
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m2_run1.txt

#BEAR
""eeeeettttttttttteeeee	chr1:59121783-59122049(-)$1	266	16	39	22.0508
e[eeeeeuuuuuuuuuuuueeee	chr17:62496621-62496891(-)$1	270	113	136	23.0187
!ccccccuuuuuuuuuuuuccc]	chr20:61536764-61536993(-)$1	229	44	67	23.3269
hhhhhhvvvvvvvvvvvvvhhhh	chr17:54941933-54942157(+)$1	224	59	82	20.8909
##ddddwwwwwwwwwwwwwwddd	chr7:129471418-129471651(-)$1	233	173	196	22.6078
c[ddddvvvvvvvvvvvvvdddd	chr7:99173180-99173433(+)$1	253	178	201	23.4154
ggggg[atttttttttttagggg	chr2:228421521-228421765(+)$1	244	68	91	22.1999
ddddddddtttttttttttdddd	chr20:30754565-30754832(+)$1	267	165	188	21.0136
:eeeeevvvvvvvvvvvvveeee	chr6:159058599-159058842(-)$1	243	23	46	22.5184
========ttttttttttt====	chr1:63903687-63903917(+)$1	230	69	92	21.3585
dddd[awwwwwwwwwwwwwwa]d	chr1:224348922-224349156(+)$1	234	113	136	21.7535
fff[bbvvvvvvvvvvvvvbb]f	chr2:204293206-204293478(+)$1	272	22	45	21.7812
ffffffvvvvvvvvvvvvvffff	chr7:150270855-150271091(+)$1	236	103	126	22.1619
=!!cccvvvvvvvvvvvvvccc2	chr16:67209725-67210202(-)$1	477	352	375	23.4135
:ddddwwwwwwwwwwwwwwdddd	chr1:33149820-33150115(+)$1	295	191	214	21.0747
###bbccctttttttttttccc]	chrX:134494927-134495164(+)$1	237	88	111	21.3744
ccddddvvvvvvvvvvvvvdddd	chr1:160248357-160248604(-)$1	247	60	83	23.2172
"""dddduuuuuuuuuuuudddd	chr15:56990764-56991002(-)$1	238	146	169	23.0231
ffeeeeettttttttttteeeee	chr19:21475144-21475373(-)$1	229	16	39	21.4616
:eeeeeuuuuuuuuuuuueeeee	chr19:49993122-49993355(+)$1	233	117	140	21.8265
!ddddccctttttttttttccc>	chr11:33794460-33794758(-)$1	298	177	200	21.8245
ffffffwwwwwwwwwwwwwwfff	chrX:79931794-79932032(-)$1	238	33	56	21.3027
ee[cccvvvvvvvvvvvvvccc]	chr3:171064645-171064893(-)$1	248	31	54	23.2056
[dddd[bbtttttttttttbbdd	chr19:41096926-41097186(+)$1	260	79	102	20.9460
ccc[cccuuuuuuuuuuuucccc	chr6:45517524-45517785(+)$1	261	233	256	23.0109
::ddddvvvvvvvvvvvvvdddd	chr17:35800569-35800792(+)$1	223	173	196	21.4514
!!fffffftttttttttttffff	chrX:103220138-103220381(+)$1	243	45	68	20.8395
[cccyyyyyyyyyyyyyyyyccc	chr17:48829245-48829479(+)$1	234	177	200	21.8103
[bbyyyyyyyyyyyyyyyybbcc	chr2:27170884-27171114(+)$1	230	97	120	20.1050
((dddduuuuuuuuuuuudddd>	chr11:118967420-118967672(-)$1	252	172	195	21.2164
""cccyyyyyyyyyyyyyyyycc	chr16:278072-278345(-)$1	273	149	172	22.1053
[eeeeewwwwwwwwwwwwwweee	chr4:40198561-40198828(+)$1	267	78	101	22.5566
ceeeeevvvvvvvvvvvvveeee	chr11:71712912-71713338(+)$1	426	122	145	23.3260
ffffffwwwwwwwwwwwwwwfff	chr9:123941668-123941906(-)$1	238	26	49	21.3027
eeeeyyyyyyyyyyyyyyyyeee	chr10:124923397-124923629(+)$1	232	71	94	21.6957
ffffffvvvvvvvvvvvvvffff	chr1:159997756-159998003(-)$1	247	107	130	22.1619
""cccyyyyyyyyyyyyyyyycc	chr12:112079889-112080117(-)$1	228	95	118	22.1053
ffffffvvvvvvvvvvvvvffff	chr1:75231699-75231942(+)$1	243	47	70	22.1619
ffffffwwwwwwwwwwwwwwfff	chr2:135206782-135207024(+)$1	242	14	37	21.3027
%%ddddvvvvvvvvvvvvvdddd	chr10:38345804-38346046(+)$1	242	52	75	22.4251
gggggguuuuuuuuuuuuggggg	chr7:99816898-99817211(-)$1	313	70	93	22.0433
cceeeeettttttttttteeeee	chr7:66107102-66107377(+)$1	275	182	205	21.6181
:cccyyyyyyyyyyyyyyyyccc	chr11:113146096-113146346(+)$1	250	102	125	20.7916
e[ddddvvvvvvvvvvvvvdddd	chr14:57670618-57670846(-)$1	228	28	51	23.3458
!!eeeeettttttttttteeeee	chr19:37118610-37118858(+)$1	248	70	93	22.1326
eeeeewwwwwwwwwwwwwweeee	chr7:39612271-39612502(+)$1	231	109	132	22.0226
%eeeeeyyyyyyyyyyyyyyyye	chr17:79531731-79531961(-)$1	230	106	129	21.2087
""ddddvvvvvvvvvvvvvdddd	chr12:52202485-52202736(+)$1	251	212	235	23.6499
c[dddduuuuuuuuuuuudddd3	chr16:69737262-69737635(+)$1	373	74	97	22.7050
$$ddddyyyyyyyyyyyyyyyyd	chr12:111887220-111887453(+)$1	233	93	116	21.4853
c!!bbwwwwwwwwwwwwwwbb22	chr19:53569835-53570086(-)$1	251	32	55	20.6406
!!ddddtttttttttttdddd33	chr6:76626842-76627074(+)$1	232	59	82	21.0873
ddd[cccuuuuuuuuuuuuccc4	chr12:29493977-29494226(-)$1	249	85	108	22.8190
:eeeeeuuuuuuuuuuuueeeee	chr2:232597241-232597524(-)$1	283	115	138	21.8265
eeeeeccctttttttttttccc:	chr12:55343935-55344190(-)$1	255	97	120	20.8389
""ddddvvvvvvvvvvvvvdddd	chr7:92165068-92165317(+)$1	249	117	140	23.6499
======yyyyyyyyyyyyyyyy=	chr18:33572508-33572768(-)$1	260	227	250	21.4404
ggggggwwwwwwwwwwwwwwggg	chr11:66433441-66433707(+)$1	266	34	57	21.9336
eeeeewwwwwwwwwwwwwweeee	chr9:88952084-88952326(-)$1	242	19	42	22.0226
ffffffvvvvvvvvvvvvvffff	chr12:72072890-72073126(+)$1	236	51	74	22.1619
===cccwwwwwwwwwwwwwwccc	chr13:113540398-113540772(+)$1	374	301	324	22.3761
hhhhccctttttttttttccc]h	chr22:47081218-47081511(-)$1	293	20	43	20.7700
!!ddddwwwwwwwwwwwwwwddd	chr12:56214734-56215022(+)$1	288	192	215	22.7431
iiiiiiyyyyyyyyyyyyyyyyi	chr2:128062966-128063218(-)$1	252	71	94	21.2645
eeeeyyyyyyyyyyyyyyyyeee	chr7:149187583-149187930(-)$1	347	103	126	21.6957
"""cccvvvvvvvvvvvvvccc3	chr17:27871143-27871405(+)$1	262	64	87	23.6155
!!cccyyyyyyyyyyyyyyyycc	chr3:107764850-107765153(-)$1	303	106	129	22.1871
#eeeeeuuuuuuuuuuuueeeee	chr2:135713145-135713377(+)$1	232	36	59	22.8592
eeeeeeeettttttttttteeee	chr17:42928119-42928370(-)$1	251	71	94	21.3197
dcccbbauuuuuuuuuuuua]bb	chr2:65301979-65302299(+)$1	320	219	242	21.8534
ddd[cccuuuuuuuuuuuuccc2	chr14:86090420-86090645(+)$1	225	26	49	22.6621

#otherMatches

#Seq PSSM
UUCUUUCUAUUAUUUGUUGAAAG	chr1:59121783-59122049(-)$1	266	16	39	22.0508
UUCUUUACACCUAAUAACAUAAA	chr17:62496621-62496891(-)$1	270	113	136	23.0187
UGGUAAGUAUUCGUAUUCUCUUC	chr20:61536764-61536993(-)$1	229	44	67	23.3269
UAUGAAGUUUAUCCUUUCAUUCA	chr17:54941933-54942157(+)$1	224	59	82	20.8909
CAGGAGUUGCCAUAUCAUCUCUC	chr7:129471418-129471651(-)$1	233	173	196	22.6078
GCUCCUCUCUCAUCAAUCCAGGA	chr7:99173180-99173433(+)$1	253	178	201	23.4154
cagugcgcuacgaucacaccacu	chr2:228421521-228421765(+)$1	244	68	91	22.1999
AGCCUCACCCAUCAAACCAGUGA	chr20:30754565-30754832(+)$1	267	165	188	21.0136
ACCAUUUAAAUACAUCGGUAAUG	chr6:159058599-159058842(-)$1	243	23	46	22.5184
AUAUUAAGUGGUGGUAUAUUUUA	chr1:63903687-63903917(+)$1	230	69	92	21.3585
ACUCUCUAAAAACAUAUACUGUG	chr1:224348922-224349156(+)$1	234	113	136	21.7535
GUCAGAAUUAAAACCCAUCUCAG	chr2:204293206-204293478(+)$1	272	22	45	21.7812
GGCAGGUCAUCCACACACUUCUG	chr7:150270855-150271091(+)$1	236	103	126	22.1619
UCUGGCAGAGGUUGGCAUAGCCU	chr16:67209725-67210202(-)$1	477	352	375	23.4135
AUGAGCCAAACAAUAAAAACUCA	chr1:33149820-33150115(+)$1	295	191	214	21.0747
AACAGGUCUUACACAAAUUGACA	chrX:134494927-134495164(+)$1	237	88	111	21.3744
GAAGGGCCCAUCCUAUUUCCCCU	chr1:160248357-160248604(-)$1	247	60	83	23.2172
uuguguucuauugguuaaaagca	chr15:56990764-56991002(-)$1	238	146	169	23.0231
GAAGCAGUUACUUAAACUUUGUU	chr19:21475144-21475373(-)$1	229	16	39	21.4616
CAUUCACCAUCUUUCGUUUGAGU	chr19:49993122-49993355(+)$1	233	117	140	21.8265
UGCCAGCAUACAACACACUUGCA	chr11:33794460-33794758(-)$1	298	177	200	21.8245
AUUGGUGCUUUUCCAUUUAUGCC	chrX:79931794-79932032(-)$1	238	33	56	21.3027
cucugccaccacuguccuagcac	chr3:171064645-171064893(-)$1	248	31	54	23.2056
AGUGGGCCAGACCUCCGACGGCC	chr19:41096926-41097186(+)$1	260	79	102	20.9460
UGAACCCUUAAUUUGCACUGGGU	chr6:45517524-45517785(+)$1	261	233	256	23.0109
ACACAGCCAUUCCAUUUCACUGU	chr17:35800569-35800792(+)$1	223	173	196	21.4514
UUGCCUGACAGUCUUGGUUUUAG	chrX:103220138-103220381(+)$1	243	45	68	20.8395
CUUGAUAAUUAAAAAGAAUACAA	chr17:48829245-48829479(+)$1	234	177	200	21.8103
cGGCUUCCUAUAACUUCUUCCUG	chr2:27170884-27171114(+)$1	230	97	120	20.1050
UAUGGCUUUCUGCAACUUGCUAC	chr11:118967420-118967672(-)$1	252	172	195	21.2164
UCCUAAAAUAUAUUCCUCCUCUA	chr16:278072-278345(-)$1	273	149	172	22.1053
UAAUCUCUUUUGUCACAUUCGGA	chr4:40198561-40198828(+)$1	267	78	101	22.5566
CUUUGGGUCCCUUCUCUCACCAA	chr11:71712912-71713338(+)$1	426	122	145	23.3260
ACAGUGAUCCAUUUUGCUUACAC	chr9:123941668-123941906(-)$1	238	26	49	21.3027
ACCUGAAAAUAAUGGAAAAGAGG	chr10:124923397-124923629(+)$1	232	71	94	21.6957
AUGUAUAUUCACAUUAUAAAUAC	chr1:159997756-159998003(-)$1	247	107	130	22.1619
AAAUGAACCACUUAAUAUACCCA	chr12:112079889-112080117(-)$1	228	95	118	22.1053
uaauggaccugaaaaauuccuau	chr1:75231699-75231942(+)$1	243	47	70	22.1619
CCCAUUAACUUAUUUAUUCGGGU	chr2:135206782-135207024(+)$1	242	14	37	21.3027
AAAGGUAAUAAUUAAAAUAACCu	chr10:38345804-38346046(+)$1	242	52	75	22.4251
ACCCACUACCAAUCUGAUGUGGG	chr7:99816898-99817211(-)$1	313	70	93	22.0433
CAUGCAGAAAGCAGUCAGCUGUA	chr7:66107102-66107377(+)$1	275	182	205	21.6181
cgcacacacacaaacacacaugc	chr11:113146096-113146346(+)$1	250	102	125	20.7916
CACACUCGCCCAUUUUCUAAGUG	chr14:57670618-57670846(-)$1	228	28	51	23.3458
cagcagacaaaaacuuccucugu	chr19:37118610-37118858(+)$1	248	70	93	22.1326
CUGCAUCAAACACCUCAACUGUA	chr7:39612271-39612502(+)$1	231	109	132	22.0226
CAAACACCUUUAUACCAuuuccu	chr17:79531731-79531961(-)$1	230	106	129	21.2087
GUUUCUUUCACUUAUUAUUAGAA	chr12:52202485-52202736(+)$1	251	212	235	23.6499
CAUGGUAAAUAUAAACUAACCAC	chr16:69737262-69737635(+)$1	373	74	97	22.7050
ACAUGGGCACACACAAUCUCCAC	chr12:111887220-111887453(+)$1	233	93	116	21.4853
uaaagaagaaaaagaaaaaCUGA	chr19:53569835-53570086(-)$1	251	32	55	20.6406
CAAGCCCAUGCAUGCCAGGUUAA	chr6:76626842-76627074(+)$1	232	59	82	21.0873
AGGAUGGCCACACAGACAACCAC	chr12:29493977-29494226(-)$1	249	85	108	22.8190
CUUCCCAGCAUACACACAGGGAA	chr2:232597241-232597524(-)$1	283	115	138	21.8265
CUGCACUGCCCUCAACAUCCAGC	chr12:55343935-55344190(-)$1	255	97	120	20.8389
caccaauaacuucagcacuuugg	chr7:92165068-92165317(+)$1	249	117	140	23.6499
GGGCAGAUGAAAGUCUAGAGAAC	chr18:33572508-33572768(-)$1	260	227	250	21.4404
UUGUUUUAAUCUUUCACAGUAAA	chr11:66433441-66433707(+)$1	266	34	57	21.9336
AUCUGAACAGAUUUUAUUACAGG	chr9:88952084-88952326(-)$1	242	19	42	22.0226
auuuuaaaaaucauaaaaauaaa	chr12:72072890-72073126(+)$1	236	51	74	22.1619
UACAACCACUCUUAUUUAAUGUU	chr13:113540398-113540772(+)$1	374	301	324	22.3761
UCUACCAAUGUUUGCUCCUGGUU	chr22:47081218-47081511(-)$1	293	20	43	20.7700
UGAAUCUACUUUUUAAAAAUGAU	chr12:56214734-56215022(+)$1	288	192	215	22.7431
AGGGACUCUUUUACGAUACUUUG	chr2:128062966-128063218(-)$1	252	71	94	21.2645
ugugcccccccaacccaucccac	chr7:149187583-149187930(-)$1	347	103	126	21.6957
AAUAGCCAAUUAUUUAAAUGUUU	chr17:27871143-27871405(+)$1	262	64	87	23.6155
AAACAUUCAUCACCUUCCUCCUG	chr3:107764850-107765153(-)$1	303	106	129	22.1871
AAGAAUUUUACACUACAUAUUUU	chr2:135713145-135713377(+)$1	232	36	59	22.8592
UGAACAGAACAUUCUGACCUCUG	chr17:42928119-42928370(-)$1	251	71	94	21.3197
UCUGAGCUGAAAUUGUACUGACU	chr2:65301979-65302299(+)$1	320	219	242	21.8534
AGAAUCAAGAAAAUUGAGAUGAG	chr14:86090420-86090645(+)$1	225	26	49	22.6621

#DB
..(((((...........)))))	chr1:59121783-59122049(-)$1	1	16	39	22.0508
(.(((((............))))	chr17:62496621-62496891(-)$1	1	113	136	23.0187
.((((((............))).	chr20:61536764-61536993(-)$1	1	44	67	23.3269
((((((.............))))	chr17:54941933-54942157(+)$1	1	59	82	20.8909
..((((..............)))	chr7:129471418-129471651(-)$1	1	173	196	22.6078
(.((((.............))))	chr7:99173180-99173433(+)$1	1	178	201	23.4154
(((((.(...........)))))	chr2:228421521-228421765(+)$1	1	68	91	22.1999
))))((((...........))))	chr20:30754565-30754832(+)$1	1	165	188	21.0136
.(((((.............))))	chr6:159058599-159058842(-)$1	1	23	46	22.5184
((((((((...........))))	chr1:63903687-63903917(+)$1	1	69	92	21.3585
((((.(..............).)	chr1:224348922-224349156(+)$1	1	113	136	21.7535
(((.((.............)).)	chr2:204293206-204293478(+)$1	1	22	45	21.7812
((((((.............))))	chr7:150270855-150271091(+)$1	1	103	126	22.1619
(..(((.............))).	chr16:67209725-67210202(-)$1	1	352	375	23.4135
.((((..............))))	chr1:33149820-33150115(+)$1	1	191	214	21.0747
...(((((...........))).	chrX:134494927-134495164(+)$1	1	88	111	21.3744
((((((.............))))	chr1:160248357-160248604(-)$1	1	60	83	23.2172
...((((............))))	chr15:56990764-56991002(-)$1	1	146	169	23.0231
(((((((...........)))))	chr19:21475144-21475373(-)$1	1	16	39	21.4616
.(((((............)))))	chr19:49993122-49993355(+)$1	1	117	140	21.8265
.(((((((...........))).	chr11:33794460-33794758(-)$1	1	177	200	21.8245
((((((..............)))	chrX:79931794-79932032(-)$1	1	33	56	21.3027
((.(((.............))).	chr3:171064645-171064893(-)$1	1	31	54	23.2056
.((((.((...........))))	chr19:41096926-41097186(+)$1	1	79	102	20.9460
(((.(((............))))	chr6:45517524-45517785(+)$1	1	233	256	23.0109
..((((.............))))	chr17:35800569-35800792(+)$1	1	173	196	21.4514
..((((((...........))))	chrX:103220138-103220381(+)$1	1	45	68	20.8395
.(((................)))	chr17:48829245-48829479(+)$1	1	177	200	21.8103
.((................))))	chr2:27170884-27171114(+)$1	1	97	120	20.1050
..((((............)))).	chr11:118967420-118967672(-)$1	1	172	195	21.2164
..(((................))	chr16:278072-278345(-)$1	1	149	172	22.1053
.(((((..............)))	chr4:40198561-40198828(+)$1	1	78	101	22.5566
)(((((.............))))	chr11:71712912-71713338(+)$1	1	122	145	23.3260
((((((..............)))	chr9:123941668-123941906(-)$1	1	26	49	21.3027
((((................)))	chr10:124923397-124923629(+)$1	1	71	94	21.6957
((((((.............))))	chr1:159997756-159998003(-)$1	1	107	130	22.1619
..(((................))	chr12:112079889-112080117(-)$1	1	95	118	22.1053
((((((.............))))	chr1:75231699-75231942(+)$1	1	47	70	22.1619
((((((..............)))	chr2:135206782-135207024(+)$1	1	14	37	21.3027
..((((.............))))	chr10:38345804-38346046(+)$1	1	52	75	22.4251
((((((............)))))	chr7:99816898-99817211(-)$1	1	70	93	22.0433
(((((((...........)))))	chr7:66107102-66107377(+)$1	1	182	205	21.6181
.(((................)))	chr11:113146096-113146346(+)$1	1	102	125	20.7916
(.((((.............))))	chr14:57670618-57670846(-)$1	1	28	51	23.3458
..(((((...........)))))	chr19:37118610-37118858(+)$1	1	70	93	22.1326
(((((..............))))	chr7:39612271-39612502(+)$1	1	109	132	22.0226
.(((((................)	chr17:79531731-79531961(-)$1	1	106	129	21.2087
..((((.............))))	chr12:52202485-52202736(+)$1	1	212	235	23.6499
(.((((............)))).	chr16:69737262-69737635(+)$1	1	74	97	22.7050
..((((................)	chr12:111887220-111887453(+)$1	1	93	116	21.4853
(..((..............))..	chr19:53569835-53570086(-)$1	1	32	55	20.6406
..((((...........))))..	chr6:76626842-76627074(+)$1	1	59	82	21.0873
(((.(((............))).	chr12:29493977-29494226(-)$1	1	85	108	22.8190
.(((((............)))))	chr2:232597241-232597524(-)$1	1	115	138	21.8265
)))))(((...........))).	chr12:55343935-55344190(-)$1	1	97	120	20.8389
..((((.............))))	chr7:92165068-92165317(+)$1	1	117	140	23.6499
((((((................)	chr18:33572508-33572768(-)$1	1	227	250	21.4404
((((((..............)))	chr11:66433441-66433707(+)$1	1	34	57	21.9336
(((((..............))))	chr9:88952084-88952326(-)$1	1	19	42	22.0226
((((((.............))))	chr12:72072890-72073126(+)$1	1	51	74	22.1619
((((((..............)))	chr13:113540398-113540772(+)$1	1	301	324	22.3761
(((((((...........))).)	chr22:47081218-47081511(-)$1	1	20	43	20.7700
..((((..............)))	chr12:56214734-56215022(+)$1	1	192	215	22.7431
((((((................)	chr2:128062966-128063218(-)$1	1	71	94	21.2645
((((................)))	chr7:149187583-149187930(-)$1	1	103	126	21.6957
...(((.............))).	chr17:27871143-27871405(+)$1	1	64	87	23.6155
..(((................))	chr3:107764850-107765153(-)$1	1	106	129	22.1871
.(((((............)))))	chr2:135713145-135713377(+)$1	1	36	59	22.8592
((((((((...........))))	chr17:42928119-42928370(-)$1	1	71	94	21.3197
(((((((............).))	chr2:65301979-65302299(+)$1	1	219	242	21.8534
(((.(((............))).	chr14:86090420-86090645(+)$1	1	26	49	22.6621

#PSSM
e : 0.12	f : 0.12	" : 0.09	! : 0.09	c : 0.09	: : 0.08	d : 0.07	= : 0.05	[ : 0.05	# : 0.04	g : 0.04	h : 0.02	% : 0.02	( : 0.01	$ : 0.01	i : 0.01	
e : 0.19	f : 0.12	" : 0.09	c : 0.09	d : 0.09	! : 0.09	[ : 0.05	g : 0.04	= : 0.04	h : 0.02	# : 0.02	: : 0.01	b : 0.01	( : 0.01	% : 0.01	$ : 0.01	i : 0.01	
d : 0.28	e : 0.25	f : 0.12	c : 0.11	g : 0.04	= : 0.04	h : 0.02	! : 0.02	" : 0.02	# : 0.01	[ : 0.01	b : 0.01	i : 0.01	
d : 0.26	e : 0.25	c : 0.15	f : 0.11	[ : 0.05	g : 0.04	h : 0.02	= : 0.02	b : 0.02	y : 0.01	i : 0.01	
d : 0.25	e : 0.22	c : 0.16	f : 0.11	y : 0.07	b : 0.05	g : 0.04	= : 0.02	h : 0.01	[ : 0.01	i : 0.01	
d : 0.21	e : 0.18	c : 0.16	f : 0.11	y : 0.11	w : 0.05	[ : 0.02	= : 0.02	b : 0.02	g : 0.02	h : 0.01	a : 0.01	i : 0.01	
v : 0.25	w : 0.18	y : 0.16	c : 0.11	e : 0.08	u : 0.08	a : 0.02	d : 0.02	= : 0.01	b : 0.01	f : 0.01	t : 0.01	
v : 0.25	u : 0.18	w : 0.18	y : 0.16	t : 0.09	c : 0.04	d : 0.01	= : 0.01	b : 0.01	f : 0.01	e : 0.01	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.21	u : 0.18	w : 0.18	y : 0.16	
v : 0.25	t : 0.19	u : 0.18	w : 0.18	y : 0.16	d : 0.01	
v : 0.25	w : 0.18	y : 0.16	t : 0.11	e : 0.09	u : 0.09	d : 0.04	a : 0.01	g : 0.01	c : 0.01	
e : 0.18	d : 0.18	c : 0.15	y : 0.15	w : 0.12	f : 0.07	b : 0.05	g : 0.02	h : 0.01	= : 0.01	a : 0.01	
e : 0.22	d : 0.21	c : 0.19	f : 0.11	y : 0.09	b : 0.05	g : 0.04	h : 0.01	= : 0.01	a : 0.01	] : 0.01	
c : 0.23	e : 0.22	d : 0.21	f : 0.11	y : 0.05	g : 0.04	] : 0.04	h : 0.01	= : 0.01	2 : 0.01	3 : 0.01	b : 0.01	
e : 0.23	d : 0.21	f : 0.12	c : 0.11	] : 0.04	g : 0.04	2 : 0.04	3 : 0.04	h : 0.02	= : 0.02	> : 0.02	4 : 0.01	: : 0.01	i : 0.01	b : 0.01	

#score	1563.1173616780188
#seq	71
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m2_run2.txt

#BEAR
fffffpppppppffff	chr4:57777436-57777676(+)$1	240	138	154	12.8414
fddddpppppppdddd	chr1:52826003-52826243(-)$1	240	203	219	14.3091
ee[bbpppppppbb]e	chr12:30863154-30863394(-)$1	240	95	111	12.2968
eeeeepppppppeeee	chr5:132334229-132334469(-)$1	240	96	112	13.9706
eeeeepppppppeeee	chrX:74296317-74296557(-)$1	240	167	183	13.9706
eeeeepppppppeeee	chr9:35740105-35740345(-)$1	240	175	191	13.9706
:ddddpppppppdddd	chr1:40887565-40887805(+)$1	240	2	18	13.5617
!!cccpppppppccc2	chr6:15508474-15508714(+)$1	240	17	33	13.7619
!ddddpppppppdddd	chr2:128848799-128849039(+)$1	240	14	30	14.5273
gggggpppppppgggg	chr22:41547760-41548000(+)$1	240	149	165	13.3185
eeeeepppppppeeee	chr20:49510690-49510930(-)$1	240	12	28	13.9706
gggggpppppppgggg	chr12:65082069-65082309(+)$1	240	212	228	13.3185
:ddddpppppppdddd	chr6:56443582-56443822(-)$1	240	196	212	13.5617
"ddddpppppppdddd	chr3:120049967-120050207(-)$1	240	90	106	14.4866
#ddddpppppppdddd	chr17:8280847-8281087(-)$1	240	86	102	14.4555
eeeeepppppppeeee	chr7:23349038-23349278(+)$1	240	29	45	13.9706
gddddpppppppdddd	chrX:54185707-54185947(-)$1	240	26	42	14.3587
bbcccpppppppccc]	chr3:179298850-179299090(+)$1	240	135	151	13.2613
eeeeepppppppeeee	chr14:91947849-91948089(-)$1	240	131	147	13.9706
f[cccpppppppccc]	chr7:103824472-103824712(-)$1	240	98	114	13.8095
eeeeepppppppeeee	chr3:58141589-58141829(+)$1	240	113	129	13.9706
!ddddpppppppdddd	chr5:106716832-106717072(-)$1	240	60	76	14.5273
"ddddpppppppdddd	chr22:20030785-20031025(+)$1	240	190	206	14.4866
!ddddpppppppdddd	chr14:31917364-31917604(-)$1	240	102	118	14.5273
fffffpppppppffff	chr6:149918543-149918783(-)$1	240	95	111	12.8414
!ddddpppppppdddd	chr3:49751463-49751703(+)$1	240	139	155	14.5273
dd[bbpppppppbb]d	chr16:24800647-24800887(+)$1	240	78	94	12.1390
:ddddpppppppdddd	chr9:91929996-91930236(+)$1	240	108	124	13.5617
:ddddpppppppdddd	chr19:14578342-14578658(+)$1	316	98	114	13.5617
:ddddpppppppdddd	chr17:27086191-27086431(-)$1	240	104	120	13.5617
gggggpppppppgggg	chr1:179851893-179852133(+)$1	240	172	188	13.3185
""cccpppppppccc]	chr2:62099548-62099797(-)$1	249	173	189	13.8283
bddddpppppppdddd	chr12:57456842-57457082(-)$1	240	164	180	14.1952
fffffpppppppffff	chr2:203420982-203421222(+)$1	240	186	202	12.8414
!ddddpppppppdddd	chr7:102950661-102950901(+)$1	240	78	94	14.5273
fffffpppppppffff	chr6:20113010-20113250(-)$1	240	162	178	12.8414
b[cccpppppppcccb	chr22:41753222-41753462(+)$1	240	189	205	13.2895
eeeeepppppppeeee	chr17:78111890-78112165(-)$1	275	237	253	13.9706
gggggpppppppgggg	chr13:23911757-23911997(-)$1	240	201	217	13.3185
ffffapppppppa]ff	chr3:111710390-111710642(+)$1	252	179	195	12.7786
fffffpppppppffff	chr1:11082123-11082363(+)$1	240	168	184	12.8414
!!cccpppppppccc2	chrX:71492354-71492634(-)$1	280	44	60	13.7619
""cccpppppppccc4	chr19:16772002-16772242(+)$1	240	138	154	13.7221
"ddddpppppppdddd	chr1:200522753-200522993(-)$1	240	13	29	14.4866
bddddpppppppdddd	chr17:48453014-48453254(+)$1	240	130	146	14.1952
$ddddpppppppdddd	chr12:57663076-57663316(-)$1	240	208	224	14.2705
eeeeepppppppeeee	chr8:42693198-42693438(-)$1	240	93	109	13.9706
f[cccpppppppccc]	chr1:40705236-40705476(+)$1	240	150	166	13.8095
eeeeepppppppeeee	chr10:70673117-70673357(+)$1	240	32	48	13.9706
hhh[apppppppahhh	chr3:184429055-184429295(-)$1	240	165	181	12.0674
a[cccpppppppccc2	chrX:118370261-118370535(+)$1	274	54	70	13.6662
fffffpppppppffff	chr22:40745880-40746120(+)$1	240	113	129	12.8414
fffffpppppppffff	chr2:190718571-190718811(+)$1	240	15	31	12.8414
eeeeepppppppeeee	chr18:19110220-19110460(-)$1	240	106	122	13.9706
a[cccpppppppccc]	chr1:204518226-204518479(+)$1	253	174	190	13.9098
eeeeepppppppeeee	chr8:109247184-109247424(-)$1	240	8	24	13.9706
f[cccpppppppcccf	chr19:37618661-37618901(+)$1	240	219	235	13.7127
eeeeepppppppeeee	chr11:134078701-134078941(-)$1	240	157	173	13.9706
:ddddpppppppdddd	chr8:101541706-101541986(-)$1	280	115	131	13.5617
[ddddpppppppdddd	chr6:31598325-31598565(+)$1	240	8	24	14.4710
a[cccpppppppccc]	chr16:3339555-3339795(+)$1	240	160	176	13.9098

#otherMatches

#Seq PSSM
AGUGAGCGAGUAUCAC	chr4:57777436-57777676(+)$1	240	138	154	12.8414
UGGUGGAGAUCGCACC	chr1:52826003-52826243(-)$1	240	203	219	14.3091
AUGUGCCAGUGACAAA	chr12:30863154-30863394(-)$1	240	95	111	12.2968
ucUGAUUCAGACUCAG	chr5:132334229-132334469(-)$1	240	96	112	13.9706
GUUGCAACCAUGGCAA	chrX:74296317-74296557(-)$1	240	167	183	13.9706
CUGGGGCUCUGACCUG	chr9:35740105-35740345(-)$1	240	175	191	13.9706
AAGGGACUCUCACCCU	chr1:40887565-40887805(+)$1	240	2	18	13.5617
AAGAGAUUUUUACUUA	chr6:15508474-15508714(+)$1	240	17	33	13.7619
CCGCGGGAAAGGCGCG	chr2:128848799-128849039(+)$1	240	14	30	14.5273
CUCAGGCCAUUGCUGA	chr22:41547760-41548000(+)$1	240	149	165	13.3185
CUGUACCUUCAAUGCA	chr20:49510690-49510930(-)$1	240	12	28	13.9706
UGCUGUUCUCAUUAGC	chr12:65082069-65082309(+)$1	240	212	228	13.3185
UCCAGAAAACACUUGG	chr6:56443582-56443822(-)$1	240	196	212	13.5617
AGAGUGAAUCUGACUC	chr3:120049967-120050207(-)$1	240	90	106	14.4866
ACUAGGCUAAAACUGG	chr17:8280847-8281087(-)$1	240	86	102	14.4555
CUCAGAUAGCACCUGA	chr7:23349038-23349278(+)$1	240	29	45	13.9706
UGCUCUGAAACUGAGC	chrX:54185707-54185947(-)$1	240	26	42	14.3587
UGUGUGAUAUUGACAU	chr3:179298850-179299090(+)$1	240	135	151	13.2613
AUCUUUUUCAAUAAGG	chr14:91947849-91948089(-)$1	240	131	147	13.9706
ACUUAAUUUUCCUAAA	chr7:103824472-103824712(-)$1	240	98	114	13.8095
CAUCAAGUUCAAUGAU	chr3:58141589-58141829(+)$1	240	113	129	13.9706
CCCAGCCGCCUUUUGG	chr5:106716832-106717072(-)$1	240	60	76	14.5273
CCUGCGUGCUCAGCGG	chr22:20030785-20031025(+)$1	240	190	206	14.4866
GAAGGGUUUGAACUUU	chr14:31917364-31917604(-)$1	240	102	118	14.5273
UUAAGACGACGCCUUG	chr6:149918543-149918783(-)$1	240	95	111	12.8414
CCAGAGUGAGUAUCUG	chr3:49751463-49751703(+)$1	240	139	155	14.5273
GAUGCUGAUUCUGCCU	chr16:24800647-24800887(+)$1	240	78	94	12.1390
AACUUUCCAAACAAGU	chr9:91929996-91930236(+)$1	240	108	124	13.5617
CCGCCCUGUGCAGGUG	chr19:14578342-14578658(+)$1	316	98	114	13.5617
AGGGUCUCCAGCACCC	chr17:27086191-27086431(-)$1	240	104	120	13.5617
UCCUGUUAUGACCAGG	chr1:179851893-179852133(+)$1	240	172	188	13.3185
CUAUGUGUUAUUCGUU	chr2:62099548-62099797(-)$1	249	173	189	13.8283
CUGUACAUCACCUGCA	chr12:57456842-57457082(-)$1	240	164	180	14.1952
UGGGCCAUCAAAGCCC	chr2:203420982-203421222(+)$1	240	186	202	12.8414
UGGAAUUUUUUUUUCC	chr7:102950661-102950901(+)$1	240	78	94	14.5273
UAGGGUCUUUCCCCUU	chr6:20113010-20113250(-)$1	240	162	178	12.8414
CACCGCCACCACUGGG	chr22:41753222-41753462(+)$1	240	189	205	13.2895
GCACAGCAUCCAUGUG	chr17:78111890-78112165(-)$1	275	237	253	13.9706
AGAUCCUUUAAUGAUC	chr13:23911757-23911997(-)$1	240	201	217	13.3185
AUCACAUGUUUAGUUG	chr3:111710390-111710642(+)$1	252	179	195	12.7786
UUUGGUGGUAAUCCAG	chr1:11082123-11082363(+)$1	240	168	184	12.8414
AAAGGGUAUCCGCCUC	chrX:71492354-71492634(-)$1	280	44	60	13.7619
AGUAUGAGCCAGGUGA	chr19:16772002-16772242(+)$1	240	138	154	13.7221
AAGAUAUCUAGAGUCU	chr1:200522753-200522993(-)$1	240	13	29	14.4866
CCUUCCACCCCAGAAG	chr17:48453014-48453254(+)$1	240	130	146	14.1952
CUGGUAAGAGAAACCA	chr12:57663076-57663316(-)$1	240	208	224	14.2705
CCACAACUAUACUGUG	chr8:42693198-42693438(-)$1	240	93	109	13.9706
UUUGAAAUGUAAUCAU	chr1:40705236-40705476(+)$1	240	150	166	13.8095
AUCAUAUUCGAAAUGG	chr10:70673117-70673357(+)$1	240	32	48	13.9706
GGGAGGAGAUGGCCCC	chr3:184429055-184429295(-)$1	240	165	181	12.0674
CUCCAGAGAUCAUGGC	chrX:118370261-118370535(+)$1	274	54	70	13.6662
CAUUAUUCACCUUGGU	chr22:40745880-40746120(+)$1	240	113	129	12.8414
UCAGUUGAAUUUGCUG	chr2:190718571-190718811(+)$1	240	15	31	12.8414
ACUGGUCAAUUUCUGG	chr18:19110220-19110460(-)$1	240	106	122	13.9706
AAGGAAAUGAUGUCCC	chr1:204518226-204518479(+)$1	253	174	190	13.9098
GUUUUGACCUCAAAGA	chr8:109247184-109247424(-)$1	240	8	24	13.9706
AAUGGGGAAAAACCAU	chr19:37618661-37618901(+)$1	240	219	235	13.7127
UCUCCCAUUCAUGGAG	chr11:134078701-134078941(-)$1	240	157	173	13.9706
UGCAUAAAUUCGGUGC	chr8:101541706-101541986(-)$1	280	115	131	13.5617
UAGGAUUAUUUUUCUU	chr6:31598325-31598565(+)$1	240	8	24	14.4710
AGACUGUGUAUGGGUG	chr16:3339555-3339795(+)$1	240	160	176	13.9098

#DB
(((((.......))))	chr4:57777436-57777676(+)$1	1	138	154	12.8414
)((((.......))))	chr1:52826003-52826243(-)$1	1	203	219	14.3091
((.((.......)).)	chr12:30863154-30863394(-)$1	1	95	111	12.2968
(((((.......))))	chr5:132334229-132334469(-)$1	1	96	112	13.9706
(((((.......))))	chrX:74296317-74296557(-)$1	1	167	183	13.9706
(((((.......))))	chr9:35740105-35740345(-)$1	1	175	191	13.9706
.((((.......))))	chr1:40887565-40887805(+)$1	1	2	18	13.5617
..(((.......))).	chr6:15508474-15508714(+)$1	1	17	33	13.7619
.((((.......))))	chr2:128848799-128849039(+)$1	1	14	30	14.5273
(((((.......))))	chr22:41547760-41548000(+)$1	1	149	165	13.3185
(((((.......))))	chr20:49510690-49510930(-)$1	1	12	28	13.9706
(((((.......))))	chr12:65082069-65082309(+)$1	1	212	228	13.3185
.((((.......))))	chr6:56443582-56443822(-)$1	1	196	212	13.5617
.((((.......))))	chr3:120049967-120050207(-)$1	1	90	106	14.4866
.((((.......))))	chr17:8280847-8281087(-)$1	1	86	102	14.4555
(((((.......))))	chr7:23349038-23349278(+)$1	1	29	45	13.9706
(((((.......))))	chrX:54185707-54185947(-)$1	1	26	42	14.3587
(((((.......))).	chr3:179298850-179299090(+)$1	1	135	151	13.2613
(((((.......))))	chr14:91947849-91948089(-)$1	1	131	147	13.9706
(.(((.......))).	chr7:103824472-103824712(-)$1	1	98	114	13.8095
(((((.......))))	chr3:58141589-58141829(+)$1	1	113	129	13.9706
.((((.......))))	chr5:106716832-106717072(-)$1	1	60	76	14.5273
.((((.......))))	chr22:20030785-20031025(+)$1	1	190	206	14.4866
.((((.......))))	chr14:31917364-31917604(-)$1	1	102	118	14.5273
(((((.......))))	chr6:149918543-149918783(-)$1	1	95	111	12.8414
.((((.......))))	chr3:49751463-49751703(+)$1	1	139	155	14.5273
((.((.......)).)	chr16:24800647-24800887(+)$1	1	78	94	12.1390
.((((.......))))	chr9:91929996-91930236(+)$1	1	108	124	13.5617
.((((.......))))	chr19:14578342-14578658(+)$1	1	98	114	13.5617
.((((.......))))	chr17:27086191-27086431(-)$1	1	104	120	13.5617
(((((.......))))	chr1:179851893-179852133(+)$1	1	172	188	13.3185
..(((.......))).	chr2:62099548-62099797(-)$1	1	173	189	13.8283
(((((.......))))	chr12:57456842-57457082(-)$1	1	164	180	14.1952
(((((.......))))	chr2:203420982-203421222(+)$1	1	186	202	12.8414
.((((.......))))	chr7:102950661-102950901(+)$1	1	78	94	14.5273
(((((.......))))	chr6:20113010-20113250(-)$1	1	162	178	12.8414
(.(((.......))))	chr22:41753222-41753462(+)$1	1	189	205	13.2895
(((((.......))))	chr17:78111890-78112165(-)$1	1	237	253	13.9706
(((((.......))))	chr13:23911757-23911997(-)$1	1	201	217	13.3185
(((((.......).))	chr3:111710390-111710642(+)$1	1	179	195	12.7786
(((((.......))))	chr1:11082123-11082363(+)$1	1	168	184	12.8414
..(((.......))).	chrX:71492354-71492634(-)$1	1	44	60	13.7619
..(((.......))).	chr19:16772002-16772242(+)$1	1	138	154	13.7221
.((((.......))))	chr1:200522753-200522993(-)$1	1	13	29	14.4866
(((((.......))))	chr17:48453014-48453254(+)$1	1	130	146	14.1952
.((((.......))))	chr12:57663076-57663316(-)$1	1	208	224	14.2705
(((((.......))))	chr8:42693198-42693438(-)$1	1	93	109	13.9706
(.(((.......))).	chr1:40705236-40705476(+)$1	1	150	166	13.8095
(((((.......))))	chr10:70673117-70673357(+)$1	1	32	48	13.9706
(((.(.......))))	chr3:184429055-184429295(-)$1	1	165	181	12.0674
(.(((.......))).	chrX:118370261-118370535(+)$1	1	54	70	13.6662
(((((.......))))	chr22:40745880-40746120(+)$1	1	113	129	12.8414
(((((.......))))	chr2:190718571-190718811(+)$1	1	15	31	12.8414
(((((.......))))	chr18:19110220-19110460(-)$1	1	106	122	13.9706
(.(((.......))).	chr1:204518226-204518479(+)$1	1	174	190	13.9098
(((((.......))))	chr8:109247184-109247424(-)$1	1	8	24	13.9706
(.(((.......))))	chr19:37618661-37618901(+)$1	1	219	235	13.7127
(((((.......))))	chr11:134078701-134078941(-)$1	1	157	173	13.9706
.((((.......))))	chr8:101541706-101541986(-)$1	1	115	131	13.5617
.((((.......))))	chr6:31598325-31598565(+)$1	1	8	24	14.4710
(.(((.......))).	chr16:3339555-3339795(+)$1	1	160	176	13.9098

#PSSM
e : 0.22	f : 0.19	! : 0.11	: : 0.09	g : 0.08	" : 0.08	b : 0.06	a : 0.04	# : 0.01	d : 0.01	$ : 0.01	h : 0.01	[ : 0.01	
d : 0.36	e : 0.22	f : 0.13	[ : 0.11	g : 0.06	! : 0.03	" : 0.03	b : 0.01	h : 0.01	
d : 0.34	e : 0.21	c : 0.19	f : 0.13	g : 0.06	[ : 0.03	h : 0.01	
d : 0.34	e : 0.21	c : 0.19	f : 0.13	g : 0.06	b : 0.03	[ : 0.01	
d : 0.34	e : 0.21	c : 0.19	f : 0.11	g : 0.06	b : 0.03	a : 0.03	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
p : 1.00	
d : 0.34	e : 0.21	c : 0.19	f : 0.11	g : 0.06	b : 0.03	a : 0.03	
d : 0.34	e : 0.21	c : 0.19	f : 0.11	g : 0.06	b : 0.03	] : 0.01	h : 0.01	
d : 0.34	e : 0.21	c : 0.19	f : 0.13	g : 0.06	] : 0.03	h : 0.01	
d : 0.36	e : 0.22	f : 0.14	] : 0.09	g : 0.06	2 : 0.04	b : 0.01	4 : 0.01	h : 0.01	

#score	836.2297758098623
#seq	61
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m3_run1.txt

#BEAR
gggggqqqqqqqqgggg	chr3:133969357-133969582(-)$1	225	135	152	13.5210
fffffqqqqqqqqffff	chr5:140175722-140175946(-)$1	224	146	163	12.7688
:ddddqqqqqqqqdddd	chr7:107706086-107706309(-)$1	223	21	38	13.4411
:ddddqqqqqqqqdddd	chr22:42341155-42341378(-)$1	223	126	143	13.4411
dddddqqqqqqqqdddd	chr1:167814887-167815114(+)$1	227	179	196	14.1187
ggggaqqqqqqqqa]gg	chr22:29446190-29446420(+)$1	230	186	203	13.5436
eeeeeqqqqqqqqeeee	chr15:75772101-75772323(+)$1	222	198	215	14.1884
Gddddqqqqqqqqdddd	chr10:102250472-102250695(+)$1	223	191	208	13.8657
dddbbqqqqqqqqbb]d	chr17:4859216-4859439(+)$1	223	149	166	12.7067
b[cccqqqqqqqqccc]	chr9:136598855-136599077(+)$1	222	140	157	13.3392
eee[aqqqqqqqqa]ee	chr19:56127159-56127382(+)$1	223	127	144	14.0270
#ddddqqqqqqqqdddd	chr17:43005433-43005655(+)$1	222	185	202	14.2350
eeeeeqqqqqqqqeeee	chr3:38180349-38180571(+)$1	222	190	207	14.1884
[ddddqqqqqqqqdddd	chr12:78573218-78573442(+)$1	224	130	147	14.3358
gggggqqqqqqqqgggg	chr3:52390670-52390892(-)$1	222	136	153	13.5210
ddcccqqqqqqqqccc3	chr14:96730232-96730453(+)$1	221	25	42	13.6000
eeeeeqqqqqqqqeeee	chr1:1960895-1961116(+)$1	221	5	22	14.1884
fffffqqqqqqqqffff	chr12:132250742-132250964(-)$1	222	80	97	12.7688
fffffqqqqqqqqffff	chr7:99725172-99725395(+)$1	223	139	156	12.7688
e[cccqqqqqqqqccc]	chr2:231861044-231861266(-)$1	222	183	200	13.6726
:ddddqqqqqqqqdddd	chr16:15831278-15831500(+)$1	222	140	157	13.4411
ee[bbqqqqqqqqbb]e	chr22:18111274-18111496(-)$1	222	137	154	12.7755
"ddddqqqqqqqqdddd	chr1:151509115-151509336(+)$1	221	159	176	14.2628
fffffqqqqqqqqffff	chr1:3440611-3440835(-)$1	224	192	209	12.7688
:ddddqqqqqqqqdddd	chr1:223283876-223284098(+)$1	222	15	32	13.4411
eeeeeqqqqqqqqeeee	chr19:16006330-16006551(+)$1	221	190	207	14.1884
!ddddqqqqqqqqdddd	chr19:57868366-57868587(-)$1	221	184	201	14.3700
eeeeeqqqqqqqqeeee	chr14:60591166-60591392(-)$1	226	52	69	14.1884
eeeeeqqqqqqqqeeee	chr19:12876892-12877117(+)$1	225	148	165	14.1884
eeeeeqqqqqqqqeeee	chr19:36545857-36546083(-)$1	226	117	134	14.1884
gggggqqqqqqqqgggg	chr16:86602274-86602495(-)$1	221	185	202	13.5210
[ddddqqqqqqqqdddd	chr6:160221290-160221514(-)$1	224	165	182	14.3358
dddbbqqqqqqqqbbdd	chr20:44999966-45000188(-)$1	222	113	130	12.8644
cc!!aqqqqqqqqa22c	chr14:20859030-20859255(+)$1	225	190	207	12.7947
gggggqqqqqqqqgggg	chr1:29138847-29139070(+)$1	223	120	137	13.5210
eee[aqqqqqqqqa]ee	chr2:7005700-7005921(-)$1	221	74	91	14.0270
!ddddqqqqqqqqdddd	chr17:58700982-58701205(+)$1	223	119	136	14.3700
cc!!aqqqqqqqqa22c	chr2:219738191-219738412(-)$1	221	77	94	12.7947
[ddddqqqqqqqqdddd	chr15:91500771-91500993(+)$1	222	185	202	14.3358
Gddddqqqqqqqqdddd	chr10:76863622-76863848(-)$1	226	205	222	13.8657
gggggqqqqqqqqgggg	chr16:69143571-69143792(+)$1	221	87	104	13.5210
eee[aqqqqqqqqa]ee	chr5:161524744-161524971(-)$1	227	59	76	14.0270
!ddddqqqqqqqqdddd	chrX:70323729-70323954(+)$1	225	196	213	14.3700
!!cccqqqqqqqqccc2	chr1:31478757-31478979(+)$1	222	57	74	13.5490
eeeeeqqqqqqqqeeee	chr3:141499419-141499641(+)$1	222	125	142	14.1884
:ddddqqqqqqqqdddd	chr20:34207033-34207256(-)$1	223	148	165	13.4411
:ddddqqqqqqqqdddd	chr1:40318335-40318559(-)$1	224	9	26	13.4411
ffcccqqqqqqqqccc]	chr16:67271260-67271481(-)$1	221	89	106	13.4614
!!cccqqqqqqqqccc2	chr5:176863309-176863533(-)$1	224	194	211	13.5490
fffffqqqqqqqqffff	chr1:983367-983598(+)$1	231	165	182	12.7688
iiiiiqqqqqqqqiiii	chr1:193028652-193028878(-)$1	226	107	124	13.3301
!ddddqqqqqqqqdddd	chr8:36703286-36703512(-)$1	226	150	167	14.3700
!!cccqqqqqqqqccc2	chr15:91016858-91017089(-)$1	231	45	62	13.5490
eeeeeqqqqqqqqeeee	chr3:183822007-183822228(+)$1	221	30	47	14.1884
eeeeeqqqqqqqqeeee	chr7:2394495-2394737(-)$1	242	180	197	14.1884
eecccqqqqqqqqccc3	chrX:25025404-25025626(+)$1	222	67	84	13.8184
:ddddqqqqqqqqdddd	chr14:102918715-102918941(-)$1	226	181	198	13.4411
eee[aqqqqqqqqaeee	chr1:11825955-11826178(-)$1	223	16	33	14.1226
iiiiiqqqqqqqqiiii	chr11:71693763-71693984(+)$1	221	21	38	13.3301
eeeeeqqqqqqqqeeee	chr12:111157822-111158044(+)$1	222	137	154	14.1884
eeeeeqqqqqqqqeeee	chr12:52793689-52793911(+)$1	222	184	201	14.1884
fffffqqqqqqqqffff	chr9:140611399-140611621(-)$1	222	119	136	12.7688
eeebbqqqqqqqqbb33	chr19:13135905-13136129(-)$1	224	104	121	12.7910

#otherMatches

#Seq PSSM
GGCCCGCGGCUGAGGGC	chr3:133969357-133969582(-)$1	225	135	152	13.5210
GCUCUCGCGGUCCAGGG	chr5:140175722-140175946(-)$1	224	146	163	12.7688
AGCAAUCAGUAUUUUGC	chr7:107706086-107706309(-)$1	223	21	38	13.4411
AGGUGUGUUUCCUCGCC	chr22:42341155-42341378(-)$1	223	126	143	13.4411
CGAAGCUGUUCCUCUUC	chr1:167814887-167815114(+)$1	227	179	196	14.1187
GCCCCACCUCUACGAGG	chr22:29446190-29446420(+)$1	230	186	203	13.5436
CAUUUGGGUCAUAAAAU	chr15:75772101-75772323(+)$1	222	198	215	14.1884
CUCUUGGaaaggaaaga	chr10:102250472-102250695(+)$1	223	191	208	13.8657
UUGAGAAGAAGGCCUGC	chr17:4859216-4859439(+)$1	223	149	166	12.7067
CCGCUCCCGCUCCAGCA	chr9:136598855-136599077(+)$1	222	140	157	13.3392
cugggggugaggacgca	chr19:56127159-56127382(+)$1	223	127	144	14.0270
CAGGGGGAGGAGGCCCU	chr17:43005433-43005655(+)$1	222	185	202	14.2350
GCCUCGUACCUGGGGGG	chr3:38180349-38180571(+)$1	222	190	207	14.1884
CAGCUGAAGAGCGAGCU	chr12:78573218-78573442(+)$1	224	130	147	14.3358
AGAUCCGCUCCAUGGUC	chr3:52390670-52390892(-)$1	222	136	153	13.5210
CAGCCUCUGAUCUGGUG	chr14:96730232-96730453(+)$1	221	25	42	13.6000
GACCCUCAUCCGUGGGU	chr1:1960895-1961116(+)$1	221	5	22	14.1884
CCGCAGAUACCAAUGUG	chr12:132250742-132250964(-)$1	222	80	97	12.7688
GGGGCAGGGCGUGGCCC	chr7:99725172-99725395(+)$1	223	139	156	12.7688
UGUGGAUUCAGGACUAG	chr2:231861044-231861266(-)$1	222	183	200	13.6726
CAGCUUCCGUUUCAGCU	chr16:15831278-15831500(+)$1	222	140	157	13.4411
UUGGUUGGGUCUUACGA	chr22:18111274-18111496(-)$1	222	137	154	12.7755
GGCCUGAGGAAGAAGGC	chr1:151509115-151509336(+)$1	221	159	176	14.2628
AUCCCUACCCUCUGGGG	chr1:3440611-3440835(-)$1	224	192	209	12.7688
ACCAGCCAACAUCCUGG	chr1:223283876-223284098(+)$1	222	15	32	13.4411
ugggcuaagggaugccc	chr19:16006330-16006551(+)$1	221	190	207	14.1884
CUUUCUCCAGUAUGAAA	chr19:57868366-57868587(-)$1	221	184	201	14.3700
AGUUUCUGAAUUUAAAC	chr14:60591166-60591392(-)$1	226	52	69	14.1884
GCAGGAGCGUCUCCCUG	chr19:12876892-12877117(+)$1	225	148	165	14.1884
CUGGCCCCUCCGCGCCG	chr19:36545857-36546083(-)$1	226	117	134	14.1884
GGGAGUUGAACAUCUCC	chr16:86602274-86602495(-)$1	221	185	202	13.5210
CCACGUCCAUGGCCGUG	chr6:160221290-160221514(-)$1	224	165	182	14.3358
GCACUGAACCACAAGGU	chr20:44999966-45000188(-)$1	222	113	130	12.8644
AUCCCAAUCAACAGCAG	chr14:20859030-20859255(+)$1	225	190	207	12.7947
AGCGCCUGCCCCAGCGC	chr1:29138847-29139070(+)$1	223	120	137	13.5210
GCGGCGUCGCUGAGGCG	chr2:7005700-7005921(-)$1	221	74	91	14.0270
UGGUGGGAGGUAACAUU	chr17:58700982-58701205(+)$1	223	119	136	14.3700
UCGGCGGCGUAGAGGAG	chr2:219738191-219738412(-)$1	221	77	94	12.7947
UGAGUGACUUAGUGCUU	chr15:91500771-91500993(+)$1	222	185	202	14.3358
GGGCUCCCCUCUCAGCC	chr10:76863622-76863848(-)$1	226	205	222	13.8657
GUGGUGGAUGGCAACCG	chr16:69143571-69143792(+)$1	221	87	104	13.5210
GUUUGUUUUCUUCCUAA	chr5:161524744-161524971(-)$1	227	59	76	14.0270
UGGACUUCUUUUUGUCU	chrX:70323729-70323954(+)$1	225	196	213	14.3700
CUGUUCACAUGGAAACU	chr1:31478757-31478979(+)$1	222	57	74	13.5490
UCGGGACAUGAAGCCUG	chr3:141499419-141499641(+)$1	222	125	142	14.1884
GUGAGAAGUAACCCUCA	chr20:34207033-34207256(-)$1	223	148	165	13.4411
AGCCCCAGGAGAUGGGC	chr1:40318335-40318559(-)$1	224	9	26	13.4411
ACCCUCAUCAACAAGGU	chr16:67271260-67271481(-)$1	221	89	106	13.4614
AGGGAAAGGUGCAUCCA	chr5:176863309-176863533(-)$1	224	194	211	13.5490
UUGCCAAGACCACGGCA	chr1:983367-983598(+)$1	231	165	182	12.7688
GGAUUCCAGGUUCGGUU	chr1:193028652-193028878(-)$1	226	107	124	13.3301
AAUGAACACAUCAUCAU	chr8:36703286-36703512(-)$1	226	150	167	14.3700
UCAGGCUACCAUACCUU	chr15:91016858-91017089(-)$1	231	45	62	13.5490
AGCCAAGAACCUGUGGC	chr3:183822007-183822228(+)$1	221	30	47	14.1884
UGGGCCCAACGCUGCCU	chr7:2394495-2394737(-)$1	242	180	197	14.1884
CCGGGAAGGGCAGCCCA	chrX:25025404-25025626(+)$1	222	67	84	13.8184
UGCUGCUCUGGCACAGC	chr14:102918715-102918941(-)$1	226	181	198	13.4411
GGGACUGCAGGUUGCUC	chr1:11825955-11826178(-)$1	223	16	33	14.1226
AGUGCUUGUGUUUGUGU	chr11:71693763-71693984(+)$1	221	21	38	13.3301
GUUUCUAUAAUUUGAAG	chr12:111157822-111158044(+)$1	222	137	154	14.1884
GUUGUCCAUCUUCACAA	chr12:52793689-52793911(+)$1	222	184	201	14.1884
CUGGGGAAAAGCGCUUG	chr9:140611399-140611621(-)$1	222	119	136	12.7688
GAUGCCCACUUCUGCUU	chr19:13135905-13136129(-)$1	224	104	121	12.7910

#DB
(((((........))))	chr3:133969357-133969582(-)$1	1	135	152	13.5210
(((((........))))	chr5:140175722-140175946(-)$1	1	146	163	12.7688
.((((........))))	chr7:107706086-107706309(-)$1	1	21	38	13.4411
.((((........))))	chr22:42341155-42341378(-)$1	1	126	143	13.4411
(((((........))))	chr1:167814887-167815114(+)$1	1	179	196	14.1187
(((((........).))	chr22:29446190-29446420(+)$1	1	186	203	13.5436
(((((........))))	chr15:75772101-75772323(+)$1	1	198	215	14.1884
)((((........))))	chr10:102250472-102250695(+)$1	1	191	208	13.8657
(((((........)).)	chr17:4859216-4859439(+)$1	1	149	166	12.7067
(.(((........))).	chr9:136598855-136599077(+)$1	1	140	157	13.3392
(((.(........).))	chr19:56127159-56127382(+)$1	1	127	144	14.0270
.((((........))))	chr17:43005433-43005655(+)$1	1	185	202	14.2350
(((((........))))	chr3:38180349-38180571(+)$1	1	190	207	14.1884
.((((........))))	chr12:78573218-78573442(+)$1	1	130	147	14.3358
(((((........))))	chr3:52390670-52390892(-)$1	1	136	153	13.5210
(((((........))).	chr14:96730232-96730453(+)$1	1	25	42	13.6000
(((((........))))	chr1:1960895-1961116(+)$1	1	5	22	14.1884
(((((........))))	chr12:132250742-132250964(-)$1	1	80	97	12.7688
(((((........))))	chr7:99725172-99725395(+)$1	1	139	156	12.7688
(.(((........))).	chr2:231861044-231861266(-)$1	1	183	200	13.6726
.((((........))))	chr16:15831278-15831500(+)$1	1	140	157	13.4411
((.((........)).)	chr22:18111274-18111496(-)$1	1	137	154	12.7755
.((((........))))	chr1:151509115-151509336(+)$1	1	159	176	14.2628
(((((........))))	chr1:3440611-3440835(-)$1	1	192	209	12.7688
.((((........))))	chr1:223283876-223284098(+)$1	1	15	32	13.4411
(((((........))))	chr19:16006330-16006551(+)$1	1	190	207	14.1884
.((((........))))	chr19:57868366-57868587(-)$1	1	184	201	14.3700
(((((........))))	chr14:60591166-60591392(-)$1	1	52	69	14.1884
(((((........))))	chr19:12876892-12877117(+)$1	1	148	165	14.1884
(((((........))))	chr19:36545857-36546083(-)$1	1	117	134	14.1884
(((((........))))	chr16:86602274-86602495(-)$1	1	185	202	13.5210
.((((........))))	chr6:160221290-160221514(-)$1	1	165	182	14.3358
)))((........))((	chr20:44999966-45000188(-)$1	1	113	130	12.8644
((..(........)..)	chr14:20859030-20859255(+)$1	1	190	207	12.7947
(((((........))))	chr1:29138847-29139070(+)$1	1	120	137	13.5210
(((.(........).))	chr2:7005700-7005921(-)$1	1	74	91	14.0270
.((((........))))	chr17:58700982-58701205(+)$1	1	119	136	14.3700
((..(........)..)	chr2:219738191-219738412(-)$1	1	77	94	12.7947
.((((........))))	chr15:91500771-91500993(+)$1	1	185	202	14.3358
)((((........))))	chr10:76863622-76863848(-)$1	1	205	222	13.8657
(((((........))))	chr16:69143571-69143792(+)$1	1	87	104	13.5210
(((.(........).))	chr5:161524744-161524971(-)$1	1	59	76	14.0270
.((((........))))	chrX:70323729-70323954(+)$1	1	196	213	14.3700
..(((........))).	chr1:31478757-31478979(+)$1	1	57	74	13.5490
(((((........))))	chr3:141499419-141499641(+)$1	1	125	142	14.1884
.((((........))))	chr20:34207033-34207256(-)$1	1	148	165	13.4411
.((((........))))	chr1:40318335-40318559(-)$1	1	9	26	13.4411
(((((........))).	chr16:67271260-67271481(-)$1	1	89	106	13.4614
..(((........))).	chr5:176863309-176863533(-)$1	1	194	211	13.5490
(((((........))))	chr1:983367-983598(+)$1	1	165	182	12.7688
(((((........))))	chr1:193028652-193028878(-)$1	1	107	124	13.3301
.((((........))))	chr8:36703286-36703512(-)$1	1	150	167	14.3700
..(((........))).	chr15:91016858-91017089(-)$1	1	45	62	13.5490
(((((........))))	chr3:183822007-183822228(+)$1	1	30	47	14.1884
(((((........))))	chr7:2394495-2394737(-)$1	1	180	197	14.1884
(((((........))).	chrX:25025404-25025626(+)$1	1	67	84	13.8184
.((((........))))	chr14:102918715-102918941(-)$1	1	181	198	13.4411
(((.(........))))	chr1:11825955-11826178(-)$1	1	16	33	14.1226
(((((........))))	chr11:71693763-71693984(+)$1	1	21	38	13.3301
(((((........))))	chr12:111157822-111158044(+)$1	1	137	154	14.1884
(((((........))))	chr12:52793689-52793911(+)$1	1	184	201	14.1884
(((((........))))	chr9:140611399-140611621(-)$1	1	119	136	12.7688
(((((........))..	chr19:13135905-13136129(-)$1	1	104	121	12.7910

#PSSM
e : 0.31	f : 0.11	: : 0.11	! : 0.11	g : 0.09	d : 0.06	[ : 0.04	G : 0.03	c : 0.03	i : 0.03	b : 0.01	# : 0.01	" : 0.01	
d : 0.34	e : 0.30	f : 0.11	g : 0.09	! : 0.04	[ : 0.03	c : 0.03	i : 0.03	
d : 0.33	e : 0.26	c : 0.12	g : 0.09	f : 0.09	! : 0.03	i : 0.03	[ : 0.01	
d : 0.30	e : 0.19	c : 0.12	g : 0.09	f : 0.09	b : 0.06	[ : 0.06	! : 0.03	i : 0.03	
d : 0.30	e : 0.19	c : 0.12	a : 0.11	f : 0.09	g : 0.07	b : 0.06	i : 0.03	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.30	e : 0.19	c : 0.12	a : 0.11	f : 0.09	g : 0.07	b : 0.06	i : 0.03	
d : 0.30	e : 0.20	c : 0.12	f : 0.09	g : 0.07	] : 0.06	b : 0.06	2 : 0.03	i : 0.03	
d : 0.31	e : 0.25	c : 0.12	g : 0.09	f : 0.09	] : 0.03	2 : 0.03	i : 0.03	3 : 0.01	
d : 0.33	e : 0.26	g : 0.09	f : 0.09	] : 0.04	3 : 0.04	2 : 0.04	c : 0.03	i : 0.03	

#score	861.0787098587624
#seq	63
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_CDS_m2_run2.txt

#BEAR
eddddoooooodddd2	chr19:44514904-44515117(+)$1	213	158	174	12.2237
b[cccooooooccc]b	chr5:102521999-102522300(+)$1	301	273	289	10.0549
ddd[aooooooa]ddd	chr14:72055774-72055998(+)$1	224	195	211	11.1977
#ddddoooooodddd6	chr2:219603592-219603805(+)$1	213	32	48	11.9295
dddddoooooodddd:	chr17:62496079-62496345(-)$1	266	190	206	11.5124
eeeeeooooooeeeee	chr2:233680329-233680580(+)$1	251	64	80	11.1246
gggggooooooggggg	chr1:151260583-151260797(+)$1	214	94	110	9.9223
cacccooooooccc]a	chr17:4848871-4849329(-)$1	458	274	290	10.3646
$ddddoooooodddd3	chr15:71211373-71211597(+)$1	224	80	96	12.2788
""cccooooooccccc	chr7:129916437-129916652(+)$1	215	147	163	10.4254
eeeeeooooooeeeee	chr14:69256314-69256572(-)$1	258	92	108	11.1246
:ddddoooooodddd:	chr13:32910999-32911224(+)$1	225	84	100	10.9025
eeeeeooooooeeeee	chr11:6340693-6340911(-)$1	218	37	53	11.1246
[ddddoooooodddd]	chr1:63913134-63913413(-)$1	279	180	196	12.4569
dddbboooooobb]dd	chr10:61828602-61828874(-)$1	272	206	222	9.7862
eeeeeooooooeeeee	chr16:731677-731934(-)$1	257	60	76	11.1246
!ddddoooooodddd2	chr19:58004737-58004956(+)$1	219	146	162	12.3990
eeeeeooooooeeeee	chr3:57107982-57108205(+)$1	223	124	140	11.1246
ddd[aooooooa]ddd	chr9:43890234-43890452(+)$1	218	42	58	11.1977
eeeeeooooooeeeee	chrX:117773420-117773641(+)$1	221	5	21	11.1246
[ddddoooooodddd]	chrY:4967220-4967438(+)$1	218	64	80	12.4569
eeeeeooooooeeeee	chr2:61610317-61610559(-)$1	242	142	158	11.1246
iiiiiooooooiiiii	chr19:36640789-36641062(+)$1	273	135	151	9.9787
=====oooooo=====	chr12:133147930-133148187(+)$1	257	181	197	10.2188
[ddddoooooodddd]	chr13:25886966-25887229(+)$1	263	75	91	12.4569
eeeeeooooooeeeee	chr4:154624219-154624433(+)$1	214	13	29	11.1246
:ddddoooooodddd:	chr7:121650786-121651001(+)$1	215	32	48	10.9025
[ddddoooooodddd]	chr3:58242286-58242500(+)$1	214	12	28	12.4569
!ddddoooooodddde	chr3:121206426-121206680(-)$1	254	213	229	12.4139
ggg[aooooooa]ggg	chr12:49579164-49579492(-)$1	328	13	29	10.0215
eeeeeooooooeeeee	chr14:105848781-105849001(+)$1	220	182	198	11.1246
[ddddooooooddddb	chr3:49147684-49147921(-)$1	237	26	42	12.1371
b[cccooooooccc]b	chr16:47581252-47581465(+)$1	213	143	159	10.0549
:ddddoooooodddd:	chr22:41363698-41363935(+)$1	237	21	37	10.9025
:ddddoooooodddd:	chr2:175436611-175436900(-)$1	289	2	18	10.9025
eeeeeooooooeeeee	chr16:2813049-2813269(+)$1	220	69	85	11.1246
ddd[aooooooadddd	chr1:32567955-32568173(+)$1	218	181	197	11.4861
eeeeeooooooeeeee	chr19:12059880-12060100(+)$1	220	87	103	11.1246
[ddddooooooddddd	chr12:40657567-40657782(+)$1	215	14	30	12.2929
dd[bboooooobbddd	chr19:58353686-58353964(+)$1	278	49	65	9.8671
dd[bboooooobbddd	chrX:153588387-153588614(-)$1	227	142	158	9.8671
:ddddoooooodddd:	chrX:71425365-71425588(-)$1	223	205	221	10.9025
ccc[aooooooa]ccc	chr19:57910517-57910739(+)$1	222	203	219	10.1668
#ddddoooooodddd3	chrX:105865864-105866078(+)$1	214	37	53	12.4599
dd!!aooooooa22dd	chr13:99947587-99947825(-)$1	238	83	99	10.0732
!!cccooooooccc33	chr18:12817220-12817450(-)$1	230	96	112	10.7722
eeeeeooooooeeeee	chr6:32159046-32159301(-)$1	255	54	70	11.1246
cddddoooooodddd]	chr1:158450148-158450363(+)$1	215	127	143	12.2701
:ddddoooooodddd:	chr5:133481814-133482278(+)$1	464	448	464	10.9025
:ddddooooooddddD	chr12:54920403-54920632(+)$1	229	204	220	10.6518
eeeeeooooooeeeee	chr9:125562925-125563140(+)$1	215	23	39	11.1246
b[cccooooooccc]b	chr3:186272339-186272585(-)$1	246	39	55	10.0549
!!cccooooooccc22	chr14:50241181-50241395(+)$1	214	179	195	10.4529
:ddddoooooodddd:	chr15:35152142-35152375(-)$1	233	61	77	10.9025
:ddddoooooodddde	chr22:36537780-36538036(-)$1	256	216	232	11.5393
e[cccooooooccc]e	chr22:36550529-36550773(-)$1	244	199	215	10.4958
[ddddoooooodddd2	chrX:153629058-153629350(+)$1	292	263	279	12.3503
#ddddoooooodddd2	chr15:83335502-83335730(-)$1	228	104	120	12.3140
!ddddoooooodddd2	chr5:110456683-110456898(+)$1	215	136	152	12.3990
eeeeeooooooeeeee	chr15:45007652-45007995(+)$1	343	12	28	11.1246
gggggooooooggggg	chr15:49926636-49926851(+)$1	215	35	51	9.9223

#otherMatches

#Seq PSSM
UUAGGUCAAGUCUUAA	chr19:44514904-44515117(+)$1	213	158	174	12.2237
AUCAGUGCUCUCUGUU	chr5:102521999-102522300(+)$1	301	273	289	10.0549
GCAGUACUUGAAGUGC	chr14:72055774-72055998(+)$1	224	195	211	11.1977
UGGACAAUACAGUCUU	chr2:219603592-219603805(+)$1	213	32	48	11.9295
CGGAAGUAAUGUUCCA	chr17:62496079-62496345(-)$1	266	190	206	11.5124
CCAGGCCCUGCCCUGG	chr2:233680329-233680580(+)$1	251	64	80	11.1246
GGGGGCCAUCACCUCC	chr1:151260583-151260797(+)$1	214	94	110	9.9223
GGCUGGAUGGACAGAC	chr17:4848871-4849329(-)$1	458	274	290	10.3646
UUUAAGUCAUGUUGAU	chr15:71211373-71211597(+)$1	224	80	96	12.2788
CUGGAUUUUGUUCCCU	chr7:129916437-129916652(+)$1	215	147	163	10.4254
GCCCCUAGCAUGGGGC	chr14:69256314-69256572(-)$1	258	92	108	11.1246
AGAAGAAACUACUUCA	chr13:32910999-32911224(+)$1	225	84	100	10.9025
CCUUGUGUAAUUAAGG	chr11:6340693-6340911(-)$1	218	37	53	11.1246
aaagcuaaauugcuuc	chr1:63913134-63913413(-)$1	279	180	196	12.4569
GAAGUAUGUAAACAUU	chr10:61828602-61828874(-)$1	272	206	222	9.7862
GGCCUCAAUGCAGGCC	chr16:731677-731934(-)$1	257	60	76	11.1246
GUGGAAAAUUGUUUAG	chr19:58004737-58004956(+)$1	219	146	162	12.3990
uuucuugguauggaag	chr3:57107982-57108205(+)$1	223	124	140	11.1246
UUUUCUCUAUUGUAAA	chr9:43890234-43890452(+)$1	218	42	58	11.1977
UUCGGAAUAGACCGAA	chrX:117773420-117773641(+)$1	221	5	21	11.1246
GUAGUGAAGAAACUAG	chrY:4967220-4967438(+)$1	218	64	80	12.4569
ACCUAUGUUAUUAGGU	chr2:61610317-61610559(-)$1	242	142	158	11.1246
GAGUUCCCCCUGGCUC	chr19:36640789-36641062(+)$1	273	135	151	9.9787
UGCGUAGGCCCGCGUG	chr12:133147930-133148187(+)$1	257	181	197	10.2188
CAGCUACAACAGGCUU	chr13:25886966-25887229(+)$1	263	75	91	12.4569
CCUGUCCAACAACAGG	chr4:154624219-154624433(+)$1	214	13	29	11.1246
AUUGACCAGUUUCAAG	chr7:121650786-121651001(+)$1	215	32	48	10.9025
GCCUGAAAGAGCAGGA	chr3:58242286-58242500(+)$1	214	12	28	12.4569
AGUUAUUUAUUUGGCU	chr3:121206426-121206680(-)$1	254	213	229	12.4139
UAUACUAACCUGAAUA	chr12:49579164-49579492(-)$1	328	13	29	10.0215
AGGAGAGUGGGUUCCU	chr14:105848781-105849001(+)$1	220	182	198	11.1246
AGUCAGCGCAGUGACG	chr3:49147684-49147921(-)$1	237	26	42	12.1371
CUGACUUUGGUGUCUG	chr16:47581252-47581465(+)$1	213	143	159	10.0549
GCCACUACCCUGUGGG	chr22:41363698-41363935(+)$1	237	21	37	10.9025
AGCCCAGCCCCGGGCC	chr2:175436611-175436900(-)$1	289	2	18	10.9025
UCUGUAACGCCACAGA	chr16:2813049-2813269(+)$1	220	69	85	11.1246
CAGACCAUCUCGCUGG	chr1:32567955-32568173(+)$1	218	181	197	11.4861
UUUCAAACACAUGAAA	chr19:12059880-12060100(+)$1	220	87	103	11.1246
UGCAUUUAGGCAUGCC	chr12:40657567-40657782(+)$1	215	14	30	12.2929
UCACUAGUCACAGGAG	chr19:58353686-58353964(+)$1	278	49	65	9.8671
GUCACCAUCAAGUACG	chrX:153588387-153588614(-)$1	227	142	158	9.8671
AAUACCCAGUAGUGUA	chrX:71425365-71425588(-)$1	223	205	221	10.9025
CAGAGAAUUCACACUG	chr19:57910517-57910739(+)$1	222	203	219	10.1668
CUCAUCUUGAAAUGAC	chrX:105865864-105866078(+)$1	214	37	53	12.4599
UGCUGCAAACUCUUCA	chr13:99947587-99947825(-)$1	238	83	99	10.0732
CCAGAACAAUAUCUCA	chr18:12817220-12817450(-)$1	230	96	112	10.7722
CCCCUCCCUCCAGGGG	chr6:32159046-32159301(-)$1	255	54	70	11.1246
AGUCAUUCUUCUGGCU	chr1:158450148-158450363(+)$1	215	127	143	12.2701
AGAGACCCAGAUCUCA	chr5:133481814-133482278(+)$1	464	448	464	10.9025
CGAGCAUUUUAGCUCC	chr12:54920403-54920632(+)$1	229	204	220	10.6518
AGCCUCUCUUAAGGCU	chr9:125562925-125563140(+)$1	215	23	39	11.1246
UUUCAGAUCUGUGACA	chr3:186272339-186272585(-)$1	246	39	55	10.0549
UUUGGAGGACACCAUU	chr14:50241181-50241395(+)$1	214	179	195	10.4529
AUGCCCCAGAUGGCAA	chr15:35152142-35152375(-)$1	233	61	77	10.9025
GCAGGGACGAGUCUGG	chr22:36537780-36538036(-)$1	256	216	232	11.5393
AAGGAAAAAUAUCCAU	chr22:36550529-36550773(-)$1	244	199	215	10.4958
CUUUCACUUCAGAAAC	chrX:153629058-153629350(+)$1	292	263	279	12.3503
UCGCGACCGGGCGCGC	chr15:83335502-83335730(-)$1	228	104	120	12.3140
UUAACCUUGAUGUUAU	chr5:110456683-110456898(+)$1	215	136	152	12.3990
GGAAAGUCAAAUUUCC	chr15:45007652-45007995(+)$1	343	12	28	11.1246
AAAAUUUAUAUAUUUU	chr15:49926636-49926851(+)$1	215	35	51	9.9223

#DB
(((((......)))).	chr19:44514904-44515117(+)$1	1	158	174	12.2237
(.(((......))).)	chr5:102521999-102522300(+)$1	1	273	289	10.0549
(((.(......).)))	chr14:72055774-72055998(+)$1	1	195	211	11.1977
.((((......)))).	chr2:219603592-219603805(+)$1	1	32	48	11.9295
)((((......)))).	chr17:62496079-62496345(-)$1	1	190	206	11.5124
(((((......)))))	chr2:233680329-233680580(+)$1	1	64	80	11.1246
(((((......)))))	chr1:151260583-151260797(+)$1	1	94	110	9.9223
(((((......))).)	chr17:4848871-4849329(-)$1	1	274	290	10.3646
.((((......)))).	chr15:71211373-71211597(+)$1	1	80	96	12.2788
..(((......)))))	chr7:129916437-129916652(+)$1	1	147	163	10.4254
(((((......)))))	chr14:69256314-69256572(-)$1	1	92	108	11.1246
.((((......)))).	chr13:32910999-32911224(+)$1	1	84	100	10.9025
(((((......)))))	chr11:6340693-6340911(-)$1	1	37	53	11.1246
.((((......)))).	chr1:63913134-63913413(-)$1	1	180	196	12.4569
(((((......)).))	chr10:61828602-61828874(-)$1	1	206	222	9.7862
(((((......)))))	chr16:731677-731934(-)$1	1	60	76	11.1246
.((((......)))).	chr19:58004737-58004956(+)$1	1	146	162	12.3990
(((((......)))))	chr3:57107982-57108205(+)$1	1	124	140	11.1246
(((.(......).)))	chr9:43890234-43890452(+)$1	1	42	58	11.1977
(((((......)))))	chrX:117773420-117773641(+)$1	1	5	21	11.1246
.((((......)))).	chrY:4967220-4967438(+)$1	1	64	80	12.4569
(((((......)))))	chr2:61610317-61610559(-)$1	1	142	158	11.1246
(((((......)))))	chr19:36640789-36641062(+)$1	1	135	151	9.9787
(((((......)))))	chr12:133147930-133148187(+)$1	1	181	197	10.2188
.((((......)))).	chr13:25886966-25887229(+)$1	1	75	91	12.4569
(((((......)))))	chr4:154624219-154624433(+)$1	1	13	29	11.1246
.((((......)))).	chr7:121650786-121651001(+)$1	1	32	48	10.9025
.((((......)))).	chr3:58242286-58242500(+)$1	1	12	28	12.4569
.((((......)))))	chr3:121206426-121206680(-)$1	1	213	229	12.4139
(((.(......).)))	chr12:49579164-49579492(-)$1	1	13	29	10.0215
(((((......)))))	chr14:105848781-105849001(+)$1	1	182	198	11.1246
.((((......)))))	chr3:49147684-49147921(-)$1	1	26	42	12.1371
(.(((......))).)	chr16:47581252-47581465(+)$1	1	143	159	10.0549
.((((......)))).	chr22:41363698-41363935(+)$1	1	21	37	10.9025
.((((......)))).	chr2:175436611-175436900(-)$1	1	2	18	10.9025
(((((......)))))	chr16:2813049-2813269(+)$1	1	69	85	11.1246
(((.(......)))))	chr1:32567955-32568173(+)$1	1	181	197	11.4861
(((((......)))))	chr19:12059880-12060100(+)$1	1	87	103	11.1246
.((((......)))))	chr12:40657567-40657782(+)$1	1	14	30	12.2929
((.((......)))))	chr19:58353686-58353964(+)$1	1	49	65	9.8671
((.((......)))))	chrX:153588387-153588614(-)$1	1	142	158	9.8671
.((((......)))).	chrX:71425365-71425588(-)$1	1	205	221	10.9025
(((.(......).)))	chr19:57910517-57910739(+)$1	1	203	219	10.1668
.((((......)))).	chrX:105865864-105866078(+)$1	1	37	53	12.4599
((..(......)..))	chr13:99947587-99947825(-)$1	1	83	99	10.0732
..(((......)))..	chr18:12817220-12817450(-)$1	1	96	112	10.7722
(((((......)))))	chr6:32159046-32159301(-)$1	1	54	70	11.1246
(((((......)))).	chr1:158450148-158450363(+)$1	1	127	143	12.2701
.((((......)))).	chr5:133481814-133482278(+)$1	1	448	464	10.9025
.((((......)))))	chr12:54920403-54920632(+)$1	1	204	220	10.6518
(((((......)))))	chr9:125562925-125563140(+)$1	1	23	39	11.1246
(.(((......))).)	chr3:186272339-186272585(-)$1	1	39	55	10.0549
..(((......)))..	chr14:50241181-50241395(+)$1	1	179	195	10.4529
.((((......)))).	chr15:35152142-35152375(-)$1	1	61	77	10.9025
.((((......))))(	chr22:36537780-36538036(-)$1	1	216	232	11.5393
(.(((......))).)	chr22:36550529-36550773(-)$1	1	199	215	10.4958
.((((......)))).	chrX:153629058-153629350(+)$1	1	263	279	12.3503
.((((......)))).	chr15:83335502-83335730(-)$1	1	104	120	12.3140
.((((......)))).	chr5:110456683-110456898(+)$1	1	136	152	12.3990
(((((......)))))	chr15:45007652-45007995(+)$1	1	12	28	11.1246
(((((......)))))	chr15:49926636-49926851(+)$1	1	35	51	9.9223

#PSSM
e : 0.26	: : 0.14	d : 0.13	[ : 0.11	! : 0.08	b : 0.04	# : 0.04	g : 0.04	c : 0.04	$ : 0.01	" : 0.01	i : 0.01	= : 0.01	
d : 0.54	e : 0.22	[ : 0.06	g : 0.04	! : 0.03	a : 0.01	" : 0.01	i : 0.01	= : 0.01	c : 0.01	
d : 0.49	e : 0.22	c : 0.14	g : 0.04	[ : 0.03	i : 0.01	= : 0.01	! : 0.01	
d : 0.42	e : 0.22	c : 0.13	[ : 0.08	b : 0.04	g : 0.03	i : 0.01	= : 0.01	! : 0.01	
d : 0.42	e : 0.22	c : 0.13	a : 0.09	b : 0.04	g : 0.03	i : 0.01	= : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
d : 0.42	e : 0.22	c : 0.13	a : 0.09	b : 0.04	g : 0.03	i : 0.01	= : 0.01	
d : 0.44	e : 0.22	c : 0.13	] : 0.06	b : 0.04	g : 0.03	i : 0.01	= : 0.01	2 : 0.01	
d : 0.50	e : 0.22	c : 0.14	g : 0.04	] : 0.01	i : 0.01	= : 0.01	2 : 0.01	
d : 0.54	e : 0.22	] : 0.08	g : 0.04	c : 0.03	i : 0.01	= : 0.01	3 : 0.01	2 : 0.01	
e : 0.27	d : 0.13	: : 0.13	2 : 0.09	] : 0.08	b : 0.06	g : 0.04	3 : 0.04	c : 0.03	6 : 0.01	a : 0.01	i : 0.01	= : 0.01	D : 0.01	

#score	679.4456951491055
#seq	61
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m1_run1.txt

#BEAR
###eeeeeooooooeeeee22cc	chr11:71820044-71820267(-)$1	223	133	156	10.9661
fffff[bboooooobb]ffffff	chr6:154831255-154831477(-)$1	222	11	34	11.5677
eeeeeeeeooooooeeeeeffff	chr7:24732513-24732737(+)$1	224	53	76	11.3416
c!!eeeeeooooooeeeee]ccc	chr15:90233807-90234030(+)$1	223	74	97	11.6428
cgggggggooooooggggggg]c	chr18:9254120-9254346(-)$1	226	34	57	12.9177
e$$$$$bboooooobb22eeeee	chr3:149036370-149036597(-)$1	227	134	157	10.8022
!!ffffffooooooffffffeee	chr2:169984701-169984922(-)$1	221	72	95	11.7661
[gggggggooooooggggggg]b	chr9:134452751-134452973(-)$1	222	132	155	12.7973
:gggggggooooooggggggg:H	chr17:56048847-56049072(+)$1	225	11	34	10.3758
dddd[cccoooooocccddddcc	chr1:204654358-204654589(+)$1	231	167	190	12.2985
eeeeecccooooooccc22eeee	chr1:26697084-26697308(+)$1	224	169	192	12.9530
eeeeecccooooooccc22eeee	chr15:91073162-91073387(+)$1	225	4	27	12.9530
dddd!!bboooooobb22dddd2	chr16:66649243-66649465(+)$1	222	59	82	11.2433
dddeeeeeooooooeeeee22dd	chr2:75891732-75891961(+)$1	229	26	49	10.5844
gg[bb[aooooooa]bb]ggggg	chr17:28444048-28444275(+)$1	227	174	197	10.8333
hhhhhhhhoooooohhhhhhhh2	chr11:102447445-102447670(+)$1	225	35	58	10.1133
fffffabboooooobb]a]ffff	chr4:41992523-41992750(-)$1	227	27	50	11.5377
dddd[cccooooooccc22dddd	chr10:69644376-69644599(-)$1	223	172	195	12.5546
:gggggggoooooogggggggdd	chr2:45838250-45838472(-)$1	222	43	66	11.6845
ffff!!bboooooobb333ffff	chr9:112970278-112970499(-)$1	221	139	162	12.3578
iiiiicccooooooccc]iiiii	chr5:154199844-154200074(+)$1	230	4	27	13.6291
f####cccooooooccc22ffff	chr19:3179927-3180148(+)$1	221	191	214	12.9300
f[ffffffoooooofffffffff	chr19:57136980-57137202(+)$1	222	182	205	11.5127
eaffffffooooooffffff]a]	chr4:114682330-114682555(+)$1	225	83	106	11.5612
fffff[bboooooobb]ffffff	chr1:114696314-114696548(+)$1	234	123	146	11.5677
[dddd[bboooooobbdddd]bb	chr10:48438641-48438865(-)$1	224	55	78	10.8040
hhhhhhhhoooooohhhhhhhhc	chr1:40563005-40563228(+)$1	223	10	33	10.2705
ddddddddoooooodddd]dddd	chrX:2800284-2800507(-)$1	223	68	91	10.6658
egggggggooooooggggggg:E	chr12:69326864-69327086(+)$1	222	102	125	11.1053
eccc[cccooooooccc]ccc33	chr7:130038393-130038616(+)$1	223	160	183	13.6743
e"""ddddoooooodddd333ee	chr11:65308228-65308453(+)$1	225	84	107	11.5478
e[bb!!bboooooobb22bb]ee	chr12:132623711-132623939(+)$1	228	163	186	11.4628
[a!!a[bboooooobba22accc	chr11:62340601-62340827(+)$1	226	161	184	12.2692
c"""ddddoooooodddd333cc	chr14:103192929-103193152(-)$1	223	180	203	11.4994
:gggggggoooooogggggggGG	chr15:72117896-72118124(+)$1	228	177	200	10.8603
====!!cccnnnnnccc22====	chr12:27573983-27574211(-)$1	228	120	143	8.7921
!!bb[cccooooooccc]bbeee	chr3:50131099-50131409(-)$1	310	44	67	12.8258
ffbb[cccooooooccc]bb22f	chr12:4835789-4836012(-)$1	223	13	36	12.1077
gggggg[aooooooa]ggggggg	chr18:23615740-23615961(+)$1	221	26	49	12.7442
ffff[cccooooooccc]fffff	chr11:44957853-44958076(-)$1	223	162	185	13.2100
g!!eeeeeooooooeeeeegggg	chr8:135725123-135725346(+)$1	223	83	106	11.9211
eccc[cccooooooccc]ccc22	chr19:35616302-35616525(+)$1	223	11	34	13.2708
ccc[ccc[allla]ccc]ccc]f	chr14:90446801-90447030(+)$1	229	7	30	8.7768
eeeeecccooooooccc]eeeee	chr22:38453123-38453345(-)$1	222	71	94	13.1258
gggg[cccooooooccc]ggggg	chr7:134131947-134132173(-)$1	226	112	135	14.0169
eee!!cccooooooccceeeee:	chr19:47507517-47507740(+)$1	223	120	143	12.1536
"eeeee[aooooooa]eeeeedd	chr17:41246212-41246435(+)$1	223	126	149	11.4359
d:ccccccooooooccc]ccc::	chr17:33307929-33308150(+)$1	221	170	193	10.3917
[ddddcccooooooccc]dddd]	chr8:41166753-41166976(+)$1	223	155	178	12.5966
ggggg[cccnnnnnccc]ggggg	chr16:84599757-84599979(+)$1	222	10	33	9.0033
========oooooo=========	chr20:2128298-2128524(-)$1	226	115	138	12.9410
!gggggggooooooggggggg44	chrX:119393906-119394128(-)$1	222	62	85	12.9051
ccccccccooooooccc]ccc]c	chr2:128145716-128145937(-)$1	221	44	67	13.3211
!cccddddoooooodddd]ccc3	chr5:140699812-140700034(+)$1	222	41	64	11.6356
eee####aooooooa4444eeee	chr16:56623980-56624204(+)$1	224	86	109	11.8075
dddd[cccooooooccc]ddddd	chr2:122125159-122125384(-)$1	225	2	25	12.6199
!!bbddddoooooodddd]bb22	chr1:26437749-26437971(+)$1	222	194	217	10.4299
eeffffffooooooffffff]ee	chr7:44424745-44424968(-)$1	223	29	52	11.5833

#otherMatches

#Seq PSSM
AGGUCAGUGUAGAGGCUGAAAGA	chr11:71820044-71820267(-)$1	223	133	156	10.9661
GCUGCAGCUGGACUGUGGCAGCU	chr6:154831255-154831477(-)$1	222	11	34	11.5677
GAUAUUAAUCCACUUUAGUUAUU	chr7:24732513-24732737(+)$1	224	53	76	11.3416
CACGAGUCGCACGGGGCUCAGGC	chr15:90233807-90234030(+)$1	223	74	97	11.6428
GGGAAGUAUCUGUUUACUUUCAC	chr18:9254120-9254346(-)$1	226	34	57	12.9177
uauaggcugaaaaaagaaagcau	chr3:149036370-149036597(-)$1	227	134	157	10.8022
UGAUCAUUAUAGUAAAUGAUCCA	chr2:169984701-169984922(-)$1	221	72	95	11.7661
AGCAGGCAGAACCGUGUCUGUGG	chr9:134452751-134452973(-)$1	222	132	155	12.7973
AUUAUCAGAGCAAACUGAUGAAG	chr17:56048847-56049072(+)$1	225	11	34	10.3758
GGGGACGCUGGUCCGCGCCCUCC	chr1:204654358-204654589(+)$1	231	167	190	12.2985
AGAUGGCAGGAAGGUGUUACAUU	chr1:26697084-26697308(+)$1	224	169	192	12.9530
gcggcggcUCCUCUGCCGGGUCG	chr15:91073162-91073387(+)$1	225	4	27	12.9530
GGACCAGACAUAACUCACGUCCU	chr16:66649243-66649465(+)$1	222	59	82	11.2433
AUUAAAAUUUUAGCAUUUUCCAA	chr2:75891732-75891961(+)$1	229	26	49	10.5844
GCAGUGUGAAGAGAGACAGUUCC	chr17:28444048-28444275(+)$1	227	174	197	10.8333
UAGGUUUAUCCACCUAAGCCUAC	chr11:102447445-102447670(+)$1	225	35	58	10.1133
ACAGGGAGGACCAGCUACAUCUG	chr4:41992523-41992750(-)$1	227	27	50	11.5377
CGCGCGGCACUGGCGCCCCCGCG	chr10:69644376-69644599(-)$1	223	172	195	12.5546
ACUUCCGGCGGGAACCGGAAGGU	chr2:45838250-45838472(-)$1	222	43	66	11.6845
AAGGACCUGGAAUAAGACACCUU	chr9:112970278-112970499(-)$1	221	139	162	12.3578
CAGCCAGGAUGACACUUAGGCUG	chr5:154199844-154200074(+)$1	230	4	27	13.6291
CCAUGGUCACCCUGGACAAGGAG	chr19:3179927-3180148(+)$1	221	191	214	12.9300
ggcugggcuccagugcccagcag	chr19:57136980-57137202(+)$1	222	182	205	11.5127
GCGUGGGGUCUCCUCCCCACAGU	chr4:114682330-114682555(+)$1	225	83	106	11.5612
CCCCGGCCGCACUGGGGCGGGGC	chr1:114696314-114696548(+)$1	234	123	146	11.5677
CCGCGCGCCCUACUGCCGCGAGG	chr10:48438641-48438865(-)$1	224	55	78	10.8040
GAUGCCCAGCCUGAUGGGCGUCG	chr1:40563005-40563228(+)$1	223	10	33	10.2705
AUCCAGCUGACACAGGCUAGGAU	chrX:2800284-2800507(-)$1	223	68	91	10.6658
ggccggguguuauagcccgguca	chr12:69326864-69327086(+)$1	222	102	125	11.1053
UCCUGAGGUGGCCUCCUGAGGGG	chr7:130038393-130038616(+)$1	223	160	183	13.6743
CGGGGCGGGCGGAGCCGCAGGGC	chr11:65308228-65308453(+)$1	225	84	107	11.5478
ACACUCUGUCCCCUCAUCGUCUG	chr12:132623711-132623939(+)$1	228	163	186	11.4628
UGUCGCGAAUAUCAUCCCUCCGG	chr11:62340601-62340827(+)$1	226	161	184	12.2692
UAUAUGCCUUUUUUGGUAAUAGC	chr14:103192929-103193152(-)$1	223	180	203	11.4994
UUAGGGAUCACCAUGUCUCUGGG	chr15:72117896-72118124(+)$1	228	177	200	10.8603
UAAGCAAGAAAUCAUCUCACUUA	chr12:27573983-27574211(-)$1	228	120	143	8.7921
AAGCUCAAAGUUCAUUGUGCCUA	chr3:50131099-50131409(-)$1	310	44	67	12.8258
CCACCUGUAGUCUCGCGUGUCGG	chr12:4835789-4836012(-)$1	223	13	36	12.1077
GUGUAUGUGUGUGAAGGUAUAUA	chr18:23615740-23615961(+)$1	221	26	49	12.7442
AGGAUUUGGAAUUACAAUUUUUA	chr11:44957853-44958076(-)$1	223	162	185	13.2100
uauuuuuauuuuuuuaaGAAAAG	chr8:135725123-135725346(+)$1	223	83	106	11.9211
AGCUGGUCCCUGGCGAUGAGCAG	chr19:35616302-35616525(+)$1	223	11	34	13.2708
UACAUUUGCAUUGGAAAGGUAUU	chr14:90446801-90447030(+)$1	229	7	30	8.7768
UCGCUGUUAGUAGGAACAAGCGA	chr22:38453123-38453345(-)$1	222	71	94	13.1258
GAGAACUUUAAGGUAAGAUCUUG	chr7:134131947-134132173(-)$1	226	112	135	14.0169
CCACUGCUGACCUGGGCUGGCCU	chr19:47507517-47507740(+)$1	223	120	143	12.1536
AGACUCCCCAUCAUGUGAGUCAU	chr17:41246212-41246435(+)$1	223	126	149	11.4359
AAGCCCUUCGAGAAAAGCGGCGG	chr17:33307929-33308150(+)$1	221	170	193	10.3917
GGCUCCCGGAGGUGCGGCGAGCA	chr8:41166753-41166976(+)$1	223	155	178	12.5966
GUAAGUUUUAAGGCAAAUUUUAU	chr16:84599757-84599979(+)$1	222	10	33	9.0033
CUGUCUGGGGGCUGCCAGACAGG	chr20:2128298-2128524(-)$1	226	115	138	12.9410
GGGAACAGGAUGUAUUGUUCCGG	chrX:119393906-119394128(-)$1	222	62	85	12.9051
GGAGACCUUUUCACGGGAUCUAC	chr2:128145716-128145937(-)$1	221	44	67	13.3211
AGUUCAUUAAAUCAGAUGCAAUG	chr5:140699812-140700034(+)$1	222	41	64	11.6356
cagaagacuccaauggcagcugg	chr16:56623980-56624204(+)$1	224	86	109	11.8075
CCCCUGCCACUGAGGGCCGGGGG	chr2:122125159-122125384(-)$1	225	2	25	12.6199
AGGCCGCGGCCGGGCGCGCGCAG	chr1:26437749-26437971(+)$1	222	194	217	10.4299
AGCGGGGAUUCUGUUCUCUGACU	chr7:44424745-44424968(-)$1	223	29	52	11.5833

#DB
...(((((......)))))..))	chr11:71820044-71820267(-)$1	1	133	156	10.9661
(((((.((......)).))))))	chr6:154831255-154831477(-)$1	1	11	34	11.5677
)))(((((......)))))((((	chr7:24732513-24732737(+)$1	1	53	76	11.3416
(..(((((......))))).)))	chr15:90233807-90234030(+)$1	1	74	97	11.6428
((((((((......))))))).)	chr18:9254120-9254346(-)$1	1	34	57	12.9177
(.....((......))..)))))	chr3:149036370-149036597(-)$1	1	134	157	10.8022
..((((((......)))))))))	chr2:169984701-169984922(-)$1	1	72	95	11.7661
.(((((((......))))))).)	chr9:134452751-134452973(-)$1	1	132	155	12.7973
.(((((((......))))))).(	chr17:56048847-56049072(+)$1	1	11	34	10.3758
((((.(((......)))))))))	chr1:204654358-204654589(+)$1	1	167	190	12.2985
((((((((......)))..))))	chr1:26697084-26697308(+)$1	1	169	192	12.9530
((((((((......)))..))))	chr15:91073162-91073387(+)$1	1	4	27	12.9530
((((..((......))..)))).	chr16:66649243-66649465(+)$1	1	59	82	11.2433
((((((((......)))))..))	chr2:75891732-75891961(+)$1	1	26	49	10.5844
((.((.(......).)).)))))	chr17:28444048-28444275(+)$1	1	174	197	10.8333
((((((((......)))))))).	chr11:102447445-102447670(+)$1	1	35	58	10.1133
((((((((......)).).))))	chr4:41992523-41992750(-)$1	1	27	50	11.5377
((((.(((......)))..))))	chr10:69644376-69644599(-)$1	1	172	195	12.5546
.(((((((......)))))))((	chr2:45838250-45838472(-)$1	1	43	66	11.6845
((((..((......))...))))	chr9:112970278-112970499(-)$1	1	139	162	12.3578
((((((((......))).)))))	chr5:154199844-154200074(+)$1	1	4	27	13.6291
(....(((......)))..))))	chr19:3179927-3180148(+)$1	1	191	214	12.9300
(.((((((......)))))))))	chr19:57136980-57137202(+)$1	1	182	205	11.5127
((((((((......)))))).).	chr4:114682330-114682555(+)$1	1	83	106	11.5612
(((((.((......)).))))))	chr1:114696314-114696548(+)$1	1	123	146	11.5677
.((((.((......)))))).))	chr10:48438641-48438865(-)$1	1	55	78	10.8040
((((((((......))))))))(	chr1:40563005-40563228(+)$1	1	10	33	10.2705
((((((((......)))).))))	chrX:2800284-2800507(-)$1	1	68	91	10.6658
)(((((((......))))))).)	chr12:69326864-69327086(+)$1	1	102	125	11.1053
((((.(((......))).)))..	chr7:130038393-130038616(+)$1	1	160	183	13.6743
(...((((......))))...))	chr11:65308228-65308453(+)$1	1	84	107	11.5478
(.((..((......))..)).))	chr12:132623711-132623939(+)$1	1	163	186	11.4628
.(..(.((......)))..))))	chr11:62340601-62340827(+)$1	1	161	184	12.2692
(...((((......))))...))	chr14:103192929-103193152(-)$1	1	180	203	11.4994
.(((((((......)))))))))	chr15:72117896-72118124(+)$1	1	177	200	10.8603
((((..(((.....)))..))))	chr12:27573983-27574211(-)$1	1	120	143	8.7921
..((.(((......))).)))))	chr3:50131099-50131409(-)$1	1	44	67	12.8258
((((.(((......))).))..)	chr12:4835789-4836012(-)$1	1	13	36	12.1077
((((((.(......).)))))))	chr18:23615740-23615961(+)$1	1	26	49	12.7442
((((.(((......))).)))))	chr11:44957853-44958076(-)$1	1	162	185	13.2100
(..(((((......)))))))))	chr8:135725123-135725346(+)$1	1	83	106	11.9211
((((.(((......))).)))..	chr19:35616302-35616525(+)$1	1	11	34	13.2708
(((.(((.(...).))).))).)	chr14:90446801-90447030(+)$1	1	7	30	8.7768
((((((((......))).)))))	chr22:38453123-38453345(-)$1	1	71	94	13.1258
((((.(((......))).)))))	chr7:134131947-134132173(-)$1	1	112	135	14.0169
(((..(((......)))))))).	chr19:47507517-47507740(+)$1	1	120	143	12.1536
.(((((.(......).)))))))	chr17:41246212-41246435(+)$1	1	126	149	11.4359
).((((((......))).)))..	chr17:33307929-33308150(+)$1	1	170	193	10.3917
.(((((((......))).)))).	chr8:41166753-41166976(+)$1	1	155	178	12.5966
(((((.(((.....))).)))))	chr16:84599757-84599979(+)$1	1	10	33	9.0033
((((((((......)))))))))	chr20:2128298-2128524(-)$1	1	115	138	12.9410
.(((((((......)))))))..	chrX:119393906-119394128(-)$1	1	62	85	12.9051
((((((((......))).))).)	chr2:128145716-128145937(-)$1	1	44	67	13.3211
.(((((((......)))).))).	chr5:140699812-140700034(+)$1	1	41	64	11.6356
(((....(......)....))))	chr16:56623980-56624204(+)$1	1	86	109	11.8075
((((.(((......))).))))(	chr2:122125159-122125384(-)$1	1	2	25	12.6199
..((((((......)))).))..	chr1:26437749-26437971(+)$1	1	194	217	10.4299
((((((((......)))))).))	chr7:44424745-44424968(-)$1	1	29	52	11.5833

#PSSM
e : 0.24	f : 0.13	d : 0.12	c : 0.08	! : 0.08	g : 0.08	[ : 0.06	: : 0.05	h : 0.03	= : 0.03	# : 0.01	i : 0.01	" : 0.01	
g : 0.18	e : 0.13	d : 0.13	f : 0.10	! : 0.08	c : 0.08	# : 0.03	h : 0.03	[ : 0.03	a : 0.03	" : 0.03	= : 0.03	$ : 0.01	i : 0.01	: : 0.01	
g : 0.17	f : 0.15	d : 0.13	e : 0.12	c : 0.10	b : 0.06	! : 0.05	# : 0.03	h : 0.03	" : 0.03	= : 0.03	$ : 0.01	[ : 0.01	i : 0.01	
g : 0.17	e : 0.15	f : 0.15	d : 0.12	b : 0.08	c : 0.08	h : 0.03	# : 0.03	" : 0.03	! : 0.03	= : 0.03	$ : 0.01	i : 0.01	[ : 0.01	
e : 0.15	g : 0.15	[ : 0.15	f : 0.12	d : 0.12	! : 0.08	c : 0.05	h : 0.03	# : 0.03	$ : 0.01	b : 0.01	i : 0.01	a : 0.01	= : 0.01	
c : 0.32	g : 0.13	e : 0.10	[ : 0.10	d : 0.08	f : 0.06	! : 0.06	h : 0.03	$ : 0.01	a : 0.01	= : 0.01	# : 0.01	
c : 0.36	b : 0.15	g : 0.12	e : 0.08	d : 0.08	f : 0.06	h : 0.03	[ : 0.03	a : 0.01	= : 0.01	# : 0.01	
c : 0.34	b : 0.15	g : 0.12	e : 0.08	d : 0.08	f : 0.06	a : 0.05	h : 0.03	o : 0.01	[ : 0.01	= : 0.01	
o : 0.94	c : 0.03	a : 0.01	
o : 0.94	n : 0.03	l : 0.01	
o : 0.94	n : 0.03	l : 0.01	
o : 0.94	n : 0.03	l : 0.01	
o : 0.94	n : 0.03	a : 0.01	
o : 0.93	n : 0.03	a : 0.01	] : 0.01	
c : 0.36	b : 0.15	g : 0.12	e : 0.08	d : 0.08	f : 0.06	a : 0.05	h : 0.03	] : 0.01	= : 0.01	
c : 0.36	b : 0.17	g : 0.12	e : 0.08	d : 0.08	f : 0.06	h : 0.03	] : 0.03	= : 0.01	4 : 0.01	
c : 0.36	g : 0.13	e : 0.10	d : 0.10	f : 0.06	] : 0.05	2 : 0.05	h : 0.03	b : 0.01	3 : 0.01	a : 0.01	= : 0.01	4 : 0.01	
] : 0.25	2 : 0.15	g : 0.13	e : 0.12	d : 0.12	f : 0.10	h : 0.03	a : 0.01	3 : 0.01	= : 0.01	4 : 0.01	
g : 0.18	e : 0.15	f : 0.12	2 : 0.10	d : 0.08	c : 0.08	] : 0.06	3 : 0.05	b : 0.05	h : 0.03	i : 0.01	= : 0.01	4 : 0.01	
g : 0.20	f : 0.18	e : 0.12	d : 0.12	c : 0.10	b : 0.06	2 : 0.03	h : 0.03	3 : 0.03	= : 0.03	] : 0.01	i : 0.01	a : 0.01	
g : 0.20	e : 0.15	f : 0.13	c : 0.13	d : 0.10	] : 0.06	2 : 0.05	h : 0.03	3 : 0.03	= : 0.03	i : 0.01	b : 0.01	
e : 0.18	f : 0.13	d : 0.13	c : 0.10	g : 0.08	] : 0.06	: : 0.05	2 : 0.05	h : 0.03	= : 0.03	i : 0.01	a : 0.01	b : 0.01	3 : 0.01	G : 0.01	4 : 0.01	
f : 0.17	e : 0.17	c : 0.13	d : 0.10	g : 0.08	2 : 0.06	b : 0.03	] : 0.03	3 : 0.03	= : 0.03	: : 0.03	H : 0.01	i : 0.01	E : 0.01	G : 0.01	4 : 0.01	

#score	682.269332188259
#seq	58
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m1_run1.txt

#BEAR
!!ffffffuuuuuuuuuuuuffff	chr13:21364570-21364822(-)$1	252	125	149	23.1857
2bb:ddddwwwwwwwwwwwwwwdd	chr1:229568274-229568514(-)$1	240	80	104	20.2718
e[ccc[ccctttttttttttccc]	chr12:98993635-98993914(+)$1	279	177	201	22.3896
ccc[ddddvvvvvvvvvvvvvddd	chr20:49509883-49510163(-)$1	280	228	252	23.1502
c[ddddccctttttttttttccc]	chr16:16372473-16372741(+)$1	268	97	121	21.9791
iiiiiiiivvvvvvvvvvvvviii	chr4:164066871-164067114(-)$1	243	181	205	23.4133
ddd[bbwwwwwwwwwwwwwwbb]d	chr15:49426438-49426700(-)$1	262	43	67	20.7103
ffffffxxxxxxxxxxxxxxxfff	chr19:1440260-1440595(+)$1	335	244	268	18.4673
hhhhhhhvvvvvvvvvvvvvhhhh	chr12:66547066-66547302(-)$1	236	61	85	20.9458
eeeee[avvvvvvvvvvvvva]ee	chr7:64168712-64168966(+)$1	254	113	137	22.6831
d"""cccwwwwwwwwwwwwwwccc	chr10:129907073-129907410(-)$1	337	14	38	22.8528
ee[cccwwwwwwwwwwwwwwccc2	chr1:26798971-26799217(+)$1	246	126	150	22.0329
ff[eeeeewwwwwwwwwwwwwwee	chr11:8017398-8017678(+)$1	280	136	160	22.2344
gggggggwwwwwwwwwwwwwwggg	chr1:245017641-245017884(-)$1	243	209	233	22.9960
fffff[bbvvvvvvvvvvvvvbb2	chr19:20117493-20117750(-)$1	257	105	129	22.2676
ggg[dddduuuuuuuuuuuudddd	chr20:61834054-61834322(-)$1	268	152	176	23.3847
ee"""cccuuuuuuuuuuuuccc4	chr12:56693856-56694096(-)$1	240	70	94	23.6342
dggggggguuuuuuuuuuuugggg	chr8:54960500-54960765(-)$1	265	231	255	23.5411
f[ddddxxxxxxxxxxxxxxxddd	chr22:41223049-41223320(-)$1	271	36	60	18.3354
""fffffftttttttttttfffff	chr15:48784627-48784888(-)$1	261	15	39	20.9941
ffff!!bbyyyyyyyyyyyyyyyy	chr12:109017404-109017690(-)$1	286	231	255	19.9795
ccc!!cccvvvvvvvvvvvvvccc	chr1:90050170-90050429(+)$1	259	84	108	23.7808
cc!!dddduuuuuuuuuuuudddd	chr16:67708989-67709258(-)$1	269	150	174	23.3068
iiiiii[auuuuuuuuuuuua]ii	chrX:134930542-134930838(-)$1	296	81	105	24.0177
]a:eeeeewwwwwwwwwwwwwwee	chr6:27798989-27799276(-)$1	287	107	131	20.9668
dd[eeeeevvvvvvvvvvvvveee	chr5:118728740-118728984(+)$1	244	187	211	22.7078
ffffffyyyyyyyyyyyyyyyyff	chr1:197055833-197056111(-)$1	278	246	270	20.9579
3ccceeeeettttttttttteeee	chr11:62295420-62295661(-)$1	241	63	87	20.9607
b!!ddddwwwwwwwwwwwwwwddd	chr10:17271573-17271835(+)$1	262	186	210	22.1987
c"""ddddvvvvvvvvvvvvvddd	chr10:116614894-116615150(+)$1	256	200	224	23.0976
c[ffffffuuuuuuuuuuuuffff	chr1:149858593-149859013(+)$1	420	220	244	23.3227
========wwwwwwwwwwwwww==	chr9:97177402-97177644(+)$1	242	189	213	22.7563
gggggccctttttttttttcccdd	chr5:151183350-151183605(+)$1	255	123	147	22.3470
gggggggwwwwwwwwwwwwwwggg	chr11:61732844-61733104(-)$1	260	148	172	22.9960
ccc:ddddyyyyyyyyyyyyyyyy	chr19:23159696-23159963(-)$1	267	239	263	19.1606
gggg[cccuuuuuuuuuuuuccc]	chr14:57741123-57741362(+)$1	239	193	217	24.2739
d[a[ddddvvvvvvvvvvvvvddd	chr8:42938176-42938428(+)$1	252	3	27	23.1600
hhhhhh[awwwwwwwwwwwwwwa]	chr7:5567527-5567802(-)$1	275	145	169	21.7218
!ggggggguuuuuuuuuuuugggg	chr12:70178415-70178643(+)$1	228	179	203	23.5881
Fgggggggtttttttttttggggg	chr1:149812581-149812873(-)$1	292	17	41	21.1483
hh!!ddddwwwwwwwwwwwwwwdd	chr3:93783197-93783436(+)$1	239	27	51	22.2505
:ffffffvvvvvvvvvvvvvffff	chr19:11557827-11558067(+)$1	240	20	44	21.5484
hhhhhhhhwwwwwwwwwwwwwwhh	chr2:198359292-198359579(-)$1	287	110	134	20.8175
ccc!!ccctttttttttttccccc	chr3:169846498-169846755(-)$1	257	209	233	22.3345
##fffffftttttttttttfffff	chr7:27824721-27824968(+)$1	247	38	62	20.9155
GGffffffuuuuuuuuuuuuffff	chr7:75070153-75070465(-)$1	312	185	209	21.9765
fffff[bbvvvvvvvvvvvvvbb]	chr6:90383034-90383277(-)$1	243	93	117	22.5007
iggggggguuuuuuuuuuuugggg	chr12:49579197-49579552(-)$1	355	238	262	23.6758
f[cccyyyyyyyyyyyyyyyyccc	chr16:11857350-11857591(-)$1	241	94	118	21.2030
dddeeeeewwwwwwwwwwwwwwee	chr19:56109021-56109293(-)$1	272	1	25	21.7102
d[ffffffuuuuuuuuuuuuffff	chr1:24021071-24021342(+)$1	271	136	160	23.1893
a[ffffffuuuuuuuuuuuuffff	chr12:49318730-49318991(-)$1	261	143	167	23.2159
cc"""ddddtttttttttttdddd	chr6:44219055-44219318(+)$1	263	53	77	21.1603
eeee[cccuuuuuuuuuuuuccc2	chr11:763685-763991(+)$1	306	77	101	23.4032
gggggggvvvvvvvvvvvvvgggg	chr3:23960832-23961150(+)$1	318	259	283	23.1906
f!!ccc[bbtttttttttttbb]c	chr12:64813789-64814105(+)$1	316	178	202	21.3043
e[bbyyyyyyyyyyyyyyyybbee	chr2:178095898-178096155(-)$1	257	103	127	19.3770
cc####ccctttttttttttccc4	chr11:64084235-64084487(-)$1	252	79	103	21.8406
ffffffwwwwwwwwwwwwwwffff	chr18:21095811-21096053(+)$1	242	89	113	21.6726
ddddyyyyyyyyyyyyyyyydddd	chr7:8094981-8095262(+)$1	281	167	191	19.1700
]cccdddduuuuuuuuuuuudddd	chr7:99689192-99689472(+)$1	280	109	133	22.9566
gg[eeeeewwwwwwwwwwwwwwee	chr2:55461877-55462120(+)$1	243	127	151	22.4559

#otherMatches

#Seq PSSM
GCCAGGUCAAGCAGCAAACAGAUC	chr13:21364570-21364822(-)$1	252	125	149	23.1857
CCGAGGCCCCCCUCAAUCCCAAGG	chr1:229568274-229568514(-)$1	240	80	104	20.2718
UUGAAGCACUGUACAAGUUUGUGG	chr12:98993635-98993914(+)$1	279	177	201	22.3896
ACACUUCCUCAACUCAAAAGUGGA	chr20:49509883-49510163(-)$1	280	228	252	23.1502
CAUCCUCACAGAUGAUCGAGGUGC	chr16:16372473-16372741(+)$1	268	97	121	21.9791
GUUUGUAAAACAUUUCAAAUCUUA	chr4:164066871-164067114(-)$1	243	181	205	23.4133
GCUUUGGAAAUUCAAAUGUACACA	chr15:49426438-49426700(-)$1	262	43	67	20.7103
AGCUUGUUCUUCCUGGCGUCCCGA	chr19:1440260-1440595(+)$1	335	244	268	18.4673
UUUUCUCUUUUAGCCUUUCUGAGA	chr12:66547066-66547302(-)$1	236	61	85	20.9458
CUUCAGAGAAACCCUACAAAUGUG	chr7:64168712-64168966(+)$1	254	113	137	22.6831
GCAUCCUAAAAAGAGGUCAGAAGG	chr10:129907073-129907410(-)$1	337	14	38	22.8528
GCCACCAUGCCCAAGAGAAAGGUA	chr1:26798971-26799217(+)$1	246	126	150	22.0329
AGAUUGCACUCAAUGAAAAACUUG	chr11:8017398-8017678(+)$1	280	136	160	22.2344
ACUUUUUAAACAUUCCACAAGAGG	chr1:245017641-245017884(-)$1	243	209	233	22.9960
UCACACUGGAGAGAAACCAUACAA	chr19:20117493-20117750(-)$1	257	105	129	22.2676
UCACAGCUACAACCCGAAAGAGUU	chr20:61834054-61834322(-)$1	268	152	176	23.3847
CCCUUUCUUACCUCCCCACCAGAU	chr12:56693856-56694096(-)$1	240	70	94	23.6342
UUUUGCAGUGUUAAAAUGUUUUGC	chr8:54960500-54960765(-)$1	265	231	255	23.5411
GUGUCAGAAUAUUUGGGAGUAUGA	chr22:41223049-41223320(-)$1	271	36	60	18.3354
AAAUGGGGAAUAAUUAUGACUCUA	chr15:48784627-48784888(-)$1	261	15	39	20.9941
AUGGAAGCACAGACCACUCCACCA	chr12:109017404-109017690(-)$1	286	231	255	19.9795
UUAUUUGGAUCUAAGCUAUAACCA	chr1:90050170-90050429(+)$1	259	84	108	23.7808
CCCGACACCAACCAGAACCUGUGU	chr16:67708989-67709258(-)$1	269	150	174	23.3068
UCUCUGGAGAUGACCUAGAAUGCA	chrX:134930542-134930838(-)$1	296	81	105	24.0177
GCAUCUCCGGCCUCAUCUACGAGG	chr6:27798989-27799276(-)$1	287	107	131	20.9668
AGUCACAUGGACGGGUUAAUAAUG	chr5:118728740-118728984(+)$1	244	187	211	22.7078
gagcacuuaccauaaacaagaugu	chr1:197055833-197056111(-)$1	278	246	270	20.9579
AGGGAAGCUGAAGGGCCCCAAGCU	chr11:62295420-62295661(-)$1	241	63	87	20.9607
CUUCGCCAACUACAUCGACAAGGU	chr10:17271573-17271835(+)$1	262	186	210	22.1987
AUCAGGUAAUACAUUUUAAAAUAC	chr10:116614894-116615150(+)$1	256	200	224	23.0976
UGCUGGGCAAAGUCACCAUCGCCC	chr1:149858593-149859013(+)$1	420	220	244	23.3227
CACGUAUCACUGUGUAUGUCUAGA	chr9:97177402-97177644(+)$1	242	189	213	22.7563
UGAAUGUCGAAGAGAAGAAGACUC	chr5:151183350-151183605(+)$1	255	123	147	22.3470
UGAAGAACUUUGCCAAAUACUUUC	chr11:61732844-61733104(-)$1	260	148	172	22.9960
ACUACACAAAGCAAAGUAUUUCAA	chr19:23159696-23159963(-)$1	267	239	263	19.1606
UCAGGUCAAAAAAAUGACUCUGAG	chr14:57741123-57741362(+)$1	239	193	217	24.2739
cuccguuucagaaaaaaaaaaaaa	chr8:42938176-42938428(+)$1	252	3	27	23.1600
CACCCAGCACAAUGAAGAUCAAGG	chr7:5567527-5567802(-)$1	275	145	169	21.7218
GGUUGGUCUAUUUACAUCUUGGCC	chr12:70178415-70178643(+)$1	228	179	203	23.5881
CGCGGGAUUUUCAAUUAUUGUUCC	chr1:149812581-149812873(-)$1	292	17	41	21.1483
CGUUCAGUAAAUUUGUAAUAUCAC	chr3:93783197-93783436(+)$1	239	27	51	22.2505
CGUGGUGGCCUAGAUCUUGACACC	chr19:11557827-11558067(+)$1	240	20	44	21.5484
CGAUUUCUGCAAACGGAGACAAAG	chr2:198359292-198359579(-)$1	287	110	134	20.8175
CAGACUCUUCCUCCUCCACAGACU	chr3:169846498-169846755(-)$1	257	209	233	22.3345
AUACCUUGUUGUCACUUCUCAGGG	chr7:27824721-27824968(+)$1	247	38	62	20.9155
UGGAGGAAGAAGACCAAAUAUUCC	chr7:75070153-75070465(-)$1	312	185	209	21.9765
CAGGAAAGAUUUUGAAGUUUGCUC	chr6:90383034-90383277(-)$1	243	93	117	22.5007
GAGAAAGCCUACCAUGAACAGCUU	chr12:49579197-49579552(-)$1	355	238	262	23.6758
GCGAGAGACAACAGUAAAAUACUC	chr16:11857350-11857591(-)$1	241	94	118	21.2030
CUCCUCUGUCUCCCCACUACUCCA	chr19:56109021-56109293(-)$1	272	1	25	21.7102
GGAUCCAGGAACACAUCGAUCUGG	chr1:24021071-24021342(+)$1	271	136	160	23.1893
CGCUUCACAUACACUACACGGUGA	chr12:49318730-49318991(-)$1	261	143	167	23.2159
GGUCUAGCUGUUUUUUACUGAGCU	chr6:44219055-44219318(+)$1	263	53	77	21.1603
UAAAAUCUACAACUACUACAAGAA	chr11:763685-763991(+)$1	306	77	101	23.4032
UUCUUGAAUGCUUUGUCAAAUUAA	chr3:23960832-23961150(+)$1	318	259	283	23.1906
GUCAGUGCCUUGAAGUAGUUGGGG	chr12:64813789-64814105(+)$1	316	178	202	21.3043
GAGAAAGAAUUGCCUGUAAGUCCU	chr2:178095898-178096155(-)$1	257	103	127	19.3770
GGAAUCUGGACGUAUGUUCCCCAU	chr11:64084235-64084487(-)$1	252	79	103	21.8406
GCCGUGAUCUUGCUGUCUACCACG	chr18:21095811-21096053(+)$1	242	89	113	21.6726
UGGCAACCAUAUAACAAUCAGUCA	chr7:8094981-8095262(+)$1	281	167	191	19.1700
CUCGGCACCAUCACCAAAACGUGC	chr7:99689192-99689472(+)$1	280	109	133	22.9566
UGCUAAGAAAAGGAAGAAGAAGUC	chr2:55461877-55462120(+)$1	243	127	151	22.4559

#DB
..((((((............))))	chr13:21364570-21364822(-)$1	1	125	149	23.1857
.)).((((..............))	chr1:229568274-229568514(-)$1	1	80	104	20.2718
(.(((.(((...........))).	chr12:98993635-98993914(+)$1	1	177	201	22.3896
(((.((((.............)))	chr20:49509883-49510163(-)$1	1	228	252	23.1502
(.(((((((...........))).	chr16:16372473-16372741(+)$1	1	97	121	21.9791
((((((((.............)))	chr4:164066871-164067114(-)$1	1	181	205	23.4133
(((.((..............)).)	chr15:49426438-49426700(-)$1	1	43	67	20.7103
((((((...............)))	chr19:1440260-1440595(+)$1	1	244	268	18.4673
(((((((.............))))	chr12:66547066-66547302(-)$1	1	61	85	20.9458
(((((.(.............).))	chr7:64168712-64168966(+)$1	1	113	137	22.6831
(...(((..............)))	chr10:129907073-129907410(-)$1	1	14	38	22.8528
((.(((..............))).	chr1:26798971-26799217(+)$1	1	126	150	22.0329
((.(((((..............))	chr11:8017398-8017678(+)$1	1	136	160	22.2344
(((((((..............)))	chr1:245017641-245017884(-)$1	1	209	233	22.9960
(((((.((.............)).	chr19:20117493-20117750(-)$1	1	105	129	22.2676
(((.((((............))))	chr20:61834054-61834322(-)$1	1	152	176	23.3847
((...(((............))).	chr12:56693856-56694096(-)$1	1	70	94	23.6342
((((((((............))))	chr8:54960500-54960765(-)$1	1	231	255	23.5411
(.((((...............)))	chr22:41223049-41223320(-)$1	1	36	60	18.3354
..((((((...........)))))	chr15:48784627-48784888(-)$1	1	15	39	20.9941
((((..((................	chr12:109017404-109017690(-)$1	1	231	255	19.9795
(((..(((.............)))	chr1:90050170-90050429(+)$1	1	84	108	23.7808
((..((((............))))	chr16:67708989-67709258(-)$1	1	150	174	23.3068
((((((.(............).))	chrX:134930542-134930838(-)$1	1	81	105	24.0177
.).(((((..............))	chr6:27798989-27799276(-)$1	1	107	131	20.9668
((.(((((.............)))	chr5:118728740-118728984(+)$1	1	187	211	22.7078
((((((................))	chr1:197055833-197056111(-)$1	1	246	270	20.9579
.)))(((((...........))))	chr11:62295420-62295661(-)$1	1	63	87	20.9607
(..((((..............)))	chr10:17271573-17271835(+)$1	1	186	210	22.1987
(...((((.............)))	chr10:116614894-116615150(+)$1	1	200	224	23.0976
(.((((((............))))	chr1:149858593-149859013(+)$1	1	220	244	23.3227
((((((((..............))	chr9:97177402-97177644(+)$1	1	189	213	22.7563
)))))(((...........)))((	chr5:151183350-151183605(+)$1	1	123	147	22.3470
(((((((..............)))	chr11:61732844-61733104(-)$1	1	148	172	22.9960
))).((((................	chr19:23159696-23159963(-)$1	1	239	263	19.1606
((((.(((............))).	chr14:57741123-57741362(+)$1	1	193	217	24.2739
(.(.((((.............)))	chr8:42938176-42938428(+)$1	1	3	27	23.1600
((((((.(..............).	chr7:5567527-5567802(-)$1	1	145	169	21.7218
.(((((((............))))	chr12:70178415-70178643(+)$1	1	179	203	23.5881
((((((((...........)))))	chr1:149812581-149812873(-)$1	1	17	41	21.1483
((..((((..............))	chr3:93783197-93783436(+)$1	1	27	51	22.2505
.((((((.............))))	chr19:11557827-11558067(+)$1	1	20	44	21.5484
((((((((..............))	chr2:198359292-198359579(-)$1	1	110	134	20.8175
(((..(((...........)))))	chr3:169846498-169846755(-)$1	1	209	233	22.3345
..((((((...........)))))	chr7:27824721-27824968(+)$1	1	38	62	20.9155
))((((((............))))	chr7:75070153-75070465(-)$1	1	185	209	21.9765
(((((.((.............)).	chr6:90383034-90383277(-)$1	1	93	117	22.5007
((((((((............))))	chr12:49579197-49579552(-)$1	1	238	262	23.6758
(.(((................)))	chr16:11857350-11857591(-)$1	1	94	118	21.2030
((((((((..............))	chr19:56109021-56109293(-)$1	1	1	25	21.7102
(.((((((............))))	chr1:24021071-24021342(+)$1	1	136	160	23.1893
(.((((((............))))	chr12:49318730-49318991(-)$1	1	143	167	23.2159
((...((((...........))))	chr6:44219055-44219318(+)$1	1	53	77	21.1603
((((.(((............))).	chr11:763685-763991(+)$1	1	77	101	23.4032
(((((((.............))))	chr3:23960832-23961150(+)$1	1	259	283	23.1906
(..(((.((...........)).)	chr12:64813789-64814105(+)$1	1	178	202	21.3043
(.((................))))	chr2:178095898-178096155(-)$1	1	103	127	19.3770
((....(((...........))).	chr11:64084235-64084487(-)$1	1	79	103	21.8406
((((((..............))))	chr18:21095811-21096053(+)$1	1	89	113	21.6726
((((................))))	chr7:8094981-8095262(+)$1	1	167	191	19.1700
.)))((((............))))	chr7:99689192-99689472(+)$1	1	109	133	22.9566
((.(((((..............))	chr2:55461877-55462120(+)$1	1	127	151	22.4559

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

#score	1367.790668724779
#seq	62
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m3_run1.txt

#BEAR
::ddddqqqqqqqqdddd	chr2:170487223-170487540(+)$1	317	212	230	13.5234
d!!cccqqqqqqqqccc]	chr6:90368249-90368666(+)$1	417	17	35	14.2423
bb[cccqqqqqqqqccc]	chr2:113404447-113404723(+)$1	276	231	249	13.7573
c[ddddqqqqqqqqdddd	chr10:71103547-71103877(+)$1	330	159	177	15.1981
[eeeeeqqqqqqqqeeee	chr10:120801823-120802200(+)$1	377	256	274	14.0540
c!!cccqqqqqqqqccc]	chr4:57860759-57861051(+)$1	292	175	193	14.3972
b[ddddqqqqqqqqdddd	chr12:112888127-112888424(+)$1	297	87	105	15.1133
BBddddqqqqqqqqdddd	chr12:109683383-109683675(+)$1	292	183	201	13.6155
d!!cccqqqqqqqqccc4	chr12:110734398-110734699(+)$1	301	90	108	14.1903
%%ddddqqqqqqqqdddd	chr14:56094559-56094921(+)$1	362	249	267	14.1800
$$$cccqqqqqqqqcccb	chr11:985407-985694(+)$1	287	217	235	13.3751
"""cccqqqqqqqqccc3	chrX:131202389-131202709(+)$1	320	263	281	14.3556
!!ddddqqqqqqqqdddd	chr16:89952203-89952491(+)$1	288	178	196	15.4214
deeeeeqqqqqqqqeeee	chr7:134644666-134644970(+)$1	304	146	164	13.7919
cc[cccqqqqqqqqcccc	chr15:63336188-63336470(+)$1	282	164	182	13.9580
ggggggqqqqqqqqgggg	chr2:234198873-234199125(+)$1	252	149	167	13.4918
iiiiiiqqqqqqqqiiii	chr12:76446866-76447153(+)$1	287	57	75	13.6126
ggggggqqqqqqqqgggg	chr14:103412698-103412964(+)$1	266	206	224	13.4918
feeeeeqqqqqqqqeeee	chr8:101724763-101725035(+)$1	272	97	115	13.7765
======qqqqqqqq====	chr8:38879081-38879399(+)$1	318	215	233	13.9124
ffddddqqqqqqqqdddd	chr20:25264696-25264980(+)$1	284	43	61	14.6390
$$ddddqqqqqqqqdddd	chr6:35854359-35854622(+)$1	263	155	173	14.9764
c[ddddqqqqqqqqdddd	chr8:38281884-38282193(+)$1	309	134	152	15.1981
::ddddqqqqqqqqdddd	chr18:3277211-3277546(+)$1	335	148	166	13.5234
""ddddqqqqqqqqdddd	chr1:90475586-90475961(+)$1	375	294	312	15.3604
!!ddddqqqqqqqqdddd	chr12:8866350-8866668(+)$1	318	258	276	15.4214
::ddddqqqqqqqqdddd	chr12:67692717-67693046(+)$1	329	157	175	13.5234
$$ddddqqqqqqqqdddd	chrX:132458344-132458604(+)$1	260	188	206	14.9764
"""cccqqqqqqqqccc3	chr19:41784956-41785221(+)$1	265	97	115	14.3556
""ddddqqqqqqqqdddd	chr1:164532446-164532717(+)$1	271	175	193	15.3604
!eeeeeqqqqqqqqeeee	chr2:196581443-196581694(+)$1	251	50	68	14.1219
eee[bbqqqqqqqqbbee	chr7:888015-888365(+)$1	350	71	89	13.0234
eeee[aqqqqqqqqa]ee	chr1:36769511-36769765(+)$1	254	132	150	13.4527
bbddddqqqqqqqqdddd	chr10:64958226-64958495(+)$1	269	215	233	14.6583
a!!cccqqqqqqqqccc2	chr21:27269767-27270017(+)$1	250	152	170	14.2089
[eeeeeqqqqqqqqeeee	chr9:15468624-15468887(+)$1	263	73	91	14.0540
:eeeeeqqqqqqqqeeee	chr20:39795266-39795624(+)$1	358	139	157	13.2890
ccc[bbqqqqqqqqbb]c	chrX:84502441-84502765(+)$1	324	150	168	12.7980
fffcccqqqqqqqqccc]	chr1:1423138-1423467(+)$1	329	230	248	13.5244
!!ddddqqqqqqqqdddd	chr8:104778612-104778894(+)$1	282	89	107	15.4214
e[ddddqqqqqqqqdddd	chrX:153786673-153786987(+)$1	314	76	94	15.0648
e"""bbqqqqqqqqbb33	chr13:28196918-28197237(+)$1	319	206	224	12.8452
eee[bbqqqqqqqqbb]e	chr1:193110976-193111309(+)$1	333	160	178	12.8844
gccc[aqqqqqqqqaccc	chr7:33397397-33397692(+)$1	295	193	211	13.5813
b[ddddqqqqqqqqdddd	chr4:79403441-79403733(+)$1	292	174	192	15.1133
dddd[aqqqqqqqqaddd	chr6:33414308-33414701(+)$1	393	49	67	14.0401
======qqqqqqqq====	chr7:35923458-35923731(+)$1	273	134	152	13.9124
ggg[bbqqqqqqqqbb]g	chr9:15470953-15471208(+)$1	255	116	134	12.9042
iiddddqqqqqqqqdddd	chr10:27822606-27822906(+)$1	300	88	106	14.9842
!!ddddqqqqqqqqdddd	chr19:59058940-59059207(+)$1	267	172	190	15.4214
ccddddqqqqqqqqdddd	chrX:70513979-70514450(+)$1	471	343	361	14.9189
ggggggqqqqqqqqgggg	chr1:93599203-93599478(+)$1	275	215	233	13.4918
:eeeeeqqqqqqqqeeee	chr1:233362841-233363187(+)$1	346	23	41	13.2890
E:ddddqqqqqqqqdddd	chr20:17581518-17581842(+)$1	324	271	289	13.4066
======qqqqqqqq====	chr22:46747966-46748423(+)$1	457	301	319	13.9124
beeeeeqqqqqqqqeeee	chr2:234344429-234344692(+)$1	263	139	157	13.8619
gggcccqqqqqqqqccc]	chr7:33423322-33423601(+)$1	279	116	134	14.0285
ggg[bbqqqqqqqqbb]g	chr1:23383921-23384241(+)$1	320	271	289	12.9042
e"""bbqqqqqqqqbbee	chr8:103848403-103848653(+)$1	250	6	24	13.1100
ggg[bbqqqqqqqqbbgg	chr3:141632411-141632806(+)$1	395	248	266	12.9634
::ddddqqqqqqqqdddd	chr17:5250005-5250349(+)$1	344	192	210	13.5234
[eeeeeqqqqqqqqeeee	chr11:373152-373407(+)$1	255	207	225	14.0540
ggggggqqqqqqqqgggg	chr7:139060738-139061041(+)$1	303	192	210	13.4918
:eeeeeqqqqqqqqeeee	chr7:26232755-26233018(+)$1	263	46	64	13.2890
a[ddddqqqqqqqqdddd	chr17:62510324-62510652(+)$1	328	87	105	15.2511
dddcccqqqqqqqqccc]	chr7:104752484-104752849(+)$1	365	315	333	13.8496
C:ddddqqqqqqqqdddd	chr10:17271632-17271951(+)$1	319	86	104	13.3188
[eeeeeqqqqqqqqeeee	chr5:134099615-134099898(+)$1	283	123	141	14.0540
b[ddddqqqqqqqqdddd	chr9:103323649-103323939(+)$1	290	196	214	15.1133
e[ddddqqqqqqqqdddd	chr5:90002004-90002302(+)$1	298	72	90	15.0648
!eeeeeqqqqqqqqeeee	chr1:10035668-10036004(+)$1	336	134	152	14.1219
bb[cccqqqqqqqqccc]	chr17:2888200-2888567(+)$1	367	99	117	13.7573

#otherMatches

#Seq PSSM
CAUCGGAAAAAUUCCCGA	chr2:170487223-170487540(+)$1	317	212	230	13.5234
AUAAGGUGACUUCUCCUC	chr6:90368249-90368666(+)$1	417	17	35	14.2423
GUGGAGAUGUACAACUCG	chr2:113404447-113404723(+)$1	276	231	249	13.7573
UGUUGCCAACAUUCGUAA	chr10:71103547-71103877(+)$1	330	159	177	15.1981
AUCGUCUGCCCCACGACG	chr10:120801823-120802200(+)$1	377	256	274	14.0540
ACUGCCUUUUGAAUGGCU	chr4:57860759-57861051(+)$1	292	175	193	14.3972
GGUCCAGUAUUACAUGGA	chr12:112888127-112888424(+)$1	297	87	105	15.1133
GGAGCCUAACCCCUGGCU	chr12:109683383-109683675(+)$1	292	183	201	13.6155
UGCAGCGGAUUAAAGCUA	chr12:110734398-110734699(+)$1	301	90	108	14.1903
AAAUUGUCCAUAAUCAGU	chr14:56094559-56094921(+)$1	362	249	267	14.1800
CACACGUUCCUUCUCGUU	chr11:985407-985694(+)$1	287	217	235	13.3751
CACUAUCCUAGUUAAUAC	chrX:131202389-131202709(+)$1	320	263	281	14.3556
ccccgcccuucucugcgg	chr16:89952203-89952491(+)$1	288	178	196	15.4214
AGAAAGGGAAUGUGUUUU	chr7:134644666-134644970(+)$1	304	146	164	13.7919
UAAGUGCACGCUCACACU	chr15:63336188-63336470(+)$1	282	164	182	13.9580
GGAGGCACAUAAGAGUCU	chr2:234198873-234199125(+)$1	252	149	167	13.4918
AGAAGCUAAGCAAUGCUU	chr12:76446866-76447153(+)$1	287	57	75	13.6126
AAGGAUGGACUGGAGUCC	chr14:103412698-103412964(+)$1	266	206	224	13.4918
UGUUCAAUUAAAAAUGAA	chr8:101724763-101725035(+)$1	272	97	115	13.7765
UUAAAAAUGUCUCAUUUU	chr8:38879081-38879399(+)$1	318	215	233	13.9124
GAGAACAAGCUCAAGUUC	chr20:25264696-25264980(+)$1	284	43	61	14.6390
CCUGAUAUUUUAAAGUCA	chr6:35854359-35854622(+)$1	263	155	173	14.9764
AUGAUUACCUUCAAGAUC	chr8:38281884-38282193(+)$1	309	134	152	15.1981
UCCUGAAGAUGUCAUCAG	chr18:3277211-3277546(+)$1	335	148	166	13.5234
ACUUUUUAUUUUUUAAAA	chr1:90475586-90475961(+)$1	375	294	312	15.3604
GGUGCUGACAAUCGAGCA	chr12:8866350-8866668(+)$1	318	258	276	15.4214
GGUAUUGCAAAUUAAAUA	chr12:67692717-67693046(+)$1	329	157	175	13.5234
CUCUGCAUUUUCAAGUAG	chrX:132458344-132458604(+)$1	260	188	206	14.9764
UCCCUGGACUCCUGCAGC	chr19:41784956-41785221(+)$1	265	97	115	14.3556
uuauuuaaauauuaaaau	chr1:164532446-164532717(+)$1	271	175	193	15.3604
UGAUGGAUUACAUACCAU	chr2:196581443-196581694(+)$1	251	50	68	14.1219
UGGCUGGCCAGAUACACU	chr7:888015-888365(+)$1	350	71	89	13.0234
CCAGGGGAGAGAGGCGCU	chr1:36769511-36769765(+)$1	254	132	150	13.4527
AGAGAAACCAUCUAUUCU	chr10:64958226-64958495(+)$1	269	215	233	14.6583
GUCGGAAUUCUGCAUCCA	chr21:27269767-27270017(+)$1	250	152	170	14.2089
AUGCUGUCUUUGUUCAGC	chr9:15468624-15468887(+)$1	263	73	91	14.0540
CCUCAUCAGCUACUAUGA	chr20:39795266-39795624(+)$1	358	139	157	13.2890
GUGGAAGUCUUGGAUUGC	chrX:84502441-84502765(+)$1	324	150	168	12.7980
GCAGCCCUUaagcuggcu	chr1:1423138-1423467(+)$1	329	230	248	13.5244
AGCAUUCUAUUAAAAAUG	chr8:104778612-104778894(+)$1	282	89	107	15.4214
AUGGCUGAGGACAAGGCC	chrX:153786673-153786987(+)$1	314	76	94	15.0648
AAGACCAUACCCUAGGAA	chr13:28196918-28197237(+)$1	319	206	224	12.8452
AUUGUCAGCAGAGAGAGA	chr1:193110976-193111309(+)$1	333	160	178	12.8844
UCUUAGUCUCUUCCCAGG	chr7:33397397-33397692(+)$1	295	193	211	13.5813
CAGCUCAGCACAAGGAGC	chr4:79403441-79403733(+)$1	292	174	192	15.1133
GAGUACGAGGAGGAGAUU	chr6:33414308-33414701(+)$1	393	49	67	14.0401
UGAAGGUAAGAUUUUCUU	chr7:35923458-35923731(+)$1	273	134	152	13.9124
UCCAUCAAUGGGGGGAAG	chr9:15470953-15471208(+)$1	255	116	134	12.9042
UAAACUGGAUAAUUGGUU	chr10:27822606-27822906(+)$1	300	88	106	14.9842
CCAGGGCAGCAAGACCCU	chr19:59058940-59059207(+)$1	267	172	190	15.4214
CCAGCUGCUCGGAAAGCU	chrX:70513979-70514450(+)$1	471	343	361	14.9189
GAGAAGCUAGUAUUUUUU	chr1:93599203-93599478(+)$1	275	215	233	13.4918
AACUUGAAAAUGUGCAAG	chr1:233362841-233363187(+)$1	346	23	41	13.2890
CAGUUGUUGUCAUUUAAU	chr20:17581518-17581842(+)$1	324	271	289	13.4066
GAGCUGUGGCGUUUCAGC	chr22:46747966-46748423(+)$1	457	301	319	13.9124
GGGUAUGUUAAGAAAUAC	chr2:234344429-234344692(+)$1	263	139	157	13.8619
CAUCAUUUUGAGGUAUGU	chr7:33423322-33423601(+)$1	279	116	134	14.0285
GUGGAAAAUGUAAAUUGU	chr1:23383921-23384241(+)$1	320	271	289	12.9042
UAAAUCAAUAACCAGAAA	chr8:103848403-103848653(+)$1	250	6	24	13.1100
UCUUGUGAAAAUGAACAG	chr3:141632411-141632806(+)$1	395	248	266	12.9634
ACUGCGGAAAGAAUUGCA	chr17:5250005-5250349(+)$1	344	192	210	13.5234
CUUGGGAAUGAGGACCCG	chr11:373152-373407(+)$1	255	207	225	14.0540
UUACUGAUAUGCUGCAGU	chr7:139060738-139061041(+)$1	303	192	210	13.4918
CCCUUUAAGUCACAAAAG	chr7:26232755-26233018(+)$1	263	46	64	13.2890
GGAAAUAUUUGAUGGUUU	chr17:62510324-62510652(+)$1	328	87	105	15.2511
CAGUUUAACCAACAAAGU	chr7:104752484-104752849(+)$1	365	315	333	13.8496
CGCACCAACGAGAAGGUG	chr10:17271632-17271951(+)$1	319	86	104	13.3188
AGGGAUAAAAGAAGAUCU	chr5:134099615-134099898(+)$1	283	123	141	14.0540
CAAUGGUUGUUGCUCUAU	chr9:103323649-103323939(+)$1	290	196	214	15.1133
CCUGGAAUGCUGAGUCUG	chr5:90002004-90002302(+)$1	298	72	90	15.0648
AGGAGUGGAAAGAGACUC	chr1:10035668-10036004(+)$1	336	134	152	14.1219
UGAUGAGCAUGAAGUCAA	chr17:2888200-2888567(+)$1	367	99	117	13.7573

#DB
..((((........))))	chr2:170487223-170487540(+)$1	1	212	230	13.5234
(..(((........))).	chr6:90368249-90368666(+)$1	1	17	35	14.2423
((.(((........))).	chr2:113404447-113404723(+)$1	1	231	249	13.7573
(.((((........))))	chr10:71103547-71103877(+)$1	1	159	177	15.1981
.(((((........))))	chr10:120801823-120802200(+)$1	1	256	274	14.0540
(..(((........))).	chr4:57860759-57861051(+)$1	1	175	193	14.3972
(.((((........))))	chr12:112888127-112888424(+)$1	1	87	105	15.1133
))((((........))))	chr12:109683383-109683675(+)$1	1	183	201	13.6155
(..(((........))).	chr12:110734398-110734699(+)$1	1	90	108	14.1903
..((((........))))	chr14:56094559-56094921(+)$1	1	249	267	14.1800
...(((........))))	chr11:985407-985694(+)$1	1	217	235	13.3751
...(((........))).	chrX:131202389-131202709(+)$1	1	263	281	14.3556
..((((........))))	chr16:89952203-89952491(+)$1	1	178	196	15.4214
((((((........))))	chr7:134644666-134644970(+)$1	1	146	164	13.7919
((.(((........))))	chr15:63336188-63336470(+)$1	1	164	182	13.9580
((((((........))))	chr2:234198873-234199125(+)$1	1	149	167	13.4918
((((((........))))	chr12:76446866-76447153(+)$1	1	57	75	13.6126
((((((........))))	chr14:103412698-103412964(+)$1	1	206	224	13.4918
)(((((........))))	chr8:101724763-101725035(+)$1	1	97	115	13.7765
((((((........))))	chr8:38879081-38879399(+)$1	1	215	233	13.9124
((((((........))))	chr20:25264696-25264980(+)$1	1	43	61	14.6390
..((((........))))	chr6:35854359-35854622(+)$1	1	155	173	14.9764
(.((((........))))	chr8:38281884-38282193(+)$1	1	134	152	15.1981
..((((........))))	chr18:3277211-3277546(+)$1	1	148	166	13.5234
..((((........))))	chr1:90475586-90475961(+)$1	1	294	312	15.3604
..((((........))))	chr12:8866350-8866668(+)$1	1	258	276	15.4214
..((((........))))	chr12:67692717-67693046(+)$1	1	157	175	13.5234
..((((........))))	chrX:132458344-132458604(+)$1	1	188	206	14.9764
...(((........))).	chr19:41784956-41785221(+)$1	1	97	115	14.3556
..((((........))))	chr1:164532446-164532717(+)$1	1	175	193	15.3604
.(((((........))))	chr2:196581443-196581694(+)$1	1	50	68	14.1219
(((.((........))))	chr7:888015-888365(+)$1	1	71	89	13.0234
((((.(........).))	chr1:36769511-36769765(+)$1	1	132	150	13.4527
((((((........))))	chr10:64958226-64958495(+)$1	1	215	233	14.6583
(..(((........))).	chr21:27269767-27270017(+)$1	1	152	170	14.2089
.(((((........))))	chr9:15468624-15468887(+)$1	1	73	91	14.0540
.(((((........))))	chr20:39795266-39795624(+)$1	1	139	157	13.2890
(((.((........)).)	chrX:84502441-84502765(+)$1	1	150	168	12.7980
((((((........))).	chr1:1423138-1423467(+)$1	1	230	248	13.5244
..((((........))))	chr8:104778612-104778894(+)$1	1	89	107	15.4214
(.((((........))))	chrX:153786673-153786987(+)$1	1	76	94	15.0648
(...((........))..	chr13:28196918-28197237(+)$1	1	206	224	12.8452
(((.((........)).)	chr1:193110976-193111309(+)$1	1	160	178	12.8844
((((.(........))))	chr7:33397397-33397692(+)$1	1	193	211	13.5813
(.((((........))))	chr4:79403441-79403733(+)$1	1	174	192	15.1133
((((.(........))))	chr6:33414308-33414701(+)$1	1	49	67	14.0401
((((((........))))	chr7:35923458-35923731(+)$1	1	134	152	13.9124
(((.((........)).)	chr9:15470953-15471208(+)$1	1	116	134	12.9042
))((((........))))	chr10:27822606-27822906(+)$1	1	88	106	14.9842
..((((........))))	chr19:59058940-59059207(+)$1	1	172	190	15.4214
))((((........))))	chrX:70513979-70514450(+)$1	1	343	361	14.9189
((((((........))))	chr1:93599203-93599478(+)$1	1	215	233	13.4918
.(((((........))))	chr1:233362841-233363187(+)$1	1	23	41	13.2890
).((((........))))	chr20:17581518-17581842(+)$1	1	271	289	13.4066
((((((........))))	chr22:46747966-46748423(+)$1	1	301	319	13.9124
((((((........))))	chr2:234344429-234344692(+)$1	1	139	157	13.8619
((((((........))).	chr7:33423322-33423601(+)$1	1	116	134	14.0285
(((.((........)).)	chr1:23383921-23384241(+)$1	1	271	289	12.9042
(...((........))))	chr8:103848403-103848653(+)$1	1	6	24	13.1100
(((.((........))))	chr3:141632411-141632806(+)$1	1	248	266	12.9634
..((((........))))	chr17:5250005-5250349(+)$1	1	192	210	13.5234
.(((((........))))	chr11:373152-373407(+)$1	1	207	225	14.0540
((((((........))))	chr7:139060738-139061041(+)$1	1	192	210	13.4918
.(((((........))))	chr7:26232755-26233018(+)$1	1	46	64	13.2890
(.((((........))))	chr17:62510324-62510652(+)$1	1	87	105	15.2511
((((((........))).	chr7:104752484-104752849(+)$1	1	315	333	13.8496
(.((((........))))	chr10:17271632-17271951(+)$1	1	86	104	13.3188
.(((((........))))	chr5:134099615-134099898(+)$1	1	123	141	14.0540
(.((((........))))	chr9:103323649-103323939(+)$1	1	196	214	15.1133
(.((((........))))	chr5:90002004-90002302(+)$1	1	72	90	15.0648
.(((((........))))	chr1:10035668-10036004(+)$1	1	134	152	14.1219
((.(((........))).	chr17:2888200-2888567(+)$1	1	99	117	13.7573

#PSSM
g : 0.12	: : 0.09	b : 0.09	e : 0.09	c : 0.08	! : 0.08	d : 0.06	[ : 0.05	" : 0.05	$ : 0.04	f : 0.04	= : 0.04	i : 0.02	a : 0.02	B : 0.01	% : 0.01	E : 0.01	C : 0.01	
e : 0.20	! : 0.11	[ : 0.11	g : 0.11	: : 0.08	" : 0.08	c : 0.05	b : 0.04	$ : 0.04	= : 0.04	i : 0.02	f : 0.02	d : 0.02	B : 0.01	% : 0.01	
d : 0.41	e : 0.20	g : 0.11	! : 0.05	" : 0.05	[ : 0.04	= : 0.04	c : 0.02	$ : 0.01	i : 0.01	f : 0.01	
d : 0.40	c : 0.19	e : 0.18	[ : 0.08	g : 0.05	= : 0.04	" : 0.02	i : 0.01	
d : 0.38	c : 0.18	e : 0.16	b : 0.11	g : 0.05	= : 0.04	[ : 0.04	i : 0.01	
d : 0.38	c : 0.18	e : 0.16	b : 0.11	g : 0.05	= : 0.04	a : 0.04	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.38	c : 0.18	e : 0.16	b : 0.11	g : 0.05	= : 0.04	a : 0.04	i : 0.01	
d : 0.40	c : 0.19	e : 0.16	b : 0.11	g : 0.05	= : 0.04	i : 0.01	] : 0.01	
d : 0.40	e : 0.20	c : 0.19	g : 0.06	] : 0.05	= : 0.04	i : 0.01	3 : 0.01	
d : 0.40	e : 0.22	] : 0.09	g : 0.09	3 : 0.04	c : 0.04	= : 0.04	4 : 0.01	b : 0.01	i : 0.01	2 : 0.01	

#score	1012.8756456688681
#seq	72
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m3_run2.txt

#BEAR
!ddddqqqqqqqqddddee	chr16:8953025-8953242(-)$1	217	167	186	13.5243
eeeeeqqqqqqqqeeeee:	chr12:121078945-121079174(+)$1	229	129	148	12.7591
cccccqqqqqqqqccc22c	chr6:31238078-31238296(-)$1	218	187	206	14.2884
bb[bbqqqqqqqqbbbb]b	chr20:44691401-44691618(-)$1	217	100	119	12.6993
b!!bbqqqqqqqqbb22bb	chr1:8926419-8926657(-)$1	238	159	178	13.1874
eeeeeqqqqqqqqeeeee]	chr4:110772564-110772787(+)$1	223	133	152	13.6694
fff[aqqqqqqqqafffff	chr17:4891716-4891935(+)$1	219	167	186	14.0831
fffffqqqqqqqqffffff	chrX:100103510-100103731(+)$1	221	167	186	13.8275
gggggqqqqqqqqgggggg	chr16:70913551-70913781(+)$1	230	51	70	14.3400
a[cccqqqqqqqqccc]a]	chr19:648277-648492(-)$1	215	92	111	14.6987
ff[bbqqqqqqqqbb]fff	chr14:101295425-101295646(+)$1	221	174	193	13.9362
====aqqqqqqqqa]====	chr13:95363798-95364021(-)$1	223	86	105	14.4858
&&cccqqqqqqqqccc444	chr9:87317014-87317242(+)$1	228	43	62	13.3821
cccbbqqqqqqqqbb]ccc	chr11:43964340-43964566(+)$1	226	148	167	13.9581
eeeeeqqqqqqqqeeeee]	chr6:43399738-43399971(+)$1	233	89	108	13.6694
$$cccqqqqqqqqccc22c	chr12:21799825-21800044(-)$1	219	186	205	13.9854
i"""aqqqqqqqqa333ii	chr1:103345153-103345377(-)$1	224	45	64	14.2054
g!!bbqqqqqqqqbb22gg	chr11:12923467-12923685(-)$1	218	58	77	13.9380
[ddddqqqqqqqqdddd]d	chr1:27480380-27480613(-)$1	233	16	35	13.6291
ffcccqqqqqqqqccc444	chr14:65253110-65253336(-)$1	226	23	42	14.5353
ddd[aqqqqqqqqadddd2	chr8:23147607-23147826(+)$1	219	125	144	13.4530
$$cccqqqqqqqqccc444	chr22:19026483-19026702(-)$1	219	62	81	14.2280
[ddddqqqqqqqqdddd]e	chrX:19947832-19948065(-)$1	233	130	149	13.6444
!!cccqqqqqqqqccc22d	chr7:5568044-5568283(-)$1	239	179	198	14.4358
fffffqqqqqqqqffffff	chr1:145534867-145535082(+)$1	215	181	200	13.8275
bbcccqqqqqqqqccc]bb	chr16:142568-142789(-)$1	221	33	52	13.6809
d!!bbqqqqqqqqbb22dd	chr2:241658423-241658641(-)$1	218	28	47	13.4420
##cccqqqqqqqqccc444	chr12:133303882-133304101(-)$1	219	48	67	14.5696
fffffqqqqqqqqffffff	chr2:96040044-96040267(+)$1	223	8	27	13.8275
c!!bbqqqqqqqqbb]ccc	chrX:101153005-101153221(-)$1	216	75	94	14.0851
eeeeeqqqqqqqqeeeeeb	chr5:756006-756235(-)$1	229	155	174	13.4306
gggggqqqqqqqqgggggg	chr15:63881057-63881278(+)$1	221	76	95	14.3400
d[cccqqqqqqqqccc]dd	chr7:1477746-1477964(-)$1	218	14	33	14.3433
[ddddqqqqqqqqdddd]d	chr12:10124139-10124357(-)$1	218	11	30	13.6291
[cccaqqqqqqqqa]ccc]	chr22:42266898-42267118(+)$1	220	128	147	14.4653
gggggqqqqqqqqgggggg	chr17:1630765-1630987(+)$1	222	33	52	14.3400
iiiiiqqqqqqqqiiiiii	chr2:32476471-32476686(-)$1	215	155	174	14.1186
b!!bbqqqqqqqqbb]bbd	chr17:72959758-72959974(-)$1	216	17	36	13.2135
cccbbqqqqqqqqbb]ccc	chr9:136259384-136259599(+)$1	215	124	143	13.9581
[ddddqqqqqqqqddddgg	chr14:50582483-50582711(-)$1	228	40	59	13.7239
gggggqqqqqqqqgggggg	chr8:104419795-104420013(-)$1	218	141	160	14.3400
gggggqqqqqqqqgggggg	chr8:103341449-103341677(-)$1	228	120	139	14.3400
eeeeeqqqqqqqqeeeee]	chr17:27869689-27869912(+)$1	223	89	108	13.6694
+ddddqqqqqqqqdddd>>	chr8:80677487-80677707(-)$1	220	142	161	12.5714
d[cccqqqqqqqqccc]dd	chr4:113567429-113567644(+)$1	215	13	32	14.3433
!ddddqqqqqqqqdddd22	chr17:54939426-54939650(+)$1	224	151	170	13.3537
eeeeeqqqqqqqqeeeee]	chr19:5914972-5915191(-)$1	219	151	170	13.6694
fffffqqqqqqqqffffff	chr7:22175582-22175805(+)$1	223	25	44	13.8275
dddbbqqqqqqqqbb]ddd	chrM:8870-9090(+)$1	220	152	171	13.3695
!ddddqqqqqqqqddddbb	chr22:32590325-32590542(+)$1	217	102	121	13.2078
dddbbqqqqqqqqbb]ddd	chr15:65628126-65628343(-)$1	217	52	71	13.3695
ggg[aqqqqqqqqa]gggg	chr2:97403563-97403793(-)$1	230	54	73	14.3535
bcccaqqqqqqqqa]ccc5	chr21:44296723-44296938(+)$1	215	32	51	13.3174
eecccqqqqqqqqccc]ee	chr7:44104618-44104833(+)$1	215	12	31	14.4235
[ddddqqqqqqqqdddd]d	chr17:6663739-6663959(+)$1	220	19	38	13.6291
c!!bbqqqqqqqqbb22cc	chr6:116573913-116574137(-)$1	224	109	128	13.8128
c[cccqqqqqqqqccc]cc	chr19:36237266-36237488(+)$1	222	53	72	14.7140
$$cccqqqqqqqqccc444	chr4:71555353-71555575(+)$1	222	40	59	14.2280
fffffqqqqqqqqffffff	chr14:64749513-64749731(+)$1	218	19	38	13.8275
[ddddqqqqqqqqdddd]a	chr12:56398637-56398857(+)$1	220	41	60	13.7142
eeeeeqqqqqqqqeeeee:	chr14:105246390-105246609(-)$1	219	100	119	12.7591
gggggqqqqqqqqgggggg	chr2:241684817-241685038(-)$1	221	161	180	14.3400
gggggqqqqqqqqgggggg	chr16:30780586-30780819(+)$1	233	147	166	14.3400
fff[aqqqqqqqqafffff	chr19:1827664-1827881(-)$1	217	133	152	14.0831
eeeeeqqqqqqqqeeeeeb	chr16:67181188-67181420(+)$1	232	188	207	13.4306
bbcccqqqqqqqqccc]bb	chr10:97096236-97096453(-)$1	217	181	200	13.6809
ee[bbqqqqqqqqbbeeee	chr20:61980921-61981145(-)$1	224	123	142	13.7191
fffffqqqqqqqqffffff	chr3:184144319-184144536(+)$1	217	3	22	13.8275
ccc[aqqqqqqqqaccc22	chr10:73579953-73580182(-)$1	229	97	116	14.0710
fffffqqqqqqqqffffff	chr4:128590153-128590370(+)$1	217	134	153	13.8275
eeeeeqqqqqqqqeeeee:	chr17:19290068-19290291(+)$1	223	127	146	12.7591
gg[bbqqqqqqqqbbgggg	chr3:47161679-47161898(-)$1	219	19	38	14.1684
f[cccqqqqqqqqcccfff	chr11:1025145-1025366(+)$1	221	118	137	14.5844
fffffqqqqqqqqffffff	chr12:49432455-49432679(-)$1	224	103	122	13.8275
gggggqqqqqqqqgggggg	chr11:9771338-9771558(-)$1	220	163	182	14.3400
fffffqqqqqqqqffffff	chr8:104210238-104210463(+)$1	225	173	192	13.8275

#otherMatches

#Seq PSSM
CGUGGUCCCAAGCCCACUG	chr16:8953025-8953242(-)$1	217	167	186	13.5243
CCGCCGCGUCCGAGGCGGA	chr12:121078945-121079174(+)$1	229	129	148	12.7591
GGCCAGCAGGAGAUGGAAC	chr6:31238078-31238296(-)$1	218	187	206	14.2884
CCGCCAACCACUCGGGGCG	chr20:44691401-44691618(-)$1	217	100	119	12.6993
GAUCCUCCCAGUCGGUGCA	chr1:8926419-8926657(-)$1	238	159	178	13.1874
CUACGAACCUCCCCGUGGA	chr4:110772564-110772787(+)$1	223	133	152	13.6694
AAAAGUAGGUCUUCUUUCC	chr17:4891716-4891935(+)$1	219	167	186	14.0831
GGUUUUCUGUUUCAGACCU	chrX:100103510-100103731(+)$1	221	167	186	13.8275
GGCAAUGCACAUCUUGCUG	chr16:70913551-70913781(+)$1	230	51	70	14.3400
ACGGCUGCAUCGUGCCCUG	chr19:648277-648492(-)$1	215	92	111	14.6987
CUUGUGUUCACCUGCUAGC	chr14:101295425-101295646(+)$1	221	174	193	13.9362
cggccUGGUGCCUGAGUCG	chr13:95363798-95364021(-)$1	223	86	105	14.4858
CUCUGCUUUGUUACAGUUU	chr9:87317014-87317242(+)$1	228	43	62	13.3821
GCUCCAGUUACCAGGCGGU	chr11:43964340-43964566(+)$1	226	148	167	13.9581
UGGCUCCUGAGUCAGCCAC	chr6:43399738-43399971(+)$1	233	89	108	13.6694
GACACCUAAAAUUGUGGCA	chr12:21799825-21800044(-)$1	219	186	205	13.9854
UUAUGACAAAGCACUUCGC	chr1:103345153-103345377(-)$1	224	45	64	14.2054
GCCCUUUCCAAACAGUUCC	chr11:12923467-12923685(-)$1	218	58	77	13.9380
UCCGUCACUGAUCAUGGCA	chr1:27480380-27480613(-)$1	233	16	35	13.6291
GGGGAGAAAGUGAUCCAAG	chr14:65253110-65253336(-)$1	226	23	42	14.5353
GUGUGAGAAUGAGCCACUG	chr8:23147607-23147826(+)$1	219	125	144	13.4530
CUGCAGACGAUGAUGCUUU	chr22:19026483-19026702(-)$1	219	62	81	14.2280
AAGUUCAGAGAAAGAUUAA	chrX:19947832-19948065(-)$1	233	130	149	13.6444
GCCGAGCGGGAAAUCGUGC	chr7:5568044-5568283(-)$1	239	179	198	14.4358
acagcauagcauagcuguu	chr1:145534867-145535082(+)$1	215	181	200	13.8275
GCUGCACUCACUGGCAUGC	chr16:142568-142789(-)$1	221	33	52	13.6809
CGAUCGUUUCCAAGAAGGG	chr2:241658423-241658641(-)$1	218	28	47	13.4420
ACAGUUCUUUCUUGCUUUC	chr12:133303882-133304101(-)$1	219	48	67	14.5696
ACAGUGAGCUGGAGCUGUC	chr2:96040044-96040267(+)$1	223	8	27	13.8275
GGAACAAAAUGAAGUGCCU	chrX:101153005-101153221(-)$1	216	75	94	14.0851
GUGAGUGCCCGCCCUCGCC	chr5:756006-756235(-)$1	229	155	174	13.4306
GUUCUGUAGCCUGAGAACA	chr15:63881057-63881278(+)$1	221	76	95	14.3400
GCGAGACGGUGACCUCCCC	chr7:1477746-1477964(-)$1	218	14	33	14.3433
CAAGUCUAUAACCACUUCU	chr12:10124139-10124357(-)$1	218	11	30	13.6291
CCUUCAAGUACCAGUAAGA	chr22:42266898-42267118(+)$1	220	128	147	14.4653
GGCCUGUCUCCCAGGGCCU	chr17:1630765-1630987(+)$1	222	33	52	14.3400
CACAGAACCUGUCCUGUGG	chr2:32476471-32476686(-)$1	215	155	174	14.1186
AAGGAGAAGCAGAUCGUCC	chr17:72959758-72959974(-)$1	216	17	36	13.2135
GGACAUGACCAGCUGCUCC	chr9:136259384-136259599(+)$1	215	124	143	13.9581
GAAUUAUUAAAACAAUUGA	chr14:50582483-50582711(-)$1	228	40	59	13.7239
UACUUUUUCUUGUGAGUAG	chr8:104419795-104420013(-)$1	218	141	160	14.3400
UUUAUCAGUGGAAAUGGAG	chr8:103341449-103341677(-)$1	228	120	139	14.3400
UGGGGGUCCAGGACCUCAC	chr17:27869689-27869912(+)$1	223	89	108	13.6694
UGGCCUCCCUGUCGGCCUU	chr8:80677487-80677707(-)$1	220	142	161	12.5714
AAUUGUACCAAAUUGAAUU	chr4:113567429-113567644(+)$1	215	13	32	14.3433
AUCCUUUUCGAAUAGGACA	chr17:54939426-54939650(+)$1	224	151	170	13.3537
GUCGUCCACCGUCACGACG	chr19:5914972-5915191(-)$1	219	151	170	13.6694
AUUUCUGAAAUAUGAAAUU	chr7:22175582-22175805(+)$1	223	25	44	13.8275
GCAGGCCACCUACUCAUGC	chrM:8870-9090(+)$1	220	152	171	13.3695
UCCCACCUCCCACUGGGUC	chr22:32590325-32590542(+)$1	217	102	121	13.2078
UGUCGGACUUCCACGUGCA	chr15:65628126-65628343(-)$1	217	52	71	13.3695
AUCCGCCUUACCCCAGAUA	chr2:97403563-97403793(-)$1	230	54	73	14.3535
UGGUCCCAUUAUCGAACCA	chr21:44296723-44296938(+)$1	215	32	51	13.3174
UGCUUUCCCUCCCAAGCCA	chr7:44104618-44104833(+)$1	215	12	31	14.4235
AGUUCUGCAAACUGGACAU	chr17:6663739-6663959(+)$1	220	19	38	13.6291
CUACAAUACUACCUGAUGG	chr6:116573913-116574137(-)$1	224	109	128	13.8128
GGGGGUUUGCUUUCCUGCC	chr19:36237266-36237488(+)$1	222	53	72	14.7140
AAGAAAGAACUGAUUCCAA	chr4:71555353-71555575(+)$1	222	40	59	14.2280
GCUGUAAUUCAUCACAGCA	chr14:64749513-64749731(+)$1	218	19	38	13.8275
GGAACUGAACAUUGUUUGU	chr12:56398637-56398857(+)$1	220	41	60	13.7142
AAUGAUGGCACCUUCAUUG	chr14:105246390-105246609(-)$1	219	100	119	12.7591
AGGCCCCCCACUUGGCUUC	chr2:241684817-241685038(-)$1	221	161	180	14.3400
AGCUUGCAGACUGGAGCUG	chr16:30780586-30780819(+)$1	233	147	166	14.3400
GGGACCUCCAGCCGCCCCC	chr19:1827664-1827881(-)$1	217	133	152	14.0831
CUGUGACUGAGGACACAGG	chr16:67181188-67181420(+)$1	232	188	207	13.4306
ACUGCAGCAUGCCGCGUGU	chr10:97096236-97096453(-)$1	217	181	200	13.6809
GAAGACACAGACUUCUCGG	chr20:61980921-61981145(-)$1	224	123	142	13.7191
AUUGUAAAUCUUAAUAAUG	chr3:184144319-184144536(+)$1	217	3	22	13.8275
AGGUCCCAGCAAAGUCUGA	chr10:73579953-73580182(-)$1	229	97	116	14.0710
UAACUGGGACACAAGUUAC	chr4:128590153-128590370(+)$1	217	134	153	13.8275
AGAGAUCCCCUGUUCUCUU	chr17:19290068-19290291(+)$1	223	127	146	12.7591
AAAGUGAUGGUGAGCUUCA	chr3:47161679-47161898(-)$1	219	19	38	14.1684
AUGUCCACGACAAGGCUCA	chr11:1025145-1025366(+)$1	221	118	137	14.5844
GCGGGAAUUUCCACCCGUC	chr12:49432455-49432679(-)$1	224	103	122	13.8275
GCUUUAAAUACAGGAAGUA	chr11:9771338-9771558(-)$1	220	163	182	14.3400
UGUAAAAUAGGCAUUGCAA	chr8:104210238-104210463(+)$1	225	173	192	13.8275

#DB
.((((........))))))	chr16:8953025-8953242(-)$1	1	167	186	13.5243
(((((........))))).	chr12:121078945-121079174(+)$1	1	129	148	12.7591
(((((........)))..)	chr6:31238078-31238296(-)$1	1	187	206	14.2884
((.((........)))).)	chr20:44691401-44691618(-)$1	1	100	119	12.6993
(..((........))..))	chr1:8926419-8926657(-)$1	1	159	178	13.1874
(((((........))))).	chr4:110772564-110772787(+)$1	1	133	152	13.6694
(((.(........))))))	chr17:4891716-4891935(+)$1	1	167	186	14.0831
(((((........))))))	chrX:100103510-100103731(+)$1	1	167	186	13.8275
(((((........))))))	chr16:70913551-70913781(+)$1	1	51	70	14.3400
(.(((........))).).	chr19:648277-648492(-)$1	1	92	111	14.6987
((.((........)).)))	chr14:101295425-101295646(+)$1	1	174	193	13.9362
(((((........).))))	chr13:95363798-95364021(-)$1	1	86	105	14.4858
..(((........)))...	chr9:87317014-87317242(+)$1	1	43	62	13.3821
(((((........)).)))	chr11:43964340-43964566(+)$1	1	148	167	13.9581
(((((........))))).	chr6:43399738-43399971(+)$1	1	89	108	13.6694
..(((........)))..)	chr12:21799825-21800044(-)$1	1	186	205	13.9854
(...(........)...))	chr1:103345153-103345377(-)$1	1	45	64	14.2054
(..((........))..))	chr11:12923467-12923685(-)$1	1	58	77	13.9380
.((((........)))).)	chr1:27480380-27480613(-)$1	1	16	35	13.6291
(((((........)))...	chr14:65253110-65253336(-)$1	1	23	42	14.5353
(((.(........))))).	chr8:23147607-23147826(+)$1	1	125	144	13.4530
..(((........)))...	chr22:19026483-19026702(-)$1	1	62	81	14.2280
.((((........)))).)	chrX:19947832-19948065(-)$1	1	130	149	13.6444
..(((........)))..)	chr7:5568044-5568283(-)$1	1	179	198	14.4358
(((((........))))))	chr1:145534867-145535082(+)$1	1	181	200	13.8275
(((((........))).))	chr16:142568-142789(-)$1	1	33	52	13.6809
(..((........))..))	chr2:241658423-241658641(-)$1	1	28	47	13.4420
..(((........)))...	chr12:133303882-133304101(-)$1	1	48	67	14.5696
(((((........))))))	chr2:96040044-96040267(+)$1	1	8	27	13.8275
(..((........)).)))	chrX:101153005-101153221(-)$1	1	75	94	14.0851
(((((........))))))	chr5:756006-756235(-)$1	1	155	174	13.4306
(((((........))))))	chr15:63881057-63881278(+)$1	1	76	95	14.3400
(.(((........))).))	chr7:1477746-1477964(-)$1	1	14	33	14.3433
.((((........)))).)	chr12:10124139-10124357(-)$1	1	11	30	13.6291
.((((........).))).	chr22:42266898-42267118(+)$1	1	128	147	14.4653
(((((........))))))	chr17:1630765-1630987(+)$1	1	33	52	14.3400
(((((........))))))	chr2:32476471-32476686(-)$1	1	155	174	14.1186
(..((........)).)))	chr17:72959758-72959974(-)$1	1	17	36	13.2135
(((((........)).)))	chr9:136259384-136259599(+)$1	1	124	143	13.9581
.((((........))))))	chr14:50582483-50582711(-)$1	1	40	59	13.7239
(((((........))))))	chr8:104419795-104420013(-)$1	1	141	160	14.3400
(((((........))))))	chr8:103341449-103341677(-)$1	1	120	139	14.3400
(((((........))))).	chr17:27869689-27869912(+)$1	1	89	108	13.6694
.((((........))))..	chr8:80677487-80677707(-)$1	1	142	161	12.5714
(.(((........))).))	chr4:113567429-113567644(+)$1	1	13	32	14.3433
.((((........))))..	chr17:54939426-54939650(+)$1	1	151	170	13.3537
(((((........))))).	chr19:5914972-5915191(-)$1	1	151	170	13.6694
(((((........))))))	chr7:22175582-22175805(+)$1	1	25	44	13.8275
(((((........)).)))	chrM:8870-9090(+)$1	1	152	171	13.3695
.((((........))))))	chr22:32590325-32590542(+)$1	1	102	121	13.2078
(((((........)).)))	chr15:65628126-65628343(-)$1	1	52	71	13.3695
(((.(........).))))	chr2:97403563-97403793(-)$1	1	54	73	14.3535
(((((........).))).	chr21:44296723-44296938(+)$1	1	32	51	13.3174
(((((........))).))	chr7:44104618-44104833(+)$1	1	12	31	14.4235
.((((........)))).)	chr17:6663739-6663959(+)$1	1	19	38	13.6291
(..((........))..))	chr6:116573913-116574137(-)$1	1	109	128	13.8128
(.(((........))).))	chr19:36237266-36237488(+)$1	1	53	72	14.7140
..(((........)))...	chr4:71555353-71555575(+)$1	1	40	59	14.2280
(((((........))))))	chr14:64749513-64749731(+)$1	1	19	38	13.8275
.((((........)))).)	chr12:56398637-56398857(+)$1	1	41	60	13.7142
(((((........))))).	chr14:105246390-105246609(-)$1	1	100	119	12.7591
(((((........))))))	chr2:241684817-241685038(-)$1	1	161	180	14.3400
(((((........))))))	chr16:30780586-30780819(+)$1	1	147	166	14.3400
(((.(........))))))	chr19:1827664-1827881(-)$1	1	133	152	14.0831
(((((........))))))	chr16:67181188-67181420(+)$1	1	188	207	13.4306
(((((........))).))	chr10:97096236-97096453(-)$1	1	181	200	13.6809
((.((........))))))	chr20:61980921-61981145(-)$1	1	123	142	13.7191
(((((........))))))	chr3:184144319-184144536(+)$1	1	3	22	13.8275
(((.(........))))..	chr10:73579953-73580182(-)$1	1	97	116	14.0710
(((((........))))))	chr4:128590153-128590370(+)$1	1	134	153	13.8275
(((((........))))).	chr17:19290068-19290291(+)$1	1	127	146	12.7591
((.((........))))))	chr3:47161679-47161898(-)$1	1	19	38	14.1684
(.(((........))))))	chr11:1025145-1025366(+)$1	1	118	137	14.5844
(((((........))))))	chr12:49432455-49432679(-)$1	1	103	122	13.8275
(((((........))))))	chr11:9771338-9771558(-)$1	1	163	182	14.3400
(((((........))))))	chr8:104210238-104210463(+)$1	1	173	192	13.8275

#PSSM
f : 0.18	e : 0.14	g : 0.14	c : 0.09	[ : 0.09	b : 0.07	d : 0.07	! : 0.05	$ : 0.03	i : 0.02	a : 0.01	= : 0.01	& : 0.01	# : 0.01	+ : 0.01	
d : 0.17	f : 0.17	e : 0.14	g : 0.13	! : 0.09	c : 0.07	[ : 0.06	b : 0.03	$ : 0.03	= : 0.01	& : 0.01	" : 0.01	# : 0.01	i : 0.01	
c : 0.27	d : 0.17	f : 0.14	e : 0.11	g : 0.11	! : 0.07	[ : 0.05	= : 0.01	" : 0.01	i : 0.01	
c : 0.23	b : 0.18	d : 0.13	e : 0.11	f : 0.11	g : 0.10	[ : 0.06	= : 0.01	" : 0.01	i : 0.01	
c : 0.21	b : 0.18	d : 0.13	e : 0.11	a : 0.11	f : 0.11	g : 0.10	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.21	b : 0.18	d : 0.13	e : 0.11	a : 0.11	f : 0.11	g : 0.10	i : 0.01	
c : 0.22	b : 0.18	d : 0.14	f : 0.14	e : 0.11	g : 0.10	] : 0.05	3 : 0.01	i : 0.01	
c : 0.24	d : 0.14	f : 0.14	e : 0.13	g : 0.13	] : 0.09	2 : 0.05	b : 0.01	= : 0.01	3 : 0.01	i : 0.01	
d : 0.17	f : 0.17	e : 0.13	g : 0.13	2 : 0.09	] : 0.09	c : 0.07	4 : 0.06	b : 0.02	= : 0.01	3 : 0.01	i : 0.01	
f : 0.17	e : 0.15	g : 0.15	c : 0.09	] : 0.07	d : 0.07	2 : 0.06	b : 0.06	4 : 0.06	i : 0.02	a : 0.01	= : 0.01	> : 0.01	
f : 0.17	g : 0.15	d : 0.13	c : 0.09	b : 0.09	] : 0.07	4 : 0.06	e : 0.05	: : 0.03	2 : 0.03	i : 0.02	= : 0.01	> : 0.01	5 : 0.01	a : 0.01	

#score	1053.2284620753967
#seq	76
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m1_run2.txt

#BEAR
"bb[eeeee####bbnnnnnbb4444eeeee22bb	chr9:340100-340318(+)$1	218	77	112	13.4044
iiiiiiii[bb[ccclllcccbbiiiiiiiii:ff	chr3:47462092-47462316(+)$1	224	76	111	11.3823
e[a"""eeeeeddddnnnnndddd22eeeee]a]e	chr6:26468090-26468321(+)$1	231	116	151	12.4010
dd[ccc[dddd!!bbnnnnnbb]dddd]cccdddd	chr17:45623174-45623395(+)$1	221	79	114	12.5668
ffffff!!ccc!!bboooooobbcccffffff]a:	chr19:1421148-1421377(+)$1	229	15	50	11.3541
e!!bb[bb"""ddddnnnnndddd22bb333bb22	chr11:8985670-8985890(-)$1	220	123	158	12.7679
=========="""bboooooobb]===========	chr17:40761083-40761310(-)$1	227	22	57	15.6687
ggggggg"""ddddoooooodddd4444ggggggg	chr17:56387884-56388100(-)$1	216	6	41	13.7936
iiiiiiiii!!ddddnnnnndddd4444iiiiiii	chr2:226447517-226447732(-)$1	215	141	176	15.4907
c[bb####gggggggnnnnnggggggg]bb]ccc:	chr4:68610257-68610475(-)$1	218	158	193	12.1556
::iiiiiiiii!!bbnnnnnbb]iiiiiiiiiiii	chr6:34497445-34497677(+)$1	232	91	126	13.3425
ff$$$$$ccc[ddddnnnnndddd22ccc333fff	chr17:76089673-76089896(+)$1	223	5	40	13.2463
dddeeeeebbcccbbnnnnnbb]ccc]bb]eeeee	chr2:25466717-25466938(-)$1	221	120	155	11.9422
iii"""bb!!a[cccooooooccc]a22bb]iiii	chr11:65389724-65389939(-)$1	215	152	187	14.1893
ddd"""dddd!!cccnnnnnccc22dddddddd22	chr4:89602285-89602502(+)$1	217	37	72	12.4048
((eeeee$$$$$cccnnnnnccc4444eeeeeggg	chr16:2814073-2814309(+)$1	236	67	102	12.6070
ccggggggg!!ddddooooooddddggggggg]cc	chrX:47086749-47086965(+)$1	216	178	213	12.4625
===========[cccnnnnnccc============	chr7:122000892-122001114(-)$1	222	165	200	16.9545
fffccc[bb####bbnnnnnbb4444bb]ccc]ff	chr10:88990602-88990831(-)$1	229	154	189	14.4187
[ggggggg!!a[ddddmmmmdddd]a]ggggggg]	chr16:8906830-8907046(+)$1	216	13	48	11.4073
eee[ccc[bb!!bboooooobb333bb]ccceeee	chr1:36053918-36054139(+)$1	221	128	163	13.0570
====="""bbeeeeennnnneeeee4444bb333=	chr1:22986001-22986224(+)$1	223	78	113	13.3861
========[a!!bboooooobb333a]========	chr19:51021621-51021840(-)$1	219	149	184	16.1776
e!!ccc[a[bb[cccmmmmcccbb]a]ccceeeee	chr16:552904-553122(+)$1	218	129	164	10.7643
ff"""bb[ccc!!bboooooobb]ccc]bb333ff	chr16:1827016-1827242(+)$1	226	187	222	13.3667
ff[ccc[bb"""bboooooobb4444bb]ccc]ff	chr7:78256395-78256610(-)$1	215	54	89	13.5643
!!cccbb[ccc[bboooooobb]ccc]bb333ccc	chr3:47957836-47958071(-)$1	235	89	124	13.1856
[eeeee!!bb[ddddnnnnndddd333bb333eee	chr13:77566211-77566429(+)$1	218	135	170	14.2446
eeeee[a[bb!!cccnnnnnccc22bb]a]eeeee	chr3:118865382-118865599(+)$1	217	178	213	13.9418
"""ccc"""bb!!bboooooobb22bb]ccc22cc	chr13:115090684-115090900(+)$1	216	34	69	13.5966
b[ffffff[a[ddddnnnnndddd]affffff]bb	chr17:61678455-61678675(+)$1	220	51	86	12.0192
fffffdddd"""cccnnnnncccdddd]ffffff:	chr2:74275107-74275332(+)$1	225	42	77	12.0040
b"""bb"""ccccccnnnnnccc]ccc]bb]bb]b	chr6:152621745-152621968(-)$1	223	113	148	13.8800
ggg[a[ccc"""ddddmmmmdddd22ccc]agggg	chr11:118868873-118869094(+)$1	221	7	42	11.2139
dd[eeeee####cccnnnnnccc4444eeeeeddd	chr16:58231460-58231681(+)$1	221	65	100	14.0431
b!!bb[bbbb[ddddnnnnndddd]bb]bb]bbbb	chr20:43532620-43532843(+)$1	223	163	198	11.6880
"""ccc!!ccc[bboooooobbccc]ccc333bbb	chr11:65618712-65618928(+)$1	216	154	189	13.6154
[dddd####bb[cccooooooccc333bb333ddd	chr4:139966193-139966411(+)$1	218	72	107	14.1081
ggggeeeee[a[bboooooobb]a]eeeee333gg	chr1:115053277-115053499(-)$1	222	65	100	12.7689
!dddd"""dddd[bbnnnnnbb]dddd]dddd22b	chr13:99100454-99100677(+)$1	223	44	79	12.1600
[bb[a####ccc[bbnnnnnbbccca]bb]cccdd	chr5:44809226-44809452(+)$1	226	121	156	14.0257
ff$$$$$==========lll==========22fff	chr1:149879134-149879364(-)$1	230	156	191	11.9047
iiiiiiii[ccccccnnnnnccc]ccc]iiiiiii	chr16:70516611-70516832(+)$1	221	50	85	15.3029
====="""ccc[cccnnnnncccccc22=======	chr12:49666513-49666738(+)$1	225	73	108	16.3597
!!gggggggbb[cccmmmmcccbb]ggggggg22c	chr16:70291906-70292123(-)$1	217	82	117	10.8062
gggggg===========lll===========cccl	chr22:45571708-45571927(+)$1	219	73	108	12.7689
[ccc============lll============]ccc	chr1:32084850-32085065(+)$1	215	133	168	13.4054
bbbb[dddd"""cccnnnnnccc333dddd]bb]b	chr2:73437886-73438102(+)$1	216	146	181	13.3647
gggggg!!ddddcccooooooccc4444dddd22g	chr12:440861-441089(-)$1	228	13	48	13.0638
ggggg"""ccc[cccmmmmccc]ccc333gggggg	chr15:43804365-43804580(+)$1	215	120	155	12.4967
ccc!!dddd!!bb[annnnna]bb22ddddcccdd	chr19:17716954-17717174(-)$1	220	45	80	11.4447
eeee===========oooooo===========888	chr20:1286459-1286693(+)$1	234	131	166	12.6190

#otherMatches

#Seq PSSM
UUCUACAGCUCCAGAGAUCAUCAAUUGCUGUCUGA	chr9:340100-340318(+)$1	218	77	112	13.4044
CAGCCAGCUGCCGCUCGUAGCGCGUUGGCUGUCCC	chr3:47462092-47462316(+)$1	224	76	111	11.3823
UCCCGAUCUCUUCCUGUCAGAGGACCGGAGAAGUG	chr6:26468090-26468321(+)$1	231	116	151	12.4010
UGAUUUUCCUUUUCCCCUUAGGUGAGGCAGGCGAC	chr17:45623174-45623395(+)$1	221	79	114	12.5668
CGAUAACAGUAAAUCAAAUAAGAUAUUUGUCGGUG	chr19:1421148-1421377(+)$1	229	15	50	11.3541
GACGCCGCCAAGGUGAGUCCCGCCCAGCCUCGCUC	chr11:8985670-8985890(-)$1	220	123	158	12.7679
UUCAGGGGCCGCCGAGAUGUGUCAGGCUCCUGGGA	chr17:40761083-40761310(-)$1	227	22	57	15.6687
GUGCUGGGCACCUCAGAGGAGAGGACAGCCAGCAC	chr17:56387884-56388100(-)$1	216	6	41	13.7936
CUUGGCCCCAUCUUGCGACACGGGUCUGGGGGUCG	chr2:226447517-226447732(-)$1	215	141	176	15.4907
CCUGACACGGGUCCUUCAUCAGGACCCCCACGGUA	chr4:68610257-68610475(-)$1	218	158	193	12.1556
AAUUUGAGGAAAAGCGGCUGGUCUUCCUCAAGGAG	chr6:34497445-34497677(+)$1	232	91	126	13.3425
CUCAUUUUGGUUUCUUAAACAGAAUUCCAUCCGGG	chr17:76089673-76089896(+)$1	223	5	40	13.2463
GAGAAGAGGAAGCCCAUCCGGGUGCUGUCUCUCUU	chr2:25466717-25466938(-)$1	221	120	155	11.9422
GCGGCCAGGGAGAAGCCAGUACUUGUAACUAUGCU	chr11:65389724-65389939(-)$1	215	152	187	14.1893
ACAACUGGUUUCACUUGAUUGGUAUAACCUGUGGA	chr4:89602285-89602502(+)$1	217	37	72	12.4048
CACACUUAGAACCCCGCCAAGGGAAAGAAGUGGUG	chr16:2814073-2814309(+)$1	236	67	102	12.6070
GCCAGCUGGCGGGUUGUGUAGGAUUCUGGCUGUGC	chrX:47086749-47086965(+)$1	216	178	213	12.4625
UUAACUGUUGUCAUAGUACUUAUAUGGCAGUUAAA	chr7:122000892-122001114(-)$1	222	165	200	16.9545
GCUGUAAACCAGUGCAGUCAGUCUCAGUCUAUAAG	chr10:88990602-88990831(-)$1	229	154	189	14.4187
GCAGGAGGCCAGAUCAGCUUUGAUGUCUUUCCUGA	chr16:8906830-8907046(+)$1	216	13	48	11.4073
CUGCUCAGCUCAACGUCCAAGUACAAGGUGACGGU	chr1:36053918-36054139(+)$1	221	128	163	13.0570
CUGGGACACCUGGCCCCGAUGGCCAACCUGGGACC	chr1:22986001-22986224(+)$1	223	78	113	13.3861
ACCGUGCAGGACACGGGCCAGUACACGUGCAUGGU	chr19:51021621-51021840(-)$1	219	149	184	16.1776
GGAGGCCCUGGAGGACCCUUCCCCCGAGCUCAUGG	chr16:552904-553122(+)$1	218	129	164	10.7643
CAACUCAUGCUCAGGACCCAGCCCAGCUUGUUGUG	chr16:1827016-1827242(+)$1	226	187	222	13.3667
GGCACCACAAGGCCACAUAAGGAGGGUGAGGUCCC	chr7:78256395-78256610(-)$1	215	54	89	13.5643
CCUGGCCAGGGACAUGACACUGCCCCCGGAAACCA	chr3:47957836-47958071(-)$1	235	89	124	13.1856
UCCGGGCUGGUCCCGGGUCUCGGGCAUCCCCUCCC	chr13:77566211-77566429(+)$1	218	135	170	14.2446
CAGACAGACCGACCACAGAAUGGCAGGCCAGUCUG	chr3:118865382-118865599(+)$1	217	178	213	13.9418
UCCCAGAAAAGUUCCCGUGGUGGUUCUCCUGAUCU	chr13:115090684-115090900(+)$1	216	34	69	13.5966
CCGGGGUCAGGGCGGCUCCUCCGCGCGACCCCCGG	chr17:61678455-61678675(+)$1	220	51	86	12.0192
UGCCGAUGACAAGCUGGAAGAGCUCAUCCGGCAGU	chr2:74275107-74275332(+)$1	225	42	77	12.0040
GAACCAACAGUGAGAUUUCCUCUCCACCUGCCUGU	chr6:152621745-152621968(-)$1	223	113	148	13.8800
GUGGUGGUGAUACCGGGUACCCGGGCUAUGGCGCC	chr11:118868873-118869094(+)$1	221	7	42	11.2139
gACGGCUUUACCCCCAGCUCGGGACGUGAGCCUCG	chr16:58231460-58231681(+)$1	221	65	100	14.0431
CGACCAGUAAUGGAGCCAGUCUUCUUUCACAGGGA	chr20:43532620-43532843(+)$1	223	163	198	11.6880
CUAAGGACGUGAGGACUCCCCCCACCCCUACCCUC	chr11:65618712-65618928(+)$1	216	154	189	13.6154
ACCCAAGGAGCCAAGAUUCCCCUUAUUGUGUGUGG	chr4:139966193-139966411(+)$1	218	72	107	14.1081
AGUUGCCGGGGGCGCAGUAUCGACGCCGGCUCCAG	chr1:115053277-115053499(-)$1	222	65	100	12.7689
AGUGAUCCGCAGUGCCACCAGCUCUGCCUCGCGAC	chr13:99100454-99100677(+)$1	223	44	79	12.1600
CGCAGACCUUCGCGCUGAAUGCCGACCGCUGGUAC	chr5:44809226-44809452(+)$1	226	121	156	14.0257
GGACCUUGAUGAGAAGGAACCUUUUUCAUUCACUA	chr1:149879134-149879364(-)$1	230	156	191	11.9047
GCUGUUGAUCCAAGGCUGCACCUGUGGCUUGAUGG	chr16:70516611-70516832(+)$1	221	50	85	15.3029
UGGUAAAUACAUGGCUUGCUGCCUGUUAUACCGUG	chr12:49666513-49666738(+)$1	225	73	108	16.3597
CUGACCCUGUGCGAGUCGUCUCCAUUGGGGUCCCG	chr16:70291906-70292123(-)$1	217	82	117	10.8062
CUGGAGGAGCCUUUAAAGGUUUUAAAGGUUUGGUG	chr22:45571708-45571927(+)$1	219	73	108	12.7689
ACACGCUGGGUAGGUCCAGGGCUUGCCCGGCAGUG	chr1:32084850-32085065(+)$1	215	133	168	13.4054
UGCCGAGUCAGGAGUGGACGGCUGAAGACUGGGAC	chr2:73437886-73438102(+)$1	216	146	181	13.3647
AGUUUGUUGUGACAUUUCCUCGUGCCUAUCACUCU	chr12:440861-441089(-)$1	228	13	48	13.0638
AAAGGUUAGGACUAAUGUUUUAUUUCAGUCCUUUG	chr15:43804365-43804580(+)$1	215	120	155	12.4967
GAGCUGCAGGUGUGCGUCAAGGACUACUGCUUCGC	chr19:17716954-17717174(-)$1	220	45	80	11.4447
CUGCUGCGGGGCUGCUGCACUGUGGCCUUGCACUC	chr20:1286459-1286693(+)$1	234	131	166	12.6190

#DB
.((.(((((....((.....))....)))))..))	chr9:340100-340318(+)$1	1	77	112	13.4044
((((((((.((.(((...)))))))))))))).((	chr3:47462092-47462316(+)$1	1	76	111	11.3823
(.(...(((((((((.....))))..))))).).)	chr6:26468090-26468321(+)$1	1	116	151	12.4010
((.(((.((((..((.....)).)))).)))))))	chr17:45623174-45623395(+)$1	1	79	114	12.5668
((((((..(((..((......))))))))))).).	chr19:1421148-1421377(+)$1	1	15	50	11.3541
(..((.((...((((.....))))..))...))..	chr11:8985670-8985890(-)$1	1	123	158	12.7679
((((((((((...((......)).)))))))))))	chr17:40761083-40761310(-)$1	1	22	57	15.6687
(((((((...((((......))))....)))))))	chr17:56387884-56388100(-)$1	1	6	41	13.7936
(((((((((..((((.....))))....)))))))	chr2:226447517-226447732(-)$1	1	141	176	15.4907
(.((....(((((((.....))))))).)).))).	chr4:68610257-68610475(-)$1	1	158	193	12.1556
..(((((((((..((.....)).)))))))))(((	chr6:34497445-34497677(+)$1	1	91	126	13.3425
((.....(((.((((.....))))..)))...)))	chr17:76089673-76089896(+)$1	1	5	40	13.2463
)))((((((((((((.....)).))).)).)))))	chr2:25466717-25466938(-)$1	1	120	155	11.9422
(((...((..(.(((......))).)..)).))))	chr11:65389724-65389939(-)$1	1	152	187	14.1893
(((...((((..(((.....)))..))))))))..	chr4:89602285-89602502(+)$1	1	37	72	12.4048
..(((((.....(((.....)))....))))))))	chr16:2814073-2814309(+)$1	1	67	102	12.6070
(((((((((..((((......))))))))))).))	chrX:47086749-47086965(+)$1	1	178	213	12.4625
(((((((((((.(((.....)))))))))))))))	chr7:122000892-122001114(-)$1	1	165	200	16.9545
((((((.((....((.....))....)).))).))	chr10:88990602-88990831(-)$1	1	154	189	14.4187
.(((((((..(.((((....)))).).))))))).	chr16:8906830-8907046(+)$1	1	13	48	11.4073
(((.(((.((..((......))...)).)))))))	chr1:36053918-36054139(+)$1	1	128	163	13.0570
(((((...(((((((.....)))))....))...)	chr1:22986001-22986224(+)$1	1	78	113	13.3861
((((((((.(..((......))...).))))))))	chr19:51021621-51021840(-)$1	1	149	184	16.1776
(..(((.(.((.(((....))))).).))))))))	chr16:552904-553122(+)$1	1	129	164	10.7643
((...((.(((..((......)).))).))...))	chr16:1827016-1827242(+)$1	1	187	222	13.3667
((.(((.((...((......))....)).))).))	chr7:78256395-78256610(-)$1	1	54	89	13.5643
..(((((.(((.((......)).))).))...)))	chr3:47957836-47958071(-)$1	1	89	124	13.1856
.(((((..((.((((.....))))...))...)))	chr13:77566211-77566429(+)$1	1	135	170	14.2446
(((((.(.((..(((.....)))..)).).)))))	chr3:118865382-118865599(+)$1	1	178	213	13.9418
...(((...((..((......))..)).)))..))	chr13:115090684-115090900(+)$1	1	34	69	13.5966
(.((((((.(.((((.....)))).))))))).))	chr17:61678455-61678675(+)$1	1	51	86	12.0192
(((((((((...(((.....))))))).)))))).	chr2:74275107-74275332(+)$1	1	42	77	12.0040
(...((...((((((.....))).))).)).)).)	chr6:152621745-152621968(-)$1	1	113	148	13.8800
(((.(.(((...((((....))))..))).)))))	chr11:118868873-118869094(+)$1	1	7	42	11.2139
((.(((((....(((.....)))....))))))))	chr16:58231460-58231681(+)$1	1	65	100	14.0431
(..((.((((.((((.....)))).)).)).))))	chr20:43532620-43532843(+)$1	1	163	198	11.6880
...(((..(((.((......))))).)))...)))	chr11:65618712-65618928(+)$1	1	154	189	13.6154
.((((....((.(((......)))...))...)))	chr4:139966193-139966411(+)$1	1	72	107	14.1081
(((((((((.(.((......)).).)))))...))	chr1:115053277-115053499(-)$1	1	65	100	12.7689
.((((...((((.((.....)).)))).))))..)	chr13:99100454-99100677(+)$1	1	44	79	12.1600
.((.(....(((.((.....)))))).)).)))))	chr5:44809226-44809452(+)$1	1	121	156	14.0257
((.....((((((((((...))))))))))..)))	chr1:149879134-149879364(-)$1	1	156	191	11.9047
((((((((.((((((.....))).))).)))))))	chr16:70516611-70516832(+)$1	1	50	85	15.3029
(((((...(((.(((.....))))))..)))))))	chr12:49666513-49666738(+)$1	1	73	108	16.3597
..(((((((((.(((....))))).)))))))..)	chr16:70291906-70292123(-)$1	1	82	117	10.8062
))))))(((((((((((...)))))))))))(((.	chr22:45571708-45571927(+)$1	1	73	108	12.7689
.(((((((((((((((...)))))))))))).)))	chr1:32084850-32085065(+)$1	1	133	168	13.4054
((((.((((...(((.....)))...)))).)).)	chr2:73437886-73438102(+)$1	1	146	181	13.3647
((((((..(((((((......)))....))))..)	chr12:440861-441089(-)$1	1	13	48	13.0638
(((((...(((.(((....))).)))...))))))	chr15:43804365-43804580(+)$1	1	120	155	12.4967
(((..((((..((.(.....).))..)))))))))	chr19:17716954-17717174(-)$1	1	45	80	11.4447
(((((((((((((((......)))))))))))...	chr20:1286459-1286693(+)$1	1	131	166	12.6190

#PSSM
f : 0.13	e : 0.11	g : 0.11	= : 0.09	[ : 0.09	i : 0.07	d : 0.07	b : 0.07	" : 0.05	c : 0.05	! : 0.05	: : 0.01	( : 0.01	
f : 0.13	g : 0.13	d : 0.11	! : 0.09	= : 0.09	i : 0.07	e : 0.07	b : 0.05	[ : 0.05	c : 0.05	" : 0.05	: : 0.01	( : 0.01	
g : 0.17	i : 0.09	= : 0.09	e : 0.09	b : 0.07	f : 0.07	d : 0.07	" : 0.07	[ : 0.05	! : 0.05	c : 0.05	$ : 0.03	a : 0.01	
c : 0.15	g : 0.15	e : 0.11	" : 0.09	= : 0.09	[ : 0.07	i : 0.07	b : 0.07	f : 0.05	$ : 0.03	d : 0.03	! : 0.01	
c : 0.15	e : 0.13	= : 0.13	g : 0.13	i : 0.07	" : 0.07	f : 0.05	b : 0.05	$ : 0.03	a : 0.03	d : 0.03	# : 0.01	[ : 0.01	! : 0.01	
" : 0.13	c : 0.13	e : 0.11	g : 0.11	= : 0.09	i : 0.07	[ : 0.07	# : 0.05	b : 0.05	d : 0.05	f : 0.03	$ : 0.03	
e : 0.11	= : 0.11	" : 0.11	b : 0.09	i : 0.07	[ : 0.07	! : 0.07	g : 0.07	d : 0.07	# : 0.05	$ : 0.03	c : 0.03	a : 0.01	f : 0.01	
= : 0.13	" : 0.13	e : 0.09	d : 0.09	b : 0.09	i : 0.07	! : 0.07	[ : 0.07	# : 0.05	g : 0.05	c : 0.03	$ : 0.01	a : 0.01	f : 0.01	
c : 0.15	b : 0.15	d : 0.13	= : 0.11	[ : 0.09	" : 0.07	e : 0.05	g : 0.05	# : 0.05	i : 0.03	! : 0.03	$ : 0.01	
b : 0.21	c : 0.19	" : 0.11	= : 0.11	! : 0.09	d : 0.07	# : 0.05	a : 0.03	e : 0.01	g : 0.01	i : 0.01	$ : 0.01	[ : 0.01	
c : 0.19	! : 0.13	" : 0.11	b : 0.09	= : 0.09	d : 0.07	[ : 0.07	# : 0.05	a : 0.05	e : 0.03	g : 0.01	i : 0.01	$ : 0.01	
[ : 0.23	d : 0.21	! : 0.17	" : 0.09	c : 0.07	= : 0.07	# : 0.05	g : 0.01	$ : 0.01	e : 0.01	b : 0.01	
c : 0.34	d : 0.21	b : 0.13	! : 0.09	= : 0.07	# : 0.03	[ : 0.03	" : 0.01	g : 0.01	e : 0.01	
b : 0.32	c : 0.32	d : 0.21	= : 0.07	g : 0.01	e : 0.01	[ : 0.01	
c : 0.32	b : 0.21	d : 0.19	o : 0.13	= : 0.07	g : 0.01	e : 0.01	a : 0.01	
n : 0.51	o : 0.30	m : 0.05	= : 0.05	d : 0.03	l : 0.01	
n : 0.51	o : 0.30	m : 0.09	l : 0.03	= : 0.03	
n : 0.51	o : 0.30	m : 0.09	l : 0.07	
n : 0.51	o : 0.30	m : 0.09	l : 0.05	c : 0.01	
n : 0.51	o : 0.30	c : 0.07	m : 0.03	l : 0.03	= : 0.01	
c : 0.26	b : 0.24	d : 0.19	o : 0.17	= : 0.05	g : 0.01	e : 0.01	a : 0.01	
b : 0.34	c : 0.30	d : 0.21	= : 0.07	g : 0.01	e : 0.01	] : 0.01	
c : 0.28	d : 0.21	b : 0.15	] : 0.13	= : 0.07	4 : 0.05	3 : 0.03	g : 0.01	e : 0.01	
d : 0.26	c : 0.19	4 : 0.09	= : 0.09	] : 0.07	2 : 0.05	3 : 0.05	b : 0.05	i : 0.03	g : 0.01	e : 0.01	a : 0.01	
c : 0.19	4 : 0.15	2 : 0.15	] : 0.13	= : 0.11	3 : 0.09	d : 0.07	i : 0.03	g : 0.01	e : 0.01	
4 : 0.17	c : 0.15	= : 0.11	a : 0.11	2 : 0.09	d : 0.07	b : 0.07	g : 0.05	3 : 0.05	i : 0.03	] : 0.01	e : 0.01	
b : 0.13	d : 0.11	= : 0.11	4 : 0.11	c : 0.11	] : 0.11	e : 0.05	g : 0.05	3 : 0.05	i : 0.03	f : 0.03	2 : 0.03	
] : 0.21	b : 0.15	= : 0.13	e : 0.09	4 : 0.07	c : 0.07	d : 0.05	g : 0.05	i : 0.03	f : 0.03	2 : 0.03	3 : 0.01	
b : 0.19	= : 0.15	c : 0.13	e : 0.09	d : 0.09	i : 0.07	g : 0.07	f : 0.05	3 : 0.03	] : 0.03	4 : 0.01	a : 0.01	
= : 0.15	c : 0.11	3 : 0.11	b : 0.11	e : 0.09	g : 0.09	d : 0.09	i : 0.07	] : 0.07	f : 0.05	
3 : 0.15	e : 0.13	c : 0.13	= : 0.13	g : 0.09	] : 0.09	i : 0.07	f : 0.05	d : 0.05	b : 0.01	a : 0.01	2 : 0.01	
3 : 0.15	g : 0.11	c : 0.11	e : 0.11	i : 0.09	= : 0.09	d : 0.07	b : 0.07	2 : 0.05	f : 0.05	] : 0.03	
c : 0.11	2 : 0.09	] : 0.09	b : 0.09	g : 0.09	e : 0.09	d : 0.07	= : 0.07	i : 0.07	f : 0.05	3 : 0.05	: : 0.01	a : 0.01	8 : 0.01	
f : 0.13	g : 0.11	c : 0.11	d : 0.09	2 : 0.09	e : 0.09	b : 0.07	= : 0.07	i : 0.07	] : 0.05	a : 0.01	3 : 0.01	8 : 0.01	
b : 0.13	f : 0.11	e : 0.11	g : 0.11	d : 0.09	= : 0.09	c : 0.09	i : 0.07	: : 0.05	2 : 0.03	] : 0.01	l : 0.01	8 : 0.01	

#score	684.3105581599617
#seq	52
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m2_run2.txt

#BEAR
###==========oooooo==========4444	chr16:24834710-24834963(+)$1	253	151	184	15.9206
[hhhhhhhh[cccooooooccc]hhhhhhhhee	chrX:84519259-84519497(+)$1	238	166	199	11.9563
eebb####eeeeeooooooeeeeebb]eeeee=	chr3:39140805-39141028(-)$1	223	107	140	13.4134
c!!ddddffffffooooooffffff]dddd]cc	chr6:144184488-144184750(+)$1	262	30	63	13.1841
d[cccdddd[cccooooooccc22dddd22ccc	chr12:6702489-6702711(-)$1	222	96	129	13.1619
==========[bboooooobb]==========:	chr10:70765442-70765670(+)$1	228	2	35	15.0806
[ffffff[eeeeeooooooeeeeeffffff]cc	chr7:98963416-98963670(+)$1	254	30	63	12.8182
ffff"""ffffffooooooffffff4444ffff	chr2:62103202-62103444(-)$1	242	2	35	14.2693
ddd"""a[eeeeeooooooeeeee]a333dddd	chr3:49049158-49049404(+)$1	246	115	148	15.0293
#dddd!!bb[cccooooooccc]bb22dddd33	chr19:50183309-50183565(+)$1	256	135	168	13.8430
deeeeegggggggooooooggggggg:gggggg	chr17:72868955-72869178(-)$1	223	32	65	13.6024
gggg[bbbb[cccooooooccc]bb]bbggggg	chr1:200378118-200378349(-)$1	231	22	55	13.2846
dd!!ffffff!!aooooooa22ffffff22ddd	chr6:18249921-18250157(-)$1	236	17	50	13.2046
ffffff!!eeeeeooooooeeeee>>>>>>>>>	chr10:33221342-33221579(-)$1	237	128	161	12.0171
eee[eeeeeddddoooooodddd]eeeee]eee	chr7:26237176-26237439(-)$1	263	220	253	12.6017
[ccc####bb[bboooooobbbb666666ccc]	chr1:46743743-46743971(+)$1	228	157	190	12.0311
cc####ffffffooooooffffffccc333ddd	chr11:9603019-9603283(+)$1	264	136	169	13.5002
dddd"""ccc[aooooooa]ccc333ddddeee	chr10:93719712-93719940(+)$1	228	105	138	13.5834
eeeee"""eeeeeooooooeeeee333eeeee:	chr21:40568153-40568390(-)$1	237	190	223	13.8028
cc[eeeee[ddddoooooodddd]eeeee333c	chr19:58906002-58906242(+)$1	240	22	55	13.0521
cc####bb[ddddooooooddddbb22ccc]cc	chr7:30639486-30639716(+)$1	230	69	102	13.8223
ggg!!eeeee[bboooooobb]eeeee]ggggg	chr1:78193991-78194217(-)$1	226	30	63	14.5519
ee[ccca!!eeeeeooooooeeeee333a]ccc	chr1:11148106-11148335(-)$1	229	158	191	13.7307
========="""cccmmmmccc333========	chr7:26235952-26236201(-)$1	249	200	233	10.4582
$$$dddd[bb[bboooooobb]bb]dddd22cc	chr17:79219592-79219813(-)$1	221	54	87	12.5132
ddd####ccc[bbammmma]bb]ccc333dddd	chr15:68500441-68500713(-)$1	272	14	47	11.0440
4eeeeegggggggooooooggggggg::eeeee	chr3:129034374-129034598(-)$1	224	24	57	12.3573
((((((gggggggooooooggggggg22ggggg	chr14:77935439-77935660(+)$1	221	172	205	11.9749
eeee"""ffffffooooooffffff]eeeee44	chr9:136917344-136917572(-)$1	228	119	152	14.0787
eeee"""gggggggmmmmggggggg333eeeee	chr6:83885655-83885877(-)$1	222	63	96	10.9279
!!ccc[a!!ddddoooooodddd22accc22bb	chr21:27354629-27354880(-)$1	251	211	244	13.2159
cc[a!!ccc[cccoooooocccccc22a]cccd	chr12:110783024-110783255(+)$1	231	157	190	15.7604
hhhh[accc!!bboooooobb22ccc]a]hhhh	chr1:44069286-44069517(+)$1	231	54	87	13.7848
####hhhhhhhhaooooooa]hhhhhhhh22ee	chr12:50149396-50149638(+)$1	242	127	160	12.1491
eeeee!!dddd[aooooooa]dddd22eeeeed	chr6:28268506-28268742(+)$1	236	82	115	13.8273
""ggggggg[a[aooooooa]a]gggggggddd	chr3:12880826-12881059(-)$1	233	158	191	14.9168
ee[a!!gggggggooooooggggggg22a]eee	chrX:118374232-118374457(+)$1	225	33	66	16.0740
iii"""dddd[bboooooobb22dddd]iiiii	chr11:94908647-94908878(-)$1	231	45	78	14.4481
ffffff!!bb[bboooooobb]bb4444fffff	chr6:26104368-26104631(+)$1	263	202	235	13.4727
##ccc[gggggggoooooogggggggccc22ee	chr1:150550714-150550978(-)$1	264	37	70	14.9581
$$$$ffffff[bboooooobbffffff4444bb	chr6:133136035-133136276(+)$1	241	136	169	13.2377
""iiiiiiiii[aooooooa]iiiiiiiiiiii	chr20:34240850-34241076(-)$1	226	121	154	15.3761
d"""dddd[ccc[allla]ccc]dddd333ddd	chr14:60337143-60337368(-)$1	225	70	103	10.2547
ii!!ccc####bboooooobb22ccc22iiiii	chr1:245027044-245027310(-)$1	266	47	80	15.3288
h$$$$$iiiiiiiiillliiiiiiiii333hhh	chr22:29696025-29696256(+)$1	231	15	48	10.4001
##eeeee[eeeeeooooooeeeee]eeeee333	chr18:20716241-20716464(+)$1	223	103	136	13.4201
fff####ffffffooooooffffff22ffffff	chrX:41205723-41205975(+)$1	252	146	179	13.9211
dddd!!ccc[cccooooooccc]ccc333dddd	chr7:26236364-26236595(-)$1	231	2	35	15.5560
eeeeebb[ddddoooooodddd333bb]eeeee	chr17:7144046-7144293(-)$1	247	36	69	11.3984
b!!ccc[bb[aooooooa]bb22ccc22bb22a	chr5:52397923-52398147(-)$1	224	34	67	11.2486
hffffff[cccbboooooobb]ccc333fffff	chr12:49433886-49434144(-)$1	258	90	123	14.3059
hhhhhccc[a[bboooooobb]accc22hhhhh	chr6:138413138-138413377(-)$1	239	183	216	13.4494
gg[bbccc[a!!bboooooobb22a22ccc]bb	chr22:38881915-38882167(-)$1	252	22	55	12.1182

#otherMatches

#Seq PSSM
CUCGGGUCCAGCCAGAGCCGGCUGGGCUCCCUC	chr16:24834710-24834963(+)$1	253	151	184	15.9206
UGUUGAAAUAGGUACAAACACUAAUUUUAAUUU	chrX:84519259-84519497(+)$1	238	166	199	11.9563
CAGACCCUGAUGGACUUCCCCAUUUCAUGGAGA	chr3:39140805-39141028(-)$1	223	107	140	13.4134
UGAAUAAUACAAGUAUAUUCUUGUACUUAUAAC	chr6:144184488-144184750(+)$1	262	30	63	13.1841
CAUUCGUGGUGGCAAGAAGGCCUCCCGCAUGAA	chr12:6702489-6702711(-)$1	222	96	129	13.1619
aaguaaaccauuacacaaauauugguuUAUUUU	chr10:70765442-70765670(+)$1	228	2	35	15.0806
UGGUGUCAUACCUACCUCGGGGUAGACACUCCU	chr7:98963416-98963670(+)$1	254	30	63	12.8182
UUUUCGCUUAAAAUUCUACUUUUAAACUUAAAA	chr2:62103202-62103444(-)$1	242	2	35	14.2693
CACUUCUGGGAGCUUUGGCGCUCUGGCCUGUGG	chr3:49049158-49049404(+)$1	246	115	148	15.0293
UCCCCAGCUGUGGGCUGAGCUAGAGACGGGGUC	chr19:50183309-50183565(+)$1	256	135	168	13.8430
GGGCCCGGGCAGGAGCGGGCUUGCCCUGCGGAG	chr17:72868955-72869178(-)$1	223	32	65	13.6024
GAGUCACGGCGUCAUCCAGGACCUCAGUAUUCU	chr1:200378118-200378349(-)$1	231	22	55	13.2846
AAGUUUUCAAGAAGAGAAUUGAUUGAAAUAUUA	chr6:18249921-18250157(-)$1	236	17	50	13.2046
ACAAAUUCAGUAAGUAAGGUUGCUCAAGUCCUU	chr10:33221342-33221579(-)$1	237	128	161	12.0171
ACUGGAUAUUAGUCUUUUAGCUGUAUGUUAAGU	chr7:26237176-26237439(-)$1	263	220	253	12.6017
AUCACCUUCGUCUUCCACCAGCGUUCUCAUGAG	chr1:46743743-46743971(+)$1	228	157	190	12.0311
CUUUUGCAAGUUGGCCGAGGCUUGAGGUAUAUU	chr11:9603019-9603283(+)$1	264	136	169	13.5002
UGUGGAUGUGCUGCUAAAAUUACUUACACAAGA	chr10:93719712-93719940(+)$1	228	105	138	13.5834
UGGUUGCACCUUAUGACCUUGAGGGAAAGCCAG	chr21:40568153-40568390(-)$1	237	190	223	13.8028
UCAGAGCUGUGUGUCUCCUUGCAGGGCUCCUCG	chr19:58906002-58906242(+)$1	240	22	55	13.0521
CUAACAGGAGCUGGCGUUACAGCCCAAAGAUGA	chr7:30639486-30639716(+)$1	230	69	102	13.8223
GAAGAUAAUAAUGAAACAACAAUGUUAAUUCAG	chr1:78193991-78194217(-)$1	226	30	63	14.5519
UAGUACCCAGCCUUAGUUUAAAGGUGCCGUGUA	chr1:11148106-11148335(-)$1	229	158	191	13.7307
UGUUUAAAGGAUGAGUGUGCUUUUAUUUUAAAU	chr7:26235952-26236201(-)$1	249	200	233	10.4582
GAAAGGCCCGCGGGGGGGACCAUGUGCCUGUGU	chr17:79219592-79219813(-)$1	221	54	87	12.5132
UUCGCCAUGCUGGCCCUCGUCCUGCACCAGAAG	chr15:68500441-68500713(-)$1	272	14	47	11.0440
AGGCUGGGCGAGCGCAACGGCUCGUCGCUGGCC	chr3:129034374-129034598(-)$1	224	24	57	12.3573
CAGCCUGCUGGACACUUCAGUCCAGCUCUCUCC	chr14:77935439-77935660(+)$1	221	172	205	11.9749
UUACAAAUUGUUACAUUUAUAACAAGGUAAGAA	chr9:136917344-136917572(-)$1	228	119	152	14.0787
UAAUUGCUGUAUUUCUUUAAAUGCAUGUGUUAU	chr6:83885655-83885877(-)$1	222	63	96	10.9279
GAGAAUGUCCCAGGUAAGUCUGGCUCUUCCAUC	chr21:27354629-27354880(-)$1	251	211	244	13.2159
CAACAGGUUAGUGCACCUUCACGGCAGGCUGAG	chr12:110783024-110783255(+)$1	231	157	190	15.7604
UGGCACCCACCCAAGGAACUGCCUGGCGAGCUG	chr1:44069286-44069517(+)$1	231	54	87	13.7848
UUGCAUUCCUUACAGGUACGUUAAGGGAUUUGU	chr12:50149396-50149638(+)$1	242	127	160	12.1491
GGUGAUUUGUGGGCCCGCAUGCACAUCUCAUCC	chr6:28268506-28268742(+)$1	236	82	115	13.8273
GAAGUUCCUGGUCCACAACGUCAAGGAGCUGGA	chr3:12880826-12881059(-)$1	233	158	191	14.9168
UUGAAGAGGGGCCGUAUGGGGUCUUUGCUGGAA	chrX:118374232-118374457(+)$1	225	33	66	16.0740
AUAAAGCUAUUGUUGUAUUGCUCGUAGGUAUGA	chr11:94908647-94908878(-)$1	231	45	78	14.4481
UCGUUUAAAGAGCUGAAAUGCGUUGCGAGAAUG	chr6:26104368-26104631(+)$1	263	202	235	13.4727
AACGAAGACGAUGUGAAAUCGUUGUCUCGAGUG	chr1:150550714-150550978(-)$1	264	37	70	14.9581
CUCAUCCACGAUGGCCUAGCACGUGGAAUUCGC	chr6:133136035-133136276(+)$1	241	136	169	13.2377
GGUCUAGGACUGGAUGUUCCGGGUUUUGGAGGU	chr20:34240850-34241076(-)$1	226	121	154	15.3761
CGGGUCCCAGUGGCUCAGGCACCGGGGGGAGGG	chr14:60337143-60337368(-)$1	225	70	103	10.2547
CCGACUCGGGCCCGAUGGAGGAGGAGGAGGCCG	chr1:245027044-245027310(-)$1	266	47	80	15.3288
GCACCUGGGGGCUCUGGAAGGGCUUCCUCACCC	chr22:29696025-29696256(+)$1	231	15	48	10.4001
GAGUUGGAGGAGGACGAUGCCUUUAUCAGCGUG	chr18:20716241-20716464(+)$1	223	103	136	13.4201
ACCUUGGUAAGUAUUUGAUUACUUGAUGGUUUC	chrX:41205723-41205975(+)$1	252	146	179	13.9211
UGUUGGCGGAAUUAAAGAAGAUACUGAGGAACA	chr7:26236364-26236595(-)$1	231	2	35	15.5560
UUUUCUGCUUUCAUCCCAGGAACACCAUGAAGA	chr17:7144046-7144293(-)$1	247	36	69	11.3984
GUUGUUGAGUGUUUUACCCCUAGGACUUCUGUU	chr5:52397923-52398147(-)$1	224	34	67	11.2486
CGGGGCCAGCAGGUGAGCUCCAUGCCAAGGUCC	chr12:49433886-49434144(-)$1	258	90	123	14.3059
CUACACAUCUGCCUAACUUGGGAAUGAAUGUGG	chr6:138413138-138413377(-)$1	239	183	216	13.4494
CUAGUAGCACCACCUCAACUGGGAGAAGUUCAC	chr22:38881915-38882167(-)$1	252	22	55	12.1182

