
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m1_run1.nuc.txt

#NT
uuua	chr1:204520014-204520254(+)$1	240	43	47	12.0000
UUUA	chr8:86194253-86194478(+)$1	225	159	163	12.0000
UUUA	chr11:71712912-71713338(+)$1	426	406	410	12.0000
uuua	chr14:100606174-100606432(+)$1	258	57	61	12.0000
UUUA	chr20:57604797-57605036(-)$1	239	67	71	12.0000
uuua	chr19:9761907-9762145(-)$1	238	72	76	12.0000
UUUA	chr16:69737262-69737635(+)$1	373	0	4	12.0000
UUUA	chr11:65622497-65622745(-)$1	248	230	234	12.0000
UUUA	chr16:11771482-11771714(+)$1	232	62	66	12.0000
UUUA	chr17:4850278-4850563(-)$1	285	150	154	12.0000
UUUA	chr11:108029067-108029334(-)$1	267	118	122	12.0000
uuua	chr5:81569584-81569827(-)$1	243	18	22	12.0000
UUUA	chr3:37029409-37029652(-)$1	243	29	33	12.0000
UUUA	chr18:32720524-32720780(+)$1	256	143	147	12.0000
UUUA	chr12:393224-393457(-)$1	233	38	42	12.0000
UUUA	chr2:69696423-69696648(-)$1	225	128	132	12.0000
UUUA	chr2:128521544-128521791(-)$1	247	36	40	12.0000
UUUA	chr2:27884627-27884858(-)$1	231	40	44	12.0000
uuua	chr11:61089958-61090255(-)$1	297	36	40	12.0000
UUUA	chr3:194998144-194998380(-)$1	236	27	31	12.0000
uuua	chr3:183890902-183891217(+)$1	315	141	145	12.0000
UUUA	chr3:178741778-178742018(-)$1	240	182	186	12.0000
UUUA	chr4:122735586-122735835(+)$1	249	21	25	12.0000
uuua	chr5:158712076-158712343(+)$1	267	2	6	12.0000
UUUA	chr7:104746928-104747159(+)$1	231	41	45	12.0000
UUUA	chr14:31915166-31915391(-)$1	225	93	97	12.0000
UUUA	chr3:9426899-9427120(+)$1	221	6	10	12.0000
UUUA	chr11:94230293-94230528(+)$1	235	5	9	12.0000
UUUA	chr9:125866170-125866418(+)$1	248	154	158	12.0000
UUUA	chr15:78887444-78887675(+)$1	231	4	8	12.0000
UUUA	chr16:24229722-24229970(+)$1	248	169	173	12.0000
UUUA	chr8:38177455-38177724(-)$1	269	2	6	12.0000
UUUA	chr17:45760777-45761031(+)$1	254	2	6	12.0000
UUUA	chr1:63903687-63903917(+)$1	230	26	30	12.0000
uuua	chr8:43056465-43056714(+)$1	249	151	155	12.0000
UUUA	chr19:15918757-15918977(-)$1	220	20	24	12.0000
UUUA	chr19:16551480-16551720(-)$1	240	210	214	12.0000
uuua	chr4:1947527-1947755(+)$1	228	132	136	12.0000
UUUA	chr10:7390038-7390284(-)$1	246	171	175	12.0000
UUUA	chr15:63557620-63557848(+)$1	228	37	41	12.0000
UUUA	chrX:118752430-118752759(-)$1	329	65	69	12.0000
UUUA	chr19:32975024-32975256(+)$1	232	18	22	12.0000
UUUA	chr12:110475882-110476161(+)$1	279	77	81	12.0000
UUUA	chr4:114375350-114375573(-)$1	223	77	81	12.0000
UUUA	chr20:5975401-5975676(+)$1	275	244	248	12.0000
UUUA	chr7:99172627-99172891(+)$1	264	51	55	12.0000
UUUA	chr5:142602541-142602811(+)$1	270	13	17	12.0000
UUUA	chr5:56190394-56190627(+)$1	233	29	33	12.0000
UUUA	chr2:174773590-174773854(-)$1	264	26	30	12.0000
UUUA	chr5:137906729-137907000(-)$1	271	165	169	12.0000
UUUA	chr2:238673456-238673717(+)$1	261	10	14	12.0000
UUUA	chr7:139788140-139788403(-)$1	263	32	36	12.0000
UUUA	chr2:179368592-179368822(+)$1	230	123	127	12.0000
UUUA	chr9:123941323-123941552(-)$1	229	54	58	12.0000
UUUA	chr9:85860972-85861193(-)$1	221	187	191	12.0000
UUUA	chrX:19934736-19934971(-)$1	235	146	150	12.0000
UUUA	chr12:15067224-15067499(-)$1	275	53	57	12.0000
UUUA	chr5:111066218-111066454(-)$1	236	7	11	12.0000
UUUA	chr8:104083310-104083551(+)$1	241	187	191	12.0000
UUUA	chr5:39106411-39106663(-)$1	252	25	29	12.0000
UUUA	chr19:37118479-37118723(+)$1	244	56	60	12.0000
UUUA	chr17:40673237-40673456(+)$1	219	30	34	12.0000
UUUA	chr4:40245851-40246138(+)$1	287	42	46	12.0000
UUUA	chrX:56311736-56311981(+)$1	245	71	75	12.0000
UUUA	chr11:125646782-125647024(-)$1	242	28	32	12.0000
UUUA	chr5:79773135-79773367(+)$1	232	9	13	12.0000
UUUA	chr1:22051349-22051581(-)$1	232	149	153	12.0000
UUUA	chr2:143995065-143995376(+)$1	311	95	99	12.0000
UUUA	chr2:228421521-228421765(+)$1	244	156	160	12.0000
UUUA	chr22:38169756-38170164(+)$1	408	311	315	12.0000
UUUA	chr9:88161367-88161612(-)$1	245	9	13	12.0000
UUUA	chrX:135956451-135956742(-)$1	291	6	10	12.0000
UUUA	chrX:74523641-74523878(+)$1	237	73	77	12.0000
UUUA	chr22:21242451-21242750(+)$1	299	132	136	12.0000
UUUA	chr3:169505522-169505775(+)$1	253	0	4	12.0000
UUUA	chr12:22838752-22838972(+)$1	220	41	45	12.0000
UUUA	chr7:106850261-106850552(-)$1	291	142	146	12.0000
uuua	chrX:71686769-71687020(-)$1	251	6	10	12.0000
uuua	chr11:108165806-108166088(+)$1	282	91	95	12.0000
UUUA	chr7:129471300-129471552(-)$1	252	52	56	12.0000
UUUA	chr7:100276512-100276750(+)$1	238	207	211	12.0000
UUUA	chr1:206636663-206636903(+)$1	240	116	120	12.0000
UUUA	chr1:21102170-21102478(-)$1	308	40	44	12.0000
uuua	chr12:58196509-58196740(+)$1	231	74	78	12.0000
UUUA	chr10:89727037-89727281(+)$1	244	13	17	12.0000

#otherMatches

#Struct PSSM
ffff	chr7:107259643-107259873(+)$1	230	125	129	12.0000
^^^^	chr1:204520014-204520254(+)$1	240	43	47	12.0000
cc^^	chr8:86194253-86194478(+)$1	225	159	163	12.0000
~~~~	chr11:71712912-71713338(+)$1	426	406	410	12.0000
dd00	chr14:100606174-100606432(+)$1	258	57	61	12.0000
::::	chr20:57604797-57605036(-)$1	239	67	71	12.0000
oooo	chr19:9761907-9762145(-)$1	238	72	76	12.0000
::::	chr16:69737262-69737635(+)$1	373	0	4	12.0000
::::	chr11:65622497-65622745(-)$1	248	230	234	12.0000
::::	chr16:11771482-11771714(+)$1	232	62	66	12.0000
::::	chr17:4850278-4850563(-)$1	285	150	154	12.0000
dd::	chr11:108029067-108029334(-)$1	267	118	122	12.0000
DDKK	chr5:81569584-81569827(-)$1	243	18	22	12.0000
ffff	chr3:37029409-37029652(-)$1	243	29	33	12.0000
wwww	chr18:32720524-32720780(+)$1	256	143	147	12.0000
::::	chr12:393224-393457(-)$1	233	38	42	12.0000
oooo	chr2:69696423-69696648(-)$1	225	128	132	12.0000
::::	chr2:128521544-128521791(-)$1	247	36	40	12.0000
ffoo	chr2:27884627-27884858(-)$1	231	40	44	12.0000
eee[	chr11:61089958-61090255(-)$1	297	36	40	12.0000
IIII	chr3:194998144-194998380(-)$1	236	27	31	12.0000
PPPP	chr3:183890902-183891217(+)$1	315	141	145	12.0000
:::G	chr3:178741778-178742018(-)$1	240	182	186	12.0000
HHH:	chr4:122735586-122735835(+)$1	249	21	25	12.0000
::::	chr5:158712076-158712343(+)$1	267	2	6	12.0000
c!!b	chr7:104746928-104747159(+)$1	231	41	45	12.0000
c===	chr14:31915166-31915391(-)$1	225	93	97	12.0000
gggg	chr3:9426899-9427120(+)$1	221	6	10	12.0000
FNNN	chr11:94230293-94230528(+)$1	235	5	9	12.0000
oddd	chr9:125866170-125866418(+)$1	248	154	158	12.0000
::::	chr15:78887444-78887675(+)$1	231	4	8	12.0000
tttt	chr16:24229722-24229970(+)$1	248	169	173	12.0000
::::	chr8:38177455-38177724(-)$1	269	2	6	12.0000
::DD	chr17:45760777-45761031(+)$1	254	2	6	12.0000
MMMM	chr1:63903687-63903917(+)$1	230	26	30	12.0000
::::	chr8:43056465-43056714(+)$1	249	151	155	12.0000
ee::	chr19:15918757-15918977(-)$1	220	20	24	12.0000
FFFF	chr19:16551480-16551720(-)$1	240	210	214	12.0000
dd[e	chr4:1947527-1947755(+)$1	228	132	136	12.0000
ff::	chr10:7390038-7390284(-)$1	246	171	175	12.0000
h[dd	chr15:63557620-63557848(+)$1	228	37	41	12.0000
ffff	chrX:118752430-118752759(-)$1	329	65	69	12.0000
##bb	chr19:32975024-32975256(+)$1	232	18	22	12.0000
llff	chr12:110475882-110476161(+)$1	279	77	81	12.0000
c!!c	chr4:114375350-114375573(-)$1	223	77	81	12.0000
eeee	chr20:5975401-5975676(+)$1	275	244	248	12.0000
EDDD	chr7:99172627-99172891(+)$1	264	51	55	12.0000
ddd:	chr5:142602541-142602811(+)$1	270	13	17	12.0000
gggm	chr5:56190394-56190627(+)$1	233	29	33	12.0000
KKFF	chr2:174773590-174773854(-)$1	264	26	30	12.0000
HHHH	chr5:137906729-137907000(-)$1	271	165	169	12.0000
C{DD	chr2:238673456-238673717(+)$1	261	10	14	12.0000
::::	chr7:139788140-139788403(-)$1	263	32	36	12.0000
iiii	chr2:179368592-179368822(+)$1	230	123	127	12.0000
mmmd	chr9:123941323-123941552(-)$1	229	54	58	12.0000
C:::	chr9:85860972-85861193(-)$1	221	187	191	12.0000
""bb	chrX:19934736-19934971(-)$1	235	146	150	12.0000
::::	chr12:15067224-15067499(-)$1	275	53	57	12.0000
::::	chr5:111066218-111066454(-)$1	236	7	11	12.0000
::::	chr8:104083310-104083551(+)$1	241	187	191	12.0000
ffff	chr5:39106411-39106663(-)$1	252	25	29	12.0000
::::	chr19:37118479-37118723(+)$1	244	56	60	12.0000
rrgg	chr17:40673237-40673456(+)$1	219	30	34	12.0000
cccf	chr4:40245851-40246138(+)$1	287	42	46	12.0000
ffff	chrX:56311736-56311981(+)$1	245	71	75	12.0000
#ggg	chr11:125646782-125647024(-)$1	242	28	32	12.0000
fnnn	chr5:79773135-79773367(+)$1	232	9	13	12.0000
JJJJ	chr1:22051349-22051581(-)$1	232	149	153	12.0000
::::	chr2:143995065-143995376(+)$1	311	95	99	12.0000
h::e	chr2:228421521-228421765(+)$1	244	156	160	12.0000
::HH	chr22:38169756-38170164(+)$1	408	311	315	12.0000
GGGG	chr9:88161367-88161612(-)$1	245	9	13	12.0000
::::	chrX:135956451-135956742(-)$1	291	6	10	12.0000
ddd]	chrX:74523641-74523878(+)$1	237	73	77	12.0000
c###	chr22:21242451-21242750(+)$1	299	132	136	12.0000
::::	chr3:169505522-169505775(+)$1	253	0	4	12.0000
]ccc	chr12:22838752-22838972(+)$1	220	41	45	12.0000
::::	chr7:106850261-106850552(-)$1	291	142	146	12.0000
:EEE	chrX:71686769-71687020(-)$1	251	6	10	12.0000
+fff	chr11:108165806-108166088(+)$1	282	91	95	12.0000
ddd$	chr7:129471300-129471552(-)$1	252	52	56	12.0000
GGG~	chr7:100276512-100276750(+)$1	238	207	211	12.0000
::::	chr1:206636663-206636903(+)$1	240	116	120	12.0000
::::	chr1:21102170-21102478(-)$1	308	40	44	12.0000
ccqq	chr12:58196509-58196740(+)$1	231	74	78	12.0000
!ccc	chr10:89727037-89727281(+)$1	244	13	17	12.0000

#DB
))))	chr7:107259643-107259873(+)$1	1	125	129	12.0000
....	chr1:204520014-204520254(+)$1	1	43	47	12.0000
((..	chr8:86194253-86194478(+)$1	1	159	163	12.0000
....	chr11:71712912-71713338(+)$1	1	406	410	12.0000
))..	chr14:100606174-100606432(+)$1	1	57	61	12.0000
....	chr20:57604797-57605036(-)$1	1	67	71	12.0000
....	chr19:9761907-9762145(-)$1	1	72	76	12.0000
....	chr16:69737262-69737635(+)$1	1	0	4	12.0000
....	chr11:65622497-65622745(-)$1	1	230	234	12.0000
....	chr16:11771482-11771714(+)$1	1	62	66	12.0000
....	chr17:4850278-4850563(-)$1	1	150	154	12.0000
))..	chr11:108029067-108029334(-)$1	1	118	122	12.0000
((..	chr5:81569584-81569827(-)$1	1	18	22	12.0000
((((	chr3:37029409-37029652(-)$1	1	29	33	12.0000
....	chr18:32720524-32720780(+)$1	1	143	147	12.0000
....	chr12:393224-393457(-)$1	1	38	42	12.0000
....	chr2:69696423-69696648(-)$1	1	128	132	12.0000
....	chr2:128521544-128521791(-)$1	1	36	40	12.0000
((..	chr2:27884627-27884858(-)$1	1	40	44	12.0000
(((.	chr11:61089958-61090255(-)$1	1	36	40	12.0000
((((	chr3:194998144-194998380(-)$1	1	27	31	12.0000
....	chr3:183890902-183891217(+)$1	1	141	145	12.0000
...)	chr3:178741778-178742018(-)$1	1	182	186	12.0000
(((.	chr4:122735586-122735835(+)$1	1	21	25	12.0000
....	chr5:158712076-158712343(+)$1	1	2	6	12.0000
(..(	chr7:104746928-104747159(+)$1	1	41	45	12.0000
))))	chr14:31915166-31915391(-)$1	1	93	97	12.0000
((((	chr3:9426899-9427120(+)$1	1	6	10	12.0000
(...	chr11:94230293-94230528(+)$1	1	5	9	12.0000
.)))	chr9:125866170-125866418(+)$1	1	154	158	12.0000
....	chr15:78887444-78887675(+)$1	1	4	8	12.0000
....	chr16:24229722-24229970(+)$1	1	169	173	12.0000
....	chr8:38177455-38177724(-)$1	1	2	6	12.0000
..((	chr17:45760777-45761031(+)$1	1	2	6	12.0000
....	chr1:63903687-63903917(+)$1	1	26	30	12.0000
....	chr8:43056465-43056714(+)$1	1	151	155	12.0000
))..	chr19:15918757-15918977(-)$1	1	20	24	12.0000
))))	chr19:16551480-16551720(-)$1	1	210	214	12.0000
((.(	chr4:1947527-1947755(+)$1	1	132	136	12.0000
))..	chr10:7390038-7390284(-)$1	1	171	175	12.0000
(.((	chr15:63557620-63557848(+)$1	1	37	41	12.0000
))))	chrX:118752430-118752759(-)$1	1	65	69	12.0000
..((	chr19:32975024-32975256(+)$1	1	18	22	12.0000
..))	chr12:110475882-110476161(+)$1	1	77	81	12.0000
(..(	chr4:114375350-114375573(-)$1	1	77	81	12.0000
))))	chr20:5975401-5975676(+)$1	1	244	248	12.0000
((((	chr7:99172627-99172891(+)$1	1	51	55	12.0000
))).	chr5:142602541-142602811(+)$1	1	13	17	12.0000
(((.	chr5:56190394-56190627(+)$1	1	29	33	12.0000
..((	chr2:174773590-174773854(-)$1	1	26	30	12.0000
))))	chr5:137906729-137907000(-)$1	1	165	169	12.0000
(.((	chr2:238673456-238673717(+)$1	1	10	14	12.0000
....	chr7:139788140-139788403(-)$1	1	32	36	12.0000
((((	chr2:179368592-179368822(+)$1	1	123	127	12.0000
...)	chr9:123941323-123941552(-)$1	1	54	58	12.0000
)...	chr9:85860972-85861193(-)$1	1	187	191	12.0000
..((	chrX:19934736-19934971(-)$1	1	146	150	12.0000
....	chr12:15067224-15067499(-)$1	1	53	57	12.0000
....	chr5:111066218-111066454(-)$1	1	7	11	12.0000
....	chr8:104083310-104083551(+)$1	1	187	191	12.0000
((((	chr5:39106411-39106663(-)$1	1	25	29	12.0000
....	chr19:37118479-37118723(+)$1	1	56	60	12.0000
..))	chr17:40673237-40673456(+)$1	1	30	34	12.0000
))))	chr4:40245851-40246138(+)$1	1	42	46	12.0000
))))	chrX:56311736-56311981(+)$1	1	71	75	12.0000
.(((	chr11:125646782-125647024(-)$1	1	28	32	12.0000
(...	chr5:79773135-79773367(+)$1	1	9	13	12.0000
))))	chr1:22051349-22051581(-)$1	1	149	153	12.0000
....	chr2:143995065-143995376(+)$1	1	95	99	12.0000
)..(	chr2:228421521-228421765(+)$1	1	156	160	12.0000
..))	chr22:38169756-38170164(+)$1	1	311	315	12.0000
((((	chr9:88161367-88161612(-)$1	1	9	13	12.0000
....	chrX:135956451-135956742(-)$1	1	6	10	12.0000
))).	chrX:74523641-74523878(+)$1	1	73	77	12.0000
(...	chr22:21242451-21242750(+)$1	1	132	136	12.0000
....	chr3:169505522-169505775(+)$1	1	0	4	12.0000
.)))	chr12:22838752-22838972(+)$1	1	41	45	12.0000
....	chr7:106850261-106850552(-)$1	1	142	146	12.0000
.(((	chrX:71686769-71687020(-)$1	1	6	10	12.0000
.(((	chr11:108165806-108166088(+)$1	1	91	95	12.0000
(((.	chr7:129471300-129471552(-)$1	1	52	56	12.0000
))).	chr7:100276512-100276750(+)$1	1	207	211	12.0000
....	chr1:206636663-206636903(+)$1	1	116	120	12.0000
....	chr1:21102170-21102478(-)$1	1	40	44	12.0000
((..	chr12:58196509-58196740(+)$1	1	74	78	12.0000
.(((	chr10:89727037-89727281(+)$1	1	13	17	12.0000

#PSSM
U : 0.86	u : 0.13	
U : 0.86	u : 0.13	
U : 0.86	u : 0.13	
A : 0.86	a : 0.13	

#score	1032.0000000000002
#seq	86
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m2_run1.nuc.txt

#NT
CCU	chr11:62038498-62038713(+)$1	215	58	61	9.0000
CCU	chrX:135956452-135956742(-)$1	290	13	16	9.0000
CCU	chr11:8009159-8009484(+)$1	325	38	41	9.0000
CCU	chr9:131455901-131456116(+)$1	215	94	97	9.0000
CCU	chr1:19446710-19447010(-)$1	300	80	83	9.0000
CCu	chr2:24905886-24906097(+)$1	211	160	163	9.0000
CCU	chr14:94780682-94780901(-)$1	219	29	32	9.0000
CCU	chrX:53574618-53574949(-)$1	331	38	41	9.0000
CCU	chr20:23347612-23347859(+)$1	247	46	49	9.0000
CCU	chr12:110937240-110937476(-)$1	236	74	77	9.0000
CCU	chr16:75203752-75203969(+)$1	217	17	20	9.0000
CCU	chr3:49201238-49201457(-)$1	219	7	10	9.0000
CCU	chr12:40651014-40651230(+)$1	216	72	75	9.0000
CCU	chr2:103335032-103335252(-)$1	220	30	33	9.0000
CCU	chr12:49666218-49666567(+)$1	349	5	8	9.0000
CCU	chr12:44166737-44166952(+)$1	215	187	190	9.0000
CCU	chr17:72205271-72205521(+)$1	250	33	36	9.0000
CCU	chr5:178392516-178392727(+)$1	211	35	38	9.0000
CCU	chr1:100586886-100587120(-)$1	234	61	64	9.0000
CCU	chr14:74086024-74086235(+)$1	211	42	45	9.0000
CCU	chr11:82595764-82595985(-)$1	221	12	15	9.0000
CCU	chrX:154113467-154113682(+)$1	215	21	24	9.0000
CCU	chr5:71491766-71491980(+)$1	214	39	42	9.0000
CCU	chr7:17382507-17382740(+)$1	233	145	148	9.0000
CCU	chr2:220412468-220412683(+)$1	215	8	11	9.0000
CCU	chr8:25343227-25343441(+)$1	214	36	39	9.0000
CCU	chr11:33047475-33047691(+)$1	216	19	22	9.0000
CCU	chr19:18649100-18649322(-)$1	222	2	5	9.0000
CCU	chr2:152463965-152464189(-)$1	224	45	48	9.0000
CCU	chr2:127956924-127957143(-)$1	219	113	116	9.0000
CCU	chr5:153857413-153857643(-)$1	230	80	83	9.0000
CCU	chr4:39474641-39474857(+)$1	216	96	99	9.0000
CCU	chr21:47423292-47423511(+)$1	219	21	24	9.0000
CCU	chr1:40524981-40525194(+)$1	213	87	90	9.0000
CCU	chr16:630810-631023(+)$1	213	25	28	9.0000
CCU	chr22:41545841-41546204(+)$1	363	10	13	9.0000
CCU	chr11:118968511-118968734(-)$1	223	10	13	9.0000
CCU	chr4:89363497-89363725(+)$1	228	15	18	9.0000
CCU	chr14:103803419-103803664(+)$1	245	76	79	9.0000
CCU	chr6:7581154-7581368(+)$1	214	31	34	9.0000
CCU	chr21:48071588-48071894(+)$1	306	20	23	9.0000
CCU	chr5:134690701-134690942(-)$1	241	21	24	9.0000
CCU	chr16:89777186-89777435(-)$1	249	2	5	9.0000
CCU	chrX:103042703-103042915(+)$1	212	36	39	9.0000
CCU	chr5:64103471-64103717(+)$1	246	53	56	9.0000
CCU	chr17:33884090-33884309(-)$1	219	17	20	9.0000
CCU	chr6:149700157-149700400(+)$1	243	46	49	9.0000
CCU	chr16:30200171-30200481(+)$1	310	126	129	9.0000
CCU	chr6:132891369-132891581(+)$1	212	31	34	9.0000
CCU	chr11:118764329-118764545(+)$1	216	12	15	9.0000
CCU	chr1:52249549-52249764(+)$1	215	43	46	9.0000
CCU	chr22:22890923-22891139(-)$1	216	8	11	9.0000
CCU	chr1:14108139-14108371(+)$1	232	20	23	9.0000
CCU	chr11:57509531-57509745(+)$1	214	49	52	9.0000
CCU	chr2:128522122-128522358(-)$1	236	75	78	9.0000
CCU	chr15:92690208-92690423(+)$1	215	25	28	9.0000
CCU	chr7:135304228-135304448(+)$1	220	13	16	9.0000
CCU	chr5:126860338-126860613(+)$1	275	6	9	9.0000
CCU	chr1:161332125-161332381(+)$1	256	1	4	9.0000
CCU	chrX:135429408-135429623(+)$1	215	1	4	9.0000
CCU	chr11:5221277-5221504(-)$1	227	5	8	9.0000
CCU	chr4:1018949-1019253(+)$1	304	72	75	9.0000
ccU	chr5:35014083-35014303(-)$1	220	21	24	9.0000
CCU	chr17:62496646-62496891(-)$1	245	38	41	9.0000
CCU	chr16:22545315-22545631(+)$1	316	12	15	9.0000
CCU	chr2:70392149-70392369(-)$1	220	27	30	9.0000
CCU	chr5:118582702-118582920(+)$1	218	3	6	9.0000
CCU	chr16:75203603-75203814(+)$1	211	63	66	9.0000
CCU	chr12:29493975-29494226(-)$1	251	1	4	9.0000
CCU	chr1:228584340-228584607(-)$1	267	4	7	9.0000
CCU	chr19:58213340-58213559(-)$1	219	0	3	9.0000
CCU	chr1:70697741-70697987(+)$1	246	217	220	9.0000
CCU	chr15:35274040-35274260(-)$1	220	50	53	9.0000
CCU	chr16:3119217-3119651(+)$1	434	0	3	9.0000
CCU	chr22:24125613-24125830(+)$1	217	9	12	9.0000
CCU	chr21:26959948-26960201(-)$1	253	117	120	9.0000
CCU	chr18:34376861-34377098(-)$1	237	6	9	9.0000
CCU	chr12:112843630-112843890(-)$1	260	15	18	9.0000
CCU	chr6:32083391-32083639(-)$1	248	2	5	9.0000
CCU	chr8:99053886-99054148(-)$1	262	121	124	9.0000
CCU	chr10:17278204-17278448(+)$1	244	71	74	9.0000
CCU	chr1:155448231-155448531(-)$1	300	23	26	9.0000
CCU	chr10:43089167-43089488(-)$1	321	203	206	9.0000
CCU	chr19:56089629-56089844(-)$1	215	32	35	9.0000
CCU	chr20:49509437-49509680(-)$1	243	53	56	9.0000
CCU	chr12:49522397-49522676(-)$1	279	28	31	9.0000
CCU	chr2:61021086-61021310(+)$1	224	1	4	9.0000
CCU	chr19:12016601-12016816(+)$1	215	39	42	9.0000
CCU	chr6:45514600-45514844(+)$1	244	18	21	9.0000
CCU	chr15:50884575-50884801(-)$1	226	89	92	9.0000
CCU	chr16:22546084-22546353(+)$1	269	0	3	9.0000
CCU	chr3:129233133-129233350(+)$1	217	16	19	9.0000
CCU	chr11:72403711-72404038(-)$1	327	19	22	9.0000
CCU	chr17:42474927-42475305(-)$1	378	43	46	9.0000
CCU	chr12:58140359-58140573(+)$1	214	101	104	9.0000
CCU	chr9:135554375-135554589(+)$1	214	81	84	9.0000
CCU	chr8:117671051-117671280(-)$1	229	42	45	9.0000
CCU	chr6:29141999-29142212(+)$1	213	9	12	9.0000
CCU	chr10:86273281-86273527(+)$1	246	115	118	9.0000

#otherMatches

#Struct PSSM
ccb	chr11:62286892-62287140(-)$1	248	6	9	9.0000
yhh	chr11:62038498-62038713(+)$1	215	58	61	9.0000
BBL	chrX:135956452-135956742(-)$1	290	13	16	9.0000
ee]	chr11:8009159-8009484(+)$1	325	38	41	9.0000
2gg	chr9:131455901-131456116(+)$1	215	94	97	9.0000
EEE	chr1:19446710-19447010(-)$1	300	80	83	9.0000
GGG	chr2:24905886-24906097(+)$1	211	160	163	9.0000
EEd	chr14:94780682-94780901(-)$1	219	29	32	9.0000
:::	chrX:53574618-53574949(-)$1	331	38	41	9.0000
mmd	chr20:23347612-23347859(+)$1	247	46	49	9.0000
c::	chr12:110937240-110937476(-)$1	236	74	77	9.0000
Ecc	chr16:75203752-75203969(+)$1	217	17	20	9.0000
:::	chr3:49201238-49201457(-)$1	219	7	10	9.0000
ccc	chr12:40651014-40651230(+)$1	216	72	75	9.0000
xxx	chr2:103335032-103335252(-)$1	220	30	33	9.0000
E::	chr12:49666218-49666567(+)$1	349	5	8	9.0000
DDD	chr12:44166737-44166952(+)$1	215	187	190	9.0000
ccc	chr17:72205271-72205521(+)$1	250	33	36	9.0000
occ	chr5:178392516-178392727(+)$1	211	35	38	9.0000
cc[	chr1:100586886-100587120(-)$1	234	61	64	9.0000
EE:	chr14:74086024-74086235(+)$1	211	42	45	9.0000
xxx	chr11:82595764-82595985(-)$1	221	12	15	9.0000
ddd	chrX:154113467-154113682(+)$1	215	21	24	9.0000
abb	chr5:71491766-71491980(+)$1	214	39	42	9.0000
:::	chr7:17382507-17382740(+)$1	233	145	148	9.0000
cc$	chr2:220412468-220412683(+)$1	215	8	11	9.0000
ggg	chr8:25343227-25343441(+)$1	214	36	39	9.0000
:dd	chr11:33047475-33047691(+)$1	216	19	22	9.0000
CEE	chr19:18649100-18649322(-)$1	222	2	5	9.0000
CC:	chr2:152463965-152464189(-)$1	224	45	48	9.0000
eee	chr2:127956924-127957143(-)$1	219	113	116	9.0000
lle	chr5:153857413-153857643(-)$1	230	80	83	9.0000
]dd	chr4:39474641-39474857(+)$1	216	96	99	9.0000
WWW	chr21:47423292-47423511(+)$1	219	21	24	9.0000
===	chr1:40524981-40525194(+)$1	213	87	90	9.0000
!bb	chr16:630810-631023(+)$1	213	25	28	9.0000
:::	chr22:41545841-41546204(+)$1	363	10	13	9.0000
nnn	chr11:118968511-118968734(-)$1	223	10	13	9.0000
HHH	chr4:89363497-89363725(+)$1	228	15	18	9.0000
ddl	chr14:103803419-103803664(+)$1	245	76	79	9.0000
ddd	chr6:7581154-7581368(+)$1	214	31	34	9.0000
ff:	chr21:48071588-48071894(+)$1	306	20	23	9.0000
NNN	chr5:134690701-134690942(-)$1	241	21	24	9.0000
:::	chr16:89777186-89777435(-)$1	249	2	5	9.0000
EEE	chrX:103042703-103042915(+)$1	212	36	39	9.0000
e66	chr5:64103471-64103717(+)$1	246	53	56	9.0000
obb	chr17:33884090-33884309(-)$1	219	17	20	9.0000
ddd	chr6:149700157-149700400(+)$1	243	46	49	9.0000
eee	chr16:30200171-30200481(+)$1	310	126	129	9.0000
eee	chr6:132891369-132891581(+)$1	212	31	34	9.0000
CKK	chr11:118764329-118764545(+)$1	216	12	15	9.0000
epp	chr1:52249549-52249764(+)$1	215	43	46	9.0000
{DD	chr22:22890923-22891139(-)$1	216	8	11	9.0000
nnn	chr1:14108139-14108371(+)$1	232	20	23	9.0000
ooo	chr11:57509531-57509745(+)$1	214	49	52	9.0000
==:	chr2:128522122-128522358(-)$1	236	75	78	9.0000
EEM	chr15:92690208-92690423(+)$1	215	25	28	9.0000
ttt	chr7:135304228-135304448(+)$1	220	13	16	9.0000
:::	chr5:126860338-126860613(+)$1	275	6	9	9.0000
::d	chr1:161332125-161332381(+)$1	256	1	4	9.0000
:::	chrX:135429408-135429623(+)$1	215	1	4	9.0000
:cc	chr11:5221277-5221504(-)$1	227	5	8	9.0000
:::	chr4:1018949-1019253(+)$1	304	72	75	9.0000
eee	chr5:35014083-35014303(-)$1	220	21	24	9.0000
:::	chr17:62496646-62496891(-)$1	245	38	41	9.0000
fam	chr16:22545315-22545631(+)$1	316	12	15	9.0000
III	chr2:70392149-70392369(-)$1	220	27	30	9.0000
:::	chr5:118582702-118582920(+)$1	218	3	6	9.0000
88e	chr16:75203603-75203814(+)$1	211	63	66	9.0000
::H	chr12:29493975-29494226(-)$1	251	1	4	9.0000
!ee	chr1:228584340-228584607(-)$1	267	4	7	9.0000
eee	chr19:58213340-58213559(-)$1	219	0	3	9.0000
EEE	chr1:70697741-70697987(+)$1	246	217	220	9.0000
ee[	chr15:35274040-35274260(-)$1	220	50	53	9.0000
:hh	chr16:3119217-3119651(+)$1	434	0	3	9.0000
'''	chr22:24125613-24125830(+)$1	217	9	12	9.0000
^^^	chr21:26959948-26960201(-)$1	253	117	120	9.0000
:::	chr18:34376861-34377098(-)$1	237	6	9	9.0000
QCC	chr12:112843630-112843890(-)$1	260	15	18	9.0000
GGG	chr6:32083391-32083639(-)$1	248	2	5	9.0000
nff	chr8:99053886-99054148(-)$1	262	121	124	9.0000
ggg	chr10:17278204-17278448(+)$1	244	71	74	9.0000
:::	chr1:155448231-155448531(-)$1	300	23	26	9.0000
qqq	chr10:43089167-43089488(-)$1	321	203	206	9.0000
MMM	chr19:56089629-56089844(-)$1	215	32	35	9.0000
eed	chr20:49509437-49509680(-)$1	243	53	56	9.0000
[bb	chr12:49522397-49522676(-)$1	279	28	31	9.0000
:::	chr2:61021086-61021310(+)$1	224	1	4	9.0000
occ	chr19:12016601-12016816(+)$1	215	39	42	9.0000
qqq	chr6:45514600-45514844(+)$1	244	18	21	9.0000
[cc	chr15:50884575-50884801(-)$1	226	89	92	9.0000
:::	chr16:22546084-22546353(+)$1	269	0	3	9.0000
d!!	chr3:129233133-129233350(+)$1	217	16	19	9.0000
e::	chr11:72403711-72404038(-)$1	327	19	22	9.0000
:::	chr17:42474927-42475305(-)$1	378	43	46	9.0000
QBB	chr12:58140359-58140573(+)$1	214	101	104	9.0000
ddd	chr9:135554375-135554589(+)$1	214	81	84	9.0000
:::	chr8:117671051-117671280(-)$1	229	42	45	9.0000
&&&	chr6:29141999-29142212(+)$1	213	9	12	9.0000
___	chr10:86273281-86273527(+)$1	246	115	118	9.0000

#DB
(((	chr11:62286892-62287140(-)$1	1	6	9	9.0000
.))	chr11:62038498-62038713(+)$1	1	58	61	9.0000
((.	chrX:135956452-135956742(-)$1	1	13	16	9.0000
)).	chr11:8009159-8009484(+)$1	1	38	41	9.0000
.))	chr9:131455901-131456116(+)$1	1	94	97	9.0000
(((	chr1:19446710-19447010(-)$1	1	80	83	9.0000
)))	chr2:24905886-24906097(+)$1	1	160	163	9.0000
(((	chr14:94780682-94780901(-)$1	1	29	32	9.0000
...	chrX:53574618-53574949(-)$1	1	38	41	9.0000
..)	chr20:23347612-23347859(+)$1	1	46	49	9.0000
)..	chr12:110937240-110937476(-)$1	1	74	77	9.0000
(((	chr16:75203752-75203969(+)$1	1	17	20	9.0000
...	chr3:49201238-49201457(-)$1	1	7	10	9.0000
)))	chr12:40651014-40651230(+)$1	1	72	75	9.0000
...	chr2:103335032-103335252(-)$1	1	30	33	9.0000
(..	chr12:49666218-49666567(+)$1	1	5	8	9.0000
)))	chr12:44166737-44166952(+)$1	1	187	190	9.0000
(((	chr17:72205271-72205521(+)$1	1	33	36	9.0000
.))	chr5:178392516-178392727(+)$1	1	35	38	9.0000
((.	chr1:100586886-100587120(-)$1	1	61	64	9.0000
((.	chr14:74086024-74086235(+)$1	1	42	45	9.0000
...	chr11:82595764-82595985(-)$1	1	12	15	9.0000
(((	chrX:154113467-154113682(+)$1	1	21	24	9.0000
)))	chr5:71491766-71491980(+)$1	1	39	42	9.0000
...	chr7:17382507-17382740(+)$1	1	145	148	9.0000
((.	chr2:220412468-220412683(+)$1	1	8	11	9.0000
(((	chr8:25343227-25343441(+)$1	1	36	39	9.0000
.((	chr11:33047475-33047691(+)$1	1	19	22	9.0000
(((	chr19:18649100-18649322(-)$1	1	2	5	9.0000
((.	chr2:152463965-152464189(-)$1	1	45	48	9.0000
)))	chr2:127956924-127957143(-)$1	1	113	116	9.0000
..)	chr5:153857413-153857643(-)$1	1	80	83	9.0000
.))	chr4:39474641-39474857(+)$1	1	96	99	9.0000
...	chr21:47423292-47423511(+)$1	1	21	24	9.0000
)))	chr1:40524981-40525194(+)$1	1	87	90	9.0000
.((	chr16:630810-631023(+)$1	1	25	28	9.0000
...	chr22:41545841-41546204(+)$1	1	10	13	9.0000
...	chr11:118968511-118968734(-)$1	1	10	13	9.0000
(((	chr4:89363497-89363725(+)$1	1	15	18	9.0000
((.	chr14:103803419-103803664(+)$1	1	76	79	9.0000
(((	chr6:7581154-7581368(+)$1	1	31	34	9.0000
)).	chr21:48071588-48071894(+)$1	1	20	23	9.0000
...	chr5:134690701-134690942(-)$1	1	21	24	9.0000
...	chr16:89777186-89777435(-)$1	1	2	5	9.0000
(((	chrX:103042703-103042915(+)$1	1	36	39	9.0000
)..	chr5:64103471-64103717(+)$1	1	53	56	9.0000
.))	chr17:33884090-33884309(-)$1	1	17	20	9.0000
(((	chr6:149700157-149700400(+)$1	1	46	49	9.0000
)))	chr16:30200171-30200481(+)$1	1	126	129	9.0000
)))	chr6:132891369-132891581(+)$1	1	31	34	9.0000
(..	chr11:118764329-118764545(+)$1	1	12	15	9.0000
(..	chr1:52249549-52249764(+)$1	1	43	46	9.0000
.((	chr22:22890923-22891139(-)$1	1	8	11	9.0000
...	chr1:14108139-14108371(+)$1	1	20	23	9.0000
...	chr11:57509531-57509745(+)$1	1	49	52	9.0000
)).	chr2:128522122-128522358(-)$1	1	75	78	9.0000
((.	chr15:92690208-92690423(+)$1	1	25	28	9.0000
...	chr7:135304228-135304448(+)$1	1	13	16	9.0000
...	chr5:126860338-126860613(+)$1	1	6	9	9.0000
..(	chr1:161332125-161332381(+)$1	1	1	4	9.0000
...	chrX:135429408-135429623(+)$1	1	1	4	9.0000
.((	chr11:5221277-5221504(-)$1	1	5	8	9.0000
...	chr4:1018949-1019253(+)$1	1	72	75	9.0000
(((	chr5:35014083-35014303(-)$1	1	21	24	9.0000
...	chr17:62496646-62496891(-)$1	1	38	41	9.0000
((.	chr16:22545315-22545631(+)$1	1	12	15	9.0000
(((	chr2:70392149-70392369(-)$1	1	27	30	9.0000
...	chr5:118582702-118582920(+)$1	1	3	6	9.0000
..)	chr16:75203603-75203814(+)$1	1	63	66	9.0000
..(	chr12:29493975-29494226(-)$1	1	1	4	9.0000
.((	chr1:228584340-228584607(-)$1	1	4	7	9.0000
(((	chr19:58213340-58213559(-)$1	1	0	3	9.0000
)))	chr1:70697741-70697987(+)$1	1	217	220	9.0000
((.	chr15:35274040-35274260(-)$1	1	50	53	9.0000
.((	chr16:3119217-3119651(+)$1	1	0	3	9.0000
...	chr22:24125613-24125830(+)$1	1	9	12	9.0000
...	chr21:26959948-26960201(-)$1	1	117	120	9.0000
...	chr18:34376861-34377098(-)$1	1	6	9	9.0000
.((	chr12:112843630-112843890(-)$1	1	15	18	9.0000
(((	chr6:32083391-32083639(-)$1	1	2	5	9.0000
.))	chr8:99053886-99054148(-)$1	1	121	124	9.0000
(((	chr10:17278204-17278448(+)$1	1	71	74	9.0000
...	chr1:155448231-155448531(-)$1	1	23	26	9.0000
...	chr10:43089167-43089488(-)$1	1	203	206	9.0000
...	chr19:56089629-56089844(-)$1	1	32	35	9.0000
))(	chr20:49509437-49509680(-)$1	1	53	56	9.0000
.((	chr12:49522397-49522676(-)$1	1	28	31	9.0000
...	chr2:61021086-61021310(+)$1	1	1	4	9.0000
.))	chr19:12016601-12016816(+)$1	1	39	42	9.0000
...	chr6:45514600-45514844(+)$1	1	18	21	9.0000
.((	chr15:50884575-50884801(-)$1	1	89	92	9.0000
...	chr16:22546084-22546353(+)$1	1	0	3	9.0000
(..	chr3:129233133-129233350(+)$1	1	16	19	9.0000
)..	chr11:72403711-72404038(-)$1	1	19	22	9.0000
...	chr17:42474927-42475305(-)$1	1	43	46	9.0000
.((	chr12:58140359-58140573(+)$1	1	101	104	9.0000
)))	chr9:135554375-135554589(+)$1	1	81	84	9.0000
...	chr8:117671051-117671280(-)$1	1	42	45	9.0000
...	chr6:29141999-29142212(+)$1	1	9	12	9.0000
...	chr10:86273281-86273527(+)$1	1	115	118	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m1_run1.nuc.txt

#NT
UGAAA	chrX:40570310-40570561(+)$1	251	118	123	15.0000
UGAAA	chr8:104709334-104709603(+)$1	269	199	204	15.0000
UGAAA	chr1:94012376-94012665(+)$1	289	39	44	15.0000
UGAAA	chr1:182845213-182845515(+)$1	302	87	92	15.0000
UGAAA	chr1:205696689-205696939(+)$1	250	1	6	15.0000
UGAAA	chr7:27839530-27839841(+)$1	311	105	110	15.0000
UGAAA	chr2:196573369-196573635(+)$1	266	110	115	15.0000
UGAAA	chr4:77941642-77941987(+)$1	345	19	24	15.0000
UGAAA	chr6:64394506-64394931(+)$1	425	289	294	15.0000
UGAAA	chr6:4037646-4037943(+)$1	297	17	22	15.0000
UGAAA	chr1:237540609-237540895(+)$1	286	113	118	15.0000
UGAAA	chr5:162902486-162902758(+)$1	272	111	116	15.0000
UGAAA	chr17:78286747-78287154(+)$1	407	84	89	15.0000
UGAAA	chrX:147013934-147014223(+)$1	289	282	287	15.0000
UGAAA	chr6:33414308-33414701(+)$1	393	74	79	15.0000
UGAAA	chr15:69718342-69718659(+)$1	317	140	145	15.0000
UGAAA	chr8:30361783-30362071(+)$1	288	36	41	15.0000
UGAAA	chr9:37126753-37127010(+)$1	257	166	171	15.0000
UGAAA	chr19:1418167-1418428(+)$1	261	89	94	15.0000
UGAAA	chr17:4796636-4796906(+)$1	270	105	110	15.0000
UGAAA	chr16:24551800-24552133(+)$1	333	262	267	15.0000
UGAAA	chr17:48818964-48819268(+)$1	304	163	168	15.0000
UGAAA	chrX:16850670-16851001(+)$1	331	167	172	15.0000
UGAAA	chr6:111306180-111306483(+)$1	303	85	90	15.0000
UGAAA	chr17:38317956-38318289(+)$1	333	95	100	15.0000
UGAAA	chr22:19468406-19468661(+)$1	255	49	54	15.0000
UGAAA	chr10:70096908-70097235(+)$1	327	83	88	15.0000
UGAAA	chr5:151176790-151177093(+)$1	303	81	86	15.0000
UGAAA	chr8:1824718-1824988(+)$1	270	19	24	15.0000
UGAAA	chr5:149755302-149755555(+)$1	253	79	84	15.0000
UGAAA	chr16:53288371-53288628(+)$1	257	81	86	15.0000
UGAAA	chr8:42260822-42261081(+)$1	259	60	65	15.0000
UGAAA	chr16:1810377-1810722(+)$1	345	149	154	15.0000
UGAAA	chrX:123195004-123195336(+)$1	332	127	132	15.0000
UGAAA	chr1:23383921-23384241(+)$1	320	47	52	15.0000
UGAAA	chr6:144795736-144795986(+)$1	250	14	19	15.0000
UGAAA	chr14:62203564-62203898(+)$1	334	119	124	15.0000
UGAAA	chr5:132424693-132425008(+)$1	315	35	40	15.0000
ugaaa	chr12:67692717-67693046(+)$1	329	114	119	15.0000
UGAAA	chr1:40535793-40536063(+)$1	270	83	88	15.0000
UGAAA	chr10:70525601-70525996(+)$1	395	24	29	15.0000
UGAAA	chr7:27831619-27831875(+)$1	256	168	173	15.0000
UGAAA	chr6:4044034-4044363(+)$1	329	181	186	15.0000
UGAAA	chr9:112898546-112898881(+)$1	335	279	284	15.0000
UGAAA	chr13:20580533-20580893(+)$1	360	238	243	15.0000
UGAAA	chr9:72895643-72895922(+)$1	279	81	86	15.0000
UGAAA	chr1:39494382-39494745(+)$1	363	121	126	15.0000
UGAAA	chr20:57480347-57480688(+)$1	341	244	249	15.0000
UGAAA	chr19:30503249-30503521(+)$1	272	35	40	15.0000
UGAAA	chr12:99109165-99109415(+)$1	250	155	160	15.0000
UGAAA	chr17:73237594-73237862(+)$1	268	184	189	15.0000

#otherMatches

#Struct PSSM
wwwww	chr1:39853418-39853722(+)$1	304	161	166	15.0000
:::::	chrX:40570310-40570561(+)$1	251	118	123	15.0000
ddd55	chr8:104709334-104709603(+)$1	269	199	204	15.0000
DDDDK	chr1:94012376-94012665(+)$1	289	39	44	15.0000
gggnn	chr1:182845213-182845515(+)$1	302	87	92	15.0000
:::ee	chr1:205696689-205696939(+)$1	250	1	6	15.0000
EEEEE	chr7:27839530-27839841(+)$1	311	105	110	15.0000
e22==	chr2:196573369-196573635(+)$1	266	110	115	15.0000
&&fff	chr4:77941642-77941987(+)$1	345	19	24	15.0000
c:::G	chr6:64394506-64394931(+)$1	425	289	294	15.0000
GGGGG	chr6:4037646-4037943(+)$1	297	17	22	15.0000
&&&&f	chr1:237540609-237540895(+)$1	286	113	118	15.0000
b5555	chr5:162902486-162902758(+)$1	272	111	116	15.0000
FF::f	chr17:78286747-78287154(+)$1	407	84	89	15.0000
GGG::	chrX:147013934-147014223(+)$1	289	282	287	15.0000
e::::	chr6:33414308-33414701(+)$1	393	74	79	15.0000
hhh77	chr15:69718342-69718659(+)$1	317	140	145	15.0000
ceeee	chr8:30361783-30362071(+)$1	288	36	41	15.0000
ddd!!	chr9:37126753-37127010(+)$1	257	166	171	15.0000
ooooo	chr19:1418167-1418428(+)$1	261	89	94	15.0000
FF::d	chr17:4796636-4796906(+)$1	270	105	110	15.0000
dllld	chr16:24551800-24552133(+)$1	333	262	267	15.0000
dddd:	chr17:48818964-48819268(+)$1	304	163	168	15.0000
ffnnn	chrX:16850670-16851001(+)$1	331	167	172	15.0000
:::::	chr6:111306180-111306483(+)$1	303	85	90	15.0000
ccmmm	chr17:38317956-38318289(+)$1	333	95	100	15.0000
=====	chr22:19468406-19468661(+)$1	255	49	54	15.0000
iiiii	chr10:70096908-70097235(+)$1	327	83	88	15.0000
dd999	chr5:151176790-151177093(+)$1	303	81	86	15.0000
eeeem	chr8:1824718-1824988(+)$1	270	19	24	15.0000
dmmmm	chr5:149755302-149755555(+)$1	253	79	84	15.0000
lllff	chr16:53288371-53288628(+)$1	257	81	86	15.0000
ppppp	chr8:42260822-42261081(+)$1	259	60	65	15.0000
:::::	chr16:1810377-1810722(+)$1	345	149	154	15.0000
CFFFF	chrX:123195004-123195336(+)$1	332	127	132	15.0000
e%%%%	chr1:23383921-23384241(+)$1	320	47	52	15.0000
ccc""	chr6:144795736-144795986(+)$1	250	14	19	15.0000
dddd3	chr14:62203564-62203898(+)$1	334	119	124	15.0000
:::::	chr5:132424693-132425008(+)$1	315	35	40	15.0000
ddd:F	chr12:67692717-67693046(+)$1	329	114	119	15.0000
:::::	chr1:40535793-40536063(+)$1	270	83	88	15.0000
uuggg	chr10:70525601-70525996(+)$1	395	24	29	15.0000
:::::	chr7:27831619-27831875(+)$1	256	168	173	15.0000
e::::	chr6:4044034-4044363(+)$1	329	181	186	15.0000
ff:::	chr9:112898546-112898881(+)$1	335	279	284	15.0000
iiiii	chr13:20580533-20580893(+)$1	360	238	243	15.0000
e$$$$	chr9:72895643-72895922(+)$1	279	81	86	15.0000
cc333	chr1:39494382-39494745(+)$1	363	121	126	15.0000
qqqqq	chr20:57480347-57480688(+)$1	341	244	249	15.0000
bmmmm	chr19:30503249-30503521(+)$1	272	35	40	15.0000
}DDDD	chr12:99109165-99109415(+)$1	250	155	160	15.0000
5ccc]	chr17:73237594-73237862(+)$1	268	184	189	15.0000

#DB
.....	chr1:39853418-39853722(+)$1	1	161	166	15.0000
.....	chrX:40570310-40570561(+)$1	1	118	123	15.0000
)))..	chr8:104709334-104709603(+)$1	1	199	204	15.0000
((((.	chr1:94012376-94012665(+)$1	1	39	44	15.0000
(((..	chr1:182845213-182845515(+)$1	1	87	92	15.0000
...((	chr1:205696689-205696939(+)$1	1	1	6	15.0000
)))))	chr7:27839530-27839841(+)$1	1	105	110	15.0000
)..))	chr2:196573369-196573635(+)$1	1	110	115	15.0000
..(((	chr4:77941642-77941987(+)$1	1	19	24	15.0000
)...)	chr6:64394506-64394931(+)$1	1	289	294	15.0000
(((((	chr6:4037646-4037943(+)$1	1	17	22	15.0000
....(	chr1:237540609-237540895(+)$1	1	113	118	15.0000
)....	chr5:162902486-162902758(+)$1	1	111	116	15.0000
((..(	chr17:78286747-78287154(+)$1	1	84	89	15.0000
)))..	chrX:147013934-147014223(+)$1	1	282	287	15.0000
)....	chr6:33414308-33414701(+)$1	1	74	79	15.0000
)))..	chr15:69718342-69718659(+)$1	1	140	145	15.0000
)))))	chr8:30361783-30362071(+)$1	1	36	41	15.0000
(((..	chr9:37126753-37127010(+)$1	1	166	171	15.0000
.....	chr19:1418167-1418428(+)$1	1	89	94	15.0000
((..(	chr17:4796636-4796906(+)$1	1	105	110	15.0000
(...)	chr16:24551800-24552133(+)$1	1	262	267	15.0000
)))).	chr17:48818964-48819268(+)$1	1	163	168	15.0000
((...	chrX:16850670-16851001(+)$1	1	167	172	15.0000
.....	chr6:111306180-111306483(+)$1	1	85	90	15.0000
((...	chr17:38317956-38318289(+)$1	1	95	100	15.0000
)))))	chr22:19468406-19468661(+)$1	1	49	54	15.0000
)))))	chr10:70096908-70097235(+)$1	1	83	88	15.0000
))...	chr5:151176790-151177093(+)$1	1	81	86	15.0000
((((.	chr8:1824718-1824988(+)$1	1	19	24	15.0000
(....	chr5:149755302-149755555(+)$1	1	79	84	15.0000
...))	chr16:53288371-53288628(+)$1	1	81	86	15.0000
.....	chr8:42260822-42261081(+)$1	1	60	65	15.0000
.....	chr16:1810377-1810722(+)$1	1	149	154	15.0000
)))))	chrX:123195004-123195336(+)$1	1	127	132	15.0000
(....	chr1:23383921-23384241(+)$1	1	47	52	15.0000
(((..	chr6:144795736-144795986(+)$1	1	14	19	15.0000
)))).	chr14:62203564-62203898(+)$1	1	119	124	15.0000
.....	chr5:132424693-132425008(+)$1	1	35	40	15.0000
))).(	chr12:67692717-67693046(+)$1	1	114	119	15.0000
.....	chr1:40535793-40536063(+)$1	1	83	88	15.0000
..)))	chr10:70525601-70525996(+)$1	1	24	29	15.0000
.....	chr7:27831619-27831875(+)$1	1	168	173	15.0000
)....	chr6:4044034-4044363(+)$1	1	181	186	15.0000
))...	chr9:112898546-112898881(+)$1	1	279	284	15.0000
(((((	chr13:20580533-20580893(+)$1	1	238	243	15.0000
(....	chr9:72895643-72895922(+)$1	1	81	86	15.0000
))...	chr1:39494382-39494745(+)$1	1	121	126	15.0000
.....	chr20:57480347-57480688(+)$1	1	244	249	15.0000
(....	chr19:30503249-30503521(+)$1	1	35	40	15.0000
.))))	chr12:99109165-99109415(+)$1	1	155	160	15.0000
.))).	chr17:73237594-73237862(+)$1	1	184	189	15.0000

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

#score	780.0000000000001
#seq	52
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m1_run2.nuc.txt

#NT
GAAACCA	chr15:40917172-40917408(+)$1	236	180	187	11.9803
AAAAUCA	chr5:169291327-169291588(+)$1	261	120	127	12.5686
AAACCCA	chr3:152058228-152058528(+)$1	300	189	196	12.6666
UAAACCA	chr16:46694343-46694590(-)$1	247	43	50	11.8823
AAAACCU	chr10:43088413-43088737(-)$1	324	185	192	13.0588
AAAAUCA	chr2:86361810-86362071(+)$1	261	110	117	12.5686
AAACCCA	chr5:176396162-176396418(-)$1	256	8	15	12.6666
GAAACCA	chr6:28121505-28121981(+)$1	476	331	338	11.9803
AAAACUA	chr1:24297606-24297886(-)$1	280	75	82	12.5686
AAACCCA	chr7:64167156-64167416(+)$1	260	81	88	12.6666
AAAACCU	chr9:95609830-95610067(-)$1	237	57	64	13.0588
AAAACCU	chr3:184429053-184429274(-)$1	221	111	118	13.0588
AAAACAA	chr18:23615625-23615921(-)$1	296	266	273	12.4705
AAAUCCA	chr17:62496567-62496918(-)$1	351	305	312	12.8627
AAAGCCA	chr2:24260830-24261071(-)$1	241	34	41	12.3725
AAAACCU	chr10:38345174-38345413(+)$1	239	198	205	13.0588
AAAACUA	chr13:37596307-37596652(-)$1	345	92	99	12.5686
aaaucca	chr4:99952702-99952954(+)$1	252	73	80	12.8627
AAAACUA	chr12:29493969-29494205(-)$1	236	11	18	12.5686
AAAACCU	chr1:111494643-111494881(-)$1	238	128	135	13.0588
AAAACUA	chr5:38950124-38950393(-)$1	269	227	234	12.5686
AAAUCCA	chr4:148554834-148555088(+)$1	254	41	48	12.8627
AACACCA	chr2:38976210-38976435(-)$1	225	199	206	11.6862
AAAACAA	chr17:65882157-65882425(+)$1	268	8	15	12.4705
AAAAACA	chr11:19256368-19256608(-)$1	240	74	81	12.6666
AAAACCA	chr6:159058600-159058846(-)$1	246	24	31	16.1960
AACACCA	chr18:29126445-29126790(+)$1	345	120	127	11.6862
AAAAACA	chr14:62207525-62207781(+)$1	256	159	166	12.6666
AAAAACA	chr3:141708243-141708554(-)$1	311	179	186	12.6666
AAAACCC	chr1:150436951-150437227(+)$1	276	218	225	12.5686
AAAUCCA	chr18:32825602-32825949(+)$1	347	148	155	12.8627
AAAACCU	chr1:40928847-40929084(+)$1	237	84	91	13.0588
AAACCCA	chr10:70202575-70202811(-)$1	236	8	15	12.6666
AAAACUA	chr7:138763854-138764139(-)$1	285	1	8	12.5686
AAAAGCA	chr12:49087301-49087563(-)$1	262	89	96	12.2745
AAAACCC	chr5:74646884-74647123(+)$1	239	118	125	12.5686
AAAACCA	chr17:4848905-4849307(-)$1	402	228	235	16.1960
AAAACAA	chr9:99581300-99581559(-)$1	259	3	10	12.4705
AAAACCC	chr14:103803408-103803678(+)$1	270	144	151	12.5686
GAAACCA	chr5:180662253-180662622(+)$1	369	153	160	11.9803
aaaaccu	chr19:55677110-55677328(-)$1	218	169	176	13.0588
AAAAUCA	chr14:24707940-24708356(+)$1	416	276	283	12.5686
AAAAUCA	chr19:58290754-58291007(+)$1	253	4	11	12.5686
AAAAACA	chr15:50884565-50884805(-)$1	240	111	118	12.6666
AAAUCCA	chr1:111778181-111778424(+)$1	243	112	119	12.8627
AAAACCU	chr19:37975977-37976224(+)$1	247	59	66	13.0588
AAAACAA	chr13:48985615-48985905(+)$1	290	86	93	12.4705
UAAACCA	chr1:28793052-28793324(+)$1	272	192	199	11.8823
AAAUCCA	chr12:1017813-1018093(+)$1	280	100	107	12.8627
aauacca	chr7:64452756-64453010(-)$1	254	160	167	11.5882

#otherMatches

#Struct PSSM
:::::::	chr10:129902229-129902475(-)$1	246	109	116	12.6666
4444bb]	chr15:40917172-40917408(+)$1	236	180	187	11.9803
&&&&ccc	chr5:169291327-169291588(+)$1	261	120	127	12.5686
:::::::	chr3:152058228-152058528(+)$1	300	189	196	12.6666
lldddd:	chr16:46694343-46694590(-)$1	247	43	50	11.8823
%%%%%ee	chr10:43088413-43088737(-)$1	324	185	192	13.0588
vvvvfff	chr2:86361810-86362071(+)$1	261	110	117	12.5686
ooooeee	chr5:176396162-176396418(-)$1	256	8	15	12.6666
cc::BB}	chr6:28121505-28121981(+)$1	476	331	338	11.9803
:::::ee	chr1:24297606-24297886(-)$1	280	75	82	12.5686
NNNNCCC	chr7:64167156-64167416(+)$1	260	81	88	12.6666
:::::::	chr9:95609830-95610067(-)$1	237	57	64	13.0588
++++eee	chr3:184429053-184429274(-)$1	221	111	118	13.0588
~DDDD::	chr18:23615625-23615921(-)$1	296	266	273	12.4705
:::EEEE	chr17:62496567-62496918(-)$1	351	305	312	12.8627
BKKBB{D	chr2:24260830-24261071(-)$1	241	34	41	12.3725
ggg]ccc	chr10:38345174-38345413(+)$1	239	198	205	13.0588
eee[ddd	chr13:37596307-37596652(-)$1	345	92	99	12.5686
:::dddd	chr4:99952702-99952954(+)$1	252	73	80	12.8627
ccceeee	chr12:29493969-29494205(-)$1	236	11	18	12.5686
:::::::	chr1:111494643-111494881(-)$1	238	128	135	13.0588
ccnnnnn	chr5:38950124-38950393(-)$1	269	227	234	12.5686
mmccc33	chr4:148554834-148555088(+)$1	254	41	48	12.8627
E~~~~CC	chr2:38976210-38976435(-)$1	225	199	206	11.6862
::::::f	chr17:65882157-65882425(+)$1	268	8	15	12.4705
eeuuuuu	chr11:19256368-19256608(-)$1	240	74	81	12.6666
::::eee	chr6:159058600-159058846(-)$1	246	24	31	16.1960
e4444bb	chr18:29126445-29126790(+)$1	345	120	127	11.6862
@@@@@@@	chr14:62207525-62207781(+)$1	256	159	166	12.6666
$$$$$bb	chr3:141708243-141708554(-)$1	311	179	186	12.6666
wwwwwwf	chr1:150436951-150437227(+)$1	276	218	225	12.5686
lllccc:	chr18:32825602-32825949(+)$1	347	148	155	12.8627
bvvvvvv	chr1:40928847-40929084(+)$1	237	84	91	13.0588
::::CCC	chr10:70202575-70202811(-)$1	236	8	15	12.6666
:::ccc[	chr7:138763854-138764139(-)$1	285	1	8	12.5686
^^^^^^^	chr12:49087301-49087563(-)$1	262	89	96	12.2745
::::DDD	chr5:74646884-74647123(+)$1	239	118	125	12.5686
:::::::	chr17:4848905-4849307(-)$1	402	228	235	16.1960
d''''''	chr9:99581300-99581559(-)$1	259	3	10	12.4705
:::::EE	chr14:103803408-103803678(+)$1	270	144	151	12.5686
qqqqqbb	chr5:180662253-180662622(+)$1	369	153	160	11.9803
::::iii	chr19:55677110-55677328(-)$1	218	169	176	13.0588
\\\\\\\	chr14:24707940-24708356(+)$1	416	276	283	12.5686
:::::CC	chr19:58290754-58291007(+)$1	253	4	11	12.5686
vvvvbb2	chr15:50884565-50884805(-)$1	240	111	118	12.6666
sssccc6	chr1:111778181-111778424(+)$1	243	112	119	12.8627
%%%%bbm	chr19:37975977-37976224(+)$1	247	59	66	13.0588
:::::::	chr13:48985615-48985905(+)$1	290	86	93	12.4705
:::eeee	chr1:28793052-28793324(+)$1	272	192	199	11.8823
:::ffff	chr12:1017813-1018093(+)$1	280	100	107	12.8627
+++++++	chr7:64452756-64453010(-)$1	254	160	167	11.5882

#DB
.......	chr10:129902229-129902475(-)$1	1	109	116	12.6666
....)).	chr15:40917172-40917408(+)$1	1	180	187	11.9803
....(((	chr5:169291327-169291588(+)$1	1	120	127	12.5686
.......	chr3:152058228-152058528(+)$1	1	189	196	12.6666
..)))).	chr16:46694343-46694590(-)$1	1	43	50	11.8823
.....((	chr10:43088413-43088737(-)$1	1	185	192	13.0588
....)))	chr2:86361810-86362071(+)$1	1	110	117	12.5686
....)))	chr5:176396162-176396418(-)$1	1	8	15	12.6666
))..)).	chr6:28121505-28121981(+)$1	1	331	338	11.9803
.....((	chr1:24297606-24297886(-)$1	1	75	82	12.5686
....(((	chr7:64167156-64167416(+)$1	1	81	88	12.6666
.......	chr9:95609830-95610067(-)$1	1	57	64	13.0588
....(((	chr3:184429053-184429274(-)$1	1	111	118	13.0588
.))))..	chr18:23615625-23615921(-)$1	1	266	273	12.4705
...))))	chr17:62496567-62496918(-)$1	1	305	312	12.8627
(..((.(	chr2:24260830-24261071(-)$1	1	34	41	12.3725
))).)))	chr10:38345174-38345413(+)$1	1	198	205	13.0588
(((.(((	chr13:37596307-37596652(-)$1	1	92	99	12.5686
...((((	chr4:99952702-99952954(+)$1	1	73	80	12.8627
(((((((	chr12:29493969-29494205(-)$1	1	11	18	12.5686
.......	chr1:111494643-111494881(-)$1	1	128	135	13.0588
((.....	chr5:38950124-38950393(-)$1	1	227	234	12.5686
..)))..	chr4:148554834-148555088(+)$1	1	41	48	12.8627
)....))	chr2:38976210-38976435(-)$1	1	199	206	11.6862
......(	chr17:65882157-65882425(+)$1	1	8	15	12.4705
((.....	chr11:19256368-19256608(-)$1	1	74	81	12.6666
....(((	chr6:159058600-159058846(-)$1	1	24	31	16.1960
)....))	chr18:29126445-29126790(+)$1	1	120	127	11.6862
.......	chr14:62207525-62207781(+)$1	1	159	166	12.6666
.....((	chr3:141708243-141708554(-)$1	1	179	186	12.6666
......)	chr1:150436951-150437227(+)$1	1	218	225	12.5686
...))).	chr18:32825602-32825949(+)$1	1	148	155	12.8627
(......	chr1:40928847-40929084(+)$1	1	84	91	13.0588
....(((	chr10:70202575-70202811(-)$1	1	8	15	12.6666
...(((.	chr7:138763854-138764139(-)$1	1	1	8	12.5686
.......	chr12:49087301-49087563(-)$1	1	89	96	12.2745
....(((	chr5:74646884-74647123(+)$1	1	118	125	12.5686
.......	chr17:4848905-4849307(-)$1	1	228	235	16.1960
(......	chr9:99581300-99581559(-)$1	1	3	10	12.4705
.....((	chr14:103803408-103803678(+)$1	1	144	151	12.5686
.....))	chr5:180662253-180662622(+)$1	1	153	160	11.9803
....(((	chr19:55677110-55677328(-)$1	1	169	176	13.0588
.......	chr14:24707940-24708356(+)$1	1	276	283	12.5686
.....((	chr19:58290754-58291007(+)$1	1	4	11	12.5686
....)).	chr15:50884565-50884805(-)$1	1	111	118	12.6666
...))).	chr1:111778181-111778424(+)$1	1	112	119	12.8627
....((.	chr19:37975977-37976224(+)$1	1	59	66	13.0588
.......	chr13:48985615-48985905(+)$1	1	86	93	12.4705
...((((	chr1:28793052-28793324(+)$1	1	192	199	11.8823
...((((	chr12:1017813-1018093(+)$1	1	100	107	12.8627
.......	chr7:64452756-64453010(-)$1	1	160	167	11.5882

#PSSM
A : 0.84	G : 0.05	a : 0.05	U : 0.03	
A : 0.94	a : 0.05	
A : 0.90	a : 0.03	C : 0.03	u : 0.01	
A : 0.74	U : 0.09	C : 0.07	a : 0.03	G : 0.01	u : 0.01	
C : 0.74	A : 0.09	U : 0.07	c : 0.05	G : 0.01	
C : 0.76	U : 0.09	A : 0.07	c : 0.05	
A : 0.74	U : 0.13	C : 0.05	a : 0.03	u : 0.01	

#score	648.0588235294124
#seq	51
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m3_run2.nuc.txt

#NT
AAAAUAAAAAAC	chr10:96168434-96168648(+)$1	214	47	59	17.9387
aaaagaaaaaGU	chr11:93477733-93477965(+)$1	232	71	83	16.4081
AAAAUACAAUAU	chr13:41195337-41195635(-)$1	298	116	128	14.2653
ACUUUAAAAAAU	chr13:74382586-74382816(-)$1	230	51	63	12.9387
aaaaaaaaaaaU	chr18:12668448-12668721(+)$1	273	169	181	24.1632
CAAAAUAAAGAU	chr2:175967979-175968221(-)$1	242	187	199	13.1428
AGGAAGAAAAAU	chr10:12473137-12473376(+)$1	239	46	58	14.4693
auaaagaaaaag	chr5:99901432-99901664(+)$1	232	77	89	14.3673
uaaaaaaaaaau	chr10:38332247-38332501(+)$1	254	189	201	20.4897
UUAAAAAAAACU	chr12:88404944-88405162(-)$1	218	167	179	14.0612
AUUAAAUAAAAU	chr11:30354238-30354470(+)$1	232	105	117	14.9795
AAAACUAGAAAU	chr17:59381320-59381582(+)$1	262	67	79	14.1632
AAAGAAAUAACU	chr1:207039340-207039554(+)$1	214	151	163	12.5306
aauaaaaaaacu	chr3:4839822-4840069(+)$1	247	117	129	16.9183
agauaaaaaaau	chr9:72880696-72880934(+)$1	238	167	179	18.4489
AAAAUACAAUAU	chrX:106454340-106454556(+)$1	216	186	198	14.2653
aaaaaaaaaaaa	chr9:118052470-118052742(+)$1	272	151	163	19.9795
AAAAUAACAACU	chr18:46706587-46706826(-)$1	239	100	112	13.9591
AAAAAAAAAAAA	chr2:198121837-198122158(-)$1	321	48	60	19.9795
AACAAGUAAAAU	chr11:94934099-94934368(-)$1	269	3	15	13.7551
gaaauuaaaaau	chr16:27427372-27427656(+)$1	284	47	59	15.2857
aaaaaaaaaaau	chr17:1777170-1777463(+)$1	293	126	138	24.1632
agaaagacaaau	chr13:108953753-108953976(+)$1	223	135	147	14.2653
aaaaaaggaaaU	chrX:48436324-48436579(+)$1	255	145	157	16.9183
AUAUAAAGAAAU	chr10:32799810-32800071(+)$1	261	173	185	15.0816
UAUUAAAAAAAU	chr8:100110837-100111073(+)$1	236	154	166	14.3673
AAAAAAAAAAAU	chr6:16371477-16371729(-)$1	252	174	186	24.1632
GAAAAUGAAAAU	chr8:32202471-32202686(+)$1	215	190	202	13.9591
ACCAAAAAGAAU	chr10:68822157-68822384(-)$1	227	117	129	13.4489
AUAUAAAUAAAU	chr5:130664477-130664761(+)$1	284	138	150	14.8775
AGUUUAaaaaau	chr5:49707914-49708148(-)$1	234	207	219	13.1428
auuaaaaacaaU	chr7:35922691-35922945(+)$1	254	104	116	14.2653
aaaaaaaaggau	chr6:102083865-102084093(+)$1	228	180	192	15.5918
caaaaaaaaaaU	chr4:128914202-128914486(+)$1	284	25	37	20.3877
uaaaaggaaaau	chr14:39880994-39881241(-)$1	247	153	165	13.8571
ACCAAACAAAAU	chr8:54635634-54635873(-)$1	239	102	114	14.2653
auaauucaaaau	chr3:43379219-43379455(+)$1	236	161	173	13.4489
agacaaaaaaau	chr4:164718370-164718620(-)$1	250	171	183	17.8367
aaauuagaaaau	chr11:118650116-118650354(-)$1	238	152	164	15.5918
aaaaaaaaaaaU	chr14:75575148-75575379(-)$1	231	104	116	24.1632
AAACAAAAAAAU	chr18:77136070-77136333(+)$1	263	150	162	20.5918
AAAUUAAAAAAC	chr6:143245176-143245410(-)$1	234	117	129	14.9795
AAAAAAAAAAAC	chr1:8521084-8521324(-)$1	240	40	52	20.0816
aaaaaaaaaaaU	chr1:151017632-151017863(+)$1	231	123	135	24.1632
AUAAUAAAGAAU	chr4:81195855-81196073(+)$1	218	111	123	15.4897
CAAAAUAGAAAU	chr7:37298387-37298618(-)$1	231	44	56	13.7551
AUAAUUCAAAAU	chr5:50139715-50139958(+)$1	243	110	122	13.4489
AAAAUAAAUAAU	chr16:19666576-19666790(+)$1	214	88	100	17.6326

#otherMatches

#Struct PSSM
odddd0000000	chr9:123684564-123684808(-)$1	244	63	75	14.5714
::::::::dddd	chr10:96168434-96168648(+)$1	214	47	59	17.9387
::::::::::::	chr11:93477733-93477965(+)$1	232	71	83	16.4081
[eeeeellleee	chr13:41195337-41195635(-)$1	298	116	128	14.2653
ddssssssssss	chr13:74382586-74382816(-)$1	230	51	63	12.9387
::::::::::ee	chr18:12668448-12668721(+)$1	273	169	181	24.1632
evvvvvvvvvvv	chr2:175967979-175968221(-)$1	242	187	199	13.1428
ddd]bb::::::	chr10:12473137-12473376(+)$1	239	46	58	14.4693
IIIIII:::::c	chr5:99901432-99901664(+)$1	232	77	89	14.3673
::::::::::::	chr10:38332247-38332501(+)$1	254	189	201	20.4897
::::::::::dd	chr12:88404944-88405162(-)$1	218	167	179	14.0612
eehhhhhhhh[f	chr11:30354238-30354470(+)$1	232	105	117	14.9795
:::::::CCC{F	chr17:59381320-59381582(+)$1	262	67	79	14.1632
hhhh''''''''	chr1:207039340-207039554(+)$1	214	151	163	12.5306
>>>>>>>>>>>e	chr3:4839822-4840069(+)$1	247	117	129	16.9183
2ccc:::::::e	chr9:72880696-72880934(+)$1	238	167	179	18.4489
::::::::::dd	chrX:106454340-106454556(+)$1	216	186	198	14.2653
::::::::::::	chr9:118052470-118052742(+)$1	272	151	163	19.9795
dd++++++++++	chr18:46706587-46706826(-)$1	239	100	112	13.9591
::::::::::::	chr2:198121837-198122158(-)$1	321	48	60	19.9795
:CCC{BBMMMMJ	chr11:94934099-94934368(-)$1	269	3	15	13.7551
b]hhhhhhhhdd	chr16:27427372-27427656(+)$1	284	47	59	15.2857
::::::::::hh	chr17:1777170-1777463(+)$1	293	126	138	24.1632
%%%%%%bb"""d	chr13:108953753-108953976(+)$1	223	135	147	14.2653
::::::cccccc	chrX:48436324-48436579(+)$1	255	145	157	16.9183
}CCC}CCC::::	chr10:32799810-32800071(+)$1	261	173	185	15.0816
mmmggggggg::	chr8:100110837-100111073(+)$1	236	154	166	14.3673
::::::iiiiii	chr6:16371477-16371729(-)$1	252	174	186	24.1632
CYYGGGGGGG~~	chr8:32202471-32202686(+)$1	215	190	202	13.9591
>>>>>eeeee]c	chr10:68822157-68822384(-)$1	227	117	129	13.4489
::::::::::::	chr5:130664477-130664761(+)$1	284	138	150	14.8775
oohhhhhhhh::	chr5:49707914-49708148(-)$1	234	207	219	13.1428
pppppeeeee::	chr7:35922691-35922945(+)$1	254	104	116	14.2653
e::::::GGGGG	chr6:102083865-102084093(+)$1	228	180	192	15.5918
dhhhhhhhhmmm	chr4:128914202-128914486(+)$1	284	25	37	20.3877
^^^^^^^^^^^^	chr14:39880994-39881241(-)$1	247	153	165	13.8571
>>>>>dddd22e	chr8:54635634-54635873(-)$1	239	102	114	14.2653
hhhhhhh:::::	chr3:43379219-43379455(+)$1	236	161	173	13.4489
eeeqqqqqqqqe	chr4:164718370-164718620(-)$1	250	171	183	17.8367
hhh22ggggggg	chr11:118650116-118650354(-)$1	238	152	164	15.5918
WWWWWWWWWWWJ	chr14:75575148-75575379(-)$1	231	104	116	24.1632
^^^^^^^^^^^e	chr18:77136070-77136333(+)$1	263	150	162	20.5918
::::::::::::	chr6:143245176-143245410(-)$1	234	117	129	14.9795
^^^^^^^^^^^^	chr1:8521084-8521324(-)$1	240	40	52	20.0816
::::::::::::	chr1:151017632-151017863(+)$1	231	123	135	24.1632
''''''ffffff	chr4:81195855-81196073(+)$1	218	111	123	15.4897
zzzzzzzzzzzz	chr7:37298387-37298618(-)$1	231	44	56	13.7551
:::::cccqqqq	chr5:50139715-50139958(+)$1	243	110	122	13.4489
::::::::::::	chr16:19666576-19666790(+)$1	214	88	100	17.6326

#DB
.)))).......	chr9:123684564-123684808(-)$1	1	63	75	14.5714
........((((	chr10:96168434-96168648(+)$1	1	47	59	17.9387
............	chr11:93477733-93477965(+)$1	1	71	83	16.4081
.(((((...)))	chr13:41195337-41195635(-)$1	1	116	128	14.2653
((..........	chr13:74382586-74382816(-)$1	1	51	63	12.9387
..........((	chr18:12668448-12668721(+)$1	1	169	181	24.1632
(...........	chr2:175967979-175968221(-)$1	1	187	199	13.1428
))).))......	chr10:12473137-12473376(+)$1	1	46	58	14.4693
((((((.....(	chr5:99901432-99901664(+)$1	1	77	89	14.3673
............	chr10:38332247-38332501(+)$1	1	189	201	20.4897
..........((	chr12:88404944-88405162(-)$1	1	167	179	14.0612
))((((((((.(	chr11:30354238-30354470(+)$1	1	105	117	14.9795
.......(((.(	chr17:59381320-59381582(+)$1	1	67	79	14.1632
((((........	chr1:207039340-207039554(+)$1	1	151	163	12.5306
...........)	chr3:4839822-4840069(+)$1	1	117	129	16.9183
.))).......(	chr9:72880696-72880934(+)$1	1	167	179	18.4489
..........((	chrX:106454340-106454556(+)$1	1	186	198	14.2653
............	chr9:118052470-118052742(+)$1	1	151	163	19.9795
((..........	chr18:46706587-46706826(-)$1	1	100	112	13.9591
............	chr2:198121837-198122158(-)$1	1	48	60	19.9795
.(((.((....(	chr11:94934099-94934368(-)$1	1	3	15	13.7551
).))))))))((	chr16:27427372-27427656(+)$1	1	47	59	15.2857
..........((	chr17:1777170-1777463(+)$1	1	126	138	24.1632
......((...(	chr13:108953753-108953976(+)$1	1	135	147	14.2653
......((((((	chrX:48436324-48436579(+)$1	1	145	157	16.9183
.))).)))....	chr10:32799810-32800071(+)$1	1	173	185	15.0816
...)))))))..	chr8:100110837-100111073(+)$1	1	154	166	14.3673
......((((((	chr6:16371477-16371729(-)$1	1	174	186	24.1632
)..)))))))..	chr8:32202471-32202686(+)$1	1	190	202	13.9591
.....))))).)	chr10:68822157-68822384(-)$1	1	117	129	13.4489
............	chr5:130664477-130664761(+)$1	1	138	150	14.8775
..))))))))..	chr5:49707914-49708148(-)$1	1	207	219	13.1428
.....)))))..	chr7:35922691-35922945(+)$1	1	104	116	14.2653
)......)))))	chr6:102083865-102084093(+)$1	1	180	192	15.5918
)((((((((...	chr4:128914202-128914486(+)$1	1	25	37	20.3877
............	chr14:39880994-39881241(-)$1	1	153	165	13.8571
.....))))..)	chr8:54635634-54635873(-)$1	1	102	114	14.2653
))))))).....	chr3:43379219-43379455(+)$1	1	161	173	13.4489
(((........)	chr4:164718370-164718620(-)$1	1	171	183	17.8367
)))..)))))))	chr11:118650116-118650354(-)$1	1	152	164	15.5918
...........(	chr14:75575148-75575379(-)$1	1	104	116	24.1632
...........)	chr18:77136070-77136333(+)$1	1	150	162	20.5918
............	chr6:143245176-143245410(-)$1	1	117	129	14.9795
............	chr1:8521084-8521324(-)$1	1	40	52	20.0816
............	chr1:151017632-151017863(+)$1	1	123	135	24.1632
......((((((	chr4:81195855-81196073(+)$1	1	111	123	15.4897
............	chr7:37298387-37298618(-)$1	1	44	56	13.7551
.....(((....	chr5:50139715-50139958(+)$1	1	110	122	13.4489
............	chr16:19666576-19666790(+)$1	1	88	100	17.6326

#PSSM
A : 0.46	a : 0.34	C : 0.04	u : 0.04	U : 0.04	g : 0.02	G : 0.02	c : 0.02	
A : 0.34	a : 0.30	U : 0.12	C : 0.06	u : 0.06	g : 0.06	G : 0.04	
A : 0.40	a : 0.36	U : 0.08	u : 0.06	C : 0.06	G : 0.02	
A : 0.40	a : 0.34	U : 0.12	u : 0.04	g : 0.02	G : 0.02	c : 0.02	C : 0.02	
a : 0.34	A : 0.34	U : 0.20	u : 0.06	g : 0.02	C : 0.02	
A : 0.42	a : 0.30	U : 0.10	u : 0.06	g : 0.06	G : 0.04	
A : 0.40	a : 0.36	C : 0.08	g : 0.06	U : 0.04	G : 0.02	c : 0.02	
A : 0.42	a : 0.40	G : 0.06	U : 0.04	C : 0.02	c : 0.02	g : 0.02	
A : 0.48	a : 0.40	G : 0.04	c : 0.02	g : 0.02	U : 0.02	
A : 0.48	a : 0.42	U : 0.04	G : 0.02	g : 0.02	
A : 0.48	a : 0.40	C : 0.06	G : 0.02	c : 0.02	
U : 0.61	u : 0.26	C : 0.06	g : 0.02	a : 0.02	A : 0.02	

#score	805.0204081632658
#seq	49
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m2_run2.nuc.txt

#NT
CUGU	chr13:30084481-30084714(-)$1	233	74	78	11.9999
CUGU	chr10:61410556-61410787(-)$1	231	210	214	11.9999
CUGU	chr5:130977840-130978061(-)$1	221	15	19	11.9999
CUGU	chr5:56216250-56216474(-)$1	224	58	62	11.9999
CUGU	chr7:100277621-100277875(-)$1	254	51	55	11.9999
CUGU	chr19:46970445-46970685(-)$1	240	14	18	11.9999
CUGU	chr12:120649070-120649297(-)$1	227	16	20	11.9999
CUGU	chr19:30193723-30193975(-)$1	252	97	101	11.9999
CUGU	chr5:43526424-43526655(-)$1	231	105	109	11.9999
CUGU	chr19:58906007-58906264(+)$1	257	23	27	11.9999
CUGU	chr22:39262013-39262263(-)$1	250	143	147	11.9999
CUGU	chr9:139007598-139007846(-)$1	248	74	78	11.9999
CUGU	chr11:47488296-47488546(-)$1	250	126	130	11.9999
CUGU	chr9:14085705-14085933(-)$1	228	107	111	11.9999
CUGU	chr17:74138483-74138708(-)$1	225	35	39	11.9999
CUGU	chr6:31506825-31507046(-)$1	221	39	43	11.9999
CUGU	chr6:111650640-111650864(-)$1	224	25	29	11.9999
CUGU	chr10:62629181-62629405(-)$1	224	96	100	11.9999
CUGU	chr15:78777957-78778182(+)$1	225	81	85	11.9999
CUGU	chr2:113288637-113288857(+)$1	220	98	102	11.9999
CUGU	chr10:79800302-79800546(+)$1	244	102	106	11.9999
CUGU	chr19:4442988-4443239(+)$1	251	106	110	11.9999
CUGU	chr7:44605281-44605512(-)$1	231	185	189	11.9999
CUGU	chrX:128725425-128725651(+)$1	226	30	34	11.9999
CUGU	chr3:42706843-42707081(+)$1	238	19	23	11.9999
CUGU	chr20:61826848-61827074(-)$1	226	163	167	11.9999
CUGU	chr17:1248276-1248509(-)$1	233	41	45	11.9999
CUGU	chr4:155471378-155471601(-)$1	223	71	75	11.9999
CUGU	chr1:154441527-154441749(+)$1	222	61	65	11.9999
CUGU	chr7:106300164-106300406(-)$1	242	100	104	11.9999
CUGU	chr2:109400945-109401174(+)$1	229	11	15	11.9999
CUGU	chr3:14526872-14527098(+)$1	226	66	70	11.9999
CUGU	chr16:1415699-1415925(-)$1	226	28	32	11.9999
CUGU	chr3:57125497-57125721(-)$1	224	138	142	11.9999
CUGU	chr12:74933978-74934217(+)$1	239	55	59	11.9999
CUGU	chr8:27989767-27989988(+)$1	221	35	39	11.9999
CUGU	chr4:103717032-103717258(-)$1	226	151	155	11.9999
cugu	chr3:9807722-9807943(+)$1	221	108	112	11.9999
CUGU	chr2:20251223-20251478(-)$1	255	189	193	11.9999
CUGU	chr1:26604775-26605000(+)$1	225	199	203	11.9999
CUGU	chr14:69926529-69926752(+)$1	223	46	50	11.9999
CUGU	chr2:172413028-172413251(+)$1	223	148	152	11.9999
CUGU	chr13:53049771-53049997(+)$1	226	75	79	11.9999
CUGU	chr20:58511858-58512089(-)$1	231	31	35	11.9999
CUGU	chr16:18803095-18803328(-)$1	233	11	15	11.9999
CUGU	chr6:118782356-118782607(-)$1	251	0	4	11.9999
CUGU	chr9:140195080-140195359(-)$1	279	68	72	11.9999
CUGU	chr17:26881144-26881391(-)$1	247	74	78	11.9999
CUGU	chr19:14071716-14071970(+)$1	254	23	27	11.9999
CUGU	chr18:66341939-66342161(-)$1	222	10	14	11.9999
CUGU	chr16:71886591-71886813(+)$1	222	43	47	11.9999
CUGU	chr14:102606226-102606456(+)$1	230	100	104	11.9999
cugu	chrX:123041716-123041943(+)$1	227	65	69	11.9999
CUGU	chr3:50296368-50296641(+)$1	273	15	19	11.9999
CUGU	chr17:27591247-27591473(-)$1	226	191	195	11.9999
cugu	chr5:132091777-132091998(-)$1	221	3	7	11.9999
CUGU	chr11:61732431-61732648(-)$1	217	72	76	11.9999
CUGU	chr17:19809400-19809624(-)$1	224	191	195	11.9999
CUGU	chr16:71764027-71764258(-)$1	231	98	102	11.9999
CUGU	chr3:49449241-49449486(-)$1	245	2	6	11.9999
CUGU	chr1:35649672-35649910(-)$1	238	78	82	11.9999
CUGU	chr18:28573375-28573606(-)$1	231	222	226	11.9999
CUGU	chr17:45905894-45906125(-)$1	231	110	114	11.9999
CUGU	chr7:157061214-157061513(+)$1	299	32	36	11.9999
CUGU	chr15:37184045-37184266(-)$1	221	90	94	11.9999
CUGU	chr19:2041809-2042025(-)$1	216	73	77	11.9999
CUGU	chr12:112518773-112518998(-)$1	225	16	20	11.9999
CUGU	chr8:103839502-103839725(-)$1	223	82	86	11.9999
CUGU	chr20:61827803-61828072(-)$1	269	197	201	11.9999
CUGU	chr17:57771651-57771884(+)$1	233	29	33	11.9999
CUGU	chr15:76584680-76584909(-)$1	229	110	114	11.9999
CUGU	chr22:38880549-38880770(-)$1	221	90	94	11.9999
CUGU	chr2:113421173-113421395(+)$1	222	39	43	11.9999
CUGU	chr13:31735679-31735901(-)$1	222	28	32	11.9999
cugu	chr19:48893621-48893874(-)$1	253	14	18	11.9999
CUGU	chr17:2587707-2587944(+)$1	237	105	109	11.9999
CUGU	chr1:203277818-203278046(+)$1	228	35	39	11.9999
CUGU	chr10:15149813-15150044(-)$1	231	83	87	11.9999

#otherMatches

#Struct PSSM
GGGG	chr3:27416109-27416353(-)$1	244	94	98	11.9999
====	chr13:30084481-30084714(-)$1	233	74	78	11.9999
qqqq	chr10:61410556-61410787(-)$1	231	210	214	11.9999
booo	chr5:130977840-130978061(-)$1	221	15	19	11.9999
J{DD	chr5:56216250-56216474(-)$1	224	58	62	11.9999
^^^^	chr7:100277621-100277875(-)$1	254	51	55	11.9999
cttt	chr19:46970445-46970685(-)$1	240	14	18	11.9999
qqqq	chr12:120649070-120649297(-)$1	227	16	20	11.9999
c[cc	chr19:30193723-30193975(-)$1	252	97	101	11.9999
uubb	chr5:43526424-43526655(-)$1	231	105	109	11.9999
ee[d	chr19:58906007-58906264(+)$1	257	23	27	11.9999
fff[	chr22:39262013-39262263(-)$1	250	143	147	11.9999
nnnn	chr9:139007598-139007846(-)$1	248	74	78	11.9999
[bbp	chr11:47488296-47488546(-)$1	250	126	130	11.9999
rddd	chr9:14085705-14085933(-)$1	228	107	111	11.9999
!!ff	chr17:74138483-74138708(-)$1	225	35	39	11.9999
iiii	chr6:31506825-31507046(-)$1	221	39	43	11.9999
MFFF	chr6:111650640-111650864(-)$1	224	25	29	11.9999
==pp	chr10:62629181-62629405(-)$1	224	96	100	11.9999
d]cc	chr15:78777957-78778182(+)$1	225	81	85	11.9999
::::	chr2:113288637-113288857(+)$1	220	98	102	11.9999
FKKE	chr10:79800302-79800546(+)$1	244	102	106	11.9999
hhhh	chr19:4442988-4443239(+)$1	251	106	110	11.9999
FFFF	chr7:44605281-44605512(-)$1	231	185	189	11.9999
fDDD	chrX:128725425-128725651(+)$1	226	30	34	11.9999
[bbd	chr3:42706843-42707081(+)$1	238	19	23	11.9999
22a2	chr20:61826848-61827074(-)$1	226	163	167	11.9999
ffff	chr17:1248276-1248509(-)$1	233	41	45	11.9999
cc22	chr4:155471378-155471601(-)$1	223	71	75	11.9999
:ccc	chr1:154441527-154441749(+)$1	222	61	65	11.9999
ccc2	chr7:106300164-106300406(-)$1	242	100	104	11.9999
pppp	chr2:109400945-109401174(+)$1	229	11	15	11.9999
ffff	chr3:14526872-14527098(+)$1	226	66	70	11.9999
mmcc	chr16:1415699-1415925(-)$1	226	28	32	11.9999
}BB:	chr3:57125497-57125721(-)$1	224	138	142	11.9999
FFFF	chr12:74933978-74934217(+)$1	239	55	59	11.9999
ffff	chr8:27989767-27989988(+)$1	221	35	39	11.9999
$$$c	chr4:103717032-103717258(-)$1	226	151	155	11.9999
ccc]	chr3:9807722-9807943(+)$1	221	108	112	11.9999
dd]a	chr2:20251223-20251478(-)$1	255	189	193	11.9999
eeee	chr1:26604775-26605000(+)$1	225	199	203	11.9999
::::	chr14:69926529-69926752(+)$1	223	46	50	11.9999
ddd$	chr2:172413028-172413251(+)$1	223	148	152	11.9999
!!a"	chr13:53049771-53049997(+)$1	226	75	79	11.9999
EE{C	chr20:58511858-58512089(-)$1	231	31	35	11.9999
[ggg	chr16:18803095-18803328(-)$1	233	11	15	11.9999
:CCC	chr6:118782356-118782607(-)$1	251	0	4	11.9999
^^^^	chr9:140195080-140195359(-)$1	279	68	72	11.9999
KKDD	chr17:26881144-26881391(-)$1	247	74	78	11.9999
GGGG	chr19:14071716-14071970(+)$1	254	23	27	11.9999
:::E	chr18:66341939-66342161(-)$1	222	10	14	11.9999
c]ee	chr16:71886591-71886813(+)$1	222	43	47	11.9999
ee::	chr14:102606226-102606456(+)$1	230	100	104	11.9999
uuuu	chrX:123041716-123041943(+)$1	227	65	69	11.9999
::::	chr3:50296368-50296641(+)$1	273	15	19	11.9999
IIII	chr17:27591247-27591473(-)$1	226	191	195	11.9999
BB{C	chr5:132091777-132091998(-)$1	221	3	7	11.9999
aooo	chr11:61732431-61732648(-)$1	217	72	76	11.9999
YYBB	chr17:19809400-19809624(-)$1	224	191	195	11.9999
bb]e	chr16:71764027-71764258(-)$1	231	98	102	11.9999
:eee	chr3:49449241-49449486(-)$1	245	2	6	11.9999
hhhh	chr1:35649672-35649910(-)$1	238	78	82	11.9999
BB::	chr18:28573375-28573606(-)$1	231	222	226	11.9999
ccc]	chr17:45905894-45906125(-)$1	231	110	114	11.9999
dd[d	chr7:157061214-157061513(+)$1	299	32	36	11.9999
b]gg	chr15:37184045-37184266(-)$1	221	90	94	11.9999
nndd	chr19:2041809-2042025(-)$1	216	73	77	11.9999
EEE{	chr12:112518773-112518998(-)$1	225	16	20	11.9999
gggg	chr8:103839502-103839725(-)$1	223	82	86	11.9999
22==	chr20:61827803-61828072(-)$1	269	197	201	11.9999
Gddd	chr17:57771651-57771884(+)$1	233	29	33	11.9999
oddd	chr15:76584680-76584909(-)$1	229	110	114	11.9999
pppp	chr22:38880549-38880770(-)$1	221	90	94	11.9999
ffff	chr2:113421173-113421395(+)$1	222	39	43	11.9999
CCee	chr13:31735679-31735901(-)$1	222	28	32	11.9999
E:::	chr19:48893621-48893874(-)$1	253	14	18	11.9999
ddd[	chr17:2587707-2587944(+)$1	237	105	109	11.9999
####	chr1:203277818-203278046(+)$1	228	35	39	11.9999
oooe	chr10:15149813-15150044(-)$1	231	83	87	11.9999

#DB
((((	chr3:27416109-27416353(-)$1	1	94	98	11.9999
))))	chr13:30084481-30084714(-)$1	1	74	78	11.9999
....	chr10:61410556-61410787(-)$1	1	210	214	11.9999
(...	chr5:130977840-130978061(-)$1	1	15	19	11.9999
(.((	chr5:56216250-56216474(-)$1	1	58	62	11.9999
....	chr7:100277621-100277875(-)$1	1	51	55	11.9999
(...	chr19:46970445-46970685(-)$1	1	14	18	11.9999
....	chr12:120649070-120649297(-)$1	1	16	20	11.9999
(.((	chr19:30193723-30193975(-)$1	1	97	101	11.9999
..))	chr5:43526424-43526655(-)$1	1	105	109	11.9999
((.(	chr19:58906007-58906264(+)$1	1	23	27	11.9999
(((.	chr22:39262013-39262263(-)$1	1	143	147	11.9999
....	chr9:139007598-139007846(-)$1	1	74	78	11.9999
.((.	chr11:47488296-47488546(-)$1	1	126	130	11.9999
.)))	chr9:14085705-14085933(-)$1	1	107	111	11.9999
..((	chr17:74138483-74138708(-)$1	1	35	39	11.9999
((((	chr6:31506825-31507046(-)$1	1	39	43	11.9999
.(((	chr6:111650640-111650864(-)$1	1	25	29	11.9999
((..	chr10:62629181-62629405(-)$1	1	96	100	11.9999
).))	chr15:78777957-78778182(+)$1	1	81	85	11.9999
....	chr2:113288637-113288857(+)$1	1	98	102	11.9999
(..(	chr10:79800302-79800546(+)$1	1	102	106	11.9999
((((	chr19:4442988-4443239(+)$1	1	106	110	11.9999
))))	chr7:44605281-44605512(-)$1	1	185	189	11.9999
)(((	chrX:128725425-128725651(+)$1	1	30	34	11.9999
.(((	chr3:42706843-42707081(+)$1	1	19	23	11.9999
..).	chr20:61826848-61827074(-)$1	1	163	167	11.9999
))))	chr17:1248276-1248509(-)$1	1	41	45	11.9999
))..	chr4:155471378-155471601(-)$1	1	71	75	11.9999
.(((	chr1:154441527-154441749(+)$1	1	61	65	11.9999
))).	chr7:106300164-106300406(-)$1	1	100	104	11.9999
....	chr2:109400945-109401174(+)$1	1	11	15	11.9999
((((	chr3:14526872-14527098(+)$1	1	66	70	11.9999
..))	chr16:1415699-1415925(-)$1	1	28	32	11.9999
.)).	chr3:57125497-57125721(-)$1	1	138	142	11.9999
((((	chr12:74933978-74934217(+)$1	1	55	59	11.9999
))))	chr8:27989767-27989988(+)$1	1	35	39	11.9999
...(	chr4:103717032-103717258(-)$1	1	151	155	11.9999
))).	chr3:9807722-9807943(+)$1	1	108	112	11.9999
)).)	chr2:20251223-20251478(-)$1	1	189	193	11.9999
))))	chr1:26604775-26605000(+)$1	1	199	203	11.9999
....	chr14:69926529-69926752(+)$1	1	46	50	11.9999
(((.	chr2:172413028-172413251(+)$1	1	148	152	11.9999
..(.	chr13:53049771-53049997(+)$1	1	75	79	11.9999
((.(	chr20:58511858-58512089(-)$1	1	31	35	11.9999
.(((	chr16:18803095-18803328(-)$1	1	11	15	11.9999
.(((	chr6:118782356-118782607(-)$1	1	0	4	11.9999
....	chr9:140195080-140195359(-)$1	1	68	72	11.9999
..((	chr17:26881144-26881391(-)$1	1	74	78	11.9999
((((	chr19:14071716-14071970(+)$1	1	23	27	11.9999
...(	chr18:66341939-66342161(-)$1	1	10	14	11.9999
).))	chr16:71886591-71886813(+)$1	1	43	47	11.9999
))..	chr14:102606226-102606456(+)$1	1	100	104	11.9999
....	chrX:123041716-123041943(+)$1	1	65	69	11.9999
....	chr3:50296368-50296641(+)$1	1	15	19	11.9999
))))	chr17:27591247-27591473(-)$1	1	191	195	11.9999
((.(	chr5:132091777-132091998(-)$1	1	3	7	11.9999
(...	chr11:61732431-61732648(-)$1	1	72	76	11.9999
..))	chr17:19809400-19809624(-)$1	1	191	195	11.9999
)).)	chr16:71764027-71764258(-)$1	1	98	102	11.9999
.(((	chr3:49449241-49449486(-)$1	1	2	6	11.9999
))))	chr1:35649672-35649910(-)$1	1	78	82	11.9999
))..	chr18:28573375-28573606(-)$1	1	222	226	11.9999
))).	chr17:45905894-45906125(-)$1	1	110	114	11.9999
((.(	chr7:157061214-157061513(+)$1	1	32	36	11.9999
).))	chr15:37184045-37184266(-)$1	1	90	94	11.9999
..))	chr19:2041809-2042025(-)$1	1	73	77	11.9999
(((.	chr12:112518773-112518998(-)$1	1	16	20	11.9999
((((	chr8:103839502-103839725(-)$1	1	82	86	11.9999
..))	chr20:61827803-61828072(-)$1	1	197	201	11.9999
((((	chr17:57771651-57771884(+)$1	1	29	33	11.9999
.)))	chr15:76584680-76584909(-)$1	1	110	114	11.9999
....	chr22:38880549-38880770(-)$1	1	90	94	11.9999
))))	chr2:113421173-113421395(+)$1	1	39	43	11.9999
((((	chr13:31735679-31735901(-)$1	1	28	32	11.9999
(...	chr19:48893621-48893874(-)$1	1	14	18	11.9999
(((.	chr17:2587707-2587944(+)$1	1	105	109	11.9999
....	chr1:203277818-203278046(+)$1	1	35	39	11.9999
...)	chr10:15149813-15150044(-)$1	1	83	87	11.9999

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

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m3_run1.nuc.txt

#NT
UGG	chr14:21829234-21829472(-)$1	238	55	58	9.0000
UGG	chr1:1689800-1690048(-)$1	248	53	56	9.0000
UGG	chr14:24779841-24780094(+)$1	253	74	77	9.0000
UGG	chr16:30537630-30537896(-)$1	266	35	38	9.0000
UGG	chr3:42701146-42701406(+)$1	260	45	48	9.0000
UGG	chr10:89265031-89265292(+)$1	261	20	23	9.0000
UGG	chr19:3983007-3983235(-)$1	228	96	99	9.0000
UGG	chr3:47777452-47777716(-)$1	264	16	19	9.0000
UGG	chrX:118603734-118603984(+)$1	250	1	4	9.0000
UGG	chr6:30570559-30570807(-)$1	248	10	13	9.0000
UGG	chr3:184039616-184039932(+)$1	316	50	53	9.0000
UGG	chr6:158541399-158541644(-)$1	245	39	42	9.0000
UGG	chr11:71726469-71726745(-)$1	276	13	16	9.0000
UGG	chr5:179045112-179045375(-)$1	263	119	122	9.0000
UGG	chr4:144474183-144474440(+)$1	257	104	107	9.0000
UGG	chr9:136208378-136208679(-)$1	301	4	7	9.0000
UGG	chr12:50480468-50480714(+)$1	246	1	4	9.0000
UGG	chr17:43012136-43012396(-)$1	260	50	53	9.0000
UGG	chr17:57758179-57758428(+)$1	249	196	199	9.0000
UGG	chr8:145741824-145742092(-)$1	268	137	140	9.0000
UGG	chr22:24129185-24129476(+)$1	291	181	184	9.0000
ugg	chr19:48982343-48982582(+)$1	239	2	5	9.0000
UGG	chr5:179049962-179050234(-)$1	272	34	37	9.0000
UGG	chr17:42398743-42399011(-)$1	268	7	10	9.0000
UGG	chr3:93803070-93803339(+)$1	269	78	81	9.0000
UGG	chr19:49118486-49118717(-)$1	231	92	95	9.0000
UGG	chr16:2806269-2806504(+)$1	235	2	5	9.0000
UGG	chr1:113459890-113460162(-)$1	272	48	51	9.0000
UGG	chr17:41246542-41246785(-)$1	243	49	52	9.0000
UGG	chr10:70738535-70738790(+)$1	255	119	122	9.0000
UGG	chr12:21807454-21807708(-)$1	254	47	50	9.0000
ugg	chr1:19653651-19653890(+)$1	239	0	3	9.0000
UGG	chr9:139735108-139735377(+)$1	269	3	6	9.0000
UGG	chr16:2813096-2813364(+)$1	268	225	228	9.0000
UGG	chr9:140472989-140473305(-)$1	316	73	76	9.0000
UGG	chr22:29181976-29182215(+)$1	239	27	30	9.0000
UGG	chr9:124921840-124922104(-)$1	264	5	8	9.0000
UGG	chr22:43575559-43575841(-)$1	282	18	21	9.0000
UGG	chr19:19648176-19648413(+)$1	237	5	8	9.0000
UGG	chr15:75498900-75499133(+)$1	233	15	18	9.0000
UGG	chr15:68503942-68504218(-)$1	276	84	87	9.0000
UGG	chr6:31600101-31600365(+)$1	264	10	13	9.0000
UGG	chr1:45266075-45266331(+)$1	256	61	64	9.0000
UGG	chr15:65855047-65855282(+)$1	235	18	21	9.0000
UGG	chr19:2807471-2807814(+)$1	343	22	25	9.0000
UGG	chr12:112756940-112757187(-)$1	247	42	45	9.0000
UGG	chr16:3024001-3024253(-)$1	252	2	5	9.0000
UGG	chr14:95562682-95562965(-)$1	283	36	39	9.0000
UGG	chr10:70100868-70101103(+)$1	235	4	7	9.0000
UGG	chr5:43294097-43294358(-)$1	261	52	55	9.0000
UGG	chr5:179301912-179302159(-)$1	247	50	53	9.0000
UGG	chr6:26124399-26124640(+)$1	241	33	36	9.0000
UGG	chr5:886662-886895(-)$1	233	59	62	9.0000
UGG	chrX:99890472-99890717(-)$1	245	0	3	9.0000
ugg	chr5:31515468-31515696(-)$1	228	58	61	9.0000
Ugg	chr22:39262864-39263127(-)$1	263	229	232	9.0000
UGG	chr11:47196481-47196734(-)$1	253	17	20	9.0000
UGG	chr1:203768450-203768688(+)$1	238	19	22	9.0000
UGG	chr1:16263779-16264041(+)$1	262	69	72	9.0000
UGG	chr11:14380276-14380517(-)$1	241	82	85	9.0000
UGG	chr10:129913902-129914132(-)$1	230	24	27	9.0000
UGG	chr4:25156653-25156873(-)$1	220	84	87	9.0000
UGG	chr20:32441262-32441499(+)$1	237	78	81	9.0000
UGG	chr19:2247767-2248040(+)$1	273	23	26	9.0000
UGG	chr13:23907585-23907816(-)$1	231	52	55	9.0000
UGG	chr10:32310989-32311245(-)$1	256	103	106	9.0000
UGG	chr17:11924093-11924344(+)$1	251	111	114	9.0000
UGG	chr13:77900626-77900896(-)$1	270	122	125	9.0000
UGG	chr20:34081227-34081467(+)$1	240	36	39	9.0000
UGG	chr7:2701226-2701467(+)$1	241	19	22	9.0000
UGG	chr14:31574497-31574754(-)$1	257	82	85	9.0000
UGG	chr6:150023008-150023242(-)$1	234	192	195	9.0000
UGG	chr13:98658444-98658700(+)$1	256	133	136	9.0000
UGG	chr19:55752591-55752848(-)$1	257	14	17	9.0000
ugg	chr12:82748174-82748411(-)$1	237	216	219	9.0000
UGG	chr20:61574790-61575053(+)$1	263	11	14	9.0000
UGG	chr12:132401908-132402148(+)$1	240	57	60	9.0000
UGG	chr19:33696894-33697152(+)$1	258	56	59	9.0000
UGG	chr17:79478842-79479088(-)$1	246	15	18	9.0000
Ugg	chr6:90121542-90121778(-)$1	236	12	15	9.0000
UGG	chr10:63957699-63957933(-)$1	234	10	13	9.0000
UGG	chr16:29821536-29821786(+)$1	250	10	13	9.0000
UGG	chr22:24109920-24110190(-)$1	270	193	196	9.0000
UGG	chr19:1106523-1106867(+)$1	344	61	64	9.0000
UGG	chr6:56336790-56337021(-)$1	231	35	38	9.0000
UGG	chrX:117819603-117819843(+)$1	240	1	4	9.0000
UGG	chr19:50165612-50165850(-)$1	238	7	10	9.0000
UGG	chr12:56553311-56553563(+)$1	252	13	16	9.0000
UGG	chr12:50480438-50480651(+)$1	213	31	34	9.0000
UGG	chr2:232003414-232003664(+)$1	250	9	12	9.0000
UGG	chr1:39835601-39835824(+)$1	223	16	19	9.0000
UGG	chr2:26257407-26257644(+)$1	237	4	7	9.0000
UGG	chr2:74757994-74758234(+)$1	240	65	68	9.0000
UGG	chr1:91403131-91403364(-)$1	233	24	27	9.0000
UGG	chr10:120936469-120936713(-)$1	244	75	78	9.0000
UGG	chr7:4721907-4722209(+)$1	302	33	36	9.0000
UGG	chr1:247320360-247320593(-)$1	233	20	23	9.0000
UGG	chr22:39711361-39711619(-)$1	258	10	13	9.0000
UGG	chr15:59102331-59102570(+)$1	239	2	5	9.0000

#otherMatches

#Struct PSSM
ddd	chr15:75499587-75499828(+)$1	241	31	34	9.0000
""d	chr14:21829234-21829472(-)$1	238	55	58	9.0000
ddm	chr1:1689800-1690048(-)$1	248	53	56	9.0000
ddd	chr14:24779841-24780094(+)$1	253	74	77	9.0000
:a[	chr16:30537630-30537896(-)$1	266	35	38	9.0000
2ee	chr3:42701146-42701406(+)$1	260	45	48	9.0000
OEE	chr10:89265031-89265292(+)$1	261	20	23	9.0000
hhl	chr19:3983007-3983235(-)$1	228	96	99	9.0000
JJJ	chr3:47777452-47777716(-)$1	264	16	19	9.0000
:DD	chrX:118603734-118603984(+)$1	250	1	4	9.0000
hhh	chr6:30570559-30570807(-)$1	248	10	13	9.0000
ddd	chr3:184039616-184039932(+)$1	316	50	53	9.0000
hhh	chr6:158541399-158541644(-)$1	245	39	42	9.0000
F{A	chr11:71726469-71726745(-)$1	276	13	16	9.0000
$$g	chr5:179045112-179045375(-)$1	263	119	122	9.0000
ddd	chr4:144474183-144474440(+)$1	257	104	107	9.0000
GGG	chr9:136208378-136208679(-)$1	301	4	7	9.0000
eee	chr12:50480468-50480714(+)$1	246	1	4	9.0000
[cc	chr17:43012136-43012396(-)$1	260	50	53	9.0000
[dd	chr17:57758179-57758428(+)$1	249	196	199	9.0000
eee	chr8:145741824-145742092(-)$1	268	137	140	9.0000
{DD	chr22:24129185-24129476(+)$1	291	181	184	9.0000
::e	chr19:48982343-48982582(+)$1	239	2	5	9.0000
4ee	chr5:179049962-179050234(-)$1	272	34	37	9.0000
MDD	chr17:42398743-42399011(-)$1	268	7	10	9.0000
bb5	chr3:93803070-93803339(+)$1	269	78	81	9.0000
MMM	chr19:49118486-49118717(-)$1	231	92	95	9.0000
A{E	chr16:2806269-2806504(+)$1	235	2	5	9.0000
ggg	chr1:113459890-113460162(-)$1	272	48	51	9.0000
H::	chr17:41246542-41246785(-)$1	243	49	52	9.0000
cc2	chr10:70738535-70738790(+)$1	255	119	122	9.0000
ee[	chr12:21807454-21807708(-)$1	254	47	50	9.0000
:A{	chr1:19653651-19653890(+)$1	239	0	3	9.0000
:::	chr9:139735108-139735377(+)$1	269	3	6	9.0000
eee	chr16:2813096-2813364(+)$1	268	225	228	9.0000
dd!	chr9:140472989-140473305(-)$1	316	73	76	9.0000
GGG	chr22:29181976-29182215(+)$1	239	27	30	9.0000
cc!	chr9:124921840-124922104(-)$1	264	5	8	9.0000
HHH	chr22:43575559-43575841(-)$1	282	18	21	9.0000
E{D	chr19:19648176-19648413(+)$1	237	5	8	9.0000
MFF	chr15:75498900-75499133(+)$1	233	15	18	9.0000
>ff	chr15:68503942-68504218(-)$1	276	84	87	9.0000
eel	chr6:31600101-31600365(+)$1	264	10	13	9.0000
bb!	chr1:45266075-45266331(+)$1	256	61	64	9.0000
III	chr15:65855047-65855282(+)$1	235	18	21	9.0000
cc]	chr19:2807471-2807814(+)$1	343	22	25	9.0000
ell	chr12:112756940-112757187(-)$1	247	42	45	9.0000
:hh	chr16:3024001-3024253(-)$1	252	2	5	9.0000
ccc	chr14:95562682-95562965(-)$1	283	36	39	9.0000
FFL	chr10:70100868-70101103(+)$1	235	4	7	9.0000
{DD	chr5:43294097-43294358(-)$1	261	52	55	9.0000
"ff	chr5:179301912-179302159(-)$1	247	50	53	9.0000
b##	chr6:26124399-26124640(+)$1	241	33	36	9.0000
fff	chr5:886662-886895(-)$1	233	59	62	9.0000
:CC	chrX:99890472-99890717(-)$1	245	0	3	9.0000
ddd	chr5:31515468-31515696(-)$1	228	58	61	9.0000
ZZA	chr22:39262864-39263127(-)$1	263	229	232	9.0000
LA{	chr11:47196481-47196734(-)$1	253	17	20	9.0000
e]c	chr1:203768450-203768688(+)$1	238	19	22	9.0000
ddd	chr1:16263779-16264041(+)$1	262	69	72	9.0000
e]g	chr11:14380276-14380517(-)$1	241	82	85	9.0000
EEE	chr10:129913902-129914132(-)$1	230	24	27	9.0000
[dd	chr4:25156653-25156873(-)$1	220	84	87	9.0000
EEE	chr20:32441262-32441499(+)$1	237	78	81	9.0000
ddd	chr19:2247767-2248040(+)$1	273	23	26	9.0000
ccc	chr13:23907585-23907816(-)$1	231	52	55	9.0000
eee	chr10:32310989-32311245(-)$1	256	103	106	9.0000
ccc	chr17:11924093-11924344(+)$1	251	111	114	9.0000
EEE	chr13:77900626-77900896(-)$1	270	122	125	9.0000
eee	chr20:34081227-34081467(+)$1	240	36	39	9.0000
FFF	chr7:2701226-2701467(+)$1	241	19	22	9.0000
^^^	chr14:31574497-31574754(-)$1	257	82	85	9.0000
ddd	chr6:150023008-150023242(-)$1	234	192	195	9.0000
sss	chr13:98658444-98658700(+)$1	256	133	136	9.0000
DDN	chr19:55752591-55752848(-)$1	257	14	17	9.0000
F}E	chr12:82748174-82748411(-)$1	237	216	219	9.0000
ooo	chr20:61574790-61575053(+)$1	263	11	14	9.0000
{HH	chr12:132401908-132402148(+)$1	240	57	60	9.0000
GGi	chr19:33696894-33697152(+)$1	258	56	59	9.0000
dd"	chr17:79478842-79479088(-)$1	246	15	18	9.0000
KKC	chr6:90121542-90121778(-)$1	236	12	15	9.0000
fff	chr10:63957699-63957933(-)$1	234	10	13	9.0000
ddd	chr16:29821536-29821786(+)$1	250	10	13	9.0000
FFF	chr22:24109920-24110190(-)$1	270	193	196	9.0000
FFF	chr19:1106523-1106867(+)$1	344	61	64	9.0000
!dd	chr6:56336790-56337021(-)$1	231	35	38	9.0000
:::	chrX:117819603-117819843(+)$1	240	1	4	9.0000
:cc	chr19:50165612-50165850(-)$1	238	7	10	9.0000
Jee	chr12:56553311-56553563(+)$1	252	13	16	9.0000
!dd	chr12:50480438-50480651(+)$1	213	31	34	9.0000
III	chr2:232003414-232003664(+)$1	250	9	12	9.0000
FFF	chr1:39835601-39835824(+)$1	223	16	19	9.0000
eee	chr2:26257407-26257644(+)$1	237	4	7	9.0000
2dd	chr2:74757994-74758234(+)$1	240	65	68	9.0000
nbb	chr1:91403131-91403364(-)$1	233	24	27	9.0000
ccc	chr10:120936469-120936713(-)$1	244	75	78	9.0000
NEE	chr7:4721907-4722209(+)$1	302	33	36	9.0000
ppp	chr1:247320360-247320593(-)$1	233	20	23	9.0000
iii	chr22:39711361-39711619(-)$1	258	10	13	9.0000
:DD	chr15:59102331-59102570(+)$1	239	2	5	9.0000

#DB
(((	chr15:75499587-75499828(+)$1	1	31	34	9.0000
..(	chr14:21829234-21829472(-)$1	1	55	58	9.0000
((.	chr1:1689800-1690048(-)$1	1	53	56	9.0000
)))	chr14:24779841-24780094(+)$1	1	74	77	9.0000
.(.	chr16:30537630-30537896(-)$1	1	35	38	9.0000
.))	chr3:42701146-42701406(+)$1	1	45	48	9.0000
.((	chr10:89265031-89265292(+)$1	1	20	23	9.0000
((.	chr19:3983007-3983235(-)$1	1	96	99	9.0000
(((	chr3:47777452-47777716(-)$1	1	16	19	9.0000
.((	chrX:118603734-118603984(+)$1	1	1	4	9.0000
(((	chr6:30570559-30570807(-)$1	1	10	13	9.0000
)))	chr3:184039616-184039932(+)$1	1	50	53	9.0000
(((	chr6:158541399-158541644(-)$1	1	39	42	9.0000
(.(	chr11:71726469-71726745(-)$1	1	13	16	9.0000
..(	chr5:179045112-179045375(-)$1	1	119	122	9.0000
(((	chr4:144474183-144474440(+)$1	1	104	107	9.0000
(((	chr9:136208378-136208679(-)$1	1	4	7	9.0000
(((	chr12:50480468-50480714(+)$1	1	1	4	9.0000
.((	chr17:43012136-43012396(-)$1	1	50	53	9.0000
.((	chr17:57758179-57758428(+)$1	1	196	199	9.0000
(((	chr8:145741824-145742092(-)$1	1	137	140	9.0000
.((	chr22:24129185-24129476(+)$1	1	181	184	9.0000
..(	chr19:48982343-48982582(+)$1	1	2	5	9.0000
.))	chr5:179049962-179050234(-)$1	1	34	37	9.0000
.((	chr17:42398743-42399011(-)$1	1	7	10	9.0000
)).	chr3:93803070-93803339(+)$1	1	78	81	9.0000
...	chr19:49118486-49118717(-)$1	1	92	95	9.0000
(.(	chr16:2806269-2806504(+)$1	1	2	5	9.0000
(((	chr1:113459890-113460162(-)$1	1	48	51	9.0000
(..	chr17:41246542-41246785(-)$1	1	49	52	9.0000
)).	chr10:70738535-70738790(+)$1	1	119	122	9.0000
((.	chr12:21807454-21807708(-)$1	1	47	50	9.0000
.(.	chr1:19653651-19653890(+)$1	1	0	3	9.0000
...	chr9:139735108-139735377(+)$1	1	3	6	9.0000
)))	chr16:2813096-2813364(+)$1	1	225	228	9.0000
((.	chr9:140472989-140473305(-)$1	1	73	76	9.0000
(((	chr22:29181976-29182215(+)$1	1	27	30	9.0000
((.	chr9:124921840-124922104(-)$1	1	5	8	9.0000
(((	chr22:43575559-43575841(-)$1	1	18	21	9.0000
(.(	chr19:19648176-19648413(+)$1	1	5	8	9.0000
.((	chr15:75498900-75499133(+)$1	1	15	18	9.0000
.))	chr15:68503942-68504218(-)$1	1	84	87	9.0000
((.	chr6:31600101-31600365(+)$1	1	10	13	9.0000
((.	chr1:45266075-45266331(+)$1	1	61	64	9.0000
(((	chr15:65855047-65855282(+)$1	1	18	21	9.0000
)).	chr19:2807471-2807814(+)$1	1	22	25	9.0000
(..	chr12:112756940-112757187(-)$1	1	42	45	9.0000
.((	chr16:3024001-3024253(-)$1	1	2	5	9.0000
(((	chr14:95562682-95562965(-)$1	1	36	39	9.0000
((.	chr10:70100868-70101103(+)$1	1	4	7	9.0000
.((	chr5:43294097-43294358(-)$1	1	52	55	9.0000
.((	chr5:179301912-179302159(-)$1	1	50	53	9.0000
(..	chr6:26124399-26124640(+)$1	1	33	36	9.0000
(((	chr5:886662-886895(-)$1	1	59	62	9.0000
.((	chrX:99890472-99890717(-)$1	1	0	3	9.0000
(((	chr5:31515468-31515696(-)$1	1	58	61	9.0000
..)	chr22:39262864-39263127(-)$1	1	229	232	9.0000
.(.	chr11:47196481-47196734(-)$1	1	17	20	9.0000
).)	chr1:203768450-203768688(+)$1	1	19	22	9.0000
)))	chr1:16263779-16264041(+)$1	1	69	72	9.0000
).)	chr11:14380276-14380517(-)$1	1	82	85	9.0000
(((	chr10:129913902-129914132(-)$1	1	24	27	9.0000
.((	chr4:25156653-25156873(-)$1	1	84	87	9.0000
(((	chr20:32441262-32441499(+)$1	1	78	81	9.0000
)))	chr19:2247767-2248040(+)$1	1	23	26	9.0000
)))	chr13:23907585-23907816(-)$1	1	52	55	9.0000
)))	chr10:32310989-32311245(-)$1	1	103	106	9.0000
)))	chr17:11924093-11924344(+)$1	1	111	114	9.0000
)))	chr13:77900626-77900896(-)$1	1	122	125	9.0000
(((	chr20:34081227-34081467(+)$1	1	36	39	9.0000
(((	chr7:2701226-2701467(+)$1	1	19	22	9.0000
...	chr14:31574497-31574754(-)$1	1	82	85	9.0000
)))	chr6:150023008-150023242(-)$1	1	192	195	9.0000
...	chr13:98658444-98658700(+)$1	1	133	136	9.0000
((.	chr19:55752591-55752848(-)$1	1	14	17	9.0000
).)	chr12:82748174-82748411(-)$1	1	216	219	9.0000
...	chr20:61574790-61575053(+)$1	1	11	14	9.0000
.((	chr12:132401908-132402148(+)$1	1	57	60	9.0000
(((	chr19:33696894-33697152(+)$1	1	56	59	9.0000
((.	chr17:79478842-79479088(-)$1	1	15	18	9.0000
..(	chr6:90121542-90121778(-)$1	1	12	15	9.0000
(((	chr10:63957699-63957933(-)$1	1	10	13	9.0000
(((	chr16:29821536-29821786(+)$1	1	10	13	9.0000
)))	chr22:24109920-24110190(-)$1	1	193	196	9.0000
(((	chr19:1106523-1106867(+)$1	1	61	64	9.0000
.((	chr6:56336790-56337021(-)$1	1	35	38	9.0000
...	chrX:117819603-117819843(+)$1	1	1	4	9.0000
.((	chr19:50165612-50165850(-)$1	1	7	10	9.0000
(((	chr12:56553311-56553563(+)$1	1	13	16	9.0000
.((	chr12:50480438-50480651(+)$1	1	31	34	9.0000
(((	chr2:232003414-232003664(+)$1	1	9	12	9.0000
(((	chr1:39835601-39835824(+)$1	1	16	19	9.0000
(((	chr2:26257407-26257644(+)$1	1	4	7	9.0000
.))	chr2:74757994-74758234(+)$1	1	65	68	9.0000
.))	chr1:91403131-91403364(-)$1	1	24	27	9.0000
)))	chr10:120936469-120936713(-)$1	1	75	78	9.0000
.((	chr7:4721907-4722209(+)$1	1	33	36	9.0000
...	chr1:247320360-247320593(-)$1	1	20	23	9.0000
(((	chr22:39711361-39711619(-)$1	1	10	13	9.0000
.((	chr15:59102331-59102570(+)$1	1	2	5	9.0000

#PSSM
U : 0.96	u : 0.04	
G : 0.94	g : 0.06	
G : 0.94	g : 0.06	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_transcript_m3_run2.nuc.txt

#NT
uuuauuuc	chr1:236439090-236439327(-)$1	237	196	204	15.5624
uuuauuug	chr1:174991534-174991755(-)$1	221	93	101	15.3541
uuuauuuu	chr1:151877711-151878019(-)$1	308	34	42	19.7291
uuaauuuu	chr16:22267670-22267919(+)$1	249	48	56	15.5624
uuuauuuu	chr1:18681353-18681568(+)$1	215	79	87	19.7291
UUUAUUUA	chr11:73432549-73432792(-)$1	243	116	124	15.3541
uuuauuuu	chr1:109346080-109346295(+)$1	215	28	36	19.7291
uuuuuuuu	chr4:108578882-108579106(-)$1	224	193	201	16.6041
uuuauuuc	chrX:50061031-50061246(+)$1	215	117	125	15.5624
UCUAUUUU	chr2:61537852-61538098(-)$1	246	27	35	15.2499
uuuuuuuu	chr2:197017899-197018228(-)$1	329	237	245	16.6041
UUUAUUUU	chr2:89000909-89001133(+)$1	224	23	31	19.7291
UUUAUUUC	chr22:40473363-40473586(+)$1	223	166	174	15.5624
UUUAUUUU	chr2:179647666-179647883(-)$1	217	69	77	19.7291
UUUAUUGU	chr8:133025481-133025729(+)$1	248	64	72	15.1458
uuuguuuu	chr2:148774194-148774420(-)$1	226	141	149	16.2916
uguauuuu	chr10:104029954-104030175(+)$1	221	143	151	15.3541
uuuauugu	chr7:4084356-4084584(+)$1	228	43	51	15.1458
UUCAUUUU	chr3:42184046-42184268(+)$1	222	209	217	16.0833
UUUAGUUU	chr12:8249919-8250165(+)$1	246	95	103	15.1458
uuuguuuu	chr1:192611831-192612046(+)$1	215	154	162	16.2916
uuuUUUUU	chr1:171513073-171513326(+)$1	253	177	185	16.6041
UUCAUUUU	chr3:185634628-185634872(-)$1	244	234	242	16.0833
uuuauuuu	chr13:92173655-92173877(+)$1	222	210	218	19.7291
UUUAAUUU	chr6:21085123-21085395(+)$1	272	180	188	15.2500
AUCAUUUU	chr9:123679210-123679523(-)$1	313	216	224	12.5416
UGUAUUUU	chr5:50127861-50128099(+)$1	238	203	211	15.3541
uuuuuuuu	chr21:45480674-45480937(+)$1	263	154	162	16.6041
guuauuuu	chr11:77956282-77956525(-)$1	243	99	107	15.6666
uucauuuu	chr18:34575990-34576242(+)$1	252	126	134	16.0833
uuuaauuu	chr11:114098564-114098778(+)$1	214	0	8	15.2500
AUUAUUUU	chr10:72311974-72312191(+)$1	217	179	187	16.1874
aucauuuu	chrX:62935589-62935842(-)$1	253	9	17	12.5416
UAUAUUUU	chr21:18957246-18957460(+)$1	214	9	17	15.2499
UUUGUUUU	chr3:59735804-59736031(-)$1	227	132	140	16.2916
uucauuuu	chrX:5934567-5934788(-)$1	221	108	116	16.0833
uuucuuuu	chr1:33479906-33480205(-)$1	299	140	148	16.2916
uuucuuuu	chr20:507540-507859(-)$1	319	255	263	16.2916
uuuuuuuu	chr17:65204167-65204411(-)$1	244	26	34	16.6041
AUUAUUUU	chr17:533868-534113(-)$1	245	181	189	16.1874
auuauuuu	chr16:69005216-69005434(+)$1	218	133	141	16.1874
UUUAUUUU	chr2:233938518-233938751(+)$1	233	187	195	19.7291
auuauuuu	chrX:135799078-135799318(-)$1	240	117	125	16.1874
uuucuuuu	chrX:135270607-135270820(+)$1	213	149	157	16.2916
uuuuuuuu	chr9:131456518-131456772(+)$1	254	0	8	16.6041
CUUAUUUU	chr6:74362257-74362500(-)$1	243	42	50	15.6666
UUUAUUUU	chr15:55569175-55569435(-)$1	260	218	226	19.7291

#otherMatches

#Struct PSSM
::::::::	chr4:143193544-143193793(-)$1	249	179	187	19.7291
fffff[bb	chr1:236439090-236439327(-)$1	237	196	204	15.5624
mmmmeeee	chr1:174991534-174991755(-)$1	221	93	101	15.3541
DDD{HHHH	chr1:151877711-151878019(-)$1	308	34	42	19.7291
ii::::::	chr16:22267670-22267919(+)$1	249	48	56	15.5624
d22fffff	chr1:18681353-18681568(+)$1	215	79	87	19.7291
:ccc[ccc	chr11:73432549-73432792(-)$1	243	116	124	15.3541
::::::::	chr1:109346080-109346295(+)$1	215	28	36	19.7291
>>>>>>>>	chr4:108578882-108579106(-)$1	224	193	201	16.6041
e)))))))	chrX:50061031-50061246(+)$1	215	117	125	15.5624
ddddllld	chr2:61537852-61538098(-)$1	246	27	35	15.2499
####eeee	chr2:197017899-197018228(-)$1	329	237	245	16.6041
d[cccuuu	chr2:89000909-89001133(+)$1	224	23	31	19.7291
:::::::i	chr22:40473363-40473586(+)$1	223	166	174	15.5624
:::ggggg	chr2:179647666-179647883(-)$1	217	69	77	19.7291
KKJJJJJJ	chr8:133025481-133025729(+)$1	248	64	72	15.1458
ggggg###	chr2:148774194-148774420(-)$1	226	141	149	16.2916
::::::::	chr10:104029954-104030175(+)$1	221	143	151	15.3541
iiiiiiii	chr7:4084356-4084584(+)$1	228	43	51	15.1458
FF______	chr3:42184046-42184268(+)$1	222	209	217	16.0833
gggppppp	chr12:8249919-8250165(+)$1	246	95	103	15.1458
::::::::	chr1:192611831-192612046(+)$1	215	154	162	16.2916
ccvvvvvv	chr1:171513073-171513326(+)$1	253	177	185	16.6041
::::::::	chr3:185634628-185634872(-)$1	244	234	242	16.0833
~~~DDDD:	chr13:92173655-92173877(+)$1	222	210	218	19.7291
eeoooooo	chr6:21085123-21085395(+)$1	272	180	188	15.2500
&&&&&&&e	chr9:123679210-123679523(-)$1	313	216	224	12.5416
ggggggg:	chr5:50127861-50128099(+)$1	238	203	211	15.3541
::::::::	chr21:45480674-45480937(+)$1	263	154	162	16.6041
e22ccc33	chr11:77956282-77956525(-)$1	243	99	107	15.6666
::::::::	chr18:34575990-34576242(+)$1	252	126	134	16.0833
FFFFFFLL	chr11:114098564-114098778(+)$1	214	0	8	15.2500
[iiiiiii	chr10:72311974-72312191(+)$1	217	179	187	16.1874
::::::::	chrX:62935589-62935842(-)$1	253	9	17	12.5416
JJJJJJJJ	chr21:18957246-18957460(+)$1	214	9	17	15.2499
dddd4444	chr3:59735804-59736031(-)$1	227	132	140	16.2916
::::::::	chrX:5934567-5934788(-)$1	221	108	116	16.0833
hhhh^^^^	chr1:33479906-33480205(-)$1	299	140	148	16.2916
^^^^^^^^	chr20:507540-507859(-)$1	319	255	263	16.2916
::::eeee	chr17:65204167-65204411(-)$1	244	26	34	16.6041
ppgggggg	chr17:533868-534113(-)$1	245	181	189	16.1874
emmmmeee	chr16:69005216-69005434(+)$1	218	133	141	16.1874
"=======	chr2:233938518-233938751(+)$1	233	187	195	19.7291
^^^^^^^^	chrX:135799078-135799318(-)$1	240	117	125	16.1874
eeeee22b	chrX:135270607-135270820(+)$1	213	149	157	16.2916
::::::gg	chr9:131456518-131456772(+)$1	254	0	8	16.6041
ccoooooo	chr6:74362257-74362500(-)$1	243	42	50	15.6666
ddddmmmm	chr15:55569175-55569435(-)$1	260	218	226	19.7291

#DB
........	chr4:143193544-143193793(-)$1	1	179	187	19.7291
(((((.((	chr1:236439090-236439327(-)$1	1	196	204	15.5624
....))))	chr1:174991534-174991755(-)$1	1	93	101	15.3541
(((.((((	chr1:151877711-151878019(-)$1	1	34	42	19.7291
))......	chr16:22267670-22267919(+)$1	1	48	56	15.5624
)..)))))	chr1:18681353-18681568(+)$1	1	79	87	19.7291
.(((.(((	chr11:73432549-73432792(-)$1	1	116	124	15.3541
........	chr1:109346080-109346295(+)$1	1	28	36	19.7291
........	chr4:108578882-108579106(-)$1	1	193	201	16.6041
(.......	chrX:50061031-50061246(+)$1	1	117	125	15.5624
((((...)	chr2:61537852-61538098(-)$1	1	27	35	15.2499
....((((	chr2:197017899-197018228(-)$1	1	237	245	16.6041
(.(((...	chr2:89000909-89001133(+)$1	1	23	31	19.7291
.......(	chr22:40473363-40473586(+)$1	1	166	174	15.5624
...(((((	chr2:179647666-179647883(-)$1	1	69	77	19.7291
..((((((	chr8:133025481-133025729(+)$1	1	64	72	15.1458
(((((...	chr2:148774194-148774420(-)$1	1	141	149	16.2916
........	chr10:104029954-104030175(+)$1	1	143	151	15.3541
((((((((	chr7:4084356-4084584(+)$1	1	43	51	15.1458
))......	chr3:42184046-42184268(+)$1	1	209	217	16.0833
(((.....	chr12:8249919-8250165(+)$1	1	95	103	15.1458
........	chr1:192611831-192612046(+)$1	1	154	162	16.2916
((......	chr1:171513073-171513326(+)$1	1	177	185	16.6041
........	chr3:185634628-185634872(-)$1	1	234	242	16.0833
...)))).	chr13:92173655-92173877(+)$1	1	210	218	19.7291
((......	chr6:21085123-21085395(+)$1	1	180	188	15.2500
.......(	chr9:123679210-123679523(-)$1	1	216	224	12.5416
))))))).	chr5:50127861-50128099(+)$1	1	203	211	15.3541
........	chr21:45480674-45480937(+)$1	1	154	162	16.6041
)..)))..	chr11:77956282-77956525(-)$1	1	99	107	15.6666
........	chr18:34575990-34576242(+)$1	1	126	134	16.0833
((((((..	chr11:114098564-114098778(+)$1	1	0	8	15.2500
.(((((((	chr10:72311974-72312191(+)$1	1	179	187	16.1874
........	chrX:62935589-62935842(-)$1	1	9	17	12.5416
((((((((	chr21:18957246-18957460(+)$1	1	9	17	15.2499
))))....	chr3:59735804-59736031(-)$1	1	132	140	16.2916
........	chrX:5934567-5934788(-)$1	1	108	116	16.0833
((((....	chr1:33479906-33480205(-)$1	1	140	148	16.2916
........	chr20:507540-507859(-)$1	1	255	263	16.2916
....((((	chr17:65204167-65204411(-)$1	1	26	34	16.6041
..))))))	chr17:533868-534113(-)$1	1	181	189	16.1874
(....)))	chr16:69005216-69005434(+)$1	1	133	141	16.1874
.(((((((	chr2:233938518-233938751(+)$1	1	187	195	19.7291
........	chrX:135799078-135799318(-)$1	1	117	125	16.1874
)))))..)	chrX:135270607-135270820(+)$1	1	149	157	16.2916
......((	chr9:131456518-131456772(+)$1	1	0	8	16.6041
((......	chr6:74362257-74362500(-)$1	1	42	50	15.6666
((((....	chr15:55569175-55569435(-)$1	1	218	226	19.7291

#PSSM
u : 0.49	U : 0.33	A : 0.06	a : 0.06	g : 0.02	C : 0.02	
u : 0.56	U : 0.35	C : 0.02	g : 0.02	G : 0.02	A : 0.02	
u : 0.49	U : 0.35	C : 0.06	c : 0.06	a : 0.02	
A : 0.39	a : 0.35	u : 0.10	c : 0.06	g : 0.04	U : 0.02	G : 0.02	
u : 0.54	U : 0.39	G : 0.02	A : 0.02	a : 0.02	
u : 0.56	U : 0.43	
u : 0.54	U : 0.41	G : 0.02	g : 0.02	
u : 0.49	U : 0.39	c : 0.04	g : 0.02	A : 0.02	C : 0.02	

#score	790.5416666666664
#seq	48
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m1_run2.nuc.txt

#NT
GAAG	chr10:33208712-33208939(-)$1	227	14	18	12.0000
GAAG	chr20:3838306-3838539(+)$1	233	116	120	12.0000
GAAG	chr6:26033414-26033640(-)$1	226	68	72	12.0000
GAAG	chr20:62591191-62591445(-)$1	254	18	22	12.0000
GAAG	chr16:30750159-30750438(+)$1	279	11	15	12.0000
GAAG	chr14:94526398-94526620(-)$1	222	132	136	12.0000
gaag	chr8:98725820-98726041(+)$1	221	143	147	12.0000
GAAG	chr9:117848800-117849024(-)$1	224	11	15	12.0000
GAAG	chr19:19626947-19627193(+)$1	246	79	83	12.0000
GAAG	chr17:7406832-7407055(+)$1	223	91	95	12.0000
GAAG	chr12:66703628-66703856(+)$1	228	19	23	12.0000
GAAG	chr3:25662133-25662355(-)$1	222	16	20	12.0000
GAAG	chr17:39977901-39978130(+)$1	229	123	127	12.0000
GAAG	chr12:56385782-56386013(+)$1	231	52	56	12.0000
GAAG	chr7:156962978-156963200(+)$1	222	32	36	12.0000
GAAG	chr2:24881464-24881692(+)$1	228	69	73	12.0000
GAAG	chr17:72862864-72863156(-)$1	292	35	39	12.0000
GAAG	chr6:31797511-31797767(+)$1	256	3	7	12.0000
GAAG	chr8:144671412-144671650(-)$1	238	103	107	12.0000
GAAG	chr1:3649247-3649480(+)$1	233	77	81	12.0000
GAAG	chr17:58740464-58740691(+)$1	227	53	57	12.0000
GAAG	chr1:149857635-149857925(-)$1	290	264	268	12.0000
GAAG	chr15:44058060-44058292(+)$1	232	49	53	12.0000
GAAG	chr7:117424268-117424499(-)$1	231	116	120	12.0000
GAAG	chrX:118377086-118377312(+)$1	226	55	59	12.0000
GAAG	chr3:194154400-194154625(-)$1	225	82	86	12.0000
GAAG	chr3:169496465-169496685(+)$1	220	15	19	12.0000
GAAG	chr21:38311034-38311265(-)$1	231	40	44	12.0000
GAAG	chr2:86279928-86280171(-)$1	243	60	64	12.0000
GAAG	chr3:128889271-128889497(-)$1	226	130	134	12.0000
GAAG	chr1:153610670-153610893(+)$1	223	96	100	12.0000
GAAG	chr12:69783951-69784178(+)$1	227	10	14	12.0000
GAAG	chr13:77581329-77581548(-)$1	219	26	30	12.0000
GAAG	chr17:61770939-61771162(+)$1	223	27	31	12.0000
GAAG	chr9:115166271-115166493(+)$1	222	160	164	12.0000
GAAG	chr21:33719964-33720186(-)$1	222	176	180	12.0000
GAAG	chr4:6882472-6882674(+)$1	202	56	60	12.0000
GAAG	chr12:122989980-122990206(-)$1	226	6	10	12.0000
GAAG	chr12:56575208-56575435(-)$1	227	86	90	12.0000
GAAG	chr4:74026857-74027082(-)$1	225	64	68	12.0000
GAAG	chr6:26156577-26156815(+)$1	238	88	92	12.0000
GAAG	chrX:102931422-102931663(-)$1	241	4	8	12.0000
GAAG	chr7:36492032-36492255(+)$1	223	16	20	12.0000
GAAG	chr11:62400440-62400658(-)$1	218	53	57	12.0000
gaag	chr11:6238799-6239030(-)$1	231	36	40	12.0000
GAAG	chrX:53224076-53224298(-)$1	222	10	14	12.0000
GAAG	chr2:222298776-222299012(-)$1	236	34	38	12.0000
GAAG	chr22:40755198-40755410(+)$1	212	154	158	12.0000
GAAG	chr9:117853047-117853272(-)$1	225	35	39	12.0000
GAAG	chr17:33680918-33681144(-)$1	226	195	199	12.0000
GAAG	chr1:234509955-234510178(+)$1	223	53	57	12.0000
GAAG	chr5:179041774-179042025(-)$1	251	104	108	12.0000
GAAG	chr20:61833787-61834037(-)$1	250	101	105	12.0000
GAAG	chr3:24003417-24003653(+)$1	236	117	121	12.0000
GAAG	chr6:31237664-31237895(-)$1	231	142	146	12.0000
GAAG	chr13:30093503-30093725(-)$1	222	64	68	12.0000
GAAG	chr21:27263965-27264211(-)$1	246	43	47	12.0000
GAAG	chr10:75863510-75863735(+)$1	225	6	10	12.0000
GAAG	chr22:38881917-38882146(-)$1	229	25	29	12.0000
GAAG	chr11:111622838-111623069(-)$1	231	61	65	12.0000
GAAG	chr7:150753580-150753809(-)$1	229	21	25	12.0000
GAAG	chr4:38097462-38097687(+)$1	225	118	122	12.0000
GAAG	chr9:117848690-117848931(-)$1	241	43	47	12.0000
GAAG	chr12:80014846-80015072(-)$1	226	100	104	12.0000
GAAG	chr6:3298325-3298549(-)$1	224	11	15	12.0000
GAAG	chr1:244217072-244217299(+)$1	227	22	26	12.0000
GAAG	chr1:161093554-161093778(-)$1	224	154	158	12.0000
GAAG	chr6:27115182-27115425(+)$1	243	81	85	12.0000
GAAG	chr20:40084474-40084705(-)$1	231	155	159	12.0000
GAAG	chr14:30046408-30046630(-)$1	222	57	61	12.0000
gaag	chr20:51870075-51870301(+)$1	226	6	10	12.0000
GAAG	chr7:99227018-99227239(+)$1	221	24	28	12.0000
GAAG	chr7:50513102-50513333(-)$1	231	17	21	12.0000
GAAG	chr8:42977728-42977950(+)$1	222	72	76	12.0000
GAAG	chr4:83977996-83978221(+)$1	225	118	122	12.0000
GAAG	chr7:155090278-155090496(+)$1	218	154	158	12.0000
GAAG	chr2:182756752-182756976(+)$1	224	112	116	12.0000
GAAG	chr20:62153045-62153278(+)$1	233	24	28	12.0000
GAAG	chr1:68151040-68151284(+)$1	244	169	173	12.0000
GAAG	chr7:150934673-150934906(+)$1	233	49	53	12.0000
GAAG	chr20:52192852-52193075(-)$1	223	21	25	12.0000

#otherMatches

#Struct PSSM
ffdd	chr2:48027154-48027376(+)$1	222	86	90	12.0000
:HHH	chr10:33208712-33208939(-)$1	227	14	18	12.0000
e!!a	chr20:3838306-3838539(+)$1	233	116	120	12.0000
vvva	chr6:26033414-26033640(-)$1	226	68	72	12.0000
ccyy	chr20:62591191-62591445(-)$1	254	18	22	12.0000
DDDD	chr16:30750159-30750438(+)$1	279	11	15	12.0000
:::e	chr14:94526398-94526620(-)$1	222	132	136	12.0000
FFFF	chr8:98725820-98726041(+)$1	221	143	147	12.0000
C::D	chr9:117848800-117849024(-)$1	224	11	15	12.0000
hhhh	chr19:19626947-19627193(+)$1	246	79	83	12.0000
nnnc	chr17:7406832-7407055(+)$1	223	91	95	12.0000
====	chr12:66703628-66703856(+)$1	228	19	23	12.0000
c:cc	chr3:25662133-25662355(-)$1	222	16	20	12.0000
mmmd	chr17:39977901-39978130(+)$1	229	123	127	12.0000
fff[	chr12:56385782-56386013(+)$1	231	52	56	12.0000
IIII	chr7:156962978-156963200(+)$1	222	32	36	12.0000
ff[d	chr2:24881464-24881692(+)$1	228	69	73	12.0000
c!!c	chr17:72862864-72863156(-)$1	292	35	39	12.0000
{JJJ	chr6:31797511-31797767(+)$1	256	3	7	12.0000
iiii	chr8:144671412-144671650(-)$1	238	103	107	12.0000
h[dd	chr1:3649247-3649480(+)$1	233	77	81	12.0000
gggg	chr17:58740464-58740691(+)$1	227	53	57	12.0000
eeee	chr1:149857635-149857925(-)$1	290	264	268	12.0000
bccc	chr15:44058060-44058292(+)$1	232	49	53	12.0000
iiii	chr7:117424268-117424499(-)$1	231	116	120	12.0000
qqqq	chrX:118377086-118377312(+)$1	226	55	59	12.0000
::::	chr3:194154400-194154625(-)$1	225	82	86	12.0000
ffff	chr3:169496465-169496685(+)$1	220	15	19	12.0000
hhhh	chr21:38311034-38311265(-)$1	231	40	44	12.0000
cDDD	chr2:86279928-86280171(-)$1	243	60	64	12.0000
EEEE	chr3:128889271-128889497(-)$1	226	130	134	12.0000
fff!	chr1:153610670-153610893(+)$1	223	96	100	12.0000
:::c	chr12:69783951-69784178(+)$1	227	10	14	12.0000
dddp	chr13:77581329-77581548(-)$1	219	26	30	12.0000
:::c	chr17:61770939-61771162(+)$1	223	27	31	12.0000
oooo	chr9:115166271-115166493(+)$1	222	160	164	12.0000
d::E	chr21:33719964-33720186(-)$1	222	176	180	12.0000
qqqq	chr4:6882472-6882674(+)$1	202	56	60	12.0000
NNBB	chr12:122989980-122990206(-)$1	226	6	10	12.0000
OOCC	chr12:56575208-56575435(-)$1	227	86	90	12.0000
ooob	chr4:74026857-74027082(-)$1	225	64	68	12.0000
bbee	chr6:26156577-26156815(+)$1	238	88	92	12.0000
ettt	chrX:102931422-102931663(-)$1	241	4	8	12.0000
dddl	chr7:36492032-36492255(+)$1	223	16	20	12.0000
ffdd	chr11:62400440-62400658(-)$1	218	53	57	12.0000
::::	chr11:6238799-6239030(-)$1	231	36	40	12.0000
:FFF	chrX:53224076-53224298(-)$1	222	10	14	12.0000
::::	chr2:222298776-222299012(-)$1	236	34	38	12.0000
cc]c	chr22:40755198-40755410(+)$1	212	154	158	12.0000
cc]g	chr9:117853047-117853272(-)$1	225	35	39	12.0000
dddd	chr17:33680918-33681144(-)$1	226	195	199	12.0000
rrrr	chr1:234509955-234510178(+)$1	223	53	57	12.0000
ggg:	chr5:179041774-179042025(-)$1	251	104	108	12.0000
cccd	chr20:61833787-61834037(-)$1	250	101	105	12.0000
###f	chr3:24003417-24003653(+)$1	236	117	121	12.0000
FFFF	chr6:31237664-31237895(-)$1	231	142	146	12.0000
oeee	chr13:30093503-30093725(-)$1	222	64	68	12.0000
eeee	chr21:27263965-27264211(-)$1	246	43	47	12.0000
KJJJ	chr10:75863510-75863735(+)$1	225	6	10	12.0000
cc[d	chr22:38881917-38882146(-)$1	229	25	29	12.0000
hhh>	chr11:111622838-111623069(-)$1	231	61	65	12.0000
cc::	chr7:150753580-150753809(-)$1	229	21	25	12.0000
wwcc	chr4:38097462-38097687(+)$1	225	118	122	12.0000
qqqq	chr9:117848690-117848931(-)$1	241	43	47	12.0000
eeee	chr12:80014846-80015072(-)$1	226	100	104	12.0000
hhll	chr6:3298325-3298549(-)$1	224	11	15	12.0000
GGGG	chr1:244217072-244217299(+)$1	227	22	26	12.0000
csss	chr1:161093554-161093778(-)$1	224	154	158	12.0000
^^^^	chr6:27115182-27115425(+)$1	243	81	85	12.0000
tttt	chr20:40084474-40084705(-)$1	231	155	159	12.0000
###c	chr14:30046408-30046630(-)$1	222	57	61	12.0000
::::	chr20:51870075-51870301(+)$1	226	6	10	12.0000
ee!!	chr7:99227018-99227239(+)$1	221	24	28	12.0000
GGGG	chr7:50513102-50513333(-)$1	231	17	21	12.0000
ff22	chr8:42977728-42977950(+)$1	222	72	76	12.0000
ee##	chr4:83977996-83978221(+)$1	225	118	122	12.0000
eeee	chr7:155090278-155090496(+)$1	218	154	158	12.0000
CYYD	chr2:182756752-182756976(+)$1	224	112	116	12.0000
eerr	chr20:62153045-62153278(+)$1	233	24	28	12.0000
::::	chr1:68151040-68151284(+)$1	244	169	173	12.0000
e22d	chr7:150934673-150934906(+)$1	233	49	53	12.0000
FFFF	chr20:52192852-52193075(-)$1	223	21	25	12.0000

#DB
))))	chr2:48027154-48027376(+)$1	1	86	90	12.0000
.(((	chr10:33208712-33208939(-)$1	1	14	18	12.0000
(..(	chr20:3838306-3838539(+)$1	1	116	120	12.0000
...)	chr6:26033414-26033640(-)$1	1	68	72	12.0000
((..	chr20:62591191-62591445(-)$1	1	18	22	12.0000
((((	chr16:30750159-30750438(+)$1	1	11	15	12.0000
...(	chr14:94526398-94526620(-)$1	1	132	136	12.0000
))))	chr8:98725820-98726041(+)$1	1	143	147	12.0000
(..(	chr9:117848800-117849024(-)$1	1	11	15	12.0000
))))	chr19:19626947-19627193(+)$1	1	79	83	12.0000
...)	chr17:7406832-7407055(+)$1	1	91	95	12.0000
((((	chr12:66703628-66703856(+)$1	1	19	23	12.0000
).((	chr3:25662133-25662355(-)$1	1	16	20	12.0000
...)	chr17:39977901-39978130(+)$1	1	123	127	12.0000
(((.	chr12:56385782-56386013(+)$1	1	52	56	12.0000
((((	chr7:156962978-156963200(+)$1	1	32	36	12.0000
((.(	chr2:24881464-24881692(+)$1	1	69	73	12.0000
(..(	chr17:72862864-72863156(-)$1	1	35	39	12.0000
.(((	chr6:31797511-31797767(+)$1	1	3	7	12.0000
((((	chr8:144671412-144671650(-)$1	1	103	107	12.0000
(.((	chr1:3649247-3649480(+)$1	1	77	81	12.0000
((((	chr17:58740464-58740691(+)$1	1	53	57	12.0000
))))	chr1:149857635-149857925(-)$1	1	264	268	12.0000
((((	chr15:44058060-44058292(+)$1	1	49	53	12.0000
))))	chr7:117424268-117424499(-)$1	1	116	120	12.0000
....	chrX:118377086-118377312(+)$1	1	55	59	12.0000
....	chr3:194154400-194154625(-)$1	1	82	86	12.0000
))))	chr3:169496465-169496685(+)$1	1	15	19	12.0000
((((	chr21:38311034-38311265(-)$1	1	40	44	12.0000
)(((	chr2:86279928-86280171(-)$1	1	60	64	12.0000
))))	chr3:128889271-128889497(-)$1	1	130	134	12.0000
(((.	chr1:153610670-153610893(+)$1	1	96	100	12.0000
...(	chr12:69783951-69784178(+)$1	1	10	14	12.0000
(((.	chr13:77581329-77581548(-)$1	1	26	30	12.0000
...(	chr17:61770939-61771162(+)$1	1	27	31	12.0000
....	chr9:115166271-115166493(+)$1	1	160	164	12.0000
)..)	chr21:33719964-33720186(-)$1	1	176	180	12.0000
....	chr4:6882472-6882674(+)$1	1	56	60	12.0000
..((	chr12:122989980-122990206(-)$1	1	6	10	12.0000
..((	chr12:56575208-56575435(-)$1	1	86	90	12.0000
...)	chr4:74026857-74027082(-)$1	1	64	68	12.0000
))((	chr6:26156577-26156815(+)$1	1	88	92	12.0000
(...	chrX:102931422-102931663(-)$1	1	4	8	12.0000
(((.	chr7:36492032-36492255(+)$1	1	16	20	12.0000
((((	chr11:62400440-62400658(-)$1	1	53	57	12.0000
....	chr11:6238799-6239030(-)$1	1	36	40	12.0000
.(((	chrX:53224076-53224298(-)$1	1	10	14	12.0000
....	chr2:222298776-222299012(-)$1	1	34	38	12.0000
)).)	chr22:40755198-40755410(+)$1	1	154	158	12.0000
)).)	chr9:117853047-117853272(-)$1	1	35	39	12.0000
))))	chr17:33680918-33681144(-)$1	1	195	199	12.0000
....	chr1:234509955-234510178(+)$1	1	53	57	12.0000
))).	chr5:179041774-179042025(-)$1	1	104	108	12.0000
))))	chr20:61833787-61834037(-)$1	1	101	105	12.0000
...(	chr3:24003417-24003653(+)$1	1	117	121	12.0000
))))	chr6:31237664-31237895(-)$1	1	142	146	12.0000
.)))	chr13:30093503-30093725(-)$1	1	64	68	12.0000
))))	chr21:27263965-27264211(-)$1	1	43	47	12.0000
.(((	chr10:75863510-75863735(+)$1	1	6	10	12.0000
((.(	chr22:38881917-38882146(-)$1	1	25	29	12.0000
))).	chr11:111622838-111623069(-)$1	1	61	65	12.0000
))..	chr7:150753580-150753809(-)$1	1	21	25	12.0000
..))	chr4:38097462-38097687(+)$1	1	118	122	12.0000
....	chr9:117848690-117848931(-)$1	1	43	47	12.0000
))))	chr12:80014846-80015072(-)$1	1	100	104	12.0000
((..	chr6:3298325-3298549(-)$1	1	11	15	12.0000
((((	chr1:244217072-244217299(+)$1	1	22	26	12.0000
(...	chr1:161093554-161093778(-)$1	1	154	158	12.0000
....	chr6:27115182-27115425(+)$1	1	81	85	12.0000
....	chr20:40084474-40084705(-)$1	1	155	159	12.0000
...(	chr14:30046408-30046630(-)$1	1	57	61	12.0000
....	chr20:51870075-51870301(+)$1	1	6	10	12.0000
((..	chr7:99227018-99227239(+)$1	1	24	28	12.0000
((((	chr7:50513102-50513333(-)$1	1	17	21	12.0000
))..	chr8:42977728-42977950(+)$1	1	72	76	12.0000
((..	chr4:83977996-83978221(+)$1	1	118	122	12.0000
))))	chr7:155090278-155090496(+)$1	1	154	158	12.0000
)..)	chr2:182756752-182756976(+)$1	1	112	116	12.0000
((..	chr20:62153045-62153278(+)$1	1	24	28	12.0000
....	chr1:68151040-68151284(+)$1	1	169	173	12.0000
)..)	chr7:150934673-150934906(+)$1	1	49	53	12.0000
((((	chr20:52192852-52193075(-)$1	1	21	25	12.0000

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

#score	984.0000000000001
#seq	82
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m2_run1.nuc.txt

#NT
CUU	chrX:152969422-152969648(-)$1	226	50	53	8.9999
CUU	chr1:204380093-204380324(-)$1	231	16	19	8.9999
CUU	chr3:121447934-121448145(-)$1	211	0	3	8.9999
CUU	chr12:44238440-44238663(+)$1	223	25	28	8.9999
CUU	chr2:217005875-217006097(+)$1	222	12	15	8.9999
CUU	chr13:25672020-25672257(+)$1	237	5	8	8.9999
CUU	chr12:56646214-56646438(-)$1	224	12	15	8.9999
CUU	chr2:24881464-24881692(+)$1	228	6	9	8.9999
CUU	chr2:36805787-36806031(-)$1	244	10	13	8.9999
CUU	chr1:1239367-1239622(-)$1	255	0	3	8.9999
CUU	chr17:73841960-73842182(-)$1	222	7	10	8.9999
CUU	chrX:135081016-135081227(+)$1	211	44	47	8.9999
CUU	chr1:40027929-40028181(-)$1	252	53	56	8.9999
CUU	chr16:24834830-24835056(+)$1	226	11	14	8.9999
CUU	chr16:30002398-30002659(+)$1	261	26	29	8.9999
CUU	chr6:27100184-27100422(-)$1	238	125	128	8.9999
CUU	chr17:61898863-61899088(-)$1	225	45	48	8.9999
CUU	chr11:9606729-9606981(+)$1	252	13	16	8.9999
CUU	chr3:98234493-98234742(-)$1	249	1	4	8.9999
CUU	chr4:187539798-187540024(-)$1	226	17	20	8.9999
CUU	chr4:76580214-76580438(-)$1	224	25	28	8.9999
CUU	chr2:219602445-219602674(+)$1	229	7	10	8.9999
CUU	chr16:30976597-30976818(+)$1	221	26	29	8.9999
CUU	chr3:168834061-168834292(-)$1	231	28	31	8.9999
CUU	chr17:56083112-56083337(-)$1	225	194	197	8.9999
CUU	chr5:179047808-179048062(-)$1	254	19	22	8.9999
CUU	chr10:112057275-112057494(-)$1	219	0	3	8.9999
CUU	chrX:118603701-118603932(+)$1	231	17	20	8.9999
CUU	chr20:47887578-47887803(-)$1	225	0	3	8.9999
CUU	chr19:1020841-1021081(-)$1	240	53	56	8.9999
CUU	chr5:179135186-179135408(+)$1	222	5	8	8.9999
CUU	chr18:33647206-33647433(-)$1	227	74	77	8.9999
CUU	chr12:82748175-82748399(-)$1	224	29	32	8.9999
CUU	chr2:198414939-198415161(+)$1	222	44	47	8.9999
CUU	chr7:98507692-98507958(+)$1	266	64	67	8.9999
CUU	chr10:13699361-13699583(-)$1	222	12	15	8.9999
CUU	chr7:158494429-158494654(-)$1	225	136	139	8.9999
CUU	chr9:117825174-117825428(-)$1	254	161	164	8.9999
CUU	chr22:44332946-44333177(+)$1	231	80	83	8.9999
CUU	chr17:57888935-57889157(+)$1	222	53	56	8.9999
CUU	chr9:136216763-136216981(+)$1	218	14	17	8.9999
CUU	chr16:66860327-66860553(-)$1	226	7	10	8.9999
CUU	chr2:30863180-30863425(+)$1	245	10	13	8.9999
CUU	chrX:107978908-107979161(-)$1	253	45	48	8.9999
CUU	chr12:56641807-56642028(-)$1	221	12	15	8.9999
CUU	chr12:98993726-98993972(+)$1	246	72	75	8.9999
CUU	chr1:16257914-16258145(+)$1	231	6	9	8.9999
CUU	chr1:114133130-114133351(+)$1	221	54	57	8.9999
CUU	chr9:123945107-123945332(-)$1	225	15	18	8.9999
CUU	chr5:1063942-1064164(-)$1	222	100	103	8.9999
CUU	chr17:79804305-79804550(-)$1	245	31	34	8.9999
CUU	chr2:9547598-9547827(-)$1	229	82	85	8.9999
CUU	chr7:158694970-158695201(+)$1	231	61	64	8.9999
cuu	chr19:49964016-49964254(+)$1	238	12	15	8.9999
CUU	chr17:28772891-28773112(+)$1	221	61	64	8.9999
CUU	chr19:11226677-11226902(+)$1	225	12	15	8.9999
CUU	chr6:30530168-30530389(+)$1	221	67	70	8.9999
CUU	chr17:77082109-77082340(+)$1	231	45	48	8.9999
CUU	chr6:139229733-139229956(-)$1	223	21	24	8.9999
CUU	chr8:22865128-22865349(+)$1	221	0	3	8.9999
CUU	chr14:95582864-95583086(-)$1	222	17	20	8.9999
CUU	chr6:75970503-75970727(-)$1	224	16	19	8.9999
CUU	chr4:2701388-2701619(+)$1	231	2	5	8.9999
CUU	chr2:97531123-97531347(-)$1	224	35	38	8.9999
CUU	chr1:212273689-212273915(+)$1	226	20	23	8.9999
CUU	chr1:93575814-93576036(+)$1	222	16	19	8.9999
CUU	chr19:19822890-19823115(-)$1	225	26	29	8.9999
CUU	chr17:73235404-73235658(-)$1	254	15	18	8.9999
CUU	chr1:3807345-3807569(-)$1	224	14	17	8.9999
CUU	chr10:22019817-22020040(+)$1	223	26	29	8.9999
CUU	chr12:57005580-57005826(-)$1	246	24	27	8.9999
CUU	chr1:52260088-52260311(-)$1	223	22	25	8.9999
CUU	chr6:107955200-107955431(+)$1	231	38	41	8.9999
CUU	chr11:61183663-61183922(-)$1	259	2	5	8.9999
CUU	chr14:53138283-53138516(-)$1	233	38	41	8.9999
CUU	chr12:57618809-57619038(+)$1	229	108	111	8.9999
CUU	chr14:102453689-102453906(+)$1	217	90	93	8.9999
CUU	chr4:159789243-159789466(+)$1	223	15	18	8.9999
CUU	chr2:10008321-10008540(+)$1	219	156	159	8.9999
CUU	chr17:7399261-7399484(+)$1	223	64	67	8.9999
CUU	chr12:58151840-58152084(+)$1	244	13	16	8.9999
CUU	chr22:50280315-50280546(+)$1	231	3	6	8.9999
CUU	chr1:2341709-2341917(-)$1	208	85	88	8.9999
CUU	chr17:48437512-48437733(+)$1	221	183	186	8.9999
CUU	chr19:58906007-58906264(+)$1	257	8	11	8.9999
CUU	chr5:179147376-179147595(+)$1	219	195	198	8.9999
CUU	chr4:148456942-148457167(+)$1	225	4	7	8.9999
CUU	chr8:144996191-144996435(-)$1	244	3	6	8.9999
CUU	chr12:99020019-99020242(-)$1	223	144	147	8.9999
CUU	chr3:139062764-139063016(+)$1	252	1	4	8.9999
CUU	chr1:249144427-249144664(-)$1	237	30	33	8.9999
CUU	chr6:3226361-3226584(-)$1	223	28	31	8.9999
CUU	chr15:69072654-69072880(-)$1	226	6	9	8.9999
CUU	chr8:119122361-119122587(-)$1	226	9	12	8.9999
CUU	chr21:26961057-26961283(-)$1	226	32	35	8.9999

#otherMatches

#Struct PSSM
rrr	chr20:42087724-42087964(+)$1	240	33	36	8.9999
HHH	chrX:152969422-152969648(-)$1	226	50	53	8.9999
b[b	chr1:204380093-204380324(-)$1	231	16	19	8.9999
ddd	chr3:121447934-121448145(-)$1	211	0	3	8.9999
lll	chr12:44238440-44238663(+)$1	223	25	28	8.9999
===	chr2:217005875-217006097(+)$1	222	12	15	8.9999
DDD	chr13:25672020-25672257(+)$1	237	5	8	8.9999
III	chr12:56646214-56646438(-)$1	224	12	15	8.9999
cpp	chr2:24881464-24881692(+)$1	228	6	9	8.9999
===	chr2:36805787-36806031(-)$1	244	10	13	8.9999
fff	chr1:1239367-1239622(-)$1	255	0	3	8.9999
ggg	chr17:73841960-73842182(-)$1	222	7	10	8.9999
###	chrX:135081016-135081227(+)$1	211	44	47	8.9999
000	chr1:40027929-40028181(-)$1	252	53	56	8.9999
:::	chr16:24834830-24835056(+)$1	226	11	14	8.9999
dmm	chr16:30002398-30002659(+)$1	261	26	29	8.9999
lll	chr6:27100184-27100422(-)$1	238	125	128	8.9999
ggg	chr17:61898863-61899088(-)$1	225	45	48	8.9999
ooo	chr11:9606729-9606981(+)$1	252	13	16	8.9999
BQQ	chr3:98234493-98234742(-)$1	249	1	4	8.9999
$$$	chr4:187539798-187540024(-)$1	226	17	20	8.9999
ccc	chr4:76580214-76580438(-)$1	224	25	28	8.9999
GGG	chr2:219602445-219602674(+)$1	229	7	10	8.9999
fff	chr16:30976597-30976818(+)$1	221	26	29	8.9999
CCC	chr3:168834061-168834292(-)$1	231	28	31	8.9999
f!!	chr17:56083112-56083337(-)$1	225	194	197	8.9999
!!d	chr5:179047808-179048062(-)$1	254	19	22	8.9999
eee	chr10:112057275-112057494(-)$1	219	0	3	8.9999
%%%	chrX:118603701-118603932(+)$1	231	17	20	8.9999
eee	chr20:47887578-47887803(-)$1	225	0	3	8.9999
ggg	chr19:1020841-1021081(-)$1	240	53	56	8.9999
:::	chr5:179135186-179135408(+)$1	222	5	8	8.9999
ggg	chr18:33647206-33647433(-)$1	227	74	77	8.9999
ddd	chr12:82748175-82748399(-)$1	224	29	32	8.9999
===	chr2:198414939-198415161(+)$1	222	44	47	8.9999
GGG	chr7:98507692-98507958(+)$1	266	64	67	8.9999
d::	chr10:13699361-13699583(-)$1	222	12	15	8.9999
ddd	chr7:158494429-158494654(-)$1	225	136	139	8.9999
c::	chr9:117825174-117825428(-)$1	254	161	164	8.9999
f]d	chr22:44332946-44333177(+)$1	231	80	83	8.9999
$ff	chr17:57888935-57889157(+)$1	222	53	56	8.9999
EE:	chr9:136216763-136216981(+)$1	218	14	17	8.9999
:::	chr16:66860327-66860553(-)$1	226	7	10	8.9999
fff	chr2:30863180-30863425(+)$1	245	10	13	8.9999
FFF	chrX:107978908-107979161(-)$1	253	45	48	8.9999
llb	chr12:56641807-56642028(-)$1	221	12	15	8.9999
===	chr12:98993726-98993972(+)$1	246	72	75	8.9999
:::	chr1:16257914-16258145(+)$1	231	6	9	8.9999
C{D	chr1:114133130-114133351(+)$1	221	54	57	8.9999
II:	chr9:123945107-123945332(-)$1	225	15	18	8.9999
bff	chr5:1063942-1064164(-)$1	222	100	103	8.9999
{HH	chr17:79804305-79804550(-)$1	245	31	34	8.9999
"""	chr2:9547598-9547827(-)$1	229	82	85	8.9999
DDD	chr7:158694970-158695201(+)$1	231	61	64	8.9999
sss	chr19:49964016-49964254(+)$1	238	12	15	8.9999
eee	chr17:28772891-28773112(+)$1	221	61	64	8.9999
ddl	chr19:11226677-11226902(+)$1	225	12	15	8.9999
ees	chr6:30530168-30530389(+)$1	221	67	70	8.9999
:ii	chr17:77082109-77082340(+)$1	231	45	48	8.9999
2ff	chr6:139229733-139229956(-)$1	223	21	24	8.9999
:::	chr8:22865128-22865349(+)$1	221	0	3	8.9999
=="	chr14:95582864-95583086(-)$1	222	17	20	8.9999
[cc	chr6:75970503-75970727(-)$1	224	16	19	8.9999
HHH	chr4:2701388-2701619(+)$1	231	2	5	8.9999
GGG	chr2:97531123-97531347(-)$1	224	35	38	8.9999
GGG	chr1:212273689-212273915(+)$1	226	20	23	8.9999
^^^	chr1:93575814-93576036(+)$1	222	16	19	8.9999
%%%	chr19:19822890-19823115(-)$1	225	26	29	8.9999
DD{	chr17:73235404-73235658(-)$1	254	15	18	8.9999
eee	chr1:3807345-3807569(-)$1	224	14	17	8.9999
fff	chr10:22019817-22020040(+)$1	223	26	29	8.9999
ffn	chr12:57005580-57005826(-)$1	246	24	27	8.9999
IKK	chr1:52260088-52260311(-)$1	223	22	25	8.9999
mmm	chr6:107955200-107955431(+)$1	231	38	41	8.9999
:::	chr11:61183663-61183922(-)$1	259	2	5	8.9999
===	chr14:53138283-53138516(-)$1	233	38	41	8.9999
eee	chr12:57618809-57619038(+)$1	229	108	111	8.9999
ggg	chr14:102453689-102453906(+)$1	217	90	93	8.9999
GGG	chr4:159789243-159789466(+)$1	223	15	18	8.9999
d[d	chr2:10008321-10008540(+)$1	219	156	159	8.9999
ddd	chr17:7399261-7399484(+)$1	223	64	67	8.9999
dnn	chr12:58151840-58152084(+)$1	244	13	16	8.9999
HHH	chr22:50280315-50280546(+)$1	231	3	6	8.9999
ooo	chr1:2341709-2341917(-)$1	208	85	88	8.9999
:::	chr17:48437512-48437733(+)$1	221	183	186	8.9999
BKK	chr19:58906007-58906264(+)$1	257	8	11	8.9999
:::	chr5:179147376-179147595(+)$1	219	195	198	8.9999
EE{	chr4:148456942-148457167(+)$1	225	4	7	8.9999
HHH	chr8:144996191-144996435(-)$1	244	3	6	8.9999
eed	chr12:99020019-99020242(-)$1	223	144	147	8.9999
:::	chr3:139062764-139063016(+)$1	252	1	4	8.9999
"""	chr1:249144427-249144664(-)$1	237	30	33	8.9999
b""	chr6:3226361-3226584(-)$1	223	28	31	8.9999
GGG	chr15:69072654-69072880(-)$1	226	6	9	8.9999
iii	chr8:119122361-119122587(-)$1	226	9	12	8.9999
B{D	chr21:26961057-26961283(-)$1	226	32	35	8.9999

#DB
...	chr20:42087724-42087964(+)$1	1	33	36	8.9999
(((	chrX:152969422-152969648(-)$1	1	50	53	8.9999
(.(	chr1:204380093-204380324(-)$1	1	16	19	8.9999
(((	chr3:121447934-121448145(-)$1	1	0	3	8.9999
...	chr12:44238440-44238663(+)$1	1	25	28	8.9999
(((	chr2:217005875-217006097(+)$1	1	12	15	8.9999
(((	chr13:25672020-25672257(+)$1	1	5	8	8.9999
(((	chr12:56646214-56646438(-)$1	1	12	15	8.9999
(..	chr2:24881464-24881692(+)$1	1	6	9	8.9999
(((	chr2:36805787-36806031(-)$1	1	10	13	8.9999
(((	chr1:1239367-1239622(-)$1	1	0	3	8.9999
(((	chr17:73841960-73842182(-)$1	1	7	10	8.9999
...	chrX:135081016-135081227(+)$1	1	44	47	8.9999
...	chr1:40027929-40028181(-)$1	1	53	56	8.9999
...	chr16:24834830-24835056(+)$1	1	11	14	8.9999
(..	chr16:30002398-30002659(+)$1	1	26	29	8.9999
...	chr6:27100184-27100422(-)$1	1	125	128	8.9999
)))	chr17:61898863-61899088(-)$1	1	45	48	8.9999
...	chr11:9606729-9606981(+)$1	1	13	16	8.9999
(..	chr3:98234493-98234742(-)$1	1	1	4	8.9999
...	chr4:187539798-187540024(-)$1	1	17	20	8.9999
(((	chr4:76580214-76580438(-)$1	1	25	28	8.9999
(((	chr2:219602445-219602674(+)$1	1	7	10	8.9999
(((	chr16:30976597-30976818(+)$1	1	26	29	8.9999
(((	chr3:168834061-168834292(-)$1	1	28	31	8.9999
(..	chr17:56083112-56083337(-)$1	1	194	197	8.9999
..(	chr5:179047808-179048062(-)$1	1	19	22	8.9999
(((	chr10:112057275-112057494(-)$1	1	0	3	8.9999
...	chrX:118603701-118603932(+)$1	1	17	20	8.9999
(((	chr20:47887578-47887803(-)$1	1	0	3	8.9999
)))	chr19:1020841-1021081(-)$1	1	53	56	8.9999
...	chr5:179135186-179135408(+)$1	1	5	8	8.9999
(((	chr18:33647206-33647433(-)$1	1	74	77	8.9999
(((	chr12:82748175-82748399(-)$1	1	29	32	8.9999
(((	chr2:198414939-198415161(+)$1	1	44	47	8.9999
(((	chr7:98507692-98507958(+)$1	1	64	67	8.9999
)..	chr10:13699361-13699583(-)$1	1	12	15	8.9999
)))	chr7:158494429-158494654(-)$1	1	136	139	8.9999
)..	chr9:117825174-117825428(-)$1	1	161	164	8.9999
).)	chr22:44332946-44333177(+)$1	1	80	83	8.9999
.((	chr17:57888935-57889157(+)$1	1	53	56	8.9999
((.	chr9:136216763-136216981(+)$1	1	14	17	8.9999
...	chr16:66860327-66860553(-)$1	1	7	10	8.9999
(((	chr2:30863180-30863425(+)$1	1	10	13	8.9999
(((	chrX:107978908-107979161(-)$1	1	45	48	8.9999
..)	chr12:56641807-56642028(-)$1	1	12	15	8.9999
(((	chr12:98993726-98993972(+)$1	1	72	75	8.9999
...	chr1:16257914-16258145(+)$1	1	6	9	8.9999
(.(	chr1:114133130-114133351(+)$1	1	54	57	8.9999
((.	chr9:123945107-123945332(-)$1	1	15	18	8.9999
(((	chr5:1063942-1064164(-)$1	1	100	103	8.9999
.((	chr17:79804305-79804550(-)$1	1	31	34	8.9999
...	chr2:9547598-9547827(-)$1	1	82	85	8.9999
(((	chr7:158694970-158695201(+)$1	1	61	64	8.9999
...	chr19:49964016-49964254(+)$1	1	12	15	8.9999
(((	chr17:28772891-28773112(+)$1	1	61	64	8.9999
((.	chr19:11226677-11226902(+)$1	1	12	15	8.9999
((.	chr6:30530168-30530389(+)$1	1	67	70	8.9999
.((	chr17:77082109-77082340(+)$1	1	45	48	8.9999
.))	chr6:139229733-139229956(-)$1	1	21	24	8.9999
...	chr8:22865128-22865349(+)$1	1	0	3	8.9999
((.	chr14:95582864-95583086(-)$1	1	17	20	8.9999
.((	chr6:75970503-75970727(-)$1	1	16	19	8.9999
(((	chr4:2701388-2701619(+)$1	1	2	5	8.9999
(((	chr2:97531123-97531347(-)$1	1	35	38	8.9999
(((	chr1:212273689-212273915(+)$1	1	20	23	8.9999
...	chr1:93575814-93576036(+)$1	1	16	19	8.9999
...	chr19:19822890-19823115(-)$1	1	26	29	8.9999
((.	chr17:73235404-73235658(-)$1	1	15	18	8.9999
(((	chr1:3807345-3807569(-)$1	1	14	17	8.9999
)))	chr10:22019817-22020040(+)$1	1	26	29	8.9999
((.	chr12:57005580-57005826(-)$1	1	24	27	8.9999
(..	chr1:52260088-52260311(-)$1	1	22	25	8.9999
...	chr6:107955200-107955431(+)$1	1	38	41	8.9999
...	chr11:61183663-61183922(-)$1	1	2	5	8.9999
(((	chr14:53138283-53138516(-)$1	1	38	41	8.9999
(((	chr12:57618809-57619038(+)$1	1	108	111	8.9999
(((	chr14:102453689-102453906(+)$1	1	90	93	8.9999
(((	chr4:159789243-159789466(+)$1	1	15	18	8.9999
(.(	chr2:10008321-10008540(+)$1	1	156	159	8.9999
(((	chr17:7399261-7399484(+)$1	1	64	67	8.9999
(..	chr12:58151840-58152084(+)$1	1	13	16	8.9999
(((	chr22:50280315-50280546(+)$1	1	3	6	8.9999
...	chr1:2341709-2341917(-)$1	1	85	88	8.9999
...	chr17:48437512-48437733(+)$1	1	183	186	8.9999
(..	chr19:58906007-58906264(+)$1	1	8	11	8.9999
...	chr5:179147376-179147595(+)$1	1	195	198	8.9999
((.	chr4:148456942-148457167(+)$1	1	4	7	8.9999
(((	chr8:144996191-144996435(-)$1	1	3	6	8.9999
)))	chr12:99020019-99020242(-)$1	1	144	147	8.9999
...	chr3:139062764-139063016(+)$1	1	1	4	8.9999
...	chr1:249144427-249144664(-)$1	1	30	33	8.9999
(..	chr6:3226361-3226584(-)$1	1	28	31	8.9999
(((	chr15:69072654-69072880(-)$1	1	6	9	8.9999
(((	chr8:119122361-119122587(-)$1	1	9	12	8.9999
(.(	chr21:26961057-26961283(-)$1	1	32	35	8.9999

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

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m2_run2.nuc.txt

#NT
CAG	chr20:62328381-62328604(+)$1	223	191	194	9.0000
CAG	chr6:139308723-139308948(+)$1	225	34	37	9.0000
CAG	chr8:38021010-38021233(-)$1	223	23	26	9.0000
CAG	chr4:763515-763750(-)$1	235	63	66	9.0000
CAG	chr11:68522281-68522503(-)$1	222	19	22	9.0000
CAG	chr22:41165505-41165735(-)$1	230	136	139	9.0000
CAG	chr22:46509471-46509697(+)$1	226	0	3	9.0000
CAG	chr1:15443323-15443550(+)$1	227	37	40	9.0000
CAG	chr6:5086827-5087052(+)$1	225	135	138	9.0000
cag	chr19:9964478-9964700(+)$1	222	72	75	9.0000
CAG	chr12:51663489-51663710(+)$1	221	4	7	9.0000
CAG	chr1:109707093-109707315(-)$1	222	8	11	9.0000
CAG	chr20:19702676-19702898(-)$1	222	71	74	9.0000
CAG	chr15:40212864-40213088(+)$1	224	55	58	9.0000
CAG	chr13:95858692-95858916(+)$1	224	165	168	9.0000
CAG	chr6:2766177-2766399(-)$1	222	73	76	9.0000
CAG	chr5:132087507-132087738(+)$1	231	147	150	9.0000
cag	chr19:19496790-19497034(+)$1	244	39	42	9.0000
CAG	chr7:127667478-127667699(-)$1	221	96	99	9.0000
CAG	chr16:20975006-20975228(-)$1	222	27	30	9.0000
CAG	chr3:137749802-137750030(-)$1	228	145	148	9.0000
CAG	chr20:3627374-3627601(+)$1	227	8	11	9.0000
CAG	chr8:64099733-64099955(+)$1	222	184	187	9.0000
CAG	chr11:62559485-62559707(-)$1	222	25	28	9.0000
CAG	chr3:128751647-128751873(-)$1	226	9	12	9.0000
CAG	chr7:31096527-31096749(+)$1	222	7	10	9.0000
cag	chr7:40169307-40169531(-)$1	224	27	30	9.0000
CAG	chr12:7088612-7088835(+)$1	223	31	34	9.0000
CAG	chr17:41246209-41246433(-)$1	224	16	19	9.0000
CAG	chr22:37336271-37336496(+)$1	225	160	163	9.0000
CAG	chr17:4884433-4884658(-)$1	225	37	40	9.0000
CAG	chr7:90015330-90015552(-)$1	222	107	110	9.0000
CAG	chr14:67708058-67708286(-)$1	228	6	9	9.0000
CAG	chr7:151874637-151874859(+)$1	222	39	42	9.0000
CAG	chr4:174447622-174447844(-)$1	222	169	172	9.0000
CAG	chr1:32050482-32050704(+)$1	222	1	4	9.0000
CAG	chr12:50350139-50350367(-)$1	228	77	80	9.0000
CAG	chr1:228468363-228468585(-)$1	222	8	11	9.0000
cag	chr19:17002768-17002994(-)$1	226	1	4	9.0000
CAG	chr17:26989198-26989420(+)$1	222	31	34	9.0000
CAg	chr8:8750937-8751161(-)$1	224	44	47	9.0000
CAG	chr12:123237201-123237423(+)$1	222	134	137	9.0000
CAG	chr2:40340803-40341030(-)$1	227	44	47	9.0000
CAG	chr13:75923239-75923465(-)$1	226	54	57	9.0000
CAG	chr13:77580030-77580253(-)$1	223	13	16	9.0000
CAG	chr7:44240489-44240717(-)$1	228	13	16	9.0000
CAG	chrX:49044976-49045199(+)$1	223	113	116	9.0000
CAG	chr16:54149744-54149966(-)$1	222	48	51	9.0000
CAG	chr2:88472215-88472436(-)$1	221	12	15	9.0000
CAG	chr5:154199844-154200074(+)$1	230	4	7	9.0000
CAG	chr3:16345757-16345982(+)$1	225	0	3	9.0000
CAG	chr1:44386055-44386282(-)$1	227	20	23	9.0000
cag	chr6:2786885-2787108(+)$1	223	216	219	9.0000
CAG	chr1:220972086-220972310(-)$1	224	40	43	9.0000
CAG	chr15:66679351-66679574(+)$1	223	73	76	9.0000
CAG	chr15:72117896-72118124(+)$1	228	89	92	9.0000
CAG	chr8:135725123-135725346(+)$1	223	180	183	9.0000
CAG	chr14:96705472-96705695(+)$1	223	26	29	9.0000
CAG	chr2:96051105-96051333(+)$1	228	11	14	9.0000
CAG	chr16:70415108-70415331(-)$1	223	12	15	9.0000
CAG	chr16:30845696-30845921(-)$1	225	62	65	9.0000
CAG	chr16:27356530-27356753(+)$1	223	4	7	9.0000
cag	chr17:27383557-27383779(-)$1	222	11	14	9.0000
CAG	chr1:153521544-153521766(-)$1	222	0	3	9.0000
CAG	chrX:100306867-100307096(+)$1	229	39	42	9.0000
CAG	chr16:730471-730694(+)$1	223	33	36	9.0000
CAG	chr20:3758321-3758549(+)$1	228	21	24	9.0000
CAG	chr5:198832-199054(-)$1	222	12	15	9.0000
CAG	chr13:28874762-28874983(-)$1	221	61	64	9.0000
cag	chr12:69326864-69327086(+)$1	222	13	16	9.0000
CAG	chr17:28444048-28444275(+)$1	227	71	74	9.0000
CAG	chr2:122125159-122125384(-)$1	225	50	53	9.0000
CAG	chr18:32721665-32721889(-)$1	224	67	70	9.0000
CAG	chr6:163736178-163736402(-)$1	224	25	28	9.0000
CAG	chr13:50108138-50108362(+)$1	224	32	35	9.0000
CAG	chr22:46546427-46546650(-)$1	223	156	159	9.0000
CAG	chr16:56390714-56390936(+)$1	222	29	32	9.0000
CAG	chr1:249152820-249153046(-)$1	226	15	18	9.0000
CAG	chr17:41939471-41939694(+)$1	223	62	65	9.0000
CAG	chr19:19609188-19609409(-)$1	221	14	17	9.0000
CAG	chr17:73886739-73886966(+)$1	227	15	18	9.0000
CAG	chr19:1230316-1230538(-)$1	222	4	7	9.0000
CAG	chr7:2281903-2282125(+)$1	222	13	16	9.0000
CAG	chr11:105782988-105783209(+)$1	221	20	23	9.0000
CAG	chr6:37321618-37321855(+)$1	237	74	77	9.0000
CAG	chr11:71693763-71693984(+)$1	221	12	15	9.0000
CAG	chr20:61981207-61981430(+)$1	223	0	3	9.0000
CAG	chr7:135661804-135662027(-)$1	223	43	46	9.0000
CAG	chr8:37716143-37716364(-)$1	221	50	53	9.0000
CAG	chr1:231906678-231906905(-)$1	227	15	18	9.0000
CAG	chr7:150813760-150813981(+)$1	221	50	53	9.0000
cag	chr1:45286075-45286297(-)$1	222	124	127	9.0000
CAG	chr15:33060685-33060907(+)$1	222	52	55	9.0000
CAG	chr2:74143676-74143898(+)$1	222	12	15	9.0000

#otherMatches

#Struct PSSM
qqq	chr4:57371494-57371717(-)$1	223	15	18	9.0000
~~B	chr20:62328381-62328604(+)$1	223	191	194	9.0000
BHH	chr6:139308723-139308948(+)$1	225	34	37	9.0000
:::	chr8:38021010-38021233(-)$1	223	23	26	9.0000
::D	chr4:763515-763750(-)$1	235	63	66	9.0000
obb	chr11:68522281-68522503(-)$1	222	19	22	9.0000
cco	chr22:41165505-41165735(-)$1	230	136	139	9.0000
fff	chr22:46509471-46509697(+)$1	226	0	3	9.0000
ppp	chr1:15443323-15443550(+)$1	227	37	40	9.0000
c:c	chr6:5086827-5087052(+)$1	225	135	138	9.0000
b::	chr19:9964478-9964700(+)$1	222	72	75	9.0000
DDD	chr12:51663489-51663710(+)$1	221	4	7	9.0000
:dd	chr1:109707093-109707315(-)$1	222	8	11	9.0000
:::	chr20:19702676-19702898(-)$1	222	71	74	9.0000
!dd	chr15:40212864-40213088(+)$1	224	55	58	9.0000
ggg	chr13:95858692-95858916(+)$1	224	165	168	9.0000
mmb	chr6:2766177-2766399(-)$1	222	73	76	9.0000
Dgg	chr5:132087507-132087738(+)$1	231	147	150	9.0000
ggg	chr19:19496790-19497034(+)$1	244	39	42	9.0000
===	chr7:127667478-127667699(-)$1	221	96	99	9.0000
ann	chr16:20975006-20975228(-)$1	222	27	30	9.0000
ddm	chr3:137749802-137750030(-)$1	228	145	148	9.0000
ddd	chr20:3627374-3627601(+)$1	227	8	11	9.0000
GG}	chr8:64099733-64099955(+)$1	222	184	187	9.0000
::B	chr11:62559485-62559707(-)$1	222	25	28	9.0000
JJJ	chr3:128751647-128751873(-)$1	226	9	12	9.0000
GGG	chr7:31096527-31096749(+)$1	222	7	10	9.0000
"dd	chr7:40169307-40169531(-)$1	224	27	30	9.0000
enn	chr12:7088612-7088835(+)$1	223	31	34	9.0000
::D	chr17:41246209-41246433(-)$1	224	16	19	9.0000
a]c	chr22:37336271-37336496(+)$1	225	160	163	9.0000
eee	chr17:4884433-4884658(-)$1	225	37	40	9.0000
b22	chr7:90015330-90015552(-)$1	222	107	110	9.0000
CCC	chr14:67708058-67708286(-)$1	228	6	9	9.0000
fff	chr7:151874637-151874859(+)$1	222	39	42	9.0000
"cc	chr4:174447622-174447844(-)$1	222	169	172	9.0000
DDD	chr1:32050482-32050704(+)$1	222	1	4	9.0000
ccc	chr12:50350139-50350367(-)$1	228	77	80	9.0000
ccn	chr1:228468363-228468585(-)$1	222	8	11	9.0000
b!!	chr19:17002768-17002994(-)$1	226	1	4	9.0000
ooo	chr17:26989198-26989420(+)$1	222	31	34	9.0000
ppd	chr8:8750937-8751161(-)$1	224	44	47	9.0000
uud	chr12:123237201-123237423(+)$1	222	134	137	9.0000
EEE	chr2:40340803-40341030(-)$1	227	44	47	9.0000
HHH	chr13:75923239-75923465(-)$1	226	54	57	9.0000
WWW	chr13:77580030-77580253(-)$1	223	13	16	9.0000
b##	chr7:44240489-44240717(-)$1	228	13	16	9.0000
66c	chrX:49044976-49045199(+)$1	223	113	116	9.0000
qqq	chr16:54149744-54149966(-)$1	222	48	51	9.0000
ppe	chr2:88472215-88472436(-)$1	221	12	15	9.0000
iii	chr5:154199844-154200074(+)$1	230	4	7	9.0000
FFF	chr3:16345757-16345982(+)$1	225	0	3	9.0000
'''	chr1:44386055-44386282(-)$1	227	20	23	9.0000
fff	chr6:2786885-2787108(+)$1	223	216	219	9.0000
::B	chr1:220972086-220972310(-)$1	224	40	43	9.0000
ggg	chr15:66679351-66679574(+)$1	223	73	76	9.0000
ff]	chr15:72117896-72118124(+)$1	228	89	92	9.0000
H::	chr8:135725123-135725346(+)$1	223	180	183	9.0000
[bb	chr14:96705472-96705695(+)$1	223	26	29	9.0000
HHH	chr2:96051105-96051333(+)$1	228	11	14	9.0000
E{I	chr16:70415108-70415331(-)$1	223	12	15	9.0000
::e	chr16:30845696-30845921(-)$1	225	62	65	9.0000
C{B	chr16:27356530-27356753(+)$1	223	4	7	9.0000
e[b	chr17:27383557-27383779(-)$1	222	11	14	9.0000
::F	chr1:153521544-153521766(-)$1	222	0	3	9.0000
ee]	chrX:100306867-100307096(+)$1	229	39	42	9.0000
ggg	chr16:730471-730694(+)$1	223	33	36	9.0000
d!!	chr20:3758321-3758549(+)$1	228	21	24	9.0000
!ff	chr5:198832-199054(-)$1	222	12	15	9.0000
ddd	chr13:28874762-28874983(-)$1	221	61	64	9.0000
ggg	chr12:69326864-69327086(+)$1	222	13	16	9.0000
=!!	chr17:28444048-28444275(+)$1	227	71	74	9.0000
mmm	chr2:122125159-122125384(-)$1	225	50	53	9.0000
c[d	chr18:32721665-32721889(-)$1	224	67	70	9.0000
RRG	chr6:163736178-163736402(-)$1	224	25	28	9.0000
DRR	chr13:50108138-50108362(+)$1	224	32	35	9.0000
c[d	chr22:46546427-46546650(-)$1	223	156	159	9.0000
fff	chr16:56390714-56390936(+)$1	222	29	32	9.0000
ddd	chr1:249152820-249153046(-)$1	226	15	18	9.0000
GGC	chr17:41939471-41939694(+)$1	223	62	65	9.0000
GGG	chr19:19609188-19609409(-)$1	221	14	17	9.0000
hhh	chr17:73886739-73886966(+)$1	227	15	18	9.0000
dnn	chr19:1230316-1230538(-)$1	222	4	7	9.0000
DLL	chr7:2281903-2282125(+)$1	222	13	16	9.0000
DDD	chr11:105782988-105783209(+)$1	221	20	23	9.0000
hhh	chr6:37321618-37321855(+)$1	237	74	77	9.0000
dd"	chr11:71693763-71693984(+)$1	221	12	15	9.0000
::D	chr20:61981207-61981430(+)$1	223	0	3	9.0000
eee	chr7:135661804-135662027(-)$1	223	43	46	9.0000
===	chr8:37716143-37716364(-)$1	221	50	53	9.0000
::D	chr1:231906678-231906905(-)$1	227	15	18	9.0000
dd[	chr7:150813760-150813981(+)$1	221	50	53	9.0000
eee	chr1:45286075-45286297(-)$1	222	124	127	9.0000
[cc	chr15:33060685-33060907(+)$1	222	52	55	9.0000
DDD	chr2:74143676-74143898(+)$1	222	12	15	9.0000

#DB
...	chr4:57371494-57371717(-)$1	1	15	18	9.0000
..)	chr20:62328381-62328604(+)$1	1	191	194	9.0000
(((	chr6:139308723-139308948(+)$1	1	34	37	9.0000
...	chr8:38021010-38021233(-)$1	1	23	26	9.0000
..(	chr4:763515-763750(-)$1	1	63	66	9.0000
.))	chr11:68522281-68522503(-)$1	1	19	22	9.0000
((.	chr22:41165505-41165735(-)$1	1	136	139	9.0000
(((	chr22:46509471-46509697(+)$1	1	0	3	9.0000
...	chr1:15443323-15443550(+)$1	1	37	40	9.0000
).(	chr6:5086827-5087052(+)$1	1	135	138	9.0000
)..	chr19:9964478-9964700(+)$1	1	72	75	9.0000
(((	chr12:51663489-51663710(+)$1	1	4	7	9.0000
.((	chr1:109707093-109707315(-)$1	1	8	11	9.0000
...	chr20:19702676-19702898(-)$1	1	71	74	9.0000
.((	chr15:40212864-40213088(+)$1	1	55	58	9.0000
)))	chr13:95858692-95858916(+)$1	1	165	168	9.0000
..)	chr6:2766177-2766399(-)$1	1	73	76	9.0000
)((	chr5:132087507-132087738(+)$1	1	147	150	9.0000
)))	chr19:19496790-19497034(+)$1	1	39	42	9.0000
(((	chr7:127667478-127667699(-)$1	1	96	99	9.0000
(..	chr16:20975006-20975228(-)$1	1	27	30	9.0000
((.	chr3:137749802-137750030(-)$1	1	145	148	9.0000
)))	chr20:3627374-3627601(+)$1	1	8	11	9.0000
)).	chr8:64099733-64099955(+)$1	1	184	187	9.0000
..(	chr11:62559485-62559707(-)$1	1	25	28	9.0000
(((	chr3:128751647-128751873(-)$1	1	9	12	9.0000
(((	chr7:31096527-31096749(+)$1	1	7	10	9.0000
.((	chr7:40169307-40169531(-)$1	1	27	30	9.0000
(..	chr12:7088612-7088835(+)$1	1	31	34	9.0000
..(	chr17:41246209-41246433(-)$1	1	16	19	9.0000
).)	chr22:37336271-37336496(+)$1	1	160	163	9.0000
(((	chr17:4884433-4884658(-)$1	1	37	40	9.0000
)..	chr7:90015330-90015552(-)$1	1	107	110	9.0000
(((	chr14:67708058-67708286(-)$1	1	6	9	9.0000
)))	chr7:151874637-151874859(+)$1	1	39	42	9.0000
.((	chr4:174447622-174447844(-)$1	1	169	172	9.0000
(((	chr1:32050482-32050704(+)$1	1	1	4	9.0000
)))	chr12:50350139-50350367(-)$1	1	77	80	9.0000
((.	chr1:228468363-228468585(-)$1	1	8	11	9.0000
(..	chr19:17002768-17002994(-)$1	1	1	4	9.0000
...	chr17:26989198-26989420(+)$1	1	31	34	9.0000
..)	chr8:8750937-8751161(-)$1	1	44	47	9.0000
..)	chr12:123237201-123237423(+)$1	1	134	137	9.0000
(((	chr2:40340803-40341030(-)$1	1	44	47	9.0000
(((	chr13:75923239-75923465(-)$1	1	54	57	9.0000
...	chr13:77580030-77580253(-)$1	1	13	16	9.0000
(..	chr7:44240489-44240717(-)$1	1	13	16	9.0000
..)	chrX:49044976-49045199(+)$1	1	113	116	9.0000
...	chr16:54149744-54149966(-)$1	1	48	51	9.0000
..)	chr2:88472215-88472436(-)$1	1	12	15	9.0000
(((	chr5:154199844-154200074(+)$1	1	4	7	9.0000
(((	chr3:16345757-16345982(+)$1	1	0	3	9.0000
...	chr1:44386055-44386282(-)$1	1	20	23	9.0000
)))	chr6:2786885-2787108(+)$1	1	216	219	9.0000
..(	chr1:220972086-220972310(-)$1	1	40	43	9.0000
)))	chr15:66679351-66679574(+)$1	1	73	76	9.0000
)).	chr15:72117896-72118124(+)$1	1	89	92	9.0000
)..	chr8:135725123-135725346(+)$1	1	180	183	9.0000
.((	chr14:96705472-96705695(+)$1	1	26	29	9.0000
(((	chr2:96051105-96051333(+)$1	1	11	14	9.0000
(.(	chr16:70415108-70415331(-)$1	1	12	15	9.0000
..(	chr16:30845696-30845921(-)$1	1	62	65	9.0000
(.(	chr16:27356530-27356753(+)$1	1	4	7	9.0000
(.(	chr17:27383557-27383779(-)$1	1	11	14	9.0000
..(	chr1:153521544-153521766(-)$1	1	0	3	9.0000
)).	chrX:100306867-100307096(+)$1	1	39	42	9.0000
)))	chr16:730471-730694(+)$1	1	33	36	9.0000
(..	chr20:3758321-3758549(+)$1	1	21	24	9.0000
.((	chr5:198832-199054(-)$1	1	12	15	9.0000
(((	chr13:28874762-28874983(-)$1	1	61	64	9.0000
(((	chr12:69326864-69327086(+)$1	1	13	16	9.0000
(..	chr17:28444048-28444275(+)$1	1	71	74	9.0000
...	chr2:122125159-122125384(-)$1	1	50	53	9.0000
(.(	chr18:32721665-32721889(-)$1	1	67	70	9.0000
..(	chr6:163736178-163736402(-)$1	1	25	28	9.0000
(..	chr13:50108138-50108362(+)$1	1	32	35	9.0000
(.(	chr22:46546427-46546650(-)$1	1	156	159	9.0000
(((	chr16:56390714-56390936(+)$1	1	29	32	9.0000
(((	chr1:249152820-249153046(-)$1	1	15	18	9.0000
(((	chr17:41939471-41939694(+)$1	1	62	65	9.0000
(((	chr19:19609188-19609409(-)$1	1	14	17	9.0000
)))	chr17:73886739-73886966(+)$1	1	15	18	9.0000
(..	chr19:1230316-1230538(-)$1	1	4	7	9.0000
(..	chr7:2281903-2282125(+)$1	1	13	16	9.0000
(((	chr11:105782988-105783209(+)$1	1	20	23	9.0000
)))	chr6:37321618-37321855(+)$1	1	74	77	9.0000
((.	chr11:71693763-71693984(+)$1	1	12	15	9.0000
..(	chr20:61981207-61981430(+)$1	1	0	3	9.0000
)))	chr7:135661804-135662027(-)$1	1	43	46	9.0000
)))	chr8:37716143-37716364(-)$1	1	50	53	9.0000
..(	chr1:231906678-231906905(-)$1	1	15	18	9.0000
((.	chr7:150813760-150813981(+)$1	1	50	53	9.0000
)))	chr1:45286075-45286297(-)$1	1	124	127	9.0000
.((	chr15:33060685-33060907(+)$1	1	52	55	9.0000
(((	chr2:74143676-74143898(+)$1	1	12	15	9.0000

#PSSM
C : 0.91	c : 0.08	
A : 0.91	a : 0.08	
G : 0.90	g : 0.09	

#score	855.0000000000001
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m3_run1.nuc.txt

#NT
GAA	chr3:140772267-140772527(+)$1	260	71	74	9.0000
GAA	chrX:10639339-10639585(-)$1	246	17	20	9.0000
GAA	chr1:87416776-87417070(+)$1	294	5	8	9.0000
GAA	chr3:33449056-33449303(-)$1	247	97	100	9.0000
GAA	chr17:64408929-64409248(+)$1	319	88	91	9.0000
GAA	chr12:108961814-108962060(+)$1	246	36	39	9.0000
GAA	chr3:133931249-133931522(-)$1	273	15	18	9.0000
gaa	chr5:49719295-49719644(-)$1	349	99	102	9.0000
gaa	chr17:55067696-55067933(+)$1	237	41	44	9.0000
gaa	chr3:100457705-100457957(+)$1	252	73	76	9.0000
gaa	chr10:70769140-70769377(+)$1	237	131	134	9.0000
GAA	chr2:159992251-159992505(+)$1	254	62	65	9.0000
GAA	chr5:179676090-179676367(-)$1	277	12	15	9.0000
GAA	chr2:42883105-42883364(+)$1	259	2	5	9.0000
gaa	chr19:36112341-36112598(+)$1	257	99	102	9.0000
gaa	chr6:83612218-83612468(-)$1	250	65	68	9.0000
GAA	chr16:56970050-56970278(+)$1	228	32	35	9.0000
gaa	chrX:138901755-138902048(-)$1	293	37	40	9.0000
gaa	chr2:202115487-202115778(+)$1	291	18	21	9.0000
GAA	chr1:111672194-111672428(-)$1	234	37	40	9.0000
GAA	chr2:183581297-183581585(+)$1	288	1	4	9.0000
GAA	chr5:107343493-107343757(-)$1	264	67	70	9.0000
gaa	chr3:141805888-141806193(-)$1	305	99	102	9.0000
GAA	chr6:81042303-81042566(+)$1	263	50	53	9.0000
gaa	chr3:150904194-150904430(+)$1	236	228	231	9.0000
gaa	chr20:30138715-30138940(+)$1	225	4	7	9.0000
GAA	chr3:59925126-59925367(-)$1	241	6	9	9.0000
gaa	chr19:40712458-40712772(+)$1	314	30	33	9.0000
GAA	chr1:233369077-233369355(-)$1	278	18	21	9.0000
gaa	chr11:86052096-86052365(+)$1	269	31	34	9.0000
gaa	chr2:159157039-159157293(-)$1	254	82	85	9.0000
GAA	chr22:41239413-41239676(-)$1	263	99	102	9.0000
gaa	chr5:79491871-79492314(-)$1	443	12	15	9.0000
GAA	chr2:149010626-149010879(+)$1	253	11	14	9.0000
GAA	chr17:75199383-75199619(+)$1	236	140	143	9.0000
GAA	chr2:191838040-191838415(-)$1	375	1	4	9.0000
GAA	chr3:35808449-35808808(+)$1	359	34	37	9.0000
GAA	chr2:231322717-231322999(+)$1	282	22	25	9.0000
GAA	chr4:26703246-26703502(+)$1	256	63	66	9.0000
gaa	chr14:93768517-93768784(-)$1	267	40	43	9.0000
gaa	chr1:113096210-113096449(-)$1	239	96	99	9.0000
GAA	chr22:40832900-40833136(-)$1	236	46	49	9.0000
GAA	chr3:28305635-28305875(+)$1	240	193	196	9.0000
GAA	chr5:80933004-80933286(-)$1	282	39	42	9.0000
GAA	chr1:143912202-143912455(-)$1	253	3	6	9.0000
GAA	chr12:54672598-54672879(-)$1	281	89	92	9.0000
GAA	chr5:111085475-111085771(-)$1	296	4	7	9.0000
gaa	chr8:105573737-105573992(-)$1	255	14	17	9.0000
GAA	chr14:92446962-92447207(-)$1	245	99	102	9.0000
GAA	chr10:63996970-63997258(-)$1	288	50	53	9.0000
gaa	chr19:35509220-35509469(+)$1	249	5	8	9.0000
GAA	chr2:227773184-227773449(+)$1	265	75	78	9.0000
gaa	chr10:131521906-131522216(+)$1	310	10	13	9.0000
GAA	chr17:35343139-35343417(+)$1	278	24	27	9.0000
GAA	chr13:95236524-95236812(-)$1	288	5	8	9.0000
GAA	chr1:209954190-209954428(+)$1	238	129	132	9.0000
GAA	chr13:100173462-100173704(+)$1	242	18	21	9.0000
GAA	chr15:41602179-41602415(-)$1	236	1	4	9.0000
gaa	chr3:154869752-154870217(+)$1	465	47	50	9.0000
gaa	chr3:196869071-196869311(-)$1	240	73	76	9.0000
GAA	chr5:157172851-157173108(+)$1	257	9	12	9.0000
GAA	chr6:146223110-146223368(-)$1	258	95	98	9.0000
gaa	chr6:99324563-99324815(-)$1	252	24	27	9.0000
gaa	chr3:160056723-160057009(-)$1	286	99	102	9.0000
gaa	chr2:211322550-211322819(-)$1	269	37	40	9.0000
GAA	chr1:72743988-72744224(-)$1	236	11	14	9.0000
gaa	chr7:128600409-128600708(-)$1	299	198	201	9.0000
GAA	chr2:68977990-68978266(+)$1	276	6	9	9.0000
GAA	chr10:3206276-3206555(-)$1	279	64	67	9.0000
gaa	chr10:76160530-76160786(+)$1	256	99	102	9.0000
gaa	chr2:203547222-203547512(+)$1	290	15	18	9.0000
GAA	chr3:182755008-182755240(-)$1	232	78	81	9.0000
GAA	chr1:233101988-233102243(+)$1	255	155	158	9.0000
GAA	chr4:124079057-124079322(+)$1	265	3	6	9.0000
GAA	chrX:138808692-138808935(-)$1	243	20	23	9.0000
GAA	chr8:74530045-74530301(-)$1	256	97	100	9.0000
GAA	chr2:26606928-26607164(+)$1	236	7	10	9.0000
gaa	chr9:133622051-133622374(+)$1	323	62	65	9.0000
GAA	chr10:27819974-27820210(+)$1	236	13	16	9.0000
gaa	chr4:174132405-174132691(+)$1	286	78	81	9.0000
GAA	chr4:125604188-125604486(-)$1	298	93	96	9.0000
gaa	chr22:42905747-42906038(-)$1	291	142	145	9.0000
GAA	chr4:152592709-152592936(-)$1	227	36	39	9.0000
GAA	chr17:49956146-49956392(-)$1	246	5	8	9.0000
GAA	chrX:74057880-74058147(-)$1	267	51	54	9.0000
gaa	chr11:57496397-57496677(+)$1	280	83	86	9.0000
gaa	chr1:9639193-9639425(+)$1	232	34	37	9.0000
GAA	chr18:43929889-43930259(+)$1	370	63	66	9.0000
GAA	chr10:18966695-18966931(+)$1	236	29	32	9.0000
GAA	chr21:36347716-36348032(-)$1	316	34	37	9.0000
gaa	chr5:134042301-134042577(+)$1	276	13	16	9.0000
GAA	chr8:91634278-91634541(-)$1	263	42	45	9.0000
GAA	chr2:68775898-68776135(+)$1	237	3	6	9.0000
GAA	chr15:59207771-59208103(-)$1	332	21	24	9.0000
gaa	chr3:192573084-192573314(-)$1	230	4	7	9.0000
GAA	chr10:101508795-101509050(+)$1	255	99	102	9.0000

#otherMatches

#Struct PSSM
GGG	chrX:133561948-133562191(+)$1	243	20	23	9.0000
bbp	chr3:140772267-140772527(+)$1	260	71	74	9.0000
===	chrX:10639339-10639585(-)$1	246	17	20	9.0000
eee	chr1:87416776-87417070(+)$1	294	5	8	9.0000
eee	chr3:33449056-33449303(-)$1	247	97	100	9.0000
===	chr17:64408929-64409248(+)$1	319	88	91	9.0000
HHH	chr12:108961814-108962060(+)$1	246	36	39	9.0000
:::	chr3:133931249-133931522(-)$1	273	15	18	9.0000
d]f	chr5:49719295-49719644(-)$1	349	99	102	9.0000
fff	chr17:55067696-55067933(+)$1	237	41	44	9.0000
dd:	chr3:100457705-100457957(+)$1	252	73	76	9.0000
gg:	chr10:70769140-70769377(+)$1	237	131	134	9.0000
ee>	chr2:159992251-159992505(+)$1	254	62	65	9.0000
nnn	chr5:179676090-179676367(-)$1	277	12	15	9.0000
:::	chr2:42883105-42883364(+)$1	259	2	5	9.0000
EE:	chr19:36112341-36112598(+)$1	257	99	102	9.0000
BB{	chr6:83612218-83612468(-)$1	250	65	68	9.0000
fff	chr16:56970050-56970278(+)$1	228	32	35	9.0000
DD:	chrX:138901755-138902048(-)$1	293	37	40	9.0000
Jee	chr2:202115487-202115778(+)$1	291	18	21	9.0000
OOO	chr1:111672194-111672428(-)$1	234	37	40	9.0000
:::	chr2:183581297-183581585(+)$1	288	1	4	9.0000
ggg	chr5:107343493-107343757(-)$1	264	67	70	9.0000
eee	chr3:141805888-141806193(-)$1	305	99	102	9.0000
b22	chr6:81042303-81042566(+)$1	263	50	53	9.0000
GGG	chr3:150904194-150904430(+)$1	236	228	231	9.0000
e[d	chr20:30138715-30138940(+)$1	225	4	7	9.0000
CCC	chr3:59925126-59925367(-)$1	241	6	9	9.0000
d::	chr19:40712458-40712772(+)$1	314	30	33	9.0000
NCC	chr1:233369077-233369355(-)$1	278	18	21	9.0000
hhh	chr11:86052096-86052365(+)$1	269	31	34	9.0000
^^^	chr2:159157039-159157293(-)$1	254	82	85	9.0000
FFF	chr22:41239413-41239676(-)$1	263	99	102	9.0000
eee	chr5:79491871-79492314(-)$1	443	12	15	9.0000
MMM	chr2:149010626-149010879(+)$1	253	11	14	9.0000
000	chr17:75199383-75199619(+)$1	236	140	143	9.0000
:::	chr2:191838040-191838415(-)$1	375	1	4	9.0000
GGG	chr3:35808449-35808808(+)$1	359	34	37	9.0000
III	chr2:231322717-231322999(+)$1	282	22	25	9.0000
[dd	chr4:26703246-26703502(+)$1	256	63	66	9.0000
gg:	chr14:93768517-93768784(-)$1	267	40	43	9.0000
b]d	chr1:113096210-113096449(-)$1	239	96	99	9.0000
eee	chr22:40832900-40833136(-)$1	236	46	49	9.0000
eee	chr3:28305635-28305875(+)$1	240	193	196	9.0000
nnn	chr5:80933004-80933286(-)$1	282	39	42	9.0000
DDN	chr1:143912202-143912455(-)$1	253	3	6	9.0000
ggo	chr12:54672598-54672879(-)$1	281	89	92	9.0000
:::	chr5:111085475-111085771(-)$1	296	4	7	9.0000
D::	chr8:105573737-105573992(-)$1	255	14	17	9.0000
ddd	chr14:92446962-92447207(-)$1	245	99	102	9.0000
!!b	chr10:63996970-63997258(-)$1	288	50	53	9.0000
mmm	chr19:35509220-35509469(+)$1	249	5	8	9.0000
:::	chr2:227773184-227773449(+)$1	265	75	78	9.0000
ddd	chr10:131521906-131522216(+)$1	310	10	13	9.0000
c::	chr17:35343139-35343417(+)$1	278	24	27	9.0000
[bb	chr13:95236524-95236812(-)$1	288	5	8	9.0000
FFF	chr1:209954190-209954428(+)$1	238	129	132	9.0000
nng	chr13:100173462-100173704(+)$1	242	18	21	9.0000
:::	chr15:41602179-41602415(-)$1	236	1	4	9.0000
ggg	chr3:154869752-154870217(+)$1	465	47	50	9.0000
fff	chr3:196869071-196869311(-)$1	240	73	76	9.0000
:::	chr5:157172851-157173108(+)$1	257	9	12	9.0000
ggg	chr6:146223110-146223368(-)$1	258	95	98	9.0000
CCC	chr6:99324563-99324815(-)$1	252	24	27	9.0000
:::	chr3:160056723-160057009(-)$1	286	99	102	9.0000
eee	chr2:211322550-211322819(-)$1	269	37	40	9.0000
DDD	chr1:72743988-72744224(-)$1	236	11	14	9.0000
77f	chr7:128600409-128600708(-)$1	299	198	201	9.0000
:::	chr2:68977990-68978266(+)$1	276	6	9	9.0000
eeq	chr10:3206276-3206555(-)$1	279	64	67	9.0000
:::	chr10:76160530-76160786(+)$1	256	99	102	9.0000
EEE	chr2:203547222-203547512(+)$1	290	15	18	9.0000
rrr	chr3:182755008-182755240(-)$1	232	78	81	9.0000
dd4	chr1:233101988-233102243(+)$1	255	155	158	9.0000
ddo	chr4:124079057-124079322(+)$1	265	3	6	9.0000
:::	chrX:138808692-138808935(-)$1	243	20	23	9.0000
GGG	chr8:74530045-74530301(-)$1	256	97	100	9.0000
ccc	chr2:26606928-26607164(+)$1	236	7	10	9.0000
RRR	chr9:133622051-133622374(+)$1	323	62	65	9.0000
FKK	chr10:27819974-27820210(+)$1	236	13	16	9.0000
:::	chr4:174132405-174132691(+)$1	286	78	81	9.0000
f%%	chr4:125604188-125604486(-)$1	298	93	96	9.0000
iii	chr22:42905747-42906038(-)$1	291	142	145	9.0000
]ad	chr4:152592709-152592936(-)$1	227	36	39	9.0000
:::	chr17:49956146-49956392(-)$1	246	5	8	9.0000
ppp	chrX:74057880-74058147(-)$1	267	51	54	9.0000
FFF	chr11:57496397-57496677(+)$1	280	83	86	9.0000
hhh	chr1:9639193-9639425(+)$1	232	34	37	9.0000
fff	chr18:43929889-43930259(+)$1	370	63	66	9.0000
===	chr10:18966695-18966931(+)$1	236	29	32	9.0000
fff	chr21:36347716-36348032(-)$1	316	34	37	9.0000
EEE	chr5:134042301-134042577(+)$1	276	13	16	9.0000
DDM	chr8:91634278-91634541(-)$1	263	42	45	9.0000
qqq	chr2:68775898-68776135(+)$1	237	3	6	9.0000
iii	chr15:59207771-59208103(-)$1	332	21	24	9.0000
CCK	chr3:192573084-192573314(-)$1	230	4	7	9.0000
B{G	chr10:101508795-101509050(+)$1	255	99	102	9.0000

#DB
(((	chrX:133561948-133562191(+)$1	1	20	23	9.0000
((.	chr3:140772267-140772527(+)$1	1	71	74	9.0000
(((	chrX:10639339-10639585(-)$1	1	17	20	9.0000
(((	chr1:87416776-87417070(+)$1	1	5	8	9.0000
)))	chr3:33449056-33449303(-)$1	1	97	100	9.0000
(((	chr17:64408929-64409248(+)$1	1	88	91	9.0000
(((	chr12:108961814-108962060(+)$1	1	36	39	9.0000
...	chr3:133931249-133931522(-)$1	1	15	18	9.0000
).)	chr5:49719295-49719644(-)$1	1	99	102	9.0000
)))	chr17:55067696-55067933(+)$1	1	41	44	9.0000
)).	chr3:100457705-100457957(+)$1	1	73	76	9.0000
)).	chr10:70769140-70769377(+)$1	1	131	134	9.0000
)).	chr2:159992251-159992505(+)$1	1	62	65	9.0000
...	chr5:179676090-179676367(-)$1	1	12	15	9.0000
...	chr2:42883105-42883364(+)$1	1	2	5	9.0000
)).	chr19:36112341-36112598(+)$1	1	99	102	9.0000
((.	chr6:83612218-83612468(-)$1	1	65	68	9.0000
(((	chr16:56970050-56970278(+)$1	1	32	35	9.0000
((.	chrX:138901755-138902048(-)$1	1	37	40	9.0000
(((	chr2:202115487-202115778(+)$1	1	18	21	9.0000
...	chr1:111672194-111672428(-)$1	1	37	40	9.0000
...	chr2:183581297-183581585(+)$1	1	1	4	9.0000
)))	chr5:107343493-107343757(-)$1	1	67	70	9.0000
(((	chr3:141805888-141806193(-)$1	1	99	102	9.0000
)..	chr6:81042303-81042566(+)$1	1	50	53	9.0000
)))	chr3:150904194-150904430(+)$1	1	228	231	9.0000
(.(	chr20:30138715-30138940(+)$1	1	4	7	9.0000
(((	chr3:59925126-59925367(-)$1	1	6	9	9.0000
)..	chr19:40712458-40712772(+)$1	1	30	33	9.0000
.((	chr1:233369077-233369355(-)$1	1	18	21	9.0000
(((	chr11:86052096-86052365(+)$1	1	31	34	9.0000
...	chr2:159157039-159157293(-)$1	1	82	85	9.0000
(((	chr22:41239413-41239676(-)$1	1	99	102	9.0000
(((	chr5:79491871-79492314(-)$1	1	12	15	9.0000
...	chr2:149010626-149010879(+)$1	1	11	14	9.0000
...	chr17:75199383-75199619(+)$1	1	140	143	9.0000
...	chr2:191838040-191838415(-)$1	1	1	4	9.0000
(((	chr3:35808449-35808808(+)$1	1	34	37	9.0000
(((	chr2:231322717-231322999(+)$1	1	22	25	9.0000
.((	chr4:26703246-26703502(+)$1	1	63	66	9.0000
)).	chr14:93768517-93768784(-)$1	1	40	43	9.0000
).)	chr1:113096210-113096449(-)$1	1	96	99	9.0000
)))	chr22:40832900-40833136(-)$1	1	46	49	9.0000
(((	chr3:28305635-28305875(+)$1	1	193	196	9.0000
...	chr5:80933004-80933286(-)$1	1	39	42	9.0000
((.	chr1:143912202-143912455(-)$1	1	3	6	9.0000
((.	chr12:54672598-54672879(-)$1	1	89	92	9.0000
...	chr5:111085475-111085771(-)$1	1	4	7	9.0000
(..	chr8:105573737-105573992(-)$1	1	14	17	9.0000
(((	chr14:92446962-92447207(-)$1	1	99	102	9.0000
..(	chr10:63996970-63997258(-)$1	1	50	53	9.0000
...	chr19:35509220-35509469(+)$1	1	5	8	9.0000
...	chr2:227773184-227773449(+)$1	1	75	78	9.0000
)))	chr10:131521906-131522216(+)$1	1	10	13	9.0000
)..	chr17:35343139-35343417(+)$1	1	24	27	9.0000
.((	chr13:95236524-95236812(-)$1	1	5	8	9.0000
)))	chr1:209954190-209954428(+)$1	1	129	132	9.0000
..)	chr13:100173462-100173704(+)$1	1	18	21	9.0000
...	chr15:41602179-41602415(-)$1	1	1	4	9.0000
)))	chr3:154869752-154870217(+)$1	1	47	50	9.0000
)))	chr3:196869071-196869311(-)$1	1	73	76	9.0000
...	chr5:157172851-157173108(+)$1	1	9	12	9.0000
))(	chr6:146223110-146223368(-)$1	1	95	98	9.0000
(((	chr6:99324563-99324815(-)$1	1	24	27	9.0000
...	chr3:160056723-160057009(-)$1	1	99	102	9.0000
(((	chr2:211322550-211322819(-)$1	1	37	40	9.0000
(((	chr1:72743988-72744224(-)$1	1	11	14	9.0000
..)	chr7:128600409-128600708(-)$1	1	198	201	9.0000
...	chr2:68977990-68978266(+)$1	1	6	9	9.0000
((.	chr10:3206276-3206555(-)$1	1	64	67	9.0000
...	chr10:76160530-76160786(+)$1	1	99	102	9.0000
(((	chr2:203547222-203547512(+)$1	1	15	18	9.0000
...	chr3:182755008-182755240(-)$1	1	78	81	9.0000
)).	chr1:233101988-233102243(+)$1	1	155	158	9.0000
((.	chr4:124079057-124079322(+)$1	1	3	6	9.0000
...	chrX:138808692-138808935(-)$1	1	20	23	9.0000
)))	chr8:74530045-74530301(-)$1	1	97	100	9.0000
(((	chr2:26606928-26607164(+)$1	1	7	10	9.0000
...	chr9:133622051-133622374(+)$1	1	62	65	9.0000
(..	chr10:27819974-27820210(+)$1	1	13	16	9.0000
...	chr4:174132405-174132691(+)$1	1	78	81	9.0000
(..	chr4:125604188-125604486(-)$1	1	93	96	9.0000
)))	chr22:42905747-42906038(-)$1	1	142	145	9.0000
.))	chr4:152592709-152592936(-)$1	1	36	39	9.0000
...	chr17:49956146-49956392(-)$1	1	5	8	9.0000
...	chrX:74057880-74058147(-)$1	1	51	54	9.0000
)))	chr11:57496397-57496677(+)$1	1	83	86	9.0000
(((	chr1:9639193-9639425(+)$1	1	34	37	9.0000
(((	chr18:43929889-43930259(+)$1	1	63	66	9.0000
)))	chr10:18966695-18966931(+)$1	1	29	32	9.0000
(((	chr21:36347716-36348032(-)$1	1	34	37	9.0000
(((	chr5:134042301-134042577(+)$1	1	13	16	9.0000
((.	chr8:91634278-91634541(-)$1	1	42	45	9.0000
...	chr2:68775898-68776135(+)$1	1	3	6	9.0000
)))	chr15:59207771-59208103(-)$1	1	21	24	9.0000
((.	chr3:192573084-192573314(-)$1	1	4	7	9.0000
(.(	chr10:101508795-101509050(+)$1	1	99	102	9.0000

#PSSM
G : 0.63	g : 0.36	
A : 0.63	a : 0.36	
A : 0.63	a : 0.36	

#score	873.0
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m1_run2.nuc.txt

#NT
CUGGUGA	chr7:2405939-2406180(+)$1	241	16	23	13.0833
CUGCAGA	chr4:83774640-83774884(-)$1	244	57	64	13.5000
CUGGAGA	chr12:72091084-72091315(+)$1	231	143	150	17.3333
CUGGAGG	chr9:139341676-139341918(-)$1	242	51	58	14.1666
CUGGAGC	chr12:7076396-7076649(-)$1	253	163	170	13.9166
CUGGAGG	chr9:139310678-139310914(+)$1	236	105	112	14.1666
CUGGCGA	chr12:48298311-48298535(-)$1	224	6	13	12.9166
CUGCAGA	chr1:118486069-118486300(+)$1	231	1	8	13.5000
CUGGAGA	chr11:66463843-66464073(-)$1	230	149	156	17.3333
CUGGAGU	chr9:35738012-35738234(+)$1	222	137	144	13.5833
CUGGAGG	chr1:220284089-220284321(+)$1	232	108	115	14.1666
CUGGAGA	chr12:120637066-120637299(-)$1	233	179	186	17.3333
CUGGACA	chr22:36901894-36902135(-)$1	241	116	123	13.0000
CUGGUGA	chr7:30639474-30639717(+)$1	243	0	7	13.0833
CUGGAGG	chr21:45217203-45217453(+)$1	250	196	203	14.1666
CCGGAGA	chr3:14220258-14220487(+)$1	229	40	47	13.1666
GUGGAGA	chr10:74658680-74658901(-)$1	221	73	80	12.5833
CAGGAGA	chr2:74595114-74595344(-)$1	230	110	117	13.2500
CUGGAGA	chr7:107580416-107580646(-)$1	230	52	59	17.3333
CAGGAGA	chr6:110424571-110424817(-)$1	246	203	210	13.2500
CUGUAGA	chr1:201816316-201816560(+)$1	244	117	124	13.4166
CGGGAGA	chr5:176958256-176958485(-)$1	229	2	9	13.2500
CUGGGGA	chr19:14677576-14677833(-)$1	257	23	30	13.0000
CUGGAGA	chr6:90491078-90491312(-)$1	234	71	78	17.3333
CUGGAGA	chr21:42540336-42540571(+)$1	235	133	140	17.3333
CUGGGGA	chr1:116941561-116941811(+)$1	250	100	107	13.0000
CUGGAGA	chr14:102822059-102822285(-)$1	226	136	143	17.3333
CUGGUGA	chr1:70716379-70716627(+)$1	248	35	42	13.0833
CUGGAGC	chr19:10257057-10257302(-)$1	245	160	167	13.9166
CUGCAGA	chr21:44479256-44479498(-)$1	242	113	120	13.5000
CUGGAGG	chr11:118918870-118919123(-)$1	253	131	138	14.1666
CUGGAGA	chr17:80040156-80040390(-)$1	234	118	125	17.3333
CUGUAGA	chr19:35450302-35450529(-)$1	227	105	112	13.4166
CUGGAGA	chr1:6524646-6524875(-)$1	229	110	117	17.3333
CUGGAGA	chr2:192543279-192543510(+)$1	231	142	149	17.3333
CGGGAGA	chr14:91738993-91739215(+)$1	222	103	110	13.2500
CUGGAGC	chr6:44219782-44220022(+)$1	240	111	118	13.9166
CUGAAGA	chr3:51426342-51426587(+)$1	245	22	29	13.4166
CUGGAGA	chr1:36101854-36102087(-)$1	233	111	118	17.3333
uuggaga	chr16:31193827-31194061(+)$1	234	225	232	12.5833
CUGUAGA	chr16:30094909-30095143(+)$1	234	60	67	13.4166
CCGGAGA	chr16:2816058-2816318(+)$1	260	158	165	13.1666
CUGGAGA	chr17:7212851-7213084(+)$1	233	6	13	17.3333
CUGGACA	chr2:20512023-20512256(-)$1	233	111	118	13.0000
CUGGAGG	chr1:934251-934549(-)$1	298	89	96	14.1666
CUGCAGA	chr19:47181771-47181993(+)$1	222	149	156	13.5000
CAGGAGA	chr8:100155238-100155468(+)$1	230	19	26	13.2500
CUGGAGC	chr19:50983859-50984090(+)$1	231	107	114	13.9166
CUGGAGC	chr19:39208527-39208770(+)$1	243	117	124	13.9166
CUGGACA	chr5:134223420-134223649(+)$1	229	110	117	13.0000
CUGGAGA	chr1:153742566-153742810(+)$1	244	178	185	17.3333
CUGGACA	chr22:41553115-41553363(+)$1	248	118	125	13.0000
CUGGAGA	chr22:20078859-20079164(+)$1	305	121	128	17.3333
CUGGAGA	chr1:153908529-153908760(-)$1	231	165	172	17.3333
CUGGAGA	chr17:74392377-74392670(-)$1	293	113	120	17.3333
CUGAAGA	chr16:30435490-30435735(-)$1	245	117	124	13.4166
CGGGAGA	chr2:97017545-97017795(+)$1	250	156	163	13.2500
CUGGAGG	chr1:64100417-64100652(+)$1	235	159	166	14.1666
CUGAAGA	chr14:91948339-91948565(-)$1	226	80	87	13.4166

#otherMatches

#Struct PSSM
2ccc:DD	chr19:5231369-5231608(-)$1	239	179	186	14.1666
DDDccc[	chr7:2405939-2406180(+)$1	241	16	23	13.0833
ee]bb33	chr4:83774640-83774884(-)$1	244	57	64	13.5000
ccfffff	chr12:72091084-72091315(+)$1	231	143	150	17.3333
KKDDDDO	chr9:139341676-139341918(-)$1	242	51	58	14.1666
bb####e	chr12:7076396-7076649(-)$1	253	163	170	13.9166
dddGGGG	chr9:139310678-139310914(+)$1	236	105	112	14.1666
ldddd::	chr12:48298311-48298535(-)$1	224	6	13	12.9166
DDD{AKK	chr1:118486069-118486300(+)$1	231	1	8	13.5000
Ecccooo	chr11:66463843-66464073(-)$1	230	149	156	17.3333
::DDDDY	chr9:35738012-35738234(+)$1	222	137	144	13.5833
!bb!!ff	chr1:220284089-220284321(+)$1	232	108	115	14.1666
eeccc::	chr12:120637066-120637299(-)$1	233	179	186	17.3333
eeee[bb	chr22:36901894-36902135(-)$1	241	116	123	13.0000
::dddd[	chr7:30639474-30639717(+)$1	243	0	7	13.0833
ddd!!ff	chr21:45217203-45217453(+)$1	250	196	203	14.1666
e''''''	chr3:14220258-14220487(+)$1	229	40	47	13.1666
gggggg]	chr10:74658680-74658901(-)$1	221	73	80	12.5833
fffff::	chr2:74595114-74595344(-)$1	230	110	117	13.2500
eee22a:	chr7:107580416-107580646(-)$1	230	52	59	17.3333
22dddd]	chr6:110424571-110424817(-)$1	246	203	210	13.2500
mmmccc]	chr1:201816316-201816560(+)$1	244	117	124	13.4166
:DDDDLL	chr5:176958256-176958485(-)$1	229	2	9	13.2500
eeeeemm	chr19:14677576-14677833(-)$1	257	23	30	13.0000
((((((d	chr6:90491078-90491312(-)$1	234	71	78	17.3333
ff$$$$$	chr21:42540336-42540571(+)$1	235	133	140	17.3333
mcccccc	chr1:116941561-116941811(+)$1	250	100	107	13.0000
dddd]a2	chr14:102822059-102822285(-)$1	226	136	143	17.3333
:::a[ee	chr1:70716379-70716627(+)$1	248	35	42	13.0833
dddd:GG	chr19:10257057-10257302(-)$1	245	160	167	13.9166
:::::::	chr21:44479256-44479498(-)$1	242	113	120	13.5000
abb$$$$	chr11:118918870-118919123(-)$1	253	131	138	14.1666
!!ggggg	chr17:80040156-80040390(-)$1	234	118	125	17.3333
4444fff	chr19:35450302-35450529(-)$1	227	105	112	13.4166
fffffoo	chr1:6524646-6524875(-)$1	229	110	117	17.3333
:CCC}GG	chr2:192543279-192543510(+)$1	231	142	149	17.3333
dddmmmm	chr14:91738993-91739215(+)$1	222	103	110	13.2500
ddd333b	chr6:44219782-44220022(+)$1	240	111	118	13.9166
KCCC:::	chr3:51426342-51426587(+)$1	245	22	29	13.4166
ccc[ddd	chr1:36101854-36102087(-)$1	233	111	118	17.3333
qqeeeee	chr16:31193827-31194061(+)$1	234	225	232	12.5833
DDDMMMM	chr16:30094909-30095143(+)$1	234	60	67	13.4166
pppppcc	chr16:2816058-2816318(+)$1	260	158	165	13.1666
G:hhhhh	chr17:7212851-7213084(+)$1	233	6	13	17.3333
ddd::==	chr2:20512023-20512256(-)$1	233	111	118	13.0000
eeee]cc	chr1:934251-934549(-)$1	298	89	96	14.1666
eeeCCC}	chr19:47181771-47181993(+)$1	222	149	156	13.5000
JJJJJJM	chr8:100155238-100155468(+)$1	230	19	26	13.2500
ccc[eee	chr19:50983859-50984090(+)$1	231	107	114	13.9166
EEEE{BB	chr19:39208527-39208770(+)$1	243	117	124	13.9166
dddd333	chr5:134223420-134223649(+)$1	229	110	117	13.0000
I______	chr1:153742566-153742810(+)$1	244	178	185	17.3333
accciii	chr22:41553115-41553363(+)$1	248	118	125	13.0000
D}IIIII	chr22:20078859-20079164(+)$1	305	121	128	17.3333
qqqqqcc	chr1:153908529-153908760(-)$1	231	165	172	17.3333
gggggff	chr17:74392377-74392670(-)$1	293	113	120	17.3333
ddd8888	chr16:30435490-30435735(-)$1	245	117	124	13.4166
ffffffl	chr2:97017545-97017795(+)$1	250	156	163	13.2500
bgggggg	chr1:64100417-64100652(+)$1	235	159	166	14.1666
ggGGGGG	chr14:91948339-91948565(-)$1	226	80	87	13.4166

#DB
.))).))	chr19:5231369-5231608(-)$1	1	179	186	14.1666
((((((.	chr7:2405939-2406180(+)$1	1	16	23	13.0833
)).))..	chr4:83774640-83774884(-)$1	1	57	64	13.5000
)))))))	chr12:72091084-72091315(+)$1	1	143	150	17.3333
..((((.	chr9:139341676-139341918(-)$1	1	51	58	14.1666
((....(	chr12:7076396-7076649(-)$1	1	163	170	13.9166
)))((((	chr9:139310678-139310914(+)$1	1	105	112	14.1666
.))))..	chr12:48298311-48298535(-)$1	1	6	13	12.9166
(((.(..	chr1:118486069-118486300(+)$1	1	1	8	13.5000
((((...	chr11:66463843-66464073(-)$1	1	149	156	17.3333
..)))).	chr9:35738012-35738234(+)$1	1	137	144	13.5833
.((..((	chr1:220284089-220284321(+)$1	1	108	115	14.1666
)))))..	chr12:120637066-120637299(-)$1	1	179	186	17.3333
((((.((	chr22:36901894-36902135(-)$1	1	116	123	13.0000
..((((.	chr7:30639474-30639717(+)$1	1	0	7	13.0833
(((..((	chr21:45217203-45217453(+)$1	1	196	203	14.1666
(......	chr3:14220258-14220487(+)$1	1	40	47	13.1666
)))))).	chr10:74658680-74658901(-)$1	1	73	80	12.5833
)))))..	chr2:74595114-74595344(-)$1	1	110	117	13.2500
)))..).	chr7:107580416-107580646(-)$1	1	52	59	17.3333
..)))).	chr6:110424571-110424817(-)$1	1	203	210	13.2500
...))).	chr1:201816316-201816560(+)$1	1	117	124	13.4166
.((((..	chr5:176958256-176958485(-)$1	1	2	9	13.2500
(((((..	chr19:14677576-14677833(-)$1	1	23	30	13.0000
......(	chr6:90491078-90491312(-)$1	1	71	78	17.3333
((.....	chr21:42540336-42540571(+)$1	1	133	140	17.3333
.))))))	chr1:116941561-116941811(+)$1	1	100	107	13.0000
)))).).	chr14:102822059-102822285(-)$1	1	136	143	17.3333
...(.((	chr1:70716379-70716627(+)$1	1	35	42	13.0833
)))).))	chr19:10257057-10257302(-)$1	1	160	167	13.9166
.......	chr21:44479256-44479498(-)$1	1	113	120	13.5000
(((....	chr11:118918870-118919123(-)$1	1	131	138	14.1666
..(((((	chr17:80040156-80040390(-)$1	1	118	125	17.3333
....)))	chr19:35450302-35450529(-)$1	1	105	112	13.4166
(((((..	chr1:6524646-6524875(-)$1	1	110	117	17.3333
.))).))	chr2:192543279-192543510(+)$1	1	142	149	17.3333
(((....	chr14:91738993-91739215(+)$1	1	103	110	13.2500
)))...)	chr6:44219782-44220022(+)$1	1	111	118	13.9166
.(((...	chr3:51426342-51426587(+)$1	1	22	29	13.4166
(((.(((	chr1:36101854-36102087(-)$1	1	111	118	17.3333
..)))))	chr16:31193827-31194061(+)$1	1	225	232	12.5833
(((....	chr16:30094909-30095143(+)$1	1	60	67	13.4166
.....))	chr16:2816058-2816318(+)$1	1	158	165	13.1666
(.(((((	chr17:7212851-7213084(+)$1	1	6	13	17.3333
)))..((	chr2:20512023-20512256(-)$1	1	111	118	13.0000
)))).))	chr1:934251-934549(-)$1	1	89	96	14.1666
)))))).	chr19:47181771-47181993(+)$1	1	149	156	13.5000
((((((.	chr8:100155238-100155468(+)$1	1	19	26	13.2500
(((.(((	chr19:50983859-50984090(+)$1	1	107	114	13.9166
((((.((	chr19:39208527-39208770(+)$1	1	117	124	13.9166
))))...	chr5:134223420-134223649(+)$1	1	110	117	13.0000
)......	chr1:153742566-153742810(+)$1	1	178	185	17.3333
)))))))	chr22:41553115-41553363(+)$1	1	118	125	13.0000
).)))))	chr22:20078859-20079164(+)$1	1	121	128	17.3333
.....))	chr1:153908529-153908760(-)$1	1	165	172	17.3333
)))))((	chr17:74392377-74392670(-)$1	1	113	120	17.3333
)))....	chr16:30435490-30435735(-)$1	1	117	124	13.4166
((((((.	chr2:97017545-97017795(+)$1	1	156	163	13.2500
)))))))	chr1:64100417-64100652(+)$1	1	159	166	14.1666
))(((((	chr14:91948339-91948565(-)$1	1	80	87	13.4166

#PSSM
C : 0.96	G : 0.01	u : 0.01	
U : 0.85	A : 0.05	G : 0.05	C : 0.03	u : 0.01	
G : 0.98	g : 0.01	
G : 0.81	C : 0.06	U : 0.05	A : 0.05	g : 0.01	
A : 0.88	U : 0.05	G : 0.03	C : 0.01	a : 0.01	
G : 0.91	C : 0.06	g : 0.01	
A : 0.75	G : 0.13	C : 0.08	U : 0.01	a : 0.01	

#score	869.5000000000018
#seq	60
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m1_run2.nuc.txt

#NT
GGAG	chr9:131446073-131446308(+)$1	235	63	67	12.0000
GGAG	chr10:103920575-103920805(+)$1	230	28	32	12.0000
GGAG	chr1:147091320-147091590(+)$1	270	71	75	12.0000
GGAG	chr1:206905819-206906043(+)$1	224	99	103	12.0000
GGAG	chr7:75959222-75959481(-)$1	259	116	120	12.0000
GGAG	chr5:137843923-137844157(-)$1	234	125	129	12.0000
GGAG	chr6:151672985-151673228(+)$1	243	128	132	12.0000
GGAG	chr17:79652536-79652785(+)$1	249	5	9	12.0000
GGAG	chr7:2402613-2402853(+)$1	240	2	6	12.0000
GGAG	chr6:160164606-160164836(+)$1	230	145	149	12.0000
GGAG	chr20:42315562-42315800(+)$1	238	69	73	12.0000
GGAG	chr15:41745022-41745264(+)$1	242	86	90	12.0000
GGAG	chr17:7480805-7481042(+)$1	237	15	19	12.0000
GGAG	chr17:79478898-79479181(-)$1	283	186	190	12.0000
GGAG	chr3:10312127-10312357(+)$1	230	118	122	12.0000
GGAG	chr1:149400385-149400626(-)$1	241	29	33	12.0000
GGAG	chr1:149814082-149814326(-)$1	244	30	34	12.0000
GGAG	chr16:89627894-89628205(+)$1	311	146	150	12.0000
GGAG	chr2:152991988-152992219(-)$1	231	16	20	12.0000
GGAG	chr15:69076635-69076919(-)$1	284	116	120	12.0000
GGAG	chr4:74005654-74005903(-)$1	249	105	109	12.0000
ggag	chrX:150156164-150156403(+)$1	239	180	184	12.0000
GGAG	chr17:7834927-7835167(-)$1	240	112	116	12.0000
GGAG	chr22:32111189-32111427(-)$1	238	207	211	12.0000
GGAG	chr12:56814743-56814984(-)$1	241	1	5	12.0000
GGAG	chr17:11984650-11984887(+)$1	237	134	138	12.0000
GGAG	chr14:70234884-70235099(+)$1	215	14	18	12.0000
GGAG	chr11:67235426-67235663(-)$1	237	40	44	12.0000
GGAG	chr16:75600649-75600883(+)$1	234	25	29	12.0000
GGAG	chr16:3900671-3900938(-)$1	267	68	72	12.0000
GGAG	chr6:157803040-157803278(+)$1	238	87	91	12.0000
GGAG	chr8:144662102-144662332(-)$1	230	123	127	12.0000
GGAG	chr16:3443651-3443885(-)$1	234	9	13	12.0000
GGAG	chr16:90097727-90097987(+)$1	260	8	12	12.0000
GGAG	chr1:144164433-144164670(+)$1	237	40	44	12.0000
GGAG	chr6:170068017-170068256(-)$1	239	118	122	12.0000
GGAG	chr19:49863154-49863403(-)$1	249	142	146	12.0000
GGAG	chr19:50412158-50412450(-)$1	292	169	173	12.0000
GGAG	chr1:149812289-149812538(-)$1	249	90	94	12.0000
GGAG	chr1:149813993-149814257(-)$1	264	13	17	12.0000
GGAG	chr11:117263625-117263887(+)$1	262	146	150	12.0000
GGAG	chr6:31856951-31857192(-)$1	241	177	181	12.0000
GGAG	chr7:63982069-63982292(-)$1	223	28	32	12.0000
GGAG	chr16:2049410-2049653(-)$1	243	101	105	12.0000
GGAG	chr2:242179114-242179335(-)$1	221	24	28	12.0000
GGAG	chr1:148267732-148267962(-)$1	230	84	88	12.0000
GGAG	chr9:131371379-131371654(+)$1	275	67	71	12.0000
GGAG	chr9:103275490-103275715(+)$1	225	121	125	12.0000
GGAG	chr17:33464036-33464279(-)$1	243	2	6	12.0000
GGAG	chr16:70594286-70594517(+)$1	231	201	205	12.0000
GGAG	chr5:82876115-82876349(+)$1	234	122	126	12.0000
GGAG	chr15:73865914-73866156(-)$1	242	135	139	12.0000
GGAG	chr22:39077923-39078202(+)$1	279	146	150	12.0000
GGAG	chr16:29808268-29808501(+)$1	233	123	127	12.0000
GGAG	chr15:101718432-101718667(-)$1	235	68	72	12.0000
GGAG	chr5:52942066-52942329(+)$1	263	14	18	12.0000
GGAG	chr19:51857413-51857662(-)$1	249	183	187	12.0000
GGAG	chr20:3027159-3027435(+)$1	276	118	122	12.0000
GGAG	chr12:110023757-110024003(+)$1	246	78	82	12.0000
GGAG	chr17:2598434-2598674(-)$1	240	36	40	12.0000
GGAG	chr17:80042917-80043132(-)$1	215	6	10	12.0000
GGAG	chrX:153052919-153053152(-)$1	233	186	190	12.0000
GGAG	chr17:79977653-79977885(-)$1	232	99	103	12.0000

#otherMatches

#Struct PSSM
BB{D	chr16:56643106-56643336(+)$1	230	1	5	12.0000
EEEE	chr9:131446073-131446308(+)$1	235	63	67	12.0000
DDDD	chr10:103920575-103920805(+)$1	230	28	32	12.0000
ffff	chr1:147091320-147091590(+)$1	270	71	75	12.0000
ddff	chr1:206905819-206906043(+)$1	224	99	103	12.0000
>>>>	chr7:75959222-75959481(-)$1	259	116	120	12.0000
BB}H	chr5:137843923-137844157(-)$1	234	125	129	12.0000
0000	chr6:151672985-151673228(+)$1	243	128	132	12.0000
rrrr	chr17:79652536-79652785(+)$1	249	5	9	12.0000
bb!!	chr7:2402613-2402853(+)$1	240	2	6	12.0000
dmmm	chr6:160164606-160164836(+)$1	230	145	149	12.0000
MMHH	chr20:42315562-42315800(+)$1	238	69	73	12.0000
eeee	chr15:41745022-41745264(+)$1	242	86	90	12.0000
dd[c	chr17:7480805-7481042(+)$1	237	15	19	12.0000
b[ee	chr17:79478898-79479181(-)$1	283	186	190	12.0000
}EEE	chr3:10312127-10312357(+)$1	230	118	122	12.0000
ggge	chr1:149400385-149400626(-)$1	241	29	33	12.0000
BBPP	chr1:149814082-149814326(-)$1	244	30	34	12.0000
eeee	chr16:89627894-89628205(+)$1	311	146	150	12.0000
AKKA	chr2:152991988-152992219(-)$1	231	16	20	12.0000
qqqa	chr15:69076635-69076919(-)$1	284	116	120	12.0000
ggg:	chr4:74005654-74005903(-)$1	249	105	109	12.0000
GGGG	chrX:150156164-150156403(+)$1	239	180	184	12.0000
ffff	chr17:7834927-7835167(-)$1	240	112	116	12.0000
EEE}	chr22:32111189-32111427(-)$1	238	207	211	12.0000
:CCC	chr12:56814743-56814984(-)$1	241	1	5	12.0000
DD:f	chr17:11984650-11984887(+)$1	237	134	138	12.0000
bmmm	chr14:70234884-70235099(+)$1	215	14	18	12.0000
mmme	chr11:67235426-67235663(-)$1	237	40	44	12.0000
DD{A	chr16:75600649-75600883(+)$1	234	25	29	12.0000
iiii	chr16:3900671-3900938(-)$1	267	68	72	12.0000
bb[e	chr6:157803040-157803278(+)$1	238	87	91	12.0000
qqqq	chr8:144662102-144662332(-)$1	230	123	127	12.0000
!ddd	chr16:3443651-3443885(-)$1	234	9	13	12.0000
oooo	chr16:90097727-90097987(+)$1	260	8	12	12.0000
bbmm	chr1:144164433-144164670(+)$1	237	40	44	12.0000
FFFF	chr6:170068017-170068256(-)$1	239	118	122	12.0000
6666	chr19:49863154-49863403(-)$1	249	142	146	12.0000
HHHH	chr19:50412158-50412450(-)$1	292	169	173	12.0000
EEbb	chr1:149812289-149812538(-)$1	249	90	94	12.0000
EEEE	chr1:149813993-149814257(-)$1	264	13	17	12.0000
CC}C	chr11:117263625-117263887(+)$1	262	146	150	12.0000
HHHH	chr6:31856951-31857192(-)$1	241	177	181	12.0000
:ccc	chr7:63982069-63982292(-)$1	223	28	32	12.0000
DDCC	chr16:2049410-2049653(-)$1	243	101	105	12.0000
FFFF	chr2:242179114-242179335(-)$1	221	24	28	12.0000
dddd	chr1:148267732-148267962(-)$1	230	84	88	12.0000
FFFF	chr9:131371379-131371654(+)$1	275	67	71	12.0000
====	chr9:103275490-103275715(+)$1	225	121	125	12.0000
FFFF	chr17:33464036-33464279(-)$1	243	2	6	12.0000
ddd]	chr16:70594286-70594517(+)$1	231	201	205	12.0000
ddd"	chr5:82876115-82876349(+)$1	234	122	126	12.0000
?BBZ	chr15:73865914-73866156(-)$1	242	135	139	12.0000
cc]c	chr22:39077923-39078202(+)$1	279	146	150	12.0000
ffff	chr16:29808268-29808501(+)$1	233	123	127	12.0000
oooo	chr15:101718432-101718667(-)$1	235	68	72	12.0000
FFFF	chr5:52942066-52942329(+)$1	263	14	18	12.0000
EEEE	chr19:51857413-51857662(-)$1	249	183	187	12.0000
pppp	chr20:3027159-3027435(+)$1	276	118	122	12.0000
2eee	chr12:110023757-110024003(+)$1	246	78	82	12.0000
&&&&	chr17:2598434-2598674(-)$1	240	36	40	12.0000
ff[b	chr17:80042917-80043132(-)$1	215	6	10	12.0000
gg:D	chrX:153052919-153053152(-)$1	233	186	190	12.0000
ii]a	chr17:79977653-79977885(-)$1	232	99	103	12.0000

#DB
((.(	chr16:56643106-56643336(+)$1	1	1	5	12.0000
((((	chr9:131446073-131446308(+)$1	1	63	67	12.0000
((((	chr10:103920575-103920805(+)$1	1	28	32	12.0000
))))	chr1:147091320-147091590(+)$1	1	71	75	12.0000
))))	chr1:206905819-206906043(+)$1	1	99	103	12.0000
....	chr7:75959222-75959481(-)$1	1	116	120	12.0000
)).)	chr5:137843923-137844157(-)$1	1	125	129	12.0000
....	chr6:151672985-151673228(+)$1	1	128	132	12.0000
....	chr17:79652536-79652785(+)$1	1	5	9	12.0000
((..	chr7:2402613-2402853(+)$1	1	2	6	12.0000
(...	chr6:160164606-160164836(+)$1	1	145	149	12.0000
..((	chr20:42315562-42315800(+)$1	1	69	73	12.0000
))))	chr15:41745022-41745264(+)$1	1	86	90	12.0000
((.(	chr17:7480805-7481042(+)$1	1	15	19	12.0000
(.((	chr17:79478898-79479181(-)$1	1	186	190	12.0000
.)))	chr3:10312127-10312357(+)$1	1	118	122	12.0000
)))(	chr1:149400385-149400626(-)$1	1	29	33	12.0000
((..	chr1:149814082-149814326(-)$1	1	30	34	12.0000
((((	chr16:89627894-89628205(+)$1	1	146	150	12.0000
(..(	chr2:152991988-152992219(-)$1	1	16	20	12.0000
...)	chr15:69076635-69076919(-)$1	1	116	120	12.0000
))).	chr4:74005654-74005903(-)$1	1	105	109	12.0000
))))	chrX:150156164-150156403(+)$1	1	180	184	12.0000
((((	chr17:7834927-7835167(-)$1	1	112	116	12.0000
))).	chr22:32111189-32111427(-)$1	1	207	211	12.0000
.(((	chr12:56814743-56814984(-)$1	1	1	5	12.0000
)).(	chr17:11984650-11984887(+)$1	1	134	138	12.0000
(...	chr14:70234884-70235099(+)$1	1	14	18	12.0000
...)	chr11:67235426-67235663(-)$1	1	40	44	12.0000
((.(	chr16:75600649-75600883(+)$1	1	25	29	12.0000
))))	chr16:3900671-3900938(-)$1	1	68	72	12.0000
((.(	chr6:157803040-157803278(+)$1	1	87	91	12.0000
....	chr8:144662102-144662332(-)$1	1	123	127	12.0000
.(((	chr16:3443651-3443885(-)$1	1	9	13	12.0000
....	chr16:90097727-90097987(+)$1	1	8	12	12.0000
((..	chr1:144164433-144164670(+)$1	1	40	44	12.0000
))((	chr6:170068017-170068256(-)$1	1	118	122	12.0000
....	chr19:49863154-49863403(-)$1	1	142	146	12.0000
))))	chr19:50412158-50412450(-)$1	1	169	173	12.0000
((((	chr1:149812289-149812538(-)$1	1	90	94	12.0000
((((	chr1:149813993-149814257(-)$1	1	13	17	12.0000
)).)	chr11:117263625-117263887(+)$1	1	146	150	12.0000
))))	chr6:31856951-31857192(-)$1	1	177	181	12.0000
.(((	chr7:63982069-63982292(-)$1	1	28	32	12.0000
((((	chr16:2049410-2049653(-)$1	1	101	105	12.0000
((((	chr2:242179114-242179335(-)$1	1	24	28	12.0000
))))	chr1:148267732-148267962(-)$1	1	84	88	12.0000
((((	chr9:131371379-131371654(+)$1	1	67	71	12.0000
((((	chr9:103275490-103275715(+)$1	1	121	125	12.0000
((((	chr17:33464036-33464279(-)$1	1	2	6	12.0000
))).	chr16:70594286-70594517(+)$1	1	201	205	12.0000
(((.	chr5:82876115-82876349(+)$1	1	122	126	12.0000
.)).	chr15:73865914-73866156(-)$1	1	135	139	12.0000
)).)	chr22:39077923-39078202(+)$1	1	146	150	12.0000
((((	chr16:29808268-29808501(+)$1	1	123	127	12.0000
....	chr15:101718432-101718667(-)$1	1	68	72	12.0000
((((	chr5:52942066-52942329(+)$1	1	14	18	12.0000
))))	chr19:51857413-51857662(-)$1	1	183	187	12.0000
....	chr20:3027159-3027435(+)$1	1	118	122	12.0000
.)))	chr12:110023757-110024003(+)$1	1	78	82	12.0000
....	chr17:2598434-2598674(-)$1	1	36	40	12.0000
((.(	chr17:80042917-80043132(-)$1	1	6	10	12.0000
)).)	chrX:153052919-153053152(-)$1	1	186	190	12.0000
)).)	chr17:79977653-79977885(-)$1	1	99	103	12.0000

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

#score	768.0
#seq	64
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m3_run1.nuc.txt

#NT
GGC	chr6:28327308-28327559(+)$1	251	30	33	9.0000
GGC	chr17:34942483-34942726(+)$1	243	63	66	9.0000
GGC	chrX:54048605-54048861(-)$1	256	54	57	9.0000
GGC	chr22:38087080-38087294(+)$1	214	5	8	9.0000
GGC	chr21:37771741-37771987(+)$1	246	113	116	9.0000
GGC	chr11:71810157-71810389(-)$1	232	13	16	9.0000
GGC	chr16:89590305-89590539(+)$1	234	101	104	9.0000
GGC	chr11:67236389-67236609(-)$1	220	9	12	9.0000
GGC	chr19:39976310-39976547(+)$1	237	110	113	9.0000
GGC	chr19:19162768-19163004(+)$1	236	20	23	9.0000
GGC	chr21:47703484-47703727(-)$1	243	37	40	9.0000
GGC	chr14:24680659-24680891(-)$1	232	34	37	9.0000
GGC	chr2:27716879-27717101(-)$1	222	50	53	9.0000
GGC	chr6:33170236-33170485(+)$1	249	30	33	9.0000
GGC	chr1:155733165-155733407(-)$1	242	74	77	9.0000
GGC	chr19:11461471-11461711(+)$1	240	29	32	9.0000
GGC	chr17:37563629-37563881(-)$1	252	83	86	9.0000
GGC	chr6:155129164-155129402(+)$1	238	38	41	9.0000
GGC	chr9:88694108-88694338(-)$1	230	77	80	9.0000
GGC	chr1:1597221-1597465(-)$1	244	42	45	9.0000
GGC	chr6:144779827-144780067(+)$1	240	80	83	9.0000
GGC	chr1:148202160-148202417(-)$1	257	7	10	9.0000
GGC	chr13:73345866-73346098(-)$1	232	101	104	9.0000
GGC	chr9:19379384-19379621(-)$1	237	29	32	9.0000
GGC	chr17:73238849-73239083(-)$1	234	138	141	9.0000
GGC	chr5:6378442-6378673(-)$1	231	20	23	9.0000
GGC	chr17:43481925-43482147(-)$1	222	67	70	9.0000
GGC	chr6:143749648-143749863(-)$1	215	6	9	9.0000
GGC	chr20:60879449-60879683(+)$1	234	15	18	9.0000
GGC	chr19:12246540-12246770(-)$1	230	4	7	9.0000
GGC	chr19:12157405-12157635(-)$1	230	68	71	9.0000
GGC	chr15:29997815-29998051(-)$1	236	150	153	9.0000
GGC	chr11:294331-294574(+)$1	243	2	5	9.0000
GGC	chr6:90372542-90372788(-)$1	246	8	11	9.0000
GGC	chr5:10262571-10262816(+)$1	245	1	4	9.0000
GGC	chr3:48460563-48460808(-)$1	245	38	41	9.0000
GGC	chr2:86361983-86362216(+)$1	233	60	63	9.0000
GGC	chr17:35310441-35310696(+)$1	255	31	34	9.0000
GGC	chr6:114181136-114181438(+)$1	302	3	6	9.0000
GGC	chr6:31504293-31504551(-)$1	258	81	84	9.0000
GGC	chrX:153629053-153629285(+)$1	232	10	13	9.0000
GGC	chr19:8056540-8056775(-)$1	235	55	58	9.0000
ggc	chr19:17430271-17430520(+)$1	249	32	35	9.0000
GGC	chr16:3795202-3795442(-)$1	240	109	112	9.0000
GGC	chr10:88854137-88854377(-)$1	240	15	18	9.0000
GGC	chr17:66518849-66519085(+)$1	236	52	55	9.0000
GGC	chr22:50832424-50832662(+)$1	238	26	29	9.0000
GGC	chr1:29379641-29379892(+)$1	251	7	10	9.0000
GGC	chr3:12632198-12632431(-)$1	233	15	18	9.0000
GGC	chr12:125397926-125398169(-)$1	243	9	12	9.0000
GGC	chr19:37869936-37870145(+)$1	209	11	14	9.0000
GGC	chr16:2052987-2053223(-)$1	236	18	21	9.0000
GGC	chr9:131477358-131477614(+)$1	256	10	13	9.0000
GGC	chr1:148278118-148278356(-)$1	238	58	61	9.0000
GGC	chr17:2323598-2323842(-)$1	244	5	8	9.0000
GGC	chr10:102678039-102678289(+)$1	250	209	212	9.0000
GGC	chr2:88095170-88095403(-)$1	233	78	81	9.0000
GGC	chr8:144895768-144895998(-)$1	230	17	20	9.0000
GGC	chr15:41819587-41819831(-)$1	244	23	26	9.0000
GGC	chr12:58114102-58114343(+)$1	241	6	9	9.0000
GGC	chr19:49469751-49469987(+)$1	236	26	29	9.0000
GGC	chr1:39322608-39322842(-)$1	234	206	209	9.0000
GGC	chr1:144200118-144200351(+)$1	233	138	141	9.0000
GGC	chr13:46553860-46554120(-)$1	260	217	220	9.0000
GGC	chr3:42555207-42555441(+)$1	234	49	52	9.0000
GGC	chr1:205689528-205689819(-)$1	291	86	89	9.0000
GGC	chr4:1730090-1730338(+)$1	248	4	7	9.0000
GGC	chr16:2807418-2807680(+)$1	262	84	87	9.0000
GGC	chr15:69727938-69728196(+)$1	258	147	150	9.0000
GGC	chr11:64805989-64806231(+)$1	242	1	4	9.0000
GGC	chr12:77202744-77202995(+)$1	251	147	150	9.0000
GGC	chr16:16485645-16485894(+)$1	249	37	40	9.0000
GGC	chr19:54695496-54695753(+)$1	257	23	26	9.0000
GGC	chr2:217526480-217526725(+)$1	245	38	41	9.0000
GGC	chr12:123343959-123344177(+)$1	218	41	44	9.0000
GGC	chr4:129208899-129209137(-)$1	238	1	4	9.0000
GGC	chr17:16120530-16120778(+)$1	248	23	26	9.0000
GGC	chr12:111800889-111801133(-)$1	244	8	11	9.0000
GGC	chrX:51931669-51931915(+)$1	246	44	47	9.0000
GGC	chr7:63981795-63982040(-)$1	245	58	61	9.0000
GGC	chr15:75651364-75651594(-)$1	230	19	22	9.0000
GGC	chr5:150515716-150515942(-)$1	226	78	81	9.0000
GGC	chr19:8553497-8553773(+)$1	276	76	79	9.0000
GGC	chr17:4849043-4849299(-)$1	256	24	27	9.0000
GGC	chr1:1636305-1636543(-)$1	238	89	92	9.0000
GGC	chr19:14640388-14640623(+)$1	235	0	3	9.0000
GGC	chr17:45745577-45745815(+)$1	238	39	42	9.0000
GGC	chr6:30553855-30554112(+)$1	257	20	23	9.0000
GGC	chr11:46817091-46817322(-)$1	231	103	106	9.0000
GGC	chr11:65746015-65746260(+)$1	245	2	5	9.0000
GGC	chr1:27648645-27648894(+)$1	249	2	5	9.0000
GGC	chrX:39922783-39923054(-)$1	271	15	18	9.0000
GGC	chr6:151670727-151670975(+)$1	248	46	49	9.0000
GGC	chr12:6692305-6692553(-)$1	248	85	88	9.0000

#otherMatches

#Struct PSSM
lll	chr14:65390698-65390930(+)$1	232	55	58	9.0000
FFF	chr6:28327308-28327559(+)$1	251	30	33	9.0000
bbo	chr17:34942483-34942726(+)$1	243	63	66	9.0000
b[c	chrX:54048605-54048861(-)$1	256	54	57	9.0000
DD:	chr22:38087080-38087294(+)$1	214	5	8	9.0000
JJJ	chr21:37771741-37771987(+)$1	246	113	116	9.0000
EEE	chr11:71810157-71810389(-)$1	232	13	16	9.0000
ccc	chr16:89590305-89590539(+)$1	234	101	104	9.0000
eee	chr11:67236389-67236609(-)$1	220	9	12	9.0000
"cc	chr19:39976310-39976547(+)$1	237	110	113	9.0000
ddd	chr19:19162768-19163004(+)$1	236	20	23	9.0000
ddd	chr21:47703484-47703727(-)$1	243	37	40	9.0000
GGG	chr14:24680659-24680891(-)$1	232	34	37	9.0000
GGG	chr2:27716879-27717101(-)$1	222	50	53	9.0000
A{E	chr6:33170236-33170485(+)$1	249	30	33	9.0000
EYY	chr1:155733165-155733407(-)$1	242	74	77	9.0000
!bb	chr19:11461471-11461711(+)$1	240	29	32	9.0000
::c	chr17:37563629-37563881(-)$1	252	83	86	9.0000
ddd	chr6:155129164-155129402(+)$1	238	38	41	9.0000
ggg	chr9:88694108-88694338(-)$1	230	77	80	9.0000
ccc	chr1:1597221-1597465(-)$1	244	42	45	9.0000
ddd	chr6:144779827-144780067(+)$1	240	80	83	9.0000
EEE	chr1:148202160-148202417(-)$1	257	7	10	9.0000
bbe	chr13:73345866-73346098(-)$1	232	101	104	9.0000
eee	chr9:19379384-19379621(-)$1	237	29	32	9.0000
FF@	chr17:73238849-73239083(-)$1	234	138	141	9.0000
EEE	chr5:6378442-6378673(-)$1	231	20	23	9.0000
gg]	chr17:43481925-43482147(-)$1	222	67	70	9.0000
EEE	chr6:143749648-143749863(-)$1	215	6	9	9.0000
ddd	chr20:60879449-60879683(+)$1	234	15	18	9.0000
eee	chr19:12246540-12246770(-)$1	230	4	7	9.0000
ddd	chr19:12157405-12157635(-)$1	230	68	71	9.0000
ggg	chr15:29997815-29998051(-)$1	236	150	153	9.0000
CCC	chr11:294331-294574(+)$1	243	2	5	9.0000
fff	chr6:90372542-90372788(-)$1	246	8	11	9.0000
cc[	chr5:10262571-10262816(+)$1	245	1	4	9.0000
ddd	chr3:48460563-48460808(-)$1	245	38	41	9.0000
FFF	chr2:86361983-86362216(+)$1	233	60	63	9.0000
GGG	chr17:35310441-35310696(+)$1	255	31	34	9.0000
C{D	chr6:114181136-114181438(+)$1	302	3	6	9.0000
"""	chr6:31504293-31504551(-)$1	258	81	84	9.0000
EEE	chrX:153629053-153629285(+)$1	232	10	13	9.0000
f[c	chr19:8056540-8056775(-)$1	235	55	58	9.0000
ddd	chr19:17430271-17430520(+)$1	249	32	35	9.0000
ggg	chr16:3795202-3795442(-)$1	240	109	112	9.0000
:ee	chr10:88854137-88854377(-)$1	240	15	18	9.0000
3ff	chr17:66518849-66519085(+)$1	236	52	55	9.0000
gg:	chr22:50832424-50832662(+)$1	238	26	29	9.0000
:cc	chr1:29379641-29379892(+)$1	251	7	10	9.0000
CCC	chr3:12632198-12632431(-)$1	233	15	18	9.0000
:DD	chr12:125397926-125398169(-)$1	243	9	12	9.0000
fff	chr19:37869936-37870145(+)$1	209	11	14	9.0000
f[h	chr16:2052987-2053223(-)$1	236	18	21	9.0000
FFF	chr9:131477358-131477614(+)$1	256	10	13	9.0000
ddc	chr1:148278118-148278356(-)$1	238	58	61	9.0000
DDD	chr17:2323598-2323842(-)$1	244	5	8	9.0000
dd:	chr10:102678039-102678289(+)$1	250	209	212	9.0000
ee"	chr2:88095170-88095403(-)$1	233	78	81	9.0000
c[d	chr8:144895768-144895998(-)$1	230	17	20	9.0000
DDD	chr15:41819587-41819831(-)$1	244	23	26	9.0000
F{E	chr12:58114102-58114343(+)$1	241	6	9	9.0000
bb:	chr19:49469751-49469987(+)$1	236	26	29	9.0000
ddd	chr1:39322608-39322842(-)$1	234	206	209	9.0000
b22	chr1:144200118-144200351(+)$1	233	138	141	9.0000
e""	chr13:46553860-46554120(-)$1	260	217	220	9.0000
:::	chr3:42555207-42555441(+)$1	234	49	52	9.0000
KKB	chr1:205689528-205689819(-)$1	291	86	89	9.0000
:EE	chr4:1730090-1730338(+)$1	248	4	7	9.0000
22d	chr16:2807418-2807680(+)$1	262	84	87	9.0000
EDD	chr15:69727938-69728196(+)$1	258	147	150	9.0000
GGG	chr11:64805989-64806231(+)$1	242	1	4	9.0000
22f	chr12:77202744-77202995(+)$1	251	147	150	9.0000
:dd	chr16:16485645-16485894(+)$1	249	37	40	9.0000
JJJ	chr19:54695496-54695753(+)$1	257	23	26	9.0000
GGG	chr2:217526480-217526725(+)$1	245	38	41	9.0000
bb2	chr12:123343959-123344177(+)$1	218	41	44	9.0000
{GG	chr4:129208899-129209137(-)$1	238	1	4	9.0000
(((	chr17:16120530-16120778(+)$1	248	23	26	9.0000
CC{	chr12:111800889-111801133(-)$1	244	8	11	9.0000
KKD	chrX:51931669-51931915(+)$1	246	44	47	9.0000
BB{	chr7:63981795-63982040(-)$1	245	58	61	9.0000
dd[	chr15:75651364-75651594(-)$1	230	19	22	9.0000
ddd	chr5:150515716-150515942(-)$1	226	78	81	9.0000
FFF	chr19:8553497-8553773(+)$1	276	76	79	9.0000
DD:	chr17:4849043-4849299(-)$1	256	24	27	9.0000
[cc	chr1:1636305-1636543(-)$1	238	89	92	9.0000
eee	chr19:14640388-14640623(+)$1	235	0	3	9.0000
ccc	chr17:45745577-45745815(+)$1	238	39	42	9.0000
ggg	chr6:30553855-30554112(+)$1	257	20	23	9.0000
cc[	chr11:46817091-46817322(-)$1	231	103	106	9.0000
:HH	chr11:65746015-65746260(+)$1	245	2	5	9.0000
ccc	chr1:27648645-27648894(+)$1	249	2	5	9.0000
ggg	chrX:39922783-39923054(-)$1	271	15	18	9.0000
!!b	chr6:151670727-151670975(+)$1	248	46	49	9.0000
[bb	chr12:6692305-6692553(-)$1	248	85	88	9.0000

#DB
...	chr14:65390698-65390930(+)$1	1	55	58	9.0000
(((	chr6:28327308-28327559(+)$1	1	30	33	9.0000
((.	chr17:34942483-34942726(+)$1	1	63	66	9.0000
(.(	chrX:54048605-54048861(-)$1	1	54	57	9.0000
((.	chr22:38087080-38087294(+)$1	1	5	8	9.0000
(((	chr21:37771741-37771987(+)$1	1	113	116	9.0000
(((	chr11:71810157-71810389(-)$1	1	13	16	9.0000
)))	chr16:89590305-89590539(+)$1	1	101	104	9.0000
(((	chr11:67236389-67236609(-)$1	1	9	12	9.0000
.((	chr19:39976310-39976547(+)$1	1	110	113	9.0000
(((	chr19:19162768-19163004(+)$1	1	20	23	9.0000
(((	chr21:47703484-47703727(-)$1	1	37	40	9.0000
(((	chr14:24680659-24680891(-)$1	1	34	37	9.0000
(((	chr2:27716879-27717101(-)$1	1	50	53	9.0000
(.(	chr6:33170236-33170485(+)$1	1	30	33	9.0000
)..	chr1:155733165-155733407(-)$1	1	74	77	9.0000
.((	chr19:11461471-11461711(+)$1	1	29	32	9.0000
..(	chr17:37563629-37563881(-)$1	1	83	86	9.0000
(((	chr6:155129164-155129402(+)$1	1	38	41	9.0000
)))	chr9:88694108-88694338(-)$1	1	77	80	9.0000
)))	chr1:1597221-1597465(-)$1	1	42	45	9.0000
)))	chr6:144779827-144780067(+)$1	1	80	83	9.0000
(((	chr1:148202160-148202417(-)$1	1	7	10	9.0000
(((	chr13:73345866-73346098(-)$1	1	101	104	9.0000
)))	chr9:19379384-19379621(-)$1	1	29	32	9.0000
)).	chr17:73238849-73239083(-)$1	1	138	141	9.0000
(((	chr5:6378442-6378673(-)$1	1	20	23	9.0000
)).	chr17:43481925-43482147(-)$1	1	67	70	9.0000
(((	chr6:143749648-143749863(-)$1	1	6	9	9.0000
(((	chr20:60879449-60879683(+)$1	1	15	18	9.0000
(((	chr19:12246540-12246770(-)$1	1	4	7	9.0000
(((	chr19:12157405-12157635(-)$1	1	68	71	9.0000
)))	chr15:29997815-29998051(-)$1	1	150	153	9.0000
(((	chr11:294331-294574(+)$1	1	2	5	9.0000
(((	chr6:90372542-90372788(-)$1	1	8	11	9.0000
((.	chr5:10262571-10262816(+)$1	1	1	4	9.0000
)))	chr3:48460563-48460808(-)$1	1	38	41	9.0000
(((	chr2:86361983-86362216(+)$1	1	60	63	9.0000
(((	chr17:35310441-35310696(+)$1	1	31	34	9.0000
(.(	chr6:114181136-114181438(+)$1	1	3	6	9.0000
...	chr6:31504293-31504551(-)$1	1	81	84	9.0000
(((	chrX:153629053-153629285(+)$1	1	10	13	9.0000
(.(	chr19:8056540-8056775(-)$1	1	55	58	9.0000
)))	chr19:17430271-17430520(+)$1	1	32	35	9.0000
(((	chr16:3795202-3795442(-)$1	1	109	112	9.0000
.((	chr10:88854137-88854377(-)$1	1	15	18	9.0000
.))	chr17:66518849-66519085(+)$1	1	52	55	9.0000
)).	chr22:50832424-50832662(+)$1	1	26	29	9.0000
.((	chr1:29379641-29379892(+)$1	1	7	10	9.0000
(((	chr3:12632198-12632431(-)$1	1	15	18	9.0000
.((	chr12:125397926-125398169(-)$1	1	9	12	9.0000
(((	chr19:37869936-37870145(+)$1	1	11	14	9.0000
(.(	chr16:2052987-2053223(-)$1	1	18	21	9.0000
(((	chr9:131477358-131477614(+)$1	1	10	13	9.0000
(((	chr1:148278118-148278356(-)$1	1	58	61	9.0000
(((	chr17:2323598-2323842(-)$1	1	5	8	9.0000
)).	chr10:102678039-102678289(+)$1	1	209	212	9.0000
((.	chr2:88095170-88095403(-)$1	1	78	81	9.0000
(.(	chr8:144895768-144895998(-)$1	1	17	20	9.0000
(((	chr15:41819587-41819831(-)$1	1	23	26	9.0000
(.(	chr12:58114102-58114343(+)$1	1	6	9	9.0000
)).	chr19:49469751-49469987(+)$1	1	26	29	9.0000
(((	chr1:39322608-39322842(-)$1	1	206	209	9.0000
)..	chr1:144200118-144200351(+)$1	1	138	141	9.0000
(..	chr13:46553860-46554120(-)$1	1	217	220	9.0000
...	chr3:42555207-42555441(+)$1	1	49	52	9.0000
..(	chr1:205689528-205689819(-)$1	1	86	89	9.0000
.((	chr4:1730090-1730338(+)$1	1	4	7	9.0000
..)	chr16:2807418-2807680(+)$1	1	84	87	9.0000
(((	chr15:69727938-69728196(+)$1	1	147	150	9.0000
(((	chr11:64805989-64806231(+)$1	1	1	4	9.0000
..)	chr12:77202744-77202995(+)$1	1	147	150	9.0000
.((	chr16:16485645-16485894(+)$1	1	37	40	9.0000
(((	chr19:54695496-54695753(+)$1	1	23	26	9.0000
(((	chr2:217526480-217526725(+)$1	1	38	41	9.0000
)).	chr12:123343959-123344177(+)$1	1	41	44	9.0000
.((	chr4:129208899-129209137(-)$1	1	1	4	9.0000
...	chr17:16120530-16120778(+)$1	1	23	26	9.0000
((.	chr12:111800889-111801133(-)$1	1	8	11	9.0000
..(	chrX:51931669-51931915(+)$1	1	44	47	9.0000
((.	chr7:63981795-63982040(-)$1	1	58	61	9.0000
((.	chr15:75651364-75651594(-)$1	1	19	22	9.0000
(((	chr5:150515716-150515942(-)$1	1	78	81	9.0000
(((	chr19:8553497-8553773(+)$1	1	76	79	9.0000
((.	chr17:4849043-4849299(-)$1	1	24	27	9.0000
.((	chr1:1636305-1636543(-)$1	1	89	92	9.0000
(((	chr19:14640388-14640623(+)$1	1	0	3	9.0000
)))	chr17:45745577-45745815(+)$1	1	39	42	9.0000
(((	chr6:30553855-30554112(+)$1	1	20	23	9.0000
((.	chr11:46817091-46817322(-)$1	1	103	106	9.0000
.((	chr11:65746015-65746260(+)$1	1	2	5	9.0000
(((	chr1:27648645-27648894(+)$1	1	2	5	9.0000
(((	chrX:39922783-39923054(-)$1	1	15	18	9.0000
..(	chr6:151670727-151670975(+)$1	1	46	49	9.0000
.((	chr12:6692305-6692553(-)$1	1	85	88	9.0000

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

#score	855.0000000000002
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m1_run1.nuc.txt

#NT
AAA	chr1:35649274-35649504(-)$1	230	26	29	9.0000
AAA	chr16:71890547-71890779(+)$1	232	7	10	9.0000
AAA	chr12:122498684-122498913(+)$1	229	62	65	9.0000
AAA	chr12:95694454-95694692(+)$1	238	38	41	9.0000
AAA	chr1:203769115-203769341(+)$1	226	33	36	9.0000
AAA	chr17:47368570-47368794(-)$1	224	35	38	9.0000
AAA	chr6:47594485-47594738(+)$1	253	14	17	9.0000
AAA	chr14:103985994-103986226(-)$1	232	20	23	9.0000
AAA	chr22:38880098-38880331(-)$1	233	10	13	9.0000
AAA	chr15:55911549-55911771(-)$1	222	113	116	9.0000
AAA	chr9:14083662-14083882(-)$1	220	12	15	9.0000
AAA	chr2:113287760-113288011(+)$1	251	19	22	9.0000
AAA	chr14:99635923-99636154(-)$1	231	3	6	9.0000
AAA	chr7:100286675-100286939(-)$1	264	107	110	9.0000
AAA	chr19:4045353-4045571(-)$1	218	10	13	9.0000
AAA	chr2:60684888-60685120(-)$1	232	1	4	9.0000
AAA	chr5:74657712-74657935(+)$1	223	5	8	9.0000
AAA	chr19:55998477-55998734(+)$1	257	140	143	9.0000
AAA	chr17:62499262-62499510(-)$1	248	0	3	9.0000
AAA	chr9:127909189-127909449(-)$1	260	31	34	9.0000
AAA	chr6:111650640-111650864(-)$1	224	72	75	9.0000
AAA	chrX:84500827-84501069(+)$1	242	1	4	9.0000
AAA	chr9:77561818-77562071(-)$1	253	55	58	9.0000
AAA	chr3:42706271-42706508(+)$1	237	89	92	9.0000
AAA	chr10:73576059-73576310(-)$1	251	158	161	9.0000
AAA	chrX:103436291-103436509(+)$1	218	13	16	9.0000
AAA	chr11:1296691-1296911(-)$1	220	7	10	9.0000
AAA	chr17:40864281-40864512(-)$1	231	37	40	9.0000
AAA	chr20:42091199-42091441(+)$1	242	5	8	9.0000
AAA	chr16:18803329-18803566(-)$1	237	38	41	9.0000
AAA	chr12:104513262-104513504(-)$1	242	22	25	9.0000
AAA	chr5:172742280-172742504(-)$1	224	33	36	9.0000
AAA	chr11:34121618-34121863(+)$1	245	43	46	9.0000
AAA	chr12:14923908-14924132(-)$1	224	17	20	9.0000
AAA	chr12:4413279-4413511(+)$1	232	45	48	9.0000
AAA	chr9:86275553-86275773(-)$1	220	21	24	9.0000
AAA	chr17:42282979-42283202(-)$1	223	45	48	9.0000
AAA	chr11:10326613-10326847(+)$1	234	225	228	9.0000
AAA	chr7:36364498-36364721(-)$1	223	34	37	9.0000
AAA	chr17:47005569-47005813(+)$1	244	132	135	9.0000
AAA	chr10:70104032-70104267(-)$1	235	43	46	9.0000
AAA	chr13:74265024-74265250(-)$1	226	14	17	9.0000
AAA	chr8:74705906-74706145(-)$1	239	41	44	9.0000
AAA	chr11:65306166-65306389(-)$1	223	72	75	9.0000
aaa	chr1:227848147-227848373(+)$1	226	27	30	9.0000
AAA	chr20:48697896-48698127(-)$1	231	2	5	9.0000
AAA	chr3:169805426-169805664(-)$1	238	27	30	9.0000
AAA	chr8:91636665-91636916(-)$1	251	28	31	9.0000
AAA	chr14:53243497-53243720(-)$1	223	32	35	9.0000
aaa	chr2:100895529-100895751(-)$1	222	4	7	9.0000
AAA	chr19:47113234-47113474(+)$1	240	129	132	9.0000
AAA	chr4:160279956-160280210(+)$1	254	97	100	9.0000
AAA	chrX:107327548-107327772(-)$1	224	15	18	9.0000
AAA	chr6:15520708-15520960(+)$1	252	6	9	9.0000
AAA	chr14:55535783-55536014(+)$1	231	15	18	9.0000
aaa	chr15:81268520-81268744(-)$1	224	68	71	9.0000
AAA	chr15:75663805-75664030(-)$1	225	100	103	9.0000
AAA	chrX:149933097-149933320(+)$1	223	72	75	9.0000
AAA	chr1:228681752-228681979(+)$1	227	18	21	9.0000
AAA	chr4:174243247-174243481(+)$1	234	136	139	9.0000
AAA	chr19:10801585-10801821(+)$1	236	29	32	9.0000
AAA	chr10:112658844-112659070(+)$1	226	19	22	9.0000
aaa	chr6:26469562-26469784(+)$1	222	7	10	9.0000
AAA	chr14:21968665-21968888(-)$1	223	28	31	9.0000
AAA	chr7:148427077-148427306(+)$1	229	10	13	9.0000
AAA	chr2:242291647-242291880(+)$1	233	140	143	9.0000
AAA	chr9:89559478-89559703(-)$1	225	35	38	9.0000
AAA	chr8:22477543-22477766(+)$1	223	178	181	9.0000
AAA	chr3:107527402-107527630(+)$1	228	47	50	9.0000
AAA	chr15:77241669-77241900(+)$1	231	47	50	9.0000
AAA	chr7:44100902-44101126(+)$1	224	81	84	9.0000
AAA	chr16:57286877-57287106(+)$1	229	56	59	9.0000
AAA	chr17:76967818-76968060(-)$1	242	200	203	9.0000
AAA	chr17:77759097-77759317(+)$1	220	8	11	9.0000
AAA	chr17:80201943-80202169(-)$1	226	131	134	9.0000
AAA	chr8:126450195-126450414(+)$1	219	1	4	9.0000
AAA	chr4:85570108-85570336(+)$1	228	6	9	9.0000
AAA	chr6:24535399-24535642(+)$1	243	1	4	9.0000
AAA	chr6:35802687-35802928(-)$1	241	72	75	9.0000
AAA	chr11:9611034-9611297(+)$1	263	20	23	9.0000
AAA	chr17:73234355-73234570(-)$1	215	0	3	9.0000
AAA	chr17:80726215-80726446(+)$1	231	87	90	9.0000
aaa	chr11:15990387-15990611(-)$1	224	12	15	9.0000
AAA	chr5:81571025-81571249(-)$1	224	18	21	9.0000
aaa	chr10:3821028-3821252(-)$1	224	0	3	9.0000
AAA	chr4:41957699-41957923(+)$1	224	81	84	9.0000
AAA	chr6:11579844-11580067(+)$1	223	44	47	9.0000
AAA	chr1:3730680-3730903(-)$1	223	199	202	9.0000
AAA	chr11:47491088-47491348(-)$1	260	61	64	9.0000
AAA	chr10:22825876-22826096(-)$1	220	28	31	9.0000
AAA	chr11:57439426-57439658(+)$1	232	19	22	9.0000
AAA	chr6:142540450-142540683(+)$1	233	53	56	9.0000
AAA	chr1:180083776-180084007(+)$1	231	2	5	9.0000
AAA	chr1:92146227-92146462(-)$1	235	5	8	9.0000
AAA	chr7:27211273-27211505(-)$1	232	206	209	9.0000
AAA	chr4:20255316-20255557(+)$1	241	77	80	9.0000
AAA	chr15:75221356-75221571(-)$1	215	111	114	9.0000
AAA	chrX:47088216-47088435(+)$1	219	96	99	9.0000
AAA	chr9:79000534-79000781(-)$1	247	0	3	9.0000

#otherMatches

#Struct PSSM
:::	chr19:4047429-4047665(-)$1	236	0	3	9.0000
bbf	chr1:35649274-35649504(-)$1	230	26	29	9.0000
:::	chr16:71890547-71890779(+)$1	232	7	10	9.0000
eee	chr12:122498684-122498913(+)$1	229	62	65	9.0000
b##	chr12:95694454-95694692(+)$1	238	38	41	9.0000
DDD	chr1:203769115-203769341(+)$1	226	33	36	9.0000
C::	chr17:47368570-47368794(-)$1	224	35	38	9.0000
"""	chr6:47594485-47594738(+)$1	253	14	17	9.0000
[ee	chr14:103985994-103986226(-)$1	232	20	23	9.0000
DEE	chr22:38880098-38880331(-)$1	233	10	13	9.0000
ppp	chr15:55911549-55911771(-)$1	222	113	116	9.0000
B{D	chr9:14083662-14083882(-)$1	220	12	15	9.0000
I::	chr2:113287760-113288011(+)$1	251	19	22	9.0000
fff	chr14:99635923-99636154(-)$1	231	3	6	9.0000
d""	chr7:100286675-100286939(-)$1	264	107	110	9.0000
hhh	chr19:4045353-4045571(-)$1	218	10	13	9.0000
:::	chr2:60684888-60685120(-)$1	232	1	4	9.0000
:::	chr5:74657712-74657935(+)$1	223	5	8	9.0000
:::	chr19:55998477-55998734(+)$1	257	140	143	9.0000
:::	chr17:62499262-62499510(-)$1	248	0	3	9.0000
::e	chr9:127909189-127909449(-)$1	260	31	34	9.0000
eee	chr6:111650640-111650864(-)$1	224	72	75	9.0000
:DD	chrX:84500827-84501069(+)$1	242	1	4	9.0000
oof	chr9:77561818-77562071(-)$1	253	55	58	9.0000
:::	chr3:42706271-42706508(+)$1	237	89	92	9.0000
:::	chr10:73576059-73576310(-)$1	251	158	161	9.0000
DLL	chrX:103436291-103436509(+)$1	218	13	16	9.0000
::g	chr11:1296691-1296911(-)$1	220	7	10	9.0000
::H	chr17:40864281-40864512(-)$1	231	37	40	9.0000
EEE	chr20:42091199-42091441(+)$1	242	5	8	9.0000
sss	chr16:18803329-18803566(-)$1	237	38	41	9.0000
:::	chr12:104513262-104513504(-)$1	242	22	25	9.0000
hff	chr5:172742280-172742504(-)$1	224	33	36	9.0000
$$$	chr11:34121618-34121863(+)$1	245	43	46	9.0000
ooo	chr12:14923908-14924132(-)$1	224	17	20	9.0000
sss	chr12:4413279-4413511(+)$1	232	45	48	9.0000
:::	chr9:86275553-86275773(-)$1	220	21	24	9.0000
e77	chr17:42282979-42283202(-)$1	223	45	48	9.0000
ooo	chr11:10326613-10326847(+)$1	234	225	228	9.0000
EE:	chr7:36364498-36364721(-)$1	223	34	37	9.0000
GGG	chr17:47005569-47005813(+)$1	244	132	135	9.0000
ddd	chr10:70104032-70104267(-)$1	235	43	46	9.0000
:::	chr13:74265024-74265250(-)$1	226	14	17	9.0000
dd[	chr8:74705906-74706145(-)$1	239	41	44	9.0000
b!!	chr11:65306166-65306389(-)$1	223	72	75	9.0000
HHK	chr1:227848147-227848373(+)$1	226	27	30	9.0000
:::	chr20:48697896-48698127(-)$1	231	2	5	9.0000
HHH	chr3:169805426-169805664(-)$1	238	27	30	9.0000
EEE	chr8:91636665-91636916(-)$1	251	28	31	9.0000
DKK	chr14:53243497-53243720(-)$1	223	32	35	9.0000
:::	chr2:100895529-100895751(-)$1	222	4	7	9.0000
]ff	chr19:47113234-47113474(+)$1	240	129	132	9.0000
"""	chr4:160279956-160280210(+)$1	254	97	100	9.0000
DDD	chrX:107327548-107327772(-)$1	224	15	18	9.0000
GG:	chr6:15520708-15520960(+)$1	252	6	9	9.0000
!!c	chr14:55535783-55536014(+)$1	231	15	18	9.0000
$$$	chr15:81268520-81268744(-)$1	224	68	71	9.0000
:::	chr15:75663805-75664030(-)$1	225	100	103	9.0000
rrr	chrX:149933097-149933320(+)$1	223	72	75	9.0000
:::	chr1:228681752-228681979(+)$1	227	18	21	9.0000
fff	chr4:174243247-174243481(+)$1	234	136	139	9.0000
ooo	chr19:10801585-10801821(+)$1	236	29	32	9.0000
qqq	chr10:112658844-112659070(+)$1	226	19	22	9.0000
:::	chr6:26469562-26469784(+)$1	222	7	10	9.0000
:::	chr14:21968665-21968888(-)$1	223	28	31	9.0000
eee	chr7:148427077-148427306(+)$1	229	10	13	9.0000
ooo	chr2:242291647-242291880(+)$1	233	140	143	9.0000
EEE	chr9:89559478-89559703(-)$1	225	35	38	9.0000
EEE	chr8:22477543-22477766(+)$1	223	178	181	9.0000
33b	chr3:107527402-107527630(+)$1	228	47	50	9.0000
III	chr15:77241669-77241900(+)$1	231	47	50	9.0000
dd]	chr7:44100902-44101126(+)$1	224	81	84	9.0000
33b	chr16:57286877-57287106(+)$1	229	56	59	9.0000
ee$	chr17:76967818-76968060(-)$1	242	200	203	9.0000
FKK	chr17:77759097-77759317(+)$1	220	8	11	9.0000
h%%	chr17:80201943-80202169(-)$1	226	131	134	9.0000
:::	chr8:126450195-126450414(+)$1	219	1	4	9.0000
:::	chr4:85570108-85570336(+)$1	228	6	9	9.0000
:::	chr6:24535399-24535642(+)$1	243	1	4	9.0000
:::	chr6:35802687-35802928(-)$1	241	72	75	9.0000
###	chr11:9611034-9611297(+)$1	263	20	23	9.0000
:::	chr17:73234355-73234570(-)$1	215	0	3	9.0000
ff:	chr17:80726215-80726446(+)$1	231	87	90	9.0000
HHH	chr11:15990387-15990611(-)$1	224	12	15	9.0000
b[f	chr5:81571025-81571249(-)$1	224	18	21	9.0000
:::	chr10:3821028-3821252(-)$1	224	0	3	9.0000
===	chr4:41957699-41957923(+)$1	224	81	84	9.0000
:::	chr6:11579844-11580067(+)$1	223	44	47	9.0000
|||	chr1:3730680-3730903(-)$1	223	199	202	9.0000
lgg	chr11:47491088-47491348(-)$1	260	61	64	9.0000
g##	chr10:22825876-22826096(-)$1	220	28	31	9.0000
CCL	chr11:57439426-57439658(+)$1	232	19	22	9.0000
xxx	chr6:142540450-142540683(+)$1	233	53	56	9.0000
:::	chr1:180083776-180084007(+)$1	231	2	5	9.0000
:::	chr1:92146227-92146462(-)$1	235	5	8	9.0000
cc]	chr7:27211273-27211505(-)$1	232	206	209	9.0000
>>>	chr4:20255316-20255557(+)$1	241	77	80	9.0000
ooo	chr15:75221356-75221571(-)$1	215	111	114	9.0000
LLC	chrX:47088216-47088435(+)$1	219	96	99	9.0000
:::	chr9:79000534-79000781(-)$1	247	0	3	9.0000

#DB
...	chr19:4047429-4047665(-)$1	1	0	3	9.0000
(((	chr1:35649274-35649504(-)$1	1	26	29	9.0000
...	chr16:71890547-71890779(+)$1	1	7	10	9.0000
(((	chr12:122498684-122498913(+)$1	1	62	65	9.0000
(..	chr12:95694454-95694692(+)$1	1	38	41	9.0000
(((	chr1:203769115-203769341(+)$1	1	33	36	9.0000
(..	chr17:47368570-47368794(-)$1	1	35	38	9.0000
...	chr6:47594485-47594738(+)$1	1	14	17	9.0000
.((	chr14:103985994-103986226(-)$1	1	20	23	9.0000
(((	chr22:38880098-38880331(-)$1	1	10	13	9.0000
...	chr15:55911549-55911771(-)$1	1	113	116	9.0000
(.(	chr9:14083662-14083882(-)$1	1	12	15	9.0000
(..	chr2:113287760-113288011(+)$1	1	19	22	9.0000
(((	chr14:99635923-99636154(-)$1	1	3	6	9.0000
(..	chr7:100286675-100286939(-)$1	1	107	110	9.0000
(((	chr19:4045353-4045571(-)$1	1	10	13	9.0000
...	chr2:60684888-60685120(-)$1	1	1	4	9.0000
...	chr5:74657712-74657935(+)$1	1	5	8	9.0000
...	chr19:55998477-55998734(+)$1	1	140	143	9.0000
...	chr17:62499262-62499510(-)$1	1	0	3	9.0000
..(	chr9:127909189-127909449(-)$1	1	31	34	9.0000
(((	chr6:111650640-111650864(-)$1	1	72	75	9.0000
.((	chrX:84500827-84501069(+)$1	1	1	4	9.0000
..)	chr9:77561818-77562071(-)$1	1	55	58	9.0000
...	chr3:42706271-42706508(+)$1	1	89	92	9.0000
...	chr10:73576059-73576310(-)$1	1	158	161	9.0000
(..	chrX:103436291-103436509(+)$1	1	13	16	9.0000
..(	chr11:1296691-1296911(-)$1	1	7	10	9.0000
..(	chr17:40864281-40864512(-)$1	1	37	40	9.0000
(((	chr20:42091199-42091441(+)$1	1	5	8	9.0000
...	chr16:18803329-18803566(-)$1	1	38	41	9.0000
...	chr12:104513262-104513504(-)$1	1	22	25	9.0000
)((	chr5:172742280-172742504(-)$1	1	33	36	9.0000
...	chr11:34121618-34121863(+)$1	1	43	46	9.0000
...	chr12:14923908-14924132(-)$1	1	17	20	9.0000
...	chr12:4413279-4413511(+)$1	1	45	48	9.0000
...	chr9:86275553-86275773(-)$1	1	21	24	9.0000
)..	chr17:42282979-42283202(-)$1	1	45	48	9.0000
...	chr11:10326613-10326847(+)$1	1	225	228	9.0000
((.	chr7:36364498-36364721(-)$1	1	34	37	9.0000
(((	chr17:47005569-47005813(+)$1	1	132	135	9.0000
(((	chr10:70104032-70104267(-)$1	1	43	46	9.0000
...	chr13:74265024-74265250(-)$1	1	14	17	9.0000
((.	chr8:74705906-74706145(-)$1	1	41	44	9.0000
(..	chr11:65306166-65306389(-)$1	1	72	75	9.0000
((.	chr1:227848147-227848373(+)$1	1	27	30	9.0000
...	chr20:48697896-48698127(-)$1	1	2	5	9.0000
(((	chr3:169805426-169805664(-)$1	1	27	30	9.0000
(((	chr8:91636665-91636916(-)$1	1	28	31	9.0000
(..	chr14:53243497-53243720(-)$1	1	32	35	9.0000
...	chr2:100895529-100895751(-)$1	1	4	7	9.0000
.))	chr19:47113234-47113474(+)$1	1	129	132	9.0000
...	chr4:160279956-160280210(+)$1	1	97	100	9.0000
(((	chrX:107327548-107327772(-)$1	1	15	18	9.0000
((.	chr6:15520708-15520960(+)$1	1	6	9	9.0000
..(	chr14:55535783-55536014(+)$1	1	15	18	9.0000
...	chr15:81268520-81268744(-)$1	1	68	71	9.0000
...	chr15:75663805-75664030(-)$1	1	100	103	9.0000
...	chrX:149933097-149933320(+)$1	1	72	75	9.0000
...	chr1:228681752-228681979(+)$1	1	18	21	9.0000
(((	chr4:174243247-174243481(+)$1	1	136	139	9.0000
...	chr19:10801585-10801821(+)$1	1	29	32	9.0000
...	chr10:112658844-112659070(+)$1	1	19	22	9.0000
...	chr6:26469562-26469784(+)$1	1	7	10	9.0000
...	chr14:21968665-21968888(-)$1	1	28	31	9.0000
(((	chr7:148427077-148427306(+)$1	1	10	13	9.0000
...	chr2:242291647-242291880(+)$1	1	140	143	9.0000
(((	chr9:89559478-89559703(-)$1	1	35	38	9.0000
)))	chr8:22477543-22477766(+)$1	1	178	181	9.0000
..)	chr3:107527402-107527630(+)$1	1	47	50	9.0000
(((	chr15:77241669-77241900(+)$1	1	47	50	9.0000
)).	chr7:44100902-44101126(+)$1	1	81	84	9.0000
..)	chr16:57286877-57287106(+)$1	1	56	59	9.0000
((.	chr17:76967818-76968060(-)$1	1	200	203	9.0000
(..	chr17:77759097-77759317(+)$1	1	8	11	9.0000
(..	chr17:80201943-80202169(-)$1	1	131	134	9.0000
...	chr8:126450195-126450414(+)$1	1	1	4	9.0000
...	chr4:85570108-85570336(+)$1	1	6	9	9.0000
...	chr6:24535399-24535642(+)$1	1	1	4	9.0000
...	chr6:35802687-35802928(-)$1	1	72	75	9.0000
...	chr11:9611034-9611297(+)$1	1	20	23	9.0000
...	chr17:73234355-73234570(-)$1	1	0	3	9.0000
)).	chr17:80726215-80726446(+)$1	1	87	90	9.0000
(((	chr11:15990387-15990611(-)$1	1	12	15	9.0000
(.(	chr5:81571025-81571249(-)$1	1	18	21	9.0000
...	chr10:3821028-3821252(-)$1	1	0	3	9.0000
(((	chr4:41957699-41957923(+)$1	1	81	84	9.0000
...	chr6:11579844-11580067(+)$1	1	44	47	9.0000
...	chr1:3730680-3730903(-)$1	1	199	202	9.0000
.))	chr11:47491088-47491348(-)$1	1	61	64	9.0000
(..	chr10:22825876-22826096(-)$1	1	28	31	9.0000
((.	chr11:57439426-57439658(+)$1	1	19	22	9.0000
...	chr6:142540450-142540683(+)$1	1	53	56	9.0000
...	chr1:180083776-180084007(+)$1	1	2	5	9.0000
...	chr1:92146227-92146462(-)$1	1	5	8	9.0000
)).	chr7:27211273-27211505(-)$1	1	206	209	9.0000
...	chr4:20255316-20255557(+)$1	1	77	80	9.0000
...	chr15:75221356-75221571(-)$1	1	111	114	9.0000
..(	chrX:47088216-47088435(+)$1	1	96	99	9.0000
...	chr9:79000534-79000781(-)$1	1	0	3	9.0000

#PSSM
A : 0.94	a : 0.06	
A : 0.94	a : 0.06	
A : 0.94	a : 0.06	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_UTR_m1_run2.nuc.txt

#NT
UUUCAUAA	chr16:46694343-46694590(-)$1	247	123	131	15.5000
UUUUAAAA	chr1:116235451-116235706(+)$1	255	3	11	15.7000
UUUUAUUA	chr3:170022243-170022480(+)$1	237	150	158	15.1000
UUUUUUAA	chr6:57049467-57049746(+)$1	279	216	224	16.2000
UUUUUUAA	chr2:201687879-201688126(+)$1	247	153	161	16.2000
uuguauaa	chr10:101472884-101473169(-)$1	285	131	139	15.1000
UUUUAUAA	chr2:61350111-61350348(+)$1	237	122	130	19.6000
UUCUAUAA	chr10:38412015-38412322(+)$1	307	275	283	15.2000
GUUUAUAA	chr13:20247413-20247642(+)$1	229	29	37	15.4000
UUUUGUAA	chr12:124242563-124242810(+)$1	247	179	187	15.7000
UCUUAUAA	chr12:110369747-110369992(-)$1	245	218	226	14.8000
UUUUAUAA	chr5:134191714-134192037(+)$1	323	172	180	19.6000
UUUUAUAG	chr2:197643243-197643534(-)$1	291	241	249	15.4000
GUUUAUAA	chr4:170650523-170650752(-)$1	229	129	137	15.4000
UUUUAUAA	chr2:242053137-242053396(-)$1	259	62	70	19.6000
uuuuuuaa	chr2:213864692-213865004(-)$1	312	90	98	16.2000
CUUUAUAA	chr1:162494148-162494399(+)$1	251	229	237	15.2000
UUUUAUCA	chr11:9302679-9302910(-)$1	231	153	161	15.1000
UUUGAUAA	chr5:72209825-72210067(+)$1	242	216	224	15.7000
UUUUAAAA	chr6:79647225-79647501(-)$1	276	28	36	15.7000
UUUUAUGA	chr3:160151000-160151408(+)$1	408	306	314	15.2000
UUUUAAAA	chr11:66433754-66434072(+)$1	318	286	294	15.7000
UUUAAUAA	chr2:54045783-54046024(-)$1	241	58	66	15.8000
uuuuuuaa	chr1:146629880-146630158(-)$1	278	2	10	16.2000
GUUuauaa	chr17:57777534-57777788(-)$1	254	38	46	15.4000
UUUAAUAA	chr3:20025693-20025966(+)$1	273	121	129	15.8000
UUUGAUAA	chr5:132216556-132216825(-)$1	269	213	221	15.7000
UUUAAUAA	chr4:175240779-175241023(+)$1	244	68	76	15.8000
UUUUGUAA	chr3:160151822-160152142(+)$1	320	227	235	15.7000
uuuuuuaa	chr18:32838262-32838493(-)$1	231	143	151	16.2000
uuuuauga	chr12:66253198-66253453(+)$1	255	225	233	15.2000
UUUUAAAA	chr6:139236846-139237119(-)$1	273	218	226	15.7000
UUAUAUAA	chr5:138207360-138207610(-)$1	250	83	91	15.1000
UUUUAGAA	chr13:52989349-52989599(-)$1	250	91	99	15.4000
AUUUAUAA	chr2:209170017-209170321(+)$1	304	24	32	15.2000
uuuuuuAA	chr22:38881636-38881872(-)$1	236	44	52	16.2000
uuuaauaa	chr3:3171761-3172051(+)$1	290	225	233	15.8000
UUUGAUAA	chr5:39105868-39106154(-)$1	286	132	140	15.7000
UUUUAUAA	chr1:159997754-159998007(-)$1	253	17	25	19.6000
UUUUAUAC	chr12:56347457-56347903(+)$1	446	370	378	15.4000
uuuuauau	chr5:110077350-110077590(+)$1	240	70	78	15.4000
UUUUAUAA	chr14:95555553-95555849(-)$1	296	58	66	19.6000
UUUUAUAG	chr17:4070048-4070358(-)$1	310	82	90	15.4000
UUUUAUAA	chr3:121140650-121140915(+)$1	265	101	109	19.6000
UUUUUUAA	chr1:113454949-113455202(-)$1	253	63	71	16.2000
UUUUACAA	chr17:15933701-15933961(-)$1	260	54	62	15.5000
UUUUACAA	chr2:128063520-128063763(-)$1	243	43	51	15.5000
UUUUAUAU	chr12:105764574-105764852(+)$1	278	183	191	15.4000
UUCUAUAA	chr5:75912166-75912400(-)$1	234	135	143	15.2000

#otherMatches

#Struct PSSM
ffff333g	chr15:91465110-91465348(+)$1	238	125	133	15.4000
::::::::	chr16:46694343-46694590(-)$1	247	123	131	15.5000
:::::::F	chr1:116235451-116235706(+)$1	255	3	11	15.7000
e:eeeeen	chr3:170022243-170022480(+)$1	237	150	158	15.1000
wwwwwwww	chr6:57049467-57049746(+)$1	279	216	224	16.2000
::::gggg	chr2:201687879-201688126(+)$1	247	153	161	16.2000
cbbddddf	chr10:101472884-101473169(-)$1	285	131	139	15.1000
sssssssc	chr2:61350111-61350348(+)$1	237	122	130	19.6000
ee::::::	chr10:38412015-38412322(+)$1	307	275	283	15.2000
g$$$$$hh	chr13:20247413-20247642(+)$1	229	29	37	15.4000
&&hhhhhh	chr12:124242563-124242810(+)$1	247	179	187	15.7000
ndddd]cc	chr12:110369747-110369992(-)$1	245	218	226	14.8000
YYFFFFFF	chr5:134191714-134192037(+)$1	323	172	180	19.6000
ZZBBYYDD	chr2:197643243-197643534(-)$1	291	241	249	15.4000
ffffff:d	chr4:170650523-170650752(-)$1	229	129	137	15.4000
eeee$$$$	chr2:242053137-242053396(-)$1	259	62	70	19.6000
::::::::	chr2:213864692-213865004(-)$1	312	90	98	16.2000
iiiiiiii	chr1:162494148-162494399(+)$1	251	229	237	15.2000
gggggrrr	chr11:9302679-9302910(-)$1	231	153	161	15.1000
eeeee]cc	chr5:72209825-72210067(+)$1	242	216	224	15.7000
$$$$eeee	chr6:79647225-79647501(-)$1	276	28	36	15.7000
}FFFFFFY	chr3:160151000-160151408(+)$1	408	306	314	15.2000
]bb333cc	chr11:66433754-66434072(+)$1	318	286	294	15.7000
ssssssss	chr2:54045783-54046024(-)$1	241	58	66	15.8000
:::::::g	chr1:146629880-146630158(-)$1	278	2	10	16.2000
fffffqqq	chr17:57777534-57777788(-)$1	254	38	46	15.4000
iiiii777	chr3:20025693-20025966(+)$1	273	121	129	15.8000
eeeeoooo	chr5:132216556-132216825(-)$1	269	213	221	15.7000
GGGFFFFF	chr4:175240779-175241023(+)$1	244	68	76	15.8000
[dddd&&&	chr3:160151822-160152142(+)$1	320	227	235	15.7000
^^ffffff	chr18:32838262-32838493(-)$1	231	143	151	16.2000
::::::::	chr12:66253198-66253453(+)$1	255	225	233	15.2000
^^^hhhhh	chr6:139236846-139237119(-)$1	273	218	226	15.7000
77hhhhhh	chr5:138207360-138207610(-)$1	250	83	91	15.1000
eeeccc22	chr13:52989349-52989599(-)$1	250	91	99	15.4000
hhhhhhll	chr2:209170017-209170321(+)$1	304	24	32	15.2000
JJJJJJJ:	chr22:38881636-38881872(-)$1	236	44	52	16.2000
:::::JJJ	chr3:3171761-3172051(+)$1	290	225	233	15.8000
iiddddqq	chr5:39105868-39106154(-)$1	286	132	140	15.7000
::::gggg	chr1:159997754-159998007(-)$1	253	17	25	19.6000
^^^^^^^^	chr12:56347457-56347903(+)$1	446	370	378	15.4000
ffffffnn	chr5:110077350-110077590(+)$1	240	70	78	15.4000
!eeeee""	chr14:95555553-95555849(-)$1	296	58	66	19.6000
ddmmmmdd	chr17:4070048-4070358(-)$1	310	82	90	15.4000
d]ffffff	chr3:121140650-121140915(+)$1	265	101	109	19.6000
ffffff!!	chr1:113454949-113455202(-)$1	253	63	71	16.2000
mma22ddd	chr17:15933701-15933961(-)$1	260	54	62	15.5000
!eeeee!!	chr2:128063520-128063763(-)$1	243	43	51	15.5000
^^^^^^^^	chr12:105764574-105764852(+)$1	278	183	191	15.4000
c:::::::	chr5:75912166-75912400(-)$1	234	135	143	15.2000

