371(-)$1	311	106	113	13.3809
UCUCUCU	chr10:106256389-106256638(+)$1	249	118	125	12.9047
UCUGUCU	chr7:104877404-104877644(-)$1	240	25	32	16.7142
UCUCUCU	chr8:96491846-96492107(+)$1	261	70	77	12.9047
UCUGUCA	chr7:129771219-129771472(+)$1	253	137	144	12.1904
UGUGUCU	chr13:74309433-74309675(-)$1	242	177	184	13.1428
UGUGUCU	chr13:78336959-78337194(-)$1	235	127	134	13.1428
UCUGGCU	chr11:60530652-60530893(-)$1	241	124	131	13.2222
UUUGUCU	chr8:47292820-47293064(-)$1	244	77	84	13.3809

#otherMatches

#Struct PSSM
FFFF{BB	chr16:14153931-14154176(-)$1	245	99	106	13.2222
dcccsss	chr16:35299447-35299697(+)$1	250	82	89	16.7142
c]ccc::	chr9:30959798-30960060(-)$1	262	189	196	12.4285
eeeemmm	chr6:4706066-4706310(+)$1	244	3	10	12.7460
iiiiiif	chr7:17501488-17501778(-)$1	290	183	190	13.2222
]eeeee]	chr14:76818619-76818854(+)$1	235	135	142	12.9047
[dddd&&	chr2:71114420-71114661(-)$1	241	68	75	16.7142
rrggggg	chr11:100888528-100888792(+)$1	264	194	201	13.1428
""ggggg	chr4:148761180-148761417(-)$1	237	25	32	12.7460
bbmmmmb	chr3:95023988-95024224(-)$1	236	94	101	12.1904
llccc]c	chr13:94994830-94995082(-)$1	252	49	56	16.7142
E{EEEEE	chr11:87794612-87794923(-)$1	311	161	168	12.4285
bb22ccc	chr3:19968893-19969128(+)$1	235	43	50	12.9047
ddddbb[	chr9:58430182-58430417(+)$1	235	111	118	13.2222
B{CCC::	chr7:106603330-106603565(+)$1	235	20	27	13.2222
bbnnnnn	chrX:10172306-10172551(+)$1	245	120	127	12.4285
iiiiccc	chr12:111865180-111865415(+)$1	235	171	178	12.9047
ogggggg	chr7:149573591-149573839(-)$1	248	91	98	13.2222
444ffff	chr11:109528789-109529095(+)$1	306	118	125	12.1904
vvvccc:	chr5:104508405-104508686(-)$1	281	30	37	13.3809
cGGGGGG	chr1:174215791-174216026(-)$1	235	41	48	16.7142
fff]ccc	chr8:67071868-67072108(-)$1	240	108	115	12.9047
FKKBBSS	chr10:29067362-29067599(-)$1	237	23	30	13.3809
FFFa!!d	chr11:59220569-59220827(-)$1	258	34	41	13.2222
$$$$fff	chr3:146395453-146395688(-)$1	235	91	98	13.1428
"""dddd	chr14:65673532-65673769(-)$1	237	48	55	12.1904
f[ccc##	chr5:137736972-137737209(-)$1	237	32	39	12.6666
>>>>iii	chr4:126707100-126707361(+)$1	261	135	142	13.3809
GGGGGGG	chrX:133369561-133369797(+)$1	236	52	59	12.9047
YYEEEEE	chrX:148326258-148326496(+)$1	238	204	211	12.4285
FFFFggg	chr5:125546130-125546365(-)$1	235	77	84	12.4285
JJJJJJJ	chr6:108491854-108492100(+)$1	246	18	25	12.4285
LLLEEEE	chr11:4964001-4964239(-)$1	238	2	9	13.2222
fff]ccc	chr11:78138010-78138267(+)$1	257	69	76	12.4285
hhhhhhh	chr11:87863329-87863588(+)$1	259	134	141	13.1428
i333bb3	chr16:35293974-35294230(+)$1	256	125	132	16.7142
dFFFFFF	chr1:83273913-83274169(-)$1	256	243	250	12.4285
:eeeeen	chr2:131762809-131763094(+)$1	285	224	231	12.4285
#ddddnn	chr8:56140641-56140894(+)$1	253	73	80	16.7142
EEEEE{A	chr19:4726530-4726776(+)$1	246	26	33	12.4285
ccc333c	chr5:104513928-104514170(-)$1	242	210	217	12.4285
ffffbbo	chrX:148317008-148317269(+)$1	261	6	13	13.3809
[axxxxx	chr19:7289793-7290030(-)$1	237	35	42	12.9047
OOOOOBB	chr15:9104843-9105086(+)$1	243	91	98	13.3809
###cccp	chr2:129444097-129444360(+)$1	263	46	53	12.1904
mdddd]d	chr10:34018422-34018682(+)$1	260	191	198	16.7142
hhhheee	chr1:193602238-193602475(+)$1	237	6	13	16.7142
::bb[dd	chr1:135533828-135534091(-)$1	263	36	43	13.3809
bb22eee	chr17:24642176-24642411(+)$1	235	40	47	12.4285
:::cccs	chr19:10058581-10058825(+)$1	244	85	92	12.1904
xxxxxxx	chr7:65047791-65048042(+)$1	251	55	62	12.9047
cnnnnnc	chr9:36557080-36557315(-)$1	235	43	50	12.1904
###ccco	chrX:162824700-162824996(+)$1	296	107	114	12.1904
FFFFFF{	chr1:174210640-174210877(-)$1	237	15	22	12.9047
YYDDDD:	chr11:50014060-50014371(-)$1	311	106	113	13.3809
D{CCCDD	chr10:106256389-106256638(+)$1	249	118	125	12.9047
ddd[fff	chr7:104877404-104877644(-)$1	240	25	32	16.7142
ccc4444	chr8:96491846-96492107(+)$1	261	70	77	12.9047
::ggggg	chr7:129771219-129771472(+)$1	253	137	144	12.1904
~IIIIII	chr13:74309433-74309675(-)$1	242	177	184	13.1428
ddd[eee	chr13:78336959-78337194(-)$1	235	127	134	13.1428
dd:cccd	chr11:60530652-60530893(-)$1	241	124	131	13.2222
##fffff	chr8:47292820-47293064(-)$1	244	77	84	13.3809

#DB
((((.((	chr16:14153931-14154176(-)$1	1	99	106	13.2222
((((...	chr16:35299447-35299697(+)$1	1	82	89	16.7142
).)))..	chr9:30959798-30960060(-)$1	1	189	196	12.4285
((((...	chr6:4706066-4706310(+)$1	1	3	10	12.7460
(((((((	chr7:17501488-17501778(-)$1	1	183	190	13.2222
.))))).	chr14:76818619-76818854(+)$1	1	135	142	12.9047
.((((..	chr2:71114420-71114661(-)$1	1	68	75	16.7142
..)))))	chr11:100888528-100888792(+)$1	1	194	201	13.1428
..(((((	chr4:148761180-148761417(-)$1	1	25	32	12.7460
((....)	chr3:95023988-95024224(-)$1	1	94	101	12.1904
..))).)	chr13:94994830-94995082(-)$1	1	49	56	16.7142
(.(((((	chr11:87794612-87794923(-)$1	1	161	168	12.4285
))..)))	chr3:19968893-19969128(+)$1	1	43	50	12.9047
((((((.	chr9:58430182-58430417(+)$1	1	111	118	13.2222
(.(((..	chr7:106603330-106603565(+)$1	1	20	27	13.2222
((.....	chrX:10172306-10172551(+)$1	1	120	127	12.4285
(((((((	chr12:111865180-111865415(+)$1	1	171	178	12.9047
.))))))	chr7:149573591-149573839(-)$1	1	91	98	13.2222
...))))	chr11:109528789-109529095(+)$1	1	118	125	12.1904
...))).	chr5:104508405-104508686(-)$1	1	30	37	13.3809
)((((((	chr1:174215791-174216026(-)$1	1	41	48	16.7142
))).)))	chr8:67071868-67072108(-)$1	1	108	115	12.9047
(..((..	chr10:29067362-29067599(-)$1	1	23	30	13.3809
((((..(	chr11:59220569-59220827(-)$1	1	34	41	13.2222
....(((	chr3:146395453-146395688(-)$1	1	91	98	13.1428
...((((	chr14:65673532-65673769(-)$1	1	48	55	12.1904
(.(((..	chr5:137736972-137737209(-)$1	1	32	39	12.6666
....)))	chr4:126707100-126707361(+)$1	1	135	142	13.3809
(((((((	chrX:133369561-133369797(+)$1	1	52	59	12.9047
..)))))	chrX:148326258-148326496(+)$1	1	204	211	12.4285
))))(((	chr5:125546130-125546365(-)$1	1	77	84	12.4285
(((((((	chr6:108491854-108492100(+)$1	1	18	25	12.4285
...((((	chr11:4964001-4964239(-)$1	1	2	9	13.2222
))).)))	chr11:78138010-78138267(+)$1	1	69	76	12.4285
(((((((	chr11:87863329-87863588(+)$1	1	134	141	13.1428
)...)).	chr16:35293974-35294230(+)$1	1	125	132	16.7142
)))))))	chr1:83273913-83274169(-)$1	1	243	250	12.4285
.(((((.	chr2:131762809-131763094(+)$1	1	224	231	12.4285
.((((..	chr8:56140641-56140894(+)$1	1	73	80	16.7142
(((((.(	chr19:4726530-4726776(+)$1	1	26	33	12.4285
)))...)	chr5:104513928-104514170(-)$1	1	210	217	12.4285
((((((.	chrX:148317008-148317269(+)$1	1	6	13	13.3809
.(.....	chr19:7289793-7290030(-)$1	1	35	42	12.9047
.....((	chr15:9104843-9105086(+)$1	1	91	98	13.3809
...(((.	chr2:129444097-129444360(+)$1	1	46	53	12.1904
.)))).)	chr10:34018422-34018682(+)$1	1	191	198	16.7142
(((((((	chr1:193602238-193602475(+)$1	1	6	13	16.7142
..((.((	chr1:135533828-135534091(-)$1	1	36	43	13.3809
))..)))	chr17:24642176-24642411(+)$1	1	40	47	12.4285
...(((.	chr19:10058581-10058825(+)$1	1	85	92	12.1904
.......	chr7:65047791-65048042(+)$1	1	55	62	12.9047
(.....)	chr9:36557080-36557315(-)$1	1	43	50	12.1904
...(((.	chrX:162824700-162824996(+)$1	1	107	114	12.1904
((((((.	chr1:174210640-174210877(-)$1	1	15	22	12.9047
..)))).	chr11:50014060-50014371(-)$1	1	106	113	13.3809
(.(((((	chr10:106256389-106256638(+)$1	1	118	125	12.9047
(((.(((	chr7:104877404-104877644(-)$1	1	25	32	16.7142
)))....	chr8:96491846-96492107(+)$1	1	70	77	12.9047
..(((((	chr7:129771219-129771472(+)$1	1	137	144	12.1904
.))))))	chr13:74309433-74309675(-)$1	1	177	184	13.1428
(((.(((	chr13:78336959-78337194(-)$1	1	127	134	13.1428
)).((((	chr11:60530652-60530893(-)$1	1	124	131	13.2222
..(((((	chr8:47292820-47293064(-)$1	1	77	84	13.3809

#PSSM
U : 0.90	G : 0.04	C : 0.04	
C : 0.79	U : 0.12	G : 0.07	
U : 0.92	C : 0.03	A : 0.03	u : 0.01	
G : 0.82	C : 0.07	U : 0.07	g : 0.01	
U : 0.80	G : 0.12	C : 0.03	A : 0.01	u : 0.01	
C : 0.90	U : 0.04	G : 0.03	g : 0.01	
U : 0.92	G : 0.03	A : 0.03	u : 0.01	

#score	842.8412698412686
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Nova_Zhang2011b_mm9_transcript_m2_run1.nuc.txt

#NT
auu	chr8:23180588-23180789(+)$1	201	6	9	9.0000
AUU	chr1:46864645-46864846(-)$1	201	13	16	9.0000
auu	chr3:123359654-123359855(-)$1	201	38	41	9.0000
AUU	chr2:112995698-112995899(-)$1	201	48	51	9.0000
AUU	chr17:6147854-6148055(+)$1	201	8	11	9.0000
AUU	chr9:30957340-30957541(-)$1	201	54	57	9.0000
auu	chr18:82730410-82730611(+)$1	201	79	82	9.0000
auu	chr13:118462180-118462381(+)$1	201	108	111	9.0000
AUU	chr17:67593150-67593351(-)$1	201	8	11	9.0000
AUU	chr13:111190917-111191118(+)$1	201	14	17	9.0000
AUU	chr6:144187975-144188176(-)$1	201	1	4	9.0000
auu	chr7:127840678-127840879(+)$1	201	27	30	9.0000
AUU	chr11:66026343-66026544(-)$1	201	89	92	9.0000
AUU	chr12:30474140-30474341(+)$1	201	35	38	9.0000
AUU	chr2:6462806-6463007(-)$1	201	20	23	9.0000
AUU	chr6:39092292-39092493(-)$1	201	99	102	9.0000
auu	chr12:62792504-62792705(+)$1	201	26	29	9.0000
auu	chr14:9129410-9129611(-)$1	201	86	89	9.0000
AUU	chr11:79226117-79226318(+)$1	201	84	87	9.0000
AUU	chr14:39710915-39711116(-)$1	201	11	14	9.0000
AUU	chr3:138610969-138611170(-)$1	201	60	63	9.0000
AUU	chr8:48340648-48340849(-)$1	201	59	62	9.0000
AUU	chr8:16827674-16827875(-)$1	201	71	74	9.0000
AUU	chr10:114138767-114138968(-)$1	201	25	28	9.0000
AUU	chr16:92061700-92061901(+)$1	201	47	50	9.0000
auu	chr5:9475812-9476013(-)$1	201	8	11	9.0000
AUU	chr12:4109978-4110179(+)$1	201	11	14	9.0000
AUU	chr2:42216182-42216383(-)$1	201	20	23	9.0000
AUU	chr6:46524704-46524905(+)$1	201	0	3	9.0000
AUU	chr5:136385376-136385577(-)$1	201	24	27	9.0000
AUU	chr6:122678022-122678223(-)$1	201	99	102	9.0000
AUU	chr2:91435493-91435694(+)$1	201	86	89	9.0000
auu	chr1:94024580-94024781(-)$1	201	8	11	9.0000
auu	chr3:86450069-86450270(+)$1	201	3	6	9.0000
AUU	chr14:39642006-39642207(-)$1	201	39	42	9.0000
AUU	chr12:110803573-110803774(+)$1	201	30	33	9.0000
AUU	chr9:66298263-66298464(+)$1	201	20	23	9.0000
AUU	chr2:21751289-21751490(+)$1	201	40	43	9.0000
AUU	chr3:81836110-81836311(-)$1	201	52	55	9.0000
AUU	chr12:110802943-110803144(+)$1	201	85	88	9.0000
auu	chr3:25761398-25761599(-)$1	201	81	84	9.0000
AUU	chr7:71695213-71695414(+)$1	201	13	16	9.0000
AUU	chr1:182683490-182683691(+)$1	201	32	35	9.0000
AUU	chr12:75028435-75028636(+)$1	201	2	5	9.0000
AUU	chr14:120830152-120830353(+)$1	201	14	17	9.0000
AUU	chr13:41733023-41733224(+)$1	201	62	65	9.0000
AUU	chr2:141813459-141813660(+)$1	201	36	39	9.0000
AUU	chr5:68010708-68010909(-)$1	201	15	18	9.0000
AUU	chr7:85445626-85445827(-)$1	201	78	81	9.0000
AUU	chr18:35024319-35024520(+)$1	201	33	36	9.0000
AUU	chr3:58395576-58395777(+)$1	201	13	16	9.0000
AUU	chr6:8981496-8981697(+)$1	201	28	31	9.0000
AUU	chr9:83028977-83029178(-)$1	201	14	17	9.0000
AUU	chr14:68359943-68360144(+)$1	201	0	3	9.0000
AUU	chr10:48986788-48986989(-)$1	201	24	27	9.0000
AUU	chr10:116789816-116790017(-)$1	201	22	25	9.0000
auu	chr4:82133749-82133950(-)$1	201	99	102	9.0000
AUU	chr2:91435494-91435695(+)$1	201	85	88	9.0000
AUU	chr11:30007000-30007201(-)$1	201	81	84	9.0000
AUU	chr8:4257633-4257834(-)$1	201	131	134	9.0000
auu	chr2:104512737-104512938(-)$1	201	7	10	9.0000
AUU	chr2:4363163-4363364(+)$1	201	7	10	9.0000
AUU	chr13:36817821-36818022(-)$1	201	86	89	9.0000
auu	chr17:8776203-8776404(+)$1	201	55	58	9.0000
AUU	chr6:50151169-50151370(+)$1	201	0	3	9.0000
AUU	chr11:97373719-97373920(-)$1	201	50	53	9.0000
AUU	chr5:72161405-72161606(+)$1	201	3	6	9.0000
AUU	chr19:5797872-5798073(-)$1	201	13	16	9.0000
auu	chr9:8956682-8956883(+)$1	201	14	17	9.0000
AUU	chr16:97372159-97372360(-)$1	201	44	47	9.0000
AUU	chr2:6565647-6565848(-)$1	201	65	68	9.0000
AUU	chr3:57585243-57585444(+)$1	201	11	14	9.0000
AUU	chr1:43872628-43872829(-)$1	201	0	3	9.0000
AUU	chrM:14780-14981(+)$1	201	15	18	9.0000
AUU	chr6:31393263-31393464(+)$1	201	5	8	9.0000
AUU	chr17:13208393-13208594(+)$1	201	56	59	9.0000
auu	chr2:61942114-61942315(+)$1	201	11	14	9.0000
AUU	chr4:76068305-76068506(-)$1	201	96	99	9.0000
auu	chr14:124726707-124726908(-)$1	201	58	61	9.0000
AUU	chr15:30957734-30957935(+)$1	201	150	153	9.0000
AUU	chr19:4786382-4786583(-)$1	201	13	16	9.0000
auu	chrX:100578553-100578754(+)$1	201	17	20	9.0000
AUU	chr19:7501149-7501350(-)$1	201	99	102	9.0000
AUu	chr18:13151299-13151500(+)$1	201	7	10	9.0000
AUU	chr13:97379011-97379212(+)$1	201	15	18	9.0000
AUU	chr2:125500116-125500317(+)$1	201	34	37	9.0000
AUU	chr8:87125194-87125395(+)$1	201	177	180	9.0000
AUU	chr14:33022729-33022930(+)$1	201	79	82	9.0000
AUU	chr2:29857311-29857512(+)$1	201	38	41	9.0000
AUU	chr16:44085560-44085761(-)$1	201	4	7	9.0000
auu	chr18:5617073-5617274(+)$1	201	7	10	9.0000
AUU	chr5:18870740-18870941(+)$1	201	17	20	9.0000
AUU	chr12:76552899-76553100(-)$1	201	14	17	9.0000
AUU	chr3:55339649-55339850(+)$1	201	5	8	9.0000
AUU	chr12:120397614-120397815(-)$1	201	61	64	9.0000
AUU	chr16:67559937-67560138(-)$1	201	19	22	9.0000
AUU	chr14:39727801-39728002(-)$1	201	80	83	9.0000
auu	chr1:181908778-181908979(+)$1	201	54	57	9.0000
AUU	chr5:48607801-48608002(+)$1	201	20	23	9.0000

#otherMatches

#Struct PSSM
cc]	chr1:183105921-183106122(-)$1	201	55	58	9.0000
HHH	chr8:23180588-23180789(+)$1	201	6	9	9.0000
eee	chr1:46864645-46864846(-)$1	201	13	16	9.0000
:FF	chr3:123359654-123359855(-)$1	201	38	41	9.0000
(((	chr2:112995698-112995899(-)$1	201	48	51	9.0000
!!d	chr17:6147854-6148055(+)$1	201	8	11	9.0000
:::	chr9:30957340-30957541(-)$1	201	54	57	9.0000
:::	chr18:82730410-82730611(+)$1	201	79	82	9.0000
vvv	chr13:118462180-118462381(+)$1	201	108	111	9.0000
sss	chr17:67593150-67593351(-)$1	201	8	11	9.0000
cnn	chr13:111190917-111191118(+)$1	201	14	17	9.0000
:::	chr6:144187975-144188176(-)$1	201	1	4	9.0000
JJJ	chr7:127840678-127840879(+)$1	201	27	30	9.0000
333	chr11:66026343-66026544(-)$1	201	89	92	9.0000
a22	chr12:30474140-30474341(+)$1	201	35	38	9.0000
CCL	chr2:6462806-6463007(-)$1	201	20	23	9.0000
www	chr6:39092292-39092493(-)$1	201	99	102	9.0000
hhh	chr12:62792504-62792705(+)$1	201	26	29	9.0000
fff	chr14:9129410-9129611(-)$1	201	86	89	9.0000
$$$	chr11:79226117-79226318(+)$1	201	84	87	9.0000
(((	chr14:39710915-39711116(-)$1	201	11	14	9.0000
xxx	chr3:138610969-138611170(-)$1	201	60	63	9.0000
emm	chr8:48340648-48340849(-)$1	201	59	62	9.0000
fff	chr8:16827674-16827875(-)$1	201	71	74	9.0000
:::	chr10:114138767-114138968(-)$1	201	25	28	9.0000
dd]	chr16:92061700-92061901(+)$1	201	47	50	9.0000
qqq	chr5:9475812-9476013(-)$1	201	8	11	9.0000
:::	chr12:4109978-4110179(+)$1	201	11	14	9.0000
hhh	chr2:42216182-42216383(-)$1	201	20	23	9.0000
EEE	chr6:46524704-46524905(+)$1	201	0	3	9.0000
HH{	chr5:136385376-136385577(-)$1	201	24	27	9.0000
:::	chr6:122678022-122678223(-)$1	201	99	102	9.0000
:::	chr2:91435493-91435694(+)$1	201	86	89	9.0000
:::	chr1:94024580-94024781(-)$1	201	8	11	9.0000
:::	chr3:86450069-86450270(+)$1	201	3	6	9.0000
qqq	chr14:39642006-39642207(-)$1	201	39	42	9.0000
sss	chr12:110803573-110803774(+)$1	201	30	33	9.0000
EMM	chr9:66298263-66298464(+)$1	201	20	23	9.0000
iil	chr2:21751289-21751490(+)$1	201	40	43	9.0000
qqq	chr3:81836110-81836311(-)$1	201	52	55	9.0000
dd]	chr12:110802943-110803144(+)$1	201	85	88	9.0000
dd!	chr3:25761398-25761599(-)$1	201	81	84	9.0000
pgg	chr7:71695213-71695414(+)$1	201	13	16	9.0000
iii	chr1:182683490-182683691(+)$1	201	32	35	9.0000
:::	chr12:75028435-75028636(+)$1	201	2	5	9.0000
)))	chr14:120830152-120830353(+)$1	201	14	17	9.0000
:::	chr13:41733023-41733224(+)$1	201	62	65	9.0000
^^^	chr2:141813459-141813660(+)$1	201	36	39	9.0000
{FF	chr5:68010708-68010909(-)$1	201	15	18	9.0000
%%%	chr7:85445626-85445827(-)$1	201	78	81	9.0000
FFF	chr18:35024319-35024520(+)$1	201	33	36	9.0000
nee	chr3:58395576-58395777(+)$1	201	13	16	9.0000
eee	chr6:8981496-8981697(+)$1	201	28	31	9.0000
UUU	chr9:83028977-83029178(-)$1	201	14	17	9.0000
:::	chr14:68359943-68360144(+)$1	201	0	3	9.0000
LLE	chr10:48986788-48986989(-)$1	201	24	27	9.0000
NNN	chr10:116789816-116790017(-)$1	201	22	25	9.0000
:::	chr4:82133749-82133950(-)$1	201	99	102	9.0000
:::	chr2:91435494-91435695(+)$1	201	85	88	9.0000
ppp	chr11:30007000-30007201(-)$1	201	81	84	9.0000
vvv	chr8:4257633-4257834(-)$1	201	131	134	9.0000
BMM	chr2:104512737-104512938(-)$1	201	7	10	9.0000
:::	chr2:4363163-4363364(+)$1	201	7	10	9.0000
[dd	chr13:36817821-36818022(-)$1	201	86	89	9.0000
DD:	chr17:8776203-8776404(+)$1	201	55	58	9.0000
:::	chr6:50151169-50151370(+)$1	201	0	3	9.0000
:::	chr11:97373719-97373920(-)$1	201	50	53	9.0000
fff	chr5:72161405-72161606(+)$1	201	3	6	9.0000
ooo	chr19:5797872-5798073(-)$1	201	13	16	9.0000
:::	chr9:8956682-8956883(+)$1	201	14	17	9.0000
:::	chr16:97372159-97372360(-)$1	201	44	47	9.0000
qqq	chr2:6565647-6565848(-)$1	201	65	68	9.0000
bmm	chr3:57585243-57585444(+)$1	201	11	14	9.0000
:ee	chr1:43872628-43872829(-)$1	201	0	3	9.0000
DDK	chrM:14780-14981(+)$1	201	15	18	9.0000
b!!	chr6:31393263-31393464(+)$1	201	5	8	9.0000
ddd	chr17:13208393-13208594(+)$1	201	56	59	9.0000
:::	chr2:61942114-61942315(+)$1	201	11	14	9.0000
fff	chr4:76068305-76068506(-)$1	201	96	99	9.0000
b::	chr14:124726707-124726908(-)$1	201	58	61	9.0000
]hh	chr15:30957734-30957935(+)$1	201	150	153	9.0000
h$$	chr19:4786382-4786583(-)$1	201	13	16	9.0000
:::	chrX:100578553-100578754(+)$1	201	17	20	9.0000
000	chr19:7501149-7501350(-)$1	201	99	102	9.0000
:::	chr18:13151299-13151500(+)$1	201	7	10	9.0000
:::	chr13:97379011-97379212(+)$1	201	15	18	9.0000
===	chr2:125500116-125500317(+)$1	201	34	37	9.0000
:::	chr8:87125194-87125395(+)$1	201	177	180	9.0000
hhh	chr14:33022729-33022930(+)$1	201	79	82	9.0000
###	chr2:29857311-29857512(+)$1	201	38	41	9.0000
:::	chr16:44085560-44085761(-)$1	201	4	7	9.0000
:::	chr18:5617073-5617274(+)$1	201	7	10	9.0000
ccq	chr5:18870740-18870941(+)$1	201	17	20	9.0000
$==	chr12:76552899-76553100(-)$1	201	14	17	9.0000
:::	chr3:55339649-55339850(+)$1	201	5	8	9.0000
)))	chr12:120397614-120397815(-)$1	201	61	64	9.0000
b""	chr16:67559937-67560138(-)$1	201	19	22	9.0000
b[b	chr14:39727801-39728002(-)$1	201	80	83	9.0000
:::	chr1:181908778-181908979(+)$1	201	54	57	9.0000
EEK	chr5:48607801-48608002(+)$1	201	20	23	9.0000

#DB
)).	chr1:183105921-183106122(-)$1	1	55	58	9.0000
(((	chr8:23180588-23180789(+)$1	1	6	9	9.0000
(((	chr1:46864645-46864846(-)$1	1	13	16	9.0000
.((	chr3:123359654-123359855(-)$1	1	38	41	9.0000
...	chr2:112995698-112995899(-)$1	1	48	51	9.0000
..(	chr17:6147854-6148055(+)$1	1	8	11	9.0000
...	chr9:30957340-30957541(-)$1	1	54	57	9.0000
...	chr18:82730410-82730611(+)$1	1	79	82	9.0000
...	chr13:118462180-118462381(+)$1	1	108	111	9.0000
...	chr17:67593150-67593351(-)$1	1	8	11	9.0000
(..	chr13:111190917-111191118(+)$1	1	14	17	9.0000
...	chr6:144187975-144188176(-)$1	1	1	4	9.0000
(((	chr7:127840678-127840879(+)$1	1	27	30	9.0000
...	chr11:66026343-66026544(-)$1	1	89	92	9.0000
)..	chr12:30474140-30474341(+)$1	1	35	38	9.0000
((.	chr2:6462806-6463007(-)$1	1	20	23	9.0000
...	chr6:39092292-39092493(-)$1	1	99	102	9.0000
(((	chr12:62792504-62792705(+)$1	1	26	29	9.0000
(((	chr14:9129410-9129611(-)$1	1	86	89	9.0000
...	chr11:79226117-79226318(+)$1	1	84	87	9.0000
...	chr14:39710915-39711116(-)$1	1	11	14	9.0000
...	chr3:138610969-138611170(-)$1	1	60	63	9.0000
(..	chr8:48340648-48340849(-)$1	1	59	62	9.0000
(((	chr8:16827674-16827875(-)$1	1	71	74	9.0000
...	chr10:114138767-114138968(-)$1	1	25	28	9.0000
)).	chr16:92061700-92061901(+)$1	1	47	50	9.0000
...	chr5:9475812-9476013(-)$1	1	8	11	9.0000
...	chr12:4109978-4110179(+)$1	1	11	14	9.0000
(((	chr2:42216182-42216383(-)$1	1	20	23	9.0000
(((	chr6:46524704-46524905(+)$1	1	0	3	9.0000
((.	chr5:136385376-136385577(-)$1	1	24	27	9.0000
...	chr6:122678022-122678223(-)$1	1	99	102	9.0000
...	chr2:91435493-91435694(+)$1	1	86	89	9.0000
...	chr1:94024580-94024781(-)$1	1	8	11	9.0000
...	chr3:86450069-86450270(+)$1	1	3	6	9.0000
...	chr14:39642006-39642207(-)$1	1	39	42	9.0000
...	chr12:110803573-110803774(+)$1	1	30	33	9.0000
(..	chr9:66298263-66298464(+)$1	1	20	23	9.0000
((.	chr2:21751289-21751490(+)$1	1	40	43	9.0000
...	chr3:81836110-81836311(-)$1	1	52	55	9.0000
)).	chr12:110802943-110803144(+)$1	1	85	88	9.0000
((.	chr3:25761398-25761599(-)$1	1	81	84	9.0000
.))	chr7:71695213-71695414(+)$1	1	13	16	9.0000
)))	chr1:182683490-182683691(+)$1	1	32	35	9.0000
...	chr12:75028435-75028636(+)$1	1	2	5	9.0000
...	chr14:120830152-120830353(+)$1	1	14	17	9.0000
...	chr13:41733023-41733224(+)$1	1	62	65	9.0000
...	chr2:141813459-141813660(+)$1	1	36	39	9.0000
.((	chr5:68010708-68010909(-)$1	1	15	18	9.0000
...	chr7:85445626-85445827(-)$1	1	78	81	9.0000
(((	chr18:35024319-35024520(+)$1	1	33	36	9.0000
.))	chr3:58395576-58395777(+)$1	1	13	16	9.0000
(((	chr6:8981496-8981697(+)$1	1	28	31	9.0000
...	chr9:83028977-83029178(-)$1	1	14	17	9.0000
...	chr14:68359943-68360144(+)$1	1	0	3	9.0000
..(	chr10:48986788-48986989(-)$1	1	24	27	9.0000
...	chr10:116789816-116790017(-)$1	1	22	25	9.0000
...	chr4:82133749-82133950(-)$1	1	99	102	9.0000
...	chr2:91435494-91435695(+)$1	1	85	88	9.0000
...	chr11:30007000-30007201(-)$1	1	81	84	9.0000
...	chr8:4257633-4257834(-)$1	1	131	134	9.0000
(..	chr2:104512737-104512938(-)$1	1	7	10	9.0000
...	chr2:4363163-4363364(+)$1	1	7	10	9.0000
.((	chr13:36817821-36818022(-)$1	1	86	89	9.0000
((.	chr17:8776203-8776404(+)$1	1	55	58	9.0000
...	chr6:50151169-50151370(+)$1	1	0	3	9.0000
...	chr11:97373719-97373920(-)$1	1	50	53	9.0000
(((	chr5:72161405-72161606(+)$1	1	3	6	9.0000
...	chr19:5797872-5798073(-)$1	1	13	16	9.0000
...	chr9:8956682-8956883(+)$1	1	14	17	9.0000
...	chr16:97372159-97372360(-)$1	1	44	47	9.0000
...	chr2:6565647-6565848(-)$1	1	65	68	9.0000
(..	chr3:57585243-57585444(+)$1	1	11	14	9.0000
.((	chr1:43872628-43872829(-)$1	1	0	3	9.0000
((.	chrM:14780-14981(+)$1	1	15	18	9.0000
(..	chr6:31393263-31393464(+)$1	1	5	8	9.0000
)))	chr17:13208393-13208594(+)$1	1	56	59	9.0000
...	chr2:61942114-61942315(+)$1	1	11	14	9.0000
)))	chr4:76068305-76068506(-)$1	1	96	99	9.0000
)..	chr14:124726707-124726908(-)$1	1	58	61	9.0000
.))	chr15:30957734-30957935(+)$1	1	150	153	9.0000
(..	chr19:4786382-4786583(-)$1	1	13	16	9.0000
...	chrX:100578553-100578754(+)$1	1	17	20	9.0000
...	chr19:7501149-7501350(-)$1	1	99	102	9.0000
...	chr18:13151299-13151500(+)$1	1	7	10	9.0000
...	chr13:97379011-97379212(+)$1	1	15	18	9.0000
(((	chr2:125500116-125500317(+)$1	1	34	37	9.0000
...	chr8:87125194-87125395(+)$1	1	177	180	9.0000
(((	chr14:33022729-33022930(+)$1	1	79	82	9.0000
...	chr2:29857311-29857512(+)$1	1	38	41	9.0000
...	chr16:44085560-44085761(-)$1	1	4	7	9.0000
...	chr18:5617073-5617274(+)$1	1	7	10	9.0000
((.	chr5:18870740-18870941(+)$1	1	17	20	9.0000
.((	chr12:76552899-76553100(-)$1	1	14	17	9.0000
...	chr3:55339649-55339850(+)$1	1	5	8	9.0000
...	chr12:120397614-120397815(-)$1	1	61	64	9.0000
(..	chr16:67559937-67560138(-)$1	1	19	22	9.0000
(.(	chr14:39727801-39728002(-)$1	1	80	83	9.0000
...	chr1:181908778-181908979(+)$1	1	54	57	9.0000
((.	chr5:48607801-48608002(+)$1	1	20	23	9.0000

#PSSM
A : 0.80	a : 0.20	
U : 0.80	u : 0.20	
U : 0.79	u : 0.21	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_nElavl_InceDunn2012_mm9_CDS_m2_run2.nuc.txt