#DB
...((((((((((......))))))))))....	chr16:24834710-24834963(+)$1	1	151	184	15.9206
.((((((((.(((......))).))))))))))	chrX:84519259-84519497(+)$1	1	166	199	11.9563
((((....(((((......))))))).)))))(	chr3:39140805-39141028(-)$1	1	107	140	13.4134
(..((((((((((......)))))).)))).))	chr6:144184488-144184750(+)$1	1	30	63	13.1841
(.(((((((.(((......)))..))))..)))	chr12:6702489-6702711(-)$1	1	96	129	13.1619
((((((((((.((......)).)))))))))).	chr10:70765442-70765670(+)$1	1	2	35	15.0806
.((((((.(((((......))))))))))).))	chr7:98963416-98963670(+)$1	1	30	63	12.8182
((((...((((((......))))))....))))	chr2:62103202-62103444(-)$1	1	2	35	14.2693
(((...(.(((((......))))).)...))))	chr3:49049158-49049404(+)$1	1	115	148	15.0293
.((((..((.(((......))).))..))))..	chr19:50183309-50183565(+)$1	1	135	168	13.8430
))))))(((((((......))))))).((((((	chr17:72868955-72869178(-)$1	1	32	65	13.6024
((((.((((.(((......))).)).)))))))	chr1:200378118-200378349(-)$1	1	22	55	13.2846
((..((((((..(......)..))))))..)))	chr6:18249921-18250157(-)$1	1	17	50	13.2046
((((((..(((((......))))).........	chr10:33221342-33221579(-)$1	1	128	161	12.0171
(((.(((((((((......)))).))))).)))	chr7:26237176-26237439(-)$1	1	220	253	12.6017
.(((....((.((......))))......))).	chr1:46743743-46743971(+)$1	1	157	190	12.0311
((....((((((......)))))))))...)))	chr11:9603019-9603283(+)$1	1	136	169	13.5002
((((...(((.(......).)))...))))(((	chr10:93719712-93719940(+)$1	1	105	138	13.5834
(((((...(((((......)))))...))))).	chr21:40568153-40568390(-)$1	1	190	223	13.8028
((.(((((.((((......)))).)))))...)	chr19:58906002-58906242(+)$1	1	22	55	13.0521
((....((.((((......))))))..))).))	chr7:30639486-30639716(+)$1	1	69	102	13.8223
(((..(((((.((......)).))))).)))))	chr1:78193991-78194217(-)$1	1	30	63	14.5519
((.((((..(((((......)))))...).)))	chr1:11148106-11148335(-)$1	1	158	191	13.7307
(((((((((...(((....)))...))))))))	chr7:26235952-26236201(-)$1	1	200	233	10.4582
...((((.((.((......)).)).))))..))	chr17:79219592-79219813(-)$1	1	54	87	12.5132
(((....(((.(((....).)).)))...))))	chr15:68500441-68500713(-)$1	1	14	47	11.0440
.)))))(((((((......)))))))..(((((	chr3:129034374-129034598(-)$1	1	24	57	12.3573
......(((((((......)))))))..)))))	chr14:77935439-77935660(+)$1	1	172	205	11.9749
((((...((((((......)))))).)))))..	chr9:136917344-136917572(-)$1	1	119	152	14.0787
((((...(((((((....)))))))...)))))	chr6:83885655-83885877(-)$1	1	63	96	10.9279
..(((.(..((((......))))..))))..))	chr21:27354629-27354880(-)$1	1	211	244	13.2159
((.(..(((.(((......))))))..).))))	chr12:110783024-110783255(+)$1	1	157	190	15.7604
((((.((((..((......))..))).).))))	chr1:44069286-44069517(+)$1	1	54	87	13.7848
....(((((((((......).))))))))..))	chr12:50149396-50149638(+)$1	1	127	160	12.1491
(((((..((((.(......).))))..)))))(	chr6:28268506-28268742(+)$1	1	82	115	13.8273
..(((((((.(.(......).).))))))))))	chr3:12880826-12881059(-)$1	1	158	191	14.9168
((.(..(((((((......)))))))..).)))	chrX:118374232-118374457(+)$1	1	33	66	16.0740
(((...((((.((......))..)))).)))))	chr11:94908647-94908878(-)$1	1	45	78	14.4481
((((((..((.((......)).))....)))))	chr6:26104368-26104631(+)$1	1	202	235	13.4727
..(((.(((((((......))))))))))..))	chr1:150550714-150550978(-)$1	1	37	70	14.9581
....((((((.((......))))))))....))	chr6:133136035-133136276(+)$1	1	136	169	13.2377
..(((((((((.(......).))))))))))))	chr20:34240850-34241076(-)$1	1	121	154	15.3761
(...((((.(((.(...).))).))))...)))	chr14:60337143-60337368(-)$1	1	70	103	10.2547
((..(((....((......))..)))..)))))	chr1:245027044-245027310(-)$1	1	47	80	15.3288
(.....(((((((((...)))))))))...)))	chr22:29696025-29696256(+)$1	1	15	48	10.4001
..(((((.(((((......))))).)))))...	chr18:20716241-20716464(+)$1	1	103	136	13.4201
(((....((((((......))))))..))))))	chrX:41205723-41205975(+)$1	1	146	179	13.9211
((((..(((.(((......))).)))...))))	chr7:26236364-26236595(-)$1	1	2	35	15.5560
(((((((.((((......))))...)).)))))	chr17:7144046-7144293(-)$1	1	36	69	11.3984
(..(((.((.(......).))..)))..))..)	chr5:52397923-52398147(-)$1	1	34	67	11.2486
(((((((.(((((......)).)))...)))))	chr12:49433886-49434144(-)$1	1	90	123	14.3059
((((((((.(.((......)).))))..)))))	chr6:138413138-138413377(-)$1	1	183	216	13.4494
((.(((((.(..((......))..)..))).))	chr22:38881915-38882167(-)$1	1	22	55	12.1182

#PSSM
e : 0.16	d : 0.15	# : 0.09	c : 0.09	f : 0.07	h : 0.07	[ : 0.05	g : 0.05	= : 0.03	$ : 0.03	" : 0.03	i : 0.03	4 : 0.01	( : 0.01	! : 0.01	b : 0.01	
e : 0.20	f : 0.11	d : 0.11	c : 0.09	# : 0.07	h : 0.05	! : 0.05	g : 0.05	$ : 0.05	" : 0.05	= : 0.03	i : 0.03	[ : 0.01	( : 0.01	
e : 0.16	f : 0.11	d : 0.09	[ : 0.09	# : 0.07	! : 0.07	c : 0.07	h : 0.05	g : 0.05	$ : 0.05	= : 0.03	i : 0.03	b : 0.01	( : 0.01	" : 0.01	
e : 0.16	c : 0.11	d : 0.09	f : 0.09	# : 0.09	= : 0.05	h : 0.05	" : 0.05	! : 0.05	b : 0.03	g : 0.03	a : 0.03	$ : 0.03	[ : 0.01	( : 0.01	i : 0.01	
e : 0.15	# : 0.11	c : 0.11	f : 0.11	" : 0.11	d : 0.07	! : 0.07	= : 0.05	h : 0.05	[ : 0.03	( : 0.01	g : 0.01	i : 0.01	$ : 0.01	b : 0.01	
" : 0.13	# : 0.11	f : 0.11	e : 0.11	! : 0.09	c : 0.09	d : 0.07	= : 0.05	h : 0.03	b : 0.03	[ : 0.03	( : 0.01	a : 0.01	g : 0.01	i : 0.01	$ : 0.01	
g : 0.11	c : 0.11	d : 0.09	f : 0.09	" : 0.09	# : 0.07	! : 0.07	e : 0.07	= : 0.05	a : 0.05	b : 0.05	h : 0.03	i : 0.03	[ : 0.01	
f : 0.13	g : 0.13	c : 0.13	[ : 0.11	d : 0.07	b : 0.07	! : 0.07	= : 0.05	# : 0.05	e : 0.05	h : 0.03	i : 0.03	" : 0.01	
e : 0.15	f : 0.13	g : 0.13	b : 0.11	c : 0.11	[ : 0.09	d : 0.07	= : 0.05	h : 0.03	! : 0.03	i : 0.03	# : 0.01	
[ : 0.15	e : 0.15	f : 0.13	d : 0.13	g : 0.11	c : 0.07	b : 0.05	= : 0.03	i : 0.03	a : 0.03	" : 0.01	! : 0.01	h : 0.01	# : 0.01	
[ : 0.18	c : 0.15	e : 0.13	g : 0.11	d : 0.11	f : 0.09	! : 0.05	a : 0.03	i : 0.03	= : 0.01	" : 0.01	h : 0.01	# : 0.01	
b : 0.22	c : 0.13	e : 0.13	g : 0.11	f : 0.09	d : 0.09	[ : 0.05	! : 0.03	= : 0.01	a : 0.01	" : 0.01	h : 0.01	i : 0.01	o : 0.01	
b : 0.24	c : 0.13	e : 0.13	g : 0.11	a : 0.09	f : 0.07	d : 0.07	o : 0.07	= : 0.01	[ : 0.01	i : 0.01	
o : 0.86	a : 0.03	e : 0.01	c : 0.01	g : 0.01	i : 0.01	b : 0.01	
o : 0.90	m : 0.03	c : 0.01	l : 0.01	i : 0.01	
o : 0.90	m : 0.05	l : 0.03	
o : 0.90	m : 0.05	l : 0.03	
o : 0.88	m : 0.05	a : 0.03	l : 0.01	
o : 0.83	a : 0.03	] : 0.03	f : 0.01	m : 0.01	g : 0.01	i : 0.01	d : 0.01	
b : 0.22	c : 0.15	e : 0.11	g : 0.11	f : 0.09	a : 0.09	d : 0.09	] : 0.03	o : 0.03	= : 0.01	i : 0.01	
b : 0.26	c : 0.16	e : 0.13	g : 0.11	f : 0.09	d : 0.09	] : 0.07	= : 0.01	2 : 0.01	i : 0.01	
c : 0.16	e : 0.13	f : 0.11	] : 0.11	g : 0.11	d : 0.11	2 : 0.09	b : 0.05	i : 0.03	= : 0.01	h : 0.01	a : 0.01	
e : 0.15	] : 0.13	f : 0.13	2 : 0.11	g : 0.11	d : 0.09	b : 0.05	c : 0.05	= : 0.03	3 : 0.03	i : 0.03	h : 0.01	a : 0.01	
e : 0.15	c : 0.15	f : 0.13	g : 0.13	b : 0.09	2 : 0.05	3 : 0.05	d : 0.05	= : 0.03	h : 0.03	] : 0.03	i : 0.03	6 : 0.01	
c : 0.16	f : 0.13	g : 0.13	b : 0.07	d : 0.07	e : 0.07	3 : 0.07	] : 0.05	= : 0.03	h : 0.03	i : 0.03	> : 0.01	6 : 0.01	2 : 0.01	4 : 0.01	a : 0.01	
c : 0.13	2 : 0.11	g : 0.11	3 : 0.09	d : 0.07	e : 0.07	= : 0.05	] : 0.05	f : 0.05	h : 0.03	b : 0.03	4 : 0.03	a : 0.03	i : 0.03	> : 0.01	6 : 0.01	
2 : 0.20	3 : 0.13	d : 0.11	e : 0.09	= : 0.05	f : 0.05	c : 0.05	h : 0.03	] : 0.03	4 : 0.03	: : 0.03	b : 0.03	i : 0.03	> : 0.01	6 : 0.01	g : 0.01	
3 : 0.16	e : 0.13	d : 0.09	2 : 0.09	c : 0.07	= : 0.05	f : 0.05	4 : 0.05	] : 0.05	h : 0.03	g : 0.03	a : 0.03	b : 0.01	> : 0.01	6 : 0.01	: : 0.01	i : 0.01	
e : 0.18	3 : 0.11	g : 0.09	d : 0.07	f : 0.07	c : 0.07	= : 0.05	h : 0.05	i : 0.05	2 : 0.03	4 : 0.03	a : 0.03	] : 0.03	> : 0.01	6 : 0.01	b : 0.01	
e : 0.15	d : 0.11	2 : 0.11	f : 0.09	g : 0.09	c : 0.07	3 : 0.07	h : 0.05	] : 0.05	i : 0.05	4 : 0.03	= : 0.03	> : 0.01	b : 0.01	
e : 0.18	d : 0.15	2 : 0.09	h : 0.07	] : 0.07	c : 0.07	f : 0.07	g : 0.07	i : 0.05	4 : 0.03	= : 0.03	3 : 0.03	> : 0.01	
e : 0.22	c : 0.15	d : 0.13	f : 0.07	g : 0.07	3 : 0.05	b : 0.05	h : 0.05	i : 0.05	4 : 0.03	= : 0.03	> : 0.01	2 : 0.01	
e : 0.16	d : 0.16	c : 0.13	f : 0.07	g : 0.07	b : 0.05	h : 0.05	i : 0.05	4 : 0.03	= : 0.03	: : 0.03	3 : 0.03	> : 0.01	] : 0.01	a : 0.01	

#score	707.4409806812488
#seq	53
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m2_run2.txt

#BEAR
::==========lll==========::	chr4:71588020-71588262(+)$1	242	60	87	14.6797
:==========nnnnn==========:	chr12:123893004-123893246(+)$1	242	130	157	16.2025
===========oooooo==========	chr17:78367605-78367845(+)$1	240	195	222	18.7156
##a[gggggggmmmmggggggg]a333	chr8:67772773-67773013(+)$1	240	189	216	13.3283
===========oooooo==========	chr18:2803190-2803440(+)$1	250	10	37	18.7156
===========mmmm===========3	chr3:107880268-107880508(-)$1	240	184	211	19.5663
ggiiiiiiiiimmmmiiiiiiiii22g	chr2:42557639-42557879(+)$1	240	125	152	16.5433
===========mmmm============	chr21:18938816-18939056(+)$1	240	52	79	19.5031
:==========mmmm==========ff	chr17:46626896-46627137(-)$1	241	124	151	17.6693
!!iiiiiiiiimmmmiiiiiiiii22c	chr6:150046780-150047020(-)$1	240	59	86	16.8219
========[bbmmmmbb]=========	chr3:133876299-133876539(-)$1	240	194	221	16.9080
iiiiiii[cccnnnnnccc22iiiiii	chr14:31364018-31364258(-)$1	240	181	208	12.8754
ggg==========lll==========:	chr9:116169621-116169867(-)$1	246	50	77	16.8621
c:iiiiiiiiillliiiiiiiiigggg	chr19:46053312-46053561(-)$1	249	158	185	14.6136
========[bbmmmmbb==========	chr12:69968693-69968933(+)$1	240	89	116	17.2054
iiiiiiii[bblllbb]iiiiiiiii5	chr5:154267201-154267441(-)$1	240	70	97	14.3707
"==========mmmm==========ee	chr20:48506066-48506306(+)$1	240	59	86	18.8632
eee[gggggggmmmmggggggg]eeee	chr7:11142253-11142493(+)$1	240	149	176	11.5703
==========oooooo==========:	chr4:108969198-108969438(-)$1	240	157	184	18.1037
==========oooooo==========b	chr6:64291036-64291276(+)$1	240	138	165	18.6643
==iiiiiiiiimmmmiiiiiiiii::A	chr3:142778452-142778692(+)$1	240	174	201	14.3767
==========oooooo==========:	chr10:71910196-71910438(-)$1	242	25	52	18.1037
===========rrrrrrrrr=======	chr2:207178865-207179106(+)$1	241	195	222	14.5645
[==========nnnnn==========b	chr19:6585875-6586121(-)$1	246	216	243	17.8865
============lll============	chr4:52781243-52781483(+)$1	240	151	178	19.2073
e==========mmmm==========]e	chr2:37479934-37480176(-)$1	242	203	230	18.7833
===========oooooo==========	chr2:97475472-97475712(+)$1	240	59	86	18.7156
:==========mmmm==========::	chr4:48426050-48426290(+)$1	240	94	121	16.4753
==========oooooo==========h	chr13:108885554-108885794(+)$1	240	96	123	18.3907
iiiii"""cccmmmmccc22iiiiiii	chr6:89872170-89872410(+)$1	240	131	158	13.8236
ggggggg[ccclllccc]ggggggg33	chr17:49239124-49239364(+)$1	240	147	174	12.2421
$$$iiiiiiiiillliiiiiiiiiddd	chr6:76625440-76625680(+)$1	240	35	62	14.8518
d[==========lll==========]d	chr6:36078443-36078683(+)$1	240	89	116	18.2584
==========ammmma]==========	chr10:82279081-82279321(+)$1	240	144	171	18.7571
f!!iiiiiiiiillliiiiiiiii22f	chr14:51721782-51722062(+)$1	280	45	72	15.5274
!==========mmmm==========cc	chr6:7417823-7418063(+)$1	240	190	217	19.1196
+==========mmmm==========>>	chr6:86320868-86321108(-)$1	240	125	152	18.3461
==========ammmma]==========	chr6:151677482-151677722(+)$1	240	60	87	18.7571
===========mmmm===========:	chr17:61823831-61824072(-)$1	241	44	71	18.8063
##iiiiiiiiinnnnniiiiiiiiicc	chr6:109689677-109689917(-)$1	240	168	195	15.7451
[iiiiiiiiiooooooiiiiiiiiibb	chr2:100892452-100892692(-)$1	240	181	208	16.5289
$==========mmmm==========66	chr17:57188708-57188950(-)$1	242	111	138	18.2986

#otherMatches

#Seq PSSM
UAGAAUUGUUUAUCUUGAGCAGUUUGU	chr4:71588020-71588262(+)$1	242	60	87	14.6797
cuuuuuuuugcuuuuuGUAGAAGAGAU	chr12:123893004-123893246(+)$1	242	130	157	16.2025
UUUUUUGUCUUCUCACAAAGACAAGAA	chr17:78367605-78367845(+)$1	240	195	222	18.7156
UUUGUAUUUGCUUUUGCAAAUAGGUAU	chr8:67772773-67773013(+)$1	240	189	216	13.3283
uauauauauauauauaaauauauauau	chr18:2803190-2803440(+)$1	250	10	37	18.7156
aaaaauaauuuuaaaaaguuauuuuuu	chr3:107880268-107880508(-)$1	240	184	211	19.5663
UUUUUUUUUUUCCUGAAAAAGAAACCA	chr2:42557639-42557879(+)$1	240	125	152	16.5433
GAUAUUUUUCUUAUUAGAAAAAUAUUA	chr21:18938816-18939056(+)$1	240	52	79	19.5031
uacauuuuuuuuuaaGGAAAAGUGUGG	chr17:46626896-46627137(-)$1	241	124	151	17.6693
CUUUAUCCUUGUCUGCAGGGAUAAUAA	chr6:150046780-150047020(-)$1	240	59	86	16.8219
CUGCUUUCGUGUUUUUGGGAAAGCAGG	chr3:133876299-133876539(-)$1	240	194	221	16.9080
AUAUUUUAGCAUUAGUUGCACAAAAUG	chr14:31364018-31364258(-)$1	240	181	208	12.8754
UUAUUUUGUGAAGCCCCUUCACAAAAA	chr9:116169621-116169867(-)$1	246	50	77	16.8621
uagcuccgucacccugacggagugcag	chr19:46053312-46053561(-)$1	249	158	185	14.6136
UGAAGAUGCAAGUGCUUCAUUUUCAUU	chr12:69968693-69968933(+)$1	240	89	116	17.2054
UUGAGAUGGAGUUGCUGCAUUUUAGGA	chr5:154267201-154267441(-)$1	240	70	97	14.3707
GUUUACUUUUUGCAUGAAAAGUAAAUG	chr20:48506066-48506306(+)$1	240	59	86	18.8632
CACUUAUCAGAAAUAUUUGAUGUGUGC	chr7:11142253-11142493(+)$1	240	149	176	11.5703
GAGCUUUUAAAUAAAAUUGAAAGUUCU	chr4:108969198-108969438(-)$1	240	157	184	18.1037
UGUUUUAUUAUGUAAUUGAUAAAAUGG	chr6:64291036-64291276(+)$1	240	138	165	18.6643
AGAUACUAGUGAAGAUACUAGUAUAAG	chr3:142778452-142778692(+)$1	240	174	201	14.3767
AUUUUUAAUUUCCUUUGGUUAAAGGUC	chr10:71910196-71910438(-)$1	242	25	52	18.1037
UAAUGUGAAGACUAAUGUAUUUUUUAU	chr2:207178865-207179106(+)$1	241	195	222	14.5645
CAAGAGAAGGCAUUGAGCUUUUUCUUU	chr19:6585875-6586121(-)$1	246	216	243	17.8865
GUAUGUAUAUACAGUGUGUGUGUAUAC	chr4:52781243-52781483(+)$1	240	151	178	19.2073
GUUUGUUUUUUUAAUGAAAAACAAGUC	chr2:37479934-37480176(-)$1	242	203	230	18.7833
UUUUUUUUAAAUAUCAUUUUGGGAAGG	chr2:97475472-97475712(+)$1	240	59	86	18.7156
CAGAAAAAAAUGUCuauuuuuuuuuau	chr4:48426050-48426290(+)$1	240	94	121	16.4753
AAGAGUGAAGGCCAUAUUUCAUUUUUU	chr13:108885554-108885794(+)$1	240	96	123	18.3907
UAAAAUAUGUUAGUAAACCUUUUUGUA	chr6:89872170-89872410(+)$1	240	131	158	13.8236
CUGUAGGAAAUCUAGUUAUUUACAGGA	chr17:49239124-49239364(+)$1	240	147	174	12.2421
GUUUUGAGAUAAGUUUUGUUUCAAUUA	chr6:76625440-76625680(+)$1	240	35	62	14.8518
UUUAGUGAGUUUCUCAAGUUUAUUAUA	chr6:36078443-36078683(+)$1	240	89	116	18.2584
AGUGUACAUUCUAGUGUGGUGUAUACU	chr10:82279081-82279321(+)$1	240	144	171	18.7571
ACUGAUUUAGGAAGUUUUUAAGUUCAU	chr14:51721782-51722062(+)$1	280	45	72	15.5274
ACAUGAGUGUCCAGAGGCACUCAUGGG	chr6:7417823-7418063(+)$1	240	190	217	19.1196
UCAUUAAUAUAAAUGUGUGUUAGUGUA	chr6:86320868-86321108(-)$1	240	125	152	18.3461
CUUUCUAACCCAGUGGAGGUUAGAAAG	chr6:151677482-151677722(+)$1	240	60	87	18.7571
AGAUAAUCAAAUUAUUUUGAUUAUUUU	chr17:61823831-61824072(-)$1	241	44	71	18.8063
AAAUGUUGUCUUGUGCAGACAACAUCA	chr6:109689677-109689917(-)$1	240	168	195	15.7451
AUUUCUAAUUGGAUCAGAUUAGGGACC	chr2:100892452-100892692(-)$1	240	181	208	16.5289
Cuuuaaaauaacuauuuauuuuaaaau	chr17:57188708-57188950(-)$1	242	111	138	18.2986

#DB
..((((((((((...))))))))))..	chr4:71588020-71588262(+)$1	1	60	87	14.6797
.((((((((((.....)))))))))).	chr12:123893004-123893246(+)$1	1	130	157	16.2025
(((((((((((......))))))))))	chr17:78367605-78367845(+)$1	1	195	222	18.7156
..(.(((((((....))))))).)...	chr8:67772773-67773013(+)$1	1	189	216	13.3283
(((((((((((......))))))))))	chr18:2803190-2803440(+)$1	1	10	37	18.7156
(((((((((((....))))))))))).	chr3:107880268-107880508(-)$1	1	184	211	19.5663
(((((((((((....)))))))))..)	chr2:42557639-42557879(+)$1	1	125	152	16.5433
(((((((((((....))))))))))))	chr21:18938816-18939056(+)$1	1	52	79	19.5031
.((((((((((....))))))))))((	chr17:46626896-46627137(-)$1	1	124	151	17.6693
..(((((((((....)))))))))..)	chr6:150046780-150047020(-)$1	1	59	86	16.8219
((((((((.((....)).)))))))))	chr3:133876299-133876539(-)$1	1	194	221	16.9080
(((((((.(((.....)))..))))))	chr14:31364018-31364258(-)$1	1	181	208	12.8754
)))((((((((((...)))))))))).	chr9:116169621-116169867(-)$1	1	50	77	16.8621
).(((((((((...)))))))))((((	chr19:46053312-46053561(-)$1	1	158	185	14.6136
((((((((.((....))))))))))))	chr12:69968693-69968933(+)$1	1	89	116	17.2054
((((((((.((...)).))))))))).	chr5:154267201-154267441(-)$1	1	70	97	14.3707
.((((((((((....))))))))))))	chr20:48506066-48506306(+)$1	1	59	86	18.8632
(((.(((((((....))))))).))))	chr7:11142253-11142493(+)$1	1	149	176	11.5703
((((((((((......)))))))))).	chr4:108969198-108969438(-)$1	1	157	184	18.1037
((((((((((......)))))))))))	chr6:64291036-64291276(+)$1	1	138	165	18.6643
))(((((((((....)))))))))..)	chr3:142778452-142778692(+)$1	1	174	201	14.3767
((((((((((......)))))))))).	chr10:71910196-71910438(-)$1	1	25	52	18.1037
(((((((((((.........)))))))	chr2:207178865-207179106(+)$1	1	195	222	14.5645
.((((((((((.....)))))))))))	chr19:6585875-6586121(-)$1	1	216	243	17.8865
((((((((((((...))))))))))))	chr4:52781243-52781483(+)$1	1	151	178	19.2073
(((((((((((....)))))))))).)	chr2:37479934-37480176(-)$1	1	203	230	18.7833
(((((((((((......))))))))))	chr2:97475472-97475712(+)$1	1	59	86	18.7156
.((((((((((....))))))))))..	chr4:48426050-48426290(+)$1	1	94	121	16.4753
((((((((((......))))))))))(	chr13:108885554-108885794(+)$1	1	96	123	18.3907
(((((...(((....)))..)))))))	chr6:89872170-89872410(+)$1	1	131	158	13.8236
(((((((.(((...))).)))))))..	chr17:49239124-49239364(+)$1	1	147	174	12.2421
...(((((((((...))))))))))))	chr6:76625440-76625680(+)$1	1	35	62	14.8518
(.((((((((((...)))))))))).)	chr6:36078443-36078683(+)$1	1	89	116	18.2584
(((((((((((....).))))))))))	chr10:82279081-82279321(+)$1	1	144	171	18.7571
(..(((((((((...)))))))))..)	chr14:51721782-51722062(+)$1	1	45	72	15.5274
.((((((((((....))))))))))))	chr6:7417823-7418063(+)$1	1	190	217	19.1196
.((((((((((....))))))))))..	chr6:86320868-86321108(-)$1	1	125	152	18.3461
(((((((((((....).))))))))))	chr6:151677482-151677722(+)$1	1	60	87	18.7571
(((((((((((....))))))))))).	chr17:61823831-61824072(-)$1	1	44	71	18.8063
..(((((((((.....)))))))))))	chr6:109689677-109689917(-)$1	1	168	195	15.7451
.(((((((((......)))))))))))	chr2:100892452-100892692(-)$1	1	181	208	16.5289
.((((((((((....))))))))))..	chr17:57188708-57188950(-)$1	1	111	138	18.2986

#PSSM
= : 0.40	: : 0.09	g : 0.07	i : 0.07	# : 0.04	! : 0.04	e : 0.04	[ : 0.04	$ : 0.04	c : 0.02	" : 0.02	d : 0.02	f : 0.02	+ : 0.02	
= : 0.61	i : 0.09	g : 0.07	: : 0.04	# : 0.04	! : 0.04	e : 0.02	$ : 0.02	[ : 0.02	
= : 0.64	i : 0.21	g : 0.04	a : 0.02	e : 0.02	$ : 0.02	! : 0.02	
= : 0.66	i : 0.26	[ : 0.04	g : 0.02	
= : 0.66	i : 0.26	g : 0.07	
= : 0.66	i : 0.23	g : 0.07	" : 0.02	
= : 0.66	i : 0.23	g : 0.07	" : 0.02	
= : 0.66	i : 0.21	g : 0.04	[ : 0.04	" : 0.02	
= : 0.61	i : 0.19	[ : 0.07	c : 0.07	g : 0.04	
= : 0.61	i : 0.19	b : 0.07	c : 0.07	g : 0.04	
= : 0.47	i : 0.16	o : 0.11	b : 0.07	c : 0.07	g : 0.04	a : 0.04	
m : 0.47	o : 0.19	= : 0.09	n : 0.09	l : 0.07	i : 0.04	r : 0.02	
m : 0.47	l : 0.19	o : 0.19	n : 0.09	= : 0.02	r : 0.02	
m : 0.47	l : 0.21	o : 0.19	n : 0.09	r : 0.02	
m : 0.47	o : 0.19	l : 0.14	n : 0.09	i : 0.02	b : 0.02	r : 0.02	c : 0.02	
= : 0.30	o : 0.19	i : 0.14	n : 0.09	b : 0.07	g : 0.04	c : 0.04	a : 0.04	l : 0.02	r : 0.02	
= : 0.47	i : 0.19	o : 0.07	c : 0.07	] : 0.07	g : 0.04	b : 0.04	r : 0.02	
= : 0.61	i : 0.21	g : 0.04	] : 0.04	c : 0.04	r : 0.02	
= : 0.64	i : 0.21	g : 0.07	c : 0.02	r : 0.02	2 : 0.02	
= : 0.64	i : 0.21	g : 0.07	2 : 0.04	r : 0.02	
= : 0.66	i : 0.23	g : 0.07	2 : 0.02	
= : 0.66	i : 0.26	g : 0.07	
= : 0.66	i : 0.26	] : 0.04	g : 0.02	
= : 0.66	i : 0.23	g : 0.04	a : 0.02	e : 0.02	
= : 0.66	i : 0.11	2 : 0.07	g : 0.04	3 : 0.02	e : 0.02	: : 0.02	d : 0.02	
= : 0.45	: : 0.07	2 : 0.07	i : 0.07	3 : 0.04	e : 0.04	] : 0.04	c : 0.04	f : 0.02	g : 0.02	d : 0.02	> : 0.02	b : 0.02	6 : 0.02	
= : 0.23	: : 0.16	3 : 0.07	c : 0.07	e : 0.07	b : 0.07	g : 0.04	f : 0.04	i : 0.04	d : 0.04	5 : 0.02	A : 0.02	h : 0.02	> : 0.02	6 : 0.02	

#score	707.350329863031
#seq	42
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m2_run1.txt

#BEAR
cc[bbuuuuuuuuuuuubb]cc	chr17:17158084-17158343(-)$1	259	101	123	22.4026
eeeevvvvvvvvvvvvveeeee	chr8:42176790-42177049(+)$1	259	176	198	23.2972
ddccctttttttttttccc]dd	chr3:157823474-157823703(+)$1	229	63	85	22.1532
eeeeeuuuuuuuuuuuueeeee	chr2:43768192-43768451(+)$1	259	17	39	23.5214
acccvvvvvvvvvvvvvccc]a	chr9:114448939-114449168(+)$1	229	133	155	23.2625
cccyyyyyyyyyyyyyyyyccc	chrX:99917065-99917294(+)$1	229	81	103	20.3258
cc[bbuuuuuuuuuuuubb]cc	chr15:33952394-33952623(+)$1	229	35	57	22.4026
eeeeeuuuuuuuuuuuueeeee	chr8:146015752-146016011(+)$1	259	175	197	23.5214
!eeeeettttttttttteeeee	chr15:41228745-41228974(-)$1	229	139	161	22.4407
""cccuuuuuuuuuuuuccc33	chr1:74867400-74867663(-)$1	263	41	63	23.6763
c[cccuuuuuuuuuuuuccccc	chr19:11491779-11492038(+)$1	259	206	228	23.6698
cbbccctttttttttttccc]b	chr3:175473094-175473365(+)$1	271	94	116	21.6489
e[ccctttttttttttccc]ee	chr3:188592048-188592307(+)$1	259	38	60	22.6856
hhhhvvvvvvvvvvvvvhhhhh	chr6:160478956-160479215(+)$1	259	126	148	21.1948
!!cccwwwwwwwwwwwwwwccc	chr9:115013203-115013462(-)$1	259	58	80	21.8808
eeeeeuuuuuuuuuuuueeeee	chr12:461342-461571(+)$1	229	106	128	23.5214
cc[bbvvvvvvvvvvvvvbb]c	chr6:161560393-161560652(+)$1	259	57	79	21.9667
eeeeeuuuuuuuuuuuueeeee	chr19:56758647-56758906(-)$1	259	41	63	23.5214
eeeeeuuuuuuuuuuuueeeee	chr7:138529114-138529343(+)$1	229	129	151	23.5214
eeeevvvvvvvvvvvvveeeee	chr17:7403903-7404132(+)$1	229	111	133	23.2972
ffffvvvvvvvvvvvvvfffff	chr9:110247972-110248201(+)$1	229	13	35	22.2258
fffffuuuuuuuuuuuufffff	chr3:133293733-133293992(-)$1	259	1	23	22.3819
eeewwwwwwwwwwwwwweeeee	chr14:105916341-105916600(+)$1	259	47	69	21.8735
cbb[bbtttttttttttbbbb2	chr8:145154176-145154435(+)$1	259	88	110	19.9421
:eeeeettttttttttteeeee	chr9:126143716-126143975(-)$1	259	162	184	21.4373
[dddduuuuuuuuuuuudddd]	chr21:46226808-46227037(+)$1	229	47	69	23.1034
b[ddddtttttttttttdddd]	chr9:139741057-139741316(-)$1	259	117	139	21.7052
fffffuuuuuuuuuuuufffff	chr2:203914495-203914754(+)$1	259	156	178	22.3819
[ddddwwwwwwwwwwwwwwddd	chr19:6852876-6853105(-)$1	229	63	85	21.2840
gggggwwwwwwwwwwwwwwggg	chr3:142226736-142226995(-)$1	259	155	177	21.2922
eeeeeuuuuuuuuuuuueeeee	chr17:73321842-73322101(-)$1	259	8	30	23.5214
##ccctttttttttttccc444	chr4:89020495-89020754(-)$1	259	183	205	22.3633
cccccwwwwwwwwwwwwwwccc	chr12:57872908-57873137(+)$1	229	166	188	21.7404
iiyyyyyyyyyyyyyyyyiiii	chrX:64743822-64744081(-)$1	259	12	34	20.0303
ddddvvvvvvvvvvvvvdddd:	chr11:71671821-71672050(+)$1	229	143	165	21.7065
[cccauuuuuuuuuuuua]ccc	chr1:154143766-154144025(-)$1	259	215	237	23.5199
bbcccvvvvvvvvvvvvvccc]	chr12:50616016-50616275(+)$1	259	215	237	22.7159
eeeeeuuuuuuuuuuuueeeee	chr9:131073132-131073391(-)$1	259	86	108	23.5214
fffffuuuuuuuuuuuufffff	chr9:117692286-117692545(+)$1	259	87	109	22.3819
::ccctttttttttttcccggg	chr7:140396526-140396785(-)$1	259	126	148	20.5600
eeeevvvvvvvvvvvvveeeee	chr16:70177337-70177596(+)$1	259	96	118	23.2972
ccc[attttttttttta]ccc:	chr16:67063279-67063508(-)$1	229	113	135	21.6934
=====vvvvvvvvvvvvv====	chr10:64957023-64957282(-)$1	259	231	253	22.9329
eeeeeuuuuuuuuuuuueeeee	chr17:40028144-40028403(-)$1	259	210	232	23.5214
%ddddtttttttttttdddd66	chr9:132397334-132397593(+)$1	259	134	156	20.1520
e[cccuuuuuuuuuuuuccc]e	chr2:168997079-168997338(+)$1	259	127	149	23.8236
======ttttttttttt=====	chr15:71125327-71125586(+)$1	259	49	71	22.0064
a[ddddtttttttttttdddd]	chr18:32345815-32346078(+)$1	263	167	189	21.9493
eecccuuuuuuuuuuuuccc]e	chr9:138590807-138591066(+)$1	259	17	39	23.8195
ee[bbtttttttttttbb]eee	chr1:33429494-33429753(-)$1	259	233	255	21.5141
f[cccuuuuuuuuuuuucccff	chr17:34077137-34077396(+)$1	259	88	110	23.4782
ffcccwwwwwwwwwwwwwwccc	chr2:192543266-192543525(+)$1	259	114	136	21.5739
:eeeeettttttttttteeeee	chr18:11851713-11851972(+)$1	259	223	245	21.4373
ccddddtttttttttttdddd]	chr7:131817683-131817942(+)$1	259	108	130	21.8912
eeyyyyyyyyyyyyyyyyeeee	chr18:10681944-10682203(-)$1	259	111	133	20.4335
ddddvvvvvvvvvvvvvdddd3	chr5:10429929-10430158(+)$1	229	187	209	22.6955
$$cccuuuuuuuuuuuuccc66	chr13:92345424-92345683(+)$1	259	12	34	22.1750
ffffvvvvvvvvvvvvvfffff	chr7:144077021-144077250(+)$1	229	151	173	22.2258
!cccvvvvvvvvvvvvvccc]e	chr12:49225800-49226059(+)$1	259	51	73	23.4923
dddbbuuuuuuuuuuuubb]dd	chr9:86591769-86592028(-)$1	259	87	109	22.1386
"ddddtttttttttttdddd33	chr12:57937509-57937768(-)$1	259	210	232	21.8421
"ddddvvvvvvvvvvvvvdddd	chrX:71825070-71825329(+)$1	259	65	87	22.5755

#otherMatches

#Seq PSSM
AUUACAAGAUAUGGCAAGUCGU	chr17:17158084-17158343(-)$1	259	101	123	22.4026
AAGACACCAUUUUUUUUUCUUU	chr8:42176790-42177049(+)$1	259	176	198	23.2972
AGAGCGCccuccuccagcuccu	chr3:157823474-157823703(+)$1	229	63	85	22.1532
AACCUUUUUUUAGAGUUGGGUU	chr2:43768192-43768451(+)$1	259	17	39	23.5214
GCCCAUCAACUCUACCAGGGAC	chr9:114448939-114449168(+)$1	229	133	155	23.2625
AGCUUGCCUUUCUUCUAUUGCU	chrX:99917065-99917294(+)$1	229	81	103	20.3258
GAGUGAAGAGAAGAACCCAGUC	chr15:33952394-33952623(+)$1	229	35	57	22.4026
AUGCACCUUCCCAAUACUGCAU	chr8:146015752-146016011(+)$1	259	175	197	23.5214
CACUGCCACCAUGCCCAGCAGU	chr15:41228745-41228974(-)$1	229	139	161	22.4407
AAGCAUACACCUGAAAUUGCAU	chr1:74867400-74867663(-)$1	263	41	63	23.6763
UGCCCUAGAAUUGCAAUGGGAC	chr19:11491779-11492038(+)$1	259	206	228	23.6698
ACCACCAGGUUUUUAUAGGUAG	chr3:175473094-175473365(+)$1	271	94	116	21.6489
GUGUACUUAACGUUUUUACUUA	chr3:188592048-188592307(+)$1	259	38	60	22.6856
GAUUUGUGUUUAAUCUUAAUCC	chr6:160478956-160479215(+)$1	259	126	148	21.1948
UCCCUUUCUUACAUGCUUUAGG	chr9:115013203-115013462(-)$1	259	58	80	21.8808
AGCUUGUUCAAAUCCAAAGGCU	chr12:461342-461571(+)$1	229	106	128	23.5214
CACCCACAAAGAAGACGAGGAU	chr6:161560393-161560652(+)$1	259	57	79	21.9667
CAUCCUUCACAUUCUCUGGGUG	chr19:56758647-56758906(-)$1	259	41	63	23.5214
UCAGGACUCCACUGCACCCUGG	chr7:138529114-138529343(+)$1	229	129	151	23.5214
CCGGCCAUCCUAAAGCCCCGGC	chr17:7403903-7404132(+)$1	229	111	133	23.2972
ACUGAAUUCUCUUCUGGCAGUG	chr9:110247972-110248201(+)$1	229	13	35	22.2258
GUUAUCUAAACACAUUUGUAAC	chr3:133293733-133293992(-)$1	259	1	23	22.3819
CUUCAGGGGAAAUAGAAGAGGA	chr14:105916341-105916600(+)$1	259	47	69	21.8735
AGGCACACACAGGCACCGUCCG	chr8:145154176-145154435(+)$1	259	88	110	19.9421
UUUGUUACAGAAAACCAAGCAA	chr9:126143716-126143975(-)$1	259	162	184	21.4373
GACGGGCCCUCUAGAAACUGUG	chr21:46226808-46227037(+)$1	229	47	69	23.1034
GUGGGGGAUAGCAGCAGCCCCU	chr9:139741057-139741316(-)$1	259	117	139	21.7052
CAAGCCUUGUCAAUUUUGCUUG	chr2:203914495-203914754(+)$1	259	156	178	22.3819
GCAAGGUGGUGUCCAGAGACUU	chr19:6852876-6853105(-)$1	229	63	85	21.2840
UAAUGCACUUUGAAUCAUUUAU	chr3:142226736-142226995(-)$1	259	155	177	21.2922
UUGGCAAAAUCCCCAGAGCCAA	chr17:73321842-73322101(-)$1	259	8	30	23.5214
UGUCAUCUUAUUUCCUUGGAAA	chr4:89020495-89020754(-)$1	259	183	205	22.3633
CUGCCCCAGUAUAAGUAAAGGC	chr12:57872908-57873137(+)$1	229	166	188	21.7404
GCACUCCCAGAACUUCACGCAG	chrX:64743822-64744081(-)$1	259	12	34	20.0303
GUCUGUCAGUCAUCAAGAGACC	chr11:71671821-71672050(+)$1	229	143	165	21.7065
AUUCCAUAUAUAAUCCAGUGAG	chr1:154143766-154144025(-)$1	259	215	237	23.5199
UCCCCUUUCUAAAGUGCUGGGA	chr12:50616016-50616275(+)$1	259	215	237	22.7159
CAGGUACUCCAACCUCGACCUG	chr9:131073132-131073391(-)$1	259	86	108	23.5214
GAGGAGUCCACUUACCGUCCUC	chr9:117692286-117692545(+)$1	259	87	109	22.3819
CCCAGCCCCACACUCACUGACG	chr7:140396526-140396785(-)$1	259	126	148	20.5600
GAAGUUCUACAGUACCUCUUCU	chr16:70177337-70177596(+)$1	259	96	118	23.2972
GCCUCACCUCACACUCGCGGCU	chr16:67063279-67063508(-)$1	229	113	135	21.6934
UUUUCAGUUUGUUUUUAAGAGG	chr10:64957023-64957282(-)$1	259	231	253	22.9329
UGAGUGUAAAACCCAGUGCUCA	chr17:40028144-40028403(-)$1	259	210	232	23.5214
UGCCUCUGCCCUCCCCAGGCCA	chr9:132397334-132397593(+)$1	259	134	156	20.1520
UUUUCUUACUUUAUUUCGGGUA	chr2:168997079-168997338(+)$1	259	127	149	23.8236
GGUCCUCAUUCAACUCAAGGAC	chr15:71125327-71125586(+)$1	259	49	71	22.0064
GUUUGUUCAGAAGAAAUGCAAU	chr18:32345815-32346078(+)$1	263	167	189	21.9493
AGGCACCACCACUCACCUGCGC	chr9:138590807-138591066(+)$1	259	17	39	23.8195
AUCAGGCAAGCCCAGACUAGUG	chr1:33429494-33429753(-)$1	259	233	255	21.5141
GGCGCCGCAACACCAAAGCGCC	chr17:34077137-34077396(+)$1	259	88	110	23.4782
UUAAGCCCGGACUGAAAAACUU	chr2:192543266-192543525(+)$1	259	114	136	21.5739
ACCACUCCCCAGAACCAAGUGG	chr18:11851713-11851972(+)$1	259	223	245	21.4373
GCAGGGCAAAGCUUACCUCCUC	chr7:131817683-131817942(+)$1	259	108	130	21.8912
UGUGCACACCCCACCUACCAGA	chr18:10681944-10682203(-)$1	259	111	133	20.4335
UUAUGAACAUAUUAAAAAUGAC	chr5:10429929-10430158(+)$1	229	187	209	22.6955
ACAGAAACCCUUGAAACUCUCA	chr13:92345424-92345683(+)$1	259	12	34	22.1750
GAGCUGAAGAACAAGCUGCUCA	chr7:144077021-144077250(+)$1	229	151	173	22.2258
CAGACACACCCCCAUCUUCUCC	chr12:49225800-49226059(+)$1	259	51	73	23.4923
GAGGCAAGAAUAUUAAGGCUCU	chr9:86591769-86592028(-)$1	259	87	109	22.1386
UACAAGAAGAGCUGAAUUGUUU	chr12:57937509-57937768(-)$1	259	210	232	21.8421
AGUGGGCCAGUUCUGUUGCCAU	chrX:71825070-71825329(+)$1	259	65	87	22.5755

#DB
((.((............)).))	chr17:17158084-17158343(-)$1	1	101	123	22.4026
((((.............)))))	chr8:42176790-42177049(+)$1	1	176	198	23.2972
(((((...........))).))	chr3:157823474-157823703(+)$1	1	63	85	22.1532
(((((............)))))	chr2:43768192-43768451(+)$1	1	17	39	23.5214
((((.............))).)	chr9:114448939-114449168(+)$1	1	133	155	23.2625
(((................)))	chrX:99917065-99917294(+)$1	1	81	103	20.3258
((.((............)).))	chr15:33952394-33952623(+)$1	1	35	57	22.4026
(((((............)))))	chr8:146015752-146016011(+)$1	1	175	197	23.5214
.(((((...........)))))	chr15:41228745-41228974(-)$1	1	139	161	22.4407
..(((............)))..	chr1:74867400-74867663(-)$1	1	41	63	23.6763
(.(((............)))))	chr19:11491779-11492038(+)$1	1	206	228	23.6698
((((((...........))).)	chr3:175473094-175473365(+)$1	1	94	116	21.6489
(.(((...........))).))	chr3:188592048-188592307(+)$1	1	38	60	22.6856
((((.............)))))	chr6:160478956-160479215(+)$1	1	126	148	21.1948
..(((..............)))	chr9:115013203-115013462(-)$1	1	58	80	21.8808
(((((............)))))	chr12:461342-461571(+)$1	1	106	128	23.5214
((.((.............)).)	chr6:161560393-161560652(+)$1	1	57	79	21.9667
(((((............)))))	chr19:56758647-56758906(-)$1	1	41	63	23.5214
(((((............)))))	chr7:138529114-138529343(+)$1	1	129	151	23.5214
((((.............)))))	chr17:7403903-7404132(+)$1	1	111	133	23.2972
((((.............)))))	chr9:110247972-110248201(+)$1	1	13	35	22.2258
(((((............)))))	chr3:133293733-133293992(-)$1	1	1	23	22.3819
(((..............)))))	chr14:105916341-105916600(+)$1	1	47	69	21.8735
(((.((...........)))).	chr8:145154176-145154435(+)$1	1	88	110	19.9421
.(((((...........)))))	chr9:126143716-126143975(-)$1	1	162	184	21.4373
.((((............)))).	chr21:46226808-46227037(+)$1	1	47	69	23.1034
(.((((...........)))).	chr9:139741057-139741316(-)$1	1	117	139	21.7052
(((((............)))))	chr2:203914495-203914754(+)$1	1	156	178	22.3819
.((((..............)))	chr19:6852876-6853105(-)$1	1	63	85	21.2840
(((((..............)))	chr3:142226736-142226995(-)$1	1	155	177	21.2922
(((((............)))))	chr17:73321842-73322101(-)$1	1	8	30	23.5214
..(((...........)))...	chr4:89020495-89020754(-)$1	1	183	205	22.3633
(((((..............)))	chr12:57872908-57873137(+)$1	1	166	188	21.7404
((................))))	chrX:64743822-64744081(-)$1	1	12	34	20.0303
((((.............)))).	chr11:71671821-71672050(+)$1	1	143	165	21.7065
.((((............).)))	chr1:154143766-154144025(-)$1	1	215	237	23.5199
(((((.............))).	chr12:50616016-50616275(+)$1	1	215	237	22.7159
(((((............)))))	chr9:131073132-131073391(-)$1	1	86	108	23.5214
(((((............)))))	chr9:117692286-117692545(+)$1	1	87	109	22.3819
..(((...........)))(((	chr7:140396526-140396785(-)$1	1	126	148	20.5600
((((.............)))))	chr16:70177337-70177596(+)$1	1	96	118	23.2972
(((.(...........).))).	chr16:67063279-67063508(-)$1	1	113	135	21.6934
(((((.............))))	chr10:64957023-64957282(-)$1	1	231	253	22.9329
(((((............)))))	chr17:40028144-40028403(-)$1	1	210	232	23.5214
.((((...........))))..	chr9:132397334-132397593(+)$1	1	134	156	20.1520
(.(((............))).)	chr2:168997079-168997338(+)$1	1	127	149	23.8236
((((((...........)))))	chr15:71125327-71125586(+)$1	1	49	71	22.0064
(.((((...........)))).	chr18:32345815-32346078(+)$1	1	167	189	21.9493
(((((............))).)	chr9:138590807-138591066(+)$1	1	17	39	23.8195
((.((...........)).)))	chr1:33429494-33429753(-)$1	1	233	255	21.5141
(.(((............)))))	chr17:34077137-34077396(+)$1	1	88	110	23.4782
(((((..............)))	chr2:192543266-192543525(+)$1	1	114	136	21.5739
.(((((...........)))))	chr18:11851713-11851972(+)$1	1	223	245	21.4373
((((((...........)))).	chr7:131817683-131817942(+)$1	1	108	130	21.8912
((................))))	chr18:10681944-10682203(-)$1	1	111	133	20.4335
((((.............)))).	chr5:10429929-10430158(+)$1	1	187	209	22.6955
..(((............)))..	chr13:92345424-92345683(+)$1	1	12	34	22.1750
((((.............)))))	chr7:144077021-144077250(+)$1	1	151	173	22.2258
.(((.............))).)	chr12:49225800-49226059(+)$1	1	51	73	23.4923
(((((............)).))	chr9:86591769-86592028(-)$1	1	87	109	22.1386
.((((...........))))..	chr12:57937509-57937768(-)$1	1	210	232	21.8421
.((((.............))))	chrX:71825070-71825329(+)$1	1	65	87	22.5755

#PSSM
e : 0.27	c : 0.16	f : 0.11	d : 0.06	! : 0.04	" : 0.04	: : 0.04	[ : 0.04	a : 0.03	b : 0.03	= : 0.03	h : 0.01	g : 0.01	# : 0.01	i : 0.01	% : 0.01	$ : 0.01	
e : 0.29	c : 0.16	d : 0.14	[ : 0.09	f : 0.09	b : 0.04	= : 0.03	" : 0.01	h : 0.01	! : 0.01	g : 0.01	# : 0.01	i : 0.01	: : 0.01	$ : 0.01	
c : 0.30	e : 0.24	d : 0.17	f : 0.08	[ : 0.06	b : 0.03	y : 0.03	= : 0.03	h : 0.01	g : 0.01	
c : 0.29	e : 0.22	d : 0.16	b : 0.08	f : 0.08	y : 0.04	[ : 0.03	= : 0.03	h : 0.01	w : 0.01	g : 0.01	
c : 0.24	e : 0.17	v : 0.16	d : 0.12	b : 0.09	y : 0.04	f : 0.04	a : 0.03	= : 0.03	w : 0.01	g : 0.01	
u : 0.35	v : 0.22	t : 0.12	w : 0.09	y : 0.04	e : 0.04	d : 0.04	c : 0.01	b : 0.01	= : 0.01	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	t : 0.27	v : 0.22	w : 0.09	y : 0.04	
u : 0.35	v : 0.22	t : 0.14	w : 0.09	c : 0.06	y : 0.04	d : 0.03	a : 0.01	b : 0.01	
e : 0.24	c : 0.20	d : 0.12	b : 0.08	w : 0.08	f : 0.08	v : 0.06	y : 0.04	h : 0.01	a : 0.01	] : 0.01	= : 0.01	
e : 0.25	c : 0.24	d : 0.14	b : 0.08	w : 0.08	f : 0.08	] : 0.03	= : 0.03	y : 0.01	h : 0.01	i : 0.01	
e : 0.27	c : 0.25	d : 0.16	] : 0.08	f : 0.08	b : 0.03	g : 0.03	= : 0.03	h : 0.01	4 : 0.01	i : 0.01	
e : 0.29	c : 0.16	d : 0.16	] : 0.09	f : 0.09	3 : 0.03	g : 0.03	= : 0.03	6 : 0.03	h : 0.01	b : 0.01	4 : 0.01	i : 0.01	
e : 0.33	c : 0.14	f : 0.09	] : 0.08	d : 0.06	3 : 0.04	g : 0.03	: : 0.03	= : 0.03	6 : 0.03	a : 0.01	b : 0.01	h : 0.01	2 : 0.01	4 : 0.01	i : 0.01	

#score	1384.2713973830719
#seq	62
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_UTR_m2_run1.txt

#BEAR
dddd[ccc[ccc!!ggggggglllggggggg]ccc]ccc2	chr17:72199722-72199960(+)$1	238	178	218	12.2051
d!!eeeee[===========lll===========22eeee	chr21:34931877-34932138(+)$1	261	201	241	14.7368
!!bb[eeeee[a[a[ccc[allla]ccc]a]a]eeeee]b	chr11:67165694-67165953(-)$1	259	149	189	12.6413
gggggg"""eeeee[cccnnnnnccceeeee]ggggggg2	chr17:76203583-76203808(+)$1	225	135	175	14.0794
hhhhhbb####bb!!cccooooooccc4444bb4444bb3	chr16:74657103-74657360(-)$1	257	180	220	16.0520
ggggg"""ddddccc[ccclllccc]ccc22dddd333gg	chr5:180669210-180669445(-)$1	235	29	69	13.3074
!!dddd[bb[ccc!!cccooooooccc4444cccbb]ddd	chr14:77494699-77494959(-)$1	260	130	170	15.4217
f!!bb[bb[ddddccc[aooooooa]ccc]ddddbb]bb3	chr8:141570402-141570660(-)$1	258	77	117	13.4861
===ffffffccc!!ddddoooooodddd22ccc22fffff	chr11:94608293-94608529(+)$1	236	53	93	13.7343
ggg"""dddd!!ccccccooooooccc]ccc]ddddgggg	chr17:56167084-56167332(+)$1	248	58	98	15.8022
ggggggg[bb!!eeeeeccclllccc]eeeee4444bb]g	chr15:66629025-66629247(-)$1	222	5	45	12.0106
ggggg[==========[aqqqqqqqqa==========ggg	chr1:51702096-51702327(+)$1	231	41	81	13.7674
#ggggggg"""cccddddllldddd]ccc333ggggggg3	chr5:38938422-38938662(-)$1	240	100	140	13.9567
b[bb[==========[bbnnnnnbb]==========]bb]	chr6:75964449-75964694(-)$1	245	24	64	14.8740
::::==========acccooooooccc]a]==========	chr7:44604930-44605162(-)$1	232	33	73	15.4060
=====####iiiiiiiiiooooooiiiiiiiii=======	chr15:64434562-64434808(+)$1	246	9	49	18.8766
ee!!eeeee!!cccacccooooooccc]a]ccceeeee22	chr17:4848896-4849219(-)$1	323	151	191	15.5920
hhhhhh"""bb"""ddddoooooodddd333bb333hhhh	chr10:28908412-28908646(+)$1	234	48	88	15.0994
eeeeeeee!!==========mmmm==========eeeee:	chr16:87866004-87866287(-)$1	283	50	90	12.4494
b!!iiiiiiiii$$$$$cccmmmmccc333iiiiiiiii2	chr21:45406208-45406483(+)$1	275	167	207	14.1739
hhh"""ffffffa[ddddoooooodddd]a333ffffff]	chr2:183902732-183902975(-)$1	243	82	122	14.0046
c[dddd[ccc[==========lll==========22ccc]	chrX:70473837-70474079(-)$1	242	34	74	14.7266
cccc[ccc[ffffff!!aooooooa22ffffff]cccccc	chr17:43226189-43226441(+)$1	252	148	188	13.8156
####===========[bbnnnnnbb]===========444	chrX:84527638-84527882(+)$1	244	50	90	15.5479
cc[iiiiiiiiifffffflllffffff333iiiiiiiii]	chr19:18548383-18548610(-)$1	227	75	115	13.8028
iiiiiiii[a[bb[bbbbnnnnnbb]bb]bb333a]iiii	chr20:62331236-62331507(-)$1	271	81	121	12.5130
ggg[ccc"""eeeeecccooooooccc]eeeee]ccc]gg	chr9:138902282-138902541(-)$1	259	120	160	16.1884
[dddd"""dddd!!ddddoooooodddd22dddd333ddd	chr17:79879772-79880020(-)$1	248	149	189	13.9783
=========ggggggg[aooooooa]ggggggg333====	chr13:101322665-101322896(-)$1	231	25	65	18.2588
eee[ccc[ccc[ffffffooooooffffffccc]ccc]ee	chr5:10390375-10390606(+)$1	231	121	161	13.9044
::::===========[bboooooobb===========a!!	chr16:3333486-3333771(+)$1	285	137	177	13.7308
ooccc:=============oooooo=============:J	chr17:38078530-38078808(-)$1	278	9	49	13.9227
c============a[aqqqqqqqqa]a]============	chr6:99849390-99849606(-)$1	216	84	124	13.9825
cccggggggg$$$$$cccooooooccc333ggggggg22c	chr7:5460907-5461167(-)$1	260	199	239	16.6171
gggggg!!ggggggg[bboooooobb]ggggggggggggg	chr12:76453477-76453744(-)$1	267	17	57	16.4837
ddddbb"""ccc"""a[cccmmmmccc]a333ccc4444b	chr16:421201-421482(-)$1	281	156	196	12.9130
cccccc!!gggggggddddnnnnndddd]gggggggccc]	chr7:99698818-99699090(-)$1	272	10	50	13.2972
[cccccc"""eeeee[annnnna]eeeee333ccc]ccc]	chr1:224573113-224573359(-)$1	246	46	86	12.8912
bb[bb[ccc!!bb!!cccooooooccc333bb4444ccc2	chr2:20647968-20648231(+)$1	263	134	174	16.3199
bccc!!dddd[ccc[cccooooooccc]cccdddd22ccc	chr6:150047008-150047248(-)$1	240	114	154	15.0724
:eeeee!!bb[ddddcccooooooccc22ddddbb]eeee	chr5:179674111-179674349(-)$1	238	4	44	12.7302
ggggggg[ccc"""ddddnnnnndddd333ccc]gggggg	chr17:62657898-62658162(-)$1	264	50	90	14.5949
eeeee####gggggggrrrrrrrrrggggggg333eeeee	chr13:108866912-108867170(-)$1	258	214	254	12.5317
eee[ggggggg!!ccc[bbnnnnnbb]ccc22ggggggg2	chr12:110368464-110368687(-)$1	223	165	205	12.6130
ggggggg####eeeeeooooooeeeee4444ggggggg::	chr1:118409525-118409772(-)$1	247	165	205	12.6138
==[dddd####ggggggglllggggggg4444dddd]===	chr19:4304587-4304853(+)$1	266	219	259	12.8656
ggggg"""eeeee[ggggggglllggggggg]eeeee22g	chr19:39220167-39220405(+)$1	238	78	118	11.8397
ggggg$$$$$cccddddoooooodddd333ccc4444ggg	chr17:4798939-4799182(+)$1	243	157	197	15.3346
gggggg[bb!!ccc[cccoooooocccccc22bbgggggg	chr15:83876277-83876551(-)$1	274	121	161	16.3010
==============[bb[ammmma]bb]============	chrX:153279475-153279711(-)$1	236	118	158	15.2475
b[ggggggg####eeeeeooooooeeeeeggggggg]bba	chr1:226819651-226819900(-)$1	249	80	120	14.8660
cc"""bb!!ffffffcccooooooccc333ffffffbbcc	chr22:50247432-50247705(+)$1	273	163	203	15.2210
bb"""eeeee!!ffffffooooooffffff22eeeee444	chr5:154194652-154194906(+)$1	254	77	117	12.9586

#otherMatches

#Seq PSSM
CACUGCCAGGUGAAAUCUGGGGACCCCAGGUCCGCGUGGA	chr17:72199722-72199960(+)$1	238	178	218	12.2051
GAGGUAAGUAGGAGGAAUAUUAUGUAUUUUUCCUUUUUUA	chr21:34931877-34932138(+)$1	261	201	241	14.7368
GACUGUGAGCAGGAUCCUGGGGCCGAGGCUGCAGCUCAGG	chr11:67165694-67165953(-)$1	259	149	189	12.6413
aacauguaaaaauuauauaaaacguaaauuuccauguuga	chr17:76203583-76203808(+)$1	225	135	175	14.0794
UGGCAGGCCCAGUGAUGGAAGCAGCUAGUGAACGAUUCCC	chr16:74657103-74657360(-)$1	257	180	220	16.0520
AGUGAAUUAUCCAGUGUGUUAAACGGGCUGCGGGUUCCUC	chr5:180669210-180669445(-)$1	235	29	69	13.3074
UGCACUCCUCUCCUCUGCUCUCGUGCGUCCUGGAAGCAGU	chr14:77494699-77494959(-)$1	260	130	170	15.4217
UCACCGCGUCCGAAGGCUGCUCUAACCCUCUUGGCGGGGG	chr8:141570402-141570660(-)$1	258	77	117	13.4861
GAGUUUGCCUCUGACGUGUGGCUCCAUGGGAGAUAGGCAA	chr11:94608293-94608529(+)$1	236	53	93	13.7343
UUGAUCUAGUACCAGGGAGAAUAUUCCACUGAACUGUGAU	chr17:56167084-56167332(+)$1	248	58	98	15.8022
UUACUAUGUAUUUUUUCUUCUUGGAGUGAAAAUCCUUAGA	chr15:66629025-66629247(-)$1	222	5	45	12.0106
gggggcggggUGGGGAAGUGCUUCGUCUCCCCGCCCCCCC	chr1:51702096-51702327(+)$1	231	41	81	13.7674
AAUUUUGCUACUUGGUUGAUUUAGCACAAAAUGCAAAGUC	chr5:38938422-38938662(-)$1	240	100	140	13.9567
UGGAGUAUGUACAUGAUAAAUUAUAAUAUGUAUAUGGUUG	chr6:75964449-75964694(-)$1	245	24	64	14.8740
UUCCUCUCCCCGAGCACACGCACAUGUAGAUUCGGGGGGA	chr7:44604930-44605162(-)$1	232	33	73	15.4060
AGUAGGGGAGAUAGAGUUAAAGGAGGCUUUGUUUUAUUUA	chr15:64434562-64434808(+)$1	246	9	49	18.8766
GGCUGGGGGCCAGGGCUGGAUGGACAGACACCUCCCCCUA	chr17:4848896-4849219(-)$1	323	151	191	15.5920
UUCAGGAUACUAUUUUUGAGACAACAAAUUAAGGAACUUG	chr10:28908412-28908646(+)$1	234	48	88	15.0994
UUAAGGAGCUGGGGGAAGGCAGGAGCCUUCCUUUCUCCUG	chr16:87866004-87866287(-)$1	283	50	90	12.4494
UAAAUUGUAUUACAUUAAACUGGAGUUACUUGAUACAAUG	chr21:45406208-45406483(+)$1	275	167	207	14.1739
UGCGAAGGCCGCGGGCCCGUGACUgggcgcgaggcggccg	chr2:183902732-183902975(-)$1	243	82	122	14.0046
CACCGCCCGCCCGCCUGGUGCAGAGCGCUGGGCGCUGCGA	chrX:70473837-70474079(-)$1	242	34	74	14.7266
ACUGUGGGCGCUUAACCCUUUACUGACUUGAGCUCCCCAG	chr17:43226189-43226441(+)$1	252	148	188	13.8156
UUUUUUAGGACAGUCUUAGCAAGUAUGAUUGUUCUAGUCU	chrX:84527638-84527882(+)$1	244	50	90	15.5479
CGCCCGGCAGGUGCCCCGGCUCGGGGUCAUGCUUGUCGGC	chr19:18548383-18548610(-)$1	227	75	115	13.8028
CGUGGCUGUCUCCGCCCCAUCGAGGAGGAGGCCCGUCAGC	chr20:62331236-62331507(-)$1	271	81	121	12.5130
GUGUCCCUGUCCCCAGCCCACCAUGGCUUGGGGUGGGUCA	chr9:138902282-138902541(-)$1	259	120	160	16.1884
AGACCAAAUCUCUGGUUGUGCGCUUAACGUGAGGGUGGGU	chr17:79879772-79880020(-)$1	248	149	189	13.9783
UAAGCAUAGAGGUUGGGGUCUGUGUGCUAACCUGUGUUGU	chr13:101322665-101322896(-)$1	231	25	65	18.2588
UGUGUGCAUUCAUCAGCCUGGUGUGGUUGAGAGAGCAGAU	chr5:10390375-10390606(+)$1	231	121	161	13.9044
GUGGCGGCGCCUGGGACCGACUGAGGCCUAGGCGCCGGAG	chr16:3333486-3333771(+)$1	285	137	177	13.7308
UGCAGCCCCUUCCCCUGCCCAGGGUGGCAGGGGAGGGGUA	chr17:38078530-38078808(-)$1	278	9	49	13.9227
UCUUUUUCUGUUUCAGAAGAAAAGCAGCAAACAGAAAGGG	chr6:99849390-99849606(-)$1	216	84	124	13.9825
CUCUGGGACUACGCCGAGGCCGAACUUUUAGGUCCCACUG	chr7:5460907-5461167(-)$1	260	199	239	16.6171
UGAGAAACCACUGGUUUUAGCUUGGAUGCCAGUGUUUUUA	chr12:76453477-76453744(-)$1	267	17	57	16.4837
UGGGGGUUUGGCCCAGAAGGAACCCCUACCCAGCCCUGUC	chr16:421201-421482(-)$1	281	156	196	12.9130
CCUUGUCCGAUUGGCCCGCACGCAGUGGCGCCGGUCACGU	chr7:99698818-99699090(-)$1	272	10	50	13.2972
AUUUCUAAAUUGUCAAGAUUUACAUGGCAUUGUGGUGGAA	chr1:224573113-224573359(-)$1	246	46	86	12.8912
GGCUGUGUGUCUGUUCGACUCCCCUCGCCCCAUUUUCACC	chr2:20647968-20648231(+)$1	263	134	174	16.3199
CCAAACUGGACAUUGUGCAAUAAAGUAGAAUUCUAUAUUG	chr6:150047008-150047248(-)$1	240	114	154	15.0724
CGUAAAAUCCACUCCAGACUGUGUUCUAAGGGGGGCUUUA	chr5:179674111-179674349(-)$1	238	4	44	12.7302
GCGGCCGAGGCGCCGGCUGCUCGGGCCCCAGCCCCGGCCG	chr17:62657898-62658162(-)$1	264	50	90	14.5949
aaccaucaagaucucauuuuacagcugggauucucugguu	chr13:108866912-108867170(-)$1	258	214	254	12.5317
UUGCCUUUAUGGCCCUAGAGAAAGUCAAGGAACAUGGGGA	chr12:110368464-110368687(-)$1	223	165	205	12.6130
UGGUUCUAGUGGCAGUGGAUUGAUUGUAUUAAGGACCAAA	chr1:118409525-118409772(-)$1	247	165	205	12.6138
GAAGGGGACCAGGUGUUGCCGCAGCGCCCCCACUCCCUCC	chr19:4304587-4304853(+)$1	266	219	259	12.8656
UGGCCAGGAGGUUCCCCCGACCAGGUUGGGGAGACUUGGG	chr19:39220167-39220405(+)$1	238	78	118	11.8397
GACAUGGAGGGCUGCGGGCACUACCGUGUUGGUGAGGAUG	chr17:4798939-4799182(+)$1	243	157	197	15.3346
CUUGGCGCGGCCGGACGCGGGCGAGCGCCGAACGGCCGGG	chr15:83876277-83876551(-)$1	274	121	161	16.3010
CCAGGCCCGGGCCCUGCCCACCUGAGCUGGGCCUGGGCCU	chrX:153279475-153279711(-)$1	236	118	158	15.2475
AUUUUUAAGUUAUAUUUAUUUUGUUGGGUUUUAAAAUUGC	chr1:226819651-226819900(-)$1	249	80	120	14.8660
CGUCCGCAGCCGGCCGGGAGCCGCCCCAGAGGCCGGGCCG	chr22:50247432-50247705(+)$1	273	163	203	15.2210
GAGAGUUGGGAGUGGCUCGAAUCAGAGCCGUGCCCAAGAU	chr5:154194652-154194906(+)$1	254	77	117	12.9586

#DB
((((.(((.(((..(((((((...))))))).))).))).	chr17:72199722-72199960(+)$1	1	178	218	12.2051
(..(((((.(((((((((((...)))))))))))..))))	chr21:34931877-34932138(+)$1	1	201	241	14.7368
..((.(((((.(.(.(((.(...).))).).).))))).)	chr11:67165694-67165953(-)$1	1	149	189	12.6413
((((((...(((((.(((.....)))))))).))))))).	chr17:76203583-76203808(+)$1	1	135	175	14.0794
(((((((....((..(((......)))....))....)).	chr16:74657103-74657360(-)$1	1	180	220	16.0520
(((((...(((((((.(((...))).)))..))))...))	chr5:180669210-180669445(-)$1	1	29	69	13.3074
..((((.((.(((..(((......)))....))))).)))	chr14:77494699-77494959(-)$1	1	130	170	15.4217
(..((.((.(((((((.(......).))).)))))).)).	chr8:141570402-141570660(-)$1	1	77	117	13.4861
)))(((((((((..((((......))))..)))..)))))	chr11:94608293-94608529(+)$1	1	53	93	13.7343
(((...((((..((((((......))).))).))))))))	chr17:56167084-56167332(+)$1	1	58	98	15.8022
(((((((.((..((((((((...))).)))))....)).)	chr15:66629025-66629247(-)$1	1	5	45	12.0106
(((((.((((((((((.(........))))))))))))))	chr1:51702096-51702327(+)$1	1	41	81	13.7674
.(((((((...(((((((...)))).)))...))))))).	chr5:38938422-38938662(-)$1	1	100	140	13.9567
(.((.((((((((((.((.....)).)))))))))).)).	chr6:75964449-75964694(-)$1	1	24	64	14.8740
....((((((((((((((......))).).))))))))))	chr7:44604930-44605162(-)$1	1	33	73	15.4060
(((((....(((((((((......))))))))))))))))	chr15:64434562-64434808(+)$1	1	9	49	18.8766
((..(((((..(((((((......))).).))))))))..	chr17:4848896-4849219(-)$1	1	151	191	15.5920
((((((...((...((((......))))...))...))))	chr10:28908412-28908646(+)$1	1	48	88	15.0994
)))(((((..((((((((((....))))))))))))))).	chr16:87866004-87866287(-)$1	1	50	90	12.4494
(..(((((((((.....(((....)))...))))))))).	chr21:45406208-45406483(+)$1	1	167	207	14.1739
(((...(((((((.((((......)))).)...)))))).	chr2:183902732-183902975(-)$1	1	82	122	14.0046
(.((((.(((.((((((((((...))))))))))..))).	chrX:70473837-70474079(-)$1	1	34	74	14.7266
((((.(((.((((((..(......)..)))))).))))))	chr17:43226189-43226441(+)$1	1	148	188	13.8156
....(((((((((((.((.....)).)))))))))))...	chrX:84527638-84527882(+)$1	1	50	90	15.5479
((.(((((((((((((((...))))))...))))))))).	chr19:18548383-18548610(-)$1	1	75	115	13.8028
((((((((.(.((.((((.....)).)).))...).))))	chr20:62331236-62331507(-)$1	1	81	121	12.5130
(((.(((...((((((((......))).))))).))).))	chr9:138902282-138902541(-)$1	1	120	160	16.1884
.((((...((((..((((......))))..))))...)))	chr17:79879772-79880020(-)$1	1	149	189	13.9783
((((((((((((((((.(......).)))))))...))))	chr13:101322665-101322896(-)$1	1	25	65	18.2588
(((.(((.(((.((((((......))))))))).))).))	chr5:10390375-10390606(+)$1	1	121	161	13.9044
....(((((((((((.((......)))))))))))))(..	chr16:3333486-3333771(+)$1	1	137	177	13.7308
..))).(((((((((((((......))))))))))))).(	chr17:38078530-38078808(-)$1	1	9	49	13.9227
)(((((((((((((.(........).).))))))))))))	chr6:99849390-99849606(-)$1	1	84	124	13.9825
((((((((((.....(((......)))...)))))))..)	chr7:5460907-5461167(-)$1	1	199	239	16.6171
((((((..(((((((.((......)).)))))))))))))	chr12:76453477-76453744(-)$1	1	17	57	16.4837
((((((...(((...(.(((....))).)...)))....)	chr16:421201-421482(-)$1	1	156	196	12.9130
((((((..(((((((((((.....)))).)))))))))).	chr7:99698818-99699090(-)$1	1	10	50	13.2972
.((((((...(((((.(.....).)))))...))).))).	chr1:224573113-224573359(-)$1	1	46	86	12.8912
((.((.(((..((..(((......)))...))....))).	chr2:20647968-20648231(+)$1	1	134	174	16.3199
((((..((((.(((.(((......))).)))))))..)))	chr6:150047008-150047248(-)$1	1	114	154	15.0724
.(((((..((.(((((((......)))..)))))).))))	chr5:179674111-179674349(-)$1	1	4	44	12.7302
(((((((.(((...((((.....))))...))).))))))	chr17:62657898-62658162(-)$1	1	50	90	14.5949
(((((....(((((((.........)))))))...)))))	chr13:108866912-108867170(-)$1	1	214	254	12.5317
(((.(((((((..(((.((.....)).)))..))))))).	chr12:110368464-110368687(-)$1	1	165	205	12.6130
(((((((....(((((......)))))....)))))))..	chr1:118409525-118409772(-)$1	1	165	205	12.6138
((.((((....(((((((...)))))))....)))).)))	chr19:4304587-4304853(+)$1	1	219	259	12.8656
(((((...(((((.(((((((...))))))).)))))..)	chr19:39220167-39220405(+)$1	1	78	118	11.8397
(((((.....(((((((......))))...)))....)))	chr17:4798939-4799182(+)$1	1	157	197	15.3346
((((((.((..(((.(((......))))))..))))))))	chr15:83876277-83876551(-)$1	1	121	161	16.3010
((((((((((((((.((.(....).)).))))))))))))	chrX:153279475-153279711(-)$1	1	118	158	15.2475
(.(((((((....(((((......)))))))))))).)))	chr1:226819651-226819900(-)$1	1	80	120	14.8660
((...((..(((((((((......)))...))))))))))	chr22:50247432-50247705(+)$1	1	163	203	15.2210
((...(((((..((((((......))))))..)))))...	chr5:154194652-154194906(+)$1	1	77	117	12.9586

#PSSM
g : 0.22	c : 0.13	b : 0.11	= : 0.09	e : 0.09	d : 0.05	h : 0.05	: : 0.05	! : 0.03	# : 0.03	[ : 0.03	f : 0.01	i : 0.01	o : 0.01	
g : 0.24	c : 0.13	= : 0.11	e : 0.11	! : 0.09	d : 0.05	h : 0.05	[ : 0.05	: : 0.03	b : 0.03	# : 0.01	i : 0.01	o : 0.01	
g : 0.26	c : 0.11	d : 0.09	= : 0.09	e : 0.09	! : 0.07	h : 0.05	[ : 0.05	b : 0.03	: : 0.03	" : 0.03	# : 0.01	i : 0.01	
g : 0.24	d : 0.11	c : 0.09	e : 0.07	b : 0.07	" : 0.07	= : 0.07	i : 0.05	[ : 0.05	h : 0.03	: : 0.03	f : 0.01	! : 0.01	# : 0.01	
g : 0.26	= : 0.13	e : 0.09	c : 0.09	[ : 0.07	d : 0.07	" : 0.07	b : 0.05	i : 0.05	h : 0.03	f : 0.01	! : 0.01	
g : 0.18	= : 0.13	c : 0.11	e : 0.11	" : 0.09	b : 0.05	d : 0.05	[ : 0.05	i : 0.05	# : 0.03	f : 0.01	h : 0.01	: : 0.01	! : 0.01	$ : 0.01	
= : 0.16	g : 0.13	c : 0.11	" : 0.11	e : 0.09	b : 0.05	[ : 0.05	d : 0.05	i : 0.05	! : 0.05	f : 0.03	# : 0.03	$ : 0.01	
= : 0.16	" : 0.15	e : 0.09	# : 0.09	c : 0.07	g : 0.07	! : 0.07	b : 0.05	[ : 0.05	i : 0.05	f : 0.03	d : 0.03	$ : 0.01	
= : 0.16	" : 0.11	[ : 0.09	# : 0.09	g : 0.09	e : 0.07	d : 0.07	b : 0.07	c : 0.07	f : 0.03	! : 0.03	i : 0.03	$ : 0.01	
= : 0.16	c : 0.11	g : 0.11	d : 0.09	e : 0.07	# : 0.07	! : 0.07	b : 0.05	" : 0.05	i : 0.05	f : 0.05	[ : 0.01	a : 0.01	$ : 0.01	
= : 0.18	c : 0.13	! : 0.11	[ : 0.09	g : 0.09	e : 0.07	# : 0.07	d : 0.05	i : 0.05	f : 0.05	" : 0.01	b : 0.01	$ : 0.01	
= : 0.20	c : 0.16	e : 0.09	g : 0.09	d : 0.07	! : 0.07	b : 0.05	i : 0.05	f : 0.05	" : 0.03	a : 0.01	[ : 0.01	$ : 0.01	# : 0.01	
= : 0.20	c : 0.15	e : 0.11	f : 0.09	g : 0.09	! : 0.07	b : 0.05	" : 0.05	d : 0.03	$ : 0.03	[ : 0.01	i : 0.01	a : 0.01	# : 0.01	
= : 0.18	c : 0.15	! : 0.11	e : 0.11	f : 0.09	g : 0.09	" : 0.05	[ : 0.05	a : 0.03	$ : 0.03	d : 0.03	i : 0.01	
= : 0.15	d : 0.15	g : 0.13	[ : 0.11	e : 0.09	f : 0.09	c : 0.07	! : 0.05	a : 0.03	$ : 0.03	i : 0.01	b : 0.01	" : 0.01	
c : 0.30	d : 0.15	[ : 0.11	g : 0.09	= : 0.09	e : 0.05	f : 0.05	b : 0.03	a : 0.03	i : 0.01	$ : 0.01	! : 0.01	
c : 0.28	d : 0.15	b : 0.11	[ : 0.09	= : 0.07	g : 0.05	f : 0.05	e : 0.03	i : 0.01	$ : 0.01	! : 0.01	q : 0.01	a : 0.01	r : 0.01	o : 0.01	
c : 0.33	d : 0.13	b : 0.11	= : 0.07	a : 0.07	g : 0.05	f : 0.05	o : 0.03	i : 0.01	q : 0.01	n : 0.01	r : 0.01	[ : 0.01	e : 0.01	
o : 0.50	n : 0.11	= : 0.07	c : 0.07	l : 0.05	g : 0.03	q : 0.03	[ : 0.01	d : 0.01	r : 0.01	b : 0.01	a : 0.01	
o : 0.52	n : 0.15	l : 0.07	= : 0.05	c : 0.05	g : 0.03	q : 0.03	a : 0.01	r : 0.01	m : 0.01	
o : 0.52	n : 0.15	l : 0.13	m : 0.07	g : 0.03	q : 0.03	= : 0.01	r : 0.01	
o : 0.52	n : 0.15	l : 0.13	m : 0.07	q : 0.03	d : 0.01	f : 0.01	r : 0.01	g : 0.01	
o : 0.50	n : 0.13	l : 0.11	m : 0.07	q : 0.03	c : 0.01	d : 0.01	f : 0.01	a : 0.01	r : 0.01	e : 0.01	g : 0.01	
o : 0.49	l : 0.05	c : 0.05	d : 0.05	b : 0.05	m : 0.05	a : 0.03	q : 0.03	n : 0.03	= : 0.01	f : 0.01	] : 0.01	r : 0.01	e : 0.01	g : 0.01	
c : 0.32	d : 0.15	b : 0.11	a : 0.07	g : 0.05	= : 0.05	f : 0.05	e : 0.05	] : 0.03	q : 0.01	i : 0.01	o : 0.01	r : 0.01	
c : 0.32	] : 0.15	d : 0.13	g : 0.07	= : 0.07	b : 0.07	f : 0.05	e : 0.05	q : 0.01	i : 0.01	2 : 0.01	
c : 0.33	= : 0.13	d : 0.13	g : 0.09	e : 0.07	] : 0.05	f : 0.05	a : 0.03	b : 0.03	i : 0.01	2 : 0.01	
= : 0.15	] : 0.15	3 : 0.13	g : 0.11	c : 0.11	d : 0.09	e : 0.07	4 : 0.05	f : 0.05	i : 0.01	b : 0.01	2 : 0.01	
= : 0.18	3 : 0.15	c : 0.13	g : 0.09	e : 0.09	] : 0.07	4 : 0.07	2 : 0.05	a : 0.05	f : 0.05	i : 0.01	
3 : 0.20	= : 0.18	g : 0.13	4 : 0.07	c : 0.07	e : 0.05	2 : 0.05	] : 0.05	f : 0.05	a : 0.03	i : 0.01	b : 0.01	d : 0.01	
= : 0.20	g : 0.15	c : 0.13	3 : 0.09	4 : 0.07	2 : 0.07	e : 0.05	d : 0.05	i : 0.05	f : 0.03	b : 0.03	] : 0.01	
= : 0.20	g : 0.13	c : 0.11	d : 0.09	3 : 0.09	] : 0.07	b : 0.05	i : 0.05	2 : 0.05	e : 0.03	f : 0.03	a : 0.01	4 : 0.01	
= : 0.20	c : 0.16	g : 0.16	d : 0.13	b : 0.05	i : 0.05	3 : 0.05	e : 0.05	4 : 0.03	f : 0.03	] : 0.01	
= : 0.22	g : 0.15	d : 0.11	c : 0.07	e : 0.07	4 : 0.07	3 : 0.07	] : 0.07	i : 0.03	f : 0.03	b : 0.03	2 : 0.01	
g : 0.18	= : 0.16	c : 0.11	e : 0.09	4 : 0.07	d : 0.07	3 : 0.07	2 : 0.05	b : 0.05	i : 0.03	f : 0.03	a : 0.01	
g : 0.18	= : 0.16	e : 0.11	4 : 0.09	] : 0.07	3 : 0.07	2 : 0.05	f : 0.05	c : 0.05	b : 0.03	d : 0.03	i : 0.03	
g : 0.16	= : 0.16	c : 0.15	e : 0.15	] : 0.09	4 : 0.05	i : 0.05	3 : 0.03	f : 0.03	b : 0.03	h : 0.01	2 : 0.01	
g : 0.18	c : 0.13	= : 0.13	e : 0.11	b : 0.11	i : 0.05	4 : 0.05	d : 0.03	f : 0.03	] : 0.03	2 : 0.03	3 : 0.01	h : 0.01	a : 0.01	
g : 0.20	c : 0.15	= : 0.11	e : 0.09	b : 0.07	2 : 0.05	i : 0.05	4 : 0.05	] : 0.03	d : 0.03	f : 0.03	: : 0.03	h : 0.01	! : 0.01	
g : 0.18	2 : 0.11	] : 0.11	= : 0.11	e : 0.07	c : 0.07	3 : 0.05	b : 0.03	d : 0.03	: : 0.03	4 : 0.03	f : 0.01	h : 0.01	i : 0.01	! : 0.01	J : 0.01	a : 0.01	

#score	759.3635306427676
#seq	53
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_CDS_m3_run1.txt

#BEAR
[eeeeeqqqqqqqqeeeee	chr6:121563321-121563557(-)$1	236	95	114	14.3067
ee[cccqqqqqqqqcccee	chr15:86124998-86125239(+)$1	241	35	54	14.8309
ffffffqqqqqqqqfffff	chrX:110931116-110931382(+)$1	266	193	212	13.0113
ccccccqqqqqqqqccc]c	chr2:46815208-46815454(-)$1	246	196	215	14.7463
ffffffqqqqqqqqfffff	chr12:6646688-6646996(+)$1	308	201	220	13.0113
e[ddddqqqqqqqqdddde	chr20:49509454-49509680(-)$1	226	32	51	14.6373
bb[cccqqqqqqqqcccbb	chr12:52943008-52943232(-)$1	224	95	114	13.8296
geeeeeqqqqqqqqeeeee	chr3:48728706-48728928(-)$1	222	16	35	14.2045
bb[cccqqqqqqqqccc]b	chrX:34961966-34962180(+)$1	214	163	182	14.2099
:eeeeeqqqqqqqqeeeee	chr11:102220890-102221114(+)$1	224	123	142	13.4023
iiiiiiqqqqqqqqiiiii	chr15:42987847-42988064(+)$1	217	82	101	13.9491
ccccccqqqqqqqqccc]c	chr11:5968888-5969109(+)$1	221	88	107	14.7463
bbddddqqqqqqqqdddd]	chr9:138454114-138454335(+)$1	221	35	54	14.2162
c[ddddqqqqqqqqdddd3	chr12:92818574-92818788(+)$1	214	121	140	14.8260
ffffffqqqqqqqqfffff	chr1:185276978-185277284(-)$1	306	259	278	13.0113
d!!cccqqqqqqqqccc44	chr18:56204317-56204540(-)$1	223	43	62	14.9833
""ddddqqqqqqqqdddd2	chr18:8624843-8625059(+)$1	216	93	112	14.5399
d!!cccqqqqqqqqccc]d	chr4:675694-675907(+)$1	213	28	47	14.8094
###cccqqqqqqqqccc44	chr8:67507769-67507998(-)$1	229	33	52	14.8749
cc[cccqqqqqqqqccccc	chr14:31553930-31554187(+)$1	257	190	209	14.8032
[eeeeeqqqqqqqqeeeee	chr19:12885286-12885516(-)$1	230	51	70	14.3067
cc[cccqqqqqqqqccc]c	chr15:44951286-44951587(-)$1	301	13	32	14.8733
eeee[aqqqqqqqqa]eee	chr19:40740857-40741079(-)$1	222	111	130	14.1831
====[aqqqqqqqqa====	chr6:42996841-42997109(+)$1	268	211	230	14.3769
b!!cccqqqqqqqqccc66	chr2:179826059-179826291(-)$1	232	25	44	13.9148
[eeeeeqqqqqqqqeeeee	chr22:41545798-41546212(+)$1	414	353	372	14.3067
d[ddddqqqqqqqqdddd3	chr4:24577965-24578241(-)$1	276	100	119	14.7061
eee[bbqqqqqqqqbb]ee	chr19:54783730-54783949(-)$1	219	176	195	13.2224
gg[cccqqqqqqqqcccgg	chr3:50004879-50005124(+)$1	245	28	47	14.7687
cc[cccqqqqqqqqccccc	chr14:97000807-97001038(+)$1	231	35	54	14.8032
:eeeeeqqqqqqqqeeeee	chr16:70432046-70432263(-)$1	217	4	23	13.4023
eee[bbqqqqqqqqbb333	chr12:54920403-54920632(+)$1	229	164	183	13.3016
b[ddddqqqqqqqqddddb	chr12:98927293-98927553(+)$1	260	31	50	14.2806
ddcccaqqqqqqqqa]ccc	chr1:154229448-154229784(+)$1	336	72	91	14.1509
f[ddddqqqqqqqqdddd]	chr12:7045390-7045614(+)$1	224	30	49	14.7121
dddcccqqqqqqqqccc::	chr19:15533727-15534019(-)$1	292	268	287	12.7339
======qqqqqqqq=====	chr1:16380072-16380285(+)$1	213	14	33	14.2694
[ccc[aqqqqqqqqacccb	chr17:3594887-3595104(-)$1	217	182	201	14.3140
ccccccqqqqqqqqccc33	chr3:122334538-122334751(+)$1	213	156	175	14.8625
eeeeeeqqqqqqqqeeeee	chr10:102896528-102896739(+)$1	211	146	165	14.1326
ffffffqqqqqqqqfffff	chr13:99947587-99947825(-)$1	238	207	226	13.0113
f[ddddqqqqqqqqddddf	chr14:94776084-94776302(-)$1	218	143	162	14.5422
$$$cccqqqqqqqqccc33	chr3:57302386-57302606(+)$1	220	124	143	14.3527
eee[bbqqqqqqqqbb]ee	chr15:52357014-52357272(+)$1	258	17	36	13.2224
ffbb[aqqqqqqqqa]bb]	chr11:1097723-1097938(+)$1	215	51	70	12.7594
Fccc[aqqqqqqqqa]ccc	chrX:64959638-64959955(+)$1	317	255	274	13.8830
ccc[bbqqqqqqqqbb]cc	chr8:25287263-25287508(-)$1	245	168	187	13.1378
[eeeeeqqqqqqqqeeeee	chr19:55175605-55175820(+)$1	215	15	34	14.3067
dd!!bbqqqqqqqqbb]dd	chr16:68324324-68324591(+)$1	267	149	168	12.9876
$$ddddqqqqqqqqddddf	chr20:3784035-3784254(+)$1	219	104	123	14.1849
ii[cccqqqqqqqqccc]i	chr11:6540639-6540939(+)$1	300	11	30	14.8861
:eeeeeqqqqqqqqeeeee	chr11:93778907-93779121(+)$1	214	185	204	13.4023
a!!cccqqqqqqqqccca]	chr13:33110187-33110410(-)$1	223	53	72	15.0131
[eeeeeqqqqqqqqeeeee	chr16:30507455-30507776(+)$1	321	277	296	14.3067
dddd[aqqqqqqqqa]ddd	chr15:68378786-68379050(+)$1	264	158	177	13.9992
f:ddddqqqqqqqqdddd:	chr15:49926636-49926851(+)$1	215	149	168	12.6569
dd[cccqqqqqqqqccc]d	chr17:729162-729389(-)$1	227	128	147	14.5382
e[ddddqqqqqqqqdddde	chr2:219498336-219498551(+)$1	215	44	63	14.6373
""ddddqqqqqqqqdddd]	chr9:5919884-5920174(-)$1	290	251	270	14.7765
ffddddqqqqqqqqdddd:	chr7:102292782-102293094(-)$1	312	160	179	13.5106
d:ddddqqqqqqqqddddd	chr10:1175148-1175364(+)$1	216	158	177	13.3646
:eeeeeqqqqqqqqeeeee	chr12:48527141-48527356(+)$1	215	15	34	13.4023
##ddddqqqqqqqqdddd4	chr20:47782463-47782705(-)$1	242	32	51	14.7146
b[ddddqqqqqqqqdddd]	chr8:22864626-22864859(+)$1	233	166	185	14.6406
:eeeeeqqqqqqqqeeeee	chr12:119624774-119624987(+)$1	213	114	133	13.4023
##ddddqqqqqqqqdddde	chr19:57910517-57910739(+)$1	222	21	40	14.6633
ggggggqqqqqqqqggggg	chr19:11943320-11943535(+)$1	215	171	190	13.8641
[ccc[aqqqqqqqqaccc]	chr1:68614153-68614371(-)$1	218	22	41	14.6740
ccccccqqqqqqqqccc]c	chr11:64535510-64535790(-)$1	280	168	187	14.7463

#otherMatches

#Seq PSSM
UAGAUGAUUUACUACAUUU	chr6:121563321-121563557(-)$1	236	95	114	14.3067
AGACUUGAUAGAGGAGGCU	chr15:86124998-86125239(+)$1	241	35	54	14.8309
uauauuuacaaaauaauau	chrX:110931116-110931382(+)$1	266	193	212	13.0113
gguacugugaaaugaguaa	chr2:46815208-46815454(-)$1	246	196	215	14.7463
UGAGCUGAACGGGAAGCUC	chr12:6646688-6646996(+)$1	308	201	220	13.0113
CACAUUGAUGAAGAGAUGG	chr20:49509454-49509680(-)$1	226	32	51	14.6373
GUAUGAGGAGGAAAUCAAC	chr12:52943008-52943232(-)$1	224	95	114	13.8296
UAAGUUAGAAGAAGAAUUU	chr3:48728706-48728928(-)$1	222	16	35	14.2045
GCCCCAUCUCCGCCUGGUG	chrX:34961966-34962180(+)$1	214	163	182	14.2099
GGAACAUAGUAGCUUGUUC	chr11:102220890-102221114(+)$1	224	123	142	13.4023
GUCCUUCCCAGGAAGAGGA	chr15:42987847-42988064(+)$1	217	82	101	13.9491
UGAGAUAUCCAUCAAUCAU	chr11:5968888-5969109(+)$1	221	88	107	14.7463
CCUGGCACUCCAUGGCCAU	chr9:138454114-138454335(+)$1	221	35	54	14.2162
GUGUGAGCAAUAUGUCACU	chr12:92818574-92818788(+)$1	214	121	140	14.8260
AUAGCAUUUCAAUUUGUUG	chr1:185276978-185277284(-)$1	306	259	278	13.0113
ACCAGCCAGUUAUAGUUCA	chr18:56204317-56204540(-)$1	223	43	62	14.9833
UGUUGACUUCAAAAUCAAA	chr18:8624843-8625059(+)$1	216	93	112	14.5399
CAACCUGGACUACAAGGCG	chr4:675694-675907(+)$1	213	28	47	14.8094
GAAUUCUACUAUGCGAAGA	chr8:67507769-67507998(-)$1	229	33	52	14.8749
GUAUGGGAGACACACCAAC	chr14:31553930-31554187(+)$1	257	190	209	14.8032
GAUUAGAGGACAGACUGGU	chr19:12885286-12885516(-)$1	230	51	70	14.3067
GUUUAUCAAAUCAAAUGUA	chr15:44951286-44951587(-)$1	301	13	32	14.8733
CACACCCCCUGACCGCUGU	chr19:40740857-40741079(-)$1	222	111	130	14.1831
GGCAAGGAUCACAGCUGCC	chr6:42996841-42997109(+)$1	268	211	230	14.3769
GCUGUAUAAAAGCUUGCUA	chr2:179826059-179826291(-)$1	232	25	44	13.9148
UCUGUUCCUACCCCAACAG	chr22:41545798-41546212(+)$1	414	353	372	14.3067
AAAGCUUCCCAUUCAGCUC	chr4:24577965-24578241(-)$1	276	100	119	14.7061
GCUUGUGAAGAACGGCCAG	chr19:54783730-54783949(-)$1	219	176	195	13.2224
GCCAAGAAGAAAGGUUUGC	chr3:50004879-50005124(+)$1	245	28	47	14.7687
AGUGCUAUUGAAACAGCCU	chr14:97000807-97001038(+)$1	231	35	54	14.8032
CGCCUCAGCAAGGAGAGGC	chr16:70432046-70432263(-)$1	217	4	23	13.4023
UGUUGGCACUUUUUCCUUU	chr12:54920403-54920632(+)$1	229	164	183	13.3016
UAGACUGAGUGAGAAGUCA	chr12:98927293-98927553(+)$1	260	31	50	14.2806
CUGCUCCCCCUUUUGAAGC	chr1:154229448-154229784(+)$1	336	72	91	14.1509
UCUCCCCACGCCAUGGGAC	chr12:7045390-7045614(+)$1	224	30	49	14.7121
CCGGGCACACUACAGCCAG	chr19:15533727-15534019(-)$1	292	268	287	12.7339
CUCACAUCCCUGACUGUGG	chr1:16380072-16380285(+)$1	213	14	33	14.2694
UAGCACACGGCCAAGGCUG	chr17:3594887-3595104(-)$1	217	182	201	14.3140
GAUACCCAAGGUCUGGUAA	chr3:122334538-122334751(+)$1	213	156	175	14.8625
GCCCAUUCUGCCCUGUGGG	chr10:102896528-102896739(+)$1	211	146	165	14.1326
AUGUUGCAAUUAUUCAACA	chr13:99947587-99947825(-)$1	238	207	226	13.0113
CCUUCCGGACAAGGGGAAG	chr14:94776084-94776302(-)$1	218	143	162	14.5422
aaaAGGUAUACAGUCCUAA	chr3:57302386-57302606(+)$1	220	124	143	14.3527
GUUCCUCUUUAACAAGCAG	chr15:52357014-52357272(+)$1	258	17	36	13.2224
CUGGUGAACGACCCCUCCA	chr11:1097723-1097938(+)$1	215	51	70	12.7594
UGGGACCAAACCUAGCCCC	chrX:64959638-64959955(+)$1	317	255	274	13.8830
UGAAAAUGUUUUCCUUAUC	chr8:25287263-25287508(-)$1	245	168	187	13.1378
CCUCCUUCUCUCCUAGGAG	chr19:55175605-55175820(+)$1	215	15	34	14.3067
GCUUGGCUGGAACUCCUGC	chr16:68324324-68324591(+)$1	267	149	168	12.9876
CCUCAUUUUCCACUGUGAA	chr20:3784035-3784254(+)$1	219	104	123	14.1849
UCUGGUCAAAUAAAAUUUG	chr11:6540639-6540939(+)$1	300	11	30	14.8861
AAUCCUUUAUUACUGGGGU	chr11:93778907-93779121(+)$1	214	185	204	13.4023
UCAGUAUAUCCUUUUAUAG	chr13:33110187-33110410(-)$1	223	53	72	15.0131
UGGCAAUUUCUUUCUUGCU	chr16:30507455-30507776(+)$1	321	277	296	14.3067
UCCCUGUUUCUCUUCUGGG	chr15:68378786-68379050(+)$1	264	158	177	13.9992
UCAUCUGCAAAAAAGGAUU	chr15:49926636-49926851(+)$1	215	149	168	12.6569
GCCACCACUGGGAAGGUUG	chr17:729162-729389(-)$1	227	128	147	14.5382
GUCUGUCUCAUUCCGCAGC	chr2:219498336-219498551(+)$1	215	44	63	14.6373
CCCAGUAAUCCUCCACUGC	chr9:5919884-5920174(-)$1	290	251	270	14.7765
CAUCCACCACCUCCUGGAG	chr7:102292782-102293094(-)$1	312	160	179	13.5106
CACUGUUUGCCAGCACAGA	chr10:1175148-1175364(+)$1	216	158	177	13.3646
GGGUCAAUUGACAAUGACU	chr12:48527141-48527356(+)$1	215	15	34	13.4023
CAAGAACCAGUCUCUUCUC	chr20:47782463-47782705(-)$1	242	32	51	14.7146
UGACGUGUGCGAGAGCGUG	chr8:22864626-22864859(+)$1	233	166	185	14.6406
AUCCAGUAAGUAACCUGGA	chr12:119624774-119624987(+)$1	213	114	133	13.4023
CAUUUGUUAGACAUCAGAG	chr19:57910517-57910739(+)$1	222	21	40	14.6633
CCUUUUGAUAUCAUGAAAG	chr19:11943320-11943535(+)$1	215	171	190	13.8641
CCUCAGGAUCAGCACGAGC	chr1:68614153-68614371(-)$1	218	22	41	14.6740
AGCGCACCUCGUCCUGCUG	chr11:64535510-64535790(-)$1	280	168	187	14.7463

#DB
.(((((........)))))	chr6:121563321-121563557(-)$1	1	95	114	14.3067
((.(((........)))))	chr15:86124998-86125239(+)$1	1	35	54	14.8309
((((((........)))))	chrX:110931116-110931382(+)$1	1	193	212	13.0113
((((((........))).)	chr2:46815208-46815454(-)$1	1	196	215	14.7463
((((((........)))))	chr12:6646688-6646996(+)$1	1	201	220	13.0113
(.((((........)))))	chr20:49509454-49509680(-)$1	1	32	51	14.6373
((.(((........)))))	chr12:52943008-52943232(-)$1	1	95	114	13.8296
((((((........)))))	chr3:48728706-48728928(-)$1	1	16	35	14.2045
((.(((........))).)	chrX:34961966-34962180(+)$1	1	163	182	14.2099
.(((((........)))))	chr11:102220890-102221114(+)$1	1	123	142	13.4023
((((((........)))))	chr15:42987847-42988064(+)$1	1	82	101	13.9491
((((((........))).)	chr11:5968888-5969109(+)$1	1	88	107	14.7463
((((((........)))).	chr9:138454114-138454335(+)$1	1	35	54	14.2162
(.((((........)))).	chr12:92818574-92818788(+)$1	1	121	140	14.8260
((((((........)))))	chr1:185276978-185277284(-)$1	1	259	278	13.0113
(..(((........)))..	chr18:56204317-56204540(-)$1	1	43	62	14.9833
..((((........)))).	chr18:8624843-8625059(+)$1	1	93	112	14.5399
(..(((........))).)	chr4:675694-675907(+)$1	1	28	47	14.8094
...(((........)))..	chr8:67507769-67507998(-)$1	1	33	52	14.8749
((.(((........)))))	chr14:31553930-31554187(+)$1	1	190	209	14.8032
.(((((........)))))	chr19:12885286-12885516(-)$1	1	51	70	14.3067
((.(((........))).)	chr15:44951286-44951587(-)$1	1	13	32	14.8733
((((.(........).)))	chr19:40740857-40741079(-)$1	1	111	130	14.1831
((((.(........)))))	chr6:42996841-42997109(+)$1	1	211	230	14.3769
(..(((........)))..	chr2:179826059-179826291(-)$1	1	25	44	13.9148
.(((((........)))))	chr22:41545798-41546212(+)$1	1	353	372	14.3067
(.((((........)))).	chr4:24577965-24578241(-)$1	1	100	119	14.7061
(((.((........)).))	chr19:54783730-54783949(-)$1	1	176	195	13.2224
((.(((........)))))	chr3:50004879-50005124(+)$1	1	28	47	14.7687
((.(((........)))))	chr14:97000807-97001038(+)$1	1	35	54	14.8032
.(((((........)))))	chr16:70432046-70432263(-)$1	1	4	23	13.4023
(((.((........))...	chr12:54920403-54920632(+)$1	1	164	183	13.3016
(.((((........)))))	chr12:98927293-98927553(+)$1	1	31	50	14.2806
((((((........).)))	chr1:154229448-154229784(+)$1	1	72	91	14.1509
(.((((........)))).	chr12:7045390-7045614(+)$1	1	30	49	14.7121
)))(((........)))..	chr19:15533727-15534019(-)$1	1	268	287	12.7339
((((((........)))))	chr1:16380072-16380285(+)$1	1	14	33	14.2694
.(((.(........)))))	chr17:3594887-3595104(-)$1	1	182	201	14.3140
((((((........)))..	chr3:122334538-122334751(+)$1	1	156	175	14.8625
((((((........)))))	chr10:102896528-102896739(+)$1	1	146	165	14.1326
((((((........)))))	chr13:99947587-99947825(-)$1	1	207	226	13.0113
(.((((........)))))	chr14:94776084-94776302(-)$1	1	143	162	14.5422
...(((........)))..	chr3:57302386-57302606(+)$1	1	124	143	14.3527
(((.((........)).))	chr15:52357014-52357272(+)$1	1	17	36	13.2224
((((.(........).)).	chr11:1097723-1097938(+)$1	1	51	70	12.7594
((((.(........).)))	chrX:64959638-64959955(+)$1	1	255	274	13.8830
(((.((........)).))	chr8:25287263-25287508(-)$1	1	168	187	13.1378
.(((((........)))))	chr19:55175605-55175820(+)$1	1	15	34	14.3067
((..((........)).))	chr16:68324324-68324591(+)$1	1	149	168	12.9876
..((((........)))))	chr20:3784035-3784254(+)$1	1	104	123	14.1849
((.(((........))).)	chr11:6540639-6540939(+)$1	1	11	30	14.8861
.(((((........)))))	chr11:93778907-93779121(+)$1	1	185	204	13.4023
(..(((........)))).	chr13:33110187-33110410(-)$1	1	53	72	15.0131
.(((((........)))))	chr16:30507455-30507776(+)$1	1	277	296	14.3067
((((.(........).)))	chr15:68378786-68379050(+)$1	1	158	177	13.9992
).((((........)))).	chr15:49926636-49926851(+)$1	1	149	168	12.6569
((.(((........))).)	chr17:729162-729389(-)$1	1	128	147	14.5382
(.((((........)))))	chr2:219498336-219498551(+)$1	1	44	63	14.6373
..((((........)))).	chr9:5919884-5920174(-)$1	1	251	270	14.7765
))((((........)))).	chr7:102292782-102293094(-)$1	1	160	179	13.5106
).((((........))))(	chr10:1175148-1175364(+)$1	1	158	177	13.3646
.(((((........)))))	chr12:48527141-48527356(+)$1	1	15	34	13.4023
..((((........)))).	chr20:47782463-47782705(-)$1	1	32	51	14.7146
(.((((........)))).	chr8:22864626-22864859(+)$1	1	166	185	14.6406
.(((((........)))))	chr12:119624774-119624987(+)$1	1	114	133	13.4023
..((((........)))))	chr19:57910517-57910739(+)$1	1	21	40	14.6633
((((((........)))))	chr19:11943320-11943535(+)$1	1	171	190	13.8641
.(((.(........)))).	chr1:68614153-68614371(-)$1	1	22	41	14.6740
((((((........))).)	chr11:64535510-64535790(-)$1	1	168	187	14.7463

#PSSM
f : 0.13	c : 0.13	d : 0.13	e : 0.11	[ : 0.10	b : 0.08	: : 0.07	g : 0.04	# : 0.04	i : 0.02	" : 0.02	= : 0.02	$ : 0.02	F : 0.01	a : 0.01	
e : 0.24	c : 0.15	[ : 0.11	f : 0.08	d : 0.07	! : 0.05	b : 0.04	# : 0.04	i : 0.02	" : 0.02	= : 0.02	g : 0.02	$ : 0.02	: : 0.02	
d : 0.27	e : 0.23	[ : 0.13	c : 0.13	! : 0.07	f : 0.05	= : 0.02	i : 0.01	# : 0.01	$ : 0.01	b : 0.01	g : 0.01	
c : 0.34	d : 0.26	e : 0.18	f : 0.05	[ : 0.05	= : 0.02	i : 0.01	b : 0.01	! : 0.01	g : 0.01	
c : 0.30	d : 0.24	e : 0.17	[ : 0.10	b : 0.07	f : 0.05	i : 0.01	= : 0.01	g : 0.01	
c : 0.28	d : 0.24	e : 0.17	a : 0.11	b : 0.07	f : 0.05	i : 0.01	= : 0.01	g : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.28	d : 0.24	e : 0.17	a : 0.11	b : 0.07	f : 0.05	i : 0.01	= : 0.01	g : 0.01	
c : 0.31	d : 0.24	e : 0.17	] : 0.07	b : 0.07	f : 0.05	= : 0.02	i : 0.01	g : 0.01	
c : 0.34	d : 0.26	e : 0.18	f : 0.05	] : 0.05	= : 0.02	i : 0.01	3 : 0.01	b : 0.01	g : 0.01	
d : 0.27	e : 0.23	] : 0.11	c : 0.10	f : 0.05	3 : 0.04	b : 0.02	4 : 0.02	= : 0.02	g : 0.02	i : 0.01	6 : 0.01	: : 0.01	a : 0.01	
e : 0.27	c : 0.13	] : 0.10	f : 0.08	3 : 0.07	d : 0.07	b : 0.05	4 : 0.04	: : 0.04	i : 0.02	= : 0.02	g : 0.02	2 : 0.01	6 : 0.01	

#score	974.162069663796
#seq	69
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_CDS_m1_run2.txt

#BEAR
=======[ccc"""bboooooobb333ccc333=======	chr13:100193789-100194022(+)$1	233	76	116	17.9692
$$dddd####ccc[aooooooaccc333ddddccc]hhhh	chr19:45422374-45422598(+)$1	224	74	114	13.1782
eee[ccc[a[cccrrrrrrrrrccc]accc]eeeeehhhh	chr16:31473888-31474111(+)$1	223	128	168	12.0498
::cccdddd####cccooooooccc4444dddd333ccc:	chr5:131925275-131925507(+)$1	232	111	151	12.5916
eeee!!ggggggg[cccnnnnncccggggggg4444eeee	chr22:42273253-42273487(+)$1	234	167	207	15.2383
eeee[dddd"""eeeeeooooooeeeee]ddddeeeee22	chr13:98086775-98087002(+)$1	227	50	90	11.6074
!ccc[eeeee[ccc[bboooooobb]ccc]eeeee]ccc2	chr12:57037222-57037452(-)$1	230	165	205	13.7962
###a[a[ccc[ggggggglllgggggggccc]a]a4444e	chr8:103230974-103231199(-)$1	225	41	81	12.7053
c[ggggggg!!a!!cccnnnnnccc]a22ggggggg]ccc	chr11:107799211-107799433(-)$1	222	48	88	16.5687
h[eeeee[ccc####bboooooobb4444ccc]eeeee]h	chr9:134349845-134350075(+)$1	230	155	195	14.9426
iiiiiii[bb####ddddmmmmdddd4444bbiiiiiiii	chr21:34123402-34123635(-)$1	233	189	229	12.0834
hhhhhhhh[ccc"""bbnnnnnbb333ccc333hhhhhhh	chr7:56079359-56079589(-)$1	230	12	52	13.4171
==========="""cccssssssssssccc22========	chr16:89869575-89869807(-)$1	232	12	52	12.6608
dddd"""ccc!!ddddoooooodddd]ccc4444ddddee	chr6:160148170-160148398(-)$1	228	15	55	13.2010
e[dddd[eeeee!!cccnnnnnccc333eeeeeddddeee	chr12:70195308-70195538(+)$1	230	89	129	14.2426
cccccc[ccc[bb[bb[aooooooa]bbbb]ccc]ccc]c	chr16:28500515-28500740(-)$1	225	40	80	13.1075
g[ccc!!bb[a"""bboooooobb333a]bb4444ccc]g	chr13:114789631-114789855(+)$1	224	103	143	15.5079
gggg"""==========oooooo==========4444ggg	chr17:8451547-8451775(-)$1	228	82	122	16.6740
cc"""eeeee[bb[ccclllcccbb22eeeee333ccc22	chr15:69733209-69733458(+)$1	249	97	137	12.7061
$$ccc!!cccgggggggnnnnnggggggg]ccc333ccc3	chr2:232576518-232576762(+)$1	244	55	95	13.7372
fff!!dddd!!ccccccnnnnnccc]ccc333dddd]fff	chr12:994776-995005(+)$1	229	185	225	14.6004
[==========[bb!!aooooooa22bb]==========]	chr6:106969142-106969363(-)$1	221	79	119	16.4564
::==========[cccooooooccc]==========::::	chr1:36101857-36102087(-)$1	230	189	229	12.1762
[dddd!!ccc!!a[cccnnnnnccc]a22ccc]dddd22b	chr7:149430446-149430675(+)$1	229	14	54	15.0795
!eeeee[ccc[bb[cccmmmmccc22bbccceeeee]fff	chr1:204379649-204379878(-)$1	229	141	181	12.4406
ccggggggg[ccc!!ccclllccc22cccggggggg]ccc	chr5:140023094-140023327(+)$1	233	175	215	14.5283
b[dddda[ccc"""cccnnnnnccc333ccc]a]ddddbb	chr19:12772027-12772257(-)$1	230	31	71	15.4541
[eeeee!!ddddbbcccnnnnnccc]bb]dddd22eeeee	chr5:5466454-5466689(+)$1	235	103	143	12.9854
ggggg[eeeee!!cccooooooccc22eeeee]ggggggg	chr10:74776518-74776747(-)$1	229	66	106	14.8442
e:==========!!bbrrrrrrrrrbb22==========C	chr3:156266627-156266857(-)$1	230	174	214	11.9935
eeeeeeee!!iiiiiiiiillliiiiiiiii333eeeee:	chr9:130674460-130674685(-)$1	225	146	186	12.3496
:ggggggg[ccc[bbccclllccc333bbcccgggggggd	chr21:34926675-34926907(+)$1	232	60	100	13.0516
eeee"""ccc####ccclllccc333ccc333eeeee22d	chr19:36276208-36276430(+)$1	222	99	139	14.9432
[ccc[dddd!!bb[cccnnnnnccc]bbdddd]ccc22ee	chr14:32560091-32560320(+)$1	229	186	226	13.9090
=============[cccnnnnnccc]==============	chrX:21861222-21861453(+)$1	231	151	191	18.4499
iiiiiiiiccc"""cccooooooccc333ccc>>>>>>>>	chr6:170844187-170844421(-)$1	234	159	199	15.0704
ffffeeeeeccc[ddddmmmmdddd]ccc333eeeee333	chr19:1053360-1053584(+)$1	224	116	156	11.3210
dd[ggggggg"""ddddooooooddddggggggg]dddd:	chr3:134201607-134201834(-)$1	227	95	135	12.4865
cc!!eeeee[ccc[cccmmmmcccccc]eeeeeccc]ddd	chr12:54115205-54115435(-)$1	230	180	220	11.8291
gggggg[ggggggg!!ccclllccc]gggggggggggggg	chr13:23912005-23912235(-)$1	230	76	116	14.0284
eeeee"""iiiiiiiiillliiiiiiiii333eeeee]cc	chr6:170594648-170594873(-)$1	225	158	198	13.5219
$$ggggggg[cccrrrrrrrrrccc]ggggggg]eeeeed	chr9:136339076-136339300(-)$1	224	132	172	12.6671
iiiiiiiii"""cccpppppppccc4444iiiiiiiii]c	chr2:85534691-85534917(-)$1	226	141	181	12.8399
####bb!!eeeee!!bbnnnnnbb22eeeee22bbggggg	chr11:64543882-64544174(-)$1	292	233	273	11.6104
F:==========eeeeennnnneeeee333==========	chr9:99417249-99417490(-)$1	241	39	79	13.5721
:==========[bbrrrrrrrrrbb]==========ffff	chr17:62500015-62500247(-)$1	232	83	123	13.0865
eeeedddd[dddd!!bbnnnnnbb333dddd]dddd333e	chr19:40882469-40882692(-)$1	223	136	176	12.6037
ee===========vvvvvvvvvvvvv===========]ee	chr2:239009023-239009248(+)$1	225	142	182	12.1554
bb[ccc[ccc[bb[cccnnnnnccc]bb333ccc]ccc33	chr15:41812551-41812780(-)$1	229	122	162	15.5041
d!!a[bb[bb[ccc[bboooooobb]cccbb]bb]a]ddd	chr17:72428286-72428510(+)$1	224	162	202	12.2381
cc[eeeee[ccc[ddddnnnnndddd]ccc333eeeee]c	chr2:3461276-3461505(+)$1	229	80	120	13.6923
==========[gggggggmmmmggggggg]==========	chr2:142567783-142568012(-)$1	229	50	90	13.6701

#otherMatches

#Seq PSSM
UUAUGUUACGGACACUGCACAAAGAUAUUGCUAGAUAUAA	chr13:100193789-100194022(+)$1	233	76	116	17.9692
UUUCAGAAAGUGAAGGAGAAACUCAAGAUUGACUCAUGAG	chr19:45422374-45422598(+)$1	224	74	114	13.1782
AAGCGCAUGGCACCCUCGUAUUGUGGCUGCCCUUGUGGGG	chr16:31473888-31474111(+)$1	223	128	168	12.0498
CUGGACUGGGAAGAAUAAUUGAGUUAAAAUCAGAAAUCCU	chr5:131925275-131925507(+)$1	232	111	151	12.5916
GUCAGGUAGGUGGAGGCCCCUUGCCCCACCUGGGCAUGGC	chr22:42273253-42273487(+)$1	234	167	207	15.2383
CACCAUCGAGGACUUCUACCGCAAGGAGAUCGAGGUGGAU	chr13:98086775-98087002(+)$1	227	50	90	11.6074
CUGUGUUUGCUGGUGUUGGUGAGAGGACCCGUGAAGGCAA	chr12:57037222-57037452(-)$1	230	165	205	13.7962
UUUGCUGCUGUAGAAGGAGUUUUCUUCUCAGGAUCUUUUG	chr8:103230974-103231199(-)$1	225	41	81	12.7053
CCUGGGUGAAGCGGUGCAGGAGGCAGGACUUGCCCACGGU	chr11:107799211-107799433(-)$1	222	48	88	16.5687
CUUUUGUUUCCACCCCAAGAAAAUGUUCAGGAUGCAGGUG	chr9:134349845-134350075(+)$1	230	155	195	14.9426
GAGCGGGAGGCCAGGAGGUAAUUCUCAAAACCCUUGCUCU	chr21:34123402-34123635(-)$1	233	189	229	12.0834
UUUCUUCCUUCUUAGGAUGCUUUCAUUGGAUUUGGAGGAA	chr7:56079359-56079589(-)$1	230	12	52	13.4171
GGAGACCAUGAUGUCCAUAAAUAACUUUGGUUUUAUGGUU	chr16:89869575-89869807(-)$1	232	12	52	12.6608
GCCUUCUGGCCCACUCACAGGAGAGUCGCCUUUCAGGCGU	chr6:160148170-160148398(-)$1	228	15	55	13.2010
GCUGUUCUGGAGGCUGUGGAAAACAAUACUCUAAGCAUUG	chr12:70195308-70195538(+)$1	230	89	129	14.2426
GGCCUUUGCAACAACUUCUCUUAUGUGGUGAUGCUGAGUG	chr16:28500515-28500740(-)$1	225	40	80	13.1075
GCGGAGCCUGGUUUUCUCACCUGAUUUCGAGCUUGUCCAC	chr13:114789631-114789855(+)$1	224	103	143	15.5079
UUGGAAAUAUUUCUUUCAAAAAGGAGAGAAAUACUGAUCA	chr17:8451547-8451775(-)$1	228	82	122	16.6740
CAAAACUUGUAUCGUGUCAGACAGAAGGCGAGGGAUGUAC	chr15:69733209-69733458(+)$1	249	97	137	12.7061
GACAUGGCCUGUUUUCUGUCGAGGAGAAUGAGGAAAAUGG	chr2:232576518-232576762(+)$1	244	55	95	13.7372
UGAACACAGCUCAUCUGGAGCUCAGCAUGCCUCUGUCUCA	chr12:994776-995005(+)$1	229	185	225	14.6004
CAUACCGGCUUGAUUUGAAAAGACCCAUGAAGUCGGUGUC	chr6:106969142-106969363(-)$1	221	79	119	16.4564
UACAGUUUUAGUUGGCAuaugaguuuacuagggcugccau	chr1:36101857-36102087(-)$1	230	189	229	12.1762
CGGUGCUGCCCUUGCGGAGAAGCUGGAUCGGCUCGCCACA	chr7:149430446-149430675(+)$1	229	14	54	15.0795
AGCCGCUGAGUGCAGAACUCAUUCCGGCCUCGUGGCAGGG	chr1:204379649-204379878(-)$1	229	141	181	12.4406
GAUGUCAGGUGAAAUUCUGGGAGAUGUUUCUUGAUACUCU	chr5:140023094-140023327(+)$1	233	175	215	14.5283
GAUCCUCUGGCUUCAGGACUCCCCUCUUGCCUGCAGGGCC	chr19:12772027-12772257(-)$1	230	31	71	15.4541
CGGCAACUCGGAGACUUGGAAAGAGCUCGUUUGUUUUGCU	chr5:5466454-5466689(+)$1	235	103	143	12.9854
UCAUGCUUUGUGUCUUUCCUUCAGGUAGCAAAUUAUGGAG	chr10:74776518-74776747(-)$1	229	66	106	14.8442
UGUUUAAAGUAUGGCCAUCAUAAAAGGGGGUACUUUGAAG	chr3:156266627-156266857(-)$1	230	174	214	11.9935
UGGGGCCUGCCUGCUGGGGUCUCUCUGGCAGCUGGGGCCU	chr9:130674460-130674685(-)$1	225	146	186	12.3496
AGUGAGACCGUUACUUCCUAAGGACAUGGAACGUCUUACA	chr21:34926675-34926907(+)$1	232	60	100	13.0516
CAGGCAGCAGACCCGACACCGUCACACUGAGAUCUGCCAA	chr19:36276208-36276430(+)$1	222	99	139	14.9432
ACUGAUCAGCUAGGCUUAGAACAAGACUUUGAACAGAAGC	chr14:32560091-32560320(+)$1	229	186	226	13.9090
UGCUGUUUUCAAUCGUGCCUUUUACAGUUGGGGACGGCGG	chrX:21861222-21861453(+)$1	231	151	191	18.4499
UACUUUGGAACUGUACCUUGGAUGGUUUUGUUUAUUAAAA	chr6:170844187-170844421(-)$1	234	159	199	15.0704
CUGGCGGAGCUGAGGCUCACUGGCUACGGGAUCUCCGACA	chr19:1053360-1053584(+)$1	224	116	156	11.3210
GUGAGGUUCAGAGAGAUGGAAGGAUCUUGGAUUUGAUUGA	chr3:134201607-134201834(-)$1	227	95	135	12.4865
GACAGGUGAGGGGAGUCCACUGACCCCGUCACUUCCUCUC	chr12:54115205-54115435(-)$1	230	180	220	11.8291
UCAUGAUGAUUUUUCUGUAAUUUGCCAAGGAUUUUAUGAA	chr13:23912005-23912235(-)$1	230	76	116	14.0284
CCAGCAGCCCUGGCAGUGCAACUGCCAGGAAGGCUGGGGG	chr6:170594648-170594873(-)$1	225	158	198	13.5219
CUGUCCGUGCUGAUCGCCGCCCUCACCAUGGACCUCGCAG	chr9:136339076-136339300(-)$1	224	132	172	12.6671
CUUUUUCUUACCCUGGAAAAUACAGCCAAAGGAAGAGGUA	chr2:85534691-85534917(-)$1	226	141	181	12.8399
CUUUGAGAUUGUUACGAUUUAUUCUGAGCAAGAUCUGCAU	chr11:64543882-64544174(-)$1	292	233	273	11.6104
CGGUGCUGGACGCCCGCGGGCAGCGGGUACCGUUCGGCGC	chr9:99417249-99417490(-)$1	241	39	79	13.5721
AGUUGCUCUAAGUGGAUUGGAUAUGGUUGGAGUGGCACAG	chr17:62500015-62500247(-)$1	232	83	123	13.0865
AGGUGGCCCGCCGCAGCCCAUCGUCAAUGGCAGGCCAGAA	chr19:40882469-40882692(-)$1	223	136	176	12.6037
GGGGCCGGCCUGGUUCACCACGCCACCCGGGCUGGCCACC	chr2:239009023-239009248(+)$1	225	142	182	12.1554
CACCUUGCGCCUUGCCCUCUUUGGGGAACACGUGGGAGCC	chr15:41812551-41812780(-)$1	229	122	162	15.5041
CCCGCGCGAGAGCGAGCAACCCAGCGCGCCUGGCUCAGCC	chr17:72428286-72428510(+)$1	224	162	202	12.2381
CAUGAUUUUGUCCUUCUCAUUUGGAAUGAUUGCAGAUCCU	chr2:3461276-3461505(+)$1	229	80	120	13.6923
UUGUGUGAUCCUGGUGAAUUUCUUUGCCACGAUCACGUGA	chr2:142567783-142568012(-)$1	229	50	90	13.6701

#DB
(((((((.(((...((......))...)))...)))))))	chr13:100193789-100194022(+)$1	1	76	116	17.9692
..((((....(((.(......))))...))))))).))))	chr19:45422374-45422598(+)$1	1	74	114	13.1782
(((.(((.(.(((.........))).)))).)))))((((	chr16:31473888-31474111(+)$1	1	128	168	12.0498
..(((((((....(((......)))....))))...))).	chr5:131925275-131925507(+)$1	1	111	151	12.5916
((((..(((((((.(((.....))))))))))....))))	chr22:42273253-42273487(+)$1	1	167	207	15.2383
((((.((((...(((((......))))).)))))))))..	chr13:98086775-98087002(+)$1	1	50	90	11.6074
.(((.(((((.(((.((......)).))).))))).))).	chr12:57037222-57037452(-)$1	1	165	205	13.7962
...(.(.(((.(((((((...)))))))))).).)....)	chr8:103230974-103231199(-)$1	1	41	81	12.7053
(.(((((((..(..(((.....))).)..))))))).)))	chr11:107799211-107799433(-)$1	1	48	88	16.5687
(.(((((.(((....((......))....))).))))).)	chr9:134349845-134350075(+)$1	1	155	195	14.9426
(((((((.((....((((....))))....))))))))))	chr21:34123402-34123635(-)$1	1	189	229	12.0834
((((((((.(((...((.....))...)))...)))))))	chr7:56079359-56079589(-)$1	1	12	52	13.4171
(((((((((((...(((..........)))..))))))))	chr16:89869575-89869807(-)$1	1	12	52	12.6608
((((...(((..((((......)))).)))....))))((	chr6:160148170-160148398(-)$1	1	15	55	13.2010
(.((((.(((((..(((.....)))...))))))))))))	chr12:70195308-70195538(+)$1	1	89	129	14.2426
((((((.(((.((.((.(......).)))).))).))).)	chr16:28500515-28500740(-)$1	1	40	80	13.1075
(.(((..((.(...((......))...).))....))).)	chr13:114789631-114789855(+)$1	1	103	143	15.5079
((((...((((((((((......))))))))))....)))	chr17:8451547-8451775(-)$1	1	82	122	16.6740
((...(((((.((.(((...)))))..)))))...)))..	chr15:69733209-69733458(+)$1	1	97	137	12.7061
..(((..((((((((((.....))))))).)))...))).	chr2:232576518-232576762(+)$1	1	55	95	13.7372
(((..((((..((((((.....))).)))...)))).)))	chr12:994776-995005(+)$1	1	185	225	14.6004
.((((((((((.((..(......)..)).)))))))))).	chr6:106969142-106969363(-)$1	1	79	119	16.4564
..((((((((((.(((......))).))))))))))....	chr1:36101857-36102087(-)$1	1	189	229	12.1762
.((((..(((..(.(((.....))).)..))).))))..)	chr7:149430446-149430675(+)$1	1	14	54	15.0795
.(((((.(((.((.(((....)))..)))))))))).)))	chr1:204379649-204379878(-)$1	1	141	181	12.4406
(((((((((.(((..(((...)))..)))))))))).)))	chr5:140023094-140023327(+)$1	1	175	215	14.5283
(.(((((.(((...(((.....)))...))).).))))))	chr19:12772027-12772257(-)$1	1	31	71	15.4541
.(((((..(((((((((.....))).)).))))..)))))	chr5:5466454-5466689(+)$1	1	103	143	12.9854
(((((.(((((..(((......)))..))))).)))))))	chr10:74776518-74776747(-)$1	1	66	106	14.8442
).((((((((((..((.........))..)))))))))))	chr3:156266627-156266857(-)$1	1	174	214	11.9935
)))(((((..(((((((((...)))))))))...))))).	chr9:130674460-130674685(-)$1	1	146	186	12.3496
.(((((((.(((.(((((...)))...))))))))))))(	chr21:34926675-34926907(+)$1	1	60	100	13.0516
((((...(((....(((...)))...)))...)))))..)	chr19:36276208-36276430(+)$1	1	99	139	14.9432
.(((.((((..((.(((.....))).)))))).)))..))	chr14:32560091-32560320(+)$1	1	186	226	13.9090
(((((((((((((.(((.....))).))))))))))))))	chrX:21861222-21861453(+)$1	1	151	191	18.4499
(((((((((((...(((......)))...)))........	chr6:170844187-170844421(-)$1	1	159	199	15.0704
((((((((((((.((((....)))).)))...)))))...	chr19:1053360-1053584(+)$1	1	116	156	11.3210
((.(((((((...((((......))))))))))).)))).	chr3:134201607-134201834(-)$1	1	95	135	12.4865
((..(((((.(((.(((....)))))).)))))))).)))	chr12:54115205-54115435(-)$1	1	180	220	11.8291
((((((.(((((((..(((...))).))))))))))))))	chr13:23912005-23912235(-)$1	1	76	116	14.0284
(((((...(((((((((...)))))))))...))))).))	chr6:170594648-170594873(-)$1	1	158	198	13.5219
..(((((((.(((.........))).))))))).))))))	chr9:136339076-136339300(-)$1	1	132	172	12.6671
(((((((((...(((.......)))....))))))))).)	chr2:85534691-85534917(-)$1	1	141	181	12.8399
....((..(((((..((.....))..)))))..)))))))	chr11:64543882-64544174(-)$1	1	233	273	11.6104
(.(((((((((((((((.....)))))...))))))))))	chr9:99417249-99417490(-)$1	1	39	79	13.5721
.((((((((((.((.........)).))))))))))((((	chr17:62500015-62500247(-)$1	1	83	123	13.0865
((((((((.((((..((.....))...)))).))))...)	chr19:40882469-40882692(-)$1	1	136	176	12.6037
(((((((((((((.............))))))))))).))	chr2:239009023-239009248(+)$1	1	142	182	12.1554
((.(((.(((.((.(((.....))).))...))).)))..	chr15:41812551-41812780(-)$1	1	122	162	15.5041
(..(.((.((.(((.((......)).))))).)).).)))	chr17:72428286-72428510(+)$1	1	162	202	12.2381
((.(((((.(((.((((.....)))).)))...))))).)	chr2:3461276-3461505(+)$1	1	80	120	13.6923
((((((((((.(((((((....))))))).))))))))))	chr2:142567783-142568012(-)$1	1	50	90	13.6701

#PSSM
e : 0.19	c : 0.11	= : 0.07	: : 0.07	g : 0.07	[ : 0.07	$ : 0.05	i : 0.05	d : 0.05	! : 0.03	# : 0.03	h : 0.03	f : 0.03	b : 0.03	F : 0.01	
e : 0.19	c : 0.13	= : 0.11	[ : 0.09	: : 0.07	g : 0.07	$ : 0.05	i : 0.05	d : 0.05	# : 0.03	f : 0.03	h : 0.01	b : 0.01	! : 0.01	
= : 0.19	e : 0.19	g : 0.13	c : 0.11	d : 0.09	i : 0.05	[ : 0.05	# : 0.03	f : 0.03	! : 0.03	h : 0.01	" : 0.01	
= : 0.19	e : 0.19	g : 0.15	c : 0.13	d : 0.09	i : 0.05	a : 0.03	! : 0.03	[ : 0.01	h : 0.01	" : 0.01	f : 0.01	# : 0.01	
= : 0.19	e : 0.15	g : 0.13	c : 0.11	d : 0.09	[ : 0.09	" : 0.07	i : 0.05	! : 0.03	h : 0.01	b : 0.01	
= : 0.19	e : 0.17	d : 0.15	g : 0.11	! : 0.07	" : 0.07	c : 0.05	i : 0.05	b : 0.03	a : 0.01	h : 0.01	[ : 0.01	
= : 0.19	e : 0.15	g : 0.11	[ : 0.11	d : 0.09	! : 0.09	" : 0.07	i : 0.05	# : 0.01	c : 0.01	h : 0.01	a : 0.01	b : 0.01	
= : 0.19	e : 0.15	c : 0.15	g : 0.13	[ : 0.11	d : 0.09	! : 0.03	i : 0.03	# : 0.01	h : 0.01	b : 0.01	" : 0.01	
c : 0.23	= : 0.19	e : 0.13	g : 0.11	d : 0.09	[ : 0.07	b : 0.05	i : 0.03	# : 0.01	a : 0.01	! : 0.01	
c : 0.30	= : 0.19	[ : 0.09	e : 0.09	! : 0.07	g : 0.05	# : 0.03	" : 0.03	b : 0.03	d : 0.03	i : 0.01	
c : 0.24	= : 0.17	[ : 0.15	! : 0.09	# : 0.05	g : 0.05	" : 0.05	e : 0.05	d : 0.03	i : 0.03	a : 0.01	
c : 0.23	" : 0.15	= : 0.11	g : 0.09	b : 0.09	# : 0.07	! : 0.05	e : 0.03	[ : 0.03	d : 0.03	i : 0.03	a : 0.01	
c : 0.17	b : 0.15	" : 0.13	g : 0.09	# : 0.07	! : 0.07	[ : 0.07	e : 0.05	= : 0.05	d : 0.03	i : 0.03	a : 0.01	
[ : 0.19	c : 0.13	" : 0.11	! : 0.11	g : 0.07	d : 0.07	b : 0.07	# : 0.05	r : 0.03	e : 0.03	i : 0.03	= : 0.01	v : 0.01	
c : 0.38	b : 0.09	d : 0.09	! : 0.09	r : 0.05	g : 0.05	e : 0.03	[ : 0.03	i : 0.03	a : 0.01	# : 0.01	" : 0.01	= : 0.01	v : 0.01	
c : 0.40	b : 0.19	d : 0.09	r : 0.05	g : 0.05	e : 0.03	! : 0.03	i : 0.03	o : 0.01	= : 0.01	p : 0.01	v : 0.01	
c : 0.36	o : 0.13	b : 0.11	r : 0.07	d : 0.07	g : 0.05	e : 0.03	i : 0.03	[ : 0.01	= : 0.01	a : 0.01	p : 0.01	v : 0.01	
n : 0.30	o : 0.28	r : 0.07	l : 0.05	m : 0.05	c : 0.05	g : 0.03	d : 0.01	s : 0.01	a : 0.01	i : 0.01	p : 0.01	v : 0.01	
o : 0.30	n : 0.30	l : 0.11	m : 0.09	r : 0.07	s : 0.01	i : 0.01	c : 0.01	p : 0.01	v : 0.01	
o : 0.30	n : 0.30	l : 0.15	m : 0.09	r : 0.07	s : 0.01	p : 0.01	v : 0.01	
o : 0.30	n : 0.30	l : 0.09	m : 0.09	r : 0.07	c : 0.03	s : 0.01	i : 0.01	p : 0.01	v : 0.01	
n : 0.30	o : 0.28	c : 0.11	r : 0.07	m : 0.03	l : 0.03	a : 0.01	g : 0.01	s : 0.01	d : 0.01	i : 0.01	p : 0.01	v : 0.01	
c : 0.46	o : 0.17	b : 0.09	d : 0.07	g : 0.05	r : 0.03	i : 0.03	s : 0.01	e : 0.01	v : 0.01	
c : 0.44	b : 0.19	d : 0.09	g : 0.05	e : 0.03	i : 0.03	s : 0.01	o : 0.01	= : 0.01	a : 0.01	r : 0.01	3 : 0.01	v : 0.01	
c : 0.38	3 : 0.11	b : 0.09	d : 0.09	2 : 0.07	g : 0.05	e : 0.03	i : 0.03	s : 0.01	a : 0.01	= : 0.01	r : 0.01	v : 0.01	
] : 0.30	3 : 0.17	2 : 0.11	g : 0.07	d : 0.07	4 : 0.05	e : 0.03	i : 0.03	c : 0.03	s : 0.01	= : 0.01	b : 0.01	v : 0.01	
3 : 0.17	c : 0.13	b : 0.13	g : 0.11	= : 0.09	4 : 0.07	a : 0.05	e : 0.05	] : 0.03	2 : 0.03	i : 0.03	s : 0.01	d : 0.01	
c : 0.23	g : 0.13	b : 0.13	3 : 0.09	= : 0.09	4 : 0.07	e : 0.07	2 : 0.05	i : 0.03	a : 0.01	] : 0.01	d : 0.01	
c : 0.28	g : 0.11	e : 0.09	= : 0.09	4 : 0.07	] : 0.07	d : 0.05	2 : 0.05	3 : 0.05	b : 0.03	i : 0.03	
c : 0.24	= : 0.13	d : 0.11	g : 0.11	3 : 0.11	e : 0.09	] : 0.05	b : 0.05	i : 0.03	4 : 0.01	
= : 0.17	3 : 0.15	c : 0.15	d : 0.11	g : 0.11	e : 0.11	b : 0.05	] : 0.03	i : 0.03	2 : 0.01	4 : 0.01	
= : 0.17	3 : 0.15	e : 0.13	c : 0.13	g : 0.11	d : 0.09	] : 0.07	2 : 0.03	4 : 0.03	b : 0.01	i : 0.01	
= : 0.19	e : 0.15	g : 0.11	3 : 0.09	d : 0.09	c : 0.07	] : 0.07	4 : 0.05	a : 0.03	i : 0.03	> : 0.01	2 : 0.01	b : 0.01	
= : 0.19	e : 0.17	g : 0.11	c : 0.09	3 : 0.07	4 : 0.07	d : 0.07	] : 0.05	i : 0.03	b : 0.03	h : 0.01	2 : 0.01	> : 0.01	
e : 0.21	= : 0.19	d : 0.11	g : 0.09	] : 0.07	c : 0.05	3 : 0.05	4 : 0.05	i : 0.03	a : 0.01	h : 0.01	2 : 0.01	> : 0.01	b : 0.01	
e : 0.21	= : 0.19	d : 0.13	g : 0.11	c : 0.11	4 : 0.05	] : 0.03	3 : 0.03	i : 0.03	h : 0.01	> : 0.01	a : 0.01	
e : 0.19	= : 0.15	c : 0.13	] : 0.11	d : 0.09	g : 0.07	h : 0.05	4 : 0.03	i : 0.03	: : 0.01	2 : 0.01	> : 0.01	f : 0.01	3 : 0.01	
c : 0.17	e : 0.15	= : 0.13	d : 0.09	g : 0.09	h : 0.05	f : 0.05	2 : 0.05	i : 0.03	3 : 0.03	] : 0.03	4 : 0.01	: : 0.01	> : 0.01	
e : 0.15	= : 0.13	c : 0.11	] : 0.09	g : 0.09	2 : 0.07	h : 0.05	f : 0.05	3 : 0.05	d : 0.05	4 : 0.01	i : 0.01	: : 0.01	b : 0.01	> : 0.01	
e : 0.15	c : 0.11	= : 0.09	g : 0.09	d : 0.09	h : 0.07	: : 0.07	2 : 0.05	3 : 0.05	f : 0.05	b : 0.03	i : 0.01	] : 0.01	C : 0.01	> : 0.01	

#score	713.1461665008674
#seq	52
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m3_run1.txt

#BEAR
ceeeee!!cccmmmmccceeeee]c	chr12:49333347-49333604(-)$1	257	145	170	12.1185
gggggggddddmmmmdddd4444gg	chr19:917475-917704(+)$1	229	95	120	10.4414
ggggg[a[cccmmmmccc]a]gggg	chr19:34890097-34890336(+)$1	239	118	143	13.6865
$eeeee!!cccmmmmccc]eeeee7	chr22:50956069-50956305(+)$1	236	46	71	11.9029
eeee####cccmmmmccc]eeeee]	chr10:105201983-105202213(+)$1	230	147	172	13.4244
ccc!!ccc[cccmmmmccc]ccc]c	chr15:40755981-40756219(+)$1	238	211	236	10.0942
ccc[ccc!!bbmmmmbb22ccc]cc	chr3:122632306-122632531(+)$1	225	143	168	10.9045
hhh[ccc[cccmmmmccc]ccc]hh	chr4:47514591-47514813(-)$1	222	64	89	12.5373
ddd[bb[cccammmma]ccc]bb]d	chr4:24538595-24538823(-)$1	228	38	63	10.0616
fff[bb!!cccmmmmccc4444bb2	chrM:14246-14492(-)$1	246	22	47	12.3932
::ccc"""cccmmmmccc333ccc:	chr7:143095353-143095577(-)$1	224	197	222	11.8391
bbdddd!!cccmmmmccc22dddd2	chr17:15341053-15341290(-)$1	237	57	82	12.0744
eeee[ccccccmmmmccc]ccc]ee	chr22:42273974-42274205(+)$1	231	60	85	12.3389
eeeee[a[cccmmmmccc]aeeeee	chr1:116931492-116931722(+)$1	230	146	171	12.5808
fffff####ccclllccc22fffff	chr12:123641324-123641556(-)$1	232	90	115	9.9974
:ccc####cccmmmmccc4444ccc	chrX:44922698-44922935(+)$1	237	1	26	13.1099
ccc[ccc[cccmmmmccc]ccc]cc	chr14:53619187-53619416(-)$1	229	58	83	13.2433
ccc[gggggggmmmmggggggg333	chr1:154247771-154248028(+)$1	257	209	234	10.7899
hhhhh"""cccmmmmccc4444hhh	chr17:4925287-4925522(+)$1	235	195	220	12.8378
d[ccc####bbmmmmbb4444ccc]	chr13:95847031-95847260(-)$1	229	4	29	11.9061
[bb$$$$$cccmmmmccc333bb]f	chr1:183111657-183111893(+)$1	236	158	183	12.5201
f[dddd!!cccmmmmccc22dddd2	chr17:27005838-27006075(+)$1	237	192	217	12.6039
"gggggggcccmmmmccc]gggggg	chr1:64100472-64100702(+)$1	230	9	34	12.9689
:ccc####cccmmmmccc333ccc:	chr22:41911669-41911901(+)$1	232	0	25	12.8422
Hggggggg[bbmmmmbb]ggggggg	chr17:26967560-26967791(-)$1	231	24	49	9.7139
eee$$$$$cccmmmmccc22eeeee	chrX:135055732-135055973(-)$1	241	30	55	12.7532
a[bbddddcccmmmmccc22dddd]	chr9:134473537-134473774(-)$1	237	6	31	11.1769
ddddd"""cccmmmmccc333dddd	chr13:100206481-100206719(+)$1	238	169	194	13.4180
ccc[ccc[cccmmmmccc]cccccc	chr3:13373753-13373992(-)$1	239	110	135	13.1921
iiii####cccmmmmccciiiiiii	chr17:30806246-30806474(+)$1	228	139	164	13.7586
d[dddd!!cccmmmmcccdddd]dd	chr17:45745459-45745698(+)$1	239	14	39	11.6537
ee[a"""ddddmmmmdddd]aeeee	chr11:62494310-62494548(-)$1	238	36	61	10.5988
d[gggggggbbmmmmbb]ggggggg	chr1:227504693-227504921(-)$1	228	111	136	10.2556
d"""ccc[cccmmmmcccccc22dd	chr2:61711083-61711358(-)$1	275	210	235	11.5967
$$ggggggg[ammmma22ggggggg	chr5:1802355-1802589(+)$1	234	94	119	9.8002
[dddd"""cccmmmmccc333dddd	chrX:149930960-149931186(+)$1	226	4	29	13.5914
fffffff[cccmmmmccc22fffff	chr16:4700337-4700566(+)$1	229	178	203	11.9114
gggg"""ddddmmmmddddgggggg	chr17:38318027-38318259(+)$1	232	183	208	11.2244
eeee"""ddddmmmmddddeeeee]	chr16:70588303-70588553(+)$1	250	135	160	10.4372
ffffff!!cccmmmmcccffffff:	chr12:21807468-21807709(-)$1	241	197	222	10.9208
iiiiiiiicccmmmmccc]iiiiii	chr1:101455979-101456210(-)$1	231	46	71	13.0109
%%%%ccc[cccmmmmccc]ccc444	chr15:68500463-68500705(-)$1	242	30	55	10.1830
##iiiiiiiiimmmmiiiiiiiii3	chr9:128069672-128069902(+)$1	230	59	84	10.9613
eee$$$$$cccmmmmccc22eeeee	chr11:66453270-66453500(-)$1	230	189	214	12.7532
ggggg[bbcccmmmmccc]bb]ggg	chr3:132347087-132347322(-)$1	235	49	74	11.7778
ffffff!!cccmmmmccc22fffff	chr13:76414108-76414350(+)$1	242	13	38	12.6395
bggggggg!!ammmma333gggggg	chrX:39934196-39934425(-)$1	229	58	83	11.2628
gggggg!!ccclllcccggggggg]	chr7:5460731-5460952(+)$1	221	66	91	10.5009
!!ccc!!ddddmmmmdddd22ccc2	chr6:122767904-122768155(-)$1	251	215	240	10.9358
gg"""ccc[bbmmmmbbcccggggg	chr15:65849078-65849343(+)$1	265	5	30	10.5327
gggg[a[ddddmmmmdddd333a]g	chr5:32444628-32444857(-)$1	229	179	204	11.1776

#otherMatches

#Seq PSSM
CCUUGUCUUUGCAAACAAACAGGUG	chr12:49333347-49333604(-)$1	257	145	170	12.1185
GGGCUGUGGCGCCAACGCCUCGGAC	chr19:917475-917704(+)$1	229	95	120	10.4414
CCUUGAGAGGCUGCUGCCACAUAAG	chr19:34890097-34890336(+)$1	239	118	143	13.6865
CGCCCACUGUGUGUUUGCCUGGGCU	chr22:50956069-50956305(+)$1	236	46	71	11.9029
GCAGUACAUGGCUUUCCACCUGCAG	chr10:105201983-105202213(+)$1	230	147	172	13.4244
CUGCCCUCUGGGAGAACCCCGAGUC	chr15:40755981-40756219(+)$1	238	211	236	10.0942
GUUGCUGCUGCACUUGCUCCAGGAG	chr3:122632306-122632531(+)$1	225	143	168	10.9045
AUACUCAUCCUUGAAGGGCUGGAUG	chr4:47514591-47514813(-)$1	222	64	89	12.5373
UUUGUUCGCCCCACGGAGGCCAAGA	chr4:24538595-24538823(-)$1	228	38	63	10.0616
UAUACUACAGCGAUGGCUAUUGAGG	chrM:14246-14492(-)$1	246	22	47	12.3932
CCAUGCCCGGGCACACCCCAACAUU	chr7:143095353-143095577(-)$1	224	197	222	11.8391
UCGGUAUUGGCCAUGGCUCCUACCA	chr17:15341053-15341290(-)$1	237	57	82	12.0744
CUGGUUCAUGGGGAGCCAGUGAUCC	chr22:42273974-42274205(+)$1	231	60	85	12.3389
AAGGUAGGCCAUUUUUGGGCACUUU	chr1:116931492-116931722(+)$1	230	146	171	12.5808
UUUUCACCUAGGAAGCCUUGGAAGA	chr12:123641324-123641556(-)$1	232	90	115	9.9974
ACUGGAAUUCCUAAUGGGCCAACAG	chrX:44922698-44922935(+)$1	237	1	26	13.1099
CCGGCACCGCUAUGAGGUAGUGACG	chr14:53619187-53619416(-)$1	229	58	83	13.2433
UUCAUCUCAAGAUUCCUUGGGGAAG	chr1:154247771-154248028(+)$1	257	209	234	10.7899
ACGGUCCAGACCAUUGUCAAACGCU	chr17:4925287-4925522(+)$1	235	195	220	12.8378
GUGACUUUUGUUUGUGCUUUUGUUU	chr13:95847031-95847260(-)$1	229	4	29	11.9061
ACUAUAACCGAGAUAUCGAGGAGAU	chr1:183111657-183111893(+)$1	236	158	183	12.5201
GCUGGCCCUGCAGGAGCACUGUUAA	chr17:27005838-27006075(+)$1	237	192	217	12.6039
AUUCCAUGCUGUAUAUAGUUGUGGG	chr1:64100472-64100702(+)$1	230	9	34	12.9689
ACCAAUAAGCAGCAAUGUGAAUGGC	chr22:41911669-41911901(+)$1	232	0	25	12.8422
GGCAUUUCGGGAGAACUGGGAGUGU	chr17:26967560-26967791(-)$1	231	24	49	9.7139
GGACUUCAGUGACGUCAUCUUUCUG	chrX:135055732-135055973(-)$1	241	30	55	12.7532
CUGCCUUGGCCUCCAGGCAUCGGGA	chr9:134473537-134473774(-)$1	237	6	31	11.1769
GGGAUUUUGCCCUUUGGCUGCAUCU	chr13:100206481-100206719(+)$1	238	169	194	13.4180
GUUUGAGAAGCUGCAGCUGCUCAAC	chr3:13373753-13373992(-)$1	239	110	135	13.1921
AGAGUACAGGUGAGAACCCUCUGGG	chr17:30806246-30806474(+)$1	228	139	164	13.7586
CAAGAGUAGUCAGAGGACCUUUAGA	chr17:45745459-45745698(+)$1	239	14	39	11.6537
CGAGAUGCUCGAGGACGAggccggc	chr11:62494310-62494548(-)$1	238	36	61	10.5988
GCUUCAGUGUGGAGACAUUACUGGA	chr1:227504693-227504921(-)$1	228	111	136	10.2556
ACCUACACAGUUUAAACUUGUUUUG	chr2:61711083-61711358(-)$1	275	210	235	11.5967
GACUACAGGAGAAUUCGGUUUGUAG	chr5:1802355-1802589(+)$1	234	94	119	9.8002
ACAGCAUCUCCAUGUGGAAACGCUG	chrX:149930960-149931186(+)$1	226	4	29	13.5914
GUGGGGGUGGGAGGCCCCUGUCCCC	chr16:4700337-4700566(+)$1	229	178	203	11.9114
UCUUGAGGCUUGGAAGAGUAAGGAU	chr17:38318027-38318259(+)$1	232	183	208	11.2244
GGUUCCUGGGGACCACCCCGACCUU	chr16:70588303-70588553(+)$1	250	135	160	10.4372
GUUGGUAUGGCGUGUGCUAUCAGCA	chr12:21807468-21807709(-)$1	241	197	222	10.9208
GUUGGCUUAGCCAGGGUUGGAGCCG	chr1:101455979-101456210(-)$1	231	46	71	13.0109
CACCAGAAGCGCAAGCGCCUCUUCC	chr15:68500463-68500705(-)$1	242	30	55	10.1830
GUGCAGUGGAGACCCCUCCAUUGUC	chr9:128069672-128069902(+)$1	230	59	84	10.9613
CCUCCGUUCAGGAAACUGCCAGGGA	chr11:66453270-66453500(-)$1	230	189	214	12.7532
UCUUCUGGGAAAUAAUUCAUCUGAG	chr3:132347087-132347322(-)$1	235	49	74	11.7778
AGAGACAGCUAAUGAUAGAAGUUUC	chr13:76414108-76414350(+)$1	242	13	38	12.6395
AUCCGGGAAGGGCUGCGGGUCCCGG	chrX:39934196-39934425(-)$1	229	58	83	11.2628
CUGUCCAUGGCCAGGCCGGACAGCA	chr7:5460731-5460952(+)$1	221	66	91	10.5009
UGACCCUUACCAACUGGUACAGGUA	chr6:122767904-122768155(-)$1	251	215	240	10.9358
ACAAACUGACCCAGAGGCAGGUAAA	chr15:65849078-65849343(+)$1	265	5	30	10.5327
CCGGGCAGCGGGGAGCCGCGGGGGU	chr5:32444628-32444857(-)$1	229	179	204	11.1776

#DB
((((((..(((....)))))))).)	chr12:49333347-49333604(-)$1	1	145	170	12.1185
(((((((((((....))))....))	chr19:917475-917704(+)$1	1	95	120	10.4414
(((((.(.(((....))).).))))	chr19:34890097-34890336(+)$1	1	118	143	13.6865
.(((((..(((....))).))))).	chr22:50956069-50956305(+)$1	1	46	71	11.9029
((((....(((....))).))))).	chr10:105201983-105202213(+)$1	1	147	172	13.4244
(((..(((.(((....))).))).)	chr15:40755981-40756219(+)$1	1	211	236	10.0942
(((.(((..((....))..))).))	chr3:122632306-122632531(+)$1	1	143	168	10.9045
(((.(((.(((....))).))).))	chr4:47514591-47514813(-)$1	1	64	89	12.5373
(((.((.((((....).))).)).)	chr4:24538595-24538823(-)$1	1	38	63	10.0616
(((.((..(((....)))....)).	chrM:14246-14492(-)$1	1	22	47	12.3932
..(((...(((....)))...))).	chr7:143095353-143095577(-)$1	1	197	222	11.8391
((((((..(((....)))..)))).	chr17:15341053-15341290(-)$1	1	57	82	12.0744
((((.((((((....))).))).))	chr22:42273974-42274205(+)$1	1	60	85	12.3389
(((((.(.(((....))).))))))	chr1:116931492-116931722(+)$1	1	146	171	12.5808
(((((....(((...)))..)))))	chr12:123641324-123641556(-)$1	1	90	115	9.9974
.(((....(((....)))....)))	chrX:44922698-44922935(+)$1	1	1	26	13.1099
(((.(((.(((....))).))).))	chr14:53619187-53619416(-)$1	1	58	83	13.2433
(((.(((((((....)))))))...	chr1:154247771-154248028(+)$1	1	209	234	10.7899
(((((...(((....)))....)))	chr17:4925287-4925522(+)$1	1	195	220	12.8378
(.(((....((....))....))).	chr13:95847031-95847260(-)$1	1	4	29	11.9061
.((.....(((....)))...)).)	chr1:183111657-183111893(+)$1	1	158	183	12.5201
(.((((..(((....)))..)))).	chr17:27005838-27006075(+)$1	1	192	217	12.6039
.((((((((((....))).))))))	chr1:64100472-64100702(+)$1	1	9	34	12.9689
.(((....(((....)))...))).	chr22:41911669-41911901(+)$1	1	0	25	12.8422
((((((((.((....)).)))))))	chr17:26967560-26967791(-)$1	1	24	49	9.7139
(((.....(((....)))..)))))	chrX:135055732-135055973(-)$1	1	30	55	12.7532
(.(((((((((....)))..)))).	chr9:134473537-134473774(-)$1	1	6	31	11.1769
(((((...(((....)))...))))	chr13:100206481-100206719(+)$1	1	169	194	13.4180
(((.(((.(((....))).))))))	chr3:13373753-13373992(-)$1	1	110	135	13.1921
((((....(((....))))))))))	chr17:30806246-30806474(+)$1	1	139	164	13.7586
(.((((..(((....))))))).))	chr17:45745459-45745698(+)$1	1	14	39	11.6537
((.(...((((....)))).)))))	chr11:62494310-62494548(-)$1	1	36	61	10.5988
(.(((((((((....)).)))))))	chr1:227504693-227504921(-)$1	1	111	136	10.2556
(...(((.(((....))))))..))	chr2:61711083-61711358(-)$1	1	210	235	11.5967
..(((((((.(....)..)))))))	chr5:1802355-1802589(+)$1	1	94	119	9.8002
.((((...(((....)))...))))	chrX:149930960-149931186(+)$1	1	4	29	13.5914
(((((((.(((....)))..)))))	chr16:4700337-4700566(+)$1	1	178	203	11.9114
((((...((((....))))))))))	chr17:38318027-38318259(+)$1	1	183	208	11.2244
((((...((((....))))))))).	chr16:70588303-70588553(+)$1	1	135	160	10.4372
((((((..(((....))))))))).	chr12:21807468-21807709(-)$1	1	197	222	10.9208
(((((((((((....))).))))))	chr1:101455979-101456210(-)$1	1	46	71	13.0109
....(((.(((....))).)))...	chr15:68500463-68500705(-)$1	1	30	55	10.1830
..(((((((((....))))))))).	chr9:128069672-128069902(+)$1	1	59	84	10.9613
(((.....(((....)))..)))))	chr11:66453270-66453500(-)$1	1	189	214	12.7532
(((((.(((((....))).)).)))	chr3:132347087-132347322(-)$1	1	49	74	11.7778
((((((..(((....)))..)))))	chr13:76414108-76414350(+)$1	1	13	38	12.6395
((((((((..(....)...))))))	chrX:39934196-39934425(-)$1	1	58	83	11.2628
((((((..(((...)))))))))).	chr7:5460731-5460952(+)$1	1	66	91	10.5009
..(((..((((....))))..))).	chr6:122767904-122768155(-)$1	1	215	240	10.9358
((...(((.((....))))))))))	chr15:65849078-65849343(+)$1	1	5	30	10.5327
((((.(.((((....))))...).)	chr5:32444628-32444857(-)$1	1	179	204	11.1776

#PSSM
g : 0.13	e : 0.13	c : 0.11	d : 0.11	f : 0.11	: : 0.05	$ : 0.03	h : 0.03	b : 0.03	[ : 0.03	i : 0.03	" : 0.01	H : 0.01	a : 0.01	% : 0.01	# : 0.01	! : 0.01	
g : 0.19	e : 0.17	c : 0.13	f : 0.09	[ : 0.09	d : 0.05	h : 0.03	b : 0.03	i : 0.03	: : 0.01	" : 0.01	$ : 0.01	% : 0.01	# : 0.01	! : 0.01	
g : 0.21	c : 0.19	e : 0.15	d : 0.11	f : 0.09	i : 0.05	h : 0.03	b : 0.03	" : 0.03	[ : 0.01	% : 0.01	
g : 0.21	[ : 0.13	e : 0.11	c : 0.09	d : 0.09	f : 0.07	$ : 0.05	i : 0.05	" : 0.03	! : 0.01	h : 0.01	b : 0.01	a : 0.01	% : 0.01	
g : 0.19	c : 0.17	d : 0.11	# : 0.07	f : 0.07	" : 0.07	e : 0.05	$ : 0.05	b : 0.03	[ : 0.03	i : 0.03	! : 0.01	h : 0.01	
c : 0.17	g : 0.15	" : 0.13	# : 0.11	d : 0.07	[ : 0.05	$ : 0.05	f : 0.05	e : 0.03	b : 0.03	i : 0.03	! : 0.01	a : 0.01	
! : 0.19	c : 0.17	g : 0.13	" : 0.13	# : 0.11	$ : 0.05	a : 0.03	[ : 0.03	i : 0.03	d : 0.01	f : 0.01	b : 0.01	
! : 0.19	[ : 0.15	d : 0.13	# : 0.11	g : 0.11	c : 0.07	" : 0.07	$ : 0.05	i : 0.03	b : 0.01	
c : 0.66	d : 0.11	[ : 0.05	g : 0.05	! : 0.03	# : 0.03	i : 0.01	
c : 0.70	d : 0.11	b : 0.09	g : 0.01	[ : 0.01	i : 0.01	! : 0.01	
c : 0.68	d : 0.11	b : 0.09	a : 0.05	g : 0.01	i : 0.01	
m : 0.94	c : 0.03	l : 0.01	
m : 0.96	l : 0.03	
m : 0.96	l : 0.03	
m : 0.96	l : 0.01	c : 0.01	
c : 0.66	d : 0.11	b : 0.09	a : 0.05	m : 0.01	g : 0.01	i : 0.01	
c : 0.68	d : 0.11	b : 0.09	] : 0.01	g : 0.01	2 : 0.01	i : 0.01	3 : 0.01	
c : 0.70	d : 0.11	2 : 0.03	g : 0.03	] : 0.03	4 : 0.01	i : 0.01	3 : 0.01	
] : 0.23	2 : 0.17	d : 0.13	3 : 0.11	g : 0.09	c : 0.07	4 : 0.07	i : 0.03	e : 0.01	f : 0.01	
c : 0.17	2 : 0.17	g : 0.15	3 : 0.11	4 : 0.09	e : 0.07	i : 0.05	a : 0.03	] : 0.03	d : 0.01	f : 0.01	b : 0.01	
g : 0.17	c : 0.15	e : 0.13	3 : 0.11	4 : 0.09	d : 0.07	f : 0.07	i : 0.05	] : 0.03	a : 0.01	b : 0.01	2 : 0.01	
c : 0.21	g : 0.19	e : 0.15	d : 0.11	4 : 0.07	f : 0.07	i : 0.05	b : 0.03	2 : 0.01	] : 0.01	3 : 0.01	
g : 0.19	e : 0.15	c : 0.13	] : 0.09	d : 0.09	f : 0.07	b : 0.05	i : 0.05	4 : 0.03	3 : 0.01	h : 0.01	2 : 0.01	a : 0.01	
g : 0.21	e : 0.15	c : 0.15	d : 0.13	] : 0.09	f : 0.07	i : 0.05	h : 0.03	b : 0.01	3 : 0.01	4 : 0.01	
g : 0.21	c : 0.11	] : 0.09	d : 0.09	e : 0.09	2 : 0.07	f : 0.07	: : 0.05	h : 0.03	3 : 0.03	i : 0.03	7 : 0.01	4 : 0.01	

#score	600.958065420875
#seq	51
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m2_run2.txt

#BEAR
!ddddwwwwwwwwwwwwwwdd	chr20:30345246-30345476(+)$1	230	73	94	20.1011
FFFccctttttttttttcccc	chr6:159204539-159204778(-)$1	239	175	196	19.4783
ddddtttttttttttddddFF	chr22:42334975-42335239(-)$1	264	0	21	18.6541
hhhhhttttttttttthhhhh	chr21:43319141-43319364(-)$1	223	56	77	19.9303
fffavvvvvvvvvvvvva]ff	chr11:93469221-93469456(-)$1	235	153	174	21.3622
ffffuuuuuuuuuuuufffff	chr9:15423827-15424078(+)$1	251	194	215	21.0862
'cccuuuuuuuuuuuuccc44	chr1:47765577-47765818(-)$1	241	125	146	20.9773
fffffvvvvvvvvvvvvvfff	chr5:68417424-68417657(+)$1	233	35	56	21.3871
d[ccctttttttttttcccdd	chr1:6697172-6697410(-)$1	238	117	138	22.3097
:ddddtttttttttttdddd:	chr10:25273679-25273905(+)$1	226	24	45	20.0521
eeeeeyyyyyyyyyyyyyyyy	chr16:30036598-30036821(-)$1	223	104	125	19.5450
iiiiiwwwwwwwwwwwwwwii	chr5:36166571-36166804(+)$1	233	136	157	20.1257
ddddwwwwwwwwwwwwwwddd	chr1:161070477-161070719(-)$1	242	115	136	19.8586
ffffftttttttttttfffff	chr4:41262655-41262893(+)$1	238	17	38	21.7352
ff[bbtttttttttttbb]ff	chr6:151277069-151277297(+)$1	228	37	58	21.2776
ffffftttttttttttfffff	chr6:134495585-134495811(-)$1	226	76	97	21.7352
hhhhhwwwwwwwwwwwwwwhh	chr19:39589606-39589829(-)$1	223	3	24	18.8180
=====ttttttttttt=====	chr1:10523483-10523720(-)$1	237	24	45	22.2962
::ccctttttttttttccchh	chr21:27372259-27372490(-)$1	231	28	49	20.0174
gggggtttttttttttggggg	chr16:58572040-58572273(-)$1	233	210	231	22.0448
=====ttttttttttt=====	chr17:47119612-47119840(+)$1	228	194	215	22.2962
e[cccyyyyyyyyyyyyyyyy	chr8:29927200-29927479(-)$1	279	207	228	19.6108
[ddddwwwwwwwwwwwwwwdd	chr1:38039924-38040156(-)$1	232	17	38	20.1274
ffffftttttttttttfffff	chr17:29226063-29226319(-)$1	256	41	62	21.7352
eeeeewwwwwwwwwwwwwwee	chr11:64088040-64088282(+)$1	242	41	62	20.2442
!!ccctttttttttttccc22	chr8:48830778-48831010(-)$1	232	144	165	22.1180
===bbuuuuuuuuuuuubb22	chrM:10447-10714(-)$1	267	188	209	20.8558
eeeeettttttttttteeeee	chr8:145727026-145727256(+)$1	230	38	59	22.0832
eeeeettttttttttteeeee	chr7:6068455-6068692(-)$1	237	132	153	22.0832
iiiauuuuuuuuuuuua]iii	chr1:120285519-120285759(+)$1	240	196	217	21.6467
!!cccwwwwwwwwwwwwwwcc	chr4:87693846-87694073(+)$1	227	46	67	20.3089
eeeeewwwwwwwwwwwwwwee	chr17:28750475-28750738(+)$1	263	188	209	20.2442
""cccuuuuuuuuuuuuccc]	chr6:26156606-26156835(+)$1	229	67	88	22.1591
:ddddtttttttttttdddd:	chr7:70254713-70254940(+)$1	227	202	223	20.0521
iiiiivvvvvvvvvvvvviii	chr16:9012858-9013087(-)$1	229	177	198	21.6127
fffffvvvvvvvvvvvvvfff	chr1:173797391-173797619(+)$1	228	33	54	21.3871
!ddddtttttttttttdddd3	chr9:35100530-35100768(-)$1	238	111	132	21.9923
[bbvvvvvvvvvvvvvbb]dd	chr19:58805692-58805921(+)$1	229	110	131	19.6944
eeeeuuuuuuuuuuuueeeee	chr2:271941-272186(+)$1	245	22	43	21.3971
cc[bbwwwwwwwwwwwwwwbb	chr11:47236669-47236899(+)$1	230	20	41	19.1062
eeeeewwwwwwwwwwwwwwee	chr11:34112048-34112276(+)$1	228	58	79	20.2442
[dddduuuuuuuuuuuudddd	chr7:158485450-158485712(-)$1	262	172	193	21.8974
fffffyyyyyyyyyyyyyyyy	chr17:45747972-45748231(+)$1	259	55	76	19.3296
eeeeettttttttttteeeee	chr17:28791682-28791911(+)$1	229	32	53	22.0832
cddddtttttttttttdddd:	chr18:51729286-51729513(-)$1	227	170	191	20.9677
:cccuuuuuuuuuuuucccGG	chr12:108932727-108932966(-)$1	239	120	141	19.5070
iiiiitttttttttttiiiii	chr17:8161108-8161337(+)$1	229	12	33	21.9560
eeeeettttttttttteeeee	chr16:89869576-89869810(-)$1	234	125	146	22.0832
[ddddtttttttttttdddd]	chr12:125396167-125396410(-)$1	243	84	105	22.0410
ffffftttttttttttfffff	chr12:12974048-12974296(+)$1	248	23	44	21.7352
ddddattttttttttta]ddd	chr15:65863836-65864069(+)$1	233	61	82	22.1128
ffffftttttttttttfffff	chr14:21556120-21556353(+)$1	233	9	30	21.7352
ddddwwwwwwwwwwwwwwddd	chr3:155547430-155547663(-)$1	233	48	69	19.8586
eeeeettttttttttteeeee	chr11:34135236-34135470(+)$1	234	206	227	22.0832

#otherMatches

#Seq PSSM
CGGAUUUCAUCAAUUUUUCAU	chr20:30345246-30345476(+)$1	230	73	94	20.1011
UUUGGCUUGGAGUUGAUGCCC	chr6:159204539-159204778(-)$1	239	175	196	19.4783
AGCAUUCUAUCUCACUGCUGU	chr22:42334975-42335239(-)$1	264	0	21	18.6541
AGGAGGACGAGCUAGACUCCU	chr21:43319141-43319364(-)$1	223	56	77	19.9303
AAGCAUAUAGAAAAAACGACU	chr11:93469221-93469456(-)$1	235	153	174	21.3622
ACAUUUUUUCAACAUUAUGUU	chr9:15423827-15424078(+)$1	251	194	215	21.0862
AGCAAAUAACUUUAAAUGCAC	chr1:47765577-47765818(-)$1	241	125	146	20.9773
UUAAAUAACAAGUCUAUUUUU	chr5:68417424-68417657(+)$1	233	35	56	21.3871
AAGGACUCGAAGCUCAUCCUC	chr1:6697172-6697410(-)$1	238	117	138	22.3097
CCAAUGUCGUGUUCUAGUUGU	chr10:25273679-25273905(+)$1	226	24	45	20.0521
GGUGCUGCUCUUUCCCUACCU	chr16:30036598-30036821(-)$1	223	104	125	19.5450
GAUUGCCUUCCGCUGCCCACG	chr5:36166571-36166804(+)$1	233	136	157	20.1257
GGAAAAGAACUAAAUGAAUUC	chr1:161070477-161070719(-)$1	242	115	136	19.8586
UUCAGGAAAAAGCAGAUUGAA	chr4:41262655-41262893(+)$1	238	17	38	21.7352
aaugaCUAAUCUGUUCUCUUU	chr6:151277069-151277297(+)$1	228	37	58	21.2776
UUCAUCCACAGCUUUCAUGAA	chr6:134495585-134495811(-)$1	226	76	97	21.7352
cgcgccccccaccgucccugc	chr19:39589606-39589829(-)$1	223	3	24	18.8180
GUCUGUGUUUGUUUGUUAGAU	chr1:10523483-10523720(-)$1	237	24	45	22.2962
CGAGCAAUGAUCUCCCGCUGG	chr21:27372259-27372490(-)$1	231	28	49	20.0174
AGGUAUGGAAGGAAUUUACUU	chr16:58572040-58572273(-)$1	233	210	231	22.0448
AGGGUGAUGGACAUGUGCCCU	chr17:47119612-47119840(+)$1	228	194	215	22.2962
GACGGGCAGUAUUCUCCUCCA	chr8:29927200-29927479(-)$1	279	207	228	19.6108
CUGGGACAACUGAAAUACCCC	chr1:38039924-38040156(-)$1	232	17	38	20.1274
CUACUGAACUACAAAGAGUAG	chr17:29226063-29226319(-)$1	256	41	62	21.7352
GGGGGUCAGAUGCAGUUAUCC	chr11:64088040-64088282(+)$1	242	41	62	20.2442
CAUCUGAAGAAGACAAAGAAC	chr8:48830778-48831010(-)$1	232	144	165	22.1180
AUUCCUAGAAGUGAGAUGGUA	chrM:10447-10714(-)$1	267	188	209	20.8558
CUGGCUGACCUGAAGCGCCAG	chr8:145727026-145727256(+)$1	230	38	59	22.0832
GAAACGGGAAGAGUAAGUUUU	chr7:6068455-6068692(-)$1	237	132	153	22.0832
GGUCUGCCCUGGAAUUGAACU	chr1:120285519-120285759(+)$1	240	196	217	21.6467
AUGUAUUUAAAAAUAGUCUUA	chr4:87693846-87694073(+)$1	227	46	67	20.3089
AUUCACCUUAUGCCAUCCAUG	chr17:28750475-28750738(+)$1	263	188	209	20.2442
CCGUGAAGAAGAAGGCCCGCA	chr6:26156606-26156835(+)$1	229	67	88	22.1591
CCGCCGACGAGCACAAGGCGA	chr7:70254713-70254940(+)$1	227	202	223	20.0521
UUUUCACGAAUCAGCUACGAA	chr16:9012858-9013087(-)$1	229	177	198	21.6127
GAGAUUUUAUCUUAAAAUGUU	chr1:173797391-173797619(+)$1	228	33	54	21.3871
AAGGACUCCAACACUAUCCUA	chr9:35100530-35100768(-)$1	238	111	132	21.9923
CAGAACAUAACUCCAGCUUAG	chr19:58805692-58805921(+)$1	229	110	131	19.6944
GAGGCCAACCUGAACUCCUCU	chr2:271941-272186(+)$1	245	22	43	21.3971
GGCUCCCAAGAAACGCCCAGA	chr11:47236669-47236899(+)$1	230	20	41	19.1062
CAGCAUCAUCAUCCCUUCCUG	chr11:34112048-34112276(+)$1	228	58	79	20.2442
UUAAAUGGUGAGUUGAUUUUG	chr7:158485450-158485712(-)$1	262	172	193	21.8974
GGUUCUUUCAGGAUUAACAUU	chr17:45747972-45748231(+)$1	259	55	76	19.3296
UGAGUAUGAAGAUGAAAUUCG	chr17:28791682-28791911(+)$1	229	32	53	22.0832
aagacccagcuucauugucuc	chr18:51729286-51729513(-)$1	227	170	191	20.9677
GGCUGGCAGAAUAUCAAGCAU	chr12:108932727-108932966(-)$1	239	120	141	19.5070
CCAGGUUACAAUCUGCCCUGG	chr17:8161108-8161337(+)$1	229	12	33	21.9560
GCCUGAAAAAAUGCCGCAGGU	chr16:89869576-89869810(-)$1	234	125	146	22.0832
GUCUGACUACAACAUCCAGAA	chr12:125396167-125396410(-)$1	243	84	105	22.0410
uguGUCAUUGUAGAAAACACA	chr12:12974048-12974296(+)$1	248	23	44	21.7352
CAUGCUGACGUGCAUUGACAU	chr15:65863836-65864069(+)$1	233	61	82	22.1128
CAGAAACACUUGACUCUUCUG	chr14:21556120-21556353(+)$1	233	9	30	21.7352
CAUGACCCUUUUAAAUACCGU	chr3:155547430-155547663(-)$1	233	48	69	19.8586
GUUCUGCUUUCUUUAAAGAAU	chr11:34135236-34135470(+)$1	234	206	227	22.0832

#DB
.((((..............))	chr20:30345246-30345476(+)$1	1	73	94	20.1011
)))(((...........)))(	chr6:159204539-159204778(-)$1	1	175	196	19.4783
((((...........))))((	chr22:42334975-42335239(-)$1	1	0	21	18.6541
(((((...........)))))	chr21:43319141-43319364(-)$1	1	56	77	19.9303
((((.............).))	chr11:93469221-93469456(-)$1	1	153	174	21.3622
((((............)))))	chr9:15423827-15424078(+)$1	1	194	215	21.0862
.(((............)))..	chr1:47765577-47765818(-)$1	1	125	146	20.9773
(((((.............)))	chr5:68417424-68417657(+)$1	1	35	56	21.3871
(.(((...........)))))	chr1:6697172-6697410(-)$1	1	117	138	22.3097
.((((...........)))).	chr10:25273679-25273905(+)$1	1	24	45	20.0521
(((((................	chr16:30036598-30036821(-)$1	1	104	125	19.5450
(((((..............))	chr5:36166571-36166804(+)$1	1	136	157	20.1257
((((..............)))	chr1:161070477-161070719(-)$1	1	115	136	19.8586
(((((...........)))))	chr4:41262655-41262893(+)$1	1	17	38	21.7352
((.((...........)).))	chr6:151277069-151277297(+)$1	1	37	58	21.2776
(((((...........)))))	chr6:134495585-134495811(-)$1	1	76	97	21.7352
(((((..............))	chr19:39589606-39589829(-)$1	1	3	24	18.8180
(((((...........)))))	chr1:10523483-10523720(-)$1	1	24	45	22.2962
..(((...........)))((	chr21:27372259-27372490(-)$1	1	28	49	20.0174
(((((...........)))))	chr16:58572040-58572273(-)$1	1	210	231	22.0448
(((((...........)))))	chr17:47119612-47119840(+)$1	1	194	215	22.2962
(.(((................	chr8:29927200-29927479(-)$1	1	207	228	19.6108
.((((..............))	chr1:38039924-38040156(-)$1	1	17	38	20.1274
(((((...........)))))	chr17:29226063-29226319(-)$1	1	41	62	21.7352
(((((..............))	chr11:64088040-64088282(+)$1	1	41	62	20.2442
..(((...........)))..	chr8:48830778-48831010(-)$1	1	144	165	22.1180
(((((............))..	chrM:10447-10714(-)$1	1	188	209	20.8558
(((((...........)))))	chr8:145727026-145727256(+)$1	1	38	59	22.0832
(((((...........)))))	chr7:6068455-6068692(-)$1	1	132	153	22.0832
((((............).)))	chr1:120285519-120285759(+)$1	1	196	217	21.6467
..(((..............))	chr4:87693846-87694073(+)$1	1	46	67	20.3089
(((((..............))	chr17:28750475-28750738(+)$1	1	188	209	20.2442
..(((............))).	chr6:26156606-26156835(+)$1	1	67	88	22.1591
.((((...........)))).	chr7:70254713-70254940(+)$1	1	202	223	20.0521
(((((.............)))	chr16:9012858-9013087(-)$1	1	177	198	21.6127
(((((.............)))	chr1:173797391-173797619(+)$1	1	33	54	21.3871
.((((...........)))).	chr9:35100530-35100768(-)$1	1	111	132	21.9923
.((.............)).))	chr19:58805692-58805921(+)$1	1	110	131	19.6944
((((............)))))	chr2:271941-272186(+)$1	1	22	43	21.3971
((.((..............))	chr11:47236669-47236899(+)$1	1	20	41	19.1062
(((((..............))	chr11:34112048-34112276(+)$1	1	58	79	20.2442
.((((............))))	chr7:158485450-158485712(-)$1	1	172	193	21.8974
(((((................	chr17:45747972-45748231(+)$1	1	55	76	19.3296
(((((...........)))))	chr17:28791682-28791911(+)$1	1	32	53	22.0832
)((((...........)))).	chr18:51729286-51729513(-)$1	1	170	191	20.9677
.(((............)))))	chr12:108932727-108932966(-)$1	1	120	141	19.5070
(((((...........)))))	chr17:8161108-8161337(+)$1	1	12	33	21.9560
(((((...........)))))	chr16:89869576-89869810(-)$1	1	125	146	22.0832
.((((...........)))).	chr12:125396167-125396410(-)$1	1	84	105	22.0410
(((((...........)))))	chr12:12974048-12974296(+)$1	1	23	44	21.7352
(((((...........).)))	chr15:65863836-65864069(+)$1	1	61	82	22.1128
(((((...........)))))	chr14:21556120-21556353(+)$1	1	9	30	21.7352
((((..............)))	chr3:155547430-155547663(-)$1	1	48	69	19.8586
(((((...........)))))	chr11:34135236-34135470(+)$1	1	206	227	22.0832

#PSSM
f : 0.20	e : 0.20	d : 0.09	! : 0.07	: : 0.07	i : 0.07	[ : 0.07	= : 0.05	h : 0.03	c : 0.03	F : 0.01	' : 0.01	g : 0.01	" : 0.01	
d : 0.22	f : 0.20	e : 0.18	i : 0.07	c : 0.05	= : 0.05	h : 0.03	[ : 0.03	! : 0.03	F : 0.01	: : 0.01	g : 0.01	" : 0.01	b : 0.01	
d : 0.22	f : 0.18	e : 0.18	c : 0.14	i : 0.07	= : 0.05	h : 0.03	[ : 0.03	F : 0.01	g : 0.01	b : 0.01	
d : 0.22	e : 0.18	c : 0.16	f : 0.16	i : 0.05	b : 0.05	h : 0.03	a : 0.03	= : 0.03	g : 0.01	v : 0.01	
e : 0.16	d : 0.14	f : 0.14	c : 0.12	u : 0.09	i : 0.05	b : 0.05	h : 0.03	v : 0.03	w : 0.03	= : 0.03	t : 0.01	g : 0.01	a : 0.01	
t : 0.48	w : 0.20	u : 0.14	v : 0.09	y : 0.05	c : 0.01	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.49	w : 0.20	u : 0.14	v : 0.09	y : 0.05	
t : 0.48	w : 0.20	u : 0.14	v : 0.09	y : 0.05	d : 0.01	
w : 0.20	d : 0.11	f : 0.11	e : 0.11	c : 0.09	v : 0.07	y : 0.05	u : 0.05	b : 0.03	= : 0.03	a : 0.03	t : 0.01	h : 0.01	g : 0.01	i : 0.01	
w : 0.20	c : 0.12	d : 0.12	f : 0.11	e : 0.11	v : 0.05	y : 0.05	b : 0.05	= : 0.03	] : 0.03	h : 0.01	a : 0.01	g : 0.01	i : 0.01	
d : 0.18	w : 0.16	f : 0.14	c : 0.12	e : 0.11	] : 0.05	y : 0.05	i : 0.05	= : 0.03	h : 0.01	g : 0.01	b : 0.01	
d : 0.24	f : 0.18	e : 0.16	i : 0.07	c : 0.05	h : 0.05	y : 0.05	= : 0.03	2 : 0.03	F : 0.01	4 : 0.01	g : 0.01	b : 0.01	G : 0.01	
f : 0.18	e : 0.16	d : 0.14	i : 0.07	h : 0.05	: : 0.05	y : 0.05	c : 0.03	= : 0.03	2 : 0.03	] : 0.03	F : 0.01	4 : 0.01	g : 0.01	3 : 0.01	b : 0.01	G : 0.01	

#score	1131.1833536649735
#seq	54
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m2_run2.txt

#BEAR
!!bb####===========oooooo===========333b	chr7:77569489-77569747(+)$1	258	83	123	15.6879
b[ccc[bb"""eeeeecccmmmmccc]eeeee4444bb]c	chr9:136405902-136406129(+)$1	227	33	73	14.3776
fffffcccdddd####cccmmmmcccdddd4444ccc]ff	chr11:67048829-67049139(+)$1	310	25	65	14.6524
ccceeeeeccc!!ffffffmmmmffffff333ccc]eeee	chr5:33998721-33998968(-)$1	247	177	217	12.0500
c[ggggggga!!ccc[cccmmmmccc]ccc22a]gggggg	chr7:87792355-87792587(+)$1	232	76	116	16.2729
eeee####ccc[bb"""bbmmmmbb]bb]ccc22eeeee3	chr14:104641395-104641676(+)$1	281	130	170	13.6572
!!ccc"""dddd[bb[cccmmmmcccbb333dddd333cc	chr1:54666149-54666364(+)$1	215	34	74	15.0857
dddd!!ccc[dddd!!cccoooooocccdddd]ccc4444	chr19:2115263-2115535(-)$1	272	89	129	14.3143
[ccc[ccc[ffffffacccmmmmccc]a]ffffff333cc	chr1:156532824-156533130(-)$1	306	25	65	15.0851
ddd[ccchhhhhhhh[cccmmmmccc4444hhhhhhhh]c	chr19:41798045-41798313(+)$1	268	161	201	12.3299
ddd[ccc"""ffffffcccmmmmccc333ffffff22ccc	chr6:31526058-31526309(+)$1	251	106	146	14.3978
hhhh$$$$$a[bb[a[cccmmmmccc]a]bba4444hhhh	chr8:144800877-144801128(-)$1	251	167	207	14.3633
===========[eeeeebbmmmmbb4444eeeee======	chr10:74969898-74970149(+)$1	251	80	120	13.6921
ffffffbb[ccc####cccmmmmccc4444ccc]bb333f	chrX:21958839-21959083(+)$1	244	23	63	15.5016
d[bbbb[bb[ggggggg[aooooooaggggggg4444bb]	chrX:149905710-149905941(+)$1	231	71	111	12.3195
E{Aiiiiiiiii[a!!cccmmmmccc]a]iiiiiiiii:d	chr22:21064885-21065125(-)$1	240	166	206	12.9483
ggggg!!bb[a[cccddddmmmmdddd22ccc]a]bb22g	chr10:134008297-134008556(-)$1	259	193	233	13.2150
cccccc!!dddd[a[ddddmmmmdddd]adddd]ccc]cc	chr17:7797265-7797683(+)$1	418	189	229	12.6491
eee"""eeeee[a[cccbbnnnnnbb]ccc]a]eeeee]e	chr3:33134785-33135022(-)$1	237	87	127	11.5541
B:ggggggg"""a!!cccooooooccc22a333ggggggg	chr15:41191004-41191274(+)$1	270	140	180	13.3572
eeeee"""ccc"""cccooooooccc]ccc22eeeee22d	chr17:1578733-1579208(-)$1	475	115	155	14.0839
ccc!!bb[cccbb####bbmmmmbb333bb]cccbb]ccc	chr11:108059819-108060044(-)$1	225	29	69	13.0551
c$$$$$ggggggg"""cccnnnnncccgggggggccc]bb	chr2:33498620-33498872(+)$1	252	167	207	12.6066
FFbb!!iiiiiiiii"""bblllbb333iiiiiiiii]bb	chr16:772453-772683(+)$1	230	179	219	12.2823
ccc!!accc!!dddd[bboooooobb]dddd333ccc22a	chr7:66482820-66483074(+)$1	254	85	125	13.5627
ggg$$$$$dddd####cccooooooccc4444ddddgggg	chr3:56694841-56695112(-)$1	271	5	45	13.8684
eeeee[ffffff[bb[cccooooooccc]bbffffff]ee	chr18:60237297-60237565(+)$1	268	27	67	12.3051
iiiiii[iiiiiiiii!!aooooooa22iiiiiiiiiiii	chr5:102469152-102469453(+)$1	301	90	130	14.3730
ee!!ccc[ffffff!!cccmmmmcccffffff]ccc]eee	chr16:89178477-89178720(+)$1	243	124	164	14.6095
c!!cccggggggg####bbmmmmbb22ggggggg]ccc22	chr1:214788093-214788489(+)$1	396	42	82	13.6550
gggg####ffffffcccooooooccc]ffffff22ggggg	chr15:43939398-43939618(-)$1	220	114	154	13.7336
[ccc$$$$$gggggggcccmmmmccc]ggggggg22ccc]	chr14:93180638-93180865(-)$1	227	131	171	15.3115
dddda[ccc!!dddd[cccmmmmccc]dddd22ccc333a	chr19:42392162-42392452(+)$1	290	130	170	15.4836
===####dddd$$$$$cccmmmmccc333dddd22=====	chr6:44414242-44414538(+)$1	296	94	134	15.7270
fffeeeee[eeeee!!cccooooooccc]eeeee22eeee	chr6:152570197-152570424(-)$1	227	155	195	12.3412
dd!!dddd[eeeee!!cccmmmmccceeeee]dddd333d	chr3:121207245-121207507(-)$1	262	194	234	13.6032
ggggggg!!ccc####cccmmmmccc4444ccc]gggggg	chr12:112601913-112602182(-)$1	269	88	128	16.6563
eeee[cccffffff!!cccmmmmcccffffff22ccceee	chr4:153245316-153245553(-)$1	237	82	122	14.4904
ffff"""bb"""ccc[cccmmmmccc]ccc]bb4444fff	chr13:51508957-51509269(+)$1	312	223	263	16.1916
dddd"""ccc[ccc[ddddllldddd]ccc]ccc333ddd	chr11:4128573-4128828(+)$1	255	136	176	13.1634
eeee[ffffff"""eeeeemmmmeeeeeffffff333eee	chr17:15466649-15466902(-)$1	253	192	232	11.8255
eee"""==========cccmmmmccc22==========44	chr10:49612854-49613124(+)$1	270	176	216	17.5182
dddd:eeeee!!ccc[cccoooooocccccc333eeeee:	chr4:151749372-151749682(-)$1	310	218	258	12.0538
eeeee!!bb!!ccc[ddddoooooodddd22ccc22bb44	chr2:128712749-128713018(-)$1	269	12	52	11.9011
eeeee!!ccc[a####cccmmmmccc22accc22eeeeed	chr5:36961493-36961785(+)$1	292	91	131	16.0336
dddd[ggggggg[bb[cccmmmmcccbb333ggggggg]d	chr22:38204011-38204261(+)$1	250	183	223	14.9100
d!!ggggggg!!gggggggmmmmggggggg4444gggggg	chr1:63999185-63999422(+)$1	237	118	158	14.7992
!a[ddddggggggg!!cccmmmmccc22ggggggg333dd	chr4:8229068-8229312(+)$1	244	37	77	15.4921
dd[a[bb[ggggggg!!bbmmmmbb]ggggggg4444bb]	chr14:101004175-101004420(-)$1	245	46	86	13.6542
fff####bb####ggggggglllggggggg4444bb22ff	chr11:61493391-61493651(+)$1	260	90	130	12.7475
"""bb[ccc!!dddd[a[aooooooa]adddd22ccc]bb	chr20:61473282-61473552(-)$1	270	47	87	12.5261
dddd!!bb####ccc[ddddllldddd]ccc4444bb22d	chr1:183506212-183506450(+)$1	238	125	165	12.6802
gggg[a[a[eeeee[cccnnnnnccc]eeeee]a]a]ggg	chr9:139617702-139617944(-)$1	242	26	66	12.7855
eeeee[bb####ccc[ddddmmmmdddd]ccc4444bb]e	chr6:35212277-35212563(-)$1	286	78	118	12.6059
eeeee[ccc==========lll==========4444ccc]	chr17:75493255-75493549(+)$1	294	202	242	14.6738
=====####dddd[cccooooooccc]dddd=========	chr2:37450398-37450643(-)$1	245	81	121	14.5185
:ffffff$$$$$bb!!cccmmmmccc22bb4444ffffff	chrX:1553871-1554077(-)$1	206	134	174	12.7502
"ffffff!!a"""ffffffmmmmffffff333a22fffff	chr12:77252678-77252904(-)$1	226	115	155	12.3481

#otherMatches

#Seq PSSM
GGAUUUUCUUUUUUUUGCUCUGUGUAGCAGAAAGAACUUA	chr7:77569489-77569747(+)$1	258	83	123	15.6879
GUGGCGGCCCCGGGGCCUGGCCACAGCGCCCUCCCAGCAG	chr9:136405902-136406129(+)$1	227	33	73	14.3776
CCUCAAGCGCCCCCUGAGGCAGCCCUGGGCCCCUGCUCUG	chr11:67048829-67049139(+)$1	310	25	65	14.6524
GCUGUUGGAGCAAUAGAACCCCAGUUCUACGAGCUGCUGA	chr5:33998721-33998968(-)$1	247	177	217	12.0500
GGCUUCUUUCAACUUUAGUACUUGCUUGAGCAGUAAAGAA	chr7:87792355-87792587(+)$1	232	76	116	16.2729
UCAGACCGGGAGCUCACCGACAACGAAGGUCCGCCUGACU	chr14:104641395-104641676(+)$1	281	130	170	13.6572
UCGCCCCCUCUUCACGAGCAUCCGCUGUACAAAGACCAGG	chr1:54666149-54666364(+)$1	215	34	74	15.0857
CUGAGUGGCUGCCCGCUGCCGGCCCGCAGGGCUGCCUAUG	chr19:2115263-2115535(-)$1	272	89	129	14.3143
GUCCAUGCAGCUGUUCUUGCCAUCAAUGAAGCAGUGGAGC	chr1:156532824-156533130(-)$1	306	25	65	15.0851
GGCAUUGCUUUCCGAAUCCAGAAGGAAGCCUUGGGGGGUC	chr19:41798045-41798313(+)$1	268	161	201	12.3299
GGGACCCAGAGGCCAUGGCUGCAGCCCUGGUGGCCAGGGG	chr6:31526058-31526309(+)$1	251	106	146	14.3978
UGCGUUCAGGUCAGUGUCUGCAGAGAGGGUGCGCACUGCA	chr8:144800877-144801128(-)$1	251	167	207	14.3633
UGAAGUCUUUCCUUCUUGCUUCUGUUACAGAGAAGAGGGA	chr10:74969898-74970149(+)$1	251	80	120	13.6921
GGCCGCAGCCUGACACGCCGCGCGGCCCCCCAGUCUCCCG	chrX:21958839-21959083(+)$1	244	23	63	15.5016
UUGCAGCGACGGUUGGGACCGAACAGCCCAGCUCACAUCU	chrX:149905710-149905941(+)$1	231	71	111	12.3195
GGCGGAGGGGGUGUGUGGAACGUUCUGAGAUCCCCUUUAG	chr22:21064885-21065125(-)$1	240	166	206	12.9483
GGAAGACGUGGUCCACUGUGAAGGCAGCAUGGUCAGCAGC	chr10:134008297-134008556(-)$1	259	193	233	13.2150
GUCCUGAACCAGAGGCUGAGGAAUCAGACCUGGACAGUGG	chr17:7797265-7797683(+)$1	418	189	229	12.6491
AGCCUCGGUCCUGCGGACGGCUGUCGCUCCUCUGGGCCAG	chr3:33134785-33135022(-)$1	237	87	127	11.5541
CUGGGACGUAAGGAUGACGCAAAAGUUCACAAGAUGUUCC	chr15:41191004-41191274(+)$1	270	140	180	13.3572
UCAUGGAUCUGUAUAGCCACCUCGUUCCAGUAUAUGAUGU	chr17:1578733-1579208(-)$1	475	115	155	14.0839
AGCUUGCAUCUCAAACAGCUCCAGCCAGUGCAGAGUUGCU	chr11:108059819-108060044(-)$1	225	29	69	13.0551
AGAUAUACCUGUAUAUGCUACGAGGGCUACAGGUUCAGUG	chr2:33498620-33498872(+)$1	252	167	207	12.6066
UGCUGGCUGAGGAGCUCUGCUCUGCUCUGCUCCUUGGGAG	chr16:772453-772683(+)$1	230	179	219	12.2823
GGCGACUGCGACGUGGUUAAAAGCAAGCACGGCAGCAUUG	chr7:66482820-66483074(+)$1	254	85	125	13.5627
GUUAAGAUUGCUAGAGUUGAAAAUACAGAUAAGGCAAACA	chr3:56694841-56695112(-)$1	271	5	45	13.8684
GUUAUUUUUAGAUGUGAAUUUGGACAUUGGCUCUGGACAU	chr18:60237297-60237565(+)$1	268	27	67	12.3051
CUCCUUAUUUAAAUAUAUCACAGUAGUAGUAUUUGAAGAG	chr5:102469152-102469453(+)$1	301	90	130	14.3730
ACCCAGCCGCACGCCCAGGAUUUCUUGCGUGCAGUUUGUG	chr16:89178477-89178720(+)$1	243	124	164	14.6095
AAAUAAGGGAGUUAUUGUCUUCUGAACAAUUCUCAUUAGG	chr1:214788093-214788489(+)$1	396	42	82	13.6550
UGGGUCCUUGAGUGUAUCCUUUCAUGUCACUCAUUUUUAU	chr15:43939398-43939618(-)$1	220	114	154	13.7336
UUCCCAAUGAAGAUGUGAGUUUUCUUAACGUUUUAAGGAC	chr14:93180638-93180865(-)$1	227	131	171	15.3115
GUUCCCGUCAGCAUCAUCGGGGCUGAGGAUGAGGAUUUUG	chr19:42392162-42392452(+)$1	290	130	170	15.4836
CUUUAAGUGUCUAAAAGAAGACGUUCAGCGACAACAAGAA	chr6:44414242-44414538(+)$1	296	94	134	15.7270
GAGAAAAUGCAUAGAGGAGAUAUGACUUACUAUGAAAUUU	chr6:152570197-152570424(-)$1	227	155	195	12.3412
UUACUAUUUGAUAGCUUCAGUGAUGACUAUCUAGUAAAAG	chr3:121207245-121207507(-)$1	262	194	234	13.6032
GCCUCCACCCUCCAGAUCAAUGAUGAGACCGAGCUGGAGG	chr12:112601913-112602182(-)$1	269	88	128	16.6563
AUUCACACGUUAACAGGGCACCAGUCGUUAACAAGUGGAA	chr4:153245316-153245553(-)$1	237	82	122	14.4904
UUGCCUAAGAACGUGGCUGCUUACAGACACACUGAAUGUA	chr13:51508957-51509269(+)$1	312	223	263	16.1916
AACACUCUCCCAUGGUGGCCAAGUCAACAUUGGAUAUUGU	chr11:4128573-4128828(+)$1	255	136	176	13.1634
GGACUGGCUCUGCAGGUUCCGUGGGACUGGAGCCCGCGUC	chr17:15466649-15466902(-)$1	253	192	232	11.8255
GAACAUUUUUGGUUUCCUAAGUAUAGAUGAAAUCAAGAUU	chr10:49612854-49613124(+)$1	270	176	216	17.5182
ACAUUCUCCGAAGCUUGGUUAACAUACCAGCAGAUGGAGU	chr4:151749372-151749682(-)$1	310	218	258	12.0538
AAUUGGACAAAUACUCAUCCUCUGAGAUGUUGUAGAUGAA	chr2:128712749-128713018(-)$1	269	12	52	11.9011
GGAAUGAUGAUGUCUCAGUAUAAACUUUCUCAGAAUUCCA	chr5:36961493-36961785(+)$1	292	91	131	16.0336
UCCAAGACCUUUCCCGAGCUUGCGCUGGAAUGGAGGUCCU	chr22:38204011-38204261(+)$1	250	183	223	14.9100
AACAUUCUUAAAUAAAGGUAUUUACUUUUAACACUAAGAA	chr1:63999185-63999422(+)$1	237	118	158	14.7992
UCUGCUUCCUCCUGGGGCGGCUGUGCAGCAGGAGGCUCAA	chr4:8229068-8229312(+)$1	244	37	77	15.4921
GGUGGCUCGGGGCUGAGCCGCAAGGACAGCCUCACCAAGG	chr14:101004175-101004420(-)$1	245	46	86	13.6542
GGGUCAAGCCACCAGCUGGUCGCGCCGGCUCAAAGUGUUC	chr11:61493391-61493651(+)$1	260	90	130	12.7475
ACAGCAGUUUUCAUGUCAGUUAAUUCAGUAUGUUAACCGU	chr20:61473282-61473552(-)$1	270	47	87	12.5261
UCAAGUAUUAGUGGUAAGGGCUACCCUAACCUUGUGUUGU	chr1:183506212-183506450(+)$1	238	125	165	12.6802
GCAGGAAGCGGCGCACGGUGGCCUCGGGUGCCACCUGCUG	chr9:139617702-139617944(-)$1	242	26	66	12.7855
GGCACAGCGAAUACAGCGGUGGAUGCUGGUGUUGUAGUAG	chr6:35212277-35212563(-)$1	286	78	118	12.6059
AGGGUGCUUGGGUGGGGCUGACGGCUUCACCCCUAAGAGG	chr17:75493255-75493549(+)$1	294	202	242	14.6738
CUUGGUUUUGUUUUGCAGGAAGAUGUUGGAUCCAGGGUUG	chr2:37450398-37450643(-)$1	245	81	121	14.5185
UGUCGCGAUCGUCCACUGCUCCAGCAAAGGUAACCGCGGC	chrX:1553871-1554077(-)$1	206	134	174	12.7502
UGGGCCCAAGGGAUUUGGCUAUGGCCAAGGAGCAGGGGCU	chr12:77252678-77252904(-)$1	226	115	155	12.3481

#DB
..((....(((((((((((......)))))))))))...)	chr7:77569489-77569747(+)$1	1	83	123	15.6879
(.(((.((...((((((((....))).)))))....)).)	chr9:136405902-136406129(+)$1	1	33	73	14.3776
((((((((((((....(((....)))))))....))).))	chr11:67048829-67049139(+)$1	1	25	65	14.6524
(((((((((((..((((((....))))))...))).))))	chr5:33998721-33998968(-)$1	1	177	217	12.0500
(.((((((((..(((.(((....))).)))..).))))))	chr7:87792355-87792587(+)$1	1	76	116	16.2729
((((....(((.((...((....)).)).)))..))))).	chr14:104641395-104641676(+)$1	1	130	170	13.6572
..(((...((((.((.(((....)))))...))))...))	chr1:54666149-54666364(+)$1	1	34	74	15.0857
((((..(((.((((..(((......))))))).)))....	chr19:2115263-2115535(-)$1	1	89	129	14.3143
.(((.(((.((((((((((....))).).))))))...))	chr1:156532824-156533130(-)$1	1	25	65	15.0851
(((.(((((((((((.(((....)))....)))))))).)	chr19:41798045-41798313(+)$1	1	161	201	12.3299
(((.(((...(((((((((....)))...))))))..)))	chr6:31526058-31526309(+)$1	1	106	146	14.3978
((((.....(.((.(.(((....))).).)))....))))	chr8:144800877-144801128(-)$1	1	167	207	14.3633
(((((((((((.(((((((....))....)))))))))))	chr10:74969898-74970149(+)$1	1	80	120	13.6921
((((((((.(((....(((....)))....))).))...)	chrX:21958839-21959083(+)$1	1	23	63	15.5016
(.((((.((.(((((((.(......))))))))....)).	chrX:149905710-149905941(+)$1	1	71	111	12.3195
(.((((((((((.(..(((....))).).))))))))).(	chr22:21064885-21065125(-)$1	1	166	206	12.9483
(((((..((.(.(((((((....))))..))).).))..)	chr10:134008297-134008556(-)$1	1	193	233	13.2150
((((((..((((.(.((((....)))).))))).))).))	chr17:7797265-7797683(+)$1	1	189	229	12.6491
(((...(((((.(.(((((.....)).))).).))))).)	chr3:33134785-33135022(-)$1	1	87	127	11.5541
(.(((((((...(..(((......)))..)...)))))))	chr15:41191004-41191274(+)$1	1	140	180	13.3572
(((((...(((...(((......))).)))..)))))..)	chr17:1578733-1579208(-)$1	1	115	155	14.0839
(((..((.(((((....((....))...)).))))).)))	chr11:108059819-108060044(-)$1	1	29	69	13.0551
(.....(((((((...(((.....))))))))))))).))	chr2:33498620-33498872(+)$1	1	167	207	12.6066
))((..(((((((((...((...))...))))))))).))	chr16:772453-772683(+)$1	1	179	219	12.2823
(((..((((..((((.((......)).))))...)))..)	chr7:66482820-66483074(+)$1	1	85	125	13.5627
(((.....((((....(((......)))....))))))))	chr3:56694841-56695112(-)$1	1	5	45	13.8684
(((((.((((((.((.(((......))).)))))))).))	chr18:60237297-60237565(+)$1	1	27	67	12.3051
((((((.(((((((((..(......)..))))))))))))	chr5:102469152-102469453(+)$1	1	90	130	14.3730
((..(((.((((((..(((....))))))))).))).)))	chr16:89178477-89178720(+)$1	1	124	164	14.6095
(..((((((((((....((....))..))))))).)))..	chr1:214788093-214788489(+)$1	1	42	82	13.6550
((((....(((((((((......))).))))))..)))))	chr15:43939398-43939618(-)$1	1	114	154	13.7336
.(((.....((((((((((....))).)))))))..))).	chr14:93180638-93180865(-)$1	1	131	171	15.3115
(((((.(((..((((.(((....))).))))..)))...)	chr19:42392162-42392452(+)$1	1	130	170	15.4836
(((....((((.....(((....)))...))))..)))))	chr6:44414242-44414538(+)$1	1	94	134	15.7270
)))(((((.(((((..(((......))).)))))..))))	chr6:152570197-152570424(-)$1	1	155	195	12.3412
((..((((.(((((..(((....)))))))).))))...)	chr3:121207245-121207507(-)$1	1	194	234	13.6032
(((((((..(((....(((....)))....))).))))))	chr12:112601913-112602182(-)$1	1	88	128	16.6563
((((.(((((((((..(((....)))))))))..))))))	chr4:153245316-153245553(-)$1	1	82	122	14.4904
((((...((...(((.(((....))).))).))....)))	chr13:51508957-51509269(+)$1	1	223	263	16.1916
((((...(((.(((.((((...)))).))).)))...)))	chr11:4128573-4128828(+)$1	1	136	176	13.1634
((((.((((((...(((((....)))))))))))...)))	chr17:15466649-15466902(-)$1	1	192	232	11.8255
(((...(((((((((((((....)))..))))))))))..	chr10:49612854-49613124(+)$1	1	176	216	17.5182
)))).(((((..(((.(((......))))))...))))).	chr4:151749372-151749682(-)$1	1	218	258	12.0538
(((((..((..(((.((((......))))..)))..))..	chr2:128712749-128713018(-)$1	1	12	52	11.9011
(((((..(((.(....(((....)))..))))..))))))	chr5:36961493-36961785(+)$1	1	91	131	16.0336
((((.(((((((.((.(((....)))))...))))))).)	chr22:38204011-38204261(+)$1	1	183	223	14.9100
(..(((((((..(((((((....)))))))....))))))	chr1:63999185-63999422(+)$1	1	118	158	14.7992
.(.(((((((((((..(((....)))..)))))))...))	chr4:8229068-8229312(+)$1	1	37	77	15.4921
((.(.((.(((((((..((....)).)))))))....)).	chr14:101004175-101004420(-)$1	1	46	86	13.6542
(((....((....(((((((...)))))))....))..))	chr11:61493391-61493651(+)$1	1	90	130	12.7475
...((.(((..((((.(.(......).)))))..))).))	chr20:61473282-61473552(-)$1	1	47	87	12.5261
((((..((....(((.((((...)))).)))....))..)	chr1:183506212-183506450(+)$1	1	125	165	12.6802
((((.(.(.(((((.(((.....))).))))).).).)))	chr9:139617702-139617944(-)$1	1	26	66	12.7855
(((((.((....(((.((((....)))).)))....)).)	chr6:35212277-35212563(-)$1	1	78	118	12.6059
(((((.(((((((((((((...))))))))))....))).	chr17:75493255-75493549(+)$1	1	202	242	14.6738
(((((....((((.(((......))).)))))))))))))	chr2:37450398-37450643(-)$1	1	81	121	14.5185
.((((((.....((..(((....)))..))....))))))	chrX:1553871-1554077(-)$1	1	134	174	12.7502
.((((((..(...((((((....))))))...)..)))))	chr12:77252678-77252904(-)$1	1	115	155	12.3481

#PSSM
e : 0.20	d : 0.20	c : 0.12	f : 0.08	g : 0.08	! : 0.05	= : 0.05	[ : 0.03	" : 0.03	b : 0.01	h : 0.01	E : 0.01	B : 0.01	F : 0.01	i : 0.01	: : 0.01	
e : 0.20	d : 0.17	f : 0.12	c : 0.10	g : 0.08	! : 0.06	[ : 0.05	= : 0.05	h : 0.01	{ : 0.01	: : 0.01	$ : 0.01	F : 0.01	i : 0.01	a : 0.01	" : 0.01	
e : 0.18	c : 0.13	d : 0.13	f : 0.12	g : 0.12	! : 0.06	b : 0.05	= : 0.05	[ : 0.03	h : 0.01	A : 0.01	$ : 0.01	i : 0.01	" : 0.01	
e : 0.18	g : 0.12	d : 0.12	c : 0.10	f : 0.08	b : 0.06	! : 0.06	[ : 0.03	= : 0.03	i : 0.03	" : 0.03	$ : 0.03	# : 0.03	h : 0.01	a : 0.01	
e : 0.13	c : 0.12	[ : 0.10	# : 0.08	g : 0.08	! : 0.08	f : 0.06	$ : 0.06	" : 0.06	= : 0.03	b : 0.03	i : 0.03	d : 0.03	a : 0.01	: : 0.01	
c : 0.13	# : 0.10	[ : 0.10	" : 0.10	! : 0.10	g : 0.08	$ : 0.06	f : 0.06	e : 0.05	b : 0.05	i : 0.03	a : 0.03	d : 0.03	= : 0.01	
c : 0.18	g : 0.12	# : 0.10	b : 0.10	e : 0.06	" : 0.06	! : 0.06	f : 0.06	$ : 0.05	[ : 0.05	= : 0.03	i : 0.03	d : 0.03	
c : 0.17	b : 0.15	g : 0.12	# : 0.06	e : 0.06	$ : 0.06	" : 0.05	i : 0.05	! : 0.05	[ : 0.05	= : 0.03	f : 0.03	d : 0.03	h : 0.01	a : 0.01	
c : 0.18	g : 0.13	d : 0.08	[ : 0.08	b : 0.08	f : 0.08	= : 0.05	$ : 0.05	i : 0.05	# : 0.05	" : 0.03	e : 0.03	! : 0.03	h : 0.01	
c : 0.13	g : 0.12	d : 0.10	f : 0.10	e : 0.08	= : 0.06	" : 0.06	! : 0.06	a : 0.05	[ : 0.05	i : 0.05	# : 0.05	h : 0.01	$ : 0.01	
d : 0.12	! : 0.12	f : 0.12	g : 0.12	c : 0.10	= : 0.06	" : 0.06	e : 0.06	[ : 0.05	i : 0.05	# : 0.05	h : 0.01	a : 0.01	$ : 0.01	
d : 0.15	g : 0.12	f : 0.10	" : 0.08	e : 0.06	! : 0.06	[ : 0.06	c : 0.06	= : 0.05	i : 0.05	# : 0.05	b : 0.03	$ : 0.03	h : 0.01	a : 0.01	
c : 0.13	g : 0.12	# : 0.10	e : 0.08	[ : 0.08	d : 0.08	f : 0.08	b : 0.06	= : 0.05	" : 0.05	a : 0.03	i : 0.03	! : 0.01	h : 0.01	$ : 0.01	
c : 0.13	# : 0.12	f : 0.12	g : 0.10	e : 0.08	b : 0.08	d : 0.06	= : 0.05	[ : 0.05	" : 0.05	a : 0.03	i : 0.03	h : 0.01	! : 0.01	$ : 0.01	
c : 0.17	! : 0.15	# : 0.12	g : 0.08	f : 0.06	[ : 0.06	= : 0.05	e : 0.05	b : 0.05	d : 0.05	" : 0.03	i : 0.03	h : 0.01	a : 0.01	$ : 0.01	
[ : 0.22	! : 0.15	# : 0.12	c : 0.10	g : 0.06	d : 0.06	= : 0.05	e : 0.05	f : 0.05	" : 0.05	a : 0.01	i : 0.01	$ : 0.01	
c : 0.60	d : 0.10	g : 0.05	= : 0.03	f : 0.03	" : 0.03	e : 0.03	# : 0.03	! : 0.03	b : 0.01	a : 0.01	
c : 0.53	b : 0.12	d : 0.10	o : 0.05	= : 0.03	f : 0.03	[ : 0.03	g : 0.03	" : 0.01	! : 0.01	e : 0.01	
c : 0.49	b : 0.12	d : 0.10	o : 0.08	a : 0.05	= : 0.03	f : 0.03	g : 0.03	e : 0.01	n : 0.01	
m : 0.58	o : 0.25	n : 0.05	l : 0.03	d : 0.03	b : 0.01	g : 0.01	
m : 0.60	o : 0.25	l : 0.08	n : 0.05	
m : 0.60	o : 0.25	l : 0.08	n : 0.05	
m : 0.60	o : 0.25	n : 0.05	l : 0.05	d : 0.01	= : 0.01	
c : 0.46	o : 0.20	b : 0.10	d : 0.06	f : 0.03	n : 0.03	g : 0.03	e : 0.01	m : 0.01	= : 0.01	
c : 0.49	o : 0.17	b : 0.13	d : 0.08	f : 0.03	g : 0.03	e : 0.01	= : 0.01	
c : 0.58	d : 0.10	a : 0.05	= : 0.03	f : 0.03	] : 0.03	b : 0.03	3 : 0.03	g : 0.03	4 : 0.01	2 : 0.01	e : 0.01	
] : 0.27	c : 0.12	d : 0.10	2 : 0.10	f : 0.06	4 : 0.06	3 : 0.06	g : 0.06	b : 0.05	= : 0.03	e : 0.03	
c : 0.17	g : 0.12	2 : 0.12	d : 0.10	f : 0.08	e : 0.06	a : 0.06	4 : 0.06	3 : 0.06	b : 0.05	= : 0.03	] : 0.03	
g : 0.13	d : 0.12	c : 0.12	] : 0.12	f : 0.10	4 : 0.08	3 : 0.06	= : 0.05	e : 0.05	2 : 0.03	a : 0.03	b : 0.03	i : 0.03	
c : 0.18	d : 0.13	g : 0.13	f : 0.10	e : 0.08	3 : 0.06	4 : 0.06	b : 0.06	= : 0.05	i : 0.05	a : 0.01	2 : 0.01	
c : 0.13	d : 0.12	f : 0.10	g : 0.10	e : 0.08	4 : 0.08	3 : 0.08	] : 0.06	= : 0.05	2 : 0.05	i : 0.05	b : 0.03	h : 0.01	
c : 0.15	f : 0.12	g : 0.12	4 : 0.10	3 : 0.08	d : 0.08	= : 0.06	e : 0.06	2 : 0.05	i : 0.05	a : 0.03	h : 0.01	] : 0.01	b : 0.01	
4 : 0.15	g : 0.12	c : 0.10	2 : 0.08	d : 0.08	] : 0.08	f : 0.08	= : 0.05	e : 0.05	i : 0.05	3 : 0.05	a : 0.03	h : 0.01	b : 0.01	
4 : 0.20	c : 0.12	2 : 0.12	g : 0.10	] : 0.06	f : 0.06	e : 0.06	= : 0.05	d : 0.05	i : 0.05	a : 0.03	3 : 0.03	h : 0.01	
c : 0.17	4 : 0.13	g : 0.10	2 : 0.10	e : 0.08	= : 0.06	f : 0.06	d : 0.05	b : 0.05	i : 0.05	] : 0.05	3 : 0.03	h : 0.01	
c : 0.17	4 : 0.12	g : 0.10	= : 0.08	e : 0.08	3 : 0.08	b : 0.08	2 : 0.06	i : 0.05	f : 0.05	d : 0.03	] : 0.01	h : 0.01	a : 0.01	
3 : 0.15	c : 0.15	e : 0.12	g : 0.12	b : 0.08	4 : 0.06	= : 0.06	i : 0.05	] : 0.05	f : 0.05	h : 0.03	2 : 0.03	
e : 0.15	g : 0.13	3 : 0.12	] : 0.10	b : 0.08	c : 0.08	2 : 0.08	= : 0.06	f : 0.05	h : 0.03	i : 0.03	4 : 0.01	d : 0.01	
e : 0.15	g : 0.12	c : 0.12	] : 0.08	f : 0.08	b : 0.08	2 : 0.08	3 : 0.06	4 : 0.05	= : 0.05	d : 0.03	h : 0.01	: : 0.01	i : 0.01	
e : 0.13	g : 0.13	d : 0.13	c : 0.12	f : 0.10	b : 0.06	] : 0.06	4 : 0.05	= : 0.05	a : 0.03	3 : 0.01	h : 0.01	i : 0.01	2 : 0.01	: : 0.01	

#score	804.4405290801053
#seq	58
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_CDS_m3_run2.txt

#BEAR
ggggxxxxxxxxxxxxxxxgggggg	chr17:35508148-35508396(-)$1	248	11	36	17.6481
ggggxxxxxxxxxxxxxxxgggggg	chr2:175979442-175979665(-)$1	223	186	211	17.6481
"eeeeevvvvvvvvvvvvveeeee]	chr16:29822298-29822529(+)$1	231	98	123	22.6468
c[bb[ccctttttttttttcccbb]	chr3:23848651-23848890(+)$1	239	8	33	21.1406
=======yyyyyyyyyyyyyyyy==	chr17:45734151-45734375(+)$1	224	44	69	20.9520
gga[ccctttttttttttccc]a]g	chr2:74372293-74372520(-)$1	227	88	113	22.1979
eeeeewwwwwwwwwwwwwweeeee7	chr6:3155786-3156048(-)$1	262	28	53	21.3839
eeee[bbvvvvvvvvvvvvvbbeee	chr22:35688892-35689116(+)$1	224	54	79	22.1604
d!!ddddwwwwwwwwwwwwwwdddd	chr6:155116121-155116350(+)$1	229	181	206	21.9293
eeee[ccctttttttttttccceee	chr16:426144-426368(+)$1	224	48	73	22.1518
a[fffffftttttttttttffffff	chr19:11728146-11728368(+)$1	222	121	146	20.8542
hhhhhhhyyyyyyyyyyyyyyyyhh	chr16:58577171-58577400(-)$1	229	104	129	19.4123
ccc!!bbuuuuuuuuuuuubb22cc	chr19:39205016-39205299(+)$1	283	6	31	22.6178
hhhhhhhuuuuuuuuuuuuhhhhhh	chr1:156563145-156563373(+)$1	228	182	207	21.2409
[ccc[ccctttttttttttccc]cc	chr9:140093662-140093894(-)$1	232	164	189	22.1076
eeeeexxxxxxxxxxxxxxxeeeee	chr15:42058599-42058826(+)$1	227	25	50	17.6969
gggdddduuuuuuuuuuuudddd]g	chr1:46073099-46073367(+)$1	268	142	167	23.6017
ffff[bbuuuuuuuuuuuubbffff	chr10:88197238-88197462(-)$1	224	32	57	22.5147
!!eeeeevvvvvvvvvvvvveeeee	chrX:152807692-152807914(-)$1	222	150	175	22.8903
gg:ddddyyyyyyyyyyyyyyyydd	chr5:36985715-36985945(+)$1	230	142	167	19.4510
c[eeeeevvvvvvvvvvvvveeeee	chr17:74732277-74732504(-)$1	227	166	191	22.8680
"eeeeevvvvvvvvvvvvveeeee3	chr8:9564278-9564511(+)$1	233	98	123	22.6499
cc!!ddddtttttttttttdddd33	chr15:101112032-101112262(-)$1	230	90	115	21.8465
gbbdddduuuuuuuuuuuudddd]b	chr2:85133410-85133668(+)$1	258	88	113	22.5635
[bb[cccvvvvvvvvvvvvvccc]b	chr5:72383351-72383575(+)$1	224	75	100	22.5685
c[eeeeeyyyyyyyyyyyyyyyyee	chr9:19379384-19379626(-)$1	242	189	214	20.8070
ffeeeeettttttttttteeeee22	chr7:12382639-12382869(-)$1	230	123	148	20.8058
gggggggtttttttttttggggggg	chr3:49569972-49570196(+)$1	224	15	40	21.4169
ccc[cccvvvvvvvvvvvvvccc]c	chr1:114524206-114524429(-)$1	223	151	176	23.3359
ggg[bbvvvvvvvvvvvvvbb]ggg	chr3:47866432-47866659(+)$1	227	32	57	22.6483
!ffffffuuuuuuuuuuuuffffff	chr1:179833954-179834184(-)$1	230	118	143	22.5561
cccyyyyyyyyyyyyyyyycccddd	chr8:82583144-82583374(-)$1	230	50	75	20.0775
fffffwwwwwwwwwwwwwwffffff	chr4:3136065-3136310(+)$1	245	7	32	21.3679
h:fffffftttttttttttffffff	chr13:96547389-96547617(-)$1	228	152	177	19.6567
hhhhhhhwwwwwwwwwwwwwwhhhh	chr20:47768134-47768375(-)$1	241	110	135	20.6072
d[ddddvvvvvvvvvvvvvdddd]d	chr5:108704306-108704535(-)$1	229	121	146	22.4607
cccdddduuuuuuuuuuuudddd]c	chr8:73848501-73848724(+)$1	223	135	160	23.3287
[ffffffxxxxxxxxxxxxxxxfff	chr5:177717254-177717478(+)$1	224	49	74	17.0911
ggggggguuuuuuuuuuuugggggg	chr14:61445862-61446093(-)$1	231	48	73	23.5921
d"""ddddtttttttttttdddd55	chr1:153617580-153617809(+)$1	229	84	109	19.6420
cc!!bbvvvvvvvvvvvvvbb22cc	chr6:112041062-112041312(-)$1	250	144	169	21.9549
ddd[ddddtttttttttttdddddd	chr1:38511999-38512222(+)$1	223	9	34	20.9633
eeee[bbvvvvvvvvvvvvvbbeee	chr19:49593628-49593857(+)$1	229	144	169	22.1604
ggggggvvvvvvvvvvvvvgggggg	chr15:100246834-100247060(+)$1	226	66	91	23.0691
ffffbbvvvvvvvvvvvvvbb]fff	chr4:57219526-57219752(-)$1	226	108	133	21.7686
ca[dddduuuuuuuuuuuudddd]a	chr9:95947337-95947566(+)$1	229	65	90	23.3094
ggggggvvvvvvvvvvvvvgggggg	chr8:103311047-103311281(-)$1	234	168	193	23.0691
ggggggvvvvvvvvvvvvvgggggg	chr6:132207723-132207964(+)$1	241	167	192	23.0691
eee[cccxxxxxxxxxxxxxxxccc	chr2:223499105-223499334(-)$1	229	117	142	17.8192
gggggggtttttttttttggggggg	chr22:36912662-36912891(-)$1	229	53	78	21.4169
fffffwwwwwwwwwwwwwwffffff	chr18:56390248-56390500(+)$1	252	74	99	21.3679
b!!ddddwwwwwwwwwwwwwwdddd	chr6:43141564-43141790(-)$1	226	92	117	21.7504
e!!dddduuuuuuuuuuuuddddee	chr12:123425292-123425520(-)$1	228	118	143	23.3216
====[bbuuuuuuuuuuuubb22==	chr19:46812469-46812693(-)$1	224	86	111	22.8716
eeecccxxxxxxxxxxxxxxxccc]	chrX:153195355-153195591(-)$1	236	178	203	17.8718
ggggggwwwwwwwwwwwwwwggggg	chr4:20525325-20525555(+)$1	230	9	34	22.8776
eee[ddddtttttttttttdddd]e	chrX:114874647-114874874(+)$1	227	147	172	21.7557
####cccvvvvvvvvvvvvvccc]e	chr14:24619805-24620027(+)$1	222	100	125	22.9101
ccceeeeettttttttttteeeee2	chr17:45735796-45736024(+)$1	228	147	172	21.4022
d"""cccuuuuuuuuuuuuccc444	chr8:124518566-124518788(-)$1	222	7	32	23.3179