#DB
))))...)	chr15:91465110-91465348(+)$1	1	125	133	15.4000
........	chr16:46694343-46694590(-)$1	1	123	131	15.5000
.......(	chr1:116235451-116235706(+)$1	1	3	11	15.7000
).(((((.	chr3:170022243-170022480(+)$1	1	150	158	15.1000
........	chr6:57049467-57049746(+)$1	1	216	224	16.2000
....((((	chr2:201687879-201688126(+)$1	1	153	161	16.2000
))))))))	chr10:101472884-101473169(-)$1	1	131	139	15.1000
.......)	chr2:61350111-61350348(+)$1	1	122	130	19.6000
))......	chr10:38412015-38412322(+)$1	1	275	283	15.2000
(.....((	chr13:20247413-20247642(+)$1	1	29	37	15.4000
..((((((	chr12:124242563-124242810(+)$1	1	179	187	15.7000
.)))).))	chr12:110369747-110369992(-)$1	1	218	226	14.8000
..))))))	chr5:134191714-134192037(+)$1	1	172	180	19.6000
..))..))	chr2:197643243-197643534(-)$1	1	241	249	15.4000
)))))).(	chr4:170650523-170650752(-)$1	1	129	137	15.4000
((((....	chr2:242053137-242053396(-)$1	1	62	70	19.6000
........	chr2:213864692-213865004(-)$1	1	90	98	16.2000
))))))))	chr1:162494148-162494399(+)$1	1	229	237	15.2000
(((((...	chr11:9302679-9302910(-)$1	1	153	161	15.1000
))))).))	chr5:72209825-72210067(+)$1	1	216	224	15.7000
....((((	chr6:79647225-79647501(-)$1	1	28	36	15.7000
.)))))).	chr3:160151000-160151408(+)$1	1	306	314	15.2000
.))...))	chr11:66433754-66434072(+)$1	1	286	294	15.7000
........	chr2:54045783-54046024(-)$1	1	58	66	15.8000
.......(	chr1:146629880-146630158(-)$1	1	2	10	16.2000
(((((...	chr17:57777534-57777788(-)$1	1	38	46	15.4000
)))))...	chr3:20025693-20025966(+)$1	1	121	129	15.8000
((((....	chr5:132216556-132216825(-)$1	1	213	221	15.7000
((((((((	chr4:175240779-175241023(+)$1	1	68	76	15.8000
.((((...	chr3:160151822-160152142(+)$1	1	227	235	15.7000
..))))))	chr18:32838262-32838493(-)$1	1	143	151	16.2000
........	chr12:66253198-66253453(+)$1	1	225	233	15.2000
...)))))	chr6:139236846-139237119(-)$1	1	218	226	15.7000
..))))))	chr5:138207360-138207610(-)$1	1	83	91	15.1000
))))))..	chr13:52989349-52989599(-)$1	1	91	99	15.4000
((((((..	chr2:209170017-209170321(+)$1	1	24	32	15.2000
(((((((.	chr22:38881636-38881872(-)$1	1	44	52	16.2000
.....)))	chr3:3171761-3172051(+)$1	1	225	233	15.8000
))((((..	chr5:39105868-39106154(-)$1	1	132	140	15.7000
....((((	chr1:159997754-159998007(-)$1	1	17	25	19.6000
........	chr12:56347457-56347903(+)$1	1	370	378	15.4000
((((((..	chr5:110077350-110077590(+)$1	1	70	78	15.4000
.(((((..	chr14:95555553-95555849(-)$1	1	58	66	19.6000
((....))	chr17:4070048-4070358(-)$1	1	82	90	15.4000
).))))))	chr3:121140650-121140915(+)$1	1	101	109	19.6000
((((((..	chr1:113454949-113455202(-)$1	1	63	71	16.2000
..)..)))	chr17:15933701-15933961(-)$1	1	54	62	15.5000
.(((((..	chr2:128063520-128063763(-)$1	1	43	51	15.5000
........	chr12:105764574-105764852(+)$1	1	183	191	15.4000
).......	chr5:75912166-75912400(-)$1	1	135	143	15.2000

#PSSM
U : 0.72	u : 0.18	G : 0.06	C : 0.02	A : 0.02	
U : 0.80	u : 0.18	C : 0.02	
U : 0.76	u : 0.16	C : 0.04	g : 0.02	A : 0.02	
U : 0.66	u : 0.18	G : 0.06	A : 0.06	C : 0.02	a : 0.02	
A : 0.70	a : 0.12	u : 0.08	U : 0.06	G : 0.04	
U : 0.66	u : 0.19	A : 0.08	C : 0.04	G : 0.02	
A : 0.76	a : 0.16	U : 0.02	C : 0.02	G : 0.02	g : 0.02	
A : 0.74	a : 0.14	G : 0.04	c : 0.02	C : 0.02	u : 0.02	U : 0.02	

#score	802.400000000001
#seq	50
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m2_run1.nuc.txt

#NT
CUGUGG	chr20:60791057-60791285(-)$1	228	86	92	15.0192
CUGUGG	chr7:148112411-148112649(+)$1	238	106	112	15.0192
CUGUGG	chr15:91503550-91503772(-)$1	222	209	215	15.0192
AUGUGG	chr19:21476066-21476291(-)$1	225	47	53	12.5192
CUGUGG	chrX:47061656-47061877(+)$1	221	22	28	15.0192
CAGUGG	chr15:48703185-48703404(-)$1	219	66	72	10.7884
CUGUGG	chr17:1686607-1686828(-)$1	221	108	114	15.0192
CUGUGG	chr2:170002233-170002449(-)$1	216	2	8	15.0192
GUGUGG	chr7:34981303-34981518(+)$1	215	109	115	12.7115
CUGUGG	chr3:51994038-51994258(+)$1	220	139	145	15.0192
AUGUGG	chr7:134644714-134644942(+)$1	228	91	97	12.5192
CAGUGG	chr12:93788308-93788532(+)$1	224	109	115	10.7884
GUGUGG	chr19:19339047-19339280(+)$1	233	191	197	12.7115
GUGUGG	chrX:152342209-152342429(-)$1	220	165	171	12.7115
UUGUGG	chr10:97423938-97424156(-)$1	218	145	151	12.5192
AUGUGG	chr1:115268793-115269017(-)$1	224	110	116	12.5192
UUGUGG	chr19:36727229-36727451(-)$1	222	26	32	12.5192
CUGUGG	chr1:240370301-240370532(+)$1	231	86	92	15.0192
UUGUGG	chr12:130926702-130926934(-)$1	232	29	35	12.5192
CUGUGG	chr11:129746614-129746832(-)$1	218	103	109	15.0192
GUGUGG	chr19:1105317-1105535(+)$1	218	143	149	12.7115
CUGUGG	chr4:2260572-2260787(-)$1	215	37	43	15.0192
CUCUGG	chr12:50294832-50295081(-)$1	249	83	89	11.3653
CUGUGG	chrX:151886392-151886607(+)$1	215	16	22	15.0192
CUCUGG	chr12:58158966-58159186(+)$1	220	64	70	11.3653
CAGUGG	chr14:50914098-50914315(-)$1	217	146	152	10.7884
CUGUGG	chr3:186314694-186314916(+)$1	222	119	125	15.0192
CUGUGG	chr11:47303094-47303314(+)$1	220	191	197	15.0192
GUGUGG	chr7:140156464-140156685(-)$1	221	87	93	12.7115
CUGUGG	chr3:12854385-12854607(+)$1	222	38	44	15.0192
CUCUGG	chr2:197705956-197706196(-)$1	240	135	141	11.3653
CUGUGG	chr16:28834616-28834864(+)$1	248	145	151	15.0192
CUCUGG	chr9:19379392-19379616(-)$1	224	112	118	11.3653
CUCUGG	chr7:1516146-1516370(-)$1	224	52	58	11.3653
GUGUGG	chr9:119413910-119414131(-)$1	221	167	173	12.7115
CUGUGG	chr2:114399515-114399751(-)$1	236	49	55	15.0192
CAGUGG	chr8:144357152-144357385(+)$1	233	48	54	10.7884
UUGUGG	chrX:70607130-70607351(+)$1	221	95	101	12.5192
CUCUGG	chr15:42740222-42740440(-)$1	218	113	119	11.3653
AUGUGG	chr17:4712504-4712758(+)$1	254	178	184	12.5192
CUCUGG	chr1:47042155-47042374(-)$1	219	155	161	11.3653
CUGUGG	chr17:61600699-61600919(+)$1	220	43	49	15.0192
CUGUGG	chr3:52510412-52510638(+)$1	226	198	204	15.0192
AUGUGG	chr2:54892996-54893219(+)$1	223	6	12	12.5192
UUGUGG	chrX:103042695-103042924(+)$1	229	32	38	12.5192
CUGUGG	chr15:102264480-102264698(-)$1	218	180	186	15.0192
UUGUGG	chr6:57246858-57247082(+)$1	224	55	61	12.5192
GUGUGG	chr21:31062166-31062399(-)$1	233	115	121	12.7115
GUGUGG	chr1:26355612-26355833(+)$1	221	39	45	12.7115
CUGUGG	chr5:149509250-149509471(-)$1	221	110	116	15.0192
CUGUGG	chr18:21735593-21735820(-)$1	227	124	130	15.0192

#otherMatches

#Struct PSSM
c:dddd	chr7:138588285-138588512(-)$1	227	134	140	12.5192
ccc[dd	chr20:60791057-60791285(-)$1	228	86	92	15.0192
ccgggg	chr7:148112411-148112649(+)$1	238	106	112	15.0192
FFFFFF	chr15:91503550-91503772(-)$1	222	209	215	15.0192
teeeee	chr19:21476066-21476291(-)$1	225	47	53	12.5192
D:a[ii	chrX:47061656-47061877(+)$1	221	22	28	15.0192
66hhhh	chr15:48703185-48703404(-)$1	219	66	72	10.7884
JJJJJJ	chr17:1686607-1686828(-)$1	221	108	114	15.0192
dddddd	chr2:170002233-170002449(-)$1	216	2	8	15.0192
b=====	chr7:34981303-34981518(+)$1	215	109	115	12.7115
5cccdd	chr3:51994038-51994258(+)$1	220	139	145	15.0192
c[eeee	chr7:134644714-134644942(+)$1	228	91	97	12.5192
ddd[a!	chr12:93788308-93788532(+)$1	224	109	115	10.7884
dd::ee	chr19:19339047-19339280(+)$1	233	191	197	12.7115
ffffff	chrX:152342209-152342429(-)$1	220	165	171	12.7115
ffffff	chr10:97423938-97424156(-)$1	218	145	151	12.5192
dEEEEE	chr1:115268793-115269017(-)$1	224	110	116	12.5192
KEEEEE	chr19:36727229-36727451(-)$1	222	26	32	12.5192
EEEEEK	chr1:240370301-240370532(+)$1	231	86	92	15.0192
ddddEE	chr12:130926702-130926934(-)$1	232	29	35	12.5192
))))cc	chr11:129746614-129746832(-)$1	218	103	109	15.0192
======	chr19:1105317-1105535(+)$1	218	143	149	12.7115
dd[a[a	chr4:2260572-2260787(-)$1	215	37	43	15.0192
HHHHHH	chr12:50294832-50295081(-)$1	249	83	89	11.3653
oeeeee	chrX:151886392-151886607(+)$1	215	16	22	15.0192
hhhhhh	chr12:58158966-58159186(+)$1	220	64	70	11.3653
oogggg	chr14:50914098-50914315(-)$1	217	146	152	10.7884
gg]ccc	chr3:186314694-186314916(+)$1	222	119	125	15.0192
d]gggg	chr11:47303094-47303314(+)$1	220	191	197	15.0192
ffffff	chr7:140156464-140156685(-)$1	221	87	93	12.7115
ccc333	chr3:12854385-12854607(+)$1	222	38	44	15.0192
pppccc	chr2:197705956-197706196(-)$1	240	135	141	11.3653
33====	chr16:28834616-28834864(+)$1	248	145	151	15.0192
ffffff	chr9:19379392-19379616(-)$1	224	112	118	11.3653
ccc::f	chr7:1516146-1516370(-)$1	224	52	58	11.3653
dddqqq	chr9:119413910-119414131(-)$1	221	167	173	12.7115
ddd]cc	chr2:114399515-114399751(-)$1	236	49	55	15.0192
qqeeee	chr8:144357152-144357385(+)$1	233	48	54	10.7884
###ccc	chrX:70607130-70607351(+)$1	221	95	101	12.5192
biiiii	chr15:42740222-42740440(-)$1	218	113	119	11.3653
hhhhhh	chr17:4712504-4712758(+)$1	254	178	184	12.5192
ffffGG	chr1:47042155-47042374(-)$1	219	155	161	11.3653
gggggg	chr17:61600699-61600919(+)$1	220	43	49	15.0192
4fffff	chr3:52510412-52510638(+)$1	226	198	204	15.0192
ccc[cc	chr2:54892996-54893219(+)$1	223	6	12	12.5192
xfffff	chrX:103042695-103042924(+)$1	229	32	38	12.5192
emmmme	chr15:102264480-102264698(-)$1	218	180	186	15.0192
ttdddd	chr6:57246858-57247082(+)$1	224	55	61	12.5192
FFFFFF	chr21:31062166-31062399(-)$1	233	115	121	12.7115
A{EEEE	chr1:26355612-26355833(+)$1	221	39	45	12.7115
d]ccc]	chr5:149509250-149509471(-)$1	221	110	116	15.0192
gggggg	chr18:21735593-21735820(-)$1	227	124	130	15.0192

#DB
).((((	chr7:138588285-138588512(-)$1	1	134	140	12.5192
(((.((	chr20:60791057-60791285(-)$1	1	86	92	15.0192
))((((	chr7:148112411-148112649(+)$1	1	106	112	15.0192
))))))	chr15:91503550-91503772(-)$1	1	209	215	15.0192
.)))))	chr19:21476066-21476291(-)$1	1	47	53	12.5192
(.(.((	chrX:47061656-47061877(+)$1	1	22	28	15.0192
..))))	chr15:48703185-48703404(-)$1	1	66	72	10.7884
))))))	chr17:1686607-1686828(-)$1	1	108	114	15.0192
((((((	chr2:170002233-170002449(-)$1	1	2	8	15.0192
))))))	chr7:34981303-34981518(+)$1	1	109	115	12.7115
.)))))	chr3:51994038-51994258(+)$1	1	139	145	15.0192
(.((((	chr7:134644714-134644942(+)$1	1	91	97	12.5192
(((.(.	chr12:93788308-93788532(+)$1	1	109	115	10.7884
))..((	chr19:19339047-19339280(+)$1	1	191	197	12.7115
))))))	chrX:152342209-152342429(-)$1	1	165	171	12.7115
((((((	chr10:97423938-97424156(-)$1	1	145	151	12.5192
)(((((	chr1:115268793-115269017(-)$1	1	110	116	12.5192
.(((((	chr19:36727229-36727451(-)$1	1	26	32	12.5192
(((((.	chr1:240370301-240370532(+)$1	1	86	92	15.0192
))))((	chr12:130926702-130926934(-)$1	1	29	35	12.5192
....((	chr11:129746614-129746832(-)$1	1	103	109	15.0192
))))))	chr19:1105317-1105535(+)$1	1	143	149	12.7115
((.(.(	chr4:2260572-2260787(-)$1	1	37	43	15.0192
((((((	chr12:50294832-50295081(-)$1	1	83	89	11.3653
.)))))	chrX:151886392-151886607(+)$1	1	16	22	15.0192
))))))	chr12:58158966-58159186(+)$1	1	64	70	11.3653
..))))	chr14:50914098-50914315(-)$1	1	146	152	10.7884
)).)))	chr3:186314694-186314916(+)$1	1	119	125	15.0192
).))))	chr11:47303094-47303314(+)$1	1	191	197	15.0192
((((((	chr7:140156464-140156685(-)$1	1	87	93	12.7115
)))...	chr3:12854385-12854607(+)$1	1	38	44	15.0192
...)))	chr2:197705956-197706196(-)$1	1	135	141	11.3653
..))))	chr16:28834616-28834864(+)$1	1	145	151	15.0192
((((((	chr9:19379392-19379616(-)$1	1	112	118	11.3653
)))..(	chr7:1516146-1516370(-)$1	1	52	58	11.3653
(((...	chr9:119413910-119414131(-)$1	1	167	173	12.7115
))).))	chr2:114399515-114399751(-)$1	1	49	55	15.0192
..))))	chr8:144357152-144357385(+)$1	1	48	54	10.7884
...(((	chrX:70607130-70607351(+)$1	1	95	101	12.5192
)(((((	chr15:42740222-42740440(-)$1	1	113	119	11.3653
))))))	chr17:4712504-4712758(+)$1	1	178	184	12.5192
))))))	chr1:47042155-47042374(-)$1	1	155	161	11.3653
((((((	chr17:61600699-61600919(+)$1	1	43	49	15.0192
.)))))	chr3:52510412-52510638(+)$1	1	198	204	15.0192
(((.((	chr2:54892996-54893219(+)$1	1	6	12	12.5192
.)))))	chrX:103042695-103042924(+)$1	1	32	38	12.5192
(....)	chr15:102264480-102264698(-)$1	1	180	186	15.0192
..))))	chr6:57246858-57247082(+)$1	1	55	61	12.5192
((((((	chr21:31062166-31062399(-)$1	1	115	121	12.7115
(.((((	chr1:26355612-26355833(+)$1	1	39	45	12.7115
).))).	chr5:149509250-149509471(-)$1	1	110	116	15.0192
))))))	chr18:21735593-21735820(-)$1	1	124	130	15.0192

#PSSM
C : 0.61	G : 0.15	A : 0.11	U : 0.11	
U : 0.92	A : 0.07	
G : 0.86	C : 0.13	
U : 1.00	
G : 1.00	
G : 1.00	

#score	690.0384615384626
#seq	52
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m1_run1.nuc.txt

#NT
AUCACU	chr12:9822254-9822483(+)$1	229	51	57	13.2631
CUCACU	chr20:55070173-55070413(+)$1	240	112	118	10.1052
AUCUCU	chr5:134705702-134705960(-)$1	258	111	117	9.5789
AUCACA	chr12:977071-977361(+)$1	290	7	13	9.3157
AACACU	chr3:33867883-33868117(+)$1	234	208	214	9.6447
AUCUCU	chr6:31603656-31603926(+)$1	270	87	93	9.5789
AACACU	chr6:139264612-139264847(-)$1	235	113	119	9.6447
UUCACU	chr16:30734950-30735256(+)$1	306	105	111	10.1710
UUCACU	chr7:102738869-102739099(+)$1	230	5	11	10.1710
ACCACU	chr4:174450083-174450302(-)$1	219	88	94	9.3815
AUCACC	chr1:204588054-204588274(-)$1	220	102	108	8.9868
AUCAGU	chr11:62438631-62438917(-)$1	286	49	55	9.7763
UUCACU	chr1:160186593-160186981(-)$1	388	163	169	10.1710
AUCACU	chr7:134719253-134719491(+)$1	238	112	118	13.2631
AUCAAU	chr10:38344201-38344476(+)$1	275	88	94	9.5789
AACACU	chr1:198661371-198661603(+)$1	232	212	218	9.6447
UUCACU	chr7:107399361-107399620(+)$1	259	79	85	10.1710
CUCACU	chr16:21416083-21416347(-)$1	264	15	21	10.1052
CUCACU	chr20:43251412-43251671(-)$1	259	55	61	10.1052
AUCAGU	chr6:150018187-150018453(-)$1	266	22	28	9.7763
AUCAUU	chr5:68660732-68660974(-)$1	242	57	63	9.6447
AGCACU	chr1:205760515-205760768(-)$1	253	47	53	9.4473
AUCUCU	chr16:15697982-15698210(-)$1	228	11	17	9.5789
AUCUCU	chr11:68216381-68216657(+)$1	276	113	119	9.5789
aucucu	chr20:57266002-57266290(+)$1	288	119	125	9.5789
AUCACU	chr2:136418809-136419051(+)$1	242	61	67	13.2631
AUCAAU	chr1:203316352-203316569(-)$1	217	143	149	9.5789
AACACU	chr10:43089167-43089500(-)$1	333	82	88	9.6447
AUCAGU	chr12:993963-994208(+)$1	245	110	116	9.7763
UUCACU	chr11:92881653-92881897(-)$1	244	51	57	10.1710
AGCACU	chr1:151400556-151400807(-)$1	251	109	115	9.4473
AUCCCU	chr5:154200776-154201004(-)$1	228	2	8	9.5131
GUCACU	chr17:2226521-2226745(-)$1	224	22	28	9.7763
AACACU	chr3:169847068-169847440(-)$1	372	21	27	9.6447
UUCACU	chr5:137502121-137502370(-)$1	249	19	25	10.1710
aucucu	chr11:77332968-77333226(-)$1	258	102	108	9.5789
AACACU	chrX:70330003-70330260(-)$1	257	140	146	9.6447
ACCACU	chr2:203630229-203630482(+)$1	253	102	108	9.3815
AUCACA	chr12:49444826-49445077(-)$1	251	101	107	9.3157
AUCAGU	chr5:32126468-32126723(-)$1	255	11	17	9.7763
AUCCCU	chr14:100762130-100762405(-)$1	275	259	265	9.5131
CUCACU	chr1:31405914-31406168(-)$1	254	147	153	10.1052
AUCACA	chr8:94935336-94935576(+)$1	240	116	122	9.3157
AUCAAU	chr17:62496621-62496891(-)$1	270	23	29	9.5789
GUCACU	chr12:54920403-54920640(+)$1	237	7	13	9.7763
AUCAGU	chr19:3550912-3551182(-)$1	270	253	259	9.7763
AUCUCU	chr1:169446426-169446701(-)$1	275	78	84	9.5789
AUCAGU	chr4:2673888-2674143(+)$1	255	59	65	9.7763
UUCACU	chr13:39587825-39588050(-)$1	225	155	161	10.1710
AGCACU	chr3:169846560-169846976(-)$1	416	3	9	9.4473
AGCACU	chr9:134145767-134145986(-)$1	219	112	118	9.4473
UUCACU	chr5:42800733-42800989(+)$1	256	5	11	10.1710
cucacu	chr2:25522729-25523122(-)$1	393	333	339	10.1052
aucaca	chr20:391025-391295(+)$1	270	72	78	9.3157
AUCAGU	chr6:149699813-149700081(+)$1	268	96	102	9.7763
CUCACU	chr16:22545729-22545989(+)$1	260	3	9	10.1052
CUCACU	chr12:994890-995117(+)$1	227	107	113	10.1052
AUCCCU	chr1:185276991-185277256(-)$1	265	7	13	9.5131
AUCCCU	chr1:42656940-42657182(-)$1	242	107	113	9.5131
ACCACU	chr17:42475014-42475290(-)$1	276	45	51	9.3815
GUCACU	chr19:37853846-37854216(+)$1	370	193	199	9.7763
AUCACC	chr17:46923297-46923541(+)$1	244	128	134	8.9868
AUCACU	chr3:49137093-49137335(-)$1	242	104	110	13.2631
AUCCCU	chr16:67576772-67577015(+)$1	243	144	150	9.5131
AUCACA	chr15:59416925-59417161(+)$1	236	20	26	9.3157
AUCAUU	chr15:44951286-44951579(-)$1	293	124	130	9.6447
AUCAUU	chr16:29815763-29816099(+)$1	336	1	7	9.6447
AUCACA	chr20:25656687-25656943(-)$1	256	109	115	9.3157
AUCAUU	chr7:110762862-110763105(-)$1	243	106	112	9.6447
AACACU	chr3:148744640-148744879(+)$1	239	81	87	9.6447
AUCCCU	chr1:169446301-169446539(-)$1	238	108	114	9.5131
AUCAUU	chr6:26452468-26452739(+)$1	271	1	7	9.6447
AUCAAU	chr1:171526980-171527259(+)$1	279	144	150	9.5789
CUCACU	chr1:42657059-42657299(-)$1	240	78	84	10.1052
AUCACA	chr11:5686020-5686286(-)$1	266	125	131	9.3157

#otherMatches

#Struct PSSM
DDGGGG	chr13:99575415-99575684(-)$1	269	159	165	10.1710
HHHHKK	chr12:9822254-9822483(+)$1	229	51	57	13.2631
::::::	chr20:55070173-55070413(+)$1	240	112	118	10.1052
iiiiii	chr5:134705702-134705960(-)$1	258	111	117	9.5789
::::::	chr12:977071-977361(+)$1	290	7	13	9.3157
eeee33	chr3:33867883-33868117(+)$1	234	208	214	9.6447
IIIIII	chr6:31603656-31603926(+)$1	270	87	93	9.5789
wwwwwf	chr6:139264612-139264847(-)$1	235	113	119	9.6447
::::::	chr16:30734950-30735256(+)$1	306	105	111	10.1710
Ecccff	chr7:102738869-102739099(+)$1	230	5	11	10.1710
ccc[ee	chr4:174450083-174450302(-)$1	219	88	94	9.3815
2fffff	chr1:204588054-204588274(-)$1	220	102	108	8.9868
JJJJJJ	chr11:62438631-62438917(-)$1	286	49	55	9.7763
B{A{HH	chr1:160186593-160186981(-)$1	388	163	169	10.1710
d22ccc	chr7:134719253-134719491(+)$1	238	112	118	13.2631
55555c	chr10:38344201-38344476(+)$1	275	88	94	9.5789
DDDD:e	chr1:198661371-198661603(+)$1	232	212	218	9.6447
eee!!c	chr7:107399361-107399620(+)$1	259	79	85	10.1710
:ccc[c	chr16:21416083-21416347(-)$1	264	15	21	10.1052
eeee22	chr20:43251412-43251671(-)$1	259	55	61	10.1052
PFFFFF	chr6:150018187-150018453(-)$1	266	22	28	9.7763
nnn===	chr5:68660732-68660974(-)$1	242	57	63	9.6447
dddd]b	chr1:205760515-205760768(-)$1	253	47	53	9.4473
EEEE{D	chr16:15697982-15698210(-)$1	228	11	17	9.5789
]dddd:	chr11:68216381-68216657(+)$1	276	113	119	9.5789
xxxeee	chr20:57266002-57266290(+)$1	288	119	125	9.5789
vvvvvv	chr2:136418809-136419051(+)$1	242	61	67	13.2631
c55555	chr1:203316352-203316569(-)$1	217	143	149	9.5789
::::EE	chr10:43089167-43089500(-)$1	333	82	88	9.6447
tttttt	chr12:993963-994208(+)$1	245	110	116	9.7763
ffff::	chr11:92881653-92881897(-)$1	244	51	57	10.1710
^^^^^^	chr1:151400556-151400807(-)$1	251	109	115	9.4473
::::::	chr5:154200776-154201004(-)$1	228	2	8	9.5131
eeeee)	chr17:2226521-2226745(-)$1	224	22	28	9.7763
C:ffff	chr3:169847068-169847440(-)$1	372	21	27	9.6447
##ccc[	chr5:137502121-137502370(-)$1	249	19	25	10.1710
eeee!!	chr11:77332968-77333226(-)$1	258	102	108	9.5789
DZZZDD	chrX:70330003-70330260(-)$1	257	140	146	9.6447
3eeeee	chr2:203630229-203630482(+)$1	253	102	108	9.3815
333ccc	chr12:49444826-49445077(-)$1	251	101	107	9.3157
[bbooo	chr5:32126468-32126723(-)$1	255	11	17	9.7763
ZDDDD}	chr14:100762130-100762405(-)$1	275	259	265	9.5131
bbffff	chr1:31405914-31406168(-)$1	254	147	153	10.1052
FFFFFC	chr8:94935336-94935576(+)$1	240	116	122	9.3157
SSSSSS	chr17:62496621-62496891(-)$1	270	23	29	9.5789
DDDKKF	chr12:54920403-54920640(+)$1	237	7	13	9.7763
??CCC}	chr19:3550912-3551182(-)$1	270	253	259	9.7763
IIINNN	chr1:169446426-169446701(-)$1	275	78	84	9.5789
:EEEEE	chr4:2673888-2674143(+)$1	255	59	65	9.7763
YYA}BB	chr13:39587825-39588050(-)$1	225	155	161	10.1710
DDKKCC	chr3:169846560-169846976(-)$1	416	3	9	9.4473
DDD}BB	chr9:134145767-134145986(-)$1	219	112	118	9.4473
::::==	chr5:42800733-42800989(+)$1	256	5	11	10.1710
ffffGG	chr2:25522729-25523122(-)$1	393	333	339	10.1052
::::::	chr20:391025-391295(+)$1	270	72	78	9.3157
:::ccc	chr6:149699813-149700081(+)$1	268	96	102	9.7763
dd^^^^	chr16:22545729-22545989(+)$1	260	3	9	10.1052
]fffff	chr12:994890-995117(+)$1	227	107	113	10.1052
::::::	chr1:185276991-185277256(-)$1	265	7	13	9.5131
::::::	chr1:42656940-42657182(-)$1	242	107	113	9.5131
::::::	chr17:42475014-42475290(-)$1	276	45	51	9.3815
}BB}CC	chr19:37853846-37854216(+)$1	370	193	199	9.7763
>>ccc3	chr17:46923297-46923541(+)$1	244	128	134	8.9868
d:::::	chr3:49137093-49137335(-)$1	242	104	110	13.2631
ddqqqq	chr16:67576772-67577015(+)$1	243	144	150	9.5131
EEEENN	chr15:59416925-59417161(+)$1	236	20	26	9.3157
C}A:::	chr15:44951286-44951579(-)$1	293	124	130	9.6447
::::::	chr16:29815763-29816099(+)$1	336	1	7	9.6447
::::::	chr20:25656687-25656943(-)$1	256	109	115	9.3157
IIIIII	chr7:110762862-110763105(-)$1	243	106	112	9.6447
nnnndd	chr3:148744640-148744879(+)$1	239	81	87	9.6447
:::fff	chr1:169446301-169446539(-)$1	238	108	114	9.5131
::::::	chr6:26452468-26452739(+)$1	271	1	7	9.6447
::::::	chr1:171526980-171527259(+)$1	279	144	150	9.5789
oooodd	chr1:42657059-42657299(-)$1	240	78	84	10.1052
:::::d	chr11:5686020-5686286(-)$1	266	125	131	9.3157

#DB
((((((	chr13:99575415-99575684(-)$1	1	159	165	10.1710
((((..	chr12:9822254-9822483(+)$1	1	51	57	13.2631
......	chr20:55070173-55070413(+)$1	1	112	118	10.1052
((((((	chr5:134705702-134705960(-)$1	1	111	117	9.5789
......	chr12:977071-977361(+)$1	1	7	13	9.3157
))))..	chr3:33867883-33868117(+)$1	1	208	214	9.6447
((((((	chr6:31603656-31603926(+)$1	1	87	93	9.5789
.....)	chr6:139264612-139264847(-)$1	1	113	119	9.6447
......	chr16:30734950-30735256(+)$1	1	105	111	10.1710
((((((	chr7:102738869-102739099(+)$1	1	5	11	10.1710
(((.((	chr4:174450083-174450302(-)$1	1	88	94	9.3815
.)))))	chr1:204588054-204588274(-)$1	1	102	108	8.9868
((((((	chr11:62438631-62438917(-)$1	1	49	55	9.7763
(.(.((	chr1:160186593-160186981(-)$1	1	163	169	10.1710
)..)))	chr7:134719253-134719491(+)$1	1	112	118	13.2631
.....)	chr10:38344201-38344476(+)$1	1	88	94	9.5789
)))).(	chr1:198661371-198661603(+)$1	1	212	218	9.6447
(((..(	chr7:107399361-107399620(+)$1	1	79	85	10.1710
.(((.(	chr16:21416083-21416347(-)$1	1	15	21	10.1052
))))..	chr20:43251412-43251671(-)$1	1	55	61	10.1052
.(((((	chr6:150018187-150018453(-)$1	1	22	28	9.7763
...)))	chr5:68660732-68660974(-)$1	1	57	63	9.6447
)))).)	chr1:205760515-205760768(-)$1	1	47	53	9.4473
((((.(	chr16:15697982-15698210(-)$1	1	11	17	9.5789
.)))).	chr11:68216381-68216657(+)$1	1	113	119	9.5789
...)))	chr20:57266002-57266290(+)$1	1	119	125	9.5789
......	chr2:136418809-136419051(+)$1	1	61	67	13.2631
).....	chr1:203316352-203316569(-)$1	1	143	149	9.5789
....((	chr10:43089167-43089500(-)$1	1	82	88	9.6447
......	chr12:993963-994208(+)$1	1	110	116	9.7763
))))..	chr11:92881653-92881897(-)$1	1	51	57	10.1710
......	chr1:151400556-151400807(-)$1	1	109	115	9.4473
......	chr5:154200776-154201004(-)$1	1	2	8	9.5131
(((((.	chr17:2226521-2226745(-)$1	1	22	28	9.7763
(.((((	chr3:169847068-169847440(-)$1	1	21	27	9.6447
..(((.	chr5:137502121-137502370(-)$1	1	19	25	10.1710
((((..	chr11:77332968-77333226(-)$1	1	102	108	9.5789
)...))	chrX:70330003-70330260(-)$1	1	140	146	9.6447
.)))))	chr2:203630229-203630482(+)$1	1	102	108	9.3815
...)))	chr12:49444826-49445077(-)$1	1	101	107	9.3157
.((...	chr5:32126468-32126723(-)$1	1	11	17	9.7763
.)))).	chr14:100762130-100762405(-)$1	1	259	265	9.5131
((((((	chr1:31405914-31406168(-)$1	1	147	153	10.1052
))))))	chr8:94935336-94935576(+)$1	1	116	122	9.3157
......	chr17:62496621-62496891(-)$1	1	23	29	9.5789
(((..(	chr12:54920403-54920640(+)$1	1	7	13	9.7763
..))).	chr19:3550912-3551182(-)$1	1	253	259	9.7763
(((...	chr1:169446426-169446701(-)$1	1	78	84	9.5789
.(((((	chr4:2673888-2674143(+)$1	1	59	65	9.7763
..).))	chr13:39587825-39588050(-)$1	1	155	161	10.1710
((..((	chr3:169846560-169846976(-)$1	1	3	9	9.4473
))).))	chr9:134145767-134145986(-)$1	1	112	118	9.4473
....((	chr5:42800733-42800989(+)$1	1	5	11	10.1710
))))))	chr2:25522729-25523122(-)$1	1	333	339	10.1052
......	chr20:391025-391295(+)$1	1	72	78	9.3157
...(((	chr6:149699813-149700081(+)$1	1	96	102	9.7763
((....	chr16:22545729-22545989(+)$1	1	3	9	10.1052
.)))))	chr12:994890-995117(+)$1	1	107	113	10.1052
......	chr1:185276991-185277256(-)$1	1	7	13	9.5131
......	chr1:42656940-42657182(-)$1	1	107	113	9.5131
......	chr17:42475014-42475290(-)$1	1	45	51	9.3815
.)).))	chr19:37853846-37854216(+)$1	1	193	199	9.7763
..))).	chr17:46923297-46923541(+)$1	1	128	134	8.9868
).....	chr3:49137093-49137335(-)$1	1	104	110	13.2631
((....	chr16:67576772-67577015(+)$1	1	144	150	9.5131
((((..	chr15:59416925-59417161(+)$1	1	20	26	9.3157
).)...	chr15:44951286-44951579(-)$1	1	124	130	9.6447
......	chr16:29815763-29816099(+)$1	1	1	7	9.6447
......	chr20:25656687-25656943(-)$1	1	109	115	9.3157
((((((	chr7:110762862-110763105(-)$1	1	106	112	9.6447
....))	chr3:148744640-148744879(+)$1	1	81	87	9.6447
...(((	chr1:169446301-169446539(-)$1	1	108	114	9.5131
......	chr6:26452468-26452739(+)$1	1	1	7	9.6447
......	chr1:171526980-171527259(+)$1	1	144	150	9.5789
....))	chr1:42657059-42657299(-)$1	1	78	84	10.1052
.....(	chr11:5686020-5686286(-)$1	1	125	131	9.3157

#PSSM
A : 0.69	U : 0.11	C : 0.09	a : 0.03	G : 0.03	c : 0.01	
U : 0.76	A : 0.09	G : 0.05	u : 0.05	C : 0.03	
C : 0.94	c : 0.05	
A : 0.80	C : 0.07	U : 0.06	u : 0.02	a : 0.02	
C : 0.73	G : 0.09	U : 0.06	A : 0.05	c : 0.05	
U : 0.84	A : 0.07	u : 0.03	C : 0.02	a : 0.01	

#score	750.5000000000008
#seq	76
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m2_run2.nuc.txt

#NT
AGU	chr19:803478-803737(+)$1	259	0	3	8.9999
AGU	chr2:62991331-62991590(+)$1	259	168	171	8.9999
AGU	chr9:95003070-95003329(-)$1	259	7	10	8.9999
AGU	chr7:105099539-105099798(+)$1	259	41	44	8.9999
AGU	chr15:73562640-73562869(+)$1	229	37	40	8.9999
AGU	chrX:53106575-53106804(+)$1	229	154	157	8.9999
AGU	chr3:123218335-123218594(+)$1	259	26	29	8.9999
AGU	chr8:33230199-33230458(+)$1	259	36	39	8.9999
AGU	chr5:118533409-118533668(+)$1	259	20	23	8.9999
AGU	chr3:126214779-126215038(+)$1	259	50	53	8.9999
AGU	chr19:36389535-36389794(+)$1	259	31	34	8.9999
AGU	chr19:16535876-16536135(+)$1	259	158	161	8.9999
AGU	chr2:209358189-209358418(-)$1	229	14	17	8.9999
AGU	chr4:154624511-154624740(+)$1	229	12	15	8.9999
AGU	chr5:128324253-128324512(+)$1	259	62	65	8.9999
AGU	chr1:16271060-16271319(+)$1	259	126	129	8.9999
AGU	chr14:93652762-93653021(-)$1	259	18	21	8.9999
AGU	chr19:49564822-49565051(+)$1	229	26	29	8.9999
AGU	chr2:99224678-99224907(+)$1	229	102	105	8.9999
AGU	chr15:72637737-72637996(-)$1	259	3	6	8.9999
AGU	chr22:21344637-21344896(+)$1	259	46	49	8.9999
AGU	chr12:49375151-49375380(-)$1	229	19	22	8.9999
AGU	chr10:94694011-94694240(-)$1	229	0	3	8.9999
AGU	chr12:57872908-57873137(+)$1	229	100	103	8.9999
AGU	chr12:70732232-70732461(-)$1	229	5	8	8.9999
AGU	chr3:47742640-47742869(-)$1	229	5	8	8.9999
AGU	chr17:65941737-65941996(+)$1	259	42	45	8.9999
AGU	chr22:20113884-20114143(+)$1	259	137	140	8.9999
AGU	chr13:107220076-107220335(+)$1	259	239	242	8.9999
AGU	chr17:36666826-36667085(+)$1	259	167	170	8.9999
AGU	chr14:75935905-75936134(-)$1	229	122	125	8.9999
AGU	chr15:63000764-63000993(+)$1	229	53	56	8.9999
AGU	chr1:177250530-177250759(-)$1	229	74	77	8.9999
AGU	chr19:5595259-5595518(+)$1	259	40	43	8.9999
AGU	chr3:39373890-39374149(-)$1	259	18	21	8.9999
AGU	chr7:107115407-107115636(+)$1	229	27	30	8.9999
AGU	chr13:76055331-76055590(-)$1	259	2	5	8.9999
AGU	chr14:59930620-59930879(+)$1	259	100	103	8.9999
AGU	chr5:167631470-167631729(+)$1	259	51	54	8.9999
AGU	chr5:236572-236831(+)$1	259	127	130	8.9999
AGU	chr19:4171630-4171889(+)$1	259	20	23	8.9999
AGU	chr19:4793713-4793972(-)$1	259	98	101	8.9999
AGU	chr16:55690703-55690932(+)$1	229	30	33	8.9999
AGU	chr17:80059569-80059832(+)$1	263	5	8	8.9999
AGU	chr12:6858944-6859203(+)$1	259	87	90	8.9999
AGU	chr20:61576160-61576419(-)$1	259	39	42	8.9999
AGU	chrX:153694981-153695240(+)$1	259	154	157	8.9999
AGU	chr6:3456064-3456323(+)$1	259	116	119	8.9999
AGU	chr8:70980500-70980729(+)$1	229	159	162	8.9999
AGU	chr4:3768638-3768897(+)$1	259	167	170	8.9999
AGU	chr22:20229613-20229842(+)$1	229	2	5	8.9999
AGU	chr11:66611303-66611562(+)$1	259	210	213	8.9999
AGU	chr13:52604892-52605151(-)$1	259	60	63	8.9999
AGU	chr5:90119152-90119381(+)$1	229	119	122	8.9999
AGU	chr11:771237-771496(+)$1	259	68	71	8.9999
AGU	chr20:16347763-16347992(+)$1	229	3	6	8.9999
AGU	chr3:159744298-159744527(-)$1	229	88	91	8.9999
AGU	chr7:2472444-2472673(+)$1	229	32	35	8.9999
AGU	chr7:97854312-97854571(+)$1	259	200	203	8.9999
AGU	chr3:47953448-47953677(+)$1	229	8	11	8.9999
AGU	chr16:30596539-30596798(-)$1	259	101	104	8.9999
AGU	chr2:171807734-171807993(+)$1	259	60	63	8.9999
AGU	chr11:65545329-65545588(-)$1	259	10	13	8.9999
AGU	chr10:105200396-105200625(-)$1	229	65	68	8.9999
AGU	chr11:56431925-56432154(+)$1	229	50	53	8.9999
AGU	chr11:119215578-119215837(+)$1	259	212	215	8.9999
AGU	chr6:37447781-37448010(+)$1	229	36	39	8.9999
AGU	chr15:38766325-38766584(+)$1	259	26	29	8.9999
AGU	chr11:59344395-59344654(+)$1	259	33	36	8.9999
AGU	chr11:35684618-35684877(+)$1	259	52	55	8.9999
AGU	chr2:242194706-242194965(+)$1	259	76	79	8.9999
AGU	chr7:99047849-99048108(+)$1	259	20	23	8.9999
AGU	chr8:145750002-145750261(+)$1	259	42	45	8.9999
AGU	chr5:140188912-140189171(-)$1	259	32	35	8.9999
AGU	chr11:73811586-73811845(-)$1	259	59	62	8.9999
AGU	chr1:156784819-156785078(+)$1	259	64	67	8.9999
AGU	chr6:17826211-17826470(+)$1	259	64	67	8.9999
AGU	chr16:66643546-66643805(-)$1	259	126	129	8.9999
AGU	chr19:4311808-4312067(+)$1	259	28	31	8.9999
AGU	chrX:118221619-118221881(+)$1	262	27	30	8.9999
AGU	chr15:78894171-78894400(+)$1	229	7	10	8.9999
AGU	chr1:201181311-201181570(+)$1	259	195	198	8.9999
AGU	chrX:78010602-78010861(+)$1	259	160	163	8.9999
AGU	chr7:50467965-50468272(+)$1	307	187	190	8.9999
AGU	chr7:107717274-107717503(-)$1	229	80	83	8.9999
AGU	chr12:10365830-10366089(-)$1	259	12	15	8.9999

#otherMatches

#Struct PSSM
hhh	chr1:200628083-200628342(+)$1	259	102	105	8.9999
:::	chr19:803478-803737(+)$1	259	0	3	8.9999
33c	chr2:62991331-62991590(+)$1	259	168	171	8.9999
::D	chr9:95003070-95003329(-)$1	259	7	10	8.9999
""=	chr7:105099539-105099798(+)$1	259	41	44	8.9999
PPP	chr15:73562640-73562869(+)$1	229	37	40	8.9999
bb[	chrX:53106575-53106804(+)$1	229	154	157	8.9999
%%%	chr3:123218335-123218594(+)$1	259	26	29	8.9999
e]c	chr8:33230199-33230458(+)$1	259	36	39	8.9999
:::	chr5:118533409-118533668(+)$1	259	20	23	8.9999
KDD	chr3:126214779-126215038(+)$1	259	50	53	8.9999
Cee	chr19:36389535-36389794(+)$1	259	31	34	8.9999
HHb	chr19:16535876-16536135(+)$1	259	158	161	8.9999
:A{	chr2:209358189-209358418(-)$1	229	14	17	8.9999
[cc	chr4:154624511-154624740(+)$1	229	12	15	8.9999
qqq	chr5:128324253-128324512(+)$1	259	62	65	8.9999
}BB	chr1:16271060-16271319(+)$1	259	126	129	8.9999
fff	chr14:93652762-93653021(-)$1	259	18	21	8.9999
:cc	chr19:49564822-49565051(+)$1	229	26	29	8.9999
oee	chr2:99224678-99224907(+)$1	229	102	105	8.9999
:::	chr15:72637737-72637996(-)$1	259	3	6	8.9999
EEE	chr22:21344637-21344896(+)$1	259	46	49	8.9999
c[b	chr12:49375151-49375380(-)$1	229	19	22	8.9999
::D	chr10:94694011-94694240(-)$1	229	0	3	8.9999
22d	chr12:57872908-57873137(+)$1	229	100	103	8.9999
:::	chr12:70732232-70732461(-)$1	229	5	8	8.9999
:::	chr3:47742640-47742869(-)$1	229	5	8	8.9999
:::	chr17:65941737-65941996(+)$1	259	42	45	8.9999
bcc	chr22:20113884-20114143(+)$1	259	137	140	8.9999
:EE	chr13:107220076-107220335(+)$1	259	239	242	8.9999
eee	chr17:36666826-36667085(+)$1	259	167	170	8.9999
eee	chr14:75935905-75936134(-)$1	229	122	125	8.9999
eee	chr15:63000764-63000993(+)$1	229	53	56	8.9999
FFF	chr1:177250530-177250759(-)$1	229	74	77	8.9999
GGK	chr19:5595259-5595518(+)$1	259	40	43	8.9999
FFF	chr3:39373890-39374149(-)$1	259	18	21	8.9999
e##	chr7:107115407-107115636(+)$1	229	27	30	8.9999
:::	chr13:76055331-76055590(-)$1	259	2	5	8.9999
]ff	chr14:59930620-59930879(+)$1	259	100	103	8.9999
hhh	chr5:167631470-167631729(+)$1	259	51	54	8.9999
ddd	chr5:236572-236831(+)$1	259	127	130	8.9999
:::	chr19:4171630-4171889(+)$1	259	20	23	8.9999
4dd	chr19:4793713-4793972(-)$1	259	98	101	8.9999
[ee	chr16:55690703-55690932(+)$1	229	30	33	8.9999
F{B	chr17:80059569-80059832(+)$1	263	5	8	8.9999
000	chr12:6858944-6859203(+)$1	259	87	90	8.9999
:::	chr20:61576160-61576419(-)$1	259	39	42	8.9999
888	chrX:153694981-153695240(+)$1	259	154	157	8.9999
[bb	chr6:3456064-3456323(+)$1	259	116	119	8.9999
:::	chr8:70980500-70980729(+)$1	229	159	162	8.9999
d::	chr4:3768638-3768897(+)$1	259	167	170	8.9999
:::	chr22:20229613-20229842(+)$1	229	2	5	8.9999
eee	chr11:66611303-66611562(+)$1	259	210	213	8.9999
III	chr13:52604892-52605151(-)$1	259	60	63	8.9999
e^^	chr5:90119152-90119381(+)$1	229	119	122	8.9999
KCC	chr11:771237-771496(+)$1	259	68	71	8.9999
bb[	chr20:16347763-16347992(+)$1	229	3	6	8.9999
bpp	chr3:159744298-159744527(-)$1	229	88	91	8.9999
""g	chr7:2472444-2472673(+)$1	229	32	35	8.9999
:DD	chr7:97854312-97854571(+)$1	259	200	203	8.9999
::G	chr3:47953448-47953677(+)$1	229	8	11	8.9999
fff	chr16:30596539-30596798(-)$1	259	101	104	8.9999
d33	chr2:171807734-171807993(+)$1	259	60	63	8.9999
{DD	chr11:65545329-65545588(-)$1	259	10	13	8.9999
ddd	chr10:105200396-105200625(-)$1	229	65	68	8.9999
9bb	chr11:56431925-56432154(+)$1	229	50	53	8.9999
ddd	chr11:119215578-119215837(+)$1	259	212	215	8.9999
===	chr6:37447781-37448010(+)$1	229	36	39	8.9999
{DD	chr15:38766325-38766584(+)$1	259	26	29	8.9999
III	chr11:59344395-59344654(+)$1	259	33	36	8.9999
]cc	chr11:35684618-35684877(+)$1	259	52	55	8.9999
:::	chr2:242194706-242194965(+)$1	259	76	79	8.9999
DD{	chr7:99047849-99048108(+)$1	259	20	23	8.9999
2cc	chr8:145750002-145750261(+)$1	259	42	45	8.9999
ggg	chr5:140188912-140189171(-)$1	259	32	35	8.9999
:::	chr11:73811586-73811845(-)$1	259	59	62	8.9999
"""	chr1:156784819-156785078(+)$1	259	64	67	8.9999
CC{	chr6:17826211-17826470(+)$1	259	64	67	8.9999
fff	chr16:66643546-66643805(-)$1	259	126	129	8.9999
{DD	chr19:4311808-4312067(+)$1	259	28	31	8.9999
ddl	chrX:118221619-118221881(+)$1	262	27	30	8.9999
[cc	chr15:78894171-78894400(+)$1	229	7	10	8.9999
b[h	chr1:201181311-201181570(+)$1	259	195	198	8.9999
ggg	chrX:78010602-78010861(+)$1	259	160	163	8.9999
ddd	chr7:50467965-50468272(+)$1	307	187	190	8.9999
HHH	chr7:107717274-107717503(-)$1	229	80	83	8.9999
hhh	chr12:10365830-10366089(-)$1	259	12	15	8.9999

#DB
(((	chr1:200628083-200628342(+)$1	1	102	105	8.9999
...	chr19:803478-803737(+)$1	1	0	3	8.9999
..)	chr2:62991331-62991590(+)$1	1	168	171	8.9999
..(	chr9:95003070-95003329(-)$1	1	7	10	8.9999
..(	chr7:105099539-105099798(+)$1	1	41	44	8.9999
...	chr15:73562640-73562869(+)$1	1	37	40	8.9999
((.	chrX:53106575-53106804(+)$1	1	154	157	8.9999
...	chr3:123218335-123218594(+)$1	1	26	29	8.9999
).)	chr8:33230199-33230458(+)$1	1	36	39	8.9999
...	chr5:118533409-118533668(+)$1	1	20	23	8.9999
.((	chr3:126214779-126215038(+)$1	1	50	53	8.9999
(((	chr19:36389535-36389794(+)$1	1	31	34	8.9999
))(	chr19:16535876-16536135(+)$1	1	158	161	8.9999
.(.	chr2:209358189-209358418(-)$1	1	14	17	8.9999
.((	chr4:154624511-154624740(+)$1	1	12	15	8.9999
...	chr5:128324253-128324512(+)$1	1	62	65	8.9999
.))	chr1:16271060-16271319(+)$1	1	126	129	8.9999
(((	chr14:93652762-93653021(-)$1	1	18	21	8.9999
.((	chr19:49564822-49565051(+)$1	1	26	29	8.9999
.))	chr2:99224678-99224907(+)$1	1	102	105	8.9999
...	chr15:72637737-72637996(-)$1	1	3	6	8.9999
(((	chr22:21344637-21344896(+)$1	1	46	49	8.9999
(.(	chr12:49375151-49375380(-)$1	1	19	22	8.9999
..(	chr10:94694011-94694240(-)$1	1	0	3	8.9999
..)	chr12:57872908-57873137(+)$1	1	100	103	8.9999
...	chr12:70732232-70732461(-)$1	1	5	8	8.9999
...	chr3:47742640-47742869(-)$1	1	5	8	8.9999
...	chr17:65941737-65941996(+)$1	1	42	45	8.9999
)))	chr22:20113884-20114143(+)$1	1	137	140	8.9999
.))	chr13:107220076-107220335(+)$1	1	239	242	8.9999
)))	chr17:36666826-36667085(+)$1	1	167	170	8.9999
)))	chr14:75935905-75936134(-)$1	1	122	125	8.9999
)))	chr15:63000764-63000993(+)$1	1	53	56	8.9999
)))	chr1:177250530-177250759(-)$1	1	74	77	8.9999
((.	chr19:5595259-5595518(+)$1	1	40	43	8.9999
(((	chr3:39373890-39374149(-)$1	1	18	21	8.9999
(..	chr7:107115407-107115636(+)$1	1	27	30	8.9999
...	chr13:76055331-76055590(-)$1	1	2	5	8.9999
.))	chr14:59930620-59930879(+)$1	1	100	103	8.9999
(((	chr5:167631470-167631729(+)$1	1	51	54	8.9999
(((	chr5:236572-236831(+)$1	1	127	130	8.9999
...	chr19:4171630-4171889(+)$1	1	20	23	8.9999
.))	chr19:4793713-4793972(-)$1	1	98	101	8.9999
.((	chr16:55690703-55690932(+)$1	1	30	33	8.9999
(.(	chr17:80059569-80059832(+)$1	1	5	8	8.9999
...	chr12:6858944-6859203(+)$1	1	87	90	8.9999
...	chr20:61576160-61576419(-)$1	1	39	42	8.9999
...	chrX:153694981-153695240(+)$1	1	154	157	8.9999
.((	chr6:3456064-3456323(+)$1	1	116	119	8.9999
...	chr8:70980500-70980729(+)$1	1	159	162	8.9999
)..	chr4:3768638-3768897(+)$1	1	167	170	8.9999
...	chr22:20229613-20229842(+)$1	1	2	5	8.9999
)))	chr11:66611303-66611562(+)$1	1	210	213	8.9999
)))	chr13:52604892-52605151(-)$1	1	60	63	8.9999
(..	chr5:90119152-90119381(+)$1	1	119	122	8.9999
.((	chr11:771237-771496(+)$1	1	68	71	8.9999
((.	chr20:16347763-16347992(+)$1	1	3	6	8.9999
(..	chr3:159744298-159744527(-)$1	1	88	91	8.9999
..(	chr7:2472444-2472673(+)$1	1	32	35	8.9999
.))	chr7:97854312-97854571(+)$1	1	200	203	8.9999
..(	chr3:47953448-47953677(+)$1	1	8	11	8.9999
)))	chr16:30596539-30596798(-)$1	1	101	104	8.9999
)..	chr2:171807734-171807993(+)$1	1	60	63	8.9999
.((	chr11:65545329-65545588(-)$1	1	10	13	8.9999
(((	chr10:105200396-105200625(-)$1	1	65	68	8.9999
.))	chr11:56431925-56432154(+)$1	1	50	53	8.9999
)))	chr11:119215578-119215837(+)$1	1	212	215	8.9999
(((	chr6:37447781-37448010(+)$1	1	36	39	8.9999
.((	chr15:38766325-38766584(+)$1	1	26	29	8.9999
(((	chr11:59344395-59344654(+)$1	1	33	36	8.9999
.))	chr11:35684618-35684877(+)$1	1	52	55	8.9999
...	chr2:242194706-242194965(+)$1	1	76	79	8.9999
((.	chr7:99047849-99048108(+)$1	1	20	23	8.9999
.))	chr8:145750002-145750261(+)$1	1	42	45	8.9999
(((	chr5:140188912-140189171(-)$1	1	32	35	8.9999
...	chr11:73811586-73811845(-)$1	1	59	62	8.9999
...	chr1:156784819-156785078(+)$1	1	64	67	8.9999
((.	chr6:17826211-17826470(+)$1	1	64	67	8.9999
)))	chr16:66643546-66643805(-)$1	1	126	129	8.9999
.((	chr19:4311808-4312067(+)$1	1	28	31	8.9999
((.	chrX:118221619-118221881(+)$1	1	27	30	8.9999
.((	chr15:78894171-78894400(+)$1	1	7	10	8.9999
(.(	chr1:201181311-201181570(+)$1	1	195	198	8.9999
(((	chrX:78010602-78010861(+)$1	1	160	163	8.9999
(((	chr7:50467965-50468272(+)$1	1	187	190	8.9999
(((	chr7:107717274-107717503(-)$1	1	80	83	8.9999
(((	chr12:10365830-10366089(-)$1	1	12	15	8.9999

#PSSM
A : 0.99	
G : 0.99	
U : 0.99	

#score	782.9999999999998
#seq	87
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m2_run1.nuc.txt

#NT
CUGG	chr22:46859945-46860168(+)$1	223	22	26	12.0000
CUGG	chr16:18849377-18849598(-)$1	221	89	93	12.0000
CUGG	chr1:155145121-155145344(-)$1	223	33	37	12.0000
CUGG	chr11:59271257-59271481(+)$1	224	37	41	12.0000
CUGG	chr22:19028544-19028768(+)$1	224	10	14	12.0000
CUGG	chr11:71693763-71693984(+)$1	221	7	11	12.0000
CUGG	chr14:20845409-20845635(+)$1	226	51	55	12.0000
CUGG	chr19:13319572-13319794(+)$1	222	28	32	12.0000
CUGG	chr6:160113643-160113865(+)$1	222	38	42	12.0000
CUGG	chr14:68086680-68086901(+)$1	221	132	136	12.0000
CUGG	chrX:49021240-49021462(+)$1	222	42	46	12.0000
CUGG	chr14:103995438-103995685(-)$1	247	3	7	12.0000
CUGG	chr2:99438365-99438590(+)$1	225	1	5	12.0000
CUGG	chrX:80533769-80533993(+)$1	224	130	134	12.0000
CUGG	chr3:52390670-52390892(-)$1	222	152	156	12.0000
cUGG	chr19:36208978-36209200(-)$1	222	10	14	12.0000
cugg	chr3:32859585-32859814(+)$1	229	132	136	12.0000
CUGG	chr7:75694040-75694261(+)$1	221	8	12	12.0000
CUGG	chr1:53676187-53676409(-)$1	222	185	189	12.0000
CUGG	chr1:228582796-228583019(-)$1	223	38	42	12.0000
CUGG	chr11:63766907-63767132(-)$1	225	137	141	12.0000
CUGG	chr16:30670940-30671161(+)$1	221	113	117	12.0000
CUGG	chr15:74220121-74220343(+)$1	222	144	148	12.0000
CUGG	chr19:7533737-7533960(-)$1	223	52	56	12.0000
CUGG	chr4:882617-882839(-)$1	222	3	7	12.0000
CUGG	chr11:105880250-105880475(-)$1	225	94	98	12.0000
CUGG	chr4:144616526-144616748(-)$1	222	66	70	12.0000
CUGG	chr12:7640502-7640726(-)$1	224	60	64	12.0000
CUGG	chr4:144380474-144380700(-)$1	226	103	107	12.0000
CUGG	chrX:153537683-153537907(-)$1	224	3	7	12.0000
CUGG	chr19:40030572-40030793(+)$1	221	185	189	12.0000
CUGG	chr11:10786024-10786246(-)$1	222	51	55	12.0000
CUGG	chr2:242438571-242438801(+)$1	230	18	22	12.0000
cugg	chr7:134131947-134132173(-)$1	226	0	4	12.0000
CUGG	chr2:106498134-106498355(-)$1	221	69	73	12.0000
CUGG	chr22:24086010-24086236(+)$1	226	73	77	12.0000
CUGG	chr2:70890652-70890875(+)$1	223	2	6	12.0000
CUGG	chr1:70616721-70616945(+)$1	224	141	145	12.0000
CUGG	chr19:39805474-39805697(-)$1	223	37	41	12.0000
CUGG	chr12:56221286-56221518(-)$1	232	54	58	12.0000
CUGG	chr15:75772101-75772323(+)$1	222	134	138	12.0000
CUGG	chr14:65438511-65438755(-)$1	244	157	161	12.0000
CUGG	chr12:29486509-29486733(+)$1	224	15	19	12.0000
CUGG	chr5:180670650-180670874(+)$1	224	90	94	12.0000
CUGG	chr16:29884883-29885108(-)$1	225	76	80	12.0000
CUGG	chr6:27218439-27218664(+)$1	225	23	27	12.0000
CUGG	chr2:189931063-189931285(+)$1	222	63	67	12.0000
CUGG	chr11:47203953-47204175(-)$1	222	33	37	12.0000
CUGG	chr15:31283539-31283760(+)$1	221	22	26	12.0000
CUGG	chrX:46433827-46434053(+)$1	226	120	124	12.0000
CUGG	chr15:40580886-40581108(+)$1	222	44	48	12.0000
CUGG	chr19:46308107-46308329(-)$1	222	148	152	12.0000
CUGG	chrX:9900256-9900480(+)$1	224	176	180	12.0000
CUGG	chr19:2222150-2222373(+)$1	223	169	173	12.0000
CUGG	chr14:24785504-24785725(-)$1	221	112	116	12.0000
CUGG	chr22:26164898-26165124(+)$1	226	129	133	12.0000
CUGG	chr9:136598855-136599077(+)$1	222	10	14	12.0000
CUGG	chr3:47446120-47446341(+)$1	221	146	150	12.0000
CUGG	chr19:48204712-48204936(+)$1	224	56	60	12.0000
CUGG	chr15:40588396-40588619(+)$1	223	11	15	12.0000
CUGG	chr11:71940482-71940705(-)$1	223	142	146	12.0000
CUGG	chr1:207224000-207224221(-)$1	221	137	141	12.0000
CUGG	chr9:94123839-94124060(+)$1	221	176	180	12.0000
CUGG	chr7:148936904-148937125(+)$1	221	8	12	12.0000
CUGG	chr15:74483433-74483657(-)$1	224	7	11	12.0000
CUGG	chr2:171822470-171822691(-)$1	221	107	111	12.0000
CUGG	chr15:40583563-40583790(+)$1	227	109	113	12.0000
CUGG	chr3:42734135-42734358(+)$1	223	59	63	12.0000
CUGG	chr1:31478757-31478979(+)$1	222	104	108	12.0000
CUGG	chr19:19609188-19609409(-)$1	221	58	62	12.0000
CUGG	chr1:22915606-22915831(+)$1	225	7	11	12.0000
CUGG	chr3:64008217-64008440(-)$1	223	138	142	12.0000
CUGG	chrX:55035652-55035874(-)$1	222	109	113	12.0000
CUGG	chr3:50137863-50138140(-)$1	277	121	125	12.0000
CUGG	chr4:108969747-108969968(+)$1	221	50	54	12.0000
CUGG	chr9:133506864-133507086(-)$1	222	0	4	12.0000
CUGG	chr8:126114533-126114759(+)$1	226	73	77	12.0000
CUGG	chr17:43005433-43005655(+)$1	222	32	36	12.0000
CUGG	chr16:86602274-86602495(-)$1	221	120	124	12.0000
CUGG	chr3:43073733-43073955(+)$1	222	152	156	12.0000
CUGG	chr1:108742638-108742859(+)$1	221	35	39	12.0000
CUGG	chr1:74506954-74507177(-)$1	223	174	178	12.0000
CUGG	chr1:167814887-167815114(+)$1	227	85	89	12.0000
CUGG	chr5:154284020-154284243(+)$1	223	48	52	12.0000
CUGG	chr16:730471-730694(+)$1	223	90	94	12.0000
CUGG	chr3:13363178-13363401(-)$1	223	143	147	12.0000
CUGG	chr16:88876160-88876383(+)$1	223	88	92	12.0000
CUGG	chr9:32526055-32526282(+)$1	227	70	74	12.0000

#otherMatches

#Struct PSSM
d555	chr19:33334694-33334918(+)$1	224	43	47	12.0000
LGGG	chr22:46859945-46860168(+)$1	223	22	26	12.0000
g000	chr16:18849377-18849598(-)$1	221	89	93	12.0000
b]ee	chr1:155145121-155145344(-)$1	223	33	37	12.0000
22cc	chr11:59271257-59271481(+)$1	224	37	41	12.0000
ooff	chr22:19028544-19028768(+)$1	224	10	14	12.0000
"a[d	chr11:71693763-71693984(+)$1	221	7	11	12.0000
eeee	chr14:20845409-20845635(+)$1	226	51	55	12.0000
nncc	chr19:13319572-13319794(+)$1	222	28	32	12.0000
JJJJ	chr6:160113643-160113865(+)$1	222	38	42	12.0000
h]cc	chr14:68086680-68086901(+)$1	221	132	136	12.0000
F:ee	chrX:49021240-49021462(+)$1	222	42	46	12.0000
IIII	chr14:103995438-103995685(-)$1	247	3	7	12.0000
::HH	chr2:99438365-99438590(+)$1	225	1	5	12.0000
ccce	chrX:80533769-80533993(+)$1	224	130	134	12.0000
gggg	chr3:52390670-52390892(-)$1	222	152	156	12.0000
eeee	chr19:36208978-36209200(-)$1	222	10	14	12.0000
2eee	chr3:32859585-32859814(+)$1	229	132	136	12.0000
C{FF	chr7:75694040-75694261(+)$1	221	8	12	12.0000
dddd	chr1:53676187-53676409(-)$1	222	185	189	12.0000
ffff	chr1:228582796-228583019(-)$1	223	38	42	12.0000
ddpp	chr11:63766907-63767132(-)$1	225	137	141	12.0000
dddd	chr16:30670940-30671161(+)$1	221	113	117	12.0000
2eee	chr15:74220121-74220343(+)$1	222	144	148	12.0000
rrrr	chr19:7533737-7533960(-)$1	223	52	56	12.0000
{CCC	chr4:882617-882839(-)$1	222	3	7	12.0000
iiii	chr11:105880250-105880475(-)$1	225	94	98	12.0000
====	chr4:144616526-144616748(-)$1	222	66	70	12.0000
annn	chr12:7640502-7640726(-)$1	224	60	64	12.0000
bb]c	chr4:144380474-144380700(-)$1	226	103	107	12.0000
!!ee	chrX:153537683-153537907(-)$1	224	3	7	12.0000
dddd	chr19:40030572-40030793(+)$1	221	185	189	12.0000
bbmm	chr11:10786024-10786246(-)$1	222	51	55	12.0000
ccuu	chr2:242438571-242438801(+)$1	230	18	22	12.0000
::dd	chr7:134131947-134132173(-)$1	226	0	4	12.0000
::ii	chr2:106498134-106498355(-)$1	221	69	73	12.0000
eeee	chr22:24086010-24086236(+)$1	226	73	77	12.0000
:::D	chr2:70890652-70890875(+)$1	223	2	6	12.0000
ggg+	chr1:70616721-70616945(+)$1	224	141	145	12.0000
ddd=	chr19:39805474-39805697(-)$1	223	37	41	12.0000
ffff	chr12:56221286-56221518(-)$1	232	54	58	12.0000
occc	chr15:75772101-75772323(+)$1	222	134	138	12.0000
====	chr14:65438511-65438755(-)$1	244	157	161	12.0000
$$ff	chr12:29486509-29486733(+)$1	224	15	19	12.0000
IIII	chr5:180670650-180670874(+)$1	224	90	94	12.0000
IIII	chr16:29884883-29885108(-)$1	225	76	80	12.0000
d[cc	chr6:27218439-27218664(+)$1	225	23	27	12.0000
FFFF	chr2:189931063-189931285(+)$1	222	63	67	12.0000
""dd	chr11:47203953-47204175(-)$1	222	33	37	12.0000
ceee	chr15:31283539-31283760(+)$1	221	22	26	12.0000
bfff	chrX:46433827-46434053(+)$1	226	120	124	12.0000
mmdd	chr15:40580886-40581108(+)$1	222	44	48	12.0000
e22a	chr19:46308107-46308329(-)$1	222	148	152	12.0000
JJJJ	chrX:9900256-9900480(+)$1	224	176	180	12.0000
peee	chr19:2222150-2222373(+)$1	223	169	173	12.0000
DDee	chr14:24785504-24785725(-)$1	221	112	116	12.0000
ddcc	chr22:26164898-26165124(+)$1	226	129	133	12.0000
ffff	chr9:136598855-136599077(+)$1	222	10	14	12.0000
qqbb	chr3:47446120-47446341(+)$1	221	146	150	12.0000
LEEE	chr19:48204712-48204936(+)$1	224	56	60	12.0000
cccq	chr15:40588396-40588619(+)$1	223	11	15	12.0000
eeee	chr11:71940482-71940705(-)$1	223	142	146	12.0000
EEEE	chr1:207224000-207224221(-)$1	221	137	141	12.0000
::ff	chr9:94123839-94124060(+)$1	221	176	180	12.0000
G{CC	chr7:148936904-148937125(+)$1	221	8	12	12.0000
lllg	chr15:74483433-74483657(-)$1	224	7	11	12.0000
ddde	chr2:171822470-171822691(-)$1	221	107	111	12.0000
CYYD	chr15:40583563-40583790(+)$1	227	109	113	12.0000
gggg	chr3:42734135-42734358(+)$1	223	59	63	12.0000
]ddd	chr1:31478757-31478979(+)$1	222	104	108	12.0000
ccc#	chr19:19609188-19609409(-)$1	221	58	62	12.0000
c[bb	chr1:22915606-22915831(+)$1	225	7	11	12.0000
GGGG	chr3:64008217-64008440(-)$1	223	138	142	12.0000
cc22	chrX:55035652-55035874(-)$1	222	109	113	12.0000
:ddd	chr3:50137863-50138140(-)$1	277	121	125	12.0000
:::b	chr4:108969747-108969968(+)$1	221	50	54	12.0000
:BB{	chr9:133506864-133507086(-)$1	222	0	4	12.0000
$$ee	chr8:126114533-126114759(+)$1	226	73	77	12.0000
EEEE	chr17:43005433-43005655(+)$1	222	32	36	12.0000
]a]b	chr16:86602274-86602495(-)$1	221	120	124	12.0000
eeee	chr3:43073733-43073955(+)$1	222	152	156	12.0000
{CCC	chr1:108742638-108742859(+)$1	221	35	39	12.0000
lbb2	chr1:74506954-74507177(-)$1	223	174	178	12.0000
:eee	chr1:167814887-167815114(+)$1	227	85	89	12.0000
ccdd	chr5:154284020-154284243(+)$1	223	48	52	12.0000
ccdd	chr16:730471-730694(+)$1	223	90	94	12.0000
cc]c	chr3:13363178-13363401(-)$1	223	143	147	12.0000
eeee	chr16:88876160-88876383(+)$1	223	88	92	12.0000
====	chr9:32526055-32526282(+)$1	227	70	74	12.0000

#DB
)...	chr19:33334694-33334918(+)$1	1	43	47	12.0000
.(((	chr22:46859945-46860168(+)$1	1	22	26	12.0000
)...	chr16:18849377-18849598(-)$1	1	89	93	12.0000
).))	chr1:155145121-155145344(-)$1	1	33	37	12.0000
..))	chr11:59271257-59271481(+)$1	1	37	41	12.0000
..))	chr22:19028544-19028768(+)$1	1	10	14	12.0000
.(.(	chr11:71693763-71693984(+)$1	1	7	11	12.0000
))))	chr14:20845409-20845635(+)$1	1	51	55	12.0000
..))	chr19:13319572-13319794(+)$1	1	28	32	12.0000
((((	chr6:160113643-160113865(+)$1	1	38	42	12.0000
).))	chr14:68086680-68086901(+)$1	1	132	136	12.0000
(.((	chrX:49021240-49021462(+)$1	1	42	46	12.0000
((((	chr14:103995438-103995685(-)$1	1	3	7	12.0000
..((	chr2:99438365-99438590(+)$1	1	1	5	12.0000
)))(	chrX:80533769-80533993(+)$1	1	130	134	12.0000
))))	chr3:52390670-52390892(-)$1	1	152	156	12.0000
))))	chr19:36208978-36209200(-)$1	1	10	14	12.0000
.)))	chr3:32859585-32859814(+)$1	1	132	136	12.0000
(.((	chr7:75694040-75694261(+)$1	1	8	12	12.0000
((((	chr1:53676187-53676409(-)$1	1	185	189	12.0000
((((	chr1:228582796-228583019(-)$1	1	38	42	12.0000
((..	chr11:63766907-63767132(-)$1	1	137	141	12.0000
))))	chr16:30670940-30671161(+)$1	1	113	117	12.0000
.)))	chr15:74220121-74220343(+)$1	1	144	148	12.0000
....	chr19:7533737-7533960(-)$1	1	52	56	12.0000
.(((	chr4:882617-882839(-)$1	1	3	7	12.0000
((((	chr11:105880250-105880475(-)$1	1	94	98	12.0000
((((	chr4:144616526-144616748(-)$1	1	66	70	12.0000
(...	chr12:7640502-7640726(-)$1	1	60	64	12.0000
)).)	chr4:144380474-144380700(-)$1	1	103	107	12.0000
..((	chrX:153537683-153537907(-)$1	1	3	7	12.0000
))))	chr19:40030572-40030793(+)$1	1	185	189	12.0000
((..	chr11:10786024-10786246(-)$1	1	51	55	12.0000
((..	chr2:242438571-242438801(+)$1	1	18	22	12.0000
..((	chr7:134131947-134132173(-)$1	1	0	4	12.0000
..((	chr2:106498134-106498355(-)$1	1	69	73	12.0000
))))	chr22:24086010-24086236(+)$1	1	73	77	12.0000
...(	chr2:70890652-70890875(+)$1	1	2	6	12.0000
(((.	chr1:70616721-70616945(+)$1	1	141	145	12.0000
((((	chr19:39805474-39805697(-)$1	1	37	41	12.0000
((((	chr12:56221286-56221518(-)$1	1	54	58	12.0000
.)))	chr15:75772101-75772323(+)$1	1	134	138	12.0000
((((	chr14:65438511-65438755(-)$1	1	157	161	12.0000
..((	chr12:29486509-29486733(+)$1	1	15	19	12.0000
((((	chr5:180670650-180670874(+)$1	1	90	94	12.0000
((((	chr16:29884883-29885108(-)$1	1	76	80	12.0000
(.((	chr6:27218439-27218664(+)$1	1	23	27	12.0000
((((	chr2:189931063-189931285(+)$1	1	63	67	12.0000
..((	chr11:47203953-47204175(-)$1	1	33	37	12.0000
((((	chr15:31283539-31283760(+)$1	1	22	26	12.0000
)(((	chrX:46433827-46434053(+)$1	1	120	124	12.0000
..))	chr15:40580886-40581108(+)$1	1	44	48	12.0000
)..)	chr19:46308107-46308329(-)$1	1	148	152	12.0000
))))	chrX:9900256-9900480(+)$1	1	176	180	12.0000
.)))	chr19:2222150-2222373(+)$1	1	169	173	12.0000
((((	chr14:24785504-24785725(-)$1	1	112	116	12.0000
((((	chr22:26164898-26165124(+)$1	1	129	133	12.0000
((((	chr9:136598855-136599077(+)$1	1	10	14	12.0000
..))	chr3:47446120-47446341(+)$1	1	146	150	12.0000
.(((	chr19:48204712-48204936(+)$1	1	56	60	12.0000
(((.	chr15:40588396-40588619(+)$1	1	11	15	12.0000
((((	chr11:71940482-71940705(-)$1	1	142	146	12.0000
((((	chr1:207224000-207224221(-)$1	1	137	141	12.0000
..((	chr9:94123839-94124060(+)$1	1	176	180	12.0000
(.((	chr7:148936904-148937125(+)$1	1	8	12	12.0000
...)	chr15:74483433-74483657(-)$1	1	7	11	12.0000
((((	chr2:171822470-171822691(-)$1	1	107	111	12.0000
)..)	chr15:40583563-40583790(+)$1	1	109	113	12.0000
))))	chr3:42734135-42734358(+)$1	1	59	63	12.0000
.)))	chr1:31478757-31478979(+)$1	1	104	108	12.0000
(((.	chr19:19609188-19609409(-)$1	1	58	62	12.0000
(.((	chr1:22915606-22915831(+)$1	1	7	11	12.0000
))))	chr3:64008217-64008440(-)$1	1	138	142	12.0000
))..	chrX:55035652-55035874(-)$1	1	109	113	12.0000
.(((	chr3:50137863-50138140(-)$1	1	121	125	12.0000
...(	chr4:108969747-108969968(+)$1	1	50	54	12.0000
.((.	chr9:133506864-133507086(-)$1	1	0	4	12.0000
..((	chr8:126114533-126114759(+)$1	1	73	77	12.0000
((((	chr17:43005433-43005655(+)$1	1	32	36	12.0000
.).)	chr16:86602274-86602495(-)$1	1	120	124	12.0000
))))	chr3:43073733-43073955(+)$1	1	152	156	12.0000
.(((	chr1:108742638-108742859(+)$1	1	35	39	12.0000
.)).	chr1:74506954-74507177(-)$1	1	174	178	12.0000
.(((	chr1:167814887-167815114(+)$1	1	85	89	12.0000
))((	chr5:154284020-154284243(+)$1	1	48	52	12.0000
((((	chr16:730471-730694(+)$1	1	90	94	12.0000
)).)	chr3:13363178-13363401(-)$1	1	143	147	12.0000
))))	chr16:88876160-88876383(+)$1	1	88	92	12.0000
))))	chr9:32526055-32526282(+)$1	1	70	74	12.0000

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

#score	1068.0000000000007
#seq	89
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m2_run2.nuc.txt

#NT
GAG	chr5:175815767-175816014(+)$1	247	5	8	9.0000
GAG	chr15:69745155-69745428(+)$1	273	40	43	9.0000
GAG	chr3:49049654-49049914(+)$1	260	37	40	9.0000
GAG	chr11:10820440-10820678(-)$1	238	107	110	9.0000
GAG	chr14:102551577-102551817(-)$1	240	0	3	9.0000
GAG	chr2:101009807-101010031(-)$1	224	55	58	9.0000
GAG	chr12:56641225-56641474(-)$1	249	6	9	9.0000
GAG	chr1:226573163-226573403(-)$1	240	32	35	9.0000
GAG	chr6:17785741-17785965(-)$1	224	39	42	9.0000
GAG	chr10:32304407-32304663(-)$1	256	1	4	9.0000
GAG	chr17:65955799-65956047(+)$1	248	60	63	9.0000
GAG	chr6:153292221-153292458(-)$1	237	9	12	9.0000
GAG	chr19:45496124-45496397(+)$1	273	10	13	9.0000
GAG	chr3:186504249-186504504(+)$1	255	100	103	9.0000
GAG	chr16:24583021-24583247(+)$1	226	34	37	9.0000
GAG	chr3:10290960-10291178(+)$1	218	5	8	9.0000
GAG	chr10:112659992-112660221(-)$1	229	23	26	9.0000
GAG	chr11:20409534-20409753(+)$1	219	47	50	9.0000
GAG	chr6:31797532-31797765(+)$1	233	80	83	9.0000
GAG	chr8:141582895-141583117(-)$1	222	197	200	9.0000
GAG	chr2:74441178-74441442(+)$1	264	27	30	9.0000
GAG	chr16:30537555-30537852(-)$1	297	0	3	9.0000
GAG	chr8:42977264-42977499(+)$1	235	6	9	9.0000
GAG	chr9:123943571-123943802(-)$1	231	39	42	9.0000
GAG	chr7:44620668-44620897(-)$1	229	21	24	9.0000
GAG	chr6:42179432-42179668(-)$1	236	152	155	9.0000
GAG	chr1:220151896-220152161(-)$1	265	38	41	9.0000
GAG	chr19:45494404-45494646(+)$1	242	21	24	9.0000
GAG	chr5:68471150-68471415(+)$1	265	82	85	9.0000
GAG	chr16:58581064-58581300(-)$1	236	127	130	9.0000
GAG	chr16:29821468-29821733(+)$1	265	36	39	9.0000
GAG	chr17:73036086-73036321(-)$1	235	90	93	9.0000
GAG	chr5:138643055-138643302(+)$1	247	35	38	9.0000
GAG	chr1:18962685-18962911(+)$1	226	42	45	9.0000
GAG	chr2:105665551-105665811(+)$1	260	152	155	9.0000
GAG	chr7:98963416-98963670(+)$1	254	17	20	9.0000
GAG	chr22:31924647-31924869(+)$1	222	112	115	9.0000
GAG	chr1:228680695-228680926(+)$1	231	13	16	9.0000
GAG	chr2:85769707-85769968(+)$1	261	44	47	9.0000
GAG	chr17:56082813-56083037(-)$1	224	77	80	9.0000
GAG	chr4:141589997-141590220(-)$1	223	5	8	9.0000
GAG	chr1:46743743-46743971(+)$1	228	118	121	9.0000
GAG	chr1:17355105-17355329(-)$1	224	19	22	9.0000
GAG	chr4:1695263-1695494(-)$1	231	16	19	9.0000
GAG	chr6:122779605-122779851(-)$1	246	131	134	9.0000
GAG	chr1:52703368-52703672(+)$1	304	15	18	9.0000
GAG	chr4:20611634-20611859(+)$1	225	5	8	9.0000
GAG	chr8:42977220-42977461(+)$1	241	41	44	9.0000
GAG	chr1:169439106-169439335(-)$1	229	64	67	9.0000
GAG	chr11:10827422-10827668(-)$1	246	8	11	9.0000
GAG	chr11:94908647-94908878(-)$1	231	92	95	9.0000
GAG	chrX:84519298-84519536(+)$1	238	5	8	9.0000
GAG	chr3:51423624-51423857(+)$1	233	59	62	9.0000
GAG	chr6:151286030-151286250(+)$1	220	0	3	9.0000
GAG	chr15:74032420-74032642(-)$1	222	18	21	9.0000
GAG	chr1:233518326-233518571(+)$1	245	40	43	9.0000
GAG	chr15:77239718-77239954(+)$1	236	153	156	9.0000
GAG	chr19:45476323-45476567(+)$1	244	58	61	9.0000
GAG	chr5:10564459-10564718(+)$1	259	36	39	9.0000
gag	chr8:26365671-26365891(-)$1	220	99	102	9.0000
GAG	chr19:46341741-46341963(-)$1	222	2	5	9.0000
GAG	chr21:28212145-28212379(-)$1	234	39	42	9.0000
GAG	chr15:89444696-89444937(-)$1	241	128	131	9.0000
GAG	chr20:62572060-62572286(-)$1	226	4	7	9.0000
GAG	chr11:62334794-62335029(-)$1	235	35	38	9.0000
GAG	chr20:42087839-42088084(+)$1	245	120	123	9.0000
GAG	chr19:58906002-58906242(+)$1	240	25	28	9.0000
gag	chr7:87514237-87514472(+)$1	235	1	4	9.0000
GAG	chr7:27147455-27147686(-)$1	231	66	69	9.0000
GAG	chr12:14923566-14923823(-)$1	257	27	30	9.0000
GAG	chr1:44069286-44069517(+)$1	231	81	84	9.0000
GAG	chr13:100189984-100190210(+)$1	226	24	27	9.0000
GAG	chr12:98993687-98993957(+)$1	270	3	6	9.0000
GAG	chr6:56966191-56966436(+)$1	245	92	95	9.0000
GAG	chr15:69747483-69747722(+)$1	239	48	51	9.0000
GAG	chr1:240371743-240371990(+)$1	247	118	121	9.0000
GAG	chr19:50001105-50001342(+)$1	237	93	96	9.0000
GAG	chr7:150774981-150775241(-)$1	260	137	140	9.0000
GAG	chr19:50001075-50001323(+)$1	248	22	25	9.0000
GAG	chr9:96326659-96326908(+)$1	249	3	6	9.0000
GAG	chr17:80543805-80544045(+)$1	240	234	237	9.0000
GAG	chr11:836150-836367(+)$1	217	5	8	9.0000
GAG	chr5:177021062-177021305(+)$1	243	5	8	9.0000
GAG	chr10:119805258-119805481(-)$1	223	5	8	9.0000
GAG	chr16:2817899-2818150(+)$1	251	151	154	9.0000
GAG	chr12:67688767-67688996(+)$1	229	163	166	9.0000
GAG	chr1:8601225-8601446(-)$1	221	32	35	9.0000
GAG	chr8:48955516-48955743(+)$1	227	39	42	9.0000
GAG	chr11:62443893-62444148(-)$1	255	85	88	9.0000
GAG	chr3:122121573-122121804(+)$1	231	57	60	9.0000
GAG	chr21:28209790-28210030(-)$1	240	47	50	9.0000
GAG	chr1:151372032-151372303(+)$1	271	149	152	9.0000
GAG	chr11:122930498-122930758(-)$1	260	2	5	9.0000
GAG	chr19:45488405-45488644(+)$1	239	13	16	9.0000
GAG	chr3:52558541-52558773(-)$1	232	1	4	9.0000
GAG	chr3:112280235-112280468(-)$1	233	10	13	9.0000
GAG	chr5:179046228-179046483(-)$1	255	124	127	9.0000
GAG	chr19:3976060-3976328(-)$1	268	21	24	9.0000
GAG	chr4:122739146-122739375(-)$1	229	155	158	9.0000

#otherMatches

#Struct PSSM
eee	chr13:23903512-23903741(-)$1	229	5	8	9.0000
ee!	chr5:175815767-175816014(+)$1	247	5	8	9.0000
eee	chr15:69745155-69745428(+)$1	273	40	43	9.0000
:ii	chr3:49049654-49049914(+)$1	260	37	40	9.0000
dd[	chr11:10820440-10820678(-)$1	238	107	110	9.0000
:::	chr14:102551577-102551817(-)$1	240	0	3	9.0000
""b	chr2:101009807-101010031(-)$1	224	55	58	9.0000
ccc	chr12:56641225-56641474(-)$1	249	6	9	9.0000
GGG	chr1:226573163-226573403(-)$1	240	32	35	9.0000
fff	chr6:17785741-17785965(-)$1	224	39	42	9.0000
FFF	chr10:32304407-32304663(-)$1	256	1	4	9.0000
ddd	chr17:65955799-65956047(+)$1	248	60	63	9.0000
:::	chr6:153292221-153292458(-)$1	237	9	12	9.0000
b[c	chr19:45496124-45496397(+)$1	273	10	13	9.0000
[dd	chr3:186504249-186504504(+)$1	255	100	103	9.0000
ccp	chr16:24583021-24583247(+)$1	226	34	37	9.0000
E{D	chr3:10290960-10291178(+)$1	218	5	8	9.0000
fff	chr10:112659992-112660221(-)$1	229	23	26	9.0000
b&&	chr11:20409534-20409753(+)$1	219	47	50	9.0000
bhh	chr6:31797532-31797765(+)$1	233	80	83	9.0000
ggg	chr8:141582895-141583117(-)$1	222	197	200	9.0000
eee	chr2:74441178-74441442(+)$1	264	27	30	9.0000
CCC	chr16:30537555-30537852(-)$1	297	0	3	9.0000
CCc	chr8:42977264-42977499(+)$1	235	6	9	9.0000
{CC	chr9:123943571-123943802(-)$1	231	39	42	9.0000
ccc	chr7:44620668-44620897(-)$1	229	21	24	9.0000
???	chr6:42179432-42179668(-)$1	236	152	155	9.0000
EEE	chr1:220151896-220152161(-)$1	265	38	41	9.0000
{CC	chr19:45494404-45494646(+)$1	242	21	24	9.0000
qqq	chr5:68471150-68471415(+)$1	265	82	85	9.0000
eee	chr16:58581064-58581300(-)$1	236	127	130	9.0000
ggg	chr16:29821468-29821733(+)$1	265	36	39	9.0000
cc2	chr17:73036086-73036321(-)$1	235	90	93	9.0000
cco	chr5:138643055-138643302(+)$1	247	35	38	9.0000
c!!	chr1:18962685-18962911(+)$1	226	42	45	9.0000
ddd	chr2:105665551-105665811(+)$1	260	152	155	9.0000
mme	chr7:98963416-98963670(+)$1	254	17	20	9.0000
ccc	chr22:31924647-31924869(+)$1	222	112	115	9.0000
d::	chr1:228680695-228680926(+)$1	231	13	16	9.0000
c##	chr2:85769707-85769968(+)$1	261	44	47	9.0000
EEE	chr17:56082813-56083037(-)$1	224	77	80	9.0000
:::	chr4:141589997-141590220(-)$1	223	5	8	9.0000
a[d	chr1:46743743-46743971(+)$1	228	118	121	9.0000
FFF	chr1:17355105-17355329(-)$1	224	19	22	9.0000
EEE	chr4:1695263-1695494(-)$1	231	16	19	9.0000
ddd	chr6:122779605-122779851(-)$1	246	131	134	9.0000
qgg	chr1:52703368-52703672(+)$1	304	15	18	9.0000
GGG	chr4:20611634-20611859(+)$1	225	5	8	9.0000
qqq	chr8:42977220-42977461(+)$1	241	41	44	9.0000
eee	chr1:169439106-169439335(-)$1	229	64	67	9.0000
CCC	chr11:10827422-10827668(-)$1	246	8	11	9.0000
rrr	chr11:94908647-94908878(-)$1	231	92	95	9.0000
EEE	chrX:84519298-84519536(+)$1	238	5	8	9.0000
ddd	chr3:51423624-51423857(+)$1	233	59	62	9.0000
FFF	chr6:151286030-151286250(+)$1	220	0	3	9.0000
a]f	chr15:74032420-74032642(-)$1	222	18	21	9.0000
{CC	chr1:233518326-233518571(+)$1	245	40	43	9.0000
:::	chr15:77239718-77239954(+)$1	236	153	156	9.0000
c[e	chr19:45476323-45476567(+)$1	244	58	61	9.0000
ggg	chr5:10564459-10564718(+)$1	259	36	39	9.0000
eee	chr8:26365671-26365891(-)$1	220	99	102	9.0000
GGG	chr19:46341741-46341963(-)$1	222	2	5	9.0000
"""	chr21:28212145-28212379(-)$1	234	39	42	9.0000
!!b	chr15:89444696-89444937(-)$1	241	128	131	9.0000
a[d	chr20:62572060-62572286(-)$1	226	4	7	9.0000
::C	chr11:62334794-62335029(-)$1	235	35	38	9.0000
ZZB	chr20:42087839-42088084(+)$1	245	120	123	9.0000
eee	chr19:58906002-58906242(+)$1	240	25	28	9.0000
ddd	chr7:87514237-87514472(+)$1	235	1	4	9.0000
a]c	chr7:27147455-27147686(-)$1	231	66	69	9.0000
ff]	chr12:14923566-14923823(-)$1	257	27	30	9.0000
a]h	chr1:44069286-44069517(+)$1	231	81	84	9.0000
eee	chr13:100189984-100190210(+)$1	226	24	27	9.0000
C{G	chr12:98993687-98993957(+)$1	270	3	6	9.0000
eee	chr6:56966191-56966436(+)$1	245	92	95	9.0000
cco	chr15:69747483-69747722(+)$1	239	48	51	9.0000
fff	chr1:240371743-240371990(+)$1	247	118	121	9.0000
ff'	chr19:50001105-50001342(+)$1	237	93	96	9.0000
mmm	chr7:150774981-150775241(-)$1	260	137	140	9.0000
:::	chr19:50001075-50001323(+)$1	248	22	25	9.0000
c[b	chr9:96326659-96326908(+)$1	249	3	6	9.0000
b]d	chr17:80543805-80544045(+)$1	240	234	237	9.0000
e[b	chr11:836150-836367(+)$1	217	5	8	9.0000
HHH	chr5:177021062-177021305(+)$1	243	5	8	9.0000
::H	chr10:119805258-119805481(-)$1	223	5	8	9.0000
]a]	chr16:2817899-2818150(+)$1	251	151	154	9.0000
Ghh	chr12:67688767-67688996(+)$1	229	163	166	9.0000
eee	chr1:8601225-8601446(-)$1	221	32	35	9.0000
ddd	chr8:48955516-48955743(+)$1	227	39	42	9.0000
eee	chr11:62443893-62444148(-)$1	255	85	88	9.0000
ggg	chr3:122121573-122121804(+)$1	231	57	60	9.0000
&&&	chr21:28209790-28210030(-)$1	240	47	50	9.0000
%ff	chr1:151372032-151372303(+)$1	271	149	152	9.0000
eee	chr11:122930498-122930758(-)$1	260	2	5	9.0000
eee	chr19:45488405-45488644(+)$1	239	13	16	9.0000
hhh	chr3:52558541-52558773(-)$1	232	1	4	9.0000
!dd	chr3:112280235-112280468(-)$1	233	10	13	9.0000
ccc	chr5:179046228-179046483(-)$1	255	124	127	9.0000
KKE	chr19:3976060-3976328(-)$1	268	21	24	9.0000
:ii	chr4:122739146-122739375(-)$1	229	155	158	9.0000

#DB
(((	chr13:23903512-23903741(-)$1	1	5	8	9.0000
((.	chr5:175815767-175816014(+)$1	1	5	8	9.0000
)))	chr15:69745155-69745428(+)$1	1	40	43	9.0000
.((	chr3:49049654-49049914(+)$1	1	37	40	9.0000
((.	chr11:10820440-10820678(-)$1	1	107	110	9.0000
...	chr14:102551577-102551817(-)$1	1	0	3	9.0000
..(	chr2:101009807-101010031(-)$1	1	55	58	9.0000
(((	chr12:56641225-56641474(-)$1	1	6	9	9.0000
(((	chr1:226573163-226573403(-)$1	1	32	35	9.0000
(((	chr6:17785741-17785965(-)$1	1	39	42	9.0000
(((	chr10:32304407-32304663(-)$1	1	1	4	9.0000
)))	chr17:65955799-65956047(+)$1	1	60	63	9.0000
...	chr6:153292221-153292458(-)$1	1	9	12	9.0000
(.(	chr19:45496124-45496397(+)$1	1	10	13	9.0000
.((	chr3:186504249-186504504(+)$1	1	100	103	9.0000
((.	chr16:24583021-24583247(+)$1	1	34	37	9.0000
(.(	chr3:10290960-10291178(+)$1	1	5	8	9.0000
)))	chr10:112659992-112660221(-)$1	1	23	26	9.0000
(..	chr11:20409534-20409753(+)$1	1	47	50	9.0000
(((	chr6:31797532-31797765(+)$1	1	80	83	9.0000
)))	chr8:141582895-141583117(-)$1	1	197	200	9.0000
)))	chr2:74441178-74441442(+)$1	1	27	30	9.0000
(((	chr16:30537555-30537852(-)$1	1	0	3	9.0000
(((	chr8:42977264-42977499(+)$1	1	6	9	9.0000
.((	chr9:123943571-123943802(-)$1	1	39	42	9.0000
(((	chr7:44620668-44620897(-)$1	1	21	24	9.0000
...	chr6:42179432-42179668(-)$1	1	152	155	9.0000
(((	chr1:220151896-220152161(-)$1	1	38	41	9.0000
.((	chr19:45494404-45494646(+)$1	1	21	24	9.0000
...	chr5:68471150-68471415(+)$1	1	82	85	9.0000
(((	chr16:58581064-58581300(-)$1	1	127	130	9.0000
(((	chr16:29821468-29821733(+)$1	1	36	39	9.0000
)).	chr17:73036086-73036321(-)$1	1	90	93	9.0000
((.	chr5:138643055-138643302(+)$1	1	35	38	9.0000
(..	chr1:18962685-18962911(+)$1	1	42	45	9.0000
)))	chr2:105665551-105665811(+)$1	1	152	155	9.0000
..)	chr7:98963416-98963670(+)$1	1	17	20	9.0000
)((	chr22:31924647-31924869(+)$1	1	112	115	9.0000
)..	chr1:228680695-228680926(+)$1	1	13	16	9.0000
(..	chr2:85769707-85769968(+)$1	1	44	47	9.0000
(((	chr17:56082813-56083037(-)$1	1	77	80	9.0000
...	chr4:141589997-141590220(-)$1	1	5	8	9.0000
(.(	chr1:46743743-46743971(+)$1	1	118	121	9.0000
(((	chr1:17355105-17355329(-)$1	1	19	22	9.0000
(((	chr4:1695263-1695494(-)$1	1	16	19	9.0000
)))	chr6:122779605-122779851(-)$1	1	131	134	9.0000
.))	chr1:52703368-52703672(+)$1	1	15	18	9.0000
(((	chr4:20611634-20611859(+)$1	1	5	8	9.0000
...	chr8:42977220-42977461(+)$1	1	41	44	9.0000
(((	chr1:169439106-169439335(-)$1	1	64	67	9.0000
(((	chr11:10827422-10827668(-)$1	1	8	11	9.0000
...	chr11:94908647-94908878(-)$1	1	92	95	9.0000
(((	chrX:84519298-84519536(+)$1	1	5	8	9.0000
(((	chr3:51423624-51423857(+)$1	1	59	62	9.0000
(((	chr6:151286030-151286250(+)$1	1	0	3	9.0000
).)	chr15:74032420-74032642(-)$1	1	18	21	9.0000
.((	chr1:233518326-233518571(+)$1	1	40	43	9.0000
...	chr15:77239718-77239954(+)$1	1	153	156	9.0000
(.(	chr19:45476323-45476567(+)$1	1	58	61	9.0000
)))	chr5:10564459-10564718(+)$1	1	36	39	9.0000
(((	chr8:26365671-26365891(-)$1	1	99	102	9.0000
(((	chr19:46341741-46341963(-)$1	1	2	5	9.0000
...	chr21:28212145-28212379(-)$1	1	39	42	9.0000
..(	chr15:89444696-89444937(-)$1	1	128	131	9.0000
(.(	chr20:62572060-62572286(-)$1	1	4	7	9.0000
..(	chr11:62334794-62335029(-)$1	1	35	38	9.0000
..)	chr20:42087839-42088084(+)$1	1	120	123	9.0000
(((	chr19:58906002-58906242(+)$1	1	25	28	9.0000
(((	chr7:87514237-87514472(+)$1	1	1	4	9.0000
).)	chr7:27147455-27147686(-)$1	1	66	69	9.0000
)).	chr12:14923566-14923823(-)$1	1	27	30	9.0000
).)	chr1:44069286-44069517(+)$1	1	81	84	9.0000
(((	chr13:100189984-100190210(+)$1	1	24	27	9.0000
(.(	chr12:98993687-98993957(+)$1	1	3	6	9.0000
(((	chr6:56966191-56966436(+)$1	1	92	95	9.0000
((.	chr15:69747483-69747722(+)$1	1	48	51	9.0000
)))	chr1:240371743-240371990(+)$1	1	118	121	9.0000
((.	chr19:50001105-50001342(+)$1	1	93	96	9.0000
...	chr7:150774981-150775241(-)$1	1	137	140	9.0000
...	chr19:50001075-50001323(+)$1	1	22	25	9.0000
(.(	chr9:96326659-96326908(+)$1	1	3	6	9.0000
).)	chr17:80543805-80544045(+)$1	1	234	237	9.0000
(.(	chr11:836150-836367(+)$1	1	5	8	9.0000
(((	chr5:177021062-177021305(+)$1	1	5	8	9.0000
..(	chr10:119805258-119805481(-)$1	1	5	8	9.0000
.).	chr16:2817899-2818150(+)$1	1	151	154	9.0000
)((	chr12:67688767-67688996(+)$1	1	163	166	9.0000
)))	chr1:8601225-8601446(-)$1	1	32	35	9.0000
(((	chr8:48955516-48955743(+)$1	1	39	42	9.0000
(((	chr11:62443893-62444148(-)$1	1	85	88	9.0000
(((	chr3:122121573-122121804(+)$1	1	57	60	9.0000
...	chr21:28209790-28210030(-)$1	1	47	50	9.0000
.((	chr1:151372032-151372303(+)$1	1	149	152	9.0000
(((	chr11:122930498-122930758(-)$1	1	2	5	9.0000
(((	chr19:45488405-45488644(+)$1	1	13	16	9.0000
(((	chr3:52558541-52558773(-)$1	1	1	4	9.0000
.((	chr3:112280235-112280468(-)$1	1	10	13	9.0000
(((	chr5:179046228-179046483(-)$1	1	124	127	9.0000
..(	chr19:3976060-3976328(-)$1	1	21	24	9.0000
.((	chr4:122739146-122739375(-)$1	1	155	158	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m1_run1.nuc.txt

#NT
UUAUUUUUAUUUUGUUU	chr5:78618205-78618449(+)$1	244	11	28	28.2916
UUUUCUUUUGUUUUUUU	chr4:71895154-71895394(+)$1	240	113	130	33.1874
Cuuuuuuuuuuuuuuuu	chr10:28340707-28340953(-)$1	246	122	139	36.8333
UUAUUUUCUUUUUUGUU	chr5:143537858-143538110(-)$1	252	94	111	29.4374
UUUUUAUUUUUGUUUUU	chr2:204161753-204162033(+)$1	280	108	125	33.2916
uuuuuuuauuuuuauuu	chr1:32636719-32637002(+)$1	283	104	121	32.9791
uuuuuuuuuuuuuuuuu	chrX:118673385-118673625(-)$1	240	112	129	40.8958
AUUUUUUUUUUCUUUUU	chr11:118622026-118622266(-)$1	240	114	131	32.8749
uuuuuuuauuuuuCUUU	chr5:145665617-145665857(+)$1	240	67	84	33.0833
UUUCUUCUUUCUUUUUU	chr12:21669415-21669655(+)$1	240	112	129	30.0624
UUUUUUUCUUUUUUUUU	chr7:23650728-23650968(+)$1	240	118	135	37.6666
UUUUCUUUUUCUUUUUU	chr6:85446238-85446478(-)$1	240	118	135	33.6041
UUAUUAUUAuuuuuuuu	chr5:70953134-70953376(+)$1	242	118	135	29.1249
uuuucuucuuuucuuuu	chr13:107141998-107142238(-)$1	240	161	178	29.5416
uuuauucuuuuuuuuuu	chr2:37334174-37334415(-)$1	241	210	227	33.8124
uuuuuguuuuuuuuuuu	chr2:232319508-232319749(-)$1	241	172	189	37.0416
UUUGUUUGUUUGUUUUU	chr2:201839074-201839314(-)$1	240	10	27	29.2291
UUUUUUUUUUUUUCUGU	chr2:145146351-145146640(-)$1	289	170	187	32.2499
UUUUUUCUUUUUUUUGU	chr5:114950771-114951051(-)$1	280	123	140	33.3958
uuuuuuuuuuuuuuuuu	chr12:19671040-19671280(+)$1	240	112	129	40.8958
UUUUUUUUCCUGUUUUU	chr6:139693855-139694105(-)$1	250	11	28	28.1874
UUUUAGUUUUUAUUUUU	chr12:56634860-56635100(-)$1	240	113	130	29.0208
AUUUGUUUUUUUUUUUU	chr8:37612201-37612481(+)$1	280	147	164	33.6041
UUUUGAUUUUUUUUUUU	chr1:114519744-114519984(+)$1	240	107	124	33.7083
UUUUUUUCUUCUUUCUU	chr22:38879952-38880205(-)$1	253	113	130	29.3333
UGAUUUUUUUUUUUUCU	chr1:179814753-179814993(-)$1	240	121	138	27.9791
UUUUCUUUUUCUUUUUU	chr7:131177027-131177268(+)$1	241	102	119	33.6041
UUUUUUCCUUUUUUUUU	chr16:79631542-79631782(-)$1	240	116	133	34.4374
cuuuuucuuucuuuuuu	chr16:15690168-15690408(-)$1	240	52	69	29.8541
UUUUUUUUUAUUUUAUU	chr3:70015095-70015335(+)$1	240	119	136	32.1458
uuuuguuuucuuguuuu	chr7:48003928-48004169(-)$1	241	174	191	28.6041
UUUUUUUUUUUUUUUUU	chr7:100163398-100163645(+)$1	247	114	131	40.8958
UUUCAUCUUUUUUUUUU	chr4:170015958-170016200(-)$1	242	116	133	30.0624
uuuuuuuauuuuauuuu	chr22:40731627-40731867(+)$1	240	47	64	32.8749
AUUUUUUUUUUUUUUUU	chr5:151183831-151184145(+)$1	314	114	131	37.1458
UUCAUUGUUUUUUUUUU	chr5:174954356-174954596(+)$1	240	216	233	28.9166
UUUUUGUUUUUGUUUGU	chr11:45950786-45951026(-)$1	240	37	54	28.8124
uuucuuucuuuuuuuuu	chr4:100801649-100801889(-)$1	240	116	133	33.8124
UUAAUUUAUUUUUUUUU	chr13:32973616-32973856(+)$1	240	112	129	29.9583
uuuuuuuuuuuuuuuuu	chr7:65619047-65619293(+)$1	246	121	138	40.8958
uuuuuuuuuuuuuuuuu	chr15:65295199-65295479(-)$1	280	157	174	40.8958
AUUUGUUUUUUUUUUUU	chr7:98258632-98258872(+)$1	240	115	132	33.6041
UUAGUUUUUAUUUUUUU	chr12:69970769-69971009(+)$1	240	157	174	29.1249
UUUUUUUUUGUUUUUUU	chr1:33321776-33322016(+)$1	240	102	119	36.7291
UUUUUUCUUUAUUUUUU	chr12:120899546-120899826(-)$1	280	20	37	33.6041
uuuuuuuuuuuuuuuuu	chr1:151668989-151669229(+)$1	240	138	155	40.8958
AUUUUACUUUUUUUUUU	chr12:106632258-106632513(-)$1	255	122	139	30.2708

#otherMatches

#Struct PSSM
iiiiiiiii[ddddhhh	chr14:75748691-75748931(+)$1	240	114	131	33.1874
guuuuuuuuuuuugggg	chr5:78618205-78618449(+)$1	244	11	28	28.2916
HHHHHHHHiiiiiiiii	chr4:71895154-71895394(+)$1	240	113	130	33.1874
iiiiiiiiiJJJJJJJJ	chr10:28340707-28340953(-)$1	246	122	139	36.8333
]hhhhhhhh::::gggg	chr5:143537858-143538110(-)$1	252	94	111	29.4374
==========%%%%%%d	chr2:204161753-204162033(+)$1	280	108	125	33.2916
ee:::::::::::::::	chr1:32636719-32637002(+)$1	283	104	121	32.9791
^^^^^^^^^^^^^^^^^	chrX:118673385-118673625(-)$1	240	112	129	40.8958
ddd:::EEEEELLLFFF	chr11:118622026-118622266(-)$1	240	114	131	32.8749
^^^^^^^^^^^^^^^^^	chr5:145665617-145665857(+)$1	240	67	84	33.0833
^^^^^^^^^^^^^^^^^	chr12:21669415-21669655(+)$1	240	112	129	30.0624
qqqqqqeeeee22gggg	chr7:23650728-23650968(+)$1	240	118	135	37.6666
e"""eeeeeqqqqqqqq	chr6:85446238-85446478(-)$1	240	118	135	33.6041
dddxxxxxxxxxxxxxx	chr5:70953134-70953376(+)$1	242	118	135	29.1249
hhhhDDDD______JJJ	chr13:107141998-107142238(-)$1	240	161	178	29.5416
:::eeeee[eeeeeooo	chr2:37334174-37334415(-)$1	241	210	227	33.8124
:================	chr2:232319508-232319749(-)$1	241	172	189	37.0416
e[eeeee[bb[dddd""	chr2:201839074-201839314(-)$1	240	10	27	29.2291
[gggggggrrrrrrrrr	chr2:145146351-145146640(-)$1	289	170	187	32.2499
3ffffff::::::::::	chr5:114950771-114951051(-)$1	280	123	140	33.3958
ddd999999999=====	chr12:19671040-19671280(+)$1	240	112	129	40.8958
:::HHHHHHHH::::::	chr6:139693855-139694105(-)$1	250	11	28	28.1874
:::::::::::::::::	chr12:56634860-56635100(-)$1	240	113	130	29.0208
cc:::::::::::::::	chr8:37612201-37612481(+)$1	280	147	164	33.6041
======0000000000i	chr1:114519744-114519984(+)$1	240	107	124	33.7083
ee:::::::::::cccq	chr22:38879952-38880205(-)$1	253	113	130	29.3333
e]hhhhhhhhffffff!	chr1:179814753-179814993(-)$1	240	121	138	27.9791
qdddd::::::::::::	chr7:131177027-131177268(+)$1	241	102	119	33.6041
:::::::::JJJJJJJJ	chr16:79631542-79631782(-)$1	240	116	133	34.4374
::::::::::::hhhhh	chr16:15690168-15690408(-)$1	240	52	69	29.8541
gggg:::::::::::::	chr3:70015095-70015335(+)$1	240	119	136	32.1458
qqqeeeeebb]dddd::	chr7:48003928-48004169(-)$1	241	174	191	28.6041
:::::::::========	chr7:100163398-100163645(+)$1	247	114	131	40.8958
JJJJJJJJJJdddd[ff	chr4:170015958-170016200(-)$1	242	116	133	30.0624
iiiiiii[dddd[dddd	chr22:40731627-40731867(+)$1	240	47	64	32.8749
c22ccc]==========	chr5:151183831-151184145(+)$1	314	114	131	37.1458
iiiiii:::::::::::	chr5:174954356-174954596(+)$1	240	216	233	28.9166
66666dddd::::iiii	chr11:45950786-45951026(-)$1	240	37	54	28.8124
::::::ffffffppppp	chr4:100801649-100801889(-)$1	240	116	133	33.8124
c$$$$$iiiiiiiii++	chr13:32973616-32973856(+)$1	240	112	129	29.9583
^^^^^^^^^^^^^^^^^	chr7:65619047-65619293(+)$1	246	121	138	40.8958
IIIIIIII:::::::::	chr15:65295199-65295479(-)$1	280	157	174	40.8958
C:============rrr	chr7:98258632-98258872(+)$1	240	115	132	33.6041
!!bbqqqqqqqqbb22e	chr12:69970769-69971009(+)$1	240	157	174	29.1249
dd[eeeee[ddddrrrr	chr1:33321776-33322016(+)$1	240	102	119	36.7291
IIIIIIIIIOOOOOOEE	chr12:120899546-120899826(-)$1	280	20	37	33.6041
:::::::::::::::::	chr1:151668989-151669229(+)$1	240	138	155	40.8958
:::::JJJJJJJJJJJJ	chr12:106632258-106632513(-)$1	255	122	139	30.2708

#DB
(((((((((.(((((((	chr14:75748691-75748931(+)$1	1	114	131	33.1874
(............))))	chr5:78618205-78618449(+)$1	1	11	28	28.2916
))))))))(((((((((	chr4:71895154-71895394(+)$1	1	113	130	33.1874
)))))))))))))))))	chr10:28340707-28340953(-)$1	1	122	139	36.8333
.))))))))....((((	chr5:143537858-143538110(-)$1	1	94	111	29.4374
((((((((((......(	chr2:204161753-204162033(+)$1	1	108	125	33.2916
))...............	chr1:32636719-32637002(+)$1	1	104	121	32.9791
.................	chrX:118673385-118673625(-)$1	1	112	129	40.8958
)))...(((((...(((	chr11:118622026-118622266(-)$1	1	114	131	32.8749
.................	chr5:145665617-145665857(+)$1	1	67	84	33.0833
.................	chr12:21669415-21669655(+)$1	1	112	129	30.0624
......)))))..))))	chr7:23650728-23650968(+)$1	1	118	135	37.6666
(...(((((........	chr6:85446238-85446478(-)$1	1	118	135	33.6041
(((..............	chr5:70953134-70953376(+)$1	1	118	135	29.1249
))))))))......)))	chr13:107141998-107142238(-)$1	1	161	178	29.5416
...(((((.(((((...	chr2:37334174-37334415(-)$1	1	210	227	33.8124
.((((((((((((((((	chr2:232319508-232319749(-)$1	1	172	189	37.0416
(.(((((.((.((((..	chr2:201839074-201839314(-)$1	1	10	27	29.2291
.(((((((.........	chr2:145146351-145146640(-)$1	1	170	187	32.2499
.))))))..........	chr5:114950771-114951051(-)$1	1	123	140	33.3958
))).........)))))	chr12:19671040-19671280(+)$1	1	112	129	40.8958
...((((((((......	chr6:139693855-139694105(-)$1	1	11	28	28.1874
.................	chr12:56634860-56635100(-)$1	1	113	130	29.0208
))...............	chr8:37612201-37612481(+)$1	1	147	164	33.6041
))))))..........)	chr1:114519744-114519984(+)$1	1	107	124	33.7083
))...........(((.	chr22:38879952-38880205(-)$1	1	113	130	29.3333
).))))))))((((((.	chr1:179814753-179814993(-)$1	1	121	138	27.9791
.))))............	chr7:131177027-131177268(+)$1	1	102	119	33.6041
.........))))))))	chr16:79631542-79631782(-)$1	1	116	133	34.4374
............(((((	chr16:15690168-15690408(-)$1	1	52	69	29.8541
)))).............	chr3:70015095-70015335(+)$1	1	119	136	32.1458
...))))))).))))..	chr7:48003928-48004169(-)$1	1	174	191	28.6041
.........((((((((	chr7:100163398-100163645(+)$1	1	114	131	40.8958
((((((((((((((.((	chr4:170015958-170016200(-)$1	1	116	133	30.0624
(((((((.((((.((((	chr22:40731627-40731867(+)$1	1	47	64	32.8749
)..))).))))))))))	chr5:151183831-151184145(+)$1	1	114	131	37.1458
))))))...........	chr5:174954356-174954596(+)$1	1	216	233	28.9166
.....))))....((((	chr11:45950786-45951026(-)$1	1	37	54	28.8124
......((((((.....	chr4:100801649-100801889(-)$1	1	116	133	33.8124
(.....(((((((((..	chr13:32973616-32973856(+)$1	1	112	129	29.9583
.................	chr7:65619047-65619293(+)$1	1	121	138	40.8958
)))))))).........	chr15:65295199-65295479(-)$1	1	157	174	40.8958
(.((((((((((((...	chr7:98258632-98258872(+)$1	1	115	132	33.6041
..((........))..)	chr12:69970769-69971009(+)$1	1	157	174	29.1249
((.(((((.((((....	chr1:33321776-33322016(+)$1	1	102	119	36.7291
(((((((((......((	chr12:120899546-120899826(-)$1	1	20	37	33.6041
.................	chr1:151668989-151669229(+)$1	1	138	155	40.8958
.....))))))))))))	chr12:106632258-106632513(-)$1	1	122	139	30.2708

#PSSM
U : 0.56	u : 0.29	A : 0.10	C : 0.02	c : 0.02	
U : 0.64	u : 0.33	G : 0.02	
U : 0.52	u : 0.33	A : 0.12	C : 0.02	
U : 0.54	u : 0.29	C : 0.04	G : 0.04	A : 0.04	a : 0.02	c : 0.02	
U : 0.49	u : 0.29	C : 0.06	G : 0.06	A : 0.04	c : 0.02	g : 0.02	
U : 0.54	u : 0.29	A : 0.08	G : 0.04	a : 0.02	g : 0.02	
U : 0.52	u : 0.29	C : 0.12	c : 0.04	G : 0.02	
U : 0.54	u : 0.22	C : 0.08	a : 0.06	c : 0.04	G : 0.02	A : 0.02	
U : 0.60	u : 0.33	A : 0.04	C : 0.02	
U : 0.54	u : 0.33	G : 0.04	A : 0.04	C : 0.02	c : 0.02	
U : 0.54	u : 0.31	C : 0.08	a : 0.02	c : 0.02	A : 0.02	
U : 0.52	u : 0.35	G : 0.08	C : 0.02	A : 0.02	
U : 0.64	u : 0.29	c : 0.02	g : 0.02	a : 0.02	
U : 0.60	u : 0.31	C : 0.04	G : 0.02	a : 0.02	
U : 0.60	u : 0.33	G : 0.02	C : 0.02	A : 0.02	
U : 0.58	u : 0.33	G : 0.06	C : 0.02	
U : 0.66	u : 0.33	

#score	1589.666666666666
#seq	48
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m2_run2.nuc.txt

#NT
UAUUGUUUU	chr10:94372735-94373009(+)$1	274	48	57	15.3333
UUUUGUUUU	chr10:70502102-70502428(+)$1	326	17	26	19.5000
UUUUUUGUU	chr8:73939106-73939453(+)$1	347	206	215	18.0714
UUUUUUUUU	chr1:171535758-171536093(+)$1	335	303	312	22.5952
UUUUUUUUU	chr7:91669952-91670287(+)$1	335	8	17	22.5952
UUUCUCUUU	chr16:53281250-53281552(+)$1	302	256	265	15.4523
uuuuuuuuu	chr17:45646703-45647026(+)$1	323	278	287	22.5952
uuuuuuuuu	chr18:55912582-55912916(+)$1	334	324	333	22.5952
UUUCUGUUU	chr10:75864706-75865041(+)$1	335	84	93	15.4523
UUUGAUUUU	chr2:233655430-233655702(+)$1	272	33	42	15.3333
UUAUUUUUU	chr5:151176790-151177093(+)$1	303	235	244	17.8333
UUUUUAUUU	chrX:123034317-123034634(+)$1	317	13	22	18.7857
uuuuuuuuu	chr10:71129184-71129513(+)$1	329	318	327	22.5952
UUUUUGUUU	chrX:123195004-123195336(+)$1	332	209	218	19.1428
UUUCUUUUU	chr20:47839789-47840115(+)$1	326	316	325	18.9047
UUUUCUUUU	chr7:86803871-86804186(+)$1	315	24	33	19.2619
UGUUUUUUU	chr14:89040929-89041268(+)$1	339	20	29	18.4285
UGUUUUUUU	chr17:48821026-48821356(+)$1	330	15	24	18.4285
UUUUUUUUU	chr18:662117-662570(+)$1	453	387	396	22.5952
UUUUCCUUU	chrX:19376997-19377308(+)$1	311	298	307	15.8095
uuucauuuU	chr14:56094559-56094921(+)$1	362	1	10	15.5714
UUUUUCUUU	chr14:94545775-94546040(+)$1	265	20	29	19.1428
CUUUUUUUU	chr7:33427603-33427857(+)$1	254	194	203	17.9523
uuuuuuuuu	chr1:39494382-39494745(+)$1	363	284	293	22.5952
UUUAUUUUU	chrX:96638892-96639203(+)$1	311	209	218	18.5476
UUUUUUUUU	chr7:33397397-33397692(+)$1	295	9	18	22.5952
UUUUAUUUU	chr4:57860759-57861051(+)$1	292	39	48	19.2619
UUUGUUUUU	chrX:96603067-96603448(+)$1	381	202	211	18.6666
uuuuuuuuu	chr12:98938691-98938943(+)$1	252	216	225	22.5952
UUUUUGUUU	chr14:92601679-92601978(+)$1	299	239	248	19.1428
UUUUUUGUU	chr18:76886213-76886525(+)$1	312	4	13	18.0714
UUUUUUUUU	chr2:190323432-190323739(+)$1	307	29	38	22.5952
UUUUGCUUU	chr4:88973069-88973365(+)$1	296	60	69	16.0476
AUUUUUUUU	chr4:123797418-123797734(+)$1	316	38	47	17.9523
UUUUUUUUU	chr22:29682872-29683193(+)$1	321	9	18	22.5952
UUUUGUUUU	chr20:62626673-62626977(+)$1	304	211	220	19.5000
UUUUUUUUU	chr6:76331194-76331527(+)$1	333	154	163	22.5952
UUUUUGUUU	chr2:170487223-170487540(+)$1	317	42	51	19.1428
UUUUGUUUU	chr12:124071305-124071575(+)$1	270	81	90	19.5000
UUUUUUUUU	chr8:95676892-95677168(+)$1	276	222	231	22.5952
UAUUCUUUU	chr18:33724819-33725142(+)$1	323	28	37	15.0952