#NT
CCUU	chr6:103661054-103661291(+)$1	237	199	203	12.0000
CCUU	chr9:49352689-49352925(-)$1	236	204	208	12.0000
CCUU	chrX:45228231-45228503(-)$1	272	88	92	12.0000
CCUU	chr4:147991693-147991943(-)$1	250	3	7	12.0000
CCUU	chr11:69482151-69482382(-)$1	231	12	16	12.0000
CCUU	chr12:62940733-62940964(+)$1	231	105	109	12.0000
CCUU	chr9:57638165-57638419(-)$1	254	72	76	12.0000
CCUU	chr17:30781546-30781781(-)$1	235	192	196	12.0000
ccuu	chr7:48904979-48905210(+)$1	231	11	15	12.0000
CCUU	chr2:122512614-122512845(-)$1	231	45	49	12.0000
CCUU	chr2:180838260-180838550(-)$1	290	70	74	12.0000
CCUU	chr7:149265963-149266201(-)$1	238	31	35	12.0000
CCUU	chrX:130431117-130431351(-)$1	234	39	43	12.0000
CCUU	chr1:66485568-66485811(+)$1	243	21	25	12.0000
CCUU	chr14:59853963-59854220(+)$1	257	219	223	12.0000
CCUU	chr11:50193314-50193558(+)$1	244	109	113	12.0000
CCUU	chr17:81785166-81785471(-)$1	305	25	29	12.0000
CCUU	chrM:9802-10062(+)$1	260	84	88	12.0000
CCUU	chr7:85449066-85449342(-)$1	276	176	180	12.0000
CCUU	chr6:71348255-71348489(-)$1	234	195	199	12.0000
CCUU	chr15:90058312-90058573(+)$1	261	20	24	12.0000
CCUU	chr9:49328159-49328404(-)$1	245	42	46	12.0000
CCUU	chr12:99930982-99931220(-)$1	238	0	4	12.0000
CCUU	chr2:154343458-154343712(+)$1	254	94	98	12.0000
CCUU	chr14:122020484-122020733(-)$1	249	178	182	12.0000
CCUU	chr9:14125577-14125813(+)$1	236	211	215	12.0000
CCUU	chr2:121260514-121260758(+)$1	244	82	86	12.0000
CCUU	chr4:135883221-135883452(+)$1	231	65	69	12.0000
CCUU	chr18:43493536-43493786(-)$1	250	87	91	12.0000
CCUU	chr11:83237889-83238120(-)$1	231	90	94	12.0000
CCUU	chr8:13294878-13295109(+)$1	231	170	174	12.0000
CCUU	chr8:26751177-26751412(+)$1	235	12	16	12.0000
CCUU	chr8:56132504-56132744(+)$1	240	52	56	12.0000
CCUU	chr7:31224872-31225103(-)$1	231	3	7	12.0000
CCUU	chr8:87245563-87245795(-)$1	232	48	52	12.0000
CCUU	chr18:61727901-61728146(+)$1	245	73	77	12.0000
CCUU	chr19:44628092-44628325(-)$1	233	36	40	12.0000
CCUU	chr3:36465916-36466166(-)$1	250	169	173	12.0000
CCUU	chr5:115548045-115548303(+)$1	258	31	35	12.0000
CCUU	chr9:49376447-49376696(-)$1	249	36	40	12.0000
CCUU	chr19:9017892-9018123(+)$1	231	94	98	12.0000
CCUU	chr2:72809049-72809284(-)$1	235	71	75	12.0000
ccuu	chr2:98507083-98507435(-)$1	352	53	57	12.0000
CCUU	chr8:26677170-26677423(+)$1	253	81	85	12.0000
ccuu	chr12:49657228-49657460(-)$1	232	61	65	12.0000
CCUU	chr14:20600291-20600527(+)$1	236	224	228	12.0000
CCUU	chr3:80493101-80493332(-)$1	231	52	56	12.0000
CCUU	chr7:104666158-104666389(+)$1	231	79	83	12.0000
CCUU	chr1:68607100-68607334(-)$1	234	190	194	12.0000
CCUU	chr1:71697096-71697332(-)$1	236	48	52	12.0000
CCUU	chr1:71700955-71701192(-)$1	237	159	163	12.0000
CCUU	chr11:97031113-97031373(-)$1	260	115	119	12.0000
CCUU	chr5:89093039-89093270(-)$1	231	31	35	12.0000
CCUU	chr6:128386551-128386784(-)$1	233	2	6	12.0000
CCUU	chr4:108297531-108297762(+)$1	231	106	110	12.0000
CCUU	chr19:32761673-32761904(-)$1	231	127	131	12.0000
CCUU	chr6:134456118-134456358(-)$1	240	63	67	12.0000
CCUU	chr15:12095852-12096109(+)$1	257	247	251	12.0000
CCUU	chr18:37967705-37967953(+)$1	248	57	61	12.0000
CCUU	chr17:28947372-28947603(+)$1	231	111	115	12.0000
CCUU	chr9:47658277-47658508(+)$1	231	63	67	12.0000
CCUU	chr14:13273278-13273509(-)$1	231	159	163	12.0000
CCUU	chr7:52155660-52155896(-)$1	236	2	6	12.0000
CCUU	chr9:4303004-4303235(-)$1	231	150	154	12.0000
CCUU	chr5:71353043-71353276(-)$1	233	108	112	12.0000
CCUU	chr19:45850594-45850830(-)$1	236	34	38	12.0000
CCUU	chr9:36668323-36668558(+)$1	235	63	67	12.0000
CCUU	chr3:144259781-144260068(+)$1	287	222	226	12.0000
CCUU	chr3:103766069-103766325(+)$1	256	0	4	12.0000
CCUU	chr18:16791454-16791686(-)$1	232	94	98	12.0000
CCUU	chr9:44733793-44734051(-)$1	258	6	10	12.0000
CCUU	chr5:52542954-52543210(-)$1	256	234	238	12.0000
CCUU	chr13:14106897-14107128(-)$1	231	131	135	12.0000
CCUU	chr4:128244438-128244671(-)$1	233	36	40	12.0000
CCUU	chr1:167535688-167535955(-)$1	267	79	83	12.0000
CCUU	chr12:111896047-111896297(+)$1	250	116	120	12.0000

#otherMatches

#Struct PSSM
c]cc	chr14:67483810-67484042(-)$1	232	84	88	12.0000
gggg	chr6:103661054-103661291(+)$1	237	199	203	12.0000
ZZZC	chr9:49352689-49352925(-)$1	236	204	208	12.0000
FFFF	chrX:45228231-45228503(-)$1	272	88	92	12.0000
eell	chr4:147991693-147991943(-)$1	250	3	7	12.0000
eeee	chr11:69482151-69482382(-)$1	231	12	16	12.0000
E:::	chr12:62940733-62940964(+)$1	231	105	109	12.0000
::ee	chr9:57638165-57638419(-)$1	254	72	76	12.0000
pccc	chr17:30781546-30781781(-)$1	235	192	196	12.0000
oooo	chr7:48904979-48905210(+)$1	231	11	15	12.0000
====	chr2:122512614-122512845(-)$1	231	45	49	12.0000
zzze	chr2:180838260-180838550(-)$1	290	70	74	12.0000
::::	chr7:149265963-149266201(-)$1	238	31	35	12.0000
wwww	chrX:130431117-130431351(-)$1	234	39	43	12.0000
EEEE	chr1:66485568-66485811(+)$1	243	21	25	12.0000
c333	chr14:59853963-59854220(+)$1	257	219	223	12.0000
bbmm	chr11:50193314-50193558(+)$1	244	109	113	12.0000
f!!i	chr17:81785166-81785471(-)$1	305	25	29	12.0000
::::	chrM:9802-10062(+)$1	260	84	88	12.0000
g$$$	chr7:85449066-85449342(-)$1	276	176	180	12.0000
::GG	chr6:71348255-71348489(-)$1	234	195	199	12.0000
DDDD	chr15:90058312-90058573(+)$1	261	20	24	12.0000
::dd	chr9:49328159-49328404(-)$1	245	42	46	12.0000
::::	chr12:99930982-99931220(-)$1	238	0	4	12.0000
eett	chr2:154343458-154343712(+)$1	254	94	98	12.0000
ffff	chr14:122020484-122020733(-)$1	249	178	182	12.0000
eeee	chr9:14125577-14125813(+)$1	236	211	215	12.0000
mmmm	chr2:121260514-121260758(+)$1	244	82	86	12.0000
4444	chr4:135883221-135883452(+)$1	231	65	69	12.0000
wwww	chr18:43493536-43493786(-)$1	250	87	91	12.0000
22ee	chr11:83237889-83238120(-)$1	231	90	94	12.0000
qqqq	chr8:13294878-13295109(+)$1	231	170	174	12.0000
{DDD	chr8:26751177-26751412(+)$1	235	12	16	12.0000
e!!b	chr8:56132504-56132744(+)$1	240	52	56	12.0000
eeec	chr7:31224872-31225103(-)$1	231	3	7	12.0000
::::	chr8:87245563-87245795(-)$1	232	48	52	12.0000
%%ff	chr18:61727901-61728146(+)$1	245	73	77	12.0000
gggg	chr19:44628092-44628325(-)$1	233	36	40	12.0000
dnnn	chr3:36465916-36466166(-)$1	250	169	173	12.0000
ccc)	chr5:115548045-115548303(+)$1	258	31	35	12.0000
:::G	chr9:49376447-49376696(-)$1	249	36	40	12.0000
ssss	chr19:9017892-9018123(+)$1	231	94	98	12.0000
::::	chr2:72809049-72809284(-)$1	235	71	75	12.0000
::::	chr2:98507083-98507435(-)$1	352	53	57	12.0000
7777	chr8:26677170-26677423(+)$1	253	81	85	12.0000
BMMM	chr12:49657228-49657460(-)$1	232	61	65	12.0000
E~~~	chr14:20600291-20600527(+)$1	236	224	228	12.0000
^^^f	chr3:80493101-80493332(-)$1	231	52	56	12.0000
pppp	chr7:104666158-104666389(+)$1	231	79	83	12.0000
nnng	chr1:68607100-68607334(-)$1	234	190	194	12.0000
VVVG	chr1:71697096-71697332(-)$1	236	48	52	12.0000
ccff	chr1:71700955-71701192(-)$1	237	159	163	12.0000
::hh	chr11:97031113-97031373(-)$1	260	115	119	12.0000
ffff	chr5:89093039-89093270(-)$1	231	31	35	12.0000
CKKD	chr6:128386551-128386784(-)$1	233	2	6	12.0000
tttt	chr4:108297531-108297762(+)$1	231	106	110	12.0000
b22e	chr19:32761673-32761904(-)$1	231	127	131	12.0000
bb!!	chr6:134456118-134456358(-)$1	240	63	67	12.0000
cc]e	chr15:12095852-12096109(+)$1	257	247	251	12.0000
dddd	chr18:37967705-37967953(+)$1	248	57	61	12.0000
eeee	chr17:28947372-28947603(+)$1	231	111	115	12.0000
#fff	chr9:47658277-47658508(+)$1	231	63	67	12.0000
eeee	chr14:13273278-13273509(-)$1	231	159	163	12.0000
::::	chr7:52155660-52155896(-)$1	236	2	6	12.0000
nnne	chr9:4303004-4303235(-)$1	231	150	154	12.0000
mmcc	chr5:71353043-71353276(-)$1	233	108	112	12.0000
nnnn	chr19:45850594-45850830(-)$1	236	34	38	12.0000
ffff	chr9:36668323-36668558(+)$1	235	63	67	12.0000
CC::	chr3:144259781-144260068(+)$1	287	222	226	12.0000
::EE	chr3:103766069-103766325(+)$1	256	0	4	12.0000
hhhh	chr18:16791454-16791686(-)$1	232	94	98	12.0000
::::	chr9:44733793-44734051(-)$1	258	6	10	12.0000
::::	chr5:52542954-52543210(-)$1	256	234	238	12.0000
eeee	chr13:14106897-14107128(-)$1	231	131	135	12.0000
rrhh	chr4:128244438-128244671(-)$1	233	36	40	12.0000
bb]d	chr1:167535688-167535955(-)$1	267	79	83	12.0000
::::	chr12:111896047-111896297(+)$1	250	116	120	12.0000

#DB
).))	chr14:67483810-67484042(-)$1	1	84	88	12.0000
))))	chr6:103661054-103661291(+)$1	1	199	203	12.0000
...)	chr9:49352689-49352925(-)$1	1	204	208	12.0000
((((	chrX:45228231-45228503(-)$1	1	88	92	12.0000
((..	chr4:147991693-147991943(-)$1	1	3	7	12.0000
))))	chr11:69482151-69482382(-)$1	1	12	16	12.0000
(...	chr12:62940733-62940964(+)$1	1	105	109	12.0000
..((	chr9:57638165-57638419(-)$1	1	72	76	12.0000
.)))	chr17:30781546-30781781(-)$1	1	192	196	12.0000
....	chr7:48904979-48905210(+)$1	1	11	15	12.0000
((((	chr2:122512614-122512845(-)$1	1	45	49	12.0000
...)	chr2:180838260-180838550(-)$1	1	70	74	12.0000
....	chr7:149265963-149266201(-)$1	1	31	35	12.0000
....	chrX:130431117-130431351(-)$1	1	39	43	12.0000
((((	chr1:66485568-66485811(+)$1	1	21	25	12.0000
)...	chr14:59853963-59854220(+)$1	1	219	223	12.0000
((..	chr11:50193314-50193558(+)$1	1	109	113	12.0000
(..(	chr17:81785166-81785471(-)$1	1	25	29	12.0000
....	chrM:9802-10062(+)$1	1	84	88	12.0000
(...	chr7:85449066-85449342(-)$1	1	176	180	12.0000
..))	chr6:71348255-71348489(-)$1	1	195	199	12.0000
((((	chr15:90058312-90058573(+)$1	1	20	24	12.0000
..((	chr9:49328159-49328404(-)$1	1	42	46	12.0000
....	chr12:99930982-99931220(-)$1	1	0	4	12.0000
((..	chr2:154343458-154343712(+)$1	1	94	98	12.0000
((((	chr14:122020484-122020733(-)$1	1	178	182	12.0000
((((	chr9:14125577-14125813(+)$1	1	211	215	12.0000
....	chr2:121260514-121260758(+)$1	1	82	86	12.0000
....	chr4:135883221-135883452(+)$1	1	65	69	12.0000
....	chr18:43493536-43493786(-)$1	1	87	91	12.0000
..))	chr11:83237889-83238120(-)$1	1	90	94	12.0000
....	chr8:13294878-13295109(+)$1	1	170	174	12.0000
.(((	chr8:26751177-26751412(+)$1	1	12	16	12.0000
(..(	chr8:56132504-56132744(+)$1	1	52	56	12.0000
((((	chr7:31224872-31225103(-)$1	1	3	7	12.0000
....	chr8:87245563-87245795(-)$1	1	48	52	12.0000
..((	chr18:61727901-61728146(+)$1	1	73	77	12.0000
))))	chr19:44628092-44628325(-)$1	1	36	40	12.0000
(...	chr3:36465916-36466166(-)$1	1	169	173	12.0000
(((.	chr5:115548045-115548303(+)$1	1	31	35	12.0000
...(	chr9:49376447-49376696(-)$1	1	36	40	12.0000
....	chr19:9017892-9018123(+)$1	1	94	98	12.0000
....	chr2:72809049-72809284(-)$1	1	71	75	12.0000
....	chr2:98507083-98507435(-)$1	1	53	57	12.0000
....	chr8:26677170-26677423(+)$1	1	81	85	12.0000
(...	chr12:49657228-49657460(-)$1	1	61	65	12.0000
)...	chr14:20600291-20600527(+)$1	1	224	228	12.0000
...)	chr3:80493101-80493332(-)$1	1	52	56	12.0000
....	chr7:104666158-104666389(+)$1	1	79	83	12.0000
...)	chr1:68607100-68607334(-)$1	1	190	194	12.0000
...(	chr1:71697096-71697332(-)$1	1	48	52	12.0000
))))	chr1:71700955-71701192(-)$1	1	159	163	12.0000
..((	chr11:97031113-97031373(-)$1	1	115	119	12.0000
((((	chr5:89093039-89093270(-)$1	1	31	35	12.0000
(..(	chr6:128386551-128386784(-)$1	1	2	6	12.0000
....	chr4:108297531-108297762(+)$1	1	106	110	12.0000
)..)	chr19:32761673-32761904(-)$1	1	127	131	12.0000
((..	chr6:134456118-134456358(-)$1	1	63	67	12.0000
)).)	chr15:12095852-12096109(+)$1	1	247	251	12.0000
((((	chr18:37967705-37967953(+)$1	1	57	61	12.0000
((((	chr17:28947372-28947603(+)$1	1	111	115	12.0000
.(((	chr9:47658277-47658508(+)$1	1	63	67	12.0000
((((	chr14:13273278-13273509(-)$1	1	159	163	12.0000
....	chr7:52155660-52155896(-)$1	1	2	6	12.0000
...)	chr9:4303004-4303235(-)$1	1	150	154	12.0000
..))	chr5:71353043-71353276(-)$1	1	108	112	12.0000
....	chr19:45850594-45850830(-)$1	1	34	38	12.0000
((((	chr9:36668323-36668558(+)$1	1	63	67	12.0000
))..	chr3:144259781-144260068(+)$1	1	222	226	12.0000
..((	chr3:103766069-103766325(+)$1	1	0	4	12.0000
))))	chr18:16791454-16791686(-)$1	1	94	98	12.0000
....	chr9:44733793-44734051(-)$1	1	6	10	12.0000
....	chr5:52542954-52543210(-)$1	1	234	238	12.0000
))))	chr13:14106897-14107128(-)$1	1	131	135	12.0000
..))	chr4:128244438-128244671(-)$1	1	36	40	12.0000
)).)	chr1:167535688-167535955(-)$1	1	79	83	12.0000
....	chr12:111896047-111896297(+)$1	1	116	120	12.0000

#PSSM
C : 0.96	c : 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
HITSCLIP_FUS_Nakaya2013b_mm9_CDS_m3_run2.nuc.txt

#NT
CUGGA	chr17:7160660-7160876(+)$1	216	43	48	15.0000
CUGGA	chr11:74650211-74650449(+)$1	238	124	129	15.0000
CUGGA	chr15:80754461-80754685(+)$1	224	61	66	15.0000
CUGGA	chr5:37358890-37359114(-)$1	224	109	114	15.0000
CUGGA	chr7:116170043-116170266(-)$1	223	103	108	15.0000
CUGGA	chr11:60302144-60302365(+)$1	221	29	34	15.0000
CUGGA	chr9:104025295-104025532(+)$1	237	95	100	15.0000
CUGGA	chr11:115041577-115041798(+)$1	221	209	214	15.0000
CUGGA	chr4:118032886-118033107(+)$1	221	64	69	15.0000
CUGGA	chr10:64465181-64465404(-)$1	223	3	8	15.0000
CUGGA	chr8:26681196-26681417(+)$1	221	62	67	15.0000
CUGGA	chr8:47294515-47294739(-)$1	224	165	170	15.0000
CUGGA	chr7:26124428-26124645(+)$1	217	73	78	15.0000
CUGGA	chr15:90371592-90371816(-)$1	224	9	14	15.0000
CUGGA	chr9:106595520-106595740(-)$1	220	34	39	15.0000
CUGGA	chr15:98675398-98675630(-)$1	232	121	126	15.0000
CUGGA	chr4:108731473-108731723(+)$1	250	60	65	15.0000
CUGGA	chr19:42031539-42031765(-)$1	226	114	119	15.0000
CUGGA	chr7:37554401-37554639(+)$1	238	180	185	15.0000
CUGGA	chr8:13122713-13122936(+)$1	223	120	125	15.0000
CUGGA	chr8:112554420-112554641(+)$1	221	88	93	15.0000
CUGGA	chr12:13384141-13384371(+)$1	230	144	149	15.0000
CUGGA	chr7:99807975-99808203(-)$1	228	100	105	15.0000
CUGGA	chr7:97533474-97533698(+)$1	224	113	118	15.0000
CUGGA	chr5:144935839-144936067(+)$1	228	217	222	15.0000
CUGGA	chr7:151031340-151031573(+)$1	233	28	33	15.0000
CUGGA	chr13:100201966-100202187(+)$1	221	134	139	15.0000
CUGGA	chr1:51346293-51346515(+)$1	222	119	124	15.0000
CUGGA	chr1:163171739-163171963(+)$1	224	75	80	15.0000
CUGGA	chr11:50590153-50590368(+)$1	215	193	198	15.0000
CUGGA	chr10:89268688-89268913(+)$1	225	85	90	15.0000
CUGGA	chr9:20152772-20153008(-)$1	236	72	77	15.0000
CUGGA	chr7:31308251-31308471(-)$1	220	207	212	15.0000
CUGGA	chr16:38144345-38144592(+)$1	247	144	149	15.0000
CUGGA	chr6:4705630-4705874(+)$1	244	112	117	15.0000
CUGGA	chr7:147410219-147410440(+)$1	221	64	69	15.0000
CUGGA	chr10:116798113-116798367(-)$1	254	95	100	15.0000
CUGGA	chr7:125288889-125289117(-)$1	228	204	209	15.0000
CUGGA	chr15:36173746-36173983(-)$1	237	134	139	15.0000
CUGGA	chr15:39366342-39366573(+)$1	231	184	189	15.0000
CUGGA	chr17:56243967-56244194(+)$1	227	55	60	15.0000
CUGGA	chr11:69730843-69731065(+)$1	222	86	91	15.0000
CUGGA	chr18:12201654-12201903(-)$1	249	162	167	15.0000
CUGGA	chr7:52966479-52966739(-)$1	260	46	51	15.0000
CUGGA	chr1:154715370-154715602(-)$1	232	128	133	15.0000
CUGGA	chr17:56245535-56245758(+)$1	223	71	76	15.0000
CUGGA	chr11:60016846-60017070(-)$1	224	36	41	15.0000
CUGGA	chr18:37977059-37977281(-)$1	222	72	77	15.0000
CUGGA	chr4:120657734-120657955(-)$1	221	38	43	15.0000
CUGGA	chr19:44476146-44476381(-)$1	235	149	154	15.0000
CUGGA	chr16:26676802-26677025(+)$1	223	140	145	15.0000
CUGGA	chr9:120336626-120336847(+)$1	221	98	103	15.0000
CUGGA	chr7:63445199-63445423(+)$1	224	75	80	15.0000
CUGGA	chr14:7269219-7269456(-)$1	237	70	75	15.0000

#otherMatches

#Struct PSSM
ggggg	chr17:6233028-6233259(+)$1	231	161	166	15.0000
IIIII	chr17:7160660-7160876(+)$1	216	43	48	15.0000
::ddd	chr11:74650211-74650449(+)$1	238	124	129	15.0000
!!ccc	chr15:80754461-80754685(+)$1	224	61	66	15.0000
eee22	chr5:37358890-37359114(-)$1	224	109	114	15.0000
bdddd	chr7:116170043-116170266(-)$1	223	103	108	15.0000
eeenn	chr11:60302144-60302365(+)$1	221	29	34	15.0000
bb[cc	chr9:104025295-104025532(+)$1	237	95	100	15.0000
YYDDD	chr11:115041577-115041798(+)$1	221	209	214	15.0000
e[bb!	chr4:118032886-118033107(+)$1	221	64	69	15.0000
:EEEE	chr10:64465181-64465404(-)$1	223	3	8	15.0000
22bb]	chr8:26681196-26681417(+)$1	221	62	67	15.0000
iiiii	chr8:47294515-47294739(-)$1	224	165	170	15.0000
::eee	chr7:26124428-26124645(+)$1	217	73	78	15.0000
::DDD	chr15:90371592-90371816(-)$1	224	9	14	15.0000
FFFFF	chr9:106595520-106595740(-)$1	220	34	39	15.0000
:ccc[	chr15:98675398-98675630(-)$1	232	121	126	15.0000
iiiii	chr4:108731473-108731723(+)$1	250	60	65	15.0000
=====	chr19:42031539-42031765(-)$1	226	114	119	15.0000
HHhhh	chr7:37554401-37554639(+)$1	238	180	185	15.0000
gg]dd	chr8:13122713-13122936(+)$1	223	120	125	15.0000
mmccc	chr8:112554420-112554641(+)$1	221	88	93	15.0000
cc[dd	chr12:13384141-13384371(+)$1	230	144	149	15.0000
ddd""	chr7:99807975-99808203(-)$1	228	100	105	15.0000
2dddd	chr7:97533474-97533698(+)$1	224	113	118	15.0000
ddddd	chr5:144935839-144936067(+)$1	228	217	222	15.0000
7ccc2	chr7:151031340-151031573(+)$1	233	28	33	15.0000
YDDDD	chr13:100201966-100202187(+)$1	221	134	139	15.0000
c[bb$	chr1:51346293-51346515(+)$1	222	119	124	15.0000
33fff	chr1:163171739-163171963(+)$1	224	75	80	15.0000
ldddd	chr11:50590153-50590368(+)$1	215	193	198	15.0000
eeee]	chr10:89268688-89268913(+)$1	225	85	90	15.0000
%ccc+	chr9:20152772-20153008(-)$1	236	72	77	15.0000
ggggg	chr7:31308251-31308471(-)$1	220	207	212	15.0000
DDDZZ	chr16:38144345-38144592(+)$1	247	144	149	15.0000
:ffff	chr6:4705630-4705874(+)$1	244	112	117	15.0000
ccc]e	chr7:147410219-147410440(+)$1	221	64	69	15.0000
FFFFL	chr10:116798113-116798367(-)$1	254	95	100	15.0000
eeeel	chr7:125288889-125289117(-)$1	228	204	209	15.0000
CCC{E	chr15:36173746-36173983(-)$1	237	134	139	15.0000
EEEEE	chr15:39366342-39366573(+)$1	231	184	189	15.0000
:FFFF	chr17:56243967-56244194(+)$1	227	55	60	15.0000
ccc44	chr11:69730843-69731065(+)$1	222	86	91	15.0000
dd[a[	chr18:12201654-12201903(-)$1	249	162	167	15.0000
!bbcc	chr7:52966479-52966739(-)$1	260	46	51	15.0000
DDDYY	chr1:154715370-154715602(-)$1	232	128	133	15.0000
hhhhh	chr17:56245535-56245758(+)$1	223	71	76	15.0000
EEEE{	chr11:60016846-60017070(-)$1	224	36	41	15.0000
bb]cc	chr18:37977059-37977281(-)$1	222	72	77	15.0000
eeeoo	chr4:120657734-120657955(-)$1	221	38	43	15.0000
eeeee	chr19:44476146-44476381(-)$1	235	149	154	15.0000
nnnnf	chr16:26676802-26677025(+)$1	223	140	145	15.0000
iiiii	chr9:120336626-120336847(+)$1	221	98	103	15.0000
22fff	chr7:63445199-63445423(+)$1	224	75	80	15.0000
accc:	chr14:7269219-7269456(-)$1	237	70	75	15.0000

#DB
(((((	chr17:6233028-6233259(+)$1	1	161	166	15.0000
(((((	chr17:7160660-7160876(+)$1	1	43	48	15.0000
..(((	chr11:74650211-74650449(+)$1	1	124	129	15.0000
..(((	chr15:80754461-80754685(+)$1	1	61	66	15.0000
)))..	chr5:37358890-37359114(-)$1	1	109	114	15.0000
(((((	chr7:116170043-116170266(-)$1	1	103	108	15.0000
(((..	chr11:60302144-60302365(+)$1	1	29	34	15.0000
((.((	chr9:104025295-104025532(+)$1	1	95	100	15.0000
..)))	chr11:115041577-115041798(+)$1	1	209	214	15.0000
(.((.	chr4:118032886-118033107(+)$1	1	64	69	15.0000
.((((	chr10:64465181-64465404(-)$1	1	3	8	15.0000
..)).	chr8:26681196-26681417(+)$1	1	62	67	15.0000
)))))	chr8:47294515-47294739(-)$1	1	165	170	15.0000
..(((	chr7:26124428-26124645(+)$1	1	73	78	15.0000
..(((	chr15:90371592-90371816(-)$1	1	9	14	15.0000
(((((	chr9:106595520-106595740(-)$1	1	34	39	15.0000
.(((.	chr15:98675398-98675630(-)$1	1	121	126	15.0000
(((((	chr4:108731473-108731723(+)$1	1	60	65	15.0000
(((((	chr19:42031539-42031765(-)$1	1	114	119	15.0000
))(((	chr7:37554401-37554639(+)$1	1	180	185	15.0000
)).))	chr8:13122713-13122936(+)$1	1	120	125	15.0000
..)))	chr8:112554420-112554641(+)$1	1	88	93	15.0000
((.((	chr12:13384141-13384371(+)$1	1	144	149	15.0000
(((..	chr7:99807975-99808203(-)$1	1	100	105	15.0000
.))))	chr7:97533474-97533698(+)$1	1	113	118	15.0000
)))))	chr5:144935839-144936067(+)$1	1	217	222	15.0000
.))).	chr7:151031340-151031573(+)$1	1	28	33	15.0000
.))))	chr13:100201966-100202187(+)$1	1	134	139	15.0000
(.((.	chr1:51346293-51346515(+)$1	1	119	124	15.0000
..)))	chr1:163171739-163171963(+)$1	1	75	80	15.0000
.))))	chr11:50590153-50590368(+)$1	1	193	198	15.0000
)))).	chr10:89268688-89268913(+)$1	1	85	90	15.0000
.(((.	chr9:20152772-20153008(-)$1	1	72	77	15.0000
)))))	chr7:31308251-31308471(-)$1	1	207	212	15.0000
)))..	chr16:38144345-38144592(+)$1	1	144	149	15.0000
.((((	chr6:4705630-4705874(+)$1	1	112	117	15.0000
))).)	chr7:147410219-147410440(+)$1	1	64	69	15.0000
((((.	chr10:116798113-116798367(-)$1	1	95	100	15.0000
((((.	chr7:125288889-125289117(-)$1	1	204	209	15.0000
(((.(	chr15:36173746-36173983(-)$1	1	134	139	15.0000
)))))	chr15:39366342-39366573(+)$1	1	184	189	15.0000
.((((	chr17:56243967-56244194(+)$1	1	55	60	15.0000
)))..	chr11:69730843-69731065(+)$1	1	86	91	15.0000
((.(.	chr18:12201654-12201903(-)$1	1	162	167	15.0000
.((((	chr7:52966479-52966739(-)$1	1	46	51	15.0000
)))..	chr1:154715370-154715602(-)$1	1	128	133	15.0000
)))))	chr17:56245535-56245758(+)$1	1	71	76	15.0000
((((.	chr11:60016846-60017070(-)$1	1	36	41	15.0000
)).))	chr18:37977059-37977281(-)$1	1	72	77	15.0000
(((..	chr4:120657734-120657955(-)$1	1	38	43	15.0000
(((((	chr19:44476146-44476381(-)$1	1	149	154	15.0000
....)	chr16:26676802-26677025(+)$1	1	140	145	15.0000
)))))	chr9:120336626-120336847(+)$1	1	98	103	15.0000
..)))	chr7:63445199-63445423(+)$1	1	75	80	15.0000
)))).	chr14:7269219-7269456(-)$1	1	70	75	15.0000

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

#score	825.0000000000001
#seq	55
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_LIN28_Cho2012c_mm9_CDS_m1_run2.nuc.txt

#NT
GGAAGA	chr6:113065414-113065649(+)$1	235	116	122	14.9791
GGAAGA	chr15:77746140-77746360(-)$1	220	14	20	14.9791
GGAAGA	chr11:105137117-105137342(+)$1	225	149	155	14.9791
AGAAGA	chr1:89120862-89121082(+)$1	220	21	27	12.2708
GGAAGA	chr1:166210364-166210584(+)$1	220	156	162	14.9791
GGAAGA	chr18:80418832-80419052(+)$1	220	145	151	14.9791
UGAAGA	chrX:12681691-12681911(+)$1	220	190	196	12.3750
UGAAGA	chr3:69356857-69357087(+)$1	230	85	91	12.3750
GGAAGA	chr9:53198524-53198744(+)$1	220	46	52	14.9791
AGAAGA	chr18:58063714-58063934(+)$1	220	100	106	12.2708
GGAAGC	chr17:75169541-75169765(+)$1	224	113	119	11.2291
GGAAGC	chr10:57939950-57940170(+)$1	220	105	111	11.2291
AGAAGA	chr4:42993311-42993540(-)$1	229	109	115	12.2708
GGAAGC	chr12:4085858-4086078(+)$1	220	14	20	11.2291
GGAAGA	chr4:130318776-130318997(+)$1	221	67	73	14.9791
GGAAGA	chr1:88033530-88033750(+)$1	220	102	108	14.9791
GGAAGA	chr6:88043839-88044073(+)$1	234	38	44	14.9791
GAAAGA	chr9:99146673-99146895(+)$1	222	155	161	11.6458
GAAAGA	chr19:32565828-32566048(+)$1	220	79	85	11.6458
UGAAGA	chr7:4759928-4760148(-)$1	220	142	148	12.3750
GAAAGA	chr1:136489837-136490057(+)$1	220	31	37	11.6458
UGAAGA	chr7:13892817-13893037(+)$1	220	51	57	12.3750
AGAAGA	chr2:75731998-75732218(+)$1	220	13	19	12.2708
GGAAGA	chr9:121369522-121369742(+)$1	220	96	102	14.9791
GGAAGA	chr5:5736317-5736538(-)$1	221	43	49	14.9791
ggaaga	chr11:106992559-106992798(-)$1	239	83	89	14.9791
UGAAGA	chr3:130412073-130412293(-)$1	220	55	61	12.3750
AGAAGA	chr4:135892115-135892338(+)$1	223	138	144	12.2708
UGAAGA	chr15:36532618-36532839(-)$1	221	25	31	12.3750
UGAAGA	chr8:87380931-87381151(+)$1	220	123	129	12.3750
GGAAGC	chr2:29847321-29847541(+)$1	220	2	8	11.2291
GGAAGC	chrX:101608968-101609188(-)$1	220	172	178	11.2291
GGAAGA	chr9:14312200-14312420(+)$1	220	114	120	14.9791
GGAAGA	chr18:73799987-73800207(-)$1	220	30	36	14.9791
GGAAGA	chr1:38078517-38078740(+)$1	223	87	93	14.9791
GAAAGA	chr16:91858424-91858660(+)$1	236	111	117	11.6458
GGAAGA	chr1:9736791-9737011(-)$1	220	21	27	14.9791
AGAAGA	chr4:131895805-131896025(-)$1	220	108	114	12.2708
GGAAGC	chr2:129034048-129034302(+)$1	254	102	108	11.2291
GAAAGA	chr1:120548778-120548998(+)$1	220	63	69	11.6458
GGAAGA	chr7:97617514-97617750(-)$1	236	107	113	14.9791
AGAAGA	chr7:135685340-135685560(+)$1	220	158	164	12.2708
UGAAGA	chr9:53366141-53366361(+)$1	220	105	111	12.3750
GAAAGA	chr2:75699894-75700116(+)$1	222	168	174	11.6458
GGAAGA	chr17:24580817-24581037(-)$1	220	130	136	14.9791
GGAAGA	chr11:87356770-87356990(+)$1	220	28	34	14.9791
GAAAGA	chr18:42734153-42734381(+)$1	228	54	60	11.6458

#otherMatches

#Struct PSSM
=====5	chr18:31995004-31995227(+)$1	223	115	121	11.6458
]fffff	chr6:113065414-113065649(+)$1	235	116	122	14.9791
DD{BB:	chr15:77746140-77746360(-)$1	220	14	20	14.9791
======	chr11:105137117-105137342(+)$1	225	149	155	14.9791
ee:FFF	chr1:89120862-89121082(+)$1	220	21	27	12.2708
::::::	chr1:166210364-166210584(+)$1	220	156	162	14.9791
FFFFFF	chr18:80418832-80419052(+)$1	220	145	151	14.9791
eeee]a	chrX:12681691-12681911(+)$1	220	190	196	12.3750
:::::e	chr3:69356857-69357087(+)$1	230	85	91	12.3750
cc::::	chr9:53198524-53198744(+)$1	220	46	52	14.9791
iiiiii	chr18:58063714-58063934(+)$1	220	100	106	12.2708
IIIDDD	chr17:75169541-75169765(+)$1	224	113	119	11.2291
HH::::	chr10:57939950-57940170(+)$1	220	105	111	11.2291
::::::	chr4:42993311-42993540(-)$1	229	109	115	12.2708
BLLLCC	chr12:4085858-4086078(+)$1	220	14	20	11.2291
======	chr4:130318776-130318997(+)$1	221	67	73	14.9791
EE::dd	chr1:88033530-88033750(+)$1	220	102	108	14.9791
cc22dd	chr6:88043839-88044073(+)$1	234	38	44	14.9791
gggggg	chr9:99146673-99146895(+)$1	222	155	161	11.6458
feeeee	chr19:32565828-32566048(+)$1	220	79	85	11.6458
ttgggg	chr7:4759928-4760148(-)$1	220	142	148	12.3750
Dhhhhh	chr1:136489837-136490057(+)$1	220	31	37	11.6458
cc"""d	chr7:13892817-13893037(+)$1	220	51	57	12.3750
:::eee	chr2:75731998-75732218(+)$1	220	13	19	12.2708
ff]bb3	chr9:121369522-121369742(+)$1	220	96	102	14.9791
"""bbo	chr5:5736317-5736538(-)$1	221	43	49	14.9791
D::::C	chr11:106992559-106992798(-)$1	239	83	89	14.9791
:::ccc	chr3:130412073-130412293(-)$1	220	55	61	12.3750
::::::	chr4:135892115-135892338(+)$1	223	138	144	12.2708
eeeenn	chr15:36532618-36532839(-)$1	221	25	31	12.3750
d333ad	chr8:87380931-87381151(+)$1	220	123	129	12.3750
eee[bb	chr2:29847321-29847541(+)$1	220	2	8	11.2291
EEEE}B	chrX:101608968-101609188(-)$1	220	172	178	11.2291
======	chr9:14312200-14312420(+)$1	220	114	120	14.9791
dd((((	chr18:73799987-73800207(-)$1	220	30	36	14.9791
::::::	chr1:38078517-38078740(+)$1	223	87	93	14.9791
pppppp	chr16:91858424-91858660(+)$1	236	111	117	11.6458
::::::	chr1:9736791-9737011(-)$1	220	21	27	14.9791
hhhhhh	chr4:131895805-131896025(-)$1	220	108	114	12.2708
eee[dd	chr2:129034048-129034302(+)$1	254	102	108	11.2291
::::::	chr1:120548778-120548998(+)$1	220	63	69	11.6458
dddd]d	chr7:97617514-97617750(-)$1	236	107	113	14.9791
tdddd>	chr7:135685340-135685560(+)$1	220	158	164	12.2708
fwwwww	chr9:53366141-53366361(+)$1	220	105	111	12.3750
hhhh""	chr2:75699894-75700116(+)$1	222	168	174	11.6458
E?????	chr17:24580817-24581037(-)$1	220	130	136	14.9791
cc]ccc	chr11:87356770-87356990(+)$1	220	28	34	14.9791
lllbb]	chr18:42734153-42734381(+)$1	228	54	60	11.6458