#otherMatches

#Seq PSSM
UGUUUAACAUUCAUAAUUUGACAUG	chr17:35508148-35508396(-)$1	248	11	36	17.6481
GUACCUUCACCAACCUCAAGUACUG	chr2:175979442-175979665(-)$1	223	186	211	17.6481
UCGUGUUCCUGUGUCCCCUGCAUGU	chr16:29822298-29822529(+)$1	231	98	123	22.6468
ACCCGAGUUCCUUAUUUACACUGGC	chr3:23848651-23848890(+)$1	239	8	33	21.1406
UUGUAUCUUUUGUCUUUUUUUUUGG	chr17:45734151-45734375(+)$1	224	44	69	20.9520
AGCUUCCACUUCACCAUCGGAUGUU	chr2:74372293-74372520(-)$1	227	88	113	22.1979
CUGUGAGUCCCUCCCCAAGCACAGG	chr6:3155786-3156048(-)$1	262	28	53	21.3839
GGAGUGUGACUCAAGCAACAACCUC	chr22:35688892-35689116(+)$1	224	54	79	22.1604
AAUUUAGAAUUUAAUAUUUUCCUAA	chr6:155116121-155116350(+)$1	229	181	206	21.9293
GCGCAGCCGCAUCACGGAGGGCGUG	chr16:426144-426368(+)$1	224	48	73	22.1518
CUUGUCUUGCAAGUGUUAGAAGACA	chr19:11728146-11728368(+)$1	222	121	146	20.8542
auguuugacagauaguagauaccca	chr16:58577171-58577400(-)$1	229	104	129	19.4123
AUGGACCAGCUGCUUUCAAGGGACG	chr19:39205016-39205299(+)$1	283	6	31	22.6178
CAGCAUCGACAUUCCCUCAGGUGCU	chr1:156563145-156563373(+)$1	228	182	207	21.2409
UGCCAGGCCUCUGCACCCUGCCAGG	chr9:140093662-140093894(-)$1	232	164	189	22.1076
AUCUCAAGGACUCAAGCAUAGAGAU	chr15:42058599-42058826(+)$1	227	25	50	17.6969
AAGGACCGAAUGAAGCUGAGGUCAC	chr1:46073099-46073367(+)$1	268	142	167	23.6017
UUUAUACUUCUUAAAAUCUGUUAAA	chr10:88197238-88197462(-)$1	224	32	57	22.5147
CAGAGGCCUUUCUCCCCACCGCCUC	chrX:152807692-152807914(-)$1	222	150	175	22.8903
AUAGUUCAAAAACUGAUAAACUAGA	chr5:36985715-36985945(+)$1	230	142	167	19.4510
AGUCCUCCCCCAGUGUCCAAGAGGG	chr17:74732277-74732504(-)$1	227	166	191	22.8680
UGCUUCCAAGAACCGUGUAGAAGUC	chr8:9564278-9564511(+)$1	233	98	123	22.6499
GUUUUCAUAGAACAAGACGAUGACA	chr15:101112032-101112262(-)$1	230	90	115	21.8465
CCCGCUCUCCACAGCCAUUGAGCAG	chr2:85133410-85133668(+)$1	258	88	113	22.5635
CUCCGAGCAAAAUUUGAUCUUUCAG	chr5:72383351-72383575(+)$1	224	75	100	22.5685
CGCCAUUGGUAACUGGUAUUUGGAA	chr9:19379384-19379626(-)$1	242	189	214	20.8070
UUGUCCUUAUGGUUUUGUAGGACCA	chr7:12382639-12382869(-)$1	230	123	148	20.8058
GCUGAGGAUGAUGGAAAACCUCGGC	chr3:49569972-49570196(+)$1	224	15	40	21.4169
CAUAUCUGCGGGGAAAAUAAGGGAG	chr1:114524206-114524429(-)$1	223	151	176	23.3359
cggccgcUCCCGUUCUCUUCGCCCG	chr3:47866432-47866659(+)$1	227	32	57	22.6483
UGAGAAAGCUUGCCAUCCAUUUCUU	chr1:179833954-179834184(-)$1	230	118	143	22.5561
UUCUAGAAGUCUAAAUAUUGAAACC	chr8:82583144-82583374(-)$1	230	50	75	20.0775
CGGGUACUGAGUGGGACUAACCUGC	chr4:3136065-3136310(+)$1	245	7	32	21.3679
AUUGUUGAAAAUAUGGGAAUCAACG	chr13:96547389-96547617(-)$1	228	152	177	19.6567
GUUCCACCUUUACUUUAUCAAGUGG	chr20:47768134-47768375(-)$1	241	110	135	20.6072
UUUGCCUCAUCGAUUUUCUGGUACA	chr5:108704306-108704535(-)$1	229	121	146	22.4607
UUCCAGCCUGGUAUUUUUUGCUGAG	chr8:73848501-73848724(+)$1	223	135	160	23.3287
AGAGAGAGAACCAAACAUCUUAUCU	chr5:177717254-177717478(+)$1	224	49	74	17.0911
CCUGAAGGUCAAGAUGUAACUUCAG	chr14:61445862-61446093(-)$1	231	48	73	23.5921
UAUAUGUCGAAAACAAAAGGACACC	chr1:153617580-153617809(+)$1	229	84	109	19.6420
CUAUGGCACAGACCCCACCCCUCAG	chr6:112041062-112041312(-)$1	250	144	169	21.9549
UGGUGCGCUGUGCUGCCCUGCGCCC	chr1:38511999-38512222(+)$1	223	9	34	20.9633
AAUGUGUAAGUCUCUCAUCCACCAU	chr19:49593628-49593857(+)$1	229	144	169	22.1604
UCAGAACACAUUUUCUCUUUUUUGA	chr15:100246834-100247060(+)$1	226	66	91	23.0691
UGCAGAAAUAUCUUCCAAGUCAUGC	chr4:57219526-57219752(-)$1	226	108	133	21.7686
CCCGCAGCCCCCGCAGCCCCUGCAG	chr9:95947337-95947566(+)$1	229	65	90	23.3094
GUUCUCCAGCCCUAUCUACGAGAAC	chr8:103311047-103311281(-)$1	234	168	193	23.0691
GCAUGUUGAAAAUCUAGACAUAUGC	chr6:132207723-132207964(+)$1	241	167	192	23.0691
UUGUCGGGCCCAUUUACUUAUACUG	chr2:223499105-223499334(-)$1	229	117	142	17.8192
GGGGAAGGAAAGAUACAACUUCCCC	chr22:36912662-36912891(-)$1	229	53	78	21.4169
GGAGCACCCCAAGCUCAAAGCUCCU	chr18:56390248-56390500(+)$1	252	74	99	21.3679
CUCACUGGUGAUCAUGGGCUGCAGU	chr6:43141564-43141790(-)$1	226	92	117	21.7504
GAAUGUGACCUUCACCUACCGCACU	chr12:123425292-123425520(-)$1	228	118	143	23.3216
CAGUAGGUGAACUUCAUGUCCAGGC	chr19:46812469-46812693(-)$1	224	86	111	22.8716
ACGAGCUUUCACAAUAAAUUCGCUC	chrX:153195355-153195591(-)$1	236	178	203	17.8718
AGUUAAUAAGAUGCUACACUUUAAU	chr4:20525325-20525555(+)$1	230	9	34	22.8776
AUUAACAUGUCAGGUUUCAAUGUAA	chrX:114874647-114874874(+)$1	227	147	172	21.7557
AACCGGACUAGUAGCCCCAUUCCAG	chr14:24619805-24620027(+)$1	222	100	125	22.9101
AGCCUAGUAAUAAUGUGAAGCUAGC	chr17:45735796-45736024(+)$1	228	147	172	21.4022
CCUUUGUGCCUACAACUGAACAUCA	chr8:124518566-124518788(-)$1	222	7	32	23.3179

#DB
((((...............))))))	chr17:35508148-35508396(-)$1	1	11	36	17.6481
((((...............))))))	chr2:175979442-175979665(-)$1	1	186	211	17.6481
.(((((.............))))).	chr16:29822298-29822529(+)$1	1	98	123	22.6468
(.((.(((...........))))).	chr3:23848651-23848890(+)$1	1	8	33	21.1406
(((((((................))	chr17:45734151-45734375(+)$1	1	44	69	20.9520
(((.(((...........))).).)	chr2:74372293-74372520(-)$1	1	88	113	22.1979
(((((..............))))).	chr6:3155786-3156048(-)$1	1	28	53	21.3839
((((.((.............)))))	chr22:35688892-35689116(+)$1	1	54	79	22.1604
(..((((..............))))	chr6:155116121-155116350(+)$1	1	181	206	21.9293
((((.(((...........))))))	chr16:426144-426368(+)$1	1	48	73	22.1518
(.((((((...........))))))	chr19:11728146-11728368(+)$1	1	121	146	20.8542
(((((((................))	chr16:58577171-58577400(-)$1	1	104	129	19.4123
(((..((............))..))	chr19:39205016-39205299(+)$1	1	6	31	22.6178
(((((((............))))))	chr1:156563145-156563373(+)$1	1	182	207	21.2409
.(((.(((...........))).))	chr9:140093662-140093894(-)$1	1	164	189	22.1076
(((((...............)))))	chr15:42058599-42058826(+)$1	1	25	50	17.6969
(((((((............)))).)	chr1:46073099-46073367(+)$1	1	142	167	23.6017
((((.((............))))))	chr10:88197238-88197462(-)$1	1	32	57	22.5147
..(((((.............)))))	chrX:152807692-152807914(-)$1	1	150	175	22.8903
)).((((................))	chr5:36985715-36985945(+)$1	1	142	167	19.4510
(.(((((.............)))))	chr17:74732277-74732504(-)$1	1	166	191	22.8680
.(((((.............))))).	chr8:9564278-9564511(+)$1	1	98	123	22.6499
((..((((...........))))..	chr15:101112032-101112262(-)$1	1	90	115	21.8465
(((((((............)))).)	chr2:85133410-85133668(+)$1	1	88	113	22.5635
.((.(((.............))).)	chr5:72383351-72383575(+)$1	1	75	100	22.5685
(.(((((................))	chr9:19379384-19379626(-)$1	1	189	214	20.8070
(((((((...........)))))..	chr7:12382639-12382869(-)$1	1	123	148	20.8058
(((((((...........)))))))	chr3:49569972-49570196(+)$1	1	15	40	21.4169
(((.(((.............))).)	chr1:114524206-114524429(-)$1	1	151	176	23.3359
(((.((.............)).)))	chr3:47866432-47866659(+)$1	1	32	57	22.6483
.((((((............))))))	chr1:179833954-179834184(-)$1	1	118	143	22.5561
(((................))))))	chr8:82583144-82583374(-)$1	1	50	75	20.0775
(((((..............))))))	chr4:3136065-3136310(+)$1	1	7	32	21.3679
).((((((...........))))))	chr13:96547389-96547617(-)$1	1	152	177	19.6567
(((((((..............))))	chr20:47768134-47768375(-)$1	1	110	135	20.6072
(.((((.............)))).)	chr5:108704306-108704535(-)$1	1	121	146	22.4607
(((((((............)))).)	chr8:73848501-73848724(+)$1	1	135	160	23.3287
.((((((...............)))	chr5:177717254-177717478(+)$1	1	49	74	17.0911
(((((((............))))))	chr14:61445862-61446093(-)$1	1	48	73	23.5921
(...((((...........))))..	chr1:153617580-153617809(+)$1	1	84	109	19.6420
((..((.............))..))	chr6:112041062-112041312(-)$1	1	144	169	21.9549
(((.((((...........))))))	chr1:38511999-38512222(+)$1	1	9	34	20.9633
((((.((.............)))))	chr19:49593628-49593857(+)$1	1	144	169	22.1604
((((((.............))))))	chr15:100246834-100247060(+)$1	1	66	91	23.0691
((((((.............)).)))	chr4:57219526-57219752(-)$1	1	108	133	21.7686
((.((((............)))).)	chr9:95947337-95947566(+)$1	1	65	90	23.3094
((((((.............))))))	chr8:103311047-103311281(-)$1	1	168	193	23.0691
((((((.............))))))	chr6:132207723-132207964(+)$1	1	167	192	23.0691
(((.(((...............)))	chr2:223499105-223499334(-)$1	1	117	142	17.8192
(((((((...........)))))))	chr22:36912662-36912891(-)$1	1	53	78	21.4169
(((((..............))))))	chr18:56390248-56390500(+)$1	1	74	99	21.3679
(..((((..............))))	chr6:43141564-43141790(-)$1	1	92	117	21.7504
(..((((............))))))	chr12:123425292-123425520(-)$1	1	118	143	23.3216
((((.((............))..))	chr19:46812469-46812693(-)$1	1	86	111	22.8716
((((((...............))).	chrX:153195355-153195591(-)$1	1	178	203	17.8718
((((((..............)))))	chr4:20525325-20525555(+)$1	1	9	34	22.8776
(((.((((...........)))).)	chrX:114874647-114874874(+)$1	1	147	172	21.7557
....(((.............))).)	chr14:24619805-24620027(+)$1	1	100	125	22.9101
((((((((...........))))).	chr17:45735796-45736024(+)$1	1	147	172	21.4022
(...(((............)))...	chr8:124518566-124518788(-)$1	1	7	32	23.3179

#PSSM
g : 0.23	c : 0.18	e : 0.15	d : 0.08	f : 0.08	h : 0.06	[ : 0.05	" : 0.03	= : 0.03	! : 0.03	a : 0.01	b : 0.01	# : 0.01	
g : 0.21	e : 0.16	c : 0.13	f : 0.11	[ : 0.08	! : 0.06	h : 0.05	= : 0.03	b : 0.03	" : 0.03	: : 0.01	d : 0.01	a : 0.01	# : 0.01	
e : 0.23	g : 0.18	f : 0.13	c : 0.09	! : 0.08	b : 0.05	h : 0.05	= : 0.03	d : 0.03	" : 0.03	a : 0.01	: : 0.01	[ : 0.01	# : 0.01	
e : 0.19	g : 0.15	d : 0.15	f : 0.13	[ : 0.11	h : 0.05	! : 0.05	= : 0.03	c : 0.03	" : 0.03	b : 0.01	y : 0.01	# : 0.01	
d : 0.21	e : 0.15	[ : 0.11	c : 0.11	g : 0.11	f : 0.09	h : 0.05	b : 0.05	x : 0.03	= : 0.01	! : 0.01	y : 0.01	
d : 0.21	c : 0.16	b : 0.13	e : 0.11	g : 0.11	f : 0.06	x : 0.05	w : 0.05	h : 0.05	= : 0.01	y : 0.01	
d : 0.19	v : 0.15	c : 0.15	b : 0.08	e : 0.08	x : 0.06	w : 0.06	f : 0.06	h : 0.05	g : 0.05	= : 0.01	y : 0.01	
v : 0.26	u : 0.19	w : 0.11	x : 0.09	y : 0.08	t : 0.06	d : 0.06	c : 0.05	f : 0.03	e : 0.01	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	t : 0.23	u : 0.19	w : 0.11	x : 0.09	y : 0.08	
v : 0.26	u : 0.19	t : 0.16	w : 0.11	x : 0.09	y : 0.08	g : 0.03	c : 0.01	e : 0.01	
d : 0.16	g : 0.13	v : 0.11	c : 0.09	b : 0.09	e : 0.08	f : 0.08	y : 0.06	w : 0.06	x : 0.06	h : 0.01	
d : 0.16	g : 0.15	c : 0.15	e : 0.13	b : 0.13	f : 0.08	y : 0.06	w : 0.05	x : 0.05	h : 0.01	
d : 0.19	g : 0.15	c : 0.15	e : 0.13	f : 0.09	y : 0.06	] : 0.05	2 : 0.05	b : 0.03	h : 0.03	x : 0.03	
d : 0.21	e : 0.18	g : 0.16	f : 0.13	c : 0.08	y : 0.06	2 : 0.05	h : 0.03	b : 0.01	a : 0.01	] : 0.01	4 : 0.01	
e : 0.19	g : 0.16	] : 0.16	f : 0.13	d : 0.08	c : 0.08	h : 0.05	= : 0.03	b : 0.01	3 : 0.01	2 : 0.01	5 : 0.01	4 : 0.01	
g : 0.19	e : 0.16	f : 0.13	d : 0.09	c : 0.09	] : 0.05	h : 0.05	= : 0.03	3 : 0.03	b : 0.03	2 : 0.03	7 : 0.01	5 : 0.01	a : 0.01	4 : 0.01	

#score	1292.1863423214995
#seq	60
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m2_run1.txt

#BEAR
###ggggggg[ccc[aooooooa]ccc]ggggggg	chr2:152276617-152276842(+)$1	225	145	180	15.8120
:iiiiiiiii!!ddddnnnnndddd22iiiiiiii	chr7:131172354-131172582(+)$1	228	188	223	11.3910
eeee####ccc[ddddnnnnndddd22ccc333ee	chr17:76089629-76089863(+)$1	234	48	83	11.9476
ccc"""bb[ccc[cccoooooocccccc]bb333c	chr4:74012407-74012634(-)$1	227	100	135	15.4133
gggggg"""bb[ddddoooooodddd4444bb333	chrX:48386627-48386877(+)$1	250	134	169	15.5684
i[iiiiiiiii####aqqqqqqqqa333iiiiiii	chr2:136605548-136605773(-)$1	225	172	207	10.6640
ddd$$$$$ffffffbboooooobb]ffffff22dd	chr18:9399301-9399522(+)$1	221	134	169	11.7290
"""dddd[bb[eeeeeooooooeeeee]bbdddd]	chr15:73067297-73067519(-)$1	222	76	111	12.7416
eebb!!a$$$$$ddddoooooodddd4444a22bb	chr19:1584525-1584761(-)$1	236	168	203	13.8807
$$bb[ccc[gggggggooooooggggggg22ccc2	chr6:111912886-111913111(-)$1	225	33	68	13.9876
:eeeee[eeeee[cccooooooccc]eeeee]eee	chr18:33706828-33707050(-)$1	222	11	46	13.4859
cc[bb[hhhhhhhh[aooooooa]hhhhhhhh]bb	chr21:30698396-30698618(+)$1	222	6	41	12.0667
d[cccccc[dddd[bboooooobb]dddd]ccc22	chr2:55214582-55214821(-)$1	239	72	107	14.0825
dddd!!ccc!!eeeeeooooooeeeeeccc22ddd	chr17:56572909-56573140(-)$1	231	167	202	13.6999
==========cccrrrrrrrrrccc]=========	chr1:92604838-92605073(+)$1	235	196	231	12.0128
####ggggggg"""bboooooobb]ggggggg22d	chr1:55590063-55590287(-)$1	224	109	144	15.5395
e[ccc!!ccc[a[cccooooooccc]a333ccc22	chr16:22358826-22359057(-)$1	231	125	160	17.3149
:dddd"""hhhhhhhhoooooohhhhhhhh4444d	chr1:112003456-112003693(+)$1	237	195	230	11.9032
eeee[dddd####cccooooooccc4444dddd]e	chr17:5311973-5312200(-)$1	227	116	151	15.3073
=====[dddd"""cccooooooccc22dddd22==	chr11:120200898-120201118(+)$1	220	94	129	15.6520
fffffaccc####cccnnnnnccc4444ccc]a]f	chr4:114232424-114232651(+)$1	227	94	129	11.9990
c!!ccc[dddd"""ccclllccc333ddddccc22	chr14:68156943-68157174(-)$1	231	173	208	10.8757
fffffeeeeeaeeeeeooooooeeeee]a]eeeee	chr1:155451377-155451608(-)$1	231	97	132	12.5570
ff!!eeeeeccc!!bboooooobb22ccc22eeee	chr11:129979310-129979539(+)$1	229	15	50	14.3194
####ccc[bb[a[cccannnnna]ccca]bb]ccc	chrX:24006336-24006567(-)$1	231	166	201	11.7895
eeedddd!!ccc!!bboooooobb22ccc22dddd	chr6:151670607-151670838(+)$1	231	53	88	14.5265
d[iiiiiiiii!!cccooooooccciiiiiiiiid	chr2:54871431-54871653(+)$1	222	183	218	16.8772
a[dddd[ccc!!eeeeennnnneeeee22ccc333	chr6:47251727-47251975(-)$1	248	139	174	11.0409
bb[ggggggg"""cccooooooccc]ggggggg]b	chr12:125509529-125509752(+)$1	223	43	78	16.1710
iiiiii[a!!bb!!bboooooobb22bb22a22ii	chr15:59139448-59139672(+)$1	224	31	66	14.7320
hhhhhhhh####ddddooooooddddhhhhhhhha	chr12:9847327-9847554(+)$1	227	18	53	12.7330
bb!!ccc!!bb[a[bboooooobb]a]bb4444cc	chr19:39138274-39138490(+)$1	216	92	127	14.5892
dd[ccc!!ccc"""bboooooobb]ccccccdddd	chr6:170852652-170852914(-)$1	262	44	79	15.4796
ddddggggggg!!cccooooooccc]ggggggg99	chr8:48746775-48747000(-)$1	225	114	149	14.7000
gggggg"""bb[ddddoooooodddd]bb333ggg	chr11:67800524-67800747(+)$1	223	5	40	15.3675
d"""bb[cccffffffooooooffffff]cccbb2	chr2:97030214-97030429(+)$1	215	174	209	12.5562
b[ccc!!dddd[ddddnnnnndddd]ddddccc]b	chr6:105232957-105233185(-)$1	228	179	214	10.7268
eeeee$$$$$dddd[aooooooa]ddddeeeeedd	chr16:2009519-2009765(+)$1	246	12	47	12.9353
::dddd"""gggggggooooooggggggg22dddd	chr4:56277752-56277975(+)$1	223	4	39	12.5144
b[eeeee!!dddd!!aooooooa22ddddeeeee4	chr19:579421-579673(+)$1	252	133	168	13.7129
ffffff[ccc[ccc[aooooooa]ccc]ccc]fff	chr11:764233-764466(+)$1	233	12	47	14.8477
""dddd!!ccc[ddddooooooddddccc]dddd4	chr8:33406868-33407099(-)$1	231	154	189	15.3284
ccca[eeeee[a!!bboooooobb333a]eeeee]	chr12:49418576-49418808(-)$1	232	95	130	14.9621
fffff[ccc!!bbcccooooooccc]bb22ccc]f	chr1:153747946-153748192(+)$1	246	186	221	14.5143
e[iiiiiiiii[cccqqqqqqqqccc]iiiiiiii	chr5:179247872-179248163(+)$1	291	132	167	10.5006
dccc!!dddd"""ddddnnnnndddd4444dddd3	chr9:92003713-92003938(-)$1	225	110	145	11.2784
eee[bb!!ccc[ddddoooooodddd333ccc]bb	chr5:179046233-179046480(-)$1	247	77	112	15.1552
!!eeeee!!cccacccooooooccc]a]ccceeee	chr17:4849006-4849302(-)$1	296	236	271	16.0302
ee####==========oooooo==========444	chr16:24834830-24835056(+)$1	226	28	63	16.2535
ggg!!ffffff[ddddoooooodddd]ffffff22	chr4:54257143-54257345(+)$1	202	44	79	13.5632
!ffffff[a[a[cccaooooooa]ccc]a22a]ff	chr19:49458916-49459165(+)$1	249	43	78	15.1143
[a[eeeee!!bb[cccooooooccc]bb]eeeeea	chr12:14923566-14923823(-)$1	257	62	97	14.6836

#otherMatches

#Seq PSSM
UCAUACCUUUAGUGGUUCAUUCAGCACAAAAGGUA	chr2:152276617-152276842(+)$1	225	145	180	15.8120
GAUUGCAGCUCCACUGACUGACAGUAAAGCUGCAG	chr7:131172354-131172582(+)$1	228	188	223	11.3910
UCUCAUUUUGGUUUCUUAAACAGAAUUCCAUCCGG	chr17:76089629-76089863(+)$1	234	48	83	11.9476
GAAAAUGGUCAUACUGAUGUAGCAGAUGUCUUACU	chr4:74012407-74012634(-)$1	227	100	135	15.4133
GUGCUUGAUGCUGUGAAGCACCUCACUCAUGCCCA	chrX:48386627-48386877(+)$1	250	134	169	15.5684
CUGUUUUGGAGUUAGGGACCAAAACAUUUUCUGAG	chr2:136605548-136605773(-)$1	225	172	207	10.6640
UGGUUUCAUAAUGCCUGCUGCGAGUGCAUUGGUCC	chr18:9399301-9399522(+)$1	221	134	169	11.7290
UCUAGAGUCAAUGCAUGUGUUGAUGUGGUGCUCUC	chr15:73067297-73067519(-)$1	222	76	111	12.7416
CCCCAGCAACAAGGUCAAGAGCGACCCGCAGAAGG	chr19:1584525-1584761(-)$1	236	168	203	13.8807
AUCACCAGCGGCCUGUAUCCCGGCAGGUCACCUGC	chr6:111912886-111913111(-)$1	225	33	68	13.9876
UUUCUUAAUUCAAUUUGUUUUAGAAGUGAGUCAAG	chr18:33706828-33707050(-)$1	222	11	46	13.4859
UUUAAUUCAGUUUGCCUACACUGCUAAACUGAUUU	chr21:30698396-30698618(+)$1	222	6	41	12.0667
AUUCAGCAUUGUGAGCGUAACAGCCUACAUUGCCU	chr2:55214582-55214821(-)$1	239	72	107	14.0825
AUCUCCCACCAGGAACAACUGAGUUCUGUGCCGGA	chr17:56572909-56573140(-)$1	231	167	202	13.6999
GCUUUGUUGAGCUGUGUUGCAAAGUGUUAAUGAAG	chr1:92604838-92605073(+)$1	235	196	231	12.0128
UGUCCUGCUGGAAUUCGAAACAGACUCAGCAGUUC	chr1:55590063-55590287(-)$1	224	109	144	15.5395
CAGGUGCCUACCGAGCACGGGCGCUGGAACUAGAG	chr16:22358826-22359057(-)$1	231	125	160	17.3149
UGACUGACUAAAUGGAAACUAGUCUAUUUGACAAA	chr1:112003456-112003693(+)$1	237	195	230	11.9032
ACUUUCCUGACAUACAUCAGUCUGUUACACAGGUA	chr17:5311973-5312200(-)$1	227	116	151	15.3073
AGGAGUGAGGAUUGGUGUGGGAGCUUGCCUCCUUU	chr11:120200898-120201118(+)$1	220	94	129	15.6520
ACCUGCGAUACAGCUUGGAGGGAGGACGAUCUGAC	chr4:114232424-114232651(+)$1	227	94	129	11.9990
GCAGGCCUGGCCUACUGUCACAGCAAGCUAGCCAA	chr14:68156943-68157174(-)$1	231	173	208	10.8757
GCCAAGGACUGUGCAAAGAAGAUUGUAGCAAGUUC	chr1:155451377-155451608(-)$1	231	97	132	12.5570
UCUUGCAGCCAAUGCCGGAACAGGAUUUGCUGUUG	chr11:129979310-129979539(+)$1	229	15	50	14.3194
UUCUUACAAUGGCAAGCUUUAUGUCUUCGGUGGUG	chrX:24006336-24006567(-)$1	231	166	201	11.7895
CUGCCCUCAGAGGAGCAAGUCAGUGGCUCGCAGGG	chr6:151670607-151670838(+)$1	231	53	88	14.5265
GAGCUGUGCAGAUCUAGACAAAUGGCUGCACGGCC	chr2:54871431-54871653(+)$1	222	183	218	16.8772
GUGCUUGUGGUGAUUGUGGUGUGCAGUAUCCGGAA	chr6:47251727-47251975(-)$1	248	139	174	11.0409
UGUCCAGCAGCCCGGCCCGCGCGCUCCUGCUGGUC	chr12:125509529-125509752(+)$1	223	43	78	16.1710
GUUACUUCUUAUUAAGGGUCAACUGUAUUUGUUGG	chr15:59139448-59139672(+)$1	224	31	66	14.7320
UCUCUUGCAGGUUUCCUAUCCUGGGAGCAGGAGAG	chr12:9847327-9847554(+)$1	227	18	53	12.7330
GCGAGCGAGAGGCGGCGGAAUGGUGGACUACCACG	chr19:39138274-39138490(+)$1	216	92	127	14.5892
UCUAUAAUGGCCUCUGCCUCUACAUGCCUGUGACU	chr6:170852652-170852914(-)$1	262	44	79	15.4796
UCUGACUCCUUGCUGUUUGCCCACAAGAGGAGUGA	chr8:48746775-48747000(-)$1	225	114	149	14.7000
CAUGGGGGAGGAGGGUGCCCCUGCCCACCACACCC	chr11:67800524-67800747(+)$1	223	5	40	15.3675
UUCUCAUGUCCCCAUUUUAUAUGGUGGGAGACUGU	chr2:97030214-97030429(+)$1	215	174	209	12.5562
UGGCACAAGGGAAUCUAAACCAGAUGCUCUUGCAG	chr6:105232957-105233185(-)$1	228	179	214	10.7268
GUCCUCUGUAGCGGGCGACCUAGGCCGCGGGACCC	chr16:2009519-2009765(+)$1	246	12	47	12.9353
AAGUAACUGAUUUUUUUUUUCCAGAAAAUAUUUAC	chr4:56277752-56277975(+)$1	223	4	39	12.5144
CUCCUUGAAUGACAGCGCCACAGAGGUCACAGGGC	chr19:579421-579673(+)$1	252	133	168	13.7129
GGGACAUGGAGCAGGCAUGGAAGGCUGGUUCUUGU	chr11:764233-764466(+)$1	233	12	47	14.8477
ACACGCCUUUCACCGCAAGUACGUGGGAAUGUGUC	chr8:33406868-33407099(-)$1	231	154	189	15.3284
CAUUGAGCCUGUGGCUGCCAUGAGAAAAGAGGCUG	chr12:49418576-49418808(-)$1	232	95	130	14.9621
GCUGCCGCCGACCCGGAAGGUCCCGAGGGGGGCUG	chr1:153747946-153748192(+)$1	246	186	221	14.5143
CAGCUUCUGCUGCAGCCCCGAGCCUGAGGCGGAAG	chr5:179247872-179248163(+)$1	291	132	167	10.5006
CCUGAAGGUGCCUGUGUUCUAUGCACUCUUCACCC	chr9:92003713-92003938(-)$1	225	110	145	11.2784
GAAAUCGUGCCAAAUGGGAUAACAUUGCCGGUGGA	chr5:179046233-179046480(-)$1	247	77	112	15.1552
CUGGGGGCCAGGGCUGGAUGGACAGACACCUCCCC	chr17:4849006-4849302(-)$1	296	236	271	16.0302
UCUCUCGGGUCCAGCCAGAGCCGGCUGGGCUCCCU	chr16:24834830-24835056(+)$1	226	28	63	16.2535
CUGAUUAUUUUAAUUAUGGGUUUAAUGAAGAUACC	chr4:54257143-54257345(+)$1	202	44	79	13.5632
GCAGGGCGAAUGGGGGGGGAGGCACCCGAGCUGGC	chr19:49458916-49459165(+)$1	249	43	78	15.1143
UGUGGUGUACGCGCUGAAACGCCAGGGUCGCACCC	chr12:14923566-14923823(-)$1	257	62	97	14.6836

#DB
...(((((((.(((.(......).))).)))))))	chr2:152276617-152276842(+)$1	1	145	180	15.8120
.(((((((((..((((.....))))..))))))))	chr7:131172354-131172582(+)$1	1	188	223	11.3910
((((....(((.((((.....))))..)))...))	chr17:76089629-76089863(+)$1	1	48	83	11.9476
(((...((.(((.(((......)))))).))...)	chr4:74012407-74012634(-)$1	1	100	135	15.4133
((((((...((.((((......))))....))...	chrX:48386627-48386877(+)$1	1	134	169	15.5684
(.(((((((((....(........)...)))))))	chr2:136605548-136605773(-)$1	1	172	207	10.6640
(((.....((((((((......)).))))))..))	chr18:9399301-9399522(+)$1	1	134	169	11.7290
...((((.((.(((((......))))).)))))).	chr15:73067297-73067519(-)$1	1	76	111	12.7416
((((..(.....((((......))))....)..))	chr19:1584525-1584761(-)$1	1	168	203	13.8807
..((.(((.(((((((......)))))))..))).	chr6:111912886-111913111(-)$1	1	33	68	13.9876
.(((((.(((((.(((......))).))))).)))	chr18:33706828-33707050(-)$1	1	11	46	13.4859
((.((.((((((((.(......).)))))))).))	chr21:30698396-30698618(+)$1	1	6	41	12.0667
(.((((((.((((.((......)).)))).)))..	chr2:55214582-55214821(-)$1	1	72	107	14.0825
((((..(((..(((((......))))))))..)))	chr17:56572909-56573140(-)$1	1	167	202	13.6999
(((((((((((((.........))).)))))))))	chr1:92604838-92605073(+)$1	1	196	231	12.0128
....(((((((...((......)).)))))))..)	chr1:55590063-55590287(-)$1	1	109	144	15.5395
(.(((..(((.(.(((......))).)...)))..	chr16:22358826-22359057(-)$1	1	125	160	17.3149
.((((...((((((((......))))))))....)	chr1:112003456-112003693(+)$1	1	195	230	11.9032
((((.((((....(((......)))....)))).)	chr17:5311973-5312200(-)$1	1	116	151	15.3073
(((((.((((...(((......)))..))))..))	chr11:120200898-120201118(+)$1	1	94	129	15.6520
(((((((((....(((.....)))....))).).)	chr4:114232424-114232651(+)$1	1	94	129	11.9990
(..(((.((((...(((...)))...)))))))..	chr14:68156943-68157174(-)$1	1	173	208	10.8757
)))))(((((((((((......))))).).)))))	chr1:155451377-155451608(-)$1	1	97	132	12.5570
((..((((((((..((......))..)))..))))	chr11:129979310-129979539(+)$1	1	15	50	14.3194
....(((.((.(.((((.....).)))).)).)))	chrX:24006336-24006567(-)$1	1	166	201	11.7895
)))((((..(((..((......))..)))..))))	chr6:151670607-151670838(+)$1	1	53	88	14.5265
(.(((((((((..(((......)))))))))))))	chr2:54871431-54871653(+)$1	1	183	218	16.8772
(.((((.(((..(((((.....)))))..)))...	chr6:47251727-47251975(-)$1	1	139	174	11.0409
((.(((((((...(((......))).))))))).)	chr12:125509529-125509752(+)$1	1	43	78	16.1710
((((((.(..((..((......))..))..)..))	chr15:59139448-59139672(+)$1	1	31	66	14.7320
((((((((....((((......))))))))))))(	chr12:9847327-9847554(+)$1	1	18	53	12.7330
((..(((..((.(.((......)).).))....))	chr19:39138274-39138490(+)$1	1	92	127	14.5892
((.(((..(((...((......)).))))))))))	chr6:170852652-170852914(-)$1	1	44	79	15.4796
(((((((((((..(((......))).)))))))..	chr8:48746775-48747000(-)$1	1	114	149	14.7000
((((((...((.((((......)))).))...)))	chr11:67800524-67800747(+)$1	1	5	40	15.3675
(...((.(((((((((......)))))).))))).	chr2:97030214-97030429(+)$1	1	174	209	12.5562
(.(((..((((.((((.....)))).))))))).)	chr6:105232957-105233185(-)$1	1	179	214	10.7268
(((((.....((((.(......).)))))))))))	chr16:2009519-2009765(+)$1	1	12	47	12.9353
..((((...(((((((......)))))))..))))	chr4:56277752-56277975(+)$1	1	4	39	12.5144
(.(((((..((((..(......)..))))))))).	chr19:579421-579673(+)$1	1	133	168	13.7129
((((((.(((.(((.(......).))).))).)))	chr11:764233-764466(+)$1	1	12	47	14.8477
..((((..(((.((((......))))))).)))).	chr8:33406868-33407099(-)$1	1	154	189	15.3284
((((.(((((.(..((......))...).))))).	chr12:49418576-49418808(-)$1	1	95	130	14.9621
(((((.(((..(((((......))).))..))).)	chr1:153747946-153748192(+)$1	1	186	221	14.5143
(.(((((((((.(((........))).))))))))	chr5:179247872-179248163(+)$1	1	132	167	10.5006
((((..((((...((((.....))))....)))).	chr9:92003713-92003938(-)$1	1	110	145	11.2784
(((.((..(((.((((......))))...))).))	chr5:179046233-179046480(-)$1	1	77	112	15.1552
..(((((..(((((((......))).).)))))))	chr17:4849006-4849302(-)$1	1	236	271	16.0302
((....((((((((((......))))))))))...	chr16:24834830-24835056(+)$1	1	28	63	16.2535
(((..((((((.((((......)))).))))))..	chr4:54257143-54257345(+)$1	1	44	79	13.5632
.((((((.(.(.((((......).))).)..).))	chr19:49458916-49459165(+)$1	1	43	78	15.1143
.(.(((((..((.(((......))).)).))))))	chr12:14923566-14923823(-)$1	1	62	97	14.6836

#PSSM
e : 0.17	d : 0.15	f : 0.09	: : 0.07	c : 0.07	b : 0.07	# : 0.05	g : 0.05	i : 0.03	" : 0.03	= : 0.03	! : 0.03	$ : 0.01	a : 0.01	h : 0.01	[ : 0.01	
e : 0.15	[ : 0.15	f : 0.11	d : 0.09	c : 0.07	# : 0.05	g : 0.05	" : 0.05	i : 0.03	= : 0.03	! : 0.03	b : 0.03	$ : 0.01	h : 0.01	: : 0.01	a : 0.01	
e : 0.15	d : 0.13	c : 0.11	i : 0.09	f : 0.09	# : 0.07	[ : 0.07	g : 0.05	! : 0.05	" : 0.03	b : 0.03	= : 0.03	h : 0.01	
d : 0.15	e : 0.13	c : 0.11	i : 0.09	f : 0.09	g : 0.07	b : 0.05	# : 0.05	! : 0.05	" : 0.03	= : 0.03	$ : 0.01	h : 0.01	a : 0.01	[ : 0.01	
c : 0.13	g : 0.11	d : 0.11	e : 0.11	i : 0.09	f : 0.09	! : 0.07	[ : 0.05	b : 0.05	# : 0.03	= : 0.03	" : 0.01	$ : 0.01	h : 0.01	
e : 0.13	g : 0.11	d : 0.11	c : 0.11	i : 0.09	! : 0.09	[ : 0.05	f : 0.05	# : 0.03	" : 0.03	$ : 0.03	b : 0.03	= : 0.01	a : 0.01	h : 0.01	
c : 0.13	[ : 0.11	e : 0.11	d : 0.09	! : 0.09	g : 0.07	i : 0.07	" : 0.07	$ : 0.03	h : 0.03	= : 0.03	f : 0.03	# : 0.01	b : 0.01	a : 0.01	
c : 0.17	! : 0.13	e : 0.09	d : 0.09	g : 0.07	i : 0.07	" : 0.07	$ : 0.05	[ : 0.05	h : 0.03	= : 0.03	# : 0.01	b : 0.01	a : 0.01	f : 0.01	
c : 0.21	! : 0.11	d : 0.09	g : 0.07	i : 0.07	e : 0.07	[ : 0.05	" : 0.05	f : 0.03	b : 0.03	$ : 0.03	h : 0.03	= : 0.03	# : 0.01	a : 0.01	
c : 0.23	g : 0.11	d : 0.11	b : 0.09	i : 0.07	! : 0.07	e : 0.05	# : 0.05	f : 0.03	$ : 0.03	h : 0.03	= : 0.03	[ : 0.01	
c : 0.17	[ : 0.11	b : 0.09	d : 0.09	! : 0.07	g : 0.07	i : 0.05	f : 0.05	# : 0.05	" : 0.05	h : 0.03	a : 0.03	$ : 0.01	e : 0.01	= : 0.01	
[ : 0.19	c : 0.13	" : 0.11	! : 0.07	# : 0.07	e : 0.07	d : 0.05	a : 0.05	b : 0.05	f : 0.03	g : 0.03	h : 0.03	$ : 0.01	= : 0.01	
d : 0.24	" : 0.11	! : 0.11	c : 0.09	[ : 0.09	e : 0.07	# : 0.05	f : 0.03	g : 0.03	h : 0.03	a : 0.03	b : 0.01	= : 0.01	
c : 0.32	d : 0.23	! : 0.09	e : 0.07	" : 0.05	f : 0.03	g : 0.03	h : 0.03	[ : 0.03	# : 0.01	r : 0.01	= : 0.01	
c : 0.30	d : 0.21	b : 0.17	[ : 0.07	e : 0.07	g : 0.03	# : 0.01	r : 0.01	h : 0.01	f : 0.01	! : 0.01	= : 0.01	
c : 0.26	d : 0.21	b : 0.17	a : 0.13	e : 0.07	g : 0.03	r : 0.01	h : 0.01	f : 0.01	q : 0.01	= : 0.01	
o : 0.78	n : 0.07	q : 0.03	r : 0.01	c : 0.01	a : 0.01	e : 0.01	d : 0.01	
o : 0.78	n : 0.13	q : 0.03	r : 0.01	l : 0.01	
o : 0.78	n : 0.13	q : 0.03	r : 0.01	l : 0.01	
o : 0.78	n : 0.13	q : 0.03	r : 0.01	l : 0.01	
o : 0.78	n : 0.13	q : 0.03	r : 0.01	c : 0.01	
o : 0.78	d : 0.05	n : 0.05	q : 0.03	c : 0.03	r : 0.01	
c : 0.26	d : 0.21	b : 0.17	a : 0.13	e : 0.07	q : 0.03	g : 0.03	h : 0.01	f : 0.01	= : 0.01	
c : 0.26	d : 0.21	b : 0.17	] : 0.11	e : 0.07	g : 0.03	q : 0.01	h : 0.01	3 : 0.01	f : 0.01	2 : 0.01	= : 0.01	
c : 0.32	d : 0.23	] : 0.09	e : 0.07	2 : 0.07	g : 0.03	h : 0.03	3 : 0.03	a : 0.01	4 : 0.01	f : 0.01	= : 0.01	
d : 0.21	] : 0.17	c : 0.13	2 : 0.11	e : 0.07	3 : 0.05	g : 0.05	f : 0.03	h : 0.03	4 : 0.03	i : 0.01	a : 0.01	= : 0.01	
c : 0.17	4 : 0.09	e : 0.09	g : 0.09	d : 0.09	] : 0.07	2 : 0.05	3 : 0.05	h : 0.05	b : 0.05	f : 0.03	= : 0.03	a : 0.03	i : 0.01	
c : 0.13	] : 0.11	d : 0.11	4 : 0.09	g : 0.09	b : 0.09	i : 0.05	3 : 0.05	f : 0.05	h : 0.05	= : 0.03	a : 0.03	e : 0.01	2 : 0.01	
c : 0.17	g : 0.11	] : 0.09	d : 0.09	i : 0.07	4 : 0.07	b : 0.05	h : 0.05	2 : 0.05	f : 0.03	e : 0.03	= : 0.03	3 : 0.03	a : 0.03	
c : 0.17	2 : 0.13	e : 0.09	g : 0.07	i : 0.07	4 : 0.07	d : 0.07	b : 0.05	h : 0.05	] : 0.05	f : 0.03	= : 0.03	3 : 0.03	
c : 0.23	2 : 0.11	e : 0.11	d : 0.09	g : 0.07	i : 0.07	b : 0.05	3 : 0.03	f : 0.03	a : 0.03	h : 0.03	= : 0.03	4 : 0.03	
c : 0.17	d : 0.13	e : 0.13	2 : 0.09	g : 0.07	i : 0.07	] : 0.07	3 : 0.05	h : 0.03	= : 0.03	4 : 0.03	b : 0.01	f : 0.01	a : 0.01	
d : 0.15	e : 0.15	c : 0.13	2 : 0.09	g : 0.07	i : 0.07	3 : 0.07	] : 0.05	4 : 0.05	f : 0.03	= : 0.01	a : 0.01	h : 0.01	b : 0.01	
d : 0.17	e : 0.15	i : 0.09	2 : 0.09	] : 0.09	b : 0.07	3 : 0.05	c : 0.05	g : 0.03	= : 0.03	4 : 0.03	f : 0.03	h : 0.01	9 : 0.01	
d : 0.17	e : 0.11	2 : 0.11	b : 0.09	i : 0.07	f : 0.07	c : 0.05	3 : 0.05	4 : 0.05	g : 0.03	] : 0.03	= : 0.03	a : 0.03	9 : 0.01	

#score	716.636948307454
#seq	52
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m1_run1.txt

#BEAR
[bb^^^^^^^^^^^^^^^^^^^^^bb33	chr17:42475053-42475290(-)$1	237	151	179	26.9617
[eeeeecccuuuuuuuuuuuuccc]eee	chr10:70256072-70256315(-)$1	243	103	131	18.6877
eeeccc^^^^^^^^^^^^^^^^^^^ccc	chr7:107399420-107399691(+)$1	271	38	66	27.0645
gggg^^^^^^^^^^^^^^^^^^^ggggg	chr19:4690652-4691001(-)$1	349	154	182	26.5551
fff^^^^^^^^^^^^^^^^^^^ffffff	chr6:83847985-83848240(+)$1	255	172	200	25.5934
!!eeeeeuuuuuuuuuuuueeeee4444	chr14:55510779-55511026(+)$1	247	26	54	18.9881
ffffff^^^^^^^^^^^^^^^^^^ffff	chr19:58384437-58384680(-)$1	243	167	195	26.2892
!!a[eeeeevvvvvvvvvvvvveeeee]	chr4:102014848-102015088(-)$1	240	92	120	18.5133
ffffffxxxxxxxxxxxxxxxffffff6	chr2:206927595-206927847(-)$1	252	16	44	20.6043
[dddd^^^^^^^^^^^^^^^^^^^^ddd	chr3:44612694-44612924(+)$1	230	98	126	27.3450
dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr4:1215463-1215716(-)$1	253	33	61	28.1723
gg!!bbyyyyyyyyyyyyyyyybb22gg	chr2:46787591-46787841(+)$1	250	32	60	23.0755
ffffffyyyyyyyyyyyyyyyyffffff	chr12:980342-980642(+)$1	300	24	52	23.6572
cc:cccyyyyyyyyyyyyyyyyccc:::	chr16:23695265-23695501(+)$1	236	43	71	20.7253
======vvvvvvvvvvvvv=========	chr16:4855073-4855400(-)$1	327	204	232	18.1672
:eeeee^^^^^^^^^^^^^^^^^^^^^^	chr5:157232755-157233158(-)$1	403	108	136	27.1263
[ccc^^^^^^^^^^^^^^^^^^^^^^^^	chr4:17825197-17825433(+)$1	236	98	126	28.9027
+dddd^^^^^^^^^^^^^^^^^^dddd9	chr13:39587475-39587904(-)$1	429	289	317	25.2852
ggggg[bbwwwwwwwwwwwwwwbb]ggg	chr17:65882157-65882425(+)$1	268	229	257	19.6029
c[bb^^^^^^^^^^^^^^^^^^bbccc]	chr12:121448752-121448983(-)$1	231	97	125	25.4860
ggggggyyyyyyyyyyyyyyyygggggg	chr2:74755310-74755600(-)$1	290	185	213	23.7676
####ddddwwwwwwwwwwwwwwdddd77	chr10:27052739-27052989(-)$1	250	204	232	18.8298
======^^^^^^^^^^^^^^^^^^^===	chr8:75276306-75276548(+)$1	242	68	96	27.2281
!!ccc^^^^^^^^^^^^^^^^^^ccc33	chr1:35650087-35650369(-)$1	282	125	153	27.4032
ffffff^^^^^^^^^^^^^^^^^^^^^^	chr5:110097185-110097476(+)$1	291	68	96	27.7325
[ddddbbxxxxxxxxxxxxxxxbb]ddd	chr5:133473698-133473934(+)$1	236	130	158	20.6444
#eeeeeyyyyyyyyyyyyyyyyeeeee4	chr1:150325244-150325517(+)$1	273	217	245	24.7978
!!ccc^^^^^^^^^^^^^^^^^^^^^^^	chr1:205589240-205589525(-)$1	285	87	115	28.7191
[eeeee^^^^^^^^^^^^^^^^^^^^ee	chr19:58353610-58353953(+)$1	343	262	290	27.7271
"ccc^^^^^^^^^^^^^^^^^^^^^^^^	chr20:49509418-49509706(-)$1	288	192	220	28.8353
::ddddyyyyyyyyyyyyyyyydddd::	chr10:119805423-119805679(-)$1	256	93	121	19.9634
ee^^^^^^^^^^^^^^^^^^^^eeeee8	chr7:138968983-138969231(+)$1	248	76	104	25.5818
dddd^^^^^^^^^^^^^^^^^^^dddd]	chr6:26452500-26452754(+)$1	254	195	223	26.2159
fffff[awwwwwwwwwwwwwwaffffff	chr19:40504158-40504417(+)$1	259	137	165	20.6163
[eeeee^^^^^^^^^^^^^^^^^^^^^^	chr11:62438556-62438917(-)$1	361	207	235	28.4266
[ccc^^^^^^^^^^^^^^^^^^^^ccc]	chr10:43088914-43089283(-)$1	369	243	271	27.9004
ffffff^^^^^^^^^^^^^^^^^^^^^^	chr13:39586814-39587249(-)$1	435	54	82	27.7325
####bbwwwwwwwwwwwwwwbb4444dd	chr4:17804891-17805374(-)$1	483	345	373	19.9901
fff^^^^^^^^^^^^^^^^^^^ffffff	chr1:235628817-235629072(-)$1	255	117	145	25.5934
ffffff^^^^^^^^^^^^^^^^^^^^^^	chr11:134180201-134180603(+)$1	402	16	44	27.7325
eeeccc^^^^^^^^^^^^^^^^^^^ccc	chr7:107399112-107399521(+)$1	409	346	374	27.0645
a[ddddyyyyyyyyyyyyyyyydddd]a	chr11:10822397-10822659(-)$1	262	210	238	23.7051
ddddcccxxxxxxxxxxxxxxxccc]dd	chr14:75248445-75248781(+)$1	336	299	327	20.7347
!eeeee^^^^^^^^^^^^^^^^^^^eee	chr14:62207525-62207781(+)$1	256	94	122	27.4401
^^^^^^^^^^^^^^^^^^^^^^^dddd]	chr12:111080063-111080406(+)$1	343	190	218	26.0766
[ccc^^^^^^^^^^^^^^^^^^^^ccc]	chr10:38344182-38344528(+)$1	346	227	255	27.9004
[eeeeeyyyyyyyyyyyyyyyyeeeee]	chr16:3486321-3486554(-)$1	233	81	109	24.7363
$eeeee^^^^^^^^^^^^^^^^^^^^^^	chr1:185277001-185277262(-)$1	261	183	211	28.1380
[dddd^^^^^^^^^^^^^^^^^^^dddd	chr1:198685830-198686082(+)$1	252	22	50	26.8354
gggggg^^^^^^^^^^^^^^^^^^^^^^	chr11:18536221-18536487(-)$1	266	26	54	27.8474
[ffffffxxxxxxxxxxxxxxxffffff	chr10:129901861-129902151(-)$1	290	233	261	20.9947
ggggg[bbvvvvvvvvvvvvvbb]gggg	chr1:40928847-40929084(+)$1	237	77	105	18.0680
[ccc^^^^^^^^^^^^^^^^^^^^^ccc	chr1:197053383-197053615(-)$1	232	188	216	28.1125
ffffffyyyyyyyyyyyyyyyyffffff	chrX:38422221-38422577(+)$1	356	170	198	23.6572
#eeeee^^^^^^^^^^^^^^^^^^^^^^	chr9:95609830-95610067(-)$1	237	98	126	28.3270
"dddd^^^^^^^^^^^^^^^^^^^^^^^	chr19:41255490-41255734(-)$1	244	168	196	28.3883
""eeeeexxxxxxxxxxxxxxxeeeee2	chr1:150436951-150437227(+)$1	276	56	84	21.4602
ffff^^^^^^^^^^^^^^^^^^^^^^^^	chr1:150678976-150679199(-)$1	223	63	91	28.4598
dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr9:95277074-95277349(+)$1	275	17	45	28.1723
"eeeeeyyyyyyyyyyyyyyyyeeeee3	chr19:57911022-57911258(+)$1	236	160	188	24.7923
$a[eeeeevvvvvvvvvvvvveeeee]a	chr10:102249255-102249567(-)$1	312	180	208	18.4279
fff^^^^^^^^^^^^^^^^^^^ffffff	chr6:83848127-83848368(+)$1	241	30	58	25.5934

#otherMatches

#Seq PSSM
AGCCAUCCCAUCCACAUCAUUCCCGCCU	chr17:42475053-42475290(-)$1	237	151	179	26.9617
GCUGUUACCACCACUAUUCAAGGUAAGC	chr10:70256072-70256315(-)$1	243	103	131	18.6877
ACUCUGAGCCCUCCAUUUACACAACCAG	chr7:107399420-107399691(+)$1	271	38	66	27.0645
GUGUUUUacacacauacacucacacaca	chr19:4690652-4691001(-)$1	349	154	182	26.5551
GCCAUUACCCAACUCAUGUCAAGGUUAC	chr6:83847985-83848240(+)$1	255	172	200	25.5934
CUGUGUCUUCCAUUCUCCUGACAUUACU	chr14:55510779-55511026(+)$1	247	26	54	18.9881
UGUGGAAAAUCAUUUACCCACAGCUCUA	chr19:58384437-58384680(-)$1	243	167	195	26.2892
GAAAUGAGAAGACUCAGGAACAUUUCAC	chr4:102014848-102015088(-)$1	240	92	120	18.5133
UAAAUCUGCCUUAUACUCUCUGAUUUAU	chr2:206927595-206927847(-)$1	252	16	44	20.6043
CGUUCCACUUUUAAUCACCACCAGCGAA	chr3:44612694-44612924(+)$1	230	98	126	27.3450
uuucuuuccucccuccuucccuuccuuc	chr4:1215463-1215716(-)$1	253	33	61	28.1723
GCUCCUGAUGAAUUAAUAAAGAAGUUGC	chr2:46787591-46787841(+)$1	250	32	60	23.0755
GCCUGACCUCUAUACACUUACUUUAGGC	chr12:980342-980642(+)$1	300	24	52	23.6572
CCCGUCUCCCCAUCACCUGCCUGACCAU	chr16:23695265-23695501(+)$1	236	43	71	20.7253
GACCCCCUCUUCCUCACAUGGGGUCGGG	chr16:4855073-4855400(-)$1	327	204	232	18.1672
ACUGUGACGACAAAGCAUAUUCAUAUCA	chr5:157232755-157233158(-)$1	403	108	136	27.1263
AGAUUCUUAUUUUACCCACAAUCCCAAU	chr4:17825197-17825433(+)$1	236	98	126	28.9027
CUGCAUAUUUCAUCUACCCCUGCUGCAA	chr13:39587475-39587904(-)$1	429	289	317	25.2852
GGAGAAAGAGAAUCUCAUACACCUGUCU	chr17:65882157-65882425(+)$1	268	229	257	19.6029
AAGUuucacuuauucaacaaauacugau	chr12:121448752-121448983(-)$1	231	97	125	25.4860
CUGUGGUCACUUUUCGUCCCUUUCACGG	chr2:74755310-74755600(-)$1	290	185	213	23.7676
CCAUUGAACUCACUUUACAUAAUUCAUA	chr10:27052739-27052989(-)$1	250	204	232	18.8298
UUGAAGAGAAAAACAUUUAACAAGGUUU	chr8:75276306-75276548(+)$1	242	68	96	27.2281
CACAUGGACAUCAACUACUUAUAAUGAA	chr1:35650087-35650369(-)$1	282	125	153	27.4032
UCAAGGAACACGCACAAUAAUUGACAAU	chr5:110097185-110097476(+)$1	291	68	96	27.7325
CACCUGCGGACAUCAGCCAGAAGCAAGG	chr5:133473698-133473934(+)$1	236	130	158	20.6444
UGCAAGCCCUUGCCUCUCCUCCCUUGCC	chr1:150325244-150325517(+)$1	273	217	245	24.7978
AUGACUGCUUUUGCCACCACACCACCCA	chr1:205589240-205589525(-)$1	285	87	115	28.7191
UGUGAAAAAAAAUUUAGGAAAAGCUCUU	chr19:58353610-58353953(+)$1	343	262	290	27.7271
UGCUUACCAUGCCCAAAAUAAUCCUCCA	chr20:49509418-49509706(-)$1	288	192	220	28.8353
AAAGUGGUACCAAUGACACAUACACUAU	chr10:119805423-119805679(-)$1	256	93	121	19.9634
CUUCCACCUACAAAAAAUCUUCAGGCCC	chr7:138968983-138969231(+)$1	248	76	104	25.5818
ccccuuauacagauaaggaaacuggggu	chr6:26452500-26452754(+)$1	254	195	223	26.2159
UCUGCACUCACUUUCUAUAAUGGUAGAG	chr19:40504158-40504417(+)$1	259	137	165	20.6163
UAAUAGUUACUUAUCUUUAACAUUUAUU	chr11:62438556-62438917(-)$1	361	207	235	28.4266
AUUCACACCUUACAGUACACCAGAGAAC	chr10:43088914-43089283(-)$1	369	243	271	27.9004
GCUGCCACCUCCACAUCUCUCCCUCAUC	chr13:39586814-39587249(-)$1	435	54	82	27.7325
UUCUCAGUCAAACUCUCUUAUGCCCUGG	chr4:17804891-17805374(-)$1	483	345	373	19.9901
AGGGUAAGUUUGCUAGUUGAAACUUGAA	chr1:235628817-235629072(-)$1	255	117	145	25.5934
guuugCAUUAGAAAGUGAAGAAGUGGGG	chr11:134180201-134180603(+)$1	402	16	44	27.7325
ACUCUGAGCCCUCCAUUUACACAACCAG	chr7:107399112-107399521(+)$1	409	346	374	27.0645
AGUGUGUUCUUCCCCCUAAUUUCAUAGU	chr11:10822397-10822659(-)$1	262	210	238	23.7051
AGACCAGCACUGCUUCCUACUCCUGUGU	chr14:75248445-75248781(+)$1	336	299	327	20.7347
CAGCAGACUCAAAUACAAGAACCUACUG	chr14:62207525-62207781(+)$1	256	94	122	27.4401
CUUUUCCCCAUUUUAAUCAAAUCUCUGC	chr12:111080063-111080406(+)$1	343	190	218	26.0766
CUUCGCACCUUAAAGUACACCAGAGAAC	chr10:38344182-38344528(+)$1	346	227	255	27.9004
AUUUGCAUCUCAUUACUCAUAAGCGAAC	chr16:3486321-3486554(-)$1	233	81	109	24.7363
GUUUCAUGAAGCCUUACCAAAUUAUUCU	chr1:185277001-185277262(-)$1	261	183	211	28.1380
AUUUGCAAAAUUUAAAACCUUAUACGAA	chr1:198685830-198686082(+)$1	252	22	50	26.8354
UCUGUUCCUUUAACCAUUCUUCaauuua	chr11:18536221-18536487(-)$1	266	26	54	27.8474
AGAAGGUACAAGUAAAAGAAGAGCCUUC	chr10:129901861-129902151(-)$1	290	233	261	20.9947
AUGUAGUAAAACCUUCAGCCAUAGUACA	chr1:40928847-40929084(+)$1	237	77	105	18.0680
AGUGUAAAGAAAUAUUAAAGCCAAUCAU	chr1:197053383-197053615(-)$1	232	188	216	28.1125
GGUAUGGACUCCCCAGACCACACAUACC	chrX:38422221-38422577(+)$1	356	170	198	23.6572
AGAAUUCAAACCUUAAUAUACAUAAAAA	chr9:95609830-95610067(-)$1	237	98	126	28.3270
AGCAGACCCCUGUUCCCCCACCGCUCCC	chr19:41255490-41255734(-)$1	244	168	196	28.3883
AGUCCUGCAUCAAGACCUUCUCCAGGAA	chr1:150436951-150437227(+)$1	276	56	84	21.4602
AUGGAAAAUAUUGACUCAACUAUACUAU	chr1:150678976-150679199(-)$1	223	63	91	28.4598
GGGuccuccucguccuccucauccuccu	chr9:95277074-95277349(+)$1	275	17	45	28.1723
GUGGGGAAUUCUUUAGCUAAAACUCCAA	chr19:57911022-57911258(+)$1	236	160	188	24.7923
AGUCAGUCCUUCCCCUUCUCAGACUGUC	chr10:102249255-102249567(-)$1	312	180	208	18.4279
GCCAUUACCCAACUCAUGUCAAGGUUAC	chr6:83848127-83848368(+)$1	241	30	58	25.5934

#DB
.((.....................))..	chr17:42475053-42475290(-)$1	1	151	179	26.9617
.((((((((............))).)))	chr10:70256072-70256315(-)$1	1	103	131	18.6877
)))(((...................)))	chr7:107399420-107399691(+)$1	1	38	66	27.0645
((((...................)))))	chr19:4690652-4691001(-)$1	1	154	182	26.5551
(((...................))))))	chr6:83847985-83848240(+)$1	1	172	200	25.5934
..(((((............)))))....	chr14:55510779-55511026(+)$1	1	26	54	18.9881
((((((..................))))	chr19:58384437-58384680(-)$1	1	167	195	26.2892
..(.(((((.............))))).	chr4:102014848-102015088(-)$1	1	92	120	18.5133
((((((...............)))))).	chr2:206927595-206927847(-)$1	1	16	44	20.6043
.((((....................)))	chr3:44612694-44612924(+)$1	1	98	126	27.3450
((((........................	chr4:1215463-1215716(-)$1	1	33	61	28.1723
((..((................))..))	chr2:46787591-46787841(+)$1	1	32	60	23.0755
((((((................))))))	chr12:980342-980642(+)$1	1	24	52	23.6572
)).(((................)))...	chr16:23695265-23695501(+)$1	1	43	71	20.7253
((((((.............)))))))))	chr16:4855073-4855400(-)$1	1	204	232	18.1672
.(((((......................	chr5:157232755-157233158(-)$1	1	108	136	27.1263
.(((........................	chr4:17825197-17825433(+)$1	1	98	126	28.9027
.((((..................)))).	chr13:39587475-39587904(-)$1	1	289	317	25.2852
(((((.((..............)).)))	chr17:65882157-65882425(+)$1	1	229	257	19.6029
(.((..................))))).	chr12:121448752-121448983(-)$1	1	97	125	25.4860
((((((................))))))	chr2:74755310-74755600(-)$1	1	185	213	23.7676
....((((..............))))..	chr10:27052739-27052989(-)$1	1	204	232	18.8298
((((((...................)))	chr8:75276306-75276548(+)$1	1	68	96	27.2281
..(((..................)))..	chr1:35650087-35650369(-)$1	1	125	153	27.4032
((((((......................	chr5:110097185-110097476(+)$1	1	68	96	27.7325
.((((((...............)).)))	chr5:133473698-133473934(+)$1	1	130	158	20.6444
.(((((................))))).	chr1:150325244-150325517(+)$1	1	217	245	24.7978
..(((.......................	chr1:205589240-205589525(-)$1	1	87	115	28.7191
.(((((....................))	chr19:58353610-58353953(+)$1	1	262	290	27.7271
.(((........................	chr20:49509418-49509706(-)$1	1	192	220	28.8353
..((((................))))..	chr10:119805423-119805679(-)$1	1	93	121	19.9634
((....................))))).	chr7:138968983-138969231(+)$1	1	76	104	25.5818
((((...................)))).	chr6:26452500-26452754(+)$1	1	195	223	26.2159
(((((.(..............)))))))	chr19:40504158-40504417(+)$1	1	137	165	20.6163
.(((((......................	chr11:62438556-62438917(-)$1	1	207	235	28.4266
.(((....................))).	chr10:43088914-43089283(-)$1	1	243	271	27.9004
((((((......................	chr13:39586814-39587249(-)$1	1	54	82	27.7325
....((..............))....))	chr4:17804891-17805374(-)$1	1	345	373	19.9901
(((...................))))))	chr1:235628817-235629072(-)$1	1	117	145	25.5934
((((((......................	chr11:134180201-134180603(+)$1	1	16	44	27.7325
)))(((...................)))	chr7:107399112-107399521(+)$1	1	346	374	27.0645
(.((((................)))).)	chr11:10822397-10822659(-)$1	1	210	238	23.7051
(((((((...............))).))	chr14:75248445-75248781(+)$1	1	299	327	20.7347
.(((((...................)))	chr14:62207525-62207781(+)$1	1	94	122	27.4401
.......................)))).	chr12:111080063-111080406(+)$1	1	190	218	26.0766
.(((....................))).	chr10:38344182-38344528(+)$1	1	227	255	27.9004
.(((((................))))).	chr16:3486321-3486554(-)$1	1	81	109	24.7363
.(((((......................	chr1:185277001-185277262(-)$1	1	183	211	28.1380
.((((...................))))	chr1:198685830-198686082(+)$1	1	22	50	26.8354
((((((......................	chr11:18536221-18536487(-)$1	1	26	54	27.8474
.((((((...............))))))	chr10:129901861-129902151(-)$1	1	233	261	20.9947
(((((.((.............)).))))	chr1:40928847-40929084(+)$1	1	77	105	18.0680
.(((.....................)))	chr1:197053383-197053615(-)$1	1	188	216	28.1125
((((((................))))))	chrX:38422221-38422577(+)$1	1	170	198	23.6572
.(((((......................	chr9:95609830-95610067(-)$1	1	98	126	28.3270
.((((.......................	chr19:41255490-41255734(-)$1	1	168	196	28.3883
..(((((...............))))).	chr1:150436951-150437227(+)$1	1	56	84	21.4602
((((........................	chr1:150678976-150679199(-)$1	1	63	91	28.4598
((((........................	chr9:95277074-95277349(+)$1	1	17	45	28.1723
.(((((................))))).	chr19:57911022-57911258(+)$1	1	160	188	24.7923
.(.(((((.............))))).)	chr10:102249255-102249567(-)$1	1	180	208	18.4279
(((...................))))))	chr6:83848127-83848368(+)$1	1	30	58	25.5934

#PSSM
[ : 0.20	f : 0.19	g : 0.09	! : 0.08	d : 0.06	# : 0.06	" : 0.06	e : 0.04	c : 0.03	= : 0.03	: : 0.03	$ : 0.03	+ : 0.01	a : 0.01	^ : 0.01	
e : 0.20	f : 0.20	d : 0.14	g : 0.09	c : 0.09	! : 0.06	= : 0.03	[ : 0.03	# : 0.03	b : 0.01	: : 0.01	^ : 0.01	" : 0.01	a : 0.01	
e : 0.22	f : 0.20	d : 0.17	c : 0.11	g : 0.08	b : 0.03	= : 0.03	# : 0.03	^ : 0.03	a : 0.01	! : 0.01	: : 0.01	[ : 0.01	
e : 0.20	d : 0.17	c : 0.16	f : 0.16	^ : 0.09	g : 0.08	= : 0.03	# : 0.03	[ : 0.01	! : 0.01	b : 0.01	
^ : 0.27	e : 0.22	f : 0.14	d : 0.12	c : 0.09	g : 0.06	b : 0.03	= : 0.03	
^ : 0.37	e : 0.22	f : 0.12	c : 0.06	b : 0.04	[ : 0.04	d : 0.04	= : 0.03	g : 0.03	
^ : 0.59	y : 0.16	e : 0.06	b : 0.04	c : 0.03	x : 0.01	v : 0.01	d : 0.01	a : 0.01	w : 0.01	f : 0.01	
^ : 0.59	y : 0.16	x : 0.08	e : 0.03	b : 0.03	w : 0.03	c : 0.01	u : 0.01	v : 0.01	d : 0.01	
^ : 0.59	y : 0.16	x : 0.08	w : 0.06	v : 0.04	c : 0.01	u : 0.01	e : 0.01	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	v : 0.06	w : 0.06	u : 0.03	
^ : 0.59	y : 0.16	x : 0.08	w : 0.06	v : 0.04	u : 0.01	e : 0.01	= : 0.01	
^ : 0.59	y : 0.16	x : 0.08	v : 0.04	w : 0.04	u : 0.01	e : 0.01	= : 0.01	b : 0.01	
^ : 0.59	y : 0.16	x : 0.06	e : 0.03	w : 0.03	b : 0.03	c : 0.01	v : 0.01	f : 0.01	= : 0.01	a : 0.01	
^ : 0.51	f : 0.12	e : 0.12	b : 0.08	c : 0.04	d : 0.04	= : 0.01	g : 0.01	4 : 0.01	
^ : 0.43	f : 0.12	e : 0.12	d : 0.09	c : 0.06	b : 0.06	g : 0.03	= : 0.01	4 : 0.01	] : 0.01	
^ : 0.35	f : 0.14	e : 0.11	d : 0.11	c : 0.09	] : 0.04	g : 0.04	4 : 0.03	b : 0.01	2 : 0.01	= : 0.01	
^ : 0.25	e : 0.14	f : 0.14	d : 0.14	c : 0.11	g : 0.06	4 : 0.03	= : 0.03	b : 0.01	2 : 0.01	: : 0.01	] : 0.01	
^ : 0.24	e : 0.14	f : 0.14	d : 0.12	c : 0.09	g : 0.08	3 : 0.03	: : 0.03	= : 0.03	] : 0.03	4 : 0.01	7 : 0.01	
^ : 0.24	f : 0.12	] : 0.11	g : 0.08	d : 0.08	3 : 0.04	e : 0.04	c : 0.04	4 : 0.03	: : 0.03	= : 0.03	a : 0.03	6 : 0.01	9 : 0.01	7 : 0.01	8 : 0.01	2 : 0.01	

#score	1537.175569249842
#seq	62
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m2_run2.txt

#BEAR
"cccvvvvvvvvvvvvvcccff	chr7:35673900-35674119(+)$1	219	45	67	22.1711
dddwwwwwwwwwwwwwwdddd:	chr11:122929785-122930006(-)$1	221	193	215	20.3584
hhhhwwwwwwwwwwwwwwhhhh	chr6:42620122-42620366(+)$1	244	31	53	20.4300
:cccvvvvvvvvvvvvvccc::	chr2:136418809-136419041(+)$1	232	53	75	19.4811
iiiiuuuuuuuuuuuuiiiiii	chr15:83345167-83345383(+)$1	216	44	66	22.4250
dddduuuuuuuuuuuudddd]d	chr13:41794603-41794823(+)$1	220	114	136	21.7754
eeewwwwwwwwwwwwwweeeee	chr18:77477826-77478047(+)$1	221	155	177	21.4587
ggggvvvvvvvvvvvvvggggg	chr10:78708871-78709089(-)$1	218	156	178	22.0476
cccxxxxxxxxxxxxxxxccc:	chr12:79988055-79988281(-)$1	226	125	147	17.5665
ffffuuuuuuuuuuuuffffff	chr16:3433165-3433392(+)$1	227	167	189	22.1910
dd[auuuuuuuuuuuuadddd]	chr12:88560121-88560346(+)$1	225	36	58	22.4194
eeeyyyyyyyyyyyyyyyyeee	chr19:42880474-42880694(+)$1	220	13	35	20.5638
bbwwwwwwwwwwwwwwbb]hhh	chr19:40221925-40222142(-)$1	217	9	31	19.6529
eeeeuuuuuuuuuuuueeeee:	chr11:130749418-130749665(-)$1	247	40	62	21.5380
:ccctttttttttttcccdddd	chr11:14535116-14535331(-)$1	215	173	195	19.6173
eeeeuuuuuuuuuuuueeeee:	chr8:118540802-118541017(+)$1	215	112	134	21.5380
dddduuuuuuuuuuuudddd]c	chr19:16640425-16640643(-)$1	218	3	25	21.9408
cccyyyyyyyyyyyyyyyyccc	chr5:179233435-179233663(-)$1	228	131	153	20.8476
ccbbxxxxxxxxxxxxxxxbb]	chr17:40315248-40315464(-)$1	216	64	86	17.4193
fffftttttttttttffffffE	chr2:27844048-27844270(+)$1	222	192	214	19.3298
ffffvvvvvvvvvvvvvfffff	chr3:172428686-172428924(-)$1	238	37	59	21.7642
====uuuuuuuuuuuu======	chr4:36212116-36212332(+)$1	216	154	176	22.6579
fffftttttttttttffffff:	chr4:114277907-114278131(+)$1	224	65	87	19.4564
ffffuuuuuuuuuuuuffffff	chr6:96651135-96651351(+)$1	216	191	213	22.1910
bbwwwwwwwwwwwwwwbb]bb]	chr22:21354571-21354793(+)$1	222	156	178	19.8071
fffftttttttttttffffff:	chr10:7841935-7842154(+)$1	219	57	79	19.4564
iiiivvvvvvvvvvvvviiiii	chr12:58131451-58131677(-)$1	226	52	74	22.0135
ggggyyyyyyyyyyyyyyyygg	chr21:18971030-18971247(+)$1	217	170	192	20.5145
addddtttttttttttdddd33	chr18:64218305-64218542(-)$1	237	155	177	19.7483
ccccwwwwwwwwwwwwwwcccH	chr7:107557208-107557423(+)$1	215	102	124	21.6177
eeeeuuuuuuuuuuuueeeee]	chr22:24718627-24718866(+)$1	239	166	188	22.3824
ccbbwwwwwwwwwwwwwwbb]c	chr10:75551135-75551384(+)$1	249	203	225	21.2239
eeeewwwwwwwwwwwwwweeee	chr10:126096981-126097223(-)$1	242	122	144	21.7331
dddduuuuuuuuuuuuddddii	chr8:126087163-126087380(-)$1	217	43	65	21.9489
#cccuuuuuuuuuuuuccc333	chr1:7737578-7737805(+)$1	227	33	55	22.7601
hhhhwwwwwwwwwwwwwwhhhh	chr9:139732258-139732473(+)$1	215	155	177	20.4300
gggxxxxxxxxxxxxxxxgggg	chr1:10327374-10327597(+)$1	223	43	65	18.3079
ffffwwwwwwwwwwwwwwffff	chr19:39369993-39370214(-)$1	221	186	208	21.7516
====xxxxxxxxxxxxxxx===	chr7:106938497-106938714(-)$1	217	104	126	18.2230
ffffuuuuuuuuuuuuffffff	chr7:100807133-100807358(-)$1	225	183	205	22.1910
=====ttttttttttt======	chr17:16285382-16285608(+)$1	226	6	28	20.2874
eeeevvvvvvvvvvvvveeeee	chr19:20735242-20735463(-)$1	221	147	169	21.7614
[cccuuuuuuuuuuuuccc]cc	chr5:55271951-55272168(-)$1	217	109	131	22.8716
iiiiwwwwwwwwwwwwwwiiii	chr16:75033488-75033712(-)$1	224	190	212	22.0128
!!bbuuuuuuuuuuuubb5555	chr12:116428891-116429128(-)$1	237	7	29	18.6360
c[bbtttttttttttbb]ccc:	chr10:61564110-61564351(-)$1	241	40	62	19.3565
ddddtttttttttttdddd22d	chr4:7056366-7056591(+)$1	225	129	151	19.1953
dccctttttttttttccc]ddd	chr1:43829616-43829835(-)$1	219	10	32	20.6533
bbxxxxxxxxxxxxxxxbbccc	chr7:94248107-94248327(+)$1	220	50	72	16.8973
dccctttttttttttccc]ddd	chr22:23603507-23603749(+)$1	242	55	77	20.6533
ggggyyyyyyyyyyyyyyyygg	chr6:158919616-158919841(+)$1	225	185	207	20.5145
ggggwwwwwwwwwwwwwwgggg	chr19:42797183-42797404(+)$1	221	127	149	22.0400
f[ccctttttttttttccc]ff	chr7:134871785-134872009(-)$1	224	128	150	20.7167
eddddtttttttttttdddd33	chr19:7987355-7987594(-)$1	239	76	98	19.8104
fffavvvvvvvvvvvvva]fff	chr12:57976858-57977089(+)$1	231	175	197	22.1159
ee[bbtttttttttttbbeeee	chr15:69011449-69011671(+)$1	222	161	183	19.9444
ddddvvvvvvvvvvvvvdddd:	chr7:13971066-13971296(-)$1	230	123	145	20.6088
"ccctttttttttttcccffff	chr16:16443025-16443245(+)$1	220	180	202	20.8731
eeeewwwwwwwwwwwwwweeee	chrX:47062277-47062506(+)$1	229	13	35	21.7331
ccbbuuuuuuuuuuuubb]ccc	chrX:16772983-16773214(+)$1	231	108	130	22.2619
ffxxxxxxxxxxxxxxxfffff	chr3:1134359-1134577(-)$1	218	162	184	17.5198
ffffuuuuuuuuuuuuffffff	chrX:53613676-53613895(-)$1	219	180	202	22.1910
e[bbuuuuuuuuuuuubb]eee	chr16:21415469-21415691(-)$1	222	137	159	22.0973
eeeeuuuuuuuuuuuueeeee2	chr4:134071232-134071464(+)$1	232	190	212	22.1098
ffffwwwwwwwwwwwwwwffff	chr2:210570247-210570478(+)$1	231	152	174	21.7516

#otherMatches

#Seq PSSM
UGCAUUUUGCCCAUCAUUGUUA	chr7:35673900-35674119(+)$1	219	45	67	22.1711
AGACCUUCACUACCUAUUCUGA	chr11:122929785-122930006(-)$1	221	193	215	20.3584
UAUCAAAAGUAACAAAGAGAUA	chr6:42620122-42620366(+)$1	244	31	53	20.4300
AGGCCACUAUCACUCCAGCCAA	chr2:136418809-136419041(+)$1	232	53	75	19.4811
CCUGUUUAGAGUUGGUCAGGUA	chr15:83345167-83345383(+)$1	216	44	66	22.4250
UCCAAGGAUAGGAAUGUGGAAU	chr13:41794603-41794823(+)$1	220	114	136	21.7754
UCCCUACCCAUCCGCCAGGAGC	chr18:77477826-77478047(+)$1	221	155	177	21.4587
GCUUCAUAACUUCCCCAAAGUG	chr10:78708871-78709089(-)$1	218	156	178	22.0476
GAGGAAAUGAUUGGAAAACUCA	chr12:79988055-79988281(-)$1	226	125	147	17.5665
CGAACAAGAUAAGAACUUCGGC	chr16:3433165-3433392(+)$1	227	167	189	22.1910
UAACUACCUCCUUCCUGUGAAU	chr12:88560121-88560346(+)$1	225	36	58	22.4194
UCACCGUCUGCUUCCCACCUGA	chr19:42880474-42880694(+)$1	220	13	35	20.5638
GGCCAAUCCUCUUACACCUUUG	chr19:40221925-40222142(-)$1	217	9	31	19.6529
UCUGUUUUUUCCUCCUCAGAUC	chr11:130749418-130749665(-)$1	247	40	62	21.5380
GCUCGUACUUACUUGGAGAGAC	chr11:14535116-14535331(-)$1	215	173	195	19.6173
CUGGAACAUAUCAAGACCGGUU	chr8:118540802-118541017(+)$1	215	112	134	21.5380
CCUCAAGACGCAGCACGAGGAG	chr19:16640425-16640643(-)$1	218	3	25	21.9408
GCCUUCCUCUCGCUGUCCUGGU	chr5:179233435-179233663(-)$1	228	131	153	20.8476
GCCCUUACCCUCACCCCAUGGU	chr17:40315248-40315464(-)$1	216	64	86	17.4193
CUGUAAGGAACCAGAGCAGGAG	chr2:27844048-27844270(+)$1	222	192	214	19.3298
UUAUAAGAAACGCGUGAAUGAG	chr3:172428686-172428924(-)$1	238	37	59	21.7642
CAGUGUCUAUCAAAAAAUUGUU	chr4:36212116-36212332(+)$1	216	154	176	22.6579
AGAAGAAGAAAAAGAUUCUGAA	chr4:114277907-114278131(+)$1	224	65	87	19.4564
UGUACAACAAAUCCCAUGCAGU	chr6:96651135-96651351(+)$1	216	191	213	22.1910
AGGGGGAAGAGAGAGACUGAUG	chr22:21354571-21354793(+)$1	222	156	178	19.8071
UGUCAUCUCCUAUAAGACAGAA	chr10:7841935-7842154(+)$1	219	57	79	19.4564
CGCCCCCACCUCCUCCCGGCGC	chr12:58131451-58131677(-)$1	226	52	74	22.0135
UCCAUAAAAACAAAGAGAUCUG	chr21:18971030-18971247(+)$1	217	170	192	20.5145
CAAGUGUAUUAAUUAAACUUUC	chr18:64218305-64218542(-)$1	237	155	177	19.7483
ACCCUUUACUAAGAAUUUGGGA	chr7:107557208-107557423(+)$1	215	102	124	21.6177
AAAGAAAAAGCAGAGACUUUGG	chr22:24718627-24718866(+)$1	239	166	188	22.3824
AGACAUACCAUGAUUUUAGUCC	chr10:75551135-75551384(+)$1	249	203	225	21.2239
AUUAAAUAUUAACUUCUAUGAU	chr10:126096981-126097223(-)$1	242	122	144	21.7331
UGGGGAUCACAGUUAAUCUAGU	chr8:126087163-126087380(-)$1	217	43	65	21.9489
UAGGUACCCACCCAUCCCUUGA	chr1:7737578-7737805(+)$1	227	33	55	22.7601
CGCCAGGGACGAGAAGAAGGUG	chr9:139732258-139732473(+)$1	215	155	177	20.4300
CUUUACUAAUUUGUUCAUAGGU	chr1:10327374-10327597(+)$1	223	43	65	18.3079
ACCCUCUCCCCACCCCAUGGGU	chr19:39369993-39370214(-)$1	221	186	208	21.7516
CAUACCAAAAAAGCCAGAUUAU	chr7:106938497-106938714(-)$1	217	104	126	18.2230
CCGCGGCGCAGGAAGAGCGGCU	chr7:100807133-100807358(-)$1	225	183	205	22.1910
UUCUGACUACAACAUCCAGAAG	chr17:16285382-16285608(+)$1	226	6	28	20.2874
CCAUGAAGAAACAUGAGAUGGU	chr19:20735242-20735463(-)$1	221	147	169	21.7614
CACCACUGAAUCUACAGGUAAG	chr5:55271951-55272168(-)$1	217	109	131	22.8716
CCCCACUUCUCAGCAGCAGGGG	chr16:75033488-75033712(-)$1	224	190	212	22.0128
AAGGAACCAAAAAACCCCAGGA	chr12:116428891-116429128(-)$1	237	7	29	18.6360
GUGGUUUUAUCGUUUCCUCCUC	chr10:61564110-61564351(-)$1	241	40	62	19.3565
CUCCAAACGGGGAAAGGAGGAC	chr4:7056366-7056591(+)$1	225	129	151	19.1953
GUCUUUCUCUAUCCUAGAUCCA	chr1:43829616-43829835(-)$1	219	10	32	20.6533
GCCACACAUUUUUCACUGCGCC	chr7:94248107-94248327(+)$1	220	50	72	16.8973
GCUGCCACCACCUCUCAGCCGG	chr22:23603507-23603749(+)$1	242	55	77	20.6533
UUCAACCCAAAUGUUUUCAGUG	chr6:158919616-158919841(+)$1	225	185	207	20.5145
GGGCAGCCCACACCACCAGCCC	chr19:42797183-42797404(+)$1	221	127	149	22.0400
CCGAGUACAGCCUCCCCUCAGA	chr7:134871785-134872009(-)$1	224	128	150	20.7167
UCUCCUCUGGUGCCUUGGAGCC	chr19:7987355-7987594(-)$1	239	76	98	19.8104
UUGCUUCCCUUCUUGCUGACAG	chr12:57976858-57977089(+)$1	231	175	197	22.1159
GCAGCCUUUGCCUUCAGCGCAG	chr15:69011449-69011671(+)$1	222	161	183	19.9444
UCCUCUGAUGAUUAAACAGGAA	chr7:13971066-13971296(-)$1	230	123	145	20.6088
AGGAAUCCACAUCUCUCCAGAG	chr16:16443025-16443245(+)$1	220	180	202	20.8731
UCAGGCCCCUGUUAACCACUGA	chrX:47062277-47062506(+)$1	229	13	35	21.7331
GAACUACUUUUACCGCGUCUCC	chrX:16772983-16773214(+)$1	231	108	130	22.2619
GAUUAAAUUCACCCUCCUCUUU	chr3:1134359-1134577(-)$1	218	162	184	17.5198
UUCGUUUCUAUUUCCCUGGGAC	chrX:53613676-53613895(-)$1	219	180	202	22.1910
GAUGAUAAUAUCAAGACACCUG	chr16:21415469-21415691(-)$1	222	137	159	22.0973
UGGACAUUACAAAACUUUCGGC	chr4:134071232-134071464(+)$1	232	190	212	22.1098
AAUUCCUUCUCUCUCAACAGUU	chr2:210570247-210570478(+)$1	231	152	174	21.7516

#DB
.(((.............)))))	chr7:35673900-35674119(+)$1	1	45	67	22.1711
(((..............)))).	chr11:122929785-122930006(-)$1	1	193	215	20.3584
((((..............))))	chr6:42620122-42620366(+)$1	1	31	53	20.4300
.(((.............)))..	chr2:136418809-136419041(+)$1	1	53	75	19.4811
((((............))))))	chr15:83345167-83345383(+)$1	1	44	66	22.4250
((((............)))).)	chr13:41794603-41794823(+)$1	1	114	136	21.7754
(((..............)))))	chr18:77477826-77478047(+)$1	1	155	177	21.4587
((((.............)))))	chr10:78708871-78709089(-)$1	1	156	178	22.0476
(((...............))).	chr12:79988055-79988281(-)$1	1	125	147	17.5665
((((............))))))	chr16:3433165-3433392(+)$1	1	167	189	22.1910
((.(............))))).	chr12:88560121-88560346(+)$1	1	36	58	22.4194
(((................)))	chr19:42880474-42880694(+)$1	1	13	35	20.5638
((..............)).)))	chr19:40221925-40222142(-)$1	1	9	31	19.6529
((((............))))).	chr11:130749418-130749665(-)$1	1	40	62	21.5380
.(((...........)))((((	chr11:14535116-14535331(-)$1	1	173	195	19.6173
((((............))))).	chr8:118540802-118541017(+)$1	1	112	134	21.5380
((((............)))).)	chr19:16640425-16640643(-)$1	1	3	25	21.9408
(((................)))	chr5:179233435-179233663(-)$1	1	131	153	20.8476
((((...............)).	chr17:40315248-40315464(-)$1	1	64	86	17.4193
((((...........)))))))	chr2:27844048-27844270(+)$1	1	192	214	19.3298
((((.............)))))	chr3:172428686-172428924(-)$1	1	37	59	21.7642
((((............))))))	chr4:36212116-36212332(+)$1	1	154	176	22.6579
((((...........)))))).	chr4:114277907-114278131(+)$1	1	65	87	19.4564
((((............))))))	chr6:96651135-96651351(+)$1	1	191	213	22.1910
((..............)).)).	chr22:21354571-21354793(+)$1	1	156	178	19.8071
((((...........)))))).	chr10:7841935-7842154(+)$1	1	57	79	19.4564
((((.............)))))	chr12:58131451-58131677(-)$1	1	52	74	22.0135
((((................))	chr21:18971030-18971247(+)$1	1	170	192	20.5145
(((((...........))))..	chr18:64218305-64218542(-)$1	1	155	177	19.7483
)(((..............))))	chr7:107557208-107557423(+)$1	1	102	124	21.6177
((((............))))).	chr22:24718627-24718866(+)$1	1	166	188	22.3824
((((..............)).)	chr10:75551135-75551384(+)$1	1	203	225	21.2239
((((..............))))	chr10:126096981-126097223(-)$1	1	122	144	21.7331
((((............))))))	chr8:126087163-126087380(-)$1	1	43	65	21.9489
.(((............)))...	chr1:7737578-7737805(+)$1	1	33	55	22.7601
((((..............))))	chr9:139732258-139732473(+)$1	1	155	177	20.4300
(((...............))))	chr1:10327374-10327597(+)$1	1	43	65	18.3079
((((..............))))	chr19:39369993-39370214(-)$1	1	186	208	21.7516
((((...............)))	chr7:106938497-106938714(-)$1	1	104	126	18.2230
((((............))))))	chr7:100807133-100807358(-)$1	1	183	205	22.1910
(((((...........))))))	chr17:16285382-16285608(+)$1	1	6	28	20.2874
((((.............)))))	chr19:20735242-20735463(-)$1	1	147	169	21.7614
.(((............))).))	chr5:55271951-55272168(-)$1	1	109	131	22.8716
((((..............))))	chr16:75033488-75033712(-)$1	1	190	212	22.0128
..((............))....	chr12:116428891-116429128(-)$1	1	7	29	18.6360
(.((...........)).))).	chr10:61564110-61564351(-)$1	1	40	62	19.3565
((((...........))))..)	chr4:7056366-7056591(+)$1	1	129	151	19.1953
((((...........))).)))	chr1:43829616-43829835(-)$1	1	10	32	20.6533
((...............)))))	chr7:94248107-94248327(+)$1	1	50	72	16.8973
((((...........))).)))	chr22:23603507-23603749(+)$1	1	55	77	20.6533
((((................))	chr6:158919616-158919841(+)$1	1	185	207	20.5145
((((..............))))	chr19:42797183-42797404(+)$1	1	127	149	22.0400
(.(((...........))).))	chr7:134871785-134872009(-)$1	1	128	150	20.7167
(((((...........))))..	chr19:7987355-7987594(-)$1	1	76	98	19.8104
((((.............).)))	chr12:57976858-57977089(+)$1	1	175	197	22.1159
((.((...........))))))	chr15:69011449-69011671(+)$1	1	161	183	19.9444
((((.............)))).	chr7:13971066-13971296(-)$1	1	123	145	20.6088
.(((...........)))))))	chr16:16443025-16443245(+)$1	1	180	202	20.8731
((((..............))))	chrX:47062277-47062506(+)$1	1	13	35	21.7331
((((............)).)))	chrX:16772983-16773214(+)$1	1	108	130	22.2619
((...............)))))	chr3:1134359-1134577(-)$1	1	162	184	17.5198
((((............))))))	chrX:53613676-53613895(-)$1	1	180	202	22.1910
(.((............)).)))	chr16:21415469-21415691(-)$1	1	137	159	22.0973
((((............))))).	chr4:134071232-134071464(+)$1	1	190	212	22.1098
((((..............))))	chr2:210570247-210570478(+)$1	1	152	174	21.7516

#PSSM
f : 0.20	e : 0.18	d : 0.13	c : 0.10	g : 0.07	i : 0.04	b : 0.04	= : 0.04	" : 0.03	h : 0.03	: : 0.03	a : 0.01	# : 0.01	[ : 0.01	! : 0.01	
c : 0.21	f : 0.18	e : 0.15	d : 0.13	g : 0.07	i : 0.04	b : 0.04	= : 0.04	[ : 0.04	h : 0.03	! : 0.01	
c : 0.18	f : 0.16	e : 0.13	d : 0.12	b : 0.09	g : 0.07	i : 0.04	= : 0.04	h : 0.03	[ : 0.03	w : 0.03	x : 0.03	
c : 0.15	f : 0.15	d : 0.10	e : 0.10	b : 0.10	w : 0.06	g : 0.06	x : 0.06	i : 0.04	= : 0.04	h : 0.03	a : 0.03	y : 0.03	
u : 0.29	w : 0.21	t : 0.13	v : 0.12	x : 0.09	y : 0.06	d : 0.03	= : 0.01	c : 0.01	b : 0.01	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	t : 0.21	v : 0.12	x : 0.09	y : 0.06	
u : 0.29	w : 0.21	v : 0.12	x : 0.09	t : 0.07	y : 0.06	c : 0.06	f : 0.04	b : 0.01	d : 0.01	
w : 0.18	v : 0.12	f : 0.10	b : 0.10	c : 0.10	d : 0.09	x : 0.09	y : 0.06	e : 0.06	= : 0.03	i : 0.01	a : 0.01	
w : 0.15	c : 0.13	d : 0.13	f : 0.13	b : 0.10	e : 0.09	x : 0.06	y : 0.06	i : 0.03	= : 0.03	g : 0.01	] : 0.01	a : 0.01	
f : 0.18	d : 0.15	e : 0.13	c : 0.12	] : 0.10	y : 0.06	i : 0.04	g : 0.04	h : 0.03	x : 0.03	= : 0.03	b : 0.03	5 : 0.01	
f : 0.20	d : 0.16	e : 0.16	c : 0.12	h : 0.04	i : 0.04	g : 0.04	b : 0.04	= : 0.04	y : 0.03	] : 0.03	3 : 0.01	5 : 0.01	2 : 0.01	
f : 0.23	e : 0.16	c : 0.10	d : 0.09	g : 0.07	i : 0.06	h : 0.04	] : 0.04	= : 0.04	3 : 0.04	b : 0.03	: : 0.01	5 : 0.01	2 : 0.01	
f : 0.18	: : 0.13	e : 0.10	c : 0.09	d : 0.07	g : 0.07	i : 0.06	] : 0.06	h : 0.04	= : 0.04	3 : 0.04	E : 0.01	H : 0.01	5 : 0.01	2 : 0.01	

#score	1353.5670632202266
#seq	65
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m1_run2.txt

#BEAR
======^^^^^^^^^^^^^^^^^^^^^^^^========	chr14:88419351-88419598(-)$1	247	65	103	42.1262
bb[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr14:24456691-24456939(+)$1	248	141	179	43.0803
b!!ccc^^^^^^^^^^^^^^^^^^^ccc333bb22a]d	chr21:37912286-37912513(-)$1	227	68	106	35.0363
hh[ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc]hhh	chr2:71574610-71574864(+)$1	254	85	123	41.1310
ffff^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff3	chr6:144009892-144010129(+)$1	237	44	82	41.9548
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^bb]fffff	chr15:38758910-38759132(+)$1	222	64	102	41.9880
dd[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^bb]ddd	chr17:70822087-70822319(-)$1	232	98	136	41.7411
fffffffffff^^^^^^^^^^^^^^^^^^^ffffff33	chr15:75121288-75121529(+)$1	241	83	121	33.2341
ii^^^^^^^^^^^^^^^^^^^^^^^^^^^^^iiiiiii	chr1:167634212-167634475(+)$1	263	60	98	43.2403
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^iiiiiiii	chr8:28771884-28772110(+)$1	226	79	117	42.7128
dd[ccc!!ccc^^^^^^^^^^^^^^^^^^^ccc22ccc	chr1:26876341-26876557(+)$1	216	79	117	35.5909
d^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]cc	chr6:36887482-36887711(+)$1	229	144	182	42.9605
=a[ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc]a]==	chr1:203765353-203765636(+)$1	283	34	72	42.2577
=====^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^===	chr3:79590851-79591097(-)$1	246	112	150	44.1367
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr12:51182406-51182632(+)$1	226	32	70	43.1381
eeeeebb^^^^^^^^^^^^^^^^^^^^^bb]eeeee44	chrX:21525290-21525540(+)$1	250	139	177	36.7041
e^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee]ff	chr13:72181563-72181796(-)$1	233	60	98	42.3225
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr3:114373438-114373661(-)$1	223	73	111	42.7422
!!bb^^^^^^^^^^^^^^^^^^^^^^^^^^^^^bb22c	chr1:159019342-159019611(+)$1	269	60	98	42.7947
ggggg[bb^^^^^^^^^^^^^^^^^^^^^^bbgggggg	chr12:65806400-65806628(+)$1	228	81	119	38.5399
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]cc	chr15:77158480-77158722(-)$1	242	108	146	43.1392
dd^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr18:60960611-60960966(-)$1	355	191	229	43.7332
b[dddd^^^^^^^^^^^^^^^^^^^^^ddddbb22fff	chr4:42515536-42515825(-)$1	289	156	194	35.2114
ffffff^^^^^^^^^^^^^^^^^^^^^ffffffeeeee	chr14:61176674-61176895(-)$1	221	102	140	35.6169
iiiiii!!ccc^^^^^^^^^^^^^^^^^^ccc22iiii	chrX:137858567-137858787(-)$1	220	5	43	34.1127
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr8:125624702-125624961(-)$1	259	53	91	43.5549
ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^c	chr3:141136119-141136358(+)$1	239	107	145	44.2402
i!!ccc^^^^^^^^^^^^^^^^^^^^^^^^ccciiiii	chr4:114521203-114521456(-)$1	253	117	155	42.0919
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd2	chr2:149485327-149485611(+)$1	284	129	167	41.9466
d[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^cccddd	chr7:106527331-106527556(+)$1	225	96	134	42.6169
"""ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^cc	chr2:225822806-225823119(-)$1	313	163	201	43.8714
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^a]gggggg	chr8:124040505-124040777(-)$1	272	63	101	42.9817
gggggg^^^^^^^^^^^^^^^^^^^^^^^^gggggggc	chr22:36659419-36659636(+)$1	217	140	178	41.1822
eeeeeeee^^^^^^^^^^^^^^^^^^eeeee]eeeeed	chr12:88472345-88472566(-)$1	221	119	157	32.1754
fffffeeeee^^^^^^^^^^^^^^^^^^^^eeeee]ff	chr12:69647728-69648037(+)$1	309	70	108	35.2412
ffffff^^^^^^^^^^^^^^^^^^^^^^^^^^^fffff	chr8:11313299-11313536(-)$1	237	99	137	41.8142
ggiiiiiiiii^^^^^^^^^^^^^^^^^^^iiiiiiii	chr6:70400270-70400501(-)$1	231	135	173	33.8363
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr4:36209222-36209511(-)$1	289	124	162	40.4452
iiiiiiiii^^^^^^^^^^^^^^^^^^^iiiiiiiii:	chr12:44337831-44338051(+)$1	220	101	139	33.1656
=====[bb^^^^^^^^^^^^^^^^^^^^^bb=======	chr1:28223942-28224165(-)$1	223	180	218	38.1130
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ddddffff	chr3:49046533-49046837(+)$1	304	104	142	41.9150
ee[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^^bb]ee	chr13:39587770-39588050(-)$1	280	101	139	42.4639
[dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr4:47427290-47427540(+)$1	250	112	150	42.9120
d"""eeeee^^^^^^^^^^^^^^^^^^^^eeeee333d	chr8:100213300-100213536(+)$1	236	12	50	36.4354
[eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr15:65982579-65982820(-)$1	241	125	163	43.1858
ieeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr11:48087165-48087407(+)$1	242	103	141	42.9075
e:eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeee:::	chr5:93699072-93699301(-)$1	229	96	134	36.0449
$$$ffffff^^^^^^^^^^^^^^^^^^^^^ffffffcc	chr11:86519412-86519626(+)$1	214	31	69	36.5015
$eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:103290885-103291115(+)$1	230	98	136	42.9936
[ggggggg^^^^^^^^^^^^^^^^^^^^^ggggggg]h	chr22:30740148-30740394(-)$1	246	153	191	37.1579
[ccc[a^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:67018528-67018778(-)$1	250	108	146	43.5418
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhhh	chr10:92638027-92638255(+)$1	228	26	64	40.4452
dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd::	chr14:76869177-76869406(+)$1	229	0	38	40.3956
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^b	chr14:102877932-102878167(+)$1	235	100	138	44.4490
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc]cc	chr6:3014799-3015046(+)$1	247	36	74	44.0927
bb!!dddd^^^^^^^^^^^^^^^^^^^^^^dddd4444	chr14:61792020-61792282(+)$1	262	146	184	38.2820
!eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr13:49717981-49718260(+)$1	279	170	208	43.2313

#otherMatches

#Seq PSSM
UCUGAGACCUUCCUAACUGCUGCUUCAGACUUCAGACC	chr14:88419351-88419598(-)$1	247	65	103	42.1262
ccaucugcuuucaucaucuuuucugaaacaaaacacua	chr14:24456691-24456939(+)$1	248	141	179	43.0803
gacugUAUAAacacacacacaccacacaccacacacac	chr21:37912286-37912513(-)$1	227	68	106	35.0363
ACAUUUUCCACCAUGCAUUUCAAUCACACAUAAAAGUG	chr2:71574610-71574864(+)$1	254	85	123	41.1310
guucccacccuucugcaauucauuuuccacagaacagc	chr6:144009892-144010129(+)$1	237	44	82	41.9548
aaucuuagaaaauacauaaaacauaaagaagaaaagca	chr15:38758910-38759132(+)$1	222	64	102	41.9880
ggacacaaauccaaaccauaucauuccaucccuggccc	chr17:70822087-70822319(-)$1	232	98	136	41.7411
UGAAUUGAAUGACCAAAUAUAUGAACAUCACauucacu	chr15:75121288-75121529(+)$1	241	83	121	33.2341
ucaccaaaaaaaaaaaaaaaaagaagaagaagauauag	chr1:167634212-167634475(+)$1	263	60	98	43.2403
CUUAAAAAAAUCGCCUCAUCAGAAUCAUCUUUUCCCAC	chr8:28771884-28772110(+)$1	226	79	117	42.7128
agugcaauggugcaaucucggcucaucacaaccucugc	chr1:26876341-26876557(+)$1	216	79	117	35.5909
UUAGAAAUGAAACAACUUAAUGAGAAAACAUAGCAGAA	chr6:36887482-36887711(+)$1	229	144	182	42.9605
GCGCUGAAUUUACCUACUCUCAUUCCUCUCCAGGGUCC	chr1:203765353-203765636(+)$1	283	34	72	42.2577
uauauacacacacacacacacacauauauauacacaua	chr3:79590851-79591097(-)$1	246	112	150	44.1367
uuugccuacuugauaaaauuuauuucuaacuccaaaaa	chr12:51182406-51182632(+)$1	226	32	70	43.1381
UGUCCCUUCUGCAUCUUAUUAUCCUAAUAGUGGACAAU	chrX:21525290-21525540(+)$1	250	139	177	36.7041
GAAACAAUAAAUAAAACACAAAUAAACAAGCUCCUAAG	chr13:72181563-72181796(-)$1	233	60	98	42.3225
aggcagaaaaucaguaagaauacacaagaaauuaaaaa	chr3:114373438-114373661(-)$1	223	73	111	42.7422
CUUCCCAAUACAUUCCCCUCGCUACUAUAUAAUGACAA	chr1:159019342-159019611(+)$1	269	60	98	42.7947
UGGUAAGUUGUUCuauuaguccauucucaugcugcuau	chr12:65806400-65806628(+)$1	228	81	119	38.5399
UacacacacacacgcacacacacacacacacUCAGUGU	chr15:77158480-77158722(-)$1	242	108	146	43.1392
AAACCCACACUCACACUACCACAACACAUACACUGUUU	chr18:60960611-60960966(-)$1	355	191	229	43.7332
acgucacuucaucuaucauuuccauacugacugaaugg	chr4:42515536-42515825(-)$1	289	156	194	35.2114
CUCAUAAUAAAAAUAAUUCAGGAAAACUAUGGGGAAAU	chr14:61176674-61176895(-)$1	221	102	140	35.6169
GAAACAGAGAGGCAACAuaagagcccaaacucgauguu	chrX:137858567-137858787(-)$1	220	5	43	34.1127
UGUUucucucucucugucucucuuucucucucGUacac	chr8:125624702-125624961(-)$1	259	53	91	43.5549
UCACAACCUUCAUUAUCCACCUCCCAAACCAGCUCUUU	chr3:141136119-141136358(+)$1	239	107	145	44.2402
guugcauugcccuaaaaaucuucugucuucugccuguu	chr4:114521203-114521456(-)$1	253	117	155	42.0919
UACACUCUCCACUCCAACCACCCCUCCUUUAUAAGUGA	chr2:149485327-149485611(+)$1	284	129	167	41.9466
gaugaucuaaaaaaaaaaaucacaaaaaagccucacag	chr7:106527331-106527556(+)$1	225	96	134	42.6169
ACCUCAACACAAUUACUUUAUAAUCCAACUUacaacug	chr2:225822806-225823119(-)$1	313	163	201	43.8714
acucuuuaccucccacuuucccuccucccagccuuugg	chr8:124040505-124040777(-)$1	272	63	101	42.9817
guugaucacacggaaagaacacagauuaaaaucagccu	chr22:36659419-36659636(+)$1	217	140	178	41.1822
aguccaaguuuaccucuauuuuagcucuugguauuuua	chr12:88472345-88472566(-)$1	221	119	157	32.1754
GAGAAuauuuucaaaauauaugcagagucugaauacuu	chr12:69647728-69648037(+)$1	309	70	108	35.2412
GCAGGGCAACCACCCCUCACACUCACACUCACACUCUG	chr8:11313299-11313536(-)$1	237	99	137	41.8142
GCAUUCAGGAGAUUUCUUGUUGGCUAAUUCCUCUUGAG	chr6:70400270-70400501(-)$1	231	135	173	33.8363
CUUAAAGACAUGCACAUAAAUUAUCAAAAUACAAUUGU	chr4:36209222-36209511(-)$1	289	124	162	40.4452
AAGAUUCAUUAAAAUAAAGCAAAGAUCCAUGAAUUUUG	chr12:44337831-44338051(+)$1	220	101	139	33.1656
UUUUAACCUUAACAUGAAAUUAACAGAAUGGUAAAGAA	chr1:28223942-28224165(-)$1	223	180	218	38.1130
UCAUuuccuguuccauccaccauacucaaugcucuugc	chr3:49046533-49046837(+)$1	304	104	142	41.9150
CACCAAUUUAAUCAACUCCUCUGCUUUAUCCUCUGCUG	chr13:39587770-39588050(-)$1	280	101	139	42.4639
cacacacacacacacacacacacacacacacacaAGUG	chr4:47427290-47427540(+)$1	250	112	150	42.9120
AUUUUAGACUAUUUUUCUUUCCUUUCUCUGUUUAUCUU	chr8:100213300-100213536(+)$1	236	12	50	36.4354
AAAAGCCCCUUACUCGUUUUAACUAUUCUUCUAAACAU	chr15:65982579-65982820(-)$1	241	125	163	43.1858
uacacauuaccuuacuaacccaccccaaccauccauug	chr11:48087165-48087407(+)$1	242	103	141	42.9075
UCUGCCUCACCUUAUAAUCCCACCCACUCAAGGUAACA	chr5:93699072-93699301(-)$1	229	96	134	36.0449
AAAGCCCCACAAGAGAAAAUUUAUGAAGAUUGGGGUGA	chr11:86519412-86519626(+)$1	214	31	69	36.5015
ugacaauauuacuucacuccccuccauuccugcccuuu	chr13:103290885-103291115(+)$1	230	98	136	42.9936
cacuuuacagaagagaaaauugaggugcagugaaguua	chr22:30740148-30740394(-)$1	246	153	191	37.1579
acacacacauacacacacacacacacacacacacaaaa	chr17:67018528-67018778(-)$1	250	108	146	43.5418
AACUUUUAUUAUACUUUUUCUUUUUACAAAAUAAGAGA	chr10:92638027-92638255(+)$1	228	26	64	40.4452
GGAAUUCUUUCUUUUUCUuucuuuuuuucuuuuuccug	chr14:76869177-76869406(+)$1	229	0	38	40.3956
gcucaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaga	chr14:102877932-102878167(+)$1	235	100	138	44.4490
UUCACUCCAUUUCCCUACUUUCCCUUUUUUUCUGAUAG	chr6:3014799-3015046(+)$1	247	36	74	44.0927
ucacauccuacaaagacauuaauucaaaauggauuaua	chr14:61792020-61792282(+)$1	262	146	184	38.2820
acuacuacuacuacuacuaAUAAUAAUAAUAAUAAUAA	chr13:49717981-49718260(+)$1	279	170	208	43.2313

#DB
((((((........................))))))))	chr14:88419351-88419598(-)$1	1	65	103	42.1262
((.(((................................	chr14:24456691-24456939(+)$1	1	141	179	43.0803
(..(((...................)))...))..).)	chr21:37912286-37912513(-)$1	1	68	106	35.0363
((.(((.........................))).)))	chr2:71574610-71574864(+)$1	1	85	123	41.1310
((((...........................)))))).	chr6:144009892-144010129(+)$1	1	44	82	41.9548
..............................)).)))))	chr15:38758910-38759132(+)$1	1	64	102	41.9880
((.((...........................)).)))	chr17:70822087-70822319(-)$1	1	98	136	41.7411
(((((((((((...................))))))..	chr15:75121288-75121529(+)$1	1	83	121	33.2341
((.............................)))))))	chr1:167634212-167634475(+)$1	1	60	98	43.2403
..............................))))))))	chr8:28771884-28772110(+)$1	1	79	117	42.7128
((.(((..(((...................)))..)))	chr1:26876341-26876557(+)$1	1	79	117	35.5909
(..............................)))).))	chr6:36887482-36887711(+)$1	1	144	182	42.9605
((.(((........................))).).))	chr1:203765353-203765636(+)$1	1	34	72	42.2577
(((((..............................)))	chr3:79590851-79591097(-)$1	1	112	150	44.1367
..((((................................	chr12:51182406-51182632(+)$1	1	32	70	43.1381
(((((((.....................)).)))))..	chrX:21525290-21525540(+)$1	1	139	177	36.7041
(.............................))))).))	chr13:72181563-72181796(-)$1	1	60	98	42.3225
((((((................................	chr3:114373438-114373661(-)$1	1	73	111	42.7422
..((.............................))..)	chr1:159019342-159019611(+)$1	1	60	98	42.7947
(((((.((......................))))))))	chr12:65806400-65806628(+)$1	1	81	119	38.5399
...............................)))).))	chr15:77158480-77158722(-)$1	1	108	146	43.1392
((.................................)))	chr18:60960611-60960966(-)$1	1	191	229	43.7332
(.((((.....................))))))..)))	chr4:42515536-42515825(-)$1	1	156	194	35.2114
((((((.....................))))))(((((	chr14:61176674-61176895(-)$1	1	102	140	35.6169
((((((..(((..................)))..))))	chrX:137858567-137858787(-)$1	1	5	43	34.1127
(((...............................))))	chr8:125624702-125624961(-)$1	1	53	91	43.5549
(((..................................)	chr3:141136119-141136358(+)$1	1	107	145	44.2402
(..(((........................))))))))	chr4:114521203-114521456(-)$1	1	117	155	42.0919
..((((...........................)))).	chr2:149485327-149485611(+)$1	1	129	167	41.9466
(.(((...........................))))))	chr7:106527331-106527556(+)$1	1	96	134	42.6169
...(((..............................))	chr2:225822806-225823119(-)$1	1	163	201	43.8714
..............................).))))))	chr8:124040505-124040777(-)$1	1	63	101	42.9817
((((((........................))))))))	chr22:36659419-36659636(+)$1	1	140	178	41.1822
((((((((..................))))).)))))(	chr12:88472345-88472566(-)$1	1	119	157	32.1754
((((((((((....................))))).))	chr12:69647728-69648037(+)$1	1	70	108	35.2412
((((((...........................)))))	chr8:11313299-11313536(-)$1	1	99	137	41.8142
))(((((((((...................))))))))	chr6:70400270-70400501(-)$1	1	135	173	33.8363
..............................))))))))	chr4:36209222-36209511(-)$1	1	124	162	40.4452
(((((((((...................))))))))).	chr12:44337831-44338051(+)$1	1	101	139	33.1656
(((((.((.....................)))))))))	chr1:28223942-28224165(-)$1	1	180	218	38.1130
..............................))))((((	chr3:49046533-49046837(+)$1	1	104	142	41.9150
((.((............................)).))	chr13:39587770-39588050(-)$1	1	101	139	42.4639
.((((..............................)))	chr4:47427290-47427540(+)$1	1	112	150	42.9120
(...(((((....................)))))...)	chr8:100213300-100213536(+)$1	1	12	50	36.4354
.(((((................................	chr15:65982579-65982820(-)$1	1	125	163	43.1858
)(((((..............................))	chr11:48087165-48087407(+)$1	1	103	141	42.9075
).(((((.......................)))))...	chr5:93699072-93699301(-)$1	1	96	134	36.0449
...((((((.....................))))))))	chr11:86519412-86519626(+)$1	1	31	69	36.5015
.(((((................................	chr13:103290885-103291115(+)$1	1	98	136	42.9936
.(((((((.....................))))))).)	chr22:30740148-30740394(-)$1	1	153	191	37.1579
.(((.(................................	chr17:67018528-67018778(-)$1	1	108	146	43.5418
..............................))))))))	chr10:92638027-92638255(+)$1	1	26	64	40.4452
((((............................))))..	chr14:76869177-76869406(+)$1	1	0	38	40.3956
.....................................)	chr14:102877932-102878167(+)$1	1	100	138	44.4490
................................))).))	chr6:3014799-3015046(+)$1	1	36	74	44.0927
((..((((......................))))....	chr14:61792020-61792282(+)$1	1	146	184	38.2820
.(((((................................	chr13:49717981-49718260(+)$1	1	170	208	43.2313

#PSSM
^ : 0.15	d : 0.12	f : 0.10	e : 0.10	i : 0.08	= : 0.07	b : 0.07	! : 0.07	[ : 0.07	g : 0.05	$ : 0.03	h : 0.01	c : 0.01	" : 0.01	
^ : 0.19	e : 0.14	f : 0.10	! : 0.08	d : 0.08	g : 0.07	= : 0.05	i : 0.05	b : 0.03	[ : 0.03	c : 0.03	" : 0.03	h : 0.01	a : 0.01	: : 0.01	$ : 0.01	
^ : 0.22	e : 0.14	[ : 0.10	f : 0.10	d : 0.08	= : 0.05	! : 0.05	g : 0.05	i : 0.05	c : 0.05	" : 0.03	b : 0.01	$ : 0.01	
^ : 0.26	c : 0.15	f : 0.12	e : 0.12	d : 0.08	= : 0.05	b : 0.05	g : 0.05	i : 0.05	" : 0.01	! : 0.01	
^ : 0.31	c : 0.14	e : 0.14	f : 0.10	d : 0.08	= : 0.05	g : 0.05	i : 0.05	b : 0.03	[ : 0.01	
^ : 0.40	e : 0.14	c : 0.12	f : 0.08	d : 0.07	i : 0.05	[ : 0.03	g : 0.03	= : 0.01	b : 0.01	a : 0.01	
^ : 0.73	e : 0.07	b : 0.05	f : 0.03	! : 0.03	i : 0.03	g : 0.01	d : 0.01	
^ : 0.77	e : 0.05	f : 0.03	! : 0.03	b : 0.03	i : 0.03	g : 0.01	d : 0.01	
^ : 0.85	f : 0.03	c : 0.03	e : 0.03	i : 0.03	
^ : 0.91	c : 0.03	f : 0.01	e : 0.01	i : 0.01	
^ : 0.92	c : 0.03	f : 0.01	i : 0.01	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 0.98	c : 0.01	
^ : 0.96	c : 0.01	e : 0.01	
^ : 0.92	c : 0.01	d : 0.01	f : 0.01	e : 0.01	
^ : 0.89	3 : 0.01	b : 0.01	d : 0.01	f : 0.01	e : 0.01	i : 0.01	
^ : 0.82	b : 0.03	e : 0.03	3 : 0.01	d : 0.01	f : 0.01	c : 0.01	i : 0.01	g : 0.01	
^ : 0.49	e : 0.08	c : 0.07	b : 0.05	f : 0.05	i : 0.05	d : 0.05	g : 0.03	h : 0.03	= : 0.01	3 : 0.01	] : 0.01	a : 0.01	
^ : 0.40	c : 0.08	e : 0.08	b : 0.07	f : 0.07	i : 0.07	d : 0.07	= : 0.03	] : 0.03	g : 0.03	h : 0.03	
^ : 0.33	c : 0.10	e : 0.10	d : 0.08	f : 0.07	i : 0.07	g : 0.07	b : 0.05	= : 0.03	h : 0.03	] : 0.01	2 : 0.01	
^ : 0.26	e : 0.12	d : 0.10	f : 0.08	i : 0.08	2 : 0.07	g : 0.07	c : 0.05	b : 0.05	= : 0.03	h : 0.03	] : 0.01	
^ : 0.24	e : 0.12	f : 0.10	i : 0.10	d : 0.07	g : 0.07	2 : 0.05	= : 0.03	] : 0.03	b : 0.03	c : 0.03	h : 0.03	a : 0.01	3 : 0.01	4 : 0.01	
^ : 0.19	f : 0.12	] : 0.12	d : 0.10	i : 0.10	e : 0.07	g : 0.07	= : 0.05	h : 0.05	a : 0.01	c : 0.01	2 : 0.01	3 : 0.01	: : 0.01	4 : 0.01	
^ : 0.15	f : 0.12	i : 0.10	c : 0.10	d : 0.08	e : 0.08	= : 0.07	h : 0.05	g : 0.05	] : 0.03	3 : 0.03	4 : 0.03	: : 0.03	2 : 0.01	
c : 0.15	^ : 0.12	d : 0.12	f : 0.10	i : 0.08	= : 0.07	h : 0.07	e : 0.07	: : 0.05	3 : 0.03	4 : 0.03	g : 0.03	2 : 0.01	b : 0.01	

#score	2303.480236296944
#seq	57
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m3_run2.txt

#BEAR
[a[ccctttttttttttccc]a	chr9:134166640-134166869(+)$1	229	159	181	21.4518
:ddddvvvvvvvvvvvvvdddd	chr6:39869834-39870093(+)$1	259	134	156	21.6308
cdddduuuuuuuuuuuudddd:	chr2:107502269-107502498(+)$1	229	68	90	22.6659
[dddduuuuuuuuuuuudddd]	chr22:46725918-46726177(+)$1	259	36	58	24.0554
gggggtttttttttttgggggg	chr6:72013067-72013326(-)$1	259	69	91	21.0980
[ddddvvvvvvvvvvvvvdddd	chr17:76495195-76495454(-)$1	259	52	74	22.8673
[dddduuuuuuuuuuuudddda	chr15:63617374-63617604(+)$1	230	14	36	23.7973
""ccctttttttttttccc]ee	chr19:3537171-3537430(-)$1	259	54	76	21.6552
[dddduuuuuuuuuuuuddddc	chr9:27546673-27546902(+)$1	229	154	176	23.7900
ecccwwwwwwwwwwwwwwccc]	chr6:43970565-43970794(+)$1	229	168	190	22.3879
eeeeevvvvvvvvvvvvveeee	chr8:134309893-134310122(+)$1	229	154	176	22.5253
eeeeeuuuuuuuuuuuueeeee	chr1:10075728-10075987(+)$1	259	27	49	23.3379
dyyyyyyyyyyyyyyyydddd3	chr6:44221267-44221496(+)$1	229	139	161	20.7862
fffffvvvvvvvvvvvvvffff	chr10:1094384-1094613(+)$1	229	50	72	21.3930
eeeeeuuuuuuuuuuuueeeee	chr8:133854881-133855140(+)$1	259	159	181	23.3379
eeeeeuuuuuuuuuuuueeeee	chr2:37423614-37423873(+)$1	259	134	156	23.3379
cccxxxxxxxxxxxxxxxccc]	chr2:191555726-191555985(+)$1	259	36	58	18.4440
eeeevvvvvvvvvvvvveeeee	chr18:59829412-59829671(-)$1	259	211	233	22.6723
dd[bbuuuuuuuuuuuubb]dd	chr17:33330051-33330310(+)$1	259	5	27	22.0360
a[ccctttttttttttccc]a]	chr1:86622275-86622534(+)$1	259	196	218	21.6786
!dddduuuuuuuuuuuudddd2	chr2:215275046-215275275(+)$1	229	148	170	23.6834
[bbyyyyyyyyyyyyyyyybb]	chr13:96258101-96258360(+)$1	259	110	132	20.1316
ggggwwwwwwwwwwwwwwgggg	chr21:45114485-45114714(+)$1	229	9	31	22.0691
ee[bbvvvvvvvvvvvvvbb]e	chr11:126159468-126159727(-)$1	259	173	195	21.3355
gggggtttttttttttgggggg	chr6:26217078-26217307(+)$1	229	88	110	21.0980
eecccuuuuuuuuuuuuccc]e	chr22:36885932-36886191(-)$1	259	139	161	23.3068
dddwwwwwwwwwwwwwwdddd3	chr3:185435004-185435233(-)$1	229	160	182	22.3313
[dddduuuuuuuuuuuudddd]	chr5:134779761-134780020(+)$1	259	155	177	24.0554
[dddduuuuuuuuuuuudddda	chr11:46418848-46419107(+)$1	259	139	161	23.7973
fffffuuuuuuuuuuuufffff	chr17:28794169-28794428(+)$1	259	164	186	22.0734
eeeeettttttttttteeeee]	chr22:32353054-32353313(+)$1	259	190	212	21.8252
fffwwwwwwwwwwwwwwfffff	chr3:113372916-113373145(-)$1	229	56	78	21.1473
[cccxxxxxxxxxxxxxxxccc	chr7:5632351-5632610(+)$1	259	130	152	18.2390
d[cccuuuuuuuuuuuucccdd	chr1:41086877-41087136(+)$1	259	141	163	23.1128
fffffuuuuuuuuuuuufffff	chr7:73111892-73112121(+)$1	229	95	117	22.0734
eeewwwwwwwwwwwwwweeeee	chr1:151668097-151668356(-)$1	259	64	86	22.1521
"""bbuuuuuuuuuuuubb444	chr4:103266181-103266410(-)$1	229	60	82	21.7509
ddxxxxxxxxxxxxxxxdddd]	chr17:40125587-40125846(-)$1	259	93	115	18.4220
eeeevvvvvvvvvvvvveeeee	chr18:28573459-28573718(+)$1	259	152	174	22.6723
"eeeeettttttttttteeeee	chr6:165746244-165746473(+)$1	229	8	30	21.4472
eeewwwwwwwwwwwwwweeeee	chr5:132441202-132441431(-)$1	229	75	97	22.1521
ccyyyyyyyyyyyyyyyyccc]	chr8:22550325-22550584(+)$1	259	184	206	21.2123
ccyyyyyyyyyyyyyyyyccc]	chr3:30734737-30734966(-)$1	229	32	54	21.2123
ggggguuuuuuuuuuuuggggg	chr17:6553577-6553836(+)$1	259	57	79	22.9508
"cccyyyyyyyyyyyyyyyycc	chr2:114648107-114648367(+)$1	260	141	163	20.6499
ddddvvvvvvvvvvvvvdddd]	chr3:38032515-38032774(-)$1	259	65	87	23.0093
fffwwwwwwwwwwwwwwfffff	chr17:37687604-37687833(-)$1	229	126	148	21.1473
:dddduuuuuuuuuuuudddde	chr1:52344203-52344432(+)$1	229	77	99	22.6373
!ddddvvvvvvvvvvvvvdddd	chr1:167097933-167098162(-)$1	229	25	47	22.8170
[ddddtttttttttttdddda:	chr17:7612796-7613055(+)$1	259	112	134	21.0221
eeeeevvvvvvvvvvvvveeee	chr17:3796093-3796352(+)$1	259	174	196	22.5253
[dddduuuuuuuuuuuuddddf	chr8:145617647-145617876(+)$1	229	186	208	23.7961
ggggguuuuuuuuuuuuggggg	chr11:117198621-117198850(+)$1	229	76	98	22.9508
ggggwwwwwwwwwwwwwwgggg	chr19:7562305-7562564(+)$1	259	223	245	22.0691
ggggguuuuuuuuuuuuggggg	chr20:13280329-13280558(-)$1	229	51	73	22.9508
[dddduuuuuuuuuuuuddddc	chr16:318479-318738(+)$1	259	4	26	23.7900
gggggtttttttttttgggggg	chr11:506068-506297(+)$1	229	200	222	21.0980
ggggguuuuuuuuuuuuggggg	chr9:112932264-112932523(+)$1	259	125	147	22.9508
ddddvvvvvvvvvvvvvdddd]	chr19:9452100-9452359(-)$1	259	114	136	23.0093

#otherMatches

#Seq PSSM
AGUUACAAUAAAAACACGUAUC	chr9:134166640-134166869(+)$1	229	159	181	21.4518
UCCCCACGCUUACCUUAAGGGG	chr6:39869834-39870093(+)$1	259	134	156	21.6308
GGGGCACAACUGUAUCCGCCCG	chr2:107502269-107502498(+)$1	229	68	90	22.6659
GAGCUCCCCUCUGAUCCAGCUG	chr22:46725918-46726177(+)$1	259	36	58	24.0554
GAAUUUCUUAUUUUUUAAUUCU	chr6:72013067-72013326(-)$1	259	69	91	21.0980
UGGCUCUUCCUCGUGUCCAGCC	chr17:76495195-76495454(-)$1	259	52	74	22.8673
AGAGAAGUAGAUAAAAGUCUCC	chr15:63617374-63617604(+)$1	230	14	36	23.7973
CUCCCAACCACUGCCAGGGUCG	chr19:3537171-3537430(-)$1	259	54	76	21.6552
ACAUCUUUCUGAUUCAUGAUGG	chr9:27546673-27546902(+)$1	229	154	176	23.7900
CCUCCUACAACACACCCCGAGC	chr6:43970565-43970794(+)$1	229	168	190	22.3879
AGGCUCCCUCCGAUUCUCAGCC	chr8:134309893-134310122(+)$1	229	154	176	22.5253
AACACAAUAAAAAAUAAGUGUU	chr1:10075728-10075987(+)$1	259	27	49	23.3379
UGCCCCUGUCCCACCUGGCUCC	chr6:44221267-44221496(+)$1	229	139	161	20.7862
UUUCUGAAUUCUCUAAGGGGAG	chr10:1094384-1094613(+)$1	229	50	72	21.3930
UGGAAGAAGAACAAGAAUUCCA	chr8:133854881-133855140(+)$1	259	159	181	23.3379
GCCUCGUCACAGUUCUGGGGGC	chr2:37423614-37423873(+)$1	259	134	156	23.3379
UCUUAAACUAGUUGACCUAGAU	chr2:191555726-191555985(+)$1	259	36	58	18.4440
AAUGUUUCAUAUUGCUUCGUUU	chr18:59829412-59829671(-)$1	259	211	233	22.6723
GCAGGAGAUAGAACAGCCCGGC	chr17:33330051-33330310(+)$1	259	5	27	22.0360
GGCCUGGGAGGAGAAAGGGGUG	chr1:86622275-86622534(+)$1	259	196	218	21.6786
UGUUACUAAUAAAAAAAUAACU	chr2:215275046-215275275(+)$1	229	148	170	23.6834
GGUGGCAACUGCACAUAAAACG	chr13:96258101-96258360(+)$1	259	110	132	20.1316
UGGCGUGCAGCUCUCCCAGCCA	chr21:45114485-45114714(+)$1	229	9	31	22.0691
AGAUCAAAACAAACCUGAGAAC	chr11:126159468-126159727(-)$1	259	173	195	21.3355
GUGGAUUGUUAGUUCUUCUGCU	chr6:26217078-26217307(+)$1	229	88	110	21.0980
GUCCCUUCCUAAGCUGUGGGCA	chr22:36885932-36886191(-)$1	259	139	161	23.3068
UGAAAUACAUGCCAGAGUCACG	chr3:185435004-185435233(-)$1	229	160	182	22.3313
AGGUUUUAUUUCACUUUAAUCC	chr5:134779761-134780020(+)$1	259	155	177	24.0554
CAACGUUUGUCUCUACCUGUUC	chr11:46418848-46419107(+)$1	259	139	161	23.7973
UUAAUAAAAGCAAAGUGAUUGA	chr17:28794169-28794428(+)$1	259	164	186	22.0734
GAGAGACAACUUGCUCCUUUCC	chr22:32353054-32353313(+)$1	259	190	212	21.8252
AGCCGUAAAUAUAGAAAGCUAA	chr3:113372916-113373145(-)$1	229	56	78	21.1473
AGCCGAACAAAGGAGCAGGGGC	chr7:5632351-5632610(+)$1	259	130	152	18.2390
UGUCUCAUCAUUACACAAGAAU	chr1:41086877-41087136(+)$1	259	141	163	23.1128
UGCUGGAGAAGAAGGAGCGGCA	chr7:73111892-73112121(+)$1	229	95	117	22.0734
UGCUUUCUUUCCUCUAUGUAAG	chr1:151668097-151668356(-)$1	259	64	86	22.1521
GCGGCGGAGAGAAUAAAGCAGA	chr4:103266181-103266410(-)$1	229	60	82	21.7509
GCUGCCCCCCUUCUCCUGCCGC	chr17:40125587-40125846(-)$1	259	93	115	18.4220
GGCACUUCAACACAUUUUGCCU	chr18:28573459-28573718(+)$1	259	152	174	22.6723
GCAAGUCAAAUGGAGUCACUUG	chr6:165746244-165746473(+)$1	229	8	30	21.4472
UGUAACAGUUUCUUAAAGCAGG	chr5:132441202-132441431(-)$1	229	75	97	22.1521
CUCCUAACGCAGCUUCCAGGCA	chr8:22550325-22550584(+)$1	259	184	206	21.2123
UCAAAAAGUUUUAAAAAAGAGA	chr3:30734737-30734966(-)$1	229	32	54	21.2123
AUUAAUAGCUACUCAAUUUAAU	chr17:6553577-6553836(+)$1	259	57	79	22.9508
CGGCUUUCCUUUCCCUCCGCGC	chr2:114648107-114648367(+)$1	260	141	163	20.6499
GCCCUUCCUUCUUUUGUGGGUA	chr3:38032515-38032774(-)$1	259	65	87	23.0093
AGGAAUACAACGGACAGCUUUG	chr17:37687604-37687833(-)$1	229	126	148	21.1473
UCAGCAUUCACCACCAAGCUGG	chr1:52344203-52344432(+)$1	229	77	99	22.6373
ACACUGCCAAAUACAUUAAGUG	chr1:167097933-167098162(-)$1	229	25	47	22.8170
UGGCUAUCCUGAAUCCAGCCCU	chr17:7612796-7613055(+)$1	259	112	134	21.0221
gcggccccACUCGCUCCUGCUG	chr17:3796093-3796352(+)$1	259	174	196	22.5253
UGCGCAACAUCAACACCGUGCG	chr8:145617647-145617876(+)$1	229	186	208	23.7961
UGGGGGAUAGUUGAGGACCUCA	chr11:117198621-117198850(+)$1	229	76	98	22.9508
AAUUUUCUAAaacucauugauu	chr19:7562305-7562564(+)$1	259	223	245	22.0691
UGUAUUAAAUAAGUUAUAUAUA	chr20:13280329-13280558(-)$1	229	51	73	22.9508
ACUUGGGGGAUGGGGAGCAAGG	chr16:318479-318738(+)$1	259	4	26	23.7900
GGCCUGCCUGGUUCUAAGGCCC	chr11:506068-506297(+)$1	229	200	222	21.0980
UUUAAUCUUUCUGUCAUUUAAA	chr9:112932264-112932523(+)$1	259	125	147	22.9508
UGCCAUUUUCAUUGCAAGGCAU	chr19:9452100-9452359(-)$1	259	114	136	23.0093

#DB
.(.(((...........))).)	chr9:134166640-134166869(+)$1	1	159	181	21.4518
.((((.............))))	chr6:39869834-39870093(+)$1	1	134	156	21.6308
)((((............)))).	chr2:107502269-107502498(+)$1	1	68	90	22.6659
.((((............)))).	chr22:46725918-46726177(+)$1	1	36	58	24.0554
(((((...........))))))	chr6:72013067-72013326(-)$1	1	69	91	21.0980
.((((.............))))	chr17:76495195-76495454(-)$1	1	52	74	22.8673
.((((............)))))	chr15:63617374-63617604(+)$1	1	14	36	23.7973
..(((...........))).))	chr19:3537171-3537430(-)$1	1	54	76	21.6552
.((((............)))))	chr9:27546673-27546902(+)$1	1	154	176	23.7900
((((..............))).	chr6:43970565-43970794(+)$1	1	168	190	22.3879
(((((.............))))	chr8:134309893-134310122(+)$1	1	154	176	22.5253
(((((............)))))	chr1:10075728-10075987(+)$1	1	27	49	23.3379
(................)))).	chr6:44221267-44221496(+)$1	1	139	161	20.7862
(((((.............))))	chr10:1094384-1094613(+)$1	1	50	72	21.3930
(((((............)))))	chr8:133854881-133855140(+)$1	1	159	181	23.3379
(((((............)))))	chr2:37423614-37423873(+)$1	1	134	156	23.3379
(((...............))).	chr2:191555726-191555985(+)$1	1	36	58	18.4440
((((.............)))))	chr18:59829412-59829671(-)$1	1	211	233	22.6723
((.((............)).))	chr17:33330051-33330310(+)$1	1	5	27	22.0360
(.(((...........))).).	chr1:86622275-86622534(+)$1	1	196	218	21.6786
.((((............)))).	chr2:215275046-215275275(+)$1	1	148	170	23.6834
.((................)).	chr13:96258101-96258360(+)$1	1	110	132	20.1316
((((..............))))	chr21:45114485-45114714(+)$1	1	9	31	22.0691
((.((.............)).)	chr11:126159468-126159727(-)$1	1	173	195	21.3355
(((((...........))))))	chr6:26217078-26217307(+)$1	1	88	110	21.0980
(((((............))).)	chr22:36885932-36886191(-)$1	1	139	161	23.3068
(((..............)))).	chr3:185435004-185435233(-)$1	1	160	182	22.3313
.((((............)))).	chr5:134779761-134780020(+)$1	1	155	177	24.0554
.((((............)))))	chr11:46418848-46419107(+)$1	1	139	161	23.7973
(((((............)))))	chr17:28794169-28794428(+)$1	1	164	186	22.0734
(((((...........))))).	chr22:32353054-32353313(+)$1	1	190	212	21.8252
(((..............)))))	chr3:113372916-113373145(-)$1	1	56	78	21.1473
.(((...............)))	chr7:5632351-5632610(+)$1	1	130	152	18.2390
(.(((............)))))	chr1:41086877-41087136(+)$1	1	141	163	23.1128
(((((............)))))	chr7:73111892-73112121(+)$1	1	95	117	22.0734
(((..............)))))	chr1:151668097-151668356(-)$1	1	64	86	22.1521
...((............))...	chr4:103266181-103266410(-)$1	1	60	82	21.7509
((...............)))).	chr17:40125587-40125846(-)$1	1	93	115	18.4220
((((.............)))))	chr18:28573459-28573718(+)$1	1	152	174	22.6723
.(((((...........)))))	chr6:165746244-165746473(+)$1	1	8	30	21.4472
(((..............)))))	chr5:132441202-132441431(-)$1	1	75	97	22.1521
((................))).	chr8:22550325-22550584(+)$1	1	184	206	21.2123
((................))).	chr3:30734737-30734966(-)$1	1	32	54	21.2123
(((((............)))))	chr17:6553577-6553836(+)$1	1	57	79	22.9508
.(((................))	chr2:114648107-114648367(+)$1	1	141	163	20.6499
((((.............)))).	chr3:38032515-38032774(-)$1	1	65	87	23.0093
(((..............)))))	chr17:37687604-37687833(-)$1	1	126	148	21.1473
.((((............))))(	chr1:52344203-52344432(+)$1	1	77	99	22.6373
.((((.............))))	chr1:167097933-167098162(-)$1	1	25	47	22.8170
.((((...........))))).	chr17:7612796-7613055(+)$1	1	112	134	21.0221
(((((.............))))	chr17:3796093-3796352(+)$1	1	174	196	22.5253
.((((............)))))	chr8:145617647-145617876(+)$1	1	186	208	23.7961
(((((............)))))	chr11:117198621-117198850(+)$1	1	76	98	22.9508
((((..............))))	chr19:7562305-7562564(+)$1	1	223	245	22.0691
(((((............)))))	chr20:13280329-13280558(-)$1	1	51	73	22.9508
.((((............)))))	chr16:318479-318738(+)$1	1	4	26	23.7900
(((((...........))))))	chr11:506068-506297(+)$1	1	200	222	21.0980
(((((............)))))	chr9:112932264-112932523(+)$1	1	125	147	22.9508
((((.............)))).	chr19:9452100-9452359(-)$1	1	114	136	23.0093

#PSSM
e : 0.22	[ : 0.20	g : 0.15	d : 0.11	f : 0.08	c : 0.06	" : 0.06	: : 0.03	! : 0.03	a : 0.01	
d : 0.32	e : 0.22	g : 0.15	c : 0.10	f : 0.08	" : 0.03	[ : 0.03	a : 0.01	y : 0.01	b : 0.01	
d : 0.28	e : 0.18	g : 0.15	c : 0.13	f : 0.08	[ : 0.05	y : 0.05	b : 0.01	" : 0.01	x : 0.01	
d : 0.27	g : 0.15	e : 0.15	c : 0.13	w : 0.08	y : 0.06	f : 0.05	b : 0.05	x : 0.03	
d : 0.23	w : 0.13	g : 0.11	e : 0.11	c : 0.08	y : 0.08	v : 0.06	f : 0.05	x : 0.05	b : 0.05	
u : 0.38	v : 0.18	w : 0.13	t : 0.11	y : 0.08	x : 0.05	c : 0.01	e : 0.01	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	t : 0.15	w : 0.13	y : 0.08	x : 0.05	
u : 0.38	v : 0.18	w : 0.13	y : 0.08	g : 0.05	x : 0.05	t : 0.03	c : 0.03	e : 0.01	d : 0.01	
d : 0.27	e : 0.15	v : 0.11	g : 0.11	c : 0.08	y : 0.06	f : 0.06	w : 0.05	x : 0.03	b : 0.03	
d : 0.32	e : 0.18	c : 0.15	g : 0.15	f : 0.08	b : 0.05	y : 0.03	x : 0.01	
d : 0.32	e : 0.18	g : 0.15	c : 0.13	f : 0.08	] : 0.05	b : 0.03	4 : 0.01	y : 0.01	
d : 0.33	e : 0.20	g : 0.15	c : 0.10	f : 0.08	] : 0.05	a : 0.03	b : 0.01	4 : 0.01	
e : 0.23	] : 0.20	g : 0.15	f : 0.10	d : 0.08	c : 0.06	a : 0.05	: : 0.03	3 : 0.03	2 : 0.01	4 : 0.01	

#score	1305.6261966339746
#seq	59
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m1_run1.txt

#BEAR
eeffffffwwwwwwwwwwwwwwffff	chr14:56101166-56101546(+)$1	380	6	32	21.4855
:ffffffuuuuuuuuuuuuffffff:	chr11:66947574-66947825(+)$1	251	70	96	20.7357
hhh[cccvvvvvvvvvvvvvccc]hh	chr2:136362394-136362652(+)$1	258	114	140	22.8097
cgggggggtttttttttttggggggg	chr17:27443316-27443576(+)$1	260	180	206	24.2443
!cccddddtttttttttttdddd]cc	chr11:70271340-70271687(+)$1	347	254	280	22.5427
hhhhhhhhvvvvvvvvvvvvvhhhhh	chr19:55493479-55493772(+)$1	293	110	136	21.8479
%gggggggyyyyyyyyyyyyyyyygg	chr12:67692717-67693046(+)$1	329	234	260	20.9808
#gggggggvvvvvvvvvvvvvggggg	chr5:151170457-151170751(+)$1	294	253	279	24.7502
====!!bbvvvvvvvvvvvvvbb===	chr17:8508018-8508285(+)$1	267	139	165	23.5550
:ggggggguuuuuuuuuuuugggggg	chr18:3277211-3277546(+)$1	335	268	294	24.0447
!ddddccctttttttttttccc]ddd	chr5:179047722-179048089(+)$1	367	33	59	22.6481
hhhhhhhhwwwwwwwwwwwwwwhhhh	chr5:131915551-131915844(+)$1	293	261	287	20.4877
egggggggwwwwwwwwwwwwwwgggg	chr14:70234869-70235173(+)$1	304	239	265	22.8571
ggffffffvvvvvvvvvvvvvfffff	chr10:33200846-33201099(+)$1	253	39	65	23.4026
:gggggggtttttttttttggggggg	chr1:33059069-33059493(+)$1	424	185	211	23.7388
========vvvvvvvvvvvvv=====	chr12:32875449-32875752(+)$1	303	221	247	24.5882
3ddddcccuuuuuuuuuuuuccc::J	chr12:7027094-7027401(+)$1	307	118	144	19.5540
:dddd[bbvvvvvvvvvvvvvbbddd	chr2:55209567-55209831(+)$1	264	61	87	21.3407
:ggggggguuuuuuuuuuuugggggg	chr1:218475598-218475887(+)$1	289	228	254	24.0447
:eeeeevvvvvvvvvvvvveeeeeff	chr6:76343206-76343552(+)$1	346	256	282	20.8565
ggggg[bbuuuuuuuuuuuubbgggg	chr21:27269767-27270017(+)$1	250	219	245	23.7543
ccc!!cccyyyyyyyyyyyyyyyycc	chr10:64948795-64949095(+)$1	300	169	195	20.8871
gg"""ccctttttttttttccc333g	chr12:123003293-123003597(+)$1	304	64	90	23.6170
b[ffffffyyyyyyyyyyyyyyyyff	chr12:16516797-16517122(+)$1	325	68	94	20.4458
:ccc[bbvvvvvvvvvvvvvbb]ccc	chr17:78263436-78263753(+)$1	317	134	160	22.1598
ffffddddtttttttttttdddd22f	chr15:35083207-35083466(+)$1	259	100	126	21.4813
c[a!!avvvvvvvvvvvvva22a]cc	chr12:112888127-112888424(+)$1	297	143	169	22.0615
:gggggggtttttttttttggggggg	chr2:102493462-102493752(+)$1	290	260	286	23.7388
iiii[cccuuuuuuuuuuuuccciii	chr5:72161375-72161664(+)$1	289	190	216	24.5063
d[ffffffuuuuuuuuuuuuffffff	chr17:34149659-34149990(+)$1	331	21	47	23.1209
Hgggggggtttttttttttggggggg	chr1:153735156-153735446(+)$1	290	264	290	23.8600
=====cccvvvvvvvvvvvvvccc22	chr16:31004330-31004603(+)$1	273	228	254	24.0514
dgggggggtttttttttttggggggg	chr2:136511693-136511965(+)$1	272	192	218	24.0187
c[ffffffwwwwwwwwwwwwwwffff	chr9:130985028-130985305(+)$1	277	203	229	21.9825
+gggggggwwwwwwwwwwwwwwgggg	chr13:98662298-98662650(+)$1	352	44	70	22.7215
!!bb[cccwwwwwwwwwwwwwwcccb	chr2:191769746-191770004(+)$1	258	24	50	21.9332
Hffffffvvvvvvvvvvvvvffffff	chr9:100767206-100767559(+)$1	353	33	59	22.3889
"""eeeeeyyyyyyyyyyyyyyyyee	chr11:62649353-62649700(+)$1	347	157	183	20.2495
cc[eeeeeuuuuuuuuuuuueeeee2	chr10:112343898-112344316(+)$1	418	347	373	23.0943
[gggggggtttttttttttggggggg	chr5:138661058-138661498(+)$1	440	270	296	24.2977
:ccc[ccctttttttttttcccccc:	chr4:48851919-48852230(+)$1	311	246	272	22.5326
h[cccyyyyyyyyyyyyyyyyccc22	chr6:4044034-4044363(+)$1	329	7	33	20.2139
::fffffftttttttttttffffff:	chr12:76446866-76447153(+)$1	287	13	39	20.5619
fffffwwwwwwwwwwwwwwffffff]	chr19:35500712-35501045(+)$1	333	203	229	19.8015
a!!eeeeettttttttttteeeee22	chr15:85402411-85402696(+)$1	285	81	107	22.8894
:eeeeewwwwwwwwwwwwwweeeee:	chr2:198353580-198353833(+)$1	253	145	171	19.5534
cc[eeeeevvvvvvvvvvvvveeeee	chr2:219612306-219612609(+)$1	303	8	34	23.1923
===[ddddvvvvvvvvvvvvvdddd2	chr12:56575345-56575610(+)$1	265	59	85	22.7951
gggeeeeettttttttttteeeee55	chr5:154179119-154179473(+)$1	354	180	206	21.3071
b!!eeeeevvvvvvvvvvvvveeeee	chr21:34926995-34927330(+)$1	335	85	111	23.2332
hhhh[ccctttttttttttccchhhh	chr16:89383246-89383513(+)$1	267	84	110	22.7136
ff:cccbbtttttttttttbb]ccc:	chr4:48859223-48859486(+)$1	263	123	149	20.5247
::fffffftttttttttttffffff:	chr4:174253017-174253358(+)$1	341	281	307	20.5619
:gggggggvvvvvvvvvvvvvggggg	chr21:34931883-34932179(+)$1	296	149	175	24.1533
========ttttttttttt=======	chr15:41770665-41770947(+)$1	282	4	30	24.3851
========vvvvvvvvvvvvv=====	chr1:24975279-24975682(+)$1	403	108	134	24.5882
###dddduuuuuuuuuuuudddd444	chr7:134552386-134552713(+)$1	327	185	211	21.2278
"ggggggguuuuuuuuuuuugggggg	chr6:30546173-30546491(+)$1	318	118	144	24.6590
""ccc[bbtttttttttttbb]ccc3	chr6:99914428-99914693(+)$1	265	116	142	23.1136
iiiiiiiitttttttttttiiiiiii	chr19:1418167-1418428(+)$1	261	122	148	24.0719
========ttttttttttt=======	chr15:40504670-40504963(+)$1	293	112	138	24.3851
!!dddd[auuuuuuuuuuuuadddd2	chr5:179757557-179757836(+)$1	279	171	197	22.9007
::eeeeeuuuuuuuuuuuueeeeehh	chr10:43089612-43089922(+)$1	310	57	83	20.1959
:ccc!!bbtttttttttttbb22ccc	chr7:33397397-33397692(+)$1	295	127	153	21.9859

#otherMatches

#Seq PSSM
AAGUAUGUUUUGUUUAUUUCUUAUAU	chr14:56101166-56101546(+)$1	380	6	32	21.4855
CAACAAAUAUAAUGCCAAUUUUGUUA	chr11:66947574-66947825(+)$1	251	70	96	20.7357
CUUAUCAAAUCAGAAAACUAUGGGAA	chr2:136362394-136362652(+)$1	258	114	140	22.8097
CAGCAUGCAAAGAAAAACAGUGUGUU	chr17:27443316-27443576(+)$1	260	180	206	24.2443
UGCACCACUAGUUGAAAGCGUGGUUG	chr11:70271340-70271687(+)$1	347	254	280	22.5427
GGCCUGGAGAUAGCAAAGAGGUCCAG	chr19:55493479-55493772(+)$1	293	110	136	21.8479
GUACUGUUUGUUUUAUuuaguuauaa	chr12:67692717-67693046(+)$1	329	234	260	20.9808
aauuucagacuuacagaaaacuugga	chr5:151170457-151170751(+)$1	294	253	279	24.7502
CUGUAAGCAGAUUCAGAUAUAGCAUA	chr17:8508018-8508285(+)$1	267	139	165	23.5550
GGUUUUCUUUUUUUACCUUUAGAAAA	chr18:3277211-3277546(+)$1	335	268	294	24.0447
UCUAGGAAGAAAACAUUAAUUCAUUG	chr5:179047722-179048089(+)$1	367	33	59	22.6481
caugauguuuugauauaaguauacau	chr5:131915551-131915844(+)$1	293	261	287	20.4877
CAGCCUUAUGUCUGAAUUUUAUUGAG	chr14:70234869-70235173(+)$1	304	239	265	22.8571
CAUUUGUAUUAUCCCUCUUCCUACAA	chr10:33200846-33201099(+)$1	253	39	65	23.4026
CCAGUCUGAAGAACAAGCACAGAUUG	chr1:33059069-33059493(+)$1	424	185	211	23.7388
UCUAUAAAACAAAAAUAUAACUUUGU	chr12:32875449-32875752(+)$1	303	221	247	24.5882
GUGCAGAGGUCUACCAUACACUCAAG	chr12:7027094-7027401(+)$1	307	118	144	19.5540
AUGAAAGGCAAAAUAAACUUACCUUC	chr2:55209567-55209831(+)$1	264	61	87	21.3407
AUUCUGGUCAAAAAUAAGAAGCUGGA	chr1:218475598-218475887(+)$1	289	228	254	24.0447
AUUCCUACAGAAAAGAUAAAGGAAGA	chr6:76343206-76343552(+)$1	346	256	282	20.8565
UGUAUUACAUCAUAAUUAAAGUAUGC	chr21:27269767-27270017(+)$1	250	219	245	23.7543
UUACUGCUAUUCUUAUAAUCCUUAAG	chr10:64948795-64949095(+)$1	300	169	195	20.8871
UACUACAUUAUAAUACAACAUGACUU	chr12:123003293-123003597(+)$1	304	64	90	23.6170
CAUAUUUGACACCCCUUCCCCAGCCA	chr12:16516797-16517122(+)$1	325	68	94	20.4458
AGCUGCUGUGAAAAACGAGAAGGAGC	chr17:78263436-78263753(+)$1	317	134	160	22.1598
UCUUUACCUUAAUCUUCAUGGUGCUA	chr15:35083207-35083466(+)$1	259	100	126	21.4813
UUGAGCUUAAAUAUCCUCUGAACUGU	chr12:112888127-112888424(+)$1	297	143	169	22.0615
CCACAUUGAGACUUGACAAUAAUGUG	chr2:102493462-102493752(+)$1	290	260	286	23.7388
UUGCCAGUACUAAUUGAUUAACUGUG	chr5:72161375-72161664(+)$1	289	190	216	24.5063
UAUGGUCAACAAGAUUCAUAUGACCA	chr17:34149659-34149990(+)$1	331	21	47	23.1209
CCUGUGAGUUAAAGUUUUGUUCACAG	chr1:153735156-153735446(+)$1	290	264	290	23.8600
UCCCUGCAGACAGAGGAGACAUGCAC	chr16:31004330-31004603(+)$1	273	228	254	24.0514
GUCAGGAAUUGGAuuuuuuuuuuuga	chr2:136511693-136511965(+)$1	272	192	218	24.0187
AAGGACUGAAAGCUCUGUUCCCCAGU	chr9:130985028-130985305(+)$1	277	203	229	21.9825
UUCUCCGUUAAUAGCCCAAGACAUGG	chr13:98662298-98662650(+)$1	352	44	70	22.7215
CCUGUGUAAAACCUUUGAAAUAUGCC	chr2:191769746-191770004(+)$1	258	24	50	21.9332
CUUCAGAAAAAGUUAGAAUGUCUGAA	chr9:100767206-100767559(+)$1	353	33	59	22.3889
AGUCUCUUGCAAUCGGCUAAAAAAAA	chr11:62649353-62649700(+)$1	347	157	183	20.2495
CUACAUGUUGCUCUUAAAAUAUAUGA	chr10:112343898-112344316(+)$1	418	347	373	23.0943
AUAUCAGCCCAAUGUUCCUGUUGGUG	chr5:138661058-138661498(+)$1	440	270	296	24.2977
CUCAUGGCUCAAAAACAUUGCCUGAA	chr4:48851919-48852230(+)$1	311	246	272	22.5326
UACAGAAAUAUAAAUACCUUGCUGAA	chr6:4044034-4044363(+)$1	329	7	33	20.2139
ACUCUCAGGAACUGCAAAAUUGAGAA	chr12:76446866-76447153(+)$1	287	13	39	20.5619
CUGUGACUCUCCGCCAGCCCGCGGGC	chr19:35500712-35501045(+)$1	333	203	229	19.8015
GAUUCGGGUGGAGCAGUUUCCUGAUG	chr15:85402411-85402696(+)$1	285	81	107	22.8894
CUUCAGCACAGCCACUCCAUCUGAAA	chr2:198353580-198353833(+)$1	253	145	171	19.5534
UGUAGGUAUCUACACAAACCCUACCU	chr2:219612306-219612609(+)$1	303	8	34	23.1923
AAUGUCAGCCUACAAUCCCCACUGAA	chr12:56575345-56575610(+)$1	265	59	85	22.7951
GCACUACCAAAAGGAGACAGGUAGGU	chr5:154179119-154179473(+)$1	354	180	206	21.3071
AAAGAGAUCAUCUAAGUCCAAGUCUC	chr21:34926995-34927330(+)$1	335	85	111	23.2332
GCAGCAUUACCUUUUUCCCAGUCUGC	chr16:89383246-89383513(+)$1	267	84	110	22.7136
UCAGGCCUAUGCAUGAAAGAGUGCCA	chr4:48859223-48859486(+)$1	263	123	149	20.5247
cugguucguucuucuucuuUGAGCCU	chr4:174253017-174253358(+)$1	341	281	307	20.5619
AGAAAACAAAGAUGAUGAUAAUGUUU	chr21:34931883-34932179(+)$1	296	149	175	24.1533
UAUUUGCCUGUGAGCUUAUGGUGAAU	chr15:41770665-41770947(+)$1	282	4	30	24.3851
AUUUUUGAAUGGAAAAAAUGCUCGAG	chr1:24975279-24975682(+)$1	403	108	134	24.5882
AAAAAUACUUGUAUUCCCUUAUUAAC	chr7:134552386-134552713(+)$1	327	185	211	21.2278
GAGGAGGAGGAAGAAAAACAUCCUCC	chr6:30546173-30546491(+)$1	318	118	144	24.6590
UACAUUUGCACAUUCUUCACACAUGA	chr6:99914428-99914693(+)$1	265	116	142	23.1136
UUGGGUUUGUCAAAUUUAAAGACCCA	chr19:1418167-1418428(+)$1	261	122	148	24.0719
CAGCUGUUAUCAAUAUCAAGAUGGCU	chr15:40504670-40504963(+)$1	293	112	138	24.3851
UUGAAAACGUAAUGUCCUCAGUUUCU	chr5:179757557-179757836(+)$1	279	171	197	22.9007
UCUGCAUUCUCUCUCUUCCGUGUAUU	chr10:43089612-43089922(+)$1	310	57	83	20.1959
AGGUCAGCCUUCAAAAACUGCAAGCC	chr7:33397397-33397692(+)$1	295	127	153	21.9859

#DB
((((((((..............))))	chr14:56101166-56101546(+)$1	1	6	32	21.4855
.((((((............)))))).	chr11:66947574-66947825(+)$1	1	70	96	20.7357
(((.(((.............))).))	chr2:136362394-136362652(+)$1	1	114	140	22.8097
((((((((...........)))))))	chr17:27443316-27443576(+)$1	1	180	206	24.2443
.(((((((...........)))).))	chr11:70271340-70271687(+)$1	1	254	280	22.5427
((((((((.............)))))	chr19:55493479-55493772(+)$1	1	110	136	21.8479
.(((((((................))	chr12:67692717-67693046(+)$1	1	234	260	20.9808
.(((((((.............)))))	chr5:151170457-151170751(+)$1	1	253	279	24.7502
((((..((.............)))))	chr17:8508018-8508285(+)$1	1	139	165	23.5550
.(((((((............))))))	chr18:3277211-3277546(+)$1	1	268	294	24.0447
.(((((((...........))).)))	chr5:179047722-179048089(+)$1	1	33	59	22.6481
((((((((..............))))	chr5:131915551-131915844(+)$1	1	261	287	20.4877
)(((((((..............))))	chr14:70234869-70235173(+)$1	1	239	265	22.8571
))((((((.............)))))	chr10:33200846-33201099(+)$1	1	39	65	23.4026
.(((((((...........)))))))	chr1:33059069-33059493(+)$1	1	185	211	23.7388
((((((((.............)))))	chr12:32875449-32875752(+)$1	1	221	247	24.5882
.))))(((............)))..)	chr12:7027094-7027401(+)$1	1	118	144	19.5540
.((((.((.............)))))	chr2:55209567-55209831(+)$1	1	61	87	21.3407
.(((((((............))))))	chr1:218475598-218475887(+)$1	1	228	254	24.0447
.(((((.............)))))((	chr6:76343206-76343552(+)$1	1	256	282	20.8565
(((((.((............))))))	chr21:27269767-27270017(+)$1	1	219	245	23.7543
(((..(((................))	chr10:64948795-64949095(+)$1	1	169	195	20.8871
((...(((...........)))...)	chr12:123003293-123003597(+)$1	1	64	90	23.6170
(.((((((................))	chr12:16516797-16517122(+)$1	1	68	94	20.4458
.(((.((.............)).)))	chr17:78263436-78263753(+)$1	1	134	160	22.1598
((((((((...........))))..)	chr15:35083207-35083466(+)$1	1	100	126	21.4813
(.(..(.............)..).))	chr12:112888127-112888424(+)$1	1	143	169	22.0615
.(((((((...........)))))))	chr2:102493462-102493752(+)$1	1	260	286	23.7388
((((.(((............))))))	chr5:72161375-72161664(+)$1	1	190	216	24.5063
(.((((((............))))))	chr17:34149659-34149990(+)$1	1	21	47	23.1209
)(((((((...........)))))))	chr1:153735156-153735446(+)$1	1	264	290	23.8600
((((((((.............)))..	chr16:31004330-31004603(+)$1	1	228	254	24.0514
)(((((((...........)))))))	chr2:136511693-136511965(+)$1	1	192	218	24.0187
(.((((((..............))))	chr9:130985028-130985305(+)$1	1	203	229	21.9825
.(((((((..............))))	chr13:98662298-98662650(+)$1	1	44	70	22.7215
..((.(((..............))))	chr2:191769746-191770004(+)$1	1	24	50	21.9332
(((((((.............))))))	chr9:100767206-100767559(+)$1	1	33	59	22.3889
...(((((................))	chr11:62649353-62649700(+)$1	1	157	183	20.2495
((.(((((............))))).	chr10:112343898-112344316(+)$1	1	347	373	23.0943
.(((((((...........)))))))	chr5:138661058-138661498(+)$1	1	270	296	24.2977
.(((.(((...........)))))).	chr4:48851919-48852230(+)$1	1	246	272	22.5326
(.(((................)))..	chr6:4044034-4044363(+)$1	1	7	33	20.2139
..((((((...........)))))).	chr12:76446866-76447153(+)$1	1	13	39	20.5619
(((((..............)))))).	chr19:35500712-35501045(+)$1	1	203	229	19.8015
(..(((((...........)))))..	chr15:85402411-85402696(+)$1	1	81	107	22.8894
.(((((..............))))).	chr2:198353580-198353833(+)$1	1	145	171	19.5534
((.(((((.............)))))	chr2:219612306-219612609(+)$1	1	8	34	23.1923
(((.((((.............)))).	chr12:56575345-56575610(+)$1	1	59	85	22.7951
((((((((...........)))))..	chr5:154179119-154179473(+)$1	1	180	206	21.3071
(..(((((.............)))))	chr21:34926995-34927330(+)$1	1	85	111	23.2332
((((.(((...........)))))))	chr16:89383246-89383513(+)$1	1	84	110	22.7136
)).(((((...........)).))).	chr4:48859223-48859486(+)$1	1	123	149	20.5247
..((((((...........)))))).	chr4:174253017-174253358(+)$1	1	281	307	20.5619
.(((((((.............)))))	chr21:34931883-34932179(+)$1	1	149	175	24.1533
((((((((...........)))))))	chr15:41770665-41770947(+)$1	1	4	30	24.3851
((((((((.............)))))	chr1:24975279-24975682(+)$1	1	108	134	24.5882
...((((............))))...	chr7:134552386-134552713(+)$1	1	185	211	21.2278
.(((((((............))))))	chr6:30546173-30546491(+)$1	1	118	144	24.6590
..(((.((...........)).))).	chr6:99914428-99914693(+)$1	1	116	142	23.1136
((((((((...........)))))))	chr19:1418167-1418428(+)$1	1	122	148	24.0719
((((((((...........)))))))	chr15:40504670-40504963(+)$1	1	112	138	24.3851
..((((.(............))))).	chr5:179757557-179757836(+)$1	1	171	197	22.9007
..(((((............)))))((	chr10:43089612-43089922(+)$1	1	57	83	20.1959
.(((..((...........))..)))	chr7:33397397-33397692(+)$1	1	127	153	21.9859

#PSSM
: : 0.23	= : 0.10	c : 0.09	h : 0.07	! : 0.06	g : 0.06	f : 0.04	" : 0.04	e : 0.03	# : 0.03	b : 0.03	i : 0.03	d : 0.03	H : 0.03	% : 0.01	3 : 0.01	+ : 0.01	[ : 0.01	a : 0.01	
g : 0.28	c : 0.10	= : 0.10	f : 0.07	[ : 0.07	h : 0.06	! : 0.06	e : 0.04	d : 0.04	: : 0.04	i : 0.03	" : 0.03	# : 0.01	
g : 0.25	f : 0.17	c : 0.10	= : 0.10	h : 0.06	d : 0.06	e : 0.04	" : 0.03	i : 0.03	[ : 0.03	! : 0.03	a : 0.01	b : 0.01	: : 0.01	# : 0.01	
g : 0.23	f : 0.17	e : 0.14	c : 0.10	= : 0.09	d : 0.07	h : 0.04	[ : 0.03	! : 0.03	i : 0.03	" : 0.01	b : 0.01	
g : 0.23	f : 0.15	e : 0.14	d : 0.12	= : 0.07	[ : 0.07	c : 0.06	! : 0.06	h : 0.03	" : 0.01	i : 0.01	
g : 0.21	c : 0.17	f : 0.14	e : 0.14	d : 0.07	= : 0.06	[ : 0.04	h : 0.03	! : 0.03	b : 0.01	a : 0.01	y : 0.01	w : 0.01	i : 0.01	
g : 0.21	c : 0.15	f : 0.14	b : 0.10	e : 0.10	d : 0.06	= : 0.06	h : 0.03	v : 0.03	w : 0.03	y : 0.01	i : 0.01	[ : 0.01	
g : 0.21	c : 0.14	f : 0.10	b : 0.09	e : 0.09	v : 0.07	= : 0.06	u : 0.04	d : 0.04	h : 0.03	w : 0.03	y : 0.01	i : 0.01	a : 0.01	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
t : 0.34	v : 0.26	u : 0.18	w : 0.12	y : 0.07	
v : 0.23	u : 0.14	w : 0.10	g : 0.09	y : 0.07	f : 0.06	c : 0.06	e : 0.06	d : 0.04	b : 0.04	= : 0.03	a : 0.01	i : 0.01	
v : 0.18	g : 0.14	c : 0.10	w : 0.09	f : 0.09	e : 0.09	y : 0.07	b : 0.07	d : 0.04	= : 0.03	2 : 0.01	i : 0.01	a : 0.01	
g : 0.17	c : 0.14	e : 0.12	f : 0.10	w : 0.09	d : 0.07	y : 0.06	b : 0.06	= : 0.06	2 : 0.03	] : 0.03	h : 0.01	i : 0.01	
g : 0.21	f : 0.14	c : 0.14	e : 0.12	d : 0.07	y : 0.06	= : 0.06	h : 0.04	b : 0.03	] : 0.03	3 : 0.01	a : 0.01	i : 0.01	2 : 0.01	
g : 0.21	f : 0.14	e : 0.12	c : 0.12	= : 0.07	y : 0.06	d : 0.06	] : 0.04	h : 0.04	i : 0.03	: : 0.01	3 : 0.01	2 : 0.01	4 : 0.01	
g : 0.23	f : 0.17	c : 0.14	h : 0.07	= : 0.07	e : 0.07	d : 0.06	2 : 0.06	i : 0.03	: : 0.01	3 : 0.01	5 : 0.01	4 : 0.01	
g : 0.25	f : 0.12	: : 0.09	2 : 0.09	h : 0.07	c : 0.07	= : 0.07	e : 0.04	d : 0.03	i : 0.03	J : 0.01	b : 0.01	] : 0.01	5 : 0.01	4 : 0.01	3 : 0.01	

#score	1440.4358121507682
#seq	64
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m1_run1.txt

#BEAR
d[ccc[bb[dddd!!cccooooooccc]ddddbb]ccc3	chr5:180651318-180651642(+)$1	324	148	187	12.7246
iiccc[ccc[bb[cccooooooccc]bb]ccc]ccc]ii	chr16:11439417-11439687(+)$1	270	23	62	15.3759
d!!ccc[ddddccc[cccmmmmcccccc]dddd4444cc	chr20:61538467-61538698(-)$1	231	18	57	12.6205
ccffffffccc!!cccooooooccc333ccc]ffffff]	chrX:153197682-153197979(-)$1	297	124	163	16.2342
===========[cccccclllccc4444ccc]=======	chr11:6568168-6568430(+)$1	262	32	71	16.9986
bb####ccc!!eeeeeooooooeeeeeccc333bb]===	chr10:120936469-120936713(-)$1	244	163	202	12.9109
hh[bbcccdddd!!cccooooooccc22dddd]ccc444	chr1:45266075-45266331(+)$1	256	9	48	14.8002
fffffa[ccc[gggggggooooooggggggg22ccc]a]	chr3:9807369-9807601(-)$1	232	1	40	13.4850
e!!ccc####ccc[ddddnnnnndddd]ccc333ccc77	chrX:133620417-133620660(+)$1	243	100	139	11.8811
==eeeeeggggggg[cccmmmmccc333ggggggg22ee	chr17:1564242-1564514(-)$1	272	10	49	14.0850
ee[ggggggg[ggggggglllggggggg]ggggggg]ee	chr16:24741473-24741691(+)$1	218	76	115	12.2956
ccc[dddd!!bb[cccnnnnncccbb22dddd22ccc]d	chr15:69709621-69709861(+)$1	240	40	79	12.1613
fff[ccc[bb!!bb[ccclllcccbb]bb]cccffffff	chr2:183826786-183826995(-)$1	209	151	190	11.9510
!!ccc!!ccca!!cccnnnnnccc22a]ccc22ccc22b	chr11:46404051-46404323(+)$1	272	178	217	14.3417
======="""cccbb[bbmmmmbb]bb]ccc]=======	chr19:18391675-18391950(-)$1	275	154	193	13.0535
d[iiiiiiiii!!cccooooooccciiiiiiiiidddde	chr2:54871431-54871662(+)$1	231	183	222	15.6085
=####dddd[ccccccooooooccc4444ccc]dddd==	chr2:74386153-74386409(-)$1	256	196	235	15.8897
fffffffff!!ccc!!cccoooooocccccc22ffffff	chr7:127992159-127992430(-)$1	271	205	244	12.2500
ee####ccc"""ggggggglllggggggg4444ccceee	chr19:47249513-47249750(-)$1	237	135	174	12.3951
:::gggggggccccccooooooccc22ccc4444ggggg	chr2:242203821-242204056(-)$1	235	140	179	12.9594
[ccc[dddd[a[a!!bboooooobb22a]a]dddd]ccc	chr7:3341068-3341346(+)$1	278	88	127	13.9529
c!!ccc!!dddd"""cccmmmmccc333ddddccc22cc	chr19:59060294-59060556(+)$1	262	125	164	14.7878
iiiiiiii[a"""eeeeellleeeee4444a]iiiiiii	chr17:65163505-65163742(-)$1	237	138	177	13.6132
ggggg!!eeeee[a[cccmmmmcccaeeeee]ggggggg	chr9:138852867-138853130(-)$1	263	59	98	12.7378
[eeeeedddd####cccnnnnnccc333dddd22eeeee	chr16:30537127-30537407(-)$1	280	238	277	13.8311
FFFFFFccc[ccc[cccooooooccc333ccc]ccc:ff	chr2:232322908-232323200(-)$1	292	130	169	12.9656
[ggggggg[bb####cccmmmmcccbb]ggggggg]bbF	chrX:102931630-102931895(-)$1	265	67	106	13.2909
gggggg!!agggggggbbnnnnnbb]ggggggg333a22	chr7:4830885-4831118(+)$1	233	169	208	12.0099
iiiiiii!!ccc####bboooooobb22ccc22iiiiii	chr1:245027102-245027375(-)$1	273	107	146	15.8339
[bb"""dddd####bboooooobb4444dddd333bb]c	chr14:23777263-23777491(+)$1	228	34	73	14.3979
fff[bb[ffffff####aooooooa4444ffffffbbff	chr12:49444136-49444382(-)$1	246	156	195	12.0347
ggggggccc!!ccc[cccmmmmccc333ccc22cccDDD	chr16:846912-847190(+)$1	278	229	268	13.4510
iiiiiii$$$$$ddddooooooddddiiiiiiiii333b	chr5:61733097-61733328(+)$1	231	50	89	13.8697
=========="""cccooooooccc==========ccc!	chr14:53224360-53224584(+)$1	224	1	40	17.5291
$$$$==========[cccmmmmccc]==========555	chr15:101815359-101815599(-)$1	240	124	163	12.4396
c[ccc[eeeee[bb[cccmmmmccc]bb]eeeeeccc]c	chr11:67169123-67169396(-)$1	273	168	207	11.7400
eee"""ccc!!ccc!!bboooooobb22ccc22ccc22e	chr20:31421443-31421693(+)$1	250	173	212	15.0893
::ccciiiiiiiii[ccclllccc333iiiiiiiii]cc	chr6:26216454-26216749(-)$1	295	233	272	13.4985
!ccc[ccc"""fffffflllffffff22ccc22ccc22d	chr19:3053876-3054120(-)$1	244	89	128	12.0203
===!!ccc[bb"""ddddllldddd4444bb22ccc===	chr1:227171711-227171955(+)$1	244	31	70	14.3659
=========####ddddannnnna]dddd==========	chr7:150776689-150776995(-)$1	306	161	200	13.6832
bbiiiiiiiiibb!!aooooooa22bb]iiiiiiiii]b	chr18:72997379-72997614(+)$1	235	147	186	13.7889
a[dddd[bb"""bb[aooooooabb333bb]dddd]a]e	chr1:16721570-16721816(+)$1	246	162	201	14.3443
0gggggggdddd[cccooooooccc22ddddeeeee!!a	chr10:112338285-112338526(+)$1	241	144	183	12.8615
fffffggggggg"""cccmmmmccc333ggggggg22ff	chr2:71297564-71297816(+)$1	252	169	208	14.9514
"ggggggg[a[ccc[aooooooa]ccc]a]ggggggg44	chr9:140082351-140082655(-)$1	304	88	127	15.6411
!ccc$$$$$bb!!a[cccmmmmccc]a]bb4444ccc22	chr10:102766558-102766797(+)$1	239	27	66	12.9873
]cccdddd!!ddddcccooooooccc]dddd22dddd:G	chr1:245018734-245018988(-)$1	254	137	176	11.7687
ee####dddda####ccclllccc4444a]dddd333ee	chr2:54876924-54877155(+)$1	231	132	171	14.5381
====[ccc[a!!bb!!ammmma22bba]ccc========	chr9:101558623-101558875(-)$1	252	143	182	13.8331
eeffffff$$$$$cccooooooccc333ffffff66666	chr5:171303354-171303594(-)$1	240	61	100	12.8915
=====!!ccc!!ddddnnnnndddd333ccc========	chr2:73678319-73678550(+)$1	231	55	94	14.6314
dd[dddd[ccc####bboooooobb333ccc]ddddddd	chr10:69672552-69672813(+)$1	261	190	229	14.6255
a!!ffffff[ccc"""bbnnnnnbb333ccc22ffffff	chr14:24901414-24901667(+)$1	253	128	167	13.6041
ffffggggggg!!cccoooooocccggggggg]ffffff	chr9:71395015-71395273(+)$1	258	207	246	14.8635
e[dddd!!bb####cccnnnnnccc4444bb22dddd]e	chr5:10417286-10417558(+)$1	272	149	188	13.9595

#otherMatches

#Seq PSSM
gcuggaggagguugaggaagaggaUCUAGACCCCGUCAC	chr5:180651318-180651642(+)$1	324	148	187	12.7246
cgggcgcguggcggcugucacgggcggcggcgggccgcg	chr16:11439417-11439687(+)$1	270	23	62	15.3759
UUGGCCCCGGGUGCUGUCACGUGGCGCAGCCCGACUCGG	chr20:61538467-61538698(-)$1	231	18	57	12.6205
UCUGGCUCAGAAACUGAUGGACCAGGCCUCUCGAGCCAU	chrX:153197682-153197979(-)$1	297	124	163	16.2342
GGCUGGCAGCCAUGGAGGACACCUCAACCCAAGGCUGCC	chr11:6568168-6568430(+)$1	262	32	71	16.9986
CAAAAUUAUUCAGCACCAGUAAGUGUUAUGUCAUGUCUU	chr10:120936469-120936713(-)$1	244	163	202	12.9109
ggggccgggcggAACCGAGAAGCCGGGACCGCGCUGCGA	chr1:45266075-45266331(+)$1	256	9	48	14.8002
ACCUUGUGAAUCCCCUCUCCCGAUAGGGGGGCCUUCUCG	chr3:9807369-9807601(-)$1	232	1	40	13.4850
AAAAGUAAUUGGUGGAGAUGAUCUCUCAACUUUAACUGG	chrX:133620417-133620660(+)$1	243	100	139	11.8811
GGGGCAAUAGGCACCCAGAAGCUUGACCGUGCCUGCCUU	chr17:1564242-1564514(-)$1	272	10	49	14.0850
uuuguuuuuguuuuuUUGUUUCAGAGAAUUGGAAGCUAA	chr16:24741473-24741691(+)$1	218	76	115	12.2956
AAGUGAAAAAUCAGGCAAAAGGUCGAACUUUCUUCUUAA	chr15:69709621-69709861(+)$1	240	40	79	12.1613
AAGGCAAGAAAAUGUGCUUUUAGCCAGUUGUUGUUUUAC	chr2:183826786-183826995(-)$1	209	151	190	11.9510
AUGCUCAGUGCCAGGAGACCAUCCGCGUCACCAAGCCCU	chr11:46404051-46404323(+)$1	272	178	217	14.3417
gGGGGGCCCUCGGGCACGGCCACGGGCUccgcgcccccc	chr19:18391675-18391950(-)$1	275	154	193	13.0535
GAGCUGUGCAGAUCUAGACAAAUGGCUGCACGGCCUGGA	chr2:54871431-54871662(+)$1	231	183	222	15.6085
GUUGAUCCAUGUUGAUUUCUGUGUCCUGUGACUUGGACU	chr2:74386153-74386409(-)$1	256	196	235	15.8897
ggUGCCCCACCGGCCUGGCUGCGCUGCUGCUCCUGGGGC	chr7:127992159-127992430(-)$1	271	205	244	12.2500
GGCCCUGGCCCCACUggggcggccccggucuccgccccu	chr19:47249513-47249750(-)$1	237	135	174	12.3951
UCUGGAGCCUGGGGGAACAAGAUCCGACCCAUCAAGGCU	chr2:242203821-242204056(-)$1	235	140	179	12.9594
CGUCCCGCCUGUCCUGCCCGCCCGUCCGUCCGGCGCGGC	chr7:3341068-3341346(+)$1	278	88	127	13.9529
GCCUGGACCUGGACCUCACAGCUGACAGCCAGCCACCCG	chr19:59060294-59060556(+)$1	262	125	164	14.7878
AUCUUCGGCCUGACUGUGACACACAGGUAUGUUUGAAGG	chr17:65163505-65163742(-)$1	237	138	177	13.6132
CCGCCUUCCCGGUGACCUUCAggggcccggguggcgggc	chr9:138852867-138853130(-)$1	263	59	98	12.7378
CCUGAGUUUGCACCCAGAAGCCCUGAAUCAGAUUCUCAG	chr16:30537127-30537407(-)$1	280	238	277	13.8311
AUCUCCCUUACAAAGUCACUCAGGAUGAAUUGAAAGAAG	chr2:232322908-232323200(-)$1	292	130	169	12.9656
CAGCUGGUCCACAGCAGAAAAAUCUUGAACCAGCUCUCC	chrX:102931630-102931895(-)$1	265	67	106	13.2909
CUGGGCAGCCAGCUUGCUACUGAGGCCAGGCUGAUAGGA	chr7:4830885-4831118(+)$1	233	169	208	12.0099
GGCGGCCGACUCGGGCCCGAUGGAGGAGGAGGAGGCCGC	chr1:245027102-245027375(-)$1	273	107	146	15.8339
GCUGAGAGUGUCAACAAGGAGAUGGAACCACUGGUGGGA	chr14:23777263-23777491(+)$1	228	34	73	14.3979
CUGUCCGUUCCCUCCCCGUUGAGUCCCAUAGGGAAGGUA	chr12:49444136-49444382(-)$1	246	156	195	12.0347
GGUGUGGCUAGGGCAGUCAUGAGGCGGGGCCAAGGCACC	chr16:846912-847190(+)$1	278	229	268	13.4510
AACACAGGCCACCAGUCAGGAUACUGCUGUGUUAAAACC	chr5:61733097-61733328(+)$1	231	50	89	13.8697
GAUUAUAGUAUAUAAGGAGUUACUUUACUGUGGUUUCAA	chr14:53224360-53224584(+)$1	224	1	40	17.5291
GGAAAAACUGAAACAAGUAUGAACUGGUUUCAGUUUGAA	chr15:101815359-101815599(-)$1	240	124	163	12.4396
UGGACUCGAUCAUCGGGCGCCUGCUGGAAGGUUGGUcgg	chr11:67169123-67169396(-)$1	273	168	207	11.7400
CCAGAACUUCAAAAUACUACAAGCAGGUUUUAAGAGAAU	chr20:31421443-31421693(+)$1	250	173	212	15.0893
UCACCAAGUAUACAAGCUCCAAGUAAAUGUGUGCUUAGG	chr6:26216454-26216749(-)$1	295	233	272	13.4985
UCCAAGCCCACCAGCUGUCCCAGCUGCAGGCCCUGGCCC	chr19:3053876-3054120(-)$1	244	89	128	12.0203
GGGACGGUGUGGAGGGCCUGUGGCUAGGGCGUGACCUCC	chr1:227171711-227171955(+)$1	244	31	70	14.3659
GCGGCUUCUGGAACAGGCGAAGAGCCCUGGGGAGCUGCU	chr7:150776689-150776995(-)$1	306	161	200	13.6832
GGCGCAGAGCUACCAGAACUCCCCAGUCAGCUCUGCGAC	chr18:72997379-72997614(+)$1	235	147	186	13.7889
GAGGGAACGACCUGACUUACUUGCACUGUGAUCCCCCUU	chr1:16721570-16721816(+)$1	246	162	201	14.3443
GAAGCAAUCCUUAUUAUAUUGUUAAACAAGGAAAGGUAA	chr10:112338285-112338526(+)$1	241	144	183	12.8615
GGGAUCAGAGGGCUUGGUUCUGAUUUUAUUCUCUGUAAU	chr2:71297564-71297816(+)$1	252	169	208	14.9514
UCUGCACCCCAGGUGUCUUCCCGGACCAGCGGUGCAGUC	chr9:140082351-140082655(-)$1	304	88	127	15.6411
GGCCAAAGUGCAGCGGGCAGCAGCCGGGGUUGGGGGCAG	chr10:102766558-102766797(+)$1	239	27	66	12.9873
GGUGGAGGAAGUGGUGGAAUCGGCUAUCCAUACCCUCGU	chr1:245018734-245018988(-)$1	254	137	176	11.7687
GAACACAGUGGAGACCUUACAGAGAAUGCACACUACAUU	chr2:54876924-54877155(+)$1	231	132	171	14.5381
GCGCGCGUGUGACCAGGGCGACAcggagacggcgcggcg	chr9:101558623-101558875(-)$1	252	143	182	13.8331
GGGAUGUGAACACGGGUGAAGUUCUUAACACAUUGAUCC	chr5:171303354-171303594(-)$1	240	61	100	12.8915
GAGAGAAGCCGAUUGUUAACUACAAACAGGCCUUUCCAG	chr2:73678319-73678550(+)$1	231	55	94	14.6314
UGGCCUAAUAGAGUGGCAAAGGAGCAGAUUAGUAGGCGG	chr10:69672552-69672813(+)$1	261	190	229	14.6255
GCCCUCCACCUGCACCGGAACCCCCAUGGCACUGUGGAG	chr14:24901414-24901667(+)$1	253	128	167	13.6041
CGCCGGUGUUCCAGGCCGAGGCGCCGAGCGCCAGGCGGA	chr9:71395015-71395273(+)$1	258	207	246	14.8635
CUGGGGCUCCUGUUUGAGCUGGUCAUUGUGGCUCCCCUG	chr5:10417286-10417558(+)$1	272	149	188	13.9595

#DB
(.(((.((.((((..(((......))).)))))).))).	chr5:180651318-180651642(+)$1	1	148	187	12.7246
(((((.(((.((.(((......))).)).))).))).))	chr16:11439417-11439687(+)$1	1	23	62	15.3759
(..(((.(((((((.(((....)))))).))))....))	chr20:61538467-61538698(-)$1	1	18	57	12.6205
(((((((((((..(((......)))...))).)))))).	chrX:153197682-153197979(-)$1	1	124	163	16.2342
(((((((((((.((((((...)))....))).)))))))	chr11:6568168-6568430(+)$1	1	32	71	16.9986
((....(((..(((((......))))))))...)).)))	chr10:120936469-120936713(-)$1	1	163	202	12.9109
((.(((((((((..(((......)))..)))).)))...	chr1:45266075-45266331(+)$1	1	9	48	14.8002
((((((.(((.(((((((......)))))))..))).).	chr3:9807369-9807601(-)$1	1	1	40	13.4850
(..(((....(((.((((.....)))).)))...)))..	chrX:133620417-133620660(+)$1	1	100	139	11.8811
((((((((((((((.(((....)))...)))))))..))	chr17:1564242-1564514(-)$1	1	10	49	14.0850
((.(((((((.(((((((...))))))).))))))).))	chr16:24741473-24741691(+)$1	1	76	115	12.2956
(((.((((..((.(((.....)))))..))))..))).)	chr15:69709621-69709861(+)$1	1	40	79	12.1613
(((.(((.((..((.(((...))))).)).)))))))))	chr2:183826786-183826995(-)$1	1	151	190	11.9510
..(((..((((..(((.....)))..).)))..)))..)	chr11:46404051-46404323(+)$1	1	178	217	14.3417
(((((((...(((((.((....)).)).))).)))))))	chr19:18391675-18391950(-)$1	1	154	193	13.0535
(.(((((((((..(((......)))))))))))))))))	chr2:54871431-54871662(+)$1	1	183	222	15.6085
(....((((.((((((......)))....))).))))))	chr2:74386153-74386409(-)$1	1	196	235	15.8897
)))((((((..(((..(((......))))))..))))))	chr7:127992159-127992430(-)$1	1	205	244	12.2500
((....(((...(((((((...)))))))....))))))	chr19:47249513-47249750(-)$1	1	135	174	12.3951
...(((((((((((((......)))..)))....)))))	chr2:242203821-242204056(-)$1	1	140	179	12.9594
.(((.((((.(.(..((......))..).).)))).)))	chr7:3341068-3341346(+)$1	1	88	127	13.9529
(..(((..((((...(((....)))...)))))))..))	chr19:59060294-59060556(+)$1	1	125	164	14.7878
((((((((.(...(((((...)))))....).)))))))	chr17:65163505-65163742(-)$1	1	138	177	13.6132
(((((..(((((.(.(((....))))))))).)))))))	chr9:138852867-138853130(-)$1	1	59	98	12.7378
.(((((((((....(((.....)))...))))..)))))	chr16:30537127-30537407(-)$1	1	238	277	13.8311
(((((((((.(((.(((......)))...))).))).((	chr2:232322908-232323200(-)$1	1	130	169	12.9656
.(((((((.((....(((....))))).))))))).))(	chrX:102931630-102931895(-)$1	1	67	106	13.2909
((((((..((((((((((.....)).)))))))...)..	chr7:4830885-4831118(+)$1	1	169	208	12.0099
(((((((..(((....((......))..)))..))))))	chr1:245027102-245027375(-)$1	1	107	146	15.8339
.((...((((....((......))....))))...)).)	chr14:23777263-23777491(+)$1	1	34	73	14.3979
(((.((.((((((....(......)....))))))))))	chr12:49444136-49444382(-)$1	1	156	195	12.0347
))))))(((..(((.(((....)))...)))..))))))	chr16:846912-847190(+)$1	1	229	268	13.4510
(((((((.....((((......)))))))))))))...)	chr5:61733097-61733328(+)$1	1	50	89	13.8697
((((((((((...(((......)))))))))))))(((.	chr14:53224360-53224584(+)$1	1	1	40	17.5291
....((((((((((.(((....))).))))))))))...	chr15:101815359-101815599(-)$1	1	124	163	12.4396
(.(((.(((((.((.(((....))).)).)))))))).)	chr11:67169123-67169396(-)$1	1	168	207	11.7400
(((...(((..(((..((......))..)))..)))..)	chr20:31421443-31421693(+)$1	1	173	212	15.0893
..((((((((((((.(((...)))...))))))))).))	chr6:26216454-26216749(-)$1	1	233	272	13.4985
.(((.(((...((((((...))))))..)))..)))..)	chr19:3053876-3054120(-)$1	1	89	128	12.0203
(((..(((.((...((((...))))....))..))))))	chr1:227171711-227171955(+)$1	1	31	70	14.3659
(((((((((....(((((.....).))))))))))))))	chr7:150776689-150776995(-)$1	1	161	200	13.6832
(((((((((((((..(......)..)).))))))))).)	chr18:72997379-72997614(+)$1	1	147	186	13.7889
(.((((.((...((.(......)))...)).)))).).)	chr1:16721570-16721816(+)$1	1	162	201	14.3443
.)))))))((((.(((......)))..))))(((((..(	chr10:112338285-112338526(+)$1	1	144	183	12.8615
((((((((((((...(((....)))...)))))))..))	chr2:71297564-71297816(+)$1	1	169	208	14.9514
.(((((((.(.(((.(......).))).).)))))))..	chr9:140082351-140082655(-)$1	1	88	127	15.6411
.(((.....((..(.(((....))).).))....)))..	chr10:102766558-102766797(+)$1	1	27	66	12.9873
.)))((((..(((((((......))).))))..)))).)	chr1:245018734-245018988(-)$1	1	137	176	11.7687
((....(((((....(((...)))....).))))...))	chr2:54876924-54877155(+)$1	1	132	171	14.5381
((((.(((.(..((..(....)..))).)))))))))))	chr9:101558623-101558875(-)$1	1	143	182	13.8331
((((((((.....(((......)))...)))))).....	chr5:171303354-171303594(-)$1	1	61	100	12.8915
(((((..(((..((((.....))))...)))))))))))	chr2:73678319-73678550(+)$1	1	55	94	14.6314
((.((((.(((....((......))...))).)))))))	chr10:69672552-69672813(+)$1	1	190	229	14.6255
(..((((((.(((...((.....))...)))..))))))	chr14:24901414-24901667(+)$1	1	128	167	13.6041
(((((((((((..(((......)))))))))).))))))	chr9:71395015-71395273(+)$1	1	207	246	14.8635
(.((((..((....(((.....)))....))..)))).)	chr5:10417286-10417558(+)$1	1	149	188	13.9595

#PSSM
= : 0.16	e : 0.12	f : 0.10	d : 0.07	i : 0.07	c : 0.07	[ : 0.07	! : 0.05	g : 0.05	b : 0.03	: : 0.03	a : 0.03	h : 0.01	F : 0.01	$ : 0.01	0 : 0.01	" : 0.01	] : 0.01	
= : 0.14	c : 0.10	f : 0.10	e : 0.10	g : 0.10	[ : 0.08	! : 0.08	i : 0.07	b : 0.05	: : 0.03	h : 0.01	# : 0.01	F : 0.01	$ : 0.01	d : 0.01	
c : 0.17	f : 0.14	= : 0.12	g : 0.10	i : 0.08	! : 0.07	# : 0.07	[ : 0.05	e : 0.05	d : 0.03	: : 0.01	F : 0.01	b : 0.01	$ : 0.01	
c : 0.21	g : 0.14	f : 0.12	= : 0.10	i : 0.08	# : 0.07	[ : 0.05	d : 0.05	e : 0.03	" : 0.03	b : 0.01	F : 0.01	$ : 0.01	! : 0.01	
c : 0.16	g : 0.16	f : 0.10	= : 0.10	d : 0.08	i : 0.08	# : 0.07	[ : 0.05	b : 0.03	e : 0.03	" : 0.03	F : 0.01	! : 0.01	$ : 0.01	
g : 0.16	c : 0.14	d : 0.12	i : 0.10	= : 0.08	f : 0.07	[ : 0.05	# : 0.05	! : 0.05	e : 0.03	" : 0.03	a : 0.01	F : 0.01	b : 0.01	$ : 0.01	
c : 0.19	d : 0.14	g : 0.12	! : 0.10	i : 0.10	= : 0.08	[ : 0.07	f : 0.07	e : 0.03	b : 0.01	# : 0.01	$ : 0.01	
c : 0.23	d : 0.14	g : 0.14	f : 0.08	= : 0.07	i : 0.07	! : 0.07	b : 0.03	[ : 0.03	e : 0.03	$ : 0.03	# : 0.01	" : 0.01	
c : 0.19	d : 0.16	[ : 0.10	g : 0.08	= : 0.07	! : 0.05	b : 0.05	i : 0.05	f : 0.05	$ : 0.05	" : 0.03	e : 0.03	# : 0.01	a : 0.01	
d : 0.14	c : 0.10	! : 0.10	g : 0.10	[ : 0.08	b : 0.08	" : 0.07	= : 0.05	i : 0.05	a : 0.05	# : 0.03	e : 0.03	$ : 0.03	f : 0.01	
c : 0.16	! : 0.12	d : 0.10	b : 0.08	" : 0.08	g : 0.07	# : 0.07	[ : 0.05	a : 0.05	i : 0.05	= : 0.03	e : 0.03	$ : 0.03	f : 0.01	
c : 0.21	! : 0.14	# : 0.12	d : 0.08	g : 0.08	" : 0.08	b : 0.05	[ : 0.05	e : 0.03	f : 0.03	$ : 0.03	= : 0.01	i : 0.01	
c : 0.21	# : 0.14	! : 0.10	g : 0.08	b : 0.08	" : 0.08	d : 0.07	[ : 0.07	f : 0.03	e : 0.01	a : 0.01	= : 0.01	i : 0.01	$ : 0.01	
c : 0.30	# : 0.14	g : 0.08	b : 0.08	! : 0.07	" : 0.07	d : 0.07	e : 0.03	[ : 0.03	a : 0.03	= : 0.01	i : 0.01	f : 0.01	
c : 0.30	[ : 0.19	! : 0.10	d : 0.08	# : 0.08	g : 0.07	" : 0.05	e : 0.03	b : 0.03	f : 0.01	
c : 0.55	d : 0.08	g : 0.07	! : 0.05	b : 0.05	a : 0.05	e : 0.03	# : 0.03	[ : 0.01	f : 0.01	" : 0.01	
c : 0.37	o : 0.26	b : 0.12	g : 0.05	d : 0.05	n : 0.05	e : 0.01	# : 0.01	f : 0.01	a : 0.01	
o : 0.35	c : 0.28	n : 0.08	b : 0.08	g : 0.05	d : 0.03	a : 0.03	e : 0.01	l : 0.01	m : 0.01	
o : 0.44	m : 0.21	n : 0.16	l : 0.14	c : 0.01	g : 0.01	
o : 0.46	m : 0.21	l : 0.16	n : 0.16	
o : 0.46	m : 0.21	n : 0.16	l : 0.14	f : 0.01	
o : 0.46	m : 0.19	c : 0.10	n : 0.10	d : 0.03	g : 0.01	l : 0.01	e : 0.01	f : 0.01	a : 0.01	
c : 0.48	o : 0.19	n : 0.07	d : 0.05	a : 0.05	e : 0.03	g : 0.03	b : 0.03	f : 0.01	2 : 0.01	
c : 0.53	b : 0.12	o : 0.10	d : 0.07	e : 0.03	g : 0.03	2 : 0.03	f : 0.01	a : 0.01	] : 0.01	
c : 0.46	b : 0.17	d : 0.07	4 : 0.05	g : 0.05	e : 0.03	2 : 0.03	] : 0.03	o : 0.01	a : 0.01	3 : 0.01	f : 0.01	
3 : 0.21	b : 0.14	c : 0.12	4 : 0.12	] : 0.08	g : 0.07	2 : 0.07	d : 0.05	e : 0.03	i : 0.01	a : 0.01	= : 0.01	f : 0.01	
3 : 0.23	4 : 0.14	2 : 0.14	b : 0.08	g : 0.08	c : 0.07	a : 0.05	e : 0.03	d : 0.03	] : 0.03	i : 0.03	= : 0.03	
3 : 0.21	] : 0.16	4 : 0.14	2 : 0.08	g : 0.08	c : 0.07	b : 0.05	i : 0.05	d : 0.05	= : 0.03	a : 0.01	e : 0.01	
c : 0.28	d : 0.16	g : 0.12	] : 0.08	4 : 0.08	i : 0.07	b : 0.05	= : 0.03	a : 0.03	e : 0.01	3 : 0.01	f : 0.01	
c : 0.33	d : 0.16	g : 0.12	i : 0.07	b : 0.07	] : 0.05	= : 0.05	4 : 0.03	e : 0.03	f : 0.03	a : 0.01	
c : 0.32	d : 0.17	g : 0.14	i : 0.07	4 : 0.05	= : 0.05	] : 0.03	e : 0.03	f : 0.03	b : 0.03	3 : 0.01	a : 0.01	
2 : 0.19	d : 0.17	g : 0.12	] : 0.10	= : 0.08	c : 0.07	i : 0.07	4 : 0.05	3 : 0.03	f : 0.03	e : 0.03	
2 : 0.23	= : 0.12	g : 0.12	] : 0.08	d : 0.08	i : 0.08	f : 0.05	3 : 0.05	4 : 0.05	c : 0.03	e : 0.03	b : 0.01	
c : 0.19	f : 0.12	= : 0.12	d : 0.12	g : 0.10	i : 0.10	4 : 0.05	3 : 0.05	b : 0.03	2 : 0.03	e : 0.03	
c : 0.26	= : 0.12	g : 0.12	d : 0.12	f : 0.10	i : 0.08	3 : 0.05	e : 0.03	] : 0.01	4 : 0.01	b : 0.01	6 : 0.01	
c : 0.28	= : 0.10	f : 0.08	d : 0.08	] : 0.07	g : 0.07	i : 0.07	2 : 0.05	3 : 0.05	e : 0.03	b : 0.03	4 : 0.01	6 : 0.01	
c : 0.12	= : 0.12	2 : 0.10	f : 0.08	d : 0.08	] : 0.07	g : 0.05	i : 0.05	b : 0.05	4 : 0.03	e : 0.03	a : 0.03	3 : 0.03	: : 0.01	D : 0.01	5 : 0.01	! : 0.01	6 : 0.01	
f : 0.14	= : 0.14	c : 0.10	] : 0.10	e : 0.08	2 : 0.08	i : 0.05	4 : 0.03	d : 0.03	g : 0.03	a : 0.01	7 : 0.01	b : 0.01	D : 0.01	3 : 0.01	5 : 0.01	! : 0.01	: : 0.01	6 : 0.01	
e : 0.16	= : 0.14	f : 0.12	c : 0.10	i : 0.05	d : 0.05	b : 0.05	] : 0.03	4 : 0.03	g : 0.03	2 : 0.03	3 : 0.01	7 : 0.01	F : 0.01	D : 0.01	! : 0.01	5 : 0.01	a : 0.01	G : 0.01	6 : 0.01	

#score	770.4565718613408
#seq	56
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m1_run2.txt

#BEAR
:fffffftttttttttttffffff	chr7:128619915-128620193(-)$1	278	59	83	21.7927
dd[cccuuuuuuuuuuuuccc]dd	chr2:3627596-3627943(+)$1	347	298	322	22.4979
a!!dddduuuuuuuuuuuudddd2	chr6:37336718-37336961(+)$1	243	65	89	23.0044
gggggggvvvvvvvvvvvvvgggg	chr11:4140980-4141256(+)$1	276	21	45	23.9479
###dddduuuuuuuuuuuudddd2	chrX:153609318-153609597(+)$1	279	176	200	22.7682
"fffffftttttttttttffffff	chr4:57896970-57897267(+)$1	297	253	277	22.8201
&ddddvvvvvvvvvvvvvddddgg	chr5:68662229-68662505(-)$1	276	48	72	21.3613
!bb[cccvvvvvvvvvvvvvccc]	chr1:89237344-89237660(+)$1	316	197	221	23.3302
e[ddddvvvvvvvvvvvvvdddd]	chr11:67053812-67054130(+)$1	318	97	121	23.0364
[ddddvvvvvvvvvvvvvdddd22	chr16:74666317-74666575(-)$1	258	136	160	21.5909
gggggggyyyyyyyyyyyyyyyyg	chr10:102748774-102749037(+)$1	263	150	174	20.0595
ffffffvvvvvvvvvvvvvfffff	chr12:21794792-21795077(-)$1	285	240	264	22.8177
ggbb[bbtttttttttttbbbb]g	chr1:149822527-149822874(+)$1	347	63	87	21.7895
hhhhhhhwwwwwwwwwwwwwwhhh	chr2:198359290-198359571(-)$1	281	103	127	20.3749
g!!ddddwwwwwwwwwwwwwwddd	chrX:47087861-47088141(+)$1	280	105	129	21.5699
eeee[bbtttttttttttbbeeee	chr10:43882170-43882430(-)$1	260	2	26	22.0919
d[eeeeettttttttttteeeee]	chr6:168317691-168317969(+)$1	278	144	168	22.6612
iiiiiiiwwwwwwwwwwwwwwiii	chr7:35930177-35930460(+)$1	283	7	31	22.1051
ccc[cccuuuuuuuuuuuuccc]c	chr16:71961469-71961744(+)$1	275	225	249	23.4442
[a[ddddtttttttttttddddab	chr1:206757745-206758103(+)$1	358	282	306	22.6828
gccccccvvvvvvvvvvvvvccc]	chr6:43480992-43481280(-)$1	288	133	157	23.7167
hhhhhhhvvvvvvvvvvvvvhhhh	chr21:33757838-33758084(-)$1	246	166	190	21.8102
beeeeeuuuuuuuuuuuueeeee]	chr4:170613234-170613510(+)$1	276	134	158	21.8420
iiiiiiiwwwwwwwwwwwwwwiii	chr1:28537010-28537249(-)$1	239	108	132	22.1051
gggggggvvvvvvvvvvvvvgggg	chr3:184025640-184025897(+)$1	257	202	226	23.9479
dd[ddddwwwwwwwwwwwwwwddd	chr6:74001606-74001955(+)$1	349	79	103	21.1193
d!!ddddvvvvvvvvvvvvvdddd	chr6:44217309-44217671(+)$1	362	56	80	22.9660
GGdddduuuuuuuuuuuuddddFF	chr1:11190659-11190924(-)$1	265	70	94	20.4932
gggggggtttttttttttgggggg	chr12:42745670-42745943(+)$1	273	180	204	23.7614
=======ttttttttttt======	chr10:33212506-33212746(-)$1	240	168	192	23.8833
=====bbtttttttttttbb]===	chr17:42428808-42429050(+)$1	242	175	199	23.1200
g!!dddduuuuuuuuuuuuddddg	chr21:30439866-30440125(-)$1	259	152	176	23.3185
"bbddddtttttttttttdddd44	chr11:62292335-62292797(-)$1	462	118	142	22.2407
:fffffftttttttttttffffff	chr22:38266084-38266431(+)$1	347	164	188	21.7927
gggggggtttttttttttgggggg	chr6:159057662-159058025(-)$1	363	152	176	23.7614
###cccuuuuuuuuuuuucccccc	chr12:53860916-53861183(+)$1	267	117	141	22.8648
dd[ddddtttttttttttdddd22	chr1:156262747-156263029(-)$1	282	148	172	22.4367
iiiiiiyyyyyyyyyyyyyyyyii	chr17:49238476-49238740(+)$1	264	163	187	20.5620
a[ddddvvvvvvvvvvvvvdddd]	chr3:178951851-178952115(+)$1	264	84	108	23.1095
ccc[ccctttttttttttccc]cc	chr1:193053608-193053895(+)$1	287	102	126	23.5046
gggggggtttttttttttgggggg	chr8:48801031-48801310(-)$1	279	2	26	23.7614
gggggggtttttttttttgggggg	chr9:20769970-20770270(+)$1	300	210	234	23.7614
ffffffvvvvvvvvvvvvvfffff	chr16:25139706-25139996(+)$1	290	260	284	22.8177
ggggccctttttttttttccc]gg	chr1:161007681-161007941(-)$1	260	63	87	24.0378
ffffffwwwwwwwwwwwwwwffff	chr7:155090140-155090423(+)$1	283	213	237	21.5548
gggggggtttttttttttgggggg	chr1:154232327-154232629(+)$1	302	272	296	23.7614
ddddavvvvvvvvvvvvva]dddd	chr6:158330835-158331161(+)$1	326	82	106	21.6216
ffffffuuuuuuuuuuuuffffff	chr7:72397254-72397523(+)$1	269	200	224	22.1659
ggggggguuuuuuuuuuuuggggg	chr8:124824829-124825128(+)$1	299	89	113	23.8103
!!eeeeettttttttttteeeee2	chr6:38029375-38029646(+)$1	271	211	235	22.6947
[ffffffwwwwwwwwwwwwwwfff	chr1:78193953-78194231(-)$1	278	6	30	21.5132
[ffffffuuuuuuuuuuuufffff	chr15:74489619-74489867(-)$1	248	25	49	22.9465
ffff[bbtttttttttttbb]fff	chrX:77224593-77224893(-)$1	300	148	172	22.3881
eeee[bbtttttttttttbb]eee	chr16:18800219-18800536(-)$1	317	290	314	22.1271
ddd[cccwwwwwwwwwwwwwwccc	chr17:66038138-66038408(+)$1	270	202	226	21.4384
cc!!cccvvvvvvvvvvvvvccc4	chr9:130698744-130699000(-)$1	256	27	51	23.5459
iiiiiiuuuuuuuuuuuuiiiiii	chr3:139097793-139098089(-)$1	296	42	66	23.0127
gggggggtttttttttttgggggg	chr16:81051283-81051549(+)$1	266	94	118	23.7614

#otherMatches

#Seq PSSM
CAGUGAAAUUGGUCUUUGUUCACU	chr7:128619915-128620193(-)$1	278	59	83	21.7927
GAGUGGAUUUUAGUGUAACCAGUC	chr2:3627596-3627943(+)$1	347	298	322	22.4979
GAUUCUGAGGCUCAAAAUACAGAU	chr6:37336718-37336961(+)$1	243	65	89	23.0044
AAAAGAAUGGGGCCAUUUUUUUCU	chr11:4140980-4141256(+)$1	276	21	45	23.9479
UUUGUGAUCGUCCUCUUCUUCAUU	chrX:153609318-153609597(+)$1	279	176	200	22.7682
AAUGACAAAUAUGUACUGUGUUGU	chr4:57896970-57897267(+)$1	297	253	277	22.8201
UCACAAACAGUAUUUUUCUGUGGC	chr5:68662229-68662505(-)$1	276	48	72	21.3613
CCAAACCAGCAGCACUAACAGGUA	chr1:89237344-89237660(+)$1	316	197	221	23.3302
UUGGCGCACCCUCCCCUCCCGUCU	chr11:67053812-67054130(+)$1	318	97	121	23.0364
ACACUAUUAAACUGACCAGGUGAG	chr16:74666317-74666575(-)$1	258	136	160	21.5909
UUGUUUGCACGAAAACUGAACCCC	chr10:102748774-102749037(+)$1	263	150	174	20.0595
UUUGAAUUUUUCAUUUUAUUUCAA	chr12:21794792-21795077(-)$1	285	240	264	22.8177
UUCUGUCUAUAAAAAGGUGAAGCA	chr1:149822527-149822874(+)$1	347	63	87	21.7895
GAUUUCUGCAAACGGAGACAAAGA	chr2:198359290-198359571(-)$1	281	103	127	20.3749
UACUUCCAUAUUUGCACUAAAGGA	chrX:47087861-47088141(+)$1	280	105	129	21.5699
AGAACGACAUUUACAACUUCUUCU	chr10:43882170-43882430(-)$1	260	2	26	22.0919
UUAAGUUAAAUUCAUUACAACUUC	chr6:168317691-168317969(+)$1	278	144	168	22.6612
UUUGGUAAAAUUUUGAAUUCAUAU	chr7:35930177-35930460(+)$1	283	7	31	22.1051
AGAGCUGAAAAAGAAAACAUAGGU	chr16:71961469-71961744(+)$1	275	225	249	23.4442
AGUGAACCCAACCAGACCGUUCCC	chr1:206757745-206758103(+)$1	358	282	306	22.6828
ACUCUGGUUGCUAUCCUACUCCAU	chr6:43480992-43481280(-)$1	288	133	157	23.7167
AGAUUUCUGUUGAGUGUGUCGAAA	chr21:33757838-33758084(-)$1	246	166	190	21.8102
UUUAGGAAAAGAAGGUCCCCUGGU	chr4:170613234-170613510(+)$1	276	134	158	21.8420
UCUUGGUGCAUCCUGACAAAAAUC	chr1:28537010-28537249(-)$1	239	108	132	22.1051
GGCUCUGACUCCACCCUUUCCAGG	chr3:184025640-184025897(+)$1	257	202	226	23.9479
UGGCGGGGUACGACUUAACUACUC	chr6:74001606-74001955(+)$1	349	79	103	21.1193
UUUUUGCUUCUUUAAAACUUGUGA	chr6:44217309-44217671(+)$1	362	56	80	22.9660
UUGCCUUUCUCCCCAACCAGGCCU	chr1:11190659-11190924(-)$1	265	70	94	20.4932
AGUAUGUAAAUUUCCCCCAUGUAC	chr12:42745670-42745943(+)$1	273	180	204	23.7614
AUUGUUUUACCAAAUGAUGGACAA	chr10:33212506-33212746(-)$1	240	168	192	23.8833
ACCUGUGAACAGGGGCCCCACCAG	chr17:42428808-42429050(+)$1	242	175	199	23.1200
AGAAGUUGGAGAUGGCACAAACUU	chr21:30439866-30440125(-)$1	259	152	176	23.3185
AGAGGGAAAGUUGAAAGGUCCCAA	chr11:62292335-62292797(-)$1	462	118	142	22.2407
CGUUCCAAUCCCAAAAUCUGGAAU	chr22:38266084-38266431(+)$1	347	164	188	21.7927
GGACUGUCUAUUUGACCUGCAGUC	chr6:159057662-159058025(-)$1	363	152	176	23.7614
ACAGUCUCAUUUUCCCAUGACGCA	chr12:53860916-53861183(+)$1	267	117	141	22.8648
UGCUGCUGCACCACAAGAAGUACU	chr1:156262747-156263029(-)$1	282	148	172	22.4367
UUUUGGUAUUUUUCCCCCUUUUCC	chr17:49238476-49238740(+)$1	264	163	187	20.5620
CUUCAUAAAUCUUUUCUCAAUGAU	chr3:178951851-178952115(+)$1	264	84	108	23.1095
AAUGGAUAUUCCAGCUAAAUUGAU	chr1:193053608-193053895(+)$1	287	102	126	23.5046
UGUUUGCUUCAUAACAGUGCAAAC	chr8:48801031-48801310(-)$1	279	2	26	23.7614
GGUGAAUGUUCAUCUUCAAUUCAC	chr9:20769970-20770270(+)$1	300	210	234	23.7614
GUGUGCUCCCUUUccagcugugcg	chr16:25139706-25139996(+)$1	290	260	284	22.8177
UCCACUCCUCCAGUGUCCGAGUUG	chr1:161007681-161007941(-)$1	260	63	87	24.0378
CCACCAUCUUUUCCUCCGCCUGGU	chr7:155090140-155090423(+)$1	283	213	237	21.5548
CAGGAUUGGUAGAUUCAAAAUCCU	chr1:154232327-154232629(+)$1	302	272	296	23.7614
UUCUCUUUCCCUUAUUUUGUAGAA	chr6:158330835-158331161(+)$1	326	82	106	21.6216
GAGGAAGAAGACCAAAUAUUCCUU	chr7:72397254-72397523(+)$1	269	200	224	22.1659
UUAUUGCUAAUCUCCAUUUGCAAU	chr8:124824829-124825128(+)$1	299	89	113	23.8103
CAGCUUAAGAACUUUAGAUGAGCA	chr6:38029375-38029646(+)$1	271	211	235	22.6947
AUAGAGCAGAAAAUGAAAAUGGCU	chr1:78193953-78194231(-)$1	278	6	30	21.5132
CCUGAGUCCAAGCCCUCAAACUCA	chr15:74489619-74489867(-)$1	248	25	49	22.9465
CCUUUCUACAGCAACAUCAGUAAG	chrX:77224593-77224893(-)$1	300	148	172	22.3881
UCCUGUAGAAAUUAAUUAUGGGGG	chr16:18800219-18800536(-)$1	317	290	314	22.1271
CUUCUGGGACAUCAGAACAAACCA	chr17:66038138-66038408(+)$1	270	202	226	21.4384
GGCAAGCAAGACACACCAGAGCUC	chr9:130698744-130699000(-)$1	256	27	51	23.5459
AGGGAUGAUGGUUUUAAAAUUUCU	chr3:139097793-139098089(-)$1	296	42	66	23.0127
UUUUUGAUAUGAAACAAUUUAAAA	chr16:81051283-81051549(+)$1	266	94	118	23.7614

#DB
.((((((...........))))))	chr7:128619915-128620193(-)$1	1	59	83	21.7927
((.(((............))).))	chr2:3627596-3627943(+)$1	1	298	322	22.4979
(..((((............)))).	chr6:37336718-37336961(+)$1	1	65	89	23.0044
(((((((.............))))	chr11:4140980-4141256(+)$1	1	21	45	23.9479
...((((............)))).	chrX:153609318-153609597(+)$1	1	176	200	22.7682
.((((((...........))))))	chr4:57896970-57897267(+)$1	1	253	277	22.8201
.((((.............))))))	chr5:68662229-68662505(-)$1	1	48	72	21.3613
.((.(((.............))).	chr1:89237344-89237660(+)$1	1	197	221	23.3302
(.((((.............)))).	chr11:67053812-67054130(+)$1	1	97	121	23.0364
.((((.............))))..	chr16:74666317-74666575(-)$1	1	136	160	21.5909
(((((((................)	chr10:102748774-102749037(+)$1	1	150	174	20.0595
((((((.............)))))	chr12:21794792-21795077(-)$1	1	240	264	22.8177
((((.((...........)))).)	chr1:149822527-149822874(+)$1	1	63	87	21.7895
(((((((..............)))	chr2:198359290-198359571(-)$1	1	103	127	20.3749
(..((((..............)))	chrX:47087861-47088141(+)$1	1	105	129	21.5699
((((.((...........))))))	chr10:43882170-43882430(-)$1	1	2	26	22.0919
(.(((((...........))))).	chr6:168317691-168317969(+)$1	1	144	168	22.6612
(((((((..............)))	chr7:35930177-35930460(+)$1	1	7	31	22.1051
(((.(((............))).)	chr16:71961469-71961744(+)$1	1	225	249	23.4442
.(.((((...........))))))	chr1:206757745-206758103(+)$1	1	282	306	22.6828
(((((((.............))).	chr6:43480992-43481280(-)$1	1	133	157	23.7167
(((((((.............))))	chr21:33757838-33758084(-)$1	1	166	190	21.8102
((((((............))))).	chr4:170613234-170613510(+)$1	1	134	158	21.8420
(((((((..............)))	chr1:28537010-28537249(-)$1	1	108	132	22.1051
(((((((.............))))	chr3:184025640-184025897(+)$1	1	202	226	23.9479
((.((((..............)))	chr6:74001606-74001955(+)$1	1	79	103	21.1193
(..((((.............))))	chr6:44217309-44217671(+)$1	1	56	80	22.9660
((((((............))))((	chr1:11190659-11190924(-)$1	1	70	94	20.4932
(((((((...........))))))	chr12:42745670-42745943(+)$1	1	180	204	23.7614
(((((((...........))))))	chr10:33212506-33212746(-)$1	1	168	192	23.8833
(((((((...........)).)))	chr17:42428808-42429050(+)$1	1	175	199	23.1200
(..((((............)))))	chr21:30439866-30440125(-)$1	1	152	176	23.3185
.((((((...........))))..	chr11:62292335-62292797(-)$1	1	118	142	22.2407
.((((((...........))))))	chr22:38266084-38266431(+)$1	1	164	188	21.7927
(((((((...........))))))	chr6:159057662-159058025(-)$1	1	152	176	23.7614
...(((............))))))	chr12:53860916-53861183(+)$1	1	117	141	22.8648
((.((((...........))))..	chr1:156262747-156263029(-)$1	1	148	172	22.4367
((((((................))	chr17:49238476-49238740(+)$1	1	163	187	20.5620
(.((((.............)))).	chr3:178951851-178952115(+)$1	1	84	108	23.1095
(((.(((...........))).))	chr1:193053608-193053895(+)$1	1	102	126	23.5046
(((((((...........))))))	chr8:48801031-48801310(-)$1	1	2	26	23.7614
(((((((...........))))))	chr9:20769970-20770270(+)$1	1	210	234	23.7614
((((((.............)))))	chr16:25139706-25139996(+)$1	1	260	284	22.8177
(((((((...........))).))	chr1:161007681-161007941(-)$1	1	63	87	24.0378
((((((..............))))	chr7:155090140-155090423(+)$1	1	213	237	21.5548
(((((((...........))))))	chr1:154232327-154232629(+)$1	1	272	296	23.7614
(((((.............).))))	chr6:158330835-158331161(+)$1	1	82	106	21.6216
((((((............))))))	chr7:72397254-72397523(+)$1	1	200	224	22.1659
(((((((............)))))	chr8:124824829-124825128(+)$1	1	89	113	23.8103
..(((((...........))))).	chr6:38029375-38029646(+)$1	1	211	235	22.6947
.((((((..............)))	chr1:78193953-78194231(-)$1	1	6	30	21.5132
.((((((............)))))	chr15:74489619-74489867(-)$1	1	25	49	22.9465
((((.((...........)).)))	chrX:77224593-77224893(-)$1	1	148	172	22.3881
((((.((...........)).)))	chr16:18800219-18800536(-)$1	1	290	314	22.1271
(((.(((..............)))	chr17:66038138-66038408(+)$1	1	202	226	21.4384
((..(((.............))).	chr9:130698744-130699000(-)$1	1	27	51	23.5459
((((((............))))))	chr3:139097793-139098089(-)$1	1	42	66	23.0127
(((((((...........))))))	chr16:81051283-81051549(+)$1	1	94	118	23.7614

#PSSM
g : 0.25	d : 0.12	f : 0.08	[ : 0.06	i : 0.06	e : 0.05	c : 0.05	: : 0.03	a : 0.03	# : 0.03	" : 0.03	! : 0.03	h : 0.03	= : 0.03	& : 0.01	b : 0.01	G : 0.01	
g : 0.20	f : 0.17	d : 0.12	! : 0.08	i : 0.06	c : 0.06	[ : 0.05	e : 0.05	# : 0.03	b : 0.03	h : 0.03	= : 0.03	a : 0.01	G : 0.01	
g : 0.18	f : 0.17	d : 0.12	! : 0.08	e : 0.08	[ : 0.06	i : 0.06	b : 0.05	c : 0.05	# : 0.03	h : 0.03	= : 0.03	
d : 0.25	g : 0.18	f : 0.17	e : 0.08	[ : 0.06	i : 0.06	c : 0.05	h : 0.03	= : 0.03	b : 0.01	! : 0.01	
d : 0.24	g : 0.17	f : 0.15	c : 0.15	[ : 0.06	i : 0.06	e : 0.05	h : 0.03	= : 0.03	a : 0.01	
d : 0.20	g : 0.17	f : 0.15	c : 0.15	b : 0.08	i : 0.06	v : 0.05	e : 0.05	h : 0.03	= : 0.01	
g : 0.17	d : 0.15	v : 0.12	c : 0.12	u : 0.10	f : 0.08	b : 0.08	h : 0.03	e : 0.03	i : 0.03	= : 0.01	y : 0.01	w : 0.01	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
t : 0.37	v : 0.24	u : 0.20	w : 0.13	y : 0.03	
v : 0.18	w : 0.13	u : 0.10	d : 0.10	g : 0.10	b : 0.08	f : 0.06	c : 0.06	e : 0.05	y : 0.03	= : 0.01	a : 0.01	i : 0.01	
d : 0.18	w : 0.13	f : 0.12	v : 0.12	g : 0.12	c : 0.08	b : 0.08	e : 0.05	y : 0.03	= : 0.01	] : 0.01	i : 0.01	
d : 0.22	g : 0.15	f : 0.13	c : 0.13	w : 0.12	e : 0.06	] : 0.05	y : 0.03	b : 0.01	h : 0.01	= : 0.01	i : 0.01	
d : 0.25	f : 0.17	g : 0.15	c : 0.10	e : 0.08	] : 0.05	i : 0.05	y : 0.03	h : 0.03	= : 0.03	b : 0.01	
g : 0.18	f : 0.17	d : 0.17	c : 0.10	e : 0.08	i : 0.06	2 : 0.03	] : 0.03	h : 0.03	= : 0.03	y : 0.01	a : 0.01	F : 0.01	4 : 0.01	
g : 0.24	f : 0.17	] : 0.10	d : 0.08	2 : 0.08	i : 0.06	c : 0.06	h : 0.03	e : 0.03	= : 0.03	4 : 0.03	b : 0.01	F : 0.01	

#score	1308.8262587963454
#seq	58
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m1_run1.txt

#BEAR
[ffffffvvvvvvvvvvvvvfffff	chr12:31825120-31825384(-)$1	264	172	197	23.8217
[ccc[ccctttttttttttccc]cc	chr3:56656759-56657038(-)$1	279	68	93	23.3262
hhhhhhhuuuuuuuuuuuuhhhhhh	chr12:69232954-69233250(+)$1	296	42	67	21.4569
bffffffuuuuuuuuuuuuffffff	chr19:17514395-17514638(-)$1	243	197	222	23.5909
eeee[bbtttttttttttbb]eeee	chr2:33808749-33809087(-)$1	338	162	187	22.2259
hh!!bbvvvvvvvvvvvvvbb]hhh	chr2:65539801-65540105(-)$1	304	122	147	22.2399
=gggggggtttttttttttgggggg	chr2:39212614-39212879(-)$1	265	205	230	22.8764
gggg[bbtttttttttttbb]gggg	chr20:34214523-34214787(-)$1	264	77	102	22.6970
======vvvvvvvvvvvvv======	chr8:54959676-54959928(-)$1	252	76	101	24.2202
iiiiiiiwwwwwwwwwwwwwwiiii	chr6:116579516-116579780(-)$1	264	26	51	22.3807
eeeeyyyyyyyyyyyyyyyyeeeee	chr10:115806333-115806769(+)$1	436	304	329	21.1552
ffffffvvvvvvvvvvvvvffffff	chr7:151926922-151927187(-)$1	265	204	229	23.5694
:ffffffuuuuuuuuuuuuffffff	chr9:123943123-123943372(-)$1	249	37	62	22.9139
ggggggvvvvvvvvvvvvvgggggg	chr8:66630650-66630904(-)$1	254	6	31	24.1070
eccccccuuuuuuuuuuuuccc]cc	chr12:123776813-123777118(-)$1	305	9	34	24.1699
fffffbbtttttttttttbb]ffff	chr11:61068236-61068506(-)$1	270	189	214	22.2132
=======uuuuuuuuuuuu======	chr20:49506555-49506797(+)$1	242	83	108	24.5240
ggggcccvvvvvvvvvvvvvccc22	chr2:232578059-232578351(+)$1	292	58	83	23.8533
fffffwwwwwwwwwwwwwwffffff	chr5:137895509-137895774(-)$1	265	21	46	22.3134
:ffffffuuuuuuuuuuuuffffff	chr15:34525356-34525620(-)$1	264	185	210	22.9139
[ffffffuuuuuuuuuuuuffffff	chr12:1604918-1605199(+)$1	281	52	77	24.1527
!!eeeeevvvvvvvvvvvvveeeee	chr12:42481006-42481362(-)$1	356	113	138	23.5155
[fffffftttttttttttffffffb	chr7:92243997-92244326(-)$1	329	159	184	22.6060
[ddddyyyyyyyyyyyyyyyydddd	chr12:56631580-56631850(-)$1	270	49	74	20.8143
[ddddyyyyyyyyyyyyyyyydddd	chr6:34212523-34212805(+)$1	282	75	100	20.8143
[fffffftttttttttttffffff]	chr3:186507210-186507573(+)$1	363	217	242	22.9351
gccccccvvvvvvvvvvvvvccc]c	chr6:43480992-43481280(-)$1	288	133	158	23.9524
ffff[bbvvvvvvvvvvvvvbbfff	chr2:220074548-220074825(-)$1	277	183	208	22.9110
"""dddduuuuuuuuuuuudddd22	chr1:160968720-160968985(-)$1	265	115	140	23.5302
ee[cccvvvvvvvvvvvvvccceee	chr17:73314211-73314477(-)$1	266	76	101	24.0604
[cccyyyyyyyyyyyyyyyyccc]b	chr11:494466-494742(-)$1	276	57	82	21.4384
dddddwwwwwwwwwwwwwwdddd33	chr8:107763831-107764109(+)$1	278	159	184	21.8403
###dddduuuuuuuuuuuudddd22	chr10:70744597-70744916(+)$1	319	155	180	23.4065
dd[cccwwwwwwwwwwwwwwccc]d	chr9:14150074-14150343(-)$1	269	35	60	22.5953
gg[ddddvvvvvvvvvvvvvdddd3	chr9:5775643-5775973(+)$1	330	238	263	23.5561
=======uuuuuuuuuuuu======	chr16:30959159-30959435(+)$1	276	83	108	24.5240
cc!!ddddtttttttttttdddd22	chr1:70717471-70717832(+)$1	361	191	216	22.1906
ee[dddduuuuuuuuuuuuddddee	chr7:100849408-100849687(-)$1	279	47	72	23.7522
gg[dddduuuuuuuuuuuudddd]g	chr17:76168599-76168874(+)$1	275	178	203	24.0866
!ffffffwwwwwwwwwwwwwwffff	chr19:46393181-46393461(-)$1	280	227	252	22.3677
!eeeeewwwwwwwwwwwwwweeeee	chr1:155141779-155142130(-)$1	351	112	137	22.6936
cfffffftttttttttttffffff]	chr7:99752225-99752470(-)$1	245	88	113	22.5939
ffffyyyyyyyyyyyyyyyyfffff	chr15:34651223-34651489(-)$1	266	69	94	21.2467
eeeecccuuuuuuuuuuuuccc333	chr8:141569400-141569683(-)$1	283	170	195	24.3607
!eeeeewwwwwwwwwwwwwweeeee	chr15:72499366-72499720(-)$1	354	230	255	22.6936
eeee[bbuuuuuuuuuuuubbeeee	chr17:6917628-6917878(+)$1	250	96	121	23.4373
ee!!bbvvvvvvvvvvvvvbb22ee	chr8:52732260-52732563(-)$1	303	204	229	22.5099
[bb[ddddtttttttttttdddd]b	chr16:89629190-89629645(+)$1	455	138	163	21.9830
"eeeeevvvvvvvvvvvvveeeee]	chr16:29822319-29822587(+)$1	268	77	102	23.6532
""a[cccuuuuuuuuuuuuccc]a3	chr20:48521283-48521587(-)$1	304	149	174	24.3933
gggggwwwwwwwwwwwwwwgggggg	chr4:144336694-144336965(+)$1	271	236	261	22.8170
ggggggvvvvvvvvvvvvvgggggg	chr20:45838563-45838836(-)$1	273	137	162	24.1070
ee[ddddvvvvvvvvvvvvvdddd]	chr11:67053812-67054130(+)$1	318	96	121	23.3661
:fffffftttttttttttffffffd	chr22:37524025-37524325(-)$1	300	179	204	21.4767
ggggggguuuuuuuuuuuugggggg	chr7:13940264-13940514(-)$1	250	166	191	24.3254
""eeeeeuuuuuuuuuuuueeeee3	chr7:104747523-104747776(+)$1	253	203	228	23.7561
ee[dddduuuuuuuuuuuudddd]e	chr5:86686777-86687038(+)$1	261	211	236	23.8670
[ccc[ccctttttttttttccc]cc	chr11:102267468-102267743(-)$1	275	83	108	23.3262
eeeeewwwwwwwwwwwwwweeeee3	chr4:146058088-146058355(-)$1	267	159	184	22.2642
"""ddddtttttttttttdddd]ee	chrX:64743892-64744159(-)$1	267	17	42	22.4221
Hddddbbuuuuuuuuuuuubb]ddd	chr21:45193947-45194251(-)$1	304	8	33	22.0787
eeeeddddtttttttttttdddd]e	chr16:1415604-1415898(-)$1	294	60	85	22.4046
[bb[ddddtttttttttttddddbb	chr1:154990262-154990539(+)$1	277	237	262	21.5101
bb!!cccuuuuuuuuuuuuccc22b	chr6:30461104-30461357(+)$1	253	123	148	23.2448
[cccccctttttttttttccc]ccc	chr11:120358283-120358552(+)$1	269	219	244	23.1987
ggggggguuuuuuuuuuuugggggg	chr1:53513439-53513697(+)$1	258	144	169	24.3254
#gggggggtttttttttttgggggg	chr19:46190631-46190899(-)$1	268	151	176	22.9064