#otherMatches

#Struct PSSM
gggggggmm	chr2:172582656-172582987(+)$1	331	34	43	18.3095
qqqqccc]i	chr10:94372735-94373009(+)$1	274	48	57	15.3333
###ccc!!e	chr10:70502102-70502428(+)$1	326	17	26	19.5000
444hhhhhh	chr8:73939106-73939453(+)$1	347	206	215	18.0714
d22hhhhhh	chr1:171535758-171536093(+)$1	335	303	312	22.5952
JJJJJJ:::	chr7:91669952-91670287(+)$1	335	8	17	22.5952
:::::::ee	chr16:53281250-53281552(+)$1	302	256	265	15.4523
:::::::::	chr17:45646703-45647026(+)$1	323	278	287	22.5952
F}EEEEE::	chr18:55912582-55912916(+)$1	334	324	333	22.5952
333eeeee]	chr10:75864706-75865041(+)$1	335	84	93	15.4523
DDDD::ddd	chr2:233655430-233655702(+)$1	272	33	42	15.3333
!!ggggggg	chr5:151176790-151177093(+)$1	303	235	244	17.8333
FFFFF::::	chrX:123034317-123034634(+)$1	317	13	22	18.7857
JJJJJJJJJ	chr10:71129184-71129513(+)$1	329	318	327	22.5952
$$$ddddmm	chrX:123195004-123195336(+)$1	332	209	218	19.1428
JJJJJJJJJ	chr20:47839789-47840115(+)$1	326	316	325	18.9047
iiiii[ddd	chr7:86803871-86804186(+)$1	315	24	33	19.2619
ggggggooo	chr14:89040929-89041268(+)$1	339	20	29	18.4285
piiiiiiii	chr17:48821026-48821356(+)$1	330	15	24	18.4285
EE:::::::	chr18:662117-662570(+)$1	453	387	396	22.5952
~~~BBYYEE	chrX:19376997-19377308(+)$1	311	298	307	15.8095
::::::::F	chr14:56094559-56094921(+)$1	362	1	10	15.5714
::::::GGG	chr14:94545775-94546040(+)$1	265	20	29	19.1428
ff::FFFFF	chr7:33427603-33427857(+)$1	254	194	203	17.9523
+++++++++	chr1:39494382-39494745(+)$1	363	284	293	22.5952
ggg]fffff	chrX:96638892-96639203(+)$1	311	209	218	18.5476
b$$$$$ddd	chr7:33397397-33397692(+)$1	295	9	18	22.5952
ggggooooo	chr4:57860759-57861051(+)$1	292	39	48	19.2619
ggg::::::	chrX:96603067-96603448(+)$1	381	202	211	18.6666
f]=======	chr12:98938691-98938943(+)$1	252	216	225	22.5952
GGGGG}GGG	chr14:92601679-92601978(+)$1	299	239	248	19.1428
:::::eeee	chr18:76886213-76886525(+)$1	312	4	13	18.0714
IIIIIIOOO	chr2:190323432-190323739(+)$1	307	29	38	22.5952
ggggg[eee	chr4:88973069-88973365(+)$1	296	60	69	16.0476
mmeeeee44	chr4:123797418-123797734(+)$1	316	38	47	17.9523
JJJPPPPPP	chr22:29682872-29683193(+)$1	321	9	18	22.5952
ppffffff:	chr20:62626673-62626977(+)$1	304	211	220	19.5000
qqqqqqqqc	chr6:76331194-76331527(+)$1	333	154	163	22.5952
ggggg[eee	chr2:170487223-170487540(+)$1	317	42	51	19.1428
^^^^^^^^^	chr12:124071305-124071575(+)$1	270	81	90	19.5000
DD?????EE	chr8:95676892-95677168(+)$1	276	222	231	22.5952
::ddddmmm	chr18:33724819-33725142(+)$1	323	28	37	15.0952

#DB
(((((((..	chr2:172582656-172582987(+)$1	1	34	43	18.3095
....))).)	chr10:94372735-94373009(+)$1	1	48	57	15.3333
...(((..(	chr10:70502102-70502428(+)$1	1	17	26	19.5000
...))))))	chr8:73939106-73939453(+)$1	1	206	215	18.0714
)..))))))	chr1:171535758-171536093(+)$1	1	303	312	22.5952
((((((...	chr7:91669952-91670287(+)$1	1	8	17	22.5952
.......((	chr16:53281250-53281552(+)$1	1	256	265	15.4523
.........	chr17:45646703-45647026(+)$1	1	278	287	22.5952
).)))))..	chr18:55912582-55912916(+)$1	1	324	333	22.5952
...))))).	chr10:75864706-75865041(+)$1	1	84	93	15.4523
((((..(((	chr2:233655430-233655702(+)$1	1	33	42	15.3333
..(((((((	chr5:151176790-151177093(+)$1	1	235	244	17.8333
(((((....	chrX:123034317-123034634(+)$1	1	13	22	18.7857
)))))))))	chr10:71129184-71129513(+)$1	1	318	327	22.5952
...((((..	chrX:123195004-123195336(+)$1	1	209	218	19.1428
)))))))))	chr20:47839789-47840115(+)$1	1	316	325	18.9047
(((((.(((	chr7:86803871-86804186(+)$1	1	24	33	19.2619
((((((...	chr14:89040929-89041268(+)$1	1	20	29	18.4285
.))))))))	chr17:48821026-48821356(+)$1	1	15	24	18.4285
)).......	chr18:662117-662570(+)$1	1	387	396	22.5952
...))..))	chrX:19376997-19377308(+)$1	1	298	307	15.8095
........(	chr14:56094559-56094921(+)$1	1	1	10	15.5714
......(((	chr14:94545775-94546040(+)$1	1	20	29	19.1428
))..)))))	chr7:33427603-33427857(+)$1	1	194	203	17.9523
.........	chr1:39494382-39494745(+)$1	1	284	293	22.5952
))).)))))	chrX:96638892-96639203(+)$1	1	209	218	18.5476
(.....(((	chr7:33397397-33397692(+)$1	1	9	18	22.5952
((((.....	chr4:57860759-57861051(+)$1	1	39	48	19.2619
)))......	chrX:96603067-96603448(+)$1	1	202	211	18.6666
).)))))))	chr12:98938691-98938943(+)$1	1	216	225	22.5952
))))).)))	chr14:92601679-92601978(+)$1	1	239	248	19.1428
.....((((	chr18:76886213-76886525(+)$1	1	4	13	18.0714
((((((...	chr2:190323432-190323739(+)$1	1	29	38	22.5952
(((((.(((	chr4:88973069-88973365(+)$1	1	60	69	16.0476
..)))))..	chr4:123797418-123797734(+)$1	1	38	47	17.9523
(((......	chr22:29682872-29683193(+)$1	1	9	18	22.5952
..)))))).	chr20:62626673-62626977(+)$1	1	211	220	19.5000
........)	chr6:76331194-76331527(+)$1	1	154	163	22.5952
(((((.(((	chr2:170487223-170487540(+)$1	1	42	51	19.1428
.........	chr12:124071305-124071575(+)$1	1	81	90	19.5000
)).....))	chr8:95676892-95677168(+)$1	1	222	231	22.5952
..((((...	chr18:33724819-33725142(+)$1	1	28	37	15.0952

#PSSM
U : 0.80	u : 0.14	C : 0.02	A : 0.02	
U : 0.73	u : 0.14	A : 0.04	G : 0.04	C : 0.02	
U : 0.83	u : 0.14	A : 0.02	
U : 0.71	u : 0.11	C : 0.07	G : 0.04	c : 0.02	A : 0.02	
U : 0.61	G : 0.11	u : 0.11	C : 0.07	A : 0.04	a : 0.02	
U : 0.64	u : 0.14	C : 0.09	G : 0.09	A : 0.02	
U : 0.80	u : 0.14	G : 0.04	
U : 0.85	u : 0.14	
U : 0.88	u : 0.11	

#score	811.3809523809525
#seq	42
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_CDS_m1_run2.nuc.txt

#NT
CAGA	chr9:117786228-117786450(-)$1	222	60	64	11.9999
CAGA	chr19:8056446-8056673(-)$1	227	58	62	11.9999
CAGA	chr3:52325719-52325972(+)$1	253	99	103	11.9999
CAGA	chr19:2037623-2037878(-)$1	255	116	120	11.9999
CAGA	chr7:120428558-120428787(-)$1	229	154	158	11.9999
CAGA	chr2:98408778-98409001(-)$1	223	3	7	11.9999
CAGA	chr17:8110488-8110721(-)$1	233	163	167	11.9999
CAGA	chr19:45494486-45494726(+)$1	240	6	10	11.9999
CAGA	chr1:94047985-94048216(-)$1	231	36	40	11.9999
CAGA	chrX:53230631-53230849(-)$1	218	20	24	11.9999
caga	chr2:242196110-242196321(-)$1	211	24	28	11.9999
CAGA	chr20:419159-419390(-)$1	231	165	169	11.9999
CAGA	chr1:6291903-6292130(-)$1	227	64	68	11.9999
CAGA	chr4:123151115-123151339(+)$1	224	86	90	11.9999
CAGA	chr4:174223121-174223356(+)$1	235	155	159	11.9999
CAGA	chr6:36653462-36653693(+)$1	231	62	66	11.9999
CAGA	chr11:62342641-62342874(-)$1	233	154	158	11.9999
CAGA	chr2:74597647-74597863(-)$1	216	195	199	11.9999
CAGA	chr4:55593914-55594146(+)$1	232	140	144	11.9999
CAGA	chr19:46190671-46190927(-)$1	256	135	139	11.9999
CAGA	chr13:46559572-46559798(-)$1	226	29	33	11.9999
CAGA	chr21:28306720-28306954(-)$1	234	56	60	11.9999
CAGA	chr9:34635527-34635791(-)$1	264	244	248	11.9999
CAGA	chr1:35447555-35447782(-)$1	227	169	173	11.9999
CAGA	chr5:141014362-141014587(-)$1	225	139	143	11.9999
CAGA	chr16:2223414-2223632(+)$1	218	64	68	11.9999
CAGA	chr19:10221344-10221599(+)$1	255	25	29	11.9999
CAGA	chr8:55060168-55060399(+)$1	231	9	13	11.9999
CAGA	chr8:21995751-21996004(-)$1	253	152	156	11.9999
CAGA	chr1:101455979-101456233(-)$1	254	99	103	11.9999
CAGA	chr19:39926389-39926632(-)$1	243	6	10	11.9999
CAGA	chr19:50880768-50880992(+)$1	224	179	183	11.9999
CAGA	chr10:98715218-98715457(+)$1	239	99	103	11.9999
CAGA	chr11:9609952-9610194(+)$1	242	40	44	11.9999
CAGA	chr17:78188313-78188554(-)$1	241	124	128	11.9999
CAGA	chr14:86088293-86088512(+)$1	219	165	169	11.9999
CAGA	chr19:33696765-33696986(+)$1	221	88	92	11.9999
CAGA	chr1:226566790-226567017(-)$1	227	204	208	11.9999
CAGA	chr5:114878572-114878807(-)$1	235	134	138	11.9999
CAGA	chr3:197553648-197553862(+)$1	214	97	101	11.9999
CAGA	chr20:5166345-5166568(+)$1	223	166	170	11.9999
CAGA	chr11:17190365-17190590(-)$1	225	2	6	11.9999
CAGA	chr12:14943452-14943678(-)$1	226	37	41	11.9999
caga	chr10:70951380-70951604(+)$1	224	204	208	11.9999
CAGA	chr17:29508394-29508607(+)$1	213	42	46	11.9999
CAGA	chr20:47887927-47888155(-)$1	228	151	155	11.9999
CAGA	chr8:23106760-23106989(+)$1	229	143	147	11.9999
CAGA	chr10:49628123-49628372(+)$1	249	196	200	11.9999
CAGA	chr3:9488758-9489004(+)$1	246	62	66	11.9999
CAGA	chr8:2048671-2048904(+)$1	233	143	147	11.9999
CAGA	chr7:102963112-102963338(-)$1	226	125	129	11.9999
CAGA	chr7:64852755-64852977(+)$1	222	166	170	11.9999
CAGA	chr2:24991038-24991268(+)$1	230	10	14	11.9999
CAGA	chr17:79846966-79847229(-)$1	263	100	104	11.9999
CAGA	chr15:23060716-23060947(-)$1	231	53	57	11.9999
CAGA	chr1:1500156-1500391(-)$1	235	201	205	11.9999
CAGA	chr17:17174008-17174221(-)$1	213	3	7	11.9999
CAGA	chr12:62918220-62918442(+)$1	222	123	127	11.9999
CAGA	chr6:27777952-27778181(+)$1	229	64	68	11.9999
CAGA	chr3:129023405-129023628(+)$1	223	50	54	11.9999
CAGA	chr14:56763610-56763850(+)$1	240	157	161	11.9999
CAGA	chr7:87011305-87011530(+)$1	225	88	92	11.9999
CAGA	chr17:41246542-41246778(-)$1	236	3	7	11.9999
CAGA	chr1:76253113-76253345(+)$1	232	14	18	11.9999
CAGA	chr12:56998431-56998662(-)$1	231	137	141	11.9999
CAGA	chr3:56680514-56680735(-)$1	221	66	70	11.9999
CAGA	chr5:134131586-134131812(+)$1	226	88	92	11.9999
CAGA	chr1:52257948-52258163(-)$1	215	208	212	11.9999
CAGA	chr17:45773475-45773710(+)$1	235	230	234	11.9999
CAGA	chr1:76215036-76215267(+)$1	231	92	96	11.9999
CAGA	chr5:5461194-5461417(+)$1	223	10	14	11.9999
CAGA	chr4:138452992-138453214(-)$1	222	83	87	11.9999
CAGA	chr16:31091334-31091553(+)$1	219	68	72	11.9999
CAGA	chr1:11137370-11137600(-)$1	230	16	20	11.9999
CAGA	chrX:99887383-99887636(-)$1	253	105	109	11.9999
CAGA	chr6:26156842-26157074(+)$1	232	58	62	11.9999
CAGA	chr22:51041646-51041871(+)$1	225	180	184	11.9999

#otherMatches

#Struct PSSM
qqqd	chr6:29576316-29576547(-)$1	231	44	48	11.9999
fff[	chr9:117786228-117786450(-)$1	222	60	64	11.9999
ccc:	chr19:8056446-8056673(-)$1	227	58	62	11.9999
eee[	chr3:52325719-52325972(+)$1	253	99	103	11.9999
e"""	chr19:2037623-2037878(-)$1	255	116	120	11.9999
ddd>	chr7:120428558-120428787(-)$1	229	154	158	11.9999
::::	chr2:98408778-98409001(-)$1	223	3	7	11.9999
qqbb	chr17:8110488-8110721(-)$1	233	163	167	11.9999
:iii	chr19:45494486-45494726(+)$1	240	6	10	11.9999
::::	chr1:94047985-94048216(-)$1	231	36	40	11.9999
[bb"	chrX:53230631-53230849(-)$1	218	20	24	11.9999
dd33	chr2:242196110-242196321(-)$1	211	24	28	11.9999
CCC:	chr20:419159-419390(-)$1	231	165	169	11.9999
[ddd	chr1:6291903-6292130(-)$1	227	64	68	11.9999
hhh]	chr4:123151115-123151339(+)$1	224	86	90	11.9999
ccmm	chr4:174223121-174223356(+)$1	235	155	159	11.9999
dddd	chr6:36653462-36653693(+)$1	231	62	66	11.9999
dd[c	chr11:62342641-62342874(-)$1	233	154	158	11.9999
eee]	chr2:74597647-74597863(-)$1	216	195	199	11.9999
ff::	chr4:55593914-55594146(+)$1	232	140	144	11.9999
eee:	chr19:46190671-46190927(-)$1	256	135	139	11.9999
b:cc	chr13:46559572-46559798(-)$1	226	29	33	11.9999
eeee	chr21:28306720-28306954(-)$1	234	56	60	11.9999
mmdd	chr9:34635527-34635791(-)$1	264	244	248	11.9999
oooo	chr1:35447555-35447782(-)$1	227	169	173	11.9999
::::	chr5:141014362-141014587(-)$1	225	139	143	11.9999
dd[a	chr16:2223414-2223632(+)$1	218	64	68	11.9999
fff(	chr19:10221344-10221599(+)$1	255	25	29	11.9999
{HHH	chr8:55060168-55060399(+)$1	231	9	13	11.9999
ddd]	chr8:21995751-21996004(-)$1	253	152	156	11.9999
::::	chr1:101455979-101456233(-)$1	254	99	103	11.9999
IIII	chr19:39926389-39926632(-)$1	243	6	10	11.9999
FFF:	chr19:50880768-50880992(+)$1	224	179	183	11.9999
fffl	chr10:98715218-98715457(+)$1	239	99	103	11.9999
]ggg	chr11:9609952-9610194(+)$1	242	40	44	11.9999
oooo	chr17:78188313-78188554(-)$1	241	124	128	11.9999
ccc3	chr14:86088293-86088512(+)$1	219	165	169	11.9999
cc[c	chr19:33696765-33696986(+)$1	221	88	92	11.9999
IIII	chr1:226566790-226567017(-)$1	227	204	208	11.9999
[ggg	chr5:114878572-114878807(-)$1	235	134	138	11.9999
====	chr3:197553648-197553862(+)$1	214	97	101	11.9999
JJJJ	chr20:5166345-5166568(+)$1	223	166	170	11.9999
::::	chr11:17190365-17190590(-)$1	225	2	6	11.9999
gggg	chr12:14943452-14943678(-)$1	226	37	41	11.9999
hhhh	chr10:70951380-70951604(+)$1	224	204	208	11.9999
lggg	chr17:29508394-29508607(+)$1	213	42	46	11.9999
ddd]	chr20:47887927-47888155(-)$1	228	151	155	11.9999
gggg	chr8:23106760-23106989(+)$1	229	143	147	11.9999
3bb]	chr10:49628123-49628372(+)$1	249	196	200	11.9999
JJJJ	chr3:9488758-9489004(+)$1	246	62	66	11.9999
::bb	chr8:2048671-2048904(+)$1	233	143	147	11.9999
bqqq	chr7:102963112-102963338(-)$1	226	125	129	11.9999
cccm	chr7:64852755-64852977(+)$1	222	166	170	11.9999
cc""	chr2:24991038-24991268(+)$1	230	10	14	11.9999
GGGG	chr17:79846966-79847229(-)$1	263	100	104	11.9999
fff"	chr15:23060716-23060947(-)$1	231	53	57	11.9999
:ddd	chr1:1500156-1500391(-)$1	235	201	205	11.9999
::::	chr17:17174008-17174221(-)$1	213	3	7	11.9999
dddd	chr12:62918220-62918442(+)$1	222	123	127	11.9999
oooo	chr6:27777952-27778181(+)$1	229	64	68	11.9999
ff!!	chr3:129023405-129023628(+)$1	223	50	54	11.9999
CCC}	chr14:56763610-56763850(+)$1	240	157	161	11.9999
:ggg	chr7:87011305-87011530(+)$1	225	88	92	11.9999
::::	chr17:41246542-41246778(-)$1	236	3	7	11.9999
dddp	chr1:76253113-76253345(+)$1	232	14	18	11.9999
fff]	chr12:56998431-56998662(-)$1	231	137	141	11.9999
ee]b	chr3:56680514-56680735(-)$1	221	66	70	11.9999
FFFF	chr5:134131586-134131812(+)$1	226	88	92	11.9999
EEE:	chr1:52257948-52258163(-)$1	215	208	212	11.9999
EEE:	chr17:45773475-45773710(+)$1	235	230	234	11.9999
dd[b	chr1:76215036-76215267(+)$1	231	92	96	11.9999
FFF{	chr5:5461194-5461417(+)$1	223	10	14	11.9999
cc22	chr4:138452992-138453214(-)$1	222	83	87	11.9999
KKEE	chr16:31091334-31091553(+)$1	219	68	72	11.9999
leee	chr1:11137370-11137600(-)$1	230	16	20	11.9999
ccc]	chrX:99887383-99887636(-)$1	253	105	109	11.9999
mmmd	chr6:26156842-26157074(+)$1	232	58	62	11.9999
ccc]	chr22:51041646-51041871(+)$1	225	180	184	11.9999

#DB
...)	chr6:29576316-29576547(-)$1	1	44	48	11.9999
(((.	chr9:117786228-117786450(-)$1	1	60	64	11.9999
))).	chr19:8056446-8056673(-)$1	1	58	62	11.9999
(((.	chr3:52325719-52325972(+)$1	1	99	103	11.9999
(...	chr19:2037623-2037878(-)$1	1	116	120	11.9999
))).	chr7:120428558-120428787(-)$1	1	154	158	11.9999
....	chr2:98408778-98409001(-)$1	1	3	7	11.9999
..))	chr17:8110488-8110721(-)$1	1	163	167	11.9999
.(((	chr19:45494486-45494726(+)$1	1	6	10	11.9999
....	chr1:94047985-94048216(-)$1	1	36	40	11.9999
.((.	chrX:53230631-53230849(-)$1	1	20	24	11.9999
))..	chr2:242196110-242196321(-)$1	1	24	28	11.9999
))).	chr20:419159-419390(-)$1	1	165	169	11.9999
.(((	chr1:6291903-6292130(-)$1	1	64	68	11.9999
))).	chr4:123151115-123151339(+)$1	1	86	90	11.9999
((..	chr4:174223121-174223356(+)$1	1	155	159	11.9999
))))	chr6:36653462-36653693(+)$1	1	62	66	11.9999
((.(	chr11:62342641-62342874(-)$1	1	154	158	11.9999
))).	chr2:74597647-74597863(-)$1	1	195	199	11.9999
))..	chr4:55593914-55594146(+)$1	1	140	144	11.9999
))).	chr19:46190671-46190927(-)$1	1	135	139	11.9999
).((	chr13:46559572-46559798(-)$1	1	29	33	11.9999
))))	chr21:28306720-28306954(-)$1	1	56	60	11.9999
..))	chr9:34635527-34635791(-)$1	1	244	248	11.9999
....	chr1:35447555-35447782(-)$1	1	169	173	11.9999
....	chr5:141014362-141014587(-)$1	1	139	143	11.9999
((.(	chr16:2223414-2223632(+)$1	1	64	68	11.9999
(((.	chr19:10221344-10221599(+)$1	1	25	29	11.9999
.(((	chr8:55060168-55060399(+)$1	1	9	13	11.9999
))).	chr8:21995751-21996004(-)$1	1	152	156	11.9999
....	chr1:101455979-101456233(-)$1	1	99	103	11.9999
((((	chr19:39926389-39926632(-)$1	1	6	10	11.9999
))).	chr19:50880768-50880992(+)$1	1	179	183	11.9999
(((.	chr10:98715218-98715457(+)$1	1	99	103	11.9999
.)))	chr11:9609952-9610194(+)$1	1	40	44	11.9999
....	chr17:78188313-78188554(-)$1	1	124	128	11.9999
))).	chr14:86088293-86088512(+)$1	1	165	169	11.9999
((.(	chr19:33696765-33696986(+)$1	1	88	92	11.9999
))))	chr1:226566790-226567017(-)$1	1	204	208	11.9999
.(((	chr5:114878572-114878807(-)$1	1	134	138	11.9999
))))	chr3:197553648-197553862(+)$1	1	97	101	11.9999
))))	chr20:5166345-5166568(+)$1	1	166	170	11.9999
....	chr11:17190365-17190590(-)$1	1	2	6	11.9999
((((	chr12:14943452-14943678(-)$1	1	37	41	11.9999
((((	chr10:70951380-70951604(+)$1	1	204	208	11.9999
.)))	chr17:29508394-29508607(+)$1	1	42	46	11.9999
))).	chr20:47887927-47888155(-)$1	1	151	155	11.9999
((((	chr8:23106760-23106989(+)$1	1	143	147	11.9999
.)).	chr10:49628123-49628372(+)$1	1	196	200	11.9999
((((	chr3:9488758-9489004(+)$1	1	62	66	11.9999
..((	chr8:2048671-2048904(+)$1	1	143	147	11.9999
(...	chr7:102963112-102963338(-)$1	1	125	129	11.9999
(((.	chr7:64852755-64852977(+)$1	1	166	170	11.9999
((..	chr2:24991038-24991268(+)$1	1	10	14	11.9999
))))	chr17:79846966-79847229(-)$1	1	100	104	11.9999
(((.	chr15:23060716-23060947(-)$1	1	53	57	11.9999
.(((	chr1:1500156-1500391(-)$1	1	201	205	11.9999
....	chr17:17174008-17174221(-)$1	1	3	7	11.9999
))))	chr12:62918220-62918442(+)$1	1	123	127	11.9999
....	chr6:27777952-27778181(+)$1	1	64	68	11.9999
((..	chr3:129023405-129023628(+)$1	1	50	54	11.9999
))).	chr14:56763610-56763850(+)$1	1	157	161	11.9999
.(((	chr7:87011305-87011530(+)$1	1	88	92	11.9999
....	chr17:41246542-41246778(-)$1	1	3	7	11.9999
(((.	chr1:76253113-76253345(+)$1	1	14	18	11.9999
))).	chr12:56998431-56998662(-)$1	1	137	141	11.9999
)).)	chr3:56680514-56680735(-)$1	1	66	70	11.9999
((((	chr5:134131586-134131812(+)$1	1	88	92	11.9999
))).	chr1:52257948-52258163(-)$1	1	208	212	11.9999
))).	chr17:45773475-45773710(+)$1	1	230	234	11.9999
((.(	chr1:76215036-76215267(+)$1	1	92	96	11.9999
(((.	chr5:5461194-5461417(+)$1	1	10	14	11.9999
))..	chr4:138452992-138453214(-)$1	1	83	87	11.9999
..((	chr16:31091334-31091553(+)$1	1	68	72	11.9999
.)))	chr1:11137370-11137600(-)$1	1	16	20	11.9999
))).	chrX:99887383-99887636(-)$1	1	105	109	11.9999
...)	chr6:26156842-26157074(+)$1	1	58	62	11.9999
))).	chr22:51041646-51041871(+)$1	1	180	184	11.9999

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

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m1_run2.nuc.txt

#NT
ACAAGUAUUUGCCAGUAGACAGCUGCCAUAUUUAUUCAUAAAUGCAAUUAAUUGAGAUUUAGUAUCUAACCUCAAAAUCAGUAUAUGACUUUACCUGCCAAGAUGCUAAAGUUGUUUUCCAUCCUGGAAAUUUACAUGUCUGUUUUCCUUAACACAGUUCCAAAGGAUGGCCUCAAAAGCCAGGCUGCAUUUGAAGAAAUGAGGACAAAUUACAUCAAAGAACUGAGGAAGAUGGUAACUAAGUGUCCCAACAAUUCU	chr4:149035310-149035569(-)$1	259	0	258	326.5000

#otherMatches

#Struct PSSM
::::cccffffff####ccc[ddddllldddd22cccffffff]cccFFFFFFffffff$$$$$ffffffpppppppffffffffffff:::FFFFFF{FFFFFF:bb[dddd[cccuuuuuuuuuuuuccc]dddd]bb:cccddddllldddd333ccc::FFFFFFZZZFFFFFF::ddddbbddddqqqqqqqqdddd]bb]ddddggggggglllgggggggFFFFFF:ccc[eeeeellleeeee]ccc:::	chr16:18816646-18816905(-)$1	259	0	258	326.5000
CCCKKBB{FFFFFF:FFFFFF::ccc"""eeeeemmmmeeeeeccc:::::::::::==========%%%%%%ccc[cccnnnnnccc]ccc88888888==========bb"""fffffflllffffff333bb:FFFFFFGGGGGGGNNNNNFFFFFFNNNNNDDDDddddqqqqqqqqdddd::eeeeemmmmeeeee:::::::::::DDDDZZZFFFFFFGGGGGGGFFFFFF}BBYYCCC::::::::::::	chr4:149035310-149035569(-)$1	259	0	258	326.5000

#DB
....(((((((((....(((.((((...))))..))))))))).)))((((((((((((.....((((((.......))))))))))))...((((((.((((((.((.((((.(((............))).)))).)).(((((((...))))...)))..))))))...))))))..((((((((((........)))).)).))))(((((((...))))))))))))).(((.(((((...))))).)))...	chr16:18816646-18816905(-)$1	1	0	258	326.5000
(((..((.((((((.((((((..(((...(((((....))))))))...........((((((((((......(((.(((.....))).)))........))))))))))((...((((((...))))))...)).))))))(((((((.....((((((.....((((((((........))))..(((((....)))))...........))))...))))))))))))))))))).))..)))............	chr4:149035310-149035569(-)$1	1	0	258	326.5000

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

#score	653.0
#seq	2
#width	258
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m3_run1.nuc.txt

#NT

#otherMatches

#Struct PSSM
{CCC::::iiiiiiiii"""a[ddddnnnnndddd]a333iiiiiiiiieeeee!!iiiiiiiiitttttttttttiiiiiiiiieeeee:::ffffff[bbmmmmbb]ffffff::::::CCC}CCC}CCCFFFFFFEEEEE}EEEEE::::::::::::::hhhhhhhh[a[ffffff[cccooooooccc]ffffffahhhhhhhhFFFFFF::::::::::dddd[hhhhhhhh[eeeee[annnnna]eeeee]hhhhhhhh22dddd:::::::::::::::::::::::::::::::	chr3:150177001-150177425(+)$1	424	85	389	912.0000

#DB
.(((....(((((((((...(.((((.....)))).)...)))))))))(((((..(((((((((...........))))))))))))))...((((((.((....)).))))))......))).))).)))))))))))))).)))))..............((((((((.(.((((((.(((......))).)))))))))))))))))))))..........((((.((((((((.(((((.(.....).))))).))))))))..))))...............................	chr3:150177001-150177425(+)$1	1	85	389	912.0000

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

#score	912.0
#seq	1
#width	304
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m2_run1.nuc.txt

#NT
UGCU	chr5:148874786-148875028(-)$1	242	127	131	11.9999
UGCU	chr1:16266692-16266925(+)$1	233	73	77	11.9999
UGCU	chr1:244220638-244220866(+)$1	228	59	63	11.9999
UGCU	chr17:35294906-35295159(+)$1	253	2	6	11.9999
UGCU	chr6:20492561-20492792(+)$1	231	225	229	11.9999
UGCU	chr17:79478336-79478588(-)$1	252	221	225	11.9999
UGCU	chr1:16721645-16721929(+)$1	284	16	20	11.9999
UGCU	chr2:10194687-10194934(+)$1	247	58	62	11.9999
UGCU	chr3:38526259-38526485(+)$1	226	171	175	11.9999
UGCU	chr9:74298531-74298753(-)$1	222	108	112	11.9999
UGCU	chr17:38175378-38175603(-)$1	225	25	29	11.9999
UGCU	chr17:74732016-74732249(-)$1	233	118	122	11.9999
UGCU	chr17:61898864-61899090(-)$1	226	95	99	11.9999
UGCU	chr7:27181234-27181495(-)$1	261	221	225	11.9999
ugcu	chr1:42643284-42643539(-)$1	255	70	74	11.9999
UGCU	chr18:3458008-3458242(+)$1	234	38	42	11.9999
UGCU	chr17:7833773-7834002(-)$1	229	215	219	11.9999
UGCU	chr1:6281449-6281700(-)$1	251	57	61	11.9999
ugcu	chr19:4047187-4047418(-)$1	231	161	165	11.9999
UGCU	chr1:204374518-204374766(-)$1	248	68	72	11.9999
UGCU	chr11:126132779-126133019(-)$1	240	45	49	11.9999
UGCU	chr11:8705701-8705941(+)$1	240	25	29	11.9999
UGCU	chr6:15522033-15522278(+)$1	245	33	37	11.9999
UGCU	chr9:138900854-138901126(-)$1	272	154	158	11.9999
UGCU	chr20:18464205-18464440(+)$1	235	118	122	11.9999
UGCU	chr2:99236248-99236481(-)$1	233	124	128	11.9999
UGCU	chr18:47008332-47008553(-)$1	221	75	79	11.9999
UGCU	chr5:154194281-154194549(+)$1	268	62	66	11.9999
UGCU	chr6:159057508-159057732(-)$1	224	114	118	11.9999
UGCU	chr1:112255069-112255312(+)$1	243	135	139	11.9999
UGCU	chr6:36654832-36655119(+)$1	287	40	44	11.9999
UGCU	chr16:53524700-53524958(+)$1	258	188	192	11.9999
UGCU	chr5:139494868-139495092(+)$1	224	114	118	11.9999
UGCU	chr2:109400945-109401179(+)$1	234	228	232	11.9999
UGCU	chr21:28296124-28296355(-)$1	231	79	83	11.9999
UGCU	chr16:18804410-18804670(-)$1	260	103	107	11.9999
UGCU	chr16:24836822-24837049(+)$1	227	21	25	11.9999
UGCU	chr14:61177191-61177426(-)$1	235	104	108	11.9999
UGCU	chr11:47489626-47489869(-)$1	243	172	176	11.9999
UGCU	chr18:19445862-19446090(+)$1	228	114	118	11.9999
UGCU	chr1:46713563-46713794(+)$1	231	3	7	11.9999
UGCU	chr12:49521537-49521814(-)$1	277	106	110	11.9999
UGCU	chr9:113018594-113018855(-)$1	261	82	86	11.9999
UGCU	chr3:23961437-23961681(+)$1	244	188	192	11.9999
UGCU	chr17:46128136-46128404(+)$1	268	171	175	11.9999
UGCU	chr18:77662488-77662719(-)$1	231	126	130	11.9999
UGCU	chr9:134373335-134373588(+)$1	253	119	123	11.9999
UGCU	chr11:19245689-19245923(-)$1	234	72	76	11.9999
UGCU	chr2:120021039-120021260(+)$1	221	188	192	11.9999
UGCU	chr12:56632569-56632812(-)$1	243	20	24	11.9999
UGCU	chr3:63987962-63988205(+)$1	243	111	115	11.9999
UGCU	chr15:101812513-101812762(-)$1	249	30	34	11.9999
UGCU	chr12:6602262-6602498(-)$1	236	169	173	11.9999
UGCU	chr14:21820243-21820501(-)$1	258	158	162	11.9999
UGCU	chr5:153854584-153854829(-)$1	245	167	171	11.9999
UGCU	chr6:158929569-158929794(+)$1	225	99	103	11.9999
UGCU	chr20:33096866-33097104(+)$1	238	91	95	11.9999
UGCU	chr2:85771838-85772105(+)$1	267	99	103	11.9999
UGCU	chr5:43289912-43290135(-)$1	223	114	118	11.9999
UGCU	chr15:73925398-73925688(-)$1	290	121	125	11.9999
UGCU	chr1:203277241-203277484(+)$1	243	68	72	11.9999
UGCU	chr1:101446074-101446297(+)$1	223	174	178	11.9999
UGCU	chr6:26055893-26056141(-)$1	248	48	52	11.9999
UGCU	chr7:27202596-27202846(-)$1	250	56	60	11.9999
UGCU	chr20:5171592-5171827(+)$1	235	94	98	11.9999
UGCU	chr7:27180858-27181093(-)$1	235	106	110	11.9999
UGCU	chr12:8249758-8249989(+)$1	231	107	111	11.9999
UGCU	chr1:47842913-47843173(+)$1	260	30	34	11.9999
UGCU	chr1:35649494-35649727(-)$1	233	32	36	11.9999
UGCU	chr1:1169076-1169314(+)$1	238	120	124	11.9999
UGCU	chr4:53732800-53733043(+)$1	243	17	21	11.9999
ugcu	chr11:2159776-2160062(-)$1	286	16	20	11.9999
UGCU	chr1:185278441-185278680(-)$1	239	231	235	11.9999
UGCU	chr6:109688014-109688247(-)$1	233	165	169	11.9999
UGCU	chr4:169848079-169848301(+)$1	222	101	105	11.9999
UGCU	chr6:18225773-18226001(-)$1	228	175	179	11.9999
UGCU	chr22:37964685-37964925(+)$1	240	111	115	11.9999
UGCU	chr1:115292352-115292579(-)$1	227	77	81	11.9999
UGCU	chr1:155106905-155107173(+)$1	268	70	74	11.9999

#otherMatches

#Struct PSSM
[ddd	chr11:4127304-4127536(+)$1	232	42	46	11.9999
ffff	chr5:148874786-148875028(-)$1	242	127	131	11.9999
pppp	chr1:16266692-16266925(+)$1	233	73	77	11.9999
gggg	chr1:244220638-244220866(+)$1	228	59	63	11.9999
{BB:	chr17:35294906-35295159(+)$1	253	2	6	11.9999
E}CC	chr6:20492561-20492792(+)$1	231	225	229	11.9999
hccc	chr17:79478336-79478588(-)$1	252	221	225	11.9999
mbb]	chr1:16721645-16721929(+)$1	284	16	20	11.9999
qqqq	chr2:10194687-10194934(+)$1	247	58	62	11.9999
ccc5	chr3:38526259-38526485(+)$1	226	171	175	11.9999
:bb[	chr9:74298531-74298753(-)$1	222	108	112	11.9999
tttt	chr17:38175378-38175603(-)$1	225	25	29	11.9999
dddd	chr17:74732016-74732249(-)$1	233	118	122	11.9999
!!a[	chr17:61898864-61899090(-)$1	226	95	99	11.9999
!bbn	chr7:27181234-27181495(-)$1	261	221	225	11.9999
====	chr1:42643284-42643539(-)$1	255	70	74	11.9999
DD::	chr18:3458008-3458242(+)$1	234	38	42	11.9999
2bb:	chr17:7833773-7834002(-)$1	229	215	219	11.9999
d]cc	chr1:6281449-6281700(-)$1	251	57	61	11.9999
d22f	chr19:4047187-4047418(-)$1	231	161	165	11.9999
ccc(	chr1:204374518-204374766(-)$1	248	68	72	11.9999
eeee	chr11:126132779-126133019(-)$1	240	45	49	11.9999
sccc	chr11:8705701-8705941(+)$1	240	25	29	11.9999
GG{B	chr6:15522033-15522278(+)$1	245	33	37	11.9999
c"""	chr9:138900854-138901126(-)$1	272	154	158	11.9999
cggg	chr20:18464205-18464440(+)$1	235	118	122	11.9999
dd[f	chr2:99236248-99236481(-)$1	233	124	128	11.9999
gqqq	chr18:47008332-47008553(-)$1	221	75	79	11.9999
ooee	chr5:154194281-154194549(+)$1	268	62	66	11.9999
GGGG	chr6:159057508-159057732(-)$1	224	114	118	11.9999
dd[c	chr1:112255069-112255312(+)$1	243	135	139	11.9999
fffn	chr6:36654832-36655119(+)$1	287	40	44	11.9999
ffff	chr16:53524700-53524958(+)$1	258	188	192	11.9999
dd::	chr5:139494868-139495092(+)$1	224	114	118	11.9999
::::	chr2:109400945-109401179(+)$1	234	228	232	11.9999
b]gg	chr21:28296124-28296355(-)$1	231	79	83	11.9999
ddd[	chr16:18804410-18804670(-)$1	260	103	107	11.9999
ffff	chr16:24836822-24837049(+)$1	227	21	25	11.9999
cc33	chr14:61177191-61177426(-)$1	235	104	108	11.9999
::::	chr11:47489626-47489869(-)$1	243	172	176	11.9999
::::	chr18:19445862-19446090(+)$1	228	114	118	11.9999
CCC{	chr1:46713563-46713794(+)$1	231	3	7	11.9999
eeee	chr12:49521537-49521814(-)$1	277	106	110	11.9999
ffff	chr9:113018594-113018855(-)$1	261	82	86	11.9999
ffff	chr3:23961437-23961681(+)$1	244	188	192	11.9999
pppp	chr17:46128136-46128404(+)$1	268	171	175	11.9999
FBBY	chr18:77662488-77662719(-)$1	231	126	130	11.9999
4bb5	chr9:134373335-134373588(+)$1	253	119	123	11.9999
ffff	chr11:19245689-19245923(-)$1	234	72	76	11.9999
BB}F	chr2:120021039-120021260(+)$1	221	188	192	11.9999
bb33	chr12:56632569-56632812(-)$1	243	20	24	11.9999
g]cc	chr3:63987962-63988205(+)$1	243	111	115	11.9999
====	chr15:101812513-101812762(-)$1	249	30	34	11.9999
a[bb	chr12:6602262-6602498(-)$1	236	169	173	11.9999
dddd	chr14:21820243-21820501(-)$1	258	158	162	11.9999
pppp	chr5:153854584-153854829(-)$1	245	167	171	11.9999
[ccc	chr6:158929569-158929794(+)$1	225	99	103	11.9999
ccc"	chr20:33096866-33097104(+)$1	238	91	95	11.9999
dddd	chr2:85771838-85772105(+)$1	267	99	103	11.9999
e[bb	chr5:43289912-43290135(-)$1	223	114	118	11.9999
::::	chr15:73925398-73925688(-)$1	290	121	125	11.9999
gg[g	chr1:203277241-203277484(+)$1	243	68	72	11.9999
ffff	chr1:101446074-101446297(+)$1	223	174	178	11.9999
hhhh	chr6:26055893-26056141(-)$1	248	48	52	11.9999
mmmf	chr7:27202596-27202846(-)$1	250	56	60	11.9999
:bb[	chr20:5171592-5171827(+)$1	235	94	98	11.9999
ddd4	chr7:27180858-27181093(-)$1	235	106	110	11.9999
mmme	chr12:8249758-8249989(+)$1	231	107	111	11.9999
:DDD	chr1:47842913-47843173(+)$1	260	30	34	11.9999
FFFF	chr1:35649494-35649727(-)$1	233	32	36	11.9999
d:bb	chr1:1169076-1169314(+)$1	238	120	124	11.9999
:ccc	chr4:53732800-53733043(+)$1	243	17	21	11.9999
dddn	chr11:2159776-2160062(-)$1	286	16	20	11.9999
FFF:	chr1:185278441-185278680(-)$1	239	231	235	11.9999
:::f	chr6:109688014-109688247(-)$1	233	165	169	11.9999
>>>>	chr4:169848079-169848301(+)$1	222	101	105	11.9999
hhhh	chr6:18225773-18226001(-)$1	228	175	179	11.9999
eeee	chr22:37964685-37964925(+)$1	240	111	115	11.9999
eeee	chr1:115292352-115292579(-)$1	227	77	81	11.9999
====	chr1:155106905-155107173(+)$1	268	70	74	11.9999

#DB
.(((	chr11:4127304-4127536(+)$1	1	42	46	11.9999
))))	chr5:148874786-148875028(-)$1	1	127	131	11.9999
....	chr1:16266692-16266925(+)$1	1	73	77	11.9999
))))	chr1:244220638-244220866(+)$1	1	59	63	11.9999
.((.	chr17:35294906-35295159(+)$1	1	2	6	11.9999
).))	chr6:20492561-20492792(+)$1	1	225	229	11.9999
))))	chr17:79478336-79478588(-)$1	1	221	225	11.9999
.)).	chr1:16721645-16721929(+)$1	1	16	20	11.9999
....	chr2:10194687-10194934(+)$1	1	58	62	11.9999
))).	chr3:38526259-38526485(+)$1	1	171	175	11.9999
.((.	chr9:74298531-74298753(-)$1	1	108	112	11.9999
....	chr17:38175378-38175603(-)$1	1	25	29	11.9999
((((	chr17:74732016-74732249(-)$1	1	118	122	11.9999
..(.	chr17:61898864-61899090(-)$1	1	95	99	11.9999
.((.	chr7:27181234-27181495(-)$1	1	221	225	11.9999
((((	chr1:42643284-42643539(-)$1	1	70	74	11.9999
((..	chr18:3458008-3458242(+)$1	1	38	42	11.9999
.)).	chr17:7833773-7834002(-)$1	1	215	219	11.9999
).))	chr1:6281449-6281700(-)$1	1	57	61	11.9999
)..)	chr19:4047187-4047418(-)$1	1	161	165	11.9999
(((.	chr1:204374518-204374766(-)$1	1	68	72	11.9999
))))	chr11:126132779-126133019(-)$1	1	45	49	11.9999
.)))	chr11:8705701-8705941(+)$1	1	25	29	11.9999
((.(	chr6:15522033-15522278(+)$1	1	33	37	11.9999
(...	chr9:138900854-138901126(-)$1	1	154	158	11.9999
)(((	chr20:18464205-18464440(+)$1	1	118	122	11.9999
((.(	chr2:99236248-99236481(-)$1	1	124	128	11.9999
(...	chr18:47008332-47008553(-)$1	1	75	79	11.9999
..))	chr5:154194281-154194549(+)$1	1	62	66	11.9999
))))	chr6:159057508-159057732(-)$1	1	114	118	11.9999
((.(	chr1:112255069-112255312(+)$1	1	135	139	11.9999
(((.	chr6:36654832-36655119(+)$1	1	40	44	11.9999
((((	chr16:53524700-53524958(+)$1	1	188	192	11.9999
))..	chr5:139494868-139495092(+)$1	1	114	118	11.9999
....	chr2:109400945-109401179(+)$1	1	228	232	11.9999
).))	chr21:28296124-28296355(-)$1	1	79	83	11.9999
(((.	chr16:18804410-18804670(-)$1	1	103	107	11.9999
((((	chr16:24836822-24837049(+)$1	1	21	25	11.9999
))..	chr14:61177191-61177426(-)$1	1	104	108	11.9999
....	chr11:47489626-47489869(-)$1	1	172	176	11.9999
....	chr18:19445862-19446090(+)$1	1	114	118	11.9999
(((.	chr1:46713563-46713794(+)$1	1	3	7	11.9999
))))	chr12:49521537-49521814(-)$1	1	106	110	11.9999
))))	chr9:113018594-113018855(-)$1	1	82	86	11.9999
))))	chr3:23961437-23961681(+)$1	1	188	192	11.9999
....	chr17:46128136-46128404(+)$1	1	171	175	11.9999
))).	chr18:77662488-77662719(-)$1	1	126	130	11.9999
.)).	chr9:134373335-134373588(+)$1	1	119	123	11.9999
))))	chr11:19245689-19245923(-)$1	1	72	76	11.9999
)).)	chr2:120021039-120021260(+)$1	1	188	192	11.9999
))..	chr12:56632569-56632812(-)$1	1	20	24	11.9999
).))	chr3:63987962-63988205(+)$1	1	111	115	11.9999
((((	chr15:101812513-101812762(-)$1	1	30	34	11.9999
(.((	chr12:6602262-6602498(-)$1	1	169	173	11.9999
))))	chr14:21820243-21820501(-)$1	1	158	162	11.9999
....	chr5:153854584-153854829(-)$1	1	167	171	11.9999
.(((	chr6:158929569-158929794(+)$1	1	99	103	11.9999
(((.	chr20:33096866-33097104(+)$1	1	91	95	11.9999
((((	chr2:85771838-85772105(+)$1	1	99	103	11.9999
(.((	chr5:43289912-43290135(-)$1	1	114	118	11.9999
....	chr15:73925398-73925688(-)$1	1	121	125	11.9999
((.(	chr1:203277241-203277484(+)$1	1	68	72	11.9999
))))	chr1:101446074-101446297(+)$1	1	174	178	11.9999
((((	chr6:26055893-26056141(-)$1	1	48	52	11.9999
...)	chr7:27202596-27202846(-)$1	1	56	60	11.9999
.((.	chr20:5171592-5171827(+)$1	1	94	98	11.9999
))).	chr7:27180858-27181093(-)$1	1	106	110	11.9999
...)	chr12:8249758-8249989(+)$1	1	107	111	11.9999
.(((	chr1:47842913-47843173(+)$1	1	30	34	11.9999
((((	chr1:35649494-35649727(-)$1	1	32	36	11.9999
).((	chr1:1169076-1169314(+)$1	1	120	124	11.9999
.(((	chr4:53732800-53733043(+)$1	1	17	21	11.9999
(((.	chr11:2159776-2160062(-)$1	1	16	20	11.9999
))).	chr1:185278441-185278680(-)$1	1	231	235	11.9999
...(	chr6:109688014-109688247(-)$1	1	165	169	11.9999
....	chr4:169848079-169848301(+)$1	1	101	105	11.9999
))))	chr6:18225773-18226001(-)$1	1	175	179	11.9999
))))	chr22:37964685-37964925(+)$1	1	111	115	11.9999
))))	chr1:115292352-115292579(-)$1	1	77	81	11.9999
))))	chr1:155106905-155107173(+)$1	1	70	74	11.9999

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

#score	959.9999999999995
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m2_run2.nuc.txt

#NT

#otherMatches

#Struct PSSM
::::::DDDDhhhhhhhh!!bb[dddd!!bb$$$$$ddddmmmmddddbb22dddd]bb22hhhhhhhh::::::::FFFFFFPPPPPPPJJJJJJJJJJ::::::::::::gggggggbb!!dddd$$$$$ffffff[eeeeeuuuuuuuuuuuueeeee]ffffff]dddd22bb]gggggggeeeeemmmmeeeee:::::JJJJJJJJJJFFFFFFDDDD::::::::	chr6:88384883-88385117(-)$1	234	2	234	696.0000

#DB
......((((((((((((..((.((((..((.....((((....))))))..)))).))..))))))))........((((((.......((((((((((............(((((((((..((((.....((((((.(((((............))))).)))))).))))..)).)))))))(((((....))))).....))))))))))))))))))))........	chr6:88384883-88385117(-)$1	1	2	234	696.0000

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

#score	696.0
#seq	1
#width	232
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m2_run2.nuc.txt

#NT
CCUUC	chr4:1215476-1215716(-)$1	240	21	26	15.0000
CCUUC	chr3:113374079-113374307(-)$1	228	104	109	15.0000
ccUUC	chr17:26369872-26370164(+)$1	292	128	133	15.0000
CCUUC	chr14:24788980-24789226(-)$1	246	7	12	15.0000
CCUUC	chr22:32894099-32894384(+)$1	285	162	167	15.0000
CCUUC	chr14:100762130-100762405(-)$1	275	155	160	15.0000
CCUUC	chr11:66260194-66260423(+)$1	229	142	147	15.0000
CCUUC	chrX:44919758-44919987(+)$1	229	78	83	15.0000
CCUUC	chr17:65941779-65942076(+)$1	297	200	205	15.0000
CCUUC	chr3:101572152-101572437(+)$1	285	243	248	15.0000
CCUUC	chr7:104746928-104747159(+)$1	231	117	122	15.0000
CCUUC	chr6:28121530-28121810(+)$1	280	20	25	15.0000
CCUUC	chr3:49137093-49137335(-)$1	242	192	197	15.0000
CCUUC	chr1:198665767-198666018(+)$1	251	45	50	15.0000
CCUUC	chr12:133634092-133634325(+)$1	233	20	25	15.0000
CCUUC	chr14:75248294-75248563(+)$1	269	69	74	15.0000
CCUUC	chr11:59568227-59568472(+)$1	245	15	20	15.0000
CCUUC	chr5:81046581-81046918(-)$1	337	149	154	15.0000
ccuuc	chr12:2690745-2690964(+)$1	219	79	84	15.0000
CCUUC	chr17:78292981-78293258(+)$1	277	87	92	15.0000
CCUUC	chr5:137906729-137907000(-)$1	271	203	208	15.0000
CCUUC	chrX:70330003-70330260(-)$1	257	54	59	15.0000
CCUUC	chr3:53326492-53326767(-)$1	275	114	119	15.0000
CCUUC	chr16:89804380-89804615(-)$1	235	110	115	15.0000
CCUUC	chr1:243349171-243349395(-)$1	224	109	114	15.0000
CCUUC	chr19:16551480-16551720(-)$1	240	119	124	15.0000
CCUUC	chr10:38344444-38344784(+)$1	340	205	210	15.0000
CCUUC	chr1:203316352-203316569(-)$1	217	36	41	15.0000
CCUUC	chr1:39799670-39799912(+)$1	242	151	156	15.0000
CCUUC	chr19:10502171-10502400(-)$1	229	4	9	15.0000
CCUUC	chr1:150468857-150469085(+)$1	228	55	60	15.0000
CCUUC	chr12:977071-977361(+)$1	290	111	116	15.0000
CCUUC	chr19:17434165-17434438(-)$1	273	127	132	15.0000
CCUUC	chr1:151400556-151400807(-)$1	251	26	31	15.0000
CCUUC	chr12:108147615-108147868(-)$1	253	29	34	15.0000
CCUUC	chr16:67576772-67577015(+)$1	243	25	30	15.0000
CCUUC	chr5:180662269-180662503(+)$1	234	55	60	15.0000
CCUUC	chr10:38344201-38344476(+)$1	275	196	201	15.0000
CCUUC	chr8:94935336-94935576(+)$1	240	39	44	15.0000
CCUUC	chr16:22545729-22545989(+)$1	260	11	16	15.0000
CCUUC	chr10:93749124-93749354(+)$1	230	70	75	15.0000
CCUUC	chr5:134690669-134690972(-)$1	303	51	56	15.0000
CCUUC	chr10:38343949-38344282(+)$1	333	56	61	15.0000
CCUUC	chr6:26452468-26452739(+)$1	271	111	116	15.0000
CCUUC	chr2:24260830-24261071(-)$1	241	15	20	15.0000
CCUUC	chr13:39588087-39588384(-)$1	297	13	18	15.0000
CCUUC	chr6:45514552-45514858(+)$1	306	230	235	15.0000
CCUUC	chr19:19105762-19106015(-)$1	253	107	112	15.0000
CCUUC	chr9:15453038-15453272(+)$1	234	74	79	15.0000

#otherMatches

#Struct PSSM
g:eee	chr2:191844392-191844637(-)$1	245	70	75	15.0000
NNGGG	chr4:1215476-1215716(-)$1	240	21	26	15.0000
:::::	chr3:113374079-113374307(-)$1	228	104	109	15.0000
:::::	chr17:26369872-26370164(+)$1	292	128	133	15.0000
JJJJJ	chr14:24788980-24789226(-)$1	246	7	12	15.0000
GGGG:	chr22:32894099-32894384(+)$1	285	162	167	15.0000
[dddd	chr14:100762130-100762405(-)$1	275	155	160	15.0000
bbooo	chr11:66260194-66260423(+)$1	229	142	147	15.0000
ggggg	chrX:44919758-44919987(+)$1	229	78	83	15.0000
ddddl	chr17:65941779-65942076(+)$1	297	200	205	15.0000
gggg!	chr3:101572152-101572437(+)$1	285	243	248	15.0000
:::::	chr7:104746928-104747159(+)$1	231	117	122	15.0000
ggg[a	chr6:28121530-28121810(+)$1	280	20	25	15.0000
bbppp	chr3:49137093-49137335(-)$1	242	192	197	15.0000
]iiii	chr1:198665767-198666018(+)$1	251	45	50	15.0000
qqqqq	chr12:133634092-133634325(+)$1	233	20	25	15.0000
:::ff	chr14:75248294-75248563(+)$1	269	69	74	15.0000
:::::	chr11:59568227-59568472(+)$1	245	15	20	15.0000
hhhhh	chr5:81046581-81046918(-)$1	337	149	154	15.0000
iiiii	chr12:2690745-2690964(+)$1	219	79	84	15.0000
B::dd	chr17:78292981-78293258(+)$1	277	87	92	15.0000
:DDDD	chr5:137906729-137907000(-)$1	271	203	208	15.0000
ggggg	chrX:70330003-70330260(-)$1	257	54	59	15.0000
cDDDD	chr3:53326492-53326767(-)$1	275	114	119	15.0000
f[ggg	chr16:89804380-89804615(-)$1	235	110	115	15.0000
dffff	chr1:243349171-243349395(-)$1	224	109	114	15.0000
ggggg	chr19:16551480-16551720(-)$1	240	119	124	15.0000
$dddd	chr10:38344444-38344784(+)$1	340	205	210	15.0000
dd%%%	chr1:203316352-203316569(-)$1	217	36	41	15.0000
C:EEE	chr1:39799670-39799912(+)$1	242	151	156	15.0000
DDDDK	chr19:10502171-10502400(-)$1	229	4	9	15.0000
=nnnn	chr1:150468857-150469085(+)$1	228	55	60	15.0000
c::::	chr12:977071-977361(+)$1	290	111	116	15.0000
)))))	chr19:17434165-17434438(-)$1	273	127	132	15.0000
wffff	chr1:151400556-151400807(-)$1	251	26	31	15.0000
MMMMG	chr12:108147615-108147868(-)$1	253	29	34	15.0000
:::::	chr16:67576772-67577015(+)$1	243	25	30	15.0000
ggggg	chr5:180662269-180662503(+)$1	234	55	60	15.0000
nnddd	chr10:38344201-38344476(+)$1	275	196	201	15.0000
llldd	chr8:94935336-94935576(+)$1	240	39	44	15.0000
^^^^^	chr16:22545729-22545989(+)$1	260	11	16	15.0000
sssss	chr10:93749124-93749354(+)$1	230	70	75	15.0000
NNNNN	chr5:134690669-134690972(-)$1	303	51	56	15.0000
ffffm	chr10:38343949-38344282(+)$1	333	56	61	15.0000
FFeee	chr6:26452468-26452739(+)$1	271	111	116	15.0000
ldddd	chr2:24260830-24261071(-)$1	241	15	20	15.0000
:::::	chr13:39588087-39588384(-)$1	297	13	18	15.0000
###cc	chr6:45514552-45514858(+)$1	306	230	235	15.0000
biiii	chr19:19105762-19106015(-)$1	253	107	112	15.0000
cchhh	chr9:15453038-15453272(+)$1	234	74	79	15.0000

#DB
).(((	chr2:191844392-191844637(-)$1	1	70	75	15.0000
..(((	chr4:1215476-1215716(-)$1	1	21	26	15.0000
.....	chr3:113374079-113374307(-)$1	1	104	109	15.0000
.....	chr17:26369872-26370164(+)$1	1	128	133	15.0000
(((((	chr14:24788980-24789226(-)$1	1	7	12	15.0000
)))).	chr22:32894099-32894384(+)$1	1	162	167	15.0000
.((((	chr14:100762130-100762405(-)$1	1	155	160	15.0000
((...	chr11:66260194-66260423(+)$1	1	142	147	15.0000
)))))	chrX:44919758-44919987(+)$1	1	78	83	15.0000
((((.	chr17:65941779-65942076(+)$1	1	200	205	15.0000
((((.	chr3:101572152-101572437(+)$1	1	243	248	15.0000
.....	chr7:104746928-104747159(+)$1	1	117	122	15.0000
(((.(	chr6:28121530-28121810(+)$1	1	20	25	15.0000
((...	chr3:49137093-49137335(-)$1	1	192	197	15.0000
.))))	chr1:198665767-198666018(+)$1	1	45	50	15.0000
.....	chr12:133634092-133634325(+)$1	1	20	25	15.0000
...((	chr14:75248294-75248563(+)$1	1	69	74	15.0000
.....	chr11:59568227-59568472(+)$1	1	15	20	15.0000
(((((	chr5:81046581-81046918(-)$1	1	149	154	15.0000
(((((	chr12:2690745-2690964(+)$1	1	79	84	15.0000
(..((	chr17:78292981-78293258(+)$1	1	87	92	15.0000
.))))	chr5:137906729-137907000(-)$1	1	203	208	15.0000
)))))	chrX:70330003-70330260(-)$1	1	54	59	15.0000
)((((	chr3:53326492-53326767(-)$1	1	114	119	15.0000
(.(((	chr16:89804380-89804615(-)$1	1	110	115	15.0000
)((((	chr1:243349171-243349395(-)$1	1	109	114	15.0000
)))))	chr19:16551480-16551720(-)$1	1	119	124	15.0000
.((((	chr10:38344444-38344784(+)$1	1	205	210	15.0000
((...	chr1:203316352-203316569(-)$1	1	36	41	15.0000
).(((	chr1:39799670-39799912(+)$1	1	151	156	15.0000
((((.	chr19:10502171-10502400(-)$1	1	4	9	15.0000
(....	chr1:150468857-150469085(+)$1	1	55	60	15.0000
)....	chr12:977071-977361(+)$1	1	111	116	15.0000
.....	chr19:17434165-17434438(-)$1	1	127	132	15.0000
.))))	chr1:151400556-151400807(-)$1	1	26	31	15.0000
....(	chr12:108147615-108147868(-)$1	1	29	34	15.0000
.....	chr16:67576772-67577015(+)$1	1	25	30	15.0000
)))))	chr5:180662269-180662503(+)$1	1	55	60	15.0000
..)))	chr10:38344201-38344476(+)$1	1	196	201	15.0000
...))	chr8:94935336-94935576(+)$1	1	39	44	15.0000
.....	chr16:22545729-22545989(+)$1	1	11	16	15.0000
.....	chr10:93749124-93749354(+)$1	1	70	75	15.0000
.....	chr5:134690669-134690972(-)$1	1	51	56	15.0000
((((.	chr10:38343949-38344282(+)$1	1	56	61	15.0000
))(((	chr6:26452468-26452739(+)$1	1	111	116	15.0000
.))))	chr2:24260830-24261071(-)$1	1	15	20	15.0000
.....	chr13:39588087-39588384(-)$1	1	13	18	15.0000
...((	chr6:45514552-45514858(+)$1	1	230	235	15.0000
)))))	chr19:19105762-19106015(-)$1	1	107	112	15.0000
)))))	chr9:15453038-15453272(+)$1	1	74	79	15.0000

#PSSM
C : 0.96	c : 0.04	
C : 0.96	c : 0.04	
U : 0.98	u : 0.02	
U : 0.98	u : 0.02	
C : 0.98	c : 0.02	

#score	750.0000000000001
#seq	50
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m2_run2.nuc.txt

#NT
GCCGGG	chr6:3118958-3119179(-)$1	221	6	12	12.0566
GCCUGG	chr3:50141577-50141847(+)$1	270	55	61	12.4339
UCCAGG	chr10:70051823-70052044(+)$1	221	90	96	11.7735
ACCAGG	chr2:176945026-176945249(-)$1	223	14	20	11.5849
ACCAGG	chr12:48372040-48372265(-)$1	225	98	104	11.5849
GCCAGG	chr1:10713364-10713590(-)$1	226	108	114	14.7924
UCCAGG	chr9:140400006-140400230(-)$1	224	18	24	11.7735
GCCAGG	chr1:144339981-144340206(-)$1	225	45	51	14.7924
GCCUGG	chr20:2378500-2378722(+)$1	222	7	13	12.4339
CCCAGG	chr9:101006195-101006418(+)$1	223	92	98	11.6792
GCCCGG	chr14:21859520-21859741(+)$1	221	162	168	12.0566
UCCAGG	chr5:141313968-141314190(-)$1	222	85	91	11.7735
GCCCGG	chr20:50048546-50048772(-)$1	226	13	19	12.0566
GCCAGG	chr11:86382824-86383049(-)$1	225	44	50	14.7924
ACCAGG	chr2:109379920-109380146(+)$1	226	5	11	11.5849
GCCUGG	chr1:208061053-208061276(+)$1	223	87	93	12.4339
GCCAGG	chr17:26881367-26881590(+)$1	223	84	90	14.7924
CCCAGG	chr11:67262447-67262668(+)$1	221	89	95	11.6792
gccagg	chrX:100912303-100912525(-)$1	222	101	107	14.7924
CCCAGG	chr1:28948450-28948674(+)$1	224	8	14	11.6792
GCCAGG	chr3:184059736-184059959(-)$1	223	147	153	14.7924
CCCAGG	chr20:34568364-34568589(+)$1	225	11	17	11.6792
GCCGGG	chr10:134755473-134755697(+)$1	224	188	194	12.0566
GCCGGG	chr1:31897538-31897762(+)$1	224	15	21	12.0566
GCCAGG	chr16:69143571-69143792(+)$1	221	103	109	14.7924
UCCAGG	chr20:35672519-35672746(-)$1	227	220	226	11.7735
GCCUGG	chr8:119122727-119122950(+)$1	223	106	112	12.4339
GCCUGG	chr1:6636437-6636659(+)$1	222	133	139	12.4339
CCCAGG	chrX:72673394-72673619(-)$1	225	137	143	11.6792
UCCAGG	chr1:171752843-171753064(+)$1	221	31	37	11.7735
ACCAGG	chr19:5789498-5789719(+)$1	221	44	50	11.5849
GCCAGG	chr19:54967476-54967699(+)$1	223	197	203	14.7924
GCCCGG	chr20:52192262-52192485(+)$1	223	57	63	12.0566
GCCUGG	chr17:46052435-46052656(-)$1	221	11	17	12.4339
GCCUGG	chr9:133333752-133333974(-)$1	222	75	81	12.4339
GCCAGG	chr14:60591166-60591392(-)$1	226	172	178	14.7924
GCCAGG	chr1:159898118-159898342(-)$1	224	191	197	14.7924
GCCAGG	chr19:54969610-54969835(-)$1	225	56	62	14.7924
GCCAGG	chr1:29138841-29139073(+)$1	232	164	170	14.7924
GCCAGG	chr19:46996750-46996975(-)$1	225	59	65	14.7924
gcccgg	chr20:30555902-30556127(-)$1	225	34	40	12.0566
GCCAGG	chr16:31075381-31075603(+)$1	222	4	10	14.7924
gccagg	chr12:120117675-120117897(-)$1	222	12	18	14.7924
GCCGGG	chr1:38511992-38512222(+)$1	230	4	10	12.0566
GCCUGG	chr17:3561329-3561553(-)$1	224	21	27	12.4339
UCCAGG	chr19:3977983-3978205(-)$1	222	0	6	11.7735
gccggg	chr7:2394514-2394737(-)$1	223	58	64	12.0566
GCCCGG	chr4:961247-961473(-)$1	226	5	11	12.0566
gccagg	chr4:27023075-27023297(+)$1	222	69	75	14.7924
GCCAGG	chr17:4884434-4884658(-)$1	224	198	204	14.7924
GCCAGG	chr12:54795291-54795512(-)$1	221	150	156	14.7924
GCCUGG	chr16:2987085-2987314(-)$1	229	75	81	12.4339

#otherMatches

#Struct PSSM
FFFFFC	chr14:23856920-23857143(+)$1	223	204	210	14.7924
[eeeee	chr6:3118958-3119179(-)$1	221	6	12	12.0566
ccdddd	chr3:50141577-50141847(+)$1	270	55	61	12.4339
cclllc	chr10:70051823-70052044(+)$1	221	90	96	11.7735
ODDDDb	chr2:176945026-176945249(-)$1	223	14	20	11.5849
ceeeee	chr12:48372040-48372265(-)$1	225	98	104	11.5849
i22ddd	chr1:10713364-10713590(-)$1	226	108	114	14.7924
F{DDDD	chr9:140400006-140400230(-)$1	224	18	24	11.7735
CLLLBB	chr1:144339981-144340206(-)$1	225	45	51	14.7924
EEDDDD	chr20:2378500-2378722(+)$1	222	7	13	12.4339
444ggg	chr9:101006195-101006418(+)$1	223	92	98	11.6792
cc22bb	chr14:21859520-21859741(+)$1	221	162	168	12.0566
CLLLGG	chr5:141313968-141314190(-)$1	222	85	91	11.7735
bb!!dd	chr20:50048546-50048772(-)$1	226	13	19	12.0566
ffffff	chr11:86382824-86383049(-)$1	225	44	50	14.7924
:BB:cc	chr2:109379920-109380146(+)$1	226	5	11	11.5849
cc22cc	chr1:208061053-208061276(+)$1	223	87	93	12.4339
ffffff	chr17:26881367-26881590(+)$1	223	84	90	14.7924
&eeeee	chr11:67262447-67262668(+)$1	221	89	95	11.6792
eeee]d	chrX:100912303-100912525(-)$1	222	101	107	14.7924
llffff	chr1:28948450-28948674(+)$1	224	8	14	11.6792
iii555	chr3:184059736-184059959(-)$1	223	147	153	14.7924
[fffff	chr20:34568364-34568589(+)$1	225	11	17	11.6792
DDdddd	chr10:134755473-134755697(+)$1	224	188	194	12.0566
JJJJdd	chr1:31897538-31897762(+)$1	224	15	21	12.0566
ggggff	chr16:69143571-69143792(+)$1	221	103	109	14.7924
BB::::	chr20:35672519-35672746(-)$1	227	220	226	11.7735
ccc$$$	chr8:119122727-119122950(+)$1	223	106	112	12.4339
ccc[gg	chr1:6636437-6636659(+)$1	222	133	139	12.4339
c!!bbn	chrX:72673394-72673619(-)$1	225	137	143	11.6792
C{DDDD	chr1:171752843-171753064(+)$1	221	31	37	11.7735
$$$$$e	chr19:5789498-5789719(+)$1	221	44	50	11.5849
:cccll	chr19:54967476-54967699(+)$1	223	197	203	14.7924
!!a[ff	chr20:52192262-52192485(+)$1	223	57	63	12.0566
eee:CC	chr17:46052435-46052656(-)$1	221	11	17	12.4339
eeeeee	chr9:133333752-133333974(-)$1	222	75	81	12.4339
ddd22g	chr14:60591166-60591392(-)$1	226	172	178	14.7924
DZZZCC	chr1:159898118-159898342(-)$1	224	191	197	14.7924
eee22a	chr19:54969610-54969835(-)$1	225	56	62	14.7924
ffffff	chr1:29138841-29139073(+)$1	232	164	170	14.7924
ccc!!a	chr19:46996750-46996975(-)$1	225	59	65	14.7924
eeeedd	chr20:30555902-30556127(-)$1	225	34	40	12.0566
EE{CCC	chr16:31075381-31075603(+)$1	222	4	10	14.7924
FLLLA{	chr12:120117675-120117897(-)$1	222	12	18	14.7924
cc!!ff	chr1:38511992-38512222(+)$1	230	4	10	12.0566
CCDDDD	chr17:3561329-3561553(-)$1	224	21	27	12.4339
:::::g	chr19:3977983-3978205(-)$1	222	0	6	11.7735
IIIIII	chr7:2394514-2394737(-)$1	223	58	64	12.0566
bbcccp	chr4:961247-961473(-)$1	226	5	11	12.0566
nnnna3	chr4:27023075-27023297(+)$1	222	69	75	14.7924
::GGGG	chr17:4884434-4884658(-)$1	224	198	204	14.7924
ccc]cc	chr12:54795291-54795512(-)$1	221	150	156	14.7924
eee::D	chr16:2987085-2987314(-)$1	229	75	81	12.4339

#DB
))))))	chr14:23856920-23857143(+)$1	1	204	210	14.7924
.(((((	chr6:3118958-3119179(-)$1	1	6	12	12.0566
((((((	chr3:50141577-50141847(+)$1	1	55	61	12.4339
((...)	chr10:70051823-70052044(+)$1	1	90	96	11.7735
.(((((	chr2:176945026-176945249(-)$1	1	14	20	11.5849
((((((	chr12:48372040-48372265(-)$1	1	98	104	11.5849
)..)))	chr1:10713364-10713590(-)$1	1	108	114	14.7924
(.((((	chr9:140400006-140400230(-)$1	1	18	24	11.7735
(...((	chr1:144339981-144340206(-)$1	1	45	51	14.7924
((((((	chr20:2378500-2378722(+)$1	1	7	13	12.4339
...)))	chr9:101006195-101006418(+)$1	1	92	98	11.6792
))..))	chr14:21859520-21859741(+)$1	1	162	168	12.0566
(...((	chr5:141313968-141314190(-)$1	1	85	91	11.7735
((..((	chr20:50048546-50048772(-)$1	1	13	19	12.0566
))))))	chr11:86382824-86383049(-)$1	1	44	50	14.7924
.((.((	chr2:109379920-109380146(+)$1	1	5	11	11.5849
))..))	chr1:208061053-208061276(+)$1	1	87	93	12.4339
))))))	chr17:26881367-26881590(+)$1	1	84	90	14.7924
.(((((	chr11:67262447-67262668(+)$1	1	89	95	11.6792
)))).)	chrX:100912303-100912525(-)$1	1	101	107	14.7924
..))))	chr1:28948450-28948674(+)$1	1	8	14	11.6792
)))...	chr3:184059736-184059959(-)$1	1	147	153	14.7924
.(((((	chr20:34568364-34568589(+)$1	1	11	17	11.6792
))((((	chr10:134755473-134755697(+)$1	1	188	194	12.0566
((((((	chr1:31897538-31897762(+)$1	1	15	21	12.0566
))))((	chr16:69143571-69143792(+)$1	1	103	109	14.7924
))....	chr20:35672519-35672746(-)$1	1	220	226	11.7735
(((...	chr8:119122727-119122950(+)$1	1	106	112	12.4339
(((.((	chr1:6636437-6636659(+)$1	1	133	139	12.4339
(..((.	chrX:72673394-72673619(-)$1	1	137	143	11.6792
(.((((	chr1:171752843-171753064(+)$1	1	31	37	11.7735
.....(	chr19:5789498-5789719(+)$1	1	44	50	11.5849
.(((..	chr19:54967476-54967699(+)$1	1	197	203	14.7924
..(.((	chr20:52192262-52192485(+)$1	1	57	63	12.0566
))).((	chr17:46052435-46052656(-)$1	1	11	17	12.4339
))))))	chr9:133333752-133333974(-)$1	1	75	81	12.4339
)))..)	chr14:60591166-60591392(-)$1	1	172	178	14.7924
)...))	chr1:159898118-159898342(-)$1	1	191	197	14.7924
)))..)	chr19:54969610-54969835(-)$1	1	56	62	14.7924
((((((	chr1:29138841-29139073(+)$1	1	164	170	14.7924
(((..(	chr19:46996750-46996975(-)$1	1	59	65	14.7924
))))))	chr20:30555902-30556127(-)$1	1	34	40	12.0566
((.(((	chr16:31075381-31075603(+)$1	1	4	10	14.7924
(...(.	chr12:120117675-120117897(-)$1	1	12	18	14.7924
((..((	chr1:38511992-38512222(+)$1	1	4	10	12.0566
((((((	chr17:3561329-3561553(-)$1	1	21	27	12.4339
.....(	chr19:3977983-3978205(-)$1	1	0	6	11.7735
((((((	chr7:2394514-2394737(-)$1	1	58	64	12.0566
(((((.	chr4:961247-961473(-)$1	1	5	11	12.0566
....).	chr4:27023075-27023297(+)$1	1	69	75	14.7924
..))))	chr17:4884434-4884658(-)$1	1	198	204	14.7924
))).))	chr12:54795291-54795512(-)$1	1	150	156	14.7924
)))..(	chr16:2987085-2987314(-)$1	1	75	81	12.4339

#PSSM
G : 0.62	U : 0.11	C : 0.09	g : 0.09	A : 0.07	
C : 0.90	c : 0.09	
C : 0.90	c : 0.09	
A : 0.58	U : 0.16	G : 0.07	C : 0.07	a : 0.05	c : 0.01	g : 0.01	
G : 0.90	g : 0.09	
G : 0.90	g : 0.09	

#score	688.9056603773587
#seq	53
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m2_run2.nuc.txt

#NT
GCA	chr15:91347365-91347580(-)$1	215	64	67	9.0000
GCA	chrX:153630334-153630549(+)$1	215	39	42	9.0000
GCA	chr10:46550695-46550910(-)$1	215	50	53	9.0000
GCA	chr8:35648390-35648611(+)$1	221	12	15	9.0000
GCA	chr1:90058925-90059157(+)$1	232	125	128	9.0000
GCA	chr2:86442318-86442544(-)$1	226	91	94	9.0000
GCA	chr11:35276652-35276872(-)$1	220	25	28	9.0000
GCA	chr11:35274298-35274532(-)$1	234	48	51	9.0000
gca	chr1:151024168-151024389(+)$1	221	6	9	9.0000
GCA	chr2:113158631-113158852(-)$1	221	5	8	9.0000
gca	chr17:6352598-6352845(-)$1	247	3	6	9.0000
GCA	chr6:135732471-135732704(-)$1	233	29	32	9.0000
GCA	chr11:66130636-66130858(-)$1	222	82	85	9.0000
GCA	chr16:4854748-4854990(-)$1	242	159	162	9.0000
GCA	chr11:45263582-45263809(-)$1	227	21	24	9.0000
GCA	chr7:42003670-42003934(-)$1	264	0	3	9.0000
GCA	chr12:57522766-57522994(+)$1	228	85	88	9.0000
GCA	chr3:42825754-42825974(-)$1	220	32	35	9.0000
GCA	chr1:240621514-240621731(-)$1	217	35	38	9.0000
GCA	chr16:29821889-29822111(+)$1	222	58	61	9.0000
GCA	chr8:66630942-66631158(-)$1	216	6	9	9.0000
GCA	chr14:68255980-68256198(-)$1	218	47	50	9.0000
GCA	chr12:122702754-122702977(-)$1	223	63	66	9.0000
GCA	chr5:138270324-138270551(+)$1	227	14	17	9.0000
GCA	chr1:15894411-15894628(+)$1	217	88	91	9.0000
GCA	chr14:70924031-70924259(-)$1	228	77	80	9.0000
GCA	chr11:62574676-62574897(-)$1	221	8	11	9.0000
GCA	chr7:44424420-44424654(-)$1	234	187	190	9.0000
GCA	chr12:56634528-56634747(-)$1	219	0	3	9.0000
GCA	chr10:133772934-133773150(+)$1	216	117	120	9.0000
GCA	chr3:49705075-49705299(+)$1	224	2	5	9.0000
gca	chr20:32226792-32227014(+)$1	222	25	28	9.0000
GCA	chr9:86618730-86618975(+)$1	245	18	21	9.0000
GCA	chr5:89689661-89689890(-)$1	229	40	43	9.0000
GCA	chr13:97638202-97638417(-)$1	215	18	21	9.0000
GCA	chrX:65858723-65858939(-)$1	216	74	77	9.0000
GCA	chr2:26411269-26411533(+)$1	264	0	3	9.0000
gcA	chr16:30680512-30680735(+)$1	223	49	52	9.0000
GCA	chr19:58266051-58266268(+)$1	217	11	14	9.0000
GCA	chr17:5288360-5288590(-)$1	230	146	149	9.0000
GCA	chr12:50264121-50264340(-)$1	219	26	29	9.0000
GCA	chr1:205116095-205116322(-)$1	227	140	143	9.0000
GCA	chr12:118474064-118474286(-)$1	222	29	32	9.0000
GCA	chr19:5784048-5784286(-)$1	238	88	91	9.0000
GCA	chr16:70208029-70208244(-)$1	215	14	17	9.0000
GCA	chr14:104163938-104164178(+)$1	240	1	4	9.0000
GCA	chr19:13250758-13250979(+)$1	221	34	37	9.0000
GCA	chr1:107599265-107599483(+)$1	218	58	61	9.0000
GCA	chr5:156768713-156768933(-)$1	220	62	65	9.0000
GCA	chr11:9160280-9160500(-)$1	220	73	76	9.0000
GCA	chr19:55898839-55899062(+)$1	223	188	191	9.0000
gca	chr8:143853783-143854008(-)$1	225	22	25	9.0000
gca	chr20:34256011-34256228(+)$1	217	27	30	9.0000
GCA	chr18:23612342-23612567(-)$1	225	129	132	9.0000
GCA	chr19:40720013-40720244(+)$1	231	24	27	9.0000
GCA	chr11:82692517-82692736(-)$1	219	48	51	9.0000
GCA	chr13:33091793-33092016(-)$1	223	110	113	9.0000
GCA	chr7:5567597-5567862(-)$1	265	46	49	9.0000
GCA	chr1:20977855-20978071(+)$1	216	32	35	9.0000
GCA	chr6:3273133-3273364(+)$1	231	58	61	9.0000
GCA	chr13:39611547-39611787(-)$1	240	46	49	9.0000
GCA	chr4:3432517-3432757(+)$1	240	7	10	9.0000
GCA	chr17:15443389-15443605(-)$1	216	162	165	9.0000
GCA	chr10:64927307-64927535(-)$1	228	160	163	9.0000
GCA	chr11:63527086-63527316(-)$1	230	51	54	9.0000
GCA	chr19:55940770-55940999(-)$1	229	53	56	9.0000
GCA	chrX:153042682-153042918(+)$1	236	26	29	9.0000
GCA	chr8:77778315-77778543(+)$1	228	124	127	9.0000
GCA	chr19:39220120-39220340(+)$1	220	3	6	9.0000
GCA	chr12:39299309-39299527(-)$1	218	210	213	9.0000
GCA	chr5:150089551-150089776(-)$1	225	36	39	9.0000
GCA	chr17:49824973-49825191(-)$1	218	9	12	9.0000
GCA	chr14:105055359-105055581(-)$1	222	20	23	9.0000
GCA	chr9:138012744-138012980(+)$1	236	124	127	9.0000
GCA	chr5:130540486-130540712(+)$1	226	25	28	9.0000
GCA	chr5:142661146-142661365(-)$1	219	45	48	9.0000
GCA	chr1:249151596-249151817(-)$1	221	149	152	9.0000
GCA	chr21:46270597-46270830(-)$1	233	116	119	9.0000
GCA	chr6:80409322-80409569(+)$1	247	2	5	9.0000
GCA	chr10:98278900-98279122(-)$1	222	99	102	9.0000
GCA	chr17:16220443-16220673(+)$1	230	5	8	9.0000
GCA	chr17:26698804-26699020(+)$1	216	30	33	9.0000
GCA	chr8:134062068-134062285(-)$1	217	84	87	9.0000
GCA	chr14:24593277-24593503(+)$1	226	44	47	9.0000
GCA	chr12:56599546-56599817(-)$1	271	2	5	9.0000
GCA	chr1:101444923-101445142(+)$1	219	99	102	9.0000
GCA	chr7:102738752-102738981(+)$1	229	32	35	9.0000
GCA	chr8:119206266-119206482(-)$1	216	133	136	9.0000
GCA	chr3:123001732-123001953(-)$1	221	2	5	9.0000
GCA	chr19:23926071-23926289(-)$1	218	6	9	9.0000
GCA	chr7:103112271-103112489(-)$1	218	137	140	9.0000
GCA	chr9:132996848-132997073(+)$1	225	72	75	9.0000
GCA	chr14:23778276-23778499(+)$1	223	14	17	9.0000
GCA	chr17:38326705-38326925(+)$1	220	82	85	9.0000
GCA	chr11:62565981-62566220(-)$1	239	37	40	9.0000
GCA	chr11:133786635-133786860(-)$1	225	25	28	9.0000
GCA	chr15:64449517-64449734(+)$1	217	16	19	9.0000
GCA	chr4:56296271-56296501(-)$1	230	120	123	9.0000
GCA	chrX:49857130-49857355(+)$1	225	58	61	9.0000

#otherMatches

#Struct PSSM
d::	chr2:110613651-110613889(+)$1	238	86	89	9.0000
ggg	chr15:91347365-91347580(-)$1	215	64	67	9.0000
hhh	chrX:153630334-153630549(+)$1	215	39	42	9.0000
eee	chr10:46550695-46550910(-)$1	215	50	53	9.0000
fff	chr8:35648390-35648611(+)$1	221	12	15	9.0000
GGY	chr1:90058925-90059157(+)$1	232	125	128	9.0000
2bb	chr2:86442318-86442544(-)$1	226	91	94	9.0000
fff	chr11:35276652-35276872(-)$1	220	25	28	9.0000
fff	chr11:35274298-35274532(-)$1	234	48	51	9.0000
:::	chr1:151024168-151024389(+)$1	221	6	9	9.0000
:::	chr2:113158631-113158852(-)$1	221	5	8	9.0000
EED	chr17:6352598-6352845(-)$1	247	3	6	9.0000
nnn	chr6:135732471-135732704(-)$1	233	29	32	9.0000
333	chr11:66130636-66130858(-)$1	222	82	85	9.0000
777	chr16:4854748-4854990(-)$1	242	159	162	9.0000
mmm	chr11:45263582-45263809(-)$1	227	21	24	9.0000
FFF	chr7:42003670-42003934(-)$1	264	0	3	9.0000
===	chr12:57522766-57522994(+)$1	228	85	88	9.0000
)))	chr3:42825754-42825974(-)$1	220	32	35	9.0000
vvv	chr1:240621514-240621731(-)$1	217	35	38	9.0000
ddd	chr16:29821889-29822111(+)$1	222	58	61	9.0000
fff	chr8:66630942-66631158(-)$1	216	6	9	9.0000
f!!	chr14:68255980-68256198(-)$1	218	47	50	9.0000
bb]	chr12:122702754-122702977(-)$1	223	63	66	9.0000
ggg	chr5:138270324-138270551(+)$1	227	14	17	9.0000
ccc	chr1:15894411-15894628(+)$1	217	88	91	9.0000
ttt	chr14:70924031-70924259(-)$1	228	77	80	9.0000
DDD	chr11:62574676-62574897(-)$1	221	8	11	9.0000
CCC	chr7:44424420-44424654(-)$1	234	187	190	9.0000
:::	chr12:56634528-56634747(-)$1	219	0	3	9.0000
c88	chr10:133772934-133773150(+)$1	216	117	120	9.0000
DD{	chr3:49705075-49705299(+)$1	224	2	5	9.0000
FFF	chr20:32226792-32227014(+)$1	222	25	28	9.0000
III	chr9:86618730-86618975(+)$1	245	18	21	9.0000
ppp	chr5:89689661-89689890(-)$1	229	40	43	9.0000
DBB	chr13:97638202-97638417(-)$1	215	18	21	9.0000
eee	chrX:65858723-65858939(-)$1	216	74	77	9.0000
EEE	chr2:26411269-26411533(+)$1	264	0	3	9.0000
bb]	chr16:30680512-30680735(+)$1	223	49	52	9.0000
cc[	chr19:58266051-58266268(+)$1	217	11	14	9.0000
d]f	chr17:5288360-5288590(-)$1	230	146	149	9.0000
DDD	chr12:50264121-50264340(-)$1	219	26	29	9.0000
ddd	chr1:205116095-205116322(-)$1	227	140	143	9.0000
ddd	chr12:118474064-118474286(-)$1	222	29	32	9.0000
^^^	chr19:5784048-5784286(-)$1	238	88	91	9.0000
ccc	chr16:70208029-70208244(-)$1	215	14	17	9.0000
FFF	chr14:104163938-104164178(+)$1	240	1	4	9.0000
qqq	chr19:13250758-13250979(+)$1	221	34	37	9.0000
dd"	chr1:107599265-107599483(+)$1	218	58	61	9.0000
b[c	chr5:156768713-156768933(-)$1	220	62	65	9.0000
bb3	chr11:9160280-9160500(-)$1	220	73	76	9.0000
FFF	chr19:55898839-55899062(+)$1	223	188	191	9.0000
$$$	chr8:143853783-143854008(-)$1	225	22	25	9.0000
"""	chr20:34256011-34256228(+)$1	217	27	30	9.0000
b22	chr18:23612342-23612567(-)$1	225	129	132	9.0000
ppp	chr19:40720013-40720244(+)$1	231	24	27	9.0000
eee	chr11:82692517-82692736(-)$1	219	48	51	9.0000
ddd	chr13:33091793-33092016(-)$1	223	110	113	9.0000
HHH	chr7:5567597-5567862(-)$1	265	46	49	9.0000
EEE	chr1:20977855-20978071(+)$1	216	32	35	9.0000
fff	chr6:3273133-3273364(+)$1	231	58	61	9.0000
d[f	chr13:39611547-39611787(-)$1	240	46	49	9.0000
EEE	chr4:3432517-3432757(+)$1	240	7	10	9.0000
ggg	chr17:15443389-15443605(-)$1	216	162	165	9.0000
ooo	chr10:64927307-64927535(-)$1	228	160	163	9.0000
b[c	chr11:63527086-63527316(-)$1	230	51	54	9.0000
ccc	chr19:55940770-55940999(-)$1	229	53	56	9.0000
ff[	chrX:153042682-153042918(+)$1	236	26	29	9.0000
fff	chr8:77778315-77778543(+)$1	228	124	127	9.0000
{FF	chr19:39220120-39220340(+)$1	220	3	6	9.0000
BBD	chr12:39299309-39299527(-)$1	218	210	213	9.0000
:::	chr5:150089551-150089776(-)$1	225	36	39	9.0000
{EE	chr17:49824973-49825191(-)$1	218	9	12	9.0000
uuu	chr14:105055359-105055581(-)$1	222	20	23	9.0000
777	chr9:138012744-138012980(+)$1	236	124	127	9.0000
qqq	chr5:130540486-130540712(+)$1	226	25	28	9.0000
+++	chr5:142661146-142661365(-)$1	219	45	48	9.0000
{A:	chr1:249151596-249151817(-)$1	221	149	152	9.0000
eee	chr21:46270597-46270830(-)$1	233	116	119	9.0000
fff	chr6:80409322-80409569(+)$1	247	2	5	9.0000
dpp	chr10:98278900-98279122(-)$1	222	99	102	9.0000
eee	chr17:16220443-16220673(+)$1	230	5	8	9.0000
ttt	chr17:26698804-26699020(+)$1	216	30	33	9.0000
2hh	chr8:134062068-134062285(-)$1	217	84	87	9.0000
ccc	chr14:24593277-24593503(+)$1	226	44	47	9.0000
FFF	chr12:56599546-56599817(-)$1	271	2	5	9.0000
ddd	chr1:101444923-101445142(+)$1	219	99	102	9.0000
ee#	chr7:102738752-102738981(+)$1	229	32	35	9.0000
$$$	chr8:119206266-119206482(-)$1	216	133	136	9.0000
EEE	chr3:123001732-123001953(-)$1	221	2	5	9.0000
ccq	chr19:23926071-23926289(-)$1	218	6	9	9.0000
CYY	chr7:103112271-103112489(-)$1	218	137	140	9.0000
fff	chr9:132996848-132997073(+)$1	225	72	75	9.0000
bb[	chr14:23778276-23778499(+)$1	223	14	17	9.0000
ddn	chr17:38326705-38326925(+)$1	220	82	85	9.0000
]a:	chr11:62565981-62566220(-)$1	239	37	40	9.0000
F::	chr11:133786635-133786860(-)$1	225	25	28	9.0000
DD:	chr15:64449517-64449734(+)$1	217	16	19	9.0000
DDY	chr4:56296271-56296501(-)$1	230	120	123	9.0000
eee	chrX:49857130-49857355(+)$1	225	58	61	9.0000

#DB
)..	chr2:110613651-110613889(+)$1	1	86	89	9.0000
(((	chr15:91347365-91347580(-)$1	1	64	67	9.0000
(((	chrX:153630334-153630549(+)$1	1	39	42	9.0000
)))	chr10:46550695-46550910(-)$1	1	50	53	9.0000
(((	chr8:35648390-35648611(+)$1	1	12	15	9.0000
)).	chr1:90058925-90059157(+)$1	1	125	128	9.0000
.))	chr2:86442318-86442544(-)$1	1	91	94	9.0000
(((	chr11:35276652-35276872(-)$1	1	25	28	9.0000
(((	chr11:35274298-35274532(-)$1	1	48	51	9.0000
...	chr1:151024168-151024389(+)$1	1	6	9	9.0000
...	chr2:113158631-113158852(-)$1	1	5	8	9.0000
(((	chr17:6352598-6352845(-)$1	1	3	6	9.0000
...	chr6:135732471-135732704(-)$1	1	29	32	9.0000
...	chr11:66130636-66130858(-)$1	1	82	85	9.0000
...	chr16:4854748-4854990(-)$1	1	159	162	9.0000
...	chr11:45263582-45263809(-)$1	1	21	24	9.0000
(((	chr7:42003670-42003934(-)$1	1	0	3	9.0000
(((	chr12:57522766-57522994(+)$1	1	85	88	9.0000
...	chr3:42825754-42825974(-)$1	1	32	35	9.0000
...	chr1:240621514-240621731(-)$1	1	35	38	9.0000
)))	chr16:29821889-29822111(+)$1	1	58	61	9.0000
(((	chr8:66630942-66631158(-)$1	1	6	9	9.0000
(..	chr14:68255980-68256198(-)$1	1	47	50	9.0000
)).	chr12:122702754-122702977(-)$1	1	63	66	9.0000
(((	chr5:138270324-138270551(+)$1	1	14	17	9.0000
(((	chr1:15894411-15894628(+)$1	1	88	91	9.0000
...	chr14:70924031-70924259(-)$1	1	77	80	9.0000
(((	chr11:62574676-62574897(-)$1	1	8	11	9.0000
)))	chr7:44424420-44424654(-)$1	1	187	190	9.0000
...	chr12:56634528-56634747(-)$1	1	0	3	9.0000
)..	chr10:133772934-133773150(+)$1	1	117	120	9.0000
((.	chr3:49705075-49705299(+)$1	1	2	5	9.0000
(((	chr20:32226792-32227014(+)$1	1	25	28	9.0000
(((	chr9:86618730-86618975(+)$1	1	18	21	9.0000
...	chr5:89689661-89689890(-)$1	1	40	43	9.0000
(((	chr13:97638202-97638417(-)$1	1	18	21	9.0000
)))	chrX:65858723-65858939(-)$1	1	74	77	9.0000
(((	chr2:26411269-26411533(+)$1	1	0	3	9.0000
)).	chr16:30680512-30680735(+)$1	1	49	52	9.0000
((.	chr19:58266051-58266268(+)$1	1	11	14	9.0000
).)	chr17:5288360-5288590(-)$1	1	146	149	9.0000
(((	chr12:50264121-50264340(-)$1	1	26	29	9.0000
)))	chr1:205116095-205116322(-)$1	1	140	143	9.0000
(((	chr12:118474064-118474286(-)$1	1	29	32	9.0000
...	chr19:5784048-5784286(-)$1	1	88	91	9.0000
(((	chr16:70208029-70208244(-)$1	1	14	17	9.0000
(((	chr14:104163938-104164178(+)$1	1	1	4	9.0000
...	chr19:13250758-13250979(+)$1	1	34	37	9.0000
((.	chr1:107599265-107599483(+)$1	1	58	61	9.0000
(.(	chr5:156768713-156768933(-)$1	1	62	65	9.0000
)).	chr11:9160280-9160500(-)$1	1	73	76	9.0000
)))	chr19:55898839-55899062(+)$1	1	188	191	9.0000
...	chr8:143853783-143854008(-)$1	1	22	25	9.0000
...	chr20:34256011-34256228(+)$1	1	27	30	9.0000
)..	chr18:23612342-23612567(-)$1	1	129	132	9.0000
...	chr19:40720013-40720244(+)$1	1	24	27	9.0000
)))	chr11:82692517-82692736(-)$1	1	48	51	9.0000
)))	chr13:33091793-33092016(-)$1	1	110	113	9.0000
(((	chr7:5567597-5567862(-)$1	1	46	49	9.0000
(((	chr1:20977855-20978071(+)$1	1	32	35	9.0000
(((	chr6:3273133-3273364(+)$1	1	58	61	9.0000
(.(	chr13:39611547-39611787(-)$1	1	46	49	9.0000
(((	chr4:3432517-3432757(+)$1	1	7	10	9.0000
(((	chr17:15443389-15443605(-)$1	1	162	165	9.0000
...	chr10:64927307-64927535(-)$1	1	160	163	9.0000
(.(	chr11:63527086-63527316(-)$1	1	51	54	9.0000
)))	chr19:55940770-55940999(-)$1	1	53	56	9.0000
((.	chrX:153042682-153042918(+)$1	1	26	29	9.0000
(((	chr8:77778315-77778543(+)$1	1	124	127	9.0000
.((	chr19:39220120-39220340(+)$1	1	3	6	9.0000
)))	chr12:39299309-39299527(-)$1	1	210	213	9.0000
...	chr5:150089551-150089776(-)$1	1	36	39	9.0000
.((	chr17:49824973-49825191(-)$1	1	9	12	9.0000
...	chr14:105055359-105055581(-)$1	1	20	23	9.0000
...	chr9:138012744-138012980(+)$1	1	124	127	9.0000
...	chr5:130540486-130540712(+)$1	1	25	28	9.0000
...	chr5:142661146-142661365(-)$1	1	45	48	9.0000
.(.	chr1:249151596-249151817(-)$1	1	149	152	9.0000
(((	chr21:46270597-46270830(-)$1	1	116	119	9.0000
(((	chr6:80409322-80409569(+)$1	1	2	5	9.0000
(..	chr10:98278900-98279122(-)$1	1	99	102	9.0000
(((	chr17:16220443-16220673(+)$1	1	5	8	9.0000
...	chr17:26698804-26699020(+)$1	1	30	33	9.0000
.))	chr8:134062068-134062285(-)$1	1	84	87	9.0000
(((	chr14:24593277-24593503(+)$1	1	44	47	9.0000
(((	chr12:56599546-56599817(-)$1	1	2	5	9.0000
(((	chr1:101444923-101445142(+)$1	1	99	102	9.0000
((.	chr7:102738752-102738981(+)$1	1	32	35	9.0000
...	chr8:119206266-119206482(-)$1	1	133	136	9.0000
(((	chr3:123001732-123001953(-)$1	1	2	5	9.0000
((.	chr19:23926071-23926289(-)$1	1	6	9	9.0000
)..	chr7:103112271-103112489(-)$1	1	137	140	9.0000
(((	chr9:132996848-132997073(+)$1	1	72	75	9.0000
((.	chr14:23778276-23778499(+)$1	1	14	17	9.0000
((.	chr17:38326705-38326925(+)$1	1	82	85	9.0000
.).	chr11:62565981-62566220(-)$1	1	37	40	9.0000
(..	chr11:133786635-133786860(-)$1	1	25	28	9.0000
((.	chr15:64449517-64449734(+)$1	1	16	19	9.0000
)).	chr4:56296271-56296501(-)$1	1	120	123	9.0000
(((	chrX:49857130-49857355(+)$1	1	58	61	9.0000

#PSSM
G : 0.94	g : 0.06	
C : 0.94	c : 0.06	
A : 0.95	a : 0.05	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m2_run2.nuc.txt

#NT
AAGACAAA	chr4:41262582-41263007(+)$1	425	214	222	15.6666
AAAACAAA	chr14:32559736-32560059(+)$1	323	149	157	20.2222
AAAACAGA	chr20:31436602-31436944(+)$1	342	162	170	16.1111
aaaaaaaa	chr13:79188294-79188722(+)$1	428	46	54	16.8888
AAAACAAA	chr12:32875449-32875752(+)$1	303	226	234	20.2222
AAAAUAAA	chr4:164440524-164440783(+)$1	259	160	168	16.6666
AAAACAAC	chr14:64465594-64465892(+)$1	298	75	83	15.7777
AAAACAAA	chr1:169100775-169101168(+)$1	393	71	79	20.2222
ACAACAAA	chr11:9303194-9303472(+)$1	278	154	162	16.0000
AAAACAUA	chr1:70610397-70610750(+)$1	353	72	80	16.3333
AAAACACA	chr19:10787811-10788132(+)$1	321	88	96	16.3333
GAAACAAA	chr12:133311078-133311332(+)$1	254	89	97	16.1111
GAAACAAA	chr5:112174577-112174912(+)$1	335	44	52	16.1111
AAAACCAA	chr9:115232686-115232952(+)$1	266	32	40	15.7777
AAAAAAAA	chr7:27868277-27868533(+)$1	256	206	214	16.8888
AAAACAAA	chr2:55517854-55518117(+)$1	263	108	116	20.2222
AAAACAAA	chr15:89803961-89804222(+)$1	261	239	247	20.2222
AAAACAAU	chr14:56128197-56128447(+)$1	250	125	133	15.6666
AAAACAAA	chrX:153068121-153068383(+)$1	262	155	163	20.2222
AAAACAUA	chr10:105048782-105049064(+)$1	282	38	46	16.3333
AAAUCAAA	chr19:30503249-30503521(+)$1	272	149	157	15.4444
AAAACAAA	chr21:34931883-34932179(+)$1	296	151	159	20.2222
ACAACAAA	chr12:30903850-30904112(+)$1	262	6	14	16.0000
AAAAAAAA	chr3:109045181-109045513(+)$1	332	251	259	16.8888
AGAACAAA	chr7:134644666-134644970(+)$1	304	10	18	15.7777
AAAACAAC	chr4:185548764-185549034(+)$1	270	51	59	15.7777
aaaacaca	chr2:29129300-29129612(+)$1	312	296	304	16.3333
AAAACAAA	chr2:44115434-44115773(+)$1	339	280	288	20.2222
AAAACAAA	chr7:23561535-23561894(+)$1	359	21	29	20.2222
AAAACUAA	chr10:118644437-118644884(+)$1	447	290	298	15.6666
GAAACAAA	chr17:57771306-57771682(+)$1	376	233	241	16.1111
GAAACAAA	chr2:61575388-61575652(+)$1	264	236	244	16.1111
AAAACAAA	chr12:123745636-123746010(+)$1	374	252	260	20.2222
AAAAAAAA	chr2:10924014-10924265(+)$1	251	40	48	16.8888
AAAAGAAA	chr5:151170457-151170751(+)$1	294	209	217	16.5555
AAAACAUA	chr11:69466522-69466878(+)$1	356	21	29	16.3333
AAAAUAAA	chr20:5527041-5527310(+)$1	269	75	83	16.6666
AAAACAAA	chr2:219093427-219093723(+)$1	296	77	85	20.2222
AAAAGAAA	chr4:129192332-129192593(+)$1	261	250	258	16.5555
ACAACAAA	chr5:169017998-169018308(+)$1	310	148	156	16.0000
AAAACACA	chr10:61788069-61788322(+)$1	253	61	69	16.3333
AAAAAAAA	chr1:109239897-109240171(+)$1	274	215	223	16.8888
AAAACCAA	chr15:58001234-58001569(+)$1	335	311	319	15.7777
AAGACAAA	chr2:9725103-9725361(+)$1	258	133	141	15.6666

#otherMatches

#Struct PSSM
::::::hh	chr1:93299057-93299407(+)$1	350	92	100	16.6666
cqqqqqqq	chr4:41262582-41263007(+)$1	425	214	222	15.6666
uuuuuuuu	chr14:32559736-32560059(+)$1	323	149	157	20.2222
nnnnccc:	chr20:31436602-31436944(+)$1	342	162	170	16.1111
gg::::::	chr13:79188294-79188722(+)$1	428	46	54	16.8888
===vvvvv	chr12:32875449-32875752(+)$1	303	226	234	20.2222
:::::::i	chr4:164440524-164440783(+)$1	259	160	168	16.6666
C:::::::	chr14:64465594-64465892(+)$1	298	75	83	15.7777
^^^^^^^^	chr1:169100775-169101168(+)$1	393	71	79	20.2222
::::::::	chr11:9303194-9303472(+)$1	278	154	162	16.0000
FFFF::::	chr1:70610397-70610750(+)$1	353	72	80	16.3333
qqqqeeee	chr19:10787811-10788132(+)$1	321	88	96	16.3333
CWWWWWWW	chr12:133311078-133311332(+)$1	254	89	97	16.1111
gggggg::	chr5:112174577-112174912(+)$1	335	44	52	16.1111
ffff::::	chr9:115232686-115232952(+)$1	266	32	40	15.7777
dd]eeeee	chr7:27868277-27868533(+)$1	256	206	214	16.8888
ssssssss	chr2:55517854-55518117(+)$1	263	108	116	20.2222
::FFFFFF	chr15:89803961-89804222(+)$1	261	239	247	20.2222
::::::::	chr14:56128197-56128447(+)$1	250	125	133	15.6666
::::::::	chrX:153068121-153068383(+)$1	262	155	163	20.2222
EEEELLLD	chr10:105048782-105049064(+)$1	282	38	46	16.3333
::::ffff	chr19:30503249-30503521(+)$1	272	149	157	15.4444
ggggggvv	chr21:34931883-34932179(+)$1	296	151	159	20.2222
::::::::	chr12:30903850-30904112(+)$1	262	6	14	16.0000
wwwwwwww	chr3:109045181-109045513(+)$1	332	251	259	16.8888
::::::::	chr7:134644666-134644970(+)$1	304	10	18	15.7777
::::::::	chr4:185548764-185549034(+)$1	270	51	59	15.7777
::::::::	chr2:29129300-29129612(+)$1	312	296	304	16.3333
qqqqqqqq	chr2:44115434-44115773(+)$1	339	280	288	20.2222
DQQQQQQQ	chr7:23561535-23561894(+)$1	359	21	29	20.2222
::::::::	chr10:118644437-118644884(+)$1	447	290	298	15.6666
====::dd	chr17:57771306-57771682(+)$1	376	233	241	16.1111
::::::::	chr2:61575388-61575652(+)$1	264	236	244	16.1111
EE{CCCLL	chr12:123745636-123746010(+)$1	374	252	260	20.2222
yyyyyyyy	chr2:10924014-10924265(+)$1	251	40	48	16.8888
::::::::	chr5:151170457-151170751(+)$1	294	209	217	16.5555
eeeee:::	chr11:69466522-69466878(+)$1	356	21	29	16.3333
ffffffff	chr20:5527041-5527310(+)$1	269	75	83	16.6666
88888ccc	chr2:219093427-219093723(+)$1	296	77	85	20.2222
DDD:::::	chr4:129192332-129192593(+)$1	261	250	258	16.5555
^^^^^^^^	chr5:169017998-169018308(+)$1	310	148	156	16.0000
::::::::	chr10:61788069-61788322(+)$1	253	61	69	16.3333
::::::::	chr1:109239897-109240171(+)$1	274	215	223	16.8888
:::::BB}	chr15:58001234-58001569(+)$1	335	311	319	15.7777
^^^^^^^^	chr2:9725103-9725361(+)$1	258	133	141	15.6666

#DB
......((	chr1:93299057-93299407(+)$1	1	92	100	16.6666
(.......	chr4:41262582-41263007(+)$1	1	214	222	15.6666
........	chr14:32559736-32560059(+)$1	1	149	157	20.2222
....))).	chr20:31436602-31436944(+)$1	1	162	170	16.1111
))......	chr13:79188294-79188722(+)$1	1	46	54	16.8888
(((.....	chr12:32875449-32875752(+)$1	1	226	234	20.2222
.......(	chr4:164440524-164440783(+)$1	1	160	168	16.6666
(.......	chr14:64465594-64465892(+)$1	1	75	83	15.7777
........	chr1:169100775-169101168(+)$1	1	71	79	20.2222
........	chr11:9303194-9303472(+)$1	1	154	162	16.0000
((((....	chr1:70610397-70610750(+)$1	1	72	80	16.3333
....))))	chr19:10787811-10788132(+)$1	1	88	96	16.3333
(.......	chr12:133311078-133311332(+)$1	1	89	97	16.1111
))))))..	chr5:112174577-112174912(+)$1	1	44	52	16.1111
))))....	chr9:115232686-115232952(+)$1	1	32	40	15.7777
)).)))))	chr7:27868277-27868533(+)$1	1	206	214	16.8888
........	chr2:55517854-55518117(+)$1	1	108	116	20.2222
..))))))	chr15:89803961-89804222(+)$1	1	239	247	20.2222
........	chr14:56128197-56128447(+)$1	1	125	133	15.6666
........	chrX:153068121-153068383(+)$1	1	155	163	20.2222
((((...(	chr10:105048782-105049064(+)$1	1	38	46	16.3333
....((((	chr19:30503249-30503521(+)$1	1	149	157	15.4444
((((((..	chr21:34931883-34932179(+)$1	1	151	159	20.2222
........	chr12:30903850-30904112(+)$1	1	6	14	16.0000
........	chr3:109045181-109045513(+)$1	1	251	259	16.8888
........	chr7:134644666-134644970(+)$1	1	10	18	15.7777
........	chr4:185548764-185549034(+)$1	1	51	59	15.7777
........	chr2:29129300-29129612(+)$1	1	296	304	16.3333
........	chr2:44115434-44115773(+)$1	1	280	288	20.2222
(.......	chr7:23561535-23561894(+)$1	1	21	29	20.2222
........	chr10:118644437-118644884(+)$1	1	290	298	15.6666
))))..((	chr17:57771306-57771682(+)$1	1	233	241	16.1111
........	chr2:61575388-61575652(+)$1	1	236	244	16.1111
((.(((..	chr12:123745636-123746010(+)$1	1	252	260	20.2222
........	chr2:10924014-10924265(+)$1	1	40	48	16.8888
........	chr5:151170457-151170751(+)$1	1	209	217	16.5555
)))))...	chr11:69466522-69466878(+)$1	1	21	29	16.3333
((((((((	chr20:5527041-5527310(+)$1	1	75	83	16.6666
.....)))	chr2:219093427-219093723(+)$1	1	77	85	20.2222
))).....	chr4:129192332-129192593(+)$1	1	250	258	16.5555
........	chr5:169017998-169018308(+)$1	1	148	156	16.0000
........	chr10:61788069-61788322(+)$1	1	61	69	16.3333
........	chr1:109239897-109240171(+)$1	1	215	223	16.8888
.....)).	chr15:58001234-58001569(+)$1	1	311	319	15.7777
........	chr2:9725103-9725361(+)$1	1	133	141	15.6666

#PSSM
A : 0.86	G : 0.08	a : 0.04	
A : 0.86	C : 0.06	a : 0.04	G : 0.02	
A : 0.91	G : 0.04	a : 0.04	
A : 0.93	a : 0.04	U : 0.02	
C : 0.75	A : 0.08	U : 0.06	G : 0.04	a : 0.02	c : 0.02	
A : 0.88	a : 0.04	C : 0.04	U : 0.02	
A : 0.82	U : 0.06	C : 0.04	G : 0.02	a : 0.02	c : 0.02	
A : 0.88	a : 0.04	C : 0.04	U : 0.02	

#score	773.5555555555559
#seq	45
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_UTR_m1_run2.nuc.txt

#NT
GAAG	chr10:124766441-124766674(-)$1	233	55	59	12.0000
GAAG	chr11:95522832-95523077(-)$1	245	45	49	12.0000
GAAG	chr13:31037676-31037925(-)$1	249	128	132	12.0000
GAAG	chr19:58324578-58324818(-)$1	240	45	49	12.0000
GAAG	chr13:96277003-96277263(-)$1	260	107	111	12.0000
GAAG	chr6:170713750-170713987(+)$1	237	214	218	12.0000
GAAG	chr3:128598426-128598669(+)$1	243	67	71	12.0000
GAAG	chr16:69943216-69943450(+)$1	234	54	58	12.0000
GAAG	chr7:39745673-39745910(+)$1	237	90	94	12.0000
GAAG	chr16:15128213-15128436(+)$1	223	1	5	12.0000
GAAG	chr17:41107776-41108032(-)$1	256	66	70	12.0000
GAAG	chr6:24415198-24415432(+)$1	234	156	160	12.0000
GAAG	chr19:16192659-16192941(+)$1	282	66	70	12.0000
GAAG	chr19:59066143-59066398(-)$1	255	0	4	12.0000
GAAG	chr7:140082211-140082448(-)$1	237	51	55	12.0000
GAAG	chr19:36001152-36001393(-)$1	241	109	113	12.0000
GAAG	chr3:58410528-58410795(+)$1	267	146	150	12.0000
GAAG	chr17:37617919-37618162(+)$1	243	8	12	12.0000
GAAG	chrX:132473192-132473437(-)$1	245	78	82	12.0000
GAAG	chr1:220267443-220267682(+)$1	239	170	174	12.0000
GAAG	chr2:26357730-26358004(+)$1	274	141	145	12.0000
GAAG	chr12:120634492-120634751(-)$1	259	116	120	12.0000
GAAG	chr1:203764707-203764951(+)$1	244	146	150	12.0000
GAAG	chr12:110386105-110386345(-)$1	240	112	116	12.0000
GAAG	chr17:73059745-73060003(+)$1	258	122	126	12.0000
GAAG	chr2:233655648-233655896(+)$1	248	93	97	12.0000
GAAG	chr11:14521178-14521446(-)$1	268	212	216	12.0000
GAAG	chr9:131851214-131851441(+)$1	227	152	156	12.0000
GAAG	chr3:197559022-197559277(+)$1	255	109	113	12.0000
GAAG	chr16:1559997-1560264(+)$1	267	75	79	12.0000
GAAG	chr9:129266480-129266758(+)$1	278	157	161	12.0000
GAAG	chr5:65460364-65460598(+)$1	234	119	123	12.0000
GAAG	chr17:36968987-36969219(-)$1	232	102	106	12.0000
GAAG	chr12:125432231-125432480(-)$1	249	244	248	12.0000
GAAG	chr19:1438705-1438947(+)$1	242	103	107	12.0000
GAAG	chr1:156280640-156280884(-)$1	244	205	209	12.0000
GAAG	chr6:144416519-144416776(-)$1	257	124	128	12.0000
GAAG	chr13:77825313-77825559(-)$1	246	104	108	12.0000
GAAG	chr5:141017108-141017349(+)$1	241	80	84	12.0000
GAAG	chr3:196658305-196658555(+)$1	250	43	47	12.0000
GAAG	chr4:1729665-1729984(+)$1	319	41	45	12.0000
GAAG	chr7:56099535-56099772(-)$1	237	103	107	12.0000
GAAG	chr2:73461338-73461595(+)$1	257	36	40	12.0000
GAAG	chr16:29511255-29511509(-)$1	254	132	136	12.0000
GAAG	chr19:8528376-8528625(+)$1	249	119	123	12.0000
GAAG	chr5:72794376-72794589(+)$1	213	59	63	12.0000
GAAG	chr19:4498200-4498426(+)$1	226	118	122	12.0000
GAAG	chr2:176049009-176049242(+)$1	233	58	62	12.0000
GAAG	chr19:12385687-12385930(-)$1	243	213	217	12.0000
gaag	chrX:154005043-154005277(+)$1	234	47	51	12.0000
GAAG	chr7:23351616-23351853(-)$1	237	129	133	12.0000
GAAG	chr17:47684577-47684819(-)$1	242	115	119	12.0000
GAAG	chr11:130005408-130005652(+)$1	244	12	16	12.0000
GAAG	chrX:149102127-149102333(-)$1	206	92	96	12.0000
GAAG	chr6:4891876-4892116(+)$1	240	108	112	12.0000
GAAG	chr1:59249384-59249622(-)$1	238	198	202	12.0000
GAAG	chr19:18420517-18420762(-)$1	245	234	238	12.0000
GAAG	chr17:62500757-62501062(-)$1	305	125	129	12.0000
GAAG	chr6:36181909-36182144(+)$1	235	60	64	12.0000
GAAG	chr22:38902052-38902311(-)$1	259	16	20	12.0000
GAAG	chr3:56627623-56627855(+)$1	232	64	68	12.0000
GAAG	chr2:26068249-26068483(-)$1	234	114	118	12.0000
GAAG	chr17:56429365-56429606(-)$1	241	0	4	12.0000
GAAG	chr4:17811958-17812235(-)$1	277	28	32	12.0000
GAAG	chr1:146037338-146037604(-)$1	266	16	20	12.0000
GAAG	chr13:53217492-53217742(+)$1	250	87	91	12.0000
GAAG	chr19:51302435-51302696(-)$1	261	87	91	12.0000
GAAG	chr8:142011181-142011428(-)$1	247	130	134	12.0000
GAAG	chr4:122734929-122735174(+)$1	245	12	16	12.0000
GAAG	chr12:76451474-76451724(+)$1	250	16	20	12.0000
GAAG	chr22:42290806-42291037(+)$1	231	102	106	12.0000
GAAG	chr16:84004928-84005180(+)$1	252	63	67	12.0000
GAAG	chrX:118986781-118987017(-)$1	236	128	132	12.0000
GAAG	chr7:99661835-99662064(-)$1	229	55	59	12.0000
GAAG	chrX:153999005-153999243(+)$1	238	133	137	12.0000
GAAG	chr7:102963944-102964174(-)$1	230	104	108	12.0000
gaag	chr6:32945613-32945854(+)$1	241	67	71	12.0000
GAAG	chr6:75994241-75994506(-)$1	265	172	176	12.0000
GAAG	chr1:36235415-36235665(-)$1	250	4	8	12.0000
GAAG	chr19:18420432-18420683(-)$1	251	155	159	12.0000
GAAG	chr17:73143578-73143809(-)$1	231	36	40	12.0000
GAAG	chr15:91560934-91561191(-)$1	257	28	32	12.0000
GAAG	chr19:8538950-8539212(+)$1	262	2	6	12.0000
GAAG	chr7:27181300-27181506(-)$1	206	148	152	12.0000
GAAG	chr11:74660293-74660526(+)$1	233	65	69	12.0000
GAAG	chr19:58899403-58899630(+)$1	227	163	167	12.0000
GAAG	chr19:11024450-11024681(+)$1	231	62	66	12.0000
GAAG	chr22:30165667-30165899(+)$1	232	67	71	12.0000
GAAG	chr4:20255106-20255364(+)$1	258	23	27	12.0000
GAAG	chr19:4499397-4499639(+)$1	242	125	129	12.0000
GAAG	chr7:139090414-139090633(+)$1	219	44	48	12.0000

#otherMatches

#Struct PSSM
cc22	chrX:153276913-153277175(-)$1	262	78	82	12.0000
''''	chr10:124766441-124766674(-)$1	233	55	59	12.0000
]ccc	chr11:95522832-95523077(-)$1	245	45	49	12.0000
D::c	chr13:31037676-31037925(-)$1	249	128	132	12.0000
ssss	chr19:58324578-58324818(-)$1	240	45	49	12.0000
nnnn	chr13:96277003-96277263(-)$1	260	107	111	12.0000
hhhh	chr6:170713750-170713987(+)$1	237	214	218	12.0000
:::G	chr3:128598426-128598669(+)$1	243	67	71	12.0000
::EE	chr16:69943216-69943450(+)$1	234	54	58	12.0000
eeee	chr7:39745673-39745910(+)$1	237	90	94	12.0000
dddd	chr16:15128213-15128436(+)$1	223	1	5	12.0000
dfff	chr17:41107776-41108032(-)$1	256	66	70	12.0000
ffff	chr6:24415198-24415432(+)$1	234	156	160	12.0000
C{CC	chr19:16192659-16192941(+)$1	282	66	70	12.0000
FFFF	chr19:59066143-59066398(-)$1	255	0	4	12.0000
eeec	chr7:140082211-140082448(-)$1	237	51	55	12.0000
JJJJ	chr19:36001152-36001393(-)$1	241	109	113	12.0000
ddll	chr3:58410528-58410795(+)$1	267	146	150	12.0000
D::f	chr17:37617919-37618162(+)$1	243	8	12	12.0000
pppd	chrX:132473192-132473437(-)$1	245	78	82	12.0000
e22=	chr1:220267443-220267682(+)$1	239	170	174	12.0000
dd[a	chr2:26357730-26358004(+)$1	274	141	145	12.0000
BBII	chr12:120634492-120634751(-)$1	259	116	120	12.0000
ffff	chr1:203764707-203764951(+)$1	244	146	150	12.0000
ee]d	chr12:110386105-110386345(-)$1	240	112	116	12.0000
oood	chr17:73059745-73060003(+)$1	258	122	126	12.0000
ddff	chr2:233655648-233655896(+)$1	248	93	97	12.0000
eeee	chr11:14521178-14521446(-)$1	268	212	216	12.0000
dddd	chr9:131851214-131851441(+)$1	227	152	156	12.0000
>>>>	chr3:197559022-197559277(+)$1	255	109	113	12.0000
gggg	chr16:1559997-1560264(+)$1	267	75	79	12.0000
{HHH	chr9:129266480-129266758(+)$1	278	157	161	12.0000
nnnn	chr5:65460364-65460598(+)$1	234	119	123	12.0000
rrrr	chr17:36968987-36969219(-)$1	232	102	106	12.0000
::::	chr12:125432231-125432480(-)$1	249	244	248	12.0000
:::A	chr19:1438705-1438947(+)$1	242	103	107	12.0000
ggdd	chr1:156280640-156280884(-)$1	244	205	209	12.0000
bbGG	chr6:144416519-144416776(-)$1	257	124	128	12.0000
%%%%	chr13:77825313-77825559(-)$1	246	104	108	12.0000
d22=	chr5:141017108-141017349(+)$1	241	80	84	12.0000
MDDD	chr3:196658305-196658555(+)$1	250	43	47	12.0000
dd[a	chr4:1729665-1729984(+)$1	319	41	45	12.0000
g[a[	chr7:56099535-56099772(-)$1	237	103	107	12.0000
FFFF	chr2:73461338-73461595(+)$1	257	36	40	12.0000
ssss	chr16:29511255-29511509(-)$1	254	132	136	12.0000
eeee	chr19:8528376-8528625(+)$1	249	119	123	12.0000
::::	chr5:72794376-72794589(+)$1	213	59	63	12.0000
dd::	chr19:4498200-4498426(+)$1	226	118	122	12.0000
clll	chr2:176049009-176049242(+)$1	233	58	62	12.0000
eeee	chr19:12385687-12385930(-)$1	243	213	217	12.0000
9999	chrX:154005043-154005277(+)$1	234	47	51	12.0000
dnnn	chr7:23351616-23351853(-)$1	237	129	133	12.0000
####	chr17:47684577-47684819(-)$1	242	115	119	12.0000
rrre	chr11:130005408-130005652(+)$1	244	12	16	12.0000
333g	chrX:149102127-149102333(-)$1	206	92	96	12.0000
gggg	chr6:4891876-4892116(+)$1	240	108	112	12.0000
666f	chr1:59249384-59249622(-)$1	238	198	202	12.0000
\\\\	chr19:18420517-18420762(-)$1	245	234	238	12.0000
d:::	chr17:62500757-62501062(-)$1	305	125	129	12.0000
""cc	chr6:36181909-36182144(+)$1	235	60	64	12.0000
d[cc	chr22:38902052-38902311(-)$1	259	16	20	12.0000
HHHH	chr3:56627623-56627855(+)$1	232	64	68	12.0000
::HH	chr2:26068249-26068483(-)$1	234	114	118	12.0000
::ee	chr17:56429365-56429606(-)$1	241	0	4	12.0000
mmmm	chr4:17811958-17812235(-)$1	277	28	32	12.0000
IIII	chr1:146037338-146037604(-)$1	266	16	20	12.0000
::::	chr13:53217492-53217742(+)$1	250	87	91	12.0000
KKEE	chr19:51302435-51302696(-)$1	261	87	91	12.0000
cc[b	chr8:142011181-142011428(-)$1	247	130	134	12.0000
nddd	chr4:122734929-122735174(+)$1	245	12	16	12.0000
:::=	chr12:76451474-76451724(+)$1	250	16	20	12.0000
qqqq	chr22:42290806-42291037(+)$1	231	102	106	12.0000
CC:h	chr16:84004928-84005180(+)$1	252	63	67	12.0000
____	chrX:118986781-118987017(-)$1	236	128	132	12.0000
oocc	chr7:99661835-99662064(-)$1	229	55	59	12.0000
ccnn	chrX:153999005-153999243(+)$1	238	133	137	12.0000
====	chr7:102963944-102964174(-)$1	230	104	108	12.0000
nngg	chr6:32945613-32945854(+)$1	241	67	71	12.0000
]a22	chr6:75994241-75994506(-)$1	265	172	176	12.0000
::::	chr1:36235415-36235665(-)$1	250	4	8	12.0000
pppb	chr19:18420432-18420683(-)$1	251	155	159	12.0000
mmmd	chr17:73143578-73143809(-)$1	231	36	40	12.0000
gggg	chr15:91560934-91561191(-)$1	257	28	32	12.0000
::DD	chr19:8538950-8539212(+)$1	262	2	6	12.0000
mmee	chr7:27181300-27181506(-)$1	206	148	152	12.0000
a!!b	chr11:74660293-74660526(+)$1	233	65	69	12.0000
BYYH	chr19:58899403-58899630(+)$1	227	163	167	12.0000
e$$$	chr19:11024450-11024681(+)$1	231	62	66	12.0000
2ddd	chr22:30165667-30165899(+)$1	232	67	71	12.0000
rrrr	chr4:20255106-20255364(+)$1	258	23	27	12.0000
ccc:	chr19:4499397-4499639(+)$1	242	125	129	12.0000
eeFF	chr7:139090414-139090633(+)$1	219	44	48	12.0000

#DB
))..	chrX:153276913-153277175(-)$1	1	78	82	12.0000
....	chr10:124766441-124766674(-)$1	1	55	59	12.0000
.)))	chr11:95522832-95523077(-)$1	1	45	49	12.0000
)..(	chr13:31037676-31037925(-)$1	1	128	132	12.0000
....	chr19:58324578-58324818(-)$1	1	45	49	12.0000
....	chr13:96277003-96277263(-)$1	1	107	111	12.0000
((((	chr6:170713750-170713987(+)$1	1	214	218	12.0000
...(	chr3:128598426-128598669(+)$1	1	67	71	12.0000
..((	chr16:69943216-69943450(+)$1	1	54	58	12.0000
))))	chr7:39745673-39745910(+)$1	1	90	94	12.0000
((((	chr16:15128213-15128436(+)$1	1	1	5	12.0000
))))	chr17:41107776-41108032(-)$1	1	66	70	12.0000
))))	chr6:24415198-24415432(+)$1	1	156	160	12.0000
(.((	chr19:16192659-16192941(+)$1	1	66	70	12.0000
((((	chr19:59066143-59066398(-)$1	1	0	4	12.0000
)))(	chr7:140082211-140082448(-)$1	1	51	55	12.0000
))))	chr19:36001152-36001393(-)$1	1	109	113	12.0000
((..	chr3:58410528-58410795(+)$1	1	146	150	12.0000
(..(	chr17:37617919-37618162(+)$1	1	8	12	12.0000
...)	chrX:132473192-132473437(-)$1	1	78	82	12.0000
)..)	chr1:220267443-220267682(+)$1	1	170	174	12.0000
((.(	chr2:26357730-26358004(+)$1	1	141	145	12.0000
))))	chr12:120634492-120634751(-)$1	1	116	120	12.0000
))))	chr1:203764707-203764951(+)$1	1	146	150	12.0000
)).)	chr12:110386105-110386345(-)$1	1	112	116	12.0000
...)	chr17:73059745-73060003(+)$1	1	122	126	12.0000
((((	chr2:233655648-233655896(+)$1	1	93	97	12.0000
((((	chr11:14521178-14521446(-)$1	1	212	216	12.0000
((((	chr9:131851214-131851441(+)$1	1	152	156	12.0000
....	chr3:197559022-197559277(+)$1	1	109	113	12.0000
))))	chr16:1559997-1560264(+)$1	1	75	79	12.0000
.(((	chr9:129266480-129266758(+)$1	1	157	161	12.0000
....	chr5:65460364-65460598(+)$1	1	119	123	12.0000
....	chr17:36968987-36969219(-)$1	1	102	106	12.0000
....	chr12:125432231-125432480(-)$1	1	244	248	12.0000
...(	chr19:1438705-1438947(+)$1	1	103	107	12.0000
))((	chr1:156280640-156280884(-)$1	1	205	209	12.0000
))))	chr6:144416519-144416776(-)$1	1	124	128	12.0000
....	chr13:77825313-77825559(-)$1	1	104	108	12.0000
)..)	chr5:141017108-141017349(+)$1	1	80	84	12.0000
.(((	chr3:196658305-196658555(+)$1	1	43	47	12.0000
((.(	chr4:1729665-1729984(+)$1	1	41	45	12.0000
(.(.	chr7:56099535-56099772(-)$1	1	103	107	12.0000
((((	chr2:73461338-73461595(+)$1	1	36	40	12.0000
....	chr16:29511255-29511509(-)$1	1	132	136	12.0000
))))	chr19:8528376-8528625(+)$1	1	119	123	12.0000
....	chr5:72794376-72794589(+)$1	1	59	63	12.0000
))..	chr19:4498200-4498426(+)$1	1	118	122	12.0000
(...	chr2:176049009-176049242(+)$1	1	58	62	12.0000
))))	chr19:12385687-12385930(-)$1	1	213	217	12.0000
....	chrX:154005043-154005277(+)$1	1	47	51	12.0000
(...	chr7:23351616-23351853(-)$1	1	129	133	12.0000
....	chr17:47684577-47684819(-)$1	1	115	119	12.0000
...)	chr11:130005408-130005652(+)$1	1	12	16	12.0000
...)	chrX:149102127-149102333(-)$1	1	92	96	12.0000
))))	chr6:4891876-4892116(+)$1	1	108	112	12.0000
...)	chr1:59249384-59249622(-)$1	1	198	202	12.0000
....	chr19:18420517-18420762(-)$1	1	234	238	12.0000
)...	chr17:62500757-62501062(-)$1	1	125	129	12.0000
..((	chr6:36181909-36182144(+)$1	1	60	64	12.0000
(.((	chr22:38902052-38902311(-)$1	1	16	20	12.0000
((((	chr3:56627623-56627855(+)$1	1	64	68	12.0000
..((	chr2:26068249-26068483(-)$1	1	114	118	12.0000
..((	chr17:56429365-56429606(-)$1	1	0	4	12.0000
....	chr4:17811958-17812235(-)$1	1	28	32	12.0000
((((	chr1:146037338-146037604(-)$1	1	16	20	12.0000
....	chr13:53217492-53217742(+)$1	1	87	91	12.0000
..((	chr19:51302435-51302696(-)$1	1	87	91	12.0000
((.(	chr8:142011181-142011428(-)$1	1	130	134	12.0000
.)))	chr4:122734929-122735174(+)$1	1	12	16	12.0000
...(	chr12:76451474-76451724(+)$1	1	16	20	12.0000
....	chr22:42290806-42291037(+)$1	1	102	106	12.0000
((.(	chr16:84004928-84005180(+)$1	1	63	67	12.0000
....	chrX:118986781-118987017(-)$1	1	128	132	12.0000
..))	chr7:99661835-99662064(-)$1	1	55	59	12.0000
((..	chrX:153999005-153999243(+)$1	1	133	137	12.0000
))))	chr7:102963944-102964174(-)$1	1	104	108	12.0000
..))	chr6:32945613-32945854(+)$1	1	67	71	12.0000
.)..	chr6:75994241-75994506(-)$1	1	172	176	12.0000
....	chr1:36235415-36235665(-)$1	1	4	8	12.0000
...)	chr19:18420432-18420683(-)$1	1	155	159	12.0000
...)	chr17:73143578-73143809(-)$1	1	36	40	12.0000
((((	chr15:91560934-91561191(-)$1	1	28	32	12.0000
..((	chr19:8538950-8539212(+)$1	1	2	6	12.0000
..))	chr7:27181300-27181506(-)$1	1	148	152	12.0000
(..(	chr11:74660293-74660526(+)$1	1	65	69	12.0000
)..)	chr19:58899403-58899630(+)$1	1	163	167	12.0000
(...	chr19:11024450-11024681(+)$1	1	62	66	12.0000
.)))	chr22:30165667-30165899(+)$1	1	67	71	12.0000
....	chr4:20255106-20255364(+)$1	1	23	27	12.0000
))).	chr19:4499397-4499639(+)$1	1	125	129	12.0000
))((	chr7:139090414-139090633(+)$1	1	44	48	12.0000

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

#score	1104.0000000000007
#seq	92
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_CDS_m1_run2.nuc.txt

#NT
UGGA	chr11:9459252-9459477(+)$1	225	64	68	11.9999
UGGA	chr17:28599516-28599747(-)$1	231	124	128	11.9999
UGGA	chrX:47497376-47497601(-)$1	225	72	76	11.9999
UGGA	chr19:15226748-15226978(-)$1	230	176	180	11.9999
UGGA	chr15:41812551-41812780(-)$1	229	40	44	11.9999
UGGA	chr10:26986563-26986787(+)$1	224	116	120	11.9999
UGGA	chr1:43224777-43224999(+)$1	222	105	109	11.9999
UGGA	chr12:6601392-6601629(-)$1	237	52	56	11.9999
UGGA	chr19:17691488-17691719(+)$1	231	45	49	11.9999
UGGA	chrX:9914784-9915008(+)$1	224	116	120	11.9999
UGGA	chr4:122593650-122593883(-)$1	233	51	55	11.9999
UGGA	chr9:131750266-131750490(+)$1	224	175	179	11.9999
UGGA	chr3:78987727-78987957(-)$1	230	30	34	11.9999
UGGA	chr1:78045083-78045313(-)$1	230	7	11	11.9999
UGGA	chr3:142281627-142281851(-)$1	224	113	117	11.9999
UGGA	chr1:46206722-46206946(-)$1	224	69	73	11.9999
UGGA	chr3:31663655-31663890(+)$1	235	89	93	11.9999
UGGA	chr17:36863666-36863894(+)$1	228	122	126	11.9999
UGGA	chr19:57061812-57062038(+)$1	226	122	126	11.9999
UGGA	chr13:113973820-113974052(+)$1	232	56	60	11.9999
UGGA	chr19:18650400-18650630(-)$1	230	87	91	11.9999
UGGA	chr17:53040657-53040885(-)$1	228	158	162	11.9999
UGGA	chr2:201756596-201756830(+)$1	234	152	156	11.9999
UGGA	chr5:180670191-180670467(-)$1	276	15	19	11.9999
UGGA	chr20:30156893-30157126(+)$1	233	109	113	11.9999
UGGA	chr17:29669993-29670220(+)$1	227	70	74	11.9999
UGGA	chr20:5154087-5154314(+)$1	227	107	111	11.9999
UGGA	chr9:134360385-134360615(+)$1	230	83	87	11.9999
UGGA	chr19:48626104-48626328(-)$1	224	85	89	11.9999
UGGA	chr19:4491457-4491679(-)$1	222	83	87	11.9999
UGGA	chr13:79933661-79933897(-)$1	236	112	116	11.9999
UGGA	chr15:69076664-69076909(-)$1	245	138	142	11.9999
UGGA	chr18:43418826-43419051(-)$1	225	98	102	11.9999
UGGA	chr15:68500468-68500702(-)$1	234	52	56	11.9999
UGGA	chr15:83826124-83826352(-)$1	228	68	72	11.9999
UGGA	chr4:113570691-113570921(+)$1	230	6	10	11.9999
UGGA	chr20:9560786-9561009(+)$1	223	8	12	11.9999
UGGA	chr20:36488258-36488481(+)$1	223	106	110	11.9999
UGGA	chr19:45648339-45648565(+)$1	226	63	67	11.9999
UGGA	chr1:29070355-29070578(+)$1	223	27	31	11.9999
UGGA	chr4:108955377-108955609(+)$1	232	29	33	11.9999
UGGA	chr7:100410389-100410614(-)$1	225	163	167	11.9999
UGGA	chr14:106321781-106322004(+)$1	223	61	65	11.9999
UGGA	chr17:38457722-38457948(+)$1	226	46	50	11.9999
UGGA	chr17:45741484-45741712(+)$1	228	125	129	11.9999
UGGA	chr22:37708015-37708236(+)$1	221	52	56	11.9999
UGGA	chrX:19376996-19377225(+)$1	229	132	136	11.9999
UGGA	chr1:222734639-222734868(-)$1	229	36	40	11.9999
UGGA	chr11:46783519-46783748(-)$1	229	11	15	11.9999
UGGA	chrX:154157344-154157567(+)$1	223	175	179	11.9999
UGGA	chr11:61895604-61895842(+)$1	238	63	67	11.9999
UGGA	chr12:100707180-100707410(+)$1	230	147	151	11.9999
UGGA	chr12:122677290-122677512(+)$1	222	59	63	11.9999
UGGA	chr9:35725570-35725820(-)$1	250	23	27	11.9999
UGGA	chr14:58701107-58701332(+)$1	225	91	95	11.9999
UGGA	chr6:123318857-123319081(+)$1	224	102	106	11.9999
UGGA	chr11:47660445-47660677(-)$1	232	30	34	11.9999
UGGA	chrM:12564-12820(-)$1	256	67	71	11.9999
UGGA	chr1:89289921-89290151(+)$1	230	82	86	11.9999
UGGA	chr2:62105932-62106172(-)$1	240	68	72	11.9999
UGGA	chr5:139006249-139006491(+)$1	242	29	33	11.9999
UGGA	chr19:5705792-5706041(-)$1	249	39	43	11.9999
UGGA	chr17:62589505-62589730(-)$1	225	45	49	11.9999
UGGA	chr1:93309586-93309808(-)$1	222	118	122	11.9999
UGGA	chr11:46797765-46797992(-)$1	227	129	133	11.9999
UGGA	chr14:102514121-102514349(+)$1	228	35	39	11.9999
UGGA	chr13:79932316-79932548(-)$1	232	31	35	11.9999
UGGA	chr17:43111583-43111811(-)$1	228	116	120	11.9999
UGGA	chr7:129987555-129987778(+)$1	223	110	114	11.9999
UGGA	chr1:38046869-38047098(-)$1	229	15	19	11.9999
UGGA	chr22:50716975-50717206(-)$1	231	120	124	11.9999
UGGA	chr3:145789099-145789321(-)$1	222	73	77	11.9999
UGGA	chr17:30179752-30179983(-)$1	231	12	16	11.9999
UGGA	chr22:39125396-39125618(-)$1	222	115	119	11.9999
UGGA	chr21:31587773-31587995(-)$1	222	117	121	11.9999
UGGA	chr5:118877575-118877803(+)$1	228	140	144	11.9999
UGGA	chr17:26890378-26890604(-)$1	226	18	22	11.9999
UGGA	chr12:122248491-122248720(+)$1	229	65	69	11.9999
UGGA	chr3:128350752-128350977(-)$1	225	74	78	11.9999
UGGA	chr17:66251741-66251982(+)$1	241	20	24	11.9999
UGGA	chr5:876194-876424(-)$1	230	144	148	11.9999
UGGA	chr1:156182728-156182964(+)$1	236	60	64	11.9999
UGGA	chr11:22647104-22647325(-)$1	221	141	145	11.9999
UGGA	chr8:25364092-25364316(+)$1	224	207	211	11.9999
UGGA	chr8:28575547-28575774(+)$1	227	114	118	11.9999
UGGA	chr12:56397930-56398157(+)$1	227	84	88	11.9999

#otherMatches

#Struct PSSM
HHHK	chr12:121951027-121951253(-)$1	226	9	13	11.9999
]ddd	chr11:9459252-9459477(+)$1	225	64	68	11.9999
bb]c	chr17:28599516-28599747(-)$1	231	124	128	11.9999
oodd	chrX:47497376-47497601(-)$1	225	72	76	11.9999
[ccc	chr19:15226748-15226978(-)$1	230	176	180	11.9999
EEE{	chr15:41812551-41812780(-)$1	229	40	44	11.9999
rrrr	chr10:26986563-26986787(+)$1	224	116	120	11.9999
ennn	chr1:43224777-43224999(+)$1	222	105	109	11.9999
gg""	chr12:6601392-6601629(-)$1	237	52	56	11.9999
GKKD	chr19:17691488-17691719(+)$1	231	45	49	11.9999
dddd	chrX:9914784-9915008(+)$1	224	116	120	11.9999
ffff	chr4:122593650-122593883(-)$1	233	51	55	11.9999
GGGY	chr9:131750266-131750490(+)$1	224	175	179	11.9999
[bb"	chr3:78987727-78987957(-)$1	230	30	34	11.9999
eell	chr1:78045083-78045313(-)$1	230	7	11	11.9999
gggg	chr3:142281627-142281851(-)$1	224	113	117	11.9999
dddd	chr1:46206722-46206946(-)$1	224	69	73	11.9999
dddd	chr3:31663655-31663890(+)$1	235	89	93	11.9999
"a[g	chr17:36863666-36863894(+)$1	228	122	126	11.9999
FFFF	chr19:57061812-57062038(+)$1	226	122	126	11.9999
ccc4	chr13:113973820-113974052(+)$1	232	56	60	11.9999
dd33	chr19:18650400-18650630(-)$1	230	87	91	11.9999
3ccc	chr17:53040657-53040885(-)$1	228	158	162	11.9999
[ccc	chr2:201756596-201756830(+)$1	234	152	156	11.9999
!ddd	chr5:180670191-180670467(-)$1	276	15	19	11.9999
FFF}	chr20:30156893-30157126(+)$1	233	109	113	11.9999
ffff	chr17:29669993-29670220(+)$1	227	70	74	11.9999
bb[h	chr20:5154087-5154314(+)$1	227	107	111	11.9999
oddd	chr9:134360385-134360615(+)$1	230	83	87	11.9999
FFF~	chr19:48626104-48626328(-)$1	224	85	89	11.9999
eeee	chr19:4491457-4491679(-)$1	222	83	87	11.9999
{FFF	chr13:79933661-79933897(-)$1	236	112	116	11.9999
C}DD	chr15:69076664-69076909(-)$1	245	138	142	11.9999
EE::	chr18:43418826-43419051(-)$1	225	98	102	11.9999
4ddd	chr15:68500468-68500702(-)$1	234	52	56	11.9999
ZZFF	chr15:83826124-83826352(-)$1	228	68	72	11.9999
ffff	chr4:113570691-113570921(+)$1	230	6	10	11.9999
::bb	chr20:9560786-9561009(+)$1	223	8	12	11.9999
eeee	chr20:36488258-36488481(+)$1	223	106	110	11.9999
qqqq	chr19:45648339-45648565(+)$1	226	63	67	11.9999
gggg	chr1:29070355-29070578(+)$1	223	27	31	11.9999
DDDD	chr4:108955377-108955609(+)$1	232	29	33	11.9999
ccc[	chr7:100410389-100410614(-)$1	225	163	167	11.9999
{BBM	chr14:106321781-106322004(+)$1	223	61	65	11.9999
nnnn	chr17:38457722-38457948(+)$1	226	46	50	11.9999
eeeo	chr17:45741484-45741712(+)$1	228	125	129	11.9999
dbbd	chr22:37708015-37708236(+)$1	221	52	56	11.9999
]eee	chrX:19376996-19377225(+)$1	229	132	136	11.9999
::::	chr1:222734639-222734868(-)$1	229	36	40	11.9999
c!!c	chr11:46783519-46783748(-)$1	229	11	15	11.9999
ccmm	chrX:154157344-154157567(+)$1	223	175	179	11.9999
""dd	chr11:61895604-61895842(+)$1	238	63	67	11.9999
ghhh	chr12:100707180-100707410(+)$1	230	147	151	11.9999
ABB:	chr12:122677290-122677512(+)$1	222	59	63	11.9999
ccc+	chr9:35725570-35725820(-)$1	250	23	27	11.9999
DDDM	chr14:58701107-58701332(+)$1	225	91	95	11.9999
eee#	chr6:123318857-123319081(+)$1	224	102	106	11.9999
yyyy	chr11:47660445-47660677(-)$1	232	30	34	11.9999
gooo	chrM:12564-12820(-)$1	256	67	71	11.9999
5fff	chr1:89289921-89290151(+)$1	230	82	86	11.9999
ffff	chr2:62105932-62106172(-)$1	240	68	72	11.9999
::::	chr5:139006249-139006491(+)$1	242	29	33	11.9999
eee[	chr19:5705792-5706041(-)$1	249	39	43	11.9999
HHHH	chr17:62589505-62589730(-)$1	225	45	49	11.9999
a]dd	chr1:93309586-93309808(-)$1	222	118	122	11.9999
eeee	chr11:46797765-46797992(-)$1	227	129	133	11.9999
ccc:	chr14:102514121-102514349(+)$1	228	35	39	11.9999
eeet	chr13:79932316-79932548(-)$1	232	31	35	11.9999
gggg	chr17:43111583-43111811(-)$1	228	116	120	11.9999
GGGG	chr7:129987555-129987778(+)$1	223	110	114	11.9999
[ccc	chr1:38046869-38047098(-)$1	229	15	19	11.9999
gggg	chr22:50716975-50717206(-)$1	231	120	124	11.9999
eeee	chr3:145789099-145789321(-)$1	222	73	77	11.9999
BBKK	chr17:30179752-30179983(-)$1	231	12	16	11.9999
na]c	chr22:39125396-39125618(-)$1	222	115	119	11.9999
b444	chr21:31587773-31587995(-)$1	222	117	121	11.9999
eee>	chr5:118877575-118877803(+)$1	228	140	144	11.9999
{ABB	chr17:26890378-26890604(-)$1	226	18	22	11.9999
gggg	chr12:122248491-122248720(+)$1	229	65	69	11.9999
cc99	chr3:128350752-128350977(-)$1	225	74	78	11.9999
ggoo	chr17:66251741-66251982(+)$1	241	20	24	11.9999
ddd[	chr5:876194-876424(-)$1	230	144	148	11.9999
HHHH	chr1:156182728-156182964(+)$1	236	60	64	11.9999
:eee	chr11:22647104-22647325(-)$1	221	141	145	11.9999
c444	chr8:25364092-25364316(+)$1	224	207	211	11.9999
cccp	chr8:28575547-28575774(+)$1	227	114	118	11.9999
:hhh	chr12:56397930-56398157(+)$1	227	84	88	11.9999

#DB
(((.	chr12:121951027-121951253(-)$1	1	9	13	11.9999
.)))	chr11:9459252-9459477(+)$1	1	64	68	11.9999
)).)	chr17:28599516-28599747(-)$1	1	124	128	11.9999
..))	chrX:47497376-47497601(-)$1	1	72	76	11.9999
.(((	chr19:15226748-15226978(-)$1	1	176	180	11.9999
(((.	chr15:41812551-41812780(-)$1	1	40	44	11.9999
....	chr10:26986563-26986787(+)$1	1	116	120	11.9999
(...	chr1:43224777-43224999(+)$1	1	105	109	11.9999
((..	chr12:6601392-6601629(-)$1	1	52	56	11.9999
(..(	chr19:17691488-17691719(+)$1	1	45	49	11.9999
((((	chrX:9914784-9915008(+)$1	1	116	120	11.9999
))))	chr4:122593650-122593883(-)$1	1	51	55	11.9999
))).	chr9:131750266-131750490(+)$1	1	175	179	11.9999
.((.	chr3:78987727-78987957(-)$1	1	30	34	11.9999
((..	chr1:78045083-78045313(-)$1	1	7	11	11.9999
))))	chr3:142281627-142281851(-)$1	1	113	117	11.9999
))))	chr1:46206722-46206946(-)$1	1	69	73	11.9999
))))	chr3:31663655-31663890(+)$1	1	89	93	11.9999
.(.(	chr17:36863666-36863894(+)$1	1	122	126	11.9999
))))	chr19:57061812-57062038(+)$1	1	122	126	11.9999
))).	chr13:113973820-113974052(+)$1	1	56	60	11.9999
))..	chr19:18650400-18650630(-)$1	1	87	91	11.9999
.)))	chr17:53040657-53040885(-)$1	1	158	162	11.9999
.(((	chr2:201756596-201756830(+)$1	1	152	156	11.9999
.(((	chr5:180670191-180670467(-)$1	1	15	19	11.9999
))).	chr20:30156893-30157126(+)$1	1	109	113	11.9999
))))	chr17:29669993-29670220(+)$1	1	70	74	11.9999
((.(	chr20:5154087-5154314(+)$1	1	107	111	11.9999
.)))	chr9:134360385-134360615(+)$1	1	83	87	11.9999
))).	chr19:48626104-48626328(-)$1	1	85	89	11.9999
))))	chr19:4491457-4491679(-)$1	1	83	87	11.9999
.(((	chr13:79933661-79933897(-)$1	1	112	116	11.9999
).))	chr15:69076664-69076909(-)$1	1	138	142	11.9999
((..	chr18:43418826-43419051(-)$1	1	98	102	11.9999
.)))	chr15:68500468-68500702(-)$1	1	52	56	11.9999
..))	chr15:83826124-83826352(-)$1	1	68	72	11.9999
((((	chr4:113570691-113570921(+)$1	1	6	10	11.9999
..((	chr20:9560786-9561009(+)$1	1	8	12	11.9999
))))	chr20:36488258-36488481(+)$1	1	106	110	11.9999
....	chr19:45648339-45648565(+)$1	1	63	67	11.9999
))))	chr1:29070355-29070578(+)$1	1	27	31	11.9999
((((	chr4:108955377-108955609(+)$1	1	29	33	11.9999
(((.	chr7:100410389-100410614(-)$1	1	163	167	11.9999
.((.	chr14:106321781-106322004(+)$1	1	61	65	11.9999
....	chr17:38457722-38457948(+)$1	1	46	50	11.9999
(((.	chr17:45741484-45741712(+)$1	1	125	129	11.9999
((((	chr22:37708015-37708236(+)$1	1	52	56	11.9999
.)))	chrX:19376996-19377225(+)$1	1	132	136	11.9999
....	chr1:222734639-222734868(-)$1	1	36	40	11.9999
(..(	chr11:46783519-46783748(-)$1	1	11	15	11.9999
((..	chrX:154157344-154157567(+)$1	1	175	179	11.9999
..((	chr11:61895604-61895842(+)$1	1	63	67	11.9999
))))	chr12:100707180-100707410(+)$1	1	147	151	11.9999
(((.	chr12:122677290-122677512(+)$1	1	59	63	11.9999
(((.	chr9:35725570-35725820(-)$1	1	23	27	11.9999
(((.	chr14:58701107-58701332(+)$1	1	91	95	11.9999
(((.	chr6:123318857-123319081(+)$1	1	102	106	11.9999
....	chr11:47660445-47660677(-)$1	1	30	34	11.9999
(...	chrM:12564-12820(-)$1	1	67	71	11.9999
.)))	chr1:89289921-89290151(+)$1	1	82	86	11.9999
))))	chr2:62105932-62106172(-)$1	1	68	72	11.9999
....	chr5:139006249-139006491(+)$1	1	29	33	11.9999
(((.	chr19:5705792-5706041(-)$1	1	39	43	11.9999
((((	chr17:62589505-62589730(-)$1	1	45	49	11.9999
).))	chr1:93309586-93309808(-)$1	1	118	122	11.9999
))))	chr11:46797765-46797992(-)$1	1	129	133	11.9999
))).	chr14:102514121-102514349(+)$1	1	35	39	11.9999
(((.	chr13:79932316-79932548(-)$1	1	31	35	11.9999
))))	chr17:43111583-43111811(-)$1	1	116	120	11.9999
))))	chr7:129987555-129987778(+)$1	1	110	114	11.9999
.(((	chr1:38046869-38047098(-)$1	1	15	19	11.9999
))))	chr22:50716975-50717206(-)$1	1	120	124	11.9999
((((	chr3:145789099-145789321(-)$1	1	73	77	11.9999
((..	chr17:30179752-30179983(-)$1	1	12	16	11.9999
.).)	chr22:39125396-39125618(-)$1	1	115	119	11.9999
)...	chr21:31587773-31587995(-)$1	1	117	121	11.9999
))).	chr5:118877575-118877803(+)$1	1	140	144	11.9999
.(((	chr17:26890378-26890604(-)$1	1	18	22	11.9999
))))	chr12:122248491-122248720(+)$1	1	65	69	11.9999
))..	chr3:128350752-128350977(-)$1	1	74	78	11.9999
((..	chr17:66251741-66251982(+)$1	1	20	24	11.9999
(((.	chr5:876194-876424(-)$1	1	144	148	11.9999
((((	chr1:156182728-156182964(+)$1	1	60	64	11.9999
.(((	chr11:22647104-22647325(-)$1	1	141	145	11.9999
)...	chr8:25364092-25364316(+)$1	1	207	211	11.9999
(((.	chr8:28575547-28575774(+)$1	1	114	118	11.9999
.(((	chr12:56397930-56398157(+)$1	1	84	88	11.9999

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

#score	1043.9999999999998
#seq	87
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m3_run2.nuc.txt

#NT
CAG	chr9:36003068-36003283(-)$1	215	14	17	8.9999
CAG	chr6:33166087-33166307(+)$1	220	14	17	8.9999
CAG	chr10:52834539-52834759(-)$1	220	26	29	8.9999
CAG	chr11:12283929-12284177(+)$1	248	94	97	8.9999
CAG	chr9:88592250-88592467(-)$1	217	8	11	8.9999
CAG	chr7:44154871-44155091(-)$1	220	25	28	8.9999
CAG	chr19:40886822-40887041(+)$1	219	19	22	8.9999
CAG	chr17:25950558-25950780(+)$1	222	78	81	8.9999
CAG	chrX:153135158-153135375(-)$1	217	12	15	8.9999
CAG	chr7:139305046-139305264(-)$1	218	22	25	8.9999
CAG	chr6:46655933-46656151(+)$1	218	22	25	8.9999
CAG	chr17:42945086-42945306(-)$1	220	19	22	8.9999
CAG	chr21:46697946-46698161(-)$1	215	0	3	8.9999
CAG	chr10:70992750-70992967(+)$1	217	16	19	8.9999
CAG	chr22:18220819-18221042(+)$1	223	74	77	8.9999
CAG	chr5:79616055-79616275(+)$1	220	146	149	8.9999
CAG	chr10:103588852-103589074(-)$1	222	53	56	8.9999
CAG	chr5:134686446-134686663(-)$1	217	29	32	8.9999
CAG	chr1:149882388-149882619(-)$1	231	21	24	8.9999
CAG	chr5:80809367-80809583(+)$1	216	31	34	8.9999
CAG	chr17:29663781-29664004(+)$1	223	13	16	8.9999
CAG	chr13:86368132-86368351(+)$1	219	0	3	8.9999
CAG	chr20:17587635-17587850(+)$1	215	76	79	8.9999
CAG	chr2:55806773-55807001(-)$1	228	54	57	8.9999
CAG	chr2:101883088-101883308(+)$1	220	105	108	8.9999
CAG	chr5:160761788-160762009(-)$1	221	108	111	8.9999
CAG	chr1:3544995-3545216(+)$1	221	41	44	8.9999
CAG	chr4:156135929-156136145(-)$1	216	0	3	8.9999
CAG	chr17:79662779-79663004(+)$1	225	14	17	8.9999
CAG	chr17:40843135-40843352(+)$1	217	16	19	8.9999
CAG	chr1:183513481-183513702(+)$1	221	3	6	8.9999
CAG	chr9:35555496-35555730(+)$1	234	36	39	8.9999
CAG	chr16:21985165-21985386(+)$1	221	27	30	8.9999
CAG	chr2:204009330-204009545(-)$1	215	55	58	8.9999
CAG	chr9:100675598-100675813(-)$1	215	25	28	8.9999
CAG	chr2:70070180-70070395(+)$1	215	43	46	8.9999
CAG	chr19:3902400-3902619(+)$1	219	81	84	8.9999
CAG	chr12:57598423-57598647(+)$1	224	114	117	8.9999
CAG	chr6:29589827-29590046(-)$1	219	121	124	8.9999
CAG	chr16:30036590-30036813(-)$1	223	22	25	8.9999
CAG	chr3:186793418-186793633(-)$1	215	46	49	8.9999
cag	chr15:51386743-51386962(-)$1	219	45	48	8.9999
CAG	chrX:70389704-70389938(+)$1	234	159	162	8.9999
CAG	chr16:2156048-2156266(+)$1	218	1	4	8.9999
CAG	chr22:50658922-50659152(-)$1	230	27	30	8.9999
CAG	chr17:6364751-6364975(-)$1	224	10	13	8.9999
CAG	chr3:32569951-32570177(-)$1	226	124	127	8.9999
CAG	chr9:104184053-104184277(+)$1	224	50	53	8.9999
CAG	chr17:56658905-56659124(+)$1	219	89	92	8.9999
CAG	chr11:64537726-64537948(-)$1	222	36	39	8.9999
CAG	chr9:101606370-101606587(-)$1	217	64	67	8.9999
CAG	chr16:85682187-85682410(+)$1	223	22	25	8.9999
CAG	chrX:147010149-147010366(+)$1	217	24	27	8.9999
CAG	chrX:38128810-38129026(-)$1	216	8	11	8.9999
CAG	chr22:32010686-32010905(+)$1	219	21	24	8.9999
CAG	chr21:43267117-43267337(-)$1	220	40	43	8.9999
CAG	chr17:38249326-38249549(+)$1	223	33	36	8.9999
CAG	chr5:139201425-139201649(+)$1	224	17	20	8.9999
cag	chr5:74848194-74848409(-)$1	215	200	203	8.9999
CAG	chr3:44670869-44671097(+)$1	228	14	17	8.9999
CAG	chr1:87538689-87538935(+)$1	246	39	42	8.9999
cag	chr17:39279932-39280148(+)$1	216	5	8	8.9999
CAG	chr20:4162362-4162578(+)$1	216	62	65	8.9999
CAG	chr14:102550168-102550390(-)$1	222	20	23	8.9999
CAG	chr11:109294460-109294677(+)$1	217	11	14	8.9999
CAG	chr1:173941594-173941823(-)$1	229	81	84	8.9999
CAG	chr19:53518022-53518238(+)$1	216	6	9	8.9999
CAG	chr7:150814091-150814311(+)$1	220	87	90	8.9999
CAG	chr6:135303557-135303776(+)$1	219	27	30	8.9999
CAG	chrX:49126760-49126979(+)$1	219	155	158	8.9999
CAG	chr12:78400501-78400731(+)$1	230	17	20	8.9999
CAG	chr11:73073548-73073769(+)$1	221	9	12	8.9999
CAG	chr17:28445056-28445274(-)$1	218	11	14	8.9999
CAG	chr8:3432428-3432647(-)$1	219	56	59	8.9999
CAG	chr10:50149737-50149953(+)$1	216	2	5	8.9999
CAG	chr22:50728715-50728930(+)$1	215	1	4	8.9999
CAG	chr17:80579406-80579628(-)$1	222	24	27	8.9999
CAG	chr16:54145689-54145906(-)$1	217	94	97	8.9999
CAG	chr16:67516906-67517122(-)$1	216	106	109	8.9999
CAG	chr9:87359872-87360104(+)$1	232	27	30	8.9999
CAG	chr5:108713942-108714158(-)$1	216	40	43	8.9999
CAG	chr10:73579920-73580150(-)$1	230	21	24	8.9999
CAG	chr9:114137272-114137505(-)$1	233	45	48	8.9999
CAG	chr19:56662919-56663137(-)$1	218	16	19	8.9999
CAG	chr2:242432231-242432449(-)$1	218	23	26	8.9999
cag	chr2:231072665-231072887(+)$1	222	6	9	8.9999
CAG	chr19:19368849-19369067(-)$1	218	7	10	8.9999
CAG	chr1:237948074-237948309(+)$1	235	46	49	8.9999
CAG	chr16:87525173-87525388(+)$1	215	26	29	8.9999
CAG	chr3:66433483-66433701(-)$1	218	40	43	8.9999
CAG	chr1:225488626-225488841(-)$1	215	44	47	8.9999
CAG	chr7:99955760-99955977(+)$1	217	37	40	8.9999
CAG	chr10:96072970-96073185(-)$1	215	34	37	8.9999
CAG	chr5:167622176-167622393(+)$1	217	1	4	8.9999
CAG	chr2:21361717-21361932(+)$1	215	45	48	8.9999
CAG	chr1:2522406-2522631(+)$1	225	3	6	8.9999

#otherMatches

#Struct PSSM
ff]	chr17:80696345-80696560(+)$1	215	16	19	8.9999
!bb	chr9:36003068-36003283(-)$1	215	14	17	8.9999
fff	chr6:33166087-33166307(+)$1	220	14	17	8.9999
^^^	chr10:52834539-52834759(-)$1	220	26	29	8.9999
ccc	chr11:12283929-12284177(+)$1	248	94	97	8.9999
LCC	chr9:88592250-88592467(-)$1	217	8	11	8.9999
cc!	chr7:44154871-44155091(-)$1	220	25	28	8.9999
ddd	chr19:40886822-40887041(+)$1	219	19	22	8.9999
3cc	chr17:25950558-25950780(+)$1	222	78	81	8.9999
FFF	chrX:153135158-153135375(-)$1	217	12	15	8.9999
vvv	chr7:139305046-139305264(-)$1	218	22	25	8.9999
===	chr6:46655933-46656151(+)$1	218	22	25	8.9999
eee	chr17:42945086-42945306(-)$1	220	19	22	8.9999
:::	chr21:46697946-46698161(-)$1	215	0	3	8.9999
EEG	chr10:70992750-70992967(+)$1	217	16	19	8.9999
ggg	chr22:18220819-18221042(+)$1	223	74	77	8.9999
ddd	chr5:79616055-79616275(+)$1	220	146	149	8.9999
EEg	chr10:103588852-103589074(-)$1	222	53	56	8.9999
eee	chr5:134686446-134686663(-)$1	217	29	32	8.9999
NNN	chr1:149882388-149882619(-)$1	231	21	24	8.9999
:BB	chr5:80809367-80809583(+)$1	216	31	34	8.9999
{EE	chr17:29663781-29664004(+)$1	223	13	16	8.9999
::c	chr13:86368132-86368351(+)$1	219	0	3	8.9999
::d	chr20:17587635-17587850(+)$1	215	76	79	8.9999
fff	chr2:55806773-55807001(-)$1	228	54	57	8.9999
:::	chr2:101883088-101883308(+)$1	220	105	108	8.9999
9a]	chr5:160761788-160762009(-)$1	221	108	111	8.9999
foo	chr1:3544995-3545216(+)$1	221	41	44	8.9999
:::	chr4:156135929-156136145(-)$1	216	0	3	8.9999
ccc	chr17:79662779-79663004(+)$1	225	14	17	8.9999
fff	chr17:40843135-40843352(+)$1	217	16	19	8.9999
:EE	chr1:183513481-183513702(+)$1	221	3	6	8.9999
rrc	chr9:35555496-35555730(+)$1	234	36	39	8.9999
c::	chr16:21985165-21985386(+)$1	221	27	30	8.9999
ggg	chr2:204009330-204009545(-)$1	215	55	58	8.9999
fff	chr9:100675598-100675813(-)$1	215	25	28	8.9999
EEE	chr2:70070180-70070395(+)$1	215	43	46	8.9999
ddd	chr19:3902400-3902619(+)$1	219	81	84	8.9999
::a	chr12:57598423-57598647(+)$1	224	114	117	8.9999
nee	chr6:29589827-29590046(-)$1	219	121	124	8.9999
ccc	chr16:30036590-30036813(-)$1	223	22	25	8.9999
##a	chr3:186793418-186793633(-)$1	215	46	49	8.9999
llb	chr15:51386743-51386962(-)$1	219	45	48	8.9999
ddn	chrX:70389704-70389938(+)$1	234	159	162	8.9999
ccc	chr16:2156048-2156266(+)$1	218	1	4	8.9999
d""	chr22:50658922-50659152(-)$1	230	27	30	8.9999
KFF	chr17:6364751-6364975(-)$1	224	10	13	8.9999
ffl	chr3:32569951-32570177(-)$1	226	124	127	8.9999
ccf	chr9:104184053-104184277(+)$1	224	50	53	8.9999
ccc	chr17:56658905-56659124(+)$1	219	89	92	8.9999
E{D	chr11:64537726-64537948(-)$1	222	36	39	8.9999
:DD	chr9:101606370-101606587(-)$1	217	64	67	8.9999
::F	chr16:85682187-85682410(+)$1	223	22	25	8.9999
{FF	chrX:147010149-147010366(+)$1	217	24	27	8.9999
[a!	chrX:38128810-38129026(-)$1	216	8	11	8.9999
LLB	chr22:32010686-32010905(+)$1	219	21	24	8.9999
HHH	chr21:43267117-43267337(-)$1	220	40	43	8.9999
A{D	chr17:38249326-38249549(+)$1	223	33	36	8.9999
eee	chr5:139201425-139201649(+)$1	224	17	20	8.9999
:::	chr5:74848194-74848409(-)$1	215	200	203	8.9999
ALL	chr3:44670869-44671097(+)$1	228	14	17	8.9999
cc[	chr1:87538689-87538935(+)$1	246	39	42	8.9999
eee	chr17:39279932-39280148(+)$1	216	5	8	8.9999
bb]	chr20:4162362-4162578(+)$1	216	62	65	8.9999
eee	chr14:102550168-102550390(-)$1	222	20	23	8.9999
ooo	chr11:109294460-109294677(+)$1	217	11	14	8.9999
eee	chr1:173941594-173941823(-)$1	229	81	84	8.9999
CC{	chr19:53518022-53518238(+)$1	216	6	9	8.9999
bgg	chr7:150814091-150814311(+)$1	220	87	90	8.9999
dff	chr6:135303557-135303776(+)$1	219	27	30	8.9999
HHH	chrX:49126760-49126979(+)$1	219	155	158	8.9999
ddd	chr12:78400501-78400731(+)$1	230	17	20	8.9999
FFF	chr11:73073548-73073769(+)$1	221	9	12	8.9999
WWW	chr17:28445056-28445274(-)$1	218	11	14	8.9999
ppp	chr8:3432428-3432647(-)$1	219	56	59	8.9999
:::	chr10:50149737-50149953(+)$1	216	2	5	8.9999
EEE	chr22:50728715-50728930(+)$1	215	1	4	8.9999
bbn	chr17:80579406-80579628(-)$1	222	24	27	8.9999
eee	chr16:54145689-54145906(-)$1	217	94	97	8.9999
KJJ	chr16:67516906-67517122(-)$1	216	106	109	8.9999
EE{	chr9:87359872-87360104(+)$1	232	27	30	8.9999
G:f	chr5:108713942-108714158(-)$1	216	40	43	8.9999
DDD	chr10:73579920-73580150(-)$1	230	21	24	8.9999
fff	chr9:114137272-114137505(-)$1	233	45	48	8.9999
::F	chr19:56662919-56663137(-)$1	218	16	19	8.9999
bb"	chr2:242432231-242432449(-)$1	218	23	26	8.9999
:gg	chr2:231072665-231072887(+)$1	222	6	9	8.9999
mmm	chr19:19368849-19369067(-)$1	218	7	10	8.9999
[ee	chr1:237948074-237948309(+)$1	235	46	49	8.9999
EEE	chr16:87525173-87525388(+)$1	215	26	29	8.9999
dd[	chr3:66433483-66433701(-)$1	218	40	43	8.9999
A::	chr1:225488626-225488841(-)$1	215	44	47	8.9999
ppc	chr7:99955760-99955977(+)$1	217	37	40	8.9999
!ee	chr10:96072970-96073185(-)$1	215	34	37	8.9999
::=	chr5:167622176-167622393(+)$1	217	1	4	8.9999
ttt	chr2:21361717-21361932(+)$1	215	45	48	8.9999
:::	chr1:2522406-2522631(+)$1	225	3	6	8.9999

#DB
)).	chr17:80696345-80696560(+)$1	1	16	19	8.9999
.((	chr9:36003068-36003283(-)$1	1	14	17	8.9999
(((	chr6:33166087-33166307(+)$1	1	14	17	8.9999
...	chr10:52834539-52834759(-)$1	1	26	29	8.9999
(((	chr11:12283929-12284177(+)$1	1	94	97	8.9999
.((	chr9:88592250-88592467(-)$1	1	8	11	8.9999
((.	chr7:44154871-44155091(-)$1	1	25	28	8.9999
(((	chr19:40886822-40887041(+)$1	1	19	22	8.9999
.))	chr17:25950558-25950780(+)$1	1	78	81	8.9999
(((	chrX:153135158-153135375(-)$1	1	12	15	8.9999
...	chr7:139305046-139305264(-)$1	1	22	25	8.9999
(((	chr6:46655933-46656151(+)$1	1	22	25	8.9999
)))	chr17:42945086-42945306(-)$1	1	19	22	8.9999
...	chr21:46697946-46698161(-)$1	1	0	3	8.9999
(((	chr10:70992750-70992967(+)$1	1	16	19	8.9999
)))	chr22:18220819-18221042(+)$1	1	74	77	8.9999
(((	chr5:79616055-79616275(+)$1	1	146	149	8.9999
(((	chr10:103588852-103589074(-)$1	1	53	56	8.9999
(((	chr5:134686446-134686663(-)$1	1	29	32	8.9999
...	chr1:149882388-149882619(-)$1	1	21	24	8.9999
.((	chr5:80809367-80809583(+)$1	1	31	34	8.9999
.((	chr17:29663781-29664004(+)$1	1	13	16	8.9999
..(	chr13:86368132-86368351(+)$1	1	0	3	8.9999
..(	chr20:17587635-17587850(+)$1	1	76	79	8.9999
)))	chr2:55806773-55807001(-)$1	1	54	57	8.9999
...	chr2:101883088-101883308(+)$1	1	105	108	8.9999
.).	chr5:160761788-160762009(-)$1	1	108	111	8.9999
(..	chr1:3544995-3545216(+)$1	1	41	44	8.9999
...	chr4:156135929-156136145(-)$1	1	0	3	8.9999
(((	chr17:79662779-79663004(+)$1	1	14	17	8.9999
(((	chr17:40843135-40843352(+)$1	1	16	19	8.9999
.((	chr1:183513481-183513702(+)$1	1	3	6	8.9999
..)	chr9:35555496-35555730(+)$1	1	36	39	8.9999
)..	chr16:21985165-21985386(+)$1	1	27	30	8.9999
)))	chr2:204009330-204009545(-)$1	1	55	58	8.9999
(((	chr9:100675598-100675813(-)$1	1	25	28	8.9999
(((	chr2:70070180-70070395(+)$1	1	43	46	8.9999
(((	chr19:3902400-3902619(+)$1	1	81	84	8.9999
..(	chr12:57598423-57598647(+)$1	1	114	117	8.9999
.))	chr6:29589827-29590046(-)$1	1	121	124	8.9999
)))	chr16:30036590-30036813(-)$1	1	22	25	8.9999
..(	chr3:186793418-186793633(-)$1	1	46	49	8.9999
..)	chr15:51386743-51386962(-)$1	1	45	48	8.9999
((.	chrX:70389704-70389938(+)$1	1	159	162	8.9999
(((	chr16:2156048-2156266(+)$1	1	1	4	8.9999
(..	chr22:50658922-50659152(-)$1	1	27	30	8.9999
.((	chr17:6364751-6364975(-)$1	1	10	13	8.9999
((.	chr3:32569951-32570177(-)$1	1	124	127	8.9999
(((	chr9:104184053-104184277(+)$1	1	50	53	8.9999
(((	chr17:56658905-56659124(+)$1	1	89	92	8.9999
(.(	chr11:64537726-64537948(-)$1	1	36	39	8.9999
.((	chr9:101606370-101606587(-)$1	1	64	67	8.9999
..(	chr16:85682187-85682410(+)$1	1	22	25	8.9999
.((	chrX:147010149-147010366(+)$1	1	24	27	8.9999
.(.	chrX:38128810-38129026(-)$1	1	8	11	8.9999
..(	chr22:32010686-32010905(+)$1	1	21	24	8.9999
(((	chr21:43267117-43267337(-)$1	1	40	43	8.9999
(.(	chr17:38249326-38249549(+)$1	1	33	36	8.9999
(((	chr5:139201425-139201649(+)$1	1	17	20	8.9999
...	chr5:74848194-74848409(-)$1	1	200	203	8.9999
(..	chr3:44670869-44671097(+)$1	1	14	17	8.9999
((.	chr1:87538689-87538935(+)$1	1	39	42	8.9999
(((	chr17:39279932-39280148(+)$1	1	5	8	8.9999
)).	chr20:4162362-4162578(+)$1	1	62	65	8.9999
(((	chr14:102550168-102550390(-)$1	1	20	23	8.9999
...	chr11:109294460-109294677(+)$1	1	11	14	8.9999
(((	chr1:173941594-173941823(-)$1	1	81	84	8.9999
((.	chr19:53518022-53518238(+)$1	1	6	9	8.9999
)))	chr7:150814091-150814311(+)$1	1	87	90	8.9999
)))	chr6:135303557-135303776(+)$1	1	27	30	8.9999
)))	chrX:49126760-49126979(+)$1	1	155	158	8.9999
)))	chr12:78400501-78400731(+)$1	1	17	20	8.9999
(((	chr11:73073548-73073769(+)$1	1	9	12	8.9999
...	chr17:28445056-28445274(-)$1	1	11	14	8.9999
...	chr8:3432428-3432647(-)$1	1	56	59	8.9999
...	chr10:50149737-50149953(+)$1	1	2	5	8.9999
(((	chr22:50728715-50728930(+)$1	1	1	4	8.9999
((.	chr17:80579406-80579628(-)$1	1	24	27	8.9999
(((	chr16:54145689-54145906(-)$1	1	94	97	8.9999
.((	chr16:67516906-67517122(-)$1	1	106	109	8.9999
((.	chr9:87359872-87360104(+)$1	1	27	30	8.9999
(.(	chr5:108713942-108714158(-)$1	1	40	43	8.9999
(((	chr10:73579920-73580150(-)$1	1	21	24	8.9999
(((	chr9:114137272-114137505(-)$1	1	45	48	8.9999
..(	chr19:56662919-56663137(-)$1	1	16	19	8.9999
((.	chr2:242432231-242432449(-)$1	1	23	26	8.9999
.((	chr2:231072665-231072887(+)$1	1	6	9	8.9999
...	chr19:19368849-19369067(-)$1	1	7	10	8.9999
.((	chr1:237948074-237948309(+)$1	1	46	49	8.9999
(((	chr16:87525173-87525388(+)$1	1	26	29	8.9999
((.	chr3:66433483-66433701(-)$1	1	40	43	8.9999
(..	chr1:225488626-225488841(-)$1	1	44	47	8.9999
..)	chr7:99955760-99955977(+)$1	1	37	40	8.9999
.((	chr10:96072970-96073185(-)$1	1	34	37	8.9999
..(	chr5:167622176-167622393(+)$1	1	1	4	8.9999
...	chr2:21361717-21361932(+)$1	1	45	48	8.9999
...	chr1:2522406-2522631(+)$1	1	3	6	8.9999

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

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m1_run2.nuc.txt

#NT
UUU	chr6:29911933-29912277(+)$1	344	301	304	9.0000
UUU	chr13:28014419-28014683(-)$1	264	66	69	9.0000
UUU	chr1:206903241-206903549(+)$1	308	9	12	9.0000
UUU	chr17:57756736-57756988(+)$1	252	16	19	9.0000
UUU	chr19:14516495-14516847(+)$1	352	138	141	9.0000
UUU	chr1:19523581-19523830(-)$1	249	1	4	9.0000
UUU	chr19:39330812-39331089(-)$1	277	54	57	9.0000
UUU	chr17:19850616-19850889(-)$1	273	36	39	9.0000
UUU	chr17:60028225-60028464(-)$1	239	43	46	9.0000
UUU	chr3:150285901-150286174(+)$1	273	22	25	9.0000
UUU	chr8:101721588-101721957(-)$1	369	28	31	9.0000
UUU	chr19:47285549-47285854(-)$1	305	18	21	9.0000
UUU	chr17:45747055-45747319(+)$1	264	67	70	9.0000
UUU	chr8:120650562-120650866(-)$1	304	24	27	9.0000
UUU	chr3:155654116-155654391(+)$1	275	1	4	9.0000
UUU	chr2:198272995-198273256(-)$1	261	191	194	9.0000
UUU	chr2:198359910-198360196(-)$1	286	13	16	9.0000
UUU	chr1:1720498-1720752(-)$1	254	9	12	9.0000
UUU	chr5:140699419-140699667(-)$1	248	5	8	9.0000
UUU	chr2:86406457-86406702(-)$1	245	47	50	9.0000
UUU	chr2:234345921-234346179(+)$1	258	42	45	9.0000
UUU	chr10:79795166-79795572(+)$1	406	30	33	9.0000
UUU	chr17:57744051-57744372(+)$1	321	17	20	9.0000
UUU	chr1:109337358-109337598(+)$1	240	3	6	9.0000
UUU	chr5:151170401-151170706(+)$1	305	0	3	9.0000
UUU	chr2:113308355-113308684(+)$1	329	56	59	9.0000
UUU	chr17:61829998-61830256(-)$1	258	56	59	9.0000
UUU	chr5:37052489-37052728(+)$1	239	58	61	9.0000
UUU	chr6:36070258-36070527(+)$1	269	29	32	9.0000
UUU	chr1:8926240-8926681(-)$1	441	239	242	9.0000
UUU	chr6:106555167-106555494(+)$1	327	40	43	9.0000
UUU	chr12:50829193-50829479(+)$1	286	33	36	9.0000
UUU	chr2:203104249-203104525(+)$1	276	10	13	9.0000
UUU	chr17:58531576-58531831(-)$1	255	54	57	9.0000
UUU	chr15:48766671-48766955(-)$1	284	14	17	9.0000
UUU	chr11:118888882-118889150(-)$1	268	35	38	9.0000
UUU	chr12:96410721-96410995(-)$1	274	6	9	9.0000
UUU	chr7:140159534-140159825(-)$1	291	71	74	9.0000
UUU	chr5:154179154-154179431(+)$1	277	103	106	9.0000
UUU	chr19:49403947-49404279(+)$1	332	274	277	9.0000
UUU	chr2:73476016-73476396(+)$1	380	8	11	9.0000
UUU	chr1:161179560-161179823(+)$1	263	54	57	9.0000
UUU	chr12:57920744-57921025(+)$1	281	55	58	9.0000
UUU	chr1:161017803-161018116(-)$1	313	141	144	9.0000
UUU	chr17:10608499-10608741(+)$1	242	103	106	9.0000
UUU	chr12:58144897-58145204(-)$1	307	65	68	9.0000
uuu	chr16:8994883-8995157(-)$1	274	0	3	9.0000
UUU	chr13:48523555-48523819(-)$1	264	17	20	9.0000
UUU	chr3:49050351-49050635(+)$1	284	44	47	9.0000
UUU	chr6:106554183-106554465(+)$1	282	94	97	9.0000
uuu	chr17:57728493-57728765(+)$1	272	39	42	9.0000
UUU	chr5:180664508-180664818(-)$1	310	13	16	9.0000
UUU	chr5:85915069-85915367(+)$1	298	18	21	9.0000
UUU	chr5:134086349-134086619(+)$1	270	4	7	9.0000
UUU	chr5:75964407-75964656(+)$1	249	24	27	9.0000
UUU	chr19:20807531-20807783(-)$1	252	64	67	9.0000
UUU	chr17:26902045-26902446(-)$1	401	79	82	9.0000
UUU	chr6:33243473-33243761(+)$1	288	18	21	9.0000
UUU	chr15:78578304-78578575(-)$1	271	33	36	9.0000
UUU	chr11:85694835-85695094(-)$1	259	54	57	9.0000
UUU	chr12:26580818-26581086(-)$1	268	8	11	9.0000
UUU	chr7:156971297-156971637(+)$1	340	41	44	9.0000
UUU	chr12:49666857-49667239(+)$1	382	12	15	9.0000
UUU	chrX:71492350-71492637(-)$1	287	2	5	9.0000
UUU	chr14:103802041-103802321(+)$1	280	27	30	9.0000
UUU	chr19:10505630-10505907(-)$1	277	15	18	9.0000
UUU	chrX:53573325-53573580(-)$1	255	17	20	9.0000
UUU	chr1:154562655-154562916(-)$1	261	16	19	9.0000
UUU	chr6:127608609-127608882(+)$1	273	86	89	9.0000
UUU	chr14:97018716-97019048(+)$1	332	2	5	9.0000
UUU	chr3:52720701-52720939(+)$1	238	47	50	9.0000
UUU	chr13:98670684-98671021(+)$1	337	7	10	9.0000
UUU	chr1:76253057-76253392(+)$1	335	7	10	9.0000
UUU	chr11:20448227-20448473(+)$1	246	27	30	9.0000
UUU	chr20:30137762-30138007(+)$1	245	87	90	9.0000
UUU	chr5:85913737-85913999(+)$1	262	8	11	9.0000
UUU	chr17:47018242-47018523(-)$1	281	1	4	9.0000
UUU	chr17:1553828-1554151(-)$1	323	21	24	9.0000
UUU	chr8:103287849-103288167(-)$1	318	7	10	9.0000
UUU	chr5:94833970-94834244(-)$1	274	110	113	9.0000
UUU	chr19:42737154-42737456(-)$1	302	92	95	9.0000
UUU	chr1:206941810-206942131(-)$1	321	7	10	9.0000
UUU	chr1:56961948-56962350(-)$1	402	3	6	9.0000
UUU	chr16:89627889-89628151(+)$1	262	6	9	9.0000
UUU	chr8:120612800-120613091(-)$1	291	11	14	9.0000
UUU	chr12:49521656-49521987(-)$1	331	73	76	9.0000
UUU	chr12:12976752-12976998(+)$1	246	32	35	9.0000
UUU	chr10:89516447-89516720(-)$1	273	0	3	9.0000
UUU	chr1:224586563-224586830(-)$1	267	25	28	9.0000
UUU	chr12:56530921-56531239(+)$1	318	22	25	9.0000
UUU	chr22:23243367-23243720(+)$1	353	255	258	9.0000
UUU	chr3:128060093-128060311(+)$1	218	72	75	9.0000
UUU	chr8:42251629-42251900(+)$1	271	65	68	9.0000
UUU	chrX:120181754-120182123(+)$1	369	272	275	9.0000
UUU	chr17:1565100-1565404(-)$1	304	2	5	9.0000
UUU	chr15:90814548-90814828(+)$1	280	111	114	9.0000
UUU	chr5:177019173-177019424(+)$1	251	159	162	9.0000
UUU	chr6:26123811-26124179(-)$1	368	16	19	9.0000
UUU	chr16:16387923-16388183(+)$1	260	63	66	9.0000

#otherMatches

#Struct PSSM
LLL	chr22:24953520-24953822(+)$1	302	8	11	9.0000
DDD	chr6:29911933-29912277(+)$1	344	301	304	9.0000
ccc	chr13:28014419-28014683(-)$1	264	66	69	9.0000
fff	chr1:206903241-206903549(+)$1	308	9	12	9.0000
::e	chr17:57756736-57756988(+)$1	252	16	19	9.0000
III	chr19:14516495-14516847(+)$1	352	138	141	9.0000
:::	chr1:19523581-19523830(-)$1	249	1	4	9.0000
HHH	chr19:39330812-39331089(-)$1	277	54	57	9.0000
HHH	chr17:19850616-19850889(-)$1	273	36	39	9.0000
::e	chr17:60028225-60028464(-)$1	239	43	46	9.0000
===	chr3:150285901-150286174(+)$1	273	22	25	9.0000
{CC	chr8:101721588-101721957(-)$1	369	28	31	9.0000
{HH	chr19:47285549-47285854(-)$1	305	18	21	9.0000
cc[	chr17:45747055-45747319(+)$1	264	67	70	9.0000
:DD	chr8:120650562-120650866(-)$1	304	24	27	9.0000
::B	chr3:155654116-155654391(+)$1	275	1	4	9.0000
:::	chr2:198272995-198273256(-)$1	261	191	194	9.0000
d[e	chr2:198359910-198360196(-)$1	286	13	16	9.0000
B::	chr1:1720498-1720752(-)$1	254	9	12	9.0000
CC{	chr5:140699419-140699667(-)$1	248	5	8	9.0000
ggg	chr2:86406457-86406702(-)$1	245	47	50	9.0000
OOO	chr2:234345921-234346179(+)$1	258	42	45	9.0000
hhh	chr10:79795166-79795572(+)$1	406	30	33	9.0000
DDD	chr17:57744051-57744372(+)$1	321	17	20	9.0000
:::	chr1:109337358-109337598(+)$1	240	3	6	9.0000
:::	chr5:151170401-151170706(+)$1	305	0	3	9.0000
rrr	chr2:113308355-113308684(+)$1	329	56	59	9.0000
ppp	chr17:61829998-61830256(-)$1	258	56	59	9.0000
cc:	chr5:37052489-37052728(+)$1	239	58	61	9.0000
III	chr6:36070258-36070527(+)$1	269	29	32	9.0000
eee	chr1:8926240-8926681(-)$1	441	239	242	9.0000
GGG	chr6:106555167-106555494(+)$1	327	40	43	9.0000
nnh	chr12:50829193-50829479(+)$1	286	33	36	9.0000
mdd	chr2:203104249-203104525(+)$1	276	10	13	9.0000
333	chr17:58531576-58531831(-)$1	255	54	57	9.0000
EEE	chr15:48766671-48766955(-)$1	284	14	17	9.0000
DKK	chr11:118888882-118889150(-)$1	268	35	38	9.0000
:::	chr12:96410721-96410995(-)$1	274	6	9	9.0000
#dd	chr7:140159534-140159825(-)$1	291	71	74	9.0000
ZEE	chr5:154179154-154179431(+)$1	277	103	106	9.0000
hhh	chr19:49403947-49404279(+)$1	332	274	277	9.0000
ggg	chr2:73476016-73476396(+)$1	380	8	11	9.0000
GGL	chr1:161179560-161179823(+)$1	263	54	57	9.0000
:::	chr12:57920744-57921025(+)$1	281	55	58	9.0000
fff	chr1:161017803-161018116(-)$1	313	141	144	9.0000
rrr	chr17:10608499-10608741(+)$1	242	103	106	9.0000
mee	chr12:58144897-58145204(-)$1	307	65	68	9.0000
:GG	chr16:8994883-8995157(-)$1	274	0	3	9.0000
ooo	chr13:48523555-48523819(-)$1	264	17	20	9.0000
JJJ	chr3:49050351-49050635(+)$1	284	44	47	9.0000
ggg	chr6:106554183-106554465(+)$1	282	94	97	9.0000
ooo	chr17:57728493-57728765(+)$1	272	39	42	9.0000
dd#	chr5:180664508-180664818(-)$1	310	13	16	9.0000
nnn	chr5:85915069-85915367(+)$1	298	18	21	9.0000
LLL	chr5:134086349-134086619(+)$1	270	4	7	9.0000
%%%	chr5:75964407-75964656(+)$1	249	24	27	9.0000
:::	chr19:20807531-20807783(-)$1	252	64	67	9.0000
JJe	chr17:26902045-26902446(-)$1	401	79	82	9.0000
ggg	chr6:33243473-33243761(+)$1	288	18	21	9.0000
dd:	chr15:78578304-78578575(-)$1	271	33	36	9.0000
{GG	chr11:85694835-85695094(-)$1	259	54	57	9.0000
:::	chr12:26580818-26581086(-)$1	268	8	11	9.0000
GGG	chr7:156971297-156971637(+)$1	340	41	44	9.0000
PPP	chr12:49666857-49667239(+)$1	382	12	15	9.0000
eee	chrX:71492350-71492637(-)$1	287	2	5	9.0000
mmm	chr14:103802041-103802321(+)$1	280	27	30	9.0000
CEE	chr19:10505630-10505907(-)$1	277	15	18	9.0000
iii	chrX:53573325-53573580(-)$1	255	17	20	9.0000
GGG	chr1:154562655-154562916(-)$1	261	16	19	9.0000
:hh	chr6:127608609-127608882(+)$1	273	86	89	9.0000
###	chr14:97018716-97019048(+)$1	332	2	5	9.0000
===	chr3:52720701-52720939(+)$1	238	47	50	9.0000
nnn	chr13:98670684-98671021(+)$1	337	7	10	9.0000
ggg	chr1:76253057-76253392(+)$1	335	7	10	9.0000
44e	chr11:20448227-20448473(+)$1	246	27	30	9.0000
cc4	chr20:30137762-30138007(+)$1	245	87	90	9.0000
GGG	chr5:85913737-85913999(+)$1	262	8	11	9.0000
:DD	chr17:47018242-47018523(-)$1	281	1	4	9.0000
ggg	chr17:1553828-1554151(-)$1	323	21	24	9.0000
:::	chr8:103287849-103288167(-)$1	318	7	10	9.0000
:::	chr5:94833970-94834244(-)$1	274	110	113	9.0000
000	chr19:42737154-42737456(-)$1	302	92	95	9.0000
DKK	chr1:206941810-206942131(-)$1	321	7	10	9.0000
d%%	chr1:56961948-56962350(-)$1	402	3	6	9.0000
GGG	chr16:89627889-89628151(+)$1	262	6	9	9.0000
:::	chr8:120612800-120613091(-)$1	291	11	14	9.0000
ccc	chr12:49521656-49521987(-)$1	331	73	76	9.0000
ddi	chr12:12976752-12976998(+)$1	246	32	35	9.0000
:::	chr10:89516447-89516720(-)$1	273	0	3	9.0000
ggg	chr1:224586563-224586830(-)$1	267	25	28	9.0000
GGG	chr12:56530921-56531239(+)$1	318	22	25	9.0000
qqq	chr22:23243367-23243720(+)$1	353	255	258	9.0000
ggg	chr3:128060093-128060311(+)$1	218	72	75	9.0000
ddd	chr8:42251629-42251900(+)$1	271	65	68	9.0000
sss	chrX:120181754-120182123(+)$1	369	272	275	9.0000
:::	chr17:1565100-1565404(-)$1	304	2	5	9.0000
""e	chr15:90814548-90814828(+)$1	280	111	114	9.0000
eee	chr5:177019173-177019424(+)$1	251	159	162	9.0000
GGG	chr6:26123811-26124179(-)$1	368	16	19	9.0000
>>>	chr16:16387923-16388183(+)$1	260	63	66	9.0000

#DB
...	chr22:24953520-24953822(+)$1	1	8	11	9.0000
)))	chr6:29911933-29912277(+)$1	1	301	304	9.0000
(((	chr13:28014419-28014683(-)$1	1	66	69	9.0000
(((	chr1:206903241-206903549(+)$1	1	9	12	9.0000
..(	chr17:57756736-57756988(+)$1	1	16	19	9.0000
)))	chr19:14516495-14516847(+)$1	1	138	141	9.0000
...	chr1:19523581-19523830(-)$1	1	1	4	9.0000
(((	chr19:39330812-39331089(-)$1	1	54	57	9.0000
(((	chr17:19850616-19850889(-)$1	1	36	39	9.0000
..(	chr17:60028225-60028464(-)$1	1	43	46	9.0000
(((	chr3:150285901-150286174(+)$1	1	22	25	9.0000
.((	chr8:101721588-101721957(-)$1	1	28	31	9.0000
.((	chr19:47285549-47285854(-)$1	1	18	21	9.0000
((.	chr17:45747055-45747319(+)$1	1	67	70	9.0000
.((	chr8:120650562-120650866(-)$1	1	24	27	9.0000
..(	chr3:155654116-155654391(+)$1	1	1	4	9.0000
...	chr2:198272995-198273256(-)$1	1	191	194	9.0000
(.(	chr2:198359910-198360196(-)$1	1	13	16	9.0000
(..	chr1:1720498-1720752(-)$1	1	9	12	9.0000
((.	chr5:140699419-140699667(-)$1	1	5	8	9.0000
)))	chr2:86406457-86406702(-)$1	1	47	50	9.0000
...	chr2:234345921-234346179(+)$1	1	42	45	9.0000
)))	chr10:79795166-79795572(+)$1	1	30	33	9.0000
(((	chr17:57744051-57744372(+)$1	1	17	20	9.0000
...	chr1:109337358-109337598(+)$1	1	3	6	9.0000
...	chr5:151170401-151170706(+)$1	1	0	3	9.0000
...	chr2:113308355-113308684(+)$1	1	56	59	9.0000
...	chr17:61829998-61830256(-)$1	1	56	59	9.0000
)).	chr5:37052489-37052728(+)$1	1	58	61	9.0000
(((	chr6:36070258-36070527(+)$1	1	29	32	9.0000
)))	chr1:8926240-8926681(-)$1	1	239	242	9.0000
(((	chr6:106555167-106555494(+)$1	1	40	43	9.0000
..)	chr12:50829193-50829479(+)$1	1	33	36	9.0000
.))	chr2:203104249-203104525(+)$1	1	10	13	9.0000
...	chr17:58531576-58531831(-)$1	1	54	57	9.0000
(((	chr15:48766671-48766955(-)$1	1	14	17	9.0000
(..	chr11:118888882-118889150(-)$1	1	35	38	9.0000
...	chr12:96410721-96410995(-)$1	1	6	9	9.0000
.((	chr7:140159534-140159825(-)$1	1	71	74	9.0000
.))	chr5:154179154-154179431(+)$1	1	103	106	9.0000
(((	chr19:49403947-49404279(+)$1	1	274	277	9.0000
(((	chr2:73476016-73476396(+)$1	1	8	11	9.0000
((.	chr1:161179560-161179823(+)$1	1	54	57	9.0000
...	chr12:57920744-57921025(+)$1	1	55	58	9.0000
(((	chr1:161017803-161018116(-)$1	1	141	144	9.0000
...	chr17:10608499-10608741(+)$1	1	103	106	9.0000
.))	chr12:58144897-58145204(-)$1	1	65	68	9.0000
.((	chr16:8994883-8995157(-)$1	1	0	3	9.0000
...	chr13:48523555-48523819(-)$1	1	17	20	9.0000
(((	chr3:49050351-49050635(+)$1	1	44	47	9.0000
(((	chr6:106554183-106554465(+)$1	1	94	97	9.0000
...	chr17:57728493-57728765(+)$1	1	39	42	9.0000
((.	chr5:180664508-180664818(-)$1	1	13	16	9.0000
...	chr5:85915069-85915367(+)$1	1	18	21	9.0000
...	chr5:134086349-134086619(+)$1	1	4	7	9.0000
...	chr5:75964407-75964656(+)$1	1	24	27	9.0000
...	chr19:20807531-20807783(-)$1	1	64	67	9.0000
(((	chr17:26902045-26902446(-)$1	1	79	82	9.0000
(((	chr6:33243473-33243761(+)$1	1	18	21	9.0000
)).	chr15:78578304-78578575(-)$1	1	33	36	9.0000
.((	chr11:85694835-85695094(-)$1	1	54	57	9.0000
...	chr12:26580818-26581086(-)$1	1	8	11	9.0000
(((	chr7:156971297-156971637(+)$1	1	41	44	9.0000
...	chr12:49666857-49667239(+)$1	1	12	15	9.0000
(((	chrX:71492350-71492637(-)$1	1	2	5	9.0000
...	chr14:103802041-103802321(+)$1	1	27	30	9.0000
(((	chr19:10505630-10505907(-)$1	1	15	18	9.0000
(((	chrX:53573325-53573580(-)$1	1	17	20	9.0000
(((	chr1:154562655-154562916(-)$1	1	16	19	9.0000
.((	chr6:127608609-127608882(+)$1	1	86	89	9.0000
...	chr14:97018716-97019048(+)$1	1	2	5	9.0000
)))	chr3:52720701-52720939(+)$1	1	47	50	9.0000
...	chr13:98670684-98671021(+)$1	1	7	10	9.0000
(((	chr1:76253057-76253392(+)$1	1	7	10	9.0000
..)	chr11:20448227-20448473(+)$1	1	27	30	9.0000
)).	chr20:30137762-30138007(+)$1	1	87	90	9.0000
(((	chr5:85913737-85913999(+)$1	1	8	11	9.0000
.((	chr17:47018242-47018523(-)$1	1	1	4	9.0000
(((	chr17:1553828-1554151(-)$1	1	21	24	9.0000
...	chr8:103287849-103288167(-)$1	1	7	10	9.0000
...	chr5:94833970-94834244(-)$1	1	110	113	9.0000
...	chr19:42737154-42737456(-)$1	1	92	95	9.0000
(..	chr1:206941810-206942131(-)$1	1	7	10	9.0000
(..	chr1:56961948-56962350(-)$1	1	3	6	9.0000
(((	chr16:89627889-89628151(+)$1	1	6	9	9.0000
...	chr8:120612800-120613091(-)$1	1	11	14	9.0000
(((	chr12:49521656-49521987(-)$1	1	73	76	9.0000
)))	chr12:12976752-12976998(+)$1	1	32	35	9.0000
...	chr10:89516447-89516720(-)$1	1	0	3	9.0000
)))	chr1:224586563-224586830(-)$1	1	25	28	9.0000
(((	chr12:56530921-56531239(+)$1	1	22	25	9.0000
...	chr22:23243367-23243720(+)$1	1	255	258	9.0000
(((	chr3:128060093-128060311(+)$1	1	72	75	9.0000
)))	chr8:42251629-42251900(+)$1	1	65	68	9.0000
...	chrX:120181754-120182123(+)$1	1	272	275	9.0000
...	chr17:1565100-1565404(-)$1	1	2	5	9.0000
..(	chr15:90814548-90814828(+)$1	1	111	114	9.0000
(((	chr5:177019173-177019424(+)$1	1	159	162	9.0000
(((	chr6:26123811-26124179(-)$1	1	16	19	9.0000
...	chr16:16387923-16388183(+)$1	1	63	66	9.0000

#PSSM
U : 0.98	u : 0.02	
U : 0.98	u : 0.02	
U : 0.98	u : 0.02	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m2_run2.nuc.txt

#NT
acacaaacacac	chr9:119321710-119321943(-)$1	233	150	162	24.0769
ACACUGACAAAC	chr4:175417799-175418263(-)$1	464	125	137	15.2307
AAACAUACAUUC	chr3:18430809-18431047(-)$1	238	110	122	14.4615
ucacauacacac	chr1:47164304-47164549(-)$1	245	151	163	22.5384
UAAAAUACACAC	chr13:29032915-29033169(-)$1	254	65	77	15.6153
AAACAUACACCU	chr11:63655429-63655677(+)$1	248	101	113	15.1025
ACCCACUCACAC	chr16:89647529-89647753(+)$1	224	111	123	15.4871
acacauacacac	chr4:128950366-128950667(+)$1	301	158	170	26.2564
ACACAUACACAC	chr2:44707341-44707573(+)$1	232	103	115	26.2564
ACACAUAUACAC	chr14:75560730-75561002(-)$1	272	103	115	22.6666
ACACAAACACUC	chr6:111988934-111989157(-)$1	223	186	198	19.7179
acacagagacaa	chr2:230045383-230045836(-)$1	453	59	71	17.0256
ACACAUACACAG	chr13:99179028-99179319(-)$1	291	70	82	22.5384
acuaauaaacac	chr7:108092538-108092766(-)$1	228	20	32	14.7179
acacauacacac	chr16:27591078-27591320(+)$1	242	103	115	26.2564
AAAUAUAAACAC	chr5:100152029-100152271(-)$1	242	112	124	15.8717
ccucaaacacac	chr19:18470104-18470416(+)$1	312	118	130	16.2564
AAACAUACCCAC	chr11:84630574-84630844(-)$1	270	129	141	18.8205
ACACAUGCACAG	chr11:84637513-84637748(-)$1	235	88	100	18.3076
ACACAUACACAC	chr14:91774070-91774371(-)$1	301	139	151	26.2564
acacauacacac	chr20:3265389-3265640(-)$1	251	118	130	26.2564
acagaaacacau	chr7:111123705-111123931(-)$1	226	143	155	16.6410
acacucacacac	chr2:64785902-64786150(+)$1	248	101	113	19.5897
ACAUAAACUCAC	chr6:90784705-90784950(-)$1	245	6	18	15.8717
ACAGAUAGACAA	chr2:48560386-48560703(+)$1	317	249	261	15.6153
UGUCAUACACAC	chr1:243625627-243625891(+)$1	264	136	148	14.8461
ACACAUGCACAU	chr11:73066327-73066557(+)$1	230	64	76	18.4358
CCACAUAGACAC	chr1:50913800-50914077(-)$1	277	169	181	19.3333
ACACAUACCCAC	chr17:7252034-7252381(+)$1	347	121	133	21.8974
acauauauacac	chr3:33091986-33092280(-)$1	294	238	250	18.9487
acacacacacac	chr6:97500857-97501098(+)$1	241	102	114	24.0769
CCACAGACACAA	chr11:75061903-75062293(-)$1	390	310	322	16.5128
agacauucaaac	chr19:12387422-12387721(-)$1	299	228	240	14.3333
AAACAAACAAAC	chr3:65968474-65968709(-)$1	235	140	152	16.8974
GCACAUAGACAC	chr1:39821696-39821971(+)$1	275	190	202	19.0769
acacacacacac	chr18:70425468-70425707(-)$1	239	62	74	24.0769
AUACAGAGACAC	chr6:158792153-158792418(+)$1	265	13	25	16.8974
acacacacacac	chr8:133084024-133084248(-)$1	224	2	14	24.0769

#otherMatches

#Struct PSSM
FFFFF:::::::	chr2:143964958-143965232(+)$1	274	88	100	24.0769
ssssssccc22d	chr9:119321710-119321943(-)$1	233	150	162	24.0769
qqqqffffff::	chr4:175417799-175418263(-)$1	464	125	137	15.2307
:::::::BBJJJ	chr3:18430809-18431047(-)$1	238	110	122	14.4615
^^^^^^^^^^^^	chr1:47164304-47164549(-)$1	245	151	163	22.5384
"dddd$$$$$dd	chr13:29032915-29033169(-)$1	254	65	77	15.6153
EEEEE:::EEEE	chr11:63655429-63655677(+)$1	248	101	113	15.1025
:::::::::::d	chr16:89647529-89647753(+)$1	224	111	123	15.4871
::::::::CCCL	chr4:128950366-128950667(+)$1	301	158	170	26.2564
::::::::::::	chr2:44707341-44707573(+)$1	232	103	115	26.2564
::::::::::::	chr14:75560730-75561002(-)$1	272	103	115	22.6666
::::::::::::	chr6:111988934-111989157(-)$1	223	186	198	19.7179
ddddrrrrrrrr	chr2:230045383-230045836(-)$1	453	59	71	17.0256
eeeaggggggge	chr13:99179028-99179319(-)$1	291	70	82	22.5384
::::::::ffff	chr7:108092538-108092766(-)$1	228	20	32	14.7179
::::::::::::	chr16:27591078-27591320(+)$1	242	103	115	26.2564
gg[dddd"""ff	chr5:100152029-100152271(-)$1	242	112	124	15.8717
22ccc:::::::	chr19:18470104-18470416(+)$1	312	118	130	16.2564
::ddddoooooo	chr11:84630574-84630844(-)$1	270	129	141	18.8205
>>>>eeeee22d	chr11:84637513-84637748(-)$1	235	88	100	18.3076
>>>>>>>>>>>>	chr14:91774070-91774371(-)$1	301	139	151	26.2564
^^^^^^^^^^^^	chr20:3265389-3265640(-)$1	251	118	130	26.2564
qqqccc666666	chr7:111123705-111123931(-)$1	226	143	155	16.6410
b>>>>>>>>>>>	chr2:64785902-64786150(+)$1	248	101	113	19.5897
:::::FFFFFF:	chr6:90784705-90784950(-)$1	245	6	18	15.8717
dddd:DDDD}DD	chr2:48560386-48560703(+)$1	317	249	261	15.6153
ffff]ccc]ddd	chr1:243625627-243625891(+)$1	264	136	148	14.8461
bb22iiiiiiii	chr11:73066327-73066557(+)$1	230	64	76	18.4358
:::::::::::b	chr1:50913800-50914077(-)$1	277	169	181	19.3333
cc::::::HHHH	chr17:7252034-7252381(+)$1	347	121	133	21.8974
"ffffffooooo	chr3:33091986-33092280(-)$1	294	238	250	18.9487
^^^^^^^^^^^^	chr6:97500857-97501098(+)$1	241	102	114	24.0769
pppccc:::::E	chr11:75061903-75062293(-)$1	390	310	322	16.5128
ee4444eeeee2	chr19:12387422-12387721(-)$1	299	228	240	14.3333
::::::::::::	chr3:65968474-65968709(-)$1	235	140	152	16.8974
oohhhhhhhh::	chr1:39821696-39821971(+)$1	275	190	202	19.0769
e:::::::::::	chr18:70425468-70425707(-)$1	239	62	74	24.0769
bb!!ddddllld	chr6:158792153-158792418(+)$1	265	13	25	16.8974
::::::::::EE	chr8:133084024-133084248(-)$1	224	2	14	24.0769

#DB
(((((.......	chr2:143964958-143965232(+)$1	1	88	100	24.0769
......)))..)	chr9:119321710-119321943(-)$1	1	150	162	24.0769
....))))))..	chr4:175417799-175418263(-)$1	1	125	137	15.2307
.......)))))	chr3:18430809-18431047(-)$1	1	110	122	14.4615
............	chr1:47164304-47164549(-)$1	1	151	163	22.5384
.((((.....((	chr13:29032915-29033169(-)$1	1	65	77	15.6153
)))))...((((	chr11:63655429-63655677(+)$1	1	101	113	15.1025
...........(	chr16:89647529-89647753(+)$1	1	111	123	15.4871
........(((.	chr4:128950366-128950667(+)$1	1	158	170	26.2564
............	chr2:44707341-44707573(+)$1	1	103	115	26.2564
............	chr14:75560730-75561002(-)$1	1	103	115	22.6666
............	chr6:111988934-111989157(-)$1	1	186	198	19.7179
((((........	chr2:230045383-230045836(-)$1	1	59	71	17.0256
))))))))))))	chr13:99179028-99179319(-)$1	1	70	82	22.5384
........((((	chr7:108092538-108092766(-)$1	1	20	32	14.7179
............	chr16:27591078-27591320(+)$1	1	103	115	26.2564
((.((((...((	chr5:100152029-100152271(-)$1	1	112	124	15.8717
..))).......	chr19:18470104-18470416(+)$1	1	118	130	16.2564
..((((......	chr11:84630574-84630844(-)$1	1	129	141	18.8205
....)))))..)	chr11:84637513-84637748(-)$1	1	88	100	18.3076
............	chr14:91774070-91774371(-)$1	1	139	151	26.2564
............	chr20:3265389-3265640(-)$1	1	118	130	26.2564
...)))......	chr7:111123705-111123931(-)$1	1	143	155	16.6410
)...........	chr2:64785902-64786150(+)$1	1	101	113	19.5897
.....((((((.	chr6:90784705-90784950(-)$1	1	6	18	15.8717
)))).)))).))	chr2:48560386-48560703(+)$1	1	249	261	15.6153
)))).))).)))	chr1:243625627-243625891(+)$1	1	136	148	14.8461
))..))))))))	chr11:73066327-73066557(+)$1	1	64	76	18.4358
...........(	chr1:50913800-50914077(-)$1	1	169	181	19.3333
))......))))	chr17:7252034-7252381(+)$1	1	121	133	21.8974
.((((((.....	chr3:33091986-33092280(-)$1	1	238	250	18.9487
............	chr6:97500857-97501098(+)$1	1	102	114	24.0769
...))).....)	chr11:75061903-75062293(-)$1	1	310	322	16.5128
))....))))).	chr19:12387422-12387721(-)$1	1	228	240	14.3333
............	chr3:65968474-65968709(-)$1	1	140	152	16.8974
..))))))))..	chr1:39821696-39821971(+)$1	1	190	202	19.0769
)...........	chr18:70425468-70425707(-)$1	1	62	74	24.0769
((..((((...)	chr6:158792153-158792418(+)$1	1	13	25	16.8974
..........((	chr8:133084024-133084248(-)$1	1	2	14	24.0769

#PSSM
A : 0.46	a : 0.35	U : 0.05	C : 0.05	u : 0.02	c : 0.02	G : 0.02	
c : 0.38	C : 0.38	A : 0.15	G : 0.02	g : 0.02	U : 0.02	
A : 0.53	a : 0.35	u : 0.05	C : 0.02	U : 0.02	
C : 0.48	c : 0.33	U : 0.05	A : 0.02	a : 0.02	g : 0.02	G : 0.02	u : 0.02	
A : 0.56	a : 0.38	U : 0.02	u : 0.02	
U : 0.41	u : 0.17	c : 0.12	a : 0.07	G : 0.07	A : 0.07	C : 0.02	g : 0.02	
A : 0.51	a : 0.38	G : 0.05	U : 0.02	u : 0.02	
C : 0.43	c : 0.33	G : 0.10	U : 0.02	g : 0.02	a : 0.02	A : 0.02	u : 0.02	
A : 0.51	a : 0.41	C : 0.05	U : 0.02	
C : 0.51	c : 0.38	A : 0.05	U : 0.02	a : 0.02	
A : 0.51	a : 0.41	U : 0.05	C : 0.02	
C : 0.43	c : 0.35	U : 0.05	G : 0.05	A : 0.05	a : 0.02	u : 0.02	

#score	760.9230769230775
#seq	39
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m3_run1.nuc.txt

#NT
AAAAU	chr6:157529401-157529627(+)$1	226	9	14	15.0000
AAAAU	chr11:47738062-47738305(-)$1	243	17	22	15.0000
AAAAU	chr20:43118726-43118951(+)$1	225	208	213	15.0000
AAAAU	chr1:233520652-233520907(+)$1	255	102	107	15.0000
AAAAU	chr12:42481142-42481369(-)$1	227	29	34	15.0000
AAAAU	chr3:180694782-180695041(+)$1	259	204	209	15.0000
AAAAU	chr3:151150521-151150739(+)$1	218	120	125	15.0000
AAAAU	chr1:155059823-155060068(+)$1	245	167	172	15.0000
AAAAU	chr2:203071618-203071853(-)$1	235	101	106	15.0000
AAAAU	chr13:46109052-46109289(+)$1	237	8	13	15.0000
AAAAU	chr3:9519168-9519416(+)$1	248	143	148	15.0000
AAAAU	chr6:97242455-97242693(-)$1	238	17	22	15.0000
AAAAU	chr1:204374714-204374954(-)$1	240	160	165	15.0000
AAAAU	chr16:24836822-24837049(+)$1	227	57	62	15.0000
AAAAU	chr3:63987734-63987965(+)$1	231	76	81	15.0000
AAAAU	chrX:24002835-24003087(-)$1	252	194	199	15.0000
AAAAU	chr4:95587454-95587706(+)$1	252	237	242	15.0000
AAAAU	chr15:99500867-99501119(+)$1	252	158	163	15.0000
AAAAU	chr17:27585753-27585986(-)$1	233	77	82	15.0000
AAAAU	chr12:50146146-50146359(+)$1	213	171	176	15.0000
AAAAU	chr4:41269968-41270243(+)$1	275	170	175	15.0000
AAAAU	chr1:116234038-116234274(+)$1	236	46	51	15.0000
AAAAU	chr8:26151105-26151355(+)$1	250	170	175	15.0000
AAAAU	chr14:20925935-20926160(-)$1	225	174	179	15.0000
AAAAU	chr18:47017924-47018189(-)$1	265	245	250	15.0000
AAAAU	chr13:95280387-95280638(+)$1	251	138	143	15.0000
AAAAU	chr7:63980727-63980962(-)$1	235	43	48	15.0000
AAAAU	chr10:28971243-28971477(+)$1	234	196	201	15.0000
AAAAU	chr13:80910064-80910288(-)$1	224	145	150	15.0000
aaaaU	chr14:31363943-31364175(-)$1	232	83	88	15.0000
AAAAU	chr9:79000560-79000783(-)$1	223	78	83	15.0000
AAAAU	chr12:118470670-118470893(-)$1	223	133	138	15.0000
AAAAU	chr13:113538154-113538378(+)$1	224	100	105	15.0000
aaaau	chr13:52706797-52707026(-)$1	229	89	94	15.0000
AAAAU	chr10:73577007-73577246(-)$1	239	148	153	15.0000
AAAAU	chr1:243667530-243667752(-)$1	222	86	91	15.0000
AAAAU	chr10:93038595-93038820(+)$1	225	144	149	15.0000
AAAAU	chr10:103922408-103922636(+)$1	228	48	53	15.0000
AAAAU	chr12:42481156-42481379(-)$1	223	39	44	15.0000
AAAAU	chr1:145441644-145441913(+)$1	269	61	66	15.0000
AAAAU	chr2:20232822-20233085(-)$1	263	75	80	15.0000
AAAAU	chr5:137088527-137088777(-)$1	250	232	237	15.0000
AAAAU	chr5:10435430-10435678(+)$1	248	53	58	15.0000
AAAAU	chr6:138203111-138203334(+)$1	223	29	34	15.0000
AAAAU	chr6:89793997-89794228(+)$1	231	40	45	15.0000
AAAAU	chr10:43881463-43881696(-)$1	233	25	30	15.0000
AAAAU	chr10:102123841-102124076(+)$1	235	74	79	15.0000
AAAAU	chr15:73852292-73852539(-)$1	247	161	166	15.0000
AAAAU	chr12:69663895-69664153(+)$1	258	136	141	15.0000
AAAAU	chr5:114951325-114951572(-)$1	247	54	59	15.0000
AAAAU	chr12:76746019-76746261(-)$1	242	188	193	15.0000
AAAAU	chr1:204372882-204373107(-)$1	225	29	34	15.0000
AAAAU	chr17:46684696-46684939(-)$1	243	82	87	15.0000
AAAAU	chr16:29822290-29822520(+)$1	230	186	191	15.0000
AAAAU	chr12:72180135-72180362(+)$1	227	179	184	15.0000
AAAAU	chr8:126450010-126450232(+)$1	222	120	125	15.0000
AAAAU	chr9:33112940-33113173(-)$1	233	1	6	15.0000
AAAAU	chr12:66359786-66360041(+)$1	255	150	155	15.0000
aaaau	chr5:154194281-154194549(+)$1	268	130	135	15.0000
AAAAU	chr5:10433922-10434156(+)$1	234	151	156	15.0000
AAAAU	chr10:103909731-103909992(+)$1	261	188	193	15.0000
AAAAU	chr7:27202717-27202969(-)$1	252	50	55	15.0000
AAAAU	chr2:65315492-65315747(-)$1	255	73	78	15.0000

#otherMatches

#Struct PSSM
lffff	chr17:27875129-27875368(+)$1	239	40	45	15.0000
CC::g	chr6:157529401-157529627(+)$1	226	9	14	15.0000
d::::	chr11:47738062-47738305(-)$1	243	17	22	15.0000
5555f	chr20:43118726-43118951(+)$1	225	208	213	15.0000
>>>>>	chr1:233520652-233520907(+)$1	255	102	107	15.0000
oofff	chr12:42481142-42481369(-)$1	227	29	34	15.0000
mmiii	chr3:180694782-180695041(+)$1	259	204	209	15.0000
eeeee	chr3:151150521-151150739(+)$1	218	120	125	15.0000
ppppb	chr1:155059823-155060068(+)$1	245	167	172	15.0000
^^^^^	chr2:203071618-203071853(-)$1	235	101	106	15.0000
:::::	chr13:46109052-46109289(+)$1	237	8	13	15.0000
:::::	chr3:9519168-9519416(+)$1	248	143	148	15.0000
HKKEE	chr6:97242455-97242693(-)$1	238	17	22	15.0000
fff]f	chr1:204374714-204374954(-)$1	240	160	165	15.0000
llddd	chr16:24836822-24837049(+)$1	227	57	62	15.0000
::::A	chr3:63987734-63987965(+)$1	231	76	81	15.0000
F:::h	chrX:24002835-24003087(-)$1	252	194	199	15.0000
ff]bb	chr4:95587454-95587706(+)$1	252	237	242	15.0000
:::::	chr15:99500867-99501119(+)$1	252	158	163	15.0000
ggggg	chr17:27585753-27585986(-)$1	233	77	82	15.0000
eee::	chr12:50146146-50146359(+)$1	213	171	176	15.0000
dd:::	chr4:41269968-41270243(+)$1	275	170	175	15.0000
:::::	chr1:116234038-116234274(+)$1	236	46	51	15.0000
gggg[	chr8:26151105-26151355(+)$1	250	170	175	15.0000
e:EEE	chr14:20925935-20926160(-)$1	225	174	179	15.0000
mmmdd	chr18:47017924-47018189(-)$1	265	245	250	15.0000
'''''	chr13:95280387-95280638(+)$1	251	138	143	15.0000
nnngg	chr7:63980727-63980962(-)$1	235	43	48	15.0000
2ffff	chr10:28971243-28971477(+)$1	234	196	201	15.0000
lllcc	chr13:80910064-80910288(-)$1	224	145	150	15.0000
GGGGG	chr14:31363943-31364175(-)$1	232	83	88	15.0000
mmmee	chr9:79000560-79000783(-)$1	223	78	83	15.0000
!!ggg	chr12:118470670-118470893(-)$1	223	133	138	15.0000
dddd]	chr13:113538154-113538378(+)$1	224	100	105	15.0000
d>>>>	chr13:52706797-52707026(-)$1	229	89	94	15.0000
h####	chr10:73577007-73577246(-)$1	239	148	153	15.0000
:::::	chr1:243667530-243667752(-)$1	222	86	91	15.0000
&&&&&	chr10:93038595-93038820(+)$1	225	144	149	15.0000
cmmmm	chr10:103922408-103922636(+)$1	228	48	53	15.0000
oofff	chr12:42481156-42481379(-)$1	223	39	44	15.0000
7777c	chr1:145441644-145441913(+)$1	269	61	66	15.0000
fffff	chr2:20232822-20233085(-)$1	263	75	80	15.0000
eeooo	chr5:137088527-137088777(-)$1	250	232	237	15.0000
ooood	chr5:10435430-10435678(+)$1	248	53	58	15.0000
mmmmf	chr6:138203111-138203334(+)$1	223	29	34	15.0000
leeee	chr6:89793997-89794228(+)$1	231	40	45	15.0000
gggmm	chr10:43881463-43881696(-)$1	233	25	30	15.0000
$$bb[	chr10:102123841-102124076(+)$1	235	74	79	15.0000
ppppp	chr15:73852292-73852539(-)$1	247	161	166	15.0000
rrrrr	chr12:69663895-69664153(+)$1	258	136	141	15.0000
KBB{E	chr5:114951325-114951572(-)$1	247	54	59	15.0000
ooocc	chr12:76746019-76746261(-)$1	242	188	193	15.0000
:::::	chr1:204372882-204373107(-)$1	225	29	34	15.0000
rrr==	chr17:46684696-46684939(-)$1	243	82	87	15.0000
eoooo	chr16:29822290-29822520(+)$1	230	186	191	15.0000
iiiii	chr12:72180135-72180362(+)$1	227	179	184	15.0000
:::::	chr8:126450010-126450232(+)$1	222	120	125	15.0000
::eee	chr9:33112940-33113173(-)$1	233	1	6	15.0000
dddll	chr12:66359786-66360041(+)$1	255	150	155	15.0000
::::F	chr5:154194281-154194549(+)$1	268	130	135	15.0000
yy===	chr5:10433922-10434156(+)$1	234	151	156	15.0000
hhhhh	chr10:103909731-103909992(+)$1	261	188	193	15.0000
:::::	chr7:27202717-27202969(-)$1	252	50	55	15.0000
wwwwc	chr2:65315492-65315747(-)$1	255	73	78	15.0000

#DB
.))))	chr17:27875129-27875368(+)$1	1	40	45	15.0000
((..(	chr6:157529401-157529627(+)$1	1	9	14	15.0000
)....	chr11:47738062-47738305(-)$1	1	17	22	15.0000
....)	chr20:43118726-43118951(+)$1	1	208	213	15.0000
.....	chr1:233520652-233520907(+)$1	1	102	107	15.0000
..)))	chr12:42481142-42481369(-)$1	1	29	34	15.0000
..)))	chr3:180694782-180695041(+)$1	1	204	209	15.0000
)))))	chr3:151150521-151150739(+)$1	1	120	125	15.0000
....)	chr1:155059823-155060068(+)$1	1	167	172	15.0000
.....	chr2:203071618-203071853(-)$1	1	101	106	15.0000
.....	chr13:46109052-46109289(+)$1	1	8	13	15.0000
.....	chr3:9519168-9519416(+)$1	1	143	148	15.0000
(..((	chr6:97242455-97242693(-)$1	1	17	22	15.0000
))).)	chr1:204374714-204374954(-)$1	1	160	165	15.0000
..)))	chr16:24836822-24837049(+)$1	1	57	62	15.0000
....(	chr3:63987734-63987965(+)$1	1	76	81	15.0000
)...(	chrX:24002835-24003087(-)$1	1	194	199	15.0000
)).))	chr4:95587454-95587706(+)$1	1	237	242	15.0000
.....	chr15:99500867-99501119(+)$1	1	158	163	15.0000
(((((	chr17:27585753-27585986(-)$1	1	77	82	15.0000
)))..	chr12:50146146-50146359(+)$1	1	171	176	15.0000
))...	chr4:41269968-41270243(+)$1	1	170	175	15.0000
.....	chr1:116234038-116234274(+)$1	1	46	51	15.0000
((((.	chr8:26151105-26151355(+)$1	1	170	175	15.0000
).)))	chr14:20925935-20926160(-)$1	1	174	179	15.0000
...))	chr18:47017924-47018189(-)$1	1	245	250	15.0000
.....	chr13:95280387-95280638(+)$1	1	138	143	15.0000
...))	chr7:63980727-63980962(-)$1	1	43	48	15.0000
.))))	chr10:28971243-28971477(+)$1	1	196	201	15.0000
...))	chr13:80910064-80910288(-)$1	1	145	150	15.0000
(((((	chr14:31363943-31364175(-)$1	1	83	88	15.0000
...))	chr9:79000560-79000783(-)$1	1	78	83	15.0000
..(((	chr12:118470670-118470893(-)$1	1	133	138	15.0000
)))).	chr13:113538154-113538378(+)$1	1	100	105	15.0000
)....	chr13:52706797-52707026(-)$1	1	89	94	15.0000
(....	chr10:73577007-73577246(-)$1	1	148	153	15.0000
.....	chr1:243667530-243667752(-)$1	1	86	91	15.0000
.....	chr10:93038595-93038820(+)$1	1	144	149	15.0000
(....	chr10:103922408-103922636(+)$1	1	48	53	15.0000
..)))	chr12:42481156-42481379(-)$1	1	39	44	15.0000
....)	chr1:145441644-145441913(+)$1	1	61	66	15.0000
)))))	chr2:20232822-20233085(-)$1	1	75	80	15.0000
((...	chr5:137088527-137088777(-)$1	1	232	237	15.0000
....)	chr5:10435430-10435678(+)$1	1	53	58	15.0000
....)	chr6:138203111-138203334(+)$1	1	29	34	15.0000
.))))	chr6:89793997-89794228(+)$1	1	40	45	15.0000
(((..	chr10:43881463-43881696(-)$1	1	25	30	15.0000
..((.	chr10:102123841-102124076(+)$1	1	74	79	15.0000
.....	chr15:73852292-73852539(-)$1	1	161	166	15.0000
.....	chr12:69663895-69664153(+)$1	1	136	141	15.0000
.((.(	chr5:114951325-114951572(-)$1	1	54	59	15.0000
...))	chr12:76746019-76746261(-)$1	1	188	193	15.0000
.....	chr1:204372882-204373107(-)$1	1	29	34	15.0000
...))	chr17:46684696-46684939(-)$1	1	82	87	15.0000
(....	chr16:29822290-29822520(+)$1	1	186	191	15.0000
(((((	chr12:72180135-72180362(+)$1	1	179	184	15.0000
.....	chr8:126450010-126450232(+)$1	1	120	125	15.0000
..(((	chr9:33112940-33113173(-)$1	1	1	6	15.0000
(((..	chr12:66359786-66360041(+)$1	1	150	155	15.0000
....)	chr5:154194281-154194549(+)$1	1	130	135	15.0000
..)))	chr5:10433922-10434156(+)$1	1	151	156	15.0000
(((((	chr10:103909731-103909992(+)$1	1	188	193	15.0000
.....	chr7:27202717-27202969(-)$1	1	50	55	15.0000
....)	chr2:65315492-65315747(-)$1	1	73	78	15.0000

#PSSM
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	
A : 0.95	a : 0.04	
U : 0.96	u : 0.03	

#score	960.0
#seq	64
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_CDS_m2_run2.nuc.txt

#NT
CUGG	chr1:27876809-27877046(-)$1	237	85	89	11.9999
CUGG	chr3:4726760-4726985(+)$1	225	100	104	11.9999
CUGG	chr2:216288827-216289046(-)$1	219	175	179	11.9999
CUGG	chr1:9655925-9656143(+)$1	218	52	56	11.9999
CUGG	chr11:64681223-64681451(-)$1	228	82	86	11.9999
CUGG	chr16:4852282-4852506(-)$1	224	66	70	11.9999
CUGG	chr1:55352490-55352715(-)$1	225	15	19	11.9999
CUGG	chr7:100487786-100488010(-)$1	224	35	39	11.9999
CUGG	chr19:49173815-49174031(-)$1	216	72	76	11.9999
CUGG	chr17:19186442-19186664(+)$1	222	199	203	11.9999
CUGG	chr7:99725600-99725824(+)$1	224	78	82	11.9999
CUGG	chr17:72832710-72832941(+)$1	231	31	35	11.9999
CUGG	chr16:18795968-18796192(-)$1	224	89	93	11.9999
CUGG	chr19:16436236-16436471(+)$1	235	12	16	11.9999
CUGG	chr17:73657669-73657888(-)$1	219	42	46	11.9999
CUGG	chr17:62496077-62496292(-)$1	215	61	65	11.9999
CUGG	chr1:621869-622093(-)$1	224	51	55	11.9999
CUGG	chr8:144992064-144992310(-)$1	246	10	14	11.9999
CUGG	chr8:12168507-12168723(+)$1	216	124	128	11.9999
CUGG	chr22:32108029-32108254(-)$1	225	169	173	11.9999
CUGG	chr19:10904394-10904625(+)$1	231	68	72	11.9999
CUGG	chr21:46876667-46876902(+)$1	235	43	47	11.9999
CUGG	chr7:1479502-1479741(-)$1	239	48	52	11.9999
CUGG	chr1:32121900-32122125(-)$1	225	87	91	11.9999
CUGG	chr4:25415179-25415397(+)$1	218	1	5	11.9999
CUGG	chr14:105416601-105416825(-)$1	224	180	184	11.9999
CUGG	chr9:134612686-134612905(-)$1	219	154	158	11.9999
CUGG	chr11:11963781-11964017(+)$1	236	169	173	11.9999
cugg	chr22:46189476-46189697(+)$1	221	207	211	11.9999
CUGG	chr6:32796606-32796838(-)$1	232	35	39	11.9999
CUGG	chr17:19282112-19282332(-)$1	220	187	191	11.9999
CUGG	chr22:32109407-32109631(-)$1	224	160	164	11.9999
CUGG	chr14:64636939-64637170(+)$1	231	97	101	11.9999
CUGG	chr15:73593653-73593874(-)$1	221	24	28	11.9999
CUGG	chr12:56994018-56994252(-)$1	234	61	65	11.9999
CUGG	chr10:17156022-17156240(-)$1	218	77	81	11.9999
CUGG	chr1:145532508-145532738(+)$1	230	126	130	11.9999
CUGG	chr6:30858755-30858982(+)$1	227	63	67	11.9999
CUGG	chr6:24522905-24523129(+)$1	224	31	35	11.9999
CUGG	chr12:124826470-124826697(-)$1	227	44	48	11.9999
CUGG	chr5:161300103-161300318(+)$1	215	51	55	11.9999
CUGG	chr7:73811399-73811624(+)$1	225	32	36	11.9999
CUGG	chr15:64005683-64005901(-)$1	218	115	119	11.9999
CUGG	chr1:6154406-6154627(+)$1	221	11	15	11.9999
CUGG	chr10:26512725-26512948(+)$1	223	51	55	11.9999
CUGG	chr12:49220699-49220928(+)$1	229	75	79	11.9999
CUGG	chr2:120251943-120252161(+)$1	218	60	64	11.9999
CUGG	chr3:97806229-97806444(+)$1	215	36	40	11.9999
CUGG	chr10:123987271-123987492(+)$1	221	16	20	11.9999
CUGG	chr2:9516946-9517164(+)$1	218	63	67	11.9999
CUGG	chr5:43700147-43700383(+)$1	236	105	109	11.9999
CUGG	chr6:33141549-33141784(-)$1	235	115	119	11.9999
CUGG	chr12:122399823-122400047(+)$1	224	44	48	11.9999
CUGG	chr22:25424097-25424318(+)$1	221	134	138	11.9999
CUGG	chr16:30744568-30744798(+)$1	230	118	122	11.9999
CUGG	chr2:191785814-191786048(+)$1	234	81	85	11.9999
CUGG	chr7:47925405-47925622(-)$1	217	5	9	11.9999
CUGG	chr8:23290443-23290664(-)$1	221	36	40	11.9999
CUGG	chr19:18391802-18392028(-)$1	226	10	14	11.9999
CUGG	chr11:129998908-129999135(+)$1	227	91	95	11.9999
CUGG	chr11:46515111-46515345(-)$1	234	119	123	11.9999
CUGG	chr9:134357014-134357231(-)$1	217	98	102	11.9999
CUGG	chr3:49162480-49162706(-)$1	226	27	31	11.9999
CUGG	chr1:156246810-156247039(-)$1	229	52	56	11.9999
CUGG	chr1:31414838-31415070(-)$1	232	151	155	11.9999
CUGG	chr17:36873746-36873966(+)$1	220	24	28	11.9999
CUGG	chr9:139394985-139395213(-)$1	228	75	79	11.9999
CUGG	chr19:1041864-1042080(+)$1	216	8	12	11.9999
CUGG	chr1:9107563-9107778(+)$1	215	38	42	11.9999
CUGG	chr18:61324532-61324749(+)$1	217	165	169	11.9999
CUGG	chr7:26192476-26192693(-)$1	217	131	135	11.9999
CUGG	chr8:27463812-27464051(-)$1	239	90	94	11.9999
CUGG	chr6:56340911-56341144(-)$1	233	12	16	11.9999
CUGG	chr6:111632225-111632450(-)$1	225	75	79	11.9999
CUGG	chr3:56044355-56044587(-)$1	232	117	121	11.9999
CUGG	chr16:29401158-29401391(+)$1	233	109	113	11.9999
CUGG	chr19:9965229-9965445(-)$1	216	113	117	11.9999
CUGG	chr12:98993642-98993884(+)$1	242	114	118	11.9999
CUGG	chr12:7355952-7356172(+)$1	220	89	93	11.9999
CUGG	chr2:227920686-227920901(-)$1	215	121	125	11.9999
cugg	chr10:99619120-99619353(+)$1	233	2	6	11.9999
CUGG	chr11:126146943-126147166(+)$1	223	46	50	11.9999
CUGG	chr12:125609378-125609603(+)$1	225	29	33	11.9999
cugg	chr11:67052217-67052434(+)$1	217	15	19	11.9999

#otherMatches

#Struct PSSM
ffff	chr15:39885272-39885501(+)$1	229	53	57	11.9999
eeee	chr1:27876809-27877046(-)$1	237	85	89	11.9999
gggg	chr3:4726760-4726985(+)$1	225	100	104	11.9999
lddd	chr2:216288827-216289046(-)$1	219	175	179	11.9999
c[ff	chr1:9655925-9656143(+)$1	218	52	56	11.9999
e]cc	chr11:64681223-64681451(-)$1	228	82	86	11.9999
b[gg	chr16:4852282-4852506(-)$1	224	66	70	11.9999
BB{A	chr1:55352490-55352715(-)$1	225	15	19	11.9999
[fff	chr7:100487786-100488010(-)$1	224	35	39	11.9999
^^dd	chr19:49173815-49174031(-)$1	216	72	76	11.9999
HHHH	chr17:19186442-19186664(+)$1	222	199	203	11.9999
c]a]	chr7:99725600-99725824(+)$1	224	78	82	11.9999
llee	chr17:72832710-72832941(+)$1	231	31	35	11.9999
:ddd	chr16:18795968-18796192(-)$1	224	89	93	11.9999
B{BB	chr19:16436236-16436471(+)$1	235	12	16	11.9999
c[ff	chr17:73657669-73657888(-)$1	219	42	46	11.9999
eeeb	chr17:62496077-62496292(-)$1	215	61	65	11.9999
hhhh	chr1:621869-622093(-)$1	224	51	55	11.9999
HHHH	chr8:144992064-144992310(-)$1	246	10	14	11.9999
""dd	chr8:12168507-12168723(+)$1	216	124	128	11.9999
EEEE	chr22:32108029-32108254(-)$1	225	169	173	11.9999
eeee	chr19:10904394-10904625(+)$1	231	68	72	11.9999
ffff	chr21:46876667-46876902(+)$1	235	43	47	11.9999
33dd	chr7:1479502-1479741(-)$1	239	48	52	11.9999
dd==	chr1:32121900-32122125(-)$1	225	87	91	11.9999
FFFF	chr4:25415179-25415397(+)$1	218	1	5	11.9999
eeee	chr14:105416601-105416825(-)$1	224	180	184	11.9999
gggp	chr9:134612686-134612905(-)$1	219	154	158	11.9999
c:cc	chr11:11963781-11964017(+)$1	236	169	173	11.9999
eemm	chr22:46189476-46189697(+)$1	221	207	211	11.9999
ddda	chr6:32796606-32796838(-)$1	232	35	39	11.9999
====	chr17:19282112-19282332(-)$1	220	187	191	11.9999
eeee	chr22:32109407-32109631(-)$1	224	160	164	11.9999
##gg	chr14:64636939-64637170(+)$1	231	97	101	11.9999
gggg	chr15:73593653-73593874(-)$1	221	24	28	11.9999
22cc	chr12:56994018-56994252(-)$1	234	61	65	11.9999
ehhh	chr10:17156022-17156240(-)$1	218	77	81	11.9999
====	chr1:145532508-145532738(+)$1	230	126	130	11.9999
BBMM	chr6:30858755-30858982(+)$1	227	63	67	11.9999
++++	chr6:24522905-24523129(+)$1	224	31	35	11.9999
bbee	chr12:124826470-124826697(-)$1	227	44	48	11.9999
gggg	chr5:161300103-161300318(+)$1	215	51	55	11.9999
EEKK	chr7:73811399-73811624(+)$1	225	32	36	11.9999
ee22	chr15:64005683-64005901(-)$1	218	115	119	11.9999
:DDD	chr1:6154406-6154627(+)$1	221	11	15	11.9999
gggg	chr10:26512725-26512948(+)$1	223	51	55	11.9999
dddd	chr12:49220699-49220928(+)$1	229	75	79	11.9999
ffff	chr2:120251943-120252161(+)$1	218	60	64	11.9999
c[dd	chr3:97806229-97806444(+)$1	215	36	40	11.9999
[eee	chr10:123987271-123987492(+)$1	221	16	20	11.9999
gggc	chr2:9516946-9517164(+)$1	218	63	67	11.9999
ddgg	chr5:43700147-43700383(+)$1	236	105	109	11.9999
b]ff	chr6:33141549-33141784(-)$1	235	115	119	11.9999
CCCg	chr12:122399823-122400047(+)$1	224	44	48	11.9999
eeee	chr22:25424097-25424318(+)$1	221	134	138	11.9999
ennn	chr16:30744568-30744798(+)$1	230	118	122	11.9999
b:FF	chr2:191785814-191786048(+)$1	234	81	85	11.9999
FFFF	chr7:47925405-47925622(-)$1	217	5	9	11.9999
ffff	chr8:23290443-23290664(-)$1	221	36	40	11.9999
DDDD	chr19:18391802-18392028(-)$1	226	10	14	11.9999
DDee	chr11:129998908-129999135(+)$1	227	91	95	11.9999
66dd	chr11:46515111-46515345(-)$1	234	119	123	11.9999
ffff	chr9:134357014-134357231(-)$1	217	98	102	11.9999
cc::	chr3:49162480-49162706(-)$1	226	27	31	11.9999
MMCC	chr1:156246810-156247039(-)$1	229	52	56	11.9999
eeee	chr1:31414838-31415070(-)$1	232	151	155	11.9999
gggg	chr17:36873746-36873966(+)$1	220	24	28	11.9999
qqcc	chr9:139394985-139395213(-)$1	228	75	79	11.9999
GGGG	chr19:1041864-1042080(+)$1	216	8	12	11.9999
DDD{	chr1:9107563-9107778(+)$1	215	38	42	11.9999
]hhh	chr18:61324532-61324749(+)$1	217	165	169	11.9999
d[cc	chr7:26192476-26192693(-)$1	217	131	135	11.9999
ffff	chr8:27463812-27464051(-)$1	239	90	94	11.9999
mmme	chr6:56340911-56341144(-)$1	233	12	16	11.9999
FFFF	chr6:111632225-111632450(-)$1	225	75	79	11.9999
fff:	chr3:56044355-56044587(-)$1	232	117	121	11.9999
mmff	chr16:29401158-29401391(+)$1	233	109	113	11.9999
2ccc	chr19:9965229-9965445(-)$1	216	113	117	11.9999
dnnn	chr12:98993642-98993884(+)$1	242	114	118	11.9999
rrrr	chr12:7355952-7356172(+)$1	220	89	93	11.9999
mmbb	chr2:227920686-227920901(-)$1	215	121	125	11.9999
eeeb	chr10:99619120-99619353(+)$1	233	2	6	11.9999
hhhh	chr11:126146943-126147166(+)$1	223	46	50	11.9999
DDDd	chr12:125609378-125609603(+)$1	225	29	33	11.9999
{DDD	chr11:67052217-67052434(+)$1	217	15	19	11.9999

#DB
))))	chr15:39885272-39885501(+)$1	1	53	57	11.9999
((((	chr1:27876809-27877046(-)$1	1	85	89	11.9999
))))	chr3:4726760-4726985(+)$1	1	100	104	11.9999
.)))	chr2:216288827-216289046(-)$1	1	175	179	11.9999
(.((	chr1:9655925-9656143(+)$1	1	52	56	11.9999
).))	chr11:64681223-64681451(-)$1	1	82	86	11.9999
(.((	chr16:4852282-4852506(-)$1	1	66	70	11.9999
((.(	chr1:55352490-55352715(-)$1	1	15	19	11.9999
.(((	chr7:100487786-100488010(-)$1	1	35	39	11.9999
..))	chr19:49173815-49174031(-)$1	1	72	76	11.9999
))))	chr17:19186442-19186664(+)$1	1	199	203	11.9999
).).	chr7:99725600-99725824(+)$1	1	78	82	11.9999
..))	chr17:72832710-72832941(+)$1	1	31	35	11.9999
.(((	chr16:18795968-18796192(-)$1	1	89	93	11.9999
(.((	chr19:16436236-16436471(+)$1	1	12	16	11.9999
(.((	chr17:73657669-73657888(-)$1	1	42	46	11.9999
((((	chr17:62496077-62496292(-)$1	1	61	65	11.9999
))))	chr1:621869-622093(-)$1	1	51	55	11.9999
((((	chr8:144992064-144992310(-)$1	1	10	14	11.9999
..((	chr8:12168507-12168723(+)$1	1	124	128	11.9999
))))	chr22:32108029-32108254(-)$1	1	169	173	11.9999
))))	chr19:10904394-10904625(+)$1	1	68	72	11.9999
((((	chr21:46876667-46876902(+)$1	1	43	47	11.9999
..))	chr7:1479502-1479741(-)$1	1	48	52	11.9999
))))	chr1:32121900-32122125(-)$1	1	87	91	11.9999
((((	chr4:25415179-25415397(+)$1	1	1	5	11.9999
((((	chr14:105416601-105416825(-)$1	1	180	184	11.9999
(((.	chr9:134612686-134612905(-)$1	1	154	158	11.9999
).((	chr11:11963781-11964017(+)$1	1	169	173	11.9999
((..	chr22:46189476-46189697(+)$1	1	207	211	11.9999
((((	chr6:32796606-32796838(-)$1	1	35	39	11.9999
((((	chr17:19282112-19282332(-)$1	1	187	191	11.9999
))))	chr22:32109407-32109631(-)$1	1	160	164	11.9999
..((	chr14:64636939-64637170(+)$1	1	97	101	11.9999
((((	chr15:73593653-73593874(-)$1	1	24	28	11.9999
..))	chr12:56994018-56994252(-)$1	1	61	65	11.9999
)(((	chr10:17156022-17156240(-)$1	1	77	81	11.9999
((((	chr1:145532508-145532738(+)$1	1	126	130	11.9999
((..	chr6:30858755-30858982(+)$1	1	63	67	11.9999
....	chr6:24522905-24523129(+)$1	1	31	35	11.9999
))))	chr12:124826470-124826697(-)$1	1	44	48	11.9999
((((	chr5:161300103-161300318(+)$1	1	51	55	11.9999
((..	chr7:73811399-73811624(+)$1	1	32	36	11.9999
))..	chr15:64005683-64005901(-)$1	1	115	119	11.9999
.(((	chr1:6154406-6154627(+)$1	1	11	15	11.9999
))))	chr10:26512725-26512948(+)$1	1	51	55	11.9999
))))	chr12:49220699-49220928(+)$1	1	75	79	11.9999
((((	chr2:120251943-120252161(+)$1	1	60	64	11.9999
(.((	chr3:97806229-97806444(+)$1	1	36	40	11.9999
.(((	chr10:123987271-123987492(+)$1	1	16	20	11.9999
)))(	chr2:9516946-9517164(+)$1	1	63	67	11.9999
((((	chr5:43700147-43700383(+)$1	1	105	109	11.9999
).))	chr6:33141549-33141784(-)$1	1	115	119	11.9999
((((	chr12:122399823-122400047(+)$1	1	44	48	11.9999
))))	chr22:25424097-25424318(+)$1	1	134	138	11.9999
(...	chr16:30744568-30744798(+)$1	1	118	122	11.9999
).((	chr2:191785814-191786048(+)$1	1	81	85	11.9999
((((	chr7:47925405-47925622(-)$1	1	5	9	11.9999
))))	chr8:23290443-23290664(-)$1	1	36	40	11.9999
((((	chr19:18391802-18392028(-)$1	1	10	14	11.9999
((((	chr11:129998908-129999135(+)$1	1	91	95	11.9999
..))	chr11:46515111-46515345(-)$1	1	119	123	11.9999
))))	chr9:134357014-134357231(-)$1	1	98	102	11.9999
))..	chr3:49162480-49162706(-)$1	1	27	31	11.9999
..((	chr1:156246810-156247039(-)$1	1	52	56	11.9999
))))	chr1:31414838-31415070(-)$1	1	151	155	11.9999
((((	chr17:36873746-36873966(+)$1	1	24	28	11.9999
..))	chr9:139394985-139395213(-)$1	1	75	79	11.9999
((((	chr19:1041864-1042080(+)$1	1	8	12	11.9999
(((.	chr1:9107563-9107778(+)$1	1	38	42	11.9999
.)))	chr18:61324532-61324749(+)$1	1	165	169	11.9999
(.((	chr7:26192476-26192693(-)$1	1	131	135	11.9999
))))	chr8:27463812-27464051(-)$1	1	90	94	11.9999
...)	chr6:56340911-56341144(-)$1	1	12	16	11.9999
((((	chr6:111632225-111632450(-)$1	1	75	79	11.9999
))).	chr3:56044355-56044587(-)$1	1	117	121	11.9999
..))	chr16:29401158-29401391(+)$1	1	109	113	11.9999
.)))	chr19:9965229-9965445(-)$1	1	113	117	11.9999
(...	chr12:98993642-98993884(+)$1	1	114	118	11.9999
....	chr12:7355952-7356172(+)$1	1	89	93	11.9999
..))	chr2:227920686-227920901(-)$1	1	121	125	11.9999
((((	chr10:99619120-99619353(+)$1	1	2	6	11.9999
((((	chr11:126146943-126147166(+)$1	1	46	50	11.9999
((((	chr12:125609378-125609603(+)$1	1	29	33	11.9999
.(((	chr11:67052217-67052434(+)$1	1	15	19	11.9999

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

#score	1019.9999999999998
#seq	85
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m2_run1.nuc.txt

#NT
UUUAAAAUUU	chr1:879533-879773(-)$1	240	121	131	17.1698
UUUUCAUUUU	chr5:64886265-64886512(-)$1	247	65	75	18.6792
UUUAAAUUCU	chr2:211298424-211298664(-)$1	240	15	25	17.2641
UUUAUAUUUU	chr13:30340198-30340439(-)$1	241	218	228	23.3018
uuaauauuuu	chr19:18687349-18687600(+)$1	251	25	35	18.5849
UUUAUAUUUU	chr9:108536862-108537102(+)$1	240	22	32	23.3018
UUUUUAUUUU	chr6:114181876-114182156(+)$1	280	0	10	21.6981
AUUUUAUUUU	chr17:75494688-75494934(+)$1	246	125	135	16.9811
UUUACAUUUU	chr17:46626527-46626767(-)$1	240	28	38	20.2830
UUCUUAUUUU	chr14:97032509-97032753(+)$1	244	15	25	16.9811
UUUAAAUUAU	chr20:57608541-57608787(-)$1	246	116	126	16.9811
UUUAAAUUUC	chr22:38881374-38881614(-)$1	240	121	131	16.2264
uuuuuaauuu	chr13:98675613-98675853(+)$1	240	103	113	17.8301
UUUAUAAUUU	chr16:69735262-69735502(+)$1	240	37	47	19.4339
UAUAUAuuuu	chr16:19089618-19089860(+)$1	242	161	171	19.2452
UUUAUAUCUU	chr13:27261973-27262213(+)$1	240	115	125	18.5849
UAUAUAUUUU	chr11:64084076-64084316(-)$1	240	117	127	19.2452
UGUUUAUUUU	chr10:98280665-98280905(-)$1	240	26	36	17.6415
UUUAAAUUCU	chr2:178085073-178085317(+)$1	244	119	129	17.2641
uauauauUUU	chr9:131493320-131493560(-)$1	240	123	133	19.2452
UUUAAAUUUU	chr3:183401841-183402081(+)$1	240	149	159	21.0377
UUUAAAUUUU	chr3:136056604-136056844(-)$1	240	36	46	21.0377
UUUUAAUUUU	chr8:125325509-125325749(-)$1	240	127	137	19.4339
UGUAUAUUUU	chr8:21863115-21863355(+)$1	240	54	64	19.2452
UUUGUAUUUU	chr1:200827426-200827666(+)$1	240	201	211	20.5660
UUUAUCUUUU	chr7:114655867-114656107(+)$1	240	125	135	19.0566
UGUAGAUUUU	chr10:94113298-94113540(+)$1	242	79	89	15.9433
uuuauuuuuu	chr17:45196358-45196598(-)$1	240	112	122	18.9622
uuuauauuuu	chr7:64390982-64391222(+)$1	240	111	121	23.3018
UUUAAAUUUU	chr20:43536169-43536409(+)$1	240	22	32	21.0377
uuuuuauuau	chr8:33356834-33357082(+)$1	248	114	124	17.6415
UUUGCAUUUU	chr9:101912425-101912665(+)$1	240	83	93	17.5471
UUUAUACUUU	chr6:79607972-79608212(+)$1	240	122	132	19.1509
UUUAUAUUUU	chr7:34970223-34970463(-)$1	240	100	110	23.3018
UUUGUACUUU	chr11:27519476-27519716(-)$1	240	40	50	16.4150
UUUAUAUUCU	chr3:57546658-57546898(+)$1	240	102	112	19.5283
UUUUUCUUUU	chr1:115249132-115249372(-)$1	240	128	138	17.4528
UUUAUAUUUU	chr3:159976000-159976240(-)$1	240	112	122	23.3018
uuuaaauuuu	chr1:61927461-61927701(+)$1	240	187	197	21.0377
UUUUUAUUUU	chr1:93618823-93619063(-)$1	240	7	17	21.6981
uuuuuaauuu	chr11:74689644-74689884(+)$1	240	90	100	17.8301
UUUAUAUUUU	chr18:11852621-11852861(+)$1	240	220	230	23.3018
UUUUCAUUUU	chr18:43845920-43846165(+)$1	245	69	79	18.6792
UUUAAAUUCU	chr2:178085030-178085270(+)$1	240	162	172	17.2641
UUUAUAUUUU	chr4:39781713-39781953(+)$1	240	143	153	23.3018
UUUAUCUUUU	chr2:204295512-204295761(+)$1	249	111	121	19.0566
UUUGUAUAUU	chrX:150573674-150573915(+)$1	241	12	22	15.8490
UCUUUAUUUU	chr5:53841075-53841315(+)$1	240	142	152	17.4528
UUUUUUUUUU	chr1:68168145-68168425(-)$1	280	122	132	17.3584
UUUAAAAUUU	chr1:97279114-97279354(+)$1	240	79	89	17.1698
UUUUUAUUGU	chr3:78647791-78648031(-)$1	240	131	141	17.5471
CUUUUAUUUU	chr6:97590309-97590549(-)$1	240	119	129	16.9811

#otherMatches

#Struct PSSM
gg"""fffff	chr22:40724497-40724740(+)$1	243	129	139	19.5283
::::::::::	chr1:879533-879773(-)$1	240	121	131	17.1698
ggggqqqqqq	chr5:64886265-64886512(-)$1	247	65	75	18.6792
uuuuuuuuuu	chr2:211298424-211298664(-)$1	240	15	25	17.2641
==========	chr13:30340198-30340439(-)$1	241	218	228	23.3018
"cccmmmmcc	chr19:18687349-18687600(+)$1	251	25	35	18.5849
iiiiiiiill	chr9:108536862-108537102(+)$1	240	22	32	23.3018
::::::::::	chr6:114181876-114182156(+)$1	280	0	10	21.6981
::::::::::	chr17:75494688-75494934(+)$1	246	125	135	16.9811
iiiiiiiiim	chr17:46626527-46626767(-)$1	240	28	38	20.2830
::::::::::	chr14:97032509-97032753(+)$1	244	15	25	16.9811
iii:::::::	chr20:57608541-57608787(-)$1	246	116	126	16.9811
ddd333ffff	chr22:38881374-38881614(-)$1	240	121	131	16.2264
f:::::::::	chr13:98675613-98675853(+)$1	240	103	113	17.8301
^^^^^^^^^^	chr16:69735262-69735502(+)$1	240	37	47	19.4339
:eeeeevvvv	chr16:19089618-19089860(+)$1	242	161	171	19.2452
::::::::::	chr13:27261973-27262213(+)$1	240	115	125	18.5849
::::::::::	chr11:64084076-64084316(-)$1	240	117	127	19.2452
::::::::::	chr10:98280665-98280905(-)$1	240	26	36	17.6415
:::::hhhhh	chr2:178085073-178085317(+)$1	244	119	129	17.2641
==========	chr9:131493320-131493560(-)$1	240	123	133	19.2452
iiiiiiiii[	chr3:183401841-183402081(+)$1	240	149	159	21.0377
[eeeeehhhh	chr3:136056604-136056844(-)$1	240	36	46	21.0377
::========	chr8:125325509-125325749(-)$1	240	127	137	19.4339
vbb333ffff	chr8:21863115-21863355(+)$1	240	54	64	19.2452
mmmhhhhhhh	chr1:200827426-200827666(+)$1	240	201	211	20.5660
ddd:eeeee[	chr7:114655867-114656107(+)$1	240	125	135	19.0566
bb[dddd$$$	chr10:94113298-94113540(+)$1	242	79	89	15.9433
>>>>>>>>>>	chr17:45196358-45196598(-)$1	240	112	122	18.9622
^^^ffffff3	chr7:64390982-64391222(+)$1	240	111	121	23.3018
::::::::::	chr20:43536169-43536409(+)$1	240	22	32	21.0377
::::::::::	chr8:33356834-33357082(+)$1	248	114	124	17.6415
22ccc:ffff	chr9:101912425-101912665(+)$1	240	83	93	17.5471
yyydddd444	chr6:79607972-79608212(+)$1	240	122	132	19.1509
ff::::::::	chr7:34970223-34970463(-)$1	240	100	110	23.3018
33dddd333e	chr11:27519476-27519716(-)$1	240	40	50	16.4150
dyyyyyyyyy	chr3:57546658-57546898(+)$1	240	102	112	19.5283
::eeeeettt	chr1:115249132-115249372(-)$1	240	128	138	17.4528
iiii&&&&&&	chr3:159976000-159976240(-)$1	240	112	122	23.3018
^^^^^^^^^^	chr1:61927461-61927701(+)$1	240	187	197	21.0377
::::::::::	chr1:93618823-93619063(-)$1	240	7	17	21.6981
22dddd22gg	chr11:74689644-74689884(+)$1	240	90	100	17.8301
eeee22gggg	chr18:11852621-11852861(+)$1	240	220	230	23.3018
NNEEEEE{JJ	chr18:43845920-43846165(+)$1	245	69	79	18.6792
:::::hhhhh	chr2:178085030-178085270(+)$1	240	162	172	17.2641
ggggnnnnng	chr4:39781713-39781953(+)$1	240	143	153	23.3018
::::::::::	chr2:204295512-204295761(+)$1	249	111	121	19.0566
LLLCCC{FFF	chrX:150573674-150573915(+)$1	241	12	22	15.8490
bbqqqqqqqq	chr5:53841075-53841315(+)$1	240	142	152	17.4528
::::ffffff	chr1:68168145-68168425(-)$1	280	122	132	17.3584
ooffffff::	chr1:97279114-97279354(+)$1	240	79	89	17.1698
iiiiiidddd	chr3:78647791-78648031(-)$1	240	131	141	17.5471
::::::::::	chr6:97590309-97590549(-)$1	240	119	129	16.9811

#DB
((...(((((	chr22:40724497-40724740(+)$1	1	129	139	19.5283
..........	chr1:879533-879773(-)$1	1	121	131	17.1698
((((......	chr5:64886265-64886512(-)$1	1	65	75	18.6792
..........	chr2:211298424-211298664(-)$1	1	15	25	17.2641
))))))))))	chr13:30340198-30340439(-)$1	1	218	228	23.3018
.(((....))	chr19:18687349-18687600(+)$1	1	25	35	18.5849
((((((((..	chr9:108536862-108537102(+)$1	1	22	32	23.3018
..........	chr6:114181876-114182156(+)$1	1	0	10	21.6981
..........	chr17:75494688-75494934(+)$1	1	125	135	16.9811
(((((((((.	chr17:46626527-46626767(-)$1	1	28	38	20.2830
..........	chr14:97032509-97032753(+)$1	1	15	25	16.9811
))).......	chr20:57608541-57608787(-)$1	1	116	126	16.9811
)))...))))	chr22:38881374-38881614(-)$1	1	121	131	16.2264
).........	chr13:98675613-98675853(+)$1	1	103	113	17.8301
..........	chr16:69735262-69735502(+)$1	1	37	47	19.4339
.(((((....	chr16:19089618-19089860(+)$1	1	161	171	19.2452
..........	chr13:27261973-27262213(+)$1	1	115	125	18.5849
..........	chr11:64084076-64084316(-)$1	1	117	127	19.2452
..........	chr10:98280665-98280905(-)$1	1	26	36	17.6415
.....(((((	chr2:178085073-178085317(+)$1	1	119	129	17.2641
))))))))))	chr9:131493320-131493560(-)$1	1	123	133	19.2452
(((((((((.	chr3:183401841-183402081(+)$1	1	149	159	21.0377
.(((((((((	chr3:136056604-136056844(-)$1	1	36	46	21.0377
..((((((((	chr8:125325509-125325749(-)$1	1	127	137	19.4339
.))...))))	chr8:21863115-21863355(+)$1	1	54	64	19.2452
...)))))))	chr1:200827426-200827666(+)$1	1	201	211	20.5660
))).(((((.	chr7:114655867-114656107(+)$1	1	125	135	19.0566
((.((((...	chr10:94113298-94113540(+)$1	1	79	89	15.9433
..........	chr17:45196358-45196598(-)$1	1	112	122	18.9622
...)))))).	chr7:64390982-64391222(+)$1	1	111	121	23.3018
..........	chr20:43536169-43536409(+)$1	1	22	32	21.0377
..........	chr8:33356834-33357082(+)$1	1	114	124	17.6415
..))).((((	chr9:101912425-101912665(+)$1	1	83	93	17.5471
...))))...	chr6:79607972-79608212(+)$1	1	122	132	19.1509
))........	chr7:34970223-34970463(-)$1	1	100	110	23.3018
..))))...)	chr11:27519476-27519716(-)$1	1	40	50	16.4150
(.........	chr3:57546658-57546898(+)$1	1	102	112	19.5283
..(((((...	chr1:115249132-115249372(-)$1	1	128	138	17.4528
((((......	chr3:159976000-159976240(-)$1	1	112	122	23.3018
..........	chr1:61927461-61927701(+)$1	1	187	197	21.0377
..........	chr1:93618823-93619063(-)$1	1	7	17	21.6981
..))))..))	chr11:74689644-74689884(+)$1	1	90	100	17.8301
))))..))))	chr18:11852621-11852861(+)$1	1	220	230	23.3018
..(((((.((	chr18:43845920-43846165(+)$1	1	69	79	18.6792
.....(((((	chr2:178085030-178085270(+)$1	1	162	172	17.2641
((((.....)	chr4:39781713-39781953(+)$1	1	143	153	23.3018
..........	chr2:204295512-204295761(+)$1	1	111	121	19.0566
...(((.(((	chrX:150573674-150573915(+)$1	1	12	22	15.8490
((........	chr5:53841075-53841315(+)$1	1	142	152	17.4528
....((((((	chr1:68168145-68168425(-)$1	1	122	132	17.3584
..))))))..	chr1:97279114-97279354(+)$1	1	79	89	17.1698
))))))((((	chr3:78647791-78648031(-)$1	1	131	141	17.5471
..........	chr6:97590309-97590549(-)$1	1	119	129	16.9811

#PSSM
U : 0.81	u : 0.15	A : 0.01	C : 0.01	
U : 0.73	u : 0.13	G : 0.05	A : 0.03	a : 0.01	C : 0.01	
U : 0.83	u : 0.13	a : 0.01	C : 0.01	
A : 0.52	U : 0.24	a : 0.09	G : 0.07	u : 0.05	
U : 0.54	A : 0.20	u : 0.13	C : 0.07	G : 0.01	a : 0.01	
A : 0.77	a : 0.13	C : 0.05	u : 0.01	U : 0.01	
U : 0.73	u : 0.13	A : 0.05	a : 0.03	C : 0.03	
U : 0.81	u : 0.15	C : 0.01	A : 0.01	
U : 0.71	u : 0.13	C : 0.09	A : 0.01	a : 0.01	G : 0.01	
U : 0.83	u : 0.15	C : 0.01	

#score	1013.9622641509433
#seq	53
#width	10
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m1_run2.nuc.txt

#NT
CCU	chr15:85213182-85213404(-)$1	222	51	54	9.0000
CCU	chr14:74532124-74532345(+)$1	221	77	80	9.0000
CCU	chr12:104697381-104697618(-)$1	237	50	53	9.0000
ccu	chr20:5975236-5975458(+)$1	222	88	91	9.0000
CCU	chr1:185286074-185286305(-)$1	231	56	59	9.0000
CCU	chr12:104512360-104512582(-)$1	222	33	36	9.0000
CCU	chr17:4884433-4884658(-)$1	225	59	62	9.0000
CCU	chr19:55973415-55973637(+)$1	222	49	52	9.0000
CCU	chr20:4667081-4667315(-)$1	234	28	31	9.0000
CCU	chr11:118964976-118965198(+)$1	222	32	35	9.0000
CCU	chr1:53793558-53793779(+)$1	221	90	93	9.0000
CCU	chr19:1154168-1154390(-)$1	222	60	63	9.0000
CCU	chr4:57371494-57371717(-)$1	223	28	31	9.0000
CCU	chr9:97321084-97321313(-)$1	229	21	24	9.0000
CCU	chr16:31094919-31095154(-)$1	235	5	8	9.0000
CCU	chr8:134467967-134468189(-)$1	222	56	59	9.0000
CCU	chr22:31477280-31477501(+)$1	221	53	56	9.0000
CCU	chr6:46097661-46097884(-)$1	223	9	12	9.0000
CCU	chr6:163736178-163736402(-)$1	224	1	4	9.0000
CCU	chr4:185011881-185012104(+)$1	223	27	30	9.0000
CCU	chr3:127309303-127309529(+)$1	226	53	56	9.0000
CCU	chr18:77208863-77209086(-)$1	223	1	4	9.0000
CCU	chr15:40708370-40708592(-)$1	222	58	61	9.0000
CCU	chr1:26697084-26697308(+)$1	224	4	7	9.0000
CCU	chr2:70166926-70167150(-)$1	224	113	116	9.0000
CCU	chr1:211651830-211652052(-)$1	222	14	17	9.0000
CCU	chr14:66974802-66975024(-)$1	222	218	221	9.0000
CCU	chr10:99400376-99400601(+)$1	225	22	25	9.0000
CCU	chr8:22876801-22877023(+)$1	222	12	15	9.0000
CCU	chr3:9860842-9861066(-)$1	224	17	20	9.0000
CCU	chr17:64731679-64731900(+)$1	221	46	49	9.0000
CCU	chr8:39782190-39782415(+)$1	225	7	10	9.0000
CCU	chr12:113900109-113900330(+)$1	221	3	6	9.0000
CCU	chr8:97346374-97346595(-)$1	221	2	5	9.0000
CCU	chr11:44285085-44285307(+)$1	222	6	9	9.0000
CCU	chr7:44240489-44240717(-)$1	228	7	10	9.0000
CCU	chr19:38796019-38796241(-)$1	222	64	67	9.0000
CCU	chr15:42606327-42606551(-)$1	224	47	50	9.0000
CCU	chr1:17934331-17934562(+)$1	231	12	15	9.0000
CCU	chr14:24563298-24563530(+)$1	232	25	28	9.0000
ccu	chr11:71145739-71145964(-)$1	225	1	4	9.0000
CCU	chr22:38453123-38453345(-)$1	222	9	12	9.0000
CCU	chr7:97838595-97838818(+)$1	223	0	3	9.0000
CCU	chr6:139308723-139308948(+)$1	225	11	14	9.0000
CCU	chr16:47733157-47733388(+)$1	231	9	12	9.0000
CCU	chr19:41859098-41859319(+)$1	221	50	53	9.0000
CCU	chr2:231772279-231772503(-)$1	224	67	70	9.0000
CCU	chr6:119399599-119399823(+)$1	224	32	35	9.0000
CCU	chr1:44386055-44386282(-)$1	227	27	30	9.0000
CCU	chr5:153825834-153826056(-)$1	222	25	28	9.0000
CCU	chrX:153173037-153173266(-)$1	229	15	18	9.0000
CCU	chr15:64366522-64366744(-)$1	222	13	16	9.0000
CCU	chr20:2781137-2781369(-)$1	232	131	134	9.0000
CCU	chr14:39639516-39639739(-)$1	223	35	38	9.0000
CCU	chr11:8160775-8160997(-)$1	222	9	12	9.0000
CCU	chr22:46635284-46635507(+)$1	223	20	23	9.0000
ccu	chr11:71820044-71820267(-)$1	223	3	6	9.0000
CCU	chr6:7541906-7542128(+)$1	222	6	9	9.0000
CCU	chr7:135661804-135662027(-)$1	223	29	32	9.0000
CCU	chr14:71249891-71250113(-)$1	222	59	62	9.0000
CCU	chr3:169496721-169496948(-)$1	227	84	87	9.0000
ccu	chr19:16186858-16187087(-)$1	229	5	8	9.0000
CCU	chr12:53730059-53730281(-)$1	222	51	54	9.0000
CCU	chr1:231473203-231473426(-)$1	223	54	57	9.0000
CCU	chr1:204945702-204945923(-)$1	221	18	21	9.0000
CCU	chr13:52026766-52026989(+)$1	223	33	36	9.0000
CCU	chr17:39988568-39988795(-)$1	227	40	43	9.0000
CCU	chr1:2325368-2325592(+)$1	224	8	11	9.0000
CCU	chr6:53213419-53213641(+)$1	222	92	95	9.0000
CCU	chrX:70323729-70323954(+)$1	225	6	9	9.0000
CCU	chr16:66649243-66649465(+)$1	222	17	20	9.0000
CCU	chr5:109025110-109025336(-)$1	226	82	85	9.0000
CCU	chr20:19702676-19702898(-)$1	222	85	88	9.0000
ccu	chr19:54490675-54490904(-)$1	229	38	41	9.0000
CCU	chr19:5686802-5687027(+)$1	225	64	67	9.0000
ccu	chr20:62717769-62717992(-)$1	223	68	71	9.0000
CCU	chr2:99757716-99757940(-)$1	224	68	71	9.0000
CCU	chr2:32503044-32503265(-)$1	221	130	133	9.0000
CCU	chr19:11606668-11606893(-)$1	225	22	25	9.0000
CCU	chr8:21972029-21972255(-)$1	226	15	18	9.0000
CCU	chr12:123868240-123868463(+)$1	223	170	173	9.0000
CCU	chr13:77456670-77456896(+)$1	226	24	27	9.0000
ccu	chrX:134481988-134482209(-)$1	221	101	104	9.0000
CCU	chr3:125899247-125899468(+)$1	221	23	26	9.0000
CCU	chr17:4890528-4890749(+)$1	221	35	38	9.0000
CCU	chr14:59950503-59950724(+)$1	221	22	25	9.0000
ccu	chr2:228336928-228337150(-)$1	222	94	97	9.0000
CCU	chr2:171822470-171822691(-)$1	221	131	134	9.0000
CCU	chr7:101896636-101896857(-)$1	221	61	64	9.0000
CCU	chr1:151964941-151965163(+)$1	222	17	20	9.0000
CCU	chr20:3905265-3905489(+)$1	224	17	20	9.0000
CCU	chr11:76737315-76737540(+)$1	225	27	30	9.0000
CCU	chr1:3566535-3566763(-)$1	228	4	7	9.0000
CCU	chr3:130613366-130613610(+)$1	244	19	22	9.0000
CCU	chr6:26031773-26031995(-)$1	222	2	5	9.0000
CCU	chr10:28966485-28966707(+)$1	222	15	18	9.0000
CCU	chrX:54070314-54070536(+)$1	222	61	64	9.0000
CCU	chr1:200939403-200939625(+)$1	222	11	14	9.0000
CCU	chr2:98928950-98929176(+)$1	226	5	8	9.0000

#otherMatches

#Struct PSSM
ddd	chr3:142839021-142839243(+)$1	222	58	61	9.0000
ff[	chr15:85213182-85213404(-)$1	222	51	54	9.0000
:::	chr14:74532124-74532345(+)$1	221	77	80	9.0000
:::	chr12:104697381-104697618(-)$1	237	50	53	9.0000
ddd	chr20:5975236-5975458(+)$1	222	88	91	9.0000
bb:	chr1:185286074-185286305(-)$1	231	56	59	9.0000
ddd	chr12:104512360-104512582(-)$1	222	33	36	9.0000
ccc	chr17:4884433-4884658(-)$1	225	59	62	9.0000
cc#	chr19:55973415-55973637(+)$1	222	49	52	9.0000
ffq	chr20:4667081-4667315(-)$1	234	28	31	9.0000
cca	chr11:118964976-118965198(+)$1	222	32	35	9.0000
d##	chr1:53793558-53793779(+)$1	221	90	93	9.0000
""c	chr19:1154168-1154390(-)$1	222	60	63	9.0000
ccc	chr4:57371494-57371717(-)$1	223	28	31	9.0000
&&&	chr9:97321084-97321313(-)$1	229	21	24	9.0000
:::	chr16:31094919-31095154(-)$1	235	5	8	9.0000
3ii	chr8:134467967-134468189(-)$1	222	56	59	9.0000
eee	chr22:31477280-31477501(+)$1	221	53	56	9.0000
ccc	chr6:46097661-46097884(-)$1	223	9	12	9.0000
BKK	chr6:163736178-163736402(-)$1	224	1	4	9.0000
CGG	chr4:185011881-185012104(+)$1	223	27	30	9.0000
cpp	chr3:127309303-127309529(+)$1	226	53	56	9.0000
BCC	chr18:77208863-77209086(-)$1	223	1	4	9.0000
ddd	chr15:40708370-40708592(-)$1	222	58	61	9.0000
CFF	chr1:26697084-26697308(+)$1	224	4	7	9.0000
ggg	chr2:70166926-70167150(-)$1	224	113	116	9.0000
cbb	chr1:211651830-211652052(-)$1	222	14	17	9.0000
ccc	chr14:66974802-66975024(-)$1	222	218	221	9.0000
ccc	chr10:99400376-99400601(+)$1	225	22	25	9.0000
hhh	chr8:22876801-22877023(+)$1	222	12	15	9.0000
FFF	chr3:9860842-9861066(-)$1	224	17	20	9.0000
lll	chr17:64731679-64731900(+)$1	221	46	49	9.0000
&&&	chr8:39782190-39782415(+)$1	225	7	10	9.0000
:::	chr12:113900109-113900330(+)$1	221	3	6	9.0000
:::	chr8:97346374-97346595(-)$1	221	2	5	9.0000
:EE	chr11:44285085-44285307(+)$1	222	6	9	9.0000
ddd	chr7:44240489-44240717(-)$1	228	7	10	9.0000
ggg	chr19:38796019-38796241(-)$1	222	64	67	9.0000
bmm	chr15:42606327-42606551(-)$1	224	47	50	9.0000
ggg	chr1:17934331-17934562(+)$1	231	12	15	9.0000
bdd	chr14:24563298-24563530(+)$1	232	25	28	9.0000
CCL	chr11:71145739-71145964(-)$1	225	1	4	9.0000
DDD	chr22:38453123-38453345(-)$1	222	9	12	9.0000
FFF	chr7:97838595-97838818(+)$1	223	0	3	9.0000
ooo	chr6:139308723-139308948(+)$1	225	11	14	9.0000
!!d	chr16:47733157-47733388(+)$1	231	9	12	9.0000
GGG	chr19:41859098-41859319(+)$1	221	50	53	9.0000
2cc	chr2:231772279-231772503(-)$1	224	67	70	9.0000
eee	chr6:119399599-119399823(+)$1	224	32	35	9.0000
eee	chr1:44386055-44386282(-)$1	227	27	30	9.0000
BDD	chr5:153825834-153826056(-)$1	222	25	28	9.0000
===	chrX:153173037-153173266(-)$1	229	15	18	9.0000
:::	chr15:64366522-64366744(-)$1	222	13	16	9.0000
ggg	chr20:2781137-2781369(-)$1	232	131	134	9.0000
mmm	chr14:39639516-39639739(-)$1	223	35	38	9.0000
:::	chr11:8160775-8160997(-)$1	222	9	12	9.0000
lld	chr22:46635284-46635507(+)$1	223	20	23	9.0000
D{D	chr11:71820044-71820267(-)$1	223	3	6	9.0000
ELL	chr6:7541906-7542128(+)$1	222	6	9	9.0000
ees	chr7:135661804-135662027(-)$1	223	29	32	9.0000
OOO	chr14:71249891-71250113(-)$1	222	59	62	9.0000
eee	chr3:169496721-169496948(-)$1	227	84	87	9.0000
:::	chr19:16186858-16187087(-)$1	229	5	8	9.0000
iii	chr12:53730059-53730281(-)$1	222	51	54	9.0000
qee	chr1:231473203-231473426(-)$1	223	54	57	9.0000
ff!	chr1:204945702-204945923(-)$1	221	18	21	9.0000
ggg	chr13:52026766-52026989(+)$1	223	33	36	9.0000
FFF	chr17:39988568-39988795(-)$1	227	40	43	9.0000
FFF	chr1:2325368-2325592(+)$1	224	8	11	9.0000
"""	chr6:53213419-53213641(+)$1	222	92	95	9.0000
cgg	chrX:70323729-70323954(+)$1	225	6	9	9.0000
eff	chr16:66649243-66649465(+)$1	222	17	20	9.0000
GGG	chr5:109025110-109025336(-)$1	226	82	85	9.0000
nnd	chr20:19702676-19702898(-)$1	222	85	88	9.0000
:dd	chr19:54490675-54490904(-)$1	229	38	41	9.0000
eel	chr19:5686802-5687027(+)$1	225	64	67	9.0000
!!b	chr20:62717769-62717992(-)$1	223	68	71	9.0000
ccm	chr2:99757716-99757940(-)$1	224	68	71	9.0000
cmm	chr2:32503044-32503265(-)$1	221	130	133	9.0000
ADD	chr19:11606668-11606893(-)$1	225	22	25	9.0000
ooo	chr8:21972029-21972255(-)$1	226	15	18	9.0000
fff	chr12:123868240-123868463(+)$1	223	170	173	9.0000
vvv	chr13:77456670-77456896(+)$1	226	24	27	9.0000
bb[	chrX:134481988-134482209(-)$1	221	101	104	9.0000
d[d	chr3:125899247-125899468(+)$1	221	23	26	9.0000
ddd	chr17:4890528-4890749(+)$1	221	35	38	9.0000
ddd	chr14:59950503-59950724(+)$1	221	22	25	9.0000
fff	chr2:228336928-228337150(-)$1	222	94	97	9.0000
ggg	chr2:171822470-171822691(-)$1	221	131	134	9.0000
:gg	chr7:101896636-101896857(-)$1	221	61	64	9.0000
mmd	chr1:151964941-151965163(+)$1	222	17	20	9.0000
###	chr20:3905265-3905489(+)$1	224	17	20	9.0000
'''	chr11:76737315-76737540(+)$1	225	27	30	9.0000
:::	chr1:3566535-3566763(-)$1	228	4	7	9.0000
:::	chr3:130613366-130613610(+)$1	244	19	22	9.0000
eee	chr6:26031773-26031995(-)$1	222	2	5	9.0000
bb:	chr10:28966485-28966707(+)$1	222	15	18	9.0000
HHg	chrX:54070314-54070536(+)$1	222	61	64	9.0000
:::	chr1:200939403-200939625(+)$1	222	11	14	9.0000
:::	chr2:98928950-98929176(+)$1	226	5	8	9.0000

#DB
(((	chr3:142839021-142839243(+)$1	1	58	61	9.0000
((.	chr15:85213182-85213404(-)$1	1	51	54	9.0000
...	chr14:74532124-74532345(+)$1	1	77	80	9.0000
...	chr12:104697381-104697618(-)$1	1	50	53	9.0000
)))	chr20:5975236-5975458(+)$1	1	88	91	9.0000
)).	chr1:185286074-185286305(-)$1	1	56	59	9.0000
(((	chr12:104512360-104512582(-)$1	1	33	36	9.0000
)))	chr17:4884433-4884658(-)$1	1	59	62	9.0000
((.	chr19:55973415-55973637(+)$1	1	49	52	9.0000
((.	chr20:4667081-4667315(-)$1	1	28	31	9.0000
(((	chr11:118964976-118965198(+)$1	1	32	35	9.0000
(..	chr1:53793558-53793779(+)$1	1	90	93	9.0000
..(	chr19:1154168-1154390(-)$1	1	60	63	9.0000
(((	chr4:57371494-57371717(-)$1	1	28	31	9.0000
...	chr9:97321084-97321313(-)$1	1	21	24	9.0000
...	chr16:31094919-31095154(-)$1	1	5	8	9.0000
.))	chr8:134467967-134468189(-)$1	1	56	59	9.0000
)))	chr22:31477280-31477501(+)$1	1	53	56	9.0000
(((	chr6:46097661-46097884(-)$1	1	9	12	9.0000
(..	chr6:163736178-163736402(-)$1	1	1	4	9.0000
(((	chr4:185011881-185012104(+)$1	1	27	30	9.0000
(..	chr3:127309303-127309529(+)$1	1	53	56	9.0000
(((	chr18:77208863-77209086(-)$1	1	1	4	9.0000
)))	chr15:40708370-40708592(-)$1	1	58	61	9.0000
(((	chr1:26697084-26697308(+)$1	1	4	7	9.0000
(((	chr2:70166926-70167150(-)$1	1	113	116	9.0000
(((	chr1:211651830-211652052(-)$1	1	14	17	9.0000
)))	chr14:66974802-66975024(-)$1	1	218	221	9.0000
)))	chr10:99400376-99400601(+)$1	1	22	25	9.0000
(((	chr8:22876801-22877023(+)$1	1	12	15	9.0000
(((	chr3:9860842-9861066(-)$1	1	17	20	9.0000
...	chr17:64731679-64731900(+)$1	1	46	49	9.0000
...	chr8:39782190-39782415(+)$1	1	7	10	9.0000
...	chr12:113900109-113900330(+)$1	1	3	6	9.0000
...	chr8:97346374-97346595(-)$1	1	2	5	9.0000
.((	chr11:44285085-44285307(+)$1	1	6	9	9.0000
(((	chr7:44240489-44240717(-)$1	1	7	10	9.0000
)))	chr19:38796019-38796241(-)$1	1	64	67	9.0000
(..	chr15:42606327-42606551(-)$1	1	47	50	9.0000
(((	chr1:17934331-17934562(+)$1	1	12	15	9.0000
(((	chr14:24563298-24563530(+)$1	1	25	28	9.0000
((.	chr11:71145739-71145964(-)$1	1	1	4	9.0000
(((	chr22:38453123-38453345(-)$1	1	9	12	9.0000
(((	chr7:97838595-97838818(+)$1	1	0	3	9.0000
...	chr6:139308723-139308948(+)$1	1	11	14	9.0000
..(	chr16:47733157-47733388(+)$1	1	9	12	9.0000
(((	chr19:41859098-41859319(+)$1	1	50	53	9.0000
.))	chr2:231772279-231772503(-)$1	1	67	70	9.0000
)))	chr6:119399599-119399823(+)$1	1	32	35	9.0000
(((	chr1:44386055-44386282(-)$1	1	27	30	9.0000
(((	chr5:153825834-153826056(-)$1	1	25	28	9.0000
(((	chrX:153173037-153173266(-)$1	1	15	18	9.0000
...	chr15:64366522-64366744(-)$1	1	13	16	9.0000
)))	chr20:2781137-2781369(-)$1	1	131	134	9.0000
...	chr14:39639516-39639739(-)$1	1	35	38	9.0000
...	chr11:8160775-8160997(-)$1	1	9	12	9.0000
..)	chr22:46635284-46635507(+)$1	1	20	23	9.0000
(.(	chr11:71820044-71820267(-)$1	1	3	6	9.0000
(..	chr6:7541906-7542128(+)$1	1	6	9	9.0000
((.	chr7:135661804-135662027(-)$1	1	29	32	9.0000
...	chr14:71249891-71250113(-)$1	1	59	62	9.0000
(((	chr3:169496721-169496948(-)$1	1	84	87	9.0000
...	chr19:16186858-16187087(-)$1	1	5	8	9.0000
(((	chr12:53730059-53730281(-)$1	1	51	54	9.0000
.))	chr1:231473203-231473426(-)$1	1	54	57	9.0000
((.	chr1:204945702-204945923(-)$1	1	18	21	9.0000
(((	chr13:52026766-52026989(+)$1	1	33	36	9.0000
(((	chr17:39988568-39988795(-)$1	1	40	43	9.0000
(((	chr1:2325368-2325592(+)$1	1	8	11	9.0000
...	chr6:53213419-53213641(+)$1	1	92	95	9.0000
(((	chrX:70323729-70323954(+)$1	1	6	9	9.0000
(((	chr16:66649243-66649465(+)$1	1	17	20	9.0000
)))	chr5:109025110-109025336(-)$1	1	82	85	9.0000
..)	chr20:19702676-19702898(-)$1	1	85	88	9.0000
.((	chr19:54490675-54490904(-)$1	1	38	41	9.0000
((.	chr19:5686802-5687027(+)$1	1	64	67	9.0000
..(	chr20:62717769-62717992(-)$1	1	68	71	9.0000
((.	chr2:99757716-99757940(-)$1	1	68	71	9.0000
(..	chr2:32503044-32503265(-)$1	1	130	133	9.0000
(((	chr19:11606668-11606893(-)$1	1	22	25	9.0000
...	chr8:21972029-21972255(-)$1	1	15	18	9.0000
)))	chr12:123868240-123868463(+)$1	1	170	173	9.0000
...	chr13:77456670-77456896(+)$1	1	24	27	9.0000
((.	chrX:134481988-134482209(-)$1	1	101	104	9.0000
(.(	chr3:125899247-125899468(+)$1	1	23	26	9.0000
(((	chr17:4890528-4890749(+)$1	1	35	38	9.0000
)))	chr14:59950503-59950724(+)$1	1	22	25	9.0000
)))	chr2:228336928-228337150(-)$1	1	94	97	9.0000
(((	chr2:171822470-171822691(-)$1	1	131	134	9.0000
.((	chr7:101896636-101896857(-)$1	1	61	64	9.0000
..)	chr1:151964941-151965163(+)$1	1	17	20	9.0000
...	chr20:3905265-3905489(+)$1	1	17	20	9.0000
...	chr11:76737315-76737540(+)$1	1	27	30	9.0000
...	chr1:3566535-3566763(-)$1	1	4	7	9.0000
...	chr3:130613366-130613610(+)$1	1	19	22	9.0000
(((	chr6:26031773-26031995(-)$1	1	2	5	9.0000
)).	chr10:28966485-28966707(+)$1	1	15	18	9.0000
(((	chrX:54070314-54070536(+)$1	1	61	64	9.0000
...	chr1:200939403-200939625(+)$1	1	11	14	9.0000
...	chr2:98928950-98929176(+)$1	1	5	8	9.0000

#PSSM
C : 0.92	c : 0.08	
C : 0.92	c : 0.08	
U : 0.92	u : 0.08	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m1_run2.nuc.txt

#NT
CUU	chr3:185639769-185639987(-)$1	218	2	5	9.0000
CUU	chr3:180665581-180665811(+)$1	230	29	32	9.0000
CUU	chrX:118752307-118752519(-)$1	212	20	23	9.0000
CUU	chr12:49521755-49521993(-)$1	238	105	108	9.0000
CUU	chr12:121138107-121138322(+)$1	215	21	24	9.0000
CUU	chrX:1505148-1505366(-)$1	218	69	72	9.0000
CUU	chr17:31268096-31268342(+)$1	246	75	78	9.0000
CUU	chr7:151919583-151919789(-)$1	206	14	17	9.0000
CUU	chr16:18820463-18820691(-)$1	228	61	64	9.0000
CUU	chr18:32915818-32916031(-)$1	213	135	138	9.0000
CUU	chr1:32372997-32373230(-)$1	233	25	28	9.0000
CUU	chr17:40993738-40993959(+)$1	221	27	30	9.0000
CUU	chr16:2326088-2326300(-)$1	212	141	144	9.0000
CUU	chr9:134400040-134400250(-)$1	210	36	39	9.0000
CUU	chr2:172822849-172823078(+)$1	229	56	59	9.0000
CUU	chr19:10655631-10655865(+)$1	234	26	29	9.0000
CUU	chr6:20491757-20491993(+)$1	236	37	40	9.0000
CUU	chr4:100869268-100869489(-)$1	221	16	19	9.0000
CUU	chr11:74352920-74353172(+)$1	252	32	35	9.0000
CUU	chr19:29698350-29698585(-)$1	235	15	18	9.0000
CUU	chr1:56961061-56961279(-)$1	218	23	26	9.0000
CUU	chr2:75883114-75883329(+)$1	215	188	191	9.0000
CUU	chr8:87573393-87573614(+)$1	221	0	3	9.0000
CUU	chr17:1421540-1421760(-)$1	220	21	24	9.0000
CUU	chr3:23932602-23932822(+)$1	220	23	26	9.0000
CUU	chr3:185636076-185636296(-)$1	220	42	45	9.0000
CUU	chr19:35988071-35988306(-)$1	235	5	8	9.0000
CUU	chr6:13588555-13588759(+)$1	204	98	101	9.0000
CUU	chrX:131337333-131337535(-)$1	202	45	48	9.0000
CUU	chr6:10756943-10757178(+)$1	235	10	13	9.0000
CUU	chr19:10260213-10260423(-)$1	210	28	31	9.0000
CUU	chr1:229459905-229460130(-)$1	225	20	23	9.0000
CUU	chr22:30977231-30977441(-)$1	210	28	31	9.0000
CUU	chrX:77083334-77083566(-)$1	232	111	114	9.0000
CUU	chr6:64292365-64292576(+)$1	211	20	23	9.0000
CUU	chr18:77896892-77897094(+)$1	202	56	59	9.0000
CUU	chr1:110174338-110174542(+)$1	204	44	47	9.0000
CUU	chr22:21802276-21802524(+)$1	248	67	70	9.0000
CUU	chr14:51713724-51713944(+)$1	220	79	82	9.0000
cuu	chr7:30119276-30119490(+)$1	214	49	52	9.0000
CUU	chr1:25169858-25170125(+)$1	267	65	68	9.0000
CUU	chr1:180017651-180017859(+)$1	208	51	54	9.0000
CUU	chr19:38874113-38874472(+)$1	359	8	11	9.0000
CUU	chr7:151074476-151074707(+)$1	231	20	23	9.0000
CUU	chr6:11137114-11137319(+)$1	205	87	90	9.0000
CUU	chr3:49757944-49758173(-)$1	229	15	18	9.0000
CUU	chr1:67469838-67470045(-)$1	207	34	37	9.0000
CUU	chr1:111983361-111983584(-)$1	223	14	17	9.0000
CUU	chr6:19837737-19837951(+)$1	214	1	4	9.0000
cuu	chr12:46636895-46637113(-)$1	218	2	5	9.0000
CUU	chr3:51425185-51425387(+)$1	202	84	87	9.0000
CUU	chrX:73752484-73752690(+)$1	206	89	92	9.0000
CUU	chr18:22033133-22033341(+)$1	208	12	15	9.0000
CUU	chr12:62926213-62926447(+)$1	234	4	7	9.0000
CUU	chrX:153609576-153609787(+)$1	211	2	5	9.0000
CUU	chr9:5786869-5787074(-)$1	205	52	55	9.0000
CUU	chr10:81113760-81114011(+)$1	251	11	14	9.0000
CUU	chr6:30461260-30461488(+)$1	228	4	7	9.0000
CUU	chr21:34930187-34930410(+)$1	223	16	19	9.0000
CUU	chr10:122650216-122650445(+)$1	229	4	7	9.0000
CUU	chr6:136610761-136611020(-)$1	259	98	101	9.0000
CUU	chr8:29931363-29931572(-)$1	209	30	33	9.0000
CUU	chr2:170495480-170495694(+)$1	214	1	4	9.0000
CUU	chr15:45009907-45010137(+)$1	230	28	31	9.0000
CUU	chr2:27249570-27249780(+)$1	210	4	7	9.0000
CUU	chr12:98991572-98991857(+)$1	285	45	48	9.0000
CUU	chr1:151376018-151376257(-)$1	239	25	28	9.0000
CUU	chr3:49021691-49021912(+)$1	221	35	38	9.0000
CUU	chr12:51089557-51089761(+)$1	204	50	53	9.0000
CUU	chr14:99864639-99864868(-)$1	229	16	19	9.0000
CUU	chr3:131102175-131102388(+)$1	213	50	53	9.0000
CUU	chr18:55216650-55216858(-)$1	208	5	8	9.0000
CUU	chr5:177022584-177022816(+)$1	232	88	91	9.0000
CUU	chr11:27389053-27389255(-)$1	202	82	85	9.0000
CUU	chr8:26265691-26265921(+)$1	230	42	45	9.0000
CUU	chr6:126299541-126299756(+)$1	215	4	7	9.0000
CUU	chr19:35176977-35177192(+)$1	215	5	8	9.0000
CUU	chr15:44817699-44817922(+)$1	223	39	42	9.0000
CUU	chr8:54959467-54959683(-)$1	216	37	40	9.0000
CUU	chr6:53133419-53133626(-)$1	207	34	37	9.0000
CUU	chr1:236647023-236647240(+)$1	217	193	196	9.0000
CUU	chr20:55093373-55093603(+)$1	230	8	11	9.0000
CUU	chr7:150070339-150070577(+)$1	238	49	52	9.0000
CUU	chr5:43174864-43175090(+)$1	226	44	47	9.0000
CUU	chr7:151851400-151851620(-)$1	220	61	64	9.0000
CUU	chr7:103767106-103767337(-)$1	231	6	9	9.0000
CUU	chr4:5822917-5823146(-)$1	229	144	147	9.0000
CUU	chr9:108397915-108398141(+)$1	226	49	52	9.0000
CUU	chr8:8641812-8642051(-)$1	239	79	82	9.0000
CUU	chr15:69728452-69728683(+)$1	231	200	203	9.0000
CUU	chr5:38481457-38481692(-)$1	235	12	15	9.0000
CUU	chr11:62392538-62392766(-)$1	228	47	50	9.0000
CUU	chr17:27586595-27586840(-)$1	245	67	70	9.0000
CUU	chr3:49020840-49021057(+)$1	217	2	5	9.0000
CUU	chr1:171561342-171561579(+)$1	237	67	70	9.0000
CUU	chr15:64975216-64975423(+)$1	207	10	13	9.0000
CUU	chr11:67938428-67938665(-)$1	237	7	10	9.0000
CUU	chr13:27261476-27261720(+)$1	244	123	126	9.0000
CUU	chr12:69222467-69222676(+)$1	209	70	73	9.0000

#otherMatches

#Struct PSSM
g:f	chr1:32637774-32638024(+)$1	250	20	23	9.0000
eee	chr3:185639769-185639987(-)$1	218	2	5	9.0000
##g	chr3:180665581-180665811(+)$1	230	29	32	9.0000
GGG	chrX:118752307-118752519(-)$1	212	20	23	9.0000
ggg	chr12:49521755-49521993(-)$1	238	105	108	9.0000
PPI	chr12:121138107-121138322(+)$1	215	21	24	9.0000
ppp	chrX:1505148-1505366(-)$1	218	69	72	9.0000
JJJ	chr17:31268096-31268342(+)$1	246	75	78	9.0000
dd!	chr7:151919583-151919789(-)$1	206	14	17	9.0000
!!e	chr16:18820463-18820691(-)$1	228	61	64	9.0000
ddc	chr18:32915818-32916031(-)$1	213	135	138	9.0000
JJJ	chr1:32372997-32373230(-)$1	233	25	28	9.0000
BBK	chr17:40993738-40993959(+)$1	221	27	30	9.0000
HHH	chr16:2326088-2326300(-)$1	212	141	144	9.0000
BFF	chr9:134400040-134400250(-)$1	210	36	39	9.0000
eee	chr2:172822849-172823078(+)$1	229	56	59	9.0000
III	chr19:10655631-10655865(+)$1	234	26	29	9.0000
ddd	chr6:20491757-20491993(+)$1	236	37	40	9.0000
c]f	chr4:100869268-100869489(-)$1	221	16	19	9.0000
JJJ	chr11:74352920-74353172(+)$1	252	32	35	9.0000
ggg	chr19:29698350-29698585(-)$1	235	15	18	9.0000
fff	chr1:56961061-56961279(-)$1	218	23	26	9.0000
GGG	chr2:75883114-75883329(+)$1	215	188	191	9.0000
:EE	chr8:87573393-87573614(+)$1	221	0	3	9.0000
c::	chr17:1421540-1421760(-)$1	220	21	24	9.0000
JJK	chr3:23932602-23932822(+)$1	220	23	26	9.0000
::g	chr3:185636076-185636296(-)$1	220	42	45	9.0000
:::	chr19:35988071-35988306(-)$1	235	5	8	9.0000
iii	chr6:13588555-13588759(+)$1	204	98	101	9.0000
eee	chrX:131337333-131337535(-)$1	202	45	48	9.0000
fff	chr6:10756943-10757178(+)$1	235	10	13	9.0000
===	chr19:10260213-10260423(-)$1	210	28	31	9.0000
555	chr1:229459905-229460130(-)$1	225	20	23	9.0000
c""	chr22:30977231-30977441(-)$1	210	28	31	9.0000
cmm	chrX:77083334-77083566(-)$1	232	111	114	9.0000
FF:	chr6:64292365-64292576(+)$1	211	20	23	9.0000
qqq	chr18:77896892-77897094(+)$1	202	56	59	9.0000
)))	chr1:110174338-110174542(+)$1	204	44	47	9.0000
c22	chr22:21802276-21802524(+)$1	248	67	70	9.0000
KKC	chr14:51713724-51713944(+)$1	220	79	82	9.0000
EEE	chr7:30119276-30119490(+)$1	214	49	52	9.0000
cc[	chr1:25169858-25170125(+)$1	267	65	68	9.0000
ddd	chr1:180017651-180017859(+)$1	208	51	54	9.0000
GG{	chr19:38874113-38874472(+)$1	359	8	11	9.0000
ggg	chr7:151074476-151074707(+)$1	231	20	23	9.0000
ttt	chr6:11137114-11137319(+)$1	205	87	90	9.0000
a""	chr3:49757944-49758173(-)$1	229	15	18	9.0000
hhh	chr1:67469838-67470045(-)$1	207	34	37	9.0000
dd[	chr1:111983361-111983584(-)$1	223	14	17	9.0000
::D	chr6:19837737-19837951(+)$1	214	1	4	9.0000
:EE	chr12:46636895-46637113(-)$1	218	2	5	9.0000
CGG	chr3:51425185-51425387(+)$1	202	84	87	9.0000
%%%	chrX:73752484-73752690(+)$1	206	89	92	9.0000
ggm	chr18:22033133-22033341(+)$1	208	12	15	9.0000
:DD	chr12:62926213-62926447(+)$1	234	4	7	9.0000
ddm	chrX:153609576-153609787(+)$1	211	2	5	9.0000
:dd	chr9:5786869-5787074(-)$1	205	52	55	9.0000
::G	chr10:81113760-81114011(+)$1	251	11	14	9.0000
:ff	chr6:30461260-30461488(+)$1	228	4	7	9.0000
FF:	chr21:34930187-34930410(+)$1	223	16	19	9.0000
fff	chr10:122650216-122650445(+)$1	229	4	7	9.0000
dd:	chr6:136610761-136611020(-)$1	259	98	101	9.0000
B{E	chr8:29931363-29931572(-)$1	209	30	33	9.0000
BDD	chr2:170495480-170495694(+)$1	214	1	4	9.0000
KKD	chr15:45009907-45010137(+)$1	230	28	31	9.0000
:::	chr2:27249570-27249780(+)$1	210	4	7	9.0000
fff	chr12:98991572-98991857(+)$1	285	45	48	9.0000
f::	chr1:151376018-151376257(-)$1	239	25	28	9.0000
eem	chr3:49021691-49021912(+)$1	221	35	38	9.0000
ppp	chr12:51089557-51089761(+)$1	204	50	53	9.0000
EEE	chr14:99864639-99864868(-)$1	229	16	19	9.0000
55c	chr3:131102175-131102388(+)$1	213	50	53	9.0000
FFF	chr18:55216650-55216858(-)$1	208	5	8	9.0000
hhh	chr5:177022584-177022816(+)$1	232	88	91	9.0000
2ee	chr11:27389053-27389255(-)$1	202	82	85	9.0000
rrr	chr8:26265691-26265921(+)$1	230	42	45	9.0000
:::	chr6:126299541-126299756(+)$1	215	4	7	9.0000
EED	chr19:35176977-35177192(+)$1	215	5	8	9.0000
eee	chr15:44817699-44817922(+)$1	223	39	42	9.0000
:gg	chr8:54959467-54959683(-)$1	216	37	40	9.0000
b55	chr6:53133419-53133626(-)$1	207	34	37	9.0000
JJJ	chr1:236647023-236647240(+)$1	217	193	196	9.0000
fff	chr20:55093373-55093603(+)$1	230	8	11	9.0000
ff#	chr7:150070339-150070577(+)$1	238	49	52	9.0000
ddd	chr5:43174864-43175090(+)$1	226	44	47	9.0000
boo	chr7:151851400-151851620(-)$1	220	61	64	9.0000
BBB	chr7:103767106-103767337(-)$1	231	6	9	9.0000
ccc	chr4:5822917-5823146(-)$1	229	144	147	9.0000
MMD	chr9:108397915-108398141(+)$1	226	49	52	9.0000
EEE	chr8:8641812-8642051(-)$1	239	79	82	9.0000
:::	chr15:69728452-69728683(+)$1	231	200	203	9.0000
:::	chr5:38481457-38481692(-)$1	235	12	15	9.0000
ddd	chr11:62392538-62392766(-)$1	228	47	50	9.0000
:EE	chr17:27586595-27586840(-)$1	245	67	70	9.0000
::F	chr3:49020840-49021057(+)$1	217	2	5	9.0000
:hh	chr1:171561342-171561579(+)$1	237	67	70	9.0000
vvv	chr15:64975216-64975423(+)$1	207	10	13	9.0000
hhh	chr11:67938428-67938665(-)$1	237	7	10	9.0000
ccc	chr13:27261476-27261720(+)$1	244	123	126	9.0000
KHH	chr12:69222467-69222676(+)$1	209	70	73	9.0000

#DB
).(	chr1:32637774-32638024(+)$1	1	20	23	9.0000
(((	chr3:185639769-185639987(-)$1	1	2	5	9.0000
..(	chr3:180665581-180665811(+)$1	1	29	32	9.0000
(((	chrX:118752307-118752519(-)$1	1	20	23	9.0000
(((	chr12:49521755-49521993(-)$1	1	105	108	9.0000
..(	chr12:121138107-121138322(+)$1	1	21	24	9.0000
...	chrX:1505148-1505366(-)$1	1	69	72	9.0000
(((	chr17:31268096-31268342(+)$1	1	75	78	9.0000
((.	chr7:151919583-151919789(-)$1	1	14	17	9.0000
..(	chr16:18820463-18820691(-)$1	1	61	64	9.0000
)))	chr18:32915818-32916031(-)$1	1	135	138	9.0000
(((	chr1:32372997-32373230(-)$1	1	25	28	9.0000
((.	chr17:40993738-40993959(+)$1	1	27	30	9.0000
)))	chr16:2326088-2326300(-)$1	1	141	144	9.0000
(((	chr9:134400040-134400250(-)$1	1	36	39	9.0000
(((	chr2:172822849-172823078(+)$1	1	56	59	9.0000
(((	chr19:10655631-10655865(+)$1	1	26	29	9.0000
)))	chr6:20491757-20491993(+)$1	1	37	40	9.0000
).)	chr4:100869268-100869489(-)$1	1	16	19	9.0000
(((	chr11:74352920-74353172(+)$1	1	32	35	9.0000
(((	chr19:29698350-29698585(-)$1	1	15	18	9.0000
(((	chr1:56961061-56961279(-)$1	1	23	26	9.0000
)))	chr2:75883114-75883329(+)$1	1	188	191	9.0000
.((	chr8:87573393-87573614(+)$1	1	0	3	9.0000
)..	chr17:1421540-1421760(-)$1	1	21	24	9.0000
((.	chr3:23932602-23932822(+)$1	1	23	26	9.0000
..(	chr3:185636076-185636296(-)$1	1	42	45	9.0000
...	chr19:35988071-35988306(-)$1	1	5	8	9.0000
(((	chr6:13588555-13588759(+)$1	1	98	101	9.0000
(((	chrX:131337333-131337535(-)$1	1	45	48	9.0000
(((	chr6:10756943-10757178(+)$1	1	10	13	9.0000
(((	chr19:10260213-10260423(-)$1	1	28	31	9.0000
...	chr1:229459905-229460130(-)$1	1	20	23	9.0000
(..	chr22:30977231-30977441(-)$1	1	28	31	9.0000
(..	chrX:77083334-77083566(-)$1	1	111	114	9.0000
((.	chr6:64292365-64292576(+)$1	1	20	23	9.0000
...	chr18:77896892-77897094(+)$1	1	56	59	9.0000
...	chr1:110174338-110174542(+)$1	1	44	47	9.0000
)..	chr22:21802276-21802524(+)$1	1	67	70	9.0000
..(	chr14:51713724-51713944(+)$1	1	79	82	9.0000
(((	chr7:30119276-30119490(+)$1	1	49	52	9.0000
((.	chr1:25169858-25170125(+)$1	1	65	68	9.0000
(((	chr1:180017651-180017859(+)$1	1	51	54	9.0000
((.	chr19:38874113-38874472(+)$1	1	8	11	9.0000
)))	chr7:151074476-151074707(+)$1	1	20	23	9.0000
...	chr6:11137114-11137319(+)$1	1	87	90	9.0000
(..	chr3:49757944-49758173(-)$1	1	15	18	9.0000
)))	chr1:67469838-67470045(-)$1	1	34	37	9.0000
((.	chr1:111983361-111983584(-)$1	1	14	17	9.0000
..(	chr6:19837737-19837951(+)$1	1	1	4	9.0000
.((	chr12:46636895-46637113(-)$1	1	2	5	9.0000
(((	chr3:51425185-51425387(+)$1	1	84	87	9.0000
...	chrX:73752484-73752690(+)$1	1	89	92	9.0000
((.	chr18:22033133-22033341(+)$1	1	12	15	9.0000
.((	chr12:62926213-62926447(+)$1	1	4	7	9.0000
((.	chrX:153609576-153609787(+)$1	1	2	5	9.0000
.((	chr9:5786869-5787074(-)$1	1	52	55	9.0000
..(	chr10:81113760-81114011(+)$1	1	11	14	9.0000
.((	chr6:30461260-30461488(+)$1	1	4	7	9.0000
((.	chr21:34930187-34930410(+)$1	1	16	19	9.0000
(((	chr10:122650216-122650445(+)$1	1	4	7	9.0000
)).	chr6:136610761-136611020(-)$1	1	98	101	9.0000
(.(	chr8:29931363-29931572(-)$1	1	30	33	9.0000
(((	chr2:170495480-170495694(+)$1	1	1	4	9.0000
..(	chr15:45009907-45010137(+)$1	1	28	31	9.0000
...	chr2:27249570-27249780(+)$1	1	4	7	9.0000
(((	chr12:98991572-98991857(+)$1	1	45	48	9.0000
)..	chr1:151376018-151376257(-)$1	1	25	28	9.0000
((.	chr3:49021691-49021912(+)$1	1	35	38	9.0000
...	chr12:51089557-51089761(+)$1	1	50	53	9.0000
(((	chr14:99864639-99864868(-)$1	1	16	19	9.0000
..)	chr3:131102175-131102388(+)$1	1	50	53	9.0000
(((	chr18:55216650-55216858(-)$1	1	5	8	9.0000
(((	chr5:177022584-177022816(+)$1	1	88	91	9.0000
.))	chr11:27389053-27389255(-)$1	1	82	85	9.0000
...	chr8:26265691-26265921(+)$1	1	42	45	9.0000
...	chr6:126299541-126299756(+)$1	1	4	7	9.0000
(((	chr19:35176977-35177192(+)$1	1	5	8	9.0000
)))	chr15:44817699-44817922(+)$1	1	39	42	9.0000
.((	chr8:54959467-54959683(-)$1	1	37	40	9.0000
)..	chr6:53133419-53133626(-)$1	1	34	37	9.0000
)))	chr1:236647023-236647240(+)$1	1	193	196	9.0000
(((	chr20:55093373-55093603(+)$1	1	8	11	9.0000
((.	chr7:150070339-150070577(+)$1	1	49	52	9.0000
(((	chr5:43174864-43175090(+)$1	1	44	47	9.0000
(..	chr7:151851400-151851620(-)$1	1	61	64	9.0000
(((	chr7:103767106-103767337(-)$1	1	6	9	9.0000
(((	chr4:5822917-5823146(-)$1	1	144	147	9.0000
..(	chr9:108397915-108398141(+)$1	1	49	52	9.0000
(((	chr8:8641812-8642051(-)$1	1	79	82	9.0000
...	chr15:69728452-69728683(+)$1	1	200	203	9.0000
...	chr5:38481457-38481692(-)$1	1	12	15	9.0000
)))	chr11:62392538-62392766(-)$1	1	47	50	9.0000
.((	chr17:27586595-27586840(-)$1	1	67	70	9.0000
..(	chr3:49020840-49021057(+)$1	1	2	5	9.0000
.((	chr1:171561342-171561579(+)$1	1	67	70	9.0000
...	chr15:64975216-64975423(+)$1	1	10	13	9.0000
(((	chr11:67938428-67938665(-)$1	1	7	10	9.0000
)))	chr13:27261476-27261720(+)$1	1	123	126	9.0000
.((	chr12:69222467-69222676(+)$1	1	70	73	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m3_run2.nuc.txt

#NT
GCUUU	chr11:64537375-64537600(-)$1	225	60	65	11.0000
ACUUU	chr1:245019949-245020211(-)$1	262	39	44	11.6363
CCUUU	chr9:139723746-139723987(+)$1	241	22	27	10.8181
ACUUU	chr6:97344571-97344794(-)$1	223	52	57	11.6363
CCUUU	chr9:130209883-130210105(-)$1	222	59	64	10.8181
UCUUU	chr18:19353540-19353762(+)$1	222	18	23	11.5454
GCUUU	chr15:66170120-66170341(+)$1	221	163	168	11.0000
CCUUU	chr4:52765420-52765644(+)$1	224	169	174	10.8181
GCUUU	chr20:42087839-42088084(+)$1	245	17	22	11.0000
UCUUU	chr17:79801327-79801614(-)$1	287	65	70	11.5454
UCUUU	chr1:35649973-35650240(-)$1	267	239	244	11.5454
UCUUU	chr12:6861364-6861603(-)$1	239	66	71	11.5454
UCUUU	chrX:153609331-153609606(+)$1	275	25	30	11.5454
ACUUU	chr17:66042532-66042764(+)$1	232	172	177	11.6363
ACUUU	chr3:112280235-112280468(-)$1	233	209	214	11.6363
UCUUU	chr3:51423624-51423857(+)$1	233	4	9	11.5454
GCUUU	chr6:26199022-26199276(-)$1	254	217	222	11.0000
ACUUU	chr1:76253108-76253344(+)$1	236	58	63	11.6363
CCUUU	chr21:28212145-28212379(-)$1	234	2	7	10.8181
ACUUU	chr5:138643531-138643766(+)$1	235	120	125	11.6363
GCUUU	chr14:32560757-32560987(+)$1	230	150	155	11.0000
GCUUU	chr11:63765087-63765337(+)$1	250	165	170	11.0000
UCUUU	chrX:118374209-118374454(+)$1	245	41	46	11.5454
UCUUU	chr1:231509656-231509876(-)$1	220	192	197	11.5454
UCUUU	chr19:59067973-59068199(-)$1	226	20	25	11.5454
ACUUU	chr3:113508550-113508773(+)$1	223	199	204	11.6363
UCUUU	chr15:102185217-102185438(-)$1	221	56	61	11.5454
ACUUU	chr16:58581064-58581300(-)$1	236	27	32	11.6363
CCUUU	chr6:30690603-30690831(+)$1	228	162	167	10.8181
CCUUU	chr6:44219397-44219659(+)$1	262	245	250	10.8181
UCUUU	chr20:5095833-5096069(-)$1	236	214	219	11.5454
UCUUU	chr1:245022502-245022726(-)$1	224	158	163	11.5454
ACUUU	chr17:38567857-38568110(-)$1	253	4	9	11.6363
ACUUU	chr15:77239718-77239954(+)$1	236	8	13	11.6363
GCUUU	chr4:77969606-77969840(-)$1	234	2	7	11.0000
CCUUU	chr6:26104342-26104593(+)$1	251	205	210	10.8181
ACUUU	chr10:49628116-49628350(+)$1	234	12	17	11.6363
UCUUU	chr3:167405354-167405579(-)$1	225	38	43	11.5454
GCUUU	chr8:103855702-103855947(-)$1	245	224	229	11.0000
ACUUU	chr3:121151096-121151342(-)$1	246	5	10	11.6363
ccuuu	chr22:38881845-38882100(-)$1	255	221	226	10.8181
ACUUU	chr11:9610040-9610296(+)$1	256	228	233	11.6363
UCUUU	chr1:150550714-150550978(-)$1	264	127	132	11.5454
UCUUU	chr15:59102343-59102562(+)$1	219	26	31	11.5454
GCUUU	chr10:72164051-72164288(+)$1	237	15	20	11.0000
GCUUU	chr19:2328291-2328522(-)$1	231	33	38	11.0000
ACUUU	chr8:95900145-95900370(-)$1	225	118	123	11.6363
UCUUU	chr16:29821468-29821733(+)$1	265	153	158	11.5454
GCUUU	chr17:49083407-49083640(-)$1	233	46	51	11.0000
ACUUU	chr6:26031725-26032012(-)$1	287	145	150	11.6363
UCUUU	chr1:224377666-224377889(+)$1	223	32	37	11.5454
ACUUU	chr1:240371743-240371990(+)$1	247	125	130	11.6363
ACUUU	chr2:10584133-10584384(-)$1	251	108	113	11.6363
CCUUU	chr19:8528383-8528627(+)$1	244	77	82	10.8181

#otherMatches

#Struct PSSM
ppggg	chr3:57271436-57271660(+)$1	224	39	44	11.6363
iiiii	chr11:64537375-64537600(-)$1	225	60	65	11.0000
siiii	chr1:245019949-245020211(-)$1	262	39	44	11.6363
sshhh	chr9:139723746-139723987(+)$1	241	22	27	10.8181
BB{EE	chr6:97344571-97344794(-)$1	223	52	57	11.6363
cc444	chr9:130209883-130210105(-)$1	222	59	64	10.8181
GGGGG	chr18:19353540-19353762(+)$1	222	18	23	11.5454
eeeee	chr15:66170120-66170341(+)$1	221	163	168	11.0000
:::::	chr4:52765420-52765644(+)$1	224	169	174	10.8181
cnnnn	chr20:42087839-42088084(+)$1	245	17	22	11.0000
::::=	chr17:79801327-79801614(-)$1	287	65	70	11.5454
eeee:	chr1:35649973-35650240(-)$1	267	239	244	11.5454
DDDDK	chr12:6861364-6861603(-)$1	239	66	71	11.5454
DDDDD	chrX:153609331-153609606(+)$1	275	25	30	11.5454
dddd3	chr17:66042532-66042764(+)$1	232	172	177	11.6363
eeeee	chr3:112280235-112280468(-)$1	233	209	214	11.6363
GGGGG	chr3:51423624-51423857(+)$1	233	4	9	11.5454
bffff	chr6:26199022-26199276(-)$1	254	217	222	11.0000
:dddd	chr1:76253108-76253344(+)$1	236	58	63	11.6363
DDDD{	chr21:28212145-28212379(-)$1	234	2	7	10.8181
}FFFF	chr5:138643531-138643766(+)$1	235	120	125	11.6363
fffff	chr14:32560757-32560987(+)$1	230	150	155	11.0000
bb444	chr11:63765087-63765337(+)$1	250	165	170	11.0000
ccc]f	chrX:118374209-118374454(+)$1	245	41	46	11.5454
ggggg	chr1:231509656-231509876(-)$1	220	192	197	11.5454
dddtt	chr19:59067973-59068199(-)$1	226	20	25	11.5454
^^^^^	chr3:113508550-113508773(+)$1	223	199	204	11.6363
eeee7	chr15:102185217-102185438(-)$1	221	56	61	11.5454
JJJJJ	chr16:58581064-58581300(-)$1	236	27	32	11.6363
dd333	chr6:30690603-30690831(+)$1	228	162	167	10.8181
eeeee	chr6:44219397-44219659(+)$1	262	245	250	10.8181
|||||	chr20:5095833-5096069(-)$1	236	214	219	11.5454
GGGGG	chr1:245022502-245022726(-)$1	224	158	163	11.5454
:::::	chr17:38567857-38568110(-)$1	253	4	9	11.6363
::JJJ	chr15:77239718-77239954(+)$1	236	8	13	11.6363
DD:::	chr4:77969606-77969840(-)$1	234	2	7	11.0000
fffmm	chr6:26104342-26104593(+)$1	251	205	210	10.8181
oooof	chr10:49628116-49628350(+)$1	234	12	17	11.6363
hhhhh	chr3:167405354-167405579(-)$1	225	38	43	11.5454
:::::	chr8:103855702-103855947(-)$1	245	224	229	11.0000
FFFFF	chr3:121151096-121151342(-)$1	246	5	10	11.6363
ffff:	chr22:38881845-38882100(-)$1	255	221	226	10.8181
C}GGG	chr11:9610040-9610296(+)$1	256	228	233	11.6363
cbb!!	chr1:150550714-150550978(-)$1	264	127	132	11.5454
GG:::	chr15:59102343-59102562(+)$1	219	26	31	11.5454
hhhh:	chr10:72164051-72164288(+)$1	237	15	20	11.0000
[cccc	chr19:2328291-2328522(-)$1	231	33	38	11.0000
nnnnb	chr8:95900145-95900370(-)$1	225	118	123	11.6363
=====	chr16:29821468-29821733(+)$1	265	153	158	11.5454
dddee	chr17:49083407-49083640(-)$1	233	46	51	11.0000
hhhh:	chr6:26031725-26032012(-)$1	287	145	150	11.6363
xxxxx	chr1:224377666-224377889(+)$1	223	32	37	11.5454
cc!!d	chr1:240371743-240371990(+)$1	247	125	130	11.6363
fffff	chr2:10584133-10584384(-)$1	251	108	113	11.6363
eefff	chr19:8528383-8528627(+)$1	244	77	82	10.8181

#DB
..)))	chr3:57271436-57271660(+)$1	1	39	44	11.6363
)))))	chr11:64537375-64537600(-)$1	1	60	65	11.0000
.))))	chr1:245019949-245020211(-)$1	1	39	44	11.6363
..)))	chr9:139723746-139723987(+)$1	1	22	27	10.8181
((.((	chr6:97344571-97344794(-)$1	1	52	57	11.6363
))...	chr9:130209883-130210105(-)$1	1	59	64	10.8181
(((((	chr18:19353540-19353762(+)$1	1	18	23	11.5454
)))))	chr15:66170120-66170341(+)$1	1	163	168	11.0000
.....	chr4:52765420-52765644(+)$1	1	169	174	10.8181
(....	chr20:42087839-42088084(+)$1	1	17	22	11.0000
....(	chr17:79801327-79801614(-)$1	1	65	70	11.5454
)))).	chr1:35649973-35650240(-)$1	1	239	244	11.5454
((((.	chr12:6861364-6861603(-)$1	1	66	71	11.5454
(((((	chrX:153609331-153609606(+)$1	1	25	30	11.5454
)))).	chr17:66042532-66042764(+)$1	1	172	177	11.6363
)))))	chr3:112280235-112280468(-)$1	1	209	214	11.6363
(((((	chr3:51423624-51423857(+)$1	1	4	9	11.5454
)))))	chr6:26199022-26199276(-)$1	1	217	222	11.0000
.((((	chr1:76253108-76253344(+)$1	1	58	63	11.6363
((((.	chr21:28212145-28212379(-)$1	1	2	7	10.8181
.))))	chr5:138643531-138643766(+)$1	1	120	125	11.6363
(((((	chr14:32560757-32560987(+)$1	1	150	155	11.0000
))...	chr11:63765087-63765337(+)$1	1	165	170	11.0000
))).)	chrX:118374209-118374454(+)$1	1	41	46	11.5454
)))))	chr1:231509656-231509876(-)$1	1	192	197	11.5454
(((..	chr19:59067973-59068199(-)$1	1	20	25	11.5454
.....	chr3:113508550-113508773(+)$1	1	199	204	11.6363
)))).	chr15:102185217-102185438(-)$1	1	56	61	11.5454
(((((	chr16:58581064-58581300(-)$1	1	27	32	11.6363
))...	chr6:30690603-30690831(+)$1	1	162	167	10.8181
)))))	chr6:44219397-44219659(+)$1	1	245	250	10.8181
.....	chr20:5095833-5096069(-)$1	1	214	219	11.5454
)))))	chr1:245022502-245022726(-)$1	1	158	163	11.5454
.....	chr17:38567857-38568110(-)$1	1	4	9	11.6363
..(((	chr15:77239718-77239954(+)$1	1	8	13	11.6363
((...	chr4:77969606-77969840(-)$1	1	2	7	11.0000
(((..	chr6:26104342-26104593(+)$1	1	205	210	10.8181
....)	chr10:49628116-49628350(+)$1	1	12	17	11.6363
(((((	chr3:167405354-167405579(-)$1	1	38	43	11.5454
.....	chr8:103855702-103855947(-)$1	1	224	229	11.0000
(((((	chr3:121151096-121151342(-)$1	1	5	10	11.6363
)))).	chr22:38881845-38882100(-)$1	1	221	226	10.8181
).)))	chr11:9610040-9610296(+)$1	1	228	233	11.6363
(((..	chr1:150550714-150550978(-)$1	1	127	132	11.5454
((...	chr15:59102343-59102562(+)$1	1	26	31	11.5454
)))).	chr10:72164051-72164288(+)$1	1	15	20	11.0000
.((((	chr19:2328291-2328522(-)$1	1	33	38	11.0000
....)	chr8:95900145-95900370(-)$1	1	118	123	11.6363
)))))	chr16:29821468-29821733(+)$1	1	153	158	11.5454
(((((	chr17:49083407-49083640(-)$1	1	46	51	11.0000
)))).	chr6:26031725-26032012(-)$1	1	145	150	11.6363
.....	chr1:224377666-224377889(+)$1	1	32	37	11.5454
((..(	chr1:240371743-240371990(+)$1	1	125	130	11.6363
(((((	chr2:10584133-10584384(-)$1	1	108	113	11.6363
(((((	chr19:8528383-8528627(+)$1	1	77	82	10.8181

#PSSM
A : 0.32	U : 0.30	G : 0.20	C : 0.14	c : 0.01	
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	624.0909090909091
#seq	55
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m3_run2.nuc.txt

#NT
UGA	chr17:2221146-2221386(+)$1	240	55	58	9.0000
UGA	chr1:207219941-207220181(-)$1	240	7	10	9.0000
UGA	chr10:116736110-116736350(+)$1	240	28	31	9.0000
UGA	chr14:24907433-24907673(+)$1	240	49	52	9.0000
UGA	chr16:67134445-67134685(+)$1	240	6	9	9.0000
UGA	chr12:108052590-108052830(+)$1	240	25	28	9.0000
UGA	chr2:20449809-20450049(-)$1	240	21	24	9.0000
UGA	chr17:61770929-61771169(+)$1	240	8	11	9.0000
uga	chr8:22108539-22108779(+)$1	240	31	34	9.0000
UGA	chrX:138810248-138810528(-)$1	280	29	32	9.0000
UGA	chr9:129647738-129647989(+)$1	251	9	12	9.0000
UGA	chr2:148688022-148688262(+)$1	240	1	4	9.0000
UGA	chr12:120125844-120126084(-)$1	240	78	81	9.0000
UGA	chr6:35802143-35802383(-)$1	240	3	6	9.0000
UGA	chr5:32604021-32604261(+)$1	240	19	22	9.0000
UGA	chr3:52326932-52327172(+)$1	240	38	41	9.0000
UGA	chr17:19580589-19580829(+)$1	240	4	7	9.0000
UGA	chr1:150238166-150238406(-)$1	240	6	9	9.0000
UGA	chr6:18466193-18466433(+)$1	240	55	58	9.0000
UGA	chr12:69756470-69756710(+)$1	240	197	200	9.0000
UGA	chr12:72288440-72288680(+)$1	240	56	59	9.0000
UGA	chr14:103986472-103986752(-)$1	280	106	109	9.0000
UGA	chr11:118620545-118620785(-)$1	240	7	10	9.0000
UGA	chr20:62522281-62522521(+)$1	240	44	47	9.0000
UGA	chr15:59981273-59981513(-)$1	240	181	184	9.0000
UGA	chr1:244870076-244870316(+)$1	240	90	93	9.0000
UGA	chr16:87744778-87745018(-)$1	240	81	84	9.0000
uGA	chr5:78671486-78671726(-)$1	240	0	3	9.0000
UGA	chr13:77454976-77455216(-)$1	240	14	17	9.0000
UGA	chr1:38269171-38269411(-)$1	240	45	48	9.0000
UGA	chr1:62626703-62626943(+)$1	240	20	23	9.0000
UGA	chr2:201846364-201846604(-)$1	240	14	17	9.0000
UGA	chr4:39781200-39781440(+)$1	240	1	4	9.0000
UGA	chr6:83920359-83920599(-)$1	240	13	16	9.0000
UGA	chr19:46191584-46191824(-)$1	240	24	27	9.0000
UGA	chr11:67924131-67924371(-)$1	240	4	7	9.0000
UGA	chr1:227083230-227083470(+)$1	240	47	50	9.0000
UGA	chr15:57580151-57580391(+)$1	240	137	140	9.0000
UGA	chr2:60686360-60686600(-)$1	240	29	32	9.0000
UGA	chr8:6616606-6616846(+)$1	240	30	33	9.0000
UGA	chr12:102140073-102140313(-)$1	240	6	9	9.0000
UGA	chr22:32894297-32894537(+)$1	240	83	86	9.0000
UGA	chr3:160155494-160155734(-)$1	240	124	127	9.0000
UGA	chr10:64567291-64567531(+)$1	240	19	22	9.0000
UGA	chr2:120129793-120130033(+)$1	240	48	51	9.0000
UGA	chrX:114877603-114877883(+)$1	280	29	32	9.0000
UGA	chr12:32945221-32945461(-)$1	240	101	104	9.0000
UGA	chr10:64953020-64953260(-)$1	240	31	34	9.0000
UGA	chr5:176724229-176724469(+)$1	240	7	10	9.0000
UGA	chr20:61431279-61431519(+)$1	240	18	21	9.0000
UGA	chr1:61922060-61922300(+)$1	240	83	86	9.0000
UGA	chr1:145688158-145688398(+)$1	240	28	31	9.0000
UGA	chr3:128888550-128888790(-)$1	240	68	71	9.0000
UGA	chr1:6694131-6694371(-)$1	240	1	4	9.0000
UGA	chr6:86318030-86318270(-)$1	240	8	11	9.0000
UGA	chr13:39623810-39624055(+)$1	245	52	55	9.0000
UGA	chr1:40758704-40758944(+)$1	240	7	10	9.0000
UGA	chr1:184660722-184660962(-)$1	240	135	138	9.0000
UGA	chrX:151996250-151996490(-)$1	240	20	23	9.0000
UGA	chr14:68143671-68143911(-)$1	240	86	89	9.0000
UGA	chr11:36510694-36510934(-)$1	240	17	20	9.0000
UGA	chr9:89559760-89560000(-)$1	240	25	28	9.0000
UGA	chr10:91342996-91343276(-)$1	280	14	17	9.0000
UGA	chr17:38292892-38293132(+)$1	240	64	67	9.0000
uga	chr17:33677829-33678069(-)$1	240	27	30	9.0000
UGA	chr4:99391417-99391657(-)$1	240	23	26	9.0000
UGA	chr21:35474720-35474974(+)$1	254	160	163	9.0000
UGA	chr14:52471476-52471716(-)$1	240	52	55	9.0000
UGA	chr3:97517078-97517318(+)$1	240	47	50	9.0000
UGA	chr15:96881721-96881961(+)$1	240	7	10	9.0000
UGA	chr17:46632815-46633055(-)$1	240	117	120	9.0000
UGA	chr6:24172569-24172809(-)$1	240	84	87	9.0000
UGA	chr8:124357095-124357335(-)$1	240	27	30	9.0000
UGA	chr11:19167694-19167934(+)$1	240	29	32	9.0000
UGA	chr3:37107223-37107463(-)$1	240	4	7	9.0000
UGA	chr5:77773194-77773434(+)$1	240	93	96	9.0000
UGA	chr12:57995325-57995565(+)$1	240	83	86	9.0000
UGA	chr16:15131202-15131482(+)$1	280	4	7	9.0000
UGA	chr18:20837634-20837914(+)$1	280	59	62	9.0000
UGA	chr11:4116036-4116276(+)$1	240	53	56	9.0000
UGA	chr19:45912436-45912676(+)$1	240	7	10	9.0000
UGA	chr8:94744575-94744815(-)$1	240	69	72	9.0000
UGA	chr20:30252164-30252404(-)$1	240	30	33	9.0000
uga	chr20:30824442-30824682(+)$1	240	60	63	9.0000
UGA	chr8:30436182-30436422(-)$1	240	40	43	9.0000
UGA	chr5:108672758-108672998(-)$1	240	12	15	9.0000
UGA	chr4:15606735-15606975(-)$1	240	31	34	9.0000
UGA	chr7:23682995-23683235(+)$1	240	3	6	9.0000
UGA	chr6:99286343-99286583(+)$1	240	107	110	9.0000
UGA	chr1:226419898-226420138(-)$1	240	103	106	9.0000
UGA	chr6:82457313-82457553(-)$1	240	40	43	9.0000
UGA	chr17:73941587-73941827(-)$1	240	74	77	9.0000
UGA	chr1:109856414-109856654(-)$1	240	169	172	9.0000
UGA	chr7:75958552-75958792(-)$1	240	36	39	9.0000
UGA	chr3:15293680-15293920(+)$1	240	4	7	9.0000
UGA	chr12:80169528-80169768(-)$1	240	14	17	9.0000
UGA	chr10:75531047-75531287(+)$1	240	48	51	9.0000

#otherMatches

#Struct PSSM
^^^	chr5:130540710-130540950(+)$1	240	43	46	9.0000
:::	chr17:2221146-2221386(+)$1	240	55	58	9.0000
ddd	chr1:207219941-207220181(-)$1	240	7	10	9.0000
eee	chr10:116736110-116736350(+)$1	240	28	31	9.0000
[cc	chr14:24907433-24907673(+)$1	240	49	52	9.0000
cce	chr16:67134445-67134685(+)$1	240	6	9	9.0000
]ff	chr12:108052590-108052830(+)$1	240	25	28	9.0000
eee	chr2:20449809-20450049(-)$1	240	21	24	9.0000
DD{	chr17:61770929-61771169(+)$1	240	8	11	9.0000
HH:	chr8:22108539-22108779(+)$1	240	31	34	9.0000
!!g	chrX:138810248-138810528(-)$1	280	29	32	9.0000
[ee	chr9:129647738-129647989(+)$1	251	9	12	9.0000
:::	chr2:148688022-148688262(+)$1	240	1	4	9.0000
qqq	chr12:120125844-120126084(-)$1	240	78	81	9.0000
A{D	chr6:35802143-35802383(-)$1	240	3	6	9.0000
cc!	chr5:32604021-32604261(+)$1	240	19	22	9.0000
HHH	chr3:52326932-52327172(+)$1	240	38	41	9.0000
ggg	chr17:19580589-19580829(+)$1	240	4	7	9.0000
{DD	chr1:150238166-150238406(-)$1	240	6	9	9.0000
hhJ	chr6:18466193-18466433(+)$1	240	55	58	9.0000
ffm	chr12:69756470-69756710(+)$1	240	197	200	9.0000
ee]	chr12:72288440-72288680(+)$1	240	56	59	9.0000
ggg	chr14:103986472-103986752(-)$1	280	106	109	9.0000
DD:	chr11:118620545-118620785(-)$1	240	7	10	9.0000
ddd	chr20:62522281-62522521(+)$1	240	44	47	9.0000
bb3	chr15:59981273-59981513(-)$1	240	181	184	9.0000
ccc	chr1:244870076-244870316(+)$1	240	90	93	9.0000
cc!	chr16:87744778-87745018(-)$1	240	81	84	9.0000
::G	chr5:78671486-78671726(-)$1	240	0	3	9.0000
eel	chr13:77454976-77455216(-)$1	240	14	17	9.0000
eee	chr1:38269171-38269411(-)$1	240	45	48	9.0000
eee	chr1:62626703-62626943(+)$1	240	20	23	9.0000
hhh	chr2:201846364-201846604(-)$1	240	14	17	9.0000
:::	chr4:39781200-39781440(+)$1	240	1	4	9.0000
HHH	chr6:83920359-83920599(-)$1	240	13	16	9.0000
]cc	chr19:46191584-46191824(-)$1	240	24	27	9.0000
GGG	chr11:67924131-67924371(-)$1	240	4	7	9.0000
ddd	chr1:227083230-227083470(+)$1	240	47	50	9.0000
ddd	chr15:57580151-57580391(+)$1	240	137	140	9.0000
DD:	chr2:60686360-60686600(-)$1	240	29	32	9.0000
ttt	chr8:6616606-6616846(+)$1	240	30	33	9.0000
gg(	chr12:102140073-102140313(-)$1	240	6	9	9.0000
cc[	chr22:32894297-32894537(+)$1	240	83	86	9.0000
HH:	chr3:160155494-160155734(-)$1	240	124	127	9.0000
JJ{	chr10:64567291-64567531(+)$1	240	19	22	9.0000
:::	chr2:120129793-120130033(+)$1	240	48	51	9.0000
2dd	chrX:114877603-114877883(+)$1	280	29	32	9.0000
eee	chr12:32945221-32945461(-)$1	240	101	104	9.0000
fff	chr10:64953020-64953260(-)$1	240	31	34	9.0000
ccn	chr5:176724229-176724469(+)$1	240	7	10	9.0000
FF{	chr20:61431279-61431519(+)$1	240	18	21	9.0000
eee	chr1:61922060-61922300(+)$1	240	83	86	9.0000
bb"	chr1:145688158-145688398(+)$1	240	28	31	9.0000
eee	chr3:128888550-128888790(-)$1	240	68	71	9.0000
:HH	chr1:6694131-6694371(-)$1	240	1	4	9.0000
ddd	chr6:86318030-86318270(-)$1	240	8	11	9.0000
hhh	chr13:39623810-39624055(+)$1	245	52	55	9.0000
EEe	chr1:40758704-40758944(+)$1	240	7	10	9.0000
fff	chr1:184660722-184660962(-)$1	240	135	138	9.0000
A{D	chrX:151996250-151996490(-)$1	240	20	23	9.0000
mmd	chr14:68143671-68143911(-)$1	240	86	89	9.0000
rdd	chr11:36510694-36510934(-)$1	240	17	20	9.0000
!dd	chr9:89559760-89560000(-)$1	240	25	28	9.0000
&&&	chr10:91342996-91343276(-)$1	280	14	17	9.0000
4dd	chr17:38292892-38293132(+)$1	240	64	67	9.0000
bbo	chr17:33677829-33678069(-)$1	240	27	30	9.0000
mbb	chr4:99391417-99391657(-)$1	240	23	26	9.0000
FFF	chr21:35474720-35474974(+)$1	254	160	163	9.0000
doo	chr14:52471476-52471716(-)$1	240	52	55	9.0000
cc!	chr3:97517078-97517318(+)$1	240	47	50	9.0000
III	chr15:96881721-96881961(+)$1	240	7	10	9.0000
ggg	chr17:46632815-46633055(-)$1	240	117	120	9.0000
eee	chr6:24172569-24172809(-)$1	240	84	87	9.0000
mmm	chr8:124357095-124357335(-)$1	240	27	30	9.0000
ggg	chr11:19167694-19167934(+)$1	240	29	32	9.0000
EEE	chr3:37107223-37107463(-)$1	240	4	7	9.0000
%cc	chr5:77773194-77773434(+)$1	240	93	96	9.0000
2ff	chr12:57995325-57995565(+)$1	240	83	86	9.0000
MMM	chr16:15131202-15131482(+)$1	280	4	7	9.0000
d!!	chr18:20837634-20837914(+)$1	280	59	62	9.0000
[a!	chr11:4116036-4116276(+)$1	240	53	56	9.0000
CCK	chr19:45912436-45912676(+)$1	240	7	10	9.0000
!cc	chr8:94744575-94744815(-)$1	240	69	72	9.0000
JJJ	chr20:30252164-30252404(-)$1	240	30	33	9.0000
cmm	chr20:30824442-30824682(+)$1	240	60	63	9.0000
c:H	chr8:30436182-30436422(-)$1	240	40	43	9.0000
qdd	chr5:108672758-108672998(-)$1	240	12	15	9.0000
eee	chr4:15606735-15606975(-)$1	240	31	34	9.0000
:::	chr7:23682995-23683235(+)$1	240	3	6	9.0000
+++	chr6:99286343-99286583(+)$1	240	107	110	9.0000
dd:	chr1:226419898-226420138(-)$1	240	103	106	9.0000
:::	chr6:82457313-82457553(-)$1	240	40	43	9.0000
CDD	chr17:73941587-73941827(-)$1	240	74	77	9.0000
:dd	chr1:109856414-109856654(-)$1	240	169	172	9.0000
GGG	chr7:75958552-75958792(-)$1	240	36	39	9.0000
:ee	chr3:15293680-15293920(+)$1	240	4	7	9.0000
EHH	chr12:80169528-80169768(-)$1	240	14	17	9.0000
$$$	chr10:75531047-75531287(+)$1	240	48	51	9.0000

#DB
...	chr5:130540710-130540950(+)$1	1	43	46	9.0000
...	chr17:2221146-2221386(+)$1	1	55	58	9.0000
(((	chr1:207219941-207220181(-)$1	1	7	10	9.0000
)))	chr10:116736110-116736350(+)$1	1	28	31	9.0000
.((	chr14:24907433-24907673(+)$1	1	49	52	9.0000
(((	chr16:67134445-67134685(+)$1	1	6	9	9.0000
.))	chr12:108052590-108052830(+)$1	1	25	28	9.0000
(((	chr2:20449809-20450049(-)$1	1	21	24	9.0000
((.	chr17:61770929-61771169(+)$1	1	8	11	9.0000
((.	chr8:22108539-22108779(+)$1	1	31	34	9.0000
..(	chrX:138810248-138810528(-)$1	1	29	32	9.0000
.((	chr9:129647738-129647989(+)$1	1	9	12	9.0000
...	chr2:148688022-148688262(+)$1	1	1	4	9.0000
...	chr12:120125844-120126084(-)$1	1	78	81	9.0000
(.(	chr6:35802143-35802383(-)$1	1	3	6	9.0000
((.	chr5:32604021-32604261(+)$1	1	19	22	9.0000
(((	chr3:52326932-52327172(+)$1	1	38	41	9.0000
(((	chr17:19580589-19580829(+)$1	1	4	7	9.0000
.((	chr1:150238166-150238406(-)$1	1	6	9	9.0000
))(	chr6:18466193-18466433(+)$1	1	55	58	9.0000
((.	chr12:69756470-69756710(+)$1	1	197	200	9.0000
)).	chr12:72288440-72288680(+)$1	1	56	59	9.0000
)))	chr14:103986472-103986752(-)$1	1	106	109	9.0000
((.	chr11:118620545-118620785(-)$1	1	7	10	9.0000
)))	chr20:62522281-62522521(+)$1	1	44	47	9.0000
)).	chr15:59981273-59981513(-)$1	1	181	184	9.0000
)))	chr1:244870076-244870316(+)$1	1	90	93	9.0000
((.	chr16:87744778-87745018(-)$1	1	81	84	9.0000
..(	chr5:78671486-78671726(-)$1	1	0	3	9.0000
((.	chr13:77454976-77455216(-)$1	1	14	17	9.0000
)))	chr1:38269171-38269411(-)$1	1	45	48	9.0000
(((	chr1:62626703-62626943(+)$1	1	20	23	9.0000
(((	chr2:201846364-201846604(-)$1	1	14	17	9.0000
...	chr4:39781200-39781440(+)$1	1	1	4	9.0000
(((	chr6:83920359-83920599(-)$1	1	13	16	9.0000
.))	chr19:46191584-46191824(-)$1	1	24	27	9.0000
(((	chr11:67924131-67924371(-)$1	1	4	7	9.0000
)))	chr1:227083230-227083470(+)$1	1	47	50	9.0000
(((	chr15:57580151-57580391(+)$1	1	137	140	9.0000
((.	chr2:60686360-60686600(-)$1	1	29	32	9.0000
...	chr8:6616606-6616846(+)$1	1	30	33	9.0000
((.	chr12:102140073-102140313(-)$1	1	6	9	9.0000
((.	chr22:32894297-32894537(+)$1	1	83	86	9.0000
)).	chr3:160155494-160155734(-)$1	1	124	127	9.0000
((.	chr10:64567291-64567531(+)$1	1	19	22	9.0000
...	chr2:120129793-120130033(+)$1	1	48	51	9.0000
.))	chrX:114877603-114877883(+)$1	1	29	32	9.0000
)))	chr12:32945221-32945461(-)$1	1	101	104	9.0000
(((	chr10:64953020-64953260(-)$1	1	31	34	9.0000
((.	chr5:176724229-176724469(+)$1	1	7	10	9.0000
((.	chr20:61431279-61431519(+)$1	1	18	21	9.0000
)))	chr1:61922060-61922300(+)$1	1	83	86	9.0000
((.	chr1:145688158-145688398(+)$1	1	28	31	9.0000
)))	chr3:128888550-128888790(-)$1	1	68	71	9.0000
.((	chr1:6694131-6694371(-)$1	1	1	4	9.0000
(((	chr6:86318030-86318270(-)$1	1	8	11	9.0000
(((	chr13:39623810-39624055(+)$1	1	52	55	9.0000
(((	chr1:40758704-40758944(+)$1	1	7	10	9.0000
(((	chr1:184660722-184660962(-)$1	1	135	138	9.0000
(.(	chrX:151996250-151996490(-)$1	1	20	23	9.0000
..)	chr14:68143671-68143911(-)$1	1	86	89	9.0000
.))	chr11:36510694-36510934(-)$1	1	17	20	9.0000
.((	chr9:89559760-89560000(-)$1	1	25	28	9.0000
...	chr10:91342996-91343276(-)$1	1	14	17	9.0000
.))	chr17:38292892-38293132(+)$1	1	64	67	9.0000
((.	chr17:33677829-33678069(-)$1	1	27	30	9.0000
.))	chr4:99391417-99391657(-)$1	1	23	26	9.0000
)))	chr21:35474720-35474974(+)$1	1	160	163	9.0000
(..	chr14:52471476-52471716(-)$1	1	52	55	9.0000
((.	chr3:97517078-97517318(+)$1	1	47	50	9.0000
(((	chr15:96881721-96881961(+)$1	1	7	10	9.0000
(((	chr17:46632815-46633055(-)$1	1	117	120	9.0000
)))	chr6:24172569-24172809(-)$1	1	84	87	9.0000
...	chr8:124357095-124357335(-)$1	1	27	30	9.0000
(((	chr11:19167694-19167934(+)$1	1	29	32	9.0000
(((	chr3:37107223-37107463(-)$1	1	4	7	9.0000
.((	chr5:77773194-77773434(+)$1	1	93	96	9.0000
.))	chr12:57995325-57995565(+)$1	1	83	86	9.0000
...	chr16:15131202-15131482(+)$1	1	4	7	9.0000
(..	chr18:20837634-20837914(+)$1	1	59	62	9.0000
.(.	chr11:4116036-4116276(+)$1	1	53	56	9.0000
((.	chr19:45912436-45912676(+)$1	1	7	10	9.0000
.((	chr8:94744575-94744815(-)$1	1	69	72	9.0000
(((	chr20:30252164-30252404(-)$1	1	30	33	9.0000
(..	chr20:30824442-30824682(+)$1	1	60	63	9.0000
).(	chr8:30436182-30436422(-)$1	1	40	43	9.0000
.))	chr5:108672758-108672998(-)$1	1	12	15	9.0000
(((	chr4:15606735-15606975(-)$1	1	31	34	9.0000
...	chr7:23682995-23683235(+)$1	1	3	6	9.0000
...	chr6:99286343-99286583(+)$1	1	107	110	9.0000
)).	chr1:226419898-226420138(-)$1	1	103	106	9.0000
...	chr6:82457313-82457553(-)$1	1	40	43	9.0000
(((	chr17:73941587-73941827(-)$1	1	74	77	9.0000
.((	chr1:109856414-109856654(-)$1	1	169	172	9.0000
(((	chr7:75958552-75958792(-)$1	1	36	39	9.0000
.((	chr3:15293680-15293920(+)$1	1	4	7	9.0000
(((	chr12:80169528-80169768(-)$1	1	14	17	9.0000
...	chr10:75531047-75531287(+)$1	1	48	51	9.0000

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

#score	882.0000000000002
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m3_run1.nuc.txt

#NT

#otherMatches

#Struct PSSM
:::CCC{BB{EEEEE:dddd&&&&&&&bb"""a[ggggggg$$$$$ccc!!bb!!hhhhhhhh"""annnnna333hhhhhhhh88888888bb22ccc55555ggggggg]a333bb7777777dddd::::::ddddnnnnndddd::::::::ddddzzzzzzzzzzzzzzzzzdddd:::::dddd[bbpppppppbb22dddd::::::gggggggooooooggggggg:EEEEE}BB}CCC::::	chr17:34171676-34171931(+)$1	255	1	252	753.0000

#DB
...(((.((.(((((.((((.......((...(.(((((((.....(((..((..((((((((...(.....)...))))))))........))..))).....))))))).)...)).......))))......((((.....))))........((((.................)))).....((((.((.......))..))))......(((((((......))))))).))))).)).)))....	chr17:34171676-34171931(+)$1	1	1	252	753.0000

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

#score	753.0
#seq	1
#width	251
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_CDS_m2_run2.nuc.txt

#NT
UUC	chr4:156825110-156825325(+)$1	215	16	19	9.0000
UUC	chr2:86710989-86711218(+)$1	229	60	63	9.0000
UUC	chr15:44888886-44889109(-)$1	223	11	14	9.0000
UUC	chr7:141478993-141479250(+)$1	257	13	16	9.0000
UUC	chr4:118006022-118006243(-)$1	221	24	27	9.0000
UUC	chr2:44547314-44547567(-)$1	253	44	47	9.0000
UUC	chr11:55860691-55860905(+)$1	214	34	37	9.0000
UUC	chr12:60154828-60155043(+)$1	215	103	106	9.0000
UUC	chr4:123255504-123255783(+)$1	279	5	8	9.0000
UUC	chr1:193149501-193149779(+)$1	278	7	10	9.0000
UUC	chr15:35152142-35152375(-)$1	233	6	9	9.0000
UUC	chr15:83335502-83335730(-)$1	228	30	33	9.0000
UUC	chr2:178095783-178096049(-)$1	266	39	42	9.0000
UUC	chr3:47451946-47452164(+)$1	218	69	72	9.0000
UUC	chrX:103042702-103042915(+)$1	213	102	105	9.0000
UUC	chr11:102195456-102195725(+)$1	269	66	69	9.0000
UUC	chr15:75308934-75309148(+)$1	214	86	89	9.0000
UUC	chr3:57302386-57302606(+)$1	220	10	13	9.0000
UUC	chr11:6630688-6630952(+)$1	264	48	51	9.0000
UUC	chr16:630102-630315(+)$1	213	83	86	9.0000
UUC	chr17:33884088-33884309(-)$1	221	68	71	9.0000
UUC	chr11:62438636-62438915(-)$1	279	25	28	9.0000
UUC	chr17:4848871-4849329(-)$1	458	16	19	9.0000
UUC	chr11:125765167-125765424(+)$1	257	11	14	9.0000
UUC	chr14:34985382-34985629(-)$1	247	41	44	9.0000
UUC	chr19:22847596-22847820(+)$1	224	3	6	9.0000
UUC	chr12:1137235-1137459(+)$1	224	76	79	9.0000
uuc	chr5:140028450-140028670(+)$1	220	68	71	9.0000
UUC	chr19:12059880-12060100(+)$1	220	4	7	9.0000
UUC	chr3:52326932-52327180(+)$1	248	84	87	9.0000
UUC	chr15:91461446-91461661(+)$1	215	104	107	9.0000
UUC	chr12:56214129-56214366(+)$1	237	11	14	9.0000
UUC	chr1:33149479-33149746(+)$1	267	112	115	9.0000
UUC	chr2:61610317-61610559(-)$1	242	15	18	9.0000
UUC	chr14:75373653-75373881(-)$1	228	63	66	9.0000
UUC	chr18:61378469-61378690(+)$1	221	62	65	9.0000
UUC	chr2:103335032-103335253(-)$1	221	17	20	9.0000
UUC	chr1:40960879-40961112(+)$1	233	108	111	9.0000
UUC	chr17:8079199-8079430(-)$1	231	9	12	9.0000
UUC	chr6:121563321-121563557(-)$1	236	20	23	9.0000
UUC	chr6:139694907-139695166(-)$1	259	66	69	9.0000
UUC	chr15:42171944-42172161(-)$1	217	91	94	9.0000
UUC	chr22:36545718-36545950(-)$1	232	59	62	9.0000
UUC	chr19:46811406-46811621(+)$1	215	101	104	9.0000
UUC	chr1:151400546-151400796(-)$1	250	17	20	9.0000
UUC	chr4:123229196-123229410(+)$1	214	60	63	9.0000
UUC	chr3:141162265-141162479(+)$1	214	5	8	9.0000
UUC	chr20:42169596-42169810(+)$1	214	65	68	9.0000
UUC	chr6:42824831-42825057(+)$1	226	55	58	9.0000
UUC	chr19:21366644-21366894(+)$1	250	59	62	9.0000
UUC	chr3:169847036-169847440(-)$1	404	10	13	9.0000
UUC	chr17:3324308-3324524(+)$1	216	36	39	9.0000
UUC	chr1:25153427-25153641(+)$1	214	28	31	9.0000
uuc	chr6:167357123-167357375(-)$1	252	104	107	9.0000
UUC	chr14:23459199-23459419(-)$1	220	33	36	9.0000
UUC	chr19:21240190-21240403(+)$1	213	20	23	9.0000
UUC	chr7:99811309-99811545(-)$1	236	77	80	9.0000
UUC	chr17:29631978-29632265(-)$1	287	1	4	9.0000
UUC	chr16:2813049-2813269(+)$1	220	137	140	9.0000
UUC	chr1:152733140-152733352(+)$1	212	67	70	9.0000
UUC	chr6:12124871-12125129(+)$1	258	56	59	9.0000
UUC	chr17:72205269-72205516(+)$1	247	15	18	9.0000
UUC	chr13:99947587-99947825(-)$1	238	3	6	9.0000
UUC	chr8:101733573-101733811(-)$1	238	90	93	9.0000
UUC	chr12:59270155-59270385(-)$1	230	24	27	9.0000
UUC	chr7:99710407-99710638(-)$1	231	51	54	9.0000
UUC	chr4:1018908-1019206(+)$1	298	6	9	9.0000
UUC	chr12:119624774-119624987(+)$1	213	42	45	9.0000
UUC	chr19:44514904-44515117(+)$1	213	2	5	9.0000
UUC	chr3:58242286-58242500(+)$1	214	101	104	9.0000
UUC	chr9:104170933-104171187(+)$1	254	16	19	9.0000
UUC	chr11:35232701-35233051(+)$1	350	19	22	9.0000
UUC	chr7:40173886-40174122(-)$1	236	34	37	9.0000
uuc	chr4:81560854-81561074(+)$1	220	68	71	9.0000
UUC	chr1:87025884-87026099(+)$1	215	2	5	9.0000
UUC	chr10:134997307-134997522(+)$1	215	40	43	9.0000
UUC	chr1:101705354-101705594(+)$1	240	2	5	9.0000
UUC	chr20:2945472-2945768(+)$1	296	10	13	9.0000
UUC	chr6:144745062-144745275(+)$1	213	162	165	9.0000
UUC	chr17:77090462-77090680(-)$1	218	61	64	9.0000
UUC	chr10:70516189-70516482(+)$1	293	16	19	9.0000
UUC	chr6:35260311-35260555(+)$1	244	63	66	9.0000
UUC	chr5:53815393-53815608(+)$1	215	1	4	9.0000
UUC	chrX:30872735-30873028(-)$1	293	77	80	9.0000
UUC	chr8:95802004-95802218(+)$1	214	43	46	9.0000
UUC	chr17:62496079-62496345(-)$1	266	201	204	9.0000
UUC	chr21:18937704-18937918(+)$1	214	6	9	9.0000
UUC	chr1:153963982-153964228(+)$1	246	50	53	9.0000
UUC	chr17:19314631-19314851(+)$1	220	2	5	9.0000
UUC	chr20:20601074-20601336(-)$1	262	45	48	9.0000
UUC	chr1:154229448-154229784(+)$1	336	3	6	9.0000
UUC	chr11:802288-802507(-)$1	219	31	34	9.0000
UUC	chr4:57797676-57797891(+)$1	215	28	31	9.0000
UUC	chr1:248525400-248525614(+)$1	214	4	7	9.0000
UUC	chr1:159504848-159505069(-)$1	221	66	69	9.0000
UUC	chr8:67047175-67047390(+)$1	215	200	203	9.0000
UUC	chr16:28845785-28846085(+)$1	300	35	38	9.0000

#otherMatches

#Struct PSSM
ccc	chr7:143175290-143175503(+)$1	213	29	32	9.0000
fmm	chr4:156825110-156825325(+)$1	215	16	19	9.0000
555	chr2:86710989-86711218(+)$1	229	60	63	9.0000
FFF	chr15:44888886-44889109(-)$1	223	11	14	9.0000
:::	chr7:141478993-141479250(+)$1	257	13	16	9.0000
!!c	chr4:118006022-118006243(-)$1	221	24	27	9.0000
ee:	chr2:44547314-44547567(-)$1	253	44	47	9.0000
c[b	chr11:55860691-55860905(+)$1	214	34	37	9.0000
hhh	chr12:60154828-60155043(+)$1	215	103	106	9.0000
:::	chr4:123255504-123255783(+)$1	279	5	8	9.0000
:::	chr1:193149501-193149779(+)$1	278	7	10	9.0000
:cc	chr15:35152142-35152375(-)$1	233	6	9	9.0000
{HH	chr15:83335502-83335730(-)$1	228	30	33	9.0000
:::	chr2:178095783-178096049(-)$1	266	39	42	9.0000
555	chr3:47451946-47452164(+)$1	218	69	72	9.0000
:::	chrX:103042702-103042915(+)$1	213	102	105	9.0000
fff	chr11:102195456-102195725(+)$1	269	66	69	9.0000
ppp	chr15:75308934-75309148(+)$1	214	86	89	9.0000
:::	chr3:57302386-57302606(+)$1	220	10	13	9.0000
GGG	chr11:6630688-6630952(+)$1	264	48	51	9.0000
ddd	chr16:630102-630315(+)$1	213	83	86	9.0000
ggg	chr17:33884088-33884309(-)$1	221	68	71	9.0000
JJ:	chr11:62438636-62438915(-)$1	279	25	28	9.0000
:::	chr17:4848871-4849329(-)$1	458	16	19	9.0000
euu	chr11:125765167-125765424(+)$1	257	11	14	9.0000
%%d	chr14:34985382-34985629(-)$1	247	41	44	9.0000
DDC	chr19:22847596-22847820(+)$1	224	3	6	9.0000
]ee	chr12:1137235-1137459(+)$1	224	76	79	9.0000
]bb	chr5:140028450-140028670(+)$1	220	68	71	9.0000
:::	chr19:12059880-12060100(+)$1	220	4	7	9.0000
tcc	chr3:52326932-52327180(+)$1	248	84	87	9.0000
55f	chr15:91461446-91461661(+)$1	215	104	107	9.0000
ooo	chr12:56214129-56214366(+)$1	237	11	14	9.0000
fff	chr1:33149479-33149746(+)$1	267	112	115	9.0000
===	chr2:61610317-61610559(-)$1	242	15	18	9.0000
333	chr14:75373653-75373881(-)$1	228	63	66	9.0000
b>>	chr18:61378469-61378690(+)$1	221	62	65	9.0000
"""	chr2:103335032-103335253(-)$1	221	17	20	9.0000
:::	chr1:40960879-40961112(+)$1	233	108	111	9.0000
GGG	chr17:8079199-8079430(-)$1	231	9	12	9.0000
ff]	chr6:121563321-121563557(-)$1	236	20	23	9.0000
fff	chr6:139694907-139695166(-)$1	259	66	69	9.0000
EEE	chr15:42171944-42172161(-)$1	217	91	94	9.0000
"bb	chr22:36545718-36545950(-)$1	232	59	62	9.0000
mmb	chr19:46811406-46811621(+)$1	215	101	104	9.0000
:::	chr1:151400546-151400796(-)$1	250	17	20	9.0000
KCC	chr4:123229196-123229410(+)$1	214	60	63	9.0000
FFF	chr3:141162265-141162479(+)$1	214	5	8	9.0000
iii	chr20:42169596-42169810(+)$1	214	65	68	9.0000
:::	chr6:42824831-42825057(+)$1	226	55	58	9.0000
::C	chr19:21366644-21366894(+)$1	250	59	62	9.0000
FFF	chr3:169847036-169847440(-)$1	404	10	13	9.0000
sss	chr17:3324308-3324524(+)$1	216	36	39	9.0000
ddd	chr1:25153427-25153641(+)$1	214	28	31	9.0000
b33	chr6:167357123-167357375(-)$1	252	104	107	9.0000
##e	chr14:23459199-23459419(-)$1	220	33	36	9.0000
fff	chr19:21240190-21240403(+)$1	213	20	23	9.0000
ff]	chr7:99811309-99811545(-)$1	236	77	80	9.0000
:::	chr17:29631978-29632265(-)$1	287	1	4	9.0000
ggg	chr16:2813049-2813269(+)$1	220	137	140	9.0000
mmm	chr1:152733140-152733352(+)$1	212	67	70	9.0000
ccc	chr6:12124871-12125129(+)$1	258	56	59	9.0000
rrr	chr17:72205269-72205516(+)$1	247	15	18	9.0000
::c	chr13:99947587-99947825(-)$1	238	3	6	9.0000
:::	chr8:101733573-101733811(-)$1	238	90	93	9.0000
qqq	chr12:59270155-59270385(-)$1	230	24	27	9.0000
WWW	chr7:99710407-99710638(-)$1	231	51	54	9.0000
GGE	chr4:1018908-1019206(+)$1	298	6	9	9.0000
eeb	chr12:119624774-119624987(+)$1	213	42	45	9.0000
:::	chr19:44514904-44515117(+)$1	213	2	5	9.0000
e]d	chr3:58242286-58242500(+)$1	214	101	104	9.0000
:::	chr9:104170933-104171187(+)$1	254	16	19	9.0000
gg[	chr11:35232701-35233051(+)$1	350	19	22	9.0000
C{C	chr7:40173886-40174122(-)$1	236	34	37	9.0000
G::	chr4:81560854-81561074(+)$1	220	68	71	9.0000
:::	chr1:87025884-87026099(+)$1	215	2	5	9.0000
22i	chr10:134997307-134997522(+)$1	215	40	43	9.0000
:::	chr1:101705354-101705594(+)$1	240	2	5	9.0000
FFC	chr20:2945472-2945768(+)$1	296	10	13	9.0000
fff	chr6:144745062-144745275(+)$1	213	162	165	9.0000
e[b	chr17:77090462-77090680(-)$1	218	61	64	9.0000
BB{	chr10:70516189-70516482(+)$1	293	16	19	9.0000
ccc	chr6:35260311-35260555(+)$1	244	63	66	9.0000
:::	chr5:53815393-53815608(+)$1	215	1	4	9.0000
ddd	chrX:30872735-30873028(-)$1	293	77	80	9.0000
888	chr8:95802004-95802218(+)$1	214	43	46	9.0000
ddd	chr17:62496079-62496345(-)$1	266	201	204	9.0000
CCC	chr21:18937704-18937918(+)$1	214	6	9	9.0000
]ff	chr1:153963982-153964228(+)$1	246	50	53	9.0000
eee	chr17:19314631-19314851(+)$1	220	2	5	9.0000
PPP	chr20:20601074-20601336(-)$1	262	45	48	9.0000
:::	chr1:154229448-154229784(+)$1	336	3	6	9.0000
zzz	chr11:802288-802507(-)$1	219	31	34	9.0000
ddd	chr4:57797676-57797891(+)$1	215	28	31	9.0000
::d	chr1:248525400-248525614(+)$1	214	4	7	9.0000
ccc	chr1:159504848-159505069(-)$1	221	66	69	9.0000
HHH	chr8:67047175-67047390(+)$1	215	200	203	9.0000
:::	chr16:28845785-28846085(+)$1	300	35	38	9.0000

#DB
(((	chr7:143175290-143175503(+)$1	1	29	32	9.0000
(..	chr4:156825110-156825325(+)$1	1	16	19	9.0000
...	chr2:86710989-86711218(+)$1	1	60	63	9.0000
(((	chr15:44888886-44889109(-)$1	1	11	14	9.0000
...	chr7:141478993-141479250(+)$1	1	13	16	9.0000
..(	chr4:118006022-118006243(-)$1	1	24	27	9.0000
)).	chr2:44547314-44547567(-)$1	1	44	47	9.0000
(.(	chr11:55860691-55860905(+)$1	1	34	37	9.0000
(((	chr12:60154828-60155043(+)$1	1	103	106	9.0000
...	chr4:123255504-123255783(+)$1	1	5	8	9.0000
...	chr1:193149501-193149779(+)$1	1	7	10	9.0000
.((	chr15:35152142-35152375(-)$1	1	6	9	9.0000
.((	chr15:83335502-83335730(-)$1	1	30	33	9.0000
...	chr2:178095783-178096049(-)$1	1	39	42	9.0000
...	chr3:47451946-47452164(+)$1	1	69	72	9.0000
...	chrX:103042702-103042915(+)$1	1	102	105	9.0000
(((	chr11:102195456-102195725(+)$1	1	66	69	9.0000
...	chr15:75308934-75309148(+)$1	1	86	89	9.0000
...	chr3:57302386-57302606(+)$1	1	10	13	9.0000
(((	chr11:6630688-6630952(+)$1	1	48	51	9.0000
(((	chr16:630102-630315(+)$1	1	83	86	9.0000
(((	chr17:33884088-33884309(-)$1	1	68	71	9.0000
((.	chr11:62438636-62438915(-)$1	1	25	28	9.0000
...	chr17:4848871-4849329(-)$1	1	16	19	9.0000
(..	chr11:125765167-125765424(+)$1	1	11	14	9.0000
..(	chr14:34985382-34985629(-)$1	1	41	44	9.0000
(((	chr19:22847596-22847820(+)$1	1	3	6	9.0000
.))	chr12:1137235-1137459(+)$1	1	76	79	9.0000
.))	chr5:140028450-140028670(+)$1	1	68	71	9.0000
...	chr19:12059880-12060100(+)$1	1	4	7	9.0000
.))	chr3:52326932-52327180(+)$1	1	84	87	9.0000
..)	chr15:91461446-91461661(+)$1	1	104	107	9.0000
...	chr12:56214129-56214366(+)$1	1	11	14	9.0000
(((	chr1:33149479-33149746(+)$1	1	112	115	9.0000
(((	chr2:61610317-61610559(-)$1	1	15	18	9.0000
...	chr14:75373653-75373881(-)$1	1	63	66	9.0000
)..	chr18:61378469-61378690(+)$1	1	62	65	9.0000
...	chr2:103335032-103335253(-)$1	1	17	20	9.0000
...	chr1:40960879-40961112(+)$1	1	108	111	9.0000
(((	chr17:8079199-8079430(-)$1	1	9	12	9.0000
)).	chr6:121563321-121563557(-)$1	1	20	23	9.0000
(((	chr6:139694907-139695166(-)$1	1	66	69	9.0000
(((	chr15:42171944-42172161(-)$1	1	91	94	9.0000
.((	chr22:36545718-36545950(-)$1	1	59	62	9.0000
..)	chr19:46811406-46811621(+)$1	1	101	104	9.0000
...	chr1:151400546-151400796(-)$1	1	17	20	9.0000
.((	chr4:123229196-123229410(+)$1	1	60	63	9.0000
(((	chr3:141162265-141162479(+)$1	1	5	8	9.0000
(((	chr20:42169596-42169810(+)$1	1	65	68	9.0000
...	chr6:42824831-42825057(+)$1	1	55	58	9.0000
..(	chr19:21366644-21366894(+)$1	1	59	62	9.0000
(((	chr3:169847036-169847440(-)$1	1	10	13	9.0000
...	chr17:3324308-3324524(+)$1	1	36	39	9.0000
(((	chr1:25153427-25153641(+)$1	1	28	31	9.0000
)..	chr6:167357123-167357375(-)$1	1	104	107	9.0000
..(	chr14:23459199-23459419(-)$1	1	33	36	9.0000
(((	chr19:21240190-21240403(+)$1	1	20	23	9.0000
)).	chr7:99811309-99811545(-)$1	1	77	80	9.0000
...	chr17:29631978-29632265(-)$1	1	1	4	9.0000
)))	chr16:2813049-2813269(+)$1	1	137	140	9.0000
...	chr1:152733140-152733352(+)$1	1	67	70	9.0000
)))	chr6:12124871-12125129(+)$1	1	56	59	9.0000
...	chr17:72205269-72205516(+)$1	1	15	18	9.0000
..(	chr13:99947587-99947825(-)$1	1	3	6	9.0000
...	chr8:101733573-101733811(-)$1	1	90	93	9.0000
...	chr12:59270155-59270385(-)$1	1	24	27	9.0000
...	chr7:99710407-99710638(-)$1	1	51	54	9.0000
(((	chr4:1018908-1019206(+)$1	1	6	9	9.0000
(((	chr12:119624774-119624987(+)$1	1	42	45	9.0000
...	chr19:44514904-44515117(+)$1	1	2	5	9.0000
).)	chr3:58242286-58242500(+)$1	1	101	104	9.0000
...	chr9:104170933-104171187(+)$1	1	16	19	9.0000
((.	chr11:35232701-35233051(+)$1	1	19	22	9.0000
(.(	chr7:40173886-40174122(-)$1	1	34	37	9.0000
(..	chr4:81560854-81561074(+)$1	1	68	71	9.0000
...	chr1:87025884-87026099(+)$1	1	2	5	9.0000
..)	chr10:134997307-134997522(+)$1	1	40	43	9.0000
...	chr1:101705354-101705594(+)$1	1	2	5	9.0000
(((	chr20:2945472-2945768(+)$1	1	10	13	9.0000
(((	chr6:144745062-144745275(+)$1	1	162	165	9.0000
(.(	chr17:77090462-77090680(-)$1	1	61	64	9.0000
((.	chr10:70516189-70516482(+)$1	1	16	19	9.0000
)))	chr6:35260311-35260555(+)$1	1	63	66	9.0000
...	chr5:53815393-53815608(+)$1	1	1	4	9.0000
)))	chrX:30872735-30873028(-)$1	1	77	80	9.0000
...	chr8:95802004-95802218(+)$1	1	43	46	9.0000
)))	chr17:62496079-62496345(-)$1	1	201	204	9.0000
(((	chr21:18937704-18937918(+)$1	1	6	9	9.0000
.))	chr1:153963982-153964228(+)$1	1	50	53	9.0000
(((	chr17:19314631-19314851(+)$1	1	2	5	9.0000
...	chr20:20601074-20601336(-)$1	1	45	48	9.0000
...	chr1:154229448-154229784(+)$1	1	3	6	9.0000
...	chr11:802288-802507(-)$1	1	31	34	9.0000
)))	chr4:57797676-57797891(+)$1	1	28	31	9.0000
..(	chr1:248525400-248525614(+)$1	1	4	7	9.0000
)))	chr1:159504848-159505069(-)$1	1	66	69	9.0000
)))	chr8:67047175-67047390(+)$1	1	200	203	9.0000
...	chr16:28845785-28846085(+)$1	1	35	38	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_FUS_Nakaya2013e_hg19_CDS_m1_run2.nuc.txt

#NT
GAG	chr6:83848398-83848613(+)$1	215	43	46	9.0000
GAG	chr4:83424111-83424341(-)$1	230	166	169	9.0000
GAG	chr10:73122084-73122300(+)$1	216	182	185	9.0000
GAG	chr4:164087670-164087912(-)$1	242	4	7	9.0000
GAG	chr10:105037814-105038031(+)$1	217	39	42	9.0000
GAG	chr9:139873450-139873688(+)$1	238	35	38	9.0000
GAG	chr6:42625688-42625906(-)$1	218	15	18	9.0000
GAG	chr13:110435924-110436154(-)$1	230	13	16	9.0000
GAG	chr2:219562116-219562332(+)$1	216	85	88	9.0000
GAG	chr3:49094332-49094565(-)$1	233	7	10	9.0000
GAG	chr6:149833190-149833410(-)$1	220	75	78	9.0000
GAG	chr16:139711-139958(-)$1	247	7	10	9.0000
GAG	chr19:3808823-3809041(-)$1	218	66	69	9.0000
GAG	chr15:24921121-24921364(+)$1	243	99	102	9.0000
GAG	chr19:56171473-56171704(+)$1	231	21	24	9.0000
GAG	chr4:79856264-79856486(-)$1	222	68	71	9.0000
GAG	chr2:65298989-65299208(+)$1	219	32	35	9.0000
GAG	chr16:11478003-11478219(-)$1	216	84	87	9.0000
GAG	chr1:179833830-179834052(-)$1	222	51	54	9.0000
GAG	chr19:45490484-45490706(+)$1	222	44	47	9.0000
GAG	chr11:67378410-67378629(+)$1	219	55	58	9.0000
GAG	chr10:22615333-22615557(+)$1	224	59	62	9.0000
GAG	chr8:195838-196061(-)$1	223	169	172	9.0000
GAG	chr6:43480994-43481236(-)$1	242	3	6	9.0000
GAG	chr8:144994756-144994972(-)$1	216	6	9	9.0000
GAG	chr20:62337659-62337882(-)$1	223	25	28	9.0000
GAG	chr16:71509055-71509274(-)$1	219	50	53	9.0000
GAG	chr9:137979810-137980043(+)$1	233	7	10	9.0000
GAG	chrX:101139404-101139622(-)$1	218	46	49	9.0000
GAG	chr22:35660624-35660841(+)$1	217	150	153	9.0000
GAG	chr11:64535112-64535333(-)$1	221	37	40	9.0000
GAG	chr16:1258027-1258247(+)$1	220	29	32	9.0000
GAG	chr19:10745707-10745952(+)$1	245	0	3	9.0000
GAG	chr17:72926524-72926743(+)$1	219	64	67	9.0000
GAG	chr1:43904910-43905146(+)$1	236	64	67	9.0000
GAG	chr15:63988350-63988585(-)$1	235	6	9	9.0000
GAG	chr22:39909988-39910212(+)$1	224	130	133	9.0000
GAG	chr12:112219676-112219891(+)$1	215	19	22	9.0000
GAG	chr15:101417959-101418179(-)$1	220	3	6	9.0000
GAG	chr12:80696454-80696669(-)$1	215	88	91	9.0000
GAG	chrX:53626990-53627232(-)$1	242	58	61	9.0000
GAG	chr20:61869857-61870072(-)$1	215	24	27	9.0000
GAG	chr14:94756653-94756874(+)$1	221	5	8	9.0000
GAG	chr15:75304925-75305143(+)$1	218	59	62	9.0000
gag	chr1:52237712-52237951(+)$1	239	231	234	9.0000
GAG	chr17:21731435-21731655(+)$1	220	68	71	9.0000
GAG	chr9:131776985-131777201(-)$1	216	60	63	9.0000
GAG	chr4:985807-986029(+)$1	222	172	175	9.0000
GAG	chr1:16256607-16256823(+)$1	216	40	43	9.0000
GAG	chr12:6166033-6166260(-)$1	227	33	36	9.0000
GAG	chr6:82924166-82924389(-)$1	223	102	105	9.0000
GAG	chr16:53243424-53243650(+)$1	226	31	34	9.0000
GAG	chr19:18391802-18392028(-)$1	226	37	40	9.0000
GAG	chr5:71495445-71495665(+)$1	220	22	25	9.0000
GAG	chr2:210558109-210558327(+)$1	218	9	12	9.0000
GAG	chr14:102472275-102472502(+)$1	227	126	129	9.0000
GAG	chr2:236817311-236817538(+)$1	227	97	100	9.0000
GAG	chr10:125526555-125526775(-)$1	220	4	7	9.0000
GAG	chr1:72241754-72241971(-)$1	217	80	83	9.0000
gag	chr9:135984926-135985163(-)$1	237	20	23	9.0000
GAG	chr2:17864851-17865066(-)$1	215	53	56	9.0000
GAG	chr1:97270330-97270554(+)$1	224	34	37	9.0000
GAG	chr12:112665857-112666082(-)$1	225	50	53	9.0000
GAG	chr12:39713608-39713826(-)$1	218	48	51	9.0000
GAG	chr3:186504874-186505111(+)$1	237	74	77	9.0000
GAG	chr5:140884858-140885074(+)$1	216	23	26	9.0000
GAG	chr1:156622450-156622676(+)$1	226	8	11	9.0000
GAG	chr12:56647764-56647992(-)$1	228	4	7	9.0000
GAG	chr9:117052996-117053218(+)$1	222	26	29	9.0000
GAG	chr12:111169518-111169735(-)$1	217	30	33	9.0000
GAG	chr11:62550180-62550395(+)$1	215	82	85	9.0000
GAG	chr1:177250325-177250581(+)$1	256	150	153	9.0000
GAG	chr13:52604032-52604258(+)$1	226	35	38	9.0000
GAG	chr1:55555218-55555436(-)$1	218	124	127	9.0000
GAG	chr7:103155762-103155981(-)$1	219	37	40	9.0000
GAG	chr10:70404502-70404728(+)$1	226	99	102	9.0000
GAG	chr13:53603072-53603290(-)$1	218	16	19	9.0000
GAG	chr12:112650246-112650477(-)$1	231	46	49	9.0000
GAG	chr20:4162976-4163192(+)$1	216	23	26	9.0000
GAG	chr13:77834486-77834707(-)$1	221	97	100	9.0000
GAG	chr9:137981934-137982169(+)$1	235	124	127	9.0000
GAG	chr7:1484281-1484498(-)$1	217	96	99	9.0000
GAG	chr7:150775805-150776031(-)$1	226	19	22	9.0000
GAG	chrX:153247631-153247847(-)$1	216	49	52	9.0000
GAG	chr19:17766037-17766264(-)$1	227	6	9	9.0000
GAG	chr4:170057422-170057638(+)$1	216	10	13	9.0000
GAG	chr17:40842751-40842972(+)$1	221	4	7	9.0000
GAG	chr12:133432953-133433175(-)$1	222	65	68	9.0000
GAG	chr3:111718299-111718528(+)$1	229	4	7	9.0000
GAG	chr6:121625393-121625622(-)$1	229	7	10	9.0000
gag	chr3:99514412-99514639(-)$1	227	192	195	9.0000
GAG	chr14:21769184-21769400(+)$1	216	16	19	9.0000
GAG	chr19:55644182-55644403(+)$1	221	2	5	9.0000
GAG	chr5:149602041-149602267(-)$1	226	31	34	9.0000
GAG	chr17:80763705-80763926(-)$1	221	8	11	9.0000
GAG	chr9:113006963-113007200(+)$1	237	68	71	9.0000
GAG	chr3:39225554-39225770(+)$1	216	33	36	9.0000
GAG	chr7:142568305-142568532(+)$1	227	62	65	9.0000
GAG	chr17:78086303-78086525(+)$1	222	25	28	9.0000

#otherMatches

#Struct PSSM
fff	chr17:11282669-11282893(+)$1	224	91	94	9.0000
c22	chr6:83848398-83848613(+)$1	215	43	46	9.0000
mmc	chr4:83424111-83424341(-)$1	230	166	169	9.0000
]ee	chr10:73122084-73122300(+)$1	216	182	185	9.0000
ggg	chr4:164087670-164087912(-)$1	242	4	7	9.0000
ooo	chr10:105037814-105038031(+)$1	217	39	42	9.0000
###	chr9:139873450-139873688(+)$1	238	35	38	9.0000
KGG	chr6:42625688-42625906(-)$1	218	15	18	9.0000
c[c	chr13:110435924-110436154(-)$1	230	13	16	9.0000
ddd	chr2:219562116-219562332(+)$1	216	85	88	9.0000
:::	chr3:49094332-49094565(-)$1	233	7	10	9.0000
mdd	chr6:149833190-149833410(-)$1	220	75	78	9.0000
DDD	chr16:139711-139958(-)$1	247	7	10	9.0000
oob	chr19:3808823-3809041(-)$1	218	66	69	9.0000
bbe	chr15:24921121-24921364(+)$1	243	99	102	9.0000
!!b	chr19:56171473-56171704(+)$1	231	21	24	9.0000
bb3	chr4:79856264-79856486(-)$1	222	68	71	9.0000
fff	chr2:65298989-65299208(+)$1	219	32	35	9.0000
qqq	chr16:11478003-11478219(-)$1	216	84	87	9.0000
c]c	chr1:179833830-179834052(-)$1	222	51	54	9.0000
:::	chr19:45490484-45490706(+)$1	222	44	47	9.0000
ccc	chr11:67378410-67378629(+)$1	219	55	58	9.0000
DDD	chr10:22615333-22615557(+)$1	224	59	62	9.0000
fff	chr8:195838-196061(-)$1	223	169	172	9.0000
eee	chr6:43480994-43481236(-)$1	242	3	6	9.0000
:::	chr8:144994756-144994972(-)$1	216	6	9	9.0000
DDD	chr20:62337659-62337882(-)$1	223	25	28	9.0000
HHH	chr16:71509055-71509274(-)$1	219	50	53	9.0000
EEE	chr9:137979810-137980043(+)$1	233	7	10	9.0000
FFF	chrX:101139404-101139622(-)$1	218	46	49	9.0000
c::	chr22:35660624-35660841(+)$1	217	150	153	9.0000
eee	chr11:64535112-64535333(-)$1	221	37	40	9.0000
D:e	chr16:1258027-1258247(+)$1	220	29	32	9.0000
ccc	chr19:10745707-10745952(+)$1	245	0	3	9.0000
eee	chr17:72926524-72926743(+)$1	219	64	67	9.0000
qqd	chr1:43904910-43905146(+)$1	236	64	67	9.0000
ff%	chr15:63988350-63988585(-)$1	235	6	9	9.0000
d]e	chr22:39909988-39910212(+)$1	224	130	133	9.0000
c22	chr12:112219676-112219891(+)$1	215	19	22	9.0000
GGG	chr15:101417959-101418179(-)$1	220	3	6	9.0000
g::	chr12:80696454-80696669(-)$1	215	88	91	9.0000
eee	chrX:53626990-53627232(-)$1	242	58	61	9.0000
::e	chr20:61869857-61870072(-)$1	215	24	27	9.0000
eee	chr14:94756653-94756874(+)$1	221	5	8	9.0000
B{E	chr15:75304925-75305143(+)$1	218	59	62	9.0000
ff:	chr1:52237712-52237951(+)$1	239	231	234	9.0000
D:c	chr17:21731435-21731655(+)$1	220	68	71	9.0000
::d	chr9:131776985-131777201(-)$1	216	60	63	9.0000
e]f	chr4:985807-986029(+)$1	222	172	175	9.0000
fff	chr1:16256607-16256823(+)$1	216	40	43	9.0000
dcc	chr12:6166033-6166260(-)$1	227	33	36	9.0000
eee	chr6:82924166-82924389(-)$1	223	102	105	9.0000
ood	chr16:53243424-53243650(+)$1	226	31	34	9.0000
GGG	chr19:18391802-18392028(-)$1	226	37	40	9.0000
ddd	chr5:71495445-71495665(+)$1	220	22	25	9.0000
:::	chr2:210558109-210558327(+)$1	218	9	12	9.0000
ddd	chr14:102472275-102472502(+)$1	227	126	129	9.0000
eee	chr2:236817311-236817538(+)$1	227	97	100	9.0000
DDD	chr10:125526555-125526775(-)$1	220	4	7	9.0000
d]c	chr1:72241754-72241971(-)$1	217	80	83	9.0000
eee	chr9:135984926-135985163(-)$1	237	20	23	9.0000
eeq	chr2:17864851-17865066(-)$1	215	53	56	9.0000
dhh	chr1:97270330-97270554(+)$1	224	34	37	9.0000
ddd	chr12:112665857-112666082(-)$1	225	50	53	9.0000
!!e	chr12:39713608-39713826(-)$1	218	48	51	9.0000
ddd	chr3:186504874-186505111(+)$1	237	74	77	9.0000
III	chr5:140884858-140885074(+)$1	216	23	26	9.0000
DOO	chr1:156622450-156622676(+)$1	226	8	11	9.0000
EEE	chr12:56647764-56647992(-)$1	228	4	7	9.0000
CCC	chr9:117052996-117053218(+)$1	222	26	29	9.0000
555	chr12:111169518-111169735(-)$1	217	30	33	9.0000
mmm	chr11:62550180-62550395(+)$1	215	82	85	9.0000
eee	chr1:177250325-177250581(+)$1	256	150	153	9.0000
h!!	chr13:52604032-52604258(+)$1	226	35	38	9.0000
q==	chr1:55555218-55555436(-)$1	218	124	127	9.0000
fff	chr7:103155762-103155981(-)$1	219	37	40	9.0000
dd:	chr10:70404502-70404728(+)$1	226	99	102	9.0000
B{C	chr13:53603072-53603290(-)$1	218	16	19	9.0000
FFF	chr12:112650246-112650477(-)$1	231	46	49	9.0000
{CC	chr20:4162976-4163192(+)$1	216	23	26	9.0000
[bb	chr13:77834486-77834707(-)$1	221	97	100	9.0000
d[b	chr9:137981934-137982169(+)$1	235	124	127	9.0000
eee	chr7:1484281-1484498(-)$1	217	96	99	9.0000
:::	chr7:150775805-150776031(-)$1	226	19	22	9.0000
bbb	chrX:153247631-153247847(-)$1	216	49	52	9.0000
!!d	chr19:17766037-17766264(-)$1	227	6	9	9.0000
ggg	chr4:170057422-170057638(+)$1	216	10	13	9.0000
DMM	chr17:40842751-40842972(+)$1	221	4	7	9.0000
vvv	chr12:133432953-133433175(-)$1	222	65	68	9.0000
LLL	chr3:111718299-111718528(+)$1	229	4	7	9.0000
BBC	chr6:121625393-121625622(-)$1	229	7	10	9.0000
:ff	chr3:99514412-99514639(-)$1	227	192	195	9.0000
B:c	chr14:21769184-21769400(+)$1	216	16	19	9.0000
FFF	chr19:55644182-55644403(+)$1	221	2	5	9.0000
d""	chr5:149602041-149602267(-)$1	226	31	34	9.0000
MCC	chr17:80763705-80763926(-)$1	221	8	11	9.0000
ggg	chr9:113006963-113007200(+)$1	237	68	71	9.0000
ggg	chr3:39225554-39225770(+)$1	216	33	36	9.0000
dpp	chr7:142568305-142568532(+)$1	227	62	65	9.0000
:::	chr17:78086303-78086525(+)$1	222	25	28	9.0000

#DB
(((	chr17:11282669-11282893(+)$1	1	91	94	9.0000
)..	chr6:83848398-83848613(+)$1	1	43	46	9.0000
..)	chr4:83424111-83424341(-)$1	1	166	169	9.0000
.))	chr10:73122084-73122300(+)$1	1	182	185	9.0000
(((	chr4:164087670-164087912(-)$1	1	4	7	9.0000
...	chr10:105037814-105038031(+)$1	1	39	42	9.0000
...	chr9:139873450-139873688(+)$1	1	35	38	9.0000
.((	chr6:42625688-42625906(-)$1	1	15	18	9.0000
(.(	chr13:110435924-110436154(-)$1	1	13	16	9.0000
)))	chr2:219562116-219562332(+)$1	1	85	88	9.0000
...	chr3:49094332-49094565(-)$1	1	7	10	9.0000
.))	chr6:149833190-149833410(-)$1	1	75	78	9.0000
(((	chr16:139711-139958(-)$1	1	7	10	9.0000
..)	chr19:3808823-3809041(-)$1	1	66	69	9.0000
(((	chr15:24921121-24921364(+)$1	1	99	102	9.0000
..(	chr19:56171473-56171704(+)$1	1	21	24	9.0000
)).	chr4:79856264-79856486(-)$1	1	68	71	9.0000
(((	chr2:65298989-65299208(+)$1	1	32	35	9.0000
...	chr16:11478003-11478219(-)$1	1	84	87	9.0000
).)	chr1:179833830-179834052(-)$1	1	51	54	9.0000
...	chr19:45490484-45490706(+)$1	1	44	47	9.0000
)))	chr11:67378410-67378629(+)$1	1	55	58	9.0000
(((	chr10:22615333-22615557(+)$1	1	59	62	9.0000
)))	chr8:195838-196061(-)$1	1	169	172	9.0000
(((	chr6:43480994-43481236(-)$1	1	3	6	9.0000
...	chr8:144994756-144994972(-)$1	1	6	9	9.0000
(((	chr20:62337659-62337882(-)$1	1	25	28	9.0000
(((	chr16:71509055-71509274(-)$1	1	50	53	9.0000
(((	chr9:137979810-137980043(+)$1	1	7	10	9.0000
(((	chrX:101139404-101139622(-)$1	1	46	49	9.0000
)..	chr22:35660624-35660841(+)$1	1	150	153	9.0000
)))	chr11:64535112-64535333(-)$1	1	37	40	9.0000
(.(	chr16:1258027-1258247(+)$1	1	29	32	9.0000
(((	chr19:10745707-10745952(+)$1	1	0	3	9.0000
(((	chr17:72926524-72926743(+)$1	1	64	67	9.0000
..)	chr1:43904910-43905146(+)$1	1	64	67	9.0000
((.	chr15:63988350-63988585(-)$1	1	6	9	9.0000
).)	chr22:39909988-39910212(+)$1	1	130	133	9.0000
)..	chr12:112219676-112219891(+)$1	1	19	22	9.0000
(((	chr15:101417959-101418179(-)$1	1	3	6	9.0000
)..	chr12:80696454-80696669(-)$1	1	88	91	9.0000
(((	chrX:53626990-53627232(-)$1	1	58	61	9.0000
..(	chr20:61869857-61870072(-)$1	1	24	27	9.0000
(((	chr14:94756653-94756874(+)$1	1	5	8	9.0000
(.(	chr15:75304925-75305143(+)$1	1	59	62	9.0000
)).	chr1:52237712-52237951(+)$1	1	231	234	9.0000
(.(	chr17:21731435-21731655(+)$1	1	68	71	9.0000
..(	chr9:131776985-131777201(-)$1	1	60	63	9.0000
).)	chr4:985807-986029(+)$1	1	172	175	9.0000
(((	chr1:16256607-16256823(+)$1	1	40	43	9.0000
(((	chr12:6166033-6166260(-)$1	1	33	36	9.0000
)))	chr6:82924166-82924389(-)$1	1	102	105	9.0000
..)	chr16:53243424-53243650(+)$1	1	31	34	9.0000
(((	chr19:18391802-18392028(-)$1	1	37	40	9.0000
(((	chr5:71495445-71495665(+)$1	1	22	25	9.0000
...	chr2:210558109-210558327(+)$1	1	9	12	9.0000
(((	chr14:102472275-102472502(+)$1	1	126	129	9.0000
)))	chr2:236817311-236817538(+)$1	1	97	100	9.0000
(((	chr10:125526555-125526775(-)$1	1	4	7	9.0000
).)	chr1:72241754-72241971(-)$1	1	80	83	9.0000
)))	chr9:135984926-135985163(-)$1	1	20	23	9.0000
((.	chr2:17864851-17865066(-)$1	1	53	56	9.0000
)))	chr1:97270330-97270554(+)$1	1	34	37	9.0000
)))	chr12:112665857-112666082(-)$1	1	50	53	9.0000
..(	chr12:39713608-39713826(-)$1	1	48	51	9.0000
(((	chr3:186504874-186505111(+)$1	1	74	77	9.0000
(((	chr5:140884858-140885074(+)$1	1	23	26	9.0000
(..	chr1:156622450-156622676(+)$1	1	8	11	9.0000
(((	chr12:56647764-56647992(-)$1	1	4	7	9.0000
(((	chr9:117052996-117053218(+)$1	1	26	29	9.0000
...	chr12:111169518-111169735(-)$1	1	30	33	9.0000
...	chr11:62550180-62550395(+)$1	1	82	85	9.0000
)))	chr1:177250325-177250581(+)$1	1	150	153	9.0000
(..	chr13:52604032-52604258(+)$1	1	35	38	9.0000
.))	chr1:55555218-55555436(-)$1	1	124	127	9.0000
(((	chr7:103155762-103155981(-)$1	1	37	40	9.0000
)).	chr10:70404502-70404728(+)$1	1	99	102	9.0000
(.(	chr13:53603072-53603290(-)$1	1	16	19	9.0000
(((	chr12:112650246-112650477(-)$1	1	46	49	9.0000
.((	chr20:4162976-4163192(+)$1	1	23	26	9.0000
.((	chr13:77834486-77834707(-)$1	1	97	100	9.0000
(.(	chr9:137981934-137982169(+)$1	1	124	127	9.0000
(((	chr7:1484281-1484498(-)$1	1	96	99	9.0000
...	chr7:150775805-150776031(-)$1	1	19	22	9.0000
(((	chrX:153247631-153247847(-)$1	1	49	52	9.0000
..(	chr19:17766037-17766264(-)$1	1	6	9	9.0000
(((	chr4:170057422-170057638(+)$1	1	10	13	9.0000
(..	chr17:40842751-40842972(+)$1	1	4	7	9.0000
...	chr12:133432953-133433175(-)$1	1	65	68	9.0000
...	chr3:111718299-111718528(+)$1	1	4	7	9.0000
(((	chr6:121625393-121625622(-)$1	1	7	10	9.0000
.((	chr3:99514412-99514639(-)$1	1	192	195	9.0000
(.(	chr14:21769184-21769400(+)$1	1	16	19	9.0000
(((	chr19:55644182-55644403(+)$1	1	2	5	9.0000
(..	chr5:149602041-149602267(-)$1	1	31	34	9.0000
.((	chr17:80763705-80763926(-)$1	1	8	11	9.0000
(((	chr9:113006963-113007200(+)$1	1	68	71	9.0000
(((	chr3:39225554-39225770(+)$1	1	33	36	9.0000
(..	chr7:142568305-142568532(+)$1	1	62	65	9.0000
...	chr17:78086303-78086525(+)$1	1	25	28	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m2_run1.nuc.txt

#NT
ugcc	chr1:171526967-171527238(+)$1	271	1	5	11.9999
UGCC	chr18:29709006-29709236(+)$1	230	180	184	11.9999
UGCC	chr19:2137660-2137906(-)$1	246	32	36	11.9999
UGCC	chr8:96166587-96166840(+)$1	253	23	27	11.9999
UGCC	chr17:79477852-79478132(-)$1	280	122	126	11.9999
UGCC	chr3:47162890-47163181(-)$1	291	133	137	11.9999
UGCC	chr2:55825867-55826143(-)$1	276	44	48	11.9999
UGCC	chr1:43166443-43166732(+)$1	289	244	248	11.9999
ugcc	chr5:137088959-137089203(-)$1	244	143	147	11.9999
UGCC	chr12:57006848-57007093(-)$1	245	139	143	11.9999
UGCC	chr2:86992160-86992418(+)$1	258	136	140	11.9999
UGCC	chr19:41781966-41782205(+)$1	239	191	195	11.9999
UGCC	chr15:44038665-44038921(+)$1	256	119	123	11.9999
UGCC	chr5:140056195-140056445(-)$1	250	142	146	11.9999
UGCC	chr19:15379611-15379954(-)$1	343	54	58	11.9999
UGCC	chr1:161007681-161007941(-)$1	260	32	36	11.9999
UGCC	chr5:14508368-14508642(+)$1	274	149	153	11.9999
UGCC	chr12:121203976-121204225(-)$1	249	31	35	11.9999
UGCC	chr1:93301782-93302039(+)$1	257	59	63	11.9999
UGCC	chr15:93499710-93499994(+)$1	284	159	163	11.9999
UGCC	chr19:17937540-17937807(-)$1	267	204	208	11.9999
UGCC	chr16:18538767-18539050(-)$1	283	176	180	11.9999
UGCC	chr6:27776116-27776532(+)$1	416	196	200	11.9999
UGCC	chr14:92600261-92600524(+)$1	263	150	154	11.9999
UGCC	chr15:81592443-81592715(+)$1	272	99	103	11.9999
UGCC	chr7:135358741-135359132(+)$1	391	144	148	11.9999
UGCC	chr16:58614459-58614760(-)$1	301	167	171	11.9999
UGCC	chr1:160276868-160277137(-)$1	269	53	57	11.9999
UGCC	chr1:149400376-149400643(-)$1	267	70	74	11.9999
UGCC	chr11:62299495-62299797(-)$1	302	4	8	11.9999
UGCC	chr20:49510415-49510668(-)$1	253	59	63	11.9999
UGCC	chr5:1321774-1322012(-)$1	238	10	14	11.9999
UGCC	chr1:155145148-155145432(-)$1	284	0	4	11.9999
UGCC	chr2:183866770-183867080(-)$1	310	199	203	11.9999
UGCC	chr15:59009726-59009999(-)$1	273	161	165	11.9999
UGCC	chr8:104447759-104448069(+)$1	310	264	268	11.9999
UGCC	chr17:1579789-1580032(-)$1	243	37	41	11.9999
UGCC	chr1:8927077-8927412(-)$1	335	140	144	11.9999
UGCC	chr1:155223322-155223594(-)$1	272	106	110	11.9999
UGCC	chr11:66392699-66392974(+)$1	275	144	148	11.9999
UGCC	chr19:4676472-4676764(-)$1	292	11	15	11.9999
UGCC	chr6:31601588-31601850(+)$1	262	108	112	11.9999
UGCC	chr1:145439488-145439771(+)$1	283	20	24	11.9999
UGCC	chr11:62338953-62339235(-)$1	282	70	74	11.9999
UGCC	chr6:532369-532637(-)$1	268	153	157	11.9999
UGCC	chr4:48895917-48896169(-)$1	252	132	136	11.9999
ugcc	chr11:47861290-47861546(-)$1	256	250	254	11.9999
UGCC	chr6:44219053-44219320(+)$1	267	134	138	11.9999
UGCC	chr5:14387520-14387766(+)$1	246	88	92	11.9999
UGCC	chr19:18652616-18652873(-)$1	257	52	56	11.9999
UGCC	chr17:1581951-1582204(-)$1	253	139	143	11.9999
UGCC	chrX:47045360-47045609(+)$1	249	15	19	11.9999
UGCC	chr1:200377023-200377307(-)$1	284	72	76	11.9999
UGCC	chr11:8706169-8706541(+)$1	372	159	163	11.9999
UGCC	chr7:133692415-133692681(+)$1	266	50	54	11.9999
UGCC	chr1:160326806-160327105(+)$1	299	128	132	11.9999
UGCC	chr16:2303594-2303884(-)$1	290	58	62	11.9999
UGCC	chr18:43667204-43667558(-)$1	354	101	105	11.9999
UGCC	chr12:95888661-95888924(+)$1	263	167	171	11.9999
UGCC	chr1:206945617-206945931(-)$1	314	3	7	11.9999
UGCC	chr19:34891288-34891651(+)$1	363	32	36	11.9999
UGCC	chr11:62291599-62291858(-)$1	259	183	187	11.9999
UGCC	chr2:176043740-176044049(-)$1	309	166	170	11.9999
UGCC	chr14:77934335-77934579(+)$1	244	53	57	11.9999
UGCC	chr16:58568073-58568370(-)$1	297	190	194	11.9999
UGCC	chr12:8075459-8075726(-)$1	267	25	29	11.9999
UGCC	chr17:57758548-57758891(+)$1	343	194	198	11.9999
UGCC	chr2:99155915-99156155(+)$1	240	85	89	11.9999
UGCC	chr15:48719745-48720028(-)$1	283	36	40	11.9999
UGCC	chr17:1565100-1565404(-)$1	304	102	106	11.9999
UGCC	chr2:96959020-96959287(-)$1	267	153	157	11.9999
UGCC	chr1:120484203-120484476(-)$1	273	1	5	11.9999
UGCC	chr5:72182792-72183065(+)$1	273	120	124	11.9999
UGCC	chr19:10940796-10941061(+)$1	265	251	255	11.9999
UGCC	chr2:203104249-203104525(+)$1	276	158	162	11.9999
UGCC	chr12:109017396-109017700(-)$1	304	26	30	11.9999
UGCC	chr17:6920181-6920422(+)$1	241	33	37	11.9999
UGCC	chr19:39127441-39127698(+)$1	257	177	181	11.9999

#otherMatches

#Struct PSSM
dccc	chr12:95905564-95905859(+)$1	295	172	176	11.9999
:::C	chr1:171526967-171527238(+)$1	271	1	5	11.9999
dddC	chr18:29709006-29709236(+)$1	230	180	184	11.9999
[bbm	chr19:2137660-2137906(-)$1	246	32	36	11.9999
ddee	chr8:96166587-96166840(+)$1	253	23	27	11.9999
oocc	chr17:79477852-79478132(-)$1	280	122	126	11.9999
ggg:	chr3:47162890-47163181(-)$1	291	133	137	11.9999
d:::	chr2:55825867-55826143(-)$1	276	44	48	11.9999
bb]e	chr1:43166443-43166732(+)$1	289	244	248	11.9999
eeee	chr5:137088959-137089203(-)$1	244	143	147	11.9999
ddcc	chr12:57006848-57007093(-)$1	245	139	143	11.9999
ffa[	chr2:86992160-86992418(+)$1	258	136	140	11.9999
EEEE	chr19:41781966-41782205(+)$1	239	191	195	11.9999
qqqq	chr15:44038665-44038921(+)$1	256	119	123	11.9999
c[cc	chr5:140056195-140056445(-)$1	250	142	146	11.9999
DKKA	chr19:15379611-15379954(-)$1	343	54	58	11.9999
DDDD	chr1:161007681-161007941(-)$1	260	32	36	11.9999
IIII	chr5:14508368-14508642(+)$1	274	149	153	11.9999
KCCC	chr12:121203976-121204225(-)$1	249	31	35	11.9999
2hhh	chr1:93301782-93302039(+)$1	257	59	63	11.9999
HHHH	chr15:93499710-93499994(+)$1	284	159	163	11.9999
gggg	chr19:17937540-17937807(-)$1	267	204	208	11.9999
fDDD	chr16:18538767-18539050(-)$1	283	176	180	11.9999
ffff	chr6:27776116-27776532(+)$1	416	196	200	11.9999
:ddd	chr14:92600261-92600524(+)$1	263	150	154	11.9999
$bbl	chr15:81592443-81592715(+)$1	272	99	103	11.9999
llee	chr7:135358741-135359132(+)$1	391	144	148	11.9999
EEEZ	chr16:58614459-58614760(-)$1	301	167	171	11.9999
hhhh	chr1:160276868-160277137(-)$1	269	53	57	11.9999
]ddd	chr1:149400376-149400643(-)$1	267	70	74	11.9999
:ddd	chr11:62299495-62299797(-)$1	302	4	8	11.9999
occc	chr20:49510415-49510668(-)$1	253	59	63	11.9999
FFFF	chr5:1321774-1322012(-)$1	238	10	14	11.9999
hhhh	chr1:155145148-155145432(-)$1	284	0	4	11.9999
cccf	chr2:183866770-183867080(-)$1	310	199	203	11.9999
c555	chr15:59009726-59009999(-)$1	273	161	165	11.9999
oooo	chr8:104447759-104448069(+)$1	310	264	268	11.9999
GGGG	chr17:1579789-1580032(-)$1	243	37	41	11.9999
HHHH	chr1:8927077-8927412(-)$1	335	140	144	11.9999
dddd	chr1:155223322-155223594(-)$1	272	106	110	11.9999
d===	chr11:66392699-66392974(+)$1	275	144	148	11.9999
KDDD	chr19:4676472-4676764(-)$1	292	11	15	11.9999
gggg	chr6:31601588-31601850(+)$1	262	108	112	11.9999
bbnn	chr1:145439488-145439771(+)$1	283	20	24	11.9999
GGGG	chr11:62338953-62339235(-)$1	282	70	74	11.9999
33ee	chr6:532369-532637(-)$1	268	153	157	11.9999
cccq	chr4:48895917-48896169(-)$1	252	132	136	11.9999
ddd:	chr11:47861290-47861546(-)$1	256	250	254	11.9999
:::D	chr6:44219053-44219320(+)$1	267	134	138	11.9999
CCCC	chr5:14387520-14387766(+)$1	246	88	92	11.9999
E{BB	chr19:18652616-18652873(-)$1	257	52	56	11.9999
22cc	chr17:1581951-1582204(-)$1	253	139	143	11.9999
:::D	chrX:47045360-47045609(+)$1	249	15	19	11.9999
ccc"	chr1:200377023-200377307(-)$1	284	72	76	11.9999
{DDD	chr11:8706169-8706541(+)$1	372	159	163	11.9999
fffb	chr7:133692415-133692681(+)$1	266	50	54	11.9999
JJJJ	chr1:160326806-160327105(+)$1	299	128	132	11.9999
eee[	chr16:2303594-2303884(-)$1	290	58	62	11.9999
====	chr18:43667204-43667558(-)$1	354	101	105	11.9999
::::	chr12:95888661-95888924(+)$1	263	167	171	11.9999
::::	chr1:206945617-206945931(-)$1	314	3	7	11.9999
lccc	chr19:34891288-34891651(+)$1	363	32	36	11.9999
JJYY	chr11:62291599-62291858(-)$1	259	183	187	11.9999
IIII	chr2:176043740-176044049(-)$1	309	166	170	11.9999
JJJJ	chr14:77934335-77934579(+)$1	244	53	57	11.9999
fff:	chr16:58568073-58568370(-)$1	297	190	194	11.9999
{DDD	chr12:8075459-8075726(-)$1	267	25	29	11.9999
ddd]	chr17:57758548-57758891(+)$1	343	194	198	11.9999
EKKF	chr2:99155915-99156155(+)$1	240	85	89	11.9999
LEEE	chr15:48719745-48720028(-)$1	283	36	40	11.9999
eee:	chr17:1565100-1565404(-)$1	304	102	106	11.9999
hh33	chr2:96959020-96959287(-)$1	267	153	157	11.9999
cccn	chr1:120484203-120484476(-)$1	273	1	5	11.9999
CCCF	chr5:72182792-72183065(+)$1	273	120	124	11.9999
FF~~	chr19:10940796-10941061(+)$1	265	251	255	11.9999
llee	chr2:203104249-203104525(+)$1	276	158	162	11.9999
eeee	chr12:109017396-109017700(-)$1	304	26	30	11.9999
DDDD	chr17:6920181-6920422(+)$1	241	33	37	11.9999
g%%%	chr19:39127441-39127698(+)$1	257	177	181	11.9999

#DB
))))	chr12:95905564-95905859(+)$1	1	172	176	11.9999
...(	chr1:171526967-171527238(+)$1	1	1	5	11.9999
))))	chr18:29709006-29709236(+)$1	1	180	184	11.9999
.((.	chr19:2137660-2137906(-)$1	1	32	36	11.9999
))((	chr8:96166587-96166840(+)$1	1	23	27	11.9999
..))	chr17:79477852-79478132(-)$1	1	122	126	11.9999
))).	chr3:47162890-47163181(-)$1	1	133	137	11.9999
)...	chr2:55825867-55826143(-)$1	1	44	48	11.9999
)).)	chr1:43166443-43166732(+)$1	1	244	248	11.9999
((((	chr5:137088959-137089203(-)$1	1	143	147	11.9999
((((	chr12:57006848-57007093(-)$1	1	139	143	11.9999
(((.	chr2:86992160-86992418(+)$1	1	136	140	11.9999
))))	chr19:41781966-41782205(+)$1	1	191	195	11.9999
....	chr15:44038665-44038921(+)$1	1	119	123	11.9999
(.((	chr5:140056195-140056445(-)$1	1	142	146	11.9999
(..(	chr19:15379611-15379954(-)$1	1	54	58	11.9999
((((	chr1:161007681-161007941(-)$1	1	32	36	11.9999
))))	chr5:14508368-14508642(+)$1	1	149	153	11.9999
.(((	chr12:121203976-121204225(-)$1	1	31	35	11.9999
.)))	chr1:93301782-93302039(+)$1	1	59	63	11.9999
((((	chr15:93499710-93499994(+)$1	1	159	163	11.9999
((((	chr19:17937540-17937807(-)$1	1	204	208	11.9999
))))	chr16:18538767-18539050(-)$1	1	176	180	11.9999
))))	chr6:27776116-27776532(+)$1	1	196	200	11.9999
.(((	chr14:92600261-92600524(+)$1	1	150	154	11.9999
.((.	chr15:81592443-81592715(+)$1	1	99	103	11.9999
..))	chr7:135358741-135359132(+)$1	1	144	148	11.9999
))).	chr16:58614459-58614760(-)$1	1	167	171	11.9999
))))	chr1:160276868-160277137(-)$1	1	53	57	11.9999
.)))	chr1:149400376-149400643(-)$1	1	70	74	11.9999
.(((	chr11:62299495-62299797(-)$1	1	4	8	11.9999
.)))	chr20:49510415-49510668(-)$1	1	59	63	11.9999
((((	chr5:1321774-1322012(-)$1	1	10	14	11.9999
((((	chr1:155145148-155145432(-)$1	1	0	4	11.9999
((((	chr2:183866770-183867080(-)$1	1	199	203	11.9999
)...	chr15:59009726-59009999(-)$1	1	161	165	11.9999
....	chr8:104447759-104448069(+)$1	1	264	268	11.9999
((((	chr17:1579789-1580032(-)$1	1	37	41	11.9999
))))	chr1:8927077-8927412(-)$1	1	140	144	11.9999
((((	chr1:155223322-155223594(-)$1	1	106	110	11.9999
))))	chr11:66392699-66392974(+)$1	1	144	148	11.9999
.(((	chr19:4676472-4676764(-)$1	1	11	15	11.9999
))))	chr6:31601588-31601850(+)$1	1	108	112	11.9999
((..	chr1:145439488-145439771(+)$1	1	20	24	11.9999
((((	chr11:62338953-62339235(-)$1	1	70	74	11.9999
..))	chr6:532369-532637(-)$1	1	153	157	11.9999
(((.	chr4:48895917-48896169(-)$1	1	132	136	11.9999
))).	chr11:47861290-47861546(-)$1	1	250	254	11.9999
...)	chr6:44219053-44219320(+)$1	1	134	138	11.9999
((((	chr5:14387520-14387766(+)$1	1	88	92	11.9999
(.((	chr19:18652616-18652873(-)$1	1	52	56	11.9999
..))	chr17:1581951-1582204(-)$1	1	139	143	11.9999
...(	chrX:47045360-47045609(+)$1	1	15	19	11.9999
(((.	chr1:200377023-200377307(-)$1	1	72	76	11.9999
.(((	chr11:8706169-8706541(+)$1	1	159	163	11.9999
((((	chr7:133692415-133692681(+)$1	1	50	54	11.9999
((((	chr1:160326806-160327105(+)$1	1	128	132	11.9999
(((.	chr16:2303594-2303884(-)$1	1	58	62	11.9999
((((	chr18:43667204-43667558(-)$1	1	101	105	11.9999
....	chr12:95888661-95888924(+)$1	1	167	171	11.9999
....	chr1:206945617-206945931(-)$1	1	3	7	11.9999
.)))	chr19:34891288-34891651(+)$1	1	32	36	11.9999
))..	chr11:62291599-62291858(-)$1	1	183	187	11.9999
((((	chr2:176043740-176044049(-)$1	1	166	170	11.9999
((((	chr14:77934335-77934579(+)$1	1	53	57	11.9999
))).	chr16:58568073-58568370(-)$1	1	190	194	11.9999
.(((	chr12:8075459-8075726(-)$1	1	25	29	11.9999
))).	chr17:57758548-57758891(+)$1	1	194	198	11.9999
(..(	chr2:99155915-99156155(+)$1	1	85	89	11.9999
.(((	chr15:48719745-48720028(-)$1	1	36	40	11.9999
))).	chr17:1565100-1565404(-)$1	1	102	106	11.9999
))..	chr2:96959020-96959287(-)$1	1	153	157	11.9999
(((.	chr1:120484203-120484476(-)$1	1	1	5	11.9999
((((	chr5:72182792-72183065(+)$1	1	120	124	11.9999
))..	chr19:10940796-10941061(+)$1	1	251	255	11.9999
..))	chr2:203104249-203104525(+)$1	1	158	162	11.9999
))))	chr12:109017396-109017700(-)$1	1	26	30	11.9999
((((	chr17:6920181-6920422(+)$1	1	33	37	11.9999
(...	chr19:39127441-39127698(+)$1	1	177	181	11.9999

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

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m1_run1.nuc.txt

#NT
CUUC	chr16:2048323-2048563(-)$1	240	114	118	11.9999
CUUC	chr9:131285983-131286223(+)$1	240	78	82	11.9999
CUUC	chr2:32772904-32773144(+)$1	240	103	107	11.9999
CUUC	chr11:59416930-59417170(-)$1	240	79	83	11.9999
CUUC	chr16:67768762-67769002(-)$1	240	128	132	11.9999
CUUC	chr5:173317149-173317389(+)$1	240	44	48	11.9999
CUUC	chr3:43389680-43389920(+)$1	240	42	46	11.9999
CUUC	chr19:47207479-47207719(-)$1	240	117	121	11.9999
CUUC	chr19:5690457-5690697(+)$1	240	36	40	11.9999
cuuc	chr6:97702463-97702703(-)$1	240	9	13	11.9999
CUUC	chr10:104135111-104135351(+)$1	240	144	148	11.9999
CUUC	chr17:5336950-5337190(-)$1	240	64	68	11.9999
CUUC	chr20:33162826-33163066(-)$1	240	68	72	11.9999
CUUC	chr7:27147837-27148077(-)$1	240	99	103	11.9999
CUUC	chr20:49510198-49510438(-)$1	240	59	63	11.9999
CUUC	chr18:54283402-54283642(-)$1	240	31	35	11.9999
CUUC	chr1:10479586-10479826(+)$1	240	114	118	11.9999
CUUC	chr6:31515926-31516166(+)$1	240	4	8	11.9999
CUUC	chrX:134427841-134428081(-)$1	240	167	171	11.9999
CUUC	chr4:24534419-24534659(-)$1	240	13	17	11.9999
CUUC	chr17:37818400-37818640(+)$1	240	124	128	11.9999
CUUC	chr1:151958538-151958778(-)$1	240	52	56	11.9999
CUUC	chr17:1680571-1680811(+)$1	240	60	64	11.9999
CUUC	chr12:118471942-118472182(-)$1	240	95	99	11.9999
CUUC	chr20:25255162-25255402(+)$1	240	54	58	11.9999
CUUC	chr14:95560230-95560470(-)$1	240	152	156	11.9999
CUUC	chrX:138884296-138884536(-)$1	240	21	25	11.9999
CUUC	chr1:109794546-109794786(+)$1	240	119	123	11.9999
CUUC	chr15:40099155-40099395(-)$1	240	51	55	11.9999
CUUC	chr1:223985818-223986058(-)$1	240	2	6	11.9999
CUUC	chr5:133537443-133537691(-)$1	248	6	10	11.9999
CUUC	chr12:57625927-57626167(+)$1	240	28	32	11.9999
CUUC	chr1:32636236-32636476(+)$1	240	41	45	11.9999
CUUC	chr1:54237958-54238198(-)$1	240	57	61	11.9999
CUUC	chr6:31604201-31604441(+)$1	240	107	111	11.9999
CUUC	chr5:43655859-43656099(+)$1	240	32	36	11.9999
CUUC	chr5:114462327-114462567(-)$1	240	66	70	11.9999
CUUC	chr4:25823600-25823840(-)$1	240	72	76	11.9999
CUUC	chr5:32126484-32126724(-)$1	240	88	92	11.9999
CUUC	chr3:130398129-130398369(-)$1	240	162	166	11.9999
CUUC	chr15:89007834-89008074(-)$1	240	101	105	11.9999
CUUC	chr9:107515187-107515427(+)$1	240	165	169	11.9999
CUUC	chr1:151259779-151260019(+)$1	240	76	80	11.9999
CUUC	chr13:32937356-32937596(+)$1	240	90	94	11.9999
CUUc	chr19:49403958-49404198(+)$1	240	125	129	11.9999
CUUC	chr14:31347918-31348158(+)$1	240	214	218	11.9999
CUUC	chr16:24817863-24818103(+)$1	240	231	235	11.9999
CUUC	chr16:47292472-47292712(-)$1	240	208	212	11.9999
CUUC	chr5:43174814-43175054(+)$1	240	94	98	11.9999
CUUC	chr7:5104293-5104533(+)$1	240	188	192	11.9999
CUUC	chr15:101717921-101718161(-)$1	240	40	44	11.9999
CUUC	chr10:32576023-32576263(-)$1	240	174	178	11.9999
CUUC	chr11:62415546-62415786(-)$1	240	138	142	11.9999
CUUC	chr2:73678933-73679173(+)$1	240	131	135	11.9999
CUUC	chr3:13417744-13417984(-)$1	240	46	50	11.9999
CUUC	chr5:172197753-172197993(-)$1	240	130	134	11.9999
CUUC	chr15:49301327-49301567(-)$1	240	19	23	11.9999
CUUC	chr4:76890369-76890609(-)$1	240	33	37	11.9999
CUUC	chr1:207222720-207222960(-)$1	240	133	137	11.9999
CUUC	chr2:220088225-220088465(-)$1	240	32	36	11.9999
CUUC	chr20:31024222-31024462(+)$1	240	232	236	11.9999
CUUC	chr5:55236993-55237233(-)$1	240	8	12	11.9999
CUUC	chr11:10821709-10821949(-)$1	240	212	216	11.9999
CUUC	chr22:50356329-50356569(+)$1	240	90	94	11.9999
CUUC	chr14:104026829-104027069(-)$1	240	79	83	11.9999
CUUC	chr4:39457936-39458176(-)$1	240	20	24	11.9999
CUUC	chr10:129903706-129903946(-)$1	240	76	80	11.9999
CUUC	chr22:24236936-24237176(+)$1	240	60	64	11.9999
CUUC	chr17:27613749-27613989(-)$1	240	95	99	11.9999
CUUC	chr11:118375798-118376038(+)$1	240	97	101	11.9999
CUUC	chr6:64421568-64421808(+)$1	240	164	168	11.9999
CUUC	chr2:192280786-192281026(+)$1	240	6	10	11.9999
CUUC	chr20:32659808-32660048(+)$1	240	38	42	11.9999
CUUC	chr4:39924207-39924469(-)$1	262	53	57	11.9999
CUUC	chr7:99091615-99091855(-)$1	240	199	203	11.9999
CUUC	chr10:74034461-74034701(+)$1	240	25	29	11.9999
CUUC	chr3:20113780-20114020(+)$1	240	185	189	11.9999
CUUC	chr17:37046607-37046847(+)$1	240	83	87	11.9999
CUUC	chr8:134270515-134270755(-)$1	240	79	83	11.9999

#otherMatches

#Struct PSSM
FFF:	chr6:44219685-44219925(+)$1	240	108	112	11.9999
eeee	chr16:2048323-2048563(-)$1	240	114	118	11.9999
b555	chr9:131285983-131286223(+)$1	240	78	82	11.9999
ffff	chr2:32772904-32773144(+)$1	240	103	107	11.9999
9999	chr11:59416930-59417170(-)$1	240	79	83	11.9999
[ggg	chr16:67768762-67769002(-)$1	240	128	132	11.9999
""dd	chr5:173317149-173317389(+)$1	240	44	48	11.9999
oooo	chr3:43389680-43389920(+)$1	240	42	46	11.9999
JJJ:	chr19:47207479-47207719(-)$1	240	117	121	11.9999
{CCC	chr19:5690457-5690697(+)$1	240	36	40	11.9999
EE{C	chr6:97702463-97702703(-)$1	240	9	13	11.9999
b]dd	chr10:104135111-104135351(+)$1	240	144	148	11.9999
::::	chr17:5336950-5337190(-)$1	240	64	68	11.9999
EEEE	chr20:33162826-33163066(-)$1	240	68	72	11.9999
555d	chr7:27147837-27148077(-)$1	240	99	103	11.9999
eee:	chr20:49510198-49510438(-)$1	240	59	63	11.9999
dd[g	chr18:54283402-54283642(-)$1	240	31	35	11.9999
::::	chr1:10479586-10479826(+)$1	240	114	118	11.9999
::::	chr6:31515926-31516166(+)$1	240	4	8	11.9999
bb]d	chrX:134427841-134428081(-)$1	240	167	171	11.9999
BBKK	chr4:24534419-24534659(-)$1	240	13	17	11.9999
gggg	chr17:37818400-37818640(+)$1	240	124	128	11.9999
FFFF	chr1:151958538-151958778(-)$1	240	52	56	11.9999
::::	chr17:1680571-1680811(+)$1	240	60	64	11.9999
oddd	chr12:118471942-118472182(-)$1	240	95	99	11.9999
ddd[	chr20:25255162-25255402(+)$1	240	54	58	11.9999
fff3	chr14:95560230-95560470(-)$1	240	152	156	11.9999
:ggg	chrX:138884296-138884536(-)$1	240	21	25	11.9999
b###	chr1:109794546-109794786(+)$1	240	119	123	11.9999
qqqq	chr15:40099155-40099395(-)$1	240	51	55	11.9999
::::	chr1:223985818-223986058(-)$1	240	2	6	11.9999
::::	chr5:133537443-133537691(-)$1	248	6	10	11.9999
BB{E	chr12:57625927-57626167(+)$1	240	28	32	11.9999
::::	chr1:32636236-32636476(+)$1	240	41	45	11.9999
dqqq	chr1:54237958-54238198(-)$1	240	57	61	11.9999
ee]d	chr6:31604201-31604441(+)$1	240	107	111	11.9999
::::	chr5:43655859-43656099(+)$1	240	32	36	11.9999
^^^^	chr5:114462327-114462567(-)$1	240	66	70	11.9999
>>>b	chr4:25823600-25823840(-)$1	240	72	76	11.9999
oooo	chr5:32126484-32126724(-)$1	240	88	92	11.9999
"fff	chr3:130398129-130398369(-)$1	240	162	166	11.9999
ccll	chr15:89007834-89008074(-)$1	240	101	105	11.9999
eeee	chr9:107515187-107515427(+)$1	240	165	169	11.9999
dddd	chr1:151259779-151260019(+)$1	240	76	80	11.9999
cc[d	chr13:32937356-32937596(+)$1	240	90	94	11.9999
hhhh	chr19:49403958-49404198(+)$1	240	125	129	11.9999
ddqq	chr14:31347918-31348158(+)$1	240	214	218	11.9999
::::	chr16:24817863-24818103(+)$1	240	231	235	11.9999
c22b	chr16:47292472-47292712(-)$1	240	208	212	11.9999
dddl	chr5:43174814-43175054(+)$1	240	94	98	11.9999
^^^^	chr7:5104293-5104533(+)$1	240	188	192	11.9999
g(((	chr15:101717921-101718161(-)$1	240	40	44	11.9999
dddq	chr10:32576023-32576263(-)$1	240	174	178	11.9999
GGGG	chr11:62415546-62415786(-)$1	240	138	142	11.9999
dddd	chr2:73678933-73679173(+)$1	240	131	135	11.9999
ssss	chr3:13417744-13417984(-)$1	240	46	50	11.9999
gggg	chr5:172197753-172197993(-)$1	240	130	134	11.9999
mmee	chr15:49301327-49301567(-)$1	240	19	23	11.9999
dddd	chr4:76890369-76890609(-)$1	240	33	37	11.9999
hhhh	chr1:207222720-207222960(-)$1	240	133	137	11.9999
ffff	chr2:220088225-220088465(-)$1	240	32	36	11.9999
EEEE	chr20:31024222-31024462(+)$1	240	232	236	11.9999
::::	chr5:55236993-55237233(-)$1	240	8	12	11.9999
::::	chr11:10821709-10821949(-)$1	240	212	216	11.9999
a:::	chr22:50356329-50356569(+)$1	240	90	94	11.9999
dddd	chr14:104026829-104027069(-)$1	240	79	83	11.9999
mmmb	chr4:39457936-39458176(-)$1	240	20	24	11.9999
dddm	chr10:129903706-129903946(-)$1	240	76	80	11.9999
EEEE	chr22:24236936-24237176(+)$1	240	60	64	11.9999
lhhh	chr17:27613749-27613989(-)$1	240	95	99	11.9999
eepp	chr11:118375798-118376038(+)$1	240	97	101	11.9999
::EE	chr6:64421568-64421808(+)$1	240	164	168	11.9999
ddmm	chr2:192280786-192281026(+)$1	240	6	10	11.9999
cc[d	chr20:32659808-32660048(+)$1	240	38	42	11.9999
EEEE	chr4:39924207-39924469(-)$1	262	53	57	11.9999
:FFF	chr7:99091615-99091855(-)$1	240	199	203	11.9999
44bb	chr10:74034461-74034701(+)$1	240	25	29	11.9999
rrrr	chr3:20113780-20114020(+)$1	240	185	189	11.9999
d[dd	chr17:37046607-37046847(+)$1	240	83	87	11.9999
[eee	chr8:134270515-134270755(-)$1	240	79	83	11.9999

#DB
(((.	chr6:44219685-44219925(+)$1	1	108	112	11.9999
((((	chr16:2048323-2048563(-)$1	1	114	118	11.9999
)...	chr9:131285983-131286223(+)$1	1	78	82	11.9999
))))	chr2:32772904-32773144(+)$1	1	103	107	11.9999
....	chr11:59416930-59417170(-)$1	1	79	83	11.9999
.(((	chr16:67768762-67769002(-)$1	1	128	132	11.9999
..((	chr5:173317149-173317389(+)$1	1	44	48	11.9999
....	chr3:43389680-43389920(+)$1	1	42	46	11.9999
))).	chr19:47207479-47207719(-)$1	1	117	121	11.9999
.(((	chr19:5690457-5690697(+)$1	1	36	40	11.9999
((.(	chr6:97702463-97702703(-)$1	1	9	13	11.9999
).))	chr10:104135111-104135351(+)$1	1	144	148	11.9999
....	chr17:5336950-5337190(-)$1	1	64	68	11.9999
((((	chr20:33162826-33163066(-)$1	1	68	72	11.9999
...)	chr7:27147837-27148077(-)$1	1	99	103	11.9999
))).	chr20:49510198-49510438(-)$1	1	59	63	11.9999
((.(	chr18:54283402-54283642(-)$1	1	31	35	11.9999
....	chr1:10479586-10479826(+)$1	1	114	118	11.9999
....	chr6:31515926-31516166(+)$1	1	4	8	11.9999
)).)	chrX:134427841-134428081(-)$1	1	167	171	11.9999
((..	chr4:24534419-24534659(-)$1	1	13	17	11.9999
((((	chr17:37818400-37818640(+)$1	1	124	128	11.9999
((((	chr1:151958538-151958778(-)$1	1	52	56	11.9999
....	chr17:1680571-1680811(+)$1	1	60	64	11.9999
.)))	chr12:118471942-118472182(-)$1	1	95	99	11.9999
(((.	chr20:25255162-25255402(+)$1	1	54	58	11.9999
))).	chr14:95560230-95560470(-)$1	1	152	156	11.9999
.(((	chrX:138884296-138884536(-)$1	1	21	25	11.9999
(...	chr1:109794546-109794786(+)$1	1	119	123	11.9999
....	chr15:40099155-40099395(-)$1	1	51	55	11.9999
....	chr1:223985818-223986058(-)$1	1	2	6	11.9999
....	chr5:133537443-133537691(-)$1	1	6	10	11.9999
((.(	chr12:57625927-57626167(+)$1	1	28	32	11.9999
....	chr1:32636236-32636476(+)$1	1	41	45	11.9999
(...	chr1:54237958-54238198(-)$1	1	57	61	11.9999
)).)	chr6:31604201-31604441(+)$1	1	107	111	11.9999
....	chr5:43655859-43656099(+)$1	1	32	36	11.9999
....	chr5:114462327-114462567(-)$1	1	66	70	11.9999
...)	chr4:25823600-25823840(-)$1	1	72	76	11.9999
....	chr5:32126484-32126724(-)$1	1	88	92	11.9999
.(((	chr3:130398129-130398369(-)$1	1	162	166	11.9999
((..	chr15:89007834-89008074(-)$1	1	101	105	11.9999
))))	chr9:107515187-107515427(+)$1	1	165	169	11.9999
((((	chr1:151259779-151260019(+)$1	1	76	80	11.9999
((.(	chr13:32937356-32937596(+)$1	1	90	94	11.9999
((((	chr19:49403958-49404198(+)$1	1	125	129	11.9999
((..	chr14:31347918-31348158(+)$1	1	214	218	11.9999
....	chr16:24817863-24818103(+)$1	1	231	235	11.9999
)..)	chr16:47292472-47292712(-)$1	1	208	212	11.9999
(((.	chr5:43174814-43175054(+)$1	1	94	98	11.9999
....	chr7:5104293-5104533(+)$1	1	188	192	11.9999
(...	chr15:101717921-101718161(-)$1	1	40	44	11.9999
(((.	chr10:32576023-32576263(-)$1	1	174	178	11.9999
))))	chr11:62415546-62415786(-)$1	1	138	142	11.9999
((((	chr2:73678933-73679173(+)$1	1	131	135	11.9999
....	chr3:13417744-13417984(-)$1	1	46	50	11.9999
))))	chr5:172197753-172197993(-)$1	1	130	134	11.9999
..))	chr15:49301327-49301567(-)$1	1	19	23	11.9999
((((	chr4:76890369-76890609(-)$1	1	33	37	11.9999
))))	chr1:207222720-207222960(-)$1	1	133	137	11.9999
((((	chr2:220088225-220088465(-)$1	1	32	36	11.9999
))))	chr20:31024222-31024462(+)$1	1	232	236	11.9999
....	chr5:55236993-55237233(-)$1	1	8	12	11.9999
....	chr11:10821709-10821949(-)$1	1	212	216	11.9999
)...	chr22:50356329-50356569(+)$1	1	90	94	11.9999
))))	chr14:104026829-104027069(-)$1	1	79	83	11.9999
...)	chr4:39457936-39458176(-)$1	1	20	24	11.9999
(((.	chr10:129903706-129903946(-)$1	1	76	80	11.9999
((((	chr22:24236936-24237176(+)$1	1	60	64	11.9999
.)))	chr17:27613749-27613989(-)$1	1	95	99	11.9999
((..	chr11:118375798-118376038(+)$1	1	97	101	11.9999
..))	chr6:64421568-64421808(+)$1	1	164	168	11.9999
((..	chr2:192280786-192281026(+)$1	1	6	10	11.9999
((.(	chr20:32659808-32660048(+)$1	1	38	42	11.9999
((((	chr4:39924207-39924469(-)$1	1	53	57	11.9999
.)))	chr7:99091615-99091855(-)$1	1	199	203	11.9999
..))	chr10:74034461-74034701(+)$1	1	25	29	11.9999
....	chr3:20113780-20114020(+)$1	1	185	189	11.9999
(.((	chr17:37046607-37046847(+)$1	1	83	87	11.9999
.(((	chr8:134270515-134270755(-)$1	1	79	83	11.9999

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

#score	959.9999999999994
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m3_run1.nuc.txt

#NT
GGAG	chr1:120457315-120457553(-)$1	238	228	232	11.9999
GGAG	chr14:75585468-75585709(-)$1	241	123	127	11.9999
GGAG	chr19:47712804-47713034(+)$1	230	46	50	11.9999
GGAG	chr11:118967417-118967640(+)$1	223	47	51	11.9999
GGAG	chr17:47865978-47866223(+)$1	245	91	95	11.9999
GGAG	chr10:43633856-43634081(+)$1	225	127	131	11.9999
GGAG	chr10:121337074-121337304(-)$1	230	127	131	11.9999
ggag	chr2:37327319-37327575(-)$1	256	88	92	11.9999
GGAG	chr4:109740870-109741098(-)$1	228	82	86	11.9999
GGAG	chr16:74506164-74506394(-)$1	230	161	165	11.9999
GGAG	chr16:1839029-1839262(+)$1	233	65	69	11.9999
GGAG	chr5:174156643-174156873(+)$1	230	114	118	11.9999
GGAG	chr19:50983859-50984090(+)$1	231	94	98	11.9999
ggag	chr10:101948159-101948388(-)$1	229	19	23	11.9999
GGAG	chr7:143599128-143599356(-)$1	228	143	147	11.9999
ggag	chr14:100605174-100605399(+)$1	225	6	10	11.9999
GGAG	chr1:225590748-225590988(-)$1	240	120	124	11.9999
GGAG	chr22:24237201-24237481(+)$1	280	184	188	11.9999
GGAG	chr20:57466553-57466798(+)$1	245	3	7	11.9999
GGAG	chr20:32077896-32078120(+)$1	224	192	196	11.9999
GGAG	chr17:1438634-1438861(-)$1	227	187	191	11.9999
GGAG	chr21:42879984-42880206(+)$1	222	135	139	11.9999
GGAG	chr17:36760750-36760976(-)$1	226	165	169	11.9999
GGAG	chr22:21982470-21982736(-)$1	266	76	80	11.9999
GGAG	chr11:6498099-6498334(-)$1	235	53	57	11.9999
GGAG	chr1:55207361-55207595(+)$1	234	132	136	11.9999
GGAG	chr18:70211647-70211869(+)$1	222	27	31	11.9999
GGAG	chr11:47544738-47544970(-)$1	232	124	128	11.9999
GGAG	chr17:62496295-62496530(-)$1	235	103	107	11.9999
GGAG	chr7:148700119-148700354(-)$1	235	52	56	11.9999
GGAG	chr11:111808055-111808294(+)$1	239	57	61	11.9999
GGAG	chr11:111930548-111930782(+)$1	234	160	164	11.9999
GGAG	chr5:154196742-154196972(+)$1	230	119	123	11.9999
GGAG	chr1:148346850-148347081(-)$1	231	164	168	11.9999
GGAG	chr12:120648912-120649142(-)$1	230	145	149	11.9999
GGAG	chr22:37098808-37099035(+)$1	227	195	199	11.9999
GGAG	chr8:103666166-103666388(+)$1	222	161	165	11.9999
GGAG	chr3:184019292-184019520(+)$1	228	79	83	11.9999
GGAG	chr6:52128836-52129073(-)$1	237	109	113	11.9999
GGAG	chr8:97343157-97343387(+)$1	230	1	5	11.9999
GGAG	chr8:101322354-101322577(+)$1	223	158	162	11.9999
GGAG	chr6:44922193-44922428(-)$1	235	130	134	11.9999
GGAG	chr6:26204749-26205025(+)$1	276	162	166	11.9999
GGAG	chr6:36076564-36076805(+)$1	241	100	104	11.9999
ggag	chr1:201852292-201852523(+)$1	231	168	172	11.9999
GGAG	chr3:42591225-42591455(-)$1	230	46	50	11.9999
GGAG	chr22:50956069-50956305(+)$1	236	5	9	11.9999
GGAG	chr14:105267290-105267514(+)$1	224	47	51	11.9999
GGAG	chrX:48380533-48380760(+)$1	227	73	77	11.9999
GGAG	chr12:50263245-50263467(-)$1	222	93	97	11.9999
GGAG	chr12:66359190-66359442(+)$1	252	87	91	11.9999
GGAG	chr15:89740730-89740960(+)$1	230	196	200	11.9999
GGAG	chr7:135322608-135322851(+)$1	243	147	151	11.9999
GGAG	chr1:157092904-157093133(-)$1	229	25	29	11.9999
GGAG	chr4:1207261-1207493(-)$1	232	193	197	11.9999
GGAG	chr9:84303905-84304130(-)$1	225	17	21	11.9999
GGAG	chr11:64889513-64889747(-)$1	234	34	38	11.9999
GGAG	chr16:30566270-30566506(-)$1	236	23	27	11.9999
GGAG	chr7:6443293-6443558(+)$1	265	224	228	11.9999
GGAG	chr7:151807566-151807795(+)$1	229	62	66	11.9999
ggag	chr17:9145036-9145264(+)$1	228	55	59	11.9999
ggag	chr11:129992220-129992464(+)$1	244	57	61	11.9999
GGAG	chr1:151584573-151584803(+)$1	230	54	58	11.9999
GGAG	chr12:70824482-70824710(+)$1	228	37	41	11.9999
GGAG	chr12:54629442-54629675(-)$1	233	107	111	11.9999
GGAG	chr12:51664255-51664481(+)$1	226	30	34	11.9999
GGAG	chr19:11561620-11561864(+)$1	244	23	27	11.9999
GGAG	chr14:102551574-102551820(-)$1	246	116	120	11.9999
GGAG	chr1:205719097-205719373(-)$1	276	83	87	11.9999
GGAG	chr12:57905988-57906220(+)$1	232	102	106	11.9999

#otherMatches

#Struct PSSM
ff##	chr17:42276446-42276672(-)$1	226	38	42	11.9999
CCCY	chr1:120457315-120457553(-)$1	238	228	232	11.9999
eebb	chr14:75585468-75585709(-)$1	241	123	127	11.9999
c[bb	chr19:47712804-47713034(+)$1	230	46	50	11.9999
dd]a	chr11:118967417-118967640(+)$1	223	47	51	11.9999
bb[c	chr17:47865978-47866223(+)$1	245	91	95	11.9999
dddd	chr10:43633856-43634081(+)$1	225	127	131	11.9999
EEEE	chr10:121337074-121337304(-)$1	230	127	131	11.9999
c[bb	chr2:37327319-37327575(-)$1	256	88	92	11.9999
DDEE	chr4:109740870-109741098(-)$1	228	82	86	11.9999
HHHH	chr16:74506164-74506394(-)$1	230	161	165	11.9999
JJJ{	chr16:1839029-1839262(+)$1	233	65	69	11.9999
GGGG	chr5:174156643-174156873(+)$1	230	114	118	11.9999
ee$$	chr19:50983859-50984090(+)$1	231	94	98	11.9999
E:::	chr10:101948159-101948388(-)$1	229	19	23	11.9999
IIII	chr7:143599128-143599356(-)$1	228	143	147	11.9999
qqqq	chr14:100605174-100605399(+)$1	225	6	10	11.9999
DDDB	chr1:225590748-225590988(-)$1	240	120	124	11.9999
ee00	chr22:24237201-24237481(+)$1	280	184	188	11.9999
dd[b	chr20:57466553-57466798(+)$1	245	3	7	11.9999
CYYB	chr20:32077896-32078120(+)$1	224	192	196	11.9999
FFFF	chr17:1438634-1438861(-)$1	227	187	191	11.9999
qggg	chr21:42879984-42880206(+)$1	222	135	139	11.9999
qqqq	chr17:36760750-36760976(-)$1	226	165	169	11.9999
gggh	chr22:21982470-21982736(-)$1	266	76	80	11.9999
GGGG	chr11:6498099-6498334(-)$1	235	53	57	11.9999
ffff	chr1:55207361-55207595(+)$1	234	132	136	11.9999
!!cc	chr18:70211647-70211869(+)$1	222	27	31	11.9999
httt	chr11:47544738-47544970(-)$1	232	124	128	11.9999
pppp	chr17:62496295-62496530(-)$1	235	103	107	11.9999
b22c	chr7:148700119-148700354(-)$1	235	52	56	11.9999
EE{C	chr11:111808055-111808294(+)$1	239	57	61	11.9999
HHHd	chr11:111930548-111930782(+)$1	234	160	164	11.9999
bb]d	chr5:154196742-154196972(+)$1	230	119	123	11.9999
====	chr1:148346850-148347081(-)$1	231	164	168	11.9999
GGGG	chr12:120648912-120649142(-)$1	230	145	149	11.9999
gggg	chr22:37098808-37099035(+)$1	227	195	199	11.9999
]a]c	chr8:103666166-103666388(+)$1	222	161	165	11.9999
iii2	chr3:184019292-184019520(+)$1	228	79	83	11.9999
====	chr6:52128836-52129073(-)$1	237	109	113	11.9999
ffff	chr8:97343157-97343387(+)$1	230	1	5	11.9999
gggg	chr8:101322354-101322577(+)$1	223	158	162	11.9999
]eee	chr6:44922193-44922428(-)$1	235	130	134	11.9999
bb[e	chr6:26204749-26205025(+)$1	276	162	166	11.9999
DD::	chr6:36076564-36076805(+)$1	241	100	104	11.9999
gggg	chr1:201852292-201852523(+)$1	231	168	172	11.9999
eeee	chr3:42591225-42591455(-)$1	230	46	50	11.9999
d!!e	chr22:50956069-50956305(+)$1	236	5	9	11.9999
IIII	chr14:105267290-105267514(+)$1	224	47	51	11.9999
gggg	chrX:48380533-48380760(+)$1	227	73	77	11.9999
eeee	chr12:50263245-50263467(-)$1	222	93	97	11.9999
====	chr12:66359190-66359442(+)$1	252	87	91	11.9999
~~~D	chr15:89740730-89740960(+)$1	230	196	200	11.9999
!!at	chr7:135322608-135322851(+)$1	243	147	151	11.9999
DDDD	chr1:157092904-157093133(-)$1	229	25	29	11.9999
EEEE	chr4:1207261-1207493(-)$1	232	193	197	11.9999
oooo	chr9:84303905-84304130(-)$1	225	17	21	11.9999
EEEE	chr11:64889513-64889747(-)$1	234	34	38	11.9999
CC:C	chr16:30566270-30566506(-)$1	236	23	27	11.9999
%%ee	chr7:6443293-6443558(+)$1	265	224	228	11.9999
gggg	chr7:151807566-151807795(+)$1	229	62	66	11.9999
bb]b	chr17:9145036-9145264(+)$1	228	55	59	11.9999
eeee	chr11:129992220-129992464(+)$1	244	57	61	11.9999
ff]f	chr1:151584573-151584803(+)$1	230	54	58	11.9999
hhhh	chr12:70824482-70824710(+)$1	228	37	41	11.9999
sfff	chr12:54629442-54629675(-)$1	233	107	111	11.9999
dddd	chr12:51664255-51664481(+)$1	226	30	34	11.9999
FFFF	chr19:11561620-11561864(+)$1	244	23	27	11.9999
cc[b	chr14:102551574-102551820(-)$1	246	116	120	11.9999
ICCC	chr1:205719097-205719373(-)$1	276	83	87	11.9999
qddd	chr12:57905988-57906220(+)$1	232	102	106	11.9999

#DB
((..	chr17:42276446-42276672(-)$1	1	38	42	11.9999
))).	chr1:120457315-120457553(-)$1	1	228	232	11.9999
))((	chr14:75585468-75585709(-)$1	1	123	127	11.9999
(.((	chr19:47712804-47713034(+)$1	1	46	50	11.9999
)).)	chr11:118967417-118967640(+)$1	1	47	51	11.9999
((.(	chr17:47865978-47866223(+)$1	1	91	95	11.9999
((((	chr10:43633856-43634081(+)$1	1	127	131	11.9999
((((	chr10:121337074-121337304(-)$1	1	127	131	11.9999
(.((	chr2:37327319-37327575(-)$1	1	88	92	11.9999
))((	chr4:109740870-109741098(-)$1	1	82	86	11.9999
))))	chr16:74506164-74506394(-)$1	1	161	165	11.9999
(((.	chr16:1839029-1839262(+)$1	1	65	69	11.9999
))))	chr5:174156643-174156873(+)$1	1	114	118	11.9999
((..	chr19:50983859-50984090(+)$1	1	94	98	11.9999
(...	chr10:101948159-101948388(-)$1	1	19	23	11.9999
))))	chr7:143599128-143599356(-)$1	1	143	147	11.9999
....	chr14:100605174-100605399(+)$1	1	6	10	11.9999
))))	chr1:225590748-225590988(-)$1	1	120	124	11.9999
))..	chr22:24237201-24237481(+)$1	1	184	188	11.9999
((.(	chr20:57466553-57466798(+)$1	1	3	7	11.9999
)..)	chr20:32077896-32078120(+)$1	1	192	196	11.9999
))))	chr17:1438634-1438861(-)$1	1	187	191	11.9999
.)))	chr21:42879984-42880206(+)$1	1	135	139	11.9999
....	chr17:36760750-36760976(-)$1	1	165	169	11.9999
)))(	chr22:21982470-21982736(-)$1	1	76	80	11.9999
((((	chr11:6498099-6498334(-)$1	1	53	57	11.9999
))))	chr1:55207361-55207595(+)$1	1	132	136	11.9999
..((	chr18:70211647-70211869(+)$1	1	27	31	11.9999
(...	chr11:47544738-47544970(-)$1	1	124	128	11.9999
....	chr17:62496295-62496530(-)$1	1	103	107	11.9999
)..)	chr7:148700119-148700354(-)$1	1	52	56	11.9999
((.(	chr11:111808055-111808294(+)$1	1	57	61	11.9999
)))(	chr11:111930548-111930782(+)$1	1	160	164	11.9999
)).)	chr5:154196742-154196972(+)$1	1	119	123	11.9999
((((	chr1:148346850-148347081(-)$1	1	164	168	11.9999
))))	chr12:120648912-120649142(-)$1	1	145	149	11.9999
))))	chr22:37098808-37099035(+)$1	1	195	199	11.9999
.).)	chr8:103666166-103666388(+)$1	1	161	165	11.9999
))).	chr3:184019292-184019520(+)$1	1	79	83	11.9999
))))	chr6:52128836-52129073(-)$1	1	109	113	11.9999
((((	chr8:97343157-97343387(+)$1	1	1	5	11.9999
))))	chr8:101322354-101322577(+)$1	1	158	162	11.9999
.)))	chr6:44922193-44922428(-)$1	1	130	134	11.9999
((.(	chr6:26204749-26205025(+)$1	1	162	166	11.9999
((..	chr6:36076564-36076805(+)$1	1	100	104	11.9999
))))	chr1:201852292-201852523(+)$1	1	168	172	11.9999
((((	chr3:42591225-42591455(-)$1	1	46	50	11.9999
(..(	chr22:50956069-50956305(+)$1	1	5	9	11.9999
))))	chr14:105267290-105267514(+)$1	1	47	51	11.9999
((((	chrX:48380533-48380760(+)$1	1	73	77	11.9999
))))	chr12:50263245-50263467(-)$1	1	93	97	11.9999
((((	chr12:66359190-66359442(+)$1	1	87	91	11.9999
...)	chr15:89740730-89740960(+)$1	1	196	200	11.9999
..(.	chr7:135322608-135322851(+)$1	1	147	151	11.9999
((((	chr1:157092904-157093133(-)$1	1	25	29	11.9999
))))	chr4:1207261-1207493(-)$1	1	193	197	11.9999
....	chr9:84303905-84304130(-)$1	1	17	21	11.9999
((((	chr11:64889513-64889747(-)$1	1	34	38	11.9999
((.(	chr16:30566270-30566506(-)$1	1	23	27	11.9999
..((	chr7:6443293-6443558(+)$1	1	224	228	11.9999
((((	chr7:151807566-151807795(+)$1	1	62	66	11.9999
)).)	chr17:9145036-9145264(+)$1	1	55	59	11.9999
((((	chr11:129992220-129992464(+)$1	1	57	61	11.9999
)).)	chr1:151584573-151584803(+)$1	1	54	58	11.9999
))))	chr12:70824482-70824710(+)$1	1	37	41	11.9999
.)))	chr12:54629442-54629675(-)$1	1	107	111	11.9999
))))	chr12:51664255-51664481(+)$1	1	30	34	11.9999
((((	chr19:11561620-11561864(+)$1	1	23	27	11.9999
((.(	chr14:102551574-102551820(-)$1	1	116	120	11.9999
((((	chr1:205719097-205719373(-)$1	1	83	87	11.9999
.)))	chr12:57905988-57906220(+)$1	1	102	106	11.9999

#PSSM
G : 0.90	g : 0.09	
G : 0.90	g : 0.09	
A : 0.90	a : 0.09	
G : 0.90	g : 0.09	

#score	851.9999999999999
#seq	71
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m2_run1.nuc.txt

#NT
UUUUUUUU	chr2:5835498-5835782(+)$1	284	199	207	16.7777
UUUUUUCA	chr3:196556573-196556809(+)$1	236	53	61	15.2962
UUUCUUUA	chr15:77242065-77242305(+)$1	240	194	202	16.0370
UUUUCUUA	chr4:134111225-134111464(+)$1	239	37	45	15.7592
UUUUUUUA	chr1:204374518-204374766(-)$1	248	11	19	20.0185
UUUUUGUA	chr22:39260294-39260575(-)$1	281	246	254	15.3888
UUUGUUUA	chr1:179814989-179815214(-)$1	225	55	63	16.0370
GUUUUUUA	chr5:67595473-67595697(+)$1	224	59	67	15.8518
UUGUUUUA	chr11:113668505-113668736(-)$1	231	132	140	15.3888
UUUUUUUA	chr11:69468109-69468375(+)$1	266	85	93	20.0185
UUUUUUGA	chr7:156765538-156765779(+)$1	241	108	116	15.2962
UUUGUUUA	chr17:79477327-79477594(-)$1	267	93	101	16.0370
UUUCUUUA	chr11:102267488-102267717(-)$1	229	107	115	16.0370
AUUUUUUA	chr11:18630222-18630474(-)$1	252	6	14	15.9444
UUUGUUUA	chr5:10434800-10435021(+)$1	221	107	115	16.0370
uuuuuuua	chr13:76100506-76100736(-)$1	230	131	139	20.0185
UUUUUUUC	chr20:5171430-5171656(+)$1	226	76	84	16.5925
UUUUGUUA	chr1:162494352-162494606(+)$1	254	239	247	15.5740
auuuuuua	chr11:35642225-35642468(+)$1	243	67	75	15.9444
uuuuuuua	chr1:203276654-203276924(+)$1	270	29	37	20.0185
GUUUUUUA	chr11:115046669-115046925(-)$1	256	185	193	15.8518
UUUUUUUU	chr13:47326952-47327186(+)$1	234	42	50	16.7777
UUUUCUUA	chr1:205684301-205684572(-)$1	271	244	252	15.7592
UUUUUUUU	chr6:111650787-111651015(-)$1	228	55	63	16.7777
UUUUUUUU	chr3:128533093-128533314(+)$1	221	161	169	16.7777
UUUUUUUG	chr4:146056900-146057142(-)$1	242	7	15	16.4999
CUUUUUUA	chr8:128753188-128753460(+)$1	272	186	194	15.8518
UAUUUUUA	chr1:94354107-94354331(-)$1	224	52	60	15.5740
UUUUUUUA	chr11:9610505-9610748(+)$1	243	83	91	20.0185
UUGUUUUA	chr1:35649494-35649727(-)$1	233	164	172	15.3888
UUUUUUUU	chr17:73132002-73132264(-)$1	262	194	202	16.7777
UUUUUUUC	chr4:166419176-166419411(+)$1	235	49	57	16.5925
uuuuuuuu	chr19:18390849-18391113(-)$1	264	236	244	16.7777
UUUUUUUC	chr4:15070824-15071077(+)$1	253	180	188	16.5925
UUUUUUUC	chr1:85112855-85113123(-)$1	268	23	31	16.5925
uuuuuuua	chr1:226170512-226170737(-)$1	225	57	65	20.0185
UUUUUUUA	chr12:12874891-12875146(+)$1	255	196	204	20.0185
UGuuuuua	chr1:244219582-244219815(+)$1	233	27	35	15.4814
UUUUUUUA	chr1:85717990-85718215(-)$1	225	61	69	20.0185
UAUUUUUA	chr12:19672990-19673226(+)$1	236	65	73	15.5740
UCUUUUUA	chr3:33431359-33431593(-)$1	234	82	90	15.4814
CUUUUUUA	chr1:27181053-27181292(+)$1	239	147	155	15.8518
UUUUUUUA	chr5:137088527-137088777(-)$1	250	190	198	20.0185
UUUUCUUA	chr8:103839533-103839782(-)$1	249	198	206	15.7592
UUUAUUUA	chr8:37556154-37556407(+)$1	253	182	190	15.9444
uuuuuuuA	chr19:1257361-1257663(+)$1	302	67	75	20.0185
UUUUAUUA	chr4:141302480-141302705(+)$1	225	65	73	15.5740
UUUCUUUA	chr4:141302156-141302418(+)$1	262	146	154	16.0370
UUUAUUUA	chr1:205682671-205682908(-)$1	237	130	138	15.9444
UUUUUUUG	chr8:42273982-42274243(-)$1	261	90	98	16.4999
UUUUUUUG	chr17:27584729-27584992(-)$1	263	73	81	16.4999
AUUUUUUA	chr10:74035579-74035801(+)$1	222	178	186	15.9444
UUUUUGUA	chr6:31797535-31797824(+)$1	289	270	278	15.3888

#otherMatches

#Struct PSSM
[ffffffm	chr6:82950391-82950622(-)$1	231	173	181	20.0185
JJJJJJJJ	chr2:5835498-5835782(+)$1	284	199	207	16.7777
ooooooag	chr3:196556573-196556809(+)$1	236	53	61	15.2962
xxxxxxxx	chr15:77242065-77242305(+)$1	240	194	202	16.0370
eee22ggg	chr4:134111225-134111464(+)$1	239	37	45	15.7592
::::::::	chr1:204374518-204374766(-)$1	248	11	19	20.0185
====mmmm	chr22:39260294-39260575(-)$1	281	246	254	15.3888
II::::::	chr1:179814989-179815214(-)$1	225	55	63	16.0370
h:::::::	chr5:67595473-67595697(+)$1	224	59	67	15.8518
e22ccc22	chr11:113668505-113668736(-)$1	231	132	140	15.3888
++++++++	chr11:69468109-69468375(+)$1	266	85	93	20.0185
ff22ccc2	chr7:156765538-156765779(+)$1	241	108	116	15.2962
:::::JJJ	chr17:79477327-79477594(-)$1	267	93	101	16.0370
::gggggg	chr11:102267488-102267717(-)$1	229	107	115	16.0370
dddd[eee	chr11:18630222-18630474(-)$1	252	6	14	15.9444
hhhhhhhl	chr5:10434800-10435021(+)$1	221	107	115	16.0370
"eeeeeqq	chr13:76100506-76100736(-)$1	230	131	139	20.0185
========	chr20:5171430-5171656(+)$1	226	76	84	16.5925
E}DDDD~~	chr1:162494352-162494606(+)$1	254	239	247	15.5740
tttttttg	chr11:35642225-35642468(+)$1	243	67	75	15.9444
========	chr1:203276654-203276924(+)$1	270	29	37	20.0185
}A::::::	chr11:115046669-115046925(-)$1	256	185	193	15.8518
[cccrrrr	chr13:47326952-47327186(+)$1	234	42	50	16.7777
::::::::	chr1:205684301-205684572(-)$1	271	244	252	15.7592
==::gggg	chr6:111650787-111651015(-)$1	228	55	63	16.7777
::::::::	chr3:128533093-128533314(+)$1	221	161	169	16.7777
ff$$$$$d	chr4:146056900-146057142(-)$1	242	7	15	16.4999
mm======	chr8:128753188-128753460(+)$1	272	186	194	15.8518
[dddd[cc	chr1:94354107-94354331(-)$1	224	52	60	15.5740
cccsssss	chr11:9610505-9610748(+)$1	243	83	91	20.0185
ddpppppp	chr1:35649494-35649727(-)$1	233	164	172	15.3888
\\\\\\\\	chr17:73132002-73132264(-)$1	262	194	202	16.7777
xxxxxxxx	chr4:166419176-166419411(+)$1	235	49	57	16.5925
::::::ii	chr19:18390849-18391113(-)$1	264	236	244	16.7777
wwwwwwww	chr4:15070824-15071077(+)$1	253	180	188	16.5925
mmmmeeee	chr1:85112855-85113123(-)$1	268	23	31	16.5925
qqqqqeee	chr1:226170512-226170737(-)$1	225	57	65	20.0185
hhhhh:::	chr12:12874891-12875146(+)$1	255	196	204	20.0185
:=======	chr1:244219582-244219815(+)$1	233	27	35	15.4814
ooofffff	chr1:85717990-85718215(-)$1	225	61	69	20.0185
========	chr12:19672990-19673226(+)$1	236	65	73	15.5740
]eeeee33	chr3:33431359-33431593(-)$1	234	82	90	15.4814
^^^^^^^^	chr1:27181053-27181292(+)$1	239	147	155	15.8518
::::::::	chr5:137088527-137088777(-)$1	250	190	198	20.0185
=======[	chr8:103839533-103839782(-)$1	249	198	206	15.7592
=====(((	chr8:37556154-37556407(+)$1	253	182	190	15.9444
::::::::	chr19:1257361-1257663(+)$1	302	67	75	20.0185
b4444ggg	chr4:141302480-141302705(+)$1	225	65	73	15.5740
zdddd]ff	chr4:141302156-141302418(+)$1	262	146	154	16.0370
========	chr1:205682671-205682908(-)$1	237	130	138	15.9444
=======q	chr8:42273982-42274243(-)$1	261	90	98	16.4999
========	chr17:27584729-27584992(-)$1	263	73	81	16.4999
>>>>>>ii	chr10:74035579-74035801(+)$1	222	178	186	15.9444
::::::::	chr6:31797535-31797824(+)$1	289	270	278	15.3888

#DB
.((((((.	chr6:82950391-82950622(-)$1	1	173	181	20.0185
))))))))	chr2:5835498-5835782(+)$1	1	199	207	16.7777
......))	chr3:196556573-196556809(+)$1	1	53	61	15.2962
........	chr15:77242065-77242305(+)$1	1	194	202	16.0370
)))..)))	chr4:134111225-134111464(+)$1	1	37	45	15.7592
........	chr1:204374518-204374766(-)$1	1	11	19	20.0185
((((....	chr22:39260294-39260575(-)$1	1	246	254	15.3888
((......	chr1:179814989-179815214(-)$1	1	55	63	16.0370
).......	chr5:67595473-67595697(+)$1	1	59	67	15.8518
)..)))..	chr11:113668505-113668736(-)$1	1	132	140	15.3888
........	chr11:69468109-69468375(+)$1	1	85	93	20.0185
))..))).	chr7:156765538-156765779(+)$1	1	108	116	15.2962
.....(((	chr17:79477327-79477594(-)$1	1	93	101	16.0370
..((((((	chr11:102267488-102267717(-)$1	1	107	115	16.0370
((((.(((	chr11:18630222-18630474(-)$1	1	6	14	15.9444
(((((((.	chr5:10434800-10435021(+)$1	1	107	115	16.0370
.(((((..	chr13:76100506-76100736(-)$1	1	131	139	20.0185
((((((((	chr20:5171430-5171656(+)$1	1	76	84	16.5925
).))))..	chr1:162494352-162494606(+)$1	1	239	247	15.5740
.......)	chr11:35642225-35642468(+)$1	1	67	75	15.9444
((((((((	chr1:203276654-203276924(+)$1	1	29	37	20.0185
.)......	chr11:115046669-115046925(-)$1	1	185	193	15.8518
.(((....	chr13:47326952-47327186(+)$1	1	42	50	16.7777
........	chr1:205684301-205684572(-)$1	1	244	252	15.7592
))..((((	chr6:111650787-111651015(-)$1	1	55	63	16.7777
........	chr3:128533093-128533314(+)$1	1	161	169	16.7777
((.....(	chr4:146056900-146057142(-)$1	1	7	15	16.4999
..))))))	chr8:128753188-128753460(+)$1	1	186	194	15.8518
.((((.((	chr1:94354107-94354331(-)$1	1	52	60	15.5740
(((.....	chr11:9610505-9610748(+)$1	1	83	91	20.0185
((......	chr1:35649494-35649727(-)$1	1	164	172	15.3888
........	chr17:73132002-73132264(-)$1	1	194	202	16.7777
........	chr4:166419176-166419411(+)$1	1	49	57	16.5925
......((	chr19:18390849-18391113(-)$1	1	236	244	16.7777
........	chr4:15070824-15071077(+)$1	1	180	188	16.5925
....))))	chr1:85112855-85113123(-)$1	1	23	31	16.5925
.....)))	chr1:226170512-226170737(-)$1	1	57	65	20.0185
)))))...	chr12:12874891-12875146(+)$1	1	196	204	20.0185
.(((((((	chr1:244219582-244219815(+)$1	1	27	35	15.4814
...)))))	chr1:85717990-85718215(-)$1	1	61	69	20.0185
))))))))	chr12:19672990-19673226(+)$1	1	65	73	15.5740
.)))))..	chr3:33431359-33431593(-)$1	1	82	90	15.4814
........	chr1:27181053-27181292(+)$1	1	147	155	15.8518
........	chr5:137088527-137088777(-)$1	1	190	198	20.0185
(((((((.	chr8:103839533-103839782(-)$1	1	198	206	15.7592
(((((...	chr8:37556154-37556407(+)$1	1	182	190	15.9444
........	chr19:1257361-1257663(+)$1	1	67	75	20.0185
)....)))	chr4:141302480-141302705(+)$1	1	65	73	15.5740
.)))).))	chr4:141302156-141302418(+)$1	1	146	154	16.0370
((((((((	chr1:205682671-205682908(-)$1	1	130	138	15.9444
(((((((.	chr8:42273982-42274243(-)$1	1	90	98	16.4999
((((((((	chr17:27584729-27584992(-)$1	1	73	81	16.4999
......))	chr10:74035579-74035801(+)$1	1	178	186	15.9444
........	chr6:31797535-31797824(+)$1	1	270	278	15.3888

#PSSM
U : 0.77	u : 0.09	G : 0.03	A : 0.03	C : 0.03	a : 0.01	
U : 0.81	u : 0.11	A : 0.03	G : 0.01	C : 0.01	
U : 0.83	u : 0.12	G : 0.03	
U : 0.72	u : 0.12	C : 0.05	G : 0.05	A : 0.03	
U : 0.77	u : 0.12	C : 0.05	G : 0.01	A : 0.01	
U : 0.83	u : 0.12	G : 0.03	
U : 0.83	u : 0.12	C : 0.01	G : 0.01	
A : 0.66	U : 0.09	a : 0.09	C : 0.07	G : 0.05	u : 0.01	

#score	908.7777777777771
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m2_run2.nuc.txt

#NT
UGG	chr12:67691103-67691383(+)$1	280	26	29	9.0000
UGG	chrX:134683490-134683730(+)$1	240	0	3	9.0000
UGG	chr22:42089445-42089685(+)$1	240	98	101	9.0000
UGG	chrX:102471291-102471531(+)$1	240	52	55	9.0000
UGG	chr16:87445638-87445878(-)$1	240	40	43	9.0000
UGG	chr17:2221146-2221386(+)$1	240	22	25	9.0000
UGG	chr15:25601014-25601254(-)$1	240	18	21	9.0000
UGG	chr3:169863129-169863369(-)$1	240	8	11	9.0000
UGG	chr14:24702622-24702862(+)$1	240	10	13	9.0000
UGG	chr17:30796033-30796273(+)$1	240	13	16	9.0000
UGG	chr17:37627471-37627711(+)$1	240	61	64	9.0000
UGG	chr3:53259694-53259934(-)$1	240	20	23	9.0000
UGG	chr4:83802957-83803197(-)$1	240	9	12	9.0000
UGG	chr12:117593611-117593851(-)$1	240	42	45	9.0000
UGG	chr4:42072489-42072729(+)$1	240	83	86	9.0000
UGG	chr19:8550535-8550775(+)$1	240	23	26	9.0000
UGG	chr7:36396536-36396776(-)$1	240	20	23	9.0000
UGG	chr10:70742192-70742432(+)$1	240	24	27	9.0000
UGG	chr17:46673878-46674118(-)$1	240	38	41	9.0000
UGG	chr10:28899597-28899837(+)$1	240	91	94	9.0000
UGG	chr2:219618990-219619230(+)$1	240	46	49	9.0000
UGG	chr7:23180328-23180568(+)$1	240	8	11	9.0000
UGG	chr19:39390709-39390949(+)$1	240	8	11	9.0000
UGG	chr3:8990102-8990342(-)$1	240	148	151	9.0000
UGG	chr16:74501576-74501816(-)$1	240	54	57	9.0000
UGG	chr17:42475014-42475254(-)$1	240	90	93	9.0000
UGG	chr3:44489086-44489326(-)$1	240	69	72	9.0000
UGG	chr10:5790037-5790277(+)$1	240	31	34	9.0000
UGG	chr2:103334766-103335006(-)$1	240	33	36	9.0000
UGG	chr14:50319356-50319596(-)$1	240	11	14	9.0000
UGG	chr22:40657995-40658235(+)$1	240	45	48	9.0000
UGG	chr14:71064244-71064484(-)$1	240	10	13	9.0000
UGG	chr6:33423363-33423603(+)$1	240	18	21	9.0000
UGG	chr1:24786888-24787128(+)$1	240	24	27	9.0000
UGG	chr7:133160087-133160327(+)$1	240	13	16	9.0000
UGG	chr7:26236924-26237164(-)$1	240	72	75	9.0000
UGG	chr15:52662449-52662689(-)$1	240	6	9	9.0000
UGG	chr14:93170405-93170645(-)$1	240	46	49	9.0000
UGG	chr3:196612416-196612656(+)$1	240	94	97	9.0000
UGG	chr21:34925817-34926057(+)$1	240	113	116	9.0000
UGG	chr19:49518743-49518983(+)$1	240	6	9	9.0000
UGG	chr15:38776736-38776976(+)$1	240	0	3	9.0000
UGG	chr19:23835956-23836196(-)$1	240	0	3	9.0000
UGG	chr17:19186294-19186534(+)$1	240	234	237	9.0000
UGG	chr6:151686744-151686984(-)$1	240	42	45	9.0000
UGG	chrX:122831438-122831678(-)$1	240	27	30	9.0000
UGG	chr15:75498395-75498675(+)$1	280	22	25	9.0000
UGG	chr19:3980490-3980730(-)$1	240	74	77	9.0000
UGG	chr2:27551327-27551567(-)$1	240	122	125	9.0000
UGG	chr22:42608499-42608739(-)$1	240	81	84	9.0000
UGG	chr16:31193752-31193992(+)$1	240	5	8	9.0000
UGG	chr1:242042119-242042359(+)$1	240	42	45	9.0000
UGG	chr20:3766449-3766689(-)$1	240	53	56	9.0000
UGG	chr11:64022607-64022847(+)$1	240	26	29	9.0000
UGG	chr20:17930884-17931124(-)$1	240	60	63	9.0000
UGG	chr10:32573645-32573885(-)$1	240	91	94	9.0000
UGG	chr2:110259131-110259371(+)$1	240	45	48	9.0000
UGG	chr14:75471380-75471620(+)$1	240	68	71	9.0000
UGG	chr20:18534813-18535053(+)$1	240	43	46	9.0000
UGG	chr19:33604593-33604833(+)$1	240	8	11	9.0000
UGG	chr2:153616160-153616400(+)$1	240	37	40	9.0000
UGG	chr19:35434231-35434471(+)$1	240	13	16	9.0000
UGG	chr6:74304638-74304918(-)$1	280	37	40	9.0000
UGG	chr1:226558034-226558274(-)$1	240	78	81	9.0000
UGG	chr12:2064506-2064746(-)$1	240	233	236	9.0000
UGG	chr17:80047054-80047294(-)$1	240	53	56	9.0000
UGG	chr6:70500145-70500385(-)$1	240	28	31	9.0000
UGG	chr19:45801062-45801302(+)$1	240	15	18	9.0000
UGG	chr19:23836191-23836431(-)$1	240	37	40	9.0000
UGG	chr5:6743802-6744042(+)$1	240	10	13	9.0000
UGG	chr2:178301437-178301677(+)$1	240	173	176	9.0000
UGG	chr1:16256668-16256908(+)$1	240	25	28	9.0000
UGG	chr1:54502251-54502491(-)$1	240	106	109	9.0000
UGG	chr5:14290942-14291182(+)$1	240	42	45	9.0000
UGG	chr10:120832964-120833373(-)$1	409	1	4	9.0000
UGG	chrX:128724125-128724365(+)$1	240	42	45	9.0000
UGG	chr4:13604996-13605236(-)$1	240	36	39	9.0000
UGG	chr3:41277189-41277429(+)$1	240	19	22	9.0000
UGG	chr14:21876480-21876720(-)$1	240	20	23	9.0000
UGG	chr3:40529628-40529868(+)$1	240	55	58	9.0000
UGG	chr2:11427682-11427922(-)$1	240	15	18	9.0000
UGG	chr5:88056904-88057144(-)$1	240	22	25	9.0000
UGG	chr16:29998798-29999038(+)$1	240	47	50	9.0000
ugG	chr17:57728515-57728755(+)$1	240	65	68	9.0000
UGG	chr10:114204855-114205095(-)$1	240	10	13	9.0000
UGG	chr3:52939128-52939368(-)$1	240	84	87	9.0000
UGG	chr1:230979418-230979658(-)$1	240	23	26	9.0000
UGG	chr12:133281250-133281490(+)$1	240	3	6	9.0000
UGG	chr6:27114226-27114466(-)$1	240	67	70	9.0000
UGG	chr11:57102459-57102699(-)$1	240	25	28	9.0000
UGG	chr1:114483735-114483975(+)$1	240	81	84	9.0000
UGG	chr6:89808241-89808481(-)$1	240	37	40	9.0000
UGG	chr7:128119340-128119580(+)$1	240	11	14	9.0000
UGG	chr10:97442770-97443010(-)$1	240	55	58	9.0000
UGG	chr1:63862127-63862367(+)$1	240	60	63	9.0000
UGG	chr4:76733237-76733477(+)$1	240	124	127	9.0000
UGG	chr12:108145768-108146008(-)$1	240	89	92	9.0000

#otherMatches

#Struct PSSM
ddd	chr2:26420496-26420736(-)$1	240	0	3	9.0000
eee	chr12:67691103-67691383(+)$1	280	26	29	9.0000
:BB	chrX:134683490-134683730(+)$1	240	0	3	9.0000
ggg	chr22:42089445-42089685(+)$1	240	98	101	9.0000
dmm	chrX:102471291-102471531(+)$1	240	52	55	9.0000
mmc	chr16:87445638-87445878(-)$1	240	40	43	9.0000
ddd	chr17:2221146-2221386(+)$1	240	22	25	9.0000
&&&	chr15:25601014-25601254(-)$1	240	18	21	9.0000
B{E	chr3:169863129-169863369(-)$1	240	8	11	9.0000
obb	chr14:24702622-24702862(+)$1	240	10	13	9.0000
FFF	chr17:30796033-30796273(+)$1	240	13	16	9.0000
{CC	chr17:37627471-37627711(+)$1	240	61	64	9.0000
EEE	chr3:53259694-53259934(-)$1	240	20	23	9.0000
{EE	chr4:83802957-83803197(-)$1	240	9	12	9.0000
bb[	chr12:117593611-117593851(-)$1	240	42	45	9.0000
ggg	chr4:42072489-42072729(+)$1	240	83	86	9.0000
ddn	chr19:8550535-8550775(+)$1	240	23	26	9.0000
eee	chr7:36396536-36396776(-)$1	240	20	23	9.0000
cc:	chr10:70742192-70742432(+)$1	240	24	27	9.0000
ccd	chr17:46673878-46674118(-)$1	240	38	41	9.0000
:dd	chr10:28899597-28899837(+)$1	240	91	94	9.0000
#gg	chr2:219618990-219619230(+)$1	240	46	49	9.0000
ddd	chr7:23180328-23180568(+)$1	240	8	11	9.0000
KDD	chr19:39390709-39390949(+)$1	240	8	11	9.0000
b==	chr3:8990102-8990342(-)$1	240	148	151	9.0000
hhh	chr16:74501576-74501816(-)$1	240	54	57	9.0000
ddd	chr17:42475014-42475254(-)$1	240	90	93	9.0000
ccc	chr3:44489086-44489326(-)$1	240	69	72	9.0000
ggg	chr10:5790037-5790277(+)$1	240	31	34	9.0000
ooo	chr2:103334766-103335006(-)$1	240	33	36	9.0000
NNN	chr14:50319356-50319596(-)$1	240	11	14	9.0000
CCC	chr22:40657995-40658235(+)$1	240	45	48	9.0000
!ee	chr14:71064244-71064484(-)$1	240	10	13	9.0000
GGG	chr6:33423363-33423603(+)$1	240	18	21	9.0000
KKG	chr1:24786888-24787128(+)$1	240	24	27	9.0000
FFF	chr7:133160087-133160327(+)$1	240	13	16	9.0000
D:e	chr7:26236924-26237164(-)$1	240	72	75	9.0000
DDD	chr15:52662449-52662689(-)$1	240	6	9	9.0000
fff	chr14:93170405-93170645(-)$1	240	46	49	9.0000
GGG	chr3:196612416-196612656(+)$1	240	94	97	9.0000
ddd	chr21:34925817-34926057(+)$1	240	113	116	9.0000
BB{	chr19:49518743-49518983(+)$1	240	6	9	9.0000
:::	chr15:38776736-38776976(+)$1	240	0	3	9.0000
CCC	chr19:23835956-23836196(-)$1	240	0	3	9.0000
llc	chr17:19186294-19186534(+)$1	240	234	237	9.0000
qdd	chr6:151686744-151686984(-)$1	240	42	45	9.0000
ddd	chrX:122831438-122831678(-)$1	240	27	30	9.0000
]dd	chr15:75498395-75498675(+)$1	280	22	25	9.0000
NA{	chr19:3980490-3980730(-)$1	240	74	77	9.0000
ccF	chr2:27551327-27551567(-)$1	240	122	125	9.0000
eee	chr22:42608499-42608739(-)$1	240	81	84	9.0000
:EE	chr16:31193752-31193992(+)$1	240	5	8	9.0000
hhh	chr1:242042119-242042359(+)$1	240	42	45	9.0000
eee	chr20:3766449-3766689(-)$1	240	53	56	9.0000
[dd	chr11:64022607-64022847(+)$1	240	26	29	9.0000
HHH	chr20:17930884-17931124(-)$1	240	60	63	9.0000
eee	chr10:32573645-32573885(-)$1	240	91	94	9.0000
boo	chr2:110259131-110259371(+)$1	240	45	48	9.0000
een	chr14:75471380-75471620(+)$1	240	68	71	9.0000
f[b	chr20:18534813-18535053(+)$1	240	43	46	9.0000
CCC	chr19:33604593-33604833(+)$1	240	8	11	9.0000
fff	chr2:153616160-153616400(+)$1	240	37	40	9.0000
[bb	chr19:35434231-35434471(+)$1	240	13	16	9.0000
CCC	chr6:74304638-74304918(-)$1	280	37	40	9.0000
fff	chr1:226558034-226558274(-)$1	240	78	81	9.0000
eee	chr12:2064506-2064746(-)$1	240	233	236	9.0000
BB{	chr17:80047054-80047294(-)$1	240	53	56	9.0000
ggg	chr6:70500145-70500385(-)$1	240	28	31	9.0000
ggg	chr19:45801062-45801302(+)$1	240	15	18	9.0000
!bb	chr19:23836191-23836431(-)$1	240	37	40	9.0000
JJJ	chr5:6743802-6744042(+)$1	240	10	13	9.0000
##e	chr2:178301437-178301677(+)$1	240	173	176	9.0000
{DD	chr1:16256668-16256908(+)$1	240	25	28	9.0000
ddd	chr1:54502251-54502491(-)$1	240	106	109	9.0000
CCC	chr5:14290942-14291182(+)$1	240	42	45	9.0000
::b	chr10:120832964-120833373(-)$1	409	1	4	9.0000
EEE	chrX:128724125-128724365(+)$1	240	42	45	9.0000
ddd	chr4:13604996-13605236(-)$1	240	36	39	9.0000
=[b	chr3:41277189-41277429(+)$1	240	19	22	9.0000
ee[	chr14:21876480-21876720(-)$1	240	20	23	9.0000
#dd	chr3:40529628-40529868(+)$1	240	55	58	9.0000
:ff	chr2:11427682-11427922(-)$1	240	15	18	9.0000
!ii	chr5:88056904-88057144(-)$1	240	22	25	9.0000
qcc	chr16:29998798-29999038(+)$1	240	47	50	9.0000
ccc	chr17:57728515-57728755(+)$1	240	65	68	9.0000
iii	chr10:114204855-114205095(-)$1	240	10	13	9.0000
ggg	chr3:52939128-52939368(-)$1	240	84	87	9.0000
fff	chr1:230979418-230979658(-)$1	240	23	26	9.0000
DDD	chr12:133281250-133281490(+)$1	240	3	6	9.0000
DDD	chr6:27114226-27114466(-)$1	240	67	70	9.0000
hhh	chr11:57102459-57102699(-)$1	240	25	28	9.0000
ddd	chr1:114483735-114483975(+)$1	240	81	84	9.0000
fff	chr6:89808241-89808481(-)$1	240	37	40	9.0000
b[g	chr7:128119340-128119580(+)$1	240	11	14	9.0000
ggg	chr10:97442770-97443010(-)$1	240	55	58	9.0000
HHH	chr1:63862127-63862367(+)$1	240	60	63	9.0000
3cc	chr4:76733237-76733477(+)$1	240	124	127	9.0000
ddd	chr12:108145768-108146008(-)$1	240	89	92	9.0000

#DB
(((	chr2:26420496-26420736(-)$1	1	0	3	9.0000
)))	chr12:67691103-67691383(+)$1	1	26	29	9.0000
.((	chrX:134683490-134683730(+)$1	1	0	3	9.0000
(((	chr22:42089445-42089685(+)$1	1	98	101	9.0000
(..	chrX:102471291-102471531(+)$1	1	52	55	9.0000
..)	chr16:87445638-87445878(-)$1	1	40	43	9.0000
)))	chr17:2221146-2221386(+)$1	1	22	25	9.0000
...	chr15:25601014-25601254(-)$1	1	18	21	9.0000
(.(	chr3:169863129-169863369(-)$1	1	8	11	9.0000
.))	chr14:24702622-24702862(+)$1	1	10	13	9.0000
(((	chr17:30796033-30796273(+)$1	1	13	16	9.0000
.((	chr17:37627471-37627711(+)$1	1	61	64	9.0000
(((	chr3:53259694-53259934(-)$1	1	20	23	9.0000
.((	chr4:83802957-83803197(-)$1	1	9	12	9.0000
((.	chr12:117593611-117593851(-)$1	1	42	45	9.0000
(((	chr4:42072489-42072729(+)$1	1	83	86	9.0000
((.	chr19:8550535-8550775(+)$1	1	23	26	9.0000
(((	chr7:36396536-36396776(-)$1	1	20	23	9.0000
)).	chr10:70742192-70742432(+)$1	1	24	27	9.0000
(((	chr17:46673878-46674118(-)$1	1	38	41	9.0000
.((	chr10:28899597-28899837(+)$1	1	91	94	9.0000
.((	chr2:219618990-219619230(+)$1	1	46	49	9.0000
(((	chr7:23180328-23180568(+)$1	1	8	11	9.0000
.((	chr19:39390709-39390949(+)$1	1	8	11	9.0000
(((	chr3:8990102-8990342(-)$1	1	148	151	9.0000
(((	chr16:74501576-74501816(-)$1	1	54	57	9.0000
(((	chr17:42475014-42475254(-)$1	1	90	93	9.0000
)))	chr3:44489086-44489326(-)$1	1	69	72	9.0000
(((	chr10:5790037-5790277(+)$1	1	31	34	9.0000
...	chr2:103334766-103335006(-)$1	1	33	36	9.0000
...	chr14:50319356-50319596(-)$1	1	11	14	9.0000
(((	chr22:40657995-40658235(+)$1	1	45	48	9.0000
.((	chr14:71064244-71064484(-)$1	1	10	13	9.0000
(((	chr6:33423363-33423603(+)$1	1	18	21	9.0000
..(	chr1:24786888-24787128(+)$1	1	24	27	9.0000
(((	chr7:133160087-133160327(+)$1	1	13	16	9.0000
(.(	chr7:26236924-26237164(-)$1	1	72	75	9.0000
(((	chr15:52662449-52662689(-)$1	1	6	9	9.0000
(((	chr14:93170405-93170645(-)$1	1	46	49	9.0000
)))	chr3:196612416-196612656(+)$1	1	94	97	9.0000
(((	chr21:34925817-34926057(+)$1	1	113	116	9.0000
((.	chr19:49518743-49518983(+)$1	1	6	9	9.0000
...	chr15:38776736-38776976(+)$1	1	0	3	9.0000
(((	chr19:23835956-23836196(-)$1	1	0	3	9.0000
..)	chr17:19186294-19186534(+)$1	1	234	237	9.0000
.))	chr6:151686744-151686984(-)$1	1	42	45	9.0000
(((	chrX:122831438-122831678(-)$1	1	27	30	9.0000
.))	chr15:75498395-75498675(+)$1	1	22	25	9.0000
.(.	chr19:3980490-3980730(-)$1	1	74	77	9.0000
))(	chr2:27551327-27551567(-)$1	1	122	125	9.0000
)))	chr22:42608499-42608739(-)$1	1	81	84	9.0000
.((	chr16:31193752-31193992(+)$1	1	5	8	9.0000
(((	chr1:242042119-242042359(+)$1	1	42	45	9.0000
)))	chr20:3766449-3766689(-)$1	1	53	56	9.0000
.((	chr11:64022607-64022847(+)$1	1	26	29	9.0000
(((	chr20:17930884-17931124(-)$1	1	60	63	9.0000
(((	chr10:32573645-32573885(-)$1	1	91	94	9.0000
(..	chr2:110259131-110259371(+)$1	1	45	48	9.0000
((.	chr14:75471380-75471620(+)$1	1	68	71	9.0000
(.(	chr20:18534813-18535053(+)$1	1	43	46	9.0000
(((	chr19:33604593-33604833(+)$1	1	8	11	9.0000
(((	chr2:153616160-153616400(+)$1	1	37	40	9.0000
.((	chr19:35434231-35434471(+)$1	1	13	16	9.0000
(((	chr6:74304638-74304918(-)$1	1	37	40	9.0000
(((	chr1:226558034-226558274(-)$1	1	78	81	9.0000
)))	chr12:2064506-2064746(-)$1	1	233	236	9.0000
((.	chr17:80047054-80047294(-)$1	1	53	56	9.0000
(((	chr6:70500145-70500385(-)$1	1	28	31	9.0000
(((	chr19:45801062-45801302(+)$1	1	15	18	9.0000
.((	chr19:23836191-23836431(-)$1	1	37	40	9.0000
(((	chr5:6743802-6744042(+)$1	1	10	13	9.0000
..(	chr2:178301437-178301677(+)$1	1	173	176	9.0000
.((	chr1:16256668-16256908(+)$1	1	25	28	9.0000
)))	chr1:54502251-54502491(-)$1	1	106	109	9.0000
(((	chr5:14290942-14291182(+)$1	1	42	45	9.0000
..(	chr10:120832964-120833373(-)$1	1	1	4	9.0000
(((	chrX:128724125-128724365(+)$1	1	42	45	9.0000
)))	chr4:13604996-13605236(-)$1	1	36	39	9.0000
(.(	chr3:41277189-41277429(+)$1	1	19	22	9.0000
((.	chr14:21876480-21876720(-)$1	1	20	23	9.0000
.((	chr3:40529628-40529868(+)$1	1	55	58	9.0000
.((	chr2:11427682-11427922(-)$1	1	15	18	9.0000
.((	chr5:88056904-88057144(-)$1	1	22	25	9.0000
.))	chr16:29998798-29999038(+)$1	1	47	50	9.0000
(((	chr17:57728515-57728755(+)$1	1	65	68	9.0000
(((	chr10:114204855-114205095(-)$1	1	10	13	9.0000
(((	chr3:52939128-52939368(-)$1	1	84	87	9.0000
(((	chr1:230979418-230979658(-)$1	1	23	26	9.0000
(((	chr12:133281250-133281490(+)$1	1	3	6	9.0000
(((	chr6:27114226-27114466(-)$1	1	67	70	9.0000
(((	chr11:57102459-57102699(-)$1	1	25	28	9.0000
)))	chr1:114483735-114483975(+)$1	1	81	84	9.0000
(((	chr6:89808241-89808481(-)$1	1	37	40	9.0000
(.(	chr7:128119340-128119580(+)$1	1	11	14	9.0000
(((	chr10:97442770-97443010(-)$1	1	55	58	9.0000
(((	chr1:63862127-63862367(+)$1	1	60	63	9.0000
.))	chr4:76733237-76733477(+)$1	1	124	127	9.0000
)))	chr12:108145768-108146008(-)$1	1	89	92	9.0000

#PSSM
U : 0.98	u : 0.01	
G : 0.98	g : 0.01	
G : 1.00	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_transcript_m1_run2.nuc.txt

#NT
UCU	chr2:71363938-71364195(+)$1	257	160	163	9.0000
ucu	chr17:26416108-26416386(+)$1	278	96	99	9.0000
UCU	chr5:49706398-49706685(-)$1	287	22	25	9.0000
ucu	chr8:63556528-63556742(+)$1	214	0	3	9.0000
UCU	chr3:112184620-112184844(-)$1	224	24	27	9.0000
UCU	chr3:170936193-170936432(-)$1	239	155	158	9.0000
ucu	chr2:135646949-135647176(+)$1	227	86	89	9.0000
ucu	chr12:120925536-120925751(+)$1	215	13	16	9.0000
UCU	chr13:77630110-77630420(-)$1	310	13	16	9.0000
ucu	chr16:3620257-3620527(-)$1	270	90	93	9.0000
UCU	chr3:143349170-143349409(-)$1	239	4	7	9.0000
UCU	chr7:4296359-4296571(+)$1	212	11	14	9.0000
ucu	chr5:65086320-65086634(+)$1	314	56	59	9.0000
UCU	chr15:67484620-67484860(+)$1	240	66	69	9.0000
ucu	chr5:147768654-147768889(+)$1	235	58	61	9.0000
ucu	chr8:38849068-38849296(-)$1	228	27	30	9.0000
UCU	chr2:225904001-225904319(-)$1	318	127	130	9.0000
UCU	chr1:156826845-156827112(-)$1	267	3	6	9.0000
UCU	chrX:96549983-96550217(+)$1	234	1	4	9.0000
ucu	chr12:124218162-124218388(+)$1	226	17	20	9.0000
ucu	chr1:12000057-12000273(+)$1	216	180	183	9.0000
UCU	chr1:236961559-236961798(+)$1	239	8	11	9.0000
ucu	chr14:71419000-71419261(+)$1	261	114	117	9.0000
UCU	chr1:66081640-66081855(+)$1	215	34	37	9.0000
UCU	chr1:84667720-84667990(+)$1	270	9	12	9.0000
ucu	chr8:22341033-22341295(+)$1	262	5	8	9.0000
ucu	chr16:88676053-88676269(+)$1	216	19	22	9.0000
UCU	chr17:5408108-5408398(-)$1	290	104	107	9.0000
UCU	chr2:161300536-161300792(-)$1	256	10	13	9.0000
ucu	chr5:131030411-131030630(-)$1	219	45	48	9.0000
UCU	chr20:51899691-51899932(+)$1	241	143	146	9.0000
UCU	chr8:61604813-61605035(+)$1	222	40	43	9.0000
ucu	chr1:22973031-22973250(+)$1	219	70	73	9.0000
ucu	chrX:108970767-108971043(-)$1	276	38	41	9.0000
ucu	chr14:35098141-35098388(-)$1	247	60	63	9.0000
UCU	chr4:83282237-83282458(-)$1	221	11	14	9.0000
ucu	chr5:10358811-10359049(+)$1	238	37	40	9.0000
ucu	chr5:118616798-118617045(+)$1	247	8	11	9.0000
UCU	chr1:62268411-62268640(+)$1	229	69	72	9.0000
ucu	chr1:228423612-228423858(+)$1	246	26	29	9.0000
UCU	chr1:160827818-160828066(-)$1	248	25	28	9.0000
UCU	chr14:65521790-65522023(-)$1	233	9	12	9.0000
ucu	chr19:41907986-41908205(+)$1	219	44	47	9.0000
UCU	chr1:90171864-90172125(+)$1	261	2	5	9.0000
UCU	chr13:103280747-103280976(+)$1	229	31	34	9.0000
UCU	chr19:58984170-58984391(+)$1	221	17	20	9.0000
UCU	chr2:175496864-175497200(-)$1	336	93	96	9.0000
ucu	chr3:99812383-99812667(+)$1	284	43	46	9.0000
UCU	chr3:114679714-114679970(-)$1	256	34	37	9.0000
ucu	chr3:31579503-31579790(+)$1	287	113	116	9.0000
ucu	chr2:114204133-114204366(+)$1	233	20	23	9.0000
UCU	chr11:93529754-93530007(+)$1	253	22	25	9.0000
ucu	chr8:48621373-48621588(+)$1	215	10	13	9.0000
UCU	chr4:100762485-100762767(+)$1	282	25	28	9.0000
ucu	chr10:114532982-114533232(+)$1	250	31	34	9.0000
UCU	chr12:69316834-69317103(-)$1	269	33	36	9.0000
UCU	chr8:102964830-102965061(-)$1	231	0	3	9.0000
UCU	chr18:201479-201731(+)$1	252	33	36	9.0000
UCU	chr2:84759410-84759626(+)$1	216	7	10	9.0000
UCU	chr17:45014048-45014274(+)$1	226	35	38	9.0000
ucu	chr9:86058121-86058343(-)$1	222	4	7	9.0000
ucu	chr17:31843262-31843550(-)$1	288	14	17	9.0000
UCU	chr21:30675046-30675290(+)$1	244	88	91	9.0000
ucu	chr7:40074546-40074760(+)$1	214	20	23	9.0000
ucu	chr2:28427573-28427809(+)$1	236	21	24	9.0000
UCU	chr2:11600899-11601119(-)$1	220	41	44	9.0000
ucu	chr21:32537592-32537860(-)$1	268	15	18	9.0000
ucu	chr11:111515769-111515988(+)$1	219	104	107	9.0000
ucu	chr16:24028683-24028941(+)$1	258	65	68	9.0000
ucu	chr11:113854781-113854995(+)$1	214	13	16	9.0000
UCU	chr22:37629103-37629346(-)$1	243	81	84	9.0000
ucu	chr6:123919929-123920149(-)$1	220	86	89	9.0000
ucu	chr9:117105001-117105271(-)$1	270	12	15	9.0000
UCU	chr2:212929608-212929872(-)$1	264	14	17	9.0000
ucu	chr17:57263848-57264109(+)$1	261	100	103	9.0000
UCU	chrX:153349065-153349357(-)$1	292	19	22	9.0000
UCU	chr12:65569107-65569329(+)$1	222	9	12	9.0000
ucu	chr8:20029081-20029315(-)$1	234	50	53	9.0000
UCU	chr8:144989691-144989916(-)$1	225	8	11	9.0000
ucu	chr9:17385523-17385762(+)$1	239	81	84	9.0000
UCU	chr4:1941810-1942045(+)$1	235	34	37	9.0000
UCU	chr2:217021115-217021369(+)$1	254	13	16	9.0000
ucu	chrX:106337856-106338122(-)$1	266	9	12	9.0000
ucu	chr5:81390655-81390897(+)$1	242	137	140	9.0000
ucu	chr1:202123640-202123923(-)$1	283	136	139	9.0000
ucu	chr3:158102240-158102495(+)$1	255	139	142	9.0000
ucu	chr4:101403593-101403815(-)$1	222	90	93	9.0000
ucu	chr4:17902349-17902584(-)$1	235	17	20	9.0000
ucu	chrX:148707359-148707593(-)$1	234	141	144	9.0000
ucu	chr18:67278626-67278868(+)$1	242	13	16	9.0000
UCU	chr22:40745659-40745894(+)$1	235	169	172	9.0000
ucu	chr3:46413993-46414217(+)$1	224	22	25	9.0000
UCU	chr13:46747321-46747725(-)$1	404	7	10	9.0000
UCU	chr6:112008617-112008968(-)$1	351	104	107	9.0000
ucu	chr3:136088988-136089286(-)$1	298	153	156	9.0000
UCU	chr2:144476967-144477285(+)$1	318	1	4	9.0000
ucu	chr17:65204167-65204411(-)$1	244	55	58	9.0000
UCU	chr11:95924976-95925342(-)$1	366	61	64	9.0000
UCU	chr2:101923495-101923754(-)$1	259	168	171	9.0000

#otherMatches

#Struct PSSM
ee[	chr11:120266503-120266724(+)$1	221	122	125	9.0000
occ	chr2:71363938-71364195(+)$1	257	160	163	9.0000
qdd	chr17:26416108-26416386(+)$1	278	96	99	9.0000
H::	chr5:49706398-49706685(-)$1	287	22	25	9.0000
:::	chr8:63556528-63556742(+)$1	214	0	3	9.0000
F:F	chr3:112184620-112184844(-)$1	224	24	27	9.0000
iii	chr3:170936193-170936432(-)$1	239	155	158	9.0000
FFF	chr2:135646949-135647176(+)$1	227	86	89	9.0000
JJJ	chr12:120925536-120925751(+)$1	215	13	16	9.0000
^^^	chr13:77630110-77630420(-)$1	310	13	16	9.0000
eeo	chr16:3620257-3620527(-)$1	270	90	93	9.0000
EEE	chr3:143349170-143349409(-)$1	239	4	7	9.0000
mee	chr7:4296359-4296571(+)$1	212	11	14	9.0000
+++	chr5:65086320-65086634(+)$1	314	56	59	9.0000
hhh	chr15:67484620-67484860(+)$1	240	66	69	9.0000
ebb	chr5:147768654-147768889(+)$1	235	58	61	9.0000
ppp	chr8:38849068-38849296(-)$1	228	27	30	9.0000
EEE	chr2:225904001-225904319(-)$1	318	127	130	9.0000
eee	chr1:156826845-156827112(-)$1	267	3	6	9.0000
:::	chrX:96549983-96550217(+)$1	234	1	4	9.0000
JJJ	chr12:124218162-124218388(+)$1	226	17	20	9.0000
ppd	chr1:12000057-12000273(+)$1	216	180	183	9.0000
hhh	chr1:236961559-236961798(+)$1	239	8	11	9.0000
:::	chr14:71419000-71419261(+)$1	261	114	117	9.0000
:::	chr1:66081640-66081855(+)$1	215	34	37	9.0000
fff	chr1:84667720-84667990(+)$1	270	9	12	9.0000
GG{	chr8:22341033-22341295(+)$1	262	5	8	9.0000
mmm	chr16:88676053-88676269(+)$1	216	19	22	9.0000
ddE	chr17:5408108-5408398(-)$1	290	104	107	9.0000
::D	chr2:161300536-161300792(-)$1	256	10	13	9.0000
ff]	chr5:131030411-131030630(-)$1	219	45	48	9.0000
i[b	chr20:51899691-51899932(+)$1	241	143	146	9.0000
:::	chr8:61604813-61605035(+)$1	222	40	43	9.0000
c::	chr1:22973031-22973250(+)$1	219	70	73	9.0000
:CC	chrX:108970767-108971043(-)$1	276	38	41	9.0000
gqq	chr14:35098141-35098388(-)$1	247	60	63	9.0000
fff	chr4:83282237-83282458(-)$1	221	11	14	9.0000
'''	chr5:10358811-10359049(+)$1	238	37	40	9.0000
fff	chr5:118616798-118617045(+)$1	247	8	11	9.0000
::e	chr1:62268411-62268640(+)$1	229	69	72	9.0000
ppc	chr1:228423612-228423858(+)$1	246	26	29	9.0000
eee	chr1:160827818-160828066(-)$1	248	25	28	9.0000
LLL	chr14:65521790-65522023(-)$1	233	9	12	9.0000
fff	chr19:41907986-41908205(+)$1	219	44	47	9.0000
:::	chr1:90171864-90172125(+)$1	261	2	5	9.0000
ppp	chr13:103280747-103280976(+)$1	229	31	34	9.0000
BBD	chr19:58984170-58984391(+)$1	221	17	20	9.0000
g::	chr2:175496864-175497200(-)$1	336	93	96	9.0000
888	chr3:99812383-99812667(+)$1	284	43	46	9.0000
hhh	chr3:114679714-114679970(-)$1	256	34	37	9.0000
ddd	chr3:31579503-31579790(+)$1	287	113	116	9.0000
dmm	chr2:114204133-114204366(+)$1	233	20	23	9.0000
III	chr11:93529754-93530007(+)$1	253	22	25	9.0000
nnn	chr8:48621373-48621588(+)$1	215	10	13	9.0000
]bb	chr4:100762485-100762767(+)$1	282	25	28	9.0000
d]e	chr10:114532982-114533232(+)$1	250	31	34	9.0000
fff	chr12:69316834-69317103(-)$1	269	33	36	9.0000
:::	chr8:102964830-102965061(-)$1	231	0	3	9.0000
ccc	chr18:201479-201731(+)$1	252	33	36	9.0000
HHH	chr2:84759410-84759626(+)$1	216	7	10	9.0000
ugg	chr17:45014048-45014274(+)$1	226	35	38	9.0000
ggg	chr9:86058121-86058343(-)$1	222	4	7	9.0000
HHH	chr17:31843262-31843550(-)$1	288	14	17	9.0000
d:g	chr21:30675046-30675290(+)$1	244	88	91	9.0000
!!c	chr7:40074546-40074760(+)$1	214	20	23	9.0000
C::	chr2:28427573-28427809(+)$1	236	21	24	9.0000
ccc	chr2:11600899-11601119(-)$1	220	41	44	9.0000
ooo	chr21:32537592-32537860(-)$1	268	15	18	9.0000
+cc	chr11:111515769-111515988(+)$1	219	104	107	9.0000
d::	chr16:24028683-24028941(+)$1	258	65	68	9.0000
:::	chr11:113854781-113854995(+)$1	214	13	16	9.0000
eee	chr22:37629103-37629346(-)$1	243	81	84	9.0000
PPP	chr6:123919929-123920149(-)$1	220	86	89	9.0000
ddn	chr9:117105001-117105271(-)$1	270	12	15	9.0000
!cc	chr2:212929608-212929872(-)$1	264	14	17	9.0000
!!f	chr17:57263848-57264109(+)$1	261	100	103	9.0000
rrr	chrX:153349065-153349357(-)$1	292	19	22	9.0000
:::	chr12:65569107-65569329(+)$1	222	9	12	9.0000
::e	chr8:20029081-20029315(-)$1	234	50	53	9.0000
ee&	chr8:144989691-144989916(-)$1	225	8	11	9.0000
::b	chr9:17385523-17385762(+)$1	239	81	84	9.0000
::c	chr4:1941810-1942045(+)$1	235	34	37	9.0000
bb[	chr2:217021115-217021369(+)$1	254	13	16	9.0000
MMM	chrX:106337856-106338122(-)$1	266	9	12	9.0000
""f	chr5:81390655-81390897(+)$1	242	137	140	9.0000
ttt	chr1:202123640-202123923(-)$1	283	136	139	9.0000
cc:	chr3:158102240-158102495(+)$1	255	139	142	9.0000
eee	chr4:101403593-101403815(-)$1	222	90	93	9.0000
eee	chr4:17902349-17902584(-)$1	235	17	20	9.0000
22f	chrX:148707359-148707593(-)$1	234	141	144	9.0000
D:d	chr18:67278626-67278868(+)$1	242	13	16	9.0000
ggg	chr22:40745659-40745894(+)$1	235	169	172	9.0000
III	chr3:46413993-46414217(+)$1	224	22	25	9.0000
:::	chr13:46747321-46747725(-)$1	404	7	10	9.0000
bbz	chr6:112008617-112008968(-)$1	351	104	107	9.0000
nnn	chr3:136088988-136089286(-)$1	298	153	156	9.0000
GGG	chr2:144476967-144477285(+)$1	318	1	4	9.0000
:::	chr17:65204167-65204411(-)$1	244	55	58	9.0000
:::	chr11:95924976-95925342(-)$1	366	61	64	9.0000
2bb	chr2:101923495-101923754(-)$1	259	168	171	9.0000