#DB
))))).	chr18:31995004-31995227(+)$1	1	115	121	11.6458
.)))))	chr6:113065414-113065649(+)$1	1	116	122	14.9791
((.((.	chr15:77746140-77746360(-)$1	1	14	20	14.9791
((((((	chr11:105137117-105137342(+)$1	1	149	155	14.9791
)).(((	chr1:89120862-89121082(+)$1	1	21	27	12.2708
......	chr1:166210364-166210584(+)$1	1	156	162	14.9791
))))))	chr18:80418832-80419052(+)$1	1	145	151	14.9791
)))).)	chrX:12681691-12681911(+)$1	1	190	196	12.3750
.....(	chr3:69356857-69357087(+)$1	1	85	91	12.3750
))....	chr9:53198524-53198744(+)$1	1	46	52	14.9791
((((((	chr18:58063714-58063934(+)$1	1	100	106	12.2708
))))))	chr17:75169541-75169765(+)$1	1	113	119	11.2291
((....	chr10:57939950-57940170(+)$1	1	105	111	11.2291
......	chr4:42993311-42993540(-)$1	1	109	115	12.2708
(...((	chr12:4085858-4086078(+)$1	1	14	20	11.2291
((((((	chr4:130318776-130318997(+)$1	1	67	73	14.9791
((..((	chr1:88033530-88033750(+)$1	1	102	108	14.9791
))..))	chr6:88043839-88044073(+)$1	1	38	44	14.9791
))))))	chr9:99146673-99146895(+)$1	1	155	161	11.6458
((((((	chr19:32565828-32566048(+)$1	1	79	85	11.6458
..))))	chr7:4759928-4760148(-)$1	1	142	148	12.3750
((((((	chr1:136489837-136490057(+)$1	1	31	37	11.6458
((...(	chr7:13892817-13893037(+)$1	1	51	57	12.3750
...(((	chr2:75731998-75732218(+)$1	1	13	19	12.2708
)).)).	chr9:121369522-121369742(+)$1	1	96	102	14.9791
...((.	chr5:5736317-5736538(-)$1	1	43	49	14.9791
(....(	chr11:106992559-106992798(-)$1	1	83	89	14.9791
...(((	chr3:130412073-130412293(-)$1	1	55	61	12.3750
......	chr4:135892115-135892338(+)$1	1	138	144	12.2708
((((..	chr15:36532618-36532839(-)$1	1	25	31	12.3750
)...))	chr8:87380931-87381151(+)$1	1	123	129	12.3750
(((.((	chr2:29847321-29847541(+)$1	1	2	8	11.2291
)))).)	chrX:101608968-101609188(-)$1	1	172	178	11.2291
))))))	chr9:14312200-14312420(+)$1	1	114	120	14.9791
((....	chr18:73799987-73800207(-)$1	1	30	36	14.9791
......	chr1:38078517-38078740(+)$1	1	87	93	14.9791
......	chr16:91858424-91858660(+)$1	1	111	117	11.6458
......	chr1:9736791-9737011(-)$1	1	21	27	14.9791
))))))	chr4:131895805-131896025(-)$1	1	108	114	12.2708
(((.((	chr2:129034048-129034302(+)$1	1	102	108	11.2291
......	chr1:120548778-120548998(+)$1	1	63	69	11.6458
)))).)	chr7:97617514-97617750(-)$1	1	107	113	14.9791
.)))).	chr7:135685340-135685560(+)$1	1	158	164	12.2708
(.....	chr9:53366141-53366361(+)$1	1	105	111	12.3750
((((..	chr2:75699894-75700116(+)$1	1	168	174	11.6458
).....	chr17:24580817-24581037(-)$1	1	130	136	14.9791
)).)))	chr11:87356770-87356990(+)$1	1	28	34	14.9791
...)).	chr18:42734153-42734381(+)$1	1	54	60	11.6458

#PSSM
G : 0.66	U : 0.16	A : 0.14	g : 0.02	
G : 0.81	A : 0.16	g : 0.02	
A : 0.97	a : 0.02	
A : 0.97	a : 0.02	
G : 0.97	g : 0.02	
A : 0.85	C : 0.12	a : 0.02	

#score	630.041666666667
#seq	48
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012d_mm9_UTR_m1_run2.nuc.txt

#NT
UUUCUUUG	chr1:54702798-54703044(-)$1	246	203	211	18.8863
UUUGUUUU	chr13:55445984-55446219(-)$1	235	3	11	14.2272
UUUCUCUG	chr7:119254506-119254741(+)$1	235	21	29	14.9090
UUUCAUUG	chr2:172179044-172179279(+)$1	235	12	20	14.3409
UUUGUUUU	chr5:15877897-15878134(+)$1	237	43	51	14.2272
UUUCUUUU	chr2:155214406-155214651(+)$1	245	233	241	16.9545
UUUCUGUG	chr7:91764019-91764255(-)$1	236	113	121	14.9090
UUUCUUUA	chr15:37297729-37297964(-)$1	235	40	48	15.8181
uuuuuuug	chr10:127514114-127514349(+)$1	235	14	22	16.0454
UGUCUUUG	chr11:60371088-60371328(+)$1	240	216	224	14.6818
UUUAUUUG	chr12:112776564-112776799(+)$1	235	178	186	15.8181
UUUGUUUG	chr18:80409144-80409381(+)$1	237	105	113	16.1590
UUUCUUUA	chr15:38419359-38419597(-)$1	238	137	145	15.8181
uuuCUUUC	chr3:60430627-60430891(+)$1	264	75	83	15.7045
UUUAUUUG	chr17:10400882-10401122(-)$1	240	175	183	15.8181
UUUCUUGG	chr16:28827388-28827623(-)$1	235	16	24	14.2272
UGUCUUUG	chr5:136386537-136386774(-)$1	237	40	48	14.6818
AUUCUUUG	chr16:36035790-36036034(+)$1	244	169	177	14.1136
UUUCAUUG	chr2:153594688-153594923(+)$1	235	159	167	14.3409
UUUCUUUG	chr2:104266800-104267037(-)$1	237	108	116	18.8863
UUUCUUUU	chr2:72241350-72241597(+)$1	247	147	155	16.9545
UUUCUCUG	chr13:21608338-21608573(-)$1	235	80	88	14.9090
UUUUUUUU	chr4:33105874-33106121(+)$1	247	167	175	14.1136
UUUCUUUU	chr2:57220188-57220427(+)$1	239	167	175	16.9545
UUUCUGUG	chrX:71549761-71549996(+)$1	235	101	109	14.9090
UUUCUUUU	chr7:35130363-35130625(-)$1	262	119	127	16.9545
UUUUUUUG	chr16:44160309-44160547(+)$1	238	107	115	16.0454
UUUCUUUU	chr2:72240598-72240836(+)$1	238	176	184	16.9545
UUUUUUUU	chr13:83802224-83802482(+)$1	258	31	39	14.1136
UUUCUUAG	chr2:14998809-14999056(+)$1	247	107	115	14.2272
UUGCUUUG	chr15:12114164-12114401(+)$1	237	115	123	14.1136
UUUGUUUG	chr5:92481805-92482063(-)$1	258	142	150	16.1590
UUUCUUUG	chr7:107789095-107789330(+)$1	235	61	69	18.8863
UUUCUUUU	chr2:155214476-155214718(+)$1	242	163	171	16.9545
UUUCUUUG	chr11:79391902-79392137(+)$1	235	151	159	18.8863
UUUCUCUG	chr4:6322128-6322363(+)$1	235	33	41	14.9090
UUUUUUUU	chr2:72244243-72244491(+)$1	248	83	91	14.1136
uuuguuug	chr9:30957160-30957421(-)$1	261	83	91	16.1590
UUUCUGUG	chr15:58614540-58614792(-)$1	252	102	110	14.9090
UUUGUUUG	chr5:32794129-32794364(+)$1	235	226	234	16.1590
UUUAUUUG	chr16:7412188-7412449(+)$1	261	155	163	15.8181
UGUCUUUG	chr16:38245760-38245995(+)$1	235	103	111	14.6818
UUUCUUUU	chr2:6465641-6465886(-)$1	245	204	212	16.9545

#otherMatches

#Struct PSSM
gg]bb:ff	chr9:14348715-14348958(-)$1	243	78	86	14.4545
cc4444dd	chr1:54702798-54703044(-)$1	246	203	211	18.8863
FFF:::::	chr13:55445984-55446219(-)$1	235	3	11	14.2272
nncccccc	chr7:119254506-119254741(+)$1	235	21	29	14.9090
{DDDD{BB	chr2:172179044-172179279(+)$1	235	12	20	14.3409
:JJJJJJJ	chr5:15877897-15878134(+)$1	237	43	51	14.2272
::::::::	chr2:155214406-155214651(+)$1	245	233	241	16.9545
bb$$$$$h	chr7:91764019-91764255(-)$1	236	113	121	14.9090
B{EEEEE:	chr15:37297729-37297964(-)$1	235	40	48	15.8181
::::::::	chr10:127514114-127514349(+)$1	235	14	22	16.0454
BB}BB}CC	chr11:60371088-60371328(+)$1	240	216	224	14.6818
pppppppd	chr12:112776564-112776799(+)$1	235	178	186	15.8181
FFFFZZZB	chr18:80409144-80409381(+)$1	237	105	113	16.1590
:::hhhhh	chr15:38419359-38419597(-)$1	238	137	145	15.8181
d]dddd44	chr3:60430627-60430891(+)$1	264	75	83	15.7045
eeee[ddd	chr17:10400882-10401122(-)$1	240	175	183	15.8181
NNNEEEEE	chr16:28827388-28827623(-)$1	235	16	24	14.2272
EEEEE{BB	chr5:136386537-136386774(-)$1	237	40	48	14.6818
hh:::::D	chr16:36035790-36036034(+)$1	244	169	177	14.1136
cddddooo	chr2:153594688-153594923(+)$1	235	159	167	14.3409
!!ffffff	chr2:104266800-104267037(-)$1	237	108	116	18.8863
eeee::::	chr2:72241350-72241597(+)$1	247	147	155	16.9545
dddd[bb!	chr13:21608338-21608573(-)$1	235	80	88	14.9090
HHHHHHHc	chr4:33105874-33106121(+)$1	247	167	175	14.1136
ggggg:::	chr2:57220188-57220427(+)$1	239	167	175	16.9545
gg&&&&&&	chrX:71549761-71549996(+)$1	235	101	109	14.9090
eeeeemmm	chr7:35130363-35130625(-)$1	262	119	127	16.9545
444eeeee	chr16:44160309-44160547(+)$1	238	107	115	16.0454
eqqqqqqq	chr2:72240598-72240836(+)$1	238	176	184	16.9545
========	chr13:83802224-83802482(+)$1	258	31	39	14.1136
c]ccciii	chr2:14998809-14999056(+)$1	247	107	115	14.2272
EEEZZZHH	chr15:12114164-12114401(+)$1	237	115	123	14.1136
[ffffffn	chr5:92481805-92482063(-)$1	258	142	150	16.1590
::::::GG	chr7:107789095-107789330(+)$1	235	61	69	18.8863
:::::GGG	chr2:155214476-155214718(+)$1	242	163	171	16.9545
[eeeee[b	chr11:79391902-79392137(+)$1	235	151	159	18.8863
FFF:::dd	chr4:6322128-6322363(+)$1	235	33	41	14.9090
22eeeee2	chr2:72244243-72244491(+)$1	248	83	91	14.1136
^^^^^^^^	chr9:30957160-30957421(-)$1	261	83	91	16.1590
pppppppe	chr15:58614540-58614792(-)$1	252	102	110	14.9090
::::::::	chr5:32794129-32794364(+)$1	235	226	234	16.1590
[iiiiiii	chr16:7412188-7412449(+)$1	261	155	163	15.8181
iiiiiiid	chr16:38245760-38245995(+)$1	235	103	111	14.6818
hhhhhhll	chr2:6465641-6465886(-)$1	245	204	212	16.9545

#DB
)).)).((	chr9:14348715-14348958(-)$1	1	78	86	14.4545
))....))	chr1:54702798-54703044(-)$1	1	203	211	18.8863
(((.....	chr13:55445984-55446219(-)$1	1	3	11	14.2272
..))))))	chr7:119254506-119254741(+)$1	1	21	29	14.9090
.((((.((	chr2:172179044-172179279(+)$1	1	12	20	14.3409
.(((((((	chr5:15877897-15878134(+)$1	1	43	51	14.2272
........	chr2:155214406-155214651(+)$1	1	233	241	16.9545
((.....(	chr7:91764019-91764255(-)$1	1	113	121	14.9090
(.(((((.	chr15:37297729-37297964(-)$1	1	40	48	15.8181
........	chr10:127514114-127514349(+)$1	1	14	22	16.0454
)).)).))	chr11:60371088-60371328(+)$1	1	216	224	14.6818
.......)	chr12:112776564-112776799(+)$1	1	178	186	15.8181
))))...)	chr18:80409144-80409381(+)$1	1	105	113	16.1590
...(((((	chr15:38419359-38419597(-)$1	1	137	145	15.8181
).))))..	chr3:60430627-60430891(+)$1	1	75	83	15.7045
((((.(((	chr17:10400882-10401122(-)$1	1	175	183	15.8181
...(((((	chr16:28827388-28827623(-)$1	1	16	24	14.2272
(((((.((	chr5:136386537-136386774(-)$1	1	40	48	14.6818
)).....)	chr16:36035790-36036034(+)$1	1	169	177	14.1136
(((((...	chr2:153594688-153594923(+)$1	1	159	167	14.3409
..((((((	chr2:104266800-104267037(-)$1	1	108	116	18.8863
))))....	chr2:72241350-72241597(+)$1	1	147	155	16.9545
((((.((.	chr13:21608338-21608573(-)$1	1	80	88	14.9090
)))))))(	chr4:33105874-33106121(+)$1	1	167	175	14.1136
)))))...	chr2:57220188-57220427(+)$1	1	167	175	16.9545
((......	chrX:71549761-71549996(+)$1	1	101	109	14.9090
(((((...	chr7:35130363-35130625(-)$1	1	119	127	16.9545
...)))))	chr16:44160309-44160547(+)$1	1	107	115	16.0454
(.......	chr2:72240598-72240836(+)$1	1	176	184	16.9545
((((((((	chr13:83802224-83802482(+)$1	1	31	39	14.1136
).))))))	chr2:14998809-14999056(+)$1	1	107	115	14.2272
)))...))	chr15:12114164-12114401(+)$1	1	115	123	14.1136
.((((((.	chr5:92481805-92482063(-)$1	1	142	150	16.1590
......((	chr7:107789095-107789330(+)$1	1	61	69	18.8863
.....(((	chr2:155214476-155214718(+)$1	1	163	171	16.9545
.(((((.(	chr11:79391902-79392137(+)$1	1	151	159	18.8863
(((...((	chr4:6322128-6322363(+)$1	1	33	41	14.9090
..))))).	chr2:72244243-72244491(+)$1	1	83	91	14.1136
........	chr9:30957160-30957421(-)$1	1	83	91	16.1590
.......)	chr15:58614540-58614792(-)$1	1	102	110	14.9090
........	chr5:32794129-32794364(+)$1	1	226	234	16.1590
.(((((((	chr16:7412188-7412449(+)$1	1	155	163	15.8181
))))))))	chr16:38245760-38245995(+)$1	1	103	111	14.6818
((((((..	chr2:6465641-6465886(-)$1	1	204	212	16.9545

#PSSM
U : 0.90	u : 0.06	A : 0.02	
U : 0.84	u : 0.06	G : 0.06	C : 0.02	
U : 0.90	u : 0.06	G : 0.02	
C : 0.68	G : 0.11	U : 0.09	A : 0.06	u : 0.02	g : 0.02	
U : 0.90	A : 0.04	u : 0.04	
U : 0.81	C : 0.06	G : 0.06	u : 0.04	
U : 0.90	u : 0.04	G : 0.02	A : 0.02	
G : 0.61	U : 0.27	A : 0.04	g : 0.04	C : 0.02	

#score	689.8636363636359
#seq	44
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago_Zhang2011a_mm9_CDS_m2_run2.nuc.txt

#NT
AGAAG	chr6:124412063-124412264(-)$1	201	172	177	14.9999
AGAAG	chr2:29866447-29866648(+)$1	201	127	132	14.9999
AGAAG	chr10:107686416-107686617(+)$1	201	106	111	14.9999
AGAAG	chr10:107686417-107686618(+)$1	201	105	110	14.9999
AGAAG	chr14:122027885-122028086(-)$1	201	123	128	14.9999
AGAAG	chrY:494799-495000(-)$1	201	78	83	14.9999
AGAAG	chr16:34016445-34016646(-)$1	201	50	55	14.9999
AGAAG	chr4:138836316-138836517(+)$1	201	67	72	14.9999
AGAAG	chr6:124997803-124998004(+)$1	201	5	10	14.9999
AGAAG	chr2:121128803-121129004(+)$1	201	40	45	14.9999
AGAAG	chr15:3225589-3225790(+)$1	201	121	126	14.9999
AGAAG	chr13:100200680-100200881(-)$1	201	29	34	14.9999
AGAAG	chr16:57136800-57137001(+)$1	201	32	37	14.9999
AGAAG	chrX:34142071-34142272(+)$1	201	111	116	14.9999
AGAAG	chr3:95738674-95738875(+)$1	201	137	142	14.9999
AGAAG	chrX:34142070-34142271(+)$1	201	112	117	14.9999
AGAAG	chr11:97317729-97317930(+)$1	201	137	142	14.9999
AGAAG	chr3:8545575-8545776(+)$1	201	76	81	14.9999
AGAAG	chr11:104285759-104285960(-)$1	201	72	77	14.9999
AGAAG	chrX:12731138-12731339(+)$1	201	178	183	14.9999
AGAAG	chr4:155089572-155089773(+)$1	201	164	169	14.9999
AGAAG	chr14:58728297-58728498(+)$1	201	9	14	14.9999
AGAAG	chr14:103553263-103553464(-)$1	201	89	94	14.9999
AGAAG	chr18:20823889-20824090(+)$1	201	14	19	14.9999
AGAAG	chr1:164632233-164632434(-)$1	201	8	13	14.9999
AGAAG	chr18:20823886-20824087(+)$1	201	17	22	14.9999
AGAAG	chr11:97317730-97317931(+)$1	201	136	141	14.9999
AGAAG	chr14:60898834-60899035(+)$1	201	28	33	14.9999
AGAAG	chr11:23333141-23333342(+)$1	201	73	78	14.9999
AGAAG	chr11:60980110-60980311(-)$1	201	160	165	14.9999
AGAAG	chr13:100204670-100204871(-)$1	201	75	80	14.9999
AGAAG	chr15:96528558-96528759(-)$1	201	124	129	14.9999
AGAAG	chr11:83822136-83822337(+)$1	201	155	160	14.9999
AGAAG	chr14:122027884-122028085(-)$1	201	122	127	14.9999
AGAAG	chr9:62221226-62221427(+)$1	201	63	68	14.9999
AGAAG	chr3:25335266-25335467(-)$1	201	47	52	14.9999
AGAAG	chr15:71292706-71292907(-)$1	201	32	37	14.9999
AGAAG	chr7:17147928-17148129(-)$1	201	130	135	14.9999
AGAAG	chr19:10163413-10163614(-)$1	201	50	55	14.9999
AGAAG	chrM:3488-3689(+)$1	201	44	49	14.9999
AGAAG	chr1:174209728-174209929(-)$1	201	14	19	14.9999
AGAAG	chr16:37536060-37536261(-)$1	201	138	143	14.9999
AGAAG	chr2:60071963-60072164(+)$1	201	138	143	14.9999

#otherMatches

#Struct PSSM
GGGG?	chr18:34476756-34476957(+)$1	201	126	131	14.9999
d0000	chr6:124412063-124412264(-)$1	201	172	177	14.9999
:::dd	chr2:29866447-29866648(+)$1	201	127	132	14.9999
qqqqq	chr10:107686416-107686617(+)$1	201	106	111	14.9999
qqqqq	chr10:107686417-107686618(+)$1	201	105	110	14.9999
qqqqe	chr14:122027885-122028086(-)$1	201	123	128	14.9999
:::::	chrY:494799-495000(-)$1	201	78	83	14.9999
cccee	chr16:34016445-34016646(-)$1	201	50	55	14.9999
cmmmm	chr4:138836316-138836517(+)$1	201	67	72	14.9999
ttttt	chr6:124997803-124998004(+)$1	201	5	10	14.9999
e[a[b	chr2:121128803-121129004(+)$1	201	40	45	14.9999
DACCC	chr15:3225589-3225790(+)$1	201	121	126	14.9999
gggll	chr13:100200680-100200881(-)$1	201	29	34	14.9999
[cccm	chr16:57136800-57137001(+)$1	201	32	37	14.9999
:::::	chrX:34142071-34142272(+)$1	201	111	116	14.9999
444bb	chr3:95738674-95738875(+)$1	201	137	142	14.9999
:::::	chrX:34142070-34142271(+)$1	201	112	117	14.9999
b4444	chr11:97317729-97317930(+)$1	201	137	142	14.9999
::::e	chr3:8545575-8545776(+)$1	201	76	81	14.9999
eee^^	chr11:104285759-104285960(-)$1	201	72	77	14.9999
:bb!!	chrX:12731138-12731339(+)$1	201	178	183	14.9999
uuucc	chr4:155089572-155089773(+)$1	201	164	169	14.9999
cc:dd	chr14:58728297-58728498(+)$1	201	9	14	14.9999
iiiii	chr14:103553263-103553464(-)$1	201	89	94	14.9999
[iiii	chr18:20823889-20824090(+)$1	201	14	19	14.9999
=====	chr1:164632233-164632434(-)$1	201	8	13	14.9999
[iiii	chr18:20823886-20824087(+)$1	201	17	22	14.9999
HHHHH	chr11:97317730-97317931(+)$1	201	136	141	14.9999
LDDDD	chr14:60898834-60899035(+)$1	201	28	33	14.9999
dddd[	chr11:23333141-23333342(+)$1	201	73	78	14.9999
GG}CC	chr11:60980110-60980311(-)$1	201	160	165	14.9999
::fff	chr13:100204670-100204871(-)$1	201	75	80	14.9999
eeeee	chr15:96528558-96528759(-)$1	201	124	129	14.9999
ddd:E	chr11:83822136-83822337(+)$1	201	155	160	14.9999
qqqqe	chr14:122027884-122028085(-)$1	201	122	127	14.9999
ppppp	chr9:62221226-62221427(+)$1	201	63	68	14.9999
::ccc	chr3:25335266-25335467(-)$1	201	47	52	14.9999
:::CC	chr15:71292706-71292907(-)$1	201	32	37	14.9999
dd]bb	chr7:17147928-17148129(-)$1	201	130	135	14.9999
:dddd	chr19:10163413-10163614(-)$1	201	50	55	14.9999
ccc[d	chrM:3488-3689(+)$1	201	44	49	14.9999
ccc!!	chr1:174209728-174209929(-)$1	201	14	19	14.9999
\\\\H	chr16:37536060-37536261(-)$1	201	138	143	14.9999
eeee]	chr2:60071963-60072164(+)$1	201	138	143	14.9999

#DB
)))).	chr18:34476756-34476957(+)$1	1	126	131	14.9999
)....	chr6:124412063-124412264(-)$1	1	172	177	14.9999
...((	chr2:29866447-29866648(+)$1	1	127	132	14.9999
.....	chr10:107686416-107686617(+)$1	1	106	111	14.9999
.....	chr10:107686417-107686618(+)$1	1	105	110	14.9999
....)	chr14:122027885-122028086(-)$1	1	123	128	14.9999
.....	chrY:494799-495000(-)$1	1	78	83	14.9999
)))((	chr16:34016445-34016646(-)$1	1	50	55	14.9999
(....	chr4:138836316-138836517(+)$1	1	67	72	14.9999
.....	chr6:124997803-124998004(+)$1	1	5	10	14.9999
(.(.(	chr2:121128803-121129004(+)$1	1	40	45	14.9999
)))))	chr15:3225589-3225790(+)$1	1	121	126	14.9999
(((..	chr13:100200680-100200881(-)$1	1	29	34	14.9999
.(((.	chr16:57136800-57137001(+)$1	1	32	37	14.9999
.....	chrX:34142071-34142272(+)$1	1	111	116	14.9999
...))	chr3:95738674-95738875(+)$1	1	137	142	14.9999
.....	chrX:34142070-34142271(+)$1	1	112	117	14.9999
)....	chr11:97317729-97317930(+)$1	1	137	142	14.9999
....(	chr3:8545575-8545776(+)$1	1	76	81	14.9999
(((..	chr11:104285759-104285960(-)$1	1	72	77	14.9999
.((..	chrX:12731138-12731339(+)$1	1	178	183	14.9999
...))	chr4:155089572-155089773(+)$1	1	164	169	14.9999
)).((	chr14:58728297-58728498(+)$1	1	9	14	14.9999
)))))	chr14:103553263-103553464(-)$1	1	89	94	14.9999
.((((	chr18:20823889-20824090(+)$1	1	14	19	14.9999
(((((	chr1:164632233-164632434(-)$1	1	8	13	14.9999
.((((	chr18:20823886-20824087(+)$1	1	17	22	14.9999
)))))	chr11:97317730-97317931(+)$1	1	136	141	14.9999
.((((	chr14:60898834-60899035(+)$1	1	28	33	14.9999
((((.	chr11:23333141-23333342(+)$1	1	73	78	14.9999
)).))	chr11:60980110-60980311(-)$1	1	160	165	14.9999
..(((	chr13:100204670-100204871(-)$1	1	75	80	14.9999
)))))	chr15:96528558-96528759(-)$1	1	124	129	14.9999
))).)	chr11:83822136-83822337(+)$1	1	155	160	14.9999
....)	chr14:122027884-122028085(-)$1	1	122	127	14.9999
.....	chr9:62221226-62221427(+)$1	1	63	68	14.9999
..(((	chr3:25335266-25335467(-)$1	1	47	52	14.9999
...((	chr15:71292706-71292907(-)$1	1	32	37	14.9999
)).))	chr7:17147928-17148129(-)$1	1	130	135	14.9999
.((((	chr19:10163413-10163614(-)$1	1	50	55	14.9999
(((.(	chrM:3488-3689(+)$1	1	44	49	14.9999
(((..	chr1:174209728-174209929(-)$1	1	14	19	14.9999
....)	chr16:37536060-37536261(-)$1	1	138	143	14.9999
)))).	chr2:60071963-60072164(+)$1	1	138	143	14.9999

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

#score	659.9999999999999
#seq	44
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_transcript_m2_run2.nuc.txt

#NT
GUG	chr17:73289029-73289285(+)$1	256	17	20	8.9999
GUG	chr4:6322057-6322292(+)$1	235	6	9	8.9999
gug	chr3:37380385-37380624(+)$1	239	31	34	8.9999
GUG	chr10:117252017-117252253(-)$1	236	112	115	8.9999
GUG	chr2:136607662-136607914(+)$1	252	68	71	8.9999
GUG	chr18:61457819-61458056(-)$1	237	55	58	8.9999
GUG	chr14:35340832-35341082(-)$1	250	118	121	8.9999
GUG	chr14:37691621-37691860(-)$1	239	11	14	8.9999
GUG	chr13:55445114-55445362(-)$1	248	22	25	8.9999
GUG	chr1:23375775-23376023(-)$1	248	23	26	8.9999
GUG	chr11:87793793-87794058(-)$1	265	8	11	8.9999
GUG	chr4:104704712-104704996(-)$1	284	7	10	8.9999
GUG	chr12:33535477-33535714(+)$1	237	20	23	8.9999
GUG	chr4:14841122-14841357(+)$1	235	17	20	8.9999
GUG	chr7:118214765-118215000(-)$1	235	56	59	8.9999
GUG	chr14:21319413-21319648(-)$1	235	53	56	8.9999
GUG	chr4:150421684-150421924(-)$1	240	2	5	8.9999
GUG	chr10:44083881-44084116(+)$1	235	106	109	8.9999
GUG	chr1:140382339-140382583(-)$1	244	70	73	8.9999
GUG	chr9:30957848-30958085(-)$1	237	47	50	8.9999
GUG	chr5:32794739-32794979(+)$1	240	59	62	8.9999
GUG	chr11:53232401-53232636(+)$1	235	106	109	8.9999
GUG	chr2:121373570-121373818(-)$1	248	62	65	8.9999
GUG	chr7:50553444-50553683(-)$1	239	20	23	8.9999
GUG	chr14:15631568-15631811(+)$1	243	64	67	8.9999
GUG	chr1:166367681-166367925(-)$1	244	67	70	8.9999
GUG	chr8:46911742-46911988(+)$1	246	47	50	8.9999
GUG	chr7:35130774-35131009(-)$1	235	81	84	8.9999
GUG	chr9:120869129-120869380(+)$1	251	50	53	8.9999
GUG	chr8:85837495-85837730(-)$1	235	115	118	8.9999
GUG	chr9:30957186-30957440(-)$1	254	22	25	8.9999
GUG	chr1:190035104-190035339(+)$1	235	0	3	8.9999
GUG	chr10:77735054-77735289(-)$1	235	197	200	8.9999
GUG	chr3:146392708-146392975(-)$1	267	86	89	8.9999
GUG	chr9:121364093-121364352(+)$1	259	19	22	8.9999
GUG	chr17:73290105-73290353(+)$1	248	133	136	8.9999
GUG	chr6:30404218-30404458(+)$1	240	37	40	8.9999
GUG	chr12:75047502-75047738(+)$1	236	11	14	8.9999
GUG	chr9:96218718-96218953(+)$1	235	19	22	8.9999
GUG	chr5:136384420-136384663(-)$1	243	32	35	8.9999
GUG	chr3:141965426-141965661(-)$1	235	51	54	8.9999
GUG	chr2:76723068-76723305(-)$1	237	111	114	8.9999
GUG	chr8:35233273-35233512(+)$1	239	12	15	8.9999
GUG	chr2:124492571-124492822(+)$1	251	64	67	8.9999
GUG	chr15:4103844-4104095(+)$1	251	69	72	8.9999
GUG	chr19:23380104-23380339(-)$1	235	94	97	8.9999
GUG	chr3:141965381-141965616(-)$1	235	6	9	8.9999
GUG	chr5:122904016-122904283(-)$1	267	16	19	8.9999
GUG	chr2:132134563-132134798(+)$1	235	47	50	8.9999
GUG	chr18:35750845-35751081(+)$1	236	3	6	8.9999
GUG	chr2:104268783-104269022(-)$1	239	20	23	8.9999
GUG	chr11:74490419-74490654(-)$1	235	0	3	8.9999
GUG	chr14:37688389-37688631(-)$1	242	20	23	8.9999
GUG	chr12:71568235-71568470(+)$1	235	24	27	8.9999
GUG	chr17:81787502-81787752(-)$1	250	52	55	8.9999
GUG	chr14:26401180-26401415(+)$1	235	9	12	8.9999
GUG	chr18:78021187-78021422(+)$1	235	61	64	8.9999
GUG	chr19:43574327-43574562(-)$1	235	32	35	8.9999
GUG	chr2:132136059-132136303(+)$1	244	30	33	8.9999
GUG	chr2:103900949-103901184(+)$1	235	86	89	8.9999
GUG	chr16:8848473-8848711(+)$1	238	44	47	8.9999
GUG	chr10:53626981-53627220(-)$1	239	130	133	8.9999
GUG	chr11:29642544-29642783(+)$1	239	8	11	8.9999
GUG	chr16:58678960-58679203(+)$1	243	42	45	8.9999
gug	chr14:18699126-18699361(+)$1	235	55	58	8.9999
GUG	chr5:32794615-32794875(+)$1	260	1	4	8.9999
GUG	chr4:154933049-154933289(+)$1	240	11	14	8.9999
GUG	chr11:51414746-51414984(-)$1	238	40	43	8.9999
GUG	chr16:37885612-37885856(+)$1	244	14	17	8.9999
GUG	chr13:29999430-29999670(-)$1	240	30	33	8.9999
gug	chr11:60371177-60371412(+)$1	235	1	4	8.9999
GUG	chr2:179769162-179769397(+)$1	235	23	26	8.9999
GUG	chr5:32794419-32794657(+)$1	238	20	23	8.9999
GUG	chr8:71425001-71425238(+)$1	237	28	31	8.9999
GUG	chrX:70604132-70604375(+)$1	243	19	22	8.9999
GUG	chr4:6321962-6322226(+)$1	264	30	33	8.9999
GUG	chr14:37688529-37688770(-)$1	241	29	32	8.9999
GUG	chr6:72561602-72561837(-)$1	235	1	4	8.9999
GUG	chr17:13208997-13209239(+)$1	242	93	96	8.9999
GUG	chr15:79657552-79657796(-)$1	244	46	49	8.9999
GUG	chr17:44174403-44174641(+)$1	238	5	8	8.9999
GUG	chr2:72241350-72241601(+)$1	251	6	9	8.9999
GUG	chr15:100233580-100233815(-)$1	235	5	8	8.9999
GUG	chr13:114384120-114384358(-)$1	238	87	90	8.9999
GUG	chr1:153210533-153210769(+)$1	236	4	7	8.9999
GUG	chrX:39150455-39150694(-)$1	239	124	127	8.9999
GUG	chr2:155214785-155215039(+)$1	254	3	6	8.9999
GUG	chr15:4103989-4104255(+)$1	266	6	9	8.9999
GUG	chr4:42970629-42970867(+)$1	238	25	28	8.9999
GUG	chr8:71430485-71430793(+)$1	308	116	119	8.9999
GUG	chr9:71352180-71352416(-)$1	236	34	37	8.9999
GUG	chr15:103029637-103029873(-)$1	236	27	30	8.9999
GUG	chr4:97780418-97780653(+)$1	235	1	4	8.9999