#otherMatches

#Seq PSSM
AGGAAAGCUUAUCAAAACUACUUUC	chr12:31825120-31825384(-)$1	264	172	197	23.8217
AAUGUUUUUUCUUUUAUUUAAAUCA	chr3:56656759-56657038(-)$1	279	68	93	23.3262
UGUGACUGAGCAGUUAAAGGGUUAC	chr12:69232954-69233250(+)$1	296	42	67	21.4569
GCGGGGCGGGGAAGCAGAGGCUCCG	chr19:17514395-17514638(-)$1	243	197	222	23.5909
GCAGGAGGCCCUUUAUUAUUGCUGC	chr2:33808749-33809087(-)$1	338	162	187	22.2259
UUCUGCCCCCCCAAAAUCUGUUGAA	chr2:65539801-65540105(-)$1	304	122	147	22.2399
AAGUGAUCUUUUGUGAAGUGAUCAU	chr2:39212614-39212879(-)$1	265	205	230	22.8764
UUGCUGCUGACUGAUGGUGCUGUGA	chr20:34214523-34214787(-)$1	264	77	102	22.6970
AGGUAUUUAAAAUCUAUUUAUGCUU	chr8:54959676-54959928(-)$1	252	76	101	24.2202
GGAGCUCAUCAAUGCUGCCAAGGGC	chr6:116579516-116579780(-)$1	264	26	51	22.3807
GUGCAAUAAAUACCAAUGAAGCACA	chr10:115806333-115806769(+)$1	436	304	329	21.1552
CAAAUAUGUAUUGAAUUUUUAUUUG	chr7:151926922-151927187(-)$1	265	204	229	23.5694
CUCACUGUACGGUUUAAUUUGGUGA	chr9:123943123-123943372(-)$1	249	37	62	22.9139
AGUUUUAUUUCAUGCACUGGAAACU	chr8:66630650-66630904(-)$1	254	6	31	24.1070
CUGGGGCAUUCAUUUGCUGGCCUCC	chr12:123776813-123777118(-)$1	305	9	34	24.1699
CCGCCCCAAGAUGCAGGAGGUGGUG	chr11:61068236-61068506(-)$1	270	189	214	22.2132
GAAAAACUCAAGGGUGUUUGUUUUU	chr20:49506555-49506797(+)$1	242	83	108	24.5240
UAAAAGGUUUCUUUUUUUUUCCUUU	chr2:232578059-232578351(+)$1	292	58	83	23.8533
GGCAGAGCCCCAAGUAAAGCUGUCA	chr5:137895509-137895774(-)$1	265	21	46	22.3134
UGUUUUGUUUCUCUUAACUCAAAAC	chr15:34525356-34525620(-)$1	264	185	210	22.9139
AUGACAUUACAAAGAAAUUGUGUUA	chr12:1604918-1605199(+)$1	281	52	77	24.1527
AAACAGUGCCAACACUCAAGACUGU	chr12:42481006-42481362(-)$1	356	113	138	23.5155
CAUUUGAUUUUUCUAACCUUGAAUG	chr7:92243997-92244326(-)$1	329	159	184	22.6060
UGCCCCACCCCUCCCCUCCCUGGGC	chr12:56631580-56631850(-)$1	270	49	74	20.8143
ACCUCACAGGAGAAGGAGGAAGAGG	chr6:34212523-34212805(+)$1	282	75	100	20.8143
UAGCAUAUCUGCCUUUAUUGUGUUU	chr3:186507210-186507573(+)$1	363	217	242	22.9351
ACUCUGGUUGCUAUCCUACUCCAUG	chr6:43480992-43481280(-)$1	288	133	158	23.9524
CCCUCUCAAAGACUAACCCAGAAGG	chr2:220074548-220074825(-)$1	277	183	208	22.9110
AGAAGGUGAUUUACAGCCAGCCUAG	chr1:160968720-160968985(-)$1	265	115	140	23.5302
UCCUGCUUCUCUUUUCCUCGCAGAU	chr17:73314211-73314477(-)$1	266	76	101	24.0604
UUCCUGCUGCUGCUCUCCCUGGACG	chr11:494466-494742(-)$1	276	57	82	21.4384
CAUAUUUCCUCAACAUACUGUGUCA	chr8:107763831-107764109(+)$1	278	159	184	21.8403
AAUGUUUUUACUAUAAAAUGAGCUA	chr10:70744597-70744916(+)$1	319	155	180	23.4065
AAAUACGAAUGUCAUUCCCAGUGCU	chr9:14150074-14150343(-)$1	269	35	60	22.5953
UGUUUCAAACCACCUUUCCCUGAAU	chr9:5775643-5775973(+)$1	330	238	263	23.5561
CGCGGGCAGCCGCUCUUCAGCUCGC	chr16:30959159-30959435(+)$1	276	83	108	24.5240
GAUAAUAAAACCCUUAAACUUAUGU	chr1:70717471-70717832(+)$1	361	191	216	22.1906
CCGCCUCACCCACUACCACGAGGGG	chr7:100849408-100849687(-)$1	279	47	72	23.7522
ACGGAAUAAAUGUUUUCUCAUUCAG	chr17:76168599-76168874(+)$1	275	178	203	24.0866
ACCUGCCCCGCCCCCUCCACAGGCA	chr19:46393181-46393461(-)$1	280	227	252	22.3677
UGGUCUGUACUACAUCAACAAGAUC	chr1:155141779-155142130(-)$1	351	112	137	22.6936
GCAAGGGUUCCCAGAGCUCCCUUGU	chr7:99752225-99752470(-)$1	245	88	113	22.5939
GGCACCUCCCAGACACCAAAUGCCU	chr15:34651223-34651489(-)$1	266	69	94	21.2467
GUUUACCAAAGAAAUUAAAGGUAAU	chr8:141569400-141569683(-)$1	283	170	195	24.3607
AGCCUGUCAUCUGUGCUACUCAGGC	chr15:72499366-72499720(-)$1	354	230	255	22.6936
GAGACUGAAUCCCUUCUCCCAUCUC	chr17:6917628-6917878(+)$1	250	96	121	23.4373
AAAAUCCCACAAAUUUUAUGAAAUU	chr8:52732260-52732563(-)$1	303	204	229	22.5099
AAGAGAAGAAUUUCAAAGCCUUCGC	chr16:89629190-89629645(+)$1	455	138	163	21.9830
UCGUGUUCCUGUGUCCCCUGCAUGU	chr16:29822319-29822587(+)$1	268	77	102	23.6532
UUGCACAUGCCCCUCUUACUGUACU	chr20:48521283-48521587(-)$1	304	149	174	24.3933
UCAAGAUAUUACUAUUCAACUUGAA	chr4:144336694-144336965(+)$1	271	236	261	22.8170
UUGUUUACAGAAGAGAAACAAACAA	chr20:45838563-45838836(-)$1	273	137	162	24.1070
GUUGGCGCACCCUCCCCUCCCGUCU	chr11:67053812-67054130(+)$1	318	96	121	23.3661
ACUUGGUGUAGACAGAUGGCCAGGG	chr22:37524025-37524325(-)$1	300	179	204	21.4767
CAGCAUUAAAAUUCAUUGAAAUGUU	chr7:13940264-13940514(-)$1	250	166	191	24.3254
CCUUAAAUUACUGGUAAAUUUUGAA	chr7:104747523-104747776(+)$1	253	203	228	23.7561
AUCUUGAUAUCUCGAACUUUCAAAA	chr5:86686777-86687038(+)$1	261	211	236	23.8670
AGUCAGUCAGAACUUCGUAGACCGA	chr11:102267468-102267743(-)$1	275	83	108	23.3262
AAGUGACAAGAAAAUAUACCAUUUG	chr4:146058088-146058355(-)$1	267	159	184	22.2642
AAAACGUGGACUUGAAUGACGUCCU	chrX:64743892-64744159(-)$1	267	17	42	22.4221
CAGAGGCUUCGCUCACUCCGCUCUC	chr21:45193947-45194251(-)$1	304	8	33	22.0787
AGUUAGAGGUUAUAAAUUGCUCUAA	chr16:1415604-1415898(-)$1	294	60	85	22.4046
GGGUGCUGGACCCCUUUUGCAGCCU	chr1:154990262-154990539(+)$1	277	237	262	21.5101
AGCCUAUUCCUUACCACCUGUAAUC	chr6:30461104-30461357(+)$1	253	123	148	23.2448
GUGUCUCCUUCCUUUUCAGAGAACA	chr11:120358283-120358552(+)$1	269	219	244	23.1987
UGACUGGUAAAAUGAAUCCUCAGUC	chr1:53513439-53513697(+)$1	258	144	169	24.3254
UGAGAAUAAUAAAGCUCUGUGUUUU	chr19:46190631-46190899(-)$1	268	151	176	22.9064

#DB
.((((((.............)))))	chr12:31825120-31825384(-)$1	1	172	197	23.8217
.(((.(((...........))).))	chr3:56656759-56657038(-)$1	1	68	93	23.3262
(((((((............))))))	chr12:69232954-69233250(+)$1	1	42	67	21.4569
)((((((............))))))	chr19:17514395-17514638(-)$1	1	197	222	23.5909
((((.((...........)).))))	chr2:33808749-33809087(-)$1	1	162	187	22.2259
((..((.............)).)))	chr2:65539801-65540105(-)$1	1	122	147	22.2399
)(((((((...........))))))	chr2:39212614-39212879(-)$1	1	205	230	22.8764
((((.((...........)).))))	chr20:34214523-34214787(-)$1	1	77	102	22.6970
((((((.............))))))	chr8:54959676-54959928(-)$1	1	76	101	24.2202
(((((((..............))))	chr6:116579516-116579780(-)$1	1	26	51	22.3807
((((................)))))	chr10:115806333-115806769(+)$1	1	304	329	21.1552
((((((.............))))))	chr7:151926922-151927187(-)$1	1	204	229	23.5694
.((((((............))))))	chr9:123943123-123943372(-)$1	1	37	62	22.9139
((((((.............))))))	chr8:66630650-66630904(-)$1	1	6	31	24.1070
(((((((............))).))	chr12:123776813-123777118(-)$1	1	9	34	24.1699
(((((((...........)).))))	chr11:61068236-61068506(-)$1	1	189	214	22.2132
(((((((............))))))	chr20:49506555-49506797(+)$1	1	83	108	24.5240
(((((((.............)))..	chr2:232578059-232578351(+)$1	1	58	83	23.8533
(((((..............))))))	chr5:137895509-137895774(-)$1	1	21	46	22.3134
.((((((............))))))	chr15:34525356-34525620(-)$1	1	185	210	22.9139
.((((((............))))))	chr12:1604918-1605199(+)$1	1	52	77	24.1527
..(((((.............)))))	chr12:42481006-42481362(-)$1	1	113	138	23.5155
.((((((...........)))))))	chr7:92243997-92244326(-)$1	1	159	184	22.6060
.((((................))))	chr12:56631580-56631850(-)$1	1	49	74	20.8143
.((((................))))	chr6:34212523-34212805(+)$1	1	75	100	20.8143
.((((((...........)))))).	chr3:186507210-186507573(+)$1	1	217	242	22.9351
(((((((.............))).)	chr6:43480992-43481280(-)$1	1	133	158	23.9524
((((.((.............)))))	chr2:220074548-220074825(-)$1	1	183	208	22.9110
...((((............))))..	chr1:160968720-160968985(-)$1	1	115	140	23.5302
((.(((.............))))))	chr17:73314211-73314477(-)$1	1	76	101	24.0604
.(((................))).)	chr11:494466-494742(-)$1	1	57	82	21.4384
(((((..............))))..	chr8:107763831-107764109(+)$1	1	159	184	21.8403
...((((............))))..	chr10:70744597-70744916(+)$1	1	155	180	23.4065
((.(((..............))).)	chr9:14150074-14150343(-)$1	1	35	60	22.5953
((.((((.............)))).	chr9:5775643-5775973(+)$1	1	238	263	23.5561
(((((((............))))))	chr16:30959159-30959435(+)$1	1	83	108	24.5240
((..((((...........))))..	chr1:70717471-70717832(+)$1	1	191	216	22.1906
((.((((............))))))	chr7:100849408-100849687(-)$1	1	47	72	23.7522
((.((((............)))).)	chr17:76168599-76168874(+)$1	1	178	203	24.0866
.((((((..............))))	chr19:46393181-46393461(-)$1	1	227	252	22.3677
.(((((..............)))))	chr1:155141779-155142130(-)$1	1	112	137	22.6936
(((((((...........)))))).	chr7:99752225-99752470(-)$1	1	88	113	22.5939
((((................)))))	chr15:34651223-34651489(-)$1	1	69	94	21.2467
(((((((............)))...	chr8:141569400-141569683(-)$1	1	170	195	24.3607
.(((((..............)))))	chr15:72499366-72499720(-)$1	1	230	255	22.6936
((((.((............))))))	chr17:6917628-6917878(+)$1	1	96	121	23.4373
((..((.............))..))	chr8:52732260-52732563(-)$1	1	204	229	22.5099
.((.((((...........)))).)	chr16:89629190-89629645(+)$1	1	138	163	21.9830
.(((((.............))))).	chr16:29822319-29822587(+)$1	1	77	102	23.6532
..(.(((............))).).	chr20:48521283-48521587(-)$1	1	149	174	24.3933
(((((..............))))))	chr4:144336694-144336965(+)$1	1	236	261	22.8170
((((((.............))))))	chr20:45838563-45838836(-)$1	1	137	162	24.1070
((.((((.............)))).	chr11:67053812-67054130(+)$1	1	96	121	23.3661
.((((((...........))))))(	chr22:37524025-37524325(-)$1	1	179	204	21.4767
(((((((............))))))	chr7:13940264-13940514(-)$1	1	166	191	24.3254
..(((((............))))).	chr7:104747523-104747776(+)$1	1	203	228	23.7561
((.((((............)))).)	chr5:86686777-86687038(+)$1	1	211	236	23.8670
.(((.(((...........))).))	chr11:102267468-102267743(-)$1	1	83	108	23.3262
(((((..............))))).	chr4:146058088-146058355(-)$1	1	159	184	22.2642
...((((...........)))).))	chrX:64743892-64744159(-)$1	1	17	42	22.4221
(((((((............)).)))	chr21:45193947-45194251(-)$1	1	8	33	22.0787
((((((((...........)))).)	chr16:1415604-1415898(-)$1	1	60	85	22.4046
.((.((((...........))))))	chr1:154990262-154990539(+)$1	1	237	262	21.5101
((..(((............)))..)	chr6:30461104-30461357(+)$1	1	123	148	23.2448
.((((((...........))).)))	chr11:120358283-120358552(+)$1	1	219	244	23.1987
(((((((............))))))	chr1:53513439-53513697(+)$1	1	144	169	24.3254
.(((((((...........))))))	chr19:46190631-46190899(-)$1	1	151	176	22.9064

#PSSM
[ : 0.17	e : 0.17	g : 0.14	f : 0.07	" : 0.07	= : 0.05	! : 0.05	: : 0.04	h : 0.02	b : 0.02	d : 0.02	# : 0.02	c : 0.02	i : 0.01	H : 0.01	
f : 0.22	e : 0.20	g : 0.16	c : 0.10	d : 0.07	" : 0.05	= : 0.04	b : 0.04	h : 0.02	i : 0.01	! : 0.01	# : 0.01	
f : 0.22	e : 0.16	g : 0.13	[ : 0.10	c : 0.08	! : 0.05	d : 0.05	= : 0.04	" : 0.02	b : 0.02	h : 0.01	i : 0.01	# : 0.01	a : 0.01	
f : 0.22	d : 0.17	e : 0.16	g : 0.13	c : 0.11	! : 0.05	= : 0.04	[ : 0.04	h : 0.01	i : 0.01	
d : 0.23	f : 0.19	c : 0.13	g : 0.10	[ : 0.08	e : 0.08	= : 0.04	y : 0.04	b : 0.02	h : 0.01	i : 0.01	
d : 0.17	f : 0.16	c : 0.16	b : 0.11	g : 0.08	y : 0.07	e : 0.07	w : 0.05	= : 0.04	h : 0.01	i : 0.01	
d : 0.17	f : 0.14	c : 0.13	v : 0.11	w : 0.10	b : 0.08	y : 0.07	g : 0.05	= : 0.02	e : 0.02	h : 0.01	i : 0.01	
u : 0.31	v : 0.22	t : 0.13	w : 0.13	y : 0.07	d : 0.05	c : 0.02	g : 0.02	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	t : 0.25	v : 0.22	w : 0.13	y : 0.07	
u : 0.31	v : 0.22	w : 0.13	t : 0.11	y : 0.07	f : 0.05	b : 0.04	d : 0.01	c : 0.01	
d : 0.16	f : 0.14	c : 0.11	v : 0.10	b : 0.10	g : 0.10	w : 0.07	y : 0.07	= : 0.04	e : 0.04	h : 0.01	
d : 0.19	f : 0.17	c : 0.17	g : 0.10	e : 0.10	b : 0.07	] : 0.04	= : 0.04	w : 0.02	y : 0.02	h : 0.01	
d : 0.22	f : 0.20	c : 0.16	e : 0.13	g : 0.11	] : 0.04	= : 0.04	h : 0.01	i : 0.01	b : 0.01	2 : 0.01	
f : 0.22	d : 0.22	e : 0.14	g : 0.11	] : 0.07	c : 0.07	= : 0.04	h : 0.02	2 : 0.02	i : 0.01	3 : 0.01	
f : 0.22	e : 0.19	g : 0.11	] : 0.10	2 : 0.07	d : 0.07	c : 0.05	= : 0.04	h : 0.02	3 : 0.02	i : 0.01	a : 0.01	b : 0.01	
e : 0.17	f : 0.16	g : 0.13	3 : 0.08	c : 0.07	b : 0.07	d : 0.07	2 : 0.05	] : 0.05	= : 0.04	h : 0.02	i : 0.01	

#score	1540.5835753993365
#seq	67
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m3_run2.txt

#BEAR
ccc[aqqqqqqqqaccc2	chr17:17749778-17750008(-)$1	230	82	100	13.5884
"""bbqqqqqqqqbb333	chr11:74551434-74551656(+)$1	222	29	47	12.6143
ee[bbqqqqqqqqbb]ee	chr10:93623969-93624194(+)$1	225	133	151	12.5112
""cccqqqqqqqqccc]d	chr1:24483124-24483346(-)$1	222	168	186	14.0876
ddcccqqqqqqqqccc]d	chr17:54941591-54941816(+)$1	225	67	85	13.9549
eeeeeqqqqqqqqeeeee	chr5:32227316-32227552(-)$1	236	86	104	13.6936
#ddddqqqqqqqqdddd4	chr8:17914325-17914549(-)$1	224	48	66	14.9871
iiiiiqqqqqqqqiiiii	chr1:115259614-115259835(-)$1	221	140	158	13.5869
eeeeeqqqqqqqqeeeee	chr1:90062943-90063173(+)$1	230	209	227	13.6936
fffffqqqqqqqqfffff	chr1:162495184-162495411(+)$1	227	29	47	13.0138
fffffqqqqqqqqfffff	chr10:64566414-64566645(+)$1	231	75	93	13.0138
Cddddqqqqqqqqdddd:	chr11:102268581-102268805(-)$1	224	28	46	12.9392
=====qqqqqqqq=====	chr6:28411128-28411354(-)$1	226	93	111	13.8458
fffffqqqqqqqqfffff	chr17:45773043-45773288(+)$1	245	120	138	13.0138
eeeeeqqqqqqqqeeeee	chr6:107979637-107979888(+)$1	251	11	29	13.6936
fffffqqqqqqqqfffff	chr17:54941079-54941307(+)$1	228	148	166	13.0138
[ddddqqqqqqqqdddd]	chr17:42477718-42477955(-)$1	237	93	111	15.1208
[ddddqqqqqqqqdddd]	chr17:79880350-79880572(-)$1	222	138	156	15.1208
gggggqqqqqqqqggggg	chr10:105356479-105356699(-)$1	220	78	96	13.5219
[ddddqqqqqqqqddddd	chr4:183811685-183811908(-)$1	223	48	66	14.8528
fffffqqqqqqqqfffff	chr16:29831049-29831324(+)$1	275	189	207	13.0138
gddddqqqqqqqqdddd]	chr1:207218114-207218345(-)$1	231	79	97	14.9248
!ddddqqqqqqqqdddd3	chr1:205758436-205758673(-)$1	237	93	111	15.1094
fffffqqqqqqqqfffff	chr1:205682375-205682599(-)$1	224	93	111	13.0138
cccccqqqqqqqqccc]c	chr20:49369135-49369368(+)$1	233	107	125	14.0577
=====qqqqqqqq=====	chr8:26218508-26218731(+)$1	223	175	193	13.8458
b[cccqqqqqqqqcccbb	chr11:4116035-4116272(+)$1	237	147	165	13.3039
eeeeeqqqqqqqqeeeee	chr6:118638649-118638881(+)$1	232	210	228	13.6936
!!cccqqqqqqqqccc]a	chr7:2473538-2473763(+)$1	225	172	190	14.2852
[ddddqqqqqqqqdddd]	chr13:28197327-28197558(+)$1	231	183	201	15.1208
[ddddqqqqqqqqdddd]	chr3:38531089-38531311(+)$1	222	125	143	15.1208
eeeeeqqqqqqqqeeeee	chr11:1296691-1296911(-)$1	220	20	38	13.6936
iiiiiqqqqqqqqiiiii	chr12:74933101-74933325(+)$1	224	6	24	13.5869
&ddddqqqqqqqqdddd9	chr17:7120482-7120723(-)$1	241	53	71	13.7363
bbcccqqqqqqqqccc33	chr17:39845069-39845333(+)$1	264	232	250	13.6671
"ddddqqqqqqqqdddd3	chr15:93569614-93569846(+)$1	232	127	145	15.0902
[ddddqqqqqqqqdddd3	chr9:137023465-137023722(+)$1	257	55	73	15.1108
""cccqqqqqqqqcccdd	chr3:122599442-122599663(+)$1	221	180	198	14.1719
cc[bbqqqqqqqqbb]cc	chr16:66650675-66650905(-)$1	230	23	41	12.4823
:ddddqqqqqqqqdddd:	chr19:11243889-11244130(+)$1	241	10	28	13.1688
#ddddqqqqqqqqddddf	chr2:29405536-29405787(+)$1	251	24	42	14.8710
:ddddqqqqqqqqdddde	chrX:150573796-150574031(+)$1	235	104	122	13.9586
"ddddqqqqqqqqdddd]	chr15:70342076-70342298(-)$1	222	146	164	15.1002
cccccqqqqqqqqccc]c	chr7:148980409-148980637(+)$1	228	181	199	14.0577
eeeeeqqqqqqqqeeeee	chr1:234519598-234519825(+)$1	227	50	68	13.6936
=====qqqqqqqq=====	chr17:36957434-36957665(-)$1	231	107	125	13.8458
:ddddqqqqqqqqdddd:	chr1:234527086-234527307(-)$1	221	181	199	13.1688
eeeeeqqqqqqqqeeeee	chr5:179135203-179135424(+)$1	221	75	93	13.6936
eeeeeqqqqqqqqeeeee	chr14:20923413-20923644(+)$1	231	33	51	13.6936
""cccqqqqqqqqccc]d	chr22:41620064-41620288(+)$1	224	200	218	14.0876
fff[aqqqqqqqqaffff	chr17:47005070-47005315(+)$1	245	104	122	13.0764
:ddddqqqqqqqqdddd:	chr13:77579311-77579538(-)$1	227	185	203	13.1688
cccccqqqqqqqqccc]c	chr19:36726477-36726719(+)$1	242	195	213	14.0577
:ddddqqqqqqqqdddde	chr17:17093134-17093365(+)$1	231	5	23	13.9586
:ddddqqqqqqqqdddde	chr11:69467790-69468029(+)$1	239	24	42	13.9586
eeeeeqqqqqqqqeeeee	chr9:116169529-116169752(-)$1	223	200	218	13.6936
h[cccqqqqqqqqccchh	chr21:44835356-44835587(-)$1	231	178	196	13.3525
fffffqqqqqqqqfffff	chr22:38881829-38882109(-)$1	280	215	233	13.0138
iiiiiqqqqqqqqiiiii	chr2:85545139-85545362(-)$1	223	167	185	13.5869
fffffqqqqqqqqfffff	chr9:138900848-138901077(-)$1	229	66	84	13.0138
b[cccqqqqqqqqccc33	chr4:77057332-77057563(-)$1	231	17	35	13.9993
d[cccqqqqqqqqccc]d	chr3:137780924-137781147(-)$1	223	92	110	13.8412
:ddddqqqqqqqqdddd:	chr8:66515930-66516161(-)$1	231	123	141	13.1688
fffffqqqqqqqqfffff	chr17:76101252-76101488(+)$1	236	2	20	13.0138
[ddddqqqqqqqqddddb	chr3:183637779-183638029(-)$1	250	9	27	14.7166
!ddddqqqqqqqqddddc	chr3:47893399-47893637(-)$1	238	161	179	14.9416
"ddddqqqqqqqqdddd]	chrX:105922423-105922654(+)$1	231	16	34	15.1002
!ddddqqqqqqqqdddd2	chr9:134375231-134375470(+)$1	239	190	208	14.8791
fddddqqqqqqqqdddd]	chr10:101910276-101910502(-)$1	226	124	142	14.8575
fffffqqqqqqqqfffff	chr14:62261658-62261889(+)$1	231	47	65	13.0138
ddd[aqqqqqqqqa]ddd	chr22:22293803-22294041(-)$1	238	186	204	13.6663
dddddqqqqqqqqdddd:	chr22:41753628-41753851(+)$1	223	129	147	13.8014
[ddddqqqqqqqqddddd	chr14:93708483-93708727(-)$1	244	188	206	14.8528

#otherMatches

#Seq PSSM
UGCUCUGCUCCCUGGCAU	chr17:17749778-17750008(-)$1	230	82	100	13.5884
UUUACUAAGUAAUGUUAU	chr11:74551434-74551656(+)$1	222	29	47	12.6143
GAAGCAUGCUUAAGCAUC	chr10:93623969-93624194(+)$1	225	133	151	12.5112
CUCCCCCAUCCCAGGGCU	chr1:24483124-24483346(-)$1	222	168	186	14.0876
aaauaccauuagcuaucu	chr17:54941591-54941816(+)$1	225	67	85	13.9549
CAAUGGAUUUAUAUAUUG	chr5:32227316-32227552(-)$1	236	86	104	13.6936
GACAGACAUUCACCUGUA	chr8:17914325-17914549(-)$1	224	48	66	14.9871
GAGGGCGGUUUUAUCUUC	chr1:115259614-115259835(-)$1	221	140	158	13.5869
GAGUGAAAGCUAGCAUUU	chr1:90062943-90063173(+)$1	230	209	227	13.6936
CCCAGUUACUUCUUUGGG	chr1:162495184-162495411(+)$1	227	29	47	13.0138
UCUGUAUUUUCUAACGGG	chr10:64566414-64566645(+)$1	231	75	93	13.0138
UGUGAGAAUAUUGUCACC	chr11:102268581-102268805(-)$1	224	28	46	12.9392
GUUUAUCAUUCUUUGGGC	chr6:28411128-28411354(-)$1	226	93	111	13.8458
GCAGGAGCCUGCCCCUGC	chr17:45773043-45773288(+)$1	245	120	138	13.0138
CUCUGCUUCUCCCCAGAG	chr6:107979637-107979888(+)$1	251	11	29	13.6936
AGCUUUAUUUAAUAAGUU	chr17:54941079-54941307(+)$1	228	148	166	13.0138
AAGGACCCAAACAUCCUA	chr17:42477718-42477955(-)$1	237	93	111	15.1208
UGGCGAAUUUGGcugccc	chr17:79880350-79880572(-)$1	222	138	156	15.1208
ACAGACACAGAUCUCUGU	chr10:105356479-105356699(-)$1	220	78	96	13.5219
UCAAUUUGGGUUUGUUGG	chr4:183811685-183811908(-)$1	223	48	66	14.8528
UGUUUUUUCUAUUGAACA	chr16:29831049-29831324(+)$1	275	189	207	13.0138
CUUAAAAUUAUUAUUGAU	chr1:207218114-207218345(-)$1	231	79	97	14.9248
CUUCCUCAUCUCUGGAAU	chr1:205758436-205758673(-)$1	237	93	111	15.1094
AUUUUGUAUUAAAAAAAU	chr1:205682375-205682599(-)$1	224	93	111	13.0138
ACUCCGCUUUGAAGGAUG	chr20:49369135-49369368(+)$1	233	107	125	14.0577
CUUUGGUGUUUGGUGAAG	chr8:26218508-26218731(+)$1	223	175	193	13.8458
CCGGCGCUUUAGAGCCGC	chr11:4116035-4116272(+)$1	237	147	165	13.3039
UUGUCUGCACUAUGACAA	chr6:118638649-118638881(+)$1	232	210	228	13.6936
CUGGAGUAAAAUAUCCCC	chr7:2473538-2473763(+)$1	225	172	190	14.2852
UGUUGACCCCUUGCAGCU	chr13:28197327-28197558(+)$1	231	183	201	15.1208
GGGGUGGGAUGGGACUCG	chr3:38531089-38531311(+)$1	222	125	143	15.1208
AUAAAUAUUUAUUUUUGU	chr11:1296691-1296911(-)$1	220	20	38	13.6936
CUUGGUCCUUAAGUCAGG	chr12:74933101-74933325(+)$1	224	6	24	13.5869
UAGGGcccccuuccccuc	chr17:7120482-7120723(-)$1	241	53	71	13.7363
CCAGAACCUCCACUCUUU	chr17:39845069-39845333(+)$1	264	232	250	13.6671
UGCUGAACCCUCACAGUU	chr15:93569614-93569846(+)$1	232	127	145	15.0902
UGGCCUCCCCUUUGGCCC	chr9:137023465-137023722(+)$1	257	55	73	15.1108
CCUGCUCCUCUCUGCACC	chr3:122599442-122599663(+)$1	221	180	198	14.1719
UGCCUGAAAAGAGAGAUG	chr16:66650675-66650905(-)$1	230	23	41	12.4823
aaUCCUCCAGUCUGGAUC	chr19:11243889-11244130(+)$1	241	10	28	13.1688
UUUAUGAAUUCAAGUAAU	chr2:29405536-29405787(+)$1	251	24	42	14.8710
CUCCACUUUACGCUGGAA	chrX:150573796-150574031(+)$1	235	104	122	13.9586
CGGUUCCCCCACAGACCC	chr15:70342076-70342298(-)$1	222	146	164	15.1002
CCCAGAAAGCACCCUGAG	chr7:148980409-148980637(+)$1	228	181	199	14.0577
GAACAUCAAUACUUGUUC	chr1:234519598-234519825(+)$1	227	50	68	13.6936
UUGCAGUCUCCAAUGUAG	chr17:36957434-36957665(-)$1	231	107	125	13.8458
GUAUUCUUCCUUUAAUAA	chr1:234527086-234527307(-)$1	221	181	199	13.1688
CAGGUGAUAAAGGACUUG	chr5:179135203-179135424(+)$1	221	75	93	13.6936
CUCUUUUGCUCAUAAGAG	chr14:20923413-20923644(+)$1	231	33	51	13.6936
GCCCCAGGCCAGAGGGAC	chr22:41620064-41620288(+)$1	224	200	218	14.0876
UCUAGAUGUAAGACAGAA	chr17:47005070-47005315(+)$1	245	104	122	13.0764
UAAACUUAAAAAUGUUUC	chr13:77579311-77579538(-)$1	227	185	203	13.1688
AAUAUAAGAAAAAAUACU	chr19:36726477-36726719(+)$1	242	195	213	14.0577
UUCCCUGCAAGCUGGGAU	chr17:17093134-17093365(+)$1	231	5	23	13.9586
ACAAAAUAGACAAUUUGC	chr11:69467790-69468029(+)$1	239	24	42	13.9586
UUGUAAUGCUUUGUACAA	chr9:116169529-116169752(-)$1	223	200	218	13.6936
CUCCCUCAGCACUGGGGU	chr21:44835356-44835587(-)$1	231	178	196	13.3525
AGGAACACUGUCuuuccu	chr22:38881829-38882109(-)$1	280	215	233	13.0138
GUUUUGUUGAACAGAAAC	chr2:85545139-85545362(-)$1	223	167	185	13.5869
AAAUUUGCACUUUAAUUU	chr9:138900848-138901077(-)$1	229	66	84	13.0138
UCAGCCUACACAAGCUCC	chr4:77057332-77057563(-)$1	231	17	35	13.9993
gugauccuggagaguuuc	chr3:137780924-137781147(-)$1	223	92	110	13.8412
CUAGAAAAACAACUCUAC	chr8:66515930-66516161(-)$1	231	123	141	13.1688
UUCAGAUUGUGGGCUGGA	chr17:76101252-76101488(+)$1	236	2	20	13.0138
UCUGCAACUUUAAGCAGC	chr3:183637779-183638029(-)$1	250	9	27	14.7166
UUCUUUUCUAACCAAGAG	chr3:47893399-47893637(-)$1	238	161	179	14.9416
CAGUUAAGCUAUAAACUU	chrX:105922423-105922654(+)$1	231	16	34	15.1002
AAAUCGAAUCGUGGAUUC	chr9:134375231-134375470(+)$1	239	190	208	14.8791
GCCCAGAUUUGAAUGGGU	chr10:101910276-101910502(-)$1	226	124	142	14.8575
AGAGCCUGGUGUAGUUUU	chr14:62261658-62261889(+)$1	231	47	65	13.0138
CAAAGGGUGACGACAUUG	chr22:22293803-22294041(-)$1	238	186	204	13.6663
GGCCCAAAGCUCAGGGCU	chr22:41753628-41753851(+)$1	223	129	147	13.8014
CAUCAAUGCCAGCUGAUA	chr14:93708483-93708727(-)$1	244	188	206	14.8528

#DB
(((.(........)))).	chr17:17749778-17750008(-)$1	1	82	100	13.5884
...((........))...	chr11:74551434-74551656(+)$1	1	29	47	12.6143
((.((........)).))	chr10:93623969-93624194(+)$1	1	133	151	12.5112
..(((........))).)	chr1:24483124-24483346(-)$1	1	168	186	14.0876
(((((........))).)	chr17:54941591-54941816(+)$1	1	67	85	13.9549
(((((........)))))	chr5:32227316-32227552(-)$1	1	86	104	13.6936
.((((........)))).	chr8:17914325-17914549(-)$1	1	48	66	14.9871
(((((........)))))	chr1:115259614-115259835(-)$1	1	140	158	13.5869
(((((........)))))	chr1:90062943-90063173(+)$1	1	209	227	13.6936
(((((........)))))	chr1:162495184-162495411(+)$1	1	29	47	13.0138
(((((........)))))	chr10:64566414-64566645(+)$1	1	75	93	13.0138
(((((........)))).	chr11:102268581-102268805(-)$1	1	28	46	12.9392
(((((........)))))	chr6:28411128-28411354(-)$1	1	93	111	13.8458
(((((........)))))	chr17:45773043-45773288(+)$1	1	120	138	13.0138
(((((........)))))	chr6:107979637-107979888(+)$1	1	11	29	13.6936
(((((........)))))	chr17:54941079-54941307(+)$1	1	148	166	13.0138
.((((........)))).	chr17:42477718-42477955(-)$1	1	93	111	15.1208
.((((........)))).	chr17:79880350-79880572(-)$1	1	138	156	15.1208
(((((........)))))	chr10:105356479-105356699(-)$1	1	78	96	13.5219
.((((........)))))	chr4:183811685-183811908(-)$1	1	48	66	14.8528
(((((........)))))	chr16:29831049-29831324(+)$1	1	189	207	13.0138
(((((........)))).	chr1:207218114-207218345(-)$1	1	79	97	14.9248
.((((........)))).	chr1:205758436-205758673(-)$1	1	93	111	15.1094
(((((........)))))	chr1:205682375-205682599(-)$1	1	93	111	13.0138
(((((........))).)	chr20:49369135-49369368(+)$1	1	107	125	14.0577
(((((........)))))	chr8:26218508-26218731(+)$1	1	175	193	13.8458
(.(((........)))))	chr11:4116035-4116272(+)$1	1	147	165	13.3039
(((((........)))))	chr6:118638649-118638881(+)$1	1	210	228	13.6936
..(((........))).)	chr7:2473538-2473763(+)$1	1	172	190	14.2852
.((((........)))).	chr13:28197327-28197558(+)$1	1	183	201	15.1208
.((((........)))).	chr3:38531089-38531311(+)$1	1	125	143	15.1208
(((((........)))))	chr11:1296691-1296911(-)$1	1	20	38	13.6936
(((((........)))))	chr12:74933101-74933325(+)$1	1	6	24	13.5869
.((((........)))).	chr17:7120482-7120723(-)$1	1	53	71	13.7363
(((((........)))..	chr17:39845069-39845333(+)$1	1	232	250	13.6671
.((((........)))).	chr15:93569614-93569846(+)$1	1	127	145	15.0902
.((((........)))).	chr9:137023465-137023722(+)$1	1	55	73	15.1108
..(((........)))))	chr3:122599442-122599663(+)$1	1	180	198	14.1719
((.((........)).))	chr16:66650675-66650905(-)$1	1	23	41	12.4823
.((((........)))).	chr19:11243889-11244130(+)$1	1	10	28	13.1688
.((((........)))))	chr2:29405536-29405787(+)$1	1	24	42	14.8710
.((((........))))(	chrX:150573796-150574031(+)$1	1	104	122	13.9586
.((((........)))).	chr15:70342076-70342298(-)$1	1	146	164	15.1002
(((((........))).)	chr7:148980409-148980637(+)$1	1	181	199	14.0577
(((((........)))))	chr1:234519598-234519825(+)$1	1	50	68	13.6936
(((((........)))))	chr17:36957434-36957665(-)$1	1	107	125	13.8458
.((((........)))).	chr1:234527086-234527307(-)$1	1	181	199	13.1688
(((((........)))))	chr5:179135203-179135424(+)$1	1	75	93	13.6936
(((((........)))))	chr14:20923413-20923644(+)$1	1	33	51	13.6936
..(((........))).)	chr22:41620064-41620288(+)$1	1	200	218	14.0876
(((.(........)))))	chr17:47005070-47005315(+)$1	1	104	122	13.0764
.((((........)))).	chr13:77579311-77579538(-)$1	1	185	203	13.1688
(((((........))).)	chr19:36726477-36726719(+)$1	1	195	213	14.0577
.((((........))))(	chr17:17093134-17093365(+)$1	1	5	23	13.9586
.((((........))))(	chr11:69467790-69468029(+)$1	1	24	42	13.9586
(((((........)))))	chr9:116169529-116169752(-)$1	1	200	218	13.6936
(.(((........)))))	chr21:44835356-44835587(-)$1	1	178	196	13.3525
(((((........)))))	chr22:38881829-38882109(-)$1	1	215	233	13.0138
(((((........)))))	chr2:85545139-85545362(-)$1	1	167	185	13.5869
(((((........)))))	chr9:138900848-138901077(-)$1	1	66	84	13.0138
(.(((........)))..	chr4:77057332-77057563(-)$1	1	17	35	13.9993
(.(((........))).)	chr3:137780924-137781147(-)$1	1	92	110	13.8412
.((((........)))).	chr8:66515930-66516161(-)$1	1	123	141	13.1688
(((((........)))))	chr17:76101252-76101488(+)$1	1	2	20	13.0138
.((((........)))))	chr3:183637779-183638029(-)$1	1	9	27	14.7166
.((((........)))))	chr3:47893399-47893637(-)$1	1	161	179	14.9416
.((((........)))).	chrX:105922423-105922654(+)$1	1	16	34	15.1002
.((((........)))).	chr9:134375231-134375470(+)$1	1	190	208	14.8791
(((((........)))).	chr10:101910276-101910502(-)$1	1	124	142	14.8575
(((((........)))))	chr14:62261658-62261889(+)$1	1	47	65	13.0138
(((.(........).)))	chr22:22293803-22294041(-)$1	1	186	204	13.6663
)((((........)))).	chr22:41753628-41753851(+)$1	1	129	147	13.8014
.((((........)))))	chr14:93708483-93708727(-)$1	1	188	206	14.8528

#PSSM
f : 0.16	e : 0.13	[ : 0.10	" : 0.09	: : 0.09	c : 0.06	d : 0.05	! : 0.05	i : 0.04	= : 0.04	b : 0.04	# : 0.02	g : 0.02	C : 0.01	& : 0.01	h : 0.01	
d : 0.41	f : 0.15	e : 0.13	c : 0.06	" : 0.05	[ : 0.05	i : 0.04	= : 0.04	g : 0.01	! : 0.01	b : 0.01	
d : 0.39	c : 0.19	f : 0.15	e : 0.12	i : 0.04	= : 0.04	[ : 0.02	" : 0.01	g : 0.01	
d : 0.38	c : 0.17	f : 0.13	e : 0.12	[ : 0.04	b : 0.04	i : 0.04	= : 0.04	g : 0.01	
d : 0.38	c : 0.17	f : 0.13	e : 0.12	a : 0.04	b : 0.04	i : 0.04	= : 0.04	g : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.38	c : 0.17	f : 0.13	e : 0.12	a : 0.04	b : 0.04	i : 0.04	= : 0.04	g : 0.01	
d : 0.38	c : 0.19	f : 0.15	e : 0.12	b : 0.04	i : 0.04	= : 0.04	g : 0.01	] : 0.01	
d : 0.39	c : 0.19	f : 0.15	e : 0.12	i : 0.04	= : 0.04	] : 0.02	3 : 0.01	g : 0.01	
d : 0.41	f : 0.15	e : 0.13	] : 0.10	3 : 0.04	i : 0.04	= : 0.04	c : 0.02	g : 0.01	b : 0.01	h : 0.01	
e : 0.17	f : 0.16	d : 0.10	] : 0.10	3 : 0.08	: : 0.08	c : 0.06	i : 0.04	= : 0.04	2 : 0.02	b : 0.02	4 : 0.01	g : 0.01	a : 0.01	9 : 0.01	h : 0.01	

#score	1012.9731550325841
#seq	73
#width	18
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m3_run2.txt

#BEAR
eeeeemmmmeeeee	chr9:129159202-129159419(+)$1	217	99	113	11.4051
eeeeemmmmeeeee	chr15:64975468-64975691(+)$1	223	147	161	11.4051
eeeeemmmmeeeee	chr6:12718841-12719059(+)$1	218	196	210	11.4051
eeeeemmmmeeeee	chr14:105862211-105862427(-)$1	216	54	68	11.4051
eeeeemmmmeeeee	chr5:179264822-179265043(+)$1	221	166	180	11.4051
eeeeemmmmeeeee	chr10:97073622-97073844(-)$1	222	170	184	11.4051
eeeeemmmmeeeee	chr5:66410215-66410432(-)$1	217	87	101	11.4051
eeeeemmmmeeeee	chrX:13791927-13792151(-)$1	224	13	27	11.4051
eeeeemmmmeeeee	chr3:178737994-178738231(-)$1	237	13	27	11.4051
eeeeemmmmeeeee	chr10:73976703-73976945(+)$1	242	140	154	11.4051
eeeeemmmmeeeee	chrX:148561602-148561827(-)$1	225	125	139	11.4051
eeeeeooooooeee	chr4:176555684-176555924(-)$1	240	96	110	9.3713
eeeeeooooooeee	chr16:71764749-71764964(+)$1	215	154	168	9.3713
eeeeemmmmeeeee	chr16:58705002-58705217(+)$1	215	47	61	11.4051
eeeeemmmmeeeee	chr4:48069167-48069383(-)$1	216	102	116	11.4051
eeeeemmmmeeeee	chr11:111966165-111966383(+)$1	218	202	216	11.4051
eeeeemmmmeeeee	chr3:86120785-86121006(+)$1	221	141	155	11.4051
eeeeemmmmeeeee	chr11:6631955-6632177(+)$1	222	44	58	11.4051
eeeeemmmmeeeee	chr1:101706689-101706917(+)$1	228	50	64	11.4051
eeeeellleeeeee	chr1:11722377-11722606(+)$1	229	159	173	9.8745
eeeeemmmmeeeee	chr4:176555926-176556142(-)$1	216	197	211	11.4051
eee[ammmma]eee	chr3:188593553-188593771(-)$1	218	173	187	9.0458
eeeeemmmmeeeee	chr6:30038721-30038939(+)$1	218	94	108	11.4051
eeeeemmmmeeeee	chr6:24705820-24706035(-)$1	215	117	131	11.4051
eeeeemmmmeeeee	chr1:205500855-205501074(+)$1	219	154	168	11.4051
eeeeeooooooeee	chr12:75816858-75817085(+)$1	227	129	143	9.3713
eeeee4444eeeee	chr5:10437069-10437294(+)$1	225	67	81	9.2792
eeeeeooooooeee	chr3:17202244-17202473(-)$1	229	52	66	9.3713
eeeeeooooooeee	chr3:47883077-47883309(+)$1	232	142	156	9.3713
eeeeeooooooeee	chr15:43487163-43487388(+)$1	225	10	24	9.3713
eeeeellleeeeee	chr1:41091754-41091977(-)$1	223	148	162	9.8745
eeeeeooooooeee	chr13:99445665-99445891(-)$1	226	196	210	9.3713
eeeeemmmmeeeee	chr10:24833938-24834175(+)$1	237	57	71	11.4051
[eeeeellleeeee	chr10:126306275-126306493(+)$1	218	50	64	9.5021
eeeeeooooooeee	chr7:99751597-99751848(+)$1	251	33	47	9.3713
eeeeemmmmeeeee	chr9:132650995-132651215(+)$1	220	66	80	11.4051
eeeee4444eeeee	chr16:29498630-29498877(-)$1	247	124	138	9.2792
eeeeemmmmeeeee	chr11:122929785-122930012(-)$1	227	42	56	11.4051
eeeee4444eeeee	chr7:151254087-151254307(+)$1	220	97	111	9.2792
eeeeemmmmeeeee	chr14:21493227-21493453(-)$1	226	27	41	11.4051
eeeeemmmmeeeee	chr10:120795325-120795544(-)$1	219	71	85	11.4051
eeeeemmmmeeeee	chr1:159888018-159888243(-)$1	225	59	73	11.4051
eeeeemmmmeeeee	chr16:30095896-30096113(-)$1	217	101	115	11.4051
#eeeeellleeeee	chr12:109490649-109490868(-)$1	219	103	117	9.2975
eeeeemmmmeeeee	chr12:57924211-57924433(-)$1	222	101	115	11.4051
eeeeemmmmeeeee	chr6:138665419-138665645(+)$1	226	141	155	11.4051
[eeeeellleeeee	chr21:27106902-27107141(-)$1	239	183	197	9.5021
eeeeemmmmeeeee	chr1:156213795-156214041(-)$1	246	182	196	11.4051
!eeeeellleeeee	chr2:225337665-225337920(-)$1	255	8	22	9.4976
eeeeellleeeee=	chr21:34400452-34400671(+)$1	219	127	141	9.2860
[eeeeellleeeee	chr15:73853009-73853229(-)$1	220	76	90	9.5021

#otherMatches

#Seq PSSM
GCUGGGGAGUCAGC	chr9:129159202-129159419(+)$1	217	99	113	11.4051
AGAGGAUCCCCUCU	chr15:64975468-64975691(+)$1	223	147	161	11.4051
UUGAGUCAGCUCAA	chr6:12718841-12719059(+)$1	218	196	210	11.4051
UGGAGACCCCUCCA	chr14:105862211-105862427(-)$1	216	54	68	11.4051
CUUUCUGCUGGAAG	chr5:179264822-179265043(+)$1	221	166	180	11.4051
AGGACGUCUGUUCU	chr10:97073622-97073844(-)$1	222	170	184	11.4051
UCAGUGAAGACUGA	chr5:66410215-66410432(-)$1	217	87	101	11.4051
CAGAUGAAAAUUUG	chrX:13791927-13792151(-)$1	224	13	27	11.4051
AGGGGAGAACCCCU	chr3:178737994-178738231(-)$1	237	13	27	11.4051
CAGUGGAAACACUG	chr10:73976703-73976945(+)$1	242	140	154	11.4051
GGUCUAGACAGACC	chrX:148561602-148561827(-)$1	225	125	139	11.4051
UUUGAAAUUUCUCA	chr4:176555684-176555924(-)$1	240	96	110	9.3713
CCUCUACACAAAGA	chr16:71764749-71764964(+)$1	215	154	168	9.3713
CAGACCAGCGUCUG	chr16:58705002-58705217(+)$1	215	47	61	11.4051
AUCACUUCAGUGAU	chr4:48069167-48069383(-)$1	216	102	116	11.4051
UUGUUCUAAAACAA	chr11:111966165-111966383(+)$1	218	202	216	11.4051
UUAUAACUUUAUAA	chr3:86120785-86121006(+)$1	221	141	155	11.4051
GCCCCAAGAGGGGC	chr11:6631955-6632177(+)$1	222	44	58	11.4051
UUGGAUUUUUCUAA	chr1:101706689-101706917(+)$1	228	50	64	11.4051
CCAGUACUGCUGGC	chr1:11722377-11722606(+)$1	229	159	173	9.8745
GUAAGGUGACUUAU	chr4:176555926-176556142(-)$1	216	197	211	11.4051
UUGGCAGUUGGCAA	chr3:188593553-188593771(-)$1	218	173	187	9.0458
GUGGGGAAUUCCAC	chr6:30038721-30038939(+)$1	218	94	108	11.4051
AUAAUCACAGUUGU	chr6:24705820-24706035(-)$1	215	117	131	11.4051
CCUGGAAUCCUAGG	chr1:205500855-205501074(+)$1	219	154	168	11.4051
GACAUACCAGAGUG	chr12:75816858-75817085(+)$1	227	129	143	9.3713
AAGUGUAAUUCUUG	chr5:10437069-10437294(+)$1	225	67	81	9.2792
GCCACCCUUCAGUG	chr3:17202244-17202473(-)$1	229	52	66	9.3713
CAGCUAAGGUGAGU	chr3:47883077-47883309(+)$1	232	142	156	9.3713
ACCAAAGAUUGUUG	chr15:43487163-43487388(+)$1	225	10	24	9.3713
CGGCCACUGGUCGG	chr1:41091754-41091977(-)$1	223	148	162	9.8745
AGGAUACCAAAAUC	chr13:99445665-99445891(-)$1	226	196	210	9.3713
GCAGUCCAAACUGC	chr10:24833938-24834175(+)$1	237	57	71	11.4051
GUCCUGGUUUAGGA	chr10:126306275-126306493(+)$1	218	50	64	9.5021
GCCUCUGUGAUGAG	chr7:99751597-99751848(+)$1	251	33	47	9.3713
AGGAGCAAUUUCCU	chr9:132650995-132651215(+)$1	220	66	80	11.4051
GCUUUAUCUGAUGA	chr16:29498630-29498877(-)$1	247	124	138	9.2792
GCUGUCCAGGCAGC	chr11:122929785-122930012(-)$1	227	42	56	11.4051
UGAUAUACAUUCUU	chr7:151254087-151254307(+)$1	220	97	111	9.2792
CUGGAAGCGUCCAG	chr14:21493227-21493453(-)$1	226	27	41	11.4051
CCAAUCUAAAUUGG	chr10:120795325-120795544(-)$1	219	71	85	11.4051
UGCUUCUACAAGUA	chr1:159888018-159888243(-)$1	225	59	73	11.4051
GGGGCUCACGCCCC	chr16:30095896-30096113(-)$1	217	101	115	11.4051
AUUGGUGUUGCCGA	chr12:109490649-109490868(-)$1	219	103	117	9.2975
GGGGUUUAUACCCC	chr12:57924211-57924433(-)$1	222	101	115	11.4051
UAUAUGUUGAUAUA	chr6:138665419-138665645(+)$1	226	141	155	11.4051
ACCCUCUCUGAGGG	chr21:27106902-27107141(-)$1	239	183	197	9.5021
GCCCAGAUUUGGGC	chr1:156213795-156214041(-)$1	246	182	196	11.4051
AGUUUUAAUGAAAU	chr2:225337665-225337920(-)$1	255	8	22	9.4976
GGGGCCUUGCUCCU	chr21:34400452-34400671(+)$1	219	127	141	9.2860
GUUAAAAUAUUUAA	chr15:73853009-73853229(-)$1	220	76	90	9.5021

#DB
(((((....)))))	chr9:129159202-129159419(+)$1	1	99	113	11.4051
(((((....)))))	chr15:64975468-64975691(+)$1	1	147	161	11.4051
(((((....)))))	chr6:12718841-12719059(+)$1	1	196	210	11.4051
(((((....)))))	chr14:105862211-105862427(-)$1	1	54	68	11.4051
(((((....)))))	chr5:179264822-179265043(+)$1	1	166	180	11.4051
(((((....)))))	chr10:97073622-97073844(-)$1	1	170	184	11.4051
(((((....)))))	chr5:66410215-66410432(-)$1	1	87	101	11.4051
(((((....)))))	chrX:13791927-13792151(-)$1	1	13	27	11.4051
(((((....)))))	chr3:178737994-178738231(-)$1	1	13	27	11.4051
(((((....)))))	chr10:73976703-73976945(+)$1	1	140	154	11.4051
(((((....)))))	chrX:148561602-148561827(-)$1	1	125	139	11.4051
(((((......)))	chr4:176555684-176555924(-)$1	1	96	110	9.3713
(((((......)))	chr16:71764749-71764964(+)$1	1	154	168	9.3713
(((((....)))))	chr16:58705002-58705217(+)$1	1	47	61	11.4051
(((((....)))))	chr4:48069167-48069383(-)$1	1	102	116	11.4051
(((((....)))))	chr11:111966165-111966383(+)$1	1	202	216	11.4051
(((((....)))))	chr3:86120785-86121006(+)$1	1	141	155	11.4051
(((((....)))))	chr11:6631955-6632177(+)$1	1	44	58	11.4051
(((((....)))))	chr1:101706689-101706917(+)$1	1	50	64	11.4051
(((((...)))))(	chr1:11722377-11722606(+)$1	1	159	173	9.8745
(((((....)))))	chr4:176555926-176556142(-)$1	1	197	211	11.4051
(((.(....).)))	chr3:188593553-188593771(-)$1	1	173	187	9.0458
(((((....)))))	chr6:30038721-30038939(+)$1	1	94	108	11.4051
(((((....)))))	chr6:24705820-24706035(-)$1	1	117	131	11.4051
(((((....)))))	chr1:205500855-205501074(+)$1	1	154	168	11.4051
(((((......)))	chr12:75816858-75817085(+)$1	1	129	143	9.3713
)))))....)))))	chr5:10437069-10437294(+)$1	1	67	81	9.2792
(((((......)))	chr3:17202244-17202473(-)$1	1	52	66	9.3713
(((((......)))	chr3:47883077-47883309(+)$1	1	142	156	9.3713
(((((......)))	chr15:43487163-43487388(+)$1	1	10	24	9.3713
(((((...))))))	chr1:41091754-41091977(-)$1	1	148	162	9.8745
(((((......)))	chr13:99445665-99445891(-)$1	1	196	210	9.3713
(((((....)))))	chr10:24833938-24834175(+)$1	1	57	71	11.4051
.(((((...)))))	chr10:126306275-126306493(+)$1	1	50	64	9.5021
(((((......)))	chr7:99751597-99751848(+)$1	1	33	47	9.3713
(((((....)))))	chr9:132650995-132651215(+)$1	1	66	80	11.4051
)))))....)))))	chr16:29498630-29498877(-)$1	1	124	138	9.2792
(((((....)))))	chr11:122929785-122930012(-)$1	1	42	56	11.4051
)))))....)))))	chr7:151254087-151254307(+)$1	1	97	111	9.2792
(((((....)))))	chr14:21493227-21493453(-)$1	1	27	41	11.4051
(((((....)))))	chr10:120795325-120795544(-)$1	1	71	85	11.4051
(((((....)))))	chr1:159888018-159888243(-)$1	1	59	73	11.4051
(((((....)))))	chr16:30095896-30096113(-)$1	1	101	115	11.4051
.(((((...)))))	chr12:109490649-109490868(-)$1	1	103	117	9.2975
(((((....)))))	chr12:57924211-57924433(-)$1	1	101	115	11.4051
(((((....)))))	chr6:138665419-138665645(+)$1	1	141	155	11.4051
.(((((...)))))	chr21:27106902-27107141(-)$1	1	183	197	9.5021
(((((....)))))	chr1:156213795-156214041(-)$1	1	182	196	11.4051
.(((((...)))))	chr2:225337665-225337920(-)$1	1	8	22	9.4976
(((((...))))))	chr21:34400452-34400671(+)$1	1	127	141	9.2860
.(((((...)))))	chr15:73853009-73853229(-)$1	1	76	90	9.5021

#PSSM
e : 0.90	[ : 0.05	# : 0.01	! : 0.01	
e : 1.00	
e : 1.00	
e : 0.98	[ : 0.01	
e : 0.98	a : 0.01	
m : 0.62	o : 0.15	e : 0.09	l : 0.05	4 : 0.05	
m : 0.62	o : 0.15	l : 0.15	4 : 0.05	
m : 0.62	o : 0.15	l : 0.15	4 : 0.05	
m : 0.62	o : 0.15	l : 0.09	e : 0.05	4 : 0.05	
e : 0.82	o : 0.15	a : 0.01	
e : 0.82	o : 0.15	] : 0.01	
e : 1.00	
e : 1.00	
e : 0.98	= : 0.01	

#score	541.752176179187
#seq	51
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m2_run1.txt

#BEAR
e"""dddd!!ddddnnnnndddd4444dddd]ee	chr16:11348551-11348775(-)$1	224	81	115	17.1186
ee[a!!ccc!!cccnnnnnccc]ccc]a]eeeee	chr19:45716168-45716391(+)$1	223	61	95	14.4786
gg[ccc####bbcccmmmmccc]bb333ccc22g	chr5:179224741-179224965(-)$1	224	74	108	10.1408
d[ffffff!!ddddnnnnndddd333ffffff]d	chr16:71316779-71317001(-)$1	222	7	41	16.2127
hhhh[dddd!!cccnnnnnccc333ddddhhhhh	chr8:22876801-22877023(+)$1	222	16	50	13.6651
f[bb[bb[a[ddddnnnnndddd]abb]bb]fff	chr13:50108138-50108362(+)$1	224	187	221	14.3350
ffff[ggggggg[annnnna]ggggggg22ffff	chr17:67144345-67144572(-)$1	227	65	99	12.4091
c!!dddd!!bb!!annnnna22bb4444dddd33	chr16:54150547-54150769(-)$1	222	104	138	14.2269
c!!bb!!dddd[bbnnnnnbb]dddd22bb]ccc	chr5:115803908-115804129(-)$1	221	2	36	12.2696
ca[ffffff!!a[annnnna]a22ffffff]a]c	chr7:100334485-100334707(+)$1	222	22	56	13.2551
bbffffffa[ddddnnnnndddd]a]ffffffbb	chr15:65360177-65360398(+)$1	221	96	130	14.0492
e[eeeee"""ddddnnnnnddddeeeee333eee	chr20:35407157-35407380(+)$1	223	124	158	16.4419
##dddd####ddddnnnnndddd4444dddd333	chr11:71639910-71640133(-)$1	223	65	99	18.3452
fffff####eeeeennnnneeeee4444ffffff	chr6:25925947-25926172(-)$1	225	103	137	14.8903
[ccc!!ccc!!cccnnnnnccc22ccc22ccchh	chr7:97838595-97838818(+)$1	223	75	109	14.5194
========####bbnnnnnbb333==========	chr13:27999192-27999413(+)$1	221	86	120	15.3970
gggg!!bb!!ddddnnnnnddddbb]gggggggd	chr9:104500411-104500635(+)$1	224	75	109	15.6406
cc!!dddd!!acccnnnnnccc]a22dddd22cc	chr19:7968278-7968500(+)$1	222	57	91	15.2257
iccc"""gggggggnnnnnggggggg22ccc444	chr3:50137866-50138143(+)$1	277	216	250	13.7868
ceeeeea[ddddbbnnnnnbb]ddddaddddggg	chr2:96051105-96051333(+)$1	228	74	108	12.8739
gggggg$$$$$cccnnnnnccc22ggggggg:ff	chrX:21857716-21857940(+)$1	224	89	123	13.7976
[bb####gggggggnnnnnggggggg333bb22e	chr11:6642867-6643089(-)$1	222	99	133	13.2414
$$dddd[dddd[bbnnnnnbb]dddd]dddd444	chr16:56390714-56390936(+)$1	222	38	72	12.6658
dd!!dddd[eeeeennnnneeeee]dddd]dddd	chr2:219433465-219433689(+)$1	224	94	128	13.6486
bb[ffffff[ddddnnnnnddddffffffbb]a]	chr12:102472715-102472940(-)$1	225	188	222	13.5960
ccc[ccc!!ddddoooooodddd22ccc]ccc44	chr4:8008976-8009199(-)$1	223	146	180	12.4386
e[eeeee"""ddddnnnnnddddeeeee4444ee	chr3:45721051-45721277(-)$1	226	144	178	16.4937
a[dddd!!a[ddddnnnnndddd]a]dddd]acc	chr7:102036681-102036905(-)$1	224	148	182	16.8081
!!eeeee[dddd[annnnna]dddd]eeeeeccc	chr15:101420677-101420902(+)$1	225	11	45	14.4422
!!dddd[a[eeeeennnnneeeeea]dddd333b	chr4:15939950-15940172(+)$1	222	108	142	15.3061
!!eeeee!!eeeeennnnneeeee4444eeeeee	chr19:48244561-48244800(-)$1	239	96	130	15.4913
=======!!bb!!annnnna22bb22========	chrX:148592985-148593212(+)$1	227	117	151	14.1421
b!!bb[ddddddddnnnnndddd22ddddbb22b	chr3:49449211-49449434(+)$1	223	65	99	14.2680
dd[ccc####ddddmmmmdddd4444cccdddd:	chr12:118573786-118574008(-)$1	222	179	213	10.4368
!!a[dddd[eeeeennnnneeeee]dddd]a22c	chr8:53024803-53025024(-)$1	221	12	46	14.8520
[dddd"""a"""ddddllldddd22a]ddddggg	chr19:12902462-12902690(+)$1	228	79	113	11.5021
eccc$$$$$eeeeennnnneeeeeccc]eeeee2	chr1:48462426-48462649(-)$1	223	122	156	13.6087
ddd!!ccc!!ddddmmmmdddd]ccc]dddd]dd	chr11:68522281-68522503(-)$1	222	71	105	10.3756
iiiiiiiixxxxxxxxxxxxxxxiiiiiiiii22	chr14:74532124-74532345(+)$1	221	118	152	10.0566
###eeeee!!ddddmmmmddddeeeee4444ggg	chr8:144873182-144873407(+)$1	225	135	169	10.5391
===!!a####ddddllldddd333a22=======	chr10:321669-321891(-)$1	222	30	64	13.1602
fff!!bb!!eeeeennnnneeeee4444bbffff	chr1:233120954-233121177(-)$1	223	7	41	14.3048
{BBeeeee!!ddddnnnnndddd333eeeeebb!	chr6:24775283-24775506(+)$1	223	43	77	13.3642
[eeeee####ddddnnnnndddd333eeeee]ff	chr20:20372966-20373194(-)$1	228	129	163	17.6989
a[cccccc[eeeeennnnneeeee333ccc]ccc	chr9:140002852-140003076(-)$1	224	21	55	15.4818
!bb[dddd"""cccnnnnnccc22dddd22bb22	chr3:9860842-9861066(-)$1	224	144	178	14.0425
gggccc####ddddnnnnnddddccc]ggggggg	chr16:81204791-81205013(+)$1	222	131	165	17.1315
hhhhhhh"""ddddnnnnndddd]hhhhhhhhdd	chr3:47458707-47458931(-)$1	224	187	221	13.8449
ffffff$$$$$cccnnnnnccc333ffffff333	chr3:69435115-69435344(+)$1	229	23	57	14.9961
cc!!dddd"""cccnnnnncccdddd22ccc22a	chr17:27086652-27086873(-)$1	221	30	64	15.3922
!!eeeee"""ddddnnnnnddddeeeee22bb77	chr16:48481389-48481611(-)$1	222	18	52	15.1140

#otherMatches

#Seq PSSM
AGCGCCCGCCGUGCACGCAGCAUUAACUGGGAUG	chr16:11348551-11348775(-)$1	224	81	115	17.1186
GUGUGGUCCCAGGCAGGGAGUCAGGAGGGGCGCC	chr19:45716168-45716391(+)$1	223	61	95	14.4786
GGAGGCCCUAGGAGCUGGUGCUgcccccgcccgc	chr5:179224741-179224965(-)$1	224	74	108	10.1408
AUGAAUUUCAGGGAAUUCAUCUCGCCAGAUUCUU	chr16:71316779-71317001(-)$1	222	7	41	16.2127
GGGGCGGCCAUGUUGUCCAGGCCCAGGCCCCUCC	chr8:22876801-22877023(+)$1	222	16	50	13.6651
GCCAAAAUGCUGCAGUCUGUGUAACUUCUGUCAA	chr13:50108138-50108362(+)$1	224	187	221	14.3350
UUUAAUUAUAAUGACAUUCUGAUUAUAAAAUAAA	chr17:67144345-67144572(-)$1	227	65	99	12.4091
CUCAGGUGAGCGAGAGAACCAGGUGAAUGCCUUC	chr16:54150547-54150769(-)$1	222	104	138	14.2269
ACAGCCGUAAUAGCGUGUAGCCGUUGAAGCCUCC	chr5:115803908-115804129(-)$1	221	2	36	12.2696
GGAGCAAGGCCCCCUCUGUGUGCACUUUGCCCAC	chr7:100334485-100334707(+)$1	222	22	56	13.2551
GCGCGCGGCCCCGGACCCGUCGGCGUCCGCGCCC	chr15:65360177-65360398(+)$1	221	96	130	14.0492
UCUUGGGAAUGGUUUGAGUGGCUUCCAAAUAAAG	chr20:35407157-35407380(+)$1	223	124	158	16.4419
CAGCUGCUUCCGCUGCUCAAGUGCUCCUAGCCAA	chr11:71639910-71640133(-)$1	223	65	99	18.3452
GGAAACUCCACCACAAAGCGUGGUACCAUUUCCC	chr6:25925947-25926172(-)$1	225	103	137	14.8903
UGAUCAUGGGGCUGGUGUAUGGAUCCACCGUCGG	chr7:97838595-97838818(+)$1	223	75	109	14.5194
GGAUUUACUAAGCAGUCAUUGAUCGUGAGUCUCG	chr13:27999192-27999413(+)$1	221	86	120	15.3970
CGCCCGGUCACUGCGCUGAGCAGGCAGGCGGGCG	chr9:104500411-104500635(+)$1	224	75	109	15.6406
CCCAAGCCGACCGUGAAAAGCGAGGAGGCUGAGG	chr19:7968278-7968500(+)$1	222	57	91	15.2257
GUCUGUACAAUUUUAAAAAAAGGUUGAAGGAGUG	chr3:50137866-50138143(+)$1	277	216	250	13.7868
CCCCAGGAGGAGAGAGAUGCUGCUCCCGCCUGAU	chr2:96051105-96051333(+)$1	228	74	108	12.8739
AGGAGGACGCCGGGGCUCGCCUUCCCUCCUCUGC	chrX:21857716-21857940(+)$1	224	89	123	13.7976
CCGACCUGGGAUGCGCACAGUGUCCCCAACGCAG	chr11:6642867-6643089(-)$1	222	99	133	13.2414
ACCCCACAGAUCAGUUUUCCUAGUCUUUGGGAAA	chr16:56390714-56390936(+)$1	222	38	72	12.6658
GCGAGCCGGAGUCGGAUGGCGGCUACGGCGGCUC	chr2:219433465-219433689(+)$1	224	94	128	13.6486
CUCAUACCUUAUCUCCCACAGAUGGGUAUAGCAA	chr12:102472715-102472940(-)$1	225	188	222	13.5960
gaccuggcuuugcagugaggcagucccaaguuca	chr4:8008976-8009199(-)$1	223	146	180	12.4386
GCUGGCUUUGGGAUCUGAAAUCCGGCCACAAUCC	chr3:45721051-45721277(-)$1	226	144	178	16.4937
GGAGGCGGGGUUGCAAGGCGCAAGCAGCCUGCUG	chr7:102036681-102036905(-)$1	224	148	182	16.8081
AGUUGGAAGACUGGGGAAGCGGGUCCUCCGAGCA	chr15:101420677-101420902(+)$1	225	11	45	14.4422
GCCCCUCCGAGGGAGCCGGUUCCUGCAGGGAAAG	chr4:15939950-15940172(+)$1	222	108	142	15.3061
GGGAGGGGGGCCGGCUCACUCGGCGGAGCCCUUG	chr19:48244561-48244800(-)$1	239	96	130	15.4913
CUUUUUAUUUGAAGAAAUGUGGCAUUUGGGAAGC	chrX:148592985-148593212(+)$1	227	117	151	14.1421
CCUCUUCGCGCCGGGGACGCCGGUCCGCGAGUCG	chr3:49449211-49449434(+)$1	223	65	99	14.2680
CCUCUGAUUGGCCGAAGCUGGCAGAGCAGGGCCU	chr12:118573786-118574008(-)$1	222	179	213	10.4368
AAUAUGAAUUAUUUAUUUGAAAUGUUUUAAAGAA	chr8:53024803-53025024(-)$1	221	12	46	14.8520
AGCGGCCCCGCAGGGACCCUCCCCAGACCGCCUG	chr19:12902462-12902690(+)$1	228	79	113	11.5021
GGGCUCCCCGCCCCGCUGAGGGGCGCCGCCCAGG	chr1:48462426-48462649(-)$1	223	122	156	13.6087
UAUGCUCUUUGGAUGUAAAUCUUAGAAAUGCAGU	chr11:68522281-68522503(-)$1	222	71	105	10.3756
UCCAAGUUACCAAUCAUAUAAACAACUUGGAAUU	chr14:74532124-74532345(+)$1	221	118	152	10.0566
GAGGUGCCUGCUCCUCUAGGAGGGCACAGGGCCC	chr8:144873182-144873407(+)$1	225	135	169	10.5391
GGGCUCCCUCGCUCAGUGAGCACAGUUCCCCGGG	chr10:321669-321891(-)$1	222	30	64	13.1602
GAGUUCCCCCACUCCUUUUGAGUGUUCAGGUUUU	chr1:233120954-233121177(-)$1	223	7	41	14.3048
AGCGUCUCCACCCAGUAAGUGGGCAAGAGGCGGC	chr6:24775283-24775506(+)$1	223	43	77	13.3642
UAGGCUGAGACGGGUACCCCCCGAAUGGCCUUGU	chr20:20372966-20373194(-)$1	228	129	163	17.6989
CAGCCAUCCACCCUAGGCAGGGGUCCAGAUAGGC	chr9:140002852-140003076(-)$1	224	21	55	15.4818
gauggauggGGAGUAUGGAGCUGACAUCAGGUAG	chr3:9860842-9861066(-)$1	224	144	178	14.0425
ugggauuacaggugcgcaccaccaucaccagcua	chr16:81204791-81205013(+)$1	222	131	165	17.1315
UGUGGGCCUUUCUGGCUGGCAGGUGCUCACAGCC	chr3:47458707-47458931(-)$1	224	187	221	13.8449
AUGCCUCCUCCUUCGCUCUGAACCCGGGCGUCCC	chr3:69435115-69435344(+)$1	229	23	57	14.9961
UGGAUGCGUAUGCUAAGAAGGUCGCAAACAACCC	chr17:27086652-27086873(-)$1	221	30	64	15.3922
ccuguccucacagcuugcugcugggacaccugcu	chr16:48481389-48481611(-)$1	222	18	52	15.1140

#DB
(...((((..((((.....))))....)))).))	chr16:11348551-11348775(-)$1	1	81	115	17.1186
((.(..(((..(((.....))).))).).)))))	chr19:45716168-45716391(+)$1	1	61	95	14.4786
((.(((....(((((....))).))...)))..)	chr5:179224741-179224965(-)$1	1	74	108	10.1408
(.((((((..((((.....))))...)))))).)	chr16:71316779-71317001(-)$1	1	7	41	16.2127
((((.((((..(((.....)))...)))))))))	chr8:22876801-22877023(+)$1	1	16	50	13.6651
(.((.((.(.((((.....)))).))).)).)))	chr13:50108138-50108362(+)$1	1	187	221	14.3350
((((.(((((((.(.....).)))))))..))))	chr17:67144345-67144572(-)$1	1	65	99	12.4091
(..((((..((..(.....)..))....))))..	chr16:54150547-54150769(-)$1	1	104	138	14.2269
(..((..((((.((.....)).))))..)).)))	chr5:115803908-115804129(-)$1	1	2	36	12.2696
((.((((((..(.(.....).)..)))))).).)	chr7:100334485-100334707(+)$1	1	22	56	13.2551
))(((((((.((((.....)))).).))))))((	chr15:65360177-65360398(+)$1	1	96	130	14.0492
(.(((((...((((.....)))))))))...)))	chr20:35407157-35407380(+)$1	1	124	158	16.4419
..((((....((((.....))))....))))...	chr11:71639910-71640133(-)$1	1	65	99	18.3452
(((((....(((((.....)))))....))))))	chr6:25925947-25926172(-)$1	1	103	137	14.8903
.(((..(((..(((.....)))..)))..)))))	chr7:97838595-97838818(+)$1	1	75	109	14.5194
((((((((....((.....))...))))))))))	chr13:27999192-27999413(+)$1	1	86	120	15.3970
((((..((..((((.....)))))).)))))))(	chr9:104500411-104500635(+)$1	1	75	109	15.6406
((..((((..((((.....))).)..))))..))	chr19:7968278-7968500(+)$1	1	57	91	15.2257
((((...(((((((.....)))))))..)))...	chr3:50137866-50138143(+)$1	1	216	250	13.7868
))))))(.((((((.....)).)))))(((((((	chr2:96051105-96051333(+)$1	1	74	108	12.8739
((((((.....(((.....)))..))))))).((	chrX:21857716-21857940(+)$1	1	89	123	13.7976
.((....(((((((.....)))))))...))..)	chr11:6642867-6643089(-)$1	1	99	133	13.2414
..((((.((((.((.....)).)))).))))...	chr16:56390714-56390936(+)$1	1	38	72	12.6658
((..((((.(((((.....))))).)))).))))	chr2:219433465-219433689(+)$1	1	94	128	13.6486
((.((((((.((((.....)))))))))))).).	chr12:102472715-102472940(-)$1	1	188	222	13.5960
(((.(((..((((......))))..))).)))..	chr4:8008976-8009199(-)$1	1	146	180	12.4386
(.(((((...((((.....)))))))))....))	chr3:45721051-45721277(-)$1	1	144	178	16.4937
(.((((..(.((((.....)))).).)))).)((	chr7:102036681-102036905(-)$1	1	148	182	16.8081
..(((((.((((.(.....).)))).))))))))	chr15:101420677-101420902(+)$1	1	11	45	14.4422
..((((.(.(((((.....)))))).))))...)	chr4:15939950-15940172(+)$1	1	108	142	15.3061
..(((((..(((((.....)))))....))))))	chr19:48244561-48244800(-)$1	1	96	130	15.4913
(((((((..((..(.....)..))..))))))))	chrX:148592985-148593212(+)$1	1	117	151	14.1421
(..((.((((((((.....))))..))))))..)	chr3:49449211-49449434(+)$1	1	65	99	14.2680
((.(((....((((....))))....))))))).	chr12:118573786-118574008(-)$1	1	179	213	10.4368
..(.((((.(((((.....))))).)))).)..)	chr8:53024803-53025024(-)$1	1	12	46	14.8520
.((((...(...((((...))))..).)))))))	chr19:12902462-12902690(+)$1	1	79	113	11.5021
((((.....(((((.....)))))))).))))).	chr1:48462426-48462649(-)$1	1	122	156	13.6087
(((..(((..((((....)))).))).)))).))	chr11:68522281-68522503(-)$1	1	71	105	10.3756
((((((((...............)))))))))..	chr14:74532124-74532345(+)$1	1	118	152	10.0566
...(((((..((((....)))))))))....)))	chr8:144873182-144873407(+)$1	1	135	169	10.5391
(((..(....((((...))))...)..)))))))	chr10:321669-321891(-)$1	1	30	64	13.1602
(((..((..(((((.....)))))....))))))	chr1:233120954-233121177(-)$1	1	7	41	14.3048
.(((((((..((((.....))))...)))))((.	chr6:24775283-24775506(+)$1	1	43	77	13.3642
.(((((....((((.....))))...))))).))	chr20:20372966-20373194(-)$1	1	129	163	17.6989
(.((((((.(((((.....)))))...))).)))	chr9:140002852-140003076(-)$1	1	21	55	15.4818
.((.((((...(((.....)))..))))..))..	chr3:9860842-9861066(-)$1	1	144	178	14.0425
((((((....((((.....))))))).)))))))	chr16:81204791-81205013(+)$1	1	131	165	17.1315
(((((((...((((.....)))).))))))))))	chr3:47458707-47458931(-)$1	1	187	221	13.8449
((((((.....(((.....)))...))))))...	chr3:69435115-69435344(+)$1	1	23	57	14.9961
((..((((...(((.....)))))))..)))..)	chr17:27086652-27086873(-)$1	1	30	64	15.3922
..(((((...((((.....)))))))))..))..	chr16:48481389-48481611(-)$1	1	18	52	15.1140

#PSSM
c : 0.13	! : 0.11	e : 0.09	f : 0.09	g : 0.07	d : 0.07	[ : 0.07	b : 0.05	= : 0.05	h : 0.03	# : 0.03	i : 0.03	a : 0.03	$ : 0.01	{ : 0.01	
! : 0.15	[ : 0.11	c : 0.11	g : 0.07	f : 0.07	b : 0.07	d : 0.07	e : 0.05	= : 0.05	h : 0.03	# : 0.03	" : 0.01	a : 0.01	$ : 0.01	i : 0.01	B : 0.01	
e : 0.13	f : 0.11	! : 0.11	d : 0.11	[ : 0.09	c : 0.09	b : 0.05	= : 0.05	g : 0.05	h : 0.03	" : 0.01	a : 0.01	i : 0.01	# : 0.01	B : 0.01	
e : 0.17	c : 0.13	f : 0.13	d : 0.11	! : 0.11	b : 0.05	[ : 0.05	h : 0.03	= : 0.03	g : 0.03	" : 0.01	a : 0.01	# : 0.01	i : 0.01	
d : 0.23	e : 0.17	! : 0.11	f : 0.11	c : 0.09	[ : 0.05	b : 0.03	= : 0.03	" : 0.01	g : 0.01	# : 0.01	$ : 0.01	i : 0.01	h : 0.01	
d : 0.23	e : 0.17	c : 0.11	f : 0.09	! : 0.07	b : 0.03	g : 0.03	# : 0.03	= : 0.03	" : 0.03	[ : 0.01	$ : 0.01	i : 0.01	a : 0.01	h : 0.01	
d : 0.17	# : 0.15	e : 0.13	c : 0.09	f : 0.07	b : 0.05	$ : 0.05	! : 0.03	= : 0.03	" : 0.03	[ : 0.03	g : 0.01	a : 0.01	i : 0.01	h : 0.01	
d : 0.19	# : 0.13	! : 0.11	" : 0.09	c : 0.07	f : 0.07	[ : 0.05	g : 0.05	$ : 0.05	e : 0.03	= : 0.01	b : 0.01	a : 0.01	i : 0.01	
! : 0.23	# : 0.15	d : 0.11	" : 0.11	a : 0.07	[ : 0.07	g : 0.05	$ : 0.05	c : 0.03	f : 0.03	x : 0.01	
! : 0.21	e : 0.15	# : 0.13	" : 0.13	d : 0.11	[ : 0.07	g : 0.05	b : 0.03	$ : 0.03	x : 0.01	
d : 0.49	e : 0.15	! : 0.07	b : 0.05	g : 0.05	" : 0.05	$ : 0.03	# : 0.01	a : 0.01	x : 0.01	
d : 0.45	c : 0.15	e : 0.15	g : 0.05	! : 0.03	[ : 0.03	b : 0.01	a : 0.01	# : 0.01	" : 0.01	x : 0.01	
d : 0.43	c : 0.17	e : 0.15	b : 0.07	[ : 0.05	! : 0.03	g : 0.03	x : 0.01	
d : 0.41	c : 0.17	e : 0.15	a : 0.09	b : 0.07	g : 0.03	o : 0.01	x : 0.01	
n : 0.84	m : 0.05	c : 0.01	o : 0.01	d : 0.01	x : 0.01	l : 0.01	
n : 0.84	m : 0.07	o : 0.01	d : 0.01	x : 0.01	l : 0.01	
n : 0.84	m : 0.07	l : 0.03	o : 0.01	x : 0.01	
n : 0.84	m : 0.07	o : 0.01	l : 0.01	x : 0.01	d : 0.01	
n : 0.84	d : 0.07	m : 0.01	o : 0.01	l : 0.01	x : 0.01	
d : 0.43	c : 0.17	e : 0.15	a : 0.09	b : 0.07	g : 0.03	x : 0.01	
d : 0.43	c : 0.17	e : 0.15	b : 0.07	] : 0.05	2 : 0.03	g : 0.03	x : 0.01	
d : 0.43	c : 0.17	e : 0.15	g : 0.05	] : 0.05	2 : 0.03	3 : 0.03	a : 0.01	x : 0.01	
d : 0.45	e : 0.17	] : 0.07	3 : 0.07	2 : 0.07	g : 0.05	b : 0.03	4 : 0.01	x : 0.01	
e : 0.23	3 : 0.13	2 : 0.13	d : 0.09	b : 0.07	] : 0.07	4 : 0.05	c : 0.05	g : 0.05	a : 0.01	f : 0.01	i : 0.01	
4 : 0.13	3 : 0.11	d : 0.11	c : 0.09	a : 0.09	2 : 0.09	g : 0.07	e : 0.07	b : 0.03	f : 0.03	] : 0.03	= : 0.01	i : 0.01	h : 0.01	
d : 0.17	4 : 0.13	c : 0.11	3 : 0.09	] : 0.09	g : 0.07	e : 0.07	f : 0.05	2 : 0.05	b : 0.01	= : 0.01	a : 0.01	i : 0.01	h : 0.01	
d : 0.15	e : 0.13	4 : 0.11	] : 0.09	f : 0.09	2 : 0.07	c : 0.07	3 : 0.05	g : 0.05	= : 0.03	b : 0.01	a : 0.01	i : 0.01	h : 0.01	
d : 0.27	e : 0.11	f : 0.09	4 : 0.09	g : 0.07	2 : 0.07	= : 0.05	c : 0.05	3 : 0.03	] : 0.03	a : 0.01	i : 0.01	h : 0.01	
d : 0.27	f : 0.11	c : 0.09	e : 0.09	2 : 0.07	b : 0.05	= : 0.05	g : 0.05	] : 0.03	3 : 0.03	4 : 0.03	i : 0.01	h : 0.01	
d : 0.21	e : 0.11	c : 0.11	b : 0.11	f : 0.09	2 : 0.05	= : 0.05	g : 0.05	h : 0.03	] : 0.03	4 : 0.03	3 : 0.01	i : 0.01	
d : 0.17	e : 0.11	f : 0.11	c : 0.09	] : 0.09	b : 0.09	= : 0.05	g : 0.05	h : 0.03	3 : 0.03	4 : 0.03	2 : 0.01	a : 0.01	i : 0.01	
2 : 0.11	f : 0.11	c : 0.09	g : 0.09	] : 0.07	e : 0.07	d : 0.05	3 : 0.05	= : 0.05	4 : 0.05	b : 0.05	h : 0.03	a : 0.03	: : 0.01	i : 0.01	
2 : 0.13	e : 0.11	f : 0.11	c : 0.09	g : 0.09	3 : 0.07	d : 0.07	= : 0.05	4 : 0.05	] : 0.03	h : 0.03	b : 0.03	a : 0.01	7 : 0.01	
c : 0.13	e : 0.11	f : 0.11	g : 0.09	d : 0.09	3 : 0.05	b : 0.05	= : 0.05	4 : 0.05	2 : 0.05	h : 0.03	] : 0.01	: : 0.01	! : 0.01	a : 0.01	7 : 0.01	

#score	721.525728448026
#seq	51
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m3_run2.txt

#BEAR
:cccnnnnnccc	chr6:139264612-139264847(-)$1	235	211	223	9.2781
[cccnnnnnccc	chr4:83740146-83740389(-)$1	243	17	29	10.0176
ddddnnnnnddd	chr10:38344444-38344784(+)$1	340	38	50	10.8211
'cccnnnnnccc	chr8:37993142-37993369(+)$1	227	172	184	9.5051
[cccnnnnnccc	chr4:1018862-1019299(+)$1	437	296	308	10.0176
:cccnnnnnccc	chr19:36332525-36332743(-)$1	218	168	180	9.2781
!cccnnnnnccc	chr5:180662269-180662503(+)$1	234	99	111	10.0748
eeeennnnneee	chr5:177636287-177636584(-)$1	297	68	80	9.1840
!cccnnnnnccc	chr9:134145767-134145986(-)$1	219	181	193	10.0748
eeeennnnneee	chr10:43089167-43089500(-)$1	333	161	173	9.1840
ccccnnnnnccc	chr1:171526980-171527259(+)$1	279	180	192	9.9713
ddddnnnnnddd	chr10:64967671-64967912(-)$1	241	76	88	10.8211
:cccnnnnnccc	chr12:2690745-2690964(+)$1	219	206	218	9.2781
ddddnnnnnddd	chr9:5919902-5920259(-)$1	357	11	23	10.8211
icccnnnnnccc	chr11:5686020-5686286(-)$1	266	214	226	9.9184
[cccnnnnnccc	chr3:49137093-49137335(-)$1	242	137	149	10.0176
ddddnnnnnddd	chr19:58290430-58290667(+)$1	237	146	158	10.8211
ddddnnnnnddd	chr15:62170811-62171030(-)$1	219	55	67	10.8211
ddddnnnnnddd	chr12:977071-977361(+)$1	290	231	243	10.8211
ddddnnnnnddd	chr9:134473588-134473822(-)$1	234	176	188	10.8211
ddddnnnnnddd	chr17:62576821-62577052(-)$1	231	3	15	10.8211
Fcccnnnnnccc	chr13:99947186-99947460(+)$1	274	46	58	9.5723
ddddnnnnnddd	chr11:124746904-124747165(+)$1	261	138	150	10.8211
eeeennnnneee	chr19:23927419-23927656(-)$1	237	52	64	9.1840
eeeennnnneee	chr19:57911022-57911271(+)$1	249	107	119	9.1840
ddddnnnnnddd	chr10:38345061-38345306(+)$1	245	223	235	10.8211
ddddnnnnnddd	chr5:81046581-81046918(-)$1	337	304	316	10.8211
ddddnnnnnddd	chr10:93749124-93749354(+)$1	230	33	45	10.8211
ddddnnnnnddd	chr1:204588054-204588274(-)$1	220	85	97	10.8211
ddddnnnnnddd	chr7:99818561-99818834(+)$1	273	55	67	10.8211
eeeennnnneee	chr3:169846560-169846976(-)$1	416	172	184	9.1840
ddddnnnnnddd	chr12:994293-994576(+)$1	283	77	89	10.8211
#cccnnnnnccc	chr14:75248525-75248781(+)$1	256	178	190	9.9507
ddddnnnnnddd	chr17:35800569-35800792(+)$1	223	159	171	10.8211
eeeennnnneee	chr12:110385090-110385321(-)$1	231	114	126	9.1840
ddddnnnnnddd	chr6:32083391-32083671(-)$1	280	2	14	10.8211
ddddnnnnnddd	chr7:94184953-94185204(+)$1	251	20	32	10.8211
:cccnnnnnccc	chr12:7077745-7077998(-)$1	253	149	161	9.2781
ddddnnnnnddd	chrX:49032198-49032437(-)$1	239	48	60	10.8211
ddddnnnnnddd	chr16:31196124-31196363(+)$1	239	88	100	10.8211
:cccnnnnnccc	chr12:994463-994907(+)$1	444	214	226	9.2781
ddddnnnnnddd	chr10:43088135-43088404(-)$1	269	239	251	10.8211
ddddnnnnnddd	chr3:53326492-53326767(-)$1	275	149	161	10.8211
[cccnnnnnccc	chr6:109835384-109835620(-)$1	236	66	78	10.0176
eeeennnnneee	chr5:108672878-108673108(-)$1	230	44	56	9.1840
ddbbnnnnnbb]	chr1:161332129-161332381(+)$1	252	23	35	8.2631
ddddnnnnnddd	chr12:56346469-56346721(+)$1	252	16	28	10.8211
:cccnnnnnccc	chr12:108147615-108147868(-)$1	253	6	18	9.2781
[cccnnnnnccc	chr12:112381042-112381273(-)$1	231	135	147	10.0176
:cccnnnnnccc	chr19:56029027-56029254(+)$1	227	97	109	9.2781
ddddnnnnnddd	chr1:185276991-185277256(-)$1	265	147	159	10.8211

#otherMatches

#Seq PSSM
AUCAUUAGUUGG	chr6:139264612-139264847(-)$1	235	211	223	9.2781
UUGCAAGGAGCA	chr4:83740146-83740389(-)$1	243	17	29	10.0176
CUUUAGUGAAAA	chr10:38344444-38344784(+)$1	340	38	50	10.8211
ACUUGAGGGAAG	chr8:37993142-37993369(+)$1	227	172	184	9.5051
ACGGGGGGGCCG	chr4:1018862-1019299(+)$1	437	296	308	10.0176
UGGAUCCAUUCC	chr19:36332525-36332743(-)$1	218	168	180	9.2781
GCUUCACUUGAG	chr5:180662269-180662503(+)$1	234	99	111	10.0748
CAAGACAGGCUU	chr5:177636287-177636584(-)$1	297	68	80	9.1840
AAGUUACAUACU	chr9:134145767-134145986(-)$1	219	181	193	10.0748
AGAGAAACACUU	chr10:43089167-43089500(-)$1	333	161	173	9.1840
CACAGAUUAUGU	chr1:171526980-171527259(+)$1	279	180	192	9.9713
GCAGUAUGCCUG	chr10:64967671-64967912(-)$1	241	76	88	10.8211
ACUGUGUUUCAG	chr12:2690745-2690964(+)$1	219	206	218	9.2781
UCCAAAAUAUGG	chr9:5919902-5920259(-)$1	357	11	23	10.8211
AGUCCCCAUGAC	chr11:5686020-5686286(-)$1	266	214	226	9.9184
GCCCGGUGAGGG	chr3:49137093-49137335(-)$1	242	137	149	10.0176
UGCAAUGAAUGU	chr19:58290430-58290667(+)$1	237	146	158	10.8211
UUCAUUUAUUGA	chr15:62170811-62171030(-)$1	219	55	67	10.8211
CUACAGCCAGUA	chr12:977071-977361(+)$1	290	231	243	10.8211
GGACGAGCUGUC	chr9:134473588-134473822(-)$1	234	176	188	10.8211
UCCAAUUAGUGG	chr17:62576821-62577052(-)$1	231	3	15	10.8211
ACAAUUAUUUUG	chr13:99947186-99947460(+)$1	274	46	58	9.5723
UUCCUUUCUGGA	chr11:124746904-124747165(+)$1	261	138	150	10.8211
AGAGACAAACUC	chr19:23927419-23927656(-)$1	237	52	64	9.1840
UGGUUCAUCACC	chr19:57911022-57911271(+)$1	249	107	119	9.1840
GGGGAAAAGCCC	chr10:38345061-38345306(+)$1	245	223	235	10.8211
CGCUGGGCGGGC	chr5:81046581-81046918(-)$1	337	304	316	10.8211
UAGUGCAAAACU	chr10:93749124-93749354(+)$1	230	33	45	10.8211
AGCUGACCAAGC	chr1:204588054-204588274(-)$1	220	85	97	10.8211
CCAGCUACUUUG	chr7:99818561-99818834(+)$1	273	55	67	10.8211
UUGGUAUCCCCA	chr3:169846560-169846976(-)$1	416	172	184	9.1840
AGGUCCUAAGCC	chr12:994293-994576(+)$1	283	77	89	10.8211
CAGCCUCCAGUU	chr14:75248525-75248781(+)$1	256	178	190	9.9507
AGCAAAAACUGC	chr17:35800569-35800792(+)$1	223	159	171	10.8211
UCUUCCUUAAAG	chr12:110385090-110385321(-)$1	231	114	126	9.1840
GGUGAUUCACAU	chr6:32083391-32083671(-)$1	280	2	14	10.8211
AGAUAACUCAUC	chr7:94184953-94185204(+)$1	251	20	32	10.8211
UUGCACAGGGCA	chr12:7077745-7077998(-)$1	253	149	161	9.2781
CGGCCCAGCGCC	chrX:49032198-49032437(-)$1	239	48	60	10.8211
ACAAUCUUUUUG	chr16:31196124-31196363(+)$1	239	88	100	10.8211
UUGGUCAUUCCA	chr12:994463-994907(+)$1	444	214	226	9.2781
GGGGAAAAGCCC	chr10:43088135-43088404(-)$1	269	239	251	10.8211
CACCACCCCGGU	chr3:53326492-53326767(-)$1	275	149	161	10.8211
AUCUAGUAAAGA	chr6:109835384-109835620(-)$1	236	66	78	10.0176
UCUCCAGUCGGG	chr5:108672878-108673108(-)$1	230	44	56	9.1840
AGCUAUACCAGU	chr1:161332129-161332381(+)$1	252	23	35	8.2631
UCCCUAACUGGG	chr12:56346469-56346721(+)$1	252	16	28	10.8211
UGGGUCCCUCCC	chr12:108147615-108147868(-)$1	253	6	18	9.2781
UUACAUCUGGUA	chr12:112381042-112381273(-)$1	231	135	147	10.0176
cugaccccauca	chr19:56029027-56029254(+)$1	227	97	109	9.2781
CUCUCCUGUAGA	chr1:185276991-185277256(-)$1	265	147	159	10.8211

#DB
.(((.....)))	chr6:139264612-139264847(-)$1	1	211	223	9.2781
.(((.....)))	chr4:83740146-83740389(-)$1	1	17	29	10.0176
((((.....)))	chr10:38344444-38344784(+)$1	1	38	50	10.8211
.(((.....)))	chr8:37993142-37993369(+)$1	1	172	184	9.5051
.(((.....)))	chr4:1018862-1019299(+)$1	1	296	308	10.0176
.(((.....)))	chr19:36332525-36332743(-)$1	1	168	180	9.2781
.(((.....)))	chr5:180662269-180662503(+)$1	1	99	111	10.0748
((((.....)))	chr5:177636287-177636584(-)$1	1	68	80	9.1840
.(((.....)))	chr9:134145767-134145986(-)$1	1	181	193	10.0748
((((.....)))	chr10:43089167-43089500(-)$1	1	161	173	9.1840
((((.....)))	chr1:171526980-171527259(+)$1	1	180	192	9.9713
((((.....)))	chr10:64967671-64967912(-)$1	1	76	88	10.8211
.(((.....)))	chr12:2690745-2690964(+)$1	1	206	218	9.2781
((((.....)))	chr9:5919902-5920259(-)$1	1	11	23	10.8211
)(((.....)))	chr11:5686020-5686286(-)$1	1	214	226	9.9184
.(((.....)))	chr3:49137093-49137335(-)$1	1	137	149	10.0176
((((.....)))	chr19:58290430-58290667(+)$1	1	146	158	10.8211
((((.....)))	chr15:62170811-62171030(-)$1	1	55	67	10.8211
((((.....)))	chr12:977071-977361(+)$1	1	231	243	10.8211
((((.....)))	chr9:134473588-134473822(-)$1	1	176	188	10.8211
((((.....)))	chr17:62576821-62577052(-)$1	1	3	15	10.8211
((((.....)))	chr13:99947186-99947460(+)$1	1	46	58	9.5723
((((.....)))	chr11:124746904-124747165(+)$1	1	138	150	10.8211
((((.....)))	chr19:23927419-23927656(-)$1	1	52	64	9.1840
((((.....)))	chr19:57911022-57911271(+)$1	1	107	119	9.1840
((((.....)))	chr10:38345061-38345306(+)$1	1	223	235	10.8211
((((.....)))	chr5:81046581-81046918(-)$1	1	304	316	10.8211
((((.....)))	chr10:93749124-93749354(+)$1	1	33	45	10.8211
((((.....)))	chr1:204588054-204588274(-)$1	1	85	97	10.8211
((((.....)))	chr7:99818561-99818834(+)$1	1	55	67	10.8211
((((.....)))	chr3:169846560-169846976(-)$1	1	172	184	9.1840
((((.....)))	chr12:994293-994576(+)$1	1	77	89	10.8211
.(((.....)))	chr14:75248525-75248781(+)$1	1	178	190	9.9507
((((.....)))	chr17:35800569-35800792(+)$1	1	159	171	10.8211
((((.....)))	chr12:110385090-110385321(-)$1	1	114	126	9.1840
((((.....)))	chr6:32083391-32083671(-)$1	1	2	14	10.8211
((((.....)))	chr7:94184953-94185204(+)$1	1	20	32	10.8211
.(((.....)))	chr12:7077745-7077998(-)$1	1	149	161	9.2781
((((.....)))	chrX:49032198-49032437(-)$1	1	48	60	10.8211
((((.....)))	chr16:31196124-31196363(+)$1	1	88	100	10.8211
.(((.....)))	chr12:994463-994907(+)$1	1	214	226	9.2781
((((.....)))	chr10:43088135-43088404(-)$1	1	239	251	10.8211
((((.....)))	chr3:53326492-53326767(-)$1	1	149	161	10.8211
.(((.....)))	chr6:109835384-109835620(-)$1	1	66	78	10.0176
((((.....)))	chr5:108672878-108673108(-)$1	1	44	56	9.1840
((((.....)).	chr1:161332129-161332381(+)$1	1	23	35	8.2631
((((.....)))	chr12:56346469-56346721(+)$1	1	16	28	10.8211
.(((.....)))	chr12:108147615-108147868(-)$1	1	6	18	9.2781
.(((.....)))	chr12:112381042-112381273(-)$1	1	135	147	10.0176
.(((.....)))	chr19:56029027-56029254(+)$1	1	97	109	9.2781
((((.....)))	chr1:185276991-185277256(-)$1	1	147	159	10.8211

#PSSM
d : 0.49	: : 0.13	e : 0.13	[ : 0.09	! : 0.03	' : 0.01	c : 0.01	i : 0.01	F : 0.01	# : 0.01	
d : 0.49	c : 0.37	e : 0.13	
d : 0.47	c : 0.37	e : 0.13	b : 0.01	
d : 0.47	c : 0.37	e : 0.13	b : 0.01	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
d : 0.47	c : 0.37	e : 0.13	b : 0.01	
d : 0.47	c : 0.37	e : 0.13	b : 0.01	
d : 0.47	c : 0.37	e : 0.13	] : 0.01	

#score	516.3631542524785
#seq	51
#width	12
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m1_run2.txt

#BEAR
dd!!a[eeeee[cccmmmmccc333eeeee]a3	chr19:44980430-44980653(-)$1	223	8	41	9.9284
eeeeee[ffffffooooooffffff]eeeee::	chr2:20450178-20450400(-)$1	222	135	168	11.2798
!bb!!bb[eeeeeooooooeeeee]bb]bb444	chr1:151025517-151025772(-)$1	255	203	236	12.9221
ggffffff!!cccooooooccc22ffffff]gg	chr17:57075523-57075761(-)$1	238	89	122	13.8713
hhhhh[gggggggooooooggggggg]hhhhhh	chr4:159827332-159827553(+)$1	221	106	139	12.8514
dffffff!!cccrrrrrrrrrccc333ffffff	chr12:132406440-132406679(+)$1	239	144	177	9.9045
!!dddd[ffffffooooooffffffdddd]ddd	chr5:78281308-78281523(-)$1	215	44	77	13.0449
gggg[ccc!!cccnnnnncccccc22ggggggg	chr7:131187446-131187679(-)$1	233	107	140	11.1770
====="""eeeeeooooooeeeee]========	chr12:49085594-49085836(-)$1	242	41	74	15.7392
acccbb[ffffffooooooffffffbb]ccc]a	chr5:72206150-72206371(+)$1	221	13	46	13.1119
dddd[bb[ccc[aooooooa]ccc]bb]dddd]	chr17:62502224-62502470(-)$1	246	106	139	13.4419
cc!!dddd[ddddoooooodddddddd4444cc	chr4:95588109-95588335(+)$1	226	112	145	13.6438
iiiiiiiii[bbaooooooa]bb]iiiiiiiii	chr3:107764807-107765032(-)$1	225	168	201	14.5685
hhhhhhh!!ddddoooooodddd333hhhhhhh	chr19:7977708-7977939(+)$1	231	95	128	13.1976
iiii[ccc[ddddmmmmdddd]ccc333iiiii	chr3:52938711-52938939(-)$1	228	100	133	10.1262
dddd!!gggggggooooooggggggg22dddd3	chr17:66528095-66528328(+)$1	233	54	87	13.6865
ddd:eeeeeddddoooooodddd333eeeee::	chr3:38531089-38531311(+)$1	222	31	64	11.0653
c!!==========oooooo==========22cc	chr15:77404924-77405175(-)$1	251	157	190	15.6943
dddd"""ffffffooooooffffffdddd333f	chr5:1463491-1463716(-)$1	225	113	146	13.5424
dd[eeeee!!cccooooooccc4444eeeee22	chr3:33133126-33133343(-)$1	217	3	36	14.5228
:ggggggg!!cccooooooccc4444ggggggg	chr1:162493525-162493753(+)$1	228	26	59	15.0870
ggggdddd!!aooooooa22dddd4444ggggg	chr22:21305465-21305687(+)$1	222	168	201	11.5402
ddddccc####bboooooobb4444ccc22ddd	chr3:12939223-12939456(-)$1	233	4	37	13.3201
!ccc!!bb[a[bboooooobb]a]bb4444ccc	chr19:39138260-39138484(+)$1	224	109	142	13.6428
ff$$$$$ffffffooooooffffff333fffff	chr3:142751610-142751833(+)$1	223	103	136	12.8303
!!dddd"""ddddooooooddddddddccc===	chr3:49049080-49049323(+)$1	243	108	141	13.9274
ggggggg"""eeeeeooooooeeeeeggggggg	chr1:19233491-19233729(-)$1	238	195	228	11.7876
!eeeee"""eeeeennnnneeeee333eeeee]	chrX:47089111-47089353(+)$1	242	161	194	10.3723
[dddd[eeeee[aooooooa]eeeeeddddccc	chr16:24802536-24802763(+)$1	227	85	118	13.3741
a[==========rrrrrrrrr==========]a	chr18:74074368-74074591(-)$1	223	56	89	11.7113
cc[adddd[ddddoooooodddd]dddd]a]cc	chr11:120894845-120895074(+)$1	229	31	64	13.7202
eeee[eeeee[bboooooobb]eeeee22eeee	chr9:123522232-123522453(-)$1	221	75	108	12.3490
ggggggg[ffffffooooooffffffggggggg	chr20:62905033-62905263(+)$1	230	140	173	12.9729
ccceeeee[ddddoooooodddd]eeeee]ccc	chr14:105476584-105476826(-)$1	242	19	52	13.7872
fff!!bb[eeeeeooooooeeeee]bb>>>>>>	chr22:36885507-36885733(-)$1	226	87	120	12.0688
iiiiiiii!!cccooooooccc333iiiiiiii	chr8:81553362-81553593(-)$1	231	184	217	16.6696
))ffffffeeeeeooooooeeeee22ffffffe	chr18:57571392-57571634(+)$1	242	113	146	11.6745
ee[ccc[ddddbboooooobb4444dddd22cc	chr7:134853584-134853822(-)$1	238	53	86	13.3533
ff[a"""ffffffooooooffffff22afffff	chr3:50363204-50363450(-)$1	246	105	138	13.3118
======[bb[cccooooooccc]bb333=====	chrX:63405242-63405473(-)$1	231	119	152	15.1365
b$$$$$gggggggoooooogggggggbb22===	chr13:77580728-77580954(-)$1	226	19	52	12.7265
bb!!dddd[ddddoooooodddd22dddd]bb]	chr9:136210571-136210824(-)$1	253	38	71	12.9142
:iiiiiiiii!!ccclllccc333iiiiiiiii	chr18:21106541-21106766(+)$1	225	183	216	10.3791
ddd:ccc[eeeeeooooooeeeee]ccc:iiii	chr10:74035564-74035801(+)$1	237	60	93	12.5904
c[ccc!!ccccccooooooccc22cccccc]cc	chr1:210016797-210017028(+)$1	231	17	50	14.7664
[cccffffff[bboooooobb]ffffff]ccc]	chr22:50356865-50357090(+)$1	225	159	192	13.1393
==========[bboooooobb============	chr17:47130170-47130411(+)$1	241	16	49	15.6189
c"""ccc"""ddddnnnnnddddccc333ccc]	chr12:132407442-132407664(+)$1	222	144	177	10.6932
"bb[ccc[ccc[aooooooa]ccc]ccc]bb]d	chr8:27685551-27685776(-)$1	225	88	121	13.6983
dd[ccc[cccrrrrrrrrrccc333cccddddc	chr12:56386647-56386888(+)$1	241	165	198	10.4954

#otherMatches

#Seq PSSM
GAAGAGAAACUCUAUGAAUGUAACUAGUUUGUA	chr19:44980430-44980653(-)$1	223	8	41	9.9284
AAAAGCCUUGCUAAUUUAGUAGUGAUGCUUUCC	chr2:20450178-20450400(-)$1	222	135	168	11.2798
GCUGAAGCCCUGGAAACCCUCAGGUCUGAGAUA	chr1:151025517-151025772(-)$1	255	203	236	12.9221
GAAUAUUGUUCACUCUUCCGUGUCUGAUGUCUU	chr17:57075523-57075761(-)$1	238	89	122	13.8713
ACUGUCAGAGCUGAUGUUACAGCUUUUACAGUU	chr4:159827332-159827553(+)$1	221	106	139	12.8514
GCAGAGGCAGUUCUUUGUUCAAGCGUUCCUCUG	chr12:132406440-132406679(+)$1	239	144	177	9.9045
aacugucagaguuguugcaggcuuuacaggaga	chr5:78281308-78281523(-)$1	215	44	77	13.0449
UUAUGGGCUCGGCAGUUAGCUGCCAUGUAGAAG	chr7:131187446-131187679(-)$1	233	107	140	11.1770
UGGGAAAGUGUUCAAAUGAGAGCAGUCUUAAGG	chr12:49085594-49085836(-)$1	242	41	74	15.7392
CUUCCAUGUGUAUUUUCUUAUAUACUGUGAAUG	chr5:72206150-72206371(+)$1	221	13	46	13.1119
GGUGUCAUCGGUGUCCUUCCUCCGCUGCCGCCC	chr17:62502224-62502470(-)$1	246	106	139	13.4419
CUUCACUAUAGAGCAUUUACUUUUAGUCUCUAG	chr4:95588109-95588335(+)$1	226	112	145	13.6438
UGUAUGUGCAUACGUAUGAGAUAGGCACAUGCA	chr3:107764807-107765032(-)$1	225	168	201	14.5685
GGCCCAGCCACCUCCUGACGGGUCCCCUGGGUC	chr19:7977708-7977939(+)$1	231	95	128	13.1976
AACCUAGGCUGCUGGAAAGCACCCUUUUGGUUG	chr3:52938711-52938939(-)$1	228	100	133	10.1262
UAGAUUUUUUUCAUAGAUUUGAAAAACUUUUAG	chr17:66528095-66528328(+)$1	233	54	87	13.6865
uucugaggucaaaaauuaguuuguaagccUUUG	chr3:38531089-38531311(+)$1	222	31	64	11.0653
guguguguguguguguauguAUACACAUGUUCA	chr15:77404924-77405175(-)$1	251	157	190	15.6943
GUGAAGUGUGUUGCAGAACCGACGCUUACUGUG	chr5:1463491-1463716(-)$1	225	113	146	13.5424
AAAGGCCUCACUGAGAAGACAGGGCUGGGCUGG	chr3:33133126-33133343(-)$1	217	3	36	14.5228
ACAAACUAGAGGAGCAGCAUCCCAGGUAGUUUG	chr1:162493525-162493753(+)$1	228	26	59	15.0870
GUGACUAGGGAGACCAUUAACUAGUUUAUCAUU	chr22:21305465-21305687(+)$1	222	168	201	11.5402
UCAUGUAUUUGUAUUUUUUUAAGUUUACCAAUG	chr3:12939223-12939456(-)$1	233	4	37	13.3201
AGCGAGAGGCGGCGGAAUGGUGGACUACCACGC	chr19:39138260-39138484(+)$1	224	109	142	13.6428
GCUGAAGCUGCUGAAGAAAUAGUGGAUUGCAUU	chr3:142751610-142751833(+)$1	223	103	136	12.8303
UAAUGGAGACCUUGACUUGGAGGCCAUGGUGGC	chr3:49049080-49049323(+)$1	243	108	141	13.9274
CUCUGGGUUUGACUGGGAUUGUGGUCCCCAGGG	chr1:19233491-19233729(-)$1	238	195	228	11.7876
AGCCCUGGGGCCCUGAAAUGGGGUGGGAGGGCA	chrX:47089111-47089353(+)$1	242	161	194	10.3723
UGGAACGAACUUGGUAAAACUAGUUCUUUCACU	chr16:24802536-24802763(+)$1	227	85	118	13.3741
GUUCUUUCCUUUUUCUCACCCAGGGGAGAGACC	chr18:74074368-74074591(-)$1	223	56	89	11.7113
GGGCCGGGGCUGGCCGGGACCAGGCCCGAGGCU	chr11:120894845-120895074(+)$1	229	31	64	13.7202
GACACUUGAGAAUUAUGCUGUCCUCAGAAUGUC	chr9:123522232-123522453(-)$1	221	75	108	12.3490
GAAGAUUGUUUUCCCAAAGUGGAGAGAAUCUUC	chr20:62905033-62905263(+)$1	230	140	173	12.9729
GAUUUUAUUUAUGUCUAUUUAUAUGUAAAUGUC	chr14:105476584-105476826(-)$1	242	19	52	13.7872
uggcaagcgcuuuaaaacaaaagcucugauauc	chr22:36885507-36885733(-)$1	226	87	120	12.0688
GUUGCUCUUACUGAGAACCCAGCUUGGAGCAGC	chr8:81553362-81553593(-)$1	231	184	217	16.6696
GUGGCAGUAAACUAUUAAAAGUUUUCACUGUUC	chr18:57571392-57571634(+)$1	242	113	146	11.6745
UCCGGGUGUGACGAGAGAACGAGAUUUACCUUC	chr7:134853584-134853822(-)$1	238	53	86	13.3533
GGUGAAGGCUAAUGGCAGAGUUAGCACCCCACU	chr3:50363204-50363450(-)$1	246	105	138	13.3118
UUUCCUGCUGUAUAUGGGGGUGGGGGUGGGGGG	chrX:63405242-63405473(-)$1	231	119	152	15.1365
UCUCUAUGCAUUUAAAAAAAAAUGUAAACUUGA	chr13:77580728-77580954(-)$1	226	19	52	12.7265
GGCCUUUCCCACAGUGCAAUGUGAUGAAAACCA	chr9:136210571-136210824(-)$1	253	38	71	12.9142
ACAGAGUAAGUUGAAUCCUUCCCCCUUGCUCUG	chr18:21106541-21106766(+)$1	225	183	216	10.3791
GAGAGGGUGGGGGCUGGAACCCCUCCCCGGGAG	chr10:74035564-74035801(+)$1	237	60	93	12.5904
AAGAUUUUGCCACAGUAUCGUGAUGCAGUCAUG	chr1:210016797-210017028(+)$1	231	17	50	14.7664
CGCCCCUCUGUGCUGCUGUGUCCGGAGGCGGCC	chr22:50356865-50357090(+)$1	225	159	192	13.1393
UAUAUAUGUGUGUGUGUGUGCUACAUAUAUAUU	chr17:47130170-47130411(+)$1	241	16	49	15.6189
UGAUAGUGCUGGACCCUUUGUCUAUUUUAAAGC	chr12:132407442-132407664(+)$1	222	144	177	10.6932
UCCCGGCCUCUCCGUUUAUGCAGAAGCUUGGCU	chr8:27685551-27685776(-)$1	225	88	121	13.6983
ACUGGUUGCCUGCAUCUUUGGCUCUGCUGUGAU	chr12:56386647-56386888(+)$1	241	165	198	10.4954

#DB
((..(.(((((.(((....)))...))))).).	chr19:44980430-44980653(-)$1	1	8	41	9.9284
)(((((.((((((......)))))).)))))..	chr2:20450178-20450400(-)$1	1	135	168	11.2798
.((..((.(((((......))))).)).))...	chr1:151025517-151025772(-)$1	1	203	236	12.9221
((((((((..(((......)))..)))))).))	chr17:57075523-57075761(-)$1	1	89	122	13.8713
(((((.(((((((......))))))).))))))	chr4:159827332-159827553(+)$1	1	106	139	12.8514
)((((((..(((.........)))...))))))	chr12:132406440-132406679(+)$1	1	144	177	9.9045
..((((.((((((......)))))))))).)))	chr5:78281308-78281523(-)$1	1	44	77	13.0449
((((.(((..(((.....))))))..)))))))	chr7:131187446-131187679(-)$1	1	107	140	11.1770
(((((...(((((......))))).))))))))	chr12:49085594-49085836(-)$1	1	41	74	15.7392
((((((.((((((......)))))))).))).)	chr5:72206150-72206371(+)$1	1	13	46	13.1119
((((.((.(((.(......).))).)).)))).	chr17:62502224-62502470(-)$1	1	106	139	13.4419
((..((((.((((......))))))))....))	chr4:95588109-95588335(+)$1	1	112	145	13.6438
(((((((((.(((......).)).)))))))))	chr3:107764807-107765032(-)$1	1	168	201	14.5685
(((((((..((((......))))...)))))))	chr19:7977708-7977939(+)$1	1	95	128	13.1976
((((.(((.((((....)))).)))...)))))	chr3:52938711-52938939(-)$1	1	100	133	10.1262
((((..(((((((......)))))))..)))).	chr17:66528095-66528328(+)$1	1	54	87	13.6865
))).(((((((((......))))...)))))..	chr3:38531089-38531311(+)$1	1	31	64	11.0653
(..((((((((((......))))))))))..))	chr15:77404924-77405175(-)$1	1	157	190	15.6943
((((...((((((......))))))))))...)	chr5:1463491-1463716(-)$1	1	113	146	13.5424
((.(((((..(((......)))....)))))..	chr3:33133126-33133343(-)$1	1	3	36	14.5228
.(((((((..(((......)))....)))))))	chr1:162493525-162493753(+)$1	1	26	59	15.0870
((((((((..(......)..))))....)))))	chr22:21305465-21305687(+)$1	1	168	201	11.5402
(((((((....((......))....)))..)))	chr3:12939223-12939456(-)$1	1	4	37	13.3201
.(((..((.(.((......)).).))....)))	chr19:39138260-39138484(+)$1	1	109	142	13.6428
((.....((((((......))))))...)))))	chr3:142751610-142751833(+)$1	1	103	136	12.8303
..((((...((((......))))))))))))))	chr3:49049080-49049323(+)$1	1	108	141	13.9274
(((((((...(((((......))))))))))))	chr1:19233491-19233729(-)$1	1	195	228	11.7876
.(((((...(((((.....)))))...))))).	chrX:47089111-47089353(+)$1	1	161	194	10.3723
.((((.(((((.(......).))))))))))))	chr16:24802536-24802763(+)$1	1	85	118	13.3741
(.((((((((((.........)))))))))).)	chr18:74074368-74074591(-)$1	1	56	89	11.7113
((.(((((.((((......)))).)))).).))	chr11:120894845-120895074(+)$1	1	31	64	13.7202
((((.(((((.((......)).)))))..))))	chr9:123522232-123522453(-)$1	1	75	108	12.3490
(((((((.((((((......)))))))))))))	chr20:62905033-62905263(+)$1	1	140	173	12.9729
((((((((.((((......)))).))))).)))	chr14:105476584-105476826(-)$1	1	19	52	13.7872
(((..((.(((((......))))).))......	chr22:36885507-36885733(-)$1	1	87	120	12.0688
((((((((..(((......)))...))))))))	chr8:81553362-81553593(-)$1	1	184	217	16.6696
..(((((((((((......)))))..)))))))	chr18:57571392-57571634(+)$1	1	113	146	11.6745
((.(((.((((((......))....))))..))	chr7:134853584-134853822(-)$1	1	53	86	13.3533
((.(...((((((......))))))..))))))	chr3:50363204-50363450(-)$1	1	105	138	13.3118
((((((.((.(((......))).))...)))))	chrX:63405242-63405473(-)$1	1	119	152	15.1365
(.....(((((((......)))))))))..)))	chr13:77580728-77580954(-)$1	1	19	52	12.7265
((..((((.((((......))))..)))).)).	chr9:136210571-136210824(-)$1	1	38	71	12.9142
.(((((((((..(((...)))...)))))))))	chr18:21106541-21106766(+)$1	1	183	216	10.3791
))).(((.(((((......))))).))).((((	chr10:74035564-74035801(+)$1	1	60	93	12.5904
(.(((..((((((......)))..)))))).))	chr1:210016797-210017028(+)$1	1	17	50	14.7664
.(((((((((.((......)).)))))).))).	chr22:50356865-50357090(+)$1	1	159	192	13.1393
((((((((((.((......))))))))))))))	chr17:47130170-47130411(+)$1	1	16	49	15.6189
(...(((...((((.....)))))))...))).	chr12:132407442-132407664(+)$1	1	144	177	10.6932
.((.(((.(((.(......).))).))).)).)	chr8:27685551-27685776(-)$1	1	88	121	13.6983
((.(((.(((.........)))...))))))))	chr12:56386647-56386888(+)$1	1	165	198	10.4954

#PSSM
d : 0.19	c : 0.12	! : 0.10	g : 0.10	e : 0.06	= : 0.06	i : 0.06	f : 0.06	h : 0.04	a : 0.04	: : 0.04	[ : 0.04	b : 0.04	) : 0.02	" : 0.02	
d : 0.19	g : 0.12	c : 0.12	e : 0.08	f : 0.08	i : 0.08	b : 0.06	! : 0.06	= : 0.06	h : 0.04	[ : 0.04	) : 0.02	$ : 0.02	" : 0.02	
d : 0.18	g : 0.10	c : 0.10	[ : 0.10	! : 0.08	f : 0.08	= : 0.08	i : 0.08	e : 0.06	b : 0.04	h : 0.04	$ : 0.04	" : 0.02	
d : 0.14	c : 0.12	! : 0.10	e : 0.10	g : 0.10	= : 0.10	i : 0.08	f : 0.06	h : 0.04	: : 0.04	$ : 0.04	a : 0.04	" : 0.02	[ : 0.02	
d : 0.14	c : 0.14	e : 0.10	= : 0.10	! : 0.08	f : 0.08	[ : 0.08	i : 0.06	g : 0.06	h : 0.04	" : 0.04	$ : 0.04	a : 0.02	b : 0.02	
c : 0.16	e : 0.12	d : 0.12	b : 0.08	f : 0.08	= : 0.08	[ : 0.06	" : 0.06	i : 0.06	! : 0.06	g : 0.06	$ : 0.04	h : 0.02	
e : 0.12	[ : 0.12	g : 0.12	c : 0.12	" : 0.10	b : 0.08	f : 0.08	d : 0.08	i : 0.06	= : 0.06	h : 0.02	$ : 0.02	! : 0.02	
f : 0.18	e : 0.12	[ : 0.12	" : 0.10	d : 0.10	g : 0.08	c : 0.08	i : 0.06	= : 0.06	! : 0.04	b : 0.04	# : 0.02	
e : 0.18	f : 0.16	! : 0.16	[ : 0.12	c : 0.08	" : 0.08	g : 0.06	= : 0.06	i : 0.04	# : 0.02	d : 0.02	b : 0.02	
e : 0.18	d : 0.18	f : 0.16	! : 0.12	c : 0.10	g : 0.06	= : 0.06	[ : 0.04	" : 0.04	# : 0.02	a : 0.02	i : 0.02	
c : 0.19	d : 0.19	e : 0.18	f : 0.14	[ : 0.08	g : 0.06	= : 0.04	b : 0.02	a : 0.02	# : 0.02	! : 0.02	r : 0.02	
d : 0.18	c : 0.16	f : 0.14	e : 0.14	b : 0.14	[ : 0.08	g : 0.06	= : 0.04	o : 0.02	! : 0.02	r : 0.02	
c : 0.18	d : 0.18	f : 0.14	e : 0.14	b : 0.12	a : 0.08	g : 0.06	r : 0.06	= : 0.02	o : 0.02	
o : 0.78	r : 0.06	c : 0.04	e : 0.04	n : 0.02	m : 0.02	f : 0.02	d : 0.02	
o : 0.80	r : 0.06	n : 0.06	c : 0.04	m : 0.02	e : 0.02	
o : 0.82	r : 0.06	n : 0.06	m : 0.04	l : 0.02	
o : 0.82	r : 0.06	n : 0.06	m : 0.04	l : 0.02	
o : 0.80	r : 0.06	n : 0.06	m : 0.02	d : 0.02	a : 0.02	l : 0.02	
o : 0.80	r : 0.06	c : 0.04	n : 0.04	m : 0.02	d : 0.02	2 : 0.02	
c : 0.19	d : 0.18	f : 0.12	e : 0.12	b : 0.12	a : 0.08	g : 0.06	r : 0.04	o : 0.04	= : 0.02	2 : 0.02	
c : 0.19	d : 0.19	f : 0.14	e : 0.12	b : 0.12	] : 0.08	g : 0.06	r : 0.04	= : 0.02	o : 0.02	
c : 0.23	d : 0.18	e : 0.16	f : 0.14	] : 0.08	g : 0.06	= : 0.06	4 : 0.04	b : 0.02	3 : 0.02	
e : 0.18	d : 0.18	f : 0.16	c : 0.10	3 : 0.08	4 : 0.08	g : 0.06	= : 0.06	2 : 0.04	b : 0.02	a : 0.02	] : 0.02	
e : 0.18	f : 0.16	3 : 0.12	c : 0.12	] : 0.08	4 : 0.08	2 : 0.06	g : 0.06	d : 0.06	= : 0.06	b : 0.02	
f : 0.18	3 : 0.14	] : 0.12	4 : 0.10	e : 0.08	g : 0.06	2 : 0.06	d : 0.06	c : 0.06	= : 0.06	i : 0.04	b : 0.04	
3 : 0.14	d : 0.14	c : 0.12	e : 0.10	b : 0.10	= : 0.08	f : 0.06	g : 0.06	2 : 0.06	i : 0.06	4 : 0.06	] : 0.02	
d : 0.16	e : 0.12	3 : 0.12	b : 0.10	c : 0.10	g : 0.08	= : 0.08	f : 0.06	i : 0.06	2 : 0.04	4 : 0.04	] : 0.02	h : 0.02	
e : 0.12	d : 0.12	c : 0.12	f : 0.08	g : 0.08	= : 0.08	3 : 0.08	] : 0.06	4 : 0.06	i : 0.06	h : 0.04	2 : 0.04	> : 0.02	a : 0.02	b : 0.02	
d : 0.16	e : 0.12	f : 0.10	g : 0.10	= : 0.10	i : 0.08	c : 0.06	2 : 0.06	] : 0.06	h : 0.04	4 : 0.04	b : 0.02	> : 0.02	: : 0.02	3 : 0.02	
e : 0.12	f : 0.10	g : 0.10	c : 0.10	i : 0.10	= : 0.08	d : 0.08	2 : 0.08	] : 0.06	b : 0.04	h : 0.04	4 : 0.04	3 : 0.02	a : 0.02	> : 0.02	
= : 0.12	c : 0.12	e : 0.10	d : 0.10	g : 0.10	i : 0.10	] : 0.08	f : 0.08	4 : 0.04	h : 0.04	2 : 0.04	b : 0.04	3 : 0.02	> : 0.02	
c : 0.19	g : 0.12	d : 0.10	= : 0.10	i : 0.10	f : 0.08	] : 0.06	: : 0.04	h : 0.04	e : 0.04	a : 0.02	4 : 0.02	3 : 0.02	2 : 0.02	> : 0.02	b : 0.02	
c : 0.18	g : 0.12	= : 0.10	] : 0.10	i : 0.10	f : 0.08	d : 0.06	3 : 0.04	: : 0.04	h : 0.04	a : 0.04	e : 0.04	4 : 0.02	2 : 0.02	> : 0.02	

#score	646.98091519672
#seq	50
#width	33
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_CDS_m2_run1.txt

#BEAR
ee[ccc!!cccnnnnnccc22ccc22ee	chr8:61654203-61654427(+)$1	224	163	191	14.3846
gg==========oooooo==========	chr2:109271512-109271730(-)$1	218	137	165	10.3578
a[dddd"""bbnnnnnbb]dddd]abb]	chr9:135554377-135554596(+)$1	219	60	88	12.1344
dd!!ccccccooooooccc333ccc22d	chrM:3886-4134(+)$1	248	44	72	10.8088
h[ccc!!ddddnnnnndddd22ccc]hh	chr7:100075288-100075512(-)$1	224	76	104	12.8136
ggggggg[cccnnnnncccggggggg55	chr11:128934642-128934866(-)$1	224	167	195	13.3853
:gggggggcccnnnnnccc333gggggg	chr5:54960558-54960782(-)$1	224	95	123	14.7469
h[ccc!!bbbbnnnnnbb]bb]ccchhh	chr2:141199988-141200212(-)$1	224	119	147	12.4353
gggggg"""bboooooobb333gggggg	chr1:26881108-26881329(+)$1	221	135	163	11.9931
gggg[bb!!bbnnnnnbb]bbggggggg	chr1:202104508-202104753(-)$1	245	100	128	13.6685
dd[bb"""cccnnnnnccc333bb]ddd	chr6:147599210-147599432(+)$1	222	34	62	13.8684
ffff[bb!!bbnnnnnbb22bb]fffff	chr3:160956459-160956680(+)$1	221	164	192	12.5395
hhhhhhh[cccnnnnnccc]hhhhhhhh	chr11:9438505-9438720(+)$1	215	174	202	12.9177
hhhhh[a[cccnnnnnccc]a]hhhhhh	chr8:8235370-8235603(-)$1	233	4	32	13.9732
c[iiiiiiiiinnnnniiiiiiiiiccc	chr11:11400534-11400767(-)$1	233	66	94	14.1292
a!!dddd[cccnnnnnccc333dddd22	chr5:177573007-177573237(-)$1	230	112	140	14.1293
eee####ddddnnnnnddddeeeee]cc	chr1:1269696-1269925(-)$1	229	40	68	11.8873
ccc[bb!!cccnnnnnccc22bb]ccc]	chr17:42987415-42987630(+)$1	215	50	78	14.5804
cc[bb[a!!bbnnnnnbb22a]bbccce	chr17:73760012-73760229(+)$1	217	162	190	13.4555
cccc[ffffffnnnnnffffff]ccc]c	chr9:139911055-139911279(-)$1	224	9	37	11.8382
fff[a[bb[bbnnnnnbb]bb]a]ffff	chr17:44590292-44590508(+)$1	216	3	31	12.0485
eeee[a[cccooooooccc333a]eeee	chr3:186299125-186299340(+)$1	215	116	144	10.9058
ccc"""eeeeennnnneeeee333ccc3	chr7:157931075-157931299(-)$1	224	141	169	12.2924
dddd!!cccbbnnnnnbb]ccc22dddd	chr19:55593703-55593948(-)$1	245	57	85	11.9091
cccccdddd[annnnna]dddd22ccc]	chr16:28414807-28415030(-)$1	223	15	43	11.7387
cc[eeeeecccnnnnnccc]eeeee]cc	chr7:75517543-75517770(+)$1	227	60	88	13.6241
fff"""bbcccnnnnnccc]bb>>>>>>	chr18:32677396-32677622(+)$1	226	18	46	11.7829
==========annnnna]==========	chr1:156131075-156131304(+)$1	229	119	147	14.7134
b[ffffff[bbnnnnnbbffffffbb33	chr6:31604006-31604262(+)$1	256	103	131	11.3443
bbffffffcccnnnnnccc22ffffff5	chr11:57080365-57080592(-)$1	227	99	127	11.9475
d[dddda[cccnnnnnccc]a]dddd]d	chrX:153441378-153441595(+)$1	217	137	165	13.6842
!!eeeee!!bbnnnnnbb22eeeee]a]	chr7:131189126-131189346(+)$1	220	117	145	13.3372
a"""gggggggnnnnnggggggga]ccc	chr11:2415108-2415338(+)$1	230	180	208	13.0682
ggggggg[cccnnnnnccc]ggggggg:	chr15:43350475-43350693(+)$1	218	31	59	14.4741
======eeeeennnnneeeee22=====	chr14:102290274-102290492(-)$1	218	81	109	12.2486
ggggg!!ddddnnnnnddddgggggggc	chr11:199868-200087(-)$1	219	2	30	13.4135
"eeeee!!cccnnnnnccc22eeeee22	chr20:35422028-35422246(-)$1	218	14	42	13.9274
ggggggg!!ccclllccc22gggggggc	chr19:38709127-38709342(+)$1	215	151	179	10.7705
iiiiiiiii[aooooooa]iiiiiiiii	chr12:98987712-98987944(+)$1	232	50	78	10.9622
ggggggg!!bboooooobb]ggggggg]	chr17:38153986-38154203(+)$1	217	177	205	11.3543
cc[dddd[cccnnnnnccc333dddd]c	chr12:56708540-56708757(-)$1	217	54	82	14.4690
ggggggg!!bboooooobb22ggggggg	chr14:101346984-101347211(+)$1	227	169	197	11.5773
[ccc!!bb[bbnnnnnbbbb22ccc]ii	chr11:1025106-1025331(+)$1	225	27	55	13.1167
e[iiiiiiiiinnnnniiiiiiiii333	chr5:130764746-130764965(-)$1	219	129	157	14.1780
iiiiii####annnnna4444iiiiiii	chr7:129110416-129110652(+)$1	236	83	111	14.8703
::cccbb[cccnnnnnccc22bb22ccc	chr17:7096282-7096507(-)$1	225	157	185	11.7678
========!!aooooooa22========	chr16:863652-863872(+)$1	220	81	109	11.7331
!!eeeee!!bbnnnnnbb22eeeee22b	chr16:67671598-67671817(-)$1	219	17	45	12.7691
gggg"""ddddnnnnndddd]ggggggg	chr12:125603198-125603429(+)$1	231	88	116	13.5114
ccc!!aaddddnnnnndddd]a]a22cc	chr1:51436066-51436283(-)$1	217	124	152	12.5042
cccc"""ddddnnnnnddddccc]cccd	chr1:11137416-11137636(-)$1	220	141	169	12.6894
ffff[a!!cccnnnnnccc22a]fffff	chr2:73450529-73450754(+)$1	225	15	43	14.4758
dddd[bb[cccnnnnnccc]bbdddd]b	chr9:70432912-70433133(-)$1	221	182	210	12.6236
ccc[ddddcccnnnnnccc]dddd]ccc	chr20:32250050-32250271(-)$1	221	85	113	13.3032
gggggggacccnnnnnccc]a]gggggg	chr1:155183216-155183444(-)$1	228	13	41	15.2837
f!!ccc[cccooooooccc]ccc333ff	chr8:113657274-113657494(-)$1	220	10	38	10.7787
"eeeee!!cccnnnnnccc22eeeee]g	chr11:111959576-111959828(+)$1	252	174	202	14.2725

#otherMatches

#Seq PSSM
UACCCUGGCAUGCAGAAUGAGAGGCAUG	chr8:61654203-61654427(+)$1	224	163	191	14.3846
UGCUCGGGGGAUUUCUUCGUUCUCUGGG	chr2:109271512-109271730(-)$1	218	137	165	10.3578
CACGGGAUAGCAGUGAGCCCCUGCGGUG	chr9:135554377-135554596(+)$1	219	60	88	12.1344
CUCAGGCUUCAACAUCGAAUACGCCGCA	chrM:3886-4134(+)$1	248	44	72	10.8088
AAGCUGCCCCACGGCCUGGGAGAGCCUU	chr7:100075288-100075512(-)$1	224	76	104	12.8136
UUAAAUUAUCUACUUAAGAAAUUUGAUA	chr11:128934642-128934866(-)$1	224	167	195	13.3853
GUUGGAUACCACUAGCUGGGAAUAUCCA	chr5:54960558-54960782(-)$1	224	95	123	14.7469
CAUCAGACGAGGCCAACUGCGGUGAGUG	chr2:141199988-141200212(-)$1	224	119	147	12.4353
AGGGGUAAAGGAUCCAGCCCAAGCcucu	chr1:26881108-26881329(+)$1	221	135	163	11.9931
UCUUAGUCCUGGGUAACAAGCGAGACCU	chr1:202104508-202104753(-)$1	245	100	128	13.6685
AAGGAAAACAAUUUAUUUGCAGUCAUUC	chr6:147599210-147599432(+)$1	222	34	62	13.8684
UUUUUCAUUUAAUCCAUAUCUGUAAAAG	chr3:160956459-160956680(+)$1	221	164	192	12.5395
CAGGGAUGUACCUAAUGUAAGUUUCUGU	chr11:9438505-9438720(+)$1	215	174	202	12.9177
CUUGUGUGUAGGUCAUCUGGAGACGAGC	chr8:8235370-8235603(-)$1	233	4	32	13.9732
GUCAGUGGCUGGAGGGCGGCCACUGCCC	chr11:11400534-11400767(-)$1	233	66	94	14.1292
CACCUGGAUCUCUACAAGGCAACCAGAG	chr5:177573007-177573237(-)$1	230	112	140	14.1293
GCUAAGUCUGGGUUCACCGGGGCUGAGA	chr1:1269696-1269925(-)$1	229	40	68	11.8873
UCAAGCUGGGCAAAGCGCCGUGUCUGAG	chr17:42987415-42987630(+)$1	215	50	78	14.5804
GAGAGACAAGCAGUACGUGAGGCUUCCG	chr17:73760012-73760229(+)$1	217	162	190	13.4555
CCUGGGUGGGCACGUGGCCCACGUGGUG	chr9:139911055-139911279(-)$1	224	9	37	11.8382
AUGCGCCUACUCUCCCAGCAGACCCGUG	chr17:44590292-44590508(+)$1	216	3	31	12.0485
UGGGCCCUGGGCGCUUCCAAAUGACCCA	chr3:186299125-186299340(+)$1	215	116	144	10.9058
GGUGAGGGGCCUGAGUGGCCUGGAGCUG	chr7:157931075-157931299(-)$1	224	141	169	12.2924
CGGCAUCCGAUGUCAGAUGCGGCCGCCG	chr19:55593703-55593948(-)$1	245	57	85	11.9091
GCUCGGGCCUCUUCGCGUGGCCGGUGAC	chr16:28414807-28415030(-)$1	223	15	43	11.7387
UGGGGCCUUGGGCACACCAGGGGCUGCA	chr7:75517543-75517770(+)$1	227	60	88	13.6241
GCCUAUUGCCAAUUCAUGGACAUGCUCU	chr18:32677396-32677622(+)$1	226	18	46	11.7829
AGCUGCUCUGCACCCAGCCGGGGCAGCU	chr1:156131075-156131304(+)$1	229	119	147	14.7134
GCUGGAGGAGUUCUCUACCCUCCACCUU	chr6:31604006-31604262(+)$1	256	103	131	11.3443
GAUGGGGAGAGUCAACCUCAAUUCCCAG	chr11:57080365-57080592(-)$1	227	99	127	11.9475
UGUGCUCGAUCUGGGCGAUGGUGGCAGA	chrX:153441378-153441595(+)$1	217	137	165	13.6842
CUGCAGCUCCUCUGUUAGCCGCUGCUAG	chr7:131189126-131189346(+)$1	220	117	145	13.3372
GUGUAGGCACCCACCUGGUGUCUCUCUC	chr11:2415108-2415338(+)$1	230	180	208	13.0682
UAUUUAUUGAUAUCUAAUUUAUAAAUAA	chr15:43350475-43350693(+)$1	218	31	59	14.4741
UGGAGUCUGUUCCUUCAACAGGAGCUCU	chr14:102290274-102290492(-)$1	218	81	109	12.2486
CCGGCGGAUCUUGUGUAGAUGCCGGGUG	chr11:199868-200087(-)$1	219	2	30	13.4135
AGAUCUCCUCCUCCCUGGACAAGGUCCA	chr20:35422028-35422246(-)$1	218	14	42	13.9274
CGGAAACUCCAGCAACUGCUGUUUCUGG	chr19:38709127-38709342(+)$1	215	151	179	10.7705
UCGUCCGUGGCGCACCUGGCGCGGGCGA	chr12:98987712-98987944(+)$1	232	50	78	10.9622
UUUGAAGCUUCGAUUAUGAUUUUUAAAC	chr17:38153986-38154203(+)$1	217	177	205	11.3543
GACCCCAAGAAGACCAUUCAGAUGGGAU	chr12:56708540-56708757(-)$1	217	54	82	14.4690
CAGGGUCAGGAACUGGCUCAGGGCCCUG	chr14:101346984-101347211(+)$1	227	169	197	11.5773
ACCCCUGCAUCAGGGAGGGCCUGGGAGG	chr11:1025106-1025331(+)$1	225	27	55	13.1167
GAUUUCUUUAGCGGACCUAAAGGAAGGA	chr5:130764746-130764965(-)$1	219	129	157	14.1780
CUGGAUUAUCCUUGCUGUACCAUCCAGG	chr7:129110416-129110652(+)$1	236	83	111	14.8703
CAGGCGCACAAGUUCAUUGAGGCCGGCC	chr17:7096282-7096507(-)$1	225	157	185	11.7678
CCGGGGCACCCCUGCCUGCCUGCCCUGG	chr16:863652-863872(+)$1	220	81	109	11.7331
CCUGGCGACGCACAAGGCUCCGCCAUCA	chr16:67671598-67671817(-)$1	219	17	45	12.7691
UCUGGGACCUGGUUGACAGGAUAGGGUA	chr12:125603198-125603429(+)$1	231	88	116	13.5114
GUCCUUCCAAAUCCAUUUUGUGCAUUGA	chr1:51436066-51436283(-)$1	217	124	152	12.5042
GGAGAAUGUUCUCUUUGGACCUCACGAC	chr1:11137416-11137636(-)$1	220	141	169	12.6894
ACCCCCCAGCUCCCUAAGCCAGUGGGUC	chr2:73450529-73450754(+)$1	225	15	43	14.4758
UGAGAGAACAAAUCGAUUGGUCCUCAUU	chr9:70432912-70433133(-)$1	221	182	210	12.6236
GCUUUGGUCCUUUUGUGGGAACUAUAGU	chr20:32250050-32250271(-)$1	221	85	113	13.3032
GGCGUUGCCCGCUGGAUGGAGACAAUGC	chr1:155183216-155183444(-)$1	228	13	41	15.2837
AUCACAUGGAUCUGUUUCUUUGUAUUUC	chr8:113657274-113657494(-)$1	220	10	38	10.7787
CCAAAUAUAGUUGUCUGCUCAGUUUGUU	chr11:111959576-111959828(+)$1	252	174	202	14.2725

#DB
((.(((..(((.....)))..)))..))	chr8:61654203-61654427(+)$1	1	163	191	14.3846
))((((((((((......))))))))))	chr2:109271512-109271730(-)$1	1	137	165	10.3578
(.((((...((.....)).)))).))).	chr9:135554377-135554596(+)$1	1	60	88	12.1344
((..((((((......)))...)))..)	chrM:3886-4134(+)$1	1	44	72	10.8088
(.(((..((((.....))))..))).))	chr7:100075288-100075512(-)$1	1	76	104	12.8136
(((((((.(((.....))))))))))..	chr11:128934642-128934866(-)$1	1	167	195	13.3853
.((((((((((.....)))...))))))	chr5:54960558-54960782(-)$1	1	95	123	14.7469
(.(((..((((.....)).)).))))))	chr2:141199988-141200212(-)$1	1	119	147	12.4353
((((((...((......))...))))))	chr1:26881108-26881329(+)$1	1	135	163	11.9931
((((.((..((.....)).)))))))))	chr1:202104508-202104753(-)$1	1	100	128	13.6685
((.((...(((.....)))...)).)))	chr6:147599210-147599432(+)$1	1	34	62	13.8684
((((.((..((.....))..)).)))))	chr3:160956459-160956680(+)$1	1	164	192	12.5395
(((((((.(((.....))).))))))))	chr11:9438505-9438720(+)$1	1	174	202	12.9177
(((((.(.(((.....))).).))))))	chr8:8235370-8235603(-)$1	1	4	32	13.9732
(.(((((((((.....))))))))))))	chr11:11400534-11400767(-)$1	1	66	94	14.1292
(..((((.(((.....)))...))))..	chr5:177573007-177573237(-)$1	1	112	140	14.1293
(((....((((.....))))))))).))	chr1:1269696-1269925(-)$1	1	40	68	11.8873
(((.((..(((.....)))..)).))).	chr17:42987415-42987630(+)$1	1	50	78	14.5804
((.((.(..((.....))..).))))))	chr17:73760012-73760229(+)$1	1	162	190	13.4555
((((.((((((.....)))))).))).)	chr9:139911055-139911279(-)$1	1	9	37	11.8382
(((.(.((.((.....)).)).).))))	chr17:44590292-44590508(+)$1	1	3	31	12.0485
((((.(.(((......)))...).))))	chr3:186299125-186299340(+)$1	1	116	144	10.9058
(((...(((((.....)))))...))).	chr7:157931075-157931299(-)$1	1	141	169	12.2924
((((..(((((.....)).)))..))))	chr19:55593703-55593948(-)$1	1	57	85	11.9091
(((((((((.(.....).))))..))).	chr16:28414807-28415030(-)$1	1	15	43	11.7387
((.((((((((.....))).))))).))	chr7:75517543-75517770(+)$1	1	60	88	13.6241
(((...(((((.....))).))......	chr18:32677396-32677622(+)$1	1	18	46	11.7829
(((((((((((.....).))))))))))	chr1:156131075-156131304(+)$1	1	119	147	14.7134
(.((((((.((.....))))))))))..	chr6:31604006-31604262(+)$1	1	103	131	11.3443
(((((((((((.....)))..)))))).	chr11:57080365-57080592(-)$1	1	99	127	11.9475
(.(((((.(((.....))).).)))).)	chrX:153441378-153441595(+)$1	1	137	165	13.6842
..(((((..((.....))..))))).).	chr7:131189126-131189346(+)$1	1	117	145	13.3372
(...(((((((.....)))))))).)))	chr11:2415108-2415338(+)$1	1	180	208	13.0682
(((((((.(((.....))).))))))).	chr15:43350475-43350693(+)$1	1	31	59	14.4741
(((((((((((.....)))))..)))))	chr14:102290274-102290492(-)$1	1	81	109	12.2486
(((((..((((.....)))))))))))(	chr11:199868-200087(-)$1	1	2	30	13.4135
.(((((..(((.....)))..)))))..	chr20:35422028-35422246(-)$1	1	14	42	13.9274
(((((((..(((...)))..))))))))	chr19:38709127-38709342(+)$1	1	151	179	10.7705
(((((((((.(......).)))))))))	chr12:98987712-98987944(+)$1	1	50	78	10.9622
(((((((..((......)).))))))).	chr17:38153986-38154203(+)$1	1	177	205	11.3543
((.((((.(((.....)))...)))).)	chr12:56708540-56708757(-)$1	1	54	82	14.4690
(((((((..((......))..)))))))	chr14:101346984-101347211(+)$1	1	169	197	11.5773
.(((..((.((.....))))..))).))	chr11:1025106-1025331(+)$1	1	27	55	13.1167
(.(((((((((.....)))))))))...	chr5:130764746-130764965(-)$1	1	129	157	14.1780
((((((....(.....)....)))))))	chr7:129110416-129110652(+)$1	1	83	111	14.8703
..(((((.(((.....)))..))..)))	chr17:7096282-7096507(-)$1	1	157	185	11.7678
((((((((..(......)..))))))))	chr16:863652-863872(+)$1	1	81	109	11.7331
..(((((..((.....))..)))))..)	chr16:67671598-67671817(-)$1	1	17	45	12.7691
((((...((((.....)))).)))))))	chr12:125603198-125603429(+)$1	1	88	116	13.5114
(((..((((((.....)))).).)..))	chr1:51436066-51436283(-)$1	1	124	152	12.5042
((((...((((.....))))))).))))	chr1:11137416-11137636(-)$1	1	141	169	12.6894
((((.(..(((.....)))..).)))))	chr2:73450529-73450754(+)$1	1	15	43	14.4758
((((.((.(((.....))).)))))).)	chr9:70432912-70433133(-)$1	1	182	210	12.6236
(((.(((((((.....))).)))).)))	chr20:32250050-32250271(-)$1	1	85	113	13.3032
(((((((((((.....))).).))))))	chr1:155183216-155183444(-)$1	1	13	41	15.2837
(..(((.(((......))).)))...))	chr8:113657274-113657494(-)$1	1	10	38	10.7787
.(((((..(((.....)))..))))).)	chr11:111959576-111959828(+)$1	1	174	202	14.2725

#PSSM
g : 0.19	c : 0.19	d : 0.08	f : 0.08	e : 0.07	h : 0.07	a : 0.05	= : 0.05	: : 0.03	b : 0.03	! : 0.03	" : 0.03	i : 0.03	[ : 0.01	
g : 0.21	c : 0.19	[ : 0.12	e : 0.08	d : 0.07	f : 0.07	! : 0.07	= : 0.05	h : 0.03	i : 0.03	b : 0.01	" : 0.01	: : 0.01	
c : 0.19	g : 0.19	f : 0.10	e : 0.10	[ : 0.08	= : 0.07	d : 0.07	i : 0.07	! : 0.05	h : 0.03	" : 0.01	
g : 0.19	c : 0.15	d : 0.10	e : 0.10	= : 0.07	f : 0.07	i : 0.07	[ : 0.05	" : 0.05	! : 0.03	b : 0.03	h : 0.03	# : 0.01	
g : 0.17	c : 0.12	[ : 0.10	d : 0.08	e : 0.08	= : 0.07	i : 0.07	" : 0.07	b : 0.05	! : 0.05	h : 0.03	f : 0.03	# : 0.01	a : 0.01	
g : 0.15	d : 0.10	! : 0.08	b : 0.08	" : 0.08	e : 0.08	= : 0.07	i : 0.07	c : 0.05	[ : 0.05	f : 0.05	a : 0.05	h : 0.01	# : 0.01	
! : 0.14	g : 0.14	b : 0.12	" : 0.08	e : 0.08	a : 0.07	d : 0.07	= : 0.05	i : 0.05	f : 0.05	c : 0.03	# : 0.03	[ : 0.03	h : 0.01	
! : 0.22	[ : 0.15	d : 0.14	c : 0.07	b : 0.07	= : 0.05	" : 0.05	i : 0.05	f : 0.05	e : 0.05	g : 0.03	# : 0.01	a : 0.01	
c : 0.43	! : 0.15	d : 0.12	i : 0.05	[ : 0.05	= : 0.03	" : 0.03	e : 0.03	b : 0.01	f : 0.01	g : 0.01	# : 0.01	
c : 0.43	b : 0.24	d : 0.10	= : 0.03	i : 0.03	e : 0.03	[ : 0.03	f : 0.01	g : 0.01	# : 0.01	! : 0.01	
c : 0.38	b : 0.24	d : 0.10	a : 0.08	o : 0.05	i : 0.03	e : 0.03	= : 0.01	f : 0.01	g : 0.01	
n : 0.82	o : 0.14	= : 0.01	c : 0.01	
n : 0.82	o : 0.15	l : 0.01	
n : 0.82	o : 0.15	l : 0.01	
n : 0.82	o : 0.15	l : 0.01	
n : 0.82	o : 0.15	c : 0.01	
c : 0.43	b : 0.19	o : 0.10	d : 0.10	a : 0.05	i : 0.03	e : 0.03	f : 0.01	g : 0.01	
c : 0.43	b : 0.24	d : 0.10	i : 0.03	e : 0.03	] : 0.03	a : 0.03	o : 0.01	f : 0.01	g : 0.01	4 : 0.01	
c : 0.42	d : 0.12	] : 0.10	2 : 0.10	b : 0.07	= : 0.03	i : 0.03	f : 0.03	e : 0.03	g : 0.01	4 : 0.01	
2 : 0.24	] : 0.19	d : 0.14	3 : 0.12	b : 0.07	i : 0.05	= : 0.03	g : 0.03	f : 0.03	e : 0.03	c : 0.01	4 : 0.01	
2 : 0.17	3 : 0.12	g : 0.10	b : 0.10	e : 0.10	a : 0.07	= : 0.05	d : 0.05	i : 0.05	c : 0.05	f : 0.03	] : 0.03	h : 0.01	4 : 0.01	
g : 0.15	3 : 0.14	] : 0.10	e : 0.10	b : 0.08	c : 0.07	i : 0.07	= : 0.05	d : 0.05	2 : 0.05	f : 0.05	a : 0.03	h : 0.01	
g : 0.21	c : 0.12	d : 0.10	e : 0.10	b : 0.07	] : 0.07	i : 0.07	= : 0.05	2 : 0.05	h : 0.03	a : 0.03	f : 0.03	3 : 0.01	> : 0.01	
g : 0.19	c : 0.10	e : 0.10	] : 0.08	d : 0.08	= : 0.07	f : 0.07	i : 0.07	2 : 0.05	b : 0.03	h : 0.03	3 : 0.03	a : 0.03	> : 0.01	
g : 0.19	c : 0.17	e : 0.12	d : 0.08	= : 0.07	f : 0.07	i : 0.07	2 : 0.05	] : 0.05	h : 0.03	a : 0.01	> : 0.01	b : 0.01	3 : 0.01	
g : 0.19	c : 0.17	d : 0.10	] : 0.08	2 : 0.07	= : 0.07	f : 0.07	h : 0.05	e : 0.05	b : 0.03	i : 0.03	3 : 0.03	> : 0.01	
c : 0.21	g : 0.17	f : 0.08	] : 0.08	= : 0.07	2 : 0.07	h : 0.07	i : 0.05	e : 0.03	d : 0.03	3 : 0.03	b : 0.01	5 : 0.01	> : 0.01	a : 0.01	
c : 0.19	g : 0.12	] : 0.08	d : 0.08	= : 0.07	h : 0.07	f : 0.07	e : 0.05	3 : 0.05	i : 0.05	5 : 0.03	2 : 0.03	b : 0.03	> : 0.01	: : 0.01	

#score	733.520724104416
#seq	57
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m2_run1.txt

#BEAR
fff"""ffffffooooooffffff4444ff	chr12:57000342-57000622(-)$1	280	84	114	14.6747
[ccc!!a!!cccooooooccc22a22ccc]	chrX:39933786-39934069(-)$1	283	40	70	15.9032
d[bb[bb[ddddoooooodddd333bb]bb	chr19:12825611-12825854(-)$1	243	161	191	11.6807
eeeddddeeeeeooooooeeeee4444ddd	chr10:120819004-120819314(-)$1	310	270	300	12.7369
ggggg####cccoooooocccggggggg::	chr9:35059394-35059660(-)$1	266	235	265	13.1786
iiiiiiiiicccooooooccc]iiiiiiii	chr16:28735623-28735887(+)$1	264	35	65	15.4360
dddd!!ffffffooooooffffff22dddd	chr2:70315759-70316036(+)$1	277	97	127	13.6834
((gggggggcccooooooccc>>>>>>>>>	chr14:23396738-23396968(-)$1	230	134	164	12.2821
b"""eeeee[bboooooobb]eeeee4444	chrX:77378592-77378929(+)$1	337	92	122	12.7051
e[bb$$$$$cccooooooccc4444bb]ee	chr5:137854342-137854649(-)$1	307	78	108	13.2292
eeeee!!eeeeeooooooeeeee22eeeee	chr13:48832156-48832465(+)$1	309	85	115	12.5027
:dddd!!a[cccooooooccc]a22dddd:	chr11:20448227-20448473(+)$1	246	41	71	12.4564
ggggg[ffffffooooooffffffgggggg	chr6:33243473-33243761(+)$1	288	18	48	13.9186
==========bboooooobb]=========	chr8:27303295-27303556(+)$1	261	131	161	14.6489
ccc[gggggggrrrrrrrrrggggggg]cc	chr7:8125737-8126096(+)$1	359	18	48	10.2122
iiiiiccc[cccoooooocccccc>>>>>>	chr9:125852519-125852764(+)$1	245	17	47	14.4182
####hhhhhhhhoooooohhhhhhhh22ee	chr1:78098331-78098659(-)$1	328	232	262	11.8143
J===========oooooo===========:	chr7:155473230-155473471(+)$1	241	182	212	13.1307
hhh[dddd[cccooooooccc22ddddhhh	chr8:82752032-82752313(-)$1	281	32	62	12.4883
[ccc$$$$$cccooooooccc333ccc]bb	chr1:3692329-3692622(+)$1	293	223	253	14.4405
#ddddgggggggooooooggggggg]dddd	chr2:198288428-198288676(-)$1	248	173	203	13.9790
cc!!hhhhhhhhoooooohhhhhhhh333c	chr17:7480560-7480907(+)$1	347	264	294	12.6669
"bb[ccc!!cccooooooccc22cccbbgg	chr17:7834251-7834569(-)$1	318	166	196	13.8286
gccc!!gggggggnnnnnggggggg333cc	chr12:58142036-58142441(-)$1	405	217	247	12.2896
cc!!a[dddd[aooooooa]dddda22ccc	chr8:145998597-145998868(-)$1	271	91	121	13.7549
ccc"""ffffffooooooffffff333ccc	chr2:26250955-26251270(-)$1	315	97	127	15.6495
ccc"""gggggggnnnnnggggggg333cc	chr8:87393649-87393917(+)$1	268	180	210	12.3677
ffffeeeee!!aooooooa]eeeee]ffff	chr1:120510628-120510867(-)$1	239	177	207	12.3831
f[aiiiiiiiiiooooooiiiiiiiii333	chr17:41132737-41132976(+)$1	239	156	186	14.8815
ddd"""ffffffooooooffffff333ddd	chr21:30304807-30305062(-)$1	255	77	107	14.8503
##ccc!!eeeeeooooooeeeee22cccgg	chr7:26236889-26237180(-)$1	291	60	90	13.5623
gccc"""eeeeeooooooeeeee]ccc:dd	chr6:32944523-32944819(+)$1	296	97	127	12.9326
eeeeegggggggooooooggggggg333ee	chr12:70195285-70195558(+)$1	273	201	231	15.0933
g!!a[ccc!!ccclllccc22ccc]a22gg	chrX:41206100-41206362(+)$1	262	195	225	10.1100
ggg!!gggggggooooooggggggg333gg	chr14:61285380-61285657(+)$1	277	174	204	16.3919
"ccc!!ffffffooooooffffff4444cc	chr5:140960216-140960477(-)$1	261	208	238	15.3842
!ccc[ccc!!cccmmmmccc22ccc]ccc]	chr19:15491247-15491495(-)$1	248	182	212	10.1139
fff!!gggggggooooooggggggg22fff	chr2:172809334-172809590(+)$1	256	149	179	14.7966
dddd[ddddcccooooooccc333dddddd	chr19:12059539-12059783(+)$1	244	10	40	13.4991
$eeeee!!ccc[aooooooa]ccc333eee	chr8:144732760-144733015(+)$1	255	208	238	13.4077
eeeeedddd[bboooooobb]dddd]eeee	chr10:111630486-111630739(-)$1	253	148	178	11.4735
dd"""ccc[cccooooooccc]ccc]dddd	chr12:56641706-56641946(-)$1	240	85	115	15.1064
=======####cccmmmmccc]========	chr17:37358476-37358796(+)$1	320	48	78	10.3014
[ccc[ddddcccccclllccc]ccc333dd	chr20:35862342-35862605(+)$1	263	150	180	11.1132
gg[eeeee[a[aooooooa]a]eeeee]gg	chr12:6687542-6687810(-)$1	268	35	65	13.4799
gggcccffffffooooooffffff22ccc2	chrX:55479188-55479519(+)$1	331	252	282	13.8166
ggggg"""ddddoooooodddd4444gggg	chr6:87968962-87969256(+)$1	294	227	257	13.7018
:ccc[ccc!!bboooooobb4444ccc]cc	chr14:102549374-102549726(-)$1	352	311	341	13.2607
ccc"""ccc[cccnnnnnccc]ccc333cc	chr14:91763577-91763848(-)$1	271	162	192	12.7027
ggggffffff[aooooooaffffff]gggg	chr1:155226017-155226304(-)$1	287	134	164	13.5344

#otherMatches

#Seq PSSM
UUUUUCUUUCUGCUCUCACAGAAACAUUGA	chr12:57000342-57000622(-)$1	280	84	114	14.6747
CUGGGUCAAUCCUUACAUGGAGGGUGCCAC	chrX:39933786-39934069(-)$1	283	40	70	15.9032
UGGCUGACGCUGGCCGAGCAGCCCAUCUGC	chr19:12825611-12825854(-)$1	243	161	191	11.6807
CAGCUUUUGGUACAGUGAUACCAUUUUAAA	chr10:120819004-120819314(-)$1	310	270	300	12.7369
UUAGUUUCUGGACAAGAUUCCACUGGGGUU	chr9:35059394-35059660(-)$1	266	235	265	13.1786
CUGCUGCAACUGCUGGUUCAGAUUGCAGCG	chr16:28735623-28735887(+)$1	264	35	65	15.4360
ACUAUCACUGGCUCUGCUGCCAGUAUUAGU	chr2:70315759-70316036(+)$1	277	97	127	13.6834
GGGUCUUCCAGCUUUCCUGCUGCCCCUUAA	chr14:23396738-23396968(-)$1	230	134	164	12.2821
UGUGUAGAUUGGCACUUCUCUGUUUGAUGA	chrX:77378592-77378929(+)$1	337	92	122	12.7051
UUCUUUCUUCCACAGCAAUGGCACCAGCAU	chr5:137854342-137854649(-)$1	307	78	108	13.2292
CUGUAUCUUUUUCUUCCCAGAAACUUACAG	chr13:48832156-48832465(+)$1	309	85	115	12.5027
AGAAUCUGUUUAACCUACUAAUCUAAUUCA	chr11:20448227-20448473(+)$1	246	41	71	12.4564
UUUGUGAGCUUUUUGAAUGAGGCUAUAAAG	chr6:33243473-33243761(+)$1	288	18	48	13.9186
CAGCAUGCGGGUAAGAGGGCUCUGCAUGCU	chr8:27303295-27303556(+)$1	261	131	161	14.6489
AAUUCAGAAAAUGCUUAACUUUUUCUGUGU	chr7:8125737-8126096(+)$1	359	18	48	10.2122
UUCUUUCUACCCUUCAGCGGGAGAAUAGGC	chr9:125852519-125852764(+)$1	245	17	47	14.4182
GUUGAUGACAGUGAUUCAGCUGUUAUAAAC	chr1:78098331-78098659(-)$1	328	232	262	11.8143
ACUGGUUUAUCACAAAUCUGAUGGAUCAGA	chr7:155473230-155473471(+)$1	241	182	212	13.1307
AUUAGUUGUUCUCUAAGUGGACUCAACAGU	chr8:82752032-82752313(-)$1	281	32	62	12.4883
UUGUACACAUGGACCCCCCCACAGACACGG	chr1:3692329-3692622(+)$1	293	223	253	14.4405
GUUAUUUUUUUGAGAGAGCAAGAAAUAUGA	chr2:198288428-198288676(-)$1	248	173	203	13.9790
GCGGGCCUGGUAGUGAGUUGUUGGGUAUAG	chr17:7480560-7480907(+)$1	347	264	294	12.6669
GGGAUCAAAGUUGUCAUGAAUACUGACUUG	chr17:7834251-7834569(-)$1	318	166	196	13.8286
GAGGCUAUGGAGGGUCCUCCUCCAUCUUUC	chr12:58142036-58142441(-)$1	405	217	247	12.2896
UCAGCACCGGAGGAUCCACACCGGGGAGAA	chr8:145998597-145998868(-)$1	271	91	121	13.7549
GAUAGAGGGCACCCUGCAGUGCCCGGAAUC	chr2:26250955-26251270(-)$1	315	97	127	15.6495
ACAAGCUCUGUUGAUACACAAUAGAAAAUG	chr8:87393649-87393917(+)$1	268	180	210	12.3677
CAGAACUUUUUCUGUUCUGUGAAGUGUCUG	chr1:120510628-120510867(-)$1	239	177	207	12.3831
UUCGCGCAGGUGCAGUUCCGCCUGCGCCAG	chr17:41132737-41132976(+)$1	239	156	186	14.8815
UUAAAGCUCGAGCUACUACUCGAGAGGUAA	chr21:30304807-30305062(-)$1	255	77	107	14.8503
AUGAGAUUAAAUGCUAAAGUUUACCCUUUG	chr7:26236889-26237180(-)$1	291	60	90	13.5623
UGGCCUUUCUAUAAACCAGUGGAUGCUUCU	chr6:32944523-32944819(+)$1	296	97	127	12.9326
AUGCGGAGGACCAAAGUAGGUUUUUACGUG	chr12:70195285-70195558(+)$1	273	201	231	15.0933
AUGGGUGUUCACUUACAGUUCAUAGUGUUU	chrX:41206100-41206362(+)$1	262	195	225	10.1100
GCAUCAAAAUGGUAAGCCUUAUUUUAAUUG	chr14:61285380-61285657(+)$1	277	174	204	16.3919
AUCAUUUUCUCUUAGUUCAGAGGACAAUUG	chr5:140960216-140960477(-)$1	261	208	238	15.3842
CGGGCCUGCCCUGUCCCCAGCUUAGUCCCC	chr19:15491247-15491495(-)$1	248	182	212	10.1139
GCAUCUAAAGUUGAUGAGAACUUUGACUGU	chr2:172809334-172809590(+)$1	256	149	179	14.7966
UCUUAUCCAUGAAAGAACUCACACUGGAGA	chr19:12059539-12059783(+)$1	244	10	40	13.4991
CCAGAGAAUUCACACCGGAGAGAGACCCUU	chr8:144732760-144733015(+)$1	255	208	238	13.4077
CAUGGUGUUGGGUCUUUUUUGAAUGUCCAU	chr10:111630486-111630739(-)$1	253	148	178	11.4735
GCCUCUGCCCUCAUCAAGGAGCGCAAGCGC	chr12:56641706-56641946(-)$1	240	85	115	15.1064
UGCUUGGGCCCCAGUUGACUGACCAGGUGC	chr17:37358476-37358796(+)$1	320	48	78	10.3014
AUGCUGGUAAGUGCCCCAGGCUGCUAAUUA	chr20:35862342-35862605(+)$1	263	150	180	11.1132
GGGUAAGGGCGAUGGUGCUGGGCUUUGGCU	chr12:6687542-6687810(-)$1	268	35	65	13.4799
GGUGCUAGGGGUUAUUCCGCCCCUUAAGUA	chrX:55479188-55479519(+)$1	331	252	282	13.8166
AAUGUGUAGUACCUACAUGUACAAAAACAU	chr6:87968962-87969256(+)$1	294	227	257	13.7018
cucugcaaaaucaugaaagacauAUUGGAG	chr14:102549374-102549726(-)$1	352	311	341	13.2607
UGGACAUCUCGCUGACCAAGCUGGACAACC	chr14:91763577-91763848(-)$1	271	162	192	12.7027
AGGCCCAGCAAGAAUUUGCUGCUGGUGUCU	chr1:155226017-155226304(-)$1	287	134	164	13.5344

#DB
(((...((((((......))))))....))	chr12:57000342-57000622(-)$1	1	84	114	14.6747
.(((..(..(((......)))..)..))).	chrX:39933786-39934069(-)$1	1	40	70	15.9032
(.((.((.((((......))))...)).))	chr19:12825611-12825854(-)$1	1	161	191	11.6807
((((((((((((......)))))....)))	chr10:120819004-120819314(-)$1	1	270	300	12.7369
(((((....(((......))))))))))..	chr9:35059394-35059660(-)$1	1	235	265	13.1786
((((((((((((......))).))))))))	chr16:28735623-28735887(+)$1	1	35	65	15.4360
((((..((((((......))))))..))))	chr2:70315759-70316036(+)$1	1	97	127	13.6834
..((((((((((......))).........	chr14:23396738-23396968(-)$1	1	134	164	12.2821
(...(((((.((......)).)))))....	chrX:77378592-77378929(+)$1	1	92	122	12.7051
(.((.....(((......)))....)).))	chr5:137854342-137854649(-)$1	1	78	108	13.2292
(((((..(((((......)))))..)))))	chr13:48832156-48832465(+)$1	1	85	115	12.5027
.((((..(.(((......))).)..)))).	chr11:20448227-20448473(+)$1	1	41	71	12.4564
(((((.((((((......))))))))))))	chr6:33243473-33243761(+)$1	1	18	48	13.9186
((((((((((((......)).)))))))))	chr8:27303295-27303556(+)$1	1	131	161	14.6489
(((.(((((((.........))))))).))	chr7:8125737-8126096(+)$1	1	18	48	10.2122
((((((((.(((......))))))......	chr9:125852519-125852764(+)$1	1	17	47	14.4182
....((((((((......))))))))..))	chr1:78098331-78098659(-)$1	1	232	262	11.8143
)(((((((((((......))))))))))).	chr7:155473230-155473471(+)$1	1	182	212	13.1307
(((.((((.(((......)))..)))))))	chr8:82752032-82752313(-)$1	1	32	62	12.4883
.(((.....(((......)))...))).))	chr1:3692329-3692622(+)$1	1	223	253	14.4405
.(((((((((((......))))))).))))	chr2:198288428-198288676(-)$1	1	173	203	13.9790
((..((((((((......))))))))...)	chr17:7480560-7480907(+)$1	1	264	294	12.6669
.((.(((..(((......)))..)))))))	chr17:7834251-7834569(-)$1	1	166	196	13.8286
((((..(((((((.....)))))))...))	chr12:58142036-58142441(-)$1	1	217	247	12.2896
((..(.((((.(......).)))))..)))	chr8:145998597-145998868(-)$1	1	91	121	13.7549
(((...((((((......))))))...)))	chr2:26250955-26251270(-)$1	1	97	127	15.6495
(((...(((((((.....)))))))...))	chr8:87393649-87393917(+)$1	1	180	210	12.3677
(((((((((..(......).))))).))))	chr1:120510628-120510867(-)$1	1	177	207	12.3831
(.((((((((((......)))))))))...	chr17:41132737-41132976(+)$1	1	156	186	14.8815
(((...((((((......))))))...)))	chr21:30304807-30305062(-)$1	1	77	107	14.8503
..(((..(((((......)))))..)))))	chr7:26236889-26237180(-)$1	1	60	90	13.5623
)(((...(((((......))))).))).((	chr6:32944523-32944819(+)$1	1	97	127	12.9326
((((((((((((......)))))))...))	chr12:70195285-70195558(+)$1	1	201	231	15.0933
(..(.(((..(((...)))..))).)..))	chrX:41206100-41206362(+)$1	1	195	225	10.1100
(((..(((((((......)))))))...))	chr14:61285380-61285657(+)$1	1	174	204	16.3919
.(((..((((((......))))))....))	chr5:140960216-140960477(-)$1	1	208	238	15.3842
.(((.(((..(((....)))..))).))).	chr19:15491247-15491495(-)$1	1	182	212	10.1139
(((..(((((((......)))))))..)))	chr2:172809334-172809590(+)$1	1	149	179	14.7966
((((.(((((((......)))...))))))	chr19:12059539-12059783(+)$1	1	10	40	13.4991
.(((((..(((.(......).)))...)))	chr8:144732760-144733015(+)$1	1	208	238	13.4077
(((((((((.((......)).)))).))))	chr10:111630486-111630739(-)$1	1	148	178	11.4735
((...(((.(((......))).))).))))	chr12:56641706-56641946(-)$1	1	85	115	15.1064
(((((((....(((....))).))))))))	chr17:37358476-37358796(+)$1	1	48	78	10.3014
.(((.((((((((((...))).)))...))	chr20:35862342-35862605(+)$1	1	150	180	11.1132
((.(((((.(.(......).).))))).))	chr12:6687542-6687810(-)$1	1	35	65	13.4799
((((((((((((......))))))..))).	chrX:55479188-55479519(+)$1	1	252	282	13.8166
(((((...((((......))))....))))	chr6:87968962-87969256(+)$1	1	227	257	13.7018
.(((.(((..((......))....))).))	chr14:102549374-102549726(-)$1	1	311	341	13.2607
(((...(((.(((.....))).)))...))	chr14:91763577-91763848(-)$1	1	162	192	12.7027
((((((((((.(......))))))).))))	chr1:155226017-155226304(-)$1	1	134	164	13.5344

#PSSM
g : 0.19	c : 0.12	d : 0.10	e : 0.10	f : 0.08	[ : 0.06	# : 0.06	i : 0.04	: : 0.04	= : 0.04	" : 0.04	( : 0.02	b : 0.02	J : 0.02	h : 0.02	! : 0.02	$ : 0.02	
c : 0.27	g : 0.14	d : 0.12	e : 0.10	f : 0.06	[ : 0.06	= : 0.06	i : 0.04	# : 0.04	( : 0.02	" : 0.02	h : 0.02	b : 0.02	! : 0.02	
c : 0.25	g : 0.14	e : 0.10	d : 0.10	f : 0.06	b : 0.06	= : 0.06	! : 0.06	i : 0.04	" : 0.04	# : 0.02	h : 0.02	a : 0.02	[ : 0.02	
c : 0.19	" : 0.14	d : 0.10	g : 0.10	e : 0.10	! : 0.08	i : 0.06	= : 0.06	[ : 0.06	b : 0.04	# : 0.02	f : 0.02	a : 0.02	
" : 0.14	e : 0.14	! : 0.12	[ : 0.12	g : 0.10	d : 0.08	i : 0.06	= : 0.06	c : 0.06	$ : 0.04	h : 0.04	a : 0.02	f : 0.02	
" : 0.14	! : 0.14	c : 0.14	g : 0.12	d : 0.10	e : 0.08	= : 0.06	i : 0.04	$ : 0.04	[ : 0.04	h : 0.04	b : 0.02	# : 0.02	f : 0.02	
f : 0.16	g : 0.16	c : 0.14	d : 0.12	! : 0.08	e : 0.06	= : 0.06	i : 0.04	$ : 0.04	h : 0.04	" : 0.04	a : 0.02	b : 0.02	# : 0.02	
f : 0.16	g : 0.16	e : 0.14	c : 0.12	d : 0.10	! : 0.06	# : 0.04	i : 0.04	$ : 0.04	= : 0.04	h : 0.04	[ : 0.02	a : 0.02	" : 0.02	
f : 0.16	g : 0.16	d : 0.12	e : 0.12	! : 0.10	[ : 0.10	# : 0.04	i : 0.04	$ : 0.04	= : 0.04	h : 0.04	c : 0.04	
c : 0.27	f : 0.16	g : 0.14	e : 0.08	! : 0.08	d : 0.06	[ : 0.06	= : 0.04	h : 0.04	i : 0.02	# : 0.02	a : 0.02	
c : 0.34	f : 0.14	g : 0.14	e : 0.08	b : 0.08	[ : 0.06	d : 0.04	h : 0.04	= : 0.02	! : 0.02	i : 0.02	# : 0.02	
c : 0.34	f : 0.14	g : 0.12	e : 0.08	b : 0.08	a : 0.08	d : 0.04	h : 0.04	r : 0.02	= : 0.02	i : 0.02	[ : 0.02	
o : 0.82	c : 0.10	g : 0.04	r : 0.02	a : 0.02	
o : 0.84	n : 0.06	c : 0.04	r : 0.02	l : 0.02	m : 0.02	
o : 0.84	n : 0.06	m : 0.04	r : 0.02	l : 0.02	c : 0.02	
o : 0.84	n : 0.06	l : 0.04	m : 0.04	r : 0.02	
o : 0.84	n : 0.06	m : 0.04	r : 0.02	c : 0.02	l : 0.02	
o : 0.84	n : 0.06	c : 0.04	r : 0.02	m : 0.02	l : 0.02	
c : 0.34	f : 0.14	g : 0.12	e : 0.08	b : 0.08	a : 0.08	d : 0.04	h : 0.04	r : 0.02	= : 0.02	i : 0.02	o : 0.02	
c : 0.32	f : 0.16	g : 0.12	e : 0.08	b : 0.08	] : 0.06	d : 0.04	h : 0.04	r : 0.02	= : 0.02	i : 0.02	2 : 0.02	a : 0.02	
c : 0.30	f : 0.16	g : 0.14	e : 0.10	] : 0.08	d : 0.06	h : 0.04	2 : 0.04	= : 0.02	i : 0.02	a : 0.02	4 : 0.02	
f : 0.16	g : 0.16	] : 0.14	e : 0.12	2 : 0.08	d : 0.08	c : 0.06	4 : 0.04	= : 0.04	h : 0.04	3 : 0.04	> : 0.02	i : 0.02	
f : 0.16	g : 0.16	e : 0.14	c : 0.14	2 : 0.06	3 : 0.06	4 : 0.06	= : 0.06	i : 0.04	h : 0.04	d : 0.04	> : 0.02	a : 0.02	
f : 0.16	g : 0.16	c : 0.16	4 : 0.08	3 : 0.06	e : 0.06	2 : 0.06	= : 0.06	d : 0.06	i : 0.04	h : 0.04	a : 0.02	> : 0.02	] : 0.02	
g : 0.18	c : 0.16	2 : 0.12	4 : 0.10	3 : 0.08	e : 0.06	= : 0.06	d : 0.06	i : 0.04	> : 0.04	h : 0.04	a : 0.02	] : 0.02	f : 0.02	
3 : 0.18	] : 0.12	2 : 0.10	c : 0.10	4 : 0.08	g : 0.06	e : 0.06	d : 0.06	= : 0.06	b : 0.04	i : 0.04	> : 0.04	h : 0.04	a : 0.02	
3 : 0.19	c : 0.14	d : 0.12	g : 0.10	4 : 0.08	2 : 0.08	b : 0.06	e : 0.06	= : 0.06	i : 0.04	> : 0.04	f : 0.02	
3 : 0.16	d : 0.14	c : 0.12	] : 0.12	g : 0.08	4 : 0.06	e : 0.06	= : 0.06	> : 0.04	2 : 0.04	f : 0.04	i : 0.02	h : 0.02	b : 0.02	: : 0.02	
c : 0.21	d : 0.18	g : 0.16	e : 0.12	f : 0.06	= : 0.06	b : 0.04	> : 0.04	3 : 0.04	: : 0.02	i : 0.02	4 : 0.02	h : 0.02	
c : 0.18	d : 0.16	g : 0.16	e : 0.12	f : 0.06	: : 0.06	] : 0.04	b : 0.04	> : 0.04	= : 0.04	i : 0.02	4 : 0.02	h : 0.02	3 : 0.02	2 : 0.02	

#score	665.9768127428919
#seq	50
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m1_run2.txt

#BEAR
ffff[==========lll==========ff	chr6:7287376-7287589(-)$1	213	120	150	12.7263
ee[ggggggg[aooooooaggggggg333e	chr1:161726508-161726738(+)$1	230	193	223	15.7472
:==========rrrrrrrrr==========	chr12:120899415-120899649(-)$1	234	83	113	11.9311
eeeee[ccc[bboooooobbccceeeee]a	chrX:41092393-41092610(+)$1	217	177	207	13.1853
e!!dddd[ddddoooooodddd22ddddee	chr1:153949170-153949413(-)$1	243	200	230	12.4016
gggggggg[cccoooooocccgggggggII	chr3:57613639-57613851(-)$1	212	88	118	13.2435
ee==========oooooo==========33	chr4:88084662-88084874(-)$1	212	117	147	17.3802
hhhhhhhcccbboooooobb]ccc22hhhh	chr6:135287416-135287654(-)$1	238	97	127	12.2481
ggggggg!!cccnnnnnccc333ggggggg	chr3:14239637-14239864(+)$1	227	14	44	12.6019
ggggg!!eeeeeooooooeeeee22ggggg	chr5:40827351-40827573(-)$1	222	89	119	13.8506
iiiiiii!!cccooooooccc333iiiiii	chr10:103923033-103923287(+)$1	254	17	47	17.5024
ggggggg!!aooooooa22ggggggg====	chr6:35802505-35802718(-)$1	213	101	131	13.5053
bb[ccc"""cccooooooccc333ccc]bb	chr2:73471709-73471933(+)$1	224	129	159	15.0782
f[a!!gggggggooooooggggggg]a]ff	chr9:127639420-127639651(+)$1	231	37	67	15.0957
ggggg####cccooooooccc333gggggg	chr15:65870446-65870658(+)$1	212	142	172	16.6483
dd[a[eeeee[aooooooa]eeeee]addd	chr14:90871541-90871786(+)$1	245	69	99	12.6697
cc==========oooooo==========::	chr15:99505318-99505540(+)$1	222	100	130	15.1974
eeedddd"""bboooooobb333dddd]ee	chr1:211919174-211919392(-)$1	218	137	167	13.4573
ggggg####cccnnnnnccc4444gggggg	chr1:180257274-180257475(-)$1	201	158	188	12.1091
iiiiiii!!cccooooooccciiiiiiiii	chr4:108832410-108832625(+)$1	215	183	213	17.2023
[gggggggddddoooooodddd22gggggg	chr7:135611877-135612091(-)$1	214	112	142	14.5069
iiiiiiii[a[aooooooa]a]iiiiiiii	chrX:47083695-47083928(+)$1	233	113	143	16.7097
gggg"""a[cccooooooccc]a22ggggg	chr17:12893502-12893708(+)$1	206	113	143	15.7779
ccc!!==========lll==========cc	chr7:133977528-133977735(-)$1	207	84	114	13.3209
eeeee[bb[cccooooooccc]bb333eee	chr15:99501484-99501694(+)$1	210	54	84	13.6936
ggggggg"""bboooooobb333ggggggg	chr3:52289302-52289547(-)$1	245	214	244	16.1081
ff!!bb!!ddddoooooodddd333bb333	chr13:25914644-25914849(+)$1	205	4	34	13.9089
[===========oooooo===========b	chr6:31110215-31110438(-)$1	223	9	39	17.3847
fffggggggg[aooooooaggggggg]fff	chr9:126142297-126142501(-)$1	204	119	149	14.7537
!!dddd[eeeeeooooooeeeeedddd444	chr11:62396258-62396536(-)$1	278	216	246	11.7707
iiiiiiii"""annnnna333iiiiiiiii	chr14:96559504-96559712(+)$1	208	82	112	13.1460
eeeee[dddd[aooooooa]ddddeeeeef	chr1:47124278-47124483(-)$1	205	52	82	12.3928
dddd===========lll===========2	chr14:103985912-103986141(-)$1	229	151	181	12.7835
eeebb==========lll==========]b	chr16:23478478-23478682(-)$1	204	12	42	12.4095
dddd####ddddoooooodddd4444dddd	chr13:48830225-48830450(+)$1	225	58	88	12.7397
==[ccc[bb[bboooooobb]bb22ccc]=	chr2:232319586-232319794(-)$1	208	34	64	13.4098
hhhh[gggggggooooooggggggg]hhhh	chr12:50872272-50872511(+)$1	239	18	48	14.0088
f"""ccc[ddddooooooddddccc333ff	chr16:68261896-68262114(+)$1	218	35	65	13.8183
=========[bblllbb]===========i	chr15:65737362-65737579(-)$1	217	86	116	12.2752
dd"""gggggggoooooogggggggddddh	chr20:35222143-35222354(+)$1	211	31	61	13.9148
####ccc[ddddooooooddddccc4444e	chr3:182662226-182662428(-)$1	202	12	42	13.5350
diiiiiiiiicccmmmmccc]iiiiiiiii	chr20:24943631-24943880(-)$1	249	28	58	11.5620
f[bbbbccc[bboooooobb]ccc333bb2	chr8:28013385-28013591(+)$1	206	65	95	12.4306
:eeeee"""cccooooooccc4444eeeee	chr4:37863512-37863740(+)$1	228	78	108	13.6807
iiiiiii!!cccooooooccciiiiiiiii	chr1:6282940-6283156(-)$1	216	131	161	17.2023
cc!!ccc"""bboooooobbccc]ccc]ff	chr11:120100445-120100648(+)$1	203	22	52	14.7569
a[eeeee[bb[aooooooabb]eeeee]a2	chr18:2784380-2784585(+)$1	205	157	187	12.8394
=======[cccrrrrrrrrrccc]======	chr16:3072200-3072439(+)$1	239	100	130	12.3641
"ccc[a!!ddddoooooodddd]a]ccc33	chr19:39437056-39437293(-)$1	237	87	117	14.1471
####a[ffffffooooooffffff]a4444	chr7:137560389-137560609(-)$1	220	146	176	12.5940
+++a[gggggggooooooggggggg]a22h	chr1:150784088-150784303(-)$1	215	89	119	12.4809
ggggggg"""aooooooa]gggggggeeee	chr9:130453577-130453815(+)$1	238	116	146	14.5308

#otherMatches

#Seq PSSM
UAAAUGGUGGUAAUGUAACAUUGCCACCUU	chr6:7287376-7287589(-)$1	213	120	150	12.7263
UUGCCUGUUUUGGGAUCACAAACAGGAAAA	chr1:161726508-161726738(+)$1	230	193	223	15.7472
UGUCUUUGUGGGUUGCUCUACUAUGGAGAU	chr12:120899415-120899649(-)$1	234	83	113	11.9311
AUGUGACAGUCUAUUUUCAGUUGCACAUAU	chrX:41092393-41092610(+)$1	217	177	207	13.1853
UUUGUGGUAGCAGAAGAGUGCUCUCCAUGC	chr1:153949170-153949413(-)$1	243	200	230	12.4016
AAAGUGGAUAUCUGUGGUGGUUCCACUUUA	chr3:57613639-57613851(-)$1	212	88	118	13.2435
GGAGCAGGAGUAGCUGUGUGUUCCUGUUUA	chr4:88084662-88084874(-)$1	212	117	147	17.3802
AGCUCUUGAGCUAUAUAAAGACUUUAAAGA	chr6:135287416-135287654(-)$1	238	97	127	12.2481
UUUGUACAGUGGCCUCUCUAAAAGUACAAA	chr3:14239637-14239864(+)$1	227	14	44	12.6019
GCUUUAAACUGCAAGCUGGCAGUGGAGGGC	chr5:40827351-40827573(-)$1	222	89	119	13.8506
AGAUUACAUUAGGUGAAAUUAUAGGUAAUC	chr10:103923033-103923287(+)$1	254	17	47	17.5024
GUCCGGGCUGCAUCAUCUUCCUGGACUGUU	chr6:35802505-35802718(-)$1	213	101	131	13.5053
UCGAGGUAAGCCUGCUGUGGCCUUCCUAGA	chr2:73471709-73471933(+)$1	224	129	159	15.0782
CGGUCUACCAGCGUGGCGGCUGGUGUUGGU	chr9:127639420-127639651(+)$1	231	37	67	15.0957
GGCAAAAUUCUGUAUUCUUAGUGAUUGUUA	chr15:65870446-65870658(+)$1	212	142	172	16.6483
GUACUUCGUGUGCUCCGACCCAUGGUGACG	chr14:90871541-90871786(+)$1	245	69	99	12.6697
CAGGGUGGCCAGACGGUGUUGGCCACUCCC	chr15:99505318-99505540(+)$1	222	100	130	15.1974
GGUUUGUUAUGUUUUUUUGCUCUGCAGUGC	chr1:211919174-211919392(-)$1	218	137	167	13.4573
ACAGUUUUGGUGAUGAACAUGUGUACUGUG	chr1:180257274-180257475(-)$1	201	158	188	12.1091
UUGGGGAAUGAGCCUGUUUUCUUUCCAGGU	chr4:108832410-108832625(+)$1	215	183	213	17.2023
UGUGGAAGCUGCAAACAAGUAGGCCUUUUA	chr7:135611877-135612091(-)$1	214	112	142	14.5069
GGGGUCUGAUGGGGAGAGUGACCAGGCUUC	chrX:47083695-47083928(+)$1	233	113	143	16.7097
UGGAAUUUGGCAGAAAAUUGUGAUCUCCAG	chr17:12893502-12893708(+)$1	206	113	143	15.7779
guuUACAGAGUAAUAAUGUGUUGCUCUGGA	chr7:133977528-133977735(-)$1	207	84	114	13.3209
GCCCAACCCCCAAGAAUCUGGUGGCCAUGG	chr15:99501484-99501694(+)$1	210	54	84	13.6936
GCAGGAAAAUGAUUGUAUUUGAGUUCCUGU	chr3:52289302-52289547(-)$1	245	214	244	16.1081
CUAUACUAGAAUCAAUUUGUUCCUUGUUAA	chr13:25914644-25914849(+)$1	205	4	34	13.9089
UGUUUGUCAAGGAGACAACCUUGACAGAUG	chr6:31110215-31110438(-)$1	223	9	39	17.3847
GGGUCUCUGGAGAUGUCACCCAGGGAGCCC	chr9:126142297-126142501(-)$1	204	119	149	14.7537
UUGGGCCAGCGAUAUUCUUUGCUGCCCUUC	chr11:62396258-62396536(-)$1	278	216	246	11.7707
GCCCUACAAAGUGGAUGGGAGUGUGGGGCU	chr14:96559504-96559712(+)$1	208	82	112	13.1460
UAUCUUGUCUUAUAUAUUUCAGACAGAUGC	chr1:47124278-47124483(-)$1	205	52	82	12.3928
UGCCUCUCCUUUCCCAGGGGGGAGGGGGAA	chr14:103985912-103986141(-)$1	229	151	181	12.7835
CAGUGUGGGAAAUGCGAAGCAUUUCUCAUC	chr16:23478478-23478682(-)$1	204	12	42	12.4095
GCUGAAAUGAGUCUUUAAACUCUCUAUAGC	chr13:48830225-48830450(+)$1	225	58	88	12.7397
AACAUUUCAAGGGCAAUACCGUGUUGGUUU	chr2:232319586-232319794(-)$1	208	34	64	13.4098
GGUUCUUUAGAUGGAGGAAUUUAAAAAAUC	chr12:50872272-50872511(+)$1	239	18	48	14.0088
UCUACUAAGGCCAGUUCAGGUCUGGGAAAG	chr16:68261896-68262114(+)$1	218	35	65	13.8183
UGGCAGGAUGAUAUGGUGGUUCUGUCGUUG	chr15:65737362-65737579(-)$1	217	86	116	12.2752
CAUUUCCCCAUUAUGUAAAAUGGGGUGUUG	chr20:35222143-35222354(+)$1	211	31	61	13.9148
UGAGAGUGAUAUAUUUAAGUGUACUGGAUC	chr3:182662226-182662428(-)$1	202	12	42	13.5350
UCAGAGAGGACUUUGCUGGGUUUCUUUCUG	chr20:24943631-24943880(-)$1	249	28	58	11.5620
GUGUACAGGGAUAUUCCAAUGCCUUUAGUU	chr8:28013385-28013591(+)$1	206	65	95	12.4306
CCAGAAAACCUAUGGAGUUAGUAAAUUCUG	chr4:37863512-37863740(+)$1	228	78	108	13.6807
UUAGGAACUUGAGUUGAAUCAUUUCUAAAC	chr1:6282940-6283156(-)$1	216	131	161	17.2023
UCCCGGACCUGGACGUUGCCUCCAGAGCAG	chr11:120100445-120100648(+)$1	203	22	52	14.7569
GCUCCUCCAAUGGAUAAACUUCGGGGAAUG	chr18:2784380-2784585(+)$1	205	157	187	12.8394
CCCAAAGCGGGGAGGAGAUAUUUAUUUUGG	chr16:3072200-3072439(+)$1	239	100	130	12.3641
UGGUGCUCCAAGAGGCAGCUUGUGGACCUG	chr19:39437056-39437293(-)$1	237	87	117	14.1471
AAUAUGGGAAAUGCAGCAAUUUCUGGACUA	chr7:137560389-137560609(-)$1	220	146	176	12.5940
UAGUGUUGAUUUGUGCUGAGAUCAAGAGGC	chr1:150784088-150784303(-)$1	215	89	119	12.4809
GGAGGUCCAAGGUGGAACAGACCUCUUUGC	chr9:130453577-130453815(+)$1	238	116	146	14.5308

#DB
((((.((((((((((...))))))))))))	chr6:7287376-7287589(-)$1	1	120	150	12.7263
((.(((((((.(......))))))))...)	chr1:161726508-161726738(+)$1	1	193	223	15.7472
.((((((((((.........))))))))))	chr12:120899415-120899649(-)$1	1	83	113	11.9311
(((((.(((.((......)))))))))).)	chrX:41092393-41092610(+)$1	1	177	207	13.1853
(..((((.((((......))))..))))))	chr1:153949170-153949413(-)$1	1	200	230	12.4016
)(((((((.(((......))))))))))((	chr3:57613639-57613851(-)$1	1	88	118	13.2435
((((((((((((......))))))))))..	chr4:88084662-88084874(-)$1	1	117	147	17.3802
((((((((((((......)).)))..))))	chr6:135287416-135287654(-)$1	1	97	127	12.2481
(((((((..(((.....)))...)))))))	chr3:14239637-14239864(+)$1	1	14	44	12.6019
(((((..(((((......)))))..)))))	chr5:40827351-40827573(-)$1	1	89	119	13.8506
(((((((..(((......)))...))))))	chr10:103923033-103923287(+)$1	1	17	47	17.5024
(((((((..(......)..)))))))))))	chr6:35802505-35802718(-)$1	1	101	131	13.5053
((.(((...(((......)))...))).))	chr2:73471709-73471933(+)$1	1	129	159	15.0782
(.(..(((((((......))))))).).))	chr9:127639420-127639651(+)$1	1	37	67	15.0957
(((((....(((......)))...))))))	chr15:65870446-65870658(+)$1	1	142	172	16.6483
((.(.(((((.(......).))))).))))	chr14:90871541-90871786(+)$1	1	69	99	12.6697
))((((((((((......))))))))))..	chr15:99505318-99505540(+)$1	1	100	130	15.1974
(((((((...((......))...)))).))	chr1:211919174-211919392(-)$1	1	137	167	13.4573
(((((....(((.....)))....))))))	chr1:180257274-180257475(-)$1	1	158	188	12.1091
(((((((..(((......))))))))))))	chr4:108832410-108832625(+)$1	1	183	213	17.2023
.(((((((((((......))))..))))))	chr7:135611877-135612091(-)$1	1	112	142	14.5069
((((((((.(.(......).).))))))))	chrX:47083695-47083928(+)$1	1	113	143	16.7097
((((...(.(((......))).)..)))))	chr17:12893502-12893708(+)$1	1	113	143	15.7779
(((..((((((((((...))))))))))))	chr7:133977528-133977735(-)$1	1	84	114	13.3209
(((((.((.(((......))).))...)))	chr15:99501484-99501694(+)$1	1	54	84	13.6936
(((((((...((......))...)))))))	chr3:52289302-52289547(-)$1	1	214	244	16.1081
((..((..((((......))))...))...	chr13:25914644-25914849(+)$1	1	4	34	13.9089
.(((((((((((......))))))))))))	chr6:31110215-31110438(-)$1	1	9	39	17.3847
((((((((((.(......)))))))).)))	chr9:126142297-126142501(-)$1	1	119	149	14.7537
..((((.(((((......)))))))))...	chr11:62396258-62396536(-)$1	1	216	246	11.7707
((((((((...(.....)...)))))))))	chr14:96559504-96559712(+)$1	1	82	112	13.1460
(((((.((((.(......).)))))))))(	chr1:47124278-47124483(-)$1	1	52	82	12.3928
(((((((((((((((...))))))))))).	chr14:103985912-103986141(-)$1	1	151	181	12.7835
(((((((((((((((...)))))))))).)	chr16:23478478-23478682(-)$1	1	12	42	12.4095
((((....((((......))))....))))	chr13:48830225-48830450(+)$1	1	58	88	12.7397
((.(((.((.((......)).))..))).)	chr2:232319586-232319794(-)$1	1	34	64	13.4098
((((.(((((((......))))))).))))	chr12:50872272-50872511(+)$1	1	18	48	14.0088
(...(((.((((......)))))))...))	chr16:68261896-68262114(+)$1	1	35	65	13.8183
(((((((((.((...)).)))))))))))(	chr15:65737362-65737579(-)$1	1	86	116	12.2752
((...(((((((......)))))))))))(	chr20:35222143-35222354(+)$1	1	31	61	13.9148
....(((.((((......)))))))....)	chr3:182662226-182662428(-)$1	1	12	42	13.5350
)((((((((((((....))).)))))))))	chr20:24943631-24943880(-)$1	1	28	58	11.5620
(.(((((((.((......)).)))...)).	chr8:28013385-28013591(+)$1	1	65	95	12.4306
.(((((...(((......)))....)))))	chr4:37863512-37863740(+)$1	1	78	108	13.6807
(((((((..(((......))))))))))))	chr1:6282940-6283156(-)$1	1	131	161	17.2023
((..(((...((......))))).))).))	chr11:120100445-120100648(+)$1	1	22	52	14.7569
(.(((((.((.(......))).))))).).	chr18:2784380-2784585(+)$1	1	157	187	12.8394
(((((((.(((.........))).))))))	chr16:3072200-3072439(+)$1	1	100	130	12.3641
.(((.(..((((......)))).).)))..	chr19:39437056-39437293(-)$1	1	87	117	14.1471
....(.((((((......)))))).)....	chr7:137560389-137560609(-)$1	1	146	176	12.5940
...(.(((((((......))))))).)..)	chr1:150784088-150784303(-)$1	1	89	119	12.4809
(((((((...(......).)))))))))))	chr9:130453577-130453815(+)$1	1	116	146	14.5308

#PSSM
g : 0.17	e : 0.15	f : 0.11	i : 0.09	d : 0.09	c : 0.05	= : 0.05	: : 0.03	h : 0.03	[ : 0.03	# : 0.03	b : 0.01	! : 0.01	a : 0.01	" : 0.01	+ : 0.01	
g : 0.19	e : 0.15	i : 0.11	= : 0.09	d : 0.07	c : 0.07	f : 0.05	[ : 0.05	! : 0.03	h : 0.03	# : 0.03	b : 0.01	" : 0.01	+ : 0.01	
g : 0.19	e : 0.13	= : 0.11	i : 0.11	[ : 0.07	! : 0.05	d : 0.05	f : 0.03	h : 0.03	c : 0.03	" : 0.03	# : 0.03	a : 0.01	b : 0.01	+ : 0.01	
g : 0.23	= : 0.11	i : 0.11	e : 0.09	d : 0.09	! : 0.07	c : 0.05	h : 0.03	a : 0.03	b : 0.03	" : 0.03	# : 0.03	f : 0.01	
g : 0.21	= : 0.13	i : 0.11	[ : 0.09	e : 0.09	c : 0.09	d : 0.05	b : 0.05	! : 0.03	" : 0.03	h : 0.01	# : 0.01	a : 0.01	
g : 0.23	= : 0.19	i : 0.11	c : 0.09	[ : 0.07	d : 0.05	# : 0.05	e : 0.05	b : 0.03	h : 0.01	! : 0.01	" : 0.01	a : 0.01	
g : 0.23	= : 0.19	i : 0.11	c : 0.09	d : 0.05	! : 0.05	" : 0.05	# : 0.05	e : 0.03	[ : 0.03	h : 0.01	b : 0.01	f : 0.01	
= : 0.17	g : 0.15	! : 0.13	" : 0.11	[ : 0.09	c : 0.05	e : 0.05	# : 0.05	i : 0.05	b : 0.03	a : 0.01	d : 0.01	f : 0.01	
= : 0.17	d : 0.15	" : 0.13	g : 0.11	! : 0.09	c : 0.07	[ : 0.07	e : 0.05	# : 0.03	b : 0.03	i : 0.01	f : 0.01	
c : 0.24	= : 0.15	d : 0.15	g : 0.11	" : 0.09	[ : 0.07	e : 0.05	a : 0.03	i : 0.01	b : 0.01	f : 0.01	
c : 0.24	= : 0.15	b : 0.15	d : 0.13	[ : 0.11	g : 0.07	e : 0.03	o : 0.01	" : 0.01	f : 0.01	a : 0.01	
c : 0.23	b : 0.15	= : 0.13	a : 0.13	d : 0.13	g : 0.07	r : 0.03	e : 0.03	o : 0.03	f : 0.01	
o : 0.78	= : 0.07	n : 0.05	r : 0.03	l : 0.01	c : 0.01	
o : 0.78	= : 0.07	n : 0.05	r : 0.03	l : 0.01	m : 0.01	
o : 0.78	= : 0.07	n : 0.05	r : 0.03	l : 0.01	m : 0.01	
o : 0.78	l : 0.07	n : 0.05	r : 0.03	b : 0.01	m : 0.01	
o : 0.76	l : 0.07	n : 0.05	r : 0.03	a : 0.01	b : 0.01	m : 0.01	
o : 0.75	l : 0.07	c : 0.05	r : 0.03	a : 0.03	2 : 0.01	] : 0.01	
c : 0.23	= : 0.15	b : 0.13	d : 0.13	a : 0.11	g : 0.07	r : 0.03	e : 0.03	2 : 0.01	3 : 0.01	f : 0.01	] : 0.01	
c : 0.23	= : 0.15	g : 0.15	b : 0.15	d : 0.13	] : 0.05	r : 0.03	e : 0.03	3 : 0.01	f : 0.01	
c : 0.23	= : 0.17	g : 0.15	d : 0.15	] : 0.07	3 : 0.07	e : 0.05	4 : 0.01	a : 0.01	b : 0.01	f : 0.01	
= : 0.17	g : 0.17	d : 0.15	3 : 0.11	c : 0.09	i : 0.07	] : 0.07	e : 0.05	4 : 0.03	b : 0.01	f : 0.01	
= : 0.17	g : 0.17	c : 0.13	3 : 0.13	i : 0.09	e : 0.07	4 : 0.05	2 : 0.03	b : 0.03	a : 0.01	d : 0.01	] : 0.01	f : 0.01	
g : 0.21	= : 0.17	2 : 0.09	i : 0.09	c : 0.07	3 : 0.07	e : 0.05	d : 0.05	4 : 0.05	] : 0.03	b : 0.01	a : 0.01	f : 0.01	
g : 0.26	= : 0.19	i : 0.11	e : 0.07	2 : 0.07	c : 0.07	d : 0.05	3 : 0.05	4 : 0.03	] : 0.03	
g : 0.23	= : 0.19	i : 0.11	e : 0.07	d : 0.07	c : 0.07	] : 0.07	3 : 0.05	4 : 0.03	2 : 0.01	b : 0.01	a : 0.01	
= : 0.21	g : 0.15	i : 0.11	e : 0.09	d : 0.09	3 : 0.07	c : 0.07	a : 0.05	h : 0.03	4 : 0.03	b : 0.01	] : 0.01	
= : 0.21	g : 0.15	i : 0.11	e : 0.09	] : 0.09	d : 0.07	3 : 0.05	4 : 0.05	h : 0.03	c : 0.03	f : 0.01	b : 0.01	2 : 0.01	
g : 0.13	= : 0.11	e : 0.11	i : 0.11	f : 0.09	3 : 0.07	] : 0.05	d : 0.05	4 : 0.05	h : 0.03	b : 0.03	I : 0.01	: : 0.01	c : 0.01	a : 0.01	2 : 0.01	
e : 0.13	g : 0.13	i : 0.13	f : 0.11	= : 0.07	h : 0.07	3 : 0.05	b : 0.05	2 : 0.05	d : 0.03	4 : 0.03	a : 0.01	I : 0.01	: : 0.01	c : 0.01	

#score	724.7415528751043
#seq	52
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m2_run2.txt

#BEAR
eeeeyyyyyyyyyyyyyyyyee	chr20:33864624-33864837(+)$1	213	98	120	22.0973
ddddyyyyyyyyyyyyyyyydd	chr1:38078066-38078305(-)$1	239	14	36	21.5415
eeeevvvvvvvvvvvvveeeee	chr11:102192871-102193098(+)$1	227	125	147	22.3387
dddduuuuuuuuuuuudddd::	chr2:29073218-29073436(+)$1	218	190	212	20.7006
eeeeettttttttttteeeee]	chr15:34679222-34679480(-)$1	258	227	249	22.3556
eeeeettttttttttteeeee]	chr4:1018949-1019253(+)$1	304	163	185	22.3556
hhhhyyyyyyyyyyyyyyyyhh	chr18:43428989-43429231(-)$1	242	77	99	20.7192
c[ccctttttttttttccc]cc	chr13:103422504-103422741(-)$1	237	137	159	22.5152
ffffuuuuuuuuuuuuffffff	chr16:18907207-18907491(-)$1	284	32	54	22.3804
gggggtttttttttttgggggg	chr2:128947965-128948195(+)$1	230	191	213	22.0363
eeeeettttttttttteeeee:	chr8:41787818-41788060(-)$1	242	31	53	21.4330
hh[auuuuuuuuuuuua]hhhh	chr2:103431318-103431535(+)$1	217	37	59	21.6783
ffffftttttttttttffffff	chr1:219385898-219386118(+)$1	220	73	95	21.5872
#cccuuuuuuuuuuuuccc22e	chr1:54562387-54562614(+)$1	227	64	86	22.8191
ffffuuuuuuuuuuuuffffff	chr2:204824825-204825186(+)$1	361	34	56	22.3804
ddddtttttttttttdddd]dd	chr11:74689530-74689801(+)$1	271	180	202	21.2713
[bbwwwwwwwwwwwwwwbb]ee	chr16:30593517-30593757(-)$1	240	58	80	20.2041
iiiiuuuuuuuuuuuuiiiiii	chr20:34843823-34844082(+)$1	259	63	85	22.9031
gggguuuuuuuuuuuugggggg	chr3:49022507-49022721(+)$1	214	55	77	22.9389
eeeevvvvvvvvvvvvveeeee	chr1:53514653-53514960(+)$1	307	23	45	22.3387
ddddvvvvvvvvvvvvvdddd>	chr2:204603318-204603556(+)$1	238	149	171	21.6035
====vvvvvvvvvvvvv=====	chr9:42717441-42717656(+)$1	215	22	44	22.2054
ccwwwwwwwwwwwwwwccc]cc	chr19:3053204-3053516(-)$1	312	68	90	20.3806
ffffftttttttttttffffff	chr3:118931616-118931898(-)$1	282	189	211	21.5872
eeewwwwwwwwwwwwwweeeee	chr3:9883054-9883362(-)$1	308	25	47	21.1273
ddddvvvvvvvvvvvvvdddd5	chr2:121980138-121980375(-)$1	237	149	171	21.0689
!ccctttttttttttccc22bb	chr1:15901664-15901901(-)$1	237	102	124	21.2118
!!bbuuuuuuuuuuuubb22ee	chr19:1440326-1440558(+)$1	232	48	70	22.1113
[bbvvvvvvvvvvvvvbb22cc	chr19:41828574-41828893(+)$1	319	50	72	20.5720
""ccctttttttttttccc]ee	chr5:87496288-87496520(-)$1	232	182	204	22.4709
eeeevvvvvvvvvvvvveeeee	chr11:47490434-47490691(-)$1	257	227	249	22.3387
ddddvvvvvvvvvvvvvdddd]	chr11:43467569-43467810(+)$1	241	49	71	21.8343
iiiiuuuuuuuuuuuuiiiiii	chr17:34136929-34137174(+)$1	245	118	140	22.9031
ddddtttttttttttdddd]ee	chr16:69733677-69733945(+)$1	268	6	28	21.5916
ddddvvvvvvvvvvvvvdddd6	chr18:56416302-56416523(+)$1	221	103	125	21.3677
ffffftttttttttttffffff	chr1:162495068-162495292(+)$1	224	1	23	21.5872
eeeevvvvvvvvvvvvveeeee	chr10:3171765-3171982(+)$1	217	98	120	22.3387
eeeeyyyyyyyyyyyyyyyyee	chr15:65869945-65870181(+)$1	236	17	39	22.0973
ffffftttttttttttffffff	chr22:40729407-40729653(+)$1	246	218	240	21.5872
ffffuuuuuuuuuuuuffffff	chrX:102005530-102005746(+)$1	216	175	197	22.3804
eeeeettttttttttteeeee:	chr4:65145405-65145626(-)$1	221	4	26	21.4330
cccyyyyyyyyyyyyyyyyccc	chr6:76425708-76425947(+)$1	239	117	139	21.5444
dddduuuuuuuuuuuudddd::	chr21:48071766-48072031(+)$1	265	116	138	20.7006
ddddtttttttttttddddccc	chr12:54448893-54449108(+)$1	215	27	49	21.2561
gggguuuuuuuuuuuugggggg	chr8:104082199-104082425(+)$1	226	98	120	22.9389
eeeeyyyyyyyyyyyyyyyyee	chrX:123506120-123506372(+)$1	252	190	212	22.0973
[cccyyyyyyyyyyyyyyyycc	chr16:3533396-3533689(+)$1	293	41	63	21.9172
ffffftttttttttttffffff	chr17:73773852-73774103(-)$1	251	228	250	21.5872
!!bbuuuuuuuuuuuubb22ee	chr11:6635306-6635559(-)$1	253	156	178	22.1113
eeeeettttttttttteeeee3	chr9:125672756-125672995(-)$1	239	155	177	22.3520
ddddyyyyyyyyyyyyyyyydd	chr15:41573220-41573484(+)$1	264	192	214	21.5415
&cccuuuuuuuuuuuuccc888	chr1:155883579-155883800(-)$1	221	97	119	20.9059
gggggtttttttttttgggggg	chr6:134308652-134308907(-)$1	255	183	205	22.0363
c[ccctttttttttttccc]cc	chr7:90015977-90016195(+)$1	218	43	65	22.5152
eeeeuuuuuuuuuuuueeeee]	chr17:62496646-62496891(-)$1	245	116	138	23.1358
dddduuuuuuuuuuuudddd33	chr15:56990670-56991003(-)$1	333	150	172	22.6134
gggguuuuuuuuuuuugggggg	chr3:88206730-88206943(+)$1	213	27	49	22.9389
ffffyyyyyyyyyyyyyyyyff	chr19:58180210-58180424(+)$1	214	24	46	21.5750
cccvvvvvvvvvvvvvccc]ee	chr19:6480014-6480461(-)$1	447	101	123	21.9746
ggggyyyyyyyyyyyyyyyygg	chr9:123618926-123619168(-)$1	242	105	127	21.9025
cccvvvvvvvvvvvvvccc333	chr1:111215455-111215679(-)$1	224	38	60	21.8838
dcccuuuuuuuuuuuuccc22d	chr1:204988501-204988730(+)$1	229	43	65	22.7496
eeewwwwwwwwwwwwwweeeee	chr12:75875605-75875846(+)$1	241	79	101	21.1273
ffffuuuuuuuuuuuuffffff	chr12:56431551-56431803(+)$1	252	63	85	22.3804
eeeeyyyyyyyyyyyyyyyyee	chr11:105852177-105852421(+)$1	244	197	219	22.0973
ddddvvvvvvvvvvvvvdddd:	chr2:179970207-179970437(-)$1	230	18	40	20.9117
gg[bbtttttttttttbb]ggg	chr22:41575755-41576065(+)$1	310	231	253	21.4522
"cccuuuuuuuuuuuuccc333	chr17:62895081-62895333(-)$1	252	73	95	23.2165

#otherMatches

#Seq PSSM
CAGUGUCAGUCACAUUUUAAAC	chr20:33864624-33864837(+)$1	213	98	120	22.0973
GACACACACGCUCAAACCCCUG	chr1:38078066-38078305(-)$1	239	14	36	21.5415
UGCAAAUUAAAGAAACAUGCAG	chr11:102192871-102193098(+)$1	227	125	147	22.3387
UCUGCCAGUUAUUAUACAGAAA	chr2:29073218-29073436(+)$1	218	190	212	20.7006
GGCAGAAAAGAAAAUGUUGCCA	chr15:34679222-34679480(-)$1	258	227	249	22.3556
AGCACAUCCACUAUCAGUGCUA	chr4:1018949-1019253(+)$1	304	163	185	22.3556
auauuuUCAGUUUUCAUCACAU	chr18:43428989-43429231(-)$1	242	77	99	20.7192
CCCUCUAACCAAUUCUGAGUGC	chr13:103422504-103422741(-)$1	237	137	159	22.5152
GGUUAACAAUGUGACCAGCCCU	chr16:18907207-18907491(-)$1	284	32	54	22.3804
UUUCUUUCCACCUUCUAGAAAA	chr2:128947965-128948195(+)$1	230	191	213	22.0363
GCAUUAACUUUUUUCAAAUGCA	chr8:41787818-41788060(-)$1	242	31	53	21.4330
GGGAUAUUUUUUUCUUUGCUAG	chr2:103431318-103431535(+)$1	217	37	59	21.6783
AUACAUUAUCCCUAuuuguaua	chr1:219385898-219386118(+)$1	220	73	95	21.5872
AGGACACCUCUAAACUUCCCCC	chr1:54562387-54562614(+)$1	227	64	86	22.8191
AGUACUCUCCUUCAAUUGCUGA	chr2:204824825-204825186(+)$1	361	34	56	22.3804
uguaaauaguuauacugcauug	chr11:74689530-74689801(+)$1	271	180	202	21.2713
GUUGACCCCAUUUUCUGAAGCU	chr16:30593517-30593757(-)$1	240	58	80	20.2041
CAGGCCUUGGUGCUAACCUGGC	chr20:34843823-34844082(+)$1	259	63	85	22.9031
UGUGAUACUGCCAUGGCACAGG	chr3:49022507-49022721(+)$1	214	55	77	22.9389
GCUUUUUCUACGUAACCAAGCA	chr1:53514653-53514960(+)$1	307	23	45	22.3387
ugcuuauuuuucuccauagcau	chr2:204603318-204603556(+)$1	238	149	171	21.6035
GAAACACAAAAACAUACUUUUA	chr9:42717441-42717656(+)$1	215	22	44	22.2054
GGCCACAGCCCUCUCACCCUGG	chr19:3053204-3053516(-)$1	312	68	90	20.3806
CAUGAAUACAUGGCUAUCAUGU	chr3:118931616-118931898(-)$1	282	189	211	21.5872
aaaaacaacaacaaAACUUUCC	chr3:9883054-9883362(-)$1	308	25	47	21.1273
cugcuuuccuaacuccugcagu	chr2:121980138-121980375(-)$1	237	149	171	21.0689
CACUCUCUUCCCAUCAGUCUCC	chr1:15901664-15901901(-)$1	237	102	124	21.2118
GAGUUCUCCAUCACCUACAAGC	chr19:1440326-1440558(+)$1	232	48	70	22.1113
CGCCACCCUUCCCACCGCCUGC	chr19:41828574-41828893(+)$1	319	50	72	20.5720
UACCUGUUAUCCUCAAAGGCUG	chr5:87496288-87496520(-)$1	232	182	204	22.4709
CUGGUUUGUUUUUUUUUCUAGA	chr11:47490434-47490691(-)$1	257	227	249	22.3387
aggauaaaauucaaacuuccua	chr11:43467569-43467810(+)$1	241	49	71	21.8343
CUGACUCACCCAUUCAUCAGGU	chr17:34136929-34137174(+)$1	245	118	140	22.9031
AGCAACUCACAUUAAUGCUUGG	chr16:69733677-69733945(+)$1	268	6	28	21.5916
auucucccauaaacacugaauu	chr18:56416302-56416523(+)$1	221	103	125	21.3677
AAAGACCUAGAAAUUUUCUUUU	chr1:162495068-162495292(+)$1	224	1	23	21.5872
UGCACACCCUUCACCUCUGCGG	chr10:3171765-3171982(+)$1	217	98	120	22.3387
AGCCUUCCAUCUCCUGCACUGG	chr15:65869945-65870181(+)$1	236	17	39	22.0973
AUAGCCUUGUCACUUUGUUAUG	chr22:40729407-40729653(+)$1	246	218	240	21.5872
GUAUCAAAUGAAUAUUAUACCU	chrX:102005530-102005746(+)$1	216	175	197	22.3804
GUAAUAAAAAGUAUAAAUUAUA	chr4:65145405-65145626(-)$1	221	4	26	21.4330
CAGCCUUUCAAUUCAUAUACUG	chr6:76425708-76425947(+)$1	239	117	139	21.5444
GGCCUUCAUCUCUCCUGGCCCA	chr21:48071766-48072031(+)$1	265	116	138	20.7006
UCUGAAGACCACUCCCAGAGCG	chr12:54448893-54449108(+)$1	215	27	49	21.2561
ggauuauaccacacacauccug	chr8:104082199-104082425(+)$1	226	98	120	22.9389
guuggacgagaaaacaauaacg	chrX:123506120-123506372(+)$1	252	190	212	22.0973
AUGUCCUCACCACCAACAACAC	chr16:3533396-3533689(+)$1	293	41	63	21.9172
AACUAACAUUCUGAACUAGUUA	chr17:73773852-73774103(-)$1	251	228	250	21.5872
CCGUUUACUCUUUCCUACCCUG	chr11:6635306-6635559(-)$1	253	156	178	22.1113
AGAGAAAUAGUGUUCCUCUCUU	chr9:125672756-125672995(-)$1	239	155	177	22.3520
UGCUCCUAAUACAUGUCCAAAG	chr15:41573220-41573484(+)$1	264	192	214	21.5415
UAGAAUCACAAAUUUAUCUCAG	chr1:155883579-155883800(-)$1	221	97	119	20.9059
AGUCUUAAGCUUGCAUAGAUUU	chr6:134308652-134308907(-)$1	255	183	205	22.0363
AUUAUCAACAAUCAAUAUAUUA	chr7:90015977-90016195(+)$1	218	43	65	22.5152
UUUACACCUAAUAACAUAAAGC	chr17:62496646-62496891(-)$1	245	116	138	23.1358
uguucuauugguuaaaagcaag	chr15:56990670-56991003(-)$1	333	150	172	22.6134
UAGUUUUUUACCUGUUACUAGG	chr3:88206730-88206943(+)$1	213	27	49	22.9389
gggcccccucuguuucaccagc	chr19:58180210-58180424(+)$1	214	24	46	21.5750
CAGGAUcacacacacacugccu	chr19:6480014-6480461(-)$1	447	101	123	21.9746
GGGACUCACCCUCUUUCAUAUC	chr9:123618926-123619168(-)$1	242	105	127	21.9025
AUGCCCUUGUUUUAUACAUUUC	chr1:111215455-111215679(-)$1	224	38	60	21.8838
UGCAAUCCCACCUAUAUGCUCA	chr1:204988501-204988730(+)$1	229	43	65	22.7496
GCUGAAGCCACCCCACAAGCUG	chr12:75875605-75875846(+)$1	241	79	101	21.1273
UUGCAUaaaaaaaaaaguaaag	chr12:56431551-56431803(+)$1	252	63	85	22.3804
cuggcgcuugcuuauuucuucc	chr11:105852177-105852421(+)$1	244	197	219	22.0973
UCCAGAAAUAAACAGAAUGGAA	chr2:179970207-179970437(-)$1	230	18	40	20.9117
UUGAUUACUUAUAAAUAUGAAC	chr22:41575755-41576065(+)$1	310	231	253	21.4522
caggccccauuuuuaucuuuua	chr17:62895081-62895333(-)$1	252	73	95	23.2165