#DB
((.	chr11:120266503-120266724(+)$1	1	122	125	9.0000
.))	chr2:71363938-71364195(+)$1	1	160	163	9.0000
.))	chr17:26416108-26416386(+)$1	1	96	99	9.0000
(..	chr5:49706398-49706685(-)$1	1	22	25	9.0000
...	chr8:63556528-63556742(+)$1	1	0	3	9.0000
(.(	chr3:112184620-112184844(-)$1	1	24	27	9.0000
(((	chr3:170936193-170936432(-)$1	1	155	158	9.0000
)))	chr2:135646949-135647176(+)$1	1	86	89	9.0000
(((	chr12:120925536-120925751(+)$1	1	13	16	9.0000
...	chr13:77630110-77630420(-)$1	1	13	16	9.0000
((.	chr16:3620257-3620527(-)$1	1	90	93	9.0000
(((	chr3:143349170-143349409(-)$1	1	4	7	9.0000
.))	chr7:4296359-4296571(+)$1	1	11	14	9.0000
...	chr5:65086320-65086634(+)$1	1	56	59	9.0000
(((	chr15:67484620-67484860(+)$1	1	66	69	9.0000
(((	chr5:147768654-147768889(+)$1	1	58	61	9.0000
...	chr8:38849068-38849296(-)$1	1	27	30	9.0000
(((	chr2:225904001-225904319(-)$1	1	127	130	9.0000
(((	chr1:156826845-156827112(-)$1	1	3	6	9.0000
...	chrX:96549983-96550217(+)$1	1	1	4	9.0000
(((	chr12:124218162-124218388(+)$1	1	17	20	9.0000
..)	chr1:12000057-12000273(+)$1	1	180	183	9.0000
(((	chr1:236961559-236961798(+)$1	1	8	11	9.0000
...	chr14:71419000-71419261(+)$1	1	114	117	9.0000
...	chr1:66081640-66081855(+)$1	1	34	37	9.0000
(((	chr1:84667720-84667990(+)$1	1	9	12	9.0000
((.	chr8:22341033-22341295(+)$1	1	5	8	9.0000
...	chr16:88676053-88676269(+)$1	1	19	22	9.0000
)))	chr17:5408108-5408398(-)$1	1	104	107	9.0000
..(	chr2:161300536-161300792(-)$1	1	10	13	9.0000
)).	chr5:131030411-131030630(-)$1	1	45	48	9.0000
(.(	chr20:51899691-51899932(+)$1	1	143	146	9.0000
...	chr8:61604813-61605035(+)$1	1	40	43	9.0000
)..	chr1:22973031-22973250(+)$1	1	70	73	9.0000
.((	chrX:108970767-108971043(-)$1	1	38	41	9.0000
(..	chr14:35098141-35098388(-)$1	1	60	63	9.0000
(((	chr4:83282237-83282458(-)$1	1	11	14	9.0000
...	chr5:10358811-10359049(+)$1	1	37	40	9.0000
(((	chr5:118616798-118617045(+)$1	1	8	11	9.0000
..(	chr1:62268411-62268640(+)$1	1	69	72	9.0000
..)	chr1:228423612-228423858(+)$1	1	26	29	9.0000
)))	chr1:160827818-160828066(-)$1	1	25	28	9.0000
...	chr14:65521790-65522023(-)$1	1	9	12	9.0000
(((	chr19:41907986-41908205(+)$1	1	44	47	9.0000
...	chr1:90171864-90172125(+)$1	1	2	5	9.0000
...	chr13:103280747-103280976(+)$1	1	31	34	9.0000
(((	chr19:58984170-58984391(+)$1	1	17	20	9.0000
)..	chr2:175496864-175497200(-)$1	1	93	96	9.0000
...	chr3:99812383-99812667(+)$1	1	43	46	9.0000
(((	chr3:114679714-114679970(-)$1	1	34	37	9.0000
(((	chr3:31579503-31579790(+)$1	1	113	116	9.0000
(..	chr2:114204133-114204366(+)$1	1	20	23	9.0000
(((	chr11:93529754-93530007(+)$1	1	22	25	9.0000
...	chr8:48621373-48621588(+)$1	1	10	13	9.0000
.))	chr4:100762485-100762767(+)$1	1	25	28	9.0000
).)	chr10:114532982-114533232(+)$1	1	31	34	9.0000
(((	chr12:69316834-69317103(-)$1	1	33	36	9.0000
...	chr8:102964830-102965061(-)$1	1	0	3	9.0000
)))	chr18:201479-201731(+)$1	1	33	36	9.0000
(((	chr2:84759410-84759626(+)$1	1	7	10	9.0000
.))	chr17:45014048-45014274(+)$1	1	35	38	9.0000
(((	chr9:86058121-86058343(-)$1	1	4	7	9.0000
(((	chr17:31843262-31843550(-)$1	1	14	17	9.0000
).(	chr21:30675046-30675290(+)$1	1	88	91	9.0000
..(	chr7:40074546-40074760(+)$1	1	20	23	9.0000
(..	chr2:28427573-28427809(+)$1	1	21	24	9.0000
(((	chr2:11600899-11601119(-)$1	1	41	44	9.0000
...	chr21:32537592-32537860(-)$1	1	15	18	9.0000
.((	chr11:111515769-111515988(+)$1	1	104	107	9.0000
)..	chr16:24028683-24028941(+)$1	1	65	68	9.0000
...	chr11:113854781-113854995(+)$1	1	13	16	9.0000
(((	chr22:37629103-37629346(-)$1	1	81	84	9.0000
...	chr6:123919929-123920149(-)$1	1	86	89	9.0000
((.	chr9:117105001-117105271(-)$1	1	12	15	9.0000
.((	chr2:212929608-212929872(-)$1	1	14	17	9.0000
..(	chr17:57263848-57264109(+)$1	1	100	103	9.0000
...	chrX:153349065-153349357(-)$1	1	19	22	9.0000
...	chr12:65569107-65569329(+)$1	1	9	12	9.0000
..(	chr8:20029081-20029315(-)$1	1	50	53	9.0000
((.	chr8:144989691-144989916(-)$1	1	8	11	9.0000
..(	chr9:17385523-17385762(+)$1	1	81	84	9.0000
..(	chr4:1941810-1942045(+)$1	1	34	37	9.0000
((.	chr2:217021115-217021369(+)$1	1	13	16	9.0000
...	chrX:106337856-106338122(-)$1	1	9	12	9.0000
..(	chr5:81390655-81390897(+)$1	1	137	140	9.0000
...	chr1:202123640-202123923(-)$1	1	136	139	9.0000
)).	chr3:158102240-158102495(+)$1	1	139	142	9.0000
(((	chr4:101403593-101403815(-)$1	1	90	93	9.0000
(((	chr4:17902349-17902584(-)$1	1	17	20	9.0000
..)	chrX:148707359-148707593(-)$1	1	141	144	9.0000
(.(	chr18:67278626-67278868(+)$1	1	13	16	9.0000
)))	chr22:40745659-40745894(+)$1	1	169	172	9.0000
(((	chr3:46413993-46414217(+)$1	1	22	25	9.0000
...	chr13:46747321-46747725(-)$1	1	7	10	9.0000
((.	chr6:112008617-112008968(-)$1	1	104	107	9.0000
...	chr3:136088988-136089286(-)$1	1	153	156	9.0000
(((	chr2:144476967-144477285(+)$1	1	1	4	9.0000
...	chr17:65204167-65204411(-)$1	1	55	58	9.0000
...	chr11:95924976-95925342(-)$1	1	61	64	9.0000
.))	chr2:101923495-101923754(-)$1	1	168	171	9.0000

#PSSM
u : 0.51	U : 0.49	
c : 0.51	C : 0.49	
u : 0.51	U : 0.49	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m2_run2.nuc.txt

#NT
AUUUUU	chr4:119179360-119179589(+)$1	229	47	53	16.6538
AUUUUU	chr10:11371683-11372025(+)$1	342	191	197	16.6538
AUUUUU	chr3:160151000-160151229(+)$1	229	148	154	16.6538
AUUUUU	chr8:101931647-101931897(-)$1	250	45	51	16.6538
AUUUUU	chr22:38881637-38881872(-)$1	235	51	57	16.6538
auuuuu	chr19:37118972-37119211(+)$1	239	83	89	16.6538
AUUUUU	chr15:65869813-65870181(+)$1	368	220	226	16.6538
CUUUUU	chr5:156820193-156820461(+)$1	268	58	64	13.8653
AUUUUU	chr9:88952084-88952326(-)$1	242	2	8	16.6538
AUUUUU	chr1:202556236-202556472(+)$1	236	14	20	16.6538
AUUUUU	chr10:38345385-38345645(+)$1	260	245	251	16.6538
AUUUUU	chr17:53121033-53121263(+)$1	230	18	24	16.6538
AUUUUU	chr14:55534639-55534885(+)$1	246	228	234	16.6538
AUUUUU	chr8:41788965-41789240(-)$1	275	240	246	16.6538
CUUUUU	chr16:29815763-29816099(+)$1	336	32	38	13.8653
AUUUUU	chr16:14358984-14359230(+)$1	246	131	137	16.6538
AUUUUU	chr10:124923397-124923629(+)$1	232	101	107	16.6538
GUUUUU	chr4:169910917-169911166(-)$1	249	40	46	13.4807
AUUUUU	chr7:94184953-94185204(+)$1	251	62	68	16.6538
CUUUUU	chr9:132651990-132652362(-)$1	372	80	86	13.8653
AUUUUU	chr7:138729790-138730113(-)$1	323	88	94	16.6538
CUUUUU	chr15:64461225-64461516(-)$1	291	247	253	13.8653
auuuuu	chr1:45285500-45285749(-)$1	249	165	171	16.6538
auuuuu	chr1:227847456-227847714(+)$1	258	86	92	16.6538
GUUUUU	chr1:160515935-160516197(-)$1	262	2	8	13.4807
AUUUUU	chr6:158518340-158518566(+)$1	226	64	70	16.6538
AUUUUU	chr8:37993142-37993369(+)$1	227	91	97	16.6538
AUUUUU	chr2:203425601-203425851(+)$1	250	17	23	16.6538
AUUUUU	chr10:76468537-76468790(+)$1	253	32	38	16.6538
AUUUUU	chr2:61275972-61276244(+)$1	272	184	190	16.6538
auuuuu	chr19:36828326-36828551(-)$1	225	198	204	16.6538
AUUUUU	chr13:37596379-37596694(-)$1	315	33	39	16.6538
AUUUUU	chr12:27955346-27955584(+)$1	238	78	84	16.6538
AUUUUU	chr11:121179063-121179315(+)$1	252	45	51	16.6538
AUUUUU	chr1:35482839-35483071(-)$1	232	13	19	16.6538
auuuuU	chr1:183596310-183596556(-)$1	246	230	236	16.6538
AUUUUU	chr5:154194157-154194432(+)$1	275	226	232	16.6538
CUUUUU	chr6:45517524-45517785(+)$1	261	75	81	13.8653
AUUUUU	chr2:62227802-62228029(+)$1	227	4	10	16.6538
AUUUUU	chr2:55626734-55626971(-)$1	237	124	130	16.6538
GUUUUU	chr7:86825026-86825257(+)$1	231	34	40	13.4807
GUUUUU	chr3:107764850-107765153(-)$1	303	261	267	13.4807
CUUUUU	chr10:70516196-70516473(+)$1	277	61	67	13.8653
AUUUUU	chr1:160186593-160186981(-)$1	388	349	355	16.6538
AUUUUU	chr1:2118281-2118538(-)$1	257	100	106	16.6538
CUUUUU	chr14:68058697-68058919(-)$1	222	146	152	13.8653
auuuuu	chr4:83848570-83848802(-)$1	232	131	137	16.6538
AUUUUU	chr5:38940194-38940464(-)$1	270	88	94	16.6538
GUUUUU	chr2:197643243-197643497(-)$1	254	202	208	13.4807
AUUUUU	chr15:23005751-23005989(-)$1	238	74	80	16.6538
CUUUUU	chr5:167983460-167983709(-)$1	249	122	128	13.8653

#otherMatches

#Struct PSSM
rrrrrr	chr11:58387746-58387983(+)$1	237	114	120	13.8653
333ddd	chr4:119179360-119179589(+)$1	229	47	53	16.6538
qeeeee	chr10:11371683-11372025(+)$1	342	191	197	16.6538
qqqqqq	chr3:160151000-160151229(+)$1	229	148	154	16.6538
bnnnnn	chr8:101931647-101931897(-)$1	250	45	51	16.6538
::::::	chr22:38881637-38881872(-)$1	235	51	57	16.6538
GGGLLL	chr19:37118972-37119211(+)$1	239	83	89	16.6538
hhhhhh	chr15:65869813-65870181(+)$1	368	220	226	16.6538
hhhhhh	chr5:156820193-156820461(+)$1	268	58	64	13.8653
::::::	chr9:88952084-88952326(-)$1	242	2	8	16.6538
::::::	chr1:202556236-202556472(+)$1	236	14	20	16.6538
dnnnnn	chr10:38345385-38345645(+)$1	260	245	251	16.6538
eeqqqq	chr17:53121033-53121263(+)$1	230	18	24	16.6538
:::HHH	chr14:55534639-55534885(+)$1	246	228	234	16.6538
::::::	chr8:41788965-41789240(-)$1	275	240	246	16.6538
ddddll	chr16:29815763-29816099(+)$1	336	32	38	13.8653
>>>>>>	chr16:14358984-14359230(+)$1	246	131	137	16.6538
fqqqqq	chr10:124923397-124923629(+)$1	232	101	107	16.6538
ff))))	chr4:169910917-169911166(-)$1	249	40	46	13.4807
eooooo	chr7:94184953-94185204(+)$1	251	62	68	16.6538
ennnnn	chr9:132651990-132652362(-)$1	372	80	86	13.8653
fff"""	chr7:138729790-138730113(-)$1	323	88	94	16.6538
crrrrr	chr15:64461225-64461516(-)$1	291	247	253	13.8653
33ffff	chr1:45285500-45285749(-)$1	249	165	171	16.6538
hh''''	chr1:227847456-227847714(+)$1	258	86	92	16.6538
EEEEEK	chr1:160515935-160516197(-)$1	262	2	8	13.4807
^^^^^^	chr6:158518340-158518566(+)$1	226	64	70	16.6538
mmeeee	chr8:37993142-37993369(+)$1	227	91	97	16.6538
%%ffff	chr2:203425601-203425851(+)$1	250	17	23	16.6538
ooobb]	chr10:76468537-76468790(+)$1	253	32	38	16.6538
]bb333	chr2:61275972-61276244(+)$1	272	184	190	16.6538
:::::G	chr19:36828326-36828551(-)$1	225	198	204	16.6538
::::::	chr13:37596379-37596694(-)$1	315	33	39	16.6538
fsssss	chr12:27955346-27955584(+)$1	238	78	84	16.6538
JJJJJJ	chr11:121179063-121179315(+)$1	252	45	51	16.6538
::::::	chr1:35482839-35483071(-)$1	232	13	19	16.6538
HHHHHH	chr1:183596310-183596556(-)$1	246	230	236	16.6538
hhhhhh	chr5:154194157-154194432(+)$1	275	226	232	16.6538
dddggg	chr6:45517524-45517785(+)$1	261	75	81	13.8653
::::::	chr2:62227802-62228029(+)$1	227	4	10	16.6538
::::::	chr2:55626734-55626971(-)$1	237	124	130	16.6538
cc[===	chr7:86825026-86825257(+)$1	231	34	40	13.4807
::::ee	chr3:107764850-107765153(-)$1	303	261	267	13.4807
cciiii	chr10:70516196-70516473(+)$1	277	61	67	13.8653
GG}JJJ	chr1:160186593-160186981(-)$1	388	349	355	16.6538
ee^^^^	chr1:2118281-2118538(-)$1	257	100	106	16.6538
cc7777	chr14:68058697-68058919(-)$1	222	146	152	13.8653
:iiiii	chr4:83848570-83848802(-)$1	232	131	137	16.6538
H:::::	chr5:38940194-38940464(-)$1	270	88	94	16.6538
nnnddd	chr2:197643243-197643497(-)$1	254	202	208	13.4807
rrrfff	chr15:23005751-23005989(-)$1	238	74	80	16.6538
a]eeee	chr5:167983460-167983709(-)$1	249	122	128	13.8653

#DB
......	chr11:58387746-58387983(+)$1	1	114	120	13.8653
...)))	chr4:119179360-119179589(+)$1	1	47	53	16.6538
.)))))	chr10:11371683-11372025(+)$1	1	191	197	16.6538
......	chr3:160151000-160151229(+)$1	1	148	154	16.6538
(.....	chr8:101931647-101931897(-)$1	1	45	51	16.6538
......	chr22:38881637-38881872(-)$1	1	51	57	16.6538
(((...	chr19:37118972-37119211(+)$1	1	83	89	16.6538
((((((	chr15:65869813-65870181(+)$1	1	220	226	16.6538
))))))	chr5:156820193-156820461(+)$1	1	58	64	13.8653
......	chr9:88952084-88952326(-)$1	1	2	8	16.6538
......	chr1:202556236-202556472(+)$1	1	14	20	16.6538
(.....	chr10:38345385-38345645(+)$1	1	245	251	16.6538
((....	chr17:53121033-53121263(+)$1	1	18	24	16.6538
...)))	chr14:55534639-55534885(+)$1	1	228	234	16.6538
......	chr8:41788965-41789240(-)$1	1	240	246	16.6538
((((..	chr16:29815763-29816099(+)$1	1	32	38	13.8653
......	chr16:14358984-14359230(+)$1	1	131	137	16.6538
(.....	chr10:124923397-124923629(+)$1	1	101	107	16.6538
((....	chr4:169910917-169911166(-)$1	1	40	46	13.4807
(.....	chr7:94184953-94185204(+)$1	1	62	68	16.6538
(.....	chr9:132651990-132652362(-)$1	1	80	86	13.8653
(((...	chr7:138729790-138730113(-)$1	1	88	94	16.6538
(.....	chr15:64461225-64461516(-)$1	1	247	253	13.8653
..))))	chr1:45285500-45285749(-)$1	1	165	171	16.6538
((....	chr1:227847456-227847714(+)$1	1	86	92	16.6538
(((((.	chr1:160515935-160516197(-)$1	1	2	8	13.4807
......	chr6:158518340-158518566(+)$1	1	64	70	16.6538
..))))	chr8:37993142-37993369(+)$1	1	91	97	16.6538
..((((	chr2:203425601-203425851(+)$1	1	17	23	16.6538
...)).	chr10:76468537-76468790(+)$1	1	32	38	16.6538
.))...	chr2:61275972-61276244(+)$1	1	184	190	16.6538
.....)	chr19:36828326-36828551(-)$1	1	198	204	16.6538
......	chr13:37596379-37596694(-)$1	1	33	39	16.6538
(.....	chr12:27955346-27955584(+)$1	1	78	84	16.6538
((((((	chr11:121179063-121179315(+)$1	1	45	51	16.6538
......	chr1:35482839-35483071(-)$1	1	13	19	16.6538
))))))	chr1:183596310-183596556(-)$1	1	230	236	16.6538
))))))	chr5:154194157-154194432(+)$1	1	226	232	16.6538
((((((	chr6:45517524-45517785(+)$1	1	75	81	13.8653
......	chr2:62227802-62228029(+)$1	1	4	10	16.6538
......	chr2:55626734-55626971(-)$1	1	124	130	16.6538
((.(((	chr7:86825026-86825257(+)$1	1	34	40	13.4807
....((	chr3:107764850-107765153(-)$1	1	261	267	13.4807
))))))	chr10:70516196-70516473(+)$1	1	61	67	13.8653
)).)))	chr1:160186593-160186981(-)$1	1	349	355	16.6538
((....	chr1:2118281-2118538(-)$1	1	100	106	16.6538
))....	chr14:68058697-68058919(-)$1	1	146	152	13.8653
.(((((	chr4:83848570-83848802(-)$1	1	131	137	16.6538
(.....	chr5:38940194-38940464(-)$1	1	88	94	16.6538
...)))	chr2:197643243-197643497(-)$1	1	202	208	13.4807
...)))	chr15:23005751-23005989(-)$1	1	74	80	16.6538
).))))	chr5:167983460-167983709(-)$1	1	122	128	13.8653

#PSSM
A : 0.61	C : 0.17	a : 0.11	G : 0.09	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.90	u : 0.09	

#score	825.0384615384628
#seq	52
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m3_run1.nuc.txt

#NT

#otherMatches

#Struct PSSM
ccc]ddddFFFFFFeeeeemmmmeeeee::CCCKKEEEEEDDDD::::GGGGGGGKKAKKHHHHHHHHKKFFFFFFEEEEECCC:::::::FFFFFF:::ccc!!ggggggg!!bb####ffffffnnnnnffffff55555bb]ggggggg333ccc:::::ddddmmmmdddd::::::::FFFFFF::::::::::cccmmmmccc:CCCZZZEEEEE}FFFFFF~~~~HHHHHHHHYYAYYGGGGGGG::::::eeeeemmmmeeeee:::::::::	chr8:48882309-48882640(+)$1	331	24	305	843.0000

#DB
))).))))(((((((((((....)))))..(((..(((((((((....(((((((..(..((((((((..((((((((((((((.......((((((...(((..(((((((..((....((((((.....)))))).....)).)))))))...))).....((((....))))........))))))..........(((....))).)))...))))).))))))....))))))))..)..)))))))......(((((....))))).........	chr8:48882309-48882640(+)$1	1	24	305	843.0000

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

#score	843.0
#seq	1
#width	281
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m2_run1.nuc.txt

#NT
AAAUGUGU	chr16:69341999-69342286(+)$1	287	117	125	11.8703
AAAUUUGU	chr12:104341510-104341808(+)$1	298	118	126	11.8703
AAAUCAGU	chr17:73314067-73314411(-)$1	344	148	156	11.1296
AAAGCUUU	chr1:31405481-31405727(-)$1	246	29	37	12.6111
CAAGCUGU	chr1:22854743-22855001(+)$1	258	74	82	12.3333
AAAGAUGU	chr15:31665358-31665631(+)$1	273	34	42	13.4444
AAACUUGU	chr6:90077578-90077856(-)$1	278	265	273	11.9629
AAAGCUUU	chr5:110835472-110835784(-)$1	312	189	197	12.6111
AAAUCUGG	chr17:72199721-72199991(+)$1	270	191	199	11.9629
AAAGCAGU	chr8:38831243-38831524(+)$1	281	19	27	12.1481
AAAGCUUU	chr1:203276968-203277302(+)$1	334	257	265	12.6111
AAAAAUGU	chr3:69154824-69155169(+)$1	345	105	113	12.2407
AAAGCUGU	chr12:8088561-8088859(-)$1	298	170	178	16.5925
AAAUCUGG	chr5:55234292-55234537(-)$1	245	41	49	11.9629
AAAACUGC	chr4:139979702-139980005(-)$1	303	66	74	11.4074
AUAGCUGU	chr17:7833864-7834149(-)$1	285	93	101	12.7962
AAUCCUGU	chr9:14085373-14085638(-)$1	265	37	45	11.1296
CAACCUGU	chr16:89629190-89629645(+)$1	455	80	88	11.4074
AAAACUGG	chr3:179341952-179342195(+)$1	243	70	78	11.7777
AAACCUGA	chr5:72801065-72801336(+)$1	271	20	28	11.5925
UAAGCUGU	chr12:392983-393248(-)$1	265	209	217	12.5185
AAAGCUGG	chr16:3022702-3023082(-)$1	380	189	197	12.9814
AAGGCUGU	chr17:66038138-66038408(+)$1	270	225	233	11.9629
AAUUCUGU	chr9:129647103-129647343(+)$1	240	35	43	11.0370
AAAACUUU	chr1:78162000-78162372(-)$1	372	4	12	11.4074
AGAACUGU	chr10:127431705-127431951(+)$1	246	215	223	11.3148
ACAACUGU	chr20:30389003-30389291(+)$1	288	23	31	11.5925
AAAUGUGU	chr12:80772710-80772951(+)$1	241	0	8	11.8703
AAAGCUGU	chr12:123349781-123350060(-)$1	279	141	149	16.5925
UAAGCUGU	chr1:206941520-206941986(-)$1	466	251	259	12.5185
AAAGCUUU	chr6:99957949-99958195(-)$1	246	120	128	12.6111
AAACCUGU	chr16:85840425-85840712(+)$1	287	126	134	15.6666
AAAGCAGU	chr9:14082737-14083020(-)$1	283	103	111	12.1481
ACAGCUGU	chr5:61681837-61682095(+)$1	258	4	12	12.7962
AAAGAUGU	chr17:36924280-36924562(-)$1	282	162	170	13.4444
AUACCUGU	chr12:50152082-50152342(+)$1	260	42	50	11.8703
UAAGCUGU	chr1:192984625-192984868(-)$1	243	137	145	12.5185
AAAGCUGC	chr8:133024043-133024310(+)$1	267	120	128	12.6111
AAAGAUGU	chr19:39127441-39127698(+)$1	257	134	142	13.4444
AAAUAUGU	chr5:125960476-125960749(+)$1	273	191	199	12.4259
AAAGCUGU	chr15:79189240-79189546(+)$1	306	157	165	16.5925
AAAAAUGU	chr10:111895080-111895412(+)$1	332	158	166	12.2407
AAACCUGG	chr2:65496936-65497263(+)$1	327	55	63	12.0555
ACACCUGU	chr17:36358753-36359061(-)$1	308	82	90	11.8703
AAACCUGU	chr11:47487738-47488115(-)$1	377	22	30	15.6666
AAACAUGU	chr11:70230063-70230355(+)$1	292	67	75	12.5185
AAAUCUGU	chr2:42559320-42559559(+)$1	239	177	185	15.5740
ACAGCUGU	chr17:73315929-73316243(-)$1	314	211	219	12.7962
UAAACUGU	chr7:115891718-115891958(+)$1	240	166	174	11.3148
AAACCUCU	chr11:67052906-67053153(+)$1	247	35	43	11.3148
AUAUCUGU	chr1:24289131-24289454(+)$1	323	9	17	11.7777
AAAAAUGU	chr9:114432016-114432317(+)$1	301	280	288	12.2407
AAAUCUGG	chr9:114124063-114124328(-)$1	265	6	14	11.9629

#otherMatches

#Struct PSSM
333dddd:	chr16:56973813-56974099(+)$1	286	48	56	11.8703
ttthhhhh	chr16:69341999-69342286(+)$1	287	117	125	11.8703
ggggggg]	chr12:104341510-104341808(+)$1	298	118	126	11.8703
666eeeee	chr17:73314067-73314411(-)$1	344	148	156	11.1296
::::dddd	chr1:31405481-31405727(-)$1	246	29	37	12.6111
eellleee	chr1:22854743-22855001(+)$1	258	74	82	12.3333
mmccc]af	chr15:31665358-31665631(+)$1	273	34	42	13.4444
mmmmdddd	chr6:90077578-90077856(-)$1	278	265	273	11.9629
:::eeeee	chr5:110835472-110835784(-)$1	312	189	197	12.6111
llffffff	chr17:72199721-72199991(+)$1	270	191	199	11.9629
Jdddd[ee	chr8:38831243-38831524(+)$1	281	19	27	12.1481
7777bb]d	chr1:203276968-203277302(+)$1	334	257	265	12.6111
tttttttt	chr3:69154824-69155169(+)$1	345	105	113	12.2407
nndddd::	chr12:8088561-8088859(-)$1	298	170	178	16.5925
qqqqqbb]	chr5:55234292-55234537(-)$1	245	41	49	11.9629
GGGGGGJJ	chr4:139979702-139980005(-)$1	303	66	74	11.4074
gggooooo	chr17:7833864-7834149(-)$1	285	93	101	12.7962
:::::eee	chr9:14085373-14085638(-)$1	265	37	45	11.1296
ggggg:::	chr16:89629190-89629645(+)$1	455	80	88	11.4074
66666ccc	chr3:179341952-179342195(+)$1	243	70	78	11.7777
JJJJ{BBC	chr5:72801065-72801336(+)$1	271	20	28	11.5925
ccnnnnnc	chr12:392983-393248(-)$1	265	209	217	12.5185
qqqqqqee	chr16:3022702-3023082(-)$1	380	189	197	12.9814
cdddd]cc	chr17:66038138-66038408(+)$1	270	225	233	11.9629
++ccc[bb	chr9:129647103-129647343(+)$1	240	35	43	11.0370
eeemmmme	chr1:78162000-78162372(-)$1	372	4	12	11.4074
:::::GGG	chr10:127431705-127431951(+)$1	246	215	223	11.3148
hhhh"""c	chr20:30389003-30389291(+)$1	288	23	31	11.5925
::::::::	chr12:80772710-80772951(+)$1	241	0	8	11.8703
eee!!bbd	chr12:123349781-123350060(-)$1	279	141	149	16.5925
%bbmmmmb	chr1:206941520-206941986(-)$1	466	251	259	12.5185
:::eeeee	chr6:99957949-99958195(-)$1	246	120	128	12.6111
dddd!!ee	chr16:85840425-85840712(+)$1	287	126	134	15.6666
>>>bb]a]	chr9:14082737-14083020(-)$1	283	103	111	12.1481
C::hhhhh	chr5:61681837-61682095(+)$1	258	4	12	12.7962
ff::::dd	chr17:36924280-36924562(-)$1	282	162	170	13.4444
eeeEEEEE	chr12:50152082-50152342(+)$1	260	42	50	11.8703
mmdddd::	chr1:192984625-192984868(-)$1	243	137	145	12.5185
:::bb[gg	chr8:133024043-133024310(+)$1	267	120	128	12.6111
ccc]bb]b	chr19:39127441-39127698(+)$1	257	134	142	13.4444
666666hh	chr5:125960476-125960749(+)$1	273	191	199	12.4259
:ccc[bb[	chr15:79189240-79189546(+)$1	306	157	165	16.5925
iiiiiiii	chr10:111895080-111895412(+)$1	332	158	166	12.2407
DDDD{HHH	chr2:65496936-65497263(+)$1	327	55	63	12.0555
=bb!!fff	chr17:36358753-36359061(-)$1	308	82	90	11.8703
ddd333dd	chr11:47487738-47488115(-)$1	377	22	30	15.6666
dd::::ii	chr11:70230063-70230355(+)$1	292	67	75	12.5185
ppccc333	chr2:42559320-42559559(+)$1	239	177	185	15.5740
FFFFF:::	chr17:73315929-73316243(-)$1	314	211	219	12.7962
qqqqqqee	chr7:115891718-115891958(+)$1	240	166	174	11.3148
::::::::	chr11:67052906-67053153(+)$1	247	35	43	11.3148
::::::::	chr1:24289131-24289454(+)$1	323	9	17	11.7777
fffmmmmf	chr9:114432016-114432317(+)$1	301	280	288	12.2407
$$$ddddq	chr9:114124063-114124328(-)$1	265	6	14	11.9629

#DB
...)))).	chr16:56973813-56974099(+)$1	1	48	56	11.8703
...)))))	chr16:69341999-69342286(+)$1	1	117	125	11.8703
))))))).	chr12:104341510-104341808(+)$1	1	118	126	11.8703
...)))))	chr17:73314067-73314411(-)$1	1	148	156	11.1296
....((((	chr1:31405481-31405727(-)$1	1	29	37	12.6111
((...)))	chr1:22854743-22855001(+)$1	1	74	82	12.3333
..))).))	chr15:31665358-31665631(+)$1	1	34	42	13.4444
....))))	chr6:90077578-90077856(-)$1	1	265	273	11.9629
...(((((	chr5:110835472-110835784(-)$1	1	189	197	12.6111
..))))))	chr17:72199721-72199991(+)$1	1	191	199	11.9629
(((((.((	chr8:38831243-38831524(+)$1	1	19	27	12.1481
....)).)	chr1:203276968-203277302(+)$1	1	257	265	12.6111
........	chr3:69154824-69155169(+)$1	1	105	113	12.2407
..))))..	chr12:8088561-8088859(-)$1	1	170	178	16.5925
.....)).	chr5:55234292-55234537(-)$1	1	41	49	11.9629
((((((((	chr4:139979702-139980005(-)$1	1	66	74	11.4074
(((.....	chr17:7833864-7834149(-)$1	1	93	101	12.7962
.....(((	chr9:14085373-14085638(-)$1	1	37	45	11.1296
)))))...	chr16:89629190-89629645(+)$1	1	80	88	11.4074
.....)))	chr3:179341952-179342195(+)$1	1	70	78	11.7777
((((.(((	chr5:72801065-72801336(+)$1	1	20	28	11.5925
((.....)	chr12:392983-393248(-)$1	1	209	217	12.5185
......))	chr16:3022702-3023082(-)$1	1	189	197	12.9814
))))).))	chr17:66038138-66038408(+)$1	1	225	233	11.9629
..(((.((	chr9:129647103-129647343(+)$1	1	35	43	11.0370
(((....)	chr1:78162000-78162372(-)$1	1	4	12	11.4074
.....)))	chr10:127431705-127431951(+)$1	1	215	223	11.3148
((((...(	chr20:30389003-30389291(+)$1	1	23	31	11.5925
........	chr12:80772710-80772951(+)$1	1	0	8	11.8703
(((..(((	chr12:123349781-123350060(-)$1	1	141	149	16.5925
.((....)	chr1:206941520-206941986(-)$1	1	251	259	12.5185
...(((((	chr6:99957949-99958195(-)$1	1	120	128	12.6111
((((..((	chr16:85840425-85840712(+)$1	1	126	134	15.6666
...)).).	chr9:14082737-14083020(-)$1	1	103	111	12.1481
(..(((((	chr5:61681837-61682095(+)$1	1	4	12	12.7962
))....((	chr17:36924280-36924562(-)$1	1	162	170	13.4444
)))(((((	chr12:50152082-50152342(+)$1	1	42	50	11.8703
..))))..	chr1:192984625-192984868(-)$1	1	137	145	12.5185
...((.((	chr8:133024043-133024310(+)$1	1	120	128	12.6111
))).)).)	chr19:39127441-39127698(+)$1	1	134	142	13.4444
......))	chr5:125960476-125960749(+)$1	1	191	199	12.4259
.(((.((.	chr15:79189240-79189546(+)$1	1	157	165	16.5925
))))))))	chr10:111895080-111895412(+)$1	1	158	166	12.2407
((((.(((	chr2:65496936-65497263(+)$1	1	55	63	12.0555
(((..(((	chr17:36358753-36359061(-)$1	1	82	90	11.8703
)))...))	chr11:47487738-47488115(-)$1	1	22	30	15.6666
))....((	chr11:70230063-70230355(+)$1	1	67	75	12.5185
..)))...	chr2:42559320-42559559(+)$1	1	177	185	15.5740
(((((...	chr17:73315929-73316243(-)$1	1	211	219	12.7962
......))	chr7:115891718-115891958(+)$1	1	166	174	11.3148
........	chr11:67052906-67053153(+)$1	1	35	43	11.3148
........	chr1:24289131-24289454(+)$1	1	9	17	11.7777
(((....)	chr9:114432016-114432317(+)$1	1	280	288	12.2407
...((((.	chr9:114124063-114124328(-)$1	1	6	14	11.9629

#PSSM
A : 0.88	U : 0.07	C : 0.03	
A : 0.83	U : 0.07	C : 0.07	G : 0.01	
A : 0.94	U : 0.03	G : 0.01	
G : 0.40	C : 0.22	U : 0.20	A : 0.16	
C : 0.77	A : 0.14	G : 0.03	U : 0.03	
U : 0.94	A : 0.05	
G : 0.88	U : 0.09	C : 0.01	
U : 0.83	G : 0.11	C : 0.03	A : 0.01	

#score	678.5925925925917
#seq	54
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m3_run1.nuc.txt

#NT
UCUG	chr6:27100725-27100968(+)$1	243	128	132	12.0000
UCUG	chr11:46798957-46799234(-)$1	277	12	16	12.0000
UCUG	chr12:7045824-7046184(+)$1	360	124	128	12.0000
UCUG	chr11:114278083-114278346(+)$1	263	9	13	12.0000
ucug	chr5:64837063-64837459(-)$1	396	143	147	12.0000
ucug	chr19:1216127-1216379(+)$1	252	150	154	12.0000
UCUG	chr20:39795397-39795773(+)$1	376	167	171	12.0000
UCUG	chr6:97247373-97247640(-)$1	267	3	7	12.0000
UCUG	chr2:85779959-85780212(-)$1	253	1	5	12.0000
UCUG	chr11:108121690-108121982(+)$1	292	69	73	12.0000
ucug	chr19:37975977-37976224(+)$1	247	221	225	12.0000
UCUG	chr2:25965437-25965680(-)$1	243	48	52	12.0000
UCUG	chr7:128449568-128449834(+)$1	266	135	139	12.0000
UCUG	chr13:39587814-39588060(-)$1	246	79	83	12.0000
UCUG	chr14:24707940-24708356(+)$1	416	131	135	12.0000
UCUG	chr7:2686400-2686667(+)$1	267	0	4	12.0000
UCUG	chr11:32954600-32954934(+)$1	334	19	23	12.0000
ucug	chr3:194338333-194338625(-)$1	292	160	164	12.0000
UCUG	chr12:978178-978453(+)$1	275	12	16	12.0000
UCUG	chr9:95219420-95219729(+)$1	309	182	186	12.0000
UCUG	chr1:169822006-169822318(+)$1	312	177	181	12.0000
UCUG	chr9:95609830-95610067(-)$1	237	24	28	12.0000
UCUG	chr2:55522369-55522632(-)$1	263	232	236	12.0000
UCUG	chr11:118183473-118183844(+)$1	371	45	49	12.0000
UCUG	chr10:15145740-15145975(+)$1	235	215	219	12.0000
UCUG	chr15:50884079-50884362(-)$1	283	109	113	12.0000
UCUG	chr1:32744985-32745318(+)$1	333	104	108	12.0000
UCUG	chr7:135073439-135073717(-)$1	278	200	204	12.0000
UCUG	chr1:26230042-26230294(-)$1	252	67	71	12.0000
UCUG	chr3:118931290-118931548(-)$1	258	49	53	12.0000
UCUG	chr2:136418795-136419051(+)$1	256	110	114	12.0000
UCUg	chr6:139236846-139237119(-)$1	273	233	237	12.0000
UCUG	chr11:62469835-62470120(-)$1	285	128	132	12.0000
UCUG	chr15:40913522-40913767(+)$1	245	74	78	12.0000
UCUG	chr11:43413364-43413639(+)$1	275	30	34	12.0000
UCUG	chr17:4883276-4883530(-)$1	254	6	10	12.0000
UCUG	chr17:41246549-41246781(-)$1	232	26	30	12.0000
UCUG	chr21:43676522-43676793(+)$1	271	140	144	12.0000
UCUG	chr1:198671434-198671797(+)$1	363	19	23	12.0000
UCUG	chr2:182340450-182340855(+)$1	405	178	182	12.0000
UCUG	chr13:33091797-33092061(-)$1	264	100	104	12.0000
UCUG	chr10:64973422-64973675(-)$1	253	91	95	12.0000
UCUG	chr9:134073264-134073504(+)$1	240	216	220	12.0000
UCUG	chr21:47613489-47613770(-)$1	281	61	65	12.0000
UCUG	chr10:38343862-38344284(+)$1	422	134	138	12.0000
UCUG	chr12:49087301-49087563(-)$1	262	49	53	12.0000
UCUG	chr8:101270910-101271183(-)$1	273	37	41	12.0000
UCUG	chr17:4848206-4848459(+)$1	253	125	129	12.0000
UCUG	chr17:44632561-44632801(-)$1	240	189	193	12.0000
UCUG	chr12:56515373-56515611(+)$1	238	140	144	12.0000
UCUG	chr13:33110662-33110900(-)$1	238	222	226	12.0000
UCUG	chr2:111395376-111395647(-)$1	271	152	156	12.0000
UCUG	chr15:44951293-44951587(-)$1	294	266	270	12.0000
UCUG	chr4:24577885-24578273(-)$1	388	189	193	12.0000
UCUG	chr2:182780781-182781030(+)$1	249	1	5	12.0000
UCUG	chr18:54443864-54444144(+)$1	280	8	12	12.0000
UCUG	chr10:43089167-43089500(-)$1	333	47	51	12.0000
UCUG	chr2:181927502-181927748(+)$1	246	2	6	12.0000
UCUG	chr10:70256072-70256315(-)$1	243	135	139	12.0000
UCUG	chr2:209169628-209169881(+)$1	253	126	130	12.0000
UCUG	chr4:1018930-1019230(+)$1	300	216	220	12.0000
UCUG	chr14:104165615-104165915(+)$1	300	23	27	12.0000
UCUG	chr17:56082805-56083103(-)$1	298	52	56	12.0000
UCUG	chr11:5566093-5566340(-)$1	247	68	72	12.0000
UCUG	chr20:49509418-49509706(-)$1	288	165	169	12.0000
UCUG	chr13:99947227-99947505(+)$1	278	121	125	12.0000
UCUG	chr14:24034999-24035283(-)$1	284	218	222	12.0000
UCUG	chr5:147819179-147819443(+)$1	264	85	89	12.0000
UCUG	chr19:44792562-44792806(-)$1	244	217	221	12.0000
UCUG	chr11:36597532-36597796(+)$1	264	47	51	12.0000
UCUG	chr1:171526950-171527244(+)$1	294	264	268	12.0000
UCUG	chr22:39425274-39425525(+)$1	251	61	65	12.0000
UCUG	chr5:180662253-180662622(+)$1	369	132	136	12.0000
UCUG	chr11:134118666-134118920(-)$1	254	40	44	12.0000
UCUG	chr5:177636317-177636576(-)$1	259	23	27	12.0000
UCUG	chr3:152058393-152058713(+)$1	320	293	297	12.0000

#otherMatches

#Struct PSSM
:ddd	chr2:46787591-46787841(+)$1	250	17	21	12.0000
:::G	chr6:27100725-27100968(+)$1	243	128	132	12.0000
ADDD	chr11:46798957-46799234(-)$1	277	12	16	12.0000
?III	chr12:7045824-7046184(+)$1	360	124	128	12.0000
RRRR	chr11:114278083-114278346(+)$1	263	9	13	12.0000
ffff	chr5:64837063-64837459(-)$1	396	143	147	12.0000
"""b	chr19:1216127-1216379(+)$1	252	150	154	12.0000
c[bb	chr20:39795397-39795773(+)$1	376	167	171	12.0000
DDDL	chr6:97247373-97247640(-)$1	267	3	7	12.0000
CC:D	chr2:85779959-85780212(-)$1	253	1	5	12.0000
dddd	chr11:108121690-108121982(+)$1	292	69	73	12.0000
!!cc	chr19:37975977-37976224(+)$1	247	221	225	12.0000
ccc]	chr2:25965437-25965680(-)$1	243	48	52	12.0000
eee:	chr7:128449568-128449834(+)$1	266	135	139	12.0000
pppp	chr13:39587814-39588060(-)$1	246	79	83	12.0000
B{GG	chr14:24707940-24708356(+)$1	416	131	135	12.0000
:FFF	chr7:2686400-2686667(+)$1	267	0	4	12.0000
eeee	chr11:32954600-32954934(+)$1	334	19	23	12.0000
====	chr3:194338333-194338625(-)$1	292	160	164	12.0000
CCMM	chr12:978178-978453(+)$1	275	12	16	12.0000
DDDD	chr9:95219420-95219729(+)$1	309	182	186	12.0000
====	chr1:169822006-169822318(+)$1	312	177	181	12.0000
dddd	chr9:95609830-95610067(-)$1	237	24	28	12.0000
mmmd	chr2:55522369-55522632(-)$1	263	232	236	12.0000
33dd	chr11:118183473-118183844(+)$1	371	45	49	12.0000
====	chr10:15145740-15145975(+)$1	235	215	219	12.0000
ffff	chr15:50884079-50884362(-)$1	283	109	113	12.0000
::::	chr1:32744985-32745318(+)$1	333	104	108	12.0000
YYCC	chr7:135073439-135073717(-)$1	278	200	204	12.0000
FFFF	chr1:26230042-26230294(-)$1	252	67	71	12.0000
d:::	chr3:118931290-118931548(-)$1	258	49	53	12.0000
occc	chr2:136418795-136419051(+)$1	256	110	114	12.0000
EEEE	chr6:139236846-139237119(-)$1	273	233	237	12.0000
dd""	chr11:62469835-62470120(-)$1	285	128	132	12.0000
cccc	chr15:40913522-40913767(+)$1	245	74	78	12.0000
ggge	chr11:43413364-43413639(+)$1	275	30	34	12.0000
HHHH	chr17:4883276-4883530(-)$1	254	6	10	12.0000
FFFF	chr17:41246549-41246781(-)$1	232	26	30	12.0000
###c	chr21:43676522-43676793(+)$1	271	140	144	12.0000
HHHH	chr1:198671434-198671797(+)$1	363	19	23	12.0000
dddd	chr2:182340450-182340855(+)$1	405	178	182	12.0000
bb[d	chr13:33091797-33092061(-)$1	264	100	104	12.0000
^^gg	chr10:64973422-64973675(-)$1	253	91	95	12.0000
::DD	chr9:134073264-134073504(+)$1	240	216	220	12.0000
iiii	chr21:47613489-47613770(-)$1	281	61	65	12.0000
ccc[	chr10:38343862-38344284(+)$1	422	134	138	12.0000
dddm	chr12:49087301-49087563(-)$1	262	49	53	12.0000
qddd	chr8:101270910-101271183(-)$1	273	37	41	12.0000
llld	chr17:4848206-4848459(+)$1	253	125	129	12.0000
ppcc	chr17:44632561-44632801(-)$1	240	189	193	12.0000
::hh	chr12:56515373-56515611(+)$1	238	140	144	12.0000
ffff	chr13:33110662-33110900(-)$1	238	222	226	12.0000
oooo	chr2:111395376-111395647(-)$1	271	152	156	12.0000
DDD~	chr15:44951293-44951587(-)$1	294	266	270	12.0000
eeee	chr4:24577885-24578273(-)$1	388	189	193	12.0000
:::F	chr2:182780781-182781030(+)$1	249	1	5	12.0000
H::h	chr18:54443864-54444144(+)$1	280	8	12	12.0000
ccc[	chr10:43089167-43089500(-)$1	333	47	51	12.0000
iiii	chr2:181927502-181927748(+)$1	246	2	6	12.0000
eee2	chr10:70256072-70256315(-)$1	243	135	139	12.0000
"""d	chr2:209169628-209169881(+)$1	253	126	130	12.0000
eeee	chr4:1018930-1019230(+)$1	300	216	220	12.0000
EEEE	chr14:104165615-104165915(+)$1	300	23	27	12.0000
meee	chr17:56082805-56083103(-)$1	298	52	56	12.0000
mmmb	chr11:5566093-5566340(-)$1	247	68	72	12.0000
%%%%	chr20:49509418-49509706(-)$1	288	165	169	12.0000
qqhh	chr13:99947227-99947505(+)$1	278	121	125	12.0000
dd]c	chr14:24034999-24035283(-)$1	284	218	222	12.0000
:ccc	chr5:147819179-147819443(+)$1	264	85	89	12.0000
dddd	chr19:44792562-44792806(-)$1	244	217	221	12.0000
FFDD	chr11:36597532-36597796(+)$1	264	47	51	12.0000
BDDD	chr1:171526950-171527244(+)$1	294	264	268	12.0000
cc]a	chr22:39425274-39425525(+)$1	251	61	65	12.0000
eeee	chr5:180662253-180662622(+)$1	369	132	136	12.0000
:ddd	chr11:134118666-134118920(-)$1	254	40	44	12.0000
:::E	chr5:177636317-177636576(-)$1	259	23	27	12.0000
EEEE	chr3:152058393-152058713(+)$1	320	293	297	12.0000

#DB
.(((	chr2:46787591-46787841(+)$1	1	17	21	12.0000
...)	chr6:27100725-27100968(+)$1	1	128	132	12.0000
((((	chr11:46798957-46799234(-)$1	1	12	16	12.0000
.)))	chr12:7045824-7046184(+)$1	1	124	128	12.0000
....	chr11:114278083-114278346(+)$1	1	9	13	12.0000
((((	chr5:64837063-64837459(-)$1	1	143	147	12.0000
...(	chr19:1216127-1216379(+)$1	1	150	154	12.0000
(.((	chr20:39795397-39795773(+)$1	1	167	171	12.0000
(((.	chr6:97247373-97247640(-)$1	1	3	7	12.0000
((.(	chr2:85779959-85780212(-)$1	1	1	5	12.0000
))))	chr11:108121690-108121982(+)$1	1	69	73	12.0000
..((	chr19:37975977-37976224(+)$1	1	221	225	12.0000
))).	chr2:25965437-25965680(-)$1	1	48	52	12.0000
))).	chr7:128449568-128449834(+)$1	1	135	139	12.0000
....	chr13:39587814-39588060(-)$1	1	79	83	12.0000
(.((	chr14:24707940-24708356(+)$1	1	131	135	12.0000
.(((	chr7:2686400-2686667(+)$1	1	0	4	12.0000
((((	chr11:32954600-32954934(+)$1	1	19	23	12.0000
))))	chr3:194338333-194338625(-)$1	1	160	164	12.0000
((..	chr12:978178-978453(+)$1	1	12	16	12.0000
))))	chr9:95219420-95219729(+)$1	1	182	186	12.0000
((((	chr1:169822006-169822318(+)$1	1	177	181	12.0000
((((	chr9:95609830-95610067(-)$1	1	24	28	12.0000
...)	chr2:55522369-55522632(-)$1	1	232	236	12.0000
..))	chr11:118183473-118183844(+)$1	1	45	49	12.0000
))))	chr10:15145740-15145975(+)$1	1	215	219	12.0000
))))	chr15:50884079-50884362(-)$1	1	109	113	12.0000
....	chr1:32744985-32745318(+)$1	1	104	108	12.0000
..))	chr7:135073439-135073717(-)$1	1	200	204	12.0000
((((	chr1:26230042-26230294(-)$1	1	67	71	12.0000
)...	chr3:118931290-118931548(-)$1	1	49	53	12.0000
.)))	chr2:136418795-136419051(+)$1	1	110	114	12.0000
))))	chr6:139236846-139237119(-)$1	1	233	237	12.0000
((..	chr11:62469835-62470120(-)$1	1	128	132	12.0000
((((	chr15:40913522-40913767(+)$1	1	74	78	12.0000
))))	chr11:43413364-43413639(+)$1	1	30	34	12.0000
((((	chr17:4883276-4883530(-)$1	1	6	10	12.0000
((((	chr17:41246549-41246781(-)$1	1	26	30	12.0000
...(	chr21:43676522-43676793(+)$1	1	140	144	12.0000
((((	chr1:198671434-198671797(+)$1	1	19	23	12.0000
))))	chr2:182340450-182340855(+)$1	1	178	182	12.0000
((.(	chr13:33091797-33092061(-)$1	1	100	104	12.0000
..))	chr10:64973422-64973675(-)$1	1	91	95	12.0000
..))	chr9:134073264-134073504(+)$1	1	216	220	12.0000
))))	chr21:47613489-47613770(-)$1	1	61	65	12.0000
(((.	chr10:38343862-38344284(+)$1	1	134	138	12.0000
(((.	chr12:49087301-49087563(-)$1	1	49	53	12.0000
.)))	chr8:101270910-101271183(-)$1	1	37	41	12.0000
...)	chr17:4848206-4848459(+)$1	1	125	129	12.0000
..))	chr17:44632561-44632801(-)$1	1	189	193	12.0000
..((	chr12:56515373-56515611(+)$1	1	140	144	12.0000
((((	chr13:33110662-33110900(-)$1	1	222	226	12.0000
....	chr2:111395376-111395647(-)$1	1	152	156	12.0000
))).	chr15:44951293-44951587(-)$1	1	266	270	12.0000
))))	chr4:24577885-24578273(-)$1	1	189	193	12.0000
...(	chr2:182780781-182781030(+)$1	1	1	5	12.0000
(..(	chr18:54443864-54444144(+)$1	1	8	12	12.0000
(((.	chr10:43089167-43089500(-)$1	1	47	51	12.0000
((((	chr2:181927502-181927748(+)$1	1	2	6	12.0000
))).	chr10:70256072-70256315(-)$1	1	135	139	12.0000
...(	chr2:209169628-209169881(+)$1	1	126	130	12.0000
((((	chr4:1018930-1019230(+)$1	1	216	220	12.0000
((((	chr14:104165615-104165915(+)$1	1	23	27	12.0000
.)))	chr17:56082805-56083103(-)$1	1	52	56	12.0000
...)	chr11:5566093-5566340(-)$1	1	68	72	12.0000
....	chr20:49509418-49509706(-)$1	1	165	169	12.0000
..))	chr13:99947227-99947505(+)$1	1	121	125	12.0000
)).)	chr14:24034999-24035283(-)$1	1	218	222	12.0000
.(((	chr5:147819179-147819443(+)$1	1	85	89	12.0000
))))	chr19:44792562-44792806(-)$1	1	217	221	12.0000
((((	chr11:36597532-36597796(+)$1	1	47	51	12.0000
))))	chr1:171526950-171527244(+)$1	1	264	268	12.0000
)).)	chr22:39425274-39425525(+)$1	1	61	65	12.0000
))))	chr5:180662253-180662622(+)$1	1	132	136	12.0000
.(((	chr11:134118666-134118920(-)$1	1	40	44	12.0000
...(	chr5:177636317-177636576(-)$1	1	23	27	12.0000
))))	chr3:152058393-152058713(+)$1	1	293	297	12.0000

#PSSM
U : 0.94	u : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	
G : 0.93	g : 0.06	

#score	924.0
#seq	77
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m3_run2.nuc.txt

#NT
UGC	chr17:43227163-43227388(-)$1	225	40	43	8.9999
UGC	chrX:37913519-37913743(-)$1	224	2	5	8.9999
UGC	chr1:246887776-246887998(+)$1	222	66	69	8.9999
UGC	chr2:37035699-37035928(-)$1	229	45	48	8.9999
UGC	chr3:195466657-195466880(+)$1	223	7	10	8.9999
UGC	chr2:32853324-32853549(+)$1	225	16	19	8.9999
UGC	chr16:70889022-70889246(+)$1	224	57	60	8.9999
UGC	chr14:68086680-68086903(+)$1	223	3	6	8.9999
UGC	chr21:34399111-34399332(-)$1	221	50	53	8.9999
UGC	chr12:65230193-65230416(+)$1	223	185	188	8.9999
UGC	chr2:122187568-122187790(-)$1	222	22	25	8.9999
UGC	chr10:75671245-75671467(-)$1	222	46	49	8.9999
UGC	chr15:56125145-56125369(+)$1	224	99	102	8.9999
UGC	chr17:26897804-26898027(+)$1	223	88	91	8.9999
UGC	chr9:90502468-90502690(-)$1	222	4	7	8.9999
UGC	chr5:1494858-1495081(-)$1	223	11	14	8.9999
UGC	chr2:219229321-219229542(-)$1	221	104	107	8.9999
UGC	chr12:132623714-132623938(+)$1	224	41	44	8.9999
UGC	chr1:231472141-231472363(+)$1	222	8	11	8.9999
UGC	chr3:154146793-154147014(-)$1	221	10	13	8.9999
UGC	chr17:11535838-11536066(+)$1	228	154	157	8.9999
UGC	chr9:130251628-130251849(-)$1	221	3	6	8.9999
UGC	chr5:72469879-72470104(-)$1	225	3	6	8.9999
UGC	chr14:38679649-38679879(-)$1	230	71	74	8.9999
UGC	chr3:52818215-52818439(+)$1	224	40	43	8.9999
UGC	chr19:47570637-47570860(-)$1	223	22	25	8.9999
UGC	chr2:95537461-95537683(-)$1	222	42	45	8.9999
UGC	chr5:140802418-140802644(-)$1	226	214	217	8.9999
UGC	chr15:48493597-48493823(+)$1	226	41	44	8.9999
UGC	chr4:3417685-3417910(-)$1	225	53	56	8.9999
UGC	chr3:49060456-49060683(-)$1	227	4	7	8.9999
UGC	chr3:52474729-52474951(+)$1	222	24	27	8.9999
UGC	chr10:127683958-127684183(+)$1	225	4	7	8.9999
UGC	chr1:151287989-151288213(+)$1	224	12	15	8.9999
UGC	chr22:29695609-29695841(+)$1	232	12	15	8.9999
UGC	chr6:90368438-90368661(-)$1	223	212	215	8.9999
UGC	chr3:69101107-69101329(+)$1	222	21	24	8.9999
UGC	chr1:38511992-38512222(+)$1	230	19	22	8.9999
UGC	chr6:3282380-3282604(+)$1	224	41	44	8.9999
UGC	chr11:7981551-7981773(-)$1	222	36	39	8.9999
UGC	chr1:43224777-43224998(+)$1	221	85	88	8.9999
UGC	chr3:50144096-50144381(-)$1	285	41	44	8.9999
UGC	chr11:45832333-45832557(-)$1	224	48	51	8.9999
UGC	chr19:4844668-4844891(-)$1	223	0	3	8.9999
UGC	chr10:104158075-104158301(+)$1	226	54	57	8.9999
UGC	chr16:85942673-85942897(+)$1	224	143	146	8.9999
UGC	chr11:674644-674866(-)$1	222	64	67	8.9999
UGC	chr16:66514958-66515182(+)$1	224	50	53	8.9999
UGC	chr16:57760747-57760969(+)$1	222	24	27	8.9999
UGC	chr1:33480077-33480299(-)$1	222	19	22	8.9999
UGC	chr14:100595872-100596095(+)$1	223	77	80	8.9999
UGC	chr14:100165740-100165969(+)$1	229	10	13	8.9999
UGC	chr1:63119578-63119800(+)$1	222	107	110	8.9999
UGC	chr1:109704523-109704745(+)$1	222	53	56	8.9999
UGC	chr16:88505256-88505480(+)$1	224	191	194	8.9999
UGC	chr19:1612094-1612340(-)$1	246	38	41	8.9999
UGC	chr2:220046007-220046232(-)$1	225	71	74	8.9999
UGC	chr7:32623381-32623602(-)$1	221	80	83	8.9999
UGC	chr7:51240032-51240257(+)$1	225	99	102	8.9999
UGC	chr17:36734888-36735110(-)$1	222	45	48	8.9999
UGC	chr20:30555902-30556127(-)$1	225	73	76	8.9999
UGC	chr1:93594774-93594996(-)$1	222	14	17	8.9999
UGC	chr17:1546907-1547130(-)$1	223	0	3	8.9999
UGC	chr3:52007753-52007978(+)$1	225	6	9	8.9999
UGC	chr18:51863421-51863642(-)$1	221	113	116	8.9999
UGC	chr6:145078950-145079173(-)$1	223	87	90	8.9999
UGC	chr16:2871498-2871719(-)$1	221	9	12	8.9999
UGC	chr2:122125159-122125384(-)$1	225	6	9	8.9999
UGC	chr19:808462-808684(+)$1	222	37	40	8.9999
UGC	chr17:40120189-40120416(+)$1	227	29	32	8.9999
UGC	chr15:40708370-40708592(-)$1	222	43	46	8.9999
UGC	chr19:12902465-12902690(+)$1	225	61	64	8.9999
UGC	chr22:24124375-24124598(-)$1	223	18	21	8.9999
UGC	chr19:56539092-56539314(+)$1	222	8	11	8.9999
UGC	chr8:145675760-145675981(-)$1	221	25	28	8.9999
UGC	chr14:61747100-61747329(-)$1	229	29	32	8.9999
ugc	chr10:11912052-11912294(+)$1	242	9	12	8.9999
UGC	chr1:98058800-98059022(-)$1	222	28	31	8.9999
UGC	chr4:126371635-126371856(-)$1	221	31	34	8.9999
UGC	chr15:64972270-64972493(-)$1	223	33	36	8.9999
UGC	chr1:153930752-153930973(+)$1	221	29	32	8.9999
ugc	chr12:109313426-109313647(-)$1	221	17	20	8.9999
UGC	chr2:166756170-166756391(-)$1	221	52	55	8.9999
UGC	chr7:82538132-82538356(+)$1	224	41	44	8.9999
UGC	chr9:35076604-35076826(-)$1	222	95	98	8.9999
UGC	chr2:202014415-202014638(+)$1	223	109	112	8.9999
UGC	chr1:45091946-45092186(-)$1	240	83	86	8.9999
UGC	chr11:6238590-6238813(+)$1	223	55	58	8.9999
UGC	chr2:207041094-207041317(-)$1	223	1	4	8.9999
UGC	chr2:206630116-206630338(+)$1	222	23	26	8.9999
UGC	chr17:33770708-33770932(+)$1	224	10	13	8.9999
UGC	chr8:94748504-94748730(+)$1	226	33	36	8.9999
UGC	chr17:72348146-72348369(-)$1	223	13	16	8.9999
ugc	chr17:34883285-34883506(+)$1	221	0	3	8.9999
UGC	chr18:29055734-29055958(+)$1	224	56	59	8.9999
UGC	chr3:48623297-48623518(+)$1	221	38	41	8.9999

#otherMatches

#Struct PSSM
B{C	chr20:23065971-23066196(-)$1	225	10	13	8.9999
]bb	chr17:43227163-43227388(-)$1	225	40	43	8.9999
:::	chrX:37913519-37913743(-)$1	224	2	5	8.9999
hhh	chr1:246887776-246887998(+)$1	222	66	69	8.9999
ddd	chr2:37035699-37035928(-)$1	229	45	48	8.9999
ccc	chr3:195466657-195466880(+)$1	223	7	10	8.9999
d]a	chr2:32853324-32853549(+)$1	225	16	19	8.9999
f[e	chr16:70889022-70889246(+)$1	224	57	60	8.9999
:HH	chr14:68086680-68086903(+)$1	223	3	6	8.9999
b]a	chr21:34399111-34399332(-)$1	221	50	53	8.9999
]dd	chr12:65230193-65230416(+)$1	223	185	188	8.9999
ccc	chr2:122187568-122187790(-)$1	222	22	25	8.9999
iii	chr10:75671245-75671467(-)$1	222	46	49	8.9999
DDD	chr15:56125145-56125369(+)$1	224	99	102	8.9999
cc4	chr17:26897804-26898027(+)$1	223	88	91	8.9999
ggg	chr9:90502468-90502690(-)$1	222	4	7	8.9999
eee	chr5:1494858-1495081(-)$1	223	11	14	8.9999
mmc	chr2:219229321-219229542(-)$1	221	104	107	8.9999
ee]	chr12:132623714-132623938(+)$1	224	41	44	8.9999
{BB	chr1:231472141-231472363(+)$1	222	8	11	8.9999
IIL	chr3:154146793-154147014(-)$1	221	10	13	8.9999
ddd	chr17:11535838-11536066(+)$1	228	154	157	8.9999
CCC	chr9:130251628-130251849(-)$1	221	3	6	8.9999
EEE	chr5:72469879-72470104(-)$1	225	3	6	8.9999
ddd	chr14:38679649-38679879(-)$1	230	71	74	8.9999
FFF	chr3:52818215-52818439(+)$1	224	40	43	8.9999
DKK	chr19:47570637-47570860(-)$1	223	22	25	8.9999
[ff	chr2:95537461-95537683(-)$1	222	42	45	8.9999
ccc	chr5:140802418-140802644(-)$1	226	214	217	8.9999
eee	chr15:48493597-48493823(+)$1	226	41	44	8.9999
eee	chr4:3417685-3417910(-)$1	225	53	56	8.9999
ddd	chr3:49060456-49060683(-)$1	227	4	7	8.9999
[cc	chr3:52474729-52474951(+)$1	222	24	27	8.9999
EEE	chr10:127683958-127684183(+)$1	225	4	7	8.9999
BB{	chr1:151287989-151288213(+)$1	224	12	15	8.9999
!ee	chr22:29695609-29695841(+)$1	232	12	15	8.9999
b]a	chr6:90368438-90368661(-)$1	223	212	215	8.9999
[ab	chr3:69101107-69101329(+)$1	222	21	24	8.9999
[dd	chr1:38511992-38512222(+)$1	230	19	22	8.9999
[cc	chr6:3282380-3282604(+)$1	224	41	44	8.9999
""c	chr11:7981551-7981773(-)$1	222	36	39	8.9999
:::	chr1:43224777-43224998(+)$1	221	85	88	8.9999
eee	chr3:50144096-50144381(-)$1	285	41	44	8.9999
:cc	chr11:45832333-45832557(-)$1	224	48	51	8.9999
:::	chr19:4844668-4844891(-)$1	223	0	3	8.9999
888	chr10:104158075-104158301(+)$1	226	54	57	8.9999
fgg	chr16:85942673-85942897(+)$1	224	143	146	8.9999
:bb	chr11:674644-674866(-)$1	222	64	67	8.9999
nnb	chr16:66514958-66515182(+)$1	224	50	53	8.9999
ggg	chr16:57760747-57760969(+)$1	222	24	27	8.9999
eee	chr1:33480077-33480299(-)$1	222	19	22	8.9999
qqq	chr14:100595872-100596095(+)$1	223	77	80	8.9999
HH{	chr14:100165740-100165969(+)$1	229	10	13	8.9999
bb[	chr1:63119578-63119800(+)$1	222	107	110	8.9999
occ	chr1:109704523-109704745(+)$1	222	53	56	8.9999
}GG	chr16:88505256-88505480(+)$1	224	191	194	8.9999
ppp	chr19:1612094-1612340(-)$1	246	38	41	8.9999
CNN	chr2:220046007-220046232(-)$1	225	71	74	8.9999
!!g	chr7:32623381-32623602(-)$1	221	80	83	8.9999
F{G	chr7:51240032-51240257(+)$1	225	99	102	8.9999
GGG	chr17:36734888-36735110(-)$1	222	45	48	8.9999
lcc	chr20:30555902-30556127(-)$1	225	73	76	8.9999
odd	chr1:93594774-93594996(-)$1	222	14	17	8.9999
:gg	chr17:1546907-1547130(-)$1	223	0	3	8.9999
ccn	chr3:52007753-52007978(+)$1	225	6	9	8.9999
c]b	chr18:51863421-51863642(-)$1	221	113	116	8.9999
ffb	chr6:145078950-145079173(-)$1	223	87	90	8.9999
eee	chr16:2871498-2871719(-)$1	221	9	12	8.9999
[cc	chr2:122125159-122125384(-)$1	225	6	9	8.9999
DD{	chr19:808462-808684(+)$1	222	37	40	8.9999
###	chr17:40120189-40120416(+)$1	227	29	32	8.9999
eee	chr15:40708370-40708592(-)$1	222	43	46	8.9999
ddd	chr19:12902465-12902690(+)$1	225	61	64	8.9999
HHH	chr22:24124375-24124598(-)$1	223	18	21	8.9999
"""	chr19:56539092-56539314(+)$1	222	8	11	8.9999
eee	chr8:145675760-145675981(-)$1	221	25	28	8.9999
eee	chr14:61747100-61747329(-)$1	229	29	32	8.9999
J==	chr10:11912052-11912294(+)$1	242	9	12	8.9999
obb	chr1:98058800-98059022(-)$1	222	28	31	8.9999
ccc	chr4:126371635-126371856(-)$1	221	31	34	8.9999
cc]	chr15:64972270-64972493(-)$1	223	33	36	8.9999
:bb	chr1:153930752-153930973(+)$1	221	29	32	8.9999
"cc	chr12:109313426-109313647(-)$1	221	17	20	8.9999
:::	chr2:166756170-166756391(-)$1	221	52	55	8.9999
eee	chr7:82538132-82538356(+)$1	224	41	44	8.9999
c]c	chr9:35076604-35076826(-)$1	222	95	98	8.9999
iii	chr2:202014415-202014638(+)$1	223	109	112	8.9999
]gg	chr1:45091946-45092186(-)$1	240	83	86	8.9999
===	chr11:6238590-6238813(+)$1	223	55	58	8.9999
:DD	chr2:207041094-207041317(-)$1	223	1	4	8.9999
ELL	chr2:206630116-206630338(+)$1	222	23	26	8.9999
ood	chr17:33770708-33770932(+)$1	224	10	13	8.9999
DDD	chr8:94748504-94748730(+)$1	226	33	36	8.9999
{BB	chr17:72348146-72348369(-)$1	223	13	16	8.9999
GGG	chr17:34883285-34883506(+)$1	221	0	3	8.9999
^^^	chr18:29055734-29055958(+)$1	224	56	59	8.9999
]bb	chr3:48623297-48623518(+)$1	221	38	41	8.9999

#DB
(.(	chr20:23065971-23066196(-)$1	1	10	13	8.9999
.))	chr17:43227163-43227388(-)$1	1	40	43	8.9999
...	chrX:37913519-37913743(-)$1	1	2	5	8.9999
)))	chr1:246887776-246887998(+)$1	1	66	69	8.9999
)))	chr2:37035699-37035928(-)$1	1	45	48	8.9999
)))	chr3:195466657-195466880(+)$1	1	7	10	8.9999
).)	chr2:32853324-32853549(+)$1	1	16	19	8.9999
(.(	chr16:70889022-70889246(+)$1	1	57	60	8.9999
.((	chr14:68086680-68086903(+)$1	1	3	6	8.9999
).)	chr21:34399111-34399332(-)$1	1	50	53	8.9999
.))	chr12:65230193-65230416(+)$1	1	185	188	8.9999
(((	chr2:122187568-122187790(-)$1	1	22	25	8.9999
(((	chr10:75671245-75671467(-)$1	1	46	49	8.9999
(((	chr15:56125145-56125369(+)$1	1	99	102	8.9999
)).	chr17:26897804-26898027(+)$1	1	88	91	8.9999
(((	chr9:90502468-90502690(-)$1	1	4	7	8.9999
(((	chr5:1494858-1495081(-)$1	1	11	14	8.9999
..)	chr2:219229321-219229542(-)$1	1	104	107	8.9999
)).	chr12:132623714-132623938(+)$1	1	41	44	8.9999
.((	chr1:231472141-231472363(+)$1	1	8	11	8.9999
((.	chr3:154146793-154147014(-)$1	1	10	13	8.9999
(((	chr17:11535838-11536066(+)$1	1	154	157	8.9999
(((	chr9:130251628-130251849(-)$1	1	3	6	8.9999
(((	chr5:72469879-72470104(-)$1	1	3	6	8.9999
)))	chr14:38679649-38679879(-)$1	1	71	74	8.9999
(((	chr3:52818215-52818439(+)$1	1	40	43	8.9999
(..	chr19:47570637-47570860(-)$1	1	22	25	8.9999
.((	chr2:95537461-95537683(-)$1	1	42	45	8.9999
)))	chr5:140802418-140802644(-)$1	1	214	217	8.9999
)))	chr15:48493597-48493823(+)$1	1	41	44	8.9999
(((	chr4:3417685-3417910(-)$1	1	53	56	8.9999
(((	chr3:49060456-49060683(-)$1	1	4	7	8.9999
.((	chr3:52474729-52474951(+)$1	1	24	27	8.9999
(((	chr10:127683958-127684183(+)$1	1	4	7	8.9999
((.	chr1:151287989-151288213(+)$1	1	12	15	8.9999
.((	chr22:29695609-29695841(+)$1	1	12	15	8.9999
).)	chr6:90368438-90368661(-)$1	1	212	215	8.9999
.((	chr3:69101107-69101329(+)$1	1	21	24	8.9999
.((	chr1:38511992-38512222(+)$1	1	19	22	8.9999
.((	chr6:3282380-3282604(+)$1	1	41	44	8.9999
..(	chr11:7981551-7981773(-)$1	1	36	39	8.9999
...	chr1:43224777-43224998(+)$1	1	85	88	8.9999
)))	chr3:50144096-50144381(-)$1	1	41	44	8.9999
.((	chr11:45832333-45832557(-)$1	1	48	51	8.9999
...	chr19:4844668-4844891(-)$1	1	0	3	8.9999
...	chr10:104158075-104158301(+)$1	1	54	57	8.9999
(((	chr16:85942673-85942897(+)$1	1	143	146	8.9999
.((	chr11:674644-674866(-)$1	1	64	67	8.9999
..)	chr16:66514958-66515182(+)$1	1	50	53	8.9999
)))	chr16:57760747-57760969(+)$1	1	24	27	8.9999
(((	chr1:33480077-33480299(-)$1	1	19	22	8.9999
...	chr14:100595872-100596095(+)$1	1	77	80	8.9999
((.	chr14:100165740-100165969(+)$1	1	10	13	8.9999
((.	chr1:63119578-63119800(+)$1	1	107	110	8.9999
.))	chr1:109704523-109704745(+)$1	1	53	56	8.9999
.))	chr16:88505256-88505480(+)$1	1	191	194	8.9999
...	chr19:1612094-1612340(-)$1	1	38	41	8.9999
(..	chr2:220046007-220046232(-)$1	1	71	74	8.9999
..(	chr7:32623381-32623602(-)$1	1	80	83	8.9999
(.(	chr7:51240032-51240257(+)$1	1	99	102	8.9999
(((	chr17:36734888-36735110(-)$1	1	45	48	8.9999
.))	chr20:30555902-30556127(-)$1	1	73	76	8.9999
.))	chr1:93594774-93594996(-)$1	1	14	17	8.9999
.((	chr17:1546907-1547130(-)$1	1	0	3	8.9999
((.	chr3:52007753-52007978(+)$1	1	6	9	8.9999
).)	chr18:51863421-51863642(-)$1	1	113	116	8.9999
(((	chr6:145078950-145079173(-)$1	1	87	90	8.9999
(((	chr16:2871498-2871719(-)$1	1	9	12	8.9999
.((	chr2:122125159-122125384(-)$1	1	6	9	8.9999
((.	chr19:808462-808684(+)$1	1	37	40	8.9999
...	chr17:40120189-40120416(+)$1	1	29	32	8.9999
(((	chr15:40708370-40708592(-)$1	1	43	46	8.9999
)))	chr19:12902465-12902690(+)$1	1	61	64	8.9999
(((	chr22:24124375-24124598(-)$1	1	18	21	8.9999
...	chr19:56539092-56539314(+)$1	1	8	11	8.9999
)))	chr8:145675760-145675981(-)$1	1	25	28	8.9999
(((	chr14:61747100-61747329(-)$1	1	29	32	8.9999
(((	chr10:11912052-11912294(+)$1	1	9	12	8.9999
.))	chr1:98058800-98059022(-)$1	1	28	31	8.9999
)))	chr4:126371635-126371856(-)$1	1	31	34	8.9999
)).	chr15:64972270-64972493(-)$1	1	33	36	8.9999
.((	chr1:153930752-153930973(+)$1	1	29	32	8.9999
.((	chr12:109313426-109313647(-)$1	1	17	20	8.9999
...	chr2:166756170-166756391(-)$1	1	52	55	8.9999
(((	chr7:82538132-82538356(+)$1	1	41	44	8.9999
).)	chr9:35076604-35076826(-)$1	1	95	98	8.9999
(((	chr2:202014415-202014638(+)$1	1	109	112	8.9999
.))	chr1:45091946-45092186(-)$1	1	83	86	8.9999
)))	chr11:6238590-6238813(+)$1	1	55	58	8.9999
.((	chr2:207041094-207041317(-)$1	1	1	4	8.9999
(..	chr2:206630116-206630338(+)$1	1	23	26	8.9999
..)	chr17:33770708-33770932(+)$1	1	10	13	8.9999
(((	chr8:94748504-94748730(+)$1	1	33	36	8.9999
.((	chr17:72348146-72348369(-)$1	1	13	16	8.9999
(((	chr17:34883285-34883506(+)$1	1	0	3	8.9999
...	chr18:29055734-29055958(+)$1	1	56	59	8.9999
.))	chr3:48623297-48623518(+)$1	1	38	41	8.9999

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

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m1_run1.nuc.txt

#NT
UCUC	chr6:31124406-31124764(-)$1	358	121	125	11.9999
UCUC	chr1:78097690-78097941(-)$1	251	90	94	11.9999
UCUC	chr9:135163888-135164140(-)$1	252	236	240	11.9999
UCUC	chr5:112458317-112458558(-)$1	241	19	23	11.9999
UCUC	chr12:7249311-7249631(-)$1	320	54	58	11.9999
UCUC	chr11:72578889-72579163(-)$1	274	85	89	11.9999
UCUC	chr2:32853264-32853547(+)$1	283	15	19	11.9999
UCUC	chr1:200572876-200573195(-)$1	319	246	250	11.9999
UCUC	chr14:23355876-23356102(-)$1	226	88	92	11.9999
UCUC	chr1:154233286-154233685(+)$1	399	68	72	11.9999
UCUC	chr2:179460254-179460502(+)$1	248	12	16	11.9999
UCUC	chr10:104231008-104231258(+)$1	250	84	88	11.9999
UCUC	chr1:161092892-161093139(+)$1	247	42	46	11.9999
UCUC	chr15:90162970-90163213(-)$1	243	34	38	11.9999
UCUC	chr12:48250821-48251064(-)$1	243	102	106	11.9999
UCUC	chr22:31838847-31839146(-)$1	299	57	61	11.9999
UCUC	chrX:19416283-19416518(-)$1	235	211	215	11.9999
UCUC	chr17:27958590-27958816(-)$1	226	186	190	11.9999
UCUC	chr19:10363146-10363386(+)$1	240	81	85	11.9999
UCUC	chr1:118439478-118439713(-)$1	235	72	76	11.9999
UCUC	chr10:99226180-99226427(+)$1	247	58	62	11.9999
UCUC	chr11:20485903-20486150(+)$1	247	127	131	11.9999
UCUC	chr2:206265635-206265948(+)$1	313	81	85	11.9999
UCUC	chr13:73401042-73401359(+)$1	317	6	10	11.9999
UCUC	chr1:151065715-151065963(+)$1	248	165	169	11.9999
UCUC	chr11:76866975-76867221(+)$1	246	23	27	11.9999
UCUC	chr20:25289981-25290313(-)$1	332	7	11	11.9999
UCUC	chr8:17104682-17104943(+)$1	261	212	216	11.9999
UCUC	chr19:19576044-19576524(+)$1	480	39	43	11.9999
UCUC	chr15:39875717-39875985(+)$1	268	35	39	11.9999
UCUC	chr1:110201344-110201595(+)$1	251	143	147	11.9999
UCUC	chr16:87453286-87453532(-)$1	246	68	72	11.9999
UCUC	chr11:67066900-67067221(+)$1	321	5	9	11.9999
UCUC	chrX:115586435-115586664(-)$1	229	68	72	11.9999
UCUC	chr5:65350086-65350310(+)$1	224	148	152	11.9999
ucuc	chr11:73536649-73536914(+)$1	265	37	41	11.9999
UCUC	chr1:115251057-115251321(-)$1	264	13	17	11.9999
UCUC	chr6:43480065-43480401(-)$1	336	86	90	11.9999
UCUC	chr4:123833653-123833880(-)$1	227	71	75	11.9999
UCUC	chr2:191796170-191796469(+)$1	299	109	113	11.9999
UCUC	chr6:152675927-152676214(-)$1	287	94	98	11.9999
UCUC	chr14:100598953-100599221(+)$1	268	89	93	11.9999
UCUC	chr12:27809444-27809763(+)$1	319	44	48	11.9999
UCUC	chr10:99229253-99229648(-)$1	395	11	15	11.9999
UCUC	chr15:40583942-40584163(-)$1	221	25	29	11.9999
UCUC	chr2:239974620-239974932(-)$1	312	38	42	11.9999
UCUC	chr14:91939276-91939579(-)$1	303	153	157	11.9999
UCUC	chr17:35831097-35831337(+)$1	240	30	34	11.9999
UCUC	chr11:70318866-70319116(-)$1	250	153	157	11.9999
UCUC	chr10:51188176-51188414(+)$1	238	28	32	11.9999
UCUC	chr7:141618545-141618778(+)$1	233	79	83	11.9999
UCUC	chr1:153914243-153914473(-)$1	230	98	102	11.9999
UCUC	chr10:75848856-75849207(+)$1	351	143	147	11.9999
UCUC	chr3:55513236-55513699(-)$1	463	91	95	11.9999
UCUC	chr13:53000061-53000294(-)$1	233	75	79	11.9999
UCUC	chr10:126448903-126449172(-)$1	269	110	114	11.9999
UCUC	chr19:53117684-53117940(-)$1	256	39	43	11.9999
UCUC	chr15:89862226-89862453(+)$1	227	21	25	11.9999
UCUC	chr7:44155862-44156197(-)$1	335	31	35	11.9999
UCUC	chr11:294360-294592(+)$1	232	4	8	11.9999
UCUC	chr2:240960686-240960956(-)$1	270	116	120	11.9999
UCUC	chr2:207012375-207012642(-)$1	267	200	204	11.9999
UCUC	chr18:32373975-32374213(+)$1	238	130	134	11.9999
UCUC	chr15:48902824-48903116(-)$1	292	247	251	11.9999
UCUC	chr13:111080713-111081014(+)$1	301	34	38	11.9999
UCUC	chr1:16202829-16203283(+)$1	454	18	22	11.9999
UCUC	chr8:23179649-23179894(-)$1	245	87	91	11.9999
UCUC	chr10:27408219-27408478(-)$1	259	84	88	11.9999
UCUC	chr14:23518253-23518529(-)$1	276	35	39	11.9999
UCUC	chr19:9061969-9062199(-)$1	230	96	100	11.9999
UCUC	chr15:42136600-42136850(+)$1	250	53	57	11.9999
UCUC	chr12:101685558-101685766(+)$1	208	195	199	11.9999
UCUC	chr9:136804116-136804438(-)$1	322	226	230	11.9999
UCUC	chr3:195456422-195456708(+)$1	286	83	87	11.9999

#otherMatches

#Struct PSSM
^^^^	chr18:67613869-67614114(-)$1	245	87	91	11.9999
eeee	chr6:31124406-31124764(-)$1	358	121	125	11.9999
eeee	chr1:78097690-78097941(-)$1	251	90	94	11.9999
DDDY	chr9:135163888-135164140(-)$1	252	236	240	11.9999
dd!!	chr5:112458317-112458558(-)$1	241	19	23	11.9999
[a[c	chr12:7249311-7249631(-)$1	320	54	58	11.9999
HH::	chr11:72578889-72579163(-)$1	274	85	89	11.9999
JJJJ	chr2:32853264-32853547(+)$1	283	15	19	11.9999
gggg	chr1:200572876-200573195(-)$1	319	246	250	11.9999
4444	chr14:23355876-23356102(-)$1	226	88	92	11.9999
wwwf	chr1:154233286-154233685(+)$1	399	68	72	11.9999
MMMB	chr2:179460254-179460502(+)$1	248	12	16	11.9999
nnne	chr10:104231008-104231258(+)$1	250	84	88	11.9999
cccd	chr1:161092892-161093139(+)$1	247	42	46	11.9999
TDDD	chr15:90162970-90163213(-)$1	243	34	38	11.9999
nnnd	chr12:48250821-48251064(-)$1	243	102	106	11.9999
{DDD	chr22:31838847-31839146(-)$1	299	57	61	11.9999
rrrr	chrX:19416283-19416518(-)$1	235	211	215	11.9999
mfff	chr17:27958590-27958816(-)$1	226	186	190	11.9999
ff!!	chr19:10363146-10363386(+)$1	240	81	85	11.9999
c777	chr1:118439478-118439713(-)$1	235	72	76	11.9999
::::	chr10:99226180-99226427(+)$1	247	58	62	11.9999
((((	chr11:20485903-20486150(+)$1	247	127	131	11.9999
d[ee	chr2:206265635-206265948(+)$1	313	81	85	11.9999
IIII	chr13:73401042-73401359(+)$1	317	6	10	11.9999
]bb2	chr1:151065715-151065963(+)$1	248	165	169	11.9999
fffv	chr11:76866975-76867221(+)$1	246	23	27	11.9999
IIII	chr20:25289981-25290313(-)$1	332	7	11	11.9999
::::	chr8:17104682-17104943(+)$1	261	212	216	11.9999
FFFF	chr19:19576044-19576524(+)$1	480	39	43	11.9999
::FF	chr15:39875717-39875985(+)$1	268	35	39	11.9999
ffff	chr1:110201344-110201595(+)$1	251	143	147	11.9999
FFFL	chr16:87453286-87453532(-)$1	246	68	72	11.9999
FFFK	chr11:67066900-67067221(+)$1	321	5	9	11.9999
::::	chrX:115586435-115586664(-)$1	229	68	72	11.9999
ssss	chr5:65350086-65350310(+)$1	224	148	152	11.9999
e^^^	chr11:73536649-73536914(+)$1	265	37	41	11.9999
WWWW	chr1:115251057-115251321(-)$1	264	13	17	11.9999
"===	chr6:43480065-43480401(-)$1	336	86	90	11.9999
ee44	chr4:123833653-123833880(-)$1	227	71	75	11.9999
gggg	chr2:191796170-191796469(+)$1	299	109	113	11.9999
iiii	chr6:152675927-152676214(-)$1	287	94	98	11.9999
ffff	chr14:100598953-100599221(+)$1	268	89	93	11.9999
eee]	chr12:27809444-27809763(+)$1	319	44	48	11.9999
GHHH	chr10:99229253-99229648(-)$1	395	11	15	11.9999
DD::	chr15:40583942-40584163(-)$1	221	25	29	11.9999
0000	chr2:239974620-239974932(-)$1	312	38	42	11.9999
mmmb	chr14:91939276-91939579(-)$1	303	153	157	11.9999
::dd	chr17:35831097-35831337(+)$1	240	30	34	11.9999
c:::	chr11:70318866-70319116(-)$1	250	153	157	11.9999
hhhh	chr10:51188176-51188414(+)$1	238	28	32	11.9999
33bb	chr7:141618545-141618778(+)$1	233	79	83	11.9999
hhhh	chr1:153914243-153914473(-)$1	230	98	102	11.9999
dd::	chr10:75848856-75849207(+)$1	351	143	147	11.9999
000e	chr3:55513236-55513699(-)$1	463	91	95	11.9999
gggg	chr13:53000061-53000294(-)$1	233	75	79	11.9999
dddd	chr10:126448903-126449172(-)$1	269	110	114	11.9999
dd[a	chr19:53117684-53117940(-)$1	256	39	43	11.9999
cmmm	chr15:89862226-89862453(+)$1	227	21	25	11.9999
bboo	chr7:44155862-44156197(-)$1	335	31	35	11.9999
eeee	chr11:294360-294592(+)$1	232	4	8	11.9999
HHHH	chr2:240960686-240960956(-)$1	270	116	120	11.9999
f22b	chr2:207012375-207012642(-)$1	267	200	204	11.9999
22dd	chr18:32373975-32374213(+)$1	238	130	134	11.9999
::::	chr15:48902824-48903116(-)$1	292	247	251	11.9999
qqqq	chr13:111080713-111081014(+)$1	301	34	38	11.9999
uuuu	chr1:16202829-16203283(+)$1	454	18	22	11.9999
GGGG	chr8:23179649-23179894(-)$1	245	87	91	11.9999
rrrr	chr10:27408219-27408478(-)$1	259	84	88	11.9999
::::	chr14:23518253-23518529(-)$1	276	35	39	11.9999
cbb]	chr19:9061969-9062199(-)$1	230	96	100	11.9999
JJ{D	chr15:42136600-42136850(+)$1	250	53	57	11.9999
oooo	chr12:101685558-101685766(+)$1	208	195	199	11.9999
]bb]	chr9:136804116-136804438(-)$1	322	226	230	11.9999
rrrr	chr3:195456422-195456708(+)$1	286	83	87	11.9999

#DB
....	chr18:67613869-67614114(-)$1	1	87	91	11.9999
((((	chr6:31124406-31124764(-)$1	1	121	125	11.9999
((((	chr1:78097690-78097941(-)$1	1	90	94	11.9999
))).	chr9:135163888-135164140(-)$1	1	236	240	11.9999
((..	chr5:112458317-112458558(-)$1	1	19	23	11.9999
.(.(	chr12:7249311-7249631(-)$1	1	54	58	11.9999
((..	chr11:72578889-72579163(-)$1	1	85	89	11.9999
((((	chr2:32853264-32853547(+)$1	1	15	19	11.9999
((((	chr1:200572876-200573195(-)$1	1	246	250	11.9999
....	chr14:23355876-23356102(-)$1	1	88	92	11.9999
...)	chr1:154233286-154233685(+)$1	1	68	72	11.9999
...(	chr2:179460254-179460502(+)$1	1	12	16	11.9999
...)	chr10:104231008-104231258(+)$1	1	84	88	11.9999
((((	chr1:161092892-161093139(+)$1	1	42	46	11.9999
.(((	chr15:90162970-90163213(-)$1	1	34	38	11.9999
...)	chr12:48250821-48251064(-)$1	1	102	106	11.9999
.(((	chr22:31838847-31839146(-)$1	1	57	61	11.9999
....	chrX:19416283-19416518(-)$1	1	211	215	11.9999
.)))	chr17:27958590-27958816(-)$1	1	186	190	11.9999
((..	chr19:10363146-10363386(+)$1	1	81	85	11.9999
)...	chr1:118439478-118439713(-)$1	1	72	76	11.9999
....	chr10:99226180-99226427(+)$1	1	58	62	11.9999
....	chr11:20485903-20486150(+)$1	1	127	131	11.9999
(.((	chr2:206265635-206265948(+)$1	1	81	85	11.9999
((((	chr13:73401042-73401359(+)$1	1	6	10	11.9999
.)).	chr1:151065715-151065963(+)$1	1	165	169	11.9999
(((.	chr11:76866975-76867221(+)$1	1	23	27	11.9999
((((	chr20:25289981-25290313(-)$1	1	7	11	11.9999
....	chr8:17104682-17104943(+)$1	1	212	216	11.9999
((((	chr19:19576044-19576524(+)$1	1	39	43	11.9999
..((	chr15:39875717-39875985(+)$1	1	35	39	11.9999
((((	chr1:110201344-110201595(+)$1	1	143	147	11.9999
(((.	chr16:87453286-87453532(-)$1	1	68	72	11.9999
(((.	chr11:67066900-67067221(+)$1	1	5	9	11.9999
....	chrX:115586435-115586664(-)$1	1	68	72	11.9999
....	chr5:65350086-65350310(+)$1	1	148	152	11.9999
(...	chr11:73536649-73536914(+)$1	1	37	41	11.9999
....	chr1:115251057-115251321(-)$1	1	13	17	11.9999
.(((	chr6:43480065-43480401(-)$1	1	86	90	11.9999
))..	chr4:123833653-123833880(-)$1	1	71	75	11.9999
((((	chr2:191796170-191796469(+)$1	1	109	113	11.9999
((((	chr6:152675927-152676214(-)$1	1	94	98	11.9999
))))	chr14:100598953-100599221(+)$1	1	89	93	11.9999
))).	chr12:27809444-27809763(+)$1	1	44	48	11.9999
((((	chr10:99229253-99229648(-)$1	1	11	15	11.9999
((..	chr15:40583942-40584163(-)$1	1	25	29	11.9999
....	chr2:239974620-239974932(-)$1	1	38	42	11.9999
...)	chr14:91939276-91939579(-)$1	1	153	157	11.9999
..((	chr17:35831097-35831337(+)$1	1	30	34	11.9999
)...	chr11:70318866-70319116(-)$1	1	153	157	11.9999
((((	chr10:51188176-51188414(+)$1	1	28	32	11.9999
..))	chr7:141618545-141618778(+)$1	1	79	83	11.9999
((((	chr1:153914243-153914473(-)$1	1	98	102	11.9999
))..	chr10:75848856-75849207(+)$1	1	143	147	11.9999
...)	chr3:55513236-55513699(-)$1	1	91	95	11.9999
))))	chr13:53000061-53000294(-)$1	1	75	79	11.9999
((((	chr10:126448903-126449172(-)$1	1	110	114	11.9999
((.(	chr19:53117684-53117940(-)$1	1	39	43	11.9999
(...	chr15:89862226-89862453(+)$1	1	21	25	11.9999
((..	chr7:44155862-44156197(-)$1	1	31	35	11.9999
((((	chr11:294360-294592(+)$1	1	4	8	11.9999
((((	chr2:240960686-240960956(-)$1	1	116	120	11.9999
)..)	chr2:207012375-207012642(-)$1	1	200	204	11.9999
..))	chr18:32373975-32374213(+)$1	1	130	134	11.9999
....	chr15:48902824-48903116(-)$1	1	247	251	11.9999
....	chr13:111080713-111081014(+)$1	1	34	38	11.9999
....	chr1:16202829-16203283(+)$1	1	18	22	11.9999
))))	chr8:23179649-23179894(-)$1	1	87	91	11.9999
....	chr10:27408219-27408478(-)$1	1	84	88	11.9999
....	chr14:23518253-23518529(-)$1	1	35	39	11.9999
))).	chr19:9061969-9062199(-)$1	1	96	100	11.9999
((.(	chr15:42136600-42136850(+)$1	1	53	57	11.9999
....	chr12:101685558-101685766(+)$1	1	195	199	11.9999
.)).	chr9:136804116-136804438(-)$1	1	226	230	11.9999
....	chr3:195456422-195456708(+)$1	1	83	87	11.9999

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

#score	899.9999999999995
#seq	75
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m3_run1.nuc.txt

#NT
acug	chr20:43535928-43536132(+)$1	204	123	127	12.0000
ACUG	chr19:44982108-44982310(-)$1	202	195	199	12.0000
ACUG	chr17:80560848-80561073(+)$1	225	121	125	12.0000
ACUG	chr1:109854820-109855026(-)$1	206	19	23	12.0000
ACUG	chr11:74548441-74548652(+)$1	211	129	133	12.0000
ACUG	chr5:112353564-112353775(+)$1	211	122	126	12.0000
ACUG	chr3:141644529-141644777(+)$1	248	188	192	12.0000
ACUG	chr16:81115866-81116073(-)$1	207	69	73	12.0000
ACUG	chr10:5807195-5807461(-)$1	266	245	249	12.0000
ACUG	chr1:44820586-44820812(-)$1	226	22	26	12.0000
ACUG	chr5:176733678-176733891(+)$1	213	156	160	12.0000
ACUG	chr20:43383106-43383320(-)$1	214	139	143	12.0000
ACUG	chr12:131357524-131357757(+)$1	233	123	127	12.0000
ACUG	chr4:108955967-108956170(+)$1	203	185	189	12.0000
ACUG	chr6:133850178-133850382(+)$1	204	35	39	12.0000
ACUG	chr4:15627141-15627377(-)$1	236	129	133	12.0000
ACUG	chr1:116947209-116947437(+)$1	228	127	131	12.0000
ACUG	chr19:3491134-3491372(-)$1	238	74	78	12.0000
ACUG	chr2:112875360-112875572(+)$1	212	179	183	12.0000
ACUG	chr14:71581389-71581632(+)$1	243	89	93	12.0000
ACUG	chr1:115313743-115313966(-)$1	223	123	127	12.0000
ACUG	chr14:89080312-89080519(-)$1	207	145	149	12.0000
ACUG	chr14:103985912-103986141(-)$1	229	100	104	12.0000
ACUG	chr17:43175715-43175945(+)$1	230	164	168	12.0000
acug	chr2:174088791-174089029(+)$1	238	148	152	12.0000
ACUG	chr11:57080304-57080510(-)$1	206	71	75	12.0000
ACUG	chr4:174252947-174253194(-)$1	247	70	74	12.0000
ACUG	chr17:41154637-41154883(+)$1	246	80	84	12.0000
ACUG	chr2:179296212-179296417(-)$1	205	92	96	12.0000
ACUG	chr3:48199369-48199575(-)$1	206	122	126	12.0000
acug	chr5:154320700-154320911(+)$1	211	189	193	12.0000
ACUG	chr11:43877127-43877343(+)$1	216	46	50	12.0000
ACUG	chr2:121980527-121980729(-)$1	202	68	72	12.0000
ACUG	chr1:234740489-234740751(-)$1	262	13	17	12.0000
ACUG	chr8:22109120-22109346(+)$1	226	43	47	12.0000
ACUG	chr1:68170189-68170422(-)$1	233	1	5	12.0000
ACUG	chr3:33133515-33133723(-)$1	208	32	36	12.0000
ACUG	chr1:36180221-36180429(-)$1	208	29	33	12.0000
ACUG	chr17:75211452-75211666(+)$1	214	38	42	12.0000
ACUG	chr12:69119413-69119615(+)$1	202	51	55	12.0000
ACUG	chr3:98515434-98515648(-)$1	214	143	147	12.0000
acug	chr3:194362204-194362412(-)$1	208	42	46	12.0000
ACUG	chr1:114310802-114311040(-)$1	238	142	146	12.0000
ACUG	chr12:53806041-53806257(+)$1	216	14	18	12.0000
ACUG	chr5:140896339-140896549(-)$1	210	174	178	12.0000
ACUG	chr12:46579018-46579294(-)$1	276	190	194	12.0000
ACUG	chr11:9610271-9610507(+)$1	236	93	97	12.0000
ACUG	chr13:107142491-107142704(-)$1	213	90	94	12.0000
ACUG	chr11:65660586-65660824(-)$1	238	60	64	12.0000
ACUG	chr8:11667101-11667317(+)$1	216	119	123	12.0000
ACUG	chr21:40714379-40714615(-)$1	236	91	95	12.0000
ACUG	chr7:100883005-100883235(-)$1	230	30	34	12.0000
ACUG	chr1:156287187-156287425(-)$1	238	87	91	12.0000
ACUG	chr2:131104041-131104251(+)$1	210	75	79	12.0000
ACUG	chr11:134020888-134021116(+)$1	228	72	76	12.0000
ACUG	chr1:157093606-157093813(-)$1	207	118	122	12.0000
ACUG	chr7:107399636-107399850(+)$1	214	55	59	12.0000
ACUG	chr17:8280853-8281064(-)$1	211	74	78	12.0000
ACUG	chr6:7882547-7882779(-)$1	232	83	87	12.0000
ACUG	chr19:19617163-19617393(+)$1	230	7	11	12.0000
ACUG	chr17:17970265-17970534(+)$1	269	141	145	12.0000
ACUG	chr15:44707192-44707400(+)$1	208	6	10	12.0000
ACUG	chr17:72199963-72200179(+)$1	216	79	83	12.0000
ACUG	chr5:179135153-179135417(+)$1	264	183	187	12.0000
ACUG	chr12:120119176-120119389(+)$1	213	202	206	12.0000
ACUG	chr11:67938428-67938665(-)$1	237	26	30	12.0000
ACUG	chr1:115260456-115260661(-)$1	205	148	152	12.0000
ACUG	chr9:80336003-80336211(-)$1	208	35	39	12.0000
ACUG	chr19:10254511-10254737(-)$1	226	1	5	12.0000
ACUG	chr10:120927393-120927606(-)$1	213	23	27	12.0000
ACUG	chr14:32624722-32624938(+)$1	216	172	176	12.0000
ACUG	chrX:49044865-49045123(-)$1	258	154	158	12.0000
ACUG	chr19:15359458-15359674(-)$1	216	177	181	12.0000
ACUG	chr15:89741555-89741761(+)$1	206	25	29	12.0000
ACUG	chr5:138761878-138762098(-)$1	220	16	20	12.0000

#otherMatches

#Struct PSSM
oooo	chr5:177576643-177576847(-)$1	204	193	197	12.0000
BB}E	chr20:43535928-43536132(+)$1	204	123	127	12.0000
:DDD	chr19:44982108-44982310(-)$1	202	195	199	12.0000
ggmm	chr17:80560848-80561073(+)$1	225	121	125	12.0000
iiii	chr1:109854820-109855026(-)$1	206	19	23	12.0000
DDDi	chr11:74548441-74548652(+)$1	211	129	133	12.0000
eeee	chr5:112353564-112353775(+)$1	211	122	126	12.0000
eenn	chr3:141644529-141644777(+)$1	248	188	192	12.0000
22dd	chr16:81115866-81116073(-)$1	207	69	73	12.0000
}CCC	chr10:5807195-5807461(-)$1	266	245	249	12.0000
nnnb	chr1:44820586-44820812(-)$1	226	22	26	12.0000
dddd	chr5:176733678-176733891(+)$1	213	156	160	12.0000
22ee	chr20:43383106-43383320(-)$1	214	139	143	12.0000
]bb:	chr12:131357524-131357757(+)$1	233	123	127	12.0000
dddd	chr4:108955967-108956170(+)$1	203	185	189	12.0000
lldd	chr6:133850178-133850382(+)$1	204	35	39	12.0000
[eee	chr4:15627141-15627377(-)$1	236	129	133	12.0000
c[bb	chr1:116947209-116947437(+)$1	228	127	131	12.0000
:::b	chr19:3491134-3491372(-)$1	238	74	78	12.0000
!eee	chr2:112875360-112875572(+)$1	212	179	183	12.0000
ffff	chr14:71581389-71581632(+)$1	243	89	93	12.0000
[ddd	chr1:115313743-115313966(-)$1	223	123	127	12.0000
IIII	chr14:89080312-89080519(-)$1	207	145	149	12.0000
rrrc	chr14:103985912-103986141(-)$1	229	100	104	12.0000
eeee	chr17:43175715-43175945(+)$1	230	164	168	12.0000
ddd:	chr2:174088791-174089029(+)$1	238	148	152	12.0000
:::f	chr11:57080304-57080510(-)$1	206	71	75	12.0000
5fff	chr4:174252947-174253194(-)$1	247	70	74	12.0000
mmdd	chr17:41154637-41154883(+)$1	246	80	84	12.0000
oogg	chr2:179296212-179296417(-)$1	205	92	96	12.0000
tttt	chr3:48199369-48199575(-)$1	206	122	126	12.0000
ffff	chr5:154320700-154320911(+)$1	211	189	193	12.0000
FFFF	chr11:43877127-43877343(+)$1	216	46	50	12.0000
ccc2	chr2:121980527-121980729(-)$1	202	68	72	12.0000
JJJJ	chr1:234740489-234740751(-)$1	262	13	17	12.0000
{DDD	chr8:22109120-22109346(+)$1	226	43	47	12.0000
:CCC	chr1:68170189-68170422(-)$1	233	1	5	12.0000
xxxx	chr3:33133515-33133723(-)$1	208	32	36	12.0000
:eee	chr1:36180221-36180429(-)$1	208	29	33	12.0000
pggg	chr17:75211452-75211666(+)$1	214	38	42	12.0000
nccc	chr12:69119413-69119615(+)$1	202	51	55	12.0000
====	chr3:98515434-98515648(-)$1	214	143	147	12.0000
::dd	chr3:194362204-194362412(-)$1	208	42	46	12.0000
eeee	chr1:114310802-114311040(-)$1	238	142	146	12.0000
ffff	chr12:53806041-53806257(+)$1	216	14	18	12.0000
E:::	chr5:140896339-140896549(-)$1	210	174	178	12.0000
fff[	chr12:46579018-46579294(-)$1	276	190	194	12.0000
GGGG	chr11:9610271-9610507(+)$1	236	93	97	12.0000
i22c	chr13:107142491-107142704(-)$1	213	90	94	12.0000
mccc	chr11:65660586-65660824(-)$1	238	60	64	12.0000
ffff	chr8:11667101-11667317(+)$1	216	119	123	12.0000
e:::	chr21:40714379-40714615(-)$1	236	91	95	12.0000
MMDD	chr7:100883005-100883235(-)$1	230	30	34	12.0000
c22h	chr1:156287187-156287425(-)$1	238	87	91	12.0000
!ccc	chr2:131104041-131104251(+)$1	210	75	79	12.0000
==%%	chr11:134020888-134021116(+)$1	228	72	76	12.0000
!bbd	chr1:157093606-157093813(-)$1	207	118	122	12.0000
====	chr7:107399636-107399850(+)$1	214	55	59	12.0000
pddd	chr17:8280853-8281064(-)$1	211	74	78	12.0000
bb[e	chr6:7882547-7882779(-)$1	232	83	87	12.0000
FF::	chr19:19617163-19617393(+)$1	230	7	11	12.0000
EBB}	chr17:17970265-17970534(+)$1	269	141	145	12.0000
++++	chr15:44707192-44707400(+)$1	208	6	10	12.0000
[bb[	chr17:72199963-72200179(+)$1	216	79	83	12.0000
:bbn	chr5:179135153-179135417(+)$1	264	183	187	12.0000
ffff	chr12:120119176-120119389(+)$1	213	202	206	12.0000
h!!c	chr11:67938428-67938665(-)$1	237	26	30	12.0000
GGGG	chr1:115260456-115260661(-)$1	205	148	152	12.0000
JJJJ	chr9:80336003-80336211(-)$1	208	35	39	12.0000
b[==	chr19:10254511-10254737(-)$1	226	1	5	12.0000
e!!b	chr10:120927393-120927606(-)$1	213	23	27	12.0000
cc[a	chr14:32624722-32624938(+)$1	216	172	176	12.0000
!bb"	chrX:49044865-49045123(-)$1	258	154	158	12.0000
GGGG	chr19:15359458-15359674(-)$1	216	177	181	12.0000
::dd	chr15:89741555-89741761(+)$1	206	25	29	12.0000
oeee	chr5:138761878-138762098(-)$1	220	16	20	12.0000

#DB
....	chr5:177576643-177576847(-)$1	1	193	197	12.0000
)).)	chr20:43535928-43536132(+)$1	1	123	127	12.0000
.)))	chr19:44982108-44982310(-)$1	1	195	199	12.0000
((..	chr17:80560848-80561073(+)$1	1	121	125	12.0000
((((	chr1:109854820-109855026(-)$1	1	19	23	12.0000
)))(	chr11:74548441-74548652(+)$1	1	129	133	12.0000
))))	chr5:112353564-112353775(+)$1	1	122	126	12.0000
((..	chr3:141644529-141644777(+)$1	1	188	192	12.0000
..))	chr16:81115866-81116073(-)$1	1	69	73	12.0000
.)))	chr10:5807195-5807461(-)$1	1	245	249	12.0000
...)	chr1:44820586-44820812(-)$1	1	22	26	12.0000
))))	chr5:176733678-176733891(+)$1	1	156	160	12.0000
..))	chr20:43383106-43383320(-)$1	1	139	143	12.0000
.)).	chr12:131357524-131357757(+)$1	1	123	127	12.0000
))))	chr4:108955967-108956170(+)$1	1	185	189	12.0000
..))	chr6:133850178-133850382(+)$1	1	35	39	12.0000
.(((	chr4:15627141-15627377(-)$1	1	129	133	12.0000
(.((	chr1:116947209-116947437(+)$1	1	127	131	12.0000
...(	chr19:3491134-3491372(-)$1	1	74	78	12.0000
.(((	chr2:112875360-112875572(+)$1	1	179	183	12.0000
((((	chr14:71581389-71581632(+)$1	1	89	93	12.0000
.(((	chr1:115313743-115313966(-)$1	1	123	127	12.0000
))))	chr14:89080312-89080519(-)$1	1	145	149	12.0000
...)	chr14:103985912-103986141(-)$1	1	100	104	12.0000
))))	chr17:43175715-43175945(+)$1	1	164	168	12.0000
))).	chr2:174088791-174089029(+)$1	1	148	152	12.0000
...(	chr11:57080304-57080510(-)$1	1	71	75	12.0000
.)))	chr4:174252947-174253194(-)$1	1	70	74	12.0000
..))	chr17:41154637-41154883(+)$1	1	80	84	12.0000
..))	chr2:179296212-179296417(-)$1	1	92	96	12.0000
....	chr3:48199369-48199575(-)$1	1	122	126	12.0000
))))	chr5:154320700-154320911(+)$1	1	189	193	12.0000
((((	chr11:43877127-43877343(+)$1	1	46	50	12.0000
))).	chr2:121980527-121980729(-)$1	1	68	72	12.0000
((((	chr1:234740489-234740751(-)$1	1	13	17	12.0000
.(((	chr8:22109120-22109346(+)$1	1	43	47	12.0000
.(((	chr1:68170189-68170422(-)$1	1	1	5	12.0000
....	chr3:33133515-33133723(-)$1	1	32	36	12.0000
.(((	chr1:36180221-36180429(-)$1	1	29	33	12.0000
.)))	chr17:75211452-75211666(+)$1	1	38	42	12.0000
.)))	chr12:69119413-69119615(+)$1	1	51	55	12.0000
((((	chr3:98515434-98515648(-)$1	1	143	147	12.0000
..((	chr3:194362204-194362412(-)$1	1	42	46	12.0000
))))	chr1:114310802-114311040(-)$1	1	142	146	12.0000
))))	chr12:53806041-53806257(+)$1	1	14	18	12.0000
)...	chr5:140896339-140896549(-)$1	1	174	178	12.0000
(((.	chr12:46579018-46579294(-)$1	1	190	194	12.0000
((((	chr11:9610271-9610507(+)$1	1	93	97	12.0000
)..)	chr13:107142491-107142704(-)$1	1	90	94	12.0000
.)))	chr11:65660586-65660824(-)$1	1	60	64	12.0000
))))	chr8:11667101-11667317(+)$1	1	119	123	12.0000
)...	chr21:40714379-40714615(-)$1	1	91	95	12.0000
..((	chr7:100883005-100883235(-)$1	1	30	34	12.0000
)..)	chr1:156287187-156287425(-)$1	1	87	91	12.0000
.(((	chr2:131104041-131104251(+)$1	1	75	79	12.0000
((..	chr11:134020888-134021116(+)$1	1	72	76	12.0000
.(((	chr1:157093606-157093813(-)$1	1	118	122	12.0000
((((	chr7:107399636-107399850(+)$1	1	55	59	12.0000
.)))	chr17:8280853-8281064(-)$1	1	74	78	12.0000
((.(	chr6:7882547-7882779(-)$1	1	83	87	12.0000
((..	chr19:19617163-19617393(+)$1	1	7	11	12.0000
))).	chr17:17970265-17970534(+)$1	1	141	145	12.0000
....	chr15:44707192-44707400(+)$1	1	6	10	12.0000
.((.	chr17:72199963-72200179(+)$1	1	79	83	12.0000
.((.	chr5:179135153-179135417(+)$1	1	183	187	12.0000
))))	chr12:120119176-120119389(+)$1	1	202	206	12.0000
(..(	chr11:67938428-67938665(-)$1	1	26	30	12.0000
))))	chr1:115260456-115260661(-)$1	1	148	152	12.0000
((((	chr9:80336003-80336211(-)$1	1	35	39	12.0000
(.((	chr19:10254511-10254737(-)$1	1	1	5	12.0000
(..(	chr10:120927393-120927606(-)$1	1	23	27	12.0000
((.(	chr14:32624722-32624938(+)$1	1	172	176	12.0000
.((.	chrX:49044865-49045123(-)$1	1	154	158	12.0000
))))	chr19:15359458-15359674(-)$1	1	177	181	12.0000
..((	chr15:89741555-89741761(+)$1	1	25	29	12.0000
.)))	chr5:138761878-138762098(-)$1	1	16	20	12.0000

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

#score	912.0000000000001
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m3_run1.nuc.txt

#NT
GAAA	chr11:47639062-47639295(-)$1	233	9	13	12.0000
GAAA	chr1:24296235-24296469(-)$1	234	134	138	12.0000
GAAA	chr4:174243520-174243763(+)$1	243	42	46	12.0000
GAAA	chr4:106162081-106162316(+)$1	235	0	4	12.0000
GAAA	chr15:62145322-62145595(-)$1	273	8	12	12.0000
GAAA	chr3:141664457-141664844(-)$1	387	34	38	12.0000
GAAA	chr6:76626842-76627074(+)$1	232	89	93	12.0000
GAAA	chr4:1947527-1947755(+)$1	228	47	51	12.0000
GAAA	chr2:178994073-178994304(+)$1	231	91	95	12.0000
gaaa	chr1:227847456-227847714(+)$1	258	40	44	12.0000
GAAA	chr3:141669655-141669888(-)$1	233	95	99	12.0000
gaaa	chr12:58196509-58196740(+)$1	231	34	38	12.0000
gaaa	chr12:55343793-55344059(-)$1	266	29	33	12.0000
GAAA	chr17:414283-414519(-)$1	236	1	5	12.0000
GAAA	chr5:134061052-134061291(+)$1	239	186	190	12.0000
gaaa	chr4:106161154-106161424(+)$1	270	203	207	12.0000
GAAA	chr7:129773859-129774122(+)$1	263	79	83	12.0000
GAAA	chr12:124245761-124246026(+)$1	265	94	98	12.0000
gaaa	chr10:38119353-38119615(-)$1	262	2	6	12.0000
GAAA	chr12:27181619-27181864(+)$1	245	0	4	12.0000
GAAA	chr11:58921538-58921770(+)$1	232	132	136	12.0000
GAAA	chr20:57252951-57253255(+)$1	304	79	83	12.0000
GAAA	chr2:46613571-46613806(+)$1	235	99	103	12.0000
GAAA	chr2:207945648-207945977(-)$1	329	47	51	12.0000
GAAA	chr5:169679115-169679407(-)$1	292	229	233	12.0000
GAAA	chr1:231990838-231991092(+)$1	254	31	35	12.0000
GAAA	chr1:161128229-161128506(+)$1	277	37	41	12.0000
GAAA	chr18:34412520-34412767(+)$1	247	75	79	12.0000
gaaa	chr5:87497037-87497288(-)$1	251	26	30	12.0000
GAAA	chr1:100614556-100614789(+)$1	233	99	103	12.0000
GAAA	chr10:104238913-104239159(-)$1	246	21	25	12.0000
GAAA	chr22:40722230-40722485(+)$1	255	52	56	12.0000
GAAA	chr16:24229722-24229970(+)$1	248	29	33	12.0000
GAAA	chr19:16551480-16551720(-)$1	240	197	201	12.0000
gaaa	chr19:52778691-52778931(+)$1	240	17	21	12.0000
GAAA	chr2:85547526-85547780(-)$1	254	71	75	12.0000
GAAA	chr2:61753079-61753319(-)$1	240	215	219	12.0000
gaaa	chr4:44707556-44707789(-)$1	233	16	20	12.0000
GAAA	chr16:85706704-85706952(+)$1	248	32	36	12.0000
GAAA	chrX:70520330-70520675(+)$1	345	172	176	12.0000
GAAA	chr2:27884627-27884858(-)$1	231	25	29	12.0000
GAAA	chr1:204525126-204525372(+)$1	246	29	33	12.0000
GAAA	chr1:154555402-154555678(-)$1	276	225	229	12.0000
GAAA	chr12:52203991-52204220(+)$1	229	7	11	12.0000
GAAA	chr18:13761362-13761614(+)$1	252	13	17	12.0000
GAAA	chr15:60787804-60788040(-)$1	236	6	10	12.0000
GAAA	chr14:57670618-57670846(-)$1	228	10	14	12.0000
GAAA	chr2:9724641-9724881(-)$1	240	8	12	12.0000
GAAA	chr21:19165306-19165562(-)$1	256	186	190	12.0000
gaaa	chr11:66963980-66964212(+)$1	232	46	50	12.0000
GAAA	chr7:129770418-129770684(+)$1	266	0	4	12.0000
GAAA	chrX:72902391-72902617(+)$1	226	23	27	12.0000
gaaa	chr8:59361756-59362125(+)$1	369	348	352	12.0000
GAAA	chr4:76857037-76857259(-)$1	222	30	34	12.0000
GAAA	chr1:26796075-26796391(+)$1	316	20	24	12.0000
gaaa	chr1:179810518-179810822(-)$1	304	250	254	12.0000
gaaa	chr1:227849265-227849503(+)$1	238	74	78	12.0000
gaaa	chr12:44180953-44181213(+)$1	260	4	8	12.0000
GAAA	chr12:95474360-95474584(-)$1	224	52	56	12.0000
GAAA	chr3:105399721-105399957(-)$1	236	156	160	12.0000
GAAA	chr7:87830477-87830708(+)$1	231	23	27	12.0000
GAAA	chr2:128494815-128495053(-)$1	238	54	58	12.0000
GAAA	chr19:58419082-58419345(-)$1	263	197	201	12.0000
GAAA	chr1:155306452-155306721(-)$1	269	3	7	12.0000
GAAA	chr1:151555687-151555929(+)$1	242	99	103	12.0000
GAAA	chr1:155883567-155883800(-)$1	233	138	142	12.0000
GAAA	chr3:194998144-194998380(-)$1	236	80	84	12.0000
GAAA	chr10:126674756-126675037(+)$1	281	18	22	12.0000
GAAA	chr20:6018085-6018319(+)$1	234	65	69	12.0000
GAAA	chr8:98287407-98287648(-)$1	241	89	93	12.0000
GAAA	chr19:58374042-58374279(+)$1	237	25	29	12.0000
gaaa	chr9:72324951-72325239(-)$1	288	35	39	12.0000
GAAA	chr1:160248357-160248604(-)$1	247	158	162	12.0000
GAAA	chr13:21356340-21356587(-)$1	247	65	69	12.0000
GAAA	chr19:58373716-58373979(+)$1	263	173	177	12.0000
GAAA	chr11:124503117-124503373(+)$1	256	193	197	12.0000
GAAA	chr2:131132106-131132366(+)$1	260	9	13	12.0000
gaaa	chr4:156265282-156265520(-)$1	238	199	203	12.0000
GAAA	chr8:101931647-101931897(-)$1	250	20	24	12.0000
GAAA	chr3:45720339-45720613(+)$1	274	89	93	12.0000
GAAA	chr22:38879780-38880101(-)$1	321	76	80	12.0000
GAAA	chr15:78886277-78886510(+)$1	233	171	175	12.0000

#otherMatches

#Struct PSSM
:eee	chr9:15886631-15886899(+)$1	268	71	75	12.0000
FF::	chr11:47639062-47639295(-)$1	233	9	13	12.0000
""dd	chr1:24296235-24296469(-)$1	234	134	138	12.0000
::::	chr4:174243520-174243763(+)$1	243	42	46	12.0000
::::	chr4:106162081-106162316(+)$1	235	0	4	12.0000
iiii	chr15:62145322-62145595(-)$1	273	8	12	12.0000
33ee	chr3:141664457-141664844(-)$1	387	34	38	12.0000
hh::	chr6:76626842-76627074(+)$1	232	89	93	12.0000
JJJJ	chr4:1947527-1947755(+)$1	228	47	51	12.0000
::::	chr2:178994073-178994304(+)$1	231	91	95	12.0000
NNGG	chr1:227847456-227847714(+)$1	258	40	44	12.0000
^^^^	chr3:141669655-141669888(-)$1	233	95	99	12.0000
eeee	chr12:58196509-58196740(+)$1	231	34	38	12.0000
HHHH	chr12:55343793-55344059(-)$1	266	29	33	12.0000
::::	chr17:414283-414519(-)$1	236	1	5	12.0000
::::	chr5:134061052-134061291(+)$1	239	186	190	12.0000
::::	chr4:106161154-106161424(+)$1	270	203	207	12.0000
ff[c	chr7:129773859-129774122(+)$1	263	79	83	12.0000
::::	chr12:124245761-124246026(+)$1	265	94	98	12.0000
iiii	chr10:38119353-38119615(-)$1	262	2	6	12.0000
::::	chr12:27181619-27181864(+)$1	245	0	4	12.0000
::::	chr11:58921538-58921770(+)$1	232	132	136	12.0000
::::	chr20:57252951-57253255(+)$1	304	79	83	12.0000
dddd	chr2:46613571-46613806(+)$1	235	99	103	12.0000
mmmm	chr2:207945648-207945977(-)$1	329	47	51	12.0000
hhhh	chr5:169679115-169679407(-)$1	292	229	233	12.0000
GGGG	chr1:231990838-231991092(+)$1	254	31	35	12.0000
::::	chr1:161128229-161128506(+)$1	277	37	41	12.0000
::::	chr18:34412520-34412767(+)$1	247	75	79	12.0000
HHH{	chr5:87497037-87497288(-)$1	251	26	30	12.0000
^^^^	chr1:100614556-100614789(+)$1	233	99	103	12.0000
mmmm	chr10:104238913-104239159(-)$1	246	21	25	12.0000
nnee	chr22:40722230-40722485(+)$1	255	52	56	12.0000
ccoo	chr16:24229722-24229970(+)$1	248	29	33	12.0000
eeee	chr19:16551480-16551720(-)$1	240	197	201	12.0000
JJJJ	chr19:52778691-52778931(+)$1	240	17	21	12.0000
CCCh	chr2:85547526-85547780(-)$1	254	71	75	12.0000
hhhh	chr2:61753079-61753319(-)$1	240	215	219	12.0000
++++	chr4:44707556-44707789(-)$1	233	16	20	12.0000
gggg	chr16:85706704-85706952(+)$1	248	32	36	12.0000
c555	chrX:70520330-70520675(+)$1	345	172	176	12.0000
eeee	chr2:27884627-27884858(-)$1	231	25	29	12.0000
""cc	chr1:204525126-204525372(+)$1	246	29	33	12.0000
cc44	chr1:154555402-154555678(-)$1	276	225	229	12.0000
EEEE	chr12:52203991-52204220(+)$1	229	7	11	12.0000
[a[g	chr18:13761362-13761614(+)$1	252	13	17	12.0000
::::	chr15:60787804-60788040(-)$1	236	6	10	12.0000
d!!d	chr14:57670618-57670846(-)$1	228	10	14	12.0000
HHHH	chr2:9724641-9724881(-)$1	240	8	12	12.0000
bb[c	chr21:19165306-19165562(-)$1	256	186	190	12.0000
d:::	chr11:66963980-66964212(+)$1	232	46	50	12.0000
::ff	chr7:129770418-129770684(+)$1	266	0	4	12.0000
DDMM	chrX:72902391-72902617(+)$1	226	23	27	12.0000
::::	chr8:59361756-59362125(+)$1	369	348	352	12.0000
nnnn	chr4:76857037-76857259(-)$1	222	30	34	12.0000
cc""	chr1:26796075-26796391(+)$1	316	20	24	12.0000
::::	chr1:179810518-179810822(-)$1	304	250	254	12.0000
hh::	chr1:227849265-227849503(+)$1	238	74	78	12.0000
EBBD	chr12:44180953-44181213(+)$1	260	4	8	12.0000
::::	chr12:95474360-95474584(-)$1	224	52	56	12.0000
ffff	chr3:105399721-105399957(-)$1	236	156	160	12.0000
eee:	chr7:87830477-87830708(+)$1	231	23	27	12.0000
HHHH	chr2:128494815-128495053(-)$1	238	54	58	12.0000
dddd	chr19:58419082-58419345(-)$1	263	197	201	12.0000
FFFF	chr1:155306452-155306721(-)$1	269	3	7	12.0000
pppp	chr1:151555687-151555929(+)$1	242	99	103	12.0000
bb##	chr1:155883567-155883800(-)$1	233	138	142	12.0000
fff[	chr3:194998144-194998380(-)$1	236	80	84	12.0000
cccl	chr10:126674756-126675037(+)$1	281	18	22	12.0000
!ccc	chr20:6018085-6018319(+)$1	234	65	69	12.0000
fff:	chr8:98287407-98287648(-)$1	241	89	93	12.0000
ddmm	chr19:58374042-58374279(+)$1	237	25	29	12.0000
eeee	chr9:72324951-72325239(-)$1	288	35	39	12.0000
ggg:	chr1:160248357-160248604(-)$1	247	158	162	12.0000
GGG:	chr13:21356340-21356587(-)$1	247	65	69	12.0000
====	chr19:58373716-58373979(+)$1	263	173	177	12.0000
HHHH	chr11:124503117-124503373(+)$1	256	193	197	12.0000
CCOO	chr2:131132106-131132366(+)$1	260	9	13	12.0000
==HH	chr4:156265282-156265520(-)$1	238	199	203	12.0000
::::	chr8:101931647-101931897(-)$1	250	20	24	12.0000
ffff	chr3:45720339-45720613(+)$1	274	89	93	12.0000
bmmm	chr22:38879780-38880101(-)$1	321	76	80	12.0000
eeee	chr15:78886277-78886510(+)$1	233	171	175	12.0000

#DB
.(((	chr9:15886631-15886899(+)$1	1	71	75	12.0000
((..	chr11:47639062-47639295(-)$1	1	9	13	12.0000
..((	chr1:24296235-24296469(-)$1	1	134	138	12.0000
....	chr4:174243520-174243763(+)$1	1	42	46	12.0000
....	chr4:106162081-106162316(+)$1	1	0	4	12.0000
((((	chr15:62145322-62145595(-)$1	1	8	12	12.0000
..))	chr3:141664457-141664844(-)$1	1	34	38	12.0000
))..	chr6:76626842-76627074(+)$1	1	89	93	12.0000
((((	chr4:1947527-1947755(+)$1	1	47	51	12.0000
....	chr2:178994073-178994304(+)$1	1	91	95	12.0000
..((	chr1:227847456-227847714(+)$1	1	40	44	12.0000
....	chr3:141669655-141669888(-)$1	1	95	99	12.0000
))))	chr12:58196509-58196740(+)$1	1	34	38	12.0000
((((	chr12:55343793-55344059(-)$1	1	29	33	12.0000
....	chr17:414283-414519(-)$1	1	1	5	12.0000
....	chr5:134061052-134061291(+)$1	1	186	190	12.0000
....	chr4:106161154-106161424(+)$1	1	203	207	12.0000
((.(	chr7:129773859-129774122(+)$1	1	79	83	12.0000
....	chr12:124245761-124246026(+)$1	1	94	98	12.0000
((((	chr10:38119353-38119615(-)$1	1	2	6	12.0000
....	chr12:27181619-27181864(+)$1	1	0	4	12.0000
....	chr11:58921538-58921770(+)$1	1	132	136	12.0000
....	chr20:57252951-57253255(+)$1	1	79	83	12.0000
))))	chr2:46613571-46613806(+)$1	1	99	103	12.0000
....	chr2:207945648-207945977(-)$1	1	47	51	12.0000
((((	chr5:169679115-169679407(-)$1	1	229	233	12.0000
((((	chr1:231990838-231991092(+)$1	1	31	35	12.0000
....	chr1:161128229-161128506(+)$1	1	37	41	12.0000
....	chr18:34412520-34412767(+)$1	1	75	79	12.0000
(((.	chr5:87497037-87497288(-)$1	1	26	30	12.0000
....	chr1:100614556-100614789(+)$1	1	99	103	12.0000
....	chr10:104238913-104239159(-)$1	1	21	25	12.0000
..))	chr22:40722230-40722485(+)$1	1	52	56	12.0000
((..	chr16:24229722-24229970(+)$1	1	29	33	12.0000
))))	chr19:16551480-16551720(-)$1	1	197	201	12.0000
((((	chr19:52778691-52778931(+)$1	1	17	21	12.0000
((((	chr2:85547526-85547780(-)$1	1	71	75	12.0000
))))	chr2:61753079-61753319(-)$1	1	215	219	12.0000
....	chr4:44707556-44707789(-)$1	1	16	20	12.0000
))))	chr16:85706704-85706952(+)$1	1	32	36	12.0000
)...	chrX:70520330-70520675(+)$1	1	172	176	12.0000
((((	chr2:27884627-27884858(-)$1	1	25	29	12.0000
..((	chr1:204525126-204525372(+)$1	1	29	33	12.0000
))..	chr1:154555402-154555678(-)$1	1	225	229	12.0000
((((	chr12:52203991-52204220(+)$1	1	7	11	12.0000
.(.(	chr18:13761362-13761614(+)$1	1	13	17	12.0000
....	chr15:60787804-60788040(-)$1	1	6	10	12.0000
(..(	chr14:57670618-57670846(-)$1	1	10	14	12.0000
((((	chr2:9724641-9724881(-)$1	1	8	12	12.0000
((.(	chr21:19165306-19165562(-)$1	1	186	190	12.0000
)...	chr11:66963980-66964212(+)$1	1	46	50	12.0000
..((	chr7:129770418-129770684(+)$1	1	0	4	12.0000
((..	chrX:72902391-72902617(+)$1	1	23	27	12.0000
....	chr8:59361756-59362125(+)$1	1	348	352	12.0000
....	chr4:76857037-76857259(-)$1	1	30	34	12.0000
((..	chr1:26796075-26796391(+)$1	1	20	24	12.0000
....	chr1:179810518-179810822(-)$1	1	250	254	12.0000
))..	chr1:227849265-227849503(+)$1	1	74	78	12.0000
((((	chr12:44180953-44181213(+)$1	1	4	8	12.0000
....	chr12:95474360-95474584(-)$1	1	52	56	12.0000
))))	chr3:105399721-105399957(-)$1	1	156	160	12.0000
))).	chr7:87830477-87830708(+)$1	1	23	27	12.0000
((((	chr2:128494815-128495053(-)$1	1	54	58	12.0000
))))	chr19:58419082-58419345(-)$1	1	197	201	12.0000
((((	chr1:155306452-155306721(-)$1	1	3	7	12.0000
....	chr1:151555687-151555929(+)$1	1	99	103	12.0000
((..	chr1:155883567-155883800(-)$1	1	138	142	12.0000
(((.	chr3:194998144-194998380(-)$1	1	80	84	12.0000
(((.	chr10:126674756-126675037(+)$1	1	18	22	12.0000
.(((	chr20:6018085-6018319(+)$1	1	65	69	12.0000
))).	chr8:98287407-98287648(-)$1	1	89	93	12.0000
((..	chr19:58374042-58374279(+)$1	1	25	29	12.0000
))))	chr9:72324951-72325239(-)$1	1	35	39	12.0000
))).	chr1:160248357-160248604(-)$1	1	158	162	12.0000
(((.	chr13:21356340-21356587(-)$1	1	65	69	12.0000
((((	chr19:58373716-58373979(+)$1	1	173	177	12.0000
))))	chr11:124503117-124503373(+)$1	1	193	197	12.0000
((..	chr2:131132106-131132366(+)$1	1	9	13	12.0000
))))	chr4:156265282-156265520(-)$1	1	199	203	12.0000
....	chr8:101931647-101931897(-)$1	1	20	24	12.0000
))))	chr3:45720339-45720613(+)$1	1	89	93	12.0000
(...	chr22:38879780-38880101(-)$1	1	76	80	12.0000
))))	chr15:78886277-78886510(+)$1	1	171	175	12.0000

#PSSM
G : 0.80	g : 0.19	
A : 0.80	a : 0.19	
A : 0.80	a : 0.19	
A : 0.80	a : 0.19	

#score	996.0000000000001
#seq	83
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m2_run1.nuc.txt

#NT
UGC	chr2:64112668-64112891(+)$1	223	8	11	9.0000
UGC	chr5:43297038-43297293(-)$1	255	43	46	9.0000
UGC	chr18:44702507-44702743(-)$1	236	44	47	9.0000
UGC	chr12:12873977-12874226(+)$1	249	30	33	9.0000
UGC	chr14:95590761-95591005(-)$1	244	17	20	9.0000
UGC	chr17:38062400-38062623(-)$1	223	85	88	9.0000
UGC	chr1:151372032-151372303(+)$1	271	15	18	9.0000
UGC	chr1:202911071-202911317(-)$1	246	4	7	9.0000
UGC	chr6:26199022-26199276(-)$1	254	55	58	9.0000
UGC	chr6:153292249-153292493(-)$1	244	3	6	9.0000
UGC	chr1:185278441-185278680(-)$1	239	111	114	9.0000
UGC	chr2:32626259-32626526(+)$1	267	33	36	9.0000
UGC	chr3:121151096-121151342(-)$1	246	110	113	9.0000
UGC	chr17:79478336-79478588(-)$1	252	60	63	9.0000
UGC	chr9:138707643-138707873(-)$1	230	13	16	9.0000
UGC	chr6:153292221-153292458(-)$1	237	2	5	9.0000
UGC	chr2:242173246-242173473(-)$1	227	66	69	9.0000
UGC	chr17:27003147-27003369(+)$1	222	5	8	9.0000
UGC	chr1:207222204-207222476(-)$1	272	22	25	9.0000
UGC	chr1:205689561-205689819(-)$1	258	33	36	9.0000
UGC	chr11:35641347-35641597(+)$1	250	2	5	9.0000
UGC	chr19:45496124-45496397(+)$1	273	49	52	9.0000
UGC	chr18:19353540-19353762(+)$1	222	67	70	9.0000
UGC	chr14:95595715-95595952(-)$1	237	27	30	9.0000
UGC	chr10:93719712-93719940(+)$1	228	48	51	9.0000
UGC	chr19:18685620-18685854(+)$1	234	54	57	9.0000
UGC	chr9:139723746-139723987(+)$1	241	121	124	9.0000
UGC	chr6:26056372-26056621(-)$1	249	6	9	9.0000
UGC	chr3:167764653-167764875(-)$1	222	14	17	9.0000
UGC	chr1:76260185-76260428(+)$1	243	38	41	9.0000
UGC	chrX:105921341-105921579(+)$1	238	0	3	9.0000
UGC	chr1:156696997-156697219(-)$1	222	20	23	9.0000
UGC	chr12:64891339-64891576(+)$1	237	101	104	9.0000
UGC	chr11:376958-377190(+)$1	232	80	83	9.0000
UGC	chr11:122929263-122929494(-)$1	231	30	33	9.0000
UGC	chr20:3129163-3129384(-)$1	221	11	14	9.0000
UGC	chr16:23646976-23647195(-)$1	219	6	9	9.0000
UGC	chr17:40725049-40725274(-)$1	225	43	46	9.0000
UGC	chr11:9595521-9595777(+)$1	256	13	16	9.0000
UGC	chr12:6861364-6861603(-)$1	239	26	29	9.0000
UGC	chr20:5095833-5096069(-)$1	236	77	80	9.0000
UGC	chr9:124103454-124103680(-)$1	226	20	23	9.0000
UGC	chr11:9461987-9462228(+)$1	241	126	129	9.0000
UGC	chr2:100015156-100015380(+)$1	224	22	25	9.0000
UGC	chr20:34240850-34241076(-)$1	226	24	27	9.0000
UGC	chr15:35275259-35275485(-)$1	226	85	88	9.0000
UGC	chr1:92711998-92712231(-)$1	233	23	26	9.0000
UGC	chr2:217365976-217366221(+)$1	245	30	33	9.0000
UGC	chr3:58295978-58296201(+)$1	223	20	23	9.0000
UGC	chr11:47311458-47311680(+)$1	222	39	42	9.0000
UGC	chr15:77348034-77348272(-)$1	238	80	83	9.0000
UGC	chrX:24006257-24006481(-)$1	224	63	66	9.0000
UGC	chr7:92122293-92122515(-)$1	222	200	203	9.0000
UGC	chr6:26056439-26056661(-)$1	222	16	19	9.0000
UGC	chr12:21796835-21797085(-)$1	250	5	8	9.0000
UGC	chr16:29820927-29821149(+)$1	222	13	16	9.0000
UGC	chr16:29822194-29822489(+)$1	295	76	79	9.0000
UGC	chr10:102114236-102114481(+)$1	245	6	9	9.0000
UGC	chr6:30690603-30690831(+)$1	228	13	16	9.0000
UGC	chr4:1695263-1695494(-)$1	231	38	41	9.0000
UGC	chr3:49049315-49049571(+)$1	256	14	17	9.0000
UGC	chr2:85838999-85839226(-)$1	227	17	20	9.0000
UGC	chr19:41270939-41271243(+)$1	304	69	72	9.0000
UGC	chr17:62500782-62501002(-)$1	220	48	51	9.0000
UGC	chr10:32304407-32304663(-)$1	256	23	26	9.0000
UGC	chrX:153993092-153993331(+)$1	239	90	93	9.0000
UGC	chr2:101622332-101622564(+)$1	232	35	38	9.0000
UGC	chr5:37333484-37333711(-)$1	227	14	17	9.0000
UGC	chr11:7273300-7273521(+)$1	221	75	78	9.0000
UGC	chr6:121768382-121768608(+)$1	226	50	53	9.0000
UGC	chr6:32942249-32942472(+)$1	223	7	10	9.0000
UGC	chr2:101898245-101898500(-)$1	255	6	9	9.0000
UGC	chr2:62103202-62103444(-)$1	242	45	48	9.0000
UGC	chr15:91453363-91453583(+)$1	220	44	47	9.0000
UGC	chr3:51423624-51423857(+)$1	233	109	112	9.0000
UGC	chr11:15197277-15197500(+)$1	223	4	7	9.0000
UGC	chr17:79477544-79477857(-)$1	313	133	136	9.0000
UGC	chr2:101009807-101010031(-)$1	224	63	66	9.0000
UGC	chr5:140953536-140953799(-)$1	263	26	29	9.0000
UGC	chr13:77672619-77672850(-)$1	231	69	72	9.0000
UGC	chr7:26236476-26236731(-)$1	255	32	35	9.0000
UGC	chr14:102551178-102551417(-)$1	239	20	23	9.0000
UGC	chr19:8381331-8381580(-)$1	249	21	24	9.0000
UGC	chr1:222838865-222839111(+)$1	246	10	13	9.0000
UGC	chr17:27086132-27086359(-)$1	227	59	62	9.0000
UGC	chr21:28210696-28210925(-)$1	229	38	41	9.0000
UGC	chr18:196595-196828(+)$1	233	26	29	9.0000
UGC	chr14:97326903-97327158(+)$1	255	74	77	9.0000
UGC	chr7:95750420-95750648(-)$1	228	3	6	9.0000
UGC	chr3:156422612-156422834(+)$1	222	28	31	9.0000
UGC	chr17:65955799-65956047(+)$1	248	3	6	9.0000
UGC	chr17:34942241-34942472(+)$1	231	116	119	9.0000
UGC	chr5:145561950-145562192(-)$1	242	20	23	9.0000
UGC	chr19:8528383-8528627(+)$1	244	2	5	9.0000
UGC	chr16:29821468-29821733(+)$1	265	43	46	9.0000
UGC	chr16:29989073-29989318(+)$1	245	21	24	9.0000
UGC	chr19:45476323-45476567(+)$1	244	2	5	9.0000

#otherMatches

#Struct PSSM
ddd	chr22:28394779-28395000(-)$1	221	51	54	9.0000
GGG	chr2:64112668-64112891(+)$1	223	8	11	9.0000
[cc	chr5:43297038-43297293(-)$1	255	43	46	9.0000
mmm	chr18:44702507-44702743(-)$1	236	44	47	9.0000
bb]	chr12:12873977-12874226(+)$1	249	30	33	9.0000
:::	chr14:95590761-95591005(-)$1	244	17	20	9.0000
NNB	chr17:38062400-38062623(-)$1	223	85	88	9.0000
[bb	chr1:151372032-151372303(+)$1	271	15	18	9.0000
GGG	chr1:202911071-202911317(-)$1	246	4	7	9.0000
dff	chr6:26199022-26199276(-)$1	254	55	58	9.0000
:::	chr6:153292249-153292493(-)$1	244	3	6	9.0000
:::	chr1:185278441-185278680(-)$1	239	111	114	9.0000
eee	chr2:32626259-32626526(+)$1	267	33	36	9.0000
cqq	chr3:121151096-121151342(-)$1	246	110	113	9.0000
ddc	chr17:79478336-79478588(-)$1	252	60	63	9.0000
iii	chr9:138707643-138707873(-)$1	230	13	16	9.0000
EEE	chr6:153292221-153292458(-)$1	237	2	5	9.0000
&dd	chr2:242173246-242173473(-)$1	227	66	69	9.0000
EEE	chr17:27003147-27003369(+)$1	222	5	8	9.0000
ddd	chr1:207222204-207222476(-)$1	272	22	25	9.0000
ooe	chr1:205689561-205689819(-)$1	258	33	36	9.0000
cee	chr11:35641347-35641597(+)$1	250	2	5	9.0000
b22	chr19:45496124-45496397(+)$1	273	49	52	9.0000
:ff	chr18:19353540-19353762(+)$1	222	67	70	9.0000
::f	chr14:95595715-95595952(-)$1	237	27	30	9.0000
eee	chr10:93719712-93719940(+)$1	228	48	51	9.0000
666	chr19:18685620-18685854(+)$1	234	54	57	9.0000
ccc	chr9:139723746-139723987(+)$1	241	121	124	9.0000
lll	chr6:26056372-26056621(-)$1	249	6	9	9.0000
nnn	chr3:167764653-167764875(-)$1	222	14	17	9.0000
:::	chr1:76260185-76260428(+)$1	243	38	41	9.0000
:::	chrX:105921341-105921579(+)$1	238	0	3	9.0000
[bb	chr1:156696997-156697219(-)$1	222	20	23	9.0000
2bb	chr12:64891339-64891576(+)$1	237	101	104	9.0000
eee	chr11:376958-377190(+)$1	232	80	83	9.0000
FKK	chr11:122929263-122929494(-)$1	231	30	33	9.0000
ooo	chr20:3129163-3129384(-)$1	221	11	14	9.0000
DDD	chr16:23646976-23647195(-)$1	219	6	9	9.0000
ggg	chr17:40725049-40725274(-)$1	225	43	46	9.0000
KCC	chr11:9595521-9595777(+)$1	256	13	16	9.0000
:::	chr12:6861364-6861603(-)$1	239	26	29	9.0000
ccc	chr20:5095833-5096069(-)$1	236	77	80	9.0000
+++	chr9:124103454-124103680(-)$1	226	20	23	9.0000
(cc	chr11:9461987-9462228(+)$1	241	126	129	9.0000
sse	chr2:100015156-100015380(+)$1	224	22	25	9.0000
mmm	chr20:34240850-34241076(-)$1	226	24	27	9.0000
hhh	chr15:35275259-35275485(-)$1	226	85	88	9.0000
bb[	chr1:92711998-92712231(-)$1	233	23	26	9.0000
ggg	chr2:217365976-217366221(+)$1	245	30	33	9.0000
mbb	chr3:58295978-58296201(+)$1	223	20	23	9.0000
:CC	chr11:47311458-47311680(+)$1	222	39	42	9.0000
cee	chr15:77348034-77348272(-)$1	238	80	83	9.0000
ggg	chrX:24006257-24006481(-)$1	224	63	66	9.0000
:cc	chr7:92122293-92122515(-)$1	222	200	203	9.0000
KEE	chr6:26056439-26056661(-)$1	222	16	19	9.0000
MMM	chr12:21796835-21797085(-)$1	250	5	8	9.0000
ggg	chr16:29820927-29821149(+)$1	222	13	16	9.0000
c44	chr16:29822194-29822489(+)$1	295	76	79	9.0000
:::	chr10:102114236-102114481(+)$1	245	6	9	9.0000
FFF	chr6:30690603-30690831(+)$1	228	13	16	9.0000
d##	chr4:1695263-1695494(-)$1	231	38	41	9.0000
hhh	chr3:49049315-49049571(+)$1	256	14	17	9.0000
EE{	chr2:85838999-85839226(-)$1	227	17	20	9.0000
bbf	chr19:41270939-41271243(+)$1	304	69	72	9.0000
{BB	chr17:62500782-62501002(-)$1	220	48	51	9.0000
DDD	chr10:32304407-32304663(-)$1	256	23	26	9.0000
ddd	chrX:153993092-153993331(+)$1	239	90	93	9.0000
b[c	chr2:101622332-101622564(+)$1	232	35	38	9.0000
DDD	chr5:37333484-37333711(-)$1	227	14	17	9.0000
qbb	chr11:7273300-7273521(+)$1	221	75	78	9.0000
ddd	chr6:121768382-121768608(+)$1	226	50	53	9.0000
BBK	chr6:32942249-32942472(+)$1	223	7	10	9.0000
nnc	chr2:101898245-101898500(-)$1	255	6	9	9.0000
:::	chr2:62103202-62103444(-)$1	242	45	48	9.0000
B{F	chr15:91453363-91453583(+)$1	220	44	47	9.0000
:::	chr3:51423624-51423857(+)$1	233	109	112	9.0000
fff	chr11:15197277-15197500(+)$1	223	4	7	9.0000
ddd	chr17:79477544-79477857(-)$1	313	133	136	9.0000
fff	chr2:101009807-101010031(-)$1	224	63	66	9.0000
!bb	chr5:140953536-140953799(-)$1	263	26	29	9.0000
]ee	chr13:77672619-77672850(-)$1	231	69	72	9.0000
fff	chr7:26236476-26236731(-)$1	255	32	35	9.0000
::D	chr14:102551178-102551417(-)$1	239	20	23	9.0000
:CC	chr19:8381331-8381580(-)$1	249	21	24	9.0000
qqq	chr1:222838865-222839111(+)$1	246	10	13	9.0000
eee	chr17:27086132-27086359(-)$1	227	59	62	9.0000
qqq	chr21:28210696-28210925(-)$1	229	38	41	9.0000
qqq	chr18:196595-196828(+)$1	233	26	29	9.0000
[cc	chr14:97326903-97327158(+)$1	255	74	77	9.0000
eee	chr7:95750420-95750648(-)$1	228	3	6	9.0000
eee	chr3:156422612-156422834(+)$1	222	28	31	9.0000
dd[	chr17:65955799-65956047(+)$1	248	3	6	9.0000
[ff	chr17:34942241-34942472(+)$1	231	116	119	9.0000
mff	chr5:145561950-145562192(-)$1	242	20	23	9.0000
:bb	chr19:8528383-8528627(+)$1	244	2	5	9.0000
cc[	chr16:29821468-29821733(+)$1	265	43	46	9.0000
occ	chr16:29989073-29989318(+)$1	245	21	24	9.0000
EEE	chr19:45476323-45476567(+)$1	244	2	5	9.0000

#DB
)))	chr22:28394779-28395000(-)$1	1	51	54	9.0000
(((	chr2:64112668-64112891(+)$1	1	8	11	9.0000
.((	chr5:43297038-43297293(-)$1	1	43	46	9.0000
...	chr18:44702507-44702743(-)$1	1	44	47	9.0000
)).	chr12:12873977-12874226(+)$1	1	30	33	9.0000
...	chr14:95590761-95591005(-)$1	1	17	20	9.0000
..(	chr17:38062400-38062623(-)$1	1	85	88	9.0000
.((	chr1:151372032-151372303(+)$1	1	15	18	9.0000
(((	chr1:202911071-202911317(-)$1	1	4	7	9.0000
(((	chr6:26199022-26199276(-)$1	1	55	58	9.0000
...	chr6:153292249-153292493(-)$1	1	3	6	9.0000
...	chr1:185278441-185278680(-)$1	1	111	114	9.0000
)))	chr2:32626259-32626526(+)$1	1	33	36	9.0000
(..	chr3:121151096-121151342(-)$1	1	110	113	9.0000
)))	chr17:79478336-79478588(-)$1	1	60	63	9.0000
(((	chr9:138707643-138707873(-)$1	1	13	16	9.0000
(((	chr6:153292221-153292458(-)$1	1	2	5	9.0000
.((	chr2:242173246-242173473(-)$1	1	66	69	9.0000
(((	chr17:27003147-27003369(+)$1	1	5	8	9.0000
(((	chr1:207222204-207222476(-)$1	1	22	25	9.0000
..)	chr1:205689561-205689819(-)$1	1	33	36	9.0000
(((	chr11:35641347-35641597(+)$1	1	2	5	9.0000
)..	chr19:45496124-45496397(+)$1	1	49	52	9.0000
.((	chr18:19353540-19353762(+)$1	1	67	70	9.0000
..(	chr14:95595715-95595952(-)$1	1	27	30	9.0000
)))	chr10:93719712-93719940(+)$1	1	48	51	9.0000
...	chr19:18685620-18685854(+)$1	1	54	57	9.0000
(((	chr9:139723746-139723987(+)$1	1	121	124	9.0000
...	chr6:26056372-26056621(-)$1	1	6	9	9.0000
...	chr3:167764653-167764875(-)$1	1	14	17	9.0000
...	chr1:76260185-76260428(+)$1	1	38	41	9.0000
...	chrX:105921341-105921579(+)$1	1	0	3	9.0000
.((	chr1:156696997-156697219(-)$1	1	20	23	9.0000
.))	chr12:64891339-64891576(+)$1	1	101	104	9.0000
(((	chr11:376958-377190(+)$1	1	80	83	9.0000
(..	chr11:122929263-122929494(-)$1	1	30	33	9.0000
...	chr20:3129163-3129384(-)$1	1	11	14	9.0000
(((	chr16:23646976-23647195(-)$1	1	6	9	9.0000
(((	chr17:40725049-40725274(-)$1	1	43	46	9.0000
.((	chr11:9595521-9595777(+)$1	1	13	16	9.0000
...	chr12:6861364-6861603(-)$1	1	26	29	9.0000
)))	chr20:5095833-5096069(-)$1	1	77	80	9.0000
...	chr9:124103454-124103680(-)$1	1	20	23	9.0000
.((	chr11:9461987-9462228(+)$1	1	126	129	9.0000
..)	chr2:100015156-100015380(+)$1	1	22	25	9.0000
...	chr20:34240850-34241076(-)$1	1	24	27	9.0000
)))	chr15:35275259-35275485(-)$1	1	85	88	9.0000
((.	chr1:92711998-92712231(-)$1	1	23	26	9.0000
)))	chr2:217365976-217366221(+)$1	1	30	33	9.0000
.))	chr3:58295978-58296201(+)$1	1	20	23	9.0000
.((	chr11:47311458-47311680(+)$1	1	39	42	9.0000
(((	chr15:77348034-77348272(-)$1	1	80	83	9.0000
(((	chrX:24006257-24006481(-)$1	1	63	66	9.0000
.((	chr7:92122293-92122515(-)$1	1	200	203	9.0000
.((	chr6:26056439-26056661(-)$1	1	16	19	9.0000
...	chr12:21796835-21797085(-)$1	1	5	8	9.0000
(((	chr16:29820927-29821149(+)$1	1	13	16	9.0000
)..	chr16:29822194-29822489(+)$1	1	76	79	9.0000
...	chr10:102114236-102114481(+)$1	1	6	9	9.0000
(((	chr6:30690603-30690831(+)$1	1	13	16	9.0000
(..	chr4:1695263-1695494(-)$1	1	38	41	9.0000
(((	chr3:49049315-49049571(+)$1	1	14	17	9.0000
((.	chr2:85838999-85839226(-)$1	1	17	20	9.0000
)))	chr19:41270939-41271243(+)$1	1	69	72	9.0000
.((	chr17:62500782-62501002(-)$1	1	48	51	9.0000
(((	chr10:32304407-32304663(-)$1	1	23	26	9.0000
)))	chrX:153993092-153993331(+)$1	1	90	93	9.0000
(.(	chr2:101622332-101622564(+)$1	1	35	38	9.0000
(((	chr5:37333484-37333711(-)$1	1	14	17	9.0000
.))	chr11:7273300-7273521(+)$1	1	75	78	9.0000
)))	chr6:121768382-121768608(+)$1	1	50	53	9.0000
((.	chr6:32942249-32942472(+)$1	1	7	10	9.0000
..)	chr2:101898245-101898500(-)$1	1	6	9	9.0000
...	chr2:62103202-62103444(-)$1	1	45	48	9.0000
(.(	chr15:91453363-91453583(+)$1	1	44	47	9.0000
...	chr3:51423624-51423857(+)$1	1	109	112	9.0000
(((	chr11:15197277-15197500(+)$1	1	4	7	9.0000
(((	chr17:79477544-79477857(-)$1	1	133	136	9.0000
(((	chr2:101009807-101010031(-)$1	1	63	66	9.0000
.((	chr5:140953536-140953799(-)$1	1	26	29	9.0000
.))	chr13:77672619-77672850(-)$1	1	69	72	9.0000
)))	chr7:26236476-26236731(-)$1	1	32	35	9.0000
..(	chr14:102551178-102551417(-)$1	1	20	23	9.0000
.((	chr19:8381331-8381580(-)$1	1	21	24	9.0000
...	chr1:222838865-222839111(+)$1	1	10	13	9.0000
)))	chr17:27086132-27086359(-)$1	1	59	62	9.0000
...	chr21:28210696-28210925(-)$1	1	38	41	9.0000
...	chr18:196595-196828(+)$1	1	26	29	9.0000
.((	chr14:97326903-97327158(+)$1	1	74	77	9.0000
(((	chr7:95750420-95750648(-)$1	1	3	6	9.0000
(((	chr3:156422612-156422834(+)$1	1	28	31	9.0000
((.	chr17:65955799-65956047(+)$1	1	3	6	9.0000
.((	chr17:34942241-34942472(+)$1	1	116	119	9.0000
.))	chr5:145561950-145562192(-)$1	1	20	23	9.0000
.((	chr19:8528383-8528627(+)$1	1	2	5	9.0000
((.	chr16:29821468-29821733(+)$1	1	43	46	9.0000
.))	chr16:29989073-29989318(+)$1	1	21	24	9.0000
(((	chr19:45476323-45476567(+)$1	1	2	5	9.0000

#PSSM
U : 1.00	
G : 1.00	
C : 1.00	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_UTR_m3_run1.nuc.txt

#NT
CUGCCCUCAGCCCCAGCCCUGGCCACCCCCCCACCCACCGGUGGUCCUGCCUCACUUGCAGCACUCUGUGGCUGGCCACCACCUGGGGCCCCCAGAGGGGCUGCCGCAGGCCGCCAUGCACGGGCAUCACACCCAGUACUGCCACAUGCAGAACCCUCCCCCGUaccaccaucaccaccaccaccaccCACCCCAGCACAUCCAGCACGCACACCAGUACCACCACGGCCCCCAUGGGGGCCACCCAGCCUACGGGGCCCAUGCCCACGGCCACCCGCCGCUGCCCUCGGCCCACGUGGGGCACACAGUGCACCACCAU	chr3:12942483-12942886(-)$1	403	14	333	462.0000

#otherMatches

#Struct PSSM
flllffffff22ddddA{EEEEEMMMMCCCBB{DDDD{CCC::eeeeellleeeee::::::::::::bbmmmmbb:::::::::::::::::::::CCC}DDDD}BB~~~~CCCZZZEEEEE}A@@@@@@@@@@BB}EEEEEA?????CCC:::::::::::::::::::::BBLLLCCC{CCCNNNNNFFFFFFEEEEE{CCCKKCCCLLLFFFFFFbbqqqqqqqqbb::::::::::::::::::::::::::::::::::::::::::::::ddddbboooooobb]ddddccc!!cccnnnnnccc22ccc::	chr14:102965078-102965517(+)$1	439	39	358	462.0000
ddd::::::BBKKFFFFFF:ggggggguuuuuuuuuuuugggggggddddpppppppdddd::eeeee[bb!!dddd[bbmmmmbbddddbbeeeeeFFFFFFYYBB:EEEEEMMMMCCC{DDDD::::::::::bb[ddddnnnnndddd]bb:::::FFFFFF::::::::::::::::::::::::::::::bbpppppppbbbbqqqqqqqqbb::::::::ffffffmmmmffffff::::::::FFFFFFDDDD}CCCZZZEEEEE::::GGGGGGGNNNNNDDDD:::dddd[ddddllldddd]dddd:::	chr3:12942483-12942886(-)$1	403	14	333	462.0000

#DB
(...))))))..))))(.(((((....(((((.((((.(((..(((((...)))))............((....)).....................))).)))).))....)))...))))).)..........)).)))))).....))).....................((...(((.(((.....(((((((((((.(((..(((...((((((((........))..............................................((((((......)).))))(((..(((.....)))..)))..	chr14:102965078-102965517(+)$1	1	39	358	462.0000
)))......((..((((((.(((((((............)))))))((((.......))))..(((((.((..((((.((....)))))))))))))))))))..)).(((((....(((.((((..........((.((((.....)))).)).....((((((..............................((.......))((........))........((((((....))))))........)))))))))).)))...)))))....(((((((.....((((...((((.((((...)))).))))...	chr3:12942483-12942886(-)$1	1	14	333	462.0000

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

#score	924.0
#seq	2
#width	319
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m1_run1.nuc.txt

#NT
CCUC	chr4:159176249-159176485(+)$1	236	25	29	11.9999
CCUC	chr20:1317298-1317523(-)$1	225	64	68	11.9999
CCUC	chr11:65622520-65622745(-)$1	225	112	116	11.9999
CCUC	chr7:140482734-140482961(-)$1	227	37	41	11.9999
CCUC	chr21:45405707-45405942(+)$1	235	169	173	11.9999
CCUC	chr3:36986275-36986491(-)$1	216	3	7	11.9999
CCUC	chr16:2505434-2505653(-)$1	219	27	31	11.9999
CCUC	chr5:55247195-55247418(-)$1	223	25	29	11.9999
CCUC	chr11:64481227-64481447(-)$1	220	13	17	11.9999
CCUC	chr10:102123669-102123892(+)$1	223	6	10	11.9999
CCUC	chr19:46518208-46518437(+)$1	229	62	66	11.9999
CCUC	chr12:57543603-57543827(+)$1	224	37	41	11.9999
CCUC	chr11:123497242-123497459(-)$1	217	103	107	11.9999
CCUC	chr6:109703533-109703751(+)$1	218	53	57	11.9999
CCUC	chr2:219139607-219139827(-)$1	220	9	13	11.9999
CCUC	chr8:29927239-29927479(-)$1	240	88	92	11.9999
CCUC	chr17:40125559-40125780(+)$1	221	112	116	11.9999
CCUC	chr1:220323100-220323318(+)$1	218	129	133	11.9999
CCUC	chr2:29025676-29025905(+)$1	229	150	154	11.9999
CCUC	chr15:31238571-31238790(-)$1	219	67	71	11.9999
CCUC	chr22:22052247-22052470(-)$1	223	56	60	11.9999
CCUC	chr17:27206912-27207162(-)$1	250	39	43	11.9999
CCUC	chr3:138121311-138121529(+)$1	218	73	77	11.9999
CCUC	chr20:1919672-1919891(+)$1	219	27	31	11.9999
CCUC	chr14:24658646-24658861(-)$1	215	48	52	11.9999
CCUC	chr11:2187803-2188018(-)$1	215	131	135	11.9999
CCUC	chr9:131584053-131584273(+)$1	220	106	110	11.9999
CCUC	chr20:45948202-45948422(-)$1	220	25	29	11.9999
CCUC	chr1:203186842-203187058(-)$1	216	38	42	11.9999
CCUC	chr7:99054860-99055083(-)$1	223	211	215	11.9999
CCUC	chr16:30959845-30960065(+)$1	220	38	42	11.9999
CCUC	chr16:50706573-50706801(-)$1	228	0	4	11.9999
CCUC	chr10:133772009-133772236(+)$1	227	183	187	11.9999
CCUC	chr8:145690233-145690451(-)$1	218	107	111	11.9999
ccuc	chr12:91570636-91570852(+)$1	216	196	200	11.9999
CCUC	chr17:34755661-34755884(-)$1	223	41	45	11.9999
CCUC	chr7:29961911-29962142(-)$1	231	30	34	11.9999
CCUC	chr17:73061431-73061656(+)$1	225	31	35	11.9999
CCUC	chr4:186508583-186508819(-)$1	236	48	52	11.9999
CCUC	chr19:15563284-15563505(-)$1	221	48	52	11.9999
CCUC	chr7:44104898-44105115(+)$1	217	118	122	11.9999
CCUC	chr18:11881155-11881380(+)$1	225	109	113	11.9999
CCUC	chr20:23614445-23614665(-)$1	220	10	14	11.9999
CCUC	chr1:160249168-160249386(-)$1	218	61	65	11.9999
CCUC	chr17:39981532-39981769(-)$1	237	41	45	11.9999
CCUC	chr3:49459770-49460008(-)$1	238	90	94	11.9999
CCUC	chr6:30512215-30512446(-)$1	231	153	157	11.9999
CCUC	chr2:189897370-189897585(-)$1	215	109	113	11.9999
CCUC	chr15:75952189-75952405(-)$1	216	159	163	11.9999
CCUC	chr11:67184914-67185143(+)$1	229	163	167	11.9999
CCUC	chr2:131806285-131806500(-)$1	215	55	59	11.9999
CCUC	chr2:128568604-128568835(-)$1	231	24	28	11.9999
CCUC	chr17:62503198-62503413(+)$1	215	7	11	11.9999
CCUC	chr16:12995710-12995933(+)$1	223	126	130	11.9999
CCUC	chr15:42450868-42451086(-)$1	218	63	67	11.9999
CCUC	chrX:153664173-153664407(+)$1	234	149	153	11.9999
CCUC	chr6:127764925-127765144(-)$1	219	91	95	11.9999
CCUC	chr17:77084051-77084271(-)$1	220	109	113	11.9999
CCUC	chr17:36882813-36883051(+)$1	238	80	84	11.9999
CCUC	chr15:90630581-90630808(-)$1	227	144	148	11.9999
CCUC	chr16:71962144-71962368(+)$1	224	114	118	11.9999
CCUC	chr14:95085547-95085765(+)$1	218	171	175	11.9999
CCUC	chr5:131608180-131608395(-)$1	215	76	80	11.9999
CCUC	chr11:61309599-61309817(-)$1	218	20	24	11.9999
CCUC	chr4:77189760-77189976(+)$1	216	137	141	11.9999
CCUC	chr2:242512999-242513221(-)$1	222	107	111	11.9999
CCUC	chr15:59150768-59150991(+)$1	223	36	40	11.9999
CCUC	chr8:87573101-87573317(-)$1	216	110	114	11.9999
CCUC	chr16:87636583-87636804(+)$1	221	53	57	11.9999
CCUC	chr19:41354406-41354650(+)$1	244	57	61	11.9999
CCUC	chr1:38269468-38269701(+)$1	233	41	45	11.9999
CCUC	chr6:30864495-30864718(+)$1	223	93	97	11.9999
CCUC	chr18:74699849-74700076(-)$1	227	111	115	11.9999
CCUC	chr5:146257552-146257771(-)$1	219	4	8	11.9999
CCUC	chr3:127395278-127395508(+)$1	230	66	70	11.9999
CCUC	chr15:23045739-23045955(-)$1	216	34	38	11.9999
CCUC	chr19:18989949-18990167(-)$1	218	102	106	11.9999
CCUC	chr2:128145206-128145428(-)$1	222	46	50	11.9999
CCUC	chr2:203241709-203241931(+)$1	222	77	81	11.9999

#otherMatches

#Struct PSSM
dddd	chr1:66839760-66839975(+)$1	215	96	100	11.9999
ddbb	chr4:159176249-159176485(+)$1	236	25	29	11.9999
eeee	chr20:1317298-1317523(-)$1	225	64	68	11.9999
::::	chr11:65622520-65622745(-)$1	225	112	116	11.9999
++++	chr7:140482734-140482961(-)$1	227	37	41	11.9999
mmmm	chr21:45405707-45405942(+)$1	235	169	173	11.9999
ee[c	chr3:36986275-36986491(-)$1	216	3	7	11.9999
a[cc	chr16:2505434-2505653(-)$1	219	27	31	11.9999
bb!!	chr5:55247195-55247418(-)$1	223	25	29	11.9999
::::	chr11:64481227-64481447(-)$1	220	13	17	11.9999
gggg	chr10:102123669-102123892(+)$1	223	6	10	11.9999
eeee	chr19:46518208-46518437(+)$1	229	62	66	11.9999
5555	chr12:57543603-57543827(+)$1	224	37	41	11.9999
eeee	chr11:123497242-123497459(-)$1	217	103	107	11.9999
ccc2	chr6:109703533-109703751(+)$1	218	53	57	11.9999
rrrr	chr2:219139607-219139827(-)$1	220	9	13	11.9999
c22e	chr8:29927239-29927479(-)$1	240	88	92	11.9999
JJJJ	chr17:40125559-40125780(+)$1	221	112	116	11.9999
''ff	chr1:220323100-220323318(+)$1	218	129	133	11.9999
dddm	chr2:29025676-29025905(+)$1	229	150	154	11.9999
f(((	chr15:31238571-31238790(-)$1	219	67	71	11.9999
CC:g	chr22:22052247-22052470(-)$1	223	56	60	11.9999
ddqq	chr17:27206912-27207162(-)$1	250	39	43	11.9999
:::c	chr3:138121311-138121529(+)$1	218	73	77	11.9999
gggg	chr20:1919672-1919891(+)$1	219	27	31	11.9999
h:::	chr14:24658646-24658861(-)$1	215	48	52	11.9999
::ff	chr11:2187803-2188018(-)$1	215	131	135	11.9999
hhhh	chr9:131584053-131584273(+)$1	220	106	110	11.9999
JJJJ	chr20:45948202-45948422(-)$1	220	25	29	11.9999
HHHK	chr1:203186842-203187058(-)$1	216	38	42	11.9999
E}BB	chr7:99054860-99055083(-)$1	223	211	215	11.9999
ffff	chr16:30959845-30960065(+)$1	220	38	42	11.9999
::::	chr16:50706573-50706801(-)$1	228	0	4	11.9999
]ddd	chr10:133772009-133772236(+)$1	227	183	187	11.9999
:ccc	chr8:145690233-145690451(-)$1	218	107	111	11.9999
::::	chr12:91570636-91570852(+)$1	216	196	200	11.9999
ddll	chr17:34755661-34755884(-)$1	223	41	45	11.9999
ggtt	chr7:29961911-29962142(-)$1	231	30	34	11.9999
{DDD	chr17:73061431-73061656(+)$1	225	31	35	11.9999
dddd	chr4:186508583-186508819(-)$1	236	48	52	11.9999
tttt	chr19:15563284-15563505(-)$1	221	48	52	11.9999
DDDD	chr7:44104898-44105115(+)$1	217	118	122	11.9999
iii!	chr18:11881155-11881380(+)$1	225	109	113	11.9999
EEee	chr20:23614445-23614665(-)$1	220	10	14	11.9999
::cc	chr1:160249168-160249386(-)$1	218	61	65	11.9999
Jccc	chr17:39981532-39981769(-)$1	237	41	45	11.9999
hhhh	chr3:49459770-49460008(-)$1	238	90	94	11.9999
ffff	chr6:30512215-30512446(-)$1	231	153	157	11.9999
rrrr	chr2:189897370-189897585(-)$1	215	109	113	11.9999
::::	chr15:75952189-75952405(-)$1	216	159	163	11.9999
d"""	chr11:67184914-67185143(+)$1	229	163	167	11.9999
ccce	chr2:131806285-131806500(-)$1	215	55	59	11.9999
CCCK	chr2:128568604-128568835(-)$1	231	24	28	11.9999
ffss	chr17:62503198-62503413(+)$1	215	7	11	11.9999
B{EE	chr16:12995710-12995933(+)$1	223	126	130	11.9999
bb%%	chr15:42450868-42451086(-)$1	218	63	67	11.9999
nfff	chrX:153664173-153664407(+)$1	234	149	153	11.9999
"""b	chr6:127764925-127765144(-)$1	219	91	95	11.9999
e999	chr17:77084051-77084271(-)$1	220	109	113	11.9999
JJJJ	chr17:36882813-36883051(+)$1	238	80	84	11.9999
cc]d	chr15:90630581-90630808(-)$1	227	144	148	11.9999
gggg	chr16:71962144-71962368(+)$1	224	114	118	11.9999
ffff	chr14:95085547-95085765(+)$1	218	171	175	11.9999
b:::	chr5:131608180-131608395(-)$1	215	76	80	11.9999
::cc	chr11:61309599-61309817(-)$1	218	20	24	11.9999
2a22	chr4:77189760-77189976(+)$1	216	137	141	11.9999
ccbb	chr2:242512999-242513221(-)$1	222	107	111	11.9999
oooo	chr15:59150768-59150991(+)$1	223	36	40	11.9999
ssss	chr8:87573101-87573317(-)$1	216	110	114	11.9999
nnnn	chr16:87636583-87636804(+)$1	221	53	57	11.9999
qqqq	chr19:41354406-41354650(+)$1	244	57	61	11.9999
ffff	chr1:38269468-38269701(+)$1	233	41	45	11.9999
ffff	chr6:30864495-30864718(+)$1	223	93	97	11.9999
dddd	chr18:74699849-74700076(-)$1	227	111	115	11.9999
FFFF	chr5:146257552-146257771(-)$1	219	4	8	11.9999
ddd2	chr3:127395278-127395508(+)$1	230	66	70	11.9999
cccs	chr15:23045739-23045955(-)$1	216	34	38	11.9999
eeoo	chr19:18989949-18990167(-)$1	218	102	106	11.9999
b!!e	chr2:128145206-128145428(-)$1	222	46	50	11.9999
^^^^	chr2:203241709-203241931(+)$1	222	77	81	11.9999

#DB
))))	chr1:66839760-66839975(+)$1	1	96	100	11.9999
((((	chr4:159176249-159176485(+)$1	1	25	29	11.9999
))))	chr20:1317298-1317523(-)$1	1	64	68	11.9999
....	chr11:65622520-65622745(-)$1	1	112	116	11.9999
....	chr7:140482734-140482961(-)$1	1	37	41	11.9999
....	chr21:45405707-45405942(+)$1	1	169	173	11.9999
((.(	chr3:36986275-36986491(-)$1	1	3	7	11.9999
(.((	chr16:2505434-2505653(-)$1	1	27	31	11.9999
((..	chr5:55247195-55247418(-)$1	1	25	29	11.9999
....	chr11:64481227-64481447(-)$1	1	13	17	11.9999
((((	chr10:102123669-102123892(+)$1	1	6	10	11.9999
))))	chr19:46518208-46518437(+)$1	1	62	66	11.9999
....	chr12:57543603-57543827(+)$1	1	37	41	11.9999
((((	chr11:123497242-123497459(-)$1	1	103	107	11.9999
))).	chr6:109703533-109703751(+)$1	1	53	57	11.9999
....	chr2:219139607-219139827(-)$1	1	9	13	11.9999
)..)	chr8:29927239-29927479(-)$1	1	88	92	11.9999
((((	chr17:40125559-40125780(+)$1	1	112	116	11.9999
..((	chr1:220323100-220323318(+)$1	1	129	133	11.9999
(((.	chr2:29025676-29025905(+)$1	1	150	154	11.9999
(...	chr15:31238571-31238790(-)$1	1	67	71	11.9999
((.(	chr22:22052247-22052470(-)$1	1	56	60	11.9999
((..	chr17:27206912-27207162(-)$1	1	39	43	11.9999
...(	chr3:138121311-138121529(+)$1	1	73	77	11.9999
((((	chr20:1919672-1919891(+)$1	1	27	31	11.9999
)...	chr14:24658646-24658861(-)$1	1	48	52	11.9999
..((	chr11:2187803-2188018(-)$1	1	131	135	11.9999
))))	chr9:131584053-131584273(+)$1	1	106	110	11.9999
((((	chr20:45948202-45948422(-)$1	1	25	29	11.9999
(((.	chr1:203186842-203187058(-)$1	1	38	42	11.9999
).))	chr7:99054860-99055083(-)$1	1	211	215	11.9999
((((	chr16:30959845-30960065(+)$1	1	38	42	11.9999
....	chr16:50706573-50706801(-)$1	1	0	4	11.9999
.)))	chr10:133772009-133772236(+)$1	1	183	187	11.9999
.(((	chr8:145690233-145690451(-)$1	1	107	111	11.9999
....	chr12:91570636-91570852(+)$1	1	196	200	11.9999
((..	chr17:34755661-34755884(-)$1	1	41	45	11.9999
((..	chr7:29961911-29962142(-)$1	1	30	34	11.9999
.(((	chr17:73061431-73061656(+)$1	1	31	35	11.9999
((((	chr4:186508583-186508819(-)$1	1	48	52	11.9999
....	chr19:15563284-15563505(-)$1	1	48	52	11.9999
))))	chr7:44104898-44105115(+)$1	1	118	122	11.9999
(((.	chr18:11881155-11881380(+)$1	1	109	113	11.9999
((((	chr20:23614445-23614665(-)$1	1	10	14	11.9999
..((	chr1:160249168-160249386(-)$1	1	61	65	11.9999
((((	chr17:39981532-39981769(-)$1	1	41	45	11.9999
((((	chr3:49459770-49460008(-)$1	1	90	94	11.9999
((((	chr6:30512215-30512446(-)$1	1	153	157	11.9999
....	chr2:189897370-189897585(-)$1	1	109	113	11.9999
....	chr15:75952189-75952405(-)$1	1	159	163	11.9999
(...	chr11:67184914-67185143(+)$1	1	163	167	11.9999
((((	chr2:131806285-131806500(-)$1	1	55	59	11.9999
(((.	chr2:128568604-128568835(-)$1	1	24	28	11.9999
((..	chr17:62503198-62503413(+)$1	1	7	11	11.9999
(.((	chr16:12995710-12995933(+)$1	1	126	130	11.9999
((..	chr15:42450868-42451086(-)$1	1	63	67	11.9999
.)))	chrX:153664173-153664407(+)$1	1	149	153	11.9999
...(	chr6:127764925-127765144(-)$1	1	91	95	11.9999
)...	chr17:77084051-77084271(-)$1	1	109	113	11.9999
((((	chr17:36882813-36883051(+)$1	1	80	84	11.9999
)).)	chr15:90630581-90630808(-)$1	1	144	148	11.9999
))))	chr16:71962144-71962368(+)$1	1	114	118	11.9999
((((	chr14:95085547-95085765(+)$1	1	171	175	11.9999
)...	chr5:131608180-131608395(-)$1	1	76	80	11.9999
..((	chr11:61309599-61309817(-)$1	1	20	24	11.9999
.)..	chr4:77189760-77189976(+)$1	1	137	141	11.9999
))))	chr2:242512999-242513221(-)$1	1	107	111	11.9999
....	chr15:59150768-59150991(+)$1	1	36	40	11.9999
....	chr8:87573101-87573317(-)$1	1	110	114	11.9999
....	chr16:87636583-87636804(+)$1	1	53	57	11.9999
....	chr19:41354406-41354650(+)$1	1	57	61	11.9999
((((	chr1:38269468-38269701(+)$1	1	41	45	11.9999
((((	chr6:30864495-30864718(+)$1	1	93	97	11.9999
))))	chr18:74699849-74700076(-)$1	1	111	115	11.9999
((((	chr5:146257552-146257771(-)$1	1	4	8	11.9999
))).	chr3:127395278-127395508(+)$1	1	66	70	11.9999
(((.	chr15:23045739-23045955(-)$1	1	34	38	11.9999
((..	chr19:18989949-18990167(-)$1	1	102	106	11.9999
(..(	chr2:128145206-128145428(-)$1	1	46	50	11.9999
....	chr2:203241709-203241931(+)$1	1	77	81	11.9999

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

#score	959.9999999999994
#seq	80
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m2_run2.nuc.txt

#NT
UGGGA	chr7:26707084-26707287(-)$1	203	157	162	15.0000
UGGGA	chr9:134400040-134400250(-)$1	210	0	5	15.0000
UGGGA	chr7:128409368-128409613(+)$1	245	130	135	15.0000
UGGGA	chr1:150191834-150192044(-)$1	210	79	84	15.0000
UGGGA	chr1:67877689-67877945(-)$1	256	152	157	15.0000
UGGGA	chr1:46828187-46828425(+)$1	238	114	119	15.0000
UGGGA	chr17:80036992-80037221(-)$1	229	35	40	15.0000
UGGGA	chr12:53805388-53805598(+)$1	210	105	110	15.0000
UGGGA	chr1:113245582-113245830(-)$1	248	104	109	15.0000
UGGGA	chr13:27260708-27260943(+)$1	235	110	115	15.0000
UGGGA	chr1:32377205-32377431(-)$1	226	128	133	15.0000
UGGGA	chr6:34555284-34555501(-)$1	217	116	121	15.0000
UGGGA	chr15:102182118-102182370(-)$1	252	63	68	15.0000
UGGGA	chr2:113289479-113289732(+)$1	253	170	175	15.0000
UGGGA	chr17:8108486-8108731(-)$1	245	199	204	15.0000
UGGGA	chr16:19090849-19091073(+)$1	224	159	164	15.0000
UGGGA	chr13:45911128-45911356(-)$1	228	171	176	15.0000
UGGGA	chr9:127996014-127996247(+)$1	233	187	192	15.0000
UGGGA	chr11:60658278-60658490(-)$1	212	52	57	15.0000
UGGGA	chr3:141644322-141644534(+)$1	212	106	111	15.0000
UGGGA	chr2:131808401-131808647(-)$1	246	13	18	15.0000
UGGGA	chr10:322005-322229(-)$1	224	68	73	15.0000
UGGGA	chr17:73886469-73886708(-)$1	239	54	59	15.0000
UGGGA	chr9:86583519-86583750(-)$1	231	124	129	15.0000
UGGGA	chr5:146771525-146771740(-)$1	215	102	107	15.0000
UGGGA	chr8:1953589-1953794(+)$1	205	91	96	15.0000
UGGGA	chr3:15293484-15293699(+)$1	215	111	116	15.0000
UGGGA	chr17:5346625-5346864(-)$1	239	146	151	15.0000
UGGGA	chr9:19378740-19378982(-)$1	242	89	94	15.0000
UGGGA	chr2:113286659-113286860(+)$1	201	8	13	15.0000
UGGGA	chr1:47124278-47124483(-)$1	205	168	173	15.0000
UGGGA	chr18:13666488-13666699(-)$1	211	18	23	15.0000
UGGGA	chr3:49145601-49145833(-)$1	232	20	25	15.0000
UGGGA	chr14:103194074-103194288(+)$1	214	28	33	15.0000
UGGGA	chr15:75136223-75136462(-)$1	239	130	135	15.0000
UGGGA	chr6:30152904-30153109(-)$1	205	101	106	15.0000
UGGGA	chr12:49085751-49085966(-)$1	215	171	176	15.0000
UGGGA	chr15:35664104-35664316(-)$1	212	127	132	15.0000
UGGGA	chr22:38879615-38879840(-)$1	225	194	199	15.0000
UGGGA	chr12:7053095-7053329(+)$1	234	110	115	15.0000
UGGGA	chr11:118621433-118621648(-)$1	215	57	62	15.0000
UGGGA	chr15:90624621-90624834(+)$1	213	55	60	15.0000
UGGGA	chr15:77348316-77348609(-)$1	293	37	42	15.0000
uggga	chr16:66978405-66978624(+)$1	219	1	6	15.0000
UGGGA	chr1:160327930-160328161(+)$1	231	190	195	15.0000
UGGGA	chr16:449544-449791(+)$1	247	85	90	15.0000
UGGGA	chr19:4724563-4724809(-)$1	246	22	27	15.0000

#otherMatches

#Struct PSSM
dcccm	chr1:934238-934480(-)$1	242	186	191	15.0000
d]aEE	chr7:26707084-26707287(-)$1	203	157	162	15.0000
:::::	chr9:134400040-134400250(-)$1	210	0	5	15.0000
HHHHH	chr7:128409368-128409613(+)$1	245	130	135	15.0000
ddd33	chr1:150191834-150192044(-)$1	210	79	84	15.0000
GGGGG	chr1:67877689-67877945(-)$1	256	152	157	15.0000
"eeee	chr1:46828187-46828425(+)$1	238	114	119	15.0000
DDfff	chr17:80036992-80037221(-)$1	229	35	40	15.0000
feeee	chr12:53805388-53805598(+)$1	210	105	110	15.0000
d[amm	chr1:113245582-113245830(-)$1	248	104	109	15.0000
GGggg	chr13:27260708-27260943(+)$1	235	110	115	15.0000
!cccg	chr1:32377205-32377431(-)$1	226	128	133	15.0000
gggg:	chr6:34555284-34555501(-)$1	217	116	121	15.0000
dddd:	chr15:102182118-102182370(-)$1	252	63	68	15.0000
EEEEJ	chr2:113289479-113289732(+)$1	253	170	175	15.0000
FFFF}	chr17:8108486-8108731(-)$1	245	199	204	15.0000
dnnnn	chr16:19090849-19091073(+)$1	224	159	164	15.0000
~~~CC	chr13:45911128-45911356(-)$1	228	171	176	15.0000
HHHHH	chr9:127996014-127996247(+)$1	233	187	192	15.0000
fffff	chr11:60658278-60658490(-)$1	212	52	57	15.0000
cqqqq	chr3:141644322-141644534(+)$1	212	106	111	15.0000
DLLLE	chr2:131808401-131808647(-)$1	246	13	18	15.0000
b[ccc	chr10:322005-322229(-)$1	224	68	73	15.0000
ppppb	chr17:73886469-73886708(-)$1	239	54	59	15.0000
ffff=	chr9:86583519-86583750(-)$1	231	124	129	15.0000
+++++	chr5:146771525-146771740(-)$1	215	102	107	15.0000
:FFFF	chr8:1953589-1953794(+)$1	205	91	96	15.0000
ffff3	chr3:15293484-15293699(+)$1	215	111	116	15.0000
]bb::	chr17:5346625-5346864(-)$1	239	146	151	15.0000
JJJJL	chr9:19378740-19378982(-)$1	242	89	94	15.0000
====!	chr2:113286659-113286860(+)$1	201	8	13	15.0000
ooocc	chr1:47124278-47124483(-)$1	205	168	173	15.0000
HLLLB	chr18:13666488-13666699(-)$1	211	18	23	15.0000
LCCC{	chr3:49145601-49145833(-)$1	232	20	25	15.0000
HHHHH	chr14:103194074-103194288(+)$1	214	28	33	15.0000
::ddd	chr15:75136223-75136462(-)$1	239	130	135	15.0000
F}GGG	chr6:30152904-30153109(-)$1	205	101	106	15.0000
=====	chr12:49085751-49085966(-)$1	215	171	176	15.0000
:EEEE	chr15:35664104-35664316(-)$1	212	127	132	15.0000
ddddg	chr22:38879615-38879840(-)$1	225	194	199	15.0000
2iiii	chr12:7053095-7053329(+)$1	234	110	115	15.0000
eeeed	chr11:118621433-118621648(-)$1	215	57	62	15.0000
cccoo	chr15:90624621-90624834(+)$1	213	55	60	15.0000
ddd!!	chr15:77348316-77348609(-)$1	293	37	42	15.0000
eeeed	chr16:66978405-66978624(+)$1	219	1	6	15.0000
leeee	chr1:160327930-160328161(+)$1	231	190	195	15.0000
EEELL	chr16:449544-449791(+)$1	247	85	90	15.0000
HDDDD	chr19:4724563-4724809(-)$1	246	22	27	15.0000

#DB
)(((.	chr1:934238-934480(-)$1	1	186	191	15.0000
).)))	chr7:26707084-26707287(-)$1	1	157	162	15.0000
.....	chr9:134400040-134400250(-)$1	1	0	5	15.0000
(((((	chr7:128409368-128409613(+)$1	1	130	135	15.0000
)))..	chr1:150191834-150192044(-)$1	1	79	84	15.0000
)))))	chr1:67877689-67877945(-)$1	1	152	157	15.0000
.((((	chr1:46828187-46828425(+)$1	1	114	119	15.0000
(((((	chr17:80036992-80037221(-)$1	1	35	40	15.0000
(((((	chr12:53805388-53805598(+)$1	1	105	110	15.0000
(.(..	chr1:113245582-113245830(-)$1	1	104	109	15.0000
))(((	chr13:27260708-27260943(+)$1	1	110	115	15.0000
.((((	chr1:32377205-32377431(-)$1	1	128	133	15.0000
)))).	chr6:34555284-34555501(-)$1	1	116	121	15.0000
)))).	chr15:102182118-102182370(-)$1	1	63	68	15.0000
)))))	chr2:113289479-113289732(+)$1	1	170	175	15.0000
)))).	chr17:8108486-8108731(-)$1	1	199	204	15.0000
(....	chr16:19090849-19091073(+)$1	1	159	164	15.0000
...))	chr13:45911128-45911356(-)$1	1	171	176	15.0000
)))))	chr9:127996014-127996247(+)$1	1	187	192	15.0000
)))((	chr11:60658278-60658490(-)$1	1	52	57	15.0000
(....	chr3:141644322-141644534(+)$1	1	106	111	15.0000
(...(	chr2:131808401-131808647(-)$1	1	13	18	15.0000
(.(((	chr10:322005-322229(-)$1	1	68	73	15.0000
....)	chr17:73886469-73886708(-)$1	1	54	59	15.0000
))))(	chr9:86583519-86583750(-)$1	1	124	129	15.0000
.....	chr5:146771525-146771740(-)$1	1	102	107	15.0000
.))))	chr8:1953589-1953794(+)$1	1	91	96	15.0000
)))).	chr3:15293484-15293699(+)$1	1	111	116	15.0000
.))..	chr17:5346625-5346864(-)$1	1	146	151	15.0000
((((.	chr9:19378740-19378982(-)$1	1	89	94	15.0000
((((.	chr2:113286659-113286860(+)$1	1	8	13	15.0000
...))	chr1:47124278-47124483(-)$1	1	168	173	15.0000
(...(	chr18:13666488-13666699(-)$1	1	18	23	15.0000
.(((.	chr3:49145601-49145833(-)$1	1	20	25	15.0000
(((((	chr14:103194074-103194288(+)$1	1	28	33	15.0000
..(((	chr15:75136223-75136462(-)$1	1	130	135	15.0000
).)))	chr6:30152904-30153109(-)$1	1	101	106	15.0000
(((((	chr12:49085751-49085966(-)$1	1	171	176	15.0000
.((((	chr15:35664104-35664316(-)$1	1	127	132	15.0000
))))(	chr22:38879615-38879840(-)$1	1	194	199	15.0000
.))))	chr12:7053095-7053329(+)$1	1	110	115	15.0000
))))(	chr11:118621433-118621648(-)$1	1	57	62	15.0000
(((..	chr15:90624621-90624834(+)$1	1	55	60	15.0000
(((..	chr15:77348316-77348609(-)$1	1	37	42	15.0000
(((((	chr16:66978405-66978624(+)$1	1	1	6	15.0000
.))))	chr1:160327930-160328161(+)$1	1	190	195	15.0000
(((..	chr16:449544-449791(+)$1	1	85	90	15.0000
(((((	chr19:4724563-4724809(-)$1	1	22	27	15.0000

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

#score	720.0000000000001
#seq	48
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m3_run2.nuc.txt

#NT
ACA	chr3:33867883-33868117(+)$1	234	2	5	8.9999
ACA	chr11:134180417-134180653(+)$1	236	80	83	8.9999
ACA	chr16:89804380-89804615(-)$1	235	1	4	8.9999
ACA	chr6:135358579-135358812(-)$1	233	91	94	8.9999
ACA	chr6:170103984-170104211(+)$1	227	90	93	8.9999
ACA	chrX:135956451-135956742(-)$1	291	46	49	8.9999
ACA	chr12:978094-978340(+)$1	246	5	8	8.9999
ACA	chr11:33374912-33375168(+)$1	256	101	104	8.9999
ACA	chr7:107115226-107115482(-)$1	256	34	37	8.9999
ACA	chr17:56051884-56052120(-)$1	236	24	27	8.9999
ACA	chr5:137502234-137502489(-)$1	255	111	114	8.9999
ACA	chr1:150468857-150469085(+)$1	228	9	12	8.9999
ACA	chr7:102738869-102739099(+)$1	230	34	37	8.9999
ACA	chr1:93736089-93736352(+)$1	263	53	56	8.9999
ACA	chr15:49327685-49327922(-)$1	237	67	70	8.9999
ACA	chr2:149240749-149241010(+)$1	261	118	121	8.9999
ACA	chr4:108985308-108985597(-)$1	289	19	22	8.9999
ACA	chr20:43251412-43251671(-)$1	259	96	99	8.9999
ACA	chr19:57803361-57803591(+)$1	230	21	24	8.9999
ACA	chr22:41545892-41546303(+)$1	411	61	64	8.9999
ACA	chr14:94776084-94776302(-)$1	218	21	24	8.9999
ACA	chr16:67576772-67577015(+)$1	243	57	60	8.9999
ACA	chr5:108672878-108673108(-)$1	230	32	35	8.9999
ACA	chr14:24788980-24789226(-)$1	246	26	29	8.9999
ACA	chr19:23927419-23927656(-)$1	237	19	22	8.9999
ACA	chr14:75248294-75248563(+)$1	269	45	48	8.9999
ACA	chr7:44092445-44092693(+)$1	248	20	23	8.9999
ACA	chr11:64891985-64892215(+)$1	230	101	104	8.9999
ACA	chr12:49666311-49666583(+)$1	272	19	22	8.9999
ACA	chr5:134705702-134705960(-)$1	258	80	83	8.9999
ACA	chr4:728642-728906(+)$1	264	54	57	8.9999
ACA	chr10:43088418-43088660(-)$1	242	34	37	8.9999
ACA	chr14:50558072-50558334(-)$1	262	20	23	8.9999
ACA	chr6:28121530-28121810(+)$1	280	48	51	8.9999
ACA	chr1:71531260-71531646(-)$1	386	10	13	8.9999
ACA	chr17:62576821-62577052(-)$1	231	16	19	8.9999
aca	chr7:64452315-64452561(-)$1	246	1	4	8.9999
ACA	chr1:204588054-204588274(-)$1	220	1	4	8.9999
ACA	chrX:44919758-44919987(+)$1	229	146	149	8.9999
ACA	chrX:118750423-118750823(-)$1	400	3	6	8.9999
ACA	chr1:54332426-54332684(-)$1	258	9	12	8.9999
ACA	chr6:36567491-36567777(+)$1	286	102	105	8.9999
ACA	chr7:107399361-107399620(+)$1	259	15	18	8.9999
ACA	chr12:7045836-7046094(+)$1	258	25	28	8.9999
ACA	chr11:5566093-5566319(-)$1	226	79	82	8.9999
ACA	chr11:68216381-68216657(+)$1	276	47	50	8.9999
aca	chr11:77332968-77333226(-)$1	258	18	21	8.9999
ACA	chr12:49522189-49522436(-)$1	247	10	13	8.9999
ACA	chr12:49434162-49434423(-)$1	261	146	149	8.9999
ACA	chr5:169291327-169291593(+)$1	266	133	136	8.9999
ACA	chr4:1215476-1215716(-)$1	240	15	18	8.9999
ACA	chr15:78837875-78838118(+)$1	243	4	7	8.9999
ACA	chr5:64103471-64103713(+)$1	242	6	9	8.9999
ACA	chr1:117119980-117120199(-)$1	219	196	199	8.9999
ACA	chr10:119805415-119805671(-)$1	256	48	51	8.9999
ACA	chr16:31196124-31196363(+)$1	239	88	91	8.9999
ACA	chr19:10502171-10502400(-)$1	229	14	17	8.9999
ACA	chr10:38344712-38345036(+)$1	324	49	52	8.9999
ACA	chr1:150811816-150812096(-)$1	280	1	4	8.9999
ACA	chr19:57911022-57911271(+)$1	249	11	14	8.9999
ACA	chr5:56532818-56533099(+)$1	281	46	49	8.9999
ACA	chr12:11174230-11174468(-)$1	238	57	60	8.9999
ACA	chr9:5920448-5920704(-)$1	256	22	25	8.9999
ACA	chr8:95892208-95892453(+)$1	245	9	12	8.9999
ACA	chr1:169446301-169446539(-)$1	238	35	38	8.9999
ACA	chr12:11138789-11139008(-)$1	219	30	33	8.9999
ACA	chr13:39586983-39587219(-)$1	236	36	39	8.9999
ACA	chr5:180662269-180662503(+)$1	234	153	156	8.9999
aca	chr8:22465380-22465628(+)$1	248	32	35	8.9999
ACA	chr7:104746928-104747159(+)$1	231	2	5	8.9999
ACA	chr16:53190859-53191139(+)$1	280	33	36	8.9999
ACA	chr22:38881911-38882238(-)$1	327	6	9	8.9999
ACA	chr17:65941779-65942076(+)$1	297	25	28	8.9999
ACA	chr12:76740121-76740363(-)$1	242	10	13	8.9999
ACA	chr13:39587475-39587717(-)$1	242	129	132	8.9999
ACA	chr15:62170811-62171030(-)$1	219	67	70	8.9999
ACA	chr3:31674496-31674726(+)$1	230	4	7	8.9999
ACA	chr5:68660732-68660974(-)$1	242	77	80	8.9999
ACA	chr2:55522369-55522618(-)$1	249	17	20	8.9999
ACA	chr1:203316352-203316569(-)$1	217	0	3	8.9999
ACA	chr12:7077745-7077998(-)$1	253	51	54	8.9999
ACA	chr17:7125973-7126225(+)$1	252	6	9	8.9999
aca	chr10:51573174-51573410(+)$1	236	7	10	8.9999
ACA	chr6:32083391-32083671(-)$1	280	10	13	8.9999
ACA	chr20:49509422-49509694(-)$1	272	30	33	8.9999
aca	chr1:33149478-33149739(+)$1	261	29	32	8.9999
ACA	chr15:44951286-44951579(-)$1	293	114	117	8.9999
ACA	chr7:150647001-150647258(-)$1	257	213	216	8.9999
ACA	chr19:56029027-56029254(+)$1	227	0	3	8.9999
ACA	chr19:16551480-16551720(-)$1	240	40	43	8.9999
ACA	chr17:7751034-7751309(+)$1	275	193	196	8.9999
ACA	chr11:19256385-19256608(-)$1	223	52	55	8.9999
ACA	chr4:159636384-159636605(-)$1	221	6	9	8.9999
ACA	chr1:63010533-63010799(-)$1	266	41	44	8.9999
ACA	chr17:4883618-4883860(-)$1	242	101	104	8.9999
ACA	chr6:109835384-109835620(-)$1	236	79	82	8.9999

#otherMatches

#Struct PSSM
eee	chr15:59373184-59373426(+)$1	242	68	71	8.9999
ddd	chr3:33867883-33868117(+)$1	234	2	5	8.9999
vvv	chr11:134180417-134180653(+)$1	236	80	83	8.9999
:cc	chr16:89804380-89804615(-)$1	235	1	4	8.9999
ZEE	chr6:135358579-135358812(-)$1	233	91	94	8.9999
===	chr6:170103984-170104211(+)$1	227	90	93	8.9999
fff	chrX:135956451-135956742(-)$1	291	46	49	8.9999
LLL	chr12:978094-978340(+)$1	246	5	8	8.9999
:::	chr11:33374912-33375168(+)$1	256	101	104	8.9999
GGG	chr7:107115226-107115482(-)$1	256	34	37	8.9999
[bb	chr17:56051884-56052120(-)$1	236	24	27	8.9999
:::	chr5:137502234-137502489(-)$1	255	111	114	8.9999
G::	chr1:150468857-150469085(+)$1	228	9	12	8.9999
eee	chr7:102738869-102739099(+)$1	230	34	37	8.9999
]ee	chr1:93736089-93736352(+)$1	263	53	56	8.9999
E::	chr15:49327685-49327922(-)$1	237	67	70	8.9999
ggg	chr2:149240749-149241010(+)$1	261	118	121	8.9999
ooo	chr4:108985308-108985597(-)$1	289	19	22	8.9999
{DD	chr20:43251412-43251671(-)$1	259	96	99	8.9999
qqq	chr19:57803361-57803591(+)$1	230	21	24	8.9999
>>>	chr22:41545892-41546303(+)$1	411	61	64	8.9999
%%%	chr14:94776084-94776302(-)$1	218	21	24	8.9999
gg$	chr16:67576772-67577015(+)$1	243	57	60	8.9999
ddd	chr5:108672878-108673108(-)$1	230	32	35	8.9999
mmg	chr14:24788980-24789226(-)$1	246	26	29	8.9999
EE:	chr19:23927419-23927656(-)$1	237	19	22	8.9999
:ff	chr14:75248294-75248563(+)$1	269	45	48	8.9999
{EE	chr7:44092445-44092693(+)$1	248	20	23	8.9999
::h	chr11:64891985-64892215(+)$1	230	101	104	8.9999
NEE	chr12:49666311-49666583(+)$1	272	19	22	8.9999
:::	chr5:134705702-134705960(-)$1	258	80	83	8.9999
#cc	chr4:728642-728906(+)$1	264	54	57	8.9999
FFF	chr10:43088418-43088660(-)$1	242	34	37	8.9999
:hh	chr14:50558072-50558334(-)$1	262	20	23	8.9999
DKK	chr6:28121530-28121810(+)$1	280	48	51	8.9999
:::	chr1:71531260-71531646(-)$1	386	10	13	8.9999
:::	chr17:62576821-62577052(-)$1	231	16	19	8.9999
eee	chr7:64452315-64452561(-)$1	246	1	4	8.9999
BBL	chr1:204588054-204588274(-)$1	220	1	4	8.9999
:::	chrX:44919758-44919987(+)$1	229	146	149	8.9999
:cc	chrX:118750423-118750823(-)$1	400	3	6	8.9999
CC:	chr1:54332426-54332684(-)$1	258	9	12	8.9999
::d	chr6:36567491-36567777(+)$1	286	102	105	8.9999
ppp	chr7:107399361-107399620(+)$1	259	15	18	8.9999
:::	chr12:7045836-7046094(+)$1	258	25	28	8.9999
c::	chr11:5566093-5566319(-)$1	226	79	82	8.9999
D:F	chr11:68216381-68216657(+)$1	276	47	50	8.9999
PPE	chr11:77332968-77333226(-)$1	258	18	21	8.9999
:::	chr12:49522189-49522436(-)$1	247	10	13	8.9999
cc:	chr12:49434162-49434423(-)$1	261	146	149	8.9999
sss	chr5:169291327-169291593(+)$1	266	133	136	8.9999
DDD	chr4:1215476-1215716(-)$1	240	15	18	8.9999
GGG	chr15:78837875-78838118(+)$1	243	4	7	8.9999
cc!	chr5:64103471-64103713(+)$1	242	6	9	8.9999
ooo	chr1:117119980-117120199(-)$1	219	196	199	8.9999
"""	chr10:119805415-119805671(-)$1	256	48	51	8.9999
ddd	chr16:31196124-31196363(+)$1	239	88	91	8.9999
:::	chr19:10502171-10502400(-)$1	229	14	17	8.9999
EEE	chr10:38344712-38345036(+)$1	324	49	52	8.9999
:EE	chr1:150811816-150812096(-)$1	280	1	4	8.9999
bdd	chr19:57911022-57911271(+)$1	249	11	14	8.9999
c[c	chr5:56532818-56533099(+)$1	281	46	49	8.9999
C::	chr12:11174230-11174468(-)$1	238	57	60	8.9999
NNN	chr9:5920448-5920704(-)$1	256	22	25	8.9999
ggg	chr8:95892208-95892453(+)$1	245	9	12	8.9999
GOO	chr1:169446301-169446539(-)$1	238	35	38	8.9999
###	chr12:11138789-11139008(-)$1	219	30	33	8.9999
^^^	chr13:39586983-39587219(-)$1	236	36	39	8.9999
:::	chr5:180662269-180662503(+)$1	234	153	156	8.9999
:a[	chr8:22465380-22465628(+)$1	248	32	35	8.9999
:::	chr7:104746928-104747159(+)$1	231	2	5	8.9999
::h	chr16:53190859-53191139(+)$1	280	33	36	8.9999
:::	chr22:38881911-38882238(-)$1	327	6	9	8.9999
BBe	chr17:65941779-65942076(+)$1	297	25	28	8.9999
:::	chr12:76740121-76740363(-)$1	242	10	13	8.9999
ddd	chr13:39587475-39587717(-)$1	242	129	132	8.9999
d>>	chr15:62170811-62171030(-)$1	219	67	70	8.9999
:::	chr3:31674496-31674726(+)$1	230	4	7	8.9999
ggg	chr5:68660732-68660974(-)$1	242	77	80	8.9999
:::	chr2:55522369-55522618(-)$1	249	17	20	8.9999
:::	chr1:203316352-203316569(-)$1	217	0	3	8.9999
ffn	chr12:7077745-7077998(-)$1	253	51	54	8.9999
OOO	chr17:7125973-7126225(+)$1	252	6	9	8.9999
DD:	chr10:51573174-51573410(+)$1	236	7	10	8.9999
ndd	chr6:32083391-32083671(-)$1	280	10	13	8.9999
emm	chr20:49509422-49509694(-)$1	272	30	33	8.9999
###	chr1:33149478-33149739(+)$1	261	29	32	8.9999
GGG	chr15:44951286-44951579(-)$1	293	114	117	8.9999
d::	chr7:150647001-150647258(-)$1	257	213	216	8.9999
:::	chr19:56029027-56029254(+)$1	227	0	3	8.9999
ooo	chr19:16551480-16551720(-)$1	240	40	43	8.9999
:::	chr17:7751034-7751309(+)$1	275	193	196	8.9999
ffn	chr11:19256385-19256608(-)$1	223	52	55	8.9999
:::	chr4:159636384-159636605(-)$1	221	6	9	8.9999
lee	chr1:63010533-63010799(-)$1	266	41	44	8.9999
ooo	chr17:4883618-4883860(-)$1	242	101	104	8.9999
33f	chr6:109835384-109835620(-)$1	236	79	82	8.9999

#DB
)))	chr15:59373184-59373426(+)$1	1	68	71	8.9999
(((	chr3:33867883-33868117(+)$1	1	2	5	8.9999
...	chr11:134180417-134180653(+)$1	1	80	83	8.9999
.((	chr16:89804380-89804615(-)$1	1	1	4	8.9999
.))	chr6:135358579-135358812(-)$1	1	91	94	8.9999
)))	chr6:170103984-170104211(+)$1	1	90	93	8.9999
(((	chrX:135956451-135956742(-)$1	1	46	49	8.9999
...	chr12:978094-978340(+)$1	1	5	8	8.9999
...	chr11:33374912-33375168(+)$1	1	101	104	8.9999
(((	chr7:107115226-107115482(-)$1	1	34	37	8.9999
.((	chr17:56051884-56052120(-)$1	1	24	27	8.9999
...	chr5:137502234-137502489(-)$1	1	111	114	8.9999
(..	chr1:150468857-150469085(+)$1	1	9	12	8.9999
(((	chr7:102738869-102739099(+)$1	1	34	37	8.9999
.))	chr1:93736089-93736352(+)$1	1	53	56	8.9999
(..	chr15:49327685-49327922(-)$1	1	67	70	8.9999
)))	chr2:149240749-149241010(+)$1	1	118	121	8.9999
...	chr4:108985308-108985597(-)$1	1	19	22	8.9999
.((	chr20:43251412-43251671(-)$1	1	96	99	8.9999
...	chr19:57803361-57803591(+)$1	1	21	24	8.9999
...	chr22:41545892-41546303(+)$1	1	61	64	8.9999
...	chr14:94776084-94776302(-)$1	1	21	24	8.9999
((.	chr16:67576772-67577015(+)$1	1	57	60	8.9999
(((	chr5:108672878-108673108(-)$1	1	32	35	8.9999
..)	chr14:24788980-24789226(-)$1	1	26	29	8.9999
((.	chr19:23927419-23927656(-)$1	1	19	22	8.9999
.((	chr14:75248294-75248563(+)$1	1	45	48	8.9999
.((	chr7:44092445-44092693(+)$1	1	20	23	8.9999
..(	chr11:64891985-64892215(+)$1	1	101	104	8.9999
.((	chr12:49666311-49666583(+)$1	1	19	22	8.9999
...	chr5:134705702-134705960(-)$1	1	80	83	8.9999
.((	chr4:728642-728906(+)$1	1	54	57	8.9999
(((	chr10:43088418-43088660(-)$1	1	34	37	8.9999
.((	chr14:50558072-50558334(-)$1	1	20	23	8.9999
(..	chr6:28121530-28121810(+)$1	1	48	51	8.9999
...	chr1:71531260-71531646(-)$1	1	10	13	8.9999
...	chr17:62576821-62577052(-)$1	1	16	19	8.9999
(((	chr7:64452315-64452561(-)$1	1	1	4	8.9999
((.	chr1:204588054-204588274(-)$1	1	1	4	8.9999
...	chrX:44919758-44919987(+)$1	1	146	149	8.9999
.((	chrX:118750423-118750823(-)$1	1	3	6	8.9999
((.	chr1:54332426-54332684(-)$1	1	9	12	8.9999
..(	chr6:36567491-36567777(+)$1	1	102	105	8.9999
...	chr7:107399361-107399620(+)$1	1	15	18	8.9999
...	chr12:7045836-7046094(+)$1	1	25	28	8.9999
)..	chr11:5566093-5566319(-)$1	1	79	82	8.9999
(.(	chr11:68216381-68216657(+)$1	1	47	50	8.9999
..(	chr11:77332968-77333226(-)$1	1	18	21	8.9999
...	chr12:49522189-49522436(-)$1	1	10	13	8.9999
)).	chr12:49434162-49434423(-)$1	1	146	149	8.9999
...	chr5:169291327-169291593(+)$1	1	133	136	8.9999
(((	chr4:1215476-1215716(-)$1	1	15	18	8.9999
(((	chr15:78837875-78838118(+)$1	1	4	7	8.9999
((.	chr5:64103471-64103713(+)$1	1	6	9	8.9999
...	chr1:117119980-117120199(-)$1	1	196	199	8.9999
...	chr10:119805415-119805671(-)$1	1	48	51	8.9999
(((	chr16:31196124-31196363(+)$1	1	88	91	8.9999
...	chr19:10502171-10502400(-)$1	1	14	17	8.9999
(((	chr10:38344712-38345036(+)$1	1	49	52	8.9999
.((	chr1:150811816-150812096(-)$1	1	1	4	8.9999
(((	chr19:57911022-57911271(+)$1	1	11	14	8.9999
(.(	chr5:56532818-56533099(+)$1	1	46	49	8.9999
(..	chr12:11174230-11174468(-)$1	1	57	60	8.9999
...	chr9:5920448-5920704(-)$1	1	22	25	8.9999
(((	chr8:95892208-95892453(+)$1	1	9	12	8.9999
(..	chr1:169446301-169446539(-)$1	1	35	38	8.9999
...	chr12:11138789-11139008(-)$1	1	30	33	8.9999
...	chr13:39586983-39587219(-)$1	1	36	39	8.9999
...	chr5:180662269-180662503(+)$1	1	153	156	8.9999
.(.	chr8:22465380-22465628(+)$1	1	32	35	8.9999
...	chr7:104746928-104747159(+)$1	1	2	5	8.9999
..(	chr16:53190859-53191139(+)$1	1	33	36	8.9999
...	chr22:38881911-38882238(-)$1	1	6	9	8.9999
(((	chr17:65941779-65942076(+)$1	1	25	28	8.9999
...	chr12:76740121-76740363(-)$1	1	10	13	8.9999
(((	chr13:39587475-39587717(-)$1	1	129	132	8.9999
)..	chr15:62170811-62171030(-)$1	1	67	70	8.9999
...	chr3:31674496-31674726(+)$1	1	4	7	8.9999
)))	chr5:68660732-68660974(-)$1	1	77	80	8.9999
...	chr2:55522369-55522618(-)$1	1	17	20	8.9999
...	chr1:203316352-203316569(-)$1	1	0	3	8.9999
((.	chr12:7077745-7077998(-)$1	1	51	54	8.9999
...	chr17:7125973-7126225(+)$1	1	6	9	8.9999
((.	chr10:51573174-51573410(+)$1	1	7	10	8.9999
.))	chr6:32083391-32083671(-)$1	1	10	13	8.9999
(..	chr20:49509422-49509694(-)$1	1	30	33	8.9999
...	chr1:33149478-33149739(+)$1	1	29	32	8.9999
)))	chr15:44951286-44951579(-)$1	1	114	117	8.9999
)..	chr7:150647001-150647258(-)$1	1	213	216	8.9999
...	chr19:56029027-56029254(+)$1	1	0	3	8.9999
...	chr19:16551480-16551720(-)$1	1	40	43	8.9999
...	chr17:7751034-7751309(+)$1	1	193	196	8.9999
((.	chr11:19256385-19256608(-)$1	1	52	55	8.9999
...	chr4:159636384-159636605(-)$1	1	6	9	8.9999
.))	chr1:63010533-63010799(-)$1	1	41	44	8.9999
...	chr17:4883618-4883860(-)$1	1	101	104	8.9999
..)	chr6:109835384-109835620(-)$1	1	79	82	8.9999

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

#score	872.9999999999998
#seq	97
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m1_run2.nuc.txt

#NT
AACUGCC	chr16:68012081-68012299(-)$1	218	174	181	12.1403
cacuucc	chr17:7417060-7417421(+)$1	361	276	283	13.8070
CCCUGCC	chr1:226054213-226054452(-)$1	239	24	31	12.8421
CACUGCU	chr17:80417910-80418139(+)$1	229	124	131	12.4912
CACUGCU	chr1:202127216-202127476(-)$1	260	152	159	12.4912
CACUCCC	chr2:44539698-44539912(+)$1	214	105	112	13.9824
CACUGCU	chr6:144081507-144081736(+)$1	229	145	152	12.4912
CACUCCC	chr1:159283493-159283715(-)$1	222	109	116	13.9824
cgcugcc	chr19:16973753-16973994(+)$1	241	68	75	12.5789
AACUGCC	chr3:49201238-49201457(-)$1	219	94	101	12.1403
CACUGCU	chr13:39587475-39587717(-)$1	242	14	21	12.4912
CACUUCC	chr7:129916435-129916652(+)$1	217	64	71	13.8070
CACUGCC	chr9:5919879-5920174(-)$1	295	264	271	16.5263
AACUGCC	chr15:98513017-98513231(+)$1	214	135	142	12.1403
CACUUCC	chr17:40836956-40837172(+)$1	216	100	107	13.8070
CACUACC	chr6:29141999-29142212(+)$1	213	60	67	13.4561
CACUGCC	chr2:220412468-220412683(+)$1	215	147	154	16.5263
CUCUGCC	chr8:145736357-145736574(+)$1	217	138	145	12.6666
CCCUGCC	chr16:30715352-30715623(+)$1	271	70	77	12.8421
CACUCCC	chr16:15045531-15045761(+)$1	230	110	117	13.9824
CAGUGCC	chr20:32336729-32336942(+)$1	213	15	22	11.7894
CACUUCC	chr15:56386926-56387201(-)$1	275	59	66	13.8070
CACUGCA	chr17:65936588-65936833(+)$1	245	15	22	12.4035
CUCUGCC	chr16:630810-631023(+)$1	213	36	43	12.6666
cccugcc	chr7:70229803-70230046(+)$1	243	20	27	12.8421
CACUUCC	chr15:44951274-44951587(-)$1	313	218	225	13.8070
CACUCCC	chr17:38146219-38146447(+)$1	228	118	125	13.9824
CAAUGCC	chr3:121206436-121206680(-)$1	244	32	39	11.7894
CACUACC	chr5:71491766-71491980(+)$1	214	103	110	13.4561
CACAGCC	chr17:47375772-47376099(-)$1	327	66	73	12.2280
CACUGCC	chr12:52450261-52450475(+)$1	214	143	150	16.5263
UACUGCC	chr1:109803762-109803978(+)$1	216	32	39	11.9649
CACUGUC	chr12:56397789-56398003(+)$1	214	108	115	12.0526
CUCUGCC	chr11:614275-614502(-)$1	227	37	44	12.6666
CCCUGCC	chr6:12124876-12125093(+)$1	217	112	119	12.8421
CCCUGCC	chr14:69256248-69256572(-)$1	324	30	37	12.8421
CACUGUC	chr1:110172375-110172591(+)$1	216	21	28	12.0526
CACUCCC	chr10:17278204-17278448(+)$1	244	103	110	13.9824
CACUACC	chrX:70330000-70330281(-)$1	281	70	77	13.4561
CACUCCC	chr16:67876885-67877101(+)$1	216	105	112	13.9824
CACUCCC	chr19:59063449-59063676(-)$1	227	76	83	13.9824
CGCUGCC	chr17:43101525-43101974(-)$1	449	116	123	12.5789
CACCGCC	chr22:39413736-39413991(+)$1	255	216	223	12.1403
CACUUCC	chr1:155448231-155448531(-)$1	300	129	136	13.8070
CACUGGC	chr22:18609088-18609301(+)$1	213	88	95	11.9649
CACUGCC	chr11:118968511-118968734(-)$1	223	118	125	16.5263
CACAGCC	chr15:44888886-44889123(-)$1	237	109	116	12.2280
CACUUCC	chr3:122439184-122439443(+)$1	259	130	137	13.8070
CACUCCC	chr11:8009159-8009484(+)$1	325	159	166	13.9824
CACUCCC	chr16:21416325-21416647(-)$1	322	203	210	13.9824
CACUGCC	chr17:56051816-56052150(-)$1	334	160	167	16.5263
CACCGCC	chr6:36567491-36567777(+)$1	286	249	256	12.1403
cacugac	chr3:14170264-14170491(+)$1	227	121	128	11.9649
CACAGCC	chr11:3838577-3838791(+)$1	214	79	86	12.2280
cacugca	chr13:25378333-25378553(+)$1	220	26	33	12.4035
CACUGCA	chr11:72403711-72404038(-)$1	327	141	148	12.4035

#otherMatches

#Struct PSSM
eee[a[b	chr2:103335032-103335252(-)$1	220	109	116	16.5263
lldddd]	chr16:68012081-68012299(-)$1	218	174	181	12.1403
^^^^^^^	chr17:7417060-7417421(+)$1	361	276	283	13.8070
FFF{GGG	chr1:226054213-226054452(-)$1	239	24	31	12.8421
$$$gggg	chr17:80417910-80418139(+)$1	229	124	131	12.4912
blllbb:	chr1:202127216-202127476(-)$1	260	152	159	12.4912
>>>eeee	chr2:44539698-44539912(+)$1	214	105	112	13.9824
ccc:ddd	chr6:144081507-144081736(+)$1	229	145	152	12.4912
^^^^^^^	chr1:159283493-159283715(-)$1	222	109	116	13.9824
g]dddd:	chr19:16973753-16973994(+)$1	241	68	75	12.5789
6666ccc	chr3:49201238-49201457(-)$1	219	94	101	12.1403
fff[ddd	chr13:39587475-39587717(-)$1	242	14	21	12.4912
hh'''''	chr7:129916435-129916652(+)$1	217	64	71	13.8070
qdddd]e	chr9:5919879-5920174(-)$1	295	264	271	16.5263
FFFFFff	chr15:98513017-98513231(+)$1	214	135	142	12.1403
e]dddd2	chr17:40836956-40837172(+)$1	216	100	107	13.8070
dd::::b	chr6:29141999-29142212(+)$1	213	60	67	13.4561
::::bbb	chr2:220412468-220412683(+)$1	215	147	154	16.5263
::::BBG	chr8:145736357-145736574(+)$1	217	138	145	12.6666
[======	chr16:30715352-30715623(+)$1	271	70	77	12.8421
ee:::::	chr16:15045531-15045761(+)$1	230	110	117	13.9824
a!!dddd	chr20:32336729-32336942(+)$1	213	15	22	11.7894
LFFFFFF	chr15:56386926-56387201(-)$1	275	59	66	13.8070
ppppddd	chr17:65936588-65936833(+)$1	245	15	22	12.4035
oooobb3	chr16:630810-631023(+)$1	213	36	43	12.6666
:::::::	chr7:70229803-70230046(+)$1	243	20	27	12.8421
bb!!ccc	chr15:44951274-44951587(-)$1	313	218	225	13.8070
bb333ff	chr17:38146219-38146447(+)$1	228	118	125	13.9824
+++++++	chr3:121206436-121206680(-)$1	244	32	39	11.7894
qqqqqbb	chr5:71491766-71491980(+)$1	214	103	110	13.4561
:::::::	chr17:47375772-47376099(-)$1	327	66	73	12.2280
CC:cccb	chr12:52450261-52450475(+)$1	214	143	150	16.5263
coooooo	chr1:109803762-109803978(+)$1	216	32	39	11.9649
bb!!ccc	chr12:56397789-56398003(+)$1	214	108	115	12.0526
sssffff	chr11:614275-614502(-)$1	227	37	44	12.6666
::::::c	chr6:12124876-12125093(+)$1	217	112	119	12.8421
:::dddd	chr14:69256248-69256572(-)$1	324	30	37	12.8421
KKCCC:d	chr1:110172375-110172591(+)$1	216	21	28	12.0526
&&&ccch	chr10:17278204-17278448(+)$1	244	103	110	13.9824
^^bb]cc	chrX:70330000-70330281(-)$1	281	70	77	13.4561
dddd!!e	chr16:67876885-67877101(+)$1	216	105	112	13.9824
^^^^^^^	chr19:59063449-59063676(-)$1	227	76	83	13.9824
dddd]cc	chr17:43101525-43101974(-)$1	449	116	123	12.5789
eee]bb2	chr22:39413736-39413991(+)$1	255	216	223	12.1403
^^fffff	chr1:155448231-155448531(-)$1	300	129	136	13.8070
emmmmee	chr22:18609088-18609301(+)$1	213	88	95	11.9649
^^^^^^^	chr11:118968511-118968734(-)$1	223	118	125	16.5263
wwggggg	chr15:44888886-44889123(-)$1	237	109	116	12.2280
^^^^^^^	chr3:122439184-122439443(+)$1	259	130	137	13.8070
444dddd	chr11:8009159-8009484(+)$1	325	159	166	13.9824
ee:::::	chr16:21416325-21416647(-)$1	322	203	210	13.9824
fffffll	chr17:56051816-56052150(-)$1	334	160	167	16.5263
CDDDD}A	chr6:36567491-36567777(+)$1	286	249	256	12.1403
333eeee	chr3:14170264-14170491(+)$1	227	121	128	11.9649
rrrdddd	chr11:3838577-3838791(+)$1	214	79	86	12.2280
ffffff5	chr13:25378333-25378553(+)$1	220	26	33	12.4035
::::bbm	chr11:72403711-72404038(-)$1	327	141	148	12.4035

#DB
(((.(.(	chr2:103335032-103335252(-)$1	1	109	116	16.5263
..)))).	chr16:68012081-68012299(-)$1	1	174	181	12.1403
.......	chr17:7417060-7417421(+)$1	1	276	283	13.8070
(((.(((	chr1:226054213-226054452(-)$1	1	24	31	12.8421
...((((	chr17:80417910-80418139(+)$1	1	124	131	12.4912
(...)).	chr1:202127216-202127476(-)$1	1	152	159	12.4912
...))))	chr2:44539698-44539912(+)$1	1	105	112	13.9824
))).(((	chr6:144081507-144081736(+)$1	1	145	152	12.4912
.......	chr1:159283493-159283715(-)$1	1	109	116	13.9824
).)))).	chr19:16973753-16973994(+)$1	1	68	75	12.5789
....)))	chr3:49201238-49201457(-)$1	1	94	101	12.1403
(((.(((	chr13:39587475-39587717(-)$1	1	14	21	12.4912
((.....	chr7:129916435-129916652(+)$1	1	64	71	13.8070
.)))).)	chr9:5919879-5920174(-)$1	1	264	271	16.5263
(((((((	chr15:98513017-98513231(+)$1	1	135	142	12.1403
).)))).	chr17:40836956-40837172(+)$1	1	100	107	13.8070
))....(	chr6:29141999-29142212(+)$1	1	60	67	13.4561
....(((	chr2:220412468-220412683(+)$1	1	147	154	16.5263
....)))	chr8:145736357-145736574(+)$1	1	138	145	12.6666
.((((((	chr16:30715352-30715623(+)$1	1	70	77	12.8421
)).....	chr16:15045531-15045761(+)$1	1	110	117	13.9824
(..((((	chr20:32336729-32336942(+)$1	1	15	22	11.7894
.((((((	chr15:56386926-56387201(-)$1	1	59	66	13.8070
....)))	chr17:65936588-65936833(+)$1	1	15	22	12.4035
....)).	chr16:630810-631023(+)$1	1	36	43	12.6666
.......	chr7:70229803-70230046(+)$1	1	20	27	12.8421
((..(((	chr15:44951274-44951587(-)$1	1	218	225	13.8070
))...))	chr17:38146219-38146447(+)$1	1	118	125	13.9824
.......	chr3:121206436-121206680(-)$1	1	32	39	11.7894
.....))	chr5:71491766-71491980(+)$1	1	103	110	13.4561
.......	chr17:47375772-47376099(-)$1	1	66	73	12.2280
)).((((	chr12:52450261-52450475(+)$1	1	143	150	16.5263
(......	chr1:109803762-109803978(+)$1	1	32	39	11.9649
((..(((	chr12:56397789-56398003(+)$1	1	108	115	12.0526
...))))	chr11:614275-614502(-)$1	1	37	44	12.6666
......(	chr6:12124876-12125093(+)$1	1	112	119	12.8421
...((((	chr14:69256248-69256572(-)$1	1	30	37	12.8421
..(((.(	chr1:110172375-110172591(+)$1	1	21	28	12.0526
...((((	chr10:17278204-17278448(+)$1	1	103	110	13.9824
..)).))	chrX:70330000-70330281(-)$1	1	70	77	13.4561
((((..(	chr16:67876885-67877101(+)$1	1	105	112	13.9824
.......	chr19:59063449-59063676(-)$1	1	76	83	13.9824
)))).))	chr17:43101525-43101974(-)$1	1	116	123	12.5789
))).)).	chr22:39413736-39413991(+)$1	1	216	223	12.1403
..)))))	chr1:155448231-155448531(-)$1	1	129	136	13.8070
(....))	chr22:18609088-18609301(+)$1	1	88	95	11.9649
.......	chr11:118968511-118968734(-)$1	1	118	125	16.5263
..)))))	chr15:44888886-44889123(-)$1	1	109	116	12.2280
.......	chr3:122439184-122439443(+)$1	1	130	137	13.8070
...))))	chr11:8009159-8009484(+)$1	1	159	166	13.9824
)).....	chr16:21416325-21416647(-)$1	1	203	210	13.9824
(((((..	chr17:56051816-56052150(-)$1	1	160	167	16.5263
))))).)	chr6:36567491-36567777(+)$1	1	249	256	12.1403
...))))	chr3:14170264-14170491(+)$1	1	121	128	11.9649
...))))	chr11:3838577-3838791(+)$1	1	79	86	12.2280
)))))).	chr13:25378333-25378553(+)$1	1	26	33	12.4035
....((.	chr11:72403711-72404038(-)$1	1	141	148	12.4035

#PSSM
C : 0.84	c : 0.08	A : 0.05	U : 0.01	
A : 0.77	C : 0.07	a : 0.05	U : 0.05	g : 0.01	c : 0.01	G : 0.01	
C : 0.87	c : 0.08	G : 0.01	A : 0.01	
U : 0.82	u : 0.08	A : 0.05	C : 0.03	
G : 0.59	C : 0.15	U : 0.10	g : 0.07	A : 0.05	u : 0.01	
C : 0.85	c : 0.07	U : 0.03	G : 0.01	a : 0.01	
C : 0.80	c : 0.07	U : 0.07	A : 0.03	a : 0.01	

#score	757.5263157894748
#seq	57
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_UTR_m3_run1.nuc.txt

#NT
UUGUUUUUUUU	chr1:61922782-61923017(+)$1	235	103	114	21.8888
UUUUUUUUUCU	chr11:118621930-118622168(-)$1	238	18	29	22.2222
AUGUCUUUUCU	chr2:112874649-112874905(+)$1	256	233	244	15.6666
CUAUUUUUUUU	chr11:118395239-118395496(+)$1	257	171	182	16.2222
AUGUAUUUUUU	chr3:185635050-185635300(-)$1	250	24	35	14.5555
UUCUUUUUUUU	chr7:75957323-75957574(-)$1	251	151	162	19.7777
UUGUUUUUUUU	chr6:114181661-114181971(+)$1	310	250	261	21.8888
UUAUUUUCUCU	chr22:41574853-41575116(+)$1	263	139	150	17.4444
UUGUUUUUUCU	chr1:78343476-78343732(+)$1	256	24	35	23.1111
UUGUAUUUUCU	chr2:183790116-183790378(-)$1	262	71	82	19.3333
UUGUUUUUGCU	chr14:77490909-77491150(-)$1	241	104	115	18.6666
uuuuuguuucu	chr5:153854550-153854823(-)$1	273	83	94	17.6666
UUAUUUUGUGU	chr20:5527381-5527640(-)$1	259	233	244	15.1111
UUGUUUUCCCU	chr12:122957718-122957961(-)$1	243	229	240	14.7777
GUACUUUUUCU	chr17:29552123-29552365(+)$1	242	158	169	13.4444
UUUCUUUUUCU	chr3:121488959-121489207(-)$1	248	183	194	18.3333
UUGUUUGGUCU	chr1:113666867-113667120(+)$1	253	1	12	14.7777
UUAUUUUAUAU	chr4:85571211-85571444(+)$1	233	67	78	15.1111
UUGGUUUUUGU	chr19:33791062-33791313(-)$1	251	101	112	16.5555
UUGCUUUUUUU	chr6:31785352-31785607(+)$1	255	232	243	18.0000
UUGUGUUUUUU	chr5:126172473-126172707(+)$1	234	161	172	18.1111
UUGAUUUUUUU	chr10:50666618-50666862(-)$1	244	217	228	18.0000
UUGUGUUUACU	chr14:105936503-105936793(+)$1	290	258	269	15.0000
UUUUAUUUUCU	chr19:41812597-41812879(+)$1	282	87	98	18.4444
UUUACUUUUCU	chr13:110406881-110407132(-)$1	251	161	172	14.4444
UGUUUUUUUCU	chr3:129370098-129370359(-)$1	261	168	179	17.8888
UUAUUUUAUCU	chr12:51637363-51637625(+)$1	262	3	14	17.5555
UUUUGUUUUCU	chr6:4954484-4954740(+)$1	256	96	107	18.4444
UUCAUUUUUUU	chr1:33238762-33239005(+)$1	243	68	79	15.8888
UUUUUUUAUAU	chr3:129369437-129369668(-)$1	231	65	76	16.0000
AUGUUUUGUCU	chrX:118718185-118718431(+)$1	246	68	79	15.7777
UUGUUUGUUUU	chr1:93602925-93603168(+)$1	243	43	54	17.3333
UAGUUUUUUAU	chr17:5344827-5345104(-)$1	277	70	81	16.6666
UUUUUUUUUCA	chr4:170911870-170912103(-)$1	233	215	226	17.4444
AUUUUUUUUCU	chr17:47131550-47131815(+)$1	265	84	95	18.6666
UAGuuuuuuuu	chr2:9629650-9629888(-)$1	238	7	18	17.8888
UUUUUUUUUUU	chr4:17625866-17626103(+)$1	237	216	227	21.0000
UUGUUUUUUUU	chr6:52128946-52129200(-)$1	254	177	188	21.8888
CUGUUAUUUCU	chr1:32663440-32663703(+)$1	263	51	62	14.6666
UACUUUUUUCU	chr22:40521686-40521925(+)$1	239	63	74	17.0000
UUGUUUUUAGU	chr1:32799675-32799911(-)$1	236	135	146	16.3333
AUUUUUUUUCU	chr4:39780073-39780330(+)$1	257	194	205	18.6666
uuguuuuuuuu	chr16:46990336-46990592(-)$1	256	207	218	21.8888
UAUUUUUUUCU	chr18:10488148-10488393(+)$1	245	191	202	18.2222

#otherMatches

#Struct PSSM
::::::EEEEE	chr10:89574185-89574461(-)$1	276	1	12	17.6666
========yyy	chr1:61922782-61923017(+)$1	235	103	114	21.8888
EEEEELLLCCC	chr11:118621930-118622168(-)$1	238	18	29	22.2222
i7777777fff	chr2:112874649-112874905(+)$1	256	233	244	15.6666
xxxxxxxxxxc	chr11:118395239-118395496(+)$1	257	171	182	16.2222
===========	chr3:185635050-185635300(-)$1	250	24	35	14.5555
ii:::::::::	chr7:75957323-75957574(-)$1	251	151	162	19.7777
JJJJJJJJJJZ	chr6:114181661-114181971(+)$1	310	250	261	21.8888
==[eeeee$$$	chr22:41574853-41575116(+)$1	263	139	150	17.4444
GGGGGGGOOOO	chr1:78343476-78343732(+)$1	256	24	35	23.1111
:ccc[eeeee[	chr2:183790116-183790378(-)$1	262	71	82	19.3333
e[bb=======	chr14:77490909-77491150(-)$1	241	104	115	18.6666
:::::dddd!!	chr5:153854550-153854823(-)$1	273	83	94	17.6666
hhhhIIIIIII	chr20:5527381-5527640(-)$1	259	233	244	15.1111
:::::::::::	chr12:122957718-122957961(-)$1	243	229	240	14.7777
zzzzzzzzzcc	chr17:29552123-29552365(+)$1	242	158	169	13.4444
::::::::DDD	chr3:121488959-121489207(-)$1	248	183	194	18.3333
::::::::EEE	chr1:113666867-113667120(+)$1	253	1	12	14.7777
hhhhhh:::::	chr4:85571211-85571444(+)$1	233	67	78	15.1111
sffffff::==	chr19:33791062-33791313(-)$1	251	101	112	16.5555
4ccc:::::::	chr6:31785352-31785607(+)$1	255	232	243	18.0000
ngggggggfff	chr5:126172473-126172707(+)$1	234	161	172	18.1111
wwwwww=====	chr10:50666618-50666862(-)$1	244	217	228	18.0000
22ffffff]dd	chr14:105936503-105936793(+)$1	290	258	269	15.0000
mmeeeee]hhh	chr19:41812597-41812879(+)$1	282	87	98	18.4444
dd]eeeeeccc	chr13:110406881-110407132(-)$1	251	161	172	14.4444
JJJJJJJJZZZ	chr3:129370098-129370359(-)$1	261	168	179	17.8888
:::::::::::	chr12:51637363-51637625(+)$1	262	3	14	17.5555
:::::::::::	chr6:4954484-4954740(+)$1	256	96	107	18.4444
ttttttttttd	chr1:33238762-33239005(+)$1	243	68	79	15.8888
22dddd:::::	chr3:129369437-129369668(-)$1	231	65	76	16.0000
qqiiiiiiiii	chrX:118718185-118718431(+)$1	246	68	79	15.7777
5==========	chr1:93602925-93603168(+)$1	243	43	54	17.3333
sssssssseee	chr17:5344827-5345104(-)$1	277	70	81	16.6666
:::::::::::	chr4:170911870-170912103(-)$1	233	215	226	17.4444
mmmiiiiiiii	chr17:47131550-47131815(+)$1	265	84	95	18.6666
D{FFFFFFLLL	chr2:9629650-9629888(-)$1	238	7	18	17.8888
zzzzzzzzzza	chr4:17625866-17626103(+)$1	237	216	227	21.0000
::=========	chr6:52128946-52129200(-)$1	254	177	188	21.8888
]dddd:::ccc	chr1:32663440-32663703(+)$1	263	51	62	14.6666
MCCC{IIIIII	chr22:40521686-40521925(+)$1	239	63	74	17.0000
pppppppccc6	chr1:32799675-32799911(-)$1	236	135	146	16.3333
drrrrrrrrrd	chr4:39780073-39780330(+)$1	257	194	205	18.6666
]ccc22hhhhh	chr16:46990336-46990592(-)$1	256	207	218	21.8888
:::::::::::	chr18:10488148-10488393(+)$1	245	191	202	18.2222

#DB
......(((((	chr10:89574185-89574461(-)$1	1	1	12	17.6666
((((((((...	chr1:61922782-61923017(+)$1	1	103	114	21.8888
(((((...(((	chr11:118621930-118622168(-)$1	1	18	29	22.2222
).......)))	chr2:112874649-112874905(+)$1	1	233	244	15.6666
..........)	chr11:118395239-118395496(+)$1	1	171	182	16.2222
)))))))))))	chr3:185635050-185635300(-)$1	1	24	35	14.5555
)).........	chr7:75957323-75957574(-)$1	1	151	162	19.7777
)))))))))).	chr6:114181661-114181971(+)$1	1	250	261	21.8888
((.(((((...	chr22:41574853-41575116(+)$1	1	139	150	17.4444
(((((((....	chr1:78343476-78343732(+)$1	1	24	35	23.1111
.(((.(((((.	chr2:183790116-183790378(-)$1	1	71	82	19.3333
(.(((((((((	chr14:77490909-77491150(-)$1	1	104	115	18.6666
.....((((..	chr5:153854550-153854823(-)$1	1	83	94	17.6666
)))))))))))	chr20:5527381-5527640(-)$1	1	233	244	15.1111
...........	chr12:122957718-122957961(-)$1	1	229	240	14.7777
.........))	chr17:29552123-29552365(+)$1	1	158	169	13.4444
........)))	chr3:121488959-121489207(-)$1	1	183	194	18.3333
........(((	chr1:113666867-113667120(+)$1	1	1	12	14.7777
)))))).....	chr4:85571211-85571444(+)$1	1	67	78	15.1111
.))))))..((	chr19:33791062-33791313(-)$1	1	101	112	16.5555
.))).......	chr6:31785352-31785607(+)$1	1	232	243	18.0000
.)))))))(((	chr5:126172473-126172707(+)$1	1	161	172	18.1111
......)))))	chr10:50666618-50666862(-)$1	1	217	228	18.0000
..)))))).))	chr14:105936503-105936793(+)$1	1	258	269	15.0000
..))))).)))	chr19:41812597-41812879(+)$1	1	87	98	18.4444
)).))))))))	chr13:110406881-110407132(-)$1	1	161	172	14.4444
))))))))...	chr3:129370098-129370359(-)$1	1	168	179	17.8888
...........	chr12:51637363-51637625(+)$1	1	3	14	17.5555
...........	chr6:4954484-4954740(+)$1	1	96	107	18.4444
..........)	chr1:33238762-33239005(+)$1	1	68	79	15.8888
..)))).....	chr3:129369437-129369668(-)$1	1	65	76	16.0000
..)))))))))	chrX:118718185-118718431(+)$1	1	68	79	15.7777
.))))))))))	chr1:93602925-93603168(+)$1	1	43	54	17.3333
........)))	chr17:5344827-5345104(-)$1	1	70	81	16.6666
...........	chr4:170911870-170912103(-)$1	1	215	226	17.4444
...))))))))	chr17:47131550-47131815(+)$1	1	84	95	18.6666
(.((((((...	chr2:9629650-9629888(-)$1	1	7	18	17.8888
..........)	chr4:17625866-17626103(+)$1	1	216	227	21.0000
..(((((((((	chr6:52128946-52129200(-)$1	1	177	188	21.8888
.))))...(((	chr1:32663440-32663703(+)$1	1	51	62	14.6666
.(((.((((((	chr22:40521686-40521925(+)$1	1	63	74	17.0000
.......))).	chr1:32799675-32799911(-)$1	1	135	146	16.3333
(.........)	chr4:39780073-39780330(+)$1	1	194	205	18.6666
.)))..)))))	chr16:46990336-46990592(-)$1	1	207	218	21.8888
...........	chr18:10488148-10488393(+)$1	1	191	202	18.2222

#PSSM
U : 0.77	A : 0.11	C : 0.04	u : 0.04	G : 0.02	
U : 0.84	A : 0.08	u : 0.04	G : 0.02	
G : 0.46	U : 0.28	A : 0.13	C : 0.06	u : 0.02	g : 0.02	
U : 0.77	u : 0.06	C : 0.06	A : 0.06	G : 0.02	
U : 0.75	A : 0.06	u : 0.06	G : 0.06	C : 0.04	
U : 0.88	u : 0.04	C : 0.02	g : 0.02	A : 0.02	
U : 0.88	u : 0.06	G : 0.04	
U : 0.75	u : 0.06	G : 0.06	A : 0.06	C : 0.04	
U : 0.84	u : 0.06	A : 0.04	G : 0.02	C : 0.02	
C : 0.53	U : 0.26	G : 0.06	A : 0.06	u : 0.04	c : 0.02	
U : 0.91	u : 0.06	A : 0.02	

#score	795.4444444444447
#seq	45
#width	11
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m3_run1.nuc.txt

#NT
ACUUUGGGGGCUCAAAUGCAAGGUGGUUUUGGAUGUGGCAACCAGUUGCCAAAAACAGAUGGAGGAAGUGAAACCAAGAAACAGCGAAGCAAACGGACUCAGAGGACGGGUGAGAAAGCAGCACCUCGCUCAAAGAAAAGGAAAAAGGACGAAGAGGAGAAACAAGCUAUGUACUCUAGCACUGACACGUUUACCCACUUGAAACAGGUGAGGGUGAGUCAUUUAGAGCAGCCUCUUUUAAAAGUCAAGGAUAUAggcugggggcagu	chr7:151855847-151856258(-)$1	411	104	372	359.0000

#otherMatches

#Struct PSSM
iiiiiiii::DDDD{AKKFFFFFF{FFFFFFDDDD{BBKKCCC{CCC{CCCiiiiiiiii[ddddvvvvvvvvvvvvvddddiiiiiiiii:dddd!!cccaqqqqqqqqa]ccc]dddd:ccclllccc:CCC}CCC}CCCZZZBBYYDDDD}FFFFFFFFFFFFYYA}DDDD::bb!!ccc[bb[ffffffeeeeea%%%%%%ffffff$$$$$bb[ffffffvvvvvvvvvvvvvffffff]bb]ffffff666666a]eeeee]	chr5:179018520-179018843(+)$1	323	33	301	359.0000
:ggggggg!!bb####ccc!!a[bb[ffffff"""ffffffmmmmffffff>>>>>>>>>>>>>>>>>>>>>>ffffff22bb]a333ccc333bb]ggggggg:::gggggggssssssssssggggggg::::::::EEEEEYYBBYYEEEEE}CCC}EEEEE::::::::ffffff"""dddd####ffffffeeeeellleeeee22ffffffdddd]ffffffiiiiiiiii"""eeeeea!!ddddffffff!!ccc[alll	chr7:151855847-151856258(-)$1	411	104	372	359.0000

#DB
))))))))..((((.(..((((((.((((((((((.((..(((.(((.((((((((((((.((((.............))))))))))))).((((..((((........).))).)))).(((...))).))).))).)))...))..)))).))))))))))))..).))))..((..(((.((.((((((((((((......((((((.....((.((((((.............)))))).)).))))))......).))))).	chr5:179018520-179018843(+)$1	1	33	301	359.0000
.(((((((..((....(((..(.((.((((((...((((((....))))))......................))))))..)).)...)))...)).)))))))...(((((((..........)))))))........)))))..))..))))).))).)))))........((((((...((((....(((((((((((...)))))..)))))))))).))))))(((((((((...((((((..((((((((((..(((.(...	chr7:151855847-151856258(-)$1	1	104	372	359.0000

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

#score	718.0
#seq	2
#width	268
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m1_run2.nuc.txt

#NT
UUU	chr16:69687075-69687369(+)$1	294	1	4	8.9999
UUU	chr2:61405801-61406103(+)$1	302	8	11	8.9999
UUU	chr6:31500430-31500691(+)$1	261	37	40	8.9999
UUU	chr16:67217037-67217298(+)$1	261	32	35	8.9999
UUU	chr9:132892187-132892459(+)$1	272	35	38	8.9999
UUU	chr19:35500712-35501045(+)$1	333	16	19	8.9999
UUU	chr15:44058073-44058408(+)$1	335	0	3	8.9999
UUU	chr1:70610397-70610750(+)$1	353	58	61	8.9999
UUU	chr5:71479508-71479814(+)$1	306	5	8	8.9999
UUU	chr10:127524707-127525039(+)$1	332	33	36	8.9999
UUU	chr14:99977080-99977387(+)$1	307	47	50	8.9999
UUU	chrX:154001356-154001649(+)$1	293	6	9	8.9999
UUU	chr7:131122550-131122855(+)$1	305	194	197	8.9999
UUU	chr1:33059069-33059493(+)$1	424	98	101	8.9999
UUU	chr2:187370420-187370693(+)$1	273	2	5	8.9999
UUU	chr17:45646703-45647026(+)$1	323	25	28	8.9999
UUU	chr12:52389196-52389461(+)$1	265	27	30	8.9999
UUU	chr13:98634688-98634982(+)$1	294	3	6	8.9999
UUU	chr3:9486860-9487181(+)$1	321	199	202	8.9999
UUU	chr12:56575345-56575610(+)$1	265	87	90	8.9999
UUU	chr11:93412597-93412869(+)$1	272	64	67	8.9999
UUU	chr20:57246193-57246485(+)$1	292	18	21	8.9999
UUU	chr5:112211977-112212286(+)$1	309	22	25	8.9999
UUU	chr14:32559736-32560059(+)$1	323	49	52	8.9999
UUU	chr6:4060875-4061210(+)$1	335	25	28	8.9999
UUU	chr12:52080857-52081177(+)$1	320	5	8	8.9999
UUU	chr12:50156631-50156970(+)$1	339	7	10	8.9999
UUU	chr13:48830325-48830682(+)$1	357	104	107	8.9999
UUU	chr8:11679247-11679526(+)$1	279	5	8	8.9999
UUU	chr2:201687103-201687437(+)$1	334	10	13	8.9999
UUU	chr9:139306480-139306756(+)$1	276	60	63	8.9999
UUU	chr1:153735156-153735446(+)$1	290	31	34	8.9999
UUU	chr22:46746209-46746546(+)$1	337	7	10	8.9999
UUU	chr1:78481883-78482257(+)$1	374	58	61	8.9999
UUU	chr11:32610075-32610390(+)$1	315	2	5	8.9999
UUU	chr4:122589293-122589595(+)$1	302	28	31	8.9999
UUU	chr1:90475586-90475961(+)$1	375	11	14	8.9999
UUU	chr14:64453153-64453440(+)$1	287	5	8	8.9999
UUU	chr2:190323432-190323739(+)$1	307	8	11	8.9999
UUU	chr10:70502102-70502428(+)$1	326	6	9	8.9999
UUU	chr12:123745636-123746010(+)$1	374	76	79	8.9999
UUU	chr5:151170457-151170751(+)$1	294	126	129	8.9999
UUU	chr17:45730109-45730397(+)$1	288	42	45	8.9999
UUU	chr18:33243569-33243908(+)$1	339	5	8	8.9999
UUU	chr19:41712540-41712854(+)$1	314	89	92	8.9999
UUU	chr14:39618397-39618662(+)$1	265	6	9	8.9999
UUU	chr5:179044409-179044674(+)$1	265	29	32	8.9999
UUU	chr2:219612306-219612609(+)$1	303	50	53	8.9999
UUU	chr12:110734398-110734699(+)$1	301	154	157	8.9999
UUU	chr11:10328504-10328830(+)$1	326	23	26	8.9999
UUU	chr16:89952203-89952491(+)$1	288	2	5	8.9999
UUU	chr22:42017939-42018228(+)$1	289	4	7	8.9999
uuu	chr11:32615328-32615646(+)$1	318	24	27	8.9999
UUU	chr2:217070010-217070348(+)$1	338	100	103	8.9999
UUU	chr5:179047722-179048089(+)$1	367	3	6	8.9999
UUU	chr7:33397397-33397692(+)$1	295	9	12	8.9999
UUU	chr8:62538427-62538684(+)$1	257	200	203	8.9999
UUU	chr2:9725103-9725361(+)$1	258	35	38	8.9999
UUU	chr15:40328107-40328360(+)$1	253	8	11	8.9999
UUU	chr14:64465594-64465892(+)$1	298	22	25	8.9999
UUU	chr22:38689121-38689375(+)$1	254	73	76	8.9999
UUU	chr2:234198873-234199125(+)$1	252	4	7	8.9999
UUU	chrX:153999005-153999286(+)$1	281	162	165	8.9999
UUU	chr1:226124154-226124537(+)$1	383	40	43	8.9999
UUU	chr18:722416-722682(+)$1	266	0	3	8.9999
UUU	chr2:198415363-198415697(+)$1	334	66	69	8.9999
UUU	chr20:61916932-61917260(+)$1	328	19	22	8.9999
UUU	chr7:6442647-6442966(+)$1	319	0	3	8.9999
UUU	chr6:64404497-64404760(+)$1	263	64	67	8.9999
UUU	chr2:8869088-8869352(+)$1	264	3	6	8.9999
UUU	chr11:71707194-71707526(+)$1	332	25	28	8.9999
UUU	chr7:86803871-86804186(+)$1	315	5	8	8.9999
UUU	chr15:42813823-42814157(+)$1	334	31	34	8.9999
UUU	chr2:170487223-170487540(+)$1	317	15	18	8.9999
UUU	chrX:5809127-5809395(+)$1	268	13	16	8.9999
UUU	chr17:40986738-40987038(+)$1	300	3	6	8.9999
UUU	chr1:85784026-85784278(+)$1	252	4	7	8.9999
UUU	chr14:73563623-73563901(+)$1	278	93	96	8.9999
UUU	chr5:140389523-140389841(+)$1	318	31	34	8.9999
UUU	chr16:29819841-29820196(+)$1	355	4	7	8.9999
uuu	chrX:47081611-47081865(+)$1	254	7	10	8.9999
UUU	chr17:48821026-48821356(+)$1	330	17	20	8.9999
UUU	chr20:31436602-31436944(+)$1	342	2	5	8.9999
UUU	chr14:75600852-75601191(+)$1	339	116	119	8.9999
UUU	chr5:115780960-115781224(+)$1	264	10	13	8.9999
UUU	chrX:147013934-147014223(+)$1	289	33	36	8.9999
UUU	chr17:38320257-38320543(+)$1	286	136	139	8.9999
UUU	chr4:141302091-141302383(+)$1	292	6	9	8.9999
UUU	chr10:64958226-64958495(+)$1	269	12	15	8.9999
UUU	chr16:3142102-3142376(+)$1	274	0	3	8.9999
UUU	chr1:109239897-109240171(+)$1	274	78	81	8.9999
UUU	chr12:105519748-105520004(+)$1	256	7	10	8.9999
UUU	chr10:96336363-96336724(+)$1	361	6	9	8.9999
UUU	chr17:61895819-61896188(+)$1	369	96	99	8.9999
UUU	chr7:33392350-33392683(+)$1	333	7	10	8.9999
UUU	chr6:44416161-44416496(+)$1	335	169	172	8.9999
UUU	chr7:99935732-99936053(+)$1	321	17	20	8.9999
UUU	chr20:57480347-57480688(+)$1	341	20	23	8.9999

#otherMatches

#Struct PSSM
:::	chr5:112352225-112352534(+)$1	309	7	10	8.9999
:::	chr16:69687075-69687369(+)$1	294	1	4	8.9999
ppp	chr2:61405801-61406103(+)$1	302	8	11	8.9999
e>>	chr6:31500430-31500691(+)$1	261	37	40	8.9999
###	chr16:67217037-67217298(+)$1	261	32	35	8.9999
:::	chr9:132892187-132892459(+)$1	272	35	38	8.9999
DDD	chr19:35500712-35501045(+)$1	333	16	19	8.9999
DDD	chr15:44058073-44058408(+)$1	335	0	3	8.9999
JJJ	chr1:70610397-70610750(+)$1	353	58	61	8.9999
:::	chr5:71479508-71479814(+)$1	306	5	8	8.9999
[bb	chr10:127524707-127525039(+)$1	332	33	36	8.9999
{HH	chr14:99977080-99977387(+)$1	307	47	50	8.9999
:::	chrX:154001356-154001649(+)$1	293	6	9	8.9999
ccc	chr7:131122550-131122855(+)$1	305	194	197	8.9999
qqq	chr1:33059069-33059493(+)$1	424	98	101	8.9999
:::	chr2:187370420-187370693(+)$1	273	2	5	8.9999
FFF	chr17:45646703-45647026(+)$1	323	25	28	8.9999
FFK	chr12:52389196-52389461(+)$1	265	27	30	8.9999
eee	chr13:98634688-98634982(+)$1	294	3	6	8.9999
c[c	chr3:9486860-9487181(+)$1	321	199	202	8.9999
===	chr12:56575345-56575610(+)$1	265	87	90	8.9999
GGG	chr11:93412597-93412869(+)$1	272	64	67	8.9999
:::	chr20:57246193-57246485(+)$1	292	18	21	8.9999
HHH	chr5:112211977-112212286(+)$1	309	22	25	8.9999
RRR	chr14:32559736-32560059(+)$1	323	49	52	8.9999
JJJ	chr6:4060875-4061210(+)$1	335	25	28	8.9999
GGG	chr12:52080857-52081177(+)$1	320	5	8	8.9999
hhh	chr12:50156631-50156970(+)$1	339	7	10	8.9999
eee	chr13:48830325-48830682(+)$1	357	104	107	8.9999
!!f	chr8:11679247-11679526(+)$1	279	5	8	8.9999
ff"	chr2:201687103-201687437(+)$1	334	10	13	8.9999
ggg	chr9:139306480-139306756(+)$1	276	60	63	8.9999
:::	chr1:153735156-153735446(+)$1	290	31	34	8.9999
:FF	chr22:46746209-46746546(+)$1	337	7	10	8.9999
hhh	chr1:78481883-78482257(+)$1	374	58	61	8.9999
:::	chr11:32610075-32610390(+)$1	315	2	5	8.9999
ggg	chr4:122589293-122589595(+)$1	302	28	31	8.9999
::H	chr1:90475586-90475961(+)$1	375	11	14	8.9999
::E	chr14:64453153-64453440(+)$1	287	5	8	8.9999
KKC	chr2:190323432-190323739(+)$1	307	8	11	8.9999
ddd	chr10:70502102-70502428(+)$1	326	6	9	8.9999
%%%	chr12:123745636-123746010(+)$1	374	76	79	8.9999
###	chr5:151170457-151170751(+)$1	294	126	129	8.9999
fff	chr17:45730109-45730397(+)$1	288	42	45	8.9999
F::	chr18:33243569-33243908(+)$1	339	5	8	8.9999
ppd	chr19:41712540-41712854(+)$1	314	89	92	8.9999
:::	chr14:39618397-39618662(+)$1	265	6	9	8.9999
^^e	chr5:179044409-179044674(+)$1	265	29	32	8.9999
GGG	chr2:219612306-219612609(+)$1	303	50	53	8.9999
nnn	chr12:110734398-110734699(+)$1	301	154	157	8.9999
EEE	chr11:10328504-10328830(+)$1	326	23	26	8.9999
===	chr16:89952203-89952491(+)$1	288	2	5	8.9999
hhh	chr22:42017939-42018228(+)$1	289	4	7	8.9999
fff	chr11:32615328-32615646(+)$1	318	24	27	8.9999
::e	chr2:217070010-217070348(+)$1	338	100	103	8.9999
:::	chr5:179047722-179048089(+)$1	367	3	6	8.9999
b$$	chr7:33397397-33397692(+)$1	295	9	12	8.9999
hhh	chr8:62538427-62538684(+)$1	257	200	203	8.9999
GGG	chr2:9725103-9725361(+)$1	258	35	38	8.9999
DDL	chr15:40328107-40328360(+)$1	253	8	11	8.9999
qqq	chr14:64465594-64465892(+)$1	298	22	25	8.9999
nnn	chr22:38689121-38689375(+)$1	254	73	76	8.9999
III	chr2:234198873-234199125(+)$1	252	4	7	8.9999
:::	chrX:153999005-153999286(+)$1	281	162	165	8.9999
vvv	chr1:226124154-226124537(+)$1	383	40	43	8.9999
:::	chr18:722416-722682(+)$1	266	0	3	8.9999
FFF	chr2:198415363-198415697(+)$1	334	66	69	8.9999
fll	chr20:61916932-61917260(+)$1	328	19	22	8.9999
::c	chr7:6442647-6442966(+)$1	319	0	3	8.9999
fff	chr6:64404497-64404760(+)$1	263	64	67	8.9999
:::	chr2:8869088-8869352(+)$1	264	3	6	8.9999
ff!	chr11:71707194-71707526(+)$1	332	25	28	8.9999
:::	chr7:86803871-86804186(+)$1	315	5	8	8.9999
ddd	chr15:42813823-42814157(+)$1	334	31	34	8.9999
eee	chr2:170487223-170487540(+)$1	317	15	18	8.9999
C{C	chrX:5809127-5809395(+)$1	268	13	16	8.9999
:HH	chr17:40986738-40987038(+)$1	300	3	6	8.9999
:::	chr1:85784026-85784278(+)$1	252	4	7	8.9999
eee	chr14:73563623-73563901(+)$1	278	93	96	8.9999
GGG	chr5:140389523-140389841(+)$1	318	31	34	8.9999
DDD	chr16:29819841-29820196(+)$1	355	4	7	8.9999
EEE	chrX:47081611-47081865(+)$1	254	7	10	8.9999
iii	chr17:48821026-48821356(+)$1	330	17	20	8.9999
FFF	chr20:31436602-31436944(+)$1	342	2	5	8.9999
fff	chr14:75600852-75601191(+)$1	339	116	119	8.9999
eec	chr5:115780960-115781224(+)$1	264	10	13	8.9999
cww	chrX:147013934-147014223(+)$1	289	33	36	8.9999
:ff	chr17:38320257-38320543(+)$1	286	136	139	8.9999
ELL	chr4:141302091-141302383(+)$1	292	6	9	8.9999
KEE	chr10:64958226-64958495(+)$1	269	12	15	8.9999
:::	chr16:3142102-3142376(+)$1	274	0	3	8.9999
fff	chr1:109239897-109240171(+)$1	274	78	81	8.9999
FKK	chr12:105519748-105520004(+)$1	256	7	10	8.9999
:::	chr10:96336363-96336724(+)$1	361	6	9	8.9999
EEE	chr17:61895819-61896188(+)$1	369	96	99	8.9999
III	chr7:33392350-33392683(+)$1	333	7	10	8.9999
iii	chr6:44416161-44416496(+)$1	335	169	172	8.9999
:::	chr7:99935732-99936053(+)$1	321	17	20	8.9999
===	chr20:57480347-57480688(+)$1	341	20	23	8.9999

#DB
...	chr5:112352225-112352534(+)$1	1	7	10	8.9999
...	chr16:69687075-69687369(+)$1	1	1	4	8.9999
...	chr2:61405801-61406103(+)$1	1	8	11	8.9999
)..	chr6:31500430-31500691(+)$1	1	37	40	8.9999
...	chr16:67217037-67217298(+)$1	1	32	35	8.9999
...	chr9:132892187-132892459(+)$1	1	35	38	8.9999
(((	chr19:35500712-35501045(+)$1	1	16	19	8.9999
(((	chr15:44058073-44058408(+)$1	1	0	3	8.9999
(((	chr1:70610397-70610750(+)$1	1	58	61	8.9999
...	chr5:71479508-71479814(+)$1	1	5	8	8.9999
.((	chr10:127524707-127525039(+)$1	1	33	36	8.9999
.((	chr14:99977080-99977387(+)$1	1	47	50	8.9999
...	chrX:154001356-154001649(+)$1	1	6	9	8.9999
)))	chr7:131122550-131122855(+)$1	1	194	197	8.9999
...	chr1:33059069-33059493(+)$1	1	98	101	8.9999
...	chr2:187370420-187370693(+)$1	1	2	5	8.9999
(((	chr17:45646703-45647026(+)$1	1	25	28	8.9999
((.	chr12:52389196-52389461(+)$1	1	27	30	8.9999
(((	chr13:98634688-98634982(+)$1	1	3	6	8.9999
(.(	chr3:9486860-9487181(+)$1	1	199	202	8.9999
)))	chr12:56575345-56575610(+)$1	1	87	90	8.9999
(((	chr11:93412597-93412869(+)$1	1	64	67	8.9999
...	chr20:57246193-57246485(+)$1	1	18	21	8.9999
(((	chr5:112211977-112212286(+)$1	1	22	25	8.9999
...	chr14:32559736-32560059(+)$1	1	49	52	8.9999
(((	chr6:4060875-4061210(+)$1	1	25	28	8.9999
(((	chr12:52080857-52081177(+)$1	1	5	8	8.9999
(((	chr12:50156631-50156970(+)$1	1	7	10	8.9999
(((	chr13:48830325-48830682(+)$1	1	104	107	8.9999
..(	chr8:11679247-11679526(+)$1	1	5	8	8.9999
((.	chr2:201687103-201687437(+)$1	1	10	13	8.9999
(((	chr9:139306480-139306756(+)$1	1	60	63	8.9999
...	chr1:153735156-153735446(+)$1	1	31	34	8.9999
.((	chr22:46746209-46746546(+)$1	1	7	10	8.9999
(((	chr1:78481883-78482257(+)$1	1	58	61	8.9999
...	chr11:32610075-32610390(+)$1	1	2	5	8.9999
(((	chr4:122589293-122589595(+)$1	1	28	31	8.9999
..(	chr1:90475586-90475961(+)$1	1	11	14	8.9999
..(	chr14:64453153-64453440(+)$1	1	5	8	8.9999
..(	chr2:190323432-190323739(+)$1	1	8	11	8.9999
(((	chr10:70502102-70502428(+)$1	1	6	9	8.9999
...	chr12:123745636-123746010(+)$1	1	76	79	8.9999
...	chr5:151170457-151170751(+)$1	1	126	129	8.9999
(((	chr17:45730109-45730397(+)$1	1	42	45	8.9999
(..	chr18:33243569-33243908(+)$1	1	5	8	8.9999
..)	chr19:41712540-41712854(+)$1	1	89	92	8.9999
...	chr14:39618397-39618662(+)$1	1	6	9	8.9999
..)	chr5:179044409-179044674(+)$1	1	29	32	8.9999
(((	chr2:219612306-219612609(+)$1	1	50	53	8.9999
...	chr12:110734398-110734699(+)$1	1	154	157	8.9999
(((	chr11:10328504-10328830(+)$1	1	23	26	8.9999
(((	chr16:89952203-89952491(+)$1	1	2	5	8.9999
(((	chr22:42017939-42018228(+)$1	1	4	7	8.9999
)))	chr11:32615328-32615646(+)$1	1	24	27	8.9999
..(	chr2:217070010-217070348(+)$1	1	100	103	8.9999
...	chr5:179047722-179048089(+)$1	1	3	6	8.9999
(..	chr7:33397397-33397692(+)$1	1	9	12	8.9999
)))	chr8:62538427-62538684(+)$1	1	200	203	8.9999
(((	chr2:9725103-9725361(+)$1	1	35	38	8.9999
((.	chr15:40328107-40328360(+)$1	1	8	11	8.9999
...	chr14:64465594-64465892(+)$1	1	22	25	8.9999
...	chr22:38689121-38689375(+)$1	1	73	76	8.9999
(((	chr2:234198873-234199125(+)$1	1	4	7	8.9999
...	chrX:153999005-153999286(+)$1	1	162	165	8.9999
...	chr1:226124154-226124537(+)$1	1	40	43	8.9999
...	chr18:722416-722682(+)$1	1	0	3	8.9999
(((	chr2:198415363-198415697(+)$1	1	66	69	8.9999
(..	chr20:61916932-61917260(+)$1	1	19	22	8.9999
..(	chr7:6442647-6442966(+)$1	1	0	3	8.9999
)))	chr6:64404497-64404760(+)$1	1	64	67	8.9999
...	chr2:8869088-8869352(+)$1	1	3	6	8.9999
((.	chr11:71707194-71707526(+)$1	1	25	28	8.9999
...	chr7:86803871-86804186(+)$1	1	5	8	8.9999
)))	chr15:42813823-42814157(+)$1	1	31	34	8.9999
(((	chr2:170487223-170487540(+)$1	1	15	18	8.9999
(.(	chrX:5809127-5809395(+)$1	1	13	16	8.9999
.((	chr17:40986738-40987038(+)$1	1	3	6	8.9999
...	chr1:85784026-85784278(+)$1	1	4	7	8.9999
(((	chr14:73563623-73563901(+)$1	1	93	96	8.9999
(((	chr5:140389523-140389841(+)$1	1	31	34	8.9999
(((	chr16:29819841-29820196(+)$1	1	4	7	8.9999
(((	chrX:47081611-47081865(+)$1	1	7	10	8.9999
)))	chr17:48821026-48821356(+)$1	1	17	20	8.9999
(((	chr20:31436602-31436944(+)$1	1	2	5	8.9999
(((	chr14:75600852-75601191(+)$1	1	116	119	8.9999
(((	chr5:115780960-115781224(+)$1	1	10	13	8.9999
(..	chrX:147013934-147014223(+)$1	1	33	36	8.9999
.((	chr17:38320257-38320543(+)$1	1	136	139	8.9999
(..	chr4:141302091-141302383(+)$1	1	6	9	8.9999
.((	chr10:64958226-64958495(+)$1	1	12	15	8.9999
...	chr16:3142102-3142376(+)$1	1	0	3	8.9999
(((	chr1:109239897-109240171(+)$1	1	78	81	8.9999
(..	chr12:105519748-105520004(+)$1	1	7	10	8.9999
...	chr10:96336363-96336724(+)$1	1	6	9	8.9999
(((	chr17:61895819-61896188(+)$1	1	96	99	8.9999
(((	chr7:33392350-33392683(+)$1	1	7	10	8.9999
(((	chr6:44416161-44416496(+)$1	1	169	172	8.9999
...	chr7:99935732-99936053(+)$1	1	17	20	8.9999
(((	chr20:57480347-57480688(+)$1	1	20	23	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m1_run1.nuc.txt

#NT
UCC	chr11:2154050-2154272(+)$1	222	104	107	9.0000
UCC	chr4:763519-763755(-)$1	236	98	101	9.0000
UCC	chr2:122125159-122125384(-)$1	225	1	4	9.0000
UCC	chr3:52474729-52474951(+)$1	222	77	80	9.0000
UCC	chr17:28444013-28444240(+)$1	227	3	6	9.0000
UCC	chr7:99668413-99668636(+)$1	223	8	11	9.0000
UCC	chr12:16035257-16035481(+)$1	224	21	24	9.0000
UCC	chr1:229736066-229736288(+)$1	222	99	102	9.0000
UCC	chr3:69435121-69435346(+)$1	225	22	25	9.0000
ucc	chrX:13699810-13700038(+)$1	228	1	4	9.0000
UCC	chr4:129190643-129190867(+)$1	224	4	7	9.0000
UCC	chr3:119883644-119883866(+)$1	222	119	122	9.0000
UCC	chr5:1295019-1295243(+)$1	224	110	113	9.0000
UCC	chr1:33480077-33480299(-)$1	222	2	5	9.0000
UCC	chr1:236444971-236445208(-)$1	237	43	46	9.0000
UCC	chr19:17660372-17660595(-)$1	223	55	58	9.0000
UCC	chr20:17693008-17693232(-)$1	224	40	43	9.0000
UCC	chr7:2281903-2282126(+)$1	223	11	14	9.0000
UCC	chr2:198283504-198283729(-)$1	225	16	19	9.0000
ucc	chr1:171181213-171181435(+)$1	222	42	45	9.0000
UCC	chr15:89055949-89056176(-)$1	227	25	28	9.0000
UCC	chr10:124816872-124817093(-)$1	221	18	21	9.0000
UCC	chr12:44229760-44230019(+)$1	259	103	106	9.0000
UCC	chr22:43902469-43902698(-)$1	229	52	55	9.0000
UCC	chr2:191208647-191208872(+)$1	225	12	15	9.0000
UCC	chr5:177031116-177031337(+)$1	221	35	38	9.0000
UCC	chr5:147821661-147821882(-)$1	221	37	40	9.0000
UCC	chr1:116383184-116383405(+)$1	221	35	38	9.0000
UCC	chr2:238395692-238395920(-)$1	228	7	10	9.0000
UCC	chr14:20845410-20845636(+)$1	226	48	51	9.0000
UCC	chr1:15443318-15443550(+)$1	232	165	168	9.0000
UCC	chr2:27598642-27598865(-)$1	223	61	64	9.0000
UCC	chr1:26857742-26857963(+)$1	221	114	117	9.0000
UCC	chr17:8633136-8633358(+)$1	222	13	16	9.0000
UCC	chr17:41052715-41052938(-)$1	223	8	11	9.0000
UCC	chr7:24732512-24732738(+)$1	226	50	53	9.0000
UCC	chr19:33334693-33334917(+)$1	224	25	28	9.0000
UCC	chr15:75312809-75313031(-)$1	222	27	30	9.0000
UCC	chr5:141233540-141233761(+)$1	221	127	130	9.0000
UCC	chr15:72546237-72546458(+)$1	221	154	157	9.0000
UCC	chr17:73060720-73060944(+)$1	224	91	94	9.0000
UCC	chr1:167370599-167370821(+)$1	222	0	3	9.0000
UCC	chr22:47169714-47169937(-)$1	223	5	8	9.0000
ucc	chr11:122929940-122930166(-)$1	226	71	74	9.0000
UCC	chr4:183838024-183838248(-)$1	224	81	84	9.0000
UCC	chr2:234228223-234228445(-)$1	222	42	45	9.0000
UCC	chr13:42142103-42142325(-)$1	222	106	109	9.0000
UCC	chr3:50140410-50140696(-)$1	286	9	12	9.0000
UCC	chr17:30228619-30228843(-)$1	224	33	36	9.0000
UCC	chr4:184210575-184210799(+)$1	224	152	155	9.0000
UCC	chr3:196083048-196083271(-)$1	223	10	13	9.0000
UCC	chr4:99363243-99363465(-)$1	222	204	207	9.0000
UCC	chr7:56032650-56032872(+)$1	222	11	14	9.0000
UCC	chr5:140699812-140700034(+)$1	222	69	72	9.0000
UCC	chr17:46137753-46137987(+)$1	234	41	44	9.0000
UCC	chr1:201374018-201374242(-)$1	224	69	72	9.0000
UCC	chr9:112970278-112970500(-)$1	222	11	14	9.0000
UCC	chr12:120881771-120881992(-)$1	221	76	79	9.0000
UCC	chr3:50229013-50229234(+)$1	221	16	19	9.0000
UCC	chr14:24902065-24902288(-)$1	223	9	12	9.0000
UCC	chr21:37507228-37507450(-)$1	222	78	81	9.0000
UCC	chr19:4714178-4714399(-)$1	221	17	20	9.0000
UCC	chr19:39672285-39672510(-)$1	225	12	15	9.0000
UCC	chr19:16524464-16524690(+)$1	226	10	13	9.0000
ucc	chr12:102472714-102472940(-)$1	226	13	16	9.0000
UCC	chr7:48128322-48128551(-)$1	229	39	42	9.0000
UCC	chr9:115983716-115983941(-)$1	225	19	22	9.0000
UCC	chr1:201977321-201977544(-)$1	223	4	7	9.0000
ucc	chr20:35491922-35492182(-)$1	260	160	163	9.0000
UCC	chr10:17243513-17243737(-)$1	224	75	78	9.0000
UCC	chr8:145749799-145750022(+)$1	223	47	50	9.0000
UCC	chr11:76737315-76737540(+)$1	225	26	29	9.0000
UCC	chr17:46606689-46606914(+)$1	225	0	3	9.0000
UCC	chr8:97307259-97307481(+)$1	222	6	9	9.0000
UCC	chr2:75891737-75891960(+)$1	223	39	42	9.0000
UCC	chr17:46052435-46052656(-)$1	221	20	23	9.0000
UCC	chr3:161089891-161090114(+)$1	223	64	67	9.0000
UCC	chr5:176023291-176023522(+)$1	231	74	77	9.0000
UCC	chr3:9798734-9798956(+)$1	222	2	5	9.0000
UCC	chr11:46722024-46722245(+)$1	221	1	4	9.0000
ucc	chr2:102960854-102961081(-)$1	227	144	147	9.0000
UCC	chr13:51858198-51858425(+)$1	227	27	30	9.0000
UCC	chr1:47683023-47683245(-)$1	222	4	7	9.0000
UCC	chr17:80197634-80197861(-)$1	227	35	38	9.0000
UCC	chr14:20841793-20842015(-)$1	222	1	4	9.0000
UCC	chr7:100959707-100959930(-)$1	223	48	51	9.0000
UCC	chr7:88388996-88389220(-)$1	224	25	28	9.0000
UCC	chr6:32973773-32973996(-)$1	223	10	13	9.0000
UCC	chr17:41113175-41113397(-)$1	222	21	24	9.0000
UCC	chr3:143709525-143709746(+)$1	221	33	36	9.0000
UCC	chr1:92709662-92709884(-)$1	222	80	83	9.0000
ucc	chr15:50606752-50606974(+)$1	222	93	96	9.0000
UCC	chr19:4279172-4279399(+)$1	227	22	25	9.0000
UCC	chr14:37126688-37126910(-)$1	222	23	26	9.0000
UCC	chr9:110252490-110252713(-)$1	223	8	11	9.0000
UCC	chr1:228871145-228871368(+)$1	223	11	14	9.0000
UCC	chr16:49522052-49522276(+)$1	224	23	26	9.0000
UCC	chr16:30546482-30546706(+)$1	224	16	19	9.0000
UCC	chr11:61920039-61920261(+)$1	222	13	16	9.0000

#otherMatches

#Struct PSSM
EEE	chr22:38035648-38035870(-)$1	222	19	22	9.0000
eee	chr11:2154050-2154272(+)$1	222	104	107	9.0000
qqc	chr4:763519-763755(-)$1	236	98	101	9.0000
:dd	chr2:122125159-122125384(-)$1	225	1	4	9.0000
===	chr3:52474729-52474951(+)$1	222	77	80	9.0000
CCB	chr17:28444013-28444240(+)$1	227	3	6	9.0000
CCK	chr7:99668413-99668636(+)$1	223	8	11	9.0000
"ff	chr12:16035257-16035481(+)$1	224	21	24	9.0000
:::	chr1:229736066-229736288(+)$1	222	99	102	9.0000
f$$	chr3:69435121-69435346(+)$1	225	22	25	9.0000
:::	chrX:13699810-13700038(+)$1	228	1	4	9.0000
CCC	chr4:129190643-129190867(+)$1	224	4	7	9.0000
ggg	chr3:119883644-119883866(+)$1	222	119	122	9.0000
FFF	chr5:1295019-1295243(+)$1	224	110	113	9.0000
:::	chr1:33480077-33480299(-)$1	222	2	5	9.0000
$hh	chr1:236444971-236445208(-)$1	237	43	46	9.0000
lle	chr19:17660372-17660595(-)$1	223	55	58	9.0000
ddd	chr20:17693008-17693232(-)$1	224	40	43	9.0000
DDD	chr7:2281903-2282126(+)$1	223	11	14	9.0000
::G	chr2:198283504-198283729(-)$1	225	16	19	9.0000
e!!	chr1:171181213-171181435(+)$1	222	42	45	9.0000
EEE	chr15:89055949-89056176(-)$1	227	25	28	9.0000
cc:	chr10:124816872-124817093(-)$1	221	18	21	9.0000
cdd	chr12:44229760-44230019(+)$1	259	103	106	9.0000
ppp	chr22:43902469-43902698(-)$1	229	52	55	9.0000
d:E	chr2:191208647-191208872(+)$1	225	12	15	9.0000
FFF	chr5:177031116-177031337(+)$1	221	35	38	9.0000
:::	chr5:147821661-147821882(-)$1	221	37	40	9.0000
e!!	chr1:116383184-116383405(+)$1	221	35	38	9.0000
HHH	chr2:238395692-238395920(-)$1	228	7	10	9.0000
c]e	chr14:20845410-20845636(+)$1	226	48	51	9.0000
eee	chr1:15443318-15443550(+)$1	232	165	168	9.0000
qqq	chr2:27598642-27598865(-)$1	223	61	64	9.0000
===	chr1:26857742-26857963(+)$1	221	114	117	9.0000
qqq	chr17:8633136-8633358(+)$1	222	13	16	9.0000
G::	chr17:41052715-41052938(-)$1	223	8	11	9.0000
:::	chr7:24732512-24732738(+)$1	226	50	53	9.0000
d::	chr19:33334693-33334917(+)$1	224	25	28	9.0000
ccc	chr15:75312809-75313031(-)$1	222	27	30	9.0000
DDD	chr5:141233540-141233761(+)$1	221	127	130	9.0000
]cc	chr15:72546237-72546458(+)$1	221	154	157	9.0000
dd:	chr17:73060720-73060944(+)$1	224	91	94	9.0000
:::	chr1:167370599-167370821(+)$1	222	0	3	9.0000
eeb	chr22:47169714-47169937(-)$1	223	5	8	9.0000
[cc	chr11:122929940-122930166(-)$1	226	71	74	9.0000
ccc	chr4:183838024-183838248(-)$1	224	81	84	9.0000
cc3	chr2:234228223-234228445(-)$1	222	42	45	9.0000
eee	chr13:42142103-42142325(-)$1	222	106	109	9.0000
CCC	chr3:50140410-50140696(-)$1	286	9	12	9.0000
fff	chr17:30228619-30228843(-)$1	224	33	36	9.0000
ccc	chr4:184210575-184210799(+)$1	224	152	155	9.0000
LDD	chr3:196083048-196083271(-)$1	223	10	13	9.0000
ccc	chr4:99363243-99363465(-)$1	222	204	207	9.0000
oee	chr7:56032650-56032872(+)$1	222	11	14	9.0000
ee:	chr5:140699812-140700034(+)$1	222	69	72	9.0000
DEE	chr17:46137753-46137987(+)$1	234	41	44	9.0000
fdd	chr1:201374018-201374242(-)$1	224	69	72	9.0000
frr	chr9:112970278-112970500(-)$1	222	11	14	9.0000
^^^	chr12:120881771-120881992(-)$1	221	76	79	9.0000
DDD	chr3:50229013-50229234(+)$1	221	16	19	9.0000
fff	chr14:24902065-24902288(-)$1	223	9	12	9.0000
ccc	chr21:37507228-37507450(-)$1	222	78	81	9.0000
ggg	chr19:4714178-4714399(-)$1	221	17	20	9.0000
DDD	chr19:39672285-39672510(-)$1	225	12	15	9.0000
E{C	chr19:16524464-16524690(+)$1	226	10	13	9.0000
:::	chr12:102472714-102472940(-)$1	226	13	16	9.0000
ppp	chr7:48128322-48128551(-)$1	229	39	42	9.0000
:::	chr9:115983716-115983941(-)$1	225	19	22	9.0000
GGG	chr1:201977321-201977544(-)$1	223	4	7	9.0000
fff	chr20:35491922-35492182(-)$1	260	160	163	9.0000
fff	chr10:17243513-17243737(-)$1	224	75	78	9.0000
nnb	chr8:145749799-145750022(+)$1	223	47	50	9.0000
'''	chr11:76737315-76737540(+)$1	225	26	29	9.0000
::d	chr17:46606689-46606914(+)$1	225	0	3	9.0000
LLL	chr8:97307259-97307481(+)$1	222	6	9	9.0000
e22	chr2:75891737-75891960(+)$1	223	39	42	9.0000
NNN	chr17:46052435-46052656(-)$1	221	20	23	9.0000
KBB	chr3:161089891-161090114(+)$1	223	64	67	9.0000
CCC	chr5:176023291-176023522(+)$1	231	74	77	9.0000
:::	chr3:9798734-9798956(+)$1	222	2	5	9.0000
ccc	chr11:46722024-46722245(+)$1	221	1	4	9.0000
ee:	chr2:102960854-102961081(-)$1	227	144	147	9.0000
:::	chr13:51858198-51858425(+)$1	227	27	30	9.0000
:::	chr1:47683023-47683245(-)$1	222	4	7	9.0000
D::	chr17:80197634-80197861(-)$1	227	35	38	9.0000
:EE	chr14:20841793-20842015(-)$1	222	1	4	9.0000
FDD	chr7:100959707-100959930(-)$1	223	48	51	9.0000
GG:	chr7:88388996-88389220(-)$1	224	25	28	9.0000
:::	chr6:32973773-32973996(-)$1	223	10	13	9.0000
MMM	chr17:41113175-41113397(-)$1	222	21	24	9.0000
qqq	chr3:143709525-143709746(+)$1	221	33	36	9.0000
eee	chr1:92709662-92709884(-)$1	222	80	83	9.0000
FFF	chr15:50606752-50606974(+)$1	222	93	96	9.0000
GGG	chr19:4279172-4279399(+)$1	227	22	25	9.0000
BLL	chr14:37126688-37126910(-)$1	222	23	26	9.0000
EEE	chr9:110252490-110252713(-)$1	223	8	11	9.0000
:::	chr1:228871145-228871368(+)$1	223	11	14	9.0000
ddd	chr16:49522052-49522276(+)$1	224	23	26	9.0000
ppp	chr16:30546482-30546706(+)$1	224	16	19	9.0000
:dd	chr11:61920039-61920261(+)$1	222	13	16	9.0000

#DB
(((	chr22:38035648-38035870(-)$1	1	19	22	9.0000
)))	chr11:2154050-2154272(+)$1	1	104	107	9.0000
..)	chr4:763519-763755(-)$1	1	98	101	9.0000
.((	chr2:122125159-122125384(-)$1	1	1	4	9.0000
)))	chr3:52474729-52474951(+)$1	1	77	80	9.0000
(((	chr17:28444013-28444240(+)$1	1	3	6	9.0000
((.	chr7:99668413-99668636(+)$1	1	8	11	9.0000
.((	chr12:16035257-16035481(+)$1	1	21	24	9.0000
...	chr1:229736066-229736288(+)$1	1	99	102	9.0000
(..	chr3:69435121-69435346(+)$1	1	22	25	9.0000
...	chrX:13699810-13700038(+)$1	1	1	4	9.0000
(((	chr4:129190643-129190867(+)$1	1	4	7	9.0000
(((	chr3:119883644-119883866(+)$1	1	119	122	9.0000
(((	chr5:1295019-1295243(+)$1	1	110	113	9.0000
...	chr1:33480077-33480299(-)$1	1	2	5	9.0000
.((	chr1:236444971-236445208(-)$1	1	43	46	9.0000
..)	chr19:17660372-17660595(-)$1	1	55	58	9.0000
)))	chr20:17693008-17693232(-)$1	1	40	43	9.0000
(((	chr7:2281903-2282126(+)$1	1	11	14	9.0000
..(	chr2:198283504-198283729(-)$1	1	16	19	9.0000
(..	chr1:171181213-171181435(+)$1	1	42	45	9.0000
(((	chr15:89055949-89056176(-)$1	1	25	28	9.0000
)).	chr10:124816872-124817093(-)$1	1	18	21	9.0000
(((	chr12:44229760-44230019(+)$1	1	103	106	9.0000
...	chr22:43902469-43902698(-)$1	1	52	55	9.0000
).(	chr2:191208647-191208872(+)$1	1	12	15	9.0000
(((	chr5:177031116-177031337(+)$1	1	35	38	9.0000
...	chr5:147821661-147821882(-)$1	1	37	40	9.0000
(..	chr1:116383184-116383405(+)$1	1	35	38	9.0000
(((	chr2:238395692-238395920(-)$1	1	7	10	9.0000
).)	chr14:20845410-20845636(+)$1	1	48	51	9.0000
(((	chr1:15443318-15443550(+)$1	1	165	168	9.0000
...	chr2:27598642-27598865(-)$1	1	61	64	9.0000
(((	chr1:26857742-26857963(+)$1	1	114	117	9.0000
...	chr17:8633136-8633358(+)$1	1	13	16	9.0000
(..	chr17:41052715-41052938(-)$1	1	8	11	9.0000
...	chr7:24732512-24732738(+)$1	1	50	53	9.0000
)..	chr19:33334693-33334917(+)$1	1	25	28	9.0000
)))	chr15:75312809-75313031(-)$1	1	27	30	9.0000
(((	chr5:141233540-141233761(+)$1	1	127	130	9.0000
.))	chr15:72546237-72546458(+)$1	1	154	157	9.0000
)).	chr17:73060720-73060944(+)$1	1	91	94	9.0000
...	chr1:167370599-167370821(+)$1	1	0	3	9.0000
(((	chr22:47169714-47169937(-)$1	1	5	8	9.0000
.((	chr11:122929940-122930166(-)$1	1	71	74	9.0000
(((	chr4:183838024-183838248(-)$1	1	81	84	9.0000
)).	chr2:234228223-234228445(-)$1	1	42	45	9.0000
)))	chr13:42142103-42142325(-)$1	1	106	109	9.0000
(((	chr3:50140410-50140696(-)$1	1	9	12	9.0000
)))	chr17:30228619-30228843(-)$1	1	33	36	9.0000
(((	chr4:184210575-184210799(+)$1	1	152	155	9.0000
.((	chr3:196083048-196083271(-)$1	1	10	13	9.0000
)))	chr4:99363243-99363465(-)$1	1	204	207	9.0000
.))	chr7:56032650-56032872(+)$1	1	11	14	9.0000
)).	chr5:140699812-140700034(+)$1	1	69	72	9.0000
(((	chr17:46137753-46137987(+)$1	1	41	44	9.0000
(((	chr1:201374018-201374242(-)$1	1	69	72	9.0000
(..	chr9:112970278-112970500(-)$1	1	11	14	9.0000
...	chr12:120881771-120881992(-)$1	1	76	79	9.0000
(((	chr3:50229013-50229234(+)$1	1	16	19	9.0000
(((	chr14:24902065-24902288(-)$1	1	9	12	9.0000
)))	chr21:37507228-37507450(-)$1	1	78	81	9.0000
(((	chr19:4714178-4714399(-)$1	1	17	20	9.0000
(((	chr19:39672285-39672510(-)$1	1	12	15	9.0000
(.(	chr19:16524464-16524690(+)$1	1	10	13	9.0000
...	chr12:102472714-102472940(-)$1	1	13	16	9.0000
...	chr7:48128322-48128551(-)$1	1	39	42	9.0000
...	chr9:115983716-115983941(-)$1	1	19	22	9.0000
(((	chr1:201977321-201977544(-)$1	1	4	7	9.0000
)))	chr20:35491922-35492182(-)$1	1	160	163	9.0000
(((	chr10:17243513-17243737(-)$1	1	75	78	9.0000
..)	chr8:145749799-145750022(+)$1	1	47	50	9.0000
...	chr11:76737315-76737540(+)$1	1	26	29	9.0000
..(	chr17:46606689-46606914(+)$1	1	0	3	9.0000
...	chr8:97307259-97307481(+)$1	1	6	9	9.0000
)..	chr2:75891737-75891960(+)$1	1	39	42	9.0000
...	chr17:46052435-46052656(-)$1	1	20	23	9.0000
.((	chr3:161089891-161090114(+)$1	1	64	67	9.0000
(((	chr5:176023291-176023522(+)$1	1	74	77	9.0000
...	chr3:9798734-9798956(+)$1	1	2	5	9.0000
(((	chr11:46722024-46722245(+)$1	1	1	4	9.0000
)).	chr2:102960854-102961081(-)$1	1	144	147	9.0000
...	chr13:51858198-51858425(+)$1	1	27	30	9.0000
...	chr1:47683023-47683245(-)$1	1	4	7	9.0000
(..	chr17:80197634-80197861(-)$1	1	35	38	9.0000
.((	chr14:20841793-20842015(-)$1	1	1	4	9.0000
(((	chr7:100959707-100959930(-)$1	1	48	51	9.0000
((.	chr7:88388996-88389220(-)$1	1	25	28	9.0000
...	chr6:32973773-32973996(-)$1	1	10	13	9.0000
...	chr17:41113175-41113397(-)$1	1	21	24	9.0000
...	chr3:143709525-143709746(+)$1	1	33	36	9.0000
(((	chr1:92709662-92709884(-)$1	1	80	83	9.0000
(((	chr15:50606752-50606974(+)$1	1	93	96	9.0000
(((	chr19:4279172-4279399(+)$1	1	22	25	9.0000
(..	chr14:37126688-37126910(-)$1	1	23	26	9.0000
(((	chr9:110252490-110252713(-)$1	1	8	11	9.0000
...	chr1:228871145-228871368(+)$1	1	11	14	9.0000
(((	chr16:49522052-49522276(+)$1	1	23	26	9.0000
...	chr16:30546482-30546706(+)$1	1	16	19	9.0000
.((	chr11:61920039-61920261(+)$1	1	13	16	9.0000

#PSSM
U : 0.93	u : 0.07	
C : 0.93	c : 0.07	
C : 0.93	c : 0.07	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m1_run2.nuc.txt

#NT
CUUUU	chr4:155748337-155748551(+)$1	214	133	138	14.9999
CUUUU	chr5:87491874-87492120(-)$1	246	7	12	14.9999
CUUUU	chr3:50138776-50139036(+)$1	260	36	41	14.9999
CUUUU	chr1:28086437-28086685(+)$1	248	188	193	14.9999
CUUUU	chr1:151030816-151031228(-)$1	412	352	357	14.9999
CUUUU	chr7:149187617-149187991(-)$1	374	75	80	14.9999
CUUUU	chr10:35468519-35468739(+)$1	220	33	38	14.9999
CUUUU	chr13:37596919-37597182(-)$1	263	35	40	14.9999
CUUUU	chr12:30782946-30783163(-)$1	217	5	10	14.9999
CUUUU	chr12:57882414-57882700(+)$1	286	46	51	14.9999
CUUUU	chr14:103808740-103809012(+)$1	272	47	52	14.9999
CUUUU	chr4:76452363-76452641(+)$1	278	207	212	14.9999
CUUUU	chr15:42861900-42862118(+)$1	218	152	157	14.9999
cuuuu	chr7:106849614-106849942(-)$1	328	117	122	14.9999
CUUUU	chr2:170911897-170912110(+)$1	213	98	103	14.9999
CUUUU	chr20:52106367-52106591(+)$1	224	128	133	14.9999
CUUUU	chr19:44678542-44678759(+)$1	217	187	192	14.9999
CUUUU	chr12:51374773-51375069(-)$1	296	10	15	14.9999
CUUUU	chr1:40145920-40146159(-)$1	239	5	10	14.9999
CUUUU	chr14:68058699-68058919(-)$1	220	146	151	14.9999
CUUUU	chr14:57878118-57878331(+)$1	213	194	199	14.9999
CUUUU	chr14:54946905-54947142(-)$1	237	167	172	14.9999
CUUUU	chr4:15606874-15607107(-)$1	233	8	13	14.9999
CUUUU	chr1:70340183-70340397(+)$1	214	34	39	14.9999
CUUUU	chr8:133024298-133024542(+)$1	244	92	97	14.9999
CUUUU	chr1:236714170-236714426(+)$1	256	85	90	14.9999
CUUUU	chr3:184556533-184556759(+)$1	226	16	21	14.9999
CUUUU	chrX:11784190-11784471(+)$1	281	4	9	14.9999
CUUUU	chr2:54888316-54888557(+)$1	241	51	56	14.9999
CUUUU	chr16:3022046-3022273(+)$1	227	99	104	14.9999
CUUUU	chr2:219319215-219319496(-)$1	281	55	60	14.9999
CUUUU	chr5:40761719-40761982(-)$1	263	64	69	14.9999
CUUUU	chr10:88494695-88494958(+)$1	263	99	104	14.9999
CUUUU	chr2:211297632-211297877(-)$1	245	205	210	14.9999
CUUUU	chr2:38960851-38961130(+)$1	279	11	16	14.9999
CUUUU	chr6:35554409-35554639(-)$1	230	27	32	14.9999
cuuuu	chr17:7572131-7572373(-)$1	242	193	198	14.9999
CUUUU	chr1:84963991-84964242(-)$1	251	231	236	14.9999
CUUUU	chrX:24095403-24095651(+)$1	248	174	179	14.9999
CUUUU	chr5:139507118-139507339(+)$1	221	93	98	14.9999
CUUUU	chr14:92248027-92248291(-)$1	264	138	143	14.9999
CUUUU	chr15:60783455-60783718(-)$1	263	6	11	14.9999
CUUUU	chr17:2586896-2587118(+)$1	222	137	142	14.9999
CUUUU	chr22:36550405-36550636(-)$1	231	170	175	14.9999
cuuuu	chr2:231268163-231268428(+)$1	265	66	71	14.9999
CUUUU	chr8:122625384-122625605(-)$1	221	23	28	14.9999
CUUUU	chr11:47593384-47593623(+)$1	239	38	43	14.9999
CUUUU	chr19:53995253-53995477(+)$1	224	76	81	14.9999
CUUUU	chr12:92823759-92823971(+)$1	212	54	59	14.9999
cuuuu	chr20:44998484-44998746(-)$1	262	186	191	14.9999
cuuuu	chr16:31770504-31770717(+)$1	213	42	47	14.9999
CUUUU	chr18:67515153-67515404(+)$1	251	153	158	14.9999
CUUUU	chr3:98240672-98240944(-)$1	272	227	232	14.9999
CUUUU	chr1:113214050-113214296(+)$1	246	203	208	14.9999
CUUUU	chr9:94972575-94972819(-)$1	244	64	69	14.9999
cuuuu	chr7:149185916-149186154(-)$1	238	71	76	14.9999
CUUUU	chr6:30654026-30654380(-)$1	354	220	225	14.9999
CUUUU	chr17:56167343-56167559(+)$1	216	50	55	14.9999

#otherMatches

#Struct PSSM
hhhhh	chr5:160716686-160716931(-)$1	245	37	42	14.9999
cc444	chr4:155748337-155748551(+)$1	214	133	138	14.9999
KEEEE	chr5:87491874-87492120(-)$1	246	7	12	14.9999
doooo	chr3:50138776-50139036(+)$1	260	36	41	14.9999
:::::	chr1:28086437-28086685(+)$1	248	188	193	14.9999
^^^^^	chr1:151030816-151031228(-)$1	412	352	357	14.9999
eeeee	chr7:149187617-149187991(-)$1	374	75	80	14.9999
:::::	chr10:35468519-35468739(+)$1	220	33	38	14.9999
uuuuu	chr13:37596919-37597182(-)$1	263	35	40	14.9999
ffff!	chr12:30782946-30783163(-)$1	217	5	10	14.9999
!!fff	chr12:57882414-57882700(+)$1	286	46	51	14.9999
EEfff	chr14:103808740-103809012(+)$1	272	47	52	14.9999
mmmee	chr4:76452363-76452641(+)$1	278	207	212	14.9999
EEEE?	chr15:42861900-42862118(+)$1	218	152	157	14.9999
:::::	chr7:106849614-106849942(-)$1	328	117	122	14.9999
dvvvv	chr2:170911897-170912110(+)$1	213	98	103	14.9999
ff!!b	chr20:52106367-52106591(+)$1	224	128	133	14.9999
meeee	chr19:44678542-44678759(+)$1	217	187	192	14.9999
GGGGM	chr12:51374773-51375069(-)$1	296	10	15	14.9999
hhhhh	chr1:40145920-40146159(-)$1	239	5	10	14.9999
cc777	chr14:68058699-68058919(-)$1	220	146	151	14.9999
B}EEE	chr14:57878118-57878331(+)$1	213	194	199	14.9999
:::::	chr14:54946905-54947142(-)$1	237	167	172	14.9999
:::::	chr4:15606874-15607107(-)$1	233	8	13	14.9999
e::JJ	chr1:70340183-70340397(+)$1	214	34	39	14.9999
:::::	chr8:133024298-133024542(+)$1	244	92	97	14.9999
oofff	chr1:236714170-236714426(+)$1	256	85	90	14.9999
c!!a[	chr3:184556533-184556759(+)$1	226	16	21	14.9999
eee&&	chrX:11784190-11784471(+)$1	281	4	9	14.9999
ddddd	chr2:54888316-54888557(+)$1	241	51	56	14.9999
::eee	chr16:3022046-3022273(+)$1	227	99	104	14.9999
ooa22	chr2:219319215-219319496(-)$1	281	55	60	14.9999
oofff	chr5:40761719-40761982(-)$1	263	64	69	14.9999
=====	chr10:88494695-88494958(+)$1	263	99	104	14.9999
ZHHHH	chr2:211297632-211297877(-)$1	245	205	210	14.9999
:::::	chr2:38960851-38961130(+)$1	279	11	16	14.9999
EEEE{	chr6:35554409-35554639(-)$1	230	27	32	14.9999
^^^^^	chr17:7572131-7572373(-)$1	242	193	198	14.9999
i22dd	chr1:84963991-84964242(-)$1	251	231	236	14.9999
d6666	chrX:24095403-24095651(+)$1	248	174	179	14.9999
d:::e	chr5:139507118-139507339(+)$1	221	93	98	14.9999
:::::	chr14:92248027-92248291(-)$1	264	138	143	14.9999
:::::	chr15:60783455-60783718(-)$1	263	6	11	14.9999
""fff	chr17:2586896-2587118(+)$1	222	137	142	14.9999
eee""	chr22:36550405-36550636(-)$1	231	170	175	14.9999
:::::	chr2:231268163-231268428(+)$1	265	66	71	14.9999
FFFFF	chr8:122625384-122625605(-)$1	221	23	28	14.9999
hhhhe	chr11:47593384-47593623(+)$1	239	38	43	14.9999
fffff	chr19:53995253-53995477(+)$1	224	76	81	14.9999
:::::	chr12:92823759-92823971(+)$1	212	54	59	14.9999
:::ee	chr20:44998484-44998746(-)$1	262	186	191	14.9999
b22dd	chr16:31770504-31770717(+)$1	213	42	47	14.9999
qqqqq	chr18:67515153-67515404(+)$1	251	153	158	14.9999
HHHHZ	chr3:98240672-98240944(-)$1	272	227	232	14.9999
sssss	chr1:113214050-113214296(+)$1	246	203	208	14.9999
eeeee	chr9:94972575-94972819(-)$1	244	64	69	14.9999
GGMMM	chr7:149185916-149186154(-)$1	238	71	76	14.9999
:::::	chr6:30654026-30654380(-)$1	354	220	225	14.9999
^^^^^	chr17:56167343-56167559(+)$1	216	50	55	14.9999

#DB
(((((	chr5:160716686-160716931(-)$1	1	37	42	14.9999
))...	chr4:155748337-155748551(+)$1	1	133	138	14.9999
.((((	chr5:87491874-87492120(-)$1	1	7	12	14.9999
(....	chr3:50138776-50139036(+)$1	1	36	41	14.9999
.....	chr1:28086437-28086685(+)$1	1	188	193	14.9999
.....	chr1:151030816-151031228(-)$1	1	352	357	14.9999
)))((	chr7:149187617-149187991(-)$1	1	75	80	14.9999
.....	chr10:35468519-35468739(+)$1	1	33	38	14.9999
.....	chr13:37596919-37597182(-)$1	1	35	40	14.9999
((((.	chr12:30782946-30783163(-)$1	1	5	10	14.9999
..(((	chr12:57882414-57882700(+)$1	1	46	51	14.9999
(((((	chr14:103808740-103809012(+)$1	1	47	52	14.9999
...))	chr4:76452363-76452641(+)$1	1	207	212	14.9999
)))).	chr15:42861900-42862118(+)$1	1	152	157	14.9999
.....	chr7:106849614-106849942(-)$1	1	117	122	14.9999
(....	chr2:170911897-170912110(+)$1	1	98	103	14.9999
((..(	chr20:52106367-52106591(+)$1	1	128	133	14.9999
.))))	chr19:44678542-44678759(+)$1	1	187	192	14.9999
((((.	chr12:51374773-51375069(-)$1	1	10	15	14.9999
(((((	chr1:40145920-40146159(-)$1	1	5	10	14.9999
))...	chr14:68058699-68058919(-)$1	1	146	151	14.9999
).)))	chr14:57878118-57878331(+)$1	1	194	199	14.9999
.....	chr14:54946905-54947142(-)$1	1	167	172	14.9999
.....	chr4:15606874-15607107(-)$1	1	8	13	14.9999
)..((	chr1:70340183-70340397(+)$1	1	34	39	14.9999
.....	chr8:133024298-133024542(+)$1	1	92	97	14.9999
..)))	chr1:236714170-236714426(+)$1	1	85	90	14.9999
(..(.	chr3:184556533-184556759(+)$1	1	16	21	14.9999
(((..	chrX:11784190-11784471(+)$1	1	4	9	14.9999
))(((	chr2:54888316-54888557(+)$1	1	51	56	14.9999
..(((	chr16:3022046-3022273(+)$1	1	99	104	14.9999
..)..	chr2:219319215-219319496(-)$1	1	55	60	14.9999
..)))	chr5:40761719-40761982(-)$1	1	64	69	14.9999
(((((	chr10:88494695-88494958(+)$1	1	99	104	14.9999
.))))	chr2:211297632-211297877(-)$1	1	205	210	14.9999
.....	chr2:38960851-38961130(+)$1	1	11	16	14.9999
((((.	chr6:35554409-35554639(-)$1	1	27	32	14.9999
.....	chr17:7572131-7572373(-)$1	1	193	198	14.9999
)..))	chr1:84963991-84964242(-)$1	1	231	236	14.9999
)....	chrX:24095403-24095651(+)$1	1	174	179	14.9999
)...(	chr5:139507118-139507339(+)$1	1	93	98	14.9999
.....	chr14:92248027-92248291(-)$1	1	138	143	14.9999
.....	chr15:60783455-60783718(-)$1	1	6	11	14.9999
..(((	chr17:2586896-2587118(+)$1	1	137	142	14.9999
(((..	chr22:36550405-36550636(-)$1	1	170	175	14.9999
.....	chr2:231268163-231268428(+)$1	1	66	71	14.9999
(((((	chr8:122625384-122625605(-)$1	1	23	28	14.9999
)))))	chr11:47593384-47593623(+)$1	1	38	43	14.9999
(((((	chr19:53995253-53995477(+)$1	1	76	81	14.9999
.....	chr12:92823759-92823971(+)$1	1	54	59	14.9999
...((	chr20:44998484-44998746(-)$1	1	186	191	14.9999
)..))	chr16:31770504-31770717(+)$1	1	42	47	14.9999
.....	chr18:67515153-67515404(+)$1	1	153	158	14.9999
)))).	chr3:98240672-98240944(-)$1	1	227	232	14.9999
.....	chr1:113214050-113214296(+)$1	1	203	208	14.9999
)))))	chr9:94972575-94972819(-)$1	1	64	69	14.9999
((...	chr7:149185916-149186154(-)$1	1	71	76	14.9999
.....	chr6:30654026-30654380(-)$1	1	220	225	14.9999
.....	chr17:56167343-56167559(+)$1	1	50	55	14.9999

#PSSM
C : 0.89	c : 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	

#score	884.9999999999995
#seq	59
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m1_run1.nuc.txt

#NT
AUAUACA	chrX:17771130-17771384(+)$1	254	129	136	12.7592
uuacaca	chr7:99374993-99375245(-)$1	252	101	108	12.1111
auacaua	chr12:51088192-51088471(+)$1	279	95	102	13.1296
aaacaca	chrX:110945660-110945945(+)$1	285	120	127	13.6851
auacaca	chr16:27617699-27617976(+)$1	277	98	105	16.7407
AUACUCA	chr8:32486615-32486828(+)$1	213	128	135	12.2037
auacaaa	chr12:9847548-9847788(+)$1	240	57	64	13.1296
AAACACA	chr8:121754083-121754355(-)$1	272	97	104	13.6851
acacaca	chr10:26799554-26799882(+)$1	328	110	117	13.6851
AUACAGA	chr7:102995434-102995660(+)$1	226	28	35	13.0370
AUCCACA	chr5:14817121-14817385(-)$1	264	42	49	12.3888
auucaca	chr9:100840044-100840258(+)$1	214	81	88	12.4814
AUACACA	chr16:85706615-85706880(+)$1	265	213	220	16.7407
AUACCCA	chr22:41256789-41257061(+)$1	272	126	133	12.1111
auacaca	chr8:12842356-12842606(+)$1	250	105	112	16.7407
AUAAACA	chr6:12087411-12087633(+)$1	222	41	48	12.5740
auaaaca	chr2:46956796-46957044(+)$1	248	81	88	12.5740
uuacaca	chr11:46645289-46645530(+)$1	241	166	173	12.1111
agacaca	chr3:15664554-15664773(+)$1	219	172	179	13.7777
auacaga	chr3:15820246-15820488(-)$1	242	196	203	13.0370
aaacaca	chr12:51852888-51853102(+)$1	214	83	90	13.6851
AUACAUA	chr5:58319412-58319682(-)$1	270	27	34	13.1296
AUACAAA	chr12:62787769-62788029(+)$1	260	89	96	13.1296
AGACACA	chr10:28498258-28498489(-)$1	231	61	68	13.7777
auacaua	chr7:11081064-11081311(+)$1	247	40	47	13.1296
acacaca	chr7:33636555-33636826(+)$1	271	127	134	13.6851
acacaca	chr13:73364452-73364712(+)$1	260	108	115	13.6851
auacaca	chr9:78610550-78610811(+)$1	261	108	115	16.7407
acacaca	chr3:156614835-156615070(+)$1	235	100	107	13.6851
AUAUACA	chr8:51109672-51109887(+)$1	215	183	190	12.7592
aaacaca	chr9:125149941-125150157(+)$1	216	96	103	13.6851
agacaca	chrX:71817294-71817528(-)$1	234	193	200	13.7777
AUACUCA	chr3:171832627-171832841(+)$1	214	2	9	12.2037
AUAUACA	chr2:63701755-63702024(-)$1	269	50	57	12.7592
AGACACA	chr8:21860883-21861104(+)$1	221	149	156	13.7777
AUACAAA	chr2:44582963-44583238(-)$1	275	191	198	13.1296
AUUCACA	chr12:73035481-73035695(+)$1	214	3	10	12.4814
AGACACA	chr17:61805375-61805606(-)$1	231	98	105	13.7777
ACACACA	chr12:65109939-65110178(-)$1	239	18	25	13.6851
auacaca	chr1:160546341-160546562(-)$1	221	39	46	16.7407
aUacaca	chr8:120617562-120617815(-)$1	253	108	115	16.7407
AUACAAA	chr9:8612256-8612475(-)$1	219	172	179	13.1296
AUACAGA	chr1:8029002-8029308(+)$1	306	51	58	13.0370
AUCCACA	chr10:103446887-103447125(-)$1	238	148	155	12.3888
AAACACA	chr6:139465125-139465367(+)$1	242	104	111	13.6851
AUAUACA	chr2:227742888-227743118(+)$1	230	71	78	12.7592
AUACACA	chr6:130170896-130171132(-)$1	236	105	112	16.7407
AUACACU	chr7:94631518-94631733(+)$1	215	66	73	12.1111
auucaca	chr3:109153021-109153256(+)$1	235	163	170	12.4814
AGACACA	chr7:133385296-133385519(+)$1	223	7	14	13.7777
auacacu	chr2:26573668-26573913(+)$1	245	118	125	12.1111
auacaca	chr14:78033803-78034033(-)$1	230	188	195	16.7407
auagaca	chr6:117864516-117864737(+)$1	221	50	57	12.4814

#otherMatches

#Struct PSSM
zzzzzzz	chr3:152166129-152166481(+)$1	352	51	58	13.1296
ffff]a]	chrX:17771130-17771384(+)$1	254	129	136	12.7592
:::::::	chr7:99374993-99375245(-)$1	252	101	108	12.1111
:::::::	chr12:51088192-51088471(+)$1	279	95	102	13.1296
^^dddd:	chrX:110945660-110945945(+)$1	285	120	127	13.6851
:::::::	chr16:27617699-27617976(+)$1	277	98	105	16.7407
iiiiiii	chr8:32486615-32486828(+)$1	213	128	135	12.2037
^^^^^^^	chr12:9847548-9847788(+)$1	240	57	64	13.1296
::EEEEE	chr8:121754083-121754355(-)$1	272	97	104	13.6851
:::::::	chr10:26799554-26799882(+)$1	328	110	117	13.6851
ddmmmmd	chr7:102995434-102995660(+)$1	226	28	35	13.0370
55dddd]	chr5:14817121-14817385(-)$1	264	42	49	12.3888
eeeeeoo	chr9:100840044-100840258(+)$1	214	81	88	12.4814
mmmeeee	chr16:85706615-85706880(+)$1	265	213	220	16.7407
ee^^^^^	chr22:41256789-41257061(+)$1	272	126	133	12.1111
:::::::	chr8:12842356-12842606(+)$1	250	105	112	16.7407
II::eee	chr6:12087411-12087633(+)$1	222	41	48	12.5740
vvvvvvb	chr2:46956796-46957044(+)$1	248	81	88	12.5740
:::JJJJ	chr11:46645289-46645530(+)$1	241	166	173	12.1111
===::::	chr3:15664554-15664773(+)$1	219	172	179	13.7777
qqqqqqq	chr3:15820246-15820488(-)$1	242	196	203	13.0370
ffffff4	chr12:51852888-51853102(+)$1	214	83	90	13.6851
FFFNNNN	chr5:58319412-58319682(-)$1	270	27	34	13.1296
dd:::::	chr12:62787769-62788029(+)$1	260	89	96	13.1296
===^^^^	chr10:28498258-28498489(-)$1	231	61	68	13.7777
======:	chr7:11081064-11081311(+)$1	247	40	47	13.1296
:::::::	chr7:33636555-33636826(+)$1	271	127	134	13.6851
:::::::	chr13:73364452-73364712(+)$1	260	108	115	13.6851
:::::::	chr9:78610550-78610811(+)$1	261	108	115	16.7407
JJJLLLD	chr3:156614835-156615070(+)$1	235	100	107	13.6851
=======	chr8:51109672-51109887(+)$1	215	183	190	12.7592
:::::::	chr9:125149941-125150157(+)$1	216	96	103	13.6851
ddddFFF	chrX:71817294-71817528(-)$1	234	193	200	13.7777
:eeeee!	chr3:171832627-171832841(+)$1	214	2	9	12.2037
"""dddd	chr2:63701755-63702024(-)$1	269	50	57	12.7592
bb]eeee	chr8:21860883-21861104(+)$1	221	149	156	13.7777
eee!!ff	chr2:44582963-44583238(-)$1	275	191	198	13.1296
FFFFFUU	chr12:73035481-73035695(+)$1	214	3	10	12.4814
^^^^^^^	chr17:61805375-61805606(-)$1	231	98	105	13.7777
C::::::	chr12:65109939-65110178(-)$1	239	18	25	13.6851
CCLLLEE	chr1:160546341-160546562(-)$1	221	39	46	16.7407
:::::::	chr8:120617562-120617815(-)$1	253	108	115	16.7407
dddhhhh	chr9:8612256-8612475(-)$1	219	172	179	13.1296
f[ccca[	chr1:8029002-8029308(+)$1	306	51	58	13.0370
=======	chr10:103446887-103447125(-)$1	238	148	155	12.3888
teeeeec	chr6:139465125-139465367(+)$1	242	104	111	13.6851
fffff33	chr2:227742888-227743118(+)$1	230	71	78	12.7592
>>>>>>>	chr6:130170896-130171132(-)$1	236	105	112	16.7407
ffff:bb	chr7:94631518-94631733(+)$1	215	66	73	12.1111
uuuuudd	chr3:109153021-109153256(+)$1	235	163	170	12.4814
!cccnnn	chr7:133385296-133385519(+)$1	223	7	14	13.7777
66666cc	chr2:26573668-26573913(+)$1	245	118	125	12.1111
::::ddd	chr14:78033803-78034033(-)$1	230	188	195	16.7407
gg::fff	chr6:117864516-117864737(+)$1	221	50	57	12.4814

#DB
.......	chr3:152166129-152166481(+)$1	1	51	58	13.1296
)))).).	chrX:17771130-17771384(+)$1	1	129	136	12.7592
.......	chr7:99374993-99375245(-)$1	1	101	108	12.1111
.......	chr12:51088192-51088471(+)$1	1	95	102	13.1296
..)))).	chrX:110945660-110945945(+)$1	1	120	127	13.6851
.......	chr16:27617699-27617976(+)$1	1	98	105	16.7407
)))))))	chr8:32486615-32486828(+)$1	1	128	135	12.2037
.......	chr12:9847548-9847788(+)$1	1	57	64	13.1296
..)))))	chr8:121754083-121754355(-)$1	1	97	104	13.6851
.......	chr10:26799554-26799882(+)$1	1	110	117	13.6851
((....)	chr7:102995434-102995660(+)$1	1	28	35	13.0370
..)))).	chr5:14817121-14817385(-)$1	1	42	49	12.3888
(((((..	chr9:100840044-100840258(+)$1	1	81	88	12.4814
...))))	chr16:85706615-85706880(+)$1	1	213	220	16.7407
((.....	chr22:41256789-41257061(+)$1	1	126	133	12.1111
.......	chr8:12842356-12842606(+)$1	1	105	112	16.7407
((..(((	chr6:12087411-12087633(+)$1	1	41	48	12.5740
......)	chr2:46956796-46957044(+)$1	1	81	88	12.5740
...((((	chr11:46645289-46645530(+)$1	1	166	173	12.1111
)))....	chr3:15664554-15664773(+)$1	1	172	179	13.7777
.......	chr3:15820246-15820488(-)$1	1	196	203	13.0370
)))))).	chr12:51852888-51853102(+)$1	1	83	90	13.6851
(((....	chr5:58319412-58319682(-)$1	1	27	34	13.1296
)).....	chr12:62787769-62788029(+)$1	1	89	96	13.1296
(((....	chr10:28498258-28498489(-)$1	1	61	68	13.7777
)))))).	chr7:11081064-11081311(+)$1	1	40	47	13.1296
.......	chr7:33636555-33636826(+)$1	1	127	134	13.6851
.......	chr13:73364452-73364712(+)$1	1	108	115	13.6851
.......	chr9:78610550-78610811(+)$1	1	108	115	16.7407
(((...(	chr3:156614835-156615070(+)$1	1	100	107	13.6851
)))))))	chr8:51109672-51109887(+)$1	1	183	190	12.7592
.......	chr9:125149941-125150157(+)$1	1	96	103	13.6851
)))))))	chrX:71817294-71817528(-)$1	1	193	200	13.7777
.(((((.	chr3:171832627-171832841(+)$1	1	2	9	12.2037
...((((	chr2:63701755-63702024(-)$1	1	50	57	12.7592
)).))))	chr8:21860883-21861104(+)$1	1	149	156	13.7777
(((..((	chr2:44582963-44583238(-)$1	1	191	198	13.1296
(((((..	chr12:73035481-73035695(+)$1	1	3	10	12.4814
.......	chr17:61805375-61805606(-)$1	1	98	105	13.7777
(......	chr12:65109939-65110178(-)$1	1	18	25	13.6851
((...((	chr1:160546341-160546562(-)$1	1	39	46	16.7407
.......	chr8:120617562-120617815(-)$1	1	108	115	16.7407
)))))))	chr9:8612256-8612475(-)$1	1	172	179	13.1296
(.((((.	chr1:8029002-8029308(+)$1	1	51	58	13.0370
(((((((	chr10:103446887-103447125(-)$1	1	148	155	12.3888
.))))))	chr6:139465125-139465367(+)$1	1	104	111	13.6851
)))))..	chr2:227742888-227743118(+)$1	1	71	78	12.7592
.......	chr6:130170896-130171132(-)$1	1	105	112	16.7407
)))).((	chr7:94631518-94631733(+)$1	1	66	73	12.1111
.....))	chr3:109153021-109153256(+)$1	1	163	170	12.4814
.(((...	chr7:133385296-133385519(+)$1	1	7	14	13.7777
.....))	chr2:26573668-26573913(+)$1	1	118	125	12.1111
....(((	chr14:78033803-78034033(-)$1	1	188	195	16.7407
))..(((	chr6:117864516-117864737(+)$1	1	50	57	12.4814

#PSSM
A : 0.51	a : 0.44	u : 0.03	
U : 0.40	u : 0.29	c : 0.07	G : 0.07	a : 0.05	A : 0.03	g : 0.03	C : 0.01	
A : 0.46	a : 0.44	C : 0.03	u : 0.03	U : 0.01	
c : 0.44	C : 0.42	U : 0.07	A : 0.01	a : 0.01	g : 0.01	
a : 0.48	A : 0.46	U : 0.03	C : 0.01	
c : 0.40	C : 0.38	A : 0.05	U : 0.03	u : 0.03	G : 0.03	a : 0.01	g : 0.01	
A : 0.49	a : 0.46	U : 0.01	u : 0.01	

#score	733.4444444444442
#seq	54
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m3_run1.nuc.txt

#NT
UCCAGG	chr6:26124610-26124889(+)$1	279	184	190	15.1698
UCCAGG	chr2:131813031-131813287(-)$1	256	14	20	15.1698
UCCAGG	chr1:26230078-26230319(-)$1	241	18	24	15.1698
UCCAGG	chrX:53576213-53576489(-)$1	276	18	24	15.1698
UCCAGG	chr2:37268227-37268495(-)$1	268	215	221	15.1698
UCCUGG	chr5:96101683-96101946(+)$1	263	146	152	12.0566
UCCAGG	chr6:26217471-26217733(+)$1	262	65	71	15.1698
UUCAGG	chr4:2896279-2896523(+)$1	244	24	30	11.3018
UCCAGC	chr1:151260669-151260910(+)$1	241	172	178	11.4905
UCCAGG	chr16:2817020-2817263(+)$1	243	43	49	15.1698
UCCAUG	chr8:48775946-48776187(-)$1	241	176	182	11.2075
UCCAGC	chr6:27858008-27858273(-)$1	265	76	82	11.4905
UCCAGC	chr16:56973860-56974130(+)$1	270	24	30	11.4905
UCCAUG	chr12:16516653-16516955(+)$1	302	280	286	11.2075
UCCAGG	chr5:179135213-179135456(+)$1	243	63	69	15.1698
UCCAGG	chr12:53854735-53855034(+)$1	299	79	85	15.1698
UCCUGG	chr17:1577815-1578077(-)$1	262	54	60	12.0566
UCCAGG	chr1:228645059-228645361(-)$1	302	177	183	15.1698
UUCAGG	chr9:35102652-35102891(-)$1	239	6	12	11.3018
UCCAUG	chr16:30081042-30081349(+)$1	307	28	34	11.2075
UCCUGG	chr8:144995306-144995546(-)$1	240	82	88	12.0566
UUCAGG	chr15:40328532-40328771(-)$1	239	65	71	11.3018
UCCAUG	chr14:74009781-74010054(+)$1	273	29	35	11.2075
UCCAGG	chr15:90814550-90814794(+)$1	244	234	240	15.1698
UCCAGG	chr4:83748620-83748882(-)$1	262	240	246	15.1698
UUCAGG	chr4:174253202-174253443(-)$1	241	49	55	11.3018
UCCAGG	chr1:153920641-153920908(-)$1	267	113	119	15.1698
UCCAGG	chr10:74834534-74834780(-)$1	246	192	198	15.1698
UCCAGG	chr6:31701514-31701805(-)$1	291	62	68	15.1698
UUCAGG	chr10:124919862-124920123(+)$1	261	13	19	11.3018
UCCAGC	chr5:74654429-74654712(+)$1	283	201	207	11.4905
UCCAGG	chr14:23745516-23745759(-)$1	243	197	203	15.1698
UCCAGC	chr6:44219148-44219411(+)$1	263	66	72	11.4905
UCCUGG	chr16:90001199-90001488(+)$1	289	6	12	12.0566
UCCAGG	chr8:145625488-145625755(-)$1	267	80	86	15.1698
UCCAGC	chr9:130582102-130582374(-)$1	272	151	157	11.4905
UCCAGG	chr1:120458002-120458276(-)$1	274	154	160	15.1698
UCCUGG	chr11:16774268-16774493(+)$1	225	49	55	12.0566
UCCAGG	chr6:26204737-26205129(+)$1	392	214	220	15.1698
UCCAAG	chr3:47957918-47958197(-)$1	279	57	63	11.1132
UCCAGG	chr5:81571935-81572173(-)$1	238	94	100	15.1698
UCCUGG	chr16:56500702-56500977(+)$1	275	74	80	12.0566
UCCUGG	chr3:48638311-48638601(-)$1	290	106	112	12.0566
UCCAGG	chr9:131386528-131386766(+)$1	238	7	13	15.1698
UCCUGG	chr16:18553831-18554101(-)$1	270	52	58	12.0566
UCCAGC	chr22:32108214-32108456(-)$1	242	19	25	11.4905
UCCUGG	chr8:104052941-104053194(+)$1	253	149	155	12.0566
UUCAGG	chr18:21095811-21096053(+)$1	242	3	9	11.3018
UCCUGG	chr6:153296260-153296509(-)$1	249	140	146	12.0566
UCCAAG	chr19:52719156-52719422(+)$1	266	30	36	11.1132
UCCAGG	chr1:27620440-27620679(+)$1	239	229	235	15.1698
UCCAGG	chr2:131414599-131414840(+)$1	241	129	135	15.1698

#otherMatches

#Struct PSSM
oooooc	chr18:47015673-47015921(-)$1	248	35	41	11.1132
eee]dd	chr6:26124610-26124889(+)$1	279	184	190	15.1698
[eeeee	chr2:131813031-131813287(-)$1	256	14	20	15.1698
FFFFFF	chr1:26230078-26230319(-)$1	241	18	24	15.1698
FF::CC	chrX:53576213-53576489(-)$1	276	18	24	15.1698
EEEJJJ	chr2:37268227-37268495(-)$1	268	215	221	15.1698
EEEddd	chr5:96101683-96101946(+)$1	263	146	152	12.0566
TTEEEE	chr6:26217471-26217733(+)$1	262	65	71	15.1698
JJJJJJ	chr4:2896279-2896523(+)$1	244	24	30	11.3018
C}GGGG	chr1:151260669-151260910(+)$1	241	172	178	11.4905
cc[ccc	chr16:2817020-2817263(+)$1	243	43	49	15.1698
e####b	chr8:48775946-48776187(-)$1	241	176	182	11.2075
mbb:ff	chr6:27858008-27858273(-)$1	265	76	82	11.4905
GGGGGN	chr16:56973860-56974130(+)$1	270	24	30	11.4905
fffffB	chr12:16516653-16516955(+)$1	302	280	286	11.2075
$$dddd	chr5:179135213-179135456(+)$1	243	63	69	15.1698
$$$$gg	chr12:53854735-53855034(+)$1	299	79	85	15.1698
f!!ddd	chr17:1577815-1578077(-)$1	262	54	60	12.0566
''''dd	chr1:228645059-228645361(-)$1	302	177	183	15.1698
ee[ddd	chr9:35102652-35102891(-)$1	239	6	12	11.3018
C{A{EE	chr16:30081042-30081349(+)$1	307	28	34	11.2075
dddddd	chr8:144995306-144995546(-)$1	240	82	88	12.0566
ee!!==	chr15:40328532-40328771(-)$1	239	65	71	11.3018
IIIIII	chr14:74009781-74010054(+)$1	273	29	35	11.2075
@@@EEE	chr15:90814550-90814794(+)$1	244	234	240	15.1698
rrrrre	chr4:83748620-83748882(-)$1	262	240	246	15.1698
gmmmmg	chr4:174253202-174253443(-)$1	241	49	55	11.3018
eeeccc	chr1:153920641-153920908(-)$1	267	113	119	15.1698
:dddd'	chr10:74834534-74834780(-)$1	246	192	198	15.1698
cccmmm	chr6:31701514-31701805(-)$1	291	62	68	15.1698
GGGGGG	chr10:124919862-124920123(+)$1	261	13	19	11.3018
!bbooo	chr5:74654429-74654712(+)$1	283	201	207	11.4905
e]ccc]	chr14:23745516-23745759(-)$1	243	197	203	15.1698
eennnn	chr6:44219148-44219411(+)$1	263	66	72	11.4905
ddeeee	chr16:90001199-90001488(+)$1	289	6	12	12.0566
ddddff	chr8:145625488-145625755(-)$1	267	80	86	15.1698
f[bbdd	chr9:130582102-130582374(-)$1	272	151	157	11.4905
flllff	chr1:120458002-120458276(-)$1	274	154	160	15.1698
eeeeeo	chr11:16774268-16774493(+)$1	225	49	55	12.0566
bbffff	chr6:26204737-26205129(+)$1	392	214	220	15.1698
oeeeee	chr3:47957918-47958197(-)$1	279	57	63	11.1132
qqqqqq	chr5:81571935-81572173(-)$1	238	94	100	15.1698
nnnnbb	chr16:56500702-56500977(+)$1	275	74	80	12.0566
ddd[ee	chr3:48638311-48638601(-)$1	290	106	112	12.0566
HHHHHH	chr9:131386528-131386766(+)$1	238	7	13	15.1698
cc!!ff	chr16:18553831-18554101(-)$1	270	52	58	12.0566
e:::::	chr22:32108214-32108456(-)$1	242	19	25	11.4905
c::::G	chr8:104052941-104053194(+)$1	253	149	155	12.0566
C{DDDD	chr18:21095811-21096053(+)$1	242	3	9	11.3018
dddmmm	chr6:153296260-153296509(-)$1	249	140	146	12.0566
&&&&&e	chr19:52719156-52719422(+)$1	266	30	36	11.1132
DDD}EE	chr1:27620440-27620679(+)$1	239	229	235	15.1698
####ee	chr2:131414599-131414840(+)$1	241	129	135	15.1698

#DB
.....)	chr18:47015673-47015921(-)$1	1	35	41	11.1132
))).))	chr6:26124610-26124889(+)$1	1	184	190	15.1698
.(((((	chr2:131813031-131813287(-)$1	1	14	20	15.1698
((((((	chr1:26230078-26230319(-)$1	1	18	24	15.1698
((..((	chrX:53576213-53576489(-)$1	1	18	24	15.1698
))))))	chr2:37268227-37268495(-)$1	1	215	221	15.1698
)))(((	chr5:96101683-96101946(+)$1	1	146	152	12.0566
..((((	chr6:26217471-26217733(+)$1	1	65	71	15.1698
((((((	chr4:2896279-2896523(+)$1	1	24	30	11.3018
).))))	chr1:151260669-151260910(+)$1	1	172	178	11.4905
((.(((	chr16:2817020-2817263(+)$1	1	43	49	15.1698
(....(	chr8:48775946-48776187(-)$1	1	176	182	11.2075
.)).((	chr6:27858008-27858273(-)$1	1	76	82	11.4905
(((((.	chr16:56973860-56974130(+)$1	1	24	30	11.4905
))))))	chr12:16516653-16516955(+)$1	1	280	286	11.2075
..((((	chr5:179135213-179135456(+)$1	1	63	69	15.1698
....((	chr12:53854735-53855034(+)$1	1	79	85	15.1698
(..(((	chr17:1577815-1578077(-)$1	1	54	60	12.0566
....((	chr1:228645059-228645361(-)$1	1	177	183	15.1698
((.(((	chr9:35102652-35102891(-)$1	1	6	12	11.3018
(.(.((	chr16:30081042-30081349(+)$1	1	28	34	11.2075
((((((	chr8:144995306-144995546(-)$1	1	82	88	12.0566
((..((	chr15:40328532-40328771(-)$1	1	65	71	11.3018
((((((	chr14:74009781-74010054(+)$1	1	29	35	11.2075
...)))	chr15:90814550-90814794(+)$1	1	234	240	15.1698
.....)	chr4:83748620-83748882(-)$1	1	240	246	15.1698
(....)	chr4:174253202-174253443(-)$1	1	49	55	11.3018
((((((	chr1:153920641-153920908(-)$1	1	113	119	15.1698
.((((.	chr10:74834534-74834780(-)$1	1	192	198	15.1698
(((...	chr6:31701514-31701805(-)$1	1	62	68	15.1698
((((((	chr10:124919862-124920123(+)$1	1	13	19	11.3018
.((...	chr5:74654429-74654712(+)$1	1	201	207	11.4905
).))).	chr14:23745516-23745759(-)$1	1	197	203	15.1698
((....	chr6:44219148-44219411(+)$1	1	66	72	11.4905
((((((	chr16:90001199-90001488(+)$1	1	6	12	12.0566
))))((	chr8:145625488-145625755(-)$1	1	80	86	15.1698
(.((((	chr9:130582102-130582374(-)$1	1	151	157	11.4905
(...))	chr1:120458002-120458276(-)$1	1	154	160	15.1698
(((((.	chr11:16774268-16774493(+)$1	1	49	55	12.0566
))))))	chr6:26204737-26205129(+)$1	1	214	220	15.1698
.)))))	chr3:47957918-47958197(-)$1	1	57	63	11.1132
......	chr5:81571935-81572173(-)$1	1	94	100	15.1698
....))	chr16:56500702-56500977(+)$1	1	74	80	12.0566
(((.((	chr3:48638311-48638601(-)$1	1	106	112	12.0566
((((((	chr9:131386528-131386766(+)$1	1	7	13	15.1698
((..((	chr16:18553831-18554101(-)$1	1	52	58	12.0566
).....	chr22:32108214-32108456(-)$1	1	19	25	11.4905
)....)	chr8:104052941-104053194(+)$1	1	149	155	12.0566
(.((((	chr18:21095811-21096053(+)$1	1	3	9	11.3018
(((...	chr6:153296260-153296509(-)$1	1	140	146	12.0566
.....(	chr19:52719156-52719422(+)$1	1	30	36	11.1132
))).))	chr1:27620440-27620679(+)$1	1	229	235	15.1698
....((	chr2:131414599-131414840(+)$1	1	129	135	15.1698

#PSSM
U : 0.99	
C : 0.88	U : 0.11	
C : 0.99	
A : 0.81	U : 0.18	
G : 0.86	U : 0.07	A : 0.05	
G : 0.86	C : 0.13	

#score	695.88679245283
#seq	53
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m3_run2.nuc.txt

#NT
UGU	chr17:27278246-27278462(-)$1	216	172	175	9.0000
UGU	chr1:53514739-53514961(+)$1	222	3	6	9.0000
UGU	chr2:109125665-109125897(+)$1	232	18	21	9.0000
UGU	chr5:79945841-79946065(-)$1	224	23	26	9.0000
UGU	chr3:120407336-120407554(-)$1	218	167	170	9.0000
UGU	chr1:40145515-40145734(-)$1	219	16	19	9.0000
UGU	chr22:49147084-49147308(+)$1	224	13	16	9.0000
UGU	chrX:73954701-73954921(+)$1	220	41	44	9.0000
UGU	chr8:56442510-56442741(+)$1	231	8	11	9.0000
UGU	chr14:102393360-102393577(+)$1	217	35	38	9.0000
UGU	chr7:29960697-29960921(-)$1	224	52	55	9.0000
UGU	chr17:40847552-40847819(+)$1	267	137	140	9.0000
UGU	chr5:172332105-172332325(-)$1	220	4	7	9.0000
UGU	chr2:203424634-203424851(+)$1	217	3	6	9.0000
UGU	chr7:140396413-140396637(+)$1	224	39	42	9.0000
UGU	chr3:127407865-127408081(-)$1	216	5	8	9.0000
UGU	chr12:110784444-110784666(+)$1	222	24	27	9.0000
UGU	chr1:2460619-2460836(-)$1	217	98	101	9.0000
UGU	chr2:204301084-204301308(+)$1	224	215	218	9.0000
UGU	chr10:81142531-81142750(-)$1	219	55	58	9.0000
UGU	chr18:44100313-44100531(+)$1	218	26	29	9.0000
UGU	chr10:93715-93963(-)$1	248	10	13	9.0000
UGU	chr18:9282703-9282924(+)$1	221	45	48	9.0000
UGU	chr1:205241237-205241460(+)$1	223	35	38	9.0000
UGU	chr4:3249476-3249691(+)$1	215	102	105	9.0000
UGU	chr7:137330130-137330347(+)$1	217	125	128	9.0000
UGU	chr11:85669715-85669943(-)$1	228	87	90	9.0000
UGU	chr22:42980839-42981071(-)$1	232	19	22	9.0000
UGU	chr21:46269671-46269887(-)$1	216	0	3	9.0000
UGU	chr19:18778530-18778766(+)$1	236	2	5	9.0000
UGU	chr8:19262147-19262377(-)$1	230	82	85	9.0000
UGU	chr5:179157676-179157897(+)$1	221	36	39	9.0000
UGU	chr15:75074767-75074993(+)$1	226	44	47	9.0000
UGU	chr9:72332902-72333121(-)$1	219	21	24	9.0000
UGU	chr15:80886247-80886463(+)$1	216	16	19	9.0000
UGU	chr14:94843714-94843929(-)$1	215	150	153	9.0000
UGU	chr8:17014927-17015154(+)$1	227	28	31	9.0000
UGU	chr3:150182509-150182732(+)$1	223	124	127	9.0000
UGU	chr1:148347159-148347378(-)$1	219	55	58	9.0000
UGU	chr11:65320575-65320794(-)$1	219	9	12	9.0000
UGU	chr19:50129030-50129246(+)$1	216	43	46	9.0000
UGU	chr16:22357588-22357803(-)$1	215	19	22	9.0000
UGU	chr3:141164953-141165171(-)$1	218	149	152	9.0000
UGU	chr5:89813791-89814007(-)$1	216	33	36	9.0000
UGU	chr17:38248212-38248430(-)$1	218	23	26	9.0000
UGU	chr10:133772823-133773047(+)$1	224	3	6	9.0000
UGU	chr19:45594208-45594436(+)$1	228	98	101	9.0000
UGU	chr2:135713254-135713492(+)$1	238	27	30	9.0000
UGU	chr7:73151269-73151487(+)$1	218	24	27	9.0000
UGU	chr22:33256161-33256390(+)$1	229	11	14	9.0000
UGU	chr8:144391453-144391675(-)$1	222	75	78	9.0000
UGU	chr19:44084614-44084830(-)$1	216	23	26	9.0000
UGU	chr16:15688688-15688903(-)$1	215	7	10	9.0000
UGU	chr19:53731553-53731768(-)$1	215	22	25	9.0000
UGU	chr2:42983009-42983226(+)$1	217	75	78	9.0000
UGU	chr3:160786948-160787164(-)$1	216	61	64	9.0000
UGU	chr2:210863738-210863961(+)$1	223	36	39	9.0000
UGU	chr1:6196486-6196706(-)$1	220	90	93	9.0000
UGU	chr6:109004126-109004367(+)$1	241	8	11	9.0000
UGU	chr11:121501013-121501228(+)$1	215	16	19	9.0000
UGU	chr5:112162725-112162943(+)$1	218	30	33	9.0000
UGU	chr16:4506286-4506511(+)$1	225	41	44	9.0000
UGU	chr4:95588885-95589108(+)$1	223	32	35	9.0000
UGU	chr12:56522207-56522433(+)$1	226	96	99	9.0000
UGU	chr17:26941810-26942029(-)$1	219	6	9	9.0000
UGU	chr16:56624811-56625042(+)$1	231	65	68	9.0000
UGU	chr3:112732725-112732946(-)$1	221	20	23	9.0000
UGU	chr8:26513459-26513703(+)$1	244	94	97	9.0000
UGU	chr15:66180796-66181018(+)$1	222	15	18	9.0000
UGU	chr5:70197527-70197743(+)$1	216	3	6	9.0000
UGU	chr11:11977768-11977989(+)$1	221	119	122	9.0000
UGU	chr17:45681239-45681470(+)$1	231	9	12	9.0000
UGU	chr8:90958378-90958601(-)$1	223	32	35	9.0000
UGU	chr19:306412-306628(-)$1	216	2	5	9.0000
UGU	chr4:139086690-139086908(+)$1	218	38	41	9.0000
UGU	chr1:205501008-205501241(+)$1	233	23	26	9.0000
UGU	chr17:18112311-18112533(+)$1	222	15	18	9.0000
UGU	chr14:39501226-39501453(-)$1	227	51	54	9.0000
UGU	chr9:108310374-108310595(-)$1	221	194	197	9.0000
ugu	chr11:101870858-101871075(-)$1	217	3	6	9.0000
UGU	chr1:155646310-155646548(-)$1	238	138	141	9.0000
UGU	chr20:3912969-3913198(-)$1	229	21	24	9.0000
UGU	chr19:36606273-36606488(+)$1	215	142	145	9.0000
UGU	chr8:142152515-142152737(+)$1	222	55	58	9.0000
UGU	chr21:42218773-42219018(-)$1	245	216	219	9.0000
UGU	chr1:86118103-86118323(-)$1	220	13	16	9.0000
UGU	chr4:185615900-185616115(+)$1	215	54	57	9.0000
UGU	chr15:42433994-42434216(-)$1	222	56	59	9.0000
UGU	chr11:130013933-130014157(+)$1	224	12	15	9.0000
UGU	chr12:47160174-47160389(-)$1	215	70	73	9.0000
UGU	chr19:10202868-10203083(-)$1	215	75	78	9.0000
UGU	chr4:184940501-184940723(+)$1	222	45	48	9.0000
UGU	chr2:233632837-233633055(+)$1	218	32	35	9.0000
UGU	chr2:69701643-69701867(-)$1	224	23	26	9.0000

#otherMatches

#Struct PSSM
bb]	chr19:46844728-46844953(+)$1	225	46	49	9.0000
HHH	chr17:27278246-27278462(-)$1	216	172	175	9.0000
DDL	chr1:53514739-53514961(+)$1	222	3	6	9.0000
fff	chr2:109125665-109125897(+)$1	232	18	21	9.0000
eee	chr5:79945841-79946065(-)$1	224	23	26	9.0000
ee!	chr3:120407336-120407554(-)$1	218	167	170	9.0000
###	chr1:40145515-40145734(-)$1	219	16	19	9.0000
iii	chr22:49147084-49147308(+)$1	224	13	16	9.0000
dee	chrX:73954701-73954921(+)$1	220	41	44	9.0000
eee	chr8:56442510-56442741(+)$1	231	8	11	9.0000
rrr	chr14:102393360-102393577(+)$1	217	35	38	9.0000
hhh	chr7:29960697-29960921(-)$1	224	52	55	9.0000
ddd	chr17:40847552-40847819(+)$1	267	137	140	9.0000
:BB	chr5:172332105-172332325(-)$1	220	4	7	9.0000
DD{	chr2:203424634-203424851(+)$1	217	3	6	9.0000
ccc	chr7:140396413-140396637(+)$1	224	39	42	9.0000
JJJ	chr3:127407865-127408081(-)$1	216	5	8	9.0000
eee	chr12:110784444-110784666(+)$1	222	24	27	9.0000
$$$	chr1:2460619-2460836(-)$1	217	98	101	9.0000
GGY	chr2:204301084-204301308(+)$1	224	215	218	9.0000
d]b	chr10:81142531-81142750(-)$1	219	55	58	9.0000
DDK	chr18:44100313-44100531(+)$1	218	26	29	9.0000
FF{	chr10:93715-93963(-)$1	248	10	13	9.0000
:::	chr18:9282703-9282924(+)$1	221	45	48	9.0000
ddd	chr1:205241237-205241460(+)$1	223	35	38	9.0000
fff	chr4:3249476-3249691(+)$1	215	102	105	9.0000
EEE	chr7:137330130-137330347(+)$1	217	125	128	9.0000
qee	chr11:85669715-85669943(-)$1	228	87	90	9.0000
ee$	chr22:42980839-42981071(-)$1	232	19	22	9.0000
:::	chr21:46269671-46269887(-)$1	216	0	3	9.0000
:bb	chr19:18778530-18778766(+)$1	236	2	5	9.0000
ddd	chr8:19262147-19262377(-)$1	230	82	85	9.0000
$bb	chr5:179157676-179157897(+)$1	221	36	39	9.0000
:cc	chr15:75074767-75074993(+)$1	226	44	47	9.0000
eee	chr9:72332902-72333121(-)$1	219	21	24	9.0000
:::	chr15:80886247-80886463(+)$1	216	16	19	9.0000
obb	chr14:94843714-94843929(-)$1	215	150	153	9.0000
ddd	chr8:17014927-17015154(+)$1	227	28	31	9.0000
ggg	chr3:150182509-150182732(+)$1	223	124	127	9.0000
mmm	chr1:148347159-148347378(-)$1	219	55	58	9.0000
:::	chr11:65320575-65320794(-)$1	219	9	12	9.0000
:::	chr19:50129030-50129246(+)$1	216	43	46	9.0000
:::	chr16:22357588-22357803(-)$1	215	19	22	9.0000
hh!	chr3:141164953-141165171(-)$1	218	149	152	9.0000
===	chr5:89813791-89814007(-)$1	216	33	36	9.0000
[ee	chr17:38248212-38248430(-)$1	218	23	26	9.0000
:::	chr10:133772823-133773047(+)$1	224	3	6	9.0000
fff	chr19:45594208-45594436(+)$1	228	98	101	9.0000
%%%	chr2:135713254-135713492(+)$1	238	27	30	9.0000
B{G	chr7:73151269-73151487(+)$1	218	24	27	9.0000
nnn	chr22:33256161-33256390(+)$1	229	11	14	9.0000
2a]	chr8:144391453-144391675(-)$1	222	75	78	9.0000
:dd	chr19:44084614-44084830(-)$1	216	23	26	9.0000
===	chr16:15688688-15688903(-)$1	215	7	10	9.0000
nnf	chr19:53731553-53731768(-)$1	215	22	25	9.0000
bb!	chr2:42983009-42983226(+)$1	217	75	78	9.0000
f[a	chr3:160786948-160787164(-)$1	216	61	64	9.0000
:CC	chr2:210863738-210863961(+)$1	223	36	39	9.0000
:::	chr1:6196486-6196706(-)$1	220	90	93	9.0000
CFF	chr6:109004126-109004367(+)$1	241	8	11	9.0000
D{C	chr11:121501013-121501228(+)$1	215	16	19	9.0000
HHH	chr5:112162725-112162943(+)$1	218	30	33	9.0000
GG:	chr16:4506286-4506511(+)$1	225	41	44	9.0000
epp	chr4:95588885-95589108(+)$1	223	32	35	9.0000
mmm	chr12:56522207-56522433(+)$1	226	96	99	9.0000
hhh	chr17:26941810-26942029(-)$1	219	6	9	9.0000
iii	chr16:56624811-56625042(+)$1	231	65	68	9.0000
{CC	chr3:112732725-112732946(-)$1	221	20	23	9.0000
c[d	chr8:26513459-26513703(+)$1	244	94	97	9.0000
FFF	chr15:66180796-66181018(+)$1	222	15	18	9.0000
B{B	chr5:70197527-70197743(+)$1	216	3	6	9.0000
eef	chr11:11977768-11977989(+)$1	221	119	122	9.0000
fff	chr17:45681239-45681470(+)$1	231	9	12	9.0000
qff	chr8:90958378-90958601(-)$1	223	32	35	9.0000
:ee	chr19:306412-306628(-)$1	216	2	5	9.0000
EEE	chr4:139086690-139086908(+)$1	218	38	41	9.0000
{FF	chr1:205501008-205501241(+)$1	233	23	26	9.0000
mcc	chr17:18112311-18112533(+)$1	222	15	18	9.0000
DD{	chr14:39501226-39501453(-)$1	227	51	54	9.0000
fff	chr9:108310374-108310595(-)$1	221	194	197	9.0000
:::	chr11:101870858-101871075(-)$1	217	3	6	9.0000
E||	chr1:155646310-155646548(-)$1	238	138	141	9.0000
nne	chr20:3912969-3913198(-)$1	229	21	24	9.0000
ddd	chr19:36606273-36606488(+)$1	215	142	145	9.0000
FFF	chr8:142152515-142152737(+)$1	222	55	58	9.0000
EEE	chr21:42218773-42219018(-)$1	245	216	219	9.0000
ggg	chr1:86118103-86118323(-)$1	220	13	16	9.0000
:a[	chr4:185615900-185616115(+)$1	215	54	57	9.0000
b[d	chr15:42433994-42434216(-)$1	222	56	59	9.0000
&&&	chr11:130013933-130014157(+)$1	224	12	15	9.0000
ddd	chr12:47160174-47160389(-)$1	215	70	73	9.0000
ooo	chr19:10202868-10203083(-)$1	215	75	78	9.0000
ddd	chr4:184940501-184940723(+)$1	222	45	48	9.0000
[ee	chr2:233632837-233633055(+)$1	218	32	35	9.0000
ddd	chr2:69701643-69701867(-)$1	224	23	26	9.0000

#DB
)).	chr19:46844728-46844953(+)$1	1	46	49	9.0000
)))	chr17:27278246-27278462(-)$1	1	172	175	9.0000
((.	chr1:53514739-53514961(+)$1	1	3	6	9.0000
(((	chr2:109125665-109125897(+)$1	1	18	21	9.0000
(((	chr5:79945841-79946065(-)$1	1	23	26	9.0000
((.	chr3:120407336-120407554(-)$1	1	167	170	9.0000
...	chr1:40145515-40145734(-)$1	1	16	19	9.0000
(((	chr22:49147084-49147308(+)$1	1	13	16	9.0000
)((	chrX:73954701-73954921(+)$1	1	41	44	9.0000
(((	chr8:56442510-56442741(+)$1	1	8	11	9.0000
...	chr14:102393360-102393577(+)$1	1	35	38	9.0000
)))	chr7:29960697-29960921(-)$1	1	52	55	9.0000
)))	chr17:40847552-40847819(+)$1	1	137	140	9.0000
.((	chr5:172332105-172332325(-)$1	1	4	7	9.0000
((.	chr2:203424634-203424851(+)$1	1	3	6	9.0000
)))	chr7:140396413-140396637(+)$1	1	39	42	9.0000
(((	chr3:127407865-127408081(-)$1	1	5	8	9.0000
(((	chr12:110784444-110784666(+)$1	1	24	27	9.0000
...	chr1:2460619-2460836(-)$1	1	98	101	9.0000
)).	chr2:204301084-204301308(+)$1	1	215	218	9.0000
).)	chr10:81142531-81142750(-)$1	1	55	58	9.0000
((.	chr18:44100313-44100531(+)$1	1	26	29	9.0000
((.	chr10:93715-93963(-)$1	1	10	13	9.0000
...	chr18:9282703-9282924(+)$1	1	45	48	9.0000
)))	chr1:205241237-205241460(+)$1	1	35	38	9.0000
(((	chr4:3249476-3249691(+)$1	1	102	105	9.0000
(((	chr7:137330130-137330347(+)$1	1	125	128	9.0000
.))	chr11:85669715-85669943(-)$1	1	87	90	9.0000
((.	chr22:42980839-42981071(-)$1	1	19	22	9.0000
...	chr21:46269671-46269887(-)$1	1	0	3	9.0000
.((	chr19:18778530-18778766(+)$1	1	2	5	9.0000
)))	chr8:19262147-19262377(-)$1	1	82	85	9.0000
.((	chr5:179157676-179157897(+)$1	1	36	39	9.0000
.((	chr15:75074767-75074993(+)$1	1	44	47	9.0000
(((	chr9:72332902-72333121(-)$1	1	21	24	9.0000
...	chr15:80886247-80886463(+)$1	1	16	19	9.0000
.))	chr14:94843714-94843929(-)$1	1	150	153	9.0000
(((	chr8:17014927-17015154(+)$1	1	28	31	9.0000
)))	chr3:150182509-150182732(+)$1	1	124	127	9.0000
...	chr1:148347159-148347378(-)$1	1	55	58	9.0000
...	chr11:65320575-65320794(-)$1	1	9	12	9.0000
...	chr19:50129030-50129246(+)$1	1	43	46	9.0000
...	chr16:22357588-22357803(-)$1	1	19	22	9.0000
((.	chr3:141164953-141165171(-)$1	1	149	152	9.0000
(((	chr5:89813791-89814007(-)$1	1	33	36	9.0000
.((	chr17:38248212-38248430(-)$1	1	23	26	9.0000
...	chr10:133772823-133773047(+)$1	1	3	6	9.0000
(((	chr19:45594208-45594436(+)$1	1	98	101	9.0000
...	chr2:135713254-135713492(+)$1	1	27	30	9.0000
(.(	chr7:73151269-73151487(+)$1	1	24	27	9.0000
...	chr22:33256161-33256390(+)$1	1	11	14	9.0000
.).	chr8:144391453-144391675(-)$1	1	75	78	9.0000
.((	chr19:44084614-44084830(-)$1	1	23	26	9.0000
(((	chr16:15688688-15688903(-)$1	1	7	10	9.0000
..)	chr19:53731553-53731768(-)$1	1	22	25	9.0000
((.	chr2:42983009-42983226(+)$1	1	75	78	9.0000
(.(	chr3:160786948-160787164(-)$1	1	61	64	9.0000
.((	chr2:210863738-210863961(+)$1	1	36	39	9.0000
...	chr1:6196486-6196706(-)$1	1	90	93	9.0000
(((	chr6:109004126-109004367(+)$1	1	8	11	9.0000
(.(	chr11:121501013-121501228(+)$1	1	16	19	9.0000
(((	chr5:112162725-112162943(+)$1	1	30	33	9.0000
((.	chr16:4506286-4506511(+)$1	1	41	44	9.0000
(..	chr4:95588885-95589108(+)$1	1	32	35	9.0000
...	chr12:56522207-56522433(+)$1	1	96	99	9.0000
(((	chr17:26941810-26942029(-)$1	1	6	9	9.0000
(((	chr16:56624811-56625042(+)$1	1	65	68	9.0000
.((	chr3:112732725-112732946(-)$1	1	20	23	9.0000
(.(	chr8:26513459-26513703(+)$1	1	94	97	9.0000
(((	chr15:66180796-66181018(+)$1	1	15	18	9.0000
(.(	chr5:70197527-70197743(+)$1	1	3	6	9.0000
)))	chr11:11977768-11977989(+)$1	1	119	122	9.0000
(((	chr17:45681239-45681470(+)$1	1	9	12	9.0000
.))	chr8:90958378-90958601(-)$1	1	32	35	9.0000
.((	chr19:306412-306628(-)$1	1	2	5	9.0000
(((	chr4:139086690-139086908(+)$1	1	38	41	9.0000
.((	chr1:205501008-205501241(+)$1	1	23	26	9.0000
.))	chr17:18112311-18112533(+)$1	1	15	18	9.0000
((.	chr14:39501226-39501453(-)$1	1	51	54	9.0000
(((	chr9:108310374-108310595(-)$1	1	194	197	9.0000
...	chr11:101870858-101871075(-)$1	1	3	6	9.0000
)..	chr1:155646310-155646548(-)$1	1	138	141	9.0000
..)	chr20:3912969-3913198(-)$1	1	21	24	9.0000
(((	chr19:36606273-36606488(+)$1	1	142	145	9.0000
(((	chr8:142152515-142152737(+)$1	1	55	58	9.0000
)))	chr21:42218773-42219018(-)$1	1	216	219	9.0000
(((	chr1:86118103-86118323(-)$1	1	13	16	9.0000
.(.	chr4:185615900-185616115(+)$1	1	54	57	9.0000
(.(	chr15:42433994-42434216(-)$1	1	56	59	9.0000
...	chr11:130013933-130014157(+)$1	1	12	15	9.0000
)))	chr12:47160174-47160389(-)$1	1	70	73	9.0000
...	chr19:10202868-10203083(-)$1	1	75	78	9.0000
)))	chr4:184940501-184940723(+)$1	1	45	48	9.0000
.((	chr2:233632837-233633055(+)$1	1	32	35	9.0000
)))	chr2:69701643-69701867(-)$1	1	23	26	9.0000

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

#score	855.0000000000002
#seq	95
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m2_run2.nuc.txt

#NT
CCUU	chr7:155569245-155569491(+)$1	246	4	8	11.9999
CCUU	chr6:27777728-27777981(+)$1	253	28	32	11.9999
CCUU	chr1:156280711-156280961(-)$1	250	81	85	11.9999
CCUU	chr15:83685904-83686150(-)$1	246	167	171	11.9999
CCUU	chr12:54631923-54632180(-)$1	257	59	63	11.9999
CCUU	chr11:625056-625284(+)$1	228	208	212	11.9999
CCUU	chr16:74486634-74486864(-)$1	230	22	26	11.9999
CCUU	chr10:99218312-99218542(-)$1	230	193	197	11.9999
CCUU	chr2:54093859-54094105(-)$1	246	144	148	11.9999
CCUU	chr8:98864105-98864341(+)$1	236	11	15	11.9999
CCUU	chr1:19426023-19426251(-)$1	228	11	15	11.9999
CCUU	chr11:118893971-118894252(+)$1	281	222	226	11.9999
CCUU	chr10:98336421-98336667(-)$1	246	22	26	11.9999
CCUU	chr12:120933832-120934079(+)$1	247	176	180	11.9999
CCUU	chr9:125865459-125865687(+)$1	228	55	59	11.9999
CCUU	chr1:25894379-25894623(+)$1	244	185	189	11.9999
CCUU	chr1:7840436-7840668(+)$1	232	32	36	11.9999
CCUU	chr19:2476025-2476271(+)$1	246	4	8	11.9999
CCUU	chr17:73820591-73820823(+)$1	232	212	216	11.9999
CCUU	chr17:58524833-58525079(-)$1	246	97	101	11.9999
CCUU	chr7:29962959-29963184(-)$1	225	200	204	11.9999
CCUU	chr11:45168286-45168515(-)$1	229	86	90	11.9999
CCUU	chr4:6644231-6644469(+)$1	238	20	24	11.9999
CCUU	chr15:44853879-44854104(+)$1	225	66	70	11.9999
CCUU	chr6:74363556-74363779(-)$1	223	127	131	11.9999
CCUU	chr14:73578287-73578526(+)$1	239	71	75	11.9999
CCUU	chr11:134038366-134038597(-)$1	231	49	53	11.9999
CCUU	chrX:152000085-152000312(-)$1	227	32	36	11.9999
CCUU	chr15:43280981-43281211(-)$1	230	5	9	11.9999
CCUU	chr16:30103837-30104070(-)$1	233	193	197	11.9999
CCUU	chr11:77043726-77043958(-)$1	232	47	51	11.9999
CCUU	chr5:180670670-180670924(-)$1	254	141	145	11.9999
CCUU	chr14:52118707-52118930(+)$1	223	34	38	11.9999
CCUU	chr1:19545512-19545739(-)$1	227	79	83	11.9999
CCUU	chr17:27237249-27237479(-)$1	230	137	141	11.9999
CCUU	chr17:76201987-76202219(+)$1	232	166	170	11.9999
CCUU	chr10:94267252-94267482(-)$1	230	47	51	11.9999
CCUU	chr18:77663278-77663506(-)$1	228	126	130	11.9999
CCUU	chr1:249105082-249105312(-)$1	230	183	187	11.9999
CCUU	chr1:227843827-227844060(+)$1	233	1	5	11.9999
CCUU	chr2:220040863-220041093(-)$1	230	7	11	11.9999
ccuu	chr17:38144862-38145113(+)$1	251	27	31	11.9999
CCUU	chr16:29822024-29822278(+)$1	254	75	79	11.9999
CCUU	chr19:47112399-47112701(+)$1	302	183	187	11.9999
CCUU	chrX:135579705-135579960(+)$1	255	62	66	11.9999
CCUU	chr17:4173182-4173419(-)$1	237	104	108	11.9999
CCUU	chr11:75283161-75283416(+)$1	255	59	63	11.9999
CCUU	chr17:38146257-38146509(+)$1	252	147	151	11.9999
CCUU	chr10:72184349-72184574(+)$1	225	137	141	11.9999
CCUU	chr9:34636944-34637176(-)$1	232	18	22	11.9999
CCUU	chr11:66053127-66053356(-)$1	229	133	137	11.9999
CCUU	chr1:26227241-26227482(-)$1	241	7	11	11.9999
CCUU	chr10:129923836-129924088(-)$1	252	21	25	11.9999
CCUU	chr19:5785561-5785802(-)$1	241	176	180	11.9999
CCUU	chr19:6413468-6413705(-)$1	237	97	101	11.9999
CCUU	chr2:97476747-97476975(+)$1	228	17	21	11.9999
CCUU	chr16:2128963-2129204(+)$1	241	1	5	11.9999
CCUU	chr1:235714292-235714542(-)$1	250	49	53	11.9999
CCUU	chr10:105153950-105154181(-)$1	231	171	175	11.9999
CCUU	chr8:37917355-37917586(+)$1	231	142	146	11.9999
CCUU	chr11:75111334-75111584(+)$1	250	1	5	11.9999
CCUU	chr11:134027766-134028000(-)$1	234	132	136	11.9999
CCUU	chr3:184049236-184049467(+)$1	231	8	12	11.9999
CCUU	chr16:58554679-58554907(-)$1	228	120	124	11.9999
CCUU	chr2:85770809-85771041(+)$1	232	95	99	11.9999
CCUU	chr1:54683809-54684057(+)$1	248	230	234	11.9999
CCUU	chr14:67708060-67708287(-)$1	227	113	117	11.9999
CCUU	chr11:3877235-3877469(+)$1	234	103	107	11.9999
CCUU	chr7:6048817-6049064(+)$1	247	138	142	11.9999
CCUU	chr11:57439406-57439636(+)$1	230	25	29	11.9999
CCUU	chr17:77756026-77756258(+)$1	232	0	4	11.9999

#otherMatches

#Struct PSSM
:ggg	chr8:56986921-56987159(-)$1	238	89	93	11.9999
:::E	chr7:155569245-155569491(+)$1	246	4	8	11.9999
HHHH	chr6:27777728-27777981(+)$1	253	28	32	11.9999
ffff	chr1:156280711-156280961(-)$1	250	81	85	11.9999
666c	chr15:83685904-83686150(-)$1	246	167	171	11.9999
::::	chr12:54631923-54632180(-)$1	257	59	63	11.9999
iiii	chr11:625056-625284(+)$1	228	208	212	11.9999
GGGG	chr16:74486634-74486864(-)$1	230	22	26	11.9999
dGGG	chr10:99218312-99218542(-)$1	230	193	197	11.9999
444c	chr2:54093859-54094105(-)$1	246	144	148	11.9999
bbmm	chr8:98864105-98864341(+)$1	236	11	15	11.9999
BBRR	chr1:19426023-19426251(-)$1	228	11	15	11.9999
]eee	chr11:118893971-118894252(+)$1	281	222	226	11.9999
rrrr	chr10:98336421-98336667(-)$1	246	22	26	11.9999
ggge	chr12:120933832-120934079(+)$1	247	176	180	11.9999
eeee	chr9:125865459-125865687(+)$1	228	55	59	11.9999
CC__	chr1:25894379-25894623(+)$1	244	185	189	11.9999
FFF{	chr1:7840436-7840668(+)$1	232	32	36	11.9999
hhhh	chr19:2476025-2476271(+)$1	246	4	8	11.9999
____	chr17:73820591-73820823(+)$1	232	212	216	11.9999
gggg	chr17:58524833-58525079(-)$1	246	97	101	11.9999
gggg	chr7:29962959-29963184(-)$1	225	200	204	11.9999
EEEE	chr11:45168286-45168515(-)$1	229	86	90	11.9999
gggl	chr4:6644231-6644469(+)$1	238	20	24	11.9999
eeee	chr15:44853879-44854104(+)$1	225	66	70	11.9999
DDDD	chr6:74363556-74363779(-)$1	223	127	131	11.9999
iiii	chr14:73578287-73578526(+)$1	239	71	75	11.9999
ffff	chr11:134038366-134038597(-)$1	231	49	53	11.9999
3fff	chrX:152000085-152000312(-)$1	227	32	36	11.9999
CCCM	chr15:43280981-43281211(-)$1	230	5	9	11.9999
}A}B	chr16:30103837-30104070(-)$1	233	193	197	11.9999
GGGG	chr11:77043726-77043958(-)$1	232	47	51	11.9999
BB::	chr5:180670670-180670924(-)$1	254	141	145	11.9999
OOOO	chr14:52118707-52118930(+)$1	223	34	38	11.9999
COOO	chr1:19545512-19545739(-)$1	227	79	83	11.9999
oooo	chr17:27237249-27237479(-)$1	230	137	141	11.9999
eee]	chr17:76201987-76202219(+)$1	232	166	170	11.9999
uuuu	chr10:94267252-94267482(-)$1	230	47	51	11.9999
f"""	chr18:77663278-77663506(-)$1	228	126	130	11.9999
DDDD	chr1:249105082-249105312(-)$1	230	183	187	11.9999
GGGG	chr1:227843827-227844060(+)$1	233	1	5	11.9999
C::D	chr2:220040863-220041093(-)$1	230	7	11	11.9999
DD::	chr17:38144862-38145113(+)$1	251	27	31	11.9999
EEEE	chr16:29822024-29822278(+)$1	254	75	79	11.9999
::cc	chr19:47112399-47112701(+)$1	302	183	187	11.9999
bb33	chrX:135579705-135579960(+)$1	255	62	66	11.9999
uuuu	chr17:4173182-4173419(-)$1	237	104	108	11.9999
cccd	chr11:75283161-75283416(+)$1	255	59	63	11.9999
2eee	chr17:38146257-38146509(+)$1	252	147	151	11.9999
qddd	chr10:72184349-72184574(+)$1	225	137	141	11.9999
::::	chr9:34636944-34637176(-)$1	232	18	22	11.9999
cc]c	chr11:66053127-66053356(-)$1	229	133	137	11.9999
::::	chr1:26227241-26227482(-)$1	241	7	11	11.9999
::::	chr10:129923836-129924088(-)$1	252	21	25	11.9999
ff[e	chr19:5785561-5785802(-)$1	241	176	180	11.9999
))))	chr19:6413468-6413705(-)$1	237	97	101	11.9999
ennn	chr2:97476747-97476975(+)$1	228	17	21	11.9999
:EEE	chr16:2128963-2129204(+)$1	241	1	5	11.9999
::::	chr1:235714292-235714542(-)$1	250	49	53	11.9999
::::	chr10:105153950-105154181(-)$1	231	171	175	11.9999
nnnn	chr8:37917355-37917586(+)$1	231	142	146	11.9999
ccc!	chr11:75111334-75111584(+)$1	250	1	5	11.9999
dddd	chr11:134027766-134028000(-)$1	234	132	136	11.9999
cggg	chr3:184049236-184049467(+)$1	231	8	12	11.9999
nnff	chr16:58554679-58554907(-)$1	228	120	124	11.9999
c:::	chr2:85770809-85771041(+)$1	232	95	99	11.9999
mccc	chr1:54683809-54684057(+)$1	248	230	234	11.9999
::::	chr14:67708060-67708287(-)$1	227	113	117	11.9999
22ee	chr11:3877235-3877469(+)$1	234	103	107	11.9999
ccll	chr7:6048817-6049064(+)$1	247	138	142	11.9999
####	chr11:57439406-57439636(+)$1	230	25	29	11.9999
CCC:	chr17:77756026-77756258(+)$1	232	0	4	11.9999

#DB
.(((	chr8:56986921-56987159(-)$1	1	89	93	11.9999
...(	chr7:155569245-155569491(+)$1	1	4	8	11.9999
((((	chr6:27777728-27777981(+)$1	1	28	32	11.9999
((((	chr1:156280711-156280961(-)$1	1	81	85	11.9999
...)	chr15:83685904-83686150(-)$1	1	167	171	11.9999
....	chr12:54631923-54632180(-)$1	1	59	63	11.9999
))))	chr11:625056-625284(+)$1	1	208	212	11.9999
((((	chr16:74486634-74486864(-)$1	1	22	26	11.9999
))))	chr10:99218312-99218542(-)$1	1	193	197	11.9999
...)	chr2:54093859-54094105(-)$1	1	144	148	11.9999
((..	chr8:98864105-98864341(+)$1	1	11	15	11.9999
((..	chr1:19426023-19426251(-)$1	1	11	15	11.9999
.)))	chr11:118893971-118894252(+)$1	1	222	226	11.9999
....	chr10:98336421-98336667(-)$1	1	22	26	11.9999
((((	chr12:120933832-120934079(+)$1	1	176	180	11.9999
))))	chr9:125865459-125865687(+)$1	1	55	59	11.9999
))..	chr1:25894379-25894623(+)$1	1	185	189	11.9999
(((.	chr1:7840436-7840668(+)$1	1	32	36	11.9999
((((	chr19:2476025-2476271(+)$1	1	4	8	11.9999
....	chr17:73820591-73820823(+)$1	1	212	216	11.9999
((((	chr17:58524833-58525079(-)$1	1	97	101	11.9999
))))	chr7:29962959-29963184(-)$1	1	200	204	11.9999
((((	chr11:45168286-45168515(-)$1	1	86	90	11.9999
(((.	chr4:6644231-6644469(+)$1	1	20	24	11.9999
))))	chr15:44853879-44854104(+)$1	1	66	70	11.9999
((((	chr6:74363556-74363779(-)$1	1	127	131	11.9999
))))	chr14:73578287-73578526(+)$1	1	71	75	11.9999
((((	chr11:134038366-134038597(-)$1	1	49	53	11.9999
.)))	chrX:152000085-152000312(-)$1	1	32	36	11.9999
(((.	chr15:43280981-43281211(-)$1	1	5	9	11.9999
.).)	chr16:30103837-30104070(-)$1	1	193	197	11.9999
((((	chr11:77043726-77043958(-)$1	1	47	51	11.9999
))..	chr5:180670670-180670924(-)$1	1	141	145	11.9999
....	chr14:52118707-52118930(+)$1	1	34	38	11.9999
(...	chr1:19545512-19545739(-)$1	1	79	83	11.9999
....	chr17:27237249-27237479(-)$1	1	137	141	11.9999
))).	chr17:76201987-76202219(+)$1	1	166	170	11.9999
....	chr10:94267252-94267482(-)$1	1	47	51	11.9999
(...	chr18:77663278-77663506(-)$1	1	126	130	11.9999
))))	chr1:249105082-249105312(-)$1	1	183	187	11.9999
((((	chr1:227843827-227844060(+)$1	1	1	5	11.9999
(..(	chr2:220040863-220041093(-)$1	1	7	11	11.9999
((..	chr17:38144862-38145113(+)$1	1	27	31	11.9999
((((	chr16:29822024-29822278(+)$1	1	75	79	11.9999
..((	chr19:47112399-47112701(+)$1	1	183	187	11.9999
))..	chrX:135579705-135579960(+)$1	1	62	66	11.9999
....	chr17:4173182-4173419(-)$1	1	104	108	11.9999
((((	chr11:75283161-75283416(+)$1	1	59	63	11.9999
.)))	chr17:38146257-38146509(+)$1	1	147	151	11.9999
.)))	chr10:72184349-72184574(+)$1	1	137	141	11.9999
....	chr9:34636944-34637176(-)$1	1	18	22	11.9999
)).)	chr11:66053127-66053356(-)$1	1	133	137	11.9999
....	chr1:26227241-26227482(-)$1	1	7	11	11.9999
....	chr10:129923836-129924088(-)$1	1	21	25	11.9999
((.(	chr19:5785561-5785802(-)$1	1	176	180	11.9999
....	chr19:6413468-6413705(-)$1	1	97	101	11.9999
(...	chr2:97476747-97476975(+)$1	1	17	21	11.9999
.(((	chr16:2128963-2129204(+)$1	1	1	5	11.9999
....	chr1:235714292-235714542(-)$1	1	49	53	11.9999
....	chr10:105153950-105154181(-)$1	1	171	175	11.9999
....	chr8:37917355-37917586(+)$1	1	142	146	11.9999
(((.	chr11:75111334-75111584(+)$1	1	1	5	11.9999
))))	chr11:134027766-134028000(-)$1	1	132	136	11.9999
((((	chr3:184049236-184049467(+)$1	1	8	12	11.9999
..))	chr16:58554679-58554907(-)$1	1	120	124	11.9999
)...	chr2:85770809-85771041(+)$1	1	95	99	11.9999
.)))	chr1:54683809-54684057(+)$1	1	230	234	11.9999
....	chr14:67708060-67708287(-)$1	1	113	117	11.9999
..))	chr11:3877235-3877469(+)$1	1	103	107	11.9999
((..	chr7:6048817-6049064(+)$1	1	138	142	11.9999
....	chr11:57439406-57439636(+)$1	1	25	29	11.9999
(((.	chr17:77756026-77756258(+)$1	1	0	4	11.9999

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

#score	863.9999999999994
#seq	72
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m3_run2.nuc.txt

#NT
agaaa	chr2:71602273-71602593(+)$1	320	164	169	15.0000
AGAAA	chr7:38299695-38299931(-)$1	236	24	29	15.0000
AGAAA	chr3:47142936-47143224(-)$1	288	5	10	15.0000
agaaa	chr18:59936613-59936838(+)$1	225	195	200	15.0000
AGAAA	chr3:50004879-50005124(+)$1	245	35	40	15.0000
AGAAA	chr1:32744993-32745323(+)$1	330	215	220	15.0000
AGAAA	chr2:152463965-152464189(-)$1	224	65	70	15.0000
AGAAA	chr19:53855346-53855559(+)$1	213	56	61	15.0000
AGAAA	chr10:86273281-86273527(+)$1	246	60	65	15.0000
AGAAA	chr13:25378333-25378553(+)$1	220	167	172	15.0000
AGAAA	chr18:32825874-32826103(+)$1	229	143	148	15.0000
AGAAA	chr5:133481814-133482070(+)$1	256	108	113	15.0000
AGAAA	chrX:153629014-153629350(+)$1	336	317	322	15.0000
AGAAA	chr15:101550619-101550836(+)$1	217	137	142	15.0000
AGAAA	chr5:71495220-71495431(+)$1	211	98	103	15.0000
AGAAA	chr2:99977627-99977843(+)$1	216	29	34	15.0000
AGAAA	chr16:30200171-30200481(+)$1	310	188	193	15.0000
AGAAA	chr5:78610307-78610577(+)$1	270	220	225	15.0000
AGAAA	chr8:22459624-22459838(+)$1	214	149	154	15.0000
AGAAA	chr2:44539698-44539912(+)$1	214	139	144	15.0000
AGAAA	chr14:23459199-23459419(-)$1	220	81	86	15.0000
AGAAA	chr11:62339984-62340252(-)$1	268	232	237	15.0000
AGAAA	chr10:38241410-38241715(-)$1	305	35	40	15.0000
AGAAA	chrX:114540791-114541005(+)$1	214	97	102	15.0000
AGAAA	chr19:21239841-21240067(+)$1	226	45	50	15.0000
AGAAA	chr17:29631694-29631930(-)$1	236	43	48	15.0000
AGAAA	chr12:49666218-49666567(+)$1	349	84	89	15.0000
AGAAA	chrX:114141584-114141799(+)$1	215	185	190	15.0000
AGAAA	chr6:24718776-24719034(-)$1	258	76	81	15.0000
AGAAA	chr10:61828602-61828865(-)$1	263	5	10	15.0000
AGAAA	chr11:8009159-8009484(+)$1	325	116	121	15.0000
AGAAA	chr6:42996854-42997115(+)$1	261	29	34	15.0000
AGAAA	chr19:54783729-54783949(-)$1	220	136	141	15.0000
AGAAA	chr17:4848167-4848447(+)$1	280	5	10	15.0000
AGAAA	chr20:5566740-5566991(-)$1	251	25	30	15.0000
AGAAA	chr1:40737510-40737725(+)$1	215	135	140	15.0000
AGAAA	chrX:17745459-17745671(+)$1	212	126	131	15.0000
AGAAA	chr11:33052991-33053205(+)$1	214	192	197	15.0000
AGAAA	chr17:62855893-62856120(-)$1	227	5	10	15.0000
AGAAA	chr16:89703814-89704028(+)$1	214	59	64	15.0000
AGAAA	chr6:35438307-35438540(+)$1	233	149	154	15.0000
AGAAA	chr17:56772340-56772557(+)$1	217	168	173	15.0000
AGAAA	chr10:124596957-124597189(-)$1	232	58	63	15.0000
AGAAA	chr4:170628113-170628327(+)$1	214	194	199	15.0000
AGAAA	chr15:38230267-38230479(+)$1	212	33	38	15.0000
AGAAA	chr19:57910847-57911114(+)$1	267	58	63	15.0000
AGAAA	chr3:121206436-121206680(-)$1	244	26	31	15.0000

#otherMatches

#Struct PSSM
uuuuu	chr12:51034444-51034694(+)$1	250	5	10	15.0000
EEEEE	chr2:71602273-71602593(+)$1	320	164	169	15.0000
c[ddd	chr7:38299695-38299931(-)$1	236	24	29	15.0000
:::::	chr3:47142936-47143224(-)$1	288	5	10	15.0000
}GGGG	chr18:59936613-59936838(+)$1	225	195	200	15.0000
qqqqq	chr3:50004879-50005124(+)$1	245	35	40	15.0000
hhFFF	chr1:32744993-32745323(+)$1	330	215	220	15.0000
"bb##	chr2:152463965-152464189(-)$1	224	65	70	15.0000
ccmmm	chr19:53855346-53855559(+)$1	213	56	61	15.0000
ddmmm	chr10:86273281-86273527(+)$1	246	60	65	15.0000
++++i	chr13:25378333-25378553(+)$1	220	167	172	15.0000
cc:::	chr18:32825874-32826103(+)$1	229	143	148	15.0000
:::::	chr5:133481814-133482070(+)$1	256	108	113	15.0000
odddd	chrX:153629014-153629350(+)$1	336	317	322	15.0000
dddd:	chr15:101550619-101550836(+)$1	217	137	142	15.0000
cc###	chr5:71495220-71495431(+)$1	211	98	103	15.0000
:::::	chr2:99977627-99977843(+)$1	216	29	34	15.0000
bqqqq	chr16:30200171-30200481(+)$1	310	188	193	15.0000
dd:::	chr5:78610307-78610577(+)$1	270	220	225	15.0000
ddd::	chr8:22459624-22459838(+)$1	214	149	154	15.0000
:::::	chr2:44539698-44539912(+)$1	214	139	144	15.0000
55555	chr14:23459199-23459419(-)$1	220	81	86	15.0000
ooodd	chr11:62339984-62340252(-)$1	268	232	237	15.0000
:::::	chr10:38241410-38241715(-)$1	305	35	40	15.0000
ebboo	chrX:114540791-114541005(+)$1	214	97	102	15.0000
ee$$$	chr19:21239841-21240067(+)$1	226	45	50	15.0000
hhh44	chr17:29631694-29631930(-)$1	236	43	48	15.0000
hhh::	chr12:49666218-49666567(+)$1	349	84	89	15.0000
rrrrr	chrX:114141584-114141799(+)$1	215	185	190	15.0000
!dddd	chr6:24718776-24719034(-)$1	258	76	81	15.0000
:::::	chr10:61828602-61828865(-)$1	263	5	10	15.0000
cc[cc	chr11:8009159-8009484(+)$1	325	116	121	15.0000
:::::	chr6:42996854-42997115(+)$1	261	29	34	15.0000
dvvvv	chr19:54783729-54783949(-)$1	220	136	141	15.0000
::::g	chr17:4848167-4848447(+)$1	280	5	10	15.0000
EE:::	chr20:5566740-5566991(-)$1	251	25	30	15.0000
^^^^^	chr1:40737510-40737725(+)$1	215	135	140	15.0000
GG:::	chrX:17745459-17745671(+)$1	212	126	131	15.0000
eee::	chr11:33052991-33053205(+)$1	214	192	197	15.0000
:::::	chr17:62855893-62856120(-)$1	227	5	10	15.0000
dddd3	chr16:89703814-89704028(+)$1	214	59	64	15.0000
ffff4	chr6:35438307-35438540(+)$1	233	149	154	15.0000
ddmmm	chr17:56772340-56772557(+)$1	217	168	173	15.0000
f:::g	chr10:124596957-124597189(-)$1	232	58	63	15.0000
:::::	chr4:170628113-170628327(+)$1	214	194	199	15.0000
ddd]c	chr15:38230267-38230479(+)$1	212	33	38	15.0000
::III	chr19:57910847-57911114(+)$1	267	58	63	15.0000
"ccc+	chr3:121206436-121206680(-)$1	244	26	31	15.0000

#DB
.....	chr12:51034444-51034694(+)$1	1	5	10	15.0000
(((((	chr2:71602273-71602593(+)$1	1	164	169	15.0000
(.(((	chr7:38299695-38299931(-)$1	1	24	29	15.0000
.....	chr3:47142936-47143224(-)$1	1	5	10	15.0000
.))))	chr18:59936613-59936838(+)$1	1	195	200	15.0000
.....	chr3:50004879-50005124(+)$1	1	35	40	15.0000
)))))	chr1:32744993-32745323(+)$1	1	215	220	15.0000
.((..	chr2:152463965-152464189(-)$1	1	65	70	15.0000
((...	chr19:53855346-53855559(+)$1	1	56	61	15.0000
((...	chr10:86273281-86273527(+)$1	1	60	65	15.0000
....(	chr13:25378333-25378553(+)$1	1	167	172	15.0000
))...	chr18:32825874-32826103(+)$1	1	143	148	15.0000
.....	chr5:133481814-133482070(+)$1	1	108	113	15.0000
.))))	chrX:153629014-153629350(+)$1	1	317	322	15.0000
)))).	chr15:101550619-101550836(+)$1	1	137	142	15.0000
((...	chr5:71495220-71495431(+)$1	1	98	103	15.0000
.....	chr2:99977627-99977843(+)$1	1	29	34	15.0000
(....	chr16:30200171-30200481(+)$1	1	188	193	15.0000
))...	chr5:78610307-78610577(+)$1	1	220	225	15.0000
)))..	chr8:22459624-22459838(+)$1	1	149	154	15.0000
.....	chr2:44539698-44539912(+)$1	1	139	144	15.0000
.....	chr14:23459199-23459419(-)$1	1	81	86	15.0000
...))	chr11:62339984-62340252(-)$1	1	232	237	15.0000
.....	chr10:38241410-38241715(-)$1	1	35	40	15.0000
(((..	chrX:114540791-114541005(+)$1	1	97	102	15.0000
((...	chr19:21239841-21240067(+)$1	1	45	50	15.0000
)))..	chr17:29631694-29631930(-)$1	1	43	48	15.0000
)))..	chr12:49666218-49666567(+)$1	1	84	89	15.0000
.....	chrX:114141584-114141799(+)$1	1	185	190	15.0000
.((((	chr6:24718776-24719034(-)$1	1	76	81	15.0000
.....	chr10:61828602-61828865(-)$1	1	5	10	15.0000
((.((	chr11:8009159-8009484(+)$1	1	116	121	15.0000
.....	chr6:42996854-42997115(+)$1	1	29	34	15.0000
(....	chr19:54783729-54783949(-)$1	1	136	141	15.0000
....(	chr17:4848167-4848447(+)$1	1	5	10	15.0000
((...	chr20:5566740-5566991(-)$1	1	25	30	15.0000
.....	chr1:40737510-40737725(+)$1	1	135	140	15.0000
))...	chrX:17745459-17745671(+)$1	1	126	131	15.0000
)))..	chr11:33052991-33053205(+)$1	1	192	197	15.0000
.....	chr17:62855893-62856120(-)$1	1	5	10	15.0000
)))).	chr16:89703814-89704028(+)$1	1	59	64	15.0000
)))).	chr6:35438307-35438540(+)$1	1	149	154	15.0000
((...	chr17:56772340-56772557(+)$1	1	168	173	15.0000
)...(	chr10:124596957-124597189(-)$1	1	58	63	15.0000
.....	chr4:170628113-170628327(+)$1	1	194	199	15.0000
))).)	chr15:38230267-38230479(+)$1	1	33	38	15.0000
..(((	chr19:57910847-57911114(+)$1	1	58	63	15.0000
.(((.	chr3:121206436-121206680(-)$1	1	26	31	15.0000

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

#score	720.0000000000001
#seq	48
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_UTR_m3_run1.nuc.txt

#NT
AAAUAAACA	chr7:90897440-90897680(+)$1	240	189	198	14.4509
aaauaaaaa	chr11:76227716-76227954(+)$1	238	146	155	18.8627
AAAAAAAAC	chr5:158712239-158712467(+)$1	228	165	174	16.3137
AAAUAUAAC	chr2:202036451-202036706(+)$1	255	206	215	15.0392
GAAUAAAAC	chr1:180083450-180083680(+)$1	230	25	34	15.3333
aaauuaaac	chr8:102212994-102213245(-)$1	251	33	42	15.8235
AAGUAAAAU	chr1:155306871-155307219(-)$1	348	321	330	13.7647
AUAUAAAAC	chr1:171672171-171672400(-)$1	229	101	110	15.3333
AAAUAAAAC	chr10:70136787-70137025(-)$1	238	51	60	19.4509
AUAUAAAAG	chr11:85371104-85371356(-)$1	252	227	236	14.4509
AAAAAAAAU	chr7:6012796-6013035(-)$1	239	108	117	15.3333
AAAAAAAAC	chr9:111779014-111779278(-)$1	264	50	59	16.3137
aaauaaaaG	chr1:24792760-24793010(+)$1	250	51	60	18.5686
AACUAAAAG	chr7:48004682-48004930(-)$1	248	117	126	13.8627
aaaaaaaaa	chr9:100848722-100849113(-)$1	391	6	15	15.7254
caauaaaaa	chr16:4737472-4737761(+)$1	289	36	45	14.5490
AAAUGAAAA	chr18:11885105-11885364(-)$1	259	235	244	15.1372
aaaaaaaaa	chr14:54416529-54416822(-)$1	293	203	212	15.7254
AAACAAAAA	chr11:6237583-6237906(-)$1	323	110	119	15.2352
AAACAAAAU	chr19:21366631-21366895(+)$1	264	143	152	14.8431
UAAUAAAAG	chr17:41246549-41246781(-)$1	232	148	157	14.3529
aaauaaaaC	chr19:46051883-46052129(-)$1	246	216	225	19.4509
aaauaaagc	chr11:96117853-96118125(-)$1	272	106	115	15.1372
AAAUUAAAC	chr2:101634645-101634872(-)$1	227	149	158	15.8235
AAAUAAAGA	chr11:59405168-59405418(-)$1	250	200	209	14.5490
AAAUGAAAC	chr1:206636662-206636903(+)$1	241	96	105	15.7254
AGAUAAAAC	chr6:160111867-160112112(-)$1	245	98	107	15.5294
AAAUAAAAA	chr1:59121073-59121323(-)$1	250	176	185	18.8627
UAAUAAAAC	chr10:93624867-93625123(+)$1	256	145	154	15.2352
AGauaaaau	chr1:235628817-235629072(-)$1	255	228	237	14.5490
AGAUAAAAG	chr20:47651456-47651821(+)$1	365	4	13	14.6470
AAAUAAAUU	chr8:59361746-59362196(+)$1	450	161	170	14.1568
AAAUAUAAU	chr8:116425157-116425382(-)$1	225	148	157	14.0588
AGAUAAAAG	chr1:150594647-150594892(-)$1	245	46	55	14.6470
ACAUAAAAG	chr2:197642882-197643118(-)$1	236	64	73	14.3529
gaauaaaAA	chr10:31818362-31818639(+)$1	277	206	215	14.7450
AAAGAAAAC	chr16:277961-278345(-)$1	384	96	105	15.9215
aaaaaaaaC	chr7:42003558-42003803(-)$1	245	133	142	16.3137
AAAGAAAAC	chr10:115668195-115668456(+)$1	261	171	180	15.9215
AAAUAUAAC	chr11:111601124-111601361(-)$1	237	53	62	15.0392
AAAUUAAAC	chr12:31944107-31944337(-)$1	230	117	126	15.8235
AAAGAAAAA	chr11:61083190-61083446(-)$1	256	85	94	15.3333
AAAUAAAAG	chr3:44894282-44894550(+)$1	268	205	214	18.5686
aaauaaaaa	chr2:201843606-201843915(-)$1	309	147	156	18.8627
AAAAAAAAG	chr18:32723204-32723440(+)$1	236	209	218	15.4313
aaauGAAAG	chr7:139107788-139108024(+)$1	236	91	100	14.8431
AAAUAACAA	chr7:26231639-26231899(-)$1	260	4	13	14.0588
AAAUUAAAU	chr3:20194966-20195204(+)$1	238	43	52	14.8431
GAAUAAAAU	chr4:76405143-76405406(-)$1	263	134	143	14.3529
AAAUGAAAU	chr7:48003568-48003829(-)$1	261	191	200	14.7450

#otherMatches

#Struct PSSM
:::::::::	chr1:7832868-7833137(+)$1	269	198	207	11.5098
hhhh:::::	chr7:90897440-90897680(+)$1	240	189	198	14.4509
gggggggvv	chr11:76227716-76227954(+)$1	238	146	155	18.8627
^^^^^^^^^	chr5:158712239-158712467(+)$1	228	165	174	16.3137
:::::::::	chr2:202036451-202036706(+)$1	255	206	215	15.0392
epppppppe	chr1:180083450-180083680(+)$1	230	25	34	15.3333
:::::::::	chr8:102212994-102213245(-)$1	251	33	42	15.8235
:::::::::	chr1:155306871-155307219(-)$1	348	321	330	13.7647
========a	chr1:171672171-171672400(-)$1	229	101	110	15.3333
DGGGGGGG{	chr10:70136787-70137025(-)$1	238	51	60	19.4509
IIII\\\\\	chr11:85371104-85371356(-)$1	252	227	236	14.4509
:::::::GG	chr7:6012796-6013035(-)$1	239	108	117	15.3333
^^^^^^^^^	chr9:111779014-111779278(-)$1	264	50	59	16.3137
:::::::::	chr1:24792760-24793010(+)$1	250	51	60	18.5686
::::::::c	chr7:48004682-48004930(-)$1	248	117	126	13.8627
:::::::::	chr9:100848722-100849113(-)$1	391	6	15	15.7254
ff^^^^^^^	chr16:4737472-4737761(+)$1	289	36	45	14.5490
gggggmmmm	chr18:11885105-11885364(-)$1	259	235	244	15.1372
:::::::::	chr14:54416529-54416822(-)$1	293	203	212	15.7254
:::::::::	chr11:6237583-6237906(-)$1	323	110	119	15.2352
ooooooeee	chr19:21366631-21366895(+)$1	264	143	152	14.8431
qqqqqqqbb	chr17:41246549-41246781(-)$1	232	148	157	14.3529
::::::::C	chr19:46051883-46052129(-)$1	246	216	225	19.4509
eeeezzzzz	chr11:96117853-96118125(-)$1	272	106	115	15.1372
LLGGGGGGG	chr2:101634645-101634872(-)$1	227	149	158	15.8235
ffffff22b	chr11:59405168-59405418(-)$1	250	200	209	14.5490
66ffffffd	chr1:206636662-206636903(+)$1	241	96	105	15.7254
$ddddoooo	chr6:160111867-160112112(-)$1	245	98	107	15.5294
==>>>>>>>	chr1:59121073-59121323(-)$1	250	176	185	18.8627
::::eeeee	chr10:93624867-93625123(+)$1	256	145	154	15.2352
ggFFFFFF}	chr1:235628817-235629072(-)$1	255	228	237	14.5490
GGG{CCCCC	chr20:47651456-47651821(+)$1	365	4	13	14.6470
:::::::::	chr8:59361746-59362196(+)$1	450	161	170	14.1568
>>>>>>>>>	chr8:116425157-116425382(-)$1	225	148	157	14.0588
llccc22bb	chr1:150594647-150594892(-)$1	245	46	55	14.6470
EEEEE:::E	chr2:197642882-197643118(-)$1	236	64	73	14.3529
f:::::fff	chr10:31818362-31818639(+)$1	277	206	215	14.7450
===ddddmm	chr16:277961-278345(-)$1	384	96	105	15.9215
ee:::::::	chr7:42003558-42003803(-)$1	245	133	142	16.3137
d:ddddqqq	chr10:115668195-115668456(+)$1	261	171	180	15.9215
fff::::CC	chr11:111601124-111601361(-)$1	237	53	62	15.0392
^^^^^^^^^	chr12:31944107-31944337(-)$1	230	117	126	15.8235
~~~HHHHHH	chr11:61083190-61083446(-)$1	256	85	94	15.3333
00000gggg	chr3:44894282-44894550(+)$1	268	205	214	18.5686
^^^^^^^^^	chr2:201843606-201843915(-)$1	309	147	156	18.8627
66ffffff]	chr18:32723204-32723440(+)$1	236	209	218	15.4313
::::ccccc	chr7:139107788-139108024(+)$1	236	91	100	14.8431
DD{EEEEE{	chr7:26231639-26231899(-)$1	260	4	13	14.0588
fff&&&&&&	chr3:20194966-20195204(+)$1	238	43	52	14.8431
dddd:::::	chr4:76405143-76405406(-)$1	263	134	143	14.3529
CC}BBGGGG	chr7:48003568-48003829(-)$1	261	191	200	14.7450