#otherMatches

#Struct PSSM
ggg	chr6:119875219-119875455(-)$1	236	11	14	8.9999
[ee	chr17:73289029-73289285(+)$1	256	17	20	8.9999
eee	chr4:6322057-6322292(+)$1	235	6	9	8.9999
CCC	chr3:37380385-37380624(+)$1	239	31	34	8.9999
::b	chr10:117252017-117252253(-)$1	236	112	115	8.9999
eee	chr2:136607662-136607914(+)$1	252	68	71	8.9999
e:d	chr18:61457819-61458056(-)$1	237	55	58	8.9999
cc6	chr14:35340832-35341082(-)$1	250	118	121	8.9999
ppp	chr14:37691621-37691860(-)$1	239	11	14	8.9999
dd:	chr13:55445114-55445362(-)$1	248	22	25	8.9999
qqq	chr1:23375775-23376023(-)$1	248	23	26	8.9999
"""	chr11:87793793-87794058(-)$1	265	8	11	8.9999
HHH	chr4:104704712-104704996(-)$1	284	7	10	8.9999
ggg	chr12:33535477-33535714(+)$1	237	20	23	8.9999
GGG	chr4:14841122-14841357(+)$1	235	17	20	8.9999
b[c	chr7:118214765-118215000(-)$1	235	56	59	8.9999
b]d	chr14:21319413-21319648(-)$1	235	53	56	8.9999
DDD	chr4:150421684-150421924(-)$1	240	2	5	8.9999
ddd	chr10:44083881-44084116(+)$1	235	106	109	8.9999
ggg	chr1:140382339-140382583(-)$1	244	70	73	8.9999
fff	chr9:30957848-30958085(-)$1	237	47	50	8.9999
ddd	chr5:32794739-32794979(+)$1	240	59	62	8.9999
III	chr11:53232401-53232636(+)$1	235	106	109	8.9999
EEE	chr2:121373570-121373818(-)$1	248	62	65	8.9999
eee	chr7:50553444-50553683(-)$1	239	20	23	8.9999
ooo	chr14:15631568-15631811(+)$1	243	64	67	8.9999
fff	chr1:166367681-166367925(-)$1	244	67	70	8.9999
ccc	chr8:46911742-46911988(+)$1	246	47	50	8.9999
HHH	chr7:35130774-35131009(-)$1	235	81	84	8.9999
III	chr9:120869129-120869380(+)$1	251	50	53	8.9999
III	chr8:85837495-85837730(-)$1	235	115	118	8.9999
fff	chr9:30957186-30957440(-)$1	254	22	25	8.9999
:::	chr1:190035104-190035339(+)$1	235	0	3	8.9999
fff	chr10:77735054-77735289(-)$1	235	197	200	8.9999
CCF	chr3:146392708-146392975(-)$1	267	86	89	8.9999
qqq	chr9:121364093-121364352(+)$1	259	19	22	8.9999
D{D	chr17:73290105-73290353(+)$1	248	133	136	8.9999
e!!	chr6:30404218-30404458(+)$1	240	37	40	8.9999
ccc	chr12:75047502-75047738(+)$1	236	11	14	8.9999
CCC	chr9:96218718-96218953(+)$1	235	19	22	8.9999
HHH	chr5:136384420-136384663(-)$1	243	32	35	8.9999
GGG	chr3:141965426-141965661(-)$1	235	51	54	8.9999
]ff	chr2:76723068-76723305(-)$1	237	111	114	8.9999
:::	chr8:35233273-35233512(+)$1	239	12	15	8.9999
b::	chr2:124492571-124492822(+)$1	251	64	67	8.9999
55b	chr15:4103844-4104095(+)$1	251	69	72	8.9999
eee	chr19:23380104-23380339(-)$1	235	94	97	8.9999
EEE	chr3:141965381-141965616(-)$1	235	6	9	8.9999
:DD	chr5:122904016-122904283(-)$1	267	16	19	8.9999
EEE	chr2:132134563-132134798(+)$1	235	47	50	8.9999
hhh	chr18:35750845-35751081(+)$1	236	3	6	8.9999
HHH	chr2:104268783-104269022(-)$1	239	20	23	8.9999
DDD	chr11:74490419-74490654(-)$1	235	0	3	8.9999
""c	chr14:37688389-37688631(-)$1	242	20	23	8.9999
ddd	chr12:71568235-71568470(+)$1	235	24	27	8.9999
DDD	chr17:81787502-81787752(-)$1	250	52	55	8.9999
:::	chr14:26401180-26401415(+)$1	235	9	12	8.9999
vvv	chr18:78021187-78021422(+)$1	235	61	64	8.9999
e[b	chr19:43574327-43574562(-)$1	235	32	35	8.9999
fll	chr2:132136059-132136303(+)$1	244	30	33	8.9999
i!!	chr2:103900949-103901184(+)$1	235	86	89	8.9999
CC{	chr16:8848473-8848711(+)$1	238	44	47	8.9999
ooo	chr10:53626981-53627220(-)$1	239	130	133	8.9999
III	chr11:29642544-29642783(+)$1	239	8	11	8.9999
gll	chr16:58678960-58679203(+)$1	243	42	45	8.9999
bbm	chr14:18699126-18699361(+)$1	235	55	58	8.9999
GGG	chr5:32794615-32794875(+)$1	260	1	4	8.9999
ddd	chr4:154933049-154933289(+)$1	240	11	14	8.9999
EEE	chr11:51414746-51414984(-)$1	238	40	43	8.9999
ggg	chr16:37885612-37885856(+)$1	244	14	17	8.9999
a[a	chr13:29999430-29999670(-)$1	240	30	33	8.9999
CCC	chr11:60371177-60371412(+)$1	235	1	4	8.9999
gge	chr2:179769162-179769397(+)$1	235	23	26	8.9999
EEE	chr5:32794419-32794657(+)$1	238	20	23	8.9999
]ee	chr8:71425001-71425238(+)$1	237	28	31	8.9999
eee	chrX:70604132-70604375(+)$1	243	19	22	8.9999
cc[	chr4:6321962-6322226(+)$1	264	30	33	8.9999
hhh	chr14:37688529-37688770(-)$1	241	29	32	8.9999
:bb	chr6:72561602-72561837(-)$1	235	1	4	8.9999
EEE	chr17:13208997-13209239(+)$1	242	93	96	8.9999
ggg	chr15:79657552-79657796(-)$1	244	46	49	8.9999
:gg	chr17:44174403-44174641(+)$1	238	5	8	8.9999
GGG	chr2:72241350-72241601(+)$1	251	6	9	8.9999
{EE	chr15:100233580-100233815(-)$1	235	5	8	8.9999
ffn	chr13:114384120-114384358(-)$1	238	87	90	8.9999
ddd	chr1:153210533-153210769(+)$1	236	4	7	8.9999
F}D	chrX:39150455-39150694(-)$1	239	124	127	8.9999
ddd	chr2:155214785-155215039(+)$1	254	3	6	8.9999
EEE	chr15:4103989-4104255(+)$1	266	6	9	8.9999
%%e	chr4:42970629-42970867(+)$1	238	25	28	8.9999
JJJ	chr8:71430485-71430793(+)$1	308	116	119	8.9999
FFF	chr9:71352180-71352416(-)$1	236	34	37	8.9999
fff	chr15:103029637-103029873(-)$1	236	27	30	8.9999
::e	chr4:97780418-97780653(+)$1	235	1	4	8.9999

#DB
(((	chr6:119875219-119875455(-)$1	1	11	14	8.9999
.((	chr17:73289029-73289285(+)$1	1	17	20	8.9999
(((	chr4:6322057-6322292(+)$1	1	6	9	8.9999
(((	chr3:37380385-37380624(+)$1	1	31	34	8.9999
..(	chr10:117252017-117252253(-)$1	1	112	115	8.9999
(((	chr2:136607662-136607914(+)$1	1	68	71	8.9999
).(	chr18:61457819-61458056(-)$1	1	55	58	8.9999
)).	chr14:35340832-35341082(-)$1	1	118	121	8.9999
...	chr14:37691621-37691860(-)$1	1	11	14	8.9999
)).	chr13:55445114-55445362(-)$1	1	22	25	8.9999
...	chr1:23375775-23376023(-)$1	1	23	26	8.9999
...	chr11:87793793-87794058(-)$1	1	8	11	8.9999
(((	chr4:104704712-104704996(-)$1	1	7	10	8.9999
)))	chr12:33535477-33535714(+)$1	1	20	23	8.9999
(((	chr4:14841122-14841357(+)$1	1	17	20	8.9999
(.(	chr7:118214765-118215000(-)$1	1	56	59	8.9999
).)	chr14:21319413-21319648(-)$1	1	53	56	8.9999
(((	chr4:150421684-150421924(-)$1	1	2	5	8.9999
(((	chr10:44083881-44084116(+)$1	1	106	109	8.9999
)))	chr1:140382339-140382583(-)$1	1	70	73	8.9999
(((	chr9:30957848-30958085(-)$1	1	47	50	8.9999
)))	chr5:32794739-32794979(+)$1	1	59	62	8.9999
)))	chr11:53232401-53232636(+)$1	1	106	109	8.9999
(((	chr2:121373570-121373818(-)$1	1	62	65	8.9999
)))	chr7:50553444-50553683(-)$1	1	20	23	8.9999
...	chr14:15631568-15631811(+)$1	1	64	67	8.9999
)))	chr1:166367681-166367925(-)$1	1	67	70	8.9999
(((	chr8:46911742-46911988(+)$1	1	47	50	8.9999
(((	chr7:35130774-35131009(-)$1	1	81	84	8.9999
(((	chr9:120869129-120869380(+)$1	1	50	53	8.9999
(((	chr8:85837495-85837730(-)$1	1	115	118	8.9999
(((	chr9:30957186-30957440(-)$1	1	22	25	8.9999
...	chr1:190035104-190035339(+)$1	1	0	3	8.9999
(((	chr10:77735054-77735289(-)$1	1	197	200	8.9999
(((	chr3:146392708-146392975(-)$1	1	86	89	8.9999
...	chr9:121364093-121364352(+)$1	1	19	22	8.9999
(.(	chr17:73290105-73290353(+)$1	1	133	136	8.9999
(..	chr6:30404218-30404458(+)$1	1	37	40	8.9999
(((	chr12:75047502-75047738(+)$1	1	11	14	8.9999
(((	chr9:96218718-96218953(+)$1	1	19	22	8.9999
(((	chr5:136384420-136384663(-)$1	1	32	35	8.9999
(((	chr3:141965426-141965661(-)$1	1	51	54	8.9999
.))	chr2:76723068-76723305(-)$1	1	111	114	8.9999
...	chr8:35233273-35233512(+)$1	1	12	15	8.9999
)..	chr2:124492571-124492822(+)$1	1	64	67	8.9999
..)	chr15:4103844-4104095(+)$1	1	69	72	8.9999
)))	chr19:23380104-23380339(-)$1	1	94	97	8.9999
(((	chr3:141965381-141965616(-)$1	1	6	9	8.9999
.((	chr5:122904016-122904283(-)$1	1	16	19	8.9999
(((	chr2:132134563-132134798(+)$1	1	47	50	8.9999
(((	chr18:35750845-35751081(+)$1	1	3	6	8.9999
(((	chr2:104268783-104269022(-)$1	1	20	23	8.9999
(((	chr11:74490419-74490654(-)$1	1	0	3	8.9999
..(	chr14:37688389-37688631(-)$1	1	20	23	8.9999
(((	chr12:71568235-71568470(+)$1	1	24	27	8.9999
(((	chr17:81787502-81787752(-)$1	1	52	55	8.9999
...	chr14:26401180-26401415(+)$1	1	9	12	8.9999
...	chr18:78021187-78021422(+)$1	1	61	64	8.9999
(.(	chr19:43574327-43574562(-)$1	1	32	35	8.9999
(..	chr2:132136059-132136303(+)$1	1	30	33	8.9999
(..	chr2:103900949-103901184(+)$1	1	86	89	8.9999
((.	chr16:8848473-8848711(+)$1	1	44	47	8.9999
...	chr10:53626981-53627220(-)$1	1	130	133	8.9999
(((	chr11:29642544-29642783(+)$1	1	8	11	8.9999
(..	chr16:58678960-58679203(+)$1	1	42	45	8.9999
((.	chr14:18699126-18699361(+)$1	1	55	58	8.9999
(((	chr5:32794615-32794875(+)$1	1	1	4	8.9999
(((	chr4:154933049-154933289(+)$1	1	11	14	8.9999
(((	chr11:51414746-51414984(-)$1	1	40	43	8.9999
(((	chr16:37885612-37885856(+)$1	1	14	17	8.9999
(.(	chr13:29999430-29999670(-)$1	1	30	33	8.9999
(((	chr11:60371177-60371412(+)$1	1	1	4	8.9999
(((	chr2:179769162-179769397(+)$1	1	23	26	8.9999
(((	chr5:32794419-32794657(+)$1	1	20	23	8.9999
.))	chr8:71425001-71425238(+)$1	1	28	31	8.9999
(((	chrX:70604132-70604375(+)$1	1	19	22	8.9999
((.	chr4:6321962-6322226(+)$1	1	30	33	8.9999
(((	chr14:37688529-37688770(-)$1	1	29	32	8.9999
.((	chr6:72561602-72561837(-)$1	1	1	4	8.9999
(((	chr17:13208997-13209239(+)$1	1	93	96	8.9999
)))	chr15:79657552-79657796(-)$1	1	46	49	8.9999
.((	chr17:44174403-44174641(+)$1	1	5	8	8.9999
(((	chr2:72241350-72241601(+)$1	1	6	9	8.9999
.((	chr15:100233580-100233815(-)$1	1	5	8	8.9999
((.	chr13:114384120-114384358(-)$1	1	87	90	8.9999
(((	chr1:153210533-153210769(+)$1	1	4	7	8.9999
).)	chrX:39150455-39150694(-)$1	1	124	127	8.9999
(((	chr2:155214785-155215039(+)$1	1	3	6	8.9999
(((	chr15:4103989-4104255(+)$1	1	6	9	8.9999
..(	chr4:42970629-42970867(+)$1	1	25	28	8.9999
)))	chr8:71430485-71430793(+)$1	1	116	119	8.9999
(((	chr9:71352180-71352416(-)$1	1	34	37	8.9999
)))	chr15:103029637-103029873(-)$1	1	27	30	8.9999
..(	chr4:97780418-97780653(+)$1	1	1	4	8.9999

#PSSM
G : 0.96	g : 0.03	
U : 0.96	u : 0.03	
G : 0.96	g : 0.03	

#score	845.9999999999998
#seq	94
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m2_run1.nuc.txt

#NT
UGGCCA	chr4:151560213-151560493(+)$1	280	176	182	11.0508
GGGCCU	chr16:36049855-36050132(-)$1	277	219	225	11.2203
GGGCCU	chr17:37114860-37115128(-)$1	268	6	12	11.2203
GGGCCA	chr11:87794792-87795066(-)$1	274	205	211	14.5254
GGGCCA	chr2:156606174-156606446(+)$1	272	265	271	14.5254
GUGCCA	chr8:74844691-74844960(+)$1	269	57	63	10.8813
GGGCCA	chr5:75006662-75006928(-)$1	266	231	237	14.5254
GGACCA	chr2:34678076-34678352(-)$1	276	186	192	10.8813
UGGCCA	chr19:5384549-5384817(-)$1	268	7	13	11.0508
GGGCCG	chr2:91803321-91803605(-)$1	284	28	34	11.0508
GGGCCA	chr8:95850590-95850858(-)$1	268	126	132	14.5254
UGGCCA	chr4:155331122-155331424(+)$1	302	162	168	11.0508
GUGCca	chr7:27949815-27950086(-)$1	271	32	38	10.8813
GUGCCA	chr1:77503123-77503392(-)$1	269	170	176	10.8813
GAGCCA	chr2:163884396-163884667(-)$1	271	142	148	10.7118
GGGCCC	chr4:33125089-33125363(+)$1	274	117	123	11.0508
GGGCCA	chr19:4792248-4792540(-)$1	292	14	20	14.5254
GGACCA	chr17:6084525-6084794(+)$1	269	93	99	10.8813
UGGCCA	chr11:117828728-117829006(-)$1	278	18	24	11.0508
GGGCCU	chr6:22240953-22241221(+)$1	268	4	10	11.2203
GGGCCA	chr5:93697524-93697801(+)$1	277	136	142	14.5254
GAGCCA	chr3:108706705-108706973(-)$1	268	1	7	10.7118
GGGCCA	chr17:35292437-35292710(-)$1	273	144	150	14.5254
UGGCCA	chr7:25670028-25670303(+)$1	275	264	270	11.0508
GGGCCA	chr11:102978353-102978633(+)$1	280	151	157	14.5254
GGGCCA	chr11:70466234-70466555(-)$1	321	142	148	14.5254
GGACCA	chr9:3411339-3411620(+)$1	281	146	152	10.8813
GGGCCU	chr2:153142656-153142935(+)$1	279	43	49	11.2203
GGACCA	chr19:29086354-29086632(+)$1	278	247	253	10.8813
UGGCCA	chr12:85733283-85733551(-)$1	268	83	89	11.0508
GGGCCA	chr14:70066969-70067240(+)$1	271	21	27	14.5254
GAGCCA	chr9:44160509-44160780(-)$1	271	8	14	10.7118
UGGCCA	chr8:63406007-63406293(-)$1	286	106	112	11.0508
GUGCCA	chr6:56728722-56729000(-)$1	278	142	148	10.8813
GAGCCA	chr13:69138020-69138287(-)$1	267	245	251	10.7118
UGGCCA	chr8:28383691-28383967(+)$1	276	14	20	11.0508
GGGCCA	chr8:74842835-74843118(+)$1	283	115	121	14.5254
GUGCCA	chr18:36908130-36908401(+)$1	271	142	148	10.8813
GGGCCU	chr13:73773815-73774087(+)$1	272	110	116	11.2203
GGACCA	chr8:23489738-23490016(-)$1	278	75	81	10.8813
GGACCA	chr2:121205212-121205496(-)$1	284	51	57	10.8813
GGGCCC	chr2:31615425-31615714(+)$1	289	1	7	11.0508
gggccg	chr7:117008949-117009223(-)$1	274	25	31	11.0508
gggccc	chr6:54767279-54767565(+)$1	286	119	125	11.0508
GGACCA	chr18:60859088-60859368(-)$1	280	115	121	10.8813
GUGCCA	chr19:7273750-7274023(-)$1	273	162	168	10.8813
GGGCCG	chr17:32498259-32498531(-)$1	272	110	116	11.0508
GGGCCA	chr2:156359397-156359677(+)$1	280	217	223	14.5254
GGGCCA	chr1:36501804-36502071(-)$1	267	57	63	14.5254
GGGCCA	chr9:97269861-97270130(-)$1	269	75	81	14.5254
GGACCA	chr14:52760734-52761005(+)$1	271	107	113	10.8813
GGGCCG	chr5:92391556-92391827(-)$1	271	127	133	11.0508
GGGCCU	chr2:174125804-174126076(+)$1	272	83	89	11.2203
GGGCCC	chr10:126721767-126722035(-)$1	268	92	98	11.0508
GGGCCA	chrX:98514856-98515126(+)$1	270	47	53	14.5254
UGGCCA	chr3:146444016-146444284(-)$1	268	13	19	11.0508
GGGCCA	chr3:96066811-96067101(-)$1	290	235	241	14.5254
GGGCCA	chr18:24743677-24743947(-)$1	270	121	127	14.5254

#otherMatches

#Struct PSSM
::::::	chr13:81930942-81931210(+)$1	268	162	168	14.5254
IIIIII	chr4:151560213-151560493(+)$1	280	176	182	11.0508
fffffp	chr16:36049855-36050132(-)$1	277	219	225	11.2203
CCC:JJ	chr17:37114860-37115128(-)$1	268	6	12	11.2203
2eeeee	chr11:87794792-87795066(-)$1	274	205	211	14.5254
C}CCC:	chr2:156606174-156606446(+)$1	272	265	271	14.5254
cccbb3	chr8:74844691-74844960(+)$1	269	57	63	10.8813
FFFFF}	chr5:75006662-75006928(-)$1	266	231	237	14.5254
dd7777	chr2:34678076-34678352(-)$1	276	186	192	10.8813
G{DDDD	chr19:5384549-5384817(-)$1	268	7	13	11.0508
BBEEEE	chr2:91803321-91803605(-)$1	284	28	34	11.0508
eee:::	chr8:95850590-95850858(-)$1	268	126	132	14.5254
eennnn	chr4:155331122-155331424(+)$1	302	162	168	11.0508
[cccqq	chr7:27949815-27950086(-)$1	271	32	38	10.8813
ddddpp	chr1:77503123-77503392(-)$1	269	170	176	10.8813
oooccc	chr2:163884396-163884667(-)$1	271	142	148	10.7118
ddccc:	chr4:33125089-33125363(+)$1	274	117	123	11.0508
eeeeex	chr19:4792248-4792540(-)$1	292	14	20	14.5254
dddd::	chr17:6084525-6084794(+)$1	269	93	99	10.8813
:DDDD:	chr11:117828728-117829006(-)$1	278	18	24	11.0508
:::HHH	chr6:22240953-22241221(+)$1	268	4	10	11.2203
bbeeee	chr5:93697524-93697801(+)$1	277	136	142	14.5254
eeeepp	chr3:108706705-108706973(-)$1	268	1	7	10.7118
:ccc[e	chr17:35292437-35292710(-)$1	273	144	150	14.5254
GGGGG:	chr7:25670028-25670303(+)$1	275	264	270	11.0508
::eeee	chr11:102978353-102978633(+)$1	280	151	157	14.5254
f"""ee	chr11:70466234-70466555(-)$1	321	142	148	14.5254
333ddd	chr9:3411339-3411620(+)$1	281	146	152	10.8813
GGgggg	chr2:153142656-153142935(+)$1	279	43	49	11.2203
cnnnnn	chr19:29086354-29086632(+)$1	278	247	253	10.8813
]ccc33	chr12:85733283-85733551(-)$1	268	83	89	11.0508
[bbbb[	chr14:70066969-70067240(+)$1	271	21	27	14.5254
:::BB:	chr9:44160509-44160780(-)$1	271	8	14	10.7118
ddddam	chr8:63406007-63406293(-)$1	286	106	112	11.0508
hhhh::	chr6:56728722-56729000(-)$1	278	142	148	10.8813
888888	chr13:69138020-69138287(-)$1	267	245	251	10.7118
DDDDdd	chr8:28383691-28383967(+)$1	276	14	20	11.0508
ccdddd	chr8:74842835-74843118(+)$1	283	115	121	14.5254
ccc]ee	chr18:36908130-36908401(+)$1	271	142	148	10.8813
dddd""	chr13:73773815-73774087(+)$1	272	110	116	11.2203
cc:ddd	chr8:23489738-23490016(-)$1	278	75	81	10.8813
EE::::	chr2:121205212-121205496(-)$1	284	51	57	10.8813
DDDUUU	chr2:31615425-31615714(+)$1	289	1	7	11.0508
CFFFFF	chr7:117008949-117009223(-)$1	274	25	31	11.0508
cc$$$$	chr6:54767279-54767565(+)$1	286	119	125	11.0508
c[abbp	chr18:60859088-60859368(-)$1	280	115	121	10.8813
ee[ddd	chr19:7273750-7274023(-)$1	273	162	168	10.8813
fffffe	chr17:32498259-32498531(-)$1	272	110	116	11.0508
FFFF:c	chr2:156359397-156359677(+)$1	280	217	223	14.5254
MMMGGG	chr1:36501804-36502071(-)$1	267	57	63	14.5254
IIIIII	chr9:97269861-97270130(-)$1	269	75	81	14.5254
EELLLB	chr14:52760734-52761005(+)$1	271	107	113	10.8813
[ddddm	chr5:92391556-92391827(-)$1	271	127	133	11.0508
mmmmee	chr2:174125804-174126076(+)$1	272	83	89	11.2203
ldddd4	chr10:126721767-126722035(-)$1	268	92	98	11.0508
fffff5	chrX:98514856-98515126(+)$1	270	47	53	14.5254
:CCC{C	chr3:146444016-146444284(-)$1	268	13	19	11.0508
fffff:	chr3:96066811-96067101(-)$1	290	235	241	14.5254
eeee22	chr18:24743677-24743947(-)$1	270	121	127	14.5254

#DB
......	chr13:81930942-81931210(+)$1	1	162	168	14.5254
))))))	chr4:151560213-151560493(+)$1	1	176	182	11.0508
(((((.	chr16:36049855-36050132(-)$1	1	219	225	11.2203
(((.((	chr17:37114860-37115128(-)$1	1	6	12	11.2203
.)))))	chr11:87794792-87795066(-)$1	1	205	211	14.5254
).))).	chr2:156606174-156606446(+)$1	1	265	271	14.5254
))))).	chr8:74844691-74844960(+)$1	1	57	63	10.8813
))))).	chr5:75006662-75006928(-)$1	1	231	237	14.5254
))....	chr2:34678076-34678352(-)$1	1	186	192	10.8813
(.((((	chr19:5384549-5384817(-)$1	1	7	13	11.0508
((((((	chr2:91803321-91803605(-)$1	1	28	34	11.0508
)))...	chr8:95850590-95850858(-)$1	1	126	132	14.5254
((....	chr4:155331122-155331424(+)$1	1	162	168	11.0508
.(((..	chr7:27949815-27950086(-)$1	1	32	38	10.8813
((((..	chr1:77503123-77503392(-)$1	1	170	176	10.8813
...)))	chr2:163884396-163884667(-)$1	1	142	148	10.7118
))))).	chr4:33125089-33125363(+)$1	1	117	123	11.0508
(((((.	chr19:4792248-4792540(-)$1	1	14	20	14.5254
))))..	chr17:6084525-6084794(+)$1	1	93	99	10.8813
.((((.	chr11:117828728-117829006(-)$1	1	18	24	11.0508
...(((	chr6:22240953-22241221(+)$1	1	4	10	11.2203
))((((	chr5:93697524-93697801(+)$1	1	136	142	14.5254
((((..	chr3:108706705-108706973(-)$1	1	1	7	10.7118
.(((.(	chr17:35292437-35292710(-)$1	1	144	150	14.5254
))))).	chr7:25670028-25670303(+)$1	1	264	270	11.0508
..((((	chr11:102978353-102978633(+)$1	1	151	157	14.5254
(...((	chr11:70466234-70466555(-)$1	1	142	148	14.5254
...)))	chr9:3411339-3411620(+)$1	1	146	152	10.8813
((((((	chr2:153142656-153142935(+)$1	1	43	49	11.2203
(.....	chr19:29086354-29086632(+)$1	1	247	253	10.8813
.)))..	chr12:85733283-85733551(-)$1	1	83	89	11.0508
.((((.	chr14:70066969-70067240(+)$1	1	21	27	14.5254
...((.	chr9:44160509-44160780(-)$1	1	8	14	10.7118
(((((.	chr8:63406007-63406293(-)$1	1	106	112	11.0508
))))..	chr6:56728722-56729000(-)$1	1	142	148	10.8813
......	chr13:69138020-69138287(-)$1	1	245	251	10.7118
((((((	chr8:28383691-28383967(+)$1	1	14	20	11.0508
))((((	chr8:74842835-74843118(+)$1	1	115	121	14.5254
))).))	chr18:36908130-36908401(+)$1	1	142	148	10.8813
((((..	chr13:73773815-73774087(+)$1	1	110	116	11.2203
)).(((	chr8:23489738-23490016(-)$1	1	75	81	10.8813
((....	chr2:121205212-121205496(-)$1	1	51	57	10.8813
(((...	chr2:31615425-31615714(+)$1	1	1	7	11.0508
((((((	chr7:117008949-117009223(-)$1	1	25	31	11.0508
((....	chr6:54767279-54767565(+)$1	1	119	125	11.0508
(.(((.	chr18:60859088-60859368(-)$1	1	115	121	10.8813
((.(((	chr19:7273750-7274023(-)$1	1	162	168	10.8813
)))))(	chr17:32498259-32498531(-)$1	1	110	116	11.0508
)))).(	chr2:156359397-156359677(+)$1	1	217	223	14.5254
...(((	chr1:36501804-36502071(-)$1	1	57	63	14.5254
((((((	chr9:97269861-97270130(-)$1	1	75	81	14.5254
((...(	chr14:52760734-52761005(+)$1	1	107	113	10.8813
.((((.	chr5:92391556-92391827(-)$1	1	127	133	11.0508
....))	chr2:174125804-174126076(+)$1	1	83	89	11.2203
.)))).	chr10:126721767-126722035(-)$1	1	92	98	11.0508
))))).	chrX:98514856-98515126(+)$1	1	47	53	14.5254
.(((.(	chr3:146444016-146444284(-)$1	1	13	19	11.0508
))))).	chr3:96066811-96067101(-)$1	1	235	241	14.5254
))))..	chr18:24743677-24743947(-)$1	1	121	127	14.5254

#PSSM
G : 0.81	U : 0.15	g : 0.03	
G : 0.79	U : 0.10	A : 0.06	g : 0.03	
G : 0.83	A : 0.13	g : 0.03	
C : 0.96	c : 0.03	
C : 0.94	c : 0.05	
A : 0.74	U : 0.10	G : 0.05	C : 0.05	a : 0.01	g : 0.01	c : 0.01	

#score	711.8305084745758
#seq	59
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m3_run2.nuc.txt

#NT
CUGCAGCC	chr19:5384549-5384817(-)$1	268	138	146	10.8367
CGGCAGCC	chr17:35119051-35119331(+)$1	280	76	84	10.7346
CAGCAAGA	chr18:36908130-36908401(+)$1	271	93	101	10.1224
CAGCCACA	chr19:8964904-8965185(+)$1	281	28	36	9.9183
CAGCAGGC	chr7:135038927-135039193(-)$1	266	36	44	11.5510
GAGCAGCC	chr3:108706705-108706973(-)$1	268	70	78	10.5306
CAGAAACA	chr4:155331122-155331424(+)$1	302	76	84	10.1224
CAGCAACC	chr14:70066969-70067240(+)$1	271	101	109	15.6326
CAGCAGCG	chr14:45912565-45912837(-)$1	272	29	37	11.7551
CAGCAGCA	chr9:66219966-66220240(+)$1	274	36	44	12.7755
cagcagca	chr7:27949815-27950086(-)$1	271	42	50	12.7755
CAGGAACC	chr8:28383691-28383967(+)$1	276	100	108	12.1632
CCGCAACC	chr5:92391556-92391827(-)$1	271	111	119	11.3469
CAGCAAUC	chr5:75006662-75006928(-)$1	266	185	193	11.6530
CAGCCACC	chr3:95464619-95464902(+)$1	283	160	168	12.0612
CAGCACCC	chr13:69138020-69138287(-)$1	267	252	260	13.8979
cagcaagc	chr5:123244349-123244627(-)$1	278	256	264	12.2653
CAGCAACA	chr2:163884396-163884667(-)$1	271	257	265	13.4897
CAGCAGCC	chr6:51413984-51414275(-)$1	291	109	117	14.9183
CAGCAUCU	chr11:117828728-117829006(-)$1	278	29	37	10.9387
CAGAAACA	chr6:22240953-22241221(+)$1	268	178	186	10.1224
CAGGAUCC	chr17:32498259-32498531(-)$1	272	6	14	10.2244
CAGCACAC	chr8:74842835-74843118(+)$1	283	121	129	9.9183
CUGCAGCC	chr19:5384494-5384777(-)$1	283	98	106	10.8367
CAGCAAGU	chr13:81930942-81931210(+)$1	268	252	260	9.5102
CAGCAAGU	chr2:40774602-40774870(-)$1	268	68	76	9.5102
CAGCGACC	chr11:120481937-120482225(-)$1	288	206	214	11.6530
CAGCAUCU	chr18:60859088-60859368(-)$1	280	26	34	10.9387
CAGCAGCU	chr9:37297061-37297336(+)$1	275	225	233	12.1632
CAGUCACC	chr3:96066811-96067101(-)$1	290	82	90	8.3877
CAGCAGCC	chr14:64225928-64226213(+)$1	285	25	33	14.9183
CAGGCACC	chr10:79879360-79879636(-)$1	276	99	107	8.5918
CAGUAACA	chr9:98390942-98391210(+)$1	268	6	14	9.8163
GAGCAGCC	chr15:76028312-76028598(-)$1	286	25	33	10.5306
CAGCACCA	chr9:97269861-97270130(-)$1	269	112	120	11.7551
CUGCAACC	chr17:37114860-37115128(-)$1	268	83	91	11.5510
CACCACCC	chr10:126721767-126722035(-)$1	268	10	18	9.3061
CGGCAGCC	chr9:64825922-64826205(+)$1	283	121	129	10.7346
GAGCAGCC	chr9:65194460-65194740(+)$1	280	89	97	10.5306
CAGCCCCC	chr2:121205212-121205496(-)$1	284	172	180	10.3265
CAGGAAGC	chr4:135883045-135883340(+)$1	295	264	272	8.7959
CAGAAACA	chr9:3411339-3411620(+)$1	281	79	87	10.1224
CAGCCACA	chr17:6084525-6084794(+)$1	269	156	164	9.9183
CAGCAACC	chr2:156606174-156606446(+)$1	272	15	23	15.6326
CAGAAGCC	chr8:86770442-86770710(-)$1	268	224	232	11.5510
CAGCGACC	chr14:52760734-52761005(+)$1	271	262	270	11.6530
CACCACCC	chrX:98514856-98515126(+)$1	270	150	158	9.3061
CAGAAGCC	chr12:85733283-85733551(-)$1	268	102	110	11.5510

#otherMatches

#Struct PSSM
::::::ee	chr13:73773815-73774087(+)$1	272	24	32	10.3265
oa]eeeee	chr19:5384549-5384817(-)$1	268	138	146	10.8367
hrrrrrrr	chr17:35119051-35119331(+)$1	280	76	84	10.7346
22ccc]bb	chr18:36908130-36908401(+)$1	271	93	101	10.1224
KKDDDD::	chr19:8964904-8965185(+)$1	281	28	36	9.9183
b[eeeeeo	chr7:135038927-135039193(-)$1	266	36	44	11.5510
::FFFFFF	chr3:108706705-108706973(-)$1	268	70	78	10.5306
a]bb333f	chr4:155331122-155331424(+)$1	302	76	84	10.1224
ggg::::c	chr14:70066969-70067240(+)$1	271	101	109	15.6326
g!!dddd[	chr14:45912565-45912837(-)$1	272	29	37	11.7551
ccc[ccc[	chr9:66219966-66220240(+)$1	274	36	44	12.7755
qqccc]a]	chr7:27949815-27950086(-)$1	271	42	50	12.7755
>>ffffff	chr8:28383691-28383967(+)$1	276	100	108	12.1632
eccc22bb	chr5:92391556-92391827(-)$1	271	111	119	11.3469
::::::::	chr5:75006662-75006928(-)$1	266	185	193	11.6530
[bbeeeee	chr3:95464619-95464902(+)$1	283	160	168	12.0612
eeee]eee	chr13:69138020-69138287(-)$1	267	252	260	13.8979
:::eeeee	chr5:123244349-123244627(-)$1	278	256	264	12.2653
ccca22ee	chr2:163884396-163884667(-)$1	271	257	265	13.4897
FFFF:FFF	chr6:51413984-51414275(-)$1	291	109	117	14.9183
::cccmmm	chr11:117828728-117829006(-)$1	278	29	37	10.9387
cffffff:	chr6:22240953-22241221(+)$1	268	178	186	10.1224
Ccccmmmm	chr17:32498259-32498531(-)$1	272	6	14	10.2244
!!cccttt	chr8:74842835-74843118(+)$1	283	121	129	9.9183
oa]eeeee	chr19:5384494-5384777(-)$1	283	98	106	10.8367
::::::FF	chr13:81930942-81931210(+)$1	268	252	260	9.5102
BBEEEEEe	chr2:40774602-40774870(-)$1	268	68	76	9.5102
f]bb::HH	chr11:120481937-120482225(-)$1	288	206	214	11.6530
mmmmdddd	chr18:60859088-60859368(-)$1	280	26	34	10.9387
gggg:BB}	chr9:37297061-37297336(+)$1	275	225	233	12.1632
333bb444	chr3:96066811-96067101(-)$1	290	82	90	8.3877
llbbffff	chr14:64225928-64226213(+)$1	285	25	33	14.9183
$$ddddcc	chr10:79879360-79879636(-)$1	276	99	107	8.5918
::::::ee	chr9:98390942-98391210(+)$1	268	6	14	9.8163
KKGGGGGG	chr15:76028312-76028598(-)$1	286	25	33	10.5306
iiiiiibb	chr9:97269861-97270130(-)$1	269	112	120	11.7551
qqqqqqqq	chr17:37114860-37115128(-)$1	268	83	91	11.5510
::::::::	chr10:126721767-126722035(-)$1	268	10	18	9.3061
:EEEEELL	chr9:64825922-64826205(+)$1	283	121	129	10.7346
]a]bbIII	chr9:65194460-65194740(+)$1	280	89	97	10.5306
cccmmmmc	chr2:121205212-121205496(-)$1	284	172	180	10.3265
gggggccc	chr4:135883045-135883340(+)$1	295	264	272	8.7959
fff$$$$$	chr9:3411339-3411620(+)$1	281	79	87	10.1224
EE:ddddg	chr17:6084525-6084794(+)$1	269	156	164	9.9183
eebbmmmm	chr2:156606174-156606446(+)$1	272	15	23	15.6326
CCCEEEEE	chr8:86770442-86770710(-)$1	268	224	232	11.5510
DDDDYYAB	chr14:52760734-52761005(+)$1	271	262	270	11.6530
ppppppbb	chrX:98514856-98515126(+)$1	270	150	158	9.3061
eeeee[hh	chr12:85733283-85733551(-)$1	268	102	110	11.5510