#DB
((((................))	chr20:33864624-33864837(+)$1	1	98	120	22.0973
((((................))	chr1:38078066-38078305(-)$1	1	14	36	21.5415
((((.............)))))	chr11:102192871-102193098(+)$1	1	125	147	22.3387
((((............))))..	chr2:29073218-29073436(+)$1	1	190	212	20.7006
(((((...........))))).	chr15:34679222-34679480(-)$1	1	227	249	22.3556
(((((...........))))).	chr4:1018949-1019253(+)$1	1	163	185	22.3556
((((................))	chr18:43428989-43429231(-)$1	1	77	99	20.7192
(.(((...........))).))	chr13:103422504-103422741(-)$1	1	137	159	22.5152
((((............))))))	chr16:18907207-18907491(-)$1	1	32	54	22.3804
(((((...........))))))	chr2:128947965-128948195(+)$1	1	191	213	22.0363
(((((...........))))).	chr8:41787818-41788060(-)$1	1	31	53	21.4330
((.(............).))))	chr2:103431318-103431535(+)$1	1	37	59	21.6783
(((((...........))))))	chr1:219385898-219386118(+)$1	1	73	95	21.5872
.(((............)))..)	chr1:54562387-54562614(+)$1	1	64	86	22.8191
((((............))))))	chr2:204824825-204825186(+)$1	1	34	56	22.3804
((((...........)))).))	chr11:74689530-74689801(+)$1	1	180	202	21.2713
.((..............)).))	chr16:30593517-30593757(-)$1	1	58	80	20.2041
((((............))))))	chr20:34843823-34844082(+)$1	1	63	85	22.9031
((((............))))))	chr3:49022507-49022721(+)$1	1	55	77	22.9389
((((.............)))))	chr1:53514653-53514960(+)$1	1	23	45	22.3387
((((.............)))).	chr2:204603318-204603556(+)$1	1	149	171	21.6035
((((.............)))))	chr9:42717441-42717656(+)$1	1	22	44	22.2054
((..............))).))	chr19:3053204-3053516(-)$1	1	68	90	20.3806
(((((...........))))))	chr3:118931616-118931898(-)$1	1	189	211	21.5872
(((..............)))))	chr3:9883054-9883362(-)$1	1	25	47	21.1273
((((.............)))).	chr2:121980138-121980375(-)$1	1	149	171	21.0689
.(((...........)))..))	chr1:15901664-15901901(-)$1	1	102	124	21.2118
..((............))..))	chr19:1440326-1440558(+)$1	1	48	70	22.1113
.((.............))..))	chr19:41828574-41828893(+)$1	1	50	72	20.5720
..(((...........))).))	chr5:87496288-87496520(-)$1	1	182	204	22.4709
((((.............)))))	chr11:47490434-47490691(-)$1	1	227	249	22.3387
((((.............)))).	chr11:43467569-43467810(+)$1	1	49	71	21.8343
((((............))))))	chr17:34136929-34137174(+)$1	1	118	140	22.9031
((((...........)))).))	chr16:69733677-69733945(+)$1	1	6	28	21.5916
((((.............)))).	chr18:56416302-56416523(+)$1	1	103	125	21.3677
(((((...........))))))	chr1:162495068-162495292(+)$1	1	1	23	21.5872
((((.............)))))	chr10:3171765-3171982(+)$1	1	98	120	22.3387
((((................))	chr15:65869945-65870181(+)$1	1	17	39	22.0973
(((((...........))))))	chr22:40729407-40729653(+)$1	1	218	240	21.5872
((((............))))))	chrX:102005530-102005746(+)$1	1	175	197	22.3804
(((((...........))))).	chr4:65145405-65145626(-)$1	1	4	26	21.4330
(((................)))	chr6:76425708-76425947(+)$1	1	117	139	21.5444
((((............))))..	chr21:48071766-48072031(+)$1	1	116	138	20.7006
((((...........))))(((	chr12:54448893-54449108(+)$1	1	27	49	21.2561
((((............))))))	chr8:104082199-104082425(+)$1	1	98	120	22.9389
((((................))	chrX:123506120-123506372(+)$1	1	190	212	22.0973
.(((................))	chr16:3533396-3533689(+)$1	1	41	63	21.9172
(((((...........))))))	chr17:73773852-73774103(-)$1	1	228	250	21.5872
..((............))..))	chr11:6635306-6635559(-)$1	1	156	178	22.1113
(((((...........))))).	chr9:125672756-125672995(-)$1	1	155	177	22.3520
((((................))	chr15:41573220-41573484(+)$1	1	192	214	21.5415
.(((............)))...	chr1:155883579-155883800(-)$1	1	97	119	20.9059
(((((...........))))))	chr6:134308652-134308907(-)$1	1	183	205	22.0363
(.(((...........))).))	chr7:90015977-90016195(+)$1	1	43	65	22.5152
((((............))))).	chr17:62496646-62496891(-)$1	1	116	138	23.1358
((((............))))..	chr15:56990670-56991003(-)$1	1	150	172	22.6134
((((............))))))	chr3:88206730-88206943(+)$1	1	27	49	22.9389
((((................))	chr19:58180210-58180424(+)$1	1	24	46	21.5750
(((.............))).))	chr19:6480014-6480461(-)$1	1	101	123	21.9746
((((................))	chr9:123618926-123619168(-)$1	1	105	127	21.9025
(((.............)))...	chr1:111215455-111215679(-)$1	1	38	60	21.8838
((((............)))..)	chr1:204988501-204988730(+)$1	1	43	65	22.7496
(((..............)))))	chr12:75875605-75875846(+)$1	1	79	101	21.1273
((((............))))))	chr12:56431551-56431803(+)$1	1	63	85	22.3804
((((................))	chr11:105852177-105852421(+)$1	1	197	219	22.0973
((((.............)))).	chr2:179970207-179970437(-)$1	1	18	40	20.9117
((.((...........)).)))	chr22:41575755-41576065(+)$1	1	231	253	21.4522
.(((............)))...	chr17:62895081-62895333(-)$1	1	73	95	23.2165

#PSSM
e : 0.23	d : 0.20	f : 0.14	g : 0.10	c : 0.08	[ : 0.04	! : 0.04	h : 0.02	i : 0.02	" : 0.02	# : 0.01	= : 0.01	& : 0.01	
e : 0.23	d : 0.19	f : 0.14	c : 0.14	g : 0.10	h : 0.02	[ : 0.02	b : 0.02	i : 0.02	! : 0.02	= : 0.01	" : 0.01	
e : 0.23	d : 0.19	c : 0.17	f : 0.14	g : 0.08	b : 0.05	[ : 0.02	i : 0.02	h : 0.01	= : 0.01	w : 0.01	
e : 0.20	d : 0.19	f : 0.14	c : 0.13	g : 0.08	w : 0.05	b : 0.04	v : 0.04	i : 0.02	h : 0.01	a : 0.01	= : 0.01	y : 0.01	
u : 0.29	v : 0.19	y : 0.16	e : 0.07	f : 0.07	t : 0.05	w : 0.05	c : 0.04	g : 0.02	b : 0.01	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.29	v : 0.19	y : 0.16	w : 0.05	
u : 0.29	t : 0.23	v : 0.19	y : 0.16	w : 0.05	d : 0.04	c : 0.01	
y : 0.16	c : 0.16	v : 0.14	f : 0.13	d : 0.08	e : 0.08	g : 0.07	b : 0.05	w : 0.04	i : 0.02	a : 0.01	
e : 0.17	y : 0.16	d : 0.16	c : 0.16	f : 0.13	g : 0.07	b : 0.07	i : 0.02	] : 0.01	= : 0.01	
e : 0.17	y : 0.16	d : 0.16	c : 0.14	f : 0.13	g : 0.07	2 : 0.05	i : 0.02	h : 0.01	b : 0.01	= : 0.01	] : 0.01	
e : 0.17	y : 0.14	f : 0.13	d : 0.11	] : 0.11	g : 0.08	2 : 0.08	i : 0.02	c : 0.02	3 : 0.02	h : 0.01	= : 0.01	8 : 0.01	
e : 0.32	f : 0.14	d : 0.11	c : 0.10	g : 0.10	3 : 0.04	: : 0.02	h : 0.02	2 : 0.02	i : 0.02	= : 0.01	b : 0.01	8 : 0.01	
e : 0.25	f : 0.14	c : 0.10	g : 0.10	: : 0.07	d : 0.05	] : 0.05	3 : 0.05	h : 0.02	i : 0.02	> : 0.01	= : 0.01	5 : 0.01	b : 0.01	6 : 0.01	8 : 0.01	

#score	1487.8590560312725
#seq	68
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m2_run1.txt

#BEAR
==========lll==========4444	chr17:17250178-17250405(+)$1	227	161	188	11.5836
a"""ffffffooooooffffff4444a	chr1:1192274-1192504(-)$1	230	119	146	12.8787
"""gggggggoooooogggggggdddd	chr19:3958605-3958834(-)$1	229	68	95	14.1937
!!ggggggg[annnnna]ggggggg22	chr11:119173892-119174122(+)$1	230	175	202	10.5061
=======[bboooooobb=========	chr7:44102689-44102912(-)$1	223	85	112	15.0773
dd"""bb[bboooooobb]bb333ddd	chr1:93297526-93297767(+)$1	241	194	221	12.2181
ggggggddddoooooodddd22ggggg	chr5:54460375-54460612(+)$1	237	43	70	12.9787
[bb"""ddddoooooodddd333bbdd	chr6:125404697-125404927(+)$1	230	30	57	12.4499
!!iiiiiiiiillliiiiiiiii333c	chr16:15130428-15130655(+)$1	227	29	56	11.1816
ee"""eeeeeooooooeeeee]eeeee	chr1:47184228-47184454(-)$1	226	103	130	12.7228
dd[gggggggooooooggggggg22dd	chr15:69696464-69696686(+)$1	222	38	65	13.8132
gggggg[a[aooooooa22a]gggggg	chr17:42295478-42295705(-)$1	227	69	96	13.9848
ffffff[cccoooooocccffffffee	chr19:46206418-46206645(+)$1	227	134	161	12.9988
baccc[ddddoooooodddd]ccc]a]	chr3:9833913-9834137(-)$1	224	33	60	12.5281
[eeeee[cccooooooccc]eeeeeee	chr16:87864642-87864870(-)$1	228	176	203	13.7370
:::gggggggoooooogggggggeeee	chr17:8168181-8168409(+)$1	228	12	39	11.2682
!!a!!eeeeeooooooeeeee22a22a	chr15:68126232-68126459(-)$1	227	105	132	13.1480
[ccc[a[cccooooooccc]accc]ee	chr21:45114260-45114489(+)$1	229	198	225	14.5595
gggg!!ddddoooooodddd]gggggg	chr1:64646108-64646335(+)$1	227	122	149	13.5437
e[bb"""cccoooooocccbb]eeeee	chr1:16890027-16890252(+)$1	225	21	48	13.4744
###gggggggooooooggggggg0000	chr17:4173182-4173407(-)$1	225	148	175	13.1687
!dddd!!cccooooooccc22dddd22	chrX:13730683-13730912(-)$1	229	138	165	12.9961
iiiiiii[bboooooobbiiiiiiiii	chr13:31711474-31711729(-)$1	255	197	224	14.5246
:iiiiiiiiiooooooiiiiiiiii::	chr13:39612019-39612248(-)$1	229	87	114	12.2476
==========mmmm==========333	chr20:33380233-33380467(-)$1	234	8	35	11.1436
fff"""acccooooooccc]a333fff	chr10:50942721-50942944(+)$1	223	103	130	14.2064
eeee!!ddddoooooodddd22eeeee	chr19:57804032-57804260(+)$1	228	113	140	12.3284
==========oooooo==========:	chr10:71910246-71910474(-)$1	228	61	88	14.8087
iiiiiiiibboooooobb]iiiiiiii	chr2:148716296-148716524(-)$1	228	162	189	14.4863
""ccc!!cccooooooccc22ccc22e	chrX:84501916-84502141(+)$1	225	47	74	14.4049
[eeeee[cccooooooccc]eeeee]a	chr15:85923770-85923999(+)$1	229	95	122	13.9100
ee"""a[cccooooooccca]eeeee3	chr1:229577311-229577539(-)$1	228	174	201	14.3437
cccgggggggooooooggggggg]ccc	chr22:42070705-42070946(-)$1	241	36	63	14.2115
ff[dddd[bboooooobb]dddd]fff	chr5:179149848-179150079(+)$1	231	90	117	11.6148
ccc[ffffffooooooffffff333cc	chr14:97002100-97002328(+)$1	228	188	215	12.6943
c[bb"""cccooooooccc333bbccc	chr7:50660525-50660755(-)$1	230	124	151	14.0672
[a[gggggggooooooggggggg]agg	chr6:27115156-27115393(+)$1	237	50	77	14.8025
!!hhhhhhhhoooooohhhhhhhh22e	chr12:48537434-48537659(+)$1	225	27	54	11.9159
dffffff[bboooooobb]ffffff33	chr1:111992034-111992257(+)$1	223	63	90	12.5465
!ggggggg[aooooooa]ggggggg22	chr20:33932957-33933210(-)$1	253	50	77	14.6928
eee[dddd[aooooooa]dddd22eee	chr7:114658857-114659085(+)$1	228	156	183	11.7811
eeeee[ccc[aooooooa]ccc]eeee	chr15:37101096-37101321(+)$1	225	166	193	11.9319
fffff"""bboooooobb22ffffffB	chr7:150738152-150738379(+)$1	227	62	89	11.4233
:iiiiiiiiiooooooiiiiiiiii:F	chr1:224585758-224585982(-)$1	224	1	28	12.7138
g[bb[a!!bboooooobb22a]bb]gg	chr14:88935244-88935467(+)$1	223	83	110	13.1290
[a[eeeee[aooooooa]eeeee]a33	chr12:49182687-49182913(+)$1	226	76	103	13.5976
"eeeee[cccooooooccc]eeeee44	chr15:75713184-75713406(-)$1	222	136	163	13.9561
###gggggggooooooggggggg6666	chr19:42752494-42752739(-)$1	245	45	72	13.1791
hhh####cccooooooccc4444hhhh	chr9:37515024-37515249(-)$1	225	21	48	12.8843
===========nnnnn===========	chr16:66878882-66879108(-)$1	226	35	62	11.2590
ddbb"""cccooooooccc333bb]dd	chr3:160129683-160129912(+)$1	229	148	175	13.6526
ggggg"""bboooooobb333gggggg	chr8:22278387-22278617(+)$1	230	135	162	14.4400
fffffeeeeeooooooeeeeeffffff	chr3:130828541-130828762(-)$1	221	118	145	11.5145
!!bb[eeeeeooooooeeeee]bb22c	chr19:50410298-50410528(-)$1	230	6	33	12.5558

#otherMatches

#Seq PSSM
GGUCUGGGAGUCCCUCCUAGACUCCUG	chr17:17250178-17250405(+)$1	227	161	188	11.5836
CGUCGGACUUCACGGUAAGUUUUAGAG	chr1:1192274-1192504(-)$1	230	119	146	12.8787
GUUCAGGCCCGGAGGAGGGUUUGCGGG	chr19:3958605-3958834(-)$1	229	68	95	14.1937
CAGUUUGuuuguucauccagcaaaugu	chr11:119173892-119174122(+)$1	230	175	202	10.5061
AGUCUGGCUGGAGUCACACUGGGCUGA	chr7:44102689-44102912(-)$1	223	85	112	15.0773
CUUUUCUUGCCCGUAUGCCAGCCUAGG	chr1:93297526-93297767(+)$1	241	194	221	12.2181
AUUUUCUAGGACUGUACUUGAUGAAAA	chr5:54460375-54460612(+)$1	237	43	70	12.9787
AGGCCCAGUAACCUUGUACUUACCCAG	chr6:125404697-125404927(+)$1	230	30	57	12.4499
AUGAGGUUGCCCGUGGCAACUUUUUGG	chr16:15130428-15130655(+)$1	227	29	56	11.1816
GCCAAGCAGUGUUGGGAUUGUAGCUGC	chr1:47184228-47184454(-)$1	226	103	130	12.7228
UAAAAAUGAAUCUUGCUUCAUUUGAUG	chr15:69696464-69696686(+)$1	222	38	65	13.8132
CGGCCAGCACGACCGAGGAGGUGGCUG	chr17:42295478-42295705(-)$1	227	69	96	13.9848
GUAAACACUUGGUCCAAAGGUUUGCAG	chr19:46206418-46206645(+)$1	227	134	161	12.9988
CCCUGGGGCCGUAGGAGGCCGCAGCGA	chr3:9833913-9834137(-)$1	224	33	60	12.5281
uggugccccaccugccuggugcauugc	chr16:87864642-87864870(-)$1	228	176	203	13.7370
ACCCCACCUGGUUCCACAGGUGGACCG	chr17:8168181-8168409(+)$1	228	12	39	11.2682
AGGGACGCCCGGGAGGGGGCGGGCAAG	chr15:68126232-68126459(-)$1	227	105	132	13.1480
CUGCACGGUGAGAGGGCACGGGCACAC	chr21:45114260-45114489(+)$1	229	198	225	14.5595
GAAGAAUUGGUUAUAUCCAGAUUUCUG	chr1:64646108-64646335(+)$1	227	122	149	13.5437
UGAAACCAGGGUAACACCUUUGGAUGA	chr1:16890027-16890252(+)$1	225	21	48	13.4744
AAUUUAAAUGCCUCUACAUUUGAUACG	chr17:4173182-4173407(-)$1	225	148	175	13.1687
UGCAGGCCACAGUGAAGUGUGUUGCUU	chrX:13730683-13730912(-)$1	229	138	165	12.9961
UUUGGUGCUGAACCUCCACAUCAGAAU	chr13:31711474-31711729(-)$1	255	197	224	14.5246
AGGUCCCCAUGAGCUGGUGGGGGCUGU	chr13:39612019-39612248(-)$1	229	87	114	12.2476
GAAAUUAAAGAAAUCUUUAAUUUCUAU	chr20:33380233-33380467(-)$1	234	8	35	11.1436
CAGGUUCGCUUCACCUGGCUGUUACUG	chr10:50942721-50942944(+)$1	223	103	130	14.2064
CAAACGGUUUGUUUGAAAACAUUUUGU	chr19:57804032-57804260(+)$1	228	113	140	12.3284
AUUUUUAAUUUCCUUUGGUUAAAGGUC	chr10:71910246-71910474(-)$1	228	61	88	14.8087
AUGGUAAGUAUGCCAUUAUUUUGCCAU	chr2:148716296-148716524(-)$1	228	162	189	14.4863
AACUGAGACAAGAGAAUGUAGUAGAGU	chrX:84501916-84502141(+)$1	225	47	74	14.4049
GCGGUGAAGCGCCUGUGCUCUGCCGAG	chr15:85923770-85923999(+)$1	229	95	122	13.9100
uucuagcugcucacauguacaaaucac	chr1:229577311-229577539(-)$1	228	174	201	14.3437
UGCCAGCUUCCCCCCUGAGGUUGUGUA	chr22:42070705-42070946(-)$1	241	36	63	14.2115
CAUUUGUGCUGAUCGAAGAAUAGUUGA	chr5:179149848-179150079(+)$1	231	90	117	11.6148
AUGUGUCCGUUUCAACACGGAUGGUCA	chr14:97002100-97002328(+)$1	228	188	215	12.6943
GCUGAAGACUGGAGGAAGUGAACACUG	chr7:50660525-50660755(-)$1	230	124	151	14.0672
AGUCACCAUCGCGCAGGGUGGUGUCUU	chr6:27115156-27115393(+)$1	237	50	77	14.8025
GUGGUGUGGAAGAUGAUUUAUACCCAA	chr12:48537434-48537659(+)$1	225	27	54	11.9159
GCCCUGACAGAUUCUCCUAUCGGGGUC	chr1:111992034-111992257(+)$1	223	63	90	12.5465
aacauuguguacucggagauaguguca	chr20:33932957-33933210(-)$1	253	50	77	14.6928
UUUCAAAACACAGUGUUCUUUUAAAAA	chr7:114658857-114659085(+)$1	228	156	183	11.7811
GGCUUCCUGACUUCUGUGACAGUAAGC	chr15:37101096-37101321(+)$1	225	166	193	11.9319
CGCUUCUACGACCCCACGGCAGGCGUG	chr7:150738152-150738379(+)$1	227	62	89	11.4233
AAAUUUGUUUGAGUUGAGGCAGAUUAA	chr1:224585758-224585982(-)$1	224	1	28	12.7138
CACUGCAGUGGACCAACAACGGAGGGU	chr14:88935244-88935467(+)$1	223	83	110	13.1290
ucccgcgguccuccgagcccgcgcguc	chr12:49182687-49182913(+)$1	226	76	103	13.5976
UGAGUCAUAGAUAGAGUUAGGAUUUCU	chr15:75713184-75713406(-)$1	222	136	163	13.9561
CCCCUCACCCCAAGGCGGGUGAGCUCU	chr19:42752494-42752739(-)$1	245	45	72	13.1791
GCUGUUCCAGUUGCUUCUGCUUGGGCU	chr9:37515024-37515249(-)$1	225	21	48	12.8843
CCGCGUCAGCCCAGGAGGCUGGUGUGG	chr16:66878882-66879108(-)$1	226	35	62	11.2590
GUCGGAGAGUUGAAAUAUUAAAUGAAC	chr3:160129683-160129912(+)$1	229	148	175	13.6526
GAGCCCUUGCCUCCGAGCUCUGGCUUC	chr8:22278387-22278617(+)$1	230	135	162	14.4400
GAAAUGAAGAGCAUAAUCUUUCAUAUU	chr3:130828541-130828762(-)$1	221	118	145	11.5145
cagguggccuucuugcagguccccgua	chr19:50410298-50410528(-)$1	230	6	33	12.5558

#DB
((((((((((...))))))))))....	chr17:17250178-17250405(+)$1	1	161	188	11.5836
(...((((((......))))))....)	chr1:1192274-1192504(-)$1	1	119	146	12.8787
...(((((((......)))))))))))	chr19:3958605-3958834(-)$1	1	68	95	14.1937
..(((((((.(.....).)))))))..	chr11:119173892-119174122(+)$1	1	175	202	10.5061
(((((((.((......)))))))))))	chr7:44102689-44102912(-)$1	1	85	112	15.0773
((...((.((......)).))...)))	chr1:93297526-93297767(+)$1	1	194	221	12.2181
((((((((((......))))..)))))	chr5:54460375-54460612(+)$1	1	43	70	12.9787
.((...((((......))))...))))	chr6:125404697-125404927(+)$1	1	30	57	12.4499
..(((((((((...)))))))))...)	chr16:15130428-15130655(+)$1	1	29	56	11.1816
((...(((((......))))).)))))	chr1:47184228-47184454(-)$1	1	103	130	12.7228
((.(((((((......)))))))..))	chr15:69696464-69696686(+)$1	1	38	65	13.8132
((((((.(.(......)..).))))))	chr17:42295478-42295705(-)$1	1	69	96	13.9848
((((((.(((......)))))))))))	chr19:46206418-46206645(+)$1	1	134	161	12.9988
(((((.((((......)))).))).).	chr3:9833913-9834137(-)$1	1	33	60	12.5281
.(((((.(((......))).)))))))	chr16:87864642-87864870(-)$1	1	176	203	13.7370
...(((((((......)))))))((((	chr17:8168181-8168409(+)$1	1	12	39	11.2682
..(..(((((......)))))..)..)	chr15:68126232-68126459(-)$1	1	105	132	13.1480
.(((.(.(((......))).)))).))	chr21:45114260-45114489(+)$1	1	198	225	14.5595
((((..((((......)))).))))))	chr1:64646108-64646335(+)$1	1	122	149	13.5437
(.((...(((......))))).)))))	chr1:16890027-16890252(+)$1	1	21	48	13.4744
...(((((((......)))))))....	chr17:4173182-4173407(-)$1	1	148	175	13.1687
.((((..(((......)))..))))..	chrX:13730683-13730912(-)$1	1	138	165	12.9961
(((((((.((......)))))))))))	chr13:31711474-31711729(-)$1	1	197	224	14.5246
.(((((((((......)))))))))..	chr13:39612019-39612248(-)$1	1	87	114	12.2476
((((((((((....))))))))))...	chr20:33380233-33380467(-)$1	1	8	35	11.1436
(((...((((......))).)...)))	chr10:50942721-50942944(+)$1	1	103	130	14.2064
((((..((((......))))..)))))	chr19:57804032-57804260(+)$1	1	113	140	12.3284
((((((((((......)))))))))).	chr10:71910246-71910474(-)$1	1	61	88	14.8087
((((((((((......)).))))))))	chr2:148716296-148716524(-)$1	1	162	189	14.4863
..(((..(((......)))..)))..)	chrX:84501916-84502141(+)$1	1	47	74	14.4049
.(((((.(((......))).))))).)	chr15:85923770-85923999(+)$1	1	95	122	13.9100
((...(.(((......)))).))))).	chr1:229577311-229577539(-)$1	1	174	201	14.3437
((((((((((......))))))).)))	chr22:42070705-42070946(-)$1	1	36	63	14.2115
((.((((.((......)).)))).)))	chr5:179149848-179150079(+)$1	1	90	117	11.6148
(((.((((((......))))))...))	chr14:97002100-97002328(+)$1	1	188	215	12.6943
(.((...(((......)))...)))))	chr7:50660525-50660755(-)$1	1	124	151	14.0672
.(.(((((((......))))))).)))	chr6:27115156-27115393(+)$1	1	50	77	14.8025
..((((((((......))))))))..)	chr12:48537434-48537659(+)$1	1	27	54	11.9159
(((((((.((......)).))))))..	chr1:111992034-111992257(+)$1	1	63	90	12.5465
.(((((((.(......).)))))))..	chr20:33932957-33933210(-)$1	1	50	77	14.6928
(((.((((.(......).))))..)))	chr7:114658857-114659085(+)$1	1	156	183	11.7811
(((((.(((.(......).))).))))	chr15:37101096-37101321(+)$1	1	166	193	11.9319
(((((...((......))..)))))))	chr7:150738152-150738379(+)$1	1	62	89	11.4233
.(((((((((......))))))))).(	chr1:224585758-224585982(-)$1	1	1	28	12.7138
(.((.(..((......))..).)).))	chr14:88935244-88935467(+)$1	1	83	110	13.1290
.(.(((((.(......).))))).)..	chr12:49182687-49182913(+)$1	1	76	103	13.5976
.(((((.(((......))).)))))..	chr15:75713184-75713406(-)$1	1	136	163	13.9561
...(((((((......)))))))....	chr19:42752494-42752739(-)$1	1	45	72	13.1791
(((....(((......)))....))))	chr9:37515024-37515249(-)$1	1	21	48	12.8843
(((((((((((.....)))))))))))	chr16:66878882-66879108(-)$1	1	35	62	11.2590
((((...(((......)))...)).))	chr3:160129683-160129912(+)$1	1	148	175	13.6526
(((((...((......))...))))))	chr8:22278387-22278617(+)$1	1	135	162	14.4400
)))))(((((......)))))((((((	chr3:130828541-130828762(-)$1	1	118	145	11.5145
..((.(((((......))))).))..)	chr19:50410298-50410528(-)$1	1	6	33	12.5558

#PSSM
! : 0.12	[ : 0.11	e : 0.11	= : 0.09	g : 0.09	f : 0.09	d : 0.07	" : 0.05	: : 0.05	c : 0.05	# : 0.03	i : 0.03	a : 0.01	b : 0.01	h : 0.01	
e : 0.14	f : 0.11	= : 0.09	! : 0.09	g : 0.09	d : 0.07	i : 0.07	" : 0.05	a : 0.05	c : 0.05	[ : 0.05	# : 0.03	b : 0.01	: : 0.01	h : 0.01	
g : 0.11	b : 0.11	e : 0.11	= : 0.09	" : 0.09	i : 0.09	f : 0.09	c : 0.09	[ : 0.07	# : 0.03	h : 0.03	: : 0.01	a : 0.01	d : 0.01	
g : 0.24	" : 0.11	e : 0.11	= : 0.09	i : 0.09	b : 0.09	f : 0.07	c : 0.05	d : 0.03	[ : 0.03	! : 0.01	h : 0.01	# : 0.01	
g : 0.22	" : 0.14	f : 0.11	= : 0.09	i : 0.09	e : 0.09	! : 0.05	[ : 0.05	d : 0.05	c : 0.03	h : 0.01	# : 0.01	
g : 0.20	e : 0.14	" : 0.12	= : 0.09	i : 0.09	f : 0.07	! : 0.07	a : 0.05	[ : 0.03	d : 0.03	b : 0.01	h : 0.01	# : 0.01	
g : 0.16	d : 0.12	[ : 0.12	= : 0.09	i : 0.09	e : 0.09	" : 0.09	f : 0.05	! : 0.05	b : 0.01	a : 0.01	h : 0.01	c : 0.01	# : 0.01	
c : 0.25	g : 0.16	d : 0.11	[ : 0.09	e : 0.09	= : 0.07	i : 0.07	f : 0.03	" : 0.03	a : 0.01	h : 0.01	! : 0.01	
c : 0.25	b : 0.16	g : 0.14	d : 0.09	= : 0.07	e : 0.07	[ : 0.07	i : 0.05	f : 0.03	h : 0.01	
c : 0.24	b : 0.16	g : 0.12	d : 0.09	= : 0.07	e : 0.07	a : 0.07	i : 0.05	f : 0.03	[ : 0.03	h : 0.01	
o : 0.88	a : 0.03	l : 0.01	i : 0.01	m : 0.01	= : 0.01	
o : 0.90	l : 0.03	n : 0.03	m : 0.01	
o : 0.90	l : 0.03	n : 0.03	m : 0.01	
o : 0.90	n : 0.03	= : 0.01	l : 0.01	m : 0.01	
o : 0.90	= : 0.03	n : 0.03	i : 0.01	
o : 0.90	= : 0.03	n : 0.03	i : 0.01	
c : 0.24	b : 0.16	g : 0.12	a : 0.09	d : 0.09	= : 0.07	e : 0.07	i : 0.05	f : 0.03	h : 0.01	o : 0.01	
c : 0.24	b : 0.16	g : 0.12	d : 0.09	= : 0.07	] : 0.07	e : 0.07	i : 0.05	f : 0.03	2 : 0.01	h : 0.01	a : 0.01	
c : 0.24	g : 0.16	d : 0.11	= : 0.09	] : 0.09	e : 0.09	i : 0.07	2 : 0.05	f : 0.03	h : 0.01	3 : 0.01	
g : 0.16	d : 0.12	= : 0.09	i : 0.09	e : 0.09	] : 0.09	f : 0.07	2 : 0.07	3 : 0.05	b : 0.03	a : 0.03	h : 0.01	c : 0.01	4 : 0.01	
g : 0.16	e : 0.14	= : 0.09	f : 0.09	i : 0.09	2 : 0.07	3 : 0.07	] : 0.07	a : 0.05	b : 0.03	d : 0.03	h : 0.01	c : 0.01	4 : 0.01	
g : 0.22	f : 0.11	= : 0.09	3 : 0.09	i : 0.09	e : 0.09	] : 0.07	c : 0.07	2 : 0.05	d : 0.05	h : 0.01	4 : 0.01	
g : 0.24	e : 0.14	= : 0.09	i : 0.09	3 : 0.07	f : 0.07	b : 0.07	c : 0.05	4 : 0.03	2 : 0.03	d : 0.03	h : 0.01	] : 0.01	
e : 0.16	g : 0.11	b : 0.09	= : 0.07	3 : 0.07	f : 0.07	i : 0.07	] : 0.07	c : 0.05	4 : 0.03	d : 0.03	2 : 0.03	h : 0.03	a : 0.01	0 : 0.01	6 : 0.01	
e : 0.18	g : 0.11	f : 0.11	2 : 0.09	] : 0.07	i : 0.07	d : 0.05	= : 0.05	3 : 0.05	4 : 0.03	c : 0.03	a : 0.03	b : 0.01	0 : 0.01	6 : 0.01	h : 0.01	
e : 0.18	2 : 0.12	g : 0.11	d : 0.09	3 : 0.07	f : 0.07	4 : 0.05	= : 0.05	c : 0.05	i : 0.03	: : 0.03	a : 0.01	0 : 0.01	] : 0.01	6 : 0.01	h : 0.01	
e : 0.20	g : 0.11	d : 0.09	c : 0.09	3 : 0.07	a : 0.05	2 : 0.05	f : 0.05	4 : 0.03	= : 0.03	i : 0.03	: : 0.03	] : 0.01	0 : 0.01	B : 0.01	F : 0.01	6 : 0.01	h : 0.01	

#score	705.9816512279867
#seq	54
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m1_run2.txt

#BEAR
ggg[bbbb!!cccqqqqqqqqccc22bb]bb]	chr2:85273168-85273393(+)$1	225	176	208	15.4910
======a[a[cccqqqqqqqqccc]a]a]===	chr19:648340-648568(-)$1	228	160	192	18.1131
d[eeeeebb[cccqqqqqqqqccc]bb333ee	chr6:31807240-31807457(+)$1	217	167	199	15.7299
d"""ccca[ddddqqqqqqqqdddd]a]ccc3	chr1:1159203-1159438(-)$1	235	197	229	16.6433
eeeeffffff[bbqqqqqqqqbb]ffffff]e	chr17:7480863-7481081(+)$1	218	79	111	14.8600
a"""dddd[ddddrrrrrrrrrdddd]dddd2	chr20:18576575-18576838(+)$1	263	140	172	11.2827
d[gggggggddddqqqqqqqqdddd22ggggg	chr14:74755336-74755546(-)$1	210	34	66	16.1272
=========[cccrrrrrrrrrccc=======	chr3:138351687-138351892(+)$1	205	84	116	14.8523
####cccbb!!bbqqqqqqqqbb22bb]ccc2	chr4:42088026-42088272(+)$1	246	82	114	15.2138
eeee####eeeeeqqqqqqqqeeeee4444ee	chr5:137525240-137525469(-)$1	229	159	191	15.5042
ccc[a[ccc!!bbqqqqqqqqbb]ccc]a]cc	chr17:52991019-52991239(+)$1	220	125	157	16.4185
e[a[dddd!!cccqqqqqqqqcccdddd]a22	chr1:120277877-120278108(+)$1	231	103	135	15.9463
""eeeee!!a[bbqqqqqqqqbb]a22eeeee	chr1:25678041-25678268(+)$1	227	72	104	15.3310
[a[ccc[bb[cccrrrrrrrrrccc22bbccc	chr1:156563736-156563960(+)$1	224	105	137	12.0410
####dddd"""bbqqqqqqqqbb]dddd333f	chr16:29819882-29820137(+)$1	255	56	88	15.8139
[bb[ffffff[bbqqqqqqqqbb]ffffff22	chr1:235597426-235597634(+)$1	208	87	119	14.9081
ggg!!bb[eeeeeqqqqqqqqeeeeebb4444	chr1:224475392-224475627(-)$1	235	87	119	15.5548
=============qqqqqqqq===========	chr1:186310144-186310382(-)$1	238	38	70	18.4381
fff[==========ppppppp==========2	chr20:24995735-24995941(-)$1	206	87	119	11.6446
!eeeee[ffffffqqqqqqqqffffffeeeee	chr18:9588053-9588297(-)$1	244	45	77	14.4956
ggggggg[ddddrrrrrrrrrddddggggggg	chr15:89018278-89018535(+)$1	257	0	32	12.3648
!!dddd"""ddddqqqqqqqqdddd333dddd	chr12:123812196-123812408(-)$1	212	149	181	15.5142
ccc[bb!!eeeeeqqqqqqqqeeeee]bbccc	chr19:41242861-41243078(+)$1	217	10	42	15.0908
======ffffffrrrrrrrrrffffff]====	chr19:34685334-34685566(+)$1	232	36	68	12.8060
iiiiiii!!ddddqqqqqqqqddddiiiiiii	chr12:102479455-102479675(-)$1	220	29	61	17.0959
ccc!!gggggggrrrrrrrrrggggggg22cc	chr7:148544191-148544415(-)$1	224	70	102	12.4205
e####eeeeecccqqqqqqqqccc]eeeee55	chr6:138583845-138584048(+)$1	203	86	118	14.6786
h$$$$$bb!!cccqqqqqqqqccc]bb66666	chr6:26285555-26285842(-)$1	287	112	144	13.5498
==============ppppppp===========	chr2:30784960-30785170(+)$1	210	5	37	12.2128
&ccc[cccccc[aqqqqqqqqa]ccc]ccc]c	chr2:109381340-109381584(+)$1	244	129	161	15.3972
ddd[ccc!!bb[aqqqqqqqqa]bb333ccc]	chr4:1902376-1902613(+)$1	237	181	213	15.6787
eeeee$$$$$cccrrrrrrrrrccc4444eee	chr19:39926161-39926397(-)$1	236	89	121	11.7139
========"""bbqqqqqqqqbb]========	chr12:51636226-51636462(+)$1	236	200	232	18.1732
fff"""dddd[arrrrrrrrradddd4444ff	chr14:102516747-102516955(+)$1	208	69	101	11.9750
fff==========qqqqqqqq==========:	chr2:172848099-172848325(+)$1	226	179	211	16.8169
iiiiiiiii[bbssssssssssbb]iiiiiii	chr1:197057383-197057607(-)$1	224	180	212	11.3122
ccc[ffffff[bbqqqqqqqqbb]ffffff]c	chr7:127361248-127361483(+)$1	235	160	192	15.5148
gggggg[ffffffqqqqqqqqffffffggggg	chr2:182783399-182783605(+)$1	206	49	81	15.7473
f!!iiiiiiiii[apppppppa]iiiiiiiii	chr22:29957510-29957721(-)$1	211	28	60	11.1498
:ffffff"""cccqqqqqqqqccc333fffff	chr10:32337306-32337554(-)$1	248	197	229	15.2746
da[ccccccddddqqqqqqqqdddd]ccc]cc	chr3:31667449-31667690(+)$1	241	187	219	15.5936
ffffffff[ddddqqqqqqqqdddd22fffff	chr2:61389941-61390142(+)$1	201	74	106	14.6766
iiiiiiiii[cccqqqqqqqqccciiiiiiii	chr17:66524995-66525210(+)$1	215	160	192	17.8193
ccc[bb"""ddddqqqqqqqqdddd]bbcccE	chr7:106820291-106820508(+)$1	217	152	184	14.6314
ddggggggg[cccqqqqqqqqccc]ggggggg	chr21:28210292-28210513(-)$1	221	77	109	16.9616
e$$$$$dddd!!aqqqqqqqqa22dddd333e	chr2:96956124-96956334(-)$1	210	96	128	14.4916
iiiiiiii[ddddrrrrrrrrrdddd]iiiii	chr19:30477150-30477402(+)$1	252	128	160	13.2204
ddd!!agggggggrrrrrrrrrggggggg]a2	chr4:57317943-57318176(+)$1	233	178	210	12.5017
e[a[eeeee[cccqqqqqqqqccc]eeeeea]	chr1:36754646-36754853(+)$1	207	124	156	16.2251
dddbb"""eeeeeqqqqqqqqeeeee333bb8	chr20:24954195-24954413(-)$1	218	15	47	14.4270
%%ffffff"""bbqqqqqqqqbb]ffffff66	chr8:103848410-103848635(-)$1	225	59	91	13.5374
ddd####ffffffqqqqqqqqffffff4444d	chr19:3982149-3982366(-)$1	217	121	153	15.5546
ggggg"""eeeeeqqqqqqqqeeeeegggggg	chr2:74441214-74441488(+)$1	274	52	84	16.0484
eeee"""ffffffqqqqqqqqffffffeeeee	chr16:70578276-70578522(+)$1	246	130	162	14.8324

#otherMatches

#Seq PSSM
CUUCUUCUCAGAGUUCAUAUUCUCCAAGCAAU	chr2:85273168-85273393(+)$1	225	176	208	15.4910
GUUCCACGACGGCUGCAUCGUGCCCUGGCUGG	chr19:648340-648568(-)$1	228	160	192	18.1131
CACCUUAUUGGGGGAAAAAUGCCUGAAAAUUA	chr6:31807240-31807457(+)$1	217	167	199	15.7299
ACUUCCGCGCCGUGGACCCUGACGGGGACGGU	chr1:1159203-1159438(-)$1	235	197	229	16.6433
AGUCAUCUUCAUCAACACCCGGAGGAAGGUGG	chr17:7480863-7481081(+)$1	218	79	111	14.8600
GAUGGACAAACAGUACGAGAUUCUGUGUGUCA	chr20:18576575-18576838(+)$1	263	140	172	11.2827
CCAGGAGGCUCUGGCUUUUUGCAGAAGGCUUC	chr14:74755336-74755546(-)$1	210	34	66	16.1272
GGUGAGUUUGUAGAUGAUGGGACUGAAACUCA	chr3:138351687-138351892(+)$1	205	84	116	14.8523
CUGAAGUUCGACAUGUAGAUUUGGAGAUACUG	chr4:42088026-42088272(+)$1	246	82	114	15.2138
UUCUUUAAUAAAAGGUUUGAAUUUUAGGCUAG	chr5:137525240-137525469(-)$1	229	159	191	15.5042
AGCGAAGUCAAAGAAGUAUACCUCGACCUGGU	chr17:52991019-52991239(+)$1	220	125	157	16.4185
GUGGAGGGAUCGUGGACGAAGGCGCCCUGCUC	chr1:120277877-120278108(+)$1	231	103	135	15.9463
CAGGAUUAAUGCAGUAUCGAAUGGACAAGUCC	chr1:25678041-25678268(+)$1	227	72	104	15.3310
ACCCUGACACCGAGUGUGUCUAUCGUCUGCAG	chr1:156563736-156563960(+)$1	224	105	137	12.0410
GUACGACACGAGGAGAAAGUGCCAUGUCACGU	chr16:29819882-29820137(+)$1	255	56	88	15.8139
UCCAGGUGCUGCGGUGUGUCGCGGGGUGCCCA	chr1:235597426-235597634(+)$1	208	87	119	14.9081
UGUGACAUGGGCAGAUAUUGGUGCCCUGGAAG	chr1:224475392-224475627(-)$1	235	87	119	15.5548
UUAAUAAUAAAUGAAUUUUUACAUUUGUUGUU	chr1:186310144-186310382(-)$1	238	38	70	18.4381
UCAACUGUGAGGCCUGGGAGUGGCUUCACAGG	chr20:24995735-24995941(-)$1	206	87	119	11.6446
GUUGUUAUUUUUCUCCUAGGUGAGGAAAACAA	chr18:9588053-9588297(-)$1	244	45	77	14.4956
UAGCUCUCUCUUAUUUCCCUGAAGAAGAGUUG	chr15:89018278-89018535(+)$1	257	0	32	12.3648
ACGGAGGUAAUGCAGUUUACGGUAUAUACUCU	chr12:123812196-123812408(-)$1	212	149	181	15.5142
UCCACACCCUGCCCUACAGAAGGCAGAUGGGA	chr19:41242861-41243078(+)$1	217	10	42	15.0908
UUUUCUUGCCAGUUCGAUCCUUUGGUACAGAA	chr19:34685334-34685566(+)$1	232	36	68	12.8060
UUCUUUUAUUAGGAUUUGGAACUUGGAAGGAG	chr12:102479455-102479675(-)$1	220	29	61	17.0959
CGGAAGCGUGUAAAAUCAGAGUACAUGCGACU	chr7:148544191-148544415(-)$1	224	70	102	12.4205
GAUGAGCUCAGCCAGGGGAAGGGCUUGAGCGA	chr6:138583845-138584048(+)$1	203	86	118	14.6786
GUCAUGUCUGGCCGUGGUAAAGGUGGAAAAGG	chr6:26285555-26285842(-)$1	287	112	144	13.5498
UUGGCAAUAAAAUUAUAGGUAAAUUUUAUUGU	chr2:30784960-30785170(+)$1	210	5	37	12.2128
AUGAGGGGAGCUCUACAAAAUGUGCUGCUUGU	chr2:109381340-109381584(+)$1	244	129	161	15.3972
GGGGGUCAUGCAGAAGUUUAACGGCCACGACG	chr4:1902376-1902613(+)$1	237	181	213	15.6787
GUCUCAUCAAGGUGAACGGGCGGCCCCUGGAG	chr19:39926161-39926397(-)$1	236	89	121	11.7139
ACCUCCCUAAAGCAUUUUGAGGUAGGGGAGGU	chr12:51636226-51636462(+)$1	236	200	232	18.1732
UUCACCGUGGACUUCGAAAUUGCUACAAAGGA	chr14:102516747-102516955(+)$1	208	69	101	11.9750
UCUGUACAGGAAGCUUGCAAAUUUUCUGUACA	chr2:172848099-172848325(+)$1	226	179	211	16.8169
UGUUUGUUGGCUAUUUUACUGAAGACAACAAA	chr1:197057383-197057607(-)$1	224	180	212	11.3122
CCUGUCCAGCAUCCGACCACCGAGGCUGGAGG	chr7:127361248-127361483(+)$1	235	160	192	15.5148
UUAGAAGUGUAAUUUUGUUAUAUUGCAUUCUA	chr2:182783399-182783605(+)$1	206	49	81	15.7473
ACACUGUCAGGAUGGAGCGCACUUCCUGGUAG	chr22:29957510-29957721(-)$1	211	28	60	11.1498
AUAAGUAAAUAAGUUUGUGAUCUUUUCUACUU	chr10:32337306-32337554(-)$1	248	197	229	15.2746
UCCAGGUAUGUGAAAGAUAGCUCACUGUGUCC	chr3:31667449-31667690(+)$1	241	187	219	15.5936
UUGUACAGAUGCAAACGGAGGUGUAGACUGUG	chr2:61389941-61390142(+)$1	201	74	106	14.6766
UUGAAUUUUAGAGGUAAAGAACUCAGAAUUUA	chr17:66524995-66525210(+)$1	215	160	192	17.8193
CAGUGUAAUGAGAAUUUGCCAUCUUCACCUGG	chr7:106820291-106820508(+)$1	217	152	184	14.6314
AGCAAGACAUUAUGUACAAAGGUGUUGUCUUG	chr21:28210292-28210513(-)$1	221	77	109	16.9616
CGGAAGACCCCAGUAUGACACCAAGGGUGAAG	chr2:96956124-96956334(-)$1	210	96	128	14.4916
UGCUCAGCAAAGCAGGCUGUAGGUUUAGUUGA	chr19:30477150-30477402(+)$1	252	128	160	13.2204
AAGGCCUGUGGAAAUUUUGGCAUUCCAUGUGA	chr4:57317943-57318176(+)$1	233	178	210	12.5017
GUGAUGGAAAAAUGAAAUCUGAUUCUUUUGCU	chr1:36754646-36754853(+)$1	207	124	156	16.2251
UCCUCCUUUUUGUGUUUUUAAACAGAUGUGAU	chr20:24954195-24954413(-)$1	218	15	47	14.4270
AGAGGGUAACAUGAAGUUUGGCACUACCCUGA	chr8:103848410-103848635(-)$1	225	59	91	13.5374
AGGUGAGCCCCGCGGGAUAUGGUGGGGGAUUC	chr19:3982149-3982366(-)$1	217	121	153	15.5546
GGCAAUGCUAAUGAAGAAUACCAUUAUUGCUG	chr2:74441214-74441488(+)$1	274	52	84	16.0484
UCUCUGAGAGUCCUAAGACAUGGACUUGAGGU	chr16:70578276-70578522(+)$1	246	130	162	14.8324

#DB
(((.((((..(((........)))..)).)).	chr2:85273168-85273393(+)$1	1	176	208	15.4910
(((((((.(.(((........))).).).)))	chr19:648340-648568(-)$1	1	160	192	18.1131
(.(((((((.(((........))).))...))	chr6:31807240-31807457(+)$1	1	167	199	15.7299
(...((((.((((........)))).).))).	chr1:1159203-1159438(-)$1	1	197	229	16.6433
((((((((((.((........)).)))))).)	chr17:7480863-7481081(+)$1	1	79	111	14.8600
(...((((.((((.........)))).)))).	chr20:18576575-18576838(+)$1	1	140	172	11.2827
(.(((((((((((........))))..)))))	chr14:74755336-74755546(-)$1	1	34	66	16.1272
(((((((((.(((.........))))))))))	chr3:138351687-138351892(+)$1	1	84	116	14.8523
....(((((..((........))..)).))).	chr4:42088026-42088272(+)$1	1	82	114	15.2138
((((....(((((........)))))....))	chr5:137525240-137525469(-)$1	1	159	191	15.5042
(((.(.(((..((........)).))).).))	chr17:52991019-52991239(+)$1	1	125	157	16.4185
(.(.((((..(((........))))))).)..	chr1:120277877-120278108(+)$1	1	103	135	15.9463
..(((((..(.((........)).)..)))))	chr1:25678041-25678268(+)$1	1	72	104	15.3310
.(.(((.((.(((.........)))..)))))	chr1:156563736-156563960(+)$1	1	105	137	12.0410
....((((...((........)).))))...)	chr16:29819882-29820137(+)$1	1	56	88	15.8139
.((.((((((.((........)).))))))..	chr1:235597426-235597634(+)$1	1	87	119	14.9081
(((..((.(((((........)))))))....	chr1:224475392-224475627(-)$1	1	87	119	15.5548
(((((((((((((........)))))))))))	chr1:186310144-186310382(-)$1	1	38	70	18.4381
(((.((((((((((.......)))))))))).	chr20:24995735-24995941(-)$1	1	87	119	11.6446
.(((((.((((((........)))))))))))	chr18:9588053-9588297(-)$1	1	45	77	14.4956
(((((((.((((.........)))))))))))	chr15:89018278-89018535(+)$1	1	0	32	12.3648
..((((...((((........))))...))))	chr12:123812196-123812408(-)$1	1	149	181	15.5142
(((.((..(((((........))))).)))))	chr19:41242861-41243078(+)$1	1	10	42	15.0908
((((((((((((.........)))))).))))	chr19:34685334-34685566(+)$1	1	36	68	12.8060
(((((((..((((........)))))))))))	chr12:102479455-102479675(-)$1	1	29	61	17.0959
(((..(((((((.........)))))))..))	chr7:148544191-148544415(-)$1	1	70	102	12.4205
(....((((((((........))).)))))..	chr6:138583845-138584048(+)$1	1	86	118	14.6786
(.....((..(((........))).)).....	chr6:26285555-26285842(-)$1	1	112	144	13.5498
((((((((((((((.......)))))))))))	chr2:30784960-30785170(+)$1	1	5	37	12.2128
.(((.((((((.(........).))).))).)	chr2:109381340-109381584(+)$1	1	129	161	15.3972
(((.(((..((.(........).))...))).	chr4:1902376-1902613(+)$1	1	181	213	15.6787
(((((.....(((.........)))....)))	chr19:39926161-39926397(-)$1	1	89	121	11.7139
((((((((...((........)).))))))))	chr12:51636226-51636462(+)$1	1	200	232	18.1732
(((...((((.(.........)))))....))	chr14:102516747-102516955(+)$1	1	69	101	11.9750
)))((((((((((........)))))))))).	chr2:172848099-172848325(+)$1	1	179	211	16.8169
(((((((((.((..........)).)))))))	chr1:197057383-197057607(-)$1	1	180	212	11.3122
(((.((((((.((........)).)))))).)	chr7:127361248-127361483(+)$1	1	160	192	15.5148
((((((.((((((........)))))))))))	chr2:182783399-182783605(+)$1	1	49	81	15.7473
(..(((((((((.(.......).)))))))))	chr22:29957510-29957721(-)$1	1	28	60	11.1498
.((((((...(((........)))...)))))	chr10:32337306-32337554(-)$1	1	197	229	15.2746
((.((((((((((........)))).))).))	chr3:31667449-31667690(+)$1	1	187	219	15.5936
))((((((.((((........))))..)))))	chr2:61389941-61390142(+)$1	1	74	106	14.6766
(((((((((.(((........)))))))))))	chr17:66524995-66525210(+)$1	1	160	192	17.8193
(((.((...((((........)))).))))))	chr7:106820291-106820508(+)$1	1	152	184	14.6314
))(((((((.(((........))).)))))))	chr21:28210292-28210513(-)$1	1	77	109	16.9616
(.....((((..(........)..))))...)	chr2:96956124-96956334(-)$1	1	96	128	14.4916
((((((((.((((.........)))).)))))	chr19:30477150-30477402(+)$1	1	128	160	13.2204
(((..((((((((.........))))))).).	chr4:57317943-57318176(+)$1	1	178	210	12.5017
(.(.(((((.(((........))).)))))).	chr1:36754646-36754853(+)$1	1	124	156	16.2251
(((((...(((((........)))))...)).	chr20:24954195-24954413(-)$1	1	15	47	14.4270
..((((((...((........)).))))))..	chr8:103848410-103848635(-)$1	1	59	91	13.5374
(((....((((((........))))))....)	chr19:3982149-3982366(-)$1	1	121	153	15.5546
(((((...(((((........)))))))))))	chr2:74441214-74441488(+)$1	1	52	84	16.0484
((((...((((((........)))))))))))	chr16:70578276-70578522(+)$1	1	130	162	14.8324

#PSSM
d : 0.16	e : 0.14	= : 0.11	g : 0.09	c : 0.09	f : 0.09	i : 0.07	# : 0.03	[ : 0.03	! : 0.03	a : 0.01	" : 0.01	h : 0.01	& : 0.01	: : 0.01	% : 0.01	
= : 0.11	c : 0.11	g : 0.09	e : 0.09	f : 0.09	d : 0.09	[ : 0.07	i : 0.07	" : 0.05	# : 0.05	a : 0.03	! : 0.03	$ : 0.03	b : 0.01	% : 0.01	
g : 0.12	e : 0.12	= : 0.11	c : 0.11	f : 0.11	d : 0.09	i : 0.07	# : 0.05	" : 0.03	a : 0.03	[ : 0.03	$ : 0.03	b : 0.01	! : 0.01	
[ : 0.18	= : 0.12	e : 0.12	g : 0.09	i : 0.09	# : 0.07	" : 0.05	c : 0.05	! : 0.05	f : 0.05	$ : 0.03	d : 0.01	b : 0.01	
= : 0.14	f : 0.11	e : 0.09	c : 0.09	g : 0.09	i : 0.09	b : 0.07	d : 0.07	# : 0.05	! : 0.05	$ : 0.03	" : 0.03	a : 0.01	[ : 0.01	
= : 0.14	c : 0.11	f : 0.11	e : 0.09	g : 0.09	i : 0.09	b : 0.07	d : 0.07	" : 0.07	$ : 0.05	# : 0.03	[ : 0.01	a : 0.01	
f : 0.12	c : 0.11	= : 0.11	d : 0.09	g : 0.09	" : 0.09	i : 0.09	e : 0.07	b : 0.05	[ : 0.05	# : 0.03	a : 0.01	! : 0.01	$ : 0.01	
f : 0.18	= : 0.11	b : 0.09	d : 0.09	" : 0.09	g : 0.07	! : 0.07	i : 0.07	[ : 0.05	c : 0.05	e : 0.03	a : 0.01	# : 0.01	$ : 0.01	
f : 0.14	e : 0.12	! : 0.11	" : 0.11	= : 0.09	[ : 0.07	g : 0.07	b : 0.05	c : 0.05	d : 0.05	i : 0.05	a : 0.01	$ : 0.01	
d : 0.22	[ : 0.14	f : 0.14	e : 0.11	! : 0.09	" : 0.07	= : 0.07	g : 0.03	a : 0.01	c : 0.01	b : 0.01	$ : 0.01	i : 0.01	
c : 0.25	d : 0.18	[ : 0.09	e : 0.09	f : 0.09	= : 0.07	! : 0.05	" : 0.05	g : 0.03	b : 0.03	i : 0.01	
c : 0.24	d : 0.18	b : 0.18	e : 0.09	f : 0.09	= : 0.07	g : 0.03	[ : 0.03	a : 0.01	i : 0.01	! : 0.01	
c : 0.24	d : 0.16	b : 0.16	e : 0.09	= : 0.07	f : 0.07	r : 0.07	a : 0.05	s : 0.01	[ : 0.01	g : 0.01	
q : 0.74	r : 0.18	= : 0.03	s : 0.01	a : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
q : 0.74	r : 0.18	p : 0.05	s : 0.01	
c : 0.18	b : 0.16	d : 0.14	r : 0.11	e : 0.09	f : 0.09	a : 0.09	= : 0.07	g : 0.01	s : 0.01	
c : 0.24	d : 0.20	b : 0.18	e : 0.09	f : 0.09	= : 0.07	] : 0.05	g : 0.03	2 : 0.01	
c : 0.25	d : 0.20	] : 0.14	e : 0.09	f : 0.09	= : 0.07	2 : 0.03	g : 0.03	b : 0.03	i : 0.01	
d : 0.25	f : 0.16	] : 0.12	c : 0.09	e : 0.09	= : 0.09	2 : 0.03	g : 0.03	i : 0.03	a : 0.01	b : 0.01	3 : 0.01	
f : 0.16	e : 0.12	d : 0.11	= : 0.11	2 : 0.09	g : 0.07	i : 0.07	b : 0.05	] : 0.05	3 : 0.05	c : 0.03	a : 0.01	4 : 0.01	
f : 0.16	b : 0.11	= : 0.11	] : 0.09	g : 0.09	2 : 0.07	3 : 0.07	i : 0.07	4 : 0.05	d : 0.05	c : 0.03	e : 0.03	a : 0.01	
g : 0.12	f : 0.11	= : 0.11	b : 0.09	e : 0.09	i : 0.09	3 : 0.07	] : 0.07	d : 0.07	4 : 0.07	c : 0.03	a : 0.01	6 : 0.01	
= : 0.12	c : 0.11	f : 0.11	g : 0.11	4 : 0.09	e : 0.09	i : 0.09	3 : 0.07	] : 0.05	d : 0.03	b : 0.03	a : 0.01	2 : 0.01	6 : 0.01	
= : 0.14	c : 0.12	f : 0.11	e : 0.11	g : 0.09	i : 0.09	4 : 0.07	3 : 0.05	] : 0.05	b : 0.03	d : 0.03	a : 0.01	2 : 0.01	6 : 0.01	
c : 0.16	= : 0.14	e : 0.11	g : 0.09	i : 0.09	] : 0.05	f : 0.05	b : 0.03	d : 0.03	2 : 0.03	3 : 0.03	4 : 0.03	6 : 0.03	a : 0.03	5 : 0.01	
e : 0.14	c : 0.12	= : 0.11	2 : 0.11	g : 0.09	i : 0.09	f : 0.07	] : 0.05	d : 0.03	6 : 0.03	3 : 0.01	4 : 0.01	5 : 0.01	: : 0.01	E : 0.01	8 : 0.01	

#score	799.4203304936625
#seq	54
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_CDS_m2_run2.txt

#BEAR
!!eeeee!!bbwwwwwwwwwwwwwwbb22	chr10:127486580-127486797(-)$1	217	34	63	22.0991
ccc[ffffffyyyyyyyyyyyyyyyyfff	chr5:173531143-173531368(+)$1	225	59	88	22.3474
:::eeeeeyyyyyyyyyyyyyyyyeeeee	chr6:149846201-149846419(+)$1	218	183	212	20.2671
eeee"""dddduuuuuuuuuuuudddd]e	chr16:3533289-3533507(+)$1	218	122	151	23.5516
bb"""fffffftttttttttttffffff3	chr5:137222966-137223191(+)$1	225	89	118	22.3696
nncccddddyyyyyyyyyyyyyyyydddd	chr5:150029636-150029864(+)$1	228	9	38	21.0217
eee[ggggggguuuuuuuuuuuugggggg	chr21:44492063-44492280(+)$1	217	117	146	24.6432
::ffffffyyyyyyyyyyyyyyyyfffff	chr1:156628753-156628976(+)$1	223	4	33	20.3193
::eeeee[ayyyyyyyyyyyyyyyyaeee	chr9:711765-711983(+)$1	218	42	71	21.3831
$$dddd!!ccctttttttttttccc333d	chr7:94180571-94180794(+)$1	223	94	123	22.8589
f::eeeee[avvvvvvvvvvvvva]eeee	chrX:101395699-101395921(-)$1	222	104	133	22.2310
eee[a[eeeeeuuuuuuuuuuuueeeee]	chr9:130430314-130430529(+)$1	215	114	143	24.7428
b[dddd!!ccctttttttttttccc]ddd	chr2:3200575-3200801(-)$1	226	102	131	22.9645
iiiiiiii[bbuuuuuuuuuuuubb]iii	chr10:3143560-3143777(+)$1	217	138	167	24.2402
ggggggeeeeewwwwwwwwwwwwwweeee	chr12:27933340-27933586(+)$1	246	56	85	23.4283
eee!!eeeeexxxxxxxxxxxxxxxeeee	chr20:45315410-45315641(-)$1	231	185	214	19.2285
ddd"""eeeeeyyyyyyyyyyyyyyyyee	chr12:49445285-49445525(-)$1	240	6	35	21.9039
""eeeeedddduuuuuuuuuuuudddd]e	chr16:29820867-29821086(+)$1	219	168	197	23.8519
[bb[bb[ddddvvvvvvvvvvvvvdddd2	chr1:10399789-10400008(+)$1	219	69	98	22.9173
$$hhhhhhhhwwwwwwwwwwwwwwhhhhh	chr15:63961765-63961982(-)$1	217	151	180	20.9826
ccc[a[bb[ccctttttttttttccc]bb	chr5:61643773-61643994(-)$1	221	112	141	22.3467
ccc"""eeeeewwwwwwwwwwwwwweeee	chr10:61832167-61832383(-)$1	216	153	182	23.5956
ccc[ggggggguuuuuuuuuuuugggggg	chr11:74911298-74911532(+)$1	234	111	140	25.0602
!!dddd!!bbwwwwwwwwwwwwwwbb333	chr19:41025265-41025482(-)$1	217	44	73	22.5214
d[a[gggggggtttttttttttggggggg	chr12:13224183-13224401(+)$1	218	85	114	23.4594
fffa!!eeeeeuuuuuuuuuuuueeeee5	chr1:161967820-161968036(-)$1	216	121	150	23.7144
ddd!!ffffffvvvvvvvvvvvvvfffff	chr11:10585516-10585739(-)$1	223	158	187	23.2635
gggggg[ddddwwwwwwwwwwwwwwdddd	chr2:133542214-133542431(+)$1	217	84	113	22.7625
gggbb"""cccuuuuuuuuuuuuccc333	chrX:64958373-64958593(-)$1	220	90	119	24.1636
iiiiiiiii[bbtttttttttttbbiiii	chr15:86311757-86311986(-)$1	229	50	79	22.7058
ffffgggggggtttttttttttggggggg	chr19:42470900-42471124(-)$1	224	96	125	22.8103
============ttttttttttt======	chr1:227441653-227441869(+)$1	216	7	36	23.4450
[cccddddddddtttttttttttdddd00	chr1:144189830-144190052(+)$1	222	36	65	21.0971
""ccc[eeeeeuuuuuuuuuuuueeeee4	chr3:41280677-41280892(+)$1	215	142	171	24.8413
d"""ccc[bbvvvvvvvvvvvvvbb]ccc	chr9:138713159-138713376(-)$1	217	35	64	23.0314
iii!!ffffffvvvvvvvvvvvvvfffff	chr2:166868602-166868824(-)$1	222	14	43	23.5863
E::ccc[dddduuuuuuuuuuuuddddcc	chr20:334110-334327(+)$1	217	54	83	21.6685
ff!!gggggggtttttttttttggggggg	chr7:73122824-73123049(-)$1	225	6	35	23.3236
d[hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr21:45725145-45725364(+)$1	219	110	139	21.3688
::==========ttttttttttt======	chr16:58712161-58712380(-)$1	219	122	151	22.1141
dbbccc!!ccctttttttttttccc22cc	chr5:149500735-149500956(+)$1	221	9	38	22.8212
ffccc[eeeeettttttttttteeeee]c	chr11:46911908-46912127(+)$1	219	64	93	23.2100
GGGGffffffvvvvvvvvvvvvvffffff	chrX:10107379-10107595(+)$1	216	154	183	20.8418
ccc[eeeeewwwwwwwwwwwwwweeeee]	chr6:132641708-132641923(-)$1	215	151	180	23.3008
hhhhhheeeeeuuuuuuuuuuuueeeee:	chr5:37206401-37206624(-)$1	223	165	194	22.5624
eee!!eeeeevvvvvvvvvvvvveeeee]	chr20:47589679-47589894(-)$1	215	115	144	24.0823
:CCCggggggguuuuuuuuuuuugggggg	chr1:180135594-180135817(+)$1	223	6	35	20.9723
F:ffffff[bbwwwwwwwwwwwwwwbb]f	chr17:7611435-7611653(+)$1	218	39	68	20.8140
llcccfffffftttttttttttffffffc	chr10:81603990-81604221(-)$1	231	119	148	21.4011
::dddd[ddddvvvvvvvvvvvvvdddd]	chr1:16046165-16046388(+)$1	223	37	66	21.8638
cc!!dddd[bbvvvvvvvvvvvvvbb]dd	chr14:32561561-32561785(+)$1	224	184	213	23.1322
B==========vvvvvvvvvvvvv=====	chr1:1309421-1309637(+)$1	216	113	142	24.0653
hhhhhheeeeevvvvvvvvvvvvveeeee	chr11:62760954-62761181(+)$1	227	25	54	23.1456
b[a[eeeeexxxxxxxxxxxxxxxeeeee	chr4:7031996-7032229(+)$1	233	141	170	19.2184
beeeee!!cccuuuuuuuuuuuuccc22e	chr7:127013555-127013779(-)$1	224	162	191	24.0871
cc!!gggggggvvvvvvvvvvvvvggggg	chr6:29455140-29455357(-)$1	217	71	100	24.6663
ff"""ccccccuuuuuuuuuuuuccc]cc	chr16:2815159-2815398(+)$1	239	63	92	24.4313
ddd[bbddddvvvvvvvvvvvvvdddd22	chr5:175749214-175749437(+)$1	223	185	214	22.2869
bffffff!!bbuuuuuuuuuuuubb4444	chr6:56470990-56471208(-)$1	218	137	166	23.3584
:ffffff[cccvvvvvvvvvvvvvccc]f	chr3:171404446-171404666(-)$1	220	67	96	23.0605
fff!!ddddyyyyyyyyyyyyyyyydddd	chr20:44987261-44987485(-)$1	224	130	159	22.2499
fccc[a!!ccctttttttttttccc22a]	chr1:36026352-36026569(+)$1	217	160	189	23.3767
bccc!!eeeeeuuuuuuuuuuuueeeee2	chr13:77672622-77672849(-)$1	227	164	193	24.7371
::a[ccc[ccctttttttttttccc]ccc	chr19:17749828-17750044(-)$1	216	180	209	22.3883
ddgggggggyyyyyyyyyyyyyyyygggg	chr3:42679618-42679834(-)$1	216	146	175	22.9796

#otherMatches

#Seq PSSM
CACAGGCACUGGCCCUGAGUUUUCACAAA	chr10:127486580-127486797(-)$1	217	34	63	22.0991
UGGAUGACUUAAUUUUGUAUUCCUCCAGG	chr5:173531143-173531368(+)$1	225	59	88	22.3474
AAGGAAGAAAGCAUUCACUCUCACUCUUC	chr6:149846201-149846419(+)$1	218	183	212	20.2671
GGACCACUGCAAAGCCAUUUACCUGCAUG	chr16:3533289-3533507(+)$1	218	122	151	23.5516
UGAAAGUGAAGAACUUUAAUAACUUUACC	chr5:137222966-137223191(+)$1	225	89	118	22.3696
CAAGGGGGCUCUCCCUCCAUCUCCUGCCC	chr5:150029636-150029864(+)$1	228	9	38	21.0217
GGGCUCCUUGGCUUCCUUAUCCUCUGGGG	chr21:44492063-44492280(+)$1	217	117	146	24.6432
CAGGCUCUGAGGAGAGGAGAAGGAAGAGC	chr1:156628753-156628976(+)$1	223	4	33	20.3193
GACUAUGAGGAGGAAGAAAUGGAGACCGU	chr9:711765-711983(+)$1	218	42	71	21.3831
UGCUGUUUGCUUUUAUUUAUCUGGCUUUG	chr7:94180571-94180794(+)$1	223	94	123	22.8589
CAUUGGAUGCAAAGAGAUGUACAGGAUCC	chrX:101395699-101395921(-)$1	222	104	133	22.2310
AUAGCACUGCGCCACAAGCACAUCGCAGA	chr9:130430314-130430529(+)$1	215	114	143	24.7428
CACAGCGAACGACACCACCCUCCGUGGCU	chr2:3200575-3200801(-)$1	226	102	131	22.9645
UCUUCCGGAAGGAGUGGAGUGGGCUGCUG	chr10:3143560-3143777(+)$1	217	138	167	24.2402
AGGCCGGCGGCCCGGAGGUGCAGCAGCUG	chr12:27933340-27933586(+)$1	246	56	85	23.4283
GGCCAGUGCUAAAAAAAUUAGAUGAAGUG	chr20:45315410-45315641(-)$1	231	185	214	19.2285
GGUAUCGCGCCUAUCCCCCCUGCCUGUGG	chr12:49445285-49445525(-)$1	240	6	35	21.9039
CGCCCCCCAGCCACAGCCCACCUGCUGAG	chr16:29820867-29821086(+)$1	219	168	197	23.8519
CGGAGCCCCUCAAAAACAAUGGCAGAGGA	chr1:10399789-10400008(+)$1	219	69	98	22.9173
AUCUUCGUUACCAACCUCUCCUUCUGAUG	chr15:63961765-63961982(-)$1	217	151	180	20.9826
AGGUCAAUCUGUUCACAACACAUACACAU	chr5:61643773-61643994(-)$1	221	112	141	22.3467
UUCUGGCUCUGAUAAUGUGAAAAAACAGA	chr10:61832167-61832383(-)$1	216	153	182	23.5956
CCCUCCUUCAUGCUCAUCCUAAGGUGAAG	chr11:74911298-74911532(+)$1	234	111	140	25.0602
UCUCCACAGCUCUCCGCUUCUCACGCACC	chr19:41025265-41025482(-)$1	217	44	73	22.5214
CAGACCAGAAGUCUGUCUUCCUCUUCUGG	chr12:13224183-13224401(+)$1	218	85	114	23.4594
GGACCAACACUCCAAACAACCUCGGUGUC	chr1:161967820-161968036(-)$1	216	121	150	23.7144
CCCAAACCCCAAGUGUGGGAAAAAUGGGG	chr11:10585516-10585739(-)$1	223	158	187	23.2635
CUCAUUUCUGGUAACAGUGACAACCCCAG	chr2:133542214-133542431(+)$1	217	84	113	22.7625
UUUGCUUUAGGCCCUGUGUCUUACCUUCU	chrX:64958373-64958593(-)$1	220	90	119	24.1636
CCAAGGCGGCGCCCAUGCUGAUUGCCCGC	chr15:86311757-86311986(-)$1	229	50	79	22.7058
CAGUCCCCCCAAUUUUGUAUUCUGGGGGG	chr19:42470900-42471124(-)$1	224	96	125	22.8103
GUUUAACAAGUAACAAGUAACAAUACUUG	chr1:227441653-227441869(+)$1	216	7	36	23.4450
GUCUGUCCCUGUCUGAAUGUAUUGCAGGA	chr1:144189830-144190052(+)$1	222	36	65	21.0971
AUACUGACCUGUAAAUCAUCCUUUAGGUA	chr3:41280677-41280892(+)$1	215	142	171	24.8413
CCAGUGCCAGGCUCUAAGAAUAACUCGCA	chr9:138713159-138713376(-)$1	217	35	64	23.0314
GUAACAUUUUCUUUAUAGGCAUUUGAAGA	chr2:166868602-166868824(-)$1	222	14	43	23.5863
GCAGCAGUUGUCACCCAUUUUCCGCAAUG	chr20:334110-334327(+)$1	217	54	83	21.6685
CUGACCACCUGGCCUUGGUCCGCAGGUGG	chr7:73122824-73123049(-)$1	225	6	35	23.3236
CAUGUUCAAGGGAGCUGCCGAGGCUUGAG	chr21:45725145-45725364(+)$1	219	110	139	21.3688
UUGGUUUCCAGAAAUAUGCCAGGUUUGGA	chr16:58712161-58712380(-)$1	219	122	151	22.1141
GCCCCACCAACACCACACGUACGUUCUUG	chr5:149500735-149500956(+)$1	221	9	38	22.8212
GCGGCGUCCAGAGCCAUCCAUGCUGGAGG	chr11:46911908-46912127(+)$1	219	64	93	23.2100
CUGCGUGGGCAGAGCCACAAAGAGCCCAU	chrX:10107379-10107595(+)$1	216	154	183	20.8418
CUUGGGUAAGAAAACUUUUAUUAUUAUUA	chr6:132641708-132641923(-)$1	215	151	180	23.3008
UCUAAUGUGUGGACAGUUGAAUAUGCACU	chr5:37206401-37206624(-)$1	223	165	194	22.5624
AGCAAUUUUGGAUAAAUCAUUUACAAGGC	chr20:47589679-47589894(-)$1	215	115	144	24.0823
ACCCCUGGGUUUUUUGUCCUUUCAGCCUG	chr1:180135594-180135817(+)$1	223	6	35	20.9723
GACCUGGAUCUCCGCUUCACCAUCAAGUU	chr17:7611435-7611653(+)$1	218	39	68	20.8140
GAGGUGUGCUGGGGAAGGUAGACAGCACC	chr10:81603990-81604221(-)$1	231	119	148	21.4011
ACGGGCCUCCUCUACUCUCUCCUCAGGAU	chr1:16046165-16046388(+)$1	223	37	66	21.8638
CCUUAGAUGGAAAAAUUUAUGAACUUGAU	chr14:32561561-32561785(+)$1	224	184	213	23.1322
CCUGCUCGGCCCCUUCCCCUAUCUGGCUG	chr1:1309421-1309637(+)$1	216	113	142	24.0653
GCGGUGAUCCCGUAGAUGAUAUUGGGGAU	chr11:62760954-62761181(+)$1	227	25	54	23.1456
CACUCGGCACCAAUCAGAGCCCCAUGCCG	chr4:7031996-7032229(+)$1	233	141	170	19.2184
CACUUCUAACUCUCCUAGUAAAAAGUAUG	chr7:127013555-127013779(-)$1	224	162	191	24.0871
CAGGUGACUCUGCUAACUUAUCAUGGAGU	chr6:29455140-29455357(-)$1	217	71	100	24.6663
CUAAAGCCAAGACAAGAACCCCACUUCGG	chr16:2815159-2815398(+)$1	239	63	92	24.4313
CCCAACCUGACAAAGAACACCAAUCAGCU	chr5:175749214-175749437(+)$1	223	185	214	22.2869
AGAUUCUAUGCAAAGUGAAGAAAGUUAUG	chr6:56470990-56471208(-)$1	218	137	166	23.3584
AAUUUCUCUAGGUUAUUUUAAUCACUAUA	chr3:171404446-171404666(-)$1	220	67	96	23.0605
GUCAGCACCAGCCACCAGCCCCUUAGGUG	chr20:44987261-44987485(-)$1	224	130	159	22.2499
CCCCUGAAUGCUACCGGGAUCUGCAGGCC	chr1:36026352-36026569(+)$1	217	160	189	23.3767
UUCUAAAUCAGACUCUUACACACUUGAUC	chr13:77672622-77672849(-)$1	227	164	193	24.7371
ACAGUGAUGCCAACUagacacaggcuuca	chr19:17749828-17750044(-)$1	216	180	209	22.3883
AUUUGGCCCUGCUUCUCUUUUUCCUGGGC	chr3:42679618-42679834(-)$1	216	146	175	22.9796

#DB
..(((((..((..............))..	chr10:127486580-127486797(-)$1	1	34	63	22.0991
(((.((((((................)))	chr5:173531143-173531368(+)$1	1	59	88	22.3474
...(((((................)))))	chr6:149846201-149846419(+)$1	1	183	212	20.2671
((((...((((............)))).)	chr16:3533289-3533507(+)$1	1	122	151	23.5516
((...((((((...........)))))).	chr5:137222966-137223191(+)$1	1	89	118	22.3696
..)))((((................))))	chr5:150029636-150029864(+)$1	1	9	38	21.0217
(((.(((((((............))))))	chr21:44492063-44492280(+)$1	1	117	146	24.6432
..((((((................)))))	chr1:156628753-156628976(+)$1	1	4	33	20.3193
..(((((.(................))))	chr9:711765-711983(+)$1	1	42	71	21.3831
..((((..(((...........)))...)	chr7:94180571-94180794(+)$1	1	94	123	22.8589
)..(((((.(.............).))))	chrX:101395699-101395921(-)$1	1	104	133	22.2310
(((.(.(((((............))))).	chr9:130430314-130430529(+)$1	1	114	143	24.7428
(.((((..(((...........))).)))	chr2:3200575-3200801(-)$1	1	102	131	22.9645
((((((((.((............)).)))	chr10:3143560-3143777(+)$1	1	138	167	24.2402
(((((((((((..............))))	chr12:27933340-27933586(+)$1	1	56	85	23.4283
(((..(((((...............))))	chr20:45315410-45315641(-)$1	1	185	214	19.2285
(((...(((((................))	chr12:49445285-49445525(-)$1	1	6	35	21.9039
..(((((((((............)))).)	chr16:29820867-29821086(+)$1	1	168	197	23.8519
.((.((.((((.............)))).	chr1:10399789-10400008(+)$1	1	69	98	22.9173
..((((((((..............)))))	chr15:63961765-63961982(-)$1	1	151	180	20.9826
(((.(.((.(((...........))).))	chr5:61643773-61643994(-)$1	1	112	141	22.3467
(((...(((((..............))))	chr10:61832167-61832383(-)$1	1	153	182	23.5956
(((.(((((((............))))))	chr11:74911298-74911532(+)$1	1	111	140	25.0602
..((((..((..............))...	chr19:41025265-41025482(-)$1	1	44	73	22.5214
(.(.(((((((...........)))))))	chr12:13224183-13224401(+)$1	1	85	114	23.4594
((((..(((((............))))).	chr1:161967820-161968036(-)$1	1	121	150	23.7144
(((..((((((.............)))))	chr11:10585516-10585739(-)$1	1	158	187	23.2635
((((((.((((..............))))	chr2:133542214-133542431(+)$1	1	84	113	22.7625
)))((...(((............)))...	chrX:64958373-64958593(-)$1	1	90	119	24.1636
(((((((((.((...........))))))	chr15:86311757-86311986(-)$1	1	50	79	22.7058
))))(((((((...........)))))))	chr19:42470900-42471124(-)$1	1	96	125	22.8103
((((((((((((...........))))))	chr1:227441653-227441869(+)$1	1	7	36	23.4450
.(((((((((((...........))))..	chr1:144189830-144190052(+)$1	1	36	65	21.0971
..(((.(((((............))))).	chr3:41280677-41280892(+)$1	1	142	171	24.8413
(...(((.((.............)).)))	chr9:138713159-138713376(-)$1	1	35	64	23.0314
(((..((((((.............)))))	chr2:166868602-166868824(-)$1	1	14	43	23.5863
(..(((.((((............))))))	chr20:334110-334327(+)$1	1	54	83	21.6685
((..(((((((...........)))))))	chr7:73122824-73123049(-)$1	1	6	35	23.3236
(.((((((((.............))))))	chr21:45725145-45725364(+)$1	1	110	139	21.3688
..((((((((((...........))))))	chr16:58712161-58712380(-)$1	1	122	151	22.1141
((((((..(((...........)))..))	chr5:149500735-149500956(+)$1	1	9	38	22.8212
))(((.(((((...........))))).)	chr11:46911908-46912127(+)$1	1	64	93	23.2100
))))((((((.............))))))	chrX:10107379-10107595(+)$1	1	154	183	20.8418
(((.(((((..............))))).	chr6:132641708-132641923(-)$1	1	151	180	23.3008
))))))(((((............))))).	chr5:37206401-37206624(-)$1	1	165	194	22.5624
(((..(((((.............))))).	chr20:47589679-47589894(-)$1	1	115	144	24.0823
.((((((((((............))))))	chr1:180135594-180135817(+)$1	1	6	35	20.9723
(.((((((.((..............)).)	chr17:7611435-7611653(+)$1	1	39	68	20.8140
..)))((((((...........))))))(	chr10:81603990-81604221(-)$1	1	119	148	21.4011
..((((.((((.............)))).	chr1:16046165-16046388(+)$1	1	37	66	21.8638
((..((((.((.............)).))	chr14:32561561-32561785(+)$1	1	184	213	23.1322
)((((((((((.............)))))	chr1:1309421-1309637(+)$1	1	113	142	24.0653
))))))(((((.............)))))	chr11:62760954-62761181(+)$1	1	25	54	23.1456
(.(.(((((...............)))))	chr4:7031996-7032229(+)$1	1	141	170	19.2184
((((((..(((............)))..)	chr7:127013555-127013779(-)$1	1	162	191	24.0871
((..(((((((.............)))))	chr6:29455140-29455357(-)$1	1	71	100	24.6663
((...((((((............))).))	chr16:2815159-2815398(+)$1	1	63	92	24.4313
(((.((((((.............))))..	chr5:175749214-175749437(+)$1	1	185	214	22.2869
(((((((..((............))....	chr6:56470990-56471208(-)$1	1	137	166	23.3584
.((((((.(((.............))).)	chr3:171404446-171404666(-)$1	1	67	96	23.0605
(((..((((................))))	chr20:44987261-44987485(-)$1	1	130	159	22.2499
((((.(..(((...........)))..).	chr1:36026352-36026569(+)$1	1	160	189	23.3767
((((..(((((............))))).	chr13:77672622-77672849(-)$1	1	164	193	24.7371
..(.(((.(((...........))).)))	chr19:17749828-17750044(-)$1	1	180	209	22.3883
(((((((((................))))	chr3:42679618-42679834(-)$1	1	146	175	22.9796

#PSSM
: : 0.12	f : 0.12	d : 0.12	c : 0.10	b : 0.09	e : 0.07	i : 0.04	g : 0.04	! : 0.03	$ : 0.03	" : 0.03	[ : 0.03	h : 0.03	n : 0.01	= : 0.01	E : 0.01	G : 0.01	F : 0.01	l : 0.01	B : 0.01	
c : 0.15	: : 0.13	f : 0.12	e : 0.09	[ : 0.06	d : 0.06	b : 0.04	i : 0.04	g : 0.04	" : 0.04	! : 0.03	$ : 0.03	= : 0.03	h : 0.03	n : 0.01	G : 0.01	C : 0.01	l : 0.01	
c : 0.18	e : 0.13	f : 0.10	d : 0.10	g : 0.06	h : 0.06	: : 0.04	" : 0.04	i : 0.04	a : 0.04	= : 0.04	! : 0.04	b : 0.03	G : 0.01	C : 0.01	
[ : 0.16	c : 0.13	! : 0.12	e : 0.10	" : 0.07	f : 0.07	d : 0.06	h : 0.06	g : 0.04	= : 0.04	i : 0.03	a : 0.01	b : 0.01	G : 0.01	C : 0.01	
g : 0.15	e : 0.12	c : 0.12	! : 0.10	f : 0.09	d : 0.09	" : 0.07	h : 0.06	b : 0.04	= : 0.04	a : 0.03	i : 0.03	[ : 0.01	
e : 0.15	f : 0.15	g : 0.15	d : 0.12	c : 0.07	" : 0.06	[ : 0.06	h : 0.06	= : 0.04	i : 0.03	b : 0.03	! : 0.03	a : 0.01	
e : 0.29	f : 0.15	g : 0.12	! : 0.09	d : 0.07	[ : 0.06	= : 0.04	c : 0.04	" : 0.03	i : 0.03	h : 0.03	b : 0.01	
e : 0.24	d : 0.16	! : 0.12	f : 0.12	g : 0.12	[ : 0.06	= : 0.04	i : 0.03	h : 0.03	b : 0.01	" : 0.01	c : 0.01	
e : 0.21	d : 0.15	c : 0.13	g : 0.12	f : 0.09	[ : 0.07	= : 0.04	! : 0.03	y : 0.03	h : 0.03	b : 0.03	a : 0.01	i : 0.01	
e : 0.18	c : 0.15	d : 0.12	b : 0.10	g : 0.10	f : 0.09	y : 0.09	= : 0.04	h : 0.03	a : 0.01	[ : 0.01	w : 0.01	x : 0.01	
c : 0.15	e : 0.15	y : 0.10	d : 0.10	g : 0.10	b : 0.09	v : 0.09	f : 0.06	w : 0.04	= : 0.04	x : 0.03	
u : 0.24	v : 0.23	t : 0.16	w : 0.12	y : 0.12	x : 0.03	= : 0.03	c : 0.01	b : 0.01	d : 0.01	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	t : 0.24	v : 0.23	w : 0.12	y : 0.12	x : 0.03	
u : 0.24	v : 0.23	w : 0.12	y : 0.12	c : 0.07	t : 0.07	g : 0.04	f : 0.03	x : 0.03	e : 0.01	
c : 0.13	v : 0.13	y : 0.12	e : 0.12	w : 0.10	g : 0.09	d : 0.07	b : 0.06	f : 0.04	x : 0.03	= : 0.03	a : 0.01	h : 0.01	
e : 0.16	c : 0.15	d : 0.10	g : 0.10	y : 0.09	f : 0.09	b : 0.09	w : 0.07	= : 0.04	h : 0.03	] : 0.01	x : 0.01	
e : 0.23	d : 0.15	g : 0.12	f : 0.09	c : 0.07	b : 0.06	] : 0.06	= : 0.04	y : 0.03	h : 0.03	2 : 0.03	a : 0.01	3 : 0.01	i : 0.01	4 : 0.01	
e : 0.24	d : 0.16	g : 0.12	f : 0.10	3 : 0.04	] : 0.04	= : 0.04	c : 0.04	2 : 0.04	b : 0.03	i : 0.03	h : 0.03	y : 0.01	4 : 0.01	
e : 0.24	g : 0.12	f : 0.10	d : 0.10	] : 0.07	c : 0.07	2 : 0.04	3 : 0.04	= : 0.04	i : 0.03	h : 0.03	b : 0.01	0 : 0.01	4 : 0.01	a : 0.01	
e : 0.18	g : 0.12	f : 0.10	c : 0.10	d : 0.09	] : 0.07	2 : 0.06	3 : 0.04	= : 0.04	i : 0.03	h : 0.03	4 : 0.03	b : 0.01	5 : 0.01	0 : 0.01	: : 0.01	

#score	1477.28806269913
#seq	65
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_transcript_m2_run2.txt

#BEAR
eeeeeyyyyyyyyyyyyyyyyee	chr7:4216126-4216349(+)$1	223	46	69	19.7004
$$dddduuuuuuuuuuuudddd5	chr14:61792029-61792297(+)$1	268	93	116	21.5907
++cccuuuuuuuuuuuuccc>>>	chr7:16286812-16287033(-)$1	221	41	64	20.5909
gggggtttttttttttggggggg	chr5:130724879-130725112(+)$1	233	201	224	20.4981
hhhhhwwwwwwwwwwwwwwhhhh	chr7:5746949-5747200(-)$1	251	166	189	22.3147
gggggguuuuuuuuuuuuggggg	chr11:94912705-94912942(-)$1	237	40	63	23.1336
eeeeevvvvvvvvvvvvveeeee	chr13:94432743-94432986(+)$1	243	154	177	24.3014
!!cccwwwwwwwwwwwwwwccc2	chr8:66962266-66962480(+)$1	214	126	149	23.3926
[bb[ccctttttttttttccc]b	chr9:8318018-8318234(-)$1	216	47	70	20.7388
eeeeewwwwwwwwwwwwwweeee	chr11:102031970-102032224(+)$1	254	177	200	23.1074
cddddvvvvvvvvvvvvvdddd]	chr4:26374065-26374297(+)$1	232	58	81	24.2382
!ddddwwwwwwwwwwwwwwdddd	chr5:39175757-39176010(-)$1	253	124	147	22.9945
[a[bbvvvvvvvvvvvvvbb]ac	chr14:91688204-91688563(+)$1	359	96	119	23.2202
hhhhhwwwwwwwwwwwwwwhhhh	chr3:87301804-87302094(+)$1	290	255	278	22.3147
gggggvvvvvvvvvvvvvggggg	chr15:84343763-84343976(+)$1	213	6	29	24.5314
eddddwwwwwwwwwwwwwwdddd	chr1:153843183-153843457(-)$1	274	50	73	22.7610
iiiiivvvvvvvvvvvvviiiii	chr2:80326882-80327098(+)$1	216	173	196	24.5670
fffffvvvvvvvvvvvvvfffff	chr5:176597576-176597844(+)$1	268	113	136	23.0312
eeeewwwwwwwwwwwwwweeeee	chr1:9755009-9755278(+)$1	269	75	98	22.5579
cccbbwwwwwwwwwwwwwwbb]c	chr2:26323046-26323321(+)$1	275	22	45	21.8526
hhhhhwwwwwwwwwwwwwwhhhh	chr13:113878944-113879159(+)$1	215	129	152	22.3147
hhhhhvvvvvvvvvvvvvhhhhh	chr1:101408581-101408827(+)$1	246	168	191	23.2614
a[cccuuuuuuuuuuuuccc]a]	chr8:48646313-48646550(+)$1	237	136	159	22.8994
hhhhhhuuuuuuuuuuuuhhhhh	chr1:62167370-62167611(-)$1	241	179	202	21.5682
bb[ddddtttttttttttdddd2	chr2:238299480-238299710(-)$1	230	152	175	20.2973
fffffwwwwwwwwwwwwwwffff	chr9:115953995-115954256(-)$1	261	106	129	21.9502
[ddddvvvvvvvvvvvvvdddd]	chr9:5695798-5696031(+)$1	233	128	151	24.4702
gggggvvvvvvvvvvvvvggggg	chr9:32419478-32419692(+)$1	214	138	161	24.5314
fffffvvvvvvvvvvvvvfffff	chr19:30463860-30464092(+)$1	232	109	132	23.0312
iiiiiwwwwwwwwwwwwwwiiii	chr14:92277954-92278215(-)$1	261	132	155	23.3983
""cccvvvvvvvvvvvvvccc22	chr18:3267783-3268008(+)$1	225	69	92	24.2420
c[cccwwwwwwwwwwwwwwccc2	chr19:42702865-42703090(-)$1	225	122	145	23.1465
eeddddtttttttttttdddd]e	chr3:33120063-33120334(-)$1	271	72	95	20.9622
eeeewwwwwwwwwwwwwweeeee	chr2:162013382-162013618(+)$1	236	30	53	22.5579
=!!cccuuuuuuuuuuuuccc22	chr4:89543166-89543438(+)$1	272	21	44	23.1592
eeeeevvvvvvvvvvvvveeeee	chr11:43408817-43409053(+)$1	236	57	80	24.3014
cccyyyyyyyyyyyyyyyyccc]	chr7:72361732-72362019(+)$1	287	125	148	19.9822
[ddddvvvvvvvvvvvvvdddd]	chr2:100014901-100015123(+)$1	222	99	122	24.4702
ffffyyyyyyyyyyyyyyyyfff	chr12:39984452-39984713(-)$1	261	96	119	19.0299
iiiiiiitttttttttttiiiii	chr3:77182738-77182953(+)$1	215	47	70	21.1347
""eeeeettttttttttteeeee	chr1:171084943-171085156(+)$1	213	96	119	21.0749
[ddddvvvvvvvvvvvvvddddb	chr11:20415420-20415653(+)$1	233	81	104	23.9527
!ddddwwwwwwwwwwwwwwdddd	chr5:175104759-175104982(+)$1	223	76	99	22.9945
gggggguuuuuuuuuuuuggggg	chr3:56619944-56620193(+)$1	249	171	194	23.1336
=====wwwwwwwwwwwwww====	chr5:37539909-37540163(+)$1	254	92	115	23.3235
!!dddduuuuuuuuuuuudddd2	chr2:228419150-228419388(+)$1	238	145	168	23.0435
gggggguuuuuuuuuuuuggggg	chr6:145144555-145144794(+)$1	239	43	66	23.1336
dd[bbwwwwwwwwwwwwwwbbdd	chr11:78624513-78624788(-)$1	275	91	114	21.6080
dddyyyyyyyyyyyyyyyydddd	chr5:169238255-169238471(+)$1	216	184	207	19.4526
iiiiiitttttttttttiiiiii	chr7:158585824-158586046(-)$1	222	31	54	21.3213
%%cccvvvvvvvvvvvvvccc66	chr5:134670484-134670713(-)$1	229	98	121	22.0475
[ddddvvvvvvvvvvvvvdddd]	chr6:56466472-56466689(-)$1	217	133	156	24.4702
bbcccwwwwwwwwwwwwwwccc]	chr2:25681909-25682170(-)$1	261	168	191	22.7536
gggggvvvvvvvvvvvvvggggg	chr4:25141292-25141544(-)$1	252	2	25	24.5314
:eeeeeuuuuuuuuuuuueeeee	chr13:33070999-33071282(-)$1	283	104	127	21.9772
&eeeeeuuuuuuuuuuuueeeee	chr12:78545674-78545901(+)$1	227	152	175	22.3769
eeeeewwwwwwwwwwwwwweeee	chr2:211308345-211308581(-)$1	236	96	119	23.1074
!eeeeettttttttttteeeee]	chr10:77742584-77742799(+)$1	215	139	162	21.5585
eeeeevvvvvvvvvvvvveeeee	chr11:14208018-14208285(+)$1	267	52	75	24.3014
eeeeettttttttttteeeeehh	chr12:51823828-51824052(+)$1	224	55	78	20.2965

#otherMatches

#Seq PSSM
caguggcauuaagcacauucaca	chr7:4216126-4216349(+)$1	223	46	69	19.7004
caacuggauagccacauacagua	chr14:61792029-61792297(+)$1	268	93	116	21.5907
ucaggccaauuaauaacccuaca	chr7:16286812-16287033(-)$1	221	41	64	20.5909
AGUCAUUUUAUUAAUCUGACUAU	chr5:130724879-130725112(+)$1	233	201	224	20.4981
aauuuauaauacaucaaaaaagu	chr7:5746949-5747200(-)$1	251	166	189	22.3147
cucagugaauguucacaaacuga	chr11:94912705-94912942(-)$1	237	40	63	23.1336
AGAUGUAACUUCUAUGCUUAUCU	chr13:94432743-94432986(+)$1	243	154	177	24.3014
CAGUGAUUUAAGAAACAUCCACA	chr8:66962266-66962480(+)$1	214	126	149	23.3926
CCUGCCACUGCUUGGAAUUGGGA	chr9:8318018-8318234(-)$1	216	47	70	20.7388
guuuuauaaccuauuuuuaaaaa	chr11:102031970-102032224(+)$1	254	177	200	23.1074
UUGUACAAUUUGAGUUCAUACAU	chr4:26374065-26374297(+)$1	232	58	81	24.2382
CUCAAUUCCAAACACUUCCUUGA	chr5:39175757-39176010(-)$1	253	124	147	22.9945
CAAGCACCCAUACACUCAGCCUC	chr14:91688204-91688563(+)$1	359	96	119	23.2202
UUUAAUAAAAUAUUGAACCUUAG	chr3:87301804-87302094(+)$1	290	255	278	22.3147
uggguuuuucauuucauuaccca	chr15:84343763-84343976(+)$1	213	6	29	24.5314
uggggaaaaacaaaaaaaaCCUC	chr1:153843183-153843457(-)$1	274	50	73	22.7610
auuuuuuuuguuguuguugagau	chr2:80326882-80327098(+)$1	216	173	196	24.5670
cuuccuauucauccauuuggaag	chr5:176597576-176597844(+)$1	268	113	136	23.0312
aaaugaacagaaaaaaaaauuug	chr1:9755009-9755278(+)$1	269	75	98	22.5579
AAUCCAAUAAGCAAAAGAAGGUG	chr2:26323046-26323321(+)$1	275	22	45	21.8526
uuauugaccauauuuuccagaug	chr13:113878944-113879159(+)$1	215	129	152	22.3147
uaguuugccugugcuucugacug	chr1:101408581-101408827(+)$1	246	168	191	23.2614
GUUGACUUUAUUCUUUUUCACCA	chr8:48646313-48646550(+)$1	237	136	159	22.8994
AAAUUAUUUUUCUGCUUCUAGUU	chr1:62167370-62167611(-)$1	241	179	202	21.5682
GUCAUUCUUUAAAAAAAUGAAUA	chr2:238299480-238299710(-)$1	230	152	175	20.2973
AGGAcucacuccuauuccugucc	chr9:115953995-115954256(-)$1	261	106	129	21.9502
CAAGCCAAACAUGCUAUUGCUUU	chr9:5695798-5696031(+)$1	233	128	151	24.4702
auguguuuaugcuuucacuacau	chr9:32419478-32419692(+)$1	214	138	161	24.5314
CAAUUCAUUAUAUCAAAAAAUUG	chr19:30463860-30464092(+)$1	232	109	132	23.0312
aacugUAAUUAGAAUACCUCAGU	chr14:92277954-92278215(-)$1	261	132	155	23.3983
aagucucccauauaaaauggcau	chr18:3267783-3268008(+)$1	225	69	92	24.2420
CUGUCCAGAGCUGAACAUAGACU	chr19:42702865-42703090(-)$1	225	122	145	23.1465
aucguaucauuucauauuacgaa	chr3:33120063-33120334(-)$1	271	72	95	20.9622
AGAGAAACAAACACCCAGUUCUG	chr2:162013382-162013618(+)$1	236	30	53	22.5579
caaugguuuuuaguauauucacg	chr4:89543166-89543438(+)$1	272	21	44	23.1592
AACCAAAUAAUAUAAGCcugguu	chr11:43408817-43409053(+)$1	236	57	80	24.3014
GGACCCAUUCACUUCCUCUUCCU	chr7:72361732-72362019(+)$1	287	125	148	19.9822
GUCAUUCUUACAACCAUCAUGAA	chr2:100014901-100015123(+)$1	222	99	122	24.4702
AGAGAAUAAUAAAAAAGUAACUC	chr12:39984452-39984713(-)$1	261	96	119	19.0299
UUUUUAUAUUUAUUCCUAAUGAA	chr3:77182738-77182953(+)$1	215	47	70	21.1347
AUGCCAAUUCACCUCUGUUUGGC	chr1:171084943-171085156(+)$1	213	96	119	21.0749
CAGUUUUUAAACCUCAGUGACUC	chr11:20415420-20415653(+)$1	233	81	104	23.9527
AGGGACCCUGCGCCACUUUUCCC	chr5:175104759-175104982(+)$1	223	76	99	22.9945
GGAAGGAAACAAGGAGAACCUUC	chr3:56619944-56620193(+)$1	249	171	194	23.1336
UUUUAGCGAUCACAUUAAAUGGA	chr5:37539909-37540163(+)$1	254	92	115	23.3235
GAUCUUAGCUUUAAACACAAGAG	chr2:228419150-228419388(+)$1	238	145	168	23.0435
AGUGGCAAAUGUGUUGAAGUUAU	chr6:145144555-145144794(+)$1	239	43	66	23.1336
AGCUGAAUUCCACCCCCGacacu	chr11:78624513-78624788(-)$1	275	91	114	21.6080
GGCUUGCUGAAAUUCUUUUGUCU	chr5:169238255-169238471(+)$1	216	184	207	19.4526
uuuuacaccaugaccaaguagga	chr7:158585824-158586046(-)$1	222	31	54	21.3213
AAGAAAAAAAAAAUCCCCUUCAC	chr5:134670484-134670713(-)$1	229	98	121	22.0475
UACAAAACauaaauauuauuguu	chr6:56466472-56466689(-)$1	217	133	156	24.4702
ggauaaacaaagagaaaacuaua	chr2:25681909-25682170(-)$1	261	168	191	22.7536
AGCAGUAAAUUCCCAUCUCUGUU	chr4:25141292-25141544(-)$1	252	2	25	24.5314
AGUUCACUUUAAUUUUUAUGAAC	chr13:33070999-33071282(-)$1	283	104	127	21.9772
AUCUUGCUUUUAAUUUCCCAGGA	chr12:78545674-78545901(+)$1	227	152	175	22.3769
agaguacuucaaauacaucacuu	chr2:211308345-211308581(-)$1	236	96	119	23.1074
ucaagagaggguaaauaucuugc	chr10:77742584-77742799(+)$1	215	139	162	21.5585
GGUAUUUUCUUUGACUCUGUACC	chr11:14208018-14208285(+)$1	267	52	75	24.3014
GGCUUUUAUGUGGAUCAGGCCUG	chr12:51823828-51824052(+)$1	224	55	78	20.2965

#DB
(((((................))	chr7:4216126-4216349(+)$1	1	46	69	19.7004
..((((............)))).	chr14:61792029-61792297(+)$1	1	93	116	21.5907
..(((............)))...	chr7:16286812-16287033(-)$1	1	41	64	20.5909
(((((...........)))))))	chr5:130724879-130725112(+)$1	1	201	224	20.4981
(((((..............))))	chr7:5746949-5747200(-)$1	1	166	189	22.3147
((((((............)))))	chr11:94912705-94912942(-)$1	1	40	63	23.1336
(((((.............)))))	chr13:94432743-94432986(+)$1	1	154	177	24.3014
..(((..............))).	chr8:66962266-66962480(+)$1	1	126	149	23.3926
.((.(((...........))).)	chr9:8318018-8318234(-)$1	1	47	70	20.7388
(((((..............))))	chr11:102031970-102032224(+)$1	1	177	200	23.1074
(((((.............)))).	chr4:26374065-26374297(+)$1	1	58	81	24.2382
.((((..............))))	chr5:39175757-39176010(-)$1	1	124	147	22.9945
.(.((.............)).))	chr14:91688204-91688563(+)$1	1	96	119	23.2202
(((((..............))))	chr3:87301804-87302094(+)$1	1	255	278	22.3147
(((((.............)))))	chr15:84343763-84343976(+)$1	1	6	29	24.5314
)((((..............))))	chr1:153843183-153843457(-)$1	1	50	73	22.7610
(((((.............)))))	chr2:80326882-80327098(+)$1	1	173	196	24.5670
(((((.............)))))	chr5:176597576-176597844(+)$1	1	113	136	23.0312
((((..............)))))	chr1:9755009-9755278(+)$1	1	75	98	22.5579
(((((..............)).)	chr2:26323046-26323321(+)$1	1	22	45	21.8526
(((((..............))))	chr13:113878944-113879159(+)$1	1	129	152	22.3147
(((((.............)))))	chr1:101408581-101408827(+)$1	1	168	191	23.2614
(.(((............))).).	chr8:48646313-48646550(+)$1	1	136	159	22.8994
((((((............)))))	chr1:62167370-62167611(-)$1	1	179	202	21.5682
((.((((...........)))).	chr2:238299480-238299710(-)$1	1	152	175	20.2973
(((((..............))))	chr9:115953995-115954256(-)$1	1	106	129	21.9502
.((((.............)))).	chr9:5695798-5696031(+)$1	1	128	151	24.4702
(((((.............)))))	chr9:32419478-32419692(+)$1	1	138	161	24.5314
(((((.............)))))	chr19:30463860-30464092(+)$1	1	109	132	23.0312
(((((..............))))	chr14:92277954-92278215(-)$1	1	132	155	23.3983
..(((.............)))..	chr18:3267783-3268008(+)$1	1	69	92	24.2420
(.(((..............))).	chr19:42702865-42703090(-)$1	1	122	145	23.1465
((((((...........)))).)	chr3:33120063-33120334(-)$1	1	72	95	20.9622
((((..............)))))	chr2:162013382-162013618(+)$1	1	30	53	22.5579
(..(((............)))..	chr4:89543166-89543438(+)$1	1	21	44	23.1592
(((((.............)))))	chr11:43408817-43409053(+)$1	1	57	80	24.3014
(((................))).	chr7:72361732-72362019(+)$1	1	125	148	19.9822
.((((.............)))).	chr2:100014901-100015123(+)$1	1	99	122	24.4702
((((................)))	chr12:39984452-39984713(-)$1	1	96	119	19.0299
(((((((...........)))))	chr3:77182738-77182953(+)$1	1	47	70	21.1347
..(((((...........)))))	chr1:171084943-171085156(+)$1	1	96	119	21.0749
.((((.............)))))	chr11:20415420-20415653(+)$1	1	81	104	23.9527
.((((..............))))	chr5:175104759-175104982(+)$1	1	76	99	22.9945
((((((............)))))	chr3:56619944-56620193(+)$1	1	171	194	23.1336
(((((..............))))	chr5:37539909-37540163(+)$1	1	92	115	23.3235
..((((............)))).	chr2:228419150-228419388(+)$1	1	145	168	23.0435
((((((............)))))	chr6:145144555-145144794(+)$1	1	43	66	23.1336
((.((..............))))	chr11:78624513-78624788(-)$1	1	91	114	21.6080
(((................))))	chr5:169238255-169238471(+)$1	1	184	207	19.4526
((((((...........))))))	chr7:158585824-158586046(-)$1	1	31	54	21.3213
..(((.............)))..	chr5:134670484-134670713(-)$1	1	98	121	22.0475
.((((.............)))).	chr6:56466472-56466689(-)$1	1	133	156	24.4702
(((((..............))).	chr2:25681909-25682170(-)$1	1	168	191	22.7536
(((((.............)))))	chr4:25141292-25141544(-)$1	1	2	25	24.5314
.(((((............)))))	chr13:33070999-33071282(-)$1	1	104	127	21.9772
.(((((............)))))	chr12:78545674-78545901(+)$1	1	152	175	22.3769
(((((..............))))	chr2:211308345-211308581(-)$1	1	96	119	23.1074
.(((((...........))))).	chr10:77742584-77742799(+)$1	1	139	162	21.5585
(((((.............)))))	chr11:14208018-14208285(+)$1	1	52	75	24.3014
(((((...........)))))))	chr12:51823828-51824052(+)$1	1	55	78	20.2965

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

#score	1352.6071117560334
#seq	60
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_UTR_m2_run2.txt

#BEAR
===[avvvvvvvvvvvvva====	chr4:763093-763330(+)$1	237	16	39	23.7328
fffffuuuuuuuuuuuuffffff	chr12:111170522-111170759(-)$1	237	15	38	23.0217
ggggggtttttttttttgggggg	chr13:37596307-37596652(-)$1	345	118	141	22.7163
eeeeevvvvvvvvvvvvveeeee	chr11:94232208-94232451(+)$1	243	116	139	24.5240
fffffftttttttttttffffff	chr19:58452567-58452829(-)$1	262	37	60	22.2287
$dddduuuuuuuuuuuudddd]h	chrX:71417589-71417840(+)$1	251	21	44	22.5933
:ddddvvvvvvvvvvvvvdddd:	chr14:21679083-21679381(-)$1	298	58	81	21.5080
eeeeevvvvvvvvvvvvveeeee	chr12:56361990-56362240(+)$1	250	80	103	24.5240
eecccuuuuuuuuuuuuccc]ee	chr4:71895204-71895487(+)$1	283	245	268	23.9749
gggccctttttttttttccc333	chr21:34963566-34963835(-)$1	269	20	43	23.2553
dd[ccctttttttttttccc]dd	chr15:49032607-49032850(-)$1	243	179	202	22.6347
eeeeettttttttttteeeeeee	chr2:9543571-9543807(+)$1	236	7	30	22.8474
eeeeevvvvvvvvvvvvveeeee	chr17:4998976-4999245(+)$1	269	147	170	24.5240
fffffftttttttttttffffff	chr3:8920830-8921070(-)$1	240	11	34	22.2287
gggggvvvvvvvvvvvvvggggg	chr6:146231186-146231494(-)$1	308	8	31	23.9560
&dddduuuuuuuuuuuudddd77	chr19:36506272-36506616(-)$1	344	215	238	21.4388
gggggvvvvvvvvvvvvvggggg	chr1:237065052-237065420(+)$1	368	61	84	23.9560
!eeeeettttttttttteeeee2	chr1:240653161-240653387(-)$1	226	162	185	23.4632
iiiccctttttttttttccc777	chr7:91829016-91829259(-)$1	243	107	130	21.3713
'eeeeettttttttttteeeee7	chr2:262557-262885(-)$1	328	24	47	22.5255
ggggguuuuuuuuuuuugggggg	chrX:108935269-108935567(-)$1	298	102	125	23.6586
eeeeeuuuuuuuuuuuueeeee:	chr10:117705417-117705646(+)$1	229	20	43	23.5037
!eeeeettttttttttteeeee3	chr7:106298209-106298488(-)$1	279	58	81	23.6920
======ttttttttttt======	chr5:134182346-134182595(+)$1	249	130	153	22.7483
gggggvvvvvvvvvvvvvggggg	chrX:53220578-53220819(-)$1	241	137	160	23.9560
=eeeeettttttttttteeeee2	chr16:56510457-56510693(+)$1	236	196	219	23.3883
hhhhhuuuuuuuuuuuuhhhhhh	chr3:42688480-42688752(+)$1	272	207	230	21.3994
fffffuuuuuuuuuuuuffffff	chr9:131303700-131303941(+)$1	241	211	234	23.0217
eeeeevvvvvvvvvvvvveeeee	chr4:102014848-102015088(-)$1	240	96	119	24.5240
::cccuuuuuuuuuuuucccddd	chr2:201735644-201735960(-)$1	316	168	191	21.3213
eeeeeettttttttttteeeee:	chr1:233508519-233508776(+)$1	257	174	197	22.7124
ggggguuuuuuuuuuuugggggg	chr15:60713883-60714127(-)$1	244	80	103	23.6586
fffffwwwwwwwwwwwwwwffff	chr9:99520192-99520428(-)$1	236	10	33	21.7166
fffffwwwwwwwwwwwwwwffff	chr1:52882908-52883171(+)$1	263	139	162	21.7166
cccwwwwwwwwwwwwwwcccggg	chr17:8370432-8370774(+)$1	342	99	122	21.4002
d[cccuuuuuuuuuuuuccc444	chr12:29493969-29494205(-)$1	236	66	89	23.5703
!!cccuuuuuuuuuuuuccc333	chr2:65249193-65249470(+)$1	277	248	271	23.9590
dd[ccctttttttttttcccddd	chr4:175240044-175240324(+)$1	280	167	190	22.5422
eee[bbtttttttttttbb]eee	chr13:41506779-41507040(-)$1	261	163	186	22.1763
"ddddtttttttttttdddd]cc	chr18:32720926-32721163(+)$1	237	128	151	21.5870
bb[ccctttttttttttccc]bb	chr4:75048671-75048903(+)$1	232	15	38	21.8428
Eeeeeettttttttttteeeee:	chr10:69829220-69829456(-)$1	236	34	57	21.6135
h!!bbuuuuuuuuuuuubb]hhh	chr1:204522612-204522837(+)$1	225	167	190	21.4141
ggggguuuuuuuuuuuugggggg	chrY:15031416-15031645(+)$1	229	41	64	23.6586
eeeeewwwwwwwwwwwwwweeee	chr2:172176735-172176970(-)$1	235	172	195	22.8013
[dddduuuuuuuuuuuudddd]c	chr6:53132164-53132460(-)$1	296	267	290	23.1357
fff[bbtttttttttttbb]fff	chr10:112658596-112658821(+)$1	225	99	122	21.4432
eeeeeuuuuuuuuuuuueeeee]	chr6:153309628-153309877(-)$1	249	22	45	24.3474
hddddvvvvvvvvvvvvvdddd:	chr10:116622454-116622715(+)$1	261	172	195	22.2863
$$cccuuuuuuuuuuuuccc666	chr19:5843621-5843841(-)$1	220	151	174	21.7882
eeeeevvvvvvvvvvvvveeeee	chr17:8193480-8193892(-)$1	412	342	365	24.5240
#ddddtttttttttttdddd333	chr9:36215382-36215653(-)$1	271	129	152	21.7839
eeeeeuuuuuuuuuuuueeeee:	chr2:242293261-242293529(+)$1	268	237	260	23.5037
fffffvvvvvvvvvvvvvfffff	chr8:91634278-91634541(-)$1	263	100	123	23.3254
b[cccvvvvvvvvvvvvvccc]b	chr10:11374712-11374963(+)$1	251	25	48	23.3981
eeeeevvvvvvvvvvvvveeeee	chr12:54105383-54105808(-)$1	425	158	181	24.5240
!!cccvvvvvvvvvvvvvccc22	chr11:82985338-82985574(-)$1	236	200	223	23.6331
eeeeeuuuuuuuuuuuueeeee4	chr2:169629908-169630170(+)$1	262	81	104	24.3396
fffffuuuuuuuuuuuuffffff	chr20:5528133-5528397(-)$1	264	241	264	23.0217
a[cccvvvvvvvvvvvvvccc]a	chr15:40759098-40759477(+)$1	379	130	153	23.8497
eeeeeuuuuuuuuuuuueeeee:	chr18:32832117-32832414(-)$1	297	114	137	23.5037
eeeeevvvvvvvvvvvvveeeee	chr3:150261494-150261757(-)$1	263	95	118	24.5240
#dddduuuuuuuuuuuudddd33	chr4:103498778-103499021(+)$1	243	162	185	23.1825
eeeeeuuuuuuuuuuuueeeeeD	chr5:40762165-40762445(-)$1	280	216	239	23.2135
iiiiiuuuuuuuuuuuuiiiiii	chr20:34843665-34843916(+)$1	251	220	243	23.3910
"cccvvvvvvvvvvvvvccc]ee	chr8:94743964-94744277(-)$1	313	285	308	23.3205
fffffftttttttttttffffff	chr17:27072253-27072505(+)$1	252	107	130	22.2287
eee[attttttttttta]eeeee	chr9:119462668-119462930(+)$1	262	166	189	23.1193
d[cccuuuuuuuuuuuucccddd	chr5:41929761-41929986(+)$1	225	98	121	23.3085
ggggguuuuuuuuuuuugggggg	chr5:169407482-169407785(+)$1	303	118	141	23.6586
[ddddwwwwwwwwwwwwwwdddd	chr1:167393972-167394198(+)$1	226	72	95	21.6394
eeeeewwwwwwwwwwwwwweeee	chr17:42879664-42879920(-)$1	256	131	154	22.8013

#otherMatches

#Seq PSSM
UGGACGUUCUGGGUACAAGCCAA	chr4:763093-763330(+)$1	237	16	39	23.7328
CUUUAUAACUGUAAAAUUAAGGU	chr12:111170522-111170759(-)$1	237	15	38	23.0217
AGUAAGAUUCCAUUAACCUUAUU	chr13:37596307-37596652(-)$1	345	118	141	22.7163
CCACAAUUUACACAAUCCUGUGG	chr11:94232208-94232451(+)$1	243	116	139	24.5240
CCAUAUGAGUGCAGUGAAUGUGG	chr19:58452567-58452829(-)$1	262	37	60	22.2287
AGCAGACUCCCUUUAACCUGUAU	chrX:71417589-71417840(+)$1	251	21	44	22.5933
AGAUCAAAUUUUUCACCAGAUCC	chr14:21679083-21679381(-)$1	298	58	81	21.5080
ACACACUCCCCUUCUUUUUGUGU	chr12:56361990-56362240(+)$1	250	80	103	24.5240
GUGCCUCUCACUUCGUUGGUGAC	chr4:71895204-71895487(+)$1	283	245	268	23.9749
AUUUCAUUCGCAUCCAUUGAGAU	chr21:34963566-34963835(-)$1	269	20	43	23.2553
GUUUGAAacaucaacaaucacac	chr15:49032607-49032850(-)$1	243	179	202	22.6347
CUCUGUUUUAAAAACUCAGAGGC	chr2:9543571-9543807(+)$1	236	7	30	22.8474
GUUCACCAUUCAUUCAUUUGAAC	chr17:4998976-4999245(+)$1	269	147	170	24.5240
ugucccgauuucuuguagggaca	chr3:8920830-8921070(-)$1	240	11	34	22.2287
CAGUGAAUAGGUAGACGCCACUG	chr6:146231186-146231494(-)$1	308	8	31	23.9560
CAGGACCCCCCAAGUCUUCCUAC	chr19:36506272-36506616(-)$1	344	215	238	21.4388
cuccaaacaccaucauucugggg	chr1:237065052-237065420(+)$1	368	61	84	23.9560
AAGGAAUUAAACUCAACUUCCUA	chr1:240653161-240653387(-)$1	226	162	185	23.4632
agacccauucuaaacAAGGGCAU	chr7:91829016-91829259(-)$1	243	107	130	21.3713
UCUUUUGUAAGUUAAAAAAAAGU	chr2:262557-262885(-)$1	328	24	47	22.5255
AGGAUACUGAUUAUAACAUCCUA	chrX:108935269-108935567(-)$1	298	102	125	23.6586
AGUCAGCACACUCUUAGUGACUC	chr10:117705417-117705646(+)$1	229	20	43	23.5037
UCCAGAGGAUUUUGAAAUUUGGC	chr7:106298209-106298488(-)$1	279	58	81	23.6920
UAUUAUCAAAACUUUCCGUGGUG	chr5:134182346-134182595(+)$1	249	130	153	22.7483
aaaguauacaauuaaauagcuuu	chrX:53220578-53220819(-)$1	241	137	160	23.9560
auacaguauuuguccuuuuguga	chr16:56510457-56510693(+)$1	236	196	219	23.3883
GGUAUAGCAUAAAUUACAUAUUU	chr3:42688480-42688752(+)$1	272	207	230	21.3994
CAGAUACUUACAUGCAAGUCUGG	chr9:131303700-131303941(+)$1	241	211	234	23.0217
UGAGAAGACUCAGGAACAUUUCA	chr4:102014848-102015088(-)$1	240	96	119	24.5240
CACAGCAAGUCCGUAUCCUGGAA	chr2:201735644-201735960(-)$1	316	168	191	21.3213
UUUGGAGAAAAAAAAAAUCCAAA	chr1:233508519-233508776(+)$1	257	174	197	22.7124
AUUAGUAAAAUUGUAUCUUGAUA	chr15:60713883-60714127(-)$1	244	80	103	23.6586
UAcaguaguccccccuuaucugu	chr9:99520192-99520428(-)$1	236	10	33	21.7166
UUGACAUUAUCCAGGCCUAGUCA	chr1:52882908-52883171(+)$1	263	139	162	21.7166
GGCUAUUUUCUCUUCUCGCCGUA	chr17:8370432-8370774(+)$1	342	99	122	21.4002
GAUGGCCACACAGACAACCACUU	chr12:29493969-29494205(-)$1	236	66	89	23.5703
CUGCUGACACGGUUCUAAGCUAA	chr2:65249193-65249470(+)$1	277	248	271	23.9590
gaugucccaaagugcuagauucc	chr4:175240044-175240324(+)$1	280	167	190	22.5422
agaugaucaccacuuucucuucu	chr13:41506779-41507040(-)$1	261	163	186	22.1763
CCAUGUCCCUUGCCCCCAUGUAG	chr18:32720926-32721163(+)$1	237	128	151	21.5870
gauuuuuuuaaaccuauaaacuc	chr4:75048671-75048903(+)$1	232	15	38	21.8428
UAUUCCAUAACUAAUAAGGAAUG	chr10:69829220-69829456(-)$1	236	34	57	21.6135
UGGGCGAAAAGUUCAGAGCAGAG	chr1:204522612-204522837(+)$1	225	167	190	21.4141
GACAGUAUUGAGGUCAUUUGUUA	chrY:15031416-15031645(+)$1	229	41	64	23.6586
UAGCCUUCCUAUUCCACAUGGCU	chr2:172176735-172176970(-)$1	235	172	195	22.8013
UGCAUUUUACAUUUUUUGUGCUG	chr6:53132164-53132460(-)$1	296	267	290	23.1357
GUAUCACUUUACUCCAUUGUUAU	chr10:112658596-112658821(+)$1	225	99	122	21.4432
ggucuuuuuuucucuucagaccu	chr6:153309628-153309877(-)$1	249	22	45	24.3474
AAGGGAACUGUCACUACCCCCUC	chr10:116622454-116622715(+)$1	261	172	195	22.2863
AACCCUCUCUCUUACCUGGGACC	chr19:5843621-5843841(-)$1	220	151	174	21.7882
ACUCACCACUGCCACCCUUGAGU	chr17:8193480-8193892(-)$1	412	342	365	24.5240
cugagccacacaaccucucAUUU	chr9:36215382-36215653(-)$1	271	129	152	21.7839
CAAAGUCUUGACAACAUCUUUGU	chr2:242293261-242293529(+)$1	268	237	260	23.5037
UUCAAAUAACCUCACAUAUUGAA	chr8:91634278-91634541(-)$1	263	100	123	23.3254
GAUGCAAAAAAACAAAAAGCAAC	chr10:11374712-11374963(+)$1	251	25	48	23.3981
GCCCAUUUUCUAUCACACUGGGC	chr12:54105383-54105808(-)$1	425	158	181	24.5240
UCUAUUUUAUUUAAUCCUGUACU	chr11:82985338-82985574(-)$1	236	200	223	23.6331
UUUCUAACAUUUAAAUAAGAAAA	chr2:169629908-169630170(+)$1	262	81	104	24.3396
AAGUAUGCUAUUUAAAUUACUUG	chr20:5528133-5528397(-)$1	264	241	264	23.0217
CACCUGAAAUCAAACCAAAGGAG	chr15:40759098-40759477(+)$1	379	130	153	23.8497
GGGACACAAACACUCCAGUCCCC	chr18:32832117-32832414(-)$1	297	114	137	23.5037
AGAUGCUUAUAGCCACAACAUCU	chr3:150261494-150261757(-)$1	263	95	118	24.5240
AGCCAUUCCGUGCUCUCUGGCAU	chr4:103498778-103499021(+)$1	243	162	185	23.1825
gcuaauuuuucguauuuuuagug	chr5:40762165-40762445(-)$1	280	216	239	23.2135
CCAGGCCUUGGUGCUAACCUGGC	chr20:34843665-34843916(+)$1	251	220	243	23.3910
AAACAUAAUUUUCCUCAGUUCUG	chr8:94743964-94744277(-)$1	313	285	308	23.3205
ACUGCCCCCUCCCCCUCGGCAGU	chr17:27072253-27072505(+)$1	252	107	130	22.2287
CUAAGGAAUUGUACAACAUAGGC	chr9:119462668-119462930(+)$1	262	166	189	23.1193
GCUGUCACUUCUUUUUUACACUC	chr5:41929761-41929986(+)$1	225	98	121	23.3085
augcaggcacacacacaugcaua	chr5:169407482-169407785(+)$1	303	118	141	23.6586
CACACCCCUAACCCACCCUGUGU	chr1:167393972-167394198(+)$1	226	72	95	21.6394
CCAGUUAAUUCUUAACAUCACUG	chr17:42879664-42879920(-)$1	256	131	154	22.8013

#DB
(((.(.............)))))	chr4:763093-763330(+)$1	1	16	39	23.7328
(((((............))))))	chr12:111170522-111170759(-)$1	1	15	38	23.0217
((((((...........))))))	chr13:37596307-37596652(-)$1	1	118	141	22.7163
(((((.............)))))	chr11:94232208-94232451(+)$1	1	116	139	24.5240
((((((...........))))))	chr19:58452567-58452829(-)$1	1	37	60	22.2287
.((((............)))).)	chrX:71417589-71417840(+)$1	1	21	44	22.5933
.((((.............)))).	chr14:21679083-21679381(-)$1	1	58	81	21.5080
(((((.............)))))	chr12:56361990-56362240(+)$1	1	80	103	24.5240
(((((............))).))	chr4:71895204-71895487(+)$1	1	245	268	23.9749
((((((...........)))...	chr21:34963566-34963835(-)$1	1	20	43	23.2553
((.(((...........))).))	chr15:49032607-49032850(-)$1	1	179	202	22.6347
(((((...........)))))((	chr2:9543571-9543807(+)$1	1	7	30	22.8474
(((((.............)))))	chr17:4998976-4999245(+)$1	1	147	170	24.5240
((((((...........))))))	chr3:8920830-8921070(-)$1	1	11	34	22.2287
(((((.............)))))	chr6:146231186-146231494(-)$1	1	8	31	23.9560
.((((............))))..	chr19:36506272-36506616(-)$1	1	215	238	21.4388
(((((.............)))))	chr1:237065052-237065420(+)$1	1	61	84	23.9560
.(((((...........))))).	chr1:240653161-240653387(-)$1	1	162	185	23.4632
((((((...........)))...	chr7:91829016-91829259(-)$1	1	107	130	21.3713
.(((((...........))))).	chr2:262557-262885(-)$1	1	24	47	22.5255
(((((............))))))	chrX:108935269-108935567(-)$1	1	102	125	23.6586
(((((............))))).	chr10:117705417-117705646(+)$1	1	20	43	23.5037
.(((((...........))))).	chr7:106298209-106298488(-)$1	1	58	81	23.6920
((((((...........))))))	chr5:134182346-134182595(+)$1	1	130	153	22.7483
(((((.............)))))	chrX:53220578-53220819(-)$1	1	137	160	23.9560
((((((...........))))).	chr16:56510457-56510693(+)$1	1	196	219	23.3883
(((((............))))))	chr3:42688480-42688752(+)$1	1	207	230	21.3994
(((((............))))))	chr9:131303700-131303941(+)$1	1	211	234	23.0217
(((((.............)))))	chr4:102014848-102015088(-)$1	1	96	119	24.5240
..(((............)))(((	chr2:201735644-201735960(-)$1	1	168	191	21.3213
)(((((...........))))).	chr1:233508519-233508776(+)$1	1	174	197	22.7124
(((((............))))))	chr15:60713883-60714127(-)$1	1	80	103	23.6586
(((((..............))))	chr9:99520192-99520428(-)$1	1	10	33	21.7166
(((((..............))))	chr1:52882908-52883171(+)$1	1	139	162	21.7166
(((..............)))(((	chr17:8370432-8370774(+)$1	1	99	122	21.4002
(.(((............)))...	chr12:29493969-29494205(-)$1	1	66	89	23.5703
..(((............)))...	chr2:65249193-65249470(+)$1	1	248	271	23.9590
((.(((...........))))))	chr4:175240044-175240324(+)$1	1	167	190	22.5422
(((.((...........)).)))	chr13:41506779-41507040(-)$1	1	163	186	22.1763
.((((...........)))).))	chr18:32720926-32721163(+)$1	1	128	151	21.5870
((.(((...........))).))	chr4:75048671-75048903(+)$1	1	15	38	21.8428
((((((...........))))).	chr10:69829220-69829456(-)$1	1	34	57	21.6135
(..((............)).)))	chr1:204522612-204522837(+)$1	1	167	190	21.4141
(((((............))))))	chrY:15031416-15031645(+)$1	1	41	64	23.6586
(((((..............))))	chr2:172176735-172176970(-)$1	1	172	195	22.8013
.((((............)))).)	chr6:53132164-53132460(-)$1	1	267	290	23.1357
(((.((...........)).)))	chr10:112658596-112658821(+)$1	1	99	122	21.4432
(((((............))))).	chr6:153309628-153309877(-)$1	1	22	45	24.3474
)((((.............)))).	chr10:116622454-116622715(+)$1	1	172	195	22.2863
..(((............)))...	chr19:5843621-5843841(-)$1	1	151	174	21.7882
(((((.............)))))	chr17:8193480-8193892(-)$1	1	342	365	24.5240
.((((...........))))...	chr9:36215382-36215653(-)$1	1	129	152	21.7839
(((((............))))).	chr2:242293261-242293529(+)$1	1	237	260	23.5037
(((((.............)))))	chr8:91634278-91634541(-)$1	1	100	123	23.3254
(.(((.............))).)	chr10:11374712-11374963(+)$1	1	25	48	23.3981
(((((.............)))))	chr12:54105383-54105808(-)$1	1	158	181	24.5240
..(((.............)))..	chr11:82985338-82985574(-)$1	1	200	223	23.6331
(((((............))))).	chr2:169629908-169630170(+)$1	1	81	104	24.3396
(((((............))))))	chr20:5528133-5528397(-)$1	1	241	264	23.0217
(.(((.............))).)	chr15:40759098-40759477(+)$1	1	130	153	23.8497
(((((............))))).	chr18:32832117-32832414(-)$1	1	114	137	23.5037
(((((.............)))))	chr3:150261494-150261757(-)$1	1	95	118	24.5240
.((((............))))..	chr4:103498778-103499021(+)$1	1	162	185	23.1825
(((((............))))))	chr5:40762165-40762445(-)$1	1	216	239	23.2135
(((((............))))))	chr20:34843665-34843916(+)$1	1	220	243	23.3910
.(((.............))).))	chr8:94743964-94744277(-)$1	1	285	308	23.3205
((((((...........))))))	chr17:27072253-27072505(+)$1	1	107	130	22.2287
(((.(...........).)))))	chr9:119462668-119462930(+)$1	1	166	189	23.1193
(.(((............))))))	chr5:41929761-41929986(+)$1	1	98	121	23.3085
(((((............))))))	chr5:169407482-169407785(+)$1	1	118	141	23.6586
.((((..............))))	chr1:167393972-167394198(+)$1	1	72	95	21.6394
(((((..............))))	chr17:42879664-42879920(-)$1	1	131	154	22.8013

#PSSM
e : 0.27	f : 0.13	g : 0.12	d : 0.05	! : 0.05	= : 0.04	h : 0.04	$ : 0.02	: : 0.02	i : 0.02	" : 0.02	b : 0.02	[ : 0.02	# : 0.02	& : 0.01	' : 0.01	c : 0.01	E : 0.01	a : 0.01	
e : 0.34	d : 0.15	f : 0.13	g : 0.12	[ : 0.05	! : 0.04	= : 0.02	i : 0.02	c : 0.02	h : 0.01	: : 0.01	b : 0.01	$ : 0.01	
e : 0.33	c : 0.15	f : 0.13	g : 0.12	d : 0.12	[ : 0.04	= : 0.02	i : 0.02	h : 0.01	! : 0.01	
e : 0.30	c : 0.20	f : 0.12	d : 0.12	g : 0.11	[ : 0.05	= : 0.01	h : 0.01	w : 0.01	b : 0.01	i : 0.01	
e : 0.30	c : 0.19	f : 0.12	d : 0.12	g : 0.11	b : 0.04	a : 0.02	= : 0.01	h : 0.01	w : 0.01	i : 0.01	v : 0.01	
u : 0.36	v : 0.25	e : 0.08	w : 0.08	c : 0.06	t : 0.05	f : 0.04	b : 0.02	g : 0.01	= : 0.01	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	t : 0.30	v : 0.25	w : 0.08	
u : 0.36	v : 0.25	t : 0.25	w : 0.08	d : 0.02	e : 0.01	a : 0.01	
v : 0.23	c : 0.18	e : 0.18	f : 0.08	d : 0.08	g : 0.06	w : 0.06	b : 0.04	= : 0.01	h : 0.01	i : 0.01	] : 0.01	
e : 0.29	c : 0.22	g : 0.11	d : 0.11	f : 0.09	w : 0.06	b : 0.04	a : 0.01	= : 0.01	h : 0.01	i : 0.01	
e : 0.31	c : 0.22	f : 0.12	d : 0.12	g : 0.11	] : 0.04	= : 0.02	h : 0.01	i : 0.01	
e : 0.33	f : 0.13	d : 0.13	g : 0.12	] : 0.06	3 : 0.04	c : 0.04	= : 0.02	h : 0.02	7 : 0.01	4 : 0.01	6 : 0.01	i : 0.01	
e : 0.36	f : 0.13	g : 0.12	d : 0.09	] : 0.05	3 : 0.05	= : 0.02	7 : 0.02	h : 0.02	4 : 0.01	c : 0.01	b : 0.01	6 : 0.01	2 : 0.01	i : 0.01	
e : 0.19	f : 0.13	g : 0.12	: : 0.09	3 : 0.06	d : 0.06	h : 0.04	7 : 0.04	2 : 0.04	= : 0.02	4 : 0.02	c : 0.02	b : 0.02	] : 0.01	6 : 0.01	a : 0.01	D : 0.01	i : 0.01	

#score	1655.405918355043
#seq	72
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_UTR_m1_run1.txt

#BEAR
gg"""dddd!!ccc"""bbmmmmbb]ccc]dddd333ggg	chr12:9086384-9086617(+)$1	233	150	190	15.0555
cc$$$$$gggggggbb!!ammmma22bb]ggggggg4444	chr12:53421694-53421932(+)$1	238	189	229	12.9061
####eeeee[eeeee[cccmmmmccc]eeeee]eeeee33	chr10:50732079-50732284(-)$1	205	91	131	14.8473
$$$$ccc[gggggggddddmmmmdddd]gggggggccc44	chr8:26149184-26149418(+)$1	234	59	99	14.2445
"bb!!dddd[iiiiiiiiimmmmiiiiiiiii]dddd22b	chr3:101298533-101298759(+)$1	226	132	172	13.7120
dddd!!ggggggg!!ddddmmmmddddggggggg22dddd	chr1:23884748-23885001(-)$1	253	86	126	14.1607
bb[ddddccc!!ccc[cccooooooccccccccc4444dd	chr19:55857508-55857748(+)$1	240	81	121	13.1640
cc[cccffffff####cccmmmmccc22ffffff]ccc22	chr19:36605037-36605253(-)$1	216	160	200	14.9622
"""a[eeeee!!eeeee[aooooooa]eeeee22eeeee]	chr3:142747340-142747574(+)$1	234	6	46	11.7563
ggggg[ffffff!!ccc[ammmma]ccc4444ffffff]g	chr2:128016877-128017116(-)$1	239	176	216	13.4766
gggggg[a####bb!!cccmmmmccc22bb4444aggggg	chr1:145209133-145209378(+)$1	245	131	171	15.2240
#ffffff!!ffffff!!bbmmmmbb22ffffff]ffffff	chr11:20417372-20417605(+)$1	233	128	168	12.6281
&&=============[ccclllccc]=============>	chr5:180278324-180278587(-)$1	263	50	90	15.2568
!ccc[ddddggggggg[bbmmmmbb]ggggggg>>>>>>>	chr5:151166089-151166333(+)$1	244	19	59	13.6569
gggggg[accc[gggggggnnnnnggggggg]ccc]a]gg	chr3:196295270-196295519(-)$1	249	48	88	12.1417
!ccceeeee!!ccc[aooooooa]ccc22eeeee22ccc4	chr12:7077506-7077739(-)$1	233	61	101	12.0400
[bb[ccc[dddd[ccc[bbmmmmbbccc]dddd]ccc]bb	chr16:90001956-90002198(+)$1	242	61	101	12.7578
ccc"""iiiiiiiii!!bbmmmmbb]iiiiiiiii333cc	chr17:37322656-37322920(+)$1	264	190	230	16.8562
cccbb[a[cccgggggggbblllbb]ggggggg]ccc]a2	chr16:2050995-2051239(-)$1	244	162	202	12.4584
ccc"""bb[ccc"""cccnnnnnccc333ccc]bbccccc	chr10:121335163-121335403(-)$1	240	128	168	13.2610
###eeeee[dddd!!cccammmma]ccc]dddd22eeeee	chr17:74714707-74714961(-)$1	254	15	55	13.5819
hhhhhh!!a"""ccc[cccmmmmccc]ccc22a22hhhhh	chr19:1370602-1370845(+)$1	243	73	113	13.3298
ccggggggg$$$$$cccooooooccc333ggggggg22cc	chr7:5460858-5461096(-)$1	238	129	169	13.4117
c[bbbb!!ccc[gggggggmmmmggggggg]ccc22bb]b	chr22:45736323-45736560(+)$1	237	77	117	12.7143
ddd!!============bbmmmmbb22============2	chr6:139255322-139255565(-)$1	243	159	199	16.7635
iiiiiiiii[ccc"""bboooooobb333ccciiiiiiii	chr16:11931781-11932025(-)$1	244	131	171	14.6610
cc!!dddda[eeeee[cccmmmmccceeeee]a4444ddd	chrX:23801258-23801504(+)$1	246	79	119	14.5794
ffffff[ccc[ccc!!cccmmmmccc22ccccccffffff	chr3:149683893-149684143(-)$1	250	74	114	14.7923
[ccc[a[ggggggg[ddddmmmmdddd]gggggggaccc]	chr1:6273036-6273267(+)$1	231	161	201	15.2281
:::================mmmm================:	chr12:27090758-27091005(-)$1	247	53	93	13.7935
""ffffff!!ccc"""cccmmmmcccccc]ffffff]eee	chr9:37592350-37592638(-)$1	288	73	113	14.9538
fffdddd[ffffff"""ccclllccc]ffffff333dddd	chr5:178044271-178044503(-)$1	232	135	175	12.7672
ccc####ccc[gggggggnnnnngggggggccc333cccd	chr17:655775-656015(-)$1	240	104	144	13.0406
fff]cccggggggg[ddddmmmmdddd4444ggggggg:d	chr7:102096945-102097212(-)$1	267	143	183	12.9211
ddd!!eeeee[ccc[cccnnnnnccc]ccc]eeeee22dd	chr17:19861356-19861610(-)$1	254	41	81	12.1498
c"""============[bbmmmmbb============333	chr14:50087653-50087904(+)$1	251	158	198	17.6958
bb============[ddddmmmmdddd]============	chrX:48566646-48566887(+)$1	241	70	110	16.5166
ddd[dddd!!eeeee[cccmmmmccc]eeeee22dddd]d	chr19:42830272-42830507(+)$1	235	133	173	13.6213
bb[eeeee[dddd####bbmmmmbb333dddd]eeeeebb	chr11:14912872-14913116(-)$1	244	52	92	13.0864
d!!==========!!ddddnnnnndddd==========]d	chr9:33281223-33281428(+)$1	205	20	60	14.0949
b!!dddd[a!!ccc[ddddoooooodddd]ccc22a]ddd	chr10:12391451-12391685(+)$1	234	107	147	12.1056
[cccggggggg[ccc!!bbmmmmbb]ccc]ggggggg]cc	chr6:10404736-10404970(+)$1	234	42	82	15.6978
Ieeeeeeeeee!!ccccccmmmmccc]ccc]eeeee]eee	chr19:13255477-13255706(-)$1	229	153	193	12.7944
dddd[ggggggg[bbddddmmmmdddd]bbgggggggddd	chr2:128615314-128615561(-)$1	247	29	69	12.6831
gggggg[a####bb!!cccmmmmccc22bb4444aggggg	chr1:120612005-120612250(-)$1	245	131	171	15.2240
f============"""bbnnnnnbb4444===========	chr1:36929750-36929986(-)$1	236	48	88	15.1625
b[eeeee####ccc!!ddddllldddd333ccc4444eee	chr2:96549822-96550052(-)$1	230	56	96	12.9262
ccc[ffffff[ccc[a[bbmmmmbba]cccffffff]ccc	chr3:128628760-128629005(+)$1	245	46	86	14.4718
:==========!!a[ddddllldddd]a4444========	chr1:100731807-100732059(+)$1	252	208	248	13.8528
ccceeeeeffffff!!cccmmmmccc22ffffff:ddddq	chr11:122930723-122930942(-)$1	219	137	177	12.7701
:=============!!cccmmmmccc333===========	chr15:45694526-45694765(+)$1	239	14	54	18.3678
[ccc[ccc[a[dddd[cccmmmmccc22dddd]a]ccc]c	chr19:5623065-5623347(+)$1	282	200	240	15.2144
ccc"""bb[eeeee!!cccmmmmccc]eeeeebb]ccc:f	chr2:234959350-234959570(+)$1	220	153	193	13.7437
===========eeeeecccmmmmccc]eeeee22======	chr2:242291281-242291510(+)$1	229	84	124	16.0521
[ccc!!ggggggg"""cccooooooccc]ggggggg4444	chrX:52987781-52988028(+)$1	247	119	159	15.4199
fbb[ddddccc[ddddcccmmmmccc]dddd]ccc]dddd	chr15:44060586-44060818(+)$1	232	127	167	13.0921
bbeeeee[ggggggg[cccmmmmccc]ggggggg22eeee	chr16:67213349-67213563(-)$1	214	74	114	15.5801
affffffccceeeee!!bbmmmmbb22eeeee333ccc22	chr1:235492984-235493222(+)$1	238	62	102	13.6440

#otherMatches

#Seq PSSM
UUCAAUGCUUCCUGCCAAGGCAUCUCCAGUAGCAGAAAGC	chr12:9086384-9086617(+)$1	233	150	190	15.0555
CUAUGAAGACCGAUAUGACAGACGGGAUGAUCGGUCGUGG	chr12:53421694-53421932(+)$1	238	189	229	12.9061
CAAGUUCUGGGGAAGAAGCUGAAGCUGCUUCUGUAGGAGA	chr10:50732079-50732284(-)$1	205	91	131	14.8473
CCCUCUCUACCCCCCCAUCCCCAGGUGAGGGGGGUGAGUU	chr8:26149184-26149418(+)$1	234	59	99	14.2445
ACUAAGACUGUUUCUUCCAGUAAUGGAGGGGAAAGUUCCA	chr3:101298533-101298759(+)$1	226	132	172	13.7120
CCCGCCCAGAACGCAGGUGCUGGCGCCCGUUCUGCCUGGG	chr1:23884748-23885001(-)$1	253	86	126	14.1607
GCAGAUGGGAACGCAGCCUGCGUGAAGGUGCUCCGGGACA	chr19:55857508-55857748(+)$1	240	81	121	13.1640
CCACCCGUGCCAAAAGUGAGCGUUCAGCUGGUACUGGGGA	chr19:36605037-36605253(-)$1	216	160	200	14.9622
GGACGGAAGAUUUUCGUAUGUUCAAAAAUGGAUCUUUUUG	chr3:142747340-142747574(+)$1	234	6	46	11.7563
CUGGCAGCCACUGACCUGGAUGCCGAGGAGGAGGUGGUGG	chr2:128016877-128017116(-)$1	239	176	216	13.4766
GAGGGGAGGAGAGAGUGGGGCUCCUCUAUCGGGACCCCCU	chr1:145209133-145209378(+)$1	245	131	171	15.2240
AAAAUGAAGUAAUUUAUCAAUCUUGCAAAAUUAAUUGUUU	chr11:20417372-20417605(+)$1	233	128	168	12.6281
UUUUAAGAGAGUGAAUAGGUGUCCUUUUCAUUUUCUUGGU	chr5:180278324-180278587(-)$1	263	50	90	15.2568
UUUCCCCUGUGUUUGAUCCUUCAGGUUUGGACAUAUUUGA	chr5:151166089-151166333(+)$1	244	19	59	13.6569
CCUCACGCCUGACGCUCGACGGGAUUGGGCGCCGGCGGGU	chr3:196295270-196295519(-)$1	249	48	88	12.1417
GGGCUGGACUACGAGGAACGAGUGUUGCCGUCCAUUGUCA	chr12:7077506-7077739(-)$1	233	61	101	12.0400
GCCAUGUUCCGGCGCAAGGCCUUCCUGCACUGGUACACGG	chr16:90001956-90002198(+)$1	242	61	101	12.7578
UGUGAAUUUCUUUCUUUGCUUAAGCUGGGGGGAAAAAAAC	chr17:37322656-37322920(+)$1	264	190	230	16.8562
GAGGCAGCGGCGCGGGGACCUGAGGAUCCCCGUGGCCCCC	chr16:2050995-2051239(-)$1	244	162	202	12.4584
GGAUUUGGUGCUCAGCCUCCCCAAGGACAAGCUCCUCCCC	chr10:121335163-121335403(-)$1	240	128	168	13.2610
CCAGUGCGAGUCUGGAUCCGAGGGCGAUGGGACAGUGCAC	chr17:74714707-74714961(-)$1	254	15	55	13.5819
UUGGGGACCAAGCUUCCUCAACUGAGCAAGGGGAGCCCCG	chr19:1370602-1370845(+)$1	243	73	113	13.3298
UCUGGGACUACGCCGAGGCCGAACUUUUAGGUCCCACUGA	chr7:5460858-5461096(-)$1	238	129	169	13.4117
UACACCAAGAGAGCCACAUGGGCAUGUGGCCCUCAAGGCU	chr22:45736323-45736560(+)$1	237	77	117	12.7143
UGACACAGUGUUCCAGCAGGAGGCUAGGUUGGAACACUGC	chr6:139255322-139255565(-)$1	243	159	199	16.7635
aggcuuugccagcaucugagaccccaaaagcugcagaguc	chr16:11931781-11932025(-)$1	244	131	171	14.6610
AGGUUCCUUGGGUCAUGGUGCCAGCCUGACUGAGAAGAGG	chrX:23801258-23801504(+)$1	246	79	119	14.5794
UUUCCUUGUGUACUCCAGCAUUGGUUAUAGUCAUGGGAAA	chr3:149683893-149684143(-)$1	250	74	114	14.7923
CCUACGUCCGCUCCAUUGCCAAGGUGAAGGAGCGGCUGGA	chr1:6273036-6273267(+)$1	231	161	201	15.2281
cccgagugcgugugugugugugcacgcgcacgcgcgcUCC	chr12:27090758-27091005(-)$1	247	53	93	13.7935
AGCGCGGCGGCUGGAAGCUGCUAAGUCAGAGCCGCGAUGU	chr9:37592350-37592638(-)$1	288	73	113	14.9538
GUGGAGACGUUCUAAGAGCAAGAUGUAUAGAAUAUUUUUC	chr5:178044271-178044503(-)$1	232	135	175	12.7672
UCCGGAACGCUGCUGUCUGGAGGGGGCGGCGCGGCAGGAG	chr17:655775-656015(-)$1	240	104	144	13.0406
GGGAUGUGAGGAGGGCAGGGAAAUCUGAGAGCCUCCUUCC	chr7:102096945-102097212(-)$1	267	143	183	12.9211
CAGCACAGUUGUUUAUGACUCAUUCAGAAGGAAUUGACCU	chr17:19861356-19861610(-)$1	254	41	81	12.1498
AGAGGUCUCGGGCCCCAGGACCCCCGGGGCCCGGGAUGAG	chr14:50087653-50087904(+)$1	251	158	198	17.6958
CCUAGGGCUCUUGGGAGCUCUGCGGUUGCUAGGGGCCCUG	chrX:48566646-48566887(+)$1	241	70	110	16.5166
GCAAGGUUCUGGCCAUGGCACUGGUUUUGGCCUUGGCCGU	chr19:42830272-42830507(+)$1	235	133	173	13.6213
UCUGCAGUCGACGAACGACUGGUGUAGGCGUUUGCUGUGA	chr11:14912872-14913116(-)$1	244	52	92	13.0864
UUCAUAUUAUGAUUCAGAAUCAUUUUCUAUUGUGGUAUUA	chr9:33281223-33281428(+)$1	205	20	60	14.0949
GAGGCUGGCAGGCGGCGGCAAAGGAGCCGGCGCGCGGCGG	chr10:12391451-12391685(+)$1	234	107	147	12.1056
CUCGGGUGGUGAGAGCCGCCGCUGCACUUCCGCCACCGUG	chr6:10404736-10404970(+)$1	234	42	82	15.6978
GCCAGGGGCUCUCGGCCACCCUGGUGUGUCUGGGCCAUCU	chr19:13255477-13255706(-)$1	229	153	193	12.7944
GCUUCGCCCAAGGCCCUGCCUCAGCGGCGGCUUGGGCAAG	chr2:128615314-128615561(-)$1	247	29	69	12.6831
GAGGGGAGGAGAGAGUGGGGCUCCUCUAUCGGGACCCCCU	chr1:120612005-120612250(-)$1	245	131	171	15.2240
CGGUCCGUGCCGCAAAGCGAAcggcggccgcggcgcgggc	chr1:36929750-36929986(-)$1	236	48	88	15.1625
CAGGCUACAGGUGAUGAGAAAGAUUCUGUUUCGAAUAUAG	chr2:96549822-96550052(-)$1	230	56	96	12.9262
CCAUGUGGGGGACUGGUCUAGGUAGUGAGUCCCCACUUGG	chr3:128628760-128629005(+)$1	245	46	86	14.4718
AAGGAGGGGAGCUCUCACCACCGGUGUGCUUACUUCUCUU	chr1:100731807-100732059(+)$1	252	208	248	13.8528
GCAAGUUCGGAUUAUUUUAAGAUUAAUUUGAUCCAUCGUA	chr11:122930723-122930942(-)$1	219	137	177	12.7701
UUCCGGCCUGCGAGCUCGGUGUUCCGCUUUUUGUGGGCCG	chr15:45694526-45694765(+)$1	239	14	54	18.3678
CGGCUCUGAGCUCCGCCUCGUCAGAGACCGGGACGCGGCG	chr19:5623065-5623347(+)$1	282	200	240	15.2144
GGUCUUGCUCAGGUAAGGUAUUCACCAACCUGGCCACCUG	chr2:234959350-234959570(+)$1	220	153	193	13.7437
GUUUUCUUUUUUCUAGAAAACACUUUCCUGGAUAAAAAAG	chr2:242291281-242291510(+)$1	229	84	124	16.0521
GACUGCGAGGGGAGAAGGCGUGGAGGUCAUCCCUUCCGGA	chrX:52987781-52988028(+)$1	247	119	159	15.4199
CCUGCAGGAUUACUUUGAUGGCAAUCUGAAGAGAUACCUG	chr15:44060586-44060818(+)$1	232	127	167	13.0921
GGCUCAGAGCACUGCCACCUGCAGGUUGUGGUGCAGCUGA	chr16:67213349-67213563(-)$1	214	74	114	15.5801
CUUCCAAGGAAUCUCAAUCAAAAGGGAGAGAUGGCUCCGA	chr1:235492984-235493222(+)$1	238	62	102	13.6440

#DB
((...((((..(((...((....)).))).))))...)))	chr12:9086384-9086617(+)$1	1	150	190	15.0555
((.....(((((((((..(....)..)).)))))))....	chr12:53421694-53421932(+)$1	1	189	229	12.9061
....(((((.(((((.(((....))).))))).)))))..	chr10:50732079-50732284(-)$1	1	91	131	14.8473
....(((.(((((((((((....)))).))))))))))..	chr8:26149184-26149418(+)$1	1	59	99	14.2445
.((..((((.(((((((((....))))))))).))))..)	chr3:101298533-101298759(+)$1	1	132	172	13.7120
((((..(((((((..((((....)))))))))))..))))	chr1:23884748-23885001(-)$1	1	86	126	14.1607
((.(((((((..(((.(((......)))))))))....))	chr19:55857508-55857748(+)$1	1	81	121	13.1640
((.(((((((((....(((....)))..)))))).)))..	chr19:36605037-36605253(-)$1	1	160	200	14.9622
...(.(((((..(((((.(......).)))))..))))).	chr3:142747340-142747574(+)$1	1	6	46	11.7563
(((((.((((((..(((.(....).)))....)))))).)	chr2:128016877-128017116(-)$1	1	176	216	13.4766
((((((.(....((..(((....)))..))....))))))	chr1:145209133-145209378(+)$1	1	131	171	15.2240
.((((((..((((((..((....))..)))))).))))))	chr11:20417372-20417605(+)$1	1	128	168	12.6281
..(((((((((((((.(((...))).))))))))))))).	chr5:180278324-180278587(-)$1	1	50	90	15.2568
.(((.(((((((((((.((....)).))))))).......	chr5:151166089-151166333(+)$1	1	19	59	13.6569
((((((.((((.(((((((.....))))))).))).).))	chr3:196295270-196295519(-)$1	1	48	88	12.1417
.((((((((..(((.(......).)))..)))))..))).	chr12:7077506-7077739(-)$1	1	61	101	12.0400
.((.(((.((((.(((.((....))))).)))).))).))	chr16:90001956-90002198(+)$1	1	61	101	12.7578
(((...(((((((((..((....)).)))))))))...))	chr17:37322656-37322920(+)$1	1	190	230	16.8562
(((((.(.((((((((((((...)).))))))).))).).	chr16:2050995-2051239(-)$1	1	162	202	12.4584
(((...((.(((...(((.....)))...))).)))))))	chr10:121335163-121335403(-)$1	1	128	168	13.2610
...(((((.((((..((((....).))).))))..)))))	chr17:74714707-74714961(-)$1	1	15	55	13.5819
((((((..(...(((.(((....))).)))..)..)))))	chr19:1370602-1370845(+)$1	1	73	113	13.3298
(((((((((.....(((......)))...)))))))..))	chr7:5460858-5461096(-)$1	1	129	169	13.4117
(.((((..(((.(((((((....))))))).)))..)).)	chr22:45736323-45736560(+)$1	1	77	117	12.7143
(((..((((((((((((((....))..)))))))))))).	chr6:139255322-139255565(-)$1	1	159	199	16.7635
(((((((((.(((...((......))...)))))))))))	chr16:11931781-11932025(-)$1	1	131	171	14.6610
((..(((((.(((((.(((....)))))))).)....)))	chrX:23801258-23801504(+)$1	1	79	119	14.5794
((((((.(((.(((..(((....)))..))))))))))))	chr3:149683893-149684143(-)$1	1	74	114	14.7923
.(((.(.(((((((.((((....)))).))))))))))).	chr1:6273036-6273267(+)$1	1	161	201	15.2281
...((((((((((((((((....)))))))))))))))).	chr12:27090758-27091005(-)$1	1	53	93	13.7935
..((((((..(((...(((....)))))).)))))).)))	chr9:37592350-37592638(-)$1	1	73	113	14.9538
(((((((.((((((...(((...))).))))))...))))	chr5:178044271-178044503(-)$1	1	135	175	12.7672
(((....(((.(((((((.....))))))))))...))))	chr17:655775-656015(-)$1	1	104	144	13.0406
))).)))(((((((.((((....))))....))))))).(	chr7:102096945-102097212(-)$1	1	143	183	12.9211
(((..(((((.(((.(((.....))).))).)))))..))	chr17:19861356-19861610(-)$1	1	41	81	12.1498
(...((((((((((((.((....))))))))))))))...	chr14:50087653-50087904(+)$1	1	158	198	17.6958
((((((((((((((.((((....)))).))))))))))))	chrX:48566646-48566887(+)$1	1	70	110	16.5166
(((.((((..(((((.(((....))).)))))..)))).)	chr19:42830272-42830507(+)$1	1	133	173	13.6213
((.(((((.((((....((....))...)))).)))))))	chr11:14912872-14913116(-)$1	1	52	92	13.0864
(..((((((((((..((((.....)))))))))))))).)	chr9:33281223-33281428(+)$1	1	20	60	14.0949
(..((((.(..(((.((((......)))).)))..).)))	chr10:12391451-12391685(+)$1	1	107	147	12.1056
.((((((((((.(((..((....)).))).))))))).))	chr6:10404736-10404970(+)$1	1	42	82	15.6978
)((((((((((..((((((....))).))).))))).)))	chr19:13255477-13255706(-)$1	1	153	193	12.7944
((((.(((((((.((((((....)))).))))))))))))	chr2:128615314-128615561(-)$1	1	29	69	12.6831
((((((.(....((..(((....)))..))....))))))	chr1:120612005-120612250(-)$1	1	131	171	15.2240
(((((((((((((...((.....))....)))))))))))	chr1:36929750-36929986(-)$1	1	48	88	15.1625
(.(((((....(((..((((...))))...)))....)))	chr2:96549822-96550052(-)$1	1	56	96	12.9262
(((.((((((.(((.(.((....))).))))))))).)))	chr3:128628760-128629005(+)$1	1	46	86	14.4718
.((((((((((..(.((((...)))).)....))))))))	chr1:100731807-100732059(+)$1	1	208	248	13.8528
))))))))((((((..(((....)))..)))))).((((.	chr11:122930723-122930942(-)$1	1	137	177	12.7701
.(((((((((((((..(((....)))...)))))))))))	chr15:45694526-45694765(+)$1	1	14	54	18.3678
.(((.(((.(.((((.(((....)))..)))).).))).)	chr19:5623065-5623347(+)$1	1	200	240	15.2144
(((...((.(((((..(((....))).))))))).))).(	chr2:234959350-234959570(+)$1	1	153	193	13.7437
(((((((((((((((((((....))).)))))..))))))	chr2:242291281-242291510(+)$1	1	84	124	16.0521
.(((..(((((((...(((......))).)))))))....	chrX:52987781-52988028(+)$1	1	119	159	15.4199
(((.(((((((.(((((((....))).)))).))).))))	chr15:44060586-44060818(+)$1	1	127	167	13.0921
))(((((.(((((((.(((....))).)))))))..))))	chr16:67213349-67213563(-)$1	1	74	114	15.5801
(((((((((((((((..((....))..)))))...)))..	chr1:235492984-235493222(+)$1	1	62	102	13.6440

#PSSM
c : 0.22	d : 0.10	b : 0.10	g : 0.08	[ : 0.08	f : 0.08	# : 0.05	" : 0.05	: : 0.05	! : 0.03	$ : 0.01	& : 0.01	h : 0.01	i : 0.01	I : 0.01	= : 0.01	a : 0.01	
c : 0.29	b : 0.12	g : 0.08	d : 0.08	f : 0.08	= : 0.06	" : 0.05	# : 0.03	[ : 0.03	! : 0.03	$ : 0.01	& : 0.01	h : 0.01	i : 0.01	: : 0.01	e : 0.01	
c : 0.22	f : 0.10	= : 0.10	d : 0.08	g : 0.08	b : 0.06	" : 0.05	[ : 0.05	! : 0.05	e : 0.05	$ : 0.03	# : 0.03	h : 0.01	i : 0.01	: : 0.01	
= : 0.13	c : 0.12	e : 0.10	" : 0.08	d : 0.08	g : 0.08	! : 0.06	f : 0.06	[ : 0.06	$ : 0.03	# : 0.03	b : 0.03	a : 0.01	h : 0.01	i : 0.01	] : 0.01	
= : 0.15	e : 0.13	d : 0.10	g : 0.10	! : 0.08	[ : 0.08	f : 0.08	" : 0.06	c : 0.06	b : 0.03	$ : 0.01	h : 0.01	i : 0.01	# : 0.01	
e : 0.17	= : 0.17	d : 0.15	g : 0.10	c : 0.08	f : 0.08	" : 0.05	! : 0.03	[ : 0.03	$ : 0.01	h : 0.01	b : 0.01	i : 0.01	a : 0.01	# : 0.01	
e : 0.17	= : 0.17	d : 0.15	f : 0.10	g : 0.08	[ : 0.08	c : 0.06	i : 0.03	b : 0.03	! : 0.03	$ : 0.01	a : 0.01	# : 0.01	
= : 0.17	g : 0.13	e : 0.13	d : 0.10	[ : 0.10	c : 0.08	f : 0.06	a : 0.05	! : 0.05	i : 0.03	b : 0.03	# : 0.01	
g : 0.17	= : 0.17	c : 0.13	e : 0.08	f : 0.08	[ : 0.08	d : 0.06	# : 0.05	! : 0.05	a : 0.05	i : 0.03	
g : 0.17	= : 0.17	c : 0.15	f : 0.10	! : 0.08	[ : 0.06	e : 0.06	# : 0.05	d : 0.05	i : 0.01	" : 0.01	$ : 0.01	a : 0.01	
g : 0.17	= : 0.17	c : 0.12	e : 0.10	! : 0.08	f : 0.08	[ : 0.08	# : 0.05	d : 0.05	i : 0.03	" : 0.01	$ : 0.01	
g : 0.18	c : 0.17	= : 0.13	e : 0.10	f : 0.08	! : 0.06	[ : 0.06	d : 0.06	i : 0.03	# : 0.03	" : 0.01	$ : 0.01	
c : 0.20	g : 0.20	= : 0.13	e : 0.12	d : 0.06	! : 0.05	f : 0.05	i : 0.03	b : 0.03	[ : 0.03	# : 0.01	" : 0.01	$ : 0.01	
c : 0.20	g : 0.17	e : 0.12	= : 0.10	" : 0.08	! : 0.06	b : 0.05	f : 0.05	i : 0.03	# : 0.03	d : 0.03	$ : 0.01	a : 0.01	
! : 0.17	[ : 0.13	" : 0.12	g : 0.12	c : 0.12	e : 0.10	= : 0.06	b : 0.03	i : 0.03	# : 0.03	d : 0.03	f : 0.01	
! : 0.18	d : 0.17	[ : 0.13	c : 0.12	" : 0.10	g : 0.08	= : 0.05	# : 0.03	e : 0.03	a : 0.03	b : 0.01	i : 0.01	
c : 0.43	d : 0.17	! : 0.08	[ : 0.06	g : 0.06	" : 0.03	= : 0.03	b : 0.03	i : 0.01	e : 0.01	o : 0.01	# : 0.01	
c : 0.41	b : 0.22	d : 0.17	g : 0.06	[ : 0.03	o : 0.03	! : 0.01	i : 0.01	= : 0.01	
c : 0.36	b : 0.20	d : 0.17	a : 0.06	n : 0.06	o : 0.05	g : 0.03	i : 0.01	= : 0.01	
m : 0.68	o : 0.12	n : 0.10	l : 0.03	b : 0.01	c : 0.01	d : 0.01	
m : 0.68	o : 0.12	n : 0.10	l : 0.08	
m : 0.68	o : 0.12	n : 0.10	l : 0.08	
m : 0.68	o : 0.10	n : 0.10	l : 0.05	c : 0.01	a : 0.01	d : 0.01	
c : 0.37	b : 0.22	d : 0.13	o : 0.08	a : 0.05	n : 0.03	g : 0.03	i : 0.01	] : 0.01	= : 0.01	
c : 0.39	b : 0.24	d : 0.15	o : 0.06	g : 0.05	] : 0.03	2 : 0.01	i : 0.01	= : 0.01	
c : 0.46	d : 0.17	] : 0.10	2 : 0.06	g : 0.05	a : 0.03	= : 0.03	i : 0.01	b : 0.01	3 : 0.01	4 : 0.01	
] : 0.22	c : 0.15	d : 0.15	2 : 0.15	g : 0.08	3 : 0.08	= : 0.05	i : 0.03	b : 0.01	e : 0.01	4 : 0.01	
c : 0.20	e : 0.12	g : 0.12	2 : 0.12	3 : 0.10	] : 0.06	= : 0.06	d : 0.05	i : 0.03	f : 0.03	4 : 0.03	b : 0.01	a : 0.01	
c : 0.15	g : 0.15	e : 0.12	= : 0.10	3 : 0.08	] : 0.06	f : 0.06	4 : 0.06	d : 0.06	b : 0.05	i : 0.03	2 : 0.01	
g : 0.20	e : 0.13	c : 0.13	= : 0.13	d : 0.08	] : 0.06	f : 0.06	4 : 0.05	b : 0.05	i : 0.03	3 : 0.01	
g : 0.20	e : 0.13	= : 0.13	c : 0.12	d : 0.10	f : 0.10	4 : 0.08	] : 0.05	i : 0.03	2 : 0.01	
g : 0.20	e : 0.15	c : 0.13	= : 0.13	f : 0.10	d : 0.08	4 : 0.06	] : 0.05	i : 0.03	2 : 0.01	
g : 0.20	= : 0.15	c : 0.13	f : 0.12	] : 0.08	d : 0.05	2 : 0.05	e : 0.05	4 : 0.03	i : 0.03	a : 0.03	b : 0.01	3 : 0.01	
g : 0.17	= : 0.15	2 : 0.10	e : 0.08	c : 0.08	f : 0.08	4 : 0.06	] : 0.05	3 : 0.05	d : 0.03	i : 0.03	b : 0.03	> : 0.01	a : 0.01	
= : 0.17	g : 0.13	2 : 0.12	e : 0.08	f : 0.08	3 : 0.06	c : 0.06	4 : 0.05	] : 0.05	d : 0.03	a : 0.03	i : 0.03	> : 0.01	b : 0.01	: : 0.01	
= : 0.17	g : 0.13	c : 0.13	e : 0.10	f : 0.08	3 : 0.06	2 : 0.06	d : 0.05	4 : 0.05	] : 0.03	a : 0.03	> : 0.01	h : 0.01	i : 0.01	
c : 0.18	= : 0.17	d : 0.10	4 : 0.08	e : 0.08	g : 0.08	] : 0.06	f : 0.05	3 : 0.03	2 : 0.03	> : 0.01	a : 0.01	h : 0.01	b : 0.01	i : 0.01	
c : 0.17	= : 0.15	e : 0.13	d : 0.13	g : 0.06	] : 0.06	4 : 0.05	2 : 0.05	f : 0.05	3 : 0.03	> : 0.01	h : 0.01	b : 0.01	i : 0.01	
d : 0.15	= : 0.13	c : 0.13	e : 0.10	] : 0.08	g : 0.06	4 : 0.05	2 : 0.05	3 : 0.03	f : 0.03	b : 0.03	: : 0.03	> : 0.01	a : 0.01	h : 0.01	i : 0.01	
d : 0.20	c : 0.10	g : 0.08	e : 0.08	= : 0.08	4 : 0.06	b : 0.06	2 : 0.06	f : 0.05	3 : 0.03	] : 0.03	> : 0.03	h : 0.01	i : 0.01	: : 0.01	q : 0.01	

#score	817.0744192214174
#seq	58
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m1_run2.txt

#BEAR
cc!!bbggggggg!!bbmmmmbb22ggggggg]bb2	chr1:1564543-1564772(+)$1	229	67	103	11.8016
ddddffffff####cccmmmmcccffffff4444dd	chr22:41863501-41863760(-)$1	259	40	76	13.3232
wgggggggddddcccooooooccc333ddddeeeee	chr11:50003551-50003810(+)$1	259	134	170	11.5667
[bb[a[eeeeebb[cccmmmmccc22bb]eeeee]a	chr10:46967539-46967798(+)$1	259	13	49	13.3127
h[ggggggg"""a[cccmmmmccca22ggggggg]h	chr3:133293796-133294055(+)$1	259	30	66	15.3261
ffffff!!bb####cccmmmmccc22bb22ffffff	chr10:82271868-82272127(+)$1	259	222	258	13.0394
ccc[==========[bblllbb22==========]c	chr2:70142359-70142588(+)$1	229	62	98	11.2220
ddd[a[dddd####cccmmmmccc333ddddadddd	chr3:127500542-127500801(+)$1	259	92	128	15.1048
eccc!!a[eeeee[cccnnnnnccc]eeeeea22cc	chr6:30994067-30994326(+)$1	259	131	167	11.5364
b!!ccceeeee"""cccmmmmccceeeee]ccc22b	chr15:102245769-102245998(-)$1	229	107	143	14.1416
rccc:ggggggg!!cccmmmmccc22ggggggg:::	chr7:75959328-75959587(+)$1	259	129	165	11.3854
[bb"""iiiiiiiii!!ammmma22iiiiiiiiibb	chr1:7993164-7993423(-)$1	259	137	173	11.5204
!!ccc!!dddd[a[cccmmmmcccadddd4444ccc	chr16:28916232-28916491(-)$1	259	123	159	14.2989
cc[ggggggg####cccmmmmccc]ggggggg]ccc	chr14:67769026-67769285(+)$1	259	210	246	15.9085
ggg"""eeeee"""cccmmmmccc333eeeee4444	chr17:56296431-56296690(+)$1	259	85	121	17.3711
eeee!!dddd[ccc[bbmmmmbbccc]dddd333ee	chr4:75250392-75250651(+)$1	259	119	155	12.5005
iiiiiiiii!!bb[cccmmmmccc]bb]iiiiiiii	chr17:54671689-54671948(-)$1	259	180	216	14.2048
cc[bb"""ggggggg[ammmma]ggggggg]bb]cc	chr17:8439129-8439358(-)$1	229	95	131	11.9015
eee[ffffff"""ddddmmmmdddd333ffffffee	chr6:131215963-131216222(+)$1	259	42	78	12.9385
eeeee!!eeeee[ddddmmmmdddd]eeeeeeeeee	chr4:39246847-39247106(+)$1	259	22	58	11.9803
a[hhhhhhhh####cccmmmmccc]hhhhhhhh]ag	chr1:9713793-9714052(+)$1	259	166	202	12.8450
dddd[ddddcccbbcccmmmmccc22bb]ccc]ddd	chr16:89778374-89778633(+)$1	259	199	235	11.8647
f[iiiiiiiii"""cccooooooccc22iiiiiiii	chr22:20229427-20229656(+)$1	229	18	54	13.5991
cc[a[ccc!!ccc[cccmmmmccc]ccc22ccc]a]	chr5:15936773-15937032(-)$1	259	140	176	14.5233
[bb"""ccc[gggggggmmmmggggggg22ccc333	chr1:21137183-21137442(+)$1	259	102	138	13.1491
ddd!!dddd[bb!!cccmmmmcccbb]dddd4444d	chr10:70516959-70517218(+)$1	259	107	143	13.8928
$$eeeee!!bb[a[cccmmmmccca]bbeeeee555	chr3:8671276-8671535(+)$1	259	82	118	11.4023
eeeee[ccc"""eeeeemmmmeeeee4444ccc22e	chr4:174449854-174450113(+)$1	259	213	249	11.5494
eeeeccc[dddda[cccmmmmccc]a]dddd]ccc2	chr2:237076506-237076765(-)$1	259	146	182	13.9120
fff!!dddd####ddddmmmmdddddddd22fffff	chr19:52940889-52941118(+)$1	229	6	42	11.7785
ggggggg[aeeeeecccmmmmccc]eeeee000000	chr10:99130700-99130959(+)$1	259	194	230	11.5240
!ccc[ggggggg!!bboooooobb22ggggggg22c	chr1:878949-879208(-)$1	259	88	124	12.2816
[eeeee[ccc####cccmmmmcccccc22eeeeebb	chr19:5243969-5244198(+)$1	229	133	169	13.7960
ddd"""dddd[a[ddddnnnnndddd]a]dddd444	chr10:101373555-101373814(+)$1	259	187	223	10.9497
###ggggggg####cccmmmmccc4444gggggggd	chrX:39931699-39931958(+)$1	259	57	93	16.0116
""bb[ffffff!!cccooooooccc22ffffff333	chr3:122353931-122354190(-)$1	259	153	189	12.2724
"a!!a!!eeeeea[bboooooobb]a]eeeee22a2	chr1:236907849-236908078(+)$1	229	149	185	12.0680
e####ggggggg!!cccoooooocccgggggggeee	chr17:79813220-79813449(+)$1	229	147	183	13.1082
"""bb"""bb####bboooooobb333bb333bb33	chr7:150439266-150439495(+)$1	229	155	191	11.9387
hh!!ffffff"""ddddmmmmdddd333ffffff>>	chr17:25628720-25628979(+)$1	259	41	77	13.1035
cbb!!a!!eeeeeacccmmmmccc]a]eeeee22a2	chr17:26731913-26732172(+)$1	259	10	46	14.2832
eee"""bb[ccc[ddddmmmmdddd]ccc]bb4444	chr18:19079975-19080204(+)$1	229	33	69	12.8813
iiiiiii[ccca!!ccclllccc22a]ccc]iiiii	chr11:76376849-76377078(+)$1	229	117	153	13.3530
dd[eeeee!!ddddddddllldddd333dddd333e	chr5:80508243-80508502(-)$1	259	85	121	10.9515
ccc"""ggggggg[cccmmmmcccggggggg66666	chr17:46655414-46655673(+)$1	259	151	187	13.6977
gg####eeeee!!cccnnnnnccc333eeeeegggg	chr5:179125406-179125665(+)$1	259	5	41	13.0285
gggggg[bb[ccc[cccmmmmccc]ccc333bbggg	chrX:117742058-117742317(-)$1	259	216	252	13.5005
eee"""eeeee"""cccnnnnnccc333eeeee22e	chr14:23011008-23011267(+)$1	259	112	148	13.6205
:eeeeea[ccc!!ddddmmmmddddccc]a]eeeee	chr11:1295814-1296043(+)$1	229	56	92	11.4038
:===============mmmm===============:	chr16:28631280-28631539(+)$1	259	32	68	11.4469
ggggggg####cccddddllldddd4444ccc333g	chr22:30928582-30928811(+)$1	229	47	83	11.9720
ggdddd!!dddd[acccmmmmccc]a]dddddddd>	chr10:135103277-135103536(+)$1	259	96	132	13.0077
c!!dddd[bb####cccmmmmcccbbdddd22ccc:	chr2:10930735-10930994(+)$1	259	17	53	12.2877
eee"""a[dddd[ddddllldddddddd]a4444ee	chr12:133354238-133354497(+)$1	259	166	202	11.1724
f$$$$$ccc!!bb!!bbmmmmbb]bb]ccc333fff	chr19:58806557-58806786(+)$1	229	6	42	11.0929
b!!ccc[dddd!!ddddmmmmdddd333ddddccc2	chr16:766454-766713(+)$1	259	208	244	13.2629
c==========[ddddoooooodddd]=========	chr9:71992525-71992784(+)$1	259	174	210	12.4817

#otherMatches

#Seq PSSM
CCACCGCGGUCGGAGCCCGCUGGACCUGGCCGCCGA	chr1:1564543-1564772(+)$1	229	67	103	11.8016
GGAGACUAGUGUAUUUCCCAGGAGACUAGUAUAUUU	chr22:41863501-41863760(-)$1	259	40	76	13.3232
AGGCCAUCACUGUCAGCAGGAUGAUCUCAGUAGCAC	chr11:50003551-50003810(+)$1	259	134	170	11.5667
UGCAGGUGCUGUGCCUUGAUCAAGCCCACCAGCAGC	chr10:46967539-46967798(+)$1	259	13	49	13.3127
GCUUAGUUAUAUGUCUACAAAUAGCUUUAAUUGAUC	chr3:133293796-133294055(+)$1	259	30	66	15.3261
CCUCCAGUGCUCUAGGAUACUUCUCUGUCAUGGAGG	chr10:82271868-82272127(+)$1	259	222	258	13.0394
GCAGUGGGGGUUGGUCCCGUGGCUCCGGCCCCCGGU	chr2:70142359-70142588(+)$1	229	62	98	11.2220
GGUCGUGGGCGAACACCAGCAGGUCCAGCCCCAUCA	chr3:127500542-127500801(+)$1	259	92	128	15.1048
UCUAGUGCAGGCUCUGGGACCACCACAGCUUCUAUG	chr6:30994067-30994326(+)$1	259	131	167	11.5364
GUACAGGUUUGUGUCCACACAUGGUAAACGCUGCUC	chr15:102245769-102245998(-)$1	229	107	143	14.1416
CCAGGAAGAGCGGCGUGCCCCCACAACGUUCUUGUA	chr7:75959328-75959587(+)$1	259	129	165	11.3854
CCUCACGCUCCGUUUCUCUGUUGUUAAACGGGGCAG	chr1:7993164-7993423(-)$1	259	137	173	11.5204
CAGGUGCGCCUAGAGCGGAUCCGCCAGGCUGAGACC	chr16:28916232-28916491(-)$1	259	123	159	14.2989
UAAUGGCAUUGAAAUUCGGGGGAAAGAUGUCAAUGA	chr14:67769026-67769285(+)$1	259	210	246	15.9085
GCGCAAGUUGCGCACGGGGUCCCGGGAGCGAUACAC	chr17:56296431-56296690(+)$1	259	85	121	17.3711
UGCCGCAAGUCUGAAUGGCGCCAUCAAACUUAUGGG	chr4:75250392-75250651(+)$1	259	119	155	12.5005
UCAGAUCCUUUUCCUUGGGGUCAAAGAUAGGGUCUG	chr17:54671689-54671948(-)$1	259	180	216	14.2048
CCUGUCAUUAUCAGGCGAACCCUCCUGGUGUACUGG	chr17:8439129-8439358(-)$1	229	95	131	11.9015
uuuauuuucuuaaaauuuuagaauuaauagaaaaga	chr6:131215963-131216222(+)$1	259	42	78	12.9385
GAUUUUUGAAAGAUAGUAAUAACUGGUUUUUGAAUC	chr4:39246847-39247106(+)$1	259	22	58	11.9803
AGUGCUCUUAAAACCCAGUUGUGgcugagagcggua	chr1:9713793-9714052(+)$1	259	166	202	12.8450
CACCCGGAGAGGCCGGGACGUCCCAGGGACCUCCUC	chr16:89778374-89778633(+)$1	259	199	235	11.8647
CGGAGCCCUCGGGCCGCACUGCAGUGAGCGGGGGCU	chr22:20229427-20229656(+)$1	229	18	54	13.5991
GCGAUGCUCAGGUACCGCAGGCGGGACUCCAGCUUG	chr5:15936773-15937032(-)$1	259	140	176	14.5233
UUCCUUCUCUGUAUCUGAGUCUAGGUACUUGAGUAA	chr1:21137183-21137442(+)$1	259	102	138	13.1491
AUGAUGGUGAAGCUAAAGAAAUUUCUACACCUACCC	chr10:70516959-70517218(+)$1	259	107	143	13.8928
CCCGUGGCAGCCGCUGCACUUGUACCGCCCACGCCC	chr3:8671276-8671535(+)$1	259	82	118	11.4023
ACUCGCGCAGUUCGGCGAAGGCGCUGUUGAUGCUCU	chr4:174449854-174450113(+)$1	259	213	249	11.5494
CGUCUAUGAGCGCAGCGUUCCCGCCGUCGCUGAUGA	chr2:237076506-237076765(-)$1	259	146	182	13.9120
UGAGUGAAGUGAUGCAGAAUCUUGUUUUCUGUCAGA	chr19:52940889-52941118(+)$1	229	6	42	11.7785
CCACGGAGCAUCCCCCAGCACUGGAGGGAUUCUGAG	chr10:99130700-99130959(+)$1	259	194	230	11.5240
GCAGUGGCAGGGUCUCCCCGUCGAUCCCCUGCUCCC	chr1:878949-879208(-)$1	259	88	124	12.2816
UAGCCGCGGAUCAGGCCGUUGGGCUCCACCGGCUCC	chr19:5243969-5244198(+)$1	229	133	169	13.7960
ACACUGGGCAGACCUUCUACAUGGAGCUGUGCCAAU	chr10:101373555-101373814(+)$1	259	187	223	10.9497
CAGCCUCAUCAGCUCCAUCUUUGGUAUAGGUGGGGG	chrX:39931699-39931958(+)$1	259	57	93	16.0116
UUUCCCAGCACAACUUCUAUUAAAGCCGUGCUGAUU	chr3:122353931-122354190(-)$1	259	153	189	12.2724
GCACGAGGCGUUCGAGAGCGACCUGGCAGCGCACCA	chr1:236907849-236908078(+)$1	229	149	185	12.0680
CAAGGACUCUGCAGCUGCGCCGUCAGGCAGGGUGGU	chr17:79813220-79813449(+)$1	229	147	183	13.1082
GUGCCAGGUGAAAACAGGAACAUGGAACGGGAGGAA	chr7:150439266-150439495(+)$1	229	155	191	11.9387
ACAUGUAUUGUUGGUUAUAUAUGAUAUCCAGUAUUU	chr17:25628720-25628979(+)$1	259	41	77	13.1035
CUGGACUUCUCUGGGGCGGGAGCCACAUAGAGCUGG	chr17:26731913-26732172(+)$1	259	10	46	14.2832
GGCCUACAGUCUCCUGGGCUCCCAGAAGAGUGGCAA	chr18:19079975-19080204(+)$1	229	33	69	12.8813
AGGGCCAGGAGCAGCAGGAUCUGGGGUCUCAUGGCU	chr11:76376849-76377078(+)$1	229	117	153	13.3530
CUUAGCAGCAGGCUGUGUCACACGCUGAGGCUCACC	chr5:80508243-80508502(-)$1	259	85	121	10.9515
GCGUAGUACCCGGGCGAGUGGUCGCUGGGUAGGUAA	chr17:46655414-46655673(+)$1	259	151	187	13.6977
CGGAGCAGUGCACGCCAAUCCGGCCAGGCGCUCGCG	chr5:179125406-179125665(+)$1	259	5	41	13.0285
UAUGAAUGAUCUUAGAUAACUAUCCAAGCCUUCUUC	chrX:117742058-117742317(-)$1	259	216	252	13.5005
GUAAAGCACCAUCUGAUUGUGUGUUUUCUGGUGGCU	chr14:23011008-23011267(+)$1	259	112	148	13.6205
AUGGCACAGUCAGGCUGUCCUUAGUGACCGCUGCCA	chr11:1295814-1296043(+)$1	229	56	92	11.4038
auuguguguguguguguguguauauACACACACAAA	chr16:28631280-28631539(+)$1	259	32	68	11.4469
AUGUGGUACCAGACAGGGCUGCCCUCACCGUCGUGG	chr22:30928582-30928811(+)$1	229	47	83	11.9720
CUGCUGCUGGACGAUGGUGUACCGCUGGUCCCAGUA	chr10:135103277-135103536(+)$1	259	96	132	13.0077
CUUUACUACCUCAUAGGGAGGCCUGGAGUAUUGGAA	chr2:10930735-10930994(+)$1	259	17	53	12.2877
AGCCACGUUGUCCAUGCCCUGCGUGACACCCACAGC	chr12:133354238-133354497(+)$1	259	166	202	11.1724
GACAGACCCUUCAAAUGUAAUCAGUGUGGGAAGUGU	chr19:58806557-58806786(+)$1	229	6	42	11.0929
GAUCGCUAGGCAUGGCCCCCAGGCCCACGUCUGUGU	chr16:766454-766713(+)$1	259	208	244	13.2629
UGUGGGUUCUGAAGACUGAAGUGUCUCCAGAACUCA	chr9:71992525-71992784(+)$1	259	174	210	12.4817

#DB
((..(((((((((..((....))..))))))).)).	chr1:1564543-1564772(+)$1	1	67	103	11.8016
((((((((((....(((....)))))))))....))	chr22:41863501-41863760(-)$1	1	40	76	13.3232
.)))))))(((((((......)))...))))(((((	chr11:50003551-50003810(+)$1	1	134	170	11.5667
.((.(.(((((((.(((....)))..)).))))).)	chr10:46967539-46967798(+)$1	1	13	49	13.3127
(.(((((((...(.(((....))))..))))))).)	chr3:133293796-133294055(+)$1	1	30	66	15.3261
((((((..((....(((....)))..))..))))))	chr10:82271868-82272127(+)$1	1	222	258	13.0394
(((.((((((((((.((...))..)))))))))).)	chr2:70142359-70142588(+)$1	1	62	98	11.2220
(((.(.((((....(((....)))...)))))))))	chr3:127500542-127500801(+)$1	1	92	128	15.1048
((((..(.(((((.(((.....))).))))))..))	chr6:30994067-30994326(+)$1	1	131	167	11.5364
(..((((((((...(((....)))))))).)))..)	chr15:102245769-102245998(-)$1	1	107	143	14.1416
.))).(((((((..(((....)))..)))))))...	chr7:75959328-75959587(+)$1	1	129	165	11.3854
.((...(((((((((..(....)..)))))))))))	chr1:7993164-7993423(-)$1	1	137	173	11.5204
..(((..((((.(.(((....))))))))....)))	chr16:28916232-28916491(-)$1	1	123	159	14.2989
((.(((((((....(((....))).))))))).)))	chr14:67769026-67769285(+)$1	1	210	246	15.9085
(((...(((((...(((....)))...)))))....	chr17:56296431-56296690(+)$1	1	85	121	17.3711
((((..((((.(((.((....))))).))))...))	chr4:75250392-75250651(+)$1	1	119	155	12.5005
(((((((((..((.(((....))).)).))))))))	chr17:54671689-54671948(-)$1	1	180	216	14.2048
((.((...(((((((.(....).))))))).)).))	chr17:8439129-8439358(-)$1	1	95	131	11.9015
(((.((((((...((((....))))...))))))))	chr6:131215963-131216222(+)$1	1	42	78	12.9385
(((((..(((((.((((....)))).))))))))))	chr4:39246847-39247106(+)$1	1	22	58	11.9803
(.((((((((....(((....))).)))))))).))	chr1:9713793-9714052(+)$1	1	166	202	12.8450
((((.((((((((((((....)))..)).))).)))	chr16:89778374-89778633(+)$1	1	199	235	11.8647
(.(((((((((...(((......)))..))))))))	chr22:20229427-20229656(+)$1	1	18	54	13.5991
((.(.(((..(((.(((....))).)))..))).).	chr5:15936773-15937032(-)$1	1	140	176	14.5233
.((...(((.(((((((....)))))))..)))...	chr1:21137183-21137442(+)$1	1	102	138	13.1491
(((..((((.((..(((....))))).))))....)	chr10:70516959-70517218(+)$1	1	107	143	13.8928
..(((((..((.(.(((....)))).)))))))...	chr3:8671276-8671535(+)$1	1	82	118	11.4023
(((((.(((...(((((....)))))....)))..)	chr4:174449854-174450113(+)$1	1	213	249	11.5494
(((((((.(((((.(((....))).).)))).))).	chr2:237076506-237076765(-)$1	1	146	182	13.9120
(((..((((....((((....))))))))..)))))	chr19:52940889-52941118(+)$1	1	6	42	11.7785
(((((((.(((((((((....))).)))))......	chr10:99130700-99130959(+)$1	1	194	230	11.5240
.(((.(((((((..((......))..)))))))..)	chr1:878949-879208(-)$1	1	88	124	12.2816
.(((((.(((....(((....))))))..)))))))	chr19:5243969-5244198(+)$1	1	133	169	13.7960
(((...((((.(.((((.....)))).).))))...	chr10:101373555-101373814(+)$1	1	187	223	10.9497
...(((((((....(((....)))....))))))))	chrX:39931699-39931958(+)$1	1	57	93	16.0116
..((.((((((..(((......)))..))))))...	chr3:122353931-122354190(-)$1	1	153	189	12.2724
.(..(..((((((.((......)).).)))))..).	chr1:236907849-236908078(+)$1	1	149	185	12.0680
(....(((((((..(((......)))))))))))))	chr17:79813220-79813449(+)$1	1	147	183	13.1082
...((...((....((......))...))...))..	chr7:150439266-150439495(+)$1	1	155	191	11.9387
((..((((((...((((....))))...))))))..	chr17:25628720-25628979(+)$1	1	41	77	13.1035
(((..(..(((((((((....))).).)))))..).	chr17:26731913-26732172(+)$1	1	10	46	14.2832
(((...((.(((.((((....)))).))).))....	chr18:19079975-19080204(+)$1	1	33	69	12.8813
(((((((.((((..(((...)))..).))).)))))	chr11:76376849-76377078(+)$1	1	117	153	13.3530
((.(((((..((((((((...))))...))))...)	chr5:80508243-80508502(-)$1	1	85	121	10.9515
(((...(((((((.(((....)))))))))).....	chr17:46655414-46655673(+)$1	1	151	187	13.6977
((....(((((..(((.....)))...)))))))))	chr5:179125406-179125665(+)$1	1	5	41	13.0285
((((((.((.(((.(((....))).)))...)))))	chrX:117742058-117742317(-)$1	1	216	252	13.5005
(((...(((((...(((.....)))...)))))..)	chr14:23011008-23011267(+)$1	1	112	148	13.6205
.((((((.(((..((((....))))))).).)))))	chr11:1295814-1296043(+)$1	1	56	92	11.4038
.(((((((((((((((....))))))))))))))).	chr16:28631280-28631539(+)$1	1	32	68	11.4469
(((((((....(((((((...))))....)))...)	chr22:30928582-30928811(+)$1	1	47	83	11.9720
((((((..((((.((((....))).).)))))))).	chr10:135103277-135103536(+)$1	1	96	132	13.0077
(..((((.((....(((....)))))))))..))).	chr2:10930735-10930994(+)$1	1	17	53	12.2877
(((...(.((((.((((...)))))))).)....))	chr12:133354238-133354497(+)$1	1	166	202	11.1724
(.....(((..((..((....)).)).)))...)))	chr19:58806557-58806786(+)$1	1	6	42	11.0929
(..(((.((((..((((....))))...))))))).	chr16:766454-766713(+)$1	1	208	244	13.2629
)((((((((((.((((......)))).)))))))))	chr9:71992525-71992784(+)$1	1	174	210	12.4817

#PSSM
e : 0.17	c : 0.15	d : 0.10	g : 0.10	[ : 0.07	f : 0.07	" : 0.05	h : 0.03	b : 0.03	! : 0.03	i : 0.03	: : 0.03	w : 0.01	r : 0.01	a : 0.01	$ : 0.01	# : 0.01	
e : 0.17	c : 0.15	g : 0.12	d : 0.10	b : 0.07	! : 0.07	[ : 0.05	f : 0.03	i : 0.03	$ : 0.03	# : 0.03	" : 0.03	= : 0.03	a : 0.01	h : 0.01	
e : 0.19	! : 0.10	d : 0.10	g : 0.10	c : 0.10	b : 0.08	[ : 0.07	i : 0.05	# : 0.05	f : 0.03	= : 0.03	h : 0.01	" : 0.01	$ : 0.01	
" : 0.14	e : 0.14	g : 0.12	! : 0.10	c : 0.10	d : 0.07	[ : 0.07	i : 0.05	b : 0.05	# : 0.03	= : 0.03	f : 0.01	h : 0.01	a : 0.01	$ : 0.01	
" : 0.14	g : 0.12	e : 0.10	! : 0.08	f : 0.07	c : 0.07	[ : 0.07	b : 0.05	a : 0.05	= : 0.05	i : 0.05	# : 0.03	d : 0.03	: : 0.01	h : 0.01	$ : 0.01	
g : 0.17	" : 0.17	f : 0.08	! : 0.08	d : 0.08	c : 0.07	e : 0.07	[ : 0.05	= : 0.05	i : 0.05	b : 0.01	h : 0.01	a : 0.01	# : 0.01	$ : 0.01	
g : 0.19	e : 0.12	d : 0.12	! : 0.10	c : 0.08	f : 0.07	i : 0.07	= : 0.05	a : 0.05	[ : 0.05	" : 0.03	h : 0.01	b : 0.01	
g : 0.15	e : 0.14	d : 0.14	[ : 0.12	c : 0.08	f : 0.07	! : 0.07	= : 0.05	i : 0.05	" : 0.03	b : 0.03	h : 0.01	# : 0.01	
d : 0.21	g : 0.15	e : 0.15	c : 0.10	f : 0.07	b : 0.07	= : 0.05	i : 0.05	! : 0.05	h : 0.01	a : 0.01	[ : 0.01	# : 0.01	
e : 0.17	d : 0.15	g : 0.14	c : 0.08	f : 0.07	b : 0.07	! : 0.07	= : 0.05	[ : 0.05	" : 0.03	i : 0.03	# : 0.03	h : 0.01	
# : 0.19	e : 0.17	g : 0.12	d : 0.12	c : 0.10	" : 0.07	= : 0.05	i : 0.03	[ : 0.03	! : 0.03	b : 0.03	f : 0.01	
# : 0.17	" : 0.14	g : 0.12	c : 0.10	d : 0.08	e : 0.08	b : 0.07	! : 0.07	[ : 0.05	= : 0.03	a : 0.03	i : 0.01	
# : 0.17	! : 0.15	" : 0.10	c : 0.08	a : 0.08	[ : 0.08	g : 0.07	b : 0.07	e : 0.07	= : 0.03	d : 0.03	i : 0.01	
[ : 0.19	d : 0.19	# : 0.15	! : 0.12	c : 0.08	" : 0.07	= : 0.03	g : 0.03	e : 0.03	a : 0.03	i : 0.01	b : 0.01	
c : 0.57	d : 0.21	b : 0.05	! : 0.03	[ : 0.03	g : 0.03	i : 0.01	e : 0.01	= : 0.01	
c : 0.56	d : 0.21	b : 0.12	o : 0.01	! : 0.01	[ : 0.01	g : 0.01	e : 0.01	= : 0.01	
c : 0.52	d : 0.19	o : 0.10	b : 0.07	! : 0.01	a : 0.01	g : 0.01	e : 0.01	n : 0.01	m : 0.01	
m : 0.68	o : 0.14	n : 0.07	l : 0.05	d : 0.03	a : 0.01	
m : 0.70	o : 0.14	l : 0.08	n : 0.07	
m : 0.70	o : 0.14	l : 0.08	n : 0.07	
m : 0.68	o : 0.14	n : 0.07	l : 0.03	b : 0.01	c : 0.01	= : 0.01	d : 0.01	
c : 0.49	d : 0.17	o : 0.12	b : 0.07	n : 0.05	m : 0.01	a : 0.01	g : 0.01	e : 0.01	= : 0.01	
c : 0.54	d : 0.21	b : 0.10	o : 0.03	2 : 0.01	a : 0.01	] : 0.01	g : 0.01	e : 0.01	= : 0.01	
c : 0.57	d : 0.21	2 : 0.07	b : 0.05	g : 0.03	e : 0.01	= : 0.01	] : 0.01	
d : 0.21	] : 0.17	2 : 0.14	c : 0.12	3 : 0.08	a : 0.05	g : 0.05	b : 0.05	= : 0.03	e : 0.03	f : 0.01	4 : 0.01	
3 : 0.17	2 : 0.12	c : 0.12	g : 0.08	d : 0.08	a : 0.08	] : 0.07	b : 0.07	e : 0.05	= : 0.03	4 : 0.03	f : 0.01	i : 0.01	h : 0.01	
3 : 0.17	] : 0.17	g : 0.14	b : 0.08	c : 0.08	e : 0.07	d : 0.07	2 : 0.05	4 : 0.05	= : 0.03	f : 0.01	i : 0.01	h : 0.01	
d : 0.17	g : 0.15	e : 0.14	c : 0.10	b : 0.08	3 : 0.08	= : 0.05	4 : 0.05	f : 0.03	2 : 0.03	i : 0.01	] : 0.01	h : 0.01	a : 0.01	
d : 0.19	e : 0.17	g : 0.15	] : 0.08	f : 0.07	2 : 0.07	= : 0.05	i : 0.05	c : 0.05	4 : 0.03	h : 0.01	b : 0.01	3 : 0.01	
e : 0.19	d : 0.17	g : 0.15	f : 0.07	2 : 0.07	c : 0.07	= : 0.05	i : 0.05	] : 0.03	4 : 0.03	3 : 0.03	a : 0.03	h : 0.01	
e : 0.17	d : 0.15	g : 0.14	c : 0.10	f : 0.07	4 : 0.05	= : 0.05	i : 0.05	] : 0.05	3 : 0.05	2 : 0.03	h : 0.01	0 : 0.01	b : 0.01	
e : 0.19	g : 0.12	c : 0.10	f : 0.08	4 : 0.07	i : 0.07	d : 0.07	= : 0.05	3 : 0.05	b : 0.05	a : 0.03	h : 0.01	] : 0.01	0 : 0.01	6 : 0.01	2 : 0.01	
e : 0.12	c : 0.12	4 : 0.10	g : 0.10	f : 0.08	i : 0.07	3 : 0.07	] : 0.05	= : 0.05	d : 0.05	2 : 0.05	b : 0.05	h : 0.01	0 : 0.01	6 : 0.01	
2 : 0.12	4 : 0.10	e : 0.10	f : 0.08	c : 0.08	3 : 0.08	g : 0.07	i : 0.07	= : 0.05	d : 0.05	] : 0.05	b : 0.03	: : 0.01	5 : 0.01	0 : 0.01	6 : 0.01	
e : 0.12	c : 0.12	3 : 0.08	d : 0.07	2 : 0.07	4 : 0.07	a : 0.07	b : 0.05	] : 0.05	f : 0.05	i : 0.05	g : 0.05	= : 0.03	: : 0.01	5 : 0.01	0 : 0.01	> : 0.01	6 : 0.01	
e : 0.17	c : 0.10	2 : 0.08	d : 0.08	g : 0.07	f : 0.05	b : 0.05	: : 0.05	4 : 0.05	i : 0.05	3 : 0.05	> : 0.03	a : 0.01	h : 0.01	] : 0.01	5 : 0.01	0 : 0.01	6 : 0.01	= : 0.01	

#score	733.4013674900627
#seq	57
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_UTR_m3_run1.txt

#BEAR
eeeee[a[ddddmmmmdddd22a]eee	chr17:47131617-47131896(+)$1	279	224	251	10.1846
cggggggg[ccclllccc22ggggggg	chr20:43118614-43118847(+)$1	233	109	136	10.0731
gggggg[cccooooooccc]ggggggg	chr3:8921821-8922052(-)$1	231	185	212	9.4514
eeee[cccddddmmmmdddd]ccc]ee	chr2:26411270-26411505(+)$1	235	80	107	10.3638
dddd####ddddmmmmdddd333dddd	chr21:35279544-35279780(-)$1	236	10	37	10.4981
hhhiiiiiiiiimmmmiiiiiiiii>>	chr8:81431766-81431990(+)$1	224	119	146	10.8461
!!dddd!!ddddmmmmdddd333dddd	chr10:104498661-104498911(+)$1	250	36	63	10.7210
eeffffff[cccmmmmcccffffffFF	chr12:50393300-50393526(-)$1	226	188	215	10.3103
nncccgggggggmmmmgggggggffff	chr17:38326640-38326900(+)$1	260	9	36	9.7469
ddd[dddd[cccmmmmccc22dddddd	chr16:1415747-1415986(-)$1	239	75	102	10.5247
+++iiiiiiiiimmmmiiiiiiiiigg	chr6:111620626-111620878(-)$1	252	143	170	10.2051
b[ffffff!!bbmmmmbb22ffffff]	chr7:5566982-5567232(-)$1	250	187	214	10.2342
[==========nnnnn==========]	chr1:236647582-236647816(+)$1	234	17	44	9.2413
ffff[a!!ddddmmmmdddd]a]ffff	chrX:41208576-41208828(+)$1	252	43	70	10.5858
ggg!!dddd[bbmmmmbbdddd]gggg	chr11:65111164-65111406(+)$1	242	144	171	10.0177
d[a[bb[a[cccmmmmcccabb22a]d	chr1:38265930-38266189(+)$1	259	167	194	10.9784
b===========mmmm===========	chr1:156712826-156713126(-)$1	300	171	198	12.5225
dddd[gggggggmmmmggggggg]ddd	chr20:34213894-34214146(-)$1	252	17	44	10.7730
[===========lll===========]	chr12:6632021-6632264(+)$1	243	18	45	10.9290
!!bb[ccc[ccclllccc333ccc]bb	chr14:105261850-105262098(-)$1	248	190	217	9.7764
ggggggg[ddddmmmmdddd333gggg	chr1:203278390-203278629(+)$1	239	18	45	11.6556
[dddd[bb[cccmmmmcccbb]dddd]	chr20:62331373-62331675(-)$1	302	194	221	10.6899
""bb[ddddcccmmmmccc]dddd]bb	chr17:79477065-79477333(-)$1	268	216	243	10.1398
fffff[ccc[bbmmmmbb]ccc]ffff	chr17:79506842-79507128(-)$1	286	111	138	10.3193
[dddd[bb[cccmmmmccc]bbdddd]	chr17:1422227-1422468(-)$1	241	117	144	11.0697
ddd[bb"""cccmmmmccc]bb]dddd	chr11:62481235-62481516(-)$1	281	222	249	10.9734
ffff####ddddmmmmdddd22fffff	chr17:79268746-79269005(-)$1	259	48	75	10.2283
dddd[gggggggmmmmggggggg]ddd	chr19:42799383-42799618(+)$1	235	119	146	10.7730
gggggg"""cccmmmmccc>>>>>>>>	chr17:76989028-76989279(-)$1	251	110	137	10.8490
fffff[bb[cccmmmmcccbb]fffff	chr19:59056287-59056530(+)$1	243	9	36	10.8126
eecccccc[cccmmmmccc22ccceee	chr12:69233063-69233347(+)$1	284	54	81	11.9691
e[a!!gggggggmmmmggggggg22ae	chr7:95034283-95034510(-)$1	227	96	123	11.1133
ccc####eeeeemmmmeeeee22ccc4	chr11:94924659-94924865(-)$1	206	128	155	9.4124
$$$$$gggggggmmmmggggggg4444	chr1:113243769-113244013(-)$1	244	15	42	10.5616
Ha[a[ccc!!bbmmmmbb22ccc]a]a	chr9:21974817-21975094(-)$1	277	212	239	10.4059
eeee!!a!!cccmmmmccc22a22eee	chr15:32930447-32930707(+)$1	260	124	151	12.0674
[a[bb"""ddddmmmmdddd22bb]ac	chr19:42365083-42365333(+)$1	250	41	68	9.9403
%gggggggddddmmmmdddd]gggggg	chr17:29701383-29701642(+)$1	259	215	242	10.7040
cc[eeeee!!bbmmmmbb333eeeeec	chr3:48199561-48199797(-)$1	236	58	85	10.4724
$$gggggggcccmmmmccc]ggggggg	chrX:41378496-41378732(-)$1	236	131	158	12.5682
!!bb!!bbddddmmmmdddd]bb333b	chr17:4851537-4851777(-)$1	240	14	41	9.8750
!===========mmmm===========	chr6:46113841-46114072(+)$1	231	184	211	12.9939
[dddd[bb[cccmmmmccc]bbdddd]	chr9:130551848-130552135(+)$1	287	150	177	11.0697
f!!ffffffcccmmmmccc]ffffff3	chr19:50979759-50979991(+)$1	232	111	138	11.4933
c[ffffff[cccmmmmcccffffff]c	chr20:62590333-62590599(-)$1	266	175	202	11.4070
d[a[ccc!!cccmmmmccc22ccc]a]	chr15:34393845-34394116(-)$1	271	53	80	12.5987
d####bbbbcccmmmmccc]bb4444b	chr9:135767579-135767812(-)$1	233	75	102	10.4047
ee[iiiiiiiiimmmmiiiiiiiii]e	chr8:30535689-30535950(-)$1	261	69	96	11.7940
$$$$eeeeecccmmmmccc4444eeee	chr8:105501922-105502167(-)$1	245	96	123	10.6862
[ccc"""eeeeemmmmeeeee333ccc	chr1:1716986-1717255(-)$1	269	207	234	10.2761
iggggggg[cccmmmmccc]ggggggg	chr17:77082109-77082382(+)$1	273	239	266	12.9980
""ccc[ccc[bbmmmmbb]ccc]ccc3	chrX:103438852-103439115(+)$1	263	12	39	11.1330
###ffffff[bbmmmmbb]ffffff]f	chr1:150190988-150191234(-)$1	246	156	183	9.9777
[ggggggg[cccmmmmccc]ggggggg	chr7:2702777-2703071(+)$1	294	74	101	13.1897
eeeee####cccmmmmccc4444eeee	chr16:30681941-30682184(+)$1	243	150	177	11.7705
+++iiiiiiiiimmmmiiiiiiiii33	chr12:6857395-6857666(-)$1	271	220	247	10.2547
c!!cccccc[bbmmmmbbccc22ccc3	chr6:26104365-26104622(+)$1	257	47	74	10.8358
[ddddccc[cccmmmmccc]ccc]ddd	chr6:36853639-36853882(+)$1	243	107	134	11.7873
ccffffff!!bbmmmmbb22fffffff	chr4:120419608-120419839(-)$1	231	65	92	10.1437
iiiiiii"""ccclllccc22iiiiii	chr16:29827555-29827839(+)$1	284	82	109	10.2675
bggggggg!!bbmmmmbb4444ggggg	chr9:139249203-139249488(+)$1	285	33	60	11.5891

#otherMatches

#Seq PSSM
GGGGAACAGGCAGGCCUGCCAGGAUCC	chr17:47131617-47131896(+)$1	279	224	251	10.1846
GGGUUUGGAAAGCACCUUAACUGAAUC	chr20:43118614-43118847(+)$1	233	109	136	10.0731
GUGUUUUCACAGUGAAGUGCAGACAUU	chr3:8921821-8922052(-)$1	231	185	212	9.4514
GGCUGGGGGCACCACUGUGUACCUGGG	chr2:26411270-26411505(+)$1	235	80	107	10.3638
UUCACUCUGGCAGAUUUGCUUGCUGAA	chr21:35279544-35279780(-)$1	236	10	37	10.4981
AAACUGUAGGGUCAAAGCCUUAUAGCa	chr8:81431766-81431990(+)$1	224	119	146	10.8461
AUUUGGAACCUUCUAAGAGGAAAUCAA	chr10:104498661-104498911(+)$1	250	36	63	10.7210
UGGUUUCUUAGAACCCUCUGGAGGCGG	chr12:50393300-50393526(-)$1	226	188	215	10.3103
AAGGCCCACUAACACUUUGGUGGUUCU	chr17:38326640-38326900(+)$1	260	9	36	9.7469
UGGUCCUGACACUACUGUGACUAGGCC	chr16:1415747-1415986(-)$1	239	75	102	10.5247
AUACAAAUGAUUUUCAAGUUGUUUGGU	chr6:111620626-111620878(-)$1	252	143	170	10.2051
CCUCUCCCAAGUCCACACAGGGGAGGU	chr7:5566982-5567232(-)$1	250	187	214	10.2342
CCUUCAUCACUGACCUGGUGGUGGGGC	chr1:236647582-236647816(+)$1	234	17	44	9.2413
UGGAGAUUGUUGAACGCAGCUUGUCUA	chrX:41208576-41208828(+)$1	252	43	70	10.5858
GUGAGGGGCCAGCGUGCUGCCUGCAUC	chr11:65111164-65111406(+)$1	242	144	171	10.0177
GGCAGGUGACUGAACUUAGCCCAGGGC	chr1:38265930-38266189(+)$1	259	167	194	10.9784
UUUCCAGGCUUCUGCUGGGGCCUGGGA	chr1:156712826-156713126(-)$1	300	171	198	12.5225
UGUGUCCCAGAGGUCCCUCUGGGCCAC	chr20:34213894-34214146(-)$1	252	17	44	10.7730
GGUACCCCAGGCCCUGUUUGGGGUGCG	chr12:6632021-6632264(+)$1	243	18	45	10.9290
cagcgccggcccgcggggaugcggagc	chr14:105261850-105262098(-)$1	248	190	217	9.7764
UGCAGGCUGUGUUCUUGCAUCUUGUCU	chr1:203278390-203278629(+)$1	239	18	45	11.6556
GCUCAGGCUGGCUUGGGCUGCAUGAGG	chr20:62331373-62331675(-)$1	302	194	221	10.6899
CGCAAUUCUCGAUUCUUUGAAGAGAUG	chr17:79477065-79477333(-)$1	268	216	243	10.1398
GUGCUCGCGCCGCUCCCGCUGCAGGCA	chr17:79506842-79507128(-)$1	286	111	138	10.3193
UCCCUGUGGCCCUCCUGGGGCAAGGGU	chr17:1422227-1422468(-)$1	241	117	144	11.0697
GUCAGCCAAGAGCUUACUCAGCAGACA	chr11:62481235-62481516(-)$1	281	222	249	10.9734
GGGGUCCGGAGGUUGACCUCGCCCCCG	chr17:79268746-79269005(-)$1	259	48	75	10.2283
AGCUCCCUCCCGGUGCUGGGGGGCAGC	chr19:42799383-42799618(+)$1	235	119	146	10.7730
CUGCAGAUCCUUGGAAAAGAAAAUGUU	chr17:76989028-76989279(-)$1	251	110	137	10.8490
CGCUGGAGCUGCUGGAGCACUGCGGCG	chr19:59056287-59056530(+)$1	243	9	36	10.8126
GUUGGGCCCUUCGUGAGAAUUGGCUUC	chr12:69233063-69233347(+)$1	284	54	81	11.9691
UCGAAUAAAGUGAAUACAUUUUGCACA	chr7:95034283-95034510(-)$1	227	96	123	11.1133
GUACUAACUUUCUUGUGGAAGAAUACU	chr11:94924659-94924865(-)$1	206	128	155	9.4124
CCUCCCUCCCAGCGCUCUGGGAGCCAC	chr1:113243769-113244013(-)$1	244	15	42	10.5616
GUGCGCUCGGCGGCUGCGGAGAGGGGG	chr9:21974817-21975094(-)$1	277	212	239	10.4059
AGACUUUACCUUUCUAAAGAAAUUGUU	chr15:32930447-32930707(+)$1	260	124	151	12.0674
AUGGGGUAGUUUGUGGAGAUGACUGAA	chr19:42365083-42365333(+)$1	250	41	68	9.9403
AUUUUUCAAGAUACAAGUUUAUGAGAG	chr17:29701383-29701642(+)$1	259	215	242	10.7040
UGAGGUCCUGGUGAGAGCGUUGGACCC	chr3:48199561-48199797(-)$1	236	58	85	10.4724
ACCAGUUUAGGCAUUUGCUAUAAACUG	chrX:41378496-41378732(-)$1	236	131	158	12.5682
CCGCCAGCCGAGGCAGCUCGAGCCCAG	chr17:4851537-4851777(-)$1	240	14	41	9.8750
CAUAAGAAUUUAUAGAUAAAUUCUUGU	chr6:46113841-46114072(+)$1	231	184	211	12.9939
GAGGGCACUGGAGCUGUCUUGUCCUUG	chr9:130551848-130552135(+)$1	287	150	177	11.0697
CGAGCCCGGGGCAGCGGCUGCCGGGCC	chr19:50979759-50979991(+)$1	232	111	138	11.4933
UCCAGUGUUCAGCCUUCUGGCACUGCA	chr20:62590333-62590599(-)$1	266	175	202	11.4070
GGUCUGAGUGCAGAGCUGCUGUCAUGG	chr15:34393845-34394116(-)$1	271	53	80	12.5987
GUUUACAUCCAGAGUUCUGUGACACAU	chr9:135767579-135767812(-)$1	233	75	102	10.4047
aaaaauauauauauauauauauauUAU	chr8:30535689-30535950(-)$1	261	69	96	11.7940
AUACAGGGUUGCGCUUGCAUUGGACCC	chr8:105501922-105502167(-)$1	245	96	123	10.6862
AGGUUCUGUGGGACCCCCCGCCCCGCC	chr1:1716986-1717255(-)$1	269	207	234	10.2761
UGGAGCCUGUCCCCAAGGAAGGGUUCC	chr17:77082109-77082382(+)$1	273	239	266	12.9980
UCAGAAAAGCUUGUUUGAUCUUCUCUA	chrX:103438852-103439115(+)$1	263	12	39	11.1330
UCCAGAUAACUUUUAAGACUUAUUUAG	chr1:150190988-150191234(-)$1	246	156	183	9.9777
GUGCAGGGGUCAAGGCUGGGCCCUGCA	chr7:2702777-2703071(+)$1	294	74	101	13.1897
ACUUGCGAAUAUUUAUAUAAAAACGAG	chr16:30681941-30682184(+)$1	243	150	177	11.7705
GCCAUGCAUUGAAGGGUCAAUGCAUUU	chr12:6857395-6857666(-)$1	271	220	247	10.2547
AAAACUGUCACAGCCAUGGAUGUAGUA	chr6:26104365-26104622(+)$1	257	47	74	10.8358
UCGCCCGGCGGCAGCUGUCCCCGAGGC	chr6:36853639-36853882(+)$1	243	107	134	11.7873
CCAGGCCAAGCGGAACUGAGUGGCCUA	chr4:120419608-120419839(-)$1	231	65	92	10.1437
CUCGGAGUACCGAACCUCGAUCUCCGG	chr16:29827555-29827839(+)$1	284	82	109	10.2675
CACACAGCAGACACCGGUGAGGGCUGU	chr9:139249203-139249488(+)$1	285	33	60	11.5891

#DB
(((((.(.((((....))))..).)))	chr17:47131617-47131896(+)$1	1	224	251	10.1846
)(((((((.(((...)))..)))))))	chr20:43118614-43118847(+)$1	1	109	136	10.0731
((((((.(((......))).)))))))	chr3:8921821-8922052(-)$1	1	185	212	9.4514
((((.(((((((....)))).))).))	chr2:26411270-26411505(+)$1	1	80	107	10.3638
((((....((((....))))...))))	chr21:35279544-35279780(-)$1	1	10	37	10.4981
((((((((((((....)))))))))..	chr8:81431766-81431990(+)$1	1	119	146	10.8461
..((((..((((....))))...))))	chr10:104498661-104498911(+)$1	1	36	63	10.7210
))((((((.(((....)))))))))))	chr12:50393300-50393526(-)$1	1	188	215	10.3103
..)))(((((((....)))))))((((	chr17:38326640-38326900(+)$1	1	9	36	9.7469
(((.((((.(((....)))..))))))	chr16:1415747-1415986(-)$1	1	75	102	10.5247
...(((((((((....)))))))))))	chr6:111620626-111620878(-)$1	1	143	170	10.2051
(.((((((..((....))..)))))).	chr7:5566982-5567232(-)$1	1	187	214	10.2342
.((((((((((.....)))))))))).	chr1:236647582-236647816(+)$1	1	17	44	9.2413
((((.(..((((....)))).).))))	chrX:41208576-41208828(+)$1	1	43	70	10.5858
(((..((((.((....)))))).))))	chr11:65111164-65111406(+)$1	1	144	171	10.0177
(.(.((.(.(((....))))))..).)	chr1:38265930-38266189(+)$1	1	167	194	10.9784
((((((((((((....)))))))))))	chr1:156712826-156713126(-)$1	1	171	198	12.5225
((((.(((((((....))))))).)))	chr20:34213894-34214146(-)$1	1	17	44	10.7730
.(((((((((((...))))))))))).	chr12:6632021-6632264(+)$1	1	18	45	10.9290
..((.(((.(((...)))...))).))	chr14:105261850-105262098(-)$1	1	190	217	9.7764
(((((((.((((....))))...))))	chr1:203278390-203278629(+)$1	1	18	45	11.6556
.((((.((.(((....))))).)))).	chr20:62331373-62331675(-)$1	1	194	221	10.6899
..((.(((((((....))).)))).))	chr17:79477065-79477333(-)$1	1	216	243	10.1398
(((((.(((.((....)).))).))))	chr17:79506842-79507128(-)$1	1	111	138	10.3193
.((((.((.(((....))).)))))).	chr17:1422227-1422468(-)$1	1	117	144	11.0697
(((.((...(((....))).)).))))	chr11:62481235-62481516(-)$1	1	222	249	10.9734
((((....((((....))))..)))))	chr17:79268746-79269005(-)$1	1	48	75	10.2283
((((.(((((((....))))))).)))	chr19:42799383-42799618(+)$1	1	119	146	10.7730
((((((...(((....)))........	chr17:76989028-76989279(-)$1	1	110	137	10.8490
(((((.((.(((....))))).)))))	chr19:59056287-59056530(+)$1	1	9	36	10.8126
)))))(((.(((....)))..)))(((	chr12:69233063-69233347(+)$1	1	54	81	11.9691
(.(..(((((((....)))))))..))	chr7:95034283-95034510(-)$1	1	96	123	11.1133
(((....(((((....)))))..))).	chr11:94924659-94924865(-)$1	1	128	155	9.4124
.....(((((((....)))))))....	chr1:113243769-113244013(-)$1	1	15	42	10.5616
)(.(.(((..((....))..))).).)	chr9:21974817-21975094(-)$1	1	212	239	10.4059
((((..(..(((....)))..)..)))	chr15:32930447-32930707(+)$1	1	124	151	12.0674
.(.((...((((....))))..)).))	chr19:42365083-42365333(+)$1	1	41	68	9.9403
.(((((((((((....)))).))))))	chr17:29701383-29701642(+)$1	1	215	242	10.7040
((.(((((..((....))...))))))	chr3:48199561-48199797(-)$1	1	58	85	10.4724
..((((((((((....))).)))))))	chrX:41378496-41378732(-)$1	1	131	158	12.5682
..((..((((((....)))).))...)	chr17:4851537-4851777(-)$1	1	14	41	9.8750
.(((((((((((....)))))))))))	chr6:46113841-46114072(+)$1	1	184	211	12.9939
.((((.((.(((....))).)))))).	chr9:130551848-130552135(+)$1	1	150	177	11.0697
(..(((((((((....))).)))))).	chr19:50979759-50979991(+)$1	1	111	138	11.4933
(.((((((.(((....))))))))).)	chr20:62590333-62590599(-)$1	1	175	202	11.4070
(.(.(((..(((....)))..))).).	chr15:34393845-34394116(-)$1	1	53	80	12.5987
(....(((((((....))).))....)	chr9:135767579-135767812(-)$1	1	75	102	10.4047
((.(((((((((....))))))))).)	chr8:30535689-30535950(-)$1	1	69	96	11.7940
....((((((((....)))....))))	chr8:105501922-105502167(-)$1	1	96	123	10.6862
.(((...(((((....)))))...)))	chr1:1716986-1717255(-)$1	1	207	234	10.2761
)(((((((.(((....))).)))))))	chr17:77082109-77082382(+)$1	1	239	266	12.9980
..(((.(((.((....)).))).))).	chrX:103438852-103439115(+)$1	1	12	39	11.1330
...((((((.((....)).)))))).)	chr1:150190988-150191234(-)$1	1	156	183	9.9777
.(((((((.(((....))).)))))))	chr7:2702777-2703071(+)$1	1	74	101	13.1897
(((((....(((....)))....))))	chr16:30681941-30682184(+)$1	1	150	177	11.7705
...(((((((((....)))))))))..	chr12:6857395-6857666(-)$1	1	220	247	10.2547
(..((((((.((....)))))..))).	chr6:26104365-26104622(+)$1	1	47	74	10.8358
.(((((((.(((....))).))).)))	chr6:36853639-36853882(+)$1	1	107	134	11.7873
))((((((..((....))..))))))(	chr4:120419608-120419839(-)$1	1	65	92	10.1437
(((((((...(((...)))..))))))	chr16:29827555-29827839(+)$1	1	82	109	10.2675
((((((((..((....))....)))))	chr9:139249203-139249488(+)$1	1	33	60	11.5891

#PSSM
[ : 0.14	e : 0.13	d : 0.13	c : 0.09	f : 0.08	g : 0.06	! : 0.06	b : 0.04	$ : 0.04	+ : 0.03	" : 0.03	i : 0.03	h : 0.01	n : 0.01	H : 0.01	% : 0.01	# : 0.01	
g : 0.14	d : 0.14	e : 0.11	! : 0.08	[ : 0.08	= : 0.06	f : 0.06	c : 0.06	$ : 0.04	+ : 0.03	" : 0.03	a : 0.03	# : 0.03	h : 0.01	n : 0.01	i : 0.01	
g : 0.16	d : 0.16	f : 0.13	c : 0.08	e : 0.06	= : 0.06	[ : 0.06	a : 0.04	b : 0.04	+ : 0.03	$ : 0.03	! : 0.03	# : 0.03	h : 0.01	i : 0.01	
f : 0.16	g : 0.14	d : 0.13	e : 0.08	i : 0.08	c : 0.08	[ : 0.06	= : 0.06	b : 0.06	! : 0.03	# : 0.03	$ : 0.03	a : 0.01	
g : 0.14	f : 0.13	[ : 0.11	d : 0.09	i : 0.08	c : 0.08	e : 0.06	# : 0.06	= : 0.06	! : 0.06	b : 0.04	$ : 0.01	" : 0.01	
g : 0.22	[ : 0.11	c : 0.11	f : 0.09	i : 0.08	# : 0.06	d : 0.06	= : 0.06	b : 0.04	! : 0.03	" : 0.03	e : 0.03	a : 0.01	
g : 0.19	c : 0.14	f : 0.09	b : 0.09	i : 0.08	# : 0.06	= : 0.06	" : 0.06	d : 0.04	a : 0.03	[ : 0.03	! : 0.03	e : 0.03	
g : 0.18	c : 0.14	f : 0.09	b : 0.09	i : 0.06	! : 0.06	= : 0.06	" : 0.06	e : 0.06	# : 0.04	d : 0.04	[ : 0.03	a : 0.01	
[ : 0.22	d : 0.19	! : 0.11	g : 0.09	c : 0.06	i : 0.06	= : 0.06	" : 0.04	e : 0.04	f : 0.03	b : 0.01	# : 0.01	
c : 0.40	d : 0.16	g : 0.08	! : 0.08	[ : 0.08	i : 0.06	= : 0.06	e : 0.03	" : 0.01	
c : 0.40	d : 0.16	b : 0.16	g : 0.08	i : 0.06	= : 0.06	e : 0.03	o : 0.01	
c : 0.40	d : 0.16	b : 0.16	g : 0.08	i : 0.06	= : 0.04	e : 0.03	o : 0.01	n : 0.01	
m : 0.90	l : 0.04	o : 0.01	n : 0.01	c : 0.01	
m : 0.90	l : 0.06	o : 0.01	n : 0.01	
m : 0.90	l : 0.06	o : 0.01	n : 0.01	
m : 0.90	c : 0.03	o : 0.01	n : 0.01	= : 0.01	l : 0.01	
c : 0.42	d : 0.16	b : 0.16	g : 0.08	i : 0.06	= : 0.06	e : 0.03	
c : 0.42	d : 0.16	b : 0.16	g : 0.08	i : 0.06	= : 0.06	e : 0.03	
c : 0.40	d : 0.18	g : 0.08	2 : 0.06	i : 0.06	= : 0.06	] : 0.04	3 : 0.03	e : 0.03	4 : 0.01	
d : 0.18	] : 0.18	2 : 0.14	g : 0.08	i : 0.06	= : 0.06	f : 0.04	c : 0.04	4 : 0.04	3 : 0.03	b : 0.03	e : 0.03	a : 0.01	> : 0.01	
g : 0.16	2 : 0.13	b : 0.11	f : 0.09	3 : 0.08	c : 0.08	] : 0.06	i : 0.06	= : 0.06	4 : 0.04	d : 0.03	e : 0.03	> : 0.01	
g : 0.18	c : 0.13	f : 0.09	b : 0.09	2 : 0.08	i : 0.08	3 : 0.06	= : 0.06	d : 0.04	4 : 0.04	a : 0.03	] : 0.03	> : 0.01	e : 0.01	
g : 0.19	f : 0.13	c : 0.09	i : 0.08	d : 0.08	] : 0.08	3 : 0.06	= : 0.06	2 : 0.06	4 : 0.04	b : 0.03	a : 0.01	> : 0.01	e : 0.01	
f : 0.18	g : 0.14	d : 0.13	c : 0.11	] : 0.08	i : 0.08	= : 0.06	2 : 0.04	e : 0.04	4 : 0.03	3 : 0.03	> : 0.01	b : 0.01	
f : 0.18	d : 0.16	g : 0.14	e : 0.09	] : 0.08	i : 0.08	= : 0.06	c : 0.06	a : 0.03	4 : 0.03	> : 0.01	2 : 0.01	3 : 0.01	
g : 0.16	d : 0.16	f : 0.13	e : 0.11	] : 0.08	= : 0.06	c : 0.06	a : 0.04	> : 0.03	b : 0.03	4 : 0.03	3 : 0.03	F : 0.01	i : 0.01	
g : 0.16	e : 0.13	d : 0.13	f : 0.11	] : 0.11	b : 0.06	c : 0.06	3 : 0.06	> : 0.03	= : 0.03	4 : 0.03	F : 0.01	a : 0.01	i : 0.01	