#DB
.........	chr1:7832868-7833137(+)$1	1	198	207	11.5098
)))).....	chr7:90897440-90897680(+)$1	1	189	198	14.4509
(((((((..	chr11:76227716-76227954(+)$1	1	146	155	18.8627
.........	chr5:158712239-158712467(+)$1	1	165	174	16.3137
.........	chr2:202036451-202036706(+)$1	1	206	215	15.0392
(.......)	chr1:180083450-180083680(+)$1	1	25	34	15.3333
.........	chr8:102212994-102213245(-)$1	1	33	42	15.8235
.........	chr1:155306871-155307219(-)$1	1	321	330	13.7647
(((((((((	chr1:171672171-171672400(-)$1	1	101	110	15.3333
((((((((.	chr10:70136787-70137025(-)$1	1	51	60	19.4509
)))).....	chr11:85371104-85371356(-)$1	1	227	236	14.4509
.......((	chr7:6012796-6013035(-)$1	1	108	117	15.3333
.........	chr9:111779014-111779278(-)$1	1	50	59	16.3137
.........	chr1:24792760-24793010(+)$1	1	51	60	18.5686
........(	chr7:48004682-48004930(-)$1	1	117	126	13.8627
.........	chr9:100848722-100849113(-)$1	1	6	15	15.7254
((.......	chr16:4737472-4737761(+)$1	1	36	45	14.5490
(((((....	chr18:11885105-11885364(-)$1	1	235	244	15.1372
.........	chr14:54416529-54416822(-)$1	1	203	212	15.7254
.........	chr11:6237583-6237906(-)$1	1	110	119	15.2352
......)))	chr19:21366631-21366895(+)$1	1	143	152	14.8431
.......))	chr17:41246549-41246781(-)$1	1	148	157	14.3529
........)	chr19:46051883-46052129(-)$1	1	216	225	19.4509
((((.....	chr11:96117853-96118125(-)$1	1	106	115	15.1372
..(((((((	chr2:101634645-101634872(-)$1	1	149	158	15.8235
))))))..)	chr11:59405168-59405418(-)$1	1	200	209	14.5490
..)))))))	chr1:206636662-206636903(+)$1	1	96	105	15.7254
.((((....	chr6:160111867-160112112(-)$1	1	98	107	15.5294
)).......	chr1:59121073-59121323(-)$1	1	176	185	18.8627
....(((((	chr10:93624867-93625123(+)$1	1	145	154	15.2352
)))))))).	chr1:235628817-235629072(-)$1	1	228	237	14.5490
(((.(((((	chr20:47651456-47651821(+)$1	1	4	13	14.6470
.........	chr8:59361746-59362196(+)$1	1	161	170	14.1568
.........	chr8:116425157-116425382(-)$1	1	148	157	14.0588
..)))..))	chr1:150594647-150594892(-)$1	1	46	55	14.6470
(((((...(	chr2:197642882-197643118(-)$1	1	64	73	14.3529
).....(((	chr10:31818362-31818639(+)$1	1	206	215	14.7450
)))((((..	chr16:277961-278345(-)$1	1	96	105	15.9215
)).......	chr7:42003558-42003803(-)$1	1	133	142	16.3137
).((((...	chr10:115668195-115668456(+)$1	1	171	180	15.9215
)))....((	chr11:111601124-111601361(-)$1	1	53	62	15.0392
.........	chr12:31944107-31944337(-)$1	1	117	126	15.8235
...))))))	chr11:61083190-61083446(-)$1	1	85	94	15.3333
.....))))	chr3:44894282-44894550(+)$1	1	205	214	18.5686
.........	chr2:201843606-201843915(-)$1	1	147	156	18.8627
..)))))).	chr18:32723204-32723440(+)$1	1	209	218	15.4313
....(((((	chr7:139107788-139108024(+)$1	1	91	100	14.8431
((.(((((.	chr7:26231639-26231899(-)$1	1	4	13	14.0588
(((......	chr3:20194966-20195204(+)$1	1	43	52	14.8431
)))).....	chr4:76405143-76405406(-)$1	1	134	143	14.3529
)).))))))	chr7:48003568-48003829(-)$1	1	191	200	14.7450

#PSSM
A : 0.68	a : 0.19	G : 0.03	U : 0.03	c : 0.01	g : 0.01	
A : 0.62	a : 0.23	G : 0.07	U : 0.03	C : 0.01	
A : 0.70	a : 0.25	G : 0.01	C : 0.01	
U : 0.56	u : 0.19	A : 0.07	a : 0.05	G : 0.05	C : 0.03	
A : 0.60	a : 0.21	U : 0.07	G : 0.07	u : 0.01	
A : 0.70	a : 0.23	U : 0.05	
A : 0.74	a : 0.23	C : 0.01	
A : 0.70	a : 0.19	U : 0.03	C : 0.01	g : 0.01	G : 0.01	
C : 0.33	G : 0.19	A : 0.15	U : 0.15	a : 0.09	c : 0.03	u : 0.01	

#score	791.5098039215691
#seq	51
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_UTR_m1_run1.nuc.txt

#NT
UUC	chr11:47736570-47736803(-)$1	233	83	86	9.0000
UUC	chr10:50859878-50860095(+)$1	217	34	37	9.0000
UUC	chr2:203630666-203630950(+)$1	284	60	63	9.0000
uuc	chr17:18639124-18639346(+)$1	222	35	38	9.0000
UUC	chr19:21366644-21366894(+)$1	250	59	62	9.0000
UUC	chr1:228285527-228285844(+)$1	317	12	15	9.0000
UUC	chr3:45719912-45720128(+)$1	216	58	61	9.0000
UUC	chr15:57839903-57840117(+)$1	214	62	65	9.0000
uuc	chr4:15606059-15606290(-)$1	231	106	109	9.0000
UUC	chr2:95955952-95956165(+)$1	213	40	43	9.0000
UUC	chr7:102193660-102194001(-)$1	341	86	89	9.0000
UUC	chr7:92759861-92760158(-)$1	297	55	58	9.0000
uuc	chr22:37636843-37637126(-)$1	283	79	82	9.0000
UUC	chr1:160186681-160186981(-)$1	300	46	49	9.0000
UUC	chr7:127011623-127011867(-)$1	244	4	7	9.0000
UUC	chr22:36876639-36876857(-)$1	218	0	3	9.0000
UUC	chr4:83344386-83344614(-)$1	228	27	30	9.0000
UUC	chr22:37334577-37334823(+)$1	246	10	13	9.0000
UUC	chr10:11372081-11372372(+)$1	291	22	25	9.0000
UUC	chr8:66634951-66635233(-)$1	282	14	17	9.0000
UUC	chr19:46811406-46811621(+)$1	215	101	104	9.0000
UUC	chr2:139328537-139328793(+)$1	256	9	12	9.0000
UUC	chr12:59270155-59270385(-)$1	230	24	27	9.0000
UUC	chr5:38962758-38963094(-)$1	336	25	28	9.0000
UUC	chr3:11598781-11599025(+)$1	244	47	50	9.0000
UUC	chr5:39106430-39106663(-)$1	233	16	19	9.0000
UUC	chr12:28459580-28459804(+)$1	224	12	15	9.0000
UUC	chr12:32896401-32896634(+)$1	233	87	90	9.0000
UUC	chr2:242291969-242292222(+)$1	253	62	65	9.0000
UUC	chr17:46627113-46627354(-)$1	241	65	68	9.0000
UUC	chr1:64605749-64605962(+)$1	213	36	39	9.0000
UUC	chr1:31405717-31405987(-)$1	270	7	10	9.0000
UUC	chr3:160141142-160141355(+)$1	213	21	24	9.0000
uuc	chr2:205912722-205912936(+)$1	214	59	62	9.0000
UUC	chr3:182989729-182989942(+)$1	213	31	34	9.0000
UUC	chr2:172411346-172411558(+)$1	212	25	28	9.0000
uuc	chr16:50070145-50070366(+)$1	221	0	3	9.0000
UUC	chr10:102800011-102800261(+)$1	250	56	59	9.0000
UUC	chr3:23934056-23934273(-)$1	217	5	8	9.0000
UUC	chr17:70121067-70121281(+)$1	214	31	34	9.0000
UUC	chr7:154876373-154876585(+)$1	212	48	51	9.0000
uuc	chr9:100848854-100849111(-)$1	257	34	37	9.0000
UUC	chr21:15745837-15746064(-)$1	227	89	92	9.0000
UUC	chr11:111609479-111609753(-)$1	274	6	9	9.0000
UUC	chr12:21622850-21623078(+)$1	228	21	24	9.0000
UUC	chr17:53240353-53240616(+)$1	263	47	50	9.0000
UUC	chr10:70502036-70502338(+)$1	302	11	14	9.0000
UUC	chr8:143784928-143785141(+)$1	213	29	32	9.0000
UUC	chr15:65869940-65870286(+)$1	346	26	29	9.0000
UUC	chr10:72643386-72643614(-)$1	228	93	96	9.0000
UUC	chr16:89395159-89395507(-)$1	348	37	40	9.0000
UUC	chr6:35549393-35549629(-)$1	236	145	148	9.0000
UUC	chr12:60154828-60155043(+)$1	215	103	106	9.0000
UUC	chr16:15131115-15131329(+)$1	214	3	6	9.0000
UUC	chrX:105937032-105937246(+)$1	214	102	105	9.0000
UUC	chr2:204824411-204824859(+)$1	448	23	26	9.0000
UUC	chr3:57302386-57302606(+)$1	220	10	13	9.0000
UUC	chr9:100843728-100843951(-)$1	223	8	11	9.0000
UUC	chr9:1056699-1056912(+)$1	213	87	90	9.0000
UUC	chr20:57252068-57252355(+)$1	287	0	3	9.0000
UUC	chr7:102741598-102741850(-)$1	252	145	148	9.0000
UUC	chr3:97673056-97673294(-)$1	238	123	126	9.0000
UUC	chr17:4850262-4850560(-)$1	298	43	46	9.0000
UUC	chr17:729162-729389(-)$1	227	48	51	9.0000
UUC	chr17:908512-908734(-)$1	222	147	150	9.0000
UUC	chr7:98445022-98445274(-)$1	252	177	180	9.0000
UUC	chr15:52413415-52413676(-)$1	261	4	7	9.0000
UUC	chr12:110385323-110385548(-)$1	225	7	10	9.0000
UUC	chrX:148073656-148073871(+)$1	215	103	106	9.0000
UUC	chr12:57493491-57493727(-)$1	236	27	30	9.0000
UUC	chr5:169675080-169675356(-)$1	276	75	78	9.0000
UUC	chrX:118750905-118751346(-)$1	441	44	47	9.0000
UUC	chr3:19389178-19389399(+)$1	221	4	7	9.0000
UUC	chr21:34967130-34967350(-)$1	220	108	111	9.0000
UUC	chr19:40504120-40504420(+)$1	300	57	60	9.0000
UUC	chr19:21300776-21300996(+)$1	220	27	30	9.0000
UUC	chr2:176041791-176042043(-)$1	252	2	5	9.0000
UUC	chr20:55093641-55093866(+)$1	225	33	36	9.0000
UUC	chr1:179323061-179323282(+)$1	221	26	29	9.0000
UUC	chr12:110369775-110369992(-)$1	217	3	6	9.0000
UUC	chr17:54942477-54942710(+)$1	233	49	52	9.0000
UUC	chr9:131770537-131770758(-)$1	221	165	168	9.0000
UUC	chr2:202025066-202025283(+)$1	217	17	20	9.0000
UUC	chr5:141368531-141368746(+)$1	215	65	68	9.0000
UUC	chr19:58375886-58376136(+)$1	250	104	107	9.0000
UUC	chr7:150270855-150271104(+)$1	249	31	34	9.0000
UUC	chr2:208477971-208478210(-)$1	239	23	26	9.0000
UUC	chr9:100848612-100848841(-)$1	229	5	8	9.0000
UUC	chr3:52290525-52290745(-)$1	220	163	166	9.0000
UUC	chr1:10436787-10437032(+)$1	245	9	12	9.0000
UUC	chr1:146629886-146630125(-)$1	239	23	26	9.0000
UUC	chr1:115259824-115260067(-)$1	243	86	89	9.0000
uuc	chr3:183890673-183890925(+)$1	252	5	8	9.0000
UUC	chr22:38339440-38339657(-)$1	217	19	22	9.0000
UUC	chr5:149781163-149781517(-)$1	354	131	134	9.0000
uuC	chr14:60762870-60763113(+)$1	243	79	82	9.0000
UUC	chr2:206860948-206861218(-)$1	270	86	89	9.0000
UUC	chr1:236713935-236714176(-)$1	241	8	11	9.0000
uuc	chrX:64742548-64742813(-)$1	265	21	24	9.0000

#otherMatches

#Struct PSSM
JJJ	chr3:152885036-152885251(+)$1	215	3	6	9.0000
ttt	chr11:47736570-47736803(-)$1	233	83	86	9.0000
eee	chr10:50859878-50860095(+)$1	217	34	37	9.0000
ccc	chr2:203630666-203630950(+)$1	284	60	63	9.0000
:::	chr17:18639124-18639346(+)$1	222	35	38	9.0000
::C	chr19:21366644-21366894(+)$1	250	59	62	9.0000
:dd	chr1:228285527-228285844(+)$1	317	12	15	9.0000
:::	chr3:45719912-45720128(+)$1	216	58	61	9.0000
qqb	chr15:57839903-57840117(+)$1	214	62	65	9.0000
FFF	chr4:15606059-15606290(-)$1	231	106	109	9.0000
qee	chr2:95955952-95956165(+)$1	213	40	43	9.0000
ttt	chr7:102193660-102194001(-)$1	341	86	89	9.0000
ee[	chr7:92759861-92760158(-)$1	297	55	58	9.0000
:::	chr22:37636843-37637126(-)$1	283	79	82	9.0000
:::	chr1:160186681-160186981(-)$1	300	46	49	9.0000
:::	chr7:127011623-127011867(-)$1	244	4	7	9.0000
:::	chr22:36876639-36876857(-)$1	218	0	3	9.0000
DDD	chr4:83344386-83344614(-)$1	228	27	30	9.0000
qqd	chr22:37334577-37334823(+)$1	246	10	13	9.0000
CC{	chr10:11372081-11372372(+)$1	291	22	25	9.0000
ooo	chr8:66634951-66635233(-)$1	282	14	17	9.0000
mmb	chr19:46811406-46811621(+)$1	215	101	104	9.0000
hhh	chr2:139328537-139328793(+)$1	256	9	12	9.0000
qqq	chr12:59270155-59270385(-)$1	230	24	27	9.0000
fff	chr5:38962758-38963094(-)$1	336	25	28	9.0000
22c	chr3:11598781-11599025(+)$1	244	47	50	9.0000
(((	chr5:39106430-39106663(-)$1	233	16	19	9.0000
ppp	chr12:28459580-28459804(+)$1	224	12	15	9.0000
c]b	chr12:32896401-32896634(+)$1	233	87	90	9.0000
:dd	chr2:242291969-242292222(+)$1	253	62	65	9.0000
]cc	chr17:46627113-46627354(-)$1	241	65	68	9.0000
ggg	chr1:64605749-64605962(+)$1	213	36	39	9.0000
ee"	chr1:31405717-31405987(-)$1	270	7	10	9.0000
[==	chr3:160141142-160141355(+)$1	213	21	24	9.0000
cc"	chr2:205912722-205912936(+)$1	214	59	62	9.0000
HH{	chr3:182989729-182989942(+)$1	213	31	34	9.0000
eee	chr2:172411346-172411558(+)$1	212	25	28	9.0000
:::	chr16:50070145-50070366(+)$1	221	0	3	9.0000
44d	chr10:102800011-102800261(+)$1	250	56	59	9.0000
:::	chr3:23934056-23934273(-)$1	217	5	8	9.0000
888	chr17:70121067-70121281(+)$1	214	31	34	9.0000
22g	chr7:154876373-154876585(+)$1	212	48	51	9.0000
:::	chr9:100848854-100849111(-)$1	257	34	37	9.0000
fff	chr21:15745837-15746064(-)$1	227	89	92	9.0000
CC{	chr11:111609479-111609753(-)$1	274	6	9	9.0000
qqq	chr12:21622850-21623078(+)$1	228	21	24	9.0000
fff	chr17:53240353-53240616(+)$1	263	47	50	9.0000
::G	chr10:70502036-70502338(+)$1	302	11	14	9.0000
ee:	chr8:143784928-143785141(+)$1	213	29	32	9.0000
yyy	chr15:65869940-65870286(+)$1	346	26	29	9.0000
xxx	chr10:72643386-72643614(-)$1	228	93	96	9.0000
333	chr16:89395159-89395507(-)$1	348	37	40	9.0000
!bb	chr6:35549393-35549629(-)$1	236	145	148	9.0000
hhh	chr12:60154828-60155043(+)$1	215	103	106	9.0000
:EE	chr16:15131115-15131329(+)$1	214	3	6	9.0000
fff	chrX:105937032-105937246(+)$1	214	102	105	9.0000
GG:	chr2:204824411-204824859(+)$1	448	23	26	9.0000
:::	chr3:57302386-57302606(+)$1	220	10	13	9.0000
fff	chr9:100843728-100843951(-)$1	223	8	11	9.0000
c33	chr9:1056699-1056912(+)$1	213	87	90	9.0000
:GG	chr20:57252068-57252355(+)$1	287	0	3	9.0000
""c	chr7:102741598-102741850(-)$1	252	145	148	9.0000
:DD	chr3:97673056-97673294(-)$1	238	123	126	9.0000
ppp	chr17:4850262-4850560(-)$1	298	43	46	9.0000
ccc	chr17:729162-729389(-)$1	227	48	51	9.0000
:::	chr17:908512-908734(-)$1	222	147	150	9.0000
eee	chr7:98445022-98445274(-)$1	252	177	180	9.0000
hhh	chr15:52413415-52413676(-)$1	261	4	7	9.0000
:::	chr12:110385323-110385548(-)$1	225	7	10	9.0000
ddd	chrX:148073656-148073871(+)$1	215	103	106	9.0000
WWW	chr12:57493491-57493727(-)$1	236	27	30	9.0000
:::	chr5:169675080-169675356(-)$1	276	75	78	9.0000
3dd	chrX:118750905-118751346(-)$1	441	44	47	9.0000
:::	chr3:19389178-19389399(+)$1	221	4	7	9.0000
:::	chr21:34967130-34967350(-)$1	220	108	111	9.0000
DDG	chr19:40504120-40504420(+)$1	300	57	60	9.0000
fff	chr19:21300776-21300996(+)$1	220	27	30	9.0000
::G	chr2:176041791-176042043(-)$1	252	2	5	9.0000
:::	chr20:55093641-55093866(+)$1	225	33	36	9.0000
ee$	chr1:179323061-179323282(+)$1	221	26	29	9.0000
eeb	chr12:110369775-110369992(-)$1	217	3	6	9.0000
III	chr17:54942477-54942710(+)$1	233	49	52	9.0000
:::	chr9:131770537-131770758(-)$1	221	165	168	9.0000
eep	chr2:202025066-202025283(+)$1	217	17	20	9.0000
8==	chr5:141368531-141368746(+)$1	215	65	68	9.0000
mee	chr19:58375886-58376136(+)$1	250	104	107	9.0000
fff	chr7:150270855-150271104(+)$1	249	31	34	9.0000
GGG	chr2:208477971-208478210(-)$1	239	23	26	9.0000
hhh	chr9:100848612-100848841(-)$1	229	5	8	9.0000
ddd	chr3:52290525-52290745(-)$1	220	163	166	9.0000
:::	chr1:10436787-10437032(+)$1	245	9	12	9.0000
ddd	chr1:146629886-146630125(-)$1	239	23	26	9.0000
:::	chr1:115259824-115260067(-)$1	243	86	89	9.0000
:::	chr3:183890673-183890925(+)$1	252	5	8	9.0000
:::	chr22:38339440-38339657(-)$1	217	19	22	9.0000
###	chr5:149781163-149781517(-)$1	354	131	134	9.0000
hh2	chr14:60762870-60763113(+)$1	243	79	82	9.0000
$$$	chr2:206860948-206861218(-)$1	270	86	89	9.0000
dmm	chr1:236713935-236714176(-)$1	241	8	11	9.0000
CBB	chrX:64742548-64742813(-)$1	265	21	24	9.0000

#DB
(((	chr3:152885036-152885251(+)$1	1	3	6	9.0000
...	chr11:47736570-47736803(-)$1	1	83	86	9.0000
(((	chr10:50859878-50860095(+)$1	1	34	37	9.0000
(((	chr2:203630666-203630950(+)$1	1	60	63	9.0000
...	chr17:18639124-18639346(+)$1	1	35	38	9.0000
..(	chr19:21366644-21366894(+)$1	1	59	62	9.0000
.((	chr1:228285527-228285844(+)$1	1	12	15	9.0000
...	chr3:45719912-45720128(+)$1	1	58	61	9.0000
..)	chr15:57839903-57840117(+)$1	1	62	65	9.0000
)))	chr4:15606059-15606290(-)$1	1	106	109	9.0000
.))	chr2:95955952-95956165(+)$1	1	40	43	9.0000
...	chr7:102193660-102194001(-)$1	1	86	89	9.0000
((.	chr7:92759861-92760158(-)$1	1	55	58	9.0000
...	chr22:37636843-37637126(-)$1	1	79	82	9.0000
...	chr1:160186681-160186981(-)$1	1	46	49	9.0000
...	chr7:127011623-127011867(-)$1	1	4	7	9.0000
...	chr22:36876639-36876857(-)$1	1	0	3	9.0000
(((	chr4:83344386-83344614(-)$1	1	27	30	9.0000
..)	chr22:37334577-37334823(+)$1	1	10	13	9.0000
((.	chr10:11372081-11372372(+)$1	1	22	25	9.0000
...	chr8:66634951-66635233(-)$1	1	14	17	9.0000
..)	chr19:46811406-46811621(+)$1	1	101	104	9.0000
(((	chr2:139328537-139328793(+)$1	1	9	12	9.0000
...	chr12:59270155-59270385(-)$1	1	24	27	9.0000
)))	chr5:38962758-38963094(-)$1	1	25	28	9.0000
..)	chr3:11598781-11599025(+)$1	1	47	50	9.0000
...	chr5:39106430-39106663(-)$1	1	16	19	9.0000
...	chr12:28459580-28459804(+)$1	1	12	15	9.0000
).)	chr12:32896401-32896634(+)$1	1	87	90	9.0000
.((	chr2:242291969-242292222(+)$1	1	62	65	9.0000
.))	chr17:46627113-46627354(-)$1	1	65	68	9.0000
)))	chr1:64605749-64605962(+)$1	1	36	39	9.0000
((.	chr1:31405717-31405987(-)$1	1	7	10	9.0000
.((	chr3:160141142-160141355(+)$1	1	21	24	9.0000
((.	chr2:205912722-205912936(+)$1	1	59	62	9.0000
((.	chr3:182989729-182989942(+)$1	1	31	34	9.0000
)))	chr2:172411346-172411558(+)$1	1	25	28	9.0000
...	chr16:50070145-50070366(+)$1	1	0	3	9.0000
..)	chr10:102800011-102800261(+)$1	1	56	59	9.0000
...	chr3:23934056-23934273(-)$1	1	5	8	9.0000
...	chr17:70121067-70121281(+)$1	1	31	34	9.0000
..)	chr7:154876373-154876585(+)$1	1	48	51	9.0000
...	chr9:100848854-100849111(-)$1	1	34	37	9.0000
)))	chr21:15745837-15746064(-)$1	1	89	92	9.0000
((.	chr11:111609479-111609753(-)$1	1	6	9	9.0000
...	chr12:21622850-21623078(+)$1	1	21	24	9.0000
)))	chr17:53240353-53240616(+)$1	1	47	50	9.0000
..(	chr10:70502036-70502338(+)$1	1	11	14	9.0000
)).	chr8:143784928-143785141(+)$1	1	29	32	9.0000
...	chr15:65869940-65870286(+)$1	1	26	29	9.0000
...	chr10:72643386-72643614(-)$1	1	93	96	9.0000
...	chr16:89395159-89395507(-)$1	1	37	40	9.0000
.((	chr6:35549393-35549629(-)$1	1	145	148	9.0000
(((	chr12:60154828-60155043(+)$1	1	103	106	9.0000
.((	chr16:15131115-15131329(+)$1	1	3	6	9.0000
)))	chrX:105937032-105937246(+)$1	1	102	105	9.0000
((.	chr2:204824411-204824859(+)$1	1	23	26	9.0000
...	chr3:57302386-57302606(+)$1	1	10	13	9.0000
(((	chr9:100843728-100843951(-)$1	1	8	11	9.0000
)..	chr9:1056699-1056912(+)$1	1	87	90	9.0000
.((	chr20:57252068-57252355(+)$1	1	0	3	9.0000
..(	chr7:102741598-102741850(-)$1	1	145	148	9.0000
.((	chr3:97673056-97673294(-)$1	1	123	126	9.0000
...	chr17:4850262-4850560(-)$1	1	43	46	9.0000
)))	chr17:729162-729389(-)$1	1	48	51	9.0000
...	chr17:908512-908734(-)$1	1	147	150	9.0000
)))	chr7:98445022-98445274(-)$1	1	177	180	9.0000
(((	chr15:52413415-52413676(-)$1	1	4	7	9.0000
...	chr12:110385323-110385548(-)$1	1	7	10	9.0000
)))	chrX:148073656-148073871(+)$1	1	103	106	9.0000
...	chr12:57493491-57493727(-)$1	1	27	30	9.0000
...	chr5:169675080-169675356(-)$1	1	75	78	9.0000
.))	chrX:118750905-118751346(-)$1	1	44	47	9.0000
...	chr3:19389178-19389399(+)$1	1	4	7	9.0000
...	chr21:34967130-34967350(-)$1	1	108	111	9.0000
(((	chr19:40504120-40504420(+)$1	1	57	60	9.0000
(((	chr19:21300776-21300996(+)$1	1	27	30	9.0000
..(	chr2:176041791-176042043(-)$1	1	2	5	9.0000
...	chr20:55093641-55093866(+)$1	1	33	36	9.0000
((.	chr1:179323061-179323282(+)$1	1	26	29	9.0000
(((	chr12:110369775-110369992(-)$1	1	3	6	9.0000
(((	chr17:54942477-54942710(+)$1	1	49	52	9.0000
...	chr9:131770537-131770758(-)$1	1	165	168	9.0000
((.	chr2:202025066-202025283(+)$1	1	17	20	9.0000
.))	chr5:141368531-141368746(+)$1	1	65	68	9.0000
.))	chr19:58375886-58376136(+)$1	1	104	107	9.0000
(((	chr7:150270855-150271104(+)$1	1	31	34	9.0000
(((	chr2:208477971-208478210(-)$1	1	23	26	9.0000
(((	chr9:100848612-100848841(-)$1	1	5	8	9.0000
)))	chr3:52290525-52290745(-)$1	1	163	166	9.0000
...	chr1:10436787-10437032(+)$1	1	9	12	9.0000
)))	chr1:146629886-146630125(-)$1	1	23	26	9.0000
...	chr1:115259824-115260067(-)$1	1	86	89	9.0000
...	chr3:183890673-183890925(+)$1	1	5	8	9.0000
...	chr22:38339440-38339657(-)$1	1	19	22	9.0000
...	chr5:149781163-149781517(-)$1	1	131	134	9.0000
)).	chr14:60762870-60763113(+)$1	1	79	82	9.0000
...	chr2:206860948-206861218(-)$1	1	86	89	9.0000
(..	chr1:236713935-236714176(-)$1	1	8	11	9.0000
(((	chrX:64742548-64742813(-)$1	1	21	24	9.0000

#PSSM
U : 0.91	u : 0.09	
U : 0.91	u : 0.09	
C : 0.92	c : 0.08	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m3_run1.nuc.txt

#NT
GCAG	chr18:57022634-57022877(-)$1	243	237	241	11.9999
GCAG	chr4:170625178-170625429(+)$1	251	15	19	11.9999
GCAG	chr5:42800842-42801072(-)$1	230	107	111	11.9999
GCAG	chr12:132393614-132393850(+)$1	236	62	66	11.9999
GCAG	chr1:202777148-202777398(-)$1	250	135	139	11.9999
GCAG	chr16:30772883-30773106(-)$1	223	78	82	11.9999
GCAG	chr15:75932133-75932387(-)$1	254	240	244	11.9999
GCAG	chr16:16139646-16139876(+)$1	230	42	46	11.9999
GCAG	chr6:7298877-7299107(-)$1	230	69	73	11.9999
GCAG	chr15:44085900-44086128(+)$1	228	22	26	11.9999
GCAG	chr5:179045062-179045325(-)$1	263	21	25	11.9999
GCAG	chr1:27177617-27177850(+)$1	233	138	142	11.9999
GCAG	chr16:66643587-66643817(+)$1	230	108	112	11.9999
GCAG	chr8:100155238-100155468(+)$1	230	74	78	11.9999
GCAG	chr1:11210139-11210371(-)$1	232	103	107	11.9999
GCAG	chr7:100853733-100853978(-)$1	245	116	120	11.9999
GCAG	chr4:99997494-99997760(-)$1	266	108	112	11.9999
GCAG	chr2:198352507-198352740(-)$1	233	36	40	11.9999
GCAG	chr1:212115151-212115380(-)$1	229	154	158	11.9999
GCAG	chr4:10082907-10083142(-)$1	235	196	200	11.9999
GCAG	chr3:196288173-196288400(-)$1	227	57	61	11.9999
GCAG	chr17:1580204-1580453(-)$1	249	24	28	11.9999
GCAG	chr4:24543434-24543678(-)$1	244	179	183	11.9999
GCAG	chr22:41650214-41650443(-)$1	229	68	72	11.9999
GCAG	chr2:74595114-74595344(-)$1	230	86	90	11.9999
GCAG	chr20:62326094-62326324(+)$1	230	8	12	11.9999
GCAG	chr12:121882194-121882415(+)$1	221	100	104	11.9999
GCAG	chr3:185638803-185639049(-)$1	246	76	80	11.9999
GCAG	chr11:66029315-66029545(+)$1	230	19	23	11.9999
GCAG	chr12:120947788-120948018(-)$1	230	40	44	11.9999
gcag	chr9:82337786-82338044(+)$1	258	240	244	11.9999
GCAG	chr5:132202486-132202726(+)$1	240	70	74	11.9999
GCAG	chr19:59061648-59061914(+)$1	266	31	35	11.9999
GCAG	chr20:20621381-20621611(-)$1	230	149	153	11.9999
GCAG	chr22:20078965-20079200(+)$1	235	107	111	11.9999
GCAG	chr4:187517801-187518025(+)$1	224	62	66	11.9999
GCAG	chr14:64855012-64855257(+)$1	245	5	9	11.9999
GCAG	chr19:5691513-5691749(+)$1	236	25	29	11.9999
GCAG	chr16:58313506-58313729(+)$1	223	84	88	11.9999
GCAG	chr17:74392377-74392670(-)$1	293	142	146	11.9999
GCAG	chr20:57290162-57290408(+)$1	246	18	22	11.9999
GCAG	chr18:29102012-29102242(+)$1	230	65	69	11.9999
GCAG	chr17:73488509-73488756(+)$1	247	78	82	11.9999
GCAG	chr7:16725477-16725714(+)$1	237	87	91	11.9999
GCAG	chr2:163204061-163204288(+)$1	227	58	62	11.9999
GCAG	chr1:161138684-161138926(+)$1	242	94	98	11.9999
GCAG	chrX:47070371-47070633(+)$1	262	161	165	11.9999
GCAG	chr14:21969037-21969265(-)$1	228	122	126	11.9999
GCAG	chr19:5210456-5210691(-)$1	235	19	23	11.9999
GCAG	chr1:224619151-224619382(-)$1	231	99	103	11.9999
GCAG	chr11:46829540-46829772(-)$1	232	4	8	11.9999
GCAG	chr12:14613379-14613606(+)$1	227	78	82	11.9999
GCAG	chr6:35262277-35262499(-)$1	222	10	14	11.9999
GCAG	chr15:90172176-90172400(-)$1	224	8	12	11.9999
GCAG	chr1:1718693-1718938(-)$1	245	183	187	11.9999
GCAG	chrX:149930960-149931186(+)$1	226	52	56	11.9999
GCAG	chr1:47903746-47903967(-)$1	221	136	140	11.9999
gcag	chr19:58024311-58024534(-)$1	223	31	35	11.9999
GCAG	chr19:5206689-5206935(-)$1	246	44	48	11.9999
GCAG	chr19:52146750-52146972(+)$1	222	25	29	11.9999
GCAG	chr1:204379649-204379879(-)$1	230	109	113	11.9999
GCAG	chr10:43882566-43882796(-)$1	230	20	24	11.9999
GCAG	chr11:64536461-64536691(-)$1	230	105	109	11.9999
GCAG	chr6:36823689-36823918(-)$1	229	43	47	11.9999
GCAG	chr5:154179431-154179684(+)$1	253	24	28	11.9999
GCAG	chr17:62496698-62496934(-)$1	236	127	131	11.9999
GCAG	chr2:220432039-220432270(-)$1	231	8	12	11.9999
GCAG	chr16:56871487-56871729(+)$1	242	28	32	11.9999
GCAG	chr20:42315505-42315762(+)$1	257	18	22	11.9999
GCAG	chr16:81398542-81398783(+)$1	241	48	52	11.9999
GCAG	chrM:11588-11820(-)$1	232	76	80	11.9999
GCAG	chr16:74524920-74525160(-)$1	240	59	63	11.9999
GCAG	chr4:1207261-1207493(-)$1	232	2	6	11.9999
GCAG	chr14:102505045-102505305(+)$1	260	50	54	11.9999
GCAG	chr12:80083587-80083811(+)$1	224	78	82	11.9999
GCAG	chr1:43828605-43828836(+)$1	231	75	79	11.9999
GCAG	chr1:55641972-55642204(-)$1	232	203	207	11.9999
GCAG	chr19:48048605-48048829(+)$1	224	1	5	11.9999
GCAG	chr22:18077202-18077434(-)$1	232	48	52	11.9999
GCAG	chr1:58992833-58993075(-)$1	242	90	94	11.9999
GCAG	chrX:39930159-39930413(-)$1	254	163	167	11.9999
GCAG	chr12:76444286-76444516(-)$1	230	110	114	11.9999
GCAG	chr2:97494633-97494856(+)$1	223	110	114	11.9999
GCAG	chr16:89713384-89713633(-)$1	249	76	80	11.9999

#otherMatches

#Struct PSSM
HHHH	chr17:80041331-80041562(-)$1	231	9	13	11.9999
CC}C	chr18:57022634-57022877(-)$1	243	237	241	11.9999
ffff	chr4:170625178-170625429(+)$1	251	15	19	11.9999
ee:d	chr5:42800842-42801072(-)$1	230	107	111	11.9999
44ii	chr12:132393614-132393850(+)$1	236	62	66	11.9999
a[bb	chr1:202777148-202777398(-)$1	250	135	139	11.9999
dddd	chr16:30772883-30773106(-)$1	223	78	82	11.9999
gggg	chr15:75932133-75932387(-)$1	254	240	244	11.9999
eeee	chr16:16139646-16139876(+)$1	230	42	46	11.9999
:a!!	chr6:7298877-7299107(-)$1	230	69	73	11.9999
BB{E	chr15:44085900-44086128(+)$1	228	22	26	11.9999
ccoo	chr5:179045062-179045325(-)$1	263	21	25	11.9999
eell	chr1:27177617-27177850(+)$1	233	138	142	11.9999
ffff	chr16:66643587-66643817(+)$1	230	108	112	11.9999
bbll	chr8:100155238-100155468(+)$1	230	74	78	11.9999
ccll	chr1:11210139-11210371(-)$1	232	103	107	11.9999
gggg	chr7:100853733-100853978(-)$1	245	116	120	11.9999
ffff	chr4:99997494-99997760(-)$1	266	108	112	11.9999
cccc	chr2:198352507-198352740(-)$1	233	36	40	11.9999
ccCC	chr1:212115151-212115380(-)$1	229	154	158	11.9999
ccc[	chr4:10082907-10083142(-)$1	235	196	200	11.9999
nnnn	chr3:196288173-196288400(-)$1	227	57	61	11.9999
eeee	chr17:1580204-1580453(-)$1	249	24	28	11.9999
eeee	chr4:24543434-24543678(-)$1	244	179	183	11.9999
2a22	chr22:41650214-41650443(-)$1	229	68	72	11.9999
oooo	chr2:74595114-74595344(-)$1	230	86	90	11.9999
bbtt	chr20:62326094-62326324(+)$1	230	8	12	11.9999
dddd	chr12:121882194-121882415(+)$1	221	100	104	11.9999
i###	chr3:185638803-185639049(-)$1	246	76	80	11.9999
gggg	chr11:66029315-66029545(+)$1	230	19	23	11.9999
cc[a	chr12:120947788-120948018(-)$1	230	40	44	11.9999
====	chr9:82337786-82338044(+)$1	258	240	244	11.9999
::::	chr5:132202486-132202726(+)$1	240	70	74	11.9999
CC{E	chr19:59061648-59061914(+)$1	266	31	35	11.9999
qqqq	chr20:20621381-20621611(-)$1	230	149	153	11.9999
3ccc	chr22:20078965-20079200(+)$1	235	107	111	11.9999
''''	chr4:187517801-187518025(+)$1	224	62	66	11.9999
BBKK	chr14:64855012-64855257(+)$1	245	5	9	11.9999
nnnn	chr19:5691513-5691749(+)$1	236	25	29	11.9999
ff[d	chr16:58313506-58313729(+)$1	223	84	88	11.9999
bbb4	chr17:74392377-74392670(-)$1	293	142	146	11.9999
MMMC	chr20:57290162-57290408(+)$1	246	18	22	11.9999
CCCg	chr18:29102012-29102242(+)$1	230	65	69	11.9999
famm	chr17:73488509-73488756(+)$1	247	78	82	11.9999
cc!!	chr7:16725477-16725714(+)$1	237	87	91	11.9999
CCC:	chr2:163204061-163204288(+)$1	227	58	62	11.9999
ffff	chr1:161138684-161138926(+)$1	242	94	98	11.9999
gggg	chrX:47070371-47070633(+)$1	262	161	165	11.9999
ff[b	chr14:21969037-21969265(-)$1	228	122	126	11.9999
EEEE	chr19:5210456-5210691(-)$1	235	19	23	11.9999
ffff	chr1:224619151-224619382(-)$1	231	99	103	11.9999
BBMM	chr11:46829540-46829772(-)$1	232	4	8	11.9999
ffff	chr12:14613379-14613606(+)$1	227	78	82	11.9999
dddJ	chr6:35262277-35262499(-)$1	222	10	14	11.9999
IIII	chr15:90172176-90172400(-)$1	224	8	12	11.9999
cc]f	chr1:1718693-1718938(-)$1	245	183	187	11.9999
====	chrX:149930960-149931186(+)$1	226	52	56	11.9999
eeee	chr1:47903746-47903967(-)$1	221	136	140	11.9999
FFFF	chr19:58024311-58024534(-)$1	223	31	35	11.9999
hh!!	chr19:5206689-5206935(-)$1	246	44	48	11.9999
d]bb	chr19:52146750-52146972(+)$1	222	25	29	11.9999
dd]g	chr1:204379649-204379879(-)$1	230	109	113	11.9999
ddd]	chr10:43882566-43882796(-)$1	230	20	24	11.9999
bbll	chr11:64536461-64536691(-)$1	230	105	109	11.9999
ffmm	chr6:36823689-36823918(-)$1	229	43	47	11.9999
DD{B	chr5:154179431-154179684(+)$1	253	24	28	11.9999
mddd	chr17:62496698-62496934(-)$1	236	127	131	11.9999
C{BB	chr2:220432039-220432270(-)$1	231	8	12	11.9999
dddl	chr16:56871487-56871729(+)$1	242	28	32	11.9999
$ddd	chr20:42315505-42315762(+)$1	257	18	22	11.9999
ffff	chr16:81398542-81398783(+)$1	241	48	52	11.9999
pppp	chrM:11588-11820(-)$1	232	76	80	11.9999
8888	chr16:74524920-74525160(-)$1	240	59	63	11.9999
dddh	chr4:1207261-1207493(-)$1	232	2	6	11.9999
{BBE	chr14:102505045-102505305(+)$1	260	50	54	11.9999
[a!!	chr12:80083587-80083811(+)$1	224	78	82	11.9999
dd:A	chr1:43828605-43828836(+)$1	231	75	79	11.9999
CCYY	chr1:55641972-55642204(-)$1	232	203	207	11.9999
::dd	chr19:48048605-48048829(+)$1	224	1	5	11.9999
ccc]	chr22:18077202-18077434(-)$1	232	48	52	11.9999
7bbe	chr1:58992833-58993075(-)$1	242	90	94	11.9999
DDD:	chrX:39930159-39930413(-)$1	254	163	167	11.9999
]ccc	chr12:76444286-76444516(-)$1	230	110	114	11.9999
eeee	chr2:97494633-97494856(+)$1	223	110	114	11.9999
gg[d	chr16:89713384-89713633(-)$1	249	76	80	11.9999

#DB
((((	chr17:80041331-80041562(-)$1	1	9	13	11.9999
)).)	chr18:57022634-57022877(-)$1	1	237	241	11.9999
((((	chr4:170625178-170625429(+)$1	1	15	19	11.9999
)).(	chr5:42800842-42801072(-)$1	1	107	111	11.9999
..))	chr12:132393614-132393850(+)$1	1	62	66	11.9999
(.((	chr1:202777148-202777398(-)$1	1	135	139	11.9999
((((	chr16:30772883-30773106(-)$1	1	78	82	11.9999
))))	chr15:75932133-75932387(-)$1	1	240	244	11.9999
))))	chr16:16139646-16139876(+)$1	1	42	46	11.9999
.(..	chr6:7298877-7299107(-)$1	1	69	73	11.9999
((.(	chr15:44085900-44086128(+)$1	1	22	26	11.9999
((..	chr5:179045062-179045325(-)$1	1	21	25	11.9999
((..	chr1:27177617-27177850(+)$1	1	138	142	11.9999
))))	chr16:66643587-66643817(+)$1	1	108	112	11.9999
((..	chr8:100155238-100155468(+)$1	1	74	78	11.9999
((..	chr1:11210139-11210371(-)$1	1	103	107	11.9999
))))	chr7:100853733-100853978(-)$1	1	116	120	11.9999
((((	chr4:99997494-99997760(-)$1	1	108	112	11.9999
))))	chr2:198352507-198352740(-)$1	1	36	40	11.9999
))))	chr1:212115151-212115380(-)$1	1	154	158	11.9999
(((.	chr4:10082907-10083142(-)$1	1	196	200	11.9999
....	chr3:196288173-196288400(-)$1	1	57	61	11.9999
((((	chr17:1580204-1580453(-)$1	1	24	28	11.9999
((((	chr4:24543434-24543678(-)$1	1	179	183	11.9999
.)..	chr22:41650214-41650443(-)$1	1	68	72	11.9999
....	chr2:74595114-74595344(-)$1	1	86	90	11.9999
((..	chr20:62326094-62326324(+)$1	1	8	12	11.9999
((((	chr12:121882194-121882415(+)$1	1	100	104	11.9999
(...	chr3:185638803-185639049(-)$1	1	76	80	11.9999
((((	chr11:66029315-66029545(+)$1	1	19	23	11.9999
((.(	chr12:120947788-120948018(-)$1	1	40	44	11.9999
))))	chr9:82337786-82338044(+)$1	1	240	244	11.9999
....	chr5:132202486-132202726(+)$1	1	70	74	11.9999
((.(	chr19:59061648-59061914(+)$1	1	31	35	11.9999
....	chr20:20621381-20621611(-)$1	1	149	153	11.9999
.)))	chr22:20078965-20079200(+)$1	1	107	111	11.9999
....	chr4:187517801-187518025(+)$1	1	62	66	11.9999
((..	chr14:64855012-64855257(+)$1	1	5	9	11.9999
....	chr19:5691513-5691749(+)$1	1	25	29	11.9999
((.(	chr16:58313506-58313729(+)$1	1	84	88	11.9999
))).	chr17:74392377-74392670(-)$1	1	142	146	11.9999
...(	chr20:57290162-57290408(+)$1	1	18	22	11.9999
((((	chr18:29102012-29102242(+)$1	1	65	69	11.9999
((..	chr17:73488509-73488756(+)$1	1	78	82	11.9999
((..	chr7:16725477-16725714(+)$1	1	87	91	11.9999
(((.	chr2:163204061-163204288(+)$1	1	58	62	11.9999
))))	chr1:161138684-161138926(+)$1	1	94	98	11.9999
))))	chrX:47070371-47070633(+)$1	1	161	165	11.9999
((.(	chr14:21969037-21969265(-)$1	1	122	126	11.9999
((((	chr19:5210456-5210691(-)$1	1	19	23	11.9999
))))	chr1:224619151-224619382(-)$1	1	99	103	11.9999
((..	chr11:46829540-46829772(-)$1	1	4	8	11.9999
((((	chr12:14613379-14613606(+)$1	1	78	82	11.9999
)))(	chr6:35262277-35262499(-)$1	1	10	14	11.9999
((((	chr15:90172176-90172400(-)$1	1	8	12	11.9999
)).)	chr1:1718693-1718938(-)$1	1	183	187	11.9999
((((	chrX:149930960-149931186(+)$1	1	52	56	11.9999
((((	chr1:47903746-47903967(-)$1	1	136	140	11.9999
((((	chr19:58024311-58024534(-)$1	1	31	35	11.9999
((..	chr19:5206689-5206935(-)$1	1	44	48	11.9999
).))	chr19:52146750-52146972(+)$1	1	25	29	11.9999
)).)	chr1:204379649-204379879(-)$1	1	109	113	11.9999
))).	chr10:43882566-43882796(-)$1	1	20	24	11.9999
((..	chr11:64536461-64536691(-)$1	1	105	109	11.9999
((..	chr6:36823689-36823918(-)$1	1	43	47	11.9999
((.(	chr5:154179431-154179684(+)$1	1	24	28	11.9999
.)))	chr17:62496698-62496934(-)$1	1	127	131	11.9999
(.((	chr2:220432039-220432270(-)$1	1	8	12	11.9999
(((.	chr16:56871487-56871729(+)$1	1	28	32	11.9999
.(((	chr20:42315505-42315762(+)$1	1	18	22	11.9999
))))	chr16:81398542-81398783(+)$1	1	48	52	11.9999
....	chrM:11588-11820(-)$1	1	76	80	11.9999
....	chr16:74524920-74525160(-)$1	1	59	63	11.9999
((((	chr4:1207261-1207493(-)$1	1	2	6	11.9999
.(((	chr14:102505045-102505305(+)$1	1	50	54	11.9999
.(..	chr12:80083587-80083811(+)$1	1	78	82	11.9999
)).)	chr1:43828605-43828836(+)$1	1	75	79	11.9999
))..	chr1:55641972-55642204(-)$1	1	203	207	11.9999
..((	chr19:48048605-48048829(+)$1	1	1	5	11.9999
))).	chr22:18077202-18077434(-)$1	1	48	52	11.9999
.)))	chr1:58992833-58993075(-)$1	1	90	94	11.9999
(((.	chrX:39930159-39930413(-)$1	1	163	167	11.9999
.)))	chr12:76444286-76444516(-)$1	1	110	114	11.9999
))))	chr2:97494633-97494856(+)$1	1	110	114	11.9999
((.(	chr16:89713384-89713633(-)$1	1	76	80	11.9999

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

#score	1019.9999999999998
#seq	85
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m2_run1.nuc.txt

#NT
AACUUGGGAGGGUUCCCUGGGGUGGGCUGGGGUGGCGGUGGCCAGUCACCUCUAACUGCUGUCCCGCCUGCUUGCAGACCUGCUGCGGAUGUUCUUUGACGCACUGUAUGACGAGGACGUGGUGAAGGAGGAUGCCUUCUACAGUUGGGAGAGUAGCAAGGACCCCGCUGAGCAGCAGGGCAAGGGUGUGGCCCUUAAAUCUGUCACAGCCUUCUUCAAGUGGCUCCGUGAAGCAGAGGAGGAGUCUGACCACAACU	chr3:184052428-184052698(+)$1	270	9	266	288.5000

#otherMatches

#Struct PSSM
EKKDDDD{BB:::::cccpppppppcccJJJJJJJJJJccclllccc:bb"""ffffff[bboooooobb]ffffff22bb::::::::::ffffff[ccc[ccc[aooooooa]ccc]ccc]ffffff:::bb[ddddrrrrrrrrrdddd]bbJJJJJJJJJJccc[eeeee[cccnnnnnccc]eeeee]ccc:::::::BB}DDDDYYEEEEE}CCCYYBB}FFFFFF:::::::::::::::::::::::::	chr1:67890717-67891000(-)$1	283	16	273	288.5000
gggggmmmmgggggggcccggggggga[a[cccbb[ddddoooooodddd]bb]ccc]a]a]ggggggg:EEEEELLLHHHHHHHHbbbb[ffffff[bb[ccc[bbrrrrrrrrrbbcccbb]ffffff]bb]bb:::::dddd[cccvvvvvvvvvvvvvccc]dddd:HHHHHHHHEEEEEccc!!cccdddd"""eeeeecccddddssssssssssdddd22ccc22eeeee]dddd]ccc22ccc::::::	chr3:184052428-184052698(+)$1	270	9	266	288.5000

#DB
(..((((.((.....(((.......)))(((((((((((((...))).((...((((((.((......)).))))))..))..........((((((.(((.(((.(......).))).))).))))))...((.((((.........)))).))))))))))))(((.(((((.(((.....))).))))).))).......)).))))..))))).)))..)).)))))).........................	chr1:67890717-67891000(-)$1	1	16	273	288.5000
(((((....))))))))))((((((((.(.(((((.((((......)))).)).))).).).))))))).(((((...((((((((((((.((((((.((.(((.((.........))))))).)))))).)).)).....((((.(((.............))).)))).)))))))))))))(((..(((((((...((((((((((((..........))))..)))..))))).)))).)))..)))......	chr3:184052428-184052698(+)$1	1	9	266	288.5000

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

#score	577.0
#seq	2
#width	257
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m1_run1.nuc.txt

#NT
UUUGUUUUU	chr7:150774981-150775241(-)$1	260	239	248	19.4418
UUUUUUUUU	chr15:99506165-99506412(+)$1	247	236	245	23.6279
UAUUUUUUU	chr14:102550149-102550376(-)$1	227	44	53	19.3255
uuuuuuuuu	chr7:100279087-100279337(-)$1	250	199	208	23.6279
UUUUCUUUU	chr22:38879461-38879702(-)$1	241	218	227	19.2093
UUCUUUUUU	chr7:123324001-123324222(-)$1	221	57	66	18.9767
UUUUUUUUU	chr16:29821852-29822088(+)$1	236	131	140	23.6279
UUUUUGUUU	chr2:26357811-26358050(+)$1	239	174	183	19.9069
UUUUUGUUU	chr1:78343294-78343563(+)$1	269	203	212	19.9069
uuuuuuuuu	chr12:74933814-74934055(+)$1	241	39	48	23.6279
UUUUUUUGU	chr19:10795886-10796159(+)$1	273	25	34	19.0930
UUUUUUUUU	chr1:156436018-156436311(-)$1	293	210	219	23.6279
UUUUUUUUU	chr1:90401376-90401630(+)$1	254	29	38	23.6279
UUUCUUUUU	chr5:133307991-133308227(-)$1	236	11	20	19.4418
UAUUUUUUU	chr5:137523619-137523880(-)$1	261	59	68	19.3255
uuuuuuuuu	chr13:47326839-47327076(+)$1	237	54	63	23.6279
UUUUUCUUU	chr12:124499014-124499269(+)$1	255	235	244	19.6744
UUUUUUUUU	chr12:106632218-106632449(-)$1	231	65	74	23.6279
UUUUUUUUU	chr2:85771641-85771881(+)$1	240	143	152	23.6279
UUUUUUCUU	chr6:7288971-7289203(-)$1	232	92	101	18.9767
UUUUUUUAU	chr2:128460571-128460816(+)$1	245	30	39	19.2093
UUUUUUUUU	chr16:29821755-29822001(+)$1	246	228	237	23.6279
UGUUUUUUU	chr2:179369596-179369826(+)$1	230	57	66	19.2093
UUUGUUUUU	chr9:139006561-139006818(-)$1	257	157	166	19.4418
UUGUUUUUU	chr14:34903301-34903531(-)$1	230	73	82	18.9767
UUUAUUUUU	chr2:55199950-55200197(-)$1	247	30	39	19.3255
uuuuuguuu	chr5:153854507-153854821(-)$1	314	81	90	19.9069
UUUUUCUUU	chr14:23779405-23779654(+)$1	249	74	83	19.6744
UUUUUGUUU	chr1:114516425-114516710(+)$1	285	179	188	19.9069
GUUUUUUUU	chr17:62500796-62501016(-)$1	220	39	48	19.0930
UCUUUUUUU	chr9:117360041-117360303(+)$1	262	220	229	19.2093
GUUUUUUUU	chr17:62500782-62501002(-)$1	220	25	34	19.0930
UUUUUAUUU	chr17:35294906-35295159(+)$1	253	209	218	19.5581
UUUUGUUUU	chr20:39751973-39752203(+)$1	230	204	213	19.4418
UUUUUUUUU	chr3:170111256-170111488(+)$1	232	111	120	23.6279
UUUUUUGUU	chr2:38536456-38536689(-)$1	233	26	35	18.9767
UUUUGUUUU	chr10:14562231-14562456(-)$1	225	19	28	19.4418
uuuuuuuuu	chr5:172662174-172662396(-)$1	222	2	11	23.6279
uuuuuuuau	chr1:32636788-32637019(+)$1	231	35	44	19.2093
uuuuguuuu	chr7:90018162-90018392(+)$1	230	209	218	19.4418
UUUCUUUUU	chr14:81942257-81942480(-)$1	223	103	112	19.4418
UUUUUUUUU	chr1:244219002-244219276(+)$1	274	31	40	23.6279

#otherMatches

#Struct PSSM
wwwwwwwww	chr7:157060789-157061015(+)$1	226	145	154	23.6279
YIIIIIIII	chr7:150774981-150775241(-)$1	260	239	248	19.4418
:::::::::	chr15:99506165-99506412(+)$1	247	236	245	23.6279
uuuuuuuue	chr14:102550149-102550376(-)$1	227	44	53	19.3255
hhhhhhhhz	chr7:100279087-100279337(-)$1	250	199	208	23.6279
H|||||||C	chr22:38879461-38879702(-)$1	241	218	227	19.2093
cc]iiiiii	chr7:123324001-123324222(-)$1	221	57	66	18.9767
^^^^^^^^^	chr16:29821852-29822088(+)$1	236	131	140	23.6279
44ggggggg	chr2:26357811-26358050(+)$1	239	174	183	19.9069
nnnnnbb44	chr1:78343294-78343563(+)$1	269	203	212	19.9069
(((((iiii	chr12:74933814-74934055(+)$1	241	39	48	23.6279
gggggggii	chr19:10795886-10796159(+)$1	273	25	34	19.0930
fff%%%%%%	chr1:156436018-156436311(-)$1	293	210	219	23.6279
=========	chr1:90401376-90401630(+)$1	254	29	38	23.6279
EEEKKFFFF	chr5:133307991-133308227(-)$1	236	11	20	19.4418
f::::::::	chr5:137523619-137523880(-)$1	261	59	68	19.3255
mmmm=====	chr13:47326839-47327076(+)$1	237	54	63	23.6279
333ccceee	chr12:124499014-124499269(+)$1	255	235	244	19.6744
:::::::::	chr12:106632218-106632449(-)$1	231	65	74	23.6279
ggggggsss	chr2:85771641-85771881(+)$1	240	143	152	23.6279
hhhhh++++	chr6:7288971-7289203(-)$1	232	92	101	18.9767
dqqqqqqqq	chr2:128460571-128460816(+)$1	245	30	39	19.2093
:::::::::	chr16:29821755-29822001(+)$1	246	228	237	23.6279
'ddddmmmm	chr2:179369596-179369826(+)$1	230	57	66	19.2093
(========	chr9:139006561-139006818(-)$1	257	157	166	19.4418
ggggggg[g	chr14:34903301-34903531(-)$1	230	73	82	18.9767
qqqqqqfff	chr2:55199950-55200197(-)$1	247	30	39	19.3255
:::::dddd	chr5:153854507-153854821(-)$1	314	81	90	19.9069
####ccc""	chr14:23779405-23779654(+)$1	249	74	83	19.6744
eeeee]fff	chr1:114516425-114516710(+)$1	285	179	188	19.9069
hhhhhhDDD	chr17:62500796-62501016(-)$1	220	39	48	19.0930
[ccc$$$$$	chr9:117360041-117360303(+)$1	262	220	229	19.2093
hhhhhhDDD	chr17:62500782-62501002(-)$1	220	25	34	19.0930
:::::::::	chr17:35294906-35295159(+)$1	253	209	218	19.5581
2dddd4444	chr20:39751973-39752203(+)$1	230	204	213	19.4418
hhhhhhppp	chr3:170111256-170111488(+)$1	232	111	120	23.6279
ccc"""fff	chr2:38536456-38536689(-)$1	233	26	35	18.9767
JJ::ggggg	chr10:14562231-14562456(-)$1	225	19	28	19.4418
:::::::::	chr5:172662174-172662396(-)$1	222	2	11	23.6279
ee:::::::	chr1:32636788-32637019(+)$1	231	35	44	19.2093
:::HHHHHH	chr7:90018162-90018392(+)$1	230	209	218	19.4418
qqqqqqqqd	chr14:81942257-81942480(-)$1	223	103	112	19.4418
FFFLLLCCC	chr1:244219002-244219276(+)$1	274	31	40	23.6279

#DB
.........	chr7:157060789-157061015(+)$1	1	145	154	23.6279
.))))))))	chr7:150774981-150775241(-)$1	1	239	248	19.4418
.........	chr15:99506165-99506412(+)$1	1	236	245	23.6279
........)	chr14:102550149-102550376(-)$1	1	44	53	19.3255
((((((((.	chr7:100279087-100279337(-)$1	1	199	208	23.6279
).......)	chr22:38879461-38879702(-)$1	1	218	227	19.2093
)).))))))	chr7:123324001-123324222(-)$1	1	57	66	18.9767
.........	chr16:29821852-29822088(+)$1	1	131	140	23.6279
..)))))))	chr2:26357811-26358050(+)$1	1	174	183	19.9069
.....))..	chr1:78343294-78343563(+)$1	1	203	212	19.9069
.....((((	chr12:74933814-74934055(+)$1	1	39	48	23.6279
(((((((((	chr19:10795886-10796159(+)$1	1	25	34	19.0930
(((......	chr1:156436018-156436311(-)$1	1	210	219	23.6279
(((((((((	chr1:90401376-90401630(+)$1	1	29	38	23.6279
(((..((((	chr5:133307991-133308227(-)$1	1	11	20	19.4418
)........	chr5:137523619-137523880(-)$1	1	59	68	19.3255
....)))))	chr13:47326839-47327076(+)$1	1	54	63	23.6279
...))))))	chr12:124499014-124499269(+)$1	1	235	244	19.6744
.........	chr12:106632218-106632449(-)$1	1	65	74	23.6279
((((((...	chr2:85771641-85771881(+)$1	1	143	152	23.6279
(((((....	chr6:7288971-7289203(-)$1	1	92	101	18.9767
(........	chr2:128460571-128460816(+)$1	1	30	39	19.2093
.........	chr16:29821755-29822001(+)$1	1	228	237	23.6279
.((((....	chr2:179369596-179369826(+)$1	1	57	66	19.2093
.((((((((	chr9:139006561-139006818(-)$1	1	157	166	19.4418
(((((((.(	chr14:34903301-34903531(-)$1	1	73	82	18.9767
......)))	chr2:55199950-55200197(-)$1	1	30	39	19.3255
.....((((	chr5:153854507-153854821(-)$1	1	81	90	19.9069
....(((..	chr14:23779405-23779654(+)$1	1	74	83	19.6744
))))).)))	chr1:114516425-114516710(+)$1	1	179	188	19.9069
))))))(((	chr17:62500796-62501016(-)$1	1	39	48	19.0930
.(((.....	chr9:117360041-117360303(+)$1	1	220	229	19.2093
))))))(((	chr17:62500782-62501002(-)$1	1	25	34	19.0930
.........	chr17:35294906-35295159(+)$1	1	209	218	19.5581
.))))....	chr20:39751973-39752203(+)$1	1	204	213	19.4418
((((((...	chr3:170111256-170111488(+)$1	1	111	120	23.6279
(((...(((	chr2:38536456-38536689(-)$1	1	26	35	18.9767
((..(((((	chr10:14562231-14562456(-)$1	1	19	28	19.4418
.........	chr5:172662174-172662396(-)$1	1	2	11	23.6279
)).......	chr1:32636788-32637019(+)$1	1	35	44	19.2093
...))))))	chr7:90018162-90018392(+)$1	1	209	218	19.4418
........)	chr14:81942257-81942480(-)$1	1	103	112	19.4418
(((...(((	chr1:244219002-244219276(+)$1	1	31	40	23.6279

#PSSM
U : 0.79	u : 0.16	G : 0.04	
U : 0.74	u : 0.16	A : 0.04	G : 0.02	C : 0.02	
U : 0.79	u : 0.16	C : 0.02	G : 0.02	
U : 0.72	u : 0.16	G : 0.04	C : 0.04	A : 0.02	
U : 0.76	u : 0.13	G : 0.04	C : 0.02	g : 0.02	
U : 0.69	u : 0.13	G : 0.06	C : 0.04	g : 0.02	A : 0.02	
U : 0.79	u : 0.16	C : 0.02	G : 0.02	
U : 0.79	u : 0.13	G : 0.02	A : 0.02	a : 0.02	
U : 0.83	u : 0.16	

#score	892.6279069767443
#seq	43
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m2_run1.nuc.txt

#NT
UUCU	chr4:962591-962813(-)$1	222	7	11	12.0000
UUCU	chr4:82125847-82126062(+)$1	215	133	137	12.0000
UUCU	chr3:54157495-54157715(+)$1	220	32	36	12.0000
UUCU	chr12:20522464-20522682(+)$1	218	180	184	12.0000
UUCU	chr6:157495929-157496149(+)$1	220	74	78	12.0000
UUCU	chr11:128844424-128844646(-)$1	222	189	193	12.0000
UUCU	chr2:178370129-178370344(+)$1	215	22	26	12.0000
UUCU	chr19:37130159-37130376(+)$1	217	4	8	12.0000
UUCU	chr1:201453036-201453268(-)$1	232	110	114	12.0000
UUCU	chr11:4615867-4616082(+)$1	215	74	78	12.0000
UUCU	chr4:39843435-39843680(+)$1	245	62	66	12.0000
UUCU	chr20:61299250-61299471(+)$1	221	213	217	12.0000
UUCU	chr19:15540361-15540579(-)$1	218	213	217	12.0000
UUCU	chr19:54692206-54692431(-)$1	225	35	39	12.0000
UUCU	chr1:223116315-223116538(+)$1	223	46	50	12.0000
UUCU	chr6:75797294-75797511(-)$1	217	172	176	12.0000
UUCU	chr4:68383757-68383976(+)$1	219	26	30	12.0000
UUCU	chrX:9864635-9864859(-)$1	224	58	62	12.0000
UUCU	chr15:51828934-51829158(-)$1	224	101	105	12.0000
UUCU	chr3:45987872-45988088(-)$1	216	123	127	12.0000
UUCU	chr7:101923258-101923477(+)$1	219	45	49	12.0000
UUCU	chr1:160213720-160213945(-)$1	225	67	71	12.0000
UUCU	chr11:113076769-113076990(+)$1	221	147	151	12.0000
UUCU	chr6:75893527-75893765(+)$1	238	68	72	12.0000
UUCU	chr1:150533772-150533993(+)$1	221	1	5	12.0000
UUCU	chr8:99960366-99960581(+)$1	215	4	8	12.0000
UUCU	chr2:220081334-220081558(-)$1	224	169	173	12.0000
UUCU	chr9:17795498-17795719(+)$1	221	12	16	12.0000
UUCU	chr16:24828084-24828311(+)$1	227	216	220	12.0000
UUCU	chrX:9914616-9914832(-)$1	216	54	58	12.0000
UUCU	chr16:14334407-14334628(+)$1	221	50	54	12.0000
UUCU	chr3:142280963-142281178(+)$1	215	17	21	12.0000
UUCU	chr9:99797753-99797972(+)$1	219	21	25	12.0000
UUCU	chr20:40827860-40828079(-)$1	219	166	170	12.0000
UUCU	chr16:18809945-18810163(-)$1	218	126	130	12.0000
UUCU	chr17:73895587-73895802(-)$1	215	177	181	12.0000
UUCU	chr6:31960190-31960406(-)$1	216	178	182	12.0000
UUCU	chr2:216995559-216995784(+)$1	225	22	26	12.0000
UUCU	chr3:113127846-113128065(+)$1	219	210	214	12.0000
UUCU	chr1:120285393-120285619(+)$1	226	24	28	12.0000
UUCU	chr19:10671784-10672002(-)$1	218	46	50	12.0000
uucu	chr1:230805137-230805355(+)$1	218	178	182	12.0000
UUCU	chr1:204403598-204403826(-)$1	228	11	15	12.0000
UUCU	chr7:107880340-107880559(-)$1	219	109	113	12.0000
UUCU	chr17:26942677-26942897(-)$1	220	54	58	12.0000
UUCU	chr9:91159261-91159484(+)$1	223	19	23	12.0000
UUCU	chr1:21934713-21934942(-)$1	229	219	223	12.0000
UUCU	chr19:40718681-40718899(-)$1	218	40	44	12.0000
UUCU	chr3:69088649-69088864(-)$1	215	3	7	12.0000
UUCU	chr20:13134538-13134761(+)$1	223	69	73	12.0000
UUCU	chr3:49749883-49750118(+)$1	235	124	128	12.0000
UUCU	chr4:118005493-118005709(-)$1	216	58	62	12.0000
UUCU	chr19:39899118-39899341(+)$1	223	211	215	12.0000
UUCU	chr15:77322739-77322969(-)$1	230	90	94	12.0000
UUCU	chr12:53451722-53451938(+)$1	216	51	55	12.0000
UUCU	chr9:128321783-128322028(-)$1	245	137	141	12.0000
UUCU	chr5:167589570-167589793(+)$1	223	17	21	12.0000
UUCU	chr2:54850589-54850808(+)$1	219	195	199	12.0000
UUCU	chr16:22360597-22360813(-)$1	216	30	34	12.0000
UUCU	chr5:74016195-74016412(+)$1	217	26	30	12.0000
UUCU	chr2:166032770-166033000(-)$1	230	32	36	12.0000
UUCU	chr1:3410833-3411075(-)$1	242	116	120	12.0000
UUCU	chr3:15621366-15621587(-)$1	221	26	30	12.0000
UUCU	chr4:160252681-160252901(+)$1	220	63	67	12.0000
UUCU	chr15:43928209-43928432(-)$1	223	7	11	12.0000
UUCU	chr13:36699980-36700199(-)$1	219	45	49	12.0000
UUCU	chr7:75912714-75912963(+)$1	249	110	114	12.0000
UUCU	chr7:100634939-100635154(-)$1	215	155	159	12.0000
UUCU	chr9:117379362-117379634(+)$1	272	10	14	12.0000
UUCU	chr7:38869731-38869964(-)$1	233	26	30	12.0000
UUCU	chr11:111866751-111866971(+)$1	220	6	10	12.0000
UUCU	chr16:331797-332022(+)$1	225	217	221	12.0000

#otherMatches

#Struct PSSM
hhhh	chr21:35172018-35172235(+)$1	217	44	48	12.0000
MMMM	chr4:962591-962813(-)$1	222	7	11	12.0000
:::f	chr4:82125847-82126062(+)$1	215	133	137	12.0000
ccc[	chr3:54157495-54157715(+)$1	220	32	36	12.0000
B}GG	chr12:20522464-20522682(+)$1	218	180	184	12.0000
::::	chr6:157495929-157496149(+)$1	220	74	78	12.0000
ssss	chr11:128844424-128844646(-)$1	222	189	193	12.0000
IIID	chr2:178370129-178370344(+)$1	215	22	26	12.0000
DDOO	chr19:37130159-37130376(+)$1	217	4	8	12.0000
hhhh	chr1:201453036-201453268(-)$1	232	110	114	12.0000
::::	chr11:4615867-4616082(+)$1	215	74	78	12.0000
tttt	chr4:39843435-39843680(+)$1	245	62	66	12.0000
HHHH	chr20:61299250-61299471(+)$1	221	213	217	12.0000
ffff	chr19:15540361-15540579(-)$1	218	213	217	12.0000
pppp	chr19:54692206-54692431(-)$1	225	35	39	12.0000
vbbd	chr1:223116315-223116538(+)$1	223	46	50	12.0000
IIII	chr6:75797294-75797511(-)$1	217	172	176	12.0000
mmme	chr4:68383757-68383976(+)$1	219	26	30	12.0000
JJJJ	chrX:9864635-9864859(-)$1	224	58	62	12.0000
5555	chr15:51828934-51829158(-)$1	224	101	105	12.0000
hhhh	chr3:45987872-45988088(-)$1	216	123	127	12.0000
D{JJ	chr7:101923258-101923477(+)$1	219	45	49	12.0000
^^^^	chr1:160213720-160213945(-)$1	225	67	71	12.0000
8888	chr11:113076769-113076990(+)$1	221	147	151	12.0000
5555	chr6:75893527-75893765(+)$1	238	68	72	12.0000
:::c	chr1:150533772-150533993(+)$1	221	1	5	12.0000
====	chr8:99960366-99960581(+)$1	215	4	8	12.0000
dddd	chr2:220081334-220081558(-)$1	224	169	173	12.0000
EEEE	chr9:17795498-17795719(+)$1	221	12	16	12.0000
DDYY	chr16:24828084-24828311(+)$1	227	216	220	12.0000
mmmm	chrX:9914616-9914832(-)$1	216	54	58	12.0000
tttt	chr16:14334407-14334628(+)$1	221	50	54	12.0000
c!!f	chr3:142280963-142281178(+)$1	215	17	21	12.0000
ccc!	chr9:99797753-99797972(+)$1	219	21	25	12.0000
ee!!	chr20:40827860-40828079(-)$1	219	166	170	12.0000
33bb	chr16:18809945-18810163(-)$1	218	126	130	12.0000
C}EE	chr17:73895587-73895802(-)$1	215	177	181	12.0000
fffn	chr6:31960190-31960406(-)$1	216	178	182	12.0000
JJJJ	chr2:216995559-216995784(+)$1	225	22	26	12.0000
FF::	chr3:113127846-113128065(+)$1	219	210	214	12.0000
rrrr	chr1:120285393-120285619(+)$1	226	24	28	12.0000
JJJJ	chr19:10671784-10672002(-)$1	218	46	50	12.0000
CCCH	chr1:230805137-230805355(+)$1	218	178	182	12.0000
qqqq	chr1:204403598-204403826(-)$1	228	11	15	12.0000
c:::	chr7:107880340-107880559(-)$1	219	109	113	12.0000
##bb	chr17:26942677-26942897(-)$1	220	54	58	12.0000
DCCC	chr9:91159261-91159484(+)$1	223	19	23	12.0000
ddDD	chr1:21934713-21934942(-)$1	229	219	223	12.0000
pppp	chr19:40718681-40718899(-)$1	218	40	44	12.0000
::::	chr3:69088649-69088864(-)$1	215	3	7	12.0000
mmmm	chr20:13134538-13134761(+)$1	223	69	73	12.0000
ffff	chr3:49749883-49750118(+)$1	235	124	128	12.0000
eEEE	chr4:118005493-118005709(-)$1	216	58	62	12.0000
??CC	chr19:39899118-39899341(+)$1	223	211	215	12.0000
::::	chr15:77322739-77322969(-)$1	230	90	94	12.0000
$$$$	chr12:53451722-53451938(+)$1	216	51	55	12.0000
DD::	chr9:128321783-128322028(-)$1	245	137	141	12.0000
::::	chr5:167589570-167589793(+)$1	223	17	21	12.0000
]eee	chr2:54850589-54850808(+)$1	219	195	199	12.0000
ccc[	chr16:22360597-22360813(-)$1	216	30	34	12.0000
Ceee	chr5:74016195-74016412(+)$1	217	26	30	12.0000
JJJJ	chr2:166032770-166033000(-)$1	230	32	36	12.0000
dnnn	chr1:3410833-3411075(-)$1	242	116	120	12.0000
gggg	chr3:15621366-15621587(-)$1	221	26	30	12.0000
b[dd	chr4:160252681-160252901(+)$1	220	63	67	12.0000
::gg	chr15:43928209-43928432(-)$1	223	7	11	12.0000
zzzz	chr13:36699980-36700199(-)$1	219	45	49	12.0000
##cc	chr7:75912714-75912963(+)$1	249	110	114	12.0000
$$ee	chr7:100634939-100635154(-)$1	215	155	159	12.0000
eee!	chr9:117379362-117379634(+)$1	272	10	14	12.0000
#ddd	chr7:38869731-38869964(-)$1	233	26	30	12.0000
::a[	chr11:111866751-111866971(+)$1	220	6	10	12.0000
33ff	chr16:331797-332022(+)$1	225	217	221	12.0000

#DB
))))	chr21:35172018-35172235(+)$1	1	44	48	12.0000
....	chr4:962591-962813(-)$1	1	7	11	12.0000
...(	chr4:82125847-82126062(+)$1	1	133	137	12.0000
(((.	chr3:54157495-54157715(+)$1	1	32	36	12.0000
).))	chr12:20522464-20522682(+)$1	1	180	184	12.0000
....	chr6:157495929-157496149(+)$1	1	74	78	12.0000
....	chr11:128844424-128844646(-)$1	1	189	193	12.0000
((((	chr2:178370129-178370344(+)$1	1	22	26	12.0000
((..	chr19:37130159-37130376(+)$1	1	4	8	12.0000
((((	chr1:201453036-201453268(-)$1	1	110	114	12.0000
....	chr11:4615867-4616082(+)$1	1	74	78	12.0000
....	chr4:39843435-39843680(+)$1	1	62	66	12.0000
))))	chr20:61299250-61299471(+)$1	1	213	217	12.0000
))))	chr19:15540361-15540579(-)$1	1	213	217	12.0000
....	chr19:54692206-54692431(-)$1	1	35	39	12.0000
.)))	chr1:223116315-223116538(+)$1	1	46	50	12.0000
))))	chr6:75797294-75797511(-)$1	1	172	176	12.0000
...)	chr4:68383757-68383976(+)$1	1	26	30	12.0000
((((	chrX:9864635-9864859(-)$1	1	58	62	12.0000
....	chr15:51828934-51829158(-)$1	1	101	105	12.0000
((((	chr3:45987872-45988088(-)$1	1	123	127	12.0000
(.((	chr7:101923258-101923477(+)$1	1	45	49	12.0000
....	chr1:160213720-160213945(-)$1	1	67	71	12.0000
....	chr11:113076769-113076990(+)$1	1	147	151	12.0000
....	chr6:75893527-75893765(+)$1	1	68	72	12.0000
...(	chr1:150533772-150533993(+)$1	1	1	5	12.0000
((((	chr8:99960366-99960581(+)$1	1	4	8	12.0000
))))	chr2:220081334-220081558(-)$1	1	169	173	12.0000
((((	chr9:17795498-17795719(+)$1	1	12	16	12.0000
))..	chr16:24828084-24828311(+)$1	1	216	220	12.0000
....	chrX:9914616-9914832(-)$1	1	54	58	12.0000
....	chr16:14334407-14334628(+)$1	1	50	54	12.0000
(..(	chr3:142280963-142281178(+)$1	1	17	21	12.0000
(((.	chr9:99797753-99797972(+)$1	1	21	25	12.0000
((..	chr20:40827860-40828079(-)$1	1	166	170	12.0000
..))	chr16:18809945-18810163(-)$1	1	126	130	12.0000
).))	chr17:73895587-73895802(-)$1	1	177	181	12.0000
(((.	chr6:31960190-31960406(-)$1	1	178	182	12.0000
((((	chr2:216995559-216995784(+)$1	1	22	26	12.0000
))..	chr3:113127846-113128065(+)$1	1	210	214	12.0000
....	chr1:120285393-120285619(+)$1	1	24	28	12.0000
((((	chr19:10671784-10672002(-)$1	1	46	50	12.0000
))))	chr1:230805137-230805355(+)$1	1	178	182	12.0000
....	chr1:204403598-204403826(-)$1	1	11	15	12.0000
)...	chr7:107880340-107880559(-)$1	1	109	113	12.0000
..((	chr17:26942677-26942897(-)$1	1	54	58	12.0000
((((	chr9:91159261-91159484(+)$1	1	19	23	12.0000
))))	chr1:21934713-21934942(-)$1	1	219	223	12.0000
....	chr19:40718681-40718899(-)$1	1	40	44	12.0000
....	chr3:69088649-69088864(-)$1	1	3	7	12.0000
....	chr20:13134538-13134761(+)$1	1	69	73	12.0000
((((	chr3:49749883-49750118(+)$1	1	124	128	12.0000
)(((	chr4:118005493-118005709(-)$1	1	58	62	12.0000
..))	chr19:39899118-39899341(+)$1	1	211	215	12.0000
....	chr15:77322739-77322969(-)$1	1	90	94	12.0000
....	chr12:53451722-53451938(+)$1	1	51	55	12.0000
))..	chr9:128321783-128322028(-)$1	1	137	141	12.0000
....	chr5:167589570-167589793(+)$1	1	17	21	12.0000
.)))	chr2:54850589-54850808(+)$1	1	195	199	12.0000
(((.	chr16:22360597-22360813(-)$1	1	30	34	12.0000
((((	chr5:74016195-74016412(+)$1	1	26	30	12.0000
((((	chr2:166032770-166033000(-)$1	1	32	36	12.0000
(...	chr1:3410833-3411075(-)$1	1	116	120	12.0000
((((	chr3:15621366-15621587(-)$1	1	26	30	12.0000
(.((	chr4:160252681-160252901(+)$1	1	63	67	12.0000
..((	chr15:43928209-43928432(-)$1	1	7	11	12.0000
....	chr13:36699980-36700199(-)$1	1	45	49	12.0000
..((	chr7:75912714-75912963(+)$1	1	110	114	12.0000
..((	chr7:100634939-100635154(-)$1	1	155	159	12.0000
(((.	chr9:117379362-117379634(+)$1	1	10	14	12.0000
.(((	chr7:38869731-38869964(-)$1	1	26	30	12.0000
..(.	chr11:111866751-111866971(+)$1	1	6	10	12.0000
..))	chr16:331797-332022(+)$1	1	217	221	12.0000

#PSSM
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	876.0000000000006
#seq	73
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m3_run2.nuc.txt

#NT
GGA	chr16:70296234-70296497(-)$1	263	14	17	8.9999
GGA	chr18:9950373-9950588(+)$1	215	26	29	8.9999
GGA	chr3:195802049-195802254(-)$1	205	29	32	8.9999
GGA	chr22:38266118-38266359(+)$1	241	3	6	8.9999
GGA	chr17:80012397-80012621(+)$1	224	30	33	8.9999
GGA	chr3:108278749-108278956(-)$1	207	86	89	8.9999
GGA	chr11:61732060-61732351(-)$1	291	78	81	8.9999
GGA	chr6:26468122-26468337(+)$1	215	66	69	8.9999
GGA	chr5:133496611-133496840(-)$1	229	45	48	8.9999
GGA	chr5:40834216-40834432(-)$1	216	24	27	8.9999
GGA	chr2:183795394-183795595(-)$1	201	115	118	8.9999
GGA	chr6:36652143-36652347(+)$1	204	2	5	8.9999
GGA	chr6:160105864-160106075(-)$1	211	11	14	8.9999
GGA	chr17:35600288-35600490(-)$1	202	125	128	8.9999
GGA	chr11:85375295-85375518(-)$1	223	1	4	8.9999
GGA	chr12:49448307-49448511(-)$1	204	16	19	8.9999
GGA	chr6:56416921-56417132(-)$1	211	8	11	8.9999
GGA	chr18:77036960-77037167(+)$1	207	43	46	8.9999
GGA	chr14:32561485-32561705(+)$1	220	3	6	8.9999
GGA	chr12:22646081-22646286(-)$1	205	188	191	8.9999
GGA	chr1:197057383-197057607(-)$1	224	101	104	8.9999
GGA	chr1:161726508-161726738(+)$1	230	140	143	8.9999
GGA	chr1:236208681-236208913(-)$1	232	34	37	8.9999
GGA	chr2:55470643-55470878(-)$1	235	0	3	8.9999
GGA	chr2:96858917-96859183(-)$1	266	7	10	8.9999
GGA	chr21:30714830-30715034(+)$1	204	168	171	8.9999
GGA	chr2:27258379-27258587(+)$1	208	10	13	8.9999
GGA	chr11:498784-498996(-)$1	212	66	69	8.9999
GGA	chr17:37627211-37627447(+)$1	236	59	62	8.9999
GGA	chr1:167889750-167889959(-)$1	209	105	108	8.9999
GGA	chr20:20512277-20512506(-)$1	229	96	99	8.9999
GGA	chr14:58718756-58718985(+)$1	229	90	93	8.9999
gga	chr6:20548757-20548996(+)$1	239	1	4	8.9999
GGA	chr12:6645570-6645784(+)$1	214	14	17	8.9999
GGA	chr18:46904894-46905125(-)$1	231	136	139	8.9999
GGA	chr20:47612304-47612508(+)$1	204	32	35	8.9999
GGA	chr9:139113595-139113852(-)$1	257	36	39	8.9999
GGA	chr1:92945838-92946043(-)$1	205	111	114	8.9999
GGA	chr5:137892129-137892342(-)$1	213	27	30	8.9999
GGA	chr7:98527669-98527873(+)$1	204	22	25	8.9999
GGA	chr19:57839145-57839362(+)$1	217	15	18	8.9999
GGA	chr2:96956333-96956562(-)$1	229	109	112	8.9999
GGA	chr11:3040313-3040516(-)$1	203	81	84	8.9999
GGA	chr10:33502352-33502556(-)$1	204	98	101	8.9999
GGA	chr22:39714323-39714539(-)$1	216	18	21	8.9999
GGA	chr6:35806054-35806293(-)$1	239	44	47	8.9999
GGA	chr20:10386010-10386245(-)$1	235	30	33	8.9999
GGA	chr19:47349253-47349467(-)$1	214	163	166	8.9999
GGA	chr1:42671374-42671583(-)$1	209	5	8	8.9999
GGA	chr12:112302994-112303210(+)$1	216	19	22	8.9999
GGA	chr6:90503464-90503678(-)$1	214	29	32	8.9999
GGA	chr3:44827858-44828069(+)$1	211	31	34	8.9999
GGA	chr1:113456625-113456844(-)$1	219	0	3	8.9999
GGA	chr2:27997199-27997429(+)$1	230	123	126	8.9999
GGA	chr2:73477416-73477650(+)$1	234	92	95	8.9999
GGA	chr19:39191209-39191445(+)$1	236	61	64	8.9999
GGA	chr2:3627664-3627877(+)$1	213	71	74	8.9999
GGA	chr1:26737808-26738031(+)$1	223	102	105	8.9999
GGA	chr1:24020242-24020488(+)$1	246	84	87	8.9999
GGA	chr1:33360328-33360562(-)$1	234	15	18	8.9999
GGA	chr19:30477150-30477402(+)$1	252	109	112	8.9999
GGA	chrX:114881837-114882045(+)$1	208	50	53	8.9999
GGA	chrX:70516729-70516941(+)$1	212	36	39	8.9999
GGA	chr9:138713920-138714146(-)$1	226	68	71	8.9999
GGA	chr15:52844016-52844251(-)$1	235	27	30	8.9999
GGA	chr12:29496064-29496294(-)$1	230	78	81	8.9999
GGA	chr2:172848099-172848325(+)$1	226	100	103	8.9999
GGA	chr3:128525267-128525504(+)$1	237	71	74	8.9999
GGA	chr12:102159841-102160079(-)$1	238	15	18	8.9999
GGA	chr17:59944901-59945110(-)$1	209	39	42	8.9999
GGA	chr17:26943331-26943552(-)$1	221	24	27	8.9999
GGA	chr1:21097389-21097594(-)$1	205	99	102	8.9999
GGA	chrX:79977984-79978221(-)$1	237	3	6	8.9999
GGA	chr16:47533657-47533884(+)$1	227	97	100	8.9999
GGA	chr9:98718115-98718353(+)$1	238	88	91	8.9999
GGA	chr3:37088949-37089172(+)$1	223	13	16	8.9999
GGA	chr18:55273018-55273259(-)$1	241	88	91	8.9999
GGA	chr6:108279069-108279314(-)$1	245	34	37	8.9999
GGA	chr5:74130235-74130445(-)$1	210	37	40	8.9999
GGA	chr8:81430606-81430839(+)$1	233	90	93	8.9999
GGA	chr6:35262875-35263098(+)$1	223	0	3	8.9999
GGA	chr12:113873128-113873351(+)$1	223	29	32	8.9999
GGA	chr7:129806160-129806409(-)$1	249	63	66	8.9999
GGA	chr16:3726006-3726212(-)$1	206	70	73	8.9999
GGA	chr11:60687232-60687449(+)$1	217	120	123	8.9999
GGA	chr1:93299013-93299240(+)$1	227	53	56	8.9999
GGA	chr15:69745197-69745449(+)$1	252	0	3	8.9999
GGA	chr15:72501976-72502218(-)$1	242	35	38	8.9999
GGA	chr17:30190359-30190566(-)$1	207	37	40	8.9999
GGA	chr5:37351315-37351523(-)$1	208	23	26	8.9999
GGA	chr16:30004897-30005136(-)$1	239	25	28	8.9999
GGA	chr5:151176701-151176919(+)$1	218	24	27	8.9999
GGA	chr5:83362262-83362495(-)$1	233	83	86	8.9999
GGA	chr7:128138017-128138241(+)$1	224	12	15	8.9999
GGA	chr3:53263308-53263537(-)$1	229	119	122	8.9999
GGA	chr16:2011694-2011960(+)$1	266	107	110	8.9999
GGA	chr12:56548850-56549059(+)$1	209	25	28	8.9999
GGA	chr16:69358091-69358298(+)$1	207	21	24	8.9999

#otherMatches

#Struct PSSM
:::	chr5:138755653-138755860(-)$1	207	3	6	8.9999
bb2	chr16:70296234-70296497(-)$1	263	14	17	8.9999
fff	chr18:9950373-9950588(+)$1	215	26	29	8.9999
bbm	chr3:195802049-195802254(-)$1	205	29	32	8.9999
FFF	chr22:38266118-38266359(+)$1	241	3	6	8.9999
ff!	chr17:80012397-80012621(+)$1	224	30	33	8.9999
hhh	chr3:108278749-108278956(-)$1	207	86	89	8.9999
eee	chr11:61732060-61732351(-)$1	291	78	81	8.9999
DDL	chr6:26468122-26468337(+)$1	215	66	69	8.9999
hhh	chr5:133496611-133496840(-)$1	229	45	48	8.9999
CC{	chr5:40834216-40834432(-)$1	216	24	27	8.9999
[dd	chr2:183795394-183795595(-)$1	201	115	118	8.9999
bdd	chr6:36652143-36652347(+)$1	204	2	5	8.9999
CC{	chr6:160105864-160106075(-)$1	211	11	14	8.9999
gg:	chr17:35600288-35600490(-)$1	202	125	128	8.9999
:::	chr11:85375295-85375518(-)$1	223	1	4	8.9999
GGG	chr12:49448307-49448511(-)$1	204	16	19	8.9999
d!!	chr6:56416921-56417132(-)$1	211	8	11	8.9999
hhh	chr18:77036960-77037167(+)$1	207	43	46	8.9999
ee#	chr14:32561485-32561705(+)$1	220	3	6	8.9999
}CC	chr12:22646081-22646286(-)$1	205	188	191	8.9999
ff[	chr1:197057383-197057607(-)$1	224	101	104	8.9999
gnn	chr1:161726508-161726738(+)$1	230	140	143	8.9999
!cc	chr1:236208681-236208913(-)$1	232	34	37	8.9999
:::	chr2:55470643-55470878(-)$1	235	0	3	8.9999
ccc	chr2:96858917-96859183(-)$1	266	7	10	8.9999
att	chr21:30714830-30715034(+)$1	204	168	171	8.9999
:ff	chr2:27258379-27258587(+)$1	208	10	13	8.9999
ddd	chr11:498784-498996(-)$1	212	66	69	8.9999
KFF	chr17:37627211-37627447(+)$1	236	59	62	8.9999
bb[	chr1:167889750-167889959(-)$1	209	105	108	8.9999
ooo	chr20:20512277-20512506(-)$1	229	96	99	8.9999
iii	chr14:58718756-58718985(+)$1	229	90	93	8.9999
ggg	chr6:20548757-20548996(+)$1	239	1	4	8.9999
iii	chr12:6645570-6645784(+)$1	214	14	17	8.9999
fff	chr18:46904894-46905125(-)$1	231	136	139	8.9999
[a!	chr20:47612304-47612508(+)$1	204	32	35	8.9999
cc]	chr9:139113595-139113852(-)$1	257	36	39	8.9999
hhh	chr1:92945838-92946043(-)$1	205	111	114	8.9999
DLL	chr5:137892129-137892342(-)$1	213	27	30	8.9999
fff	chr7:98527669-98527873(+)$1	204	22	25	8.9999
NEE	chr19:57839145-57839362(+)$1	217	15	18	8.9999
fff	chr2:96956333-96956562(-)$1	229	109	112	8.9999
ppp	chr11:3040313-3040516(-)$1	203	81	84	8.9999
e:D	chr10:33502352-33502556(-)$1	204	98	101	8.9999
fff	chr22:39714323-39714539(-)$1	216	18	21	8.9999
ccc	chr6:35806054-35806293(-)$1	239	44	47	8.9999
c!!	chr20:10386010-10386245(-)$1	235	30	33	8.9999
bb]	chr19:47349253-47349467(-)$1	214	163	166	8.9999
ggg	chr1:42671374-42671583(-)$1	209	5	8	8.9999
CCC	chr12:112302994-112303210(+)$1	216	19	22	8.9999
Edd	chr6:90503464-90503678(-)$1	214	29	32	8.9999
""c	chr3:44827858-44828069(+)$1	211	31	34	8.9999
:::	chr1:113456625-113456844(-)$1	219	0	3	8.9999
:::	chr2:27997199-27997429(+)$1	230	123	126	8.9999
fff	chr2:73477416-73477650(+)$1	234	92	95	8.9999
bee	chr19:39191209-39191445(+)$1	236	61	64	8.9999
%cc	chr2:3627664-3627877(+)$1	213	71	74	8.9999
EEE	chr1:26737808-26738031(+)$1	223	102	105	8.9999
fff	chr1:24020242-24020488(+)$1	246	84	87	8.9999
CCC	chr1:33360328-33360562(-)$1	234	15	18	8.9999
fff	chr19:30477150-30477402(+)$1	252	109	112	8.9999
bb3	chrX:114881837-114882045(+)$1	208	50	53	8.9999
d$$	chrX:70516729-70516941(+)$1	212	36	39	8.9999
CC{	chr9:138713920-138714146(-)$1	226	68	71	8.9999
d$$	chr15:52844016-52844251(-)$1	235	27	30	8.9999
cc:	chr12:29496064-29496294(-)$1	230	78	81	8.9999
ee&	chr2:172848099-172848325(+)$1	226	100	103	8.9999
ee"	chr3:128525267-128525504(+)$1	237	71	74	8.9999
eeo	chr12:102159841-102160079(-)$1	238	15	18	8.9999
fff	chr17:59944901-59945110(-)$1	209	39	42	8.9999
DDM	chr17:26943331-26943552(-)$1	221	24	27	8.9999
eec	chr1:21097389-21097594(-)$1	205	99	102	8.9999
dds	chrX:79977984-79978221(-)$1	237	3	6	8.9999
d!!	chr16:47533657-47533884(+)$1	227	97	100	8.9999
iii	chr9:98718115-98718353(+)$1	238	88	91	8.9999
ddd	chr3:37088949-37089172(+)$1	223	13	16	8.9999
c[c	chr18:55273018-55273259(-)$1	241	88	91	8.9999
ee:	chr6:108279069-108279314(-)$1	245	34	37	8.9999
nnn	chr5:74130235-74130445(-)$1	210	37	40	8.9999
ccf	chr8:81430606-81430839(+)$1	233	90	93	8.9999
::F	chr6:35262875-35263098(+)$1	223	0	3	8.9999
FFF	chr12:113873128-113873351(+)$1	223	29	32	8.9999
EEE	chr7:129806160-129806409(-)$1	249	63	66	8.9999
iii	chr16:3726006-3726212(-)$1	206	70	73	8.9999
h44	chr11:60687232-60687449(+)$1	217	120	123	8.9999
fff	chr1:93299013-93299240(+)$1	227	53	56	8.9999
bb!	chr15:69745197-69745449(+)$1	252	0	3	8.9999
dd]	chr15:72501976-72502218(-)$1	242	35	38	8.9999
ooo	chr17:30190359-30190566(-)$1	207	37	40	8.9999
eee	chr5:37351315-37351523(-)$1	208	23	26	8.9999
CCC	chr16:30004897-30005136(-)$1	239	25	28	8.9999
22g	chr5:151176701-151176919(+)$1	218	24	27	8.9999
+++	chr5:83362262-83362495(-)$1	233	83	86	8.9999
ffq	chr7:128138017-128138241(+)$1	224	12	15	8.9999
DDD	chr3:53263308-53263537(-)$1	229	119	122	8.9999
dd2	chr16:2011694-2011960(+)$1	266	107	110	8.9999
eee	chr12:56548850-56549059(+)$1	209	25	28	8.9999
CCC	chr16:69358091-69358298(+)$1	207	21	24	8.9999

#DB
...	chr5:138755653-138755860(-)$1	1	3	6	8.9999
)).	chr16:70296234-70296497(-)$1	1	14	17	8.9999
(((	chr18:9950373-9950588(+)$1	1	26	29	8.9999
((.	chr3:195802049-195802254(-)$1	1	29	32	8.9999
(((	chr22:38266118-38266359(+)$1	1	3	6	8.9999
((.	chr17:80012397-80012621(+)$1	1	30	33	8.9999
)))	chr3:108278749-108278956(-)$1	1	86	89	8.9999
(((	chr11:61732060-61732351(-)$1	1	78	81	8.9999
((.	chr6:26468122-26468337(+)$1	1	66	69	8.9999
)))	chr5:133496611-133496840(-)$1	1	45	48	8.9999
((.	chr5:40834216-40834432(-)$1	1	24	27	8.9999
.((	chr2:183795394-183795595(-)$1	1	115	118	8.9999
(((	chr6:36652143-36652347(+)$1	1	2	5	8.9999
((.	chr6:160105864-160106075(-)$1	1	11	14	8.9999
)).	chr17:35600288-35600490(-)$1	1	125	128	8.9999
...	chr11:85375295-85375518(-)$1	1	1	4	8.9999
(((	chr12:49448307-49448511(-)$1	1	16	19	8.9999
(..	chr6:56416921-56417132(-)$1	1	8	11	8.9999
)))	chr18:77036960-77037167(+)$1	1	43	46	8.9999
((.	chr14:32561485-32561705(+)$1	1	3	6	8.9999
.))	chr12:22646081-22646286(-)$1	1	188	191	8.9999
((.	chr1:197057383-197057607(-)$1	1	101	104	8.9999
(..	chr1:161726508-161726738(+)$1	1	140	143	8.9999
.((	chr1:236208681-236208913(-)$1	1	34	37	8.9999
...	chr2:55470643-55470878(-)$1	1	0	3	8.9999
(((	chr2:96858917-96859183(-)$1	1	7	10	8.9999
(..	chr21:30714830-30715034(+)$1	1	168	171	8.9999
.((	chr2:27258379-27258587(+)$1	1	10	13	8.9999
(((	chr11:498784-498996(-)$1	1	66	69	8.9999
.((	chr17:37627211-37627447(+)$1	1	59	62	8.9999
((.	chr1:167889750-167889959(-)$1	1	105	108	8.9999
...	chr20:20512277-20512506(-)$1	1	96	99	8.9999
)))	chr14:58718756-58718985(+)$1	1	90	93	8.9999
(((	chr6:20548757-20548996(+)$1	1	1	4	8.9999
(((	chr12:6645570-6645784(+)$1	1	14	17	8.9999
(((	chr18:46904894-46905125(-)$1	1	136	139	8.9999
.(.	chr20:47612304-47612508(+)$1	1	32	35	8.9999
)).	chr9:139113595-139113852(-)$1	1	36	39	8.9999
)))	chr1:92945838-92946043(-)$1	1	111	114	8.9999
(..	chr5:137892129-137892342(-)$1	1	27	30	8.9999
(((	chr7:98527669-98527873(+)$1	1	22	25	8.9999
.((	chr19:57839145-57839362(+)$1	1	15	18	8.9999
)))	chr2:96956333-96956562(-)$1	1	109	112	8.9999
...	chr11:3040313-3040516(-)$1	1	81	84	8.9999
).)	chr10:33502352-33502556(-)$1	1	98	101	8.9999
(((	chr22:39714323-39714539(-)$1	1	18	21	8.9999
(((	chr6:35806054-35806293(-)$1	1	44	47	8.9999
(..	chr20:10386010-10386245(-)$1	1	30	33	8.9999
)).	chr19:47349253-47349467(-)$1	1	163	166	8.9999
(((	chr1:42671374-42671583(-)$1	1	5	8	8.9999
(((	chr12:112302994-112303210(+)$1	1	19	22	8.9999
(((	chr6:90503464-90503678(-)$1	1	29	32	8.9999
..(	chr3:44827858-44828069(+)$1	1	31	34	8.9999
...	chr1:113456625-113456844(-)$1	1	0	3	8.9999
...	chr2:27997199-27997429(+)$1	1	123	126	8.9999
(((	chr2:73477416-73477650(+)$1	1	92	95	8.9999
)))	chr19:39191209-39191445(+)$1	1	61	64	8.9999
.((	chr2:3627664-3627877(+)$1	1	71	74	8.9999
)))	chr1:26737808-26738031(+)$1	1	102	105	8.9999
)))	chr1:24020242-24020488(+)$1	1	84	87	8.9999
(((	chr1:33360328-33360562(-)$1	1	15	18	8.9999
)))	chr19:30477150-30477402(+)$1	1	109	112	8.9999
)).	chrX:114881837-114882045(+)$1	1	50	53	8.9999
(..	chrX:70516729-70516941(+)$1	1	36	39	8.9999
((.	chr9:138713920-138714146(-)$1	1	68	71	8.9999
(..	chr15:52844016-52844251(-)$1	1	27	30	8.9999
)).	chr12:29496064-29496294(-)$1	1	78	81	8.9999
((.	chr2:172848099-172848325(+)$1	1	100	103	8.9999
((.	chr3:128525267-128525504(+)$1	1	71	74	8.9999
((.	chr12:102159841-102160079(-)$1	1	15	18	8.9999
)))	chr17:59944901-59945110(-)$1	1	39	42	8.9999
((.	chr17:26943331-26943552(-)$1	1	24	27	8.9999
)))	chr1:21097389-21097594(-)$1	1	99	102	8.9999
((.	chrX:79977984-79978221(-)$1	1	3	6	8.9999
(..	chr16:47533657-47533884(+)$1	1	97	100	8.9999
)))	chr9:98718115-98718353(+)$1	1	88	91	8.9999
(((	chr3:37088949-37089172(+)$1	1	13	16	8.9999
(.(	chr18:55273018-55273259(-)$1	1	88	91	8.9999
)).	chr6:108279069-108279314(-)$1	1	34	37	8.9999
...	chr5:74130235-74130445(-)$1	1	37	40	8.9999
(((	chr8:81430606-81430839(+)$1	1	90	93	8.9999
..(	chr6:35262875-35263098(+)$1	1	0	3	8.9999
(((	chr12:113873128-113873351(+)$1	1	29	32	8.9999
(((	chr7:129806160-129806409(-)$1	1	63	66	8.9999
(((	chr16:3726006-3726212(-)$1	1	70	73	8.9999
)..	chr11:60687232-60687449(+)$1	1	120	123	8.9999
(((	chr1:93299013-93299240(+)$1	1	53	56	8.9999
((.	chr15:69745197-69745449(+)$1	1	0	3	8.9999
)).	chr15:72501976-72502218(-)$1	1	35	38	8.9999
...	chr17:30190359-30190566(-)$1	1	37	40	8.9999
(((	chr5:37351315-37351523(-)$1	1	23	26	8.9999
(((	chr16:30004897-30005136(-)$1	1	25	28	8.9999
..)	chr5:151176701-151176919(+)$1	1	24	27	8.9999
...	chr5:83362262-83362495(-)$1	1	83	86	8.9999
((.	chr7:128138017-128138241(+)$1	1	12	15	8.9999
)))	chr3:53263308-53263537(-)$1	1	119	122	8.9999
)).	chr16:2011694-2011960(+)$1	1	107	110	8.9999
(((	chr12:56548850-56549059(+)$1	1	25	28	8.9999
(((	chr16:69358091-69358298(+)$1	1	21	24	8.9999

#PSSM
G : 0.98	g : 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_SFRS1_Sanford2009_hg19_UTR_m3_run1.nuc.txt

#NT
AGGAG	chr1:248031228-248031462(+)$1	234	109	114	15.0000
AGGAG	chr17:20903907-20904162(-)$1	255	107	112	15.0000
AGGAG	chr9:178743-178997(-)$1	254	56	61	15.0000
AGGAG	chr11:57558905-57559158(+)$1	253	136	141	15.0000
AGGAG	chr5:7878127-7878367(+)$1	240	9	14	15.0000
AGGAG	chr14:24680901-24681145(-)$1	244	116	121	15.0000
AGGAG	chr20:57226234-57226473(+)$1	239	133	138	15.0000
AGGAG	chr17:38785123-38785353(-)$1	230	108	113	15.0000
AGGAG	chr1:156278816-156279053(-)$1	237	56	61	15.0000
AGGAG	chr15:83206998-83207224(-)$1	226	36	41	15.0000
AGGAG	chr18:11884889-11885129(+)$1	240	101	106	15.0000
AGGAG	chr1:109822341-109822614(-)$1	273	247	252	15.0000
AGGAG	chr12:6648669-6648930(-)$1	261	165	170	15.0000
AGGAG	chr12:7077506-7077739(-)$1	233	32	37	15.0000
AGGAG	chr14:23791289-23791501(+)$1	212	98	103	15.0000
AGGAG	chr1:236306059-236306317(-)$1	258	103	108	15.0000
AGGAG	chr9:134371067-134371318(+)$1	251	108	113	15.0000
AGGAG	chr1:145509955-145510197(+)$1	242	88	93	15.0000
AGGAG	chr8:29207970-29208209(-)$1	239	36	41	15.0000
AGGAG	chr1:154148597-154148824(-)$1	227	167	172	15.0000
AGGAG	chr10:58117629-58117860(-)$1	231	118	123	15.0000
AGGAG	chr9:114134648-114134886(-)$1	238	115	120	15.0000
AGGAG	chr3:128628760-128629005(+)$1	245	7	12	15.0000
AGGAG	chr2:74683207-74683448(+)$1	241	65	70	15.0000
AGGAG	chr3:184039684-184039929(+)$1	245	45	50	15.0000
AGGAG	chr2:219524927-219525194(+)$1	267	22	27	15.0000
AGGAG	chr6:30545785-30546027(+)$1	242	182	187	15.0000
AGGAG	chr21:34894434-34894691(-)$1	257	100	105	15.0000
AGGAG	chr17:79478282-79478521(-)$1	239	143	148	15.0000
AGGAG	chr6:26204751-26205016(+)$1	265	159	164	15.0000
AGGAG	chr1:46079705-46079948(+)$1	243	78	83	15.0000
AGGAG	chr2:182756684-182756929(+)$1	245	143	148	15.0000
AGGAG	chr14:24606501-24606740(+)$1	239	26	31	15.0000
AGGAG	chr1:93721791-93722010(+)$1	219	140	145	15.0000
AGGAG	chr22:38883793-38884030(-)$1	237	127	132	15.0000
AGGAG	chr17:74035262-74035500(-)$1	238	21	26	15.0000
AGGAG	chr17:27235753-27235992(-)$1	239	102	107	15.0000
AGGAG	chr12:49233535-49233775(-)$1	240	102	107	15.0000
AGGAG	chr11:64012094-64012336(-)$1	242	124	129	15.0000
AGGAG	chr1:145318835-145319077(+)$1	242	3	8	15.0000
AGGAG	chr3:69153634-69153885(+)$1	251	241	246	15.0000
AGGAG	chr10:88854041-88854282(+)$1	241	100	105	15.0000
AGGAG	chr3:50137906-50138136(+)$1	230	203	208	15.0000
AGGAG	chr12:104359644-104359886(+)$1	242	15	20	15.0000
AGGAG	chr3:56647536-56647810(+)$1	274	162	167	15.0000
AGGAG	chr16:89711270-89711540(-)$1	270	45	50	15.0000
AGGAG	chr13:24796922-24797157(+)$1	235	47	52	15.0000
AGGAG	chr20:44526543-44526775(+)$1	232	170	175	15.0000
AGGAG	chr14:105936299-105936546(+)$1	247	20	25	15.0000
AGGAG	chr20:17608061-17608297(-)$1	236	21	26	15.0000
AGGAG	chr16:103434-103684(-)$1	250	141	146	15.0000
AGGAG	chr14:89038460-89038669(+)$1	209	84	89	15.0000
AGGAG	chr1:156288578-156288818(-)$1	240	147	152	15.0000
AGGAG	chr7:72361094-72361324(+)$1	230	111	116	15.0000
AGGAG	chr17:1420911-1421143(+)$1	232	125	130	15.0000
AGGAG	chr19:579475-579747(+)$1	272	144	149	15.0000
AGGAG	chr17:4085510-4085746(-)$1	236	180	185	15.0000
AGGAG	chr17:74035718-74035955(-)$1	237	160	165	15.0000
AGGAG	chr6:109323380-109323612(-)$1	232	127	132	15.0000

#otherMatches

#Struct PSSM
na22a	chr9:130630558-130630792(-)$1	234	104	109	15.0000
JJJJJ	chr1:248031228-248031462(+)$1	234	109	114	15.0000
fff::	chr17:20903907-20904162(-)$1	255	107	112	15.0000
[cccc	chr9:178743-178997(-)$1	254	56	61	15.0000
###bb	chr11:57558905-57559158(+)$1	253	136	141	15.0000
eeee!	chr5:7878127-7878367(+)$1	240	9	14	15.0000
2dddd	chr14:24680901-24681145(-)$1	244	116	121	15.0000
ba]cc	chr20:57226234-57226473(+)$1	239	133	138	15.0000
dddpp	chr17:38785123-38785353(-)$1	230	108	113	15.0000
ggggg	chr1:156278816-156279053(-)$1	237	56	61	15.0000
ggggg	chr15:83206998-83207224(-)$1	226	36	41	15.0000
::eee	chr18:11884889-11885129(+)$1	240	101	106	15.0000
]cccc	chr1:109822341-109822614(-)$1	273	247	252	15.0000
GGGGG	chr12:6648669-6648930(-)$1	261	165	170	15.0000
::::c	chr12:7077506-7077739(-)$1	233	32	37	15.0000
&&eee	chr14:23791289-23791501(+)$1	212	98	103	15.0000
xxxxx	chr1:236306059-236306317(-)$1	258	103	108	15.0000
:ffff	chr9:134371067-134371318(+)$1	251	108	113	15.0000
:cccn	chr1:145509955-145510197(+)$1	242	88	93	15.0000
EEEee	chr8:29207970-29208209(-)$1	239	36	41	15.0000
eeeee	chr1:154148597-154148824(-)$1	227	167	172	15.0000
22ccc	chr10:58117629-58117860(-)$1	231	118	123	15.0000
%cccm	chr9:114134648-114134886(-)$1	238	115	120	15.0000
bbmmm	chr3:128628760-128629005(+)$1	245	7	12	15.0000
nnnnn	chr2:74683207-74683448(+)$1	241	65	70	15.0000
nnnnn	chr3:184039684-184039929(+)$1	245	45	50	15.0000
:cccn	chr2:219524927-219525194(+)$1	267	22	27	15.0000
!a!!d	chr6:30545785-30546027(+)$1	242	182	187	15.0000
lffff	chr21:34894434-34894691(-)$1	257	100	105	15.0000
5bb]h	chr17:79478282-79478521(-)$1	239	143	148	15.0000
:bb[e	chr6:26204751-26205016(+)$1	265	159	164	15.0000
hhhhh	chr1:46079705-46079948(+)$1	243	78	83	15.0000
b]bb]	chr2:182756684-182756929(+)$1	245	143	148	15.0000
eeeee	chr14:24606501-24606740(+)$1	239	26	31	15.0000
qqccc	chr1:93721791-93722010(+)$1	219	140	145	15.0000
HHHHH	chr22:38883793-38884030(-)$1	237	127	132	15.0000
ddd[d	chr17:74035262-74035500(-)$1	238	21	26	15.0000
ddddC	chr17:27235753-27235992(-)$1	239	102	107	15.0000
gg:gg	chr12:49233535-49233775(-)$1	240	102	107	15.0000
obb::	chr11:64012094-64012336(-)$1	242	124	129	15.0000
BBKKE	chr1:145318835-145319077(+)$1	242	3	8	15.0000
??EEE	chr3:69153634-69153885(+)$1	251	241	246	15.0000
mmccc	chr10:88854041-88854282(+)$1	241	100	105	15.0000
2ccc4	chr3:50137906-50138136(+)$1	230	203	208	15.0000
g!!bb	chr12:104359644-104359886(+)$1	242	15	20	15.0000
^^^^^	chr3:56647536-56647810(+)$1	274	162	167	15.0000
FFFFF	chr16:89711270-89711540(-)$1	270	45	50	15.0000
$bb[b	chr13:24796922-24797157(+)$1	235	47	52	15.0000
|HHHH	chr20:44526543-44526775(+)$1	232	170	175	15.0000
BBB{A	chr14:105936299-105936546(+)$1	247	20	25	15.0000
nnnnb	chr20:17608061-17608297(-)$1	236	21	26	15.0000
[bb[a	chr16:103434-103684(-)$1	250	141	146	15.0000
3ffff	chr14:89038460-89038669(+)$1	209	84	89	15.0000
fffff	chr1:156288578-156288818(-)$1	240	147	152	15.0000
III{D	chr7:72361094-72361324(+)$1	230	111	116	15.0000
BB:::	chr17:1420911-1421143(+)$1	232	125	130	15.0000
###cc	chr19:579475-579747(+)$1	272	144	149	15.0000
]gggg	chr17:4085510-4085746(-)$1	236	180	185	15.0000
ggggg	chr17:74035718-74035955(-)$1	237	160	165	15.0000
obb]c	chr6:109323380-109323612(-)$1	232	127	132	15.0000

#DB
.)..)	chr9:130630558-130630792(-)$1	1	104	109	15.0000
)))))	chr1:248031228-248031462(+)$1	1	109	114	15.0000
)))..	chr17:20903907-20904162(-)$1	1	107	112	15.0000
.((((	chr9:178743-178997(-)$1	1	56	61	15.0000
...((	chr11:57558905-57559158(+)$1	1	136	141	15.0000
((((.	chr5:7878127-7878367(+)$1	1	9	14	15.0000
.))))	chr14:24680901-24681145(-)$1	1	116	121	15.0000
)).))	chr20:57226234-57226473(+)$1	1	133	138	15.0000
(((..	chr17:38785123-38785353(-)$1	1	108	113	15.0000
)))))	chr1:156278816-156279053(-)$1	1	56	61	15.0000
)))))	chr15:83206998-83207224(-)$1	1	36	41	15.0000
..(((	chr18:11884889-11885129(+)$1	1	101	106	15.0000
.))))	chr1:109822341-109822614(-)$1	1	247	252	15.0000
)))))	chr12:6648669-6648930(-)$1	1	165	170	15.0000
....(	chr12:7077506-7077739(-)$1	1	32	37	15.0000
..(((	chr14:23791289-23791501(+)$1	1	98	103	15.0000
.....	chr1:236306059-236306317(-)$1	1	103	108	15.0000
.((((	chr9:134371067-134371318(+)$1	1	108	113	15.0000
.(((.	chr1:145509955-145510197(+)$1	1	88	93	15.0000
(((((	chr8:29207970-29208209(-)$1	1	36	41	15.0000
)))))	chr1:154148597-154148824(-)$1	1	167	172	15.0000
..)))	chr10:58117629-58117860(-)$1	1	118	123	15.0000
.(((.	chr9:114134648-114134886(-)$1	1	115	120	15.0000
((...	chr3:128628760-128629005(+)$1	1	7	12	15.0000
.....	chr2:74683207-74683448(+)$1	1	65	70	15.0000
.....	chr3:184039684-184039929(+)$1	1	45	50	15.0000
.(((.	chr2:219524927-219525194(+)$1	1	22	27	15.0000
.(..(	chr6:30545785-30546027(+)$1	1	182	187	15.0000
.))))	chr21:34894434-34894691(-)$1	1	100	105	15.0000
.)).)	chr17:79478282-79478521(-)$1	1	143	148	15.0000
.((.(	chr6:26204751-26205016(+)$1	1	159	164	15.0000
)))))	chr1:46079705-46079948(+)$1	1	78	83	15.0000
).)).	chr2:182756684-182756929(+)$1	1	143	148	15.0000
)))))	chr14:24606501-24606740(+)$1	1	26	31	15.0000
..)))	chr1:93721791-93722010(+)$1	1	140	145	15.0000
(((((	chr22:38883793-38884030(-)$1	1	127	132	15.0000
(((.(	chr17:74035262-74035500(-)$1	1	21	26	15.0000
)))))	chr17:27235753-27235992(-)$1	1	102	107	15.0000
)).((	chr12:49233535-49233775(-)$1	1	102	107	15.0000
.))..	chr11:64012094-64012336(-)$1	1	124	129	15.0000
((..(	chr1:145318835-145319077(+)$1	1	3	8	15.0000
..)))	chr3:69153634-69153885(+)$1	1	241	246	15.0000
..)))	chr10:88854041-88854282(+)$1	1	100	105	15.0000
.))).	chr3:50137906-50138136(+)$1	1	203	208	15.0000
(..((	chr12:104359644-104359886(+)$1	1	15	20	15.0000
.....	chr3:56647536-56647810(+)$1	1	162	167	15.0000
(((((	chr16:89711270-89711540(-)$1	1	45	50	15.0000
.((.(	chr13:24796922-24797157(+)$1	1	47	52	15.0000
.))))	chr20:44526543-44526775(+)$1	1	170	175	15.0000
(((.(	chr14:105936299-105936546(+)$1	1	20	25	15.0000
....)	chr20:17608061-17608297(-)$1	1	21	26	15.0000
.((.(	chr16:103434-103684(-)$1	1	141	146	15.0000
.))))	chr14:89038460-89038669(+)$1	1	84	89	15.0000
(((((	chr1:156288578-156288818(-)$1	1	147	152	15.0000
(((.(	chr7:72361094-72361324(+)$1	1	111	116	15.0000
((...	chr17:1420911-1421143(+)$1	1	125	130	15.0000
...((	chr19:579475-579747(+)$1	1	144	149	15.0000
.))))	chr17:4085510-4085746(-)$1	1	180	185	15.0000
(((((	chr17:74035718-74035955(-)$1	1	160	165	15.0000
.)).)	chr6:109323380-109323612(-)$1	1	127	132	15.0000

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

#score	900.0000000000005
#seq	60
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_CDS_m1_run1.nuc.txt

#NT
UGA	chr6:26184162-26184401(+)$1	239	48	51	8.9999
UGA	chr11:93778907-93779121(+)$1	214	71	74	8.9999
UGA	chr12:32491619-32491841(+)$1	222	28	31	8.9999
UGA	chr11:93808276-93808492(+)$1	216	5	8	8.9999
UGA	chr16:70432046-70432263(-)$1	217	84	87	8.9999
UGA	chr3:127820386-127820610(-)$1	224	97	100	8.9999
UGA	chr8:21827632-21827854(+)$1	222	73	76	8.9999
UGA	chrX:70756020-70756298(+)$1	278	44	47	8.9999
UGA	chr1:151018495-151018709(+)$1	214	26	29	8.9999
UGA	chr1:186948479-186948692(+)$1	213	4	7	8.9999
UGA	chrX:133511939-133512168(+)$1	229	22	25	8.9999
UGA	chr17:46805324-46805543(-)$1	219	67	70	8.9999
uga	chr21:47613435-47613816(-)$1	381	2	5	8.9999
UGA	chr17:25639290-25639576(+)$1	286	31	34	8.9999
UGA	chr12:59270155-59270385(-)$1	230	1	4	8.9999
UGA	chr16:111538-111755(-)$1	217	31	34	8.9999
UGA	chr1:198668533-198668976(+)$1	443	20	23	8.9999
UGA	chr1:64605749-64605962(+)$1	213	54	57	8.9999
UGA	chr7:99811309-99811545(-)$1	236	48	51	8.9999
UGA	chr3:160146512-160146735(+)$1	223	32	35	8.9999
UGA	chr19:41209551-41209806(-)$1	255	3	6	8.9999
UGA	chr6:35260311-35260555(+)$1	244	233	236	8.9999
UGA	chr1:161332130-161332411(+)$1	281	10	13	8.9999
UGA	chr6:36181724-36181938(+)$1	214	25	28	8.9999
UGA	chr18:47797787-47798051(-)$1	264	214	217	8.9999
UGA	chr11:66189890-66190105(+)$1	215	51	54	8.9999
UGA	chr7:143141092-143141305(+)$1	213	19	22	8.9999
UGA	chr11:18955685-18955903(-)$1	218	75	78	8.9999
UGA	chr6:31238752-31239073(-)$1	321	15	18	8.9999
UGA	chr13:99947587-99947825(-)$1	238	124	127	8.9999
uga	chr6:167357123-167357375(-)$1	252	29	32	8.9999
UGA	chr1:205589244-205589505(-)$1	261	68	71	8.9999
UGA	chr1:70687188-70687422(+)$1	234	93	96	8.9999
UGA	chr13:39588117-39588475(-)$1	358	3	6	8.9999
UGA	chr5:71490122-71490339(+)$1	217	1	4	8.9999
UGA	chrX:119694142-119694367(-)$1	225	47	50	8.9999
uga	chr12:110370781-110371014(-)$1	233	30	33	8.9999
UGA	chr5:102530533-102530768(+)$1	235	5	8	8.9999
UGA	chr12:29493975-29494226(-)$1	251	83	86	8.9999
UGA	chr16:69220963-69221199(+)$1	236	25	28	8.9999
UGA	chr16:22094889-22095159(+)$1	270	154	157	8.9999
UGA	chr12:121861267-121861550(+)$1	283	50	53	8.9999
UGA	chr7:98509536-98509784(+)$1	248	6	9	8.9999
UGA	chr6:35438314-35438528(+)$1	214	13	16	8.9999
UGA	chr7:2278707-2278943(-)$1	236	32	35	8.9999
UGA	chr18:34376852-34377099(-)$1	247	50	53	8.9999
UGA	chr10:45891223-45891440(+)$1	217	10	13	8.9999
UGA	chr3:31674496-31674721(+)$1	225	67	70	8.9999
UGA	chr16:68025639-68025883(-)$1	244	4	7	8.9999
UGA	chr11:113281495-113281712(-)$1	217	49	52	8.9999
UGA	chrX:2779559-2779773(+)$1	214	14	17	8.9999
UGA	chrX:114141586-114141799(+)$1	213	25	28	8.9999
UGA	chr6:42658794-42659041(+)$1	247	98	101	8.9999
UGA	chr11:128910787-128911015(-)$1	228	137	140	8.9999
UGA	chr12:53676073-53676297(+)$1	224	147	150	8.9999
UGA	chr3:12942756-12943072(-)$1	316	8	11	8.9999
UGA	chr11:118882535-118882767(+)$1	232	26	29	8.9999
UGA	chr17:76082842-76083060(+)$1	218	11	14	8.9999
UGA	chr4:79697623-79697848(+)$1	225	75	78	8.9999
UGA	chr19:56012395-56012610(+)$1	215	18	21	8.9999
UGA	chr3:52283576-52283868(+)$1	292	37	40	8.9999
UGA	chr16:30393802-30394018(-)$1	216	59	62	8.9999
UGA	chr2:242282340-242282555(+)$1	215	40	43	8.9999
UGA	chr20:39985970-39986188(+)$1	218	118	121	8.9999
UGA	chr15:90768131-90768344(+)$1	213	132	135	8.9999
UGA	chr2:167298038-167298259(-)$1	221	43	46	8.9999
UGA	chr14:74960948-74961167(+)$1	219	6	9	8.9999
UGA	chr6:84645919-84646159(+)$1	240	7	10	8.9999
uga	chr9:130648947-130649186(-)$1	239	30	33	8.9999
UGA	chr1:247320550-247320804(-)$1	254	14	17	8.9999
UGA	chr2:233680329-233680580(+)$1	251	121	124	8.9999
UGA	chr4:39474641-39474857(+)$1	216	51	54	8.9999
UGA	chr19:1599303-1599561(-)$1	258	70	73	8.9999
UGA	chr11:103908173-103908393(+)$1	220	45	48	8.9999
UGA	chrX:36254847-36255062(+)$1	215	2	5	8.9999
UGA	chr8:24196957-24197172(+)$1	215	2	5	8.9999
UGA	chr11:6540639-6540939(+)$1	300	28	31	8.9999
UGA	chr5:145838699-145838974(+)$1	275	202	205	8.9999
UGA	chr19:17664202-17664418(+)$1	216	167	170	8.9999
UGA	chr4:124323389-124323611(+)$1	222	58	61	8.9999
UGA	chr19:2877935-2878148(+)$1	213	48	51	8.9999
UGA	chr19:57956610-57956939(+)$1	329	158	161	8.9999
UGA	chr2:186665915-186666131(+)$1	216	129	132	8.9999
UGA	chr17:4848871-4849329(-)$1	458	49	52	8.9999
UGA	chr7:103175703-103175927(-)$1	224	0	3	8.9999
UGA	chr11:18536219-18536488(-)$1	269	77	80	8.9999
UGA	chr12:122818494-122818751(-)$1	257	12	15	8.9999
UGA	chr19:36640789-36641062(+)$1	273	60	63	8.9999
UGA	chr10:134997307-134997522(+)$1	215	48	51	8.9999
UGA	chr1:44442906-44443132(+)$1	226	52	55	8.9999
uga	chr7:102292782-102293094(-)$1	312	2	5	8.9999
UGA	chr4:24577965-24578241(-)$1	276	0	3	8.9999
UGA	chr3:50004879-50005124(+)$1	245	143	146	8.9999
UGA	chr19:12016601-12016816(+)$1	215	98	101	8.9999
UGA	chr15:52357014-52357272(+)$1	258	1	4	8.9999

#otherMatches

#Struct PSSM
fff	chr1:205588031-205588301(-)$1	270	73	76	8.9999
qqq	chr6:26184162-26184401(+)$1	239	48	51	8.9999
bb]	chr11:93778907-93779121(+)$1	214	71	74	8.9999
f::	chr12:32491619-32491841(+)$1	222	28	31	8.9999
:::	chr11:93808276-93808492(+)$1	216	5	8	8.9999
33e	chr16:70432046-70432263(-)$1	217	84	87	8.9999
hhh	chr3:127820386-127820610(-)$1	224	97	100	8.9999
!dd	chr8:21827632-21827854(+)$1	222	73	76	8.9999
333	chrX:70756020-70756298(+)$1	278	44	47	8.9999
WWW	chr1:151018495-151018709(+)$1	214	26	29	8.9999
cbb	chr1:186948479-186948692(+)$1	213	4	7	8.9999
+++	chrX:133511939-133512168(+)$1	229	22	25	8.9999
ff:	chr17:46805324-46805543(-)$1	219	67	70	8.9999
BB{	chr21:47613435-47613816(-)$1	381	2	5	8.9999
ccc	chr17:25639290-25639576(+)$1	286	31	34	8.9999
:::	chr12:59270155-59270385(-)$1	230	1	4	8.9999
[a[	chr16:111538-111755(-)$1	217	31	34	8.9999
eee	chr1:198668533-198668976(+)$1	443	20	23	8.9999
:ff	chr1:64605749-64605962(+)$1	213	54	57	8.9999
cc!	chr7:99811309-99811545(-)$1	236	48	51	8.9999
c!!	chr3:160146512-160146735(+)$1	223	32	35	8.9999
:::	chr19:41209551-41209806(-)$1	255	3	6	8.9999
DD}	chr6:35260311-35260555(+)$1	244	233	236	8.9999
FNN	chr1:161332130-161332411(+)$1	281	10	13	8.9999
ee:	chr6:36181724-36181938(+)$1	214	25	28	8.9999
c55	chr18:47797787-47798051(-)$1	264	214	217	8.9999
HHH	chr11:66189890-66190105(+)$1	215	51	54	8.9999
EEU	chr7:143141092-143141305(+)$1	213	19	22	8.9999
f::	chr11:18955685-18955903(-)$1	218	75	78	8.9999
cc"	chr6:31238752-31239073(-)$1	321	15	18	8.9999
ggg	chr13:99947587-99947825(-)$1	238	124	127	8.9999
mmm	chr6:167357123-167357375(-)$1	252	29	32	8.9999
!cc	chr1:205589244-205589505(-)$1	261	68	71	8.9999
ff!	chr1:70687188-70687422(+)$1	234	93	96	8.9999
eee	chr13:39588117-39588475(-)$1	358	3	6	8.9999
CCC	chr5:71490122-71490339(+)$1	217	1	4	8.9999
bbm	chrX:119694142-119694367(-)$1	225	47	50	8.9999
eee	chr12:110370781-110371014(-)$1	233	30	33	8.9999
DD{	chr5:102530533-102530768(+)$1	235	5	8	8.9999
"dd	chr12:29493975-29494226(-)$1	251	83	86	8.9999
bb:	chr16:69220963-69221199(+)$1	236	25	28	8.9999
ccc	chr16:22094889-22095159(+)$1	270	154	157	8.9999
dd:	chr12:121861267-121861550(+)$1	283	50	53	8.9999
{A{	chr7:98509536-98509784(+)$1	248	6	9	8.9999
:::	chr6:35438314-35438528(+)$1	214	13	16	8.9999
fff	chr7:2278707-2278943(-)$1	236	32	35	8.9999
DD{	chr18:34376852-34377099(-)$1	247	50	53	8.9999
ggg	chr10:45891223-45891440(+)$1	217	10	13	8.9999
ddm	chr3:31674496-31674721(+)$1	225	67	70	8.9999
eee	chr16:68025639-68025883(-)$1	244	4	7	8.9999
ccc	chr11:113281495-113281712(-)$1	217	49	52	8.9999
mmm	chrX:2779559-2779773(+)$1	214	14	17	8.9999
{EE	chrX:114141586-114141799(+)$1	213	25	28	8.9999
a22	chr6:42658794-42659041(+)$1	247	98	101	8.9999
GGG	chr11:128910787-128911015(-)$1	228	137	140	8.9999
[a'	chr12:53676073-53676297(+)$1	224	147	150	8.9999
ccc	chr3:12942756-12943072(-)$1	316	8	11	8.9999
BMM	chr11:118882535-118882767(+)$1	232	26	29	8.9999
:::	chr17:76082842-76083060(+)$1	218	11	14	8.9999
ccc	chr4:79697623-79697848(+)$1	225	75	78	8.9999
:::	chr19:56012395-56012610(+)$1	215	18	21	8.9999
LLL	chr3:52283576-52283868(+)$1	292	37	40	8.9999
###	chr16:30393802-30394018(-)$1	216	59	62	8.9999
ff:	chr2:242282340-242282555(+)$1	215	40	43	8.9999
eee	chr20:39985970-39986188(+)$1	218	118	121	8.9999
ccc	chr15:90768131-90768344(+)$1	213	132	135	8.9999
d""	chr2:167298038-167298259(-)$1	221	43	46	8.9999
::d	chr14:74960948-74961167(+)$1	219	6	9	8.9999
HHH	chr6:84645919-84646159(+)$1	240	7	10	8.9999
phh	chr9:130648947-130649186(-)$1	239	30	33	8.9999
DD:	chr1:247320550-247320804(-)$1	254	14	17	8.9999
e::	chr2:233680329-233680580(+)$1	251	121	124	8.9999
ccc	chr4:39474641-39474857(+)$1	216	51	54	8.9999
d]b	chr19:1599303-1599561(-)$1	258	70	73	8.9999
:::	chr11:103908173-103908393(+)$1	220	45	48	8.9999
GGG	chrX:36254847-36255062(+)$1	215	2	5	8.9999
FFF	chr8:24196957-24197172(+)$1	215	2	5	8.9999
]ii	chr11:6540639-6540939(+)$1	300	28	31	8.9999
ee]	chr5:145838699-145838974(+)$1	275	202	205	8.9999
CC}	chr19:17664202-17664418(+)$1	216	167	170	8.9999
ddd	chr4:124323389-124323611(+)$1	222	58	61	8.9999
eeb	chr19:2877935-2878148(+)$1	213	48	51	8.9999
a[g	chr19:57956610-57956939(+)$1	329	158	161	8.9999
fff	chr2:186665915-186666131(+)$1	216	129	132	8.9999
ee2	chr17:4848871-4849329(-)$1	458	49	52	8.9999
:::	chr7:103175703-103175927(-)$1	224	0	3	8.9999
fff	chr11:18536219-18536488(-)$1	269	77	80	8.9999
ff[	chr12:122818494-122818751(-)$1	257	12	15	8.9999
KEE	chr19:36640789-36641062(+)$1	273	60	63	8.9999
iii	chr10:134997307-134997522(+)$1	215	48	51	8.9999
!bb	chr1:44442906-44443132(+)$1	226	52	55	8.9999
:dd	chr7:102292782-102293094(-)$1	312	2	5	8.9999
:::	chr4:24577965-24578241(-)$1	276	0	3	8.9999
ffn	chr3:50004879-50005124(+)$1	245	143	146	8.9999
ccc	chr19:12016601-12016816(+)$1	215	98	101	8.9999
CCL	chr15:52357014-52357272(+)$1	258	1	4	8.9999

#DB
(((	chr1:205588031-205588301(-)$1	1	73	76	8.9999
...	chr6:26184162-26184401(+)$1	1	48	51	8.9999
)).	chr11:93778907-93779121(+)$1	1	71	74	8.9999
)..	chr12:32491619-32491841(+)$1	1	28	31	8.9999
...	chr11:93808276-93808492(+)$1	1	5	8	8.9999
..)	chr16:70432046-70432263(-)$1	1	84	87	8.9999
)))	chr3:127820386-127820610(-)$1	1	97	100	8.9999
.((	chr8:21827632-21827854(+)$1	1	73	76	8.9999
...	chrX:70756020-70756298(+)$1	1	44	47	8.9999
...	chr1:151018495-151018709(+)$1	1	26	29	8.9999
(((	chr1:186948479-186948692(+)$1	1	4	7	8.9999
...	chrX:133511939-133512168(+)$1	1	22	25	8.9999
)).	chr17:46805324-46805543(-)$1	1	67	70	8.9999
((.	chr21:47613435-47613816(-)$1	1	2	5	8.9999
)))	chr17:25639290-25639576(+)$1	1	31	34	8.9999
...	chr12:59270155-59270385(-)$1	1	1	4	8.9999
.(.	chr16:111538-111755(-)$1	1	31	34	8.9999
(((	chr1:198668533-198668976(+)$1	1	20	23	8.9999
.((	chr1:64605749-64605962(+)$1	1	54	57	8.9999
((.	chr7:99811309-99811545(-)$1	1	48	51	8.9999
(..	chr3:160146512-160146735(+)$1	1	32	35	8.9999
...	chr19:41209551-41209806(-)$1	1	3	6	8.9999
)).	chr6:35260311-35260555(+)$1	1	233	236	8.9999
(..	chr1:161332130-161332411(+)$1	1	10	13	8.9999
)).	chr6:36181724-36181938(+)$1	1	25	28	8.9999
)..	chr18:47797787-47798051(-)$1	1	214	217	8.9999
(((	chr11:66189890-66190105(+)$1	1	51	54	8.9999
((.	chr7:143141092-143141305(+)$1	1	19	22	8.9999
)..	chr11:18955685-18955903(-)$1	1	75	78	8.9999
((.	chr6:31238752-31239073(-)$1	1	15	18	8.9999
)))	chr13:99947587-99947825(-)$1	1	124	127	8.9999
...	chr6:167357123-167357375(-)$1	1	29	32	8.9999
.((	chr1:205589244-205589505(-)$1	1	68	71	8.9999
((.	chr1:70687188-70687422(+)$1	1	93	96	8.9999
(((	chr13:39588117-39588475(-)$1	1	3	6	8.9999
(((	chr5:71490122-71490339(+)$1	1	1	4	8.9999
((.	chrX:119694142-119694367(-)$1	1	47	50	8.9999
)))	chr12:110370781-110371014(-)$1	1	30	33	8.9999
((.	chr5:102530533-102530768(+)$1	1	5	8	8.9999
.((	chr12:29493975-29494226(-)$1	1	83	86	8.9999
)).	chr16:69220963-69221199(+)$1	1	25	28	8.9999
)))	chr16:22094889-22095159(+)$1	1	154	157	8.9999
)).	chr12:121861267-121861550(+)$1	1	50	53	8.9999
.(.	chr7:98509536-98509784(+)$1	1	6	9	8.9999
...	chr6:35438314-35438528(+)$1	1	13	16	8.9999
(((	chr7:2278707-2278943(-)$1	1	32	35	8.9999
((.	chr18:34376852-34377099(-)$1	1	50	53	8.9999
(((	chr10:45891223-45891440(+)$1	1	10	13	8.9999
((.	chr3:31674496-31674721(+)$1	1	67	70	8.9999
(((	chr16:68025639-68025883(-)$1	1	4	7	8.9999
(((	chr11:113281495-113281712(-)$1	1	49	52	8.9999
...	chrX:2779559-2779773(+)$1	1	14	17	8.9999
.((	chrX:114141586-114141799(+)$1	1	25	28	8.9999
)..	chr6:42658794-42659041(+)$1	1	98	101	8.9999
)))	chr11:128910787-128911015(-)$1	1	137	140	8.9999
.(.	chr12:53676073-53676297(+)$1	1	147	150	8.9999
(((	chr3:12942756-12943072(-)$1	1	8	11	8.9999
(..	chr11:118882535-118882767(+)$1	1	26	29	8.9999
...	chr17:76082842-76083060(+)$1	1	11	14	8.9999
(((	chr4:79697623-79697848(+)$1	1	75	78	8.9999
...	chr19:56012395-56012610(+)$1	1	18	21	8.9999
...	chr3:52283576-52283868(+)$1	1	37	40	8.9999
...	chr16:30393802-30394018(-)$1	1	59	62	8.9999
)).	chr2:242282340-242282555(+)$1	1	40	43	8.9999
)))	chr20:39985970-39986188(+)$1	1	118	121	8.9999
)))	chr15:90768131-90768344(+)$1	1	132	135	8.9999
(..	chr2:167298038-167298259(-)$1	1	43	46	8.9999
..(	chr14:74960948-74961167(+)$1	1	6	9	8.9999
(((	chr6:84645919-84646159(+)$1	1	7	10	8.9999
.))	chr9:130648947-130649186(-)$1	1	30	33	8.9999
((.	chr1:247320550-247320804(-)$1	1	14	17	8.9999
)..	chr2:233680329-233680580(+)$1	1	121	124	8.9999
(((	chr4:39474641-39474857(+)$1	1	51	54	8.9999
).)	chr19:1599303-1599561(-)$1	1	70	73	8.9999
...	chr11:103908173-103908393(+)$1	1	45	48	8.9999
(((	chrX:36254847-36255062(+)$1	1	2	5	8.9999
(((	chr8:24196957-24197172(+)$1	1	2	5	8.9999
.))	chr11:6540639-6540939(+)$1	1	28	31	8.9999
)).	chr5:145838699-145838974(+)$1	1	202	205	8.9999
)).	chr19:17664202-17664418(+)$1	1	167	170	8.9999
)))	chr4:124323389-124323611(+)$1	1	58	61	8.9999
(((	chr19:2877935-2878148(+)$1	1	48	51	8.9999
(.(	chr19:57956610-57956939(+)$1	1	158	161	8.9999
)))	chr2:186665915-186666131(+)$1	1	129	132	8.9999
)).	chr17:4848871-4849329(-)$1	1	49	52	8.9999
...	chr7:103175703-103175927(-)$1	1	0	3	8.9999
(((	chr11:18536219-18536488(-)$1	1	77	80	8.9999
((.	chr12:122818494-122818751(-)$1	1	12	15	8.9999
.((	chr19:36640789-36641062(+)$1	1	60	63	8.9999
)))	chr10:134997307-134997522(+)$1	1	48	51	8.9999
.((	chr1:44442906-44443132(+)$1	1	52	55	8.9999
.((	chr7:102292782-102293094(-)$1	1	2	5	8.9999
...	chr4:24577965-24578241(-)$1	1	0	3	8.9999
((.	chr3:50004879-50005124(+)$1	1	143	146	8.9999
(((	chr19:12016601-12016816(+)$1	1	98	101	8.9999
((.	chr15:52357014-52357272(+)$1	1	1	4	8.9999

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

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m1_run2.nuc.txt

#NT
CCCAGC	chrX:100614984-100615206(+)$1	222	192	198	14.8478
CCCAGC	chr8:144789237-144789461(-)$1	224	140	146	14.8478
CCCAGC	chr1:35370755-35370977(+)$1	222	122	128	14.8478
UCCAGC	chr19:49631503-49631724(-)$1	221	48	54	13.5434
UCCAGC	chr17:39594404-39594634(+)$1	230	6	12	13.5434
UCCAGC	chr13:100623569-100623791(-)$1	222	1	7	13.5434
UCCAGC	chr9:990423-990648(+)$1	225	21	27	13.5434
cccAGA	chr1:171486812-171487037(-)$1	225	33	39	11.1521
GCCAGC	chrX:129159169-129159393(-)$1	224	28	34	13.2173
UCCAGC	chr10:90701012-90701246(-)$1	234	39	45	13.5434
GCCAGC	chr2:133541351-133541573(+)$1	222	210	216	13.2173
CCCAGA	chr7:15725470-15725695(-)$1	225	18	24	11.1521
UCCAGC	chr3:50137860-50138139(-)$1	279	115	121	13.5434
UCCAGC	chr11:124615308-124615531(-)$1	223	83	89	13.5434
CCCAGC	chr9:133230197-133230422(-)$1	225	214	220	14.8478
CCCAGC	chr8:144522222-144522448(-)$1	226	190	196	14.8478
ACCAGC	chr13:94482606-94482828(+)$1	222	64	70	12.7826
CCCAGC	chr16:1264958-1265180(-)$1	222	41	47	14.8478
CCCAGC	chr16:133111-133333(-)$1	222	63	69	14.8478
CCCAGC	chr10:97116664-97116888(-)$1	224	199	205	14.8478
CCCAGA	chr17:18059533-18059755(+)$1	222	7	13	11.1521
ACCAGC	chr3:168845682-168845905(-)$1	223	87	93	12.7826
UCCAGC	chr16:4559543-4559765(-)$1	222	32	38	13.5434
GCCAGC	chr12:118533445-118533667(-)$1	222	190	196	13.2173
UCCAGC	chr18:59813135-59813359(+)$1	224	61	67	13.5434
CCCAGC	chr19:6182772-6182996(-)$1	224	27	33	14.8478
GCCAGC	chr19:48205064-48205288(-)$1	224	1	7	13.2173
CCCAGC	chr1:45269986-45270208(+)$1	222	48	54	14.8478
CCCAGA	chr9:37746613-37746836(+)$1	223	121	127	11.1521
CCCAGC	chr16:66946912-66947135(-)$1	223	173	179	14.8478
GCCAGC	chr2:175200735-175200962(-)$1	227	87	93	13.2173
CCCAGC	chr17:32961993-32962217(+)$1	224	130	136	14.8478
UCCAGC	chr17:60757461-60757682(-)$1	221	36	42	13.5434
CCCAGC	chr9:130251628-130251849(-)$1	221	34	40	14.8478
ACCAGC	chr5:153856927-153857157(-)$1	230	6	12	12.7826
ACCAGC	chr22:36920562-36920794(+)$1	232	138	144	12.7826
CCCAGA	chr19:3751428-3751651(-)$1	223	32	38	11.1521
CCCAGC	chr12:132623714-132623938(+)$1	224	96	102	14.8478
CCCAGC	chr1:226037536-226037765(-)$1	229	46	52	14.8478
UCCAGC	chr1:31406069-31406291(+)$1	222	55	61	13.5434
GCCAGC	chr19:757119-757340(+)$1	221	50	56	13.2173
CCCAGC	chr16:69143571-69143792(+)$1	221	49	55	14.8478
CCCAGC	chr13:30097294-30097521(+)$1	227	160	166	14.8478
GCCAGC	chr2:233708747-233708969(+)$1	222	15	21	13.2173
GCCAGC	chr2:176958052-176958273(+)$1	221	114	120	13.2173

#otherMatches

#Struct PSSM
e:::DD	chr1:156288540-156288769(+)$1	229	20	26	11.1521
rrrrbb	chrX:100614984-100615206(+)$1	222	192	198	14.8478
5555dd	chr8:144789237-144789461(-)$1	224	140	146	14.8478
fff]bb	chr1:35370755-35370977(+)$1	222	122	128	14.8478
::::EE	chr19:49631503-49631724(-)$1	221	48	54	13.5434
CKKEEE	chr17:39594404-39594634(+)$1	230	6	12	13.5434
:::ddd	chr13:100623569-100623791(-)$1	222	1	7	13.5434
ccc###	chr9:990423-990648(+)$1	225	21	27	13.5434
KKDDDD	chr1:171486812-171487037(-)$1	225	33	39	11.1521
bmmmmb	chrX:129159169-129159393(-)$1	224	28	34	13.2173
glllgg	chr10:90701012-90701246(-)$1	234	39	45	13.5434
2ccc]d	chr2:133541351-133541573(+)$1	222	210	216	13.2173
eeeemm	chr7:15725470-15725695(-)$1	225	18	24	11.1521
22ccc:	chr3:50137860-50138139(-)$1	279	115	121	13.5434
ddd!!e	chr11:124615308-124615531(-)$1	223	83	89	13.5434
ccc:::	chr9:133230197-133230422(-)$1	225	214	220	14.8478
e333bb	chr8:144522222-144522448(-)$1	226	190	196	14.8478
3dddd:	chr13:94482606-94482828(+)$1	222	64	70	12.7826
BCCC{G	chr16:1264958-1265180(-)$1	222	41	47	14.8478
b"""cc	chr16:133111-133333(-)$1	222	63	69	14.8478
22ccc]	chr10:97116664-97116888(-)$1	224	199	205	14.8478
::::::	chr17:18059533-18059755(+)$1	222	7	13	11.1521
mmccc]	chr3:168845682-168845905(-)$1	223	87	93	12.7826
cooooo	chr16:4559543-4559765(-)$1	222	32	38	13.5434
????DD	chr12:118533445-118533667(-)$1	222	190	196	13.2173
mmccc]	chr18:59813135-59813359(+)$1	224	61	67	13.5434
^^eeee	chr19:6182772-6182996(-)$1	224	27	33	14.8478
gggggg	chr19:48205064-48205288(-)$1	224	1	7	13.2173
hhhhff	chr1:45269986-45270208(+)$1	222	48	54	14.8478
ccc[bb	chr9:37746613-37746836(+)$1	223	121	127	11.1521
eeeee:	chr16:66946912-66947135(-)$1	223	173	179	14.8478
{CCC::	chr2:175200735-175200962(-)$1	227	87	93	13.2173
eeeqqq	chr17:32961993-32962217(+)$1	224	130	136	14.8478
[cccbb	chr17:60757461-60757682(-)$1	221	36	42	13.5434
b!!ccc	chr9:130251628-130251849(-)$1	221	34	40	14.8478
CCKKBB	chr5:153856927-153857157(-)$1	230	6	12	12.7826
DDD}GG	chr22:36920562-36920794(+)$1	232	138	144	12.7826
ff::::	chr19:3751428-3751651(-)$1	223	32	38	11.1521
[a[ccc	chr12:132623714-132623938(+)$1	224	96	102	14.8478
beeeee	chr1:226037536-226037765(-)$1	229	46	52	14.8478
iiiii[	chr1:31406069-31406291(+)$1	222	55	61	13.5434
gggggg	chr19:757119-757340(+)$1	221	50	56	13.2173
DBBKKB	chr16:69143571-69143792(+)$1	221	49	55	14.8478
ebb[dd	chr13:30097294-30097521(+)$1	227	160	166	14.8478
::::::	chr2:233708747-233708969(+)$1	222	15	21	13.2173
CCC{EE	chr2:176958052-176958273(+)$1	221	114	120	13.2173

#DB
)...((	chr1:156288540-156288769(+)$1	1	20	26	11.1521
....))	chrX:100614984-100615206(+)$1	1	192	198	14.8478
....))	chr8:144789237-144789461(-)$1	1	140	146	14.8478
))).))	chr1:35370755-35370977(+)$1	1	122	128	14.8478
....((	chr19:49631503-49631724(-)$1	1	48	54	13.5434
(..(((	chr17:39594404-39594634(+)$1	1	6	12	13.5434
...(((	chr13:100623569-100623791(-)$1	1	1	7	13.5434
(((...	chr9:990423-990648(+)$1	1	21	27	13.5434
..((((	chr1:171486812-171487037(-)$1	1	33	39	11.1521
(....)	chrX:129159169-129159393(-)$1	1	28	34	13.2173
(...))	chr10:90701012-90701246(-)$1	1	39	45	13.5434
.))).)	chr2:133541351-133541573(+)$1	1	210	216	13.2173
((((..	chr7:15725470-15725695(-)$1	1	18	24	11.1521
..))).	chr3:50137860-50138139(-)$1	1	115	121	13.5434
(((..(	chr11:124615308-124615531(-)$1	1	83	89	13.5434
)))...	chr9:133230197-133230422(-)$1	1	214	220	14.8478
)...))	chr8:144522222-144522448(-)$1	1	190	196	14.8478
.)))).	chr13:94482606-94482828(+)$1	1	64	70	12.7826
((((.(	chr16:1264958-1265180(-)$1	1	41	47	14.8478
(...((	chr16:133111-133333(-)$1	1	63	69	14.8478
..))).	chr10:97116664-97116888(-)$1	1	199	205	14.8478
......	chr17:18059533-18059755(+)$1	1	7	13	11.1521
..))).	chr3:168845682-168845905(-)$1	1	87	93	12.7826
(.....	chr16:4559543-4559765(-)$1	1	32	38	13.5434
....))	chr12:118533445-118533667(-)$1	1	190	196	13.2173
..))).	chr18:59813135-59813359(+)$1	1	61	67	13.5434
..))))	chr19:6182772-6182996(-)$1	1	27	33	14.8478
((((((	chr19:48205064-48205288(-)$1	1	1	7	13.2173
((((((	chr1:45269986-45270208(+)$1	1	48	54	14.8478
(((.((	chr9:37746613-37746836(+)$1	1	121	127	11.1521
))))).	chr16:66946912-66947135(-)$1	1	173	179	14.8478
.(((..	chr2:175200735-175200962(-)$1	1	87	93	13.2173
(((...	chr17:32961993-32962217(+)$1	1	130	136	14.8478
.(((((	chr17:60757461-60757682(-)$1	1	36	42	13.5434
(..(((	chr9:130251628-130251849(-)$1	1	34	40	14.8478
((..((	chr5:153856927-153857157(-)$1	1	6	12	12.7826
))).))	chr22:36920562-36920794(+)$1	1	138	144	12.7826
))....	chr19:3751428-3751651(-)$1	1	32	38	11.1521
.(.(((	chr12:132623714-132623938(+)$1	1	96	102	14.8478
((((((	chr1:226037536-226037765(-)$1	1	46	52	14.8478
(((((.	chr1:31406069-31406291(+)$1	1	55	61	13.5434
((((((	chr19:757119-757340(+)$1	1	50	56	13.2173
)((..(	chr16:69143571-69143792(+)$1	1	49	55	14.8478
)((.((	chr13:30097294-30097521(+)$1	1	160	166	14.8478
......	chr2:233708747-233708969(+)$1	1	15	21	13.2173
(((.((	chr2:176958052-176958273(+)$1	1	114	120	13.2173

#PSSM
C : 0.47	U : 0.23	G : 0.17	A : 0.08	c : 0.02	
C : 0.97	c : 0.02	
C : 0.97	c : 0.02	
A : 0.99	
G : 0.99	
C : 0.86	A : 0.13	

#score	625.173913043478
#seq	46
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m1_run1.nuc.txt

#NT
uuauuuu	chr5:56191148-56191379(+)$1	231	37	44	17.3559
UUAUUUU	chr2:101892996-101893229(-)$1	233	189	196	17.3559
UUAUAUU	chr9:37866300-37866525(+)$1	225	11	18	13.8813
UUGUUUU	chr8:48685732-48685975(-)$1	243	208	215	14.8135
GUAUUUU	chr14:81642371-81642592(-)$1	221	26	33	13.3728
UUAAUUU	chr10:123238933-123239160(-)$1	227	99	106	13.2881
UUAUAUU	chr10:116623089-116623320(+)$1	231	171	178	13.8813
UUAUUUU	chr17:4848912-4849148(-)$1	236	29	36	17.3559
UUCUUUU	chr4:141542110-141542362(-)$1	252	150	157	14.4745
uuaauuu	chr10:50666618-50666845(-)$1	227	40	47	13.2881
GUAUUUU	chr6:74304625-74304859(-)$1	234	92	99	13.3728
UUAUUUU	chr11:67024405-67024647(+)$1	242	162	169	17.3559
UUAUUUU	chr3:191113221-191113443(+)$1	222	79	86	17.3559
UUAAUUU	chr1:229729913-229730137(-)$1	224	90	97	13.2881
UUCUUUU	chr1:203651830-203652055(+)$1	225	6	13	14.4745
UUAUUUU	chr3:156865634-156865859(-)$1	225	128	135	17.3559
UUAUCUU	chr18:56995252-56995476(-)$1	224	122	129	13.5423
UUAUGUU	chr3:128888990-128889222(-)$1	232	110	117	13.7118
UUGUUUU	chr8:104312163-104312393(+)$1	230	8	15	14.8135
UUAAUUU	chr6:20491273-20491530(+)$1	257	197	204	13.2881
UUGUUUU	chr4:77956833-77957058(+)$1	225	185	192	14.8135
UUAUUUU	chr6:118030086-118030318(+)$1	232	48	55	17.3559
UUAUAUU	chr8:20078928-20079162(+)$1	234	207	214	13.8813
uuauuuu	chr9:117406172-117406398(+)$1	226	124	131	17.3559
UUAUAUU	chr19:5152672-5152910(+)$1	238	145	152	13.8813
UUAUGUU	chr6:144145086-144145317(+)$1	231	162	169	13.7118
UUGUUUU	chr11:110041789-110042012(+)$1	223	129	136	14.8135
UUAAUUU	chr1:244220341-244220566(+)$1	225	28	35	13.2881
UUUUUUU	chr17:62541704-62541931(-)$1	227	80	87	14.2203
UUUUUUU	chr2:109300582-109300804(+)$1	222	2	9	14.2203
UUGUUUU	chr17:65073437-65073670(-)$1	233	26	33	14.8135
UUAUUUU	chr1:241792083-241792305(-)$1	222	80	87	17.3559
UUAGUUU	chr10:72640124-72640348(+)$1	224	10	17	12.9491
GUAUUUU	chr2:5841298-5841530(+)$1	232	6	13	13.3728
UUCUUUU	chr10:11376030-11376271(+)$1	241	2	9	14.4745
UUAUAUU	chr6:7252046-7252270(+)$1	224	148	155	13.8813
UUGUUUU	chr16:1749489-1749735(+)$1	246	108	115	14.8135
UUGUUUU	chr12:53582682-53582913(+)$1	231	201	208	14.8135
UUAUAUU	chr6:24425365-24425588(+)$1	223	21	28	13.8813
GUAUUUU	chr9:130648024-130648276(-)$1	252	166	173	13.3728
UUCUUUU	chr3:55502358-55502589(-)$1	231	173	180	14.4745
UUAUCUU	chr22:29951462-29951697(-)$1	235	47	54	13.5423
UUCUUUU	chr3:18389378-18389601(-)$1	223	18	25	14.4745
UUAUUUU	chr14:62214040-62214260(+)$1	220	41	48	17.3559
UUCUUUU	chr4:57801259-57801483(+)$1	224	182	189	14.4745
UUUUUUU	chr19:10578229-10578489(+)$1	260	199	206	14.2203
UUGUUUU	chr4:119201656-119201885(-)$1	229	146	153	14.8135
UUGUUUU	chr6:52362936-52363171(-)$1	235	45	52	14.8135
UUAUGUU	chr9:114695181-114695397(+)$1	216	144	151	13.7118
GUAUUUU	chr2:20511965-20512190(-)$1	225	198	205	13.3728
UUAUGUU	chr5:38478832-38479054(-)$1	222	161	168	13.7118
GUAUUUU	chr11:65622453-65622703(-)$1	250	180	187	13.3728
UUAUUUU	chr11:14892195-14892417(+)$1	222	160	167	17.3559
UUAUUUU	chr1:185266716-185266969(-)$1	253	23	30	17.3559
UUAUUUU	chr15:58913675-58913911(-)$1	236	78	85	17.3559
UUAUUUU	chr6:21597692-21597929(+)$1	237	219	226	17.3559
UUAUUUU	chr1:67876656-67876879(-)$1	223	129	136	17.3559
UUGUUUU	chr7:150774981-150775216(-)$1	235	215	222	14.8135

#otherMatches

#Struct PSSM
ggggggg	chr18:66343604-66343832(-)$1	228	195	202	17.3559
:::::::	chr5:56191148-56191379(+)$1	231	37	44	17.3559
8888888	chr2:101892996-101893229(-)$1	233	189	196	17.3559
ddeeeee	chr9:37866300-37866525(+)$1	225	11	18	13.8813
CJJJJJJ	chr8:48685732-48685975(-)$1	243	208	215	14.8135
hhhhooo	chr14:81642371-81642592(-)$1	221	26	33	13.3728
fffoooo	chr10:123238933-123239160(-)$1	227	99	106	13.2881
"eeeeem	chr10:116623089-116623320(+)$1	231	171	178	13.8813
:::::::	chr17:4848912-4849148(-)$1	236	29	36	17.3559
ZZZFFFF	chr4:141542110-141542362(-)$1	252	150	157	14.4745
=====nn	chr10:50666618-50666845(-)$1	227	40	47	13.2881
ccc333h	chr6:74304625-74304859(-)$1	234	92	99	13.3728
vvvvvvv	chr11:67024405-67024647(+)$1	242	162	169	17.3559
cc[cccm	chr3:191113221-191113443(+)$1	222	79	86	17.3559
hhhhhhh	chr1:229729913-229730137(-)$1	224	90	97	13.2881
:::::::	chr1:203651830-203652055(+)$1	225	6	13	14.4745
ecccmmm	chr3:156865634-156865859(-)$1	225	128	135	17.3559
|||||HH	chr18:56995252-56995476(-)$1	224	122	129	13.5423
d]dddd2	chr3:128888990-128889222(-)$1	232	110	117	13.7118
ddddmmm	chr8:104312163-104312393(+)$1	230	8	15	14.8135
:::::::	chr6:20491273-20491530(+)$1	257	197	204	13.2881
eeeeeww	chr4:77956833-77957058(+)$1	225	185	192	14.8135
3dddd44	chr6:118030086-118030318(+)$1	232	48	55	17.3559
iiiiiii	chr8:20078928-20079162(+)$1	234	207	214	13.8813
CC}GGGG	chr9:117406172-117406398(+)$1	226	124	131	17.3559
>>>>>>>	chr19:5152672-5152910(+)$1	238	145	152	13.8813
ggggggg	chr6:144145086-144145317(+)$1	231	162	169	13.7118
hhhhhhh	chr11:110041789-110042012(+)$1	223	129	136	14.8135
qqqiiii	chr1:244220341-244220566(+)$1	225	28	35	13.2881
JJJJJJJ	chr17:62541704-62541931(-)$1	227	80	87	14.2203
ggggggg	chr2:109300582-109300804(+)$1	222	2	9	14.2203
cccssss	chr17:65073437-65073670(-)$1	233	26	33	14.8135
rrrrree	chr1:241792083-241792305(-)$1	222	80	87	17.3559
::::::C	chr10:72640124-72640348(+)$1	224	10	17	12.9491
:::::::	chr2:5841298-5841530(+)$1	232	6	13	13.3728
:::::::	chr10:11376030-11376271(+)$1	241	2	9	14.4745
qqqqqqd	chr6:7252046-7252270(+)$1	224	148	155	13.8813
fffffff	chr16:1749489-1749735(+)$1	246	108	115	14.8135
mmeeeee	chr12:53582682-53582913(+)$1	231	201	208	14.8135
OOOEEEE	chr6:24425365-24425588(+)$1	223	21	28	13.8813
hh"""dd	chr9:130648024-130648276(-)$1	252	166	173	13.3728
^^^^^^^	chr3:55502358-55502589(-)$1	231	173	180	14.4745
$$$ffff	chr22:29951462-29951697(-)$1	235	47	54	13.5423
%%cccoo	chr3:18389378-18389601(-)$1	223	18	25	14.4745
DDDDKKE	chr14:62214040-62214260(+)$1	220	41	48	17.3559
=======	chr4:57801259-57801483(+)$1	224	182	189	14.4745
ppfffff	chr19:10578229-10578489(+)$1	260	199	206	14.2203
0ffffff	chr4:119201656-119201885(-)$1	229	146	153	14.8135
ddd333c	chr6:52362936-52363171(-)$1	235	45	52	14.8135
glllggg	chr9:114695181-114695397(+)$1	216	144	151	13.7118
=======	chr2:20511965-20512190(-)$1	225	198	205	13.3728
dddhhhh	chr5:38478832-38479054(-)$1	222	161	168	13.7118
e::::::	chr11:65622453-65622703(-)$1	250	180	187	13.3728
eeeee""	chr11:14892195-14892417(+)$1	222	160	167	17.3559
cc:::::	chr1:185266716-185266969(-)$1	253	23	30	17.3559
JJ:::::	chr15:58913675-58913911(-)$1	236	78	85	17.3559
qqqqqqq	chr6:21597692-21597929(+)$1	237	219	226	17.3559
iiiiiii	chr1:67876656-67876879(-)$1	223	129	136	17.3559
33hhhhh	chr7:150774981-150775216(-)$1	235	215	222	14.8135

#DB
)))))))	chr18:66343604-66343832(-)$1	1	195	202	17.3559
.......	chr5:56191148-56191379(+)$1	1	37	44	17.3559
.......	chr2:101892996-101893229(-)$1	1	189	196	17.3559
(((((((	chr9:37866300-37866525(+)$1	1	11	18	13.8813
)))))))	chr8:48685732-48685975(-)$1	1	208	215	14.8135
((((...	chr14:81642371-81642592(-)$1	1	26	33	13.3728
(((....	chr10:123238933-123239160(-)$1	1	99	106	13.2881
.(((((.	chr10:116623089-116623320(+)$1	1	171	178	13.8813
.......	chr17:4848912-4849148(-)$1	1	29	36	17.3559
...))))	chr4:141542110-141542362(-)$1	1	150	157	14.4745
(((((..	chr10:50666618-50666845(-)$1	1	40	47	13.2881
)))...)	chr6:74304625-74304859(-)$1	1	92	99	13.3728
.......	chr11:67024405-67024647(+)$1	1	162	169	17.3559
((.(((.	chr3:191113221-191113443(+)$1	1	79	86	17.3559
(((((((	chr1:229729913-229730137(-)$1	1	90	97	13.2881
.......	chr1:203651830-203652055(+)$1	1	6	13	14.4745
((((...	chr3:156865634-156865859(-)$1	1	128	135	17.3559
.....))	chr18:56995252-56995476(-)$1	1	122	129	13.5423
).)))).	chr3:128888990-128889222(-)$1	1	110	117	13.7118
((((...	chr8:104312163-104312393(+)$1	1	8	15	14.8135
.......	chr6:20491273-20491530(+)$1	1	197	204	13.2881
(((((..	chr4:77956833-77957058(+)$1	1	185	192	14.8135
.))))..	chr6:118030086-118030318(+)$1	1	48	55	17.3559
(((((((	chr8:20078928-20079162(+)$1	1	207	214	13.8813
)).))))	chr9:117406172-117406398(+)$1	1	124	131	17.3559
.......	chr19:5152672-5152910(+)$1	1	145	152	13.8813
(((((((	chr6:144145086-144145317(+)$1	1	162	169	13.7118
)))))))	chr11:110041789-110042012(+)$1	1	129	136	14.8135
...))))	chr1:244220341-244220566(+)$1	1	28	35	13.2881
(((((((	chr17:62541704-62541931(-)$1	1	80	87	14.2203
(((((((	chr2:109300582-109300804(+)$1	1	2	9	14.2203
(((....	chr17:65073437-65073670(-)$1	1	26	33	14.8135
.....))	chr1:241792083-241792305(-)$1	1	80	87	17.3559
......(	chr10:72640124-72640348(+)$1	1	10	17	12.9491
.......	chr2:5841298-5841530(+)$1	1	6	13	13.3728
.......	chr10:11376030-11376271(+)$1	1	2	9	14.4745
......)	chr6:7252046-7252270(+)$1	1	148	155	13.8813
)))))))	chr16:1749489-1749735(+)$1	1	108	115	14.8135
..)))))	chr12:53582682-53582913(+)$1	1	201	208	14.8135
...((((	chr6:24425365-24425588(+)$1	1	21	28	13.8813
((...((	chr9:130648024-130648276(-)$1	1	166	173	13.3728
.......	chr3:55502358-55502589(-)$1	1	173	180	14.4745
...((((	chr22:29951462-29951697(-)$1	1	47	54	13.5423
..(((..	chr3:18389378-18389601(-)$1	1	18	25	14.4745
((((..(	chr14:62214040-62214260(+)$1	1	41	48	17.3559
)))))))	chr4:57801259-57801483(+)$1	1	182	189	14.4745
..)))))	chr19:10578229-10578489(+)$1	1	199	206	14.2203
.))))))	chr4:119201656-119201885(-)$1	1	146	153	14.8135
)))...)	chr6:52362936-52363171(-)$1	1	45	52	14.8135
(...)))	chr9:114695181-114695397(+)$1	1	144	151	13.7118
(((((((	chr2:20511965-20512190(-)$1	1	198	205	13.3728
(((((((	chr5:38478832-38479054(-)$1	1	161	168	13.7118
)......	chr11:65622453-65622703(-)$1	1	180	187	13.3728
(((((..	chr11:14892195-14892417(+)$1	1	160	167	17.3559
)).....	chr1:185266716-185266969(-)$1	1	23	30	17.3559
((.....	chr15:58913675-58913911(-)$1	1	78	85	17.3559
.......	chr6:21597692-21597929(+)$1	1	219	226	17.3559
)))))))	chr1:67876656-67876879(-)$1	1	129	136	17.3559
..)))))	chr7:150774981-150775216(-)$1	1	215	222	14.8135

#PSSM
U : 0.84	G : 0.10	u : 0.05	
U : 0.94	u : 0.05	
A : 0.62	G : 0.16	C : 0.10	a : 0.05	U : 0.05	
U : 0.86	A : 0.06	u : 0.03	a : 0.01	G : 0.01	
U : 0.74	A : 0.10	G : 0.06	u : 0.05	C : 0.03	
U : 0.94	u : 0.05	
U : 0.94	u : 0.05	

#score	880.1864406779656
#seq	59
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_UTR_m1_run2.nuc.txt

#NT
CUG	chr11:71935824-71936103(+)$1	279	11	14	9.0000
CUG	chr1:25568919-25569169(-)$1	250	10	13	9.0000
CUG	chr17:48828629-48828906(+)$1	277	6	9	9.0000
CUG	chr12:48361821-48362071(+)$1	250	5	8	9.0000
CUG	chr7:86781646-86781904(+)$1	258	20	23	9.0000
CUG	chr16:29821731-29822082(+)$1	351	10	13	9.0000
CUG	chr11:58346520-58346819(+)$1	299	5	8	9.0000
CUG	chr20:62331703-62331948(-)$1	245	6	9	9.0000
CUG	chr1:114225585-114225826(+)$1	241	107	110	9.0000
CUG	chr17:40352250-40352474(-)$1	224	29	32	9.0000
CUG	chr7:150779517-150779777(-)$1	260	32	35	9.0000
CUG	chr9:134373607-134373845(+)$1	238	76	79	9.0000
CUG	chr3:183901614-183901845(+)$1	231	0	3	9.0000
CUG	chr19:39936373-39936629(+)$1	256	34	37	9.0000
CUG	chr6:155054779-155055077(+)$1	298	16	19	9.0000
CUG	chr10:43881478-43881750(-)$1	272	25	28	9.0000
CUG	chr17:42397061-42397293(-)$1	232	10	13	9.0000
CUG	chr3:18390398-18390678(-)$1	280	0	3	9.0000
CUG	chr11:64535566-64535797(-)$1	231	12	15	9.0000
CUG	chr1:1717638-1717870(-)$1	232	91	94	9.0000
CUG	chr17:47006172-47006415(+)$1	243	17	20	9.0000
CUG	chr17:61822821-61823089(-)$1	268	34	37	9.0000
CUG	chr3:48199561-48199797(-)$1	236	2	5	9.0000
CUG	chr12:27951142-27951382(+)$1	240	86	89	9.0000
CUG	chr11:66384322-66384559(+)$1	237	13	16	9.0000
CUG	chr6:114181661-114181971(+)$1	310	21	24	9.0000
CUG	chr8:145693172-145693409(+)$1	237	8	11	9.0000
CUG	chr12:51566141-51566398(-)$1	257	46	49	9.0000
CUG	chrX:118370197-118370463(+)$1	266	94	97	9.0000
CUG	chr12:56634737-56634996(-)$1	259	124	127	9.0000
CUG	chr11:1297029-1297299(-)$1	270	4	7	9.0000
CUG	chr12:50158390-50158624(+)$1	234	38	41	9.0000
CUG	chr19:57804280-57804512(+)$1	232	35	38	9.0000
CUG	chr5:32229665-32229933(-)$1	268	51	54	9.0000
CUG	chr4:95587472-95587706(+)$1	234	7	10	9.0000
CUG	chr11:61094177-61094412(-)$1	235	138	141	9.0000
CUG	chr1:47143628-47143874(-)$1	246	56	59	9.0000
CUG	chr10:70174551-70174796(-)$1	245	128	131	9.0000
CUG	chr3:141644860-141645134(+)$1	274	33	36	9.0000
CUG	chr7:100278917-100279185(-)$1	268	22	25	9.0000
CUG	chr2:20449786-20450077(-)$1	291	107	110	9.0000
CUG	chr19:50176969-50177232(+)$1	263	32	35	9.0000
CUG	chr1:178442686-178442928(+)$1	242	22	25	9.0000
CUG	chr17:77761112-77761384(+)$1	272	36	39	9.0000
CUG	chr3:42706141-42706372(+)$1	231	13	16	9.0000
CUG	chr10:113911293-113911529(-)$1	236	105	108	9.0000
CUG	chr5:133450496-133450736(+)$1	240	110	113	9.0000
CUG	chr19:50985870-50986220(+)$1	350	13	16	9.0000
CUG	chr11:69467670-69467910(+)$1	240	19	22	9.0000
cug	chr22:29663314-29663582(-)$1	268	25	28	9.0000
CUG	chr9:136901059-136901317(-)$1	258	1	4	9.0000
cug	chr17:80231330-80231641(-)$1	311	16	19	9.0000
CUG	chr21:34804422-34804670(+)$1	248	123	126	9.0000
CUG	chr7:26251609-26251865(+)$1	256	33	36	9.0000
CUG	chr13:72440895-72441172(-)$1	277	243	246	9.0000
CUG	chr15:58006865-58007158(+)$1	293	8	11	9.0000
cug	chr16:28975929-28976160(+)$1	231	92	95	9.0000
CUG	chr19:59069845-59070158(-)$1	313	21	24	9.0000
CUG	chr2:233722408-233722656(+)$1	248	15	18	9.0000
CUG	chr8:144676007-144676295(-)$1	288	12	15	9.0000
CUG	chr9:129647102-129647357(+)$1	255	0	3	9.0000
CUG	chr20:62703511-62703776(+)$1	265	15	18	9.0000
CUG	chr21:45115464-45115706(+)$1	242	65	68	9.0000
CUG	chr3:111393654-111393885(+)$1	231	47	50	9.0000
CUG	chr19:41808551-41808808(+)$1	257	50	53	9.0000
CUG	chr19:50882246-50882501(+)$1	255	1	4	9.0000
CUG	chr10:102249768-102250027(-)$1	259	11	14	9.0000
CUG	chr9:77562818-77563078(-)$1	260	22	25	9.0000
CUG	chr5:137854448-137854656(-)$1	208	17	20	9.0000
CUG	chr1:160187041-160187309(-)$1	268	122	125	9.0000
CUG	chr8:146015067-146015310(-)$1	243	36	39	9.0000
CUG	chr12:99018049-99018278(-)$1	229	51	54	9.0000
CUG	chr1:116193869-116194128(+)$1	259	37	40	9.0000
CUG	chr1:197475160-197475395(-)$1	235	112	115	9.0000
CUG	chr19:2038181-2038432(-)$1	251	104	107	9.0000
CUG	chr19:1250109-1250334(+)$1	225	65	68	9.0000
CUG	chr19:3061064-3061341(-)$1	277	2	5	9.0000
CUG	chr9:99148910-99149144(-)$1	234	228	231	9.0000
CUG	chr17:79879256-79879499(-)$1	243	138	141	9.0000
CUG	chr1:1192276-1192536(-)$1	260	3	6	9.0000
CUG	chr19:1009746-1010027(-)$1	281	1	4	9.0000
CUG	chr16:4745438-4745676(+)$1	238	0	3	9.0000
CUG	chr19:34845601-34845850(+)$1	249	62	65	9.0000
CUG	chr1:245015890-245016127(-)$1	237	42	45	9.0000
CUG	chr1:154554559-154554839(-)$1	280	21	24	9.0000
CUG	chr11:65321528-65321791(-)$1	263	15	18	9.0000
CUG	chr9:139006558-139006833(-)$1	275	2	5	9.0000
CUG	chr1:154197490-154197753(+)$1	263	3	6	9.0000
CUG	chr7:5460907-5461167(-)$1	260	28	31	9.0000
cug	chr9:117406155-117406398(+)$1	243	49	52	9.0000
CUG	chr6:148872364-148872601(+)$1	237	4	7	9.0000
CUG	chr16:29869830-29870110(-)$1	280	25	28	9.0000
CUG	chr17:30817521-30817774(+)$1	253	43	46	9.0000
CUG	chr17:79213292-79213531(+)$1	239	13	16	9.0000
CUG	chr1:26232395-26232632(-)$1	237	73	76	9.0000
CUG	chr17:73886748-73886992(-)$1	244	45	48	9.0000
CUG	chrX:39911273-39911551(-)$1	278	26	29	9.0000
CUG	chr8:94744481-94744729(-)$1	248	21	24	9.0000
CUG	chr19:34890910-34891162(+)$1	252	43	46	9.0000

#otherMatches

#Struct PSSM
JJJ	chr7:4805759-4806059(+)$1	300	40	43	9.0000
eee	chr11:71935824-71936103(+)$1	279	11	14	9.0000
ddd	chr1:25568919-25569169(-)$1	250	10	13	9.0000
cc[	chr17:48828629-48828906(+)$1	277	6	9	9.0000
GGK	chr12:48361821-48362071(+)$1	250	5	8	9.0000
fff	chr7:86781646-86781904(+)$1	258	20	23	9.0000
MMM	chr16:29821731-29822082(+)$1	351	10	13	9.0000
fff	chr11:58346520-58346819(+)$1	299	5	8	9.0000
FFF	chr20:62331703-62331948(-)$1	245	6	9	9.0000
II:	chr1:114225585-114225826(+)$1	241	107	110	9.0000
iii	chr17:40352250-40352474(-)$1	224	29	32	9.0000
fff	chr7:150779517-150779777(-)$1	260	32	35	9.0000
gg2	chr9:134373607-134373845(+)$1	238	76	79	9.0000
:::	chr3:183901614-183901845(+)$1	231	0	3	9.0000
eee	chr19:39936373-39936629(+)$1	256	34	37	9.0000
""d	chr6:155054779-155055077(+)$1	298	16	19	9.0000
:::	chr10:43881478-43881750(-)$1	272	25	28	9.0000
::=	chr17:42397061-42397293(-)$1	232	10	13	9.0000
:::	chr3:18390398-18390678(-)$1	280	0	3	9.0000
:::	chr11:64535566-64535797(-)$1	231	12	15	9.0000
mmm	chr1:1717638-1717870(-)$1	232	91	94	9.0000
!ff	chr17:47006172-47006415(+)$1	243	17	20	9.0000
HKK	chr17:61822821-61823089(-)$1	268	34	37	9.0000
::E	chr3:48199561-48199797(-)$1	236	2	5	9.0000
fff	chr12:27951142-27951382(+)$1	240	86	89	9.0000
lll	chr11:66384322-66384559(+)$1	237	13	16	9.0000
ddd	chr6:114181661-114181971(+)$1	310	21	24	9.0000
EEE	chr8:145693172-145693409(+)$1	237	8	11	9.0000
hh[	chr12:51566141-51566398(-)$1	257	46	49	9.0000
33b	chrX:118370197-118370463(+)$1	266	94	97	9.0000
ffd	chr12:56634737-56634996(-)$1	259	124	127	9.0000
GGG	chr11:1297029-1297299(-)$1	270	4	7	9.0000
dd!	chr12:50158390-50158624(+)$1	234	38	41	9.0000
::f	chr19:57804280-57804512(+)$1	232	35	38	9.0000
ddd	chr5:32229665-32229933(-)$1	268	51	54	9.0000
MMD	chr4:95587472-95587706(+)$1	234	7	10	9.0000
emm	chr11:61094177-61094412(-)$1	235	138	141	9.0000
]dd	chr1:47143628-47143874(-)$1	246	56	59	9.0000
eee	chr10:70174551-70174796(-)$1	245	128	131	9.0000
::E	chr3:141644860-141645134(+)$1	274	33	36	9.0000
AKK	chr7:100278917-100279185(-)$1	268	22	25	9.0000
fff	chr2:20449786-20450077(-)$1	291	107	110	9.0000
eee	chr19:50176969-50177232(+)$1	263	32	35	9.0000
d[f	chr1:178442686-178442928(+)$1	242	22	25	9.0000
fcc	chr17:77761112-77761384(+)$1	272	36	39	9.0000
qqq	chr3:42706141-42706372(+)$1	231	13	16	9.0000
aoo	chr10:113911293-113911529(-)$1	236	105	108	9.0000
nnn	chr5:133450496-133450736(+)$1	240	110	113	9.0000
:::	chr19:50985870-50986220(+)$1	350	13	16	9.0000
GG:	chr11:69467670-69467910(+)$1	240	19	22	9.0000
ccc	chr22:29663314-29663582(-)$1	268	25	28	9.0000
B{H	chr9:136901059-136901317(-)$1	258	1	4	9.0000
HHL	chr17:80231330-80231641(-)$1	311	16	19	9.0000
fff	chr21:34804422-34804670(+)$1	248	123	126	9.0000
C:d	chr7:26251609-26251865(+)$1	256	33	36	9.0000
^^^	chr13:72440895-72441172(-)$1	277	243	246	9.0000
GGG	chr15:58006865-58007158(+)$1	293	8	11	9.0000
f]f	chr16:28975929-28976160(+)$1	231	92	95	9.0000
EEA	chr19:59069845-59070158(-)$1	313	21	24	9.0000
cmm	chr2:233722408-233722656(+)$1	248	15	18	9.0000
III	chr8:144676007-144676295(-)$1	288	12	15	9.0000
III	chr9:129647102-129647357(+)$1	255	0	3	9.0000
eee	chr20:62703511-62703776(+)$1	265	15	18	9.0000
GGG	chr21:45115464-45115706(+)$1	242	65	68	9.0000
ee=	chr3:111393654-111393885(+)$1	231	47	50	9.0000
ooo	chr19:41808551-41808808(+)$1	257	50	53	9.0000
DDD	chr19:50882246-50882501(+)$1	255	1	4	9.0000
EEE	chr10:102249768-102250027(-)$1	259	11	14	9.0000
LDD	chr9:77562818-77563078(-)$1	260	22	25	9.0000
ccc	chr5:137854448-137854656(-)$1	208	17	20	9.0000
ggn	chr1:160187041-160187309(-)$1	268	122	125	9.0000
b[b	chr8:146015067-146015310(-)$1	243	36	39	9.0000
rrf	chr12:99018049-99018278(-)$1	229	51	54	9.0000
:::	chr1:116193869-116194128(+)$1	259	37	40	9.0000
fff	chr1:197475160-197475395(-)$1	235	112	115	9.0000
dde	chr19:2038181-2038432(-)$1	251	104	107	9.0000
ooo	chr19:1250109-1250334(+)$1	225	65	68	9.0000
:::	chr19:3061064-3061341(-)$1	277	2	5	9.0000
FF:	chr9:99148910-99149144(-)$1	234	228	231	9.0000
^^^	chr17:79879256-79879499(-)$1	243	138	141	9.0000
!!f	chr1:1192276-1192536(-)$1	260	3	6	9.0000
CCC	chr19:1009746-1010027(-)$1	281	1	4	9.0000
::D	chr16:4745438-4745676(+)$1	238	0	3	9.0000
##e	chr19:34845601-34845850(+)$1	249	62	65	9.0000
fff	chr1:245015890-245016127(-)$1	237	42	45	9.0000
CCC	chr1:154554559-154554839(-)$1	280	21	24	9.0000
bbh	chr11:65321528-65321791(-)$1	263	15	18	9.0000
FFF	chr9:139006558-139006833(-)$1	275	2	5	9.0000
CBB	chr1:154197490-154197753(+)$1	263	3	6	9.0000
!!d	chr7:5460907-5461167(-)$1	260	28	31	9.0000
eee	chr9:117406155-117406398(+)$1	243	49	52	9.0000
GGG	chr6:148872364-148872601(+)$1	237	4	7	9.0000
III	chr16:29869830-29870110(-)$1	280	25	28	9.0000
!!b	chr17:30817521-30817774(+)$1	253	43	46	9.0000
HHH	chr17:79213292-79213531(+)$1	239	13	16	9.0000
fff	chr1:26232395-26232632(-)$1	237	73	76	9.0000
fff	chr17:73886748-73886992(-)$1	244	45	48	9.0000
fff	chrX:39911273-39911551(-)$1	278	26	29	9.0000
III	chr8:94744481-94744729(-)$1	248	21	24	9.0000
ooc	chr19:34890910-34891162(+)$1	252	43	46	9.0000

#DB
(((	chr7:4805759-4806059(+)$1	1	40	43	9.0000
(((	chr11:71935824-71936103(+)$1	1	11	14	9.0000
)))	chr1:25568919-25569169(-)$1	1	10	13	9.0000
((.	chr17:48828629-48828906(+)$1	1	6	9	9.0000
((.	chr12:48361821-48362071(+)$1	1	5	8	9.0000
(((	chr7:86781646-86781904(+)$1	1	20	23	9.0000
...	chr16:29821731-29822082(+)$1	1	10	13	9.0000
(((	chr11:58346520-58346819(+)$1	1	5	8	9.0000
(((	chr20:62331703-62331948(-)$1	1	6	9	9.0000
((.	chr1:114225585-114225826(+)$1	1	107	110	9.0000
(((	chr17:40352250-40352474(-)$1	1	29	32	9.0000
(((	chr7:150779517-150779777(-)$1	1	32	35	9.0000
)).	chr9:134373607-134373845(+)$1	1	76	79	9.0000
...	chr3:183901614-183901845(+)$1	1	0	3	9.0000
(((	chr19:39936373-39936629(+)$1	1	34	37	9.0000
..(	chr6:155054779-155055077(+)$1	1	16	19	9.0000
...	chr10:43881478-43881750(-)$1	1	25	28	9.0000
..(	chr17:42397061-42397293(-)$1	1	10	13	9.0000
...	chr3:18390398-18390678(-)$1	1	0	3	9.0000
...	chr11:64535566-64535797(-)$1	1	12	15	9.0000
...	chr1:1717638-1717870(-)$1	1	91	94	9.0000
.((	chr17:47006172-47006415(+)$1	1	17	20	9.0000
(..	chr17:61822821-61823089(-)$1	1	34	37	9.0000
..(	chr3:48199561-48199797(-)$1	1	2	5	9.0000
)))	chr12:27951142-27951382(+)$1	1	86	89	9.0000
...	chr11:66384322-66384559(+)$1	1	13	16	9.0000
)))	chr6:114181661-114181971(+)$1	1	21	24	9.0000
(((	chr8:145693172-145693409(+)$1	1	8	11	9.0000
((.	chr12:51566141-51566398(-)$1	1	46	49	9.0000
..)	chrX:118370197-118370463(+)$1	1	94	97	9.0000
(((	chr12:56634737-56634996(-)$1	1	124	127	9.0000
(((	chr11:1297029-1297299(-)$1	1	4	7	9.0000
((.	chr12:50158390-50158624(+)$1	1	38	41	9.0000
..(	chr19:57804280-57804512(+)$1	1	35	38	9.0000
(((	chr5:32229665-32229933(-)$1	1	51	54	9.0000
..(	chr4:95587472-95587706(+)$1	1	7	10	9.0000
(..	chr11:61094177-61094412(-)$1	1	138	141	9.0000
.))	chr1:47143628-47143874(-)$1	1	56	59	9.0000
)))	chr10:70174551-70174796(-)$1	1	128	131	9.0000
..(	chr3:141644860-141645134(+)$1	1	33	36	9.0000
(..	chr7:100278917-100279185(-)$1	1	22	25	9.0000
)))	chr2:20449786-20450077(-)$1	1	107	110	9.0000
(((	chr19:50176969-50177232(+)$1	1	32	35	9.0000
(.(	chr1:178442686-178442928(+)$1	1	22	25	9.0000
)((	chr17:77761112-77761384(+)$1	1	36	39	9.0000
...	chr3:42706141-42706372(+)$1	1	13	16	9.0000
(..	chr10:113911293-113911529(-)$1	1	105	108	9.0000
...	chr5:133450496-133450736(+)$1	1	110	113	9.0000
...	chr19:50985870-50986220(+)$1	1	13	16	9.0000
((.	chr11:69467670-69467910(+)$1	1	19	22	9.0000
)))	chr22:29663314-29663582(-)$1	1	25	28	9.0000
(.(	chr9:136901059-136901317(-)$1	1	1	4	9.0000
((.	chr17:80231330-80231641(-)$1	1	16	19	9.0000
)))	chr21:34804422-34804670(+)$1	1	123	126	9.0000
(.(	chr7:26251609-26251865(+)$1	1	33	36	9.0000
...	chr13:72440895-72441172(-)$1	1	243	246	9.0000
(((	chr15:58006865-58007158(+)$1	1	8	11	9.0000
).)	chr16:28975929-28976160(+)$1	1	92	95	9.0000
(((	chr19:59069845-59070158(-)$1	1	21	24	9.0000
(..	chr2:233722408-233722656(+)$1	1	15	18	9.0000
(((	chr8:144676007-144676295(-)$1	1	12	15	9.0000
(((	chr9:129647102-129647357(+)$1	1	0	3	9.0000
(((	chr20:62703511-62703776(+)$1	1	15	18	9.0000
(((	chr21:45115464-45115706(+)$1	1	65	68	9.0000
(((	chr3:111393654-111393885(+)$1	1	47	50	9.0000
...	chr19:41808551-41808808(+)$1	1	50	53	9.0000
(((	chr19:50882246-50882501(+)$1	1	1	4	9.0000
(((	chr10:102249768-102250027(-)$1	1	11	14	9.0000
.((	chr9:77562818-77563078(-)$1	1	22	25	9.0000
(((	chr5:137854448-137854656(-)$1	1	17	20	9.0000
((.	chr1:160187041-160187309(-)$1	1	122	125	9.0000
(.(	chr8:146015067-146015310(-)$1	1	36	39	9.0000
..)	chr12:99018049-99018278(-)$1	1	51	54	9.0000
...	chr1:116193869-116194128(+)$1	1	37	40	9.0000
)))	chr1:197475160-197475395(-)$1	1	112	115	9.0000
)))	chr19:2038181-2038432(-)$1	1	104	107	9.0000
...	chr19:1250109-1250334(+)$1	1	65	68	9.0000
...	chr19:3061064-3061341(-)$1	1	2	5	9.0000
)).	chr9:99148910-99149144(-)$1	1	228	231	9.0000
...	chr17:79879256-79879499(-)$1	1	138	141	9.0000
..(	chr1:1192276-1192536(-)$1	1	3	6	9.0000
(((	chr19:1009746-1010027(-)$1	1	1	4	9.0000
..(	chr16:4745438-4745676(+)$1	1	0	3	9.0000
..(	chr19:34845601-34845850(+)$1	1	62	65	9.0000
(((	chr1:245015890-245016127(-)$1	1	42	45	9.0000
(((	chr1:154554559-154554839(-)$1	1	21	24	9.0000
(((	chr11:65321528-65321791(-)$1	1	15	18	9.0000
(((	chr9:139006558-139006833(-)$1	1	2	5	9.0000
(((	chr1:154197490-154197753(+)$1	1	3	6	9.0000
..(	chr7:5460907-5461167(-)$1	1	28	31	9.0000
)))	chr9:117406155-117406398(+)$1	1	49	52	9.0000
(((	chr6:148872364-148872601(+)$1	1	4	7	9.0000
(((	chr16:29869830-29870110(-)$1	1	25	28	9.0000
..(	chr17:30817521-30817774(+)$1	1	43	46	9.0000
(((	chr17:79213292-79213531(+)$1	1	13	16	9.0000
(((	chr1:26232395-26232632(-)$1	1	73	76	9.0000
(((	chr17:73886748-73886992(-)$1	1	45	48	9.0000
)))	chrX:39911273-39911551(-)$1	1	26	29	9.0000
(((	chr8:94744481-94744729(-)$1	1	21	24	9.0000
..)	chr19:34890910-34891162(+)$1	1	43	46	9.0000

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

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m3_run2.nuc.txt

#NT
CAGG	chr14:105916341-105916600(+)$1	259	32	36	12.0000
CAGG	chr13:111995054-111995313(-)$1	259	86	90	12.0000
CAGG	chr16:30772782-30773041(+)$1	259	16	20	12.0000
CAGG	chr19:48821841-48822070(+)$1	229	1	5	12.0000
CAGG	chr6:75860805-75861034(-)$1	229	125	129	12.0000
CAGG	chrX:101911437-101911696(+)$1	259	65	69	12.0000
CAGG	chr7:2041631-2041890(-)$1	259	107	111	12.0000
CAGG	chr1:236907849-236908078(+)$1	229	73	77	12.0000
CAGG	chr11:78285310-78285569(+)$1	259	202	206	12.0000
CAGG	chr18:72168581-72168810(-)$1	229	53	57	12.0000
cagg	chr11:59968920-59969179(+)$1	259	63	67	12.0000
CAGG	chr14:31495185-31495444(+)$1	259	122	126	12.0000
CAGG	chr19:36336550-36336809(+)$1	259	38	42	12.0000
CAGG	chr16:1827925-1828184(+)$1	259	61	65	12.0000
CAGG	chr7:150766910-150767139(+)$1	229	173	177	12.0000
CAGG	chr1:61553853-61554112(-)$1	259	220	224	12.0000
CAGG	chr14:102028037-102028296(+)$1	259	177	181	12.0000
CAGG	chr3:39373890-39374149(-)$1	259	81	85	12.0000
CAGG	chr12:8997769-8998028(-)$1	259	151	155	12.0000
cagg	chr7:44240702-44240961(-)$1	259	46	50	12.0000
CAGG	chr14:101348719-101348978(-)$1	259	49	53	12.0000
CAGG	chr7:97854312-97854571(+)$1	259	6	10	12.0000
CAGG	chr19:4652143-4652402(+)$1	259	53	57	12.0000
CAGG	chr11:5968957-5969186(-)$1	229	32	36	12.0000
CAGG	chr3:42602564-42602793(+)$1	229	22	26	12.0000
CAGG	chr4:79229080-79229339(+)$1	259	157	161	12.0000
CAGG	chr5:80521429-80521658(-)$1	229	50	54	12.0000
CAGG	chr4:57425486-57425745(-)$1	259	77	81	12.0000
cagg	chrX:48690409-48690668(+)$1	259	14	18	12.0000
CAGG	chr11:64331674-64331903(-)$1	229	12	16	12.0000
CAGG	chr2:175201091-175201350(-)$1	259	64	68	12.0000
CAGG	chr15:34654346-34654605(+)$1	259	126	130	12.0000
CAGG	chr15:86262285-86262514(-)$1	229	87	91	12.0000
CAGG	chr16:11945248-11945507(+)$1	259	2	6	12.0000
CAGG	chr11:85396770-85397029(+)$1	259	139	143	12.0000
CAGG	chr15:102245769-102245998(-)$1	229	110	114	12.0000
CAGG	chr1:35575915-35576174(+)$1	259	130	134	12.0000
CAGG	chr4:39301605-39301834(+)$1	229	40	44	12.0000
CAGG	chr22:17444614-17444843(+)$1	229	18	22	12.0000
CAGG	chr10:50953772-50954001(+)$1	229	23	27	12.0000
CAGG	chr17:18081881-18082140(-)$1	259	13	17	12.0000
CAGG	chr18:5489088-5489317(+)$1	229	129	133	12.0000
cagg	chr17:76235802-76236061(+)$1	259	128	132	12.0000
CAGG	chr6:30522786-30523045(+)$1	259	51	55	12.0000
CAGG	chr4:85414349-85414578(+)$1	229	6	10	12.0000
CAGG	chr3:124605622-124605881(-)$1	259	101	105	12.0000
CAGG	chr7:140396526-140396785(-)$1	259	3	7	12.0000
CAGG	chr19:6692939-6693198(-)$1	259	10	14	12.0000
CAGG	chr19:1488156-1488385(+)$1	229	52	56	12.0000
CAGG	chr10:17275797-17276026(-)$1	229	31	35	12.0000
CAGG	chr7:6189728-6189957(-)$1	229	29	33	12.0000
CAGG	chr11:17424091-17424350(+)$1	259	202	206	12.0000
CAGG	chr7:131122568-131122827(+)$1	259	185	189	12.0000
CAGG	chr16:1712551-1712810(-)$1	259	28	32	12.0000
CAGG	chr12:53207329-53207588(+)$1	259	1	5	12.0000
CAGG	chr15:41228745-41228974(-)$1	229	45	49	12.0000
CAGG	chr11:76873933-76874192(+)$1	259	74	78	12.0000
CAGG	chrX:75650926-75651155(+)$1	229	175	179	12.0000
CAGG	chr7:107115407-107115636(+)$1	229	33	37	12.0000
CAGG	chr19:1918027-1918286(-)$1	259	20	24	12.0000
CAGG	chr16:2288297-2288556(-)$1	259	99	103	12.0000
CAGG	chr2:27436050-27436309(+)$1	259	10	14	12.0000
CAGG	chr8:22429140-22429399(+)$1	259	27	31	12.0000
CAGG	chr3:127785675-127785934(+)$1	259	11	15	12.0000
CAGG	chr17:17070832-17071061(+)$1	229	21	25	12.0000
CAGG	chrX:41193872-41194131(-)$1	259	119	123	12.0000
CAGG	chr4:875716-875945(+)$1	229	70	74	12.0000
CAGG	chr19:58514472-58514731(-)$1	259	26	30	12.0000
CAGG	chr17:76171110-76171369(+)$1	259	7	11	12.0000
CAGG	chr19:52954535-52954794(-)$1	259	67	71	12.0000
CAGG	chr2:234365538-234365797(-)$1	259	9	13	12.0000
CAGG	chr15:63941909-63942138(+)$1	229	136	140	12.0000
CAGG	chr11:134158564-134158823(+)$1	259	72	76	12.0000
CAGG	chr15:54556346-54556605(+)$1	259	101	105	12.0000
CAGG	chr19:17644279-17644508(-)$1	229	7	11	12.0000
CAGG	chr19:54584425-54584684(+)$1	259	22	26	12.0000
CAGG	chr12:1893014-1893273(-)$1	259	51	55	12.0000
CAGG	chr10:118439152-118439411(+)$1	259	11	15	12.0000
CAGG	chr22:36691590-36691849(+)$1	259	85	89	12.0000
CAGG	chr11:1295814-1296043(+)$1	229	66	70	12.0000
CAGG	chr16:845823-846082(+)$1	259	210	214	12.0000
CAGG	chr19:2247526-2247785(+)$1	259	28	32	12.0000

#otherMatches

#Struct PSSM
eEEE	chr17:10534769-10535028(-)$1	259	52	56	12.0000
c:cc	chr14:105916341-105916600(+)$1	259	32	36	12.0000
EEEE	chr13:111995054-111995313(-)$1	259	86	90	12.0000
KKCC	chr16:30772782-30773041(+)$1	259	16	20	12.0000
FFFF	chr19:48821841-48822070(+)$1	229	1	5	12.0000
ddoo	chr6:75860805-75861034(-)$1	229	125	129	12.0000
qqdd	chrX:101911437-101911696(+)$1	259	65	69	12.0000
B{DD	chr7:2041631-2041890(-)$1	259	107	111	12.0000
dddd	chr1:236907849-236908078(+)$1	229	73	77	12.0000
ZZCC	chr11:78285310-78285569(+)$1	259	202	206	12.0000
!fff	chr18:72168581-72168810(-)$1	229	53	57	12.0000
LDDD	chr11:59968920-59969179(+)$1	259	63	67	12.0000
""ff	chr14:31495185-31495444(+)$1	259	122	126	12.0000
mmmf	chr19:36336550-36336809(+)$1	259	38	42	12.0000
%%%%	chr16:1827925-1828184(+)$1	259	61	65	12.0000
CCCD	chr7:150766910-150767139(+)$1	229	173	177	12.0000
]ccc	chr1:61553853-61554112(-)$1	259	220	224	12.0000
@@@E	chr14:102028037-102028296(+)$1	259	177	181	12.0000
c[dd	chr3:39373890-39374149(-)$1	259	81	85	12.0000
ffff	chr12:8997769-8998028(-)$1	259	151	155	12.0000
EEEE	chr7:44240702-44240961(-)$1	259	46	50	12.0000
KKEE	chr14:101348719-101348978(-)$1	259	49	53	12.0000
EEE:	chr7:97854312-97854571(+)$1	259	6	10	12.0000
:eee	chr19:4652143-4652402(+)$1	259	53	57	12.0000
e:::	chr11:5968957-5969186(-)$1	229	32	36	12.0000
GGGG	chr3:42602564-42602793(+)$1	229	22	26	12.0000
c]cc	chr4:79229080-79229339(+)$1	259	157	161	12.0000
44ff	chr5:80521429-80521658(-)$1	229	50	54	12.0000
JJJJ	chr4:57425486-57425745(-)$1	259	77	81	12.0000
EEEE	chrX:48690409-48690668(+)$1	259	14	18	12.0000
hhhh	chr11:64331674-64331903(-)$1	229	12	16	12.0000
oooo	chr2:175201091-175201350(-)$1	259	64	68	12.0000
rrcc	chr15:34654346-34654605(+)$1	259	126	130	12.0000
pppp	chr15:86262285-86262514(-)$1	229	87	91	12.0000
dddd	chr16:11945248-11945507(+)$1	259	2	6	12.0000
ffff	chr11:85396770-85397029(+)$1	259	139	143	12.0000
ccce	chr15:102245769-102245998(-)$1	229	110	114	12.0000
JJJJ	chr1:35575915-35576174(+)$1	259	130	134	12.0000
dddd	chr4:39301605-39301834(+)$1	229	40	44	12.0000
b22e	chr22:17444614-17444843(+)$1	229	18	22	12.0000
::cc	chr10:50953772-50954001(+)$1	229	23	27	12.0000
cc[b	chr17:18081881-18082140(-)$1	259	13	17	12.0000
##bb	chr18:5489088-5489317(+)$1	229	129	133	12.0000
c]dd	chr17:76235802-76236061(+)$1	259	128	132	12.0000
]bbd	chr6:30522786-30523045(+)$1	259	51	55	12.0000
cc[b	chr4:85414349-85414578(+)$1	229	6	10	12.0000
qqqq	chr3:124605622-124605881(-)$1	259	101	105	12.0000
EEEc	chr7:140396526-140396785(-)$1	259	3	7	12.0000
BBKK	chr19:6692939-6693198(-)$1	259	10	14	12.0000
HHHH	chr19:1488156-1488385(+)$1	229	52	56	12.0000
"eee	chr10:17275797-17276026(-)$1	229	31	35	12.0000
gggg	chr7:6189728-6189957(-)$1	229	29	33	12.0000
iiim	chr11:17424091-17424350(+)$1	259	202	206	12.0000
cccg	chr7:131122568-131122827(+)$1	259	185	189	12.0000
C:cc	chr16:1712551-1712810(-)$1	259	28	32	12.0000
:::E	chr12:53207329-53207588(+)$1	259	1	5	12.0000
C::c	chr15:41228745-41228974(-)$1	229	45	49	12.0000
DDDD	chr11:76873933-76874192(+)$1	259	74	78	12.0000
yycc	chrX:75650926-75651155(+)$1	229	175	179	12.0000
ddds	chr7:107115407-107115636(+)$1	229	33	37	12.0000
peee	chr19:1918027-1918286(-)$1	259	20	24	12.0000
llla	chr16:2288297-2288556(-)$1	259	99	103	12.0000
GGGb	chr2:27436050-27436309(+)$1	259	10	14	12.0000
::CC	chr8:22429140-22429399(+)$1	259	27	31	12.0000
!!cc	chr3:127785675-127785934(+)$1	259	11	15	12.0000
bbFF	chr17:17070832-17071061(+)$1	229	21	25	12.0000
b[ee	chrX:41193872-41194131(-)$1	259	119	123	12.0000
:CCC	chr4:875716-875945(+)$1	229	70	74	12.0000
FFFF	chr19:58514472-58514731(-)$1	259	26	30	12.0000
ADDD	chr17:76171110-76171369(+)$1	259	7	11	12.0000
oddd	chr19:52954535-52954794(-)$1	259	67	71	12.0000
:GGG	chr2:234365538-234365797(-)$1	259	9	13	12.0000
::dd	chr15:63941909-63942138(+)$1	229	136	140	12.0000
#eee	chr11:134158564-134158823(+)$1	259	72	76	12.0000
::bb	chr15:54556346-54556605(+)$1	259	101	105	12.0000
MMHH	chr19:17644279-17644508(-)$1	229	7	11	12.0000
dddD	chr19:54584425-54584684(+)$1	259	22	26	12.0000
44cc	chr12:1893014-1893273(-)$1	259	51	55	12.0000
DD{D	chr10:118439152-118439411(+)$1	259	11	15	12.0000
hhhh	chr22:36691590-36691849(+)$1	259	85	89	12.0000
c!!d	chr11:1295814-1296043(+)$1	229	66	70	12.0000
FFFF	chr16:845823-846082(+)$1	259	210	214	12.0000
eeee	chr19:2247526-2247785(+)$1	259	28	32	12.0000

#DB
)(((	chr17:10534769-10535028(-)$1	1	52	56	12.0000
).((	chr14:105916341-105916600(+)$1	1	32	36	12.0000
((((	chr13:111995054-111995313(-)$1	1	86	90	12.0000
..((	chr16:30772782-30773041(+)$1	1	16	20	12.0000
((((	chr19:48821841-48822070(+)$1	1	1	5	12.0000
((..	chr6:75860805-75861034(-)$1	1	125	129	12.0000
..))	chrX:101911437-101911696(+)$1	1	65	69	12.0000
(.((	chr7:2041631-2041890(-)$1	1	107	111	12.0000
))))	chr1:236907849-236908078(+)$1	1	73	77	12.0000
..))	chr11:78285310-78285569(+)$1	1	202	206	12.0000
.(((	chr18:72168581-72168810(-)$1	1	53	57	12.0000
.(((	chr11:59968920-59969179(+)$1	1	63	67	12.0000
..((	chr14:31495185-31495444(+)$1	1	122	126	12.0000
...)	chr19:36336550-36336809(+)$1	1	38	42	12.0000
....	chr16:1827925-1828184(+)$1	1	61	65	12.0000
))))	chr7:150766910-150767139(+)$1	1	173	177	12.0000
.)))	chr1:61553853-61554112(-)$1	1	220	224	12.0000
...)	chr14:102028037-102028296(+)$1	1	177	181	12.0000
(.((	chr3:39373890-39374149(-)$1	1	81	85	12.0000
((((	chr12:8997769-8998028(-)$1	1	151	155	12.0000
((((	chr7:44240702-44240961(-)$1	1	46	50	12.0000
..((	chr14:101348719-101348978(-)$1	1	49	53	12.0000
(((.	chr7:97854312-97854571(+)$1	1	6	10	12.0000
.(((	chr19:4652143-4652402(+)$1	1	53	57	12.0000
)...	chr11:5968957-5969186(-)$1	1	32	36	12.0000
((((	chr3:42602564-42602793(+)$1	1	22	26	12.0000
).))	chr4:79229080-79229339(+)$1	1	157	161	12.0000
..))	chr5:80521429-80521658(-)$1	1	50	54	12.0000
((((	chr4:57425486-57425745(-)$1	1	77	81	12.0000
((((	chrX:48690409-48690668(+)$1	1	14	18	12.0000
((((	chr11:64331674-64331903(-)$1	1	12	16	12.0000
....	chr2:175201091-175201350(-)$1	1	64	68	12.0000
..))	chr15:34654346-34654605(+)$1	1	126	130	12.0000
....	chr15:86262285-86262514(-)$1	1	87	91	12.0000
((((	chr16:11945248-11945507(+)$1	1	2	6	12.0000
))))	chr11:85396770-85397029(+)$1	1	139	143	12.0000
((((	chr15:102245769-102245998(-)$1	1	110	114	12.0000
))))	chr1:35575915-35576174(+)$1	1	130	134	12.0000
((((	chr4:39301605-39301834(+)$1	1	40	44	12.0000
)..)	chr22:17444614-17444843(+)$1	1	18	22	12.0000
..((	chr10:50953772-50954001(+)$1	1	23	27	12.0000
((.(	chr17:18081881-18082140(-)$1	1	13	17	12.0000
..((	chr18:5489088-5489317(+)$1	1	129	133	12.0000
).))	chr17:76235802-76236061(+)$1	1	128	132	12.0000
.))(	chr6:30522786-30523045(+)$1	1	51	55	12.0000
((.(	chr4:85414349-85414578(+)$1	1	6	10	12.0000
....	chr3:124605622-124605881(-)$1	1	101	105	12.0000
((((	chr7:140396526-140396785(-)$1	1	3	7	12.0000
((..	chr19:6692939-6693198(-)$1	1	10	14	12.0000
((((	chr19:1488156-1488385(+)$1	1	52	56	12.0000
.(((	chr10:17275797-17276026(-)$1	1	31	35	12.0000
((((	chr7:6189728-6189957(-)$1	1	29	33	12.0000
(((.	chr11:17424091-17424350(+)$1	1	202	206	12.0000
)))(	chr7:131122568-131122827(+)$1	1	185	189	12.0000
(.((	chr16:1712551-1712810(-)$1	1	28	32	12.0000
...(	chr12:53207329-53207588(+)$1	1	1	5	12.0000
(..(	chr15:41228745-41228974(-)$1	1	45	49	12.0000
((((	chr11:76873933-76874192(+)$1	1	74	78	12.0000
..))	chrX:75650926-75651155(+)$1	1	175	179	12.0000
(((.	chr7:107115407-107115636(+)$1	1	33	37	12.0000
.)))	chr19:1918027-1918286(-)$1	1	20	24	12.0000
...)	chr16:2288297-2288556(-)$1	1	99	103	12.0000
((((	chr2:27436050-27436309(+)$1	1	10	14	12.0000
..((	chr8:22429140-22429399(+)$1	1	27	31	12.0000
..((	chr3:127785675-127785934(+)$1	1	11	15	12.0000
))((	chr17:17070832-17071061(+)$1	1	21	25	12.0000
(.((	chrX:41193872-41194131(-)$1	1	119	123	12.0000
.(((	chr4:875716-875945(+)$1	1	70	74	12.0000
((((	chr19:58514472-58514731(-)$1	1	26	30	12.0000
((((	chr17:76171110-76171369(+)$1	1	7	11	12.0000
.)))	chr19:52954535-52954794(-)$1	1	67	71	12.0000
.(((	chr2:234365538-234365797(-)$1	1	9	13	12.0000
..((	chr15:63941909-63942138(+)$1	1	136	140	12.0000
.(((	chr11:134158564-134158823(+)$1	1	72	76	12.0000
..((	chr15:54556346-54556605(+)$1	1	101	105	12.0000
..((	chr19:17644279-17644508(-)$1	1	7	11	12.0000
)))(	chr19:54584425-54584684(+)$1	1	22	26	12.0000
..))	chr12:1893014-1893273(-)$1	1	51	55	12.0000
((.(	chr10:118439152-118439411(+)$1	1	11	15	12.0000
((((	chr22:36691590-36691849(+)$1	1	85	89	12.0000
(..(	chr11:1295814-1296043(+)$1	1	66	70	12.0000
))))	chr16:845823-846082(+)$1	1	210	214	12.0000
))))	chr19:2247526-2247785(+)$1	1	28	32	12.0000

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

#score	996.0000000000002
#seq	83
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_CDS_m1_run2.nuc.txt

#NT
UUUCUUUUU	chr5:33461211-33461451(+)$1	240	24	33	19.5000
CUUAUUUUU	chr12:102154933-102155173(-)$1	240	120	129	18.6666
UUUAUUUUU	chr3:183585586-183585826(-)$1	240	155	164	23.1666
UUUAUUUUU	chr15:55474223-55474463(-)$1	240	13	22	23.1666
UUUAUUUUU	chr2:223773430-223773710(+)$1	280	181	190	23.1666
UUUAUUUUA	chr4:83276373-83276613(-)$1	240	49	58	18.8333
UUUUUUUUU	chr1:205683511-205683751(-)$1	240	115	124	19.6666
UUUUUUUUU	chr15:41672272-41672552(+)$1	280	169	178	19.6666
UUUAUUUUU	chr1:243858798-243859038(-)$1	240	183	192	23.1666
UUUGUUUUU	chr13:113459214-113459454(+)$1	240	36	45	19.3333
UUUAUUUCU	chr14:31107239-31107479(+)$1	240	130	139	18.7500
UUUACUUUU	chr4:17813907-17814147(+)$1	240	122	131	19.0833
uuuauuuuu	chr20:33703106-33703349(-)$1	243	129	138	23.1666
UUUUUUUUU	chr18:214495-214735(-)$1	240	114	123	19.6666
UUUAUAUUU	chr14:62213692-62213938(+)$1	246	172	181	18.5833
UUUAUUUCU	chr3:169802047-169802298(+)$1	251	125	134	18.7500
UUUAUAUUU	chr7:73096986-73097226(-)$1	240	143	152	18.5833
UUUAUUUUU	chr12:85695145-85695385(+)$1	240	121	130	23.1666
GUUAUUUUU	chr6:149900986-149901226(+)$1	240	217	226	18.5833
UUUAUUUUG	chr7:65419249-65419489(+)$1	240	85	94	18.9166
UUGAUUUUU	chr8:29961732-29961972(+)$1	240	2	11	18.5833
UUUAUUCUU	chr14:74363092-74363332(+)$1	240	117	126	18.5833
UUUAUUUCU	chr19:38055997-38056237(-)$1	240	105	114	18.7500
CUUAUUUUU	chr16:66592071-66592311(+)$1	240	110	119	18.6666
UUUAUUUUU	chr3:108298112-108298352(-)$1	240	7	16	23.1666
uuuuuuuuu	chr8:144940061-144940301(-)$1	240	210	219	19.6666
UUUAUUUUU	chr3:122591304-122591544(+)$1	240	111	120	23.1666
UUUAAUUUU	chr7:23509626-23509866(-)$1	240	85	94	18.9166
UUUAUUUAU	chr3:100013903-100014143(+)$1	240	111	120	18.5833
UUUAUUUUU	chr12:120899722-120899971(-)$1	249	172	181	23.1666
UUUAGUUUU	chr6:88372722-88372962(+)$1	240	152	161	18.8333
UUUCUUUUU	chr10:122619627-122619867(+)$1	240	125	134	19.5000
UUCAUUUUU	chr5:54948256-54948496(-)$1	240	111	120	18.7500
UUUAUUUUU	chr6:70410568-70410848(-)$1	280	132	141	23.1666
UUUAAUUUU	chr7:77379176-77379416(+)$1	240	118	127	18.9166
uuuuuuuuu	chr5:94005816-94006056(+)$1	240	225	234	19.6666
UUUACUUUU	chr1:193038434-193038674(+)$1	240	125	134	19.0833
UUUAUCUUU	chr6:76540070-76540310(+)$1	240	3	12	18.5000
UUUAUUUUC	chr5:131008395-131008645(-)$1	250	115	124	19.0833
UGUAUUUUU	chr17:80724042-80724282(+)$1	240	57	66	18.4166
UUCAUUUUU	chr13:103443206-103443446(-)$1	240	174	183	18.7500
uuuuuuuuu	chr5:179041678-179041958(-)$1	280	151	160	19.6666
UUUAUUUUC	chr7:63981671-63981911(-)$1	240	111	120	19.0833
UUUAUUUUU	chr8:441569-441809(-)$1	240	62	71	23.1666
AUUAUUUUU	chr2:70064587-70064827(+)$1	240	130	139	18.5833
UUUACUUUU	chr3:194140543-194140783(-)$1	240	64	73	19.0833
UUUAUUCUU	chr21:30698993-30699233(+)$1	240	110	119	18.5833
UUUAUUUUU	chr19:32928002-32928242(+)$1	240	113	122	23.1666
UUUGUUUUU	chrX:48435822-48436072(+)$1	250	136	145	19.3333
UUUAUUUUU	chr15:89859560-89859802(-)$1	242	111	120	23.1666
UUUAUUUUU	chr1:40756527-40756767(+)$1	240	118	127	23.1666
UUUAUUAUU	chr15:48434387-48434667(-)$1	280	140	149	18.5000
UUUCUUUUU	chr11:125472605-125472845(+)$1	240	32	41	19.5000
UUUACUUUU	chr21:26957895-26958135(-)$1	240	222	231	19.0833
UUUAUUUUG	chr12:111890403-111890643(-)$1	240	114	123	18.9166
UUUAUUUUC	chr6:96034241-96034481(+)$1	240	125	134	19.0833
UUUCUUUUU	chr5:70860606-70860846(+)$1	240	122	131	19.5000
UUCAUUUUU	chr2:86344115-86344361(+)$1	246	64	73	18.7500
UAUAUUUUU	chr5:74893735-74893975(+)$1	240	92	101	18.4166

#otherMatches

#Struct PSSM
ddd::::::	chr1:165697112-165697363(-)$1	251	116	125	19.0833
ffff[eeee	chr5:33461211-33461451(+)$1	240	24	33	19.5000
eeeeeuuuu	chr12:102154933-102155173(-)$1	240	120	129	18.6666
fffff>>>>	chr3:183585586-183585826(-)$1	240	155	164	23.1666
fff[eeeee	chr15:55474223-55474463(-)$1	240	13	22	23.1666
dd[gggggg	chr2:223773430-223773710(+)$1	280	181	190	23.1666
vvvvvvddd	chr4:83276373-83276613(-)$1	240	49	58	18.8333
ccc55555d	chr1:205683511-205683751(-)$1	240	115	124	19.6666
@@@@@@@@G	chr15:41672272-41672552(+)$1	280	169	178	19.6666
EEEEEHHHH	chr1:243858798-243859038(-)$1	240	183	192	23.1666
cddddtttt	chr13:113459214-113459454(+)$1	240	36	45	19.3333
9999999gg	chr14:31107239-31107479(+)$1	240	130	139	18.7500
FFFFF:hhh	chr4:17813907-17814147(+)$1	240	122	131	19.0833
nffffff99	chr20:33703106-33703349(-)$1	243	129	138	23.1666
JJJJJ::::	chr18:214495-214735(-)$1	240	114	123	19.6666
)))))))ff	chr14:62213692-62213938(+)$1	246	172	181	18.5833
i[bbooooo	chr3:169802047-169802298(+)$1	251	125	134	18.7500
^^^^^^^^^	chr7:73096986-73097226(-)$1	240	143	152	18.5833
bb%%%%%%h	chr12:85695145-85695385(+)$1	240	121	130	23.1666
=========	chr6:149900986-149901226(+)$1	240	217	226	18.5833
SSBB{EEEE	chr7:65419249-65419489(+)$1	240	85	94	18.9166
:::::::::	chr8:29961732-29961972(+)$1	240	2	11	18.5833
00000000d	chr14:74363092-74363332(+)$1	240	117	126	18.5833
qqqqfffff	chr19:38055997-38056237(-)$1	240	105	114	18.7500
b22dddd00	chr16:66592071-66592311(+)$1	240	110	119	18.6666
::::::::E	chr3:108298112-108298352(-)$1	240	7	16	23.1666
?????FFFF	chr8:144940061-144940301(-)$1	240	210	219	19.6666
+++++++++	chr3:122591304-122591544(+)$1	240	111	120	23.1666
dddd99999	chr7:23509626-23509866(-)$1	240	85	94	18.9166
((iiiiiii	chr3:100013903-100014143(+)$1	240	111	120	18.5833
]ffffff::	chr12:120899722-120899971(-)$1	249	172	181	23.1666
ggggggccc	chr6:88372722-88372962(+)$1	240	152	161	18.8333
c========	chr10:122619627-122619867(+)$1	240	125	134	19.5000
dddd+++++	chr5:54948256-54948496(-)$1	240	111	120	18.7500
#dddd"""c	chr6:70410568-70410848(-)$1	280	132	141	23.1666
::::::iii	chr7:77379176-77379416(+)$1	240	118	127	18.9166
:::::::::	chr5:94005816-94006056(+)$1	240	225	234	19.6666
eee[ccc!!	chr1:193038434-193038674(+)$1	240	125	134	19.0833
ggggmmmmg	chr6:76540070-76540310(+)$1	240	3	12	18.5000
=========	chr5:131008395-131008645(-)$1	250	115	124	19.0833
b]a]bb]ee	chr17:80724042-80724282(+)$1	240	57	66	18.4166
:dddd[fff	chr13:103443206-103443446(-)$1	240	174	183	18.7500
:::::::::	chr5:179041678-179041958(-)$1	280	151	160	19.6666
iiiii^^^^	chr7:63981671-63981911(-)$1	240	111	120	19.0833
2ggggggg2	chr8:441569-441809(-)$1	240	62	71	23.1666
ggggggmmm	chr2:70064587-70064827(+)$1	240	130	139	18.5833
iiiiiii!!	chr3:194140543-194140783(-)$1	240	64	73	19.0833
::::HHHHH	chr21:30698993-30699233(+)$1	240	110	119	18.5833
HHcccmmmm	chr19:32928002-32928242(+)$1	240	113	122	23.1666
rrccc333d	chrX:48435822-48436072(+)$1	250	136	145	19.3333
dd[======	chr15:89859560-89859802(-)$1	242	111	120	23.1666
D::::::::	chr1:40756527-40756767(+)$1	240	118	127	23.1666
^^ggggggg	chr15:48434387-48434667(-)$1	280	140	149	18.5000
:::::::::	chr11:125472605-125472845(+)$1	240	32	41	19.5000
e::::::::	chr21:26957895-26958135(-)$1	240	222	231	19.0833
pppeeeeef	chr12:111890403-111890643(-)$1	240	114	123	18.9166
!eeeeeqqq	chr6:96034241-96034481(+)$1	240	125	134	19.0833
dddd:::::	chr5:70860606-70860846(+)$1	240	122	131	19.5000
eeeeeeeee	chr2:86344115-86344361(+)$1	246	64	73	18.7500
qqqqqqqqe	chr5:74893735-74893975(+)$1	240	92	101	18.4166

#DB
)))......	chr1:165697112-165697363(-)$1	1	116	125	19.0833
((((.((((	chr5:33461211-33461451(+)$1	1	24	33	19.5000
(((((....	chr12:102154933-102155173(-)$1	1	120	129	18.6666
)))))....	chr3:183585586-183585826(-)$1	1	155	164	23.1666
(((.(((((	chr15:55474223-55474463(-)$1	1	13	22	23.1666
((.((((((	chr2:223773430-223773710(+)$1	1	181	190	23.1666
......)))	chr4:83276373-83276613(-)$1	1	49	58	18.8333
))).....)	chr1:205683511-205683751(-)$1	1	115	124	19.6666
........)	chr15:41672272-41672552(+)$1	1	169	178	19.6666
)))))))))	chr1:243858798-243859038(-)$1	1	183	192	23.1666
(((((....	chr13:113459214-113459454(+)$1	1	36	45	19.3333
.......))	chr14:31107239-31107479(+)$1	1	130	139	18.7500
))))).(((	chr4:17813907-17814147(+)$1	1	122	131	19.0833
.))))))..	chr20:33703106-33703349(-)$1	1	129	138	23.1666
)))))....	chr18:214495-214735(-)$1	1	114	123	19.6666
.......((	chr14:62213692-62213938(+)$1	1	172	181	18.5833
(.((.....	chr3:169802047-169802298(+)$1	1	125	134	18.7500
.........	chr7:73096986-73097226(-)$1	1	143	152	18.5833
((......(	chr12:85695145-85695385(+)$1	1	121	130	23.1666
)))))))))	chr6:149900986-149901226(+)$1	1	217	226	18.5833
..((.((((	chr7:65419249-65419489(+)$1	1	85	94	18.9166
.........	chr8:29961732-29961972(+)$1	1	2	11	18.5833
........)	chr14:74363092-74363332(+)$1	1	117	126	18.5833
....)))))	chr19:38055997-38056237(-)$1	1	105	114	18.7500
)..))))..	chr16:66592071-66592311(+)$1	1	110	119	18.6666
........(	chr3:108298112-108298352(-)$1	1	7	16	23.1666
.....))))	chr8:144940061-144940301(-)$1	1	210	219	19.6666
.........	chr3:122591304-122591544(+)$1	1	111	120	23.1666
)))).....	chr7:23509626-23509866(-)$1	1	85	94	18.9166
..(((((((	chr3:100013903-100014143(+)$1	1	111	120	18.5833
.))))))..	chr12:120899722-120899971(-)$1	1	172	181	23.1666
(((((((((	chr6:88372722-88372962(+)$1	1	152	161	18.8333
)))))))))	chr10:122619627-122619867(+)$1	1	125	134	19.5000
((((.....	chr5:54948256-54948496(-)$1	1	111	120	18.7500
.((((...(	chr6:70410568-70410848(-)$1	1	132	141	23.1666
......(((	chr7:77379176-77379416(+)$1	1	118	127	18.9166
.........	chr5:94005816-94006056(+)$1	1	225	234	19.6666
(((.(((..	chr1:193038434-193038674(+)$1	1	125	134	19.0833
((((....)	chr6:76540070-76540310(+)$1	1	3	12	18.5000
(((((((((	chr5:131008395-131008645(-)$1	1	115	124	19.0833
).).)).))	chr17:80724042-80724282(+)$1	1	57	66	18.4166
.((((.(((	chr13:103443206-103443446(-)$1	1	174	183	18.7500
.........	chr5:179041678-179041958(-)$1	1	151	160	19.6666
(((((....	chr7:63981671-63981911(-)$1	1	111	120	19.0833
.))))))).	chr8:441569-441809(-)$1	1	62	71	23.1666
((((((...	chr2:70064587-70064827(+)$1	1	130	139	18.5833
(((((((..	chr3:194140543-194140783(-)$1	1	64	73	19.0833
....)))))	chr21:30698993-30699233(+)$1	1	110	119	18.5833
(((((....	chr19:32928002-32928242(+)$1	1	113	122	23.1666
..)))...)	chrX:48435822-48436072(+)$1	1	136	145	19.3333
((.((((((	chr15:89859560-89859802(-)$1	1	111	120	23.1666
)........	chr1:40756527-40756767(+)$1	1	118	127	23.1666
..)))))))	chr15:48434387-48434667(-)$1	1	140	149	18.5000
.........	chr11:125472605-125472845(+)$1	1	32	41	19.5000
)........	chr21:26957895-26958135(-)$1	1	222	231	19.0833
...))))))	chr12:111890403-111890643(-)$1	1	114	123	18.9166
.(((((...	chr6:96034241-96034481(+)$1	1	125	134	19.0833
)))).....	chr5:70860606-70860846(+)$1	1	122	131	19.5000
(((((((((	chr2:86344115-86344361(+)$1	1	64	73	18.7500
........)	chr5:74893735-74893975(+)$1	1	92	101	18.4166

#PSSM
U : 0.86	u : 0.06	C : 0.03	G : 0.01	A : 0.01	
U : 0.90	u : 0.06	G : 0.01	A : 0.01	
U : 0.86	u : 0.06	C : 0.05	G : 0.01	
A : 0.78	C : 0.06	U : 0.05	u : 0.05	G : 0.03	a : 0.01	
U : 0.81	C : 0.06	u : 0.06	A : 0.03	G : 0.01	
U : 0.88	u : 0.06	A : 0.03	C : 0.01	
U : 0.88	u : 0.06	C : 0.03	A : 0.01	
U : 0.86	u : 0.06	C : 0.05	A : 0.01	
U : 0.81	C : 0.06	u : 0.06	G : 0.03	A : 0.01	

#score	1197.333333333335
#seq	60
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m1_run1.nuc.txt

#NT
AUUCUUUU	chr12:69042388-69042660(+)$1	272	62	70	15.5384
UUUUUUUU	chr4:90167794-90168042(-)$1	248	142	150	16.8461
UUUCUUUU	chr13:77754162-77754431(-)$1	269	227	235	19.7692
UUUAUUUU	chrX:41209246-41209541(+)$1	295	239	247	16.7692
UUUCAUUU	chr10:33218744-33219072(-)$1	328	66	74	15.8461
UUUGUUUU	chr17:65343161-65343440(-)$1	279	50	58	16.8461
GUUCUUUU	chr14:90874362-90874716(+)$1	354	46	54	15.4615
UUUGUUUU	chr3:185765179-185765442(-)$1	263	244	252	16.8461
UUUCUUUG	chr2:86370957-86371243(-)$1	286	43	51	15.3076
UUUCAUUU	chr10:35859293-35859570(+)$1	277	61	69	15.8461
UUUAUUUU	chr4:38700015-38700346(+)$1	331	133	141	16.7692
UUUCCUUU	chr10:72640256-72640511(+)$1	255	198	206	15.9999
UUUCUUUC	chr5:151179748-151179993(+)$1	245	148	156	15.3846
AUUCUUUU	chr5:102365247-102365516(+)$1	269	46	54	15.5384
UUUCUUGU	chr6:407817-408228(+)$1	411	181	189	14.9999
UUUAUUUU	chr3:172116536-172116797(+)$1	261	101	109	16.7692
GUUCUUUU	chr18:40847762-40848026(-)$1	264	93	101	15.4615
UUUAUUUU	chr13:30085412-30085684(-)$1	272	84	92	16.7692
UCUCUUUU	chr16:16387923-16388183(+)$1	260	89	97	15.3076
AUUCUUUU	chr17:1247696-1248112(-)$1	416	53	61	15.5384
uuuauuuu	chr6:75964405-75964676(-)$1	271	53	61	16.7692
UUUCUUUC	chr17:38145909-38146222(+)$1	313	64	72	15.3846
UUUCUUUU	chr3:113530703-113530988(+)$1	285	206	214	19.7692
uuucuuuu	chr12:4410738-4411162(+)$1	424	352	360	19.7692
UUGCUUUU	chr20:35869708-35870048(+)$1	340	255	263	15.3076
uuucuuuu	chr6:407357-407702(+)$1	345	261	269	19.7692
UUUCUUUU	chr8:61534218-61534468(+)$1	250	29	37	19.7692
UUUAUUUU	chr1:113213472-113213732(+)$1	260	30	38	16.7692
UUGCUUUU	chr16:1749252-1749562(+)$1	310	277	285	15.3076
UUUGUUUU	chr2:85771837-85772104(+)$1	267	15	23	16.8461
UUUCUCUU	chr12:111159847-111160110(-)$1	263	24	32	14.9999
UUACUUUU	chr20:4681752-4682027(+)$1	275	97	105	15.1538
uuuuuuuu	chr4:152025545-152025839(+)$1	294	46	54	16.8461
UUUCUUUG	chr2:38525227-38525622(-)$1	395	244	252	15.3076
UCUCUUUU	chrX:41206825-41207123(+)$1	298	44	52	15.3076
uuuuuuuu	chr9:14086083-14086324(-)$1	241	50	58	16.8461
UUUCAUUU	chr14:103809289-103809640(+)$1	351	253	261	15.8461
UUUCCUUU	chr11:119172809-119173082(+)$1	273	139	147	15.9999
UAUCUUUU	chr20:62905779-62906018(+)$1	239	194	202	15.3846
UUUUUUUU	chr8:107763354-107763635(+)$1	281	153	161	16.8461
UUUGUUUU	chr4:109588711-109589020(+)$1	309	276	284	16.8461
UUUGUUUU	chr6:133135778-133136029(+)$1	251	80	88	16.8461
CUUCUUUU	chr16:11643169-11643466(-)$1	297	98	106	15.4615
UUUCUUUC	chr7:7646972-7647231(+)$1	259	190	198	15.3846
UUUCUGUU	chr17:46942000-46942333(+)$1	333	247	255	14.9999
UUUCAUUU	chr1:67878144-67878436(-)$1	292	92	100	15.8461
UAUCUUUU	chr3:176740987-176741257(-)$1	270	203	211	15.3846
UUUCCUUU	chr4:7056977-7057242(+)$1	265	94	102	15.9999
UUUUUUUU	chr17:78368861-78369213(+)$1	352	33	41	16.8461
UUUUUUUU	chr7:112115605-112115857(+)$1	252	4	12	16.8461
UUGCUUUU	chr20:48698188-48698453(-)$1	265	234	242	15.3076
UUUCCUUU	chr5:142660796-142661037(-)$1	241	110	118	15.9999
UUUCUUCU	chr7:42959026-42959283(+)$1	257	91	99	14.9999
uuucuuuu	chr11:62392196-62392484(-)$1	288	268	276	19.7692
UUUCUUUU	chr5:224410-224684(+)$1	274	52	60	19.7692
UUUCUUUU	chr5:95091032-95091326(+)$1	294	50	58	19.7692
CUUCUUUU	chr15:77345022-77345329(-)$1	307	284	292	15.4615
UUUCUUUU	chr11:9610276-9610644(+)$1	368	305	313	19.7692
UUUCCUUU	chr2:135712862-135713231(+)$1	369	310	318	15.9999
UUUGuuuu	chr17:49255082-49255410(-)$1	328	82	90	16.8461
UUUUUUUU	chr5:98131968-98132238(+)$1	270	39	47	16.8461
UAUCUUUU	chr9:86275706-86276018(-)$1	312	279	287	15.3846
UUUCCUUU	chr18:8638158-8638524(+)$1	366	184	192	15.9999
UUUGUUUU	chr1:224599032-224599339(-)$1	307	62	70	16.8461