#DB
......((	chr13:73773815-73774087(+)$1	1	24	32	10.3265
.).)))))	chr19:5384549-5384817(-)$1	1	138	146	10.8367
(.......	chr17:35119051-35119331(+)$1	1	76	84	10.7346
..))).))	chr18:36908130-36908401(+)$1	1	93	101	10.1224
..((((..	chr19:8964904-8965185(+)$1	1	28	36	9.9183
(.(((((.	chr7:135038927-135039193(-)$1	1	36	44	11.5510
..((((((	chr3:108706705-108706973(-)$1	1	70	78	10.5306
).))...)	chr4:155331122-155331424(+)$1	1	76	84	10.1224
)))....(	chr14:70066969-70067240(+)$1	1	101	109	15.6326
(..((((.	chr14:45912565-45912837(-)$1	1	29	37	11.7551
(((.(((.	chr9:66219966-66220240(+)$1	1	36	44	12.7755
..))).).	chr7:27949815-27950086(-)$1	1	42	50	12.7755
..))))))	chr8:28383691-28383967(+)$1	1	100	108	12.1632
))))..))	chr5:92391556-92391827(-)$1	1	111	119	11.3469
........	chr5:75006662-75006928(-)$1	1	185	193	11.6530
.(((((((	chr3:95464619-95464902(+)$1	1	160	168	12.0612
)))).)))	chr13:69138020-69138287(-)$1	1	252	260	13.8979
...(((((	chr5:123244349-123244627(-)$1	1	256	264	12.2653
))))..))	chr2:163884396-163884667(-)$1	1	257	265	13.4897
)))).(((	chr6:51413984-51414275(-)$1	1	109	117	14.9183
..(((...	chr11:117828728-117829006(-)$1	1	29	37	10.9387
))))))).	chr6:22240953-22241221(+)$1	1	178	186	10.1224
((((....	chr17:32498259-32498531(-)$1	1	6	14	10.2244
..(((...	chr8:74842835-74843118(+)$1	1	121	129	9.9183
.).)))))	chr19:5384494-5384777(-)$1	1	98	106	10.8367
......))	chr13:81930942-81931210(+)$1	1	252	260	9.5102
((((((((	chr2:40774602-40774870(-)$1	1	68	76	9.5102
).))..))	chr11:120481937-120482225(-)$1	1	206	214	11.6530
....))))	chr18:60859088-60859368(-)$1	1	26	34	10.9387
)))).)).	chr9:37297061-37297336(+)$1	1	225	233	12.1632
...))...	chr3:96066811-96067101(-)$1	1	82	90	8.3877
..))((((	chr14:64225928-64226213(+)$1	1	25	33	14.9183
..((((((	chr10:79879360-79879636(-)$1	1	99	107	8.5918
......((	chr9:98390942-98391210(+)$1	1	6	14	9.8163
..((((((	chr15:76028312-76028598(-)$1	1	25	33	10.5306
((((((((	chr9:97269861-97270130(-)$1	1	112	120	11.7551
........	chr17:37114860-37115128(-)$1	1	83	91	11.5510
........	chr10:126721767-126722035(-)$1	1	10	18	9.3061
.(((((..	chr9:64825922-64826205(+)$1	1	121	129	10.7346
.).))(((	chr9:65194460-65194740(+)$1	1	89	97	10.5306
(((....)	chr2:121205212-121205496(-)$1	1	172	180	10.3265
)))))(((	chr4:135883045-135883340(+)$1	1	264	272	8.7959
(((.....	chr9:3411339-3411620(+)$1	1	79	87	10.1224
((.(((((	chr17:6084525-6084794(+)$1	1	156	164	9.9183
((((....	chr2:156606174-156606446(+)$1	1	15	23	15.6326
))))))))	chr8:86770442-86770710(-)$1	1	224	232	11.5510
))))..))	chr14:52760734-52761005(+)$1	1	262	270	11.6530
......))	chrX:98514856-98515126(+)$1	1	150	158	9.3061
(((((.((	chr12:85733283-85733551(-)$1	1	102	110	11.5510

#PSSM
C : 0.89	G : 0.06	c : 0.04	
A : 0.83	U : 0.06	G : 0.04	a : 0.04	C : 0.02	
G : 0.91	g : 0.04	C : 0.04	
C : 0.73	A : 0.10	G : 0.08	c : 0.04	U : 0.04	
A : 0.79	C : 0.12	a : 0.04	G : 0.04	
A : 0.44	G : 0.30	C : 0.12	U : 0.08	g : 0.02	a : 0.02	
C : 0.79	G : 0.12	c : 0.02	U : 0.02	g : 0.02	A : 0.02	
C : 0.63	A : 0.20	U : 0.10	G : 0.02	a : 0.02	c : 0.02	

#score	549.6734693877556
#seq	49
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012b_mm9_CDS_m1_run2.nuc.txt

#NT
UCU	chr13:74476965-74477204(-)$1	239	58	61	8.9999
UCU	chr5:90646461-90646698(-)$1	237	3	6	8.9999
UCU	chr16:35293974-35294230(+)$1	256	15	18	8.9999
UCU	chrX:69679876-69680119(-)$1	243	37	40	8.9999
UCU	chr14:65673532-65673769(-)$1	237	48	51	8.9999
UCU	chrX:148317008-148317269(+)$1	261	10	13	8.9999
UCU	chrX:143628695-143628930(+)$1	235	15	18	8.9999
UCU	chr2:156002938-156003173(-)$1	235	31	34	8.9999
UCU	chr9:30959798-30960060(-)$1	262	102	105	8.9999
UCU	chr18:50024647-50024885(+)$1	238	73	76	8.9999
UCU	chr10:41239320-41239558(+)$1	238	45	48	8.9999
UCU	chr11:4964001-4964239(-)$1	238	2	5	8.9999
UCU	chr15:27701031-27701272(-)$1	241	0	3	8.9999
UCU	chr11:31917577-31917812(+)$1	235	7	10	8.9999
UCU	chr2:25077838-25078075(-)$1	237	51	54	8.9999
UCU	chr12:113025641-113025876(+)$1	235	33	36	8.9999
UCU	chr9:95945897-95946132(+)$1	235	120	123	8.9999
UCU	chr11:41960533-41960768(-)$1	235	16	19	8.9999
UCU	chr4:126707015-126707250(+)$1	235	209	212	8.9999
UCU	chr8:107803318-107803553(+)$1	235	125	128	8.9999
UCU	chr11:78138010-78138267(+)$1	257	52	55	8.9999
UCU	chr1:174215791-174216026(-)$1	235	1	4	8.9999
UCU	chr11:86602657-86602898(-)$1	241	37	40	8.9999
UCU	chr13:94994830-94995082(-)$1	252	18	21	8.9999
UCU	chr11:41946818-41947090(-)$1	272	36	39	8.9999
UCU	chr1:175262352-175262595(-)$1	243	43	46	8.9999
UCU	chr15:83666718-83666956(+)$1	238	133	136	8.9999
UCU	chr6:4706066-4706310(+)$1	244	3	6	8.9999
UCU	chr6:36693305-36693540(-)$1	235	31	34	8.9999
UCU	chr16:90229856-90230093(-)$1	237	122	125	8.9999
UCU	chr13:67097895-67098158(+)$1	263	10	13	8.9999
UCU	chr7:149573591-149573839(-)$1	248	6	9	8.9999
UCU	chr5:29619320-29619555(-)$1	235	92	95	8.9999
UCU	chr1:135533828-135534091(-)$1	263	40	43	8.9999
UCU	chr7:129777075-129777383(+)$1	308	76	79	8.9999
UCU	chr2:71114420-71114661(-)$1	241	18	21	8.9999
UCU	chr15:58767736-58767981(+)$1	245	12	15	8.9999
UCU	chr15:31418450-31418687(-)$1	237	67	70	8.9999
UCU	chr14:37939004-37939242(-)$1	238	12	15	8.9999
UCU	chr17:24642176-24642411(+)$1	235	44	47	8.9999
UCU	chr1:193602238-193602475(+)$1	237	2	5	8.9999
UCU	chr17:82047059-82047320(-)$1	261	53	56	8.9999
UCU	chr19:57229539-57229775(-)$1	236	2	5	8.9999
UCU	chr12:21315974-21316209(+)$1	235	70	73	8.9999
UCU	chr8:41532325-41532562(+)$1	237	66	69	8.9999
UCU	chr10:57236816-57237127(-)$1	311	39	42	8.9999
UCU	chr2:129444097-129444360(+)$1	263	50	53	8.9999
UCU	chr1:174210640-174210877(-)$1	237	15	18	8.9999
UCU	chr7:31226612-31226851(-)$1	239	13	16	8.9999
UCU	chr12:73675052-73675287(+)$1	235	53	56	8.9999
UCU	chr9:58430182-58430417(+)$1	235	44	47	8.9999
UCU	chr8:63391717-63391957(-)$1	240	137	140	8.9999
UCU	chrX:10172306-10172551(+)$1	245	26	29	8.9999
UCU	chr11:78335201-78335436(+)$1	235	68	71	8.9999
UCU	chr11:60530652-60530893(-)$1	241	20	23	8.9999
UCU	chr10:12125570-12125808(-)$1	238	1	4	8.9999
UCU	chrX:141894531-141894792(-)$1	261	10	13	8.9999
UCU	chrX:39458041-39458277(+)$1	236	26	29	8.9999
UCU	chr7:137872027-137872262(+)$1	235	17	20	8.9999
UCU	chr10:34018422-34018682(+)$1	260	27	30	8.9999
UCU	chr3:107416213-107416450(-)$1	237	51	54	8.9999
UCU	chr8:56140641-56140894(+)$1	253	15	18	8.9999
UCU	chr2:9985644-9985896(-)$1	252	187	190	8.9999
UCU	chr3:95023988-95024224(-)$1	236	4	7	8.9999
UCU	chr11:50014060-50014371(-)$1	311	37	40	8.9999
ucu	chrX:10156346-10156601(+)$1	255	7	10	8.9999
UCU	chr11:70483294-70483530(-)$1	236	12	15	8.9999
UCU	chr5:137736972-137737209(-)$1	237	30	33	8.9999
UCU	chr19:47331845-47332080(+)$1	235	49	52	8.9999
UCU	chr13:6602544-6602805(-)$1	261	71	74	8.9999
UCU	chr19:10058581-10058825(+)$1	244	89	92	8.9999
UCU	chr11:70483254-70483493(-)$1	239	15	18	8.9999
UCU	chr5:131921174-131921409(-)$1	235	30	33	8.9999
UCU	chr10:106256389-106256638(+)$1	249	4	7	8.9999
UCU	chrX:162824810-162825047(+)$1	237	1	4	8.9999
UCU	chr12:4637380-4637615(+)$1	235	2	5	8.9999
UCU	chr1:59927210-59927447(+)$1	237	32	35	8.9999
UCU	chr10:53063680-53063917(+)$1	237	69	72	8.9999
UCU	chr5:138398460-138398701(-)$1	241	34	37	8.9999
UCU	chr10:29067362-29067599(-)$1	237	0	3	8.9999
UCU	chr11:87863329-87863588(+)$1	259	15	18	8.9999
UCU	chr8:46095312-46095551(+)$1	239	6	9	8.9999
UCU	chr2:181041364-181041632(-)$1	268	46	49	8.9999
UCU	chr2:32452594-32452855(+)$1	261	67	70	8.9999
UCU	chr7:20150502-20150751(-)$1	249	32	35	8.9999
UCU	chr11:90202099-90202341(-)$1	242	18	21	8.9999
UCU	chr5:104508405-104508686(-)$1	281	9	12	8.9999
UCU	chr11:100888528-100888792(+)$1	264	10	13	8.9999
ucu	chr15:31412540-31412775(-)$1	235	1	4	8.9999
UCU	chr6:108491854-108492100(+)$1	246	18	21	8.9999
UCU	chr3:87798024-87798262(-)$1	238	9	12	8.9999
UCU	chr17:34782494-34782729(+)$1	235	106	109	8.9999
UCU	chr11:55208949-55209192(-)$1	243	1	4	8.9999
UCU	chr7:129771219-129771472(+)$1	253	76	79	8.9999
UCU	chr12:111865180-111865415(+)$1	235	11	14	8.9999
UCU	chr2:181041975-181042222(-)$1	247	28	31	8.9999
UCU	chr7:17501488-17501778(-)$1	290	158	161	8.9999
UCU	chr7:148337524-148337759(+)$1	235	12	15	8.9999

#otherMatches

#Struct PSSM
:ee	chrX:162824700-162824996(+)$1	296	2	5	8.9999
iii	chr13:74476965-74477204(-)$1	239	58	61	8.9999
:CC	chr5:90646461-90646698(-)$1	237	3	6	8.9999
"ff	chr16:35293974-35294230(+)$1	256	15	18	8.9999
WWW	chrX:69679876-69680119(-)$1	243	37	40	8.9999
"""	chr14:65673532-65673769(-)$1	237	48	51	8.9999
bbo	chrX:148317008-148317269(+)$1	261	10	13	8.9999
BBL	chrX:143628695-143628930(+)$1	235	15	18	8.9999
ooo	chr2:156002938-156003173(-)$1	235	31	34	8.9999
]ee	chr9:30959798-30960060(-)$1	262	102	105	8.9999
ggg	chr18:50024647-50024885(+)$1	238	73	76	8.9999
KKD	chr10:41239320-41239558(+)$1	238	45	48	8.9999
LLL	chr11:4964001-4964239(-)$1	238	2	5	8.9999
:::	chr15:27701031-27701272(-)$1	241	0	3	8.9999
:::	chr11:31917577-31917812(+)$1	235	7	10	8.9999
DDD	chr2:25077838-25078075(-)$1	237	51	54	8.9999
fff	chr12:113025641-113025876(+)$1	235	33	36	8.9999
uuu	chr9:95945897-95946132(+)$1	235	120	123	8.9999
JJJ	chr11:41960533-41960768(-)$1	235	16	19	8.9999
eee	chr4:126707015-126707250(+)$1	235	209	212	8.9999
ggg	chr8:107803318-107803553(+)$1	235	125	128	8.9999
qqq	chr11:78138010-78138267(+)$1	257	52	55	8.9999
:::	chr1:174215791-174216026(-)$1	235	1	4	8.9999
ccc	chr11:86602657-86602898(-)$1	241	37	40	8.9999
:::	chr13:94994830-94995082(-)$1	252	18	21	8.9999
JJJ	chr11:41946818-41947090(-)$1	272	36	39	8.9999
[cc	chr1:175262352-175262595(-)$1	243	43	46	8.9999
fff	chr15:83666718-83666956(+)$1	238	133	136	8.9999
eee	chr6:4706066-4706310(+)$1	244	3	6	8.9999
eee	chr6:36693305-36693540(-)$1	235	31	34	8.9999
iii	chr16:90229856-90230093(-)$1	237	122	125	8.9999
cnn	chr13:67097895-67098158(+)$1	263	10	13	8.9999
JJJ	chr7:149573591-149573839(-)$1	248	6	9	8.9999
LGG	chr5:29619320-29619555(-)$1	235	92	95	8.9999
[dd	chr1:135533828-135534091(-)$1	263	40	43	8.9999
ggg	chr7:129777075-129777383(+)$1	308	76	79	8.9999
nne	chr2:71114420-71114661(-)$1	241	18	21	8.9999
FF:	chr15:58767736-58767981(+)$1	245	12	15	8.9999
duu	chr15:31418450-31418687(-)$1	237	67	70	8.9999
ooo	chr14:37939004-37939242(-)$1	238	12	15	8.9999
eee	chr17:24642176-24642411(+)$1	235	44	47	8.9999
hhh	chr1:193602238-193602475(+)$1	237	2	5	8.9999
GGG	chr17:82047059-82047320(-)$1	261	53	56	8.9999
:EE	chr19:57229539-57229775(-)$1	236	2	5	8.9999
cc:	chr12:21315974-21316209(+)$1	235	70	73	8.9999
666	chr8:41532325-41532562(+)$1	237	66	69	8.9999
444	chr10:57236816-57237127(-)$1	311	39	42	8.9999
ccp	chr2:129444097-129444360(+)$1	263	50	53	8.9999
FFF	chr1:174210640-174210877(-)$1	237	15	18	8.9999
FFF	chr7:31226612-31226851(-)$1	239	13	16	8.9999
ooo	chr12:73675052-73675287(+)$1	235	53	56	8.9999
eee	chr9:58430182-58430417(+)$1	235	44	47	8.9999
dd:	chr8:63391717-63391957(-)$1	240	137	140	8.9999
ddp	chrX:10172306-10172551(+)$1	245	26	29	8.9999
ccc	chr11:78335201-78335436(+)$1	235	68	71	8.9999
[cc	chr11:60530652-60530893(-)$1	241	20	23	8.9999
::f	chr10:12125570-12125808(-)$1	238	1	4	8.9999
DDD	chrX:141894531-141894792(-)$1	261	10	13	8.9999
ddd	chrX:39458041-39458277(+)$1	236	26	29	8.9999
JJJ	chr7:137872027-137872262(+)$1	235	17	20	8.9999
qqb	chr10:34018422-34018682(+)$1	260	27	30	8.9999
999	chr3:107416213-107416450(-)$1	237	51	54	8.9999
$$$	chr8:56140641-56140894(+)$1	253	15	18	8.9999
sss	chr2:9985644-9985896(-)$1	252	187	190	8.9999
DD:	chr3:95023988-95024224(-)$1	236	4	7	8.9999
:ee	chr11:50014060-50014371(-)$1	311	37	40	8.9999
d[d	chrX:10156346-10156601(+)$1	255	7	10	8.9999
hhh	chr11:70483294-70483530(-)$1	236	12	15	8.9999
fff	chr5:137736972-137737209(-)$1	237	30	33	8.9999
:::	chr19:47331845-47332080(+)$1	235	49	52	8.9999
ggc	chr13:6602544-6602805(-)$1	261	71	74	8.9999
ccs	chr19:10058581-10058825(+)$1	244	89	92	8.9999
"cc	chr11:70483254-70483493(-)$1	239	15	18	8.9999
:::	chr5:131921174-131921409(-)$1	235	30	33	8.9999
EBB	chr10:106256389-106256638(+)$1	249	4	7	8.9999
CCC	chrX:162824810-162825047(+)$1	237	1	4	8.9999
:::	chr12:4637380-4637615(+)$1	235	2	5	8.9999
obb	chr1:59927210-59927447(+)$1	237	32	35	8.9999
$$$	chr10:53063680-53063917(+)$1	237	69	72	8.9999
e::	chr5:138398460-138398701(-)$1	241	34	37	8.9999
:::	chr10:29067362-29067599(-)$1	237	0	3	8.9999
GGG	chr11:87863329-87863588(+)$1	259	15	18	8.9999
OOO	chr8:46095312-46095551(+)$1	239	6	9	8.9999
iii	chr2:181041364-181041632(-)$1	268	46	49	8.9999
ma2	chr2:32452594-32452855(+)$1	261	67	70	8.9999
ooo	chr7:20150502-20150751(-)$1	249	32	35	8.9999
sss	chr11:90202099-90202341(-)$1	242	18	21	8.9999
{GG	chr5:104508405-104508686(-)$1	281	9	12	8.9999
DDD	chr11:100888528-100888792(+)$1	264	10	13	8.9999
BBK	chr15:31412540-31412775(-)$1	235	1	4	8.9999
JJJ	chr6:108491854-108492100(+)$1	246	18	21	8.9999
FF{	chr3:87798024-87798262(-)$1	238	9	12	8.9999
eee	chr17:34782494-34782729(+)$1	235	106	109	8.9999
:::	chr11:55208949-55209192(-)$1	243	1	4	8.9999
eee	chr7:129771219-129771472(+)$1	253	76	79	8.9999
fff	chr12:111865180-111865415(+)$1	235	11	14	8.9999
KEE	chr2:181041975-181042222(-)$1	247	28	31	8.9999
FFF	chr7:17501488-17501778(-)$1	290	158	161	8.9999
eee	chr7:148337524-148337759(+)$1	235	12	15	8.9999

#DB
.((	chrX:162824700-162824996(+)$1	1	2	5	8.9999
)))	chr13:74476965-74477204(-)$1	1	58	61	8.9999
.((	chr5:90646461-90646698(-)$1	1	3	6	8.9999
.((	chr16:35293974-35294230(+)$1	1	15	18	8.9999
...	chrX:69679876-69680119(-)$1	1	37	40	8.9999
...	chr14:65673532-65673769(-)$1	1	48	51	8.9999
((.	chrX:148317008-148317269(+)$1	1	10	13	8.9999
((.	chrX:143628695-143628930(+)$1	1	15	18	8.9999
...	chr2:156002938-156003173(-)$1	1	31	34	8.9999
.))	chr9:30959798-30960060(-)$1	1	102	105	8.9999
)))	chr18:50024647-50024885(+)$1	1	73	76	8.9999
..(	chr10:41239320-41239558(+)$1	1	45	48	8.9999
...	chr11:4964001-4964239(-)$1	1	2	5	8.9999
...	chr15:27701031-27701272(-)$1	1	0	3	8.9999
...	chr11:31917577-31917812(+)$1	1	7	10	8.9999
(((	chr2:25077838-25078075(-)$1	1	51	54	8.9999
(((	chr12:113025641-113025876(+)$1	1	33	36	8.9999
...	chr9:95945897-95946132(+)$1	1	120	123	8.9999
(((	chr11:41960533-41960768(-)$1	1	16	19	8.9999
)))	chr4:126707015-126707250(+)$1	1	209	212	8.9999
)))	chr8:107803318-107803553(+)$1	1	125	128	8.9999
...	chr11:78138010-78138267(+)$1	1	52	55	8.9999
...	chr1:174215791-174216026(-)$1	1	1	4	8.9999
(((	chr11:86602657-86602898(-)$1	1	37	40	8.9999
...	chr13:94994830-94995082(-)$1	1	18	21	8.9999
(((	chr11:41946818-41947090(-)$1	1	36	39	8.9999
.((	chr1:175262352-175262595(-)$1	1	43	46	8.9999
(((	chr15:83666718-83666956(+)$1	1	133	136	8.9999
(((	chr6:4706066-4706310(+)$1	1	3	6	8.9999
(((	chr6:36693305-36693540(-)$1	1	31	34	8.9999
)))	chr16:90229856-90230093(-)$1	1	122	125	8.9999
(..	chr13:67097895-67098158(+)$1	1	10	13	8.9999
(((	chr7:149573591-149573839(-)$1	1	6	9	8.9999
.((	chr5:29619320-29619555(-)$1	1	92	95	8.9999
.((	chr1:135533828-135534091(-)$1	1	40	43	8.9999
(((	chr7:129777075-129777383(+)$1	1	76	79	8.9999
..)	chr2:71114420-71114661(-)$1	1	18	21	8.9999
((.	chr15:58767736-58767981(+)$1	1	12	15	8.9999
(..	chr15:31418450-31418687(-)$1	1	67	70	8.9999
...	chr14:37939004-37939242(-)$1	1	12	15	8.9999
)))	chr17:24642176-24642411(+)$1	1	44	47	8.9999
(((	chr1:193602238-193602475(+)$1	1	2	5	8.9999
(((	chr17:82047059-82047320(-)$1	1	53	56	8.9999
.((	chr19:57229539-57229775(-)$1	1	2	5	8.9999
)).	chr12:21315974-21316209(+)$1	1	70	73	8.9999
...	chr8:41532325-41532562(+)$1	1	66	69	8.9999
...	chr10:57236816-57237127(-)$1	1	39	42	8.9999
((.	chr2:129444097-129444360(+)$1	1	50	53	8.9999
(((	chr1:174210640-174210877(-)$1	1	15	18	8.9999
(((	chr7:31226612-31226851(-)$1	1	13	16	8.9999
...	chr12:73675052-73675287(+)$1	1	53	56	8.9999
(((	chr9:58430182-58430417(+)$1	1	44	47	8.9999
)).	chr8:63391717-63391957(-)$1	1	137	140	8.9999
((.	chrX:10172306-10172551(+)$1	1	26	29	8.9999
)))	chr11:78335201-78335436(+)$1	1	68	71	8.9999
.((	chr11:60530652-60530893(-)$1	1	20	23	8.9999
..(	chr10:12125570-12125808(-)$1	1	1	4	8.9999
(((	chrX:141894531-141894792(-)$1	1	10	13	8.9999
(((	chrX:39458041-39458277(+)$1	1	26	29	8.9999
(((	chr7:137872027-137872262(+)$1	1	17	20	8.9999
..)	chr10:34018422-34018682(+)$1	1	27	30	8.9999
...	chr3:107416213-107416450(-)$1	1	51	54	8.9999
...	chr8:56140641-56140894(+)$1	1	15	18	8.9999
...	chr2:9985644-9985896(-)$1	1	187	190	8.9999
((.	chr3:95023988-95024224(-)$1	1	4	7	8.9999
.((	chr11:50014060-50014371(-)$1	1	37	40	8.9999
(.(	chrX:10156346-10156601(+)$1	1	7	10	8.9999
(((	chr11:70483294-70483530(-)$1	1	12	15	8.9999
(((	chr5:137736972-137737209(-)$1	1	30	33	8.9999
...	chr19:47331845-47332080(+)$1	1	49	52	8.9999
(((	chr13:6602544-6602805(-)$1	1	71	74	8.9999
((.	chr19:10058581-10058825(+)$1	1	89	92	8.9999
.((	chr11:70483254-70483493(-)$1	1	15	18	8.9999
...	chr5:131921174-131921409(-)$1	1	30	33	8.9999
(((	chr10:106256389-106256638(+)$1	1	4	7	8.9999
(((	chrX:162824810-162825047(+)$1	1	1	4	8.9999
...	chr12:4637380-4637615(+)$1	1	2	5	8.9999
.))	chr1:59927210-59927447(+)$1	1	32	35	8.9999
...	chr10:53063680-53063917(+)$1	1	69	72	8.9999
)..	chr5:138398460-138398701(-)$1	1	34	37	8.9999
...	chr10:29067362-29067599(-)$1	1	0	3	8.9999
(((	chr11:87863329-87863588(+)$1	1	15	18	8.9999
...	chr8:46095312-46095551(+)$1	1	6	9	8.9999
(((	chr2:181041364-181041632(-)$1	1	46	49	8.9999
.).	chr2:32452594-32452855(+)$1	1	67	70	8.9999
...	chr7:20150502-20150751(-)$1	1	32	35	8.9999
...	chr11:90202099-90202341(-)$1	1	18	21	8.9999
.((	chr5:104508405-104508686(-)$1	1	9	12	8.9999
(((	chr11:100888528-100888792(+)$1	1	10	13	8.9999
((.	chr15:31412540-31412775(-)$1	1	1	4	8.9999
(((	chr6:108491854-108492100(+)$1	1	18	21	8.9999
((.	chr3:87798024-87798262(-)$1	1	9	12	8.9999
(((	chr17:34782494-34782729(+)$1	1	106	109	8.9999
...	chr11:55208949-55209192(-)$1	1	1	4	8.9999
)))	chr7:129771219-129771472(+)$1	1	76	79	8.9999
)))	chr12:111865180-111865415(+)$1	1	11	14	8.9999
.((	chr2:181041975-181042222(-)$1	1	28	31	8.9999
)))	chr7:17501488-17501778(-)$1	1	158	161	8.9999
(((	chr7:148337524-148337759(+)$1	1	12	15	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl2_Charizanis2012_mm9_transcript_m1_run2.nuc.txt

#NT
UUGUUUUU	chr10:115942123-115942340(-)$1	217	100	108	18.9999
UUGUUUUU	chr2:9978360-9978578(-)$1	218	120	128	18.9999
UUGUUUGU	chr12:104206068-104206289(+)$1	221	56	64	14.3260
UUAAUUUU	chr4:150435272-150435472(-)$1	200	15	23	13.5652
UUGUUUUC	chr12:85771978-85772182(-)$1	204	58	66	15.1956
UUGUUCUU	chr13:77342562-77342789(+)$1	227	2	10	14.3260
uucuuuuu	chrX:149830385-149830588(+)$1	203	123	131	16.8260
uugAUUUU	chr7:140308361-140308590(-)$1	229	4	12	15.5217
UUCUUUUU	chr17:66198929-66199142(-)$1	213	107	115	16.8260
UUGCUUUU	chr10:79336720-79336939(-)$1	219	156	164	15.7391
uuguuuua	chr13:29651550-29651785(-)$1	235	102	110	15.1956
UUGUUGUU	chr12:118470370-118470590(+)$1	220	68	76	14.3260
UUCCUUUU	chr7:91106847-91107072(-)$1	225	100	108	13.5652
UUAUUUUU	chr7:16745532-16745737(+)$1	205	185	193	17.0434
UUUUUUUU	chr7:94627673-94627890(-)$1	217	42	50	16.3913
UUGCUUUU	chr5:14252957-14253163(+)$1	206	101	109	15.7391
uuauuuuu	chr4:119059940-119060149(-)$1	209	150	158	17.0434
UUGUUUUU	chr1:82748422-82748625(+)$1	203	115	123	18.9999
UUCUUUUU	chr15:98568017-98568221(-)$1	204	40	48	16.8260
UUGUUUUC	chr3:98996724-98996944(+)$1	220	178	186	15.1956
UAGUUUUU	chrX:70602987-70603193(+)$1	206	53	61	14.2173
UUGCUUUU	chr15:36407473-36407678(-)$1	205	8	16	15.7391
uugcuuuu	chr14:52713418-52713623(-)$1	205	130	138	15.7391
UUAAUUUU	chr1:178664642-178664846(-)$1	204	9	17	13.5652
UUGUUUUG	chr2:58437882-58438087(+)$1	205	176	184	15.0869
uucuuuuu	chr4:102533343-102533544(+)$1	201	164	172	16.8260
UUAUUUUU	chr17:49101823-49102057(+)$1	234	153	161	17.0434
UUCUUUUU	chr16:43634583-43634804(+)$1	221	30	38	16.8260
UUUUUUUU	chr11:77525542-77525748(+)$1	206	77	85	16.3913
UUGUGUUU	chr12:112505164-112505371(+)$1	207	73	81	14.4347
UUGUUUUU	chr9:8567344-8567579(+)$1	235	61	69	18.9999
UUGUUUUG	chr13:41108119-41108320(+)$1	201	139	147	15.0869
Uuauuuuu	chr12:106006374-106006587(-)$1	213	92	100	17.0434
UUAUUUUU	chr10:69486894-69487095(+)$1	201	99	107	17.0434
UUGUUUUA	chr6:57702718-57702943(-)$1	225	84	92	15.1956
UUGUGUUU	chr3:117022024-117022227(-)$1	203	15	23	14.4347
UUCCUUUU	chr4:117119532-117119753(-)$1	221	128	136	13.5652
UUGUUUUC	chr3:119421754-119421954(-)$1	200	176	184	15.1956
UUUUUUUU	chr9:83672880-83673090(+)$1	210	70	78	16.3913
uuauuuuu	chr9:58724405-58724614(-)$1	209	176	184	17.0434
CUGUUUUU	chr2:180821409-180821611(-)$1	202	118	126	14.3260
UUGUUUUA	chr13:89748461-89748675(+)$1	214	50	58	15.1956
UUAUUUUU	chr8:95384298-95384527(+)$1	229	85	93	17.0434
uuguuuau	chr4:44812618-44812828(+)$1	210	5	13	14.3260
GUGUUUUU	chr16:63831709-63831943(-)$1	234	198	206	14.3260

#otherMatches

#Struct PSSM
DDDD::::	chr14:79942685-79942920(+)$1	235	226	234	15.5217
iiiiiiii	chr10:115942123-115942340(-)$1	217	100	108	18.9999
ddd[eeee	chr2:9978360-9978578(-)$1	218	120	128	18.9999
22dddd]d	chr12:104206068-104206289(+)$1	221	56	64	14.3260
++++++++	chr4:150435272-150435472(-)$1	200	15	23	13.5652
ggggg777	chr12:85771978-85772182(-)$1	204	58	66	15.1956
========	chr13:77342562-77342789(+)$1	227	2	10	14.3260
::::::::	chrX:149830385-149830588(+)$1	203	123	131	16.8260
iiiiii++	chr7:140308361-140308590(-)$1	229	4	12	15.5217
bb]ggggg	chr17:66198929-66199142(-)$1	213	107	115	16.8260
ddbbhhhh	chr10:79336720-79336939(-)$1	219	156	164	15.7391
hhhhhhhc	chr13:29651550-29651785(-)$1	235	102	110	15.1956
''hhhhhh	chr12:118470370-118470590(+)$1	220	68	76	14.3260
:EEEEEYY	chr7:91106847-91107072(-)$1	225	100	108	13.5652
___EEEEE	chr7:16745532-16745737(+)$1	205	185	193	17.0434
::::::::	chr7:94627673-94627890(-)$1	217	42	50	16.3913
eeFFFFFF	chr5:14252957-14253163(+)$1	206	101	109	15.7391
HHHHHH||	chr4:119059940-119060149(-)$1	209	150	158	17.0434
gg[bbmmm	chr1:82748422-82748625(+)$1	203	115	123	18.9999
uuuuuuuu	chr15:98568017-98568221(-)$1	204	40	48	16.8260
cccmmmmc	chr3:98996724-98996944(+)$1	220	178	186	15.1956
occc:fff	chrX:70602987-70603193(+)$1	206	53	61	14.2173
f[ccc"""	chr15:36407473-36407678(-)$1	205	8	16	15.7391
ppffffff	chr14:52713418-52713623(-)$1	205	130	138	15.7391
rrrrrrrr	chr1:178664642-178664846(-)$1	204	9	17	13.5652
::::::::	chr2:58437882-58438087(+)$1	205	176	184	15.0869
::::::::	chr4:102533343-102533544(+)$1	201	164	172	16.8260
GGGGGG::	chr17:49101823-49102057(+)$1	234	153	161	17.0434
e[eeeee+	chr16:43634583-43634804(+)$1	221	30	38	16.8260
:::iiiii	chr11:77525542-77525748(+)$1	206	77	85	16.3913
:::::::e	chr12:112505164-112505371(+)$1	207	73	81	14.4347
eeee::::	chr9:8567344-8567579(+)$1	235	61	69	18.9999
dd]eeeee	chr13:41108119-41108320(+)$1	201	139	147	15.0869
[ccc####	chr12:106006374-106006587(-)$1	213	92	100	17.0434
^^^^ffff	chr10:69486894-69487095(+)$1	201	99	107	17.0434
gggggggm	chr6:57702718-57702943(-)$1	225	84	92	15.1956
DD{EEEEE	chr3:117022024-117022227(-)$1	203	15	23	14.4347
::::::::	chr4:117119532-117119753(-)$1	221	128	136	13.5652
GGGGG@@@	chr3:119421754-119421954(-)$1	200	176	184	15.1956
ccc[eeee	chr9:83672880-83673090(+)$1	210	70	78	16.3913
eeeerrrr	chr9:58724405-58724614(-)$1	209	176	184	17.0434
dddd:::c	chr2:180821409-180821611(-)$1	202	118	126	14.3260
::::::::	chr13:89748461-89748675(+)$1	214	50	58	15.1956
8888888g	chr8:95384298-95384527(+)$1	229	85	93	17.0434
GGGGGGG{	chr4:44812618-44812828(+)$1	210	5	13	14.3260
::gggggg	chr16:63831709-63831943(-)$1	234	198	206	14.3260

#DB
))))....	chr14:79942685-79942920(+)$1	1	226	234	15.5217
((((((((	chr10:115942123-115942340(-)$1	1	100	108	18.9999
(((.((((	chr2:9978360-9978578(-)$1	1	120	128	18.9999
..)))).)	chr12:104206068-104206289(+)$1	1	56	64	14.3260
........	chr4:150435272-150435472(-)$1	1	15	23	13.5652
)))))...	chr12:85771978-85772182(-)$1	1	58	66	15.1956
((((((((	chr13:77342562-77342789(+)$1	1	2	10	14.3260
........	chrX:149830385-149830588(+)$1	1	123	131	16.8260
((((((..	chr7:140308361-140308590(-)$1	1	4	12	15.5217
)).)))))	chr17:66198929-66199142(-)$1	1	107	115	16.8260
))))))))	chr10:79336720-79336939(-)$1	1	156	164	15.7391
))))))))	chr13:29651550-29651785(-)$1	1	102	110	15.1956
..((((((	chr12:118470370-118470590(+)$1	1	68	76	14.3260
.)))))..	chr7:91106847-91107072(-)$1	1	100	108	13.5652
...)))))	chr7:16745532-16745737(+)$1	1	185	193	17.0434
........	chr7:94627673-94627890(-)$1	1	42	50	16.3913
))))))))	chr5:14252957-14253163(+)$1	1	101	109	15.7391
))))))..	chr4:119059940-119060149(-)$1	1	150	158	17.0434
((.((...	chr1:82748422-82748625(+)$1	1	115	123	18.9999
........	chr15:98568017-98568221(-)$1	1	40	48	16.8260
(((....)	chr3:98996724-98996944(+)$1	1	178	186	15.1956
.))).(((	chrX:70602987-70603193(+)$1	1	53	61	14.2173
(.(((...	chr15:36407473-36407678(-)$1	1	8	16	15.7391
..))))))	chr14:52713418-52713623(-)$1	1	130	138	15.7391
........	chr1:178664642-178664846(-)$1	1	9	17	13.5652
........	chr2:58437882-58438087(+)$1	1	176	184	15.0869
........	chr4:102533343-102533544(+)$1	1	164	172	16.8260
))))))..	chr17:49101823-49102057(+)$1	1	153	161	17.0434
(.(((((.	chr16:43634583-43634804(+)$1	1	30	38	16.8260
...(((((	chr11:77525542-77525748(+)$1	1	77	85	16.3913
.......(	chr12:112505164-112505371(+)$1	1	73	81	14.4347
))))....	chr9:8567344-8567579(+)$1	1	61	69	18.9999
)).)))))	chr13:41108119-41108320(+)$1	1	139	147	15.0869
.(((....	chr12:106006374-106006587(-)$1	1	92	100	17.0434
....))))	chr10:69486894-69487095(+)$1	1	99	107	17.0434
(((((((.	chr6:57702718-57702943(-)$1	1	84	92	15.1956
((.(((((	chr3:117022024-117022227(-)$1	1	15	23	14.4347
........	chr4:117119532-117119753(-)$1	1	128	136	13.5652
)))))...	chr3:119421754-119421954(-)$1	1	176	184	15.1956
(((.((((	chr9:83672880-83673090(+)$1	1	70	78	16.3913
((((....	chr9:58724405-58724614(-)$1	1	176	184	17.0434
))))...(	chr2:180821409-180821611(-)$1	1	118	126	14.3260
........	chr13:89748461-89748675(+)$1	1	50	58	15.1956
.......)	chr8:95384298-95384527(+)$1	1	85	93	17.0434
(((((((.	chr4:44812618-44812828(+)$1	1	5	13	14.3260
..((((((	chr16:63831709-63831943(-)$1	1	198	206	14.3260