#score	661.2572642064218
#seq	61
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m3_run1.txt

#BEAR
eeeeeddddoooooodddd22eeeee	chr13:113709593-113709865(+)$1	272	231	257	11.3253
d[ccc[cccooooooccc]ccc]ddd	chr3:59882328-59882572(-)$1	244	201	227	13.4898
===========mmmm===========	chr9:95244247-95244483(+)$1	236	160	186	10.7986
ggg####bboooooobb333gggggg	chr3:59844329-59844567(-)$1	238	73	99	13.6382
""ddddcccooooooccc22dddddd	chr16:12578402-12578647(+)$1	245	126	152	12.0303
=========nnnnn==========33	chr13:45125337-45125718(-)$1	381	216	242	11.5610
!!gggggggooooooggggggg]eee	chr11:65904566-65904792(+)$1	226	78	104	13.9924
%ccc[ddddooooooddddcccgggg	chr4:4542823-4543083(-)$1	260	36	62	12.0444
hhh"""cccooooooccchhhhhhhh	chr10:50686224-50686452(-)$1	228	172	198	11.9190
fff[a[cccooooooccc]a333fff	chr12:104860249-104860505(+)$1	256	12	38	13.6037
iiiii[cccooooooccc]iiiiiii	chr11:3991849-3992103(+)$1	254	187	213	15.0956
gdddd!!bboooooobb22dddd22g	chr10:30019205-30019430(-)$1	225	148	174	11.0866
i[gggggggooooooggggggg]iii	chr12:13817962-13818228(-)$1	266	51	77	14.4354
e[ccc!!bboooooobb22ccc]eee	chr6:89477746-89477986(-)$1	240	136	162	12.7397
"""bbddddoooooodddd]bb333d	chr3:33247795-33248051(-)$1	256	15	41	12.1607
ddd!!ddddoooooodddd4444ddd	chr14:68624705-68624932(+)$1	227	167	193	12.0832
ffff!!cccoooooocccffffff66	chr8:130939705-130940024(-)$1	319	14	40	11.8011
=====[cccooooooccc========	chr10:115478307-115478523(+)$1	216	63	89	15.4917
fffff[cccooooooccc]ffffff:	chr7:47836101-47836317(+)$1	216	164	190	11.6013
ccgggggggooooooggggggg:hhh	chr12:5672007-5672229(-)$1	222	28	54	11.9286
[eeeee[bboooooobb]eeeee]ee	chr3:44399785-44400111(+)$1	326	278	304	11.9472
=========oooooo===========	chr4:123211837-123212106(+)$1	269	179	205	15.6194
gggg[ddddoooooodddd]gggggg	chr2:152332803-152333020(+)$1	217	129	155	13.3431
b[ccc!!bboooooobb22ccc]bbb	chr11:120813713-120813971(+)$1	258	137	163	11.9350
c!!ffffffooooooffffff22ccc	chr3:43368929-43369147(+)$1	218	14	40	12.0269
dd[ffffffooooooffffff]dddd	chr5:65359584-65359894(+)$1	310	101	127	11.3367
=========lll==========333e	chr1:172628960-172629174(+)$1	214	30	56	11.6152
####eeeeeooooooeeeeedddd]a	chr3:10395214-10395435(-)$1	221	122	148	12.0477
"""ffffffooooooffffff333ee	chr11:28209862-28210077(+)$1	215	82	108	12.7189
eee!!ddddoooooodddd]eeeee4	chr12:13369364-13369585(+)$1	221	24	50	12.1441
iiiiiiiirrrrrrrrriiiiiiiii	chr9:37291668-37291918(+)$1	250	3	29	10.0799
b[eeeee[aooooooaeeeee333bb	chr5:1244130-1244352(+)$1	222	192	218	12.1460
=======rrrrrrrrr==========	chr1:32651491-32651755(+)$1	264	195	221	10.6575
iiiiiiiiillliiiiiiiii22ggg	chr1:205387377-205387594(-)$1	217	51	77	10.0015
ggggg!!cccnnnnncccggggggg3	chr16:2541858-2542089(+)$1	231	189	215	10.1470
===="""bboooooobb4444=====	chr12:58091544-58091881(+)$1	337	300	326	14.2041
ffffeeeeeooooooeeeee]fffff	chr8:67071275-67071494(+)$1	219	11	37	11.4316
iiiiii[bboooooobb22iiiiiii	chr3:188593275-188593521(+)$1	246	137	163	14.0106
ddd"""cccooooooccc22dddd33	chr5:43609788-43610066(+)$1	278	116	142	12.6788
=========oooooo===========	chr7:137300128-137300418(-)$1	290	146	172	15.6194
iiiiiiiiiooooooiiiiiiiii55	chr13:28818626-28818883(+)$1	257	35	61	13.2903
i!!ccc[cccnnnnncccccc4444i	chr1:240529879-240530113(+)$1	234	166	192	9.6344
ff[ffffffooooooffffff]ffff	chr13:40164736-40164958(-)$1	222	123	149	11.4829
iiiiiiiiiooooooiiiiiiiii:f	chr7:139833985-139834237(-)$1	252	159	185	13.6631
iiiiiiiiiooooooiiiiiiiii::	chr15:56455116-56455366(-)$1	250	221	247	12.7958
iiiiiii[bbnnnnnbb]iiiiiiii	chr13:47178797-47179027(+)$1	230	61	87	9.8863
ddd[a[ddddoooooodddd]a]ddd	chr17:62128249-62128504(-)$1	255	91	117	10.6957
"cccaddddoooooodddd]a]ccc3	chr11:19482064-19482300(+)$1	236	96	122	12.6175
gggg[ddddooooooddddggggggg	chr11:77095725-77095948(-)$1	223	193	219	13.2851
####eeeeeooooooeeeee22dddd	chr1:84632459-84632684(+)$1	225	71	97	11.9246
ggg[eeeeeooooooeeeee]ggggg	chr21:40621727-40621986(-)$1	259	218	244	13.0452
""gggggggooooooggggggg333d	chr2:73816719-73816938(+)$1	219	155	181	14.2737
eee"""cccooooooccc333eeeee	chrX:152102571-152102787(+)$1	216	38	64	13.4477
####eeeeeooooooeeeee4444ee	chr2:242263637-242263885(+)$1	248	13	39	12.6949

#otherMatches

#Seq PSSM
GUGAAACGUAGAAGAGCGUGAUUCAU	chr13:113709593-113709865(+)$1	272	231	257	11.3253
UAAAAUUAUUUCAUUAUACUUUCAUU	chr3:59882328-59882572(-)$1	244	201	227	13.4898
UAGGUACAAAUUUAGGUUUGUAUUUA	chr9:95244247-95244483(+)$1	236	160	186	10.7986
uauauauacucauuuguucaauauua	chr3:59844329-59844567(-)$1	238	73	99	13.6382
cuggaauggccauucccagauuccua	chr16:12578402-12578647(+)$1	245	126	152	12.0303
UUUGUUUUAGUUUUUGAGACAGGGUc	chr13:45125337-45125718(-)$1	381	216	242	11.5610
aaggccuuguccacuugaggcuguuu	chr11:65904566-65904792(+)$1	226	78	104	13.9924
UAAGUAGGACUCAGUUCCUCUUGAGA	chr4:4542823-4543083(-)$1	260	36	62	12.0444
GGCUAGGCCCGCUGUGGCGUCUGCCC	chr10:50686224-50686452(-)$1	228	172	198	11.9190
gccagcggccaaacagccccaaaggc	chr12:104860249-104860505(+)$1	256	12	38	13.6037
gauauacgugaaguaaugaauaucaa	chr11:3991849-3992103(+)$1	254	187	213	15.0956
GGAGGUUGAGUCUCAUCUUCUUCUAC	chr10:30019205-30019430(-)$1	225	148	174	11.0866
aaaggggggagaaagCUUUCUUGUAU	chr12:13817962-13818228(-)$1	266	51	77	14.4354
AAUGUUUGUGGCUUAAUUUACAAUUG	chr6:89477746-89477986(-)$1	240	136	162	12.7397
UGAUCCAGUCAAGCAACUGAGAGAUG	chr3:33247795-33248051(-)$1	256	15	41	12.1607
CUGCCUUGACUAAACUCAAUGAACAG	chr14:68624705-68624932(+)$1	227	167	193	12.0832
uCAUACUGUAUUUUAAUAAUGAAAAU	chr8:130939705-130940024(-)$1	319	14	40	11.8011
auccauggccaacuugcuuggauuug	chr10:115478307-115478523(+)$1	216	63	89	15.4917
uuuuacacauccaauuguuuaaaaaa	chr7:47836101-47836317(+)$1	216	164	190	11.6013
CACUGGGGUCUCUCCACCCCAGAGUC	chr12:5672007-5672229(-)$1	222	28	54	11.9286
auaaguaaucuagaaaugacuuaaag	chr3:44399785-44400111(+)$1	326	278	304	11.9472
uauuauauaacauacuauauaauaua	chr4:123211837-123212106(+)$1	269	179	205	15.6194
ACUUCUUCUUUGAAUAGAAUGAGUGA	chr2:152332803-152333020(+)$1	217	129	155	13.3431
acacacacacCCCCCUGACUGUUUGG	chr11:120813713-120813971(+)$1	258	137	163	11.9350
UUUUAGAACAUUCUAGUUCUAUUGCU	chr3:43368929-43369147(+)$1	218	14	40	12.0269
AUUUAUAUACACACUUAUAUACGUAC	chr5:65359584-65359894(+)$1	310	101	127	11.3367
CUUUUAAGUUUUGCUUGGAAGUAAAU	chr1:172628960-172629174(+)$1	214	30	56	11.6152
CUCAGAACUUCCCACAGUUCCCAGUG	chr3:10395214-10395435(-)$1	221	122	148	12.0477
UAAAAUGUCAAGUCAGAUAUUAUUCA	chr11:28209862-28210077(+)$1	215	82	108	12.7189
CAUUAUGAUUUCAUUAUCACAUGAUU	chr12:13369364-13369585(+)$1	221	24	50	12.1441
uuuguuuuuguuuuuuugagauggaa	chr9:37291668-37291918(+)$1	250	3	29	10.0799
CCCCAGGGCUGGUCUGCCUGGUCUGC	chr5:1244130-1244352(+)$1	222	192	218	12.1460
augucauaccugccuaaugacauucu	chr1:32651491-32651755(+)$1	264	195	221	10.6575
CAGGGGUCUCCAGGAUCUCUGGGCUU	chr1:205387377-205387594(-)$1	217	51	77	10.0015
ccaggcuggucuugaacuccugggcu	chr16:2541858-2542089(+)$1	231	189	215	10.1470
ucccucacuaagauaagcucugggaa	chr12:58091544-58091881(+)$1	337	300	326	14.2041
cacuaaaauuuacccauuuuaagugu	chr8:67071275-67071494(+)$1	219	11	37	11.4316
CUGCAACUGAAAUUACAUAUUGCAGG	chr3:188593275-188593521(+)$1	246	137	163	14.0106
cuacauccuccuaguagguauagguc	chr5:43609788-43610066(+)$1	278	116	142	12.6788
acauauacacaUAUAUGUAUAUGUAU	chr7:137300128-137300418(-)$1	290	146	172	15.6194
AACAUAAAGUAUAACCUUUAUGUUUU	chr13:28818626-28818883(+)$1	257	35	61	13.2903
ucuccacguuggucaggcuggucuca	chr1:240529879-240530113(+)$1	234	166	192	9.6344
UACUUACAUGAUUCAAUGUAAAUAUC	chr13:40164736-40164958(-)$1	222	123	149	11.4829
gcugugACUACUCAAGGUCAUAGCCU	chr7:139833985-139834237(-)$1	252	159	185	13.6631
GUAAGAUUUAUCUCAGAAUCUUAUUU	chr15:56455116-56455366(-)$1	250	221	247	12.7958
gcuuugAACUAGGUGAGCUUAGAGCA	chr13:47178797-47179027(+)$1	230	61	87	9.8863
ccaaccuggaaaccccuucaagcugg	chr17:62128249-62128504(-)$1	255	91	117	10.6957
acaggguggggaacaucacacacugg	chr11:19482064-19482300(+)$1	236	96	122	12.6175
ucuauggauuugccuauucuggacau	chr11:77095725-77095948(-)$1	223	193	219	13.2851
CUACAUUUUCUCCAAAAAAUCUCAUC	chr1:84632459-84632684(+)$1	225	71	97	11.9246
uuguuaaaaaauauguuuuaccagau	chr21:40621727-40621986(-)$1	259	218	244	13.0452
cccaggagcacccagguuccugucag	chr2:73816719-73816938(+)$1	219	155	181	14.2737
CAGCCUGCAUCUUUUUGCCAUCUGCA	chrX:152102571-152102787(+)$1	216	38	64	13.4477
UCUAAGGUAAGAUCAUACUUCAUGUA	chr2:242263637-242263885(+)$1	248	13	39	12.6949

#DB
(((((((((......))))..)))))	chr13:113709593-113709865(+)$1	1	231	257	11.3253
(.(((.(((......))).))).)))	chr3:59882328-59882572(-)$1	1	201	227	13.4898
(((((((((((....)))))))))))	chr9:95244247-95244483(+)$1	1	160	186	10.7986
(((....((......))...))))))	chr3:59844329-59844567(-)$1	1	73	99	13.6382
..(((((((......)))..))))))	chr16:12578402-12578647(+)$1	1	126	152	12.0303
(((((((((.....))))))))))..	chr13:45125337-45125718(-)$1	1	216	242	11.5610
..(((((((......))))))).)))	chr11:65904566-65904792(+)$1	1	78	104	13.9924
.(((.((((......)))))))))))	chr4:4542823-4543083(-)$1	1	36	62	12.0444
(((...(((......)))))))))))	chr10:50686224-50686452(-)$1	1	172	198	11.9190
(((.(.(((......))).)...)))	chr12:104860249-104860505(+)$1	1	12	38	13.6037
(((((.(((......))).)))))))	chr11:3991849-3992103(+)$1	1	187	213	15.0956
(((((..((......))..))))..)	chr10:30019205-30019430(-)$1	1	148	174	11.0866
(.(((((((......))))))).)))	chr12:13817962-13818228(-)$1	1	51	77	14.4354
(.(((..((......))..))).)))	chr6:89477746-89477986(-)$1	1	136	162	12.7397
...((((((......)))).))...)	chr3:33247795-33248051(-)$1	1	15	41	12.1607
(((..((((......))))....)))	chr14:68624705-68624932(+)$1	1	167	193	12.0832
((((..(((......)))))))))..	chr8:130939705-130940024(-)$1	1	14	40	11.8011
(((((.(((......)))))))))))	chr10:115478307-115478523(+)$1	1	63	89	15.4917
(((((.(((......))).)))))).	chr7:47836101-47836317(+)$1	1	164	190	11.6013
))(((((((......))))))).(((	chr12:5672007-5672229(-)$1	1	28	54	11.9286
.(((((.((......)).))))).))	chr3:44399785-44400111(+)$1	1	278	304	11.9472
(((((((((......)))))))))))	chr4:123211837-123212106(+)$1	1	179	205	15.6194
((((.((((......)))).))))))	chr2:152332803-152333020(+)$1	1	129	155	13.3431
(.(((..((......))..))).)))	chr11:120813713-120813971(+)$1	1	137	163	11.9350
(..((((((......))))))..)))	chr3:43368929-43369147(+)$1	1	14	40	12.0269
((.((((((......)))))).))))	chr5:65359584-65359894(+)$1	1	101	127	11.3367
(((((((((...))))))))))...)	chr1:172628960-172629174(+)$1	1	30	56	11.6152
....(((((......))))))))).)	chr3:10395214-10395435(-)$1	1	122	148	12.0477
...((((((......))))))...))	chr11:28209862-28210077(+)$1	1	82	108	12.7189
(((..((((......)))).))))).	chr12:13369364-13369585(+)$1	1	24	50	12.1441
((((((((.........)))))))))	chr9:37291668-37291918(+)$1	1	3	29	10.0799
(.(((((.(......))))))...))	chr5:1244130-1244352(+)$1	1	192	218	12.1460
(((((((.........))))))))))	chr1:32651491-32651755(+)$1	1	195	221	10.6575
(((((((((...)))))))))..)))	chr1:205387377-205387594(-)$1	1	51	77	10.0015
(((((..(((.....)))))))))).	chr16:2541858-2542089(+)$1	1	189	215	10.1470
((((...((......))....)))))	chr12:58091544-58091881(+)$1	1	300	326	14.2041
(((((((((......))))).)))))	chr8:67071275-67071494(+)$1	1	11	37	11.4316
((((((.((......))..)))))))	chr3:188593275-188593521(+)$1	1	137	163	14.0106
(((...(((......)))..))))..	chr5:43609788-43610066(+)$1	1	116	142	12.6788
(((((((((......)))))))))))	chr7:137300128-137300418(-)$1	1	146	172	15.6194
(((((((((......)))))))))..	chr13:28818626-28818883(+)$1	1	35	61	13.2903
(..(((.(((.....))))))....)	chr1:240529879-240530113(+)$1	1	166	192	9.6344
((.((((((......)))))).))))	chr13:40164736-40164958(-)$1	1	123	149	11.4829
(((((((((......))))))))).(	chr7:139833985-139834237(-)$1	1	159	185	13.6631
(((((((((......)))))))))..	chr15:56455116-56455366(-)$1	1	221	247	12.7958
(((((((.((.....)).))))))))	chr13:47178797-47179027(+)$1	1	61	87	9.8863
(((.(.((((......)))).).)))	chr17:62128249-62128504(-)$1	1	91	117	10.6957
.((((((((......)))).).))).	chr11:19482064-19482300(+)$1	1	96	122	12.6175
((((.((((......)))))))))))	chr11:77095725-77095948(-)$1	1	193	219	13.2851
....(((((......)))))..))))	chr1:84632459-84632684(+)$1	1	71	97	11.9246
(((.(((((......))))).)))))	chr21:40621727-40621986(-)$1	1	218	244	13.0452
..(((((((......)))))))...)	chr2:73816719-73816938(+)$1	1	155	181	14.2737
(((...(((......)))...)))))	chrX:152102571-152102787(+)$1	1	38	64	13.4477
....(((((......)))))....))	chr2:242263637-242263885(+)$1	1	13	39	12.6949

#PSSM
i : 0.18	= : 0.14	g : 0.11	d : 0.09	" : 0.09	f : 0.09	e : 0.07	# : 0.05	c : 0.03	b : 0.03	! : 0.01	% : 0.01	h : 0.01	[ : 0.01	
= : 0.14	i : 0.14	[ : 0.09	g : 0.09	f : 0.09	d : 0.09	e : 0.07	" : 0.07	! : 0.05	c : 0.05	# : 0.05	h : 0.01	
g : 0.16	= : 0.14	i : 0.14	e : 0.09	c : 0.09	d : 0.09	f : 0.07	# : 0.05	" : 0.03	! : 0.03	[ : 0.03	h : 0.01	
= : 0.14	i : 0.14	g : 0.12	f : 0.12	c : 0.11	# : 0.07	e : 0.05	" : 0.05	[ : 0.05	d : 0.03	! : 0.03	b : 0.01	
e : 0.14	i : 0.14	= : 0.12	g : 0.09	f : 0.09	c : 0.07	" : 0.07	[ : 0.05	a : 0.05	! : 0.05	d : 0.03	# : 0.01	b : 0.01	
d : 0.16	e : 0.12	i : 0.12	[ : 0.11	= : 0.11	! : 0.09	g : 0.07	" : 0.07	f : 0.07	# : 0.01	c : 0.01	
c : 0.18	d : 0.16	= : 0.11	e : 0.11	i : 0.11	g : 0.07	! : 0.07	f : 0.07	[ : 0.05	# : 0.01	" : 0.01	
c : 0.22	d : 0.16	b : 0.12	= : 0.09	e : 0.09	i : 0.09	g : 0.07	f : 0.07	[ : 0.03	r : 0.01	
c : 0.22	d : 0.16	b : 0.14	= : 0.09	e : 0.09	g : 0.07	f : 0.07	i : 0.07	r : 0.03	a : 0.01	
o : 0.81	l : 0.03	r : 0.03	c : 0.03	= : 0.01	n : 0.01	b : 0.01	d : 0.01	
o : 0.83	n : 0.07	l : 0.03	r : 0.03	= : 0.01	
o : 0.83	n : 0.07	l : 0.03	r : 0.03	m : 0.01	
o : 0.83	n : 0.07	r : 0.03	m : 0.01	= : 0.01	i : 0.01	
o : 0.83	n : 0.07	r : 0.03	m : 0.01	= : 0.01	i : 0.01	
o : 0.83	n : 0.05	= : 0.03	r : 0.03	m : 0.01	i : 0.01	
c : 0.22	d : 0.14	b : 0.14	= : 0.09	e : 0.09	g : 0.07	f : 0.07	i : 0.07	r : 0.03	a : 0.01	o : 0.01	
c : 0.22	d : 0.16	b : 0.14	= : 0.11	e : 0.11	g : 0.07	f : 0.07	i : 0.07	r : 0.01	
c : 0.22	d : 0.16	= : 0.11	e : 0.11	i : 0.09	g : 0.07	2 : 0.07	f : 0.07	] : 0.03	3 : 0.01	4 : 0.01	
d : 0.16	= : 0.12	e : 0.12	2 : 0.11	i : 0.11	g : 0.09	f : 0.09	] : 0.07	3 : 0.03	h : 0.01	4 : 0.01	c : 0.01	
i : 0.14	= : 0.12	e : 0.12	g : 0.11	f : 0.11	c : 0.09	] : 0.07	2 : 0.05	3 : 0.03	d : 0.03	4 : 0.03	h : 0.01	a : 0.01	
g : 0.14	i : 0.14	= : 0.12	f : 0.11	c : 0.09	d : 0.07	4 : 0.05	e : 0.05	] : 0.05	2 : 0.03	3 : 0.03	h : 0.01	b : 0.01	a : 0.01	
g : 0.16	= : 0.14	i : 0.12	e : 0.07	c : 0.07	d : 0.07	3 : 0.05	4 : 0.05	f : 0.05	2 : 0.05	] : 0.05	h : 0.01	b : 0.01	a : 0.01	
= : 0.12	i : 0.12	] : 0.11	g : 0.11	d : 0.11	3 : 0.11	e : 0.07	f : 0.07	4 : 0.05	2 : 0.03	h : 0.01	: : 0.01	c : 0.01	
d : 0.14	i : 0.14	= : 0.12	g : 0.12	e : 0.09	f : 0.09	3 : 0.09	h : 0.03	c : 0.03	4 : 0.03	2 : 0.01	] : 0.01	b : 0.01	
e : 0.14	g : 0.12	d : 0.11	= : 0.11	3 : 0.09	i : 0.09	f : 0.07	h : 0.03	b : 0.03	c : 0.03	: : 0.03	2 : 0.01	6 : 0.01	] : 0.01	5 : 0.01	4 : 0.01	
e : 0.14	d : 0.14	g : 0.12	= : 0.11	i : 0.11	3 : 0.07	f : 0.07	h : 0.03	: : 0.03	b : 0.03	6 : 0.01	c : 0.01	a : 0.01	4 : 0.01	5 : 0.01	

#score	671.2772523854887
#seq	54
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m3_run1.txt

#BEAR
"""eeeeeqqqqqqqqeeeee2	chr11:9438499-9438727(+)$1	228	144	166	15.4052
cc::ddddqqqqqqqqdddddd	chr4:139966308-139966548(+)$1	240	54	76	12.9806
ccceeeeeqqqqqqqqeeeee:	chr2:234085837-234086078(+)$1	241	218	240	14.0112
eeee!!bbqqqqqqqqbb22ee	chrM:15020-15277(-)$1	257	228	250	13.5922
[gggggggqqqqqqqqgggggg	chr6:44218756-44219026(+)$1	270	238	260	14.9095
fff!!cccqqqqqqqqcccfff	chr11:125473958-125474212(+)$1	254	15	37	15.1105
gggggggaqqqqqqqqa]gggg	chr5:174940424-174940693(+)$1	269	58	80	14.6515
ffffffffqqqqqqqqffffff	chr17:80037960-80038203(-)$1	243	150	172	13.2579
Igggggggqqqqqqqqgggggg	chr12:96421155-96421419(-)$1	264	82	104	13.5991
fffeeeeeqqqqqqqqeeeee2	chr3:145788960-145789200(-)$1	240	58	80	14.6620
cc!!ddddqqqqqqqqdddd33	chrX:69626025-69626264(+)$1	239	65	87	16.3385
[gggggggqqqqqqqqgggggg	chr15:60639735-60639986(-)$1	251	4	26	14.9095
ff"""cccqqqqqqqqccc333	chrM:14596-14889(+)$1	293	127	149	16.3140
b[dddd[aqqqqqqqqadddd]	chr5:133534715-133534990(-)$1	275	122	144	14.5575
:a[eeeeeqqqqqqqqeeeee]	chr6:31504247-31504500(-)$1	253	99	121	14.4445
fff!!cccqqqqqqqqccc22f	chr19:21909338-21909630(-)$1	292	28	50	15.4441
b[ddddbbqqqqqqqqbb]ddd	chr10:3155218-3155481(+)$1	263	183	205	13.6067
ffffffbbqqqqqqqqbbgggg	chr6:27107035-27107274(+)$1	239	170	192	13.6044
$$$eeeeeqqqqqqqqeeeee=	chrM:7668-7942(-)$1	274	217	239	14.7955
$$$$ddddqqqqqqqqdddd55	chr9:125622236-125622508(-)$1	272	99	121	14.0103
ddddddddqqqqqqqqdddd22	chr2:62103175-62103414(-)$1	239	62	84	14.7074
"""eeeeeqqqqqqqqeeeee]	chr12:49666795-49667057(+)$1	262	204	226	15.5122
ffff[cccqqqqqqqqcccfff	chr2:97008394-97008634(+)$1	240	194	216	14.6172
[dddd[bbqqqqqqqqbb]ddd	chr5:76785226-76785491(-)$1	265	202	224	13.6368
f:ccccccqqqqqqqqccc]cc	chr4:78085330-78085627(+)$1	297	126	148	14.0789
ccc"""bbqqqqqqqqbb22cc	chr3:145802917-145803162(-)$1	245	95	117	14.2701
ccc!!cccqqqqqqqqccc22c	chr14:74196254-74196496(-)$1	242	54	76	15.7592
####ddddqqqqqqqqdddd44	chr11:130131062-130131303(-)$1	241	81	103	16.2015
####ddddqqqqqqqqdddd44	chr9:15446990-15447263(+)$1	273	207	229	16.2015
%%%%ddddqqqqqqqqdddd77	chr9:135202660-135202899(-)$1	239	134	156	12.7084
:bb!!cccqqqqqqqqccc22b	chrX:16870060-16870301(-)$1	241	191	213	14.2554
d"""ddddqqqqqqqqdddd22	chr11:113688311-113688550(-)$1	239	17	39	15.8290
ddd####aqqqqqqqqa4444d	chr5:140908304-140908603(-)$1	299	50	72	14.2629
ba!!ddddqqqqqqqqdddd22	chr11:67053787-67054026(+)$1	239	15	37	15.8107
#bb[ddddqqqqqqqqdddd]b	chr6:13644807-13645046(-)$1	239	127	149	15.0634
ee[eeeeeqqqqqqqqeeeeee	chrX:77369194-77369505(+)$1	311	61	83	14.5746
::a[ddddqqqqqqqqdddd]a	chr19:2269424-2269717(+)$1	293	210	232	13.9397
d!!eeeeeqqqqqqqqeeeee]	chr5:108714757-108715025(-)$1	268	177	199	15.1809
[a####bbqqqqqqqqbb4444	chr20:49510670-49510923(-)$1	253	188	210	15.2652
!ccc[cccqqqqqqqqccc]cc	chr5:107716945-107717221(-)$1	276	7	29	15.3761
eeeeecccqqqqqqqqccc22e	chr4:2883589-2883831(+)$1	242	161	183	14.6743
fff[ddddqqqqqqqqdddd]f	chr18:67795589-67795830(-)$1	241	16	38	15.2998
cbb[ddddqqqqqqqqdddd]b	chr17:26901076-26901358(-)$1	282	223	245	14.9175
"""eeeeeqqqqqqqqeeeee3	chr13:41133592-41133833(-)$1	241	133	155	15.6235
:gggggggqqqqqqqqgggggg	chr1:224377314-224377566(+)$1	252	81	103	13.9575
eeffffffqqqqqqqqffffff	chr10:43280982-43281219(+)$1	237	81	103	13.1193
gggg[cccqqqqqqqqccc333	chr16:74496373-74496635(-)$1	262	225	247	16.0431
dd"""cccqqqqqqqqccc22d	chr9:131386528-131386766(+)$1	238	151	173	15.3349
fa[eeeeeqqqqqqqqeeeee]	chr5:167995742-167995994(-)$1	252	169	191	15.1712
"gggggggqqqqqqqqgggggg	chr12:57704061-57704352(-)$1	291	214	236	14.9249
fff!!cccqqqqqqqqcccfff	chr6:26124551-26124800(-)$1	249	160	182	15.1105
hhhhhcccqqqqqqqqccc000	chr12:53412645-53412888(+)$1	243	79	101	13.0298
"""eeeeeqqqqqqqqeeeee]	chr6:26043505-26043745(-)$1	240	36	58	15.5122
ccc[ddddqqqqqqqqdddd22	chr11:62294878-62295123(-)$1	245	184	206	15.6854
ccc"""bbqqqqqqqqbb]ccc	chr5:43297006-43297294(-)$1	288	203	225	14.4435
ccc[ddddqqqqqqqqdddd]c	chr22:46125291-46125548(+)$1	257	197	219	15.6149
[a####bbqqqqqqqqbb4444	chr9:74485041-74485280(-)$1	239	189	211	15.2652
bb!!ddddqqqqqqqqdddd22	chr11:65421895-65422187(-)$1	292	127	149	15.5830
ggg####aqqqqqqqqa333gg	chr12:57036353-57036635(-)$1	282	127	149	14.8826
))ccc[bbqqqqqqqqbbcccf	chr1:40531802-40532042(+)$1	240	153	175	13.3698
dd[eeeeeqqqqqqqqeeeee]	chr12:57063991-57064252(-)$1	261	204	226	14.8514
"ccc[cccqqqqqqqqccc]cc	chr3:128890199-128890466(-)$1	267	54	76	15.3795
iiiiiiiiqqqqqqqqiiiiii	chr3:67451083-67451356(-)$1	273	108	130	14.6594
[gggggggqqqqqqqqgggggg	chr3:12623263-12623504(+)$1	241	194	216	14.9095

#otherMatches

#Seq PSSM
GACAGAAUGGAUAGAAAUUUUA	chr11:9438499-9438727(+)$1	228	144	166	15.4052
UGAACAGCGCCUACAAGCUGCU	chr4:139966308-139966548(+)$1	240	54	76	12.9806
ACUGCCCUAAAAUCUAAGGGCU	chr2:234085837-234086078(+)$1	241	218	240	14.0112
CCUCGCCCGAUGUGUAGGAAGA	chrM:15020-15277(-)$1	257	228	250	13.5922
GGUUUUAGGCAUUCUGCUAGGA	chr6:44218756-44219026(+)$1	270	238	260	14.9095
AGAAUGGACUAGUGGAUCCUCU	chr11:125473958-125474212(+)$1	254	15	37	15.1105
UUCCCGUCACGGAUGAGAAUGG	chr5:174940424-174940693(+)$1	269	58	80	14.6515
UCUUCGUGCAGCAGUUCACGGA	chr17:80037960-80038203(-)$1	243	150	172	13.2579
AAGAAAUUGUUAUAGAAAUUUC	chr12:96421155-96421419(-)$1	264	82	104	13.5991
GGAGAAUGUAUGGCUUCAUUUU	chr3:145788960-145789200(-)$1	240	58	80	14.6620
UCUCUUCUUUUCAAAUAGAAAC	chrX:69626025-69626264(+)$1	239	65	87	16.3385
AAGCUUCAUUGUGCGUUGAGGC	chr15:60639735-60639986(-)$1	251	4	26	14.9095
UGUAUUUCAACUACAAGAACAC	chrM:14596-14889(+)$1	293	127	149	16.3140
GUAGUAACGAUUUUCAGUGCUC	chr5:133534715-133534990(-)$1	275	122	144	14.5575
CUGCCCGCAUAUCGUCGUGGGG	chr6:31504247-31504500(-)$1	253	99	121	14.4445
GAUAACUCAUACUGGAGAGAAA	chr19:21909338-21909630(-)$1	292	28	50	15.4441
AUGCCCCGACCUCUCCUGCGGG	chr10:3155218-3155481(+)$1	263	183	205	13.6067
GCCGCGGCGGCGUGAAGCGCAU	chr6:27107035-27107274(+)$1	239	170	192	13.6044
UGAGUGUUAGGAAAAGGGCAUA	chrM:7668-7942(-)$1	274	217	239	14.7955
AAAAUUGGUUCUCCACCCAAGA	chr9:125622236-125622508(-)$1	272	99	121	14.0103
GGUUUCUGACUAUGCCCAGAUG	chr2:62103175-62103414(-)$1	239	62	84	14.7074
AAGAGUAUUAACCUGUGUGCUG	chr12:49666795-49667057(+)$1	262	204	226	15.5122
AAGAAGGAUGUCCACUUUCUCU	chr2:97008394-97008634(+)$1	240	194	216	14.6172
GACUACAGGUAAGAAGCUAUAG	chr5:76785226-76785491(-)$1	265	202	224	13.6368
GAGUUGGUUUCUAAAUGCCUAG	chr4:78085330-78085627(+)$1	297	126	148	14.0789
CUGUUAGGGACUUUUGCCGUCA	chr3:145802917-145803162(-)$1	245	95	117	14.2701
GGCUCUGGCCUCUACUUCAAUG	chr14:74196254-74196496(-)$1	242	54	76	15.7592
AAGCGCAAAAGCUACAUUGUUA	chr11:130131062-130131303(-)$1	241	81	103	16.2015
GAAUUCAGCAACACUCCUGACC	chr9:15446990-15447263(+)$1	273	207	229	16.2015
ACAGUAACAGAAAACAGUUAAU	chr9:135202660-135202899(-)$1	239	134	156	12.7084
AGUCAUUCAUAAACUAGAAAAG	chrX:16870060-16870301(-)$1	241	191	213	14.2554
CUCGGUUCCCGCUCCCGGACAU	chr11:113688311-113688550(-)$1	239	17	39	15.8290
UCCCCCUCUUUUGACUGUAAUG	chr5:140908304-140908603(-)$1	299	50	72	14.2629
CCCCACAGCCCACGUCCUGUCA	chr11:67053787-67054026(+)$1	239	15	37	15.8107
GUGGUCGAUGCCAAUUUUGGGC	chr6:13644807-13645046(-)$1	239	127	149	15.0634
CCCAAGCAUCAAAUUCUGCUUG	chrX:77369194-77369505(+)$1	311	61	83	14.5746
ACUGCUUCGCCAGAGAGAAGGA	chr19:2269424-2269717(+)$1	293	210	232	13.9397
GAGAGCAGUCAAUCCUUUGUUG	chr5:108714757-108715025(-)$1	268	177	199	15.1809
CCGAGAUCCUCUUUAUGAAAUA	chr20:49510670-49510923(-)$1	253	188	210	15.2652
UGCUCUGCUUCAUCGUGCACAG	chr5:107716945-107717221(-)$1	276	7	29	15.3761
GCAGCUCCGCAAGGAGGGAUGG	chr4:2883589-2883831(+)$1	242	161	183	14.6743
AGUUUGUAAUUAUUUGUACACA	chr18:67795589-67795830(-)$1	241	16	38	15.2998
CCAUGGCAACUGUCACUGCCCU	chr17:26901076-26901358(-)$1	282	223	245	14.9175
ACAGUGUCAAGACAACGACACA	chr13:41133592-41133833(-)$1	241	133	155	15.6235
AAUGGGUCAUAUUUGGGGCCUA	chr1:224377314-224377566(+)$1	252	81	103	13.9575
GGAACUUUACCCGGCAGAAGUU	chr10:43280982-43281219(+)$1	237	81	103	13.1193
CCUGAAGCUGAGAUAUGCUGAC	chr16:74496373-74496635(-)$1	262	225	247	16.0431
CUGCAGCCCAGAGAAAGGCGAA	chr9:131386528-131386766(+)$1	238	151	173	15.3349
ACUGAAAGAUUUAACACUUUUU	chr5:167995742-167995994(-)$1	252	169	191	15.1712
CUGUAAACAAAAACAAGUUUAU	chr12:57704061-57704352(-)$1	291	214	236	14.9249
GGUCAGGUACUCUAACACCGCC	chr6:26124551-26124800(-)$1	249	160	182	15.1105
UUUCUAGGAAACCUACCCUAUG	chr12:53412645-53412888(+)$1	243	79	101	13.0298
CAUGGGGAUCAUGAAUUCCUUC	chr6:26043505-26043745(-)$1	240	36	58	15.5122
UUGAUUUCAAUUUAAAGGGACC	chr11:62294878-62295123(-)$1	245	184	206	15.6854
CAUUUUCCUUGGUUUUGGUAUG	chr5:43297006-43297294(-)$1	288	203	225	14.4435
CCAAUCUCGGGUAAAAGAGAAU	chr22:46125291-46125548(+)$1	257	197	219	15.6149
UGCUGCUGUUAUUCUUCAUUCU	chr9:74485041-74485280(-)$1	239	189	211	15.2652
UACCUGUGGCCCCCCACACAAC	chr11:65421895-65422187(-)$1	292	127	149	15.5830
UGUACUGCUAUUUAUUGAUAAC	chr12:57036353-57036635(-)$1	282	127	149	14.8826
GGAGUUCCAUACCACCGGACUG	chr1:40531802-40532042(+)$1	240	153	175	13.3698
UUAAAUGGACCUCUCCCCAUUC	chr12:57063991-57064252(-)$1	261	204	226	14.8514
UAGCCGAAUUCUUUGUUUUUGC	chr3:128890199-128890466(-)$1	267	54	76	15.3795
GGUGGUAUCGUCAACUGUGCCA	chr3:67451083-67451356(-)$1	273	108	130	14.6594
ACUUUAGCCAUCUCUAGUUGGG	chr3:12623263-12623504(+)$1	241	194	216	14.9095

#DB
...(((((........))))).	chr11:9438499-9438727(+)$1	1	144	166	15.4052
))..((((........))))((	chr4:139966308-139966548(+)$1	1	54	76	12.9806
)))(((((........))))).	chr2:234085837-234086078(+)$1	1	218	240	14.0112
((((..((........))..))	chrM:15020-15277(-)$1	1	228	250	13.5922
.(((((((........))))))	chr6:44218756-44219026(+)$1	1	238	260	14.9095
(((..(((........))))))	chr11:125473958-125474212(+)$1	1	15	37	15.1105
((((((((........).))))	chr5:174940424-174940693(+)$1	1	58	80	14.6515
((((((((........))))))	chr17:80037960-80038203(-)$1	1	150	172	13.2579
((((((((........))))))	chr12:96421155-96421419(-)$1	1	82	104	13.5991
((((((((........))))).	chr3:145788960-145789200(-)$1	1	58	80	14.6620
((..((((........))))..	chrX:69626025-69626264(+)$1	1	65	87	16.3385
.(((((((........))))))	chr15:60639735-60639986(-)$1	1	4	26	14.9095
((...(((........)))...	chrM:14596-14889(+)$1	1	127	149	16.3140
(.((((.(........))))).	chr5:133534715-133534990(-)$1	1	122	144	14.5575
.(.(((((........))))).	chr6:31504247-31504500(-)$1	1	99	121	14.4445
(((..(((........)))..)	chr19:21909338-21909630(-)$1	1	28	50	15.4441
(.((((((........)).)))	chr10:3155218-3155481(+)$1	1	183	205	13.6067
))))))((........))((((	chr6:27107035-27107274(+)$1	1	170	192	13.6044
...(((((........))))))	chrM:7668-7942(-)$1	1	217	239	14.7955
....((((........))))..	chr9:125622236-125622508(-)$1	1	99	121	14.0103
((((((((........))))..	chr2:62103175-62103414(-)$1	1	62	84	14.7074
...(((((........))))).	chr12:49666795-49667057(+)$1	1	204	226	15.5122
((((.(((........))))))	chr2:97008394-97008634(+)$1	1	194	216	14.6172
.((((.((........)).)))	chr5:76785226-76785491(-)$1	1	202	224	13.6368
).((((((........))).))	chr4:78085330-78085627(+)$1	1	126	148	14.0789
(((...((........))..))	chr3:145802917-145803162(-)$1	1	95	117	14.2701
(((..(((........)))..)	chr14:74196254-74196496(-)$1	1	54	76	15.7592
....((((........))))..	chr11:130131062-130131303(-)$1	1	81	103	16.2015
....((((........))))..	chr9:15446990-15447263(+)$1	1	207	229	16.2015
....((((........))))..	chr9:135202660-135202899(-)$1	1	134	156	12.7084
.((..(((........)))..)	chrX:16870060-16870301(-)$1	1	191	213	14.2554
(...((((........))))..	chr11:113688311-113688550(-)$1	1	17	39	15.8290
(((....(........)....)	chr5:140908304-140908603(-)$1	1	50	72	14.2629
((..((((........))))..	chr11:67053787-67054026(+)$1	1	15	37	15.8107
.((.((((........)))).)	chr6:13644807-13645046(-)$1	1	127	149	15.0634
((.(((((........))))))	chrX:77369194-77369505(+)$1	1	61	83	14.5746
..(.((((........)))).)	chr19:2269424-2269717(+)$1	1	210	232	13.9397
(..(((((........))))).	chr5:108714757-108715025(-)$1	1	177	199	15.1809
.(....((........))....	chr20:49510670-49510923(-)$1	1	188	210	15.2652
.(((.(((........))).))	chr5:107716945-107717221(-)$1	1	7	29	15.3761
((((((((........)))..)	chr4:2883589-2883831(+)$1	1	161	183	14.6743
(((.((((........)))).)	chr18:67795589-67795830(-)$1	1	16	38	15.2998
(((.((((........)))).)	chr17:26901076-26901358(-)$1	1	223	245	14.9175
...(((((........))))).	chr13:41133592-41133833(-)$1	1	133	155	15.6235
.(((((((........))))))	chr1:224377314-224377566(+)$1	1	81	103	13.9575
((((((((........))))))	chr10:43280982-43281219(+)$1	1	81	103	13.1193
((((.(((........)))...	chr16:74496373-74496635(-)$1	1	225	247	16.0431
((...(((........)))..)	chr9:131386528-131386766(+)$1	1	151	173	15.3349
)(.(((((........))))).	chr5:167995742-167995994(-)$1	1	169	191	15.1712
.(((((((........))))))	chr12:57704061-57704352(-)$1	1	214	236	14.9249
(((..(((........))))))	chr6:26124551-26124800(-)$1	1	160	182	15.1105
((((((((........)))...	chr12:53412645-53412888(+)$1	1	79	101	13.0298
...(((((........))))).	chr6:26043505-26043745(-)$1	1	36	58	15.5122
(((.((((........))))..	chr11:62294878-62295123(-)$1	1	184	206	15.6854
(((...((........)).)))	chr5:43297006-43297294(-)$1	1	203	225	14.4435
(((.((((........)))).)	chr22:46125291-46125548(+)$1	1	197	219	15.6149
.(....((........))....	chr9:74485041-74485280(-)$1	1	189	211	15.2652
((..((((........))))..	chr11:65421895-65422187(-)$1	1	127	149	15.5830
(((....(........)...))	chr12:57036353-57036635(-)$1	1	127	149	14.8826
..(((.((........))))))	chr1:40531802-40532042(+)$1	1	153	175	13.3698
((.(((((........))))).	chr12:57063991-57064252(-)$1	1	204	226	14.8514
.(((.(((........))).))	chr3:128890199-128890466(-)$1	1	54	76	15.3795
((((((((........))))))	chr3:67451083-67451356(-)$1	1	108	130	14.6594
.(((((((........))))))	chr3:12623263-12623504(+)$1	1	194	216	14.9095

#PSSM
f : 0.17	c : 0.14	" : 0.09	[ : 0.09	d : 0.09	e : 0.06	b : 0.06	: : 0.06	g : 0.04	# : 0.04	$ : 0.03	I : 0.01	% : 0.01	! : 0.01	h : 0.01	) : 0.01	i : 0.01	
c : 0.15	g : 0.14	f : 0.14	" : 0.07	a : 0.07	d : 0.07	e : 0.06	b : 0.06	[ : 0.03	$ : 0.03	: : 0.03	# : 0.03	% : 0.01	! : 0.01	h : 0.01	) : 0.01	i : 0.01	
c : 0.15	g : 0.14	f : 0.14	" : 0.10	d : 0.07	! : 0.06	[ : 0.06	# : 0.06	b : 0.04	e : 0.03	$ : 0.03	: : 0.01	% : 0.01	a : 0.01	h : 0.01	i : 0.01	
e : 0.21	g : 0.12	! : 0.12	# : 0.09	[ : 0.09	" : 0.07	f : 0.06	d : 0.06	c : 0.06	: : 0.01	$ : 0.01	% : 0.01	h : 0.01	i : 0.01	
d : 0.29	e : 0.20	g : 0.10	! : 0.09	" : 0.06	[ : 0.06	# : 0.06	f : 0.04	c : 0.03	h : 0.01	i : 0.01	
d : 0.28	c : 0.21	e : 0.18	g : 0.10	# : 0.06	f : 0.04	[ : 0.03	" : 0.03	! : 0.01	i : 0.01	
d : 0.25	c : 0.21	e : 0.18	b : 0.14	g : 0.10	f : 0.03	# : 0.03	[ : 0.01	i : 0.01	
d : 0.25	c : 0.21	e : 0.18	b : 0.14	g : 0.09	a : 0.06	f : 0.03	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.25	c : 0.21	e : 0.18	b : 0.14	g : 0.09	a : 0.06	f : 0.03	i : 0.01	
d : 0.26	c : 0.21	e : 0.18	b : 0.14	g : 0.09	f : 0.03	] : 0.01	4 : 0.01	3 : 0.01	i : 0.01	
d : 0.26	c : 0.23	e : 0.18	g : 0.12	] : 0.04	4 : 0.04	2 : 0.03	f : 0.03	3 : 0.01	i : 0.01	
d : 0.29	e : 0.18	g : 0.12	2 : 0.10	f : 0.07	3 : 0.04	] : 0.04	4 : 0.04	c : 0.03	0 : 0.01	i : 0.01	
e : 0.20	2 : 0.15	g : 0.14	c : 0.09	f : 0.07	4 : 0.07	] : 0.07	d : 0.06	3 : 0.04	5 : 0.01	7 : 0.01	0 : 0.01	i : 0.01	
g : 0.14	f : 0.12	2 : 0.10	] : 0.10	c : 0.10	d : 0.07	3 : 0.06	4 : 0.06	e : 0.04	b : 0.04	: : 0.01	= : 0.01	5 : 0.01	7 : 0.01	a : 0.01	0 : 0.01	i : 0.01	

#score	944.8217747864655
#seq	64
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m1_run1.txt

#BEAR
ddddeeeee^^^^^^^^^^^^^^^^^^^eeeee:	chr8:43056268-43056609(+)$1	341	298	332	32.8691
fffff^^^^^^^^^^^^^^^^^^^^^^^^^ffff	chr20:5527615-5527893(-)$1	278	135	169	39.6245
ggggg^^^^^^^^^^^^^^^^^^^^^^^^^^ggg	chr7:86824472-86824739(+)$1	267	72	106	40.1151
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr20:31031670-31031958(-)$1	288	157	191	39.6044
fdddd[bb^^^^^^^^^^^^^^^^^^^bb]dddd	chr2:243402-243662(-)$1	260	162	196	33.2277
c:ccc^^^^^^^^^^^^^^^^^^^^cccddddoo	chr12:100733566-100733785(+)$1	219	86	120	33.4827
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee:	chr1:2118281-2118538(-)$1	257	96	130	36.5899
####dddd^^^^^^^^^^^^^^^^^^^^dddd55	chr12:110475773-110476027(+)$1	254	102	136	33.7058
ddccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc]	chr14:24782410-24782723(+)$1	313	168	202	40.0305
[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr2:204600015-204600248(+)$1	233	89	123	40.5384
!eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee]	chr12:56347517-56347903(+)$1	386	292	326	38.6298
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr18:32838261-32838492(-)$1	231	116	150	39.6044
=[ccc^^^^^^^^^^^^^^^^^^^^^^^ccc]==	chr6:170103984-170104211(+)$1	227	57	91	39.3269
[ccceeeee^^^^^^^^^^^^^^^^^^eeeee]c	chr2:128062966-128063218(-)$1	252	210	244	33.1324
iiiiii^^^^^^^^^^^^^^^^^^^^^^iiiiii	chr6:88051110-88051369(+)$1	259	222	256	37.3914
!!eeeee^^^^^^^^^^^^^^^^^^^^^eeeeec	chr1:218509895-218510120(+)$1	225	144	178	37.3561
g^^^^^^^^^^^^^^^^^^^^^^^^^^^^^gggg	chr5:78619395-78619632(+)$1	237	9	43	40.9217
ggggg^^^^^^^^^^^^^^^^^^^^^^^^^gggg	chr12:48735946-48736174(-)$1	228	95	129	40.0110
[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:155306452-155306721(-)$1	269	84	118	40.8840
"dddd[bb^^^^^^^^^^^^^^^^^^^^bb]ddd	chr12:133307922-133308151(-)$1	229	147	181	34.7177
""ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr21:34968250-34968561(-)$1	311	157	191	40.5347
[bb^^^^^^^^^^^^^^^^^^^^^^^^^^^bb]d	chr12:110475882-110476161(+)$1	279	19	53	39.9847
ff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr17:7363305-7363543(-)$1	238	91	125	40.7208
[dddd^^^^^^^^^^^^^^^^^^^^dddd]dddd	chr12:393224-393457(-)$1	233	149	183	34.0084
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr19:21475666-21475908(-)$1	242	111	145	40.7170
fdddd^^^^^^^^^^^^^^^^^^^^^^^^dddd]	chr9:88161367-88161612(-)$1	245	168	202	39.2578
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr16:28334543-28334779(+)$1	236	103	137	40.8283
ii^^^^^^^^^^^^^^^^^^^^^^^^^^^^iiii	chr3:182638220-182638452(+)$1	232	46	80	40.7034
"dddd^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:32566521-32566772(+)$1	251	169	203	40.0321
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr15:68378786-68379050(+)$1	264	194	228	40.8283
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr3:69025691-69025943(-)$1	252	120	154	41.0345
!!dddd^^^^^^^^^^^^^^^^^^^^^dddd333	chr1:160185953-160186223(-)$1	270	101	135	36.7167
eeeee^^^^^^^^^^^^^^^^^^^^^^^eeeeec	chr1:162496010-162496250(+)$1	240	55	89	39.1765
eeeebb^^^^^^^^^^^^^^^^^^^^^^bb]eee	chr6:138734356-138734625(+)$1	269	141	175	37.2800
[ffffff^^^^^^^^^^^^^^^^^^^ffffff]b	chr17:38337349-38337595(+)$1	246	117	151	33.0853
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr12:53567477-53567703(-)$1	226	77	111	41.1794
:ccc[ccc^^^^^^^^^^^^^^^^^^^ccc]ccc	chr2:241532119-241532348(+)$1	229	43	77	33.6620
!!bb^^^^^^^^^^^^^^^^^^^^^^^^^^^bb2	chr6:109953661-109953894(-)$1	233	100	134	39.8836
fff"""dddd^^^^^^^^^^^^^^^^^^dddd]f	chr6:143810291-143810537(+)$1	246	69	103	32.0813
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee:	chr11:6634752-6635067(-)$1	315	154	188	36.5899
fffff^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr16:18817518-18817759(-)$1	241	45	79	39.8130
fffff^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr8:133858860-133859135(+)$1	275	204	238	38.4124
g^^^^^^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr5:158712242-158712468(+)$1	226	152	186	40.4716
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee:	chr18:13761362-13761614(+)$1	252	148	182	36.5899
eeee^^^^^^^^^^^^^^^^^^^^^^^^eeeee4	chr17:27587946-27588247(-)$1	301	208	242	39.6834
[bb!!bb^^^^^^^^^^^^^^^^^^^^bb22bb]	chr5:130539325-130539559(+)$1	234	133	167	34.3232
""ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc33	chr13:73329955-73330194(-)$1	239	69	103	40.4059
[dddd^^^^^^^^^^^^^^^^^^^^^^^^^dddd	chr22:17660992-17661329(-)$1	337	23	57	39.8487
&ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc66	chr9:5921882-5922141(-)$1	259	110	144	39.2179
ee[ccc^^^^^^^^^^^^^^^^^^^ccc]eeeee	chr15:100255208-100255463(+)$1	255	72	106	34.1774
eeee^^^^^^^^^^^^^^^^^^^^^^^^^eeeee	chr8:133860829-133861067(+)$1	238	123	157	40.2126
!ccc[dddd^^^^^^^^^^^^^^^^^^^dddd]c	chr11:58911365-58911637(+)$1	272	65	99	33.8534
ggggg^^^^^^^^^^^^^^^^^^^^^^^^ggggg	chr16:69733578-69733935(+)$1	357	37	71	39.5609
fffff^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr4:77958073-77958318(+)$1	245	39	73	39.8130
ggggg^^^^^^^^^^^^^^^^^^^^^^^^^gggg	chr17:8364570-8364800(+)$1	230	89	123	40.0110
fffff^^^^^^^^^^^^^^^^^^^ffffffeeee	chr12:70210188-70210413(+)$1	225	72	106	32.4249
[ccc[eeeee^^^^^^^^^^^^^^^^^^eeeee]	chr20:30754565-30754832(+)$1	267	115	149	33.0457
[ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc22	chr17:42475014-42475290(-)$1	276	225	259	40.2423
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff	chr5:39106411-39106663(-)$1	252	105	139	39.6044
fff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr12:110813528-110813773(-)$1	245	64	98	40.5724
eeee^^^^^^^^^^^^^^^^^^^^^^^^^^^eee	chr5:134191735-134192035(+)$1	300	15	49	40.5768
!!ccc^^^^^^^^^^^^^^^^^^^^^^ccc333b	chr11:118224065-118224301(+)$1	236	100	134	38.3002

#otherMatches

#Seq PSSM
ggggcuucuccugccuccaucacaucacagaagu	chr8:43056268-43056609(+)$1	341	298	332	32.8691
GGCUGCUGCCAUUUUUCCACUUAACCAAACCAGC	chr20:5527615-5527893(-)$1	278	135	169	39.6245
CUUAAUUUACCAAUUUAAAUAGCCACAGUCCUUA	chr7:86824472-86824739(+)$1	267	72	106	40.1151
CCUAAAAAUACAACAAAAAACCUAUACCACGUAG	chr20:31031670-31031958(-)$1	288	157	191	39.6044
auguugugucuucauuuuccuuaaucucaaaaua	chr2:243402-243662(-)$1	260	162	196	33.2277
UUGGAUAUAUUUAGAAUCACUUUUUUCCUCCUGU	chr12:100733566-100733785(+)$1	219	86	120	33.4827
CAGGAUUUUUCAAACCACACUUCAAUACAUCCUU	chr1:2118281-2118538(-)$1	257	96	130	36.5899
CAUUGUCAUUAUUCUUCCUCCAUCUAUCUGAUUC	chr12:110475773-110476027(+)$1	254	102	136	33.7058
ugcgguuucugcccauuuuuuucauauccucUGA	chr14:24782410-24782723(+)$1	313	168	202	40.0305
GGGAUAGGAAGACAUAUUUAAAAACCAUUAAAAC	chr2:204600015-204600248(+)$1	233	89	123	40.5384
AAGUGGUACACUUCCUUCUUUUAUACCUUCACUC	chr12:56347517-56347903(+)$1	386	292	326	38.6298
ucacccuccaacuguuaucuguuacauuuuuuaa	chr18:32838261-32838492(-)$1	231	116	150	39.6044
AAAUGGCACCAAAUAUUCCACUUAAAUGCAUAUA	chr6:170103984-170104211(+)$1	227	57	91	39.3269
CAACGCUUCUCUCAUAUUCUUAAAAUUGAAGCAG	chr2:128062966-128063218(-)$1	252	210	244	33.1324
AUAAUGUUAUUUUUAAUUUGUCAUACUUUAUUAU	chr6:88051110-88051369(+)$1	259	222	256	37.3914
UCAAGACUGUUUCUACACAAUAAUAUUUGUCUUU	chr1:218509895-218510120(+)$1	225	144	178	37.3561
AUGUGUCAACAUUUCAUAUAUCCAGUUCUUUGGG	chr5:78619395-78619632(+)$1	237	9	43	40.9217
AGCAGUAUAUACAUCACCUCUCACCCUCACCUGC	chr12:48735946-48736174(-)$1	228	95	129	40.0110
AUUCAGUUCAAAAUAAAAUCAUUUAAAAACCUAC	chr1:155306452-155306721(-)$1	269	84	118	40.8840
UGAUUGACAUACAUUAAACUAAGAAGCAGUGAAU	chr12:133307922-133308151(-)$1	229	147	181	34.7177
AAAGACACACACACACCCCUACCACUUCACCACC	chr21:34968250-34968561(-)$1	311	157	191	40.5347
UCUGAUUCCAUUCCUUCCACACCCAGCUAAAGUU	chr12:110475882-110476161(+)$1	279	19	53	39.9847
GAAAAACACACAAAAAAAAAAAUCACUAAAAAUU	chr17:7363305-7363543(-)$1	238	91	125	40.7208
UUAAAAAAAAAAAUCCCAUUCCUUCUUUGUAGUA	chr12:393224-393457(-)$1	233	149	183	34.0084
AACUUUUCUAAACAUAAAAUAAAUCAUACUGGUG	chr19:21475666-21475908(-)$1	242	111	145	40.7170
UCAUCUUCUUUAACCAGCUCAGAUUAUUUGAUGU	chr9:88161367-88161612(-)$1	245	168	202	39.2578
AAAAAAAAAAAUCACACAAAAAAUCUCCCUUGUU	chr16:28334543-28334779(+)$1	236	103	137	40.8283
AGUGUCCCCUUUGCAUAUUUCUUUAAAAUUCUUU	chr3:182638220-182638452(+)$1	232	46	80	40.7034
CAGAGGGAGAGAAGAUGAUACAGUAAAAGAAGGG	chr1:32566521-32566772(+)$1	251	169	203	40.0321
AACUCCCACAUCUUACAUCAGCUCUUCACCCAGU	chr15:68378786-68379050(+)$1	264	194	228	40.8283
uacacacacacacacacacacacacacacacgca	chr3:69025691-69025943(-)$1	252	120	154	41.0345
cauguacacacacaccacacacauacauacacac	chr1:160185953-160186223(-)$1	270	101	135	36.7167
UUUUUUUUUUUUUUACAGUUAAUUUAAUGAAAAU	chr1:162496010-162496250(+)$1	240	55	89	39.1765
ACAAUCAUAUUCCCUUUUUUUUUUCUUGGAUUUG	chr6:138734356-138734625(+)$1	269	141	175	37.2800
CACACAGUCCCCACUGAUGCUAACCUCUGUGUUU	chr17:38337349-38337595(+)$1	246	117	151	33.0853
uuuaugaaaaaaacacuuaauuguacacuuuUCA	chr12:53567477-53567703(-)$1	226	77	111	41.1794
CGCACCGCUUCUCACACUGCCACACACGCGCUGU	chr2:241532119-241532348(+)$1	229	43	77	33.6620
cucacucucacucuccccauauaaucacuccugu	chr6:109953661-109953894(-)$1	233	100	134	39.8836
UGAUUUUUCCUUCAAGAAAAACUACAGUGGGAUU	chr6:143810291-143810537(+)$1	246	69	103	32.0813
ugacugcacaucuuaaauauaucUUUaucagucc	chr11:6634752-6635067(-)$1	315	154	188	36.5899
GCUCUUGAUCUGCUUCCCUAAAUUACUUUUUUAG	chr16:18817518-18817759(-)$1	241	45	79	39.8130
UUUGCCUUCAGAAAAAAAAAAAUACAUUGUAAAU	chr8:133858860-133859135(+)$1	275	204	238	38.4124
ACAAACCAAAAAAAAAAACAAAAAAAAACUUUUU	chr5:158712242-158712468(+)$1	226	152	186	40.4716
ACAGGUAAUAAUAAUACAUGUACUUUUAGCCUGA	chr18:13761362-13761614(+)$1	252	148	182	36.5899
UUACAUAGCCUUUCUUCUAACCUCCUUAGUAAUG	chr17:27587946-27588247(-)$1	301	208	242	39.6834
GUAUUCUGUGAAAGCUACUAUAAAUAAAGUUUAG	chr5:130539325-130539559(+)$1	234	133	167	34.3232
CUCCACUCUCCCAGCCCCACUUUUUCUCUUGGUU	chr13:73329955-73330194(-)$1	239	69	103	40.4059
cugcgccgucccccacucccuacaucagaacgca	chr22:17660992-17661329(-)$1	337	23	57	39.8487
UGGUGCCAAAAUCAACAACUUCUUCCUCUGCUUU	chr9:5921882-5922141(-)$1	259	110	144	39.2179
GUACUUACUUUACUGAACUACUUACAGGCACAUU	chr15:100255208-100255463(+)$1	255	72	106	34.1774
AUCUUAUUUCCACUGUCUUAUUUCCUCUCAGAUG	chr8:133860829-133861067(+)$1	238	123	157	40.2126
uuuaucuaccaauccuaaacuuuuacccguagcu	chr11:58911365-58911637(+)$1	272	65	99	33.8534
AAGGACCUAAAUAAACUGUGAGCCACCUUUUCUU	chr16:69733578-69733935(+)$1	357	37	71	39.5609
CCUUUGUUUAAAAAAAAGACUAAAUAUAUUUAAA	chr4:77958073-77958318(+)$1	245	39	73	39.8130
UGUAUUAAAAGCACAUCCUAAAACAUCACUAUAC	chr17:8364570-8364800(+)$1	230	89	123	40.0110
CCUAAACAUUAAAUAUAUUUUCCCUUGGGUAAAC	chr12:70210188-70210413(+)$1	225	72	106	32.4249
AGGAAGAUGUCCCUCCCCUCACUGCCCCACAUUC	chr20:30754565-30754832(+)$1	267	115	149	33.0457
UGCCCUCUACCCCACCCUACUUGCUCCACGGCCU	chr17:42475014-42475290(-)$1	276	225	259	40.2423
CUCUAACAGUACAUACUCAUUCCCAAAGCAAUCC	chr5:39106411-39106663(-)$1	252	105	139	39.6044
UAAAAAUUUUUUCUUAAAAUAUAUUAACAACAUU	chr12:110813528-110813773(-)$1	245	64	98	40.5724
UUGAUUUAACCAUUAUACCUGAAAUAAUUCUUCA	chr5:134191735-134192035(+)$1	300	15	49	40.5768
AAAGCUCUCCCUCCACCGCCAUCCCCUGCUACCC	chr11:118224065-118224301(+)$1	236	100	134	38.3002

#DB
))))(((((...................))))).	chr8:43056268-43056609(+)$1	1	298	332	32.8691
(((((.........................))))	chr20:5527615-5527893(-)$1	1	135	169	39.6245
(((((..........................)))	chr7:86824472-86824739(+)$1	1	72	106	40.1151
............................))))))	chr20:31031670-31031958(-)$1	1	157	191	39.6044
(((((.((...................)).))))	chr2:243402-243662(-)$1	1	162	196	33.2277
).(((....................)))((((..	chr12:100733566-100733785(+)$1	1	86	120	33.4827
.(((((......................))))).	chr1:2118281-2118538(-)$1	1	96	130	36.5899
....((((....................))))..	chr12:110475773-110476027(+)$1	1	102	136	33.7058
(((((.........................))).	chr14:24782410-24782723(+)$1	1	168	202	40.0305
.((...............................	chr2:204600015-204600248(+)$1	1	89	123	40.5384
.(((((......................))))).	chr12:56347517-56347903(+)$1	1	292	326	38.6298
............................))))))	chr18:32838261-32838492(-)$1	1	116	150	39.6044
(.(((.......................))).))	chr6:170103984-170104211(+)$1	1	57	91	39.3269
.((((((((..................))))).)	chr2:128062966-128063218(-)$1	1	210	244	33.1324
((((((......................))))))	chr6:88051110-88051369(+)$1	1	222	256	37.3914
..(((((.....................))))))	chr1:218509895-218510120(+)$1	1	144	178	37.3561
(.............................))))	chr5:78619395-78619632(+)$1	1	9	43	40.9217
(((((.........................))))	chr12:48735946-48736174(-)$1	1	95	129	40.0110
.(((..............................	chr1:155306452-155306721(-)$1	1	84	118	40.8840
.((((.((....................)).)))	chr12:133307922-133308151(-)$1	1	147	181	34.7177
..(((.............................	chr21:34968250-34968561(-)$1	1	157	191	40.5347
.((...........................)).)	chr12:110475882-110476161(+)$1	1	19	53	39.9847
((..............................))	chr17:7363305-7363543(-)$1	1	91	125	40.7208
.((((....................)))).))))	chr12:393224-393457(-)$1	1	149	183	34.0084
..............................))))	chr19:21475666-21475908(-)$1	1	111	145	40.7170
(((((........................)))).	chr9:88161367-88161612(-)$1	1	168	202	39.2578
.............................)))))	chr16:28334543-28334779(+)$1	1	103	137	40.8283
((............................))))	chr3:182638220-182638452(+)$1	1	46	80	40.7034
.((((.............................	chr1:32566521-32566772(+)$1	1	169	203	40.0321
.............................)))))	chr15:68378786-68379050(+)$1	1	194	228	40.8283
...............................)))	chr3:69025691-69025943(-)$1	1	120	154	41.0345
..((((.....................))))...	chr1:160185953-160186223(-)$1	1	101	135	36.7167
(((((.......................))))))	chr1:162496010-162496250(+)$1	1	55	89	39.1765
((((((......................)).)))	chr6:138734356-138734625(+)$1	1	141	175	37.2800
.((((((...................)))))).)	chr17:38337349-38337595(+)$1	1	117	151	33.0853
..............................))))	chr12:53567477-53567703(-)$1	1	77	111	41.1794
.(((.(((...................))).)))	chr2:241532119-241532348(+)$1	1	43	77	33.6620
..((...........................)).	chr6:109953661-109953894(-)$1	1	100	134	39.8836
(((...((((..................)))).)	chr6:143810291-143810537(+)$1	1	69	103	32.0813
.(((((......................))))).	chr11:6634752-6635067(-)$1	1	154	188	36.5899
(((((...........................))	chr16:18817518-18817759(-)$1	1	45	79	39.8130
(((((.......................))))))	chr8:133858860-133859135(+)$1	1	204	238	38.4124
(............................)))))	chr5:158712242-158712468(+)$1	1	152	186	40.4716
.(((((......................))))).	chr18:13761362-13761614(+)$1	1	148	182	36.5899
((((........................))))).	chr17:27587946-27588247(-)$1	1	208	242	39.6834
.((..((....................))..)).	chr5:130539325-130539559(+)$1	1	133	167	34.3232
..(((........................)))..	chr13:73329955-73330194(-)$1	1	69	103	40.4059
.((((.........................))))	chr22:17660992-17661329(-)$1	1	23	57	39.8487
.(((.........................)))..	chr9:5921882-5922141(-)$1	1	110	144	39.2179
((.(((...................))).)))))	chr15:100255208-100255463(+)$1	1	72	106	34.1774
((((.........................)))))	chr8:133860829-133861067(+)$1	1	123	157	40.2126
.(((.((((...................)))).)	chr11:58911365-58911637(+)$1	1	65	99	33.8534
(((((........................)))))	chr16:69733578-69733935(+)$1	1	37	71	39.5609
(((((...........................))	chr4:77958073-77958318(+)$1	1	39	73	39.8130
(((((.........................))))	chr17:8364570-8364800(+)$1	1	89	123	40.0110
(((((...................))))))((((	chr12:70210188-70210413(+)$1	1	72	106	32.4249
.(((.(((((..................))))).	chr20:30754565-30754832(+)$1	1	115	149	33.0457
.(((.........................)))..	chr17:42475014-42475290(-)$1	1	225	259	40.2423
............................))))))	chr5:39106411-39106663(-)$1	1	105	139	39.6044
(((.............................))	chr12:110813528-110813773(-)$1	1	64	98	40.5724
((((...........................)))	chr5:134191735-134192035(+)$1	1	15	49	40.5768
..(((......................)))...)	chr11:118224065-118224301(+)$1	1	100	134	38.3002

#PSSM
f : 0.16	[ : 0.16	^ : 0.12	g : 0.09	! : 0.09	e : 0.09	: : 0.06	" : 0.06	d : 0.03	i : 0.03	c : 0.01	# : 0.01	= : 0.01	& : 0.01	
^ : 0.16	e : 0.16	f : 0.14	d : 0.12	c : 0.11	g : 0.06	! : 0.06	b : 0.04	i : 0.03	" : 0.03	: : 0.01	# : 0.01	[ : 0.01	
c : 0.20	^ : 0.19	e : 0.16	d : 0.12	f : 0.12	g : 0.06	b : 0.06	# : 0.01	i : 0.01	[ : 0.01	
^ : 0.24	c : 0.22	e : 0.16	d : 0.12	f : 0.09	g : 0.06	# : 0.01	i : 0.01	b : 0.01	" : 0.01	! : 0.01	
^ : 0.35	e : 0.12	d : 0.12	c : 0.11	f : 0.09	g : 0.06	[ : 0.04	i : 0.01	b : 0.01	" : 0.01	! : 0.01	
^ : 0.67	e : 0.12	d : 0.04	[ : 0.03	b : 0.03	c : 0.03	i : 0.01	f : 0.01	" : 0.01	
^ : 0.80	e : 0.06	b : 0.04	d : 0.04	f : 0.01	c : 0.01	
^ : 0.85	e : 0.04	d : 0.04	b : 0.03	c : 0.01	
^ : 0.91	e : 0.04	d : 0.03	
^ : 0.96	d : 0.01	e : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.98	f : 0.01	
^ : 0.93	c : 0.03	d : 0.01	f : 0.01	
^ : 0.91	c : 0.03	f : 0.03	d : 0.01	
^ : 0.82	c : 0.06	b : 0.03	d : 0.03	f : 0.03	e : 0.01	
^ : 0.49	e : 0.16	f : 0.09	d : 0.09	b : 0.06	c : 0.04	i : 0.01	] : 0.01	
^ : 0.35	e : 0.22	f : 0.09	d : 0.09	c : 0.09	] : 0.03	b : 0.03	g : 0.03	i : 0.01	2 : 0.01	
e : 0.25	^ : 0.19	d : 0.16	f : 0.09	c : 0.08	g : 0.08	] : 0.04	i : 0.03	b : 0.01	2 : 0.01	3 : 0.01	
e : 0.29	d : 0.16	^ : 0.12	f : 0.09	g : 0.09	c : 0.09	b : 0.04	i : 0.03	3 : 0.03	] : 0.01	
e : 0.27	f : 0.14	g : 0.09	d : 0.09	] : 0.08	^ : 0.06	c : 0.04	3 : 0.04	i : 0.03	b : 0.03	o : 0.01	5 : 0.01	= : 0.01	6 : 0.01	2 : 0.01	
f : 0.16	e : 0.12	g : 0.09	d : 0.09	c : 0.09	] : 0.08	: : 0.06	^ : 0.06	i : 0.03	3 : 0.03	b : 0.03	2 : 0.03	o : 0.01	5 : 0.01	= : 0.01	4 : 0.01	6 : 0.01	

#score	2361.231999493612
#seq	62
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_UTR_m1_run2.txt

#BEAR
ggg!!attttttttttta22ggggg	chr13:50366514-50366746(-)$1	232	125	150	22.5055
ee!!bbuuuuuuuuuuuubb]eeee	chr10:116623431-116623671(+)$1	240	49	74	22.5066
b[ddddtttttttttttdddd22bb	chr17:4851459-4851714(-)$1	255	91	116	20.9052
gggggggtttttttttttggggggg	chr6:136582059-136582329(-)$1	270	214	239	22.5811
[eeeeewwwwwwwwwwwwwweeeee	chr1:935306-935603(-)$1	297	92	117	21.7901
cc!!ccctttttttttttccc22cc	chr6:109307733-109308004(-)$1	271	111	136	22.4872
iiiiiyyyyyyyyyyyyyyyyiiii	chr6:1612759-1613001(+)$1	242	30	55	23.0509
ccc[abbtttttttttttbb]a]cc	chrX:109438834-109439100(-)$1	266	25	50	21.5967
ee[ccctttttttttttccc]eeee	chr19:45476268-45476501(+)$1	233	118	143	21.9658
[eeeeewwwwwwwwwwwwwweeeee	chr13:52706795-52707032(-)$1	237	127	152	21.7901
gggggggtttttttttttggggggg	chr4:57801627-57801858(+)$1	231	57	82	22.5811
=!!ddddtttttttttttdddd22=	chr15:65847168-65847398(+)$1	230	166	191	22.5918
:eeeeeuuuuuuuuuuuueeeee::	chr10:32299947-32300186(-)$1	239	128	153	20.3173
ffff[auuuuuuuuuuuua]fffff	chr10:74035564-74035812(+)$1	248	130	155	22.6834
"bbccctttttttttttccc]bb33	chr6:116599319-116599585(-)$1	266	110	135	21.5239
e[ddddxxxxxxxxxxxxxxxdddd	chr7:63981374-63981613(-)$1	239	83	108	17.7458
ddddddvvvvvvvvvvvvvdddd]d	chr17:78183238-78183509(-)$1	271	217	242	22.1461
&&dddduuuuuuuuuuuudddd666	chr1:27180997-27181252(+)$1	255	60	85	21.3390
c[dddduuuuuuuuuuuuddddccc	chr3:126755189-126755475(+)$1	286	44	69	23.5612
##dddduuuuuuuuuuuudddd444	chr16:18803237-18803485(-)$1	248	51	76	23.9370
$$ddddvvvvvvvvvvvvvdddd66	chr2:71653698-71653940(+)$1	242	185	210	21.7178
iiiiiiitttttttttttiiiiiii	chr10:23729927-23730176(+)$1	249	217	242	22.7289
======wwwwwwwwwwwwww=====	chr9:134372908-134373145(+)$1	237	180	205	22.9217
ggggggyyyyyyyyyyyyyyyyggg	chr2:32379959-32380197(+)$1	238	83	108	22.6891
gggggguuuuuuuuuuuuggggggg	chr10:51589609-51589840(+)$1	231	25	50	23.8853
::ddddwwwwwwwwwwwwwwdddd:	chr9:139253151-139253419(+)$1	268	207	232	18.7499
hhhhhhvvvvvvvvvvvvvhhhhhh	chr14:93705237-93705471(-)$1	234	105	130	20.5831
ggggggvvvvvvvvvvvvvgggggg	chr8:29193992-29194277(-)$1	285	240	265	23.1123
ggggggwwwwwwwwwwwwwwggggg	chr12:110782980-110783249(+)$1	269	17	42	22.4615
[fffffftttttttttttffffff3	chr6:32948918-32949161(+)$1	243	85	110	21.2905
hhhhhhyyyyyyyyyyyyyyyyhhh	chr2:20449372-20449651(-)$1	279	149	174	20.7972
##ddddxxxxxxxxxxxxxxxdddd	chr16:2580237-2580515(+)$1	278	112	137	17.8605
eeeeeyyyyyyyyyyyyyyyyeeee	chr6:114181661-114181971(+)$1	310	276	301	22.0348
"""cccuuuuuuuuuuuuccc7777	chr11:769014-769253(-)$1	239	26	51	22.0296
ccccyyyyyyyyyyyyyyyyccc]c	chr1:16723884-16724144(+)$1	260	153	178	22.2955
'eeeeeuuuuuuuuuuuueeeee66	chr22:22114558-22114796(-)$1	238	119	144	22.0355
eeeeewwwwwwwwwwwwwweeeee:	chr19:1257189-1257449(+)$1	260	198	223	20.3560
ffyyyyyyyyyyyyyyyyffffff3	chr1:23885776-23886060(-)$1	284	118	143	20.2446
ii!!ccctttttttttttccc4444	chr16:18817796-18818037(-)$1	241	63	88	23.2850
iiiiiiuuuuuuuuuuuuiiiiiii	chr1:224621793-224622052(-)$1	259	194	219	24.1270
iiiiiiitttttttttttiiiiiii	chr7:44100741-44100968(+)$1	227	199	224	22.7289
dddbbyyyyyyyyyyyyyyyybb]d	chr12:118587592-118587820(-)$1	228	94	119	20.9178
c[dddduuuuuuuuuuuudddd]cc	chr17:79801018-79801289(-)$1	271	75	100	23.6897
a[ddddtttttttttttdddda333	chr12:132414001-132414264(+)$1	263	171	196	22.4741
f"""ccctttttttttttccc]fff	chr21:45403443-45403698(+)$1	255	155	180	22.3417
======yyyyyyyyyyyyyyyy===	chr1:61922782-61923017(+)$1	235	105	130	23.0863
[eeeeeuuuuuuuuuuuueeeee]d	chr6:16301299-16301530(-)$1	231	196	221	23.3353
ffffffftttttttttttffffffc	chr14:102516765-102516998(+)$1	233	86	111	20.8603
"""ddddtttttttttttdddd444	chr12:56636311-56636553(-)$1	242	183	208	22.7867
###ddddtttttttttttdddd444	chr19:42752392-42752650(-)$1	258	169	194	22.7010
======wwwwwwwwwwwwww=====	chr16:30792799-30793037(-)$1	238	53	78	22.9217
ggggggwwwwwwwwwwwwwwggggg	chr7:2702630-2702905(+)$1	275	110	135	22.4615
""ddddtttttttttttdddd333e	chr12:22601647-22601886(-)$1	239	20	45	22.3478
e!!cccvvvvvvvvvvvvvccc22e	chr10:81072918-81073193(+)$1	275	95	120	22.7453
gggggggtttttttttttggggggg	chr8:104344423-104344668(+)$1	245	165	190	22.5811
gggggguuuuuuuuuuuuggggggg	chr19:47113021-47113273(+)$1	252	16	41	23.8853
ggggggvvvvvvvvvvvvvgggggg	chr14:93406176-93406438(-)$1	262	31	56	23.1123
[eeeeewwwwwwwwwwwwwweeeee	chr1:156904864-156905095(-)$1	231	124	149	21.7901
iiiiiivvvvvvvvvvvvviiiiii	chr16:30363484-30363747(-)$1	263	25	50	23.3253
======wwwwwwwwwwwwww=====	chr6:150132358-150132592(+)$1	234	128	153	22.9217
ffyyyyyyyyyyyyyyyyffffff:	chr2:120738592-120738823(+)$1	231	164	189	19.2087
ddddwwwwwwwwwwwwwwdddd444	chr8:12579577-12579819(-)$1	242	25	50	20.7028

#otherMatches

#Seq PSSM
GAGAACCACCGCAUCAAGAGCUUCA	chr13:50366514-50366746(-)$1	232	125	150	22.5055
UUUUUCUUACCUUCUGUUGACAGCU	chr10:116623431-116623671(+)$1	240	49	74	22.5066
GUGGGCUACAAGGACUCGCCCUCCG	chr17:4851459-4851714(-)$1	255	91	116	20.9052
UUUUAAGUCUUCAAAUAUCUUGAGA	chr6:136582059-136582329(-)$1	270	214	239	22.5811
GAGGCCUUAAAUAGGGAAACGGCCU	chr1:935306-935603(-)$1	297	92	117	21.7901
CAUUCAGUCUCUCUGCCUCUGCCUG	chr6:109307733-109308004(-)$1	271	111	136	22.4872
AUGAAAGUCGCUUUCUUUUUAUUCA	chr6:1612759-1613001(+)$1	242	30	55	23.0509
GGUGUGCUUCAAACAAAUGCUAGAC	chrX:109438834-109439100(-)$1	266	25	50	21.5967
CCGGCCCCUCAGGACCAGGCGGGCC	chr19:45476268-45476501(+)$1	233	118	143	21.9658
augcugACCACAGACCUUUAUAGCA	chr13:52706795-52707032(-)$1	237	127	152	21.7901
GGCAUUGAAACAUUACAACAAUGUU	chr4:57801627-57801858(+)$1	231	57	82	22.5811
AGGAAAUGAAUACCAGUAGUUUAGU	chr15:65847168-65847398(+)$1	230	166	191	22.5918
UGUUUUUCUUUUCCUAUUAAAACGU	chr10:32299947-32300186(-)$1	239	128	153	20.3173
UGAAGAUAAGAUACUCACUGUUCAU	chr10:74035564-74035812(+)$1	248	130	155	22.6834
UGCUGUUCUGGAAUAUCACAUGCUA	chr6:116599319-116599585(-)$1	266	110	135	21.5239
UAAACAUAAAAGACACCAUCCUGUU	chr7:63981374-63981613(-)$1	239	83	108	17.7458
GCCCUGCCUCCACCCACCUCGGGAG	chr17:78183238-78183509(-)$1	271	217	242	22.1461
UAAGGGAUCCCAGCCUGCCCCUCCA	chr1:27180997-27181252(+)$1	255	60	85	21.3390
CUCAUGAAGCAGUUCCCACAUGGGC	chr3:126755189-126755475(+)$1	286	44	69	23.5612
UAAUCAUUCUUAACUUCUUGGUAGC	chr16:18803237-18803485(-)$1	248	51	76	23.9370
GAACUAAAUAUGGAAGAAAUGGUAA	chr2:71653698-71653940(+)$1	242	185	210	21.7178
AAAAUGUAUUUUUGCACAACAUUUU	chr10:23729927-23730176(+)$1	249	217	242	22.7289
AGGUGCUUUACUGUUCACCUGCAUC	chr9:134372908-134373145(+)$1	237	180	205	22.9217
GUUUAUUUUCUUUUUUCGUUUUAUA	chr2:32379959-32380197(+)$1	238	83	108	22.6891
CUACAGAUGCUUCUCUUGCUGUGGG	chr10:51589609-51589840(+)$1	231	25	50	23.8853
CAUUCCAAAACCCCAAGCCAGGAAA	chr9:139253151-139253419(+)$1	268	207	232	18.7499
CCUGACACCGCAAUAACCCGUUAGG	chr14:93705237-93705471(-)$1	234	105	130	20.5831
UCAUUUCUCAGUCACCAACAGAUGA	chr8:29193992-29194277(-)$1	285	240	265	23.1123
GCCUGGACUUGGGAAAUAUACUGGG	chr12:110782980-110783249(+)$1	269	17	42	22.4615
CUGGGGGUUUCAGUCAUCUCCCCAU	chr6:32948918-32949161(+)$1	243	85	110	21.2905
UGUUCAGUGCUGAAAACUAAAAUGA	chr2:20449372-20449651(-)$1	279	149	174	20.7972
CUGCCAUCUUCUGUGUCCCCUUGGC	chr16:2580237-2580515(+)$1	278	112	137	17.8605
ACAGAUCCCAUCUCAAAUCAUUCUG	chr6:114181661-114181971(+)$1	310	276	301	22.0348
CUCGCAGAUUAGUCAGGAUGCCCAC	chr11:769014-769253(-)$1	239	26	51	22.0296
AGGCUGCUGCCCCUUUAUCUGCCUU	chr1:16723884-16724144(+)$1	260	153	178	22.2955
CUUGUAAAAAAAAAAAACUACAAAA	chr22:22114558-22114796(-)$1	238	119	144	22.0355
AGAAGucuuuuuuucuuuucuucuu	chr19:1257189-1257449(+)$1	260	198	223	20.3560
GGCACCUCUGGACUCACUCCCCAGC	chr1:23885776-23886060(-)$1	284	118	143	20.2446
AGUUCAAUCUUAAGUUUUUUGCUGU	chr16:18817796-18818037(-)$1	241	63	88	23.2850
GCUGCUGUCCCCCACCGAAGUAGCG	chr1:224621793-224622052(-)$1	259	194	219	24.1270
GAACAGUGAACGUAGAGAAUUGUUU	chr7:44100741-44100968(+)$1	227	199	224	22.7289
AAGGCUUUACUUCUUUUGCAUGCAC	chr12:118587592-118587820(-)$1	228	94	119	20.9178
CUGGCCUCUCUACAGCACGGCCUGU	chr17:79801018-79801289(-)$1	271	75	100	23.6897
GUCCGAGAGGUUAGGGGUCGGCAGA	chr12:132414001-132414264(+)$1	263	171	196	22.4741
AGAACGCUCAACUUGGUUGCGGUAC	chr21:45403443-45403698(+)$1	255	155	180	22.3417
GUUUUUUUUCCUUAAUUUGCACGAA	chr1:61922782-61923017(+)$1	235	105	130	23.0863
GUUUGUAAAAAAAAAAAAGCAGAGA	chr6:16301299-16301530(-)$1	231	196	221	23.3353
UCCUCGCAGCUUCUACGAGCGGGGU	chr14:102516765-102516998(+)$1	233	86	111	20.8603
CCUGGAGCUUUUUCCCCACUUCUGU	chr12:56636311-56636553(-)$1	242	183	208	22.7867
UAUAAAACUUUAAUUUCUUUUUUUU	chr19:42752392-42752650(-)$1	258	169	194	22.7010
UUCCCCCAAAAAAAUUACAUGGGGA	chr16:30792799-30793037(-)$1	238	53	78	22.9217
GAUCGGACGUGCUACCCCUCCCGGU	chr7:2702630-2702905(+)$1	275	110	135	22.4615
ACUCCUACCAAAUAAACAGGAUUUU	chr12:22601647-22601886(-)$1	239	20	45	22.3478
GCAGUGAGACCAGCCCACCCACCAC	chr10:81072918-81073193(+)$1	275	95	120	22.7453
GAUUGUAUUAUAACCACUUACAGUU	chr8:104344423-104344668(+)$1	245	165	190	22.5811
AGUGGGCAACACUCACAUCCCACUG	chr19:47113021-47113273(+)$1	252	16	41	23.8853
GAGGCCAUCAGAACUGCCCGGCUUU	chr14:93406176-93406438(-)$1	262	31	56	23.1123
CCCUGUAGAAAACCAGUGAAGCAGG	chr1:156904864-156905095(-)$1	231	124	149	21.7901
AGCCAGUGUCUUCCCUAAUCUGGCU	chr16:30363484-30363747(-)$1	263	25	50	23.3253
AGCUGUGUCCUAGUUCUUGAACAGU	chr6:150132358-150132592(+)$1	234	128	153	22.9217
GCAUUUCAGUCACUUAUAGUAAAUA	chr2:120738592-120738823(+)$1	231	164	189	19.2087
GGGCUUUUCACAUUAACUGCCCAUU	chr8:12579577-12579819(-)$1	242	25	50	20.7028

#DB
(((..(...........)..)))))	chr13:50366514-50366746(-)$1	1	125	150	22.5055
((..((............)).))))	chr10:116623431-116623671(+)$1	1	49	74	22.5066
(.((((...........))))..))	chr17:4851459-4851714(-)$1	1	91	116	20.9052
(((((((...........)))))))	chr6:136582059-136582329(-)$1	1	214	239	22.5811
.(((((..............)))))	chr1:935306-935603(-)$1	1	92	117	21.7901
((..(((...........)))..))	chr6:109307733-109308004(-)$1	1	111	136	22.4872
(((((................))))	chr6:1612759-1613001(+)$1	1	30	55	23.0509
(((.(((...........)).).))	chrX:109438834-109439100(-)$1	1	25	50	21.5967
((.(((...........))).))))	chr19:45476268-45476501(+)$1	1	118	143	21.9658
.(((((..............)))))	chr13:52706795-52707032(-)$1	1	127	152	21.7901
(((((((...........)))))))	chr4:57801627-57801858(+)$1	1	57	82	22.5811
(..((((...........))))..)	chr15:65847168-65847398(+)$1	1	166	191	22.5918
.(((((............)))))..	chr10:32299947-32300186(-)$1	1	128	153	20.3173
((((.(............).)))))	chr10:74035564-74035812(+)$1	1	130	155	22.6834
.(((((...........))).))..	chr6:116599319-116599585(-)$1	1	110	135	21.5239
(.((((...............))))	chr7:63981374-63981613(-)$1	1	83	108	17.7458
((((((.............)))).)	chr17:78183238-78183509(-)$1	1	217	242	22.1461
..((((............))))...	chr1:27180997-27181252(+)$1	1	60	85	21.3390
(.((((............)))))))	chr3:126755189-126755475(+)$1	1	44	69	23.5612
..((((............))))...	chr16:18803237-18803485(-)$1	1	51	76	23.9370
..((((.............))))..	chr2:71653698-71653940(+)$1	1	185	210	21.7178
(((((((...........)))))))	chr10:23729927-23730176(+)$1	1	217	242	22.7289
((((((..............)))))	chr9:134372908-134373145(+)$1	1	180	205	22.9217
((((((................)))	chr2:32379959-32380197(+)$1	1	83	108	22.6891
((((((............)))))))	chr10:51589609-51589840(+)$1	1	25	50	23.8853
..((((..............)))).	chr9:139253151-139253419(+)$1	1	207	232	18.7499
((((((.............))))))	chr14:93705237-93705471(-)$1	1	105	130	20.5831
((((((.............))))))	chr8:29193992-29194277(-)$1	1	240	265	23.1123
((((((..............)))))	chr12:110782980-110783249(+)$1	1	17	42	22.4615
.((((((...........)))))).	chr6:32948918-32949161(+)$1	1	85	110	21.2905
((((((................)))	chr2:20449372-20449651(-)$1	1	149	174	20.7972
..((((...............))))	chr16:2580237-2580515(+)$1	1	112	137	17.8605
(((((................))))	chr6:114181661-114181971(+)$1	1	276	301	22.0348
...(((............)))....	chr11:769014-769253(-)$1	1	26	51	22.0296
((((................))).)	chr1:16723884-16724144(+)$1	1	153	178	22.2955
.(((((............)))))..	chr22:22114558-22114796(-)$1	1	119	144	22.0355
(((((..............))))).	chr19:1257189-1257449(+)$1	1	198	223	20.3560
((................)))))).	chr1:23885776-23886060(-)$1	1	118	143	20.2446
((..(((...........)))....	chr16:18817796-18818037(-)$1	1	63	88	23.2850
((((((............)))))))	chr1:224621793-224622052(-)$1	1	194	219	24.1270
(((((((...........)))))))	chr7:44100741-44100968(+)$1	1	199	224	22.7289
(((((................)).)	chr12:118587592-118587820(-)$1	1	94	119	20.9178
(.((((............)))).))	chr17:79801018-79801289(-)$1	1	75	100	23.6897
(.((((...........)))))...	chr12:132414001-132414264(+)$1	1	171	196	22.4741
(...(((...........))).)))	chr21:45403443-45403698(+)$1	1	155	180	22.3417
((((((................)))	chr1:61922782-61923017(+)$1	1	105	130	23.0863
.(((((............))))).)	chr6:16301299-16301530(-)$1	1	196	221	23.3353
)((((((...........))))))(	chr14:102516765-102516998(+)$1	1	86	111	20.8603
...((((...........))))...	chr12:56636311-56636553(-)$1	1	183	208	22.7867
...((((...........))))...	chr19:42752392-42752650(-)$1	1	169	194	22.7010
((((((..............)))))	chr16:30792799-30793037(-)$1	1	53	78	22.9217
((((((..............)))))	chr7:2702630-2702905(+)$1	1	110	135	22.4615
..((((...........))))...)	chr12:22601647-22601886(-)$1	1	20	45	22.3478
(..(((.............)))..)	chr10:81072918-81073193(+)$1	1	95	120	22.7453
(((((((...........)))))))	chr8:104344423-104344668(+)$1	1	165	190	22.5811
((((((............)))))))	chr19:47113021-47113273(+)$1	1	16	41	23.8853
((((((.............))))))	chr14:93406176-93406438(-)$1	1	31	56	23.1123
.(((((..............)))))	chr1:156904864-156905095(-)$1	1	124	149	21.7901
((((((.............))))))	chr16:30363484-30363747(-)$1	1	25	50	23.3253
((((((..............)))))	chr6:150132358-150132592(+)$1	1	128	153	22.9217
((................)))))).	chr2:120738592-120738823(+)$1	1	164	189	19.2087
((((..............))))...	chr8:12579577-12579819(-)$1	1	25	50	20.7028

#PSSM
g : 0.17	e : 0.09	i : 0.09	[ : 0.08	c : 0.08	= : 0.08	f : 0.08	" : 0.06	d : 0.04	# : 0.04	: : 0.03	h : 0.03	b : 0.01	& : 0.01	$ : 0.01	' : 0.01	a : 0.01	
g : 0.17	e : 0.16	i : 0.09	[ : 0.08	f : 0.08	= : 0.06	" : 0.06	c : 0.04	d : 0.04	# : 0.04	! : 0.03	h : 0.03	b : 0.01	& : 0.01	$ : 0.01	: : 0.01	
d : 0.22	g : 0.17	e : 0.12	! : 0.08	i : 0.08	= : 0.06	f : 0.04	" : 0.04	c : 0.03	h : 0.03	y : 0.03	[ : 0.01	b : 0.01	# : 0.01	
d : 0.25	g : 0.16	e : 0.12	i : 0.08	c : 0.08	! : 0.06	= : 0.06	f : 0.04	h : 0.03	y : 0.03	[ : 0.01	b : 0.01	" : 0.01	
d : 0.24	g : 0.16	e : 0.12	c : 0.11	i : 0.08	= : 0.06	y : 0.04	b : 0.03	h : 0.03	f : 0.03	! : 0.01	a : 0.01	[ : 0.01	w : 0.01	
d : 0.24	g : 0.16	c : 0.11	e : 0.09	y : 0.09	i : 0.06	= : 0.06	a : 0.03	b : 0.03	h : 0.03	f : 0.03	w : 0.03	
u : 0.20	w : 0.17	y : 0.14	v : 0.11	t : 0.09	g : 0.04	c : 0.04	d : 0.04	x : 0.03	i : 0.03	f : 0.03	b : 0.01	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.32	u : 0.20	w : 0.17	y : 0.14	v : 0.11	x : 0.03	
t : 0.22	u : 0.20	w : 0.17	y : 0.14	v : 0.11	d : 0.04	c : 0.03	x : 0.03	a : 0.01	
d : 0.17	w : 0.16	y : 0.11	v : 0.11	c : 0.09	g : 0.08	f : 0.06	e : 0.04	i : 0.04	b : 0.03	x : 0.03	2 : 0.01	a : 0.01	
d : 0.20	w : 0.14	g : 0.11	c : 0.11	y : 0.11	e : 0.06	i : 0.06	f : 0.06	b : 0.03	x : 0.03	2 : 0.01	] : 0.01	h : 0.01	
d : 0.22	g : 0.16	e : 0.11	c : 0.09	y : 0.09	f : 0.08	] : 0.06	i : 0.06	= : 0.04	x : 0.03	h : 0.01	
d : 0.20	g : 0.16	e : 0.16	i : 0.08	f : 0.08	= : 0.04	y : 0.04	2 : 0.03	a : 0.03	b : 0.03	c : 0.03	h : 0.01	7 : 0.01	4 : 0.01	] : 0.01	3 : 0.01	
g : 0.17	e : 0.16	f : 0.09	i : 0.08	d : 0.08	4 : 0.08	2 : 0.06	= : 0.06	] : 0.03	b : 0.03	c : 0.03	h : 0.03	3 : 0.03	6 : 0.01	7 : 0.01	
g : 0.17	e : 0.11	f : 0.09	i : 0.08	4 : 0.08	c : 0.06	] : 0.06	= : 0.06	3 : 0.04	d : 0.04	6 : 0.04	2 : 0.03	h : 0.03	b : 0.01	: : 0.01	7 : 0.01	
g : 0.17	e : 0.12	c : 0.09	i : 0.08	= : 0.08	d : 0.08	4 : 0.08	: : 0.06	3 : 0.06	6 : 0.04	f : 0.03	h : 0.03	b : 0.01	7 : 0.01	

#score	1367.7402058975379
#seq	62
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m2_run2.txt

#BEAR
:eeeeeqqqqqqqqeeeee	chr1:92709662-92709884(-)$1	222	58	77	12.9004
ffffffqqqqqqqqfffff	chr9:94123838-94124060(+)$1	222	179	198	13.0430
ff[a[aqqqqqqqqa22a]	chr2:47596528-47596767(-)$1	239	128	147	13.7709
bb!!bbqqqqqqqqbb22b	chr9:136901574-136901799(-)$1	225	204	223	13.3051
:a[cccqqqqqqqqccc]a	chr20:17623627-17623849(+)$1	222	163	182	14.6156
dddcccqqqqqqqqccc]d	chr19:35616302-35616525(+)$1	223	167	186	14.7057
[eeeeeqqqqqqqqeeeee	chr20:44582465-44582690(-)$1	225	133	152	13.7706
e!!cccqqqqqqqqccc22	chr11:71928343-71928568(+)$1	225	55	74	15.4134
!!ddddqqqqqqqqdddd2	chr17:43227163-43227388(-)$1	225	13	32	14.0350
ccccccqqqqqqqqccc]c	chr6:50807803-50808027(-)$1	224	152	171	15.1010
"""cccqqqqqqqqccc33	chr10:75671245-75671467(-)$1	222	143	162	15.8587
:eeeeeqqqqqqqqeeeee	chr12:7310521-7310745(+)$1	224	163	182	12.9004
dd[cccqqqqqqqqcccdd	chr8:119122727-119122950(+)$1	223	42	61	14.7137
f!!cccqqqqqqqqccc44	chr7:38791692-38791914(+)$1	222	79	98	15.6051
####bbqqqqqqqqbb444	chr22:44004278-44004500(-)$1	222	29	48	14.3837
cc[cccqqqqqqqqccc]c	chr13:37679060-37679281(+)$1	221	78	97	15.4138
"eeeeeqqqqqqqqeeeee	chr9:133333752-133333974(-)$1	222	61	80	13.7993
gg!!bbqqqqqqqqbb]gg	chr19:4891273-4891495(+)$1	222	178	197	14.0920
:eeeeeqqqqqqqqeeeee	chr2:205986490-205986715(-)$1	225	188	207	12.9004
"""cccqqqqqqqqccc33	chr1:171752843-171753064(+)$1	221	92	111	15.8587
:eeeeeqqqqqqqqeeeee	chr11:118827836-118828069(+)$1	233	16	35	12.9004
""a[bbqqqqqqqqbb]a3	chr8:143435970-143436191(+)$1	221	79	98	14.3209
ccccccqqqqqqqqccc22	chr6:35587832-35588057(+)$1	225	73	92	15.0258
======qqqqqqqq=====	chr2:160604732-160604953(-)$1	221	194	213	14.5481
c[ddddqqqqqqqqdddd]	chr8:126021406-126021629(+)$1	223	109	128	13.9959
!!ddddqqqqqqqqdddd5	chr22:25423944-25424169(-)$1	225	165	184	13.3635
ccc[bbqqqqqqqqbb]cc	chr17:72999837-73000058(-)$1	221	185	204	13.7235
ee:cccqqqqqqqqccchh	chr1:156288540-156288769(+)$1	229	130	149	13.4409
ffffffqqqqqqqqfffff	chr3:93845042-93845265(-)$1	223	105	124	13.0430
dd[cccqqqqqqqqccc]d	chr17:19283705-19283926(+)$1	221	48	67	15.0538
$$$cccqqqqqqqqccc55	chr7:121941955-121942179(-)$1	224	9	28	13.3803
dd[cccqqqqqqqqccc44	chr15:44962148-44962370(+)$1	222	106	125	15.2605
eeddddqqqqqqqqdddd]	chr3:12779125-12779347(+)$1	222	177	196	13.6750
ff[cccqqqqqqqqccc22	chr14:36783792-36784017(-)$1	225	5	24	15.1703
b!!cccqqqqqqqqccc22	chr11:119056819-119057041(+)$1	222	131	150	15.4245
ddd[bbqqqqqqqqbb]dd	chr17:78936242-78936464(-)$1	222	200	219	13.3039
!eeeeeqqqqqqqqeeeee	chr19:989794-990016(+)$1	222	127	146	13.8064
bb[cccqqqqqqqqccc]b	chr3:49163746-49163971(-)$1	225	132	151	14.7573
e[bb[aqqqqqqqqa]bb]	chr10:77158874-77159097(+)$1	223	21	40	13.0681
iii[bbqqqqqqqqbb]ii	chr1:45091946-45092186(-)$1	240	192	211	13.9634
####bbqqqqqqqqbb444	chrX:51637758-51637980(-)$1	222	27	46	14.3837
gggcccqqqqqqqqccc]g	chr16:24801242-24801463(-)$1	221	159	178	15.1617
cc[cccqqqqqqqqccccc	chrX:103498766-103498987(-)$1	221	36	55	15.0980
b[ddddqqqqqqqqddddb	chr12:53452074-53452297(-)$1	223	157	176	13.4398
"eeeeeqqqqqqqqeeeee	chr12:55945417-55945641(-)$1	224	34	53	13.7993
f[bb[aqqqqqqqqabb]f	chr20:43538804-43539026(+)$1	222	23	42	13.5441
a[ddddqqqqqqqqdddd]	chr10:79685949-79686173(-)$1	224	53	72	14.0158
ffffffqqqqqqqqfffff	chr12:107713254-107713475(-)$1	221	142	161	13.0430
f[ddddqqqqqqqqdddd3	chr9:111617410-111617633(+)$1	223	162	181	14.0180
e!!cccqqqqqqqqccc22	chr17:58700981-58701207(+)$1	226	196	215	15.4134
iiiiiiqqqqqqqqiiiii	chr4:169374219-169374443(-)$1	224	34	53	14.1651
cc[cccqqqqqqqqccc]c	chr18:29497519-29497742(+)$1	223	33	52	15.4138
ffffbbqqqqqqqqbb]ff	chrX:70344830-70345051(+)$1	221	3	22	13.2101
bccc[aqqqqqqqqa]ccc	chr19:47570637-47570860(-)$1	223	141	160	14.0792
ff[cccqqqqqqqqccc]f	chr17:47583771-47583993(-)$1	222	72	91	15.1737
gccc[aqqqqqqqqa]ccc	chr7:75694040-75694264(+)$1	224	173	192	14.1700
cc[cccqqqqqqqqccc]c	chr11:61914204-61914429(+)$1	225	54	73	15.4138
dd[cccqqqqqqqqccc]d	chr19:36258946-36259171(+)$1	225	56	75	15.0538
dddcccqqqqqqqqccc22	chr18:51819958-51820181(+)$1	223	44	63	14.7470
b[ddddqqqqqqqqdddd2	chr15:91500771-91500994(+)$1	223	184	203	13.7973
iiiiiiqqqqqqqqiiiii	chr14:25100220-25100446(+)$1	226	133	152	14.1651
i!!cccqqqqqqqqcccii	chr14:59113165-59113386(-)$1	221	113	132	15.4187
b!!cccqqqqqqqqccc]b	chr7:148427107-148427331(-)$1	224	121	140	15.2261
[eeeeeqqqqqqqqeeeee	chrX:100662694-100662918(-)$1	224	195	214	13.7706
:eeeeeqqqqqqqqeeeee	chr20:21689768-21689990(+)$1	222	6	25	12.9004
!eeeeeqqqqqqqqeeeee	chr11:18541038-18541266(-)$1	228	121	140	13.8064
[bb[bbqqqqqqqqbbbb]	chr10:89621794-89622019(-)$1	225	75	94	12.8768
eeee[aqqqqqqqqaeeee	chr2:219558875-219559099(-)$1	224	30	49	13.8626
==!!bbqqqqqqqqbb22=	chr8:67488197-67488419(-)$1	222	80	99	14.1675

#otherMatches

#Seq PSSM
UUCUUCAGUUGACAGAAGA	chr1:92709662-92709884(-)$1	222	58	77	12.9004
GGGCCCAGAUCGCCGGGCC	chr9:94123838-94124060(+)$1	222	179	198	13.0430
GCGCGCGCCGAGAAGAggg	chr2:47596528-47596767(-)$1	239	128	147	13.7709
CCUUGGAUUUUCUGCCUUG	chr9:136901574-136901799(-)$1	225	204	223	13.3051
AGAGCUGAGACUUAGGCCC	chr20:17623627-17623849(+)$1	222	163	182	14.6156
CAGCUUGGAAGCAGAAGCC	chr19:35616302-35616525(+)$1	223	167	186	14.7057
GCAGGGUUAGCAUCCCCUG	chr20:44582465-44582690(-)$1	225	133	152	13.7706
uguggggaaggcaacuuga	chr11:71928343-71928568(+)$1	225	55	74	15.4134
CGCUCGUACGUCUCCGAGA	chr17:43227163-43227388(-)$1	225	13	32	14.0350
GCUUCUCCUGAAAAAGACA	chr6:50807803-50808027(-)$1	224	152	171	15.1010
AGGGCUCUCAUGGUGGCGA	chr10:75671245-75671467(-)$1	222	143	162	15.8587
ACCUCUCCCCACGCAGAGG	chr12:7310521-7310745(+)$1	224	163	182	12.9004
GUGCACAUACUGAGGUGAC	chr8:119122727-119122950(+)$1	223	42	61	14.7137
UUACCUUUUCAAGUGGGCA	chr7:38791692-38791914(+)$1	222	79	98	15.6051
GAAACCGAUAAUGAGGGCA	chr22:44004278-44004500(-)$1	222	29	48	14.3837
GUUGUCUUUUUCCUGACCA	chr13:37679060-37679281(+)$1	221	78	97	15.4138
GCGGGCGAUGCAGGGCCUG	chr9:133333752-133333974(-)$1	222	61	80	13.7993
UUGAUCUCUGUUGUGAAGA	chr19:4891273-4891495(+)$1	222	178	197	14.0920
UCAGGACUAUCGGUUCCUG	chr2:205986490-205986715(-)$1	225	188	207	12.9004
CUAUCGGGAUAUAGUGAAC	chr1:171752843-171753064(+)$1	221	92	111	15.8587
UGCCCCUUCUCCUUGGGGC	chr11:118827836-118828069(+)$1	233	16	35	12.9004
CAGGCCACCUCCACGGGCG	chr8:143435970-143436191(+)$1	221	79	98	14.3209
UGCCUCAAAAAAGAGAGUU	chr6:35587832-35588057(+)$1	225	73	92	15.0258
UUCUUGGAGAAACGUAAGA	chr2:160604732-160604953(-)$1	221	194	213	14.5481
GACAUUAGAGGAGAAAUGC	chr8:126021406-126021629(+)$1	223	109	128	13.9959
AAGGGCGUUAUGGAGCCCA	chr22:25423944-25424169(-)$1	225	165	184	13.3635
CGUACUUCUCCAGCAGCGC	chr17:72999837-73000058(-)$1	221	185	204	13.7235
UUUCUUGUAUUCCAGAGAA	chr1:156288540-156288769(+)$1	229	130	149	13.4409
GUGGGAGUUUAAAAUUUCA	chr3:93845042-93845265(-)$1	223	105	124	13.0430
AGAAUCUAAAACGUGAUGC	chr17:19283705-19283926(+)$1	221	48	67	15.0538
CCAGGCACUGAAccgccgc	chr7:121941955-121942179(-)$1	224	9	28	13.3803
CCUGCUUCUUCUCUAGCUU	chr15:44962148-44962370(+)$1	222	106	125	15.2605
GUGGGAUUUUCUUUUCCCU	chr3:12779125-12779347(+)$1	222	177	196	13.6750
CCAUUGGCGACCUACAAGA	chr14:36783792-36784017(-)$1	225	5	24	15.1703
GUAACCACUCACUCGGUCU	chr11:119056819-119057041(+)$1	222	131	150	15.4245
GACGCUGCCAAGAGAGGGU	chr17:78936242-78936464(-)$1	222	200	219	13.3039
ACCUGGAACUGCACCCGGG	chr19:989794-990016(+)$1	222	127	146	13.8064
CCUGAGACUCCCUACUCUG	chr3:49163746-49163971(-)$1	225	132	151	14.7573
AGUUGCAGAUGUGGGGGAG	chr10:77158874-77159097(+)$1	223	21	40	13.0681
UUGAUGGAAGCAGACAACA	chr1:45091946-45092186(-)$1	240	192	211	13.9634
AGGGGUGAAGUAGGGCAAG	chrX:51637758-51637980(-)$1	222	27	46	14.3837
GGUAAUAUUUUGAGGUUGA	chr16:24801242-24801463(-)$1	221	159	178	15.1617
UGAGGGACCACAGCCCCCA	chrX:103498766-103498987(-)$1	221	36	55	15.0980
GUCCGGUCUGUGCCCCGGC	chr12:53452074-53452297(-)$1	223	157	176	13.4398
GAGGAUGACCAUCAGUUCU	chr12:55945417-55945641(-)$1	224	34	53	13.7993
UGGGCGAUCUGCACCCCGA	chr20:43538804-43539026(+)$1	222	23	42	13.5441
GGAGCUGCUGCUCAAGCUG	chr10:79685949-79686173(-)$1	224	53	72	14.0158
GGGCCGACUUGCCGCGGCC	chr12:107713254-107713475(-)$1	221	142	161	13.0430
UCGCCCUCGGAUAUGGGCA	chr9:111617410-111617633(+)$1	223	162	181	14.0180
AUUGACCUACUACUGUCCC	chr17:58700981-58701207(+)$1	226	196	215	15.4134
CAGGAGGUGGAAGAUUUCU	chr4:169374219-169374443(-)$1	224	34	53	14.1651
GGUUCAGAAAUUCAUGAUC	chr18:29497519-29497742(+)$1	223	33	52	15.4138
CCCUACUAUGCCCUGUGAG	chrX:70344830-70345051(+)$1	221	3	22	13.2101
GCCGUGAACAUUCCCCUGG	chr19:47570637-47570860(-)$1	223	141	160	14.0792
CGUCGGAAUACGUGCCGUC	chr17:47583771-47583993(-)$1	222	72	91	15.1737
CUUCGUUAAGUCACAGGAA	chr7:75694040-75694264(+)$1	224	173	192	14.1700
cggcgcgagcaggagcggc	chr11:61914204-61914429(+)$1	225	54	73	15.4138
CCAGCCCCCUAAGAGGCCG	chr19:36258946-36259171(+)$1	225	56	75	15.0538
UAUUCUUGUGUUCUAGAAA	chr18:51819958-51820181(+)$1	223	44	63	14.7470
GUGAGUGACUUAGUGCUUC	chr15:91500771-91500994(+)$1	223	184	203	13.7973
UGUUUCGUCCAUAGGAGAC	chr14:25100220-25100446(+)$1	226	133	152	14.1651
GCCGGGAACACCAGCCUCG	chr14:59113165-59113386(-)$1	221	113	132	15.4187
AGGGAUGUUCUAAAGUCGU	chr7:148427107-148427331(-)$1	224	121	140	15.2261
CAGGAAGAGCCAGAUUCCU	chrX:100662694-100662918(-)$1	224	195	214	13.7706
UGGACGAAAACCCCCGUCU	chr20:21689768-21689990(+)$1	222	6	25	12.9004
AUACAGAGACCUAACUGUA	chr11:18541038-18541266(-)$1	228	121	140	13.8064
CAGCGGAACCCCAACCCUU	chr10:89621794-89622019(-)$1	225	75	94	12.8768
GUGAAGGUUAAAAACUUAC	chr2:219558875-219559099(-)$1	224	30	49	13.8626
CCCCAGGCAGCGAACUUAG	chr8:67488197-67488419(-)$1	222	80	99	14.1675

#DB
.(((((........)))))	chr1:92709662-92709884(-)$1	1	58	77	12.9004
((((((........)))))	chr9:94123838-94124060(+)$1	1	179	198	13.0430
((.(.(........)..).	chr2:47596528-47596767(-)$1	1	128	147	13.7709
((..((........))..)	chr9:136901574-136901799(-)$1	1	204	223	13.3051
.(.(((........))).)	chr20:17623627-17623849(+)$1	1	163	182	14.6156
((((((........))).)	chr19:35616302-35616525(+)$1	1	167	186	14.7057
.(((((........)))))	chr20:44582465-44582690(-)$1	1	133	152	13.7706
(..(((........)))..	chr11:71928343-71928568(+)$1	1	55	74	15.4134
..((((........)))).	chr17:43227163-43227388(-)$1	1	13	32	14.0350
((((((........))).)	chr6:50807803-50808027(-)$1	1	152	171	15.1010
...(((........)))..	chr10:75671245-75671467(-)$1	1	143	162	15.8587
.(((((........)))))	chr12:7310521-7310745(+)$1	1	163	182	12.9004
((.(((........)))))	chr8:119122727-119122950(+)$1	1	42	61	14.7137
(..(((........)))..	chr7:38791692-38791914(+)$1	1	79	98	15.6051
....((........))...	chr22:44004278-44004500(-)$1	1	29	48	14.3837
((.(((........))).)	chr13:37679060-37679281(+)$1	1	78	97	15.4138
.(((((........)))))	chr9:133333752-133333974(-)$1	1	61	80	13.7993
((..((........)).))	chr19:4891273-4891495(+)$1	1	178	197	14.0920
.(((((........)))))	chr2:205986490-205986715(-)$1	1	188	207	12.9004
...(((........)))..	chr1:171752843-171753064(+)$1	1	92	111	15.8587
.(((((........)))))	chr11:118827836-118828069(+)$1	1	16	35	12.9004
..(.((........)).).	chr8:143435970-143436191(+)$1	1	79	98	14.3209
((((((........)))..	chr6:35587832-35588057(+)$1	1	73	92	15.0258
((((((........)))))	chr2:160604732-160604953(-)$1	1	194	213	14.5481
(.((((........)))).	chr8:126021406-126021629(+)$1	1	109	128	13.9959
..((((........)))).	chr22:25423944-25424169(-)$1	1	165	184	13.3635
(((.((........)).))	chr17:72999837-73000058(-)$1	1	185	204	13.7235
)).(((........)))((	chr1:156288540-156288769(+)$1	1	130	149	13.4409
((((((........)))))	chr3:93845042-93845265(-)$1	1	105	124	13.0430
((.(((........))).)	chr17:19283705-19283926(+)$1	1	48	67	15.0538
...(((........)))..	chr7:121941955-121942179(-)$1	1	9	28	13.3803
((.(((........)))..	chr15:44962148-44962370(+)$1	1	106	125	15.2605
((((((........)))).	chr3:12779125-12779347(+)$1	1	177	196	13.6750
((.(((........)))..	chr14:36783792-36784017(-)$1	1	5	24	15.1703
(..(((........)))..	chr11:119056819-119057041(+)$1	1	131	150	15.4245
(((.((........)).))	chr17:78936242-78936464(-)$1	1	200	219	13.3039
.(((((........)))))	chr19:989794-990016(+)$1	1	127	146	13.8064
((.(((........))).)	chr3:49163746-49163971(-)$1	1	132	151	14.7573
(.((.(........).)).	chr10:77158874-77159097(+)$1	1	21	40	13.0681
(((.((........)).))	chr1:45091946-45092186(-)$1	1	192	211	13.9634
....((........))...	chrX:51637758-51637980(-)$1	1	27	46	14.3837
((((((........))).)	chr16:24801242-24801463(-)$1	1	159	178	15.1617
((.(((........)))))	chrX:103498766-103498987(-)$1	1	36	55	15.0980
(.((((........)))))	chr12:53452074-53452297(-)$1	1	157	176	13.4398
.(((((........)))))	chr12:55945417-55945641(-)$1	1	34	53	13.7993
(.((.(........))).)	chr20:43538804-43539026(+)$1	1	23	42	13.5441
(.((((........)))).	chr10:79685949-79686173(-)$1	1	53	72	14.0158
((((((........)))))	chr12:107713254-107713475(-)$1	1	142	161	13.0430
(.((((........)))).	chr9:111617410-111617633(+)$1	1	162	181	14.0180
(..(((........)))..	chr17:58700981-58701207(+)$1	1	196	215	15.4134
((((((........)))))	chr4:169374219-169374443(-)$1	1	34	53	14.1651
((.(((........))).)	chr18:29497519-29497742(+)$1	1	33	52	15.4138
((((((........)).))	chrX:70344830-70345051(+)$1	1	3	22	13.2101
((((.(........).)))	chr19:47570637-47570860(-)$1	1	141	160	14.0792
((.(((........))).)	chr17:47583771-47583993(-)$1	1	72	91	15.1737
((((.(........).)))	chr7:75694040-75694264(+)$1	1	173	192	14.1700
((.(((........))).)	chr11:61914204-61914429(+)$1	1	54	73	15.4138
((.(((........))).)	chr19:36258946-36259171(+)$1	1	56	75	15.0538
((((((........)))..	chr18:51819958-51820181(+)$1	1	44	63	14.7470
(.((((........)))).	chr15:91500771-91500994(+)$1	1	184	203	13.7973
((((((........)))))	chr14:25100220-25100446(+)$1	1	133	152	14.1651
(..(((........)))))	chr14:59113165-59113386(-)$1	1	113	132	15.4187
(..(((........))).)	chr7:148427107-148427331(-)$1	1	121	140	15.2261
.(((((........)))))	chrX:100662694-100662918(-)$1	1	195	214	13.7706
.(((((........)))))	chr20:21689768-21689990(+)$1	1	6	25	12.9004
.(((((........)))))	chr11:18541038-18541266(-)$1	1	121	140	13.8064
.((.((........)))).	chr10:89621794-89622019(-)$1	1	75	94	12.8768
((((.(........)))))	chr2:219558875-219559099(-)$1	1	30	49	13.8626
((..((........))..)	chr8:67488197-67488419(-)$1	1	80	99	14.1675

#PSSM
f : 0.14	c : 0.11	b : 0.10	d : 0.10	: : 0.08	e : 0.08	" : 0.07	! : 0.05	i : 0.05	[ : 0.04	g : 0.04	# : 0.02	= : 0.02	$ : 0.01	a : 0.01	
e : 0.20	c : 0.13	! : 0.11	f : 0.10	d : 0.10	[ : 0.10	b : 0.04	" : 0.04	i : 0.04	# : 0.02	g : 0.02	= : 0.02	a : 0.01	$ : 0.01	
[ : 0.18	e : 0.17	d : 0.15	! : 0.13	c : 0.07	f : 0.05	b : 0.04	i : 0.04	" : 0.02	# : 0.02	a : 0.01	= : 0.01	: : 0.01	$ : 0.01	g : 0.01	
c : 0.42	e : 0.17	d : 0.11	[ : 0.07	f : 0.05	! : 0.04	# : 0.02	b : 0.02	i : 0.02	a : 0.01	= : 0.01	
c : 0.39	e : 0.15	b : 0.15	d : 0.11	[ : 0.08	f : 0.04	i : 0.02	= : 0.01	
c : 0.39	e : 0.15	b : 0.15	d : 0.11	a : 0.08	f : 0.04	i : 0.02	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.39	e : 0.15	b : 0.15	d : 0.11	a : 0.08	f : 0.04	i : 0.02	= : 0.01	
c : 0.39	e : 0.17	b : 0.17	d : 0.11	f : 0.04	] : 0.04	i : 0.02	2 : 0.01	= : 0.01	
c : 0.42	e : 0.17	d : 0.11	] : 0.08	f : 0.04	2 : 0.04	b : 0.04	4 : 0.02	i : 0.02	= : 0.01	
] : 0.18	e : 0.17	d : 0.14	2 : 0.11	f : 0.05	4 : 0.05	c : 0.05	i : 0.05	a : 0.02	3 : 0.02	b : 0.02	g : 0.01	= : 0.01	h : 0.01	5 : 0.01	
e : 0.17	2 : 0.11	c : 0.11	f : 0.08	] : 0.08	d : 0.07	b : 0.05	3 : 0.05	4 : 0.05	i : 0.05	g : 0.02	= : 0.02	5 : 0.02	a : 0.01	h : 0.01	

#score	980.7504890927636
#seq	69
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m3_run1.txt

#BEAR
eeee"""a[cccnnnnnccc]a333	chr17:78368442-78368687(+)$1	245	173	198	10.8759
3cccbb!!ddddoooooodddd22b	chr19:5696620-5696870(-)$1	250	169	194	14.2751
gggggg"""a[ddddllldddd]a]	chr7:132469593-132469832(-)$1	239	103	128	9.7956
===$$$$$ddddoooooodddd22=	chr11:315091-315360(+)$1	269	155	180	14.6778
HHHHbb"""cccooooooccc333b	chr1:148251753-148252025(-)$1	272	41	66	11.8632
dd[a[eeeee[aooooooa]eeeee	chr14:90871531-90871813(+)$1	282	79	104	10.3155
FFFdddd[ddddoooooodddd]dd	chr19:18546233-18546473(-)$1	240	60	85	12.1642
ggggggg[ddddooooooddddggg	chr4:15069752-15069992(+)$1	240	11	36	13.3317
!!dddd"""ddddmmmmdddd333d	chr19:13058900-13059140(+)$1	240	69	94	10.8320
==[eeeeeddddoooooodddd22e	chr2:178095173-178095577(-)$1	404	63	88	14.2597
#eeeee"""cccooooooccc]eee	chrX:134874079-134874332(+)$1	253	210	235	13.7453
::dddd!!ddddoooooodddd22d	chr1:182567666-182567911(-)$1	245	26	51	13.7493
::eeeee!!cccooooooccc22ee	chr11:9610060-9610353(+)$1	293	242	267	11.8710
cc[ccc!!cccoooooocccccc]c	chr6:26157135-26157429(+)$1	294	104	129	11.7379
[ccca"""ddddoooooodddd333	chr22:42991448-42991687(-)$1	239	74	99	16.2530
""a[a[cccddddnnnnndddd]cc	chr19:2430595-2430835(-)$1	240	46	71	9.6836
dddd####ddddoooooodddd555	chr6:99847393-99847636(-)$1	243	48	73	12.9251
fffff"""ddddooooooddddfff	chr18:60794011-60794272(-)$1	261	222	247	13.7581
'dddd!!a[cccooooooccca22d	chr21:30428553-30428806(-)$1	253	196	221	13.3835
bb[ccc"""cccooooooccccccb	chr17:79477854-79478133(-)$1	279	107	132	12.6864
""eeeee[ddddoooooodddd22e	chr16:74496373-74496635(-)$1	262	64	89	15.0617
b[eeeee!!cccnnnnnccc4444e	chr15:74338953-74339195(+)$1	242	183	208	10.1533
eeeee####cccooooooccceeee	chr11:45954272-45954532(-)$1	260	103	128	13.4396
:===========oooooo=======	chr7:33046316-33046581(+)$1	265	179	204	11.1920
:==========ddddllldddd333	chr15:45010204-45010446(+)$1	242	94	119	9.5118
eee::ddddcccooooooccc4444	chr12:120636570-120636894(-)$1	324	170	195	10.6365
#eeeee"""cccooooooccc]eee	chrX:134856819-134857072(+)$1	253	210	235	13.7453
::ffffffddddoooooodddd]ff	chr6:31236589-31237018(-)$1	429	350	375	11.0932
:ffffff[ddddoooooodddd22f	chr10:79735523-79735783(-)$1	260	82	107	13.3248
ccc[a!!eeeeeooooooeeeee22	chr12:131274361-131274600(-)$1	239	53	78	12.2237
:eeeee!!ddddoooooodddd22e	chr16:9010836-9011105(-)$1	269	7	32	15.0148
gbb####eeeeeooooooeeeee33	chr9:133589348-133589637(+)$1	289	253	278	12.1329
ee[bb"""ddddoooooodddd333	chr3:96336835-96337141(-)$1	306	31	56	15.6692
##dddd!!cccoooooocccddddf	chr10:27475697-27475949(+)$1	252	207	232	11.7363
$$dddd[eeeeeooooooeeeee33	chr14:23567244-23567503(+)$1	259	129	154	12.0593
$$$eeeee[cccooooooccc333e	chr19:48885730-48885989(-)$1	259	103	128	13.0606
!aeeeee[ddddnnnnndddd]eee	chr1:40555039-40555279(-)$1	240	16	41	9.9134
deeeee"""cccnnnnnccc333ee	chr19:1244670-1244926(+)$1	256	221	246	10.5390
Edddd"""ddddoooooodddd22d	chr12:66545951-66546190(-)$1	239	95	120	14.7947
::ccc"""ddddoooooodddd333	chr17:78938369-78938608(+)$1	239	78	103	14.8478
ffffff!!ddddooooooddddfff	chr1:32639270-32639509(+)$1	239	31	56	13.1355
!eeeee"""cccnnnnnccc333ee	chr15:44085897-44086158(+)$1	261	111	136	10.9066
c"""bb[eeeeeooooooeeeee]b	chr7:155100122-155100439(+)$1	317	25	50	11.0566
e[dddd[eeeeeooooooeeeeedd	chr18:9547041-9547285(-)$1	244	110	135	10.9575
b[ccc####ddddnnnnndddd333	chr19:18288734-18289028(+)$1	294	165	190	12.3385
ggg$$$$$ddddoooooodddd666	chr8:74706009-74706289(-)$1	280	114	139	12.9082
!!bb####cccoooooocccbb22g	chr10:93808898-93809137(-)$1	239	75	100	12.1897
[eeeee$$$$$ddddllldddd22e	chr17:40351093-40351335(-)$1	242	6	31	9.4856

#otherMatches

#Seq PSSM
ACUGCAGGCAGUAACUGACUUCACA	chr17:78368442-78368687(+)$1	245	173	198	10.8759
CCCCUGAUCCUCAUCGACGAGGUGC	chr19:5696620-5696870(-)$1	250	169	194	14.2751
UUAUCAAUAUGAAGGCAACCUUGGC	chr7:132469593-132469832(-)$1	239	103	128	9.7956
AUUCAAUAAAGUGCACGUGCUUGUG	chr11:315091-315360(+)$1	269	155	180	14.6778
UUGAGGAACAGCACAUCAGCUUCGC	chr1:148251753-148252025(-)$1	272	41	66	11.8632
GUACUUCGUGUGCUCCGACCCAUGG	chr14:90871531-90871813(+)$1	282	79	104	10.3155
UGGGCGGAACCAACACACUGGUGCU	chr19:18546233-18546473(-)$1	240	60	85	12.1642
CAAGGGUGUUGCCUUAUAGCAAACC	chr4:15069752-15069992(+)$1	240	11	36	13.3317
CCCUUUUUCUUGCUGUUGCAGACCA	chr19:13058900-13059140(+)$1	240	69	94	10.8320
AGAUUUAGGAGGAUUUGACCUUUUC	chr2:178095173-178095577(-)$1	404	63	88	14.2597
UGUAUUCCCACCUGUGCUGGUAGAU	chrX:134874079-134874332(+)$1	253	210	235	13.7453
ACUGUUUAAAUAUUUAUUUAUUGUG	chr1:182567666-182567911(-)$1	245	26	51	13.7493
UUGAUGAUUGCUAUGUCAGGCUUUC	chr11:9610060-9610353(+)$1	293	242	267	11.8710
GCAGCCAAGCCAAAGAAGGCGGCAG	chr6:26157135-26157429(+)$1	294	104	129	11.7379
UCAGCCCAUUGGAAGGCACCAAGAU	chr22:42991448-42991687(-)$1	239	74	99	16.2530
ACGUGUGGGUGGGUCUCCCCCAGCC	chr19:2430595-2430835(-)$1	240	46	71	9.6836
ACUUUUCUUCCUAUUUUGGGGAUUU	chr6:99847393-99847636(-)$1	243	48	73	12.9251
AAAAAUACAUGCAUCUCAGCGUUUU	chr18:60794011-60794272(-)$1	261	222	247	13.7581
augacuuguguuccucucaaccuug	chr21:30428553-30428806(-)$1	253	196	221	13.3835
CCAUGUACCCGGGCAUUGCCGACAG	chr17:79477854-79478133(-)$1	279	107	132	12.6864
CAGGUGGAAUGUUUUGUCACAUGCU	chr16:74496373-74496635(-)$1	262	64	89	15.0617
UGCUCAGCAUCCCCAGAGGAACCAC	chr15:74338953-74339195(+)$1	242	183	208	10.1533
GGCUGACAGUCCAAUUAAGGGUAGC	chr11:45954272-45954532(-)$1	260	103	128	13.4396
AAUGUUGGAAAGCUGAUCUUUUCUG	chr7:33046316-33046581(+)$1	265	179	204	11.1920
CUGGUUUAUUUUUGUUCCACAAGUU	chr15:45010204-45010446(+)$1	242	94	119	9.5118
AGAAGACCUCCUUUUUCCAGGCUUU	chr12:120636570-120636894(-)$1	324	170	195	10.6365
UGUAUUCCCACCUGUGCUGGUAGAU	chrX:134856819-134857072(+)$1	253	210	235	13.7453
ACUUCUUACUUCCCUAAUGAAGUUA	chr6:31236589-31237018(-)$1	429	350	375	11.0932
AGGAUUAAGUUUGUUAAUGAACACU	chr10:79735523-79735783(-)$1	260	82	107	13.3248
AUGUCCCACCUUUCCUUCAAGGUCU	chr12:131274361-131274600(-)$1	239	53	78	12.2237
UAAACAUGAAGAUUAAAUUCUUACU	chr16:9010836-9011105(-)$1	269	7	32	15.0148
GCAGCGAAUGUGAAAUCCCACGUAU	chr9:133589348-133589637(+)$1	289	253	278	12.1329
AGGAGAUUUCAACUCAACUUGACCA	chr3:96336835-96337141(-)$1	306	31	56	15.6692
AAUCAUUUAAGGCCAUACUUGUGAC	chr10:27475697-27475949(+)$1	252	207	232	11.7363
AAAGCUCUGGAACUGGUAUUCCAAC	chr14:23567244-23567503(+)$1	259	129	154	12.0593
UACAGAACUGAUGGUUGAAUCUUUG	chr19:48885730-48885989(-)$1	259	103	128	13.0606
uucucacagugccuugugcauagug	chr1:40555039-40555279(-)$1	240	16	41	9.9134
CGUCCUCCAUGUCCCUUGCAAAUAG	chr19:1244670-1244926(+)$1	256	221	246	10.5390
AACAGACAUAAGUAUCCCCUUAACC	chr12:66545951-66546190(-)$1	239	95	120	14.7947
ACCUCACUUUAUUUCCAUGUAAUCA	chr17:78938369-78938608(+)$1	239	78	103	14.8478
UGUGGACAGUCUUCAUCUAGAUUCC	chr1:32639270-32639509(+)$1	239	31	56	13.1355
UGUGUGCCUGGAGCCAGUCCCACCA	chr15:44085897-44086158(+)$1	261	111	136	10.9066
GAAUGAUGACUUACCCUGAAGUCUU	chr7:155100122-155100439(+)$1	317	25	50	11.0566
CAUAUUGCUGUACACAUUUACAGAA	chr18:9547041-9547285(-)$1	244	110	135	10.9575
GUGCUAAAGUAAAACUAGUUUAAUA	chr19:18288734-18289028(+)$1	294	165	190	12.3385
GUUGAUCGCUGGUUCAGUCCAGGCA	chr8:74706009-74706289(-)$1	280	114	139	12.9082
UUUUUUGAAGGCUAUAACCUAACCU	chr10:93808898-93809137(-)$1	239	75	100	12.1897
ACCAAAAAAAAGUAUUGUGUACAAU	chr17:40351093-40351335(-)$1	242	6	31	9.4856

#DB
((((...(.(((.....))).)...	chr17:78368442-78368687(+)$1	1	173	198	10.8759
.)))((..((((......))))..)	chr19:5696620-5696870(-)$1	1	169	194	14.2751
((((((...(.((((...)))).).	chr7:132469593-132469832(-)$1	1	103	128	9.7956
(((.....((((......))))..)	chr11:315091-315360(+)$1	1	155	180	14.6778
((((((...(((......)))...)	chr1:148251753-148252025(-)$1	1	41	66	11.8632
((.(.(((((.(......).)))))	chr14:90871531-90871813(+)$1	1	79	104	10.3155
(((((((.((((......)))).))	chr19:18546233-18546473(-)$1	1	60	85	12.1642
(((((((.((((......)))))))	chr4:15069752-15069992(+)$1	1	11	36	13.3317
..((((...((((....))))...)	chr19:13058900-13059140(+)$1	1	69	94	10.8320
((.(((((((((......))))..)	chr2:178095173-178095577(-)$1	1	63	88	14.2597
.(((((...(((......))).)))	chrX:134874079-134874332(+)$1	1	210	235	13.7453
..((((..((((......))))..)	chr1:182567666-182567911(-)$1	1	26	51	13.7493
..(((((..(((......)))..))	chr11:9610060-9610353(+)$1	1	242	267	11.8710
((.(((..(((......)))))).)	chr6:26157135-26157429(+)$1	1	104	129	11.7379
.((((...((((......))))...	chr22:42991448-42991687(-)$1	1	74	99	16.2530
..(.(.(((((((.....)))).))	chr19:2430595-2430835(-)$1	1	46	71	9.6836
((((....((((......))))...	chr6:99847393-99847636(-)$1	1	48	73	12.9251
(((((...((((......)))))))	chr18:60794011-60794272(-)$1	1	222	247	13.7581
.((((..(.(((......))))..)	chr21:30428553-30428806(-)$1	1	196	221	13.3835
((.(((...(((......)))))))	chr17:79477854-79478133(-)$1	1	107	132	12.6864
..(((((.((((......))))..)	chr16:74496373-74496635(-)$1	1	64	89	15.0617
(.(((((..(((.....)))....)	chr15:74338953-74339195(+)$1	1	183	208	10.1533
(((((....(((......)))))))	chr11:45954272-45954532(-)$1	1	103	128	13.4396
.(((((((((((......)))))))	chr7:33046316-33046581(+)$1	1	179	204	11.1920
.((((((((((((((...))))...	chr15:45010204-45010446(+)$1	1	94	119	9.5118
)))..(((((((......)))....	chr12:120636570-120636894(-)$1	1	170	195	10.6365
.(((((...(((......))).)))	chrX:134856819-134857072(+)$1	1	210	235	13.7453
..((((((((((......)))).))	chr6:31236589-31237018(-)$1	1	350	375	11.0932
.((((((.((((......))))..)	chr10:79735523-79735783(-)$1	1	82	107	13.3248
(((.(..(((((......)))))..	chr12:131274361-131274600(-)$1	1	53	78	12.2237
.(((((..((((......))))..)	chr16:9010836-9011105(-)$1	1	7	32	15.0148
(((....(((((......)))))..	chr9:133589348-133589637(+)$1	1	253	278	12.1329
((.((...((((......))))...	chr3:96336835-96337141(-)$1	1	31	56	15.6692
..((((..(((......))))))))	chr10:27475697-27475949(+)$1	1	207	232	11.7363
..((((.(((((......)))))..	chr14:23567244-23567503(+)$1	1	129	154	12.0593
...(((((.(((......)))...)	chr19:48885730-48885989(-)$1	1	103	128	13.0606
.((((((.((((.....)))).)))	chr1:40555039-40555279(-)$1	1	16	41	9.9134
)(((((...(((.....)))...))	chr19:1244670-1244926(+)$1	1	221	246	10.5390
(((((...((((......))))..)	chr12:66545951-66546190(-)$1	1	95	120	14.7947
..(((...((((......))))...	chr17:78938369-78938608(+)$1	1	78	103	14.8478
((((((..((((......)))))))	chr1:32639270-32639509(+)$1	1	31	56	13.1355
.(((((...(((.....)))...))	chr15:44085897-44086158(+)$1	1	111	136	10.9066
(...((.(((((......))))).)	chr7:155100122-155100439(+)$1	1	25	50	11.0566
(.((((.(((((......)))))))	chr18:9547041-9547285(-)$1	1	110	135	10.9575
(.(((....((((.....))))...	chr19:18288734-18289028(+)$1	1	165	190	12.3385
(((.....((((......))))...	chr8:74706009-74706289(-)$1	1	114	139	12.9082
..((....(((......)))))..)	chr10:93808898-93809137(-)$1	1	75	100	12.1897
.(((((.....((((...))))..)	chr17:40351093-40351335(-)$1	1	6	31	9.4856

#PSSM
: : 0.16	e : 0.10	g : 0.08	! : 0.08	d : 0.06	# : 0.06	c : 0.06	b : 0.06	= : 0.04	[ : 0.04	" : 0.04	f : 0.04	$ : 0.04	3 : 0.02	H : 0.02	F : 0.02	' : 0.02	E : 0.02	
e : 0.20	c : 0.08	= : 0.08	d : 0.08	: : 0.08	g : 0.06	" : 0.06	f : 0.06	[ : 0.06	! : 0.04	b : 0.04	$ : 0.04	H : 0.02	F : 0.02	# : 0.02	a : 0.02	
e : 0.27	d : 0.16	c : 0.10	[ : 0.10	f : 0.08	g : 0.06	= : 0.06	b : 0.04	H : 0.02	F : 0.02	a : 0.02	$ : 0.02	" : 0.02	
e : 0.29	d : 0.18	c : 0.12	f : 0.08	g : 0.04	$ : 0.04	[ : 0.04	= : 0.04	b : 0.04	H : 0.02	a : 0.02	: : 0.02	# : 0.02	" : 0.02	
e : 0.27	d : 0.16	b : 0.08	c : 0.08	f : 0.08	a : 0.06	# : 0.06	g : 0.04	$ : 0.04	= : 0.04	" : 0.02	[ : 0.02	: : 0.02	
e : 0.27	d : 0.14	" : 0.12	# : 0.10	b : 0.06	f : 0.06	g : 0.04	$ : 0.04	c : 0.04	! : 0.04	= : 0.04	[ : 0.02	
" : 0.29	! : 0.16	e : 0.14	# : 0.10	$ : 0.06	[ : 0.06	d : 0.04	= : 0.04	f : 0.04	g : 0.02	c : 0.02	
" : 0.27	! : 0.16	e : 0.16	[ : 0.10	# : 0.08	$ : 0.06	a : 0.04	= : 0.04	c : 0.02	d : 0.02	f : 0.02	
d : 0.41	" : 0.16	e : 0.12	c : 0.08	[ : 0.06	! : 0.04	# : 0.04	= : 0.04	$ : 0.02	
d : 0.45	c : 0.33	e : 0.12	= : 0.04	a : 0.02	$ : 0.02	
d : 0.45	c : 0.33	e : 0.10	[ : 0.04	= : 0.04	$ : 0.02	
d : 0.52	c : 0.27	e : 0.10	o : 0.06	a : 0.02	= : 0.02	
o : 0.77	d : 0.12	n : 0.10	
o : 0.77	n : 0.14	d : 0.06	m : 0.02	
o : 0.77	n : 0.14	d : 0.06	m : 0.02	
o : 0.77	n : 0.14	l : 0.06	m : 0.02	
o : 0.77	n : 0.14	l : 0.06	m : 0.02	
o : 0.70	c : 0.14	l : 0.06	d : 0.04	n : 0.04	
d : 0.52	c : 0.33	e : 0.10	a : 0.02	= : 0.02	
d : 0.52	c : 0.33	e : 0.10	] : 0.02	= : 0.02	
d : 0.54	c : 0.20	e : 0.12	3 : 0.04	] : 0.02	4 : 0.02	= : 0.02	b : 0.02	
d : 0.49	e : 0.14	3 : 0.10	] : 0.06	a : 0.04	c : 0.04	4 : 0.04	2 : 0.02	= : 0.02	b : 0.02	
2 : 0.25	3 : 0.22	e : 0.20	] : 0.08	c : 0.04	f : 0.04	4 : 0.04	g : 0.02	5 : 0.02	= : 0.02	d : 0.02	6 : 0.02	
2 : 0.25	3 : 0.22	e : 0.16	d : 0.06	f : 0.06	] : 0.04	c : 0.04	4 : 0.04	a : 0.02	g : 0.02	5 : 0.02	= : 0.02	6 : 0.02	
e : 0.29	3 : 0.16	d : 0.12	f : 0.10	b : 0.08	= : 0.04	g : 0.04	c : 0.04	] : 0.02	5 : 0.02	4 : 0.02	2 : 0.02	6 : 0.02	

#score	595.3144331545835
#seq	48
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m3_run1.txt

#BEAR
ffff[iiiiiiiiimmmmiiiiiiiii22f	chr3:127335798-127336023(+)$1	225	100	130	11.5819
dccc[iiiiiiiiimmmmiiiiiiiii333	chr19:1390895-1391123(+)$1	228	57	87	12.4428
ff[dddd!!eeeeemmmmeeeee]dddd]f	chr18:52894318-52894544(-)$1	226	108	138	11.3484
c[a[bb"""eeeeemmmmeeeee22bbacc	chr3:127788806-127789034(+)$1	228	2	32	10.9876
eeeee[ccc!!cccmmmmccc22ccc22ee	chr2:74141868-74142091(-)$1	223	64	94	12.4825
hh!!eeeee[ddddmmmmddddeeeee333	chr8:134249400-134249627(-)$1	227	109	139	12.4589
"ccc[eeeee[cccmmmmccceeeee]ccc	chr19:39923782-39924029(-)$1	247	31	61	12.4849
gggg[bb!!eeeeemmmmeeeee]bb]ggg	chr2:61721019-61721315(-)$1	296	225	255	11.4512
dd[eeeee!!ddddmmmmdddd]eeeee22	chr3:48731123-48731350(-)$1	227	161	191	12.3317
"""eeeee[eeeeemmmmeeeee4444eee	chr3:155657731-155657959(+)$1	228	104	134	12.2598
[ggggggg"""ddddllldddd333ggggg	chr16:23679431-23679686(+)$1	255	194	224	11.8746
c!!dddd####cccmmmmcccdddd]ccc:	chr21:34668474-34668704(+)$1	230	124	154	11.4616
ggggg[ddddddddmmmmdddd333dddd]	chr16:58196700-58196941(-)$1	241	113	143	12.1463
[iiiiiiiiiddddllldddd4444iiiii	chr16:2124199-2124435(+)$1	236	97	127	11.0984
cc[ggggggg[ccclllccc]gggggggcc	chr15:76209583-76209832(+)$1	249	52	82	10.8278
"""ccc[gggggggmmmmggggggg]ccc6	chr2:107418429-107418652(-)$1	223	107	137	11.4241
:ffffff####cccmmmmccc333ffffff	chr15:65442739-65442963(-)$1	224	115	145	11.6179
c[eeeee!!eeeeemmmmeeeeeeeeeecc	chr7:116165398-116165619(+)$1	221	32	62	12.1333
[bbccc####ddddmmmmdddd]ccc]bb]	chr14:37132176-37132397(+)$1	221	7	37	11.7717
!iiiiiiiii!!bblllbb22iiiiiiiii	chr2:220081037-220081274(-)$1	237	144	174	9.5451
eeeee$$$$$ddddmmmmddddeeeee333	chr17:37566673-37566897(+)$1	224	123	153	11.7189
dd!!ccc"""ddddmmmmdddd]ccc22dd	chr6:43752745-43752967(+)$1	222	68	98	12.3631
)iiiiiiiiiddddmmmmdddd22iiiiii	chr18:196631-196859(+)$1	228	163	193	12.6165
fffff[ddddddddmmmmdddd4444dddd	chr20:2443731-2443963(-)$1	232	187	217	10.9407
ffffff"""eeeeemmmmeeeee333ffff	chr2:109301143-109301373(+)$1	230	150	180	11.8281
dd!!eeeeeeeeeemmmmeeeee]eeeee2	chr9:123636900-123637124(-)$1	224	109	139	11.4344
eeee"""ccc[ccclllcccccc22eeeee	chr11:68355304-68355534(+)$1	230	115	145	9.6068
c[eeeee"""ddddmmmmddddeeeee]cc	chrX:10415913-10416143(-)$1	230	78	108	12.8795
bb"""eeeee!!bbmmmmbb]eeeee22bb	chr9:130551703-130551933(+)$1	230	88	118	10.0256
dddd!!ccc!!cccmmmmccc22ccc333d	chr16:30938641-30938868(+)$1	227	50	80	12.7728
ccc[dddd"""cccmmmmccc333dddd]c	chr17:662544-662772(-)$1	228	158	188	13.0307
====ccc[ffffffmmmmffffff333ccc	chr20:30753563-30753793(+)$1	230	129	159	10.7384
####ddddccc[bbmmmmbb]ccc]dddd3	chr10:22607507-22607735(+)$1	228	69	99	10.0448
c[ccc[ccc!!cccmmmmccc22cccccc2	chr17:76791956-76792184(-)$1	228	147	177	12.8900
cccffffff[ddddmmmmddddffffff]c	chr1:32681111-32681340(-)$1	229	47	77	10.7972
beeeeeccc!!ccclllccc]ccc22eeee	chrX:139014103-139014325(-)$1	222	105	135	9.8057
bbggggggg"""bbmmmmbb333ggggggg	chr2:85824484-85824708(-)$1	224	128	158	11.8512
========eeeeennnnneeeee333====	chr12:67197814-67198041(-)$1	227	87	117	9.7764
iiiiiiiccc[cccmmmmccc]ccc333ii	chr8:20066890-20067120(+)$1	230	144	174	13.3638
!bba!!ccc!!cccmmmmccc22ccc22a]	chr5:137754591-137754818(+)$1	227	154	184	12.6578
fffeeeee[a[ccclllccca]eeeee]ff	chr12:27932848-27933074(+)$1	226	31	61	10.0571
G::dddd[a!!cccmmmmccc333a]dddd	chr16:30435381-30435610(-)$1	229	197	227	10.3303
[eeeee"""eeeeemmmmeeeee]eeeee]	chr19:33468405-33468633(+)$1	228	74	104	12.3161
[eeeeedddd[cccmmmmcccdddd4444e	chr17:38291779-38292008(+)$1	229	52	82	11.5376
e!!eeeee[eeeeemmmmeeeeeeeeee22	chr20:11900346-11900572(+)$1	226	48	78	11.7673
!ggggggg!!a[bbmmmmbb]a22gggggg	chr5:149823740-149823973(-)$1	233	72	102	12.3128
##dddd[ccc!!bbmmmmbb22ccc]dddd	chr11:71808578-71808811(-)$1	233	107	137	10.0399
===####gggggggmmmmggggggg=====	chr14:24774194-24774424(+)$1	230	141	171	12.2000
Bggggggg!!ddddmmmmdddd333ggggg	chr7:100883018-100883239(+)$1	221	16	46	13.1509
cc!!a!!gggggggmmmmggggggg22a]c	chr19:56164360-56164590(+)$1	230	171	201	11.8669
[ggggggg"""cccmmmmccc22ggggggg	chr4:25125610-25125838(-)$1	228	85	115	13.8925
####eeeee!!cccmmmmccc]eeeee444	chrX:69506467-69506690(+)$1	223	58	88	13.1045
iiiiiiiii!!cccmmmmccciiiiiiiii	chr11:8705707-8706009(+)$1	302	147	177	13.8424
:ggggggg[eeeeemmmmeeeee333gggg	chr5:179156877-179157110(+)$1	233	199	229	12.2178
dggggggg!!ddddmmmmdddd]ggggggg	chr17:62541836-62542081(-)$1	245	172	202	13.1930
=========!!cccmmmmccc=========	chr21:38574214-38574442(+)$1	228	174	204	14.4367

#otherMatches

#Seq PSSM
UUGGAGGCUGGGGCCCUGGUUCUGGCUGAC	chr3:127335798-127336023(+)$1	225	100	130	11.5819
CCGCUUUGGCGUGGUCUUCCGCGCCAGCCC	chr19:1390895-1391123(+)$1	228	57	87	12.4428
UAGUGCCAACUCUGCUUCCAGAGGGGUAGU	chr18:52894318-52894544(-)$1	226	108	138	11.3484
GUGCUGUAUGCGGCUGCAGCCGUCUCACCU	chr3:127788806-127789034(+)$1	228	2	32	10.9876
AUUGGCAGGGACUGUGGGCAGCACCUCACC	chr2:74141868-74142091(-)$1	223	64	94	12.4825
CUGAGUACGGAUGGGAAACUAUUGUGCACA	chr8:134249400-134249627(-)$1	227	109	139	12.4589
UGCUGGUAGCUGACCCUCGUCGCUGCGAGU	chr19:39923782-39924029(-)$1	247	31	61	12.4849
CUGGAAGUCAACAUUUUGAUGUUCCUCCCA	chr2:61721019-61721315(-)$1	296	225	255	11.4512
GUGCCUACCCGUGUGGGGGCACUGUGGGAA	chr3:48731123-48731350(-)$1	227	161	191	12.3317
CUAGAAUGGUGGCUACCUGGCUAAUAACAU	chr3:155657731-155657959(+)$1	228	104	134	12.2598
CCAGUUGUGGGGUUUGCAAAACAAAACAGC	chr16:23679431-23679686(+)$1	255	194	224	11.8746
CAAGCAGAAUCCUGGUGACAGCUGCAGCCU	chr21:34668474-34668704(+)$1	230	124	154	11.4616
GUUGUGUGGGCAGGGUCAUCUGAAACUCAA	chr16:58196700-58196941(-)$1	241	113	143	12.1463
AUCAUCAUCAAGGCGCUGCCUGUUCUGGUG	chr16:2124199-2124435(+)$1	236	97	127	11.0984
UUAUUAUUCCCUCAAAUUGAAGGAAUAAAA	chr15:76209583-76209832(+)$1	249	52	82	10.8278
CACUAUGAAGGUAGAACACUACCUUAAUAU	chr2:107418429-107418652(-)$1	223	107	137	11.4241
CUGUAGAUUUUACAAUAAUGUUACUCUACA	chr15:65442739-65442963(-)$1	224	115	145	11.6179
ACGCGUUUUCUGGAUGGGUCUAGGAUGCUC	chr7:116165398-116165619(+)$1	221	32	62	12.1333
CGUGGAACUGGCCCAACUGGGCAUCCGACC	chr14:37132176-37132397(+)$1	221	7	37	11.7717
ACGUCUUCCUCAAGUUCCUCCAGGGGGGUG	chr2:220081037-220081274(-)$1	237	144	174	9.5451
ACCACUCAUUGGGUUGUUGCCUGUGGUCAU	chr17:37566673-37566897(+)$1	224	123	153	11.7189
CCCACUCAGAUCCUGACAGGGAAGAGGAGG	chr6:43752745-43752967(+)$1	222	68	98	12.3631
UGUAAAUGUAAAACUUAGGUUUCCUACAUU	chr18:196631-196859(+)$1	228	163	193	12.6165
GGGGUCCUCCCCCACCUAUGGGCCGAGGAG	chr20:2443731-2443963(-)$1	232	187	217	10.9407
AUAUAUUGCUUCAGAAAACUGAAUGUGUAU	chr2:109301143-109301373(+)$1	230	150	180	11.8281
AGAAUCGAGCUCUGGAUCCAGGGACUCGGG	chr9:123636900-123637124(-)$1	224	109	139	11.4344
AAAUGACGUCCAAUUUUAUUGACCAGUUUG	chr11:68355304-68355534(+)$1	230	115	145	9.6068
AUGAAUUAAGGCUUUCUUGAGCAGUUCUUG	chrX:10415913-10416143(-)$1	230	78	108	12.8795
CAACCAGACGGAGUUUGAGCGCGUCUUCUG	chr9:130551703-130551933(+)$1	230	88	118	10.0256
GAGGGAGAGGAAGAGAAAUUUGGUUUGAGC	chr16:30938641-30938868(+)$1	227	50	80	12.7728
GGAAUUAUAUUGUGUAUUCAUUGAAUAAAU	chr17:662544-662772(-)$1	228	158	188	13.0307
GCUUCAGUGAGGUUUCCGAGCCUCUCCCUG	chr20:30753563-30753793(+)$1	230	129	159	10.7384
UUCAGUAUAGGCAGAUCUCUCCCUCAUAUA	chr10:22607507-22607735(+)$1	228	69	99	10.0448
UCUUGUACACGUAUGUAAGUAAAUGUCAAU	chr17:76791956-76792184(-)$1	228	147	177	12.8900
CUGCUUCCUCAUUUAACAAGGUAGGAAGUU	chr1:32681111-32681340(-)$1	229	47	77	10.7972
CCCGGCAGCCUUCGACGCGAUGUUCCGCCG	chrX:139014103-139014325(-)$1	222	105	135	9.8057
GCUGUUUUCGAGCCUGAAGGAAAGAAGGCA	chr2:85824484-85824708(-)$1	224	128	158	11.8512
CCUGGGUUUUGUCAAGGCGAUAAGAAGAUC	chr12:67197814-67198041(-)$1	227	87	117	9.7764
UAGUUCAGGUAAGUUUCAGCUGGCCAGCUG	chr8:20066890-20067120(+)$1	230	144	174	13.3638
AGCCGACAGCACUGACAUCAGAUCUGAAGA	chr5:137754591-137754818(+)$1	227	154	184	12.6578
UCCAGCCGGCAGGUCAGGCCGGCGGCUGGG	chr12:27932848-27933074(+)$1	226	31	61	10.0571
UCUAGAAGGUAGCCUCCUGGUGUUUGUUCU	chr16:30435381-30435610(-)$1	229	197	227	10.3303
GCAUAUGUCUUCUGCACACAGAAAGUAUGA	chr19:33468405-33468633(+)$1	228	74	104	12.3161
AAAGAGAAUAUGUCCCCAGAUUAUUAGCAC	chr17:38291779-38292008(+)$1	229	52	82	11.5376
CCAUGCGAUGUUUUACGGAGAACUUGCAGA	chr20:11900346-11900572(+)$1	226	48	78	11.7673
UCCCCUCUGACAGCACUCGCAGGAAGGGGG	chr5:149823740-149823973(-)$1	233	72	102	12.3128
GUGAGGGUAGAACCUUUUGGGACUGGCCUU	chr11:71808578-71808811(-)$1	233	107	137	10.0399
GGGCAAAAUGGGGUAUCCACCCCAUCCCUU	chr14:24774194-24774424(+)$1	230	141	171	12.2000
CGAGGAUGGACAGGCCCUCCUGGAGCGUUC	chr7:100883018-100883239(+)$1	221	16	46	13.1509
GCCUCAGCCUCUUCCUAGGAGGGGGACGUG	chr19:56164360-56164590(+)$1	230	171	201	11.8669
GCUGCAUCAGCCAUCGGAAUGAAGAUGCAG	chr4:25125610-25125838(-)$1	228	85	115	13.8925
AAAGUGUAUGAAUCUUCUGGUAGUGCAAGG	chrX:69506467-69506690(+)$1	223	58	88	13.1045
ACUGGCUGUGGGCCUUAUGGCACAGUCAGU	chr11:8705707-8706009(+)$1	302	147	177	13.8424
AUAGUGUAAUAAUGUUAUUAUUACUCUACA	chr5:179156877-179157110(+)$1	233	199	229	12.2178
UUUCAGCAGAGUUUCAAAGAAUAUGCUGAA	chr17:62541836-62542081(-)$1	245	172	202	13.1930
auuuuaauaauuuauaguuaauguuaaaau	chr21:38574214-38574442(+)$1	228	174	204	14.4367

#DB
((((.(((((((((....)))))))))..)	chr3:127335798-127336023(+)$1	1	100	130	11.5819
((((.(((((((((....)))))))))...	chr19:1390895-1391123(+)$1	1	57	87	12.4428
((.((((..(((((....))))).)))).)	chr18:52894318-52894544(-)$1	1	108	138	11.3484
(.(.((...(((((....)))))..)))))	chr3:127788806-127789034(+)$1	1	2	32	10.9876
(((((.(((..(((....)))..)))..))	chr2:74141868-74142091(-)$1	1	64	94	12.4825
((..(((((.((((....)))))))))...	chr8:134249400-134249627(-)$1	1	109	139	12.4589
.(((.(((((.(((....)))))))).)))	chr19:39923782-39924029(-)$1	1	31	61	12.4849
((((.((..(((((....))))).)).)))	chr2:61721019-61721315(-)$1	1	225	255	11.4512
((.(((((..((((....)))).)))))..	chr3:48731123-48731350(-)$1	1	161	191	12.3317
...(((((.(((((....)))))....)))	chr3:155657731-155657959(+)$1	1	104	134	12.2598
.(((((((...((((...))))...)))))	chr16:23679431-23679686(+)$1	1	194	224	11.8746
(..((((....(((....))))))).))).	chr21:34668474-34668704(+)$1	1	124	154	11.4616
(((((.((((((((....))))...)))).	chr16:58196700-58196941(-)$1	1	113	143	12.1463
.(((((((((((((...))))....)))))	chr16:2124199-2124435(+)$1	1	97	127	11.0984
((.(((((((.(((...))).)))))))))	chr15:76209583-76209832(+)$1	1	52	82	10.8278
...(((.(((((((....))))))).))).	chr2:107418429-107418652(-)$1	1	107	137	11.4241
.((((((....(((....)))...))))))	chr15:65442739-65442963(-)$1	1	115	145	11.6179
(.(((((..(((((....))))))))))))	chr7:116165398-116165619(+)$1	1	32	62	12.1333
.(((((....((((....)))).))).)).	chr14:37132176-37132397(+)$1	1	7	37	11.7717
.(((((((((..((...))..)))))))))	chr2:220081037-220081274(-)$1	1	144	174	9.5451
(((((.....((((....)))))))))...	chr17:37566673-37566897(+)$1	1	123	153	11.7189
((..(((...((((....)))).)))..))	chr6:43752745-43752967(+)$1	1	68	98	12.3631
.(((((((((((((....))))..))))))	chr18:196631-196859(+)$1	1	163	193	12.6165
(((((.((((((((....))))....))))	chr20:2443731-2443963(-)$1	1	187	217	10.9407
((((((...(((((....)))))...))))	chr2:109301143-109301373(+)$1	1	150	180	11.8281
((..((((((((((....))))).))))).	chr9:123636900-123637124(-)$1	1	109	139	11.4344
((((...(((.(((...))))))..)))))	chr11:68355304-68355534(+)$1	1	115	145	9.6068
(.(((((...((((....))))))))).))	chrX:10415913-10416143(-)$1	1	78	108	12.8795
((...(((((..((....)).)))))..))	chr9:130551703-130551933(+)$1	1	88	118	10.0256
((((..(((..(((....)))..)))...)	chr16:30938641-30938868(+)$1	1	50	80	12.7728
(((.((((...(((....)))...)))).)	chr17:662544-662772(-)$1	1	158	188	13.0307
))))(((.((((((....))))))...)))	chr20:30753563-30753793(+)$1	1	129	159	10.7384
....(((((((.((....)).))).)))).	chr10:22607507-22607735(+)$1	1	69	99	10.0448
(.(((.(((..(((....)))..)))))).	chr17:76791956-76792184(-)$1	1	147	177	12.8900
(((((((((.((((....)))))))))).)	chr1:32681111-32681340(-)$1	1	47	77	10.7972
(((((((((..(((...))).)))..))))	chrX:139014103-139014325(-)$1	1	105	135	9.8057
(((((((((...((....))...)))))))	chr2:85824484-85824708(-)$1	1	128	158	11.8512
(((((((((((((.....)))))...))))	chr12:67197814-67198041(-)$1	1	87	117	9.7764
((((((((((.(((....))).)))...))	chr8:20066890-20067120(+)$1	1	144	174	13.3638
.(((..(((..(((....)))..)))..).	chr5:137754591-137754818(+)$1	1	154	184	12.6578
((((((((.(.(((...)))).))))).))	chr12:27932848-27933074(+)$1	1	31	61	10.0571
)..((((.(..(((....)))...).))))	chr16:30435381-30435610(-)$1	1	197	227	10.3303
.(((((...(((((....))))).))))).	chr19:33468405-33468633(+)$1	1	74	104	12.3161
.(((((((((.(((....)))))))....)	chr17:38291779-38292008(+)$1	1	52	82	11.5376
(..(((((.(((((....))))))))))..	chr20:11900346-11900572(+)$1	1	48	78	11.7673
.(((((((..(.((....)).)..))))))	chr5:149823740-149823973(-)$1	1	72	102	12.3128
..((((.(((..((....))..))).))))	chr11:71808578-71808811(-)$1	1	107	137	10.0399
(((....(((((((....))))))))))))	chr14:24774194-24774424(+)$1	1	141	171	12.2000
((((((((..((((....))))...)))))	chr7:100883018-100883239(+)$1	1	16	46	13.1509
((..(..(((((((....)))))))..).)	chr19:56164360-56164590(+)$1	1	171	201	11.8669
.(((((((...(((....)))..)))))))	chr4:25125610-25125838(-)$1	1	85	115	13.8925
....(((((..(((....))).)))))...	chrX:69506467-69506690(+)$1	1	58	88	13.1045
(((((((((..(((....))))))))))))	chr11:8705707-8706009(+)$1	1	147	177	13.8424
.(((((((.(((((....)))))...))))	chr5:179156877-179157110(+)$1	1	199	229	12.2178
((((((((..((((....)))).)))))))	chr17:62541836-62542081(-)$1	1	172	202	13.1930
(((((((((..(((....))))))))))))	chr21:38574214-38574442(+)$1	1	174	204	14.4367

#PSSM
c : 0.16	d : 0.10	[ : 0.10	f : 0.08	e : 0.07	= : 0.07	" : 0.05	! : 0.05	b : 0.05	# : 0.05	g : 0.03	: : 0.03	i : 0.03	h : 0.01	) : 0.01	G : 0.01	B : 0.01	
g : 0.14	f : 0.10	c : 0.10	e : 0.10	i : 0.08	[ : 0.07	d : 0.07	b : 0.07	= : 0.07	# : 0.05	" : 0.03	! : 0.03	h : 0.01	: : 0.01	
g : 0.16	e : 0.14	! : 0.10	f : 0.08	c : 0.08	i : 0.08	= : 0.07	[ : 0.05	" : 0.05	b : 0.03	d : 0.03	# : 0.03	a : 0.01	: : 0.01	
e : 0.21	g : 0.17	f : 0.08	c : 0.08	d : 0.08	i : 0.08	! : 0.07	= : 0.05	# : 0.05	[ : 0.03	" : 0.01	a : 0.01	
e : 0.24	g : 0.16	d : 0.10	i : 0.08	c : 0.08	[ : 0.07	f : 0.07	" : 0.03	! : 0.03	= : 0.03	b : 0.01	# : 0.01	a : 0.01	
e : 0.24	g : 0.14	i : 0.12	d : 0.10	[ : 0.07	c : 0.07	f : 0.05	! : 0.05	b : 0.03	= : 0.03	$ : 0.01	" : 0.01	# : 0.01	
e : 0.19	d : 0.14	g : 0.14	i : 0.12	c : 0.12	" : 0.07	[ : 0.03	f : 0.03	# : 0.03	= : 0.03	b : 0.01	$ : 0.01	! : 0.01	
g : 0.19	e : 0.16	c : 0.14	i : 0.10	" : 0.08	d : 0.08	! : 0.05	# : 0.05	[ : 0.03	= : 0.03	$ : 0.01	f : 0.01	
c : 0.16	" : 0.14	! : 0.12	i : 0.10	e : 0.10	g : 0.08	[ : 0.07	# : 0.05	d : 0.05	f : 0.03	$ : 0.01	a : 0.01	= : 0.01	
e : 0.23	! : 0.23	" : 0.10	i : 0.08	g : 0.07	c : 0.07	# : 0.05	d : 0.05	[ : 0.03	$ : 0.01	f : 0.01	a : 0.01	
d : 0.23	! : 0.21	e : 0.19	[ : 0.10	" : 0.07	g : 0.05	i : 0.03	# : 0.03	f : 0.01	c : 0.01	a : 0.01	
c : 0.33	d : 0.24	e : 0.19	g : 0.05	! : 0.05	i : 0.03	[ : 0.03	f : 0.01	" : 0.01	
c : 0.33	d : 0.24	e : 0.19	b : 0.10	g : 0.05	i : 0.03	f : 0.01	
c : 0.33	d : 0.24	e : 0.17	b : 0.10	g : 0.05	i : 0.03	f : 0.01	n : 0.01	
m : 0.85	l : 0.10	d : 0.01	n : 0.01	
m : 0.85	l : 0.12	n : 0.01	
m : 0.85	l : 0.12	n : 0.01	
m : 0.85	c : 0.07	l : 0.01	d : 0.01	b : 0.01	n : 0.01	
c : 0.33	d : 0.24	e : 0.19	b : 0.10	g : 0.05	i : 0.03	f : 0.01	
c : 0.33	d : 0.24	e : 0.19	b : 0.08	g : 0.05	i : 0.03	2 : 0.01	f : 0.01	
c : 0.28	d : 0.24	e : 0.19	] : 0.08	g : 0.05	i : 0.03	2 : 0.03	f : 0.01	3 : 0.01	a : 0.01	
d : 0.26	e : 0.23	2 : 0.10	i : 0.07	g : 0.07	3 : 0.07	c : 0.05	] : 0.05	4 : 0.01	f : 0.01	a : 0.01	= : 0.01	
e : 0.32	2 : 0.12	3 : 0.12	c : 0.08	i : 0.07	] : 0.07	g : 0.07	d : 0.03	4 : 0.03	f : 0.03	= : 0.01	
c : 0.17	e : 0.17	3 : 0.16	g : 0.12	i : 0.07	] : 0.07	2 : 0.07	4 : 0.05	d : 0.03	f : 0.03	= : 0.01	
e : 0.21	c : 0.14	g : 0.14	3 : 0.12	i : 0.08	d : 0.07	2 : 0.05	4 : 0.05	f : 0.03	b : 0.01	] : 0.01	a : 0.01	= : 0.01	
e : 0.23	g : 0.12	i : 0.10	c : 0.10	3 : 0.08	d : 0.07	] : 0.07	4 : 0.05	b : 0.03	f : 0.03	2 : 0.03	= : 0.03	
e : 0.21	g : 0.14	d : 0.12	i : 0.10	2 : 0.08	] : 0.05	c : 0.05	f : 0.05	3 : 0.05	= : 0.05	4 : 0.03	b : 0.01	
g : 0.16	e : 0.14	d : 0.12	2 : 0.08	3 : 0.08	c : 0.08	i : 0.07	f : 0.05	= : 0.05	a : 0.03	] : 0.03	4 : 0.03	b : 0.01	
c : 0.16	g : 0.14	e : 0.10	d : 0.10	i : 0.08	3 : 0.07	] : 0.07	2 : 0.05	f : 0.05	= : 0.05	b : 0.03	4 : 0.03	a : 0.01	
c : 0.16	g : 0.14	f : 0.08	e : 0.08	i : 0.08	d : 0.08	3 : 0.07	2 : 0.07	] : 0.07	= : 0.05	: : 0.01	6 : 0.01	b : 0.01	4 : 0.01	

#score	661.141559846959
#seq	56
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m3_run1.txt

#BEAR
==========oooooo===========	chr17:35511979-35512207(-)$1	228	19	46	15.4482
eee!!ccc[aooooooa]ccc22eeee	chr2:143978982-143979248(+)$1	266	80	107	13.0336
ggggg"""cccnnnnnccc333ggggg	chr4:99446462-99446715(-)$1	253	125	152	11.4823
eee!!eeeeeooooooeeeeeeeeeec	chr6:28218069-28218331(-)$1	262	173	200	12.3764
ggg[ffffffooooooffffffggggg	chr1:35818626-35818881(+)$1	255	55	82	12.4989
c!!gggggggooooooggggggg22cc	chr22:28674767-28675093(-)$1	326	3	30	13.7777
[dddd!!cccooooooccc22dddd]c	chr9:94812483-94812720(-)$1	237	110	137	13.2871
hhhh"""cccooooooccc333hhhhh	chr14:21846659-21846915(-)$1	256	174	201	13.9374
eeeee[ddddoooooodddd4444eee	chr6:162642085-162642316(-)$1	231	180	207	12.7780
iiiiiiicccooooooccc]iiiiiii	chr17:40027085-40027376(-)$1	291	44	71	15.1082
dd[a[eeeeeooooooeeeeea]dddd	chr15:86330866-86331103(-)$1	237	2	29	11.9466
g[bb"""cccoooooocccbb]ggggg	chr3:196860627-196860897(-)$1	270	68	95	13.9476
$$hhhhhhhhoooooohhhhhhhh333	chr4:106364343-106364646(-)$1	303	224	251	10.8296
!ccciiiiiiiiillliiiiiiiii]c	chr1:1773931-1774214(-)$1	283	26	53	9.9839
iiiii"""bboooooobb333iiiiii	chr22:46621982-46622255(+)$1	273	120	147	14.8687
[a"""eeeeeooooooeeeee333aee	chr1:244833493-244833716(+)$1	223	16	43	13.7361
[eeeeeddddoooooodddd4444eee	chr13:36910288-36910509(-)$1	221	59	86	12.7263
======[a!!annnnna22a]======	chr4:109066668-109067162(-)$1	494	402	429	10.4354
[ffffff[bboooooobb]ffffff]d	chr19:14555251-14555494(+)$1	243	73	100	11.7010
#ccc####bboooooobbccc22ffff	chr3:23333978-23334222(+)$1	244	43	70	13.0721
gggggg!!bboooooobb22ggggggg	chr2:136236110-136236339(-)$1	229	135	162	13.9122
bb[gggggggoooooogggggggbb44	chr21:36412317-36412656(-)$1	339	167	194	12.8727
ccc[ffffffooooooffffffccc22	chr10:63842698-63842965(+)$1	267	53	80	11.5360
ggggg[ddddoooooodddd4444ggg	chr19:53078878-53079096(+)$1	218	153	180	13.8402
ggggg"""bboooooobb333gggggg	chr12:69250074-69250299(-)$1	225	115	142	14.6956
dddgggggggooooooggggggg333d	chr11:71718892-71719155(-)$1	263	83	110	13.5223
$$$$a!!cccooooooccc22a22bb]	chr17:28162472-28162755(-)$1	283	167	194	13.3655
==========oooooo==========:	chr5:141004420-141004660(-)$1	240	26	53	14.5110
f####eeeeeooooooeeeee22ffff	chr1:78391546-78391767(+)$1	221	54	81	12.7225
ggggggddddoooooodddd]gggggg	chr2:197646722-197646983(-)$1	261	156	183	13.5368
ggggg[ddddoooooodddd]gggggg	chr7:120596278-120596509(+)$1	231	75	102	13.7174
bb"""eeeeeooooooeeeee]bb22b	chr12:5701416-5701636(-)$1	220	30	57	11.6586
iiiiiiii[ccclllccc]iiiiiiii	chr13:74691725-74691988(-)$1	263	153	180	9.9753
###bb[ddddoooooodddd]bb333a	chr15:49544348-49544690(+)$1	342	163	190	12.3358
"ggggggg[cccmmmmccc]ggggggg	chr19:31790826-31791092(-)$1	266	47	74	9.3828
:iiiiiiiiiooooooiiiiiiiii::	chrX:6123492-6123733(-)$1	241	176	203	11.7360
ccc!!eeeeeooooooeeeee22ccc]	chr3:11648914-11649196(-)$1	282	76	103	12.9751
===========nnnnn===========	chr1:100971516-100971780(+)$1	264	231	258	11.3049
[a[gggggggooooooggggggg]aa2	chr14:95576505-95576731(-)$1	226	86	113	13.9331
eeeee!!cccooooooccc333eeeee	chr6:13290376-13290602(-)$1	226	5	32	14.6434
"""bb!!cccooooooccc22bb22ff	chrX:128951796-128952026(-)$1	230	167	194	13.4680
ffff"""cccooooooccc4444ffff	chr22:41362566-41362835(+)$1	269	91	118	14.5555
++dddd!!bboooooobb333dddd>>	chr9:140403546-140403800(-)$1	254	39	66	10.5980
eeeeeeeeeeooooooeeeee333eee	chr6:118930083-118930311(-)$1	228	131	158	12.9150
ff"""eeeeeooooooeeeee333fff	chr7:129574532-129574785(-)$1	253	112	139	13.5115
ffffbb[cccoooooocccbb]fffff	chr19:4934366-4934618(+)$1	252	3	30	12.4603
ffff[a!!bboooooobb22a]fffff	chr17:40392371-40392700(-)$1	329	235	262	12.8519
d[==========mmmm==========]	chr1:155926954-155927186(-)$1	232	38	65	10.4135
ggggg!!cccooooooccc666666gg	chr8:26483352-26483624(+)$1	272	28	55	12.5946
cceeeeecccooooooccc333eeeee	chr2:215659926-215660160(-)$1	234	5	32	14.0834
fiiiiiiiiiooooooiiiiiiiii::	chr1:180128482-180128716(+)$1	234	197	224	12.6895
eeeee!!cccooooooccc22eeeee:	chr4:83827152-83827402(+)$1	250	77	104	12.9183
eeeccc[cccoooooocccccc>>>>>	chr19:2628262-2628502(-)$1	240	170	197	12.6578
ffff"""cccooooooccc22ffffff	chr11:70125362-70125614(+)$1	252	50	77	14.0263

#otherMatches

#Seq PSSM
uauucuuaaaacauuauuuaagaauau	chr17:35511979-35512207(-)$1	228	19	46	15.4482
AUGCCUUAGCUUAUCUGAUGAACCAUA	chr2:143978982-143979248(+)$1	266	80	107	13.0336
cacacucacucagacagggaccgugug	chr4:99446462-99446715(-)$1	253	125	152	11.4823
CUGUCCACCCUUggcugggugcagugg	chr6:28218069-28218331(-)$1	262	173	200	12.3764
gaaaugacacccuguuguguuauucuu	chr1:35818626-35818881(+)$1	255	55	82	12.4989
uguaaauuuucacaauaaaauuuuaga	chr22:28674767-28675093(-)$1	326	3	30	13.7777
cuguucacccucaccugggaaaacacg	chr9:94812483-94812720(-)$1	237	110	137	13.2871
uuuuaaagacagaaaaguugaaagaau	chr14:21846659-21846915(-)$1	256	174	201	13.9374
ACCAGUCUUUCACACCAAAGCAUUCUG	chr6:162642085-162642316(-)$1	231	180	207	12.7780
UUGAGGGGACAUAUUGGUCACCUUCGG	chr17:40027085-40027376(-)$1	291	44	71	15.1082
AGUGUGAGGGUCCAUCCCCUCCUUUGU	chr15:86330866-86331103(-)$1	237	2	29	11.9466
cucucuuaaaucaacuuuuagugaggc	chr3:196860627-196860897(-)$1	270	68	95	13.9476
uuccugggaacacuccuuuccagguau	chr4:106364343-106364646(-)$1	303	224	251	10.8296
cguuuaguacauuuacaauguguugca	chr1:1773931-1774214(-)$1	283	26	53	9.9839
ugcacauaugcucacacacacgugcac	chr22:46621982-46622255(+)$1	273	120	147	14.8687
cggccucccacagugcugggauuacag	chr1:244833493-244833716(+)$1	223	16	43	13.7361
AACCUGCCACCUUUAAGUGGAAAUCAG	chr13:36910288-36910509(-)$1	221	59	86	12.7263
AUCAGUACAGUGAGGAAAGGAGCUGAU	chr4:109066668-109067162(-)$1	494	402	429	10.4354
GGUGUGUCCUGUUACAAGCACACACAG	chr19:14555251-14555494(+)$1	243	73	100	11.7010
AGAGCCCCACUCACUUGUCUCCUAGGU	chr3:23333978-23334222(+)$1	244	43	70	13.0721
uuuucaaacauaguguugagugaaaga	chr2:136236110-136236339(-)$1	229	135	162	13.9122
UGCAGGCUGCAUCUGGGCAGCUUCAUC	chr21:36412317-36412656(-)$1	339	167	194	12.8727
CUAUAAUUAUCUUUCAAUGAUUUAGAA	chr10:63842698-63842965(+)$1	267	53	80	11.5360
AUUUGUCGGAACAUUCUCUGCAAUUAA	chr19:53078878-53079096(+)$1	218	153	180	13.8402
CUGGAAUCAGGGAUUGCUCACUCCAGG	chr12:69250074-69250299(-)$1	225	115	142	14.6956
guuccccagugguagagcugggguuug	chr11:71718892-71719155(-)$1	263	83	110	13.5223
ACUUGAACUGAAUUUGCAGGGCCUGGU	chr17:28162472-28162755(-)$1	283	167	194	13.3655
uguuauuuuuaaugacaaaaguaacac	chr5:141004420-141004660(-)$1	240	26	53	14.5110
UCUAUAAUAUAUAUAAAUGUUUAAUAA	chr1:78391546-78391767(+)$1	221	54	81	12.7225
auuagguaucaacacagguauuuuggu	chr2:197646722-197646983(-)$1	261	156	183	13.5368
UUUGCAUUAAAGUAAAUUAAAGCAGAA	chr7:120596278-120596509(+)$1	231	75	102	13.7174
GCCAUGUCGCCUACCCGUGACUGCUUG	chr12:5701416-5701636(-)$1	220	30	57	11.6586
gguaucauuguaucauaucaugauauc	chr13:74691725-74691988(-)$1	263	153	180	9.9753
cuuugcuuuuucacuuaaaaccauaaa	chr15:49544348-49544690(+)$1	342	163	190	12.3358
AAGGCUUGUGGGAUCCCUCUUAGGCUU	chr19:31790826-31791092(-)$1	266	47	74	9.3828
UUCUCUUUUCUUAUCUGGGAAGAGAUC	chrX:6123492-6123733(-)$1	241	176	203	11.7360
CUUAUAAAUAUAUUCUUAUUUUGGAGG	chr3:11648914-11649196(-)$1	282	76	103	12.9751
uaaauauuaaCUAGGUGUUAAUAUUUA	chr1:100971516-100971780(+)$1	264	231	258	11.3049
agcugccaggauagacucuggcacccu	chr14:95576505-95576731(-)$1	226	86	113	13.9331
AGAGAUCCAGUUUAAUUUGUAUUCUCU	chr6:13290376-13290602(-)$1	226	5	32	14.6434
acccaagugucuaucaacagaugaaug	chrX:128951796-128952026(-)$1	230	167	194	13.4680
UUGUCUUUGUCAAAAAACAUUUCACAA	chr22:41362566-41362835(+)$1	269	91	118	14.5555
CCAGCUAAACUCACUUGUACcagcuaa	chr9:140403546-140403800(-)$1	254	39	66	10.5980
CUCCUAGAAUUAGUUUAUUCUCCAAGG	chr6:118930083-118930311(-)$1	228	131	158	12.9150
uggccucccaaagugcugggauuacag	chr7:129574532-129574785(-)$1	253	112	139	13.5115
uuaagcgcacaguucgguggcauuaaa	chr19:4934366-4934618(+)$1	252	3	30	12.4603
uggauuugccuauuccggauauuucau	chr17:40392371-40392700(-)$1	329	235	262	12.8519
uacauuuauuuuucuaaaaaugaauga	chr1:155926954-155927186(-)$1	232	38	65	10.4135
ugugugugcaguucauuguuuuaaaau	chr8:26483352-26483624(+)$1	272	28	55	12.5946
cuggucugcaaaacccuguaugggacc	chr2:215659926-215660160(-)$1	234	5	32	14.0834
ugagcugagcagaggaguuuggcuuua	chr1:180128482-180128716(+)$1	234	197	224	12.6895
UUUCUCUAGUUACUUUAUUUCAGAAAC	chr4:83827152-83827402(+)$1	250	77	104	12.9183
gcugcaaggaaaugaauucugccgaua	chr19:2628262-2628502(-)$1	240	170	197	12.6578
UGCUGAAGCUCAAACAGGCAAGGCAGA	chr11:70125362-70125614(+)$1	252	50	77	14.0263

#DB
((((((((((......)))))))))))	chr17:35511979-35512207(-)$1	1	19	46	15.4482
(((..(((.(......).)))..))))	chr2:143978982-143979248(+)$1	1	80	107	13.0336
(((((...(((.....)))...)))))	chr4:99446462-99446715(-)$1	1	125	152	11.4823
(((..(((((......)))))))))))	chr6:28218069-28218331(-)$1	1	173	200	12.3764
(((.((((((......)))))))))))	chr1:35818626-35818881(+)$1	1	55	82	12.4989
(..(((((((......)))))))..))	chr22:28674767-28675093(-)$1	1	3	30	13.7777
.((((..(((......)))..)))).)	chr9:94812483-94812720(-)$1	1	110	137	13.2871
((((...(((......)))...)))))	chr14:21846659-21846915(-)$1	1	174	201	13.9374
(((((.((((......))))....)))	chr6:162642085-162642316(-)$1	1	180	207	12.7780
((((((((((......))).)))))))	chr17:40027085-40027376(-)$1	1	44	71	15.1082
((.(.(((((......)))))).))))	chr15:86330866-86331103(-)$1	1	2	29	11.9466
(.((...(((......))))).)))))	chr3:196860627-196860897(-)$1	1	68	95	13.9476
..((((((((......))))))))...	chr4:106364343-106364646(-)$1	1	224	251	10.8296
.((((((((((((...))))))))).)	chr1:1773931-1774214(-)$1	1	26	53	9.9839
(((((...((......))...))))))	chr22:46621982-46622255(+)$1	1	120	147	14.8687
.(...(((((......)))))...)))	chr1:244833493-244833716(+)$1	1	16	43	13.7361
.(((((((((......))))....)))	chr13:36910288-36910509(-)$1	1	59	86	12.7263
((((((.(..(.....)..).))))))	chr4:109066668-109067162(-)$1	1	402	429	10.4354
.((((((.((......)).)))))).)	chr19:14555251-14555494(+)$1	1	73	100	11.7010
.(((....((......)))))..))))	chr3:23333978-23334222(+)$1	1	43	70	13.0721
((((((..((......))..)))))))	chr2:136236110-136236339(-)$1	1	135	162	13.9122
((.(((((((......)))))))))..	chr21:36412317-36412656(-)$1	1	167	194	12.8727
(((.((((((......)))))))))..	chr10:63842698-63842965(+)$1	1	53	80	11.5360
(((((.((((......))))....)))	chr19:53078878-53079096(+)$1	1	153	180	13.8402
(((((...((......))...))))))	chr12:69250074-69250299(-)$1	1	115	142	14.6956
((((((((((......)))))))...)	chr11:71718892-71719155(-)$1	1	83	110	13.5223
....(..(((......)))..)..)).	chr17:28162472-28162755(-)$1	1	167	194	13.3655
((((((((((......)))))))))).	chr5:141004420-141004660(-)$1	1	26	53	14.5110
(....(((((......)))))..))))	chr1:78391546-78391767(+)$1	1	54	81	12.7225
((((((((((......)))).))))))	chr2:197646722-197646983(-)$1	1	156	183	13.5368
(((((.((((......)))).))))))	chr7:120596278-120596509(+)$1	1	75	102	13.7174
((...(((((......))))).))..)	chr12:5701416-5701636(-)$1	1	30	57	11.6586
((((((((.(((...))).))))))))	chr13:74691725-74691988(-)$1	1	153	180	9.9753
...((.((((......)))).))...)	chr15:49544348-49544690(+)$1	1	163	190	12.3358
.(((((((.(((....))).)))))))	chr19:31790826-31791092(-)$1	1	47	74	9.3828
.(((((((((......)))))))))..	chrX:6123492-6123733(-)$1	1	176	203	11.7360
(((..(((((......)))))..))).	chr3:11648914-11649196(-)$1	1	76	103	12.9751
(((((((((((.....)))))))))))	chr1:100971516-100971780(+)$1	1	231	258	11.3049
.(.(((((((......))))))).)).	chr14:95576505-95576731(-)$1	1	86	113	13.9331
(((((..(((......)))...)))))	chr6:13290376-13290602(-)$1	1	5	32	14.6434
...((..(((......)))..))..))	chrX:128951796-128952026(-)$1	1	167	194	13.4680
((((...(((......)))....))))	chr22:41362566-41362835(+)$1	1	91	118	14.5555
..((((..((......))...))))..	chr9:140403546-140403800(-)$1	1	39	66	10.5980
((((((((((......)))))...)))	chr6:118930083-118930311(-)$1	1	131	158	12.9150
((...(((((......)))))...)))	chr7:129574532-129574785(-)$1	1	112	139	13.5115
((((((.(((......))))).)))))	chr19:4934366-4934618(+)$1	1	3	30	12.4603
((((.(..((......))..).)))))	chr17:40392371-40392700(-)$1	1	235	262	12.8519
(.((((((((((....)))))))))).	chr1:155926954-155927186(-)$1	1	38	65	10.4135
(((((..(((......)))......))	chr8:26483352-26483624(+)$1	1	28	55	12.5946
((((((((((......)))...)))))	chr2:215659926-215660160(-)$1	1	5	32	14.0834
)(((((((((......)))))))))..	chr1:180128482-180128716(+)$1	1	197	224	12.6895
(((((..(((......)))..))))).	chr4:83827152-83827402(+)$1	1	77	104	12.9183
((((((.(((......)))))).....	chr19:2628262-2628502(-)$1	1	170	197	12.6578
((((...(((......)))..))))))	chr11:70125362-70125614(+)$1	1	50	77	14.0263

#PSSM
g : 0.16	e : 0.12	f : 0.12	[ : 0.09	= : 0.07	c : 0.07	i : 0.05	d : 0.05	$ : 0.03	# : 0.03	b : 0.03	" : 0.03	h : 0.01	! : 0.01	: : 0.01	+ : 0.01	
g : 0.16	e : 0.14	f : 0.11	i : 0.09	c : 0.09	= : 0.07	d : 0.05	[ : 0.03	$ : 0.03	a : 0.03	b : 0.03	# : 0.03	! : 0.01	h : 0.01	" : 0.01	+ : 0.01	
e : 0.16	g : 0.16	= : 0.09	i : 0.09	f : 0.09	c : 0.07	" : 0.07	d : 0.05	[ : 0.05	h : 0.03	# : 0.03	! : 0.01	b : 0.01	$ : 0.01	
g : 0.22	e : 0.11	= : 0.09	i : 0.09	f : 0.09	! : 0.05	b : 0.05	c : 0.05	" : 0.05	[ : 0.03	d : 0.03	h : 0.03	a : 0.01	$ : 0.01	# : 0.01	
g : 0.22	" : 0.12	e : 0.11	i : 0.11	= : 0.09	! : 0.05	f : 0.05	b : 0.05	d : 0.03	[ : 0.03	# : 0.03	h : 0.01	a : 0.01	c : 0.01	
e : 0.18	" : 0.12	g : 0.12	! : 0.11	= : 0.09	i : 0.09	[ : 0.07	f : 0.05	c : 0.03	h : 0.01	# : 0.01	d : 0.01	b : 0.01	a : 0.01	
e : 0.16	! : 0.16	" : 0.12	d : 0.11	g : 0.09	i : 0.09	= : 0.07	f : 0.05	[ : 0.05	c : 0.01	h : 0.01	# : 0.01	
c : 0.27	e : 0.14	d : 0.11	g : 0.09	= : 0.07	i : 0.07	" : 0.05	! : 0.05	f : 0.03	h : 0.01	a : 0.01	[ : 0.01	# : 0.01	
c : 0.27	e : 0.14	b : 0.12	d : 0.11	= : 0.07	g : 0.07	[ : 0.05	i : 0.05	f : 0.03	h : 0.01	! : 0.01	
c : 0.31	e : 0.14	b : 0.12	d : 0.11	= : 0.07	g : 0.07	i : 0.05	f : 0.03	a : 0.01	h : 0.01	! : 0.01	
o : 0.87	c : 0.05	= : 0.03	i : 0.01	a : 0.01	
o : 0.87	n : 0.05	c : 0.03	i : 0.01	= : 0.01	
o : 0.87	n : 0.05	m : 0.03	i : 0.01	l : 0.01	
o : 0.87	n : 0.05	l : 0.03	m : 0.03	
o : 0.87	n : 0.05	l : 0.03	m : 0.03	
o : 0.87	n : 0.05	m : 0.03	l : 0.01	c : 0.01	
c : 0.31	e : 0.14	b : 0.12	d : 0.11	= : 0.07	g : 0.07	i : 0.05	a : 0.03	f : 0.03	h : 0.01	
c : 0.31	e : 0.14	b : 0.12	d : 0.11	= : 0.07	g : 0.07	i : 0.05	f : 0.03	] : 0.01	h : 0.01	2 : 0.01	
c : 0.33	e : 0.14	d : 0.11	= : 0.07	g : 0.07	i : 0.05	3 : 0.05	2 : 0.05	f : 0.03	] : 0.03	h : 0.01	
e : 0.14	3 : 0.12	2 : 0.12	d : 0.11	= : 0.07	g : 0.07	i : 0.07	c : 0.05	f : 0.05	] : 0.03	b : 0.03	h : 0.01	a : 0.01	4 : 0.01	6 : 0.01	
e : 0.14	3 : 0.12	g : 0.11	2 : 0.09	i : 0.09	= : 0.07	4 : 0.07	] : 0.07	c : 0.05	f : 0.05	b : 0.03	h : 0.01	a : 0.01	6 : 0.01	
g : 0.16	3 : 0.12	i : 0.11	= : 0.09	2 : 0.07	f : 0.07	4 : 0.07	] : 0.07	e : 0.03	d : 0.03	a : 0.03	b : 0.03	h : 0.01	6 : 0.01	c : 0.01	
g : 0.22	i : 0.11	= : 0.09	2 : 0.09	e : 0.07	4 : 0.07	f : 0.07	3 : 0.05	b : 0.05	d : 0.03	h : 0.03	] : 0.01	c : 0.01	6 : 0.01	> : 0.01	
g : 0.14	f : 0.12	i : 0.11	= : 0.09	e : 0.09	3 : 0.09	2 : 0.05	d : 0.05	4 : 0.05	h : 0.03	b : 0.03	c : 0.03	] : 0.01	6 : 0.01	> : 0.01	
g : 0.16	e : 0.14	f : 0.14	i : 0.11	= : 0.09	2 : 0.05	d : 0.05	3 : 0.05	a : 0.03	b : 0.03	c : 0.03	h : 0.01	6 : 0.01	> : 0.01	
g : 0.18	e : 0.16	f : 0.14	= : 0.09	] : 0.05	i : 0.05	3 : 0.05	c : 0.03	2 : 0.03	: : 0.03	> : 0.03	h : 0.01	d : 0.01	4 : 0.01	b : 0.01	a : 0.01	
g : 0.18	f : 0.14	e : 0.12	c : 0.07	: : 0.07	= : 0.05	i : 0.05	d : 0.05	] : 0.05	2 : 0.03	> : 0.03	h : 0.01	3 : 0.01	4 : 0.01	b : 0.01	a : 0.01	

#score	692.8983906718385
#seq	54
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m1_run2.txt

#BEAR
!ccctttttttttttccc]e	chrX:119746197-119746426(+)$1	229	167	187	21.5845
gggguuuuuuuuuuuugggg	chr14:67851745-67851967(+)$1	222	163	183	22.3007
eeeeettttttttttteeee	chr9:37887386-37887614(+)$1	228	58	78	21.6943
[ddddtttttttttttdddd	chr3:125871950-125872171(-)$1	221	76	96	21.9921
hhhhuuuuuuuuuuuuhhhh	chr5:43290514-43290740(-)$1	226	94	114	21.0018
!ddddtttttttttttdddd	chr3:58552041-58552289(-)$1	248	171	191	22.0254
ddddwwwwwwwwwwwwwwdd	chr15:100254898-100255126(+)$1	228	13	33	20.4887
eeeeettttttttttteeee	chr6:89814861-89815082(+)$1	221	59	79	21.6943
====uuuuuuuuuuuu====	chr1:62905366-62905581(-)$1	215	44	64	22.4473
ddddvvvvvvvvvvvvvddd	chr3:52083882-52084109(-)$1	227	79	99	22.2284
yyyyyyyyyyyyyyyydddd	chr22:24812519-24812759(+)$1	240	121	141	19.3195
eeeeettttttttttteeee	chr6:152448113-152448330(-)$1	217	82	102	21.6943
[cccvvvvvvvvvvvvvccc	chr17:38288186-38288409(+)$1	223	21	41	22.4903
%ccctttttttttttccc66	chr2:153505101-153505330(+)$1	229	135	155	19.6890
eeeeettttttttttteeee	chr2:224740230-224740447(-)$1	217	15	35	21.6943
!cccwwwwwwwwwwwwwwcc	chr16:30592824-30593055(-)$1	231	77	97	20.7145
eeeeettttttttttteeee	chr16:87731326-87731545(+)$1	219	134	154	21.6943
eeeevvvvvvvvvvvvveee	chr11:65088049-65088271(+)$1	222	122	142	22.0456
gggguuuuuuuuuuuugggg	chr15:45010221-45010442(+)$1	221	21	41	22.3007
gggguuuuuuuuuuuugggg	chr5:149599565-149599800(-)$1	235	101	121	22.3007
iiiiuuuuuuuuuuuuiiii	chr3:185866983-185867214(-)$1	231	33	53	22.3346
ddddtttttttttttdddd:	chr6:34254106-34254333(-)$1	227	22	42	20.1348
eeeeettttttttttteeee	chr13:77454788-77455006(-)$1	218	13	33	21.6943
eeeevvvvvvvvvvvvveee	chr12:54058854-54059091(-)$1	237	154	174	22.0456
!!bbvvvvvvvvvvvvvbb3	chr1:118408193-118408417(-)$1	224	181	201	21.3091
eeeeuuuuuuuuuuuueeee	chr8:110586705-110586923(-)$1	218	156	176	22.2939
ddddwwwwwwwwwwwwwwdd	chr5:143856672-143856887(+)$1	215	161	181	20.4887
:ccctttttttttttcccff	chr3:127391505-127391720(+)$1	215	96	116	20.3352
yyyyyyyyyyyyyyyydddd	chr22:41626602-41626824(+)$1	222	57	77	19.3195
cccwwwwwwwwwwwwwwccc	chr7:917531-917753(+)$1	222	50	70	20.6389
[cccwwwwwwwwwwwwwwcc	chr20:3732696-3732912(+)$1	216	96	116	20.6812
dddduuuuuuuuuuuudddd	chr11:72292335-72292555(-)$1	220	137	157	22.4936
e[bbvvvvvvvvvvvvvbb]	chr1:244572385-244572611(-)$1	226	153	173	21.2068
ddddvvvvvvvvvvvvvddd	chr17:74676330-74676560(-)$1	230	159	179	22.2284
ddccctttttttttttccc]	chr1:86195994-86196215(-)$1	221	48	68	22.2210
gggggtttttttttttgggg	chr1:51737974-51738190(+)$1	216	23	43	21.5625
Jcccuuuuuuuuuuuuccc:	chr3:44701921-44702140(+)$1	219	20	40	20.2916
!ddddtttttttttttdddd	chr9:137989528-137989765(+)$1	237	73	93	22.0254
e[ccctttttttttttccc]	chr7:2752478-2752696(+)$1	218	158	178	22.2526
ffffvvvvvvvvvvvvvfff	chr8:110659460-110659676(-)$1	216	178	198	21.2307
yyyyyyyyyyyyyyyyeeee	chr1:245017422-245017651(-)$1	229	172	192	19.2254
hhccctttttttttttccc]	chr1:25167505-25167730(+)$1	225	83	103	21.8962
[cccvvvvvvvvvvvvvccc	chr10:5494322-5494549(+)$1	227	55	75	22.4903
cddddtttttttttttdddd	chr2:68520328-68520543(+)$1	215	168	188	21.8552
ddddwwwwwwwwwwwwwwdd	chr11:47290994-47291240(+)$1	246	26	46	20.4887
!ddddtttttttttttdddd	chr6:32160740-32160958(-)$1	218	135	155	22.0254
eeeeettttttttttteeee	chr9:140062070-140062307(+)$1	237	134	154	21.6943
%%ccctttttttttttccc5	chr3:185330301-185330518(-)$1	217	20	40	19.9515
cyyyyyyyyyyyyyyyyccc	chr5:55233424-55233639(+)$1	215	4	24	19.7186
ccwwwwwwwwwwwwwwcccd	chr5:63906905-63907129(+)$1	224	81	101	20.2562
ffffvvvvvvvvvvvvvfff	chr10:116192814-116193034(-)$1	220	68	88	21.2307
hhhhhttttttttttthhhh	chr10:86275022-86275255(+)$1	233	18	38	20.0442
ddddvvvvvvvvvvvvvddd	chr21:30717802-30718017(+)$1	215	156	176	22.2284
!cccuuuuuuuuuuuuccc2	chr17:2288126-2288357(-)$1	231	114	134	22.6480
d[bbuuuuuuuuuuuubb]d	chr11:1576902-1577136(-)$1	234	32	52	21.4819
ggggvvvvvvvvvvvvvggg	chr9:99264514-99264731(-)$1	217	187	207	22.0648
ffffftttttttttttffff	chr19:6495887-6496117(-)$1	230	143	163	20.7262
dddduuuuuuuuuuuudddd	chr3:185046329-185046548(-)$1	219	171	191	22.4936
yyyyyyyyyyyyyyyyiiii	chrX:12742366-12742583(+)$1	217	87	107	19.2158
ffffftttttttttttffff	chr14:105225821-105226040(+)$1	219	155	175	20.7262
d[bbuuuuuuuuuuuubb]d	chr3:11078666-11078915(+)$1	249	90	110	21.4819
ggggvvvvvvvvvvvvvggg	chr5:53839655-53839877(+)$1	222	134	154	22.0648
ddddtttttttttttdddd:	chr11:117158348-117158580(-)$1	232	65	85	20.1348
ggwwwwwwwwwwwwwwgggg	chr18:70415207-70415432(-)$1	225	8	28	19.9735

#otherMatches

#Seq PSSM
GGCUAAUGAUAUAAGAGUGA	chrX:119746197-119746426(+)$1	229	167	187	21.5845
UGCUAACCUAAAAGACAGCA	chr14:67851745-67851967(+)$1	222	163	183	22.3007
AGAGGCUUGAGACUUUCCUU	chr9:37887386-37887614(+)$1	228	58	78	21.6943
ACCCACUUCUCUGUUCUGGG	chr3:125871950-125872171(-)$1	221	76	96	21.9921
CUGGGACAAUAAAACACUGG	chr5:43290514-43290740(-)$1	226	94	114	21.0018
AAGCACCCAGCCCUCCUGCU	chr3:58552041-58552289(-)$1	248	171	191	22.0254
CCUUUUCCUAAAAAACUCAA	chr15:100254898-100255126(+)$1	228	13	33	20.4887
UCUCCUGUGAUCACUUGGAG	chr6:89814861-89815082(+)$1	221	59	79	21.6943
UUUUUCUUCAAAUCCCAAGG	chr1:62905366-62905581(-)$1	215	44	64	22.4473
UGGUCUUUGCAUUUUCUGCC	chr3:52083882-52084109(-)$1	227	79	99	22.2284
UUCCCAACUUUAUCCCUUGC	chr22:24812519-24812759(+)$1	240	121	141	19.3195
GGUUUGGAAAAAAAGAAGAC	chr6:152448113-152448330(-)$1	217	82	102	21.6943
UAGUGAAUAGUUGUGCAACU	chr17:38288186-38288409(+)$1	223	21	41	22.4903
CAACAAGCAUUCAAGGUUAC	chr2:153505101-153505330(+)$1	229	135	155	19.6890
AUGCUAUAUUUAUUCAAGUG	chr2:224740230-224740447(-)$1	217	15	35	21.6943
AGUGCACAAACUAUCAAACA	chr16:30592824-30593055(-)$1	231	77	97	20.7145
CAAACAAAAGAACAAGGUUU	chr16:87731326-87731545(+)$1	219	134	154	21.6943
UUGAUCUCUAAUCUUUUUUA	chr11:65088049-65088271(+)$1	222	122	142	22.0456
AAGAUUCAUAUUUACUUCUU	chr15:45010221-45010442(+)$1	221	21	41	22.3007
CACACCUCCUGUCCACUGUG	chr5:149599565-149599800(-)$1	235	101	121	22.3007
GCUCCAAGAGCCCCCAGAGC	chr3:185866983-185867214(-)$1	231	33	53	22.3346
GUUCAAAUAAAUAAAGGGCA	chr6:34254106-34254333(-)$1	227	22	42	20.1348
GUCACUUAAAUUUUUUGUGA	chr13:77454788-77455006(-)$1	218	13	33	21.6943
UGUGUAUAUUUCUUUUCCAC	chr12:54058854-54059091(-)$1	237	154	174	22.0456
GUCAUACCUUUUUUUUUUGU	chr1:118408193-118408417(-)$1	224	181	201	21.3091
AUGUGUAAUUGUUCCAGCAU	chr8:110586705-110586923(-)$1	218	156	176	22.2939
AGUGGCUUCCAAAAUAUGCA	chr5:143856672-143856887(+)$1	215	161	181	20.4887
CGGGACUCAAUUAAACCCGC	chr3:127391505-127391720(+)$1	215	96	116	20.3352
GAGCCAUGUAAAUUAAGUUC	chr22:41626602-41626824(+)$1	222	57	77	19.3195
gcauucccccaccucccugc	chr7:917531-917753(+)$1	222	50	70	20.6389
AUCGACUUUCUUUCCAACUG	chr20:3732696-3732912(+)$1	216	96	116	20.6812
GCUCACCAACUACCUCGAGU	chr11:72292335-72292555(-)$1	220	137	157	22.4936
GUCAUUGUAAUCUUUGUUGU	chr1:244572385-244572611(-)$1	226	153	173	21.2068
UGCCAUAUUGAUUACAGGGC	chr17:74676330-74676560(-)$1	230	159	179	22.2284
AAGACAGACAGAUACAGUCA	chr1:86195994-86196215(-)$1	221	48	68	22.2210
CUGCAUCUCUCAUUACUGUA	chr1:51737974-51738190(+)$1	216	23	43	21.5625
AGGUAAUUUUUUAAAAGCCA	chr3:44701921-44702140(+)$1	219	20	40	20.2916
CGGUAUUUCAUUUUCUUACU	chr9:137989528-137989765(+)$1	237	73	93	22.0254
ugucaucccaucacuuugag	chr7:2752478-2752696(+)$1	218	158	178	22.2526
AUUUGUAUGUAAGGGAAGAG	chr8:110659460-110659676(-)$1	216	178	198	21.2307
CUUUUUUUUUUUUUUAUCAC	chr1:245017422-245017651(-)$1	229	172	192	19.2254
UAUACACUCCUAAGCAGUAU	chr1:25167505-25167730(+)$1	225	83	103	21.8962
AGGUCAACAGUCCCAACACC	chr10:5494322-5494549(+)$1	227	55	75	22.4903
UUUGUAUUACAUUUUCACAA	chr2:68520328-68520543(+)$1	215	168	188	21.8552
GACCUAGAACCCAGUGUCGG	chr11:47290994-47291240(+)$1	246	26	46	20.4887
GUCCCGGUAAGUAAGAGGGA	chr6:32160740-32160958(-)$1	218	135	155	22.0254
CUGUGUAUUUCUAUUUUGCA	chr9:140062070-140062307(+)$1	237	134	154	21.6943
AGUAAGAAAAUAUAUAUUAA	chr3:185330301-185330518(-)$1	217	20	40	19.9515
CUAAUCCUAAAACACUUGCC	chr5:55233424-55233639(+)$1	215	4	24	19.7186
AGCUUAAUAUCCUUUCCUGA	chr5:63906905-63907129(+)$1	224	81	101	20.2562
AGUUAUUAACACACUCAAAC	chr10:116192814-116193034(-)$1	220	68	88	21.2307
AGGGAUUGUAAACUAUUUUC	chr10:86275022-86275255(+)$1	233	18	38	20.0442
AUUUUAAAUAAGGAAAUAAG	chr21:30717802-30718017(+)$1	215	156	176	22.2284
CUGCCCACCUCUCCCUGCAU	chr17:2288126-2288357(-)$1	231	114	134	22.6480
UGCCAGGGUGUUCAGAGGGG	chr11:1576902-1577136(-)$1	234	32	52	21.4819
CAUCAUGAGAGACGGAAGAU	chr9:99264514-99264731(-)$1	217	187	207	22.0648
UGGUGGAGCCCUACAACGCC	chr19:6495887-6496117(-)$1	230	143	163	20.7262
GAGCUUCAAAUAUCUUGCUU	chr3:185046329-185046548(-)$1	219	171	191	22.4936
CACAUUCACUAAGCAUGGGG	chrX:12742366-12742583(+)$1	217	87	107	19.2158
CUCUUUAUAUUUGCACAAGA	chr14:105225821-105226040(+)$1	219	155	175	20.7262
GCGAGUCCAGACACCAUCAC	chr3:11078666-11078915(+)$1	249	90	110	21.4819
UUUCUGAUUGAAAGAGUGAA	chr5:53839655-53839877(+)$1	222	134	154	22.0648
UGGGUUCUCUUCAUUCCCAC	chr11:117158348-117158580(-)$1	232	65	85	20.1348
UGUUUUAACUGUUUUUUAUU	chr18:70415207-70415432(-)$1	225	8	28	19.9735

#DB
.(((...........))).)	chrX:119746197-119746426(+)$1	1	167	187	21.5845
((((............))))	chr14:67851745-67851967(+)$1	1	163	183	22.3007
(((((...........))))	chr9:37887386-37887614(+)$1	1	58	78	21.6943
.((((...........))))	chr3:125871950-125872171(-)$1	1	76	96	21.9921
((((............))))	chr5:43290514-43290740(-)$1	1	94	114	21.0018
.((((...........))))	chr3:58552041-58552289(-)$1	1	171	191	22.0254
((((..............))	chr15:100254898-100255126(+)$1	1	13	33	20.4887
(((((...........))))	chr6:89814861-89815082(+)$1	1	59	79	21.6943
((((............))))	chr1:62905366-62905581(-)$1	1	44	64	22.4473
((((.............)))	chr3:52083882-52084109(-)$1	1	79	99	22.2284
................))))	chr22:24812519-24812759(+)$1	1	121	141	19.3195
(((((...........))))	chr6:152448113-152448330(-)$1	1	82	102	21.6943
.(((.............)))	chr17:38288186-38288409(+)$1	1	21	41	22.4903
.(((...........)))..	chr2:153505101-153505330(+)$1	1	135	155	19.6890
(((((...........))))	chr2:224740230-224740447(-)$1	1	15	35	21.6943
.(((..............))	chr16:30592824-30593055(-)$1	1	77	97	20.7145
(((((...........))))	chr16:87731326-87731545(+)$1	1	134	154	21.6943
((((.............)))	chr11:65088049-65088271(+)$1	1	122	142	22.0456
((((............))))	chr15:45010221-45010442(+)$1	1	21	41	22.3007
((((............))))	chr5:149599565-149599800(-)$1	1	101	121	22.3007
((((............))))	chr3:185866983-185867214(-)$1	1	33	53	22.3346
((((...........)))).	chr6:34254106-34254333(-)$1	1	22	42	20.1348
(((((...........))))	chr13:77454788-77455006(-)$1	1	13	33	21.6943
((((.............)))	chr12:54058854-54059091(-)$1	1	154	174	22.0456
..((.............)).	chr1:118408193-118408417(-)$1	1	181	201	21.3091
((((............))))	chr8:110586705-110586923(-)$1	1	156	176	22.2939
((((..............))	chr5:143856672-143856887(+)$1	1	161	181	20.4887
.(((...........)))((	chr3:127391505-127391720(+)$1	1	96	116	20.3352
................))))	chr22:41626602-41626824(+)$1	1	57	77	19.3195
(((..............)))	chr7:917531-917753(+)$1	1	50	70	20.6389
.(((..............))	chr20:3732696-3732912(+)$1	1	96	116	20.6812
((((............))))	chr11:72292335-72292555(-)$1	1	137	157	22.4936
(.((.............)).	chr1:244572385-244572611(-)$1	1	153	173	21.2068
((((.............)))	chr17:74676330-74676560(-)$1	1	159	179	22.2284
(((((...........))).	chr1:86195994-86196215(-)$1	1	48	68	22.2210
(((((...........))))	chr1:51737974-51738190(+)$1	1	23	43	21.5625
((((............))).	chr3:44701921-44702140(+)$1	1	20	40	20.2916
.((((...........))))	chr9:137989528-137989765(+)$1	1	73	93	22.0254
(.(((...........))).	chr7:2752478-2752696(+)$1	1	158	178	22.2526
((((.............)))	chr8:110659460-110659676(-)$1	1	178	198	21.2307
................))))	chr1:245017422-245017651(-)$1	1	172	192	19.2254
(((((...........))).	chr1:25167505-25167730(+)$1	1	83	103	21.8962
.(((.............)))	chr10:5494322-5494549(+)$1	1	55	75	22.4903
)((((...........))))	chr2:68520328-68520543(+)$1	1	168	188	21.8552
((((..............))	chr11:47290994-47291240(+)$1	1	26	46	20.4887
.((((...........))))	chr6:32160740-32160958(-)$1	1	135	155	22.0254
(((((...........))))	chr9:140062070-140062307(+)$1	1	134	154	21.6943
..(((...........))).	chr3:185330301-185330518(-)$1	1	20	40	19.9515
(................)))	chr5:55233424-55233639(+)$1	1	4	24	19.7186
((..............))))	chr5:63906905-63907129(+)$1	1	81	101	20.2562
((((.............)))	chr10:116192814-116193034(-)$1	1	68	88	21.2307
(((((...........))))	chr10:86275022-86275255(+)$1	1	18	38	20.0442
((((.............)))	chr21:30717802-30718017(+)$1	1	156	176	22.2284
.(((............))).	chr17:2288126-2288357(-)$1	1	114	134	22.6480
(.((............)).)	chr11:1576902-1577136(-)$1	1	32	52	21.4819
((((.............)))	chr9:99264514-99264731(-)$1	1	187	207	22.0648
(((((...........))))	chr19:6495887-6496117(-)$1	1	143	163	20.7262
((((............))))	chr3:185046329-185046548(-)$1	1	171	191	22.4936
................))))	chrX:12742366-12742583(+)$1	1	87	107	19.2158
(((((...........))))	chr14:105225821-105226040(+)$1	1	155	175	20.7262
(.((............)).)	chr3:11078666-11078915(+)$1	1	90	110	21.4819
((((.............)))	chr5:53839655-53839877(+)$1	1	134	154	22.0648
((((...........)))).	chr11:117158348-117158580(-)$1	1	65	85	20.1348
((..............))))	chr18:70415207-70415432(-)$1	1	8	28	19.9735

#PSSM
d : 0.20	e : 0.18	! : 0.10	g : 0.10	[ : 0.06	y : 0.06	c : 0.06	f : 0.06	h : 0.04	% : 0.03	= : 0.01	i : 0.01	: : 0.01	J : 0.01	
d : 0.25	c : 0.17	e : 0.15	g : 0.10	y : 0.07	[ : 0.06	f : 0.06	h : 0.04	= : 0.01	i : 0.01	! : 0.01	% : 0.01	
d : 0.23	c : 0.21	e : 0.15	g : 0.09	y : 0.07	b : 0.06	f : 0.06	h : 0.03	w : 0.03	= : 0.01	i : 0.01	
d : 0.23	c : 0.20	e : 0.15	g : 0.09	y : 0.07	b : 0.06	f : 0.06	w : 0.04	h : 0.03	= : 0.01	i : 0.01	
u : 0.20	v : 0.20	w : 0.12	e : 0.10	t : 0.07	d : 0.07	y : 0.07	c : 0.06	f : 0.03	g : 0.01	h : 0.01	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.39	u : 0.20	v : 0.20	w : 0.12	y : 0.07	
t : 0.31	u : 0.20	v : 0.20	w : 0.12	y : 0.07	c : 0.04	d : 0.03	
v : 0.20	d : 0.17	c : 0.15	e : 0.14	w : 0.09	g : 0.07	h : 0.03	i : 0.03	b : 0.03	f : 0.03	= : 0.01	y : 0.01	
c : 0.21	d : 0.21	e : 0.17	g : 0.10	w : 0.07	b : 0.06	f : 0.06	h : 0.03	i : 0.03	= : 0.01	
d : 0.26	c : 0.20	e : 0.17	g : 0.10	f : 0.07	] : 0.04	h : 0.03	i : 0.03	b : 0.03	= : 0.01	6 : 0.01	
d : 0.28	e : 0.18	g : 0.10	c : 0.09	f : 0.07	] : 0.06	: : 0.04	h : 0.03	i : 0.03	= : 0.01	6 : 0.01	3 : 0.01	5 : 0.01	2 : 0.01	

#score	1364.309560849861
#seq	64
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m1_run2.txt

#BEAR
ccc!!eeeeeccc!!ccclllccc]ccc]eeeee22ccc]	chr20:44330632-44330853(-)$1	221	178	218	11.6532
:dddd[==========!!bbmmmmbb333==========2	chr9:90283417-90283638(-)$1	221	124	164	11.0225
dcccbb!!bb$$$$$cccooooooccc4444bb22bb]cc	chr14:97032237-97032461(+)$1	224	164	204	13.8053
[ccc[ccc!!dddd[cccoooooocccddddcccccc]bb	chr1:204654357-204654590(+)$1	233	158	198	13.9626
""cccccc[bb####cccrrrrrrrrrccc4444bbccc]	chr5:141243169-141243392(+)$1	223	86	126	12.7370
[ggggggg[bb[ccc[bboooooobbcccbb333gggggg	chr11:73106729-73106950(-)$1	221	115	155	14.3500
======!!dddd[bb[ddddllldddd22bb]dddd]===	chr3:112931335-112931558(+)$1	223	42	82	12.1298
a####gggggggbb!!cccnnnnnccc22bb]ggggggg3	chrX:102005998-102006222(-)$1	224	65	105	13.7056
dddd[dddd$$$$$ddddoooooodddddddddddd]ccc	chr17:46052435-46052656(-)$1	221	90	130	12.3283
b[ccc####eeeee[bboooooobb]eeeee4444ccc33	chr4:99363243-99363465(-)$1	222	80	120	12.6506
cc[ccc####hhhhhhhhoooooohhhhhhhh4444cccc	chr12:25357969-25358190(-)$1	221	1	41	11.6887
==========$$$$$bbqqqqqqqqbb4444=========	chr16:55364105-55364328(+)$1	223	38	78	12.2809
$$$$ccc[ccc!!ddddoooooodddd22ccc]ccc4444	chr4:8008974-8009199(-)$1	225	142	182	15.6844
========[bb"""eeeeellleeeee333bb]=======	chr16:30076961-30077188(+)$1	227	73	113	13.8040
b####bb!!ggggggg[ccclllccc333ggggggg22bb	chr12:120882272-120882497(+)$1	225	59	99	12.2859
$$$$$dddd[ccc!!cccooooooccc22ccc]dddd>>>	chr5:153418689-153418910(+)$1	221	153	193	15.5053
e[bb!!ffffff!!ddddoooooodddd4444ffffff22	chr14:96705472-96705695(+)$1	223	25	65	12.8944
!ccc[ccc[ccc[dddd[ccclllccc]dddd]ccc333c	chr7:150498006-150498242(-)$1	236	3	43	12.3941
!!ccc!!eeeee!!ccclllccceeeee333ccc]fffff	chr22:38453121-38453348(-)$1	227	106	146	10.9376
"""ccc!!gggggggooooooggggggg]ccc333eeeee	chr11:66721673-66721895(+)$1	222	103	143	12.1496
e[eeeee!!ccc!!cccqqqqqqqqccc]ccceeeeeeee	chr11:118926886-118927108(-)$1	222	135	175	10.7364
c[ddddbb####ffffffooooooffffff333bb]dddd	chr5:175812173-175812394(+)$1	221	106	146	11.5038
eeggggggg!!ccc[cccmmmmccc]ccc4444ggggggg	chr18:66382465-66382687(+)$1	222	74	114	12.1375
####a!!dddd!!a!!ddddllldddd22a22dddd22a4	chr14:50360097-50360319(+)$1	222	18	58	13.5195
[dddd[a[ccc[cccrrrrrrrrrccc]ccca]dddd]a]	chr3:119812866-119813087(+)$1	221	105	145	12.2693
ccc"""eeeee[bb!!cccnnnnnccc22bb]eeeee22c	chr18:60794519-60794741(-)$1	222	110	150	12.1797
iiiiiiiii[ccc!!bbqqqqqqqqbb22ccc333iiiii	chr5:122523116-122523340(+)$1	224	154	194	12.7459
$$eeeee####ccc[bboooooobb]ccc22eeeee4444	chr22:45960795-45961020(-)$1	225	148	188	12.8539
eeeeeeeeee!!a[ddddoooooodddd]a]eeeee4444	chr15:89164700-89164922(+)$1	222	131	171	13.7600
FFFccc[ccc[ccc!!bboooooobb22cccccc22ccc:	chr6:37359058-37359281(+)$1	223	29	69	11.8862
cc!!a!!bb"""ffffffooooooffffff]bb]a22ccc	chr2:238395692-238395920(-)$1	228	187	227	12.2970
####eeeee"""cccqqqqqqqqccc4444eeeee333cc	chr9:22453626-22453851(+)$1	225	175	215	11.4278
eeeee!!dddd####cccooooooccc4444ddddeeeee	chr4:124318788-124319018(+)$1	230	20	60	14.8886
d!!ccc[ddddbb"""bbnnnnnbb4444bb333dddd]c	chr12:123469749-123469970(-)$1	221	116	156	11.9536
####iiiiiiiii[ddddnnnnndddd333iiiiiiiii2	chr3:182775090-182775315(-)$1	225	142	182	14.7311
::ggggggg[a!!eeeeeooooooeeeee22a]ggggggg	chr19:4279172-4279399(+)$1	227	58	98	12.1442
fff[ccc!!dddd[ddddoooooodddd]dddd]cccfff	chr1:40975100-40975341(+)$1	241	16	56	13.1512
!!eeeee!!ccc"""ddddmmmmdddd22ccc4444eeee	chr12:120124974-120125195(+)$1	221	46	86	13.2709
$ffffff!!ccc[ccc!!bbnnnnnbb22ccc333ccc]f	chr1:172379287-172379508(+)$1	221	158	198	11.3203
ggggggg[a[eeeee[bboooooobb]eeeee22a]gggg	chr14:24682544-24682783(-)$1	239	144	184	12.4180
==========!!bb!!annnnna22bb22==========]	chrX:148592983-148593212(+)$1	229	116	156	13.3994
ffdddd####cccdddd[annnnna]dddd]ccc333ddd	chr2:27422754-27422977(+)$1	223	126	166	10.9234
gg####dddd[bbeeeeeooooooeeeee]bb]dddd444	chr2:242385428-242385651(+)$1	223	49	89	12.6778
""===========vvvvvvvvvvvvv===========333	chrX:55290922-55291143(-)$1	221	64	104	11.7609
[ggggggg"""bbzzzzzzzzzzzzzzzzzbb333ggggg	chr9:112629247-112629469(-)$1	222	94	134	10.9100
ccc[ggggggg!!cccqqqqqqqqccc22ggggggg22cc	chr3:50142407-50142679(+)$1	272	83	123	11.9545
c####dddd[dddd[cccoooooocccdddddddd22ccc	chr3:50144099-50144401(+)$1	302	189	229	13.6072
=[a[dddd[a[ccc[ddddnnnnndddd]ccc]a]dddd]	chr4:5711138-5711364(-)$1	226	122	162	12.7938
ccccccdddd"""a[ddddmmmmdddd]a4444dddd]cc	chr3:125899241-125899470(+)$1	229	38	78	12.3382
$ggggggg[bb"""bb[bblllbb]bb333bb22gggggg	chr11:67023335-67023557(-)$1	222	21	61	11.7641
##iiiiiiiiiccc[cccooooooccc22ccc]iiiiiii	chr19:36486973-36487195(-)$1	222	77	117	17.5371
[a!!cccccc!!ccccccooooooccc22ccc]ccc]ccc	chr12:6438550-6438773(-)$1	223	61	101	17.2442
bbbbbb!!cccgggggggooooooggggggg22ccc22bb	chr3:150126320-150126542(+)$1	222	43	83	11.6026
:a!!ddddbb[bb!!cccooooooccc333bb]bb]dddd	chr10:321668-321891(-)$1	223	178	218	14.0400
eeeee[dddd####ddddnnnnndddd333dddd]eeeee	chr19:5711802-5712033(+)$1	231	175	215	12.2417
[dddd[ccc[ccc!!ddddmmmmdddd333ccc]cccddd	chr19:42788403-42788625(-)$1	222	139	179	12.4651