#otherMatches

#Struct PSSM
%%eeeee[	chr1:149857643-149857963(-)$1	320	271	279	19.7692
::::::::	chr12:69042388-69042660(+)$1	272	62	70	15.5384
rrrrrrgg	chr4:90167794-90168042(-)$1	248	142	150	16.8461
d]bbHHHH	chr13:77754162-77754431(-)$1	269	227	235	19.7692
ggggggg[	chrX:41209246-41209541(+)$1	295	239	247	16.7692
EEEE{FFF	chr10:33218744-33219072(-)$1	328	66	74	15.8461
b22fffff	chr17:65343161-65343440(-)$1	279	50	58	16.8461
ssbb]hhh	chr14:90874362-90874716(+)$1	354	46	54	15.4615
}FFFFFF:	chr3:185765179-185765442(-)$1	263	244	252	16.8461
GGG::eee	chr2:86370957-86371243(-)$1	286	43	51	15.3076
========	chr10:35859293-35859570(+)$1	277	61	69	15.8461
::::====	chr4:38700015-38700346(+)$1	331	133	141	16.7692
""dddd!!	chr10:72640256-72640511(+)$1	255	198	206	15.9999
eeecccll	chr5:151179748-151179993(+)$1	245	148	156	15.3846
wwwhhhhh	chr5:102365247-102365516(+)$1	269	46	54	15.5384
gggg!!cc	chr6:407817-408228(+)$1	411	181	189	14.9999
c666666b	chr3:172116536-172116797(+)$1	261	101	109	16.7692
c]dddd33	chr18:40847762-40848026(-)$1	264	93	101	15.4615
#eeeee!!	chr13:30085412-30085684(-)$1	272	84	92	16.7692
=:CCCEEE	chr16:16387923-16388183(+)$1	260	89	97	15.3076
cnnnnncc	chr17:1247696-1248112(-)$1	416	53	61	15.5384
!!eeeeed	chr6:75964405-75964676(-)$1	271	53	61	16.7692
eeeddddF	chr17:38145909-38146222(+)$1	313	64	72	15.3846
hh22ffff	chr3:113530703-113530988(+)$1	285	206	214	19.7692
EEEE::::	chr12:4410738-4411162(+)$1	424	352	360	19.7692
========	chr20:35869708-35870048(+)$1	340	255	263	15.3076
22ffffff	chr6:407357-407702(+)$1	345	261	269	19.7692
ee::::::	chr8:61534218-61534468(+)$1	250	29	37	19.7692
ddddoooo	chr1:113213472-113213732(+)$1	260	30	38	16.7692
ffff9999	chr16:1749252-1749562(+)$1	310	277	285	15.3076
dd[eeeee	chr2:85771837-85772104(+)$1	267	15	23	16.8461
:cccgggg	chr12:111159847-111160110(-)$1	263	24	32	14.9999
eebb22cc	chr20:4681752-4682027(+)$1	275	97	105	15.1538
::::::::	chr4:152025545-152025839(+)$1	294	46	54	16.8461
333bb666	chr2:38525227-38525622(-)$1	395	244	252	15.3076
eeeee:::	chrX:41206825-41207123(+)$1	298	44	52	15.3076
====6666	chr9:14086083-14086324(-)$1	241	50	58	16.8461
gggggggm	chr14:103809289-103809640(+)$1	351	253	261	15.8461
HHHHHHH:	chr11:119172809-119173082(+)$1	273	139	147	15.9999
::::::::	chr20:62905779-62906018(+)$1	239	194	202	15.3846
^^^^^^^^	chr8:107763354-107763635(+)$1	281	153	161	16.8461
f:ddddqq	chr4:109588711-109589020(+)$1	309	276	284	16.8461
::::::::	chr6:133135778-133136029(+)$1	251	80	88	16.8461
EEENNNNN	chr16:11643169-11643466(-)$1	297	98	106	15.4615
ggccclll	chr7:7646972-7647231(+)$1	259	190	198	15.3846
iiiiiiii	chr17:46942000-46942333(+)$1	333	247	255	14.9999
::::::::	chr1:67878144-67878436(-)$1	292	92	100	15.8461
fff]gggg	chr3:176740987-176741257(-)$1	270	203	211	15.3846
eeeooooo	chr4:7056977-7057242(+)$1	265	94	102	15.9999
evvvvvvv	chr17:78368861-78369213(+)$1	352	33	41	16.8461
{BBJJJJJ	chr7:112115605-112115857(+)$1	252	4	12	16.8461
mmbb22cc	chr20:48698188-48698453(-)$1	265	234	242	15.3076
========	chr5:142660796-142661037(-)$1	241	110	118	15.9999
qqqqqddd	chr7:42959026-42959283(+)$1	257	91	99	14.9999
__HHHHHH	chr11:62392196-62392484(-)$1	288	268	276	19.7692
JJJJJJJJ	chr5:224410-224684(+)$1	274	52	60	19.7692
::::ffff	chr5:95091032-95091326(+)$1	294	50	58	19.7692
f:::HHHH	chr15:77345022-77345329(-)$1	307	284	292	15.4615
!!ccc!!c	chr11:9610276-9610644(+)$1	368	305	313	19.7692
i:::::::	chr2:135712862-135713231(+)$1	369	310	318	15.9999
c!!ccc!!	chr17:49255082-49255410(-)$1	328	82	90	16.8461
nnnneeee	chr5:98131968-98132238(+)$1	270	39	47	16.8461
iiiii22d	chr9:86275706-86276018(-)$1	312	279	287	15.3846
^^^^^^^^	chr18:8638158-8638524(+)$1	366	184	192	15.9999
ffoooooo	chr1:224599032-224599339(-)$1	307	62	70	16.8461

#DB
..(((((.	chr1:149857643-149857963(-)$1	1	271	279	19.7692
........	chr12:69042388-69042660(+)$1	1	62	70	15.5384
......))	chr4:90167794-90168042(-)$1	1	142	150	16.8461
).))))))	chr13:77754162-77754431(-)$1	1	227	235	19.7692
(((((((.	chrX:41209246-41209541(+)$1	1	239	247	16.7692
((((.(((	chr10:33218744-33219072(-)$1	1	66	74	15.8461
)..)))))	chr17:65343161-65343440(-)$1	1	50	58	16.8461
..)).)))	chr14:90874362-90874716(+)$1	1	46	54	15.4615
.)))))).	chr3:185765179-185765442(-)$1	1	244	252	16.8461
(((..(((	chr2:86370957-86371243(-)$1	1	43	51	15.3076
((((((((	chr10:35859293-35859570(+)$1	1	61	69	15.8461
....((((	chr4:38700015-38700346(+)$1	1	133	141	16.7692
..((((..	chr10:72640256-72640511(+)$1	1	198	206	15.9999
((((((..	chr5:151179748-151179993(+)$1	1	148	156	15.3846
...)))))	chr5:102365247-102365516(+)$1	1	46	54	15.5384
((((..((	chr6:407817-408228(+)$1	1	181	189	14.9999
)......)	chr3:172116536-172116797(+)$1	1	101	109	16.7692
).))))..	chr18:40847762-40848026(-)$1	1	93	101	15.4615
.(((((..	chr13:30085412-30085684(-)$1	1	84	92	16.7692
).((((((	chr16:16387923-16388183(+)$1	1	89	97	15.3076
(.....))	chr17:1247696-1248112(-)$1	1	53	61	15.5384
..((((((	chr6:75964405-75964676(-)$1	1	53	61	16.7692
)))))))(	chr17:38145909-38146222(+)$1	1	64	72	15.3846
))..))))	chr3:113530703-113530988(+)$1	1	206	214	19.7692
))))....	chr12:4410738-4411162(+)$1	1	352	360	19.7692
((((((((	chr20:35869708-35870048(+)$1	1	255	263	15.3076
..))))))	chr6:407357-407702(+)$1	1	261	269	19.7692
))......	chr8:61534218-61534468(+)$1	1	29	37	19.7692
((((....	chr1:113213472-113213732(+)$1	1	30	38	16.7692
))))....	chr16:1749252-1749562(+)$1	1	277	285	15.3076
((.(((((	chr2:85771837-85772104(+)$1	1	15	23	16.8461
.(((((((	chr12:111159847-111160110(-)$1	1	24	32	14.9999
))))..))	chr20:4681752-4682027(+)$1	1	97	105	15.1538
........	chr4:152025545-152025839(+)$1	1	46	54	16.8461
...))...	chr2:38525227-38525622(-)$1	1	244	252	15.3076
)))))...	chrX:41206825-41207123(+)$1	1	44	52	15.3076
))))....	chr9:14086083-14086324(-)$1	1	50	58	16.8461
(((((((.	chr14:103809289-103809640(+)$1	1	253	261	15.8461
(((((((.	chr11:119172809-119173082(+)$1	1	139	147	15.9999
........	chr20:62905779-62906018(+)$1	1	194	202	15.3846
........	chr8:107763354-107763635(+)$1	1	153	161	16.8461
).((((..	chr4:109588711-109589020(+)$1	1	276	284	16.8461
........	chr6:133135778-133136029(+)$1	1	80	88	16.8461
(((.....	chr16:11643169-11643466(-)$1	1	98	106	15.4615
(((((...	chr7:7646972-7647231(+)$1	1	190	198	15.3846
))))))))	chr17:46942000-46942333(+)$1	1	247	255	14.9999
........	chr1:67878144-67878436(-)$1	1	92	100	15.8461
))).))))	chr3:176740987-176741257(-)$1	1	203	211	15.3846
(((.....	chr4:7056977-7057242(+)$1	1	94	102	15.9999
(.......	chr17:78368861-78369213(+)$1	1	33	41	16.8461
.(((((((	chr7:112115605-112115857(+)$1	1	4	12	16.8461
..))..))	chr20:48698188-48698453(-)$1	1	234	242	15.3076
))))))))	chr5:142660796-142661037(-)$1	1	110	118	15.9999
.....)))	chr7:42959026-42959283(+)$1	1	91	99	14.9999
..))))))	chr11:62392196-62392484(-)$1	1	268	276	19.7692
((((((((	chr5:224410-224684(+)$1	1	52	60	19.7692
....((((	chr5:95091032-95091326(+)$1	1	50	58	19.7692
)...))))	chr15:77345022-77345329(-)$1	1	284	292	15.4615
..(((..(	chr11:9610276-9610644(+)$1	1	305	313	19.7692
).......	chr2:135712862-135713231(+)$1	1	310	318	15.9999
(..(((..	chr17:49255082-49255410(-)$1	1	82	90	16.8461
....))))	chr5:98131968-98132238(+)$1	1	39	47	16.8461
)))))..)	chr9:86275706-86276018(-)$1	1	279	287	15.3846
........	chr18:8638158-8638524(+)$1	1	184	192	15.9999
((......	chr1:224599032-224599339(-)$1	1	62	70	16.8461

#PSSM
U : 0.79	u : 0.09	A : 0.04	G : 0.03	C : 0.03	
U : 0.83	u : 0.09	A : 0.04	C : 0.03	
U : 0.84	u : 0.09	G : 0.04	A : 0.01	
C : 0.64	G : 0.10	U : 0.07	A : 0.07	c : 0.04	u : 0.03	a : 0.01	
U : 0.73	u : 0.10	C : 0.09	A : 0.06	
U : 0.86	u : 0.10	C : 0.01	G : 0.01	
U : 0.86	u : 0.10	G : 0.01	C : 0.01	
U : 0.81	u : 0.10	C : 0.04	G : 0.03	

#score	1076.6153846153834
#seq	65
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_CDS_m3_run1.nuc.txt

#NT
GCCUGGGAGGACAUCGCCUGCGUGUCCGCCCACGGGAGCAGAAGGAGUUCCAGAGCCCGGCCUCCAAAUCCCCCAAAGGAGCGGCCCCCGACAGUCACCAGCUGGCCAAAGCGCUAGCUGAGGCUGCAGACGUGGGGGCACAAAUGAUAAAGCUUGUGGGGCUGAGGGAGUUGUCCGAGGCCGAGCGGCAGCUUCGCAGCCUAGUGGUGGCCCUGAUGCAGGAGGUCUUCACAGAGU	chr11:62348817-62349107(-)$1	290	4	241	303.5000

#otherMatches

#Struct PSSM
eeeqqqqqqqqeeeeebb]dddd333eeeee::::::::gggggggggggggg[ccc+++++++++++++bb[ffffff!!ccc!!ffffff!!dddd[ccc[eeeee!!ffffffdddd[cccrrrrrrrrrccc]dddd]ffffff4444eeeee333ccc]dddd]ffffff]cccffffff]bbccc22ggggggg666666gggggggddddlllddddGGGGGGG}BBccc	chr11:62346064-62346424(-)$1	360	31	268	303.5000
CCC{DDDDeeeee[bbmmmmbbeeeee::::::CCCKKDDDDLLLCCC::CCCNNNNNDDDD{CCC:::ffffff$$$$$ffffff++++++++++++hhhhhhhhoooooohhhhhhhh]ffffff55555ffffffeeeeesssssssssseeeeeffffff!!ggggggg[cccqqqqqqqqcccggggggg]ffffff::CCC}DDDDCCC:::::ffffffccc!!ccc[an	chr11:62348817-62349107(-)$1	290	4	241	303.5000

#DB
(((........))))))).))))...)))))........((((((((((((((.(((.............((.((((((..(((..((((((..((((.(((.(((((..((((((((((.(((.........))).)))).))))))....)))))...))).)))).)))))).))))))))).)))))..)))))))......)))))))((((...))))))))))).))(((	chr11:62346064-62346424(-)$1	1	31	268	303.5000
(((.(((((((((.((....)))))))......(((..((((...(((..(((.....((((.(((...((((((.....((((((............((((((((......)))))))).)))))).....))))))(((((..........)))))((((((..(((((((.(((........)))))))))).))))))..))).))))))).....(((((((((..(((.(.	chr11:62348817-62349107(-)$1	1	4	241	303.5000

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

#score	607.0
#seq	2
#width	237
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m1_run2.nuc.txt

#NT
GGGGCC	chr20:24646013-24646272(+)$1	259	155	161	14.1904
GGGGCC	chr12:133433996-133434255(+)$1	259	246	252	14.1904
GGAGCC	chr16:85024102-85024361(+)$1	259	97	103	9.9047
GUGGCC	chr14:99864947-99865176(+)$1	229	210	216	11.6507
GCGGCC	chr1:6295755-6295984(+)$1	229	32	38	11.2539
UGGGCC	chr11:126173999-126174228(-)$1	229	191	197	9.6666
GUGGCC	chr19:7184414-7184673(-)$1	259	129	135	11.6507
GGGGAC	chr2:242615474-242615733(+)$1	259	26	32	11.1746
GAGGCC	chr8:145731190-145731449(+)$1	259	66	72	11.3333
UGGGCC	chr3:13896011-13896270(+)$1	259	237	243	9.6666
GGGGUC	chr14:34247619-34247848(-)$1	229	150	156	11.1746
GGGGAC	chr1:171756886-171757145(+)$1	259	9	15	11.1746
gcggcc	chr7:44144254-44144483(+)$1	229	4	10	11.2539
GGUGCC	chr1:32131102-32131361(-)$1	259	54	60	9.9047
GUGGCC	chr5:150175008-150175267(-)$1	259	176	182	11.6507
GGGGCC	chr14:55529796-55530055(-)$1	259	15	21	14.1904
GGGGCC	chr7:148978780-148979039(+)$1	259	6	12	14.1904
GGAGCC	chr3:49770083-49770342(-)$1	259	50	56	9.9047
GGGGGC	chr7:43687039-43687298(-)$1	259	131	137	10.9365
GGGGCC	chr10:115804025-115804284(+)$1	259	208	214	14.1904
UGGGCC	chr7:44796390-44796649(+)$1	259	171	177	9.6666
guggCC	chr16:81387913-81388172(+)$1	259	17	23	11.6507
GGGGCC	chr13:111299311-111299570(-)$1	259	204	210	14.1904
GGGGCC	chr13:98829159-98829388(+)$1	229	132	138	14.1904
GGGGCC	chr1:155232900-155233159(+)$1	259	89	95	14.1904
GGGGCC	chr1:159824535-159824794(+)$1	259	94	100	14.1904
GUGGCC	chr2:120012234-120012493(+)$1	259	225	231	11.6507
GGUGCC	chr10:75559702-75559961(-)$1	259	92	98	9.9047
GGGGAC	chr9:117228433-117228692(-)$1	259	35	41	11.1746
GGGGUC	chr13:52604892-52605151(-)$1	259	109	115	11.1746
GUGGCC	chr19:15904737-15904996(+)$1	259	112	118	11.6507
GAGGCC	chr8:70541641-70541900(-)$1	259	38	44	11.3333
GUGGCC	chr15:91150564-91150793(-)$1	229	65	71	11.6507
GAGGCC	chr1:34164287-34164546(+)$1	259	80	86	11.3333
GAGGCC	chr1:109547132-109547391(-)$1	259	75	81	11.3333
GGGGGC	chr16:1793298-1793601(+)$1	303	101	107	10.9365
GGGGUC	chr9:139865873-139866102(-)$1	229	32	38	11.1746
GGGGAC	chr9:111693124-111693383(-)$1	259	46	52	11.1746
GCGGCC	chr12:1893014-1893273(-)$1	259	149	155	11.2539
GGUGCC	chr7:99047849-99048108(+)$1	259	148	154	9.9047
GGGGUC	chr22:20779592-20779821(+)$1	229	148	154	11.1746
GGGGCC	chr20:62193212-62193471(+)$1	259	42	48	14.1904
GAGGCC	chrX:41193872-41194131(-)$1	259	46	52	11.3333
GAGGCC	chr14:59112807-59113036(+)$1	229	8	14	11.3333
GCGGCC	chr15:44038711-44038970(+)$1	259	77	83	11.2539
GGGGAC	chr19:47184829-47185088(+)$1	259	62	68	11.1746
GGGGAC	chr9:130890822-130891051(-)$1	229	143	149	11.1746
GGGGUC	chr16:30528922-30529181(-)$1	259	84	90	11.1746
ggggcc	chr11:61276354-61276613(-)$1	259	160	166	14.1904
GUGGCC	chr19:5706975-5707234(+)$1	259	42	48	11.6507
GUGGCC	chr2:206364524-206364783(+)$1	259	94	100	11.6507
GGGGCC	chr6:136598918-136599177(-)$1	259	105	111	14.1904
GGGGAC	chr4:100463143-100463372(-)$1	229	141	147	11.1746
GGGGCC	chr5:176022549-176022808(-)$1	259	125	131	14.1904
GCGGCC	chr11:6477229-6477488(+)$1	259	108	114	11.2539
GGGGUC	chr7:65435228-65435487(-)$1	259	228	234	11.1746
GGGGCC	chr1:52811686-52811915(+)$1	229	135	141	14.1904
GGGGGC	chr14:72165589-72165818(+)$1	229	220	226	10.9365
GUGGCC	chr5:140745864-140746127(+)$1	263	22	28	11.6507
GGAGCC	chr1:113245113-113245372(-)$1	259	208	214	9.9047
GGGGGC	chr2:227663161-227663420(+)$1	259	113	119	10.9365
GGGGCC	chr17:7642924-7643183(+)$1	259	203	209	14.1904

#otherMatches

#Struct PSSM
ccc]bb	chr4:169604096-169604355(+)$1	259	187	193	11.1746
GGGGGG	chr20:24646013-24646272(+)$1	259	155	161	14.1904
mfffff	chr12:133433996-133434255(+)$1	259	246	252	14.1904
rdddd4	chr16:85024102-85024361(+)$1	259	97	103	9.9047
b]ccc:	chr14:99864947-99865176(+)$1	229	210	216	11.6507
cccccd	chr1:6295755-6295984(+)$1	229	32	38	11.2539
mmmccc	chr11:126173999-126174228(-)$1	229	191	197	9.6666
ccbb]c	chr19:7184414-7184673(-)$1	259	129	135	11.6507
hhhhhh	chr2:242615474-242615733(+)$1	259	26	32	11.1746
!!a[dd	chr8:145731190-145731449(+)$1	259	66	72	11.3333
fflllf	chr3:13896011-13896270(+)$1	259	237	243	9.6666
eeee22	chr14:34247619-34247848(-)$1	229	150	156	11.1746
B{BB{D	chr1:171756886-171757145(+)$1	259	9	15	11.1746
ffffff	chr7:44144254-44144483(+)$1	229	4	10	11.2539
"eeeee	chr1:32131102-32131361(-)$1	259	54	60	9.9047
ffffff	chr5:150175008-150175267(-)$1	259	176	182	11.6507
EEEEEe	chr14:55529796-55530055(-)$1	259	15	21	14.1904
EEEIII	chr7:148978780-148979039(+)$1	259	6	12	14.1904
eeeeea	chr3:49770083-49770342(-)$1	259	50	56	9.9047
gcccff	chr7:43687039-43687298(-)$1	259	131	137	10.9365
bb]ggg	chr10:115804025-115804284(+)$1	259	208	214	14.1904
ffff!!	chr7:44796390-44796649(+)$1	259	171	177	9.6666
[eeeee	chr16:81387913-81388172(+)$1	259	17	23	11.6507
I}BB}I	chr13:111299311-111299570(-)$1	259	204	210	14.1904
eeeee!	chr13:98829159-98829388(+)$1	229	132	138	14.1904
=====3	chr1:155232900-155233159(+)$1	259	89	95	14.1904
HHHHHH	chr1:159824535-159824794(+)$1	259	94	100	14.1904
lccc22	chr2:120012234-120012493(+)$1	259	225	231	11.6507
dd]ddd	chr10:75559702-75559961(-)$1	259	92	98	9.9047
fffff:	chr9:117228433-117228692(-)$1	259	35	41	11.1746
gggggg	chr13:52604892-52605151(-)$1	259	109	115	11.1746
!eeeee	chr19:15904737-15904996(+)$1	259	112	118	11.6507
LEEEEE	chr8:70541641-70541900(-)$1	259	38	44	11.3333
ffff]f	chr15:91150564-91150793(-)$1	229	65	71	11.6507
dddeee	chr1:34164287-34164546(+)$1	259	80	86	11.3333
ooobb2	chr1:109547132-109547391(-)$1	259	75	81	11.3333
ggggg2	chr16:1793298-1793601(+)$1	303	101	107	10.9365
GGGGG:	chr9:139865873-139866102(-)$1	229	32	38	11.1746
!cccoo	chr9:111693124-111693383(-)$1	259	46	52	11.1746
b[bbbb	chr12:1893014-1893273(-)$1	259	149	155	11.2539
2iiiii	chr7:99047849-99048108(+)$1	259	148	154	9.9047
ffffmm	chr22:20779592-20779821(+)$1	229	148	154	11.1746
{DDDDC	chr20:62193212-62193471(+)$1	259	42	48	14.1904
++dddd	chrX:41193872-41194131(-)$1	259	46	52	11.3333
::CCC{	chr14:59112807-59113036(+)$1	229	8	14	11.3333
{FFFFF	chr15:44038711-44038970(+)$1	259	77	83	11.2539
eeeee:	chr19:47184829-47185088(+)$1	259	62	68	11.1746
eeeeed	chr9:130890822-130891051(-)$1	229	143	149	11.1746
eeeee!	chr16:30528922-30529181(-)$1	259	84	90	11.1746
=====[	chr11:61276354-61276613(-)$1	259	160	166	14.1904
fffff!	chr19:5706975-5707234(+)$1	259	42	48	11.6507
gqqqqq	chr2:206364524-206364783(+)$1	259	94	100	11.6507
eeeeeb	chr6:136598918-136599177(-)$1	259	105	111	14.1904
dddd22	chr4:100463143-100463372(-)$1	229	141	147	11.1746
shhhhh	chr5:176022549-176022808(-)$1	259	125	131	14.1904
ddddll	chr11:6477229-6477488(+)$1	259	108	114	11.2539
lbb]bb	chr7:65435228-65435487(-)$1	259	228	234	11.1746
gggggg	chr1:52811686-52811915(+)$1	229	135	141	14.1904
fffff:	chr14:72165589-72165818(+)$1	229	220	226	10.9365
gggggg	chr5:140745864-140746127(+)$1	263	22	28	11.6507
c[gggg	chr1:113245113-113245372(-)$1	259	208	214	9.9047
cc[eee	chr2:227663161-227663420(+)$1	259	113	119	10.9365
ma]ddd	chr17:7642924-7643183(+)$1	259	203	209	14.1904

#DB
))).))	chr4:169604096-169604355(+)$1	1	187	193	11.1746
))))))	chr20:24646013-24646272(+)$1	1	155	161	14.1904
.)))))	chr12:133433996-133434255(+)$1	1	246	252	14.1904
.)))).	chr16:85024102-85024361(+)$1	1	97	103	9.9047
).))).	chr14:99864947-99865176(+)$1	1	210	216	11.6507
((((((	chr1:6295755-6295984(+)$1	1	32	38	11.2539
...)))	chr11:126173999-126174228(-)$1	1	191	197	9.6666
)))).)	chr19:7184414-7184673(-)$1	1	129	135	11.6507
))))))	chr2:242615474-242615733(+)$1	1	26	32	11.1746
..(.((	chr8:145731190-145731449(+)$1	1	66	72	11.3333
((...)	chr3:13896011-13896270(+)$1	1	237	243	9.6666
))))..	chr14:34247619-34247848(-)$1	1	150	156	11.1746
(.((.(	chr1:171756886-171757145(+)$1	1	9	15	11.1746
((((((	chr7:44144254-44144483(+)$1	1	4	10	11.2539
.(((((	chr1:32131102-32131361(-)$1	1	54	60	9.9047
))))))	chr5:150175008-150175267(-)$1	1	176	182	11.6507
((((((	chr14:55529796-55530055(-)$1	1	15	21	14.1904
((((((	chr7:148978780-148979039(+)$1	1	6	12	14.1904
((((((	chr3:49770083-49770342(-)$1	1	50	56	9.9047
))))((	chr7:43687039-43687298(-)$1	1	131	137	10.9365
)).)))	chr10:115804025-115804284(+)$1	1	208	214	14.1904
((((..	chr7:44796390-44796649(+)$1	1	171	177	9.6666
.(((((	chr16:81387913-81388172(+)$1	1	17	23	11.6507
).)).)	chr13:111299311-111299570(-)$1	1	204	210	14.1904
(((((.	chr13:98829159-98829388(+)$1	1	132	138	14.1904
))))).	chr1:155232900-155233159(+)$1	1	89	95	14.1904
))))))	chr1:159824535-159824794(+)$1	1	94	100	14.1904
.)))..	chr2:120012234-120012493(+)$1	1	225	231	11.6507
)).)))	chr10:75559702-75559961(-)$1	1	92	98	9.9047
))))).	chr9:117228433-117228692(-)$1	1	35	41	11.1746
))))))	chr13:52604892-52605151(-)$1	1	109	115	11.1746
.(((((	chr19:15904737-15904996(+)$1	1	112	118	11.6507
.(((((	chr8:70541641-70541900(-)$1	1	38	44	11.3333
)))).)	chr15:91150564-91150793(-)$1	1	65	71	11.6507
((((((	chr1:34164287-34164546(+)$1	1	80	86	11.3333
...)).	chr1:109547132-109547391(-)$1	1	75	81	11.3333
))))).	chr16:1793298-1793601(+)$1	1	101	107	10.9365
(((((.	chr9:139865873-139866102(-)$1	1	32	38	11.1746
.(((..	chr9:111693124-111693383(-)$1	1	46	52	11.1746
(.((((	chr12:1893014-1893273(-)$1	1	149	155	11.2539
.)))))	chr7:99047849-99048108(+)$1	1	148	154	9.9047
((((..	chr22:20779592-20779821(+)$1	1	148	154	11.1746
.(((((	chr20:62193212-62193471(+)$1	1	42	48	14.1904
..((((	chrX:41193872-41194131(-)$1	1	46	52	11.3333
..(((.	chr14:59112807-59113036(+)$1	1	8	14	11.3333
.(((((	chr15:44038711-44038970(+)$1	1	77	83	11.2539
))))).	chr19:47184829-47185088(+)$1	1	62	68	11.1746
))))))	chr9:130890822-130891051(-)$1	1	143	149	11.1746
(((((.	chr16:30528922-30529181(-)$1	1	84	90	11.1746
(((((.	chr11:61276354-61276613(-)$1	1	160	166	14.1904
(((((.	chr19:5706975-5707234(+)$1	1	42	48	11.6507
(.....	chr2:206364524-206364783(+)$1	1	94	100	11.6507
)))))(	chr6:136598918-136599177(-)$1	1	105	111	14.1904
))))..	chr4:100463143-100463372(-)$1	1	141	147	11.1746
.)))))	chr5:176022549-176022808(-)$1	1	125	131	14.1904
((((..	chr11:6477229-6477488(+)$1	1	108	114	11.2539
.)).))	chr7:65435228-65435487(-)$1	1	228	234	11.1746
((((((	chr1:52811686-52811915(+)$1	1	135	141	14.1904
))))).	chr14:72165589-72165818(+)$1	1	220	226	10.9365
))))))	chr5:140745864-140746127(+)$1	1	22	28	11.6507
(.((((	chr1:113245113-113245372(-)$1	1	208	214	9.9047
((.(((	chr2:227663161-227663420(+)$1	1	113	119	10.9365
.).)))	chr17:7642924-7643183(+)$1	1	203	209	14.1904

#PSSM
G : 0.90	U : 0.04	g : 0.04	
G : 0.65	U : 0.14	A : 0.09	C : 0.06	c : 0.01	u : 0.01	g : 0.01	
G : 0.85	A : 0.04	g : 0.04	U : 0.04	
G : 0.95	g : 0.04	
C : 0.68	U : 0.11	A : 0.11	G : 0.06	c : 0.03	
C : 0.96	c : 0.03	

#score	742.2539682539667
#seq	63
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m3_run2.nuc.txt

#NT
UGA	chr7:56155189-56155431(-)$1	242	21	24	8.9999
UGA	chrX:54837283-54837507(+)$1	224	5	8	8.9999
UGA	chr2:220422872-220423093(-)$1	221	98	101	8.9999
UGA	chr3:113378664-113378887(-)$1	223	55	58	8.9999
UGA	chr9:104433281-104433496(-)$1	215	40	43	8.9999
UGA	chr2:136481528-136481754(+)$1	226	3	6	8.9999
UGA	chr17:56166514-56166731(+)$1	217	136	139	8.9999
UGA	chr19:46347275-46347492(-)$1	217	7	10	8.9999
UGA	chr11:63672353-63672574(-)$1	221	25	28	8.9999
UGA	chr15:43822210-43822432(+)$1	222	57	60	8.9999
UGA	chr5:55247178-55247394(-)$1	216	7	10	8.9999
UGA	chr1:39784169-39784386(+)$1	217	30	33	8.9999
UGA	chr16:67472465-67472683(-)$1	218	41	44	8.9999
UGA	chr16:50118073-50118299(+)$1	226	8	11	8.9999
UGA	chr2:202025324-202025541(+)$1	217	175	178	8.9999
UGA	chr4:9346212-9346460(-)$1	248	10	13	8.9999
UGA	chr19:49652814-49653058(+)$1	244	75	78	8.9999
UGA	chr22:20128066-20128297(+)$1	231	53	56	8.9999
UGA	chr3:44932030-44932246(-)$1	216	7	10	8.9999
UGA	chr8:104312393-104312609(-)$1	216	82	85	8.9999
UGA	chr9:136302764-136302984(+)$1	220	29	32	8.9999
UGA	chr11:47312247-47312485(+)$1	238	15	18	8.9999
UGA	chr14:36008638-36008875(-)$1	237	4	7	8.9999
UGA	chr16:16349854-16350075(+)$1	221	23	26	8.9999
UGA	chr2:166904115-166904339(-)$1	224	87	90	8.9999
UGA	chr15:98417126-98417345(+)$1	219	101	104	8.9999
UGA	chr1:19671603-19671821(-)$1	218	47	50	8.9999
UGA	chr3:48205684-48205905(-)$1	221	10	13	8.9999
UGA	chr14:63511721-63511936(+)$1	215	90	93	8.9999
UGA	chr5:178152260-178152487(-)$1	227	39	42	8.9999
UGA	chr17:8792097-8792315(-)$1	218	19	22	8.9999
UGA	chr5:95124365-95124594(+)$1	229	15	18	8.9999
UGA	chr17:17068767-17069010(+)$1	243	31	34	8.9999
UGA	chr6:44150738-44150958(-)$1	220	16	19	8.9999
UGA	chr1:151751499-151751724(-)$1	225	64	67	8.9999
UGA	chr12:49422549-49422792(-)$1	243	139	142	8.9999
UGA	chr8:27301652-27301879(+)$1	227	11	14	8.9999
UGA	chr13:73636462-73636678(+)$1	216	98	101	8.9999
UGA	chr6:132874505-132874720(-)$1	215	82	85	8.9999
UGA	chr5:71493077-71493306(+)$1	229	1	4	8.9999
UGA	chr13:42877115-42877344(+)$1	229	56	59	8.9999
UGA	chr1:28785559-28785777(+)$1	218	184	187	8.9999
UGA	chr19:50204770-50204992(+)$1	222	56	59	8.9999
UGA	chr1:179012988-179013220(+)$1	232	64	67	8.9999
UGA	chr8:22332406-22332621(-)$1	215	20	23	8.9999
UGA	chr2:27157462-27157697(+)$1	235	25	28	8.9999
UGA	chr9:87338440-87338665(+)$1	225	129	132	8.9999
UGA	chr1:86167782-86168006(-)$1	224	73	76	8.9999
UGA	chr11:279321-279539(+)$1	218	61	64	8.9999
UGA	chr14:58604981-58605197(+)$1	216	64	67	8.9999
UGA	chr11:33640052-33640272(+)$1	220	12	15	8.9999
UGA	chr5:140626394-140626620(+)$1	226	43	46	8.9999
UGA	chr1:12476653-12476894(+)$1	241	24	27	8.9999
UGA	chr1:173523773-173523990(+)$1	217	6	9	8.9999
UGA	chrX:70783233-70783448(+)$1	215	15	18	8.9999
UGA	chr16:30486553-30486774(+)$1	221	57	60	8.9999
UGA	chr19:57334859-57335091(-)$1	232	57	60	8.9999
UGA	chr17:17070668-17070892(+)$1	224	52	55	8.9999
UGA	chr11:67186412-67186631(+)$1	219	31	34	8.9999
UGA	chr11:133801491-133801722(-)$1	231	48	51	8.9999
UGA	chr5:71492268-71492492(+)$1	224	15	18	8.9999
UGA	chr15:91769421-91769640(+)$1	219	77	80	8.9999
UGA	chr2:37295935-37296151(+)$1	216	103	106	8.9999
UGA	chr5:102894656-102894871(-)$1	215	31	34	8.9999
UGA	chr4:114294152-114294373(+)$1	221	68	71	8.9999
UGA	chr19:36128347-36128600(-)$1	253	19	22	8.9999
UGA	chr9:112189266-112189489(-)$1	223	60	63	8.9999
UGA	chr12:51092129-51092349(-)$1	220	51	54	8.9999
UGA	chr12:8244268-8244487(+)$1	219	179	182	8.9999
UGA	chr19:34868299-34868540(+)$1	241	5	8	8.9999
UGA	chr1:237666520-237666744(+)$1	224	6	9	8.9999
UGA	chr2:173659722-173659954(+)$1	232	77	80	8.9999
UGA	chr12:72680391-72680610(-)$1	219	45	48	8.9999
UGA	chr6:31604075-31604300(+)$1	225	102	105	8.9999
UGA	chr19:42492112-42492351(-)$1	239	41	44	8.9999
UGA	chr11:1908633-1908855(-)$1	222	30	33	8.9999
UGA	chr5:140595800-140596023(-)$1	223	35	38	8.9999
UGA	chr22:30806495-30806731(+)$1	236	134	137	8.9999
UGA	chr11:118343403-118343636(+)$1	233	33	36	8.9999
UGA	chr12:123805220-123805444(-)$1	224	4	7	8.9999
UGA	chr15:43164748-43164971(-)$1	223	16	19	8.9999
UGA	chr17:73895552-73895810(-)$1	258	82	85	8.9999
UGA	chr5:141520028-141520245(+)$1	217	21	24	8.9999
UGA	chr11:47741418-47741652(-)$1	234	73	76	8.9999
UGA	chr16:24802625-24802844(+)$1	219	70	73	8.9999
UGA	chr12:57500485-57500714(-)$1	229	56	59	8.9999
UGA	chr5:176074563-176074779(+)$1	216	85	88	8.9999
UGA	chr1:237794706-237794927(+)$1	221	28	31	8.9999
UGA	chr12:58127789-58128005(-)$1	216	16	19	8.9999
UGA	chr2:39088346-39088567(-)$1	221	32	35	8.9999
UGA	chr11:61551710-61551930(+)$1	220	76	79	8.9999
UGA	chr4:156698584-156698801(-)$1	217	21	24	8.9999
UGA	chr5:176083794-176084013(+)$1	219	132	135	8.9999
UGA	chr17:61432624-61432842(+)$1	218	39	42	8.9999
UGA	chr5:71489801-71490031(+)$1	230	61	64	8.9999

#otherMatches

#Struct PSSM
ddd	chr2:149806725-149806946(+)$1	221	32	35	8.9999
dd:	chr7:56155189-56155431(-)$1	242	21	24	8.9999
FFF	chrX:54837283-54837507(+)$1	224	5	8	8.9999
555	chr2:220422872-220423093(-)$1	221	98	101	8.9999
{BB	chr3:113378664-113378887(-)$1	223	55	58	8.9999
ttt	chr9:104433281-104433496(-)$1	215	40	43	8.9999
DDD	chr2:136481528-136481754(+)$1	226	3	6	8.9999
ee!	chr17:56166514-56166731(+)$1	217	136	139	8.9999
:::	chr19:46347275-46347492(-)$1	217	7	10	8.9999
E{I	chr11:63672353-63672574(-)$1	221	25	28	8.9999
ee2	chr15:43822210-43822432(+)$1	222	57	60	8.9999
BBC	chr5:55247178-55247394(-)$1	216	7	10	8.9999
bmm	chr1:39784169-39784386(+)$1	217	30	33	8.9999
EE:	chr16:67472465-67472683(-)$1	218	41	44	8.9999
DD{	chr16:50118073-50118299(+)$1	226	8	11	8.9999
===	chr2:202025324-202025541(+)$1	217	175	178	8.9999
gee	chr4:9346212-9346460(-)$1	248	10	13	8.9999
mcc	chr19:49652814-49653058(+)$1	244	75	78	8.9999
EEA	chr22:20128066-20128297(+)$1	231	53	56	8.9999
GGG	chr3:44932030-44932246(-)$1	216	7	10	8.9999
GGG	chr8:104312393-104312609(-)$1	216	82	85	8.9999
EEE	chr9:136302764-136302984(+)$1	220	29	32	8.9999
eee	chr11:47312247-47312485(+)$1	238	15	18	8.9999
{CC	chr14:36008638-36008875(-)$1	237	4	7	8.9999
DDc	chr16:16349854-16350075(+)$1	221	23	26	8.9999
b[a	chr2:166904115-166904339(-)$1	224	87	90	8.9999
c22	chr15:98417126-98417345(+)$1	219	101	104	8.9999
dd#	chr1:19671603-19671821(-)$1	218	47	50	8.9999
HH:	chr3:48205684-48205905(-)$1	221	10	13	8.9999
qqq	chr14:63511721-63511936(+)$1	215	90	93	8.9999
b!!	chr5:178152260-178152487(-)$1	227	39	42	8.9999
CLL	chr17:8792097-8792315(-)$1	218	19	22	8.9999
eee	chr5:95124365-95124594(+)$1	229	15	18	8.9999
f$$	chr17:17068767-17069010(+)$1	243	31	34	8.9999
fnn	chr6:44150738-44150958(-)$1	220	16	19	8.9999
[bb	chr1:151751499-151751724(-)$1	225	64	67	8.9999
eee	chr12:49422549-49422792(-)$1	243	139	142	8.9999
c!!	chr8:27301652-27301879(+)$1	227	11	14	8.9999
2ff	chr13:73636462-73636678(+)$1	216	98	101	8.9999
:::	chr6:132874505-132874720(-)$1	215	82	85	8.9999
DDD	chr5:71493077-71493306(+)$1	229	1	4	8.9999
bb2	chr13:42877115-42877344(+)$1	229	56	59	8.9999
qqq	chr1:28785559-28785777(+)$1	218	184	187	8.9999
b!!	chr19:50204770-50204992(+)$1	222	56	59	8.9999
ii[	chr1:179012988-179013220(+)$1	232	64	67	8.9999
cc:	chr8:22332406-22332621(-)$1	215	20	23	8.9999
EEE	chr2:27157462-27157697(+)$1	235	25	28	8.9999
e""	chr9:87338440-87338665(+)$1	225	129	132	8.9999
%%%	chr1:86167782-86168006(-)$1	224	73	76	8.9999
xxe	chr11:279321-279539(+)$1	218	61	64	8.9999
+ff	chr14:58604981-58605197(+)$1	216	64	67	8.9999
ddd	chr11:33640052-33640272(+)$1	220	12	15	8.9999
cc:	chr5:140626394-140626620(+)$1	226	43	46	8.9999
:::	chr1:12476653-12476894(+)$1	241	24	27	8.9999
cc[	chr1:173523773-173523990(+)$1	217	6	9	8.9999
a[d	chrX:70783233-70783448(+)$1	215	15	18	8.9999
fff	chr16:30486553-30486774(+)$1	221	57	60	8.9999
eee	chr19:57334859-57335091(-)$1	232	57	60	8.9999
bb]	chr17:17070668-17070892(+)$1	224	52	55	8.9999
bb]	chr11:67186412-67186631(+)$1	219	31	34	8.9999
$$f	chr11:133801491-133801722(-)$1	231	48	51	8.9999
BB{	chr5:71492268-71492492(+)$1	224	15	18	8.9999
eee	chr15:91769421-91769640(+)$1	219	77	80	8.9999
:::	chr2:37295935-37296151(+)$1	216	103	106	8.9999
:::	chr5:102894656-102894871(-)$1	215	31	34	8.9999
ccc	chr4:114294152-114294373(+)$1	221	68	71	8.9999
fff	chr19:36128347-36128600(-)$1	253	19	22	8.9999
[ee	chr9:112189266-112189489(-)$1	223	60	63	8.9999
hhh	chr12:51092129-51092349(-)$1	220	51	54	8.9999
nff	chr12:8244268-8244487(+)$1	219	179	182	8.9999
D::	chr19:34868299-34868540(+)$1	241	5	8	8.9999
DD:	chr1:237666520-237666744(+)$1	224	6	9	8.9999
:::	chr2:173659722-173659954(+)$1	232	77	80	8.9999
DD:	chr12:72680391-72680610(-)$1	219	45	48	8.9999
fff	chr6:31604075-31604300(+)$1	225	102	105	8.9999
[a[	chr19:42492112-42492351(-)$1	239	41	44	8.9999
ggg	chr11:1908633-1908855(-)$1	222	30	33	8.9999
c))	chr5:140595800-140596023(-)$1	223	35	38	8.9999
cdd	chr22:30806495-30806731(+)$1	236	134	137	8.9999
^^^	chr11:118343403-118343636(+)$1	233	33	36	8.9999
ggg	chr12:123805220-123805444(-)$1	224	4	7	8.9999
)))	chr15:43164748-43164971(-)$1	223	16	19	8.9999
EE:	chr17:73895552-73895810(-)$1	258	82	85	8.9999
A{B	chr5:141520028-141520245(+)$1	217	21	24	8.9999
mmm	chr11:47741418-47741652(-)$1	234	73	76	8.9999
JJJ	chr16:24802625-24802844(+)$1	219	70	73	8.9999
ee"	chr12:57500485-57500714(-)$1	229	56	59	8.9999
cc]	chr5:176074563-176074779(+)$1	216	85	88	8.9999
:::	chr1:237794706-237794927(+)$1	221	28	31	8.9999
HHH	chr12:58127789-58128005(-)$1	216	16	19	8.9999
fff	chr2:39088346-39088567(-)$1	221	32	35	8.9999
fff	chr11:61551710-61551930(+)$1	220	76	79	8.9999
eem	chr4:156698584-156698801(-)$1	217	21	24	8.9999
/FF	chr5:176083794-176084013(+)$1	219	132	135	8.9999
{FF	chr17:61432624-61432842(+)$1	218	39	42	8.9999
ggg	chr5:71489801-71490031(+)$1	230	61	64	8.9999

#DB
(((	chr2:149806725-149806946(+)$1	1	32	35	8.9999
)).	chr7:56155189-56155431(-)$1	1	21	24	8.9999
(((	chrX:54837283-54837507(+)$1	1	5	8	8.9999
...	chr2:220422872-220423093(-)$1	1	98	101	8.9999
.((	chr3:113378664-113378887(-)$1	1	55	58	8.9999
...	chr9:104433281-104433496(-)$1	1	40	43	8.9999
(((	chr2:136481528-136481754(+)$1	1	3	6	8.9999
((.	chr17:56166514-56166731(+)$1	1	136	139	8.9999
...	chr19:46347275-46347492(-)$1	1	7	10	8.9999
(.(	chr11:63672353-63672574(-)$1	1	25	28	8.9999
)).	chr15:43822210-43822432(+)$1	1	57	60	8.9999
(((	chr5:55247178-55247394(-)$1	1	7	10	8.9999
(..	chr1:39784169-39784386(+)$1	1	30	33	8.9999
((.	chr16:67472465-67472683(-)$1	1	41	44	8.9999
((.	chr16:50118073-50118299(+)$1	1	8	11	8.9999
)))	chr2:202025324-202025541(+)$1	1	175	178	8.9999
(((	chr4:9346212-9346460(-)$1	1	10	13	8.9999
.))	chr19:49652814-49653058(+)$1	1	75	78	8.9999
(((	chr22:20128066-20128297(+)$1	1	53	56	8.9999
(((	chr3:44932030-44932246(-)$1	1	7	10	8.9999
(((	chr8:104312393-104312609(-)$1	1	82	85	8.9999
(((	chr9:136302764-136302984(+)$1	1	29	32	8.9999
(((	chr11:47312247-47312485(+)$1	1	15	18	8.9999
.((	chr14:36008638-36008875(-)$1	1	4	7	8.9999
(((	chr16:16349854-16350075(+)$1	1	23	26	8.9999
(.(	chr2:166904115-166904339(-)$1	1	87	90	8.9999
)..	chr15:98417126-98417345(+)$1	1	101	104	8.9999
((.	chr1:19671603-19671821(-)$1	1	47	50	8.9999
((.	chr3:48205684-48205905(-)$1	1	10	13	8.9999
...	chr14:63511721-63511936(+)$1	1	90	93	8.9999
(..	chr5:178152260-178152487(-)$1	1	39	42	8.9999
(..	chr17:8792097-8792315(-)$1	1	19	22	8.9999
))(	chr5:95124365-95124594(+)$1	1	15	18	8.9999
(..	chr17:17068767-17069010(+)$1	1	31	34	8.9999
(..	chr6:44150738-44150958(-)$1	1	16	19	8.9999
.((	chr1:151751499-151751724(-)$1	1	64	67	8.9999
(((	chr12:49422549-49422792(-)$1	1	139	142	8.9999
(..	chr8:27301652-27301879(+)$1	1	11	14	8.9999
.))	chr13:73636462-73636678(+)$1	1	98	101	8.9999
...	chr6:132874505-132874720(-)$1	1	82	85	8.9999
(((	chr5:71493077-71493306(+)$1	1	1	4	8.9999
)).	chr13:42877115-42877344(+)$1	1	56	59	8.9999
...	chr1:28785559-28785777(+)$1	1	184	187	8.9999
(..	chr19:50204770-50204992(+)$1	1	56	59	8.9999
((.	chr1:179012988-179013220(+)$1	1	64	67	8.9999
)).	chr8:22332406-22332621(-)$1	1	20	23	8.9999
(((	chr2:27157462-27157697(+)$1	1	25	28	8.9999
(..	chr9:87338440-87338665(+)$1	1	129	132	8.9999
...	chr1:86167782-86168006(-)$1	1	73	76	8.9999
..)	chr11:279321-279539(+)$1	1	61	64	8.9999
.((	chr14:58604981-58605197(+)$1	1	64	67	8.9999
(((	chr11:33640052-33640272(+)$1	1	12	15	8.9999
)).	chr5:140626394-140626620(+)$1	1	43	46	8.9999
...	chr1:12476653-12476894(+)$1	1	24	27	8.9999
((.	chr1:173523773-173523990(+)$1	1	6	9	8.9999
(.(	chrX:70783233-70783448(+)$1	1	15	18	8.9999
(((	chr16:30486553-30486774(+)$1	1	57	60	8.9999
(((	chr19:57334859-57335091(-)$1	1	57	60	8.9999
)).	chr17:17070668-17070892(+)$1	1	52	55	8.9999
)).	chr11:67186412-67186631(+)$1	1	31	34	8.9999
..(	chr11:133801491-133801722(-)$1	1	48	51	8.9999
((.	chr5:71492268-71492492(+)$1	1	15	18	8.9999
)))	chr15:91769421-91769640(+)$1	1	77	80	8.9999
...	chr2:37295935-37296151(+)$1	1	103	106	8.9999
...	chr5:102894656-102894871(-)$1	1	31	34	8.9999
)))	chr4:114294152-114294373(+)$1	1	68	71	8.9999
(((	chr19:36128347-36128600(-)$1	1	19	22	8.9999
.((	chr9:112189266-112189489(-)$1	1	60	63	8.9999
)))	chr12:51092129-51092349(-)$1	1	51	54	8.9999
.))	chr12:8244268-8244487(+)$1	1	179	182	8.9999
(..	chr19:34868299-34868540(+)$1	1	5	8	8.9999
((.	chr1:237666520-237666744(+)$1	1	6	9	8.9999
...	chr2:173659722-173659954(+)$1	1	77	80	8.9999
((.	chr12:72680391-72680610(-)$1	1	45	48	8.9999
(((	chr6:31604075-31604300(+)$1	1	102	105	8.9999
.(.	chr19:42492112-42492351(-)$1	1	41	44	8.9999
(((	chr11:1908633-1908855(-)$1	1	30	33	8.9999
(..	chr5:140595800-140596023(-)$1	1	35	38	8.9999
(((	chr22:30806495-30806731(+)$1	1	134	137	8.9999
...	chr11:118343403-118343636(+)$1	1	33	36	8.9999
(((	chr12:123805220-123805444(-)$1	1	4	7	8.9999
...	chr15:43164748-43164971(-)$1	1	16	19	8.9999
((.	chr17:73895552-73895810(-)$1	1	82	85	8.9999
(.(	chr5:141520028-141520245(+)$1	1	21	24	8.9999
...	chr11:47741418-47741652(-)$1	1	73	76	8.9999
(((	chr16:24802625-24802844(+)$1	1	70	73	8.9999
((.	chr12:57500485-57500714(-)$1	1	56	59	8.9999
)).	chr5:176074563-176074779(+)$1	1	85	88	8.9999
...	chr1:237794706-237794927(+)$1	1	28	31	8.9999
(((	chr12:58127789-58128005(-)$1	1	16	19	8.9999
(((	chr2:39088346-39088567(-)$1	1	32	35	8.9999
)))	chr11:61551710-61551930(+)$1	1	76	79	8.9999
((.	chr4:156698584-156698801(-)$1	1	21	24	8.9999
.))	chr5:176083794-176084013(+)$1	1	132	135	8.9999
.((	chr17:61432624-61432842(+)$1	1	39	42	8.9999
(((	chr5:71489801-71490031(+)$1	1	61	64	8.9999

#PSSM
U : 0.99	
G : 0.99	
A : 0.99	

#score	863.9999999999998
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m2_run1.nuc.txt

#NT
AUGCAAUGAAUGUGGGAAAGCCUUUAGCCAUAAGUCAGCCCUCACAUUACACCAGAGAACACAUACAGGGGAGAAACCCUAUCAAUGUAAUGCGUGUGGGAAAACUUUUUGCCAGAAAUCUGACCUCACUAAACAUCAGAGAACACACACAGGGCUGAAACCCUAUGAAUGUUAUGAAUGUGGAAAAUCCUUCCGUGUGACUUCGCACCUUAAAGUACACCAG	chr10:38344182-38344528(+)$1	346	27	250	646.5000

#otherMatches

#Struct PSSM
EEEEE:bbhhhhhhhh"""bb[ddddmmmmdddd333bb]hhhhhhhh]bb:::::::dddd####ddddoooooodddd4444dddd::EEEEE:ccc!!bbmmmmbb22cccBBYYEEEEE:CCC{CCC:ddddbb"""dddd!!bb[ddddoooooodddd]bb22dddd]bb]ddddccclllccc::dddd[ccc[ccc^^^^^^^^^^^^^^^^^^^	chr10:43088914-43089283(-)$1	369	43	266	646.5000
EEMMMMBBhhhhhhhh"""bb[ddddmmmmdddd333bb]hhhhhhhh::::::::::::dddd!!ddddoooooodddd4444dddd:DDDDHHHHHHHHKKIIIIIIIII{BBLLLCCC{BBDDDDMMMMDDDDDDDD:dddd!!bb[ddddoooooodddd]bb22dddd::::::::ddddnnnnnddddffffff[ccc^^^^^^^^^^^^^^^^^^^	chr10:38344182-38344528(+)$1	346	27	250	646.5000

#DB
(((((.((((((((((...((.((((....))))...)).)))))))).)).......((((....((((......))))....))))..))))).(((..((....))..)))))..))))).(((.(((.((((((...((((..((.((((......)))).))..)))).)).))))(((...)))..((((.(((.(((...................	chr10:43088914-43089283(-)$1	1	43	266	646.5000
((....((((((((((...((.((((....))))...)).))))))))............((((..((((......))))....)))).((((((((((((..(((((((((.((...(((.((((((....((((((((.((((..((.((((......)))).))..))))........((((.....))))((((((.(((...................	chr10:38344182-38344528(+)$1	1	27	250	646.5000

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

#score	1293.0
#seq	2
#width	223
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m3_run2.nuc.txt

#NT
auuauuuuuuaaaaaacuuu	chr3:145787346-145787631(-)$1	285	7	27	16.2222
GUUAUUUGCCAAAGAAGAUU	chr8:124827085-124827329(+)$1	244	31	51	14.0000
AUUGUUUAAAAAUACACAUG	chr7:35944338-35944591(+)$1	253	56	76	15.7777
UUUCUUUUGAAAAACCUUUU	chr1:100547906-100548146(+)$1	240	47	67	12.1111
GGUAUUUUGAAAGUAAAAUA	chr5:38477955-38478197(-)$1	242	42	62	15.3333
AUUGUUUUCaaaaaauuaau	chr5:114949190-114949430(-)$1	240	105	125	16.8888
CUUUUUUCUAAACAGAAAUU	chr2:203426032-203426272(+)$1	240	181	201	18.8888
GUAAUCUCAAUAAUAAAAUU	chr2:61276218-61276458(+)$1	240	139	159	15.4444
GGACGUUAAAAAAAAAAAUC	chr18:55144519-55144759(+)$1	240	23	43	11.6666
UUUUUUUCUAAAAUAAAACU	chr2:75882363-75882603(+)$1	240	178	198	22.3333
AUUUUUAAAAAUGAAAAAGU	chr12:51140018-51140258(+)$1	240	2	22	14.6666
GUUGUUUCAAAAAAAAAAUU	chr1:22418182-22418422(+)$1	240	70	90	26.8888
AUUUUGUUAAAAAGAGAAUU	chr6:108364650-108364890(-)$1	240	203	223	20.0000
UUUCUUUUAGAAAUAAACUU	chr14:45672432-45672673(-)$1	241	144	164	18.8888
UUUUUAUCAAAAGUUAAUUU	chr9:15464891-15465131(-)$1	240	111	131	16.4444
CUUAGUUUAAAAAAAAAAUC	chr15:91044356-91044596(+)$1	240	188	208	18.8888
AUAAUUGAAACAACAAAAUU	chr20:56939676-56939916(+)$1	240	16	36	13.7777
AAUUUUUCAAAAAAAUUAAA	chr12:53873437-53873677(+)$1	240	110	130	16.0000
AUCUUAUCaauaauaauaau	chr11:58921053-58921293(+)$1	240	12	32	12.8888
AGUGUUUUAAAAAUACUUUG	chr9:37357551-37357831(+)$1	280	4	24	12.6666
AUUGUUUAAAUAUAGCAAUA	chr5:121363479-121363719(+)$1	240	65	85	12.7777
GGGGUUUAAAAAAAAAAAAC	chr5:172744012-172744252(-)$1	240	214	234	13.6666
GUCCUAUGUAAAACUAAAUU	chr2:131808952-131809192(-)$1	240	10	30	11.2222
AUUCUUGUAAUCACAAAUUU	chr7:107400665-107400905(+)$1	240	37	57	10.1111
UUAAUAUCAAAAUAAGAAUA	chr3:194997173-194997453(-)$1	280	203	223	13.2222
UUUUUUCCAAAUAAAUUACU	chr17:37688078-37688318(+)$1	240	109	129	12.1111
UAUAUUUUAGAAAUAAUAUA	chr3:185362677-185362921(-)$1	244	69	89	15.7777
AUUUUUUCAUAAUUUAAUUU	chr12:40150553-40150793(-)$1	240	112	132	16.2222
AAUUUUUAAAAAUUUAGCUU	chr4:141303286-141303526(+)$1	240	123	143	13.2222
GUUUUUUAAGAUAUUAAACA	chr18:13664315-13664555(-)$1	240	78	98	11.2222
UUUUUUUCUCAAAAUAAGCU	chr5:10265010-10265250(+)$1	240	198	218	12.8888
AUUAUUUUAAAAGAGUUAUU	chr4:140394938-140395178(+)$1	240	82	102	17.2222
AUUAUUUUUAAAAAAACAAA	chr1:213166664-213166904(-)$1	240	117	137	18.0000
CAUUUUUCAAAAAGGGAAGU	chr12:66357530-66357783(+)$1	253	196	216	12.8888
AAUGUAUGAAAAAAAUCAUU	chr12:72095345-72095585(+)$1	240	63	83	15.1111
UUUGUUUAUAAUAAAAAAUA	chr16:67323232-67323472(+)$1	240	119	139	18.7777
AUCUUAUUAAAAGAAAAAGC	chrX:132436224-132436464(-)$1	240	23	43	13.7777
UUCUUUUGCACAGAAAUAUU	chr1:227177662-227177902(-)$1	240	206	226	11.7777
AAUUUUUUUAAACAAAAAUU	chr4:6623062-6623302(+)$1	240	110	130	20.6666
GUUGUGUCAAAAAUAAGGGU	chr1:101446095-101446335(+)$1	240	3	23	13.4444
UCUGUGUAGAAAUGAAAAUU	chr1:78414192-78414432(-)$1	240	167	187	12.3333
uauauuuaaaaaauauaaaa	chr11:12959333-12959573(+)$1	240	192	212	15.7777
UUUAUUUCAAACAUACAUUA	chr21:43220504-43220784(-)$1	280	123	143	14.8888
UUUUUAUCAACACUAAACUU	chr12:77415993-77416274(-)$1	281	116	136	14.6666

#otherMatches

#Struct PSSM
))))gggggggqqqqqqqqg	chr10:74646577-74646817(+)$1	240	143	163	12.8888
::::::::::::EEEEELLL	chr3:145787346-145787631(-)$1	285	7	27	16.2222
!hhhhhhhh!!dddd[dddd	chr8:124827085-124827329(+)$1	244	31	51	14.0000
ffcccqqqqqqqqccc]fff	chr7:35944338-35944591(+)$1	253	56	76	15.7777
ddddmmmmdddd::::::::	chr1:100547906-100548146(+)$1	240	47	67	12.1111
CCC============!!ddd	chr5:38477955-38478197(-)$1	242	42	62	15.3333
ff::::::::::::::::::	chr5:114949190-114949430(-)$1	240	105	125	16.8888
[a!!eeeeemmmmeeeee22	chr2:203426032-203426272(+)$1	240	181	201	18.8888
dddd0000000000ffffff	chr2:61276218-61276458(+)$1	240	139	159	15.4444
CCWWWWWWWWWWWWWWWGGG	chr18:55144519-55144759(+)$1	240	23	43	11.6666
d4444dddd333eeeee:::	chr2:75882363-75882603(+)$1	240	178	198	22.3333
::::::::::::::::dddd	chr12:51140018-51140258(+)$1	240	2	22	14.6666
=oooooo==========:::	chr1:22418182-22418422(+)$1	240	70	90	26.8888
f4444eeeeecccdddd]gg	chr6:108364650-108364890(-)$1	240	203	223	20.0000
:::::::hhhhhhhhmmmmh	chr14:45672432-45672673(-)$1	241	144	164	18.8888
eeeemmmmeeeee:::::::	chr9:15464891-15465131(-)$1	240	111	131	16.4444
gggg::::::::::::::::	chr15:91044356-91044596(+)$1	240	188	208	18.8888
c####eeeeeuuuuuuuuuu	chr20:56939676-56939916(+)$1	240	16	36	13.7777
e:::::IIIIIIIIIYYCCC	chr12:53873437-53873677(+)$1	240	110	130	16.0000
i!!ddddqqqqqqqqdddd3	chr11:58921053-58921293(+)$1	240	12	32	12.8888
iiiiiiillliiiiiiiii:	chr9:37357551-37357831(+)$1	280	4	24	12.6666
ffffffpppppppffffff:	chr5:121363479-121363719(+)$1	240	65	85	12.7777
ggggggg::::::::::::G	chr5:172744012-172744252(-)$1	240	214	234	13.6666
EEEEE:::::::::::::::	chr2:131808952-131809192(-)$1	240	10	30	11.2222
)))))eeeeeqqqqqqqqee	chr7:107400665-107400905(+)$1	240	37	57	10.1111
HHHHHH~~~~GGGGGGGGGG	chr3:194997173-194997453(-)$1	280	203	223	13.2222
:::EEEEE::::::::::::	chr17:37688078-37688318(+)$1	240	109	129	12.1111
ggggggqqqqqqqqgggggg	chr3:185362677-185362921(-)$1	244	69	89	15.7777
ttthhhhhhhhEEEEEGGGG	chr12:40150553-40150793(-)$1	240	112	132	16.2222
b!!bb[ccc"""ffffff&&	chr4:141303286-141303526(+)$1	240	123	143	13.2222
qqqqqqqqbb333ffffff]	chr18:13664315-13664555(-)$1	240	78	98	11.2222
=====4444cccddddccc]	chr5:10265010-10265250(+)$1	240	198	218	12.8888
]dddd::::::JJJJJJJJJ	chr4:140394938-140395178(+)$1	240	82	102	17.2222
^^^^^^^^^^^^^^^^^^^^	chr1:213166664-213166904(-)$1	240	117	137	18.0000
:::::DDDDZZZEEEEEccc	chr12:66357530-66357783(+)$1	253	196	216	12.8888
e[dddd[bb[dddd[bb[dd	chr12:72095345-72095585(+)$1	240	63	83	15.1111
ggpppppppggggggg::dd	chr16:67323232-67323472(+)$1	240	119	139	18.7777
[eeeee!!iiiiiiiii[cc	chrX:132436224-132436464(-)$1	240	23	43	13.7777
ooooooa]ddddFFFFFFYY	chr1:227177662-227177902(-)$1	240	206	226	11.7777
hhhhhhhoooooohhhhhhh	chr4:6623062-6623302(+)$1	240	110	130	20.6666
EEE{FFFFFF:::::::HHH	chr1:101446095-101446335(+)$1	240	3	23	13.4444
fffmmmmffffff4444hhh	chr1:78414192-78414432(-)$1	240	167	187	12.3333
gggg''''''''eeeeemmm	chr11:12959333-12959573(+)$1	240	192	212	15.7777
iiiiii::::eeeeelllee	chr21:43220504-43220784(-)$1	280	123	143	14.8888
:::::::::::::ggggggg	chr12:77415993-77416274(-)$1	281	116	136	14.6666

#DB
....(((((((........)	chr10:74646577-74646817(+)$1	1	143	163	12.8888
............(((((...	chr3:145787346-145787631(-)$1	1	7	27	16.2222
.((((((((..((((.((((	chr8:124827085-124827329(+)$1	1	31	51	14.0000
(((((........))).)))	chr7:35944338-35944591(+)$1	1	56	76	15.7777
((((....))))........	chr1:100547906-100548146(+)$1	1	47	67	12.1111
(((((((((((((((..(((	chr5:38477955-38478197(-)$1	1	42	62	15.3333
))..................	chr5:114949190-114949430(-)$1	1	105	125	16.8888
.(..(((((....)))))..	chr2:203426032-203426272(+)$1	1	181	201	18.8888
))))..........))))))	chr2:61276218-61276458(+)$1	1	139	159	15.4444
((...............(((	chr18:55144519-55144759(+)$1	1	23	43	11.6666
)....))))...)))))...	chr2:75882363-75882603(+)$1	1	178	198	22.3333
................((((	chr12:51140018-51140258(+)$1	1	2	22	14.6666
(......))))))))))...	chr1:22418182-22418422(+)$1	1	70	90	26.8888
)....)))))))))))).))	chr6:108364650-108364890(-)$1	1	203	223	20.0000
.......((((((((....)	chr14:45672432-45672673(-)$1	1	144	164	18.8888
((((....))))).......	chr9:15464891-15465131(-)$1	1	111	131	16.4444
))))................	chr15:91044356-91044596(+)$1	1	188	208	18.8888
(....(((((..........	chr20:56939676-56939916(+)$1	1	16	36	13.7777
).....)))))))))..)))	chr12:53873437-53873677(+)$1	1	110	130	16.0000
(..((((........)))).	chr11:58921053-58921293(+)$1	1	12	32	12.8888
(((((((...))))))))).	chr9:37357551-37357831(+)$1	1	4	24	12.6666
((((((.......)))))).	chr5:121363479-121363719(+)$1	1	65	85	12.7777
)))))))............)	chr5:172744012-172744252(-)$1	1	214	234	13.6666
(((((...............	chr2:131808952-131809192(-)$1	1	10	30	11.2222
.....(((((........))	chr7:107400665-107400905(+)$1	1	37	57	10.1111
))))))....))))))))))	chr3:194997173-194997453(-)$1	1	203	223	13.2222
...)))))............	chr17:37688078-37688318(+)$1	1	109	129	12.1111
((((((........))))))	chr3:185362677-185362921(-)$1	1	69	89	15.7777
...)))))))))))))))))	chr12:40150553-40150793(-)$1	1	112	132	16.2222
(..((.(((...((((((..	chr4:141303286-141303526(+)$1	1	123	143	13.2222
........))...)))))).	chr18:13664315-13664555(-)$1	1	78	98	11.2222
)))))....)))))))))).	chr5:10265010-10265250(+)$1	1	198	218	12.8888
.))))......(((((((((	chr4:140394938-140395178(+)$1	1	82	102	17.2222
....................	chr1:213166664-213166904(-)$1	1	117	137	18.0000
.....))))...)))))(((	chr12:66357530-66357783(+)$1	1	196	216	12.8888
(.((((.((.((((.((.((	chr12:72095345-72095585(+)$1	1	63	83	15.1111
((.......)))))))..((	chr16:67323232-67323472(+)$1	1	119	139	18.7777
.(((((..(((((((((.((	chrX:132436224-132436464(-)$1	1	23	43	13.7777
......).))))))))))..	chr1:227177662-227177902(-)$1	1	206	226	11.7777
(((((((......)))))))	chr4:6623062-6623302(+)$1	1	110	130	20.6666
(((.((((((.......(((	chr1:101446095-101446335(+)$1	1	3	23	13.4444
(((....))))))....)))	chr1:78414192-78414432(-)$1	1	167	187	12.3333
((((........(((((...	chr11:12959333-12959573(+)$1	1	192	212	15.7777
))))))....(((((...))	chr21:43220504-43220784(-)$1	1	123	143	14.8888
.............(((((((	chr12:77415993-77416274(-)$1	1	116	136	14.6666

#PSSM
A : 0.39	U : 0.28	G : 0.20	C : 0.06	a : 0.02	u : 0.02	
U : 0.71	A : 0.13	G : 0.08	u : 0.02	C : 0.02	a : 0.02	
U : 0.75	A : 0.08	C : 0.08	u : 0.04	G : 0.02	
U : 0.39	A : 0.22	G : 0.22	C : 0.11	a : 0.04	
U : 0.91	u : 0.04	G : 0.04	
U : 0.71	A : 0.15	G : 0.06	u : 0.04	C : 0.02	
U : 0.86	u : 0.04	G : 0.04	A : 0.02	C : 0.02	
C : 0.35	U : 0.28	A : 0.22	G : 0.08	u : 0.02	a : 0.02	
A : 0.62	U : 0.17	C : 0.06	G : 0.06	a : 0.04	u : 0.02	
A : 0.75	a : 0.06	G : 0.06	U : 0.04	C : 0.04	u : 0.02	
A : 0.77	a : 0.06	U : 0.06	C : 0.06	u : 0.02	
A : 0.75	U : 0.11	a : 0.08	C : 0.04	
A : 0.55	U : 0.13	G : 0.13	C : 0.08	a : 0.08	
A : 0.44	U : 0.31	G : 0.08	C : 0.06	a : 0.04	u : 0.04	
A : 0.62	U : 0.15	a : 0.08	G : 0.08	C : 0.04	
A : 0.66	C : 0.08	U : 0.08	G : 0.06	a : 0.04	u : 0.04	
A : 0.62	U : 0.15	G : 0.06	C : 0.06	u : 0.04	c : 0.02	a : 0.02	
A : 0.66	U : 0.13	a : 0.06	C : 0.06	G : 0.04	u : 0.02	
U : 0.66	C : 0.08	G : 0.08	a : 0.06	A : 0.06	u : 0.02	
U : 0.57	A : 0.20	C : 0.08	u : 0.06	G : 0.04	a : 0.02	

#score	684.4444444444451
#seq	45
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m2_run2.nuc.txt

#NT
GGA	chr1:205500476-205500705(-)$1	229	19	22	8.9999
GGA	chr2:9562593-9562822(+)$1	229	49	52	8.9999
gga	chr19:1216185-1216444(+)$1	259	114	117	8.9999
GGA	chr19:48968297-48968556(-)$1	259	232	235	8.9999
GGA	chr5:80521429-80521658(-)$1	229	45	48	8.9999
GGA	chr17:10600730-10600989(+)$1	259	78	81	8.9999
GGA	chr11:118901442-118901671(+)$1	229	8	11	8.9999
GGA	chr22:46508672-46508931(+)$1	259	1	4	8.9999
GGA	chr8:92998375-92998634(+)$1	259	2	5	8.9999
GGA	chr2:63631253-63631482(+)$1	229	27	30	8.9999
GGA	chr9:130871137-130871397(+)$1	260	14	17	8.9999
GGA	chr21:40557281-40557540(+)$1	259	24	27	8.9999
GGA	chr12:102113878-102114137(-)$1	259	114	117	8.9999
GGA	chr16:89615295-89615524(+)$1	229	112	115	8.9999
GGA	chr6:16586016-16586275(+)$1	259	19	22	8.9999
GGA	chr16:48386676-48386905(+)$1	229	20	23	8.9999
GGA	chr14:53241099-53241358(+)$1	259	15	18	8.9999
GGA	chr9:139958624-139958883(-)$1	259	53	56	8.9999
GGA	chr10:1094384-1094613(+)$1	229	0	3	8.9999
GGA	chrX:38547520-38547779(+)$1	259	51	54	8.9999
gga	chr17:38249557-38249816(-)$1	259	7	10	8.9999
GGA	chr17:76168112-76168371(+)$1	259	34	37	8.9999
GGA	chr1:204043366-204043595(+)$1	229	35	38	8.9999
GGA	chr17:46058722-46058981(+)$1	259	7	10	8.9999
GGA	chr11:61512381-61512610(-)$1	229	47	50	8.9999
gga	chr19:54752558-54752817(+)$1	259	61	64	8.9999
GGA	chr11:70319036-70319265(-)$1	229	16	19	8.9999
GGA	chr17:27139349-27139578(+)$1	229	20	23	8.9999
GGA	chr17:42271326-42271555(+)$1	229	18	21	8.9999
gga	chr15:45360253-45360482(+)$1	229	14	17	8.9999
GGA	chr6:33420659-33420918(+)$1	259	29	32	8.9999
GGA	chr1:197410054-197410313(+)$1	259	19	22	8.9999
GGA	chr14:105916341-105916600(+)$1	259	54	57	8.9999
GGA	chr16:19566626-19566855(-)$1	229	37	40	8.9999
GGA	chr10:124739409-124739668(-)$1	259	10	13	8.9999
GGA	chr11:8128743-8128972(+)$1	229	30	33	8.9999
GGA	chr22:30091628-30091857(-)$1	229	6	9	8.9999
GGA	chr22:31600624-31600853(+)$1	229	43	46	8.9999
gga	chr20:35380965-35381224(+)$1	259	32	35	8.9999
GGA	chr3:113372916-113373145(-)$1	229	160	163	8.9999
GGA	chr12:95907523-95907752(+)$1	229	73	76	8.9999
gga	chr20:4705796-4706055(-)$1	259	23	26	8.9999
GGA	chr19:2429833-2430062(+)$1	229	30	33	8.9999
GGA	chr20:36720231-36720490(+)$1	259	111	114	8.9999
GGA	chr18:77663647-77663906(+)$1	259	50	53	8.9999
gga	chr1:231354880-231355139(-)$1	259	51	54	8.9999
GGA	chr9:126143326-126143555(+)$1	229	0	3	8.9999
GGA	chrX:130217525-130217784(+)$1	259	45	48	8.9999
GGA	chr12:57422817-57423076(+)$1	259	195	198	8.9999
GGA	chr2:97535998-97536258(+)$1	260	31	34	8.9999
GGA	chr2:238395112-238395341(+)$1	229	52	55	8.9999
GGA	chr3:447363-447622(-)$1	259	100	103	8.9999
GGA	chr13:99100468-99100727(+)$1	259	23	26	8.9999
GGA	chr16:50731260-50731519(+)$1	259	59	62	8.9999
GGA	chr22:34269195-34269454(+)$1	259	67	70	8.9999
GGA	chr11:117102964-117103223(-)$1	259	12	15	8.9999
gga	chrX:53247686-53247945(-)$1	259	64	67	8.9999
GGA	chr7:99170024-99170283(+)$1	259	6	9	8.9999
GGA	chr12:58166653-58166912(-)$1	259	67	70	8.9999
GGA	chr9:133579461-133579720(+)$1	259	150	153	8.9999
GGA	chr12:3862179-3862438(+)$1	259	23	26	8.9999
GGA	chr17:1494486-1494745(+)$1	259	7	10	8.9999
GGA	chr1:35246755-35247014(-)$1	259	55	58	8.9999
GGA	chr5:14694963-14695192(+)$1	229	19	22	8.9999
GGA	chr9:132597414-132597673(+)$1	259	61	64	8.9999
GGA	chr19:37063154-37063383(+)$1	229	0	3	8.9999
GGA	chr11:129940343-129940602(-)$1	259	47	50	8.9999
GGA	chr4:905443-905672(+)$1	229	8	11	8.9999
GGA	chr10:48373355-48373584(+)$1	229	92	95	8.9999
GGA	chr11:113678981-113679240(-)$1	259	145	148	8.9999
GGA	chr8:38089346-38089575(-)$1	229	91	94	8.9999
GGA	chr19:38852745-38853004(+)$1	259	22	25	8.9999
GGA	chr22:41642276-41642505(-)$1	229	94	97	8.9999
GGA	chr18:21242720-21242979(-)$1	259	10	13	8.9999
GGA	chr8:100905840-100906099(+)$1	259	2	5	8.9999
GGA	chr14:90085325-90085584(+)$1	259	15	18	8.9999
GGA	chr6:91296609-91296838(+)$1	229	20	23	8.9999
GGA	chr9:140135586-140135846(-)$1	260	54	57	8.9999
GGA	chr8:99058422-99058681(-)$1	259	72	75	8.9999
GGA	chr1:92545875-92546136(+)$1	261	56	59	8.9999
GGA	chr2:217528643-217528902(+)$1	259	48	51	8.9999
GGA	chr4:3257661-3257920(-)$1	259	10	13	8.9999
gga	chr22:46218945-46219204(+)$1	259	75	78	8.9999
GGA	chr7:101926278-101926537(+)$1	259	199	202	8.9999
GGA	chr19:18901842-18902071(+)$1	229	82	85	8.9999
GGA	chr8:22451637-22451896(+)$1	259	81	84	8.9999
GGA	chrX:15804751-15805010(+)$1	259	114	117	8.9999
GGA	chr8:28633229-28633488(+)$1	259	6	9	8.9999
GGA	chr9:91091005-91091264(-)$1	259	108	111	8.9999
GGA	chr10:127511541-127511770(+)$1	229	62	65	8.9999
GGA	chr11:10562216-10562475(+)$1	259	13	16	8.9999
GGA	chr12:113736695-113736924(+)$1	229	60	63	8.9999
GGA	chr12:70732232-70732461(-)$1	229	23	26	8.9999
GGA	chr2:37480070-37480329(-)$1	259	31	34	8.9999
GGA	chr19:13223657-13223919(+)$1	262	85	88	8.9999
GGA	chrX:52780197-52780456(+)$1	259	22	25	8.9999
GGA	chr1:214522446-214522705(+)$1	259	46	49	8.9999
GGA	chrX:100183362-100183621(+)$1	259	30	33	8.9999

#otherMatches

#Struct PSSM
fff	chr16:30016510-30016769(-)$1	259	14	17	8.9999
EEE	chr1:205500476-205500705(-)$1	229	19	22	8.9999
cc:	chr2:9562593-9562822(+)$1	229	49	52	8.9999
ddd	chr19:1216185-1216444(+)$1	259	114	117	8.9999
dd:	chr19:48968297-48968556(-)$1	259	232	235	8.9999
fff	chr5:80521429-80521658(-)$1	229	45	48	8.9999
NCC	chr17:10600730-10600989(+)$1	259	78	81	8.9999
:::	chr11:118901442-118901671(+)$1	229	8	11	8.9999
ddd	chr22:46508672-46508931(+)$1	259	1	4	8.9999
fff	chr8:92998375-92998634(+)$1	259	2	5	8.9999
GGG	chr2:63631253-63631482(+)$1	229	27	30	8.9999
ddd	chr9:130871137-130871397(+)$1	260	14	17	8.9999
htt	chr21:40557281-40557540(+)$1	259	24	27	8.9999
555	chr12:102113878-102114137(-)$1	259	114	117	8.9999
dbb	chr16:89615295-89615524(+)$1	229	112	115	8.9999
ddm	chr6:16586016-16586275(+)$1	259	19	22	8.9999
EEE	chr16:48386676-48386905(+)$1	229	20	23	8.9999
eee	chr14:53241099-53241358(+)$1	259	15	18	8.9999
mhh	chr9:139958624-139958883(-)$1	259	53	56	8.9999
BBd	chr10:1094384-1094613(+)$1	229	0	3	8.9999
ee[	chrX:38547520-38547779(+)$1	259	51	54	8.9999
DDD	chr17:38249557-38249816(-)$1	259	7	10	8.9999
eee	chr17:76168112-76168371(+)$1	259	34	37	8.9999
fff	chr1:204043366-204043595(+)$1	229	35	38	8.9999
FFF	chr17:46058722-46058981(+)$1	259	7	10	8.9999
DDK	chr11:61512381-61512610(-)$1	229	47	50	8.9999
###	chr19:54752558-54752817(+)$1	259	61	64	8.9999
DDD	chr11:70319036-70319265(-)$1	229	16	19	8.9999
===	chr17:27139349-27139578(+)$1	229	20	23	8.9999
HHH	chr17:42271326-42271555(+)$1	229	18	21	8.9999
EEE	chr15:45360253-45360482(+)$1	229	14	17	8.9999
ee]	chr6:33420659-33420918(+)$1	259	29	32	8.9999
iii	chr1:197410054-197410313(+)$1	259	19	22	8.9999
www	chr14:105916341-105916600(+)$1	259	54	57	8.9999
DDD	chr16:19566626-19566855(-)$1	229	37	40	8.9999
ccc	chr10:124739409-124739668(-)$1	259	10	13	8.9999
ddd	chr11:8128743-8128972(+)$1	229	30	33	8.9999
DDb	chr22:30091628-30091857(-)$1	229	6	9	8.9999
cmm	chr22:31600624-31600853(+)$1	229	43	46	8.9999
Dcc	chr20:35380965-35381224(+)$1	259	32	35	8.9999
bqq	chr3:113372916-113373145(-)$1	229	160	163	8.9999
eee	chr12:95907523-95907752(+)$1	229	73	76	8.9999
oob	chr20:4705796-4706055(-)$1	259	23	26	8.9999
cBB	chr19:2429833-2430062(+)$1	229	30	33	8.9999
:hh	chr20:36720231-36720490(+)$1	259	111	114	8.9999
BBL	chr18:77663647-77663906(+)$1	259	50	53	8.9999
:::	chr1:231354880-231355139(-)$1	259	51	54	8.9999
BBK	chr9:126143326-126143555(+)$1	229	0	3	8.9999
bb3	chrX:130217525-130217784(+)$1	259	45	48	8.9999
ddq	chr12:57422817-57423076(+)$1	259	195	198	8.9999
lld	chr2:97535998-97536258(+)$1	260	31	34	8.9999
ee%	chr2:238395112-238395341(+)$1	229	52	55	8.9999
eee	chr3:447363-447622(-)$1	259	100	103	8.9999
dd!	chr13:99100468-99100727(+)$1	259	23	26	8.9999
FFF	chr16:50731260-50731519(+)$1	259	59	62	8.9999
dd:	chr22:34269195-34269454(+)$1	259	67	70	8.9999
DD:	chr11:117102964-117103223(-)$1	259	12	15	8.9999
emm	chrX:53247686-53247945(-)$1	259	64	67	8.9999
:::	chr7:99170024-99170283(+)$1	259	6	9	8.9999
bbm	chr12:58166653-58166912(-)$1	259	67	70	8.9999
dd!	chr9:133579461-133579720(+)$1	259	150	153	8.9999
LLL	chr12:3862179-3862438(+)$1	259	23	26	8.9999
ff"	chr17:1494486-1494745(+)$1	259	7	10	8.9999
JJJ	chr1:35246755-35247014(-)$1	259	55	58	8.9999
Hcc	chr5:14694963-14695192(+)$1	229	19	22	8.9999
eee	chr9:132597414-132597673(+)$1	259	61	64	8.9999
eee	chr19:37063154-37063383(+)$1	229	0	3	8.9999
cc[	chr11:129940343-129940602(-)$1	259	47	50	8.9999
HHH	chr4:905443-905672(+)$1	229	8	11	8.9999
eee	chr10:48373355-48373584(+)$1	229	92	95	8.9999
a]d	chr11:113678981-113679240(-)$1	259	145	148	8.9999
eee	chr8:38089346-38089575(-)$1	229	91	94	8.9999
CC{	chr19:38852745-38853004(+)$1	259	22	25	8.9999
FFF	chr22:41642276-41642505(-)$1	229	94	97	8.9999
BB{	chr18:21242720-21242979(-)$1	259	10	13	8.9999
FFF	chr8:100905840-100906099(+)$1	259	2	5	8.9999
eee	chr14:90085325-90085584(+)$1	259	15	18	8.9999
cc!	chr6:91296609-91296838(+)$1	229	20	23	8.9999
f!!	chr9:140135586-140135846(-)$1	260	54	57	8.9999
a22	chr8:99058422-99058681(-)$1	259	72	75	8.9999
ddd	chr1:92545875-92546136(+)$1	261	56	59	8.9999
ggg	chr2:217528643-217528902(+)$1	259	48	51	8.9999
ooo	chr4:3257661-3257920(-)$1	259	10	13	8.9999
a!!	chr22:46218945-46219204(+)$1	259	75	78	8.9999
ddd	chr7:101926278-101926537(+)$1	259	199	202	8.9999
ffl	chr19:18901842-18902071(+)$1	229	82	85	8.9999
JJJ	chr8:22451637-22451896(+)$1	259	81	84	8.9999
hhh	chrX:15804751-15805010(+)$1	259	114	117	8.9999
E::	chr8:28633229-28633488(+)$1	259	6	9	8.9999
CCJ	chr9:91091005-91091264(-)$1	259	108	111	8.9999
EEE	chr10:127511541-127511770(+)$1	229	62	65	8.9999
IIL	chr11:10562216-10562475(+)$1	259	13	16	8.9999
hhq	chr12:113736695-113736924(+)$1	229	60	63	8.9999
EEE	chr12:70732232-70732461(-)$1	229	23	26	8.9999
ccg	chr2:37480070-37480329(-)$1	259	31	34	8.9999
ddd	chr19:13223657-13223919(+)$1	262	85	88	8.9999
eee	chrX:52780197-52780456(+)$1	259	22	25	8.9999
e]c	chr1:214522446-214522705(+)$1	259	46	49	8.9999
DDD	chrX:100183362-100183621(+)$1	259	30	33	8.9999

#DB
(((	chr16:30016510-30016769(-)$1	1	14	17	8.9999
(((	chr1:205500476-205500705(-)$1	1	19	22	8.9999
)).	chr2:9562593-9562822(+)$1	1	49	52	8.9999
(((	chr19:1216185-1216444(+)$1	1	114	117	8.9999
)).	chr19:48968297-48968556(-)$1	1	232	235	8.9999
)))	chr5:80521429-80521658(-)$1	1	45	48	8.9999
.((	chr17:10600730-10600989(+)$1	1	78	81	8.9999
...	chr11:118901442-118901671(+)$1	1	8	11	8.9999
(((	chr22:46508672-46508931(+)$1	1	1	4	8.9999
(((	chr8:92998375-92998634(+)$1	1	2	5	8.9999
(((	chr2:63631253-63631482(+)$1	1	27	30	8.9999
(((	chr9:130871137-130871397(+)$1	1	14	17	8.9999
(..	chr21:40557281-40557540(+)$1	1	24	27	8.9999
...	chr12:102113878-102114137(-)$1	1	114	117	8.9999
(((	chr16:89615295-89615524(+)$1	1	112	115	8.9999
((.	chr6:16586016-16586275(+)$1	1	19	22	8.9999
(((	chr16:48386676-48386905(+)$1	1	20	23	8.9999
(((	chr14:53241099-53241358(+)$1	1	15	18	8.9999
.))	chr9:139958624-139958883(-)$1	1	53	56	8.9999
(((	chr10:1094384-1094613(+)$1	1	0	3	8.9999
((.	chrX:38547520-38547779(+)$1	1	51	54	8.9999
(((	chr17:38249557-38249816(-)$1	1	7	10	8.9999
)))	chr17:76168112-76168371(+)$1	1	34	37	8.9999
(((	chr1:204043366-204043595(+)$1	1	35	38	8.9999
(((	chr17:46058722-46058981(+)$1	1	7	10	8.9999
((.	chr11:61512381-61512610(-)$1	1	47	50	8.9999
...	chr19:54752558-54752817(+)$1	1	61	64	8.9999
(((	chr11:70319036-70319265(-)$1	1	16	19	8.9999
(((	chr17:27139349-27139578(+)$1	1	20	23	8.9999
(((	chr17:42271326-42271555(+)$1	1	18	21	8.9999
(((	chr15:45360253-45360482(+)$1	1	14	17	8.9999
)).	chr6:33420659-33420918(+)$1	1	29	32	8.9999
(((	chr1:197410054-197410313(+)$1	1	19	22	8.9999
...	chr14:105916341-105916600(+)$1	1	54	57	8.9999
(((	chr16:19566626-19566855(-)$1	1	37	40	8.9999
(((	chr10:124739409-124739668(-)$1	1	10	13	8.9999
(((	chr11:8128743-8128972(+)$1	1	30	33	8.9999
(((	chr22:30091628-30091857(-)$1	1	6	9	8.9999
(..	chr22:31600624-31600853(+)$1	1	43	46	8.9999
(((	chr20:35380965-35381224(+)$1	1	32	35	8.9999
(..	chr3:113372916-113373145(-)$1	1	160	163	8.9999
)))	chr12:95907523-95907752(+)$1	1	73	76	8.9999
..)	chr20:4705796-4706055(-)$1	1	23	26	8.9999
)((	chr19:2429833-2430062(+)$1	1	30	33	8.9999
.((	chr20:36720231-36720490(+)$1	1	111	114	8.9999
((.	chr18:77663647-77663906(+)$1	1	50	53	8.9999
...	chr1:231354880-231355139(-)$1	1	51	54	8.9999
((.	chr9:126143326-126143555(+)$1	1	0	3	8.9999
)).	chrX:130217525-130217784(+)$1	1	45	48	8.9999
((.	chr12:57422817-57423076(+)$1	1	195	198	8.9999
..)	chr2:97535998-97536258(+)$1	1	31	34	8.9999
((.	chr2:238395112-238395341(+)$1	1	52	55	8.9999
(((	chr3:447363-447622(-)$1	1	100	103	8.9999
((.	chr13:99100468-99100727(+)$1	1	23	26	8.9999
(((	chr16:50731260-50731519(+)$1	1	59	62	8.9999
)).	chr22:34269195-34269454(+)$1	1	67	70	8.9999
((.	chr11:117102964-117103223(-)$1	1	12	15	8.9999
(..	chrX:53247686-53247945(-)$1	1	64	67	8.9999
...	chr7:99170024-99170283(+)$1	1	6	9	8.9999
((.	chr12:58166653-58166912(-)$1	1	67	70	8.9999
((.	chr9:133579461-133579720(+)$1	1	150	153	8.9999
...	chr12:3862179-3862438(+)$1	1	23	26	8.9999
((.	chr17:1494486-1494745(+)$1	1	7	10	8.9999
(((	chr1:35246755-35247014(-)$1	1	55	58	8.9999
(((	chr5:14694963-14695192(+)$1	1	19	22	8.9999
(((	chr9:132597414-132597673(+)$1	1	61	64	8.9999
(((	chr19:37063154-37063383(+)$1	1	0	3	8.9999
((.	chr11:129940343-129940602(-)$1	1	47	50	8.9999
(((	chr4:905443-905672(+)$1	1	8	11	8.9999
(((	chr10:48373355-48373584(+)$1	1	92	95	8.9999
).)	chr11:113678981-113679240(-)$1	1	145	148	8.9999
(((	chr8:38089346-38089575(-)$1	1	91	94	8.9999
((.	chr19:38852745-38853004(+)$1	1	22	25	8.9999
)))	chr22:41642276-41642505(-)$1	1	94	97	8.9999
((.	chr18:21242720-21242979(-)$1	1	10	13	8.9999
(((	chr8:100905840-100906099(+)$1	1	2	5	8.9999
(((	chr14:90085325-90085584(+)$1	1	15	18	8.9999
((.	chr6:91296609-91296838(+)$1	1	20	23	8.9999
(..	chr9:140135586-140135846(-)$1	1	54	57	8.9999
)..	chr8:99058422-99058681(-)$1	1	72	75	8.9999
(((	chr1:92545875-92546136(+)$1	1	56	59	8.9999
)))	chr2:217528643-217528902(+)$1	1	48	51	8.9999
...	chr4:3257661-3257920(-)$1	1	10	13	8.9999
(..	chr22:46218945-46219204(+)$1	1	75	78	8.9999
)))	chr7:101926278-101926537(+)$1	1	199	202	8.9999
((.	chr19:18901842-18902071(+)$1	1	82	85	8.9999
(((	chr8:22451637-22451896(+)$1	1	81	84	8.9999
)))	chrX:15804751-15805010(+)$1	1	114	117	8.9999
(..	chr8:28633229-28633488(+)$1	1	6	9	8.9999
)))	chr9:91091005-91091264(-)$1	1	108	111	8.9999
(((	chr10:127511541-127511770(+)$1	1	62	65	8.9999
((.	chr11:10562216-10562475(+)$1	1	13	16	8.9999
((.	chr12:113736695-113736924(+)$1	1	60	63	8.9999
(((	chr12:70732232-70732461(-)$1	1	23	26	8.9999
)))	chr2:37480070-37480329(-)$1	1	31	34	8.9999
)))	chr19:13223657-13223919(+)$1	1	85	88	8.9999
)))	chrX:52780197-52780456(+)$1	1	22	25	8.9999
).)	chr1:214522446-214522705(+)$1	1	46	49	8.9999
(((	chrX:100183362-100183621(+)$1	1	30	33	8.9999

#PSSM
G : 0.90	g : 0.09	
G : 0.90	g : 0.09	
A : 0.90	a : 0.09	

#score	890.9999999999998
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_CDS_m3_run1.nuc.txt

#NT
CUCUUCC	chr9:115592926-115593155(+)$1	229	79	86	13.4468
CUCUUCC	chr1:204402924-204403146(-)$1	222	202	209	13.4468
CUUUGCC	chr15:43813146-43813378(+)$1	232	136	143	12.0638
CUCUACC	chr2:171902582-171902801(-)$1	219	28	35	13.1276
CUCUUCC	chr19:40357405-40357634(-)$1	229	104	111	13.4468
CUCUGCA	chr6:37012813-37013030(+)$1	217	209	216	12.2765
gucugcc	chr17:17707170-17707386(+)$1	216	140	147	12.5957
CUCAGCC	chr9:130889698-130889925(-)$1	227	195	202	12.0638
CCCUGCC	chr3:52325781-52326033(+)$1	252	147	154	12.7021
CUCUGCC	chr3:43618339-43618573(-)$1	234	197	204	16.5319
CACUGCC	chr19:58982109-58982340(-)$1	231	21	28	12.5957
CUCUCCC	chr17:37339907-37340145(-)$1	238	170	177	13.5531
CUCUGCC	chr1:228362292-228362511(+)$1	219	9	16	16.5319
CACUGCC	chr2:29368070-29368285(-)$1	215	138	145	12.5957
AUCUGCC	chr11:65545289-65545504(+)$1	215	124	131	12.5957
CUCUGCC	chr2:97530698-97530917(-)$1	219	81	88	16.5319
CCCUGCC	chr1:203316797-203317051(-)$1	254	170	177	12.7021
CUCUCCC	chr11:63449035-63449253(+)$1	218	20	27	13.5531
UUCUGCC	chr6:42036221-42036445(+)$1	224	136	143	12.8085
AUCUGCC	chr1:183616776-183616995(+)$1	219	66	73	12.5957
CUCUGGC	chr12:7026672-7026907(+)$1	235	105	112	12.1702
CCCUGCC	chr9:130707865-130708085(-)$1	220	30	37	12.7021
cugugcc	chr20:36760746-36760984(-)$1	238	4	11	11.9574
CUUUGCC	chr16:28743071-28743296(+)$1	225	66	73	12.0638
CUCUUCC	chr17:1558689-1558909(-)$1	220	51	58	13.4468
CUCUCCC	chr10:104233519-104233740(+)$1	221	39	46	13.5531
UUCUGCC	chr9:35044113-35044331(-)$1	218	194	201	12.8085
CCCUGCC	chr17:67283745-67283965(-)$1	220	43	50	12.7021
UUCUGCC	chr15:79214377-79214612(-)$1	235	55	62	12.8085
CUCUGCC	chr12:7026096-7026311(+)$1	215	47	54	16.5319
CUCUACC	chr16:57693353-57693594(+)$1	241	164	171	13.1276
CUCUGCC	chr3:64085414-64085653(-)$1	239	218	225	16.5319
CACUGCC	chr1:20975520-20975740(+)$1	220	133	140	12.5957
CUCUCCC	chrX:123217211-123217428(-)$1	217	110	117	13.5531
CUCUGCA	chr9:1056601-1056819(-)$1	218	62	69	12.2765
CUCUUCC	chr21:40604245-40604472(-)$1	227	32	39	13.4468
CUCUGCG	chr12:18793348-18793563(+)$1	215	28	35	12.0638
CUCAGCC	chr8:39442057-39442273(-)$1	216	134	141	12.0638
CUCUCCC	chr9:34977944-34978177(+)$1	233	202	209	13.5531
CUCGGCC	chr19:407520-407739(-)$1	219	37	44	11.9574
CUCUGCA	chr15:75646712-75646938(+)$1	226	154	161	12.2765
GUCUGCC	chr11:1770201-1770423(+)$1	222	9	16	12.5957
CUCUGUC	chr19:12830005-12830252(-)$1	247	69	76	12.1702
CUCUGUC	chr9:139282784-139283000(+)$1	216	181	188	12.1702
CUCUGGC	chr15:83678980-83679200(+)$1	220	121	128	12.1702
CUCUCCC	chr18:31802871-31803089(+)$1	218	4	11	13.5531

#otherMatches

#Struct PSSM
GGGGGGD	chr9:96021500-96021723(+)$1	223	29	36	12.8085
ffffff!	chr9:115592926-115593155(+)$1	229	79	86	13.4468
:::::::	chr1:204402924-204403146(-)$1	222	202	209	13.4468
eee[ccc	chr15:43813146-43813378(+)$1	232	136	143	12.0638
:::::::	chr2:171902582-171902801(-)$1	219	28	35	13.1276
rrrrrrr	chr19:40357405-40357634(-)$1	229	104	111	13.4468
|||CCC:	chr6:37012813-37013030(+)$1	217	209	216	12.2765
ddddmmm	chr17:17707170-17707386(+)$1	216	140	147	12.5957
33hhhhh	chr9:130889698-130889925(-)$1	227	195	202	12.0638
D}EEEEE	chr3:52325781-52326033(+)$1	252	147	154	12.7021
22ccc]d	chr3:43618339-43618573(-)$1	234	197	204	16.5319
bb[bb""	chr19:58982109-58982340(-)$1	231	21	28	12.5957
eeooooo	chr17:37339907-37340145(-)$1	238	170	177	13.5531
E{CCC:e	chr1:228362292-228362511(+)$1	219	9	16	16.5319
D::ccco	chr2:29368070-29368285(-)$1	215	138	145	12.5957
pppdddd	chr11:65545289-65545504(+)$1	215	124	131	12.5957
glllggg	chr2:97530698-97530917(-)$1	219	81	88	16.5319
eFFFFFF	chr1:203316797-203317051(-)$1	254	170	177	12.7021
:::::::	chr11:63449035-63449253(+)$1	218	20	27	13.5531
333ccc7	chr6:42036221-42036445(+)$1	224	136	143	12.8085
ffffff]	chr1:183616776-183616995(+)$1	219	66	73	12.5957
555eeee	chr12:7026672-7026907(+)$1	235	105	112	12.1702
44dddd:	chr9:130707865-130708085(-)$1	220	30	37	12.7021
GGGGbbf	chr20:36760746-36760984(-)$1	238	4	11	11.9574
DDKKDDD	chr16:28743071-28743296(+)$1	225	66	73	12.0638
ff22ccc	chr17:1558689-1558909(-)$1	220	51	58	13.4468
:::CCCA	chr10:104233519-104233740(+)$1	221	39	46	13.5531
EEEEE}C	chr9:35044113-35044331(-)$1	218	194	201	12.8085
HH{CCC:	chr17:67283745-67283965(-)$1	220	43	50	12.7021
::BB{DD	chr15:79214377-79214612(-)$1	235	55	62	12.8085
dddeeee	chr12:7026096-7026311(+)$1	215	47	54	16.5319
=======	chr16:57693353-57693594(+)$1	241	164	171	13.1276
##ddddl	chr3:64085414-64085653(-)$1	239	218	225	16.5319
b333ccc	chr1:20975520-20975740(+)$1	220	133	140	12.5957
:::::bb	chrX:123217211-123217428(-)$1	217	110	117	13.5531
FF::ddd	chr9:1056601-1056819(-)$1	218	62	69	12.2765
^^^^^^^	chr21:40604245-40604472(-)$1	227	32	39	13.4468
cc:eeee	chr12:18793348-18793563(+)$1	215	28	35	12.0638
fff[bbo	chr8:39442057-39442273(-)$1	216	134	141	12.0638
DD}DDDD	chr9:34977944-34978177(+)$1	233	202	209	13.5531
""dddd[	chr19:407520-407739(-)$1	219	37	44	11.9574
ddddeee	chr15:75646712-75646938(+)$1	226	154	161	12.2765
gggggdd	chr11:1770201-1770423(+)$1	222	9	16	12.5957
mmmmggg	chr19:12830005-12830252(-)$1	247	69	76	12.1702
::BB}HH	chr9:139282784-139283000(+)$1	216	181	188	12.1702
ciiiiii	chr15:83678980-83679200(+)$1	220	121	128	12.1702
:::::::	chr18:31802871-31803089(+)$1	218	4	11	13.5531

#DB
(((((((	chr9:96021500-96021723(+)$1	1	29	36	12.8085
((((((.	chr9:115592926-115593155(+)$1	1	79	86	13.4468
.......	chr1:204402924-204403146(-)$1	1	202	209	13.4468
(((.(((	chr15:43813146-43813378(+)$1	1	136	143	12.0638
.......	chr2:171902582-171902801(-)$1	1	28	35	13.1276
.......	chr19:40357405-40357634(-)$1	1	104	111	13.4468
...))).	chr6:37012813-37013030(+)$1	1	209	216	12.2765
((((...	chr17:17707170-17707386(+)$1	1	140	147	12.5957
..)))))	chr9:130889698-130889925(-)$1	1	195	202	12.0638
).)))))	chr3:52325781-52326033(+)$1	1	147	154	12.7021
..))).)	chr3:43618339-43618573(-)$1	1	197	204	16.5319
((.((..	chr19:58982109-58982340(-)$1	1	21	28	12.5957
((.....	chr17:37339907-37340145(-)$1	1	170	177	13.5531
(.(((.(	chr1:228362292-228362511(+)$1	1	9	16	16.5319
)..(((.	chr2:29368070-29368285(-)$1	1	138	145	12.5957
...))))	chr11:65545289-65545504(+)$1	1	124	131	12.5957
(...)))	chr2:97530698-97530917(-)$1	1	81	88	16.5319
)))))))	chr1:203316797-203317051(-)$1	1	170	177	12.7021
.......	chr11:63449035-63449253(+)$1	1	20	27	13.5531
...))).	chr6:42036221-42036445(+)$1	1	136	143	12.8085
)))))).	chr1:183616776-183616995(+)$1	1	66	73	12.5957
...))))	chr12:7026672-7026907(+)$1	1	105	112	12.1702
..)))).	chr9:130707865-130708085(-)$1	1	30	37	12.7021
(((((((	chr20:36760746-36760984(-)$1	1	4	11	11.9574
((..(((	chr16:28743071-28743296(+)$1	1	66	73	12.0638
))..)))	chr17:1558689-1558909(-)$1	1	51	58	13.4468
...((((	chr10:104233519-104233740(+)$1	1	39	46	13.5531
))))).)	chr9:35044113-35044331(-)$1	1	194	201	12.8085
((.(((.	chr17:67283745-67283965(-)$1	1	43	50	12.7021
..((.((	chr15:79214377-79214612(-)$1	1	55	62	12.8085
)))))))	chr12:7026096-7026311(+)$1	1	47	54	16.5319
(((((((	chr16:57693353-57693594(+)$1	1	164	171	13.1276
..((((.	chr3:64085414-64085653(-)$1	1	218	225	16.5319
)...)))	chr1:20975520-20975740(+)$1	1	133	140	12.5957
.....((	chrX:123217211-123217428(-)$1	1	110	117	13.5531
((..(((	chr9:1056601-1056819(-)$1	1	62	69	12.2765
.......	chr21:40604245-40604472(-)$1	1	32	39	13.4468
)).((((	chr12:18793348-18793563(+)$1	1	28	35	12.0638
(((.((.	chr8:39442057-39442273(-)$1	1	134	141	12.0638
)).))))	chr9:34977944-34978177(+)$1	1	202	209	13.5531
..((((.	chr19:407520-407739(-)$1	1	37	44	11.9574
(((((((	chr15:75646712-75646938(+)$1	1	154	161	12.2765
(((((((	chr11:1770201-1770423(+)$1	1	9	16	12.5957
....)))	chr19:12830005-12830252(-)$1	1	69	76	12.1702
..)).))	chr9:139282784-139283000(+)$1	1	181	188	12.1702
)))))))	chr15:83678980-83679200(+)$1	1	121	128	12.1702
.......	chr18:31802871-31803089(+)$1	1	4	11	13.5531

#PSSM
C : 0.80	U : 0.08	A : 0.04	g : 0.02	c : 0.02	G : 0.02	
U : 0.80	C : 0.08	A : 0.06	u : 0.04	
C : 0.91	U : 0.04	c : 0.02	g : 0.02	
U : 0.89	u : 0.04	A : 0.04	G : 0.02	
G : 0.68	C : 0.12	U : 0.10	A : 0.04	g : 0.04	
C : 0.87	c : 0.04	G : 0.04	U : 0.04	
C : 0.87	A : 0.06	c : 0.04	G : 0.02	

#score	617.4255319148938
#seq	47
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m1_run2.nuc.txt

#NT
CCUGGG	chr7:104773357-104773585(-)$1	228	113	119	15.6923
CCUGGG	chr2:95976137-95976368(+)$1	231	216	222	15.6923
CCUGGG	chr11:47609240-47609465(-)$1	225	162	168	15.6923
CCUGGG	chr19:54969871-54970095(+)$1	224	150	156	15.6923
CCUGGG	chr17:38251976-38252194(+)$1	218	94	100	15.6923
CCUGGG	chr19:17678214-17678430(+)$1	216	147	153	15.6923
CCUGAG	chr12:56995784-56996007(-)$1	223	33	39	14.1538
CCUGAG	chr6:147091642-147091857(-)$1	215	111	117	14.1538
CCUGUG	chr3:49755679-49755898(+)$1	219	68	74	14.1538
CCUGGG	chr3:48685277-48685498(-)$1	221	60	66	15.6923
CCUGAG	chr17:7230658-7230874(-)$1	216	7	13	14.1538
CCUGUG	chr9:135946549-135946766(+)$1	217	14	20	14.1538
CCUGGG	chr12:49521757-49521976(-)$1	219	39	45	15.6923
CCUGGG	chrX:153072150-153072372(-)$1	222	154	160	15.6923
CCUGGG	chr9:91995884-91996106(-)$1	222	38	44	15.6923
ccuggg	chr15:41804207-41804427(-)$1	220	167	173	15.6923
CCUGGG	chr11:119058959-119059181(+)$1	222	3	9	15.6923
CCUGGG	chr10:27443032-27443250(+)$1	218	73	79	15.6923
CCUGUG	chr4:71555353-71555575(+)$1	222	113	119	14.1538
CCUGUG	chr3:5241246-5241467(+)$1	221	9	15	14.1538
CCUGUG	chr8:22005809-22006027(-)$1	218	15	21	14.1538
CCUGGG	chr7:99755254-99755485(-)$1	231	184	190	15.6923
CCUGAG	chr12:49445258-49445482(-)$1	224	12	18	14.1538
CCUGUG	chr3:65415628-65415850(-)$1	222	62	68	14.1538
CCUGGG	chr2:1915712-1915936(-)$1	224	208	214	15.6923
CCUGUG	chr20:43545383-43545598(+)$1	215	1	7	14.1538
CCUGGG	chr19:50387476-50387700(+)$1	224	162	168	15.6923
CCUGGG	chr1:17322637-17322855(-)$1	218	18	24	15.6923
CCUGAG	chr19:39879828-39880054(-)$1	226	4	10	14.1538
CCUGAG	chr6:33646457-33646673(-)$1	216	29	35	14.1538
CCUGUG	chr1:26349106-26349333(+)$1	227	57	63	14.1538
CCUGGG	chr14:103986180-103986397(-)$1	217	73	79	15.6923
CCUGAG	chr11:62343317-62343566(-)$1	249	13	19	14.1538
CCUGAG	chr7:45004006-45004221(+)$1	215	111	117	14.1538
CCUGGG	chr3:100091336-100091552(+)$1	216	112	118	15.6923
ccuggg	chr19:17783180-17783400(-)$1	220	38	44	15.6923
CCUGUG	chr3:97167462-97167679(-)$1	217	206	212	14.1538
CCUGGG	chr9:124536528-124536744(+)$1	216	96	102	15.6923

#otherMatches

#Struct PSSM
YYEEEE	chr11:3381356-3381572(-)$1	216	202	208	14.1538
fffff[	chr7:104773357-104773585(-)$1	228	113	119	15.6923
GGGGGG	chr2:95976137-95976368(+)$1	231	216	222	15.6923
cc22gg	chr11:47609240-47609465(-)$1	225	162	168	15.6923
2eeeee	chr19:54969871-54970095(+)$1	224	150	156	15.6923
3eeeee	chr17:38251976-38252194(+)$1	218	94	100	15.6923
======	chr19:17678214-17678430(+)$1	216	147	153	15.6923
pphhhh	chr12:56995784-56996007(-)$1	223	33	39	14.1538
eeeeec	chr6:147091642-147091857(-)$1	215	111	117	14.1538
ccffff	chr3:49755679-49755898(+)$1	219	68	74	14.1538
+eeeee	chr3:48685277-48685498(-)$1	221	60	66	15.6923
MMMMDD	chr17:7230658-7230874(-)$1	216	7	13	14.1538
hhhhhh	chr9:135946549-135946766(+)$1	217	14	20	14.1538
eee===	chr12:49521757-49521976(-)$1	219	39	45	15.6923
BB::dd	chrX:153072150-153072372(-)$1	222	154	160	15.6923
GGGGGG	chr9:91995884-91996106(-)$1	222	38	44	15.6923
bb22bb	chr15:41804207-41804427(-)$1	220	167	173	15.6923
EE{AKK	chr11:119058959-119059181(+)$1	222	3	9	15.6923
bbiiii	chr10:27443032-27443250(+)$1	218	73	79	15.6923
ggggg[	chr4:71555353-71555575(+)$1	222	113	119	14.1538
{GGGGG	chr3:5241246-5241467(+)$1	221	9	15	14.1538
BB{EEE	chr8:22005809-22006027(-)$1	218	15	21	14.1538
====dd	chr7:99755254-99755485(-)$1	231	184	190	15.6923
b[bb[c	chr12:49445258-49445482(-)$1	224	12	18	14.1538
d:ffff	chr3:65415628-65415850(-)$1	222	62	68	14.1538
hh:GGG	chr2:1915712-1915936(-)$1	224	208	214	15.6923
JJJJJJ	chr20:43545383-43545598(+)$1	215	1	7	14.1538
gggEEE	chr19:50387476-50387700(+)$1	224	162	168	15.6923
JJJccc	chr1:17322637-17322855(-)$1	218	18	24	15.6923
ECCCA{	chr19:39879828-39880054(-)$1	226	4	10	14.1538
eeeeee	chr6:33646457-33646673(-)$1	216	29	35	14.1538
$$$$$g	chr1:26349106-26349333(+)$1	227	57	63	14.1538
dd!!ff	chr14:103986180-103986397(-)$1	217	73	79	15.6923
:ccc[f	chr11:62343317-62343566(-)$1	249	13	19	14.1538
]iiiii	chr7:45004006-45004221(+)$1	215	111	117	14.1538
:::ddd	chr3:100091336-100091552(+)$1	216	112	118	15.6923
KKCCCD	chr19:17783180-17783400(-)$1	220	38	44	15.6923
FFFFYY	chr3:97167462-97167679(-)$1	217	206	212	14.1538
hh:CCC	chr9:124536528-124536744(+)$1	216	96	102	15.6923

#DB
..))))	chr11:3381356-3381572(-)$1	1	202	208	14.1538
(((((.	chr7:104773357-104773585(-)$1	1	113	119	15.6923
))))))	chr2:95976137-95976368(+)$1	1	216	222	15.6923
))..))	chr11:47609240-47609465(-)$1	1	162	168	15.6923
.)))))	chr19:54969871-54970095(+)$1	1	150	156	15.6923
.)))))	chr17:38251976-38252194(+)$1	1	94	100	15.6923
))))))	chr19:17678214-17678430(+)$1	1	147	153	15.6923
..))))	chr12:56995784-56996007(-)$1	1	33	39	14.1538
))))))	chr6:147091642-147091857(-)$1	1	111	117	14.1538
))))))	chr3:49755679-49755898(+)$1	1	68	74	14.1538
.(((((	chr3:48685277-48685498(-)$1	1	60	66	15.6923
....((	chr17:7230658-7230874(-)$1	1	7	13	14.1538
((((((	chr9:135946549-135946766(+)$1	1	14	20	14.1538
((((((	chr12:49521757-49521976(-)$1	1	39	45	15.6923
))..((	chrX:153072150-153072372(-)$1	1	154	160	15.6923
((((((	chr9:91995884-91996106(-)$1	1	38	44	15.6923
))..))	chr15:41804207-41804427(-)$1	1	167	173	15.6923
((.(..	chr11:119058959-119059181(+)$1	1	3	9	15.6923
))((((	chr10:27443032-27443250(+)$1	1	73	79	15.6923
(((((.	chr4:71555353-71555575(+)$1	1	113	119	14.1538
.(((((	chr3:5241246-5241467(+)$1	1	9	15	14.1538
((.(((	chr8:22005809-22006027(-)$1	1	15	21	14.1538
))))((	chr7:99755254-99755485(-)$1	1	184	190	15.6923
(.((.(	chr12:49445258-49445482(-)$1	1	12	18	14.1538
).((((	chr3:65415628-65415850(-)$1	1	62	68	14.1538
)).)))	chr2:1915712-1915936(-)$1	1	208	214	15.6923
((((((	chr20:43545383-43545598(+)$1	1	1	7	14.1538
))))))	chr19:50387476-50387700(+)$1	1	162	168	15.6923
((((((	chr1:17322637-17322855(-)$1	1	18	24	15.6923
(((((.	chr19:39879828-39880054(-)$1	1	4	10	14.1538
((((((	chr6:33646457-33646673(-)$1	1	29	35	14.1538
.....(	chr1:26349106-26349333(+)$1	1	57	63	14.1538
((..((	chr14:103986180-103986397(-)$1	1	73	79	15.6923
.(((.(	chr11:62343317-62343566(-)$1	1	13	19	14.1538
.)))))	chr7:45004006-45004221(+)$1	1	111	117	14.1538
...(((	chr3:100091336-100091552(+)$1	1	112	118	15.6923
..((((	chr19:17783180-17783400(-)$1	1	38	44	15.6923
))))..	chr3:97167462-97167679(-)$1	1	206	212	14.1538
)).(((	chr9:124536528-124536744(+)$1	1	96	102	15.6923

#PSSM
C : 0.94	c : 0.05	
C : 0.94	c : 0.05	
U : 0.94	u : 0.05	
G : 0.94	g : 0.05	
G : 0.48	A : 0.23	U : 0.23	g : 0.05	
G : 0.94	g : 0.05	

#score	584.3076923076923
#seq	39
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m2_run1.nuc.txt

#NT
uuuuaaa	chr3:141613394-141613789(+)$1	395	24	31	18.0175
uuuuuaa	chr15:85308093-85308419(+)$1	326	88	95	14.0701
UCUUAAA	chr11:85755274-85755558(-)$1	284	248	255	14.9473
UUUUAua	chr15:80378676-80378928(+)$1	252	11	18	14.0701
uuuucaa	chr12:49887351-49887616(+)$1	265	206	213	13.8947
uuuuaaa	chr12:129859807-129860064(-)$1	257	18	25	18.0175
uuuuaca	chr11:77128397-77128646(-)$1	249	75	82	14.5964
UAUUAAA	chr11:108121990-108122227(+)$1	237	2	9	14.9473
UUUUAAA	chr12:10761453-10761697(-)$1	244	39	46	18.0175
UCUUAAA	chr1:44320685-44321087(+)$1	402	3	10	14.9473
uuuuaaa	chr3:113449911-113450166(-)$1	255	136	143	18.0175
uuuuaaa	chr10:35666040-35666299(+)$1	259	39	46	18.0175
UGUUAAA	chr4:42057553-42057791(+)$1	238	98	105	14.7719
uuuuaaa	chr3:186266091-186266318(-)$1	227	26	33	18.0175
UUUUACA	chr10:51571768-51572004(+)$1	236	102	109	14.5964
UUUUAAA	chr6:1893891-1894128(-)$1	237	63	70	18.0175
UUUUAAA	chr2:233682047-233682292(+)$1	245	14	21	18.0175
uauuaaa	chr7:110915596-110915874(-)$1	278	20	27	14.9473
uuuuaca	chr12:100653048-100653308(-)$1	260	102	109	14.5964
uuuuaaa	chr2:128501828-128502308(-)$1	480	217	224	18.0175
UGUUAAA	chr19:4419891-4420248(+)$1	357	165	172	14.7719
UUUUAAA	chr11:75136023-75136254(-)$1	231	62	69	18.0175
uuuuaaa	chr2:173646350-173646625(+)$1	275	227	234	18.0175
ucuuaaa	chr13:49834490-49834761(+)$1	271	108	115	14.9473
uuuuaaa	chr12:105543674-105543932(+)$1	258	51	58	18.0175
UUUUAAA	chr1:243915865-243916101(-)$1	236	151	158	18.0175
uuuuaaa	chr4:42020769-42021015(+)$1	246	179	186	18.0175
UUUUGAA	chr10:103446151-103446427(-)$1	276	85	92	13.8947
uuuuaaa	chr3:129178567-129178836(+)$1	269	197	204	18.0175
UUUUAAA	chr9:26884358-26884668(-)$1	310	65	72	18.0175
UUUUGAA	chr7:140097408-140097642(-)$1	234	34	41	13.8947
UGUUAAA	chr4:48357696-48357946(+)$1	250	16	23	14.7719
UUUUAAA	chr2:216816980-216817214(-)$1	234	6	13	18.0175
UUUUAAA	chr3:136392054-136392392(-)$1	338	57	64	18.0175
UCUUAAA	chr1:59121073-59121323(-)$1	250	6	13	14.9473
UUUUUAA	chr6:81053084-81053324(+)$1	240	178	185	14.0701
UUUUUAA	chr15:64666159-64666418(-)$1	259	0	7	14.0701
ucuuaaa	chr10:114248673-114248925(+)$1	252	112	119	14.9473
UUUUAUA	chr4:169805175-169805393(+)$1	218	64	71	14.0701
UUUUAAA	chrX:119588962-119589209(-)$1	247	63	70	18.0175
UUUUAAA	chr3:13458269-13458592(-)$1	323	104	111	18.0175
uuuuaca	chr4:151633251-151633483(-)$1	232	161	168	14.5964
uauuaaa	chr2:214183757-214184039(+)$1	282	121	128	14.9473
UUUUAAA	chr14:60164750-60164995(-)$1	245	4	11	18.0175
UGUUAAA	chr3:115892380-115892646(-)$1	266	66	73	14.7719
UUUUACA	chrX:100084513-100084825(+)$1	312	48	55	14.5964
UCUUAAA	chr5:68472848-68473107(+)$1	259	87	94	14.9473
UUUUACA	chr6:42640252-42640551(+)$1	299	25	32	14.5964
uauuaaa	chr10:38412015-38412322(+)$1	307	162	169	14.9473
UUUUACA	chr6:146244252-146244540(-)$1	288	6	13	14.5964
uuuuaaa	chr1:244589100-244589417(-)$1	317	134	141	18.0175
UUUUUAA	chr10:86197673-86197904(+)$1	231	7	14	14.0701
uauuaaa	chr2:136333063-136333393(+)$1	330	213	220	14.9473
uuuuaaa	chr5:176473765-176474045(+)$1	280	201	208	18.0175
UUUUACA	chr4:74076930-74077210(-)$1	280	43	50	14.5964
UUUUCAA	chr4:145585651-145585969(+)$1	318	87	94	13.8947

#otherMatches

#Struct PSSM
yyyyyyy	chr18:672384-672623(-)$1	239	44	51	14.9473
gggggg[	chr3:141613394-141613789(+)$1	395	24	31	18.0175
CCCLLLB	chr15:85308093-85308419(+)$1	326	88	95	14.0701
EEE????	chr11:85755274-85755558(-)$1	284	248	255	14.9473
:::::::	chr15:80378676-80378928(+)$1	252	11	18	14.0701
::::::d	chr12:49887351-49887616(+)$1	265	206	213	13.8947
TTTTTTT	chr12:129859807-129860064(-)$1	257	18	25	18.0175
oooccc:	chr11:77128397-77128646(-)$1	249	75	82	14.5964
:::::::	chr11:108121990-108122227(+)$1	237	2	9	14.9473
EEEE:::	chr12:10761453-10761697(-)$1	244	39	46	18.0175
DD:::::	chr1:44320685-44321087(+)$1	402	3	10	14.9473
ggglllg	chr3:113449911-113450166(-)$1	255	136	143	18.0175
>>>>>>>	chr10:35666040-35666299(+)$1	259	39	46	18.0175
hhhhhhh	chr4:42057553-42057791(+)$1	238	98	105	14.7719
ddppppp	chr3:186266091-186266318(-)$1	227	26	33	18.0175
ffff[bb	chr10:51571768-51572004(+)$1	236	102	109	14.5964
++++++c	chr6:1893891-1894128(-)$1	237	63	70	18.0175
:::::::	chr2:233682047-233682292(+)$1	245	14	21	18.0175
ttttttt	chr7:110915596-110915874(-)$1	278	20	27	14.9473
qqqqqbb	chr12:100653048-100653308(-)$1	260	102	109	14.5964
MMMMFFF	chr2:128501828-128502308(-)$1	480	217	224	18.0175
mmmmggg	chr19:4419891-4420248(+)$1	357	165	172	14.7719
dddd%%%	chr11:75136023-75136254(-)$1	231	62	69	18.0175
8888888	chr2:173646350-173646625(+)$1	275	227	234	18.0175
:::::::	chr13:49834490-49834761(+)$1	271	108	115	14.9473
=iiiiii	chr12:105543674-105543932(+)$1	258	51	58	18.0175
ggggggg	chr1:243915865-243916101(-)$1	236	151	158	18.0175
=mmmm==	chr4:42020769-42021015(+)$1	246	179	186	18.0175
drrrrrr	chr10:103446151-103446427(-)$1	276	85	92	13.8947
$$$$ccc	chr3:129178567-129178836(+)$1	269	197	204	18.0175
ffffff:	chr9:26884358-26884668(-)$1	310	65	72	18.0175
$$ccc!!	chr7:140097408-140097642(-)$1	234	34	41	13.8947
ggggg::	chr4:48357696-48357946(+)$1	250	16	23	14.7719
:::::::	chr2:216816980-216817214(-)$1	234	6	13	18.0175
FFKKBB{	chr3:136392054-136392392(-)$1	338	57	64	18.0175
:::::ff	chr1:59121073-59121323(-)$1	250	6	13	14.9473
ee22fff	chr6:81053084-81053324(+)$1	240	178	185	14.0701
:::::::	chr15:64666159-64666418(-)$1	259	0	7	14.0701
fff]ddd	chr10:114248673-114248925(+)$1	252	112	119	14.9473
gggg::f	chr4:169805175-169805393(+)$1	218	64	71	14.0701
ggmmmmg	chrX:119588962-119589209(-)$1	247	63	70	18.0175
pppdddd	chr3:13458269-13458592(-)$1	323	104	111	18.0175
ellleee	chr4:151633251-151633483(-)$1	232	161	168	14.5964
WWWWWWW	chr2:214183757-214184039(+)$1	282	121	128	14.9473
:::::::	chr14:60164750-60164995(-)$1	245	4	11	18.0175
FFKKGGG	chr3:115892380-115892646(-)$1	266	66	73	14.7719
SSSSSSS	chrX:100084513-100084825(+)$1	312	48	55	14.5964
ccc::::	chr5:68472848-68473107(+)$1	259	87	94	14.9473
:::::::	chr6:42640252-42640551(+)$1	299	25	32	14.5964
eeee555	chr10:38412015-38412322(+)$1	307	162	169	14.9473
:::CCCC	chr6:146244252-146244540(-)$1	288	6	13	14.5964
)))))))	chr1:244589100-244589417(-)$1	317	134	141	18.0175
HHHHHLL	chr10:86197673-86197904(+)$1	231	7	14	14.0701
::::::d	chr2:136333063-136333393(+)$1	330	213	220	14.9473
====:::	chr5:176473765-176474045(+)$1	280	201	208	18.0175
ooooddd	chr4:74076930-74077210(-)$1	280	43	50	14.5964
hhhhhhh	chr4:145585651-145585969(+)$1	318	87	94	13.8947

#DB
.......	chr18:672384-672623(-)$1	1	44	51	14.9473
((((((.	chr3:141613394-141613789(+)$1	1	24	31	18.0175
(((...(	chr15:85308093-85308419(+)$1	1	88	95	14.0701
)))....	chr11:85755274-85755558(-)$1	1	248	255	14.9473
.......	chr15:80378676-80378928(+)$1	1	11	18	14.0701
......(	chr12:49887351-49887616(+)$1	1	206	213	13.8947
.......	chr12:129859807-129860064(-)$1	1	18	25	18.0175
...))).	chr11:77128397-77128646(-)$1	1	75	82	14.5964
.......	chr11:108121990-108122227(+)$1	1	2	9	14.9473
((((...	chr12:10761453-10761697(-)$1	1	39	46	18.0175
((.....	chr1:44320685-44321087(+)$1	1	3	10	14.9473
(((...)	chr3:113449911-113450166(-)$1	1	136	143	18.0175
.......	chr10:35666040-35666299(+)$1	1	39	46	18.0175
(((((((	chr4:42057553-42057791(+)$1	1	98	105	14.7719
((.....	chr3:186266091-186266318(-)$1	1	26	33	18.0175
((((.((	chr10:51571768-51572004(+)$1	1	102	109	14.5964
......(	chr6:1893891-1894128(-)$1	1	63	70	18.0175
.......	chr2:233682047-233682292(+)$1	1	14	21	18.0175
.......	chr7:110915596-110915874(-)$1	1	20	27	14.9473
.....))	chr12:100653048-100653308(-)$1	1	102	109	14.5964
....(((	chr2:128501828-128502308(-)$1	1	217	224	18.0175
....)))	chr19:4419891-4420248(+)$1	1	165	172	14.7719
((((...	chr11:75136023-75136254(-)$1	1	62	69	18.0175
.......	chr2:173646350-173646625(+)$1	1	227	234	18.0175
.......	chr13:49834490-49834761(+)$1	1	108	115	14.9473
)((((((	chr12:105543674-105543932(+)$1	1	51	58	18.0175
(((((((	chr1:243915865-243916101(-)$1	1	151	158	18.0175
(....))	chr4:42020769-42021015(+)$1	1	179	186	18.0175
(......	chr10:103446151-103446427(-)$1	1	85	92	13.8947
....(((	chr3:129178567-129178836(+)$1	1	197	204	18.0175
)))))).	chr9:26884358-26884668(-)$1	1	65	72	18.0175
..(((..	chr7:140097408-140097642(-)$1	1	34	41	13.8947
)))))..	chr4:48357696-48357946(+)$1	1	16	23	14.7719
.......	chr2:216816980-216817214(-)$1	1	6	13	18.0175
((..((.	chr3:136392054-136392392(-)$1	1	57	64	18.0175
.....((	chr1:59121073-59121323(-)$1	1	6	13	14.9473
))..)))	chr6:81053084-81053324(+)$1	1	178	185	14.0701
.......	chr15:64666159-64666418(-)$1	1	0	7	14.0701
))).)))	chr10:114248673-114248925(+)$1	1	112	119	14.9473
))))..(	chr4:169805175-169805393(+)$1	1	64	71	14.0701
((....)	chrX:119588962-119589209(-)$1	1	63	70	18.0175
...))))	chr3:13458269-13458592(-)$1	1	104	111	18.0175
(...)))	chr4:151633251-151633483(-)$1	1	161	168	14.5964
.......	chr2:214183757-214184039(+)$1	1	121	128	14.9473
.......	chr14:60164750-60164995(-)$1	1	4	11	18.0175
((..(((	chr3:115892380-115892646(-)$1	1	66	73	14.7719
.......	chrX:100084513-100084825(+)$1	1	48	55	14.5964
)))....	chr5:68472848-68473107(+)$1	1	87	94	14.9473
.......	chr6:42640252-42640551(+)$1	1	25	32	14.5964
))))...	chr10:38412015-38412322(+)$1	1	162	169	14.9473
...((((	chr6:146244252-146244540(-)$1	1	6	13	14.5964
.......	chr1:244589100-244589417(-)$1	1	134	141	18.0175
(((((..	chr10:86197673-86197904(+)$1	1	7	14	14.0701
......(	chr2:136333063-136333393(+)$1	1	213	220	14.9473
))))...	chr5:176473765-176474045(+)$1	1	201	208	18.0175
....)))	chr4:74076930-74077210(-)$1	1	43	50	14.5964
)))))))	chr4:145585651-145585969(+)$1	1	87	94	13.8947

#PSSM
U : 0.59	u : 0.40	
U : 0.42	u : 0.29	C : 0.07	G : 0.07	a : 0.07	A : 0.03	c : 0.03	
U : 0.59	u : 0.40	
U : 0.59	u : 0.40	
A : 0.49	a : 0.36	U : 0.05	G : 0.03	u : 0.01	c : 0.01	C : 0.01	
A : 0.47	a : 0.35	C : 0.08	c : 0.05	u : 0.01	U : 0.01	
A : 0.57	a : 0.42	

#score	909.6315789473684
#seq	57
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m1_run2.nuc.txt

#NT
GUU	chr12:7032098-7032363(+)$1	265	68	71	8.9999
GUU	chr21:28295246-28295477(-)$1	231	74	77	8.9999
GUU	chr12:8249758-8249989(+)$1	231	7	10	8.9999
GUU	chr15:60785446-60785671(-)$1	225	6	9	8.9999
GUU	chr1:28607250-28607514(+)$1	264	86	89	8.9999
GUU	chr3:42707350-42707587(+)$1	237	35	38	8.9999
GUU	chr6:105529014-105529245(+)$1	231	19	22	8.9999
GUU	chr15:77345059-77345303(-)$1	244	39	42	8.9999
GUU	chr1:162493238-162493475(+)$1	237	20	23	8.9999
GUU	chr11:63743805-63744069(+)$1	264	48	51	8.9999
GUU	chr14:23794663-23794951(+)$1	288	114	117	8.9999
GUU	chr12:42481142-42481369(-)$1	227	1	4	8.9999
GUU	chr22:32080657-32080894(-)$1	237	31	34	8.9999
GUU	chr22:21982292-21982522(-)$1	230	67	70	8.9999
GUU	chr1:246887619-246887850(+)$1	231	15	18	8.9999
GUU	chr10:93623788-93624047(+)$1	259	11	14	8.9999
GUU	chr11:47800400-47800638(-)$1	238	182	185	8.9999
GUU	chr14:95553444-95553692(-)$1	248	104	107	8.9999
GUU	chr11:64789331-64789585(+)$1	254	64	67	8.9999
GUU	chr2:217364579-217364836(+)$1	257	61	64	8.9999
GUU	chr1:155306246-155306477(-)$1	231	9	12	8.9999
GUU	chr12:12873977-12874226(+)$1	249	4	7	8.9999
GUU	chr8:61778958-61779204(+)$1	246	13	16	8.9999
GUU	chrX:24003858-24004110(-)$1	252	10	13	8.9999
GUU	chr16:30535466-30535686(-)$1	220	23	26	8.9999
GUU	chr10:101910041-101910304(-)$1	263	49	52	8.9999
GUU	chr11:69467086-69467334(+)$1	248	12	15	8.9999
GUU	chr5:179041711-179041971(-)$1	260	87	90	8.9999
GUU	chr8:95900145-95900370(-)$1	225	51	54	8.9999
GUU	chr11:35642225-35642468(+)$1	243	9	12	8.9999
guu	chr12:56145202-56145428(+)$1	226	13	16	8.9999
GUU	chr1:15897945-15898165(+)$1	220	47	50	8.9999
GUU	chr19:13049388-13049634(+)$1	246	65	68	8.9999
GUU	chr1:207218754-207218981(-)$1	227	78	81	8.9999
GUU	chr2:61765075-61765315(-)$1	240	22	25	8.9999
GUU	chr16:70605737-70606010(+)$1	273	16	19	8.9999
GUU	chr15:99673828-99674064(+)$1	236	85	88	8.9999
GUU	chr7:27202438-27202664(-)$1	226	1	4	8.9999
GUU	chr1:162497206-162497445(+)$1	239	51	54	8.9999
GUU	chr1:32799708-32799946(-)$1	238	50	53	8.9999
GUU	chr19:50001075-50001323(+)$1	248	41	44	8.9999
GUU	chr7:30123794-30124032(+)$1	238	63	66	8.9999
GUU	chr8:27661807-27662054(+)$1	247	28	31	8.9999
GUU	chr5:150409437-150409659(-)$1	222	30	33	8.9999
GUU	chr5:148874786-148875028(-)$1	242	197	200	8.9999
GUU	chr7:26230358-26230584(-)$1	226	21	24	8.9999
GUU	chr5:179157331-179157581(+)$1	250	10	13	8.9999
GUU	chr16:30094002-30094230(+)$1	228	28	31	8.9999
GUU	chr2:111925802-111926070(+)$1	268	38	41	8.9999
GUU	chrX:39910810-39911032(-)$1	222	57	60	8.9999
GUU	chr18:43432252-43432487(-)$1	235	8	11	8.9999
GUU	chr1:85112855-85113123(-)$1	268	39	42	8.9999
GUU	chr6:36654832-36655119(+)$1	287	16	19	8.9999
GUU	chr7:94295905-94296147(+)$1	242	94	97	8.9999
GUU	chr3:120048013-120048244(-)$1	231	88	91	8.9999
GUU	chr15:48064286-48064504(+)$1	218	30	33	8.9999
GUU	chr22:51041646-51041870(+)$1	224	73	76	8.9999
GUU	chr7:5568196-5568432(-)$1	236	87	90	8.9999
GUU	chr14:68214586-68214874(-)$1	288	6	9	8.9999
GUU	chr5:132214921-132215145(-)$1	224	12	15	8.9999
GUU	chr15:64365077-64365302(-)$1	225	40	43	8.9999
GUU	chr1:154990521-154990764(+)$1	243	69	72	8.9999
GUU	chrX:109439332-109439557(-)$1	225	40	43	8.9999
GUU	chrX:53406475-53406762(-)$1	287	107	110	8.9999
GUU	chr5:68425889-68426111(+)$1	222	10	13	8.9999
GUU	chr3:78647099-78647322(-)$1	223	5	8	8.9999
GUU	chr19:1257741-1258000(+)$1	259	126	129	8.9999
GUU	chr6:21598486-21598731(+)$1	245	80	83	8.9999
GUU	chr1:28607645-28607919(+)$1	274	179	182	8.9999
GUU	chr2:101622546-101622777(+)$1	231	62	65	8.9999
GUU	chr1:33322211-33322448(+)$1	237	121	124	8.9999
GUU	chr17:27585368-27585593(-)$1	225	2	5	8.9999
GUU	chr6:24718876-24719106(-)$1	230	13	16	8.9999
GUU	chr11:9610610-9610840(+)$1	230	95	98	8.9999
GUU	chr17:7363419-7363666(-)$1	247	52	55	8.9999
GUU	chr1:181059164-181059389(+)$1	225	66	69	8.9999
GUU	chr1:203278430-203278675(+)$1	245	82	85	8.9999
GUU	chr7:36364980-36365225(-)$1	245	70	73	8.9999
GUU	chr1:247003434-247003663(-)$1	229	33	36	8.9999
GUU	chr17:53854451-53854676(+)$1	225	4	7	8.9999
GUU	chr16:66755635-66755897(-)$1	262	7	10	8.9999
GUU	chr12:122756951-122757191(-)$1	240	6	9	8.9999
GUU	chr6:31783244-31783478(+)$1	234	133	136	8.9999
GUU	chr4:41961498-41961721(+)$1	223	71	74	8.9999
GUU	chr14:95553727-95553950(-)$1	223	79	82	8.9999
GUU	chr6:82950268-82950493(-)$1	225	140	143	8.9999
Guu	chr8:37614498-37614722(+)$1	224	5	8	8.9999
GUU	chr2:74405703-74405953(-)$1	250	208	211	8.9999
GUU	chr17:47130615-47130907(+)$1	292	0	3	8.9999
GUU	chr21:34804427-34804668(+)$1	241	18	21	8.9999
GUU	chr3:113442708-113442942(-)$1	234	45	48	8.9999
GUU	chr7:128411149-128411401(+)$1	252	25	28	8.9999
GUU	chr4:170017268-170017492(-)$1	224	5	8	8.9999
GUU	chr12:123775952-123776206(-)$1	254	19	22	8.9999
GUU	chr20:33096866-33097104(+)$1	238	55	58	8.9999
GUU	chr17:26521629-26521863(+)$1	234	105	108	8.9999
GUU	chr7:127010416-127010654(-)$1	238	41	44	8.9999
GUU	chr3:50362678-50362922(-)$1	244	43	46	8.9999

#otherMatches

#Struct PSSM
ddd	chr15:73853053-73853325(-)$1	272	0	3	8.9999
dd3	chr12:7032098-7032363(+)$1	265	68	71	8.9999
:::	chr21:28295246-28295477(-)$1	231	74	77	8.9999
ii"	chr12:8249758-8249989(+)$1	231	7	10	8.9999
c!!	chr15:60785446-60785671(-)$1	225	6	9	8.9999
eee	chr1:28607250-28607514(+)$1	264	86	89	8.9999
g&&	chr3:42707350-42707587(+)$1	237	35	38	8.9999
fff	chr6:105529014-105529245(+)$1	231	19	22	8.9999
fff	chr15:77345059-77345303(-)$1	244	39	42	8.9999
qdd	chr1:162493238-162493475(+)$1	237	20	23	8.9999
ooo	chr11:63743805-63744069(+)$1	264	48	51	8.9999
===	chr14:23794663-23794951(+)$1	288	114	117	8.9999
DDD	chr12:42481142-42481369(-)$1	227	1	4	8.9999
ppp	chr22:32080657-32080894(-)$1	237	31	34	8.9999
DDD	chr22:21982292-21982522(-)$1	230	67	70	8.9999
===	chr1:246887619-246887850(+)$1	231	15	18	8.9999
:::	chr10:93623788-93624047(+)$1	259	11	14	8.9999
eee	chr11:47800400-47800638(-)$1	238	182	185	8.9999
mmm	chr14:95553444-95553692(-)$1	248	104	107	8.9999
===	chr11:64789331-64789585(+)$1	254	64	67	8.9999
:hh	chr2:217364579-217364836(+)$1	257	61	64	8.9999
:::	chr1:155306246-155306477(-)$1	231	9	12	8.9999
ggg	chr12:12873977-12874226(+)$1	249	4	7	8.9999
ddo	chr8:61778958-61779204(+)$1	246	13	16	8.9999
GGG	chrX:24003858-24004110(-)$1	252	10	13	8.9999
eee	chr16:30535466-30535686(-)$1	220	23	26	8.9999
gcc	chr10:101910041-101910304(-)$1	263	49	52	8.9999
iii	chr11:69467086-69467334(+)$1	248	12	15	8.9999
===	chr5:179041711-179041971(-)$1	260	87	90	8.9999
ygg	chr8:95900145-95900370(-)$1	225	51	54	8.9999
DKK	chr11:35642225-35642468(+)$1	243	9	12	8.9999
HHH	chr12:56145202-56145428(+)$1	226	13	16	8.9999
ggg	chr1:15897945-15898165(+)$1	220	47	50	8.9999
[bb	chr19:13049388-13049634(+)$1	246	65	68	8.9999
fff	chr1:207218754-207218981(-)$1	227	78	81	8.9999
[dd	chr2:61765075-61765315(-)$1	240	22	25	8.9999
fff	chr16:70605737-70606010(+)$1	273	16	19	8.9999
::e	chr15:99673828-99674064(+)$1	236	85	88	8.9999
:::	chr7:27202438-27202664(-)$1	226	1	4	8.9999
eee	chr1:162497206-162497445(+)$1	239	51	54	8.9999
:::	chr1:32799708-32799946(-)$1	238	50	53	8.9999
e::	chr19:50001075-50001323(+)$1	248	41	44	8.9999
HHH	chr7:30123794-30124032(+)$1	238	63	66	8.9999
HHH	chr8:27661807-27662054(+)$1	247	28	31	8.9999
lld	chr5:150409437-150409659(-)$1	222	30	33	8.9999
ddd	chr5:148874786-148875028(-)$1	242	197	200	8.9999
:::	chr7:26230358-26230584(-)$1	226	21	24	8.9999
eeg	chr5:179157331-179157581(+)$1	250	10	13	8.9999
II:	chr16:30094002-30094230(+)$1	228	28	31	8.9999
dnn	chr2:111925802-111926070(+)$1	268	38	41	8.9999
F{I	chrX:39910810-39911032(-)$1	222	57	60	8.9999
===	chr18:43432252-43432487(-)$1	235	8	11	8.9999
ggg	chr1:85112855-85113123(-)$1	268	39	42	8.9999
GGG	chr6:36654832-36655119(+)$1	287	16	19	8.9999
:::	chr7:94295905-94296147(+)$1	242	94	97	8.9999
>>>	chr3:120048013-120048244(-)$1	231	88	91	8.9999
f''	chr15:48064286-48064504(+)$1	218	30	33	8.9999
::d	chr22:51041646-51041870(+)$1	224	73	76	8.9999
mmm	chr7:5568196-5568432(-)$1	236	87	90	8.9999
ooo	chr14:68214586-68214874(-)$1	288	6	9	8.9999
CKK	chr5:132214921-132215145(-)$1	224	12	15	8.9999
ddd	chr15:64365077-64365302(-)$1	225	40	43	8.9999
c::	chr1:154990521-154990764(+)$1	243	69	72	8.9999
fff	chrX:109439332-109439557(-)$1	225	40	43	8.9999
{EE	chrX:53406475-53406762(-)$1	287	107	110	8.9999
:::	chr5:68425889-68426111(+)$1	222	10	13	8.9999
:::	chr3:78647099-78647322(-)$1	223	5	8	8.9999
brr	chr19:1257741-1258000(+)$1	259	126	129	8.9999
eee	chr6:21598486-21598731(+)$1	245	80	83	8.9999
fff	chr1:28607645-28607919(+)$1	274	179	182	8.9999
3ee	chr2:101622546-101622777(+)$1	231	62	65	8.9999
dd:	chr1:33322211-33322448(+)$1	237	121	124	8.9999
:::	chr17:27585368-27585593(-)$1	225	2	5	8.9999
hhh	chr6:24718876-24719106(-)$1	230	13	16	8.9999
:::	chr11:9610610-9610840(+)$1	230	95	98	8.9999
h$$	chr17:7363419-7363666(-)$1	247	52	55	8.9999
b!!	chr1:181059164-181059389(+)$1	225	66	69	8.9999
ddd	chr1:203278430-203278675(+)$1	245	82	85	8.9999
cc[	chr7:36364980-36365225(-)$1	245	70	73	8.9999
::g	chr1:247003434-247003663(-)$1	229	33	36	8.9999
:::	chr17:53854451-53854676(+)$1	225	4	7	8.9999
fff	chr16:66755635-66755897(-)$1	262	7	10	8.9999
BBF	chr12:122756951-122757191(-)$1	240	6	9	8.9999
eee	chr6:31783244-31783478(+)$1	234	133	136	8.9999
^^^	chr4:41961498-41961721(+)$1	223	71	74	8.9999
ff3	chr14:95553727-95553950(-)$1	223	79	82	8.9999
===	chr6:82950268-82950493(-)$1	225	140	143	8.9999
ddd	chr8:37614498-37614722(+)$1	224	5	8	8.9999
eee	chr2:74405703-74405953(-)$1	250	208	211	8.9999
:::	chr17:47130615-47130907(+)$1	292	0	3	8.9999
eeo	chr21:34804427-34804668(+)$1	241	18	21	8.9999
fff	chr3:113442708-113442942(-)$1	234	45	48	8.9999
CCC	chr7:128411149-128411401(+)$1	252	25	28	8.9999
"ff	chr4:170017268-170017492(-)$1	224	5	8	8.9999
:::	chr12:123775952-123776206(-)$1	254	19	22	8.9999
d::	chr20:33096866-33097104(+)$1	238	55	58	8.9999
ddd	chr17:26521629-26521863(+)$1	234	105	108	8.9999
fff	chr7:127010416-127010654(-)$1	238	41	44	8.9999
eee	chr3:50362678-50362922(-)$1	244	43	46	8.9999

#DB
(((	chr15:73853053-73853325(-)$1	1	0	3	8.9999
)).	chr12:7032098-7032363(+)$1	1	68	71	8.9999
...	chr21:28295246-28295477(-)$1	1	74	77	8.9999
((.	chr12:8249758-8249989(+)$1	1	7	10	8.9999
(..	chr15:60785446-60785671(-)$1	1	6	9	8.9999
)))	chr1:28607250-28607514(+)$1	1	86	89	8.9999
(..	chr3:42707350-42707587(+)$1	1	35	38	8.9999
(((	chr6:105529014-105529245(+)$1	1	19	22	8.9999
(((	chr15:77345059-77345303(-)$1	1	39	42	8.9999
.))	chr1:162493238-162493475(+)$1	1	20	23	8.9999
...	chr11:63743805-63744069(+)$1	1	48	51	8.9999
(((	chr14:23794663-23794951(+)$1	1	114	117	8.9999
(((	chr12:42481142-42481369(-)$1	1	1	4	8.9999
...	chr22:32080657-32080894(-)$1	1	31	34	8.9999
(((	chr22:21982292-21982522(-)$1	1	67	70	8.9999
)))	chr1:246887619-246887850(+)$1	1	15	18	8.9999
...	chr10:93623788-93624047(+)$1	1	11	14	8.9999
)))	chr11:47800400-47800638(-)$1	1	182	185	8.9999
...	chr14:95553444-95553692(-)$1	1	104	107	8.9999
(((	chr11:64789331-64789585(+)$1	1	64	67	8.9999
.((	chr2:217364579-217364836(+)$1	1	61	64	8.9999
...	chr1:155306246-155306477(-)$1	1	9	12	8.9999
(((	chr12:12873977-12874226(+)$1	1	4	7	8.9999
((.	chr8:61778958-61779204(+)$1	1	13	16	8.9999
(((	chrX:24003858-24004110(-)$1	1	10	13	8.9999
)))	chr16:30535466-30535686(-)$1	1	23	26	8.9999
(((	chr10:101910041-101910304(-)$1	1	49	52	8.9999
(((	chr11:69467086-69467334(+)$1	1	12	15	8.9999
(((	chr5:179041711-179041971(-)$1	1	87	90	8.9999
.))	chr8:95900145-95900370(-)$1	1	51	54	8.9999
(..	chr11:35642225-35642468(+)$1	1	9	12	8.9999
(((	chr12:56145202-56145428(+)$1	1	13	16	8.9999
)))	chr1:15897945-15898165(+)$1	1	47	50	8.9999
.((	chr19:13049388-13049634(+)$1	1	65	68	8.9999
)))	chr1:207218754-207218981(-)$1	1	78	81	8.9999
.((	chr2:61765075-61765315(-)$1	1	22	25	8.9999
(((	chr16:70605737-70606010(+)$1	1	16	19	8.9999
..(	chr15:99673828-99674064(+)$1	1	85	88	8.9999
...	chr7:27202438-27202664(-)$1	1	1	4	8.9999
(((	chr1:162497206-162497445(+)$1	1	51	54	8.9999
...	chr1:32799708-32799946(-)$1	1	50	53	8.9999
)..	chr19:50001075-50001323(+)$1	1	41	44	8.9999
(((	chr7:30123794-30124032(+)$1	1	63	66	8.9999
(((	chr8:27661807-27662054(+)$1	1	28	31	8.9999
..)	chr5:150409437-150409659(-)$1	1	30	33	8.9999
(((	chr5:148874786-148875028(-)$1	1	197	200	8.9999
...	chr7:26230358-26230584(-)$1	1	21	24	8.9999
(((	chr5:179157331-179157581(+)$1	1	10	13	8.9999
((.	chr16:30094002-30094230(+)$1	1	28	31	8.9999
(..	chr2:111925802-111926070(+)$1	1	38	41	8.9999
(.(	chrX:39910810-39911032(-)$1	1	57	60	8.9999
(((	chr18:43432252-43432487(-)$1	1	8	11	8.9999
)))	chr1:85112855-85113123(-)$1	1	39	42	8.9999
(((	chr6:36654832-36655119(+)$1	1	16	19	8.9999
...	chr7:94295905-94296147(+)$1	1	94	97	8.9999
...	chr3:120048013-120048244(-)$1	1	88	91	8.9999
(..	chr15:48064286-48064504(+)$1	1	30	33	8.9999
..(	chr22:51041646-51041870(+)$1	1	73	76	8.9999
...	chr7:5568196-5568432(-)$1	1	87	90	8.9999
...	chr14:68214586-68214874(-)$1	1	6	9	8.9999
(..	chr5:132214921-132215145(-)$1	1	12	15	8.9999
(((	chr15:64365077-64365302(-)$1	1	40	43	8.9999
)..	chr1:154990521-154990764(+)$1	1	69	72	8.9999
(((	chrX:109439332-109439557(-)$1	1	40	43	8.9999
.((	chrX:53406475-53406762(-)$1	1	107	110	8.9999
...	chr5:68425889-68426111(+)$1	1	10	13	8.9999
...	chr3:78647099-78647322(-)$1	1	5	8	8.9999
(..	chr19:1257741-1258000(+)$1	1	126	129	8.9999
(((	chr6:21598486-21598731(+)$1	1	80	83	8.9999
)))	chr1:28607645-28607919(+)$1	1	179	182	8.9999
.))	chr2:101622546-101622777(+)$1	1	62	65	8.9999
)).	chr1:33322211-33322448(+)$1	1	121	124	8.9999
...	chr17:27585368-27585593(-)$1	1	2	5	8.9999
(((	chr6:24718876-24719106(-)$1	1	13	16	8.9999
...	chr11:9610610-9610840(+)$1	1	95	98	8.9999
(..	chr17:7363419-7363666(-)$1	1	52	55	8.9999
(..	chr1:181059164-181059389(+)$1	1	66	69	8.9999
(((	chr1:203278430-203278675(+)$1	1	82	85	8.9999
((.	chr7:36364980-36365225(-)$1	1	70	73	8.9999
..(	chr1:247003434-247003663(-)$1	1	33	36	8.9999
...	chr17:53854451-53854676(+)$1	1	4	7	8.9999
(((	chr16:66755635-66755897(-)$1	1	7	10	8.9999
(((	chr12:122756951-122757191(-)$1	1	6	9	8.9999
)))	chr6:31783244-31783478(+)$1	1	133	136	8.9999
...	chr4:41961498-41961721(+)$1	1	71	74	8.9999
)).	chr14:95553727-95553950(-)$1	1	79	82	8.9999
)))	chr6:82950268-82950493(-)$1	1	140	143	8.9999
(((	chr8:37614498-37614722(+)$1	1	5	8	8.9999
(((	chr2:74405703-74405953(-)$1	1	208	211	8.9999
...	chr17:47130615-47130907(+)$1	1	0	3	8.9999
((.	chr21:34804427-34804668(+)$1	1	18	21	8.9999
(((	chr3:113442708-113442942(-)$1	1	45	48	8.9999
(((	chr7:128411149-128411401(+)$1	1	25	28	8.9999
.((	chr4:170017268-170017492(-)$1	1	5	8	8.9999
...	chr12:123775952-123776206(-)$1	1	19	22	8.9999
)..	chr20:33096866-33097104(+)$1	1	55	58	8.9999
(((	chr17:26521629-26521863(+)$1	1	105	108	8.9999
(((	chr7:127010416-127010654(-)$1	1	41	44	8.9999
)))	chr3:50362678-50362922(-)$1	1	43	46	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m2_run2.nuc.txt

#NT
AUUUUUUU	chr10:71910234-71910474(-)$1	240	148	156	20.2500
AUUUUUUU	chr7:44922116-44922396(-)$1	280	76	84	20.2500
AGUUUUUU	chr5:110464626-110464866(+)$1	240	142	150	16.2656
AUUAUUUU	chr6:1612717-1612957(+)$1	240	29	37	15.4843
AUUUUUGU	chr3:181431163-181431403(+)$1	240	200	208	15.7187
AUUUUUUU	chr3:124947917-124948157(-)$1	240	178	186	20.2500
AUUUUAUU	chr6:47594673-47594913(+)$1	240	188	196	16.1093
AUUUAUUU	chr13:41130470-41130710(-)$1	240	106	114	16.2656
AUUUUGUU	chr3:63987710-63987950(+)$1	240	91	99	16.1093
AUUUUUUU	chr6:37300532-37300772(+)$1	240	132	140	20.2500
ACUUUUUU	chr19:34718794-34719036(+)$1	242	86	94	16.2656
AUUUCUUU	chr19:17453379-17453619(+)$1	240	170	178	15.9531
AUUUUUUU	chr4:140396301-140396541(+)$1	240	79	87	20.2500
AUUUUUUU	chr14:75129681-75129921(-)$1	240	88	96	20.2500
AUUUUAUU	chr3:149236122-149236362(-)$1	240	15	23	16.1093
AUUUAUUU	chr11:32999538-32999778(+)$1	240	81	89	16.2656
CUUUUUUU	chr16:24930734-24930974(-)$1	240	159	167	15.9531
AUUUUUUU	chr7:141357997-141358237(-)$1	240	226	234	20.2500
AUUUUUGU	chr1:25687341-25687581(+)$1	240	84	92	15.7187
AUUUGUUU	chrX:74519589-74519829(+)$1	240	155	163	16.0312
AUUUUAUU	chr16:87442011-87442251(-)$1	240	9	17	16.1093
AUUUUUUA	chr1:156712194-156712434(-)$1	240	72	80	15.5625
AUCUUUUU	chr9:5774920-5775160(+)$1	240	38	46	16.1875
ACuuuuuu	chr5:137772526-137772766(+)$1	240	62	70	16.2656
AUUUUCUU	chr4:55604728-55604968(+)$1	240	58	66	16.0312
AUUUUUUU	chr5:10265050-10265290(+)$1	240	155	163	20.2500
AUCUUUUU	chr6:110421493-110421733(-)$1	240	200	208	16.1875
AUUUUUUU	chr7:19155261-19155501(-)$1	240	40	48	20.2500
ACUUUUUU	chr9:99150157-99150437(-)$1	280	83	91	16.2656
AUUUUUUC	chr14:54944604-54944844(-)$1	240	26	34	15.6406
GUUUUUUU	chr17:65073387-65073627(-)$1	240	12	20	15.7187
AUGUUUUU	chr1:20235057-20235297(+)$1	240	64	72	16.2656
AUUUUUAU	chr21:18966092-18966372(-)$1	280	83	91	15.6406
AUUUUUUU	chr1:236371845-236372085(+)$1	240	192	200	20.2500
AUUUUCuu	chr16:58553474-58553714(+)$1	240	67	75	16.0312
CUUUUUUU	chr3:143708592-143708872(+)$1	280	107	115	15.9531
CUUUUUUU	chr15:56383057-56383297(-)$1	240	48	56	15.9531
ACUUUUUU	chr1:40026386-40026626(-)$1	240	35	43	16.2656
AUUUUUUU	chr8:105501501-105501741(-)$1	240	22	30	20.2500
AUUUGUUU	chr7:99634922-99635162(+)$1	240	39	47	16.0312
AAUUUUUU	chr14:35044880-35045120(-)$1	240	52	60	16.0312
AUUUUUUC	chr8:121550255-121550495(-)$1	240	206	214	15.6406
AUUUUUUU	chr2:203634039-203634279(+)$1	240	217	225	20.2500
AUGUUUUU	chr13:79894308-79894548(-)$1	240	27	35	16.2656
AUUUAUUU	chrX:118722664-118722904(-)$1	240	117	125	16.2656
CUUUUUUU	chr16:47189453-47189693(-)$1	240	229	237	15.9531
AGUUUUUU	chr2:11322001-11322241(-)$1	240	80	88	16.2656
AUUUUGUU	chr17:27953754-27953994(-)$1	240	47	55	16.1093
AUAUUUUU	chr12:12272601-12272841(-)$1	240	183	191	16.1093
AUUUAUUU	chr7:102742196-102742436(-)$1	240	187	195	16.2656
AGUUUUUU	chr2:64859849-64860089(-)$1	240	63	71	16.2656
AUUUUUUU	chr12:56366384-56366624(+)$1	240	74	82	20.2500
AUAUUUUU	chr6:160176541-160176781(+)$1	240	101	109	16.1093
AUUUUUUU	chr6:126360174-126360414(+)$1	240	67	75	20.2500
AUUGUUUU	chr5:54711804-54712044(+)$1	240	213	221	15.4843
AUUUUUUU	chr3:160137183-160137423(+)$1	240	206	214	20.2500
AUUUUUCU	chr2:182794792-182795032(+)$1	240	126	134	15.6406
AGUUUUUU	chrX:133634328-133634568(+)$1	240	98	106	16.2656
AUUUAUUU	chr9:138701409-138701649(-)$1	240	169	177	16.2656
AUGuuuuu	chr6:132781753-132781993(-)$1	240	160	168	16.2656
auuuuuuu	chr6:15520441-15520681(+)$1	240	72	80	20.2500
AUCUUUUU	chr2:64320430-64320670(-)$1	240	135	143	16.1875
AUGUUUUU	chr5:95131923-95132163(+)$1	240	86	94	16.2656

#otherMatches

#Struct PSSM
G::::ccc	chr19:16628607-16628847(-)$1	240	12	20	16.1093
::::::::	chr10:71910234-71910474(-)$1	240	148	156	20.2500
c[cccmmm	chr7:44922116-44922396(-)$1	280	76	84	20.2500
2bb:::::	chr5:110464626-110464866(+)$1	240	142	150	16.2656
dooooood	chr6:1612717-1612957(+)$1	240	29	37	15.4843
mmdddd]b	chr3:181431163-181431403(+)$1	240	200	208	15.7187
:::::ggg	chr3:124947917-124948157(-)$1	240	178	186	20.2500
JJJJJJJ}	chr6:47594673-47594913(+)$1	240	188	196	16.1093
^^^^^^^^	chr13:41130470-41130710(-)$1	240	106	114	16.2656
nnnndddd	chr3:63987710-63987950(+)$1	240	91	99	16.1093
]ccc22gg	chr6:37300532-37300772(+)$1	240	132	140	20.2500
%%%%gggg	chr19:34718794-34719036(+)$1	242	86	94	16.2656
ccdddddd	chr19:17453379-17453619(+)$1	240	170	178	15.9531
hhhhhhhh	chr4:140396301-140396541(+)$1	240	79	87	20.2500
::======	chr14:75129681-75129921(-)$1	240	88	96	20.2500
mmffffff	chr3:149236122-149236362(-)$1	240	15	23	16.1093
iiiiiiii	chr11:32999538-32999778(+)$1	240	81	89	16.2656
::::::::	chr16:24930734-24930974(-)$1	240	159	167	15.9531
C~~~~DDD	chr7:141357997-141358237(-)$1	240	226	234	20.2500
::::ccc[	chr1:25687341-25687581(+)$1	240	84	92	15.7187
???EEEEE	chrX:74519589-74519829(+)$1	240	155	163	16.0312
::::::::	chr16:87442011-87442251(-)$1	240	9	17	16.1093
oddddeee	chr1:156712194-156712434(-)$1	240	72	80	15.5625
[eeeee[d	chr9:5774920-5775160(+)$1	240	38	46	16.1875
ffffff[c	chr5:137772526-137772766(+)$1	240	62	70	16.2656
xxxxxxxx	chr4:55604728-55604968(+)$1	240	58	66	16.0312
========	chr5:10265050-10265290(+)$1	240	155	163	20.2500
%%%%%ggg	chr6:110421493-110421733(-)$1	240	200	208	16.1875
hhhhhhhc	chr7:19155261-19155501(-)$1	240	40	48	20.2500
::::eeee	chr9:99150157-99150437(-)$1	280	83	91	16.2656
c####eee	chr14:54944604-54944844(-)$1	240	26	34	15.6406
yyyyyyyy	chr17:65073387-65073627(-)$1	240	12	20	15.7187
eee333ff	chr1:20235057-20235297(+)$1	240	64	72	16.2656
::::::::	chr21:18966092-18966372(-)$1	280	83	91	15.6406
gnnnnngg	chr1:236371845-236372085(+)$1	240	192	200	20.2500
:HHHHHHH	chr16:58553474-58553714(+)$1	240	67	75	16.0312
ttttttcc	chr3:143708592-143708872(+)$1	280	107	115	15.9531
^^^^^^^^	chr15:56383057-56383297(-)$1	240	48	56	15.9531
##======	chr1:40026386-40026626(-)$1	240	35	43	16.2656
iiiiiiif	chr8:105501501-105501741(-)$1	240	22	30	20.2500
2iiiiiii	chr7:99634922-99635162(+)$1	240	39	47	16.0312
eee::JJJ	chr14:35044880-35045120(-)$1	240	52	60	16.0312
gg22hhhh	chr8:121550255-121550495(-)$1	240	206	214	15.6406
hhhh::::	chr2:203634039-203634279(+)$1	240	217	225	20.2500
dddmmmmd	chr13:79894308-79894548(-)$1	240	27	35	16.2656
++++++++	chrX:118722664-118722904(-)$1	240	117	125	16.2656
CJJJJJJJ	chr16:47189453-47189693(-)$1	240	229	237	15.9531
ndddd555	chr2:11322001-11322241(-)$1	240	80	88	16.2656
::::::::	chr17:27953754-27953994(-)$1	240	47	55	16.1093
::::::::	chr12:12272601-12272841(-)$1	240	183	191	16.1093
wwwwwwww	chr7:102742196-102742436(-)$1	240	187	195	16.2656
hhhhhhh:	chr2:64859849-64860089(-)$1	240	63	71	16.2656
m=======	chr12:56366384-56366624(+)$1	240	74	82	20.2500
ffffff::	chr6:160176541-160176781(+)$1	240	101	109	16.1093
eeeee:::	chr6:126360174-126360414(+)$1	240	67	75	20.2500
:ffffffn	chr5:54711804-54712044(+)$1	240	213	221	15.4843
>>>>>>>f	chr3:160137183-160137423(+)$1	240	206	214	20.2500
e]ffffff	chr2:182794792-182795032(+)$1	240	126	134	15.6406
iiiimmmm	chrX:133634328-133634568(+)$1	240	98	106	16.2656
::::::::	chr9:138701409-138701649(-)$1	240	169	177	16.2656
66iiiiii	chr6:132781753-132781993(-)$1	240	160	168	16.2656
dooooood	chr6:15520441-15520681(+)$1	240	72	80	20.2500
eooooooe	chr2:64320430-64320670(-)$1	240	135	143	16.1875
ssssseee	chr5:95131923-95132163(+)$1	240	86	94	16.2656

#DB
(....(((	chr19:16628607-16628847(-)$1	1	12	20	16.1093
........	chr10:71910234-71910474(-)$1	1	148	156	20.2500
(.(((...	chr7:44922116-44922396(-)$1	1	76	84	20.2500
.)).....	chr5:110464626-110464866(+)$1	1	142	150	16.2656
(......)	chr6:1612717-1612957(+)$1	1	29	37	15.4843
..)))).)	chr3:181431163-181431403(+)$1	1	200	208	15.7187
.....(((	chr3:124947917-124948157(-)$1	1	178	186	20.2500
))))))).	chr6:47594673-47594913(+)$1	1	188	196	16.1093
........	chr13:41130470-41130710(-)$1	1	106	114	16.2656
....))))	chr3:63987710-63987950(+)$1	1	91	99	16.1093
.)))..))	chr6:37300532-37300772(+)$1	1	132	140	20.2500
....((((	chr19:34718794-34719036(+)$1	1	86	94	16.2656
((((((((	chr19:17453379-17453619(+)$1	1	170	178	15.9531
((((((((	chr4:140396301-140396541(+)$1	1	79	87	20.2500
..((((((	chr14:75129681-75129921(-)$1	1	88	96	20.2500
..))))))	chr3:149236122-149236362(-)$1	1	15	23	16.1093
)))))))(	chr11:32999538-32999778(+)$1	1	81	89	16.2656
........	chr16:24930734-24930974(-)$1	1	159	167	15.9531
)....)))	chr7:141357997-141358237(-)$1	1	226	234	20.2500
....(((.	chr1:25687341-25687581(+)$1	1	84	92	15.7187
...)))))	chrX:74519589-74519829(+)$1	1	155	163	16.0312
........	chr16:87442011-87442251(-)$1	1	9	17	16.1093
.))))(((	chr1:156712194-156712434(-)$1	1	72	80	15.5625
.(((((.(	chr9:5774920-5775160(+)$1	1	38	46	16.1875
((((((.(	chr5:137772526-137772766(+)$1	1	62	70	16.2656
........	chr4:55604728-55604968(+)$1	1	58	66	16.0312
))))))))	chr5:10265050-10265290(+)$1	1	155	163	20.2500
.....(((	chr6:110421493-110421733(-)$1	1	200	208	16.1875
))))))))	chr7:19155261-19155501(-)$1	1	40	48	20.2500
....((((	chr9:99150157-99150437(-)$1	1	83	91	16.2656
(....(((	chr14:54944604-54944844(-)$1	1	26	34	15.6406
........	chr17:65073387-65073627(-)$1	1	12	20	15.7187
)))...))	chr1:20235057-20235297(+)$1	1	64	72	16.2656
........	chr21:18966092-18966372(-)$1	1	83	91	15.6406
(.....))	chr1:236371845-236372085(+)$1	1	192	200	20.2500
.(((((((	chr16:58553474-58553714(+)$1	1	67	75	16.0312
......))	chr3:143708592-143708872(+)$1	1	107	115	15.9531
........	chr15:56383057-56383297(-)$1	1	48	56	15.9531
..((((((	chr1:40026386-40026626(-)$1	1	35	43	16.2656
((((((((	chr8:105501501-105501741(-)$1	1	22	30	20.2500
.)))))))	chr7:99634922-99635162(+)$1	1	39	47	16.0312
)))..)))	chr14:35044880-35045120(-)$1	1	52	60	16.0312
))..))))	chr8:121550255-121550495(-)$1	1	206	214	15.6406
))))....	chr2:203634039-203634279(+)$1	1	217	225	20.2500
(((....)	chr13:79894308-79894548(-)$1	1	27	35	16.2656
........	chrX:118722664-118722904(-)$1	1	117	125	16.2656
))))))))	chr16:47189453-47189693(-)$1	1	229	237	15.9531
.))))...	chr2:11322001-11322241(-)$1	1	80	88	16.2656
........	chr17:27953754-27953994(-)$1	1	47	55	16.1093
........	chr12:12272601-12272841(-)$1	1	183	191	16.1093
........	chr7:102742196-102742436(-)$1	1	187	195	16.2656
))))))).	chr2:64859849-64860089(-)$1	1	63	71	16.2656
.)))))))	chr12:56366384-56366624(+)$1	1	74	82	20.2500
))))))..	chr6:160176541-160176781(+)$1	1	101	109	16.1093
)))))...	chr6:126360174-126360414(+)$1	1	67	75	20.2500
.((((((.	chr5:54711804-54712044(+)$1	1	213	221	15.4843
.......)	chr3:160137183-160137423(+)$1	1	206	214	20.2500
).))))))	chr2:182794792-182795032(+)$1	1	126	134	15.6406
((((....	chrX:133634328-133634568(+)$1	1	98	106	16.2656
........	chr9:138701409-138701649(-)$1	1	169	177	16.2656
..))))))	chr6:132781753-132781993(-)$1	1	160	168	16.2656
(......)	chr6:15520441-15520681(+)$1	1	72	80	20.2500
(......)	chr2:64320430-64320670(-)$1	1	135	143	16.1875
.....)))	chr5:95131923-95132163(+)$1	1	86	94	16.2656

#PSSM
A : 0.90	C : 0.06	G : 0.01	a : 0.01	
U : 0.84	G : 0.06	C : 0.06	A : 0.01	u : 0.01	
U : 0.82	G : 0.06	C : 0.04	u : 0.03	A : 0.03	
U : 0.92	u : 0.04	A : 0.01	G : 0.01	
U : 0.82	A : 0.07	u : 0.04	G : 0.03	C : 0.01	
U : 0.82	G : 0.04	A : 0.04	u : 0.04	C : 0.03	
U : 0.87	u : 0.06	G : 0.03	A : 0.01	C : 0.01	
U : 0.89	u : 0.06	C : 0.03	A : 0.01	

#score	1094.125
#seq	64
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m3_run2.nuc.txt

#NT
cauccauucauccaugcauccaucuguccauucauccauccauccauccauccaucuaaccauccauccauccaggcauccaugcauccauccacuuguucauucauccauucaggcaugcaccaguccuugcauccauccaugcauccaccuguccauccauccauccauccauccauccauccauccauccaugcaucaacccaugcauccaccuguccauccauccauccauccaugcauccaccuguccauucauccauccaauuauccauccauccaauuauccauccauccauccauccauccauccgugcaucaa	chr11:63881308-63881796(-)$1	488	74	396	646.0000

#otherMatches

#Struct PSSM
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::ddddqqqqqqqqdddd:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::	chr6:109200305-109200641(+)$1	336	2	324	646.0000
:::::::::::::ffffff$$$$$dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd333ffffff:::::::::::::::::::::::::DDDD{EEEEE:ccc####eeeeeooooooeeeee55555ccc:::::::::::::::::::::::::::::::::::::::ffffffooooooffffff:::::::::::::::::::::::::::EEEEEZZZDDDD:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::ffffffooo	chr11:63881308-63881796(-)$1	488	74	396	646.0000

#DB
.......................................................................................................................................................................................................................................((((........))))...........................................................................	chr6:109200305-109200641(+)$1	1	2	324	646.0000
.............((((((.....((((..............................................))))...)))))).........................((((.(((((.(((....(((((......))))).....))).......................................((((((......))))))...........................)))))...))))...............................................................((((((...	chr11:63881308-63881796(-)$1	1	74	396	646.0000

#PSSM
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
u : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 0.50	u : 0.50	
a : 0.50	g : 0.50	
u : 1.00	
c : 1.00	
c : 1.00	
g : 0.50	a : 0.50	
c : 0.50	u : 0.50	
u : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
a : 0.50	c : 0.50	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 1.00	
c : 0.50	u : 0.50	
a : 1.00	
c : 0.50	a : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 0.50	g : 0.50	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 0.50	c : 0.50	
c : 0.50	u : 0.50	
u : 1.00	
g : 1.00	
u : 1.00	
c : 0.50	u : 0.50	
u : 0.50	c : 0.50	
a : 1.00	
c : 0.50	u : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 1.00	
u : 0.50	g : 0.50	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
a : 0.50	g : 0.50	
u : 0.50	c : 0.50	
a : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
u : 0.50	a : 0.50	
c : 0.50	g : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 0.50	u : 0.50	
u : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
u : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
c : 0.50	u : 0.50	
a : 0.50	g : 0.50	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
u : 0.50	c : 0.50	
g : 0.50	a : 0.50	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	a : 0.50	
a : 1.00	
c : 1.00	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 0.50	c : 0.50	
c : 1.00	
c : 0.50	u : 0.50	
a : 0.50	g : 0.50	
u : 1.00	
a : 0.50	c : 0.50	
u : 0.50	c : 0.50	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
c : 0.50	u : 0.50	
c : 1.00	
c : 1.00	
a : 1.00	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
g : 0.50	a : 0.50	
u : 1.00	
c : 1.00	
u : 0.50	c : 0.50	
a : 1.00	
c : 0.50	u : 0.50	
c : 0.50	g : 0.50	
c : 1.00	
a : 1.00	
u : 1.00	
g : 0.50	c : 0.50	
c : 1.00	
a : 1.00	
g : 0.50	c : 0.50	
c : 1.00	
u : 1.00	
a : 0.50	g : 0.50	
g : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
u : 1.00	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	a : 0.50	
u : 1.00	
a : 0.50	u : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
a : 0.50	u : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
a : 0.50	u : 0.50	
u : 0.50	c : 0.50	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
c : 0.50	u : 0.50	
u : 0.50	c : 0.50	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	a : 0.50	
u : 1.00	
c : 1.00	
a : 0.50	c : 0.50	
u : 0.50	g : 0.50	
c : 0.50	u : 0.50	
c : 0.50	g : 0.50	
a : 0.50	c : 0.50	
c : 0.50	a : 0.50	
c : 0.50	u : 0.50	
c : 1.00	
a : 1.00	
u : 0.50	a : 0.50	

#score	1292.0
#seq	2
#width	322
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_transcript_m2_run2.nuc.txt

#NT
ACU	chr2:208598347-208598623(+)$1	276	22	25	9.0000
ACU	chr1:145335044-145335283(+)$1	239	14	17	9.0000
ACU	chr3:13675352-13675611(+)$1	259	20	23	9.0000
ACU	chr6:106652746-106653007(-)$1	261	42	45	9.0000
ACU	chr8:38847090-38847338(-)$1	248	98	101	9.0000
acu	chr9:6235909-6236163(+)$1	254	27	30	9.0000
ACU	chr13:99456404-99456650(-)$1	246	122	125	9.0000
acu	chr5:159645134-159645351(+)$1	217	64	67	9.0000
acu	chr6:158751573-158751830(+)$1	257	23	26	9.0000
ACU	chr8:120757834-120758056(-)$1	222	91	94	9.0000
ACU	chr2:97626937-97627180(-)$1	243	156	159	9.0000
ACU	chr13:73321335-73321559(+)$1	224	14	17	9.0000
ACU	chr3:54780559-54780774(+)$1	215	13	16	9.0000
acu	chr3:129179004-129179242(+)$1	238	92	95	9.0000
ACU	chr7:100159982-100160229(+)$1	247	137	140	9.0000
acu	chr1:151877711-151878019(-)$1	308	23	26	9.0000
acu	chr6:3101642-3101876(+)$1	234	6	9	9.0000
ACU	chr22:23428814-23429035(-)$1	221	27	30	9.0000
ACU	chr11:125249641-125249856(+)$1	215	2	5	9.0000
acu	chr1:92265763-92266020(-)$1	257	10	13	9.0000
ACU	chr4:103787609-103787838(-)$1	229	14	17	9.0000
ACU	chr20:20485355-20485623(-)$1	268	84	87	9.0000
acu	chr8:103395002-103395259(-)$1	257	14	17	9.0000
ACU	chr6:45485264-45485508(+)$1	244	111	114	9.0000
acu	chr3:52240846-52241063(+)$1	217	74	77	9.0000
ACU	chr6:152279832-152280055(+)$1	223	114	117	9.0000
ACU	chr18:77056249-77056480(+)$1	231	61	64	9.0000
ACU	chr2:150243314-150243528(+)$1	214	28	31	9.0000
ACU	chr1:7833737-7833966(+)$1	229	8	11	9.0000
ACU	chr2:70509335-70509573(-)$1	238	115	118	9.0000
acu	chr8:61758347-61758575(+)$1	228	8	11	9.0000
ACU	chr5:78126195-78126443(-)$1	248	29	32	9.0000
ACU	chr9:117661887-117662236(-)$1	349	45	48	9.0000
ACU	chr1:46183963-46184182(-)$1	219	136	139	9.0000
ACU	chr4:103261960-103262254(-)$1	294	16	19	9.0000
ACU	chr1:18637534-18637754(+)$1	220	165	168	9.0000
ACU	chr1:174809281-174809519(+)$1	238	132	135	9.0000
ACU	chr8:26380738-26380961(+)$1	223	44	47	9.0000
ACU	chr19:20218952-20219166(+)$1	214	76	79	9.0000
ACU	chr1:24221632-24221851(-)$1	219	100	103	9.0000
ACU	chr2:231622397-231622653(+)$1	256	26	29	9.0000
acu	chr8:100079591-100079810(+)$1	219	56	59	9.0000
acu	chr2:178123044-178123337(-)$1	293	94	97	9.0000
ACU	chr8:141957561-141957788(-)$1	227	64	67	9.0000
ACU	chr3:17271810-17272088(-)$1	278	8	11	9.0000
acu	chr6:90976335-90976604(-)$1	269	46	49	9.0000
acu	chr1:115112058-115112306(-)$1	248	54	57	9.0000
ACU	chr1:42371204-42371442(-)$1	238	14	17	9.0000
acu	chr7:70229803-70230046(+)$1	243	77	80	9.0000
acu	chr2:201408621-201408852(+)$1	231	23	26	9.0000
acu	chr1:89292140-89292384(+)$1	244	169	172	9.0000
acu	chr4:86652021-86652239(+)$1	218	46	49	9.0000
acu	chr8:42769655-42769875(+)$1	220	23	26	9.0000
ACU	chrX:64959646-64959955(+)$1	309	24	27	9.0000
ACU	chr17:6019632-6019855(+)$1	223	74	77	9.0000
acu	chr2:75884986-75885236(+)$1	250	113	116	9.0000
acu	chr20:51735482-51735777(+)$1	295	43	46	9.0000
acu	chr3:12402199-12402431(+)$1	232	49	52	9.0000
ACU	chr18:72409616-72409850(+)$1	234	32	35	9.0000
acu	chrX:117545867-117546085(+)$1	218	29	32	9.0000
ACU	chr3:12557139-12557429(+)$1	290	9	12	9.0000
acu	chr4:81862983-81863196(+)$1	213	20	23	9.0000
acu	chr8:94728737-94728951(+)$1	214	25	28	9.0000
ACU	chr2:222422866-222423158(-)$1	292	42	45	9.0000
acu	chr1:42036291-42036513(-)$1	222	105	108	9.0000
ACU	chr5:125824675-125824890(+)$1	215	166	169	9.0000
ACU	chr12:41445587-41445841(+)$1	254	56	59	9.0000
ACU	chr14:45601949-45602208(-)$1	259	51	54	9.0000
ACU	chr8:37693451-37693719(+)$1	268	219	222	9.0000
acu	chr1:244598413-244598645(-)$1	232	38	41	9.0000
ACU	chr18:60969654-60969925(-)$1	271	44	47	9.0000
ACU	chr16:48385938-48386190(+)$1	252	0	3	9.0000
acu	chrX:70790911-70791175(+)$1	264	28	31	9.0000
ACU	chr15:69619794-69620013(+)$1	219	25	28	9.0000
ACU	chr3:143158835-143159059(-)$1	224	108	111	9.0000
ACU	chr4:8407311-8407544(-)$1	233	16	19	9.0000
ACU	chr3:160119859-160120102(+)$1	243	39	42	9.0000
ACU	chrX:9522334-9522558(+)$1	224	25	28	9.0000
ACU	chr5:78576081-78576336(+)$1	255	28	31	9.0000
ACU	chr2:233680352-233680580(+)$1	228	102	105	9.0000
acu	chr7:110788675-110788939(-)$1	264	18	21	9.0000
ACU	chr6:5392854-5393114(+)$1	260	45	48	9.0000
ACu	chr1:10350003-10350239(+)$1	236	111	114	9.0000
ACU	chr10:37490799-37491013(+)$1	214	50	53	9.0000
acu	chr11:126192186-126192404(+)$1	218	3	6	9.0000
ACU	chr9:33135780-33136031(-)$1	251	24	27	9.0000
acu	chr9:88918842-88919064(-)$1	222	108	111	9.0000
ACU	chr11:17320480-17320756(+)$1	276	119	122	9.0000
acu	chr3:141263472-141263744(+)$1	272	29	32	9.0000
ACU	chr18:6565094-6565320(+)$1	226	101	104	9.0000
ACU	chr15:25614201-25614433(-)$1	232	26	29	9.0000
ACU	chr18:13410643-13410857(+)$1	214	110	113	9.0000
ACU	chr7:70029516-70029730(+)$1	214	110	113	9.0000
acu	chr2:234171031-234171311(+)$1	280	232	235	9.0000
acu	chr8:105031277-105031503(+)$1	226	37	40	9.0000
acu	chr3:156577429-156577665(+)$1	236	104	107	9.0000
ACU	chr18:32821120-32821366(+)$1	246	83	86	9.0000

#otherMatches

#Struct PSSM
eee	chr10:31781632-31781868(+)$1	236	52	55	9.0000
vvv	chr2:208598347-208598623(+)$1	276	22	25	9.0000
HH:	chr1:145335044-145335283(+)$1	239	14	17	9.0000
GGG	chr3:13675352-13675611(+)$1	259	20	23	9.0000
:cc	chr6:106652746-106653007(-)$1	261	42	45	9.0000
ddd	chr8:38847090-38847338(-)$1	248	98	101	9.0000
ppp	chr9:6235909-6236163(+)$1	254	27	30	9.0000
!dd	chr13:99456404-99456650(-)$1	246	122	125	9.0000
nnn	chr5:159645134-159645351(+)$1	217	64	67	9.0000
CCC	chr6:158751573-158751830(+)$1	257	23	26	9.0000
hhb	chr8:120757834-120758056(-)$1	222	91	94	9.0000
mme	chr2:97626937-97627180(-)$1	243	156	159	9.0000
B::	chr13:73321335-73321559(+)$1	224	14	17	9.0000
GCC	chr3:54780559-54780774(+)$1	215	13	16	9.0000
ggg	chr3:129179004-129179242(+)$1	238	92	95	9.0000
uuu	chr7:100159982-100160229(+)$1	247	137	140	9.0000
{EE	chr1:151877711-151878019(-)$1	308	23	26	9.0000
"""	chr6:3101642-3101876(+)$1	234	6	9	9.0000
LLL	chr22:23428814-23429035(-)$1	221	27	30	9.0000
:dd	chr11:125249641-125249856(+)$1	215	2	5	9.0000
nnn	chr1:92265763-92266020(-)$1	257	10	13	9.0000
KDD	chr4:103787609-103787838(-)$1	229	14	17	9.0000
::d	chr20:20485355-20485623(-)$1	268	84	87	9.0000
&&&	chr8:103395002-103395259(-)$1	257	14	17	9.0000
E::	chr6:45485264-45485508(+)$1	244	111	114	9.0000
bb]	chr3:52240846-52241063(+)$1	217	74	77	9.0000
ggg	chr6:152279832-152280055(+)$1	223	114	117	9.0000
e]a	chr18:77056249-77056480(+)$1	231	61	64	9.0000
FFF	chr2:150243314-150243528(+)$1	214	28	31	9.0000
FMM	chr1:7833737-7833966(+)$1	229	8	11	9.0000
::e	chr2:70509335-70509573(-)$1	238	115	118	9.0000
dap	chr8:61758347-61758575(+)$1	228	8	11	9.0000
d]c	chr5:78126195-78126443(-)$1	248	29	32	9.0000
zzz	chr9:117661887-117662236(-)$1	349	45	48	9.0000
ddd	chr1:46183963-46184182(-)$1	219	136	139	9.0000
DDM	chr4:103261960-103262254(-)$1	294	16	19	9.0000
JJJ	chr1:18637534-18637754(+)$1	220	165	168	9.0000
GGG	chr1:174809281-174809519(+)$1	238	132	135	9.0000
SSS	chr8:26380738-26380961(+)$1	223	44	47	9.0000
www	chr19:20218952-20219166(+)$1	214	76	79	9.0000
cc"	chr1:24221632-24221851(-)$1	219	100	103	9.0000
'dd	chr2:231622397-231622653(+)$1	256	26	29	9.0000
FFD	chr8:100079591-100079810(+)$1	219	56	59	9.0000
::b	chr2:178123044-178123337(-)$1	293	94	97	9.0000
:::	chr8:141957561-141957788(-)$1	227	64	67	9.0000
:EE	chr3:17271810-17272088(-)$1	278	8	11	9.0000
eee	chr6:90976335-90976604(-)$1	269	46	49	9.0000
:EE	chr1:115112058-115112306(-)$1	248	54	57	9.0000
b[e	chr1:42371204-42371442(-)$1	238	14	17	9.0000
bbz	chr7:70229803-70230046(+)$1	243	77	80	9.0000
::e	chr2:201408621-201408852(+)$1	231	23	26	9.0000
bcc	chr1:89292140-89292384(+)$1	244	169	172	9.0000
fff	chr4:86652021-86652239(+)$1	218	46	49	9.0000
c[c	chr8:42769655-42769875(+)$1	220	23	26	9.0000
[a[	chrX:64959646-64959955(+)$1	309	24	27	9.0000
CCD	chr17:6019632-6019855(+)$1	223	74	77	9.0000
d::	chr2:75884986-75885236(+)$1	250	113	116	9.0000
bb[	chr20:51735482-51735777(+)$1	295	43	46	9.0000
555	chr3:12402199-12402431(+)$1	232	49	52	9.0000
::f	chr18:72409616-72409850(+)$1	234	32	35	9.0000
l==	chrX:117545867-117546085(+)$1	218	29	32	9.0000
:::	chr3:12557139-12557429(+)$1	290	9	12	9.0000
:::	chr4:81862983-81863196(+)$1	213	20	23	9.0000
uuu	chr8:94728737-94728951(+)$1	214	25	28	9.0000
ccr	chr2:222422866-222423158(-)$1	292	42	45	9.0000
fff	chr1:42036291-42036513(-)$1	222	105	108	9.0000
eee	chr5:125824675-125824890(+)$1	215	166	169	9.0000
&&&	chr12:41445587-41445841(+)$1	254	56	59	9.0000
dnn	chr14:45601949-45602208(-)$1	259	51	54	9.0000
ggg	chr8:37693451-37693719(+)$1	268	219	222	9.0000
ii!	chr1:244598413-244598645(-)$1	232	38	41	9.0000
:cc	chr18:60969654-60969925(-)$1	271	44	47	9.0000
:dd	chr16:48385938-48386190(+)$1	252	0	3	9.0000
qqq	chrX:70790911-70791175(+)$1	264	28	31	9.0000
:BB	chr15:69619794-69620013(+)$1	219	25	28	9.0000
f((	chr3:143158835-143159059(-)$1	224	108	111	9.0000
DKK	chr4:8407311-8407544(-)$1	233	16	19	9.0000
:::	chr3:160119859-160120102(+)$1	243	39	42	9.0000
BB{	chrX:9522334-9522558(+)$1	224	25	28	9.0000
C{C	chr5:78576081-78576336(+)$1	255	28	31	9.0000
llc	chr2:233680352-233680580(+)$1	228	102	105	9.0000
===	chr7:110788675-110788939(-)$1	264	18	21	9.0000
[bb	chr6:5392854-5393114(+)$1	260	45	48	9.0000
c22	chr1:10350003-10350239(+)$1	236	111	114	9.0000
gDD	chr10:37490799-37491013(+)$1	214	50	53	9.0000
:::	chr11:126192186-126192404(+)$1	218	3	6	9.0000
dmm	chr9:33135780-33136031(-)$1	251	24	27	9.0000
^^^	chr9:88918842-88919064(-)$1	222	108	111	9.0000
FFF	chr11:17320480-17320756(+)$1	276	119	122	9.0000
===	chr3:141263472-141263744(+)$1	272	29	32	9.0000
eee	chr18:6565094-6565320(+)$1	226	101	104	9.0000
IIE	chr15:25614201-25614433(-)$1	232	26	29	9.0000
EEE	chr18:13410643-13410857(+)$1	214	110	113	9.0000
hhh	chr7:70029516-70029730(+)$1	214	110	113	9.0000
^^^	chr2:234171031-234171311(+)$1	280	232	235	9.0000
mmf	chr8:105031277-105031503(+)$1	226	37	40	9.0000
>>>	chr3:156577429-156577665(+)$1	236	104	107	9.0000
ooe	chr18:32821120-32821366(+)$1	246	83	86	9.0000

#DB
(((	chr10:31781632-31781868(+)$1	1	52	55	9.0000
...	chr2:208598347-208598623(+)$1	1	22	25	9.0000
((.	chr1:145335044-145335283(+)$1	1	14	17	9.0000
(((	chr3:13675352-13675611(+)$1	1	20	23	9.0000
.((	chr6:106652746-106653007(-)$1	1	42	45	9.0000
(((	chr8:38847090-38847338(-)$1	1	98	101	9.0000
...	chr9:6235909-6236163(+)$1	1	27	30	9.0000
.((	chr13:99456404-99456650(-)$1	1	122	125	9.0000
...	chr5:159645134-159645351(+)$1	1	64	67	9.0000
(((	chr6:158751573-158751830(+)$1	1	23	26	9.0000
(((	chr8:120757834-120758056(-)$1	1	91	94	9.0000
..)	chr2:97626937-97627180(-)$1	1	156	159	9.0000
(..	chr13:73321335-73321559(+)$1	1	14	17	9.0000
(((	chr3:54780559-54780774(+)$1	1	13	16	9.0000
(((	chr3:129179004-129179242(+)$1	1	92	95	9.0000
...	chr7:100159982-100160229(+)$1	1	137	140	9.0000
.((	chr1:151877711-151878019(-)$1	1	23	26	9.0000
...	chr6:3101642-3101876(+)$1	1	6	9	9.0000
...	chr22:23428814-23429035(-)$1	1	27	30	9.0000
.((	chr11:125249641-125249856(+)$1	1	2	5	9.0000
...	chr1:92265763-92266020(-)$1	1	10	13	9.0000
.((	chr4:103787609-103787838(-)$1	1	14	17	9.0000
..(	chr20:20485355-20485623(-)$1	1	84	87	9.0000
...	chr8:103395002-103395259(-)$1	1	14	17	9.0000
)..	chr6:45485264-45485508(+)$1	1	111	114	9.0000
)).	chr3:52240846-52241063(+)$1	1	74	77	9.0000
)))	chr6:152279832-152280055(+)$1	1	114	117	9.0000
).)	chr18:77056249-77056480(+)$1	1	61	64	9.0000
(((	chr2:150243314-150243528(+)$1	1	28	31	9.0000
(..	chr1:7833737-7833966(+)$1	1	8	11	9.0000
..(	chr2:70509335-70509573(-)$1	1	115	118	9.0000
((.	chr8:61758347-61758575(+)$1	1	8	11	9.0000
).)	chr5:78126195-78126443(-)$1	1	29	32	9.0000
...	chr9:117661887-117662236(-)$1	1	45	48	9.0000
)))	chr1:46183963-46184182(-)$1	1	136	139	9.0000
((.	chr4:103261960-103262254(-)$1	1	16	19	9.0000
)))	chr1:18637534-18637754(+)$1	1	165	168	9.0000
(((	chr1:174809281-174809519(+)$1	1	132	135	9.0000
...	chr8:26380738-26380961(+)$1	1	44	47	9.0000
...	chr19:20218952-20219166(+)$1	1	76	79	9.0000
((.	chr1:24221632-24221851(-)$1	1	100	103	9.0000
.((	chr2:231622397-231622653(+)$1	1	26	29	9.0000
(((	chr8:100079591-100079810(+)$1	1	56	59	9.0000
..(	chr2:178123044-178123337(-)$1	1	94	97	9.0000
...	chr8:141957561-141957788(-)$1	1	64	67	9.0000
.((	chr3:17271810-17272088(-)$1	1	8	11	9.0000
)))	chr6:90976335-90976604(-)$1	1	46	49	9.0000
.((	chr1:115112058-115112306(-)$1	1	54	57	9.0000
(.(	chr1:42371204-42371442(-)$1	1	14	17	9.0000
((.	chr7:70229803-70230046(+)$1	1	77	80	9.0000
..(	chr2:201408621-201408852(+)$1	1	23	26	9.0000
(((	chr1:89292140-89292384(+)$1	1	169	172	9.0000
)))	chr4:86652021-86652239(+)$1	1	46	49	9.0000
(.(	chr8:42769655-42769875(+)$1	1	23	26	9.0000
.(.	chrX:64959646-64959955(+)$1	1	24	27	9.0000
(((	chr17:6019632-6019855(+)$1	1	74	77	9.0000
)..	chr2:75884986-75885236(+)$1	1	113	116	9.0000
((.	chr20:51735482-51735777(+)$1	1	43	46	9.0000
...	chr3:12402199-12402431(+)$1	1	49	52	9.0000
..(	chr18:72409616-72409850(+)$1	1	32	35	9.0000
.))	chrX:117545867-117546085(+)$1	1	29	32	9.0000
...	chr3:12557139-12557429(+)$1	1	9	12	9.0000
...	chr4:81862983-81863196(+)$1	1	20	23	9.0000
...	chr8:94728737-94728951(+)$1	1	25	28	9.0000
((.	chr2:222422866-222423158(-)$1	1	42	45	9.0000
)))	chr1:42036291-42036513(-)$1	1	105	108	9.0000
(((	chr5:125824675-125824890(+)$1	1	166	169	9.0000
...	chr12:41445587-41445841(+)$1	1	56	59	9.0000
(..	chr14:45601949-45602208(-)$1	1	51	54	9.0000
(((	chr8:37693451-37693719(+)$1	1	219	222	9.0000
((.	chr1:244598413-244598645(-)$1	1	38	41	9.0000
.((	chr18:60969654-60969925(-)$1	1	44	47	9.0000
.((	chr16:48385938-48386190(+)$1	1	0	3	9.0000
...	chrX:70790911-70791175(+)$1	1	28	31	9.0000
.((	chr15:69619794-69620013(+)$1	1	25	28	9.0000
(..	chr3:143158835-143159059(-)$1	1	108	111	9.0000
(..	chr4:8407311-8407544(-)$1	1	16	19	9.0000
...	chr3:160119859-160120102(+)$1	1	39	42	9.0000
((.	chrX:9522334-9522558(+)$1	1	25	28	9.0000
(.(	chr5:78576081-78576336(+)$1	1	28	31	9.0000
..)	chr2:233680352-233680580(+)$1	1	102	105	9.0000
(((	chr7:110788675-110788939(-)$1	1	18	21	9.0000
.((	chr6:5392854-5393114(+)$1	1	45	48	9.0000
)..	chr1:10350003-10350239(+)$1	1	111	114	9.0000
)((	chr10:37490799-37491013(+)$1	1	50	53	9.0000
...	chr11:126192186-126192404(+)$1	1	3	6	9.0000
(..	chr9:33135780-33136031(-)$1	1	24	27	9.0000
...	chr9:88918842-88919064(-)$1	1	108	111	9.0000
(((	chr11:17320480-17320756(+)$1	1	119	122	9.0000
)))	chr3:141263472-141263744(+)$1	1	29	32	9.0000
)))	chr18:6565094-6565320(+)$1	1	101	104	9.0000
(((	chr15:25614201-25614433(-)$1	1	26	29	9.0000
(((	chr18:13410643-13410857(+)$1	1	110	113	9.0000
)))	chr7:70029516-70029730(+)$1	1	110	113	9.0000
...	chr2:234171031-234171311(+)$1	1	232	235	9.0000
..)	chr8:105031277-105031503(+)$1	1	37	40	9.0000
...	chr3:156577429-156577665(+)$1	1	104	107	9.0000
..)	chr18:32821120-32821366(+)$1	1	83	86	9.0000

#PSSM
A : 0.64	a : 0.35	
C : 0.64	c : 0.35	
U : 0.63	u : 0.36	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m3_run2.nuc.txt

#NT
AGG	chr12:132623711-132623939(+)$1	228	56	59	8.9999
AGG	chr8:134467967-134468189(-)$1	222	20	23	8.9999
AGG	chr6:53213419-53213641(+)$1	222	34	37	8.9999
AGG	chr20:3219211-3219448(+)$1	237	161	164	8.9999
AGG	chr14:91738993-91739214(+)$1	221	31	34	8.9999
AGG	chr2:37470996-37471222(-)$1	226	14	17	8.9999
agg	chr6:111136340-111136569(-)$1	229	16	19	8.9999
agg	chr3:9860842-9861066(-)$1	224	61	64	8.9999
AGG	chr2:33172209-33172448(-)$1	239	7	10	8.9999
AGG	chr7:137562152-137562373(+)$1	221	91	94	8.9999
AGG	chr16:54149744-54149966(-)$1	222	53	56	8.9999
AGG	chr1:160854768-160854990(+)$1	222	60	63	8.9999
AGG	chr3:69435115-69435344(+)$1	229	180	183	8.9999
AGG	chr10:127683960-127684182(+)$1	222	104	107	8.9999
AGG	chr17:4997152-4997377(-)$1	225	37	40	8.9999
AGG	chr11:65308228-65308453(+)$1	225	78	81	8.9999
AGG	chr9:97321084-97321313(-)$1	229	41	44	8.9999
AGG	chr15:41245245-41245469(+)$1	224	88	91	8.9999
AGG	chr15:75313415-75313636(+)$1	221	121	124	8.9999
AGG	chr19:23941522-23941747(-)$1	225	116	119	8.9999
AGG	chr17:77775167-77775388(+)$1	221	4	7	8.9999
AGG	chr5:132208680-132208901(+)$1	221	78	81	8.9999
AGG	chr1:6273084-6273305(-)$1	221	105	108	8.9999
AGG	chr11:66839220-66839441(-)$1	221	1	4	8.9999
AGG	chr16:11348551-11348775(-)$1	224	176	179	8.9999
agg	chr10:82288243-82288468(-)$1	225	0	3	8.9999
AGG	chr6:149771545-149771773(-)$1	228	80	83	8.9999
agg	chr16:25026494-25026716(+)$1	222	129	132	8.9999
AGG	chr11:71935764-71935986(+)$1	222	62	65	8.9999
agg	chr2:100895459-100895680(-)$1	221	31	34	8.9999
AGG	chr12:123868240-123868463(+)$1	223	29	32	8.9999
AGG	chr1:36786725-36786952(+)$1	227	2	5	8.9999
AGG	chr9:140009372-140009593(-)$1	221	39	42	8.9999
AGG	chr16:1823038-1823259(+)$1	221	20	23	8.9999
AGG	chr20:62328381-62328604(+)$1	223	34	37	8.9999
AGG	chr19:41859098-41859319(+)$1	221	5	8	8.9999
AGG	chr16:11933741-11933971(-)$1	230	18	21	8.9999
AGG	chr17:21146080-21146303(-)$1	223	4	7	8.9999
AGG	chr13:77580030-77580253(-)$1	223	28	31	8.9999
AGG	chr17:54968152-54968377(-)$1	225	41	44	8.9999
AGG	chr1:26437749-26437971(+)$1	222	28	31	8.9999
AGG	chr6:163835358-163835580(+)$1	222	55	58	8.9999
agg	chr6:158097780-158098003(-)$1	223	30	33	8.9999
AGG	chr18:56936094-56936317(+)$1	223	44	47	8.9999
AGG	chr19:52430588-52430818(+)$1	230	37	40	8.9999
AGG	chr12:56388276-56388497(+)$1	221	65	68	8.9999
AGG	chr8:37592478-37592703(-)$1	225	15	18	8.9999
AGG	chr3:50137863-50138140(-)$1	277	155	158	8.9999
AGG	chr1:151675107-151675330(+)$1	223	17	20	8.9999
AGG	chr2:75879202-75879426(-)$1	224	113	116	8.9999
AGG	chr1:233120954-233121177(-)$1	223	108	111	8.9999
AGG	chr3:187420220-187420443(-)$1	223	8	11	8.9999
AGG	chr1:185286339-185286560(-)$1	221	3	6	8.9999
AGG	chr1:204523375-204523605(-)$1	230	41	44	8.9999
AGG	chr12:58005472-58005695(-)$1	223	141	144	8.9999
AGG	chr19:49968945-49969169(-)$1	224	82	85	8.9999
AGG	chr4:763515-763750(-)$1	235	135	138	8.9999
AGG	chr12:48131744-48131966(+)$1	222	95	98	8.9999
AGG	chr9:20345800-20346021(-)$1	221	19	22	8.9999
AGG	chr3:50129400-50129715(+)$1	315	26	29	8.9999
AGG	chr14:100142365-100142593(+)$1	228	26	29	8.9999
AGG	chrX:54070314-54070536(+)$1	222	70	73	8.9999
AGG	chr19:45572360-45572586(-)$1	226	26	29	8.9999
AGG	chr12:51663489-51663710(+)$1	221	17	20	8.9999
AGG	chr16:136523-136745(-)$1	222	1	4	8.9999
AGG	chr11:17407750-17407973(-)$1	223	10	13	8.9999
AGG	chr8:145158762-145158993(+)$1	231	92	95	8.9999
agg	chr15:75971526-75971749(-)$1	223	40	43	8.9999
agg	chr3:149036370-149036597(-)$1	227	93	96	8.9999
AGG	chr12:132250742-132250964(-)$1	222	40	43	8.9999
AGG	chr22:31477280-31477501(+)$1	221	32	35	8.9999
AGG	chr15:66801100-66801321(+)$1	221	99	102	8.9999
AGG	chr8:12612834-12613063(+)$1	229	67	70	8.9999
agg	chr20:4990716-4990940(+)$1	224	44	47	8.9999
AGG	chr21:45224293-45224516(+)$1	223	103	106	8.9999
AGG	chr6:3118957-3119179(-)$1	222	82	85	8.9999
agg	chr2:31557444-31557670(-)$1	226	84	87	8.9999
AGG	chr6:5086827-5087052(+)$1	225	36	39	8.9999
AGG	chr3:50131099-50131409(-)$1	310	126	129	8.9999
AGG	chr13:28874762-28874983(-)$1	221	170	173	8.9999
AGG	chr6:25925947-25926172(-)$1	225	0	3	8.9999
agg	chr3:9987618-9987839(+)$1	221	40	43	8.9999
AGG	chr6:41159380-41159602(-)$1	222	134	137	8.9999
AGG	chrX:14938612-14938837(+)$1	225	140	143	8.9999
AGG	chr11:130345413-130345634(-)$1	221	12	15	8.9999
AGG	chr12:109490314-109490538(-)$1	224	69	72	8.9999
AGG	chr11:118964976-118965198(+)$1	222	11	14	8.9999
AGG	chr19:7712242-7712463(-)$1	221	1	4	8.9999
AGG	chr16:84599757-84599979(+)$1	222	20	23	8.9999
AGG	chr20:19702676-19702898(-)$1	222	159	162	8.9999
agg	chr15:68484576-68484798(-)$1	222	47	50	8.9999
agg	chr19:4542909-4543131(-)$1	222	10	13	8.9999
AGG	chr17:3375470-3375692(+)$1	222	1	4	8.9999
AGG	chr8:37716143-37716364(-)$1	221	4	7	8.9999
AGG	chr4:44701879-44702100(-)$1	221	5	8	8.9999

#otherMatches

#Struct PSSM
ddd	chr1:167510353-167510577(+)$1	224	61	64	8.9999
hhh	chr12:132623711-132623939(+)$1	228	56	59	8.9999
c!!	chr8:134467967-134468189(-)$1	222	20	23	8.9999
##d	chr6:53213419-53213641(+)$1	222	34	37	8.9999
:ee	chr20:3219211-3219448(+)$1	237	161	164	8.9999
GGG	chr14:91738993-91739214(+)$1	221	31	34	8.9999
eee	chr2:37470996-37471222(-)$1	226	14	17	8.9999
nbb	chr6:111136340-111136569(-)$1	229	16	19	8.9999
%%%	chr3:9860842-9861066(-)$1	224	61	64	8.9999
KBB	chr2:33172209-33172448(-)$1	239	7	10	8.9999
iii	chr7:137562152-137562373(+)$1	221	91	94	8.9999
qdd	chr16:54149744-54149966(-)$1	222	53	56	8.9999
%bb	chr1:160854768-160854990(+)$1	222	60	63	8.9999
fff	chr3:69435115-69435344(+)$1	229	180	183	8.9999
[cc	chr10:127683960-127684182(+)$1	222	104	107	8.9999
DD:	chr17:4997152-4997377(-)$1	225	37	40	8.9999
##e	chr11:65308228-65308453(+)$1	225	78	81	8.9999
edd	chr9:97321084-97321313(-)$1	229	41	44	8.9999
ccc	chr15:41245245-41245469(+)$1	224	88	91	8.9999
"""	chr15:75313415-75313636(+)$1	221	121	124	8.9999
ggg	chr19:23941522-23941747(-)$1	225	116	119	8.9999
:DD	chr17:77775167-77775388(+)$1	221	4	7	8.9999
ccc	chr5:132208680-132208901(+)$1	221	78	81	8.9999
:::	chr1:6273084-6273305(-)$1	221	105	108	8.9999
::D	chr11:66839220-66839441(-)$1	221	1	4	8.9999
III	chr16:11348551-11348775(-)$1	224	176	179	8.9999
::E	chr10:82288243-82288468(-)$1	225	0	3	8.9999
ddd	chr6:149771545-149771773(-)$1	228	80	83	8.9999
iii	chr16:25026494-25026716(+)$1	222	129	132	8.9999
ccd	chr11:71935764-71935986(+)$1	222	62	65	8.9999
ddd	chr2:100895459-100895680(-)$1	221	31	34	8.9999
mmm	chr12:123868240-123868463(+)$1	223	29	32	8.9999
:EE	chr1:36786725-36786952(+)$1	227	2	5	8.9999
LLC	chr9:140009372-140009593(-)$1	221	39	42	8.9999
::c	chr16:1823038-1823259(+)$1	221	20	23	8.9999
eee	chr20:62328381-62328604(+)$1	223	34	37	8.9999
::d	chr19:41859098-41859319(+)$1	221	5	8	8.9999
aee	chr16:11933741-11933971(-)$1	230	18	21	8.9999
EEE	chr17:21146080-21146303(-)$1	223	4	7	8.9999
WCC	chr13:77580030-77580253(-)$1	223	28	31	8.9999
22i	chr17:54968152-54968377(-)$1	225	41	44	8.9999
{BB	chr1:26437749-26437971(+)$1	222	28	31	8.9999
KCC	chr6:163835358-163835580(+)$1	222	55	58	8.9999
bb2	chr6:158097780-158098003(-)$1	223	30	33	8.9999
fff	chr18:56936094-56936317(+)$1	223	44	47	8.9999
ddd	chr19:52430588-52430818(+)$1	230	37	40	8.9999
:gg	chr12:56388276-56388497(+)$1	221	65	68	8.9999
oee	chr8:37592478-37592703(-)$1	225	15	18	8.9999
ddd	chr3:50137863-50138140(-)$1	277	155	158	8.9999
qcc	chr1:151675107-151675330(+)$1	223	17	20	8.9999
ddd	chr2:75879202-75879426(-)$1	224	113	116	8.9999
cc[	chr1:233120954-233121177(-)$1	223	108	111	8.9999
[cc	chr3:187420220-187420443(-)$1	223	8	11	8.9999
:cc	chr1:185286339-185286560(-)$1	221	3	6	8.9999
$$$	chr1:204523375-204523605(-)$1	230	41	44	8.9999
]==	chr12:58005472-58005695(-)$1	223	141	144	8.9999
nff	chr19:49968945-49969169(-)$1	224	82	85	8.9999
eee	chr4:763515-763750(-)$1	235	135	138	8.9999
]dd	chr12:48131744-48131966(+)$1	222	95	98	8.9999
!!d	chr9:20345800-20346021(-)$1	221	19	22	8.9999
hhz	chr3:50129400-50129715(+)$1	315	26	29	8.9999
:ee	chr14:100142365-100142593(+)$1	228	26	29	8.9999
[ff	chrX:54070314-54070536(+)$1	222	70	73	8.9999
Hdd	chr19:45572360-45572586(-)$1	226	26	29	8.9999
MMC	chr12:51663489-51663710(+)$1	221	17	20	8.9999
FFF	chr16:136523-136745(-)$1	222	1	4	8.9999
[ee	chr11:17407750-17407973(-)$1	223	10	13	8.9999
mmd	chr8:145158762-145158993(+)$1	231	92	95	8.9999
b$$	chr15:75971526-75971749(-)$1	223	40	43	8.9999
ddd	chr3:149036370-149036597(-)$1	227	93	96	8.9999
fff	chr12:132250742-132250964(-)$1	222	40	43	8.9999
lll	chr22:31477280-31477501(+)$1	221	32	35	8.9999
ddd	chr15:66801100-66801321(+)$1	221	99	102	8.9999
fff	chr8:12612834-12613063(+)$1	229	67	70	8.9999
FFF	chr20:4990716-4990940(+)$1	224	44	47	8.9999
hhh	chr21:45224293-45224516(+)$1	223	103	106	8.9999
]bb	chr6:3118957-3119179(-)$1	222	82	85	8.9999
nna	chr2:31557444-31557670(-)$1	226	84	87	8.9999
[a[	chr6:5086827-5087052(+)$1	225	36	39	8.9999
[bb	chr3:50131099-50131409(-)$1	310	126	129	8.9999
EEE	chr13:28874762-28874983(-)$1	221	170	173	8.9999
:ee	chr6:25925947-25926172(-)$1	225	0	3	8.9999
eee	chr3:9987618-9987839(+)$1	221	40	43	8.9999
ggg	chr6:41159380-41159602(-)$1	222	134	137	8.9999
ddd	chrX:14938612-14938837(+)$1	225	140	143	8.9999
JJJ	chr11:130345413-130345634(-)$1	221	12	15	8.9999
fff	chr12:109490314-109490538(-)$1	224	69	72	8.9999
[ff	chr11:118964976-118965198(+)$1	222	11	14	8.9999
:HH	chr19:7712242-7712463(-)$1	221	1	4	8.9999
nnn	chr16:84599757-84599979(+)$1	222	20	23	8.9999
"""	chr20:19702676-19702898(-)$1	222	159	162	8.9999
eee	chr15:68484576-68484798(-)$1	222	47	50	8.9999
KGG	chr19:4542909-4543131(-)$1	222	10	13	8.9999
::B	chr17:3375470-3375692(+)$1	222	1	4	8.9999
hhh	chr8:37716143-37716364(-)$1	221	4	7	8.9999
CCC	chr4:44701879-44702100(-)$1	221	5	8	8.9999

#DB
(((	chr1:167510353-167510577(+)$1	1	61	64	8.9999
(((	chr12:132623711-132623939(+)$1	1	56	59	8.9999
(..	chr8:134467967-134468189(-)$1	1	20	23	8.9999
..(	chr6:53213419-53213641(+)$1	1	34	37	8.9999
.((	chr20:3219211-3219448(+)$1	1	161	164	8.9999
(((	chr14:91738993-91739214(+)$1	1	31	34	8.9999
)))	chr2:37470996-37471222(-)$1	1	14	17	8.9999
.))	chr6:111136340-111136569(-)$1	1	16	19	8.9999
...	chr3:9860842-9861066(-)$1	1	61	64	8.9999
.((	chr2:33172209-33172448(-)$1	1	7	10	8.9999
)))	chr7:137562152-137562373(+)$1	1	91	94	8.9999
.))	chr16:54149744-54149966(-)$1	1	53	56	8.9999
.((	chr1:160854768-160854990(+)$1	1	60	63	8.9999
)))	chr3:69435115-69435344(+)$1	1	180	183	8.9999
.((	chr10:127683960-127684182(+)$1	1	104	107	8.9999
((.	chr17:4997152-4997377(-)$1	1	37	40	8.9999
..(	chr11:65308228-65308453(+)$1	1	78	81	8.9999
)))	chr9:97321084-97321313(-)$1	1	41	44	8.9999
(((	chr15:41245245-41245469(+)$1	1	88	91	8.9999
...	chr15:75313415-75313636(+)$1	1	121	124	8.9999
(((	chr19:23941522-23941747(-)$1	1	116	119	8.9999
.((	chr17:77775167-77775388(+)$1	1	4	7	8.9999
)))	chr5:132208680-132208901(+)$1	1	78	81	8.9999
...	chr1:6273084-6273305(-)$1	1	105	108	8.9999
..(	chr11:66839220-66839441(-)$1	1	1	4	8.9999
)))	chr16:11348551-11348775(-)$1	1	176	179	8.9999
..(	chr10:82288243-82288468(-)$1	1	0	3	8.9999
)))	chr6:149771545-149771773(-)$1	1	80	83	8.9999
(((	chr16:25026494-25026716(+)$1	1	129	132	8.9999
))(	chr11:71935764-71935986(+)$1	1	62	65	8.9999
(((	chr2:100895459-100895680(-)$1	1	31	34	8.9999
...	chr12:123868240-123868463(+)$1	1	29	32	8.9999
.((	chr1:36786725-36786952(+)$1	1	2	5	8.9999
..(	chr9:140009372-140009593(-)$1	1	39	42	8.9999
..(	chr16:1823038-1823259(+)$1	1	20	23	8.9999
)))	chr20:62328381-62328604(+)$1	1	34	37	8.9999
..(	chr19:41859098-41859319(+)$1	1	5	8	8.9999
(((	chr16:11933741-11933971(-)$1	1	18	21	8.9999
(((	chr17:21146080-21146303(-)$1	1	4	7	8.9999
.((	chr13:77580030-77580253(-)$1	1	28	31	8.9999
..)	chr17:54968152-54968377(-)$1	1	41	44	8.9999
.((	chr1:26437749-26437971(+)$1	1	28	31	8.9999
.((	chr6:163835358-163835580(+)$1	1	55	58	8.9999
)).	chr6:158097780-158098003(-)$1	1	30	33	8.9999
(((	chr18:56936094-56936317(+)$1	1	44	47	8.9999
)))	chr19:52430588-52430818(+)$1	1	37	40	8.9999
.((	chr12:56388276-56388497(+)$1	1	65	68	8.9999
.))	chr8:37592478-37592703(-)$1	1	15	18	8.9999
)))	chr3:50137863-50138140(-)$1	1	155	158	8.9999
.))	chr1:151675107-151675330(+)$1	1	17	20	8.9999
)))	chr2:75879202-75879426(-)$1	1	113	116	8.9999
((.	chr1:233120954-233121177(-)$1	1	108	111	8.9999
.((	chr3:187420220-187420443(-)$1	1	8	11	8.9999
.((	chr1:185286339-185286560(-)$1	1	3	6	8.9999
...	chr1:204523375-204523605(-)$1	1	41	44	8.9999
.))	chr12:58005472-58005695(-)$1	1	141	144	8.9999
.))	chr19:49968945-49969169(-)$1	1	82	85	8.9999
)))	chr4:763515-763750(-)$1	1	135	138	8.9999
.))	chr12:48131744-48131966(+)$1	1	95	98	8.9999
..(	chr9:20345800-20346021(-)$1	1	19	22	8.9999
((.	chr3:50129400-50129715(+)$1	1	26	29	8.9999
.((	chr14:100142365-100142593(+)$1	1	26	29	8.9999
.((	chrX:54070314-54070536(+)$1	1	70	73	8.9999
(((	chr19:45572360-45572586(-)$1	1	26	29	8.9999
..(	chr12:51663489-51663710(+)$1	1	17	20	8.9999
(((	chr16:136523-136745(-)$1	1	1	4	8.9999
.((	chr11:17407750-17407973(-)$1	1	10	13	8.9999
..)	chr8:145158762-145158993(+)$1	1	92	95	8.9999
(..	chr15:75971526-75971749(-)$1	1	40	43	8.9999
)))	chr3:149036370-149036597(-)$1	1	93	96	8.9999
(((	chr12:132250742-132250964(-)$1	1	40	43	8.9999
...	chr22:31477280-31477501(+)$1	1	32	35	8.9999
(((	chr15:66801100-66801321(+)$1	1	99	102	8.9999
))(	chr8:12612834-12613063(+)$1	1	67	70	8.9999
(((	chr20:4990716-4990940(+)$1	1	44	47	8.9999
)))	chr21:45224293-45224516(+)$1	1	103	106	8.9999
.))	chr6:3118957-3119179(-)$1	1	82	85	8.9999
..)	chr2:31557444-31557670(-)$1	1	84	87	8.9999
.(.	chr6:5086827-5087052(+)$1	1	36	39	8.9999
.((	chr3:50131099-50131409(-)$1	1	126	129	8.9999
)))	chr13:28874762-28874983(-)$1	1	170	173	8.9999
.((	chr6:25925947-25926172(-)$1	1	0	3	8.9999
)))	chr3:9987618-9987839(+)$1	1	40	43	8.9999
)))	chr6:41159380-41159602(-)$1	1	134	137	8.9999
)))	chrX:14938612-14938837(+)$1	1	140	143	8.9999
(((	chr11:130345413-130345634(-)$1	1	12	15	8.9999
(((	chr12:109490314-109490538(-)$1	1	69	72	8.9999
.((	chr11:118964976-118965198(+)$1	1	11	14	8.9999
.((	chr19:7712242-7712463(-)$1	1	1	4	8.9999
...	chr16:84599757-84599979(+)$1	1	20	23	8.9999
...	chr20:19702676-19702898(-)$1	1	159	162	8.9999
(((	chr15:68484576-68484798(-)$1	1	47	50	8.9999
.((	chr19:4542909-4543131(-)$1	1	10	13	8.9999
..(	chr17:3375470-3375692(+)$1	1	1	4	8.9999
(((	chr8:37716143-37716364(-)$1	1	4	7	8.9999
(((	chr4:44701879-44702100(-)$1	1	5	8	8.9999

#PSSM
A : 0.86	a : 0.13	
G : 0.86	g : 0.13	
G : 0.86	g : 0.13	

#score	863.9999999999999
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m2_run1.nuc.txt

#NT
CUGG	chr15:40212864-40213088(+)$1	224	3	7	11.9999
CUGG	chr16:66946912-66947135(-)$1	223	5	9	11.9999
CUGG	chr11:71693763-71693984(+)$1	221	7	11	11.9999
CUGG	chr2:112785995-112786225(+)$1	230	77	81	11.9999
CUGG	chr19:14040259-14040487(+)$1	228	32	36	11.9999
cugg	chr11:8021888-8022110(+)$1	222	52	56	11.9999
CUGG	chr10:135113409-135113634(-)$1	225	107	111	11.9999
CUGG	chr6:139308723-139308948(+)$1	225	159	163	11.9999
CUGG	chr2:74875325-74875559(+)$1	234	95	99	11.9999
CUGG	chr2:65301591-65301813(+)$1	222	36	40	11.9999
CUGG	chr3:128751644-128751868(-)$1	224	13	17	11.9999
CUGG	chr8:42911805-42912026(+)$1	221	18	22	11.9999
CUGG	chr8:81882734-81882955(+)$1	221	27	31	11.9999
CUGG	chr8:145752137-145752359(+)$1	222	176	180	11.9999
CUGG	chr1:204523375-204523603(-)$1	228	86	90	11.9999
CUGG	chr19:49132638-49132859(-)$1	221	154	158	11.9999
CUGG	chr1:228871145-228871368(+)$1	223	140	144	11.9999
CUGG	chr1:167510354-167510577(+)$1	223	199	203	11.9999
cugg	chr16:48573448-48573671(+)$1	223	57	61	11.9999
CUGG	chr3:127309303-127309529(+)$1	226	13	17	11.9999
CUGG	chr7:99130821-99131044(+)$1	223	31	35	11.9999
CUGG	chr2:31557445-31557670(-)$1	225	212	216	11.9999
CUGG	chr19:52430593-52430818(+)$1	225	121	125	11.9999
CUGG	chr21:46645897-46646121(+)$1	224	43	47	11.9999
CUGG	chr7:4805362-4805584(-)$1	222	4	8	11.9999
CUGG	chr6:160148200-160148421(-)$1	221	43	47	11.9999
CUGG	chr11:17407743-17407972(-)$1	229	5	9	11.9999
cugg	chr2:47596528-47596767(-)$1	239	225	229	11.9999
CUGG	chr7:130038393-130038616(+)$1	223	6	10	11.9999
CUGG	chr19:10802934-10803156(-)$1	222	103	107	11.9999
CUGG	chr12:123093852-123094076(-)$1	224	39	43	11.9999
CUGG	chr2:20401465-20401688(+)$1	223	29	33	11.9999
CUGG	chr19:56110442-56110668(-)$1	226	25	29	11.9999
CUGG	chr1:156863411-156863637(+)$1	226	107	111	11.9999
CUGG	chr19:17660372-17660595(-)$1	223	41	45	11.9999
CUGG	chr2:75879201-75879427(-)$1	226	53	57	11.9999
CUGG	chr3:50145402-50145668(-)$1	266	117	121	11.9999
CUGG	chr19:1418604-1418825(+)$1	221	134	138	11.9999
CUGG	chr1:231906681-231906906(-)$1	225	194	198	11.9999
CUGG	chr7:30451884-30452107(+)$1	223	106	110	11.9999
CUGG	chr12:108079719-108079941(+)$1	222	36	40	11.9999
CUGG	chr12:46579350-46579574(-)$1	224	66	70	11.9999
CUGG	chr17:46052435-46052656(-)$1	221	13	17	11.9999
CUGG	chr2:28615900-28616125(+)$1	225	73	77	11.9999
CUGG	chr16:30003281-30003512(+)$1	231	0	4	11.9999
CUGG	chr3:154797762-154797983(+)$1	221	25	29	11.9999
CUGG	chr6:160560761-160560983(-)$1	222	47	51	11.9999
CUGG	chr3:184059736-184059959(-)$1	223	53	57	11.9999
CUGG	chr19:1980613-1980838(+)$1	225	45	49	11.9999
CUGG	chr1:197127717-197127942(-)$1	225	163	167	11.9999
cugg	chr15:40623610-40623833(-)$1	223	41	45	11.9999
CUGG	chr15:56125145-56125369(+)$1	224	192	196	11.9999
CUGG	chr19:4697538-4697761(-)$1	223	122	126	11.9999
CUGG	chr13:111175884-111176108(-)$1	224	80	84	11.9999
CUGG	chr6:166825779-166826000(-)$1	221	204	208	11.9999
CUGG	chr11:58939846-58940070(+)$1	224	57	61	11.9999
CUGG	chr17:16346478-16346701(-)$1	223	107	111	11.9999
CUGG	chr4:37841106-37841330(-)$1	224	37	41	11.9999
CUGG	chr2:171569828-171570057(-)$1	229	182	186	11.9999
CUGG	chr17:80674560-80674781(+)$1	221	95	99	11.9999
CUGG	chr4:170533485-170533707(+)$1	222	110	114	11.9999
CUGG	chr17:58524326-58524547(-)$1	221	197	201	11.9999
CUGG	chr7:17833547-17833769(-)$1	222	118	122	11.9999
CUGG	chr5:111065646-111065869(-)$1	223	26	30	11.9999
CUGG	chr16:58741694-58741916(-)$1	222	33	37	11.9999
CUGG	chr19:46388960-46389182(+)$1	222	42	46	11.9999
CUGG	chr2:43519205-43519428(+)$1	223	108	112	11.9999
CUGG	chr2:98928951-98929176(+)$1	225	54	58	11.9999
CUGG	chr18:54694932-54695157(+)$1	225	32	36	11.9999
CUGG	chr6:161560477-161560701(-)$1	224	120	124	11.9999
CUGG	chr9:100410334-100410562(+)$1	228	2	6	11.9999
CUGG	chr1:222885707-222885932(-)$1	225	174	178	11.9999
CUGG	chr16:4852698-4852925(-)$1	227	20	24	11.9999
CUGG	chr19:16524464-16524690(+)$1	226	129	133	11.9999
CUGG	chr2:103353173-103353394(+)$1	221	215	219	11.9999
CUGG	chr8:124194870-124195110(-)$1	240	25	29	11.9999
CUGG	chr12:4959910-4960131(+)$1	221	1	5	11.9999

#otherMatches

#Struct PSSM
iiii	chr1:221052766-221052990(+)$1	224	126	130	11.9999
::CC	chr15:40212864-40213088(+)$1	224	3	7	11.9999
::::	chr16:66946912-66947135(-)$1	223	5	9	11.9999
"a[d	chr11:71693763-71693984(+)$1	221	7	11	11.9999
b[bb	chr2:112785995-112786225(+)$1	230	77	81	11.9999
eemm	chr19:14040259-14040487(+)$1	228	32	36	11.9999
DDDD	chr11:8021888-8022110(+)$1	222	52	56	11.9999
bccc	chr10:135113409-135113634(-)$1	225	107	111	11.9999
bbgg	chr6:139308723-139308948(+)$1	225	159	163	11.9999
CC{D	chr2:74875325-74875559(+)$1	234	95	99	11.9999
::ff	chr2:65301591-65301813(+)$1	222	36	40	11.9999
eeee	chr3:128751644-128751868(-)$1	224	13	17	11.9999
eeee	chr8:42911805-42912026(+)$1	221	18	22	11.9999
nccc	chr8:81882734-81882955(+)$1	221	27	31	11.9999
dddd	chr8:145752137-145752359(+)$1	222	176	180	11.9999
:ccc	chr1:204523375-204523603(-)$1	228	86	90	11.9999
gggg	chr19:49132638-49132859(-)$1	221	154	158	11.9999
cccf	chr1:228871145-228871368(+)$1	223	140	144	11.9999
qqbb	chr1:167510354-167510577(+)$1	223	199	203	11.9999
iiii	chr16:48573448-48573671(+)$1	223	57	61	11.9999
LDDD	chr3:127309303-127309529(+)$1	226	13	17	11.9999
ffff	chr7:99130821-99131044(+)$1	223	31	35	11.9999
EEEE	chr2:31557445-31557670(-)$1	225	212	216	11.9999
====	chr19:52430593-52430818(+)$1	225	121	125	11.9999
H{BB	chr21:46645897-46646121(+)$1	224	43	47	11.9999
e[cc	chr7:4805362-4805584(-)$1	222	4	8	11.9999
HHHH	chr6:160148200-160148421(-)$1	221	43	47	11.9999
eeee	chr11:17407743-17407972(-)$1	229	5	9	11.9999
clll	chr2:47596528-47596767(-)$1	239	225	229	11.9999
::::	chr7:130038393-130038616(+)$1	223	6	10	11.9999
i]bb	chr19:10802934-10803156(-)$1	222	103	107	11.9999
:::g	chr12:123093852-123094076(-)$1	224	39	43	11.9999
ffff	chr2:20401465-20401688(+)$1	223	29	33	11.9999
JJJJ	chr19:56110442-56110668(-)$1	226	25	29	11.9999
YYDD	chr1:156863411-156863637(+)$1	226	107	111	11.9999
KGGG	chr19:17660372-17660595(-)$1	223	41	45	11.9999
##cc	chr2:75879201-75879427(-)$1	226	53	57	11.9999
a]cc	chr3:50145402-50145668(-)$1	266	117	121	11.9999
JJJd	chr19:1418604-1418825(+)$1	221	134	138	11.9999
dddd	chr1:231906681-231906906(-)$1	225	194	198	11.9999
YYDD	chr7:30451884-30452107(+)$1	223	106	110	11.9999
ffff	chr12:108079719-108079941(+)$1	222	36	40	11.9999
d[bb	chr12:46579350-46579574(-)$1	224	66	70	11.9999
e:CC	chr17:46052435-46052656(-)$1	221	13	17	11.9999
qqdd	chr2:28615900-28616125(+)$1	225	73	77	11.9999
::gg	chr16:30003281-30003512(+)$1	231	0	4	11.9999
dddd	chr3:154797762-154797983(+)$1	221	25	29	11.9999
ff[a	chr6:160560761-160560983(-)$1	222	47	51	11.9999
eee[	chr3:184059736-184059959(-)$1	223	53	57	11.9999
2a]e	chr19:1980613-1980838(+)$1	225	45	49	11.9999
gggg	chr1:197127717-197127942(-)$1	225	163	167	11.9999
b[cc	chr15:40623610-40623833(-)$1	223	41	45	11.9999
DDDD	chr15:56125145-56125369(+)$1	224	192	196	11.9999
dddb	chr19:4697538-4697761(-)$1	223	122	126	11.9999
bfff	chr13:111175884-111176108(-)$1	224	80	84	11.9999
gggg	chr6:166825779-166826000(-)$1	221	204	208	11.9999
gggg	chr11:58939846-58940070(+)$1	224	57	61	11.9999
eeee	chr17:16346478-16346701(-)$1	223	107	111	11.9999
555f	chr4:37841106-37841330(-)$1	224	37	41	11.9999
ddrr	chr2:171569828-171570057(-)$1	229	182	186	11.9999
gggg	chr17:80674560-80674781(+)$1	221	95	99	11.9999
!ccc	chr4:170533485-170533707(+)$1	222	110	114	11.9999
:CCC	chr17:58524326-58524547(-)$1	221	197	201	11.9999
22ff	chr7:17833547-17833769(-)$1	222	118	122	11.9999
cc!!	chr5:111065646-111065869(-)$1	223	26	30	11.9999
cmmm	chr16:58741694-58741916(-)$1	222	33	37	11.9999
[eee	chr19:46388960-46389182(+)$1	222	42	46	11.9999
hhhb	chr2:43519205-43519428(+)$1	223	108	112	11.9999
HHHH	chr2:98928951-98929176(+)$1	225	54	58	11.9999
EEEE	chr18:54694932-54695157(+)$1	225	32	36	11.9999
e[dd	chr6:161560477-161560701(-)$1	224	120	124	11.9999
C:gg	chr9:100410334-100410562(+)$1	228	2	6	11.9999
====	chr1:222885707-222885932(-)$1	225	174	178	11.9999
JJJJ	chr16:4852698-4852925(-)$1	227	20	24	11.9999
b:cc	chr19:16524464-16524690(+)$1	226	129	133	11.9999
~~CC	chr2:103353173-103353394(+)$1	221	215	219	11.9999
CCC{	chr8:124194870-124195110(-)$1	240	25	29	11.9999
cc[c	chr12:4959910-4960131(+)$1	221	1	5	11.9999

#DB
((((	chr1:221052766-221052990(+)$1	1	126	130	11.9999
..((	chr15:40212864-40213088(+)$1	1	3	7	11.9999
....	chr16:66946912-66947135(-)$1	1	5	9	11.9999
.(.(	chr11:71693763-71693984(+)$1	1	7	11	11.9999
(.((	chr2:112785995-112786225(+)$1	1	77	81	11.9999
((..	chr19:14040259-14040487(+)$1	1	32	36	11.9999
((((	chr11:8021888-8022110(+)$1	1	52	56	11.9999
((((	chr10:135113409-135113634(-)$1	1	107	111	11.9999
))))	chr6:139308723-139308948(+)$1	1	159	163	11.9999
((.(	chr2:74875325-74875559(+)$1	1	95	99	11.9999
..((	chr2:65301591-65301813(+)$1	1	36	40	11.9999
))))	chr3:128751644-128751868(-)$1	1	13	17	11.9999
((((	chr8:42911805-42912026(+)$1	1	18	22	11.9999
.)))	chr8:81882734-81882955(+)$1	1	27	31	11.9999
))))	chr8:145752137-145752359(+)$1	1	176	180	11.9999
.(((	chr1:204523375-204523603(-)$1	1	86	90	11.9999
))))	chr19:49132638-49132859(-)$1	1	154	158	11.9999
))))	chr1:228871145-228871368(+)$1	1	140	144	11.9999
..))	chr1:167510354-167510577(+)$1	1	199	203	11.9999
((((	chr16:48573448-48573671(+)$1	1	57	61	11.9999
.(((	chr3:127309303-127309529(+)$1	1	13	17	11.9999
))))	chr7:99130821-99131044(+)$1	1	31	35	11.9999
))))	chr2:31557445-31557670(-)$1	1	212	216	11.9999
))))	chr19:52430593-52430818(+)$1	1	121	125	11.9999
(.((	chr21:46645897-46646121(+)$1	1	43	47	11.9999
(.((	chr7:4805362-4805584(-)$1	1	4	8	11.9999
((((	chr6:160148200-160148421(-)$1	1	43	47	11.9999
((((	chr11:17407743-17407972(-)$1	1	5	9	11.9999
(...	chr2:47596528-47596767(-)$1	1	225	229	11.9999
....	chr7:130038393-130038616(+)$1	1	6	10	11.9999
).))	chr19:10802934-10803156(-)$1	1	103	107	11.9999
...(	chr12:123093852-123094076(-)$1	1	39	43	11.9999
))))	chr2:20401465-20401688(+)$1	1	29	33	11.9999
((((	chr19:56110442-56110668(-)$1	1	25	29	11.9999
..))	chr1:156863411-156863637(+)$1	1	107	111	11.9999
.(((	chr19:17660372-17660595(-)$1	1	41	45	11.9999
..((	chr2:75879201-75879427(-)$1	1	53	57	11.9999
).))	chr3:50145402-50145668(-)$1	1	117	121	11.9999
)))(	chr19:1418604-1418825(+)$1	1	134	138	11.9999
((((	chr1:231906681-231906906(-)$1	1	194	198	11.9999
..))	chr7:30451884-30452107(+)$1	1	106	110	11.9999
((((	chr12:108079719-108079941(+)$1	1	36	40	11.9999
(.((	chr12:46579350-46579574(-)$1	1	66	70	11.9999
).((	chr17:46052435-46052656(-)$1	1	13	17	11.9999
..))	chr2:28615900-28616125(+)$1	1	73	77	11.9999
..((	chr16:30003281-30003512(+)$1	1	0	4	11.9999
((((	chr3:154797762-154797983(+)$1	1	25	29	11.9999
((.(	chr6:160560761-160560983(-)$1	1	47	51	11.9999
(((.	chr3:184059736-184059959(-)$1	1	53	57	11.9999
.).)	chr19:1980613-1980838(+)$1	1	45	49	11.9999
))))	chr1:197127717-197127942(-)$1	1	163	167	11.9999
(.((	chr15:40623610-40623833(-)$1	1	41	45	11.9999
))))	chr15:56125145-56125369(+)$1	1	192	196	11.9999
))))	chr19:4697538-4697761(-)$1	1	122	126	11.9999
))))	chr13:111175884-111176108(-)$1	1	80	84	11.9999
))))	chr6:166825779-166826000(-)$1	1	204	208	11.9999
))))	chr11:58939846-58940070(+)$1	1	57	61	11.9999
))))	chr17:16346478-16346701(-)$1	1	107	111	11.9999
...)	chr4:37841106-37841330(-)$1	1	37	41	11.9999
((..	chr2:171569828-171570057(-)$1	1	182	186	11.9999
))))	chr17:80674560-80674781(+)$1	1	95	99	11.9999
.(((	chr4:170533485-170533707(+)$1	1	110	114	11.9999
.)))	chr17:58524326-58524547(-)$1	1	197	201	11.9999
..))	chr7:17833547-17833769(-)$1	1	118	122	11.9999
((..	chr5:111065646-111065869(-)$1	1	26	30	11.9999
(...	chr16:58741694-58741916(-)$1	1	33	37	11.9999
.(((	chr19:46388960-46389182(+)$1	1	42	46	11.9999
)))(	chr2:43519205-43519428(+)$1	1	108	112	11.9999
((((	chr2:98928951-98929176(+)$1	1	54	58	11.9999
((((	chr18:54694932-54695157(+)$1	1	32	36	11.9999
(.((	chr6:161560477-161560701(-)$1	1	120	124	11.9999
(.((	chr9:100410334-100410562(+)$1	1	2	6	11.9999
((((	chr1:222885707-222885932(-)$1	1	174	178	11.9999
((((	chr16:4852698-4852925(-)$1	1	20	24	11.9999
).((	chr19:16524464-16524690(+)$1	1	129	133	11.9999
..))	chr2:103353173-103353394(+)$1	1	215	219	11.9999
(((.	chr8:124194870-124195110(-)$1	1	25	29	11.9999
((.(	chr12:4959910-4960131(+)$1	1	1	5	11.9999

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

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m1_run1.nuc.txt

#NT
UUUCU	chr17:15948048-15948264(-)$1	216	56	61	15.0000
UUUCU	chr1:200828450-200828671(+)$1	221	14	19	15.0000
UUUCU	chr16:47653068-47653284(-)$1	216	75	80	15.0000
UUUCU	chr19:37641312-37641529(-)$1	217	70	75	15.0000
UUUCU	chr5:77782040-77782258(-)$1	218	38	43	15.0000
UUUCU	chr15:79214377-79214612(-)$1	235	54	59	15.0000
UUUCU	chr17:70121368-70121586(-)$1	218	125	130	15.0000
UUUCU	chr10:73819533-73819772(-)$1	239	66	71	15.0000
UUUCU	chr1:176832660-176832878(-)$1	218	9	14	15.0000
UUUCU	chr5:83237579-83237809(-)$1	230	90	95	15.0000
UUUCU	chr7:148114378-148114594(+)$1	216	12	17	15.0000
uuucu	chr1:32958516-32958732(+)$1	216	9	14	15.0000
UUUCU	chr1:109855947-109856164(-)$1	217	103	108	15.0000
UUUCU	chr8:13372184-13372403(+)$1	219	4	9	15.0000
UUUCU	chr20:62375152-62375371(-)$1	219	66	71	15.0000
UUUCU	chr10:97631578-97631798(-)$1	220	137	142	15.0000
UUUCU	chr12:109016073-109016322(-)$1	249	103	108	15.0000
UUUCU	chrX:154467521-154467738(+)$1	217	18	23	15.0000
UUUCU	chr16:64980718-64980933(+)$1	215	68	73	15.0000
UUUCU	chr8:86037071-86037289(-)$1	218	53	58	15.0000
UUUCU	chr10:135039678-135039907(+)$1	229	211	216	15.0000
UUUCU	chr6:55299187-55299405(-)$1	218	180	185	15.0000
UUUCU	chr5:102433324-102433542(-)$1	218	103	108	15.0000
UUUCU	chr5:141000887-141001106(-)$1	219	102	107	15.0000
UUUCU	chr12:68688518-68688733(-)$1	215	129	134	15.0000
UUUCU	chr15:74421808-74422023(-)$1	215	29	34	15.0000
UUUCU	chr7:120389463-120389681(+)$1	218	180	185	15.0000
UUUCU	chr9:117052996-117053218(+)$1	222	82	87	15.0000
UUUCU	chr3:183354330-183354555(+)$1	225	7	12	15.0000
UUUCU	chr9:36216970-36217214(-)$1	244	46	51	15.0000
UUUCU	chr2:160624088-160624304(-)$1	216	73	78	15.0000
UUUCU	chr21:38573824-38574041(+)$1	217	105	110	15.0000
UUUCU	chr15:44817257-44817473(-)$1	216	195	200	15.0000
UUUCU	chr11:11979417-11979633(-)$1	216	107	112	15.0000
UUUCU	chr5:73923389-73923622(-)$1	233	152	157	15.0000
UUUCU	chr2:192289591-192289811(+)$1	220	152	157	15.0000
UUUCU	chr20:62566484-62566712(+)$1	228	168	173	15.0000
UUUCU	chr4:113970707-113970935(+)$1	228	156	161	15.0000
UUUCU	chr2:210598578-210598796(+)$1	218	105	110	15.0000
UUUCU	chr1:879440-879662(-)$1	222	5	10	15.0000
UUUCU	chr11:109295872-109296089(+)$1	217	60	65	15.0000
UUUCU	chr17:26722699-26722929(+)$1	230	211	216	15.0000
UUUCU	chr10:82288099-82288316(+)$1	217	49	54	15.0000
UUUCU	chr7:32338675-32338894(-)$1	219	26	31	15.0000
UUUCU	chr1:47683737-47683973(-)$1	236	0	5	15.0000
UUUCU	chr1:183221082-183221298(-)$1	216	17	22	15.0000
UUUCU	chr8:29193954-29194171(+)$1	217	101	106	15.0000
UUUCU	chr4:83345304-83345525(+)$1	221	48	53	15.0000

#otherMatches

#Struct PSSM
IIIII	chr17:45209550-45209766(-)$1	216	153	158	15.0000
dd[dd	chr17:15948048-15948264(-)$1	216	56	61	15.0000
EEEPP	chr1:200828450-200828671(+)$1	221	14	19	15.0000
qdddd	chr16:47653068-47653284(-)$1	216	75	80	15.0000
hhhhh	chr19:37641312-37641529(-)$1	217	70	75	15.0000
:::::	chr5:77782040-77782258(-)$1	218	38	43	15.0000
:::BB	chr15:79214377-79214612(-)$1	235	54	59	15.0000
!!bbm	chr17:70121368-70121586(-)$1	218	125	130	15.0000
hhhhh	chr10:73819533-73819772(-)$1	239	66	71	15.0000
IIPPP	chr1:176832660-176832878(-)$1	218	9	14	15.0000
ddmmm	chr5:83237579-83237809(-)$1	230	90	95	15.0000
eeee=	chr7:148114378-148114594(+)$1	216	12	17	15.0000
ddppp	chr1:32958516-32958732(+)$1	216	9	14	15.0000
::::F	chr1:109855947-109856164(-)$1	217	103	108	15.0000
:::::	chr8:13372184-13372403(+)$1	219	4	9	15.0000
::::f	chr20:62375152-62375371(-)$1	219	66	71	15.0000
ff444	chr10:97631578-97631798(-)$1	220	137	142	15.0000
coooo	chr12:109016073-109016322(-)$1	249	103	108	15.0000
HMMMM	chrX:154467521-154467738(+)$1	217	18	23	15.0000
eeeee	chr16:64980718-64980933(+)$1	215	68	73	15.0000
ff22c	chr8:86037071-86037289(-)$1	218	53	58	15.0000
YYFFF	chr10:135039678-135039907(+)$1	229	211	216	15.0000
bmmmm	chr6:55299187-55299405(-)$1	218	180	185	15.0000
'''''	chr5:102433324-102433542(-)$1	218	103	108	15.0000
:hhhh	chr5:141000887-141001106(-)$1	219	102	107	15.0000
fff))	chr12:68688518-68688733(-)$1	215	129	134	15.0000
:::::	chr15:74421808-74422023(-)$1	215	29	34	15.0000
GGGGG	chr7:120389463-120389681(+)$1	218	180	185	15.0000
=====	chr9:117052996-117053218(+)$1	222	82	87	15.0000
ddmmm	chr3:183354330-183354555(+)$1	225	7	12	15.0000
nnnnn	chr9:36216970-36217214(-)$1	244	46	51	15.0000
FFFFF	chr2:160624088-160624304(-)$1	216	73	78	15.0000
zccc]	chr21:38573824-38574041(+)$1	217	105	110	15.0000
::::D	chr15:44817257-44817473(-)$1	216	195	200	15.0000
FFFFF	chr11:11979417-11979633(-)$1	216	107	112	15.0000
rrrrr	chr5:73923389-73923622(-)$1	233	152	157	15.0000
iiii8	chr2:192289591-192289811(+)$1	220	152	157	15.0000
ee]dd	chr20:62566484-62566712(+)$1	228	168	173	15.0000
JJJJJ	chr4:113970707-113970935(+)$1	228	156	161	15.0000
GGGGG	chr2:210598578-210598796(+)$1	218	105	110	15.0000
hhhhh	chr1:879440-879662(-)$1	222	5	10	15.0000
=====	chr11:109295872-109296089(+)$1	217	60	65	15.0000
c]ccc	chr17:26722699-26722929(+)$1	230	211	216	15.0000
::eee	chr10:82288099-82288316(+)$1	217	49	54	15.0000
ggggg	chr7:32338675-32338894(-)$1	219	26	31	15.0000
:::dd	chr1:47683737-47683973(-)$1	236	0	5	15.0000
eeccc	chr1:183221082-183221298(-)$1	216	17	22	15.0000
fffft	chr8:29193954-29194171(+)$1	217	101	106	15.0000
KKEEE	chr4:83345304-83345525(+)$1	221	48	53	15.0000

#DB
)))))	chr17:45209550-45209766(-)$1	1	153	158	15.0000
((.((	chr17:15948048-15948264(-)$1	1	56	61	15.0000
(((..	chr1:200828450-200828671(+)$1	1	14	19	15.0000
.))))	chr16:47653068-47653284(-)$1	1	75	80	15.0000
)))))	chr19:37641312-37641529(-)$1	1	70	75	15.0000
.....	chr5:77782040-77782258(-)$1	1	38	43	15.0000
...((	chr15:79214377-79214612(-)$1	1	54	59	15.0000
..((.	chr17:70121368-70121586(-)$1	1	125	130	15.0000
)))))	chr10:73819533-73819772(-)$1	1	66	71	15.0000
((...	chr1:176832660-176832878(-)$1	1	9	14	15.0000
((...	chr5:83237579-83237809(-)$1	1	90	95	15.0000
))))(	chr7:148114378-148114594(+)$1	1	12	17	15.0000
((...	chr1:32958516-32958732(+)$1	1	9	14	15.0000
....(	chr1:109855947-109856164(-)$1	1	103	108	15.0000
.....	chr8:13372184-13372403(+)$1	1	4	9	15.0000
....(	chr20:62375152-62375371(-)$1	1	66	71	15.0000
))...	chr10:97631578-97631798(-)$1	1	137	142	15.0000
(....	chr12:109016073-109016322(-)$1	1	103	108	15.0000
(....	chrX:154467521-154467738(+)$1	1	18	23	15.0000
(((((	chr16:64980718-64980933(+)$1	1	68	73	15.0000
))..)	chr8:86037071-86037289(-)$1	1	53	58	15.0000
..)))	chr10:135039678-135039907(+)$1	1	211	216	15.0000
(....	chr6:55299187-55299405(-)$1	1	180	185	15.0000
.....	chr5:102433324-102433542(-)$1	1	103	108	15.0000
.((((	chr5:141000887-141001106(-)$1	1	102	107	15.0000
(((..	chr12:68688518-68688733(-)$1	1	129	134	15.0000
.....	chr15:74421808-74422023(-)$1	1	29	34	15.0000
)))))	chr7:120389463-120389681(+)$1	1	180	185	15.0000
(((((	chr9:117052996-117053218(+)$1	1	82	87	15.0000
((...	chr3:183354330-183354555(+)$1	1	7	12	15.0000
.....	chr9:36216970-36217214(-)$1	1	46	51	15.0000
(((((	chr2:160624088-160624304(-)$1	1	73	78	15.0000
.))).	chr21:38573824-38574041(+)$1	1	105	110	15.0000
....)	chr15:44817257-44817473(-)$1	1	195	200	15.0000
(((((	chr11:11979417-11979633(-)$1	1	107	112	15.0000
.....	chr5:73923389-73923622(-)$1	1	152	157	15.0000
)))).	chr2:192289591-192289811(+)$1	1	152	157	15.0000
)).))	chr20:62566484-62566712(+)$1	1	168	173	15.0000
(((((	chr4:113970707-113970935(+)$1	1	156	161	15.0000
)))))	chr2:210598578-210598796(+)$1	1	105	110	15.0000
(((((	chr1:879440-879662(-)$1	1	5	10	15.0000
)))))	chr11:109295872-109296089(+)$1	1	60	65	15.0000
).)))	chr17:26722699-26722929(+)$1	1	211	216	15.0000
..(((	chr10:82288099-82288316(+)$1	1	49	54	15.0000
(((((	chr7:32338675-32338894(-)$1	1	26	31	15.0000
...((	chr1:47683737-47683973(-)$1	1	0	5	15.0000
(((((	chr1:183221082-183221298(-)$1	1	17	22	15.0000
((((.	chr8:29193954-29194171(+)$1	1	101	106	15.0000
..(((	chr4:83345304-83345525(+)$1	1	48	53	15.0000

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

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m2_run1.nuc.txt

#NT
UGCAG	chr8:22423787-22424014(+)$1	227	65	70	15.0000
UGCAG	chr2:10584502-10584750(-)$1	248	72	77	15.0000
UGCAG	chr1:1192276-1192536(-)$1	260	21	26	15.0000
UGCAG	chr19:6413432-6413685(-)$1	253	97	102	15.0000
UGCAG	chr11:129979298-129979565(+)$1	267	30	35	15.0000
UGCAG	chr16:28884918-28885167(+)$1	249	137	142	15.0000
UGCAG	chr8:41476183-41476425(+)$1	242	112	117	15.0000
UGCAG	chr19:12848227-12848499(+)$1	272	248	253	15.0000
UGCAG	chr9:139617658-139617896(+)$1	238	38	43	15.0000
UGCAG	chrX:153609307-153609555(+)$1	248	221	226	15.0000
UGCAG	chr16:2580640-2580895(+)$1	255	230	235	15.0000
UGCAG	chr19:36223452-36223719(+)$1	267	221	226	15.0000
UGCAG	chr10:102286136-102286367(-)$1	231	11	16	15.0000
UGCAG	chrX:102931630-102931895(-)$1	265	25	30	15.0000
UGCAG	chr17:57744062-57744301(+)$1	239	183	188	15.0000
UGCAG	chr9:131493530-131493769(-)$1	239	112	117	15.0000
UGCAG	chr17:1554082-1554350(-)$1	268	205	210	15.0000
UGCAG	chr17:27086403-27086670(-)$1	267	166	171	15.0000
UGCAG	chr2:5834019-5834261(+)$1	242	194	199	15.0000
UGCAG	chr6:168281008-168281245(+)$1	237	50	55	15.0000
UGCAG	chr22:19504245-19504509(+)$1	264	53	58	15.0000
UGCAG	chrX:153284052-153284311(-)$1	259	101	106	15.0000
UGCAG	chr19:2249420-2249662(+)$1	242	170	175	15.0000
UGCAG	chr7:135612425-135612665(-)$1	240	17	22	15.0000
UGCAG	chr1:226566826-226567073(-)$1	247	23	28	15.0000
UGCAG	chr1:19473291-19473522(-)$1	231	53	58	15.0000
UGCAG	chr1:92946378-92946634(-)$1	256	97	102	15.0000
UGCAG	chr9:139616512-139616787(+)$1	275	14	19	15.0000
UGCAG	chr16:28877957-28878216(+)$1	259	197	202	15.0000
UGCAG	chr1:27023437-27023702(+)$1	265	7	12	15.0000
UGCAG	chr1:84944864-84945116(+)$1	252	183	188	15.0000
UGCAG	chr19:12841662-12841956(-)$1	294	240	245	15.0000
UGCAG	chr1:33237289-33237538(+)$1	249	141	146	15.0000
UGCAG	chr1:248020772-248020993(+)$1	221	170	175	15.0000
UGCAG	chr19:49129447-49129717(+)$1	270	219	224	15.0000
UGCAG	chr1:17359454-17359667(-)$1	213	103	108	15.0000
UGCAG	chr19:47290665-47290943(-)$1	278	48	53	15.0000
UGCAG	chr14:51223835-51224099(-)$1	264	203	208	15.0000
UGCAG	chr12:48177843-48178079(-)$1	236	97	102	15.0000
UGCAG	chr5:140081551-140081789(+)$1	238	48	53	15.0000
UGCAG	chr4:71690975-71691208(-)$1	233	164	169	15.0000

#otherMatches

#Struct PSSM
bmmmm	chr17:38191439-38191695(-)$1	256	180	185	15.0000
fffff	chr8:22423787-22424014(+)$1	227	65	70	15.0000
ccc[d	chr2:10584502-10584750(-)$1	248	72	77	15.0000
cccDD	chr1:1192276-1192536(-)$1	260	21	26	15.0000
ldddd	chr19:6413432-6413685(-)$1	253	97	102	15.0000
!eeee	chr11:129979298-129979565(+)$1	267	30	35	15.0000
ee!!d	chr16:28884918-28885167(+)$1	249	137	142	15.0000
ggggg	chr8:41476183-41476425(+)$1	242	112	117	15.0000
gCCC}	chr19:12848227-12848499(+)$1	272	248	253	15.0000
FFFFF	chr9:139617658-139617896(+)$1	238	38	43	15.0000
6dddd	chrX:153609307-153609555(+)$1	248	221	226	15.0000
ff!!b	chr16:2580640-2580895(+)$1	255	230	235	15.0000
lbb22	chr19:36223452-36223719(+)$1	267	221	226	15.0000
[iiii	chr10:102286136-102286367(-)$1	231	11	16	15.0000
ccc::	chrX:102931630-102931895(-)$1	265	25	30	15.0000
cca]c	chr17:57744062-57744301(+)$1	239	183	188	15.0000
ppddd	chr9:131493530-131493769(-)$1	239	112	117	15.0000
mmmmf	chr17:1554082-1554350(-)$1	268	205	210	15.0000
ff[bb	chr17:27086403-27086670(-)$1	267	166	171	15.0000
FFFFF	chr2:5834019-5834261(+)$1	242	194	199	15.0000
:dddd	chr6:168281008-168281245(+)$1	237	50	55	15.0000
ppppd	chr22:19504245-19504509(+)$1	264	53	58	15.0000
pccc2	chrX:153284052-153284311(-)$1	259	101	106	15.0000
[aa[a	chr19:2249420-2249662(+)$1	242	170	175	15.0000
$$ccc	chr7:135612425-135612665(-)$1	240	17	22	15.0000
IIIII	chr1:226566826-226567073(-)$1	247	23	28	15.0000
[a!!d	chr1:19473291-19473522(-)$1	231	53	58	15.0000
c]fff	chr1:92946378-92946634(-)$1	256	97	102	15.0000
eeee[	chr9:139616512-139616787(+)$1	275	14	19	15.0000
!!ccc	chr16:28877957-28878216(+)$1	259	197	202	15.0000
EEE{F	chr1:27023437-27023702(+)$1	265	7	12	15.0000
EEE}F	chr1:84944864-84945116(+)$1	252	183	188	15.0000
::ccc	chr19:12841662-12841956(-)$1	294	240	245	15.0000
mbb]b	chr1:33237289-33237538(+)$1	249	141	146	15.0000
=gggg	chr1:248020772-248020993(+)$1	221	170	175	15.0000
GGGGG	chr19:49129447-49129717(+)$1	270	219	224	15.0000
uuuua	chr1:17359454-17359667(-)$1	213	103	108	15.0000
fffff	chr19:47290665-47290943(-)$1	278	48	53	15.0000
b[bb#	chr14:51223835-51224099(-)$1	264	203	208	15.0000
bbddd	chr12:48177843-48178079(-)$1	236	97	102	15.0000
::::c	chr5:140081551-140081789(+)$1	238	48	53	15.0000
llddd	chr4:71690975-71691208(-)$1	233	164	169	15.0000

#DB
(....	chr17:38191439-38191695(-)$1	1	180	185	15.0000
)))))	chr8:22423787-22424014(+)$1	1	65	70	15.0000
(((.(	chr2:10584502-10584750(-)$1	1	72	77	15.0000
)))((	chr1:1192276-1192536(-)$1	1	21	26	15.0000
.))))	chr19:6413432-6413685(-)$1	1	97	102	15.0000
.((((	chr11:129979298-129979565(+)$1	1	30	35	15.0000
((..(	chr16:28884918-28885167(+)$1	1	137	142	15.0000
)))))	chr8:41476183-41476425(+)$1	1	112	117	15.0000
)))).	chr19:12848227-12848499(+)$1	1	248	253	15.0000
(((((	chr9:139617658-139617896(+)$1	1	38	43	15.0000
.))))	chrX:153609307-153609555(+)$1	1	221	226	15.0000
((..(	chr16:2580640-2580895(+)$1	1	230	235	15.0000
.))..	chr19:36223452-36223719(+)$1	1	221	226	15.0000
.((((	chr10:102286136-102286367(-)$1	1	11	16	15.0000
)))..	chrX:102931630-102931895(-)$1	1	25	30	15.0000
))).)	chr17:57744062-57744301(+)$1	1	183	188	15.0000
..)))	chr9:131493530-131493769(-)$1	1	112	117	15.0000
....)	chr17:1554082-1554350(-)$1	1	205	210	15.0000
((.((	chr17:27086403-27086670(-)$1	1	166	171	15.0000
)))))	chr2:5834019-5834261(+)$1	1	194	199	15.0000
.((((	chr6:168281008-168281245(+)$1	1	50	55	15.0000
....)	chr22:19504245-19504509(+)$1	1	53	58	15.0000
.))).	chrX:153284052-153284311(-)$1	1	101	106	15.0000
.((.(	chr19:2249420-2249662(+)$1	1	170	175	15.0000
..(((	chr7:135612425-135612665(-)$1	1	17	22	15.0000
(((((	chr1:226566826-226567073(-)$1	1	23	28	15.0000
.(..(	chr1:19473291-19473522(-)$1	1	53	58	15.0000
).)))	chr1:92946378-92946634(-)$1	1	97	102	15.0000
((((.	chr9:139616512-139616787(+)$1	1	14	19	15.0000
..(((	chr16:28877957-28878216(+)$1	1	197	202	15.0000
(((.(	chr1:27023437-27023702(+)$1	1	7	12	15.0000
))).)	chr1:84944864-84945116(+)$1	1	183	188	15.0000
..(((	chr19:12841662-12841956(-)$1	1	240	245	15.0000
.)).)	chr1:33237289-33237538(+)$1	1	141	146	15.0000
)))))	chr1:248020772-248020993(+)$1	1	170	175	15.0000
)))))	chr19:49129447-49129717(+)$1	1	219	224	15.0000
....)	chr1:17359454-17359667(-)$1	1	103	108	15.0000
)))))	chr19:47290665-47290943(-)$1	1	48	53	15.0000
(.((.	chr14:51223835-51224099(-)$1	1	203	208	15.0000
(((((	chr12:48177843-48178079(-)$1	1	97	102	15.0000
....(	chr5:140081551-140081789(+)$1	1	48	53	15.0000
..)))	chr4:71690975-71691208(-)$1	1	164	169	15.0000

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

#score	630.0000000000001
#seq	42
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m2_run1.nuc.txt

#NT
CCUU	chr10:75135444-75135698(-)$1	254	6	10	12.0000
CCUU	chr2:178094948-178095242(-)$1	294	223	227	12.0000
CCUU	chr17:61497864-61498152(+)$1	288	75	79	12.0000
CCUU	chr1:149822527-149822865(+)$1	338	221	225	12.0000
CCUU	chr1:150191385-150191658(-)$1	273	18	22	12.0000
CCUU	chr7:139107724-139107989(+)$1	265	128	132	12.0000
CCUU	chr9:123942328-123942571(-)$1	243	7	11	12.0000
CCUU	chr12:125515408-125515653(+)$1	245	134	138	12.0000
CCUU	chr19:21909338-21909630(-)$1	292	13	17	12.0000
CCUU	chr6:26378291-26378537(+)$1	246	117	121	12.0000
CCUU	chr1:165877043-165877285(+)$1	242	144	148	12.0000
CCUU	chr16:24829828-24830083(+)$1	255	46	50	12.0000
CCUU	chr6:36654599-36654897(+)$1	298	90	94	12.0000
CCUU	chr7:128097379-128097619(+)$1	240	104	108	12.0000
CCUU	chr1:154243156-154243425(+)$1	269	167	171	12.0000
CCUU	chr11:8009041-8009295(+)$1	254	111	115	12.0000
CCUU	chr1:149814081-149814419(-)$1	338	222	226	12.0000
CCUU	chr19:13250756-13251001(+)$1	245	82	86	12.0000
CCUU	chr15:52842811-52843066(-)$1	255	110	114	12.0000
CCUU	chr11:57468509-57468757(+)$1	248	79	83	12.0000
CCUU	chr17:67273768-67274007(-)$1	239	145	149	12.0000
CCUU	chr2:61705377-61705621(-)$1	244	43	47	12.0000
CCUU	chr12:125396089-125396341(-)$1	252	88	92	12.0000
CCUU	chr5:68505507-68505752(+)$1	245	28	32	12.0000
CCUU	chr17:26900035-26900339(-)$1	304	102	106	12.0000
CCUU	chr6:64286671-64286944(+)$1	273	199	203	12.0000
CCUU	chr5:162945164-162945415(+)$1	251	104	108	12.0000
CCUU	chr12:110784955-110785216(+)$1	261	31	35	12.0000
CCUU	chr19:11243928-11244175(+)$1	247	161	165	12.0000
CCUU	chr18:48701166-48701415(-)$1	249	30	34	12.0000
CCUU	chr12:120638451-120638739(-)$1	288	194	198	12.0000
CCUU	chr2:70316168-70316407(+)$1	239	180	184	12.0000
CCUU	chr19:48833486-48833725(+)$1	239	92	96	12.0000
CCUU	chr19:18418082-18418322(-)$1	240	159	163	12.0000
CCUU	chr6:106557080-106557330(+)$1	250	3	7	12.0000
CCUU	chr9:125622236-125622508(-)$1	272	68	72	12.0000
CCUU	chr8:97243942-97244232(-)$1	290	134	138	12.0000
CCUU	chr11:9611127-9611402(+)$1	275	172	176	12.0000
CCUU	chr11:62392443-62392730(-)$1	287	10	14	12.0000
CCUU	chr17:38248944-38249217(-)$1	273	30	34	12.0000
CCUU	chr4:99982927-99983215(+)$1	288	123	127	12.0000
CCUU	chr17:47371952-47372213(-)$1	261	8	12	12.0000
CCUU	chr7:104753006-104753283(+)$1	277	113	117	12.0000
CCUU	chr19:42799773-42800050(+)$1	277	77	81	12.0000
CCUU	chr2:173431509-173431765(+)$1	256	44	48	12.0000
CCUU	chr3:41281768-41282036(+)$1	268	42	46	12.0000
CCUU	chr9:88886846-88887093(-)$1	247	107	111	12.0000
CCUU	chrX:77381241-77381501(+)$1	260	52	56	12.0000
CCUU	chr9:82341279-82341518(+)$1	239	33	37	12.0000
CCUU	chr12:77417503-77417742(-)$1	239	41	45	12.0000
CCUU	chr16:48573047-48573280(-)$1	233	138	142	12.0000
CCUU	chr17:79477854-79478133(-)$1	279	29	33	12.0000
CCUU	chr12:54635236-54635492(-)$1	256	16	20	12.0000
CCUU	chr12:58088433-58088685(+)$1	252	55	59	12.0000
CCUU	chr4:2517081-2517337(+)$1	256	173	177	12.0000
CCUU	chr16:30958450-30958691(+)$1	241	57	61	12.0000
CCUU	chr17:42113165-42113404(-)$1	239	61	65	12.0000
CCUU	chr17:65739954-65740186(+)$1	232	34	38	12.0000
CCUU	chr17:77766418-77766672(-)$1	254	67	71	12.0000
CCUU	chr13:41834885-41835144(-)$1	259	22	26	12.0000
CCUU	chr7:104747831-104748070(+)$1	239	13	17	12.0000
CCUU	chr17:20902926-20903193(-)$1	267	189	193	12.0000
CCUU	chr17:76220975-76221235(+)$1	260	253	257	12.0000
CCUU	chr6:34213232-34213480(+)$1	248	13	17	12.0000
CCUU	chr10:23729813-23730073(+)$1	260	31	35	12.0000
CCUU	chr10:72183581-72183843(+)$1	262	209	213	12.0000
CCUU	chr17:40023072-40023363(-)$1	291	218	222	12.0000
CCUU	chr12:49412900-49413218(-)$1	318	128	132	12.0000
CCUU	chr10:98982373-98982613(-)$1	240	63	67	12.0000
CCUU	chr22:19035867-19036123(-)$1	256	233	237	12.0000
CCUU	chr2:242292445-242292711(+)$1	266	30	34	12.0000
CCUU	chr6:30568803-30569040(-)$1	237	6	10	12.0000
CCUU	chr1:156713060-156713302(-)$1	242	27	31	12.0000
CCUU	chr10:102123105-102123475(+)$1	370	29	33	12.0000
CCUU	chr20:47674920-47675188(+)$1	268	51	55	12.0000
CCUU	chr7:107555990-107556236(+)$1	246	67	71	12.0000
CCUU	chr4:1694785-1695026(-)$1	241	128	132	12.0000
CCUU	chr16:46711121-46711372(-)$1	251	36	40	12.0000
CCUU	chr17:17168006-17168271(-)$1	265	8	12	12.0000
CCUU	chr16:1375164-1375427(+)$1	263	52	56	12.0000
CCUU	chr19:4657500-4657740(-)$1	240	66	70	12.0000
CCUU	chr14:75129736-75130001(-)$1	265	19	23	12.0000

#otherMatches

#Struct PSSM
::dd	chr2:204299788-204300027(-)$1	239	54	58	12.0000
::::	chr10:75135444-75135698(-)$1	254	6	10	12.0000
gggg	chr2:178094948-178095242(-)$1	294	223	227	12.0000
::::	chr17:61497864-61498152(+)$1	288	75	79	12.0000
eeee	chr1:149822527-149822865(+)$1	338	221	225	12.0000
ooof	chr1:150191385-150191658(-)$1	273	18	22	12.0000
::gg	chr7:139107724-139107989(+)$1	265	128	132	12.0000
IIII	chr9:123942328-123942571(-)$1	243	7	11	12.0000
llcc	chr12:125515408-125515653(+)$1	245	134	138	12.0000
::::	chr19:21909338-21909630(-)$1	292	13	17	12.0000
hhhc	chr6:26378291-26378537(+)$1	246	117	121	12.0000
E:::	chr1:165877043-165877285(+)$1	242	144	148	12.0000
MMMB	chr16:24829828-24830083(+)$1	255	46	50	12.0000
:JJJ	chr6:36654599-36654897(+)$1	298	90	94	12.0000
dbb:	chr7:128097379-128097619(+)$1	240	104	108	12.0000
5ggg	chr1:154243156-154243425(+)$1	269	167	171	12.0000
g777	chr11:8009041-8009295(+)$1	254	111	115	12.0000
eeee	chr1:149814081-149814419(-)$1	338	222	226	12.0000
GGG{	chr19:13250756-13251001(+)$1	245	82	86	12.0000
7777	chr15:52842811-52843066(-)$1	255	110	114	12.0000
::::	chr11:57468509-57468757(+)$1	248	79	83	12.0000
b!!c	chr17:67273768-67274007(-)$1	239	145	149	12.0000
bggg	chr2:61705377-61705621(-)$1	244	43	47	12.0000
====	chr12:125396089-125396341(-)$1	252	88	92	12.0000
ccco	chr5:68505507-68505752(+)$1	245	28	32	12.0000
$$$c	chr17:26900035-26900339(-)$1	304	102	106	12.0000
eeee	chr6:64286671-64286944(+)$1	273	199	203	12.0000
c333	chr5:162945164-162945415(+)$1	251	104	108	12.0000
cc]b	chr12:110784955-110785216(+)$1	261	31	35	12.0000
eenn	chr19:11243928-11244175(+)$1	247	161	165	12.0000
ccnn	chr18:48701166-48701415(-)$1	249	30	34	12.0000
ff::	chr12:120638451-120638739(-)$1	288	194	198	12.0000
gggg	chr2:70316168-70316407(+)$1	239	180	184	12.0000
ff99	chr19:48833486-48833725(+)$1	239	92	96	12.0000
ffff	chr19:18418082-18418322(-)$1	240	159	163	12.0000
gggg	chr6:106557080-106557330(+)$1	250	3	7	12.0000
ff]d	chr9:125622236-125622508(-)$1	272	68	72	12.0000
yyyy	chr8:97243942-97244232(-)$1	290	134	138	12.0000
33ee	chr11:9611127-9611402(+)$1	275	172	176	12.0000
DMMM	chr11:62392443-62392730(-)$1	287	10	14	12.0000
ba]e	chr17:38248944-38249217(-)$1	273	30	34	12.0000
qqqq	chr4:99982927-99983215(+)$1	288	123	127	12.0000
FFFM	chr17:47371952-47372213(-)$1	261	8	12	12.0000
"""b	chr7:104753006-104753283(+)$1	277	113	117	12.0000
::HH	chr19:42799773-42800050(+)$1	277	77	81	12.0000
beee	chr2:173431509-173431765(+)$1	256	44	48	12.0000
RRRR	chr3:41281768-41282036(+)$1	268	42	46	12.0000
ffff	chr9:88886846-88887093(-)$1	247	107	111	12.0000
[bb!	chrX:77381241-77381501(+)$1	260	52	56	12.0000
%%%%	chr9:82341279-82341518(+)$1	239	33	37	12.0000
FEEE	chr12:77417503-77417742(-)$1	239	41	45	12.0000
9999	chr16:48573047-48573280(-)$1	233	138	142	12.0000
ceee	chr17:79477854-79478133(-)$1	279	29	33	12.0000
::::	chr12:54635236-54635492(-)$1	256	16	20	12.0000
EEEE	chr12:58088433-58088685(+)$1	252	55	59	12.0000
333c	chr4:2517081-2517337(+)$1	256	173	177	12.0000
d$$$	chr16:30958450-30958691(+)$1	241	57	61	12.0000
^^^^	chr17:42113165-42113404(-)$1	239	61	65	12.0000
EEff	chr17:65739954-65740186(+)$1	232	34	38	12.0000
pppp	chr17:77766418-77766672(-)$1	254	67	71	12.0000
FFFN	chr13:41834885-41835144(-)$1	259	22	26	12.0000
D:::	chr7:104747831-104748070(+)$1	239	13	17	12.0000
^^^^	chr17:20902926-20903193(-)$1	267	189	193	12.0000
bb::	chr17:76220975-76221235(+)$1	260	253	257	12.0000
FFFF	chr6:34213232-34213480(+)$1	248	13	17	12.0000
::::	chr10:23729813-23730073(+)$1	260	31	35	12.0000
f!!d	chr10:72183581-72183843(+)$1	262	209	213	12.0000
::::	chr17:40023072-40023363(-)$1	291	218	222	12.0000
[ccc	chr12:49412900-49413218(-)$1	318	128	132	12.0000
ccco	chr10:98982373-98982613(-)$1	240	63	67	12.0000
IIII	chr22:19035867-19036123(-)$1	256	233	237	12.0000
nngg	chr2:242292445-242292711(+)$1	266	30	34	12.0000
IIII	chr6:30568803-30569040(-)$1	237	6	10	12.0000
++++	chr1:156713060-156713302(-)$1	242	27	31	12.0000
ffff	chr10:102123105-102123475(+)$1	370	29	33	12.0000
::::	chr20:47674920-47675188(+)$1	268	51	55	12.0000
d:::	chr7:107555990-107556236(+)$1	246	67	71	12.0000
ccc]	chr4:1694785-1695026(-)$1	241	128	132	12.0000
uuuu	chr16:46711121-46711372(-)$1	251	36	40	12.0000
bb[b	chr17:17168006-17168271(-)$1	265	8	12	12.0000
IIIF	chr16:1375164-1375427(+)$1	263	52	56	12.0000
DDDM	chr19:4657500-4657740(-)$1	240	66	70	12.0000
GGGG	chr14:75129736-75130001(-)$1	265	19	23	12.0000

#DB
..((	chr2:204299788-204300027(-)$1	1	54	58	12.0000
....	chr10:75135444-75135698(-)$1	1	6	10	12.0000
))))	chr2:178094948-178095242(-)$1	1	223	227	12.0000
....	chr17:61497864-61498152(+)$1	1	75	79	12.0000
((((	chr1:149822527-149822865(+)$1	1	221	225	12.0000
...)	chr1:150191385-150191658(-)$1	1	18	22	12.0000
..((	chr7:139107724-139107989(+)$1	1	128	132	12.0000
((((	chr9:123942328-123942571(-)$1	1	7	11	12.0000
..))	chr12:125515408-125515653(+)$1	1	134	138	12.0000
....	chr19:21909338-21909630(-)$1	1	13	17	12.0000
))))	chr6:26378291-26378537(+)$1	1	117	121	12.0000
)...	chr1:165877043-165877285(+)$1	1	144	148	12.0000
...(	chr16:24829828-24830083(+)$1	1	46	50	12.0000
.)))	chr6:36654599-36654897(+)$1	1	90	94	12.0000
))).	chr7:128097379-128097619(+)$1	1	104	108	12.0000
.)))	chr1:154243156-154243425(+)$1	1	167	171	12.0000
)...	chr11:8009041-8009295(+)$1	1	111	115	12.0000
((((	chr1:149814081-149814419(-)$1	1	222	226	12.0000
(((.	chr19:13250756-13251001(+)$1	1	82	86	12.0000
....	chr15:52842811-52843066(-)$1	1	110	114	12.0000
....	chr11:57468509-57468757(+)$1	1	79	83	12.0000
(..(	chr17:67273768-67274007(-)$1	1	145	149	12.0000
((((	chr2:61705377-61705621(-)$1	1	43	47	12.0000
))))	chr12:125396089-125396341(-)$1	1	88	92	12.0000
(((.	chr5:68505507-68505752(+)$1	1	28	32	12.0000
...(	chr17:26900035-26900339(-)$1	1	102	106	12.0000
((((	chr6:64286671-64286944(+)$1	1	199	203	12.0000
)...	chr5:162945164-162945415(+)$1	1	104	108	12.0000
)).)	chr12:110784955-110785216(+)$1	1	31	35	12.0000
((..	chr19:11243928-11244175(+)$1	1	161	165	12.0000
((..	chr18:48701166-48701415(-)$1	1	30	34	12.0000
))..	chr12:120638451-120638739(-)$1	1	194	198	12.0000
((((	chr2:70316168-70316407(+)$1	1	180	184	12.0000
))..	chr19:48833486-48833725(+)$1	1	92	96	12.0000
))))	chr19:18418082-18418322(-)$1	1	159	163	12.0000
((((	chr6:106557080-106557330(+)$1	1	3	7	12.0000
)).)	chr9:125622236-125622508(-)$1	1	68	72	12.0000
....	chr8:97243942-97244232(-)$1	1	134	138	12.0000
..))	chr11:9611127-9611402(+)$1	1	172	176	12.0000
(...	chr11:62392443-62392730(-)$1	1	10	14	12.0000
)).)	chr17:38248944-38249217(-)$1	1	30	34	12.0000
....	chr4:99982927-99983215(+)$1	1	123	127	12.0000
(((.	chr17:47371952-47372213(-)$1	1	8	12	12.0000
...(	chr7:104753006-104753283(+)$1	1	113	117	12.0000
..((	chr19:42799773-42800050(+)$1	1	77	81	12.0000
))))	chr2:173431509-173431765(+)$1	1	44	48	12.0000
....	chr3:41281768-41282036(+)$1	1	42	46	12.0000
))))	chr9:88886846-88887093(-)$1	1	107	111	12.0000
.((.	chrX:77381241-77381501(+)$1	1	52	56	12.0000
....	chr9:82341279-82341518(+)$1	1	33	37	12.0000
((((	chr12:77417503-77417742(-)$1	1	41	45	12.0000
....	chr16:48573047-48573280(-)$1	1	138	142	12.0000
((((	chr17:79477854-79478133(-)$1	1	29	33	12.0000
....	chr12:54635236-54635492(-)$1	1	16	20	12.0000
((((	chr12:58088433-58088685(+)$1	1	55	59	12.0000
...)	chr4:2517081-2517337(+)$1	1	173	177	12.0000
(...	chr16:30958450-30958691(+)$1	1	57	61	12.0000
....	chr17:42113165-42113404(-)$1	1	61	65	12.0000
((((	chr17:65739954-65740186(+)$1	1	34	38	12.0000
....	chr17:77766418-77766672(-)$1	1	67	71	12.0000
(((.	chr13:41834885-41835144(-)$1	1	22	26	12.0000
(...	chr7:104747831-104748070(+)$1	1	13	17	12.0000
....	chr17:20902926-20903193(-)$1	1	189	193	12.0000
))..	chr17:76220975-76221235(+)$1	1	253	257	12.0000
((((	chr6:34213232-34213480(+)$1	1	13	17	12.0000
....	chr10:23729813-23730073(+)$1	1	31	35	12.0000
(..(	chr10:72183581-72183843(+)$1	1	209	213	12.0000
....	chr17:40023072-40023363(-)$1	1	218	222	12.0000
.(((	chr12:49412900-49413218(-)$1	1	128	132	12.0000
(((.	chr10:98982373-98982613(-)$1	1	63	67	12.0000
))))	chr22:19035867-19036123(-)$1	1	233	237	12.0000
..))	chr2:242292445-242292711(+)$1	1	30	34	12.0000
((((	chr6:30568803-30569040(-)$1	1	6	10	12.0000
....	chr1:156713060-156713302(-)$1	1	27	31	12.0000
((((	chr10:102123105-102123475(+)$1	1	29	33	12.0000
....	chr20:47674920-47675188(+)$1	1	51	55	12.0000
)...	chr7:107555990-107556236(+)$1	1	67	71	12.0000
))).	chr4:1694785-1695026(-)$1	1	128	132	12.0000
....	chr16:46711121-46711372(-)$1	1	36	40	12.0000
((.(	chr17:17168006-17168271(-)$1	1	8	12	12.0000
((((	chr16:1375164-1375427(+)$1	1	52	56	12.0000
(((.	chr19:4657500-4657740(-)$1	1	66	70	12.0000
((((	chr14:75129736-75130001(-)$1	1	19	23	12.0000

#PSSM
C : 0.98	c : 0.01	
C : 0.98	c : 0.01	
U : 1.00	
U : 1.00	

#score	996.0000000000005
#seq	83
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m3_run1.nuc.txt

#NT
UCCC	chr12:31743571-31743794(+)$1	223	8	12	12.0000
UCCC	chr7:150748850-150749077(-)$1	227	178	182	12.0000
UCCC	chr11:45230462-45230686(+)$1	224	86	90	12.0000
UCCC	chr1:19476139-19476362(-)$1	223	64	68	12.0000
UCCC	chr16:31500334-31500555(+)$1	221	162	166	12.0000
UCCC	chr11:18503185-18503407(+)$1	222	36	40	12.0000
UCCC	chr9:18777188-18777415(+)$1	227	114	118	12.0000
UCCC	chr20:44519406-44519627(-)$1	221	62	66	12.0000
UCCC	chr22:32009271-32009495(+)$1	224	59	63	12.0000
UCCC	chr4:142053634-142053862(+)$1	228	62	66	12.0000
UCCC	chr3:195466659-195466883(+)$1	224	8	12	12.0000
UCCC	chr18:74680149-74680372(-)$1	223	159	163	12.0000
UCCC	chr20:44582467-44582688(-)$1	221	72	76	12.0000
UCCC	chr22:20779667-20779895(+)$1	228	40	44	12.0000
UCCC	chr16:70986266-70986488(+)$1	222	22	26	12.0000
UCCC	chr1:45288167-45288389(+)$1	222	117	121	12.0000
UCCC	chr9:139324649-139324871(-)$1	222	153	157	12.0000
UCCC	chr9:101006195-101006419(+)$1	224	90	94	12.0000
UCCC	chr10:105362442-105362666(+)$1	224	16	20	12.0000
UCCC	chr10:127683960-127684182(+)$1	222	135	139	12.0000
UCCC	chr2:148602636-148602857(+)$1	221	66	70	12.0000
UCCC	chr12:132623711-132623939(+)$1	228	80	84	12.0000
UCCC	chr10:83635385-83635607(-)$1	222	189	193	12.0000
UCCC	chr3:47458707-47458931(-)$1	224	21	25	12.0000
UCCC	chr1:1474981-1475203(-)$1	222	91	95	12.0000
UCCC	chr17:1546909-1547130(-)$1	221	198	202	12.0000
UCCC	chr3:50142413-50142662(+)$1	249	86	90	12.0000
UCCC	chr20:44999966-45000188(-)$1	222	43	47	12.0000
UCCC	chr16:51174155-51174376(-)$1	221	66	70	12.0000
UCCC	chr12:50474239-50474461(-)$1	222	178	182	12.0000
UCCC	chr7:72396740-72396962(-)$1	222	152	156	12.0000
uccc	chr15:40583563-40583790(+)$1	227	10	14	12.0000
UCCC	chr1:150526385-150526606(-)$1	221	39	43	12.0000
UCCC	chr12:31478115-31478343(-)$1	228	179	183	12.0000
UCCC	chr18:21269814-21270039(-)$1	225	25	29	12.0000
UCCC	chr19:40745915-40746139(+)$1	224	200	204	12.0000
uccc	chr17:73892587-73892827(-)$1	240	48	52	12.0000
UCCC	chr10:119134509-119134745(+)$1	236	32	36	12.0000
UCCC	chr12:56651527-56651750(+)$1	223	66	70	12.0000
UCCC	chr17:34195585-34195809(-)$1	224	3	7	12.0000
UCCC	chr5:159707433-159707656(-)$1	223	168	172	12.0000
UCCC	chr7:134131947-134132173(-)$1	226	53	57	12.0000
UCCC	chr19:10476282-10476503(+)$1	221	37	41	12.0000
UCCC	chr17:42289608-42289833(+)$1	225	20	24	12.0000
UCCC	chr19:12842056-12842282(+)$1	226	134	138	12.0000
UCCC	chr9:133228408-133228632(+)$1	224	37	41	12.0000
UCCC	chr16:89357333-89357560(+)$1	227	51	55	12.0000
UCCC	chr1:55223566-55223793(+)$1	227	48	52	12.0000
UCCC	chr14:20859030-20859255(+)$1	225	12	16	12.0000
UCCC	chr15:52241899-52242120(+)$1	221	66	70	12.0000
UCCC	chr8:36703286-36703512(-)$1	226	49	53	12.0000
UCCC	chr9:101552354-101552579(+)$1	225	78	82	12.0000
UCCC	chr6:3227596-3227823(+)$1	227	28	32	12.0000
UCCC	chr11:2441348-2441575(+)$1	227	3	7	12.0000
UCCC	chrX:153537683-153537907(-)$1	224	160	164	12.0000
UCCC	chr6:150341989-150342212(+)$1	223	1	5	12.0000
UCCC	chr2:28843041-28843263(-)$1	222	75	79	12.0000
UCCC	chr3:52390670-52390892(-)$1	222	64	68	12.0000
UCCC	chr17:31348149-31348373(+)$1	224	10	14	12.0000
UCCC	chr9:139835947-139836179(-)$1	232	34	38	12.0000
UCCC	chr8:104427188-104427423(+)$1	235	210	214	12.0000
UCCC	chr22:44287569-44287791(-)$1	222	2	6	12.0000
UCCC	chr1:223718045-223718266(+)$1	221	55	59	12.0000
UCCC	chr9:33271082-33271304(-)$1	222	134	138	12.0000
UCCC	chr11:82892893-82893117(+)$1	224	197	201	12.0000
UCCC	chr19:4697538-4697761(-)$1	223	89	93	12.0000
UCCC	chrX:47486866-47487089(+)$1	223	111	115	12.0000
UCCC	chr7:70254996-70255218(-)$1	222	134	138	12.0000
UCCC	chr11:65308228-65308453(+)$1	225	41	45	12.0000
UCCC	chr16:31088641-31088863(+)$1	222	37	41	12.0000
UCCC	chr8:120577017-120577238(-)$1	221	214	218	12.0000
UCCC	chr22:37420403-37420633(+)$1	230	13	17	12.0000
UCCC	chr18:28574193-28574415(+)$1	222	70	74	12.0000
UCCC	chr1:108742638-108742859(+)$1	221	15	19	12.0000
UCCC	chr19:5668177-5668406(-)$1	229	142	146	12.0000
UCCC	chr5:131606557-131606780(-)$1	223	98	102	12.0000

#otherMatches

#Struct PSSM
ssss	chr9:140355055-140355281(+)$1	226	79	83	12.0000
EEEE	chr12:31743571-31743794(+)$1	223	8	12	12.0000
ffll	chr7:150748850-150749077(-)$1	227	178	182	12.0000
ffff	chr11:45230462-45230686(+)$1	224	86	90	12.0000
pppp	chr1:19476139-19476362(-)$1	223	64	68	12.0000
"hhh	chr16:31500334-31500555(+)$1	221	162	166	12.0000
EEEE	chr11:18503185-18503407(+)$1	222	36	40	12.0000
333e	chr9:18777188-18777415(+)$1	227	114	118	12.0000
333f	chr20:44519406-44519627(-)$1	221	62	66	12.0000
ssss	chr22:32009271-32009495(+)$1	224	59	63	12.0000
::::	chr4:142053634-142053862(+)$1	228	62	66	12.0000
EGGG	chr3:195466659-195466883(+)$1	224	8	12	12.0000
::::	chr18:74680149-74680372(-)$1	223	159	163	12.0000
ceee	chr20:44582467-44582688(-)$1	221	72	76	12.0000
::ff	chr22:20779667-20779895(+)$1	228	40	44	12.0000
ufff	chr16:70986266-70986488(+)$1	222	22	26	12.0000
C}DD	chr1:45288167-45288389(+)$1	222	117	121	12.0000
eeee	chr9:139324649-139324871(-)$1	222	153	157	12.0000
d444	chr9:101006195-101006419(+)$1	224	90	94	12.0000
##==	chr10:105362442-105362666(+)$1	224	16	20	12.0000
]ccc	chr10:127683960-127684182(+)$1	222	135	139	12.0000
::cc	chr2:148602636-148602857(+)$1	221	66	70	12.0000
addd	chr12:132623711-132623939(+)$1	228	80	84	12.0000
eeee	chr10:83635385-83635607(-)$1	222	189	193	12.0000
dttt	chr3:47458707-47458931(-)$1	224	21	25	12.0000
ffff	chr1:1474981-1475203(-)$1	222	91	95	12.0000
mmme	chr17:1546909-1547130(-)$1	221	198	202	12.0000
ccc:	chr3:50142413-50142662(+)$1	249	86	90	12.0000
44dd	chr20:44999966-45000188(-)$1	222	43	47	12.0000
ee::	chr16:51174155-51174376(-)$1	221	66	70	12.0000
hhhh	chr12:50474239-50474461(-)$1	222	178	182	12.0000
FFFF	chr7:72396740-72396962(-)$1	222	152	156	12.0000
EEEC	chr15:40583563-40583790(+)$1	227	10	14	12.0000
ccc!	chr1:150526385-150526606(-)$1	221	39	43	12.0000
ddae	chr12:31478115-31478343(-)$1	228	179	183	12.0000
oeee	chr18:21269814-21270039(-)$1	225	25	29	12.0000
GGGG	chr19:40745915-40746139(+)$1	224	200	204	12.0000
ffqq	chr17:73892587-73892827(-)$1	240	48	52	12.0000
ccc[	chr10:119134509-119134745(+)$1	236	32	36	12.0000
ccc2	chr12:56651527-56651750(+)$1	223	66	70	12.0000
::::	chr17:34195585-34195809(-)$1	224	3	7	12.0000
ppdd	chr5:159707433-159707656(-)$1	223	168	172	12.0000
fff[	chr7:134131947-134132173(-)$1	226	53	57	12.0000
DDDD	chr19:10476282-10476503(+)$1	221	37	41	12.0000
DDDD	chr17:42289608-42289833(+)$1	225	20	24	12.0000
:ccc	chr19:12842056-12842282(+)$1	226	134	138	12.0000
gggg	chr9:133228408-133228632(+)$1	224	37	41	12.0000
ffff	chr16:89357333-89357560(+)$1	227	51	55	12.0000
ddd:	chr1:55223566-55223793(+)$1	227	48	52	12.0000
nfff	chr14:20859030-20859255(+)$1	225	12	16	12.0000
KKDD	chr15:52241899-52242120(+)$1	221	66	70	12.0000
cccF	chr8:36703286-36703512(-)$1	226	49	53	12.0000
]add	chr9:101552354-101552579(+)$1	225	78	82	12.0000
nnbb	chr6:3227596-3227823(+)$1	227	28	32	12.0000
DDCC	chr11:2441348-2441575(+)$1	227	3	7	12.0000
dddd	chrX:153537683-153537907(-)$1	224	160	164	12.0000
:::E	chr6:150341989-150342212(+)$1	223	1	5	12.0000
::::	chr2:28843041-28843263(-)$1	222	75	79	12.0000
leee	chr3:52390670-52390892(-)$1	222	64	68	12.0000
B{DD	chr17:31348149-31348373(+)$1	224	10	14	12.0000
[fff	chr9:139835947-139836179(-)$1	232	34	38	12.0000
hmmm	chr8:104427188-104427423(+)$1	235	210	214	12.0000
::EE	chr22:44287569-44287791(-)$1	222	2	6	12.0000
bbmm	chr1:223718045-223718266(+)$1	221	55	59	12.0000
b###	chr9:33271082-33271304(-)$1	222	134	138	12.0000
nnnn	chr11:82892893-82893117(+)$1	224	197	201	12.0000
>>>>	chr19:4697538-4697761(-)$1	223	89	93	12.0000
eeee	chrX:47486866-47487089(+)$1	223	111	115	12.0000
FFF:	chr7:70254996-70255218(-)$1	222	134	138	12.0000
DDD{	chr11:65308228-65308453(+)$1	225	41	45	12.0000
====	chr16:31088641-31088863(+)$1	222	37	41	12.0000
ff::	chr8:120577017-120577238(-)$1	221	214	218	12.0000
FFFG	chr22:37420403-37420633(+)$1	230	13	17	12.0000
&&ff	chr18:28574193-28574415(+)$1	222	70	74	12.0000
KKDD	chr1:108742638-108742859(+)$1	221	15	19	12.0000
gddd	chr19:5668177-5668406(-)$1	229	142	146	12.0000
ffff	chr5:131606557-131606780(-)$1	223	98	102	12.0000

#DB
....	chr9:140355055-140355281(+)$1	1	79	83	12.0000
((((	chr12:31743571-31743794(+)$1	1	8	12	12.0000
((..	chr7:150748850-150749077(-)$1	1	178	182	12.0000
((((	chr11:45230462-45230686(+)$1	1	86	90	12.0000
....	chr1:19476139-19476362(-)$1	1	64	68	12.0000
.(((	chr16:31500334-31500555(+)$1	1	162	166	12.0000
((((	chr11:18503185-18503407(+)$1	1	36	40	12.0000
...)	chr9:18777188-18777415(+)$1	1	114	118	12.0000
...)	chr20:44519406-44519627(-)$1	1	62	66	12.0000
....	chr22:32009271-32009495(+)$1	1	59	63	12.0000
....	chr4:142053634-142053862(+)$1	1	62	66	12.0000
((((	chr3:195466659-195466883(+)$1	1	8	12	12.0000
....	chr18:74680149-74680372(-)$1	1	159	163	12.0000
))))	chr20:44582467-44582688(-)$1	1	72	76	12.0000
..((	chr22:20779667-20779895(+)$1	1	40	44	12.0000
.)))	chr16:70986266-70986488(+)$1	1	22	26	12.0000
).))	chr1:45288167-45288389(+)$1	1	117	121	12.0000
))))	chr9:139324649-139324871(-)$1	1	153	157	12.0000
)...	chr9:101006195-101006419(+)$1	1	90	94	12.0000
..((	chr10:105362442-105362666(+)$1	1	16	20	12.0000
.)))	chr10:127683960-127684182(+)$1	1	135	139	12.0000
..((	chr2:148602636-148602857(+)$1	1	66	70	12.0000
))))	chr12:132623711-132623939(+)$1	1	80	84	12.0000
))))	chr10:83635385-83635607(-)$1	1	189	193	12.0000
(...	chr3:47458707-47458931(-)$1	1	21	25	12.0000
((((	chr1:1474981-1475203(-)$1	1	91	95	12.0000
...)	chr17:1546909-1547130(-)$1	1	198	202	12.0000
))).	chr3:50142413-50142662(+)$1	1	86	90	12.0000
..))	chr20:44999966-45000188(-)$1	1	43	47	12.0000
))..	chr16:51174155-51174376(-)$1	1	66	70	12.0000
((((	chr12:50474239-50474461(-)$1	1	178	182	12.0000
))))	chr7:72396740-72396962(-)$1	1	152	156	12.0000
((((	chr15:40583563-40583790(+)$1	1	10	14	12.0000
(((.	chr1:150526385-150526606(-)$1	1	39	43	12.0000
((((	chr12:31478115-31478343(-)$1	1	179	183	12.0000
.)))	chr18:21269814-21270039(-)$1	1	25	29	12.0000
))))	chr19:40745915-40746139(+)$1	1	200	204	12.0000
((..	chr17:73892587-73892827(-)$1	1	48	52	12.0000
(((.	chr10:119134509-119134745(+)$1	1	32	36	12.0000
))).	chr12:56651527-56651750(+)$1	1	66	70	12.0000
....	chr17:34195585-34195809(-)$1	1	3	7	12.0000
..))	chr5:159707433-159707656(-)$1	1	168	172	12.0000
(((.	chr7:134131947-134132173(-)$1	1	53	57	12.0000
((((	chr19:10476282-10476503(+)$1	1	37	41	12.0000
((((	chr17:42289608-42289833(+)$1	1	20	24	12.0000
.(((	chr19:12842056-12842282(+)$1	1	134	138	12.0000
((((	chr9:133228408-133228632(+)$1	1	37	41	12.0000
((((	chr16:89357333-89357560(+)$1	1	51	55	12.0000
))).	chr1:55223566-55223793(+)$1	1	48	52	12.0000
.)))	chr14:20859030-20859255(+)$1	1	12	16	12.0000
..((	chr15:52241899-52242120(+)$1	1	66	70	12.0000
)))(	chr8:36703286-36703512(-)$1	1	49	53	12.0000
.)))	chr9:101552354-101552579(+)$1	1	78	82	12.0000
..))	chr6:3227596-3227823(+)$1	1	28	32	12.0000
((((	chr11:2441348-2441575(+)$1	1	3	7	12.0000
))))	chrX:153537683-153537907(-)$1	1	160	164	12.0000
...(	chr6:150341989-150342212(+)$1	1	1	5	12.0000
....	chr2:28843041-28843263(-)$1	1	75	79	12.0000
.)))	chr3:52390670-52390892(-)$1	1	64	68	12.0000
(.((	chr17:31348149-31348373(+)$1	1	10	14	12.0000
.(((	chr9:139835947-139836179(-)$1	1	34	38	12.0000
(...	chr8:104427188-104427423(+)$1	1	210	214	12.0000
..((	chr22:44287569-44287791(-)$1	1	2	6	12.0000
((..	chr1:223718045-223718266(+)$1	1	55	59	12.0000
(...	chr9:33271082-33271304(-)$1	1	134	138	12.0000
....	chr11:82892893-82893117(+)$1	1	197	201	12.0000
....	chr19:4697538-4697761(-)$1	1	89	93	12.0000
))))	chrX:47486866-47487089(+)$1	1	111	115	12.0000
))).	chr7:70254996-70255218(-)$1	1	134	138	12.0000
(((.	chr11:65308228-65308453(+)$1	1	41	45	12.0000
((((	chr16:31088641-31088863(+)$1	1	37	41	12.0000
))..	chr8:120577017-120577238(-)$1	1	214	218	12.0000
((((	chr22:37420403-37420633(+)$1	1	13	17	12.0000
..((	chr18:28574193-28574415(+)$1	1	70	74	12.0000
..((	chr1:108742638-108742859(+)$1	1	15	19	12.0000
)(((	chr19:5668177-5668406(-)$1	1	142	146	12.0000
))))	chr5:131606557-131606780(-)$1	1	98	102	12.0000

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

#score	924.0000000000001
#seq	77
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m3_run2.nuc.txt

#NT
UUUG	chr1:1336091-1336320(+)$1	229	201	205	12.0000
UUUG	chr1:52485824-52486085(-)$1	261	71	75	12.0000
UUUG	chr4:56283241-56283472(+)$1	231	2	6	12.0000
UUUG	chr8:22879046-22879272(-)$1	226	15	19	12.0000
UUUG	chr1:32637231-32637474(+)$1	243	144	148	12.0000
UUUG	chr8:103661632-103661860(-)$1	228	73	77	12.0000
UUUG	chr1:245017531-245017757(-)$1	226	135	139	12.0000
UUUG	chr17:45695697-45695923(+)$1	226	83	87	12.0000
UUUG	chr2:71415381-71415602(-)$1	221	5	9	12.0000
UUUG	chr11:33731226-33731451(-)$1	225	36	40	12.0000
UUUG	chr19:4443097-4443320(+)$1	223	12	16	12.0000
UUUG	chr18:19781644-19781871(+)$1	227	28	32	12.0000
UUUG	chr12:96051903-96052126(-)$1	223	147	151	12.0000
UUUG	chr13:39623042-39623277(+)$1	235	47	51	12.0000
UUUG	chr3:57557402-57557627(-)$1	225	63	67	12.0000
UUUG	chr11:129734123-129734377(-)$1	254	128	132	12.0000
UUUG	chr3:141012240-141012466(+)$1	226	104	108	12.0000
uuug	chr10:127569351-127569572(-)$1	221	21	25	12.0000
UUUG	chr19:49122301-49122536(-)$1	235	149	153	12.0000
UUUG	chr2:174771651-174771877(-)$1	226	133	137	12.0000
UUUG	chr14:20926183-20926417(-)$1	234	93	97	12.0000
UUUG	chr12:12271864-12272087(-)$1	223	1	5	12.0000
UUUG	chr19:47504327-47504589(+)$1	262	204	208	12.0000
UUUG	chr15:65869992-65870217(+)$1	225	44	48	12.0000
UUUG	chr6:150140019-150140239(-)$1	220	5	9	12.0000
UUUG	chr14:81645462-81645694(-)$1	232	212	216	12.0000
UUUG	chr12:56635063-56635308(-)$1	245	24	28	12.0000
UUUG	chr16:87364706-87364932(-)$1	226	117	121	12.0000
UUUG	chr12:39687110-39687333(-)$1	223	118	122	12.0000
UUUG	chr19:4046416-4046663(-)$1	247	122	126	12.0000
UUUG	chr1:156712157-156712399(-)$1	242	101	105	12.0000
UUUG	chr1:109817512-109817750(+)$1	238	16	20	12.0000
UUUG	chr9:127909189-127909449(-)$1	260	56	60	12.0000
UUUG	chr2:128460034-128460267(+)$1	233	89	93	12.0000
UUUG	chr16:31202225-31202485(+)$1	260	48	52	12.0000
UUUG	chr20:48521309-48521540(-)$1	231	39	43	12.0000
UUUG	chr13:78338093-78338324(+)$1	231	34	38	12.0000
UUUG	chr2:220149900-220150126(+)$1	226	101	105	12.0000
UUUG	chr12:131360614-131360835(+)$1	221	44	48	12.0000
UUUG	chr11:120207756-120207979(+)$1	223	11	15	12.0000
UUUG	chr2:113287171-113287396(+)$1	225	5	9	12.0000
UUUG	chr6:31802736-31802958(+)$1	222	54	58	12.0000
UUUG	chr19:47724079-47724321(-)$1	242	173	177	12.0000
UUUG	chr20:61827803-61828072(-)$1	269	43	47	12.0000
UUUG	chr10:105360914-105361159(-)$1	245	1	5	12.0000
UUUG	chr22:38880589-38880840(-)$1	251	39	43	12.0000
UUUG	chr7:106842019-106842240(+)$1	221	16	20	12.0000
UUUG	chr6:32948678-32948930(+)$1	252	156	160	12.0000
UUUG	chr1:152004886-152005113(-)$1	227	148	152	12.0000
UUUG	chr6:52147379-52147600(-)$1	221	65	69	12.0000
UUUG	chr6:7249454-7249672(+)$1	218	77	81	12.0000
UUUG	chr6:44201266-44201567(+)$1	301	191	195	12.0000
UUUG	chr17:27871061-27871301(+)$1	240	41	45	12.0000
UUUG	chr21:30717056-30717277(+)$1	221	114	118	12.0000
UUUG	chr2:42580299-42580530(-)$1	231	89	93	12.0000
UUUG	chr1:115292530-115292761(-)$1	231	78	82	12.0000
UUUG	chr14:57676220-57676445(-)$1	225	28	32	12.0000
UUUG	chr18:8638498-8638745(+)$1	247	132	136	12.0000
UUUG	chr11:118895060-118895280(-)$1	220	205	209	12.0000
UUUG	chr11:12696152-12696379(+)$1	227	35	39	12.0000
UUUG	chr19:57803871-57804125(+)$1	254	162	166	12.0000
UUUG	chr10:105356479-105356699(-)$1	220	62	66	12.0000
UUUG	chr1:180083776-180084007(+)$1	231	84	88	12.0000
UUUG	chr15:70340903-70341126(-)$1	223	73	77	12.0000
uuug	chr19:36259740-36259960(+)$1	220	208	212	12.0000
UUUG	chr21:43176840-43177070(-)$1	230	79	83	12.0000
UUUG	chr22:42070045-42070276(-)$1	231	186	190	12.0000
UUUG	chr6:114178690-114178922(+)$1	232	19	23	12.0000
UUUG	chr6:43147629-43147860(+)$1	231	12	16	12.0000
UUUG	chr2:5836959-5837197(+)$1	238	153	157	12.0000
UUUG	chr6:97246109-97246336(-)$1	227	9	13	12.0000
UUUG	chr1:150548403-150548627(-)$1	224	40	44	12.0000
UUUG	chr5:130536378-130536603(+)$1	225	7	11	12.0000
UUUG	chr17:42282979-42283202(-)$1	223	48	52	12.0000
UUUG	chr1:153781102-153781355(-)$1	253	54	58	12.0000

#otherMatches

#Struct PSSM
&&&d	chr20:50217262-50217493(-)$1	231	57	61	12.0000
mmdd	chr1:1336091-1336320(+)$1	229	201	205	12.0000
e!!e	chr1:52485824-52486085(-)$1	261	71	75	12.0000
DDEE	chr4:56283241-56283472(+)$1	231	2	6	12.0000
OOOO	chr8:22879046-22879272(-)$1	226	15	19	12.0000
"""e	chr1:32637231-32637474(+)$1	243	144	148	12.0000
::BB	chr8:103661632-103661860(-)$1	228	73	77	12.0000
7fff	chr1:245017531-245017757(-)$1	226	135	139	12.0000
rrdd	chr17:45695697-45695923(+)$1	226	83	87	12.0000
::::	chr2:71415381-71415602(-)$1	221	5	9	12.0000
dqqq	chr11:33731226-33731451(-)$1	225	36	40	12.0000
gggg	chr19:4443097-4443320(+)$1	223	12	16	12.0000
$$cc	chr18:19781644-19781871(+)$1	227	28	32	12.0000
ee55	chr12:96051903-96052126(-)$1	223	147	151	12.0000
dddd	chr13:39623042-39623277(+)$1	235	47	51	12.0000
BKKD	chr3:57557402-57557627(-)$1	225	63	67	12.0000
HZZZ	chr11:129734123-129734377(-)$1	254	128	132	12.0000
cc]c	chr3:141012240-141012466(+)$1	226	104	108	12.0000
iiii	chr10:127569351-127569572(-)$1	221	21	25	12.0000
GGGG	chr19:49122301-49122536(-)$1	235	149	153	12.0000
eeee	chr2:174771651-174771877(-)$1	226	133	137	12.0000
::ee	chr14:20926183-20926417(-)$1	234	93	97	12.0000
eeee	chr12:12271864-12272087(-)$1	223	1	5	12.0000
nnnn	chr19:47504327-47504589(+)$1	262	204	208	12.0000
hhhh	chr15:65869992-65870217(+)$1	225	44	48	12.0000
ffff	chr6:150140019-150140239(-)$1	220	5	9	12.0000
ccqq	chr14:81645462-81645694(-)$1	232	212	216	12.0000
"""b	chr12:56635063-56635308(-)$1	245	24	28	12.0000
:eee	chr16:87364706-87364932(-)$1	226	117	121	12.0000
hhhh	chr12:39687110-39687333(-)$1	223	118	122	12.0000
#ggg	chr19:4046416-4046663(-)$1	247	122	126	12.0000
55ee	chr1:156712157-156712399(-)$1	242	101	105	12.0000
ooob	chr1:109817512-109817750(+)$1	238	16	20	12.0000
mmmf	chr9:127909189-127909449(-)$1	260	56	60	12.0000
gggg	chr2:128460034-128460267(+)$1	233	89	93	12.0000
]bb]	chr16:31202225-31202485(+)$1	260	48	52	12.0000
vvvv	chr20:48521309-48521540(-)$1	231	39	43	12.0000
333c	chr13:78338093-78338324(+)$1	231	34	38	12.0000
fff4	chr2:220149900-220150126(+)$1	226	101	105	12.0000
c[dd	chr12:131360614-131360835(+)$1	221	44	48	12.0000
###f	chr11:120207756-120207979(+)$1	223	11	15	12.0000
MMMC	chr2:113287171-113287396(+)$1	225	5	9	12.0000
gggg	chr6:31802736-31802958(+)$1	222	54	58	12.0000
CC}E	chr19:47724079-47724321(-)$1	242	173	177	12.0000
dddq	chr20:61827803-61828072(-)$1	269	43	47	12.0000
::::	chr10:105360914-105361159(-)$1	245	1	5	12.0000
:::e	chr22:38880589-38880840(-)$1	251	39	43	12.0000
mfff	chr7:106842019-106842240(+)$1	221	16	20	12.0000
hhhh	chr6:32948678-32948930(+)$1	252	156	160	12.0000
??EE	chr1:152004886-152005113(-)$1	227	148	152	12.0000
mmmm	chr6:52147379-52147600(-)$1	221	65	69	12.0000
6666	chr6:7249454-7249672(+)$1	218	77	81	12.0000
ZZZE	chr6:44201266-44201567(+)$1	301	191	195	12.0000
====	chr17:27871061-27871301(+)$1	240	41	45	12.0000
EEE}	chr21:30717056-30717277(+)$1	221	114	118	12.0000
::::	chr2:42580299-42580530(-)$1	231	89	93	12.0000
ceee	chr1:115292530-115292761(-)$1	231	78	82	12.0000
d!!g	chr14:57676220-57676445(-)$1	225	28	32	12.0000
ggg:	chr18:8638498-8638745(+)$1	247	132	136	12.0000
ffff	chr11:118895060-118895280(-)$1	220	205	209	12.0000
GGGG	chr11:12696152-12696379(+)$1	227	35	39	12.0000
llee	chr19:57803871-57804125(+)$1	254	162	166	12.0000
qqqb	chr10:105356479-105356699(-)$1	220	62	66	12.0000
mmee	chr1:180083776-180084007(+)$1	231	84	88	12.0000
nngg	chr15:70340903-70341126(-)$1	223	73	77	12.0000
mmgg	chr19:36259740-36259960(+)$1	220	208	212	12.0000
dddd	chr21:43176840-43177070(-)$1	230	79	83	12.0000
iiii	chr22:42070045-42070276(-)$1	231	186	190	12.0000
GGG:	chr6:114178690-114178922(+)$1	232	19	23	12.0000
:::d	chr6:43147629-43147860(+)$1	231	12	16	12.0000
dddb	chr2:5836959-5837197(+)$1	238	153	157	12.0000
GGGG	chr6:97246109-97246336(-)$1	227	9	13	12.0000
SSSS	chr1:150548403-150548627(-)$1	224	40	44	12.0000
mmee	chr5:130536378-130536603(+)$1	225	7	11	12.0000
7777	chr17:42282979-42283202(-)$1	223	48	52	12.0000
[ddd	chr1:153781102-153781355(-)$1	253	54	58	12.0000