#PSSM
U : 0.78	u : 0.17	C : 0.02	G : 0.02	
U : 0.78	u : 0.19	A : 0.02	
G : 0.49	A : 0.13	C : 0.10	g : 0.08	U : 0.06	a : 0.06	c : 0.04	
U : 0.63	u : 0.15	C : 0.10	A : 0.08	c : 0.02	
U : 0.78	u : 0.17	G : 0.04	
U : 0.78	u : 0.17	C : 0.02	G : 0.02	
U : 0.80	u : 0.15	G : 0.02	a : 0.02	
U : 0.67	u : 0.15	C : 0.06	G : 0.04	A : 0.04	a : 0.02	

#score	727.2608695652173
#seq	46
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012e_mm9_UTR_m1_run1.nuc.txt

#NT
CUU	chr19:7350360-7350621(-)$1	261	4	7	9.0000
CUU	chrX:12253094-12253356(-)$1	262	4	7	9.0000
CUU	chr10:52058384-52058650(-)$1	266	7	10	9.0000
CUU	chr13:89795492-89795751(-)$1	259	10	13	9.0000
CUU	chr6:52182178-52182415(-)$1	237	7	10	9.0000
CUU	chr9:24216586-24216831(-)$1	245	90	93	9.0000
CUU	chr17:71343559-71343821(-)$1	262	18	21	9.0000
CUU	chr6:138105063-138105298(+)$1	235	35	38	9.0000
CUU	chr8:86493855-86494116(+)$1	261	23	26	9.0000
CUU	chr10:66474349-66474639(-)$1	290	4	7	9.0000
CUU	chr2:14958608-14958848(-)$1	240	24	27	9.0000
CUU	chr10:58627290-58627570(-)$1	280	113	116	9.0000
CUU	chr11:52066673-52066928(-)$1	255	75	78	9.0000
CUU	chr8:72856419-72856657(-)$1	238	3	6	9.0000
CUU	chr11:48620501-48620775(-)$1	274	24	27	9.0000
CUU	chr10:127838447-127838704(-)$1	257	13	16	9.0000
CUU	chr11:8332767-8333031(-)$1	264	0	3	9.0000
CUU	chr12:25393064-25393377(+)$1	313	53	56	9.0000
CUU	chr7:7236417-7236655(-)$1	238	19	22	9.0000
CUU	chr13:73952749-73952998(+)$1	249	26	29	9.0000
CUU	chr11:60371581-60371844(+)$1	263	59	62	9.0000
CUU	chr16:11074900-11075144(+)$1	244	130	133	9.0000
CUU	chr1:158578178-158578433(+)$1	255	21	24	9.0000
CUU	chr2:35170062-35170319(-)$1	257	20	23	9.0000
CUU	chr11:100232361-100232625(-)$1	264	21	24	9.0000
CUU	chrX:93291338-93291579(+)$1	241	46	49	9.0000
CUU	chr15:99473762-99474018(-)$1	256	19	22	9.0000
CUU	chr11:55208421-55208707(-)$1	286	5	8	9.0000
CUU	chr2:104268108-104268346(-)$1	238	130	133	9.0000
CUU	chr16:37883725-37883990(+)$1	265	13	16	9.0000
cuu	chr16:15554315-15554553(-)$1	238	33	36	9.0000
CUU	chr2:155213866-155214154(+)$1	288	3	6	9.0000
CUU	chr3:95433013-95433251(+)$1	238	4	7	9.0000
CUU	chr10:126975169-126975431(-)$1	262	12	15	9.0000
CUU	chr13:110851684-110851943(-)$1	259	29	32	9.0000
CUU	chr7:5032131-5032426(+)$1	295	61	64	9.0000
CUU	chr2:6463612-6463884(-)$1	272	20	23	9.0000
CUU	chr1:16334657-16334913(-)$1	256	57	60	9.0000
CUU	chr7:17082036-17082278(-)$1	242	2	5	9.0000
CUU	chr18:34761550-34761805(-)$1	255	53	56	9.0000
CUU	chr11:32645002-32645288(+)$1	286	23	26	9.0000
CUU	chrX:71471507-71471746(-)$1	239	9	12	9.0000
CUU	chr9:21560329-21560569(-)$1	240	45	48	9.0000
CUU	chr15:36407866-36408105(-)$1	239	55	58	9.0000
CUU	chr4:15211102-15211338(+)$1	236	8	11	9.0000
Cuu	chr5:149363475-149363722(-)$1	247	0	3	9.0000
CUU	chr15:81745270-81745506(+)$1	236	56	59	9.0000
CUU	chr1:87973832-87974071(+)$1	239	78	81	9.0000
CUU	chr10:126434598-126434852(+)$1	254	21	24	9.0000
CUU	chr7:105053172-105053421(+)$1	249	164	167	9.0000
cuu	chr7:16534802-16535077(-)$1	275	46	49	9.0000
CUU	chr10:79373597-79373886(-)$1	289	70	73	9.0000
CUU	chr5:125368137-125368372(+)$1	235	8	11	9.0000
CUU	chr2:113672936-113673203(-)$1	267	67	70	9.0000
CUU	chr4:102278196-102278444(+)$1	248	3	6	9.0000
CUU	chr8:97094084-97094319(+)$1	235	40	43	9.0000
CUU	chr10:76171941-76172200(-)$1	259	15	18	9.0000
CUU	chr7:126118247-126118495(-)$1	248	86	89	9.0000
CUU	chr1:162133232-162133487(-)$1	255	42	45	9.0000
CUU	chr19:58870900-58871211(-)$1	311	16	19	9.0000
CUU	chrX:147418086-147418321(-)$1	235	34	37	9.0000
CUU	chr13:55771472-55771731(+)$1	259	31	34	9.0000
CUU	chr2:44843935-44844170(-)$1	235	94	97	9.0000
CUU	chrX:35773857-35774146(-)$1	289	34	37	9.0000
CUU	chr15:32963087-32963330(+)$1	243	7	10	9.0000
CUU	chr4:137798539-137798776(+)$1	237	12	15	9.0000
CUU	chr2:76467997-76468236(-)$1	239	76	79	9.0000
CUU	chr2:80193324-80193579(+)$1	255	82	85	9.0000
CUU	chr11:86508251-86508550(-)$1	299	21	24	9.0000
CUU	chr11:77994727-77994968(-)$1	241	79	82	9.0000
CUU	chr18:33596852-33597106(-)$1	254	72	75	9.0000
CUU	chr4:109058828-109059081(+)$1	253	48	51	9.0000
CUU	chr17:27327227-27327470(-)$1	243	6	9	9.0000
Cuu	chr1:93744236-93744480(+)$1	244	43	46	9.0000
CUU	chr8:23278928-23279163(-)$1	235	20	23	9.0000
CUU	chr11:86547128-86547390(-)$1	262	5	8	9.0000
CUU	chr9:66875589-66875853(-)$1	264	20	23	9.0000
CUU	chr2:131003574-131003830(-)$1	256	0	3	9.0000
CUU	chr5:149317595-149317856(-)$1	261	7	10	9.0000
CUU	chr16:92605657-92605947(-)$1	290	113	116	9.0000
CUU	chr14:37935140-37935416(-)$1	276	97	100	9.0000
CUU	chr3:31017461-31017718(+)$1	257	111	114	9.0000
CUU	chr15:102844374-102844629(+)$1	255	46	49	9.0000
CUU	chr5:93602910-93603221(+)$1	311	19	22	9.0000
CUU	chr2:26776600-26776846(-)$1	246	26	29	9.0000
CUU	chr9:49324972-49325215(-)$1	243	31	34	9.0000
CUU	chr6:29325894-29326143(+)$1	249	27	30	9.0000
CUU	chr10:82359212-82359508(+)$1	296	35	38	9.0000
CUU	chr14:21852347-21852647(+)$1	300	31	34	9.0000
CUU	chr2:6465606-6465870(-)$1	264	26	29	9.0000
CUU	chr19:7028185-7028431(-)$1	246	2	5	9.0000
CUU	chr6:91222377-91222615(+)$1	238	165	168	9.0000
CUU	chr10:76171566-76171875(-)$1	309	11	14	9.0000
CUU	chr18:38001270-38001581(+)$1	311	32	35	9.0000
CUU	chr15:82957993-82958234(-)$1	241	47	50	9.0000
CUU	chr16:77115749-77115993(+)$1	244	68	71	9.0000
cuu	chr5:77396049-77396327(+)$1	278	25	28	9.0000
CUU	chr9:44757793-44758028(-)$1	235	6	9	9.0000
CUU	chr4:41239466-41239746(-)$1	280	0	3	9.0000

#otherMatches

#Struct PSSM
xxx	chr7:3297647-3297951(+)$1	304	57	60	9.0000
:hh	chr19:7350360-7350621(-)$1	261	4	7	9.0000
FFN	chrX:12253094-12253356(-)$1	262	4	7	9.0000
fff	chr10:52058384-52058650(-)$1	266	7	10	9.0000
JKK	chr13:89795492-89795751(-)$1	259	10	13	9.0000
:hh	chr6:52182178-52182415(-)$1	237	7	10	9.0000
hh:	chr9:24216586-24216831(-)$1	245	90	93	9.0000
bss	chr17:71343559-71343821(-)$1	262	18	21	9.0000
uuu	chr6:138105063-138105298(+)$1	235	35	38	9.0000
b!!	chr8:86493855-86494116(+)$1	261	23	26	9.0000
GGG	chr10:66474349-66474639(-)$1	290	4	7	9.0000
{EE	chr2:14958608-14958848(-)$1	240	24	27	9.0000
NNN	chr10:58627290-58627570(-)$1	280	113	116	9.0000
nnd	chr11:52066673-52066928(-)$1	255	75	78	9.0000
:::	chr8:72856419-72856657(-)$1	238	3	6	9.0000
DDD	chr11:48620501-48620775(-)$1	274	24	27	9.0000
CLL	chr10:127838447-127838704(-)$1	257	13	16	9.0000
:::	chr11:8332767-8333031(-)$1	264	0	3	9.0000
'''	chr12:25393064-25393377(+)$1	313	53	56	9.0000
dd(	chr7:7236417-7236655(-)$1	238	19	22	9.0000
cc]	chr13:73952749-73952998(+)$1	249	26	29	9.0000
555	chr11:60371581-60371844(+)$1	263	59	62	9.0000
!ff	chr16:11074900-11075144(+)$1	244	130	133	9.0000
ggg	chr1:158578178-158578433(+)$1	255	21	24	9.0000
ff!	chr2:35170062-35170319(-)$1	257	20	23	9.0000
OOO	chr11:100232361-100232625(-)$1	264	21	24	9.0000
d]d	chrX:93291338-93291579(+)$1	241	46	49	9.0000
FFF	chr15:99473762-99474018(-)$1	256	19	22	9.0000
fff	chr11:55208421-55208707(-)$1	286	5	8	9.0000
88d	chr2:104268108-104268346(-)$1	238	130	133	9.0000
:::	chr16:37883725-37883990(+)$1	265	13	16	9.0000
:::	chr16:15554315-15554553(-)$1	238	33	36	9.0000
DDD	chr2:155213866-155214154(+)$1	288	3	6	9.0000
dqq	chr3:95433013-95433251(+)$1	238	4	7	9.0000
iii	chr10:126975169-126975431(-)$1	262	12	15	9.0000
OOO	chr13:110851684-110851943(-)$1	259	29	32	9.0000
c33	chr7:5032131-5032426(+)$1	295	61	64	9.0000
ddd	chr2:6463612-6463884(-)$1	272	20	23	9.0000
ccb	chr1:16334657-16334913(-)$1	256	57	60	9.0000
:::	chr7:17082036-17082278(-)$1	242	2	5	9.0000
""e	chr18:34761550-34761805(-)$1	255	53	56	9.0000
PPP	chr11:32645002-32645288(+)$1	286	23	26	9.0000
III	chrX:71471507-71471746(-)$1	239	9	12	9.0000
ggg	chr9:21560329-21560569(-)$1	240	45	48	9.0000
###	chr15:36407866-36408105(-)$1	239	55	58	9.0000
===	chr4:15211102-15211338(+)$1	236	8	11	9.0000
:::	chr5:149363475-149363722(-)$1	247	0	3	9.0000
ccq	chr15:81745270-81745506(+)$1	236	56	59	9.0000
mmm	chr1:87973832-87974071(+)$1	239	78	81	9.0000
ppf	chr10:126434598-126434852(+)$1	254	21	24	9.0000
cc"	chr7:105053172-105053421(+)$1	249	164	167	9.0000
vvb	chr7:16534802-16535077(-)$1	275	46	49	9.0000
b33	chr10:79373597-79373886(-)$1	289	70	73	9.0000
ERR	chr5:125368137-125368372(+)$1	235	8	11	9.0000
GGG	chr2:113672936-113673203(-)$1	267	67	70	9.0000
C{H	chr4:102278196-102278444(+)$1	248	3	6	9.0000
^^^	chr8:97094084-97094319(+)$1	235	40	43	9.0000
:::	chr10:76171941-76172200(-)$1	259	15	18	9.0000
:::	chr7:126118247-126118495(-)$1	248	86	89	9.0000
]bb	chr1:162133232-162133487(-)$1	255	42	45	9.0000
fff	chr19:58870900-58871211(-)$1	311	16	19	9.0000
(((	chrX:147418086-147418321(-)$1	235	34	37	9.0000
ooo	chr13:55771472-55771731(+)$1	259	31	34	9.0000
:JJ	chr2:44843935-44844170(-)$1	235	94	97	9.0000
'''	chrX:35773857-35774146(-)$1	289	34	37	9.0000
CCK	chr15:32963087-32963330(+)$1	243	7	10	9.0000
eeo	chr4:137798539-137798776(+)$1	237	12	15	9.0000
bbm	chr2:76467997-76468236(-)$1	239	76	79	9.0000
:::	chr2:80193324-80193579(+)$1	255	82	85	9.0000
E::	chr11:86508251-86508550(-)$1	299	21	24	9.0000
FFF	chr11:77994727-77994968(-)$1	241	79	82	9.0000
:::	chr18:33596852-33597106(-)$1	254	72	75	9.0000
iii	chr4:109058828-109059081(+)$1	253	48	51	9.0000
EEL	chr17:27327227-27327470(-)$1	243	6	9	9.0000
555	chr1:93744236-93744480(+)$1	244	43	46	9.0000
iii	chr8:23278928-23279163(-)$1	235	20	23	9.0000
:::	chr11:86547128-86547390(-)$1	262	5	8	9.0000
FFF	chr9:66875589-66875853(-)$1	264	20	23	9.0000
FFF	chr2:131003574-131003830(-)$1	256	0	3	9.0000
:::	chr5:149317595-149317856(-)$1	261	7	10	9.0000
eee	chr16:92605657-92605947(-)$1	290	113	116	9.0000
ddd	chr14:37935140-37935416(-)$1	276	97	100	9.0000
444	chr3:31017461-31017718(+)$1	257	111	114	9.0000
hhh	chr15:102844374-102844629(+)$1	255	46	49	9.0000
GG:	chr5:93602910-93603221(+)$1	311	19	22	9.0000
eee	chr2:26776600-26776846(-)$1	246	26	29	9.0000
bbm	chr9:49324972-49325215(-)$1	243	31	34	9.0000
NNC	chr6:29325894-29326143(+)$1	249	27	30	9.0000
fff	chr10:82359212-82359508(+)$1	296	35	38	9.0000
hhh	chr14:21852347-21852647(+)$1	300	31	34	9.0000
ddd	chr2:6465606-6465870(-)$1	264	26	29	9.0000
::E	chr19:7028185-7028431(-)$1	246	2	5	9.0000
nnn	chr6:91222377-91222615(+)$1	238	165	168	9.0000
:::	chr10:76171566-76171875(-)$1	309	11	14	9.0000
""d	chr18:38001270-38001581(+)$1	311	32	35	9.0000
KKB	chr15:82957993-82958234(-)$1	241	47	50	9.0000
nnn	chr16:77115749-77115993(+)$1	244	68	71	9.0000
c""	chr5:77396049-77396327(+)$1	278	25	28	9.0000
GGG	chr9:44757793-44758028(-)$1	235	6	9	9.0000
:::	chr4:41239466-41239746(-)$1	280	0	3	9.0000

#DB
...	chr7:3297647-3297951(+)$1	1	57	60	9.0000
.((	chr19:7350360-7350621(-)$1	1	4	7	9.0000
((.	chrX:12253094-12253356(-)$1	1	4	7	9.0000
(((	chr10:52058384-52058650(-)$1	1	7	10	9.0000
(..	chr13:89795492-89795751(-)$1	1	10	13	9.0000
.((	chr6:52182178-52182415(-)$1	1	7	10	9.0000
)).	chr9:24216586-24216831(-)$1	1	90	93	9.0000
(..	chr17:71343559-71343821(-)$1	1	18	21	9.0000
...	chr6:138105063-138105298(+)$1	1	35	38	9.0000
(..	chr8:86493855-86494116(+)$1	1	23	26	9.0000
(((	chr10:66474349-66474639(-)$1	1	4	7	9.0000
.((	chr2:14958608-14958848(-)$1	1	24	27	9.0000
...	chr10:58627290-58627570(-)$1	1	113	116	9.0000
..)	chr11:52066673-52066928(-)$1	1	75	78	9.0000
...	chr8:72856419-72856657(-)$1	1	3	6	9.0000
(((	chr11:48620501-48620775(-)$1	1	24	27	9.0000
(..	chr10:127838447-127838704(-)$1	1	13	16	9.0000
...	chr11:8332767-8333031(-)$1	1	0	3	9.0000
...	chr12:25393064-25393377(+)$1	1	53	56	9.0000
((.	chr7:7236417-7236655(-)$1	1	19	22	9.0000
)).	chr13:73952749-73952998(+)$1	1	26	29	9.0000
...	chr11:60371581-60371844(+)$1	1	59	62	9.0000
.((	chr16:11074900-11075144(+)$1	1	130	133	9.0000
(((	chr1:158578178-158578433(+)$1	1	21	24	9.0000
((.	chr2:35170062-35170319(-)$1	1	20	23	9.0000
...	chr11:100232361-100232625(-)$1	1	21	24	9.0000
).)	chrX:93291338-93291579(+)$1	1	46	49	9.0000
(((	chr15:99473762-99474018(-)$1	1	19	22	9.0000
(((	chr11:55208421-55208707(-)$1	1	5	8	9.0000
..)	chr2:104268108-104268346(-)$1	1	130	133	9.0000
...	chr16:37883725-37883990(+)$1	1	13	16	9.0000
...	chr16:15554315-15554553(-)$1	1	33	36	9.0000
(((	chr2:155213866-155214154(+)$1	1	3	6	9.0000
(..	chr3:95433013-95433251(+)$1	1	4	7	9.0000
(((	chr10:126975169-126975431(-)$1	1	12	15	9.0000
...	chr13:110851684-110851943(-)$1	1	29	32	9.0000
)..	chr7:5032131-5032426(+)$1	1	61	64	9.0000
)))	chr2:6463612-6463884(-)$1	1	20	23	9.0000
(((	chr1:16334657-16334913(-)$1	1	57	60	9.0000
...	chr7:17082036-17082278(-)$1	1	2	5	9.0000
..(	chr18:34761550-34761805(-)$1	1	53	56	9.0000
...	chr11:32645002-32645288(+)$1	1	23	26	9.0000
(((	chrX:71471507-71471746(-)$1	1	9	12	9.0000
)))	chr9:21560329-21560569(-)$1	1	45	48	9.0000
...	chr15:36407866-36408105(-)$1	1	55	58	9.0000
(((	chr4:15211102-15211338(+)$1	1	8	11	9.0000
...	chr5:149363475-149363722(-)$1	1	0	3	9.0000
((.	chr15:81745270-81745506(+)$1	1	56	59	9.0000
...	chr1:87973832-87974071(+)$1	1	78	81	9.0000
..)	chr10:126434598-126434852(+)$1	1	21	24	9.0000
((.	chr7:105053172-105053421(+)$1	1	164	167	9.0000
..)	chr7:16534802-16535077(-)$1	1	46	49	9.0000
)..	chr10:79373597-79373886(-)$1	1	70	73	9.0000
(..	chr5:125368137-125368372(+)$1	1	8	11	9.0000
(((	chr2:113672936-113673203(-)$1	1	67	70	9.0000
(.(	chr4:102278196-102278444(+)$1	1	3	6	9.0000
...	chr8:97094084-97094319(+)$1	1	40	43	9.0000
...	chr10:76171941-76172200(-)$1	1	15	18	9.0000
...	chr7:126118247-126118495(-)$1	1	86	89	9.0000
.))	chr1:162133232-162133487(-)$1	1	42	45	9.0000
(((	chr19:58870900-58871211(-)$1	1	16	19	9.0000
...	chrX:147418086-147418321(-)$1	1	34	37	9.0000
...	chr13:55771472-55771731(+)$1	1	31	34	9.0000
.))	chr2:44843935-44844170(-)$1	1	94	97	9.0000
...	chrX:35773857-35774146(-)$1	1	34	37	9.0000
((.	chr15:32963087-32963330(+)$1	1	7	10	9.0000
((.	chr4:137798539-137798776(+)$1	1	12	15	9.0000
((.	chr2:76467997-76468236(-)$1	1	76	79	9.0000
...	chr2:80193324-80193579(+)$1	1	82	85	9.0000
(..	chr11:86508251-86508550(-)$1	1	21	24	9.0000
(((	chr11:77994727-77994968(-)$1	1	79	82	9.0000
...	chr18:33596852-33597106(-)$1	1	72	75	9.0000
)))	chr4:109058828-109059081(+)$1	1	48	51	9.0000
((.	chr17:27327227-27327470(-)$1	1	6	9	9.0000
...	chr1:93744236-93744480(+)$1	1	43	46	9.0000
(((	chr8:23278928-23279163(-)$1	1	20	23	9.0000
...	chr11:86547128-86547390(-)$1	1	5	8	9.0000
(((	chr9:66875589-66875853(-)$1	1	20	23	9.0000
(((	chr2:131003574-131003830(-)$1	1	0	3	9.0000
...	chr5:149317595-149317856(-)$1	1	7	10	9.0000
(((	chr16:92605657-92605947(-)$1	1	113	116	9.0000
)))	chr14:37935140-37935416(-)$1	1	97	100	9.0000
...	chr3:31017461-31017718(+)$1	1	111	114	9.0000
(((	chr15:102844374-102844629(+)$1	1	46	49	9.0000
((.	chr5:93602910-93603221(+)$1	1	19	22	9.0000
(((	chr2:26776600-26776846(-)$1	1	26	29	9.0000
((.	chr9:49324972-49325215(-)$1	1	31	34	9.0000
..(	chr6:29325894-29326143(+)$1	1	27	30	9.0000
(((	chr10:82359212-82359508(+)$1	1	35	38	9.0000
)))	chr14:21852347-21852647(+)$1	1	31	34	9.0000
)))	chr2:6465606-6465870(-)$1	1	26	29	9.0000
..(	chr19:7028185-7028431(-)$1	1	2	5	9.0000
...	chr6:91222377-91222615(+)$1	1	165	168	9.0000
...	chr10:76171566-76171875(-)$1	1	11	14	9.0000
..(	chr18:38001270-38001581(+)$1	1	32	35	9.0000
..(	chr15:82957993-82958234(-)$1	1	47	50	9.0000
...	chr16:77115749-77115993(+)$1	1	68	71	9.0000
(..	chr5:77396049-77396327(+)$1	1	25	28	9.0000
(((	chr9:44757793-44758028(-)$1	1	6	9	9.0000
...	chr4:41239466-41239746(-)$1	1	0	3	9.0000

#PSSM
C : 0.97	c : 0.03	
U : 0.95	u : 0.05	
U : 0.95	u : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013a_mm9_CDS_m2_run2.nuc.txt

#NT
CUUC	chr11:70787302-70787529(-)$1	227	16	20	11.9999
CUUC	chr6:99601672-99601891(-)$1	219	76	80	11.9999
CUUC	chr1:127923167-127923389(-)$1	222	112	116	11.9999
CUUC	chr16:73928225-73928449(-)$1	224	63	67	11.9999
CUUC	chr9:44629379-44629599(+)$1	220	43	47	11.9999
CUUC	chr11:120936795-120937017(-)$1	222	150	154	11.9999
CUUC	chr10:61302712-61302929(+)$1	217	3	7	11.9999
CUUC	chr17:35033184-35033423(+)$1	239	47	51	11.9999
CUUC	chr2:171867623-171867885(-)$1	262	4	8	11.9999
CUUC	chr5:144951859-144952080(-)$1	221	85	89	11.9999
CUUC	chr5:143051153-143051399(-)$1	246	84	88	11.9999
CUUC	chr11:87862613-87862834(-)$1	221	48	52	11.9999
CUUC	chr14:55682075-55682309(-)$1	234	104	108	11.9999
CUUC	chr11:75259176-75259392(+)$1	216	99	103	11.9999
CUUC	chr4:106386630-106386852(+)$1	222	81	85	11.9999
CUUC	chr5:112904502-112904724(-)$1	222	107	111	11.9999
CUUC	chr7:26074028-26074269(+)$1	241	99	103	11.9999
CUUC	chr3:101638927-101639148(+)$1	221	31	35	11.9999
CUUC	chr13:59713941-59714184(+)$1	243	50	54	11.9999
CUUC	chr3:126542982-126543212(+)$1	230	39	43	11.9999
CUUC	chr9:108477121-108477346(-)$1	225	105	109	11.9999
CUUC	chr3:5242285-5242510(+)$1	225	19	23	11.9999
CUUC	chr4:134101363-134101584(-)$1	221	56	60	11.9999
CUUC	chr17:66868601-66868819(-)$1	218	25	29	11.9999
CUUC	chr10:39541811-39542032(-)$1	221	5	9	11.9999
CUUC	chr3:38787893-38788124(+)$1	231	22	26	11.9999
CUUC	chr2:22808941-22809172(-)$1	231	113	117	11.9999
CUUC	chr1:157160276-157160515(-)$1	239	89	93	11.9999
CUUC	chrX:7507478-7507708(-)$1	230	29	33	11.9999
CUUC	chr11:79353740-79353966(+)$1	226	73	77	11.9999
CUUC	chrX:54754166-54754383(-)$1	217	14	18	11.9999
CUUC	chr16:55822009-55822229(-)$1	220	164	168	11.9999
CUUC	chr2:32076807-32077028(+)$1	221	48	52	11.9999
CUUC	chr10:31670922-31671146(-)$1	224	11	15	11.9999
CUUC	chr5:145659939-145660161(-)$1	222	27	31	11.9999
CUUC	chr7:19147316-19147538(-)$1	222	80	84	11.9999
CUUC	chr1:52264073-52264302(-)$1	229	144	148	11.9999
CUUC	chr3:98656359-98656580(+)$1	221	192	196	11.9999
CUUC	chr1:36528735-36528955(+)$1	220	68	72	11.9999
CUUC	chr8:65824536-65824766(+)$1	230	70	74	11.9999
CUUC	chr5:27988073-27988295(-)$1	222	133	137	11.9999
CUUC	chr14:56369934-56370156(+)$1	222	57	61	11.9999
CUUC	chr10:20043322-20043559(+)$1	237	24	28	11.9999
CUUC	chr7:139439465-139439680(-)$1	215	28	32	11.9999
CUUC	chr7:117118297-117118527(-)$1	230	74	78	11.9999
CUUC	chr1:157882977-157883197(+)$1	220	19	23	11.9999
CUUC	chr15:99257625-99257845(+)$1	220	37	41	11.9999
CUUC	chr7:6413530-6413755(+)$1	225	8	12	11.9999
CUUC	chr19:10343648-10343871(-)$1	223	135	139	11.9999
CUUC	chr13:97436482-97436718(-)$1	236	33	37	11.9999
CUUC	chr9:86399942-86400169(+)$1	227	88	92	11.9999
CUUC	chr11:48651282-48651503(+)$1	221	49	53	11.9999
CUUC	chr1:72475309-72475554(-)$1	245	112	116	11.9999
CUUC	chr17:46259598-46259813(-)$1	215	51	55	11.9999
CUUC	chr19:6062943-6063170(-)$1	227	2	6	11.9999
CUUC	chr7:52779149-52779373(-)$1	224	55	59	11.9999
CUUC	chr13:54653879-54654126(-)$1	247	94	98	11.9999
CUUC	chr6:17047430-17047656(+)$1	226	119	123	11.9999
CUUC	chr3:96510246-96510468(+)$1	222	189	193	11.9999
CUUC	chr19:29791701-29791926(-)$1	225	28	32	11.9999
CUUC	chr13:40800924-40801143(-)$1	219	23	27	11.9999
CUUC	chr13:54840609-54840830(-)$1	221	49	53	11.9999
CUUC	chr18:9917000-9917225(-)$1	225	24	28	11.9999
CUUC	chr11:46484374-46484592(-)$1	218	72	76	11.9999
CUUC	chr8:108948741-108948961(+)$1	220	80	84	11.9999
CUUC	chr2:49113053-49113272(+)$1	219	136	140	11.9999
CUUC	chr1:174043181-174043410(+)$1	229	109	113	11.9999
CUUC	chr15:37919154-37919405(-)$1	251	30	34	11.9999
CUUC	chr9:108745884-108746105(+)$1	221	25	29	11.9999
CUUC	chr17:26355018-26355237(-)$1	219	109	113	11.9999
CUUC	chr11:30720810-30721032(+)$1	222	91	95	11.9999
CUUC	chr14:35551000-35551218(+)$1	218	133	137	11.9999
CUUC	chr7:135025429-135025651(-)$1	222	64	68	11.9999
CUUC	chr4:123191022-123191239(-)$1	217	110	114	11.9999

#otherMatches

#Struct PSSM
oood	chr8:74147307-74147541(+)$1	234	102	106	11.9999
d"""	chr11:70787302-70787529(-)$1	227	16	20	11.9999
::::	chr6:99601672-99601891(-)$1	219	76	80	11.9999
wwww	chr1:127923167-127923389(-)$1	222	112	116	11.9999
ffff	chr16:73928225-73928449(-)$1	224	63	67	11.9999
bb33	chr9:44629379-44629599(+)$1	220	43	47	11.9999
]ccc	chr11:120936795-120937017(-)$1	222	150	154	11.9999
::DD	chr10:61302712-61302929(+)$1	217	3	7	11.9999
cccb	chr17:35033184-35033423(+)$1	239	47	51	11.9999
GGGG	chr2:171867623-171867885(-)$1	262	4	8	11.9999
cooo	chr5:144951859-144952080(-)$1	221	85	89	11.9999
++++	chr5:143051153-143051399(-)$1	246	84	88	11.9999
333c	chr11:87862613-87862834(-)$1	221	48	52	11.9999
ssss	chr14:55682075-55682309(-)$1	234	104	108	11.9999
oooo	chr11:75259176-75259392(+)$1	216	99	103	11.9999
c22d	chr4:106386630-106386852(+)$1	222	81	85	11.9999
==""	chr5:112904502-112904724(-)$1	222	107	111	11.9999
ddd2	chr7:26074028-26074269(+)$1	241	99	103	11.9999
::::	chr3:101638927-101639148(+)$1	221	31	35	11.9999
d%%%	chr13:59713941-59714184(+)$1	243	50	54	11.9999
!!bb	chr3:126542982-126543212(+)$1	230	39	43	11.9999
bbcc	chr9:108477121-108477346(-)$1	225	105	109	11.9999
LLLD	chr3:5242285-5242510(+)$1	225	19	23	11.9999
"""a	chr4:134101363-134101584(-)$1	221	56	60	11.9999
aqqq	chr17:66868601-66868819(-)$1	218	25	29	11.9999
HHHH	chr10:39541811-39542032(-)$1	221	5	9	11.9999
EEEE	chr3:38787893-38788124(+)$1	231	22	26	11.9999
^^^^	chr2:22808941-22809172(-)$1	231	113	117	11.9999
dddd	chr1:157160276-157160515(-)$1	239	89	93	11.9999
##dd	chrX:7507478-7507708(-)$1	230	29	33	11.9999
xxxc	chr11:79353740-79353966(+)$1	226	73	77	11.9999
GGGG	chrX:54754166-54754383(-)$1	217	14	18	11.9999
44dd	chr16:55822009-55822229(-)$1	220	164	168	11.9999
pppp	chr2:32076807-32077028(+)$1	221	48	52	11.9999
::::	chr10:31670922-31671146(-)$1	224	11	15	11.9999
]ccc	chr5:145659939-145660161(-)$1	222	27	31	11.9999
ppcc	chr7:19147316-19147538(-)$1	222	80	84	11.9999
h:::	chr1:52264073-52264302(-)$1	229	144	148	11.9999
xxxd	chr3:98656359-98656580(+)$1	221	192	196	11.9999
oocc	chr1:36528735-36528955(+)$1	220	68	72	11.9999
!!dd	chr8:65824536-65824766(+)$1	230	70	74	11.9999
IIII	chr5:27988073-27988295(-)$1	222	133	137	11.9999
DD{A	chr14:56369934-56370156(+)$1	222	57	61	11.9999
ddd3	chr10:20043322-20043559(+)$1	237	24	28	11.9999
eeee	chr7:139439465-139439680(-)$1	215	28	32	11.9999
ee[b	chr7:117118297-117118527(-)$1	230	74	78	11.9999
DDDD	chr1:157882977-157883197(+)$1	220	19	23	11.9999
hhhh	chr15:99257625-99257845(+)$1	220	37	41	11.9999
::::	chr7:6413530-6413755(+)$1	225	8	12	11.9999
B{CC	chr19:10343648-10343871(-)$1	223	135	139	11.9999
a!!c	chr13:97436482-97436718(-)$1	236	33	37	11.9999
hhhh	chr9:86399942-86400169(+)$1	227	88	92	11.9999
::::	chr11:48651282-48651503(+)$1	221	49	53	11.9999
ffff	chr1:72475309-72475554(-)$1	245	112	116	11.9999
hhhh	chr17:46259598-46259813(-)$1	215	51	55	11.9999
::::	chr19:6062943-6063170(-)$1	227	2	6	11.9999
dddd	chr7:52779149-52779373(-)$1	224	55	59	11.9999
dddd	chr13:54653879-54654126(-)$1	247	94	98	11.9999
FFFF	chr6:17047430-17047656(+)$1	226	119	123	11.9999
JJJJ	chr3:96510246-96510468(+)$1	222	189	193	11.9999
:ccc	chr19:29791701-29791926(-)$1	225	28	32	11.9999
mmmc	chr13:40800924-40801143(-)$1	219	23	27	11.9999
ddd8	chr13:54840609-54840830(-)$1	221	49	53	11.9999
$$$$	chr18:9917000-9917225(-)$1	225	24	28	11.9999
elll	chr11:46484374-46484592(-)$1	218	72	76	11.9999
gggg	chr8:108948741-108948961(+)$1	220	80	84	11.9999
dddd	chr2:49113053-49113272(+)$1	219	136	140	11.9999
====	chr1:174043181-174043410(+)$1	229	109	113	11.9999
b]dd	chr15:37919154-37919405(-)$1	251	30	34	11.9999
""bb	chr9:108745884-108746105(+)$1	221	25	29	11.9999
bb""	chr17:26355018-26355237(-)$1	219	109	113	11.9999
^^^^	chr11:30720810-30721032(+)$1	222	91	95	11.9999
hhhh	chr14:35551000-35551218(+)$1	218	133	137	11.9999
^^^^	chr7:135025429-135025651(-)$1	222	64	68	11.9999
ggg3	chr4:123191022-123191239(-)$1	217	110	114	11.9999