#otherMatches

#Seq PSSM
GCAAAGUGGAGGCCCAGUGUGACUAGCCUUUCACCGUGUA	chr20:44330632-44330853(-)$1	221	178	218	11.6532
GUCCUGUUGGAGAAAAAUGCAUUAGUUUCUUUUCUCUGAA	chr9:90283417-90283638(-)$1	221	124	164	11.0225
GGGAUGGCCAUUUGAUCUCUAAAAGGAAUUUUGUACACUC	chr14:97032237-97032461(+)$1	224	164	204	13.8053
GGGCCGGGCUGGGGACGCUGGUCCGCGCCCUCCCGCCGCG	chr1:204654357-204654590(+)$1	233	158	198	13.9626
CCGCUGUCUGCAGUAGCGCACAAGAACCGCCAGGGCGAUG	chr5:141243169-141243392(+)$1	223	86	126	12.7370
AUCCCGUGGGCUCCUAGGAUCCAGCCAGGGCAGGCACGGG	chr11:73106729-73106950(-)$1	221	115	155	14.3500
UCUCAUAGUUGGCGUCUUCUAAAGGAAAAACACUAAAAUG	chr3:112931335-112931558(+)$1	223	42	82	12.1298
UAGUAGCAAAAUUAAAAUUGAACAAAUAAUACAUUUUGUC	chrX:102005998-102006222(-)$1	224	65	105	13.7056
UCUCAUAGUUGACAUUCCGAACCAGGAGGCUAGAGAGUUC	chr17:46052435-46052656(-)$1	221	90	130	12.3283
UAUUAGAACAUCACAUGCAUGCACAAGUGGUAUGGUAGAG	chr4:99363243-99363465(-)$1	222	80	120	12.6506
UUACAGUGACUAUGAGUGUGUAUUUAUUCAUGAAAUUUGA	chr12:25357969-25358190(-)$1	221	1	41	11.6887
CCCAGAGGUUUCCUAAGAAUUGCCACUAAACAGCCUUUGG	chr16:55364105-55364328(+)$1	223	38	78	12.2809
gaaagaccuggcuuugcagugaggcagucccaaguucaaa	chr4:8008974-8009199(-)$1	225	142	182	15.6844
GAGGGCGGAGUGGUGCCUUUAAAAGGCCGGGCGCCGCCUU	chr16:30076961-30077188(+)$1	227	73	113	13.8040
AAAUCAAGAGGUCAGGCAGCUCUGCUCAUCCUGACUAGUU	chr12:120882272-120882497(+)$1	225	59	99	12.2859
aacaaacgggauuaucuaaggugguaguaagugcuguaaa	chr5:153418689-153418910(+)$1	221	153	193	15.5053
ACAGCACAGGGCACUGGGAAAAUGCCCaaugaguccugcc	chr14:96705472-96705695(+)$1	223	25	65	12.8944
UGGCUGCCUGUGGAGCUCCUGUGCCAGCAGCUGCGCCCCG	chr7:150498006-150498242(-)$1	236	3	43	12.3941
AACGGUCUGGACAGGCUGACAGCGUCUAACCCCGCCCUUU	chr22:38453121-38453348(-)$1	227	106	146	10.9376
AACGCCAAGAUGAAGCAAGCUUUUCAUUCGGUAAGUAAGA	chr11:66721673-66721895(+)$1	222	103	143	12.1496
AUGAAUCUUACAGCCUCUCCGUUCUGGGAUGUGAUUCUGU	chr11:118926886-118927108(-)$1	222	135	175	10.7364
GACAGAGUAUUUCCUUUCUUUUCUGGAAGGCUGGCUUCUG	chr5:175812173-175812394(+)$1	221	106	146	11.5038
GUUCACUGGGGCGCGUUUCCGGGAAGGUGAAUACCGGUGA	chr18:66382465-66382687(+)$1	222	74	114	12.1375
AGAGGAAGGCGGAGGAGCGGGAACCGCGGCGGCGCUCGCG	chr14:50360097-50360319(+)$1	222	18	58	13.5195
CGGAGGCAGCUCCCUUCAGACCCCAGGCAGCGGCUCCUCG	chr3:119812866-119813087(+)$1	221	105	145	12.2693
CUGUAGAGGGAAGGAACAGAGGCCCUGGGCCCUUCCUAUC	chr18:60794519-60794741(-)$1	222	110	150	12.1797
GGUUCUCGUUGCACCUUUUUUUAGUAACAUGUUUCAUGGG	chr5:122523116-122523340(+)$1	224	154	194	12.7459
CUAGGCAUCAAGGUGGGUAUCCUCCAACCCCUGCUUCCAU	chr22:45960795-45961020(-)$1	225	148	188	12.8539
UGGUCGUUGGGACUCGGCCCAGCUGCCGCGGCCAGCAAGU	chr15:89164700-89164922(+)$1	222	131	171	13.7600
GCUCAUAGAUUACAACCAAGAAAGUGACUGUAUCAGAUGA	chr6:37359058-37359281(+)$1	223	29	69	11.8862
CGGAUACUCGACCCCCAAGCCAGUUUGGGGAGAAAGACGG	chr2:238395692-238395920(-)$1	228	187	227	12.2970
AAUCCACUUAUUGAAUGCUAUUUUUCUGAAAAGUGCUAGA	chr9:22453626-22453851(+)$1	225	175	215	11.4278
GCGCUGCCCGGGAGAGGCUGACCUGCCGGGACCGGAGUGC	chr4:124318788-124319018(+)$1	230	20	60	14.8886
CCUGGCCGCCUCUUCCGCUCCCUGCCAUCAGUCAAGGCCG	chr12:123469749-123469970(-)$1	221	116	156	11.9536
AAUGCUGUGUACUUGUUUGAAAGAGACUGUAGUGUGCAGA	chr3:182775090-182775315(-)$1	225	142	182	14.7311
acgcggcggaggggaggugggggAGCCUUGACGCUGCUGC	chr19:4279172-4279399(+)$1	227	58	98	12.1442
UUUCAGGGAGCAGGGAUUGGAUCAAGUCAUUGCAUCUAGA	chr1:40975100-40975341(+)$1	241	16	56	13.1512
AAGGGGGCAGCACAUGCAGUGAACUGCCAUGCAGAACUCC	chr12:120124974-120125195(+)$1	221	46	86	13.2709
AAGAUGGGAAUGUAGCUUAAUGAUUUUCUGUUUCCCAUAC	chr1:172379287-172379508(+)$1	221	158	198	11.3203
GGUCUCGGCAGGCUCUUCGGGAAGGGUGAGCCAGGGUGGG	chr14:24682544-24682783(-)$1	239	144	184	12.4180
CUGCUUUUUAUUUGAAGAAAUGUGGCAUUUGGGAAGCAGC	chrX:148592983-148593212(+)$1	229	116	156	13.3994
AGGGGAAGCAGCUUCCAGUUUUAUGGUGGAGAGUCAGUCC	chr2:27422754-27422977(+)$1	223	126	166	10.9234
AUUUAAGUUUCCAAAAGUCCAGGUACUUUAUGUAGGCCAA	chr2:242385428-242385651(+)$1	223	49	89	12.6778
GGCCUUUGUCGUCGUUUCUGGGCCAGGACGACGGAGGAAG	chrX:55290922-55291143(-)$1	221	64	104	11.7609
GUUCUUACAAACUGCAAAUACCAUAGAAUAAGACAGUGGG	chr9:112629247-112629469(-)$1	222	94	134	10.9100
GGAUCACUUUCCCUUCUAGACUCUGAACAGGAAGUGCCUC	chr3:50142407-50142679(+)$1	272	83	123	11.9545
UGCCAGAAAGUGAGUGGCUUCAUUGUCCUUAUUUCAAACU	chr3:50144099-50144401(+)$1	302	189	229	13.6072
UUGUCCAUGUUAGGUCAGGAAAGGCCUGUCCUUGGAUGGU	chr4:5711138-5711364(-)$1	226	122	162	12.7938
CGCCGGGAGUCCAGCGCUCUCGAGAGCCCAGAAACUCACC	chr3:125899241-125899470(+)$1	229	38	78	12.3382
ACAGGCCUGGGCUCAGGGGGCUCCGCUAAACCAGAGGCCU	chr11:67023335-67023557(-)$1	222	21	61	11.7641
UUUGGGGGUCUUCAGUUGAUCAACCAGGGUGAUAGACCCC	chr19:36486973-36487195(-)$1	222	77	117	17.5371
AGGGCUGAGCGACCACGAGAUCGAUCGGCUGGAGCUGCAG	chr12:6438550-6438773(-)$1	223	61	101	17.2442
GCCGCCCGCCCGCAGGGGUGGUUCCCCCUGUAAGGGGAGG	chr3:150126320-150126542(+)$1	222	43	83	11.6026
AGCUCACCUGUGCACUUCUAAAUUGAAUUGGCCCACGGUG	chr10:321668-321891(-)$1	223	178	218	14.0400
UCGGGCUCCACCUCCAGCUGUCUGCUGAUAUGGACUCUGA	chr19:5711802-5712033(+)$1	231	175	215	12.2417
cggggcggggcgcgacgCGCGUGCGCGGGGGCGgcccccu	chr19:42788403-42788625(-)$1	222	139	179	12.4651

#DB
(((..((((((((..(((...))).))).)))))..))).	chr20:44330632-44330853(-)$1	1	178	218	11.6532
.((((.((((((((((..((....))...)))))))))).	chr9:90283417-90283638(-)$1	1	124	164	11.0225
((((((..((.....(((......)))....))..)).))	chr14:97032237-97032461(+)$1	1	164	204	13.8053
.(((.(((..((((.(((......))))))))))))).))	chr1:204654357-204654590(+)$1	1	158	198	13.9626
..((((((.((....(((.........)))....))))).	chr5:141243169-141243392(+)$1	1	86	126	12.7370
.(((((((.((.(((.((......)))))))...))))))	chr11:73106729-73106950(-)$1	1	115	155	14.3500
((((((..((((.((.((((...))))..)).)))).)))	chr3:112931335-112931558(+)$1	1	42	82	12.1298
(....(((((((((..(((.....)))..)).))))))).	chrX:102005998-102006222(-)$1	1	65	105	13.7056
((((.((((.....((((......)))))))))))).)))	chr17:46052435-46052656(-)$1	1	90	130	12.3283
(.(((....(((((.((......)).)))))....)))..	chr4:99363243-99363465(-)$1	1	80	120	12.6506
((.(((....((((((((......))))))))....))))	chr12:25357969-25358190(-)$1	1	1	41	11.6887
((((((((((.....((........))....)))))))))	chr16:55364105-55364328(+)$1	1	38	78	12.2809
....(((.(((..((((......))))..))).)))....	chr4:8008974-8009199(-)$1	1	142	182	15.6844
((((((((.((...(((((...)))))...)).)))))))	chr16:30076961-30077188(+)$1	1	73	113	13.8040
(....((..(((((((.(((...)))...)))))))..))	chr12:120882272-120882497(+)$1	1	59	99	12.2859
.....((((.(((..(((......)))..))).))))...	chr5:153418689-153418910(+)$1	1	153	193	15.5053
(.((..((((((..((((......))))....))))))..	chr14:96705472-96705695(+)$1	1	25	65	12.8944
.(((.(((.(((.((((.(((...))).)))).)))...)	chr7:150498006-150498242(-)$1	1	3	43	12.3941
..(((..(((((..(((...))))))))...))).)))))	chr22:38453121-38453348(-)$1	1	106	146	10.9376
...(((..(((((((......))))))).)))...)))))	chr11:66721673-66721895(+)$1	1	103	143	12.1496
(.(((((..(((..(((........))).)))))))))))	chr11:118926886-118927108(-)$1	1	135	175	10.7364
(.((((((....((((((......))))))...)).))))	chr5:175812173-175812394(+)$1	1	106	146	11.5038
))(((((((..(((.(((....))).)))....)))))))	chr18:66382465-66382687(+)$1	1	74	114	12.1375
....(..((((..(..((((...))))..)..))))..).	chr14:50360097-50360319(+)$1	1	18	58	13.5195
.((((.(.(((.(((.........))).)))).)))).).	chr3:119812866-119813087(+)$1	1	105	145	12.2693
(((...(((((.((..(((.....)))..)).)))))..)	chr18:60794519-60794741(-)$1	1	110	150	12.1797
(((((((((.(((..((........))..)))...)))))	chr5:122523116-122523340(+)$1	1	154	194	12.7459
..(((((....(((.((......)).)))..)))))....	chr22:45960795-45961020(-)$1	1	148	188	12.8539
((((((((((..(.((((......)))).).)))))....	chr15:89164700-89164922(+)$1	1	131	171	13.7600
((((((.(((.(((..((......))..))))))..))).	chr6:37359058-37359281(+)$1	1	29	69	11.8862
((..(..((...((((((......)))))).)).)..)))	chr2:238395692-238395920(-)$1	1	187	227	12.2970
....(((((...(((........)))....)))))...))	chr9:22453626-22453851(+)$1	1	175	215	11.4278
(((((..((((....(((......)))....)))))))))	chr4:124318788-124319018(+)$1	1	20	60	14.8886
(..(((.((((((...((.....))....))...)))).)	chr12:123469749-123469970(-)$1	1	116	156	11.9536
....(((((((((.((((.....))))...))))))))).	chr3:182775090-182775315(-)$1	1	142	182	14.7311
..(((((((.(..(((((......)))))..).)))))))	chr19:4279172-4279399(+)$1	1	58	98	12.1442
(((.(((..((((.((((......)))).)))).))))))	chr1:40975100-40975341(+)$1	1	16	56	13.1512
..(((((..(((...((((....))))..)))....))))	chr12:120124974-120125195(+)$1	1	46	86	13.2709
.((((((..(((.(((..((.....))..)))...))).)	chr1:172379287-172379508(+)$1	1	158	198	11.3203
(((((((.(.(((((.((......)).)))))..).))))	chr14:24682544-24682783(-)$1	1	144	184	12.4180
((((((((((..((..(.....)..))..)))))))))).	chrX:148592983-148593212(+)$1	1	116	156	13.3994
))((((....(((((((.(.....).)))).)))...)))	chr2:27422754-27422977(+)$1	1	126	166	10.9234
((....((((.(((((((......))))).)).))))...	chr2:242385428-242385651(+)$1	1	49	89	12.6778
..(((((((((((.............)))))))))))...	chrX:55290922-55291143(-)$1	1	64	104	11.7609
.(((((((...((.................))...)))))	chr9:112629247-112629469(-)$1	1	94	134	10.9100
(((.(((((((..(((........)))..)))))))..))	chr3:50142407-50142679(+)$1	1	83	123	11.9545
(....((((.((((.(((......)))))))))))..)))	chr3:50144099-50144401(+)$1	1	189	229	13.6072
(.(.((((.(.(((.((((.....)))).))).).)))).	chr4:5711138-5711364(-)$1	1	122	162	12.7938
((((((((((...(.((((....)))).)....)))).))	chr3:125899241-125899470(+)$1	1	38	78	12.3382
.(((((((.((...((.((...)).))...))..))))))	chr11:67023335-67023557(-)$1	1	21	61	11.7641
..((((((((((((.(((......)))..))).)))))))	chr19:36486973-36487195(-)$1	1	77	117	17.5371
.(..((((((..((((((......)))..))).))).)))	chr12:6438550-6438773(-)$1	1	61	101	17.2442
((((((..((((((((((......)))))))..)))..))	chr3:150126320-150126542(+)$1	1	43	83	11.6026
.(..((((((.((..(((......)))...)).)).))))	chr10:321668-321891(-)$1	1	178	218	14.0400
(((((.((((....((((.....))))...)))).)))))	chr19:5711802-5712033(+)$1	1	175	215	12.2417
.((((.(((.(((..((((....))))...))).))))))	chr19:42788403-42788625(-)$1	1	139	179	12.4651

#PSSM
c : 0.14	[ : 0.10	e : 0.10	= : 0.08	$ : 0.08	# : 0.07	: : 0.05	d : 0.05	" : 0.05	b : 0.05	! : 0.05	f : 0.03	g : 0.03	a : 0.01	i : 0.01	F : 0.01	
c : 0.16	# : 0.12	g : 0.08	[ : 0.08	d : 0.07	= : 0.07	e : 0.07	" : 0.05	$ : 0.05	! : 0.05	f : 0.05	a : 0.03	i : 0.01	F : 0.01	: : 0.01	b : 0.01	
c : 0.17	# : 0.12	d : 0.10	g : 0.10	e : 0.10	= : 0.08	! : 0.07	$ : 0.03	b : 0.03	i : 0.03	f : 0.03	[ : 0.01	" : 0.01	F : 0.01	a : 0.01	
c : 0.19	# : 0.12	d : 0.10	g : 0.10	e : 0.10	= : 0.08	! : 0.07	[ : 0.05	$ : 0.03	b : 0.03	i : 0.03	" : 0.01	f : 0.01	
c : 0.19	d : 0.12	g : 0.12	e : 0.12	= : 0.08	# : 0.07	[ : 0.05	i : 0.05	! : 0.03	b : 0.03	a : 0.03	$ : 0.01	" : 0.01	f : 0.01	
c : 0.19	g : 0.14	d : 0.12	e : 0.10	= : 0.08	! : 0.08	[ : 0.07	b : 0.05	i : 0.05	# : 0.03	" : 0.01	f : 0.01	
! : 0.14	g : 0.14	d : 0.14	e : 0.12	c : 0.12	= : 0.08	# : 0.05	i : 0.05	b : 0.03	f : 0.03	[ : 0.03	a : 0.01	
d : 0.19	! : 0.16	g : 0.12	c : 0.10	e : 0.08	= : 0.08	# : 0.07	[ : 0.05	i : 0.05	b : 0.03	f : 0.01	
d : 0.17	! : 0.10	[ : 0.10	c : 0.10	e : 0.08	g : 0.08	# : 0.08	= : 0.07	b : 0.05	i : 0.05	f : 0.01	a : 0.01	" : 0.01	
c : 0.16	d : 0.14	b : 0.10	[ : 0.10	e : 0.08	= : 0.07	g : 0.07	# : 0.07	" : 0.05	! : 0.03	i : 0.03	$ : 0.01	f : 0.01	a : 0.01	
c : 0.21	d : 0.12	b : 0.07	g : 0.07	e : 0.07	! : 0.07	[ : 0.07	" : 0.07	$ : 0.05	# : 0.05	= : 0.03	i : 0.03	h : 0.01	f : 0.01	a : 0.01	
c : 0.24	! : 0.12	" : 0.08	d : 0.07	# : 0.07	g : 0.07	b : 0.07	$ : 0.05	[ : 0.05	e : 0.05	= : 0.03	h : 0.01	f : 0.01	i : 0.01	
c : 0.24	b : 0.12	! : 0.12	" : 0.07	$ : 0.05	d : 0.05	# : 0.05	[ : 0.05	g : 0.05	= : 0.03	e : 0.03	f : 0.03	h : 0.01	a : 0.01	i : 0.01	
c : 0.19	! : 0.14	d : 0.08	b : 0.07	e : 0.07	" : 0.07	$ : 0.05	# : 0.05	g : 0.05	[ : 0.05	f : 0.03	a : 0.03	= : 0.01	h : 0.01	v : 0.01	z : 0.01	
! : 0.17	d : 0.16	[ : 0.14	c : 0.14	e : 0.07	g : 0.05	$ : 0.03	# : 0.03	b : 0.03	f : 0.03	" : 0.03	= : 0.01	h : 0.01	v : 0.01	z : 0.01	
c : 0.26	d : 0.23	! : 0.08	b : 0.08	[ : 0.05	e : 0.05	g : 0.03	f : 0.03	= : 0.01	h : 0.01	o : 0.01	r : 0.01	q : 0.01	" : 0.01	v : 0.01	z : 0.01	
c : 0.26	d : 0.26	b : 0.14	e : 0.05	! : 0.03	[ : 0.03	f : 0.03	q : 0.03	h : 0.01	o : 0.01	r : 0.01	a : 0.01	v : 0.01	z : 0.01	g : 0.01	
c : 0.24	d : 0.21	b : 0.08	q : 0.08	o : 0.07	e : 0.05	! : 0.03	[ : 0.03	f : 0.03	h : 0.01	l : 0.01	r : 0.01	n : 0.01	v : 0.01	z : 0.01	g : 0.01	
o : 0.44	d : 0.10	q : 0.08	c : 0.07	n : 0.07	b : 0.05	l : 0.03	r : 0.03	e : 0.01	m : 0.01	a : 0.01	v : 0.01	z : 0.01	
o : 0.44	n : 0.14	q : 0.08	l : 0.07	m : 0.07	b : 0.03	r : 0.03	d : 0.03	c : 0.03	v : 0.01	z : 0.01	
o : 0.44	n : 0.16	l : 0.10	m : 0.08	q : 0.08	r : 0.03	c : 0.03	v : 0.01	z : 0.01	
o : 0.42	n : 0.16	l : 0.10	m : 0.08	q : 0.08	c : 0.03	r : 0.03	g : 0.01	v : 0.01	z : 0.01	
o : 0.42	n : 0.14	q : 0.08	m : 0.07	l : 0.07	c : 0.05	r : 0.03	e : 0.01	g : 0.01	a : 0.01	v : 0.01	z : 0.01	b : 0.01	
o : 0.37	d : 0.14	n : 0.08	c : 0.07	b : 0.07	q : 0.07	r : 0.03	e : 0.03	m : 0.01	l : 0.01	g : 0.01	2 : 0.01	v : 0.01	z : 0.01	
c : 0.28	d : 0.23	b : 0.12	e : 0.07	q : 0.05	] : 0.03	g : 0.03	f : 0.03	r : 0.01	h : 0.01	n : 0.01	2 : 0.01	a : 0.01	v : 0.01	z : 0.01	
c : 0.30	d : 0.23	b : 0.16	] : 0.07	e : 0.07	g : 0.03	f : 0.03	r : 0.01	h : 0.01	4 : 0.01	v : 0.01	z : 0.01	
c : 0.32	d : 0.24	e : 0.08	b : 0.08	3 : 0.03	g : 0.03	f : 0.03	4 : 0.03	r : 0.01	h : 0.01	2 : 0.01	] : 0.01	= : 0.01	z : 0.01	
2 : 0.24	3 : 0.14	d : 0.14	c : 0.10	4 : 0.08	e : 0.08	] : 0.05	g : 0.03	f : 0.03	h : 0.01	= : 0.01	z : 0.01	
2 : 0.23	3 : 0.16	] : 0.10	4 : 0.10	c : 0.10	d : 0.08	e : 0.07	f : 0.03	h : 0.01	= : 0.01	z : 0.01	a : 0.01	g : 0.01	
c : 0.23	4 : 0.12	3 : 0.12	d : 0.10	b : 0.08	e : 0.05	= : 0.05	g : 0.05	f : 0.03	a : 0.03	2 : 0.03	h : 0.01	] : 0.01	z : 0.01	
c : 0.23	b : 0.17	4 : 0.12	d : 0.10	e : 0.07	= : 0.05	g : 0.05	2 : 0.05	] : 0.05	3 : 0.03	h : 0.01	i : 0.01	
c : 0.26	b : 0.12	d : 0.10	e : 0.08	4 : 0.08	= : 0.07	3 : 0.05	] : 0.05	g : 0.03	2 : 0.03	a : 0.03	h : 0.01	i : 0.01	
] : 0.19	3 : 0.12	d : 0.12	e : 0.10	4 : 0.10	c : 0.08	= : 0.07	g : 0.05	2 : 0.05	b : 0.03	f : 0.01	i : 0.01	
d : 0.17	c : 0.14	e : 0.10	3 : 0.10	= : 0.08	g : 0.08	4 : 0.07	2 : 0.05	] : 0.05	b : 0.03	i : 0.03	f : 0.01	a : 0.01	
d : 0.17	c : 0.12	g : 0.12	= : 0.08	3 : 0.08	e : 0.08	2 : 0.05	b : 0.05	4 : 0.05	] : 0.05	a : 0.03	i : 0.03	f : 0.01	
c : 0.16	d : 0.16	g : 0.14	e : 0.12	= : 0.08	2 : 0.07	] : 0.05	i : 0.05	b : 0.03	4 : 0.03	f : 0.03	3 : 0.03	
c : 0.16	d : 0.14	g : 0.12	2 : 0.10	e : 0.10	= : 0.08	] : 0.05	4 : 0.05	3 : 0.05	i : 0.05	f : 0.03	b : 0.01	
c : 0.17	g : 0.12	d : 0.10	= : 0.08	2 : 0.08	e : 0.08	] : 0.07	4 : 0.07	f : 0.05	3 : 0.05	i : 0.05	> : 0.01	
c : 0.21	g : 0.12	= : 0.08	e : 0.08	d : 0.08	4 : 0.07	b : 0.05	3 : 0.05	i : 0.05	2 : 0.03	f : 0.03	a : 0.03	] : 0.03	> : 0.01	
c : 0.21	g : 0.10	] : 0.08	4 : 0.08	e : 0.08	d : 0.07	2 : 0.05	b : 0.05	= : 0.05	3 : 0.05	f : 0.05	i : 0.03	> : 0.01	: : 0.01	

#score	716.4277567180317
#seq	56
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_CDS_m3_run2.txt

#BEAR
""ccc[ddddrrrrrrrrrdddd]ccc333	chr14:55818247-55818469(+)$1	222	127	157	9.3869
[ccc!!ggggggglllggggggg]ccc]cc	chr8:21835222-21835454(+)$1	232	199	229	9.4029
gggggg[eeeeeooooooeeeee]gggggg	chr7:129317434-129317660(+)$1	226	164	194	14.3908
cc[ccc"""ddddoooooodddd]ccc]cc	chr2:73315238-73315467(-)$1	229	2	32	13.2068
dddddd"""bboooooobb4444dddd]dd	chr12:6140531-6140756(-)$1	225	130	160	11.5113
ccc[ccc!!cccmmmmcccccc333ccc]b	chr6:17779759-17779979(-)$1	220	181	211	9.2694
e!!dddd!!cccooooooccc22dddd22e	chr2:216189875-216190113(+)$1	238	126	156	13.0442
ffffff:eeeeeooooooeeeeeddddfff	chr1:249142664-249142880(-)$1	216	81	111	11.6117
###ccc[eeeeeooooooeeeeecccbb]b	chr1:155838313-155838535(+)$1	222	190	220	13.5606
ddd"""bb!!bboooooobb22bb333ddd	chr2:37229375-37229590(-)$1	215	119	149	12.3631
ggg!!cccbb[aooooooa]bb]cccgggg	chr4:40810731-40810953(-)$1	222	20	50	12.8142
h!!dddd"""bboooooobb333dddd22h	chr14:45414983-45415199(-)$1	216	163	193	12.7291
[eeeee[eeeeeooooooeeeee4444eee	chr1:207131867-207132083(+)$1	216	156	186	14.4318
ee:ccc[eeeeeooooooeeeee]cccddd	chr9:139757644-139757863(-)$1	219	115	145	13.7287
geeeee[a[cccooooooccc]a]eeeee2	chr1:33237658-33237877(+)$1	219	73	103	13.6827
::ccceeeee[aooooooa]eeeee]ccc:	chr7:94056914-94057134(+)$1	220	106	136	11.3004
gggggg[bb[bboooooobbbbggggggg]	chr2:1926261-1926491(-)$1	230	101	131	12.4413
hhhhhh[eeeeeooooooeeeeehhhhhhh	chr10:118956964-118957182(+)$1	218	161	191	12.0487
[dddd[ffffffooooooffffff]ddddc	chr15:27572058-27572274(+)$1	216	182	212	12.5967
ddd[ccceeeeeooooooeeeee]ccc]dd	chr1:146410841-146411057(+)$1	216	56	86	14.6990
dddddddd[cccoooooocccdddd]dddd	chr1:43913737-43913954(-)$1	217	37	67	13.0013
""eeeee[ddddooooooddddeeeeeeee	chr9:124094686-124094940(+)$1	254	11	41	12.9555
cc!!ccc[ddddooooooddddccc66666	chr14:60749496-60749733(+)$1	237	32	62	11.5689
ee"""gggggggooooooggggggg]eeee	chr12:32552675-32552896(+)$1	221	120	150	13.0060
hh[accc[eeeeellleeeee333ccc]a]	chr5:149576598-149576818(+)$1	220	6	36	9.5688
b!!ccc[ccc[aooooooa]ccc]ccc]bb	chr21:47401753-47401972(-)$1	219	75	105	14.0082
eee[cccbb!!bboooooobb4444bb]cc	chr3:126070744-126070984(-)$1	240	51	81	11.4670
g[eeeee[a[bboooooobbaeeeeegggg	chr7:102137220-102137461(-)$1	241	138	168	13.0374
ccc"""eeeeeddddllldddd333eeeee	chr19:812500-812716(-)$1	216	87	117	9.0569
[cccccceeeeeooooooeeeee333ccc]	chr19:14273773-14273989(-)$1	216	23	53	15.0767
[ccc####ddddoooooodddd4444ccc]	chr1:160140966-160141198(-)$1	232	101	131	14.4982
dddd!!ffffffooooooffffff333ddd	chrX:148564456-148564676(-)$1	220	39	69	12.8691
eeee"""bbcccooooooccc]bb333eee	chr22:35726321-35726539(+)$1	218	133	163	13.1523
ccc[dddd[cccooooooccc333dddd>>	chr9:113233682-113233898(-)$1	216	45	75	13.7077
ddd[dddd"""bboooooobbdddd]dddd	chr2:27552249-27552473(-)$1	224	193	223	11.0140
iiiiieeeee[aooooooa]eeeee]iiii	chr5:145857955-145858172(+)$1	217	53	83	13.7273
"cccbb[eeeeeooooooeeeee]bb]ccc	chr16:24816304-24816527(+)$1	223	46	76	13.4877
a[ffffff!!bboooooobbffffff]a]c	chr19:54946664-54946921(+)$1	257	73	103	12.1353
!dddd!!ccc[aooooooa]ccc22dddd4	chr10:64967122-64967353(-)$1	231	159	189	13.8732
eee!!dddd[bboooooobb]ddddeeeee	chr20:62851138-62851362(-)$1	224	77	107	12.5573
dddd[a[eeeeeooooooeeeeea]dddd:	chr4:41635488-41635704(-)$1	216	49	79	13.3225
:ffffff!!cccooooooccc]ffffffdd	chr19:14065316-14065539(+)$1	223	170	200	11.6375
ggccc$$$$$bboooooobb4444cccFFF	chrX:71425154-71425369(+)$1	215	93	123	11.8343
eeeee"""ddddooooooddddeeeee]bb	chr1:240374358-240374576(+)$1	218	43	73	12.9239
ccccc!!bbcccooooooccc]bb22ccc4	chr18:60630575-60630805(+)$1	230	171	201	13.2883
!!eeeee[ddddoooooodddd333eeeee	chrM:12585-12831(+)$1	246	184	214	13.8599
ccc[a[ffffffooooooffffff]a]ccc	chr11:35308330-35308545(-)$1	215	71	101	12.7939
!!ccc[bb!!bboooooobb]bb]ccc]ff	chr19:54930241-54930478(+)$1	237	197	227	13.3702
###ccc[eeeeeooooooeeeee]ccc555	chr6:152768572-152768788(-)$1	216	40	70	12.6255
dddd[a[ddddoooooodddd]adddd]dd	chr1:44467012-44467231(-)$1	219	29	59	11.9714

#otherMatches

#Seq PSSM
CAAGCCUCUGAAUUGCCCACAGAUGCUGUU	chr14:55818247-55818469(+)$1	222	127	157	9.3869
AUAUUCGUUUUGUUUUAUAAAAUUAUACAA	chr8:21835222-21835454(+)$1	232	199	229	9.4029
GUAAGUCAGAACCAAGCUGUUCUCAUUUGC	chr7:129317434-129317660(+)$1	226	164	194	14.3908
GCUACCAGAGGGCAAGCCAGUCCAGGUUGC	chr2:73315238-73315467(-)$1	229	2	32	13.2068
AGCUGUUUGACGGGGAGGUAAGUGCAGCCU	chr12:6140531-6140756(-)$1	225	130	160	11.5113
gggcgcaguggcucaugccuguaaucccag	chr6:17779759-17779979(-)$1	220	181	211	9.2694
UGGCUUCUCCAGGUGUAACUGUUGAGGAGG	chr2:216189875-216190113(+)$1	238	126	156	13.0442
AGCCGGCCCCUCAAAGACGAGGGCAGUGCC	chr1:249142664-249142880(-)$1	216	81	111	11.6117
CAUGGUGCCACUGGCAGGGGUGGACCCCAG	chr1:155838313-155838535(+)$1	222	190	220	13.5606
ACCAUCCCUUUGUUCACCCGCUGGUACGGU	chr2:37229375-37229590(-)$1	215	119	149	12.3631
UGAGUAGGGAGGAAGGUGUGUCAUCUUUAG	chr4:40810731-40810953(-)$1	222	20	50	12.8142
CGAACUCUGUGACAUCAUUCUUCGAGUAGG	chr14:45414983-45415199(-)$1	216	163	193	12.7291
GCAGAGACACAGAGCAGACUGUGAGGGUUC	chr1:207131867-207132083(+)$1	216	156	186	14.4318
CUGGCCACGGUGAGGCUGCGCCGGGGCUCU	chr9:139757644-139757863(-)$1	219	115	145	13.7287
GCGGCCCGUGUCCCCUGAGACCCAGGCUGA	chr1:33237658-33237877(+)$1	219	73	103	13.6827
ACAGGGCUGACCAGCCUCGCUCAGCACCUU	chr7:94056914-94057134(+)$1	220	106	136	11.3004
GGCUGGAGGAGCAGUUGAGCCCCCGGUCGA	chr2:1926261-1926491(-)$1	230	101	131	12.4413
GCCAUUGAGGACGGCCAGGUCCUGGUGGCA	chr10:118956964-118957182(+)$1	218	161	191	12.0487
GUAGGAAUGAGACCCUAUUUUCAUCUCUAA	chr15:27572058-27572274(+)$1	216	182	212	12.5967
UGGUUCACUCUCAGGAACGAGAGCUGACCC	chr1:146410841-146411057(+)$1	216	56	86	14.6990
GGUCCAGGCGCUAGAAUAAGCCCUGAGGCC	chr1:43913737-43913954(-)$1	217	37	67	13.0013
ACGUGUGUCUGCAGCUAAGCGGUACAUCGA	chr9:124094686-124094940(+)$1	254	11	41	12.9555
GGAGGAUGCACAUACGGCUGUGAUCGGUUU	chr14:60749496-60749733(+)$1	237	32	62	11.5689
GCCGCCCGGGGUGCCCCGGCCCUGGAGCAG	chr12:32552675-32552896(+)$1	221	120	150	13.0060
GCGCCGGCGCAGCCAUGCUGCUCAUCGUGG	chr5:149576598-149576818(+)$1	220	6	36	9.5688
GGGGGUCUGGAGCCUGCACCCCAAGCCACC	chr21:47401753-47401972(-)$1	219	75	105	14.0082
UUGUGCGCAUUGCCCCUGUGCCCAUUGCCG	chr3:126070744-126070984(-)$1	240	51	81	11.4670
CUGUGCCACGAGGUCAAGCUGGGCAUGCAG	chr7:102137220-102137461(-)$1	241	138	168	13.0374
GCGGAGGCGGAGGCCGAGGGCUACUUCCGC	chr19:812500-812716(-)$1	216	87	117	9.0569
GUGCCGUCUUCUACAACAAGGAGCGCACGC	chr19:14273773-14273989(-)$1	216	23	53	15.0767
ACCCUUCAUCAUCAGUACGUGGGUCUGGGA	chr1:160140966-160141198(-)$1	232	101	131	14.4982
GUGCAGAGAAGGCAAGAACCUUCUGAAGCA	chrX:148564456-148564676(-)$1	220	39	69	12.8691
UGUUCCUGCGCCAUGAACGGUAGCCCCAGC	chr22:35726321-35726539(+)$1	218	133	163	13.1523
GAAAUGAUACCCUUGAAUGGGAAAAUCAGC	chr9:113233682-113233898(-)$1	216	45	75	13.7077
GCUGUGCGUACCCUUCAAUGGUGCAAAGCU	chr2:27552249-27552473(-)$1	224	193	223	11.0140
AAUAUGUUCUGUAACAUAAGAGAAUGAUAU	chr5:145857955-145858172(+)$1	217	53	83	13.7273
UGUUUGGUGUUGGAAACACAGCAGCACAAC	chr16:24816304-24816527(+)$1	223	46	76	13.4877
UGCGGGGCCUGUGCGAAGACGCCCUGGAAG	chr19:54946664-54946921(+)$1	257	73	103	12.1353
GUGGUUCAGAAGUAAUUUCCUCUUUAUCAA	chr10:64967122-64967353(-)$1	231	159	189	13.8732
GCCGGUCCCACUCGUCCUGGCGGGAGGCCU	chr20:62851138-62851362(-)$1	224	77	107	12.5573
CAGUCCACUGCCACUCCAGGCAGGAGCUGU	chr4:41635488-41635704(-)$1	216	49	79	13.3225
AACACCAGGCUGGCCCUUCAGAUGgugugg	chr19:14065316-14065539(+)$1	223	170	200	11.6375
AGGACCCUUUGCUUCACUGCUGUCGUCAAG	chrX:71425154-71425369(+)$1	215	93	123	11.8343
CUUCACUUAUUUGGGAAAAAAUUGAAGAGC	chr1:240374358-240374576(+)$1	218	43	73	12.9239
UGUCUCACUCCUUUAGUUGGGUAGAAAGAA	chr18:60630575-60630805(+)$1	230	171	201	13.2883
GAGGGCGUAGGAAUUAUAUCCUUCUUGCUC	chrM:12585-12831(+)$1	246	184	214	13.8599
UCGUUGCCUGGAAGAAAAUCUGGGGAUUGA	chr11:35308330-35308545(-)$1	215	71	101	12.7939
CUGCGUCACCUGGAGCUGCAUUGUCGCCCU	chr19:54930241-54930478(+)$1	237	197	227	13.3702
AAUGGUGUUACCAAAAGGGGUGAGACCCUC	chr6:152768572-152768788(-)$1	216	40	70	12.6255
GUGGAUGUGUCCCGUGUGGCAGACCACGGC	chr1:44467012-44467231(-)$1	219	29	59	11.9714

#DB
..(((.((((.........)))).)))...	chr14:55818247-55818469(+)$1	1	127	157	9.3869
.(((..(((((((...))))))).))).))	chr8:21835222-21835454(+)$1	1	199	229	9.4029
((((((.(((((......))))).))))))	chr7:129317434-129317660(+)$1	1	164	194	14.3908
((.(((...((((......)))).))).))	chr2:73315238-73315467(-)$1	1	2	32	13.2068
((((((...((......))....)))).))	chr12:6140531-6140756(-)$1	1	130	160	11.5113
(((.(((..(((....))))))...))).)	chr6:17779759-17779979(-)$1	1	181	211	9.2694
(..((((..(((......)))..))))..)	chr2:216189875-216190113(+)$1	1	126	156	13.0442
)))))).(((((......)))))(((((((	chr1:249142664-249142880(-)$1	1	81	111	11.6117
...(((.(((((......)))))))))).)	chr1:155838313-155838535(+)$1	1	190	220	13.5606
(((...((..((......))..))...)))	chr2:37229375-37229590(-)$1	1	119	149	12.3631
(((..(((((.(......).)).)))))))	chr4:40810731-40810953(-)$1	1	20	50	12.8142
(..((((...((......))...))))..)	chr14:45414983-45415199(-)$1	1	163	193	12.7291
.(((((.(((((......)))))....)))	chr1:207131867-207132083(+)$1	1	156	186	14.4318
)).(((.(((((......))))).)))(((	chr9:139757644-139757863(-)$1	1	115	145	13.7287
((((((.(.(((......))).).))))).	chr1:33237658-33237877(+)$1	1	73	103	13.6827
..((((((((.(......).))))).))).	chr7:94056914-94057134(+)$1	1	106	136	11.3004
((((((.((.((......))))))))))).	chr2:1926261-1926491(-)$1	1	101	131	12.4413
((((((.(((((......))))))))))))	chr10:118956964-118957182(+)$1	1	161	191	12.0487
.((((.((((((......)))))).)))))	chr15:27572058-27572274(+)$1	1	182	212	12.5967
(((.((((((((......))))).))).))	chr1:146410841-146411057(+)$1	1	56	86	14.6990
((((((((.(((......))))))).))))	chr1:43913737-43913954(-)$1	1	37	67	13.0013
..(((((.((((......))))))))))))	chr9:124094686-124094940(+)$1	1	11	41	12.9555
((..(((.((((......))))))).....	chr14:60749496-60749733(+)$1	1	32	62	11.5689
((...(((((((......))))))).))))	chr12:32552675-32552896(+)$1	1	120	150	13.0060
((.((((.(((((...)))))...))).).	chr5:149576598-149576818(+)$1	1	6	36	9.5688
(..(((.(((.(......).))).))).))	chr21:47401753-47401972(-)$1	1	75	105	14.0082
(((.(((((..((......))....)).))	chr3:126070744-126070984(-)$1	1	51	81	11.4670
(.(((((.(.((......))))))))))))	chr7:102137220-102137461(-)$1	1	138	168	13.0374
(((...(((((((((...))))...)))))	chr19:812500-812716(-)$1	1	87	117	9.0569
.(((((((((((......)))))...))).	chr19:14273773-14273989(-)$1	1	23	53	15.0767
.(((....((((......))))....))).	chr1:160140966-160141198(-)$1	1	101	131	14.4982
((((..((((((......))))))...)))	chrX:148564456-148564676(-)$1	1	39	69	12.8691
((((...(((((......))).))...)))	chr22:35726321-35726539(+)$1	1	133	163	13.1523
(((.((((.(((......)))...))))..	chr9:113233682-113233898(-)$1	1	45	75	13.7077
(((.((((...((......)))))).))))	chr2:27552249-27552473(-)$1	1	193	223	11.0140
((((((((((.(......).))))).))))	chr5:145857955-145858172(+)$1	1	53	83	13.7273
.(((((.(((((......))))).)).)))	chr16:24816304-24816527(+)$1	1	46	76	13.4877
(.((((((..((......)))))))).).)	chr19:54946664-54946921(+)$1	1	73	103	12.1353
.((((..(((.(......).)))..)))).	chr10:64967122-64967353(-)$1	1	159	189	13.8732
(((..((((.((......)).)))))))))	chr20:62851138-62851362(-)$1	1	77	107	12.5573
((((.(.(((((......)))))).)))).	chr4:41635488-41635704(-)$1	1	49	79	13.3225
.((((((..(((......))).))))))((	chr19:14065316-14065539(+)$1	1	170	200	11.6375
))(((.....((......))....)))(((	chrX:71425154-71425369(+)$1	1	93	123	11.8343
(((((...((((......))))))))).))	chr1:240374358-240374576(+)$1	1	43	73	12.9239
(((((..(((((......))).))..))).	chr18:60630575-60630805(+)$1	1	171	201	13.2883
..(((((.((((......))))...)))))	chrM:12585-12831(+)$1	1	184	214	13.8599
(((.(.((((((......)))))).).)))	chr11:35308330-35308545(-)$1	1	71	101	12.7939
..(((.((..((......)).)).))).))	chr19:54930241-54930478(+)$1	1	197	227	13.3702
...(((.(((((......))))).)))...	chr6:152768572-152768788(-)$1	1	40	70	12.6255
((((.(.((((......)))).))))).))	chr1:44467012-44467231(-)$1	1	29	59	11.9714

#PSSM
d : 0.16	c : 0.14	e : 0.14	g : 0.12	[ : 0.10	" : 0.06	h : 0.06	! : 0.06	# : 0.04	: : 0.04	f : 0.02	b : 0.02	i : 0.02	a : 0.02	
c : 0.21	d : 0.19	e : 0.16	! : 0.10	g : 0.08	" : 0.04	f : 0.04	# : 0.04	h : 0.04	[ : 0.04	: : 0.02	i : 0.02	
c : 0.25	d : 0.19	e : 0.18	! : 0.08	g : 0.06	f : 0.06	[ : 0.04	# : 0.04	: : 0.02	h : 0.02	" : 0.02	i : 0.02	
c : 0.27	d : 0.18	e : 0.14	[ : 0.12	f : 0.06	" : 0.06	! : 0.06	g : 0.04	h : 0.02	a : 0.02	i : 0.02	
c : 0.32	d : 0.16	e : 0.12	! : 0.08	" : 0.08	f : 0.06	g : 0.04	[ : 0.04	h : 0.02	# : 0.02	i : 0.02	b : 0.02	a : 0.02	
c : 0.23	d : 0.14	e : 0.14	[ : 0.08	! : 0.08	" : 0.08	g : 0.06	f : 0.06	a : 0.04	h : 0.02	# : 0.02	b : 0.02	$ : 0.02	
[ : 0.23	d : 0.14	c : 0.14	e : 0.12	f : 0.10	" : 0.08	g : 0.04	b : 0.04	! : 0.04	: : 0.02	# : 0.02	$ : 0.02	
e : 0.27	d : 0.12	b : 0.12	[ : 0.10	" : 0.08	f : 0.08	! : 0.06	c : 0.06	g : 0.04	a : 0.02	# : 0.02	$ : 0.02	
e : 0.30	d : 0.16	! : 0.12	b : 0.10	" : 0.08	[ : 0.06	f : 0.06	g : 0.04	c : 0.04	a : 0.02	$ : 0.02	
e : 0.30	c : 0.19	d : 0.16	! : 0.08	[ : 0.06	f : 0.06	g : 0.04	b : 0.04	" : 0.04	$ : 0.02	
e : 0.25	b : 0.18	c : 0.16	d : 0.14	[ : 0.10	f : 0.06	g : 0.04	r : 0.02	! : 0.02	" : 0.02	
e : 0.23	b : 0.19	c : 0.16	d : 0.14	a : 0.10	f : 0.06	g : 0.04	o : 0.04	r : 0.02	
o : 0.84	d : 0.04	b : 0.04	r : 0.02	g : 0.02	m : 0.02	e : 0.02	
o : 0.90	l : 0.04	r : 0.02	m : 0.02	d : 0.02	
o : 0.90	l : 0.04	r : 0.02	m : 0.02	d : 0.02	
o : 0.90	l : 0.06	r : 0.02	m : 0.02	
o : 0.90	r : 0.02	g : 0.02	c : 0.02	e : 0.02	l : 0.02	
o : 0.86	r : 0.02	g : 0.02	b : 0.02	c : 0.02	e : 0.02	l : 0.02	d : 0.02	
e : 0.23	b : 0.18	c : 0.16	d : 0.14	a : 0.10	o : 0.06	f : 0.06	g : 0.04	r : 0.02	
e : 0.23	b : 0.19	d : 0.18	c : 0.16	] : 0.10	f : 0.06	g : 0.04	4 : 0.02	
e : 0.27	c : 0.19	d : 0.18	b : 0.08	f : 0.08	g : 0.04	4 : 0.04	] : 0.04	2 : 0.02	3 : 0.02	a : 0.02	
e : 0.27	d : 0.21	] : 0.10	f : 0.08	4 : 0.06	c : 0.06	b : 0.06	3 : 0.06	g : 0.04	2 : 0.04	
e : 0.32	3 : 0.12	d : 0.10	f : 0.10	4 : 0.08	b : 0.08	g : 0.06	c : 0.06	a : 0.04	2 : 0.02	] : 0.02	
] : 0.21	d : 0.16	3 : 0.12	e : 0.10	f : 0.10	4 : 0.08	c : 0.06	b : 0.06	g : 0.04	h : 0.02	2 : 0.02	a : 0.02	
c : 0.25	d : 0.18	3 : 0.14	e : 0.12	g : 0.06	4 : 0.06	] : 0.06	f : 0.04	2 : 0.04	h : 0.02	b : 0.02	
c : 0.25	d : 0.18	e : 0.14	] : 0.10	3 : 0.08	g : 0.04	4 : 0.04	b : 0.04	f : 0.04	h : 0.02	6 : 0.02	2 : 0.02	a : 0.02	
c : 0.30	d : 0.21	e : 0.14	g : 0.08	3 : 0.06	] : 0.06	b : 0.04	4 : 0.02	h : 0.02	6 : 0.02	i : 0.02	f : 0.02	
] : 0.19	d : 0.18	e : 0.16	c : 0.14	g : 0.08	2 : 0.04	f : 0.04	3 : 0.02	b : 0.02	h : 0.02	6 : 0.02	i : 0.02	a : 0.02	F : 0.02	5 : 0.02	
d : 0.23	c : 0.18	e : 0.16	g : 0.08	] : 0.06	2 : 0.04	f : 0.04	b : 0.04	3 : 0.02	h : 0.02	6 : 0.02	a : 0.02	> : 0.02	i : 0.02	F : 0.02	5 : 0.02	
d : 0.18	e : 0.16	c : 0.14	b : 0.08	] : 0.08	g : 0.06	f : 0.04	h : 0.04	: : 0.04	4 : 0.04	3 : 0.02	2 : 0.02	6 : 0.02	> : 0.02	i : 0.02	F : 0.02	5 : 0.02	

#score	629.6188860047961
#seq	50
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m3_run1.txt

#BEAR
[ccc"""bbnnnnnbb333cccaa	chr1:2521236-2521500(+)$1	264	192	216	12.6157
==========mmmm==========	chr7:135613988-135614248(-)$1	260	234	258	8.6478
gggg[ddddnnnnnddddgggggg	chr5:54654334-54654559(+)$1	225	58	82	12.3374
####eeeeennnnneeeee333cc	chr7:99054821-99055032(+)$1	211	158	182	11.7088
ee[dddd[annnnna]ddddeeee	chr1:156005441-156005671(-)$1	230	130	154	10.9094
[a[ccc!!annnnna4444ccc]a	chr15:55649001-55649211(-)$1	210	103	127	12.6678
!bb"""cccnnnnnccc4444bb4	chr4:71849550-71849784(+)$1	234	138	162	12.1918
eeee!!cccnnnnnccc22eeeee	chr3:15609847-15610101(-)$1	254	195	219	12.1352
:ccc[ddddnnnnndddd]ccccc	chr11:118915194-118915413(-)$1	219	109	133	11.0421
""iiiiiiiiillliiiiiiiii2	chrX:128580495-128580704(-)$1	209	73	97	8.9606
dd####cccnnnnnccc4444ddd	chr4:166263062-166263273(+)$1	211	45	69	12.0695
fff"""cccnnnnnccc22fffff	chr12:14923880-14924148(-)$1	268	195	219	11.7314
!iiiiiiiiimmmmiiiiiiiiic	chr14:55835809-55836028(-)$1	219	138	162	8.1233
Gdddd[cccnnnnnccc333dddd	chr11:3047844-3048101(-)$1	257	29	53	11.3132
iiiiiiiiinnnnniiiiiiiii]	chr1:220957577-220957783(+)$1	206	93	117	13.7001
eeee!!cccnnnnnccceeeee]d	chr4:129191937-129192164(-)$1	227	54	78	12.2474
ggggg!!bbnnnnnbb]ggggggg	chr14:57676234-57676447(-)$1	213	35	59	12.5098
[hhhhhhhhnnnnnhhhhhhhh]f	chr17:17970064-17970271(+)$1	207	29	53	10.5919
==========mmmm==========	chr8:17422831-17423040(+)$1	209	75	99	8.6478
b[ccc!!bbnnnnnbb22ccc]bb	chr20:3734091-3734320(-)$1	229	35	59	11.0789
=!!ffffffnnnnnffffff333=	chr5:126172409-126172619(+)$1	210	151	175	11.3785
ccc!!cccooooooccc22ccc]b	chr10:5807195-5807461(-)$1	266	59	83	8.4001
ddddeeeeennnnneeeee22ddd	chr22:21804774-21804975(+)$1	201	21	45	10.0208
iiiiiiiiinnnnniiiiiiiii:	chr22:26848817-26849055(-)$1	238	97	121	12.7743
[a!!cccbbnnnnnbb]ccc22a]	chr5:154196625-154196839(+)$1	214	145	169	12.0221
ccc[eeeeennnnneeeee]cccb	chr12:6979673-6979951(+)$1	278	227	251	11.1829
eee[a[cccnnnnncccaeeeee:	chr11:8706194-8706482(+)$1	288	20	44	11.3529
ddd!!ddddnnnnndddddddd]c	chr3:149237055-149237292(-)$1	237	202	226	11.0990
iiiiiddddnnnnndddd]iiiii	chr20:62374532-62374763(+)$1	231	109	133	12.8675
!ddddddddnnnnndddd]dddd2	chr1:173456911-173457130(+)$1	219	27	51	10.9566
eeee[ddddnnnnndddd>>>>>>	chr22:32081014-32081220(-)$1	206	93	117	10.2227
=========nnnnn==========	chr18:13018993-13019212(+)$1	219	31	55	14.0311
==========mmmm==========	chr5:179157358-179157599(+)$1	241	214	238	8.6478
!hhhhhhhhnnnnnhhhhhhhh22	chr11:8969035-8969245(-)$1	210	58	82	10.5947
d!!ffffffnnnnnffffff22dd	chr17:76220613-76220846(+)$1	233	9	33	10.1271
[hhhhhhhhnnnnnhhhhhhhh22	chr3:47888841-47889045(+)$1	204	93	117	10.5960
gggggggbbnnnnnbb]ggggggg	chr1:184763747-184763960(-)$1	213	17	41	12.2452
g!!dddd[annnnna]dddd22gg	chr14:66209436-66209672(+)$1	236	11	35	11.4720
eeeee[cccnnnnnccc]eeeee]	chr14:69865815-69866047(+)$1	232	100	124	12.1191
iii[eeeeennnnneeeee22iii	chrX:129758392-129758596(-)$1	204	68	92	11.8215
===[bb[bbnnnnnbbbb]=====	chr2:113289479-113289732(+)$1	253	217	241	11.8229
iiiiiiiiinnnnniiiiiiiii:	chr15:23044011-23044236(-)$1	225	10	34	12.7743
iiiiiiiiinnnnniiiiiiiii:	chr10:63853847-63854061(+)$1	214	37	61	12.7743
####eeeeennnnneeeeebb333	chr7:158526509-158526723(-)$1	214	140	164	11.3837
hhh"""cccnnnnnccc333hhhh	chr12:49717012-49717216(+)$1	204	154	178	12.4501
c:ccc"""annnnna22ccc====	chr14:69926889-69927128(+)$1	239	152	176	10.9716
"""ffffffnnnnnffffff]bb2	chr19:812142-812369(+)$1	227	93	117	10.3374
!!bb[ddddnnnnndddd]bb22c	chr2:242265406-242265621(+)$1	215	124	148	11.1517
eeeee[cccnnnnnccc]eeeee2	chr6:111346612-111346833(+)$1	221	24	48	12.0405
[ccc[ddddnnnnndddd]cccee	chr6:42979650-42979853(+)$1	203	160	184	12.1378
#ffffff[annnnna]ffffff33	chr7:75695682-75695884(+)$1	202	22	46	10.9785
#ccc[ddddnnnnndddd]ccc33	chr8:103217103-103217306(-)$1	203	27	51	12.6218
ggggg!!bbnnnnnbb22gggggg	chr3:48636980-48637184(-)$1	204	130	154	12.2788
====!!cccnnnnnccc22=====	chr12:110972168-110972385(-)$1	217	145	169	14.0013
eeee"""bbnnnnnbb]eeeeeff	chr17:79477562-79477800(-)$1	238	195	219	11.1403

#otherMatches

#Seq PSSM
UCAGAAUCAUUGUUUGCACCUGCU	chr1:2521236-2521500(+)$1	264	192	216	12.6157
AGAUAAAACUGACUAGUUUUAUUU	chr7:135613988-135614248(-)$1	260	234	258	8.6478
UCAUUCAGAUUUCUUCUGGUGAAU	chr5:54654334-54654559(+)$1	225	58	82	12.3374
UAAAGCUUGUUUUUUAAGCCAUGU	chr7:99054821-99055032(+)$1	211	158	182	11.7088
UAACCCAGAGGUAAUGUGGGUACC	chr1:156005441-156005671(-)$1	230	130	154	10.9094
CGGCCAGGGGAUGACAGUAUGGAC	chr15:55649001-55649211(-)$1	210	103	127	12.6678
AUCUUGUCCAUAUAGGAAAAUGAA	chr4:71849550-71849784(+)$1	234	138	162	12.1918
UCAUUAUAAUGUGUUUAAUAUGAA	chr3:15609847-15610101(-)$1	254	195	219	12.1352
ACCUCCCUCUCUCUGAGGCAGGCC	chr11:118915194-118915413(-)$1	219	109	133	11.0421
AAUAUUUUUUUCCUAAAGGAAUAA	chrX:128580495-128580704(-)$1	209	73	97	8.9606
GUAAACCUUCCUGAAAGAUAAACG	chr4:166263062-166263273(+)$1	211	45	69	12.0695
GCUGCGGGACAAUAUCCAAGGCAU	chr12:14923880-14924148(-)$1	268	195	219	11.7314
AAAAGCUCUUUAAUAAGAGUUUUU	chr14:55835809-55836028(-)$1	219	138	162	8.1233
CGGGUCUGUUAGAUGCACCCACCC	chr11:3047844-3048101(-)$1	257	29	53	11.3132
UGUGUCCUGAUGUGCAGGACGCAU	chr1:220957577-220957783(+)$1	206	93	117	13.7001
GUAUUUGCUACUCAAGUGUACAGA	chr4:129191937-129192164(-)$1	227	54	78	12.2474
UGGAACUUGGAGUACGUUUUCAUC	chr14:57676234-57676447(-)$1	213	35	59	12.5098
UUGACAUAUGUACUGUAUGUUACU	chr17:17970064-17970271(+)$1	207	29	53	10.5919
guauguauguaucuauguauAUGC	chr8:17422831-17423040(+)$1	209	75	99	8.6478
CCACUGCUGUCCACCAUGAGUAGG	chr20:3734091-3734320(-)$1	229	35	59	11.0789
AGAUUCUUAAUUCAUGAGGAGGGU	chr5:126172409-126172619(+)$1	210	151	175	11.3785
UAUGUGGUGUUUUAACCUAAUAAA	chr10:5807195-5807461(-)$1	266	59	83	8.4001
GGCCAUCCUGAGUUGGGGUGAGGC	chr22:21804774-21804975(+)$1	201	21	45	10.0208
GGGGCCGGGACGGGCUUGGCUCCC	chr22:26848817-26849055(-)$1	238	97	121	12.7743
AGUACCUCCUGUGUGGAAGGGUCC	chr5:154196625-154196839(+)$1	214	145	169	12.0221
AGAAGGCAGGAGUGCUGCCCUCUC	chr12:6979673-6979951(+)$1	278	227	251	11.1829
AUAGCAUCUUAAUUGGAGUGUGUA	chr11:8706194-8706482(+)$1	288	20	44	11.3529
UAAUCCUGUUUGCUACAGUUGGUA	chr3:149237055-149237292(-)$1	237	202	226	11.0990
CGUAGAUUUAUCAAGGGUGUUAUG	chr20:62374532-62374763(+)$1	231	109	133	12.8675
AGGAGUCUUCACCAAAGAGCUCCC	chr1:173456911-173457130(+)$1	219	27	51	10.9566
UACGGUGGUGCUAGACCAAGAUUA	chr22:32081014-32081220(-)$1	206	93	117	10.2227
UGUUAGAUUACUCAGAUUUGAUGU	chr18:13018993-13019212(+)$1	219	31	55	14.0311
UGAGCUUUAAAUCAUUAGAGCUUA	chr5:179157358-179157599(+)$1	241	214	238	8.6478
CAAACUGGCCAUUUGCUAGUUUAC	chr11:8969035-8969245(-)$1	210	58	82	10.5947
CAGCAGCUCCCGCAGGGCUGAAGU	chr17:76220613-76220846(+)$1	233	9	33	10.1271
CUUCCUGCCUGGGUGGCAGGAGAU	chr3:47888841-47889045(+)$1	204	93	117	10.5960
UUGUGGACAUGAAUUGUUCUACGA	chr1:184763747-184763960(-)$1	213	17	41	12.2452
UGACACAGACAUUUUGUGUGAGAC	chr14:66209436-66209672(+)$1	236	11	35	11.4720
GGUACGUUCAAGAGGAAGGUGCCU	chr14:69865815-69866047(+)$1	232	100	124	12.1191
GUUCAGUUUUCUGUGAAUUAAAAU	chrX:129758392-129758596(-)$1	204	68	92	11.8215
ACUGUGAUCGAAGUGACAAAGUGU	chr2:113289479-113289732(+)$1	253	217	241	11.8229
gggaUGGUUCUUCAAAUUGUUUCU	chr15:23044011-23044236(-)$1	225	10	34	12.7743
AUAUUUGUGGGCUGCACAGAUAUU	chr10:63853847-63854061(+)$1	214	37	61	12.7743
UUAUAUAUCACUGAGGUAUACUAU	chr7:158526509-158526723(-)$1	214	140	164	11.3837
GCUGGGUUCAUAGGGAGGAGGGCA	chr12:49717012-49717216(+)$1	204	154	178	12.4501
AAGUAGCACAAAUAGGAUACAGUU	chr14:69926889-69927128(+)$1	239	152	176	10.9716
CCUGUGUUCGCUGUGGACGCUGUA	chr19:812142-812369(+)$1	227	93	117	10.3374
AAGAAAUUAAUCUAUAGUCUCCAA	chr2:242265406-242265621(+)$1	215	124	148	11.1517
CUUUUGGUACAACUUAUGGAAGGA	chr6:111346612-111346833(+)$1	221	24	48	12.0405
GAGCGGUGCCCCAAGCAUGGCUCC	chr6:42979650-42979853(+)$1	203	160	184	12.1378
GAUUUCGUGAAGACCCUGAAGUGA	chr7:75695682-75695884(+)$1	202	22	46	10.9785
AGAAUUGAAAUCUCUUUGUUUCCC	chr8:103217103-103217306(-)$1	203	27	51	12.6218
GGGGUCUGCUCUUUGUUUAUUUCC	chr3:48636980-48637184(-)$1	204	130	154	12.2788
UGUUAAUUAUAUUUUAAGCAACAC	chr12:110972168-110972385(-)$1	217	145	169	14.0013
UCGAAAAGAAAUUGUCCUUGAAGC	chr17:79477562-79477800(-)$1	238	195	219	11.1403

#DB
.(((...((.....))...)))))	chr1:2521236-2521500(+)$1	1	192	216	12.6157
((((((((((....))))))))))	chr7:135613988-135614248(-)$1	1	234	258	8.6478
((((.((((.....))))))))))	chr5:54654334-54654559(+)$1	1	58	82	12.3374
....(((((.....)))))...))	chr7:99054821-99055032(+)$1	1	158	182	11.7088
((.((((.(.....).))))))))	chr1:156005441-156005671(-)$1	1	130	154	10.9094
.(.(((..(.....)....))).)	chr15:55649001-55649211(-)$1	1	103	127	12.6678
.((...(((.....)))....)).	chr4:71849550-71849784(+)$1	1	138	162	12.1918
((((..(((.....)))..)))))	chr3:15609847-15610101(-)$1	1	195	219	12.1352
.(((.((((.....)))).)))((	chr11:118915194-118915413(-)$1	1	109	133	11.0421
..(((((((((...))))))))).	chrX:128580495-128580704(-)$1	1	73	97	8.9606
((....(((.....)))....)))	chr4:166263062-166263273(+)$1	1	45	69	12.0695
(((...(((.....)))..)))))	chr12:14923880-14924148(-)$1	1	195	219	11.7314
.(((((((((....))))))))))	chr14:55835809-55836028(-)$1	1	138	162	8.1233
(((((.(((.....)))...))))	chr11:3047844-3048101(-)$1	1	29	53	11.3132
(((((((((.....))))))))).	chr1:220957577-220957783(+)$1	1	93	117	13.7001
((((..(((.....)))))))).)	chr4:129191937-129192164(-)$1	1	54	78	12.2474
(((((..((.....)).)))))))	chr14:57676234-57676447(-)$1	1	35	59	12.5098
.((((((((.....)))))))).)	chr17:17970064-17970271(+)$1	1	29	53	10.5919
((((((((((....))))))))))	chr8:17422831-17423040(+)$1	1	75	99	8.6478
(.(((..((.....))..))).))	chr20:3734091-3734320(-)$1	1	35	59	11.0789
(..((((((.....))))))...)	chr5:126172409-126172619(+)$1	1	151	175	11.3785
(((..(((......)))..))).)	chr10:5807195-5807461(-)$1	1	59	83	8.4001
(((((((((.....)))))..)))	chr22:21804774-21804975(+)$1	1	21	45	10.0208
(((((((((.....))))))))).	chr22:26848817-26849055(-)$1	1	97	121	12.7743
.(..(((((.....)).)))..).	chr5:154196625-154196839(+)$1	1	145	169	12.0221
(((.(((((.....))))).))))	chr12:6979673-6979951(+)$1	1	227	251	11.1829
(((.(.(((.....))))))))).	chr11:8706194-8706482(+)$1	1	20	44	11.3529
(((..((((.....)))))))).)	chr3:149237055-149237292(-)$1	1	202	226	11.0990
(((((((((.....)))).)))))	chr20:62374532-62374763(+)$1	1	109	133	12.8675
.((((((((.....)))).)))).	chr1:173456911-173457130(+)$1	1	27	51	10.9566
((((.((((.....))))......	chr22:32081014-32081220(-)$1	1	93	117	10.2227
(((((((((.....))))))))))	chr18:13018993-13019212(+)$1	1	31	55	14.0311
((((((((((....))))))))))	chr5:179157358-179157599(+)$1	1	214	238	8.6478
.((((((((.....))))))))..	chr11:8969035-8969245(-)$1	1	58	82	10.5947
(..((((((.....))))))..))	chr17:76220613-76220846(+)$1	1	9	33	10.1271
.((((((((.....))))))))..	chr3:47888841-47889045(+)$1	1	93	117	10.5960
(((((((((.....)).)))))))	chr1:184763747-184763960(-)$1	1	17	41	12.2452
(..((((.(.....).))))..))	chr14:66209436-66209672(+)$1	1	11	35	11.4720
(((((.(((.....))).))))).	chr14:69865815-69866047(+)$1	1	100	124	12.1191
(((.(((((.....)))))..)))	chrX:129758392-129758596(-)$1	1	68	92	11.8215
(((.((.((.....)))).)))))	chr2:113289479-113289732(+)$1	1	217	241	11.8229
(((((((((.....))))))))).	chr15:23044011-23044236(-)$1	1	10	34	12.7743
(((((((((.....))))))))).	chr10:63853847-63854061(+)$1	1	37	61	12.7743
....(((((.....)))))))...	chr7:158526509-158526723(-)$1	1	140	164	11.3837
(((...(((.....)))...))))	chr12:49717012-49717216(+)$1	1	154	178	12.4501
).(((...(.....)..)))((((	chr14:69926889-69927128(+)$1	1	152	176	10.9716
...((((((.....)))))).)).	chr19:812142-812369(+)$1	1	93	117	10.3374
..((.((((.....)))).))..)	chr2:242265406-242265621(+)$1	1	124	148	11.1517
(((((.(((.....))).))))).	chr6:111346612-111346833(+)$1	1	24	48	12.0405
.(((.((((.....)))).)))))	chr6:42979650-42979853(+)$1	1	160	184	12.1378
.((((((.(.....).))))))..	chr7:75695682-75695884(+)$1	1	22	46	10.9785
.(((.((((.....)))).)))..	chr8:103217103-103217306(-)$1	1	27	51	12.6218
(((((..((.....))..))))))	chr3:48636980-48637184(-)$1	1	130	154	12.2788
((((..(((.....)))..)))))	chr12:110972168-110972385(-)$1	1	145	169	14.0013
((((...((.....)).)))))))	chr17:79477562-79477800(-)$1	1	195	219	11.1403

#PSSM
e : 0.14	= : 0.12	[ : 0.10	i : 0.10	g : 0.09	! : 0.09	# : 0.07	d : 0.07	c : 0.05	" : 0.03	: : 0.01	f : 0.01	G : 0.01	b : 0.01	h : 0.01	
e : 0.14	i : 0.12	c : 0.10	= : 0.10	d : 0.09	g : 0.07	h : 0.07	! : 0.07	# : 0.03	a : 0.03	" : 0.03	f : 0.03	b : 0.01	[ : 0.01	: : 0.01	
c : 0.14	i : 0.14	e : 0.12	= : 0.10	g : 0.07	d : 0.07	h : 0.07	! : 0.07	# : 0.05	[ : 0.03	b : 0.03	f : 0.03	" : 0.01	
c : 0.12	i : 0.12	e : 0.10	= : 0.09	d : 0.09	g : 0.07	f : 0.07	[ : 0.07	# : 0.05	" : 0.05	h : 0.05	! : 0.05	b : 0.01	
e : 0.12	i : 0.12	[ : 0.10	" : 0.09	! : 0.09	= : 0.07	d : 0.07	c : 0.07	f : 0.07	g : 0.05	h : 0.05	# : 0.01	a : 0.01	b : 0.01	
d : 0.20	" : 0.10	! : 0.10	i : 0.10	e : 0.09	= : 0.07	[ : 0.07	f : 0.07	c : 0.05	h : 0.05	# : 0.01	g : 0.01	b : 0.01	
c : 0.23	d : 0.20	i : 0.10	e : 0.09	= : 0.07	! : 0.07	f : 0.07	" : 0.05	h : 0.05	g : 0.01	[ : 0.01	
c : 0.21	d : 0.16	b : 0.14	i : 0.10	e : 0.09	= : 0.07	[ : 0.05	h : 0.05	f : 0.05	! : 0.01	" : 0.01	
c : 0.20	d : 0.16	b : 0.14	i : 0.10	e : 0.09	a : 0.09	= : 0.07	h : 0.05	f : 0.05	o : 0.01	
n : 0.89	= : 0.05	i : 0.03	o : 0.01	
n : 0.89	m : 0.07	i : 0.01	o : 0.01	
n : 0.89	m : 0.07	l : 0.01	o : 0.01	
n : 0.89	m : 0.07	l : 0.01	o : 0.01	
n : 0.89	m : 0.07	l : 0.01	o : 0.01	
c : 0.21	d : 0.16	b : 0.14	i : 0.10	e : 0.09	a : 0.09	= : 0.07	h : 0.05	f : 0.05	
c : 0.21	d : 0.16	b : 0.14	i : 0.10	e : 0.09	= : 0.07	] : 0.05	h : 0.05	f : 0.05	4 : 0.01	2 : 0.01	
c : 0.21	d : 0.20	i : 0.10	e : 0.09	= : 0.07	] : 0.07	f : 0.07	h : 0.05	2 : 0.05	3 : 0.01	4 : 0.01	b : 0.01	
d : 0.20	e : 0.12	2 : 0.10	i : 0.10	= : 0.07	f : 0.07	3 : 0.05	4 : 0.05	h : 0.05	g : 0.03	c : 0.03	] : 0.03	a : 0.01	b : 0.01	
e : 0.18	] : 0.12	i : 0.10	= : 0.07	g : 0.07	2 : 0.07	f : 0.07	3 : 0.05	d : 0.05	4 : 0.05	h : 0.05	c : 0.05	> : 0.01	
c : 0.16	i : 0.12	= : 0.10	e : 0.10	f : 0.09	g : 0.07	d : 0.07	3 : 0.05	h : 0.05	4 : 0.03	2 : 0.03	b : 0.03	] : 0.01	> : 0.01	
c : 0.14	= : 0.12	e : 0.12	i : 0.12	2 : 0.09	g : 0.07	h : 0.07	d : 0.05	3 : 0.03	4 : 0.03	f : 0.03	b : 0.03	> : 0.01	] : 0.01	
i : 0.14	c : 0.12	= : 0.12	e : 0.12	d : 0.09	g : 0.07	h : 0.07	2 : 0.07	3 : 0.05	b : 0.03	f : 0.03	] : 0.01	> : 0.01	
i : 0.14	= : 0.12	e : 0.10	g : 0.09	] : 0.09	d : 0.09	3 : 0.07	c : 0.05	b : 0.05	2 : 0.05	a : 0.03	f : 0.03	> : 0.01	h : 0.01	
= : 0.14	2 : 0.10	g : 0.09	c : 0.09	d : 0.09	: : 0.07	e : 0.05	f : 0.05	] : 0.05	b : 0.05	3 : 0.05	a : 0.03	i : 0.03	4 : 0.01	> : 0.01	h : 0.01	

#score	628.029521760793
#seq	55
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m3_run2.txt

#BEAR
ggggcccqqqqqqqqccc]gggg	chr12:19427437-19427655(+)$1	218	9	32	16.4112
ddddcccqqqqqqqqccc22ddd	chr18:22029799-22030018(+)$1	219	102	125	15.7159
gggggggqqqqqqqqgggggggc	chr22:35819135-35819354(-)$1	219	86	109	15.7458
cc!!cccqqqqqqqqccc22ccc	chr15:35274901-35275138(-)$1	237	33	56	16.7614
eeee[bbqqqqqqqqbb]eeeee	chr3:113672666-113672883(+)$1	217	13	36	14.1648
iii[cccqqqqqqqqccciiiii	chr2:166245337-166245556(+)$1	219	22	45	16.6142
==eeeeeqqqqqqqqeeeee>>>	chr4:77095345-77095599(-)$1	254	93	116	14.6321
ddd[cccqqqqqqqqccc22ddd	chr2:191302184-191302402(-)$1	218	17	40	15.8076
gggggggqqqqqqqqggggggg2	chrX:40522183-40522413(-)$1	230	126	149	15.5323
=======qqqqqqqq========	chr11:122929785-122930006(-)$1	221	79	102	16.3643
"""ddddqqqqqqqqdddd22cc	chr11:6432050-6432276(-)$1	226	99	122	16.3748
"""ddddqqqqqqqqdddd333c	chr6:12163466-12163706(+)$1	240	43	66	16.6655
e!!ddddqqqqqqqqdddd4444	chr19:10251719-10251934(+)$1	215	74	97	16.2506
dd[ddddqqqqqqqqdddd22dd	chr8:110587376-110587608(-)$1	232	173	196	15.9301
hh[ddddqqqqqqqqddddhhhh	chr7:5770329-5770548(-)$1	219	69	92	15.1632
gggggggqqqqqqqqggggggg3	chr1:210761295-210761513(+)$1	218	164	187	15.7617
dd[ddddqqqqqqqqdddd]ddd	chr6:84664996-84665214(-)$1	218	170	193	15.8085
gggggbbqqqqqqqqbb]ggggg	chr17:4072439-4072654(-)$1	215	86	109	14.9946
gggggggqqqqqqqqggggggg:	chr13:36382285-36382504(-)$1	219	174	197	14.7123
ddddabbqqqqqqqqbb]a]ddd	chr14:24620314-24620535(+)$1	221	117	140	14.2866
h[ccc[aqqqqqqqqa]ccc]hh	chr22:50857682-50857902(+)$1	220	186	209	15.1113
d"""cccqqqqqqqqccc4444d	chr19:7606751-7606978(+)$1	227	18	41	16.3399
eeeeebbqqqqqqqqbb]eeeee	chr12:57590655-57590890(+)$1	235	156	179	14.1642
fffff[aqqqqqqqqa]ffffff	chr15:40396377-40396595(+)$1	218	176	199	13.7803
==[ddddqqqqqqqqdddd22==	chr11:61081747-61081972(-)$1	225	130	153	16.5547
c[a[cccqqqqqqqqccc]a]cc	chr19:57723076-57723291(+)$1	215	49	72	16.7523
iiiiiiiqqqqqqqqiiiiiiii	chr13:113976522-113976743(+)$1	221	20	43	15.9367
gggggggqqqqqqqqggggggg3	chr1:110086080-110086295(+)$1	215	174	197	15.7617
c!!ddddqqqqqqqqdddd22cc	chr8:17159668-17159892(+)$1	224	5	28	16.5637
=======qqqqqqqq========	chrX:16685677-16685892(+)$1	215	54	77	16.3643
c[a[cccqqqqqqqqccc]a]cc	chr11:212502-212729(+)$1	227	158	181	16.7523
ccc[cccqqqqqqqqccc]ccc]	chr2:20482710-20482928(+)$1	218	137	160	16.3794
c[eeeeeqqqqqqqqeeeee]cc	chr10:104141964-104142182(+)$1	218	187	210	15.6060
##eeeeeqqqqqqqqeeeee22=	chr12:64882192-64882409(+)$1	217	101	124	15.0807
iiiiiiiqqqqqqqqiiiiiiii	chr9:123230095-123230316(-)$1	221	54	77	15.9367
!!eeeeeqqqqqqqqeeeee333	chr15:89021036-89021254(+)$1	218	189	212	15.7250
ee[ddddqqqqqqqqdddd]eee	chr11:66436128-66436356(-)$1	228	151	174	15.7516
cc[ddddqqqqqqqqdddd]ccc	chr1:182811694-182811914(-)$1	220	108	131	16.4557
ccc[cccqqqqqqqqcccccccc	chr1:1273327-1273561(-)$1	234	98	121	16.2554
cc[ddddqqqqqqqqdddd]ccc	chrX:51929732-51929958(+)$1	226	128	151	16.4557
cc[ddddqqqqqqqqdddd]ccc	chr3:71027002-71027234(-)$1	232	51	74	16.4557
)))ddddqqqqqqqqddddccc]	chr16:30982883-30983106(+)$1	223	51	74	14.2598
====cccqqqqqqqqccc]====	chr2:108464871-108465092(+)$1	221	26	49	16.8685
===[cccqqqqqqqqccc=====	chr2:110656302-110656528(+)$1	226	150	173	16.8884
cceeeeeqqqqqqqqeeeee]cc	chr19:17750572-17750802(-)$1	230	113	136	15.4793
ccc[cccqqqqqqqqccc22ccc	chr22:32482130-32482346(-)$1	216	158	181	16.5350
$$eeeeeqqqqqqqqeeeee]ee	chr17:5264861-5265078(-)$1	217	88	111	14.7837
dddd[bbqqqqqqqqbbddddee	chr3:11059456-11059686(+)$1	230	94	117	14.1516
c"""cccqqqqqqqqccc22ccc	chr12:56334615-56334835(-)$1	220	17	40	16.6450
B:eeeeeqqqqqqqqeeeeefff	chr5:56111708-56111931(+)$1	223	115	138	12.8212
ddddcccqqqqqqqqccc22ddd	chr1:230492753-230492983(-)$1	230	0	23	15.7159
!ccc[bbqqqqqqqqbb22ccc2	chr17:16001625-16001854(-)$1	229	185	208	14.3338
dd!!cccqqqqqqqqccc333dd	chr17:40850662-40850891(+)$1	229	128	151	16.7032
!dddd[aqqqqqqqqadddd22d	chr12:54765240-54765461(+)$1	221	170	193	15.1231
eee[cccqqqqqqqqccc]eeee	chr4:75178622-75178837(-)$1	215	47	70	15.7625
bb[ddddqqqqqqqqddddbb22	chr9:138941972-138942200(-)$1	228	123	146	14.4915
bffffffqqqqqqqqffffff]b	chr15:59191580-59191796(-)$1	216	91	114	13.3541

#otherMatches

#Seq PSSM
CAGAGUGGACAAGAUUACAUCUG	chr12:19427437-19427655(+)$1	218	9	32	16.4112
CUACACAAAUUCACCUGUAAGUG	chr18:22029799-22030018(+)$1	219	102	125	15.7159
GAGCUGCUUCUCGAUGCGGCUCA	chr22:35819135-35819354(-)$1	219	86	109	15.7458
GCAUGUACUUAUUCAUACUGGUC	chr15:35274901-35275138(-)$1	237	33	56	16.7614
CUGCCUGUCUUCCUUCAUGUGGC	chr3:113672666-113672883(+)$1	217	13	36	14.1648
UUUGCCUAUGUUAAGAGGGAAGU	chr2:166245337-166245556(+)$1	219	22	45	16.6142
CCAGAGUCCACAUUCACUUUUUA	chr4:77095345-77095599(-)$1	254	93	116	14.6321
CAAAUUAUAAUACCUUAAAAUUG	chr2:191302184-191302402(-)$1	218	17	40	15.8076
CCAGGCCUUGUGCCCGGCCUGGC	chrX:40522183-40522413(-)$1	230	126	149	15.5323
UUCAAGAUUUGCUGCUCUUGGAU	chr11:122929785-122930006(-)$1	221	79	102	16.3643
GACCUGGCCUGAUCAUCAGCACU	chr11:6432050-6432276(-)$1	226	99	122	16.3748
AUUUAGAGCCCAUCAUCUGUAAG	chr6:12163466-12163706(+)$1	240	43	66	16.6655
CUUCCCUUUGUUUCCAGGGCUAC	chr19:10251719-10251934(+)$1	215	74	97	16.2506
GGAUGCAGAAGUUCAUGCAAACC	chr8:110587376-110587608(-)$1	232	173	196	15.9301
AGUAUGAAAGUAACAUCAUUUGU	chr7:5770329-5770548(-)$1	219	69	92	15.1632
CUGCUGUGUUAGGGGACAGUGGA	chr1:210761295-210761513(+)$1	218	164	187	15.7617
UGCUGAGAGAACAAAUUCAACAU	chr6:84664996-84665214(-)$1	218	170	193	15.8085
GAGCCUCCGUGGUGUGACGGCUC	chr17:4072439-4072654(-)$1	215	86	109	14.9946
AUUCUGUGUGUCUUAACGGAAUU	chr13:36382285-36382504(-)$1	219	174	197	14.7123
ACUGCCCUACGUCCUGGAGAUGG	chr14:24620314-24620535(+)$1	221	117	140	14.2866
UUGCUGGAAACCAGGCGGGUUGG	chr22:50857682-50857902(+)$1	220	186	209	15.1113
UUUAACUAGUUAAUCAGUCGCCA	chr19:7606751-7606978(+)$1	227	18	41	16.3399
UGCUGAUGUGGACGAGUGCAGCA	chr12:57590655-57590890(+)$1	235	156	179	14.1642
AGGAUCCACAUCUCAGCAUUCUC	chr15:40396377-40396595(+)$1	218	176	199	13.7803
GGUGGCUGUAGGCAGGGCCCUCU	chr11:61081747-61081972(-)$1	225	130	153	16.5547
CAUGAGAAAAUUCACUCUGGAGU	chr19:57723076-57723291(+)$1	215	49	72	16.7523
GUUUGCAGGCCCCUGUGUGAGCA	chr13:113976522-113976743(+)$1	221	20	43	15.9367
ACUGCCAGCUUUUUGUGGUGGUC	chr1:110086080-110086295(+)$1	215	174	197	15.7617
CCUCUAGUUCUUCCUCUAGCUGC	chr8:17159668-17159892(+)$1	224	5	28	16.5637
UUGAAGAGAGAAAAUUUUUUAAA	chrX:16685677-16685892(+)$1	215	54	77	16.3643
AGAUGCUGCGGAACAAGCUUGUC	chr11:212502-212729(+)$1	227	158	181	16.7523
CUGCUUCCAUAAAAUGAAUUAGA	chr2:20482710-20482928(+)$1	218	137	160	16.3794
UCUGGCUGUCCUGCGGGCCACAA	chr10:104141964-104142182(+)$1	218	187	210	15.6060
AACUGUUCACAAAAAGACAGAAG	chr12:64882192-64882409(+)$1	217	101	124	15.0807
UACAGCUAGUGAAGGAGCUGUAU	chr9:123230095-123230316(-)$1	221	54	77	15.9367
CACUUGGACCUGACCUCAAGCCU	chr15:89021036-89021254(+)$1	218	189	212	15.7250
CCAGAGAGUGAAUUAUCUCAGGC	chr11:66436128-66436356(-)$1	228	151	174	15.7516
CAUGAAUUUCUGCCUGUUUUUGU	chr1:182811694-182811914(-)$1	220	108	131	16.4557
GGGCUACCCCUACCAGUACCCGG	chr1:1273327-1273561(-)$1	234	98	121	16.2554
AGGCUCCCCGGCCCAGGAGGCUG	chrX:51929732-51929958(+)$1	226	128	151	16.4557
CAGUUGAAUCUGGUAUCAAGUGU	chr3:71027002-71027234(-)$1	232	51	74	16.4557
CCAGUGCCCACGCCAGCACCUGU	chr16:30982883-30983106(+)$1	223	51	74	14.2598
GUUCUCUGCUCUUGAAGAUGGGU	chr2:108464871-108465092(+)$1	221	26	49	16.8685
GUCUACAAGGAGUUCUGUGACUU	chr2:110656302-110656528(+)$1	226	150	173	16.8884
AGCUGCAUAACUCCCUGCGGAUU	chr19:17750572-17750802(-)$1	230	113	136	15.4793
CCACGUCAGCAAGCAGACAUUGG	chr22:32482130-32482346(-)$1	216	158	181	16.5350
ACGUGAGAAAGGUAACUCACCUC	chr17:5264861-5265078(-)$1	217	88	111	14.7837
CCUGACACUCAUCUUUGCGGGGG	chr3:11059456-11059686(+)$1	230	94	117	14.1516
GCUCCAGUGAAAAACCUGCCCCC	chr12:56334615-56334835(-)$1	220	17	40	16.6450
GAGCCCGGGGAGAAGCGGGCGCC	chr5:56111708-56111931(+)$1	223	115	138	12.8212
UGGUGCAGACAAACAUGUAUGCC	chr1:230492753-230492983(-)$1	230	0	23	15.7159
UUGUGAGGAAGAAAACUAAAUAU	chr17:16001625-16001854(-)$1	229	185	208	14.3338
GCCCAGGUCCCCACCCCUACAGC	chr17:40850662-40850891(+)$1	229	128	151	16.7032
ACCAGUCUCCGGAAUGCUGGGAG	chr12:54765240-54765461(+)$1	221	170	193	15.1231
CAUAUGAAGUUAAAGUCAAGUGC	chr4:75178622-75178837(-)$1	215	47	70	15.7625
GCUCGUGGUCAUGUACACGGCCG	chr9:138941972-138942200(-)$1	228	123	146	14.4915
GGGCCCUCGUCUACUGGGGCCUC	chr15:59191580-59191796(-)$1	216	91	114	13.3541

#DB
(((((((........))).))))	chr12:19427437-19427655(+)$1	1	9	32	16.4112
(((((((........)))..)))	chr18:22029799-22030018(+)$1	1	102	125	15.7159
(((((((........))))))))	chr22:35819135-35819354(-)$1	1	86	109	15.7458
((..(((........)))..)))	chr15:35274901-35275138(-)$1	1	33	56	16.7614
((((.((........)).)))))	chr3:113672666-113672883(+)$1	1	13	36	14.1648
(((.(((........))))))))	chr2:166245337-166245556(+)$1	1	22	45	16.6142
(((((((........)))))...	chr4:77095345-77095599(-)$1	1	93	116	14.6321
(((.(((........)))..)))	chr2:191302184-191302402(-)$1	1	17	40	15.8076
(((((((........))))))).	chrX:40522183-40522413(-)$1	1	126	149	15.5323
(((((((........))))))))	chr11:122929785-122930006(-)$1	1	79	102	16.3643
...((((........))))..))	chr11:6432050-6432276(-)$1	1	99	122	16.3748
...((((........))))...)	chr6:12163466-12163706(+)$1	1	43	66	16.6655
(..((((........))))....	chr19:10251719-10251934(+)$1	1	74	97	16.2506
((.((((........))))..))	chr8:110587376-110587608(-)$1	1	173	196	15.9301
((.((((........))))))))	chr7:5770329-5770548(-)$1	1	69	92	15.1632
(((((((........))))))).	chr1:210761295-210761513(+)$1	1	164	187	15.7617
((.((((........)))).)))	chr6:84664996-84665214(-)$1	1	170	193	15.8085
(((((((........)).)))))	chr17:4072439-4072654(-)$1	1	86	109	14.9946
(((((((........))))))).	chr13:36382285-36382504(-)$1	1	174	197	14.7123
(((((((........)).).)))	chr14:24620314-24620535(+)$1	1	117	140	14.2866
(.(((.(........).))).))	chr22:50857682-50857902(+)$1	1	186	209	15.1113
(...(((........)))....)	chr19:7606751-7606978(+)$1	1	18	41	16.3399
(((((((........)).)))))	chr12:57590655-57590890(+)$1	1	156	179	14.1642
(((((.(........).))))))	chr15:40396377-40396595(+)$1	1	176	199	13.7803
((.((((........))))..))	chr11:61081747-61081972(-)$1	1	130	153	16.5547
(.(.(((........))).).))	chr19:57723076-57723291(+)$1	1	49	72	16.7523
(((((((........))))))))	chr13:113976522-113976743(+)$1	1	20	43	15.9367
(((((((........))))))).	chr1:110086080-110086295(+)$1	1	174	197	15.7617
(..((((........))))..))	chr8:17159668-17159892(+)$1	1	5	28	16.5637
(((((((........))))))))	chrX:16685677-16685892(+)$1	1	54	77	16.3643
(.(.(((........))).).))	chr11:212502-212729(+)$1	1	158	181	16.7523
(((.(((........))).))).	chr2:20482710-20482928(+)$1	1	137	160	16.3794
(.(((((........))))).))	chr10:104141964-104142182(+)$1	1	187	210	15.6060
..(((((........)))))..)	chr12:64882192-64882409(+)$1	1	101	124	15.0807
(((((((........))))))))	chr9:123230095-123230316(-)$1	1	54	77	15.9367
..(((((........)))))...	chr15:89021036-89021254(+)$1	1	189	212	15.7250
((.((((........)))).)))	chr11:66436128-66436356(-)$1	1	151	174	15.7516
((.((((........)))).)))	chr1:182811694-182811914(-)$1	1	108	131	16.4557
(((.(((........))))))((	chr1:1273327-1273561(-)$1	1	98	121	16.2554
((.((((........)))).)))	chrX:51929732-51929958(+)$1	1	128	151	16.4557
((.((((........)))).)))	chr3:71027002-71027234(-)$1	1	51	74	16.4557
...((((........))))))).	chr16:30982883-30983106(+)$1	1	51	74	14.2598
(((((((........))).))))	chr2:108464871-108465092(+)$1	1	26	49	16.8685
(((.(((........))))))))	chr2:110656302-110656528(+)$1	1	150	173	16.8884
(((((((........))))).))	chr19:17750572-17750802(-)$1	1	113	136	15.4793
(((.(((........)))..)))	chr22:32482130-32482346(-)$1	1	158	181	16.5350
..(((((........))))).))	chr17:5264861-5265078(-)$1	1	88	111	14.7837
((((.((........))))))((	chr3:11059456-11059686(+)$1	1	94	117	14.1516
(...(((........)))..)))	chr12:56334615-56334835(-)$1	1	17	40	16.6450
).(((((........)))))(((	chr5:56111708-56111931(+)$1	1	115	138	12.8212
(((((((........)))..)))	chr1:230492753-230492983(-)$1	1	0	23	15.7159
.(((.((........))..))).	chr17:16001625-16001854(-)$1	1	185	208	14.3338
((..(((........)))...))	chr17:40850662-40850891(+)$1	1	128	151	16.7032
.((((.(........)))))..)	chr12:54765240-54765461(+)$1	1	170	193	15.1231
(((.(((........))).))))	chr4:75178622-75178837(-)$1	1	47	70	15.7625
((.((((........))))))..	chr9:138941972-138942200(-)$1	1	123	146	14.4915
(((((((........)))))).)	chr15:59191580-59191796(-)$1	1	91	114	13.3541

#PSSM
c : 0.22	d : 0.15	g : 0.12	= : 0.10	e : 0.08	i : 0.05	! : 0.05	" : 0.03	h : 0.03	b : 0.03	f : 0.01	# : 0.01	) : 0.01	$ : 0.01	B : 0.01	
d : 0.15	c : 0.15	g : 0.12	= : 0.10	e : 0.07	" : 0.07	[ : 0.07	i : 0.05	! : 0.05	f : 0.03	h : 0.01	# : 0.01	) : 0.01	$ : 0.01	: : 0.01	b : 0.01	
e : 0.17	[ : 0.15	g : 0.12	d : 0.10	c : 0.08	! : 0.07	= : 0.07	" : 0.07	i : 0.05	f : 0.03	a : 0.03	) : 0.01	
d : 0.33	e : 0.15	[ : 0.15	g : 0.12	= : 0.05	! : 0.03	c : 0.03	" : 0.03	f : 0.03	i : 0.03	
c : 0.31	d : 0.26	e : 0.14	g : 0.10	[ : 0.05	= : 0.03	f : 0.03	i : 0.03	a : 0.01	
c : 0.29	d : 0.24	e : 0.12	b : 0.10	g : 0.08	[ : 0.05	= : 0.03	i : 0.03	f : 0.01	
c : 0.29	d : 0.24	e : 0.12	b : 0.10	g : 0.08	a : 0.05	= : 0.03	i : 0.03	f : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.29	d : 0.24	e : 0.12	b : 0.10	g : 0.08	a : 0.05	= : 0.03	i : 0.03	f : 0.01	
c : 0.29	d : 0.26	e : 0.12	b : 0.10	g : 0.08	= : 0.03	] : 0.03	i : 0.03	f : 0.01	
c : 0.31	d : 0.28	e : 0.12	g : 0.08	] : 0.07	= : 0.03	f : 0.03	i : 0.03	2 : 0.01	
d : 0.28	e : 0.15	2 : 0.12	] : 0.10	g : 0.10	i : 0.05	= : 0.05	c : 0.03	f : 0.03	a : 0.01	4 : 0.01	3 : 0.01	
2 : 0.17	e : 0.17	g : 0.12	] : 0.10	c : 0.08	= : 0.07	i : 0.05	3 : 0.03	4 : 0.03	f : 0.03	a : 0.03	d : 0.03	h : 0.01	b : 0.01	
c : 0.17	g : 0.12	d : 0.10	2 : 0.10	] : 0.10	e : 0.07	= : 0.07	i : 0.05	3 : 0.05	f : 0.05	4 : 0.03	> : 0.01	h : 0.01	b : 0.01	
c : 0.28	g : 0.12	d : 0.12	e : 0.10	= : 0.08	i : 0.05	2 : 0.05	3 : 0.03	4 : 0.03	h : 0.03	f : 0.03	> : 0.01	] : 0.01	
c : 0.26	d : 0.15	e : 0.10	= : 0.10	i : 0.05	2 : 0.05	3 : 0.05	g : 0.03	h : 0.03	f : 0.03	] : 0.03	> : 0.01	4 : 0.01	: : 0.01	b : 0.01	

#score	891.8002620621185
#seq	57
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m1_run1.txt

#BEAR
!a[ccc!!dddd"""ddddoooooodddd333dddd]ccc	chr9:134166640-134166869(+)$1	229	59	99	13.2015
fffiiiiiiiii"""cccmmmmccc333iiiiiiiiiccc	chr12:14956436-14956665(-)$1	229	151	191	15.7216
[ggggggg"""dddd[bbnnnnnbb]ddddggggggg]ee	chr16:4896825-4897084(-)$1	259	35	75	14.1391
d!!a"""ccc"""cccooooooccc22ccc333a22dddd	chr8:99058422-99058681(-)$1	259	39	79	15.6577
iiiiiiiii!!bb[bb[bbmmmmbb22bbbb22iiiiiii	chr19:541396-541625(+)$1	229	57	97	13.3293
gggggddddccceeeeeooooooeeeee]ccc]ddddiii	chr9:85677948-85678177(+)$1	229	138	178	11.9755
ddd[bb"""bb####cccmmmmccc333bb333bb]dddd	chr6:27371386-27371645(-)$1	259	62	102	12.6335
%ggggggg!!dddd[bbnnnnnbb]dddd333ggggggga	chrX:9686907-9687166(-)$1	259	179	219	13.7151
!!adddd[ccc[a!!bboooooobb22a]cccdddd6666	chr8:81398377-81398606(-)$1	229	36	76	14.0626
g]aggggggg[bb"""ddddoooooodddd22bb]ggggg	chr1:65281491-65281720(+)$1	229	145	185	11.7124
ccc[dddd!!dddd[bboooooobb]dddd4444ddddcc	chr20:42142460-42142689(-)$1	229	71	111	14.1776
gggeeeee####eeeeeooooooeeeee333eeeee]ggg	chr2:175260770-175261029(+)$1	259	132	172	12.4072
a[===========ssssssssss===========]a333e	chr17:27589926-27590185(+)$1	259	175	215	12.9411
[iiiiiiiii"""ddddqqqqqqqqdddd333iiiiiiii	chr21:45176464-45176723(-)$1	259	30	70	13.0377
eee!!iiiiiiiii[ddddllldddd]iiiiiiiii22ee	chr13:53274472-53274701(+)$1	229	178	218	13.5773
i####ccc"""ddddoooooodddd22ccc22iiiiiiii	chr1:214214377-214214636(+)$1	259	169	209	14.7218
=========!!dddd[bbnnnnnbbdddd22=========	chr21:40720928-40721187(+)$1	259	35	75	15.4711
iiiiiiiiccc"""cccooooooccc22ccc]iiiiiiii	chrX:70798241-70798500(-)$1	259	116	156	17.9259
gggggggggccc!!bbpppppppbb22ccc4444gggggg	chr19:30165964-30166193(-)$1	229	39	79	12.6297
dd:iiiiiiiiicccddddllldddd]ccc]iiiiiiiii	chr22:24030245-24030504(-)$1	259	42	82	12.9758
[a[ccc"""dddd"""bbnnnnnbb]ddddccc]a]dddd	chr1:151262567-151262826(+)$1	259	24	64	13.6448
:iiiiiiiii!!ccccccnnnnnccc]ccciiiiiiiii:	chr15:57026036-57026296(+)$1	260	2	42	13.7324
iiiiiiiiiccc[a[cccmmmmccc]a]ccc]iiiiiiii	chr2:203742883-203743112(+)$1	229	5	45	15.6039
eeee####bbddddcccooooooccc4444dddd]bbeee	chr16:617695-617954(+)$1	259	57	97	12.4219
ggggg[==========!!bblllbb22==========]gg	chr16:89725578-89725837(-)$1	259	12	52	16.3473
iiiiiiiffffff!!aqqqqqqqqa22ffffff]iiiiii	chr2:128062573-128062832(+)$1	259	30	70	12.0047
dd[a=============oooooo=============0000	chr11:65381212-65381441(-)$1	229	40	80	15.5217
eeeeeffffffccc[cccmmmmccc]ccc333ffffff22	chr9:130573138-130573397(+)$1	259	26	66	11.2929
hh!!a==========!!aooooooa22==========]a2	chr14:53241099-53241358(+)$1	259	87	127	17.9043
ggggggg"""dddd!!bbnnnnnbb22dddd]ggggggg]	chr19:50001367-50001597(+)$1	230	98	138	15.7428
ggggg"""ccc[a[cccmmmmccc]a]ccc22ggggggg]	chr10:63661087-63661316(+)$1	229	182	222	14.1092
d[ffffff!!ccc!!bboooooobb]ccc22ffffff]dd	chr3:122170342-122170601(-)$1	259	118	158	14.7219
ggccc"""ffffff[bboooooobb]ffffffccc]gggg	chr2:71634971-71635230(+)$1	259	200	240	14.5202
fbb[a!!ggggggg!!ccclllccc22ggggggg4444a]	chr11:93466377-93466636(-)$1	259	33	73	14.3246
fff[iiiiiiiii!!bboooooobb22iiiiiiiii22ff	chr5:31532290-31532549(-)$1	259	137	177	17.9487
!iiiiiiiiiccc!!bboooooobb22ccc22iiiiiiii	chr18:56962889-56963148(+)$1	259	187	227	19.9694
ccc==========!!ccc[dddddddd!!==========a	chr2:25142513-25142772(+)$1	259	57	97	11.9614
"""bb####dddd"""bbmmmmbb333ddddbb333gggg	chr3:196014552-196014781(+)$1	229	36	76	13.1161
"""ccc"""ccc####bbmmmmbb333ccc333ccceeee	chr18:72917337-72917566(-)$1	229	94	134	15.5652
$$$gggggggccc"""ccclllccc333ccc]ggggggg]	chr15:91425032-91425291(-)$1	259	182	222	15.8508
eeeee!!==========qqqqqqqq==========4444e	chr15:41795556-41795785(+)$1	229	43	83	12.5641
eeeee!!dddd!!bb[bbnnnnnbb333bb22dddd22ee	chr16:30035597-30035856(-)$1	259	155	195	12.3424
!!ccc!!ggggggg[bboooooobb22ggggggg]ccc22	chr14:45540826-45541085(-)$1	259	127	167	16.9169
hhhhhhhh!!ccc!!bbnnnnnbb333ccc22hhhhhhhh	chr7:66205315-66205574(-)$1	259	200	240	13.6915
eeee[ccccccccc[bboooooobbccc]ccc]ccc]eee	chr15:44038711-44038970(+)$1	259	181	221	14.7212
====####gggggggrrrrrrrrrggggggg]========	chr22:47570346-47570575(+)$1	229	92	132	13.9794
d####dddd[ccc[cccooooooccc22ccc]dddd7777	chr1:193074437-193074666(+)$1	229	120	160	12.0786

#otherMatches

#Seq PSSM
ACAUGUGAGGUGGAGGUCUCAGGCAAGGCAAACAUUAACA	chr9:134166640-134166869(+)$1	229	59	99	13.2015
GGUCCUGGAAUUCUUGGGUAUUCUCUAUGGUUCCAGGGUC	chr12:14956436-14956665(-)$1	229	151	191	15.7216
CCGAGGCCGAGGGUGGCCACGUCGGGCACCGGCUUUGAUC	chr16:4896825-4897084(-)$1	259	35	75	14.1391
UCACGCUAACACAGUCACAAAAGGCGAGUUUUGGGAAACU	chr8:99058422-99058681(-)$1	259	39	79	15.6577
CUCUUCUACGACGACUACUACGAGGACGGCGAGGUGGAGG	chr19:541396-541625(+)$1	229	57	97	13.3293
CACUUUCCCGGCGGGUGCAGCUCCGCCCAGCCAGGGAGGA	chr9:85677948-85678177(+)$1	229	138	178	11.9755
cucaugaAUUGGAAAGCCAAGAGGUCAGCAUCCCAGGAGA	chr6:27371386-27371645(-)$1	259	62	102	12.6335
CUGUCCAUGGUGUUGUCCCGCUGAGAACGGGGAUGGAUAU	chrX:9686907-9687166(-)$1	259	179	219	13.7151
GAGGGUGAGAGGCACGCUAAACUGCUCGGCUCCGCCACAU	chr8:81398377-81398606(-)$1	229	36	76	14.0626
guccuuuauuagauaacauuugaaguaaugacuuagauaa	chr1:65281491-65281720(+)$1	229	145	185	11.7124
CGGCGCUAAGCUGCGGCAGGACGGUGGCAGAAACUGGUUC	chr20:42142460-42142689(-)$1	229	71	111	14.1776
AAUGACAGACagcucugcaagaacggaggcccugucuauu	chr2:175260770-175261029(+)$1	259	132	172	12.4072
UGACAUACAUGGAUAUACUAAUUUCUGUGUGUGUGAUGUG	chr17:27589926-27590185(+)$1	259	175	215	12.9411
AGCAUCUUCCUCAAGUCACUCGGCGGAUUCCUGGAAGAUG	chr21:45176464-45176723(-)$1	259	30	70	13.0377
ACACCUAUAUAUGCAUAUAGUAUAUGAGCAUGUGUAUUUG	chr13:53274472-53274701(+)$1	229	178	218	13.5773
UGCAGUAUAUAUGCAAGCUUGUGCAAAAUAAAAUAUACAU	chr1:214214377-214214636(+)$1	259	169	209	14.7218
CCGCCGCCCGAGCUGCUGAGACCCACAGCGGGGGCGGUGG	chr21:40720928-40721187(+)$1	259	35	75	15.4711
CCGGUCACCUACCUGGUGUUGCAGCCUCUGGCGUGGCCGG	chrX:70798241-70798500(-)$1	259	116	156	17.9259
GGGCCUGGUGGCACCCACAGCACGGCAGUCUCUGGCUGGG	chr19:30165964-30166193(-)$1	229	39	79	12.6297
GCGUCGAGGGUGAGGGUUGAACCAAUGUCUAUAUUCUCGG	chr22:24030245-24030504(-)$1	259	42	82	12.9758
UCCUAGUCAGUGAAAAAGUUCCCCUGUCGCCUGUGUGAGC	chr1:151262567-151262826(+)$1	259	24	64	13.6448
UGCUCGGAAUUUGCAGGCGAGGAGCCGUGCGUUCCGGGCC	chr15:57026036-57026296(+)$1	260	2	42	13.7324
GGGAAUAGGUGGGGACCAGUUCUGGAUGCCAUUUUAUUCU	chr2:203742883-203743112(+)$1	229	5	45	15.6039
CCCCAUCUGCCUCCUGCCCUGCCGCACUCCGGGGAGCGGG	chr16:617695-617954(+)$1	259	57	97	12.4219
acaggcgugagccacugcgcccagccGAGUGGUUCAUUCU	chr16:89725578-89725837(-)$1	259	12	52	16.3473
UCUUUUCAGGUGCCUUUAUUUUCUAUAGCAUUUAGAAAAG	chr2:128062573-128062832(+)$1	259	30	70	12.0047
AUGCGGGGGGCCGGGAGACAACACUCCUGGCUCCCCAGAG	chr11:65381212-65381441(-)$1	229	40	80	15.5217
GGAAGUUGGUGGACAUCCUUUCGGGGGUCUGACACCAAGU	chr9:130573138-130573397(+)$1	259	26	66	11.2929
CUUUCUUUCUUUGUUCAACAGUGCUCCGAUAAGGGAAUGC	chr14:53241099-53241358(+)$1	259	87	127	17.9043
AAGCGUUCUAcagggugaauaucucuaccugaaaugcuug	chr19:50001367-50001597(+)$1	230	98	138	15.7428
AAAAUUGAGUCGUUAUAGAAAUAUUAGGACAUAUUUUCAA	chr10:63661087-63661316(+)$1	229	182	222	14.1092
UAGGUUAUUUUCAAAGCAAAACCGCCUGACCAUGACCCGG	chr3:122170342-122170601(-)$1	259	118	158	14.7219
guggaauuguuggauuaugugguuauucuaauuccaauuu	chr2:71634971-71635230(+)$1	259	200	240	14.5202
AACGUUAUGAAAAACCAGAUAAUCUACUUUUUUACCUUAG	chr11:93466377-93466636(-)$1	259	33	73	14.3246
CGGGCGGAAGCGCUCCCUCACCCGGUUGCGUUUUCGGAUU	chr5:31532290-31532549(-)$1	259	137	177	17.9487
gguugggaggagacagagagagaUUGAUUUAACUUCUUAA	chr18:56962889-56963148(+)$1	259	187	227	19.9694
CCGCGUGCUCCGGGACGGUCCCCGCGCGGGCUGGGGCGGG	chr2:25142513-25142772(+)$1	259	57	97	11.9614
GCAGCUGAUGGAAGAGCCAGCCGGAAGUUCCGCCUACUUC	chr3:196014552-196014781(+)$1	229	36	76	13.1161
UACAGAUUUGGAGAAUGCCUGCGCCGGUCCUAUUCUUUUU	chr18:72917337-72917566(-)$1	229	94	134	15.5652
AUCAGAGGGCGCUCUGGUCUUUGAUAAAGGCGGUCCUCUC	chr15:91425032-91425291(-)$1	259	182	222	15.8508
AGGGCUUCUUCCUCAGGCCAGCUCUUCUGAGGAGGCUCUG	chr15:41795556-41795785(+)$1	229	43	83	12.5641
UGGGGGGCUUGGGCCAUGGGAAACAGAGGGGACAGGAUCC	chr16:30035597-30035856(-)$1	259	155	195	12.3424
AAACUGAGCUUUUGUGCAAAAUGGCUGUAGAAGUAAGUAA	chr14:45540826-45541085(-)$1	259	127	167	16.9169
GCGGUGGUAGCGCGAAUGGGAGGUGGAGCGGAGCUACUGC	chr7:66205315-66205574(-)$1	259	200	240	13.6915
CUUCGCCCCCUGGUGAGUCCAUUCUGCCGAGGCGGGGGAA	chr15:44038711-44038970(+)$1	259	181	221	14.7212
GUUCCUUGGGGCUCUAAGUGCGGAAGGGCCCAGAGCUGGU	chr22:47570346-47570575(+)$1	229	92	132	13.9794
GAUCCCGGGAGCCCGCCUCCUCCGGCCCGGCccccgccuu	chr1:193074437-193074666(+)$1	229	120	160	12.0786

#DB
.(.(((..((((...((((......))))...)))).)))	chr9:134166640-134166869(+)$1	1	59	99	13.2015
)))(((((((((...(((....)))...)))))))))(((	chr12:14956436-14956665(-)$1	1	151	191	15.7216
.(((((((...((((.((.....)).))))))))))).))	chr16:4896825-4897084(-)$1	1	35	75	14.1391
(..(...(((...(((......)))..)))...)..))))	chr8:99058422-99058681(-)$1	1	39	79	15.6577
(((((((((..((.((.((....))..))))..)))))))	chr19:541396-541625(+)$1	1	57	97	13.3293
)))))((((((((((((......))))).))).))))(((	chr9:85677948-85678177(+)$1	1	138	178	11.9755
(((.((...((....(((....)))...))...)).))))	chr6:27371386-27371645(-)$1	1	62	102	12.6335
.(((((((..((((.((.....)).))))...))))))))	chrX:9686907-9687166(-)$1	1	179	219	13.7151
..(((((.(((.(..((......))..).)))))))....	chr8:81398377-81398606(-)$1	1	36	76	14.0626
).)(((((((.((...((((......))))..)).)))))	chr1:65281491-65281720(+)$1	1	145	185	11.7124
(((.((((..((((.((......)).))))....))))))	chr20:42142460-42142689(-)$1	1	71	111	14.1776
((((((((....(((((......)))))...))))).)))	chr2:175260770-175261029(+)$1	1	132	172	12.4072
(.(((((((((((..........))))))))))).)...)	chr17:27589926-27590185(+)$1	1	175	215	12.9411
.(((((((((...((((........))))...))))))))	chr21:45176464-45176723(-)$1	1	30	70	13.0377
(((..(((((((((.((((...)))).)))))))))..))	chr13:53274472-53274701(+)$1	1	178	218	13.5773
(....(((...((((......))))..)))..))))))))	chr1:214214377-214214636(+)$1	1	169	209	14.7218
(((((((((..((((.((.....))))))..)))))))))	chr21:40720928-40721187(+)$1	1	35	75	15.4711
(((((((((((...(((......)))..))).))))))))	chrX:70798241-70798500(-)$1	1	116	156	17.9259
((((((((((((..((.......))..)))....))))))	chr19:30165964-30166193(-)$1	1	39	79	12.6297
)).((((((((((((((((...)))).))).)))))))))	chr22:24030245-24030504(-)$1	1	42	82	12.9758
.(.(((...((((...((.....)).))))))).).))))	chr1:151262567-151262826(+)$1	1	24	64	13.6448
.(((((((((..((((((.....))).)))))))))))).	chr15:57026036-57026296(+)$1	1	2	42	13.7324
((((((((((((.(.(((....))).).))).))))))))	chr2:203742883-203743112(+)$1	1	5	45	15.6039
((((....(((((((((......)))....)))).)))))	chr16:617695-617954(+)$1	1	57	97	12.4219
(((((.((((((((((..((...))..)))))))))).))	chr16:89725578-89725837(-)$1	1	12	52	16.3473
(((((((((((((..(........)..)))))).))))))	chr2:128062573-128062832(+)$1	1	30	70	12.0047
((.((((((((((((((......)))))))))))))....	chr11:65381212-65381441(-)$1	1	40	80	15.5217
((((((((((((((.(((....))).)))...))))))..	chr9:130573138-130573397(+)$1	1	26	66	11.2929
((..(((((((((((..(......)..)))))))))).).	chr14:53241099-53241358(+)$1	1	87	127	17.9043
(((((((...((((..((.....))..)))).))))))).	chr19:50001367-50001597(+)$1	1	98	138	15.7428
(((((...(((.(.(((....))).).)))..))))))).	chr10:63661087-63661316(+)$1	1	182	222	14.1092
(.((((((..(((..((......)).)))..)))))).))	chr3:122170342-122170601(-)$1	1	118	158	14.7219
(((((...((((((.((......)).))))))))).))))	chr2:71634971-71635230(+)$1	1	200	240	14.5202
(((.(..(((((((..(((...)))..)))))))....).	chr11:93466377-93466636(-)$1	1	33	73	14.3246
(((.(((((((((..((......))..)))))))))..))	chr5:31532290-31532549(-)$1	1	137	177	17.9487
.((((((((((((..((......))..)))..))))))))	chr18:56962889-56963148(+)$1	1	187	227	19.9694
)))((((((((((..(((.((((((((..(((((((((((	chr2:25142513-25142772(+)$1	1	57	97	11.9614
...((....((((...((....))...))))))...))))	chr3:196014552-196014781(+)$1	1	36	76	13.1161
...(((...(((....((....))...)))...)))))))	chr18:72917337-72917566(-)$1	1	94	134	15.5652
...((((((((((...(((...)))...))).))))))).	chr15:91425032-91425291(-)$1	1	182	222	15.8508
(((((..((((((((((........))))))))))....)	chr15:41795556-41795785(+)$1	1	43	83	12.5641
(((((..((((..((.((.....))...))..))))..))	chr16:30035597-30035856(-)$1	1	155	195	12.3424
..(((..(((((((.((......))..))))))).)))..	chr14:45540826-45541085(-)$1	1	127	167	16.9169
((((((((..(((..((.....))...)))..))))))))	chr7:66205315-66205574(-)$1	1	200	240	13.6915
((((.(((((((((.((......))))).))).))).)))	chr15:44038711-44038970(+)$1	1	181	221	14.7212
((((....(((((((.........))))))).))))))))	chr22:47570346-47570575(+)$1	1	92	132	13.9794
(....((((.(((.(((......)))..))).))))....	chr1:193074437-193074666(+)$1	1	120	160	12.0786

#PSSM
g : 0.17	d : 0.12	e : 0.12	i : 0.10	! : 0.08	f : 0.06	[ : 0.06	c : 0.04	= : 0.04	h : 0.04	" : 0.04	% : 0.02	a : 0.02	: : 0.02	$ : 0.02	
g : 0.19	i : 0.14	e : 0.12	! : 0.06	d : 0.06	a : 0.04	f : 0.04	c : 0.04	[ : 0.04	# : 0.04	= : 0.04	h : 0.04	" : 0.04	] : 0.02	b : 0.02	$ : 0.02	
g : 0.17	i : 0.14	e : 0.12	c : 0.08	[ : 0.06	f : 0.06	= : 0.06	! : 0.04	a : 0.04	# : 0.04	" : 0.04	d : 0.02	: : 0.02	b : 0.02	$ : 0.02	h : 0.02	
i : 0.19	g : 0.19	e : 0.12	c : 0.10	[ : 0.08	= : 0.08	a : 0.04	! : 0.04	# : 0.04	d : 0.02	f : 0.02	b : 0.02	h : 0.02	
i : 0.21	g : 0.19	c : 0.10	e : 0.08	= : 0.08	# : 0.08	b : 0.04	d : 0.04	a : 0.04	" : 0.02	! : 0.02	f : 0.02	h : 0.02	[ : 0.02	
i : 0.23	g : 0.12	c : 0.10	= : 0.10	d : 0.08	! : 0.08	" : 0.06	# : 0.06	f : 0.04	b : 0.02	e : 0.02	[ : 0.02	h : 0.02	
i : 0.23	g : 0.12	" : 0.12	= : 0.12	! : 0.10	d : 0.08	# : 0.06	c : 0.04	f : 0.04	e : 0.02	h : 0.02	
i : 0.21	g : 0.14	= : 0.14	" : 0.12	d : 0.08	c : 0.06	# : 0.06	f : 0.06	! : 0.02	[ : 0.02	e : 0.02	h : 0.02	
i : 0.19	= : 0.14	" : 0.12	g : 0.12	c : 0.10	d : 0.08	! : 0.08	f : 0.06	# : 0.04	b : 0.02	
c : 0.19	i : 0.14	! : 0.12	= : 0.12	g : 0.10	d : 0.08	" : 0.06	f : 0.06	b : 0.04	# : 0.02	[ : 0.02	
c : 0.27	d : 0.17	= : 0.12	i : 0.08	" : 0.08	! : 0.06	f : 0.06	g : 0.06	b : 0.02	[ : 0.02	# : 0.02	
c : 0.23	d : 0.21	= : 0.12	i : 0.08	" : 0.06	g : 0.06	b : 0.04	# : 0.04	[ : 0.04	! : 0.04	f : 0.04	
d : 0.19	c : 0.19	= : 0.12	" : 0.10	g : 0.06	b : 0.04	e : 0.04	# : 0.04	a : 0.04	i : 0.04	! : 0.04	f : 0.04	[ : 0.02	
d : 0.17	! : 0.17	" : 0.14	c : 0.10	= : 0.08	[ : 0.06	g : 0.06	e : 0.04	# : 0.04	s : 0.02	i : 0.02	a : 0.02	f : 0.02	b : 0.02	
! : 0.19	[ : 0.17	c : 0.14	" : 0.12	d : 0.08	= : 0.08	b : 0.06	e : 0.04	# : 0.04	s : 0.02	g : 0.02	
b : 0.25	c : 0.23	d : 0.08	" : 0.08	[ : 0.06	= : 0.06	! : 0.06	e : 0.04	s : 0.02	o : 0.02	a : 0.02	# : 0.02	r : 0.02	
b : 0.36	c : 0.25	d : 0.10	o : 0.04	e : 0.04	! : 0.04	= : 0.04	[ : 0.02	s : 0.02	p : 0.02	q : 0.02	r : 0.02	
o : 0.34	c : 0.17	b : 0.17	d : 0.08	q : 0.06	n : 0.04	s : 0.02	p : 0.02	! : 0.02	a : 0.02	m : 0.02	r : 0.02	
o : 0.36	n : 0.17	m : 0.14	d : 0.08	q : 0.06	b : 0.04	c : 0.04	s : 0.02	p : 0.02	[ : 0.02	r : 0.02	
o : 0.38	m : 0.17	n : 0.17	l : 0.08	q : 0.06	d : 0.04	s : 0.02	p : 0.02	b : 0.02	r : 0.02	
o : 0.40	m : 0.17	n : 0.17	l : 0.10	q : 0.06	s : 0.02	p : 0.02	d : 0.02	r : 0.02	
o : 0.38	n : 0.17	m : 0.14	l : 0.10	q : 0.06	d : 0.04	s : 0.02	p : 0.02	c : 0.02	r : 0.02	
o : 0.36	c : 0.17	n : 0.12	b : 0.08	d : 0.08	q : 0.06	m : 0.02	s : 0.02	p : 0.02	l : 0.02	r : 0.02	
b : 0.42	c : 0.25	d : 0.08	o : 0.06	q : 0.06	e : 0.04	= : 0.04	r : 0.02	
b : 0.34	c : 0.23	d : 0.08	3 : 0.06	o : 0.04	e : 0.04	] : 0.04	= : 0.04	q : 0.04	a : 0.04	g : 0.02	
2 : 0.27	d : 0.14	3 : 0.14	] : 0.14	c : 0.10	= : 0.06	e : 0.04	o : 0.02	a : 0.02	g : 0.02	
2 : 0.31	d : 0.19	3 : 0.14	] : 0.08	= : 0.06	c : 0.06	e : 0.04	a : 0.02	4 : 0.02	f : 0.02	g : 0.02	
c : 0.25	d : 0.21	= : 0.10	3 : 0.08	g : 0.06	e : 0.04	i : 0.04	2 : 0.04	f : 0.04	b : 0.02	a : 0.02	] : 0.02	4 : 0.02	! : 0.02	
c : 0.31	d : 0.21	= : 0.10	i : 0.06	b : 0.06	] : 0.06	g : 0.06	f : 0.04	3 : 0.02	4 : 0.02	! : 0.02	
c : 0.34	d : 0.12	= : 0.12	3 : 0.10	i : 0.06	b : 0.06	g : 0.06	2 : 0.04	f : 0.04	4 : 0.02	
3 : 0.17	c : 0.17	2 : 0.17	= : 0.12	i : 0.08	g : 0.08	d : 0.06	4 : 0.04	f : 0.04	b : 0.02	] : 0.02	
3 : 0.14	2 : 0.14	= : 0.14	] : 0.12	i : 0.10	c : 0.08	g : 0.06	f : 0.06	4 : 0.04	e : 0.02	d : 0.02	b : 0.02	
i : 0.21	= : 0.17	g : 0.14	d : 0.10	3 : 0.06	f : 0.06	] : 0.04	b : 0.04	4 : 0.04	c : 0.04	2 : 0.02	e : 0.02	h : 0.02	
i : 0.23	= : 0.17	g : 0.14	d : 0.12	c : 0.06	b : 0.04	4 : 0.04	] : 0.04	f : 0.04	a : 0.02	e : 0.02	3 : 0.02	h : 0.02	
i : 0.25	= : 0.14	d : 0.12	g : 0.12	] : 0.08	c : 0.06	f : 0.04	2 : 0.02	b : 0.02	e : 0.02	a : 0.02	4 : 0.02	3 : 0.02	h : 0.02	
i : 0.25	g : 0.14	d : 0.12	= : 0.12	] : 0.06	c : 0.06	f : 0.04	4 : 0.04	2 : 0.02	e : 0.02	a : 0.02	b : 0.02	3 : 0.02	h : 0.02	
i : 0.21	g : 0.19	d : 0.10	= : 0.10	] : 0.06	2 : 0.06	f : 0.04	4 : 0.04	6 : 0.02	3 : 0.02	b : 0.02	0 : 0.02	e : 0.02	c : 0.02	h : 0.02	7 : 0.02	
i : 0.21	g : 0.19	] : 0.08	d : 0.08	c : 0.06	2 : 0.06	= : 0.06	e : 0.06	4 : 0.04	6 : 0.02	3 : 0.02	0 : 0.02	f : 0.02	h : 0.02	7 : 0.02	
i : 0.21	g : 0.21	e : 0.12	d : 0.08	c : 0.06	= : 0.06	2 : 0.04	a : 0.04	6 : 0.02	3 : 0.02	0 : 0.02	f : 0.02	4 : 0.02	h : 0.02	7 : 0.02	
i : 0.19	e : 0.17	g : 0.12	d : 0.08	] : 0.08	c : 0.06	2 : 0.06	a : 0.04	= : 0.04	6 : 0.02	: : 0.02	0 : 0.02	f : 0.02	h : 0.02	7 : 0.02	

#score	668.6143279614403
#seq	47
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m3_run2.txt

#BEAR
ccc[aooooooaccc22	chr14:55510779-55511026(+)$1	247	73	90	10.4758
[ddddoooooodddd]c	chr15:62170811-62171030(-)$1	219	150	167	12.8839
[ddddoooooodddd]c	chr2:197705921-197706196(-)$1	275	223	240	12.8839
f[cccooooooccc333	chr19:58353098-58353401(+)$1	303	158	175	10.8625
"ddddoooooodddd33	chr10:102740871-102741128(-)$1	257	151	168	12.9167
eeeeeooooooeeeee5	chr19:21366631-21366895(+)$1	264	138	155	10.6732
[ddddoooooodddd]a	chrX:135956446-135956762(-)$1	316	73	90	12.9753
####aooooooa333ee	chr19:55677110-55677328(-)$1	218	5	22	9.7275
ddd[aooooooa]dddd	chr7:110762843-110763106(-)$1	263	150	167	10.9127
[ddddoooooodddd]d	chrX:38422221-38422577(+)$1	356	330	347	12.7317
##cccooooooccc333	chr19:57839871-57840104(+)$1	233	163	180	11.0541
!!cccooooooccc22d	chr6:135358579-135358820(-)$1	241	156	173	10.6092
:ddddoooooodddd::	chr22:41545845-41546133(+)$1	288	41	58	10.6511
[ddddoooooodddd]b	chr15:64430140-64430385(+)$1	245	11	28	12.8707
:ddddoooooodddd:f	chr1:33149788-33150101(+)$1	313	267	284	10.8285
eeeeeooooooeeeee]	chr13:39588175-39588521(-)$1	346	71	88	11.2214
[ddddoooooodddd]b	chr10:43088143-43088404(-)$1	261	69	86	12.8707
cddddoooooodddd]c	chr19:1216127-1216379(+)$1	252	171	188	12.5812
###bboooooobb4444	chr14:57713467-57713703(-)$1	236	63	80	9.2671
ggg[aooooooa]gggg	chr6:97247373-97247640(-)$1	267	95	112	10.0517
[ddddoooooodddd]b	chr10:43088914-43089283(-)$1	369	24	41	12.8707
:ddddoooooodddd:C	chr20:39795397-39795773(+)$1	376	206	223	10.4165
cccccooooooccc]cc	chr10:119805423-119805679(-)$1	256	159	176	10.4515
:ddddoooooodddd:b	chr16:4855073-4855400(-)$1	327	121	138	11.0224
eeeeeooooooeeeee2	chr3:184429053-184429274(-)$1	221	115	132	11.0719
bddddoooooodddd::	chr12:54920404-54920640(+)$1	236	203	220	11.1449
[ddddoooooodddd]h	chr21:47423292-47423511(+)$1	219	100	117	12.5191
!ddddoooooodddd]b	chrX:44919754-44919994(+)$1	240	191	208	12.8570
[cccaooooooa]ccc]	chr8:57078753-57079047(-)$1	294	260	277	10.7512
[ddddoooooodddd]b	chr10:38344182-38344528(+)$1	346	176	193	12.8707
=ddddoooooodddd44	chr2:206927595-206927847(-)$1	252	66	83	12.6144
[ddddoooooodddd]b	chr10:129901861-129902151(-)$1	290	122	139	12.8707
dddddooooooddddDD	chr4:102014848-102015088(-)$1	240	163	180	10.3654
[ddddoooooodddd]f	chr20:25657170-25657440(-)$1	270	208	225	12.6767
cccccooooooccc]cc	chr1:32744985-32745318(+)$1	333	192	209	10.4515
:ddddoooooodddd::	chr19:44792562-44792806(-)$1	244	223	240	10.6511
eeeeeooooooeeeee]	chr7:2686400-2686667(+)$1	267	160	177	11.2214
eee[aooooooa]eeee	chr19:17440205-17440461(-)$1	256	217	234	10.7063
eee[aooooooa]eeee	chr19:58452868-58453144(-)$1	276	76	93	10.7063
eeeeeooooooeeeeeb	chr9:134073264-134073504(+)$1	240	119	136	11.1109
eecccooooooccc]ee	chr15:48434160-48434464(-)$1	304	145	162	10.5989
eecccooooooccc22e	chr21:43676522-43676793(+)$1	271	4	21	10.5059
:ddddoooooodddd::	chr17:42475053-42475290(-)$1	237	125	142	10.6511
eeeeeooooooeeeee7	chr20:390843-391160(+)$1	317	141	158	10.9101
eeeeeooooooeeeee]	chr7:138968983-138969231(+)$1	248	137	154	11.2214
:ddddoooooodddd::	chr14:75248445-75248781(+)$1	336	18	35	10.6511
eeeeeooooooeeeee:	chr17:41246549-41246781(-)$1	232	167	184	10.7396
Fddddoooooodddd::	chr13:39586814-39587249(-)$1	435	226	243	10.9933
gggggoooooogggggg	chr1:197053383-197053615(-)$1	232	60	77	9.8629
eeeeeooooooeeeee:	chr14:50585229-50585471(-)$1	242	161	178	10.7396
e[cccooooooccc]ee	chr14:94776084-94776302(-)$1	218	47	64	10.4366
#ddddoooooodddd44	chr1:24297606-24297886(-)$1	280	172	189	12.7400
!ddddoooooodddd22	chr12:72056628-72056894(-)$1	266	175	192	12.5794
"""bboooooobb4444	chr1:149879150-149879414(-)$1	264	112	129	9.3511
eeeeeooooooeeeee:	chr16:89628706-89628964(+)$1	258	224	241	10.7396
gggggoooooogggggg	chr5:110097185-110097476(+)$1	291	210	227	9.8629
eeeeeooooooeeeee:	chr11:114278083-114278346(+)$1	263	48	65	10.7396
eeeeeooooooeeeee]	chr21:34944799-34945035(+)$1	236	54	71	11.2214
bddddoooooodddd::	chrX:70389704-70389966(+)$1	262	45	62	11.1449
[ddddoooooodddd]b	chr17:29631980-29632240(-)$1	260	208	225	12.8707
eeeeaooooooa]eeee	chr1:197071678-197071916(-)$1	238	189	206	10.8096
:ddddoooooodddd::	chr9:5921761-5922016(-)$1	255	200	217	10.6511
gggggoooooogggggg	chr12:2994468-2994738(+)$1	270	150	167	9.8629

#otherMatches

#Seq PSSM
AGGACCCAAGCGCCUGU	chr14:55510779-55511026(+)$1	247	73	90	10.4758
UGCAGUUCAUUCUGUCA	chr15:62170811-62171030(-)$1	219	150	167	12.8839
AUGCAACUUUAUGUAAG	chr2:197705921-197706196(-)$1	275	223	240	12.8839
UGGAGAAAGACCUUACA	chr19:58353098-58353401(+)$1	303	158	175	10.8625
UGCUGCUCUCACAGCCU	chr10:102740871-102741128(-)$1	257	151	168	12.9167
UUAUUAAACAAAAUAAU	chr19:21366631-21366895(+)$1	264	138	155	10.6732
UUCUGUAAAUUCAGAUU	chrX:135956446-135956762(-)$1	316	73	90	12.9753
ACCCCGAGCUAGAUGUG	chr19:55677110-55677328(-)$1	218	5	22	9.7275
GGUGUAAACCAAGGCCU	chr7:110762843-110763106(-)$1	263	150	167	10.9127
UCAUAUCAUCUUAUGCU	chrX:38422221-38422577(+)$1	356	330	347	12.7317
AGGCGUUCAACCGUAGG	chr19:57839871-57840104(+)$1	233	163	180	11.0541
AUUCCAGUACAGGACAG	chr6:135358579-135358820(-)$1	241	156	173	10.6092
UGUACCUAGUCGUACCC	chr22:41545845-41546133(+)$1	288	41	58	10.6511
UUACUCCUGAUGGUGCC	chr15:64430140-64430385(+)$1	245	11	28	12.8707
AAACACUUUUUUGUUCA	chr1:33149788-33150101(+)$1	313	267	284	10.8285
UCCUGUGUUCCCAGGGC	chr13:39588175-39588521(-)$1	346	71	88	11.2214
CGGGGGAGAAACCCUAU	chr10:43088143-43088404(-)$1	261	69	86	12.8707
uggauuggcuuguccug	chr19:1216127-1216379(+)$1	252	171	188	12.5812
ACUGGUCAGUUCCUAAG	chr14:57713467-57713703(-)$1	236	63	80	9.2671
GUAUGAAAACACCUACA	chr6:97247373-97247640(-)$1	267	95	112	10.0517
CAGGGGAGAAACCUUUU	chr10:43088914-43089283(-)$1	369	24	41	12.8707
aguucgugggagggccc	chr20:39795397-39795773(+)$1	376	206	223	10.4165
CUGAGAAAACCCUUGAG	chr10:119805423-119805679(-)$1	256	159	176	10.4515
UGACAACGAUAUGUCCG	chr16:4855073-4855400(-)$1	327	121	138	11.0224
CCUCUggaggaggagga	chr3:184429053-184429274(-)$1	221	115	132	11.0719
CGAGCAUUUUAGCUCCC	chr12:54920404-54920640(+)$1	236	203	220	11.1449
CGCCAAGCGCCUGGCCG	chr21:47423292-47423511(+)$1	219	100	117	12.5191
UUCUAGCCAAGUAGAUG	chrX:44919754-44919994(+)$1	240	191	208	12.8570
GAUUCAUUACAGAAAUG	chr8:57078753-57079047(-)$1	294	260	277	10.7512
CAGGGCUGAAACCCUAU	chr10:38344182-38344528(+)$1	346	176	193	12.8707
GUGGCCUUUUAGCUGAU	chr2:206927595-206927847(-)$1	252	66	83	12.6144
CUCAGGAAUCACUGACU	chr10:129901861-129902151(-)$1	290	122	139	12.8707
UAGAGAACUUGCUCUCU	chr4:102014848-102015088(-)$1	240	163	180	10.3654
CAGGAGAGAAGUCCUAU	chr20:25657170-25657440(-)$1	270	208	225	12.6767
UCAGACACACUUCUAGA	chr1:32744985-32745318(+)$1	333	192	209	10.4515
AACUCAUCAGAGAGUCC	chr19:44792562-44792806(-)$1	244	223	240	10.6511
CUGGCUGUGCUGCCGGC	chr7:2686400-2686667(+)$1	267	160	177	11.2214
GCCUCCUGCUCGCGGCC	chr19:17440205-17440461(-)$1	256	217	234	10.7063
CAGAGAGUUCACACUGG	chr19:58452868-58453144(-)$1	276	76	93	10.7063
GCCUGAGAAGCCAGGUG	chr9:134073264-134073504(+)$1	240	119	136	11.1109
AUAAAUGCAGUUUUAAU	chr15:48434160-48434464(-)$1	304	145	162	10.5989
UCACACCUUCCUGUCAG	chr21:43676522-43676793(+)$1	271	4	21	10.5059
CUGGCCACCCUGCCACC	chr17:42475053-42475290(-)$1	237	125	142	10.6511
gggagguucugcucccg	chr20:390843-391160(+)$1	317	141	158	10.9101
CUGUUGGGAAGAACAGC	chr7:138968983-138969231(+)$1	248	137	154	11.2214
UUCCCCCACCAGGGAUG	chr14:75248445-75248781(+)$1	336	18	35	10.6511
GGCUUAGCAAGGAGCCA	chr17:41246549-41246781(-)$1	232	167	184	10.7396
CAGGCUUUUCUGUCUCU	chr13:39586814-39587249(-)$1	435	226	243	10.9933
CUUAAGCCAGAUUGGGU	chr1:197053383-197053615(-)$1	232	60	77	9.8629
GACAUUAGUACGUGUCC	chr14:50585229-50585471(-)$1	242	161	178	10.7396
GUUGCAGUCGAGCACCA	chr14:94776084-94776302(-)$1	218	47	64	10.4366
AAUCUCAGUCAAGAUCA	chr1:24297606-24297886(-)$1	280	172	189	12.7400
ACGAGUGUAACUUUGAA	chr12:72056628-72056894(-)$1	266	175	192	12.5794
ACACGUUUUUCCGCAAC	chr1:149879150-149879414(-)$1	264	112	129	9.3511
GGAAAGGAACAUUUCUU	chr16:89628706-89628964(+)$1	258	224	241	10.7396
GCUGUUAUAAUACAGUA	chr5:110097185-110097476(+)$1	291	210	227	9.8629
GAAGUAUUAACAUUUCC	chr11:114278083-114278346(+)$1	263	48	65	10.7396
CAGGGCCAAAUCCUUGU	chr21:34944799-34945035(+)$1	236	54	71	11.2214
CUGCGCCUCACUGCAUU	chrX:70389704-70389966(+)$1	262	45	62	11.1449
AUUAUAAUUCAAUAGCU	chr17:29631980-29632240(-)$1	260	208	225	12.8707
AGUACAGCAAAGAUACU	chr1:197071678-197071916(-)$1	238	189	206	10.8096
UCUUCUCCCUUGAAGUC	chr9:5921761-5922016(-)$1	255	200	217	10.6511
CUGUGCAUCUACACAGC	chr12:2994468-2994738(+)$1	270	150	167	9.8629

#DB
(((.(......))))..	chr14:55510779-55511026(+)$1	1	73	90	10.4758
.((((......)))).)	chr15:62170811-62171030(-)$1	1	150	167	12.8839
.((((......)))).)	chr2:197705921-197706196(-)$1	1	223	240	12.8839
(.(((......)))...	chr19:58353098-58353401(+)$1	1	158	175	10.8625
.((((......))))..	chr10:102740871-102741128(-)$1	1	151	168	12.9167
(((((......))))).	chr19:21366631-21366895(+)$1	1	138	155	10.6732
.((((......)))).)	chrX:135956446-135956762(-)$1	1	73	90	12.9753
....(......)...))	chr19:55677110-55677328(-)$1	1	5	22	9.7275
(((.(......).))))	chr7:110762843-110763106(-)$1	1	150	167	10.9127
.((((......)))).)	chrX:38422221-38422577(+)$1	1	330	347	12.7317
..(((......)))...	chr19:57839871-57840104(+)$1	1	163	180	11.0541
..(((......)))..)	chr6:135358579-135358820(-)$1	1	156	173	10.6092
.((((......))))..	chr22:41545845-41546133(+)$1	1	41	58	10.6511
.((((......)))).)	chr15:64430140-64430385(+)$1	1	11	28	12.8707
.((((......)))).(	chr1:33149788-33150101(+)$1	1	267	284	10.8285
(((((......))))).	chr13:39588175-39588521(-)$1	1	71	88	11.2214
.((((......)))).)	chr10:43088143-43088404(-)$1	1	69	86	12.8707
(((((......)))).)	chr19:1216127-1216379(+)$1	1	171	188	12.5812
...((......))....	chr14:57713467-57713703(-)$1	1	63	80	9.2671
(((.(......).))))	chr6:97247373-97247640(-)$1	1	95	112	10.0517
.((((......)))).)	chr10:43088914-43089283(-)$1	1	24	41	12.8707
.((((......)))).(	chr20:39795397-39795773(+)$1	1	206	223	10.4165
(((((......))).))	chr10:119805423-119805679(-)$1	1	159	176	10.4515
.((((......)))).(	chr16:4855073-4855400(-)$1	1	121	138	11.0224
(((((......))))).	chr3:184429053-184429274(-)$1	1	115	132	11.0719
)((((......))))..	chr12:54920404-54920640(+)$1	1	203	220	11.1449
.((((......)))).)	chr21:47423292-47423511(+)$1	1	100	117	12.5191
.((((......)))).)	chrX:44919754-44919994(+)$1	1	191	208	12.8570
.((((......).))).	chr8:57078753-57079047(-)$1	1	260	277	10.7512
.((((......)))).)	chr10:38344182-38344528(+)$1	1	176	193	12.8707
(((((......))))..	chr2:206927595-206927847(-)$1	1	66	83	12.6144
.((((......)))).)	chr10:129901861-129902151(-)$1	1	122	139	12.8707
)((((......))))))	chr4:102014848-102015088(-)$1	1	163	180	10.3654
.((((......)))).)	chr20:25657170-25657440(-)$1	1	208	225	12.6767
(((((......))).))	chr1:32744985-32745318(+)$1	1	192	209	10.4515
.((((......))))..	chr19:44792562-44792806(-)$1	1	223	240	10.6511
(((((......))))).	chr7:2686400-2686667(+)$1	1	160	177	11.2214
(((.(......).))))	chr19:17440205-17440461(-)$1	1	217	234	10.7063
(((.(......).))))	chr19:58452868-58453144(-)$1	1	76	93	10.7063
(((((......)))))(	chr9:134073264-134073504(+)$1	1	119	136	11.1109
(((((......))).))	chr15:48434160-48434464(-)$1	1	145	162	10.5989
(((((......)))..)	chr21:43676522-43676793(+)$1	1	4	21	10.5059
.((((......))))..	chr17:42475053-42475290(-)$1	1	125	142	10.6511
(((((......))))).	chr20:390843-391160(+)$1	1	141	158	10.9101
(((((......))))).	chr7:138968983-138969231(+)$1	1	137	154	11.2214
.((((......))))..	chr14:75248445-75248781(+)$1	1	18	35	10.6511
(((((......))))).	chr17:41246549-41246781(-)$1	1	167	184	10.7396
(((((......))))..	chr13:39586814-39587249(-)$1	1	226	243	10.9933
(((((......))))))	chr1:197053383-197053615(-)$1	1	60	77	9.8629
(((((......))))).	chr14:50585229-50585471(-)$1	1	161	178	10.7396
(.(((......))).))	chr14:94776084-94776302(-)$1	1	47	64	10.4366
.((((......))))..	chr1:24297606-24297886(-)$1	1	172	189	12.7400
.((((......))))..	chr12:72056628-72056894(-)$1	1	175	192	12.5794
...((......))....	chr1:149879150-149879414(-)$1	1	112	129	9.3511
(((((......))))).	chr16:89628706-89628964(+)$1	1	224	241	10.7396
(((((......))))))	chr5:110097185-110097476(+)$1	1	210	227	9.8629
(((((......))))).	chr11:114278083-114278346(+)$1	1	48	65	10.7396
(((((......))))).	chr21:34944799-34945035(+)$1	1	54	71	11.2214
)((((......))))..	chrX:70389704-70389966(+)$1	1	45	62	11.1449
.((((......)))).)	chr17:29631980-29632240(-)$1	1	208	225	12.8707
(((((......).))))	chr1:197071678-197071916(-)$1	1	189	206	10.8096
.((((......))))..	chr9:5921761-5922016(-)$1	1	200	217	10.6511
(((((......))))))	chr12:2994468-2994738(+)$1	1	150	167	9.8629

#PSSM
e : 0.28	[ : 0.20	: : 0.12	c : 0.06	# : 0.06	g : 0.06	! : 0.04	" : 0.03	d : 0.03	b : 0.03	f : 0.01	= : 0.01	F : 0.01	
d : 0.49	e : 0.26	c : 0.06	g : 0.06	# : 0.04	[ : 0.03	! : 0.01	" : 0.01	
d : 0.49	e : 0.23	c : 0.15	g : 0.06	# : 0.03	" : 0.01	
d : 0.47	e : 0.20	c : 0.14	[ : 0.07	g : 0.04	b : 0.03	# : 0.01	
d : 0.47	e : 0.19	a : 0.12	c : 0.12	g : 0.04	b : 0.03	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
d : 0.47	e : 0.19	a : 0.12	c : 0.12	g : 0.04	b : 0.03	
d : 0.47	e : 0.19	c : 0.14	] : 0.09	g : 0.04	b : 0.03	3 : 0.01	
d : 0.49	e : 0.23	c : 0.15	g : 0.06	4 : 0.03	3 : 0.01	
d : 0.49	e : 0.23	g : 0.06	] : 0.06	3 : 0.04	c : 0.03	2 : 0.03	4 : 0.03	
e : 0.28	] : 0.22	: : 0.17	2 : 0.06	4 : 0.06	g : 0.06	3 : 0.04	c : 0.04	d : 0.01	D : 0.01	
: : 0.19	b : 0.14	e : 0.11	c : 0.07	] : 0.07	4 : 0.06	g : 0.06	2 : 0.04	3 : 0.04	d : 0.04	f : 0.03	5 : 0.01	a : 0.01	C : 0.01	h : 0.01	D : 0.01	7 : 0.01	

#score	708.2866434602452
#seq	63
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m2_run2.txt

#BEAR
hhhhhh"""dddd[cccooooooccc]dddd333hhhh	chr4:85592585-85592820(-)$1	235	98	136	12.0199
ggg==========[ddddllldddd22==========G	chr1:150238066-150238309(-)$1	243	150	188	17.1746
c!!bb"""ggggggg[bbnnnnnbb333ggggggg333	chr7:138521600-138521822(-)$1	222	37	75	11.7361
ccc!!ccc!!cccddddmmmmdddd333ccc22ccc22	chr17:27953364-27953604(-)$1	240	115	153	15.5825
$ccc[===========!!ammmma22===========c	chr7:92242532-92242766(-)$1	234	163	201	12.8491
!ggggggg[dddd[ccclllccc]dddd]ggggggg]c	chr14:102547620-102547860(-)$1	240	18	56	12.3630
eee[ccc"""dddd[ccclllcccdddd22ccceeeee	chr7:100278661-100278922(-)$1	261	152	190	11.5292
ccc!!iiiiiiiiiddddllldddd4444iiiiiiiii	chr10:102121221-102121444(+)$1	223	164	202	16.9322
bbffffff"""ccccccooooooccc]cccffffff]b	chr19:55858832-55859060(+)$1	228	106	144	11.5552
d[eeeee!!dddd[cccnnnnnccc333ddddeeeee]	chr6:26156503-26156776(+)$1	273	50	88	11.8205
iiiiiiii####eeeeemmmmeeeee22iiiiiiiii2	chr5:176726354-176726604(+)$1	250	57	95	14.7220
eeeeeeea[iiiiiiiiiooooooiiiiiiiii22a]e	chr2:111923817-111924069(+)$1	252	109	147	11.7270
cc[ccc!!eeeeeddddmmmmdddd333eeeeeccc]c	chr1:3697469-3697694(-)$1	225	33	71	14.4324
!ccc[cccbbcccddddmmmmdddd22ccc]bb22ccc	chr3:38295240-38295482(+)$1	242	189	227	12.9542
ccc"""ccc[ccc[ddddmmmmddddccc]ccc333cc	chr4:2233309-2233534(-)$1	225	55	93	13.4193
c!!hhhhhhhhbbddddmmmmdddd22bb333hhhhhh	chr15:83710452-83710684(-)$1	232	155	193	12.1054
iiiiiii"""gggggggmmmmggggggg333iiiiiii	chr5:73924955-73925181(-)$1	226	39	77	13.9873
eeeee####ccc!!ddddllldddd666666ccc333e	chr20:35240389-35240635(+)$1	246	82	120	12.4996
ggggg"""ddddrrrrrrrrrdddd333ggggggg333	chr1:179071562-179071785(-)$1	223	141	179	12.4037
hhhhhhheeeee[ddddmmmmdddd22eeeee4444hh	chr2:36776326-36776579(+)$1	253	81	119	12.1098
iiiiiii[ccc"""ddddllldddd]ccciiiiiiiii	chr13:77458820-77459044(-)$1	224	37	75	16.1923
ffffffbb"""ddddoooooodddd4444bb]ffffff	chr11:63743742-63743987(+)$1	245	93	131	12.3839
eeeee!!bb!!ddddoooooodddd22bb22eeeee>>	chr17:27585625-27585850(-)$1	225	67	105	12.1297
fff[bb[ccc$$$$$cccmmmmccc4444ccc22bbff	chr12:16052858-16053083(+)$1	225	10	48	11.7393
ddd[eeeee####ddddmmmmdddd22eeeeeddddgg	chr11:85374497-85374732(-)$1	235	125	163	13.0772
bggggggg!!bb!!ddddllldddd22bb22ggggggg	chr19:3985275-3985541(-)$1	266	215	253	15.2881
b===========[ddddmmmmdddd22===========	chr9:98209310-98209541(-)$1	231	166	204	16.9994
========"""bb[aooooooa]bb333==========	chr7:100277074-100277357(-)$1	283	89	127	15.8589
eeeee[ccc####ddddmmmmdddd22ccc22eeeee:	chr11:14479107-14479334(-)$1	227	115	153	13.5366
b[bb!!bb[iiiiiiiiimmmmiiiiiiiii333bb22	chr1:2240585-2240806(+)$1	221	54	92	11.6220
CCggggggg!!ggggggglllggggggg333ggggggg	chr12:118470670-118470922(-)$1	252	153	191	10.9358
hhhhh[ccc$$$$$ddddllldddd4444ccchhhhhh	chr1:205685786-205686035(-)$1	249	131	169	13.9221
cccggggggg####ddddllldddd4444ggggggg22	chr12:121001156-121001382(+)$1	226	152	190	16.5985
gggggg[ddddbb!!cccmmmmccc333bb]dddd]gg	chr12:49521724-49521948(-)$1	224	58	96	12.3827
"""dddd"""ccc[ddddmmmmdddd]ccc333dddd4	chr5:176662727-176662955(+)$1	228	57	95	12.9880
ccc!!eeeee####ddddlllddddeeeee333ccc44	chr16:87442655-87442877(-)$1	222	137	175	14.1122
==========[bb[ddddmmmmdddd]bb]========	chr6:90074867-90075087(-)$1	220	123	161	15.0166
=========="""ddddmmmmdddd4444=========	chr3:194123633-194123865(-)$1	232	181	219	17.7788
=========%%%%%%bboooooobb333==========	chr5:179149779-179150016(+)$1	237	26	64	12.3754
b!!eeeee[dddd[ddddmmmmdddd]dddd333eeee	chr1:205682445-205682690(-)$1	245	11	49	12.1866
gggg!!bb[iiiiiiiiinnnnniiiiiiiii22bb33	chr4:2470859-2471085(+)$1	226	137	175	11.3340
eeeeeeeeee!!a[ddddoooooodddd]a22eeeee>	chr3:185207505-185207727(-)$1	222	138	176	10.9584
ffffff[ccc"""cccooooooccc22ccc]ffffff2	chrX:71800692-71800916(-)$1	224	119	157	12.8311
:ccc####ccc"""cccooooooccc333ccc22ccc:	chr2:237039095-237039322(+)$1	227	118	156	12.7296
d:=========="""cccnnnnnccc]==========:	chr6:114182080-114182320(+)$1	240	113	151	12.1168
bbiiiiiiiii"""cccmmmmccc4444iiiiiiiii]	chr13:95279356-95279605(+)$1	249	45	83	15.8322
iiiiiiii!!eeeeeooooooeeeee22iiiiiiiii:	chr12:22839252-22839484(+)$1	232	171	209	13.1756
eeee$$$$$eeeee[ccclllccc333eeeee]eeeee	chr19:55602362-55602607(-)$1	245	49	87	11.3310
ffa[ggggggg[eeeeemmmmeeeee]ggggggg]a:c	chr11:13752883-13753104(+)$1	221	87	125	11.0787
dffffff[eeeee[cccmmmmccc4444eeeee333ff	chr3:180632601-180632859(+)$1	258	63	101	12.1158
c####eeeee!!a[ccclllccc]a333eeeeeccc]c	chr1:193028310-193028541(-)$1	231	143	181	13.0135
ff[bb[bb!!ccc[ddddlllddddccc333bb]bb]f	chr1:180083776-180084007(+)$1	231	175	213	13.1233
gg!!a[a[a[a[eeeeemmmmeeeeea]a]aa22gggg	chr19:42799781-42800031(+)$1	250	137	175	12.5087
hhhhhhh####ddddoooooodddd333hhhhhhhhGG	chr1:162493863-162494092(+)$1	229	167	205	12.2850

#otherMatches

#Seq PSSM
GAGAUUAGUUUACAGAGAAAAGGCUUGGUGGUGGGAUU	chr4:85592585-85592820(-)$1	235	98	136	12.0199
GUCCCUUUCUCCUUGGUCCCAGACCUUGGGGGAAAGGA	chr1:150238066-150238309(-)$1	243	150	188	17.1746
CGAUCGCUAAGGCCGAUCCUGUAGAAUGCGGCUUUCAA	chr7:138521600-138521822(-)$1	222	37	75	11.7361
AGCAAUGCUGGUGGCAGCGUCCUGUGUACACAUGCAGA	chr17:27953364-27953604(-)$1	240	115	153	15.5825
GCAUUAUUAAGUUGUACUGAAUUCUUUGCAGCUUAAUG	chr7:92242532-92242766(-)$1	234	163	201	12.8491
UCAUGUUGGUUUAUUUUCACAGAUUGGGGUAACGUGCA	chr14:102547620-102547860(-)$1	240	18	56	12.3630
CAGACCUGUUGUGAGCAGCUCCUGUCACUGAGGCUGGC	chr7:100278661-100278922(-)$1	261	152	190	11.5292
GUGGCUGCGGUGUUUGGCAAUGCUAAUUCAAUGCCGCA	chr10:102121221-102121444(+)$1	223	164	202	16.9322
GACCCUGGAAUGGGGUUGGUUUGGACACCCCCAGGGAU	chr19:55858832-55859060(+)$1	228	106	144	11.5552
GCUCGAGUCCCGGCCAGUGCCUCUGCUUCCGGCUCGAA	chr6:26156503-26156776(+)$1	273	50	88	11.8205
AGGUGGCCAUUGAGUUUCUCAGGGCUGGGGCCACCUUG	chr5:176726354-176726604(+)$1	250	57	95	14.7220
CAUUUCCCUCUGGCCUGGCGGCCUCCAGGCUGGCUGUG	chr2:111923817-111924069(+)$1	252	109	147	11.7270
CGUGCGCUGACGCCAGGGCCGCCUGUCCGCGUUUGUUU	chr1:3697469-3697694(-)$1	225	33	71	14.4324
CCACAUGUGCCGUGACCUUUAGGUUUUAUGAGUAGACA	chr3:38295240-38295482(+)$1	242	189	227	12.9542
GCUUUUUAUGACUUGAGCAUGUGUUUAGUGGUACUUAG	chr4:2233309-2233534(-)$1	225	55	93	13.4193
ACUUUCCUUAAUCCGGUUCCCACUGAUGACAAUUGAGG	chr15:83710452-83710684(-)$1	232	155	193	12.1054
CAGCUGUCUUCACAUGUAUGGACGUGUGUGAAUGGUUG	chr5:73924955-73925181(-)$1	226	39	77	13.9873
GUGCUCCCUAUCCAGUCCAAAGGACCCUCUUGAUUACA	chr20:35240389-35240635(+)$1	246	82	120	12.4996
AGGCUUCAGCGGUUUGUGUCUCUGUCUUAGCUUGUAUC	chr1:179071562-179071785(-)$1	223	141	179	12.4037
UUUCUUUUCUAUACAGUCACAACUGCAGUAGGCAGUGA	chr2:36776326-36776579(+)$1	253	81	119	12.1098
CCCCCAGAUGGUACUUCAGUUUGGAUCUAUUGGGGGAG	chr13:77458820-77459044(-)$1	224	37	75	16.1923
CCGGCCCAUCCUGGUCAUGUUACUGCAUUUGUGGCCGG	chr11:63743742-63743987(+)$1	245	93	131	12.3839
UGUAGCACAGCCACUAACAAGAGUGAAUGAAUUAUAAA	chr17:27585625-27585850(-)$1	225	67	105	12.1297
CUGUGUGAGAUUUAGUCCUGAUGGAGAACUCUAUGCCA	chr12:16052858-16053083(+)$1	225	10	48	11.7393
UGUAGGGGUUACAGAACAGUCGUUCCCGCCUCACAACC	chr11:85374497-85374732(-)$1	235	125	163	13.0772
CGGGGCCUACGCUGCCUAGCCUGGGACGCUGGGGCCCC	chr19:3985275-3985541(-)$1	266	215	253	15.2881
GGCCUGGGCGGAACCCCCGAGGGGGACUCUGCCCAGGC	chr9:98209310-98209541(-)$1	231	166	204	16.9994
GUGCAGGGGUCACCGUGUUCCCUGUCUGCCUUGUACCC	chr7:100277074-100277357(-)$1	283	89	127	15.8589
AAGAUUGAGUUUAAAAUUAUAGUUUGUCUUUUGUCUUA	chr11:14479107-14479334(-)$1	227	115	153	13.5366
GCGAGUCCGUUUCUUUUCAGCAGAAGGGGGAAGAGGUG	chr1:2240585-2240806(+)$1	221	54	92	11.6220
UGUCUUUUCAAAAUGAGAGGCUUUCAUUGAAGAAAAGA	chr12:118470670-118470922(-)$1	252	153	191	10.9358
CCAGGCGCUAAUGGGAACAAGGUUUAAAGGGUCCUGGU	chr1:205685786-205686035(-)$1	249	131	169	13.9221
UUAGCAGAUGACAAUCUUAAAGAGGGGACCAUUUGCAC	chr12:121001156-121001382(+)$1	226	152	190	16.5985
GCCUUUGUUCACUGGUACGUGGGUGAGGGGAUGGAGGA	chr12:49521724-49521948(-)$1	224	58	96	12.3827
UUUUUGAUUAAUGUUGAAUUUGUUUAUCAUCUUUUAGC	chr5:176662727-176662955(+)$1	228	57	95	12.9880
GGGAAGUGGUAGGACUCUGGAAGAGGCCACACACCCGA	chr16:87442655-87442877(-)$1	222	137	175	14.1122
UUGGUUAUUUUCAGUGAUGUAGAUUAGUGUGAAUGACC	chr6:90074867-90075087(-)$1	220	123	161	15.0166
UUUAAUGUAUUAAAAUUUGGUAAUUAUGUGUACAUUAA	chr3:194123633-194123865(-)$1	232	181	219	17.7788
GAAUCUGGAAACCCAGGAAAAUACCAAAUCCAGAUUUC	chr5:179149779-179150016(+)$1	237	26	64	12.3754
GGUAGAAUCGUGUGAUGGUCUUUUGUGAUACUUAAUUU	chr1:205682445-205682690(-)$1	245	11	49	12.1866
CCUUGCAGAUGCGAGGUUUAGGCAGCUUCGCGGCCUAC	chr4:2470859-2471085(+)$1	226	137	175	11.3340
UGUGGCCUUUGGUGUUCUGGAGUAGGGGGAGGGAAGGA	chr3:185207505-185207727(-)$1	222	138	176	10.9584
UGAUUGUGCAUGGAACUAAAAUGUUAUUGCCUAAUCAC	chrX:71800692-71800916(-)$1	224	119	157	12.8311
AGAGCUUUGGUAAACAGAAGACACUGGAAGCCCACUCG	chr2:237039095-237039322(+)$1	227	118	156	12.7296
GAAGUGGUGCAUAACAUUGCCAAAAUAGUGUGCCACUA	chr6:114182080-114182320(+)$1	240	113	151	12.1168
CACAAAAGUCGCCCUCAUUUCUGAUACUUGAUUUUUGU	chr13:95279356-95279605(+)$1	249	45	83	15.8322
CUUUAAAAUACUUGGAUUAUCUCAAGAUUUUUGAAGCU	chr12:22839252-22839484(+)$1	232	171	209	13.1756
GAUCAGUAGCCAGGACCAGAGUGGCCGCCUGGAGGUCC	chr19:55602362-55602607(-)$1	245	49	87	11.3310
UAAGAAAUAAAAGCAUUAUUGGGUGCCUUUGUUUGUAA	chr11:13752883-13753104(+)$1	221	87	125	11.0787
AGCCAUAAUCCACUUGCAUAUGCACUUUGUGGAAACUG	chr3:180632601-180632859(+)$1	258	63	101	12.1158
CCAGGGCCAUGACGGGCAAUGCCGGGGAGUGGUGCCUC	chr1:193028310-193028541(-)$1	231	143	181	13.0135
UUAACUGAAAUAUACUUUAAGAAAGAUAAAAUCUGUAA	chr1:180083776-180084007(+)$1	231	175	213	13.1233
CAAUGAGCGAGAUUAAAGCUGUUUAACACACCUGUGUG	chr19:42799781-42800031(+)$1	250	137	175	12.5087
CAAUUAUUGUUUGACAUUUUAGUUAUUUAUAAUUGUCA	chr1:162493863-162494092(+)$1	229	167	205	12.2850

#DB
((((((...((((.(((......))).))))...))))	chr4:85592585-85592820(-)$1	1	98	136	12.0199
)))((((((((((.((((...))))..)))))))))))	chr1:150238066-150238309(-)$1	1	150	188	17.1746
(..((...(((((((.((.....))...)))))))...	chr7:138521600-138521822(-)$1	1	37	75	11.7361
(((..(((..(((((((....))))...)))..)))..	chr17:27953364-27953604(-)$1	1	115	153	15.5825
.(((.(((((((((((..(....)..))))))))))))	chr7:92242532-92242766(-)$1	1	163	201	12.8491
.(((((((.((((.(((...))).)))).))))))).)	chr14:102547620-102547860(-)$1	1	18	56	12.3630
(((.(((...((((.(((...)))))))..))))))))	chr7:100278661-100278922(-)$1	1	152	190	11.5292
(((..(((((((((((((...))))....)))))))))	chr10:102121221-102121444(+)$1	1	164	202	16.9322
((((((((...((((((......))).))))))))).)	chr19:55858832-55859060(+)$1	1	106	144	11.5552
(.(((((..((((.(((.....)))...))))))))).	chr6:26156503-26156776(+)$1	1	50	88	11.8205
((((((((....(((((....)))))..))))))))).	chr5:176726354-176726604(+)$1	1	57	95	14.7220
))((((((.(((((((((......)))))))))..).)	chr2:111923817-111924069(+)$1	1	109	147	11.7270
((.(((..(((((((((....))))...)))))))).)	chr1:3697469-3697694(-)$1	1	33	71	14.4324
.(((.((((((((((((....))))..))).))..)))	chr3:38295240-38295482(+)$1	1	189	227	12.9542
(((...(((.(((.((((....))))))).)))...))	chr4:2233309-2233534(-)$1	1	55	93	13.4193
(..((((((((((((((....))))..))...))))))	chr15:83710452-83710684(-)$1	1	155	193	12.1054
(((((((...(((((((....)))))))...)))))))	chr5:73924955-73925181(-)$1	1	39	77	13.9873
(((((....(((..((((...))))......)))...)	chr20:35240389-35240635(+)$1	1	82	120	12.4996
(((((...((((.........))))...)))))))...	chr1:179071562-179071785(-)$1	1	141	179	12.4037
((((((((((((.((((....))))..)))))....))	chr2:36776326-36776579(+)$1	1	81	119	12.1098
(((((((.(((...((((...)))).))))))))))))	chr13:77458820-77459044(-)$1	1	37	75	16.1923
((((((((...((((......))))....)).))))))	chr11:63743742-63743987(+)$1	1	93	131	12.3839
(((((..((..((((......))))..))..)))))..	chr17:27585625-27585850(-)$1	1	67	105	12.1297
(((.((.(((.....(((....)))....)))..))))	chr12:16052858-16053083(+)$1	1	10	48	11.7393
(((.(((((....((((....))))..)))))))))))	chr11:85374497-85374732(-)$1	1	125	163	13.0772
((((((((..((..((((...))))..))..)))))))	chr19:3985275-3985541(-)$1	1	215	253	15.2881
((((((((((((.((((....))))..)))))))))))	chr9:98209310-98209541(-)$1	1	166	204	16.9994
((((((((...((.(......).))...))))))))))	chr7:100277074-100277357(-)$1	1	89	127	15.8589
(((((.(((....((((....))))..)))..))))).	chr11:14479107-14479334(-)$1	1	115	153	13.5366
(.((..((.(((((((((....)))))))))...))..	chr1:2240585-2240806(+)$1	1	54	92	11.6220
(((((((((..(((((((...)))))))...)))))))	chr12:118470670-118470922(-)$1	1	153	191	10.9358
(((((.(((.....((((...))))....)))))))))	chr1:205685786-205686035(-)$1	1	131	169	13.9221
((((((((((....((((...))))....)))))))..	chr12:121001156-121001382(+)$1	1	152	190	16.5985
((((((.((((((..(((....)))...)).)))).))	chr12:49521724-49521948(-)$1	1	58	96	12.3827
...((((...(((.((((....)))).)))...)))).	chr5:176662727-176662955(+)$1	1	57	95	12.9880
(((..(((((....((((...)))))))))...)))..	chr16:87442655-87442877(-)$1	1	137	175	14.1122
((((((((((.((.((((....)))).)).))))))))	chr6:90074867-90075087(-)$1	1	123	161	15.0166
((((((((((...((((....))))....)))))))))	chr3:194123633-194123865(-)$1	1	181	219	17.7788
(((((((((......((......))...))))))))))	chr5:179149779-179150016(+)$1	1	26	64	12.3754
(..(((((.((((.((((....)))).))))...))))	chr1:205682445-205682690(-)$1	1	11	49	12.1866
((((..((.(((((((((.....)))))))))..))..	chr4:2470859-2471085(+)$1	1	137	175	11.3340
((((((((((..(.((((......)))).)..))))).	chr3:185207505-185207727(-)$1	1	138	176	10.9584
((((((.(((...(((......)))..))).)))))).	chrX:71800692-71800916(-)$1	1	119	157	12.8311
.(((....(((...(((......)))...)))..))).	chr2:237039095-237039322(+)$1	1	118	156	12.7296
).((((((((((...(((.....))).)))))))))).	chr6:114182080-114182320(+)$1	1	113	151	12.1168
(((((((((((...(((....)))....))))))))).	chr13:95279356-95279605(+)$1	1	45	83	15.8322
((((((((..(((((......)))))..))))))))).	chr12:22839252-22839484(+)$1	1	171	209	13.1756
((((.....(((((.(((...)))...))))).)))))	chr19:55602362-55602607(-)$1	1	49	87	11.3310
))(.(((((((.(((((....))))).))))))).).(	chr11:13752883-13753104(+)$1	1	87	125	11.0787
)((((((.(((((.(((....)))....)))))...))	chr3:180632601-180632859(+)$1	1	63	101	12.1158
(....(((((..(.(((...))).)...)))))))).)	chr1:193028310-193028541(-)$1	1	143	181	13.0135
((.((.((..(((.((((...)))))))...)).)).)	chr1:180083776-180084007(+)$1	1	175	213	13.1233
((..(.(.(.(.(((((....)))))).).))..))))	chr19:42799781-42800031(+)$1	1	137	175	12.5087
(((((((....((((......))))...))))))))))	chr1:162493863-162494092(+)$1	1	167	205	12.2850

#PSSM
c : 0.16	e : 0.12	b : 0.11	g : 0.09	f : 0.09	h : 0.07	d : 0.07	i : 0.07	= : 0.07	! : 0.03	$ : 0.01	C : 0.01	" : 0.01	: : 0.01	
c : 0.16	g : 0.12	e : 0.12	f : 0.11	= : 0.09	h : 0.07	i : 0.07	! : 0.05	b : 0.03	[ : 0.03	d : 0.01	C : 0.01	" : 0.01	: : 0.01	# : 0.01	
c : 0.14	e : 0.14	g : 0.12	= : 0.11	f : 0.09	i : 0.09	h : 0.07	! : 0.07	[ : 0.03	d : 0.01	b : 0.01	" : 0.01	a : 0.01	# : 0.01	
e : 0.14	= : 0.12	g : 0.12	h : 0.09	i : 0.09	! : 0.07	c : 0.07	[ : 0.07	f : 0.07	b : 0.05	" : 0.01	d : 0.01	# : 0.01	
e : 0.14	= : 0.12	g : 0.12	h : 0.09	! : 0.09	i : 0.09	f : 0.07	b : 0.05	[ : 0.03	c : 0.03	# : 0.03	" : 0.01	d : 0.01	$ : 0.01	a : 0.01	
= : 0.14	e : 0.12	g : 0.11	i : 0.11	h : 0.07	c : 0.07	f : 0.07	[ : 0.07	" : 0.05	! : 0.05	# : 0.03	b : 0.01	d : 0.01	$ : 0.01	
= : 0.14	e : 0.12	c : 0.11	i : 0.11	g : 0.09	b : 0.07	" : 0.05	h : 0.05	[ : 0.05	f : 0.03	! : 0.03	# : 0.03	d : 0.01	$ : 0.01	a : 0.01	
= : 0.14	c : 0.12	" : 0.11	e : 0.11	g : 0.09	b : 0.09	i : 0.07	# : 0.05	[ : 0.05	! : 0.03	f : 0.01	a : 0.01	h : 0.01	d : 0.01	$ : 0.01	
" : 0.12	= : 0.12	e : 0.12	c : 0.12	! : 0.09	[ : 0.09	g : 0.07	# : 0.05	i : 0.03	b : 0.03	d : 0.03	h : 0.01	$ : 0.01	a : 0.01	
e : 0.12	d : 0.11	= : 0.11	! : 0.11	" : 0.11	i : 0.09	c : 0.09	# : 0.07	g : 0.05	[ : 0.03	b : 0.01	h : 0.01	$ : 0.01	% : 0.01	
c : 0.14	d : 0.12	# : 0.11	i : 0.09	" : 0.09	e : 0.09	= : 0.07	! : 0.07	g : 0.05	$ : 0.03	h : 0.01	b : 0.01	[ : 0.01	% : 0.01	a : 0.01	
d : 0.16	c : 0.12	# : 0.09	e : 0.09	b : 0.09	" : 0.09	= : 0.07	i : 0.07	g : 0.05	$ : 0.03	! : 0.03	[ : 0.03	% : 0.01	
d : 0.14	e : 0.12	c : 0.11	" : 0.11	i : 0.07	b : 0.07	# : 0.07	g : 0.05	= : 0.03	! : 0.03	[ : 0.03	$ : 0.03	a : 0.03	r : 0.01	% : 0.01	
[ : 0.24	d : 0.24	e : 0.09	i : 0.07	" : 0.07	g : 0.05	! : 0.05	c : 0.03	$ : 0.03	# : 0.03	= : 0.01	r : 0.01	% : 0.01	
d : 0.48	c : 0.16	e : 0.07	g : 0.05	i : 0.05	[ : 0.03	= : 0.01	r : 0.01	$ : 0.01	a : 0.01	! : 0.01	% : 0.01	" : 0.01	
d : 0.42	c : 0.25	o : 0.09	e : 0.05	i : 0.05	g : 0.03	[ : 0.01	= : 0.01	r : 0.01	b : 0.01	
d : 0.42	c : 0.24	o : 0.11	e : 0.05	i : 0.05	b : 0.03	g : 0.03	! : 0.01	r : 0.01	
m : 0.27	d : 0.25	o : 0.18	c : 0.09	i : 0.05	l : 0.03	b : 0.01	! : 0.01	n : 0.01	r : 0.01	g : 0.01	
m : 0.40	l : 0.25	o : 0.22	n : 0.07	a : 0.01	r : 0.01	
m : 0.42	l : 0.25	o : 0.22	n : 0.07	r : 0.01	
m : 0.42	o : 0.22	l : 0.22	n : 0.07	c : 0.03	r : 0.01	
d : 0.40	m : 0.14	o : 0.12	c : 0.11	n : 0.07	e : 0.07	g : 0.03	a : 0.01	
d : 0.48	c : 0.18	o : 0.11	e : 0.07	n : 0.05	g : 0.03	m : 0.01	] : 0.01	i : 0.01	
d : 0.48	c : 0.22	e : 0.07	b : 0.05	] : 0.03	o : 0.03	g : 0.03	i : 0.03	a : 0.01	
d : 0.53	c : 0.14	e : 0.07	b : 0.05	i : 0.05	g : 0.03	4 : 0.03	2 : 0.01	3 : 0.01	a : 0.01	
2 : 0.20	3 : 0.20	4 : 0.14	d : 0.12	c : 0.09	e : 0.09	i : 0.05	g : 0.03	6 : 0.01	] : 0.01	
2 : 0.22	3 : 0.22	4 : 0.14	] : 0.12	d : 0.05	i : 0.05	c : 0.05	g : 0.03	= : 0.01	6 : 0.01	e : 0.01	a : 0.01	
3 : 0.20	4 : 0.14	c : 0.14	d : 0.09	= : 0.07	b : 0.07	e : 0.07	i : 0.05	g : 0.05	2 : 0.03	6 : 0.01	] : 0.01	
c : 0.14	e : 0.12	= : 0.11	4 : 0.11	i : 0.11	b : 0.09	3 : 0.07	d : 0.05	g : 0.05	] : 0.03	2 : 0.01	6 : 0.01	a : 0.01	h : 0.01	
c : 0.16	i : 0.14	= : 0.12	e : 0.12	g : 0.09	3 : 0.07	d : 0.05	2 : 0.05	] : 0.05	b : 0.03	6 : 0.01	a : 0.01	h : 0.01	
= : 0.14	i : 0.14	c : 0.11	e : 0.11	3 : 0.11	g : 0.09	2 : 0.07	d : 0.05	] : 0.05	f : 0.01	6 : 0.01	b : 0.01	a : 0.01	h : 0.01	
= : 0.14	i : 0.14	g : 0.12	e : 0.12	3 : 0.11	c : 0.11	2 : 0.05	f : 0.03	d : 0.03	b : 0.03	] : 0.01	a : 0.01	h : 0.01	
= : 0.14	g : 0.12	i : 0.12	e : 0.12	3 : 0.09	2 : 0.09	c : 0.05	f : 0.05	h : 0.05	b : 0.03	d : 0.03	4 : 0.01	] : 0.01	
= : 0.14	g : 0.12	e : 0.11	i : 0.11	2 : 0.11	3 : 0.09	c : 0.09	f : 0.05	h : 0.05	d : 0.05	4 : 0.01	] : 0.01	
= : 0.14	g : 0.12	e : 0.12	i : 0.11	c : 0.09	h : 0.07	b : 0.07	f : 0.05	3 : 0.05	d : 0.05	2 : 0.03	4 : 0.01	] : 0.01	
= : 0.14	e : 0.12	c : 0.11	i : 0.11	3 : 0.09	g : 0.09	h : 0.07	b : 0.07	f : 0.05	a : 0.03	d : 0.03	4 : 0.01	] : 0.01	
= : 0.14	] : 0.11	e : 0.11	i : 0.11	g : 0.09	h : 0.07	3 : 0.07	f : 0.07	2 : 0.05	c : 0.05	> : 0.01	d : 0.01	4 : 0.01	: : 0.01	G : 0.01	
c : 0.12	2 : 0.09	e : 0.09	g : 0.09	= : 0.09	h : 0.07	f : 0.07	: : 0.07	3 : 0.05	i : 0.05	G : 0.03	] : 0.03	> : 0.03	4 : 0.03	b : 0.01	

#score	715.4834861491664
#seq	54
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_CDS_m1_run1.txt

#BEAR
[ddddtttttttttttdddd22	chr16:56438779-56439009(-)$1	230	166	188	20.8244
ddddwwwwwwwwwwwwwwdddd	chr5:14405905-14406134(+)$1	229	167	189	20.4823
fffffvvvvvvvvvvvvvffff	chr1:68620716-68620957(-)$1	241	1	23	21.9051
b[cccvvvvvvvvvvvvvccc]	chr7:99764657-99764872(-)$1	215	129	151	22.8272
#ddddtttttttttttdddd22	chr17:17769587-17769808(-)$1	221	84	106	20.6891
ddcccuuuuuuuuuuuuccc33	chr3:58555442-58555662(-)$1	220	127	149	23.1235
d[cccwwwwwwwwwwwwwwccc	chr6:17637608-17637836(-)$1	228	184	206	21.3473
ecccyyyyyyyyyyyyyyyycc	chr19:41112040-41112283(+)$1	243	71	93	21.1231
ggggggtttttttttttggggg	chr2:55254440-55254666(-)$1	226	32	54	22.1196
ffyyyyyyyyyyyyyyyyffff	chr6:163990389-163990632(+)$1	243	108	130	20.0666
:ddddvvvvvvvvvvvvvdddd	chr2:112588794-112589016(-)$1	222	163	185	20.9311
ffffftttttttttttffffff	chr17:55183974-55184201(+)$1	227	178	200	20.8087
"""ccctttttttttttccc]c	chr3:136196115-136196330(+)$1	215	30	52	22.1734
ggggvvvvvvvvvvvvvggggg	chr10:36811643-36811861(-)$1	218	33	55	22.1207
:eeeeettttttttttteeeee	chr19:10369986-10370208(+)$1	222	185	207	20.5870
ggggguuuuuuuuuuuuggggg	chr3:184714183-184714399(-)$1	216	154	176	23.0519
:eeeeettttttttttteeeee	chr1:15821845-15822063(-)$1	218	169	191	20.5870
:dddduuuuuuuuuuuudddd:	chr14:75248692-75248910(+)$1	218	100	122	20.4169
ddddyyyyyyyyyyyyyyyydd	chr5:42800899-42801133(+)$1	234	209	231	20.6090
:cccwwwwwwwwwwwwwwccc:	chr19:53856039-53856255(+)$1	216	0	22	19.3983
!!cccvvvvvvvvvvvvvccc]	chr16:324932-325163(-)$1	231	19	41	23.1009
eeeevvvvvvvvvvvvveeeee	chr2:241512554-241512801(-)$1	247	84	106	21.4460
iiiiiuuuuuuuuuuuuiiiii	chr21:34861247-34861465(+)$1	218	143	165	23.2339
$$ccctttttttttttccc333	chr3:122288101-122288319(-)$1	218	62	84	21.4374
hhhhhyyyyyyyyyyyyyyyyh	chr7:105122702-105122921(-)$1	219	95	117	20.1080
ggggggtttttttttttggggg	chr10:87614250-87614472(-)$1	222	148	170	22.1196
bb[ccctttttttttttcccbb	chr2:101582053-101582276(+)$1	223	128	150	21.4235
fffffuuuuuuuuuuuufffff	chr14:102900912-102901136(+)$1	224	118	140	22.2348
fffffvvvvvvvvvvvvvffff	chr15:29398809-29399028(+)$1	219	194	216	21.9051
eeewwwwwwwwwwwwwweeeee	chr17:61831703-61831935(-)$1	232	59	81	19.8912
hhhhhvvvvvvvvvvvvvhhhh	chr3:28378181-28378411(-)$1	230	38	60	21.2737
iiiiiuuuuuuuuuuuuiiiii	chr10:76936255-76936475(+)$1	220	148	170	23.2339
hhh!!attttttttttta22hh	chr12:107713702-107713924(+)$1	222	110	132	21.6320
=====uuuuuuuuuuuu=====	chr1:76211453-76211679(+)$1	226	166	188	23.2156
iiiiiwwwwwwwwwwwwwwiii	chr8:110099745-110099962(+)$1	217	54	76	21.4846
b[ccctttttttttttccc]bb	chr5:134223469-134223694(+)$1	225	32	54	21.2570
dd[bbuuuuuuuuuuuubb]dd	chrX:56590561-56590795(+)$1	234	98	120	21.6065
hhhhhwwwwwwwwwwwwwwhhh	chr13:23915612-23915827(-)$1	215	167	189	20.1847
!!cccvvvvvvvvvvvvvccc]	chr16:67472305-67472552(-)$1	247	101	123	23.1009
hhhhbbtttttttttttbb333	chr15:75558473-75558688(-)$1	215	77	99	21.0500
!!ddddtttttttttttdddd2	chr12:46320605-46320823(+)$1	218	21	43	21.6156
ddddduuuuuuuuuuuudddd]	chr5:138650271-138650518(+)$1	247	159	181	22.3810
fffffwwwwwwwwwwwwwwfff	chr2:210574748-210574968(+)$1	220	5	27	20.6473
hhhhhuuuuuuuuuuuuhhhhh	chr6:31600405-31600625(+)$1	220	182	204	21.3877
[dddduuuuuuuuuuuudddd]	chr10:100179719-100179942(-)$1	223	169	191	22.6129
iiiiiitttttttttttiiiii	chr17:56769930-56770146(+)$1	216	106	128	22.2250
fffffftttttttttttfffff	chr19:6495844-6496080(-)$1	236	105	127	21.3755
ddddyyyyyyyyyyyyyyyydd	chr11:88258405-88258637(-)$1	232	61	83	20.6090
"eeeeettttttttttteeeee	chr2:210574571-210574794(+)$1	223	94	116	21.5438
ddddyyyyyyyyyyyyyyyydd	chrM:11679-11899(+)$1	220	11	33	20.6090
fffffuuuuuuuuuuuufffff	chr1:119427461-119427682(+)$1	221	7	29	22.2348
fffffftttttttttttfffff	chr8:113650899-113651132(-)$1	233	5	27	21.3755
eeeeeettttttttttteeeee	chr11:134114745-134114969(+)$1	224	87	109	21.4549
hhhhhyyyyyyyyyyyyyyyyh	chr4:367268-367484(-)$1	216	136	158	20.1080
fffffftttttttttttfffff	chrX:11139747-11139965(+)$1	218	194	216	21.3755
hhh[awwwwwwwwwwwwwwa]h	chr7:5567590-5567838(-)$1	248	184	206	20.7337
fffffvvvvvvvvvvvvvffff	chr2:219029368-219029584(-)$1	216	132	154	21.9051
eeeeeuuuuuuuuuuuueeeee	chr13:49084675-49084896(-)$1	221	76	98	22.2924
======ttttttttttt=====	chr2:10269383-10269614(+)$1	231	163	185	22.3572
ffcccvvvvvvvvvvvvvccc]	chr8:48715837-48716076(-)$1	239	30	52	22.7948
cccyyyyyyyyyyyyyyyyccc	chr11:36458906-36459151(+)$1	245	93	115	20.9879
!dddduuuuuuuuuuuudddd2	chr2:218674462-218674697(-)$1	235	71	93	22.3944
""cccvvvvvvvvvvvvvccc4	chr5:847528-847744(-)$1	216	151	173	22.6577

#otherMatches

#Seq PSSM
UCAUGCACCAUAUUCACAUGUU	chr16:56438779-56439009(-)$1	230	166	188	20.8244
UCCCGCCACAAGACAGAAGGGA	chr5:14405905-14406134(+)$1	229	167	189	20.4823
GCUCUUUUUCCAGACUCCAGAG	chr1:68620716-68620957(-)$1	241	1	23	21.9051
GUCACCUCACCCUUCCCUGUGC	chr7:99764657-99764872(-)$1	215	129	151	22.8272
GAAGUAACCGAAGACAACUUAA	chr17:17769587-17769808(-)$1	221	84	106	20.6891
GGCCAGAAUACAGAGAGUGGAA	chr3:58555442-58555662(-)$1	220	127	149	23.1235
AGUGCAAAAUAAACCUGAAGCA	chr6:17637608-17637836(-)$1	228	184	206	21.3473
UGGCCCACCCCUCUCCUCUCGC	chr19:41112040-41112283(+)$1	243	71	93	21.1231
UCCAUGGUCACAGAAAAUAUGG	chr2:55254440-55254666(-)$1	226	32	54	22.1196
AUCAAACCUCAGAAUAUAGUAG	chr6:163990389-163990632(+)$1	243	108	130	20.0666
UGGAGUGUUACUACCUAUCUCC	chr2:112588794-112589016(-)$1	222	163	185	20.9311
UGUCCAGCCCCACCAAGGACAG	chr17:55183974-55184201(+)$1	227	178	200	20.8087
CCAGCCAACAUAUUUUAGGUAA	chr3:136196115-136196330(+)$1	215	30	52	22.1734
UGGCAAGGUGACAAAAAGCUAU	chr10:36811643-36811861(-)$1	218	33	55	22.1207
AGUCACACUAGACCACAGUGAC	chr19:10369986-10370208(+)$1	222	185	207	20.5870
CUGCUGCAAACAUAUAGAGCAG	chr3:184714183-184714399(-)$1	216	154	176	23.0519
CCUGGCAGUAACCCCGAGCCAG	chr1:15821845-15822063(-)$1	218	169	191	20.5870
ACAACUUACCAUCCUCCGUUGC	chr14:75248692-75248910(+)$1	218	100	122	20.4169
AGAGUAAUUGAUUUAUACAUCU	chr5:42800899-42801133(+)$1	234	209	231	20.6090
AGCCCUUAUAAUUCACAAGGCA	chr19:53856039-53856255(+)$1	216	0	22	19.3983
CCGGCUCGUCCCGCCCUCGCCC	chr16:324932-325163(-)$1	231	19	41	23.1009
GCCUGCGCAGCCCCAGAAGGCC	chr2:241512554-241512801(-)$1	247	84	106	21.4460
AGAGCACCUUUCUAUAAGCUUU	chr21:34861247-34861465(+)$1	218	143	165	23.2339
AGGCAUCGAUGAAACUUGCAUA	chr3:122288101-122288319(-)$1	218	62	84	21.4374
UUCAGCUAUCAAAAAAACCCAC	chr7:105122702-105122921(-)$1	219	95	117	20.1080
UCGAAUCCCUAUGUCCAGUUUG	chr10:87614250-87614472(-)$1	222	148	170	22.1196
CUACCACAUUGAUGACCUGGAG	chr2:101582053-101582276(+)$1	223	128	150	21.4235
AUGGGGAAGACAUCCAACCCAU	chr14:102900912-102901136(+)$1	224	118	140	22.2348
CUGCCAAGGCAUCAUCAAGGUA	chr15:29398809-29399028(+)$1	219	194	216	21.9051
GGUUCACUUUCUUACACACUAU	chr17:61831703-61831935(-)$1	232	59	81	19.8912
UGAGGAAUUUAAAUCCACCUUC	chr3:28378181-28378411(-)$1	230	38	60	21.2737
GUUGGCCAUUUUCAAAACCAGC	chr10:76936255-76936475(+)$1	220	148	170	23.2339
CAGCCCUACCAGCACCUGAUCU	chr12:107713702-107713924(+)$1	222	110	132	21.6320
UAGGGCCCCaaauauuauuuua	chr1:76211453-76211679(+)$1	226	166	188	23.2156
UGGCCUUAGAAUACCAGGUGGU	chr8:110099745-110099962(+)$1	217	54	76	21.4846
CAGCAGAAGAGGCCAAUGCGGU	chr5:134223469-134223694(+)$1	225	32	54	21.2570
CGCGGGAACUAACACUACCUCG	chrX:56590561-56590795(+)$1	234	98	120	21.6065
UCUUUAUAUACAUUUUUCAGAG	chr13:23915612-23915827(-)$1	215	167	189	20.1847
AACUACAUCCCUAUCUUCUAGC	chr16:67472305-67472552(-)$1	247	101	123	23.1009
CUCUGCUUUUGUUCCUUGCUAA	chr15:75558473-75558688(-)$1	215	77	99	21.0500
AUGAACUCUUACUUUUUGUUCU	chr12:46320605-46320823(+)$1	218	21	43	21.6156
AGUUUGAAAUACCUUUAAAACA	chr5:138650271-138650518(+)$1	247	159	181	22.3810
CCUGGAACCCCUAGCUAUCCCA	chr2:210574748-210574968(+)$1	220	5	27	20.6473
UUGAGUAAACGGAGCUUCUCAA	chr6:31600405-31600625(+)$1	220	182	204	21.3877
ACGGGCCACACACACUUCCCGC	chr10:100179719-100179942(-)$1	223	169	191	22.6129
GCGGGAUUUGGUGAGUUUCCCG	chr17:56769930-56770146(+)$1	216	106	128	22.2250
GUGGUGGAGCCCUACAACGCCA	chr19:6495844-6496080(-)$1	236	105	127	21.3755
CCAGGUACAAAGACAGGAGACU	chr11:88258405-88258637(-)$1	232	61	83	20.6090
GAGUGGUACCUCAACACCCACU	chr2:210574571-210574794(+)$1	223	94	116	21.5438
GGCGCAGUCAUUCUCAUAAUCG	chrM:11679-11899(+)$1	220	11	33	20.6090
GCUGUGCUCCAUCCCUGACGGC	chr1:119427461-119427682(+)$1	221	7	29	22.2348
CUUCCACACUUUUCAUUUGGAA	chr8:113650899-113651132(-)$1	233	5	27	21.3755
AGAGUCCAUCCCGAUCCGGCUC	chr11:134114745-134114969(+)$1	224	87	109	21.4549
UUUGCCACAUUCAUCACAUUUG	chr4:367268-367484(-)$1	216	136	158	20.1080
AGAUGGAAAAAUAUAAACUAUU	chrX:11139747-11139965(+)$1	218	194	216	21.3755
CCAGCACAAUGAAGAUCAAGGU	chr7:5567590-5567838(-)$1	248	184	206	20.7337
GGGACUGUCUAUGAAUCUGUCC	chr2:219029368-219029584(-)$1	216	132	154	21.9051
ACUGGCAAUAAAAGCAACCAGU	chr13:49084675-49084896(-)$1	221	76	98	22.2924
UUUUUUUUCCAUCUCAUAAGAA	chr2:10269383-10269614(+)$1	231	163	185	22.3572
UACAGAACAAUUUCUCACUUGC	chr8:48715837-48716076(-)$1	239	30	52	22.7948
CUGCAGGCAAUAUUUUAUCCAG	chr11:36458906-36459151(+)$1	245	93	115	20.9879
UGCAGACCCCACGCCAGCUGCC	chr2:218674462-218674697(-)$1	235	71	93	22.3944
GGCUUGGGGGAAUUUGGAAGGG	chr5:847528-847744(-)$1	216	151	173	22.6577

#DB
.((((...........))))..	chr16:56438779-56439009(-)$1	1	166	188	20.8244
((((..............))))	chr5:14405905-14406134(+)$1	1	167	189	20.4823
(((((.............))))	chr1:68620716-68620957(-)$1	1	1	23	21.9051
(.(((.............))).	chr7:99764657-99764872(-)$1	1	129	151	22.8272
.((((...........))))..	chr17:17769587-17769808(-)$1	1	84	106	20.6891
(((((............)))..	chr3:58555442-58555662(-)$1	1	127	149	23.1235
(.(((..............)))	chr6:17637608-17637836(-)$1	1	184	206	21.3473
((((................))	chr19:41112040-41112283(+)$1	1	71	93	21.1231
((((((...........)))))	chr2:55254440-55254666(-)$1	1	32	54	22.1196
((................))))	chr6:163990389-163990632(+)$1	1	108	130	20.0666
.((((.............))))	chr2:112588794-112589016(-)$1	1	163	185	20.9311
(((((...........))))))	chr17:55183974-55184201(+)$1	1	178	200	20.8087
...(((...........))).)	chr3:136196115-136196330(+)$1	1	30	52	22.1734
((((.............)))))	chr10:36811643-36811861(-)$1	1	33	55	22.1207
.(((((...........)))))	chr19:10369986-10370208(+)$1	1	185	207	20.5870
(((((............)))))	chr3:184714183-184714399(-)$1	1	154	176	23.0519
.(((((...........)))))	chr1:15821845-15822063(-)$1	1	169	191	20.5870
.((((............)))).	chr14:75248692-75248910(+)$1	1	100	122	20.4169
((((................))	chr5:42800899-42801133(+)$1	1	209	231	20.6090
.(((..............))).	chr19:53856039-53856255(+)$1	1	0	22	19.3983
..(((.............))).	chr16:324932-325163(-)$1	1	19	41	23.1009
((((.............)))))	chr2:241512554-241512801(-)$1	1	84	106	21.4460
(((((............)))))	chr21:34861247-34861465(+)$1	1	143	165	23.2339
..(((...........)))...	chr3:122288101-122288319(-)$1	1	62	84	21.4374
(((((................)	chr7:105122702-105122921(-)$1	1	95	117	20.1080
((((((...........)))))	chr10:87614250-87614472(-)$1	1	148	170	22.1196
((.(((...........)))))	chr2:101582053-101582276(+)$1	1	128	150	21.4235
(((((............)))))	chr14:102900912-102901136(+)$1	1	118	140	22.2348
(((((.............))))	chr15:29398809-29399028(+)$1	1	194	216	21.9051
(((..............)))))	chr17:61831703-61831935(-)$1	1	59	81	19.8912
(((((.............))))	chr3:28378181-28378411(-)$1	1	38	60	21.2737
(((((............)))))	chr10:76936255-76936475(+)$1	1	148	170	23.2339
(((..(...........)..))	chr12:107713702-107713924(+)$1	1	110	132	21.6320
(((((............)))))	chr1:76211453-76211679(+)$1	1	166	188	23.2156
(((((..............)))	chr8:110099745-110099962(+)$1	1	54	76	21.4846
(.(((...........))).))	chr5:134223469-134223694(+)$1	1	32	54	21.2570
((.((............)).))	chrX:56590561-56590795(+)$1	1	98	120	21.6065
(((((..............)))	chr13:23915612-23915827(-)$1	1	167	189	20.1847
..(((.............))).	chr16:67472305-67472552(-)$1	1	101	123	23.1009
((((((...........))...	chr15:75558473-75558688(-)$1	1	77	99	21.0500
..((((...........)))).	chr12:46320605-46320823(+)$1	1	21	43	21.6156
(((((............)))).	chr5:138650271-138650518(+)$1	1	159	181	22.3810
(((((..............)))	chr2:210574748-210574968(+)$1	1	5	27	20.6473
(((((............)))))	chr6:31600405-31600625(+)$1	1	182	204	21.3877
.((((............)))).	chr10:100179719-100179942(-)$1	1	169	191	22.6129
((((((...........)))))	chr17:56769930-56770146(+)$1	1	106	128	22.2250
((((((...........)))))	chr19:6495844-6496080(-)$1	1	105	127	21.3755
((((................))	chr11:88258405-88258637(-)$1	1	61	83	20.6090
.(((((...........)))))	chr2:210574571-210574794(+)$1	1	94	116	21.5438
((((................))	chrM:11679-11899(+)$1	1	11	33	20.6090
(((((............)))))	chr1:119427461-119427682(+)$1	1	7	29	22.2348
((((((...........)))))	chr8:113650899-113651132(-)$1	1	5	27	21.3755
((((((...........)))))	chr11:134114745-134114969(+)$1	1	87	109	21.4549
(((((................)	chr4:367268-367484(-)$1	1	136	158	20.1080
((((((...........)))))	chrX:11139747-11139965(+)$1	1	194	216	21.3755
(((.(..............).)	chr7:5567590-5567838(-)$1	1	184	206	20.7337
(((((.............))))	chr2:219029368-219029584(-)$1	1	132	154	21.9051
(((((............)))))	chr13:49084675-49084896(-)$1	1	76	98	22.2924
((((((...........)))))	chr2:10269383-10269614(+)$1	1	163	185	22.3572
(((((.............))).	chr8:48715837-48716076(-)$1	1	30	52	22.7948
(((................)))	chr11:36458906-36459151(+)$1	1	93	115	20.9879
.((((............)))).	chr2:218674462-218674697(-)$1	1	71	93	22.3944
..(((.............))).	chr5:847528-847744(-)$1	1	151	173	22.6577

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

#score	1357.8129675107962
#seq	63
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m3_run2.txt

#BEAR
bb"""ddddoooooodddd333b	chr3:121193134-121193389(-)$1	255	70	93	12.1894
ffffff[bboooooobb]fffff	chr5:129043980-129044230(+)$1	250	73	96	11.5546
"ccc[ddddoooooodddd]ccc	chr17:27082996-27083279(-)$1	283	248	271	12.3760
fffff!!bboooooobb22ffff	chr17:3567019-3567265(-)$1	246	178	201	11.4757
=========oooooo========	chr18:60194725-60194961(+)$1	236	179	202	13.6776
llddddcccooooooccceeeee	chr6:41802013-41802322(-)$1	309	44	67	10.9299
hhhhh!!bboooooobb]hhhhh	chr4:153566307-153566537(-)$1	230	12	35	11.0342
f!!dddd[aooooooadddd]ff	chr1:110926285-110926510(-)$1	225	133	156	12.3053
:dddd[cccooooooccc]dddd	chr3:126503164-126503455(+)$1	291	7	30	10.5798
"""ffffffooooooffffff44	chrX:64207372-64207608(-)$1	236	58	81	12.4884
c!!ffffffooooooffffff]c	chr18:180418-180706(+)$1	288	49	72	12.4235
ggggggg[aooooooa]gggggg	chr16:4023029-4023283(-)$1	254	170	193	13.3254
####eeeeeooooooeeeee444	chr10:74487239-74487475(+)$1	236	65	88	12.9656
####eeeeeooooooeeeee22f	chr15:76698246-76698494(-)$1	248	81	104	12.6625
b"""eeeeeooooooeeeee333	chr2:230681267-230681506(-)$1	239	41	64	13.3561
c"""eeeeeooooooeeeee444	chr15:80419894-80420145(+)$1	251	136	159	13.0895
bccc!!cccooooooccc22ccc	chr9:97667852-97668200(+)$1	348	85	108	12.5708
d[ccc!!bboooooobb22ccc9	chr16:30505777-30506053(+)$1	276	240	263	11.7082
ccc!!ddddoooooodddd]ccc	chr11:66310120-66310379(-)$1	259	81	104	12.4366
iiiiiiiiiooooooiiiiiiii	chr1:36437853-36438091(+)$1	238	78	101	13.2115
b[gggggggooooooggggggg]	chr1:53709451-53709805(-)$1	354	113	136	13.5217
##gggggggooooooggggggg8	chr1:225415474-225415734(+)$1	260	106	129	13.1003
dddffffffooooooffffff]d	chr4:57291818-57292065(-)$1	247	210	233	11.1944
ccc[a!!bboooooobb22accc	chr4:113303862-113304095(+)$1	233	69	92	12.2130
!!dddd!!aooooooa22dddd]	chr12:88526042-88526333(-)$1	291	216	239	11.8119
d!!ccc[bboooooobb]cccdd	chr10:26799617-26799913(+)$1	296	87	110	12.3113
gggggg!!aooooooa]gggggg	chr6:128793344-128793623(-)$1	279	203	226	13.3714
cc!!eeeeeooooooeeeee666	chr11:9847763-9848011(-)$1	248	68	91	11.4885
b[bb!!cccooooooccc22bb]	chr18:59740945-59741221(-)$1	276	245	268	12.1665
ccbb[ddddooooooddddbb22	chr12:120606197-120606445(-)$1	248	104	127	11.1739
eeeee!!bboooooobb]eeeee	chr4:119731192-119731435(-)$1	243	80	103	11.7051
ggggggg[aooooooaggggggg	chr11:102303731-102303993(-)$1	262	44	67	13.3922
"""ffffffooooooffffff22	chr1:115293252-115293501(-)$1	249	205	228	12.2631
====[ddddoooooodddd22==	chr2:144506469-144506755(+)$1	286	79	102	12.5130
gggg[bb[aooooooa]bb]ggg	chr10:7373535-7373762(-)$1	227	199	222	11.9265
c[bb[ddddoooooodddd]bb]	chr4:119149335-119149617(+)$1	282	23	46	11.9225
"""bb[cccoooooocccbb]ff	chr12:46288556-46288851(+)$1	295	240	263	12.0758
e[bb[eeeeeooooooeeeee22	chr1:243937609-243937864(-)$1	255	30	53	10.4441
ggggggg[aooooooa]gggggg	chr8:27662015-27662246(+)$1	231	70	93	13.3254
iiiiiiiiiooooooiiiiiiii	chr14:59941330-59941611(-)$1	281	184	207	13.2115
:ccc!!cccooooooccc333cc	chr2:191357950-191358189(+)$1	239	2	25	12.3365
hhhhhddddoooooodddd]hhh	chr10:34790655-34790891(-)$1	236	153	176	10.8503
""gggggggooooooggggggg]	chr22:22185692-22185986(-)$1	294	94	117	13.6643
::gggggggoooooogggggggd	chr14:23520101-23520346(-)$1	245	36	59	11.2450
e"""eeeeeooooooeeeeeeee	chr3:169513386-169513616(-)$1	230	55	78	12.4896
iiiiiiiiiooooooiiiiiiii	chr3:99747492-99747893(+)$1	401	219	242	13.2115
b"""eeeeeooooooeeeee22b	chr3:136651258-136651594(+)$1	336	280	303	12.5112
cc!!eeeeeooooooeeeee22c	chr9:102928757-102929012(+)$1	255	217	240	12.6007
b[eeeeebboooooobb]eeeee	chr3:49107177-49107429(-)$1	252	135	158	11.9717
b[dddd[bboooooobbddddbb	chr5:38548340-38548579(-)$1	239	83	106	11.1516
ffffff[bboooooobbffffff	chr6:38513584-38513918(-)$1	334	219	242	11.4486
ii$$$$$bboooooobbiiiiii	chr1:200627803-200628059(-)$1	256	24	47	11.8223
g[a"""cccooooooccc333a]	chr15:45324472-45324733(+)$1	261	142	165	13.4882
::gggggggooooooggggggg:	chr7:73596923-73597200(+)$1	277	57	80	10.5588
cc[ffffffooooooffffff]c	chr2:48120315-48120549(-)$1	234	70	93	12.0603
g[bb[ddddoooooodddd]bb]	chr5:102526930-102527186(+)$1	256	157	180	11.8985
eee[ccc[aooooooa]ccc]ee	chr2:10290607-10290940(+)$1	333	268	291	12.1135
eeeccccccooooooccc]ccc]	chr21:36226832-36227104(-)$1	272	243	266	12.2743
d:gggggggooooooggggggg:	chr19:38432403-38432657(+)$1	254	108	131	11.2130

#otherMatches

#Seq PSSM
UAUAGUAGAUAAUGUUCUGAAUU	chr3:121193134-121193389(-)$1	255	70	93	12.1894
UUCUUCGGAUCUUUCUUGGGAGA	chr5:129043980-129044230(+)$1	250	73	96	11.5546
GAUUAUUAUAAACCAGUAAAAAU	chr17:27082996-27083279(-)$1	283	248	271	12.3760
GCGGCAGUCGCUGCAGAAGGCCG	chr17:3567019-3567265(-)$1	246	178	201	11.4757
CAGUAGUGAAGUCACUCACUACU	chr18:60194725-60194961(+)$1	236	179	202	13.6776
cagucaccucccaccaggcccca	chr6:41802013-41802322(-)$1	309	44	67	10.9299
ACAGGAACUAAAAACAGGCUUGU	chr4:153566307-153566537(-)$1	230	12	35	11.0342
ccuggggacuagauugccuuugu	chr1:110926285-110926510(-)$1	225	133	156	12.3053
UCUGAAAACUUCCCUGUUCUCAG	chr3:126503164-126503455(+)$1	291	7	30	10.5798
uccaaaagguuuucuccuuuuuu	chrX:64207372-64207608(-)$1	236	58	81	12.4884
uuuaaugcuuuuuauaguauuua	chr18:180418-180706(+)$1	288	49	72	12.4235
AUGGAAAACAUUUAAGAUUUUCA	chr16:4023029-4023283(-)$1	254	170	193	13.3254
UCAUAAAGCCUCUUUGCUUUCUC	chr10:74487239-74487475(+)$1	236	65	88	12.9656
AUUUCCUUUACUAGAAGAGGUCU	chr15:76698246-76698494(-)$1	248	81	104	12.6625
CAGUUAAAAUUUAGUUUUUAUUA	chr2:230681267-230681506(-)$1	239	41	64	13.3561
uaaucaauaacaaaguauuguca	chr15:80419894-80420145(+)$1	251	136	159	13.0895
UCUUGUUAAAAUCUGUUAUAAAG	chr9:97667852-97668200(+)$1	348	85	108	12.5708
CUGCCUCUCCCCACAGAUUGGCU	chr16:30505777-30506053(+)$1	276	240	263	11.7082
AGUCCCGGCCCUUCAGCCGCACU	chr11:66310120-66310379(-)$1	259	81	104	12.4366
UUGUUCAACUGAAAUGUUGAACA	chr1:36437853-36438091(+)$1	238	78	101	13.2115
UCCAGUUAUCUCAGUAUGACUGC	chr1:53709451-53709805(-)$1	354	113	136	13.5217
uuaugggagcuaauauuuccauu	chr1:225415474-225415734(+)$1	260	106	129	13.1003
cuaucugggaacccaccuagagu	chr4:57291818-57292065(-)$1	247	210	233	11.1944
CAGUGAGUCUAACAUGAACCCUG	chr4:113303862-113304095(+)$1	233	69	92	12.2130
UCUUUAUUAUAGACUUUUUAAAU	chr12:88526042-88526333(-)$1	291	216	239	11.8119
aAAUGAAAAUUAGAUUUAUCAUG	chr10:26799617-26799913(+)$1	296	87	110	12.3113
AGAAGCAACACAACCGGGCUUCU	chr6:128793344-128793623(-)$1	279	203	226	13.3714
ugccuuuaguuaacucugaauau	chr11:9847763-9848011(-)$1	248	68	91	11.4885
UAAUAAGGGUAGCUUCCCAAAUC	chr18:59740945-59741221(-)$1	276	245	268	12.1665
CCGGAUGAGAAGCAGUUCACCUA	chr12:120606197-120606445(-)$1	248	104	127	11.1739
guucuuacaauagucugcaggac	chr4:119731192-119731435(-)$1	243	80	103	11.7051
gugucuguggcuuuuccagacac	chr11:102303731-102303993(-)$1	262	44	67	13.3922
AUAGUCUGUGACAUAAUAGAUAC	chr1:115293252-115293501(-)$1	249	205	228	12.2631
CCCUACAAGUCAGCUUUUGAGAG	chr2:144506469-144506755(+)$1	286	79	102	12.5130
CCACAGUGGACAGGGCGGCAGUG	chr10:7373535-7373762(-)$1	227	199	222	11.9265
AUGACAAAUACUUACAUUUUUCU	chr4:119149335-119149617(+)$1	282	23	46	11.9225
ccuucaugauucaguucagacau	chr12:46288556-46288851(+)$1	295	240	263	12.0758
UAUGCUUCUGGAACCACAGAAAU	chr1:243937609-243937864(-)$1	255	30	53	10.4441
CAAAACAUUGUUCAAAUUGUUUU	chr8:27662015-27662246(+)$1	231	70	93	13.3254
uuaucguuuuucaauagaugaua	chr14:59941330-59941611(-)$1	281	184	207	13.2115
agcuauucuuacaucagacaaag	chr2:191357950-191358189(+)$1	239	2	25	12.3365
ccuuaaucacauguaugauguaa	chr10:34790655-34790891(-)$1	236	153	176	10.8503
AAAGGGUUGGUGcagugacucuc	chr22:22185692-22185986(-)$1	294	94	117	13.6643
CCGUGUGUGUCCGUGUACACACA	chr14:23520101-23520346(-)$1	245	36	59	11.2450
AAUUAGAAAACUAAGUUUCUUGG	chr3:169513386-169513616(-)$1	230	55	78	12.4896
AUACACCUUUUUACUGAGGUGUG	chr3:99747492-99747893(+)$1	401	219	242	13.2115
auccuggaaagucccuucuaacu	chr3:136651258-136651594(+)$1	336	280	303	12.5112
auuuaucuacaaaccuagauuua	chr9:102928757-102929012(+)$1	255	217	240	12.6007
cagcucacauuaccuugaugagc	chr3:49107177-49107429(-)$1	252	135	158	11.9717
GAUGUUACAUCUUACUGAACACA	chr5:38548340-38548579(-)$1	239	83	106	11.1516
cuguucucaaaccccuggagcag	chr6:38513584-38513918(-)$1	334	219	242	11.4486
UUUUAAAGCAUUGCAGCAGGUUC	chr1:200627803-200628059(-)$1	256	24	47	11.8223
UCCCAAGACACCUCAGUCCCAGC	chr15:45324472-45324733(+)$1	261	142	165	13.4882
acagUCCCAAAGUGCUGGGACUA	chr7:73596923-73597200(+)$1	277	57	80	10.5588
ugauuuauauauauuuauaAAAC	chr2:48120315-48120549(-)$1	234	70	93	12.0603
UAAGUAGUUAGAAAGAGCUUUUA	chr5:102526930-102527186(+)$1	256	157	180	11.8985
auagaauccuacaguguguugug	chr2:10290607-10290940(+)$1	333	268	291	12.1135
ugcccaugcuggagugcaguggu	chr21:36226832-36227104(-)$1	272	243	266	12.2743
AGCCCUGGUAACCUGGCCAGGGG	chr19:38432403-38432657(+)$1	254	108	131	11.2130

#DB
((...((((......))))...)	chr3:121193134-121193389(-)$1	1	70	93	12.1894
((((((.((......)).)))))	chr5:129043980-129044230(+)$1	1	73	96	11.5546
.(((.((((......)))).)))	chr17:27082996-27083279(-)$1	1	248	271	12.3760
(((((..((......))..))))	chr17:3567019-3567265(-)$1	1	178	201	11.4757
(((((((((......))))))))	chr18:60194725-60194961(+)$1	1	179	202	13.6776
..))))(((......)))(((((	chr6:41802013-41802322(-)$1	1	44	67	10.9299
(((((..((......)).)))))	chr4:153566307-153566537(-)$1	1	12	35	11.0342
(..((((.(......))))).))	chr1:110926285-110926510(-)$1	1	133	156	12.3053
.((((.(((......))).))))	chr3:126503164-126503455(+)$1	1	7	30	10.5798
...((((((......))))))..	chrX:64207372-64207608(-)$1	1	58	81	12.4884
(..((((((......)))))).)	chr18:180418-180706(+)$1	1	49	72	12.4235
(((((((.(......).))))))	chr16:4023029-4023283(-)$1	1	170	193	13.3254
....(((((......)))))...	chr10:74487239-74487475(+)$1	1	65	88	12.9656
....(((((......)))))..)	chr15:76698246-76698494(-)$1	1	81	104	12.6625
(...(((((......)))))...	chr2:230681267-230681506(-)$1	1	41	64	13.3561
(...(((((......)))))...	chr15:80419894-80420145(+)$1	1	136	159	13.0895
((((..(((......)))..)))	chr9:97667852-97668200(+)$1	1	85	108	12.5708
(.(((..((......))..))).	chr16:30505777-30506053(+)$1	1	240	263	11.7082
(((..((((......)))).)))	chr11:66310120-66310379(-)$1	1	81	104	12.4366
(((((((((......))))))))	chr1:36437853-36438091(+)$1	1	78	101	13.2115
(.(((((((......))))))).	chr1:53709451-53709805(-)$1	1	113	136	13.5217
..(((((((......))))))).	chr1:225415474-225415734(+)$1	1	106	129	13.1003
(((((((((......)))))).)	chr4:57291818-57292065(-)$1	1	210	233	11.1944
(((.(..((......))..))))	chr4:113303862-113304095(+)$1	1	69	92	12.2130
..((((..(......)..)))).	chr12:88526042-88526333(-)$1	1	216	239	11.8119
(..(((.((......)).)))))	chr10:26799617-26799913(+)$1	1	87	110	12.3113
((((((..(......).))))))	chr6:128793344-128793623(-)$1	1	203	226	13.3714
((..(((((......)))))...	chr11:9847763-9848011(-)$1	1	68	91	11.4885
(.((..(((......)))..)).	chr18:59740945-59741221(-)$1	1	245	268	12.1665
((((.((((......))))))..	chr12:120606197-120606445(-)$1	1	104	127	11.1739
(((((..((......)).)))))	chr4:119731192-119731435(-)$1	1	80	103	11.7051
(((((((.(......))))))))	chr11:102303731-102303993(-)$1	1	44	67	13.3922
...((((((......))))))..	chr1:115293252-115293501(-)$1	1	205	228	12.2631
((((.((((......))))..))	chr2:144506469-144506755(+)$1	1	79	102	12.5130
((((.((.(......).)).)))	chr10:7373535-7373762(-)$1	1	199	222	11.9265
(.((.((((......)))).)).	chr4:119149335-119149617(+)$1	1	23	46	11.9225
...((.(((......))))).))	chr12:46288556-46288851(+)$1	1	240	263	12.0758
(.((.(((((......)))))..	chr1:243937609-243937864(-)$1	1	30	53	10.4441
(((((((.(......).))))))	chr8:27662015-27662246(+)$1	1	70	93	13.3254
(((((((((......))))))))	chr14:59941330-59941611(-)$1	1	184	207	13.2115
.(((..(((......)))...))	chr2:191357950-191358189(+)$1	1	2	25	12.3365
(((((((((......)))).)))	chr10:34790655-34790891(-)$1	1	153	176	10.8503
..(((((((......))))))).	chr22:22185692-22185986(-)$1	1	94	117	13.6643
..(((((((......)))))))(	chr14:23520101-23520346(-)$1	1	36	59	11.2450
(...(((((......))))))))	chr3:169513386-169513616(-)$1	1	55	78	12.4896
(((((((((......))))))))	chr3:99747492-99747893(+)$1	1	219	242	13.2115
(...(((((......)))))..)	chr3:136651258-136651594(+)$1	1	280	303	12.5112
((..(((((......)))))..)	chr9:102928757-102929012(+)$1	1	217	240	12.6007
(.(((((((......)).)))))	chr3:49107177-49107429(-)$1	1	135	158	11.9717
(.((((.((......))))))))	chr5:38548340-38548579(-)$1	1	83	106	11.1516
((((((.((......))))))))	chr6:38513584-38513918(-)$1	1	219	242	11.4486
((.....((......))))))))	chr1:200627803-200628059(-)$1	1	24	47	11.8223
(.(...(((......)))...).	chr15:45324472-45324733(+)$1	1	142	165	13.4882
..(((((((......))))))).	chr7:73596923-73597200(+)$1	1	57	80	10.5588
((.((((((......)))))).)	chr2:48120315-48120549(-)$1	1	70	93	12.0603
(.((.((((......)))).)).	chr5:102526930-102527186(+)$1	1	157	180	11.8985
(((.(((.(......).))).))	chr2:10290607-10290940(+)$1	1	268	291	12.1135
(((((((((......))).))).	chr21:36226832-36227104(-)$1	1	243	266	12.2743
).(((((((......))))))).	chr19:38432403-38432657(+)$1	1	108	131	11.2130

#PSSM
c : 0.15	b : 0.13	g : 0.11	" : 0.08	e : 0.08	f : 0.06	: : 0.06	d : 0.06	i : 0.06	# : 0.05	= : 0.03	h : 0.03	l : 0.01	! : 0.01	
c : 0.15	[ : 0.15	" : 0.13	g : 0.08	! : 0.06	i : 0.06	f : 0.05	# : 0.05	e : 0.05	: : 0.05	= : 0.03	h : 0.03	d : 0.03	b : 0.01	l : 0.01	
g : 0.18	" : 0.13	c : 0.10	d : 0.08	! : 0.08	b : 0.08	e : 0.06	f : 0.05	i : 0.05	= : 0.03	h : 0.03	# : 0.03	$ : 0.01	a : 0.01	[ : 0.01	
g : 0.18	f : 0.13	" : 0.10	c : 0.10	b : 0.10	d : 0.08	! : 0.05	i : 0.05	= : 0.03	h : 0.03	# : 0.03	[ : 0.03	e : 0.03	$ : 0.01	
g : 0.16	e : 0.16	f : 0.13	[ : 0.11	d : 0.08	! : 0.06	c : 0.06	i : 0.05	" : 0.03	h : 0.03	= : 0.01	a : 0.01	b : 0.01	$ : 0.01	
d : 0.20	g : 0.16	e : 0.16	! : 0.13	f : 0.11	i : 0.05	c : 0.05	[ : 0.03	= : 0.01	b : 0.01	$ : 0.01	" : 0.01	
e : 0.16	d : 0.15	c : 0.15	g : 0.15	! : 0.11	f : 0.08	[ : 0.06	i : 0.05	= : 0.01	b : 0.01	$ : 0.01	
b : 0.18	e : 0.15	d : 0.13	c : 0.13	[ : 0.10	g : 0.10	f : 0.08	i : 0.05	! : 0.03	= : 0.01	
b : 0.18	e : 0.15	d : 0.13	c : 0.13	a : 0.13	g : 0.10	f : 0.08	i : 0.05	= : 0.01	
o : 0.98	e : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
b : 0.18	d : 0.13	c : 0.13	a : 0.13	e : 0.13	g : 0.10	f : 0.08	i : 0.05	= : 0.01	o : 0.01	
b : 0.18	d : 0.15	e : 0.15	c : 0.13	g : 0.11	f : 0.08	] : 0.08	i : 0.05	= : 0.01	2 : 0.01	
d : 0.16	g : 0.16	c : 0.15	e : 0.15	f : 0.10	] : 0.08	2 : 0.06	i : 0.06	= : 0.01	b : 0.01	
e : 0.20	d : 0.18	g : 0.16	f : 0.11	2 : 0.08	i : 0.06	] : 0.03	c : 0.03	b : 0.03	3 : 0.03	= : 0.01	h : 0.01	
e : 0.20	g : 0.16	f : 0.13	] : 0.10	d : 0.06	c : 0.06	i : 0.06	3 : 0.05	2 : 0.05	b : 0.03	= : 0.01	h : 0.01	a : 0.01	
g : 0.18	f : 0.13	c : 0.11	e : 0.08	3 : 0.06	2 : 0.06	i : 0.06	b : 0.06	] : 0.05	d : 0.05	h : 0.03	4 : 0.03	= : 0.01	6 : 0.01	
g : 0.18	c : 0.11	2 : 0.10	f : 0.08	e : 0.08	i : 0.06	b : 0.06	d : 0.05	4 : 0.05	] : 0.05	3 : 0.03	= : 0.03	h : 0.03	6 : 0.01	a : 0.01	
c : 0.13	] : 0.13	f : 0.10	e : 0.08	g : 0.08	d : 0.06	i : 0.06	b : 0.05	4 : 0.05	2 : 0.05	= : 0.03	h : 0.03	: : 0.03	3 : 0.01	9 : 0.01	8 : 0.01	6 : 0.01	

#score	720.4050723478061
#seq	59
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m3_run2.txt

#BEAR
hh[bb"""ddddmmmmdddd]bb]hhhh	chr8:126034378-126034615(+)$1	237	134	162	13.0325
dd!!a"""ddddmmmmdddd333a22dd	chr1:155629298-155629544(-)$1	246	103	131	15.4441
bb[ccc[eeeeemmmmeeeeeccc]bbd	chr16:57484948-57485175(+)$1	227	48	76	10.5408
eeeeccc[ddddmmmmddddccc]eeee	chr1:156712361-156712613(-)$1	252	150	178	12.9507
[eeeee"""ddddllldddd333eeeee	chr5:10264762-10265010(+)$1	248	79	107	11.7471
cc[dddd!!ddddllldddd22dddd33	chr19:7550739-7550960(+)$1	221	105	133	10.9005
Gccc!!ccccccmmmmccc]ccc22ccc	chr11:122932712-122932949(-)$1	237	45	73	10.4935
[gggggggddddmmmmdddd22gggggg	chr17:45229154-45229381(+)$1	227	104	132	13.9230
ggggggg!!cccmmmmccc333gggggg	chrX:69664885-69665114(+)$1	229	158	186	12.4824
dddccc[eeeeemmmmeeeeeccc22dd	chr11:66278062-66278296(+)$1	234	198	226	10.8211
fffff"""ddddmmmmdddd4444ffff	chr14:91738993-91739215(+)$1	222	94	122	14.4455
"dddd"""ddddmmmmdddddddd333e	chr21:18941523-18941753(+)$1	230	171	199	13.9306
gggg"""eeeeemmmmeeeee333gggg	chr13:96295324-96295547(+)$1	223	47	75	13.1408
dddd[cccddddmmmmdddd22ccc]dd	chr16:14761778-14762008(+)$1	230	149	177	13.4196
hhhhhhh[ddddmmmmdddd]hhhhhhh	chr16:3708002-3708252(-)$1	250	74	102	11.1877
[dddd!!ccc[ammmma]ccc]ddddee	chr12:72278568-72278796(+)$1	228	181	209	10.4647
[dddd!!eeeeemmmmeeeee4444ddd	chr15:83478376-83478611(+)$1	235	136	164	11.9370
'ccc####ddddmmmmdddd666666cc	chr12:39242257-39242487(-)$1	230	170	198	12.1911
dd$$$$$eeeeemmmmeeeee333dddd	chr3:149679722-149679946(+)$1	224	158	186	11.4745
ffff####ddddllldddd4444fffff	chr8:97285425-97285653(+)$1	228	20	48	11.4974
b!!ccc"""cccmmmmccc4444ccc22	chr19:7115370-7115639(-)$1	269	121	149	12.7680
!ggggggg[cccmmmmcccggggggg]d	chr1:114301757-114301991(-)$1	234	165	193	11.0218
!!dddd!!ddddmmmmdddd22dddd22	chr7:27881995-27882219(+)$1	224	143	171	13.8522
ggggggg[ddddmmmmdddd]ggggggg	chr17:40175857-40176105(+)$1	248	34	62	13.9490
fffff"""ddddmmmmddddffffff]a	chr19:42703312-42703545(-)$1	233	181	209	13.3257
g[bb"""eeeeemmmmeeeeebb]gggg	chr17:42395600-42395827(+)$1	227	166	194	11.3106
ffffff"""cccmmmmccc4444fffff	chr8:18390254-18390491(-)$1	237	123	151	11.5301
cc[a[ccc[cccmmmmcccccc]a]ccc	chr9:113018660-113018886(-)$1	226	4	32	11.3241
eeee[a[eeeeemmmmeeeee]aeeeee	chr19:19101815-19102045(-)$1	230	28	56	11.1693
[ggggggg[cccmmmmccc22ggggggg	chr6:131931185-131931449(-)$1	264	59	87	11.1853
fff$$$$$ddddmmmmddddffffffgg	chr9:110062321-110062567(+)$1	246	91	119	12.6724
gggggg!!ddddmmmmdddd22gggggg	chrX:149934745-149934999(-)$1	254	112	140	14.7097
bdddd####ddddllldddd333dddd3	chr3:170584131-170584373(-)$1	242	137	165	11.8330
ff!!ccc!!cccmmmmcccccc]fffff	chr20:1286838-1287064(-)$1	226	89	117	11.1577
hhhhh[a[ddddmmmmdddd333a333h	chr11:18387366-18387597(+)$1	231	134	162	14.5385
c####adddd[ammmmadddd]a4444c	chr7:2770589-2770827(-)$1	238	178	206	12.1415
cc"""gggggggmmmmggggggg4444c	chr22:42334747-42335005(-)$1	258	207	235	10.5082
f[ccc!!eeeeemmmmeeeee22ccc]f	chr12:123756313-123756557(+)$1	244	189	217	12.1261
eccc[a[ddddnnnnndddd]accc444	chr4:1205789-1206038(-)$1	249	79	107	10.1160
""ccc[a[ddddmmmmdddd]a]ccc33	chr11:125453374-125453617(+)$1	243	138	166	14.6395
a!!a[cccddddmmmmdddd]ccc]a22	chr19:58024311-58024534(-)$1	223	112	140	13.9235
d!!ccc!!ddddmmmmdddd]ccc]ddd	chr11:68522281-68522504(-)$1	223	74	102	14.5609
bccc####ddddmmmmdddd333ccc]b	chr9:134323029-134323279(+)$1	250	188	216	15.4100
ddd"""dddd[ammmmaddddddddeee	chr15:88521544-88521770(-)$1	226	34	62	11.1897
eeee[bb[ddddmmmmdddd]bbeeeee	chr1:235490645-235490867(+)$1	222	128	156	12.5517
a[dddd"""cccmmmmccc333dddd]a	chr4:1205380-1205628(-)$1	248	180	208	12.1165
dd[dddd[ddddmmmmdddd]dddd]dd	chr7:143004198-143004438(+)$1	240	151	179	12.6324
ea$$$$$eeeeemmmmeeeee22a]eee	chr6:7891778-7892008(-)$1	230	132	160	11.2506
cc"""bb[ddddmmmmdddd]bb66666	chr2:191798648-191798888(+)$1	240	190	218	11.3812
:::ccc!!ddddmmmmdddd22cccggg	chr1:77557443-77557672(-)$1	229	157	185	11.8587
[eeeee!!ddddmmmmdddd]eeeee22	chr3:48731122-48731352(-)$1	230	165	193	13.2431
[bb!!bb[ddddmmmmdddd]bb22bb]	chr12:117288642-117288872(+)$1	230	178	206	12.1240