#DB
...(	chr20:50217262-50217493(-)$1	1	57	61	12.0000
..))	chr1:1336091-1336320(+)$1	1	201	205	12.0000
(..(	chr1:52485824-52486085(-)$1	1	71	75	12.0000
((((	chr4:56283241-56283472(+)$1	1	2	6	12.0000
....	chr8:22879046-22879272(-)$1	1	15	19	12.0000
...(	chr1:32637231-32637474(+)$1	1	144	148	12.0000
..((	chr8:103661632-103661860(-)$1	1	73	77	12.0000
.)))	chr1:245017531-245017757(-)$1	1	135	139	12.0000
..))	chr17:45695697-45695923(+)$1	1	83	87	12.0000
....	chr2:71415381-71415602(-)$1	1	5	9	12.0000
(...	chr11:33731226-33731451(-)$1	1	36	40	12.0000
((((	chr19:4443097-4443320(+)$1	1	12	16	12.0000
..((	chr18:19781644-19781871(+)$1	1	28	32	12.0000
))..	chr12:96051903-96052126(-)$1	1	147	151	12.0000
))))	chr13:39623042-39623277(+)$1	1	47	51	12.0000
(..(	chr3:57557402-57557627(-)$1	1	63	67	12.0000
)...	chr11:129734123-129734377(-)$1	1	128	132	12.0000
)).)	chr3:141012240-141012466(+)$1	1	104	108	12.0000
((((	chr10:127569351-127569572(-)$1	1	21	25	12.0000
))))	chr19:49122301-49122536(-)$1	1	149	153	12.0000
((((	chr2:174771651-174771877(-)$1	1	133	137	12.0000
..((	chr14:20926183-20926417(-)$1	1	93	97	12.0000
((((	chr12:12271864-12272087(-)$1	1	1	5	12.0000
....	chr19:47504327-47504589(+)$1	1	204	208	12.0000
((((	chr15:65869992-65870217(+)$1	1	44	48	12.0000
((((	chr6:150140019-150140239(-)$1	1	5	9	12.0000
((..	chr14:81645462-81645694(-)$1	1	212	216	12.0000
...(	chr12:56635063-56635308(-)$1	1	24	28	12.0000
.(((	chr16:87364706-87364932(-)$1	1	117	121	12.0000
((((	chr12:39687110-39687333(-)$1	1	118	122	12.0000
.(((	chr19:4046416-4046663(-)$1	1	122	126	12.0000
..))	chr1:156712157-156712399(-)$1	1	101	105	12.0000
...)	chr1:109817512-109817750(+)$1	1	16	20	12.0000
...)	chr9:127909189-127909449(-)$1	1	56	60	12.0000
))))	chr2:128460034-128460267(+)$1	1	89	93	12.0000
.)).	chr16:31202225-31202485(+)$1	1	48	52	12.0000
....	chr20:48521309-48521540(-)$1	1	39	43	12.0000
...)	chr13:78338093-78338324(+)$1	1	34	38	12.0000
))).	chr2:220149900-220150126(+)$1	1	101	105	12.0000
(.((	chr12:131360614-131360835(+)$1	1	44	48	12.0000
...(	chr11:120207756-120207979(+)$1	1	11	15	12.0000
...(	chr2:113287171-113287396(+)$1	1	5	9	12.0000
))))	chr6:31802736-31802958(+)$1	1	54	58	12.0000
)).)	chr19:47724079-47724321(-)$1	1	173	177	12.0000
(((.	chr20:61827803-61828072(-)$1	1	43	47	12.0000
....	chr10:105360914-105361159(-)$1	1	1	5	12.0000
...(	chr22:38880589-38880840(-)$1	1	39	43	12.0000
.)))	chr7:106842019-106842240(+)$1	1	16	20	12.0000
((((	chr6:32948678-32948930(+)$1	1	156	160	12.0000
..))	chr1:152004886-152005113(-)$1	1	148	152	12.0000
....	chr6:52147379-52147600(-)$1	1	65	69	12.0000
....	chr6:7249454-7249672(+)$1	1	77	81	12.0000
...)	chr6:44201266-44201567(+)$1	1	191	195	12.0000
))))	chr17:27871061-27871301(+)$1	1	41	45	12.0000
))).	chr21:30717056-30717277(+)$1	1	114	118	12.0000
....	chr2:42580299-42580530(-)$1	1	89	93	12.0000
))))	chr1:115292530-115292761(-)$1	1	78	82	12.0000
(..(	chr14:57676220-57676445(-)$1	1	28	32	12.0000
))).	chr18:8638498-8638745(+)$1	1	132	136	12.0000
))))	chr11:118895060-118895280(-)$1	1	205	209	12.0000
((((	chr11:12696152-12696379(+)$1	1	35	39	12.0000
..))	chr19:57803871-57804125(+)$1	1	162	166	12.0000
...)	chr10:105356479-105356699(-)$1	1	62	66	12.0000
..))	chr1:180083776-180084007(+)$1	1	84	88	12.0000
..))	chr15:70340903-70341126(-)$1	1	73	77	12.0000
..))	chr19:36259740-36259960(+)$1	1	208	212	12.0000
((((	chr21:43176840-43177070(-)$1	1	79	83	12.0000
))))	chr22:42070045-42070276(-)$1	1	186	190	12.0000
(((.	chr6:114178690-114178922(+)$1	1	19	23	12.0000
...(	chr6:43147629-43147860(+)$1	1	12	16	12.0000
))))	chr2:5836959-5837197(+)$1	1	153	157	12.0000
((((	chr6:97246109-97246336(-)$1	1	9	13	12.0000
....	chr1:150548403-150548627(-)$1	1	40	44	12.0000
..))	chr5:130536378-130536603(+)$1	1	7	11	12.0000
....	chr17:42282979-42283202(-)$1	1	48	52	12.0000
.(((	chr1:153781102-153781355(-)$1	1	54	58	12.0000

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

#score	912.0000000000002
#seq	76
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m3_run2.nuc.txt

#NT
UUUAAA	chr12:69980441-69980705(+)$1	264	248	254	18.0000
UUUAAA	chr12:111160307-111160580(-)$1	273	33	39	18.0000
UUUAAA	chr7:131176881-131177160(+)$1	279	189	195	18.0000
uuuaaa	chrX:67753046-67753336(+)$1	290	276	282	18.0000
UUUAAA	chr4:185676778-185677067(-)$1	289	49	55	18.0000
UUUAAA	chr15:59955164-59955425(-)$1	261	104	110	18.0000
UUUAAA	chr3:56656759-56657038(-)$1	279	84	90	18.0000
UUUAAA	chr5:61681905-61682187(+)$1	282	201	207	18.0000
UUUAAA	chr11:9468424-9468746(+)$1	322	265	271	18.0000
UUUAAA	chr6:105544664-105544964(-)$1	300	77	83	18.0000
UUUAAA	chr14:45590603-45590911(-)$1	308	34	40	18.0000
UUUAAA	chr12:120899623-120899876(+)$1	253	18	24	18.0000
UUUAAA	chr20:58511793-58512066(-)$1	273	129	135	18.0000
UUUAAA	chr1:164818959-164819227(+)$1	268	168	174	18.0000
UUUAAA	chr19:23541200-23541475(-)$1	275	167	173	18.0000
UUUAAA	chr12:8250151-8250469(+)$1	318	252	258	18.0000
uuuaaa	chr17:1248303-1248681(-)$1	378	95	101	18.0000
UUUAAA	chr16:84813268-84813621(+)$1	353	254	260	18.0000
UUUAAA	chr13:58298665-58299027(+)$1	362	28	34	18.0000
uuuaaa	chr3:176740987-176741257(-)$1	270	120	126	18.0000
UUUAAA	chr1:146628205-146628470(-)$1	265	9	15	18.0000
UUUAAA	chr2:132022165-132022405(+)$1	240	226	232	18.0000
UUUAAA	chr8:130853695-130853946(-)$1	251	36	42	18.0000
uuuaaa	chr1:185089409-185089688(-)$1	279	231	237	18.0000
UUUAAA	chr10:73576538-73576814(-)$1	276	132	138	18.0000
UUUAAA	chr7:26231366-26231711(-)$1	345	169	175	18.0000
UUUAAA	chr1:167511131-167511416(-)$1	285	209	215	18.0000
UUUAAA	chr6:127608609-127608882(+)$1	273	224	230	18.0000
UUUAAA	chr2:178095136-178095383(-)$1	247	14	20	18.0000
UUUAAA	chr11:75112583-75112869(+)$1	286	44	50	18.0000
UUUAAA	chr4:1205202-1205476(-)$1	274	213	219	18.0000
UUUAAA	chr17:27585353-27585698(-)$1	345	91	97	18.0000
UUUAAA	chr3:178952415-178952704(+)$1	289	24	30	18.0000
UUUAAA	chr11:118621845-118622098(-)$1	253	14	20	18.0000
UUUAAA	chr4:68483006-68483248(-)$1	242	61	67	18.0000
UUUAAA	chr1:184659632-184659963(-)$1	331	75	81	18.0000
UUUAAA	chr8:82713248-82713686(-)$1	438	18	24	18.0000
UUUAAA	chr3:45959524-45959796(-)$1	272	3	9	18.0000
UUUAAA	chr9:114124063-114124328(-)$1	265	198	204	18.0000

#otherMatches

#Struct PSSM
ssssss	chr6:116909912-116910214(+)$1	302	241	247	18.0000
::::::	chr12:69980441-69980705(+)$1	264	248	254	18.0000
======	chr12:111160307-111160580(-)$1	273	33	39	18.0000
:::::h	chr7:131176881-131177160(+)$1	279	189	195	18.0000
d4444h	chrX:67753046-67753336(+)$1	290	276	282	18.0000
oodddd	chr4:185676778-185677067(-)$1	289	49	55	18.0000
6666ee	chr15:59955164-59955425(-)$1	261	104	110	18.0000
tttccc	chr3:56656759-56657038(-)$1	279	84	90	18.0000
ooccc2	chr5:61681905-61682187(+)$1	282	201	207	18.0000
xxxxxx	chr11:9468424-9468746(+)$1	322	265	271	18.0000
::::::	chr6:105544664-105544964(-)$1	300	77	83	18.0000
:::ccc	chr14:45590603-45590911(-)$1	308	34	40	18.0000
e!!bbm	chr12:120899623-120899876(+)$1	253	18	24	18.0000
::::II	chr20:58511793-58512066(-)$1	273	129	135	18.0000
:eeeee	chr1:164818959-164819227(+)$1	268	168	174	18.0000
======	chr19:23541200-23541475(-)$1	275	167	173	18.0000
bb8888	chr12:8250151-8250469(+)$1	318	252	258	18.0000
::::::	chr17:1248303-1248681(-)$1	378	95	101	18.0000
fff:gg	chr16:84813268-84813621(+)$1	353	254	260	18.0000
%%%%%g	chr13:58298665-58299027(+)$1	362	28	34	18.0000
ggggpp	chr3:176740987-176741257(-)$1	270	120	126	18.0000
eellle	chr1:146628205-146628470(-)$1	265	9	15	18.0000
DDD:::	chr2:132022165-132022405(+)$1	240	226	232	18.0000
:::::H	chr8:130853695-130853946(-)$1	251	36	42	18.0000
HH@@@@	chr1:185089409-185089688(-)$1	279	231	237	18.0000
==4444	chr10:73576538-73576814(-)$1	276	132	138	18.0000
iiii&&	chr7:26231366-26231711(-)$1	345	169	175	18.0000
hhhhhh	chr1:167511131-167511416(-)$1	285	209	215	18.0000
dddooo	chr6:127608609-127608882(+)$1	273	224	230	18.0000
gggggo	chr2:178095136-178095383(-)$1	247	14	20	18.0000
iii333	chr11:75112583-75112869(+)$1	286	44	50	18.0000
ggglll	chr4:1205202-1205476(-)$1	274	213	219	18.0000
::::::	chr17:27585353-27585698(-)$1	345	91	97	18.0000
HHHHKK	chr3:178952415-178952704(+)$1	289	24	30	18.0000
ffff::	chr11:118621845-118622098(-)$1	253	14	20	18.0000
gggggg	chr4:68483006-68483248(-)$1	242	61	67	18.0000
MMEEEE	chr1:184659632-184659963(-)$1	331	75	81	18.0000
iiiii[	chr8:82713248-82713686(-)$1	438	18	24	18.0000
eerrrr	chr3:45959524-45959796(-)$1	272	3	9	18.0000
oogggg	chr9:114124063-114124328(-)$1	265	198	204	18.0000

#DB
......	chr6:116909912-116910214(+)$1	1	241	247	18.0000
......	chr12:69980441-69980705(+)$1	1	248	254	18.0000
))))))	chr12:111160307-111160580(-)$1	1	33	39	18.0000
.....(	chr7:131176881-131177160(+)$1	1	189	195	18.0000
)....)	chrX:67753046-67753336(+)$1	1	276	282	18.0000
..))))	chr4:185676778-185677067(-)$1	1	49	55	18.0000
....))	chr15:59955164-59955425(-)$1	1	104	110	18.0000
...)))	chr3:56656759-56657038(-)$1	1	84	90	18.0000
..))).	chr5:61681905-61682187(+)$1	1	201	207	18.0000
......	chr11:9468424-9468746(+)$1	1	265	271	18.0000
......	chr6:105544664-105544964(-)$1	1	77	83	18.0000
...(((	chr14:45590603-45590911(-)$1	1	34	40	18.0000
(..((.	chr12:120899623-120899876(+)$1	1	18	24	18.0000
....((	chr20:58511793-58512066(-)$1	1	129	135	18.0000
.(((((	chr1:164818959-164819227(+)$1	1	168	174	18.0000
((((((	chr19:23541200-23541475(-)$1	1	167	173	18.0000
))....	chr12:8250151-8250469(+)$1	1	252	258	18.0000
......	chr17:1248303-1248681(-)$1	1	95	101	18.0000
))).((	chr16:84813268-84813621(+)$1	1	254	260	18.0000
.....(	chr13:58298665-58299027(+)$1	1	28	34	18.0000
((((..	chr3:176740987-176741257(-)$1	1	120	126	18.0000
((...)	chr1:146628205-146628470(-)$1	1	9	15	18.0000
)))...	chr2:132022165-132022405(+)$1	1	226	232	18.0000
.....(	chr8:130853695-130853946(-)$1	1	36	42	18.0000
))....	chr1:185089409-185089688(-)$1	1	231	237	18.0000
))....	chr10:73576538-73576814(-)$1	1	132	138	18.0000
((((..	chr7:26231366-26231711(-)$1	1	169	175	18.0000
((((((	chr1:167511131-167511416(-)$1	1	209	215	18.0000
(((...	chr6:127608609-127608882(+)$1	1	224	230	18.0000
(((((.	chr2:178095136-178095383(-)$1	1	14	20	18.0000
)))...	chr11:75112583-75112869(+)$1	1	44	50	18.0000
(((...	chr4:1205202-1205476(-)$1	1	213	219	18.0000
......	chr17:27585353-27585698(-)$1	1	91	97	18.0000
((((..	chr3:178952415-178952704(+)$1	1	24	30	18.0000
))))..	chr11:118621845-118622098(-)$1	1	14	20	18.0000
((((((	chr4:68483006-68483248(-)$1	1	61	67	18.0000
..((((	chr1:184659632-184659963(-)$1	1	75	81	18.0000
(((((.	chr8:82713248-82713686(-)$1	1	18	24	18.0000
((....	chr3:45959524-45959796(-)$1	1	3	9	18.0000
..))))	chr9:114124063-114124328(-)$1	1	198	204	18.0000

#PSSM
U : 0.90	u : 0.10	
U : 0.90	u : 0.10	
U : 0.90	u : 0.10	
A : 0.90	a : 0.10	
A : 0.90	a : 0.10	
A : 0.90	a : 0.10	

#score	720.0000000000001
#seq	40
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m3_run2.nuc.txt

#NT
CUGG	chr1:246887620-246887845(+)$1	225	30	34	11.9999
CUGG	chr16:20749068-20749300(-)$1	232	173	177	11.9999
CUGG	chr6:133136028-133136282(+)$1	254	90	94	11.9999
CUGG	chr2:96861154-96861380(-)$1	226	146	150	11.9999
CUGG	chr6:28358356-28358591(-)$1	235	83	87	11.9999
cugg	chr12:48090058-48090280(-)$1	222	19	23	11.9999
CUGG	chrX:53565250-53565472(-)$1	222	10	14	11.9999
CUGG	chr20:35858290-35858553(+)$1	263	227	231	11.9999
CUGG	chr2:113417955-113418191(+)$1	236	24	28	11.9999
CUGG	chr9:114170789-114171017(-)$1	228	8	12	11.9999
CUGG	chr2:74755308-74755530(-)$1	222	13	17	11.9999
CUGG	chr3:128356624-128356858(-)$1	234	145	149	11.9999
CUGG	chr4:891803-892025(-)$1	222	168	172	11.9999
CUGG	chr21:27484244-27484488(-)$1	244	44	48	11.9999
CUGG	chr2:9541337-9541562(+)$1	225	205	209	11.9999
CUGG	chr21:28213297-28213529(-)$1	232	29	33	11.9999
CUGG	chr8:141557489-141557720(-)$1	231	23	27	11.9999
CUGG	chr1:150238851-150239073(-)$1	222	31	35	11.9999
CUGG	chr17:4701584-4701847(+)$1	263	40	44	11.9999
CUGG	chr7:44684896-44685128(+)$1	232	116	120	11.9999
CUGG	chr11:10821144-10821378(-)$1	234	14	18	11.9999
CUGG	chr14:21992953-21993203(-)$1	250	21	25	11.9999
CUGG	chr5:179143062-179143293(+)$1	231	72	76	11.9999
CUGG	chr1:116944090-116944314(+)$1	224	125	129	11.9999
CUGG	chrX:41206055-41206308(+)$1	253	58	62	11.9999
CUGG	chr17:57970522-57970765(+)$1	243	116	120	11.9999
CUGG	chr2:113073949-113074175(+)$1	226	193	197	11.9999
cugg	chr19:36208874-36209133(+)$1	259	83	87	11.9999
CUGG	chr14:24003988-24004213(-)$1	225	31	35	11.9999
CUGG	chr11:18425147-18425385(+)$1	238	120	124	11.9999
CUGG	chr10:99211358-99211599(+)$1	241	98	102	11.9999
CUGG	chr5:14504480-14504705(+)$1	225	208	212	11.9999
CUGG	chr4:6863916-6864136(+)$1	220	78	82	11.9999
CUGG	chr19:30193723-30193975(-)$1	252	119	123	11.9999
CUGG	chr17:80039040-80039261(-)$1	221	1	5	11.9999
CUGG	chr6:32945450-32945682(+)$1	232	27	31	11.9999
CUGG	chr19:14554232-14554459(+)$1	227	64	68	11.9999
CUGG	chr19:18548383-18548607(-)$1	224	111	115	11.9999
CUGG	chrX:24024635-24024908(-)$1	273	153	157	11.9999
CUGG	chr16:20807584-20807806(-)$1	222	205	209	11.9999
CUGG	chrX:129189756-129189975(+)$1	219	8	12	11.9999
CUGG	chr11:114057627-114057853(+)$1	226	105	109	11.9999
CUGG	chr1:234509955-234510178(+)$1	223	71	75	11.9999
CUGG	chr2:20234039-20234264(-)$1	225	21	25	11.9999
CUGG	chr11:61732431-61732648(-)$1	217	81	85	11.9999
CUGG	chr6:30690605-30690836(+)$1	231	115	119	11.9999
CUGG	chr19:18530323-18530560(+)$1	237	23	27	11.9999
CUGG	chr17:34169293-34169510(+)$1	217	194	198	11.9999
CUGG	chr17:18202782-18203002(-)$1	220	43	47	11.9999
CUGG	chr8:74233111-74233349(+)$1	238	173	177	11.9999
CUGG	chr5:82836941-82837164(+)$1	223	26	30	11.9999
CUGG	chr1:236738007-236738238(-)$1	231	140	144	11.9999
CUGG	chr11:71939324-71939547(+)$1	223	30	34	11.9999
CUGG	chrX:107977772-107978044(-)$1	272	160	164	11.9999
CUGG	chr14:74753061-74753292(-)$1	231	133	137	11.9999
CUGG	chr12:62918220-62918442(+)$1	222	104	108	11.9999
CUGG	chr22:32108735-32108958(-)$1	223	9	13	11.9999
CUGG	chr17:72771686-72771917(-)$1	231	1	5	11.9999
CUGG	chr16:29821505-29821736(+)$1	231	40	44	11.9999
CUGG	chr19:19626947-19627193(+)$1	246	226	230	11.9999
CUGG	chr16:67299944-67300182(+)$1	238	214	218	11.9999
CUGG	chr13:115090554-115090780(+)$1	226	199	203	11.9999
CUGG	chr4:185681537-185681754(-)$1	217	33	37	11.9999
CUGG	chr3:9483761-9483984(+)$1	223	197	201	11.9999
CUGG	chr11:134018343-134018564(+)$1	221	133	137	11.9999
CUGG	chr6:35803038-35803259(-)$1	221	81	85	11.9999
CUGG	chr1:27158838-27159072(+)$1	234	109	113	11.9999
CUGG	chr13:37393642-37393874(+)$1	232	9	13	11.9999
CUGG	chr5:141014362-141014587(-)$1	225	38	42	11.9999
CUGG	chr17:40021422-40021664(-)$1	242	101	105	11.9999
CUGG	chr6:170846315-170846528(-)$1	213	160	164	11.9999
CUGG	chr19:50173579-50173801(+)$1	222	40	44	11.9999
CUGG	chr6:74304786-74305032(-)$1	246	196	200	11.9999
CUGG	chr9:108147602-108147817(+)$1	215	137	141	11.9999
CUGG	chr2:200298104-200298330(-)$1	226	179	183	11.9999
CUGG	chr17:79818177-79818450(-)$1	273	127	131	11.9999
CUGG	chr20:31019040-31019261(+)$1	221	128	132	11.9999
CUGG	chr6:30865955-30866181(+)$1	226	55	59	11.9999

#otherMatches

#Struct PSSM
mmmd	chr11:70266456-70266710(+)$1	254	26	30	11.9999
[bbm	chr1:246887620-246887845(+)$1	225	30	34	11.9999
dd[d	chr16:20749068-20749300(-)$1	232	173	177	11.9999
cddd	chr6:133136028-133136282(+)$1	254	90	94	11.9999
gggg	chr2:96861154-96861380(-)$1	226	146	150	11.9999
gg[a	chr6:28358356-28358591(-)$1	235	83	87	11.9999
mddd	chr12:48090058-48090280(-)$1	222	19	23	11.9999
eeec	chrX:53565250-53565472(-)$1	222	10	14	11.9999
eeGG	chr20:35858290-35858553(+)$1	263	227	231	11.9999
555f	chr2:113417955-113418191(+)$1	236	24	28	11.9999
ffff	chr9:114170789-114171017(-)$1	228	8	12	11.9999
DDDe	chr2:74755308-74755530(-)$1	222	13	17	11.9999
ffcc	chr3:128356624-128356858(-)$1	234	145	149	11.9999
a[bb	chr4:891803-892025(-)$1	222	168	172	11.9999
JJJc	chr21:27484244-27484488(-)$1	244	44	48	11.9999
ffll	chr2:9541337-9541562(+)$1	225	205	209	11.9999
FFFF	chr21:28213297-28213529(-)$1	232	29	33	11.9999
ee:f	chr8:141557489-141557720(-)$1	231	23	27	11.9999
dddd	chr1:150238851-150239073(-)$1	222	31	35	11.9999
dddd	chr17:4701584-4701847(+)$1	263	40	44	11.9999
ccdd	chr7:44684896-44685128(+)$1	232	116	120	11.9999
eeee	chr11:10821144-10821378(-)$1	234	14	18	11.9999
$$$g	chr14:21992953-21993203(-)$1	250	21	25	11.9999
eee[	chr5:179143062-179143293(+)$1	231	72	76	11.9999
66bb	chr1:116944090-116944314(+)$1	224	125	129	11.9999
cc::	chrX:41206055-41206308(+)$1	253	58	62	11.9999
ddd2	chr17:57970522-57970765(+)$1	243	116	120	11.9999
iimm	chr2:113073949-113074175(+)$1	226	193	197	11.9999
qqqq	chr19:36208874-36209133(+)$1	259	83	87	11.9999
B{AF	chr14:24003988-24004213(-)$1	225	31	35	11.9999
GG::	chr11:18425147-18425385(+)$1	238	120	124	11.9999
cc[c	chr10:99211358-99211599(+)$1	241	98	102	11.9999
zzii	chr5:14504480-14504705(+)$1	225	208	212	11.9999
mmdd	chr4:6863916-6864136(+)$1	220	78	82	11.9999
ffff	chr19:30193723-30193975(-)$1	252	119	123	11.9999
DDD{	chr17:80039040-80039261(-)$1	221	1	5	11.9999
ffff	chr6:32945450-32945682(+)$1	232	27	31	11.9999
::cc	chr19:14554232-14554459(+)$1	227	64	68	11.9999
]ccc	chr19:18548383-18548607(-)$1	224	111	115	11.9999
pppp	chrX:24024635-24024908(-)$1	273	153	157	11.9999
::EE	chr16:20807584-20807806(-)$1	222	205	209	11.9999
GGGG	chrX:129189756-129189975(+)$1	219	8	12	11.9999
hhhh	chr11:114057627-114057853(+)$1	226	105	109	11.9999
ee:F	chr1:234509955-234510178(+)$1	223	71	75	11.9999
GGGG	chr2:20234039-20234264(-)$1	225	21	25	11.9999
dddd	chr11:61732431-61732648(-)$1	217	81	85	11.9999
HHHH	chr6:30690605-30690836(+)$1	231	115	119	11.9999
dd[a	chr19:18530323-18530560(+)$1	237	23	27	11.9999
dddd	chr17:34169293-34169510(+)$1	217	194	198	11.9999
ffff	chr17:18202782-18203002(-)$1	220	43	47	11.9999
bb55	chr8:74233111-74233349(+)$1	238	173	177	11.9999
::ff	chr5:82836941-82837164(+)$1	223	26	30	11.9999
eeee	chr1:236738007-236738238(-)$1	231	140	144	11.9999
CC{C	chr11:71939324-71939547(+)$1	223	30	34	11.9999
DDD:	chrX:107977772-107978044(-)$1	272	160	164	11.9999
IIII	chr14:74753061-74753292(-)$1	231	133	137	11.9999
!ddd	chr12:62918220-62918442(+)$1	222	104	108	11.9999
qqcc	chr22:32108735-32108958(-)$1	223	9	13	11.9999
::CC	chr17:72771686-72771917(-)$1	231	1	5	11.9999
dddd	chr16:29821505-29821736(+)$1	231	40	44	11.9999
oooo	chr19:19626947-19627193(+)$1	246	226	230	11.9999
ffBB	chr16:67299944-67300182(+)$1	238	214	218	11.9999
GGGG	chr13:115090554-115090780(+)$1	226	199	203	11.9999
:ddd	chr4:185681537-185681754(-)$1	217	33	37	11.9999
qqdd	chr3:9483761-9483984(+)$1	223	197	201	11.9999
]ddd	chr11:134018343-134018564(+)$1	221	133	137	11.9999
[fff	chr6:35803038-35803259(-)$1	221	81	85	11.9999
33ee	chr1:27158838-27159072(+)$1	234	109	113	11.9999
EEEF	chr13:37393642-37393874(+)$1	232	9	13	11.9999
nnee	chr5:141014362-141014587(-)$1	225	38	42	11.9999
tttt	chr17:40021422-40021664(-)$1	242	101	105	11.9999
iii:	chr6:170846315-170846528(-)$1	213	160	164	11.9999
gggg	chr19:50173579-50173801(+)$1	222	40	44	11.9999
:ccc	chr6:74304786-74305032(-)$1	246	196	200	11.9999
:EEE	chr9:108147602-108147817(+)$1	215	137	141	11.9999
eeee	chr2:200298104-200298330(-)$1	226	179	183	11.9999
e[bb	chr17:79818177-79818450(-)$1	273	127	131	11.9999
""ff	chr20:31019040-31019261(+)$1	221	128	132	11.9999
ciii	chr6:30865955-30866181(+)$1	226	55	59	11.9999

#DB
...)	chr11:70266456-70266710(+)$1	1	26	30	11.9999
.((.	chr1:246887620-246887845(+)$1	1	30	34	11.9999
((.(	chr16:20749068-20749300(-)$1	1	173	177	11.9999
))))	chr6:133136028-133136282(+)$1	1	90	94	11.9999
((((	chr2:96861154-96861380(-)$1	1	146	150	11.9999
((.(	chr6:28358356-28358591(-)$1	1	83	87	11.9999
.)))	chr12:48090058-48090280(-)$1	1	19	23	11.9999
((((	chrX:53565250-53565472(-)$1	1	10	14	11.9999
))))	chr20:35858290-35858553(+)$1	1	227	231	11.9999
...)	chr2:113417955-113418191(+)$1	1	24	28	11.9999
((((	chr9:114170789-114171017(-)$1	1	8	12	11.9999
((((	chr2:74755308-74755530(-)$1	1	13	17	11.9999
))((	chr3:128356624-128356858(-)$1	1	145	149	11.9999
(.((	chr4:891803-892025(-)$1	1	168	172	11.9999
((((	chr21:27484244-27484488(-)$1	1	44	48	11.9999
((..	chr2:9541337-9541562(+)$1	1	205	209	11.9999
((((	chr21:28213297-28213529(-)$1	1	29	33	11.9999
)).(	chr8:141557489-141557720(-)$1	1	23	27	11.9999
))))	chr1:150238851-150239073(-)$1	1	31	35	11.9999
))))	chr17:4701584-4701847(+)$1	1	40	44	11.9999
))))	chr7:44684896-44685128(+)$1	1	116	120	11.9999
((((	chr11:10821144-10821378(-)$1	1	14	18	11.9999
...(	chr14:21992953-21993203(-)$1	1	21	25	11.9999
(((.	chr5:179143062-179143293(+)$1	1	72	76	11.9999
..))	chr1:116944090-116944314(+)$1	1	125	129	11.9999
))..	chrX:41206055-41206308(+)$1	1	58	62	11.9999
))).	chr17:57970522-57970765(+)$1	1	116	120	11.9999
((..	chr2:113073949-113074175(+)$1	1	193	197	11.9999
....	chr19:36208874-36209133(+)$1	1	83	87	11.9999
(.((	chr14:24003988-24004213(-)$1	1	31	35	11.9999
((..	chr11:18425147-18425385(+)$1	1	120	124	11.9999
((.(	chr10:99211358-99211599(+)$1	1	98	102	11.9999
..))	chr5:14504480-14504705(+)$1	1	208	212	11.9999
..))	chr4:6863916-6864136(+)$1	1	78	82	11.9999
))))	chr19:30193723-30193975(-)$1	1	119	123	11.9999
(((.	chr17:80039040-80039261(-)$1	1	1	5	11.9999
((((	chr6:32945450-32945682(+)$1	1	27	31	11.9999
..((	chr19:14554232-14554459(+)$1	1	64	68	11.9999
.)))	chr19:18548383-18548607(-)$1	1	111	115	11.9999
....	chrX:24024635-24024908(-)$1	1	153	157	11.9999
..))	chr16:20807584-20807806(-)$1	1	205	209	11.9999
((((	chrX:129189756-129189975(+)$1	1	8	12	11.9999
((((	chr11:114057627-114057853(+)$1	1	105	109	11.9999
)).(	chr1:234509955-234510178(+)$1	1	71	75	11.9999
((((	chr2:20234039-20234264(-)$1	1	21	25	11.9999
))))	chr11:61732431-61732648(-)$1	1	81	85	11.9999
))))	chr6:30690605-30690836(+)$1	1	115	119	11.9999
((.(	chr19:18530323-18530560(+)$1	1	23	27	11.9999
((((	chr17:34169293-34169510(+)$1	1	194	198	11.9999
((((	chr17:18202782-18203002(-)$1	1	43	47	11.9999
))..	chr8:74233111-74233349(+)$1	1	173	177	11.9999
..((	chr5:82836941-82837164(+)$1	1	26	30	11.9999
))))	chr1:236738007-236738238(-)$1	1	140	144	11.9999
((.(	chr11:71939324-71939547(+)$1	1	30	34	11.9999
))).	chrX:107977772-107978044(-)$1	1	160	164	11.9999
))))	chr14:74753061-74753292(-)$1	1	133	137	11.9999
.(((	chr12:62918220-62918442(+)$1	1	104	108	11.9999
..))	chr22:32108735-32108958(-)$1	1	9	13	11.9999
..((	chr17:72771686-72771917(-)$1	1	1	5	11.9999
((((	chr16:29821505-29821736(+)$1	1	40	44	11.9999
....	chr19:19626947-19627193(+)$1	1	226	230	11.9999
))))	chr16:67299944-67300182(+)$1	1	214	218	11.9999
))))	chr13:115090554-115090780(+)$1	1	199	203	11.9999
.(((	chr4:185681537-185681754(-)$1	1	33	37	11.9999
..))	chr3:9483761-9483984(+)$1	1	197	201	11.9999
.)))	chr11:134018343-134018564(+)$1	1	133	137	11.9999
.(((	chr6:35803038-35803259(-)$1	1	81	85	11.9999
..))	chr1:27158838-27159072(+)$1	1	109	113	11.9999
((((	chr13:37393642-37393874(+)$1	1	9	13	11.9999
..))	chr5:141014362-141014587(-)$1	1	38	42	11.9999
....	chr17:40021422-40021664(-)$1	1	101	105	11.9999
))).	chr6:170846315-170846528(-)$1	1	160	164	11.9999
((((	chr19:50173579-50173801(+)$1	1	40	44	11.9999
.(((	chr6:74304786-74305032(-)$1	1	196	200	11.9999
.)))	chr9:108147602-108147817(+)$1	1	137	141	11.9999
((((	chr2:200298104-200298330(-)$1	1	179	183	11.9999
(.((	chr17:79818177-79818450(-)$1	1	127	131	11.9999
..((	chr20:31019040-31019261(+)$1	1	128	132	11.9999
)(((	chr6:30865955-30866181(+)$1	1	55	59	11.9999

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

#score	947.9999999999998
#seq	79
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m1_run2.nuc.txt

#NT
CAG	chr11:9438574-9438780(+)$1	206	61	64	9.0000
CAG	chr12:123041877-123042096(+)$1	219	3	6	9.0000
CAG	chr14:93185019-93185242(-)$1	223	14	17	9.0000
CAG	chr17:8457186-8457398(-)$1	212	13	16	9.0000
CAG	chr16:70564644-70564869(+)$1	225	0	3	9.0000
CAG	chr5:52344138-52344350(+)$1	212	75	78	9.0000
CAG	chr10:33212542-33212755(-)$1	213	133	136	9.0000
CAG	chr6:28871922-28872130(-)$1	208	41	44	9.0000
CAG	chr18:72187362-72187602(+)$1	240	11	14	9.0000
CAG	chr1:120510050-120510263(-)$1	213	16	19	9.0000
CAG	chr22:41564635-41564847(+)$1	212	40	43	9.0000
CAG	chr5:32126332-32126573(-)$1	241	10	13	9.0000
CAG	chr3:137881038-137881266(-)$1	228	50	53	9.0000
CAG	chr1:109888373-109888592(-)$1	219	49	52	9.0000
CAG	chr15:77348043-77348260(-)$1	217	52	55	9.0000
CAG	chrX:47098680-47098903(+)$1	223	6	9	9.0000
CAG	chr1:156294720-156294960(-)$1	240	38	41	9.0000
CAG	chr19:35230036-35230260(+)$1	224	13	16	9.0000
CAG	chr17:65907949-65908163(+)$1	214	2	5	9.0000
CAG	chr14:58730328-58730532(+)$1	204	64	67	9.0000
CAG	chr6:128643225-128643442(-)$1	217	11	14	9.0000
CAG	chr2:54041594-54041810(+)$1	216	82	85	9.0000
CAG	chr2:63833906-63834112(+)$1	206	47	50	9.0000
CAG	chr2:69565547-69565759(-)$1	212	59	62	9.0000
CAG	chr1:6588990-6589202(-)$1	212	48	51	9.0000
CAG	chr11:498784-498996(-)$1	212	60	63	9.0000
CAG	chr19:59063661-59063871(-)$1	210	63	66	9.0000
CAG	chr11:75112595-75112844(+)$1	249	0	3	9.0000
CAG	chr17:76219905-76220189(+)$1	284	9	12	9.0000
CAG	chr5:176867633-176867864(+)$1	231	64	67	9.0000
CAG	chr1:115273036-115273274(-)$1	238	2	5	9.0000
CAG	chrX:49028254-49028474(+)$1	220	15	18	9.0000
CAG	chr9:35738195-35738410(-)$1	215	6	9	9.0000
CAG	chr11:68131243-68131451(+)$1	208	42	45	9.0000
CAG	chr5:149390027-149390253(+)$1	226	24	27	9.0000
CAG	chr7:92077988-92078192(+)$1	204	74	77	9.0000
CAG	chr5:102364537-102364777(+)$1	240	1	4	9.0000
CAG	chr5:74016376-74016622(+)$1	246	139	142	9.0000
CAG	chr3:183670919-183671122(-)$1	203	66	69	9.0000
CAG	chr20:35443559-35443763(-)$1	204	18	21	9.0000
CAG	chr13:41323220-41323433(-)$1	213	54	57	9.0000
CAG	chr21:34922979-34923209(+)$1	230	14	17	9.0000
CAG	chr9:35102001-35102209(-)$1	208	15	18	9.0000
CAG	chr20:62373408-62373666(+)$1	258	21	24	9.0000
CAG	chr12:56548850-56549059(+)$1	209	43	46	9.0000
CAG	chr1:15959852-15960059(+)$1	207	107	110	9.0000
CAG	chr12:56619125-56619349(+)$1	224	28	31	9.0000
CAG	chr6:31500537-31500779(-)$1	242	32	35	9.0000
CAG	chr1:39494435-39494691(+)$1	256	21	24	9.0000
CAG	chr1:172558388-172558601(+)$1	213	5	8	9.0000
CAG	chr1:183091223-183091475(+)$1	252	23	26	9.0000
CAG	chr12:110929798-110930011(-)$1	213	118	121	9.0000
CAG	chr18:33706165-33706382(-)$1	217	68	71	9.0000
CAG	chrX:16887111-16887343(-)$1	232	101	104	9.0000
CAG	chr16:2826910-2827138(-)$1	228	7	10	9.0000
CAG	chrX:77373475-77373744(+)$1	269	97	100	9.0000
CAG	chrX:135308013-135308245(-)$1	232	29	32	9.0000
CAG	chr16:14693703-14693907(-)$1	204	3	6	9.0000
CAG	chr6:31760503-31760712(-)$1	209	37	40	9.0000
CAG	chr7:128645014-128645229(-)$1	215	13	16	9.0000
CAG	chr16:53498049-53498261(+)$1	212	114	117	9.0000
CAG	chrX:71417123-71417358(+)$1	235	35	38	9.0000
CAG	chr17:39974601-39974807(+)$1	206	29	32	9.0000
CAG	chr20:57484688-57484898(+)$1	210	6	9	9.0000
CAG	chr6:44413314-44413530(+)$1	216	74	77	9.0000
CAG	chr20:2637333-2637607(+)$1	274	27	30	9.0000
CAG	chr16:4802575-4802806(-)$1	231	16	19	9.0000
CAG	chr22:46749632-46749847(+)$1	215	1	4	9.0000
CAG	chr6:31593793-31594025(+)$1	232	0	3	9.0000
CAG	chr6:44219712-44219942(+)$1	230	20	23	9.0000
CAG	chr22:36690196-36690407(-)$1	211	7	10	9.0000
CAG	chr5:81573501-81573759(-)$1	258	7	10	9.0000
CAG	chr15:84286877-84287115(+)$1	238	10	13	9.0000
CAG	chr19:37917133-37917340(-)$1	207	32	35	9.0000
CAG	chr16:84101256-84101511(-)$1	255	43	46	9.0000
CAG	chr17:59820379-59820587(-)$1	208	21	24	9.0000
CAG	chr20:18576575-18576838(+)$1	263	42	45	9.0000
CAG	chr11:43380528-43380736(+)$1	208	31	34	9.0000
CAG	chr1:220310108-220310343(+)$1	235	44	47	9.0000
CAG	chr9:34241549-34241760(+)$1	211	53	56	9.0000
CAG	chr12:72316690-72316926(+)$1	236	0	3	9.0000
CAG	chrX:118723254-118723456(-)$1	202	82	85	9.0000
CAG	chr9:108536089-108536305(+)$1	216	9	12	9.0000
CAG	chr6:13658923-13659140(-)$1	217	73	76	9.0000
CAG	chr20:60713136-60713353(-)$1	217	35	38	9.0000
CAG	chr9:139370824-139371036(-)$1	212	59	62	9.0000
CAG	chr1:169930115-169930321(-)$1	206	5	8	9.0000
CAG	chr15:74948195-74948408(-)$1	213	12	15	9.0000
CAG	chr6:13634646-13634853(-)$1	207	66	69	9.0000
CAG	chr13:48830225-48830450(+)$1	225	14	17	9.0000
CAG	chr17:80040866-80041079(-)$1	213	35	38	9.0000
CAG	chr15:66811225-66811451(+)$1	226	56	59	9.0000
CAG	chr16:9017097-9017309(-)$1	212	4	7	9.0000
CAG	chr15:65748504-65748732(-)$1	228	20	23	9.0000
CAG	chr19:5207907-5208128(-)$1	221	1	4	9.0000
CAG	chr4:37636498-37636713(-)$1	215	0	3	9.0000
CAG	chr10:7830059-7830300(+)$1	241	92	95	9.0000
CAG	chr11:62327687-62328011(-)$1	324	198	201	9.0000
CAG	chr8:9592391-9592626(+)$1	235	9	12	9.0000

#otherMatches

#Struct PSSM
a[c	chr11:120302453-120302680(+)$1	227	49	52	9.0000
fff	chr11:9438574-9438780(+)$1	206	61	64	9.0000
fff	chr12:123041877-123042096(+)$1	219	3	6	9.0000
CKK	chr14:93185019-93185242(-)$1	223	14	17	9.0000
CCC	chr17:8457186-8457398(-)$1	212	13	16	9.0000
:EE	chr16:70564644-70564869(+)$1	225	0	3	9.0000
ddC	chr5:52344138-52344350(+)$1	212	75	78	9.0000
ccc	chr10:33212542-33212755(-)$1	213	133	136	9.0000
3bb	chr6:28871922-28872130(-)$1	208	41	44	9.0000
:gg	chr18:72187362-72187602(+)$1	240	11	14	9.0000
BLL	chr1:120510050-120510263(-)$1	213	16	19	9.0000
cc3	chr22:41564635-41564847(+)$1	212	40	43	9.0000
fff	chr5:32126332-32126573(-)$1	241	10	13	9.0000
ee+	chr3:137881038-137881266(-)$1	228	50	53	9.0000
ooo	chr1:109888373-109888592(-)$1	219	49	52	9.0000
ggg	chr15:77348043-77348260(-)$1	217	52	55	9.0000
[dd	chrX:47098680-47098903(+)$1	223	6	9	9.0000
CCI	chr1:156294720-156294960(-)$1	240	38	41	9.0000
H:c	chr19:35230036-35230260(+)$1	224	13	16	9.0000
::C	chr17:65907949-65908163(+)$1	214	2	5	9.0000
]ii	chr14:58730328-58730532(+)$1	204	64	67	9.0000
ggg	chr6:128643225-128643442(-)$1	217	11	14	9.0000
ddd	chr2:54041594-54041810(+)$1	216	82	85	9.0000
HHH	chr2:63833906-63834112(+)$1	206	47	50	9.0000
::E	chr2:69565547-69565759(-)$1	212	59	62	9.0000
fff	chr1:6588990-6589202(-)$1	212	48	51	9.0000
d]d	chr11:498784-498996(-)$1	212	60	63	9.0000
::e	chr19:59063661-59063871(-)$1	210	63	66	9.0000
:::	chr11:75112595-75112844(+)$1	249	0	3	9.0000
HHH	chr17:76219905-76220189(+)$1	284	9	12	9.0000
eee	chr5:176867633-176867864(+)$1	231	64	67	9.0000
EEE	chr1:115273036-115273274(-)$1	238	2	5	9.0000
c[d	chrX:49028254-49028474(+)$1	220	15	18	9.0000
iii	chr9:35738195-35738410(-)$1	215	6	9	9.0000
EEE	chr11:68131243-68131451(+)$1	208	42	45	9.0000
ggg	chr5:149390027-149390253(+)$1	226	24	27	9.0000
a[d	chr7:92077988-92078192(+)$1	204	74	77	9.0000
:::	chr5:102364537-102364777(+)$1	240	1	4	9.0000
eee	chr5:74016376-74016622(+)$1	246	139	142	9.0000
c[b	chr3:183670919-183671122(-)$1	203	66	69	9.0000
mma	chr20:35443559-35443763(-)$1	204	18	21	9.0000
bnn	chr13:41323220-41323433(-)$1	213	54	57	9.0000
i[b	chr21:34922979-34923209(+)$1	230	14	17	9.0000
eee	chr9:35102001-35102209(-)$1	208	15	18	9.0000
ff:	chr20:62373408-62373666(+)$1	258	21	24	9.0000
c::	chr12:56548850-56549059(+)$1	209	43	46	9.0000
fff	chr1:15959852-15960059(+)$1	207	107	110	9.0000
MEE	chr12:56619125-56619349(+)$1	224	28	31	9.0000
ooc	chr6:31500537-31500779(-)$1	242	32	35	9.0000
DDK	chr1:39494435-39494691(+)$1	256	21	24	9.0000
:::	chr1:172558388-172558601(+)$1	213	5	8	9.0000
fff	chr1:183091223-183091475(+)$1	252	23	26	9.0000
ddd	chr12:110929798-110930011(-)$1	213	118	121	9.0000
:::	chr18:33706165-33706382(-)$1	217	68	71	9.0000
fff	chrX:16887111-16887343(-)$1	232	101	104	9.0000
D:c	chr16:2826910-2827138(-)$1	228	7	10	9.0000
:::	chrX:77373475-77373744(+)$1	269	97	100	9.0000
ddd	chrX:135308013-135308245(-)$1	232	29	32	9.0000
::C	chr16:14693703-14693907(-)$1	204	3	6	9.0000
EEE	chr6:31760503-31760712(-)$1	209	37	40	9.0000
ccc	chr7:128645014-128645229(-)$1	215	13	16	9.0000
2cc	chr16:53498049-53498261(+)$1	212	114	117	9.0000
eee	chrX:71417123-71417358(+)$1	235	35	38	9.0000
c[c	chr17:39974601-39974807(+)$1	206	29	32	9.0000
NNN	chr20:57484688-57484898(+)$1	210	6	9	9.0000
vvv	chr6:44413314-44413530(+)$1	216	74	77	9.0000
c::	chr20:2637333-2637607(+)$1	274	27	30	9.0000
:EE	chr16:4802575-4802806(-)$1	231	16	19	9.0000
ggg	chr22:46749632-46749847(+)$1	215	1	4	9.0000
:::	chr6:31593793-31594025(+)$1	232	0	3	9.0000
EEE	chr6:44219712-44219942(+)$1	230	20	23	9.0000
D:C	chr22:36690196-36690407(-)$1	211	7	10	9.0000
::E	chr5:81573501-81573759(-)$1	258	7	10	9.0000
b^^	chr15:84286877-84287115(+)$1	238	10	13	9.0000
CLL	chr19:37917133-37917340(-)$1	207	32	35	9.0000
mmm	chr16:84101256-84101511(-)$1	255	43	46	9.0000
:ff	chr17:59820379-59820587(-)$1	208	21	24	9.0000
DDD	chr20:18576575-18576838(+)$1	263	42	45	9.0000
hhh	chr11:43380528-43380736(+)$1	208	31	34	9.0000
eed	chr1:220310108-220310343(+)$1	235	44	47	9.0000
ggg	chr9:34241549-34241760(+)$1	211	53	56	9.0000
ddd	chr12:72316690-72316926(+)$1	236	0	3	9.0000
[ee	chrX:118723254-118723456(-)$1	202	82	85	9.0000
eee	chr9:108536089-108536305(+)$1	216	9	12	9.0000
hhh	chr6:13658923-13659140(-)$1	217	73	76	9.0000
ggg	chr20:60713136-60713353(-)$1	217	35	38	9.0000
EEE	chr9:139370824-139371036(-)$1	212	59	62	9.0000
CCC	chr1:169930115-169930321(-)$1	206	5	8	9.0000
{FF	chr15:74948195-74948408(-)$1	213	12	15	9.0000
bbp	chr6:13634646-13634853(-)$1	207	66	69	9.0000
GGG	chr13:48830225-48830450(+)$1	225	14	17	9.0000
GGG	chr17:80040866-80041079(-)$1	213	35	38	9.0000
:::	chr15:66811225-66811451(+)$1	226	56	59	9.0000
FFD	chr16:9017097-9017309(-)$1	212	4	7	9.0000
ddd	chr15:65748504-65748732(-)$1	228	20	23	9.0000
:::	chr19:5207907-5208128(-)$1	221	1	4	9.0000
ccc	chr4:37636498-37636713(-)$1	215	0	3	9.0000
ggg	chr10:7830059-7830300(+)$1	241	92	95	9.0000
lll	chr11:62327687-62328011(-)$1	324	198	201	9.0000
eee	chr8:9592391-9592626(+)$1	235	9	12	9.0000

#DB
(.(	chr11:120302453-120302680(+)$1	1	49	52	9.0000
(((	chr11:9438574-9438780(+)$1	1	61	64	9.0000
(((	chr12:123041877-123042096(+)$1	1	3	6	9.0000
(..	chr14:93185019-93185242(-)$1	1	14	17	9.0000
(((	chr17:8457186-8457398(-)$1	1	13	16	9.0000
.((	chr16:70564644-70564869(+)$1	1	0	3	9.0000
))(	chr5:52344138-52344350(+)$1	1	75	78	9.0000
)))	chr10:33212542-33212755(-)$1	1	133	136	9.0000
.))	chr6:28871922-28872130(-)$1	1	41	44	9.0000
.((	chr18:72187362-72187602(+)$1	1	11	14	9.0000
(..	chr1:120510050-120510263(-)$1	1	16	19	9.0000
)).	chr22:41564635-41564847(+)$1	1	40	43	9.0000
(((	chr5:32126332-32126573(-)$1	1	10	13	9.0000
((.	chr3:137881038-137881266(-)$1	1	50	53	9.0000
...	chr1:109888373-109888592(-)$1	1	49	52	9.0000
(((	chr15:77348043-77348260(-)$1	1	52	55	9.0000
.((	chrX:47098680-47098903(+)$1	1	6	9	9.0000
(((	chr1:156294720-156294960(-)$1	1	38	41	9.0000
(.(	chr19:35230036-35230260(+)$1	1	13	16	9.0000
..(	chr17:65907949-65908163(+)$1	1	2	5	9.0000
.))	chr14:58730328-58730532(+)$1	1	64	67	9.0000
(((	chr6:128643225-128643442(-)$1	1	11	14	9.0000
(((	chr2:54041594-54041810(+)$1	1	82	85	9.0000
(((	chr2:63833906-63834112(+)$1	1	47	50	9.0000
..(	chr2:69565547-69565759(-)$1	1	59	62	9.0000
(((	chr1:6588990-6589202(-)$1	1	48	51	9.0000
).)	chr11:498784-498996(-)$1	1	60	63	9.0000
..(	chr19:59063661-59063871(-)$1	1	63	66	9.0000
...	chr11:75112595-75112844(+)$1	1	0	3	9.0000
(((	chr17:76219905-76220189(+)$1	1	9	12	9.0000
(((	chr5:176867633-176867864(+)$1	1	64	67	9.0000
(((	chr1:115273036-115273274(-)$1	1	2	5	9.0000
(.(	chrX:49028254-49028474(+)$1	1	15	18	9.0000
(((	chr9:35738195-35738410(-)$1	1	6	9	9.0000
(((	chr11:68131243-68131451(+)$1	1	42	45	9.0000
(((	chr5:149390027-149390253(+)$1	1	24	27	9.0000
(.(	chr7:92077988-92078192(+)$1	1	74	77	9.0000
...	chr5:102364537-102364777(+)$1	1	1	4	9.0000
(((	chr5:74016376-74016622(+)$1	1	139	142	9.0000
(.(	chr3:183670919-183671122(-)$1	1	66	69	9.0000
..)	chr20:35443559-35443763(-)$1	1	18	21	9.0000
(..	chr13:41323220-41323433(-)$1	1	54	57	9.0000
(.(	chr21:34922979-34923209(+)$1	1	14	17	9.0000
(((	chr9:35102001-35102209(-)$1	1	15	18	9.0000
)).	chr20:62373408-62373666(+)$1	1	21	24	9.0000
)..	chr12:56548850-56549059(+)$1	1	43	46	9.0000
(((	chr1:15959852-15960059(+)$1	1	107	110	9.0000
.((	chr12:56619125-56619349(+)$1	1	28	31	9.0000
..)	chr6:31500537-31500779(-)$1	1	32	35	9.0000
((.	chr1:39494435-39494691(+)$1	1	21	24	9.0000
...	chr1:172558388-172558601(+)$1	1	5	8	9.0000
)))	chr1:183091223-183091475(+)$1	1	23	26	9.0000
(((	chr12:110929798-110930011(-)$1	1	118	121	9.0000
...	chr18:33706165-33706382(-)$1	1	68	71	9.0000
(((	chrX:16887111-16887343(-)$1	1	101	104	9.0000
(.(	chr16:2826910-2827138(-)$1	1	7	10	9.0000
...	chrX:77373475-77373744(+)$1	1	97	100	9.0000
(((	chrX:135308013-135308245(-)$1	1	29	32	9.0000
..(	chr16:14693703-14693907(-)$1	1	3	6	9.0000
(((	chr6:31760503-31760712(-)$1	1	37	40	9.0000
(((	chr7:128645014-128645229(-)$1	1	13	16	9.0000
.))	chr16:53498049-53498261(+)$1	1	114	117	9.0000
(((	chrX:71417123-71417358(+)$1	1	35	38	9.0000
(.(	chr17:39974601-39974807(+)$1	1	29	32	9.0000
...	chr20:57484688-57484898(+)$1	1	6	9	9.0000
...	chr6:44413314-44413530(+)$1	1	74	77	9.0000
)..	chr20:2637333-2637607(+)$1	1	27	30	9.0000
.((	chr16:4802575-4802806(-)$1	1	16	19	9.0000
(((	chr22:46749632-46749847(+)$1	1	1	4	9.0000
...	chr6:31593793-31594025(+)$1	1	0	3	9.0000
(((	chr6:44219712-44219942(+)$1	1	20	23	9.0000
(.(	chr22:36690196-36690407(-)$1	1	7	10	9.0000
..(	chr5:81573501-81573759(-)$1	1	7	10	9.0000
(..	chr15:84286877-84287115(+)$1	1	10	13	9.0000
(..	chr19:37917133-37917340(-)$1	1	32	35	9.0000
...	chr16:84101256-84101511(-)$1	1	43	46	9.0000
.((	chr17:59820379-59820587(-)$1	1	21	24	9.0000
(((	chr20:18576575-18576838(+)$1	1	42	45	9.0000
(((	chr11:43380528-43380736(+)$1	1	31	34	9.0000
))(	chr1:220310108-220310343(+)$1	1	44	47	9.0000
)))	chr9:34241549-34241760(+)$1	1	53	56	9.0000
(((	chr12:72316690-72316926(+)$1	1	0	3	9.0000
.((	chrX:118723254-118723456(-)$1	1	82	85	9.0000
(((	chr9:108536089-108536305(+)$1	1	9	12	9.0000
(((	chr6:13658923-13659140(-)$1	1	73	76	9.0000
(((	chr20:60713136-60713353(-)$1	1	35	38	9.0000
(((	chr9:139370824-139371036(-)$1	1	59	62	9.0000
(((	chr1:169930115-169930321(-)$1	1	5	8	9.0000
.((	chr15:74948195-74948408(-)$1	1	12	15	9.0000
((.	chr6:13634646-13634853(-)$1	1	66	69	9.0000
(((	chr13:48830225-48830450(+)$1	1	14	17	9.0000
(((	chr17:80040866-80041079(-)$1	1	35	38	9.0000
...	chr15:66811225-66811451(+)$1	1	56	59	9.0000
(((	chr16:9017097-9017309(-)$1	1	4	7	9.0000
)))	chr15:65748504-65748732(-)$1	1	20	23	9.0000
...	chr19:5207907-5208128(-)$1	1	1	4	9.0000
(((	chr4:37636498-37636713(-)$1	1	0	3	9.0000
)))	chr10:7830059-7830300(+)$1	1	92	95	9.0000
...	chr11:62327687-62328011(-)$1	1	198	201	9.0000
(((	chr8:9592391-9592626(+)$1	1	9	12	9.0000

#PSSM
C : 1.00	
A : 1.00	
G : 1.00	

#score	900.0000000000001
#seq	100
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m3_run1.nuc.txt

#NT
GUCCUCU	chr15:89441853-89442112(+)$1	259	100	107	9.7037
uucccca	chr15:69018916-69019175(+)$1	259	26	33	9.6111
GUCCUCC	chr1:161493174-161493403(+)$1	229	33	40	11.4629
UUccucc	chr19:56173060-56173319(+)$1	259	215	222	15.5370
UUCCUCA	chr16:617695-617954(+)$1	259	4	11	13.5925
UUUCUCC	chr3:143708679-143708908(+)$1	229	25	32	11.4629
UUGCUCU	chr12:112591289-112591518(+)$1	229	12	19	9.5185
UUCCUUC	chr7:138518008-138518267(-)$1	259	112	119	10.9999
UUCCCCA	chr8:144391501-144391760(+)$1	259	39	46	9.6111
UUCCUCC	chr19:44090023-44090252(+)$1	229	89	96	15.5370
UUCCUCA	chr3:42706974-42707233(+)$1	259	54	61	13.5925
UUCCUCC	chr2:20251414-20251643(+)$1	229	56	63	15.5370
UUCCUGC	chr16:67043006-67043265(-)$1	259	203	210	10.9999
UGCCUCU	chr2:216860974-216861203(+)$1	229	117	124	10.9074
UUCCUAC	chr8:125597293-125597522(-)$1	229	54	61	11.0925
UUCCCCC	chr6:36978602-36978861(+)$1	259	105	112	11.5555
UUCCUCU	chr20:3905267-3905496(+)$1	229	101	108	13.7777
UCCCUCU	chr9:119463046-119463275(-)$1	229	190	197	10.7222
GUCCUCU	chr11:65307190-65307449(+)$1	259	112	119	9.7037
GUCCUCU	chr11:67079727-67079956(+)$1	229	35	42	9.7037
UUCCUCC	chr20:39813402-39813661(-)$1	259	51	58	15.5370
UUCCUCG	chr4:109090000-109090229(+)$1	229	3	10	12.7592
UACCUCC	chr1:46657983-46658242(-)$1	259	105	112	12.0185
UGCCUCC	chr11:31804892-31805121(-)$1	229	69	76	12.6666
GUCCUCC	chr15:29253533-29253792(+)$1	259	102	109	11.4629
UUCCUCU	chr10:95069753-95070012(-)$1	259	104	111	13.7777
UGCCUCC	chr1:180169374-180169633(+)$1	259	241	248	12.6666
UCCCUCA	chr6:36932216-36932445(-)$1	229	37	44	10.5370
UUCCACC	chr11:10530597-10530856(-)$1	259	143	150	11.1851
UUCCCCC	chr22:36885932-36886191(-)$1	259	76	83	11.5555
UUCCUAC	chrX:103411359-103411621(+)$1	262	133	140	11.0925
UCCCUCC	chr22:21801297-21801556(+)$1	259	210	217	12.4814
UGCCUCU	chr21:46189061-46189320(+)$1	259	24	31	10.9074
UCCCUCC	chr11:72297069-72297328(-)$1	259	71	78	12.4814
UUCCUCC	chr1:21106264-21106493(+)$1	229	50	57	15.5370
UGCCUCC	chr1:55529414-55529643(+)$1	229	35	42	12.6666
UUCCUCC	chr13:84455629-84455858(+)$1	229	163	170	15.5370
UCCCUCC	chr8:41754121-41754350(+)$1	229	155	162	12.4814
UUCCUCA	chr1:19775674-19775933(-)$1	259	32	39	13.5925
UUUCUCA	chr4:38825307-38825566(+)$1	259	215	222	9.5185
UUCCUCC	chr19:18672342-18672601(-)$1	259	63	70	15.5370
UUCCUCA	chr17:61498384-61498643(+)$1	259	61	68	13.5925
UUUCUCC	chr19:34989339-34989568(+)$1	229	40	47	11.4629
UGCCUCC	chr19:18004663-18004922(+)$1	259	177	184	12.6666
UUCCUCC	chr9:127113770-127114029(+)$1	259	189	196	15.5370
UCCCUCC	chr6:32976053-32976312(-)$1	259	22	29	12.4814
UUGCUCU	chr15:31849163-31849392(-)$1	229	208	215	9.5185
UUCCUCC	chr7:127948498-127948757(+)$1	259	26	33	15.5370
UGCCUCC	chr17:74023274-74023533(+)$1	259	235	242	12.6666
ugccuca	chr7:6866091-6866323(+)$1	232	126	133	10.7222
UUCCUCA	chrX:9686907-9687166(-)$1	259	33	40	13.5925
UUCCUCC	chr16:4388286-4388515(+)$1	229	103	110	15.5370
UUUCUCU	chr1:95445894-95446153(-)$1	259	77	84	9.7037

#otherMatches

#Struct PSSM
ee22ccc	chr13:41885386-41885645(-)$1	259	187	194	9.7962
YEEEEEd	chr15:89441853-89442112(+)$1	259	100	107	9.7037
hhhhhhh	chr15:69018916-69019175(+)$1	259	26	33	9.6111
""eeeee	chr1:161493174-161493403(+)$1	229	33	40	11.4629
:::GGGG	chr19:56173060-56173319(+)$1	259	215	222	15.5370
::::JJJ	chr16:617695-617954(+)$1	259	4	11	13.5925
gggg+++	chr3:143708679-143708908(+)$1	229	25	32	11.4629
::ggggg	chr12:112591289-112591518(+)$1	229	12	19	9.5185
d::::::	chr7:138518008-138518267(-)$1	259	112	119	10.9999
::::EEE	chr8:144391501-144391760(+)$1	259	39	46	9.6111
:::cccm	chr19:44090023-44090252(+)$1	229	89	96	15.5370
fffff))	chr3:42706974-42707233(+)$1	259	54	61	13.5925
##cccoo	chr2:20251414-20251643(+)$1	229	56	63	15.5370
C}ADDDD	chr16:67043006-67043265(-)$1	259	203	210	10.9999
ffffffb	chr2:216860974-216861203(+)$1	229	117	124	10.9074
:::::::	chr8:125597293-125597522(-)$1	229	54	61	11.0925
fff::::	chr6:36978602-36978861(+)$1	259	105	112	11.5555
7777777	chr20:3905267-3905496(+)$1	229	101	108	13.7777
DDDD~~~	chr9:119463046-119463275(-)$1	229	190	197	10.7222
EEEEE{D	chr11:65307190-65307449(+)$1	259	112	119	9.7037
E{CCC::	chr11:67079727-67079956(+)$1	229	35	42	9.7037
zzzzzzz	chr20:39813402-39813661(-)$1	259	51	58	15.5370
ddmmmmd	chr4:109090000-109090229(+)$1	229	3	10	12.7592
]ccc::E	chr1:46657983-46658242(-)$1	259	105	112	12.0185
JJJJJJJ	chr11:31804892-31805121(-)$1	229	69	76	12.6666
CCggggg	chr15:29253533-29253792(+)$1	259	102	109	11.4629
ttttfff	chr10:95069753-95070012(-)$1	259	104	111	13.7777
ccooooo	chr1:180169374-180169633(+)$1	259	241	248	12.6666
HHdddd"	chr6:36932216-36932445(-)$1	229	37	44	10.5370
:::::::	chr11:10530597-10530856(-)$1	259	143	150	11.1851
$$$$$ee	chr22:36885932-36886191(-)$1	259	76	83	11.5555
eeeoooo	chrX:103411359-103411621(+)$1	262	133	140	11.0925
2bb]eee	chr22:21801297-21801556(+)$1	259	210	217	12.4814
:::::::	chr21:46189061-46189320(+)$1	259	24	31	10.9074
2a]eeee	chr11:72297069-72297328(-)$1	259	71	78	12.4814
hhhhhhh	chr1:21106264-21106493(+)$1	229	50	57	15.5370
iiiiiii	chr1:55529414-55529643(+)$1	229	35	42	12.6666
nccc]dd	chr13:84455629-84455858(+)$1	229	163	170	15.5370
=====[=	chr8:41754121-41754350(+)$1	229	155	162	12.4814
#ddddpp	chr1:19775674-19775933(-)$1	259	32	39	13.5925
iiiii22	chr4:38825307-38825566(+)$1	259	215	222	9.5185
ff&&&&&	chr19:18672342-18672601(-)$1	259	63	70	15.5370
::ddddq	chr17:61498384-61498643(+)$1	259	61	68	13.5925
:::::::	chr19:34989339-34989568(+)$1	229	40	47	11.4629
lffffff	chr19:18004663-18004922(+)$1	259	177	184	12.6666
eeeeebb	chr9:127113770-127114029(+)$1	259	189	196	15.5370
GGGGGCC	chr6:32976053-32976312(-)$1	259	22	29	12.4814
ggggggg	chr15:31849163-31849392(-)$1	229	208	215	9.5185
uuuuuuu	chr7:127948498-127948757(+)$1	259	26	33	15.5370
HHHHHHH	chr17:74023274-74023533(+)$1	259	235	242	12.6666
EEE::::	chr7:6866091-6866323(+)$1	232	126	133	10.7222
33ccc::	chrX:9686907-9687166(-)$1	259	33	40	13.5925
^^^^^^^	chr16:4388286-4388515(+)$1	229	103	110	15.5370
fff:::e	chr1:95445894-95446153(-)$1	259	77	84	9.7037

#DB
))..)))	chr13:41885386-41885645(-)$1	1	187	194	9.7962
.)))))(	chr15:89441853-89442112(+)$1	1	100	107	9.7037
(((((((	chr15:69018916-69019175(+)$1	1	26	33	9.6111
..(((((	chr1:161493174-161493403(+)$1	1	33	40	11.4629
...))))	chr19:56173060-56173319(+)$1	1	215	222	15.5370
....(((	chr16:617695-617954(+)$1	1	4	11	13.5925
((((...	chr3:143708679-143708908(+)$1	1	25	32	11.4629
..(((((	chr12:112591289-112591518(+)$1	1	12	19	9.5185
)......	chr7:138518008-138518267(-)$1	1	112	119	10.9999
....(((	chr8:144391501-144391760(+)$1	1	39	46	9.6111
...(((.	chr19:44090023-44090252(+)$1	1	89	96	15.5370
(((((..	chr3:42706974-42707233(+)$1	1	54	61	13.5925
..(((..	chr2:20251414-20251643(+)$1	1	56	63	15.5370
).)))))	chr16:67043006-67043265(-)$1	1	203	210	10.9999
(((((((	chr2:216860974-216861203(+)$1	1	117	124	10.9074
.......	chr8:125597293-125597522(-)$1	1	54	61	11.0925
)))....	chr6:36978602-36978861(+)$1	1	105	112	11.5555
.......	chr20:3905267-3905496(+)$1	1	101	108	13.7777
))))...	chr9:119463046-119463275(-)$1	1	190	197	10.7222
(((((.(	chr11:65307190-65307449(+)$1	1	112	119	9.7037
(.(((..	chr11:67079727-67079956(+)$1	1	35	42	9.7037
.......	chr20:39813402-39813661(-)$1	1	51	58	15.5370
((....)	chr4:109090000-109090229(+)$1	1	3	10	12.7592
.)))..(	chr1:46657983-46658242(-)$1	1	105	112	12.0185
(((((((	chr11:31804892-31805121(-)$1	1	69	76	12.6666
(((((((	chr15:29253533-29253792(+)$1	1	102	109	11.4629
....)))	chr10:95069753-95070012(-)$1	1	104	111	13.7777
((.....	chr1:180169374-180169633(+)$1	1	241	248	12.6666
((((((.	chr6:36932216-36932445(-)$1	1	37	44	10.5370
.......	chr11:10530597-10530856(-)$1	1	143	150	11.1851
.....((	chr22:36885932-36886191(-)$1	1	76	83	11.5555
(((....	chrX:103411359-103411621(+)$1	1	133	140	11.0925
.)).)))	chr22:21801297-21801556(+)$1	1	210	217	12.4814
.......	chr21:46189061-46189320(+)$1	1	24	31	10.9074
.).))))	chr11:72297069-72297328(-)$1	1	71	78	12.4814
(((((((	chr1:21106264-21106493(+)$1	1	50	57	15.5370
(((((((	chr1:55529414-55529643(+)$1	1	35	42	12.6666
.))).))	chr13:84455629-84455858(+)$1	1	163	170	15.5370
(((((.(	chr8:41754121-41754350(+)$1	1	155	162	12.4814
.((((..	chr1:19775674-19775933(-)$1	1	32	39	13.5925
)))))..	chr4:38825307-38825566(+)$1	1	215	222	9.5185
((.....	chr19:18672342-18672601(-)$1	1	63	70	15.5370
..((((.	chr17:61498384-61498643(+)$1	1	61	68	13.5925
.......	chr19:34989339-34989568(+)$1	1	40	47	11.4629
.))))))	chr19:18004663-18004922(+)$1	1	177	184	12.6666
(((((((	chr9:127113770-127114029(+)$1	1	189	196	15.5370
(((((((	chr6:32976053-32976312(-)$1	1	22	29	12.4814
)))))))	chr15:31849163-31849392(-)$1	1	208	215	9.5185
.......	chr7:127948498-127948757(+)$1	1	26	33	15.5370
)))))))	chr17:74023274-74023533(+)$1	1	235	242	12.6666
)))....	chr7:6866091-6866323(+)$1	1	126	133	10.7222
..)))..	chrX:9686907-9687166(-)$1	1	33	40	13.5925
.......	chr16:4388286-4388515(+)$1	1	103	110	15.5370
)))...(	chr1:95445894-95446153(-)$1	1	77	84	9.7037

#PSSM
U : 0.87	G : 0.09	u : 0.03	
U : 0.70	G : 0.12	C : 0.11	u : 0.01	A : 0.01	g : 0.01	
C : 0.83	U : 0.07	c : 0.05	G : 0.03	
C : 0.94	c : 0.05	
U : 0.85	C : 0.07	u : 0.03	c : 0.01	A : 0.01	
C : 0.87	c : 0.05	A : 0.03	U : 0.01	G : 0.01	
C : 0.55	U : 0.22	A : 0.14	a : 0.03	c : 0.01	G : 0.01	

#score	663.4444444444438
#seq	54
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m1_run2.nuc.txt

#NT
AAGA	chrX:153609331-153609606(+)$1	275	206	210	12.0000
aaga	chr5:179132621-179132863(+)$1	242	179	183	12.0000
AAGA	chr8:37555849-37556105(+)$1	256	217	221	12.0000
AAGA	chr14:95570271-95570511(-)$1	240	11	15	12.0000
aaga	chr19:13054690-13054918(+)$1	228	2	6	12.0000
AAGA	chr5:138643055-138643302(+)$1	247	33	37	12.0000
AAGA	chr6:26199022-26199276(-)$1	254	27	31	12.0000
AAGA	chr17:39880856-39881075(-)$1	219	10	14	12.0000
AAGA	chr12:99059269-99059505(+)$1	236	156	160	12.0000
AAGA	chr17:56568906-56569144(-)$1	238	91	95	12.0000
AAGA	chr12:69983206-69983431(+)$1	225	81	85	12.0000
AAGA	chr10:70101430-70101662(+)$1	232	82	86	12.0000
AAGA	chr12:21796835-21797085(-)$1	250	40	44	12.0000
AAGA	chr5:72875061-72875292(+)$1	231	95	99	12.0000
AAGA	chr17:65955799-65956047(+)$1	248	58	62	12.0000
AAGA	chr2:200789809-200790080(+)$1	271	251	255	12.0000
AAGA	chr1:26135461-26135693(+)$1	232	103	107	12.0000
AAGA	chr1:6285107-6285333(-)$1	226	84	88	12.0000
aaga	chr22:51041646-51041870(+)$1	224	96	100	12.0000
AAGA	chr9:79985371-79985594(+)$1	223	31	35	12.0000
AAGA	chr20:47688773-47689019(+)$1	246	53	57	12.0000
AAGA	chr3:58413673-58413907(-)$1	234	72	76	12.0000
AAGA	chr11:63742052-63742295(+)$1	243	172	176	12.0000
AAGA	chr7:87533527-87533745(+)$1	218	196	200	12.0000
AAGA	chr3:9512082-9512313(+)$1	231	73	77	12.0000
AAGA	chr19:9271346-9271579(+)$1	233	23	27	12.0000
AAGA	chr11:122930498-122930758(-)$1	260	33	37	12.0000
AAGA	chr10:112659992-112660221(-)$1	229	63	67	12.0000
AAGA	chr4:6863673-6863912(+)$1	239	60	64	12.0000
AAGA	chr14:69847162-69847408(-)$1	246	89	93	12.0000
AAGA	chr10:17275722-17275943(+)$1	221	169	173	12.0000
AAGA	chr7:64388367-64388610(+)$1	243	11	15	12.0000
AAGA	chr6:160206326-160206564(-)$1	238	90	94	12.0000
AAGA	chr12:52056627-52056858(+)$1	231	76	80	12.0000
AAGA	chr8:141582895-141583117(-)$1	222	162	166	12.0000
AAGA	chr2:136602096-136602321(-)$1	225	67	71	12.0000
AAGA	chr10:120795443-120795689(-)$1	246	9	13	12.0000
AAGA	chr1:149858058-149858324(-)$1	266	67	71	12.0000
AAGA	chr12:50146149-50146375(+)$1	226	145	149	12.0000
AAGA	chr11:4127304-4127536(+)$1	232	125	129	12.0000
AAGA	chrX:84510325-84510583(+)$1	258	161	165	12.0000
AAGA	chr14:102516778-102517000(+)$1	222	212	216	12.0000
AAGA	chr14:102547973-102548238(-)$1	265	13	17	12.0000
AAGA	chr21:34652077-34652314(+)$1	237	83	87	12.0000
AAGA	chr19:45477638-45477871(+)$1	233	17	21	12.0000
AAGA	chr17:40721439-40721672(+)$1	233	117	121	12.0000
AAGA	chr17:79478128-79478371(-)$1	243	67	71	12.0000
AAGA	chr14:102551178-102551417(-)$1	239	101	105	12.0000
AAGA	chr1:36074871-36075102(-)$1	231	8	12	12.0000
AAGA	chr12:12873977-12874226(+)$1	249	47	51	12.0000
AAGA	chr14:70809277-70809503(-)$1	226	120	124	12.0000
AAGA	chr13:34410272-34410520(+)$1	248	118	122	12.0000
AAGA	chr3:24003417-24003640(+)$1	223	118	122	12.0000
AAGA	chr5:179046228-179046483(-)$1	255	3	7	12.0000
AAGA	chr7:95750420-95750648(-)$1	228	147	151	12.0000
AAGA	chr2:3481420-3481649(+)$1	229	79	83	12.0000
AAGA	chr13:114294429-114294654(+)$1	225	198	202	12.0000
AAGA	chr17:49083407-49083640(-)$1	233	61	65	12.0000
AAGA	chr3:101284274-101284497(+)$1	223	3	7	12.0000
AAGA	chr7:98957223-98957448(+)$1	225	76	80	12.0000
AAGA	chr5:90678783-90679015(-)$1	232	36	40	12.0000
AAGA	chr7:5567818-5568072(-)$1	254	32	36	12.0000
AAGA	chrX:71493674-71493919(-)$1	245	118	122	12.0000
AAGA	chr21:28327014-28327252(-)$1	238	150	154	12.0000
AAGA	chr1:44442733-44442970(+)$1	237	86	90	12.0000
AAGA	chr9:134346093-134346357(+)$1	264	93	97	12.0000
AAGA	chr15:64365077-64365302(-)$1	225	96	100	12.0000
AAGA	chr9:94172554-94172807(-)$1	253	1	5	12.0000
AAGA	chr5:149826335-149826576(-)$1	241	21	25	12.0000
AAGA	chr21:28210069-28210300(-)$1	231	25	29	12.0000
AAGA	chr6:26056503-26056766(-)$1	263	170	174	12.0000
AAGA	chr11:9603019-9603283(+)$1	264	4	8	12.0000
AAGA	chr18:46448029-46448267(-)$1	238	52	56	12.0000
AAGA	chr1:150550714-150550978(-)$1	264	41	45	12.0000
AAGA	chrX:107975822-107976077(-)$1	255	38	42	12.0000
AAGA	chr19:46341741-46341963(-)$1	222	120	124	12.0000
AAGA	chr1:163318729-163318964(+)$1	235	22	26	12.0000
AAGA	chr17:56083140-56083371(-)$1	231	12	16	12.0000
AAGA	chr6:112041124-112041355(-)$1	231	126	130	12.0000
AAGA	chr2:10931836-10932076(-)$1	240	46	50	12.0000

#otherMatches

#Struct PSSM
ee::	chr11:2972393-2972616(-)$1	223	22	26	12.0000
:fff	chrX:153609331-153609606(+)$1	275	206	210	12.0000
ccc]	chr5:179132621-179132863(+)$1	242	179	183	12.0000
mmmm	chr8:37555849-37556105(+)$1	256	217	221	12.0000
#ccc	chr14:95570271-95570511(-)$1	240	11	15	12.0000
FFFF	chr19:13054690-13054918(+)$1	228	2	6	12.0000
:ccc	chr5:138643055-138643302(+)$1	247	33	37	12.0000
wwww	chr6:26199022-26199276(-)$1	254	27	31	12.0000
::::	chr17:39880856-39881075(-)$1	219	10	14	12.0000
22cc	chr12:99059269-99059505(+)$1	236	156	160	12.0000
JJJJ	chr17:56568906-56569144(-)$1	238	91	95	12.0000
cc[d	chr12:69983206-69983431(+)$1	225	81	85	12.0000
eeee	chr10:70101430-70101662(+)$1	232	82	86	12.0000
++cc	chr12:21796835-21797085(-)$1	250	40	44	12.0000
ffff	chr5:72875061-72875292(+)$1	231	95	99	12.0000
22dd	chr17:65955799-65956047(+)$1	248	58	62	12.0000
eeoo	chr2:200789809-200790080(+)$1	271	251	255	12.0000
oooo	chr1:26135461-26135693(+)$1	232	103	107	12.0000
b]a2	chr1:6285107-6285333(-)$1	226	84	88	12.0000
:::E	chr22:51041646-51041870(+)$1	224	96	100	12.0000
4444	chr9:79985371-79985594(+)$1	223	31	35	12.0000
]iii	chr20:47688773-47689019(+)$1	246	53	57	12.0000
]bb:	chr3:58413673-58413907(-)$1	234	72	76	12.0000
e[ee	chr11:63742052-63742295(+)$1	243	172	176	12.0000
////	chr7:87533527-87533745(+)$1	218	196	200	12.0000
qqqq	chr3:9512082-9512313(+)$1	231	73	77	12.0000
++++	chr19:9271346-9271579(+)$1	233	23	27	12.0000
ssss	chr11:122930498-122930758(-)$1	260	33	37	12.0000
qqqq	chr10:112659992-112660221(-)$1	229	63	67	12.0000
PPPP	chr4:6863673-6863912(+)$1	239	60	64	12.0000
ccc]	chr14:69847162-69847408(-)$1	246	89	93	12.0000
YYBB	chr10:17275722-17275943(+)$1	221	169	173	12.0000
rrrr	chr7:64388367-64388610(+)$1	243	11	15	12.0000
5555	chr6:160206326-160206564(-)$1	238	90	94	12.0000
::::	chr12:52056627-52056858(+)$1	231	76	80	12.0000
G:::	chr8:141582895-141583117(-)$1	222	162	166	12.0000
hhhh	chr2:136602096-136602321(-)$1	225	67	71	12.0000
DDDD	chr10:120795443-120795689(-)$1	246	9	13	12.0000
[eee	chr1:149858058-149858324(-)$1	266	67	71	12.0000
mmff	chr12:50146149-50146375(+)$1	226	145	149	12.0000
!!cc	chr11:4127304-4127536(+)$1	232	125	129	12.0000
bb!!	chrX:84510325-84510583(+)$1	258	161	165	12.0000
fff:	chr14:102516778-102517000(+)$1	222	212	216	12.0000
:HHH	chr14:102547973-102548238(-)$1	265	13	17	12.0000
====	chr21:34652077-34652314(+)$1	237	83	87	12.0000
D{DD	chr19:45477638-45477871(+)$1	233	17	21	12.0000
8888	chr17:40721439-40721672(+)$1	233	117	121	12.0000
gggg	chr17:79478128-79478371(-)$1	243	67	71	12.0000
:DDD	chr14:102551178-102551417(-)$1	239	101	105	12.0000
C{GG	chr1:36074871-36075102(-)$1	231	8	12	12.0000
]ggg	chr12:12873977-12874226(+)$1	249	47	51	12.0000
dddd	chr14:70809277-70809503(-)$1	226	120	124	12.0000
mmee	chr13:34410272-34410520(+)$1	248	118	122	12.0000
##ff	chr3:24003417-24003640(+)$1	223	118	122	12.0000
JJJJ	chr5:179046228-179046483(-)$1	255	3	7	12.0000
====	chr7:95750420-95750648(-)$1	228	147	151	12.0000
ggmm	chr2:3481420-3481649(+)$1	229	79	83	12.0000
fffl	chr13:114294429-114294654(+)$1	225	198	202	12.0000
qqqq	chr17:49083407-49083640(-)$1	233	61	65	12.0000
:CCC	chr3:101284274-101284497(+)$1	223	3	7	12.0000
:BB{	chr7:98957223-98957448(+)$1	225	76	80	12.0000
ffff	chr5:90678783-90679015(-)$1	232	36	40	12.0000
dDDD	chr7:5567818-5568072(-)$1	254	32	36	12.0000
mmmm	chrX:71493674-71493919(-)$1	245	118	122	12.0000
b]dd	chr21:28327014-28327252(-)$1	238	150	154	12.0000
ffff	chr1:44442733-44442970(+)$1	237	86	90	12.0000
7fff	chr9:134346093-134346357(+)$1	264	93	97	12.0000
EBB{	chr15:64365077-64365302(-)$1	225	96	100	12.0000
::EE	chr9:94172554-94172807(-)$1	253	1	5	12.0000
g>>>	chr5:149826335-149826576(-)$1	241	21	25	12.0000
qqqq	chr21:28210069-28210300(-)$1	231	25	29	12.0000
ssss	chr6:26056503-26056766(-)$1	263	170	174	12.0000
eeee	chr11:9603019-9603283(+)$1	264	4	8	12.0000
f"""	chr18:46448029-46448267(-)$1	238	52	56	12.0000
c[gg	chr1:150550714-150550978(-)$1	264	41	45	12.0000
pppp	chrX:107975822-107976077(-)$1	255	38	42	12.0000
dddd	chr19:46341741-46341963(-)$1	222	120	124	12.0000
WWWW	chr1:163318729-163318964(+)$1	235	22	26	12.0000
++++	chr17:56083140-56083371(-)$1	231	12	16	12.0000
====	chr6:112041124-112041355(-)$1	231	126	130	12.0000
xxxx	chr2:10931836-10932076(-)$1	240	46	50	12.0000

#DB
))..	chr11:2972393-2972616(-)$1	1	22	26	12.0000
.(((	chrX:153609331-153609606(+)$1	1	206	210	12.0000
))).	chr5:179132621-179132863(+)$1	1	179	183	12.0000
....	chr8:37555849-37556105(+)$1	1	217	221	12.0000
.(((	chr14:95570271-95570511(-)$1	1	11	15	12.0000
((((	chr19:13054690-13054918(+)$1	1	2	6	12.0000
.(((	chr5:138643055-138643302(+)$1	1	33	37	12.0000
....	chr6:26199022-26199276(-)$1	1	27	31	12.0000
....	chr17:39880856-39881075(-)$1	1	10	14	12.0000
..))	chr12:99059269-99059505(+)$1	1	156	160	12.0000
((((	chr17:56568906-56569144(-)$1	1	91	95	12.0000
((.(	chr12:69983206-69983431(+)$1	1	81	85	12.0000
))))	chr10:70101430-70101662(+)$1	1	82	86	12.0000
..((	chr12:21796835-21797085(-)$1	1	40	44	12.0000
))))	chr5:72875061-72875292(+)$1	1	95	99	12.0000
..))	chr17:65955799-65956047(+)$1	1	58	62	12.0000
((..	chr2:200789809-200790080(+)$1	1	251	255	12.0000
....	chr1:26135461-26135693(+)$1	1	103	107	12.0000
).).	chr1:6285107-6285333(-)$1	1	84	88	12.0000
...)	chr22:51041646-51041870(+)$1	1	96	100	12.0000
....	chr9:79985371-79985594(+)$1	1	31	35	12.0000
.)))	chr20:47688773-47689019(+)$1	1	53	57	12.0000
.)).	chr3:58413673-58413907(-)$1	1	72	76	12.0000
(.((	chr11:63742052-63742295(+)$1	1	172	176	12.0000
....	chr7:87533527-87533745(+)$1	1	196	200	12.0000
....	chr3:9512082-9512313(+)$1	1	73	77	12.0000
....	chr19:9271346-9271579(+)$1	1	23	27	12.0000
....	chr11:122930498-122930758(-)$1	1	33	37	12.0000
....	chr10:112659992-112660221(-)$1	1	63	67	12.0000
....	chr4:6863673-6863912(+)$1	1	60	64	12.0000
))).	chr14:69847162-69847408(-)$1	1	89	93	12.0000
..))	chr10:17275722-17275943(+)$1	1	169	173	12.0000
....	chr7:64388367-64388610(+)$1	1	11	15	12.0000
....	chr6:160206326-160206564(-)$1	1	90	94	12.0000
....	chr12:52056627-52056858(+)$1	1	76	80	12.0000
)...	chr8:141582895-141583117(-)$1	1	162	166	12.0000
))))	chr2:136602096-136602321(-)$1	1	67	71	12.0000
((((	chr10:120795443-120795689(-)$1	1	9	13	12.0000
.(((	chr1:149858058-149858324(-)$1	1	67	71	12.0000
..))	chr12:50146149-50146375(+)$1	1	145	149	12.0000
..((	chr11:4127304-4127536(+)$1	1	125	129	12.0000
((..	chrX:84510325-84510583(+)$1	1	161	165	12.0000
))).	chr14:102516778-102517000(+)$1	1	212	216	12.0000
.(((	chr14:102547973-102548238(-)$1	1	13	17	12.0000
((((	chr21:34652077-34652314(+)$1	1	83	87	12.0000
(.((	chr19:45477638-45477871(+)$1	1	17	21	12.0000
....	chr17:40721439-40721672(+)$1	1	117	121	12.0000
))))	chr17:79478128-79478371(-)$1	1	67	71	12.0000
.)))	chr14:102551178-102551417(-)$1	1	101	105	12.0000
(.((	chr1:36074871-36075102(-)$1	1	8	12	12.0000
.)))	chr12:12873977-12874226(+)$1	1	47	51	12.0000
))))	chr14:70809277-70809503(-)$1	1	120	124	12.0000
..))	chr13:34410272-34410520(+)$1	1	118	122	12.0000
..((	chr3:24003417-24003640(+)$1	1	118	122	12.0000
((((	chr5:179046228-179046483(-)$1	1	3	7	12.0000
((((	chr7:95750420-95750648(-)$1	1	147	151	12.0000
((..	chr2:3481420-3481649(+)$1	1	79	83	12.0000
(((.	chr13:114294429-114294654(+)$1	1	198	202	12.0000
....	chr17:49083407-49083640(-)$1	1	61	65	12.0000
.(((	chr3:101284274-101284497(+)$1	1	3	7	12.0000
.((.	chr7:98957223-98957448(+)$1	1	76	80	12.0000
((((	chr5:90678783-90679015(-)$1	1	36	40	12.0000
)(((	chr7:5567818-5568072(-)$1	1	32	36	12.0000
....	chrX:71493674-71493919(-)$1	1	118	122	12.0000
).))	chr21:28327014-28327252(-)$1	1	150	154	12.0000
((((	chr1:44442733-44442970(+)$1	1	86	90	12.0000
.)))	chr9:134346093-134346357(+)$1	1	93	97	12.0000
(((.	chr15:64365077-64365302(-)$1	1	96	100	12.0000
..((	chr9:94172554-94172807(-)$1	1	1	5	12.0000
)...	chr5:149826335-149826576(-)$1	1	21	25	12.0000
....	chr21:28210069-28210300(-)$1	1	25	29	12.0000
....	chr6:26056503-26056766(-)$1	1	170	174	12.0000
((((	chr11:9603019-9603283(+)$1	1	4	8	12.0000
(...	chr18:46448029-46448267(-)$1	1	52	56	12.0000
(.((	chr1:150550714-150550978(-)$1	1	41	45	12.0000
....	chrX:107975822-107976077(-)$1	1	38	42	12.0000
))))	chr19:46341741-46341963(-)$1	1	120	124	12.0000
....	chr1:163318729-163318964(+)$1	1	22	26	12.0000
....	chr17:56083140-56083371(-)$1	1	12	16	12.0000
))))	chr6:112041124-112041355(-)$1	1	126	130	12.0000
....	chr2:10931836-10932076(-)$1	1	46	50	12.0000

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

#score	972.0000000000006
#seq	81
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m1_run2.nuc.txt

#NT
GGAGUAGAGCAGCCUCGCCUCCCAGCUGGACCUGCAAACAGGCCACCUGAGCCUCACACCCAGGUUCAGAGGGCACAAGCAGAAACAGGCCCGACUUCCUUCCCCUCCCCUGUGUCUGUCUCCAUGAAGCCUGACCUUCCAGUCUCUCUUCCCACUCAGACUGCCCCAAAACAGCCGUUGUUUGUCCCAACAACCUCUGGCCCCAGCACCCCACCAGGACUGGUUCUGCCACACACUGAAUUCCAGC	chr1:16263807-16264126(+)$1	319	15	262	326.0000

#otherMatches

#Struct PSSM
88ffffffbb22ddddEEEEE{EEEEE::::::ccc!!bbnnnnnbb22ccc::a[ggggggg!!dddd####hhhhhhhh"""dddd[bbffffff[aeeeee%%%%%%ffffff[bb"""ccc$$$$$iiiiiiiiirrrrrrrrriiiiiiiii333cccbbffffff22eeeee]a]ffffff666666bbdddd666666hhhhhhhhdddd55555ggggggga::EEEEE}EEEEE::dd	chrX:107978015-107978348(-)$1	333	44	291	326.0000
eeee!!cccmmmmccc22eeeee22dddd::cccmmmmcccccc!!hhhhhhhhppppppphhhhhhhh22ccc::::FFFFFFeeeee"""bbtttttttttttbb]eeeeeeeeee&&&&&&&dddd"""cccooooooccc333dddd55555eeeee::::::::::ccc!!ffffffooooooffffff22ccc:::dddd!!bboooooobb]ddddFFFFFF::::::cccnnnnnccc:	chr1:16263807-16264126(+)$1	319	15	262	326.0000

#DB
..))))))))..))))(((((.(((((......(((..((.....))..)))..(.(((((((..((((....((((((((...((((.((((((((.((((((......((((((.((...(((.....(((((((((.........)))))))))...)))))))))))..))))).).))))))......))))))......)))))))))))).....))))))))..))))).)))))..((	chrX:107978015-107978348(-)$1	1	44	291	326.0000
((((..(((....)))..)))))..))))..(((....)))(((..((((((((.......))))))))..)))....(((((((((((...((...........)).)))))(((((.......((((...(((......)))...)))).....)))))..........(((..((((((......))))))..)))...((((..((......)).))))))))))......(((.....))).	chr1:16263807-16264126(+)$1	1	15	262	326.0000

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

#score	652.0
#seq	2
#width	247
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m2_run1.nuc.txt

#NT
GAGGCA	chr10:105351111-105351332(+)$1	221	165	171	10.1710
GAGGUA	chr9:80032378-80032593(+)$1	215	161	167	10.0394
GAGAAA	chr2:101965921-101966157(-)$1	236	28	34	9.8421
GAGCAA	chr5:131818903-131819119(+)$1	216	49	55	9.8421
GAGAAA	chr12:13715297-13715528(-)$1	231	97	103	9.8421
GUGGAA	chr7:99631874-99632089(-)$1	215	27	33	9.5131
UAGGAA	chr7:2567804-2568028(+)$1	224	161	167	10.3026
GAGGGA	chr17:40555170-40555390(-)$1	220	20	26	10.2368
GAGGAA	chr3:51752078-51752300(+)$1	222	118	124	13.9210
UAGGAA	chr8:145649863-145650080(-)$1	217	114	120	10.3026
GAGGUA	chr6:43472251-43472480(+)$1	229	151	157	10.0394
GAGCAA	chr15:44620847-44621063(+)$1	216	34	40	9.8421
GAGGAG	chr3:85008475-85008694(+)$1	219	52	58	9.7763
GGGGAA	chr6:80412788-80413029(+)$1	241	158	164	9.5131
GAGGCA	chr18:24435300-24435522(-)$1	222	85	91	10.1710
GAGGAA	chrY:2354419-2354636(+)$1	217	189	195	13.9210
GAGGCA	chr19:58992242-58992461(-)$1	219	28	34	10.1710
GAGGGA	chrX:153073402-153073635(-)$1	233	45	51	10.2368
GAGGAG	chr19:989927-990158(+)$1	231	25	31	9.7763
GUGGAA	chr9:86584631-86584849(-)$1	218	99	105	9.5131
GAGGAA	chr11:6504355-6504573(+)$1	218	11	17	13.9210
GAGGAA	chr20:62697503-62697729(+)$1	226	185	191	13.9210
GAAGAA	chr16:6069543-6069767(+)$1	224	49	55	9.7763
GAGGAG	chr11:33795792-33796009(-)$1	217	111	117	9.7763
GAAGAA	chr2:54081844-54082067(-)$1	223	148	154	9.7763
GAGCAA	chr14:100143945-100144161(-)$1	216	88	94	9.8421
GAAGAA	chr9:34648869-34649111(+)$1	242	141	147	9.7763
AAGGAA	chr11:64895256-64895478(+)$1	222	124	130	10.6315
GAGUAA	chr11:124972159-124972378(-)$1	219	78	84	9.7105
GAGAAA	chr6:136580287-136580504(-)$1	217	71	77	9.8421
GAGGAA	chr11:96086096-96086317(-)$1	221	38	44	13.9210
GAGGAG	chr22:24030317-24030535(-)$1	218	144	150	9.7763
AAGGAA	chr15:25224642-25224858(+)$1	216	53	59	10.6315
GAGGAA	chr8:12611644-12611880(+)$1	236	69	75	13.9210
GAGCAA	chr5:108671848-108672067(-)$1	219	189	195	9.8421
GAGGAA	chr1:157092885-157093102(-)$1	217	141	147	13.9210
GGGGAA	chr11:118915290-118915516(-)$1	226	174	180	9.5131
GAGGCA	chr3:195269924-195270142(-)$1	218	161	167	10.1710
GAAGAA	chrX:40465571-40465799(+)$1	228	69	75	9.7763
UAGGAA	chr9:5468169-5468386(-)$1	217	65	71	10.3026
GAAGAA	chr17:6916672-6916903(+)$1	231	1	7	9.7763
GAUGAA	chr17:60689814-60690039(+)$1	225	206	212	9.4473
AAGGAA	chr17:61780313-61780539(+)$1	226	34	40	10.6315
GAGGAG	chr17:48560679-48560897(-)$1	218	19	25	9.7763
CAGGAA	chr9:5774461-5774699(+)$1	238	75	81	10.5657
GAGGAA	chr8:22491887-22492110(-)$1	223	8	14	13.9210
GAGGGA	chr10:74094669-74094884(+)$1	215	72	78	10.2368
GAGGCA	chr1:147142155-147142370(-)$1	215	48	54	10.1710
GAAGAA	chr7:100091976-100092196(+)$1	220	154	160	9.7763
AAGGAA	chr3:150260550-150260774(-)$1	224	17	23	10.6315
CAGGAA	chr12:110781075-110781291(-)$1	216	208	214	10.5657
AAGGAA	chr1:12939023-12939239(-)$1	216	5	11	10.6315
GAGAAA	chr6:88050385-88050602(+)$1	217	97	103	9.8421
GGGGAA	chr15:64974669-64974927(+)$1	258	184	190	9.5131
AAGGAA	chr7:124532301-124532527(-)$1	226	199	205	10.6315
GAGGAA	chr10:73993219-73993445(+)$1	226	125	131	13.9210
GAGGAC	chr17:76850672-76850893(-)$1	221	107	113	9.4473
GAGUAA	chr3:62279765-62279986(-)$1	221	47	53	9.7105
CAGGAA	chr1:146627693-146627909(+)$1	216	14	20	10.5657
GAGGUA	chr3:156423962-156424181(+)$1	219	86	92	10.0394
GAGGAA	chr8:101734601-101734823(-)$1	222	78	84	13.9210
GAGGAA	chr11:85406122-85406349(-)$1	227	10	16	13.9210
GAGGAA	chr7:44097529-44097761(+)$1	232	222	228	13.9210
GUGGAA	chr19:58211402-58211636(-)$1	234	73	79	9.5131
GAGGAA	chr15:72070821-72071039(-)$1	218	28	34	13.9210
GAGGGA	chr13:25738331-25738550(-)$1	219	60	66	10.2368
CAGGAA	chr6:142544453-142544676(+)$1	223	120	126	10.5657
CAGGAA	chr10:47087883-47088101(-)$1	218	93	99	10.5657
GAGGAA	chr5:177549333-177549551(-)$1	218	208	214	13.9210
CAGGAA	chr1:11902865-11903082(+)$1	217	48	54	10.5657
GAGGGA	chr11:65486832-65487063(+)$1	231	58	64	10.2368
AAGGAA	chr2:207945709-207945929(-)$1	220	36	42	10.6315
GAGGAG	chr1:26348981-26349197(+)$1	216	167	173	9.7763
AAGGAA	chr15:73854144-73854371(-)$1	227	57	63	10.6315
CAGGAA	chr12:56868336-56868554(+)$1	218	28	34	10.5657

#otherMatches

#Struct PSSM
[bbooo	chr22:51050559-51050778(-)$1	219	42	48	10.2368
glllgg	chr10:105351111-105351332(+)$1	221	165	171	10.1710
ddddee	chr9:80032378-80032593(+)$1	215	161	167	10.0394
::::::	chr2:101965921-101966157(-)$1	236	28	34	9.8421
ffff!!	chr5:131818903-131819119(+)$1	216	49	55	9.8421
_____E	chr12:13715297-13715528(-)$1	231	97	103	9.8421
!dddde	chr7:99631874-99632089(-)$1	215	27	33	9.5131
]dddd4	chr7:2567804-2568028(+)$1	224	161	167	10.3026
"""bb[	chr17:40555170-40555390(-)$1	220	20	26	10.2368
ddd:dd	chr3:51752078-51752300(+)$1	222	118	124	13.9210
ddd]bb	chr8:145649863-145650080(-)$1	217	114	120	10.3026
oooggg	chr6:43472251-43472480(+)$1	229	151	157	10.0394
::::::	chr15:44620847-44621063(+)$1	216	34	40	9.8421
e]bb]d	chr3:85008475-85008694(+)$1	219	52	58	9.7763
fffddd	chr6:80412788-80413029(+)$1	241	158	164	9.5131
AKKCCC	chr18:24435300-24435522(-)$1	222	85	91	10.1710
DYYA}D	chrY:2354419-2354636(+)$1	217	189	195	13.9210
d[ccco	chr19:58992242-58992461(-)$1	219	28	34	10.1710
HHHHHH	chrX:153073402-153073635(-)$1	233	45	51	10.2368
::::::	chr19:989927-990158(+)$1	231	25	31	9.7763
hhhh[e	chr9:86584631-86584849(-)$1	218	99	105	9.5131
qqbb::	chr11:6504355-6504573(+)$1	218	11	17	13.9210
hhhhhh	chr20:62697503-62697729(+)$1	226	185	191	13.9210
CFFFFF	chr16:6069543-6069767(+)$1	224	49	55	9.7763
22bb]h	chr11:33795792-33796009(-)$1	217	111	117	9.7763
cc[app	chr2:54081844-54082067(-)$1	223	148	154	9.7763
gcccoo	chr14:100143945-100144161(-)$1	216	88	94	9.8421
f####e	chr9:34648869-34649111(+)$1	242	141	147	9.7763
GGGGGG	chr11:64895256-64895478(+)$1	222	124	130	10.6315
EEEEKK	chr11:124972159-124972378(-)$1	219	78	84	9.7105
f+++++	chr6:136580287-136580504(-)$1	217	71	77	9.8421
ffffff	chr11:96086096-96086317(-)$1	221	38	44	13.9210
qhhhhh	chr22:24030317-24030535(-)$1	218	144	150	9.7763
fffff:	chr15:25224642-25224858(+)$1	216	53	59	10.6315
E}BB::	chr8:12611644-12611880(+)$1	236	69	75	13.9210
::FFFF	chr5:108671848-108672067(-)$1	219	189	195	9.8421
ppcccg	chr1:157092885-157093102(-)$1	217	141	147	13.9210
]dddd]	chr11:118915290-118915516(-)$1	226	174	180	9.5131
qqccc:	chr3:195269924-195270142(-)$1	218	161	167	10.1710
mmccc:	chrX:40465571-40465799(+)$1	228	69	75	9.7763
::dddd	chr9:5468169-5468386(-)$1	217	65	71	10.3026
:::BBL	chr17:6916672-6916903(+)$1	231	1	7	9.7763
b:::::	chr17:60689814-60690039(+)$1	225	206	212	9.4473
::bb!!	chr17:61780313-61780539(+)$1	226	34	40	10.6315
DD{BBO	chr17:48560679-48560897(-)$1	218	19	25	9.7763
""dddd	chr9:5774461-5774699(+)$1	238	75	81	10.5657
ddddnn	chr8:22491887-22492110(-)$1	223	8	14	13.9210
fffffb	chr10:74094669-74094884(+)$1	215	72	78	10.2368
HHHHHC	chr1:147142155-147142370(-)$1	215	48	54	10.1710
e22ccc	chr7:100091976-100092196(+)$1	220	154	160	9.7763
C{FFFF	chr3:150260550-150260774(-)$1	224	17	23	10.6315
CCC:::	chr12:110781075-110781291(-)$1	216	208	214	10.5657
{CCCLL	chr1:12939023-12939239(-)$1	216	5	11	10.6315
[hhhhh	chr6:88050385-88050602(+)$1	217	97	103	9.8421
ffffff	chr15:64974669-64974927(+)$1	258	184	190	9.5131
hhhhhh	chr7:124532301-124532527(-)$1	226	199	205	10.6315
gggggg	chr10:73993219-73993445(+)$1	226	125	131	13.9210
cmmmmc	chr17:76850672-76850893(-)$1	221	107	113	9.4473
eee[cc	chr3:62279765-62279986(-)$1	221	47	53	9.7105
{EEEEE	chr1:146627693-146627909(+)$1	216	14	20	10.5657
dddd]c	chr3:156423962-156424181(+)$1	219	86	92	10.0394
B{BBKK	chr8:101734601-101734823(-)$1	222	78	84	13.9210
EEEEE:	chr11:85406122-85406349(-)$1	227	10	16	13.9210
::::::	chr7:44097529-44097761(+)$1	232	222	228	13.9210
22gggg	chr19:58211402-58211636(-)$1	234	73	79	9.5131
::bb!!	chr15:72070821-72071039(-)$1	218	28	34	13.9210
&&&&ff	chr13:25738331-25738550(-)$1	219	60	66	10.2368
::ffff	chr6:142544453-142544676(+)$1	223	120	126	10.5657
bb$$$$	chr10:47087883-47088101(-)$1	218	93	99	10.5657
eeee::	chr5:177549333-177549551(-)$1	218	208	214	13.9210
a!!ddd	chr1:11902865-11903082(+)$1	217	48	54	10.5657
ggggg]	chr11:65486832-65487063(+)$1	231	58	64	10.2368
NNBB::	chr2:207945709-207945929(-)$1	220	36	42	10.6315
bccc]d	chr1:26348981-26349197(+)$1	216	167	173	9.7763
mggggg	chr15:73854144-73854371(-)$1	227	57	63	10.6315
EEEEMM	chr12:56868336-56868554(+)$1	218	28	34	10.5657

#DB
.((...	chr22:51050559-51050778(-)$1	1	42	48	10.2368
(...))	chr10:105351111-105351332(+)$1	1	165	171	10.1710
((((((	chr9:80032378-80032593(+)$1	1	161	167	10.0394
......	chr2:101965921-101966157(-)$1	1	28	34	9.8421
((((..	chr5:131818903-131819119(+)$1	1	49	55	9.8421
.....)	chr12:13715297-13715528(-)$1	1	97	103	9.8421
.(((((	chr7:99631874-99632089(-)$1	1	27	33	9.5131
.)))).	chr7:2567804-2568028(+)$1	1	161	167	10.3026
...((.	chr17:40555170-40555390(-)$1	1	20	26	10.2368
))).((	chr3:51752078-51752300(+)$1	1	118	124	13.9210
))).))	chr8:145649863-145650080(-)$1	1	114	120	10.3026
...)))	chr6:43472251-43472480(+)$1	1	151	157	10.0394
......	chr15:44620847-44621063(+)$1	1	34	40	9.8421
).)).)	chr3:85008475-85008694(+)$1	1	52	58	9.7763
)))(((	chr6:80412788-80413029(+)$1	1	158	164	9.5131
(..(((	chr18:24435300-24435522(-)$1	1	85	91	10.1710
)..).)	chrY:2354419-2354636(+)$1	1	189	195	13.9210
(.(((.	chr19:58992242-58992461(-)$1	1	28	34	10.1710
((((((	chrX:153073402-153073635(-)$1	1	45	51	10.2368
......	chr19:989927-990158(+)$1	1	25	31	9.7763
((((.(	chr9:86584631-86584849(-)$1	1	99	105	9.5131
..))..	chr11:6504355-6504573(+)$1	1	11	17	13.9210
((((((	chr20:62697503-62697729(+)$1	1	185	191	13.9210
((((((	chr16:6069543-6069767(+)$1	1	49	55	9.7763
..)).)	chr11:33795792-33796009(-)$1	1	111	117	9.7763
((.(..	chr2:54081844-54082067(-)$1	1	148	154	9.7763
)(((..	chr14:100143945-100144161(-)$1	1	88	94	9.8421
(....(	chr9:34648869-34649111(+)$1	1	141	147	9.7763
))))))	chr11:64895256-64895478(+)$1	1	124	130	10.6315
((((..	chr11:124972159-124972378(-)$1	1	78	84	9.7105
(.....	chr6:136580287-136580504(-)$1	1	71	77	9.8421
((((((	chr11:96086096-96086317(-)$1	1	38	44	13.9210
.)))))	chr22:24030317-24030535(-)$1	1	144	150	9.7763
))))).	chr15:25224642-25224858(+)$1	1	53	59	10.6315
).))..	chr8:12611644-12611880(+)$1	1	69	75	13.9210
..))))	chr5:108671848-108672067(-)$1	1	189	195	9.8421
..)))(	chr1:157092885-157093102(-)$1	1	141	147	13.9210
.)))).	chr11:118915290-118915516(-)$1	1	174	180	9.5131
..))).	chr3:195269924-195270142(-)$1	1	161	167	10.1710
..))).	chrX:40465571-40465799(+)$1	1	69	75	9.7763
..((((	chr9:5468169-5468386(-)$1	1	65	71	10.3026
...((.	chr17:6916672-6916903(+)$1	1	1	7	9.7763
).....	chr17:60689814-60690039(+)$1	1	206	212	9.4473
..((..	chr17:61780313-61780539(+)$1	1	34	40	10.6315
((.((.	chr17:48560679-48560897(-)$1	1	19	25	9.7763
..((((	chr9:5774461-5774699(+)$1	1	75	81	10.5657
((((..	chr8:22491887-22492110(-)$1	1	8	14	13.9210
((((((	chr10:74094669-74094884(+)$1	1	72	78	10.2368
((((((	chr1:147142155-147142370(-)$1	1	48	54	10.1710
)..)))	chr7:100091976-100092196(+)$1	1	154	160	9.7763
(.((((	chr3:150260550-150260774(-)$1	1	17	23	10.6315
)))...	chr12:110781075-110781291(-)$1	1	208	214	10.5657
.(((..	chr1:12939023-12939239(-)$1	1	5	11	10.6315
.(((((	chr6:88050385-88050602(+)$1	1	97	103	9.8421
))))))	chr15:64974669-64974927(+)$1	1	184	190	9.5131
))))))	chr7:124532301-124532527(-)$1	1	199	205	10.6315
((((((	chr10:73993219-73993445(+)$1	1	125	131	13.9210
(....)	chr17:76850672-76850893(-)$1	1	107	113	9.4473
(((.((	chr3:62279765-62279986(-)$1	1	47	53	9.7105
.(((((	chr1:146627693-146627909(+)$1	1	14	20	10.5657
)))).)	chr3:156423962-156424181(+)$1	1	86	92	10.0394
(.((..	chr8:101734601-101734823(-)$1	1	78	84	13.9210
(((((.	chr11:85406122-85406349(-)$1	1	10	16	13.9210
......	chr7:44097529-44097761(+)$1	1	222	228	13.9210
..))))	chr19:58211402-58211636(-)$1	1	73	79	9.5131
..((..	chr15:72070821-72071039(-)$1	1	28	34	13.9210
....((	chr13:25738331-25738550(-)$1	1	60	66	10.2368
..((((	chr6:142544453-142544676(+)$1	1	120	126	10.5657
((....	chr10:47087883-47088101(-)$1	1	93	99	10.5657
))))..	chr5:177549333-177549551(-)$1	1	208	214	13.9210
(..(((	chr1:11902865-11903082(+)$1	1	48	54	10.5657
))))).	chr11:65486832-65487063(+)$1	1	58	64	10.2368
..((..	chr2:207945709-207945929(-)$1	1	36	42	10.6315
)))).)	chr1:26348981-26349197(+)$1	1	167	173	9.7763
.)))))	chr15:73854144-73854371(-)$1	1	57	63	10.6315
((((..	chr12:56868336-56868554(+)$1	1	28	34	10.5657

#PSSM
G : 0.76	A : 0.10	C : 0.09	U : 0.03	
A : 0.92	U : 0.03	G : 0.03	
G : 0.90	A : 0.07	U : 0.01	
G : 0.86	A : 0.05	C : 0.05	U : 0.02	
A : 0.81	G : 0.07	C : 0.06	U : 0.03	
A : 0.90	G : 0.07	C : 0.01	

#score	818.6578947368432
#seq	76
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m3_run1.nuc.txt

#NT
AGA	chr2:113960478-113960705(+)$1	227	13	16	9.0000
AGA	chr1:179502867-179503091(+)$1	224	6	9	9.0000
AGA	chr3:130394314-130394538(-)$1	224	43	46	9.0000
AGA	chr1:10463046-10463276(+)$1	230	165	168	9.0000
AGA	chr3:183701656-183701906(-)$1	250	57	60	9.0000
AGA	chr19:11474993-11475219(-)$1	226	90	93	9.0000
AGA	chr9:33917843-33918069(+)$1	226	70	73	9.0000
AGA	chr7:75511077-75511302(-)$1	225	6	9	9.0000
AGA	chr9:13105777-13106012(-)$1	235	15	18	9.0000
AGA	chr1:55207713-55207949(+)$1	236	26	29	9.0000
AGA	chr16:19128690-19128915(+)$1	225	12	15	9.0000
AGA	chrX:118717681-118717910(+)$1	229	56	59	9.0000
AGA	chr3:186759628-186759850(-)$1	222	15	18	9.0000
AGA	chr7:123092616-123092841(-)$1	225	13	16	9.0000
AGA	chr4:42072564-42072794(+)$1	230	63	66	9.0000
AGA	chr2:24397426-24397647(-)$1	221	42	45	9.0000
AGA	chr17:53014435-53014659(+)$1	224	114	117	9.0000
AGA	chr19:44732933-44733157(-)$1	224	3	6	9.0000
aga	chr10:38409554-38409784(+)$1	230	27	30	9.0000
AGA	chr12:32896786-32897033(+)$1	247	2	5	9.0000
AGA	chr13:25915593-25915823(+)$1	230	67	70	9.0000
AGA	chr3:183732091-183732324(-)$1	233	137	140	9.0000
aga	chr12:81905965-81906187(+)$1	222	1	4	9.0000
AGA	chr7:116660427-116660651(+)$1	224	14	17	9.0000
AGA	chr16:30368878-30369106(-)$1	228	7	10	9.0000
AGA	chr1:110565218-110565447(+)$1	229	185	188	9.0000
AGA	chr10:98745154-98745382(+)$1	228	116	119	9.0000
AGA	chr20:47894456-47894694(-)$1	238	231	234	9.0000
AGA	chr16:28503466-28503688(+)$1	222	44	47	9.0000
AGA	chr10:35625969-35626192(+)$1	223	10	13	9.0000
AGA	chr15:69730574-69730817(+)$1	243	37	40	9.0000
AGA	chr11:62649282-62649510(+)$1	228	13	16	9.0000
AGA	chr2:85766308-85766538(+)$1	230	13	16	9.0000
AGA	chr8:117862880-117863107(-)$1	227	11	14	9.0000
AGA	chr3:57306898-57307130(+)$1	232	76	79	9.0000
AGA	chr13:45910936-45911166(-)$1	230	0	3	9.0000
AGA	chr11:1483103-1483331(+)$1	228	25	28	9.0000
AGA	chr6:111656642-111656867(-)$1	225	52	55	9.0000
AGA	chr6:13595653-13595876(-)$1	223	39	42	9.0000
AGA	chr13:67804283-67804506(-)$1	223	18	21	9.0000
AGA	chr2:61764955-61765201(-)$1	246	44	47	9.0000
AGA	chr18:8638977-8639204(+)$1	227	43	46	9.0000
AGA	chr17:61896992-61897229(-)$1	237	9	12	9.0000
AGA	chr1:32636684-32636917(+)$1	233	26	29	9.0000
AGA	chr12:109973547-109973773(+)$1	226	44	47	9.0000
AGA	chr20:50004630-50004851(-)$1	221	16	19	9.0000
AGA	chr11:112104280-112104507(+)$1	227	48	51	9.0000
AGA	chr13:107145053-107145277(-)$1	224	4	7	9.0000
AGA	chr14:31872071-31872319(-)$1	248	62	65	9.0000
AGA	chr16:84156784-84157012(-)$1	228	56	59	9.0000
AGA	chr19:36728196-36728421(+)$1	225	5	8	9.0000
AGA	chr17:1248353-1248605(-)$1	252	50	53	9.0000
AGA	chr12:49523188-49523428(-)$1	240	23	26	9.0000
AGA	chr4:56290668-56290894(+)$1	226	108	111	9.0000
AGA	chr10:120445401-120445625(-)$1	224	18	21	9.0000
AGA	chr5:149681892-149682123(+)$1	231	22	25	9.0000
AGA	chr1:100658182-100658409(-)$1	227	6	9	9.0000
AGA	chr10:75526103-75526341(+)$1	238	16	19	9.0000
AGA	chr1:43133451-43133673(-)$1	222	18	21	9.0000
AGA	chr1:1447835-1448063(+)$1	228	128	131	9.0000
AGA	chr2:145144077-145144306(-)$1	229	27	30	9.0000
AGA	chr16:29821474-29821714(+)$1	240	99	102	9.0000
AGA	chr11:134029825-134030054(-)$1	229	49	52	9.0000
AGA	chr3:45879332-45879584(-)$1	252	43	46	9.0000
AGA	chr12:3724385-3724614(-)$1	229	24	27	9.0000
AGA	chr1:32374325-32374566(-)$1	241	3	6	9.0000
AGA	chr21:46225731-46225956(-)$1	225	5	8	9.0000
AGA	chr4:2263865-2264087(+)$1	222	15	18	9.0000
AGA	chr9:132589577-132589801(-)$1	224	8	11	9.0000
AGA	chr2:201735972-201736201(-)$1	229	10	13	9.0000
AGA	chr3:132843811-132844034(-)$1	223	104	107	9.0000
AGA	chr14:104387201-104387430(-)$1	229	84	87	9.0000
AGA	chr1:201938569-201938818(+)$1	249	40	43	9.0000
AGA	chr17:26937419-26937645(-)$1	226	14	17	9.0000
AGA	chr17:75477962-75478188(+)$1	226	77	80	9.0000
AGA	chr3:107527731-107527956(+)$1	225	64	67	9.0000
AGA	chr1:227181075-227181299(-)$1	224	33	36	9.0000
AGA	chr6:76425167-76425399(+)$1	232	5	8	9.0000
AGA	chr4:177249896-177250120(-)$1	224	0	3	9.0000
AGA	chr14:92588229-92588472(+)$1	243	48	51	9.0000
AGA	chr12:96409336-96409561(-)$1	225	3	6	9.0000
AGA	chr22:19863094-19863319(-)$1	225	177	180	9.0000
AGA	chr2:27439732-27439972(+)$1	240	73	76	9.0000
AGA	chr1:120455365-120455595(-)$1	230	14	17	9.0000
AGA	chr8:41455966-41456194(+)$1	228	12	15	9.0000
AGA	chr17:6939448-6939674(+)$1	226	24	27	9.0000
AGA	chr7:129520658-129520888(-)$1	230	33	36	9.0000
AGA	chr10:69647081-69647310(+)$1	229	91	94	9.0000
AGA	chr16:11966691-11966920(-)$1	229	60	63	9.0000
AGA	chrX:154467440-154467667(+)$1	227	64	67	9.0000
AGA	chr2:97475137-97475361(-)$1	224	109	112	9.0000

#otherMatches

#Struct PSSM
:::	chr6:64394133-64394363(+)$1	230	17	20	9.0000
===	chr2:113960478-113960705(+)$1	227	13	16	9.0000
$$$	chr1:179502867-179503091(+)$1	224	6	9	9.0000
{DD	chr3:130394314-130394538(-)$1	224	43	46	9.0000
ddd	chr1:10463046-10463276(+)$1	230	165	168	9.0000
ggg	chr3:183701656-183701906(-)$1	250	57	60	9.0000
22e	chr19:11474993-11475219(-)$1	226	90	93	9.0000
{A{	chr9:33917843-33918069(+)$1	226	70	73	9.0000
:::	chr7:75511077-75511302(-)$1	225	6	9	9.0000
ooo	chr9:13105777-13106012(-)$1	235	15	18	9.0000
{DD	chr1:55207713-55207949(+)$1	236	26	29	9.0000
fff	chr16:19128690-19128915(+)$1	225	12	15	9.0000
(((	chrX:118717681-118717910(+)$1	229	56	59	9.0000
{DD	chr3:186759628-186759850(-)$1	222	15	18	9.0000
Gdd	chr7:123092616-123092841(-)$1	225	13	16	9.0000
^cc	chr4:42072564-42072794(+)$1	230	63	66	9.0000
bb]	chr2:24397426-24397647(-)$1	221	42	45	9.0000
III	chr17:53014435-53014659(+)$1	224	114	117	9.0000
:::	chr19:44732933-44733157(-)$1	224	3	6	9.0000
%%%	chr10:38409554-38409784(+)$1	230	27	30	9.0000
::g	chr12:32896786-32897033(+)$1	247	2	5	9.0000
:::	chr13:25915593-25915823(+)$1	230	67	70	9.0000
d]c	chr3:183732091-183732324(-)$1	233	137	140	9.0000
:bb	chr12:81905965-81906187(+)$1	222	1	4	9.0000
:dd	chr7:116660427-116660651(+)$1	224	14	17	9.0000
HH:	chr16:30368878-30369106(-)$1	228	7	10	9.0000
ccc	chr1:110565218-110565447(+)$1	229	185	188	9.0000
FFF	chr10:98745154-98745382(+)$1	228	116	119	9.0000
:::	chr20:47894456-47894694(-)$1	238	231	234	9.0000
fff	chr16:28503466-28503688(+)$1	222	44	47	9.0000
bbf	chr10:35625969-35626192(+)$1	223	10	13	9.0000
qqq	chr15:69730574-69730817(+)$1	243	37	40	9.0000
f""	chr11:62649282-62649510(+)$1	228	13	16	9.0000
ee:	chr2:85766308-85766538(+)$1	230	13	16	9.0000
:::	chr8:117862880-117863107(-)$1	227	11	14	9.0000
HHH	chr3:57306898-57307130(+)$1	232	76	79	9.0000
fff	chr13:45910936-45911166(-)$1	230	0	3	9.0000
:::	chr11:1483103-1483331(+)$1	228	25	28	9.0000
::e	chr6:111656642-111656867(-)$1	225	52	55	9.0000
fff	chr6:13595653-13595876(-)$1	223	39	42	9.0000
dee	chr13:67804283-67804506(-)$1	223	18	21	9.0000
qqq	chr2:61764955-61765201(-)$1	246	44	47	9.0000
bb]	chr18:8638977-8639204(+)$1	227	43	46	9.0000
MMM	chr17:61896992-61897229(-)$1	237	9	12	9.0000
DDD	chr1:32636684-32636917(+)$1	233	26	29	9.0000
]a]	chr12:109973547-109973773(+)$1	226	44	47	9.0000
boo	chr20:50004630-50004851(-)$1	221	16	19	9.0000
6cc	chr11:112104280-112104507(+)$1	227	48	51	9.0000
FF{	chr13:107145053-107145277(-)$1	224	4	7	9.0000
gg[	chr14:31872071-31872319(-)$1	248	62	65	9.0000
::d	chr16:84156784-84157012(-)$1	228	56	59	9.0000
:::	chr19:36728196-36728421(+)$1	225	5	8	9.0000
ddd	chr17:1248353-1248605(-)$1	252	50	53	9.0000
2ff	chr12:49523188-49523428(-)$1	240	23	26	9.0000
CCY	chr4:56290668-56290894(+)$1	226	108	111	9.0000
BBK	chr10:120445401-120445625(-)$1	224	18	21	9.0000
ooo	chr5:149681892-149682123(+)$1	231	22	25	9.0000
ggg	chr1:100658182-100658409(-)$1	227	6	9	9.0000
ooo	chr10:75526103-75526341(+)$1	238	16	19	9.0000
CC{	chr1:43133451-43133673(-)$1	222	18	21	9.0000
ooo	chr1:1447835-1448063(+)$1	228	128	131	9.0000
ttt	chr2:145144077-145144306(-)$1	229	27	30	9.0000
===	chr16:29821474-29821714(+)$1	240	99	102	9.0000
off	chr11:134029825-134030054(-)$1	229	49	52	9.0000
"ee	chr3:45879332-45879584(-)$1	252	43	46	9.0000
:::	chr12:3724385-3724614(-)$1	229	24	27	9.0000
:::	chr1:32374325-32374566(-)$1	241	3	6	9.0000
F:f	chr21:46225731-46225956(-)$1	225	5	8	9.0000
CC{	chr4:2263865-2264087(+)$1	222	15	18	9.0000
CC{	chr9:132589577-132589801(-)$1	224	8	11	9.0000
eee	chr2:201735972-201736201(-)$1	229	10	13	9.0000
odd	chr3:132843811-132844034(-)$1	223	104	107	9.0000
:cc	chr14:104387201-104387430(-)$1	229	84	87	9.0000
qbb	chr1:201938569-201938818(+)$1	249	40	43	9.0000
obb	chr17:26937419-26937645(-)$1	226	14	17	9.0000
555	chr17:75477962-75478188(+)$1	226	77	80	9.0000
dd7	chr3:107527731-107527956(+)$1	225	64	67	9.0000
mmc	chr1:227181075-227181299(-)$1	224	33	36	9.0000
:CC	chr6:76425167-76425399(+)$1	232	5	8	9.0000
:::	chr4:177249896-177250120(-)$1	224	0	3	9.0000
iii	chr14:92588229-92588472(+)$1	243	48	51	9.0000
EE:	chr12:96409336-96409561(-)$1	225	3	6	9.0000
ddd	chr22:19863094-19863319(-)$1	225	177	180	9.0000
ddd	chr2:27439732-27439972(+)$1	240	73	76	9.0000
:::	chr1:120455365-120455595(-)$1	230	14	17	9.0000
"""	chr8:41455966-41456194(+)$1	228	12	15	9.0000
fff	chr17:6939448-6939674(+)$1	226	24	27	9.0000
eff	chr7:129520658-129520888(-)$1	230	33	36	9.0000
eee	chr10:69647081-69647310(+)$1	229	91	94	9.0000
eee	chr16:11966691-11966920(-)$1	229	60	63	9.0000
ddd	chrX:154467440-154467667(+)$1	227	64	67	9.0000
666	chr2:97475137-97475361(-)$1	224	109	112	9.0000

#DB
...	chr6:64394133-64394363(+)$1	1	17	20	9.0000
(((	chr2:113960478-113960705(+)$1	1	13	16	9.0000
...	chr1:179502867-179503091(+)$1	1	6	9	9.0000
.((	chr3:130394314-130394538(-)$1	1	43	46	9.0000
)))	chr1:10463046-10463276(+)$1	1	165	168	9.0000
)))	chr3:183701656-183701906(-)$1	1	57	60	9.0000
..)	chr19:11474993-11475219(-)$1	1	90	93	9.0000
.(.	chr9:33917843-33918069(+)$1	1	70	73	9.0000
...	chr7:75511077-75511302(-)$1	1	6	9	9.0000
...	chr9:13105777-13106012(-)$1	1	15	18	9.0000
.((	chr1:55207713-55207949(+)$1	1	26	29	9.0000
(((	chr16:19128690-19128915(+)$1	1	12	15	9.0000
...	chrX:118717681-118717910(+)$1	1	56	59	9.0000
.((	chr3:186759628-186759850(-)$1	1	15	18	9.0000
(((	chr7:123092616-123092841(-)$1	1	13	16	9.0000
.))	chr4:42072564-42072794(+)$1	1	63	66	9.0000
)).	chr2:24397426-24397647(-)$1	1	42	45	9.0000
(((	chr17:53014435-53014659(+)$1	1	114	117	9.0000
...	chr19:44732933-44733157(-)$1	1	3	6	9.0000
...	chr10:38409554-38409784(+)$1	1	27	30	9.0000
..(	chr12:32896786-32897033(+)$1	1	2	5	9.0000
...	chr13:25915593-25915823(+)$1	1	67	70	9.0000
).)	chr3:183732091-183732324(-)$1	1	137	140	9.0000
.((	chr12:81905965-81906187(+)$1	1	1	4	9.0000
.((	chr7:116660427-116660651(+)$1	1	14	17	9.0000
((.	chr16:30368878-30369106(-)$1	1	7	10	9.0000
(((	chr1:110565218-110565447(+)$1	1	185	188	9.0000
(((	chr10:98745154-98745382(+)$1	1	116	119	9.0000
...	chr20:47894456-47894694(-)$1	1	231	234	9.0000
(((	chr16:28503466-28503688(+)$1	1	44	47	9.0000
(((	chr10:35625969-35626192(+)$1	1	10	13	9.0000
...	chr15:69730574-69730817(+)$1	1	37	40	9.0000
(..	chr11:62649282-62649510(+)$1	1	13	16	9.0000
)).	chr2:85766308-85766538(+)$1	1	13	16	9.0000
...	chr8:117862880-117863107(-)$1	1	11	14	9.0000
(((	chr3:57306898-57307130(+)$1	1	76	79	9.0000
(((	chr13:45910936-45911166(-)$1	1	0	3	9.0000
...	chr11:1483103-1483331(+)$1	1	25	28	9.0000
..(	chr6:111656642-111656867(-)$1	1	52	55	9.0000
)))	chr6:13595653-13595876(-)$1	1	39	42	9.0000
(((	chr13:67804283-67804506(-)$1	1	18	21	9.0000
...	chr2:61764955-61765201(-)$1	1	44	47	9.0000
)).	chr18:8638977-8639204(+)$1	1	43	46	9.0000
...	chr17:61896992-61897229(-)$1	1	9	12	9.0000
(((	chr1:32636684-32636917(+)$1	1	26	29	9.0000
.).	chr12:109973547-109973773(+)$1	1	44	47	9.0000
(..	chr20:50004630-50004851(-)$1	1	16	19	9.0000
.))	chr11:112104280-112104507(+)$1	1	48	51	9.0000
((.	chr13:107145053-107145277(-)$1	1	4	7	9.0000
((.	chr14:31872071-31872319(-)$1	1	62	65	9.0000
..(	chr16:84156784-84157012(-)$1	1	56	59	9.0000
...	chr19:36728196-36728421(+)$1	1	5	8	9.0000
(((	chr17:1248353-1248605(-)$1	1	50	53	9.0000
.))	chr12:49523188-49523428(-)$1	1	23	26	9.0000
)).	chr4:56290668-56290894(+)$1	1	108	111	9.0000
((.	chr10:120445401-120445625(-)$1	1	18	21	9.0000
...	chr5:149681892-149682123(+)$1	1	22	25	9.0000
(((	chr1:100658182-100658409(-)$1	1	6	9	9.0000
...	chr10:75526103-75526341(+)$1	1	16	19	9.0000
((.	chr1:43133451-43133673(-)$1	1	18	21	9.0000
...	chr1:1447835-1448063(+)$1	1	128	131	9.0000
...	chr2:145144077-145144306(-)$1	1	27	30	9.0000
(((	chr16:29821474-29821714(+)$1	1	99	102	9.0000
.))	chr11:134029825-134030054(-)$1	1	49	52	9.0000
.((	chr3:45879332-45879584(-)$1	1	43	46	9.0000
...	chr12:3724385-3724614(-)$1	1	24	27	9.0000
...	chr1:32374325-32374566(-)$1	1	3	6	9.0000
(.(	chr21:46225731-46225956(-)$1	1	5	8	9.0000
((.	chr4:2263865-2264087(+)$1	1	15	18	9.0000
((.	chr9:132589577-132589801(-)$1	1	8	11	9.0000
(((	chr2:201735972-201736201(-)$1	1	10	13	9.0000
.))	chr3:132843811-132844034(-)$1	1	104	107	9.0000
.((	chr14:104387201-104387430(-)$1	1	84	87	9.0000
.))	chr1:201938569-201938818(+)$1	1	40	43	9.0000
.))	chr17:26937419-26937645(-)$1	1	14	17	9.0000
...	chr17:75477962-75478188(+)$1	1	77	80	9.0000
)).	chr3:107527731-107527956(+)$1	1	64	67	9.0000
..)	chr1:227181075-227181299(-)$1	1	33	36	9.0000
.((	chr6:76425167-76425399(+)$1	1	5	8	9.0000
...	chr4:177249896-177250120(-)$1	1	0	3	9.0000
(((	chr14:92588229-92588472(+)$1	1	48	51	9.0000
((.	chr12:96409336-96409561(-)$1	1	3	6	9.0000
)))	chr22:19863094-19863319(-)$1	1	177	180	9.0000
(((	chr2:27439732-27439972(+)$1	1	73	76	9.0000
...	chr1:120455365-120455595(-)$1	1	14	17	9.0000
...	chr8:41455966-41456194(+)$1	1	12	15	9.0000
(((	chr17:6939448-6939674(+)$1	1	24	27	9.0000
)))	chr7:129520658-129520888(-)$1	1	33	36	9.0000
(((	chr10:69647081-69647310(+)$1	1	91	94	9.0000
)))	chr16:11966691-11966920(-)$1	1	60	63	9.0000
))(	chrX:154467440-154467667(+)$1	1	64	67	9.0000
...	chr2:97475137-97475361(-)$1	1	109	112	9.0000

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

#score	828.0000000000007
#seq	92
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m1_run1.nuc.txt

#NT
GCCAGG	chr12:67691115-67691381(+)$1	266	16	22	15.3469
GCCAGG	chr11:71164322-71164527(+)$1	205	14	20	15.3469
ACCAGG	chr1:161721578-161721830(+)$1	252	112	118	12.5918
CCCAGG	chr18:12366896-12367144(-)$1	248	23	29	13.4081
GCCAGG	chr5:427852-428118(+)$1	266	20	26	15.3469
GCCAGG	chr1:161130551-161130847(+)$1	296	43	49	15.3469
GCCAGC	chr10:70765522-70765757(+)$1	235	69	75	11.6734
CCCAGG	chr3:49154783-49155026(-)$1	243	18	24	13.4081
GCCAGG	chr17:8108473-8108712(-)$1	239	216	222	15.3469
GCCAGG	chr7:766297-766587(+)$1	290	236	242	15.3469
GCCAGG	chr19:59067973-59068199(-)$1	226	37	43	15.3469
GCCAGG	chr14:24900643-24900888(+)$1	245	168	174	15.3469
CCCAGG	chr9:139934353-139934599(-)$1	246	75	81	13.4081
gccagg	chr1:36208657-36208897(-)$1	240	211	217	15.3469
GCCAGA	chr7:100280149-100280383(-)$1	234	51	57	11.1632
GCCAGC	chr20:35812482-35812717(+)$1	235	138	144	11.6734
GCCAGG	chr14:23532596-23532871(-)$1	275	101	107	15.3469
GCCAGC	chr16:450180-450421(+)$1	241	51	57	11.6734
UCCAGG	chr6:52129341-52129572(-)$1	231	113	119	12.7959
CCCAGG	chr19:33698310-33698542(+)$1	232	25	31	13.4081
GCCAGG	chr9:140500090-140500381(+)$1	291	243	249	15.3469
GCCAGG	chr22:50942947-50943238(-)$1	291	246	252	15.3469
GCCAGG	chr9:97535314-97535550(+)$1	236	22	28	15.3469
GCCAGG	chr16:30536074-30536322(-)$1	248	217	223	15.3469
CCCAGG	chr19:55777167-55777420(-)$1	253	65	71	13.4081
UCCAGG	chr19:39905661-39905915(+)$1	254	83	89	12.7959
GCCAGG	chr1:151137621-151137861(-)$1	240	153	159	15.3469
CCCAGG	chr19:14523767-14524018(-)$1	251	41	47	13.4081
GCCAGG	chr14:24780499-24780784(+)$1	285	167	173	15.3469
CCCAGG	chr1:19653651-19653890(+)$1	239	85	91	13.4081
GCCAGC	chr11:65546512-65546743(-)$1	231	74	80	11.6734
UCCAGG	chr8:53570265-53570509(-)$1	244	36	42	12.7959
uccagg	chr5:176929976-176930221(-)$1	245	0	6	12.7959
CCCAGG	chr12:7049942-7050167(+)$1	225	16	22	13.4081
UCCAGG	chr19:34890080-34890340(+)$1	260	107	113	12.7959
CCCAGG	chr6:29571233-29571544(-)$1	311	153	159	13.4081
gccagg	chr19:4318249-4318536(+)$1	287	248	254	15.3469
GCCAGG	chr19:33072076-33072333(+)$1	257	175	181	15.3469
GCCAGG	chr20:3765888-3766158(-)$1	270	40	46	15.3469
GCCAGG	chr9:35092098-35092351(-)$1	253	175	181	15.3469
GCCAGG	chr16:29997926-29998165(+)$1	239	2	8	15.3469
CCCAGG	chr9:135973959-135974216(-)$1	257	25	31	13.4081
ACCAGG	chr19:1271278-1271530(+)$1	252	77	83	12.5918
CCCAGG	chr17:49238995-49239239(+)$1	244	88	94	13.4081
GCCAGG	chr1:155934747-155935008(-)$1	261	26	32	15.3469
GCCAGG	chr1:976601-976863(+)$1	262	137	143	15.3469
ACCAGG	chr1:171514623-171514886(+)$1	263	135	141	12.5918
GCCAGC	chr5:176885101-176885350(-)$1	249	78	84	11.6734

#otherMatches

#Struct PSSM
pppppp	chr5:180661378-180661649(+)$1	271	76	82	11.6734
EEEECC	chr12:67691115-67691381(+)$1	266	16	22	15.3469
eeeooo	chr11:71164322-71164527(+)$1	205	14	20	15.3469
gga[ff	chr1:161721578-161721830(+)$1	252	112	118	12.5918
hhhddd	chr18:12366896-12367144(-)$1	248	23	29	13.4081
hhhhhh	chr5:427852-428118(+)$1	266	20	26	15.3469
cc[ccc	chr1:161130551-161130847(+)$1	296	43	49	15.3469
bb[ccc	chr10:70765522-70765757(+)$1	235	69	75	11.6734
dEEEEE	chr3:49154783-49155026(-)$1	243	18	24	13.4081
mmccc]	chr17:8108473-8108712(-)$1	239	216	222	15.3469
cccddd	chr7:766297-766587(+)$1	290	236	242	15.3469
d22ggg	chr19:59067973-59068199(-)$1	226	37	43	15.3469
::eeee	chr14:24900643-24900888(+)$1	245	168	174	15.3469
ccc:cc	chr9:139934353-139934599(-)$1	246	75	81	13.4081
eeeeec	chr1:36208657-36208897(-)$1	240	211	217	15.3469
dddddd	chr7:100280149-100280383(-)$1	234	51	57	11.1632
gggggg	chr20:35812482-35812717(+)$1	235	138	144	11.6734
!!ffff	chr14:23532596-23532871(-)$1	275	101	107	15.3469
eeeee]	chr16:450180-450421(+)$1	241	51	57	11.6734
ccc]bb	chr6:52129341-52129572(-)$1	231	113	119	12.7959
####ee	chr19:33698310-33698542(+)$1	232	25	31	13.4081
FFFFFD	chr9:140500090-140500381(+)$1	291	243	249	15.3469
b]gggg	chr22:50942947-50943238(-)$1	291	246	252	15.3469
cccFFF	chr9:97535314-97535550(+)$1	236	22	28	15.3469
88dddd	chr16:30536074-30536322(-)$1	248	217	223	15.3469
i333dd	chr19:55777167-55777420(-)$1	253	65	71	13.4081
Dbb[cc	chr19:39905661-39905915(+)$1	254	83	89	12.7959
mmmmee	chr1:151137621-151137861(-)$1	240	153	159	15.3469
elllee	chr19:14523767-14524018(-)$1	251	41	47	13.4081
ii333d	chr14:24780499-24780784(+)$1	285	167	173	15.3469
!!ccc[	chr1:19653651-19653890(+)$1	239	85	91	13.4081
EEEE:f	chr11:65546512-65546743(-)$1	231	74	80	11.6734
&&&eee	chr8:53570265-53570509(-)$1	244	36	42	12.7959
:HHHHH	chr5:176929976-176930221(-)$1	245	0	6	12.7959
FFKKDD	chr12:7049942-7050167(+)$1	225	16	22	13.4081
ddd:::	chr19:34890080-34890340(+)$1	260	107	113	12.7959
b[eeee	chr6:29571233-29571544(-)$1	311	153	159	13.4081
ddd]dd	chr19:4318249-4318536(+)$1	287	248	254	15.3469
ffffhh	chr19:33072076-33072333(+)$1	257	175	181	15.3469
]bb:gg	chr20:3765888-3766158(-)$1	270	40	46	15.3469
22ffff	chr9:35092098-35092351(-)$1	253	175	181	15.3469
cfffff	chr16:29997926-29998165(+)$1	239	2	8	15.3469
##dddd	chr9:135973959-135974216(-)$1	257	25	31	13.4081
CCCKKD	chr19:1271278-1271530(+)$1	252	77	83	12.5918
h!!ddd	chr17:49238995-49239239(+)$1	244	88	94	13.4081
bb"""d	chr1:155934747-155935008(-)$1	261	26	32	15.3469
eeee[c	chr1:976601-976863(+)$1	262	137	143	15.3469
::::bb	chr1:171514623-171514886(+)$1	263	135	141	12.5918
4hhhhh	chr5:176885101-176885350(-)$1	249	78	84	11.6734

#DB
......	chr5:180661378-180661649(+)$1	1	76	82	11.6734
((((((	chr12:67691115-67691381(+)$1	1	16	22	15.3469
(((...	chr11:71164322-71164527(+)$1	1	14	20	15.3469
(((.((	chr1:161721578-161721830(+)$1	1	112	118	12.5918
((((((	chr18:12366896-12367144(-)$1	1	23	29	13.4081
((((((	chr5:427852-428118(+)$1	1	20	26	15.3469
((.(((	chr1:161130551-161130847(+)$1	1	43	49	15.3469
((.(((	chr10:70765522-70765757(+)$1	1	69	75	11.6734
)(((((	chr3:49154783-49155026(-)$1	1	18	24	13.4081
..))).	chr17:8108473-8108712(-)$1	1	216	222	15.3469
))))))	chr7:766297-766587(+)$1	1	236	242	15.3469
)..)))	chr19:59067973-59068199(-)$1	1	37	43	15.3469
..((((	chr14:24900643-24900888(+)$1	1	168	174	15.3469
))).((	chr9:139934353-139934599(-)$1	1	75	81	13.4081
)))))(	chr1:36208657-36208897(-)$1	1	211	217	15.3469
))))))	chr7:100280149-100280383(-)$1	1	51	57	11.1632
))))))	chr20:35812482-35812717(+)$1	1	138	144	11.6734
..((((	chr14:23532596-23532871(-)$1	1	101	107	15.3469
))))).	chr16:450180-450421(+)$1	1	51	57	11.6734
))).))	chr6:52129341-52129572(-)$1	1	113	119	12.7959
....((	chr19:33698310-33698542(+)$1	1	25	31	13.4081
))))))	chr9:140500090-140500381(+)$1	1	243	249	15.3469
).))))	chr22:50942947-50943238(-)$1	1	246	252	15.3469
)))(((	chr9:97535314-97535550(+)$1	1	22	28	15.3469
..))))	chr16:30536074-30536322(-)$1	1	217	223	15.3469
)...))	chr19:55777167-55777420(-)$1	1	65	71	13.4081
(((.((	chr19:39905661-39905915(+)$1	1	83	89	12.7959
....))	chr1:151137621-151137861(-)$1	1	153	159	15.3469
(...))	chr19:14523767-14524018(-)$1	1	41	47	13.4081
))...)	chr14:24780499-24780784(+)$1	1	167	173	15.3469
..(((.	chr1:19653651-19653890(+)$1	1	85	91	13.4081
((((.(	chr11:65546512-65546743(-)$1	1	74	80	11.6734
...(((	chr8:53570265-53570509(-)$1	1	36	42	12.7959
.(((((	chr5:176929976-176930221(-)$1	1	0	6	12.7959
((..((	chr12:7049942-7050167(+)$1	1	16	22	13.4081
)))...	chr19:34890080-34890340(+)$1	1	107	113	12.7959
(.((((	chr6:29571233-29571544(-)$1	1	153	159	13.4081
))).))	chr19:4318249-4318536(+)$1	1	248	254	15.3469
))))))	chr19:33072076-33072333(+)$1	1	175	181	15.3469
.)).((	chr20:3765888-3766158(-)$1	1	40	46	15.3469
..))))	chr9:35092098-35092351(-)$1	1	175	181	15.3469
((((((	chr16:29997926-29998165(+)$1	1	2	8	15.3469
..((((	chr9:135973959-135974216(-)$1	1	25	31	13.4081
(((..(	chr19:1271278-1271530(+)$1	1	77	83	12.5918
(..(((	chr17:49238995-49239239(+)$1	1	88	94	13.4081
((...(	chr1:155934747-155935008(-)$1	1	26	32	15.3469
((((.(	chr1:976601-976863(+)$1	1	137	143	15.3469
....((	chr1:171514623-171514886(+)$1	1	135	141	12.5918
.)))))	chr5:176885101-176885350(-)$1	1	78	84	11.6734

#PSSM
G : 0.57	C : 0.22	U : 0.08	A : 0.06	g : 0.04	u : 0.02	
C : 0.93	c : 0.06	
C : 0.93	c : 0.06	
A : 0.93	a : 0.06	
G : 0.93	g : 0.06	
G : 0.79	C : 0.12	g : 0.06	A : 0.02	

#score	683.4285714285721
#seq	49
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m3_run1.nuc.txt

#NT
CCUGG	chr1:2325401-2325623(+)$1	222	127	132	15.0000
CCUGG	chr22:39214600-39214828(-)$1	228	92	97	15.0000
CCUGG	chr12:49160953-49161179(-)$1	226	220	225	15.0000
CCUGG	chrX:153609317-153609549(+)$1	232	2	7	15.0000
CCUGG	chr7:150750930-150751151(+)$1	221	141	146	15.0000
CCUGG	chr16:70605811-70606044(+)$1	233	58	63	15.0000
CCUGG	chr5:141233335-141233590(-)$1	255	82	87	15.0000
CCUGG	chr8:143695713-143695928(+)$1	215	134	139	15.0000
CCUGG	chr9:87489182-87489399(+)$1	217	106	111	15.0000
CCUGG	chr4:1810342-1810561(+)$1	219	13	18	15.0000
CCUGG	chr4:56297532-56297758(+)$1	226	181	186	15.0000
CCUGG	chr19:47507570-47507787(+)$1	217	77	82	15.0000
CCUGG	chr5:141392108-141392327(+)$1	219	69	74	15.0000
CCUGG	chr17:73201719-73201937(+)$1	218	121	126	15.0000
CCUGG	chr2:74689818-74690035(-)$1	217	199	204	15.0000
CCUGG	chr1:181058930-181059151(-)$1	221	68	73	15.0000
CCUGG	chr22:39778751-39778970(+)$1	219	17	22	15.0000
CCUGG	chr1:155168412-155168630(-)$1	218	114	119	15.0000
CCUGG	chr16:18437987-18438207(-)$1	220	165	170	15.0000
CCUGG	chr15:58000920-58001143(+)$1	223	214	219	15.0000
CCUGG	chr5:95726329-95726553(-)$1	224	17	22	15.0000
CCUGG	chr1:11849852-11850070(-)$1	218	37	42	15.0000
CCUGG	chr20:62271900-62272117(-)$1	217	8	13	15.0000
CCUGG	chr14:56147301-56147518(+)$1	217	41	46	15.0000
CCUGG	chr8:30241949-30242175(+)$1	226	115	120	15.0000
CCUGG	chr10:99627164-99627396(+)$1	232	137	142	15.0000
CCUGG	chrX:106893595-106893817(+)$1	222	101	106	15.0000
CCUGG	chr17:39959063-39959301(-)$1	238	8	13	15.0000
CCUGG	chr17:4579984-4580205(-)$1	221	1	6	15.0000
CCUGG	chr1:1189752-1189981(-)$1	229	7	12	15.0000
CCUGG	chr22:39529430-39529664(-)$1	234	136	141	15.0000
CCUGG	chr7:75511269-75511489(+)$1	220	163	168	15.0000
CCUGG	chr17:44054527-44054759(+)$1	232	20	25	15.0000
CCUGG	chr3:141944261-141944476(+)$1	215	163	168	15.0000
CCUGG	chr16:85122596-85122818(+)$1	222	100	105	15.0000
CCUGG	chr17:29863605-29863825(+)$1	220	109	114	15.0000
CCUGG	chr6:163836122-163836340(+)$1	218	95	100	15.0000
CCUGG	chr14:23527847-23528068(+)$1	221	90	95	15.0000
CCUGG	chr8:21549560-21549779(-)$1	219	173	178	15.0000
CCUGG	chr19:1812091-1812306(+)$1	215	23	28	15.0000
CCUGG	chr22:21352744-21352959(-)$1	215	188	193	15.0000
CCUGG	chr1:33360263-33360496(-)$1	233	166	171	15.0000

#otherMatches

#Struct PSSM
peeee	chr16:29465821-29466040(+)$1	219	183	188	15.0000
fffff	chr1:2325401-2325623(+)$1	222	127	132	15.0000
xxxgg	chr22:39214600-39214828(-)$1	228	92	97	15.0000
ECCC:	chr12:49160953-49161179(-)$1	226	220	225	15.0000
:::DD	chrX:153609317-153609549(+)$1	232	2	7	15.0000
eeeeE	chr7:150750930-150751151(+)$1	221	141	146	15.0000
ooocc	chr16:70605811-70606044(+)$1	233	58	63	15.0000
:FFFF	chr5:141233335-141233590(-)$1	255	82	87	15.0000
eee]=	chr8:143695713-143695928(+)$1	215	134	139	15.0000
[a[cc	chr9:87489182-87489399(+)$1	217	106	111	15.0000
CC{BB	chr4:1810342-1810561(+)$1	219	13	18	15.0000
33ccc	chr4:56297532-56297758(+)$1	226	181	186	15.0000
CC:gg	chr19:47507570-47507787(+)$1	217	77	82	15.0000
====F	chr5:141392108-141392327(+)$1	219	69	74	15.0000
ccqqq	chr17:73201719-73201937(+)$1	218	121	126	15.0000
DDCCC	chr2:74689818-74690035(-)$1	217	199	204	15.0000
ellle	chr1:181058930-181059151(-)$1	221	68	73	15.0000
:DDDD	chr22:39778751-39778970(+)$1	219	17	22	15.0000
fffff	chr1:155168412-155168630(-)$1	218	114	119	15.0000
GGGG:	chr16:18437987-18438207(-)$1	220	165	170	15.0000
ldddd	chr15:58000920-58001143(+)$1	223	214	219	15.0000
llddd	chr5:95726329-95726553(-)$1	224	17	22	15.0000
qqqbb	chr1:11849852-11850070(-)$1	218	37	42	15.0000
EEEEE	chr20:62271900-62272117(-)$1	217	8	13	15.0000
eeee$	chr14:56147301-56147518(+)$1	217	41	46	15.0000
ccchh	chr8:30241949-30242175(+)$1	226	115	120	15.0000
a]ccc	chr10:99627164-99627396(+)$1	232	137	142	15.0000
b]ddd	chrX:106893595-106893817(+)$1	222	101	106	15.0000
HHHHH	chr17:39959063-39959301(-)$1	238	8	13	15.0000
:IIII	chr17:4579984-4580205(-)$1	221	1	6	15.0000
eeeee	chr1:1189752-1189981(-)$1	229	7	12	15.0000
ffnnn	chr22:39529430-39529664(-)$1	234	136	141	15.0000
22eee	chr7:75511269-75511489(+)$1	220	163	168	15.0000
{EEEE	chr17:44054527-44054759(+)$1	232	20	25	15.0000
G}BBd	chr3:141944261-141944476(+)$1	215	163	168	15.0000
eeedd	chr16:85122596-85122818(+)$1	222	100	105	15.0000
!!ccc	chr17:29863605-29863825(+)$1	220	109	114	15.0000
cc:bb	chr6:163836122-163836340(+)$1	218	95	100	15.0000
feeee	chr14:23527847-23528068(+)$1	221	90	95	15.0000
tttcc	chr8:21549560-21549779(-)$1	219	173	178	15.0000
Bffff	chr19:1812091-1812306(+)$1	215	23	28	15.0000
JJJJJ	chr22:21352744-21352959(-)$1	215	188	193	15.0000
ttttt	chr1:33360263-33360496(-)$1	233	166	171	15.0000

#DB
.))))	chr16:29465821-29466040(+)$1	1	183	188	15.0000
(((((	chr1:2325401-2325623(+)$1	1	127	132	15.0000
...))	chr22:39214600-39214828(-)$1	1	92	97	15.0000
)))).	chr12:49160953-49161179(-)$1	1	220	225	15.0000
...((	chrX:153609317-153609549(+)$1	1	2	7	15.0000
)))))	chr7:150750930-150751151(+)$1	1	141	146	15.0000
...))	chr16:70605811-70606044(+)$1	1	58	63	15.0000
.))))	chr5:141233335-141233590(-)$1	1	82	87	15.0000
))).)	chr8:143695713-143695928(+)$1	1	134	139	15.0000
.(.((	chr9:87489182-87489399(+)$1	1	106	111	15.0000
((.((	chr4:1810342-1810561(+)$1	1	13	18	15.0000
..)))	chr4:56297532-56297758(+)$1	1	181	186	15.0000
)).((	chr19:47507570-47507787(+)$1	1	77	82	15.0000
))))(	chr5:141392108-141392327(+)$1	1	69	74	15.0000
((...	chr17:73201719-73201937(+)$1	1	121	126	15.0000
)))))	chr2:74689818-74690035(-)$1	1	199	204	15.0000
(...)	chr1:181058930-181059151(-)$1	1	68	73	15.0000
.((((	chr22:39778751-39778970(+)$1	1	17	22	15.0000
(((((	chr1:155168412-155168630(-)$1	1	114	119	15.0000
)))).	chr16:18437987-18438207(-)$1	1	165	170	15.0000
.))))	chr15:58000920-58001143(+)$1	1	214	219	15.0000
..)))	chr5:95726329-95726553(-)$1	1	17	22	15.0000
...))	chr1:11849852-11850070(-)$1	1	37	42	15.0000
(((((	chr20:62271900-62272117(-)$1	1	8	13	15.0000
((((.	chr14:56147301-56147518(+)$1	1	41	46	15.0000
)))((	chr8:30241949-30242175(+)$1	1	115	120	15.0000
).)))	chr10:99627164-99627396(+)$1	1	137	142	15.0000
).)))	chrX:106893595-106893817(+)$1	1	101	106	15.0000
(((((	chr17:39959063-39959301(-)$1	1	8	13	15.0000
.((((	chr17:4579984-4580205(-)$1	1	1	6	15.0000
(((((	chr1:1189752-1189981(-)$1	1	7	12	15.0000
((...	chr22:39529430-39529664(-)$1	1	136	141	15.0000
..)))	chr7:75511269-75511489(+)$1	1	163	168	15.0000
.((((	chr17:44054527-44054759(+)$1	1	20	25	15.0000
).))(	chr3:141944261-141944476(+)$1	1	163	168	15.0000
)))))	chr16:85122596-85122818(+)$1	1	100	105	15.0000
..(((	chr17:29863605-29863825(+)$1	1	109	114	15.0000
)).((	chr6:163836122-163836340(+)$1	1	95	100	15.0000
(((((	chr14:23527847-23528068(+)$1	1	90	95	15.0000
...))	chr8:21549560-21549779(-)$1	1	173	178	15.0000
(((((	chr19:1812091-1812306(+)$1	1	23	28	15.0000
)))))	chr22:21352744-21352959(-)$1	1	188	193	15.0000
.....	chr1:33360263-33360496(-)$1	1	166	171	15.0000

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

#score	645.0000000000001
#seq	43
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_UTR_m2_run2.nuc.txt

#NT
UUUG	chr2:114472373-114472667(-)$1	294	52	56	11.9999
UUUg	chr1:204525013-204525275(+)$1	262	166	170	11.9999
uuug	chr12:53869716-53870066(+)$1	350	334	338	11.9999
uuug	chr14:75526490-75526808(-)$1	318	233	237	11.9999
UUUG	chr1:93619352-93619598(-)$1	246	73	77	11.9999
UUUG	chr4:71895204-71895487(+)$1	283	2	6	11.9999
UUUG	chr1:52376933-52377193(-)$1	260	51	55	11.9999
UUUG	chr15:44818973-44819198(+)$1	225	191	195	11.9999
uuug	chr11:125526593-125526835(+)$1	242	33	37	11.9999
UUUG	chr2:204293206-204293519(+)$1	313	258	262	11.9999
UUUG	chr20:24988087-24988355(-)$1	268	201	205	11.9999
UUUG	chr1:113072419-113072699(-)$1	280	15	19	11.9999
UUUG	chr2:48604943-48605266(+)$1	323	63	67	11.9999
UUUG	chr1:52373994-52374237(-)$1	243	113	117	11.9999
UUUG	chr15:59149002-59149310(+)$1	308	96	100	11.9999
UUUG	chr1:109943244-109943466(-)$1	222	23	27	11.9999
UUUG	chr19:6480015-6480456(-)$1	441	413	417	11.9999
UUUG	chrX:12994827-12995093(+)$1	266	180	184	11.9999
UUUG	chr10:104497552-104497867(+)$1	315	51	55	11.9999
UUUG	chr5:50139049-50139312(+)$1	263	63	67	11.9999
UUUG	chr4:139092153-139092418(-)$1	265	52	56	11.9999
UUUG	chr15:38782402-38782667(-)$1	265	133	137	11.9999
uuug	chr1:118408515-118408811(-)$1	296	46	50	11.9999
UUUG	chr11:61134898-61135142(+)$1	244	107	111	11.9999
UUUG	chr1:71530388-71530653(-)$1	265	46	50	11.9999
UUUG	chr2:233632518-233632754(+)$1	236	12	16	11.9999
UUUG	chr12:53805612-53805841(+)$1	229	77	81	11.9999
UUUG	chr2:171849712-171849974(-)$1	262	27	31	11.9999
uuug	chr7:150067708-150067969(+)$1	261	105	109	11.9999
UUUG	chr12:69665136-69665402(+)$1	266	80	84	11.9999
UUUG	chr15:25219005-25219270(+)$1	265	186	190	11.9999
UUUG	chr8:81432865-81433105(+)$1	240	14	18	11.9999
uuug	chr18:32913498-32913763(-)$1	265	5	9	11.9999
UUUG	chr1:52552840-52553108(+)$1	268	80	84	11.9999
UUUG	chr7:44618818-44619077(-)$1	259	7	11	11.9999
UUUG	chr9:88952068-88952327(-)$1	259	9	13	11.9999
UUUG	chr7:35939879-35940158(+)$1	279	219	223	11.9999
UUUG	chr20:18467403-18467648(-)$1	245	3	7	11.9999
UUUG	chr2:208466168-208466427(+)$1	259	185	189	11.9999
uuug	chr18:14100999-14101254(-)$1	255	192	196	11.9999
UUUG	chr6:64292696-64292939(+)$1	243	233	237	11.9999
UUUG	chr15:38781918-38782176(-)$1	258	188	192	11.9999
UUUG	chr12:112374481-112374734(-)$1	253	212	216	11.9999
UUUG	chr4:183811817-183812060(-)$1	243	15	19	11.9999
UUUG	chrX:71687278-71687527(-)$1	249	31	35	11.9999
UUUG	chr2:7181000-7181251(+)$1	251	149	153	11.9999
UUUG	chr4:7761511-7761755(-)$1	244	34	38	11.9999
UUUG	chr3:146233058-146233296(-)$1	238	147	151	11.9999
UUUG	chr11:17110023-17110271(-)$1	248	25	29	11.9999
uuug	chrX:41588230-41588485(-)$1	255	16	20	11.9999
UUUG	chr6:28123083-28123553(+)$1	470	135	139	11.9999
UUUG	chr17:57060016-57060262(+)$1	246	28	32	11.9999
UUUG	chr1:100614715-100614967(+)$1	252	11	15	11.9999
UUUG	chr14:95555370-95555602(-)$1	232	41	45	11.9999
UUUG	chr7:23350302-23350536(-)$1	234	49	53	11.9999
UUUG	chr10:76937784-76938009(+)$1	225	89	93	11.9999
UUUG	chr4:25123076-25123312(-)$1	236	27	31	11.9999
UUUG	chr1:45468639-45468875(-)$1	236	37	41	11.9999
UUUG	chr2:206860896-206861232(-)$1	336	46	50	11.9999
UUUG	chrX:135742214-135742458(+)$1	244	0	4	11.9999
UUUG	chr18:51681108-51681408(-)$1	300	26	30	11.9999
UUUG	chrX:71799648-71799906(-)$1	258	24	28	11.9999
UUUG	chr17:27072253-27072505(+)$1	252	39	43	11.9999
UUUG	chr9:127708511-127708747(-)$1	236	3	7	11.9999
UUUG	chr11:6504584-6505032(+)$1	448	13	17	11.9999
UUUG	chr7:45762248-45762555(+)$1	307	43	47	11.9999
UUUG	chr6:38644141-38644371(-)$1	230	150	154	11.9999
UUUG	chr4:76405143-76405406(-)$1	263	74	78	11.9999
UUUG	chr1:155154764-155155091(+)$1	327	48	52	11.9999
uuug	chr8:102212994-102213245(-)$1	251	44	48	11.9999
UUUG	chr11:59405420-59405666(-)$1	246	68	72	11.9999
UUUG	chr9:33043966-33044213(-)$1	247	126	130	11.9999
UUUG	chr18:48701599-48701886(-)$1	287	26	30	11.9999
UUUG	chr2:202036451-202036706(+)$1	255	128	132	11.9999
uuug	chr15:45901415-45901691(+)$1	276	20	24	11.9999
UUUG	chr11:65485157-65485431(-)$1	274	83	87	11.9999
UUUG	chr17:30662310-30662563(-)$1	253	147	151	11.9999
UUUG	chr20:418135-418372(-)$1	237	44	48	11.9999
UUUG	chr1:53514717-53514971(+)$1	254	12	16	11.9999
UUUG	chr1:243667890-243668157(-)$1	267	171	175	11.9999
UUUG	chr6:138657883-138658131(+)$1	248	26	30	11.9999
UUUG	chr5:112929930-112930193(+)$1	263	69	73	11.9999
UUUG	chr6:131201879-131202115(-)$1	236	72	76	11.9999

#otherMatches

#Struct PSSM
oooo	chr9:91090474-91090799(+)$1	325	67	71	11.9999
lldd	chr2:114472373-114472667(-)$1	294	52	56	11.9999
:::i	chr1:204525013-204525275(+)$1	262	166	170	11.9999
JJJJ	chr12:53869716-53870066(+)$1	350	334	338	11.9999
xxxx	chr14:75526490-75526808(-)$1	318	233	237	11.9999
qqqq	chr1:93619352-93619598(-)$1	246	73	77	11.9999
::::	chr4:71895204-71895487(+)$1	283	2	6	11.9999
HHHH	chr1:52376933-52377193(-)$1	260	51	55	11.9999
>>>>	chr15:44818973-44819198(+)$1	225	191	195	11.9999
ssss	chr11:125526593-125526835(+)$1	242	33	37	11.9999
eee]	chr2:204293206-204293519(+)$1	313	258	262	11.9999
qqcc	chr20:24988087-24988355(-)$1	268	201	205	11.9999
iiii	chr1:113072419-113072699(-)$1	280	15	19	11.9999
{CCC	chr2:48604943-48605266(+)$1	323	63	67	11.9999
llff	chr1:52373994-52374237(-)$1	243	113	117	11.9999
c]dd	chr15:59149002-59149310(+)$1	308	96	100	11.9999
mccc	chr1:109943244-109943466(-)$1	222	23	27	11.9999
G}FF	chr19:6480015-6480456(-)$1	441	413	417	11.9999
]ddd	chrX:12994827-12995093(+)$1	266	180	184	11.9999
ffff	chr10:104497552-104497867(+)$1	315	51	55	11.9999
eeoo	chr5:50139049-50139312(+)$1	263	63	67	11.9999
GGGG	chr4:139092153-139092418(-)$1	265	52	56	11.9999
gggg	chr15:38782402-38782667(-)$1	265	133	137	11.9999
====	chr1:118408515-118408811(-)$1	296	46	50	11.9999
gggq	chr11:61134898-61135142(+)$1	244	107	111	11.9999
###g	chr1:71530388-71530653(-)$1	265	46	50	11.9999
gggg	chr2:233632518-233632754(+)$1	236	12	16	11.9999
::::	chr12:53805612-53805841(+)$1	229	77	81	11.9999
{CCC	chr2:171849712-171849974(-)$1	262	27	31	11.9999
mmee	chr7:150067708-150067969(+)$1	261	105	109	11.9999
eeee	chr12:69665136-69665402(+)$1	266	80	84	11.9999
mmcc	chr15:25219005-25219270(+)$1	265	186	190	11.9999
rrrr	chr8:81432865-81433105(+)$1	240	14	18	11.9999
KA{D	chr18:32913498-32913763(-)$1	265	5	9	11.9999
HHHH	chr1:52552840-52553108(+)$1	268	80	84	11.9999
::::	chr7:44618818-44619077(-)$1	259	7	11	11.9999
dddd	chr9:88952068-88952327(-)$1	259	9	13	11.9999
EEEE	chr7:35939879-35940158(+)$1	279	219	223	11.9999
::::	chr20:18467403-18467648(-)$1	245	3	7	11.9999
__BB	chr2:208466168-208466427(+)$1	259	185	189	11.9999
::::	chr18:14100999-14101254(-)$1	255	192	196	11.9999
====	chr6:64292696-64292939(+)$1	243	233	237	11.9999
hhhh	chr15:38781918-38782176(-)$1	258	188	192	11.9999
cqqq	chr12:112374481-112374734(-)$1	253	212	216	11.9999
ssff	chr4:183811817-183812060(-)$1	243	15	19	11.9999
eeee	chrX:71687278-71687527(-)$1	249	31	35	11.9999
occc	chr2:7181000-7181251(+)$1	251	149	153	11.9999
mmmb	chr4:7761511-7761755(-)$1	244	34	38	11.9999
::cc	chr3:146233058-146233296(-)$1	238	147	151	11.9999
mmmh	chr11:17110023-17110271(-)$1	248	25	29	11.9999
yyyy	chrX:41588230-41588485(-)$1	255	16	20	11.9999
mfff	chr6:28123083-28123553(+)$1	470	135	139	11.9999
iiii	chr17:57060016-57060262(+)$1	246	28	32	11.9999
ffff	chr1:100614715-100614967(+)$1	252	11	15	11.9999
mmff	chr14:95555370-95555602(-)$1	232	41	45	11.9999
JJ{B	chr7:23350302-23350536(-)$1	234	49	53	11.9999
drrr	chr10:76937784-76938009(+)$1	225	89	93	11.9999
leee	chr4:25123076-25123312(-)$1	236	27	31	11.9999
pppp	chr1:45468639-45468875(-)$1	236	37	41	11.9999
iiii	chr2:206860896-206861232(-)$1	336	46	50	11.9999
::::	chrX:135742214-135742458(+)$1	244	0	4	11.9999
^^gg	chr18:51681108-51681408(-)$1	300	26	30	11.9999
:::D	chrX:71799648-71799906(-)$1	258	24	28	11.9999
NNNN	chr17:27072253-27072505(+)$1	252	39	43	11.9999
:eee	chr9:127708511-127708747(-)$1	236	3	7	11.9999
::ee	chr11:6504584-6505032(+)$1	448	13	17	11.9999
ddd[	chr7:45762248-45762555(+)$1	307	43	47	11.9999
ccc[	chr6:38644141-38644371(-)$1	230	150	154	11.9999
7777	chr4:76405143-76405406(-)$1	263	74	78	11.9999
:::f	chr1:155154764-155155091(+)$1	327	48	52	11.9999
::::	chr8:102212994-102213245(-)$1	251	44	48	11.9999
:hhh	chr11:59405420-59405666(-)$1	246	68	72	11.9999
mmme	chr9:33043966-33044213(-)$1	247	126	130	11.9999
NNDD	chr18:48701599-48701886(-)$1	287	26	30	11.9999
:::c	chr2:202036451-202036706(+)$1	255	128	132	11.9999
ddd2	chr15:45901415-45901691(+)$1	276	20	24	11.9999
g>>>	chr11:65485157-65485431(-)$1	274	83	87	11.9999
b"""	chr17:30662310-30662563(-)$1	253	147	151	11.9999
ffff	chr20:418135-418372(-)$1	237	44	48	11.9999
eddd	chr1:53514717-53514971(+)$1	254	12	16	11.9999
FFFF	chr1:243667890-243668157(-)$1	267	171	175	11.9999
DEEE	chr6:138657883-138658131(+)$1	248	26	30	11.9999
UUUU	chr5:112929930-112930193(+)$1	263	69	73	11.9999
hhhh	chr6:131201879-131202115(-)$1	236	72	76	11.9999

#DB
....	chr9:91090474-91090799(+)$1	1	67	71	11.9999
..))	chr2:114472373-114472667(-)$1	1	52	56	11.9999
...(	chr1:204525013-204525275(+)$1	1	166	170	11.9999
))))	chr12:53869716-53870066(+)$1	1	334	338	11.9999
....	chr14:75526490-75526808(-)$1	1	233	237	11.9999
....	chr1:93619352-93619598(-)$1	1	73	77	11.9999
....	chr4:71895204-71895487(+)$1	1	2	6	11.9999
((((	chr1:52376933-52377193(-)$1	1	51	55	11.9999
....	chr15:44818973-44819198(+)$1	1	191	195	11.9999
....	chr11:125526593-125526835(+)$1	1	33	37	11.9999
))).	chr2:204293206-204293519(+)$1	1	258	262	11.9999
..))	chr20:24988087-24988355(-)$1	1	201	205	11.9999
((((	chr1:113072419-113072699(-)$1	1	15	19	11.9999
.(((	chr2:48604943-48605266(+)$1	1	63	67	11.9999
..))	chr1:52373994-52374237(-)$1	1	113	117	11.9999
).))	chr15:59149002-59149310(+)$1	1	96	100	11.9999
.)))	chr1:109943244-109943466(-)$1	1	23	27	11.9999
).))	chr19:6480015-6480456(-)$1	1	413	417	11.9999
.)))	chrX:12994827-12995093(+)$1	1	180	184	11.9999
((((	chr10:104497552-104497867(+)$1	1	51	55	11.9999
((..	chr5:50139049-50139312(+)$1	1	63	67	11.9999
((((	chr4:139092153-139092418(-)$1	1	52	56	11.9999
((((	chr15:38782402-38782667(-)$1	1	133	137	11.9999
((((	chr1:118408515-118408811(-)$1	1	46	50	11.9999
(((.	chr11:61134898-61135142(+)$1	1	107	111	11.9999
...(	chr1:71530388-71530653(-)$1	1	46	50	11.9999
((((	chr2:233632518-233632754(+)$1	1	12	16	11.9999
....	chr12:53805612-53805841(+)$1	1	77	81	11.9999
.(((	chr2:171849712-171849974(-)$1	1	27	31	11.9999
..))	chr7:150067708-150067969(+)$1	1	105	109	11.9999
((((	chr12:69665136-69665402(+)$1	1	80	84	11.9999
..))	chr15:25219005-25219270(+)$1	1	186	190	11.9999
....	chr8:81432865-81433105(+)$1	1	14	18	11.9999
.(.(	chr18:32913498-32913763(-)$1	1	5	9	11.9999
((((	chr1:52552840-52553108(+)$1	1	80	84	11.9999
....	chr7:44618818-44619077(-)$1	1	7	11	11.9999
((((	chr9:88952068-88952327(-)$1	1	9	13	11.9999
))))	chr7:35939879-35940158(+)$1	1	219	223	11.9999
....	chr20:18467403-18467648(-)$1	1	3	7	11.9999
..))	chr2:208466168-208466427(+)$1	1	185	189	11.9999
....	chr18:14100999-14101254(-)$1	1	192	196	11.9999
))))	chr6:64292696-64292939(+)$1	1	233	237	11.9999
))))	chr15:38781918-38782176(-)$1	1	188	192	11.9999
(...	chr12:112374481-112374734(-)$1	1	212	216	11.9999
..))	chr4:183811817-183812060(-)$1	1	15	19	11.9999
((((	chrX:71687278-71687527(-)$1	1	31	35	11.9999
.)))	chr2:7181000-7181251(+)$1	1	149	153	11.9999
...)	chr4:7761511-7761755(-)$1	1	34	38	11.9999
..((	chr3:146233058-146233296(-)$1	1	147	151	11.9999
...)	chr11:17110023-17110271(-)$1	1	25	29	11.9999
....	chrX:41588230-41588485(-)$1	1	16	20	11.9999
.)))	chr6:28123083-28123553(+)$1	1	135	139	11.9999
))))	chr17:57060016-57060262(+)$1	1	28	32	11.9999
((((	chr1:100614715-100614967(+)$1	1	11	15	11.9999
..))	chr14:95555370-95555602(-)$1	1	41	45	11.9999
((.(	chr7:23350302-23350536(-)$1	1	49	53	11.9999
(...	chr10:76937784-76938009(+)$1	1	89	93	11.9999
.)))	chr4:25123076-25123312(-)$1	1	27	31	11.9999
....	chr1:45468639-45468875(-)$1	1	37	41	11.9999
))))	chr2:206860896-206861232(-)$1	1	46	50	11.9999
....	chrX:135742214-135742458(+)$1	1	0	4	11.9999
..))	chr18:51681108-51681408(-)$1	1	26	30	11.9999
...(	chrX:71799648-71799906(-)$1	1	24	28	11.9999
....	chr17:27072253-27072505(+)$1	1	39	43	11.9999
.(((	chr9:127708511-127708747(-)$1	1	3	7	11.9999
..((	chr11:6504584-6505032(+)$1	1	13	17	11.9999
(((.	chr7:45762248-45762555(+)$1	1	43	47	11.9999
(((.	chr6:38644141-38644371(-)$1	1	150	154	11.9999
....	chr4:76405143-76405406(-)$1	1	74	78	11.9999
...(	chr1:155154764-155155091(+)$1	1	48	52	11.9999
....	chr8:102212994-102213245(-)$1	1	44	48	11.9999
.(((	chr11:59405420-59405666(-)$1	1	68	72	11.9999
...)	chr9:33043966-33044213(-)$1	1	126	130	11.9999
..((	chr18:48701599-48701886(-)$1	1	26	30	11.9999
...(	chr2:202036451-202036706(+)$1	1	128	132	11.9999
))).	chr15:45901415-45901691(+)$1	1	20	24	11.9999
)...	chr11:65485157-65485431(-)$1	1	83	87	11.9999
(...	chr17:30662310-30662563(-)$1	1	147	151	11.9999
((((	chr20:418135-418372(-)$1	1	44	48	11.9999
((((	chr1:53514717-53514971(+)$1	1	12	16	11.9999
((((	chr1:243667890-243668157(-)$1	1	171	175	11.9999
((((	chr6:138657883-138658131(+)$1	1	26	30	11.9999
....	chr5:112929930-112930193(+)$1	1	69	73	11.9999
((((	chr6:131201879-131202115(-)$1	1	72	76	11.9999

#PSSM
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
U : 0.88	u : 0.11	
G : 0.86	g : 0.13	

#score	1007.9999999999998
#seq	84
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m3_run1.nuc.txt

#NT
UUU	chr1:154554431-154554733(-)$1	302	13	16	9.0000
UUU	chr1:2241382-2241661(+)$1	279	0	3	9.0000
UUU	chr2:9624471-9624758(+)$1	287	52	55	9.0000
UUU	chr15:35166022-35166299(-)$1	277	0	3	9.0000
UUU	chr7:30536350-30536598(-)$1	248	34	37	9.0000
UUU	chr1:89447656-89447901(-)$1	245	4	7	9.0000
UUU	chr12:74933108-74933375(+)$1	267	90	93	9.0000
UUU	chr6:138413015-138413349(-)$1	334	51	54	9.0000
UUU	chr7:13935188-13935445(-)$1	257	27	30	9.0000
UUU	chr1:26227223-26227508(-)$1	285	2	5	9.0000
UUU	chr13:28197270-28197522(+)$1	252	0	3	9.0000
UUU	chr16:56643246-56643505(+)$1	259	74	77	9.0000
UUU	chr17:80559112-80559333(-)$1	221	91	94	9.0000
UUU	chr11:33762747-33763013(-)$1	266	9	12	9.0000
UUU	chr5:172744091-172744340(-)$1	249	39	42	9.0000
UUU	chr5:77771786-77772035(+)$1	249	24	27	9.0000
UUU	chr12:4414203-4414475(+)$1	272	52	55	9.0000
UUU	chr19:39898692-39898979(+)$1	287	41	44	9.0000
UUU	chr3:15093843-15094112(-)$1	269	10	13	9.0000
UUU	chr5:179044441-179044690(-)$1	249	18	21	9.0000
UUU	chr13:28868757-28869040(+)$1	283	39	42	9.0000
UUU	chr12:51142262-51142541(+)$1	279	5	8	9.0000
UUU	chr1:109351684-109351923(+)$1	239	6	9	9.0000
UUU	chr4:124239547-124239799(+)$1	252	8	11	9.0000
UUU	chr12:122270401-122270651(+)$1	250	25	28	9.0000
UUU	chr14:89627974-89628233(-)$1	259	194	197	9.0000
UUU	chr10:74035236-74035533(+)$1	297	138	141	9.0000
UUU	chr4:146038413-146038641(+)$1	228	2	5	9.0000
UUU	chr14:35871032-35871285(-)$1	253	0	3	9.0000
UUU	chr2:204296728-204296980(+)$1	252	87	90	9.0000
UUU	chr1:118166857-118167122(+)$1	265	58	61	9.0000
UUU	chr12:93870646-93870889(+)$1	243	17	20	9.0000
UUU	chr10:133781769-133782023(-)$1	254	99	102	9.0000
UUU	chr11:129999888-130000132(+)$1	244	211	214	9.0000
UUU	chr17:28791821-28792060(+)$1	239	19	22	9.0000
UUU	chr11:10819152-10819405(-)$1	253	100	103	9.0000
UUU	chr12:120634562-120634806(-)$1	244	42	45	9.0000
UUU	chr5:179264115-179264357(+)$1	242	41	44	9.0000
UUU	chr6:150045362-150045638(-)$1	276	121	124	9.0000
UUU	chr2:71662038-71662282(+)$1	244	16	19	9.0000
UUU	chr19:3465112-3465404(+)$1	292	34	37	9.0000
UUU	chr4:140310067-140310347(+)$1	280	148	151	9.0000
UUU	chr5:138704412-138704651(+)$1	239	1	4	9.0000
UUU	chr12:112460657-112460896(+)$1	239	83	86	9.0000
UUU	chr20:33128613-33128866(+)$1	253	34	37	9.0000
UUU	chr11:93463574-93463842(-)$1	268	23	26	9.0000
UUU	chr3:141165922-141166195(+)$1	273	171	174	9.0000
UUU	chr2:230631825-230632086(-)$1	261	28	31	9.0000
UUU	chr7:151833207-151833466(-)$1	259	44	47	9.0000
UUU	chr4:10076696-10076953(-)$1	257	20	23	9.0000
UUU	chr16:4740812-4741057(+)$1	245	34	37	9.0000
uuu	chr10:111894016-111894257(+)$1	241	89	92	9.0000
UUU	chr4:166263844-166264106(+)$1	262	112	115	9.0000
UUU	chr14:102323071-102323297(+)$1	226	13	16	9.0000
UUU	chr3:186504810-186505110(+)$1	300	44	47	9.0000
UUU	chr16:89333984-89334255(-)$1	271	0	3	9.0000
UUU	chr17:46690032-46690256(+)$1	224	106	109	9.0000
UUU	chr4:68079-68337(+)$1	258	136	139	9.0000
UUU	chr3:9519665-9519915(+)$1	250	128	131	9.0000
UUU	chr17:27586587-27586849(-)$1	262	21	24	9.0000
UUU	chr11:58386899-58387188(+)$1	289	6	9	9.0000
UUU	chr1:32799061-32799331(+)$1	270	3	6	9.0000
UUU	chr9:88642153-88642409(-)$1	256	1	4	9.0000
UUU	chr6:135357195-135357444(-)$1	249	22	25	9.0000
UUU	chr6:26158254-26158525(+)$1	271	51	54	9.0000
UUU	chr1:150547055-150547342(-)$1	287	42	45	9.0000
UUU	chr4:76568175-76568446(-)$1	271	84	87	9.0000
UUU	chr6:75963887-75964151(-)$1	264	4	7	9.0000
UUU	chr1:179044674-179044913(+)$1	239	18	21	9.0000
uuu	chr10:63956385-63956624(-)$1	239	52	55	9.0000
UUU	chr21:34949483-34949709(+)$1	226	19	22	9.0000
UUU	chr17:27589934-27590175(-)$1	241	98	101	9.0000
UUU	chr8:80915230-80915500(-)$1	270	7	10	9.0000
UUU	chr3:23960832-23961150(+)$1	318	171	174	9.0000
UUU	chr4:99850996-99851237(-)$1	241	166	169	9.0000
UUU	chr19:2232148-2232426(+)$1	278	119	122	9.0000
UUU	chr9:88933762-88934034(-)$1	272	0	3	9.0000
UUU	chr2:230663897-230664145(-)$1	248	31	34	9.0000
UUU	chr19:50484859-50485107(-)$1	248	136	139	9.0000
UUU	chr3:122168312-122168551(-)$1	239	3	6	9.0000
uuu	chr12:98994858-98995098(+)$1	240	7	10	9.0000
UUU	chr8:126450455-126450745(+)$1	290	147	150	9.0000
UUU	chrX:96854550-96854819(+)$1	269	10	13	9.0000
UUU	chr13:43462146-43462417(-)$1	271	266	269	9.0000
UUU	chr3:156423843-156424085(+)$1	242	18	21	9.0000
UUU	chr1:153932121-153932370(-)$1	249	201	204	9.0000
UUU	chr17:79477227-79477649(-)$1	422	110	113	9.0000
UUU	chr6:64286671-64286944(+)$1	273	6	9	9.0000

#otherMatches

#Struct PSSM
===	chr2:150426048-150426309(-)$1	261	256	259	9.0000
bb=	chr1:154554431-154554733(-)$1	302	13	16	9.0000
:::	chr1:2241382-2241661(+)$1	279	0	3	9.0000
nnn	chr2:9624471-9624758(+)$1	287	52	55	9.0000
:::	chr15:35166022-35166299(-)$1	277	0	3	9.0000
fff	chr7:30536350-30536598(-)$1	248	34	37	9.0000
iii	chr1:89447656-89447901(-)$1	245	4	7	9.0000
ddm	chr12:74933108-74933375(+)$1	267	90	93	9.0000
dee	chr6:138413015-138413349(-)$1	334	51	54	9.0000
JJJ	chr7:13935188-13935445(-)$1	257	27	30	9.0000
:::	chr1:26227223-26227508(-)$1	285	2	5	9.0000
:::	chr13:28197270-28197522(+)$1	252	0	3	9.0000
===	chr16:56643246-56643505(+)$1	259	74	77	9.0000
3cc	chr17:80559112-80559333(-)$1	221	91	94	9.0000
nee	chr11:33762747-33763013(-)$1	266	9	12	9.0000
ggg	chr5:172744091-172744340(-)$1	249	39	42	9.0000
EEL	chr5:77771786-77772035(+)$1	249	24	27	9.0000
dJJ	chr12:4414203-4414475(+)$1	272	52	55	9.0000
===	chr19:39898692-39898979(+)$1	287	41	44	9.0000
KKD	chr3:15093843-15094112(-)$1	269	10	13	9.0000
xxx	chr5:179044441-179044690(-)$1	249	18	21	9.0000
GGG	chr13:28868757-28869040(+)$1	283	39	42	9.0000
eoo	chr12:51142262-51142541(+)$1	279	5	8	9.0000
EEE	chr1:109351684-109351923(+)$1	239	6	9	9.0000
DDD	chr4:124239547-124239799(+)$1	252	8	11	9.0000
CDD	chr12:122270401-122270651(+)$1	250	25	28	9.0000
%%%	chr14:89627974-89628233(-)$1	259	194	197	9.0000
ppp	chr10:74035236-74035533(+)$1	297	138	141	9.0000
:::	chr4:146038413-146038641(+)$1	228	2	5	9.0000
:::	chr14:35871032-35871285(-)$1	253	0	3	9.0000
:::	chr2:204296728-204296980(+)$1	252	87	90	9.0000
eee	chr1:118166857-118167122(+)$1	265	58	61	9.0000
eee	chr12:93870646-93870889(+)$1	243	17	20	9.0000
===	chr10:133781769-133782023(-)$1	254	99	102	9.0000
CCB	chr11:129999888-130000132(+)$1	244	211	214	9.0000
3ee	chr17:28791821-28792060(+)$1	239	19	22	9.0000
:::	chr11:10819152-10819405(-)$1	253	100	103	9.0000
fff	chr12:120634562-120634806(-)$1	244	42	45	9.0000
:::	chr5:179264115-179264357(+)$1	242	41	44	9.0000
:::	chr6:150045362-150045638(-)$1	276	121	124	9.0000
:::	chr2:71662038-71662282(+)$1	244	16	19	9.0000
EEE	chr19:3465112-3465404(+)$1	292	34	37	9.0000
2bb	chr4:140310067-140310347(+)$1	280	148	151	9.0000
:::	chr5:138704412-138704651(+)$1	239	1	4	9.0000
:::	chr12:112460657-112460896(+)$1	239	83	86	9.0000
KKE	chr20:33128613-33128866(+)$1	253	34	37	9.0000
eee	chr11:93463574-93463842(-)$1	268	23	26	9.0000
dd]	chr3:141165922-141166195(+)$1	273	171	174	9.0000
ggg	chr2:230631825-230632086(-)$1	261	28	31	9.0000
EEE	chr7:151833207-151833466(-)$1	259	44	47	9.0000
+++	chr4:10076696-10076953(-)$1	257	20	23	9.0000
eee	chr16:4740812-4741057(+)$1	245	34	37	9.0000
FFF	chr10:111894016-111894257(+)$1	241	89	92	9.0000
ecc	chr4:166263844-166264106(+)$1	262	112	115	9.0000
!bb	chr14:102323071-102323297(+)$1	226	13	16	9.0000
iii	chr3:186504810-186505110(+)$1	300	44	47	9.0000
:ee	chr16:89333984-89334255(-)$1	271	0	3	9.0000
qgg	chr17:46690032-46690256(+)$1	224	106	109	9.0000
===	chr4:68079-68337(+)$1	258	136	139	9.0000
ggg	chr3:9519665-9519915(+)$1	250	128	131	9.0000
c!!	chr17:27586587-27586849(-)$1	262	21	24	9.0000
:::	chr11:58386899-58387188(+)$1	289	6	9	9.0000
:::	chr1:32799061-32799331(+)$1	270	3	6	9.0000
GGG	chr9:88642153-88642409(-)$1	256	1	4	9.0000
===	chr6:135357195-135357444(-)$1	249	22	25	9.0000
eee	chr6:26158254-26158525(+)$1	271	51	54	9.0000
===	chr1:150547055-150547342(-)$1	287	42	45	9.0000
fff	chr4:76568175-76568446(-)$1	271	84	87	9.0000
:::	chr6:75963887-75964151(-)$1	264	4	7	9.0000
nnn	chr1:179044674-179044913(+)$1	239	18	21	9.0000
nee	chr10:63956385-63956624(-)$1	239	52	55	9.0000
nnn	chr21:34949483-34949709(+)$1	226	19	22	9.0000
"ee	chr17:27589934-27590175(-)$1	241	98	101	9.0000
cc[	chr8:80915230-80915500(-)$1	270	7	10	9.0000
fff	chr3:23960832-23961150(+)$1	318	171	174	9.0000
:ff	chr4:99850996-99851237(-)$1	241	166	169	9.0000
eee	chr19:2232148-2232426(+)$1	278	119	122	9.0000
:::	chr9:88933762-88934034(-)$1	272	0	3	9.0000
III	chr2:230663897-230664145(-)$1	248	31	34	9.0000
qff	chr19:50484859-50485107(-)$1	248	136	139	9.0000
EE:	chr3:122168312-122168551(-)$1	239	3	6	9.0000
JJJ	chr12:98994858-98995098(+)$1	240	7	10	9.0000
ggg	chr8:126450455-126450745(+)$1	290	147	150	9.0000
EEE	chrX:96854550-96854819(+)$1	269	10	13	9.0000
:::	chr13:43462146-43462417(-)$1	271	266	269	9.0000
ggg	chr3:156423843-156424085(+)$1	242	18	21	9.0000
HHH	chr1:153932121-153932370(-)$1	249	201	204	9.0000
g]b	chr17:79477227-79477649(-)$1	422	110	113	9.0000
:::	chr6:64286671-64286944(+)$1	273	6	9	9.0000

#DB
)))	chr2:150426048-150426309(-)$1	1	256	259	9.0000
(((	chr1:154554431-154554733(-)$1	1	13	16	9.0000
...	chr1:2241382-2241661(+)$1	1	0	3	9.0000
...	chr2:9624471-9624758(+)$1	1	52	55	9.0000
...	chr15:35166022-35166299(-)$1	1	0	3	9.0000
(((	chr7:30536350-30536598(-)$1	1	34	37	9.0000
(((	chr1:89447656-89447901(-)$1	1	4	7	9.0000
((.	chr12:74933108-74933375(+)$1	1	90	93	9.0000
)((	chr6:138413015-138413349(-)$1	1	51	54	9.0000
(((	chr7:13935188-13935445(-)$1	1	27	30	9.0000
...	chr1:26227223-26227508(-)$1	1	2	5	9.0000
...	chr13:28197270-28197522(+)$1	1	0	3	9.0000
)))	chr16:56643246-56643505(+)$1	1	74	77	9.0000
.))	chr17:80559112-80559333(-)$1	1	91	94	9.0000
.))	chr11:33762747-33763013(-)$1	1	9	12	9.0000
)))	chr5:172744091-172744340(-)$1	1	39	42	9.0000
((.	chr5:77771786-77772035(+)$1	1	24	27	9.0000
)((	chr12:4414203-4414475(+)$1	1	52	55	9.0000
(((	chr19:39898692-39898979(+)$1	1	41	44	9.0000
..(	chr3:15093843-15094112(-)$1	1	10	13	9.0000
...	chr5:179044441-179044690(-)$1	1	18	21	9.0000
(((	chr13:28868757-28869040(+)$1	1	39	42	9.0000
(..	chr12:51142262-51142541(+)$1	1	5	8	9.0000
(((	chr1:109351684-109351923(+)$1	1	6	9	9.0000
(((	chr4:124239547-124239799(+)$1	1	8	11	9.0000
(((	chr12:122270401-122270651(+)$1	1	25	28	9.0000
...	chr14:89627974-89628233(-)$1	1	194	197	9.0000
...	chr10:74035236-74035533(+)$1	1	138	141	9.0000
...	chr4:146038413-146038641(+)$1	1	2	5	9.0000
...	chr14:35871032-35871285(-)$1	1	0	3	9.0000
...	chr2:204296728-204296980(+)$1	1	87	90	9.0000
)))	chr1:118166857-118167122(+)$1	1	58	61	9.0000
(((	chr12:93870646-93870889(+)$1	1	17	20	9.0000
(((	chr10:133781769-133782023(-)$1	1	99	102	9.0000
)))	chr11:129999888-130000132(+)$1	1	211	214	9.0000
.))	chr17:28791821-28792060(+)$1	1	19	22	9.0000
...	chr11:10819152-10819405(-)$1	1	100	103	9.0000
)))	chr12:120634562-120634806(-)$1	1	42	45	9.0000
...	chr5:179264115-179264357(+)$1	1	41	44	9.0000
...	chr6:150045362-150045638(-)$1	1	121	124	9.0000
...	chr2:71662038-71662282(+)$1	1	16	19	9.0000
(((	chr19:3465112-3465404(+)$1	1	34	37	9.0000
.))	chr4:140310067-140310347(+)$1	1	148	151	9.0000
...	chr5:138704412-138704651(+)$1	1	1	4	9.0000
...	chr12:112460657-112460896(+)$1	1	83	86	9.0000
..(	chr20:33128613-33128866(+)$1	1	34	37	9.0000
(((	chr11:93463574-93463842(-)$1	1	23	26	9.0000
)).	chr3:141165922-141166195(+)$1	1	171	174	9.0000
(((	chr2:230631825-230632086(-)$1	1	28	31	9.0000
(((	chr7:151833207-151833466(-)$1	1	44	47	9.0000
...	chr4:10076696-10076953(-)$1	1	20	23	9.0000
(((	chr16:4740812-4741057(+)$1	1	34	37	9.0000
(((	chr10:111894016-111894257(+)$1	1	89	92	9.0000
(((	chr4:166263844-166264106(+)$1	1	112	115	9.0000
.((	chr14:102323071-102323297(+)$1	1	13	16	9.0000
(((	chr3:186504810-186505110(+)$1	1	44	47	9.0000
.((	chr16:89333984-89334255(-)$1	1	0	3	9.0000
.))	chr17:46690032-46690256(+)$1	1	106	109	9.0000
)))	chr4:68079-68337(+)$1	1	136	139	9.0000
(((	chr3:9519665-9519915(+)$1	1	128	131	9.0000
(..	chr17:27586587-27586849(-)$1	1	21	24	9.0000
...	chr11:58386899-58387188(+)$1	1	6	9	9.0000
...	chr1:32799061-32799331(+)$1	1	3	6	9.0000
(((	chr9:88642153-88642409(-)$1	1	1	4	9.0000
(((	chr6:135357195-135357444(-)$1	1	22	25	9.0000
(((	chr6:26158254-26158525(+)$1	1	51	54	9.0000
)))	chr1:150547055-150547342(-)$1	1	42	45	9.0000
)))	chr4:76568175-76568446(-)$1	1	84	87	9.0000
...	chr6:75963887-75964151(-)$1	1	4	7	9.0000
...	chr1:179044674-179044913(+)$1	1	18	21	9.0000
.))	chr10:63956385-63956624(-)$1	1	52	55	9.0000
...	chr21:34949483-34949709(+)$1	1	19	22	9.0000
.((	chr17:27589934-27590175(-)$1	1	98	101	9.0000
((.	chr8:80915230-80915500(-)$1	1	7	10	9.0000
(((	chr3:23960832-23961150(+)$1	1	171	174	9.0000
.((	chr4:99850996-99851237(-)$1	1	166	169	9.0000
)((	chr19:2232148-2232426(+)$1	1	119	122	9.0000
...	chr9:88933762-88934034(-)$1	1	0	3	9.0000
(((	chr2:230663897-230664145(-)$1	1	31	34	9.0000
.))	chr19:50484859-50485107(-)$1	1	136	139	9.0000
((.	chr3:122168312-122168551(-)$1	1	3	6	9.0000
(((	chr12:98994858-98995098(+)$1	1	7	10	9.0000
)))	chr8:126450455-126450745(+)$1	1	147	150	9.0000
(((	chrX:96854550-96854819(+)$1	1	10	13	9.0000
...	chr13:43462146-43462417(-)$1	1	266	269	9.0000
)))	chr3:156423843-156424085(+)$1	1	18	21	9.0000
)))	chr1:153932121-153932370(-)$1	1	201	204	9.0000
).)	chr17:79477227-79477649(-)$1	1	110	113	9.0000
...	chr6:64286671-64286944(+)$1	1	6	9	9.0000

#PSSM
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	
U : 0.96	u : 0.03	

#score	801.0000000000002
#seq	89
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m1_run1.nuc.txt

#NT
UUCU	chr1:24120090-24120333(+)$1	243	228	232	12.0000
UUCU	chr10:135176280-135176522(-)$1	242	64	68	12.0000
UUCU	chr17:7212891-7213182(+)$1	291	24	28	12.0000
UUCU	chr6:74228691-74228954(-)$1	263	91	95	12.0000
UUCU	chr10:6274753-6275006(+)$1	253	12	16	12.0000
UUCU	chr5:176636942-176637210(+)$1	268	160	164	12.0000
UUCU	chr16:21983175-21983438(+)$1	263	35	39	12.0000
UUCU	chr11:64693078-64693317(+)$1	239	218	222	12.0000
UUCU	chr8:128750786-128751031(+)$1	245	133	137	12.0000
UUCU	chr15:82821061-82821304(-)$1	243	3	7	12.0000
UUCU	chr3:180680719-180680987(+)$1	268	25	29	12.0000
UUCU	chr2:234750172-234750419(-)$1	247	31	35	12.0000
UUCU	chr11:9459492-9459733(-)$1	241	93	97	12.0000
UUCU	chr10:43280982-43281219(+)$1	237	211	215	12.0000
UUCU	chr12:56993650-56993904(-)$1	254	12	16	12.0000
UUCU	chr21:34668425-34668683(+)$1	258	91	95	12.0000
UUCU	chr19:17515098-17515339(-)$1	241	77	81	12.0000
UUCU	chr12:123031894-123032143(+)$1	249	140	144	12.0000
UUCU	chr20:52192367-52192634(-)$1	267	29	33	12.0000
UUCU	chr6:82925745-82926039(-)$1	294	8	12	12.0000
UUCU	chr14:35872328-35872583(-)$1	255	69	73	12.0000
UUCU	chr10:387093-387367(-)$1	274	122	126	12.0000
UUCU	chr2:54845147-54845393(+)$1	246	18	22	12.0000
UUCU	chr18:47015745-47015995(-)$1	250	53	57	12.0000
UUCU	chr2:224824245-224824515(+)$1	270	85	89	12.0000
UUCU	chr15:66795651-66795911(-)$1	260	36	40	12.0000
UUCU	chr6:13657300-13657561(-)$1	261	43	47	12.0000
UUCU	chr7:30661946-30662188(+)$1	242	190	194	12.0000
UUCU	chr20:49518488-49518737(-)$1	249	85	89	12.0000
UUCU	chr16:56423100-56423365(-)$1	265	1	5	12.0000
UUCU	chr18:32917201-32917475(-)$1	274	50	54	12.0000
UUCU	chr14:58895980-58896241(+)$1	261	42	46	12.0000
UUCU	chr17:80196525-80196797(+)$1	272	147	151	12.0000
UUCU	chr17:80195613-80195855(+)$1	242	2	6	12.0000
UUCU	chr19:3981255-3981510(-)$1	255	34	38	12.0000
UUCU	chr13:46725061-46725316(-)$1	255	78	82	12.0000
UUCU	chr11:46782168-46782412(-)$1	244	4	8	12.0000
UUCU	chr1:46032163-46032412(+)$1	249	61	65	12.0000
UUCU	chr16:48286103-48286353(+)$1	250	191	195	12.0000
UUCU	chr6:26045566-26045822(+)$1	256	6	10	12.0000
UUCU	chr6:29692729-29693015(+)$1	286	62	66	12.0000
UUCU	chr16:47545545-47545792(+)$1	247	24	28	12.0000
UUCU	chr1:159889355-159889608(-)$1	253	243	247	12.0000
UUCU	chr9:27562313-27562563(-)$1	250	39	43	12.0000
UUCU	chr1:8025287-8025588(+)$1	301	20	24	12.0000
UUCU	chr2:176043798-176044073(-)$1	275	82	86	12.0000
UUCU	chr17:37564958-37565208(-)$1	250	34	38	12.0000
UUCU	chr19:49469824-49470240(+)$1	416	4	8	12.0000
UUCU	chrX:64949351-64949601(+)$1	250	5	9	12.0000
UUCU	chr12:49522947-49523208(-)$1	261	18	22	12.0000
UUCU	chr1:153639951-153640218(-)$1	267	18	22	12.0000
UUCU	chr6:43013252-43013499(-)$1	247	61	65	12.0000
UUCU	chr1:35865013-35865252(+)$1	239	51	55	12.0000
UUCU	chr3:156869870-156870123(-)$1	253	177	181	12.0000
UUCU	chr6:17624770-17625033(-)$1	263	129	133	12.0000
UUCU	chr20:44526940-44527174(+)$1	234	116	120	12.0000
UUCU	chr17:35564576-35564817(-)$1	241	15	19	12.0000
UUCU	chr4:17590410-17590666(+)$1	256	18	22	12.0000
UUCU	chr6:29911041-29911303(+)$1	262	4	8	12.0000
UUCU	chr2:107040538-107040781(-)$1	243	168	172	12.0000
UUCU	chr12:49579443-49579729(-)$1	286	18	22	12.0000
UUCU	chr5:85915087-85915344(+)$1	257	63	67	12.0000
UUCU	chr19:13058900-13059140(+)$1	240	75	79	12.0000
UUCU	chr5:162945164-162945415(+)$1	251	24	28	12.0000
UUCU	chr1:8926359-8926659(-)$1	300	77	81	12.0000
UUCU	chr10:38343920-38344167(+)$1	247	1	5	12.0000
UUCU	chr11:62334208-62334480(-)$1	272	248	252	12.0000
UUCU	chr1:55560906-55561167(-)$1	261	76	80	12.0000
UUCU	chr6:32825034-32825274(+)$1	240	153	157	12.0000
UUCU	chrM:11810-12070(-)$1	260	11	15	12.0000
UUCU	chr17:44373163-44373432(+)$1	269	97	101	12.0000
UUCU	chr16:69782032-69782262(-)$1	230	6	10	12.0000
UUCU	chr2:178097132-178097380(-)$1	248	71	75	12.0000
UUCU	chr3:40503359-40503685(+)$1	326	48	52	12.0000
UUCU	chr8:95885518-95885757(+)$1	239	72	76	12.0000
UUCU	chr11:67953218-67953467(-)$1	249	50	54	12.0000
UUCU	chr5:179192350-179192599(+)$1	249	161	165	12.0000
UUCU	chr1:24077560-24077802(+)$1	242	47	51	12.0000
UUCU	chr7:99708724-99708975(-)$1	251	20	24	12.0000
UUCU	chr19:39336232-39336464(-)$1	232	13	17	12.0000

#otherMatches

#Struct PSSM
DDD{	chr17:45678938-45679204(+)$1	266	19	23	12.0000
oooo	chr1:24120090-24120333(+)$1	243	228	232	12.0000
hhhh	chr10:135176280-135176522(-)$1	242	64	68	12.0000
b!!c	chr17:7212891-7213182(+)$1	291	24	28	12.0000
dddd	chr6:74228691-74228954(-)$1	263	91	95	12.0000
))))	chr10:6274753-6275006(+)$1	253	12	16	12.0000
h:FF	chr5:176636942-176637210(+)$1	268	160	164	12.0000
ffff	chr16:21983175-21983438(+)$1	263	35	39	12.0000
pppp	chr11:64693078-64693317(+)$1	239	218	222	12.0000
fmmm	chr8:128750786-128751031(+)$1	245	133	137	12.0000
:::i	chr15:82821061-82821304(-)$1	243	3	7	12.0000
ffff	chr3:180680719-180680987(+)$1	268	25	29	12.0000
gggg	chr2:234750172-234750419(-)$1	247	31	35	12.0000
deee	chr11:9459492-9459733(-)$1	241	93	97	12.0000
EEE?	chr10:43280982-43281219(+)$1	237	211	215	12.0000
GFFF	chr12:56993650-56993904(-)$1	254	12	16	12.0000
GGGG	chr21:34668425-34668683(+)$1	258	91	95	12.0000
eeee	chr19:17515098-17515339(-)$1	241	77	81	12.0000
::::	chr12:123031894-123032143(+)$1	249	140	144	12.0000
eeee	chr20:52192367-52192634(-)$1	267	29	33	12.0000
EEEE	chr6:82925745-82926039(-)$1	294	8	12	12.0000
eeee	chr14:35872328-35872583(-)$1	255	69	73	12.0000
ggg:	chr10:387093-387367(-)$1	274	122	126	12.0000
::::	chr2:54845147-54845393(+)$1	246	18	22	12.0000
ffff	chr18:47015745-47015995(-)$1	250	53	57	12.0000
]bb]	chr2:224824245-224824515(+)$1	270	85	89	12.0000
::::	chr15:66795651-66795911(-)$1	260	36	40	12.0000
LLLC	chr6:13657300-13657561(-)$1	261	43	47	12.0000
::::	chr7:30661946-30662188(+)$1	242	190	194	12.0000
"""d	chr20:49518488-49518737(-)$1	249	85	89	12.0000
:::G	chr16:56423100-56423365(-)$1	265	1	5	12.0000
eccc	chr18:32917201-32917475(-)$1	274	50	54	12.0000
EEEE	chr14:58895980-58896241(+)$1	261	42	46	12.0000
gggg	chr17:80196525-80196797(+)$1	272	147	151	12.0000
::::	chr17:80195613-80195855(+)$1	242	2	6	12.0000
#ccc	chr19:3981255-3981510(-)$1	255	34	38	12.0000
sssf	chr13:46725061-46725316(-)$1	255	78	82	12.0000
:::=	chr11:46782168-46782412(-)$1	244	4	8	12.0000
EEEH	chr1:46032163-46032412(+)$1	249	61	65	12.0000
hhhh	chr16:48286103-48286353(+)$1	250	191	195	12.0000
fff!	chr6:26045566-26045822(+)$1	256	6	10	12.0000
%eee	chr6:29692729-29693015(+)$1	286	62	66	12.0000
++++	chr16:47545545-47545792(+)$1	247	24	28	12.0000
pppp	chr1:159889355-159889608(-)$1	253	243	247	12.0000
HHHH	chr9:27562313-27562563(-)$1	250	39	43	12.0000
FFFF	chr1:8025287-8025588(+)$1	301	20	24	12.0000
::cc	chr2:176043798-176044073(-)$1	275	82	86	12.0000
::::	chr17:37564958-37565208(-)$1	250	34	38	12.0000
GGGG	chr19:49469824-49470240(+)$1	416	4	8	12.0000
::::	chrX:64949351-64949601(+)$1	250	5	9	12.0000
dddc	chr12:49522947-49523208(-)$1	261	18	22	12.0000
ff::	chr1:153639951-153640218(-)$1	267	18	22	12.0000
cccd	chr6:43013252-43013499(-)$1	247	61	65	12.0000
hh))	chr1:35865013-35865252(+)$1	239	51	55	12.0000
ff::	chr3:156869870-156870123(-)$1	253	177	181	12.0000
ddll	chr6:17624770-17625033(-)$1	263	129	133	12.0000
g333	chr20:44526940-44527174(+)$1	234	116	120	12.0000
mmcc	chr17:35564576-35564817(-)$1	241	15	19	12.0000
:ddd	chr4:17590410-17590666(+)$1	256	18	22	12.0000
FFFF	chr6:29911041-29911303(+)$1	262	4	8	12.0000
c]bb	chr2:107040538-107040781(-)$1	243	168	172	12.0000
DDKK	chr12:49579443-49579729(-)$1	286	18	22	12.0000
((((	chr5:85915087-85915344(+)$1	257	63	67	12.0000
"""d	chr19:13058900-13059140(+)$1	240	75	79	12.0000
ffmm	chr5:162945164-162945415(+)$1	251	24	28	12.0000
b22c	chr1:8926359-8926659(-)$1	300	77	81	12.0000
::::	chr10:38343920-38344167(+)$1	247	1	5	12.0000
::::	chr11:62334208-62334480(-)$1	272	248	252	12.0000
eeee	chr1:55560906-55561167(-)$1	261	76	80	12.0000
emmm	chr6:32825034-32825274(+)$1	240	153	157	12.0000
gggg	chrM:11810-12070(-)$1	260	11	15	12.0000
iiii	chr17:44373163-44373432(+)$1	269	97	101	12.0000
:::d	chr16:69782032-69782262(-)$1	230	6	10	12.0000
::::	chr2:178097132-178097380(-)$1	248	71	75	12.0000
GGGG	chr3:40503359-40503685(+)$1	326	48	52	12.0000
RRRR	chr8:95885518-95885757(+)$1	239	72	76	12.0000
33dd	chr11:67953218-67953467(-)$1	249	50	54	12.0000
d333	chr5:179192350-179192599(+)$1	249	161	165	12.0000
JCCC	chr1:24077560-24077802(+)$1	242	47	51	12.0000
uuuu	chr7:99708724-99708975(-)$1	251	20	24	12.0000
::::	chr19:39336232-39336464(-)$1	232	13	17	12.0000

#DB
(((.	chr17:45678938-45679204(+)$1	1	19	23	12.0000
....	chr1:24120090-24120333(+)$1	1	228	232	12.0000
))))	chr10:135176280-135176522(-)$1	1	64	68	12.0000
(..(	chr17:7212891-7213182(+)$1	1	24	28	12.0000
))))	chr6:74228691-74228954(-)$1	1	91	95	12.0000
....	chr10:6274753-6275006(+)$1	1	12	16	12.0000
).))	chr5:176636942-176637210(+)$1	1	160	164	12.0000
))))	chr16:21983175-21983438(+)$1	1	35	39	12.0000
....	chr11:64693078-64693317(+)$1	1	218	222	12.0000
(...	chr8:128750786-128751031(+)$1	1	133	137	12.0000
...(	chr15:82821061-82821304(-)$1	1	3	7	12.0000
((((	chr3:180680719-180680987(+)$1	1	25	29	12.0000
))))	chr2:234750172-234750419(-)$1	1	31	35	12.0000
))))	chr11:9459492-9459733(-)$1	1	93	97	12.0000
))).	chr10:43280982-43281219(+)$1	1	211	215	12.0000
((((	chr12:56993650-56993904(-)$1	1	12	16	12.0000
((((	chr21:34668425-34668683(+)$1	1	91	95	12.0000
((((	chr19:17515098-17515339(-)$1	1	77	81	12.0000
....	chr12:123031894-123032143(+)$1	1	140	144	12.0000
))))	chr20:52192367-52192634(-)$1	1	29	33	12.0000
((((	chr6:82925745-82926039(-)$1	1	8	12	12.0000
))))	chr14:35872328-35872583(-)$1	1	69	73	12.0000
))).	chr10:387093-387367(-)$1	1	122	126	12.0000
....	chr2:54845147-54845393(+)$1	1	18	22	12.0000
))))	chr18:47015745-47015995(-)$1	1	53	57	12.0000
.)).	chr2:224824245-224824515(+)$1	1	85	89	12.0000
....	chr15:66795651-66795911(-)$1	1	36	40	12.0000
...(	chr6:13657300-13657561(-)$1	1	43	47	12.0000
....	chr7:30661946-30662188(+)$1	1	190	194	12.0000
...(	chr20:49518488-49518737(-)$1	1	85	89	12.0000
...(	chr16:56423100-56423365(-)$1	1	1	5	12.0000
)(((	chr18:32917201-32917475(-)$1	1	50	54	12.0000
((((	chr14:58895980-58896241(+)$1	1	42	46	12.0000
((((	chr17:80196525-80196797(+)$1	1	147	151	12.0000
....	chr17:80195613-80195855(+)$1	1	2	6	12.0000
.(((	chr19:3981255-3981510(-)$1	1	34	38	12.0000
...)	chr13:46725061-46725316(-)$1	1	78	82	12.0000
...(	chr11:46782168-46782412(-)$1	1	4	8	12.0000
((((	chr1:46032163-46032412(+)$1	1	61	65	12.0000
))))	chr16:48286103-48286353(+)$1	1	191	195	12.0000
(((.	chr6:26045566-26045822(+)$1	1	6	10	12.0000
.(((	chr6:29692729-29693015(+)$1	1	62	66	12.0000
....	chr16:47545545-47545792(+)$1	1	24	28	12.0000
....	chr1:159889355-159889608(-)$1	1	243	247	12.0000
((((	chr9:27562313-27562563(-)$1	1	39	43	12.0000
((((	chr1:8025287-8025588(+)$1	1	20	24	12.0000
..((	chr2:176043798-176044073(-)$1	1	82	86	12.0000
....	chr17:37564958-37565208(-)$1	1	34	38	12.0000
((((	chr19:49469824-49470240(+)$1	1	4	8	12.0000
....	chrX:64949351-64949601(+)$1	1	5	9	12.0000
((((	chr12:49522947-49523208(-)$1	1	18	22	12.0000
))..	chr1:153639951-153640218(-)$1	1	18	22	12.0000
((((	chr6:43013252-43013499(-)$1	1	61	65	12.0000
((..	chr1:35865013-35865252(+)$1	1	51	55	12.0000
))..	chr3:156869870-156870123(-)$1	1	177	181	12.0000
((..	chr6:17624770-17625033(-)$1	1	129	133	12.0000
)...	chr20:44526940-44527174(+)$1	1	116	120	12.0000
..))	chr17:35564576-35564817(-)$1	1	15	19	12.0000
.(((	chr4:17590410-17590666(+)$1	1	18	22	12.0000
((((	chr6:29911041-29911303(+)$1	1	4	8	12.0000
).))	chr2:107040538-107040781(-)$1	1	168	172	12.0000
((..	chr12:49579443-49579729(-)$1	1	18	22	12.0000
....	chr5:85915087-85915344(+)$1	1	63	67	12.0000
...(	chr19:13058900-13059140(+)$1	1	75	79	12.0000
((..	chr5:162945164-162945415(+)$1	1	24	28	12.0000
)..)	chr1:8926359-8926659(-)$1	1	77	81	12.0000
....	chr10:38343920-38344167(+)$1	1	1	5	12.0000
....	chr11:62334208-62334480(-)$1	1	248	252	12.0000
))))	chr1:55560906-55561167(-)$1	1	76	80	12.0000
(...	chr6:32825034-32825274(+)$1	1	153	157	12.0000
((((	chrM:11810-12070(-)$1	1	11	15	12.0000
))))	chr17:44373163-44373432(+)$1	1	97	101	12.0000
...(	chr16:69782032-69782262(-)$1	1	6	10	12.0000
....	chr2:178097132-178097380(-)$1	1	71	75	12.0000
((((	chr3:40503359-40503685(+)$1	1	48	52	12.0000
....	chr8:95885518-95885757(+)$1	1	72	76	12.0000
..))	chr11:67953218-67953467(-)$1	1	50	54	12.0000
)...	chr5:179192350-179192599(+)$1	1	161	165	12.0000
((((	chr1:24077560-24077802(+)$1	1	47	51	12.0000
....	chr7:99708724-99708975(-)$1	1	20	24	12.0000
....	chr19:39336232-39336464(-)$1	1	13	17	12.0000

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

#score	972.0000000000006
#seq	81
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_CDS_m3_run1.nuc.txt

#NT
CUGG	chr12:125396164-125396398(-)$1	234	41	45	12.0000
CUGG	chr12:56120872-56121110(-)$1	238	66	70	12.0000
CUGG	chr9:92002313-92002538(-)$1	225	198	202	12.0000
CUGG	chr2:131813088-131813324(-)$1	236	10	14	12.0000
CUGG	chr19:10790447-10790678(+)$1	231	99	103	12.0000
CUGG	chr13:20640890-20641110(+)$1	220	210	214	12.0000
CUGG	chr17:45787796-45788027(+)$1	231	4	8	12.0000
CUGG	chr17:26881181-26881425(-)$1	244	128	132	12.0000
CUGG	chr10:51769594-51769825(+)$1	231	19	23	12.0000
CUGG	chr2:203384730-203384961(+)$1	231	117	121	12.0000
CUGG	chr11:819692-819912(+)$1	220	131	135	12.0000
CUGG	chr8:81411742-81411965(+)$1	223	157	161	12.0000
CUGG	chr17:73132067-73132305(-)$1	238	77	81	12.0000
CUGG	chr11:62339977-62340179(-)$1	202	188	192	12.0000
CUGG	chr5:68471150-68471410(+)$1	260	196	200	12.0000
CUGG	chr20:45848866-45849075(-)$1	209	30	34	12.0000
CUGG	chr3:121195409-121195631(-)$1	222	167	171	12.0000
CUGG	chr15:68570723-68570945(+)$1	222	41	45	12.0000
CUGG	chr11:10819264-10819492(-)$1	228	81	85	12.0000
CUGG	chr1:182845197-182845433(+)$1	236	120	124	12.0000
CUGG	chr1:150938907-150939132(-)$1	225	43	47	12.0000
CUGG	chr19:3193236-3193467(+)$1	231	72	76	12.0000
CUGG	chr21:35169701-35169925(+)$1	224	9	13	12.0000
CUGG	chr16:24834680-24834954(+)$1	274	28	32	12.0000
CUGG	chr17:73237405-73237638(-)$1	233	168	172	12.0000
CUGG	chr9:99150588-99150839(-)$1	251	144	148	12.0000
CUGG	chr10:113924232-113924465(-)$1	233	145	149	12.0000
cugg	chr1:94047985-94048216(-)$1	231	84	88	12.0000
CUGG	chr1:154918056-154918298(-)$1	242	29	33	12.0000
cuGG	chr19:48893621-48893874(-)$1	253	82	86	12.0000
CUGG	chr16:20807584-20807806(-)$1	222	205	209	12.0000
CUGG	chr9:97221585-97221808(+)$1	223	57	61	12.0000
CUGG	chr8:22272220-22272445(+)$1	225	60	64	12.0000
CUGG	chr7:30395257-30395497(+)$1	240	107	111	12.0000
CUGG	chr11:86662739-86662965(-)$1	226	220	224	12.0000
CUGG	chr1:244217061-244217281(+)$1	220	126	130	12.0000
CUGG	chrX:117529180-117529401(+)$1	221	104	108	12.0000
CUGG	chr12:12871115-12871345(+)$1	230	184	188	12.0000
CUGG	chr10:13233210-13233434(+)$1	224	137	141	12.0000
CUGG	chr1:24175038-24175248(-)$1	210	162	166	12.0000
CUGG	chr12:49427397-49427624(-)$1	227	31	35	12.0000
CUGG	chr16:53261266-53261476(+)$1	210	117	121	12.0000
CUGG	chrX:47040619-47040840(+)$1	221	17	21	12.0000
CUGG	chr14:21851920-21852139(-)$1	219	65	69	12.0000
CUGG	chr17:7366377-7366599(-)$1	222	61	65	12.0000
CUGG	chr10:93619235-93619465(+)$1	230	58	62	12.0000
CUGG	chr1:153747946-153748192(+)$1	246	92	96	12.0000
CUGG	chr2:242274475-242274706(+)$1	231	140	144	12.0000
CUGG	chr1:94883922-94884146(+)$1	224	95	99	12.0000
CUGG	chr1:42693491-42693713(-)$1	222	84	88	12.0000
CUGG	chr17:2238771-2238991(-)$1	220	21	25	12.0000
CUGG	chr11:62342641-62342874(-)$1	233	61	65	12.0000
CUGG	chr3:128889271-128889497(-)$1	226	95	99	12.0000
CUGG	chrX:119673041-119673281(-)$1	240	234	238	12.0000
CUGG	chr10:13699361-13699583(-)$1	222	128	132	12.0000
CUGG	chr20:35856990-35857231(+)$1	241	49	53	12.0000
CUGG	chr18:28604266-28604492(-)$1	226	175	179	12.0000
CUGG	chr17:4607196-4607448(-)$1	252	25	29	12.0000
CUGG	chr3:120128320-120128541(-)$1	221	85	89	12.0000
CUGG	chr17:60087945-60088166(-)$1	221	130	134	12.0000
CUGG	chr6:26124343-26124592(+)$1	249	88	92	12.0000
CUGG	chr1:235826210-235826432(-)$1	222	117	121	12.0000
CUGG	chr1:87369009-87369229(-)$1	220	209	213	12.0000
CUGG	chr3:179131180-179131411(-)$1	231	54	58	12.0000
CUGG	chr2:86831838-86832089(-)$1	251	175	179	12.0000
CUGG	chr3:126451897-126452128(+)$1	231	165	169	12.0000
CUGG	chr10:101914562-101914796(-)$1	234	111	115	12.0000
CUGG	chr6:144128113-144128337(+)$1	224	22	26	12.0000
CUGG	chr2:44428952-44429183(+)$1	231	120	124	12.0000
CUGG	chr20:32659923-32660159(+)$1	236	50	54	12.0000
CUGG	chr6:83905812-83906037(+)$1	225	86	90	12.0000
CUGG	chr14:61186837-61187077(-)$1	240	87	91	12.0000
CUGG	chr20:43571663-43571887(-)$1	224	154	158	12.0000
CUGG	chr2:113073949-113074175(+)$1	226	193	197	12.0000
CUGG	chr7:2402198-2402443(+)$1	245	91	95	12.0000
CUGG	chr11:96124919-96125142(+)$1	223	85	89	12.0000
CUGG	chr1:154179800-154180037(-)$1	237	194	198	12.0000
CUGG	chr18:44470788-44471010(-)$1	222	45	49	12.0000
CUGG	chr17:80054166-80054425(-)$1	259	25	29	12.0000
CUGG	chr15:78790295-78790526(+)$1	231	33	37	12.0000
CUGG	chrX:47088171-47088425(+)$1	254	26	30	12.0000
CUGG	chr1:228288752-228288976(-)$1	224	148	152	12.0000

#otherMatches

#Struct PSSM
:DDD	chr9:78925521-78925745(+)$1	224	61	65	12.0000
dddn	chr12:125396164-125396398(-)$1	234	41	45	12.0000
fffF	chr12:56120872-56121110(-)$1	238	66	70	12.0000
cnnn	chr9:92002313-92002538(-)$1	225	198	202	12.0000
cooo	chr2:131813088-131813324(-)$1	236	10	14	12.0000
cccJ	chr19:10790447-10790678(+)$1	231	99	103	12.0000
YYCC	chr13:20640890-20641110(+)$1	220	210	214	12.0000
{EEE	chr17:45787796-45788027(+)$1	231	4	8	12.0000
EEE{	chr17:26881181-26881425(-)$1	244	128	132	12.0000
EEKK	chr10:51769594-51769825(+)$1	231	19	23	12.0000
OEEE	chr2:203384730-203384961(+)$1	231	117	121	12.0000
:bbe	chr11:819692-819912(+)$1	220	131	135	12.0000
:::H	chr8:81411742-81411965(+)$1	223	157	161	12.0000
dddd	chr17:73132067-73132305(-)$1	238	77	81	12.0000
3fff	chr11:62339977-62340179(-)$1	202	188	192	12.0000
77cc	chr5:68471150-68471410(+)$1	260	196	200	12.0000
CCCK	chr20:45848866-45849075(-)$1	209	30	34	12.0000
G}BB	chr3:121195409-121195631(-)$1	222	167	171	12.0000
::ff	chr15:68570723-68570945(+)$1	222	41	45	12.0000
MMGG	chr11:10819264-10819492(-)$1	228	81	85	12.0000
3ggg	chr1:182845197-182845433(+)$1	236	120	124	12.0000
CCCc	chr1:150938907-150939132(-)$1	225	43	47	12.0000
eee5	chr19:3193236-3193467(+)$1	231	72	76	12.0000
dddd	chr21:35169701-35169925(+)$1	224	9	13	12.0000
mmbb	chr16:24834680-24834954(+)$1	274	28	32	12.0000
dddd	chr17:73237405-73237638(-)$1	233	168	172	12.0000
bb!!	chr9:99150588-99150839(-)$1	251	144	148	12.0000
gggg	chr10:113924232-113924465(-)$1	233	145	149	12.0000
hhhh	chr1:94047985-94048216(-)$1	231	84	88	12.0000
iooo	chr1:154918056-154918298(-)$1	242	29	33	12.0000
cccn	chr19:48893621-48893874(-)$1	253	82	86	12.0000
::EE	chr16:20807584-20807806(-)$1	222	205	209	12.0000
cc[b	chr9:97221585-97221808(+)$1	223	57	61	12.0000
dddo	chr8:22272220-22272445(+)$1	225	60	64	12.0000
dd]b	chr7:30395257-30395497(+)$1	240	107	111	12.0000
22cc	chr11:86662739-86662965(-)$1	226	220	224	12.0000
dddd	chr1:244217061-244217281(+)$1	220	126	130	12.0000
ffff	chrX:117529180-117529401(+)$1	221	104	108	12.0000
DDDD	chr12:12871115-12871345(+)$1	230	184	188	12.0000
ccbb	chr10:13233210-13233434(+)$1	224	137	141	12.0000
rrrr	chr1:24175038-24175248(-)$1	210	162	166	12.0000
[ddd	chr12:49427397-49427624(-)$1	227	31	35	12.0000
}EEE	chr16:53261266-53261476(+)$1	210	117	121	12.0000
cc33	chrX:47040619-47040840(+)$1	221	17	21	12.0000
dd!!	chr14:21851920-21852139(-)$1	219	65	69	12.0000
ggoo	chr17:7366377-7366599(-)$1	222	61	65	12.0000
gggg	chr10:93619235-93619465(+)$1	230	58	62	12.0000
::ee	chr1:153747946-153748192(+)$1	246	92	96	12.0000
fffo	chr2:242274475-242274706(+)$1	231	140	144	12.0000
c]cc	chr1:94883922-94884146(+)$1	224	95	99	12.0000
:fff	chr1:42693491-42693713(-)$1	222	84	88	12.0000
ffll	chr17:2238771-2238991(-)$1	220	21	25	12.0000
E{BB	chr11:62342641-62342874(-)$1	233	61	65	12.0000
gggc	chr3:128889271-128889497(-)$1	226	95	99	12.0000
DDD:	chrX:119673041-119673281(-)$1	240	234	238	12.0000
eeef	chr10:13699361-13699583(-)$1	222	128	132	12.0000
bbzz	chr20:35856990-35857231(+)$1	241	49	53	12.0000
::DD	chr18:28604266-28604492(-)$1	226	175	179	12.0000
:::B	chr17:4607196-4607448(-)$1	252	25	29	12.0000
ffff	chr3:120128320-120128541(-)$1	221	85	89	12.0000
::dd	chr17:60087945-60088166(-)$1	221	130	134	12.0000
gg66	chr6:26124343-26124592(+)$1	249	88	92	12.0000
IIII	chr1:235826210-235826432(-)$1	222	117	121	12.0000
C}DD	chr1:87369009-87369229(-)$1	220	209	213	12.0000
gggg	chr3:179131180-179131411(-)$1	231	54	58	12.0000
ffff	chr2:86831838-86832089(-)$1	251	175	179	12.0000
hh[a	chr3:126451897-126452128(+)$1	231	165	169	12.0000
ee22	chr10:101914562-101914796(-)$1	234	111	115	12.0000
nbb]	chr6:144128113-144128337(+)$1	224	22	26	12.0000
ssss	chr2:44428952-44429183(+)$1	231	120	124	12.0000
ffff	chr20:32659923-32660159(+)$1	236	50	54	12.0000
GGGG	chr6:83905812-83906037(+)$1	225	86	90	12.0000
DDDD	chr14:61186837-61187077(-)$1	240	87	91	12.0000
!ccc	chr20:43571663-43571887(-)$1	224	154	158	12.0000
iimm	chr2:113073949-113074175(+)$1	226	193	197	12.0000
cc]d	chr7:2402198-2402443(+)$1	245	91	95	12.0000
b22a	chr11:96124919-96125142(+)$1	223	85	89	12.0000
vfff	chr1:154179800-154180037(-)$1	237	194	198	12.0000
dd[a	chr18:44470788-44471010(-)$1	222	45	49	12.0000
3ddd	chr17:80054166-80054425(-)$1	259	25	29	12.0000
CFFF	chr15:78790295-78790526(+)$1	231	33	37	12.0000
:bbe	chrX:47088171-47088425(+)$1	254	26	30	12.0000
ddcc	chr1:228288752-228288976(-)$1	224	148	152	12.0000

#DB
.(((	chr9:78925521-78925745(+)$1	1	61	65	12.0000
(((.	chr12:125396164-125396398(-)$1	1	41	45	12.0000
)))(	chr12:56120872-56121110(-)$1	1	66	70	12.0000
(...	chr9:92002313-92002538(-)$1	1	198	202	12.0000
(...	chr2:131813088-131813324(-)$1	1	10	14	12.0000
)))(	chr19:10790447-10790678(+)$1	1	99	103	12.0000
..))	chr13:20640890-20641110(+)$1	1	210	214	12.0000
.(((	chr17:45787796-45788027(+)$1	1	4	8	12.0000
(((.	chr17:26881181-26881425(-)$1	1	128	132	12.0000
((..	chr10:51769594-51769825(+)$1	1	19	23	12.0000
.(((	chr2:203384730-203384961(+)$1	1	117	121	12.0000
.(((	chr11:819692-819912(+)$1	1	131	135	12.0000
...)	chr8:81411742-81411965(+)$1	1	157	161	12.0000
))))	chr17:73132067-73132305(-)$1	1	77	81	12.0000
.)))	chr11:62339977-62340179(-)$1	1	188	192	12.0000
..))	chr5:68471150-68471410(+)$1	1	196	200	12.0000
(((.	chr20:45848866-45849075(-)$1	1	30	34	12.0000
).))	chr3:121195409-121195631(-)$1	1	167	171	12.0000
..((	chr15:68570723-68570945(+)$1	1	41	45	12.0000
..((	chr11:10819264-10819492(-)$1	1	81	85	12.0000
.)))	chr1:182845197-182845433(+)$1	1	120	124	12.0000
((((	chr1:150938907-150939132(-)$1	1	43	47	12.0000
))).	chr19:3193236-3193467(+)$1	1	72	76	12.0000
((((	chr21:35169701-35169925(+)$1	1	9	13	12.0000
..))	chr16:24834680-24834954(+)$1	1	28	32	12.0000
((((	chr17:73237405-73237638(-)$1	1	168	172	12.0000
((..	chr9:99150588-99150839(-)$1	1	144	148	12.0000
))))	chr10:113924232-113924465(-)$1	1	145	149	12.0000
))))	chr1:94047985-94048216(-)$1	1	84	88	12.0000
(...	chr1:154918056-154918298(-)$1	1	29	33	12.0000
(((.	chr19:48893621-48893874(-)$1	1	82	86	12.0000
..))	chr16:20807584-20807806(-)$1	1	205	209	12.0000
((.(	chr9:97221585-97221808(+)$1	1	57	61	12.0000
(((.	chr8:22272220-22272445(+)$1	1	60	64	12.0000
)).)	chr7:30395257-30395497(+)$1	1	107	111	12.0000
..))	chr11:86662739-86662965(-)$1	1	220	224	12.0000
))))	chr1:244217061-244217281(+)$1	1	126	130	12.0000
))))	chrX:117529180-117529401(+)$1	1	104	108	12.0000
))))	chr12:12871115-12871345(+)$1	1	184	188	12.0000
))((	chr10:13233210-13233434(+)$1	1	137	141	12.0000
....	chr1:24175038-24175248(-)$1	1	162	166	12.0000
.(((	chr12:49427397-49427624(-)$1	1	31	35	12.0000
.)))	chr16:53261266-53261476(+)$1	1	117	121	12.0000
))..	chrX:47040619-47040840(+)$1	1	17	21	12.0000
((..	chr14:21851920-21852139(-)$1	1	65	69	12.0000
((..	chr17:7366377-7366599(-)$1	1	61	65	12.0000
((((	chr10:93619235-93619465(+)$1	1	58	62	12.0000
..((	chr1:153747946-153748192(+)$1	1	92	96	12.0000
(((.	chr2:242274475-242274706(+)$1	1	140	144	12.0000
).))	chr1:94883922-94884146(+)$1	1	95	99	12.0000
.(((	chr1:42693491-42693713(-)$1	1	84	88	12.0000
((..	chr17:2238771-2238991(-)$1	1	21	25	12.0000
(.((	chr11:62342641-62342874(-)$1	1	61	65	12.0000
)))(	chr3:128889271-128889497(-)$1	1	95	99	12.0000
))).	chrX:119673041-119673281(-)$1	1	234	238	12.0000
)))(	chr10:13699361-13699583(-)$1	1	128	132	12.0000
((..	chr20:35856990-35857231(+)$1	1	49	53	12.0000
..))	chr18:28604266-28604492(-)$1	1	175	179	12.0000
...(	chr17:4607196-4607448(-)$1	1	25	29	12.0000
((((	chr3:120128320-120128541(-)$1	1	85	89	12.0000
..((	chr17:60087945-60088166(-)$1	1	130	134	12.0000
))..	chr6:26124343-26124592(+)$1	1	88	92	12.0000
((((	chr1:235826210-235826432(-)$1	1	117	121	12.0000
).))	chr1:87369009-87369229(-)$1	1	209	213	12.0000
))))	chr3:179131180-179131411(-)$1	1	54	58	12.0000
((((	chr2:86831838-86832089(-)$1	1	175	179	12.0000
((.(	chr3:126451897-126452128(+)$1	1	165	169	12.0000
))..	chr10:101914562-101914796(-)$1	1	111	115	12.0000
.)).	chr6:144128113-144128337(+)$1	1	22	26	12.0000
....	chr2:44428952-44429183(+)$1	1	120	124	12.0000
((((	chr20:32659923-32660159(+)$1	1	50	54	12.0000
((((	chr6:83905812-83906037(+)$1	1	86	90	12.0000
((((	chr14:61186837-61187077(-)$1	1	87	91	12.0000
.(((	chr20:43571663-43571887(-)$1	1	154	158	12.0000
((..	chr2:113073949-113074175(+)$1	1	193	197	12.0000
)).)	chr7:2402198-2402443(+)$1	1	91	95	12.0000
)..)	chr11:96124919-96125142(+)$1	1	85	89	12.0000
.)))	chr1:154179800-154180037(-)$1	1	194	198	12.0000
((.(	chr18:44470788-44471010(-)$1	1	45	49	12.0000
.)))	chr17:80054166-80054425(-)$1	1	25	29	12.0000
((((	chr15:78790295-78790526(+)$1	1	33	37	12.0000
.(((	chrX:47088171-47088425(+)$1	1	26	30	12.0000
))))	chr1:228288752-228288976(-)$1	1	148	152	12.0000

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

#score	996.0000000000005
#seq	83
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m2_run2.nuc.txt

#NT
CCU	chr19:50161790-50162005(+)$1	215	0	3	8.9999
ccu	chr14:53109232-53109481(-)$1	249	136	139	8.9999
CCU	chr17:38247384-38247656(+)$1	272	12	15	8.9999
CCU	chr5:55234784-55235071(-)$1	287	110	113	8.9999
ccu	chr13:28499709-28499924(+)$1	215	2	5	8.9999
CCU	chr10:22825372-22825643(-)$1	271	87	90	8.9999
CCU	chr6:143818315-143818536(-)$1	221	27	30	8.9999
CCU	chr12:57490030-57490292(-)$1	262	14	17	8.9999
CCU	chr12:393703-393930(-)$1	227	15	18	8.9999
ccu	chr17:62895081-62895333(-)$1	252	3	6	8.9999
ccu	chr13:113539472-113539844(+)$1	372	16	19	8.9999
CCU	chr13:74263721-74264033(-)$1	312	156	159	8.9999
CCU	chr1:15901664-15901901(-)$1	237	0	3	8.9999
CCU	chr12:133781621-133781864(+)$1	243	15	18	8.9999
ccu	chr14:105777138-105777369(+)$1	231	57	60	8.9999
CCU	chr15:52602590-52602821(-)$1	231	2	5	8.9999
CCU	chr1:151025019-151025414(-)$1	395	25	28	8.9999
CCU	chr19:47112367-47112591(+)$1	224	120	123	8.9999
CCU	chr1:153782344-153782583(-)$1	239	14	17	8.9999
CCU	chr19:7987762-7987971(+)$1	209	19	22	8.9999
CCU	chr2:96049814-96050066(+)$1	252	15	18	8.9999
CCU	chr1:145763632-145763845(+)$1	213	53	56	8.9999
CCU	chr5:71490125-71490339(+)$1	214	8	11	8.9999
CCU	chr2:9724878-9725140(-)$1	262	131	134	8.9999
CCU	chr20:5527445-5527682(-)$1	237	174	177	8.9999
CCU	chr3:118931616-118931898(-)$1	282	5	8	8.9999
CCU	chr6:111215210-111215433(+)$1	223	0	3	8.9999
ccu	chr7:134343203-134343418(+)$1	215	57	60	8.9999
ccu	chr20:44998484-44998746(-)$1	262	242	245	8.9999
CCU	chr17:80321159-80321376(+)$1	217	72	75	8.9999
CCU	chr6:24805086-24805352(-)$1	266	5	8	8.9999
CCU	chr6:96055877-96056102(+)$1	225	48	51	8.9999
CCU	chr1:900972-901189(+)$1	217	3	6	8.9999
CCU	chr6:158518341-158518565(+)$1	224	2	5	8.9999
CCU	chr1:213070553-213070841(+)$1	288	3	6	8.9999
CCU	chrX:64959646-64959955(+)$1	309	48	51	8.9999
ccu	chr13:45912237-45912463(-)$1	226	17	20	8.9999
CCU	chr5:133482433-133482707(+)$1	274	5	8	8.9999
CCU	chr11:68286877-68287141(+)$1	264	7	10	8.9999
ccu	chr3:44794573-44794817(-)$1	244	51	54	8.9999
CCU	chr1:145285697-145285967(+)$1	270	23	26	8.9999
CCU	chr12:123087559-123087775(+)$1	216	82	85	8.9999
ccu	chr7:35939879-35940143(+)$1	264	30	33	8.9999
CCU	chr12:9845636-9845977(+)$1	341	48	51	8.9999
CCU	chr1:70340183-70340397(+)$1	214	83	86	8.9999
CCU	chr8:57129063-57129285(+)$1	222	32	35	8.9999
CCU	chr9:86618324-86618540(+)$1	216	72	75	8.9999
CCU	chr10:115670491-115670714(+)$1	223	26	29	8.9999
CCU	chr15:63599698-63599911(+)$1	213	26	29	8.9999
CCU	chr1:59124787-59125054(-)$1	267	116	119	8.9999
CCU	chr17:73773852-73774103(-)$1	251	107	110	8.9999
ccu	chr10:102283746-102283995(-)$1	249	23	26	8.9999
ccu	chr19:17935505-17935774(-)$1	269	22	25	8.9999
CCU	chr2:63283759-63283972(+)$1	213	31	34	8.9999
CCU	chr1:202556236-202556488(+)$1	252	7	10	8.9999
CCU	chr15:38782100-38782399(-)$1	299	9	12	8.9999
CCU	chr1:24296244-24296469(-)$1	225	33	36	8.9999
ccu	chr19:53120514-53120763(-)$1	249	6	9	8.9999
CCU	chr9:5919879-5920174(-)$1	295	27	30	8.9999
ccu	chr1:40538619-40538867(-)$1	248	116	119	8.9999
CCU	chr1:204522612-204522837(+)$1	225	10	13	8.9999
CCU	chr1:7826528-7826800(+)$1	272	40	43	8.9999
CCU	chr17:4624549-4624803(+)$1	254	43	46	8.9999
ccu	chr1:158909298-158909612(+)$1	314	39	42	8.9999
CCU	chr6:111498461-111498674(+)$1	213	6	9	8.9999
CCU	chr1:236714170-236714426(+)$1	256	166	169	8.9999
CCU	chr4:2839708-2839953(+)$1	245	6	9	8.9999
ccu	chr11:89938783-89939123(-)$1	340	53	56	8.9999
CCU	chr19:49843560-49843822(+)$1	262	32	35	8.9999
CCU	chr16:68332200-68332480(+)$1	280	0	3	8.9999
CCU	chr1:40928427-40928642(+)$1	215	61	64	8.9999
CCU	chr1:162334505-162334723(+)$1	218	21	24	8.9999
CCU	chr9:35609891-35610105(+)$1	214	114	117	8.9999
ccu	chr16:50706491-50706874(-)$1	383	9	12	8.9999
ccu	chr22:25465816-25466107(+)$1	291	90	93	8.9999
CCU	chr6:143810287-143810537(+)$1	250	55	58	8.9999
CCU	chr7:66422682-66422975(+)$1	293	43	46	8.9999
CCU	chr17:73314918-73315217(-)$1	299	21	24	8.9999
CCU	chr2:99204501-99204728(+)$1	227	23	26	8.9999
CCU	chr7:127010428-127010670(-)$1	242	0	3	8.9999
CCU	chr4:57327244-57327499(+)$1	255	13	16	8.9999
CCU	chr1:161128243-161128495(+)$1	252	70	73	8.9999
CCU	chr14:24593368-24593637(+)$1	269	44	47	8.9999
CCU	chr5:162944827-162945042(+)$1	215	140	143	8.9999
CCU	chr16:15819426-15819657(+)$1	231	3	6	8.9999
CCU	chr16:75203752-75203969(+)$1	217	17	20	8.9999
CCU	chr4:103498778-103499017(+)$1	239	4	7	8.9999
CCU	chr4:144476068-144476347(+)$1	279	58	61	8.9999
CCU	chr11:124502986-124503378(+)$1	392	15	18	8.9999
CCU	chr13:73329506-73329734(-)$1	228	4	7	8.9999
CCU	chr11:64888582-64888856(-)$1	274	18	21	8.9999
CCU	chr4:55130269-55130484(+)$1	215	90	93	8.9999
CCU	chr15:41028374-41028591(-)$1	217	13	16	8.9999
CCU	chr2:207945668-207945965(-)$1	297	4	7	8.9999
CCU	chr7:150270855-150271104(+)$1	249	0	3	8.9999

#otherMatches

#Struct PSSM
mmm	chr18:72188176-72188399(+)$1	223	11	14	8.9999
:::	chr19:50161790-50162005(+)$1	215	0	3	8.9999
FLL	chr14:53109232-53109481(-)$1	249	136	139	8.9999
LLB	chr17:38247384-38247656(+)$1	272	12	15	8.9999
eee	chr5:55234784-55235071(-)$1	287	110	113	8.9999
:::	chr13:28499709-28499924(+)$1	215	2	5	8.9999
ccc	chr10:22825372-22825643(-)$1	271	87	90	8.9999
iii	chr6:143818315-143818536(-)$1	221	27	30	8.9999
Cdd	chr12:57490030-57490292(-)$1	262	14	17	8.9999
ccc	chr12:393703-393930(-)$1	227	15	18	8.9999
GGG	chr17:62895081-62895333(-)$1	252	3	6	8.9999
:::	chr13:113539472-113539844(+)$1	372	16	19	8.9999
^^^	chr13:74263721-74264033(-)$1	312	156	159	8.9999
:::	chr1:15901664-15901901(-)$1	237	0	3	8.9999
KFF	chr12:133781621-133781864(+)$1	243	15	18	8.9999
dd:	chr14:105777138-105777369(+)$1	231	57	60	8.9999
:::	chr15:52602590-52602821(-)$1	231	2	5	8.9999
:::	chr1:151025019-151025414(-)$1	395	25	28	8.9999
::c	chr19:47112367-47112591(+)$1	224	120	123	8.9999
bbd	chr1:153782344-153782583(-)$1	239	14	17	8.9999
EEE	chr19:7987762-7987971(+)$1	209	19	22	8.9999
:CC	chr2:96049814-96050066(+)$1	252	15	18	8.9999
b##	chr1:145763632-145763845(+)$1	213	53	56	8.9999
BEE	chr5:71490125-71490339(+)$1	214	8	11	8.9999
:ee	chr2:9724878-9725140(-)$1	262	131	134	8.9999
hhh	chr20:5527445-5527682(-)$1	237	174	177	8.9999
fff	chr3:118931616-118931898(-)$1	282	5	8	8.9999
:::	chr6:111215210-111215433(+)$1	223	0	3	8.9999
ggg	chr7:134343203-134343418(+)$1	215	57	60	8.9999
:::	chr20:44998484-44998746(-)$1	262	242	245	8.9999
""c	chr17:80321159-80321376(+)$1	217	72	75	8.9999
DOO	chr6:24805086-24805352(-)$1	266	5	8	8.9999
===	chr6:96055877-96056102(+)$1	225	48	51	8.9999
GGG	chr1:900972-901189(+)$1	217	3	6	8.9999
:DD	chr6:158518341-158518565(+)$1	224	2	5	8.9999
:cc	chr1:213070553-213070841(+)$1	288	3	6	8.9999
cc]	chrX:64959646-64959955(+)$1	309	48	51	8.9999
:::	chr13:45912237-45912463(-)$1	226	17	20	8.9999
BBN	chr5:133482433-133482707(+)$1	274	5	8	8.9999
ddd	chr11:68286877-68287141(+)$1	264	7	10	8.9999
+++	chr3:44794573-44794817(-)$1	244	51	54	8.9999
:::	chr1:145285697-145285967(+)$1	270	23	26	8.9999
!!b	chr12:123087559-123087775(+)$1	216	82	85	8.9999
dd:	chr7:35939879-35940143(+)$1	264	30	33	8.9999
dll	chr12:9845636-9845977(+)$1	341	48	51	8.9999
bb:	chr1:70340183-70340397(+)$1	214	83	86	8.9999
"bb	chr8:57129063-57129285(+)$1	222	32	35	8.9999
ccc	chr9:86618324-86618540(+)$1	216	72	75	8.9999
zzz	chr10:115670491-115670714(+)$1	223	26	29	8.9999
JJJ	chr15:63599698-63599911(+)$1	213	26	29	8.9999
6ee	chr1:59124787-59125054(-)$1	267	116	119	8.9999
HHH	chr17:73773852-73774103(-)$1	251	107	110	8.9999
WWW	chr10:102283746-102283995(-)$1	249	23	26	8.9999
E{J	chr19:17935505-17935774(-)$1	269	22	25	8.9999
EMM	chr2:63283759-63283972(+)$1	213	31	34	8.9999
:::	chr1:202556236-202556488(+)$1	252	7	10	8.9999
NNG	chr15:38782100-38782399(-)$1	299	9	12	8.9999
ddd	chr1:24296244-24296469(-)$1	225	33	36	8.9999
CCC	chr19:53120514-53120763(-)$1	249	6	9	8.9999
:::	chr9:5919879-5920174(-)$1	295	27	30	8.9999
###	chr1:40538619-40538867(-)$1	248	116	119	8.9999
ddd	chr1:204522612-204522837(+)$1	225	10	13	8.9999
'''	chr1:7826528-7826800(+)$1	272	40	43	8.9999
:::	chr17:4624549-4624803(+)$1	254	43	46	8.9999
KDD	chr1:158909298-158909612(+)$1	314	39	42	8.9999
ddd	chr6:111498461-111498674(+)$1	213	6	9	8.9999
ncc	chr1:236714170-236714426(+)$1	256	166	169	8.9999
:::	chr4:2839708-2839953(+)$1	245	6	9	8.9999
ddd	chr11:89938783-89939123(-)$1	340	53	56	8.9999
MMM	chr19:49843560-49843822(+)$1	262	32	35	8.9999
:::	chr16:68332200-68332480(+)$1	280	0	3	8.9999
cii	chr1:40928427-40928642(+)$1	215	61	64	8.9999
qqq	chr1:162334505-162334723(+)$1	218	21	24	8.9999
}DD	chr9:35609891-35610105(+)$1	214	114	117	8.9999
NBB	chr16:50706491-50706874(-)$1	383	9	12	8.9999
:::	chr22:25465816-25466107(+)$1	291	90	93	8.9999
bb:	chr6:143810287-143810537(+)$1	250	55	58	8.9999
a[e	chr7:66422682-66422975(+)$1	293	43	46	8.9999
hhl	chr17:73314918-73315217(-)$1	299	21	24	8.9999
eee	chr2:99204501-99204728(+)$1	227	23	26	8.9999
ddd	chr7:127010428-127010670(-)$1	242	0	3	8.9999
:::	chr4:57327244-57327499(+)$1	255	13	16	8.9999
ccc	chr1:161128243-161128495(+)$1	252	70	73	8.9999
DDD	chr14:24593368-24593637(+)$1	269	44	47	8.9999
:::	chr5:162944827-162945042(+)$1	215	140	143	8.9999
EEE	chr16:15819426-15819657(+)$1	231	3	6	8.9999
Ecc	chr16:75203752-75203969(+)$1	217	17	20	8.9999
bbq	chr4:103498778-103499017(+)$1	239	4	7	8.9999
[as	chr4:144476068-144476347(+)$1	279	58	61	8.9999
:::	chr11:124502986-124503378(+)$1	392	15	18	8.9999
:EE	chr13:73329506-73329734(-)$1	228	4	7	8.9999
^^^	chr11:64888582-64888856(-)$1	274	18	21	8.9999
DDD	chr4:55130269-55130484(+)$1	215	90	93	8.9999
:EE	chr15:41028374-41028591(-)$1	217	13	16	8.9999
::D	chr2:207945668-207945965(-)$1	297	4	7	8.9999
::d	chr7:150270855-150271104(+)$1	249	0	3	8.9999

#DB
...	chr18:72188176-72188399(+)$1	1	11	14	8.9999
...	chr19:50161790-50162005(+)$1	1	0	3	8.9999
(..	chr14:53109232-53109481(-)$1	1	136	139	8.9999
..(	chr17:38247384-38247656(+)$1	1	12	15	8.9999
)))	chr5:55234784-55235071(-)$1	1	110	113	8.9999
...	chr13:28499709-28499924(+)$1	1	2	5	8.9999
)))	chr10:22825372-22825643(-)$1	1	87	90	8.9999
)))	chr6:143818315-143818536(-)$1	1	27	30	8.9999
(((	chr12:57490030-57490292(-)$1	1	14	17	8.9999
(((	chr12:393703-393930(-)$1	1	15	18	8.9999
(((	chr17:62895081-62895333(-)$1	1	3	6	8.9999
...	chr13:113539472-113539844(+)$1	1	16	19	8.9999
...	chr13:74263721-74264033(-)$1	1	156	159	8.9999
...	chr1:15901664-15901901(-)$1	1	0	3	8.9999
.((	chr12:133781621-133781864(+)$1	1	15	18	8.9999
)).	chr14:105777138-105777369(+)$1	1	57	60	8.9999
...	chr15:52602590-52602821(-)$1	1	2	5	8.9999
...	chr1:151025019-151025414(-)$1	1	25	28	8.9999
..(	chr19:47112367-47112591(+)$1	1	120	123	8.9999
(((	chr1:153782344-153782583(-)$1	1	14	17	8.9999
(((	chr19:7987762-7987971(+)$1	1	19	22	8.9999
.((	chr2:96049814-96050066(+)$1	1	15	18	8.9999
(..	chr1:145763632-145763845(+)$1	1	53	56	8.9999
(((	chr5:71490125-71490339(+)$1	1	8	11	8.9999
.((	chr2:9724878-9725140(-)$1	1	131	134	8.9999
(((	chr20:5527445-5527682(-)$1	1	174	177	8.9999
(((	chr3:118931616-118931898(-)$1	1	5	8	8.9999
...	chr6:111215210-111215433(+)$1	1	0	3	8.9999
(((	chr7:134343203-134343418(+)$1	1	57	60	8.9999
...	chr20:44998484-44998746(-)$1	1	242	245	8.9999
..(	chr17:80321159-80321376(+)$1	1	72	75	8.9999
(..	chr6:24805086-24805352(-)$1	1	5	8	8.9999
(((	chr6:96055877-96056102(+)$1	1	48	51	8.9999
(((	chr1:900972-901189(+)$1	1	3	6	8.9999
.((	chr6:158518341-158518565(+)$1	1	2	5	8.9999
.((	chr1:213070553-213070841(+)$1	1	3	6	8.9999
)).	chrX:64959646-64959955(+)$1	1	48	51	8.9999
...	chr13:45912237-45912463(-)$1	1	17	20	8.9999
((.	chr5:133482433-133482707(+)$1	1	5	8	8.9999
(((	chr11:68286877-68287141(+)$1	1	7	10	8.9999
...	chr3:44794573-44794817(-)$1	1	51	54	8.9999
...	chr1:145285697-145285967(+)$1	1	23	26	8.9999
..(	chr12:123087559-123087775(+)$1	1	82	85	8.9999
)).	chr7:35939879-35940143(+)$1	1	30	33	8.9999
(..	chr12:9845636-9845977(+)$1	1	48	51	8.9999
)).	chr1:70340183-70340397(+)$1	1	83	86	8.9999
.((	chr8:57129063-57129285(+)$1	1	32	35	8.9999
)))	chr9:86618324-86618540(+)$1	1	72	75	8.9999
...	chr10:115670491-115670714(+)$1	1	26	29	8.9999
(((	chr15:63599698-63599911(+)$1	1	26	29	8.9999
.))	chr1:59124787-59125054(-)$1	1	116	119	8.9999
)))	chr17:73773852-73774103(-)$1	1	107	110	8.9999
...	chr10:102283746-102283995(-)$1	1	23	26	8.9999
(.(	chr19:17935505-17935774(-)$1	1	22	25	8.9999
(..	chr2:63283759-63283972(+)$1	1	31	34	8.9999
...	chr1:202556236-202556488(+)$1	1	7	10	8.9999
..(	chr15:38782100-38782399(-)$1	1	9	12	8.9999
(((	chr1:24296244-24296469(-)$1	1	33	36	8.9999
(((	chr19:53120514-53120763(-)$1	1	6	9	8.9999
...	chr9:5919879-5920174(-)$1	1	27	30	8.9999
...	chr1:40538619-40538867(-)$1	1	116	119	8.9999
(((	chr1:204522612-204522837(+)$1	1	10	13	8.9999
...	chr1:7826528-7826800(+)$1	1	40	43	8.9999
...	chr17:4624549-4624803(+)$1	1	43	46	8.9999
.((	chr1:158909298-158909612(+)$1	1	39	42	8.9999
(((	chr6:111498461-111498674(+)$1	1	6	9	8.9999
.))	chr1:236714170-236714426(+)$1	1	166	169	8.9999
...	chr4:2839708-2839953(+)$1	1	6	9	8.9999
)))	chr11:89938783-89939123(-)$1	1	53	56	8.9999
...	chr19:49843560-49843822(+)$1	1	32	35	8.9999
...	chr16:68332200-68332480(+)$1	1	0	3	8.9999
)))	chr1:40928427-40928642(+)$1	1	61	64	8.9999
...	chr1:162334505-162334723(+)$1	1	21	24	8.9999
.))	chr9:35609891-35610105(+)$1	1	114	117	8.9999
.((	chr16:50706491-50706874(-)$1	1	9	12	8.9999
...	chr22:25465816-25466107(+)$1	1	90	93	8.9999
)).	chr6:143810287-143810537(+)$1	1	55	58	8.9999
(.(	chr7:66422682-66422975(+)$1	1	43	46	8.9999
((.	chr17:73314918-73315217(-)$1	1	21	24	8.9999
(((	chr2:99204501-99204728(+)$1	1	23	26	8.9999
(((	chr7:127010428-127010670(-)$1	1	0	3	8.9999
...	chr4:57327244-57327499(+)$1	1	13	16	8.9999
(((	chr1:161128243-161128495(+)$1	1	70	73	8.9999
(((	chr14:24593368-24593637(+)$1	1	44	47	8.9999
...	chr5:162944827-162945042(+)$1	1	140	143	8.9999
(((	chr16:15819426-15819657(+)$1	1	3	6	8.9999
(((	chr16:75203752-75203969(+)$1	1	17	20	8.9999
((.	chr4:103498778-103499017(+)$1	1	4	7	8.9999
.(.	chr4:144476068-144476347(+)$1	1	58	61	8.9999
...	chr11:124502986-124503378(+)$1	1	15	18	8.9999
.((	chr13:73329506-73329734(-)$1	1	4	7	8.9999
...	chr11:64888582-64888856(-)$1	1	18	21	8.9999
)))	chr4:55130269-55130484(+)$1	1	90	93	8.9999
.((	chr15:41028374-41028591(-)$1	1	13	16	8.9999
..(	chr2:207945668-207945965(-)$1	1	4	7	8.9999
..(	chr7:150270855-150271104(+)$1	1	0	3	8.9999

#PSSM
C : 0.81	c : 0.18	
C : 0.81	c : 0.18	
U : 0.81	u : 0.18	

#score	863.9999999999999
#seq	96
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m3_run1.nuc.txt

#NT
GCUGCCCUCCCUCGCUGCCCCCUACCCUCUCCCGGGGCUCCCGGCCCUCUACUCCCUUcgggcgcgggccccucgccccgcccgggcgcgcccccccucccccgggUCCUGCGGCCCCGGAUGCCCGGGCCCCGAGGGGCUGCUGGCGGCCUGGCCCCUGAGAUGCGCggggcgggggcggcggggcugcuggcgcugcugcugcugcugcugcugcugcugcugggccugggcggcagggucgagggggg	chr11:65325294-65325551(-)$1	257	1	252	373.0000

#otherMatches

#Struct PSSM
EBB{DDDD{BBdddd[dddd[bb!!eeeee[cccooooooccc]eeeee]bb22dddddddd:dddd!!eeeee[bblllbbeeeee22dddd::bb[bb[bb[dddd[ccclllccc]dddd22bb]bb]bb::bb[ddddfffffftttttttttttffffff22dddd]bb::::BBYYDDDD}BB}EEEEE}CCC::::::::::::::::::bbmmmmbb::::DDDDYYBB}DDDDZZZFFFFFF	chr20:57466616-57466899(+)$1	283	31	282	373.0000
:A{JJJJJJJJJJJEEEEECCC:::::::::::fffffflllffffff::::::::::ffffff[ddddnnnnnddddffffffccc[dddd%%%%%%dddddddd[dddd[cccpppppppcccdddd]dddd]dddd55555ddddccc:eeeee"""bb!!bbddddeeeee[hhhhhhhh[ccclllccc]hhhhhhhh]eeeee]dddd]bb22bb333eeeee:CCC}EEEEEZZZJJJJJJJJJ	chr11:65325294-65325551(-)$1	257	1	252	373.0000

#DB
(((.((((.((((((.((((.((..(((((.(((......))).))))).))..)))))))).((((..(((((.((...)))))))..))))..((.((.((.((((.(((...))).))))..)).)).))..((.((((((((((...........))))))..)))).))....))..)))).)).))))).)))..................((....))....))))..)).))))...))))))	chr20:57466616-57466899(+)$1	1	31	282	373.0000
.(.(((((((((((((((((((...........((((((...))))))..........((((((.((((.....))))))))))(((.((((......((((((((.((((.(((.......))))))).)))).)))).....))))))).(((((...((..(((((((((((.((((((((.(((...))).)))))))).))))).)))).))..))...))))).))).)))))...)))))))))	chr11:65325294-65325551(-)$1	1	1	252	373.0000

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

#score	746.0
#seq	2
#width	251
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m3_run2.nuc.txt

#NT
UCAGGUAGCAAUCGACCUCAGGAAAUAGAAAUUGGAGAAUCUGGUUUUGCUUUAUUAUUCCCUCAAAUUGAAGGAAUAAAAAUACAACCCUUUCAUUUUAUUAAGGAUCCAAAGAAUUUAACAUUAGAAAGACAUCAACUCACUGAAGUAGGUAAGUUACUUUUAUUUAUCAUUAACUGCUCAUUUUAUUGAUUAAUUUUGUUUUCUUUUUAAUUCUGGCUAGUUGGUGGAU	chr15:76209549-76209829(+)$1	280	35	267	323.5000

#otherMatches

#Struct PSSM
qqqqqqqeeeee:::::::::::::EEEEEKKCCC:::bb!!ggggggg"""gggggggrrrrrrrrrggggggg4444ggggggg22bb:::::ddddqqqqqqqqdddd:::::BB{FFFFFF::::==========lll==========::::::ffffff[dddd[bb!!cccooooooccc22bbdddd]ffffff:::::::FFFFFFBB______CCCYYEEEEE	chr17:57647797-57648037(+)$1	240	8	240	323.5000
bb[cccmmmmcccbb]ddddccc4444a22iiiiiiiii333dddd22bb::::ggggggg[ccclllccc]ggggggg:::::::::::::::::::::::EEEEE{BB::::::::::::=========="""ccc[ccc[ffffff[dddd[ddddwwwwwwwwwwwwwwdddddddd]ffffff]ccc666666ccc333==========dddd[annnnna]dddd:	chr15:76209549-76209829(+)$1	280	35	267	323.5000

#DB
.......))))).............(((((..(((...((..(((((((...(((((((.........)))))))....)))))))..)).....((((........)))).....((.((((((....((((((((((...))))))))))......((((((.((((.((..(((......)))..)))))).)))))).......))))))))......)))..)))))	chr17:57647797-57648037(+)$1	1	8	240	323.5000
((.(((....))))).)))))))....)..)))))))))...))))..))....(((((((.(((...))).))))))).......................(((((.((............((((((((((...(((.(((.((((((.((((.((((..............)))))))).)))))).)))......)))...))))))))))((((.(.....).)))).	chr15:76209549-76209829(+)$1	1	35	267	323.5000

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

#score	647.0
#seq	2
#width	232
#escape	false
#onStep	11847
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m1_run1.nuc.txt

#NT
CUGGG	chr9:79008978-79009218(-)$1	240	56	61	15.0000
CUGGG	chr21:30428632-30428874(-)$1	242	54	59	15.0000
CUGGG	chr19:38866897-38867130(+)$1	233	9	14	15.0000
CUGGG	chr17:11466227-11466449(+)$1	222	114	119	15.0000
CUGGG	chr14:31091398-31091624(-)$1	226	106	111	15.0000
CUGGG	chr22:50956069-50956305(+)$1	236	64	69	15.0000
CUGGG	chr1:151374216-151374472(+)$1	256	219	224	15.0000
cuggg	chr12:133332172-133332402(+)$1	230	105	110	15.0000
CUGGG	chr4:99391989-99392218(-)$1	229	89	94	15.0000
CUGGG	chr4:122744892-122745125(-)$1	233	108	113	15.0000
CUGGG	chr10:105314935-105315164(-)$1	229	58	63	15.0000
CUGGG	chr1:32833983-32834254(-)$1	271	128	133	15.0000
CUGGG	chr12:109525111-109525349(+)$1	238	11	16	15.0000
CUGGG	chr1:183595724-183595969(-)$1	245	119	124	15.0000
CUGGG	chr1:40254157-40254395(+)$1	238	20	25	15.0000
CUGGG	chr9:132399685-132399935(-)$1	250	181	186	15.0000
CUGGG	chr17:27943917-27944155(-)$1	238	30	35	15.0000
CUGGG	chr9:131570844-131571085(+)$1	241	99	104	15.0000
CUGGG	chr2:176974558-176974798(+)$1	240	57	62	15.0000
CUGGG	chr4:41262655-41262893(+)$1	238	149	154	15.0000
CUGGG	chr15:77057676-77057908(-)$1	232	141	146	15.0000
CUGGG	chr8:37557328-37557605(+)$1	277	72	77	15.0000
CUGGG	chr11:122929930-122930175(-)$1	245	159	164	15.0000
CUGGG	chr6:34501673-34501903(+)$1	230	91	96	15.0000
CUGGG	chr12:3069035-3069271(+)$1	236	162	167	15.0000
CUGGG	chr17:26690387-26690608(+)$1	221	11	16	15.0000
CUGGG	chr8:22432676-22432911(+)$1	235	51	56	15.0000
CUGGG	chr2:32503000-32503233(+)$1	233	172	177	15.0000
CUGGG	chr16:30096315-30096548(+)$1	233	145	150	15.0000
CUGGG	chr19:46283567-46283837(-)$1	270	145	150	15.0000
CUGGG	chr3:66430933-66431164(-)$1	231	62	67	15.0000
CUGGG	chr7:2770589-2770827(-)$1	238	216	221	15.0000
CUGGG	chr16:29869804-29870031(-)$1	227	37	42	15.0000
CUGGG	chr8:48686764-48687000(-)$1	236	75	80	15.0000
CUGGG	chr11:118625319-118625554(-)$1	235	38	43	15.0000
cuggg	chr11:76834974-76835202(+)$1	228	13	18	15.0000
CUGGG	chr5:137727640-137727867(+)$1	227	213	218	15.0000
CUGGG	chr1:33478868-33479102(-)$1	234	2	7	15.0000
CUGGG	chr14:76117787-76118040(-)$1	253	74	79	15.0000
CUGGG	chr19:5977968-5978198(-)$1	230	62	67	15.0000
CUGGG	chr16:3110488-3110722(+)$1	234	108	113	15.0000
CUGGG	chr11:63525863-63526115(+)$1	252	138	143	15.0000
CUGGG	chr22:39083347-39083580(-)$1	233	60	65	15.0000
CUGGG	chr7:44252724-44252983(+)$1	259	12	17	15.0000
CUGGG	chr9:96051579-96051819(+)$1	240	11	16	15.0000
CUGGG	chr17:76122988-76123212(-)$1	224	91	96	15.0000
CUGGG	chr3:49142055-49142289(-)$1	234	84	89	15.0000
CUGGG	chr16:57075817-57076040(+)$1	223	92	97	15.0000

#otherMatches

#Struct PSSM
44ddd	chr11:72300731-72300953(+)$1	222	207	212	15.0000
:::bb	chr9:79008978-79009218(-)$1	240	56	61	15.0000
::fff	chr21:30428632-30428874(-)$1	242	54	59	15.0000
PPDDD	chr19:38866897-38867130(+)$1	233	9	14	15.0000
'''ii	chr17:11466227-11466449(+)$1	222	114	119	15.0000
ddaff	chr14:31091398-31091624(-)$1	226	106	111	15.0000
]eeee	chr22:50956069-50956305(+)$1	236	64	69	15.0000
ccbbo	chr1:151374216-151374472(+)$1	256	219	224	15.0000
oeeee	chr12:133332172-133332402(+)$1	230	105	110	15.0000
mmccc	chr4:99391989-99392218(-)$1	229	89	94	15.0000
BB}FF	chr4:122744892-122745125(-)$1	233	108	113	15.0000
FFFFi	chr10:105314935-105315164(-)$1	229	58	63	15.0000
]ffff	chr1:32833983-32834254(-)$1	271	128	133	15.0000
EA{CC	chr12:109525111-109525349(+)$1	238	11	16	15.0000
::ggg	chr1:183595724-183595969(-)$1	245	119	124	15.0000
fffff	chr1:40254157-40254395(+)$1	238	20	25	15.0000
ccbbo	chr9:132399685-132399935(-)$1	250	181	186	15.0000
NNNII	chr17:27943917-27944155(-)$1	238	30	35	15.0000
qqeee	chr9:131570844-131571085(+)$1	241	99	104	15.0000
DDDOO	chr2:176974558-176974798(+)$1	240	57	62	15.0000
qccc3	chr4:41262655-41262893(+)$1	238	149	154	15.0000
hhhhh	chr15:77057676-77057908(-)$1	232	141	146	15.0000
[eeee	chr8:37557328-37557605(+)$1	277	72	77	15.0000
nccc]	chr11:122929930-122930175(-)$1	245	159	164	15.0000
ddd[b	chr6:34501673-34501903(+)$1	230	91	96	15.0000
ffff!	chr12:3069035-3069271(+)$1	236	162	167	15.0000
{EEEE	chr17:26690387-26690608(+)$1	221	11	16	15.0000
22ddd	chr8:22432676-22432911(+)$1	235	51	56	15.0000
BBYYD	chr2:32503000-32503233(+)$1	233	172	177	15.0000
c]ddd	chr16:30096315-30096548(+)$1	233	145	150	15.0000
##ddd	chr19:46283567-46283837(-)$1	270	145	150	15.0000
ppphh	chr3:66430933-66431164(-)$1	231	62	67	15.0000
BGGGG	chr7:2770589-2770827(-)$1	238	216	221	15.0000
GGDDD	chr16:29869804-29870031(-)$1	227	37	42	15.0000
DDDDc	chr8:48686764-48687000(-)$1	236	75	80	15.0000
cc[dd	chr11:118625319-118625554(-)$1	235	38	43	15.0000
LLCCC	chr11:76834974-76835202(+)$1	228	13	18	15.0000
dddDD	chr5:137727640-137727867(+)$1	227	213	218	15.0000
:::CC	chr1:33478868-33479102(-)$1	234	2	7	15.0000
fffff	chr14:76117787-76118040(-)$1	253	74	79	15.0000
ddd]b	chr19:5977968-5978198(-)$1	230	62	67	15.0000
eeee[	chr16:3110488-3110722(+)$1	234	108	113	15.0000
eeeee	chr11:63525863-63526115(+)$1	252	138	143	15.0000
2hhhh	chr22:39083347-39083580(-)$1	233	60	65	15.0000
DDDDK	chr7:44252724-44252983(+)$1	259	12	17	15.0000
!!eee	chr9:96051579-96051819(+)$1	240	11	16	15.0000
4eeee	chr17:76122988-76123212(-)$1	224	91	96	15.0000
fffff	chr3:49142055-49142289(-)$1	234	84	89	15.0000
DDDDC	chr16:57075817-57076040(+)$1	223	92	97	15.0000

#DB
..)))	chr11:72300731-72300953(+)$1	1	207	212	15.0000
...((	chr9:79008978-79009218(-)$1	1	56	61	15.0000
..(((	chr21:30428632-30428874(-)$1	1	54	59	15.0000
..(((	chr19:38866897-38867130(+)$1	1	9	14	15.0000
...((	chr17:11466227-11466449(+)$1	1	114	119	15.0000
)))))	chr14:31091398-31091624(-)$1	1	106	111	15.0000
.))))	chr22:50956069-50956305(+)$1	1	64	69	15.0000
((((.	chr1:151374216-151374472(+)$1	1	219	224	15.0000
.))))	chr12:133332172-133332402(+)$1	1	105	110	15.0000
..)))	chr4:99391989-99392218(-)$1	1	89	94	15.0000
)).))	chr4:122744892-122745125(-)$1	1	108	113	15.0000
(((((	chr10:105314935-105315164(-)$1	1	58	63	15.0000
.))))	chr1:32833983-32834254(-)$1	1	128	133	15.0000
((.((	chr12:109525111-109525349(+)$1	1	11	16	15.0000
..(((	chr1:183595724-183595969(-)$1	1	119	124	15.0000
(((((	chr1:40254157-40254395(+)$1	1	20	25	15.0000
((((.	chr9:132399685-132399935(-)$1	1	181	186	15.0000
...((	chr17:27943917-27944155(-)$1	1	30	35	15.0000
..)))	chr9:131570844-131571085(+)$1	1	99	104	15.0000
(((..	chr2:176974558-176974798(+)$1	1	57	62	15.0000
.))).	chr4:41262655-41262893(+)$1	1	149	154	15.0000
(((((	chr15:77057676-77057908(-)$1	1	141	146	15.0000
.((((	chr8:37557328-37557605(+)$1	1	72	77	15.0000
.))).	chr11:122929930-122930175(-)$1	1	159	164	15.0000
(((.(	chr6:34501673-34501903(+)$1	1	91	96	15.0000
((((.	chr12:3069035-3069271(+)$1	1	162	167	15.0000
.((((	chr17:26690387-26690608(+)$1	1	11	16	15.0000
..)))	chr8:22432676-22432911(+)$1	1	51	56	15.0000
))..)	chr2:32503000-32503233(+)$1	1	172	177	15.0000
).)))	chr16:30096315-30096548(+)$1	1	145	150	15.0000
..(((	chr19:46283567-46283837(-)$1	1	145	150	15.0000
...))	chr3:66430933-66431164(-)$1	1	62	67	15.0000
)))))	chr7:2770589-2770827(-)$1	1	216	221	15.0000
(((((	chr16:29869804-29870031(-)$1	1	37	42	15.0000
(((((	chr8:48686764-48687000(-)$1	1	75	80	15.0000
((.((	chr11:118625319-118625554(-)$1	1	38	43	15.0000
..(((	chr11:76834974-76835202(+)$1	1	13	18	15.0000
)))))	chr5:137727640-137727867(+)$1	1	213	218	15.0000
...((	chr1:33478868-33479102(-)$1	1	2	7	15.0000
(((((	chr14:76117787-76118040(-)$1	1	74	79	15.0000
))).)	chr19:5977968-5978198(-)$1	1	62	67	15.0000
((((.	chr16:3110488-3110722(+)$1	1	108	113	15.0000
(((((	chr11:63525863-63526115(+)$1	1	138	143	15.0000
.))))	chr22:39083347-39083580(-)$1	1	60	65	15.0000
((((.	chr7:44252724-44252983(+)$1	1	12	17	15.0000
..(((	chr9:96051579-96051819(+)$1	1	11	16	15.0000
.))))	chr17:76122988-76123212(-)$1	1	91	96	15.0000
(((((	chr3:49142055-49142289(-)$1	1	84	89	15.0000
(((((	chr16:57075817-57076040(+)$1	1	92	97	15.0000

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

#score	735.0000000000001
#seq	49
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m3_run2.nuc.txt

#NT
AAAAGGCAGCUCUCCUGAAAGCUUCUCCCAAAAAAGCACCUGGUACUAAGGGUAcugcugcugcugcugcugcugcugcugcugcuAAAGUUCCAGCAAAAAAGAUCACCGCCGCGAGUAAAAAGGCUCCAGCCCAGAAGGUUCCUGCCCAGAAAGCCACAGGCCAGAAAGCAGCGCCUGCUCCAAAAGCUCAGAAGGGUCAAAAAGCUCCAGCCCAGAAAGCACCUGCUCCAAAGGCAUCUGGCAAGAAAGCAUAAGUGGCAAUCAUAAAAAGUAAUAAAGGUUC	chr3:40503340-40503757(+)$1	417	126	412	373.0000

#otherMatches

#Struct PSSM
A{BBMMMMGGGGGGGccc[eeeee[a[ddddnnnnndddd]a]eeeeeccc::::EEEEE{DDDDMMMMEEEEE:::cccqqqqqqqqccc:bb[bb!!dddd&&&&&&&ccc[bb!!a[eeeee"""iiiiiiiiillliiiiiiiii4444eeeee]a22bbccc666666dddd22bb]bb:::::::EEEEE|||||||DDDD}EEEEE:bbnnnnnbb:::::::ccc[dddd!!a[bbqqqqqqqqbba22dddd]cccGGGGGGGYYBB}A~~~~BB}H	chr13:25670808-25671203(+)$1	395	84	370	373.0000
g::DDDDddddqqqqqqqqdddd:::::::::::dddd[a[fffffflllffffffa]ddddFFFFFF{CCC:eeeee!!cccnnnnnccc22eeeee::::::::::::bb[a[ddddoooooodddda]bb::::::cccmmmmccc::::::ccclllcccCCCYYFFFFFFDDDDcccnnnnnccc::::::dddduuuuuuuuuuuuddddIIIIIIIII~~~~EEEEE______DDDDYYEEEEECCCGGGGGGG:::::::ffffff[cccmmmmcccf	chr3:40503340-40503757(+)$1	417	126	412	373.0000

#DB
(.((....((((((((((.(((((.(.((((.....)))).).))))))))....(((((.((((....(((((...(((........))).((.((..((((.......(((.((..(.(((((...(((((((((...)))))))))....))))).)..)))))......))))..)).)).......))))).......)))).))))).((.....)).......(((.((((..(.((........)))..)))).))))))))))..)).)....)).)	chr13:25670808-25671203(+)$1	1	84	370	373.0000
)..((((((((........))))...........((((.(.((((((...))))))).))))((((((.(((.(((((..(((.....)))..)))))............((.(.((((......))))).))......(((....)))......(((...))))))..))))))))))(((.....)))......((((............)))))))))))))....)))))......))))..))))))))))))))).......((((((.(((....))))	chr3:40503340-40503757(+)$1	1	126	412	373.0000

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

#score	746.0
#seq	2
#width	286
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m2_run1.nuc.txt

#NT
CACUGUCUGUCCCUGACCUCAGACAACUCCUAAAAGACCCGCAAGUGCUAUUUGCUGGCUACAAAGUCCCCCACCCCUUGGAGCACAAGAUCAUCAUCCGAGUGCAGACCACGCCGGACUACAGCCCCCAGGAAGCCUUUACCAACGCCAUCACCGACCUCAUCAGUGAGCUGUCCCUGCUGGAGGAGCGCUUUCGGGUGAGGGCGGGGCCUGGAGGGGCAGACGGGGUGGGCUGGACACUGGCCCGUGUGCCCAGGCCUGGGACAGCCCUGGCCUGUUUC	chr7:102114723-102115009(-)$1	286	5	286	383.0000

#otherMatches

#Struct PSSM
GGGGGGEEEEEBB:BB{JJJJJJJJJJJ{DDDD:::DDDDMMMMBBLLLCCCEEEEE{FFFFFF:ddddbbeeeee[ccc!!cccffffffbb[bbrrrrrrrrrbb]bb]ffffff]cccccceeeee]bb7777777dddd::::::::::::ddddlllddddeeeeeooooooeeeee:::FFFFFF}EEEEE}CCCZZZBBYYDDDDcccnnnnncccDDDDJJJJJJJJJJJYYBB::::::============!!ddddqqqqqqqqdddd]==	chr16:30081364-30081837(+)$1	473	181	462	383.0000
EEEffffffssssssssssffffff:::::::::::::::fffffflllffffff:EEEEEMMMMDDDDHHHHHHHHcccnnnnnccc::::::::dddd[cccpppppppcccdddd::::::bbmmmmbb::ffffff[ccc!!ccc####ccc[ggggggg[a[dddd[bb[cccnnnnnccc]bbdddd]a]ggggggg]cccccc]cccffffff::::HHHHHHHHYYDDDDYYEEEEE}EEEEE::ffffff[cccmmmmccc]ffffff::::	chr7:102114723-102115009(-)$1	286	5	286	383.0000

#DB
))))))))))))).((.(((((((((((.((((...((((....((...((((((((.((((((.(((((((((((.(((..(((((((((((.((.........)).)).)))))).))))))))))).)).......))))............((((...))))(((((......)))))...)))))).))))).)))...))..))))(((.....))))))))))))))))))..))......((((((((((((..((((........)))).))	chr16:30081364-30081837(+)$1	1	181	462	383.0000
(((((((((..........))))))...............((((((...)))))).(((((....(((((((((((((((.....)))........((((.(((.......)))))))......((....))..((((((.(((..(((....(((.(((((((.(.((((.((.(((.....))).)))))).).))))))).)))))).)))))))))....))))))))..))))..))))).)))))..((((((.(((....))).))))))....	chr7:102114723-102115009(-)$1	1	5	286	383.0000

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

#score	766.0
#seq	2
#width	281
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m1_run1.nuc.txt

#NT
cagacacaUGUAUAUACCAacauacacacauucacauauacacacauacacaaacacaugcacacaccuacauacacucaugcacauacaugcacacacaaacauauguauauccacaugcgcacacacgugcauacacucacacacaaauauacacacacacccagauacucaugcacauacacacacaugcacacaUAUACCCacaugcacacaugcaugcauacacaugcaugcacacauauacccacaugcacacaugcaugcauacacauacaugcacacaCCACCCCCCACAGAGGCACACAUUCAUGUACAUUUAUGCAAUCAUACAAAAACACAUGuacacaccuaca	chr4:187123730-187124220(+)$1	490	90	446	480.5000

#otherMatches

#Struct PSSM
:::::::::::::::::::::::::::::::FFFFFF:ffffffqqqqqqqqffffff:ccc"""dddd[eeeeepppppppeeeee]dddd22ccc::::::::::EEEEE::cccddddoooooodddd]ccc:::::::::::::eeeeerrrrrrrrreeeee:::::::::::::EEEEEYYFFFFFF:::::::::::EEEEE{CCCDDDD:::::::::::::::::::cccmmmmccc:EEEEE{IIIIIIIII::gggggggmmmmggggggg::::::::::dddd[aeeeee[a[ccc[a!!ffffff!!ccc%%%%%%dddd[ccclllccc]ddddccc]fff	chr12:131287248-131287707(-)$1	459	8	364	480.5000
qqqqqqeeeee]ccc:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::ddddoooooodddd::::::::::GGGGGGGOOOOOOGGGGGGG:::::ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff:::::::::::ddddwwwwwwwwwwwwwwdddd::::iiiiiiiiimmmmiiiiiiiii:::::::::::::eeeeemmmmeeeeeeeeee####ffffff(((((((((bbaooooooa]bb88888888ffffff4444eeeee::::::::::::::::eeeeeooooooeeee	chr4:187123730-187124220(+)$1	490	90	446	480.5000

#DB
...............................((((((.((((((........)))))).(((...((((.(((((.......))))).))))..)))..........(((((..(((((((......)))).))).............(((((.........))))).............)))))..))))))...........(((((.(((((((...................(((....))).(((((.(((((((((..(((((((....)))))))..........((((.((((((.(.(((.(..((((((..(((......((((.(((...))).))))))).)))	chr12:131287248-131287707(-)$1	1	8	364	480.5000
......))))).))).................................................................((((......))))..........(((((((......(((((((.....((((((......................................))))))...........((((..............))))....(((((((((....))))))))).............(((((....)))))(((((....((((((.........(((......).))........))))))....)))))................(((((......))))	chr4:187123730-187124220(+)$1	1	90	446	480.5000

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

#score	961.0
#seq	2
#width	356
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m1_run2.nuc.txt

#NT
UGC	chr4:5830164-5830381(-)$1	217	19	22	8.9999
UGC	chr22:50962084-50962309(+)$1	225	10	13	8.9999
Ugc	chr14:89258707-89258947(-)$1	240	32	35	8.9999
UGC	chr3:167000132-167000351(-)$1	219	136	139	8.9999
UGC	chr2:113541182-113541403(+)$1	221	19	22	8.9999
UGC	chr15:51792040-51792255(-)$1	215	50	53	8.9999
UGC	chr15:90349304-90349522(+)$1	218	16	19	8.9999
UGC	chrX:23397886-23398101(+)$1	215	59	62	8.9999
UGC	chr17:17062177-17062404(+)$1	227	53	56	8.9999
UGC	chr7:100658836-100659055(+)$1	219	25	28	8.9999
UGC	chr13:110434898-110435125(-)$1	227	9	12	8.9999
UGC	chr12:2710964-2711193(+)$1	229	50	53	8.9999
UGC	chr3:15064655-15064875(+)$1	220	54	57	8.9999
ugc	chr14:68035731-68035955(+)$1	224	10	13	8.9999
UGC	chr12:112673482-112673699(-)$1	217	47	50	8.9999
UGC	chr7:56155189-56155431(-)$1	242	69	72	8.9999
UGC	chr3:197553753-197553980(+)$1	227	7	10	8.9999
UGC	chr16:15044067-15044286(+)$1	219	20	23	8.9999
UGC	chrX:52677311-52677527(+)$1	216	78	81	8.9999
UGC	chr2:166915043-166915283(-)$1	240	129	132	8.9999
UGC	chr4:90749199-90749416(-)$1	217	105	108	8.9999
UGC	chr5:140052852-140053073(+)$1	221	29	32	8.9999
UGC	chr9:138670224-138670442(+)$1	218	73	76	8.9999
UGC	chr1:93621794-93622015(-)$1	221	6	9	8.9999
UGC	chr4:114257721-114257956(+)$1	235	21	24	8.9999
UGC	chr15:91328208-91328425(-)$1	217	37	40	8.9999
UGC	chr5:139625489-139625712(-)$1	223	65	68	8.9999
UGC	chr17:62500239-62500468(-)$1	229	27	30	8.9999
UGC	chrX:155003882-155004133(+)$1	251	31	34	8.9999
UGC	chr20:1584655-1584904(-)$1	249	3	6	8.9999
UGC	chr10:70719867-70720084(+)$1	217	104	107	8.9999
UGC	chr22:20812022-20812246(-)$1	224	0	3	8.9999
UGC	chr11:58892194-58892411(+)$1	217	17	20	8.9999
UGC	chr4:129773275-129773495(+)$1	220	15	18	8.9999
UGC	chrX:119760890-119761109(+)$1	219	9	12	8.9999
UGC	chr12:130387781-130388007(-)$1	226	39	42	8.9999
UGC	chr14:77791102-77791334(+)$1	232	140	143	8.9999
UGC	chr7:45123884-45124100(-)$1	216	64	67	8.9999
UGC	chr1:210415105-210415327(+)$1	222	13	16	8.9999
UGC	chr1:184701871-184702105(-)$1	234	13	16	8.9999
UGC	chr13:78335093-78335313(+)$1	220	50	53	8.9999
ugc	chr4:164393729-164393945(-)$1	216	60	63	8.9999
UGC	chr7:143080129-143080345(+)$1	216	171	174	8.9999
UGC	chr22:17621875-17622127(-)$1	252	7	10	8.9999
UGC	chr4:164246656-164246882(-)$1	226	63	66	8.9999
UGC	chr22:46748116-46748344(+)$1	228	48	51	8.9999
UGC	chr6:111696894-111697114(-)$1	220	67	70	8.9999
UGC	chr2:197184979-197185196(-)$1	217	28	31	8.9999
UGC	chr3:9476416-9476631(-)$1	215	79	82	8.9999
UGC	chr18:54547234-54547460(+)$1	226	49	52	8.9999
UGC	chr22:39917364-39917598(+)$1	234	21	24	8.9999
UGC	chr11:109294455-109294684(+)$1	229	5	8	8.9999
UGC	chr17:6352598-6352845(-)$1	247	51	54	8.9999
UGC	chr1:11115775-11116008(-)$1	233	2	5	8.9999
UGC	chr20:44521361-44521598(+)$1	237	94	97	8.9999
UGC	chr16:1756312-1756539(+)$1	227	85	88	8.9999
UGC	chr8:53852770-53852990(+)$1	220	21	24	8.9999
UGC	chr22:50659061-50659277(-)$1	216	68	71	8.9999
UGC	chr19:3977170-3977385(-)$1	215	152	155	8.9999
UGC	chr17:19186892-19187124(+)$1	232	10	13	8.9999
UGC	chr7:127999340-127999557(-)$1	217	12	15	8.9999
UGC	chr13:114201488-114201720(+)$1	232	72	75	8.9999
UGC	chr6:3225331-3225558(-)$1	227	8	11	8.9999
UGC	chr11:47306976-47307211(+)$1	235	7	10	8.9999
UGC	chr19:40883793-40884023(+)$1	230	69	72	8.9999
UGC	chr17:80159690-80159914(-)$1	224	54	57	8.9999
UGC	chr2:163241136-163241352(-)$1	216	104	107	8.9999
UGC	chr20:47444277-47444498(-)$1	221	53	56	8.9999
UGC	chr17:48655547-48655763(-)$1	216	1	4	8.9999
UGC	chr6:128718595-128718817(-)$1	222	56	59	8.9999
UGC	chr1:62340839-62341063(+)$1	224	48	51	8.9999
UGC	chr16:56370623-56370842(+)$1	219	7	10	8.9999
UGC	chr20:2776184-2776399(-)$1	215	12	15	8.9999
UGC	chr1:100350079-100350299(+)$1	220	63	66	8.9999
UGC	chr7:81642689-81642914(-)$1	225	116	119	8.9999
UGC	chr1:6535990-6536246(-)$1	256	35	38	8.9999
UGC	chr9:35107351-35107579(-)$1	228	19	22	8.9999
UGC	chr16:18805824-18806039(-)$1	215	28	31	8.9999
UGC	chr17:48435770-48435996(+)$1	226	20	23	8.9999
UGC	chr1:234455776-234455993(+)$1	217	95	98	8.9999
UGC	chr19:9968392-9968619(-)$1	227	3	6	8.9999
UGC	chr10:105037222-105037443(+)$1	221	38	41	8.9999
UGC	chr16:70177301-70177519(+)$1	218	38	41	8.9999
UGC	chr17:80039377-80039614(-)$1	237	2	5	8.9999
UGC	chrX:51641280-51641502(+)$1	222	24	27	8.9999
UGC	chr5:36683930-36684161(+)$1	231	50	53	8.9999
UGC	chr6:33405937-33406157(+)$1	220	4	7	8.9999
UGC	chr19:55614671-55614889(+)$1	218	141	144	8.9999
UGC	chr15:75137343-75137563(-)$1	220	6	9	8.9999
UGC	chr12:125396996-125397216(-)$1	220	10	13	8.9999
UGC	chr19:38842998-38843216(+)$1	218	81	84	8.9999
UGC	chr11:66948760-66948975(-)$1	215	47	50	8.9999
UGC	chr12:6981313-6981535(-)$1	222	97	100	8.9999
UGC	chr16:28997396-28997611(+)$1	215	66	69	8.9999
UGC	chr11:71809275-71809500(-)$1	225	8	11	8.9999
UGC	chr9:104433281-104433496(-)$1	215	47	50	8.9999
UGC	chr11:71948414-71948636(+)$1	222	16	19	8.9999
UGC	chr12:124305034-124305250(-)$1	216	86	89	8.9999

#otherMatches

#Struct PSSM
GGG	chr14:21860825-21861056(-)$1	231	121	124	8.9999
eee	chr4:5830164-5830381(-)$1	217	19	22	8.9999
===	chr22:50962084-50962309(+)$1	225	10	13	8.9999
g:=	chr14:89258707-89258947(-)$1	240	32	35	8.9999
ggg	chr3:167000132-167000351(-)$1	219	136	139	8.9999
:ff	chr2:113541182-113541403(+)$1	221	19	22	8.9999
FFF	chr15:51792040-51792255(-)$1	215	50	53	8.9999
ccc	chr15:90349304-90349522(+)$1	218	16	19	8.9999
===	chrX:23397886-23398101(+)$1	215	59	62	8.9999
C{C	chr17:17062177-17062404(+)$1	227	53	56	8.9999
e&&	chr7:100658836-100659055(+)$1	219	25	28	8.9999
nnn	chr13:110434898-110435125(-)$1	227	9	12	8.9999
$dd	chr12:2710964-2711193(+)$1	229	50	53	8.9999
dcc	chr3:15064655-15064875(+)$1	220	54	57	8.9999
EDD	chr14:68035731-68035955(+)$1	224	10	13	8.9999
rrr	chr12:112673482-112673699(-)$1	217	47	50	8.9999
]bb	chr7:56155189-56155431(-)$1	242	69	72	8.9999
fcc	chr3:197553753-197553980(+)$1	227	7	10	8.9999
dd2	chr16:15044067-15044286(+)$1	219	20	23	8.9999
mmm	chrX:52677311-52677527(+)$1	216	78	81	8.9999
iii	chr2:166915043-166915283(-)$1	240	129	132	8.9999
$hh	chr4:90749199-90749416(-)$1	217	105	108	8.9999
:::	chr5:140052852-140053073(+)$1	221	29	32	8.9999
qqq	chr9:138670224-138670442(+)$1	218	73	76	8.9999
fcc	chr1:93621794-93622015(-)$1	221	6	9	8.9999
DDD	chr4:114257721-114257956(+)$1	235	21	24	8.9999
eee	chr15:91328208-91328425(-)$1	217	37	40	8.9999
pa2	chr5:139625489-139625712(-)$1	223	65	68	8.9999
CCC	chr17:62500239-62500468(-)$1	229	27	30	8.9999
ggg	chrX:155003882-155004133(+)$1	251	31	34	8.9999
ppp	chr20:1584655-1584904(-)$1	249	3	6	8.9999
ccc	chr10:70719867-70720084(+)$1	217	104	107	8.9999
CCC	chr22:20812022-20812246(-)$1	224	0	3	8.9999
eed	chr11:58892194-58892411(+)$1	217	17	20	8.9999
ff$	chr4:129773275-129773495(+)$1	220	15	18	8.9999
GGG	chrX:119760890-119761109(+)$1	219	9	12	8.9999
a[e	chr12:130387781-130388007(-)$1	226	39	42	8.9999
ppp	chr14:77791102-77791334(+)$1	232	140	143	8.9999
JJJ	chr7:45123884-45124100(-)$1	216	64	67	8.9999
:cc	chr1:210415105-210415327(+)$1	222	13	16	8.9999
ddd	chr1:184701871-184702105(-)$1	234	13	16	8.9999
mmm	chr13:78335093-78335313(+)$1	220	50	53	8.9999
]ae	chr4:164393729-164393945(-)$1	216	60	63	8.9999
:ee	chr7:143080129-143080345(+)$1	216	171	174	8.9999
c##	chr22:17621875-17622127(-)$1	252	7	10	8.9999
555	chr4:164246656-164246882(-)$1	226	63	66	8.9999
fff	chr22:46748116-46748344(+)$1	228	48	51	8.9999
c:E	chr6:111696894-111697114(-)$1	220	67	70	8.9999
MFF	chr2:197184979-197185196(-)$1	217	28	31	8.9999
FFF	chr3:9476416-9476631(-)$1	215	79	82	8.9999
c[c	chr18:54547234-54547460(+)$1	226	49	52	8.9999
ggg	chr22:39917364-39917598(+)$1	234	21	24	8.9999
EEB	chr11:109294455-109294684(+)$1	229	5	8	8.9999
fff	chr17:6352598-6352845(-)$1	247	51	54	8.9999
:bb	chr1:11115775-11116008(-)$1	233	2	5	8.9999
lll	chr20:44521361-44521598(+)$1	237	94	97	8.9999
===	chr16:1756312-1756539(+)$1	227	85	88	8.9999
qqq	chr8:53852770-53852990(+)$1	220	21	24	8.9999
ddm	chr22:50659061-50659277(-)$1	216	68	71	8.9999
DDD	chr19:3977170-3977385(-)$1	215	152	155	8.9999
fff	chr17:19186892-19187124(+)$1	232	10	13	8.9999
fdd	chr7:127999340-127999557(-)$1	217	12	15	8.9999
{FF	chr13:114201488-114201720(+)$1	232	72	75	8.9999
:::	chr6:3225331-3225558(-)$1	227	8	11	8.9999
KA{	chr11:47306976-47307211(+)$1	235	7	10	8.9999
]cc	chr19:40883793-40884023(+)$1	230	69	72	8.9999
hh3	chr17:80159690-80159914(-)$1	224	54	57	8.9999
]dd	chr2:163241136-163241352(-)$1	216	104	107	8.9999
mmm	chr20:47444277-47444498(-)$1	221	53	56	8.9999
DDD	chr17:48655547-48655763(-)$1	216	1	4	8.9999
KKD	chr6:128718595-128718817(-)$1	222	56	59	8.9999
:::	chr1:62340839-62341063(+)$1	224	48	51	8.9999
III	chr16:56370623-56370842(+)$1	219	7	10	8.9999
Fdd	chr20:2776184-2776399(-)$1	215	12	15	8.9999
ttt	chr1:100350079-100350299(+)$1	220	63	66	8.9999
{CC	chr7:81642689-81642914(-)$1	225	116	119	8.9999
[a!	chr1:6535990-6536246(-)$1	256	35	38	8.9999
ccc	chr9:35107351-35107579(-)$1	228	19	22	8.9999
HHD	chr16:18805824-18806039(-)$1	215	28	31	8.9999
ppd	chr17:48435770-48435996(+)$1	226	20	23	8.9999
ccc	chr1:234455776-234455993(+)$1	217	95	98	8.9999
:::	chr19:9968392-9968619(-)$1	227	3	6	8.9999
[bb	chr10:105037222-105037443(+)$1	221	38	41	8.9999
ffe	chr16:70177301-70177519(+)$1	218	38	41	8.9999
:::	chr17:80039377-80039614(-)$1	237	2	5	8.9999
ooe	chrX:51641280-51641502(+)$1	222	24	27	8.9999
hhh	chr5:36683930-36684161(+)$1	231	50	53	8.9999
:cc	chr6:33405937-33406157(+)$1	220	4	7	8.9999
555	chr19:55614671-55614889(+)$1	218	141	144	8.9999
bff	chr15:75137343-75137563(-)$1	220	6	9	8.9999
OCC	chr12:125396996-125397216(-)$1	220	10	13	8.9999
eee	chr19:38842998-38843216(+)$1	218	81	84	8.9999
"cc	chr11:66948760-66948975(-)$1	215	47	50	8.9999
ddd	chr12:6981313-6981535(-)$1	222	97	100	8.9999
2cc	chr16:28997396-28997611(+)$1	215	66	69	8.9999
EEE	chr11:71809275-71809500(-)$1	225	8	11	8.9999
hhh	chr9:104433281-104433496(-)$1	215	47	50	8.9999
sss	chr11:71948414-71948636(+)$1	222	16	19	8.9999
e]b	chr12:124305034-124305250(-)$1	216	86	89	8.9999

#DB
)))	chr14:21860825-21861056(-)$1	1	121	124	8.9999
)))	chr4:5830164-5830381(-)$1	1	19	22	8.9999
(((	chr22:50962084-50962309(+)$1	1	10	13	8.9999
).(	chr14:89258707-89258947(-)$1	1	32	35	8.9999
(((	chr3:167000132-167000351(-)$1	1	136	139	8.9999
.((	chr2:113541182-113541403(+)$1	1	19	22	8.9999
(((	chr15:51792040-51792255(-)$1	1	50	53	8.9999
(((	chr15:90349304-90349522(+)$1	1	16	19	8.9999
)))	chrX:23397886-23398101(+)$1	1	59	62	8.9999
(.(	chr17:17062177-17062404(+)$1	1	53	56	8.9999
(..	chr7:100658836-100659055(+)$1	1	25	28	8.9999
...	chr13:110434898-110435125(-)$1	1	9	12	8.9999
.((	chr12:2710964-2711193(+)$1	1	50	53	8.9999
(((	chr3:15064655-15064875(+)$1	1	54	57	8.9999
(((	chr14:68035731-68035955(+)$1	1	10	13	8.9999
...	chr12:112673482-112673699(-)$1	1	47	50	8.9999
.))	chr7:56155189-56155431(-)$1	1	69	72	8.9999
(((	chr3:197553753-197553980(+)$1	1	7	10	8.9999
)).	chr16:15044067-15044286(+)$1	1	20	23	8.9999
...	chrX:52677311-52677527(+)$1	1	78	81	8.9999
)))	chr2:166915043-166915283(-)$1	1	129	132	8.9999
.((	chr4:90749199-90749416(-)$1	1	105	108	8.9999
...	chr5:140052852-140053073(+)$1	1	29	32	8.9999
...	chr9:138670224-138670442(+)$1	1	73	76	8.9999
(((	chr1:93621794-93622015(-)$1	1	6	9	8.9999
(((	chr4:114257721-114257956(+)$1	1	21	24	8.9999
(((	chr15:91328208-91328425(-)$1	1	37	40	8.9999
.).	chr5:139625489-139625712(-)$1	1	65	68	8.9999
(((	chr17:62500239-62500468(-)$1	1	27	30	8.9999
(((	chrX:155003882-155004133(+)$1	1	31	34	8.9999
...	chr20:1584655-1584904(-)$1	1	3	6	8.9999
(((	chr10:70719867-70720084(+)$1	1	104	107	8.9999
(((	chr22:20812022-20812246(-)$1	1	0	3	8.9999
(((	chr11:58892194-58892411(+)$1	1	17	20	8.9999
((.	chr4:129773275-129773495(+)$1	1	15	18	8.9999
(((	chrX:119760890-119761109(+)$1	1	9	12	8.9999
(.(	chr12:130387781-130388007(-)$1	1	39	42	8.9999
...	chr14:77791102-77791334(+)$1	1	140	143	8.9999
(((	chr7:45123884-45124100(-)$1	1	64	67	8.9999
.((	chr1:210415105-210415327(+)$1	1	13	16	8.9999
)))	chr1:184701871-184702105(-)$1	1	13	16	8.9999
...	chr13:78335093-78335313(+)$1	1	50	53	8.9999
.))	chr4:164393729-164393945(-)$1	1	60	63	8.9999
.((	chr7:143080129-143080345(+)$1	1	171	174	8.9999
(..	chr22:17621875-17622127(-)$1	1	7	10	8.9999
...	chr4:164246656-164246882(-)$1	1	63	66	8.9999
(((	chr22:46748116-46748344(+)$1	1	48	51	8.9999
).)	chr6:111696894-111697114(-)$1	1	67	70	8.9999
.((	chr2:197184979-197185196(-)$1	1	28	31	8.9999
(((	chr3:9476416-9476631(-)$1	1	79	82	8.9999
(.(	chr18:54547234-54547460(+)$1	1	49	52	8.9999
)))	chr22:39917364-39917598(+)$1	1	21	24	8.9999
(((	chr11:109294455-109294684(+)$1	1	5	8	8.9999
)))	chr17:6352598-6352845(-)$1	1	51	54	8.9999
.((	chr1:11115775-11116008(-)$1	1	2	5	8.9999
...	chr20:44521361-44521598(+)$1	1	94	97	8.9999
(((	chr16:1756312-1756539(+)$1	1	85	88	8.9999
...	chr8:53852770-53852990(+)$1	1	21	24	8.9999
((.	chr22:50659061-50659277(-)$1	1	68	71	8.9999
)))	chr19:3977170-3977385(-)$1	1	152	155	8.9999
(((	chr17:19186892-19187124(+)$1	1	10	13	8.9999
(((	chr7:127999340-127999557(-)$1	1	12	15	8.9999
.((	chr13:114201488-114201720(+)$1	1	72	75	8.9999
...	chr6:3225331-3225558(-)$1	1	8	11	8.9999
.(.	chr11:47306976-47307211(+)$1	1	7	10	8.9999
.))	chr19:40883793-40884023(+)$1	1	69	72	8.9999
)).	chr17:80159690-80159914(-)$1	1	54	57	8.9999
.))	chr2:163241136-163241352(-)$1	1	104	107	8.9999
...	chr20:47444277-47444498(-)$1	1	53	56	8.9999
(((	chr17:48655547-48655763(-)$1	1	1	4	8.9999
..(	chr6:128718595-128718817(-)$1	1	56	59	8.9999
...	chr1:62340839-62341063(+)$1	1	48	51	8.9999
(((	chr16:56370623-56370842(+)$1	1	7	10	8.9999
(((	chr20:2776184-2776399(-)$1	1	12	15	8.9999
...	chr1:100350079-100350299(+)$1	1	63	66	8.9999
.((	chr7:81642689-81642914(-)$1	1	116	119	8.9999
.(.	chr1:6535990-6536246(-)$1	1	35	38	8.9999
(((	chr9:35107351-35107579(-)$1	1	19	22	8.9999
(((	chr16:18805824-18806039(-)$1	1	28	31	8.9999
..)	chr17:48435770-48435996(+)$1	1	20	23	8.9999
)))	chr1:234455776-234455993(+)$1	1	95	98	8.9999
...	chr19:9968392-9968619(-)$1	1	3	6	8.9999
.((	chr10:105037222-105037443(+)$1	1	38	41	8.9999
))(	chr16:70177301-70177519(+)$1	1	38	41	8.9999
...	chr17:80039377-80039614(-)$1	1	2	5	8.9999
..)	chrX:51641280-51641502(+)$1	1	24	27	8.9999
(((	chr5:36683930-36684161(+)$1	1	50	53	8.9999
.((	chr6:33405937-33406157(+)$1	1	4	7	8.9999
...	chr19:55614671-55614889(+)$1	1	141	144	8.9999
(((	chr15:75137343-75137563(-)$1	1	6	9	8.9999
.((	chr12:125396996-125397216(-)$1	1	10	13	8.9999
)))	chr19:38842998-38843216(+)$1	1	81	84	8.9999
.((	chr11:66948760-66948975(-)$1	1	47	50	8.9999
)))	chr12:6981313-6981535(-)$1	1	97	100	8.9999
.))	chr16:28997396-28997611(+)$1	1	66	69	8.9999
(((	chr11:71809275-71809500(-)$1	1	8	11	8.9999
)))	chr9:104433281-104433496(-)$1	1	47	50	8.9999
...	chr11:71948414-71948636(+)$1	1	16	19	8.9999
).)	chr12:124305034-124305250(-)$1	1	86	89	8.9999

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

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m1_run1.nuc.txt

#NT
CUUUUCU	chr8:48874045-48874318(+)$1	273	6	13	13.0422
AUUUUCU	chr15:23043328-23043576(-)$1	248	15	22	12.9718
UUUUUGU	chr4:6709334-6709595(-)$1	261	109	116	13.3943
UUUUACU	chr22:41231508-41231767(-)$1	259	49	56	12.9718
UUUUUCA	chr10:111894016-111894257(+)$1	241	15	22	13.0422
uuuuuuu	chr16:31202625-31202897(+)$1	272	73	80	13.3943
UUUUUCA	chr13:31499237-31499488(+)$1	251	185	192	13.0422
UCUUUCU	chr13:98674470-98674789(+)$1	319	18	25	13.3239
UUUUUGU	chr10:3178735-3178991(+)$1	256	80	87	13.3943
UUUUUCU	chr1:245017417-245017699(-)$1	282	92	99	17.1267
UUUUUCA	chr11:33762747-33763013(-)$1	266	137	144	13.0422
UUUUUGU	chr16:3776640-3776891(-)$1	251	128	135	13.3943
UUUUUCU	chr6:45518657-45518910(+)$1	253	88	95	17.1267
UUUUUCA	chr11:65622176-65622504(-)$1	328	242	249	13.0422
UUUUUAU	chr12:49413182-49413450(-)$1	268	188	195	13.2535
UUUUGCU	chr3:156271399-156271669(-)$1	270	56	63	13.1830
UUUUUCU	chr8:67955224-67955474(-)$1	250	197	204	17.1267
UAUUUCU	chr11:33772054-33772293(-)$1	239	186	193	13.5352
GUUUUCU	chr13:42807620-42807859(+)$1	239	85	92	12.9014
UAUUUCU	chr1:153778948-153779207(-)$1	259	65	72	13.5352
UUUUUCC	chr12:16516653-16516955(+)$1	302	64	71	13.1126
UUUUUCU	chr16:50070834-50071093(+)$1	259	171	178	17.1267
UGUUUCU	chr8:103839699-103839940(-)$1	241	0	7	13.4647
UUUUUCU	chr2:135209491-135209730(+)$1	239	101	108	17.1267
UAUUUCU	chr12:56511472-56511715(+)$1	243	61	68	13.5352
uuuuucu	chr19:2070929-2071203(-)$1	274	257	264	17.1267
UUUUUUU	chrX:77381532-77381804(+)$1	272	238	245	13.3943
UUUUUCU	chrX:41378899-41379161(-)$1	262	7	14	17.1267
UUUUGCU	chr20:62605366-62605649(-)$1	283	113	120	13.1830
UUUUUAU	chr1:193056260-193056500(+)$1	240	142	149	13.2535
UUUUUCU	chr3:193412430-193412683(+)$1	253	32	39	17.1267
UUUUUCU	chr4:39780235-39780475(+)$1	240	36	43	17.1267
UGUUUCU	chr7:66703694-66703953(+)$1	259	10	17	13.4647
UUUUCCU	chr6:89321861-89322115(-)$1	254	92	99	13.0422
UAUUUCU	chr19:30314806-30315058(+)$1	252	6	13	13.5352
UUUUACU	chr8:61533329-61533598(+)$1	269	5	12	12.9718
UUUUUCU	chr17:58143539-58143778(-)$1	239	3	10	17.1267
UUUUCCU	chr1:185069733-185069973(+)$1	240	43	50	13.0422
UUUUUCU	chr16:24829828-24830083(+)$1	255	26	33	17.1267
AUUUUCU	chr18:43667257-43667496(-)$1	239	28	35	12.9718
UUUUUUU	chr6:44221295-44221722(+)$1	427	151	158	13.3943
UUUUGCU	chr17:38140590-38140841(+)$1	251	124	131	13.1830
UGUUUCU	chr11:63678345-63678586(+)$1	241	159	166	13.4647
UUUUUCC	chr17:47366839-47367085(-)$1	246	194	201	13.1126
UUUUUCU	chr15:25223448-25223711(+)$1	263	75	82	17.1267
UAUUUCU	chr5:72209856-72210095(+)$1	239	122	129	13.5352
uuuuuuu	chr7:5567067-5567315(-)$1	248	25	32	13.3943
CUUUUCU	chr5:170833328-170833593(+)$1	265	208	215	13.0422
AUUUUCU	chr15:90815267-90815527(+)$1	260	24	31	12.9718
UUUUUAU	chr8:29931328-29931588(-)$1	260	232	239	13.2535
UUUUUGU	chr14:35181752-35182023(-)$1	271	34	41	13.3943
UUUUUCC	chr18:60790967-60791211(-)$1	244	170	177	13.1126
CUUUUCU	chr5:167977803-167978061(-)$1	258	29	36	13.0422
UUUUCCU	chr9:126163886-126164138(-)$1	252	130	137	13.0422
UUUUGCU	chr16:89333936-89334175(-)$1	239	22	29	13.1830
GUUUUCU	chr3:32495953-32496269(+)$1	316	47	54	12.9014
UUUUUCC	chr2:106510269-106510511(+)$1	242	22	29	13.1126
UGUUUCU	chr17:49042922-49043164(-)$1	242	168	175	13.4647
UUUUUCU	chr4:140210985-140211297(-)$1	312	35	42	17.1267
UUUUUUU	chr2:64859555-64859787(-)$1	232	73	80	13.3943
UAUUUCU	chr16:71957095-71957392(+)$1	297	10	17	13.5352
CUUUUCU	chr2:219118638-219118886(+)$1	248	234	241	13.0422
UUUUUCU	chr19:12903615-12903855(+)$1	240	219	226	17.1267
UGUUUCU	chr14:102323071-102323297(+)$1	226	21	28	13.4647
UUUUUGU	chr14:54941998-54942273(-)$1	275	29	36	13.3943
UUUUUCU	chr13:60240523-60240764(-)$1	241	202	209	17.1267
UUUUUCC	chr7:12375678-12375923(-)$1	245	173	180	13.1126
UUUUGCU	chr8:142205548-142205792(+)$1	244	218	225	13.1830
UCUUUCU	chr11:46698734-46698981(-)$1	247	196	203	13.3239
UUUUUCU	chr3:63996134-63996375(-)$1	241	157	164	17.1267