#DB
...)	chr8:74147307-74147541(+)$1	1	102	106	11.9999
(...	chr11:70787302-70787529(-)$1	1	16	20	11.9999
....	chr6:99601672-99601891(-)$1	1	76	80	11.9999
....	chr1:127923167-127923389(-)$1	1	112	116	11.9999
))))	chr16:73928225-73928449(-)$1	1	63	67	11.9999
))..	chr9:44629379-44629599(+)$1	1	43	47	11.9999
.)))	chr11:120936795-120937017(-)$1	1	150	154	11.9999
..((	chr10:61302712-61302929(+)$1	1	3	7	11.9999
((((	chr17:35033184-35033423(+)$1	1	47	51	11.9999
((((	chr2:171867623-171867885(-)$1	1	4	8	11.9999
(...	chr5:144951859-144952080(-)$1	1	85	89	11.9999
....	chr5:143051153-143051399(-)$1	1	84	88	11.9999
...)	chr11:87862613-87862834(-)$1	1	48	52	11.9999
....	chr14:55682075-55682309(-)$1	1	104	108	11.9999
....	chr11:75259176-75259392(+)$1	1	99	103	11.9999
)..)	chr4:106386630-106386852(+)$1	1	81	85	11.9999
((..	chr5:112904502-112904724(-)$1	1	107	111	11.9999
))).	chr7:26074028-26074269(+)$1	1	99	103	11.9999
....	chr3:101638927-101639148(+)$1	1	31	35	11.9999
(...	chr13:59713941-59714184(+)$1	1	50	54	11.9999
..((	chr3:126542982-126543212(+)$1	1	39	43	11.9999
))))	chr9:108477121-108477346(-)$1	1	105	109	11.9999
...(	chr3:5242285-5242510(+)$1	1	19	23	11.9999
...(	chr4:134101363-134101584(-)$1	1	56	60	11.9999
(...	chr17:66868601-66868819(-)$1	1	25	29	11.9999
((((	chr10:39541811-39542032(-)$1	1	5	9	11.9999
((((	chr3:38787893-38788124(+)$1	1	22	26	11.9999
....	chr2:22808941-22809172(-)$1	1	113	117	11.9999
))))	chr1:157160276-157160515(-)$1	1	89	93	11.9999
..((	chrX:7507478-7507708(-)$1	1	29	33	11.9999
...)	chr11:79353740-79353966(+)$1	1	73	77	11.9999
((((	chrX:54754166-54754383(-)$1	1	14	18	11.9999
..))	chr16:55822009-55822229(-)$1	1	164	168	11.9999
....	chr2:32076807-32077028(+)$1	1	48	52	11.9999
....	chr10:31670922-31671146(-)$1	1	11	15	11.9999
.)))	chr5:145659939-145660161(-)$1	1	27	31	11.9999
..))	chr7:19147316-19147538(-)$1	1	80	84	11.9999
)...	chr1:52264073-52264302(-)$1	1	144	148	11.9999
...)	chr3:98656359-98656580(+)$1	1	192	196	11.9999
..))	chr1:36528735-36528955(+)$1	1	68	72	11.9999
..((	chr8:65824536-65824766(+)$1	1	70	74	11.9999
))))	chr5:27988073-27988295(-)$1	1	133	137	11.9999
((.(	chr14:56369934-56370156(+)$1	1	57	61	11.9999
))).	chr10:20043322-20043559(+)$1	1	24	28	11.9999
((((	chr7:139439465-139439680(-)$1	1	28	32	11.9999
((.(	chr7:117118297-117118527(-)$1	1	74	78	11.9999
((((	chr1:157882977-157883197(+)$1	1	19	23	11.9999
((((	chr15:99257625-99257845(+)$1	1	37	41	11.9999
....	chr7:6413530-6413755(+)$1	1	8	12	11.9999
(.((	chr19:10343648-10343871(-)$1	1	135	139	11.9999
(..(	chr13:97436482-97436718(-)$1	1	33	37	11.9999
((((	chr9:86399942-86400169(+)$1	1	88	92	11.9999
....	chr11:48651282-48651503(+)$1	1	49	53	11.9999
))))	chr1:72475309-72475554(-)$1	1	112	116	11.9999
((((	chr17:46259598-46259813(-)$1	1	51	55	11.9999
....	chr19:6062943-6063170(-)$1	1	2	6	11.9999
((((	chr7:52779149-52779373(-)$1	1	55	59	11.9999
))))	chr13:54653879-54654126(-)$1	1	94	98	11.9999
))))	chr6:17047430-17047656(+)$1	1	119	123	11.9999
))))	chr3:96510246-96510468(+)$1	1	189	193	11.9999
.(((	chr19:29791701-29791926(-)$1	1	28	32	11.9999
...)	chr13:40800924-40801143(-)$1	1	23	27	11.9999
))).	chr13:54840609-54840830(-)$1	1	49	53	11.9999
....	chr18:9917000-9917225(-)$1	1	24	28	11.9999
(...	chr11:46484374-46484592(-)$1	1	72	76	11.9999
((((	chr8:108948741-108948961(+)$1	1	80	84	11.9999
((((	chr2:49113053-49113272(+)$1	1	136	140	11.9999
((((	chr1:174043181-174043410(+)$1	1	109	113	11.9999
).))	chr15:37919154-37919405(-)$1	1	30	34	11.9999
..((	chr9:108745884-108746105(+)$1	1	25	29	11.9999
((..	chr17:26355018-26355237(-)$1	1	109	113	11.9999
....	chr11:30720810-30721032(+)$1	1	91	95	11.9999
((((	chr14:35551000-35551218(+)$1	1	133	137	11.9999
....	chr7:135025429-135025651(-)$1	1	64	68	11.9999
))).	chr4:123191022-123191239(-)$1	1	110	114	11.9999

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

#score	899.9999999999995
#seq	75
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011b_mm9_CDS_m3_run2.nuc.txt

#NT
AGGA	chr9:53773691-53773960(-)$1	269	155	159	12.0000
AGGA	chr13:69138016-69138287(-)$1	271	121	125	12.0000
AGGA	chr8:74844691-74844960(+)$1	269	221	225	12.0000
AGGA	chr11:87794777-87795061(-)$1	284	211	215	12.0000
AGGA	chr3:95464614-95464908(+)$1	294	13	17	12.0000
AGGA	chr9:97269861-97270130(-)$1	269	0	4	12.0000
AGGA	chr17:35292433-35292717(-)$1	284	43	47	12.0000
AGGA	chr4:45372561-45372833(+)$1	272	230	234	12.0000
AGGA	chr8:86770433-86770706(-)$1	273	7	11	12.0000
AGGA	chr2:31615419-31615714(+)$1	295	246	250	12.0000
AGGA	chr9:64825927-64826205(+)$1	278	134	138	12.0000
AGGA	chr6:22240953-22241221(+)$1	268	115	119	12.0000
AGGA	chr6:51413975-51414275(-)$1	300	63	67	12.0000
AGGA	chr7:27949815-27950085(-)$1	270	103	107	12.0000
AGGA	chr2:34678076-34678352(-)$1	276	125	129	12.0000
AGGA	chr7:25670028-25670303(+)$1	275	160	164	12.0000
AGGA	chr9:108701514-108701781(+)$1	267	204	208	12.0000
AGGA	chr3:154259844-154260110(-)$1	266	202	206	12.0000
AGGA	chr9:65194529-65194809(+)$1	280	230	234	12.0000
AGGA	chr1:93275013-93275289(-)$1	276	84	88	12.0000
AGGA	chr18:24743679-24743949(-)$1	270	20	24	12.0000
AGGA	chr7:52631892-52632163(-)$1	271	78	82	12.0000
AGGA	chr5:108863240-108863508(-)$1	268	62	66	12.0000
AGGA	chr9:107159265-107159531(-)$1	266	107	111	12.0000
AGGA	chr9:98390942-98391210(+)$1	268	93	97	12.0000
AGGA	chr7:28151313-28151603(-)$1	290	126	130	12.0000
AGGA	chr7:135038924-135039193(-)$1	269	20	24	12.0000
AGGA	chr2:40774602-40774881(-)$1	279	20	24	12.0000
AGGA	chr13:73773754-73774025(+)$1	271	161	165	12.0000
AGGA	chr19:5384494-5384771(-)$1	277	46	50	12.0000
AGGA	chr5:122096593-122096864(-)$1	271	19	23	12.0000
AGGA	chr19:8964904-8965185(+)$1	281	19	23	12.0000
AGGA	chr5:123244330-123244627(-)$1	297	33	37	12.0000
AGGA	chr8:74842841-74843113(+)$1	272	202	206	12.0000
AGGA	chr6:56728726-56729000(-)$1	274	82	86	12.0000
AGGA	chr2:174125804-174126079(+)$1	275	13	17	12.0000
AGGA	chr5:138223490-138223786(-)$1	296	172	176	12.0000
AGGA	chr19:29086354-29086641(+)$1	287	28	32	12.0000
AGGA	chr4:135883045-135883347(+)$1	302	29	33	12.0000
AGGA	chr2:156606172-156606446(+)$1	274	159	163	12.0000
AGGA	chr4:155331129-155331405(+)$1	276	58	62	12.0000
AGGA	chr11:102978337-102978633(+)$1	296	7	11	12.0000
AGGA	chr18:60859085-60859370(-)$1	285	186	190	12.0000
AGGA	chr11:97574608-97574878(+)$1	270	40	44	12.0000
AGGA	chr19:7273742-7274025(-)$1	283	147	151	12.0000
AGGA	chr14:45912564-45912838(-)$1	274	59	63	12.0000
AGGA	chr16:36049850-36050132(-)$1	282	177	181	12.0000
AGGA	chr2:121205209-121205478(-)$1	269	115	119	12.0000
AGGA	chr8:23489736-23490016(-)$1	280	74	78	12.0000

#otherMatches

#Struct PSSM
hhhh	chr2:32092890-32093158(+)$1	268	158	162	12.0000
mmcc	chr9:53773691-53773960(-)$1	269	155	159	12.0000
5555	chr13:69138016-69138287(-)$1	271	121	125	12.0000
::::	chr8:74844691-74844960(+)$1	269	221	225	12.0000
b[ff	chr11:87794777-87795061(-)$1	284	211	215	12.0000
===#	chr3:95464614-95464908(+)$1	294	13	17	12.0000
dddd	chr9:97269861-97270130(-)$1	269	0	4	12.0000
nbb2	chr17:35292433-35292717(-)$1	284	43	47	12.0000
c22h	chr4:45372561-45372833(+)$1	272	230	234	12.0000
qqqq	chr8:86770433-86770706(-)$1	273	7	11	12.0000
GZZZ	chr2:31615419-31615714(+)$1	295	246	250	12.0000
EEMM	chr9:64825927-64826205(+)$1	278	134	138	12.0000
cc::	chr6:22240953-22241221(+)$1	268	115	119	12.0000
xxxx	chr6:51413975-51414275(-)$1	300	63	67	12.0000
[bbm	chr7:27949815-27950085(-)$1	270	103	107	12.0000
dd:D	chr2:34678076-34678352(-)$1	276	125	129	12.0000
[ggg	chr7:25670028-25670303(+)$1	275	160	164	12.0000
GGG:	chr9:108701514-108701781(+)$1	267	204	208	12.0000
qqqd	chr3:154259844-154260110(-)$1	266	202	206	12.0000
}BB|	chr9:65194529-65194809(+)$1	280	230	234	12.0000
cc44	chr1:93275013-93275289(-)$1	276	84	88	12.0000
#ccc	chr18:24743679-24743949(-)$1	270	20	24	12.0000
d:::	chr7:52631892-52632163(-)$1	271	78	82	12.0000
""gg	chr5:108863240-108863508(-)$1	268	62	66	12.0000
2ddd	chr9:107159265-107159531(-)$1	266	107	111	12.0000
]bb7	chr9:98390942-98391210(+)$1	268	93	97	12.0000
::::	chr7:28151313-28151603(-)$1	290	126	130	12.0000
iiii	chr7:135038924-135039193(-)$1	269	20	24	12.0000
ccc!	chr2:40774602-40774881(-)$1	279	20	24	12.0000
?JJJ	chr13:73773754-73774025(+)$1	271	161	165	12.0000
dddd	chr19:5384494-5384771(-)$1	277	46	50	12.0000
''''	chr5:122096593-122096864(-)$1	271	19	23	12.0000
CCKK	chr19:8964904-8965185(+)$1	281	19	23	12.0000
dddd	chr5:123244330-123244627(-)$1	297	33	37	12.0000
llee	chr8:74842841-74843113(+)$1	272	202	206	12.0000
oooo	chr6:56728726-56729000(-)$1	274	82	86	12.0000
dd!!	chr2:174125804-174126079(+)$1	275	13	17	12.0000
EEEE	chr5:138223490-138223786(-)$1	296	172	176	12.0000
eee#	chr19:29086354-29086641(+)$1	287	28	32	12.0000
ffff	chr4:135883045-135883347(+)$1	302	29	33	12.0000
mbb]	chr2:156606172-156606446(+)$1	274	159	163	12.0000
[arr	chr4:155331129-155331405(+)$1	276	58	62	12.0000
:ccc	chr11:102978337-102978633(+)$1	296	7	11	12.0000
ggg4	chr18:60859085-60859370(-)$1	285	186	190	12.0000
JJJJ	chr11:97574608-97574878(+)$1	270	40	44	12.0000
pppe	chr19:7273742-7274025(-)$1	283	147	151	12.0000
:eee	chr14:45912564-45912838(-)$1	274	59	63	12.0000
:ccc	chr16:36049850-36050132(-)$1	282	177	181	12.0000
====	chr2:121205209-121205478(-)$1	269	115	119	12.0000
ccc:	chr8:23489736-23490016(-)$1	280	74	78	12.0000

#DB
))))	chr2:32092890-32093158(+)$1	1	158	162	12.0000
..))	chr9:53773691-53773960(-)$1	1	155	159	12.0000
....	chr13:69138016-69138287(-)$1	1	121	125	12.0000
....	chr8:74844691-74844960(+)$1	1	221	225	12.0000
(.((	chr11:87794777-87795061(-)$1	1	211	215	12.0000
(((.	chr3:95464614-95464908(+)$1	1	13	17	12.0000
((((	chr9:97269861-97270130(-)$1	1	0	4	12.0000
.)).	chr17:35292433-35292717(-)$1	1	43	47	12.0000
)..)	chr4:45372561-45372833(+)$1	1	230	234	12.0000
....	chr8:86770433-86770706(-)$1	1	7	11	12.0000
)...	chr2:31615419-31615714(+)$1	1	246	250	12.0000
((..	chr9:64825927-64826205(+)$1	1	134	138	12.0000
))..	chr6:22240953-22241221(+)$1	1	115	119	12.0000
....	chr6:51413975-51414275(-)$1	1	63	67	12.0000
.((.	chr7:27949815-27950085(-)$1	1	103	107	12.0000
)).(	chr2:34678076-34678352(-)$1	1	125	129	12.0000
.(((	chr7:25670028-25670303(+)$1	1	160	164	12.0000
))).	chr9:108701514-108701781(+)$1	1	204	208	12.0000
...)	chr3:154259844-154260110(-)$1	1	202	206	12.0000
.)).	chr9:65194529-65194809(+)$1	1	230	234	12.0000
))..	chr1:93275013-93275289(-)$1	1	84	88	12.0000
.(((	chr18:24743679-24743949(-)$1	1	20	24	12.0000
)...	chr7:52631892-52632163(-)$1	1	78	82	12.0000
..((	chr5:108863240-108863508(-)$1	1	62	66	12.0000
.)))	chr9:107159265-107159531(-)$1	1	107	111	12.0000
.)).	chr9:98390942-98391210(+)$1	1	93	97	12.0000
....	chr7:28151313-28151603(-)$1	1	126	130	12.0000
((((	chr7:135038924-135039193(-)$1	1	20	24	12.0000
(((.	chr2:40774602-40774881(-)$1	1	20	24	12.0000
.)))	chr13:73773754-73774025(+)$1	1	161	165	12.0000
))))	chr19:5384494-5384771(-)$1	1	46	50	12.0000
....	chr5:122096593-122096864(-)$1	1	19	23	12.0000
((..	chr19:8964904-8965185(+)$1	1	19	23	12.0000
))))	chr5:123244330-123244627(-)$1	1	33	37	12.0000
..))	chr8:74842841-74843113(+)$1	1	202	206	12.0000
....	chr6:56728726-56729000(-)$1	1	82	86	12.0000
((..	chr2:174125804-174126079(+)$1	1	13	17	12.0000
))))	chr5:138223490-138223786(-)$1	1	172	176	12.0000
(((.	chr19:29086354-29086641(+)$1	1	28	32	12.0000
))))	chr4:135883045-135883347(+)$1	1	29	33	12.0000
.)).	chr2:156606172-156606446(+)$1	1	159	163	12.0000
.(..	chr4:155331129-155331405(+)$1	1	58	62	12.0000
.(((	chr11:102978337-102978633(+)$1	1	7	11	12.0000
))).	chr18:60859085-60859370(-)$1	1	186	190	12.0000
((((	chr11:97574608-97574878(+)$1	1	40	44	12.0000
...)	chr19:7273742-7274025(-)$1	1	147	151	12.0000
.(((	chr14:45912564-45912838(-)$1	1	59	63	12.0000
.(((	chr16:36049850-36050132(-)$1	1	177	181	12.0000
))))	chr2:121205209-121205478(-)$1	1	115	119	12.0000
))).	chr8:23489736-23490016(-)$1	1	74	78	12.0000

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

#score	600.0000000000001
#seq	50
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Mbnl1_Wang2012c_mm9_UTR_m2_run1.nuc.txt

#NT
uuguuuuguuuug	chr6:119875219-119875455(-)$1	236	102	115	25.4130
UUGUUUUGUUUUA	chrX:35772881-35773116(-)$1	235	200	213	25.4130
UUAUUUUGUAUUU	chr14:121685936-121686190(-)$1	254	239	252	22.5869
UUGUUUUGUUGUU	chr3:104459972-104460212(+)$1	240	104	117	23.9999
UCCUUUUGGUUUU	chr2:104269211-104269455(-)$1	244	114	127	18.6739
UUUUUUUUUUUUU	chr11:115940745-115940980(-)$1	235	51	64	25.1956
UUGCUUUCUUUUU	chr14:70705593-70705855(-)$1	262	171	184	22.6956
UUUCUUUGUCUUU	chr12:78038429-78038664(-)$1	235	216	229	19.3260
UUGUUUUGUUUUG	chr5:32793714-32793955(+)$1	241	104	117	25.4130
UUGuuuuguuuuu	chr4:150421751-150421986(-)$1	235	179	192	28.6739
uuuuuuuuuuuuu	chr10:34003605-34003844(+)$1	239	55	68	25.1956
uuguuggguuuuu	chr12:75046634-75046871(+)$1	237	112	125	19.8695
UUGUGUUACUUUU	chr8:85837495-85837730(-)$1	235	113	126	17.4782
UUAUUUUUCUUUU	chr2:155214476-155214718(+)$1	242	158	171	20.6304
GUGUUUUGUCUUC	chr11:62215867-62216106(-)$1	239	35	48	16.8260
CUCUUUUGUUUGU	chr5:8074434-8074671(-)$1	237	3	16	18.6739
UUGUUUUGUUUUA	chr9:30957253-30957494(-)$1	241	119	132	25.4130
UUGuuuuguuuuu	chr4:150421684-150421924(-)$1	240	117	130	28.6739
UCUUUUUCUUUUU	chr10:53626981-53627220(-)$1	239	193	206	21.0652
uuguuuuguuuug	chr7:66561836-66562082(+)$1	246	60	73	25.4130
uucuuuuuuuuuu	chr4:57909670-57909907(+)$1	237	187	200	25.0869
uuauuuugcuuau	chr18:60551048-60551286(+)$1	238	29	42	18.3478
UUGUUUUGUUUUU	chr11:50108261-50108515(-)$1	254	129	142	28.6739
UUCUUGUGUUUUA	chr16:96377526-96377769(+)$1	243	107	120	19.6521
UUUUUUUUUUUUU	chr12:54249968-54250203(+)$1	235	217	230	25.1956
uuguguugguuuu	chr9:42772398-42772633(-)$1	235	99	112	20.0869
UUCUUUUGUUUGU	chr18:68426825-68427060(-)$1	235	117	130	22.9130
UUAUUUUUAUUUU	chr3:146394948-146395183(-)$1	235	49	62	20.4130
UUUUUUCCUUUUU	chr8:106942833-106943068(-)$1	235	219	232	21.1739
UUCCUUUCUUUUU	chr14:35339882-35340126(-)$1	244	71	84	21.2826
UGAUUUUAUUUUU	chr5:135657504-135657739(+)$1	235	93	106	19.5434
UUUGUUUGUUUUU	chr2:121373570-121373818(-)$1	248	26	39	23.0217
UUGUUUUGUUUUG	chr2:132136059-132136303(+)$1	244	113	126	25.4130
UUGUUUUGUUUUU	chr6:39554848-39555083(-)$1	235	109	122	28.6739
UUGUUUUGUUUUU	chr9:96233096-96233334(-)$1	238	116	129	28.6739
CUGUUUUGUUUUA	chr8:71429898-71430160(+)$1	262	194	207	21.1739
uucuuuucuucuu	chrX:149935155-149935402(+)$1	247	5	18	20.7391
UUUUUUUUUUUUU	chr5:32794615-32794875(+)$1	260	70	83	25.1956
AUGUUUCCUUUUU	chr10:117252017-117252253(-)$1	236	70	83	18.1304
UUGUUGUGUCUUA	chr5:122904087-122904383(-)$1	296	7	20	17.1521
UUCUUUACUUUUU	chr14:35340832-35341082(-)$1	250	209	222	20.9565
UUUAUUUGUCUUU	chr2:134420523-134420770(-)$1	247	112	125	19.1086
GUUUUUUGUUUUU	chr11:120242232-120242467(-)$1	235	101	114	23.1304
UUGUUUUCUGUUG	chr6:30404218-30404458(+)$1	240	110	123	19.3260
UUGUAUUCUUUUU	chr9:3478532-3478767(+)$1	235	205	218	22.2608

#otherMatches

#Struct PSSM
HHHHHH::::iii	chr17:80249097-80249332(-)$1	235	76	89	20.9565
eeeee:::::::d	chr6:119875219-119875455(-)$1	236	102	115	25.4130
>>>>>>>>>>>>f	chrX:35772881-35773116(-)$1	235	200	213	25.4130
eeee22dddd:::	chr14:121685936-121686190(-)$1	254	239	252	22.5869
22ccc22======	chr3:104459972-104460212(+)$1	240	104	117	23.9999
:bbmmmmbb::::	chr2:104269211-104269455(-)$1	244	114	127	18.6739
dddwwwwwwwwww	chr11:115940745-115940980(-)$1	235	51	64	25.1956
i[bb"""eeeee#	chr14:70705593-70705855(-)$1	262	171	184	22.6956
gg22eeeee::::	chr12:78038429-78038664(-)$1	235	216	229	19.3260
c]dddd:CCC{BB	chr5:32793714-32793955(+)$1	241	104	117	25.4130
4dddd::::::EE	chr4:150421751-150421986(-)$1	235	179	192	28.6739
c>>>>>>>>>>>>	chr10:34003605-34003844(+)$1	239	55	68	25.1956
!!===========	chr12:75046634-75046871(+)$1	237	112	125	19.8695
IIIII::::::::	chr8:85837495-85837730(-)$1	235	113	126	17.4782
::::::::::GGG	chr2:155214476-155214718(+)$1	242	158	171	20.6304
dddd"""a[ffff	chr11:62215867-62216106(-)$1	239	35	48	16.8260
:ggggggg+++++	chr5:8074434-8074671(-)$1	237	3	16	18.6739
22dddd:::::::	chr9:30957253-30957494(-)$1	241	119	132	25.4130
:::::::::HHHH	chr4:150421684-150421924(-)$1	240	117	130	28.6739
cc:::::::::::	chr10:53626981-53627220(-)$1	239	193	206	21.0652
>>>>>>>>>>>>=	chr7:66561836-66562082(+)$1	246	60	73	25.4130
:::::::::::::	chr4:57909670-57909907(+)$1	237	187	200	25.0869
eeeuuuuuuuuuu	chr18:60551048-60551286(+)$1	238	29	42	18.3478
_____EEEEEZZZ	chr11:50108261-50108515(-)$1	254	129	142	28.6739
!!a!!hhhhhhhh	chr16:96377526-96377769(+)$1	243	107	120	19.6521
88888========	chr12:54249968-54250203(+)$1	235	217	230	25.1956
cc]ccc]dddd]i	chr9:42772398-42772633(-)$1	235	99	112	20.0869
EEMMMMGGGGGGG	chr18:68426825-68427060(-)$1	235	117	130	22.9130
ooooooeeeee22	chr3:146394948-146395183(-)$1	235	49	62	20.4130
pppdddd::::::	chr8:106942833-106943068(-)$1	235	219	232	21.1739
ccbbrrrrrrrrr	chr14:35339882-35340126(-)$1	244	71	84	21.2826
5ggggggg:::::	chr5:135657504-135657739(+)$1	235	93	106	19.5434
iiiiiiii!!ddd	chr2:121373570-121373818(-)$1	248	26	39	23.0217
e]eeeee666666	chr2:132136059-132136303(+)$1	244	113	126	25.4130
::===========	chr6:39554848-39555083(-)$1	235	109	122	28.6739
::iiiiiiiiipp	chr9:96233096-96233334(-)$1	238	116	129	28.6739
[ddddeeeeeppp	chr8:71429898-71430160(+)$1	262	194	207	21.1739
:::::::::::::	chrX:149935155-149935402(+)$1	247	5	18	20.7391
^^^^^^^^^^^^^	chr5:32794615-32794875(+)$1	260	70	83	25.1956
=============	chr10:117252017-117252253(-)$1	236	70	83	18.1304
IIIIIIIbbmmmm	chr5:122904087-122904383(-)$1	296	7	20	17.1521
dddd22ggggggg	chr14:35340832-35341082(-)$1	250	209	222	20.9565
ddddqqqqqqqqd	chr2:134420523-134420770(-)$1	247	112	125	19.1086
FF}DDDD}FFFFF	chr11:120242232-120242467(-)$1	235	101	114	23.1304
hhhh55555dddd	chr6:30404218-30404458(+)$1	240	110	123	19.3260
JJJJJYYA:gggg	chr9:3478532-3478767(+)$1	235	205	218	22.2608

#DB
((((((....(((	chr17:80249097-80249332(-)$1	1	76	89	20.9565
))))).......(	chr6:119875219-119875455(-)$1	1	102	115	25.4130
............)	chrX:35772881-35773116(-)$1	1	200	213	25.4130
))))..))))...	chr14:121685936-121686190(-)$1	1	239	252	22.5869
..)))..))))))	chr3:104459972-104460212(+)$1	1	104	117	23.9999
.((....))....	chr2:104269211-104269455(-)$1	1	114	127	18.6739
(((..........	chr11:115940745-115940980(-)$1	1	51	64	25.1956
(.((...(((((.	chr14:70705593-70705855(-)$1	1	171	184	22.6956
))..)))))....	chr12:78038429-78038664(-)$1	1	216	229	19.3260
).)))).(((.((	chr5:32793714-32793955(+)$1	1	104	117	25.4130
.))))......))	chr4:150421751-150421986(-)$1	1	179	192	28.6739
)............	chr10:34003605-34003844(+)$1	1	55	68	25.1956
..(((((((((((	chr12:75046634-75046871(+)$1	1	112	125	19.8695
(((((........	chr8:85837495-85837730(-)$1	1	113	126	17.4782
..........(((	chr2:155214476-155214718(+)$1	1	158	171	20.6304
((((...(.((((	chr11:62215867-62216106(-)$1	1	35	48	16.8260
.(((((((.....	chr5:8074434-8074671(-)$1	1	3	16	18.6739
..)))).......	chr9:30957253-30957494(-)$1	1	119	132	25.4130
.........((((	chr4:150421684-150421924(-)$1	1	117	130	28.6739
))...........	chr10:53626981-53627220(-)$1	1	193	206	21.0652
............)	chr7:66561836-66562082(+)$1	1	60	73	25.4130
.............	chr4:57909670-57909907(+)$1	1	187	200	25.0869
(((..........	chr18:60551048-60551286(+)$1	1	29	42	18.3478
.....)))))...	chr11:50108261-50108515(-)$1	1	129	142	28.6739
..(..((((((((	chr16:96377526-96377769(+)$1	1	107	120	19.6521
.....))))))))	chr12:54249968-54250203(+)$1	1	217	230	25.1956
)).))).)))).)	chr9:42772398-42772633(-)$1	1	99	112	20.0869
((....(((((((	chr18:68426825-68427060(-)$1	1	117	130	22.9130
......)))))..	chr3:146394948-146395183(-)$1	1	49	62	20.4130
...))))......	chr8:106942833-106943068(-)$1	1	219	232	21.1739
((((.........	chr14:35339882-35340126(-)$1	1	71	84	21.2826
.))))))).....	chr5:135657504-135657739(+)$1	1	93	106	19.5434
((((((((..(((	chr2:121373570-121373818(-)$1	1	26	39	23.0217
).)))))......	chr2:132136059-132136303(+)$1	1	113	126	25.4130
..(((((((((((	chr6:39554848-39555083(-)$1	1	109	122	28.6739
..(((((((((..	chr9:96233096-96233334(-)$1	1	116	129	28.6739
.(((((((((...	chr8:71429898-71430160(+)$1	1	194	207	21.1739
.............	chrX:149935155-149935402(+)$1	1	5	18	20.7391
.............	chr5:32794615-32794875(+)$1	1	70	83	25.1956
)))))))))))))	chr10:117252017-117252253(-)$1	1	70	83	18.1304
(((((((((....	chr5:122904087-122904383(-)$1	1	7	20	17.1521
))))..)))))))	chr14:35340832-35341082(-)$1	1	209	222	20.9565
((((........)	chr2:134420523-134420770(-)$1	1	112	125	19.1086
)).)))).)))))	chr11:120242232-120242467(-)$1	1	101	114	23.1304
)))).....))))	chr6:30404218-30404458(+)$1	1	110	123	19.3260
)))))..).((((	chr9:3478532-3478767(+)$1	1	205	218	22.2608

#PSSM
U : 0.71	u : 0.17	G : 0.04	C : 0.04	A : 0.02	
U : 0.76	u : 0.17	C : 0.04	G : 0.02	
G : 0.39	U : 0.19	C : 0.15	g : 0.08	A : 0.08	c : 0.04	u : 0.02	a : 0.02	
U : 0.67	u : 0.21	C : 0.06	G : 0.02	A : 0.02	
U : 0.73	u : 0.19	G : 0.02	g : 0.02	A : 0.02	
U : 0.73	u : 0.19	G : 0.04	g : 0.02	
U : 0.71	u : 0.19	C : 0.04	g : 0.02	A : 0.02	
G : 0.43	C : 0.19	g : 0.15	U : 0.10	u : 0.04	A : 0.04	c : 0.02	
U : 0.69	u : 0.17	C : 0.04	G : 0.02	c : 0.02	g : 0.02	A : 0.02	
U : 0.65	u : 0.21	C : 0.08	A : 0.02	G : 0.02	
U : 0.76	u : 0.19	G : 0.02	c : 0.02	
U : 0.71	u : 0.19	G : 0.04	C : 0.02	a : 0.02	
U : 0.58	u : 0.17	A : 0.10	G : 0.06	g : 0.04	C : 0.02	

#score	1032.9130434782603
#seq	46
#width	13
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011c_mm9_CDS_m1_run2.nuc.txt

#NT
GCUG	chr17:35119051-35119331(+)$1	280	136	140	11.9999
GCUG	chr18:60859088-60859368(-)$1	280	128	132	11.9999
GCUG	chr9:44160509-44160780(-)$1	271	109	113	11.9999
GCUG	chr2:32092881-32093158(+)$1	277	11	15	11.9999
GCUG	chr2:121205212-121205496(-)$1	284	13	17	11.9999
GCUG	chr17:35292437-35292710(-)$1	273	128	132	11.9999
GCUG	chr3:102703878-102704148(-)$1	270	137	141	11.9999
GCUG	chr2:91803321-91803605(-)$1	284	142	146	11.9999
GCUG	chr8:95850590-95850858(-)$1	268	176	180	11.9999
GCUG	chr4:33125089-33125363(+)$1	274	262	266	11.9999
GCUG	chr10:126721767-126722035(-)$1	268	102	106	11.9999
GCUG	chr8:28383691-28383967(+)$1	276	1	5	11.9999
GCUG	chr17:6084525-6084794(+)$1	269	54	58	11.9999
GCUG	chr19:46681074-46681349(+)$1	275	0	4	11.9999
GCUG	chrX:98514856-98515126(+)$1	270	18	22	11.9999
GCUG	chr18:24743677-24743947(-)$1	270	81	85	11.9999
GCUG	chr5:122096592-122096861(-)$1	269	20	24	11.9999
GCUG	chr1:93275018-93275289(-)$1	271	148	152	11.9999
GCUG	chr2:34678076-34678352(-)$1	276	23	27	11.9999
GCUG	chr19:7273750-7274023(-)$1	273	9	13	11.9999
GCUG	chr3:51288320-51288589(+)$1	269	203	207	11.9999
GCUG	chr7:135038927-135039193(-)$1	266	84	88	11.9999
GCUG	chr15:76028312-76028598(-)$1	286	109	113	11.9999
GCUG	chr18:36908130-36908401(+)$1	271	46	50	11.9999
GCUG	chr14:70066969-70067240(+)$1	271	160	164	11.9999
GCUG	chr2:153142656-153142935(+)$1	279	79	83	11.9999
GCUG	chr11:87794792-87795066(-)$1	274	187	191	11.9999
GCUG	chr5:75006662-75006928(-)$1	266	164	168	11.9999
GCUG	chr11:70466234-70466555(-)$1	321	77	81	11.9999
GCUG	chr13:55651491-55651760(-)$1	269	144	148	11.9999
GCUG	chr13:73773815-73774087(+)$1	272	120	124	11.9999
GCUG	chr17:32498259-32498531(-)$1	272	49	53	11.9999
GCUG	chr4:45372561-45372833(+)$1	272	178	182	11.9999
GCUG	chr5:67078040-67078310(+)$1	270	43	47	11.9999
GCUG	chr5:93697524-93697801(+)$1	277	35	39	11.9999
GCUG	chr14:64225928-64226213(+)$1	285	169	173	11.9999
GCUG	chr7:28151330-28151601(-)$1	271	101	105	11.9999
GCUG	chr11:120481937-120482225(-)$1	288	217	221	11.9999
GCUG	chr8:74842835-74843118(+)$1	283	17	21	11.9999
GCUG	chr11:97574603-97574878(+)$1	275	33	37	11.9999
GCUG	chr2:40774602-40774870(-)$1	268	140	144	11.9999
GCUG	chr3:108706705-108706973(-)$1	268	247	251	11.9999
GCUG	chr7:27949815-27950086(-)$1	271	20	24	11.9999
GCUG	chr1:77503123-77503392(-)$1	269	107	111	11.9999
GCUG	chr6:22240953-22241221(+)$1	268	102	106	11.9999
GCUG	chr3:95464619-95464902(+)$1	283	66	70	11.9999
GCUG	chr9:97269861-97270130(-)$1	269	63	67	11.9999
gcug	chr9:37297061-37297336(+)$1	275	47	51	11.9999
GCUG	chr19:5384494-5384777(-)$1	283	7	11	11.9999
GCUG	chr3:146444016-146444284(-)$1	268	49	53	11.9999
GCUG	chr14:52760734-52761005(+)$1	271	68	72	11.9999
GCUG	chr8:86770442-86770710(-)$1	268	31	35	11.9999
GCUG	chr13:81930942-81931210(+)$1	268	130	134	11.9999
GCUG	chr8:23489738-23490016(-)$1	278	84	88	11.9999
GCUG	chr12:85733283-85733551(-)$1	268	5	9	11.9999
GCUG	chr11:102978353-102978633(+)$1	280	91	95	11.9999
GCUG	chr5:92391556-92391827(-)$1	271	23	27	11.9999
GCUG	chr7:25670028-25670303(+)$1	275	9	13	11.9999
GCUG	chr14:45912565-45912837(-)$1	272	76	80	11.9999
GCUG	chr9:3411339-3411620(+)$1	281	141	145	11.9999
GCUG	chr11:117828728-117829006(-)$1	278	88	92	11.9999
GCUG	chr9:64825922-64826205(+)$1	283	38	42	11.9999
GCUG	chr5:123244349-123244627(-)$1	278	128	132	11.9999
GCUG	chr3:154259844-154260111(-)$1	267	55	59	11.9999
GCUG	chr2:174125804-174126076(+)$1	272	200	204	11.9999
GCUG	chr19:5384549-5384817(-)$1	268	47	51	11.9999
GCUG	chr4:155331122-155331424(+)$1	302	153	157	11.9999
GCUG	chr4:135883045-135883340(+)$1	295	168	172	11.9999
GCUG	chr2:156359397-156359677(+)$1	280	149	153	11.9999
GCUG	chr13:24843895-24844178(-)$1	283	81	85	11.9999
GCUG	chr6:54767279-54767565(+)$1	286	21	25	11.9999
GCUG	chr9:98390942-98391210(+)$1	268	247	251	11.9999
GCUG	chr19:4792248-4792540(-)$1	292	175	179	11.9999
GCUG	chr9:65194460-65194740(+)$1	280	76	80	11.9999
GCUG	chr3:96066811-96067101(-)$1	290	47	51	11.9999
GCUG	chr2:31615425-31615714(+)$1	289	64	68	11.9999
GCUG	chr9:107159264-107159531(-)$1	267	6	10	11.9999
GCUG	chr1:36501804-36502071(-)$1	267	157	161	11.9999
GCUG	chr13:69138020-69138287(-)$1	267	67	71	11.9999
GCUG	chr1:184398226-184398498(-)$1	272	134	138	11.9999
GCUG	chr6:56728722-56729000(-)$1	278	151	155	11.9999
GCUG	chr5:108863239-108863508(-)$1	269	261	265	11.9999
GCUG	chr19:29086354-29086632(+)$1	278	193	197	11.9999
GCUG	chr2:156606174-156606446(+)$1	272	137	141	11.9999
GCUG	chr1:181447930-181448215(-)$1	285	89	93	11.9999
GCUG	chr7:117008949-117009223(-)$1	274	81	85	11.9999
GCUG	chr8:63406007-63406293(-)$1	286	68	72	11.9999
GCUG	chr16:36049855-36050132(-)$1	277	118	122	11.9999
GCUG	chr4:151560213-151560493(+)$1	280	44	48	11.9999

#otherMatches

#Struct PSSM
%%%%	chr2:163884396-163884667(-)$1	271	45	49	11.9999
ffff	chr17:35119051-35119331(+)$1	280	136	140	11.9999
b]a]	chr18:60859088-60859368(-)$1	280	128	132	11.9999
:eee	chr9:44160509-44160780(-)$1	271	109	113	11.9999
ffff	chr2:32092881-32093158(+)$1	277	11	15	11.9999
GGGG	chr2:121205212-121205496(-)$1	284	13	17	11.9999
dddd	chr17:35292437-35292710(-)$1	273	128	132	11.9999
f::f	chr3:102703878-102704148(-)$1	270	137	141	11.9999
hhhh	chr2:91803321-91803605(-)$1	284	142	146	11.9999
eeee	chr8:95850590-95850858(-)$1	268	176	180	11.9999
CYYG	chr4:33125089-33125363(+)$1	274	262	266	11.9999
cc]d	chr10:126721767-126722035(-)$1	268	102	106	11.9999
DDDC	chr8:28383691-28383967(+)$1	276	1	5	11.9999
E{BB	chr17:6084525-6084794(+)$1	269	54	58	11.9999
bbnn	chr19:46681074-46681349(+)$1	275	0	4	11.9999
eee"	chrX:98514856-98515126(+)$1	270	18	22	11.9999
cccr	chr18:24743677-24743947(-)$1	270	81	85	11.9999
'''h	chr5:122096592-122096861(-)$1	269	20	24	11.9999
EEEE	chr1:93275018-93275289(-)$1	271	148	152	11.9999
eeee	chr2:34678076-34678352(-)$1	276	23	27	11.9999
lddd	chr19:7273750-7274023(-)$1	273	9	13	11.9999
dddd	chr3:51288320-51288589(+)$1	269	203	207	11.9999
iiii	chr7:135038927-135039193(-)$1	266	84	88	11.9999
dddd	chr15:76028312-76028598(-)$1	286	109	113	11.9999
!ddd	chr18:36908130-36908401(+)$1	271	46	50	11.9999
ggg+	chr14:70066969-70067240(+)$1	271	160	164	11.9999
ddd"	chr2:153142656-153142935(+)$1	279	79	83	11.9999
ff]b	chr11:87794792-87795066(-)$1	274	187	191	11.9999
abbg	chr5:75006662-75006928(-)$1	266	164	168	11.9999
DDDD	chr11:70466234-70466555(-)$1	321	77	81	11.9999
eee[	chr13:55651491-55651760(-)$1	269	144	148	11.9999
eenn	chr13:73773815-73774087(+)$1	272	120	124	11.9999
GGA{	chr17:32498259-32498531(-)$1	272	49	53	11.9999
FFFF	chr4:45372561-45372833(+)$1	272	178	182	11.9999
::CC	chr5:67078040-67078310(+)$1	270	43	47	11.9999
cc[g	chr5:93697524-93697801(+)$1	277	35	39	11.9999
hhh[	chr14:64225928-64226213(+)$1	285	169	173	11.9999
fffn	chr7:28151330-28151601(-)$1	271	101	105	11.9999
HHHc	chr11:120481937-120482225(-)$1	288	217	221	11.9999
ccll	chr8:74842835-74843118(+)$1	283	17	21	11.9999
BBKK	chr11:97574603-97574878(+)$1	275	33	37	11.9999
ffff	chr2:40774602-40774870(-)$1	268	140	144	11.9999
FFFF	chr3:108706705-108706973(-)$1	268	247	251	11.9999
eeee	chr7:27949815-27950086(-)$1	271	20	24	11.9999
eee!	chr1:77503123-77503392(-)$1	269	107	111	11.9999
qqqq	chr6:22240953-22241221(+)$1	268	102	106	11.9999
FFFF	chr3:95464619-95464902(+)$1	283	66	70	11.9999
geee	chr9:97269861-97270130(-)$1	269	63	67	11.9999
FFFF	chr9:37297061-37297336(+)$1	275	47	51	11.9999
eee[	chr19:5384494-5384777(-)$1	283	7	11	11.9999
lhhh	chr3:146444016-146444284(-)$1	268	49	53	11.9999
DDDD	chr14:52760734-52761005(+)$1	271	68	72	11.9999
:fff	chr8:86770442-86770710(-)$1	268	31	35	11.9999
eeeC	chr13:81930942-81931210(+)$1	268	130	134	11.9999
cc$$	chr8:23489738-23490016(-)$1	278	84	88	11.9999
GGGG	chr12:85733283-85733551(-)$1	268	5	9	11.9999
c22f	chr11:102978353-102978633(+)$1	280	91	95	11.9999
ccc]	chr5:92391556-92391827(-)$1	271	23	27	11.9999
GGGG	chr7:25670028-25670303(+)$1	275	9	13	11.9999
dddd	chr14:45912565-45912837(-)$1	272	76	80	11.9999
2ddd	chr9:3411339-3411620(+)$1	281	141	145	11.9999
::::	chr11:117828728-117829006(-)$1	278	88	92	11.9999
gggg	chr9:64825922-64826205(+)$1	283	38	42	11.9999
ffff	chr5:123244349-123244627(-)$1	278	128	132	11.9999
ppcc	chr3:154259844-154260111(-)$1	267	55	59	11.9999
eeee	chr2:174125804-174126076(+)$1	272	200	204	11.9999
g22a	chr19:5384549-5384817(-)$1	268	47	51	11.9999
====	chr4:155331122-155331424(+)$1	302	153	157	11.9999
c[cc	chr4:135883045-135883340(+)$1	295	168	172	11.9999
pppp	chr2:156359397-156359677(+)$1	280	149	153	11.9999
e[a[	chr13:24843895-24844178(-)$1	283	81	85	11.9999
JJJJ	chr6:54767279-54767565(+)$1	286	21	25	11.9999
EEEE	chr9:98390942-98391210(+)$1	268	247	251	11.9999
!ass	chr19:4792248-4792540(-)$1	292	175	179	11.9999
ffff	chr9:65194460-65194740(+)$1	280	76	80	11.9999
iii"	chr3:96066811-96067101(-)$1	290	47	51	11.9999
ii:c	chr2:31615425-31615714(+)$1	289	64	68	11.9999
:ddd	chr9:107159264-107159531(-)$1	267	6	10	11.9999
[ddd	chr1:36501804-36502071(-)$1	267	157	161	11.9999
[ddd	chr13:69138020-69138287(-)$1	267	67	71	11.9999
eeff	chr1:184398226-184398498(-)$1	272	134	138	11.9999
GGGG	chr6:56728722-56729000(-)$1	278	151	155	11.9999
E}EE	chr5:108863239-108863508(-)$1	269	261	265	11.9999
fFFF	chr19:29086354-29086632(+)$1	278	193	197	11.9999
::::	chr2:156606174-156606446(+)$1	272	137	141	11.9999
#bb[	chr1:181447930-181448215(-)$1	285	89	93	11.9999
bb[e	chr7:117008949-117009223(-)$1	274	81	85	11.9999
BBBB	chr8:63406007-63406293(-)$1	286	68	72	11.9999
mmmd	chr16:36049855-36050132(-)$1	277	118	122	11.9999
dCCC	chr4:151560213-151560493(+)$1	280	44	48	11.9999

#DB
....	chr2:163884396-163884667(-)$1	1	45	49	11.9999
))))	chr17:35119051-35119331(+)$1	1	136	140	11.9999
).).	chr18:60859088-60859368(-)$1	1	128	132	11.9999
.(((	chr9:44160509-44160780(-)$1	1	109	113	11.9999
((((	chr2:32092881-32093158(+)$1	1	11	15	11.9999
((((	chr2:121205212-121205496(-)$1	1	13	17	11.9999
))))	chr17:35292437-35292710(-)$1	1	128	132	11.9999
)..(	chr3:102703878-102704148(-)$1	1	137	141	11.9999
))))	chr2:91803321-91803605(-)$1	1	142	146	11.9999
((((	chr8:95850590-95850858(-)$1	1	176	180	11.9999
)..)	chr4:33125089-33125363(+)$1	1	262	266	11.9999
)).)	chr10:126721767-126722035(-)$1	1	102	106	11.9999
((((	chr8:28383691-28383967(+)$1	1	1	5	11.9999
(.((	chr17:6084525-6084794(+)$1	1	54	58	11.9999
((..	chr19:46681074-46681349(+)$1	1	0	4	11.9999
(((.	chrX:98514856-98515126(+)$1	1	18	22	11.9999
(((.	chr18:24743677-24743947(-)$1	1	81	85	11.9999
...(	chr5:122096592-122096861(-)$1	1	20	24	11.9999
((((	chr1:93275018-93275289(-)$1	1	148	152	11.9999
((((	chr2:34678076-34678352(-)$1	1	23	27	11.9999
.)))	chr19:7273750-7274023(-)$1	1	9	13	11.9999
((((	chr3:51288320-51288589(+)$1	1	203	207	11.9999
((((	chr7:135038927-135039193(-)$1	1	84	88	11.9999
))))	chr15:76028312-76028598(-)$1	1	109	113	11.9999
.(((	chr18:36908130-36908401(+)$1	1	46	50	11.9999
(((.	chr14:70066969-70067240(+)$1	1	160	164	11.9999
(((.	chr2:153142656-153142935(+)$1	1	79	83	11.9999
)).)	chr11:87794792-87795066(-)$1	1	187	191	11.9999
))))	chr5:75006662-75006928(-)$1	1	164	168	11.9999
((((	chr11:70466234-70466555(-)$1	1	77	81	11.9999
(((.	chr13:55651491-55651760(-)$1	1	144	148	11.9999
((..	chr13:73773815-73774087(+)$1	1	120	124	11.9999
(((.	chr17:32498259-32498531(-)$1	1	49	53	11.9999
))))	chr4:45372561-45372833(+)$1	1	178	182	11.9999
..((	chr5:67078040-67078310(+)$1	1	43	47	11.9999
((.(	chr5:93697524-93697801(+)$1	1	35	39	11.9999
(((.	chr14:64225928-64226213(+)$1	1	169	173	11.9999
(((.	chr7:28151330-28151601(-)$1	1	101	105	11.9999
)))(	chr11:120481937-120482225(-)$1	1	217	221	11.9999
((..	chr8:74842835-74843118(+)$1	1	17	21	11.9999
((..	chr11:97574603-97574878(+)$1	1	33	37	11.9999
((((	chr2:40774602-40774870(-)$1	1	140	144	11.9999
))))	chr3:108706705-108706973(-)$1	1	247	251	11.9999
((((	chr7:27949815-27950086(-)$1	1	20	24	11.9999
(((.	chr1:77503123-77503392(-)$1	1	107	111	11.9999
....	chr6:22240953-22241221(+)$1	1	102	106	11.9999
((((	chr3:95464619-95464902(+)$1	1	66	70	11.9999
))))	chr9:97269861-97270130(-)$1	1	63	67	11.9999
))))	chr9:37297061-37297336(+)$1	1	47	51	11.9999
(((.	chr19:5384494-5384777(-)$1	1	7	11	11.9999
.)))	chr3:146444016-146444284(-)$1	1	49	53	11.9999
((((	chr14:52760734-52761005(+)$1	1	68	72	11.9999
.(((	chr8:86770442-86770710(-)$1	1	31	35	11.9999
)))(	chr13:81930942-81931210(+)$1	1	130	134	11.9999
((..	chr8:23489738-23490016(-)$1	1	84	88	11.9999
((((	chr12:85733283-85733551(-)$1	1	5	9	11.9999
)..)	chr11:102978353-102978633(+)$1	1	91	95	11.9999
))).	chr5:92391556-92391827(-)$1	1	23	27	11.9999
((((	chr7:25670028-25670303(+)$1	1	9	13	11.9999
))))	chr14:45912565-45912837(-)$1	1	76	80	11.9999
.)))	chr9:3411339-3411620(+)$1	1	141	145	11.9999
....	chr11:117828728-117829006(-)$1	1	88	92	11.9999
((((	chr9:64825922-64826205(+)$1	1	38	42	11.9999
((((	chr5:123244349-123244627(-)$1	1	128	132	11.9999
..))	chr3:154259844-154260111(-)$1	1	55	59	11.9999
))))	chr2:174125804-174126076(+)$1	1	200	204	11.9999
)..)	chr19:5384549-5384817(-)$1	1	47	51	11.9999
((((	chr4:155331122-155331424(+)$1	1	153	157	11.9999
(.((	chr4:135883045-135883340(+)$1	1	168	172	11.9999
....	chr2:156359397-156359677(+)$1	1	149	153	11.9999
(.(.	chr13:24843895-24844178(-)$1	1	81	85	11.9999
((((	chr6:54767279-54767565(+)$1	1	21	25	11.9999
))))	chr9:98390942-98391210(+)$1	1	247	251	11.9999
.(..	chr19:4792248-4792540(-)$1	1	175	179	11.9999
))))	chr9:65194460-65194740(+)$1	1	76	80	11.9999
(((.	chr3:96066811-96067101(-)$1	1	47	51	11.9999
)).(	chr2:31615425-31615714(+)$1	1	64	68	11.9999
.(((	chr9:107159264-107159531(-)$1	1	6	10	11.9999
.(((	chr1:36501804-36502071(-)$1	1	157	161	11.9999
.(((	chr13:69138020-69138287(-)$1	1	67	71	11.9999
))))	chr1:184398226-184398498(-)$1	1	134	138	11.9999
((((	chr6:56728722-56729000(-)$1	1	151	155	11.9999
).))	chr5:108863239-108863508(-)$1	1	261	265	11.9999
))))	chr19:29086354-29086632(+)$1	1	193	197	11.9999
....	chr2:156606174-156606446(+)$1	1	137	141	11.9999
.((.	chr1:181447930-181448215(-)$1	1	89	93	11.9999
((.(	chr7:117008949-117009223(-)$1	1	81	85	11.9999
((((	chr8:63406007-63406293(-)$1	1	68	72	11.9999
...)	chr16:36049855-36050132(-)$1	1	118	122	11.9999
)(((	chr4:151560213-151560493(+)$1	1	44	48	11.9999

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

#score	1079.9999999999995
#seq	90
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_Ago2_Leung2011a_mm9_UTR_m2_run1.nuc.txt

#NT
GAGG	chr17:32498275-32498549(-)$1	274	50	54	12.0000
GAGG	chr15:80766809-80767079(+)$1	270	62	66	12.0000
GAGG	chr4:33125089-33125364(+)$1	275	115	119	12.0000
GAGG	chr19:5456361-5456634(-)$1	273	24	28	12.0000
GAGG	chr7:151775188-151775455(-)$1	267	69	73	12.0000
GAGG	chr5:67078040-67078309(+)$1	269	85	89	12.0000
GAGG	chr16:98014687-98014959(-)$1	272	73	77	12.0000
GAGG	chr3:108163839-108164128(+)$1	289	276	280	12.0000
GAGG	chr8:74842841-74843113(+)$1	272	204	208	12.0000
GAGG	chr1:181447940-181448228(-)$1	288	105	109	12.0000
GAGG	chr11:117828707-117828977(-)$1	270	126	130	12.0000
GAGG	chr11:79506341-79506633(+)$1	292	56	60	12.0000
GAGG	chr4:137798692-137798972(+)$1	280	130	134	12.0000
GAGG	chr6:30079454-30079729(+)$1	275	96	100	12.0000
GAGG	chr2:144232685-144232977(+)$1	292	236	240	12.0000
GAGG	chr11:114729900-114730186(+)$1	286	107	111	12.0000
GAGG	chr1:133921794-133922065(+)$1	271	13	17	12.0000
GAGG	chr15:89012664-89012935(-)$1	271	4	8	12.0000
GAGG	chr17:57032824-57033135(-)$1	311	39	43	12.0000
GAGG	chr17:35119075-35119345(+)$1	270	106	110	12.0000
GAGG	chr2:31615419-31615714(+)$1	295	33	37	12.0000
GAGG	chr2:173526976-173527252(+)$1	276	70	74	12.0000
GAGG	chr17:37209972-37210240(+)$1	268	17	21	12.0000
GAGG	chr7:30106085-30106361(-)$1	276	189	193	12.0000
GAGG	chr16:98170671-98170948(-)$1	277	132	136	12.0000
GAGG	chr16:98170644-98170921(-)$1	277	105	109	12.0000
gagg	chr7:16451276-16451548(-)$1	272	27	31	12.0000
GAGG	chr4:99324900-99325179(+)$1	279	138	142	12.0000
GAGG	chr12:113887155-113887428(+)$1	273	91	95	12.0000
GAGG	chr14:65431215-65431492(-)$1	277	112	116	12.0000
GAGG	chr19:45079711-45079992(-)$1	281	93	97	12.0000
GAGG	chr6:140599382-140599676(+)$1	294	96	100	12.0000
GAGG	chr15:101926280-101926567(+)$1	287	149	153	12.0000
GAGG	chr17:46305889-46306172(+)$1	283	246	250	12.0000
GAGG	chr16:92084361-92084635(+)$1	274	130	134	12.0000
GAGG	chr6:56728726-56729000(-)$1	274	81	85	12.0000
GAGG	chr15:81535366-81535658(-)$1	292	85	89	12.0000
GAGG	chr10:76508552-76508827(+)$1	275	63	67	12.0000
GAGG	chr3:145309905-145310179(-)$1	274	13	17	12.0000
GAGG	chr4:140669561-140669856(-)$1	295	76	80	12.0000
GAGG	chr15:81678793-81679067(-)$1	274	158	162	12.0000
GAGG	chr2:168780769-168781049(-)$1	280	70	74	12.0000
GAGG	chr8:125096545-125096859(+)$1	314	132	136	12.0000
GAGG	chr19:5664675-5664943(-)$1	268	67	71	12.0000
GAGG	chr5:93697524-93697808(+)$1	284	39	43	12.0000
GAGG	chr16:91227771-91228065(+)$1	294	82	86	12.0000
GAGG	chr15:79656085-79656364(-)$1	279	29	33	12.0000
GAGG	chr5:123807810-123808084(+)$1	274	136	140	12.0000
GAGG	chr17:6084557-6084835(+)$1	278	143	147	12.0000
GAGG	chr15:75831591-75831877(-)$1	286	170	174	12.0000
GAGG	chr2:31071139-31071426(+)$1	287	152	156	12.0000
GAGG	chr15:98734299-98734578(-)$1	279	130	134	12.0000
GAGG	chr14:71003925-71004195(-)$1	270	6	10	12.0000
GAGG	chr9:30881655-30881942(+)$1	287	172	176	12.0000
GAGG	chr3:122242260-122242557(-)$1	297	141	145	12.0000
GAGG	chr5:137967098-137967380(+)$1	282	15	19	12.0000
GAGG	chr19:24758574-24758850(-)$1	276	2	6	12.0000
GAGG	chr3:87340651-87340919(+)$1	268	61	65	12.0000
GAGG	chr5:137968786-137969068(+)$1	282	8	12	12.0000
GAGG	chr5:138223116-138223429(-)$1	313	165	169	12.0000
GAGG	chr19:8907655-8907942(+)$1	287	66	70	12.0000
GAGG	chr17:6084525-6084804(+)$1	279	175	179	12.0000
GAGG	chr15:79655049-79655353(-)$1	304	29	33	12.0000
GAGG	chrX:11614220-11614489(-)$1	269	137	141	12.0000
GAGG	chr15:75831563-75831841(-)$1	278	134	138	12.0000
GAGG	chr4:126421180-126421460(-)$1	280	6	10	12.0000
GAGG	chr7:107985033-107985335(+)$1	302	96	100	12.0000
GAGG	chr6:140543072-140543349(+)$1	277	133	137	12.0000
GAGG	chr13:5869145-5869421(+)$1	276	133	137	12.0000
GAGG	chr5:108863235-108863508(-)$1	273	64	68	12.0000
GAGG	chr4:49669033-49669321(+)$1	288	176	180	12.0000
GAGG	chrX:11614175-11614449(-)$1	274	97	101	12.0000
GAGG	chr11:87794777-87795061(-)$1	284	133	137	12.0000
GAGG	chr11:98015256-98015533(-)$1	277	234	238	12.0000
GAGG	chr17:37114860-37115135(-)$1	275	5	9	12.0000
GAGG	chr13:69138016-69138287(-)$1	271	123	127	12.0000
GAGG	chr5:137966809-137967086(+)$1	277	218	222	12.0000
GAGG	chr6:124998807-124999094(+)$1	287	48	52	12.0000
GAGG	chr19:46147231-46147507(+)$1	276	163	167	12.0000
GAGG	chr4:140884838-140885115(+)$1	277	6	10	12.0000
GAGG	chr7:152050685-152050968(+)$1	283	37	41	12.0000
GAGG	chr4:126924673-126924951(+)$1	278	15	19	12.0000
GAGG	chr3:90057072-90057343(+)$1	271	110	114	12.0000
GAGG	chr12:8798856-8799128(+)$1	272	43	47	12.0000
GAGG	chr11:53590397-53590671(+)$1	274	85	89	12.0000

#otherMatches

#Struct PSSM
ffff	chr15:80761843-80762129(+)$1	286	52	56	12.0000
HHHH	chr17:32498275-32498549(-)$1	274	50	54	12.0000
cccf	chr15:80766809-80767079(+)$1	270	62	66	12.0000
dddd	chr4:33125089-33125364(+)$1	275	115	119	12.0000
^^^^	chr19:5456361-5456634(-)$1	273	24	28	12.0000
mmmb	chr7:151775188-151775455(-)$1	267	69	73	12.0000
f[dd	chr5:67078040-67078309(+)$1	269	85	89	12.0000
gggo	chr16:98014687-98014959(-)$1	272	73	77	12.0000
nnnn	chr3:108163839-108164128(+)$1	289	276	280	12.0000
eeee	chr8:74842841-74843113(+)$1	272	204	208	12.0000
KKBB	chr1:181447940-181448228(-)$1	288	105	109	12.0000
YCCC	chr11:117828707-117828977(-)$1	270	126	130	12.0000
]ccc	chr11:79506341-79506633(+)$1	292	56	60	12.0000
iiii	chr4:137798692-137798972(+)$1	280	130	134	12.0000
eeee	chr6:30079454-30079729(+)$1	275	96	100	12.0000
7777	chr2:144232685-144232977(+)$1	292	236	240	12.0000
!!ee	chr11:114729900-114730186(+)$1	286	107	111	12.0000
"""i	chr1:133921794-133922065(+)$1	271	13	17	12.0000
:FFF	chr15:89012664-89012935(-)$1	271	4	8	12.0000
eeee	chr17:57032824-57033135(-)$1	311	39	43	12.0000
e]bb	chr17:35119075-35119345(+)$1	270	106	110	12.0000
EKKE	chr2:31615419-31615714(+)$1	295	33	37	12.0000
FFFc	chr2:173526976-173527252(+)$1	276	70	74	12.0000
GGGC	chr17:37209972-37210240(+)$1	268	17	21	12.0000
!aqq	chr7:30106085-30106361(-)$1	276	189	193	12.0000
iiii	chr16:98170671-98170948(-)$1	277	132	136	12.0000
iiii	chr16:98170644-98170921(-)$1	277	105	109	12.0000
ccc!	chr7:16451276-16451548(-)$1	272	27	31	12.0000
a22c	chr4:99324900-99325179(+)$1	279	138	142	12.0000
oooo	chr12:113887155-113887428(+)$1	273	91	95	12.0000
DD{A	chr14:65431215-65431492(-)$1	277	112	116	12.0000
:eee	chr19:45079711-45079992(-)$1	281	93	97	12.0000
====	chr6:140599382-140599676(+)$1	294	96	100	12.0000
ffff	chr15:101926280-101926567(+)$1	287	149	153	12.0000
ddee	chr17:46305889-46306172(+)$1	283	246	250	12.0000
ffff	chr16:92084361-92084635(+)$1	274	130	134	12.0000
oooo	chr6:56728726-56729000(-)$1	274	81	85	12.0000
c]dd	chr15:81535366-81535658(-)$1	292	85	89	12.0000
!fff	chr10:76508552-76508827(+)$1	275	63	67	12.0000
ffff	chr3:145309905-145310179(-)$1	274	13	17	12.0000
b[dd	chr4:140669561-140669856(-)$1	295	76	80	12.0000
JJJJ	chr15:81678793-81679067(-)$1	274	158	162	12.0000
hhhh	chr2:168780769-168781049(-)$1	280	70	74	12.0000
[bbc	chr8:125096545-125096859(+)$1	314	132	136	12.0000
GGGG	chr19:5664675-5664943(-)$1	268	67	71	12.0000
gggg	chr5:93697524-93697808(+)$1	284	39	43	12.0000
HHHd	chr16:91227771-91228065(+)$1	294	82	86	12.0000
mmme	chr15:79656085-79656364(-)$1	279	29	33	12.0000
hhhh	chr5:123807810-123808084(+)$1	274	136	140	12.0000
rrrr	chr17:6084557-6084835(+)$1	278	143	147	12.0000
d]dd	chr15:75831591-75831877(-)$1	286	170	174	12.0000
////	chr2:31071139-31071426(+)$1	287	152	156	12.0000
]bb]	chr15:98734299-98734578(-)$1	279	130	134	12.0000
DDDD	chr14:71003925-71004195(-)$1	270	6	10	12.0000
++++	chr9:30881655-30881942(+)$1	287	172	176	12.0000
gggg	chr3:122242260-122242557(-)$1	297	141	145	12.0000
mmcc	chr5:137967098-137967380(+)$1	282	15	19	12.0000
====	chr19:24758574-24758850(-)$1	276	2	6	12.0000
RRRR	chr3:87340651-87340919(+)$1	268	61	65	12.0000
iiii	chr5:137968786-137969068(+)$1	282	8	12	12.0000
====	chr5:138223116-138223429(-)$1	313	165	169	12.0000
iiii	chr19:8907655-8907942(+)$1	287	66	70	12.0000
rrrr	chr17:6084525-6084804(+)$1	279	175	179	12.0000
ffff	chr15:79655049-79655353(-)$1	304	29	33	12.0000
::::	chrX:11614220-11614489(-)$1	269	137	141	12.0000
a[cc	chr15:75831563-75831841(-)$1	278	134	138	12.0000
###h	chr4:126421180-126421460(-)$1	280	6	10	12.0000
fff:	chr7:107985033-107985335(+)$1	302	96	100	12.0000
b!!a	chr6:140543072-140543349(+)$1	277	133	137	12.0000
cccm	chr13:5869145-5869421(+)$1	276	133	137	12.0000
gggg	chr5:108863235-108863508(-)$1	273	64	68	12.0000
ee[b	chr4:49669033-49669321(+)$1	288	176	180	12.0000
C{CC	chrX:11614175-11614449(-)$1	274	97	101	12.0000
dd33	chr11:87794777-87795061(-)$1	284	133	137	12.0000
dddd	chr11:98015256-98015533(-)$1	277	234	238	12.0000
DDDD	chr17:37114860-37115135(-)$1	275	5	9	12.0000
555e	chr13:69138016-69138287(-)$1	271	123	127	12.0000
:CCC	chr5:137966809-137967086(+)$1	277	218	222	12.0000
====	chr6:124998807-124999094(+)$1	287	48	52	12.0000
eeef	chr19:46147231-46147507(+)$1	276	163	167	12.0000
hhhh	chr4:140884838-140885115(+)$1	277	6	10	12.0000
hhhh	chr7:152050685-152050968(+)$1	283	37	41	12.0000
HH{C	chr4:126924673-126924951(+)$1	278	15	19	12.0000
====	chr3:90057072-90057343(+)$1	271	110	114	12.0000
gggg	chr12:8798856-8799128(+)$1	272	43	47	12.0000
ffff	chr11:53590397-53590671(+)$1	274	85	89	12.0000

#DB
))))	chr15:80761843-80762129(+)$1	1	52	56	12.0000
((((	chr17:32498275-32498549(-)$1	1	50	54	12.0000
)))(	chr15:80766809-80767079(+)$1	1	62	66	12.0000
))))	chr4:33125089-33125364(+)$1	1	115	119	12.0000
....	chr19:5456361-5456634(-)$1	1	24	28	12.0000
...)	chr7:151775188-151775455(-)$1	1	69	73	12.0000
(.((	chr5:67078040-67078309(+)$1	1	85	89	12.0000
(((.	chr16:98014687-98014959(-)$1	1	73	77	12.0000
....	chr3:108163839-108164128(+)$1	1	276	280	12.0000
))))	chr8:74842841-74843113(+)$1	1	204	208	12.0000
..((	chr1:181447940-181448228(-)$1	1	105	109	12.0000
.)))	chr11:117828707-117828977(-)$1	1	126	130	12.0000
.)))	chr11:79506341-79506633(+)$1	1	56	60	12.0000
))))	chr4:137798692-137798972(+)$1	1	130	134	12.0000
))))	chr6:30079454-30079729(+)$1	1	96	100	12.0000
....	chr2:144232685-144232977(+)$1	1	236	240	12.0000
..((	chr11:114729900-114730186(+)$1	1	107	111	12.0000
...(	chr1:133921794-133922065(+)$1	1	13	17	12.0000
.(((	chr15:89012664-89012935(-)$1	1	4	8	12.0000
))))	chr17:57032824-57033135(-)$1	1	39	43	12.0000
).))	chr17:35119075-35119345(+)$1	1	106	110	12.0000
(..(	chr2:31615419-31615714(+)$1	1	33	37	12.0000
((((	chr2:173526976-173527252(+)$1	1	70	74	12.0000
((((	chr17:37209972-37210240(+)$1	1	17	21	12.0000
.(..	chr7:30106085-30106361(-)$1	1	189	193	12.0000
))))	chr16:98170671-98170948(-)$1	1	132	136	12.0000
))))	chr16:98170644-98170921(-)$1	1	105	109	12.0000
(((.	chr7:16451276-16451548(-)$1	1	27	31	12.0000
)..)	chr4:99324900-99325179(+)$1	1	138	142	12.0000
....	chr12:113887155-113887428(+)$1	1	91	95	12.0000
((.(	chr14:65431215-65431492(-)$1	1	112	116	12.0000
.(((	chr19:45079711-45079992(-)$1	1	93	97	12.0000
))))	chr6:140599382-140599676(+)$1	1	96	100	12.0000
((((	chr15:101926280-101926567(+)$1	1	149	153	12.0000
((((	chr17:46305889-46306172(+)$1	1	246	250	12.0000
))))	chr16:92084361-92084635(+)$1	1	130	134	12.0000
....	chr6:56728726-56729000(-)$1	1	81	85	12.0000
).))	chr15:81535366-81535658(-)$1	1	85	89	12.0000
.(((	chr10:76508552-76508827(+)$1	1	63	67	12.0000
))))	chr3:145309905-145310179(-)$1	1	13	17	12.0000
(.((	chr4:140669561-140669856(-)$1	1	76	80	12.0000
))))	chr15:81678793-81679067(-)$1	1	158	162	12.0000
))))	chr2:168780769-168781049(-)$1	1	70	74	12.0000
.(((	chr8:125096545-125096859(+)$1	1	132	136	12.0000
))))	chr19:5664675-5664943(-)$1	1	67	71	12.0000
((((	chr5:93697524-93697808(+)$1	1	39	43	12.0000
((((	chr16:91227771-91228065(+)$1	1	82	86	12.0000
...)	chr15:79656085-79656364(-)$1	1	29	33	12.0000
((((	chr5:123807810-123808084(+)$1	1	136	140	12.0000
....	chr17:6084557-6084835(+)$1	1	143	147	12.0000
).))	chr15:75831591-75831877(-)$1	1	170	174	12.0000
....	chr2:31071139-31071426(+)$1	1	152	156	12.0000
.)).	chr15:98734299-98734578(-)$1	1	130	134	12.0000
((((	chr14:71003925-71004195(-)$1	1	6	10	12.0000
....	chr9:30881655-30881942(+)$1	1	172	176	12.0000
))))	chr3:122242260-122242557(-)$1	1	141	145	12.0000
..))	chr5:137967098-137967380(+)$1	1	15	19	12.0000
((((	chr19:24758574-24758850(-)$1	1	2	6	12.0000
....	chr3:87340651-87340919(+)$1	1	61	65	12.0000
((((	chr5:137968786-137969068(+)$1	1	8	12	12.0000
))))	chr5:138223116-138223429(-)$1	1	165	169	12.0000
))))	chr19:8907655-8907942(+)$1	1	66	70	12.0000
....	chr17:6084525-6084804(+)$1	1	175	179	12.0000
((((	chr15:79655049-79655353(-)$1	1	29	33	12.0000
....	chrX:11614220-11614489(-)$1	1	137	141	12.0000
(.((	chr15:75831563-75831841(-)$1	1	134	138	12.0000
...(	chr4:126421180-126421460(-)$1	1	6	10	12.0000
))).	chr7:107985033-107985335(+)$1	1	96	100	12.0000
(..(	chr6:140543072-140543349(+)$1	1	133	137	12.0000
(((.	chr13:5869145-5869421(+)$1	1	133	137	12.0000
((((	chr5:108863235-108863508(-)$1	1	64	68	12.0000
((.(	chr4:49669033-49669321(+)$1	1	176	180	12.0000
(.((	chrX:11614175-11614449(-)$1	1	97	101	12.0000
))..	chr11:87794777-87795061(-)$1	1	133	137	12.0000
((((	chr11:98015256-98015533(-)$1	1	234	238	12.0000
((((	chr17:37114860-37115135(-)$1	1	5	9	12.0000
...)	chr13:69138016-69138287(-)$1	1	123	127	12.0000
.)))	chr5:137966809-137967086(+)$1	1	218	222	12.0000
))))	chr6:124998807-124999094(+)$1	1	48	52	12.0000
)))(	chr19:46147231-46147507(+)$1	1	163	167	12.0000
((((	chr4:140884838-140885115(+)$1	1	6	10	12.0000
))))	chr7:152050685-152050968(+)$1	1	37	41	12.0000
((.(	chr4:126924673-126924951(+)$1	1	15	19	12.0000
((((	chr3:90057072-90057343(+)$1	1	110	114	12.0000
))))	chr12:8798856-8799128(+)$1	1	43	47	12.0000
))))	chr11:53590397-53590671(+)$1	1	85	89	12.0000

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

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000