#otherMatches

#Struct PSSM
ffnnnnn	chr2:178407855-178408107(+)$1	252	66	73	13.3239
ffffddd	chr8:48874045-48874318(+)$1	273	6	13	13.0422
iiiiiii	chr15:23043328-23043576(-)$1	248	15	22	12.9718
hhhhhhh	chr4:6709334-6709595(-)$1	261	109	116	13.3943
+++hhhh	chr22:41231508-41231767(-)$1	259	49	56	12.9718
ttttttt	chr10:111894016-111894257(+)$1	241	15	22	13.0422
:::::::	chr16:31202625-31202897(+)$1	272	73	80	13.3943
@@@@@@@	chr13:31499237-31499488(+)$1	251	185	192	13.0422
ddd"""c	chr13:98674470-98674789(+)$1	319	18	25	13.3239
$$$$$ee	chr10:3178735-3178991(+)$1	256	80	87	13.3943
:::::::	chr1:245017417-245017699(-)$1	282	92	99	17.1267
===::CC	chr11:33762747-33763013(-)$1	266	137	144	13.0422
ffffooo	chr16:3776640-3776891(-)$1	251	128	135	13.3943
cpppppp	chr6:45518657-45518910(+)$1	253	88	95	17.1267
@@@@@@@	chr11:65622176-65622504(-)$1	328	242	249	13.0422
vvvvvvv	chr12:49413182-49413450(-)$1	268	188	195	13.2535
e!!eeee	chr3:156271399-156271669(-)$1	270	56	63	13.1830
eennnnn	chr8:67955224-67955474(-)$1	250	197	204	17.1267
&&&&&&c	chr11:33772054-33772293(-)$1	239	186	193	13.5352
d]dddd2	chr13:42807620-42807859(+)$1	239	85	92	12.9014
ffffff:	chr1:153778948-153779207(-)$1	259	65	72	13.5352
hhhhhh:	chr12:16516653-16516955(+)$1	302	64	71	13.1126
e++++++	chr16:50070834-50071093(+)$1	259	171	178	17.1267
FFFFFFe	chr8:103839699-103839940(-)$1	241	0	7	13.4647
:::::::	chr2:135209491-135209730(+)$1	239	101	108	17.1267
:::::::	chr12:56511472-56511715(+)$1	243	61	68	13.5352
sgggggg	chr19:2070929-2071203(-)$1	274	257	264	17.1267
:::::::	chrX:77381532-77381804(+)$1	272	238	245	13.3943
:::::::	chrX:41378899-41379161(-)$1	262	7	14	17.1267
b[eeeee	chr20:62605366-62605649(-)$1	283	113	120	13.1830
ggggg::	chr1:193056260-193056500(+)$1	240	142	149	13.2535
DDKKEEE	chr3:193412430-193412683(+)$1	253	32	39	17.1267
rrrrrrd	chr4:39780235-39780475(+)$1	240	36	43	17.1267
:DDDDLL	chr7:66703694-66703953(+)$1	259	10	17	13.4647
77777==	chr6:89321861-89322115(-)$1	254	92	99	13.0422
NNNNGGG	chr19:30314806-30315058(+)$1	252	6	13	13.5352
:::::::	chr8:61533329-61533598(+)$1	269	5	12	12.9718
DD{GGGG	chr17:58143539-58143778(-)$1	239	3	10	17.1267
:::::::	chr1:185069733-185069973(+)$1	240	43	50	13.0422
ffff333	chr16:24829828-24830083(+)$1	255	26	33	17.1267
eeeee]c	chr18:43667257-43667496(-)$1	239	28	35	12.9718
YHHHHHH	chr6:44221295-44221722(+)$1	427	151	158	13.3943
nnnnacc	chr17:38140590-38140841(+)$1	251	124	131	13.1830
:IIIIII	chr11:63678345-63678586(+)$1	241	159	166	13.4647
=======	chr17:47366839-47367085(-)$1	246	194	201	13.1126
^^^^^^^	chr15:25223448-25223711(+)$1	263	75	82	17.1267
eeeee[g	chr5:72209856-72210095(+)$1	239	122	129	13.5352
DLLLEEE	chr7:5567067-5567315(-)$1	248	25	32	13.3943
xxxxxxx	chr5:170833328-170833593(+)$1	265	208	215	13.0422
ooooooc	chr15:90815267-90815527(+)$1	260	24	31	12.9718
JJJJJJJ	chr8:29931328-29931588(-)$1	260	232	239	13.2535
I:::eee	chr14:35181752-35182023(-)$1	271	34	41	13.3943
&&&&&&&	chr18:60790967-60791211(-)$1	244	170	177	13.1126
a::::EE	chr5:167977803-167978061(-)$1	258	29	36	13.0422
oooooob	chr9:126163886-126164138(-)$1	252	130	137	13.0422
####bb+	chr16:89333936-89334175(-)$1	239	22	29	13.1830
b4444dd	chr3:32495953-32496269(+)$1	316	47	54	12.9014
:GGGGGG	chr2:106510269-106510511(+)$1	242	22	29	13.1126
3ffffff	chr17:49042922-49043164(-)$1	242	168	175	13.4647
+++++++	chr4:140210985-140211297(-)$1	312	35	42	17.1267
ggg!!bb	chr2:64859555-64859787(-)$1	232	73	80	13.3943
{CCCLLL	chr16:71957095-71957392(+)$1	297	10	17	13.5352
666ffff	chr2:219118638-219118886(+)$1	248	234	241	13.0422
ggqqqqq	chr19:12903615-12903855(+)$1	240	219	226	17.1267
eccc[bb	chr14:102323071-102323297(+)$1	226	21	28	13.4647
pppppa]	chr14:54941998-54942273(-)$1	275	29	36	13.3943
ffffff9	chr13:60240523-60240764(-)$1	241	202	209	17.1267
ooooddd	chr7:12375678-12375923(-)$1	245	173	180	13.1126
fffcccm	chr8:142205548-142205792(+)$1	244	218	225	13.1830
[aqqqqq	chr11:46698734-46698981(-)$1	247	196	203	13.3239
ii:::::	chr3:63996134-63996375(-)$1	241	157	164	17.1267

#DB
((.....	chr2:178407855-178408107(+)$1	1	66	73	13.3239
(((((((	chr8:48874045-48874318(+)$1	1	6	13	13.0422
(((((((	chr15:23043328-23043576(-)$1	1	15	22	12.9718
)))))))	chr4:6709334-6709595(-)$1	1	109	116	13.3943
...((((	chr22:41231508-41231767(-)$1	1	49	56	12.9718
.......	chr10:111894016-111894257(+)$1	1	15	22	13.0422
.......	chr16:31202625-31202897(+)$1	1	73	80	13.3943
.......	chr13:31499237-31499488(+)$1	1	185	192	13.0422
(((...(	chr13:98674470-98674789(+)$1	1	18	25	13.3239
.....((	chr10:3178735-3178991(+)$1	1	80	87	13.3943
.......	chr1:245017417-245017699(-)$1	1	92	99	17.1267
)))..((	chr11:33762747-33763013(-)$1	1	137	144	13.0422
((((...	chr16:3776640-3776891(-)$1	1	128	135	13.3943
(......	chr6:45518657-45518910(+)$1	1	88	95	17.1267
.......	chr11:65622176-65622504(-)$1	1	242	249	13.0422
.......	chr12:49413182-49413450(-)$1	1	188	195	13.2535
(..((((	chr3:156271399-156271669(-)$1	1	56	63	13.1830
((.....	chr8:67955224-67955474(-)$1	1	197	204	17.1267
......(	chr11:33772054-33772293(-)$1	1	186	193	13.5352
).)))).	chr13:42807620-42807859(+)$1	1	85	92	12.9014
)))))).	chr1:153778948-153779207(-)$1	1	65	72	13.5352
)))))).	chr12:16516653-16516955(+)$1	1	64	71	13.1126
(......	chr16:50070834-50071093(+)$1	1	171	178	17.1267
(((((((	chr8:103839699-103839940(-)$1	1	0	7	13.4647
.......	chr2:135209491-135209730(+)$1	1	101	108	17.1267
.......	chr12:56511472-56511715(+)$1	1	61	68	13.5352
.))))))	chr19:2070929-2071203(-)$1	1	257	264	17.1267
.......	chrX:77381532-77381804(+)$1	1	238	245	13.3943
.......	chrX:41378899-41379161(-)$1	1	7	14	17.1267
(.(((((	chr20:62605366-62605649(-)$1	1	113	120	13.1830
)))))..	chr1:193056260-193056500(+)$1	1	142	149	13.2535
((..(((	chr3:193412430-193412683(+)$1	1	32	39	17.1267
......)	chr4:39780235-39780475(+)$1	1	36	43	17.1267
.((((..	chr7:66703694-66703953(+)$1	1	10	17	13.4647
.....))	chr6:89321861-89322115(-)$1	1	92	99	13.0422
....(((	chr19:30314806-30315058(+)$1	1	6	13	13.5352
.......	chr8:61533329-61533598(+)$1	1	5	12	12.9718
((.((((	chr17:58143539-58143778(-)$1	1	3	10	17.1267
.......	chr1:185069733-185069973(+)$1	1	43	50	13.0422
))))...	chr16:24829828-24830083(+)$1	1	26	33	17.1267
))))).)	chr18:43667257-43667496(-)$1	1	28	35	12.9718
.))))))	chr6:44221295-44221722(+)$1	1	151	158	13.3943
....)))	chr17:38140590-38140841(+)$1	1	124	131	13.1830
.((((((	chr11:63678345-63678586(+)$1	1	159	166	13.4647
)))))))	chr17:47366839-47367085(-)$1	1	194	201	13.1126
.......	chr15:25223448-25223711(+)$1	1	75	82	17.1267
(((((.(	chr5:72209856-72210095(+)$1	1	122	129	13.5352
(...(((	chr7:5567067-5567315(-)$1	1	25	32	13.3943
.......	chr5:170833328-170833593(+)$1	1	208	215	13.0422
......)	chr15:90815267-90815527(+)$1	1	24	31	12.9718
)))))))	chr8:29931328-29931588(-)$1	1	232	239	13.2535
(...(((	chr14:35181752-35182023(-)$1	1	34	41	13.3943
.......	chr18:60790967-60791211(-)$1	1	170	177	13.1126
)....((	chr5:167977803-167978061(-)$1	1	29	36	13.0422
......)	chr9:126163886-126164138(-)$1	1	130	137	13.0422
....((.	chr16:89333936-89334175(-)$1	1	22	29	13.1830
)....))	chr3:32495953-32496269(+)$1	1	47	54	12.9014
.((((((	chr2:106510269-106510511(+)$1	1	22	29	13.1126
.))))))	chr17:49042922-49043164(-)$1	1	168	175	13.4647
.......	chr4:140210985-140211297(-)$1	1	35	42	17.1267
(((..((	chr2:64859555-64859787(-)$1	1	73	80	13.3943
.(((...	chr16:71957095-71957392(+)$1	1	10	17	13.5352
...))))	chr2:219118638-219118886(+)$1	1	234	241	13.0422
((.....	chr19:12903615-12903855(+)$1	1	219	226	17.1267
((((.((	chr14:102323071-102323297(+)$1	1	21	28	13.4647
.....).	chr14:54941998-54942273(-)$1	1	29	36	13.3943
)))))).	chr13:60240523-60240764(-)$1	1	202	209	17.1267
....)))	chr7:12375678-12375923(-)$1	1	173	180	13.1126
((((((.	chr8:142205548-142205792(+)$1	1	218	225	13.1830
.(.....	chr11:46698734-46698981(-)$1	1	196	203	13.3239
)).....	chr3:63996134-63996375(-)$1	1	157	164	17.1267

#PSSM
U : 0.83	C : 0.05	A : 0.04	u : 0.04	G : 0.02	
U : 0.76	A : 0.08	G : 0.07	C : 0.04	u : 0.04	
U : 0.95	u : 0.04	
U : 0.95	u : 0.04	
U : 0.81	G : 0.07	u : 0.04	C : 0.04	A : 0.02	
C : 0.80	G : 0.07	A : 0.04	U : 0.04	u : 0.02	c : 0.01	
U : 0.83	C : 0.07	A : 0.05	u : 0.04	

#score	1001.8450704225348
#seq	71
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m1_run2.nuc.txt

#NT
AAAAUUAA	chr2:160087950-160088190(+)$1	240	46	54	13.5205
AAAAUCUG	chr17:38545619-38545859(-)$1	240	22	30	11.9452
AAAAUCCU	chr7:138983011-138983251(+)$1	240	112	120	12.8356
AAAAUAGC	chr2:113315505-113315745(+)$1	240	11	19	12.3561
AAAAUCCA	chr17:35980842-35981082(-)$1	240	7	15	12.9041
AAAAUUCU	chr15:99673725-99674005(+)$1	280	46	54	13.4520
AAAAUUUC	chr12:68053772-68054012(+)$1	240	85	93	12.9726
AAAAUAAA	chr9:14084339-14084579(-)$1	240	59	67	13.9315
AAAAUCUU	chr17:58524360-58524600(-)$1	240	108	116	13.2465
AAAAUUUG	chr4:139086053-139086333(-)$1	280	21	29	12.5616
AAAAUUUU	chr21:43408538-43408778(-)$1	240	13	21	13.8630
AAAAUAGA	chr21:28208539-28208779(-)$1	240	119	127	13.3150
AAAAUAUU	chr17:53470547-53470787(-)$1	240	182	190	14.2739
aaaauuau	chr20:46284357-46284597(+)$1	240	145	153	13.4520
aaaaUAAC	chr3:121448025-121448265(-)$1	240	4	12	12.9726
AAAAUGUA	chr7:914093-914333(+)$1	240	191	199	13.6575
AAAAUGAA	chr10:88950934-88951174(+)$1	240	16	24	13.2465
AAAAUUAA	chr21:40887146-40887386(+)$1	240	20	28	13.5205
AAAAUACU	chr20:43996724-43996964(+)$1	240	165	173	13.8630
AAAAUAAA	chr14:93406149-93406389(-)$1	240	156	164	13.9315
AAAAUUGC	chr11:110100795-110101035(-)$1	240	110	118	11.9452
AAAAUGAA	chr10:22045417-22045657(-)$1	240	76	84	13.2465
AAAAUUCU	chr16:97000-97240(-)$1	240	220	228	13.4520
aaaauaga	chr6:97702463-97702703(-)$1	240	19	27	13.3150
AAAAUACU	chr2:42558933-42559173(+)$1	240	75	83	13.8630
AAAAUCUC	chr8:67545137-67545377(-)$1	240	9	17	12.3561
AAAAUGCU	chr7:108213838-108214078(+)$1	240	139	147	13.1780
AAAAUCAA	chr9:79002021-79002261(-)$1	240	31	39	12.9041
AAAAUAUG	chr12:53808839-53809079(+)$1	240	110	118	12.9726
AAAAUGAA	chr7:138728737-138729057(-)$1	320	17	25	13.2465
AAAAUAUA	chr2:222290015-222290255(-)$1	240	118	126	14.3424
AAAAUGAC	chr1:151375892-151376132(-)$1	240	16	24	12.2876
AAAAUGUG	chr2:139329775-139330015(+)$1	240	2	10	12.2876
AAAAUACU	chr1:150190962-150191202(-)$1	240	18	26	13.8630
AAAAUUUC	chr2:230899611-230899851(-)$1	240	176	184	12.9726
AAAAUGUA	chr13:53049621-53049861(+)$1	240	11	19	13.6575
AAAAUUUU	chr4:83847716-83847956(-)$1	240	17	25	13.8630
AAAAUGUA	chr6:79648520-79648760(-)$1	240	4	12	13.6575
AAAAUCAU	chr17:21438594-21438834(-)$1	240	115	123	12.8356
AAAAUUCU	chr11:82642974-82643214(+)$1	240	113	121	13.4520
AAAAUACU	chr3:113437752-113437992(-)$1	240	50	58	13.8630
AAAAUUGU	chr17:33678663-33678903(-)$1	240	117	125	12.8356
AAAAUCGU	chr10:69677564-69677804(+)$1	240	232	240	12.2191
AAAAUAGC	chr8:131064594-131064834(-)$1	240	170	178	12.3561
AAAAUUCU	chr18:22032383-22032623(+)$1	240	194	202	13.4520
AAAAUGUG	chr5:90664748-90664988(-)$1	240	38	46	12.2876
AAAAUUUA	chr16:69151839-69152079(-)$1	240	3	11	13.9315
AAAAUAGA	chr3:100083945-100084185(-)$1	240	199	207	13.3150
AAAAUGGC	chr16:15154379-15154619(-)$1	240	209	217	11.6712
AAAAUGUC	chr6:89319890-89320130(-)$1	240	70	78	12.6986
AAAAUCAG	chr3:45786557-45786797(+)$1	240	3	11	11.5342
AAAAUAUA	chr2:178084968-178085208(+)$1	240	127	135	14.3424
AAAAUGAC	chr6:82879876-82880116(-)$1	240	62	70	12.2876
AAAAUUUA	chr4:68483477-68483757(-)$1	280	61	69	13.9315
AAAAUUAG	chr9:5775242-5775482(+)$1	240	33	41	12.1506
AAAAUCAA	chr9:101912471-101912711(+)$1	240	74	82	12.9041
AAAAUACA	chrX:70520779-70521019(+)$1	240	216	224	13.9315
AAAAUUCA	chr14:103372452-103372692(+)$1	240	118	126	13.5205
AAAAUACU	chrX:44970987-44971227(+)$1	240	37	45	13.8630
AAAAUUCA	chr9:111781950-111782190(-)$1	240	190	198	13.5205
AAAAUGAA	chr10:29746388-29746628(-)$1	240	51	59	13.2465
AAAAUGAA	chr2:204296419-204296659(+)$1	240	124	132	13.2465
AAAAUACU	chr7:102944321-102944561(+)$1	240	117	125	13.8630
AAAAUAUU	chr1:8072623-8072863(-)$1	240	49	57	14.2739
AAAAUAUA	chr8:59494822-59495062(+)$1	240	102	110	14.3424
AAAAUCUA	chr14:55258641-55258881(+)$1	240	10	18	13.3150
AAAAUACC	chr16:22358183-22358423(-)$1	240	107	115	12.9726
AAAAUUCU	chrX:108886560-108886800(-)$1	240	0	8	13.4520
aaaauauu	chr5:142608121-142608361(+)$1	240	35	43	14.2739
AAAAUAAU	chr2:26512750-26512990(+)$1	240	64	72	13.8630
AAAAUGGU	chr17:36891141-36891421(-)$1	280	193	201	12.5616
AAAAUAUC	chr5:135514861-135515101(+)$1	240	32	40	13.3835

#otherMatches

#Struct PSSM
::::::::	chr8:120743082-120743322(-)$1	240	232	240	13.8630
fff:::::	chr2:160087950-160088190(+)$1	240	46	54	13.5205
:::::::d	chr17:38545619-38545859(-)$1	240	22	30	11.9452
EEYYFFFF	chr7:138983011-138983251(+)$1	240	112	120	12.8356
:::::::G	chr2:113315505-113315745(+)$1	240	11	19	12.3561
eeeee[bb	chr17:35980842-35981082(-)$1	240	7	15	12.9041
:::::::b	chr15:99673725-99674005(+)$1	280	46	54	13.4520
ccc333cc	chr12:68053772-68054012(+)$1	240	85	93	12.9726
::::::::	chr9:14084339-14084579(-)$1	240	59	67	13.9315
dd22hhhh	chr17:58524360-58524600(-)$1	240	108	116	13.2465
ff666666	chr4:139086053-139086333(-)$1	280	21	29	12.5616
ooooofff	chr21:43408538-43408778(-)$1	240	13	21	13.8630
ff333eee	chr21:28208539-28208779(-)$1	240	119	127	13.3150
=======:	chr17:53470547-53470787(-)$1	240	182	190	14.2739
qqqqqqqe	chr20:46284357-46284597(+)$1	240	145	153	13.4520
::::::EE	chr3:121448025-121448265(-)$1	240	4	12	12.9726
ggggggg:	chr7:914093-914333(+)$1	240	191	199	13.6575
::ffffff	chr10:88950934-88951174(+)$1	240	16	24	13.2465
::::::::	chr21:40887146-40887386(+)$1	240	20	28	13.5205
oooooccc	chr20:43996724-43996964(+)$1	240	165	173	13.8630
c:::::::	chr14:93406149-93406389(-)$1	240	156	164	13.9315
eee]bbbb	chr11:110100795-110101035(-)$1	240	110	118	11.9452
=4444fff	chr10:22045417-22045657(-)$1	240	76	84	13.2465
cc::::::	chr16:97000-97240(-)$1	240	220	228	13.4520
:::FFFFF	chr6:97702463-97702703(-)$1	240	19	27	13.3150
goooooog	chr2:42558933-42559173(+)$1	240	75	83	13.8630
GGGGG::f	chr8:67545137-67545377(-)$1	240	9	17	12.3561
dddd[bb+	chr7:108213838-108214078(+)$1	240	139	147	13.1780
e"""cccc	chr9:79002021-79002261(-)$1	240	31	39	12.9041
:::::::d	chr12:53808839-53809079(+)$1	240	110	118	12.9726
::::::::	chr7:138728737-138729057(-)$1	320	17	25	13.2465
zzzzzzzz	chr2:222290015-222290255(-)$1	240	118	126	14.3424
cc!!bb[b	chr1:151375892-151376132(-)$1	240	16	24	12.2876
:::::ddd	chr2:139329775-139330015(+)$1	240	2	10	12.2876
b^^^^^^^	chr1:150190962-150191202(-)$1	240	18	26	13.8630
gggggmmm	chr2:230899611-230899851(-)$1	240	176	184	12.9726
gggppppp	chr13:53049621-53049861(+)$1	240	11	19	13.6575
JJJJJFFF	chr4:83847716-83847956(-)$1	240	17	25	13.8630
hhhhhhhh	chr6:79648520-79648760(-)$1	240	4	12	13.6575
xxxxxxxx	chr17:21438594-21438834(-)$1	240	115	123	12.8356
ttteeeee	chr11:82642974-82643214(+)$1	240	113	121	13.4520
::ccc[ee	chr3:113437752-113437992(-)$1	240	50	58	13.8630
eee:::::	chr17:33678663-33678903(-)$1	240	117	125	12.8356
ZZZCCC::	chr10:69677564-69677804(+)$1	240	232	240	12.2191
^^^^^^^^	chr8:131064594-131064834(-)$1	240	170	178	12.3561
qqqqffff	chr18:22032383-22032623(+)$1	240	194	202	13.4520
dllldddd	chr5:90664748-90664988(-)$1	240	38	46	12.2876
::::::::	chr16:69151839-69152079(-)$1	240	3	11	13.9315
=====22i	chr3:100083945-100084185(-)$1	240	199	207	13.3150
JJJJJGGG	chr16:15154379-15154619(-)$1	240	209	217	11.6712
55555ddd	chr6:89319890-89320130(-)$1	240	70	78	12.6986
::::::::	chr3:45786557-45786797(+)$1	240	3	11	11.5342
eeee"""b	chr2:178084968-178085208(+)$1	240	127	135	14.3424
::::::::	chr6:82879876-82880116(-)$1	240	62	70	12.2876
eeeennnn	chr4:68483477-68483757(-)$1	280	61	69	13.9315
ellleeee	chr9:5775242-5775482(+)$1	240	33	41	12.1506
ff::::gg	chr9:101912471-101912711(+)$1	240	74	82	12.9041
::::::::	chrX:70520779-70521019(+)$1	240	216	224	13.9315
zzzzzbb]	chr14:103372452-103372692(+)$1	240	118	126	13.5205
ccc!!fff	chrX:44970987-44971227(+)$1	240	37	45	13.8630
ooooo===	chr9:111781950-111782190(-)$1	240	190	198	13.5205
55555ddd	chr10:29746388-29746628(-)$1	240	51	59	13.2465
b!!fffff	chr2:204296419-204296659(+)$1	240	124	132	13.2465
dd22a]dd	chr7:102944321-102944561(+)$1	240	117	125	13.8630
eeeeeemm	chr1:8072623-8072863(-)$1	240	49	57	14.2739
""ddddmm	chr8:59494822-59495062(+)$1	240	102	110	14.3424
%%%%%ccc	chr14:55258641-55258881(+)$1	240	10	18	13.3150
yyyyyyyy	chr16:22358183-22358423(-)$1	240	107	115	12.9726
::::GGGG	chrX:108886560-108886800(-)$1	240	0	8	13.4520
JJJJJJJJ	chr5:142608121-142608361(+)$1	240	35	43	14.2739
DDD{GGGG	chr2:26512750-26512990(+)$1	240	64	72	13.8630
ffffffnn	chr17:36891141-36891421(-)$1	280	193	201	12.5616
F:::ffff	chr5:135514861-135515101(+)$1	240	32	40	13.3835

#DB
........	chr8:120743082-120743322(-)$1	1	232	240	13.8630
))).....	chr2:160087950-160088190(+)$1	1	46	54	13.5205
.......(	chr17:38545619-38545859(-)$1	1	22	30	11.9452
))..))))	chr7:138983011-138983251(+)$1	1	112	120	12.8356
.......(	chr2:113315505-113315745(+)$1	1	11	19	12.3561
(((((.((	chr17:35980842-35981082(-)$1	1	7	15	12.9041
.......(	chr15:99673725-99674005(+)$1	1	46	54	13.4520
)))...))	chr12:68053772-68054012(+)$1	1	85	93	12.9726
........	chr9:14084339-14084579(-)$1	1	59	67	13.9315
))..))))	chr17:58524360-58524600(-)$1	1	108	116	13.2465
))......	chr4:139086053-139086333(-)$1	1	21	29	12.5616
.....)))	chr21:43408538-43408778(-)$1	1	13	21	13.8630
))...)))	chr21:28208539-28208779(-)$1	1	119	127	13.3150
))))))).	chr17:53470547-53470787(-)$1	1	182	190	14.2739
.......)	chr20:46284357-46284597(+)$1	1	145	153	13.4520
......((	chr3:121448025-121448265(-)$1	1	4	12	12.9726
))))))).	chr7:914093-914333(+)$1	1	191	199	13.6575
..((((((	chr10:88950934-88951174(+)$1	1	16	24	13.2465
........	chr21:40887146-40887386(+)$1	1	20	28	13.5205
.....)))	chr20:43996724-43996964(+)$1	1	165	173	13.8630
).......	chr14:93406149-93406389(-)$1	1	156	164	13.9315
))).))))	chr11:110100795-110101035(-)$1	1	110	118	11.9452
)....)))	chr10:22045417-22045657(-)$1	1	76	84	13.2465
))......	chr16:97000-97240(-)$1	1	220	228	13.4520
...(((((	chr6:97702463-97702703(-)$1	1	19	27	13.3150
(......)	chr2:42558933-42559173(+)$1	1	75	83	13.8630
(((((..(	chr8:67545137-67545377(-)$1	1	9	17	12.3561
((((.((.	chr7:108213838-108214078(+)$1	1	139	147	13.1780
(...((((	chr9:79002021-79002261(-)$1	1	31	39	12.9041
.......(	chr12:53808839-53809079(+)$1	1	110	118	12.9726
........	chr7:138728737-138729057(-)$1	1	17	25	13.2465
........	chr2:222290015-222290255(-)$1	1	118	126	14.3424
((..((.(	chr1:151375892-151376132(-)$1	1	16	24	12.2876
.....(((	chr2:139329775-139330015(+)$1	1	2	10	12.2876
(.......	chr1:150190962-150191202(-)$1	1	18	26	13.8630
(((((...	chr2:230899611-230899851(-)$1	1	176	184	12.9726
(((.....	chr13:53049621-53049861(+)$1	1	11	19	13.6575
((((((((	chr4:83847716-83847956(-)$1	1	17	25	13.8630
((((((((	chr6:79648520-79648760(-)$1	1	4	12	13.6575
........	chr17:21438594-21438834(-)$1	1	115	123	12.8356
...)))))	chr11:82642974-82643214(+)$1	1	113	121	13.4520
..(((.((	chr3:113437752-113437992(-)$1	1	50	58	13.8630
))).....	chr17:33678663-33678903(-)$1	1	117	125	12.8356
...)))..	chr10:69677564-69677804(+)$1	1	232	240	12.2191
........	chr8:131064594-131064834(-)$1	1	170	178	12.3561
....))))	chr18:22032383-22032623(+)$1	1	194	202	13.4520
(...))))	chr5:90664748-90664988(-)$1	1	38	46	12.2876
........	chr16:69151839-69152079(-)$1	1	3	11	13.9315
)))))..)	chr3:100083945-100084185(-)$1	1	199	207	13.3150
))))))))	chr16:15154379-15154619(-)$1	1	209	217	11.6712
.....)))	chr6:89319890-89320130(-)$1	1	70	78	12.6986
........	chr3:45786557-45786797(+)$1	1	3	11	11.5342
((((...(	chr2:178084968-178085208(+)$1	1	127	135	14.3424
........	chr6:82879876-82880116(-)$1	1	62	70	12.2876
((((....	chr4:68483477-68483757(-)$1	1	61	69	13.9315
(...))))	chr9:5775242-5775482(+)$1	1	33	41	12.1506
))....((	chr9:101912471-101912711(+)$1	1	74	82	12.9041
........	chrX:70520779-70521019(+)$1	1	216	224	13.9315
.....)).	chr14:103372452-103372692(+)$1	1	118	126	13.5205
(((..(((	chrX:44970987-44971227(+)$1	1	37	45	13.8630
.....)))	chr9:111781950-111782190(-)$1	1	190	198	13.5205
.....)))	chr10:29746388-29746628(-)$1	1	51	59	13.2465
(..(((((	chr2:204296419-204296659(+)$1	1	124	132	13.2465
))..).))	chr7:102944321-102944561(+)$1	1	117	125	13.8630
((((((..	chr1:8072623-8072863(-)$1	1	49	57	14.2739
..((((..	chr8:59494822-59495062(+)$1	1	102	110	14.3424
.....(((	chr14:55258641-55258881(+)$1	1	10	18	13.3150
........	chr16:22358183-22358423(-)$1	1	107	115	12.9726
....((((	chrX:108886560-108886800(-)$1	1	0	8	13.4520
((((((((	chr5:142608121-142608361(+)$1	1	35	43	14.2739
(((.((((	chr2:26512750-26512990(+)$1	1	64	72	13.8630
((((((..	chr17:36891141-36891421(-)$1	1	193	201	12.5616
(...((((	chr5:135514861-135515101(+)$1	1	32	40	13.3835

#PSSM
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
A : 0.94	a : 0.05	
U : 0.95	u : 0.04	
A : 0.32	U : 0.26	G : 0.21	C : 0.15	a : 0.02	u : 0.01	
U : 0.32	C : 0.26	A : 0.24	G : 0.12	a : 0.01	g : 0.01	u : 0.01	
A : 0.35	U : 0.32	C : 0.17	G : 0.09	u : 0.02	a : 0.01	

#score	966.7945205479477
#seq	73
#width	8
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m3_run1.nuc.txt

#NT
GCUGCCC	chr20:24944339-24944569(-)$1	230	133	140	13.0338
CCUGGCC	chr16:74442558-74442773(-)$1	215	166	173	13.3728
GCUGCCC	chr1:27734536-27734766(-)$1	230	96	103	13.0338
CCUGCCU	chr3:58550842-58551079(-)$1	237	227	234	13.2033
cccgccc	chr2:220408207-220408442(-)$1	235	66	73	12.9491
CCUGCCC	chr17:40851418-40851639(+)$1	221	29	36	17.2711
CCUGGCC	chrX:153713055-153713278(-)$1	223	132	139	13.3728
CCUCCCC	chr5:177209820-177210038(-)$1	218	63	70	13.9661
CCUGUCC	chrX:150869515-150869734(+)$1	219	4	11	13.2033
CCUGCCC	chr22:39218235-39218456(-)$1	221	3	10	17.2711
CCUGGCC	chr12:49330511-49330744(-)$1	233	9	16	13.3728
CCUGACC	chr9:136627108-136627323(+)$1	215	25	32	13.2881
CCUGACC	chr17:48438151-48438390(-)$1	239	49	56	13.2881
CCUUCCC	chr15:43889706-43889935(+)$1	229	148	155	13.7966
CCGGCCC	chr22:39131265-39131489(-)$1	224	156	163	12.8644
CCUGCCC	chr9:139958826-139959061(-)$1	235	114	121	17.2711
CCUGCCU	chr17:6357892-6358111(-)$1	219	154	161	13.2033
CCUCCCC	chr3:125802614-125802847(+)$1	233	29	36	13.9661
CCUGUCC	chr11:86782505-86782729(+)$1	224	188	195	13.2033
CCUGGCC	chr19:15219997-15220226(+)$1	229	197	204	13.3728
CCUGCCC	chr12:1604175-1604404(+)$1	229	184	191	17.2711
CCUUCCC	chr1:99774219-99774455(+)$1	236	161	168	13.7966
CCUGCCC	chr1:226795217-226795442(+)$1	225	35	42	17.2711
CCUGCCC	chr20:36151272-36151488(-)$1	216	96	103	17.2711
CAUGCCC	chr1:167391231-167391464(+)$1	233	149	156	12.6101
CCUUCCC	chr12:56634748-56634986(-)$1	238	156	163	13.7966
CCUCCCC	chr17:17104484-17104726(-)$1	242	110	117	13.9661
CCUUCCC	chr20:35274515-35274737(+)$1	222	149	156	13.7966
CCUCCCC	chr17:80013568-80013798(+)$1	230	19	26	13.9661
CCUGCCC	chr20:62694772-62694988(-)$1	216	149	156	17.2711
CCUCCCC	chr1:167392051-167392266(-)$1	215	9	16	13.9661
CCUGCCG	chr16:70699290-70699509(-)$1	219	18	25	12.8644
CCUCCCC	chr9:27329535-27329760(-)$1	225	189	196	13.9661
CCUGCCU	chr22:38616644-38616874(-)$1	230	96	103	13.2033
CCUGACC	chr9:139905588-139905829(-)$1	241	46	53	13.2881
CCUGCCC	chr3:47893793-47894011(-)$1	218	177	184	17.2711
CCUGCCU	chr8:42698210-42698454(-)$1	244	171	178	13.2033
GCUGCCC	chr13:50570612-50570834(+)$1	222	140	147	13.0338
GCUGCCC	chr14:104195391-104195622(+)$1	231	216	223	13.0338
CCUGCCC	chr17:17719908-17720128(-)$1	220	155	162	17.2711
CCCGCCC	chr11:1298019-1298235(+)$1	216	51	58	12.9491
CCUGCAC	chr9:139933977-139934196(-)$1	219	159	166	12.5254
CCUCCCC	chr18:3498982-3499212(-)$1	230	72	79	13.9661
CCUGCGC	chr21:33784974-33785189(+)$1	215	156	163	12.5254
CCUGCCC	chr11:8131172-8131413(-)$1	241	6	13	17.2711
CCUGCCC	chr5:149600203-149600439(-)$1	236	176	183	17.2711
CCUGCCC	chr15:91455757-91455976(+)$1	219	115	122	17.2711
CCAGCCC	chr7:157406616-157406840(-)$1	224	159	166	13.0338
acugcCC	chr11:70053043-70053262(-)$1	219	23	30	12.7796
CUUGCCC	chr10:98760076-98760293(-)$1	217	3	10	12.6101
CCUGCCC	chr19:45867269-45867493(-)$1	224	34	41	17.2711
CCUGCCU	chr20:31033479-31033705(-)$1	226	53	60	13.2033
CCAGCCC	chr6:109776754-109776974(-)$1	220	10	17	13.0338
CCUUCCC	chr10:299064-299292(+)$1	228	194	201	13.7966
CCUGCCC	chr17:68165737-68165952(+)$1	215	189	196	17.2711
CCUGCCC	chr20:62589005-62589254(-)$1	249	169	176	17.2711
CGUGCCC	chr10:32217563-32217785(-)$1	222	18	25	12.6101
CCUACCC	chr16:24883410-24883632(+)$1	222	105	112	13.4576

#otherMatches

#Struct PSSM
:::::::	chr1:160187027-160187249(+)$1	222	3	10	13.0338
!ccc!!e	chr20:24944339-24944569(-)$1	230	133	140	13.0338
ZBB}FFF	chr16:74442558-74442773(-)$1	215	166	173	13.3728
ddd$$$$	chr1:27734536-27734766(-)$1	230	96	103	13.0338
dddd]ee	chr3:58550842-58551079(-)$1	237	227	234	13.2033
ccccmmm	chr2:220408207-220408442(-)$1	235	66	73	12.9491
:::::::	chr17:40851418-40851639(+)$1	221	29	36	17.2711
ZZIIIII	chrX:153713055-153713278(-)$1	223	132	139	13.3728
ee[dddd	chr5:177209820-177210038(-)$1	218	63	70	13.9661
{BB{FFF	chrX:150869515-150869734(+)$1	219	4	11	13.2033
GGGGGGC	chr22:39218235-39218456(-)$1	221	3	10	17.2711
:::CCC:	chr12:49330511-49330744(-)$1	233	9	16	13.3728
!ccc###	chr9:136627108-136627323(+)$1	215	25	32	13.2881
bb!!===	chr17:48438151-48438390(-)$1	239	49	56	13.2881
eee&&&&	chr15:43889706-43889935(+)$1	229	148	155	13.7966
eefffff	chr22:39131265-39131489(-)$1	224	156	163	12.8644
hhhhhhg	chr9:139958826-139959061(-)$1	235	114	121	17.2711
hhheeee	chr17:6357892-6358111(-)$1	219	154	161	13.2033
eeeelll	chr3:125802614-125802847(+)$1	233	29	36	13.9661
hhhhh::	chr11:86782505-86782729(+)$1	224	188	195	13.2033
C}GGGGG	chr19:15219997-15220226(+)$1	229	197	204	13.3728
eeeeccc	chr12:1604175-1604404(+)$1	229	184	191	17.2711
bbfffff	chr1:99774219-99774455(+)$1	236	161	168	13.7966
tttdddd	chr1:226795217-226795442(+)$1	225	35	42	17.2711
c"""ccc	chr20:36151272-36151488(-)$1	216	96	103	17.2711
ffffff]	chr1:167391231-167391464(+)$1	233	149	156	12.6101
d::::::	chr12:56634748-56634986(-)$1	238	156	163	13.7966
%%%%%ee	chr17:17104484-17104726(-)$1	242	110	117	13.9661
GGGGGGG	chr20:35274515-35274737(+)$1	222	149	156	13.7966
""fffff	chr17:80013568-80013798(+)$1	230	19	26	13.9661
ddd]ddd	chr20:62694772-62694988(-)$1	216	149	156	17.2711
CCEEEEE	chr1:167392051-167392266(-)$1	215	9	16	13.9661
DDDDKKD	chr16:70699290-70699509(-)$1	219	18	25	12.8644
^^^^^^^	chr9:27329535-27329760(-)$1	225	189	196	13.9661
EEEDDDD	chr22:38616644-38616874(-)$1	230	96	103	13.2033
EEKKBBL	chr9:139905588-139905829(-)$1	241	46	53	13.2881
lllbb22	chr3:47893793-47894011(-)$1	218	177	184	17.2711
G::::gg	chr8:42698210-42698454(-)$1	244	171	178	13.2033
d]ggggg	chr13:50570612-50570834(+)$1	222	140	147	13.0338
DDDZZZC	chr14:104195391-104195622(+)$1	231	216	223	13.0338
ma]eeee	chr17:17719908-17720128(-)$1	220	155	162	17.2711
FFFKKEE	chr11:1298019-1298235(+)$1	216	51	58	12.9491
b[ccc[g	chr9:139933977-139934196(-)$1	219	159	166	12.5254
^^^^^^^	chr18:3498982-3499212(-)$1	230	72	79	13.9661
bffffff	chr21:33784974-33785189(+)$1	215	156	163	12.5254
dddmmmm	chr11:8131172-8131413(-)$1	241	6	13	17.2711
=======	chr5:149600203-149600439(-)$1	236	176	183	17.2711
=======	chr15:91455757-91455976(+)$1	219	115	122	17.2711
}A::::e	chr7:157406616-157406840(-)$1	224	159	166	13.0338
qqdddd3	chr11:70053043-70053262(-)$1	219	23	30	12.7796
:EEEEEH	chr10:98760076-98760293(-)$1	217	3	10	12.6101
ceeeee4	chr19:45867269-45867493(-)$1	224	34	41	17.2711
:eeeeee	chr20:31033479-31033705(-)$1	226	53	60	13.2033
dddd22a	chr6:109776754-109776974(-)$1	220	10	17	13.0338
>>>>>>>	chr10:299064-299292(+)$1	228	194	201	13.7966
^^^^^^^	chr17:68165737-68165952(+)$1	215	189	196	17.2711
IIIIICC	chr20:62589005-62589254(-)$1	249	169	176	17.2711
JJJJJJJ	chr10:32217563-32217785(-)$1	222	18	25	12.6101
77ggggg	chr16:24883410-24883632(+)$1	222	105	112	13.4576

#DB
.......	chr1:160187027-160187249(+)$1	1	3	10	13.0338
.(((..(	chr20:24944339-24944569(-)$1	1	133	140	13.0338
.)).)))	chr16:74442558-74442773(-)$1	1	166	173	13.3728
(((....	chr1:27734536-27734766(-)$1	1	96	103	13.0338
)))).))	chr3:58550842-58551079(-)$1	1	227	234	13.2033
)(((...	chr2:220408207-220408442(-)$1	1	66	73	12.9491
.......	chr17:40851418-40851639(+)$1	1	29	36	17.2711
..)))))	chrX:153713055-153713278(-)$1	1	132	139	13.3728
((.((((	chr5:177209820-177210038(-)$1	1	63	70	13.9661
.((.(((	chrX:150869515-150869734(+)$1	1	4	11	13.2033
(((((((	chr22:39218235-39218456(-)$1	1	3	10	17.2711
...(((.	chr12:49330511-49330744(-)$1	1	9	16	13.3728
.(((...	chr9:136627108-136627323(+)$1	1	25	32	13.2881
((..(((	chr17:48438151-48438390(-)$1	1	49	56	13.2881
(((....	chr15:43889706-43889935(+)$1	1	148	155	13.7966
))(((((	chr22:39131265-39131489(-)$1	1	156	163	12.8644
))))))(	chr9:139958826-139959061(-)$1	1	114	121	17.2711
)))))))	chr17:6357892-6358111(-)$1	1	154	161	13.2033
((((...	chr3:125802614-125802847(+)$1	1	29	36	13.9661
)))))..	chr11:86782505-86782729(+)$1	1	188	195	13.2033
).)))))	chr19:15219997-15220226(+)$1	1	197	204	13.3728
))))(((	chr12:1604175-1604404(+)$1	1	184	191	17.2711
)))))))	chr1:99774219-99774455(+)$1	1	161	168	13.7966
...))))	chr1:226795217-226795442(+)$1	1	35	42	17.2711
(...(((	chr20:36151272-36151488(-)$1	1	96	103	17.2711
)))))).	chr1:167391231-167391464(+)$1	1	149	156	12.6101
)......	chr12:56634748-56634986(-)$1	1	156	163	13.7966
.....((	chr17:17104484-17104726(-)$1	1	110	117	13.9661
)))))))	chr20:35274515-35274737(+)$1	1	149	156	13.7966
..(((((	chr17:80013568-80013798(+)$1	1	19	26	13.9661
))).)))	chr20:62694772-62694988(-)$1	1	149	156	17.2711
(((((((	chr1:167392051-167392266(-)$1	1	9	16	13.9661
((((..(	chr16:70699290-70699509(-)$1	1	18	25	12.8644
.......	chr9:27329535-27329760(-)$1	1	189	196	13.9661
)))))))	chr22:38616644-38616874(-)$1	1	96	103	13.2033
((..((.	chr9:139905588-139905829(-)$1	1	46	53	13.2881
...))..	chr3:47893793-47894011(-)$1	1	177	184	17.2711
)....((	chr8:42698210-42698454(-)$1	1	171	178	13.2033
).)))))	chr13:50570612-50570834(+)$1	1	140	147	13.0338
)))...)	chr14:104195391-104195622(+)$1	1	216	223	13.0338
.).))))	chr17:17719908-17720128(-)$1	1	155	162	17.2711
(((..((	chr11:1298019-1298235(+)$1	1	51	58	12.9491
(.(((.(	chr9:139933977-139934196(-)$1	1	159	166	12.5254
.......	chr18:3498982-3499212(-)$1	1	72	79	13.9661
(((((((	chr21:33784974-33785189(+)$1	1	156	163	12.5254
(((....	chr11:8131172-8131413(-)$1	1	6	13	17.2711
)))))))	chr5:149600203-149600439(-)$1	1	176	183	17.2711
(((((((	chr15:91455757-91455976(+)$1	1	115	122	17.2711
.)....(	chr7:157406616-157406840(-)$1	1	159	166	13.0338
..)))).	chr11:70053043-70053262(-)$1	1	23	30	12.7796
.((((((	chr10:98760076-98760293(-)$1	1	3	10	12.6101
)))))).	chr19:45867269-45867493(-)$1	1	34	41	17.2711
.((((((	chr20:31033479-31033705(-)$1	1	53	60	13.2033
))))..)	chr6:109776754-109776974(-)$1	1	10	17	13.0338
.......	chr10:299064-299292(+)$1	1	194	201	13.7966
.......	chr17:68165737-68165952(+)$1	1	189	196	17.2711
)))))))	chr20:62589005-62589254(-)$1	1	169	176	17.2711
(((((((	chr10:32217563-32217785(-)$1	1	18	25	12.6101
..)))))	chr16:24883410-24883632(+)$1	1	105	112	13.4576

#PSSM
C : 0.89	G : 0.06	c : 0.01	a : 0.01	
C : 0.91	c : 0.03	A : 0.01	U : 0.01	G : 0.01	
U : 0.88	A : 0.05	c : 0.01	G : 0.01	C : 0.01	u : 0.01	
G : 0.74	C : 0.11	U : 0.08	g : 0.03	A : 0.01	
C : 0.81	G : 0.06	A : 0.05	c : 0.03	U : 0.03	
C : 0.94	c : 0.01	A : 0.01	G : 0.01	
C : 0.88	U : 0.08	c : 0.01	G : 0.01	

#score	843.5762711864403
#seq	59
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m3_run2.nuc.txt

#NT
AAUacacacacacacacacacacacacacacacacacacacacacac	chr6:143746758-143747032(-)$1	274	114	161	122.0416
uccacccauacacacacacacacacacacacacacacacacacacac	chr20:44512598-44512921(+)$1	323	137	184	112.0416
CUCUcacacacacacacacacacacacacacacacacacacacacac	chr12:8235251-8235518(+)$1	267	115	162	116.4166
Aacacacacacacacacacacacacacacacacacacacacacacac	chr2:203630669-203630973(+)$1	304	114	161	124.5416
AAUUUacacacacacacacacacacacacacacacacacacacacaG	chr5:112213542-112213854(-)$1	312	130	177	111.4166
UAUGCACAUGUacacacacacacacacacacacacacacacauacac	chrX:74589031-74589282(-)$1	251	90	137	99.5416
AUAAAUcacacacacacacacacacacacacacacacacacacaAGU	chr11:105852177-105852421(+)$1	244	97	144	100.3750
Uacacacacacacacacacacacacacacacacccccacacacacac	chr8:11279764-11280015(-)$1	251	100	147	113.0833
aacacacacacacacacacacacacacacacacacacacacacacac	chr16:28332393-28332662(+)$1	269	109	156	124.5416
CACCACcacacacacacacacacacacacacacacacacacacacac	chr2:202758694-202758941(+)$1	247	96	143	110.7916
UUcacacacacacacacacacacacacacacacacacacacacacac	chr2:17836618-17836870(+)$1	252	102	149	120.1666
AACAGAUUGCUacacacacacacacacacacacacacacacacacac	chr2:96049814-96050066(+)$1	252	92	139	99.7500
UAUAUacacacacacacacacacacacacacacacacacacUCUGAC	chr5:122165307-122165637(+)$1	330	158	205	103.7083
accacacacacacacacacacacacacacacacacacacaGAAAUAU	chr7:98445012-98445278(-)$1	266	111	158	106.0000
Aacacacacacacacacacacacacacacacacacacacacacacac	chr13:30779957-30780224(-)$1	267	103	150	124.5416
ACAUcacacacacacucacacucacauacacacacacacacacacUC	chr13:30779646-30779896(-)$1	250	101	148	98.5000
cauacacacacacacacacacacacacacacacacacacacacacac	chr1:211665277-211665537(-)$1	260	100	147	119.3333
Aacacacacacacacacacacacacacacacacacacacacacacac	chr17:38632509-38632786(-)$1	277	104	151	124.5416
Aacacacacacacacacacacacacacacacacacacacacacacac	chr16:24230874-24231249(+)$1	375	101	148	124.5416
ACcacacacacacacacacacacacacacacacacacacacacacac	chr5:158712048-158712377(+)$1	329	154	201	122.2500
AacacacacacacacacacacacacacacacacacacacacacacUC	chr7:92759862-92760183(-)$1	321	165	212	121.0000
AacacacacauguacacacacacacacacacacacacacacacCCUU	chr12:113334841-113335075(+)$1	234	96	143	100.3750
AUCAGacacacacacacacacacacacacacacacacacucgcauac	chr20:37206237-37206535(+)$1	298	99	146	106.4166

#otherMatches

#Struct PSSM
FFF:::::::ccc####ccc[ccc^^^^^^^^^^^^^^^^^^^^^^^	chr5:160716686-160716931(-)$1	245	87	134	104.3333
>>eeeee::::::::::::::::::::::::::::::::::::::::	chr6:143746758-143747032(-)$1	274	114	161	122.0416
:::::::::::::::::::::::::::::::::::::::::::::::	chr20:44512598-44512921(+)$1	323	137	184	112.0416
:::::::::::::::::::::::::::::::::::::::::::::::	chr12:8235251-8235518(+)$1	267	115	162	116.4166
::::::::::::::::::::::::::::::::::::::::::dddda	chr2:203630669-203630973(+)$1	304	114	161	124.5416
oeeeeeccc::::::::::::::::::::::::::::::::::::ee	chr5:112213542-112213854(-)$1	312	130	177	111.4166
gmmmmggggggg:::::::::::::::::::::::::::::::::::	chrX:74589031-74589282(-)$1	251	90	137	99.5416
ggg::::::::::::::::::::::::::::::::::::::::::::	chr11:105852177-105852421(+)$1	244	97	144	100.3750
e::::::::::::::::::::::::::::::::::::::::::::::	chr8:11279764-11280015(-)$1	251	100	147	113.0833
:::::::::::::::::::::::::::::::::::::::::::::::	chr16:28332393-28332662(+)$1	269	109	156	124.5416
ff]a::::::::::::::::::::::::::::::::::::::eeeee	chr2:202758694-202758941(+)$1	247	96	143	110.7916
d:::::::::::::::::::::::bb!!eeeee&&&&&&&bb[ffff	chr2:17836618-17836870(+)$1	252	102	149	120.1666
444bb]eeeee::::::::::::::::::::::::::::::::::::	chr2:96049814-96050066(+)$1	252	92	139	99.7500
:::::::::::::::::::::::::::::::::::::::::bb[eee	chr5:122165307-122165637(+)$1	330	158	205	103.7083
ccc:::::::::::::::::::::::::::::::::::::eeeee$$	chr7:98445012-98445278(-)$1	266	111	158	106.0000
:::::::::::::::::::::::::::::::::::::::::::::::	chr13:30779957-30780224(-)$1	267	103	150	124.5416
^^^^^^dddd4444eeeeeEEEEE@@@@@@@@@@@@@DDDD//////	chr13:30779646-30779896(-)$1	250	101	148	98.5000
c::::::::::::::::::::::::::::::::::::::::::::::	chr1:211665277-211665537(-)$1	260	100	147	119.3333
KKA::::::::::::::::::::::::::::::::::::::::::::	chr17:38632509-38632786(-)$1	277	104	151	124.5416
:::::::::::::::::::::::::::::::::::::::::::::::	chr16:24230874-24231249(+)$1	375	101	148	124.5416
::::::::::::::::::::::::::::::::::::::::::::ccc	chr5:158712048-158712377(+)$1	329	154	201	122.2500
:::::::::::::::::::::::::::::::::::::::::::::::	chr7:92759862-92760183(-)$1	321	165	212	121.0000
dd:::::::ggggggg"""eeeee[eeeee^^^^^^^^^^^^^^^^^	chr12:113334841-113335075(+)$1	234	96	143	100.3750
DD}BB:::::::::::::::::::::::::::::::::::::::::J	chr20:37206237-37206535(+)$1	298	99	146	106.4166

#DB
(((.......(((....(((.(((.......................	chr5:160716686-160716931(-)$1	1	87	134	104.3333
..)))))........................................	chr6:143746758-143747032(-)$1	1	114	161	122.0416
...............................................	chr20:44512598-44512921(+)$1	1	137	184	112.0416
...............................................	chr12:8235251-8235518(+)$1	1	115	162	116.4166
..........................................(((((	chr2:203630669-203630973(+)$1	1	114	161	124.5416
.))))))))....................................((	chr5:112213542-112213854(-)$1	1	130	177	111.4166
(....)))))))...................................	chrX:74589031-74589282(-)$1	1	90	137	99.5416
)))............................................	chr11:105852177-105852421(+)$1	1	97	144	100.3750
)..............................................	chr8:11279764-11280015(-)$1	1	100	147	113.0833
...............................................	chr16:28332393-28332662(+)$1	1	109	156	124.5416
)).)......................................(((((	chr2:202758694-202758941(+)$1	1	96	143	110.7916
).......................((..(((((.......((.((((	chr2:17836618-17836870(+)$1	1	102	149	120.1666
...)).)))))....................................	chr2:96049814-96050066(+)$1	1	92	139	99.7500
.........................................((.(((	chr5:122165307-122165637(+)$1	1	158	205	103.7083
))).....................................(((((..	chr7:98445012-98445278(-)$1	1	111	158	106.0000
...............................................	chr13:30779957-30780224(-)$1	1	103	150	124.5416
......))))....)))))))))).............))))......	chr13:30779646-30779896(-)$1	1	101	148	98.5000
)..............................................	chr1:211665277-211665537(-)$1	1	100	147	119.3333
..(............................................	chr17:38632509-38632786(-)$1	1	104	151	124.5416
...............................................	chr16:24230874-24231249(+)$1	1	101	148	124.5416
............................................(((	chr5:158712048-158712377(+)$1	1	154	201	122.2500
...............................................	chr7:92759862-92760183(-)$1	1	165	212	121.0000
)).......(((((((...(((((.(((((.................	chr12:113334841-113335075(+)$1	1	96	143	100.3750
)).)).........................................(	chr20:37206237-37206535(+)$1	1	99	146	106.4166

#PSSM
A : 0.58	U : 0.16	C : 0.08	a : 0.08	u : 0.04	c : 0.04	
a : 0.37	A : 0.24	U : 0.16	c : 0.08	C : 0.08	u : 0.04	
c : 0.54	U : 0.16	C : 0.16	A : 0.08	u : 0.04	
a : 0.62	A : 0.16	U : 0.12	G : 0.04	C : 0.04	
c : 0.70	U : 0.08	A : 0.08	G : 0.08	C : 0.04	
a : 0.79	A : 0.08	c : 0.04	U : 0.04	C : 0.04	
c : 0.91	C : 0.04	U : 0.04	
a : 0.91	A : 0.04	U : 0.04	
c : 0.87	u : 0.04	U : 0.04	G : 0.04	
a : 0.91	G : 0.04	C : 0.04	
c : 0.87	U : 0.08	u : 0.04	
a : 0.95	g : 0.04	
c : 0.91	g : 0.04	u : 0.04	
a : 0.95	u : 0.04	
c : 0.99	
a : 0.95	u : 0.04	
c : 0.99	
a : 0.99	
c : 0.99	
a : 0.99	
c : 0.99	
a : 0.95	u : 0.04	
c : 0.95	g : 0.04	
a : 0.95	u : 0.04	
c : 0.99	
a : 0.99	
c : 0.95	u : 0.04	
a : 0.99	
c : 0.99	
a : 0.99	
c : 0.99	
a : 0.99	
c : 0.99	
a : 0.95	c : 0.04	
c : 0.99	
a : 0.95	c : 0.04	
c : 0.99	
a : 0.99	
c : 0.99	
a : 0.95	u : 0.04	
c : 0.95	G : 0.04	
a : 0.87	U : 0.04	A : 0.04	g : 0.04	
c : 0.87	u : 0.04	C : 0.04	A : 0.04	
a : 0.87	U : 0.04	A : 0.04	C : 0.04	
c : 0.79	A : 0.04	G : 0.04	U : 0.04	C : 0.04	u : 0.04	
a : 0.74	U : 0.12	A : 0.08	G : 0.04	
c : 0.70	U : 0.12	C : 0.12	G : 0.04	

#score	2710.250000000001
#seq	24
#width	47
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_UTR_m2_run1.nuc.txt

#NT
GGCU	chr4:83350402-83350642(-)$1	240	17	21	11.9999
GGCU	chr6:161491725-161491960(+)$1	235	209	213	11.9999
GGCU	chr17:72244107-72244354(+)$1	247	118	122	11.9999
GGCU	chr14:103988054-103988262(-)$1	208	41	45	11.9999
GGCU	chr9:131851214-131851441(+)$1	227	83	87	11.9999
GGCU	chr12:101801391-101801632(-)$1	241	117	121	11.9999
GGCU	chr1:1684276-1684529(-)$1	253	2	6	11.9999
GGCU	chr17:35870712-35870952(+)$1	240	34	38	11.9999
GGCU	chr17:15948099-15948352(+)$1	253	26	30	11.9999
GGCU	chr19:1650112-1650379(-)$1	267	4	8	11.9999
GGCU	chr22:20302857-20303096(-)$1	239	171	175	11.9999
GGCU	chr20:39751852-39752095(+)$1	243	60	64	11.9999
GGCU	chr14:37641529-37641773(-)$1	244	135	139	11.9999
GGCU	chr12:113407666-113407891(+)$1	225	34	38	11.9999
GGCU	chr17:4085510-4085746(-)$1	236	227	231	11.9999
GGCU	chr14:78392071-78392301(+)$1	230	1	5	11.9999
GGCU	chr19:37427543-37427748(+)$1	205	127	131	11.9999
GGCU	chr19:46389114-46389352(-)$1	238	66	70	11.9999
GGCU	chr7:6655483-6655724(+)$1	241	208	212	11.9999
GGCU	chr16:21854709-21854946(-)$1	237	44	48	11.9999
GGCU	chr17:4692128-4692365(-)$1	237	13	17	11.9999
GGCU	chr3:113594285-113594519(+)$1	234	108	112	11.9999
GGCU	chr19:10227741-10227964(-)$1	223	17	21	11.9999
GGCU	chr5:14509776-14510021(+)$1	245	34	38	11.9999
GGCU	chr19:4714200-4714440(-)$1	240	112	116	11.9999
GGCU	chr2:198359297-198359537(-)$1	240	20	24	11.9999
GGCU	chr1:144817863-144818105(+)$1	242	22	26	11.9999
GGCU	chr3:14189307-14189540(-)$1	233	228	232	11.9999
GGCU	chr17:40266125-40266360(-)$1	235	165	169	11.9999
GGCU	chr5:68860846-68861112(+)$1	266	152	156	11.9999
GGCU	chr19:10792568-10792786(+)$1	218	122	126	11.9999
GGCU	chr12:66356950-66357183(+)$1	233	50	54	11.9999
GGCU	chr19:10692398-10692636(-)$1	238	175	179	11.9999
GGCU	chr1:145354194-145354452(+)$1	258	43	47	11.9999
GGCU	chr1:144187359-144187617(+)$1	258	43	47	11.9999
GGCU	chr11:62384358-62384588(-)$1	230	11	15	11.9999
GGCU	chr12:2926336-2926583(+)$1	247	122	126	11.9999
GGCU	chr19:17628455-17628725(+)$1	270	48	52	11.9999
GGCU	chr12:133294028-133294250(+)$1	222	6	10	11.9999
GGCU	chr2:63282837-63283079(+)$1	242	7	11	11.9999
GGCU	chr20:62589123-62589367(-)$1	244	26	30	11.9999
GGCU	chr12:48526658-48526901(+)$1	243	126	130	11.9999
GGCU	chr3:47882454-47882702(+)$1	248	243	247	11.9999
GGCU	chr1:205496914-205497145(+)$1	231	135	139	11.9999
GGCU	chr8:38275336-38275596(-)$1	260	115	119	11.9999
GGCU	chr19:46319639-46319883(-)$1	244	208	212	11.9999
GGCU	chr14:31676702-31676955(-)$1	253	147	151	11.9999
GGCU	chr6:116692112-116692342(+)$1	230	12	16	11.9999
GGCU	chr7:5567930-5568177(-)$1	247	3	7	11.9999
GGCU	chr2:97217803-97218035(+)$1	232	24	28	11.9999
GGCU	chr17:7216430-7216653(-)$1	223	108	112	11.9999
GGCU	chr12:53421785-53422029(+)$1	244	12	16	11.9999
GGCU	chr1:45101658-45101899(+)$1	241	60	64	11.9999
GGCU	chr7:100880879-100881125(-)$1	246	32	36	11.9999
GGCU	chr3:49758729-49758976(-)$1	247	11	15	11.9999
GGCU	chr17:2496924-2497181(+)$1	257	195	199	11.9999
GGCU	chrX:119077444-119077713(-)$1	269	41	45	11.9999
GGCU	chr2:74592619-74592852(-)$1	233	96	100	11.9999
GGCU	chr7:75104295-75104525(-)$1	230	94	98	11.9999
GGCU	chrX:1720097-1720331(+)$1	234	82	86	11.9999
GGCU	chr1:24143112-24143345(-)$1	233	166	170	11.9999
GGCU	chr6:13574744-13574992(+)$1	248	121	125	11.9999
GGCU	chr19:1817153-1817384(-)$1	231	92	96	11.9999
GGCU	chr16:2607711-2607953(+)$1	242	154	158	11.9999
GGCU	chr20:33866894-33867109(-)$1	215	20	24	11.9999
GGCU	chr12:113614581-113614836(-)$1	255	129	133	11.9999
GGCU	chr17:7214857-7215071(+)$1	214	16	20	11.9999
GGCU	chr12:57624568-57624850(+)$1	282	58	62	11.9999
GGCU	chr3:23960826-23961062(+)$1	236	38	42	11.9999
GGCU	chr7:150069832-150070067(+)$1	235	223	227	11.9999
GGCU	chr1:156737304-156737536(+)$1	232	119	123	11.9999
GGCU	chr1:144198537-144198803(+)$1	266	133	137	11.9999
GGCU	chr7:44106747-44106985(+)$1	238	122	126	11.9999
GGCU	chr7:43687072-43687308(-)$1	236	144	148	11.9999
GGCU	chr1:43124793-43125000(+)$1	207	16	20	11.9999
GGCU	chrX:135956236-135956481(-)$1	245	47	51	11.9999
GGCU	chr10:79735208-79735479(-)$1	271	59	63	11.9999

#otherMatches

#Struct PSSM
F}CC	chr20:36694470-36694697(+)$1	227	118	122	11.9999
fff#	chr4:83350402-83350642(-)$1	240	17	21	11.9999
^ccc	chr6:161491725-161491960(+)$1	235	209	213	11.9999
ccc[	chr17:72244107-72244354(+)$1	247	118	122	11.9999
JJJJ	chr14:103988054-103988262(-)$1	208	41	45	11.9999
eeee	chr9:131851214-131851441(+)$1	227	83	87	11.9999
dddd	chr12:101801391-101801632(-)$1	241	117	121	11.9999
C{DD	chr1:1684276-1684529(-)$1	253	2	6	11.9999
gggg	chr17:35870712-35870952(+)$1	240	34	38	11.9999
ffff	chr17:15948099-15948352(+)$1	253	26	30	11.9999
ee[b	chr19:1650112-1650379(-)$1	267	4	8	11.9999
Eccc	chr22:20302857-20303096(-)$1	239	171	175	11.9999
gggg	chr20:39751852-39752095(+)$1	243	60	64	11.9999
iiii	chr14:37641529-37641773(-)$1	244	135	139	11.9999
ffff	chr12:113407666-113407891(+)$1	225	34	38	11.9999
CCC}	chr17:4085510-4085746(-)$1	236	227	231	11.9999
DDDD	chr14:78392071-78392301(+)$1	230	1	5	11.9999
]fff	chr19:37427543-37427748(+)$1	205	127	131	11.9999
hhhh	chr19:46389114-46389352(-)$1	238	66	70	11.9999
ccc:	chr7:6655483-6655724(+)$1	241	208	212	11.9999
dd]e	chr16:21854709-21854946(-)$1	237	44	48	11.9999
eee[	chr17:4692128-4692365(-)$1	237	13	17	11.9999
ccc]	chr3:113594285-113594519(+)$1	234	108	112	11.9999
ccc[	chr19:10227741-10227964(-)$1	223	17	21	11.9999
iiii	chr5:14509776-14510021(+)$1	245	34	38	11.9999
hhh]	chr19:4714200-4714440(-)$1	240	112	116	11.9999
LLCC	chr2:198359297-198359537(-)$1	240	20	24	11.9999
ccc]	chr1:144817863-144818105(+)$1	242	22	26	11.9999
HHH:	chr3:14189307-14189540(-)$1	233	228	232	11.9999
cccm	chr17:40266125-40266360(-)$1	235	165	169	11.9999
:fff	chr5:68860846-68861112(+)$1	266	152	156	11.9999
dddd	chr19:10792568-10792786(+)$1	218	122	126	11.9999
ddd"	chr12:66356950-66357183(+)$1	233	50	54	11.9999
ddd]	chr19:10692398-10692636(-)$1	238	175	179	11.9999
HHHH	chr1:145354194-145354452(+)$1	258	43	47	11.9999
HHHH	chr1:144187359-144187617(+)$1	258	43	47	11.9999
nnnh	chr11:62384358-62384588(-)$1	230	11	15	11.9999
EEEE	chr12:2926336-2926583(+)$1	247	122	126	11.9999
FFFF	chr19:17628455-17628725(+)$1	270	48	52	11.9999
bb[b	chr12:133294028-133294250(+)$1	222	6	10	11.9999
EEEE	chr2:63282837-63283079(+)$1	242	7	11	11.9999
[fff	chr20:62589123-62589367(-)$1	244	26	30	11.9999
dd]b	chr12:48526658-48526901(+)$1	243	126	130	11.9999
mddd	chr3:47882454-47882702(+)$1	248	243	247	11.9999
IIII	chr1:205496914-205497145(+)$1	231	135	139	11.9999
dmmm	chr8:38275336-38275596(-)$1	260	115	119	11.9999
dddd	chr19:46319639-46319883(-)$1	244	208	212	11.9999
cccm	chr14:31676702-31676955(-)$1	253	147	151	11.9999
b[bb	chr6:116692112-116692342(+)$1	230	12	16	11.9999
CCC{	chr7:5567930-5568177(-)$1	247	3	7	11.9999
eeee	chr2:97217803-97218035(+)$1	232	24	28	11.9999
dd::	chr17:7216430-7216653(-)$1	223	108	112	11.9999
bb[c	chr12:53421785-53422029(+)$1	244	12	16	11.9999
dddd	chr1:45101658-45101899(+)$1	241	60	64	11.9999
ee[d	chr7:100880879-100881125(-)$1	246	32	36	11.9999
EEEE	chr3:49758729-49758976(-)$1	247	11	15	11.9999
dddd	chr17:2496924-2497181(+)$1	257	195	199	11.9999
ff33	chrX:119077444-119077713(-)$1	269	41	45	11.9999
dddd	chr2:74592619-74592852(-)$1	233	96	100	11.9999
eee2	chr7:75104295-75104525(-)$1	230	94	98	11.9999
c]gg	chrX:1720097-1720331(+)$1	234	82	86	11.9999
mmmf	chr1:24143112-24143345(-)$1	233	166	170	11.9999
meee	chr6:13574744-13574992(+)$1	248	121	125	11.9999
gggc	chr19:1817153-1817384(-)$1	231	92	96	11.9999
eeee	chr16:2607711-2607953(+)$1	242	154	158	11.9999
{BBL	chr20:33866894-33867109(-)$1	215	20	24	11.9999
dddd	chr12:113614581-113614836(-)$1	255	129	133	11.9999
dddd	chr17:7214857-7215071(+)$1	214	16	20	11.9999
eeee	chr12:57624568-57624850(+)$1	282	58	62	11.9999
hhhh	chr3:23960826-23961062(+)$1	236	38	42	11.9999
CC}C	chr7:150069832-150070067(+)$1	235	223	227	11.9999
cnnn	chr1:156737304-156737536(+)$1	232	119	123	11.9999
DDD{	chr1:144198537-144198803(+)$1	266	133	137	11.9999
sccc	chr7:44106747-44106985(+)$1	238	122	126	11.9999
cfff	chr7:43687072-43687308(-)$1	236	144	148	11.9999
GGGG	chr1:43124793-43125000(+)$1	207	16	20	11.9999
cc""	chrX:135956236-135956481(-)$1	245	47	51	11.9999
dfff	chr10:79735208-79735479(-)$1	271	59	63	11.9999

#DB
).))	chr20:36694470-36694697(+)$1	1	118	122	11.9999
(((.	chr4:83350402-83350642(-)$1	1	17	21	11.9999
.)))	chr6:161491725-161491960(+)$1	1	209	213	11.9999
(((.	chr17:72244107-72244354(+)$1	1	118	122	11.9999
((((	chr14:103988054-103988262(-)$1	1	41	45	11.9999
((((	chr9:131851214-131851441(+)$1	1	83	87	11.9999
((((	chr12:101801391-101801632(-)$1	1	117	121	11.9999
(.((	chr1:1684276-1684529(-)$1	1	2	6	11.9999
))))	chr17:35870712-35870952(+)$1	1	34	38	11.9999
))))	chr17:15948099-15948352(+)$1	1	26	30	11.9999
((.(	chr19:1650112-1650379(-)$1	1	4	8	11.9999
)(((	chr22:20302857-20303096(-)$1	1	171	175	11.9999
((((	chr20:39751852-39752095(+)$1	1	60	64	11.9999
))))	chr14:37641529-37641773(-)$1	1	135	139	11.9999
((((	chr12:113407666-113407891(+)$1	1	34	38	11.9999
))).	chr17:4085510-4085746(-)$1	1	227	231	11.9999
((((	chr14:78392071-78392301(+)$1	1	1	5	11.9999
.)))	chr19:37427543-37427748(+)$1	1	127	131	11.9999
))))	chr19:46389114-46389352(-)$1	1	66	70	11.9999
))).	chr7:6655483-6655724(+)$1	1	208	212	11.9999
)).)	chr16:21854709-21854946(-)$1	1	44	48	11.9999
(((.	chr17:4692128-4692365(-)$1	1	13	17	11.9999
))).	chr3:113594285-113594519(+)$1	1	108	112	11.9999
(((.	chr19:10227741-10227964(-)$1	1	17	21	11.9999
))))	chr5:14509776-14510021(+)$1	1	34	38	11.9999
))).	chr19:4714200-4714440(-)$1	1	112	116	11.9999
..((	chr2:198359297-198359537(-)$1	1	20	24	11.9999
))).	chr1:144817863-144818105(+)$1	1	22	26	11.9999
))).	chr3:14189307-14189540(-)$1	1	228	232	11.9999
(((.	chr17:40266125-40266360(-)$1	1	165	169	11.9999
.(((	chr5:68860846-68861112(+)$1	1	152	156	11.9999
))))	chr19:10792568-10792786(+)$1	1	122	126	11.9999
(((.	chr12:66356950-66357183(+)$1	1	50	54	11.9999
))).	chr19:10692398-10692636(-)$1	1	175	179	11.9999
((((	chr1:145354194-145354452(+)$1	1	43	47	11.9999
((((	chr1:144187359-144187617(+)$1	1	43	47	11.9999
...)	chr11:62384358-62384588(-)$1	1	11	15	11.9999
))))	chr12:2926336-2926583(+)$1	1	122	126	11.9999
((((	chr19:17628455-17628725(+)$1	1	48	52	11.9999
((.(	chr12:133294028-133294250(+)$1	1	6	10	11.9999
((((	chr2:63282837-63283079(+)$1	1	7	11	11.9999
.(((	chr20:62589123-62589367(-)$1	1	26	30	11.9999
)).)	chr12:48526658-48526901(+)$1	1	126	130	11.9999
.)))	chr3:47882454-47882702(+)$1	1	243	247	11.9999
))))	chr1:205496914-205497145(+)$1	1	135	139	11.9999
(...	chr8:38275336-38275596(-)$1	1	115	119	11.9999
))))	chr19:46319639-46319883(-)$1	1	208	212	11.9999
(((.	chr14:31676702-31676955(-)$1	1	147	151	11.9999
(.((	chr6:116692112-116692342(+)$1	1	12	16	11.9999
(((.	chr7:5567930-5568177(-)$1	1	3	7	11.9999
((((	chr2:97217803-97218035(+)$1	1	24	28	11.9999
))..	chr17:7216430-7216653(-)$1	1	108	112	11.9999
((.(	chr12:53421785-53422029(+)$1	1	12	16	11.9999
))))	chr1:45101658-45101899(+)$1	1	60	64	11.9999
((.(	chr7:100880879-100881125(-)$1	1	32	36	11.9999
((((	chr3:49758729-49758976(-)$1	1	11	15	11.9999
))))	chr17:2496924-2497181(+)$1	1	195	199	11.9999
))..	chrX:119077444-119077713(-)$1	1	41	45	11.9999
))))	chr2:74592619-74592852(-)$1	1	96	100	11.9999
))).	chr7:75104295-75104525(-)$1	1	94	98	11.9999
).))	chrX:1720097-1720331(+)$1	1	82	86	11.9999
...)	chr1:24143112-24143345(-)$1	1	166	170	11.9999
.)))	chr6:13574744-13574992(+)$1	1	121	125	11.9999
)))(	chr19:1817153-1817384(-)$1	1	92	96	11.9999
))))	chr16:2607711-2607953(+)$1	1	154	158	11.9999
.((.	chr20:33866894-33867109(-)$1	1	20	24	11.9999
((((	chr12:113614581-113614836(-)$1	1	129	133	11.9999
))))	chr17:7214857-7215071(+)$1	1	16	20	11.9999
((((	chr12:57624568-57624850(+)$1	1	58	62	11.9999
))))	chr3:23960826-23961062(+)$1	1	38	42	11.9999
)).)	chr7:150069832-150070067(+)$1	1	223	227	11.9999
(...	chr1:156737304-156737536(+)$1	1	119	123	11.9999
(((.	chr1:144198537-144198803(+)$1	1	133	137	11.9999
.)))	chr7:44106747-44106985(+)$1	1	122	126	11.9999
)(((	chr7:43687072-43687308(-)$1	1	144	148	11.9999
((((	chr1:43124793-43125000(+)$1	1	16	20	11.9999
((..	chrX:135956236-135956481(-)$1	1	47	51	11.9999
)(((	chr10:79735208-79735479(-)$1	1	59	63	11.9999

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

#score	935.9999999999995
#seq	78
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m1_run1.nuc.txt

#NT
CGGGCAAGACGCUAGGCAGGCCUGAAGCAGACUCUCCUCCUCCUCUUCCAUCCUCCAGACAAGGUGGUUGCCCGGGACCUGGUUGGAGCCAUGUUGAGCCCACUGCCGCAGCCACGCCCCUCUGCCCCCCAGGUGCUGGCCCACCCCUUCUUUUGGAGCAGAGCCAAGCAACUCCAGUUCUUCCAGGUCAGAAGGAAAGCUUGGGAAUGGCCCCCAAAAGUCCU	chr16:23703243-23703470(-)$1	227	1	225	317.0000

#otherMatches

#Struct PSSM
::::EEEEEKKBB:FFFFFFKKBB:::hhhhhhhh%%%%%%ddddllldddd55555hhhhhhhh:::::ffffffnnnnnffffff::bboooooobb:::BBYYFFFFFF:CCCNNNNNGGGGGGGBBeeeeemmmmeeeee:::::::::::ddddmmmmddddgggggggxxxxxxxxxxxxxxxggggggg::BB}GGGGGGGCCC}BBYYEEEEE:::	chr15:64388106-64388330(-)$1	224	0	224	317.0000
ggggggg!!dddd[bb[ccc"""dddd[bbuuuuuuuuuuuubbdddd333cccbb666666dddd]ggggggg:gggggggffffff"""dddd!!bb"""dddd!!bbdddd[bb[cccrrrrrrrrrccc]bbdddd>>>>>>>>>>>>>bb22dddd]bb22dddd]ffffff55555ggggggg:::dddd####eeeeepppppppeeeee333dddd	chr16:23703243-23703470(-)$1	227	1	225	317.0000

#DB
....(((((..((.((((((..((...((((((((......((((...)))).....)))))))).....((((((.....))))))..((......))...))..)))))).(((.....((((((((((((((....)))))...........((((....))))(((((((...............)))))))..)).)))))))))).))..)))))...	chr15:64388106-64388330(-)$1	1	0	224	317.0000
(((((((..((((.((.(((...((((.((............))))))...)))))......)))).))))))).(((((((((((((...((((..((...((((..((((((.((.(((.........))).)))))).............))..)))).))..)))).)))))).....)))))))...((((....(((((.......)))))...))))	chr16:23703243-23703470(-)$1	1	1	225	317.0000

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

#score	634.0
#seq	2
#width	224
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m2_run2.nuc.txt

#NT
UUUAUUU	chr17:7215168-7215408(+)$1	240	74	81	13.8030
UUUUUUU	chr2:37428698-37428928(+)$1	230	14	21	17.8181
UUUUUUU	chr2:42557623-42557861(+)$1	238	136	143	17.8181
Uuuuauu	chr15:58305972-58306197(-)$1	225	217	224	13.8787
UUAUUUU	chr3:156865631-156865857(-)$1	226	126	133	13.4999
UCUUUUU	chr16:19088541-19088773(+)$1	232	69	76	13.8030
UUUUUUU	chr3:113440600-113440829(-)$1	229	15	22	17.8181
AUUUUUU	chr3:48786407-48786650(-)$1	243	58	65	13.1212
UUUUCUU	chr16:69337336-69337565(+)$1	229	210	217	13.9545
CUUUUUU	chr1:225685223-225685446(-)$1	223	172	179	13.1212
UUUUUUU	chr1:25168658-25168884(+)$1	226	56	63	17.8181
UUUUUUU	chr1:182353337-182353579(-)$1	242	151	158	17.8181
UUUUUUU	chr8:28426280-28426504(+)$1	224	97	104	17.8181
UUUUCUU	chr10:104622592-104622821(+)$1	229	177	184	13.9545
UUUUGUU	chr11:4159920-4160155(+)$1	235	37	44	13.9545
UUUUUUU	chr5:76728700-76728940(-)$1	240	77	84	17.8181
UUUGUUU	chr1:205685013-205685271(-)$1	258	154	161	13.6515
uuuuuuu	chr4:36068436-36068664(-)$1	228	87	94	17.8181
UGUUUUU	chr18:29709014-29709244(+)$1	230	31	38	13.9545
uuuuuuu	chrX:24094795-24095063(+)$1	268	248	255	17.8181
UUUUUUU	chr1:171562214-171562450(+)$1	236	62	69	17.8181
UUUUUUU	chr1:225675491-225675718(-)$1	227	64	71	17.8181
UUUUUUU	chr5:179149739-179149968(+)$1	229	52	59	17.8181
UAUUUUU	chr8:104340456-104340686(+)$1	230	27	34	13.7272
uuguuuu	chr4:77052286-77052515(-)$1	229	44	51	13.4999
UUUUAUU	chr14:31588919-31589148(-)$1	229	62	69	13.8787
uuuuguu	chr1:43310342-43310570(+)$1	228	53	60	13.9545
UUUUUUU	chr5:149779632-149779865(+)$1	233	174	181	17.8181
UGUUUUU	chr2:32853106-32853329(+)$1	223	46	53	13.9545
uuuuuuu	chr19:18320852-18321081(+)$1	229	147	154	17.8181
UUUUUUU	chr17:25635663-25635892(+)$1	229	67	74	17.8181
UUUUUUU	chr11:108348278-108348509(-)$1	231	53	60	17.8181
UUUUUCU	chr6:126661204-126661433(+)$1	229	93	100	13.1969
UUUUGUU	chr1:224576583-224576824(-)$1	241	169	176	13.9545
UUUUUCU	chr2:3469330-3469558(+)$1	228	22	29	13.1969
UUUUUUU	chr11:94903973-94904199(-)$1	226	86	93	17.8181
UUAUUUU	chr2:200322689-200322911(-)$1	222	98	105	13.4999
uuuguuu	chr17:18763722-18763946(+)$1	224	39	46	13.6515
UUUUAUU	chr5:71503001-71503229(+)$1	228	126	133	13.8787
UUUUUAU	chr7:120607927-120608156(+)$1	229	32	39	13.1212
uucuuuu	chr3:23964970-23965198(+)$1	228	48	55	13.5757
UGUUUUU	chr17:15929758-15929984(+)$1	226	56	63	13.9545
UUUUUUU	chr12:123647483-123647712(-)$1	229	196	203	17.8181
UUUUUUU	chrX:62569090-62569318(-)$1	228	31	38	17.8181
UUCUUUU	chr9:2192628-2192857(+)$1	229	20	27	13.5757
UUUUUUU	chr16:74655438-74655664(-)$1	226	196	203	17.8181
UUUAUUU	chr12:39096562-39096786(-)$1	224	188	195	13.8030
UUUUUUU	chr11:76733421-76733652(+)$1	231	47	54	17.8181
UUUAUUU	chr4:110631910-110632138(-)$1	228	61	68	13.8030
UGUUUUU	chr4:170643283-170643508(+)$1	225	22	29	13.9545
UUUUCUU	chr17:27082883-27083104(+)$1	221	118	125	13.9545
uuuauuu	chr6:160102206-160102434(-)$1	228	199	206	13.8030
GUUUUUU	chr2:135694356-135694582(+)$1	226	1	8	13.1212
UUUUCUU	chr4:40247845-40248069(+)$1	224	27	34	13.9545
UUUUUUU	chr3:49061702-49061930(-)$1	228	140	147	17.8181
UUGUUUU	chr1:205758695-205758922(-)$1	227	184	191	13.4999
UUUUUUU	chr14:61110170-61110397(-)$1	227	42	49	17.8181
UUUAUUU	chr16:11940287-11940521(-)$1	234	50	57	13.8030
UGUUUUU	chr10:1086649-1086901(-)$1	252	101	108	13.9545
UUCUUUU	chr7:100961332-100961558(-)$1	226	48	55	13.5757
UUUUUUU	chr19:19617215-19617440(+)$1	225	208	215	17.8181
UUUGUUU	chr1:225589913-225590142(-)$1	229	14	21	13.6515
UCUUUUU	chr5:167983751-167983983(-)$1	232	196	203	13.8030
UAUUUUU	chr1:46125789-46126010(+)$1	221	3	10	13.7272
UUUUGUU	chr7:73643369-73643599(-)$1	230	9	16	13.9545

#otherMatches

#Struct PSSM
gggiiii	chr15:85213056-85213300(-)$1	244	10	17	13.8030
:::::::	chr17:7215168-7215408(+)$1	240	74	81	13.8030
hhhhhhh	chr2:37428698-37428928(+)$1	230	14	21	17.8181
ggggggg	chr2:42557623-42557861(+)$1	238	136	143	17.8181
22bb:::	chr15:58305972-58306197(-)$1	225	217	224	13.8787
nffffff	chr3:156865631-156865857(-)$1	226	126	133	13.4999
fiiiiii	chr16:19088541-19088773(+)$1	232	69	76	13.8030
:::::::	chr3:113440600-113440829(-)$1	229	15	22	17.8181
]gggggg	chr3:48786407-48786650(-)$1	243	58	65	13.1212
FFZZZFF	chr16:69337336-69337565(+)$1	229	210	217	13.9545
ccppppp	chr1:225685223-225685446(-)$1	223	172	179	13.1212
hhhhqqq	chr1:25168658-25168884(+)$1	226	56	63	17.8181
FFYYGGG	chr1:182353337-182353579(-)$1	242	151	158	17.8181
ee[eeee	chr8:28426280-28426504(+)$1	224	97	104	17.8181
[cccccc	chr10:104622592-104622821(+)$1	229	177	184	13.9545
=======	chr11:4159920-4160155(+)$1	235	37	44	13.9545
:::::::	chr5:76728700-76728940(-)$1	240	77	84	17.8181
[eeeee!	chr1:205685013-205685271(-)$1	258	154	161	13.6515
mmmmfff	chr4:36068436-36068664(-)$1	228	87	94	17.8181
:IIIIII	chr18:29709014-29709244(+)$1	230	31	38	13.9545
JJJJJJJ	chrX:24094795-24095063(+)$1	268	248	255	17.8181
gggggg$	chr1:171562214-171562450(+)$1	236	62	69	17.8181
ggggg44	chr1:225675491-225675718(-)$1	227	64	71	17.8181
dddd[ee	chr5:179149739-179149968(+)$1	229	52	59	17.8181
ggggggg	chr8:104340456-104340686(+)$1	230	27	34	13.7272
i[eeeee	chr4:77052286-77052515(-)$1	229	44	51	13.4999
=======	chr14:31588919-31589148(-)$1	229	62	69	13.8787
ooooccc	chr1:43310342-43310570(+)$1	228	53	60	13.9545
=======	chr5:149779632-149779865(+)$1	233	174	181	17.8181
[bb####	chr2:32853106-32853329(+)$1	223	46	53	13.9545
ddd9999	chr19:18320852-18321081(+)$1	229	147	154	17.8181
ggggggg	chr17:25635663-25635892(+)$1	229	67	74	17.8181
^^^^^^^	chr11:108348278-108348509(-)$1	231	53	60	17.8181
fffffan	chr6:126661204-126661433(+)$1	229	93	100	13.1969
CC}CCCY	chr1:224576583-224576824(-)$1	241	169	176	13.9545
JJJJJJJ	chr2:3469330-3469558(+)$1	228	22	29	13.1969
ggggGGG	chr11:94903973-94904199(-)$1	226	86	93	17.8181
^^^^^^^	chr2:200322689-200322911(-)$1	222	98	105	13.4999
JJJJJJJ	chr17:18763722-18763946(+)$1	224	39	46	13.6515
gg+++++	chr5:71503001-71503229(+)$1	228	126	133	13.8787
{DDDD::	chr7:120607927-120608156(+)$1	229	32	39	13.1212
eeebb[g	chr3:23964970-23965198(+)$1	228	48	55	13.5757
ccc####	chr17:15929758-15929984(+)$1	226	56	63	13.9545
ffff]ee	chr12:123647483-123647712(-)$1	229	196	203	17.8181
:::::gg	chrX:62569090-62569318(-)$1	228	31	38	17.8181
zzzzzzz	chr9:2192628-2192857(+)$1	229	20	27	13.5757
dssssss	chr16:74655438-74655664(-)$1	226	196	203	17.8181
iiiiiii	chr12:39096562-39096786(-)$1	224	188	195	13.8030
c======	chr11:76733421-76733652(+)$1	231	47	54	17.8181
gggggll	chr4:110631910-110632138(-)$1	228	61	68	13.8030
HHHHHHH	chr4:170643283-170643508(+)$1	225	22	29	13.9545
gggggg]	chr17:27082883-27083104(+)$1	221	118	125	13.9545
xxxxxxx	chr6:160102206-160102434(-)$1	228	199	206	13.8030
ddd[eee	chr2:135694356-135694582(+)$1	226	1	8	13.1212
)))))))	chr4:40247845-40248069(+)$1	224	27	34	13.9545
=======	chr3:49061702-49061930(-)$1	228	140	147	17.8181
YYDDDD@	chr1:205758695-205758922(-)$1	227	184	191	13.4999
7777eee	chr14:61110170-61110397(-)$1	227	42	49	17.8181
eeeeell	chr16:11940287-11940521(-)$1	234	50	57	13.8030
eeeee88	chr10:1086649-1086901(-)$1	252	101	108	13.9545
dddd"""	chr7:100961332-100961558(-)$1	226	48	55	13.5757
:::::::	chr19:19617215-19617440(+)$1	225	208	215	17.8181
fffffqq	chr1:225589913-225590142(-)$1	229	14	21	13.6515
dd4444e	chr5:167983751-167983983(-)$1	232	196	203	13.8030
eeeeooo	chr1:46125789-46126010(+)$1	221	3	10	13.7272
EEEEEMM	chr7:73643369-73643599(-)$1	230	9	16	13.9545

#DB
(((((((	chr15:85213056-85213300(-)$1	1	10	17	13.8030
.......	chr17:7215168-7215408(+)$1	1	74	81	13.8030
)))))))	chr2:37428698-37428928(+)$1	1	14	21	17.8181
(((((((	chr2:42557623-42557861(+)$1	1	136	143	17.8181
..))...	chr15:58305972-58306197(-)$1	1	217	224	13.8787
.))))))	chr3:156865631-156865857(-)$1	1	126	133	13.4999
(((((((	chr16:19088541-19088773(+)$1	1	69	76	13.8030
.......	chr3:113440600-113440829(-)$1	1	15	22	17.8181
.))))))	chr3:48786407-48786650(-)$1	1	58	65	13.1212
))...))	chr16:69337336-69337565(+)$1	1	210	217	13.9545
((.....	chr1:225685223-225685446(-)$1	1	172	179	13.1212
((((...	chr1:25168658-25168884(+)$1	1	56	63	17.8181
))..)))	chr1:182353337-182353579(-)$1	1	151	158	17.8181
((.((((	chr8:28426280-28426504(+)$1	1	97	104	17.8181
.((((((	chr10:104622592-104622821(+)$1	1	177	184	13.9545
(((((((	chr11:4159920-4160155(+)$1	1	37	44	13.9545
.......	chr5:76728700-76728940(-)$1	1	77	84	17.8181
.(((((.	chr1:205685013-205685271(-)$1	1	154	161	13.6515
....)))	chr4:36068436-36068664(-)$1	1	87	94	17.8181
.((((((	chr18:29709014-29709244(+)$1	1	31	38	13.9545
)))))))	chrX:24094795-24095063(+)$1	1	248	255	17.8181
((((((.	chr1:171562214-171562450(+)$1	1	62	69	17.8181
)))))..	chr1:225675491-225675718(-)$1	1	64	71	17.8181
((((.((	chr5:179149739-179149968(+)$1	1	52	59	17.8181
)))))))	chr8:104340456-104340686(+)$1	1	27	34	13.7272
(.(((((	chr4:77052286-77052515(-)$1	1	44	51	13.4999
)))))))	chr14:31588919-31589148(-)$1	1	62	69	13.8787
....)))	chr1:43310342-43310570(+)$1	1	53	60	13.9545
(((((((	chr5:149779632-149779865(+)$1	1	174	181	17.8181
.((....	chr2:32853106-32853329(+)$1	1	46	53	13.9545
)))....	chr19:18320852-18321081(+)$1	1	147	154	17.8181
(((((((	chr17:25635663-25635892(+)$1	1	67	74	17.8181
.......	chr11:108348278-108348509(-)$1	1	53	60	17.8181
((((((.	chr6:126661204-126661433(+)$1	1	93	100	13.1969
)).))).	chr1:224576583-224576824(-)$1	1	169	176	13.9545
(((((((	chr2:3469330-3469558(+)$1	1	22	29	13.1969
)))))))	chr11:94903973-94904199(-)$1	1	86	93	17.8181
.......	chr2:200322689-200322911(-)$1	1	98	105	13.4999
(((((((	chr17:18763722-18763946(+)$1	1	39	46	13.6515
((.....	chr5:71503001-71503229(+)$1	1	126	133	13.8787
.((((..	chr7:120607927-120608156(+)$1	1	32	39	13.1212
(((((.(	chr3:23964970-23965198(+)$1	1	48	55	13.5757
(((....	chr17:15929758-15929984(+)$1	1	56	63	13.9545
)))).))	chr12:123647483-123647712(-)$1	1	196	203	17.8181
.....((	chrX:62569090-62569318(-)$1	1	31	38	17.8181
.......	chr9:2192628-2192857(+)$1	1	20	27	13.5757
(......	chr16:74655438-74655664(-)$1	1	196	203	17.8181
)))))))	chr12:39096562-39096786(-)$1	1	188	195	13.8030
(((((((	chr11:76733421-76733652(+)$1	1	47	54	17.8181
(((((..	chr4:110631910-110632138(-)$1	1	61	68	13.8030
(((((((	chr4:170643283-170643508(+)$1	1	22	29	13.9545
)))))).	chr17:27082883-27083104(+)$1	1	118	125	13.9545
.......	chr6:160102206-160102434(-)$1	1	199	206	13.8030
(((.(((	chr2:135694356-135694582(+)$1	1	1	8	13.1212
.......	chr4:40247845-40248069(+)$1	1	27	34	13.9545
(((((((	chr3:49061702-49061930(-)$1	1	140	147	17.8181
..)))).	chr1:205758695-205758922(-)$1	1	184	191	13.4999
....)))	chr14:61110170-61110397(-)$1	1	42	49	17.8181
(((((..	chr16:11940287-11940521(-)$1	1	50	57	13.8030
)))))..	chr10:1086649-1086901(-)$1	1	101	108	13.9545
((((...	chr7:100961332-100961558(-)$1	1	48	55	13.5757
.......	chr19:19617215-19617440(+)$1	1	208	215	17.8181
(((((..	chr1:225589913-225590142(-)$1	1	14	21	13.6515
))....)	chr5:167983751-167983983(-)$1	1	196	203	13.8030
((((...	chr1:46125789-46126010(+)$1	1	3	10	13.7272
(((((..	chr7:73643369-73643599(-)$1	1	9	16	13.9545

#PSSM
U : 0.83	u : 0.12	A : 0.01	C : 0.01	G : 0.01	
U : 0.71	u : 0.13	G : 0.07	C : 0.04	A : 0.03	
U : 0.78	u : 0.10	A : 0.03	C : 0.03	g : 0.01	c : 0.01	G : 0.01	
U : 0.77	u : 0.10	A : 0.06	G : 0.03	g : 0.01	a : 0.01	
U : 0.72	u : 0.10	C : 0.06	G : 0.04	A : 0.03	a : 0.01	g : 0.01	
U : 0.81	u : 0.13	C : 0.03	A : 0.01	
U : 0.86	u : 0.13	

#score	1003.1212121212113
#seq	66
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m2_run1.nuc.txt

#NT
UGA	chr1:150280391-150280667(+)$1	276	28	31	9.0000
UGA	chr14:45433289-45433526(+)$1	237	2	5	9.0000
UGA	chr17:73919251-73919500(-)$1	249	45	48	9.0000
UGA	chr21:45222071-45222335(+)$1	264	61	64	9.0000
UGA	chr6:57048834-57049076(+)$1	242	9	12	9.0000
UGA	chr6:116573926-116574170(-)$1	244	155	158	9.0000
UGA	chr6:53133919-53134159(-)$1	240	131	134	9.0000
UGA	chr4:83347089-83347318(-)$1	229	11	14	9.0000
UGA	chr8:145010026-145010277(-)$1	251	3	6	9.0000
UGA	chr22:42913946-42914181(-)$1	235	47	50	9.0000
UGA	chr8:128752570-128752806(+)$1	236	16	19	9.0000
UGA	chr22:40804700-40804943(+)$1	243	55	58	9.0000
UGA	chr3:99895078-99895350(+)$1	272	51	54	9.0000
UGA	chr19:5119669-5119927(+)$1	258	101	104	9.0000
UGA	chr11:66136766-66137010(-)$1	244	56	59	9.0000
UGA	chr7:74113192-74113469(+)$1	277	102	105	9.0000
UGA	chr17:42286982-42287203(-)$1	221	28	31	9.0000
UGA	chr17:42290086-42290301(-)$1	215	116	119	9.0000
UGA	chr2:132249469-132249699(-)$1	230	119	122	9.0000
UGA	chr12:120173011-120173254(-)$1	243	45	48	9.0000
UGA	chr6:31504293-31504551(-)$1	258	64	67	9.0000
UGA	chr3:49739146-49739398(+)$1	252	1	4	9.0000
UGA	chr12:120575413-120575653(-)$1	240	57	60	9.0000
UGA	chr19:39306823-39307058(-)$1	235	41	44	9.0000
UGA	chr7:128040775-128041015(-)$1	240	9	12	9.0000
UGA	chr22:21288113-21288375(+)$1	262	37	40	9.0000
UGA	chr17:80038656-80038899(-)$1	243	155	158	9.0000
UGA	chr12:112915618-112915889(+)$1	271	15	18	9.0000
UGA	chr7:100285503-100285715(-)$1	212	57	60	9.0000
UGA	chr2:24930530-24930794(+)$1	264	76	79	9.0000
UGA	chr9:132985260-132985493(+)$1	233	138	141	9.0000
UGA	chr16:2825351-2825574(-)$1	223	19	22	9.0000
UGA	chr22:21212773-21213014(-)$1	241	184	187	9.0000
UGA	chr12:133256430-133256676(-)$1	246	31	34	9.0000
UGA	chr22:20097477-20097738(+)$1	261	49	52	9.0000
UGA	chr16:28734394-28734731(+)$1	337	21	24	9.0000
UGA	chr16:30204807-30205074(-)$1	267	4	7	9.0000
UGA	chr17:8416805-8417044(-)$1	239	21	24	9.0000
UGA	chr20:62250560-62250800(-)$1	240	13	16	9.0000
UGA	chr14:105859063-105859282(+)$1	219	86	89	9.0000
UGA	chr2:152320250-152320483(+)$1	233	70	73	9.0000
uga	chr13:53217339-53217592(+)$1	253	34	37	9.0000
UGA	chr1:40562761-40563017(-)$1	256	94	97	9.0000
UGA	chr17:11984650-11984887(+)$1	237	30	33	9.0000
UGA	chr20:57019031-57019261(+)$1	230	45	48	9.0000
UGA	chr5:78608146-78608377(+)$1	231	28	31	9.0000
UGA	chr7:6509158-6509391(-)$1	233	43	46	9.0000
UGA	chr19:50002725-50002975(+)$1	250	14	17	9.0000
UGA	chr1:14149558-14149805(+)$1	247	48	51	9.0000
UGA	chr6:30530140-30530378(-)$1	238	0	3	9.0000
UGA	chrX:16859680-16859916(+)$1	236	48	51	9.0000
UGA	chr2:27898362-27898597(+)$1	235	70	73	9.0000
UGA	chr4:435971-436192(-)$1	221	33	36	9.0000
UGA	chr15:41687117-41687341(-)$1	224	17	20	9.0000
UGA	chr10:32311700-32311931(-)$1	231	31	34	9.0000
UGA	chr2:70443263-70443495(-)$1	232	39	42	9.0000
UGA	chr11:62594946-62595185(-)$1	239	22	25	9.0000
UGA	chr6:26056325-26056577(-)$1	252	105	108	9.0000
UGA	chr16:14818072-14818321(+)$1	249	19	22	9.0000
UGA	chr1:16259722-16259953(+)$1	231	83	86	9.0000
UGA	chr22:41925175-41925431(-)$1	256	61	64	9.0000
UGA	chr19:48744125-48744375(-)$1	250	6	9	9.0000
UGA	chr1:114940224-114940491(-)$1	267	11	14	9.0000
UGA	chr17:20922379-20922598(-)$1	219	6	9	9.0000
UGA	chr17:26906282-26906517(-)$1	235	47	50	9.0000
UGA	chr1:234743112-234743393(-)$1	281	29	32	9.0000
UGA	chr6:3081205-3081444(+)$1	239	8	11	9.0000
UGA	chr9:2830912-2831128(-)$1	216	56	59	9.0000
UGA	chr1:40769635-40769841(-)$1	206	107	110	9.0000
UGA	chr3:51101852-51102089(+)$1	237	63	66	9.0000
UGA	chr5:132439562-132439809(+)$1	247	5	8	9.0000
UGA	chr8:67341254-67341535(+)$1	281	95	98	9.0000
UGA	chr5:158705206-158705437(+)$1	231	1	4	9.0000
UGA	chr17:16285178-16285426(+)$1	248	2	5	9.0000
UGA	chr7:16736454-16736695(+)$1	241	5	8	9.0000
UGA	chr5:157285842-157286081(-)$1	239	10	13	9.0000
UGA	chr1:109813918-109814170(+)$1	252	1	4	9.0000
UGA	chr7:99000925-99001215(-)$1	290	18	21	9.0000
UGA	chr7:98634593-98634840(+)$1	247	133	136	9.0000
UGA	chr1:47840802-47841032(+)$1	230	102	105	9.0000
UGA	chr6:31796399-31796691(+)$1	292	26	29	9.0000
UGA	chr15:84908493-84908723(+)$1	230	6	9	9.0000
UGA	chr11:57094145-57094354(-)$1	209	123	126	9.0000
UGA	chr22:18898309-18898542(+)$1	233	48	51	9.0000
UGA	chr4:39459757-39460021(-)$1	264	11	14	9.0000
UGA	chr21:30434710-30434916(-)$1	206	0	3	9.0000
UGA	chr11:62445296-62445562(-)$1	266	8	11	9.0000
UGA	chr19:53878951-53879202(+)$1	251	78	81	9.0000
UGA	chr17:49239006-49239265(+)$1	259	59	62	9.0000
UGA	chr19:2245369-2245648(+)$1	279	126	129	9.0000
UGA	chr13:76140747-76140984(+)$1	237	25	28	9.0000
UGA	chr6:114270245-114270477(-)$1	232	99	102	9.0000
UGA	chr4:466276-466506(-)$1	230	107	110	9.0000
UGA	chr19:10781932-10782150(+)$1	218	62	65	9.0000
UGA	chr14:70234884-70235099(+)$1	215	87	90	9.0000
UGA	chr11:10819314-10819528(-)$1	214	66	69	9.0000
UGA	chr16:15781192-15781464(+)$1	272	66	69	9.0000

#otherMatches

#Struct PSSM
GGG	chr11:114310231-114310462(+)$1	231	17	20	9.0000
rrr	chr1:150280391-150280667(+)$1	276	28	31	9.0000
DD:	chr14:45433289-45433526(+)$1	237	2	5	9.0000
ppp	chr17:73919251-73919500(-)$1	249	45	48	9.0000
DD:	chr21:45222071-45222335(+)$1	264	61	64	9.0000
II:	chr6:57048834-57049076(+)$1	242	9	12	9.0000
bb2	chr6:116573926-116574170(-)$1	244	155	158	9.0000
:::	chr6:53133919-53134159(-)$1	240	131	134	9.0000
ldd	chr4:83347089-83347318(-)$1	229	11	14	9.0000
::g	chr8:145010026-145010277(-)$1	251	3	6	9.0000
:cc	chr22:42913946-42914181(-)$1	235	47	50	9.0000
nnd	chr8:128752570-128752806(+)$1	236	16	19	9.0000
ooo	chr22:40804700-40804943(+)$1	243	55	58	9.0000
{DD	chr3:99895078-99895350(+)$1	272	51	54	9.0000
BB{	chr19:5119669-5119927(+)$1	258	101	104	9.0000
bbt	chr11:66136766-66137010(-)$1	244	56	59	9.0000
iii	chr7:74113192-74113469(+)$1	277	102	105	9.0000
"""	chr17:42286982-42287203(-)$1	221	28	31	9.0000
ooo	chr17:42290086-42290301(-)$1	215	116	119	9.0000
mmm	chr2:132249469-132249699(-)$1	230	119	122	9.0000
ttt	chr12:120173011-120173254(-)$1	243	45	48	9.0000
fff	chr6:31504293-31504551(-)$1	258	64	67	9.0000
:::	chr3:49739146-49739398(+)$1	252	1	4	9.0000
b[g	chr12:120575413-120575653(-)$1	240	57	60	9.0000
ee2	chr19:39306823-39307058(-)$1	235	41	44	9.0000
KKE	chr7:128040775-128041015(-)$1	240	9	12	9.0000
f]b	chr22:21288113-21288375(+)$1	262	37	40	9.0000
ppp	chr17:80038656-80038899(-)$1	243	155	158	9.0000
EE:	chr12:112915618-112915889(+)$1	271	15	18	9.0000
"""	chr7:100285503-100285715(-)$1	212	57	60	9.0000
f::	chr2:24930530-24930794(+)$1	264	76	79	9.0000
e55	chr9:132985260-132985493(+)$1	233	138	141	9.0000
GGG	chr16:2825351-2825574(-)$1	223	19	22	9.0000
999	chr22:21212773-21213014(-)$1	241	184	187	9.0000
JJJ	chr12:133256430-133256676(-)$1	246	31	34	9.0000
ppc	chr22:20097477-20097738(+)$1	261	49	52	9.0000
:ee	chr16:28734394-28734731(+)$1	337	21	24	9.0000
DMM	chr16:30204807-30205074(-)$1	267	4	7	9.0000
iii	chr17:8416805-8417044(-)$1	239	21	24	9.0000
:ff	chr20:62250560-62250800(-)$1	240	13	16	9.0000
dmm	chr14:105859063-105859282(+)$1	219	86	89	9.0000
eee	chr2:152320250-152320483(+)$1	233	70	73	9.0000
DD{	chr13:53217339-53217592(+)$1	253	34	37	9.0000
mcc	chr1:40562761-40563017(-)$1	256	94	97	9.0000
b[b	chr17:11984650-11984887(+)$1	237	30	33	9.0000
eee	chr20:57019031-57019261(+)$1	230	45	48	9.0000
===	chr5:78608146-78608377(+)$1	231	28	31	9.0000
Dcc	chr7:6509158-6509391(-)$1	233	43	46	9.0000
"dd	chr19:50002725-50002975(+)$1	250	14	17	9.0000
e]c	chr1:14149558-14149805(+)$1	247	48	51	9.0000
eee	chr6:30530140-30530378(-)$1	238	0	3	9.0000
e22	chrX:16859680-16859916(+)$1	236	48	51	9.0000
fff	chr2:27898362-27898597(+)$1	235	70	73	9.0000
CKK	chr4:435971-436192(-)$1	221	33	36	9.0000
FFF	chr15:41687117-41687341(-)$1	224	17	20	9.0000
dd]	chr10:32311700-32311931(-)$1	231	31	34	9.0000
ddd	chr2:70443263-70443495(-)$1	232	39	42	9.0000
::H	chr11:62594946-62595185(-)$1	239	22	25	9.0000
f>>	chr6:26056325-26056577(-)$1	252	105	108	9.0000
emm	chr16:14818072-14818321(+)$1	249	19	22	9.0000
DEE	chr1:16259722-16259953(+)$1	231	83	86	9.0000
ooo	chr22:41925175-41925431(-)$1	256	61	64	9.0000
E{H	chr19:48744125-48744375(-)$1	250	6	9	9.0000
eer	chr1:114940224-114940491(-)$1	267	11	14	9.0000
:DD	chr17:20922379-20922598(-)$1	219	6	9	9.0000
::c	chr17:26906282-26906517(-)$1	235	47	50	9.0000
cc:	chr1:234743112-234743393(-)$1	281	29	32	9.0000
:::	chr6:3081205-3081444(+)$1	239	8	11	9.0000
bhh	chr9:2830912-2831128(-)$1	216	56	59	9.0000
===	chr1:40769635-40769841(-)$1	206	107	110	9.0000
EEE	chr3:51101852-51102089(+)$1	237	63	66	9.0000
:::	chr5:132439562-132439809(+)$1	247	5	8	9.0000
:BB	chr8:67341254-67341535(+)$1	281	95	98	9.0000
:::	chr5:158705206-158705437(+)$1	231	1	4	9.0000
:::	chr17:16285178-16285426(+)$1	248	2	5	9.0000
E::	chr7:16736454-16736695(+)$1	241	5	8	9.0000
III	chr5:157285842-157286081(-)$1	239	10	13	9.0000
:cc	chr1:109813918-109814170(+)$1	252	1	4	9.0000
DDK	chr7:99000925-99001215(-)$1	290	18	21	9.0000
ggg	chr7:98634593-98634840(+)$1	247	133	136	9.0000
eee	chr1:47840802-47841032(+)$1	230	102	105	9.0000
EE:	chr6:31796399-31796691(+)$1	292	26	29	9.0000
ggg	chr15:84908493-84908723(+)$1	230	6	9	9.0000
:::	chr11:57094145-57094354(-)$1	209	123	126	9.0000
G::	chr22:18898309-18898542(+)$1	233	48	51	9.0000
[ee	chr4:39459757-39460021(-)$1	264	11	14	9.0000
EEE	chr21:30434710-30434916(-)$1	206	0	3	9.0000
CC{	chr11:62445296-62445562(-)$1	266	8	11	9.0000
)))	chr19:53878951-53879202(+)$1	251	78	81	9.0000
{BB	chr17:49239006-49239265(+)$1	259	59	62	9.0000
dmm	chr19:2245369-2245648(+)$1	279	126	129	9.0000
FFF	chr13:76140747-76140984(+)$1	237	25	28	9.0000
ccc	chr6:114270245-114270477(-)$1	232	99	102	9.0000
444	chr4:466276-466506(-)$1	230	107	110	9.0000
BBK	chr19:10781932-10782150(+)$1	218	62	65	9.0000
"cc	chr14:70234884-70235099(+)$1	215	87	90	9.0000
fff	chr11:10819314-10819528(-)$1	214	66	69	9.0000
fff	chr16:15781192-15781464(+)$1	272	66	69	9.0000

#DB
(((	chr11:114310231-114310462(+)$1	1	17	20	9.0000
...	chr1:150280391-150280667(+)$1	1	28	31	9.0000
((.	chr14:45433289-45433526(+)$1	1	2	5	9.0000
...	chr17:73919251-73919500(-)$1	1	45	48	9.0000
((.	chr21:45222071-45222335(+)$1	1	61	64	9.0000
((.	chr6:57048834-57049076(+)$1	1	9	12	9.0000
)).	chr6:116573926-116574170(-)$1	1	155	158	9.0000
...	chr6:53133919-53134159(-)$1	1	131	134	9.0000
.))	chr4:83347089-83347318(-)$1	1	11	14	9.0000
..(	chr8:145010026-145010277(-)$1	1	3	6	9.0000
.((	chr22:42913946-42914181(-)$1	1	47	50	9.0000
..)	chr8:128752570-128752806(+)$1	1	16	19	9.0000
...	chr22:40804700-40804943(+)$1	1	55	58	9.0000
.((	chr3:99895078-99895350(+)$1	1	51	54	9.0000
((.	chr19:5119669-5119927(+)$1	1	101	104	9.0000
((.	chr11:66136766-66137010(-)$1	1	56	59	9.0000
)))	chr7:74113192-74113469(+)$1	1	102	105	9.0000
...	chr17:42286982-42287203(-)$1	1	28	31	9.0000
...	chr17:42290086-42290301(-)$1	1	116	119	9.0000
...	chr2:132249469-132249699(-)$1	1	119	122	9.0000
...	chr12:120173011-120173254(-)$1	1	45	48	9.0000
)))	chr6:31504293-31504551(-)$1	1	64	67	9.0000
...	chr3:49739146-49739398(+)$1	1	1	4	9.0000
(.(	chr12:120575413-120575653(-)$1	1	57	60	9.0000
)).	chr19:39306823-39307058(-)$1	1	41	44	9.0000
..(	chr7:128040775-128041015(-)$1	1	9	12	9.0000
).)	chr22:21288113-21288375(+)$1	1	37	40	9.0000
...	chr17:80038656-80038899(-)$1	1	155	158	9.0000
((.	chr12:112915618-112915889(+)$1	1	15	18	9.0000
...	chr7:100285503-100285715(-)$1	1	57	60	9.0000
)..	chr2:24930530-24930794(+)$1	1	76	79	9.0000
)..	chr9:132985260-132985493(+)$1	1	138	141	9.0000
(((	chr16:2825351-2825574(-)$1	1	19	22	9.0000
...	chr22:21212773-21213014(-)$1	1	184	187	9.0000
(((	chr12:133256430-133256676(-)$1	1	31	34	9.0000
..)	chr22:20097477-20097738(+)$1	1	49	52	9.0000
.((	chr16:28734394-28734731(+)$1	1	21	24	9.0000
(..	chr16:30204807-30205074(-)$1	1	4	7	9.0000
(((	chr17:8416805-8417044(-)$1	1	21	24	9.0000
.((	chr20:62250560-62250800(-)$1	1	13	16	9.0000
(..	chr14:105859063-105859282(+)$1	1	86	89	9.0000
)))	chr2:152320250-152320483(+)$1	1	70	73	9.0000
((.	chr13:53217339-53217592(+)$1	1	34	37	9.0000
.))	chr1:40562761-40563017(-)$1	1	94	97	9.0000
(.(	chr17:11984650-11984887(+)$1	1	30	33	9.0000
)))	chr20:57019031-57019261(+)$1	1	45	48	9.0000
(((	chr5:78608146-78608377(+)$1	1	28	31	9.0000
(((	chr7:6509158-6509391(-)$1	1	43	46	9.0000
.((	chr19:50002725-50002975(+)$1	1	14	17	9.0000
).)	chr1:14149558-14149805(+)$1	1	48	51	9.0000
(((	chr6:30530140-30530378(-)$1	1	0	3	9.0000
)..	chrX:16859680-16859916(+)$1	1	48	51	9.0000
)))	chr2:27898362-27898597(+)$1	1	70	73	9.0000
(..	chr4:435971-436192(-)$1	1	33	36	9.0000
(((	chr15:41687117-41687341(-)$1	1	17	20	9.0000
)).	chr10:32311700-32311931(-)$1	1	31	34	9.0000
(((	chr2:70443263-70443495(-)$1	1	39	42	9.0000
..(	chr11:62594946-62595185(-)$1	1	22	25	9.0000
)..	chr6:26056325-26056577(-)$1	1	105	108	9.0000
(..	chr16:14818072-14818321(+)$1	1	19	22	9.0000
)((	chr1:16259722-16259953(+)$1	1	83	86	9.0000
...	chr22:41925175-41925431(-)$1	1	61	64	9.0000
(.(	chr19:48744125-48744375(-)$1	1	6	9	9.0000
((.	chr1:114940224-114940491(-)$1	1	11	14	9.0000
.((	chr17:20922379-20922598(-)$1	1	6	9	9.0000
..(	chr17:26906282-26906517(-)$1	1	47	50	9.0000
)).	chr1:234743112-234743393(-)$1	1	29	32	9.0000
...	chr6:3081205-3081444(+)$1	1	8	11	9.0000
)))	chr9:2830912-2831128(-)$1	1	56	59	9.0000
)))	chr1:40769635-40769841(-)$1	1	107	110	9.0000
(((	chr3:51101852-51102089(+)$1	1	63	66	9.0000
...	chr5:132439562-132439809(+)$1	1	5	8	9.0000
.))	chr8:67341254-67341535(+)$1	1	95	98	9.0000
...	chr5:158705206-158705437(+)$1	1	1	4	9.0000
...	chr17:16285178-16285426(+)$1	1	2	5	9.0000
(..	chr7:16736454-16736695(+)$1	1	5	8	9.0000
(((	chr5:157285842-157286081(-)$1	1	10	13	9.0000
.((	chr1:109813918-109814170(+)$1	1	1	4	9.0000
((.	chr7:99000925-99001215(-)$1	1	18	21	9.0000
)))	chr7:98634593-98634840(+)$1	1	133	136	9.0000
)))	chr1:47840802-47841032(+)$1	1	102	105	9.0000
((.	chr6:31796399-31796691(+)$1	1	26	29	9.0000
(((	chr15:84908493-84908723(+)$1	1	6	9	9.0000
...	chr11:57094145-57094354(-)$1	1	123	126	9.0000
(..	chr22:18898309-18898542(+)$1	1	48	51	9.0000
.((	chr4:39459757-39460021(-)$1	1	11	14	9.0000
(((	chr21:30434710-30434916(-)$1	1	0	3	9.0000
((.	chr11:62445296-62445562(-)$1	1	8	11	9.0000
...	chr19:53878951-53879202(+)$1	1	78	81	9.0000
.((	chr17:49239006-49239265(+)$1	1	59	62	9.0000
(..	chr19:2245369-2245648(+)$1	1	126	129	9.0000
(((	chr13:76140747-76140984(+)$1	1	25	28	9.0000
)))	chr6:114270245-114270477(-)$1	1	99	102	9.0000
...	chr4:466276-466506(-)$1	1	107	110	9.0000
((.	chr19:10781932-10782150(+)$1	1	62	65	9.0000
.((	chr14:70234884-70235099(+)$1	1	87	90	9.0000
)))	chr11:10819314-10819528(-)$1	1	66	69	9.0000
)))	chr16:15781192-15781464(+)$1	1	66	69	9.0000

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

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m1_run2.nuc.txt

#NT
UCU	chr4:41699123-41699364(+)$1	241	22	25	8.9999
ucu	chr6:163991663-163991892(+)$1	229	0	3	8.9999
UCU	chr3:113665485-113665707(+)$1	222	1	4	8.9999
UCU	chr10:104389996-104390272(+)$1	276	196	199	8.9999
UCU	chr19:49469983-49470201(+)$1	218	15	18	8.9999
UCU	chr3:182733072-182733291(-)$1	219	98	101	8.9999
UCU	chr17:79876188-79876422(-)$1	234	11	14	8.9999
UCU	chr11:110036456-110036694(+)$1	238	17	20	8.9999
ucu	chr19:18280279-18280517(+)$1	238	2	5	8.9999
ucu	chr3:12200520-12200752(-)$1	232	4	7	8.9999
UCU	chr3:133547059-133547284(-)$1	225	56	59	8.9999
ucu	chr17:26878313-26878544(-)$1	231	3	6	8.9999
UCU	chr4:159132172-159132392(+)$1	220	34	37	8.9999
UCU	chr7:143057392-143057609(-)$1	217	6	9	8.9999
UCU	chr5:141974694-141974921(-)$1	227	32	35	8.9999
UCU	chr4:76567881-76568104(-)$1	223	40	43	8.9999
UCU	chr8:133025115-133025330(+)$1	215	37	40	8.9999
UCU	chr19:2101780-2102001(-)$1	221	24	27	8.9999
UCU	chr2:73518396-73518616(+)$1	220	180	183	8.9999
UCU	chr19:1257270-1257489(+)$1	219	3	6	8.9999
UCU	chr12:51140314-51140555(+)$1	241	19	22	8.9999
UCU	chr1:203278264-203278489(+)$1	225	2	5	8.9999
UCU	chr20:3904712-3904931(-)$1	219	12	15	8.9999
UCU	chr12:26147906-26148154(+)$1	248	125	128	8.9999
UCU	chr11:121178615-121178833(+)$1	218	37	40	8.9999
ucu	chr5:139028430-139028659(+)$1	229	73	76	8.9999
UCU	chr11:76507765-76507981(+)$1	216	138	141	8.9999
UCU	chr14:71138682-71138908(+)$1	226	76	79	8.9999
UCU	chr2:55199255-55199491(-)$1	236	107	110	8.9999
UCU	chr3:42680256-42680471(+)$1	215	72	75	8.9999
UCU	chr8:93003779-93003998(+)$1	219	38	41	8.9999
UCU	chr16:4932675-4932896(+)$1	221	79	82	8.9999
UCU	chr15:78558217-78558454(+)$1	237	32	35	8.9999
uCU	chr12:76930701-76930919(-)$1	218	86	89	8.9999
UCU	chr16:29499640-29499874(+)$1	234	10	13	8.9999
UCU	chr8:91968485-91968718(+)$1	233	50	53	8.9999
UCU	chr1:202555647-202555868(+)$1	221	22	25	8.9999
UCU	chr22:38383188-38383414(+)$1	226	5	8	8.9999
UCU	chr14:59928986-59929205(-)$1	219	40	43	8.9999
UCU	chr1:45965427-45965642(-)$1	215	69	72	8.9999
UCU	chr18:67511186-67511410(+)$1	224	53	56	8.9999
UCU	chr2:175298955-175299177(-)$1	222	69	72	8.9999
UCU	chr11:28353798-28354026(+)$1	228	67	70	8.9999
UCU	chr3:9821753-9821978(-)$1	225	0	3	8.9999
UCU	chr11:9466830-9467047(-)$1	217	52	55	8.9999
UCU	chr3:2140490-2140705(-)$1	215	167	170	8.9999
UCU	chr12:10343500-10343715(+)$1	215	31	34	8.9999
UCU	chr12:27476917-27477137(+)$1	220	26	29	8.9999
UCU	chr1:205498376-205498621(+)$1	245	59	62	8.9999
UCU	chr2:201910166-201910386(-)$1	220	5	8	8.9999
UCU	chrX:41208272-41208505(+)$1	233	13	16	8.9999
UCU	chr11:118527508-118527730(+)$1	222	84	87	8.9999
UCU	chr2:11322346-11322575(-)$1	229	3	6	8.9999
UCU	chr14:102547923-102548153(-)$1	230	105	108	8.9999
UCU	chrX:48755667-48755889(+)$1	222	65	68	8.9999
UCU	chr9:130578028-130578250(+)$1	222	0	3	8.9999
UCU	chr9:125836535-125836754(+)$1	219	102	105	8.9999
UCU	chr1:246830922-246831165(+)$1	243	1	4	8.9999
UCU	chr12:124430280-124430501(-)$1	221	53	56	8.9999
UCU	chr8:21894127-21894347(+)$1	220	158	161	8.9999
UCU	chr16:19074945-19075166(+)$1	221	43	46	8.9999
UCU	chr19:11476039-11476277(+)$1	238	41	44	8.9999
UCU	chr15:44707805-44708028(+)$1	223	29	32	8.9999
UCU	chr8:71485765-71485988(-)$1	223	24	27	8.9999
UCU	chr17:5393455-5393679(+)$1	224	0	3	8.9999
UCU	chr8:21881565-21881785(+)$1	220	3	6	8.9999
UCU	chr14:75158790-75159018(-)$1	228	53	56	8.9999
UCU	chr1:61922705-61922926(+)$1	221	43	46	8.9999
UCU	chr19:40718924-40719142(+)$1	218	32	35	8.9999
UCU	chr8:145689217-145689436(-)$1	219	0	3	8.9999
UCU	chrX:128977184-128977407(-)$1	223	90	93	8.9999
UCU	chr16:4560655-4560876(+)$1	221	34	37	8.9999
UCU	chrX:119571450-119571669(-)$1	219	8	11	8.9999
UCU	chr5:14612535-14612750(+)$1	215	23	26	8.9999
UCU	chr7:100733395-100733618(+)$1	223	58	61	8.9999
UCU	chr16:24802508-24802734(+)$1	226	2	5	8.9999
UCU	chr20:462034-462253(+)$1	219	76	79	8.9999
UCU	chr17:29701666-29701888(-)$1	222	86	89	8.9999
UCU	chr16:31000760-31000983(-)$1	223	45	48	8.9999
UCU	chr3:49315287-49315502(-)$1	215	1	4	8.9999
UCU	chr12:133266782-133266999(-)$1	217	51	54	8.9999
UCU	chr22:43355617-43355832(-)$1	215	14	17	8.9999
UCU	chr15:40759355-40759601(+)$1	246	17	20	8.9999
UCU	chr22:50434873-50435088(-)$1	215	15	18	8.9999
UCU	chr15:66603961-66604181(+)$1	220	30	33	8.9999
UCU	chr21:34949657-34949881(+)$1	224	26	29	8.9999
UCU	chr17:73126760-73127003(-)$1	243	32	35	8.9999
UCU	chr3:124444708-124444927(+)$1	219	133	136	8.9999
UCU	chr3:138255788-138256014(-)$1	226	68	71	8.9999
UCU	chr1:145764336-145764554(+)$1	218	70	73	8.9999
UCU	chr1:22970403-22970632(+)$1	229	86	89	8.9999
UCU	chr16:16486205-16486423(+)$1	218	90	93	8.9999
ucu	chr1:29653209-29653440(+)$1	231	90	93	8.9999
UCU	chr6:157529116-157529331(-)$1	215	15	18	8.9999
UCU	chr15:45460068-45460284(+)$1	216	50	53	8.9999
UCU	chr10:102890635-102890854(-)$1	219	106	109	8.9999
UCU	chr3:151055188-151055410(-)$1	222	199	202	8.9999
UCU	chr6:39872039-39872254(+)$1	215	17	20	8.9999

#otherMatches

#Struct PSSM
CC:	chr5:137902717-137902938(-)$1	221	42	45	8.9999
d%%	chr4:41699123-41699364(+)$1	241	22	25	8.9999
:::	chr6:163991663-163991892(+)$1	229	0	3	8.9999
:JJ	chr3:113665485-113665707(+)$1	222	1	4	8.9999
$$$	chr10:104389996-104390272(+)$1	276	196	199	8.9999
ca[	chr19:49469983-49470201(+)$1	218	15	18	8.9999
:dd	chr3:182733072-182733291(-)$1	219	98	101	8.9999
:::	chr17:79876188-79876422(-)$1	234	11	14	8.9999
:::	chr11:110036456-110036694(+)$1	238	17	20	8.9999
:::	chr19:18280279-18280517(+)$1	238	2	5	8.9999
DKK	chr3:12200520-12200752(-)$1	232	4	7	8.9999
ggg	chr3:133547059-133547284(-)$1	225	56	59	8.9999
:CC	chr17:26878313-26878544(-)$1	231	3	6	8.9999
[bb	chr4:159132172-159132392(+)$1	220	34	37	8.9999
eee	chr7:143057392-143057609(-)$1	217	6	9	8.9999
mmm	chr5:141974694-141974921(-)$1	227	32	35	8.9999
::h	chr4:76567881-76568104(-)$1	223	40	43	8.9999
EEE	chr8:133025115-133025330(+)$1	215	37	40	8.9999
dcc	chr19:2101780-2102001(-)$1	221	24	27	8.9999
ccc	chr2:73518396-73518616(+)$1	220	180	183	8.9999
ddm	chr19:1257270-1257489(+)$1	219	3	6	8.9999
#ee	chr12:51140314-51140555(+)$1	241	19	22	8.9999
:::	chr1:203278264-203278489(+)$1	225	2	5	8.9999
ccc	chr20:3904712-3904931(-)$1	219	12	15	8.9999
[dd	chr12:26147906-26148154(+)$1	248	125	128	8.9999
iii	chr11:121178615-121178833(+)$1	218	37	40	8.9999
fff	chr5:139028430-139028659(+)$1	229	73	76	8.9999
iii	chr11:76507765-76507981(+)$1	216	138	141	8.9999
d]d	chr14:71138682-71138908(+)$1	226	76	79	8.9999
ggg	chr2:55199255-55199491(-)$1	236	107	110	8.9999
hhh	chr3:42680256-42680471(+)$1	215	72	75	8.9999
DDD	chr8:93003779-93003998(+)$1	219	38	41	8.9999
EEE	chr16:4932675-4932896(+)$1	221	79	82	8.9999
ooo	chr15:78558217-78558454(+)$1	237	32	35	8.9999
iii	chr12:76930701-76930919(-)$1	218	86	89	8.9999
FF:	chr16:29499640-29499874(+)$1	234	10	13	8.9999
eem	chr8:91968485-91968718(+)$1	233	50	53	8.9999
fff	chr1:202555647-202555868(+)$1	221	22	25	8.9999
HHH	chr22:38383188-38383414(+)$1	226	5	8	8.9999
ggg	chr14:59928986-59929205(-)$1	219	40	43	8.9999
::f	chr1:45965427-45965642(-)$1	215	69	72	8.9999
FFF	chr18:67511186-67511410(+)$1	224	53	56	8.9999
ccp	chr2:175298955-175299177(-)$1	222	69	72	8.9999
ddd	chr11:28353798-28354026(+)$1	228	67	70	8.9999
:::	chr3:9821753-9821978(-)$1	225	0	3	8.9999
d::	chr11:9466830-9467047(-)$1	217	52	55	8.9999
YCC	chr3:2140490-2140705(-)$1	215	167	170	8.9999
uuu	chr12:10343500-10343715(+)$1	215	31	34	8.9999
mmf	chr12:27476917-27477137(+)$1	220	26	29	8.9999
+++	chr1:205498376-205498621(+)$1	245	59	62	8.9999
JJJ	chr2:201910166-201910386(-)$1	220	5	8	8.9999
D:G	chrX:41208272-41208505(+)$1	233	13	16	8.9999
ddd	chr11:118527508-118527730(+)$1	222	84	87	8.9999
:::	chr2:11322346-11322575(-)$1	229	3	6	8.9999
)))	chr14:102547923-102548153(-)$1	230	105	108	8.9999
ccc	chrX:48755667-48755889(+)$1	222	65	68	8.9999
:EE	chr9:130578028-130578250(+)$1	222	0	3	8.9999
ee:	chr9:125836535-125836754(+)$1	219	102	105	8.9999
:::	chr1:246830922-246831165(+)$1	243	1	4	8.9999
CC:	chr12:124430280-124430501(-)$1	221	53	56	8.9999
emm	chr8:21894127-21894347(+)$1	220	158	161	8.9999
777	chr16:19074945-19075166(+)$1	221	43	46	8.9999
qqq	chr19:11476039-11476277(+)$1	238	41	44	8.9999
ccc	chr15:44707805-44708028(+)$1	223	29	32	8.9999
[a#	chr8:71485765-71485988(-)$1	223	24	27	8.9999
CCC	chr17:5393455-5393679(+)$1	224	0	3	8.9999
EEE	chr8:21881565-21881785(+)$1	220	3	6	8.9999
===	chr14:75158790-75159018(-)$1	228	53	56	8.9999
:::	chr1:61922705-61922926(+)$1	221	43	46	8.9999
!!d	chr19:40718924-40719142(+)$1	218	32	35	8.9999
:::	chr8:145689217-145689436(-)$1	219	0	3	8.9999
ddd	chrX:128977184-128977407(-)$1	223	90	93	8.9999
fff	chr16:4560655-4560876(+)$1	221	34	37	8.9999
:::	chrX:119571450-119571669(-)$1	219	8	11	8.9999
FFF	chr5:14612535-14612750(+)$1	215	23	26	8.9999
iii	chr7:100733395-100733618(+)$1	223	58	61	8.9999
FFF	chr16:24802508-24802734(+)$1	226	2	5	8.9999
55f	chr20:462034-462253(+)$1	219	76	79	8.9999
:::	chr17:29701666-29701888(-)$1	222	86	89	8.9999
DDD	chr16:31000760-31000983(-)$1	223	45	48	8.9999
:::	chr3:49315287-49315502(-)$1	215	1	4	8.9999
:cc	chr12:133266782-133266999(-)$1	217	51	54	8.9999
CQQ	chr22:43355617-43355832(-)$1	215	14	17	8.9999
ddd	chr15:40759355-40759601(+)$1	246	17	20	8.9999
c!!	chr22:50434873-50435088(-)$1	215	15	18	8.9999
fff	chr15:66603961-66604181(+)$1	220	30	33	8.9999
[a!	chr21:34949657-34949881(+)$1	224	26	29	8.9999
nnn	chr17:73126760-73127003(-)$1	243	32	35	8.9999
EEE	chr3:124444708-124444927(+)$1	219	133	136	8.9999
:::	chr3:138255788-138256014(-)$1	226	68	71	8.9999
EEE	chr1:145764336-145764554(+)$1	218	70	73	8.9999
c]e	chr1:22970403-22970632(+)$1	229	86	89	8.9999
bb3	chr16:16486205-16486423(+)$1	218	90	93	8.9999
e::	chr1:29653209-29653440(+)$1	231	90	93	8.9999
ODD	chr6:157529116-157529331(-)$1	215	15	18	8.9999
DDD	chr15:45460068-45460284(+)$1	216	50	53	8.9999
fff	chr10:102890635-102890854(-)$1	219	106	109	8.9999
ggg	chr3:151055188-151055410(-)$1	222	199	202	8.9999
fff	chr6:39872039-39872254(+)$1	215	17	20	8.9999

#DB
((.	chr5:137902717-137902938(-)$1	1	42	45	8.9999
(..	chr4:41699123-41699364(+)$1	1	22	25	8.9999
...	chr6:163991663-163991892(+)$1	1	0	3	8.9999
.((	chr3:113665485-113665707(+)$1	1	1	4	8.9999
...	chr10:104389996-104390272(+)$1	1	196	199	8.9999
((.	chr19:49469983-49470201(+)$1	1	15	18	8.9999
.((	chr3:182733072-182733291(-)$1	1	98	101	8.9999
...	chr17:79876188-79876422(-)$1	1	11	14	8.9999
...	chr11:110036456-110036694(+)$1	1	17	20	8.9999
...	chr19:18280279-18280517(+)$1	1	2	5	8.9999
(..	chr3:12200520-12200752(-)$1	1	4	7	8.9999
)))	chr3:133547059-133547284(-)$1	1	56	59	8.9999
.((	chr17:26878313-26878544(-)$1	1	3	6	8.9999
.((	chr4:159132172-159132392(+)$1	1	34	37	8.9999
(((	chr7:143057392-143057609(-)$1	1	6	9	8.9999
...	chr5:141974694-141974921(-)$1	1	32	35	8.9999
..(	chr4:76567881-76568104(-)$1	1	40	43	8.9999
(((	chr8:133025115-133025330(+)$1	1	37	40	8.9999
(((	chr19:2101780-2102001(-)$1	1	24	27	8.9999
(((	chr2:73518396-73518616(+)$1	1	180	183	8.9999
((.	chr19:1257270-1257489(+)$1	1	3	6	8.9999
.((	chr12:51140314-51140555(+)$1	1	19	22	8.9999
...	chr1:203278264-203278489(+)$1	1	2	5	8.9999
(((	chr20:3904712-3904931(-)$1	1	12	15	8.9999
.((	chr12:26147906-26148154(+)$1	1	125	128	8.9999
)))	chr11:121178615-121178833(+)$1	1	37	40	8.9999
(((	chr5:139028430-139028659(+)$1	1	73	76	8.9999
)))	chr11:76507765-76507981(+)$1	1	138	141	8.9999
).)	chr14:71138682-71138908(+)$1	1	76	79	8.9999
(((	chr2:55199255-55199491(-)$1	1	107	110	8.9999
)))	chr3:42680256-42680471(+)$1	1	72	75	8.9999
(((	chr8:93003779-93003998(+)$1	1	38	41	8.9999
(((	chr16:4932675-4932896(+)$1	1	79	82	8.9999
...	chr15:78558217-78558454(+)$1	1	32	35	8.9999
(((	chr12:76930701-76930919(-)$1	1	86	89	8.9999
((.	chr16:29499640-29499874(+)$1	1	10	13	8.9999
((.	chr8:91968485-91968718(+)$1	1	50	53	8.9999
(((	chr1:202555647-202555868(+)$1	1	22	25	8.9999
(((	chr22:38383188-38383414(+)$1	1	5	8	8.9999
(((	chr14:59928986-59929205(-)$1	1	40	43	8.9999
..(	chr1:45965427-45965642(-)$1	1	69	72	8.9999
(((	chr18:67511186-67511410(+)$1	1	53	56	8.9999
((.	chr2:175298955-175299177(-)$1	1	69	72	8.9999
(((	chr11:28353798-28354026(+)$1	1	67	70	8.9999
...	chr3:9821753-9821978(-)$1	1	0	3	8.9999
)..	chr11:9466830-9467047(-)$1	1	52	55	8.9999
.))	chr3:2140490-2140705(-)$1	1	167	170	8.9999
...	chr12:10343500-10343715(+)$1	1	31	34	8.9999
..)	chr12:27476917-27477137(+)$1	1	26	29	8.9999
...	chr1:205498376-205498621(+)$1	1	59	62	8.9999
(((	chr2:201910166-201910386(-)$1	1	5	8	8.9999
(.(	chrX:41208272-41208505(+)$1	1	13	16	8.9999
)))	chr11:118527508-118527730(+)$1	1	84	87	8.9999
...	chr2:11322346-11322575(-)$1	1	3	6	8.9999
...	chr14:102547923-102548153(-)$1	1	105	108	8.9999
)))	chrX:48755667-48755889(+)$1	1	65	68	8.9999
.((	chr9:130578028-130578250(+)$1	1	0	3	8.9999
)).	chr9:125836535-125836754(+)$1	1	102	105	8.9999
...	chr1:246830922-246831165(+)$1	1	1	4	8.9999
((.	chr12:124430280-124430501(-)$1	1	53	56	8.9999
(..	chr8:21894127-21894347(+)$1	1	158	161	8.9999
...	chr16:19074945-19075166(+)$1	1	43	46	8.9999
...	chr19:11476039-11476277(+)$1	1	41	44	8.9999
(((	chr15:44707805-44708028(+)$1	1	29	32	8.9999
.(.	chr8:71485765-71485988(-)$1	1	24	27	8.9999
(((	chr17:5393455-5393679(+)$1	1	0	3	8.9999
(((	chr8:21881565-21881785(+)$1	1	3	6	8.9999
)))	chr14:75158790-75159018(-)$1	1	53	56	8.9999
...	chr1:61922705-61922926(+)$1	1	43	46	8.9999
..(	chr19:40718924-40719142(+)$1	1	32	35	8.9999
...	chr8:145689217-145689436(-)$1	1	0	3	8.9999
)))	chrX:128977184-128977407(-)$1	1	90	93	8.9999
(((	chr16:4560655-4560876(+)$1	1	34	37	8.9999
...	chrX:119571450-119571669(-)$1	1	8	11	8.9999
(((	chr5:14612535-14612750(+)$1	1	23	26	8.9999
)))	chr7:100733395-100733618(+)$1	1	58	61	8.9999
(((	chr16:24802508-24802734(+)$1	1	2	5	8.9999
..)	chr20:462034-462253(+)$1	1	76	79	8.9999
...	chr17:29701666-29701888(-)$1	1	86	89	8.9999
(((	chr16:31000760-31000983(-)$1	1	45	48	8.9999
...	chr3:49315287-49315502(-)$1	1	1	4	8.9999
.((	chr12:133266782-133266999(-)$1	1	51	54	8.9999
(..	chr22:43355617-43355832(-)$1	1	14	17	8.9999
(((	chr15:40759355-40759601(+)$1	1	17	20	8.9999
(..	chr22:50434873-50435088(-)$1	1	15	18	8.9999
(((	chr15:66603961-66604181(+)$1	1	30	33	8.9999
.(.	chr21:34949657-34949881(+)$1	1	26	29	8.9999
...	chr17:73126760-73127003(-)$1	1	32	35	8.9999
)))	chr3:124444708-124444927(+)$1	1	133	136	8.9999
...	chr3:138255788-138256014(-)$1	1	68	71	8.9999
(((	chr1:145764336-145764554(+)$1	1	70	73	8.9999
).)	chr1:22970403-22970632(+)$1	1	86	89	8.9999
)).	chr16:16486205-16486423(+)$1	1	90	93	8.9999
)..	chr1:29653209-29653440(+)$1	1	90	93	8.9999
.((	chr6:157529116-157529331(-)$1	1	15	18	8.9999
(((	chr15:45460068-45460284(+)$1	1	50	53	8.9999
)))	chr10:102890635-102890854(-)$1	1	106	109	8.9999
)))	chr3:151055188-151055410(-)$1	1	199	202	8.9999
)))	chr6:39872039-39872254(+)$1	1	17	20	8.9999

#PSSM
U : 0.92	u : 0.07	
C : 0.93	c : 0.06	
U : 0.93	u : 0.06	

#score	890.9999999999993
#seq	99
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m2_run1.nuc.txt

#NT
UGUUUUU	chr22:22838965-22839191(-)$1	226	201	208	17.3492
UGUUUCU	chr1:51737882-51738107(+)$1	225	177	184	13.6984
UGAUUUU	chrX:112019264-112019501(-)$1	237	26	33	13.3809
UGUGUUU	chr7:27202543-27202779(-)$1	236	13	20	13.8571
UGUUUCU	chr10:75557626-75557850(+)$1	224	146	153	13.6984
UGUUUUU	chr10:112657926-112658163(+)$1	237	83	90	17.3492
UAUUUUU	chr2:8823887-8824109(+)$1	222	1	8	13.6984
UCUUUUU	chr14:54894362-54894606(-)$1	244	28	35	13.5396
UGUGUUU	chr3:125165854-125166075(-)$1	221	12	19	13.8571
UGUGUUU	chr16:24836654-24836906(+)$1	252	66	73	13.8571
UGCUUUU	chr6:86321670-86321915(-)$1	245	111	118	13.5396
UGUAUUU	chr9:37439891-37440122(-)$1	231	130	137	13.7777
UGUUUUU	chr9:138902346-138902572(-)$1	226	58	65	17.3492
UUUUUUU	chr1:2241374-2241599(+)$1	225	2	9	13.6190
UAUUUUU	chr13:77457653-77457890(-)$1	237	136	143	13.6984
UGUUUCU	chr17:46699791-46700014(-)$1	223	95	102	13.6984
UGUUUUU	chr2:38972165-38972406(-)$1	241	62	69	17.3492
uguuuuu	chr17:73884997-73885228(-)$1	231	221	228	17.3492
UGUUUUU	chr7:139246777-139247001(-)$1	224	143	150	17.3492
UGUGUUU	chr6:144144734-144144961(+)$1	227	185	192	13.8571
UUUUUUU	chr1:205685786-205686035(-)$1	249	211	218	13.6190
UGUUUUU	chr19:10244120-10244339(-)$1	219	57	64	17.3492
UGUCUUU	chr1:197122785-197123016(-)$1	231	91	98	13.5396
UGUUUUU	chr15:60782371-60782602(-)$1	231	99	106	17.3492
UGGUUUU	chr2:74331126-74331352(+)$1	226	73	80	13.3015
UGUUUUU	chr1:203278543-203278787(+)$1	244	107	114	17.3492
UGUUUUU	chr6:11138725-11138958(+)$1	233	139	146	17.3492
uuuuuuu	chr1:26227373-26227675(-)$1	302	45	52	13.6190
UGUCUUU	chr10:102312988-102313219(+)$1	231	113	120	13.5396
UGUGUUU	chr7:27193243-27193465(-)$1	222	84	91	13.8571
UAUUUUU	chr10:74035164-74035423(+)$1	259	63	70	13.6984
UGCUUUU	chr20:57478492-57478719(+)$1	227	4	11	13.5396
UGUUUAU	chr8:57074243-57074473(-)$1	230	65	72	13.3809
uauuuuu	chr14:23794524-23794746(+)$1	222	81	88	13.6984
UGUAUUU	chr16:66649783-66650009(-)$1	226	50	57	13.7777
UGUUUUU	chr2:239355341-239355564(+)$1	223	20	27	17.3492
uguuucu	chr16:18818061-18818284(-)$1	223	180	187	13.6984
UGUUUUU	chr16:84135549-84135774(-)$1	225	45	52	17.3492
UGCUUUU	chr3:142775857-142776095(+)$1	238	22	29	13.5396
UCUUUUU	chr19:21303134-21303357(+)$1	223	16	23	13.5396
UGUAUUU	chr2:40340042-40340269(-)$1	227	203	210	13.7777
UGUUUUU	chr7:131185650-131185874(-)$1	224	2	9	17.3492
UGCUUUU	chr12:31540136-31540358(-)$1	222	85	92	13.5396
UGCUUUU	chr11:9468502-9468743(+)$1	241	207	214	13.5396
UGUUUGU	chr19:47112573-47112807(+)$1	234	187	194	13.4603
UGUUUUU	chr3:138373925-138374152(-)$1	227	213	220	17.3492
UGUUUUU	chr1:70727439-70727681(-)$1	242	196	203	17.3492
UGUGUUU	chr15:44086825-44087056(+)$1	231	216	223	13.8571
UUUUUUU	chr3:160137186-160137421(+)$1	235	177	184	13.6190
UGUAUUU	chr9:129647049-129647280(+)$1	231	19	26	13.7777
UGAUUUU	chr3:160787593-160787813(+)$1	220	140	147	13.3809
UGUUUGU	chr17:47127912-47128143(+)$1	231	85	92	13.4603
UGUUUCU	chr9:116169519-116169740(-)$1	221	81	88	13.6984
UGUUUAU	chr9:100434193-100434424(+)$1	231	161	168	13.3809
UGGUUUU	chr6:7883348-7883582(-)$1	234	9	16	13.3015
UGUUUGU	chr1:167381177-167381405(+)$1	228	3	10	13.4603
UGUUUCU	chr2:219128796-219129023(-)$1	227	1	8	13.6984
ucuuuuu	chr19:1257196-1257456(+)$1	260	196	203	13.5396
UGUAUUU	chr15:38645885-38646113(+)$1	228	207	214	13.7777
UGUUUUU	chr15:77345054-77345301(-)$1	247	224	231	17.3492
UGAUUUU	chr5:140085167-140085423(+)$1	256	14	21	13.3809
UGUUUUU	chr2:201775657-201775896(-)$1	239	163	170	17.3492

#otherMatches

#Struct PSSM
::fffff	chr15:56121041-56121260(-)$1	219	164	171	13.6984
ccceeee	chr22:22838965-22839191(-)$1	226	201	208	17.3492
JJJJJJJ	chr1:51737882-51738107(+)$1	225	177	184	13.6984
:::::::	chrX:112019264-112019501(-)$1	237	26	33	13.3809
cc[dddd	chr7:27202543-27202779(-)$1	236	13	20	13.8571
DDDD}EE	chr10:75557626-75557850(+)$1	224	146	153	13.6984
mmmmhhh	chr10:112657926-112658163(+)$1	237	83	90	17.3492
:::EEEE	chr2:8823887-8824109(+)$1	222	1	8	13.6984
CPPPPPP	chr14:54894362-54894606(-)$1	244	28	35	13.5396
e[bb###	chr3:125165854-125166075(-)$1	221	12	19	13.8571
=======	chr16:24836654-24836906(+)$1	252	66	73	13.8571
IIIIIII	chr6:86321670-86321915(-)$1	245	111	118	13.5396
ffff!!b	chr9:37439891-37440122(-)$1	231	130	137	13.7777
:FFFFFF	chr9:138902346-138902572(-)$1	226	58	65	17.3492
=======	chr1:2241374-2241599(+)$1	225	2	9	13.6190
iiiiiii	chr13:77457653-77457890(-)$1	237	136	143	13.6984
cc4444f	chr17:46699791-46700014(-)$1	223	95	102	13.6984
ndddd]c	chr2:38972165-38972406(-)$1	241	62	69	17.3492
:::::::	chr17:73884997-73885228(-)$1	231	221	228	17.3492
hhhhhhm	chr7:139246777-139247001(-)$1	224	143	150	17.3492
EEEEeee	chr6:144144734-144144961(+)$1	227	185	192	13.8571
@@@@@@@	chr1:205685786-205686035(-)$1	249	211	218	13.6190
:::::::	chr19:10244120-10244339(-)$1	219	57	64	17.3492
))=====	chr1:197122785-197123016(-)$1	231	91	98	13.5396
eeee666	chr15:60782371-60782602(-)$1	231	99	106	17.3492
[dddd""	chr2:74331126-74331352(+)$1	226	73	80	13.3015
ggggggg	chr1:203278543-203278787(+)$1	244	107	114	17.3492
bffffff	chr6:11138725-11138958(+)$1	233	139	146	17.3492
eeeee""	chr1:26227373-26227675(-)$1	302	45	52	13.6190
e777777	chr10:102312988-102313219(+)$1	231	113	120	13.5396
IIIIddd	chr7:27193243-27193465(-)$1	222	84	91	13.8571
yyyyyyf	chr10:74035164-74035423(+)$1	259	63	70	13.6984
ggggggg	chr20:57478492-57478719(+)$1	227	4	11	13.5396
dddd!!c	chr8:57074243-57074473(-)$1	230	65	72	13.3809
iiiiiii	chr14:23794524-23794746(+)$1	222	81	88	13.6984
ma55555	chr16:66649783-66650009(-)$1	226	50	57	13.7777
:::::::	chr2:239355341-239355564(+)$1	223	20	27	17.3492
:::::::	chr16:18818061-18818284(-)$1	223	180	187	13.6984
qqqqqqq	chr16:84135549-84135774(-)$1	225	45	52	17.3492
IIIIIII	chr3:142775857-142776095(+)$1	238	22	29	13.5396
ggggggg	chr19:21303134-21303357(+)$1	223	16	23	13.5396
fff::FF	chr2:40340042-40340269(-)$1	227	203	210	13.7777
ddd[ddd	chr7:131185650-131185874(-)$1	224	2	9	17.3492
iiiiii2	chr12:31540136-31540358(-)$1	222	85	92	13.5396
cc333ff	chr11:9468502-9468743(+)$1	241	207	214	13.5396
eee]bb]	chr19:47112573-47112807(+)$1	234	187	194	13.4603
EEEYYII	chr3:138373925-138374152(-)$1	227	213	220	17.3492
ffffffm	chr1:70727439-70727681(-)$1	242	196	203	17.3492
ffffff:	chr15:44086825-44087056(+)$1	231	216	223	13.8571
FFFF:::	chr3:160137186-160137421(+)$1	235	177	184	13.6190
!ccc^^^	chr9:129647049-129647280(+)$1	231	19	26	13.7777
cccmmmm	chr3:160787593-160787813(+)$1	220	140	147	13.3809
cc"""dd	chr17:47127912-47128143(+)$1	231	85	92	13.4603
wwwwwww	chr9:116169519-116169740(-)$1	221	81	88	13.6984
ggg$$$$	chr9:100434193-100434424(+)$1	231	161	168	13.3809
##eeeee	chr6:7883348-7883582(-)$1	234	9	16	13.3015
EEEDDDD	chr1:167381177-167381405(+)$1	228	3	10	13.4603
:::::::	chr2:219128796-219129023(-)$1	227	1	8	13.6984
wwwwwww	chr19:1257196-1257456(+)$1	260	196	203	13.5396
YYFFFFF	chr15:38645885-38646113(+)$1	228	207	214	13.7777
DDDEEEE	chr15:77345054-77345301(-)$1	247	224	231	17.3492
GGGGLLL	chr5:140085167-140085423(+)$1	256	14	21	13.3809
=======	chr2:201775657-201775896(-)$1	239	163	170	17.3492

#DB
..(((((	chr15:56121041-56121260(-)$1	1	164	171	13.6984
)))))))	chr22:22838965-22839191(-)$1	1	201	208	17.3492
)))))))	chr1:51737882-51738107(+)$1	1	177	184	13.6984
.......	chrX:112019264-112019501(-)$1	1	26	33	13.3809
((.((((	chr7:27202543-27202779(-)$1	1	13	20	13.8571
)))).))	chr10:75557626-75557850(+)$1	1	146	153	13.6984
....)))	chr10:112657926-112658163(+)$1	1	83	90	17.3492
...((((	chr2:8823887-8824109(+)$1	1	1	8	13.6984
(......	chr14:54894362-54894606(-)$1	1	28	35	13.5396
(.((...	chr3:125165854-125166075(-)$1	1	12	19	13.8571
(((((((	chr16:24836654-24836906(+)$1	1	66	73	13.8571
)))))))	chr6:86321670-86321915(-)$1	1	111	118	13.5396
((((..(	chr9:37439891-37440122(-)$1	1	130	137	13.7777
.((((((	chr9:138902346-138902572(-)$1	1	58	65	17.3492
(((((((	chr1:2241374-2241599(+)$1	1	2	9	13.6190
(((((((	chr13:77457653-77457890(-)$1	1	136	143	13.6984
))....)	chr17:46699791-46700014(-)$1	1	95	102	13.6984
.)))).)	chr2:38972165-38972406(-)$1	1	62	69	17.3492
.......	chr17:73884997-73885228(-)$1	1	221	228	17.3492
((((((.	chr7:139246777-139247001(-)$1	1	143	150	17.3492
))))(((	chr6:144144734-144144961(+)$1	1	185	192	13.8571
.......	chr1:205685786-205686035(-)$1	1	211	218	13.6190
.......	chr19:10244120-10244339(-)$1	1	57	64	17.3492
..(((((	chr1:197122785-197123016(-)$1	1	91	98	13.5396
))))...	chr15:60782371-60782602(-)$1	1	99	106	17.3492
.((((..	chr2:74331126-74331352(+)$1	1	73	80	13.3015
)))))))	chr1:203278543-203278787(+)$1	1	107	114	17.3492
)))))))	chr6:11138725-11138958(+)$1	1	139	146	17.3492
(((((..	chr1:26227373-26227675(-)$1	1	45	52	13.6190
)......	chr10:102312988-102313219(+)$1	1	113	120	13.5396
(((((((	chr7:27193243-27193465(-)$1	1	84	91	13.8571
......)	chr10:74035164-74035423(+)$1	1	63	70	13.6984
(((((((	chr20:57478492-57478719(+)$1	1	4	11	13.5396
((((..(	chr8:57074243-57074473(-)$1	1	65	72	13.3809
(((((((	chr14:23794524-23794746(+)$1	1	81	88	13.6984
.).....	chr16:66649783-66650009(-)$1	1	50	57	13.7777
.......	chr2:239355341-239355564(+)$1	1	20	27	17.3492
.......	chr16:18818061-18818284(-)$1	1	180	187	13.6984
.......	chr16:84135549-84135774(-)$1	1	45	52	17.3492
(((((((	chr3:142775857-142776095(+)$1	1	22	29	13.5396
(((((((	chr19:21303134-21303357(+)$1	1	16	23	13.5396
)))..))	chr2:40340042-40340269(-)$1	1	203	210	13.7777
(((.(((	chr7:131185650-131185874(-)$1	1	2	9	17.3492
)))))).	chr12:31540136-31540358(-)$1	1	85	92	13.5396
))...))	chr11:9468502-9468743(+)$1	1	207	214	13.5396
))).)).	chr19:47112573-47112807(+)$1	1	187	194	13.4603
)))..))	chr3:138373925-138374152(-)$1	1	213	220	17.3492
((((((.	chr1:70727439-70727681(-)$1	1	196	203	17.3492
)))))).	chr15:44086825-44087056(+)$1	1	216	223	13.8571
))))...	chr3:160137186-160137421(+)$1	1	177	184	13.6190
.(((...	chr9:129647049-129647280(+)$1	1	19	26	13.7777
(((....	chr3:160787593-160787813(+)$1	1	140	147	13.3809
((...((	chr17:47127912-47128143(+)$1	1	85	92	13.4603
.......	chr9:116169519-116169740(-)$1	1	81	88	13.6984
(((....	chr9:100434193-100434424(+)$1	1	161	168	13.3809
..(((((	chr6:7883348-7883582(-)$1	1	9	16	13.3015
(((((((	chr1:167381177-167381405(+)$1	1	3	10	13.4603
.......	chr2:219128796-219129023(-)$1	1	1	8	13.6984
.......	chr19:1257196-1257456(+)$1	1	196	203	13.5396
..)))))	chr15:38645885-38646113(+)$1	1	207	214	13.7777
)))))))	chr15:77345054-77345301(-)$1	1	224	231	17.3492
((((...	chr5:140085167-140085423(+)$1	1	14	21	13.3809
(((((((	chr2:201775657-201775896(-)$1	1	163	170	17.3492

#PSSM
U : 0.92	u : 0.07	
G : 0.77	A : 0.06	U : 0.04	C : 0.03	g : 0.03	u : 0.01	a : 0.01	c : 0.01	
U : 0.76	C : 0.07	u : 0.07	A : 0.04	G : 0.03	
U : 0.71	G : 0.09	A : 0.07	u : 0.07	C : 0.03	
U : 0.92	u : 0.07	
U : 0.76	C : 0.07	u : 0.06	G : 0.04	A : 0.03	c : 0.01	
U : 0.92	u : 0.07	

#score	921.4126984126967
#seq	63
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m2_run1.nuc.txt

#NT
UUUUUUA	chr2:8946301-8946584(-)$1	283	224	231	13.3188
UUAUUUC	chr10:75185953-75186186(-)$1	233	31	38	13.4637
UAUUUUC	chr13:111319684-111319922(-)$1	238	220	227	13.0289
UUUUUUC	chr21:30380518-30380746(+)$1	228	199	206	17.1594
UUUUUUC	chr12:105588984-105589241(+)$1	257	75	82	17.1594
UGUUUUC	chr3:125279163-125279475(-)$1	312	98	105	13.2463
UGUUUUC	chr21:30304787-30305087(-)$1	300	43	50	13.2463
AUUUUUC	chr7:17379141-17379599(+)$1	458	1	8	13.0289
UUUUUUG	chr2:27423317-27423550(-)$1	233	29	36	13.1014
UUGUUUC	chr20:39721079-39721311(+)$1	232	153	160	13.5362
UUUUUUC	chr2:128028850-128029081(-)$1	231	10	17	17.1594
UUUUUUU	chr15:44067474-44067701(-)$1	227	219	226	13.5362
GUUUUUC	chr4:75040894-75041220(+)$1	326	90	97	13.0289
CUUUUUC	chr1:36501677-36501905(+)$1	228	79	86	13.0289
UGUUUUC	chr20:20021233-20021500(-)$1	267	80	87	13.2463
UAUUUUC	chr10:124177314-124177589(+)$1	275	122	129	13.0289
AUUUUUC	chr1:242024601-242024904(+)$1	303	32	39	13.0289
UUAUUUC	chrX:11778855-11779127(+)$1	272	70	77	13.4637
AUUUUUC	chr1:220156558-220156815(-)$1	257	58	65	13.0289
UUUUUUU	chr20:47693414-47693665(+)$1	251	207	214	13.5362
UUCUUUC	chr4:26422080-26422323(+)$1	243	81	88	13.5362
UUUUUUA	chr3:71161594-71161875(-)$1	281	22	29	13.3188
UUAUUUC	chr1:36291218-36291516(+)$1	298	49	56	13.4637
UUUUUUC	chr2:67629920-67630197(+)$1	277	52	59	17.1594
UUUUUUU	chr13:37580160-37580397(+)$1	237	183	190	13.5362
UUAUUUC	chr2:196851748-196852009(-)$1	261	51	58	13.4637
UUUCUUC	chr12:40153846-40154155(-)$1	309	105	112	12.8115
UUUUUUU	chr5:37605042-37605310(+)$1	268	80	87	13.5362
UUCUUUC	chr6:30673514-30673800(-)$1	286	37	44	13.5362
UUUUUUC	chr6:170657142-170657513(+)$1	371	81	88	17.1594
UUUUUUC	chr5:128440627-128440862(+)$1	235	9	16	17.1594
uuuuuuu	chr7:91699303-91699622(+)$1	319	2	9	13.5362
UGUUUUC	chr8:96264314-96264590(-)$1	276	16	23	13.2463
CUUUUUC	chr19:9075897-9076201(-)$1	304	151	158	13.0289
UUUUUUC	chr3:171510435-171510668(-)$1	233	84	91	17.1594
UCUUUUC	chr9:97221428-97221773(+)$1	345	68	75	13.1014
UUUUUUU	chr5:138643617-138643901(+)$1	284	188	195	13.5362
UUGUUUC	chr2:112615784-112616080(-)$1	296	218	225	13.5362
UUUUGUC	chr10:127525241-127525476(-)$1	235	33	40	12.5942
UUUUUUU	chr17:71202746-71202976(+)$1	230	31	38	13.5362
UUUUUUC	chr1:117957267-117957554(+)$1	287	47	54	17.1594
UCUUUUC	chr13:108862916-108863143(-)$1	227	134	141	13.1014
UGUUUUC	chr3:29628519-29628797(+)$1	278	74	81	13.2463
UUCUUUC	chr1:39781082-39781347(+)$1	265	41	48	13.5362
UUUCUUC	chr15:91544551-91544795(-)$1	244	91	98	12.8115
CUUUUUC	chr12:46758888-46759179(-)$1	291	77	84	13.0289
GUUUUUC	chr8:41801303-41801567(-)$1	264	17	24	13.0289
UCUUUUC	chr2:166897640-166897908(-)$1	268	98	105	13.1014
UUUUUUC	chr16:47644672-47644932(+)$1	260	55	62	17.1594
UUUUUUC	chr22:32205494-32205727(+)$1	233	158	165	17.1594
uuuuuuc	chr1:32834804-32835027(-)$1	223	78	85	17.1594
UUUUUUA	chr8:27677981-27678264(-)$1	283	37	44	13.3188
UUUUUUC	chr10:116595219-116595491(+)$1	272	59	66	17.1594
UUUUGUC	chr3:49867020-49867299(-)$1	279	174	181	12.5942
UUUUUUC	chr3:171965325-171965704(+)$1	379	195	202	17.1594
UUGUUUC	chr22:44062955-44063254(-)$1	299	291	298	13.5362
UUUGUUC	chr3:9121606-9121832(-)$1	226	41	48	12.5942
UUCUUUC	chr12:69263951-69264223(-)$1	272	29	36	13.5362
UUUCUUC	chr12:106751557-106751830(+)$1	273	77	84	12.8115
UUGUUUC	chr12:100603971-100604230(+)$1	259	38	45	13.5362
UUUCUUC	chr11:117109636-117109904(+)$1	268	256	263	12.8115
UUCUUUC	chr9:108126749-108127102(+)$1	353	59	66	13.5362
UUUUUUC	chr13:49051388-49051639(+)$1	251	160	167	17.1594
UUUUUUC	chr11:63438679-63438966(-)$1	287	42	49	17.1594
UUGUUUC	chr2:96963969-96964258(-)$1	289	7	14	13.5362
UUUUUUC	chr10:135346150-135346436(+)$1	286	29	36	17.1594
UUUUUUA	chr3:195063252-195063483(-)$1	231	49	56	13.3188
GUUUUUC	chr7:156450739-156450981(+)$1	242	70	77	13.0289

#otherMatches

#Struct PSSM
iiiiiii	chr3:9406840-9407107(+)$1	267	133	140	12.5942
YYEEEEE	chr2:8946301-8946584(-)$1	283	224	231	13.3188
:::::::	chr10:75185953-75186186(-)$1	233	31	38	13.4637
mmmeeee	chr13:111319684-111319922(-)$1	238	220	227	13.0289
\\\\\\\	chr21:30380518-30380746(+)$1	228	199	206	17.1594
KKFFFFF	chr12:105588984-105589241(+)$1	257	75	82	17.1594
fffffee	chr3:125279163-125279475(-)$1	312	98	105	13.2463
###ffff	chr21:30304787-30305087(-)$1	300	43	50	13.2463
DDD::::	chr7:17379141-17379599(+)$1	458	1	8	13.0289
%%%%%cc	chr2:27423317-27423550(-)$1	233	29	36	13.1014
:::::ff	chr20:39721079-39721311(+)$1	232	153	160	13.5362
:::::::	chr2:128028850-128029081(-)$1	231	10	17	17.1594
dd:::::	chr15:44067474-44067701(-)$1	227	219	226	13.5362
d####dd	chr4:75040894-75041220(+)$1	326	90	97	13.0289
ygggggg	chr1:36501677-36501905(+)$1	228	79	86	13.0289
2eeeee:	chr20:20021233-20021500(-)$1	267	80	87	13.2463
e::::::	chr10:124177314-124177589(+)$1	275	122	129	13.0289
66666ee	chr1:242024601-242024904(+)$1	303	32	39	13.0289
doooooo	chrX:11778855-11779127(+)$1	272	70	77	13.4637
pppppee	chr1:220156558-220156815(-)$1	257	58	65	13.0289
sss====	chr20:47693414-47693665(+)$1	251	207	214	13.5362
^^^^^^^	chr4:26422080-26422323(+)$1	243	81	88	13.5362
nneeeee	chr3:71161594-71161875(-)$1	281	22	29	13.3188
SSSSSSS	chr1:36291218-36291516(+)$1	298	49	56	13.4637
7777fff	chr2:67629920-67630197(+)$1	277	52	59	17.1594
>>>>>>>	chr13:37580160-37580397(+)$1	237	183	190	13.5362
ee333bb	chr2:196851748-196852009(-)$1	261	51	58	13.4637
KCCCHHH	chr12:40153846-40154155(-)$1	309	105	112	12.8115
:::::gg	chr5:37605042-37605310(+)$1	268	80	87	13.5362
fffff[e	chr6:30673514-30673800(-)$1	286	37	44	13.5362
]bb]eee	chr6:170657142-170657513(+)$1	371	81	88	17.1594
:::eeee	chr5:128440627-128440862(+)$1	235	9	16	17.1594
:::::::	chr7:91699303-91699622(+)$1	319	2	9	13.5362
D::::::	chr8:96264314-96264590(-)$1	276	16	23	13.2463
:::::::	chr19:9075897-9076201(-)$1	304	151	158	13.0289
ppppppg	chr3:171510435-171510668(-)$1	233	84	91	17.1594
:dddd[e	chr9:97221428-97221773(+)$1	345	68	75	13.1014
GGGGGGK	chr5:138643617-138643901(+)$1	284	188	195	13.5362
ffffffo	chr2:112615784-112616080(-)$1	296	218	225	13.5362
[eeeeen	chr10:127525241-127525476(-)$1	235	33	40	12.5942
^^^^^^^	chr17:71202746-71202976(+)$1	230	31	38	13.5362
c777777	chr1:117957267-117957554(+)$1	287	47	54	17.1594
dd[bb!!	chr13:108862916-108863143(-)$1	227	134	141	13.1014
iiiiiii	chr3:29628519-29628797(+)$1	278	74	81	13.2463
777777f	chr1:39781082-39781347(+)$1	265	41	48	13.5362
GYYAYYB	chr15:91544551-91544795(-)$1	244	91	98	12.8115
hhhhhh>	chr12:46758888-46759179(-)$1	291	77	84	13.0289
GGGNNNN	chr8:41801303-41801567(-)$1	264	17	24	13.0289
7777777	chr2:166897640-166897908(-)$1	268	98	105	13.1014
ee%%%%%	chr16:47644672-47644932(+)$1	260	55	62	17.1594
ee55555	chr22:32205494-32205727(+)$1	233	158	165	17.1594
I:=====	chr1:32834804-32835027(-)$1	223	78	85	17.1594
:::::ee	chr8:27677981-27678264(-)$1	283	37	44	13.3188
{GGGGGG	chr10:116595219-116595491(+)$1	272	59	66	17.1594
b[dddd!	chr3:49867020-49867299(-)$1	279	174	181	12.5942
^^^^^^^	chr3:171965325-171965704(+)$1	379	195	202	17.1594
g::::::	chr22:44062955-44063254(-)$1	299	291	298	13.5362
"""a###	chr3:9121606-9121832(-)$1	226	41	48	12.5942
^^^^^^^	chr12:69263951-69264223(-)$1	272	29	36	13.5362
fffff!!	chr12:106751557-106751830(+)$1	273	77	84	12.8115
iiiiiii	chr12:100603971-100604230(+)$1	259	38	45	13.5362
HHHHHHH	chr11:117109636-117109904(+)$1	268	256	263	12.8115
D{JJJJJ	chr9:108126749-108127102(+)$1	353	59	66	13.5362
ggggg[b	chr13:49051388-49051639(+)$1	251	160	167	17.1594
ooooooc	chr11:63438679-63438966(-)$1	287	42	49	17.1594
:::::::	chr2:96963969-96964258(-)$1	289	7	14	13.5362
=======	chr10:135346150-135346436(+)$1	286	29	36	17.1594
hhhhhhh	chr3:195063252-195063483(-)$1	231	49	56	13.3188
iiiiiid	chr7:156450739-156450981(+)$1	242	70	77	13.0289

#DB
)))))))	chr3:9406840-9407107(+)$1	1	133	140	12.5942
..)))))	chr2:8946301-8946584(-)$1	1	224	231	13.3188
.......	chr10:75185953-75186186(-)$1	1	31	38	13.4637
...))))	chr13:111319684-111319922(-)$1	1	220	227	13.0289
.......	chr21:30380518-30380746(+)$1	1	199	206	17.1594
..(((((	chr12:105588984-105589241(+)$1	1	75	82	17.1594
)))))))	chr3:125279163-125279475(-)$1	1	98	105	13.2463
...((((	chr21:30304787-30305087(-)$1	1	43	50	13.2463
(((....	chr7:17379141-17379599(+)$1	1	1	8	13.0289
.....((	chr2:27423317-27423550(-)$1	1	29	36	13.1014
.....((	chr20:39721079-39721311(+)$1	1	153	160	13.5362
.......	chr2:128028850-128029081(-)$1	1	10	17	17.1594
)).....	chr15:44067474-44067701(-)$1	1	219	226	13.5362
(....((	chr4:75040894-75041220(+)$1	1	90	97	13.0289
.))))))	chr1:36501677-36501905(+)$1	1	79	86	13.0289
.))))).	chr20:20021233-20021500(-)$1	1	80	87	13.2463
)......	chr10:124177314-124177589(+)$1	1	122	129	13.0289
.....))	chr1:242024601-242024904(+)$1	1	32	39	13.0289
(......	chrX:11778855-11779127(+)$1	1	70	77	13.4637
.....))	chr1:220156558-220156815(-)$1	1	58	65	13.0289
...))))	chr20:47693414-47693665(+)$1	1	207	214	13.5362
.......	chr4:26422080-26422323(+)$1	1	81	88	13.5362
..)))))	chr3:71161594-71161875(-)$1	1	22	29	13.3188
.......	chr1:36291218-36291516(+)$1	1	49	56	13.4637
....)))	chr2:67629920-67630197(+)$1	1	52	59	17.1594
.......	chr13:37580160-37580397(+)$1	1	183	190	13.5362
))...))	chr2:196851748-196852009(-)$1	1	51	58	13.4637
.((((((	chr12:40153846-40154155(-)$1	1	105	112	12.8115
.....((	chr5:37605042-37605310(+)$1	1	80	87	13.5362
(((((.(	chr6:30673514-30673800(-)$1	1	37	44	13.5362
.)).)))	chr6:170657142-170657513(+)$1	1	81	88	17.1594
...((((	chr5:128440627-128440862(+)$1	1	9	16	17.1594
.......	chr7:91699303-91699622(+)$1	1	2	9	13.5362
(......	chr8:96264314-96264590(-)$1	1	16	23	13.2463
.......	chr19:9075897-9076201(-)$1	1	151	158	13.0289
......)	chr3:171510435-171510668(-)$1	1	84	91	17.1594
.((((.(	chr9:97221428-97221773(+)$1	1	68	75	13.1014
((((((.	chr5:138643617-138643901(+)$1	1	188	195	13.5362
((((((.	chr2:112615784-112616080(-)$1	1	218	225	13.5362
.(((((.	chr10:127525241-127525476(-)$1	1	33	40	12.5942
.......	chr17:71202746-71202976(+)$1	1	31	38	13.5362
)......	chr1:117957267-117957554(+)$1	1	47	54	17.1594
((.((..	chr13:108862916-108863143(-)$1	1	134	141	13.1014
)))))))	chr3:29628519-29628797(+)$1	1	74	81	13.2463
......)	chr1:39781082-39781347(+)$1	1	41	48	13.5362
)..)..)	chr15:91544551-91544795(-)$1	1	91	98	12.8115
)))))).	chr12:46758888-46759179(-)$1	1	77	84	13.0289
(((....	chr8:41801303-41801567(-)$1	1	17	24	13.0289
.......	chr2:166897640-166897908(-)$1	1	98	105	13.1014
((.....	chr16:47644672-47644932(+)$1	1	55	62	17.1594
)).....	chr22:32205494-32205727(+)$1	1	158	165	17.1594
(.(((((	chr1:32834804-32835027(-)$1	1	78	85	17.1594
.....((	chr8:27677981-27678264(-)$1	1	37	44	13.3188
.((((((	chr10:116595219-116595491(+)$1	1	59	66	17.1594
(.((((.	chr3:49867020-49867299(-)$1	1	174	181	12.5942
.......	chr3:171965325-171965704(+)$1	1	195	202	17.1594
)......	chr22:44062955-44063254(-)$1	1	291	298	13.5362
...(...	chr3:9121606-9121832(-)$1	1	41	48	12.5942
.......	chr12:69263951-69264223(-)$1	1	29	36	13.5362
(((((..	chr12:106751557-106751830(+)$1	1	77	84	12.8115
)))))))	chr12:100603971-100604230(+)$1	1	38	45	13.5362
)))))))	chr11:117109636-117109904(+)$1	1	256	263	12.8115
(.(((((	chr9:108126749-108127102(+)$1	1	59	66	13.5362
(((((.(	chr13:49051388-49051639(+)$1	1	160	167	17.1594
......)	chr11:63438679-63438966(-)$1	1	42	49	17.1594
.......	chr2:96963969-96964258(-)$1	1	7	14	13.5362
)))))))	chr10:135346150-135346436(+)$1	1	29	36	17.1594
(((((((	chr3:195063252-195063483(-)$1	1	49	56	13.3188
)))))))	chr7:156450739-156450981(+)$1	1	70	77	13.0289

#PSSM
U : 0.84	A : 0.04	G : 0.04	C : 0.04	u : 0.02	
U : 0.82	G : 0.07	C : 0.04	A : 0.02	u : 0.02	
U : 0.76	G : 0.07	C : 0.07	A : 0.05	u : 0.02	
U : 0.89	C : 0.05	u : 0.02	G : 0.01	
U : 0.92	G : 0.04	u : 0.02	
U : 0.97	u : 0.02	
C : 0.81	U : 0.08	A : 0.05	G : 0.01	u : 0.01	c : 0.01	

#score	975.3768115942015
#seq	69
#width	7
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m3_run2.nuc.txt

#NT
GUUUU	chr8:91637676-91637913(-)$1	237	131	136	14.9999
GUUUU	chr6:161557213-161557467(-)$1	254	66	71	14.9999
GUUUU	chr10:102311911-102312163(+)$1	252	45	50	14.9999
GUUUU	chr4:54257113-54257344(+)$1	231	49	54	14.9999
GUUUU	chr4:160280511-160280776(+)$1	265	134	139	14.9999
GUUUU	chr1:35649494-35649727(-)$1	233	166	171	14.9999
GUUUU	chr12:50152377-50152632(+)$1	255	138	143	14.9999
GUUUU	chr3:178739835-178740069(-)$1	234	68	73	14.9999
GUUUU	chr9:131770326-131770553(-)$1	227	182	187	14.9999
GUUUU	chr14:102550149-102550376(-)$1	227	8	13	14.9999
GUUUU	chr2:102510727-102510951(+)$1	224	69	74	14.9999
GUUUU	chrX:112020682-112020930(-)$1	248	169	174	14.9999
GUUUU	chr5:138704397-138704640(+)$1	243	206	211	14.9999
GUUUU	chr3:197768708-197768943(+)$1	235	194	199	14.9999
GUUUU	chr17:27589341-27589624(-)$1	283	189	194	14.9999
GUUUU	chr6:158929569-158929794(+)$1	225	159	164	14.9999
GUUUU	chr1:203277056-203277323(+)$1	267	179	184	14.9999
GUUUU	chr5:179203982-179204204(+)$1	222	108	113	14.9999
GUUUU	chr18:57571222-57571447(+)$1	225	144	149	14.9999
GUUUU	chr11:69466521-69466744(+)$1	223	10	15	14.9999
GUUUU	chr2:20450110-20450345(-)$1	235	163	168	14.9999
GUUUU	chr1:183114483-183114720(+)$1	237	187	192	14.9999
GUUUU	chr12:10851737-10851965(-)$1	228	90	95	14.9999
GUUUU	chr2:20232386-20232630(-)$1	244	231	236	14.9999
GUUUU	chr3:194123632-194123863(-)$1	231	90	95	14.9999
GUUUU	chr8:38068025-38068256(+)$1	231	163	168	14.9999
GUUUU	chr8:64124879-64125115(+)$1	236	205	210	14.9999
GUUUU	chr6:97244140-97244364(-)$1	224	100	105	14.9999
GUUUU	chr11:61136516-61136742(+)$1	226	126	131	14.9999
GUUUU	chr3:88103956-88104183(-)$1	227	87	92	14.9999
GUUUU	chr16:3631090-3631324(-)$1	234	101	106	14.9999
GUUUU	chr8:95893269-95893495(-)$1	226	127	132	14.9999
GUUUU	chr4:166263292-166263528(+)$1	236	23	28	14.9999
GUUUU	chr3:194123594-194123830(-)$1	236	57	62	14.9999
guUUU	chr1:42643284-42643539(-)$1	255	110	115	14.9999
GUUUU	chr8:104344344-104344581(+)$1	237	33	38	14.9999
GUUUU	chrX:84527201-84527423(+)$1	222	131	136	14.9999
GUUUU	chr7:99667514-99667790(-)$1	276	92	97	14.9999
GUUUU	chr14:54894127-54894404(-)$1	277	44	49	14.9999
GUUUU	chr17:48211213-48211472(-)$1	259	9	14	14.9999
GUUUU	chr6:132781101-132781330(-)$1	229	83	88	14.9999
GUUUU	chr14:69847074-69847313(-)$1	239	129	134	14.9999
GUUUU	chr7:156473634-156473868(-)$1	234	28	33	14.9999
GUUUU	chr5:125962587-125962818(+)$1	231	51	56	14.9999
GUUUU	chr1:47143546-47143808(-)$1	262	172	177	14.9999
guuuu	chr1:45285466-45285725(-)$1	259	130	135	14.9999
GUUUU	chr12:120636861-120637103(-)$1	242	7	12	14.9999
GUUUU	chr7:155101242-155101467(+)$1	225	31	36	14.9999
GUUUU	chr12:12874891-12875146(+)$1	255	234	239	14.9999
GUUUU	chr5:134121127-134121360(+)$1	233	85	90	14.9999
GUUUU	chr1:203276503-203276754(+)$1	251	212	217	14.9999
GUUUU	chr22:50167735-50167989(-)$1	254	240	245	14.9999
GUUUU	chr1:222839076-222839303(+)$1	227	131	136	14.9999
GUUUU	chr1:52818265-52818515(-)$1	250	195	200	14.9999
GUUUU	chr1:203278430-203278675(+)$1	245	221	226	14.9999
GUUUU	chr1:226548923-226549163(-)$1	240	151	156	14.9999
GUUUU	chr4:185549187-185549428(-)$1	241	216	221	14.9999
GUUUU	chrX:134167384-134167633(+)$1	249	33	38	14.9999
GUUUU	chr19:14230335-14230567(-)$1	232	192	197	14.9999
GUUUU	chr6:157529401-157529627(+)$1	226	61	66	14.9999
GUUUU	chr17:27589734-27589957(-)$1	223	6	11	14.9999

#otherMatches

#Struct PSSM
hhhhh	chr1:205684301-205684572(-)$1	271	171	176	14.9999
d''''	chr8:91637676-91637913(-)$1	237	131	136	14.9999
cccmm	chr6:161557213-161557467(-)$1	254	66	71	14.9999
""ddd	chr10:102311911-102312163(+)$1	252	45	50	14.9999
nnnnb	chr4:54257113-54257344(+)$1	231	49	54	14.9999
ooooo	chr4:160280511-160280776(+)$1	265	134	139	14.9999
ppppp	chr1:35649494-35649727(-)$1	233	166	171	14.9999
ccc$$	chr12:50152377-50152632(+)$1	255	138	143	14.9999
iiiii	chr3:178739835-178740069(-)$1	234	68	73	14.9999
ee000	chr9:131770326-131770553(-)$1	227	182	187	14.9999
E{CCC	chr14:102550149-102550376(-)$1	227	8	13	14.9999
66666	chr2:102510727-102510951(+)$1	224	69	74	14.9999
ggggg	chrX:112020682-112020930(-)$1	248	169	174	14.9999
hhhhh	chr5:138704397-138704640(+)$1	243	206	211	14.9999
fffff	chr3:197768708-197768943(+)$1	235	194	199	14.9999
"ffff	chr17:27589341-27589624(-)$1	283	189	194	14.9999
a22cc	chr6:158929569-158929794(+)$1	225	159	164	14.9999
d]===	chr1:203277056-203277323(+)$1	267	179	184	14.9999
ttttg	chr5:179203982-179204204(+)$1	222	108	113	14.9999
f4444	chr18:57571222-57571447(+)$1	225	144	149	14.9999
DD{CC	chr11:69466521-69466744(+)$1	223	10	15	14.9999
))))f	chr2:20450110-20450345(-)$1	235	163	168	14.9999
:::EE	chr1:183114483-183114720(+)$1	237	187	192	14.9999
eeeed	chr12:10851737-10851965(-)$1	228	90	95	14.9999
sssss	chr2:20232386-20232630(-)$1	244	231	236	14.9999
b]a22	chr3:194123632-194123863(-)$1	231	90	95	14.9999
bbfff	chr8:38068025-38068256(+)$1	231	163	168	14.9999
fffff	chr8:64124879-64125115(+)$1	236	205	210	14.9999
?????	chr6:97244140-97244364(-)$1	224	100	105	14.9999
fffff	chr11:61136516-61136742(+)$1	226	126	131	14.9999
hhh[b	chr3:88103956-88104183(-)$1	227	87	92	14.9999
geeee	chr16:3631090-3631324(-)$1	234	101	106	14.9999
ohhhh	chr8:95893269-95893495(-)$1	226	127	132	14.9999
PPPPP	chr4:166263292-166263528(+)$1	236	23	28	14.9999
ee333	chr3:194123594-194123830(-)$1	236	57	62	14.9999
dddd3	chr1:42643284-42643539(-)$1	255	110	115	14.9999
hhhhh	chr8:104344344-104344581(+)$1	237	33	38	14.9999
GGGGG	chrX:84527201-84527423(+)$1	222	131	136	14.9999
ccc[d	chr7:99667514-99667790(-)$1	276	92	97	14.9999
HHHHH	chr14:54894127-54894404(-)$1	277	44	49	14.9999
ee[ff	chr17:48211213-48211472(-)$1	259	9	14	14.9999
ccmmm	chr6:132781101-132781330(-)$1	229	83	88	14.9999
cc]ee	chr14:69847074-69847313(-)$1	239	129	134	14.9999
=====	chr7:156473634-156473868(-)$1	234	28	33	14.9999
!!===	chr5:125962587-125962818(+)$1	231	51	56	14.9999
]dddd	chr1:47143546-47143808(-)$1	262	172	177	14.9999
ee:::	chr1:45285466-45285725(-)$1	259	130	135	14.9999
CCKKG	chr12:120636861-120637103(-)$1	242	7	12	14.9999
oooff	chr7:155101242-155101467(+)$1	225	31	36	14.9999
cc]dd	chr12:12874891-12875146(+)$1	255	234	239	14.9999
ggggm	chr5:134121127-134121360(+)$1	233	85	90	14.9999
hhhhh	chr1:203276503-203276754(+)$1	251	212	217	14.9999
DDEEE	chr22:50167735-50167989(-)$1	254	240	245	14.9999
fff[b	chr1:222839076-222839303(+)$1	227	131	136	14.9999
meeee	chr1:52818265-52818515(-)$1	250	195	200	14.9999
ggggg	chr1:203278430-203278675(+)$1	245	221	226	14.9999
nnnnn	chr1:226548923-226549163(-)$1	240	151	156	14.9999
>>>>>	chr4:185549187-185549428(-)$1	241	216	221	14.9999
sssss	chrX:134167384-134167633(+)$1	249	33	38	14.9999
=====	chr19:14230335-14230567(-)$1	232	192	197	14.9999
eeeee	chr6:157529401-157529627(+)$1	226	61	66	14.9999
HHH::	chr17:27589734-27589957(-)$1	223	6	11	14.9999

#DB
)))))	chr1:205684301-205684572(-)$1	1	171	176	14.9999
(....	chr8:91637676-91637913(-)$1	1	131	136	14.9999
(((..	chr6:161557213-161557467(-)$1	1	66	71	14.9999
..(((	chr10:102311911-102312163(+)$1	1	45	50	14.9999
....)	chr4:54257113-54257344(+)$1	1	49	54	14.9999
.....	chr4:160280511-160280776(+)$1	1	134	139	14.9999
.....	chr1:35649494-35649727(-)$1	1	166	171	14.9999
(((..	chr12:50152377-50152632(+)$1	1	138	143	14.9999
)))))	chr3:178739835-178740069(-)$1	1	68	73	14.9999
))...	chr9:131770326-131770553(-)$1	1	182	187	14.9999
(.(((	chr14:102550149-102550376(-)$1	1	8	13	14.9999
.....	chr2:102510727-102510951(+)$1	1	69	74	14.9999
)))))	chrX:112020682-112020930(-)$1	1	169	174	14.9999
)))))	chr5:138704397-138704640(+)$1	1	206	211	14.9999
)))))	chr3:197768708-197768943(+)$1	1	194	199	14.9999
.((((	chr17:27589341-27589624(-)$1	1	189	194	14.9999
)..))	chr6:158929569-158929794(+)$1	1	159	164	14.9999
).)))	chr1:203277056-203277323(+)$1	1	179	184	14.9999
....)	chr5:179203982-179204204(+)$1	1	108	113	14.9999
)....	chr18:57571222-57571447(+)$1	1	144	149	14.9999
((.((	chr11:69466521-69466744(+)$1	1	10	15	14.9999
....(	chr2:20450110-20450345(-)$1	1	163	168	14.9999
...))	chr1:183114483-183114720(+)$1	1	187	192	14.9999
)))))	chr12:10851737-10851965(-)$1	1	90	95	14.9999
.....	chr2:20232386-20232630(-)$1	1	231	236	14.9999
).)..	chr3:194123632-194123863(-)$1	1	90	95	14.9999
)))))	chr8:38068025-38068256(+)$1	1	163	168	14.9999
)))))	chr8:64124879-64125115(+)$1	1	205	210	14.9999
.....	chr6:97244140-97244364(-)$1	1	100	105	14.9999
)))))	chr11:61136516-61136742(+)$1	1	126	131	14.9999
(((.(	chr3:88103956-88104183(-)$1	1	87	92	14.9999
(((((	chr16:3631090-3631324(-)$1	1	101	106	14.9999
.))))	chr8:95893269-95893495(-)$1	1	127	132	14.9999
.....	chr4:166263292-166263528(+)$1	1	23	28	14.9999
))...	chr3:194123594-194123830(-)$1	1	57	62	14.9999
)))).	chr1:42643284-42643539(-)$1	1	110	115	14.9999
)))))	chr8:104344344-104344581(+)$1	1	33	38	14.9999
)))))	chrX:84527201-84527423(+)$1	1	131	136	14.9999
(((.(	chr7:99667514-99667790(-)$1	1	92	97	14.9999
(((((	chr14:54894127-54894404(-)$1	1	44	49	14.9999
((.((	chr17:48211213-48211472(-)$1	1	9	14	14.9999
((...	chr6:132781101-132781330(-)$1	1	83	88	14.9999
)).))	chr14:69847074-69847313(-)$1	1	129	134	14.9999
(((((	chr7:156473634-156473868(-)$1	1	28	33	14.9999
..(((	chr5:125962587-125962818(+)$1	1	51	56	14.9999
.))))	chr1:47143546-47143808(-)$1	1	172	177	14.9999
))...	chr1:45285466-45285725(-)$1	1	130	135	14.9999
((..(	chr12:120636861-120637103(-)$1	1	7	12	14.9999
...))	chr7:155101242-155101467(+)$1	1	31	36	14.9999
)).))	chr12:12874891-12875146(+)$1	1	234	239	14.9999
((((.	chr5:134121127-134121360(+)$1	1	85	90	14.9999
)))))	chr1:203276503-203276754(+)$1	1	212	217	14.9999
)))))	chr22:50167735-50167989(-)$1	1	240	245	14.9999
(((.(	chr1:222839076-222839303(+)$1	1	131	136	14.9999
.))))	chr1:52818265-52818515(-)$1	1	195	200	14.9999
)))))	chr1:203278430-203278675(+)$1	1	221	226	14.9999
.....	chr1:226548923-226549163(-)$1	1	151	156	14.9999
.....	chr4:185549187-185549428(-)$1	1	216	221	14.9999
.....	chrX:134167384-134167633(+)$1	1	33	38	14.9999
(((((	chr19:14230335-14230567(-)$1	1	192	197	14.9999
(((((	chr6:157529401-157529627(+)$1	1	61	66	14.9999
(((..	chr17:27589734-27589957(-)$1	1	6	11	14.9999

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

#score	929.9999999999999
#seq	62
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m1_run1.nuc.txt

#NT
auuuu	chr7:24864492-24864756(-)$1	264	191	196	14.9999
AUUUU	chr12:46582397-46582643(-)$1	246	103	108	14.9999
auuuu	chr6:97263380-97263613(-)$1	233	121	126	14.9999
AUUUU	chr17:27127298-27127528(-)$1	230	8	13	14.9999
auuuu	chr1:109962242-109962511(-)$1	269	235	240	14.9999
auuuu	chr19:39330385-39330620(-)$1	235	100	105	14.9999
Auuuu	chr21:17205876-17206102(+)$1	226	32	37	14.9999
auuuu	chr1:54318888-54319144(-)$1	256	226	231	14.9999
auuuu	chr2:27843159-27843391(+)$1	232	134	139	14.9999
auuuu	chr5:118616702-118617061(+)$1	359	139	144	14.9999
auuuu	chr4:74062319-74062594(-)$1	275	15	20	14.9999
auuuu	chr14:73779973-73780197(-)$1	224	6	11	14.9999
auuuu	chr10:126457738-126458063(-)$1	325	259	264	14.9999
auuuu	chr12:46200124-46200360(+)$1	236	143	148	14.9999
AUUUU	chr18:9917937-9918194(+)$1	257	62	67	14.9999
AUUUU	chr12:32497448-32497712(+)$1	264	221	226	14.9999
auuuu	chr7:37082909-37083237(-)$1	328	81	86	14.9999
AUUUU	chrX:122805866-122806123(-)$1	257	238	243	14.9999
auuuu	chr13:50490115-50490362(-)$1	247	240	245	14.9999
AUUUU	chr4:107152982-107153210(-)$1	228	17	22	14.9999
AUUUU	chr20:49172323-49172564(+)$1	241	229	234	14.9999
AUUUU	chr2:230692642-230692889(-)$1	247	197	202	14.9999
auuuu	chr2:29703121-29703348(-)$1	227	40	45	14.9999
AUUUU	chr14:56063668-56063897(+)$1	229	42	47	14.9999
AUUUU	chr16:78924673-78924934(+)$1	261	221	226	14.9999
AUUUU	chr15:66841176-66841394(-)$1	218	62	67	14.9999
AUUUU	chr1:28959150-28959427(-)$1	277	44	49	14.9999
auuuu	chr11:74713375-74713612(+)$1	237	25	30	14.9999
AUUUU	chr1:161820565-161820803(+)$1	238	210	215	14.9999
AUUUU	chr1:174856459-174856700(+)$1	241	132	137	14.9999
AUUUU	chr15:100255208-100255463(+)$1	255	56	61	14.9999
AUUUU	chr13:96345886-96346136(+)$1	250	126	131	14.9999
aUUUU	chr1:109451231-109451483(+)$1	252	236	241	14.9999
AUUUU	chr2:150430789-150431042(-)$1	253	50	55	14.9999
AUUUU	chr15:77769428-77769679(+)$1	251	70	75	14.9999
AUUUU	chr13:66975102-66975320(-)$1	218	200	205	14.9999
auuuu	chr9:130684723-130684962(-)$1	239	142	147	14.9999
auuuu	chr17:37810323-37810591(+)$1	268	134	139	14.9999
AUUUU	chr9:124828362-124828625(-)$1	263	218	223	14.9999
AUUUU	chr2:128880342-128880577(+)$1	235	225	230	14.9999
auuuu	chr15:67424855-67425120(+)$1	265	130	135	14.9999
AUUUU	chr17:46407480-46407748(-)$1	268	108	113	14.9999
AUUUU	chr5:158628798-158629045(-)$1	247	18	23	14.9999
AUUUU	chr2:32790276-32790518(+)$1	242	12	17	14.9999
AUUUU	chr3:67469983-67470213(-)$1	230	93	98	14.9999
AUUUU	chr10:34781932-34782197(-)$1	265	5	10	14.9999
AUUUU	chr3:127819804-127820047(-)$1	243	55	60	14.9999
AUUUU	chr5:70810989-70811238(+)$1	249	21	26	14.9999
AUUUU	chr7:16739590-16739823(+)$1	233	111	116	14.9999
auuuu	chr3:151064503-151064762(+)$1	259	204	209	14.9999
auuuu	chr6:90966049-90966292(-)$1	243	54	59	14.9999
Auuuu	chr17:28063078-28063349(-)$1	271	215	220	14.9999
AUUUU	chr1:167448048-167448310(-)$1	262	10	15	14.9999
AUUUU	chr1:155154764-155155100(+)$1	336	59	64	14.9999
auuuu	chr1:225445906-225446141(+)$1	235	44	49	14.9999
auuuu	chrX:20279302-20279534(-)$1	232	1	6	14.9999
AUUUU	chr11:10255640-10255891(-)$1	251	170	175	14.9999
AUUUU	chr18:51743772-51744014(-)$1	242	6	11	14.9999
auuuu	chr2:171957076-171957314(-)$1	238	69	74	14.9999
auuuu	chr6:118825861-118826118(-)$1	257	11	16	14.9999
AUUUU	chr12:105089919-105090153(+)$1	234	76	81	14.9999
auuuu	chrY:15492903-15493141(-)$1	238	118	123	14.9999

#otherMatches

#Struct PSSM
ee]cc	chr1:171549474-171549710(+)$1	236	101	106	14.9999
e::::	chr7:24864492-24864756(-)$1	264	191	196	14.9999
=^^^^	chr12:46582397-46582643(-)$1	246	103	108	14.9999
}EEEE	chr6:97263380-97263613(-)$1	233	121	126	14.9999
:::::	chr17:27127298-27127528(-)$1	230	8	13	14.9999
ggggg	chr1:109962242-109962511(-)$1	269	235	240	14.9999
:ffff	chr19:39330385-39330620(-)$1	235	100	105	14.9999
ffmmm	chr21:17205876-17206102(+)$1	226	32	37	14.9999
cc22c	chr1:54318888-54319144(-)$1	256	226	231	14.9999
:::::	chr2:27843159-27843391(+)$1	232	134	139	14.9999
e[ddd	chr5:118616702-118617061(+)$1	359	139	144	14.9999
oofff	chr4:74062319-74062594(-)$1	275	15	20	14.9999
::::=	chr14:73779973-73780197(-)$1	224	6	11	14.9999
ff:::	chr10:126457738-126458063(-)$1	325	259	264	14.9999
:::::	chr12:46200124-46200360(+)$1	236	143	148	14.9999
[====	chr18:9917937-9918194(+)$1	257	62	67	14.9999
eelll	chr12:32497448-32497712(+)$1	264	221	226	14.9999
dgggg	chr7:37082909-37083237(-)$1	328	81	86	14.9999
=====	chrX:122805866-122806123(-)$1	257	238	243	14.9999
:::::	chr13:50490115-50490362(-)$1	247	240	245	14.9999
:::::	chr4:107152982-107153210(-)$1	228	17	22	14.9999
^^fff	chr20:49172323-49172564(+)$1	241	229	234	14.9999
dddff	chr2:230692642-230692889(-)$1	247	197	202	14.9999
fffff	chr2:29703121-29703348(-)$1	227	40	45	14.9999
##hhh	chr14:56063668-56063897(+)$1	229	42	47	14.9999
ddddn	chr16:78924673-78924934(+)$1	261	221	226	14.9999
hhhhh	chr15:66841176-66841394(-)$1	218	62	67	14.9999
ggggg	chr1:28959150-28959427(-)$1	277	44	49	14.9999
cssss	chr11:74713375-74713612(+)$1	237	25	30	14.9999
eeeee	chr1:161820565-161820803(+)$1	238	210	215	14.9999
=====	chr1:174856459-174856700(+)$1	241	132	137	14.9999
emmmm	chr15:100255208-100255463(+)$1	255	56	61	14.9999
:::::	chr13:96345886-96346136(+)$1	250	126	131	14.9999
:::::	chr1:109451231-109451483(+)$1	252	236	241	14.9999
=====	chr2:150430789-150431042(-)$1	253	50	55	14.9999
ddnnn	chr15:77769428-77769679(+)$1	251	70	75	14.9999
^^^^^	chr13:66975102-66975320(-)$1	218	200	205	14.9999
:::::	chr9:130684723-130684962(-)$1	239	142	147	14.9999
66666	chr17:37810323-37810591(+)$1	268	134	139	14.9999
:::::	chr9:124828362-124828625(-)$1	263	218	223	14.9999
:::::	chr2:128880342-128880577(+)$1	235	225	230	14.9999
ee]ff	chr15:67424855-67425120(+)$1	265	130	135	14.9999
ffff2	chr17:46407480-46407748(-)$1	268	108	113	14.9999
b[hhh	chr5:158628798-158629045(-)$1	247	18	23	14.9999
IIII:	chr2:32790276-32790518(+)$1	242	12	17	14.9999
@@@@@	chr3:67469983-67470213(-)$1	230	93	98	14.9999
cc###	chr10:34781932-34782197(-)$1	265	5	10	14.9999
::JJJ	chr3:127819804-127820047(-)$1	243	55	60	14.9999
LHHHH	chr5:70810989-70811238(+)$1	249	21	26	14.9999
=====	chr7:16739590-16739823(+)$1	233	111	116	14.9999
rrrrr	chr3:151064503-151064762(+)$1	259	204	209	14.9999
OOODD	chr6:90966049-90966292(-)$1	243	54	59	14.9999
ggooo	chr17:28063078-28063349(-)$1	271	215	220	14.9999
:JJJJ	chr1:167448048-167448310(-)$1	262	10	15	14.9999
ccccc	chr1:155154764-155155100(+)$1	336	59	64	14.9999
cc666	chr1:225445906-225446141(+)$1	235	44	49	14.9999
:::::	chrX:20279302-20279534(-)$1	232	1	6	14.9999
^^^^^	chr11:10255640-10255891(-)$1	251	170	175	14.9999
JJJJ:	chr18:51743772-51744014(-)$1	242	6	11	14.9999
:::::	chr2:171957076-171957314(-)$1	238	69	74	14.9999
FFFF:	chr6:118825861-118826118(-)$1	257	11	16	14.9999
f5555	chr12:105089919-105090153(+)$1	234	76	81	14.9999
fffff	chrY:15492903-15493141(-)$1	238	118	123	14.9999

#DB
)).))	chr1:171549474-171549710(+)$1	1	101	106	14.9999
)....	chr7:24864492-24864756(-)$1	1	191	196	14.9999
(....	chr12:46582397-46582643(-)$1	1	103	108	14.9999
.))))	chr6:97263380-97263613(-)$1	1	121	126	14.9999
.....	chr17:27127298-27127528(-)$1	1	8	13	14.9999
(((((	chr1:109962242-109962511(-)$1	1	235	240	14.9999
.((((	chr19:39330385-39330620(-)$1	1	100	105	14.9999
((...	chr21:17205876-17206102(+)$1	1	32	37	14.9999
))..)	chr1:54318888-54319144(-)$1	1	226	231	14.9999
.....	chr2:27843159-27843391(+)$1	1	134	139	14.9999
(.(((	chr5:118616702-118617061(+)$1	1	139	144	14.9999
..)))	chr4:74062319-74062594(-)$1	1	15	20	14.9999
....(	chr14:73779973-73780197(-)$1	1	6	11	14.9999
))...	chr10:126457738-126458063(-)$1	1	259	264	14.9999
.....	chr12:46200124-46200360(+)$1	1	143	148	14.9999
.((((	chr18:9917937-9918194(+)$1	1	62	67	14.9999
((...	chr12:32497448-32497712(+)$1	1	221	226	14.9999
(((((	chr7:37082909-37083237(-)$1	1	81	86	14.9999
)))))	chrX:122805866-122806123(-)$1	1	238	243	14.9999
.....	chr13:50490115-50490362(-)$1	1	240	245	14.9999
.....	chr4:107152982-107153210(-)$1	1	17	22	14.9999
..)))	chr20:49172323-49172564(+)$1	1	229	234	14.9999
)))((	chr2:230692642-230692889(-)$1	1	197	202	14.9999
(((((	chr2:29703121-29703348(-)$1	1	40	45	14.9999
..(((	chr14:56063668-56063897(+)$1	1	42	47	14.9999
((((.	chr16:78924673-78924934(+)$1	1	221	226	14.9999
)))))	chr15:66841176-66841394(-)$1	1	62	67	14.9999
)))))	chr1:28959150-28959427(-)$1	1	44	49	14.9999
(....	chr11:74713375-74713612(+)$1	1	25	30	14.9999
)))))	chr1:161820565-161820803(+)$1	1	210	215	14.9999
(((((	chr1:174856459-174856700(+)$1	1	132	137	14.9999
(....	chr15:100255208-100255463(+)$1	1	56	61	14.9999
.....	chr13:96345886-96346136(+)$1	1	126	131	14.9999
.....	chr1:109451231-109451483(+)$1	1	236	241	14.9999
)))))	chr2:150430789-150431042(-)$1	1	50	55	14.9999
((...	chr15:77769428-77769679(+)$1	1	70	75	14.9999
.....	chr13:66975102-66975320(-)$1	1	200	205	14.9999
.....	chr9:130684723-130684962(-)$1	1	142	147	14.9999
.....	chr17:37810323-37810591(+)$1	1	134	139	14.9999
.....	chr9:124828362-124828625(-)$1	1	218	223	14.9999
.....	chr2:128880342-128880577(+)$1	1	225	230	14.9999
)).))	chr15:67424855-67425120(+)$1	1	130	135	14.9999
)))).	chr17:46407480-46407748(-)$1	1	108	113	14.9999
(.(((	chr5:158628798-158629045(-)$1	1	18	23	14.9999
((((.	chr2:32790276-32790518(+)$1	1	12	17	14.9999
.....	chr3:67469983-67470213(-)$1	1	93	98	14.9999
((...	chr10:34781932-34782197(-)$1	1	5	10	14.9999
..(((	chr3:127819804-127820047(-)$1	1	55	60	14.9999
.((((	chr5:70810989-70811238(+)$1	1	21	26	14.9999
(((((	chr7:16739590-16739823(+)$1	1	111	116	14.9999
.....	chr3:151064503-151064762(+)$1	1	204	209	14.9999
...((	chr6:90966049-90966292(-)$1	1	54	59	14.9999
((...	chr17:28063078-28063349(-)$1	1	215	220	14.9999
.((((	chr1:167448048-167448310(-)$1	1	10	15	14.9999
(((((	chr1:155154764-155155100(+)$1	1	59	64	14.9999
))...	chr1:225445906-225446141(+)$1	1	44	49	14.9999
.....	chrX:20279302-20279534(-)$1	1	1	6	14.9999
.....	chr11:10255640-10255891(-)$1	1	170	175	14.9999
((((.	chr18:51743772-51744014(-)$1	1	6	11	14.9999
.....	chr2:171957076-171957314(-)$1	1	69	74	14.9999
((((.	chr6:118825861-118826118(-)$1	1	11	16	14.9999
)....	chr12:105089919-105090153(+)$1	1	76	81	14.9999
)))))	chrY:15492903-15493141(-)$1	1	118	123	14.9999

#PSSM
A : 0.58	a : 0.41	
U : 0.57	u : 0.42	
U : 0.57	u : 0.42	
U : 0.57	u : 0.42	
U : 0.57	u : 0.42	

#score	944.9999999999999
#seq	63
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m2_run2.nuc.txt

#NT
CUGA	chr11:488098-488331(+)$1	233	81	85	11.9999
CUGA	chr1:109730721-109730942(+)$1	221	49	53	11.9999
CUGA	chr7:99689284-99689553(+)$1	269	124	128	11.9999
CUGA	chr9:139110422-139110679(-)$1	257	0	4	11.9999
CUGA	chr2:44566290-44566534(-)$1	244	103	107	11.9999
CUGA	chr2:128930170-128930409(+)$1	239	85	89	11.9999
CUGA	chr11:63519958-63520224(+)$1	266	105	109	11.9999
CUGA	chr17:80038660-80038885(-)$1	225	140	144	11.9999
CUGA	chr17:40053936-40054181(-)$1	245	120	124	11.9999
CUGA	chr5:140480311-140480534(+)$1	223	28	32	11.9999
CUGA	chrX:47058365-47058599(+)$1	234	161	165	11.9999
CUGA	chr12:58114556-58114813(+)$1	257	20	24	11.9999
CUGA	chr12:121784662-121784905(-)$1	243	104	108	11.9999
CUGA	chr1:183111731-183111959(+)$1	228	39	43	11.9999
CUGA	chr1:113460514-113460780(-)$1	266	146	150	11.9999
CUGA	chr19:1425765-1426029(+)$1	264	7	11	11.9999
CUGA	chr19:581213-581446(+)$1	233	176	180	11.9999
CUGA	chr14:102505045-102505305(+)$1	260	98	102	11.9999
CUGA	chr17:4577800-4578031(-)$1	231	89	93	11.9999
CUGA	chr4:24541720-24541965(-)$1	245	46	50	11.9999
CUGA	chrX:114883720-114883951(+)$1	231	3	7	11.9999
CUGA	chr22:41911669-41911901(+)$1	232	37	41	11.9999
CUGA	chr1:71536550-71536787(-)$1	237	127	131	11.9999
CUGA	chr10:79750760-79750992(-)$1	232	112	116	11.9999
CUGA	chrM:3766-4036(-)$1	270	101	105	11.9999
CUGA	chr19:54969961-54970192(+)$1	231	79	83	11.9999
CUGA	chr7:127731952-127732194(+)$1	242	36	40	11.9999
CUGA	chr16:3023340-3023571(+)$1	231	21	25	11.9999
CUGA	chr21:46193500-46193738(-)$1	238	123	127	11.9999
CUGA	chr8:56699020-56699254(+)$1	234	110	114	11.9999
CUGA	chr6:122773035-122773270(-)$1	235	28	32	11.9999
CUGA	chr20:44533360-44533592(-)$1	232	77	81	11.9999
CUGA	chr7:135285575-135285809(+)$1	234	52	56	11.9999
CUGA	chr11:65305916-65306158(+)$1	242	8	12	11.9999
CUGA	chr1:45479306-45479536(+)$1	230	68	72	11.9999
CUGA	chr6:43096698-43096920(+)$1	222	189	193	11.9999
CUGA	chrX:132439771-132440002(-)$1	231	117	121	11.9999
CUGA	chr2:10580825-10581090(-)$1	265	20	24	11.9999
CUGA	chr8:38090472-38090699(+)$1	227	8	12	11.9999
CUGA	chr7:135612088-135612316(-)$1	228	65	69	11.9999
CUGA	chr15:89848798-89849028(+)$1	230	46	50	11.9999
CUGA	chr10:62553560-62553790(+)$1	230	122	126	11.9999
CUGA	chr1:120285448-120285674(+)$1	226	189	193	11.9999
CUGA	chrX:123176342-123176587(+)$1	245	56	60	11.9999
CUGA	chr13:20656838-20657067(+)$1	229	159	163	11.9999
CUGA	chr6:42986116-42986357(+)$1	241	112	116	11.9999
CUGA	chrM:8596-8848(+)$1	252	131	135	11.9999
CUGA	chr17:7810651-7810886(+)$1	235	20	24	11.9999
CUGA	chr3:139092131-139092358(-)$1	227	78	82	11.9999
CUGA	chr16:2115433-2115661(+)$1	228	36	40	11.9999
CUGA	chr5:125896689-125896917(-)$1	228	199	203	11.9999
CUGA	chr17:45775978-45776212(+)$1	234	75	79	11.9999
CUGA	chr15:85341740-85341968(+)$1	228	22	26	11.9999
CUGA	chr19:40485899-40486145(+)$1	246	2	6	11.9999
CUGA	chr10:27437740-27437984(-)$1	244	27	31	11.9999
CUGA	chr7:44746748-44746981(+)$1	233	37	41	11.9999
CUGA	chr11:62567790-62568043(-)$1	253	92	96	11.9999
CUGA	chr11:66241101-66241324(-)$1	223	14	18	11.9999
CUGA	chr22:39910165-39910398(+)$1	233	89	93	11.9999
CUGA	chr14:24684672-24684901(-)$1	229	8	12	11.9999
CUGA	chr17:46673770-46673998(-)$1	228	59	63	11.9999
CUGA	chr11:2417004-2417246(+)$1	242	67	71	11.9999
CUGA	chr19:3979233-3979538(-)$1	305	84	88	11.9999
CUGA	chr6:17637588-17637826(-)$1	238	188	192	11.9999
CUGA	chr20:42331322-42331567(+)$1	245	20	24	11.9999
CUGA	chr1:10527238-10527473(-)$1	235	176	180	11.9999
CUGA	chr11:119535467-119535689(+)$1	222	31	35	11.9999
CUGA	chr17:47119612-47119840(+)$1	228	17	21	11.9999
CUGA	chr1:32793041-32793277(+)$1	236	74	78	11.9999
CUGA	chr20:62311149-62311380(+)$1	231	72	76	11.9999
CUGA	chr11:72406776-72407005(-)$1	229	56	60	11.9999
CUGA	chr8:101729946-101730212(-)$1	266	38	42	11.9999
CUGA	chr1:160201029-160201279(-)$1	250	234	238	11.9999
CUGA	chr14:89075620-89075845(-)$1	225	3	7	11.9999

#otherMatches

#Struct PSSM
CCC{	chr21:27372259-27372490(-)$1	231	2	6	11.9999
ff]b	chr11:488098-488331(+)$1	233	81	85	11.9999
$$$$	chr1:109730721-109730942(+)$1	221	49	53	11.9999
qqqq	chr7:99689284-99689553(+)$1	269	124	128	11.9999
HHHH	chr9:139110422-139110679(-)$1	257	0	4	11.9999
]bbc	chr2:44566290-44566534(-)$1	244	103	107	11.9999
ffff	chr2:128930170-128930409(+)$1	239	85	89	11.9999
EEE:	chr11:63519958-63520224(+)$1	266	105	109	11.9999
bppp	chr17:80038660-80038885(-)$1	225	140	144	11.9999
5ddd	chr17:40053936-40054181(-)$1	245	120	124	11.9999
fff"	chr5:140480311-140480534(+)$1	223	28	32	11.9999
::::	chrX:47058365-47058599(+)$1	234	161	165	11.9999
::::	chr12:58114556-58114813(+)$1	257	20	24	11.9999
dddd	chr12:121784662-121784905(-)$1	243	104	108	11.9999
gggg	chr1:183111731-183111959(+)$1	228	39	43	11.9999
e]dd	chr1:113460514-113460780(-)$1	266	146	150	11.9999
{HHH	chr19:1425765-1426029(+)$1	264	7	11	11.9999
iii2	chr19:581213-581446(+)$1	233	176	180	11.9999
ccc:	chr14:102505045-102505305(+)$1	260	98	102	11.9999
eee]	chr17:4577800-4578031(-)$1	231	89	93	11.9999
c$$$	chr4:24541720-24541965(-)$1	245	46	50	11.9999
DDD:	chrX:114883720-114883951(+)$1	231	3	7	11.9999
CCMM	chr22:41911669-41911901(+)$1	232	37	41	11.9999
pppd	chr1:71536550-71536787(-)$1	237	127	131	11.9999
fff[	chr10:79750760-79750992(-)$1	232	112	116	11.9999
d:gg	chrM:3766-4036(-)$1	270	101	105	11.9999
ffff	chr19:54969961-54970192(+)$1	231	79	83	11.9999
cccn	chr7:127731952-127732194(+)$1	242	36	40	11.9999
FFF:	chr16:3023340-3023571(+)$1	231	21	25	11.9999
::::	chr21:46193500-46193738(-)$1	238	123	127	11.9999
ee&&	chr8:56699020-56699254(+)$1	234	110	114	11.9999
bbpp	chr6:122773035-122773270(-)$1	235	28	32	11.9999
eee"	chr20:44533360-44533592(-)$1	232	77	81	11.9999
hhhh	chr7:135285575-135285809(+)$1	234	52	56	11.9999
EEE{	chr11:65305916-65306158(+)$1	242	8	12	11.9999
!a[c	chr1:45479306-45479536(+)$1	230	68	72	11.9999
dd::	chr6:43096698-43096920(+)$1	222	189	193	11.9999
HHH}	chrX:132439771-132440002(-)$1	231	117	121	11.9999
iill	chr2:10580825-10581090(-)$1	265	20	24	11.9999
!!ee	chr8:38090472-38090699(+)$1	227	8	12	11.9999
eeee	chr7:135612088-135612316(-)$1	228	65	69	11.9999
==dd	chr15:89848798-89849028(+)$1	230	46	50	11.9999
iiii	chr10:62553560-62553790(+)$1	230	122	126	11.9999
dddd	chr1:120285448-120285674(+)$1	226	189	193	11.9999
iiii	chrX:123176342-123176587(+)$1	245	56	60	11.9999
ffee	chr13:20656838-20657067(+)$1	229	159	163	11.9999
bb[d	chr6:42986116-42986357(+)$1	241	112	116	11.9999
cc>>	chrM:8596-8848(+)$1	252	131	135	11.9999
dd&&	chr17:7810651-7810886(+)$1	235	20	24	11.9999
B}GG	chr3:139092131-139092358(-)$1	227	78	82	11.9999
!bbr	chr16:2115433-2115661(+)$1	228	36	40	11.9999
GGGG	chr5:125896689-125896917(-)$1	228	199	203	11.9999
ddd]	chr17:45775978-45776212(+)$1	234	75	79	11.9999
{DDD	chr15:85341740-85341968(+)$1	228	22	26	11.9999
ccc"	chr19:40485899-40486145(+)$1	246	2	6	11.9999
:ddd	chr10:27437740-27437984(-)$1	244	27	31	11.9999
gggg	chr7:44746748-44746981(+)$1	233	37	41	11.9999
cccb	chr11:62567790-62568043(-)$1	253	92	96	11.9999
E:gg	chr11:66241101-66241324(-)$1	223	14	18	11.9999
ccc%	chr22:39910165-39910398(+)$1	233	89	93	11.9999
NNNN	chr14:24684672-24684901(-)$1	229	8	12	11.9999
DDD:	chr17:46673770-46673998(-)$1	228	59	63	11.9999
22cc	chr11:2417004-2417246(+)$1	242	67	71	11.9999
cc!!	chr19:3979233-3979538(-)$1	305	84	88	11.9999
5555	chr6:17637588-17637826(-)$1	238	188	192	11.9999
[bbn	chr20:42331322-42331567(+)$1	245	20	24	11.9999
ddd8	chr1:10527238-10527473(-)$1	235	176	180	11.9999
gggg	chr11:119535467-119535689(+)$1	222	31	35	11.9999
#ccc	chr17:47119612-47119840(+)$1	228	17	21	11.9999
DDD:	chr1:32793041-32793277(+)$1	236	74	78	11.9999
gggg	chr20:62311149-62311380(+)$1	231	72	76	11.9999
!ccc	chr11:72406776-72407005(-)$1	229	56	60	11.9999
qqbb	chr8:101729946-101730212(-)$1	266	38	42	11.9999
hhhh	chr1:160201029-160201279(-)$1	250	234	238	11.9999
FFFF	chr14:89075620-89075845(-)$1	225	3	7	11.9999

#DB
(((.	chr21:27372259-27372490(-)$1	1	2	6	11.9999
)).)	chr11:488098-488331(+)$1	1	81	85	11.9999
....	chr1:109730721-109730942(+)$1	1	49	53	11.9999
....	chr7:99689284-99689553(+)$1	1	124	128	11.9999
((((	chr9:139110422-139110679(-)$1	1	0	4	11.9999
.)))	chr2:44566290-44566534(-)$1	1	103	107	11.9999
))))	chr2:128930170-128930409(+)$1	1	85	89	11.9999
(((.	chr11:63519958-63520224(+)$1	1	105	109	11.9999
(...	chr17:80038660-80038885(-)$1	1	140	144	11.9999
.)))	chr17:40053936-40054181(-)$1	1	120	124	11.9999
(((.	chr5:140480311-140480534(+)$1	1	28	32	11.9999
....	chrX:47058365-47058599(+)$1	1	161	165	11.9999
....	chr12:58114556-58114813(+)$1	1	20	24	11.9999
))))	chr12:121784662-121784905(-)$1	1	104	108	11.9999
))))	chr1:183111731-183111959(+)$1	1	39	43	11.9999
).))	chr1:113460514-113460780(-)$1	1	146	150	11.9999
.(((	chr19:1425765-1426029(+)$1	1	7	11	11.9999
))).	chr19:581213-581446(+)$1	1	176	180	11.9999
))).	chr14:102505045-102505305(+)$1	1	98	102	11.9999
))).	chr17:4577800-4578031(-)$1	1	89	93	11.9999
(...	chr4:24541720-24541965(-)$1	1	46	50	11.9999
(((.	chrX:114883720-114883951(+)$1	1	3	7	11.9999
((..	chr22:41911669-41911901(+)$1	1	37	41	11.9999
...)	chr1:71536550-71536787(-)$1	1	127	131	11.9999
(((.	chr10:79750760-79750992(-)$1	1	112	116	11.9999
).((	chrM:3766-4036(-)$1	1	101	105	11.9999
))))	chr19:54969961-54970192(+)$1	1	79	83	11.9999
(((.	chr7:127731952-127732194(+)$1	1	36	40	11.9999
(((.	chr16:3023340-3023571(+)$1	1	21	25	11.9999
....	chr21:46193500-46193738(-)$1	1	123	127	11.9999
((..	chr8:56699020-56699254(+)$1	1	110	114	11.9999
((..	chr6:122773035-122773270(-)$1	1	28	32	11.9999
(((.	chr20:44533360-44533592(-)$1	1	77	81	11.9999
((((	chr7:135285575-135285809(+)$1	1	52	56	11.9999
(((.	chr11:65305916-65306158(+)$1	1	8	12	11.9999
.(.(	chr1:45479306-45479536(+)$1	1	68	72	11.9999
))..	chr6:43096698-43096920(+)$1	1	189	193	11.9999
))).	chrX:132439771-132440002(-)$1	1	117	121	11.9999
((..	chr2:10580825-10581090(-)$1	1	20	24	11.9999
..((	chr8:38090472-38090699(+)$1	1	8	12	11.9999
((((	chr7:135612088-135612316(-)$1	1	65	69	11.9999
((((	chr15:89848798-89849028(+)$1	1	46	50	11.9999
((((	chr10:62553560-62553790(+)$1	1	122	126	11.9999
))))	chr1:120285448-120285674(+)$1	1	189	193	11.9999
((((	chrX:123176342-123176587(+)$1	1	56	60	11.9999
))((	chr13:20656838-20657067(+)$1	1	159	163	11.9999
((.(	chr6:42986116-42986357(+)$1	1	112	116	11.9999
))..	chrM:8596-8848(+)$1	1	131	135	11.9999
((..	chr17:7810651-7810886(+)$1	1	20	24	11.9999
).))	chr3:139092131-139092358(-)$1	1	78	82	11.9999
.((.	chr16:2115433-2115661(+)$1	1	36	40	11.9999
))))	chr5:125896689-125896917(-)$1	1	199	203	11.9999
))).	chr17:45775978-45776212(+)$1	1	75	79	11.9999
.(((	chr15:85341740-85341968(+)$1	1	22	26	11.9999
(((.	chr19:40485899-40486145(+)$1	1	2	6	11.9999
.(((	chr10:27437740-27437984(-)$1	1	27	31	11.9999
))))	chr7:44746748-44746981(+)$1	1	37	41	11.9999
))))	chr11:62567790-62568043(-)$1	1	92	96	11.9999
(.((	chr11:66241101-66241324(-)$1	1	14	18	11.9999
(((.	chr22:39910165-39910398(+)$1	1	89	93	11.9999
....	chr14:24684672-24684901(-)$1	1	8	12	11.9999
(((.	chr17:46673770-46673998(-)$1	1	59	63	11.9999
..))	chr11:2417004-2417246(+)$1	1	67	71	11.9999
((..	chr19:3979233-3979538(-)$1	1	84	88	11.9999
....	chr6:17637588-17637826(-)$1	1	188	192	11.9999
.((.	chr20:42331322-42331567(+)$1	1	20	24	11.9999
))).	chr1:10527238-10527473(-)$1	1	176	180	11.9999
((((	chr11:119535467-119535689(+)$1	1	31	35	11.9999
.(((	chr17:47119612-47119840(+)$1	1	17	21	11.9999
(((.	chr1:32793041-32793277(+)$1	1	74	78	11.9999
((((	chr20:62311149-62311380(+)$1	1	72	76	11.9999
.(((	chr11:72406776-72407005(-)$1	1	56	60	11.9999
..))	chr8:101729946-101730212(-)$1	1	38	42	11.9999
))))	chr1:160201029-160201279(-)$1	1	234	238	11.9999
((((	chr14:89075620-89075845(-)$1	1	3	7	11.9999

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

#score	899.9999999999995
#seq	75
#width	4
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m3_run1.nuc.txt

#NT
AGG	chr22:46508532-46508760(+)$1	228	39	42	9.0000
AGG	chr7:107384779-107385002(+)$1	223	110	113	9.0000
AGG	chr22:47073170-47073393(+)$1	223	146	149	9.0000
AGG	chr12:56122992-56123215(+)$1	223	15	18	9.0000
AGG	chr9:140110854-140111077(-)$1	223	11	14	9.0000
AGG	chr22:19754605-19754839(-)$1	234	70	73	9.0000
AGG	chr2:74666698-74666924(-)$1	226	0	3	9.0000
AGG	chr12:113735961-113736188(+)$1	227	19	22	9.0000
AGG	chr19:47181751-47181992(+)$1	241	5	8	9.0000
AGG	chr12:2800671-2800894(-)$1	223	32	35	9.0000
AGG	chr14:64009616-64009839(+)$1	223	69	72	9.0000
AGG	chr2:191208647-191208872(+)$1	225	1	4	9.0000
AGG	chr2:28616164-28616387(-)$1	223	183	186	9.0000
AGG	chr17:79430812-79431034(-)$1	222	26	29	9.0000
AGG	chr10:7326148-7326371(-)$1	223	80	83	9.0000
AGG	chr19:46388960-46389182(+)$1	222	22	25	9.0000
AGG	chr5:150510691-150510913(-)$1	222	0	3	9.0000
AGG	chr10:112270705-112270928(-)$1	223	30	33	9.0000
AGG	chr7:48128322-48128551(-)$1	229	16	19	9.0000
AGG	chr11:77034122-77034348(-)$1	226	4	7	9.0000
AGG	chr11:6642867-6643089(-)$1	222	6	9	9.0000
agg	chr12:54982215-54982437(-)$1	222	84	87	9.0000
AGG	chr2:201936027-201936257(+)$1	230	60	63	9.0000
AGG	chrX:115305438-115305663(+)$1	225	45	48	9.0000
AGG	chr1:213188704-213188926(+)$1	222	96	99	9.0000
AGG	chr16:20975003-20975228(-)$1	225	41	44	9.0000
AGG	chr1:23884754-23884977(-)$1	223	76	79	9.0000
AGG	chr9:35076604-35076826(-)$1	222	5	8	9.0000
AGG	chr9:38541306-38541527(+)$1	221	43	46	9.0000
agg	chr19:4497409-4497630(+)$1	221	60	63	9.0000
AGG	chr8:110598260-110598484(+)$1	224	12	15	9.0000
AGG	chr14:102785968-102786200(+)$1	232	27	30	9.0000
AGG	chr4:146403574-146403804(+)$1	230	36	39	9.0000
AGG	chr3:50144817-50145088(+)$1	271	9	12	9.0000
AGG	chr19:49256122-49256347(-)$1	225	12	15	9.0000
AGG	chr17:1546907-1547130(-)$1	223	124	127	9.0000
AGG	chr16:50300383-50300609(+)$1	226	50	53	9.0000
AGG	chr10:60028842-60029063(+)$1	221	29	32	9.0000
AGG	chr9:140003058-140003283(-)$1	225	7	10	9.0000
AGG	chr12:110906512-110906734(-)$1	222	80	83	9.0000
AGG	chr1:33283272-33283495(+)$1	223	16	19	9.0000
AGG	chr7:150498006-150498242(-)$1	236	140	143	9.0000
Agg	chr22:19166108-19166330(-)$1	222	120	123	9.0000
agg	chr17:8024198-8024427(+)$1	229	102	105	9.0000
AGG	chr19:45998282-45998505(-)$1	223	38	41	9.0000
AGG	chr11:118098644-118098866(+)$1	222	37	40	9.0000
AGG	chr17:16251958-16252182(-)$1	224	24	27	9.0000
agg	chr11:8021888-8022110(+)$1	222	37	40	9.0000
AGG	chr17:16346478-16346701(-)$1	223	39	42	9.0000
agg	chrX:11776177-11776413(+)$1	236	18	21	9.0000
agg	chr17:75136901-75137122(-)$1	221	53	56	9.0000
AGG	chr19:39435616-39435842(-)$1	226	77	80	9.0000
AGG	chr20:6748758-6748981(-)$1	223	6	9	9.0000
AGG	chr7:134131947-134132173(-)$1	226	38	41	9.0000
AGG	chrX:148077284-148077505(-)$1	221	13	16	9.0000
AGG	chr19:2427643-2427866(-)$1	223	10	13	9.0000
AGG	chr1:154600256-154600479(-)$1	223	48	51	9.0000
AGG	chr7:30451884-30452107(+)$1	223	60	63	9.0000
AGG	chr15:44968801-44969026(-)$1	225	99	102	9.0000
AGG	chr22:41165505-41165735(-)$1	230	62	65	9.0000
AGG	chr16:71842065-71842286(-)$1	221	25	28	9.0000
AGG	chr4:3417685-3417910(-)$1	225	95	98	9.0000
AGG	chr11:47290862-47291085(+)$1	223	24	27	9.0000
AGG	chr6:119399579-119399820(+)$1	241	19	22	9.0000
AGG	chr1:40254164-40254392(+)$1	228	55	58	9.0000
AGG	chr1:236444971-236445208(-)$1	237	88	91	9.0000
agg	chr2:31557445-31557670(-)$1	225	84	87	9.0000
agg	chr11:66244464-66244686(+)$1	222	23	26	9.0000
AGG	chr17:29580554-29580781(+)$1	227	43	46	9.0000
AGG	chr21:34730307-34730529(-)$1	222	18	21	9.0000
AGG	chr1:56961301-56961527(-)$1	226	46	49	9.0000
AGG	chr1:228270384-228270623(+)$1	239	2	5	9.0000
AGG	chr1:117529495-117529717(+)$1	222	35	38	9.0000
AGG	chr2:26533646-26533867(-)$1	221	8	11	9.0000
agg	chr1:203783956-203784177(-)$1	221	59	62	9.0000
AGG	chr16:66639221-66639443(+)$1	222	83	86	9.0000
agg	chr11:57137832-57138053(+)$1	221	10	13	9.0000
AGG	chr14:21501939-21502163(+)$1	224	15	18	9.0000
AGG	chr3:13357794-13358016(-)$1	222	0	3	9.0000
AGG	chr10:73475069-73475291(+)$1	222	41	44	9.0000
AGG	chr11:3109185-3109408(+)$1	223	22	25	9.0000
AGG	chr11:18655836-18656062(+)$1	226	8	11	9.0000
AGG	chr2:86668173-86668396(-)$1	223	42	45	9.0000
AGG	chr19:18547541-18547765(+)$1	224	33	36	9.0000
AGG	chr1:180244855-180245077(-)$1	222	44	47	9.0000
AGG	chr1:153778461-153778686(+)$1	225	35	38	9.0000
AGG	chr1:15819179-15819400(+)$1	221	29	32	9.0000
AGG	chr15:72070769-72070991(-)$1	222	72	75	9.0000
AGG	chr11:77929179-77929400(-)$1	221	21	24	9.0000
AGG	chr9:125884544-125884768(+)$1	224	5	8	9.0000
AGG	chr12:91348622-91348845(-)$1	223	114	117	9.0000

#otherMatches

#Struct PSSM
fff	chr2:275073-275295(+)$1	222	17	20	9.0000
{CC	chr22:46508532-46508760(+)$1	228	39	42	9.0000
===	chr7:107384779-107385002(+)$1	223	110	113	9.0000
3gg	chr22:47073170-47073393(+)$1	223	146	149	9.0000
ncc	chr12:56122992-56123215(+)$1	223	15	18	9.0000
FFF	chr9:140110854-140111077(-)$1	223	11	14	9.0000
mee	chr22:19754605-19754839(-)$1	234	70	73	9.0000
::F	chr2:74666698-74666924(-)$1	226	0	3	9.0000
:ff	chr12:113735961-113736188(+)$1	227	19	22	9.0000
HHH	chr19:47181751-47181992(+)$1	241	5	8	9.0000
eeE	chr12:2800671-2800894(-)$1	223	32	35	9.0000
4ff	chr14:64009616-64009839(+)$1	223	69	72	9.0000
ddd	chr2:191208647-191208872(+)$1	225	1	4	9.0000
:bb	chr2:28616164-28616387(-)$1	223	183	186	9.0000
ggg	chr17:79430812-79431034(-)$1	222	26	29	9.0000
DDD	chr10:7326148-7326371(-)$1	223	80	83	9.0000
[bb	chr19:46388960-46389182(+)$1	222	22	25	9.0000
:FF	chr5:150510691-150510913(-)$1	222	0	3	9.0000
oii	chr10:112270705-112270928(-)$1	223	30	33	9.0000
:::	chr7:48128322-48128551(-)$1	229	16	19	9.0000
DDD	chr11:77034122-77034348(-)$1	226	4	7	9.0000
FFF	chr11:6642867-6643089(-)$1	222	6	9	9.0000
ooa	chr12:54982215-54982437(-)$1	222	84	87	9.0000
ppe	chr2:201936027-201936257(+)$1	230	60	63	9.0000
fff	chrX:115305438-115305663(+)$1	225	45	48	9.0000
:CC	chr1:213188704-213188926(+)$1	222	96	99	9.0000
ccc	chr16:20975003-20975228(-)$1	225	41	44	9.0000
!dd	chr1:23884754-23884977(-)$1	223	76	79	9.0000
:DD	chr9:35076604-35076826(-)$1	222	5	8	9.0000
:bb	chr9:38541306-38541527(+)$1	221	43	46	9.0000
hhh	chr19:4497409-4497630(+)$1	221	60	63	9.0000
EEE	chr8:110598260-110598484(+)$1	224	12	15	9.0000
:ii	chr14:102785968-102786200(+)$1	232	27	30	9.0000
HHF	chr4:146403574-146403804(+)$1	230	36	39	9.0000
LCC	chr3:50144817-50145088(+)$1	271	9	12	9.0000
EEE	chr19:49256122-49256347(-)$1	225	12	15	9.0000
fff	chr17:1546907-1547130(-)$1	223	124	127	9.0000
obb	chr16:50300383-50300609(+)$1	226	50	53	9.0000
:ff	chr10:60028842-60029063(+)$1	221	29	32	9.0000
{CC	chr9:140003058-140003283(-)$1	225	7	10	9.0000
b]b	chr12:110906512-110906734(-)$1	222	80	83	9.0000
GGG	chr1:33283272-33283495(+)$1	223	16	19	9.0000
$$$	chr7:150498006-150498242(-)$1	236	140	143	9.0000
bb[	chr22:19166108-19166330(-)$1	222	120	123	9.0000
DDD	chr17:8024198-8024427(+)$1	229	102	105	9.0000
!ff	chr19:45998282-45998505(-)$1	223	38	41	9.0000
ggg	chr11:118098644-118098866(+)$1	222	37	40	9.0000
ggg	chr17:16251958-16252182(-)$1	224	24	27	9.0000
88h	chr11:8021888-8022110(+)$1	222	37	40	9.0000
occ	chr17:16346478-16346701(-)$1	223	39	42	9.0000
:::	chrX:11776177-11776413(+)$1	236	18	21	9.0000
!!a	chr17:75136901-75137122(-)$1	221	53	56	9.0000
hhh	chr19:39435616-39435842(-)$1	226	77	80	9.0000
GGG	chr20:6748758-6748981(-)$1	223	6	9	9.0000
mee	chr7:134131947-134132173(-)$1	226	38	41	9.0000
oee	chrX:148077284-148077505(-)$1	221	13	16	9.0000
mmm	chr19:2427643-2427866(-)$1	223	10	13	9.0000
33e	chr1:154600256-154600479(-)$1	223	48	51	9.0000
lgg	chr7:30451884-30452107(+)$1	223	60	63	9.0000
hhc	chr15:44968801-44969026(-)$1	225	99	102	9.0000
:::	chr22:41165505-41165735(-)$1	230	62	65	9.0000
DDD	chr16:71842065-71842286(-)$1	221	25	28	9.0000
ccc	chr4:3417685-3417910(-)$1	225	95	98	9.0000
MMM	chr11:47290862-47291085(+)$1	223	24	27	9.0000
LLL	chr6:119399579-119399820(+)$1	241	19	22	9.0000
eel	chr1:40254164-40254392(+)$1	228	55	58	9.0000
mmc	chr1:236444971-236445208(-)$1	237	88	91	9.0000
nna	chr2:31557445-31557670(-)$1	225	84	87	9.0000
:::	chr11:66244464-66244686(+)$1	222	23	26	9.0000
hhh	chr17:29580554-29580781(+)$1	227	43	46	9.0000
e[a	chr21:34730307-34730529(-)$1	222	18	21	9.0000
GGG	chr1:56961301-56961527(-)$1	226	46	49	9.0000
:CC	chr1:228270384-228270623(+)$1	239	2	5	9.0000
cnn	chr1:117529495-117529717(+)$1	222	35	38	9.0000
GGG	chr2:26533646-26533867(-)$1	221	8	11	9.0000
hhh	chr1:203783956-203784177(-)$1	221	59	62	9.0000
hhh	chr16:66639221-66639443(+)$1	222	83	86	9.0000
[gg	chr11:57137832-57138053(+)$1	221	10	13	9.0000
ddd	chr14:21501939-21502163(+)$1	224	15	18	9.0000
DDD	chr3:13357794-13358016(-)$1	222	0	3	9.0000
ccm	chr10:73475069-73475291(+)$1	222	41	44	9.0000
iii	chr11:3109185-3109408(+)$1	223	22	25	9.0000
:EE	chr11:18655836-18656062(+)$1	226	8	11	9.0000
eee	chr2:86668173-86668396(-)$1	223	42	45	9.0000
eee	chr19:18547541-18547765(+)$1	224	33	36	9.0000
KDD	chr1:180244855-180245077(-)$1	222	44	47	9.0000
hhh	chr1:153778461-153778686(+)$1	225	35	38	9.0000
{CC	chr1:15819179-15819400(+)$1	221	29	32	9.0000
ooo	chr15:72070769-72070991(-)$1	222	72	75	9.0000
qqq	chr11:77929179-77929400(-)$1	221	21	24	9.0000
:::	chr9:125884544-125884768(+)$1	224	5	8	9.0000
hhh	chr12:91348622-91348845(-)$1	223	114	117	9.0000

#DB
(((	chr2:275073-275295(+)$1	1	17	20	9.0000
.((	chr22:46508532-46508760(+)$1	1	39	42	9.0000
(((	chr7:107384779-107385002(+)$1	1	110	113	9.0000
.))	chr22:47073170-47073393(+)$1	1	146	149	9.0000
.))	chr12:56122992-56123215(+)$1	1	15	18	9.0000
(((	chr9:140110854-140111077(-)$1	1	11	14	9.0000
.))	chr22:19754605-19754839(-)$1	1	70	73	9.0000
..(	chr2:74666698-74666924(-)$1	1	0	3	9.0000
.((	chr12:113735961-113736188(+)$1	1	19	22	9.0000
(((	chr19:47181751-47181992(+)$1	1	5	8	9.0000
))(	chr12:2800671-2800894(-)$1	1	32	35	9.0000
.))	chr14:64009616-64009839(+)$1	1	69	72	9.0000
(((	chr2:191208647-191208872(+)$1	1	1	4	9.0000
.((	chr2:28616164-28616387(-)$1	1	183	186	9.0000
)))	chr17:79430812-79431034(-)$1	1	26	29	9.0000
(((	chr10:7326148-7326371(-)$1	1	80	83	9.0000
.((	chr19:46388960-46389182(+)$1	1	22	25	9.0000
.((	chr5:150510691-150510913(-)$1	1	0	3	9.0000
.))	chr10:112270705-112270928(-)$1	1	30	33	9.0000
...	chr7:48128322-48128551(-)$1	1	16	19	9.0000
(((	chr11:77034122-77034348(-)$1	1	4	7	9.0000
(((	chr11:6642867-6643089(-)$1	1	6	9	9.0000
..)	chr12:54982215-54982437(-)$1	1	84	87	9.0000
..)	chr2:201936027-201936257(+)$1	1	60	63	9.0000
(((	chrX:115305438-115305663(+)$1	1	45	48	9.0000
.((	chr1:213188704-213188926(+)$1	1	96	99	9.0000
(((	chr16:20975003-20975228(-)$1	1	41	44	9.0000
.((	chr1:23884754-23884977(-)$1	1	76	79	9.0000
.((	chr9:35076604-35076826(-)$1	1	5	8	9.0000
.((	chr9:38541306-38541527(+)$1	1	43	46	9.0000
(((	chr19:4497409-4497630(+)$1	1	60	63	9.0000
(((	chr8:110598260-110598484(+)$1	1	12	15	9.0000
.((	chr14:102785968-102786200(+)$1	1	27	30	9.0000
(((	chr4:146403574-146403804(+)$1	1	36	39	9.0000
.((	chr3:50144817-50145088(+)$1	1	9	12	9.0000
(((	chr19:49256122-49256347(-)$1	1	12	15	9.0000
(((	chr17:1546907-1547130(-)$1	1	124	127	9.0000
.))	chr16:50300383-50300609(+)$1	1	50	53	9.0000
.((	chr10:60028842-60029063(+)$1	1	29	32	9.0000
.((	chr9:140003058-140003283(-)$1	1	7	10	9.0000
).)	chr12:110906512-110906734(-)$1	1	80	83	9.0000
(((	chr1:33283272-33283495(+)$1	1	16	19	9.0000
...	chr7:150498006-150498242(-)$1	1	140	143	9.0000
((.	chr22:19166108-19166330(-)$1	1	120	123	9.0000
(((	chr17:8024198-8024427(+)$1	1	102	105	9.0000
.((	chr19:45998282-45998505(-)$1	1	38	41	9.0000
(((	chr11:118098644-118098866(+)$1	1	37	40	9.0000
(((	chr17:16251958-16252182(-)$1	1	24	27	9.0000
..)	chr11:8021888-8022110(+)$1	1	37	40	9.0000
.))	chr17:16346478-16346701(-)$1	1	39	42	9.0000
...	chrX:11776177-11776413(+)$1	1	18	21	9.0000
..(	chr17:75136901-75137122(-)$1	1	53	56	9.0000
)))	chr19:39435616-39435842(-)$1	1	77	80	9.0000
(((	chr20:6748758-6748981(-)$1	1	6	9	9.0000
.))	chr7:134131947-134132173(-)$1	1	38	41	9.0000
.))	chrX:148077284-148077505(-)$1	1	13	16	9.0000
...	chr19:2427643-2427866(-)$1	1	10	13	9.0000
..)	chr1:154600256-154600479(-)$1	1	48	51	9.0000
.))	chr7:30451884-30452107(+)$1	1	60	63	9.0000
))(	chr15:44968801-44969026(-)$1	1	99	102	9.0000
...	chr22:41165505-41165735(-)$1	1	62	65	9.0000
(((	chr16:71842065-71842286(-)$1	1	25	28	9.0000
)))	chr4:3417685-3417910(-)$1	1	95	98	9.0000
...	chr11:47290862-47291085(+)$1	1	24	27	9.0000
...	chr6:119399579-119399820(+)$1	1	19	22	9.0000
((.	chr1:40254164-40254392(+)$1	1	55	58	9.0000
..)	chr1:236444971-236445208(-)$1	1	88	91	9.0000
..)	chr2:31557445-31557670(-)$1	1	84	87	9.0000
...	chr11:66244464-66244686(+)$1	1	23	26	9.0000
)))	chr17:29580554-29580781(+)$1	1	43	46	9.0000
(.(	chr21:34730307-34730529(-)$1	1	18	21	9.0000
(((	chr1:56961301-56961527(-)$1	1	46	49	9.0000
.((	chr1:228270384-228270623(+)$1	1	2	5	9.0000
(..	chr1:117529495-117529717(+)$1	1	35	38	9.0000
(((	chr2:26533646-26533867(-)$1	1	8	11	9.0000
(((	chr1:203783956-203784177(-)$1	1	59	62	9.0000
(((	chr16:66639221-66639443(+)$1	1	83	86	9.0000
.((	chr11:57137832-57138053(+)$1	1	10	13	9.0000
)))	chr14:21501939-21502163(+)$1	1	15	18	9.0000
(((	chr3:13357794-13358016(-)$1	1	0	3	9.0000
((.	chr10:73475069-73475291(+)$1	1	41	44	9.0000
)))	chr11:3109185-3109408(+)$1	1	22	25	9.0000
.((	chr11:18655836-18656062(+)$1	1	8	11	9.0000
(((	chr2:86668173-86668396(-)$1	1	42	45	9.0000
(((	chr19:18547541-18547765(+)$1	1	33	36	9.0000
.((	chr1:180244855-180245077(-)$1	1	44	47	9.0000
(((	chr1:153778461-153778686(+)$1	1	35	38	9.0000
.((	chr1:15819179-15819400(+)$1	1	29	32	9.0000
...	chr15:72070769-72070991(-)$1	1	72	75	9.0000
...	chr11:77929179-77929400(-)$1	1	21	24	9.0000
...	chr9:125884544-125884768(+)$1	1	5	8	9.0000
)))	chr12:91348622-91348845(-)$1	1	114	117	9.0000

#PSSM
A : 0.89	a : 0.10	
G : 0.88	g : 0.11	
G : 0.88	g : 0.11	

#score	828.0000000000002
#seq	92
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m1_run2.nuc.txt

#NT
UUGGAG	chr3:160282914-160283174(-)$1	260	167	173	10.3529
UUAGAG	chr12:117154322-117154552(-)$1	230	86	92	9.9852
UUUGAG	chrX:13790413-13790638(+)$1	225	49	55	14.1029
UUUGAG	chr11:3392049-3392273(-)$1	224	147	153	14.1029
UUUGAG	chr19:44039998-44040226(-)$1	228	192	198	14.1029
uuggag	chr20:30825496-30825721(+)$1	225	39	45	10.3529
UUUGAG	chr19:2272895-2273133(+)$1	238	107	113	14.1029
UAUGAG	chr1:43133451-43133673(-)$1	222	86	92	10.9411
UAUGAG	chr15:75012512-75012736(+)$1	224	214	220	10.9411
UGUGAG	chr5:137275068-137275293(-)$1	225	206	212	10.7941
UUUCAG	chr9:8315155-8315376(+)$1	221	184	190	10.3529
UUUGAG	chrX:70794993-70795243(+)$1	250	220	226	14.1029
UUUGAG	chrX:114869101-114869335(+)$1	234	162	168	14.1029
UUAGAG	chr6:35262908-35263135(+)$1	227	30	36	9.9852
UUCGAG	chrX:47426599-47426828(+)$1	229	129	135	9.9117
uuucag	chr22:22050282-22050511(+)$1	229	97	103	10.3529
UUUUAG	chr5:95224061-95224289(-)$1	228	34	40	10.5735
UGUGAG	chr4:76598369-76598601(-)$1	232	59	65	10.7941
UUUUAG	chr12:102140110-102140340(-)$1	230	177	183	10.5735
UUUGAG	chr17:37221023-37221246(+)$1	223	24	30	14.1029
UUUGUG	chr11:111745840-111746070(-)$1	230	5	11	10.2058
UCUGAG	chr1:192984313-192984538(-)$1	225	102	108	10.8676
UCUGAG	chr6:154651108-154651333(+)$1	225	21	27	10.8676
UAUGAG	chr17:40767069-40767297(+)$1	228	144	150	10.9411
UCUGAG	chr5:176301024-176301248(-)$1	224	156	162	10.8676
UGUGAG	chr17:17970239-17970469(+)$1	230	152	158	10.7941
UUUAAG	chr5:138678946-138679173(+)$1	227	66	72	10.2058
UGUGAG	chrX:53406462-53406691(-)$1	229	27	33	10.7941
uuuGAG	chr11:85989280-85989505(+)$1	225	9	15	14.1029
UUUGAG	chr8:90937841-90938065(-)$1	224	189	195	14.1029
UCUGAG	chr6:131931205-131931449(-)$1	244	129	135	10.8676
UUUGAG	chr4:41262653-41262887(+)$1	234	173	179	14.1029
UCUGAG	chr5:150408399-150408624(+)$1	225	3	9	10.8676
UUGGAG	chr4:38777297-38777519(+)$1	222	80	86	10.3529
UUUCAG	chrX:39923600-39923825(+)$1	225	13	19	10.3529
UCUGAG	chr12:66236417-66236639(-)$1	222	131	137	10.8676
UUUCAG	chr17:47129158-47129381(+)$1	223	61	67	10.3529
UUUGAG	chr15:65822870-65823095(+)$1	225	5	11	14.1029
UGUGAG	chr18:13612208-13612433(+)$1	225	55	61	10.7941
UUUGAG	chr11:62393481-62393734(-)$1	253	119	125	14.1029
uuuggg	chr7:148700605-148700853(-)$1	248	197	203	10.6470
UUGGAG	chr9:88193741-88193967(-)$1	226	57	63	10.3529
UUUGGG	chr19:10427880-10428108(-)$1	228	23	29	10.6470
UAUGAG	chr1:154574862-154575115(-)$1	253	55	61	10.9411
UUUGGG	chr2:27596007-27596230(+)$1	223	178	184	10.6470
UAUgag	chr2:204193140-204193366(+)$1	226	67	73	10.9411
UUUGUG	chr19:16662806-16663040(-)$1	234	75	81	10.2058
uuuuag	chr10:13251616-13251846(+)$1	230	181	187	10.5735
UUUGGG	chr5:60047903-60048131(-)$1	228	169	175	10.6470
UUUGAG	chr14:57700416-57700653(-)$1	237	60	66	14.1029
UUUGAG	chr22:50687484-50687711(-)$1	227	174	180	14.1029
UUGGAG	chr8:22212912-22213134(+)$1	222	115	121	10.3529
uuuaaG	chr3:41281330-41281566(+)$1	236	98	104	10.2058
UAUGAG	chrX:114883654-114883893(+)$1	239	17	23	10.9411
UUUUAG	chr6:90074948-90075177(-)$1	229	100	106	10.5735
UUUUAG	chr2:47387573-47387803(-)$1	230	70	76	10.5735
UUGGAG	chrX:101967204-101967427(-)$1	223	12	18	10.3529
uuugag	chr10:96089487-96089716(-)$1	229	180	186	14.1029
UUUGGG	chr17:67211973-67212197(-)$1	224	135	141	10.6470
UUUGGG	chr11:74548780-74549002(+)$1	222	85	91	10.6470
UUGGAG	chr3:126676236-126676469(+)$1	233	226	232	10.3529
UUUGGG	chr4:186346906-186347129(-)$1	223	64	70	10.6470
uuuggg	chr3:46061100-46061321(+)$1	221	28	34	10.6470
UUUGUG	chr8:146015074-146015310(-)$1	236	142	148	10.2058
UUUUAG	chr5:35065188-35065411(+)$1	223	169	175	10.5735
uaugag	chr10:95079542-95079765(+)$1	223	21	27	10.9411
UUUGGG	chr1:25169621-25169846(+)$1	225	203	209	10.6470

#otherMatches

#Struct PSSM
ddd]cc	chr6:132212597-132212827(+)$1	230	131	137	10.5735
cc[ccc	chr3:160282914-160283174(-)$1	260	167	173	10.3529
nccc]b	chr12:117154322-117154552(-)$1	230	86	92	9.9852
d[cccz	chrX:13790413-13790638(+)$1	225	49	55	14.1029
ccc[gg	chr11:3392049-3392273(-)$1	224	147	153	14.1029
hhhhhh	chr19:44039998-44040226(-)$1	228	192	198	14.1029
ffff22	chr20:30825496-30825721(+)$1	225	39	45	10.3529
444fff	chr19:2272895-2273133(+)$1	238	107	113	14.1029
clllcc	chr1:43133451-43133673(-)$1	222	86	92	10.9411
YBBFFF	chr15:75012512-75012736(+)$1	224	214	220	10.9411
bb]ccc	chr5:137275068-137275293(-)$1	225	206	212	10.7941
ddddll	chr9:8315155-8315376(+)$1	221	184	190	10.3529
uuuudd	chrX:70794993-70795243(+)$1	250	220	226	14.1029
::eeee	chrX:114869101-114869335(+)$1	234	162	168	14.1029
ddmmmm	chr6:35262908-35263135(+)$1	227	30	36	9.9852
(((((e	chrX:47426599-47426828(+)$1	229	129	135	9.9117
IIIIII	chr22:22050282-22050511(+)$1	229	97	103	10.3529
fffffh	chr5:95224061-95224289(-)$1	228	34	40	10.5735
iiiiii	chr4:76598369-76598601(-)$1	232	59	65	10.7941
ggglll	chr12:102140110-102140340(-)$1	230	177	183	10.5735
:::::e	chr17:37221023-37221246(+)$1	223	24	30	14.1029
:::::e	chr11:111745840-111746070(-)$1	230	5	11	10.2058
#iiiii	chr1:192984313-192984538(-)$1	225	102	108	10.8676
HHHHHH	chr6:154651108-154651333(+)$1	225	21	27	10.8676
gggggg	chr17:40767069-40767297(+)$1	228	144	150	10.9411
eee]bb	chr5:176301024-176301248(-)$1	224	156	162	10.8676
cccHHH	chr17:17970239-17970469(+)$1	230	152	158	10.7941
IIIIII	chr5:138678946-138679173(+)$1	227	66	72	10.2058
CCGGGG	chrX:53406462-53406691(-)$1	229	27	33	10.7941
EEEE{B	chr11:85989280-85989505(+)$1	225	9	15	14.1029
ffffEE	chr8:90937841-90938065(-)$1	224	189	195	14.1029
hh]bb2	chr6:131931205-131931449(-)$1	244	129	135	10.8676
qqqqa]	chr4:41262653-41262887(+)$1	234	173	179	14.1029
IIIIII	chr5:150408399-150408624(+)$1	225	3	9	10.8676
iiiiii	chr4:38777297-38777519(+)$1	222	80	86	10.3529
ggggmm	chrX:39923600-39923825(+)$1	225	13	19	10.3529
eeffff	chr12:66236417-66236639(-)$1	222	131	137	10.8676
22dddd	chr17:47129158-47129381(+)$1	223	61	67	10.3529
ee!!dd	chr15:65822870-65823095(+)$1	225	5	11	14.1029
ff]bb]	chr18:13612208-13612433(+)$1	225	55	61	10.7941
beeeee	chr11:62393481-62393734(-)$1	253	119	125	14.1029
:::III	chr7:148700605-148700853(-)$1	248	197	203	10.6470
cctttt	chr9:88193741-88193967(-)$1	226	57	63	10.3529
IIIIII	chr19:10427880-10428108(-)$1	228	23	29	10.6470
::eeee	chr1:154574862-154575115(-)$1	253	55	61	10.9411
EZZZEE	chr2:27596007-27596230(+)$1	223	178	184	10.6470
cc]ddd	chr2:204193140-204193366(+)$1	226	67	73	10.9411
##dddd	chr19:16662806-16663040(-)$1	234	75	81	10.2058
ffffff	chr10:13251616-13251846(+)$1	230	181	187	10.5735
::BB}F	chr5:60047903-60048131(-)$1	228	169	175	10.6470
EEEEEN	chr14:57700416-57700653(-)$1	237	60	66	14.1029
ffffff	chr22:50687484-50687711(-)$1	227	174	180	14.1029
]dddd4	chr8:22212912-22213134(+)$1	222	115	121	10.3529
oooeee	chr3:41281330-41281566(+)$1	236	98	104	10.2058
::ffff	chrX:114883654-114883893(+)$1	239	17	23	10.9411
"""fff	chr6:90074948-90075177(-)$1	229	100	106	10.5735
ffffff	chr2:47387573-47387803(-)$1	230	70	76	10.5735
nnnfff	chrX:101967204-101967427(-)$1	223	12	18	10.3529
FFFFFh	chr10:96089487-96089716(-)$1	229	180	186	14.1029
hhheee	chr17:67211973-67212197(-)$1	224	135	141	10.6470
::ffff	chr11:74548780-74549002(+)$1	222	85	91	10.6470
}FFFFF	chr3:126676236-126676469(+)$1	233	226	232	10.3529
:::ddd	chr4:186346906-186347129(-)$1	223	64	70	10.6470
Fggggg	chr3:46061100-46061321(+)$1	221	28	34	10.6470
pppppp	chr8:146015074-146015310(-)$1	236	142	148	10.2058
pppppp	chr5:35065188-35065411(+)$1	223	169	175	10.5735
::ffff	chr10:95079542-95079765(+)$1	223	21	27	10.9411
::::FF	chr1:25169621-25169846(+)$1	225	203	209	10.6470

#DB
))).))	chr6:132212597-132212827(+)$1	1	131	137	10.5735
((.(((	chr3:160282914-160283174(-)$1	1	167	173	10.3529
.))).)	chr12:117154322-117154552(-)$1	1	86	92	9.9852
(.(((.	chrX:13790413-13790638(+)$1	1	49	55	14.1029
(((.((	chr11:3392049-3392273(-)$1	1	147	153	14.1029
))))))	chr19:44039998-44040226(-)$1	1	192	198	14.1029
))))..	chr20:30825496-30825721(+)$1	1	39	45	10.3529
...)))	chr19:2272895-2273133(+)$1	1	107	113	14.1029
(...))	chr1:43133451-43133673(-)$1	1	86	92	10.9411
.)))))	chr15:75012512-75012736(+)$1	1	214	220	10.9411
)).)))	chr5:137275068-137275293(-)$1	1	206	212	10.7941
((((..	chr9:8315155-8315376(+)$1	1	184	190	10.3529
....))	chrX:70794993-70795243(+)$1	1	220	226	14.1029
..((((	chrX:114869101-114869335(+)$1	1	162	168	14.1029
((....	chr6:35262908-35263135(+)$1	1	30	36	9.9852
.....(	chrX:47426599-47426828(+)$1	1	129	135	9.9117
((((((	chr22:22050282-22050511(+)$1	1	97	103	10.3529
)))))(	chr5:95224061-95224289(-)$1	1	34	40	10.5735
((((((	chr4:76598369-76598601(-)$1	1	59	65	10.7941
(((...	chr12:102140110-102140340(-)$1	1	177	183	10.5735
.....(	chr17:37221023-37221246(+)$1	1	24	30	14.1029
.....(	chr11:111745840-111746070(-)$1	1	5	11	10.2058
.(((((	chr1:192984313-192984538(-)$1	1	102	108	10.8676
((((((	chr6:154651108-154651333(+)$1	1	21	27	10.8676
))))))	chr17:40767069-40767297(+)$1	1	144	150	10.9411
))).))	chr5:176301024-176301248(-)$1	1	156	162	10.8676
))))))	chr17:17970239-17970469(+)$1	1	152	158	10.7941
((((((	chr5:138678946-138679173(+)$1	1	66	72	10.2058
((((((	chrX:53406462-53406691(-)$1	1	27	33	10.7941
((((.(	chr11:85989280-85989505(+)$1	1	9	15	14.1029
))))))	chr8:90937841-90938065(-)$1	1	189	195	14.1029
)).)).	chr6:131931205-131931449(-)$1	1	129	135	10.8676
....).	chr4:41262653-41262887(+)$1	1	173	179	14.1029
((((((	chr5:150408399-150408624(+)$1	1	3	9	10.8676
((((((	chr4:38777297-38777519(+)$1	1	80	86	10.3529
((((..	chrX:39923600-39923825(+)$1	1	13	19	10.3529
))((((	chr12:66236417-66236639(-)$1	1	131	137	10.8676
..))))	chr17:47129158-47129381(+)$1	1	61	67	10.3529
((..((	chr15:65822870-65823095(+)$1	1	5	11	14.1029
)).)).	chr18:13612208-13612433(+)$1	1	55	61	10.7941
))))))	chr11:62393481-62393734(-)$1	1	119	125	14.1029
...)))	chr7:148700605-148700853(-)$1	1	197	203	10.6470
((....	chr9:88193741-88193967(-)$1	1	57	63	10.3529
((((((	chr19:10427880-10428108(-)$1	1	23	29	10.6470
..((((	chr1:154574862-154575115(-)$1	1	55	61	10.9411
)...))	chr2:27596007-27596230(+)$1	1	178	184	10.6470
)).)))	chr2:204193140-204193366(+)$1	1	67	73	10.9411
..((((	chr19:16662806-16663040(-)$1	1	75	81	10.2058
))))))	chr10:13251616-13251846(+)$1	1	181	187	10.5735
..)).)	chr5:60047903-60048131(-)$1	1	169	175	10.6470
(((((.	chr14:57700416-57700653(-)$1	1	60	66	14.1029
))))))	chr22:50687484-50687711(-)$1	1	174	180	14.1029
.)))).	chr8:22212912-22213134(+)$1	1	115	121	10.3529
...)))	chr3:41281330-41281566(+)$1	1	98	104	10.2058
..((((	chrX:114883654-114883893(+)$1	1	17	23	10.9411
...(((	chr6:90074948-90075177(-)$1	1	100	106	10.5735
))))))	chr2:47387573-47387803(-)$1	1	70	76	10.5735
...)))	chrX:101967204-101967427(-)$1	1	12	18	10.3529
)))))(	chr10:96089487-96089716(-)$1	1	180	186	14.1029
)))(((	chr17:67211973-67212197(-)$1	1	135	141	10.6470
..((((	chr11:74548780-74549002(+)$1	1	85	91	10.6470
.)))))	chr3:126676236-126676469(+)$1	1	226	232	10.3529
...(((	chr4:186346906-186347129(-)$1	1	64	70	10.6470
((((((	chr3:46061100-46061321(+)$1	1	28	34	10.6470
......	chr8:146015074-146015310(-)$1	1	142	148	10.2058
......	chr5:35065188-35065411(+)$1	1	169	175	10.5735
..((((	chr10:95079542-95079765(+)$1	1	21	27	10.9411
....))	chr1:25169621-25169846(+)$1	1	203	209	10.6470

#PSSM
U : 0.86	u : 0.13	
U : 0.61	u : 0.11	A : 0.08	C : 0.08	G : 0.07	a : 0.01	
U : 0.73	u : 0.11	G : 0.08	A : 0.02	g : 0.01	C : 0.01	
G : 0.72	U : 0.08	g : 0.08	C : 0.04	c : 0.01	A : 0.01	u : 0.01	a : 0.01	
A : 0.72	a : 0.10	G : 0.10	U : 0.04	g : 0.02	
G : 0.88	g : 0.11	

#score	771.9411764705872
#seq	68
#width	6
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_CDS_m3_run2.nuc.txt

#NT
ACAGA	chr1:156278950-156279175(-)$1	225	211	216	14.9999
ACAGA	chr16:5081751-5081977(-)$1	226	204	209	14.9999
ACAGA	chr1:10352011-10352240(+)$1	229	199	204	14.9999
ACAGA	chr11:32956551-32956777(+)$1	226	35	40	14.9999
ACAGA	chr11:122928467-122928729(-)$1	262	131	136	14.9999
ACAGA	chr5:145509540-145509763(-)$1	223	85	90	14.9999
ACAGA	chr3:100170475-100170702(-)$1	227	148	153	14.9999
ACAGA	chr14:75576454-75576684(-)$1	230	31	36	14.9999
ACAGA	chr3:31674422-31674650(+)$1	228	195	200	14.9999
ACAGA	chr17:79410427-79410674(+)$1	247	176	181	14.9999
ACAGA	chr1:25572851-25573083(-)$1	232	95	100	14.9999
ACAGA	chr11:67166479-67166718(-)$1	239	137	142	14.9999
ACAGA	chr1:70697958-70698183(+)$1	225	141	146	14.9999
ACAGA	chr16:27518339-27518568(-)$1	229	20	25	14.9999
ACAGA	chr6:139355234-139355458(+)$1	224	135	140	14.9999
ACAGA	chr6:28116270-28116508(+)$1	238	178	183	14.9999
ACAGA	chr1:154246190-154246419(+)$1	229	108	113	14.9999
ACAGA	chr6:7246619-7246847(+)$1	228	33	38	14.9999
ACAGA	chr19:39923782-39924029(-)$1	247	224	229	14.9999
ACAGA	chr3:107799034-107799264(-)$1	230	28	33	14.9999
ACAGA	chr3:47891448-47891693(+)$1	245	186	191	14.9999
ACAGA	chr22:24509456-24509681(+)$1	225	180	185	14.9999
ACAGA	chr12:70330288-70330510(-)$1	222	216	221	14.9999
ACAGA	chr19:1056016-1056259(+)$1	243	44	49	14.9999
ACAGA	chr14:21969034-21969268(-)$1	234	165	170	14.9999
ACAGA	chr3:125249264-125249490(+)$1	226	52	57	14.9999
ACAGA	chr9:131344958-131345183(+)$1	225	152	157	14.9999
ACAGA	chr8:48826457-48826715(-)$1	258	133	138	14.9999
ACAGA	chr7:66459196-66459423(-)$1	227	195	200	14.9999
ACAGA	chr1:70616733-70616960(-)$1	227	158	163	14.9999
ACAGA	chr13:72133833-72134058(-)$1	225	98	103	14.9999
ACAGA	chr10:79579585-79579807(+)$1	222	69	74	14.9999
ACAGA	chr17:4910458-4910687(+)$1	229	102	107	14.9999
ACAGA	chr12:39079225-39079449(-)$1	224	26	31	14.9999
ACAGA	chr12:120173001-120173231(-)$1	230	75	80	14.9999
ACAGA	chr2:242065723-242065947(-)$1	224	84	89	14.9999
ACAGA	chr1:245023572-245023816(-)$1	244	36	41	14.9999

#otherMatches

#Struct PSSM
==]ff	chr3:169496473-169496698(+)$1	225	194	199	14.9999
E}CCC	chr1:156278950-156279175(-)$1	225	211	216	14.9999
ggg::	chr16:5081751-5081977(-)$1	226	204	209	14.9999
=====	chr1:10352011-10352240(+)$1	229	199	204	14.9999
:iiii	chr11:32956551-32956777(+)$1	226	35	40	14.9999
!ccco	chr11:122928467-122928729(-)$1	262	131	136	14.9999
eeee:	chr5:145509540-145509763(-)$1	223	85	90	14.9999
vvvvv	chr3:100170475-100170702(-)$1	227	148	153	14.9999
hhhhh	chr14:75576454-75576684(-)$1	230	31	36	14.9999
?CCCY	chr3:31674422-31674650(+)$1	228	195	200	14.9999
uuuuu	chr17:79410427-79410674(+)$1	247	176	181	14.9999
$$$$$	chr1:25572851-25573083(-)$1	232	95	100	14.9999
[ccco	chr11:67166479-67166718(-)$1	239	137	142	14.9999
::ccc	chr1:70697958-70698183(+)$1	225	141	146	14.9999
Hcccn	chr16:27518339-27518568(-)$1	229	20	25	14.9999
nnnne	chr6:139355234-139355458(+)$1	224	135	140	14.9999
}DDDD	chr6:28116270-28116508(+)$1	238	178	183	14.9999
D}BB:	chr1:154246190-154246419(+)$1	229	108	113	14.9999
:::::	chr6:7246619-7246847(+)$1	228	33	38	14.9999
^^^^^	chr19:39923782-39924029(-)$1	247	224	229	14.9999
qqccc	chr3:107799034-107799264(-)$1	230	28	33	14.9999
444gg	chr3:47891448-47891693(+)$1	245	186	191	14.9999
::DDD	chr22:24509456-24509681(+)$1	225	180	185	14.9999
}DDDD	chr12:70330288-70330510(-)$1	222	216	221	14.9999
fff((	chr19:1056016-1056259(+)$1	243	44	49	14.9999
nneee	chr14:21969034-21969268(-)$1	234	165	170	14.9999
:eeee	chr3:125249264-125249490(+)$1	226	52	57	14.9999
2ffff	chr9:131344958-131345183(+)$1	225	152	157	14.9999
e]ccc	chr8:48826457-48826715(-)$1	258	133	138	14.9999
BBEEE	chr7:66459196-66459423(-)$1	227	195	200	14.9999
eeeee	chr1:70616733-70616960(-)$1	227	158	163	14.9999
eeee$	chr13:72133833-72134058(-)$1	225	98	103	14.9999
ppbb]	chr10:79579585-79579807(+)$1	222	69	74	14.9999
+++++	chr17:4910458-4910687(+)$1	229	102	107	14.9999
:IIII	chr12:39079225-39079449(-)$1	224	26	31	14.9999
qqqq=	chr12:120173001-120173231(-)$1	230	75	80	14.9999
d!!ee	chr2:242065723-242065947(-)$1	224	84	89	14.9999
FFFFF	chr1:245023572-245023816(-)$1	244	36	41	14.9999

#DB
)).))	chr3:169496473-169496698(+)$1	1	194	199	14.9999
).)))	chr1:156278950-156279175(-)$1	1	211	216	14.9999
)))..	chr16:5081751-5081977(-)$1	1	204	209	14.9999
(((((	chr1:10352011-10352240(+)$1	1	199	204	14.9999
.((((	chr11:32956551-32956777(+)$1	1	35	40	14.9999
.(((.	chr11:122928467-122928729(-)$1	1	131	136	14.9999
)))).	chr5:145509540-145509763(-)$1	1	85	90	14.9999
.....	chr3:100170475-100170702(-)$1	1	148	153	14.9999
(((((	chr14:75576454-75576684(-)$1	1	31	36	14.9999
.))).	chr3:31674422-31674650(+)$1	1	195	200	14.9999
.....	chr17:79410427-79410674(+)$1	1	176	181	14.9999
.....	chr1:25572851-25573083(-)$1	1	95	100	14.9999
.(((.	chr11:67166479-67166718(-)$1	1	137	142	14.9999
..(((	chr1:70697958-70698183(+)$1	1	141	146	14.9999
((((.	chr16:27518339-27518568(-)$1	1	20	25	14.9999
....)	chr6:139355234-139355458(+)$1	1	135	140	14.9999
.))))	chr6:28116270-28116508(+)$1	1	178	183	14.9999
).)).	chr1:154246190-154246419(+)$1	1	108	113	14.9999
.....	chr6:7246619-7246847(+)$1	1	33	38	14.9999
.....	chr19:39923782-39924029(-)$1	1	224	229	14.9999
..)))	chr3:107799034-107799264(-)$1	1	28	33	14.9999
...))	chr3:47891448-47891693(+)$1	1	186	191	14.9999
..)))	chr22:24509456-24509681(+)$1	1	180	185	14.9999
.))))	chr12:70330288-70330510(-)$1	1	216	221	14.9999
(((..	chr19:1056016-1056259(+)$1	1	44	49	14.9999
..)))	chr14:21969034-21969268(-)$1	1	165	170	14.9999
.((((	chr3:125249264-125249490(+)$1	1	52	57	14.9999
.))))	chr9:131344958-131345183(+)$1	1	152	157	14.9999
).)))	chr8:48826457-48826715(-)$1	1	133	138	14.9999
)))))	chr7:66459196-66459423(-)$1	1	195	200	14.9999
(((((	chr1:70616733-70616960(-)$1	1	158	163	14.9999
((((.	chr13:72133833-72134058(-)$1	1	98	103	14.9999
..)).	chr10:79579585-79579807(+)$1	1	69	74	14.9999
.....	chr17:4910458-4910687(+)$1	1	102	107	14.9999
.((((	chr12:39079225-39079449(-)$1	1	26	31	14.9999
....)	chr12:120173001-120173231(-)$1	1	75	80	14.9999
(..((	chr2:242065723-242065947(-)$1	1	84	89	14.9999
(((((	chr1:245023572-245023816(-)$1	1	36	41	14.9999

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

#score	569.9999999999999
#seq	38
#width	5
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_CDS_m2_run1.nuc.txt

#NT
AUUUUCUCU	chr14:62233544-62233784(+)$1	240	29	38	12.9259
UUGUUCUUU	chrX:119004410-119004650(-)$1	240	142	151	15.9814
UUUUUCUUC	chr13:103443206-103443446(-)$1	240	121	130	16.4444
UUUUUCUCU	chr15:48434387-48434667(-)$1	280	62	71	16.1666
ACUUUCUUU	chr17:62496654-62496894(-)$1	240	113	122	13.0185
GUUUUCUUA	chr16:29821508-29821748(+)$1	240	179	188	12.7407
UUUUUCUUU	chr8:120233750-120233990(+)$1	240	169	178	20.6111
GUUUUCUUU	chr12:44337974-44338214(+)$1	240	175	184	17.1851
uuuuuuauu	chr3:73006363-73006603(+)$1	240	122	131	14.4999
UUUCucauu	chr13:48934104-48934344(+)$1	240	187	196	14.4074
UUUCUCUUU	chr10:1087067-1087307(-)$1	240	106	115	16.5370
UUUUUCAUU	chr2:70064587-70064827(+)$1	240	71	80	18.4814
AUUUUAUUU	chr19:9676516-9676756(-)$1	240	104	113	13.5740
UAUUUCUUU	chr7:87170572-87170812(-)$1	240	112	121	16.2592
AUUUUCUUU	chr2:54150410-54150650(-)$1	240	21	30	17.3703
UCUUUCCUU	chr8:11667160-11667400(+)$1	240	121	130	14.0370
AUUUUCUUC	chr11:62344298-62344538(-)$1	240	97	106	13.2037
UUUUGCAUU	chr3:169801936-169802176(+)$1	240	143	152	14.1296
UGUUUCUUU	chr4:2940438-2940678(-)$1	240	9	18	16.1666
UUUUUCCAU	chr3:132431869-132432109(-)$1	240	24	33	13.9444
UUUUACUUU	chr3:194140543-194140783(-)$1	240	63	72	16.2592
UUUUUCUUC	chr4:122737873-122738117(-)$1	244	126	135	16.4444
GUUUUCCUU	chr7:114655867-114656107(+)$1	240	108	117	14.9629
UUUGUCUUU	chr14:90870955-90871195(+)$1	240	64	73	16.3518
UUUCUCUUU	chr11:46780416-46780656(-)$1	240	40	49	16.5370
GUUUUCUUU	chr8:95780589-95780829(+)$1	240	152	161	17.1851
UUUUUCCUU	chr6:32944009-32944249(+)$1	240	0	9	18.3888
UUUUUCUUC	chrX:138901396-138901641(-)$1	245	35	44	16.4444
UUUUUCGUU	chr7:23509626-23509866(-)$1	240	90	99	17.7407
UUUUUCUUU	chr5:94005816-94006056(+)$1	240	121	130	20.6111
UUUGUCUUU	chr2:223339207-223339447(+)$1	240	67	76	16.3518
UUUUUUUUU	chr6:70410568-70410848(-)$1	280	75	84	16.6296
UUUUACUUU	chr21:33747615-33747855(-)$1	240	51	60	16.2592
UUUUUCUUU	chr3:98234561-98234801(-)$1	240	19	28	20.6111
UUUUUCCUU	chr14:59835446-59835686(+)$1	240	228	237	18.3888
UUUUCCUUU	chr1:154524467-154524707(-)$1	240	127	136	16.1666
UAUUUCCUU	chr13:113459214-113459454(+)$1	240	119	128	14.0370
auuuuCUUU	chr12:42481534-42481774(-)$1	240	10	19	17.3703
UUUUUCCAU	chr7:107221166-107221407(+)$1	241	24	33	13.9444
uuuuuauuu	chr5:61778838-61779078(+)$1	240	64	73	16.8148
UUUUUCUUU	chr18:61067713-61067953(-)$1	240	201	210	20.6111
UUCUUCAUU	chr1:205589608-205589848(-)$1	240	115	124	13.9444
UUUUUCCUU	chr16:58584953-58585193(-)$1	240	192	201	18.3888
UUUUUAAUU	chr8:71499090-71499330(-)$1	240	73	82	14.6851
UUUUUAGUU	chr20:54945463-54945703(-)$1	240	97	106	13.9444
AUUUUAUUU	chr15:55474223-55474463(-)$1	240	182	191	13.5740
UUUUUCCUU	chr1:165638125-165638613(-)$1	488	346	355	18.3888
UUUUGCAUU	chr3:169802047-169802298(+)$1	251	32	41	14.1296
UUUUUCAUU	chr14:73653456-73653696(+)$1	240	151	160	18.4814
GUCUUCUUU	chr14:31107239-31107479(+)$1	240	47	56	12.6481
UUUUUUAUU	chr1:40735612-40735852(+)$1	240	145	154	14.4999
UUUUUCAUU	chr7:108155185-108155433(-)$1	248	63	72	18.4814
UUUUUCUUU	chr9:86584179-86584419(-)$1	240	45	54	20.6111

#otherMatches

#Struct PSSM
EEGGGGGGG	chr5:38523513-38523753(-)$1	240	42	51	16.5370
::fffffff	chr14:62233544-62233784(+)$1	240	29	38	12.9259
hhhhheeee	chrX:119004410-119004650(-)$1	240	142	151	15.9814
ccdddd]ee	chr13:103443206-103443446(-)$1	240	121	130	16.4444
ooeeeee]b	chr15:48434387-48434667(-)$1	280	62	71	16.1666
dddd[eeee	chr17:62496654-62496894(-)$1	240	113	122	13.0185
ccc!!eeee	chr16:29821508-29821748(+)$1	240	179	188	12.7407
sssssssss	chr8:120233750-120233990(+)$1	240	169	178	20.6111
cmmmmccc]	chr12:44337974-44338214(+)$1	240	175	184	17.1851
qqqdddd77	chr3:73006363-73006603(+)$1	240	122	131	14.4999
^^^^^^^^^	chr13:48934104-48934344(+)$1	240	187	196	14.4074
^^^^^^ggg	chr10:1087067-1087307(-)$1	240	106	115	16.5370
ggggg[ddd	chr2:70064587-70064827(+)$1	240	71	80	18.4814
ggggg"""c	chr19:9676516-9676756(-)$1	240	104	113	13.5740
mmmdddd::	chr7:87170572-87170812(-)$1	240	112	121	16.2592
ccqqqqqqq	chr2:54150410-54150650(-)$1	240	21	30	17.3703
FFLLLBB::	chr8:11667160-11667400(+)$1	240	121	130	14.0370
E::::::::	chr11:62344298-62344538(-)$1	240	97	106	13.2037
444bb333c	chr3:169801936-169802176(+)$1	240	143	152	14.1296
KGGGGGGGK	chr4:2940438-2940678(-)$1	240	9	18	16.1666
oooffffff	chr3:132431869-132432109(-)$1	240	24	33	13.9444
iiiiiiii!	chr3:194140543-194140783(-)$1	240	63	72	16.2592
:::::::::	chr4:122737873-122738117(-)$1	244	126	135	16.4444
oooddddff	chr7:114655867-114656107(+)$1	240	108	117	14.9629
^hhhhhhhh	chr14:90870955-90871195(+)$1	240	64	73	16.3518
d:EEEEE{E	chr11:46780416-46780656(-)$1	240	40	49	16.5370
ffwwwwwww	chr8:95780589-95780829(+)$1	240	152	161	17.1851
:::::::::	chr6:32944009-32944249(+)$1	240	0	9	18.3888
+++++++++	chrX:138901396-138901641(-)$1	245	35	44	16.4444
99999999=	chr7:23509626-23509866(-)$1	240	90	99	17.7407
7ffffff22	chr5:94005816-94006056(+)$1	240	121	130	20.6111
hhhhhauuu	chr2:223339207-223339447(+)$1	240	67	76	16.3518
2ccc:::::	chr6:70410568-70410848(-)$1	280	75	84	16.6296
ppppppggg	chr21:33747615-33747855(-)$1	240	51	60	16.2592
::ffffff!	chr3:98234561-98234801(-)$1	240	19	28	20.6111
HHHHHHHH:	chr14:59835446-59835686(+)$1	240	228	237	18.3888
eeeoooooo	chr1:154524467-154524707(-)$1	240	127	136	16.1666
f::::gggg	chr13:113459214-113459454(+)$1	240	119	128	14.0370
GGGGGGGDD	chr12:42481534-42481774(-)$1	240	10	19	17.3703
####cccdd	chr7:107221166-107221407(+)$1	241	24	33	13.9444
==4444fff	chr5:61778838-61779078(+)$1	240	64	73	16.8148
}EEEEE}GG	chr18:61067713-61067953(-)$1	240	201	210	20.6111
fffff!!cc	chr1:205589608-205589848(-)$1	240	115	124	13.9444
ff!!cccnn	chr16:58584953-58585193(-)$1	240	192	201	18.3888
tttffffff	chr8:71499090-71499330(-)$1	240	73	82	14.6851
qqqqdddd]	chr20:54945463-54945703(-)$1	240	97	106	13.9444
HHHHH:ggg	chr15:55474223-55474463(-)$1	240	182	191	13.5740
^^^^dddd5	chr1:165638125-165638613(-)$1	488	346	355	18.3888
nnnnbb22b	chr3:169802047-169802298(+)$1	251	32	41	14.1296
::ffffff!	chr14:73653456-73653696(+)$1	240	151	160	18.4814
dd[ccc"""	chr14:31107239-31107479(+)$1	240	47	56	12.6481
::hhhhhhh	chr1:40735612-40735852(+)$1	240	145	154	14.4999
iiiiii>>>	chr7:108155185-108155433(-)$1	248	63	72	18.4814
^^^^^^^^^	chr9:86584179-86584419(-)$1	240	45	54	20.6111

#DB
(((((((((	chr5:38523513-38523753(-)$1	1	42	51	16.5370
..(((((((	chr14:62233544-62233784(+)$1	1	29	38	12.9259
(((((((((	chrX:119004410-119004650(-)$1	1	142	151	15.9814
)))))).))	chr13:103443206-103443446(-)$1	1	121	130	16.4444
..))))).)	chr15:48434387-48434667(-)$1	1	62	71	16.1666
((((.((((	chr17:62496654-62496894(-)$1	1	113	122	13.0185
(((..((((	chr16:29821508-29821748(+)$1	1	179	188	12.7407
.........	chr8:120233750-120233990(+)$1	1	169	178	20.6111
(....))).	chr12:44337974-44338214(+)$1	1	175	184	17.1851
...))))..	chr3:73006363-73006603(+)$1	1	122	131	14.4999
.........	chr13:48934104-48934344(+)$1	1	187	196	14.4074
......)))	chr10:1087067-1087307(-)$1	1	106	115	16.5370
(((((.(((	chr2:70064587-70064827(+)$1	1	71	80	18.4814
(((((...(	chr19:9676516-9676756(-)$1	1	104	113	13.5740
...))))..	chr7:87170572-87170812(-)$1	1	112	121	16.2592
((.......	chr2:54150410-54150650(-)$1	1	21	30	17.3703
((...((..	chr8:11667160-11667400(+)$1	1	121	130	14.0370
(........	chr11:62344298-62344538(-)$1	1	97	106	13.2037
...))...)	chr3:169801936-169802176(+)$1	1	143	152	14.1296
.(((((((.	chr4:2940438-2940678(-)$1	1	9	18	16.1666
...))))))	chr3:132431869-132432109(-)$1	1	24	33	13.9444
((((((((.	chr3:194140543-194140783(-)$1	1	63	72	16.2592
.........	chr4:122737873-122738117(-)$1	1	126	135	16.4444
...))))))	chr7:114655867-114656107(+)$1	1	108	117	14.9629
.))))))))	chr14:90870955-90871195(+)$1	1	64	73	16.3518
).(((((.(	chr11:46780416-46780656(-)$1	1	40	49	16.5370
((.......	chr8:95780589-95780829(+)$1	1	152	161	17.1851
.........	chr6:32944009-32944249(+)$1	1	0	9	18.3888
.........	chrX:138901396-138901641(-)$1	1	35	44	16.4444
........)	chr7:23509626-23509866(-)$1	1	90	99	17.7407
.))))))..	chr5:94005816-94006056(+)$1	1	121	130	20.6111
((((((...	chr2:223339207-223339447(+)$1	1	67	76	16.3518
.))).....	chr6:70410568-70410848(-)$1	1	75	84	16.6296
......)))	chr21:33747615-33747855(-)$1	1	51	60	16.2592
..((((((.	chr3:98234561-98234801(-)$1	1	19	28	20.6111
)))))))).	chr14:59835446-59835686(+)$1	1	228	237	18.3888
(((......	chr1:154524467-154524707(-)$1	1	127	136	16.1666
)....((((	chr13:113459214-113459454(+)$1	1	119	128	14.0370
(((((((((	chr12:42481534-42481774(-)$1	1	10	19	17.3703
....(((((	chr7:107221166-107221407(+)$1	1	24	33	13.9444
))....)))	chr5:61778838-61779078(+)$1	1	64	73	16.8148
.))))).))	chr18:61067713-61067953(-)$1	1	201	210	20.6111
(((((..((	chr1:205589608-205589848(-)$1	1	115	124	13.9444
((..(((..	chr16:58584953-58585193(-)$1	1	192	201	18.3888
...))))))	chr8:71499090-71499330(-)$1	1	73	82	14.6851
....)))).	chr20:54945463-54945703(-)$1	1	97	106	13.9444
))))).(((	chr15:55474223-55474463(-)$1	1	182	191	13.5740
....)))).	chr1:165638125-165638613(-)$1	1	346	355	18.3888
....))..)	chr3:169802047-169802298(+)$1	1	32	41	14.1296
..((((((.	chr14:73653456-73653696(+)$1	1	151	160	18.4814
((.(((...	chr14:31107239-31107479(+)$1	1	47	56	12.6481
..(((((((	chr1:40735612-40735852(+)$1	1	145	154	14.4999
))))))...	chr7:108155185-108155433(-)$1	1	63	72	18.4814
.........	chr9:86584179-86584419(-)$1	1	45	54	20.6111

#PSSM
U : 0.74	A : 0.11	G : 0.09	u : 0.03	a : 0.01	
U : 0.85	u : 0.05	C : 0.03	A : 0.03	G : 0.01	
U : 0.88	u : 0.05	C : 0.03	G : 0.01	
U : 0.83	C : 0.07	u : 0.05	G : 0.03	
U : 0.83	u : 0.07	G : 0.03	A : 0.03	C : 0.01	
C : 0.83	A : 0.07	U : 0.03	u : 0.01	c : 0.01	a : 0.01	
U : 0.59	C : 0.16	A : 0.14	a : 0.03	G : 0.03	u : 0.01	
U : 0.87	u : 0.05	C : 0.03	A : 0.03	
U : 0.85	C : 0.07	u : 0.05	A : 0.01	

#score	874.1111111111101
#seq	54
#width	9
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m2_run1.nuc.txt

#NT
uug	chr2:63363594-63363864(-)$1	270	2	5	9.0000
uug	chr19:9954850-9955062(+)$1	212	7	10	9.0000
uug	chr10:15187116-15187405(-)$1	289	70	73	9.0000
UUG	chr5:156650167-156650470(+)$1	303	12	15	9.0000
uug	chr12:66614514-66614727(+)$1	213	115	118	9.0000
UUG	chr11:96012562-96012848(-)$1	286	71	74	9.0000
UUG	chr13:21365349-21365570(-)$1	221	86	89	9.0000
UUG	chr3:114287836-114288087(-)$1	251	70	73	9.0000
uug	chr7:66616824-66617055(+)$1	231	6	9	9.0000
uug	chr14:73356682-73356970(-)$1	288	4	7	9.0000
UUG	chr2:144084003-144084361(+)$1	358	21	24	9.0000
UUG	chr5:110590167-110590398(+)$1	231	112	115	9.0000
uug	chr13:52297151-52297371(+)$1	220	120	123	9.0000
uug	chr14:67481061-67481303(+)$1	242	82	85	9.0000
uug	chr1:53218754-53218972(+)$1	218	121	124	9.0000
uug	chr6:157295898-157296174(+)$1	276	88	91	9.0000
UUG	chr14:65906174-65906432(+)$1	258	6	9	9.0000
uug	chr7:133348040-133348300(+)$1	260	26	29	9.0000
uug	chr2:119708619-119708847(+)$1	228	22	25	9.0000
uug	chr16:54052686-54052935(+)$1	249	69	72	9.0000
uug	chr12:111080654-111080916(+)$1	262	76	79	9.0000
UUG	chr1:245017542-245017852(-)$1	310	8	11	9.0000
UUG	chr9:35752126-35752341(+)$1	215	13	16	9.0000
UUG	chr19:45525522-45525782(+)$1	260	39	42	9.0000
UUG	chr6:27359426-27359679(+)$1	253	116	119	9.0000
uug	chr14:48058808-48059025(-)$1	217	33	36	9.0000
UUG	chrY:16741846-16742059(+)$1	213	15	18	9.0000
UUG	chr1:10768710-10768946(-)$1	236	153	156	9.0000
uug	chr15:73397181-73397401(+)$1	220	140	143	9.0000
uug	chr10:24039467-24039682(+)$1	215	24	27	9.0000
UUG	chr15:43855890-43856137(-)$1	247	14	17	9.0000
uug	chr4:83878797-83879039(-)$1	242	21	24	9.0000
UUG	chr8:59935355-59935607(-)$1	252	69	72	9.0000
uug	chr1:44260091-44260306(+)$1	215	35	38	9.0000
UUG	chr14:56664587-56664857(+)$1	270	152	155	9.0000
UUG	chr6:65250660-65250883(-)$1	223	67	70	9.0000
uug	chr1:216156429-216156646(-)$1	217	81	84	9.0000
UUG	chr2:207945648-207945989(-)$1	341	24	27	9.0000
UUG	chr12:12699142-12699393(-)$1	251	22	25	9.0000
UUG	chrX:73994117-73994400(-)$1	283	0	3	9.0000
uug	chr1:101384126-101384372(+)$1	246	12	15	9.0000
uug	chr15:40994075-40994323(+)$1	248	37	40	9.0000
UUG	chr3:23875788-23876167(+)$1	379	58	61	9.0000
UUG	chr15:71888306-71888522(+)$1	216	53	56	9.0000
UUG	chr11:44182398-44182618(+)$1	220	65	68	9.0000
UUG	chr5:110588326-110588546(+)$1	220	68	71	9.0000
uug	chr6:38172354-38172588(-)$1	234	38	41	9.0000
UUG	chr8:56735298-56735552(+)$1	254	8	11	9.0000
uug	chr6:13059585-13059829(+)$1	244	55	58	9.0000
uug	chr1:46112022-46112255(-)$1	233	70	73	9.0000
UUG	chr9:97204531-97204813(+)$1	282	73	76	9.0000
uug	chr22:39985065-39985280(+)$1	215	93	96	9.0000
uug	chr11:76644476-76644702(+)$1	226	10	13	9.0000
uug	chr1:234386514-234386730(+)$1	216	71	74	9.0000
uug	chr3:136415229-136415594(-)$1	365	11	14	9.0000
uug	chr13:95030175-95030396(+)$1	221	66	69	9.0000
UUG	chr14:35181517-35181741(-)$1	224	4	7	9.0000
uug	chr17:35332574-35332820(+)$1	246	14	17	9.0000
uug	chr9:5749115-5749346(+)$1	231	3	6	9.0000
UUG	chr12:109179588-109179842(-)$1	254	10	13	9.0000
UUG	chr3:107764913-107765149(-)$1	236	61	64	9.0000
UUG	chr9:43728545-43728762(+)$1	217	72	75	9.0000
uug	chr1:35961121-35961391(-)$1	270	33	36	9.0000
uug	chr1:22388064-22388286(+)$1	222	1	4	9.0000
UUG	chr9:7101694-7101956(+)$1	262	27	30	9.0000
UUG	chr5:72974584-72974798(+)$1	214	132	135	9.0000
uug	chr22:29497385-29497637(+)$1	252	158	161	9.0000
UUG	chr2:54955345-54955562(+)$1	217	34	37	9.0000
UUG	chr1:198711686-198712000(+)$1	314	69	72	9.0000
uug	chr3:148873776-148874027(+)$1	251	17	20	9.0000
uug	chr12:62691606-62691846(+)$1	240	20	23	9.0000
UUG	chr10:112658621-112658888(+)$1	267	90	93	9.0000
uug	chr10:121625726-121625957(-)$1	231	5	8	9.0000
uug	chrY:9340728-9340984(+)$1	256	42	45	9.0000
uug	chr2:32993252-32993478(+)$1	226	74	77	9.0000
UUG	chr19:52714727-52714984(+)$1	257	34	37	9.0000
uug	chr1:64521389-64521612(+)$1	223	71	74	9.0000
UUG	chrX:147015260-147015497(+)$1	237	9	12	9.0000
uug	chr3:196619875-196620159(+)$1	284	30	33	9.0000
UUG	chr1:245756467-245756724(+)$1	257	2	5	9.0000
UUG	chr3:114216980-114217202(-)$1	222	50	53	9.0000
UUG	chr1:35342017-35342286(-)$1	269	36	39	9.0000
UUG	chr2:202025066-202025283(+)$1	217	33	36	9.0000
UUG	chr14:79200446-79200699(+)$1	253	24	27	9.0000
uug	chr1:36076925-36077151(-)$1	226	107	110	9.0000
uug	chr15:86175411-86175645(+)$1	234	26	29	9.0000
uug	chr2:191987441-191987683(-)$1	242	13	16	9.0000
UUG	chr8:10650255-10650479(-)$1	224	49	52	9.0000
uug	chr14:64578326-64578548(+)$1	222	64	67	9.0000
UUG	chr8:48693787-48694044(-)$1	257	27	30	9.0000
UUG	chr1:29378920-29379159(+)$1	239	41	44	9.0000
uug	chr14:66098566-66098835(+)$1	269	34	37	9.0000
UUG	chr3:173866624-173866837(+)$1	213	11	14	9.0000
uug	chrX:83609259-83609492(-)$1	233	12	15	9.0000
uug	chr9:117119608-117119997(-)$1	389	15	18	9.0000
UUG	chr3:43374150-43374383(+)$1	233	20	23	9.0000
UUG	chr1:21557599-21557879(-)$1	280	172	175	9.0000

#otherMatches

#Struct PSSM
::D	chrX:85238294-85238563(-)$1	269	18	21	9.0000
:::	chr2:63363594-63363864(-)$1	270	2	5	9.0000
KII	chr19:9954850-9955062(+)$1	212	7	10	9.0000
fff	chr10:15187116-15187405(-)$1	289	70	73	9.0000
#cc	chr5:156650167-156650470(+)$1	303	12	15	9.0000
dEE	chr12:66614514-66614727(+)$1	213	115	118	9.0000
QQD	chr11:96012562-96012848(-)$1	286	71	74	9.0000
JJJ	chr13:21365349-21365570(-)$1	221	86	89	9.0000
=""	chr3:114287836-114288087(-)$1	251	70	73	9.0000
::D	chr7:66616824-66617055(+)$1	231	6	9	9.0000
::C	chr14:73356682-73356970(-)$1	288	4	7	9.0000
HHH	chr2:144084003-144084361(+)$1	358	21	24	9.0000
GG{	chr5:110590167-110590398(+)$1	231	112	115	9.0000
::c	chr13:52297151-52297371(+)$1	220	120	123	9.0000
eee	chr14:67481061-67481303(+)$1	242	82	85	9.0000
ggg	chr1:53218754-53218972(+)$1	218	121	124	9.0000
^ii	chr6:157295898-157296174(+)$1	276	88	91	9.0000
[cc	chr14:65906174-65906432(+)$1	258	6	9	9.0000
"bb	chr7:133348040-133348300(+)$1	260	26	29	9.0000
DDD	chr2:119708619-119708847(+)$1	228	22	25	9.0000
ddd	chr16:54052686-54052935(+)$1	249	69	72	9.0000
rrr	chr12:111080654-111080916(+)$1	262	76	79	9.0000
##b	chr1:245017542-245017852(-)$1	310	8	11	9.0000
#gg	chr9:35752126-35752341(+)$1	215	13	16	9.0000
FFc	chr19:45525522-45525782(+)$1	260	39	42	9.0000
MMC	chr6:27359426-27359679(+)$1	253	116	119	9.0000
fff	chr14:48058808-48059025(-)$1	217	33	36	9.0000
EEE	chrY:16741846-16742059(+)$1	213	15	18	9.0000
===	chr1:10768710-10768946(-)$1	236	153	156	9.0000
JJJ	chr15:73397181-73397401(+)$1	220	140	143	9.0000
pdd	chr10:24039467-24039682(+)$1	215	24	27	9.0000
qqe	chr15:43855890-43856137(-)$1	247	14	17	9.0000
:::	chr4:83878797-83879039(-)$1	242	21	24	9.0000
:::	chr8:59935355-59935607(-)$1	252	69	72	9.0000
]cc	chr1:44260091-44260306(+)$1	215	35	38	9.0000
fff	chr14:56664587-56664857(+)$1	270	152	155	9.0000
fff	chr6:65250660-65250883(-)$1	223	67	70	9.0000
eee	chr1:216156429-216156646(-)$1	217	81	84	9.0000
F{B	chr2:207945648-207945989(-)$1	341	24	27	9.0000
'''	chr12:12699142-12699393(-)$1	251	22	25	9.0000
fff	chrX:73994117-73994400(-)$1	283	0	3	9.0000
GMM	chr1:101384126-101384372(+)$1	246	12	15	9.0000
hhh	chr15:40994075-40994323(+)$1	248	37	40	9.0000
eef	chr3:23875788-23876167(+)$1	379	58	61	9.0000
:dd	chr15:71888306-71888522(+)$1	216	53	56	9.0000
33i	chr11:44182398-44182618(+)$1	220	65	68	9.0000
ggg	chr5:110588326-110588546(+)$1	220	68	71	9.0000
$$f	chr6:38172354-38172588(-)$1	234	38	41	9.0000
FF:	chr8:56735298-56735552(+)$1	254	8	11	9.0000
eee	chr6:13059585-13059829(+)$1	244	55	58	9.0000
dd>	chr1:46112022-46112255(-)$1	233	70	73	9.0000
fff	chr9:97204531-97204813(+)$1	282	73	76	9.0000
ddd	chr22:39985065-39985280(+)$1	215	93	96	9.0000
E{F	chr11:76644476-76644702(+)$1	226	10	13	9.0000
ggg	chr1:234386514-234386730(+)$1	216	71	74	9.0000
:CC	chr3:136415229-136415594(-)$1	365	11	14	9.0000
i::	chr13:95030175-95030396(+)$1	221	66	69	9.0000
ggg	chr14:35181517-35181741(-)$1	224	4	7	9.0000
GGG	chr17:35332574-35332820(+)$1	246	14	17	9.0000
:CC	chr9:5749115-5749346(+)$1	231	3	6	9.0000
ggg	chr12:109179588-109179842(-)$1	254	10	13	9.0000
::C	chr3:107764913-107765149(-)$1	236	61	64	9.0000
]dd	chr9:43728545-43728762(+)$1	217	72	75	9.0000
fff	chr1:35961121-35961391(-)$1	270	33	36	9.0000
ddd	chr1:22388064-22388286(+)$1	222	1	4	9.0000
eee	chr9:7101694-7101956(+)$1	262	27	30	9.0000
2cc	chr5:72974584-72974798(+)$1	214	132	135	9.0000
fff	chr22:29497385-29497637(+)$1	252	158	161	9.0000
:::	chr2:54955345-54955562(+)$1	217	34	37	9.0000
ddd	chr1:198711686-198712000(+)$1	314	69	72	9.0000
GGG	chr3:148873776-148874027(+)$1	251	17	20	9.0000
EEE	chr12:62691606-62691846(+)$1	240	20	23	9.0000
GGG	chr10:112658621-112658888(+)$1	267	90	93	9.0000
::B	chr10:121625726-121625957(-)$1	231	5	8	9.0000
:::	chrY:9340728-9340984(+)$1	256	42	45	9.0000
eep	chr2:32993252-32993478(+)$1	226	74	77	9.0000
fff	chr19:52714727-52714984(+)$1	257	34	37	9.0000
:::	chr1:64521389-64521612(+)$1	223	71	74	9.0000
iii	chrX:147015260-147015497(+)$1	237	9	12	9.0000
ddq	chr3:196619875-196620159(+)$1	284	30	33	9.0000
:::	chr1:245756467-245756724(+)$1	257	2	5	9.0000
tcc	chr3:114216980-114217202(-)$1	222	50	53	9.0000
DDg	chr1:35342017-35342286(-)$1	269	36	39	9.0000
:dd	chr2:202025066-202025283(+)$1	217	33	36	9.0000
eee	chr14:79200446-79200699(+)$1	253	24	27	9.0000
ff]	chr1:36076925-36077151(-)$1	226	107	110	9.0000
!!b	chr15:86175411-86175645(+)$1	234	26	29	9.0000
KKB	chr2:191987441-191987683(-)$1	242	13	16	9.0000
cc[	chr8:10650255-10650479(-)$1	224	49	52	9.0000
ddd	chr14:64578326-64578548(+)$1	222	64	67	9.0000
ddd	chr8:48693787-48694044(-)$1	257	27	30	9.0000
fff	chr1:29378920-29379159(+)$1	239	41	44	9.0000
EEE	chr14:66098566-66098835(+)$1	269	34	37	9.0000
HHH	chr3:173866624-173866837(+)$1	213	11	14	9.0000
GGg	chrX:83609259-83609492(-)$1	233	12	15	9.0000
""d	chr9:117119608-117119997(-)$1	389	15	18	9.0000
hho	chr3:43374150-43374383(+)$1	233	20	23	9.0000
f[b	chr1:21557599-21557879(-)$1	280	172	175	9.0000

#DB
..(	chrX:85238294-85238563(-)$1	1	18	21	9.0000
...	chr2:63363594-63363864(-)$1	1	2	5	9.0000
.((	chr19:9954850-9955062(+)$1	1	7	10	9.0000
(((	chr10:15187116-15187405(-)$1	1	70	73	9.0000
.((	chr5:156650167-156650470(+)$1	1	12	15	9.0000
)))	chr12:66614514-66614727(+)$1	1	115	118	9.0000
..(	chr11:96012562-96012848(-)$1	1	71	74	9.0000
(((	chr13:21365349-21365570(-)$1	1	86	89	9.0000
(..	chr3:114287836-114288087(-)$1	1	70	73	9.0000
..(	chr7:66616824-66617055(+)$1	1	6	9	9.0000
..(	chr14:73356682-73356970(-)$1	1	4	7	9.0000
(((	chr2:144084003-144084361(+)$1	1	21	24	9.0000
((.	chr5:110590167-110590398(+)$1	1	112	115	9.0000
..(	chr13:52297151-52297371(+)$1	1	120	123	9.0000
)))	chr14:67481061-67481303(+)$1	1	82	85	9.0000
)))	chr1:53218754-53218972(+)$1	1	121	124	9.0000
.))	chr6:157295898-157296174(+)$1	1	88	91	9.0000
.((	chr14:65906174-65906432(+)$1	1	6	9	9.0000
.((	chr7:133348040-133348300(+)$1	1	26	29	9.0000
(((	chr2:119708619-119708847(+)$1	1	22	25	9.0000
(((	chr16:54052686-54052935(+)$1	1	69	72	9.0000
...	chr12:111080654-111080916(+)$1	1	76	79	9.0000
..(	chr1:245017542-245017852(-)$1	1	8	11	9.0000
.((	chr9:35752126-35752341(+)$1	1	13	16	9.0000
(((	chr19:45525522-45525782(+)$1	1	39	42	9.0000
..(	chr6:27359426-27359679(+)$1	1	116	119	9.0000
(((	chr14:48058808-48059025(-)$1	1	33	36	9.0000
(((	chrY:16741846-16742059(+)$1	1	15	18	9.0000
(((	chr1:10768710-10768946(-)$1	1	153	156	9.0000
)))	chr15:73397181-73397401(+)$1	1	140	143	9.0000
.))	chr10:24039467-24039682(+)$1	1	24	27	9.0000
..)	chr15:43855890-43856137(-)$1	1	14	17	9.0000
...	chr4:83878797-83879039(-)$1	1	21	24	9.0000
...	chr8:59935355-59935607(-)$1	1	69	72	9.0000
.))	chr1:44260091-44260306(+)$1	1	35	38	9.0000
(((	chr14:56664587-56664857(+)$1	1	152	155	9.0000
)))	chr6:65250660-65250883(-)$1	1	67	70	9.0000
)))	chr1:216156429-216156646(-)$1	1	81	84	9.0000
(.(	chr2:207945648-207945989(-)$1	1	24	27	9.0000
...	chr12:12699142-12699393(-)$1	1	22	25	9.0000
(((	chrX:73994117-73994400(-)$1	1	0	3	9.0000
(..	chr1:101384126-101384372(+)$1	1	12	15	9.0000
(((	chr15:40994075-40994323(+)$1	1	37	40	9.0000
(((	chr3:23875788-23876167(+)$1	1	58	61	9.0000
.((	chr15:71888306-71888522(+)$1	1	53	56	9.0000
..)	chr11:44182398-44182618(+)$1	1	65	68	9.0000
)))	chr5:110588326-110588546(+)$1	1	68	71	9.0000
..(	chr6:38172354-38172588(-)$1	1	38	41	9.0000
((.	chr8:56735298-56735552(+)$1	1	8	11	9.0000
)))	chr6:13059585-13059829(+)$1	1	55	58	9.0000
)).	chr1:46112022-46112255(-)$1	1	70	73	9.0000
)))	chr9:97204531-97204813(+)$1	1	73	76	9.0000
)))	chr22:39985065-39985280(+)$1	1	93	96	9.0000
(.(	chr11:76644476-76644702(+)$1	1	10	13	9.0000
(((	chr1:234386514-234386730(+)$1	1	71	74	9.0000
.((	chr3:136415229-136415594(-)$1	1	11	14	9.0000
)..	chr13:95030175-95030396(+)$1	1	66	69	9.0000
(((	chr14:35181517-35181741(-)$1	1	4	7	9.0000
(((	chr17:35332574-35332820(+)$1	1	14	17	9.0000
.((	chr9:5749115-5749346(+)$1	1	3	6	9.0000
(((	chr12:109179588-109179842(-)$1	1	10	13	9.0000
..(	chr3:107764913-107765149(-)$1	1	61	64	9.0000
.))	chr9:43728545-43728762(+)$1	1	72	75	9.0000
)))	chr1:35961121-35961391(-)$1	1	33	36	9.0000
(((	chr1:22388064-22388286(+)$1	1	1	4	9.0000
(((	chr9:7101694-7101956(+)$1	1	27	30	9.0000
.))	chr5:72974584-72974798(+)$1	1	132	135	9.0000
(((	chr22:29497385-29497637(+)$1	1	158	161	9.0000
...	chr2:54955345-54955562(+)$1	1	34	37	9.0000
(((	chr1:198711686-198712000(+)$1	1	69	72	9.0000
(((	chr3:148873776-148874027(+)$1	1	17	20	9.0000
(((	chr12:62691606-62691846(+)$1	1	20	23	9.0000
(((	chr10:112658621-112658888(+)$1	1	90	93	9.0000
..(	chr10:121625726-121625957(-)$1	1	5	8	9.0000
...	chrY:9340728-9340984(+)$1	1	42	45	9.0000
((.	chr2:32993252-32993478(+)$1	1	74	77	9.0000
(((	chr19:52714727-52714984(+)$1	1	34	37	9.0000
...	chr1:64521389-64521612(+)$1	1	71	74	9.0000
(((	chrX:147015260-147015497(+)$1	1	9	12	9.0000
((.	chr3:196619875-196620159(+)$1	1	30	33	9.0000
...	chr1:245756467-245756724(+)$1	1	2	5	9.0000
.))	chr3:114216980-114217202(-)$1	1	50	53	9.0000
(((	chr1:35342017-35342286(-)$1	1	36	39	9.0000
.((	chr2:202025066-202025283(+)$1	1	33	36	9.0000
)))	chr14:79200446-79200699(+)$1	1	24	27	9.0000
)).	chr1:36076925-36077151(-)$1	1	107	110	9.0000
..(	chr15:86175411-86175645(+)$1	1	26	29	9.0000
..(	chr2:191987441-191987683(-)$1	1	13	16	9.0000
((.	chr8:10650255-10650479(-)$1	1	49	52	9.0000
(((	chr14:64578326-64578548(+)$1	1	64	67	9.0000
(((	chr8:48693787-48694044(-)$1	1	27	30	9.0000
(((	chr1:29378920-29379159(+)$1	1	41	44	9.0000
(((	chr14:66098566-66098835(+)$1	1	34	37	9.0000
(((	chr3:173866624-173866837(+)$1	1	11	14	9.0000
(((	chrX:83609259-83609492(-)$1	1	12	15	9.0000
..(	chr9:117119608-117119997(-)$1	1	15	18	9.0000
((.	chr3:43374150-43374383(+)$1	1	20	23	9.0000
(.(	chr1:21557599-21557879(-)$1	1	172	175	9.0000

#PSSM
U : 0.50	u : 0.50	
U : 0.50	u : 0.50	
G : 0.50	g : 0.50	

#score	882.0000000000001
#seq	98
#width	3
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000