#otherMatches

#Seq PSSM
AAUGAAGAAUGAACUUUCGUGUCUUUUU	chr8:126034378-126034615(+)$1	237	134	162	13.0325
AGAAUAAGAGUCUGGAGACUGGGagccu	chr1:155629298-155629544(-)$1	246	103	131	15.4441
CAGCUGUGGGGCUAAGGUCUUCAGAUGA	chr16:57484948-57485175(+)$1	227	48	76	10.5408
GGAUGCUUGGGAAGACUCCUAGCUGUCC	chr1:156712361-156712613(-)$1	252	150	178	12.9507
AGAAUGAUUUUGAAGAUUGAUGACAUUC	chr5:10264762-10265010(+)$1	248	79	107	11.7471
GACCUGGCGGGACACUGUUCAACCAGAA	chr19:7550739-7550960(+)$1	221	105	133	10.9005
GCCCCUUCUGGAAGGUUCUAAGAUAGGG	chr11:122932712-122932949(-)$1	237	45	73	10.4935
CCAGUUUGGCCGAUUCUGGCAACAGACU	chr17:45229154-45229381(+)$1	227	104	132	13.9230
GCAGUGCCAUGCACAAGCACCAGCACUG	chrX:69664885-69665114(+)$1	229	158	186	12.4824
CUCGGGCAGUCUGGAAGGACUCUUAAGA	chr11:66278062-66278296(+)$1	234	198	226	10.8211
GAGCCAAAUCGGGAGACCGACCUGGGCU	chr14:91738993-91739215(+)$1	222	94	122	14.4455
uauguacauauauCUUUAUAACAUUCCU	chr21:18941523-18941753(+)$1	230	171	199	13.9306
CAGGCCUCUCAUUUCUAUGGGUCUUCUG	chr13:96295324-96295547(+)$1	223	47	75	13.1408
AGCCACCUUCCUCACAGGGACUAGGAGG	chr16:14761778-14762008(+)$1	230	149	177	13.4196
GGUGGGCCGCUUGAAUGAGCUGCUUGUC	chr16:3708002-3708252(-)$1	250	74	102	11.1877
GAGAUAGCAAACUACUGAUUGAAUCUCU	chr12:72278568-72278796(+)$1	228	181	209	10.4647
GGGUGCCGGUCCGGGAGGGCCUCUUCGC	chr15:83478376-83478611(+)$1	235	136	164	11.9370
AGACAAUAUUACUAAUGUAAGGCAGGGU	chr12:39242257-39242487(-)$1	230	170	198	12.1911
AGUUUGAAUGUUAAUAAACAUGUUUUCC	chr3:149679722-149679946(+)$1	224	158	186	11.4745
UAGAACAUGGAAAUCUUCCUUCCUCUAG	chr8:97285425-97285653(+)$1	228	20	48	11.4974
UGACGGUCCUCAGUACUGAACUCCCGGA	chr19:7115370-7115639(-)$1	269	121	149	12.7680
CGGCUGCCUCCGAAGCUGGGGCGGCCUC	chr1:114301757-114301991(-)$1	234	165	193	11.0218
AAACAUGAAGCUUUGGAGCUAAAUGUGG	chr7:27881995-27882219(+)$1	224	143	171	13.8522
GCGGCUCCUUGGAUGGCUGAAGAGCUGC	chr17:40175857-40176105(+)$1	248	34	62	13.9490
CCCCCUUAGCCUCCGGAGGCGGGGGCUG	chr19:42703312-42703545(-)$1	233	181	209	13.3257
UGCCUUGGCAGCACGGGCUGCGGAAGAA	chr17:42395600-42395827(+)$1	227	166	194	11.3106
UGGUCAUAGUGUUGUUGCAAAAUUGACC	chr8:18390254-18390491(-)$1	237	123	151	11.5301
cgacgggcgcggagguccggccgggcgc	chr9:113018660-113018886(-)$1	226	4	32	11.3241
CGCGUGAUGUGUGGUGGCACAGCCGUGU	chr19:19101815-19102045(-)$1	230	28	56	11.1693
ACAGCACAAGCAGCGCUGCCCUGUGCUG	chr6:131931185-131931449(-)$1	264	59	87	11.1853
UUCCUAUAGGUGAAAGCACUGAAAGAGA	chr9:110062321-110062567(+)$1	246	91	119	12.6724
CAUCUGUUCACGUGCUUGUGUCCAGGUG	chrX:149934745-149934999(-)$1	254	112	140	14.7097
AGGAGACCUACGAACUUCGUUACUUCCA	chr3:170584131-170584373(-)$1	242	137	165	11.8330
GGCCGGGUUGGCCCUCGCUCCCUCCCCU	chr20:1286838-1287064(-)$1	226	89	117	11.1577
AGAUGACCUCACAGGAGUGAUAAGAAAC	chr11:18387366-18387597(+)$1	231	134	162	14.5385
CAAAAGGACAUGGAAACUGUCACGUUAG	chr7:2770589-2770827(-)$1	238	178	206	12.1415
cuccauuuaagguuuccuuugaacaaaa	chr22:42334747-42335005(-)$1	258	207	235	10.5082
cgcccgcAACUUGCCAAAGUUUGGGGGG	chr12:123756313-123756557(+)$1	244	189	217	12.1261
GAGGAGGCAUCUGUGUGGUGGCCCUGGC	chr4:1205789-1206038(-)$1	249	79	107	10.1160
UCUGCAGAGAAGUUCCCUUCACCGCAUC	chr11:125453374-125453617(+)$1	243	138	166	14.6395
GUUCGGGCGccacuuguggcugucgguu	chr19:58024311-58024534(-)$1	223	112	140	13.9235
UGCUCUUUGGAUGUAAAUCUUAGAAAUG	chr11:68522281-68522504(-)$1	223	74	102	14.5609
GACGGGCAGGACCAAAGUCCAUAUGUAC	chr9:134323029-134323279(+)$1	250	188	216	15.4100
GGAAUCAGGGACAAAGGCCCUUCCUGCC	chr15:88521544-88521770(-)$1	226	34	62	11.1897
UGGGAGCGAGAUCAACAUCUGGCCCCGC	chr1:235490645-235490867(+)$1	222	128	156	12.5517
CGAAGCAGCUCCAAAAGGAAAAGCUUGG	chr4:1205380-1205628(-)$1	248	180	208	12.1165
aucauguaccaagugcuuggcacauagu	chr7:143004198-143004438(+)$1	240	151	179	12.6324
CCGAAACUGUCAAGAUUGGCAAGGUGAG	chr6:7891778-7892008(-)$1	230	132	160	11.2506
AAUUUCAAGUUUGUUGAAACCUGUUAAU	chr2:191798648-191798888(+)$1	240	190	218	11.3812
cacagucuucuauuguuggaccacuuac	chr1:77557443-77557672(-)$1	229	157	185	11.8587
GCCUACCCGUGUGGGGGCACUGUGGGAA	chr3:48731122-48731352(-)$1	230	165	193	13.2431
caaagcaugcagcauccugcuuggauua	chr12:117288642-117288872(+)$1	230	178	206	12.1240

#DB
((.((...((((....)))).)).))))	chr8:126034378-126034615(+)$1	1	134	162	13.0325
((..(...((((....))))...)..))	chr1:155629298-155629544(-)$1	1	103	131	15.4441
((.(((.(((((....)))))))).)))	chr16:57484948-57485175(+)$1	1	48	76	10.5408
(((((((.((((....))))))).))))	chr1:156712361-156712613(-)$1	1	150	178	12.9507
.(((((...((((...))))...)))))	chr5:10264762-10265010(+)$1	1	79	107	11.7471
((.((((..((((...))))..))))..	chr19:7550739-7550960(+)$1	1	105	133	10.9005
((((..((((((....))).)))..)))	chr11:122932712-122932949(-)$1	1	45	73	10.4935
.(((((((((((....))))..))))))	chr17:45229154-45229381(+)$1	1	104	132	13.9230
(((((((..(((....)))...))))))	chrX:69664885-69665114(+)$1	1	158	186	12.4824
((((((.(((((....))))))))..))	chr11:66278062-66278296(+)$1	1	198	226	10.8211
(((((...((((....))))....))))	chr14:91738993-91739215(+)$1	1	94	122	14.4455
.((((...((((....))))))))...)	chr21:18941523-18941753(+)$1	1	171	199	13.9306
((((...(((((....)))))...))))	chr13:96295324-96295547(+)$1	1	47	75	13.1408
((((.(((((((....))))..))).))	chr16:14761778-14762008(+)$1	1	149	177	13.4196
(((((((.((((....)))).)))))))	chr16:3708002-3708252(-)$1	1	74	102	11.1877
.((((..(((.(....).))).))))))	chr12:72278568-72278796(+)$1	1	181	209	10.4647
.((((..(((((....)))))....)))	chr15:83478376-83478611(+)$1	1	136	164	11.9370
.(((....((((....))))......))	chr12:39242257-39242487(-)$1	1	170	198	12.1911
((.....(((((....)))))...))))	chr3:149679722-149679946(+)$1	1	158	186	11.4745
((((....((((...))))....)))))	chr8:97285425-97285653(+)$1	1	20	48	11.4974
(..(((...(((....)))....)))..	chr19:7115370-7115639(-)$1	1	121	149	12.7680
.(((((((.(((....)))))))))).)	chr1:114301757-114301991(-)$1	1	165	193	11.0218
..((((..((((....))))..))))..	chr7:27881995-27882219(+)$1	1	143	171	13.8522
(((((((.((((....)))).)))))))	chr17:40175857-40176105(+)$1	1	34	62	13.9490
(((((...((((....)))))))))).)	chr19:42703312-42703545(-)$1	1	181	209	13.3257
(.((...(((((....))))))).))))	chr17:42395600-42395827(+)$1	1	166	194	11.3106
((((((...(((....)))....)))))	chr8:18390254-18390491(-)$1	1	123	151	11.5301
((.(.(((.(((....)))))).).)))	chr9:113018660-113018886(-)$1	1	4	32	11.3241
((((.(.(((((....))))).))))))	chr19:19101815-19102045(-)$1	1	28	56	11.1693
.(((((((.(((....)))..)))))))	chr6:131931185-131931449(-)$1	1	59	87	11.1853
(((.....((((....))))))))))))	chr9:110062321-110062567(+)$1	1	91	119	12.6724
((((((..((((....))))..))))))	chrX:149934745-149934999(-)$1	1	112	140	14.7097
(((((....((((...))))...)))).	chr3:170584131-170584373(-)$1	1	137	165	11.8330
((..(((..(((....)))))).)))))	chr20:1286838-1287064(-)$1	1	89	117	11.1577
(((((.(.((((....))))...)...)	chr11:18387366-18387597(+)$1	1	134	162	14.5385
(....(((((.(....))))).)....)	chr7:2770589-2770827(-)$1	1	178	206	12.1415
((...(((((((....)))))))....)	chr22:42334747-42335005(-)$1	1	207	235	10.5082
(.(((..(((((....)))))..))).)	chr12:123756313-123756557(+)$1	1	189	217	12.1261
((((.(.((((.....)))).))))...	chr4:1205789-1206038(-)$1	1	79	107	10.1160
..(((.(.((((....)))).).)))..	chr11:125453374-125453617(+)$1	1	138	166	14.6395
(..(.(((((((....)))).))).)..	chr19:58024311-58024534(-)$1	1	112	140	13.9235
(..(((..((((....)))).))).)))	chr11:68522281-68522504(-)$1	1	74	102	14.5609
((((....((((....))))...))).)	chr9:134323029-134323279(+)$1	1	188	216	15.4100
(((...((((.(....)))))))))(((	chr15:88521544-88521770(-)$1	1	34	62	11.1897
((((.((.((((....)))).)))))))	chr1:235490645-235490867(+)$1	1	128	156	12.5517
(.((((...(((....)))...)))).)	chr4:1205380-1205628(-)$1	1	180	208	12.1165
((.((((.((((....)))).)))).))	chr7:143004198-143004438(+)$1	1	151	179	12.6324
((.....(((((....)))))..).)))	chr6:7891778-7892008(-)$1	1	132	160	11.2506
((...((.((((....)))).)).....	chr2:191798648-191798888(+)$1	1	190	218	11.3812
...(((..((((....))))..)))(((	chr1:77557443-77557672(-)$1	1	157	185	11.8587
.(((((..((((....)))).)))))..	chr3:48731122-48731352(-)$1	1	165	193	13.2431
.((..((.((((....)))).))..)).	chr12:117288642-117288872(+)$1	1	178	206	12.1240

#PSSM
d : 0.13	[ : 0.13	f : 0.13	e : 0.09	c : 0.09	g : 0.09	b : 0.07	h : 0.05	" : 0.03	! : 0.03	a : 0.03	G : 0.01	' : 0.01	: : 0.01	
d : 0.19	c : 0.15	g : 0.13	f : 0.11	e : 0.09	! : 0.07	h : 0.05	[ : 0.05	b : 0.03	# : 0.01	" : 0.01	a : 0.01	: : 0.01	
d : 0.17	g : 0.13	c : 0.11	[ : 0.09	! : 0.09	e : 0.09	f : 0.09	h : 0.03	$ : 0.03	b : 0.03	" : 0.03	# : 0.01	: : 0.01	
c : 0.21	d : 0.17	g : 0.13	e : 0.09	f : 0.07	! : 0.05	$ : 0.05	" : 0.05	b : 0.03	h : 0.03	a : 0.03	# : 0.01	
c : 0.17	d : 0.15	g : 0.11	[ : 0.11	" : 0.09	# : 0.07	f : 0.05	$ : 0.05	e : 0.03	! : 0.03	h : 0.03	b : 0.01	a : 0.01	
c : 0.19	" : 0.15	g : 0.13	d : 0.07	! : 0.07	# : 0.07	$ : 0.05	a : 0.05	b : 0.05	e : 0.03	[ : 0.03	h : 0.01	f : 0.01	
" : 0.21	! : 0.15	c : 0.11	g : 0.11	[ : 0.07	d : 0.07	# : 0.07	$ : 0.05	b : 0.05	a : 0.03	h : 0.01	
" : 0.17	e : 0.17	[ : 0.17	! : 0.15	c : 0.09	g : 0.07	# : 0.07	d : 0.05	$ : 0.01	
d : 0.55	e : 0.17	" : 0.07	! : 0.05	[ : 0.05	c : 0.03	# : 0.01	g : 0.01	
d : 0.61	c : 0.19	e : 0.17	g : 0.01	
d : 0.57	e : 0.17	c : 0.17	[ : 0.05	g : 0.01	
d : 0.55	e : 0.17	c : 0.17	a : 0.05	g : 0.01	n : 0.01	
m : 0.90	d : 0.05	l : 0.01	n : 0.01	
m : 0.90	l : 0.07	n : 0.01	
m : 0.90	l : 0.07	n : 0.01	
m : 0.90	l : 0.05	d : 0.01	n : 0.01	
d : 0.57	e : 0.17	c : 0.17	a : 0.05	g : 0.01	
d : 0.61	e : 0.17	c : 0.17	] : 0.01	g : 0.01	
d : 0.61	c : 0.19	e : 0.17	g : 0.01	
d : 0.59	e : 0.17	c : 0.05	4 : 0.05	3 : 0.03	g : 0.03	] : 0.01	2 : 0.01	
] : 0.23	e : 0.17	3 : 0.13	2 : 0.13	c : 0.09	4 : 0.07	d : 0.05	g : 0.03	f : 0.03	6 : 0.01	
3 : 0.17	c : 0.15	2 : 0.15	b : 0.09	4 : 0.09	g : 0.07	d : 0.05	] : 0.05	f : 0.03	a : 0.03	h : 0.01	6 : 0.01	e : 0.01	
c : 0.17	3 : 0.13	d : 0.13	g : 0.13	b : 0.09	4 : 0.09	] : 0.05	f : 0.03	a : 0.03	2 : 0.03	h : 0.01	6 : 0.01	e : 0.01	
c : 0.21	d : 0.15	g : 0.11	f : 0.09	a : 0.07	e : 0.07	4 : 0.07	] : 0.05	2 : 0.03	3 : 0.03	6 : 0.03	h : 0.01	
d : 0.15	g : 0.15	c : 0.13	f : 0.11	] : 0.09	e : 0.09	2 : 0.07	4 : 0.05	h : 0.03	3 : 0.03	6 : 0.03	
g : 0.17	d : 0.15	e : 0.13	c : 0.11	f : 0.11	4 : 0.05	h : 0.03	2 : 0.03	b : 0.03	3 : 0.03	] : 0.03	6 : 0.03	a : 0.01	
g : 0.17	d : 0.15	e : 0.13	] : 0.09	3 : 0.07	f : 0.07	2 : 0.07	c : 0.05	4 : 0.05	h : 0.03	b : 0.03	6 : 0.01	
d : 0.17	g : 0.17	e : 0.15	c : 0.09	f : 0.09	2 : 0.07	h : 0.05	3 : 0.05	a : 0.03	4 : 0.01	b : 0.01	6 : 0.01	] : 0.01	

#score	644.1482575793981
#seq	52
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m1_run1.txt

#BEAR
!!ddddwwwwwwwwwwwwwwdddd22	chr10:74035263-74035527(+)$1	264	72	98	21.8232
cceeeeevvvvvvvvvvvvveeeee]	chr1:229456849-229457073(-)$1	224	178	204	22.9615
ee[dddduuuuuuuuuuuuddddeee	chr5:98129494-98129735(+)$1	241	111	137	22.6278
======yyyyyyyyyyyyyyyy====	chr1:61922792-61923017(+)$1	225	95	121	22.7944
gggggggvvvvvvvvvvvvvgggggg	chr2:85772087-85772327(+)$1	240	38	64	23.9295
ffffffwwwwwwwwwwwwwwffffff	chr4:15070824-15071077(+)$1	253	169	195	22.8554
#ffffffuuuuuuuuuuuuffffff3	chr11:47489626-47489869(-)$1	243	19	45	23.8302
!!eeeeexxxxxxxxxxxxxxxeeee	chr1:228645388-228645647(-)$1	259	48	74	18.5374
ffffffxxxxxxxxxxxxxxxfffff	chr6:31503058-31503306(-)$1	248	17	43	18.8883
""ccc[auuuuuuuuuuuuaccceee	chr1:45116875-45117138(+)$1	263	163	189	24.5811
ggeeeeevvvvvvvvvvvvveeeee4	chr10:90774650-90774883(+)$1	233	133	159	23.1116
!ffffffyyyyyyyyyyyyyyyyfff	chr19:59061839-59062125(+)$1	286	127	153	21.9764
iiiddddvvvvvvvvvvvvvddddFF	chr17:44833220-44833447(+)$1	227	36	62	21.6895
e[fffffftttttttttttffffff2	chr17:48211213-48211472(-)$1	259	10	36	22.4079
eeeee[bbtttttttttttbb22eee	chr19:1434908-1435174(+)$1	266	193	219	21.7987
"ffffffwwwwwwwwwwwwwwfffff	chr9:134371729-134371985(+)$1	256	10	36	22.7807
gggggyyyyyyyyyyyyyyyyggggg	chr22:47082376-47082623(-)$1	247	35	61	23.1105
e[ccc[bbtttttttttttbbccc]e	chr1:246887619-246887850(+)$1	231	56	82	22.4020
ggggggwwwwwwwwwwwwwwgggggg	chrX:84528133-84528395(+)$1	262	46	72	23.5317
ffff[bbuuuuuuuuuuuubb]ffff	chr13:77579300-77579537(-)$1	237	31	57	23.2653
gggggggtttttttttttgggggggg	chr5:179203982-179204204(+)$1	222	94	120	22.1499
fffff[bbtttttttttttbbfffff	chr17:38175378-38175603(-)$1	225	17	43	22.4318
===!!ccctttttttttttccc22==	chr2:62095657-62095896(-)$1	239	156	182	22.5773
Fgggggggtttttttttttggggggg	chr14:81643805-81644051(-)$1	246	19	45	22.3624
e[ddddvvvvvvvvvvvvvddddeee	chr3:23934321-23934553(-)$1	232	130	156	22.0215
e[cccxxxxxxxxxxxxxxxccceee	chr11:10818581-10818860(-)$1	279	138	164	18.7859
D:eeeeevvvvvvvvvvvvveeeee:	chr21:28208890-28209132(-)$1	242	110	136	19.6582
b[fffffftttttttttttffffff]	chr19:50001075-50001323(+)$1	248	206	232	22.3393
!!bbyyyyyyyyyyyyyyyybb22dd	chr1:203277384-203277637(+)$1	253	169	195	20.6614
eeeeeyyyyyyyyyyyyyyyyeeeee	chr16:23646976-23647195(-)$1	219	110	136	22.2411
!!fffffftttttttttttffffff2	chrX:106956475-106956762(-)$1	287	219	245	22.6070
fffffyyyyyyyyyyyyyyyyfffff	chr9:117406627-117406861(+)$1	234	2	28	22.5446
ggggggwwwwwwwwwwwwwwgggggg	chr2:111924656-111924892(+)$1	236	2	28	23.5317
=addddyyyyyyyyyyyyyyyydddd	chrX:102632672-102632901(+)$1	229	172	198	21.1969
eeeee[avvvvvvvvvvvvva]eeee	chr19:56185858-56186119(+)$1	261	141	167	23.4950
ggggggwwwwwwwwwwwwwwgggggg	chr2:111924619-111924892(+)$1	273	39	65	23.5317
hhhhhhhuuuuuuuuuuuuhhhhhhh	chr6:158363768-158364030(+)$1	262	169	195	20.8536
=====[bbtttttttttttbb=====	chr10:70743597-70743847(+)$1	250	148	174	22.7212
ggggggwwwwwwwwwwwwwwgggggg	chr1:207222106-207222352(-)$1	246	77	103	23.5317
:ffffffvvvvvvvvvvvvvffffff	chr1:2239282-2239534(+)$1	252	68	94	22.3841
b!!ddddtttttttttttdddd22bb	chr4:169848079-169848301(+)$1	222	67	93	19.7536
[dddd[ccctttttttttttccc]dd	chr8:98863673-98863935(+)$1	262	80	106	20.7113
d[a[cccuuuuuuuuuuuuccc]a22	chrX:131209333-131209560(+)$1	227	121	147	23.4547
:gggggggtttttttttttggggggg	chr17:45699886-45700112(+)$1	226	51	77	21.7644
[ffffffwwwwwwwwwwwwwwfffff	chr3:52558541-52558773(-)$1	232	162	188	22.8206
ee[bbwwwwwwwwwwwwwwbb333ee	chr19:47113411-47113709(+)$1	298	109	135	21.0647
ggggggguuuuuuuuuuuuggggggg	chr11:10818799-10819030(-)$1	231	83	109	24.2565
ggggg[awwwwwwwwwwwwwwa]ggg	chr1:28218090-28218327(-)$1	237	127	153	23.4149
ddd[cccvvvvvvvvvvvvvccc]dd	chr3:184052434-184052677(+)$1	243	145	171	22.5158
fffff[attttttttttta]ffffff	chr16:24836822-24837049(+)$1	227	164	190	22.6623
ee[cccvvvvvvvvvvvvvccc22ee	chr2:20648569-20648799(+)$1	230	160	186	22.6300
ffff[ccctttttttttttccc]fff	chr1:244219676-244219904(+)$1	228	95	121	22.7995
:ffffffuuuuuuuuuuuuffffffJ	chr3:178739750-178739976(-)$1	226	175	201	21.2093
hhhhhhhvvvvvvvvvvvvvhhhhhh	chr7:27146945-27147190(-)$1	245	210	236	20.8149
!!eeeeettttttttttteeeee22c	chr10:92617445-92617666(-)$1	221	136	162	21.3064
"""cccwwwwwwwwwwwwwwccc333	chr12:46582137-46582373(-)$1	236	68	94	23.0087
ggggggguuuuuuuuuuuuggggggg	chr14:61177191-61177426(-)$1	235	42	68	24.2565
iiiiiiiitttttttttttiiiiiii	chr2:20401659-20401886(-)$1	227	2	28	22.3093
eeeeeexxxxxxxxxxxxxxxeeeee	chr15:85923769-85923994(+)$1	225	180	206	18.5577
""ddddwwwwwwwwwwwwwwdddd22	chr19:4047010-4047291(-)$1	281	199	225	21.6334
ggggggwwwwwwwwwwwwwwgggggg	chr10:70104032-70104264(-)$1	232	133	159	23.5317
g[ccc[bbtttttttttttbb]cccg	chr6:31802939-31803189(+)$1	250	19	45	22.4619
!!fffffftttttttttttffffff3	chr20:44444400-44444647(+)$1	247	200	226	22.7761
###eeeeettttttttttteeeee33	chr10:27293938-27294160(-)$1	222	61	87	21.9309
!!eeeeeyyyyyyyyyyyyyyyyeee	chr7:98957223-98957448(+)$1	225	118	144	21.9814

#otherMatches

#Seq PSSM
AGCCGGAGGGAGGGGGGAGGUCGGAG	chr10:74035263-74035527(+)$1	264	72	98	21.8232
GCUGGGCACAUAAUCACAAAGCCCAG	chr1:229456849-229457073(-)$1	224	178	204	22.9615
UACUGUGUUUGGCUGUUUUCACAUAU	chr5:98129494-98129735(+)$1	241	111	137	22.6278
GUUUUUUUUCCUUAAUUUGCACGAAA	chr1:61922792-61923017(+)$1	225	95	121	22.7944
CCAAGGUGUCCUACAGAAAAACCUUG	chr2:85772087-85772327(+)$1	240	38	64	23.9295
AUGCAAAUUUAUUUUUUUCAUUGCAU	chr4:15070824-15071077(+)$1	253	169	195	22.8554
CGGAGAGCACCUGAACCCCCUUUCCU	chr11:47489626-47489869(-)$1	243	19	45	23.8302
UAAGGGCUCGCUGGCCUUCACUGCCC	chr1:228645388-228645647(-)$1	259	48	74	18.5374
CUACAAUUUUUUUCCUUGUUCUUGUA	chr6:31503058-31503306(-)$1	248	17	43	18.8883
AGUGGUGUAUAUUUCUUCUCCCAGAC	chr1:45116875-45117138(+)$1	263	163	189	24.5811
UUUAUUGGUGUCAUAUUAUACAAUAU	chr10:90774650-90774883(+)$1	233	133	159	23.1116
UGUCACCCCAUCCCCACUCCCCUGGU	chr19:59061839-59062125(+)$1	286	127	153	21.9764
ACUGUCUUACUCAAGAUACUGGACUA	chr17:44833220-44833447(+)$1	227	36	62	21.6895
UUUUUGUUCAUUUUUUAAAAACAGAC	chr17:48211213-48211472(-)$1	259	10	36	22.4079
AUCAGCACAAUAAAAAAAAGUCACUG	chr19:1434908-1435174(+)$1	266	193	219	21.7987
CCAUGUGUAUAGCUGAACUUUUAUAU	chr9:134371729-134371985(+)$1	256	10	36	22.7807
AGUGGUUGAUUCUCUUUGCCUUCAUU	chr22:47082376-47082623(-)$1	247	35	61	23.1105
CGCCGUGGACUCCACCCGCCCCGGGG	chr1:246887619-246887850(+)$1	231	56	82	22.4020
UGAGAAUAAAUUUUUUAUCUUUCUUA	chrX:84528133-84528395(+)$1	262	46	72	23.5317
CUUAAAAUACUUUGUCACUUUAUAAG	chr13:77579300-77579537(-)$1	237	31	57	23.2653
UCCUUUAUAUGUGUGUUUUGGGGGAG	chr5:179203982-179204204(+)$1	222	94	120	22.1499
UCUCCAUCUGCUGGCACCUGAGGAGA	chr17:38175378-38175603(-)$1	225	17	43	22.4318
UUAUUUCCUCUGAAUUUCUGGGCUUG	chr2:62095657-62095896(-)$1	239	156	182	22.5773
CACUUUCAGAAUUUGAAAAUGAAAGU	chr14:81643805-81644051(-)$1	246	19	45	22.3624
UUGGGCUAAGGUUAUUAUUGCCUGAU	chr3:23934321-23934553(-)$1	232	130	156	22.0215
GUGAGAAUUUGAAUUGGUCCCUCCUA	chr11:10818581-10818860(-)$1	279	138	164	18.7859
AAACGCCGGAACAAAAAUGAGGUGUG	chr21:28208890-28209132(-)$1	242	110	136	19.6582
UACACCUGUCCCCCUGCUUCAGGUGA	chr19:50001075-50001323(+)$1	248	206	232	22.3393
UCCCCUCCCCCUUCCCUUCUGGUCGG	chr1:203277384-203277637(+)$1	253	169	195	20.6614
ACCUUGAACACAUUCCUCCUAAAGGU	chr16:23646976-23647195(-)$1	219	110	136	22.2411
UUAUCCUGAUGUAUGGUUCCAGGAUU	chrX:106956475-106956762(-)$1	287	219	245	22.6070
ggacuccuauucaugcuucaaagucc	chr9:117406627-117406861(+)$1	234	2	28	22.5446
UAGAAAUAUUGUAUAUUUAUUUUCUG	chr2:111924656-111924892(+)$1	236	2	28	23.5317
GCUGUGAACCCUAUGUUAUUUCCAUG	chrX:102632672-102632901(+)$1	229	172	198	21.1969
CUGCCCCUCUCCUACUCUCUGUGGCA	chr19:56185858-56186119(+)$1	261	141	167	23.4950
UAGAAAUAUUGUAUAUUUAUUUUCUG	chr2:111924619-111924892(+)$1	273	39	65	23.5317
UUUUUUCCCCUAUUAUUCAGAAAAAA	chr6:158363768-158364030(+)$1	262	169	195	20.8536
GACAAACUGUAUGUGAUUAAGUUGUU	chr10:70743597-70743847(+)$1	250	148	174	22.7212
AAGGAUACAAUGCUUGAACCAUCCUU	chr1:207222106-207222352(-)$1	246	77	103	23.5317
UCUGUGCCUUCCAGCAUCUUGUACAG	chr1:2239282-2239534(+)$1	252	68	94	22.3841
UUAACAUUUUUUUUCUUUAUGUGUAG	chr4:169848079-169848301(+)$1	222	67	93	19.7536
AGCAAUAGUUCUGUUAUUUCACUUUU	chr8:98863673-98863935(+)$1	262	80	106	20.7113
AAAGUCAUUUAAAAAAAUCUGAGUAA	chrX:131209333-131209560(+)$1	227	121	147	23.4547
CAAAAACCUACCCUGUUCUGGUUUUU	chr17:45699886-45700112(+)$1	226	51	77	21.7644
CGCGUGGACUUCACCUUCUACCCACG	chr3:52558541-52558773(-)$1	232	162	188	22.8206
GCCGCUUCCUCACAUCUGUGCUCCGU	chr19:47113411-47113709(+)$1	298	109	135	21.0647
GUUACAGAAAAAUUCUUAACUGUAAU	chr11:10818799-10819030(-)$1	231	83	109	24.2565
UCAUGACUUUUUGACACACUUGCCAU	chr1:28218090-28218327(-)$1	237	127	153	23.4149
AGUUGGGAGAGUAGCAAGGACCCCGC	chr3:184052434-184052677(+)$1	243	145	171	22.5158
GAGCAUCUUUGGGAUCUUGUUGCUCA	chr16:24836822-24837049(+)$1	227	164	190	22.6623
GUAGCAUUCUGACCACACUUGUACGC	chr2:20648569-20648799(+)$1	230	160	186	22.6300
UGCAUUUAUAACAAACUUCUAAUUGC	chr1:244219676-244219904(+)$1	228	95	121	22.7995
CAGUUUGCUCCUUAAAUUCCAAACUC	chr3:178739750-178739976(-)$1	226	175	201	21.2093
GAAUAAUCUAAGUUUUAAAUAUUAUU	chr7:27146945-27147190(-)$1	245	210	236	20.8149
GGGCCGGGCGGAGCGGAACCGGUGAG	chr10:92617445-92617666(-)$1	221	136	162	21.3064
UUUGCUUUACAGAAAAAAAUGGUUUC	chr12:46582137-46582373(-)$1	236	68	94	23.0087
CCAAGGGCCAGACUCAGAACCCUUGG	chr14:61177191-61177426(-)$1	235	42	68	24.2565
UAAGAAGACUUUUUUUUUUUUUUUUU	chr2:20401659-20401886(-)$1	227	2	28	22.3093
GGCCGCCUAUUGUCUUUCUCCGCGGC	chr15:85923769-85923994(+)$1	225	180	206	18.5577
CUGAGACACAAACCUAUUUAUUUCUA	chr19:4047010-4047291(-)$1	281	199	225	21.6334
UAUAAAAAAUACAUAGAAAAUUUAUG	chr10:70104032-70104264(-)$1	232	133	159	23.5317
CUGCUGACUCAAAACAACUGUGAGUG	chr6:31802939-31803189(+)$1	250	19	45	22.4619
AAGGCUCCCUCAAACAAAAGGAGCCC	chr20:44444400-44444647(+)$1	247	200	226	22.7761
AUCAAAUUUACAUAAUUUUAAUUUUA	chr10:27293938-27294160(-)$1	222	61	87	21.9309
CUGCACCAGAAUAGCAUCACGUAGGU	chr7:98957223-98957448(+)$1	225	118	144	21.9814

#DB
..((((..............))))..	chr10:74035263-74035527(+)$1	1	72	98	21.8232
(((((((.............))))).	chr1:229456849-229457073(-)$1	1	178	204	22.9615
((.((((............)))))))	chr5:98129494-98129735(+)$1	1	111	137	22.6278
((((((................))))	chr1:61922792-61923017(+)$1	1	95	121	22.7944
(((((((.............))))))	chr2:85772087-85772327(+)$1	1	38	64	23.9295
((((((..............))))))	chr4:15070824-15071077(+)$1	1	169	195	22.8554
.((((((............)))))).	chr11:47489626-47489869(-)$1	1	19	45	23.8302
..(((((...............))))	chr1:228645388-228645647(-)$1	1	48	74	18.5374
((((((...............)))))	chr6:31503058-31503306(-)$1	1	17	43	18.8883
..(((.(............)))))))	chr1:45116875-45117138(+)$1	1	163	189	24.5811
(((((((.............))))).	chr10:90774650-90774883(+)$1	1	133	159	23.1116
.((((((................)))	chr19:59061839-59062125(+)$1	1	127	153	21.9764
)))((((.............))))((	chr17:44833220-44833447(+)$1	1	36	62	21.6895
(.((((((...........)))))).	chr17:48211213-48211472(-)$1	1	10	36	22.4079
(((((.((...........))..)))	chr19:1434908-1435174(+)$1	1	193	219	21.7987
.((((((..............)))))	chr9:134371729-134371985(+)$1	1	10	36	22.7807
(((((................)))))	chr22:47082376-47082623(-)$1	1	35	61	23.1105
(.(((.((...........))))).)	chr1:246887619-246887850(+)$1	1	56	82	22.4020
((((((..............))))))	chrX:84528133-84528395(+)$1	1	46	72	23.5317
((((.((............)).))))	chr13:77579300-77579537(-)$1	1	31	57	23.2653
(((((((...........)))))))(	chr5:179203982-179204204(+)$1	1	94	120	22.1499
(((((.((...........)))))))	chr17:38175378-38175603(-)$1	1	17	43	22.4318
(((..(((...........)))..))	chr2:62095657-62095896(-)$1	1	156	182	22.5773
((((((((...........)))))))	chr14:81643805-81644051(-)$1	1	19	45	22.3624
(.((((.............)))))))	chr3:23934321-23934553(-)$1	1	130	156	22.0215
(.(((...............))))))	chr11:10818581-10818860(-)$1	1	138	164	18.7859
(.(((((.............))))).	chr21:28208890-28209132(-)$1	1	110	136	19.6582
(.((((((...........)))))).	chr19:50001075-50001323(+)$1	1	206	232	22.3393
..((................))..))	chr1:203277384-203277637(+)$1	1	169	195	20.6614
(((((................)))))	chr16:23646976-23647195(-)$1	1	110	136	22.2411
..((((((...........)))))).	chrX:106956475-106956762(-)$1	1	219	245	22.6070
(((((................)))))	chr9:117406627-117406861(+)$1	1	2	28	22.5446
((((((..............))))))	chr2:111924656-111924892(+)$1	1	2	28	23.5317
((((((................))))	chrX:102632672-102632901(+)$1	1	172	198	21.1969
(((((.(.............).))))	chr19:56185858-56186119(+)$1	1	141	167	23.4950
((((((..............))))))	chr2:111924619-111924892(+)$1	1	39	65	23.5317
(((((((............)))))))	chr6:158363768-158364030(+)$1	1	169	195	20.8536
(((((.((...........)))))))	chr10:70743597-70743847(+)$1	1	148	174	22.7212
((((((..............))))))	chr1:207222106-207222352(-)$1	1	77	103	23.5317
.((((((.............))))))	chr1:2239282-2239534(+)$1	1	68	94	22.3841
(..((((...........))))..))	chr4:169848079-169848301(+)$1	1	67	93	19.7536
.((((.(((...........))).))	chr8:98863673-98863935(+)$1	1	80	106	20.7113
(.(.(((............))).)..	chrX:131209333-131209560(+)$1	1	121	147	23.4547
.(((((((...........)))))))	chr17:45699886-45700112(+)$1	1	51	77	21.7644
.((((((..............)))))	chr3:52558541-52558773(-)$1	1	162	188	22.8206
((.((..............))...))	chr19:47113411-47113709(+)$1	1	109	135	21.0647
(((((((............)))))))	chr11:10818799-10819030(-)$1	1	83	109	24.2565
(((((.(..............).)))	chr1:28218090-28218327(-)$1	1	127	153	23.4149
(((.(((.............))).))	chr3:184052434-184052677(+)$1	1	145	171	22.5158
(((((.(...........).))))))	chr16:24836822-24837049(+)$1	1	164	190	22.6623
((.(((.............)))..))	chr2:20648569-20648799(+)$1	1	160	186	22.6300
((((.(((...........))).)))	chr1:244219676-244219904(+)$1	1	95	121	22.7995
.((((((............)))))))	chr3:178739750-178739976(-)$1	1	175	201	21.2093
(((((((.............))))))	chr7:27146945-27147190(-)$1	1	210	236	20.8149
..(((((...........)))))..)	chr10:92617445-92617666(-)$1	1	136	162	21.3064
...(((..............)))...	chr12:46582137-46582373(-)$1	1	68	94	23.0087
(((((((............)))))))	chr14:61177191-61177426(-)$1	1	42	68	24.2565
((((((((...........)))))))	chr2:20401659-20401886(-)$1	1	2	28	22.3093
)(((((...............)))))	chr15:85923769-85923994(+)$1	1	180	206	18.5577
..((((..............))))..	chr19:4047010-4047291(-)$1	1	199	225	21.6334
((((((..............))))))	chr10:70104032-70104264(-)$1	1	133	159	23.5317
(.(((.((...........)).))))	chr6:31802939-31803189(+)$1	1	19	45	22.4619
..((((((...........)))))).	chr20:44444400-44444647(+)$1	1	200	226	22.7761
...(((((...........)))))..	chr10:27293938-27294160(-)$1	1	61	87	21.9309
..(((((................)))	chr7:98957223-98957448(+)$1	1	118	144	21.9814

#PSSM
g : 0.20	e : 0.16	! : 0.12	f : 0.10	= : 0.06	" : 0.06	: : 0.04	# : 0.03	i : 0.03	b : 0.03	h : 0.03	[ : 0.03	d : 0.03	c : 0.01	F : 0.01	D : 0.01	
g : 0.21	f : 0.20	! : 0.12	e : 0.10	[ : 0.10	= : 0.04	" : 0.04	i : 0.03	h : 0.03	d : 0.03	c : 0.01	: : 0.01	a : 0.01	# : 0.01	
f : 0.26	g : 0.20	e : 0.15	d : 0.09	c : 0.06	[ : 0.04	= : 0.04	i : 0.03	h : 0.03	b : 0.01	! : 0.01	a : 0.01	" : 0.01	# : 0.01	
f : 0.26	g : 0.20	e : 0.16	d : 0.12	c : 0.09	= : 0.03	b : 0.03	h : 0.03	[ : 0.03	! : 0.01	i : 0.01	
f : 0.23	g : 0.20	e : 0.16	d : 0.12	c : 0.12	= : 0.03	[ : 0.03	h : 0.03	! : 0.01	y : 0.01	b : 0.01	i : 0.01	
f : 0.18	g : 0.16	[ : 0.15	e : 0.12	d : 0.10	c : 0.09	y : 0.06	h : 0.03	= : 0.01	b : 0.01	x : 0.01	w : 0.01	i : 0.01	
w : 0.15	f : 0.15	e : 0.10	y : 0.09	g : 0.09	b : 0.09	c : 0.07	a : 0.06	d : 0.04	x : 0.04	v : 0.03	h : 0.03	i : 0.01	
w : 0.20	v : 0.16	u : 0.13	y : 0.12	b : 0.07	x : 0.06	f : 0.06	t : 0.06	c : 0.04	g : 0.03	i : 0.01	e : 0.01	
t : 0.29	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	c : 0.01	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.30	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	
t : 0.24	w : 0.20	v : 0.16	u : 0.13	y : 0.12	x : 0.06	g : 0.01	d : 0.01	a : 0.01	e : 0.01	
w : 0.18	v : 0.13	y : 0.12	b : 0.10	f : 0.09	g : 0.07	x : 0.06	c : 0.06	d : 0.04	e : 0.03	a : 0.01	h : 0.01	t : 0.01	] : 0.01	i : 0.01	
g : 0.16	f : 0.13	c : 0.13	b : 0.12	y : 0.10	d : 0.09	e : 0.07	x : 0.04	w : 0.04	h : 0.03	a : 0.01	i : 0.01	
f : 0.21	g : 0.18	c : 0.15	e : 0.10	d : 0.09	y : 0.06	] : 0.04	h : 0.03	x : 0.01	2 : 0.01	b : 0.01	= : 0.01	3 : 0.01	a : 0.01	i : 0.01	
f : 0.23	g : 0.18	e : 0.13	c : 0.10	d : 0.09	2 : 0.07	] : 0.04	= : 0.03	y : 0.03	h : 0.03	3 : 0.01	i : 0.01	
f : 0.26	e : 0.21	g : 0.20	2 : 0.07	d : 0.06	= : 0.03	c : 0.03	h : 0.03	] : 0.03	3 : 0.03	a : 0.01	i : 0.01	
f : 0.26	e : 0.23	g : 0.20	2 : 0.06	d : 0.06	= : 0.04	h : 0.03	3 : 0.03	F : 0.01	] : 0.01	b : 0.01	i : 0.01	c : 0.01	
g : 0.21	e : 0.20	f : 0.16	2 : 0.07	3 : 0.06	d : 0.06	= : 0.04	] : 0.03	h : 0.03	4 : 0.01	F : 0.01	: : 0.01	b : 0.01	J : 0.01	c : 0.01	i : 0.01	

#score	1444.1590283440707
#seq	65
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_CDS_m1_run1.txt

#BEAR
!!eeeee"""ccc[cccpppppppccc333ccc]eeeee4	chr3:47890998-47891224(+)$1	226	21	61	12.3318
eee[bb[bb"""bb[bboooooobb]bb4444bb]bb]ee	chr12:121756042-121756269(-)$1	227	59	99	12.8282
""ccc!!bb!!ccc[ddddoooooodddd]ccc22bb]cc	chr17:5336606-5336839(-)$1	233	54	94	14.8276
gggggg[bb$$$$$ddddnnnnndddd333bb]ggggggg	chr17:38345014-38345243(-)$1	229	126	166	12.9280
d[dddd[a"""===========lll===========333a	chr14:31617862-31618101(-)$1	239	161	201	12.4212
a[dddd####ddddrrrrrrrrrdddd22dddd]aggggg	chr2:217026607-217026834(+)$1	227	182	222	12.8229
======####cccddddoooooodddd22ccc333=====	chr17:42288119-42288365(-)$1	246	59	99	18.3693
##cccccc[ccc[ddddmmmmdddd]ccc]ccc333ccc3	chr17:18144774-18145008(+)$1	234	130	170	13.1618
""dddd[ccc[ccccccooooooccc4444ccc22ccc33	chr14:67779196-67779423(+)$1	227	72	112	19.1434
"dddd!!ccc####cccooooooccc55555ccc22dddd	chr1:19467200-19467427(-)$1	227	114	154	13.7044
caeeeee[bb[ddddccclllccc4444ddddbb]eeeee	chr17:7411511-7411739(+)$1	228	82	122	11.2934
[eeeee####ccc[cccqqqqqqqqccc]ccc333eeeee	chr8:38880602-38880832(+)$1	230	45	85	12.1226
=====!!ddddaeeeeeooooooeeeee22a]dddd====	chr16:30094909-30095143(+)$1	234	163	203	13.8448
eeee[bb[ccc$$$$$cccmmmmccc4444ccc22bbeee	chr12:16052815-16053044(+)$1	229	52	92	11.8898
"ccc[ddddccc!!ddddllldddd]ccc]dddd]ccc33	chr20:35929628-35929860(+)$1	232	9	49	12.8126
dddd[ccc!!ddddrrrrrrrrrdddd333ccc22ddddd	chr1:153907267-153907511(-)$1	244	8	48	13.8173
!!ccc"""==========oooooo==========ccc]dd	chr11:113085089-113085316(+)$1	227	172	212	15.8067
d$$$$$eeeee"""cccooooooccc22eeeee]dddd]b	chr21:28212094-28212328(-)$1	234	67	107	13.1777
ggggggg[bb"""ddddoooooodddd333bb22gggggg	chr12:53460256-53460482(-)$1	226	156	196	16.9835
ffff"""ccc[bb[cccoooooocccbb]ccc333fffff	chr1:120508041-120508265(-)$1	224	20	60	15.4777
===========[ddddoooooodddd4444==========	chr8:145139224-145139481(+)$1	257	126	166	16.8455
####=========="""bbmmmmbb333==========22	chr3:113503477-113503703(+)$1	226	74	114	12.5385
"ccc[dddd!!ffffffooooooffffff22ddddccc22	chr1:153640375-153640617(-)$1	242	171	211	12.5556
###eeeee[ccc!!cccooooooccc333ccc]eeeeeff	chr16:47001327-47001551(-)$1	224	143	183	16.4618
""eeeee!!ccc[ddddooooooddddccc]eeeeedddd	chr1:160276869-160277098(-)$1	229	112	152	14.5564
iiiiii[ccc[bb"""ddddllldddd4444bb22cccii	chr1:227171720-227171958(+)$1	238	20	60	14.1161
ffffff[ccc!!dddd!!ccclllccc22dddd22ccc]f	chr4:69188506-69188732(-)$1	226	98	138	12.1650
==========####bbqqqqqqqqbb4444==========	chr17:65145890-65146120(-)$1	230	30	70	12.7527
eeeee[cccddddddddoooooodddd333dddd]cccee	chr6:26027027-26027362(-)$1	335	134	174	15.8078
c!!ggggggg[fffffflllffffff4444gggggggccc	chr19:10794513-10794746(+)$1	233	32	72	11.1482
ddd!!ccc[dddd!!bboooooobbdddd]ccc22dddd]	chr2:220249004-220249229(-)$1	225	20	60	14.8560
!!dddd[dddd[bbbboooooobb333bb]dddd]dddd]	chr12:124110902-124111137(-)$1	235	115	155	12.3040
ccc[==========rrrrrrrrr==========22cccDD	chrM:13164-13402(-)$1	238	1	41	11.9023
a[ffffff[acccddddoooooodddd]ccc]a]ffffff	chr3:49141239-49141479(-)$1	240	175	215	14.0442
b[eeeeeeeeee[ddddooooooddddeeeee333eeeee	chr10:104210611-104210852(+)$1	241	179	219	14.1861
a[==========!!a[aooooooa]a22==========]a	chr8:145134682-145134911(+)$1	229	5	45	17.0240
$$$$$eeeee[ccc[ddddoooooodddd]ccc22eeeee	chr15:89811625-89811854(+)$1	229	18	58	13.3272
ddddeeeee"""ccccccnnnnnccc]ccc333eeeee]d	chr4:128806929-128807159(+)$1	230	179	219	11.6887
[iiiiiiiii[cccddddoooooodddd]ccc22iiiiii	chr2:161137723-161137947(+)$1	224	171	211	15.8557
::=============cccnnnnnccc]=============	chrX:53247437-53247673(-)$1	236	50	90	12.2504
!ccc"""eeeee"""bblllbbeeeee333ccc4444ccc	chr16:58580505-58580738(-)$1	233	77	117	12.3898
$$dddd!!a"""cccooooooccc22a22dddd22ggggg	chr3:97668673-97668914(-)$1	241	110	150	14.8908
####gggggggccc!!ddddmmmmdddd22ccc22ggggg	chrX:132887505-132887772(-)$1	267	18	58	12.2943
ggggggdddd"""bbccclllccc]bb22dddd22ggggg	chr6:149720182-149720413(+)$1	231	134	174	12.7379
[adddd[bb!!ffffffooooooffffff]bb]dddd22a	chr1:21179950-21180200(-)$1	250	168	208	12.0006
$$ggggggg"""bb[ddddoooooodddd]bb333ggggg	chr11:67800303-67800579(+)$1	276	223	263	14.4947
ccccc!!ccc[ddddlllddddccc]ccc]ccc22ccc22	chr17:20922326-20922565(-)$1	239	150	190	11.2548
eeee!!dddd[bb[cccoooooocccbb22dddd]eeeee	chr1:151373652-151373921(+)$1	269	129	169	14.4691
dddd!!bb[a"""ddddoooooodddd333a]bb]dddd]	chr16:30990927-30991161(+)$1	234	13	53	16.1810
fffff[ccc[dddd[cccooooooccc22dddd22ccc33	chr19:50412672-50412899(-)$1	227	142	182	15.4333
ccc[dddd####ddddnnnnndddddddd]ccc22ccc]c	chr22:18379523-18379747(-)$1	224	176	216	12.4376
&&eeeee!!bb!!a[bboooooobb]a]bb]eeeee4444	chr19:11552037-11552270(+)$1	233	92	132	11.8924
[dddd!!ccc[a!!ammmma22a]ccc22dddd22ccca2	chr17:26919463-26919709(-)$1	246	134	174	11.6662
gggg$$$$$dddd!!bboooooobb333dddd4444gggg	chr12:123345762-123346007(+)$1	245	96	136	14.2898
ccc[bb[ccc!!a[cccooooooccc]a22cccbb]ccc]	chr17:42292963-42293199(-)$1	236	86	126	15.7071

#otherMatches

#Seq PSSM
UGCUGCACAAGUCGACCAUUAACAGGUGAGGGCAUGCAGG	chr3:47890998-47891224(+)$1	226	21	61	12.3318
CAGAGCUGUACUGGCGAUCUUCCUCCCCUACCAUCGCGCU	chr12:121756042-121756269(-)$1	227	59	99	12.8282
CUAGCUUGUCCUGGAGAACCCUUCAGUUUCCCAAUAUUGU	chr17:5336606-5336839(-)$1	233	54	94	14.8276
CUGGCAUGGACACAGCUGGGCAUCAGCACGCCCUGCCAGG	chr17:38345014-38345243(-)$1	229	126	166	12.9280
AAACAAAGCAAAAGGUAUAUCUGUUGGAUGUGCUUUAUUC	chr14:31617862-31618101(-)$1	239	161	201	12.4212
AUUUAGGAGAAGCUGUUUAGUUAAGCUAACUAAUUUAAAG	chr2:217026607-217026834(+)$1	227	182	222	12.8229
GAGAAGCCCAAGCGGCCCGUGUCGGCCAUGUUCAUCUUCU	chr17:42288119-42288365(-)$1	246	59	99	18.3693
CACCAACCUGGGUGACGUCCACGUCUUCUCGGUGCCUGGC	chr17:18144774-18145008(+)$1	234	130	170	13.1618
AUGACCCCUCAGAUGACCCUUAUGUUCCAUGUCGAGAGUU	chr14:67779196-67779423(+)$1	227	72	112	19.1434
CGCAGGAACCCUCUCUGACACCACAGCAUCAGGUAACUGU	chr1:19467200-19467427(-)$1	227	114	154	13.7044
GCUCUGGCUGCGCAGUCCCUUGGAGAACCUGCCACCCAGA	chr17:7411511-7411739(+)$1	228	82	122	11.2934
UAUAUACUUUUAUUUCUUUCUUCCCAGAUGUAUAUUAUGU	chr8:38880602-38880832(+)$1	230	45	85	12.1226
UGUGUGACCUCCUCUGGUCUGACCCAGAAGGUGAGGGCAU	chr16:30094909-30095143(+)$1	234	163	203	13.8448
ACUGUGUGAGAUUUAGUCCUGAUGGAGAACUCUAUGCCAG	chr12:16052815-16053044(+)$1	229	52	92	11.8898
GAGACGUCAGGCAGCAAGCGACUUGGGCCAUGGCCUCUGA	chr20:35929628-35929860(+)$1	232	9	49	12.8126
GUGGGUAUGAGGCAGGGUUAGGGUGUCGAGGUAGGCCAUC	chr1:153907267-153907511(-)$1	244	8	48	13.8173
CUUGGAAUGCAGACUCAAAGCAGAUUGAGUCUGCUCAUGC	chr11:113085089-113085316(+)$1	227	172	212	15.8067
GAAGUACUGUGAAGGCAAACGAGUGCGCUACAGAUCCUGU	chr21:28212094-28212328(-)$1	234	67	107	13.1777
GCUUGGGGCCGAGGGUGGAAAGGCACCACAGGAGCUCAGG	chr12:53460256-53460482(-)$1	226	156	196	16.9835
GUAAAGGGAGACACAAGAUAAUCCUUUGACUCAUGUUACC	chr1:120508041-120508265(-)$1	224	20	60	15.4777
GCUGCAGGGCCUGCAGACACUGCUGCUCAUGGUUCUGCGG	chr8:145139224-145139481(+)$1	257	126	166	16.8455
CAUAUCACUGGCGGAGACAUUUAUGGAAUUGUCAGUGAGA	chr3:113503477-113503703(+)$1	226	74	114	12.5385
AGGGCAGCUUUGGUAGUGUGGAAAUUGCCUUGGCUCUUGA	chr1:153640375-153640617(-)$1	242	171	211	12.5556
UUCUCUGCUUUUAUGUUGGAAUGGAUUGGGAAUGCAGAUA	chr16:47001327-47001551(-)$1	224	143	183	16.4618
AAAUCGGUUUGCUGUCCUAGAUCGGAUGCAUUCGGUGAGU	chr1:160276869-160277098(-)$1	229	112	152	14.5564
GGGGGACGGUGUGGAGGGCCUGUGGCUAGGGCGUGACCUC	chr1:227171720-227171958(+)$1	238	20	60	14.1161
GGAAAUUGAACUUGAAUGUGGAACCCAGCUUUGUCUUCUG	chr4:69188506-69188732(-)$1	226	98	138	12.1650
CACAUUCUAUUAGAUGAAGCUGCCCAGGCCAUGGAGUGUG	chr17:65145890-65146120(-)$1	230	30	70	12.7527
AUGGAUGUGGUUUACGCGCUCAAGCGUCAAGGACGCACUC	chr6:26027027-26027362(-)$1	335	134	174	15.8078
GCCGGAGACACUGCUGGACCCCGGUAACCCUGUCUUUCCC	chr19:10794513-10794746(+)$1	233	32	72	11.1482
GGGGUGGAGGGUUGAAGGUCGGGCUGACUGUCUUACCUCU	chr2:220249004-220249229(-)$1	225	20	60	14.8560
CCUCUGCCACCUCAACGUCCCUGUCACUGUGGUGCUAGAU	chr12:124110902-124111137(-)$1	235	115	155	12.3040
UCUUGUUCAUUGUUAAGGUUGUGGAUGAUGGACCCGGAGC	chrM:13164-13402(-)$1	238	1	41	11.9023
GAGGAGGCUGUGAGUCUUUCCCCAGGCAUCGUCUGCCUCC	chr3:49141239-49141479(-)$1	240	175	215	14.0442
CAGCUGCGGCGGCGGCGGCCAGACGCCCUGUUUGGGCGGC	chr10:104210611-104210852(+)$1	241	179	219	14.1861
UGCAAGACAGAGAGCGCAAAACAGGGGGCUUUGUUUUGGA	chr8:145134682-145134911(+)$1	229	5	45	17.0240
UCACUGUGCCAUCAGGUGAACUUCGUCAUGUGGAAGGCAC	chr15:89811625-89811854(+)$1	229	18	58	13.3272
GGUCCCUGGGCUGUAUGUUUUAUACAUUACUUAUCGGGAG	chr4:128806929-128807159(+)$1	230	179	219	11.6887
GAAAGAAAUAUUGAUUUUCAUUGUAAAGCUUACCUAUUUC	chr2:161137723-161137947(+)$1	224	171	211	15.8557
GUGGGAGGGGGUGGCCAGCCUCUUUGAGCCAUUUCUUCUU	chrX:53247437-53247673(-)$1	236	50	90	12.2504
UUCUUUAGGUUUUUAGGCCACCAAACCCUUGGACAAUGGC	chr16:58580505-58580738(-)$1	233	77	117	12.3898
UUGCAGACCGGCUGGAGGGCACCAAAGAACUGCUUUCCUC	chr3:97668673-97668914(-)$1	241	110	150	14.8908
UCUUACUGCCAGGGACUGAUGAUGGUUAAACCCUGUGGCG	chrX:132887505-132887772(-)$1	267	18	58	12.2943
AAAGGUUAGUGUAUCCAUUAAAUGUGAAAACUGUUACUUU	chr6:149720182-149720413(+)$1	231	134	174	12.7379
GUCUACUCAAGGCUGGCCCGCUUGCCAGUAUGUGUGGCAA	chr1:21179950-21180200(-)$1	250	168	208	12.0006
AUGCAUGGGGGAGGAGGGUGCCCCUGCCCACCACACCCGU	chr11:67800303-67800579(+)$1	276	223	263	14.4947
ACCUCGAACUGCACCAUAGGUGGGUGGAGCGUGUCGUCAC	chr17:20922326-20922565(-)$1	239	150	190	11.2548
AACGCUGCAUGCGAGUGCUGUACUACCGAGAUGCCCGUUC	chr1:151373652-151373921(+)$1	269	129	169	14.4691
GGCCACAGAGACAUCGGACGAGGCCGAGCGCCCUAGGCCC	chr16:30990927-30991161(+)$1	234	13	53	16.1810
CUGCCACCCCAGCCAUGGCAAACCCCAGCGGCUUUGGGCU	chr19:50412672-50412899(-)$1	227	142	182	15.4333
UGCCUCCGAGAACGCCGCCUUGGUGCGGGAGCAGAACGGA	chr22:18379523-18379747(-)$1	224	176	216	12.4376
GAUCCUUAUUGAGGACUGGAAGAAGGCACGGGAGGAGAAG	chr19:11552037-11552270(+)$1	233	92	132	11.8924
UGAGGACUUAGUACCUUCUGAAAGUAACGCCUUCUUGCCU	chr17:26919463-26919709(-)$1	246	134	174	11.6662
GUGUCCUGGAGCUGGAGAAGACGCUGGAGGCUGAACGCAU	chr12:123345762-123346007(+)$1	245	96	136	14.2898
CCAAGUAUGCGAAACUCCACCCUGAGAUGAGCAACCUGGA	chr17:42292963-42293199(-)$1	236	86	126	15.7071

#DB
..(((((...(((.(((.......)))...))).))))).	chr3:47890998-47891224(+)$1	1	21	61	12.3318
(((.((.((...((.((......)).))....)).)).))	chr12:121756042-121756269(-)$1	1	59	99	12.8282
..(((..((..(((.((((......)))).)))..)).))	chr17:5336606-5336839(-)$1	1	54	94	14.8276
((((((.((.....((((.....))))...)).)))))))	chr17:38345014-38345243(-)$1	1	126	166	12.9280
(.((((.(...(((((((((((...)))))))))))...)	chr14:31617862-31618101(-)$1	1	161	201	12.4212
(.((((....((((.........))))..)))).))))))	chr2:217026607-217026834(+)$1	1	182	222	12.8229
((((((....(((((((......))))..)))...)))))	chr17:42288119-42288365(-)$1	1	59	99	18.3693
..((((((.(((.((((....)))).))).)))...))).	chr17:18144774-18145008(+)$1	1	130	170	13.1618
..((((.(((.((((((......)))....)))..)))..	chr14:67779196-67779423(+)$1	1	72	112	19.1434
.((((..(((....(((......))).....)))..))))	chr1:19467200-19467427(-)$1	1	114	154	13.7044
(((((((.((.(((((((...)))....)))))).)))))	chr17:7411511-7411739(+)$1	1	82	122	11.2934
.(((((....(((.(((........))).)))...)))))	chr8:38880602-38880832(+)$1	1	45	85	12.1226
(((((..((((((((((......)))))..).))))))))	chr16:30094909-30095143(+)$1	1	163	203	13.8448
((((.((.(((.....(((....)))....)))..)))))	chr12:16052815-16053044(+)$1	1	52	92	11.8898
.(((.(((((((..((((...)))).))).)))).)))..	chr20:35929628-35929860(+)$1	1	9	49	12.8126
((((.(((..((((.........))))...)))..)))))	chr1:153907267-153907511(-)$1	1	8	48	13.8173
..(((...((((((((((......))))))))))))).))	chr11:113085089-113085316(+)$1	1	172	212	15.8067
(.....(((((...(((......)))..))))).)))).)	chr21:28212094-28212328(-)$1	1	67	107	13.1777
(((((((.((...((((......))))...))..))))))	chr12:53460256-53460482(-)$1	1	156	196	16.9835
((((...(((.((.(((......))))).)))...)))))	chr1:120508041-120508265(-)$1	1	20	60	15.4777
(((((((((((.((((......))))....))))))))))	chr8:145139224-145139481(+)$1	1	126	166	16.8455
....((((((((((...((....))...))))))))))..	chr3:113503477-113503703(+)$1	1	74	114	12.5385
.(((.((((..((((((......))))))..)))))))..	chr1:153640375-153640617(-)$1	1	171	211	12.5556
...(((((.(((..(((......)))...))).)))))))	chr16:47001327-47001551(-)$1	1	143	183	16.4618
..(((((..(((.((((......))))))).)))))))))	chr1:160276869-160277098(-)$1	1	112	152	14.5564
((((((.(((.((...((((...))))....))..)))))	chr1:227171720-227171958(+)$1	1	20	60	14.1161
((((((.(((..((((..(((...)))..))))..))).)	chr4:69188506-69188732(-)$1	1	98	138	12.1650
((((((((((....((........))....))))))))))	chr17:65145890-65146120(-)$1	1	30	70	12.7527
(((((.(((((((((((......))))...)))).)))))	chr6:26027027-26027362(-)$1	1	134	174	15.8078
(..(((((((.((((((...))))))....))))))))))	chr19:10794513-10794746(+)$1	1	32	72	11.1482
(((..(((.((((..((......)))))).)))..)))).	chr2:220249004-220249229(-)$1	1	20	60	14.8560
..((((.((((.((((......))...)).)))).)))).	chr12:124110902-124111137(-)$1	1	115	155	12.3040
(((.((((((((((.........))))))))))..)))((	chrM:13164-13402(-)$1	1	1	41	11.9023
(.((((((.((((((((......)))).))).).))))))	chr3:49141239-49141479(-)$1	1	175	215	14.0442
(.((((((((((.((((......)))))))))...)))))	chr10:104210611-104210852(+)$1	1	179	219	14.1861
(.((((((((((..(.(......).)..)))))))))).)	chr8:145134682-145134911(+)$1	1	5	45	17.0240
.....(((((.(((.((((......)))).)))..)))))	chr15:89811625-89811854(+)$1	1	18	58	13.3272
(((((((((...((((((.....))).)))...))))).)	chr4:128806929-128807159(+)$1	1	179	219	11.6887
.(((((((((.(((((((......)))).)))..))))))	chr2:161137723-161137947(+)$1	1	171	211	15.8557
..((((((((((((((((.....))).)))))))))))))	chrX:53247437-53247673(-)$1	1	50	90	12.2504
.(((...(((((...((...)))))))...)))....)))	chr16:58580505-58580738(-)$1	1	77	117	12.3898
..((((..(...(((......)))..)..))))..)))))	chr3:97668673-97668914(-)$1	1	110	150	14.8908
....((((((((((..((((....))))..)))..)))))	chrX:132887505-132887772(-)$1	1	18	58	12.2943
((((((((((...(((((...))).))..))))..)))))	chr6:149720182-149720413(+)$1	1	134	174	12.7379
.(((((.((..((((((......)))))).)).))))..)	chr1:21179950-21180200(-)$1	1	168	208	12.0006
..(((((((...((.((((......)))).))...)))))	chr11:67800303-67800579(+)$1	1	223	263	14.4947
(((((..(((.((((...))))))).))).)))..)))..	chr17:20922326-20922565(-)$1	1	150	190	11.2548
((((..((((.((.(((......)))))..)))).)))))	chr1:151373652-151373921(+)$1	1	129	169	14.4691
((((..((.(...((((......))))...).)).)))).	chr16:30990927-30991161(+)$1	1	13	53	16.1810
(((((.(((.((((.(((......)))..))))..)))..	chr19:50412672-50412899(-)$1	1	142	182	15.4333
(((.((((....((((.....)))))))).)))..))).)	chr22:18379523-18379747(-)$1	1	176	216	12.4376
..(((((..((..(.((......)).).)).)))))....	chr19:11552037-11552270(+)$1	1	92	132	11.8924
.((((..(((.(..(....)..).)))..))))..)))).	chr17:26919463-26919709(-)$1	1	134	174	11.6662
((((.....((((..((......))...))))....))))	chr12:123345762-123346007(+)$1	1	96	136	14.2898
(((.((.(((..(.(((......))).)..))))).))).	chr17:42292963-42293199(-)$1	1	86	126	15.7071

#PSSM
" : 0.10	d : 0.10	c : 0.10	! : 0.07	e : 0.07	g : 0.07	= : 0.07	# : 0.07	[ : 0.07	a : 0.05	f : 0.05	$ : 0.05	i : 0.01	b : 0.01	: : 0.01	& : 0.01	
c : 0.12	d : 0.10	e : 0.09	[ : 0.09	! : 0.07	g : 0.07	= : 0.07	# : 0.07	$ : 0.07	" : 0.05	f : 0.05	a : 0.03	i : 0.03	: : 0.01	& : 0.01	
d : 0.21	e : 0.18	c : 0.18	= : 0.10	g : 0.09	f : 0.07	# : 0.05	$ : 0.03	i : 0.03	! : 0.01	
d : 0.20	e : 0.18	c : 0.12	g : 0.10	= : 0.10	[ : 0.07	f : 0.07	$ : 0.03	# : 0.03	i : 0.03	! : 0.01	
e : 0.16	d : 0.16	= : 0.14	g : 0.10	c : 0.07	[ : 0.07	$ : 0.05	f : 0.05	! : 0.05	b : 0.03	" : 0.03	i : 0.03	
e : 0.16	d : 0.16	! : 0.12	= : 0.12	g : 0.10	b : 0.05	c : 0.05	" : 0.05	$ : 0.03	i : 0.03	f : 0.03	[ : 0.03	
e : 0.16	[ : 0.16	! : 0.10	= : 0.10	c : 0.09	d : 0.09	g : 0.07	# : 0.05	" : 0.05	b : 0.03	f : 0.01	i : 0.01	$ : 0.01	
c : 0.23	d : 0.12	e : 0.10	= : 0.10	b : 0.09	# : 0.05	[ : 0.05	! : 0.05	g : 0.05	" : 0.03	a : 0.01	f : 0.01	i : 0.01	$ : 0.01	
c : 0.20	= : 0.12	b : 0.10	d : 0.10	[ : 0.09	e : 0.09	# : 0.07	! : 0.05	g : 0.05	" : 0.03	i : 0.01	a : 0.01	$ : 0.01	
c : 0.23	d : 0.12	= : 0.12	" : 0.10	! : 0.07	# : 0.07	e : 0.07	b : 0.05	g : 0.03	a : 0.03	$ : 0.01	i : 0.01	[ : 0.01	
[ : 0.18	c : 0.16	" : 0.14	d : 0.14	= : 0.10	! : 0.09	# : 0.05	e : 0.05	$ : 0.01	g : 0.01	b : 0.01	
c : 0.23	" : 0.14	d : 0.14	= : 0.10	# : 0.05	b : 0.05	f : 0.05	! : 0.05	$ : 0.03	a : 0.03	[ : 0.03	e : 0.03	
c : 0.20	d : 0.20	b : 0.10	= : 0.09	! : 0.09	" : 0.09	[ : 0.05	f : 0.05	$ : 0.03	# : 0.03	e : 0.01	a : 0.01	
d : 0.29	c : 0.12	! : 0.10	[ : 0.09	= : 0.09	b : 0.07	" : 0.05	f : 0.05	$ : 0.03	# : 0.03	e : 0.01	a : 0.01	
d : 0.29	c : 0.20	[ : 0.10	= : 0.05	r : 0.05	" : 0.05	f : 0.05	b : 0.05	! : 0.05	a : 0.03	e : 0.01	$ : 0.01	
d : 0.30	c : 0.25	b : 0.12	r : 0.05	f : 0.05	= : 0.03	" : 0.03	e : 0.01	$ : 0.01	[ : 0.01	o : 0.01	! : 0.01	l : 0.01	m : 0.01	
d : 0.29	c : 0.27	b : 0.09	r : 0.05	o : 0.05	f : 0.05	= : 0.03	e : 0.01	" : 0.01	! : 0.01	q : 0.01	a : 0.01	l : 0.01	n : 0.01	m : 0.01	
o : 0.45	d : 0.14	c : 0.10	r : 0.05	l : 0.05	= : 0.03	m : 0.03	q : 0.03	p : 0.01	b : 0.01	! : 0.01	n : 0.01	
o : 0.50	d : 0.10	l : 0.09	n : 0.07	r : 0.05	m : 0.03	q : 0.03	c : 0.03	p : 0.01	= : 0.01	b : 0.01	
o : 0.56	l : 0.09	n : 0.07	r : 0.05	m : 0.05	d : 0.05	q : 0.03	p : 0.01	= : 0.01	c : 0.01	a : 0.01	
o : 0.56	n : 0.07	m : 0.07	l : 0.07	r : 0.05	q : 0.03	p : 0.01	= : 0.01	c : 0.01	f : 0.01	b : 0.01	d : 0.01	2 : 0.01	
o : 0.54	d : 0.07	n : 0.05	r : 0.05	c : 0.05	m : 0.05	q : 0.03	l : 0.03	p : 0.01	= : 0.01	f : 0.01	b : 0.01	2 : 0.01	
o : 0.50	d : 0.07	c : 0.07	n : 0.05	l : 0.05	r : 0.05	m : 0.05	q : 0.03	p : 0.01	f : 0.01	b : 0.01	e : 0.01	a : 0.01	
d : 0.27	c : 0.25	b : 0.10	o : 0.10	f : 0.05	l : 0.03	q : 0.03	e : 0.03	p : 0.01	= : 0.01	a : 0.01	m : 0.01	] : 0.01	
d : 0.30	c : 0.27	b : 0.10	o : 0.05	f : 0.05	e : 0.03	= : 0.03	] : 0.03	l : 0.01	4 : 0.01	q : 0.01	3 : 0.01	2 : 0.01	
d : 0.34	c : 0.27	] : 0.09	= : 0.05	3 : 0.05	f : 0.05	e : 0.03	b : 0.03	4 : 0.01	a : 0.01	2 : 0.01	
d : 0.32	c : 0.14	4 : 0.10	b : 0.07	3 : 0.07	= : 0.05	] : 0.05	e : 0.03	2 : 0.03	f : 0.03	a : 0.03	5 : 0.01	
3 : 0.18	2 : 0.16	d : 0.12	4 : 0.12	c : 0.10	b : 0.07	= : 0.07	e : 0.03	f : 0.03	] : 0.03	5 : 0.01	a : 0.01	
2 : 0.20	3 : 0.14	4 : 0.12	d : 0.12	= : 0.10	c : 0.10	] : 0.05	e : 0.03	f : 0.03	b : 0.03	5 : 0.01	
] : 0.18	d : 0.14	c : 0.14	3 : 0.12	4 : 0.12	= : 0.10	2 : 0.09	e : 0.03	5 : 0.01	b : 0.01	
c : 0.34	d : 0.21	= : 0.14	b : 0.07	4 : 0.03	a : 0.03	e : 0.03	] : 0.03	5 : 0.01	2 : 0.01	g : 0.01	3 : 0.01	
c : 0.34	d : 0.23	= : 0.14	b : 0.09	e : 0.07	] : 0.05	4 : 0.01	g : 0.01	3 : 0.01	
c : 0.25	d : 0.21	= : 0.14	3 : 0.10	b : 0.07	] : 0.05	e : 0.05	2 : 0.03	g : 0.01	a : 0.01	4 : 0.01	
2 : 0.32	= : 0.12	d : 0.12	3 : 0.10	] : 0.07	b : 0.07	e : 0.07	g : 0.03	4 : 0.03	c : 0.01	
2 : 0.30	] : 0.12	= : 0.10	3 : 0.10	e : 0.09	d : 0.07	g : 0.05	4 : 0.03	a : 0.01	c : 0.01	f : 0.01	i : 0.01	b : 0.01	
c : 0.21	e : 0.18	g : 0.14	= : 0.12	d : 0.12	b : 0.05	f : 0.03	4 : 0.03	3 : 0.01	2 : 0.01	i : 0.01	] : 0.01	
c : 0.25	g : 0.16	e : 0.14	d : 0.14	= : 0.12	b : 0.05	f : 0.03	4 : 0.03	3 : 0.01	i : 0.01	
c : 0.27	e : 0.16	g : 0.14	= : 0.12	d : 0.12	] : 0.05	f : 0.03	3 : 0.01	i : 0.01	2 : 0.01	4 : 0.01	
e : 0.16	g : 0.14	d : 0.12	c : 0.09	= : 0.09	] : 0.09	3 : 0.07	2 : 0.07	f : 0.05	i : 0.03	D : 0.01	4 : 0.01	a : 0.01	
e : 0.14	g : 0.14	= : 0.09	d : 0.09	c : 0.07	3 : 0.07	f : 0.07	2 : 0.07	] : 0.07	a : 0.05	4 : 0.03	i : 0.03	b : 0.01	D : 0.01	

#score	758.2931418790907
#seq	55
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m1_run1.txt

#BEAR
d::eeeeettttttttttteeeee	chr17:27003147-27003369(+)$1	222	144	168	19.8562
========ttttttttttt=====	chr16:29818683-29818944(+)$1	261	90	114	21.3171
bb[dddduuuuuuuuuuuuddddb	chr10:105151904-105152126(-)$1	222	113	137	21.9660
c!!dddduuuuuuuuuuuudddd2	chr10:28897044-28897291(+)$1	247	178	202	22.8490
ee!!cccuuuuuuuuuuuuccc33	chr12:50152377-50152632(+)$1	255	32	56	23.2339
:bb[cccuuuuuuuuuuuucccbb	chr2:62103202-62103444(-)$1	242	118	142	21.3655
ddd[ddddtttttttttttdddd]	chr19:6413378-6413653(-)$1	275	7	31	21.0275
gggggggtttttttttttgggggg	chr6:26217076-26217341(+)$1	265	88	112	20.7172
!!eeeeeuuuuuuuuuuuueeeee	chr3:113440556-113440782(-)$1	226	47	71	23.8144
fffdddduuuuuuuuuuuudddd2	chr1:149858761-149858986(+)$1	225	53	77	22.3459
eeeeewwwwwwwwwwwwwweeeee	chr2:74755906-74756138(-)$1	232	198	222	21.8957
[cccyyyyyyyyyyyyyyyycccc	chr16:29817924-29818166(+)$1	242	179	203	21.6915
$ffffffwwwwwwwwwwwwwwfff	chr14:59965383-59965623(+)$1	240	9	33	20.6300
#ccc[ccctttttttttttccccc	chr5:140953536-140953799(-)$1	263	169	193	22.0421
eeeeccctttttttttttccc]ee	chrX:47088667-47088903(+)$1	236	120	144	21.5213
gggggggvvvvvvvvvvvvvgggg	chr19:45477638-45477871(+)$1	233	158	182	21.7601
d!!cccvvvvvvvvvvvvvcccdd	chr10:93608054-93608274(+)$1	220	147	171	22.2818
ggg[cccvvvvvvvvvvvvvccc]	chr7:116532968-116533193(+)$1	225	28	52	22.3183
ccbb[ccctttttttttttccc]b	chr1:224377361-224377603(+)$1	242	72	96	20.9008
eeeeewwwwwwwwwwwwwweeeee	chr15:69745155-69745428(+)$1	273	145	169	21.8957
gggggggtttttttttttgggggg	chrX:107975775-107976064(-)$1	289	263	287	20.7172
c:fffffftttttttttttfffff	chr19:50001105-50001342(+)$1	237	176	200	19.6552
fffeeeeettttttttttteeeee	chrX:123787511-123787730(-)$1	219	24	48	21.5787
!!ccc[auuuuuuuuuuuua]ccc	chr3:172486760-172486986(+)$1	226	72	96	23.6768
""eeeeevvvvvvvvvvvvveeee	chr16:29822248-29822489(+)$1	241	147	171	22.4999
cdddd[bbtttttttttttbbddd	chr17:79803682-79803916(-)$1	234	9	33	20.5530
:ccccccuuuuuuuuuuuuccc]c	chr2:217363925-217364213(+)$1	288	136	160	22.3936
!!fffffftttttttttttfffff	chr20:44444400-44444647(+)$1	247	200	224	21.0221
e"""ccctttttttttttccc333	chr1:149899520-149899759(-)$1	239	128	152	21.3274
:ffffffuuuuuuuuuuuufffff	chr15:65862413-65862639(+)$1	226	2	26	21.2055
[ddddyyyyyyyyyyyyyyyyddd	chr2:224640588-224640813(-)$1	225	85	109	21.4472
dddeeeeettttttttttteeeee	chr1:156280706-156280983(-)$1	277	100	124	21.5730
eeeeexxxxxxxxxxxxxxxeeee	chr21:34877841-34878092(-)$1	251	78	102	17.9241
ggggg[auuuuuuuuuuuua]ggg	chr17:34171577-34171838(+)$1	261	113	137	23.2465
=======vvvvvvvvvvvvv====	chr11:4127304-4127536(+)$1	232	179	203	21.9321
fffffwwwwwwwwwwwwwwfffff	chr19:18390744-18390969(-)$1	225	193	217	20.8615
fffbbwwwwwwwwwwwwwwbb]ff	chr7:30395257-30395531(+)$1	274	144	168	20.2173
!!eeeeeuuuuuuuuuuuueeeee	chr6:31604220-31604485(+)$1	265	212	236	23.8144
[gggggggtttttttttttggggg	chr10:79795015-79795271(+)$1	256	21	45	21.3227
[bb[ddddtttttttttttdddd]	chr12:125396165-125396419(-)$1	254	90	114	21.0787
hhhhhhhuuuuuuuuuuuuhhhhh	chr2:74386214-74386458(-)$1	244	190	214	20.5509
eeeeexxxxxxxxxxxxxxxeeee	chr17:33689933-33690166(-)$1	233	164	188	17.9241
e[cccwwwwwwwwwwwwwwcccee	chr3:49397526-49397772(-)$1	246	201	225	22.1488
dccc[bbtttttttttttbbccc]	chr16:18809936-18810197(-)$1	261	219	243	20.7633
#ffffffattttttttttta]fff	chr19:3984086-3984358(-)$1	272	200	224	21.3956
d[ddddvvvvvvvvvvvvvdddd]	chr1:228680695-228680926(+)$1	231	148	172	21.8859
iiiiiwwwwwwwwwwwwwwiiiii	chr6:31797535-31797824(+)$1	289	146	170	21.6187
eeeeewwwwwwwwwwwwwweeeee	chr1:91985705-91985933(+)$1	228	143	167	21.8957
::ddddwwwwwwwwwwwwwwdddd	chr9:136216724-136216989(+)$1	265	57	81	19.8498
!!ddddyyyyyyyyyyyyyyyydd	chrX:47088137-47088410(+)$1	273	188	212	21.3003
[ddddxxxxxxxxxxxxxxxdddd	chr2:47388853-47389084(-)$1	231	129	153	17.6781
[cccxxxxxxxxxxxxxxxcccee	chr10:27459384-27459620(+)$1	236	185	209	17.9115
!!cccxxxxxxxxxxxxxxxccc]	chr17:79478128-79478371(-)$1	243	174	198	18.5014
$$$eeeeettttttttttteeeee	chr2:220089696-220089952(-)$1	256	84	108	21.4785
""ddddxxxxxxxxxxxxxxxddd	chr4:122739146-122739375(-)$1	229	81	105	17.6609
!!eeeeettttttttttteeeee2	chr1:16262352-16262647(+)$1	295	61	85	21.7708
dddd!!bbtttttttttttbb22d	chr3:51423624-51423857(+)$1	233	169	193	19.8721
###cccxxxxxxxxxxxxxxxccc	chr1:78193991-78194217(-)$1	226	111	135	17.8019
[eeeee[atttttttttttaeeee	chr3:58295978-58296201(+)$1	223	182	206	22.4846
c!!dddduuuuuuuuuuuudddd3	chr1:169446804-169447064(-)$1	260	180	204	23.0443
fff[ccctttttttttttccc]ff	chr6:134303646-134303885(+)$1	239	211	235	21.1131
[a[eeeeettttttttttteeeee	chr19:42462354-42462580(-)$1	226	23	47	22.1486
dddd[bbwwwwwwwwwwwwwwbb]	chrX:47083946-47084191(+)$1	245	129	153	20.2244
::eeeeettttttttttteeeeeg	chr3:9512082-9512313(+)$1	231	38	62	19.7309
[ccc[bbtttttttttttbbccc]	chr1:246887619-246887850(+)$1	231	57	81	21.1216
!!cccxxxxxxxxxxxxxxxccc]	chr20:57605330-57605569(-)$1	239	9	33	18.5014

#otherMatches

#Seq PSSM
UGAGGGUGAAAUCCGAGUGCGCCC	chr17:27003147-27003369(+)$1	222	144	168	19.8562
GUGCUAUGAAGAUGCCGACCAUGG	chr16:29818683-29818944(+)$1	261	90	114	21.3171
GCAUUGAUUGUCUUAUAUUUCAAG	chr10:105151904-105152126(-)$1	222	113	137	21.9660
UCCCUGUUUCUCCUGUUCCACAGU	chr10:28897044-28897291(+)$1	247	178	202	22.8490
GAUUGCUUUACUUUGCCUUGGCUU	chr12:50152377-50152632(+)$1	255	32	56	23.2339
GAGUGCUGCGAGAAGAGAGAGCCU	chr2:62103202-62103444(-)$1	242	118	142	21.3655
UCUUGCUAUUUCUUUUUUUUAGUU	chr19:6413378-6413653(-)$1	275	7	31	21.0275
CAGUGGAUUGUUAGUUCUUCUGCU	chr6:26217076-26217341(+)$1	265	88	112	20.7172
GGCUUUGAGAUUAUUGAGACAAAG	chr3:113440556-113440782(-)$1	226	47	71	23.8144
GCUGGGCAAAGUCACCAUCGCCCA	chr1:149858761-149858986(+)$1	225	53	77	22.3459
UCCUCUGCUGCUAUUCCCUGAGGA	chr2:74755906-74756138(-)$1	232	198	222	21.8957
AUGAACUCCUUCCCGCCACCUCAG	chr16:29817924-29818166(+)$1	242	179	203	21.6915
AAACAUUUUUAAAACAUUUUUGAU	chr14:59965383-59965623(+)$1	240	9	33	20.6300
UUCCACCACCACCUGCUCCUGGGG	chr5:140953536-140953799(-)$1	263	169	193	22.0421
CCUGCUCCCAGCCUUUCAGAGACA	chrX:47088667-47088903(+)$1	236	120	144	21.5213
UAGCGGCGAGAACUCAGACGGCUG	chr19:45477638-45477871(+)$1	233	158	182	21.7601
CAAGCCUCAAGUGCUCAAUGGUGU	chr10:93608054-93608274(+)$1	220	147	171	22.2818
AUUCUUGAAACAUAUAACAAUAAU	chr7:116532968-116533193(+)$1	225	28	52	22.3183
AUUAACCACUCAAUGACUCUGGCU	chr1:224377361-224377603(+)$1	242	72	96	20.9008
CCGAGCUCGCCUGCAUCUACUCGG	chr15:69745155-69745428(+)$1	273	145	169	21.8957
AUUUUAGAAUUAAUUUCCCUAAAG	chrX:107975775-107976064(-)$1	289	263	287	20.7172
UACACCUGUCCCCCUGCUUCAGGU	chr19:50001105-50001342(+)$1	237	176	200	19.6552
UGAAAAGCUAAAAACCAUUGCUUU	chrX:123787511-123787730(-)$1	219	24	48	21.5787
CCACUCCAGUUCCUUCAAAGCAGU	chr3:172486760-172486986(+)$1	226	72	96	23.6768
AUCGUGUUCCUGUGUCCCCUGCAU	chr16:29822248-29822489(+)$1	241	147	171	22.4999
AGGCAUCGCCGCCCCUCACCGUGC	chr17:79803682-79803916(-)$1	234	9	33	20.5530
AUGGUGAAGAAAAUUGAAAUCAGC	chr2:217363925-217364213(+)$1	288	136	160	22.3936
AAGGCUCCCUCAAACAAAAGGAGC	chr20:44444400-44444647(+)$1	247	200	224	21.0221
CGAGCGGAAUCAGGGUAACUGGAG	chr1:149899520-149899759(-)$1	239	128	152	21.3274
GUCUUUCUAAUAGCUUCUUGGAAG	chr15:65862413-65862639(+)$1	226	2	26	21.2055
AGGUAUGCUAGUUUAUAUUUUUGC	chr2:224640588-224640813(-)$1	225	85	109	21.4472
AUGCCUUGACAGAAAAAUCCAAGG	chr1:156280706-156280983(-)$1	277	100	124	21.5730
UACAGGUAAUUAAUCAUAAACUGU	chr21:34877841-34878092(-)$1	251	78	102	17.9241
augguggggacagaggaggcggcu	chr17:34171577-34171838(+)$1	261	113	137	23.2465
GUACUCUCAGAAAAGUAAUAAGGG	chr11:4127304-4127536(+)$1	232	179	203	21.9321
UUCUUGUGUUGGUUUUUUAAAGAA	chr19:18390744-18390969(-)$1	225	193	217	20.8615
GGGAGAUACUAUAGCACGACUGCC	chr7:30395257-30395531(+)$1	274	144	168	20.2173
UUGCUGGCUUUGAUUUUCCCUGGU	chr6:31604220-31604485(+)$1	265	212	236	23.8144
AGGUCUUGGAAAAUCACAGCAAGG	chr10:79795015-79795271(+)$1	256	21	45	21.3227
CCUGUCUGACUACAACAUCCAGAA	chr12:125396165-125396419(-)$1	254	90	114	21.0787
GAGGAGGCCCACCUCAACACCUCC	chr2:74386214-74386458(-)$1	244	190	214	20.5509
ACAAGCCAUAUACAAACUACCUUG	chr17:33689933-33690166(-)$1	233	164	188	17.9241
ACUGGCCUUUUUCAUUUAUCUAUA	chr3:49397526-49397772(-)$1	246	201	225	22.1488
AAAGACUUUUUAAUAUAUAGCUUC	chr16:18809936-18810197(-)$1	261	219	243	20.7633
AGCGUUGCAUCACCAUCAAGUCAA	chr19:3984086-3984358(-)$1	272	200	224	21.3956
GAGGCUGAGAAGGAGGAGGGGCUC	chr1:228680695-228680926(+)$1	231	148	172	21.8859
UUGAGGUGGACUGUUGGGACUCAA	chr6:31797535-31797824(+)$1	289	146	170	21.6187
GUAUUAUAGAACCAAACAAAAUGC	chr1:91985705-91985933(+)$1	228	143	167	21.8957
AGCUGGCCCACAAGUACAGACCAG	chr9:136216724-136216989(+)$1	265	57	81	19.8498
UUGGCCUGUCAACCCACCCAUUGG	chrX:47088137-47088410(+)$1	273	188	212	21.3003
AUGACAAACCUUGGAGAGAAGUUA	chr2:47388853-47389084(-)$1	231	129	153	17.6781
CUUCUAAAAAUAUUUCUAUGAACU	chr10:27459384-27459620(+)$1	236	185	209	17.9115
AAAGGUUUCUACUCUUACAUCCUC	chr17:79478128-79478371(-)$1	243	174	198	18.5014
UAUCAAGUUCAUCUAUAACAUUUG	chr2:220089696-220089952(-)$1	256	84	108	21.4785
AAGUCUUAAGCCUUGUCUCAUGGA	chr4:122739146-122739375(-)$1	229	81	105	17.6609
CAGCAGCCAGGGAAGGAAGCUGCC	chr1:16262352-16262647(+)$1	295	61	85	21.7708
GGCCCUGGCUCAUGUUAACCCUCG	chr3:51423624-51423857(+)$1	233	169	193	19.8721
AUGUGCAAUAAGAUUAAUAAAGUA	chr1:78193991-78194217(-)$1	226	111	135	17.8019
UAGAUUACUUUUCUAACAUGAAUC	chr3:58295978-58296201(+)$1	223	182	206	22.4846
CUCAGCCUUAUUGUUACAUGGUUU	chr1:169446804-169447064(-)$1	260	180	204	23.0443
CUUAACAGCAAAAUCAUAUGUAAA	chr6:134303646-134303885(+)$1	239	211	235	21.1131
CCUCCCUGCACUCCUCCUCCAGGG	chr19:42462354-42462580(-)$1	226	23	47	22.1486
GAAGCUGACCCUCAAUAGCCCCAU	chrX:47083946-47084191(+)$1	245	129	153	20.2244
CCGUUGAUUUUUAUUCUUUCAGCU	chr3:9512082-9512313(+)$1	231	38	62	19.7309
GCCGUGGACUCCACCCGCCCCGGG	chr1:246887619-246887850(+)$1	231	57	81	21.1216
AAAGCGAAAACACAGUAACAGCUG	chr20:57605330-57605569(-)$1	239	9	33	18.5014

#DB
)..(((((...........)))))	chr17:27003147-27003369(+)$1	1	144	168	19.8562
((((((((...........)))))	chr16:29818683-29818944(+)$1	1	90	114	21.3171
((.((((............)))))	chr10:105151904-105152126(-)$1	1	113	137	21.9660
(..((((............)))).	chr10:28897044-28897291(+)$1	1	178	202	22.8490
((..(((............)))..	chr12:50152377-50152632(+)$1	1	32	56	23.2339
.((.(((............)))))	chr2:62103202-62103444(-)$1	1	118	142	21.3655
(((.((((...........)))).	chr19:6413378-6413653(-)$1	1	7	31	21.0275
(((((((...........))))))	chr6:26217076-26217341(+)$1	1	88	112	20.7172
..(((((............)))))	chr3:113440556-113440782(-)$1	1	47	71	23.8144
(((((((............)))).	chr1:149858761-149858986(+)$1	1	53	77	22.3459
(((((..............)))))	chr2:74755906-74756138(-)$1	1	198	222	21.8957
.(((................))))	chr16:29817924-29818166(+)$1	1	179	203	21.6915
.((((((..............)))	chr14:59965383-59965623(+)$1	1	9	33	20.6300
.(((.(((...........)))))	chr5:140953536-140953799(-)$1	1	169	193	22.0421
(((((((...........))).))	chrX:47088667-47088903(+)$1	1	120	144	21.5213
(((((((.............))))	chr19:45477638-45477871(+)$1	1	158	182	21.7601
(..(((.............)))))	chr10:93608054-93608274(+)$1	1	147	171	22.2818
(((.(((.............))).	chr7:116532968-116533193(+)$1	1	28	52	22.3183
((((.(((...........))).)	chr1:224377361-224377603(+)$1	1	72	96	20.9008
(((((..............)))))	chr15:69745155-69745428(+)$1	1	145	169	21.8957
(((((((...........))))))	chrX:107975775-107976064(-)$1	1	263	287	20.7172
).((((((...........)))))	chr19:50001105-50001342(+)$1	1	176	200	19.6552
((((((((...........)))))	chrX:123787511-123787730(-)$1	1	24	48	21.5787
..(((.(............).)))	chr3:172486760-172486986(+)$1	1	72	96	23.6768
..(((((.............))))	chr16:29822248-29822489(+)$1	1	147	171	22.4999
)((((.((...........)))))	chr17:79803682-79803916(-)$1	1	9	33	20.5530
.((((((............))).)	chr2:217363925-217364213(+)$1	1	136	160	22.3936
..((((((...........)))))	chr20:44444400-44444647(+)$1	1	200	224	21.0221
(...(((...........)))...	chr1:149899520-149899759(-)$1	1	128	152	21.3274
.((((((............)))))	chr15:65862413-65862639(+)$1	1	2	26	21.2055
.((((................)))	chr2:224640588-224640813(-)$1	1	85	109	21.4472
((((((((...........)))))	chr1:156280706-156280983(-)$1	1	100	124	21.5730
(((((...............))))	chr21:34877841-34878092(-)$1	1	78	102	17.9241
(((((.(............).)))	chr17:34171577-34171838(+)$1	1	113	137	23.2465
(((((((.............))))	chr11:4127304-4127536(+)$1	1	179	203	21.9321
(((((..............)))))	chr19:18390744-18390969(-)$1	1	193	217	20.8615
(((((..............)).))	chr7:30395257-30395531(+)$1	1	144	168	20.2173
..(((((............)))))	chr6:31604220-31604485(+)$1	1	212	236	23.8144
.(((((((...........)))))	chr10:79795015-79795271(+)$1	1	21	45	21.3227
.((.((((...........)))).	chr12:125396165-125396419(-)$1	1	90	114	21.0787
(((((((............)))))	chr2:74386214-74386458(-)$1	1	190	214	20.5509
(((((...............))))	chr17:33689933-33690166(-)$1	1	164	188	17.9241
(.(((..............)))))	chr3:49397526-49397772(-)$1	1	201	225	22.1488
((((.((...........))))).	chr16:18809936-18810197(-)$1	1	219	243	20.7633
.(((((((...........).)))	chr19:3984086-3984358(-)$1	1	200	224	21.3956
(.((((.............)))).	chr1:228680695-228680926(+)$1	1	148	172	21.8859
(((((..............)))))	chr6:31797535-31797824(+)$1	1	146	170	21.6187
(((((..............)))))	chr1:91985705-91985933(+)$1	1	143	167	21.8957
..((((..............))))	chr9:136216724-136216989(+)$1	1	57	81	19.8498
..((((................))	chrX:47088137-47088410(+)$1	1	188	212	21.3003
.((((...............))))	chr2:47388853-47389084(-)$1	1	129	153	17.6781
.(((...............)))))	chr10:27459384-27459620(+)$1	1	185	209	17.9115
..(((...............))).	chr17:79478128-79478371(-)$1	1	174	198	18.5014
...(((((...........)))))	chr2:220089696-220089952(-)$1	1	84	108	21.4785
..((((...............)))	chr4:122739146-122739375(-)$1	1	81	105	17.6609
..(((((...........))))).	chr1:16262352-16262647(+)$1	1	61	85	21.7708
((((..((...........))..)	chr3:51423624-51423857(+)$1	1	169	193	19.8721
...(((...............)))	chr1:78193991-78194217(-)$1	1	111	135	17.8019
.(((((.(...........)))))	chr3:58295978-58296201(+)$1	1	182	206	22.4846
(..((((............)))).	chr1:169446804-169447064(-)$1	1	180	204	23.0443
(((.(((...........))).))	chr6:134303646-134303885(+)$1	1	211	235	21.1131
.(.(((((...........)))))	chr19:42462354-42462580(-)$1	1	23	47	22.1486
((((.((..............)).	chrX:47083946-47084191(+)$1	1	129	153	20.2244
..(((((...........)))))(	chr3:9512082-9512313(+)$1	1	38	62	19.7309
.(((.((...........))))).	chr1:246887619-246887850(+)$1	1	57	81	21.1216
..(((...............))).	chr20:57605330-57605569(-)$1	1	9	33	18.5014

#PSSM
e : 0.13	[ : 0.13	d : 0.12	! : 0.12	c : 0.07	: : 0.07	g : 0.07	f : 0.07	# : 0.04	= : 0.03	$ : 0.03	" : 0.03	b : 0.01	h : 0.01	i : 0.01	
! : 0.16	e : 0.12	f : 0.12	d : 0.10	c : 0.10	g : 0.09	: : 0.06	b : 0.04	" : 0.04	= : 0.03	[ : 0.03	h : 0.01	i : 0.01	$ : 0.01	# : 0.01	a : 0.01	
e : 0.18	d : 0.16	f : 0.15	c : 0.15	g : 0.09	! : 0.06	b : 0.04	= : 0.03	[ : 0.03	: : 0.01	" : 0.01	h : 0.01	i : 0.01	$ : 0.01	# : 0.01	
e : 0.25	d : 0.19	c : 0.18	f : 0.09	[ : 0.07	g : 0.07	= : 0.03	b : 0.03	! : 0.01	" : 0.01	h : 0.01	i : 0.01	
e : 0.24	d : 0.19	c : 0.19	f : 0.09	g : 0.07	[ : 0.07	= : 0.03	y : 0.01	b : 0.01	h : 0.01	i : 0.01	x : 0.01	! : 0.01	
e : 0.16	c : 0.16	d : 0.15	w : 0.10	x : 0.09	f : 0.07	g : 0.06	[ : 0.04	b : 0.04	= : 0.03	y : 0.03	h : 0.01	! : 0.01	
e : 0.15	c : 0.13	w : 0.12	x : 0.12	d : 0.09	f : 0.07	b : 0.07	g : 0.06	y : 0.04	= : 0.03	v : 0.03	a : 0.03	h : 0.01	[ : 0.01	
u : 0.19	w : 0.15	t : 0.13	x : 0.12	v : 0.09	e : 0.07	y : 0.04	d : 0.03	c : 0.03	f : 0.03	b : 0.03	a : 0.03	= : 0.01	g : 0.01	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.39	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	
t : 0.25	u : 0.19	w : 0.15	x : 0.12	v : 0.09	y : 0.04	c : 0.04	g : 0.03	b : 0.03	e : 0.03	
e : 0.18	c : 0.16	d : 0.10	x : 0.10	b : 0.07	v : 0.06	f : 0.06	a : 0.06	g : 0.04	y : 0.04	w : 0.04	= : 0.01	h : 0.01	i : 0.01	
c : 0.25	e : 0.24	d : 0.13	g : 0.06	f : 0.06	] : 0.04	b : 0.04	= : 0.03	w : 0.03	y : 0.03	x : 0.03	h : 0.01	i : 0.01	
e : 0.24	c : 0.24	d : 0.18	f : 0.09	g : 0.07	] : 0.04	= : 0.03	3 : 0.01	h : 0.01	i : 0.01	y : 0.01	2 : 0.01	b : 0.01	
e : 0.28	d : 0.21	c : 0.13	f : 0.12	g : 0.07	= : 0.03	3 : 0.03	b : 0.03	] : 0.03	h : 0.01	i : 0.01	2 : 0.01	
e : 0.25	] : 0.13	f : 0.12	d : 0.12	g : 0.09	c : 0.07	b : 0.04	2 : 0.04	3 : 0.04	= : 0.03	h : 0.01	i : 0.01	

#score	1393.8570843336734
#seq	66
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_UTR_m2_run2.txt

#BEAR
eee[ccc[bboooooobb22ccce	chr15:34836965-34837203(-)$1	238	80	104	11.8194
a[a[ddddbboooooobb]dddd]	chr17:40269646-40269888(-)$1	242	164	188	12.5066
ggg[ccc[bboooooobb]ccc22	chr10:72575603-72575842(+)$1	239	129	153	12.3677
cccdddd[bboooooobb]dddd:	chr6:31946654-31946875(+)$1	221	63	87	10.9950
bb[gggggggooooooggggggg]	chrX:48433536-48433771(+)$1	235	112	136	11.8639
eeeee"""bboooooobb]eeeee	chr15:91510209-91510439(-)$1	230	130	154	11.9398
##bb[eeeeeooooooeeeeebb4	chr19:3612998-3613232(-)$1	234	25	49	11.8779
e[ccc[ddddoooooodddd]ccc	chr12:57395673-57395912(-)$1	239	88	112	14.2155
eeee!!cccaooooooa]ccceee	chr22:38690334-38690594(-)$1	260	62	86	12.8459
cc!!a[ddddoooooodddda22c	chr12:121013509-121013744(+)$1	235	83	107	14.2594
eeeea[ddddoooooodddd]a22	chr7:139256255-139256486(-)$1	231	18	42	13.8344
!dddd!!cccooooooccc]dddd	chr6:31498780-31499012(-)$1	232	60	84	12.2316
Ddddd[ddddoooooodddd]ddd	chr7:35922030-35922274(+)$1	244	49	73	12.1284
cc####ddddoooooodddd]ccc	chr5:64859120-64859375(+)$1	255	225	249	14.1383
""bb!!ddddooooooddddbb33	chr1:92182045-92182279(-)$1	234	107	131	13.2913
eeeeeeeeeeooooooeeeee]ee	chr17:73035203-73035443(-)$1	240	57	81	12.4587
==========oooooo========	chr2:86437604-86437849(+)$1	245	217	241	12.9283
!!a!!eeeeeooooooeeeee22a	chr17:47684577-47684819(-)$1	242	124	148	13.6665
ccc[ffffffooooooffffff22	chr1:20977188-20977451(+)$1	263	141	165	11.0122
bb!!a[ddddoooooodddd]a22	chr17:79803728-79803959(-)$1	231	91	115	13.8652
!!ccc[eeeeeooooooeeeeecc	chr12:120637074-120637358(-)$1	284	51	75	11.9842
!!ccc[eeeeeooooooeeeee]c	chr11:804994-805229(-)$1	235	142	166	12.0333
gggbb[ddddoooooodddd]bb:	chr11:66391589-66391822(+)$1	233	16	40	11.9434
c$$$$$ddddoooooodddd333c	chr12:49088062-49088296(-)$1	234	175	199	13.6727
!!ccc[cccooooooccc22ccch	chr17:35870712-35870952(+)$1	240	197	221	11.2561
ee"""ccc[aooooooa]ccc444	chr14:103986153-103986395(-)$1	242	155	179	13.0863
hhh[a[ddddoooooodddda]hh	chr5:133707159-133707397(+)$1	238	30	54	13.3732
hhhhhhddddoooooodddd22hh	chrX:19377661-19377923(+)$1	262	231	255	12.1714
""ccceeeeeooooooeeeee]cc	chr7:7606606-7606845(+)$1	239	101	125	13.0805
cccgggggggooooooggggggg:	chr3:32726757-32726988(+)$1	231	9	33	11.4680
c[dddd[cccoooooocccdddd]	chr17:79479659-79479900(-)$1	241	64	88	12.3723
[eeeee[cccooooooccceeeee	chr19:19416757-19416985(-)$1	228	183	207	12.3565
Cccc!!ddddoooooodddd22cc	chr21:44514664-44514896(-)$1	232	142	166	12.9652
gggggggcccooooooccca[eee	chr19:990790-991036(+)$1	246	90	114	12.1252
b[a####cccooooooccc4444a	chr3:39424762-39424993(-)$1	231	164	188	13.5666
ddd$$$$$bboooooobb4444dd	chr17:80616446-80616682(-)$1	236	80	104	11.1911
eeeeeeeeeeooooooeeeeehhh	chr19:53352296-53352537(-)$1	241	47	71	11.9943
gg"""eeeeeooooooeeeeeggg	chr17:7481742-7481997(+)$1	255	84	108	13.1331
aeeeeea[bboooooobb]a]eee	chr12:1019139-1019383(+)$1	244	106	130	11.7874
b[ccc[eeeeeooooooeeeee]c	chr17:47004566-47004809(+)$1	243	81	105	11.7941
e[ccc[a[bboooooobba]ccc]	chr19:54710453-54710686(+)$1	233	176	200	12.7240
eeee!!ddddooooooddddeeee	chr11:16776424-16776688(+)$1	264	237	261	13.6813
]cccccccccooooooccc22ccc	chr5:176731649-176731883(+)$1	234	154	178	12.2383
ff:eeeee[aooooooa]eeeee:	chr1:151028348-151028569(-)$1	221	181	205	10.4029
bb####ddddoooooodddd333b	chr22:30972934-30973210(-)$1	276	88	112	13.7876
d[ccc!!cccooooooccc333cc	chr18:9861355-9861609(+)$1	254	105	129	13.6983
a[ccc[ddddooooooddddccc]	chr19:54647872-54648084(+)$1	212	46	70	14.2323
dddd[cccbboooooobb]cccdd	chr3:11850937-11851181(-)$1	244	156	180	11.6211
cc####ddddoooooodddd5555	chr19:1275977-1276202(+)$1	225	134	158	11.2868
2ddddeeeeeooooooeeeee:ee	chr1:110943999-110944237(-)$1	238	118	142	10.8912
eee"""ddddoooooodddd4444	chr16:22096448-22096688(+)$1	240	55	79	14.3453
eee[ccc!!aooooooa22cccee	chr16:22539054-22539291(+)$1	237	89	113	12.1830
g[a!!bb!!aooooooa22bb22a	chr2:74381301-74381570(-)$1	269	153	177	11.6870
"""gggggggooooooggggggg2	chr1:165865356-165865591(+)$1	235	125	149	12.3216
fff!!eeeeeooooooeeeee22f	chr1:150192894-150193152(-)$1	258	83	107	12.6869
hhhhh[ddddoooooodddd]hhh	chr5:148878676-148878918(-)$1	242	83	107	12.6730

#otherMatches

#Seq PSSM
UCAUCGUACAAAGAAAUGCCACGU	chr15:34836965-34837203(-)$1	238	80	104	11.8194
CUGACCCUGCUGCCAUGCUGGGGC	chr17:40269646-40269888(-)$1	242	164	188	12.5066
CCGGGCCUCCAAUCUCGGCGGCGG	chr10:72575603-72575842(+)$1	239	129	153	12.3677
GCUGGGCUUCGACUUGGAUGCCCA	chr6:31946654-31946875(+)$1	221	63	87	10.9950
CAGUUUCGGACCUAUCUCUGAGGG	chrX:48433536-48433771(+)$1	235	112	136	11.8639
AAUUAUAUGGGGGUGACUUUAGUU	chr15:91510209-91510439(-)$1	230	130	154	11.9398
CCUGAUCCAGCAGAGCCUGGACGA	chr19:3612998-3613232(-)$1	234	25	49	11.8779
UUCCAAAGAAACAGGAUUUUAUGG	chr12:57395673-57395912(-)$1	239	88	112	14.2155
CCGGAAUCCCGAGGAUGUGGACCG	chr22:38690334-38690594(-)$1	260	62	86	12.8459
AGAUGAGAACAGCUUAGUUCCUCC	chr12:121013509-121013744(+)$1	235	83	107	14.2594
CAAUCUCAGCUCUUCUGUUGUGCU	chr7:139256255-139256486(-)$1	231	18	42	13.8344
AAAGAUUUUCAACGACGAAUUCUU	chr6:31498780-31499012(-)$1	232	60	84	12.2316
UUCUUCCAUUUUAGAUAAUGAAAG	chr7:35922030-35922274(+)$1	244	49	73	12.1284
AUAGUACCGGGACGAAUUGGAGUG	chr5:64859120-64859375(+)$1	255	225	249	14.1383
AUGGAUGAAGGAGAUGCUUCCCUG	chr1:92182045-92182279(-)$1	234	107	131	13.2913
AUUUCUCUUUCUUCUUAAAGGUGA	chr17:73035203-73035443(-)$1	240	57	81	12.4587
GGAUAUGUAUCUUUGUGUACAUAU	chr2:86437604-86437849(+)$1	245	217	241	12.9283
AAGGAAAUGAUGUGCUUCAUUUAC	chr17:47684577-47684819(-)$1	242	124	148	13.6665
GGAAGAACUUGAGUGAGAGUUCAG	chr1:20977188-20977451(+)$1	263	141	165	11.0122
GCCCCACCUGAUGAGCCAGGAGCU	chr17:79803728-79803959(-)$1	231	91	115	13.8652
UCUGGCUUGUUUUUUGUAGCAACU	chr12:120637074-120637358(-)$1	284	51	75	11.9842
AUCCCGAGCCUGCCUCGGGGCUGG	chr11:804994-805229(-)$1	235	142	166	12.0333
UUGUGUGUCCAAUUUGGGACCCAU	chr11:66391589-66391822(+)$1	233	16	40	11.9434
AGACACAACCAUUGCAGGUUUAAU	chr12:49088062-49088296(-)$1	234	175	199	13.6727
CUUGUCUGACUGAAAUCACUGCAG	chr17:35870712-35870952(+)$1	240	197	221	11.2561
GGGCCAGGCCAUCGACGACCUCAU	chr14:103986153-103986395(-)$1	242	155	179	13.0863
ggcggcgAUCCACAGUGAUUcggc	chr5:133707159-133707397(+)$1	238	30	54	13.3732
GUGUAGAUUGAGCAGGUAGUAAUU	chrX:19377661-19377923(+)$1	262	231	255	12.1714
GUGAGCGCGACCCGGUUCGCGUCU	chr7:7606606-7606845(+)$1	239	101	125	13.0805
GACGACGGGAACUAGCUCUCGUCA	chr3:32726757-32726988(+)$1	231	9	33	11.4680
CCGCGGUCGGUCUCAGUCGCCGCU	chr17:79479659-79479900(-)$1	241	64	88	12.3723
ACAGGCCUGGGGCUGGCCAGCCUG	chr19:19416757-19416985(-)$1	228	183	207	12.3565
AGUGGCCAGUGACGUGACUGAGCA	chr21:44514664-44514896(-)$1	232	142	166	12.9652
GCUCUCCGUCCUCUUUGACGUGUC	chr19:990790-991036(+)$1	246	90	114	12.1252
CGCUUGUCACGUGAGGGUGUUCUG	chr3:39424762-39424993(-)$1	231	164	188	13.5666
UCCUGCCCGCUAGCAUGCCCCCGG	chr17:80616446-80616682(-)$1	236	80	104	11.1911
GGUUAAAAUGUGUUUUCAUUUCAG	chr19:53352296-53352537(-)$1	241	47	71	11.9943
CCAGCCAGGGCUCAAUCUCUGGGG	chr17:7481742-7481997(+)$1	255	84	108	13.1331
GCUAGGCUUGAACAGACGUGACCU	chr12:1019139-1019383(+)$1	244	106	130	11.7874
UGGGAGUGGGGGCCUGUUCCCGGU	chr17:47004566-47004809(+)$1	243	81	105	11.7941
CAGCCUCACCUCGCUUGGGUGGUG	chr19:54710453-54710686(+)$1	233	176	200	12.7240
CUUAGUCUUUGUAUUAAAAGUAAG	chr11:16776424-16776688(+)$1	264	237	261	13.6813
CAGACCAUGACUACCUUCACCUGG	chr5:176731649-176731883(+)$1	234	154	178	12.2383
GACACUGACCUUCACUGCUCAGUU	chr1:151028348-151028569(-)$1	221	181	205	10.4029
UCACAGGCCAACAAGCUGGCGGAG	chr22:30972934-30973210(-)$1	276	88	112	13.7876
CAUCAGCACUCAGAGUAGUCAGUG	chr18:9861355-9861609(+)$1	254	105	129	13.6983
UGGGUGUAGGCGGAACCCUAGCUG	chr19:54647872-54648084(+)$1	212	46	70	14.2323
UCAUGAUCCCGACUGUGGAGAUGU	chr3:11850937-11851181(-)$1	244	156	180	11.6211
CUGAAGCCGGAGCAUGCCGGGCAG	chr19:1275977-1276202(+)$1	225	134	158	11.2868
UGUCAUAGGAACUGGAUCCUACCU	chr1:110943999-110944237(-)$1	238	118	142	10.8912
aauaauaauaauaaaauauuuaCA	chr16:22096448-22096688(+)$1	240	55	79	14.3453
UUCGAGGAAAUAAAAUUGGCCUGA	chr16:22539054-22539291(+)$1	237	89	113	12.1830
GGGAGAUAAUGGGAAGAGGAUGGC	chr2:74381301-74381570(-)$1	269	153	177	11.6870
CUGGCCUUCUACUCCCAGGAGGUA	chr1:165865356-165865591(+)$1	235	125	149	12.3216
UUUAAGAAGAAGGAGGUCUUCGAG	chr1:150192894-150193152(-)$1	258	83	107	12.6869
AUUUUAACUGAUGUUACAGUGAAG	chr5:148878676-148878918(-)$1	242	83	107	12.6730

#DB
(((.(((.((......))..))))	chr15:34836965-34837203(-)$1	1	80	104	11.8194
(.(.((((((......)).)))).	chr17:40269646-40269888(-)$1	1	164	188	12.5066
(((.(((.((......)).)))..	chr10:72575603-72575842(+)$1	1	129	153	12.3677
)))((((.((......)).)))).	chr6:31946654-31946875(+)$1	1	63	87	10.9950
((.(((((((......))))))).	chrX:48433536-48433771(+)$1	1	112	136	11.8639
(((((...((......)).)))))	chr15:91510209-91510439(-)$1	1	130	154	11.9398
..((.(((((......))))))).	chr19:3612998-3613232(-)$1	1	25	49	11.8779
(.(((.((((......)))).)))	chr12:57395673-57395912(-)$1	1	88	112	14.2155
((((..((((......).))))))	chr22:38690334-38690594(-)$1	1	62	86	12.8459
((..(.((((......)))))..)	chr12:121013509-121013744(+)$1	1	83	107	14.2594
(((((.((((......)))).)..	chr7:139256255-139256486(-)$1	1	18	42	13.8344
.((((..(((......))).))))	chr6:31498780-31499012(-)$1	1	60	84	12.2316
(((((.((((......)))).)))	chr7:35922030-35922274(+)$1	1	49	73	12.1284
((....((((......)))).)))	chr5:64859120-64859375(+)$1	1	225	249	14.1383
..((..((((......))))))..	chr1:92182045-92182279(-)$1	1	107	131	13.2913
((((((((((......))))).))	chr17:73035203-73035443(-)$1	1	57	81	12.4587
((((((((((......))))))))	chr2:86437604-86437849(+)$1	1	217	241	12.9283
..(..(((((......)))))..)	chr17:47684577-47684819(-)$1	1	124	148	13.6665
(((.((((((......))))))..	chr1:20977188-20977451(+)$1	1	141	165	11.0122
((..(.((((......)))).)..	chr17:79803728-79803959(-)$1	1	91	115	13.8652
..(((.(((((......)))))))	chr12:120637074-120637358(-)$1	1	51	75	11.9842
..(((.(((((......))))).)	chr11:804994-805229(-)$1	1	142	166	12.0333
)))((.((((......)))).)).	chr11:66391589-66391822(+)$1	1	16	40	11.9434
(.....((((......))))...)	chr12:49088062-49088296(-)$1	1	175	199	13.6727
..(((.(((......)))..))))	chr17:35870712-35870952(+)$1	1	197	221	11.2561
((...(((.(......).)))...	chr14:103986153-103986395(-)$1	1	155	179	13.0863
(((.(.((((......))))).))	chr5:133707159-133707397(+)$1	1	30	54	13.3732
((((((((((......))))..))	chrX:19377661-19377923(+)$1	1	231	255	12.1714
..((((((((......))))).))	chr7:7606606-7606845(+)$1	1	101	125	13.0805
)))(((((((......))))))).	chr3:32726757-32726988(+)$1	1	9	33	11.4680
(.((((.(((......))))))).	chr17:79479659-79479900(-)$1	1	64	88	12.3723
.(((((.(((......))))))))	chr19:19416757-19416985(-)$1	1	183	207	12.3565
((((..((((......))))..))	chr21:44514664-44514896(-)$1	1	142	166	12.9652
)))))))(((......)))(.(((	chr19:990790-991036(+)$1	1	90	114	12.1252
(.(....(((......)))....)	chr3:39424762-39424993(-)$1	1	164	188	13.5666
(((.....((......))....))	chr17:80616446-80616682(-)$1	1	80	104	11.1911
)))))(((((......)))))(((	chr19:53352296-53352537(-)$1	1	47	71	11.9943
((...(((((......))))))))	chr17:7481742-7481997(+)$1	1	84	108	13.1331
(((((((.((......)).).)))	chr12:1019139-1019383(+)$1	1	106	130	11.7874
(.(((.(((((......))))).)	chr17:47004566-47004809(+)$1	1	81	105	11.7941
(.(((.(.((......))).))).	chr19:54710453-54710686(+)$1	1	176	200	12.7240
((((..((((......))))))))	chr11:16776424-16776688(+)$1	1	237	261	13.6813
.)))((((((......)))..)))	chr5:176731649-176731883(+)$1	1	154	178	12.2383
)).(((((.(......).))))).	chr1:151028348-151028569(-)$1	1	181	205	10.4029
((....((((......))))...)	chr22:30972934-30973210(-)$1	1	88	112	13.7876
(.(((..(((......)))...))	chr18:9861355-9861609(+)$1	1	105	129	13.6983
(.(((.((((......))))))).	chr19:54647872-54648084(+)$1	1	46	70	14.2323
((((.(((((......)).)))))	chr3:11850937-11851181(-)$1	1	156	180	11.6211
((....((((......))))....	chr19:1275977-1276202(+)$1	1	134	158	11.2868
.))))(((((......))))).((	chr1:110943999-110944237(-)$1	1	118	142	10.8912
(((...((((......))))....	chr16:22096448-22096688(+)$1	1	55	79	14.3453
(((.(((..(......)..)))))	chr16:22539054-22539291(+)$1	1	89	113	12.1830
(.(..((..(......)..))..)	chr2:74381301-74381570(-)$1	1	153	177	11.6870
...(((((((......))))))).	chr1:165865356-165865591(+)$1	1	125	149	12.3216
(((..(((((......)))))..)	chr1:150192894-150193152(-)$1	1	83	107	12.6869
(((((.((((......)))).)))	chr5:148878676-148878918(-)$1	1	83	107	12.6730

#PSSM
e : 0.21	c : 0.14	g : 0.08	b : 0.08	! : 0.08	a : 0.05	" : 0.05	h : 0.05	d : 0.05	f : 0.03	# : 0.01	D : 0.01	= : 0.01	[ : 0.01	C : 0.01	] : 0.01	2 : 0.01	
e : 0.21	[ : 0.16	c : 0.14	d : 0.08	g : 0.07	! : 0.07	b : 0.05	" : 0.05	h : 0.05	f : 0.03	# : 0.01	= : 0.01	$ : 0.01	
c : 0.24	e : 0.19	d : 0.10	a : 0.07	g : 0.05	# : 0.05	" : 0.05	h : 0.05	b : 0.03	! : 0.03	[ : 0.01	= : 0.01	$ : 0.01	: : 0.01	f : 0.01	
c : 0.19	e : 0.16	[ : 0.10	d : 0.10	! : 0.08	g : 0.07	# : 0.07	b : 0.05	" : 0.05	$ : 0.03	h : 0.03	= : 0.01	
c : 0.23	! : 0.12	d : 0.10	e : 0.10	g : 0.07	a : 0.07	# : 0.07	" : 0.05	[ : 0.03	$ : 0.03	h : 0.03	= : 0.01	f : 0.01	b : 0.01	
[ : 0.24	e : 0.19	c : 0.10	! : 0.10	g : 0.07	# : 0.07	d : 0.05	" : 0.03	$ : 0.03	= : 0.01	f : 0.01	h : 0.01	b : 0.01	
d : 0.35	e : 0.21	c : 0.14	g : 0.07	! : 0.03	[ : 0.03	a : 0.03	" : 0.01	= : 0.01	f : 0.01	# : 0.01	$ : 0.01	b : 0.01	
d : 0.33	e : 0.21	c : 0.19	[ : 0.08	g : 0.05	! : 0.03	" : 0.01	= : 0.01	f : 0.01	$ : 0.01	
d : 0.32	e : 0.19	b : 0.16	c : 0.16	g : 0.05	[ : 0.03	! : 0.03	= : 0.01	f : 0.01	
d : 0.32	e : 0.19	b : 0.16	c : 0.12	a : 0.08	g : 0.05	= : 0.01	f : 0.01	o : 0.01	
o : 0.94	e : 0.05	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 0.98	c : 0.01	
d : 0.32	b : 0.16	e : 0.14	c : 0.14	a : 0.08	g : 0.05	o : 0.05	= : 0.01	f : 0.01	
d : 0.32	e : 0.19	b : 0.16	c : 0.14	g : 0.05	] : 0.05	2 : 0.03	= : 0.01	f : 0.01	
d : 0.32	e : 0.21	c : 0.16	] : 0.10	2 : 0.07	g : 0.05	= : 0.01	f : 0.01	4 : 0.01	a : 0.01	
d : 0.37	e : 0.24	c : 0.08	2 : 0.05	g : 0.05	] : 0.03	a : 0.03	4 : 0.03	= : 0.01	f : 0.01	3 : 0.01	b : 0.01	
e : 0.26	c : 0.16	] : 0.14	d : 0.07	g : 0.05	3 : 0.05	2 : 0.05	4 : 0.05	a : 0.03	b : 0.03	= : 0.01	f : 0.01	[ : 0.01	5 : 0.01	
c : 0.17	e : 0.17	2 : 0.10	d : 0.08	g : 0.07	4 : 0.07	b : 0.05	] : 0.05	3 : 0.05	a : 0.03	h : 0.03	= : 0.01	f : 0.01	5 : 0.01	: : 0.01	
c : 0.19	e : 0.17	2 : 0.14	d : 0.12	g : 0.07	h : 0.07	3 : 0.05	4 : 0.05	b : 0.03	] : 0.03	= : 0.01	5 : 0.01	
c : 0.19	e : 0.17	] : 0.08	2 : 0.08	h : 0.08	: : 0.07	d : 0.07	4 : 0.05	a : 0.05	3 : 0.01	= : 0.01	g : 0.01	b : 0.01	5 : 0.01	f : 0.01	

#score	702.0644393578734
#seq	56
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m2_run1.txt

#BEAR
cc!!bbeeeeennnnneeeee]bb333	chr19:2235679-2235904(-)$1	225	109	136	11.8344
'ffffff[cccnnnnnccc]fffffff	chr15:64428435-64428640(+)$1	205	170	197	12.6199
eeee"""ddddnnnnndddd22eeeee	chrX:41007629-41007880(+)$1	251	22	49	13.3674
eeeee[eeeeennnnneeeeeeeeee6	chr14:96001471-96001712(+)$1	241	115	142	11.5967
[a!!dddd[bbnnnnnbb22dddda]b	chr1:109439481-109439684(+)$1	203	41	68	11.4847
ggggggg[cccnnnnnccc]ggggggg	chrX:53564492-53564729(-)$1	237	88	115	14.7846
$$eeeee[cccnnnnnccc]eeeee]b	chr19:58904635-58904937(+)$1	302	48	75	13.2726
ccc[bb[ddddnnnnnddddbb]ccc]	chr16:30667452-30667716(+)$1	264	82	109	12.5898
"ccc[bb[cccnnnnncccbb]cccdd	chr20:61907752-61907969(+)$1	217	12	39	12.9613
eeee"""ddddnnnnndddd22eeeee	chr1:100459113-100459351(+)$1	238	54	81	13.3674
ffffff!!cccnnnnncccffffffff	chr7:29994702-29994909(-)$1	207	163	190	13.4090
bbggggggg[annnnna]ggggggg]b	chr7:132990578-132990789(+)$1	211	67	94	12.6916
=ccceeeeebbnnnnnbb]eeeee]cc	chr20:33594249-33594457(-)$1	208	88	115	12.2191
!!cccaeeeeennnnneeeee]a]ccc	chr3:42602591-42602802(-)$1	211	151	178	12.8022
[ccc[ccc[bbnnnnnbb]ccc]cccd	chr3:50290399-50290626(+)$1	227	81	108	12.4575
eeeee[eeeeennnnneeeee333eee	chr17:27208832-27209066(-)$1	234	21	48	12.5610
gggggg[bb[annnnna]bb]gggggg	chr1:6341173-6341392(-)$1	219	5	32	12.6929
======eeeeennnnneeeee4444==	chr20:34302040-34302272(-)$1	232	150	177	12.9691
ggggbb[ddddnnnnndddd]bb22gg	chr19:29698350-29698585(-)$1	235	18	45	12.7908
ffffffeeeeennnnneeeee]fffff	chr16:28840656-28840888(+)$1	232	3	30	11.7233
eee$$$$$cccnnnnnccceeeeefff	chr1:94946001-94946239(+)$1	238	28	55	12.9574
eeeee####bbnnnnnbb333eeeee]	chr7:82581305-82581512(-)$1	207	143	170	13.2499
ggggg!!acccooooooccc]a22ggg	chr1:43630293-43630500(-)$1	207	33	60	10.1740
""bb"""ddddnnnnndddd]bb]fff	chr15:84286877-84287115(+)$1	238	190	217	12.8889
cc!!ddddcccnnnnnccc333dddd3	chr19:40478186-40478422(+)$1	236	146	173	13.8922
hhhhhh!!cccnnnnnccc22hhhhhh	chr12:111772373-111772580(+)$1	207	152	179	13.1278
ddd[ccc!!bbnnnnnbb]ccc]dddd	chr19:1105628-1105847(+)$1	219	171	198	11.8987
ffff!!ccc[annnnna]ccc]fffff	chr7:43684845-43685066(-)$1	221	117	144	12.8454
ffffff"""bbnnnnnbbfffffffff	chr22:39714323-39714539(-)$1	216	69	96	11.9213
:dddd!!ddddnnnnndddd22dddde	chr8:19687896-19688146(+)$1	250	15	42	11.7186
!!dddd!!cccnnnnnccc22dddd33	chr16:9010884-9011104(-)$1	220	63	90	13.9424
b!!dddd!!bbnnnnnbb333dddd]b	chr9:2811450-2811664(-)$1	214	134	161	12.2754
===========nnnnn===========	chr13:98658480-98658687(+)$1	207	113	140	14.3182
hhhhhh!!cccnnnnnccc333hhhhh	chr1:16199241-16199459(+)$1	218	96	123	13.7135
iiiiiiiiibbnnnnnbb]iiiiiiii	chr17:20924388-20924625(-)$1	237	99	126	13.4413
CCiiiiiiiiinnnnniiiiiiiiicc	chr8:103324348-103324551(-)$1	203	22	49	11.2607
"ccc[a!!cccnnnnnccc]a]ccc]b	chr6:26158607-26158842(+)$1	235	99	126	14.8487
dd[ffffff[annnnna]ffffff]dd	chr15:91308438-91308646(+)$1	208	88	115	11.2370
ffff####cccnnnnnccc4444ffff	chr14:23945144-23945357(+)$1	213	171	198	14.2181
=ccc[a[ddddnnnnndddd]a]ccc:	chr14:24475007-24475218(+)$1	211	79	106	12.8206
i####bb[cccnnnnnccc]bb333ii	chr12:57906480-57906704(+)$1	224	42	69	13.7124
iiiiiiii[bbnnnnnbbiiiiiiiii	chr1:235277104-235277314(-)$1	210	128	155	13.4944
beeeee!!cccnnnnnccc22eeeee:	chr14:20917241-20917444(-)$1	203	46	73	13.1006
###bb"""cccnnnnnccc22bb22ff	chr1:64117253-64117529(+)$1	276	232	259	13.7692
!bb[gggggggnnnnnggggggg]bb2	chr5:156731218-156731427(+)$1	209	8	35	11.9894
e!!addddcccnnnnnccc22dddd]a	chrX:150573299-150573532(+)$1	233	87	114	13.2906
eeeee!!ddddnnnnndddd22eeeee	chr13:31724100-31724316(-)$1	216	94	121	13.2983
hhhhhh[ddddnnnnnddddhhhhhhh	chr19:40540670-40540881(-)$1	211	100	127	11.4687
ggggg"""cccooooooccc]gggggg	chr1:16262284-16262489(+)$1	205	22	49	10.6547
ee####eeeeennnnneeeee333eee	chrX:71417123-71417358(+)$1	235	66	93	12.6755
[dddd"""cccnnnnncccdddd]ddd	chr4:178272499-178272734(+)$1	235	120	147	13.4993
gggggg[ddddnnnnndddd22ggggg	chr6:150001232-150001442(-)$1	210	124	151	13.9299
iiiiii!!cccnnnnnccc22iiiiii	chr17:26890394-26890609(-)$1	215	162	189	15.4572
ffffffbbcccnnnnnccc]bb333ff	chr16:85839253-85839479(+)$1	226	157	184	12.6492
%%%%bb!!cccnnnnnccc]bb333gg	chr1:202699039-202699241(-)$1	202	75	102	11.6315
c!!bb!!ddddnnnnndddd]bb22cc	chr12:98993743-98993991(+)$1	248	3	30	12.9013
iiiiii[cccooooooccciiiiiiii	chrX:69719690-69719930(+)$1	240	63	90	10.2454
cc[eeeeecccnnnnnccc]eeeeecc	chr16:18542728-18542956(-)$1	228	99	126	13.6818
ddddgggggggnnnnnggggggg]ddd	chr13:77633611-77633816(-)$1	205	72	99	12.2787

#otherMatches

#Seq PSSM
AGUCGUCCGGGAAGAGCCCGGCACCUU	chr19:2235679-2235904(-)$1	225	109	136	11.8344
UGAGGUGAGAUAGAAAAUCCUACUUCU	chr15:64428435-64428640(+)$1	205	170	197	12.6199
CGUGAAAAGCUACUUGAGCUGAUACGU	chrX:41007629-41007880(+)$1	251	22	49	13.3674
UGGUGGUCUUCCUCAAGGGGACGCCGG	chr14:96001471-96001712(+)$1	241	115	142	11.5967
GAACGUCUAUGUAAAUCAGGAGACUGC	chr1:109439481-109439684(+)$1	203	41	68	11.4847
CUGGAGCGUUUAGAUGAGGGGCUCCGG	chrX:53564492-53564729(-)$1	237	88	115	14.7846
GCAUGGGGCUGGAUGUCAGGCUCAUAU	chr19:58904635-58904937(+)$1	302	48	75	13.2726
CUGAUGUGGGCCCCCUGCUCCAGCAGC	chr16:30667452-30667716(+)$1	264	82	109	12.5898
UGCUGGGUGGAGGGUGUCCCUGGGUGU	chr20:61907752-61907969(+)$1	217	12	39	12.9613
UUGGUUCUAACAAUGCGUUAUUCCAGA	chr1:100459113-100459351(+)$1	238	54	81	13.3674
UGGGGACAGGAUUUAUUUCUCCCUAAA	chr7:29994702-29994909(-)$1	207	163	190	13.4090
UCUUUGGAGGGCCCCCUGCUCCAGGUG	chr7:132990578-132990789(+)$1	211	67	94	12.6916
UACUGCAUUGUGGACAGCGAGUGUAAG	chr20:33594249-33594457(-)$1	208	88	115	12.2191
AAUGGGGUGAUGAAUGGUCACACACCG	chr3:42602591-42602802(-)$1	211	151	178	12.8022
UGUCCUGCACCGCCGAGGAGCAAGGCG	chr3:50290399-50290626(+)$1	227	81	108	12.4575
CAGCUGAGGCCCAGUUGGCCUAUGAGC	chr17:27208832-27209066(-)$1	234	21	48	12.5610
GGGUGGAGGCCGCCCUGACCCCCGCCC	chr1:6341173-6341392(-)$1	219	5	32	12.6929
GCAAGACUUGCAGAGGGUAAGUGUUUC	chr20:34302040-34302272(-)$1	232	150	177	12.9691
GCCAUGGGUCACACUAUGAUGCAUCUG	chr19:29698350-29698585(-)$1	235	18	45	12.7908
AGGGAAGUGACUUGUCGUUGCUUUUCC	chr16:28840656-28840888(+)$1	232	3	30	11.7233
GCAUGAUGGCCUACUUGGUUGUUUCUG	chr1:94946001-94946239(+)$1	238	28	55	12.9574
UUGGUUAUAGGGAUGACCACUAUCAGU	chr7:82581305-82581512(-)$1	207	143	170	13.2499
UAAACGACGGUAUAAAAACCAGAAGUU	chr1:43630293-43630500(-)$1	207	33	60	10.1740
UCGUAACUGAAAUGAAUUCACACCAGU	chr15:84286877-84287115(+)$1	238	190	217	12.8889
CAAAAGAACCUGAAAAAGGAAUUUCUC	chr19:40478186-40478422(+)$1	236	146	173	13.8922
GUGGGAAUCGGAGAGGCUGCCUCCCAC	chr12:111772373-111772580(+)$1	207	152	179	13.1278
CCUGGGAAAGUGCGUGACCUCUGGGGA	chr19:1105628-1105847(+)$1	219	171	198	11.8987
GAGCCAUCCCGAGGCACAGGAAGCUCU	chr7:43684845-43685066(-)$1	221	117	144	12.8454
CAGCCUUCCUGGGAUACAAGGCUGGCA	chr22:39714323-39714539(-)$1	216	69	96	11.9213
AGCAGAGUUCAGACGAUGAAGACUGUU	chr8:19687896-19688146(+)$1	250	15	42	11.7186
AAAAAUUCUUAUUUCUUAAUUGUUUCA	chr16:9010884-9011104(-)$1	220	63	90	13.9424
CUUUGUUAAGCUACCUGCAAGAACACG	chr9:2811450-2811664(-)$1	214	134	161	12.2754
AAGGAAAAAGUAAGUAAuuuuuuuuuu	chr13:98658480-98658687(+)$1	207	113	140	14.3182
UCUUCCCAAGAGGGGAUCUGAAGGAGG	chr1:16199241-16199459(+)$1	218	96	123	13.7135
GUACGGAGGCAUCUACUGUUUUCUGUG	chr17:20924388-20924625(-)$1	237	99	126	13.4413
UGACUCCGUGAGUUUAUUAUGGAGUUU	chr8:103324348-103324551(-)$1	203	22	49	11.2607
CCGGGGGAGCUGGCCAAGCACGCCGUG	chr6:26158607-26158842(+)$1	235	99	126	14.8487
AGGUGGUAAGAGUUUGUGUUACCAGCU	chr15:91308438-91308646(+)$1	208	88	115	11.2370
GUGUCUAAGAAAUAUGUUCCUCCACGC	chr14:23945144-23945357(+)$1	213	171	198	14.2181
UUCCCCAGGUUAGGCGAGCCAGAGGAU	chr14:24475007-24475218(+)$1	211	79	106	12.8206
CCUCUGUCCAGAGUACCUGAACUAUGA	chr12:57906480-57906704(+)$1	224	42	69	13.7124
UUGCUGUGUGUGGACAGCCACAGCAGU	chr1:235277104-235277314(-)$1	210	128	155	13.4944
CGUAUCUUUGGGGAAACCAUCGAUAUU	chr14:20917241-20917444(-)$1	203	46	73	13.1006
ACAGCGACCCAGUGGAUGGAAGCAUUU	chr1:64117253-64117529(+)$1	276	232	259	13.7692
GGGUGGCGCUGCUGUUCAGUGUCUCCA	chr5:156731218-156731427(+)$1	209	8	35	11.9894
GGCGCCCUUGGGAUGUCCAAUAGGGAC	chrX:150573299-150573532(+)$1	233	87	114	13.2906
AGUGCAGUUGAGAUUGUUGGAGGCGCU	chr13:31724100-31724316(-)$1	216	94	121	13.2983
UUCAUGCUGGUGUAAAACCAUAUGAAU	chr19:40540670-40540881(-)$1	211	100	127	11.4687
UGCCACGGGAUGUGAGGAUCAUGGUGC	chr1:16262284-16262489(+)$1	205	22	49	10.6547
GAUAUCACUUAUCUUUUGGGUUUUUCA	chrX:71417123-71417358(+)$1	235	66	93	12.6755
AGCACUGGACCUGUGUGGUGUGUACUU	chr4:178272499-178272734(+)$1	235	120	147	13.4993
UGAAUGGGUAGUUCGUCUAUAUUAUUC	chr6:150001232-150001442(-)$1	210	124	151	13.9299
UAAGGUAACAGAGAGGCUGCGACUUUG	chr17:26890394-26890609(-)$1	215	162	189	15.4572
GCGGUGCCAUGUUCUUCAUCGGUUUCA	chr16:85839253-85839479(+)$1	226	157	184	12.6492
CUUCCACCCAGAAUGACUGUUGCCGAG	chr1:202699039-202699241(-)$1	202	75	102	11.6315
UUGCUCCUCUCUGGAUGAGACAGAUAC	chr12:98993743-98993991(+)$1	248	3	30	12.9013
AGGUGGAUGGACAAGACUACCACUUUG	chrX:69719690-69719930(+)$1	240	63	90	10.2454
GACAGGCCCGUGAUGGAUGUGGCCUUU	chr16:18542728-18542956(-)$1	228	99	126	13.6818
AGCUCAGAAGCAUGUCGCUUCUGUGGU	chr13:77633611-77633816(-)$1	205	72	99	12.2787

#DB
((..(((((((.....))))).))...	chr19:2235679-2235904(-)$1	1	109	136	11.8344
.((((((.(((.....))).)))))))	chr15:64428435-64428640(+)$1	1	170	197	12.6199
((((...((((.....))))..)))))	chrX:41007629-41007880(+)$1	1	22	49	13.3674
(((((.(((((.....)))))))))).	chr14:96001471-96001712(+)$1	1	115	142	11.5967
.(..((((.((.....))..))))).)	chr1:109439481-109439684(+)$1	1	41	68	11.4847
(((((((.(((.....))).)))))))	chrX:53564492-53564729(-)$1	1	88	115	14.7846
..(((((.(((.....))).))))).)	chr19:58904635-58904937(+)$1	1	48	75	13.2726
(((.((.((((.....)))))).))).	chr16:30667452-30667716(+)$1	1	82	109	12.5898
.(((.((.(((.....))))).)))))	chr20:61907752-61907969(+)$1	1	12	39	12.9613
((((...((((.....))))..)))))	chr1:100459113-100459351(+)$1	1	54	81	13.3674
((((((..(((.....)))))))))))	chr7:29994702-29994909(-)$1	1	163	190	13.4090
(((((((((.(.....).))))))).)	chr7:132990578-132990789(+)$1	1	67	94	12.6916
(((((((((((.....)).))))).))	chr20:33594249-33594457(-)$1	1	88	115	12.2191
..(((((((((.....))))).).)))	chr3:42602591-42602802(-)$1	1	151	178	12.8022
.(((.(((.((.....)).))).))))	chr3:50290399-50290626(+)$1	1	81	108	12.4575
(((((.(((((.....)))))...)))	chr17:27208832-27209066(-)$1	1	21	48	12.5610
((((((.((.(.....).)).))))))	chr1:6341173-6341392(-)$1	1	5	32	12.6929
(((((((((((.....)))))....))	chr20:34302040-34302272(-)$1	1	150	177	12.9691
((((((.((((.....)))).))..))	chr19:29698350-29698585(-)$1	1	18	45	12.7908
(((((((((((.....))))).)))))	chr16:28840656-28840888(+)$1	1	3	30	11.7233
(((.....(((.....)))))))))))	chr1:94946001-94946239(+)$1	1	28	55	12.9574
(((((....((.....))...))))).	chr7:82581305-82581512(-)$1	1	143	170	13.2499
(((((..((((......))).)..)))	chr1:43630293-43630500(-)$1	1	33	60	10.1740
..((...((((.....)))).)).)))	chr15:84286877-84287115(+)$1	1	190	217	12.8889
((..(((((((.....)))...)))).	chr19:40478186-40478422(+)$1	1	146	173	13.8922
((((((..(((.....)))..))))))	chr12:111772373-111772580(+)$1	1	152	179	13.1278
(((.(((..((.....)).))).))))	chr19:1105628-1105847(+)$1	1	171	198	11.8987
((((..(((.(.....).))).)))))	chr7:43684845-43685066(-)$1	1	117	144	12.8454
((((((...((.....))))))))(((	chr22:39714323-39714539(-)$1	1	69	96	11.9213
.((((..((((.....))))..))))(	chr8:19687896-19688146(+)$1	1	15	42	11.7186
..((((..(((.....)))..))))..	chr16:9010884-9011104(-)$1	1	63	90	13.9424
(..((((..((.....))...)))).)	chr9:2811450-2811664(-)$1	1	134	161	12.2754
(((((((((((.....)))))))))))	chr13:98658480-98658687(+)$1	1	113	140	14.3182
((((((..(((.....)))...)))))	chr1:16199241-16199459(+)$1	1	96	123	13.7135
(((((((((((.....)).))))))))	chr17:20924388-20924625(-)$1	1	99	126	13.4413
(((((((((((.....)))))))))((	chr8:103324348-103324551(-)$1	1	22	49	11.2607
.(((.(..(((.....))).).))).)	chr6:26158607-26158842(+)$1	1	99	126	14.8487
((.((((((.(.....).)))))).))	chr15:91308438-91308646(+)$1	1	88	115	11.2370
((((....(((.....)))....))))	chr14:23945144-23945357(+)$1	1	171	198	14.2181
)(((.(.((((.....)))).).))).	chr14:24475007-24475218(+)$1	1	79	106	12.8206
(....((.(((.....))).))...))	chr12:57906480-57906704(+)$1	1	42	69	13.7124
((((((((.((.....)))))))))))	chr1:235277104-235277314(-)$1	1	128	155	13.4944
)(((((..(((.....)))..))))).	chr14:20917241-20917444(-)$1	1	46	73	13.1006
...((...(((.....)))..))..))	chr1:64117253-64117529(+)$1	1	232	259	13.7692
.((.(((((((.....))))))).)).	chr5:156731218-156731427(+)$1	1	8	35	11.9894
(..((((((((.....)))..)))).)	chrX:150573299-150573532(+)$1	1	87	114	13.2906
(((((..((((.....))))..)))))	chr13:31724100-31724316(-)$1	1	94	121	13.2983
((((((.((((.....)))))))))))	chr19:40540670-40540881(-)$1	1	100	127	11.4687
(((((...(((......))).))))))	chr1:16262284-16262489(+)$1	1	22	49	10.6547
((....(((((.....)))))...)))	chrX:71417123-71417358(+)$1	1	66	93	12.6755
.((((...(((.....))))))).)))	chr4:178272499-178272734(+)$1	1	120	147	13.4993
((((((.((((.....))))..)))))	chr6:150001232-150001442(-)$1	1	124	151	13.9299
((((((..(((.....)))..))))))	chr17:26890394-26890609(-)$1	1	162	189	15.4572
(((((((((((.....))).))...))	chr16:85839253-85839479(+)$1	1	157	184	12.6492
....((..(((.....))).))...))	chr1:202699039-202699241(-)$1	1	75	102	11.6315
(..((..((((.....)))).))..))	chr12:98993743-98993991(+)$1	1	3	30	12.9013
((((((.(((......)))))))))))	chrX:69719690-69719930(+)$1	1	63	90	10.2454
((.((((((((.....))).)))))))	chr16:18542728-18542956(-)$1	1	99	126	13.6818
(((((((((((.....))))))).)))	chr13:77633611-77633816(-)$1	1	72	99	12.2787

#PSSM
e : 0.15	g : 0.10	f : 0.10	c : 0.08	i : 0.08	= : 0.06	[ : 0.05	" : 0.05	b : 0.05	! : 0.05	h : 0.05	d : 0.05	' : 0.01	$ : 0.01	: : 0.01	C : 0.01	# : 0.01	% : 0.01	
c : 0.15	e : 0.15	f : 0.11	g : 0.10	! : 0.08	d : 0.08	i : 0.06	h : 0.05	b : 0.03	= : 0.03	# : 0.03	a : 0.01	$ : 0.01	" : 0.01	C : 0.01	% : 0.01	
e : 0.15	f : 0.11	g : 0.11	c : 0.11	! : 0.10	d : 0.08	i : 0.08	h : 0.05	# : 0.05	= : 0.03	b : 0.03	[ : 0.03	% : 0.01	
e : 0.15	f : 0.13	g : 0.11	c : 0.10	d : 0.08	i : 0.08	! : 0.05	[ : 0.05	b : 0.05	h : 0.05	= : 0.03	# : 0.03	$ : 0.01	a : 0.01	% : 0.01	
e : 0.13	g : 0.13	d : 0.11	b : 0.10	f : 0.10	i : 0.08	[ : 0.06	" : 0.05	h : 0.05	# : 0.05	c : 0.03	= : 0.03	$ : 0.01	! : 0.01	
b : 0.10	f : 0.10	" : 0.10	g : 0.10	d : 0.08	! : 0.08	i : 0.08	e : 0.06	a : 0.05	# : 0.05	h : 0.05	[ : 0.03	c : 0.03	= : 0.03	$ : 0.01	
! : 0.20	e : 0.16	" : 0.11	[ : 0.11	d : 0.06	g : 0.06	b : 0.05	c : 0.05	i : 0.05	f : 0.03	# : 0.03	$ : 0.01	= : 0.01	
d : 0.23	! : 0.16	e : 0.15	[ : 0.08	" : 0.06	g : 0.05	c : 0.05	i : 0.05	b : 0.03	# : 0.03	$ : 0.01	a : 0.01	= : 0.01	f : 0.01	
c : 0.42	d : 0.18	e : 0.13	[ : 0.05	g : 0.05	! : 0.03	i : 0.03	b : 0.01	# : 0.01	" : 0.01	= : 0.01	f : 0.01	
c : 0.40	d : 0.18	b : 0.15	e : 0.11	[ : 0.06	g : 0.03	= : 0.01	i : 0.01	
c : 0.38	d : 0.18	b : 0.15	e : 0.11	a : 0.06	g : 0.03	= : 0.01	i : 0.01	o : 0.01	
n : 0.94	o : 0.05	
n : 0.94	o : 0.05	
n : 0.94	o : 0.05	
n : 0.94	o : 0.05	
n : 0.94	o : 0.05	
c : 0.37	d : 0.18	b : 0.15	e : 0.11	a : 0.06	o : 0.03	g : 0.03	= : 0.01	i : 0.01	
c : 0.40	d : 0.18	b : 0.15	e : 0.11	] : 0.06	g : 0.03	= : 0.01	i : 0.01	
c : 0.42	d : 0.18	e : 0.11	] : 0.06	g : 0.05	3 : 0.03	f : 0.03	i : 0.03	2 : 0.01	b : 0.01	= : 0.01	
d : 0.20	e : 0.15	] : 0.13	2 : 0.11	c : 0.08	3 : 0.06	i : 0.06	f : 0.05	g : 0.05	b : 0.03	= : 0.01	4 : 0.01	
e : 0.18	2 : 0.18	] : 0.11	b : 0.08	f : 0.06	g : 0.06	3 : 0.06	i : 0.06	c : 0.05	d : 0.03	= : 0.01	a : 0.01	4 : 0.01	h : 0.01	
b : 0.13	e : 0.11	] : 0.10	g : 0.10	2 : 0.08	d : 0.08	i : 0.08	f : 0.06	3 : 0.06	c : 0.03	4 : 0.03	a : 0.03	h : 0.03	= : 0.01	
e : 0.16	d : 0.11	g : 0.11	f : 0.10	b : 0.08	3 : 0.08	i : 0.08	] : 0.06	h : 0.05	c : 0.03	4 : 0.03	a : 0.01	2 : 0.01	= : 0.01	
e : 0.16	f : 0.11	d : 0.11	g : 0.08	c : 0.08	] : 0.08	3 : 0.08	i : 0.08	2 : 0.06	h : 0.05	b : 0.01	4 : 0.01	= : 0.01	
e : 0.16	f : 0.13	d : 0.13	g : 0.10	c : 0.10	i : 0.08	3 : 0.06	2 : 0.05	h : 0.05	] : 0.03	a : 0.01	4 : 0.01	= : 0.01	b : 0.01	
f : 0.16	e : 0.13	c : 0.13	g : 0.11	d : 0.11	] : 0.10	i : 0.08	h : 0.05	3 : 0.03	= : 0.03	b : 0.01	
f : 0.16	g : 0.11	e : 0.10	d : 0.10	b : 0.08	c : 0.08	i : 0.08	3 : 0.05	h : 0.05	] : 0.03	= : 0.03	: : 0.03	6 : 0.01	2 : 0.01	a : 0.01	

#score	754.676870651788
#seq	59
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m2_run1.txt

#BEAR
[eeeee"""dddd!!ddddmmmmdddddddd4444eeeee	chr1:115292352-115292579(-)$1	227	102	142	12.1144
ggggg[eeeee####ddddooooooddddeeeeegggggg	chr1:234742561-234742808(-)$1	247	39	79	16.2295
dddd[ccc[ccc[a[ddddoooooodddd22a]ccc]ccc	chr10:93624694-93624940(+)$1	246	149	189	15.5613
[bb!!eeeee####cccrrrrrrrrrccc333eeeee444	chr9:123942571-123942806(-)$1	235	46	86	13.5178
========[a!!eeeee[cccmmmmccc22eeeee]a===	chr17:56167387-56167638(+)$1	251	74	114	13.1192
iiiiiii####ccc[ddddmmmmdddd22ccciiiiiiii	chr1:67467633-67467861(-)$1	228	12	52	14.9526
[iiiiiiiii[dddd!!bbmmmmbb]ddddiiiiiiiii3	chr6:31382823-31383094(+)$1	271	218	258	13.1969
========!!ccc[bbrrrrrrrrrbb]ccc]========	chr6:109688965-109689224(-)$1	259	75	115	14.5021
iiiiiiii[dddd!!cccmmmmccc22ddddiiiiiiiii	chr5:179156078-179156321(+)$1	243	182	222	13.4178
$ccc[eeeee####eeeeeooooooeeeee22eeeeeccc	chr19:1258264-1258514(+)$1	250	87	127	13.9506
ff[iiiiiiiii####cccpppppppccciiiiiiiii]f	chr17:79780593-79780850(-)$1	257	123	163	13.8250
d!!ggggggg!!gggggggooooooggggggg333ggggg	chr15:49419634-49419869(-)$1	235	30	70	16.9305
hhhhhhhh[eeeee!!cccooooooccc333eeeee]hhh	chr1:203276624-203276863(+)$1	239	26	66	14.2841
!ffffff"""ggggggg[aooooooaggggggg333ffff	chr3:196556573-196556809(+)$1	236	34	74	15.4447
eeeee!!ccc[a!!ccc[aooooooaccc22a]ccc22ee	chrX:41207469-41207720(+)$1	251	131	171	15.6017
E:=================lll=================:	chr1:90401376-90401630(+)$1	254	26	66	14.5793
ggggggg####eeeeecccooooooccc]eeeee4444gg	chr4:169847879-169848121(+)$1	242	186	226	16.0826
eeeee####eeeeecccrrrrrrrrrccc]eeeee333ee	chr7:26231613-26231875(-)$1	262	107	147	12.0835
cccggggggg!!ccc[cccooooooccccccggggggg]c	chr8:107282350-107282575(+)$1	225	99	139	17.2081
c::=========="""cccmmmmccc4444==========	chr13:95279352-95279583(+)$1	231	47	87	15.6587
$$$$$ggggggg####cccnnnnnccc333ggggggg22f	chr1:93308559-93308781(-)$1	222	47	87	15.1021
dd!!a[ffffff"""ddddoooooodddd]ffffff]a22	chr15:73925398-73925688(-)$1	290	145	185	15.2514
""a[iiiiiiiii"""cccooooooccc]iiiiiiiii]a	chr11:47489572-47489826(-)$1	254	145	185	19.6546
"""ccc[dddd[a!!ddddllldddd22a]dddd]ccc]d	chr14:95552537-95552773(-)$1	236	13	53	12.8324
b!!eeeee####cccddddoooooodddd]ccceeeee22	chr7:30123962-30124196(+)$1	234	107	147	15.0284
gggggggccc!!gggggggnnnnnggggggg333ccc]gg	chr12:58142084-58142330(-)$1	246	100	140	14.1219
======="""ccc[cccrrrrrrrrrccc22ccc======	chr3:98298674-98298927(-)$1	253	177	217	15.6604
======"""ggggggg[a[ammmma]a]ggggggg=====	chr7:106842049-106842270(+)$1	221	150	190	15.1733
"""ffffff!!bb"""cccmmmmccc]bbffffff4444e	chr1:32662076-32662325(+)$1	249	130	170	12.6901
ggggggg$$$$$ddddcccooooooccc]dddd333gggg	chr1:94995724-94995944(-)$1	220	113	153	15.3280
eeeee[==========cccmmmmccc]==========]ee	chr17:79825496-79825738(-)$1	242	132	172	15.6477
dccc!!eeeee####ddddlllddddeeeee333ccc444	chr16:87442654-87442880(-)$1	226	139	179	13.7497
============"""eeeeemmmmeeeee===========	chr9:79000560-79000783(-)$1	223	57	97	16.1989
cc[cccccc"""gggggggooooooggggggg4444ccc3	chr4:160280511-160280776(+)$1	265	114	154	15.9811
[dddd[ggggggg!!cccooooooccc4444ggggggg]d	chr1:162493400-162493653(+)$1	253	146	186	16.6334
f"""bb[eeeee"""ddddoooooodddd4444eeeee]b	chr17:74730283-74730515(-)$1	232	17	57	15.5443
i####ccc"""ccc[ddddnnnnnddddccc22ccc333i	chr10:102307966-102308242(+)$1	276	86	126	14.8073
##dddd=============oooooo=============]d	chr17:46626711-46626942(-)$1	231	134	174	18.1874
bb"""ggggggg"""eeeeennnnneeeeegggggggbb]	chr1:38269299-38269551(-)$1	252	158	198	12.9103
cc[iiiiiiiii####ccclllccciiiiiiiii22ccc4	chr12:69235275-69235536(+)$1	261	148	188	15.9702
"""bb$$$$$==========nnnnn==========4444b	chr1:202103323-202103575(-)$1	252	63	103	14.6017
iiiiiiccc[ccc"""cccooooooccc]ccc]ccc]iii	chr12:4411888-4412133(+)$1	245	13	53	17.9984
ccbb!!bb[ccc"""ddddllldddd]cccbbbb]ccc]d	chr19:2269570-2269829(+)$1	259	133	173	12.6340
[============!!ddddoooooodddd===========	chr1:203278306-203278543(+)$1	237	41	81	20.0984
[a[bb"""ccc[a!!cccnnnnnccc]a]ccc]bb]a]cc	chr6:26158672-26158924(+)$1	252	27	67	13.6221
dddd"""==========[annnnna22==========]dd	chr8:53535200-53535421(-)$1	221	96	136	15.3212
!!ccc[gggggggccccccmmmmccc]ccc]ggggggg]c	chr16:28875819-28876077(+)$1	258	3	43	14.6707
dddd[iiiiiiiii[ddddoooooodddd]iiiiiiiii]	chr21:15745397-15745620(-)$1	223	31	71	17.6202
ffffa!!bb!!ccc[bb[aooooooa]bb22ccc22bb22	chr5:52397923-52398147(-)$1	224	26	66	13.1596

#otherMatches

#Seq PSSM
ACUACUGAAAGUGCAAUAUUUGAGUAUCACUGCGAGGUAG	chr1:115292352-115292579(-)$1	227	102	142	12.1144
CAUGGCUGUAUAAUUUUGAUUUUUUUUGAAUACAUUGUGU	chr1:234742561-234742808(-)$1	247	39	79	16.2295
AGUACGUUGCAUGAAAUAGCUUACUUUAUAAUGAUGGAAU	chr10:93624694-93624940(+)$1	246	149	189	15.5613
ACACUAGCAGAUUCUGUUCCAUCUUUGCACUGUUGCUUAC	chr9:123942571-123942806(-)$1	235	46	86	13.5178
GUUCUCUUAGAGCAGCCCCUGUUGUUAGUUGGCUGGCAAG	chr17:56167387-56167638(+)$1	251	74	114	13.1192
AAGGGCAUAGUGAGAGCUAUUUUUAGUGAUUCUGUUCUUU	chr1:67467633-67467861(-)$1	228	12	52	14.9526
aggcugcaaaauguuaguagauaugaggcauuugcagcug	chr6:31382823-31383094(+)$1	271	218	258	13.1969
GUAUAGAGCUAAAUUGAUUUAAUUACACUUUCCUUUGUAC	chr6:109688965-109689224(-)$1	259	75	115	14.5021
AUAGAUAUAUAAGAAAAAAUUCUUUCACUUGAUGUUUGUU	chr5:179156078-179156321(+)$1	243	182	222	13.4178
UCCGUGUAGCAUUAACCCCCGUGGCGGGGUCCGCUGCUGG	chr19:1258264-1258514(+)$1	250	87	127	13.9506
UGGUUUUGUCCUUGAAGUGGUCAGGAUACAGGACAAGGGC	chr17:79780593-79780850(-)$1	257	123	163	13.8250
GAUUUUAAAUACACUGACACGCUACUGUUGGUUAAAUUUA	chr15:49419634-49419869(-)$1	235	30	70	16.9305
UUUUUAAAUGAAGAGCuauuuauauauauuauuuuuuuuu	chr1:203276624-203276863(+)$1	239	26	66	14.2841
UUAGUUUAGUUUUGUUUUGUUUUUUCAAAUAAGUAGAGAC	chr3:196556573-196556809(+)$1	236	34	74	15.4447
CUGGAUAGGUAUUUAGAACCUGAUAGUCUUUAAGCCAUUC	chrX:41207469-41207720(+)$1	251	131	171	15.6017
UCAUUUUUUUUUUUCUUUUGGGGAAAGGGAAGGAAAAAUU	chr1:90401376-90401630(+)$1	254	26	66	14.5793
AUAUUAAAUCAUAAGGAAGGAACUACUUGCCUUAAAUGUU	chr4:169847879-169848121(+)$1	242	186	226	16.0826
ACUGUGGAGGAAGGAUUGUAAAAAAAAAUGCCUUUGAGAC	chr7:26231613-26231875(-)$1	262	107	147	12.0835
CUGGGCUGCGUCAGGCUGAGCCCAUUCACCUCGCGGCCAC	chr8:107282350-107282575(+)$1	225	99	139	17.2081
GACACAAAAGUCGCCCUCAUUUCUGAUACUUGAUUUUUGU	chr13:95279352-95279583(+)$1	231	47	87	15.6587
GCCCUGUUACAUCUCCGAAGUACAUUCAUUGUGUAACUAU	chr1:93308559-93308781(-)$1	222	47	87	15.1021
CGCUGCCCAGCGCCCUGGCCCUCUCGCUGUUGCUGGUCUC	chr15:73925398-73925688(-)$1	290	145	185	15.2514
CUCCACAGCAAAAUGUGAUGCUUUGAUUuuuuuguuguug	chr11:47489572-47489826(-)$1	254	145	185	19.6546
UAUUAUUUGAUUGACAAUAAAAUAUUUACCAUCACAUGCU	chr14:95552537-95552773(-)$1	236	13	53	12.8324
AUAUGUUGGAGCCUCUUGGGACCAACCGAUGAGCGACAGU	chr7:30123962-30124196(+)$1	234	107	147	15.0284
AUCUCUGAGGCUAUGGAGGGUCCUCCUCCAUCUUUCUACA	chr12:58142084-58142330(-)$1	246	100	140	14.1219
AUCUCUGUGUGGAAGUUGAGACUAAGAAUAAUCCUAGGGA	chr3:98298674-98298927(-)$1	253	177	217	15.6604
UGUUUUAUUUUAAAUUGUACGAAAGGGGAAUUUAAAAAAU	chr7:106842049-106842270(+)$1	221	150	190	15.1733
GUUGCAAACUUGCCAGGGUAUUAGCCAGUGUUUGUGCCAA	chr1:32662076-32662325(+)$1	249	130	170	12.6901
UUGAAAUGUAACGAAUGGUACUACAACCAAUUCCAAGUUU	chr1:94995724-94995944(-)$1	220	113	153	15.3280
CCCUGAAGGAGCUGGGGGUGUCUGCUGCUUGGCUUCUCCA	chr17:79825496-79825738(-)$1	242	132	172	15.6477
UGGGAAGUGGUAGGACUCUGGAAGAGGCCACACACCCGAG	chr16:87442654-87442880(-)$1	226	139	179	13.7497
AAAACAAACAUAGGAAAUGUGAAAAUAUUUGUGUUUGUUU	chr9:79000560-79000783(-)$1	223	57	97	16.1989
CUCCACUCUAUUUUUGUGUUGUUUUGCACAGACUCCGGAA	chr4:160280511-160280776(+)$1	265	114	154	15.9811
UGAAGACAAACUAGAGGAGCAGCAUCCCAGGUAGUUUGGC	chr1:162493400-162493653(+)$1	253	146	186	16.6334
UUAAAAUGCCUGACAACUGCACUUCCAGUCACCCGGGCCU	chr17:74730283-74730515(-)$1	232	17	57	15.5443
GCAGUUGGCACUCCACUCCUAUUUGGAGGGACUUCAUACC	chr10:102307966-102308242(+)$1	276	86	126	14.8073
GGCAGGGGCUGGGCAGGGCCUGUGUGCCUUGCUCAGCCUC	chr17:46626711-46626942(-)$1	231	134	174	18.1874
UUGUAUUUUCAUAUAUCAGCCAAAAGCUGAAUGGAAAAGU	chr1:38269299-38269551(-)$1	252	158	198	12.9103
CUUGGCCUGGGUUACAUGGUUCCCAGCCUAGGUUUCAGAC	chr12:69235275-69235536(+)$1	261	148	188	15.9702
CUAAGCCCACCCCUCCUCACCCAGUGUGAGGAGGGCCCUC	chr1:202103323-202103575(-)$1	252	63	103	14.6017
AGGCUGCUUCUCUACAGAGGUGAAAUUCCAGAUGAGUCAG	chr12:4411888-4412133(+)$1	245	13	53	17.9984
UCCUAAGCCUGCACAGCCGCGGCGGCAGCAGCAGUGAGAG	chr19:2269570-2269829(+)$1	259	133	173	12.6340
GGGCCCACAGACCCAAGAGCUAAUUUUCUGGUUUGUGGGU	chr1:203278306-203278543(+)$1	237	41	81	20.0984
GCUGCUUCCGGGGGAGCUGGCCAAGCACGCCGUGUCGGAG	chr6:26158672-26158924(+)$1	252	27	67	13.6221
CUAUAUACUAUGUAACAGGGUAAACAGUGUUAUGUAGAAU	chr8:53535200-53535421(-)$1	221	96	136	15.3212
AGUUGUCCCUGCGGUUGGAGCCAUCUGAGCUUGUAGGGUC	chr16:28875819-28876077(+)$1	258	3	43	14.6707
GAUUCCCAGUUCUUACUAAAUUGUAUUAGCAGGAGCUGGU	chr21:15745397-15745620(-)$1	223	31	71	17.6202
GCCUAUAAGUUGUUGAGUGUUUUACCCCUAGGACUUCUGU	chr5:52397923-52398147(-)$1	224	26	66	13.1596

#DB
.(((((...((((..((((....))))))))....)))))	chr1:115292352-115292579(-)$1	1	102	142	12.1144
(((((.(((((....((((......)))))))))))))))	chr1:234742561-234742808(-)$1	1	39	79	16.2295
((((.(((.(((.(.((((......))))..).))).)))	chr10:93624694-93624940(+)$1	1	149	189	15.5613
.((..(((((....(((.........)))...)))))...	chr9:123942571-123942806(-)$1	1	46	86	13.5178
((((((((.(..(((((.(((....)))..))))).))))	chr17:56167387-56167638(+)$1	1	74	114	13.1192
(((((((....(((.((((....))))..)))))))))))	chr1:67467633-67467861(-)$1	1	12	52	14.9526
.(((((((((.((((..((....)).))))))))))))).	chr6:31382823-31383094(+)$1	1	218	258	13.1969
((((((((..(((.((.........)).))).))))))))	chr6:109688965-109689224(-)$1	1	75	115	14.5021
((((((((.((((..(((....)))..)))))))))))))	chr5:179156078-179156321(+)$1	1	182	222	13.4178
.(((.(((((....(((((......)))))..))))))))	chr19:1258264-1258514(+)$1	1	87	127	13.9506
((.(((((((((....(((.......)))))))))))).)	chr17:79780593-79780850(-)$1	1	123	163	13.8250
(..(((((((..(((((((......)))))))...)))))	chr15:49419634-49419869(-)$1	1	30	70	16.9305
((((((((.(((((..(((......)))...))))).)))	chr1:203276624-203276863(+)$1	1	26	66	14.2841
.((((((...(((((((.(......))))))))...))))	chr3:196556573-196556809(+)$1	1	34	74	15.4447
(((((..(((.(..(((.(......))))..).)))..))	chrX:41207469-41207720(+)$1	1	131	171	15.6017
(.(((((((((((((((((...))))))))))))))))).	chr1:90401376-90401630(+)$1	1	26	66	14.5793
(((((((....((((((((......))).)))))....))	chr4:169847879-169848121(+)$1	1	186	226	16.0826
(((((....((((((((.........))).)))))...))	chr7:26231613-26231875(-)$1	1	107	147	12.0835
((((((((((..(((.(((......))))))))))))).)	chr8:107282350-107282575(+)$1	1	99	139	17.2081
)..((((((((((...(((....)))....))))))))))	chr13:95279352-95279583(+)$1	1	47	87	15.6587
.....(((((((....(((.....)))...)))))))..)	chr1:93308559-93308781(-)$1	1	47	87	15.1021
((..(.((((((...((((......)))).)))))).)..	chr15:73925398-73925688(-)$1	1	145	185	15.2514
..(.(((((((((...(((......))).))))))))).)	chr11:47489572-47489826(-)$1	1	145	185	19.6546
...(((.((((.(..((((...))))..).)))).))).)	chr14:95552537-95552773(-)$1	1	13	53	12.8324
(..(((((....(((((((......)))).))))))))..	chr7:30123962-30124196(+)$1	1	107	147	15.0284
((((((((((..(((((((.....)))))))...))).))	chr12:58142084-58142330(-)$1	1	100	140	14.1219
(((((((...(((.(((.........)))..)))))))))	chr3:98298674-98298927(-)$1	1	177	217	15.6604
((((((...(((((((.(.(....).).))))))))))))	chr7:106842049-106842270(+)$1	1	150	190	15.1733
...((((((..((...(((....))).))))))))....)	chr1:32662076-32662325(+)$1	1	130	170	12.6901
(((((((.....(((((((......))).))))...))))	chr1:94995724-94995944(-)$1	1	113	153	15.3280
(((((.(((((((((((((....))).)))))))))).))	chr17:79825496-79825738(-)$1	1	132	172	15.6477
((((..(((((....((((...)))))))))...)))...	chr16:87442654-87442880(-)$1	1	139	179	13.7497
((((((((((((...(((((....))))))))))))))))	chr9:79000560-79000783(-)$1	1	57	97	16.1989
((.((((((...(((((((......)))))))....))).	chr4:160280511-160280776(+)$1	1	114	154	15.9811
.((((.(((((((..(((......)))....))))))).)	chr1:162493400-162493653(+)$1	1	146	186	16.6334
(...((.(((((...((((......))))....))))).)	chr17:74730283-74730515(-)$1	1	17	57	15.5443
(....(((...(((.((((.....)))))))..)))...)	chr10:102307966-102308242(+)$1	1	86	126	14.8073
..(((((((((((((((((......))))))))))))).)	chr17:46626711-46626942(-)$1	1	134	174	18.1874
((...(((((((...(((((.....)))))))))))))).	chr1:38269299-38269551(-)$1	1	158	198	12.9103
((.(((((((((....(((...))))))))))))..))).	chr12:69235275-69235536(+)$1	1	148	188	15.9702
...((.....((((((((((.....))))))))))....)	chr1:202103323-202103575(-)$1	1	63	103	14.6017
(((((((((.(((...(((......))).))).))).)))	chr12:4411888-4412133(+)$1	1	13	53	17.9984
((((..((.(((...((((...)))).))))))).))).)	chr19:2269570-2269829(+)$1	1	133	173	12.6340
.((((((((((((..((((......)))))))))))))))	chr1:203278306-203278543(+)$1	1	41	81	20.0984
.(.((...(((.(..(((.....))).).))).)).).))	chr6:26158672-26158924(+)$1	1	27	67	13.6221
((((...((((((((((.(.....)..)))))))))).))	chr8:53535200-53535421(-)$1	1	96	136	15.3212
..(((.(((((((((((((....))).))).))))))).)	chr16:28875819-28876077(+)$1	1	3	43	14.6707
((((.(((((((((.((((......)))).))))))))).	chr21:15745397-15745620(-)$1	1	31	71	17.6202
(((((..((..(((.((.(......).))..)))..))..	chr5:52397923-52398147(-)$1	1	26	66	13.1596

#PSSM
[ : 0.12	d : 0.12	= : 0.10	c : 0.10	g : 0.08	i : 0.08	" : 0.08	f : 0.06	e : 0.06	$ : 0.04	! : 0.04	b : 0.04	h : 0.02	E : 0.02	# : 0.02	
= : 0.12	c : 0.12	d : 0.10	" : 0.10	e : 0.08	g : 0.08	i : 0.08	f : 0.06	! : 0.06	b : 0.04	: : 0.04	# : 0.04	h : 0.02	$ : 0.02	a : 0.02	
= : 0.14	d : 0.10	" : 0.10	e : 0.08	g : 0.08	i : 0.08	c : 0.08	[ : 0.08	! : 0.06	b : 0.04	f : 0.04	h : 0.02	: : 0.02	$ : 0.02	a : 0.02	# : 0.02	
= : 0.16	g : 0.12	i : 0.12	e : 0.10	d : 0.10	c : 0.10	f : 0.06	b : 0.06	! : 0.04	" : 0.04	h : 0.02	$ : 0.02	[ : 0.02	# : 0.02	
= : 0.16	i : 0.14	g : 0.12	e : 0.10	[ : 0.06	! : 0.06	c : 0.06	b : 0.06	f : 0.04	a : 0.04	d : 0.04	" : 0.04	h : 0.02	$ : 0.02	# : 0.02	
= : 0.16	i : 0.16	g : 0.14	[ : 0.10	e : 0.08	c : 0.08	! : 0.08	f : 0.04	" : 0.04	h : 0.02	# : 0.02	b : 0.02	d : 0.02	$ : 0.02	
= : 0.18	g : 0.18	i : 0.14	e : 0.10	" : 0.08	c : 0.08	f : 0.06	! : 0.04	[ : 0.04	h : 0.02	# : 0.02	$ : 0.02	b : 0.02	
= : 0.18	e : 0.12	c : 0.12	i : 0.12	g : 0.12	" : 0.10	# : 0.06	f : 0.04	$ : 0.04	b : 0.04	h : 0.02	d : 0.02	
= : 0.14	g : 0.12	" : 0.10	e : 0.10	[ : 0.10	i : 0.10	c : 0.10	# : 0.08	f : 0.04	$ : 0.04	! : 0.02	d : 0.02	b : 0.02	
e : 0.14	g : 0.14	= : 0.14	c : 0.10	i : 0.10	" : 0.08	d : 0.06	# : 0.06	! : 0.06	$ : 0.04	a : 0.02	f : 0.02	[ : 0.02	
= : 0.16	c : 0.12	! : 0.12	g : 0.12	e : 0.10	# : 0.10	i : 0.08	d : 0.06	[ : 0.04	" : 0.04	f : 0.02	$ : 0.02	
c : 0.16	= : 0.16	g : 0.12	# : 0.10	! : 0.08	i : 0.08	e : 0.08	d : 0.06	[ : 0.04	a : 0.02	f : 0.02	b : 0.02	$ : 0.02	" : 0.02	
c : 0.16	# : 0.14	g : 0.14	= : 0.14	" : 0.10	d : 0.08	e : 0.08	i : 0.04	a : 0.04	[ : 0.02	! : 0.02	b : 0.02	
" : 0.18	! : 0.14	# : 0.14	c : 0.12	g : 0.10	= : 0.10	e : 0.08	d : 0.04	[ : 0.04	a : 0.02	i : 0.02	
" : 0.18	! : 0.14	c : 0.14	# : 0.10	[ : 0.10	g : 0.10	= : 0.10	e : 0.06	d : 0.04	b : 0.02	
d : 0.28	c : 0.16	e : 0.10	g : 0.10	= : 0.10	" : 0.08	# : 0.06	! : 0.04	b : 0.04	[ : 0.02	
c : 0.40	d : 0.26	e : 0.08	g : 0.08	= : 0.08	! : 0.02	r : 0.02	[ : 0.02	b : 0.02	
c : 0.32	d : 0.26	[ : 0.10	r : 0.08	e : 0.06	g : 0.06	= : 0.06	b : 0.02	a : 0.02	
c : 0.28	d : 0.26	r : 0.08	a : 0.08	e : 0.06	g : 0.06	= : 0.06	b : 0.02	m : 0.02	[ : 0.02	o : 0.02	n : 0.02	
o : 0.42	m : 0.16	l : 0.10	n : 0.10	r : 0.08	e : 0.04	c : 0.02	p : 0.02	a : 0.02	= : 0.02	
o : 0.42	m : 0.20	n : 0.14	l : 0.10	r : 0.08	c : 0.02	p : 0.02	
o : 0.42	m : 0.22	n : 0.14	l : 0.10	r : 0.08	p : 0.02	
o : 0.42	m : 0.20	n : 0.14	r : 0.08	d : 0.06	c : 0.04	p : 0.02	= : 0.02	
o : 0.42	c : 0.14	n : 0.12	d : 0.10	r : 0.08	m : 0.06	b : 0.02	p : 0.02	= : 0.02	
o : 0.40	c : 0.18	d : 0.12	r : 0.08	a : 0.04	n : 0.04	m : 0.02	b : 0.02	p : 0.02	= : 0.02	g : 0.02	e : 0.02	
c : 0.28	d : 0.26	r : 0.06	e : 0.06	g : 0.06	a : 0.06	= : 0.06	] : 0.04	2 : 0.04	b : 0.02	p : 0.02	i : 0.02	
c : 0.28	d : 0.22	] : 0.12	e : 0.08	g : 0.08	2 : 0.06	= : 0.06	b : 0.02	4 : 0.02	a : 0.02	i : 0.02	
c : 0.28	d : 0.22	= : 0.10	e : 0.08	g : 0.08	2 : 0.04	] : 0.04	4 : 0.04	b : 0.04	3 : 0.02	i : 0.02	a : 0.02	
d : 0.20	c : 0.20	g : 0.10	= : 0.10	] : 0.10	e : 0.08	2 : 0.04	3 : 0.04	4 : 0.04	b : 0.04	a : 0.02	i : 0.02	
c : 0.16	= : 0.14	e : 0.10	2 : 0.10	g : 0.10	] : 0.10	d : 0.08	3 : 0.06	i : 0.06	4 : 0.06	f : 0.02	
= : 0.16	c : 0.14	g : 0.14	e : 0.10	2 : 0.10	i : 0.10	d : 0.08	3 : 0.04	f : 0.04	4 : 0.04	b : 0.02	] : 0.02	
g : 0.18	= : 0.16	c : 0.12	i : 0.12	e : 0.10	3 : 0.06	4 : 0.04	a : 0.04	2 : 0.04	f : 0.04	d : 0.04	] : 0.02	b : 0.02	
= : 0.18	e : 0.14	i : 0.14	g : 0.14	] : 0.08	4 : 0.06	3 : 0.06	c : 0.06	f : 0.04	d : 0.04	2 : 0.02	b : 0.02	
e : 0.18	= : 0.18	i : 0.14	c : 0.12	g : 0.12	3 : 0.10	4 : 0.04	f : 0.04	b : 0.04	d : 0.02	
= : 0.20	g : 0.14	e : 0.14	c : 0.12	i : 0.12	4 : 0.06	3 : 0.06	f : 0.04	] : 0.04	2 : 0.04	b : 0.02	
= : 0.20	c : 0.16	g : 0.14	e : 0.12	i : 0.12	4 : 0.08	3 : 0.06	] : 0.04	2 : 0.04	f : 0.02	
= : 0.20	g : 0.16	i : 0.12	c : 0.12	e : 0.10	] : 0.08	4 : 0.06	a : 0.04	3 : 0.04	f : 0.02	2 : 0.02	b : 0.02	
= : 0.18	i : 0.14	g : 0.12	c : 0.12	4 : 0.10	] : 0.08	e : 0.06	2 : 0.04	3 : 0.04	b : 0.04	h : 0.02	f : 0.02	a : 0.02	
] : 0.18	= : 0.16	g : 0.10	c : 0.10	i : 0.10	e : 0.08	4 : 0.08	2 : 0.08	h : 0.02	f : 0.02	3 : 0.02	b : 0.02	d : 0.02	
= : 0.14	e : 0.10	g : 0.10	c : 0.10	d : 0.10	i : 0.08	4 : 0.06	f : 0.06	2 : 0.06	3 : 0.04	b : 0.04	] : 0.04	h : 0.02	: : 0.02	a : 0.02	

#score	738.4624532767816
#seq	49
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_CDS_m2_run1.txt

#BEAR
eeeettttttttttteeeee	chr20:47704473-47704713(+)$1	240	53	73	21.2254
eevvvvvvvvvvvvveeeee	chr5:74893735-74893975(+)$1	240	34	54	21.9043
eeeettttttttttteeeee	chr1:154524467-154524707(-)$1	240	205	225	21.2254
[ccctttttttttttcccdd	chr6:149983054-149983294(-)$1	240	36	56	21.4761
eeeuuuuuuuuuuuueeeee	chr17:62496654-62496894(-)$1	240	120	140	22.3924
[bbvvvvvvvvvvvvvbb]b	chr3:148765778-148766018(-)$1	240	150	170	20.6728
iiwwwwwwwwwwwwwwiiii	chr10:88939811-88940051(+)$1	240	30	50	20.5438
yyyyyyyyyyyyyyyggggg	chr8:141561299-141561539(-)$1	240	67	87	20.4168
cccvvvvvvvvvvvvvccc2	chr12:105238178-105238458(-)$1	280	28	48	21.6398
yyyyyyyyyyyyyyyccc]f	chr6:96034241-96034481(+)$1	240	37	57	20.6187
cccvvvvvvvvvvvvvccc]	chr3:128356670-128356918(-)$1	248	85	105	21.9100
fffwwwwwwwwwwwwwwfff	chr5:133295131-133295371(-)$1	240	156	176	19.8392
eeeettttttttttteeeee	chr3:182545851-182546091(+)$1	240	179	199	21.2254
ggwwwwwwwwwwwwwwgggg	chr13:113459214-113459454(+)$1	240	129	149	20.6197
dddwwwwwwwwwwwwwwddd	chr5:110097337-110097577(+)$1	240	1	21	19.9790
yyyyyyyyyyyyyyyggggg	chr11:62346253-62346608(-)$1	355	78	98	20.4168
fffftttttttttttfffff	chr21:34822994-34823234(-)$1	240	211	231	20.6247
cccwwwwwwwwwwwwwwccc	chr19:14203259-14203501(-)$1	242	202	222	20.3468
fffftttttttttttfffff	chr8:77617246-77617486(+)$1	240	30	50	20.6247
eeeuuuuuuuuuuuueeeee	chr14:55510767-55511007(+)$1	240	42	62	22.3924
yyyyyyyyyyyyyyybb]bb	chr19:58905805-58906045(+)$1	240	95	115	19.4809
cccuuuuuuuuuuuuccc::	chr21:30698993-30699233(+)$1	240	67	87	20.7542
eevvvvvvvvvvvvveeeee	chr11:62343128-62343408(-)$1	280	206	226	21.9043
cccuuuuuuuuuuuuccc44	chr12:44337974-44338214(+)$1	240	29	49	22.5638
ffvvvvvvvvvvvvvfffff	chr1:63884940-63885180(+)$1	240	45	65	21.3942
dddvvvvvvvvvvvvvdddd	chr13:48938928-48939168(+)$1	240	72	92	21.4089
yyyyyyyyyyyyyyyccccc	chr5:41917251-41917500(+)$1	249	114	134	20.5589
dwwwwwwwwwwwwwwddddd	chr15:76209549-76209789(+)$1	240	193	213	20.2241
!!bbtttttttttttbb22d	chr16:66592071-66592311(+)$1	240	94	114	20.0697
yyyyyyyyyyyyyyyggggg	chr9:86297795-86298035(-)$1	240	108	128	20.4168
bbvvvvvvvvvvvvvbb22f	chrX:41055464-41055704(+)$1	240	124	144	20.5368
[ccctttttttttttcccee	chr15:55474223-55474463(-)$1	240	101	121	21.6831
cccuuuuuuuuuuuuccc]i	chr9:98229448-98229688(-)$1	240	195	215	22.6540
dbbuuuuuuuuuuuubb]dd	chr14:53248433-53248673(-)$1	240	181	201	21.4831
ddvvvvvvvvvvvvvdddde	chr6:72005958-72006198(+)$1	240	123	143	21.6261
eeettttttttttteeeee]	chr3:41267075-41267315(+)$1	240	95	115	21.1358
iiiitttttttttttiiiii	chrX:48435822-48436072(+)$1	250	200	220	20.7716
yyyyyyyyyyyyyyyggggg	chr15:83686713-83686953(-)$1	240	142	162	20.4168
ddduuuuuuuuuuuuddddC	chr13:103443150-103443390(-)$1	240	218	238	20.9875
ccctttttttttttcccccc	chr17:27613749-27613989(-)$1	240	150	170	21.5186
dddtttttttttttddddbb	chr11:62348487-62348727(-)$1	240	85	105	20.3677
dddtttttttttttdddd:e	chr19:38055997-38056237(-)$1	240	123	143	20.0176
dddtttttttttttdddd33	chr3:47164330-47164570(-)$1	240	41	61	20.9252
cccuuuuuuuuuuuuccc44	chr14:60585107-60585347(+)$1	240	41	61	22.5638
gggvvvvvvvvvvvvvgggg	chr11:32953710-32953950(+)$1	240	78	98	21.5484
eeettttttttttteeeee]	chr19:34916921-34917161(+)$1	240	115	135	21.1358
yyyyyyyyyyyyyyyfffff	chr18:214495-214735(-)$1	240	200	220	20.2136
eeeettttttttttteeeee	chr2:85769938-85770178(+)$1	240	58	78	21.2254
dddvvvvvvvvvvvvvdddd	chr11:62343532-62343783(-)$1	251	31	51	21.4089
[bbtttttttttttbb]bb]	chr13:27847526-27847766(+)$1	240	21	41	19.9456
eeeuuuuuuuuuuuueeeee	chr12:102154933-102155173(-)$1	240	122	142	22.3924
fffwwwwwwwwwwwwwwfff	chr19:3976148-3976400(-)$1	252	166	186	19.8392
fffuuuuuuuuuuuufffff	chr2:8998674-8998914(-)$1	240	204	224	21.8249
cwwwwwwwwwwwwwwccc]f	chr2:48033313-48033553(+)$1	240	123	143	20.7053
!avvvvvvvvvvvvva22gg	chr1:55557613-55557853(-)$1	240	138	158	21.3591
fffwwwwwwwwwwwwwwfff	chr8:95780589-95780829(+)$1	240	151	171	19.8392
CbbuuuuuuuuuuuubbFFF	chr11:62343019-62343306(-)$1	287	26	46	19.3937
ccctttttttttttcccccc	chr6:64286729-64286969(+)$1	240	58	78	21.5186
eeeuuuuuuuuuuuueeeee	chr2:223339207-223339447(+)$1	240	130	150	22.3924
eevvvvvvvvvvvvveeeee	chr16:29822345-29822585(+)$1	240	55	75	21.9043
dddtttttttttttdddd44	chr8:57079198-57079438(-)$1	240	163	183	20.8327
dddvvvvvvvvvvvvvdddd	chr11:125472605-125472845(+)$1	240	90	110	21.4089

#otherMatches

#Seq PSSM
CUGUUUUUGUAUUUUACAGC	chr20:47704473-47704713(+)$1	240	53	73	21.2254
UGACAAAGUACUCAACAUCA	chr5:74893735-74893975(+)$1	240	34	54	21.9043
GAGGAUGCUGGCCUCCCUCC	chr1:154524467-154524707(-)$1	240	205	225	21.2254
UGCUGAUGAAAUAAAAGCUC	chr6:149983054-149983294(-)$1	240	36	56	21.4761
UUACACCUAAUAACAUAAAG	chr17:62496654-62496894(-)$1	240	120	140	22.3924
GUGGCAUAGAACAAUACAGC	chr3:148765778-148766018(-)$1	240	150	170	20.6728
GAUUAAAGCCCAGAUUUCAG	chr10:88939811-88940051(+)$1	240	30	50	20.5438
GGCAUCGAGAUCAAGGUGUG	chr8:141561299-141561539(-)$1	240	67	87	20.4168
UGUUUUAAUUACUUUUACAU	chr12:105238178-105238458(-)$1	280	28	48	21.6398
AAAACACUUACUAUUUUGGA	chr6:96034241-96034481(+)$1	240	37	57	20.6187
CAGUCAGAGAAACAGUUUGU	chr3:128356670-128356918(-)$1	248	85	105	21.9100
UGUUUACAUUACAUAUCACA	chr5:133295131-133295371(-)$1	240	156	176	19.8392
CAUAGUUUCUAAAAAUAUGU	chr3:182545851-182546091(+)$1	240	179	199	21.2254
UCAUAUUUCUGGUGCAGGUA	chr13:113459214-113459454(+)$1	240	129	149	20.6197
UGUAUCAAUACCAUAAGGCA	chr5:110097337-110097577(+)$1	240	1	21	19.9790
AUUUCACUCAGUUCAUUUCU	chr11:62346253-62346608(-)$1	355	78	98	20.4168
AUGUUUUGUUUCUUUACAUU	chr21:34822994-34823234(-)$1	240	211	231	20.6247
CUCAAAUCCAUUUUAAAGAG	chr19:14203259-14203501(-)$1	242	202	222	20.3468
CUCCGCCAUAAUACAGGGGA	chr8:77617246-77617486(+)$1	240	30	50	20.6247
GUCUUCCAUUCUCCUGACAU	chr14:55510767-55511007(+)$1	240	42	62	22.3924
CCUUCCGGAACAUUAAGACC	chr19:58905805-58906045(+)$1	240	95	115	19.4809
GUGACUCCUUUCCCCCACAA	chr21:30698993-30699233(+)$1	240	67	87	20.7542
AGAUGGACAGAAAAACUGCU	chr11:62343128-62343408(-)$1	280	206	226	21.9043
GUAUUUCAGGUCAGUUGCUC	chr12:44337974-44338214(+)$1	240	29	49	22.5638
UGAUAUGCUAUUUCACAAGU	chr1:63884940-63885180(+)$1	240	45	65	21.3942
UGAUCAUGUUGUAACUUCAU	chr13:48938928-48939168(+)$1	240	72	92	21.4089
CAAAUUUUAAACUUCUUUCA	chr5:41917251-41917500(+)$1	249	114	134	20.5589
ACUUUUAUUUAUCAUUAACU	chr15:76209549-76209789(+)$1	240	193	213	20.2241
UUGAAGUCACCGUUAUCUUA	chr16:66592071-66592311(+)$1	240	94	114	20.0697
AUCAUCAACUCCUAAUAGUA	chr9:86297795-86298035(-)$1	240	108	128	20.4168
ACUCUACUCUUUACUGUUUU	chrX:41055464-41055704(+)$1	240	124	144	20.5368
AGAUGCUCCUUAAAAAUCUC	chr15:55474223-55474463(-)$1	240	101	121	21.6831
UACACAGGAGUUUCAGUAAC	chr9:98229448-98229688(-)$1	240	195	215	22.6540
GCUUAUAAAUAAAAUGGACA	chr14:53248433-53248673(-)$1	240	181	201	21.4831
CACACUUACAUUCAAUGGUC	chr6:72005958-72006198(+)$1	240	123	143	21.6261
UGUUUUAUGCCAUUACAACU	chr3:41267075-41267315(+)$1	240	95	115	21.1358
AAAUUUUUUCUGCCUAUUUA	chrX:48435822-48436072(+)$1	250	200	220	20.7716
UUAUAAUACAUCUUGGCUAA	chr15:83686713-83686953(-)$1	240	142	162	20.4168
CCUGCAAAUUUCAAGAGGUG	chr13:103443150-103443390(-)$1	240	218	238	20.9875
GACCCAAUCAUCAAGUCGCU	chr17:27613749-27613989(-)$1	240	150	170	21.5186
GCUUCGAUGUCCAUGGCUGU	chr11:62348487-62348727(-)$1	240	85	105	20.3677
CUUAUUCAACAUCAAAGAAU	chr19:38055997-38056237(-)$1	240	123	143	20.0176
CCCCCUAAUGAACUGGGAUU	chr3:47164330-47164570(-)$1	240	41	61	20.9252
ACAACUGCCACUUUAUGUAU	chr14:60585107-60585347(+)$1	240	41	61	22.5638
UCAAUUCAGGCACAACUGAC	chr11:32953710-32953950(+)$1	240	78	98	21.5484
uuauuaauauaaauuaaaaC	chr19:34916921-34917161(+)$1	240	115	135	21.1358
AACAUUUUUAUAACAAUUGU	chr18:214495-214735(-)$1	240	200	220	20.2136
AUUCUUACGACAUUUGAAUC	chr2:85769938-85770178(+)$1	240	58	78	21.2254
GUGACCCCCCUUUCCCCACU	chr11:62343532-62343783(-)$1	251	31	51	21.4089
CGCUCUCCCAACAUGCAGGA	chr13:27847526-27847766(+)$1	240	21	41	19.9456
UAUUUUUAUUAUCUCAUGAG	chr12:102154933-102155173(-)$1	240	122	142	22.3924
UUUAACAAACGCAUUAAGAG	chr19:3976148-3976400(-)$1	252	166	186	19.8392
CUGGGGGGAAAUGGACAGUU	chr2:8998674-8998914(-)$1	240	204	224	21.8249
UCACUACCAUUCAUUAGUAG	chr2:48033313-48033553(+)$1	240	123	143	20.7053
CGGACAAAGAAGAAACUCAG	chr1:55557613-55557853(-)$1	240	138	158	21.3591
UGUUUUCUUUCUAUGUUGCA	chr8:95780589-95780829(+)$1	240	151	171	19.8392
GGCAACCAAGAGAACGCGGU	chr11:62343019-62343306(-)$1	287	26	46	19.3937
GGCUCGAAUGAACCGCCCAG	chr6:64286729-64286969(+)$1	240	58	78	21.5186
CAAUUUUCAGCUGCUUUGGG	chr2:223339207-223339447(+)$1	240	130	150	22.3924
GUUCCUGUGUCCCCUGCAUG	chr16:29822345-29822585(+)$1	240	55	75	21.9043
UCUAUUCCUGAAAAAGAACA	chr8:57079198-57079438(-)$1	240	163	183	20.8327
AGGUUUAAUGAUCACCUCUG	chr11:125472605-125472845(+)$1	240	90	110	21.4089

#DB
((((...........)))))	chr20:47704473-47704713(+)$1	1	53	73	21.2254
((.............)))))	chr5:74893735-74893975(+)$1	1	34	54	21.9043
((((...........)))))	chr1:154524467-154524707(-)$1	1	205	225	21.2254
.(((...........)))))	chr6:149983054-149983294(-)$1	1	36	56	21.4761
(((............)))))	chr17:62496654-62496894(-)$1	1	120	140	22.3924
.((.............)).)	chr3:148765778-148766018(-)$1	1	150	170	20.6728
((..............))))	chr10:88939811-88940051(+)$1	1	30	50	20.5438
...............)))))	chr8:141561299-141561539(-)$1	1	67	87	20.4168
(((.............))).	chr12:105238178-105238458(-)$1	1	28	48	21.6398
...............))).)	chr6:96034241-96034481(+)$1	1	37	57	20.6187
(((.............))).	chr3:128356670-128356918(-)$1	1	85	105	21.9100
(((..............)))	chr5:133295131-133295371(-)$1	1	156	176	19.8392
((((...........)))))	chr3:182545851-182546091(+)$1	1	179	199	21.2254
((..............))))	chr13:113459214-113459454(+)$1	1	129	149	20.6197
(((..............)))	chr5:110097337-110097577(+)$1	1	1	21	19.9790
...............)))))	chr11:62346253-62346608(-)$1	1	78	98	20.4168
((((...........)))))	chr21:34822994-34823234(-)$1	1	211	231	20.6247
(((..............)))	chr19:14203259-14203501(-)$1	1	202	222	20.3468
((((...........)))))	chr8:77617246-77617486(+)$1	1	30	50	20.6247
(((............)))))	chr14:55510767-55511007(+)$1	1	42	62	22.3924
...............)).))	chr19:58905805-58906045(+)$1	1	95	115	19.4809
(((............)))..	chr21:30698993-30699233(+)$1	1	67	87	20.7542
((.............)))))	chr11:62343128-62343408(-)$1	1	206	226	21.9043
(((............)))..	chr12:44337974-44338214(+)$1	1	29	49	22.5638
((.............)))))	chr1:63884940-63885180(+)$1	1	45	65	21.3942
(((.............))))	chr13:48938928-48939168(+)$1	1	72	92	21.4089
...............)))))	chr5:41917251-41917500(+)$1	1	114	134	20.5589
(..............)))))	chr15:76209549-76209789(+)$1	1	193	213	20.2241
..((...........))..)	chr16:66592071-66592311(+)$1	1	94	114	20.0697
...............)))))	chr9:86297795-86298035(-)$1	1	108	128	20.4168
((.............))..)	chrX:41055464-41055704(+)$1	1	124	144	20.5368
.(((...........)))))	chr15:55474223-55474463(-)$1	1	101	121	21.6831
(((............))).)	chr9:98229448-98229688(-)$1	1	195	215	22.6540
(((............)).))	chr14:53248433-53248673(-)$1	1	181	201	21.4831
((.............)))))	chr6:72005958-72006198(+)$1	1	123	143	21.6261
(((...........))))).	chr3:41267075-41267315(+)$1	1	95	115	21.1358
((((...........)))))	chrX:48435822-48436072(+)$1	1	200	220	20.7716
...............)))))	chr15:83686713-83686953(-)$1	1	142	162	20.4168
(((............)))))	chr13:103443150-103443390(-)$1	1	218	238	20.9875
(((...........)))(((	chr17:27613749-27613989(-)$1	1	150	170	21.5186
(((...........))))((	chr11:62348487-62348727(-)$1	1	85	105	20.3677
(((...........)))).(	chr19:38055997-38056237(-)$1	1	123	143	20.0176
(((...........))))..	chr3:47164330-47164570(-)$1	1	41	61	20.9252
(((............)))..	chr14:60585107-60585347(+)$1	1	41	61	22.5638
(((.............))))	chr11:32953710-32953950(+)$1	1	78	98	21.5484
(((...........))))).	chr19:34916921-34917161(+)$1	1	115	135	21.1358
...............)))))	chr18:214495-214735(-)$1	1	200	220	20.2136
((((...........)))))	chr2:85769938-85770178(+)$1	1	58	78	21.2254
(((.............))))	chr11:62343532-62343783(-)$1	1	31	51	21.4089
.((...........)).)).	chr13:27847526-27847766(+)$1	1	21	41	19.9456
(((............)))))	chr12:102154933-102155173(-)$1	1	122	142	22.3924
(((..............)))	chr19:3976148-3976400(-)$1	1	166	186	19.8392
(((............)))))	chr2:8998674-8998914(-)$1	1	204	224	21.8249
(..............))).)	chr2:48033313-48033553(+)$1	1	123	143	20.7053
.(.............)..))	chr1:55557613-55557853(-)$1	1	138	158	21.3591
(((..............)))	chr8:95780589-95780829(+)$1	1	151	171	19.8392
(((............))(((	chr11:62343019-62343306(-)$1	1	26	46	19.3937
(((...........)))(((	chr6:64286729-64286969(+)$1	1	58	78	21.5186
(((............)))))	chr2:223339207-223339447(+)$1	1	130	150	22.3924
((.............)))))	chr16:29822345-29822585(+)$1	1	55	75	21.9043
(((...........))))..	chr8:57079198-57079438(-)$1	1	163	183	20.8327
(((.............))))	chr11:125472605-125472845(+)$1	1	90	110	21.4089

#PSSM
e : 0.20	d : 0.19	c : 0.16	y : 0.12	f : 0.11	[ : 0.06	i : 0.03	g : 0.03	! : 0.03	b : 0.01	C : 0.01	
e : 0.20	c : 0.17	d : 0.16	y : 0.12	f : 0.11	b : 0.08	i : 0.03	g : 0.03	w : 0.03	! : 0.01	a : 0.01	
c : 0.17	e : 0.16	d : 0.14	y : 0.12	v : 0.11	f : 0.09	b : 0.08	w : 0.06	i : 0.01	g : 0.01	
v : 0.22	u : 0.19	w : 0.14	t : 0.14	y : 0.12	e : 0.06	c : 0.03	f : 0.03	b : 0.01	i : 0.01	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
t : 0.30	v : 0.22	u : 0.19	w : 0.14	y : 0.12	
v : 0.22	u : 0.19	t : 0.16	w : 0.14	y : 0.12	d : 0.06	e : 0.03	c : 0.03	b : 0.01	
e : 0.20	c : 0.17	v : 0.11	w : 0.11	d : 0.11	b : 0.09	f : 0.08	g : 0.06	i : 0.01	a : 0.01	
e : 0.20	c : 0.20	d : 0.16	b : 0.09	g : 0.09	w : 0.08	f : 0.08	i : 0.03	] : 0.01	2 : 0.01	
c : 0.22	e : 0.20	d : 0.17	f : 0.12	g : 0.09	2 : 0.04	b : 0.03	i : 0.03	] : 0.03	F : 0.01	
e : 0.22	d : 0.14	f : 0.12	g : 0.11	c : 0.09	] : 0.06	b : 0.04	4 : 0.04	i : 0.03	: : 0.03	2 : 0.03	3 : 0.01	F : 0.01	
e : 0.22	f : 0.17	d : 0.12	g : 0.11	] : 0.06	c : 0.06	b : 0.04	i : 0.04	4 : 0.04	2 : 0.01	: : 0.01	C : 0.01	3 : 0.01	F : 0.01	

#score	1304.44901902286
#seq	62
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m2_run2.txt

#BEAR
b!!gggggggqqqqqqqqggggggg22b	chr12:4409617-4409950(+)$1	333	128	156	16.5340
b[eeeee[bbqqqqqqqqbb]eeeee]b	chr17:77807331-77807570(-)$1	239	34	62	15.5464
eeee"""cccqqqqqqqqccc]eeeee:	chr19:18642470-18642754(-)$1	284	160	188	16.4239
dd[eeeee[aqqqqqqqqa]eeeeeddd	chr19:52729396-52729697(+)$1	301	263	291	15.1864
eeeee[ddddqqqqqqqqdddd333eee	chr22:22041847-22042117(+)$1	270	227	255	15.5554
d[bb[bbcccqqqqqqqqccc]bbbbdd	chr2:98264458-98264755(+)$1	297	69	97	15.5477
$$$$bbddddqqqqqqqqdddd]bb444	chr4:77968209-77968455(-)$1	246	119	147	14.0052
hh[ccc[cccqqqqqqqqccc]ccc22h	chr2:217364590-217364849(+)$1	259	118	146	17.0991
fff[ffffffqqqqqqqqffffffffff	chr2:174091624-174091870(+)$1	246	25	53	15.7755
cffffff[bbqqqqqqqqbb]ffffff]	chr15:69745066-69745308(+)$1	242	14	42	15.9420
ggggg!!cccqqqqqqqqcccggggggg	chr10:103545943-103546203(-)$1	260	31	59	18.0424
hhh[ffffffqqqqqqqqffffff]hhh	chr10:105785613-105785869(+)$1	256	11	39	15.1944
##bb[eeeeeqqqqqqqqeeeee]bb22	chr11:66408417-66408680(+)$1	263	110	138	14.7547
"""ccc[cccqqqqqqqqccc]ccc22d	chr20:418072-418329(-)$1	257	165	193	17.6443
eeee!!ddddqqqqqqqqdddd22eeee	chr10:72183111-72183385(+)$1	274	16	44	15.1006
!!eeeee[bbqqqqqqqqbb]eeeeeff	chr17:61909842-61910082(-)$1	240	116	144	15.8454
:iiiiiiiiiqqqqqqqqiiiiiiiii:	chr19:17342604-17342878(-)$1	274	66	94	15.2632
fffff!!cccqqqqqqqqccc22fffff	chr19:21909338-21909630(-)$1	292	26	54	17.2501
c[dddd[cccqqqqqqqqcccdddd]cc	chr3:142151537-142151788(-)$1	251	141	169	16.4966
eeee[a!!bbqqqqqqqqbb]aeeeee2	chr2:232264701-232264940(-)$1	239	63	91	16.0003
:cccffffffqqqqqqqqffffff]ccc	chr8:28573338-28573583(+)$1	245	114	142	15.4708
cccbb!!cccqqqqqqqqccc22bb]cc	chr4:1982845-1983098(+)$1	253	106	134	16.8698
cc!!ffffffqqqqqqqqffffff]ccc	chr20:30729207-30729448(+)$1	241	69	97	16.6013
=====cccbbqqqqqqqqbb]ccc]===	chr12:56386842-56387082(+)$1	240	10	38	17.0012
e####a[cccqqqqqqqqccc]a333ee	chr1:89447656-89447901(-)$1	245	156	184	18.2817
ddddddd!!aqqqqqqqqa22dddd]dd	chrX:48432819-48433058(+)$1	239	136	164	13.9995
#cccffffffqqqqqqqqffffff]ccc	chr12:6979742-6980066(+)$1	324	24	52	16.3545
cccdddd[bbqqqqqqqqbbdddd]ccc	chr5:172744091-172744340(-)$1	249	130	158	15.3950
fffff!!cccqqqqqqqqccc4444fff	chr5:14508091-14508361(+)$1	270	155	183	17.5931
======[cccqqqqqqqqccc=======	chrX:147032254-147032519(+)$1	265	205	233	18.4441
[ccc[eeeeeqqqqqqqqeeeee]ccc]	chr10:102122924-102123244(+)$1	320	271	299	16.0660
bb[gggggggqqqqqqqqggggggg]bb	chr5:14509182-14509466(+)$1	284	112	140	16.2512
bb[ccc!!bbqqqqqqqqbbccc]bbEE	chr1:17735020-17735266(-)$1	246	194	222	14.2034
dd[eeeee[aqqqqqqqqaeeeee333d	chr17:78368442-78368687(+)$1	245	96	124	16.0145
g!!ccc[cccqqqqqqqqccc22ccc22	chr17:7128429-7128688(+)$1	259	34	62	17.5599
fffff!!cccqqqqqqqqccc22fffff	chr12:48175229-48175509(+)$1	280	30	58	17.2501
fffff!!cccqqqqqqqqccc]ffffff	chr11:202990-203232(-)$1	242	131	159	17.4531
:ccc[cccbbqqqqqqqqbb]ccc]ccc	chr1:145442455-145442724(+)$1	269	78	106	15.9047
fff!!bbcccqqqqqqqqccc]bb4444	chr15:91044853-91045127(+)$1	274	3	31	16.6476
!!ccc!!cccqqqqqqqqccc333ccc5	chr19:51301638-51301880(-)$1	242	11	39	17.7514
ffbb!!ddddqqqqqqqqddddbb]fff	chr12:4410762-4411036(+)$1	274	150	178	14.7795
a[ccc"""bbqqqqqqqqbb4444ccc]	chr6:108250512-108250751(-)$1	239	142	170	16.9474
ee!!ffffffqqqqqqqqffffff]eee	chr14:35777110-35777368(+)$1	258	12	40	16.1725
:iiiiiiiiiqqqqqqqqiiiiiiiii:	chr4:144391516-144391755(+)$1	239	2	30	15.2632
gggggg[cccqqqqqqqqcccggggggg	chr17:21731178-21731474(+)$1	296	104	132	17.8949
ee[gggggggqqqqqqqqgggggggeee	chr7:108214561-108214794(+)$1	233	111	139	16.6496
dddd[a[cccqqqqqqqqccc]a]dddd	chr17:73775685-73775941(-)$1	256	91	119	16.9688
ggggggg[bbqqqqqqqqbb]ggggggg	chr19:10396313-10396561(+)$1	248	140	168	16.7969
gggg[eeeeeqqqqqqqqeeeee22ggg	chr11:102269337-102269623(-)$1	286	142	170	15.7646
####ccccccqqqqqqqqccc22cccdd	chr6:31237978-31238360(-)$1	382	246	274	17.1601
ff[a"""cccqqqqqqqqccc]a]ffff	chr12:51420014-51420253(-)$1	239	13	41	17.8688
ddddffffffqqqqqqqqffffff22dd	chr22:39917209-39917449(+)$1	240	13	41	15.1579
=========rrrrrrrrr==========	chr17:1367379-1367670(-)$1	291	32	60	11.0340
!a"""eeeeeqqqqqqqqeeeee333a2	chr8:145698994-145699236(+)$1	242	204	232	16.2621
bb[gggggggqqqqqqqqgggggggbbd	chr19:34846319-34846573(+)$1	254	36	64	16.0835
[bb####cccqqqqqqqqccc333bb]a	chr3:178952404-178952702(+)$1	298	116	144	17.3027
===####cccqqqqqqqqccc55555==	chr14:45396855-45397102(-)$1	247	177	205	14.2005

#otherMatches

#Seq PSSM
AGGAGUGUAGUUGGAUCUCUACAUUAAU	chr12:4409617-4409950(+)$1	333	128	156	16.5340
CCUCUCCUGCCCUUCCCCGCUGGAGAUG	chr17:77807331-77807570(-)$1	239	34	62	15.5464
AAAUAAAGCAUCCCACCCUGCAGUUUCC	chr19:18642470-18642754(-)$1	284	160	188	16.4239
GGUCUAGAAGUAGUUGGUCCUCUGGCCU	chr19:52729396-52729697(+)$1	301	263	291	15.1864
CUGGGUGGGCUUGUCCCUGCCCCAUCCC	chr22:22041847-22042117(+)$1	270	227	255	15.5554
GUGGAGCCCAUUACAAGCUGGUGCCCCA	chr2:98264458-98264755(+)$1	297	69	97	15.5477
CUCUGGUAGCAAUAAAAAGUUGUCCUUA	chr4:77968209-77968455(-)$1	246	119	147	14.0052
GUGGUUCCUGCAUGAAGACAGUGGCUGG	chr2:217364590-217364849(+)$1	259	118	146	17.0991
UGCCAAAUAUCUUGUAUAAUGUUUGUAU	chr2:174091624-174091870(+)$1	246	25	53	15.7755
GGUCCGCCUCUUCCGCCCGGUGCGGGCG	chr15:69745066-69745308(+)$1	242	14	42	15.9420
UAACUGCACCUUGUGAAUGGUAGUUGAG	chr10:103545943-103546203(-)$1	260	31	59	18.0424
uuuguuuuuAAGCAAAGAUGAAGGGAAA	chr10:105785613-105785869(+)$1	256	11	39	15.1944
AUGGUGAGUUGCUAUCUGAACUCUUCUU	chr11:66408417-66408680(+)$1	263	110	138	14.7547
AAUGUCGUUGGAAACUUGCAAAGACUCU	chr20:418072-418329(-)$1	257	165	193	17.6443
AAAGCCUCAUUCUUUUCUGUGACCCUUU	chr10:72183111-72183385(+)$1	274	16	44	15.1006
CUGGGGCGAGGGUCAGAGCUGGCUCUGG	chr17:61909842-61910082(-)$1	240	116	144	15.8454
GGGCUGCUCCAGUGGGCAGGGGUAGCUA	chr19:17342604-17342878(-)$1	274	66	94	15.2632
AAGAUAACUCAUACUGGAGAGAAAUCUU	chr19:21909338-21909630(-)$1	292	26	54	17.2501
UUUCAGAUGAUAAAAUCUUUACUGAUAU	chr3:142151537-142151788(-)$1	251	141	169	16.4966
CCAGACAGGCUCUCUGAUGCAGCUGGGA	chr2:232264701-232264940(-)$1	239	63	91	16.0003
GUCUGGGGAGCACACUAACUCUUCUGGA	chr8:28573338-28573583(+)$1	245	114	142	15.4708
GAGCAAGUAACACUAACUUUGAAUGUCU	chr4:1982845-1983098(+)$1	253	106	134	16.8698
UUGAUCUGUCUCUCUUACGGCAGGAGAG	chr20:30729207-30729448(+)$1	241	69	97	16.6013
GAGGAGGGACAGUUUCUGGUACCCAUCC	chr12:56386842-56387082(+)$1	240	10	38	17.0012
AAUCUGCAAGAACCUCCCCUUUCCCCUC	chr1:89447656-89447901(-)$1	245	156	184	18.2817
UUCCAGGUAAGUUGCAUAUGUCCUGCGA	chrX:48432819-48433058(+)$1	239	136	164	13.9995
GUCACCAAGGUGGCUUCUCCUUGGCUGA	chr12:6979742-6980066(+)$1	324	24	52	16.3545
UCUGGGCUGGGGGGGACACUGUCCAAGG	chr5:172744091-172744340(-)$1	249	130	158	15.3950
AUUUGCCGCUUAGACUUUAGCUUCCCAG	chr5:14508091-14508361(+)$1	270	155	183	17.5931
UGAUUCACAUGUUUUCAAAUGGAGUUGG	chrX:147032254-147032519(+)$1	265	205	233	18.4441
GUCUUUUGAGCUAUUCACCUCAGUAGAA	chr10:102122924-102123244(+)$1	320	271	299	16.0660
UCAGAUUGUGGAGCAGUACACAGUCAGA	chr5:14509182-14509466(+)$1	284	112	140	16.2512
CCUUCUCCGCUUUUUCUUGCAGAUGGGC	chr1:17735020-17735266(-)$1	246	194	222	14.2034
GGCACGGAAGGAACUGUGCUCCGUUCUC	chr17:78368442-78368687(+)$1	245	96	124	16.0145
AAAGCCGAAGCCCCUUUCCUUAAGGCCC	chr17:7128429-7128688(+)$1	259	34	62	17.5599
CUUUUCUGCCCAUACACUGGCCCAAGGG	chr12:48175229-48175509(+)$1	280	30	58	17.2501
UGCUGACUGUAAUCCCUGACACCAGUAA	chr11:202990-203232(-)$1	242	131	159	17.4531
UGGUAAAGACUAUAUUUUGUACUUAACC	chr1:145442455-145442724(+)$1	269	78	106	15.9047
GGUUACAGCCCACAGGGAGGCAUGGAGU	chr15:91044853-91045127(+)$1	274	3	31	16.6476
UCCUCCCGGCACUUCGAGGCCACUGAGC	chr19:51301638-51301880(-)$1	242	11	39	17.7514
ACCUAGCUGUAAUGUUUCACAGAGUGUG	chr12:4410762-4411036(+)$1	274	150	178	14.7795
GGAUUUCAAGAAAAAAACCUACUUAAUG	chr6:108250512-108250751(-)$1	239	142	170	16.9474
UUUUUAAUGACUAUUAUUUCAUUGCAAG	chr14:35777110-35777368(+)$1	258	12	40	16.1725
AGAAUUACGGAUUUUGUACUGUGAUUUA	chr4:144391516-144391755(+)$1	239	2	30	15.2632
AUCUUUGCAGGCAAGCAGCUGGAAGAUG	chr17:21731178-21731474(+)$1	296	104	132	17.8949
CAAUAUUUUUAAAUCCUGAGAAAUGUGU	chr7:108214561-108214794(+)$1	233	111	139	16.6496
CGGUUUGGUCGUUCGUUGGGCGGUGCUG	chr17:73775685-73775941(-)$1	256	91	119	16.9688
GAUGAUAUGUAUUUAUUCauuuguuauu	chr19:10396313-10396561(+)$1	248	140	168	16.7969
AUAUAAUGUACAGUGUAUUACGUAAAUA	chr11:102269337-102269623(-)$1	286	142	170	15.7646
GACCAGGCCAGCAGGAGAUGGAACCUUC	chr6:31237978-31238360(-)$1	382	246	274	17.1601
CAGGGACUCCAGCCAAUAGGGAUGUGCG	chr12:51420014-51420253(-)$1	239	13	41	17.8688
GGGAGGGGCAAAUACAACUGCCCUGUUC	chr22:39917209-39917449(+)$1	240	13	41	15.1579
CGGCAGGGGCAUCACCUCCUUCUGCUGC	chr17:1367379-1367670(-)$1	291	32	60	11.0340
CCGAAAAAGGUGCUACCUCCUUUCCAGA	chr8:145698994-145699236(+)$1	242	204	232	16.2621
GGACAUUGUGUGUAUAGUUACAAUGCUU	chr19:34846319-34846573(+)$1	254	36	64	16.0835
GCAAAUGUUCUAUGUUUUGAAAUGUGGA	chr3:178952404-178952702(+)$1	298	116	144	17.3027
GAUGUUUACUUGAGUAAUAGUUCUAAGU	chr14:45396855-45397102(-)$1	247	177	205	14.2005

#DB
(..(((((((........)))))))..)	chr12:4409617-4409950(+)$1	1	128	156	16.5340
(.(((((.((........)).))))).)	chr17:77807331-77807570(-)$1	1	34	62	15.5464
((((...(((........))).))))).	chr19:18642470-18642754(-)$1	1	160	188	16.4239
((.(((((.(........).))))))))	chr19:52729396-52729697(+)$1	1	263	291	15.1864
(((((.((((........))))...)))	chr22:22041847-22042117(+)$1	1	227	255	15.5554
(.((.(((((........))).))))))	chr2:98264458-98264755(+)$1	1	69	97	15.5477
....((((((........)))).))...	chr4:77968209-77968455(-)$1	1	119	147	14.0052
((.(((.(((........))).)))..)	chr2:217364590-217364849(+)$1	1	118	146	17.0991
(((.((((((........))))))))))	chr2:174091624-174091870(+)$1	1	25	53	15.7755
(((((((.((........)).)))))).	chr15:69745066-69745308(+)$1	1	14	42	15.9420
(((((..(((........))))))))))	chr10:103545943-103546203(-)$1	1	31	59	18.0424
(((.((((((........)))))).)))	chr10:105785613-105785869(+)$1	1	11	39	15.1944
..((.(((((........))))).))..	chr11:66408417-66408680(+)$1	1	110	138	14.7547
...(((.(((........))).)))..)	chr20:418072-418329(-)$1	1	165	193	17.6443
((((..((((........))))..))))	chr10:72183111-72183385(+)$1	1	16	44	15.1006
..(((((.((........)).)))))))	chr17:61909842-61910082(-)$1	1	116	144	15.8454
.(((((((((........))))))))).	chr19:17342604-17342878(-)$1	1	66	94	15.2632
(((((..(((........)))..)))))	chr19:21909338-21909630(-)$1	1	26	54	17.2501
(.((((.(((........))))))).))	chr3:142151537-142151788(-)$1	1	141	169	16.4966
((((.(..((........)).)))))).	chr2:232264701-232264940(-)$1	1	63	91	16.0003
.(((((((((........)))))).)))	chr8:28573338-28573583(+)$1	1	114	142	15.4708
(((((..(((........)))..)).))	chr4:1982845-1983098(+)$1	1	106	134	16.8698
((..((((((........)))))).)))	chr20:30729207-30729448(+)$1	1	69	97	16.6013
((((((((((........)).))).)))	chr12:56386842-56387082(+)$1	1	10	38	17.0012
(....(.(((........))).)...))	chr1:89447656-89447901(-)$1	1	156	184	18.2817
(((((((..(........)..)))).))	chrX:48432819-48433058(+)$1	1	136	164	13.9995
.(((((((((........)))))).)))	chr12:6979742-6980066(+)$1	1	24	52	16.3545
(((((((.((........)))))).)))	chr5:172744091-172744340(-)$1	1	130	158	15.3950
(((((..(((........)))....)))	chr5:14508091-14508361(+)$1	1	155	183	17.5931
((((((.(((........))))))))))	chrX:147032254-147032519(+)$1	1	205	233	18.4441
.(((.(((((........))))).))).	chr10:102122924-102123244(+)$1	1	271	299	16.0660
((.(((((((........))))))).))	chr5:14509182-14509466(+)$1	1	112	140	16.2512
((.(((..((........))))).))))	chr1:17735020-17735266(-)$1	1	194	222	14.2034
((.(((((.(........))))))...)	chr17:78368442-78368687(+)$1	1	96	124	16.0145
(..(((.(((........)))..)))..	chr17:7128429-7128688(+)$1	1	34	62	17.5599
(((((..(((........)))..)))))	chr12:48175229-48175509(+)$1	1	30	58	17.2501
(((((..(((........))).))))))	chr11:202990-203232(-)$1	1	131	159	17.4531
.(((.(((((........)).))).)))	chr1:145442455-145442724(+)$1	1	78	106	15.9047
(((..(((((........))).))....	chr15:91044853-91045127(+)$1	1	3	31	16.6476
..(((..(((........)))...))).	chr19:51301638-51301880(-)$1	1	11	39	17.7514
((((..((((........)))))).)))	chr12:4410762-4411036(+)$1	1	150	178	14.7795
(.(((...((........))....))).	chr6:108250512-108250751(-)$1	1	142	170	16.9474
((..((((((........)))))).)))	chr14:35777110-35777368(+)$1	1	12	40	16.1725
.(((((((((........))))))))).	chr4:144391516-144391755(+)$1	1	2	30	15.2632
((((((.(((........))))))))))	chr17:21731178-21731474(+)$1	1	104	132	17.8949
((.(((((((........))))))))))	chr7:108214561-108214794(+)$1	1	111	139	16.6496
((((.(.(((........))).).))))	chr17:73775685-73775941(-)$1	1	91	119	16.9688
(((((((.((........)).)))))))	chr19:10396313-10396561(+)$1	1	140	168	16.7969
((((.(((((........)))))..)))	chr11:102269337-102269623(-)$1	1	142	170	15.7646
....((((((........)))..)))))	chr6:31237978-31238360(-)$1	1	246	274	17.1601
((.(...(((........))).).))))	chr12:51420014-51420253(-)$1	1	13	41	17.8688
((((((((((........))))))..))	chr22:39917209-39917449(+)$1	1	13	41	15.1579
(((((((((.........))))))))))	chr17:1367379-1367670(-)$1	1	32	60	11.0340
.(...(((((........)))))...).	chr8:145698994-145699236(+)$1	1	204	232	16.2621
((.(((((((........)))))))))(	chr19:34846319-34846573(+)$1	1	36	64	16.0835
.((....(((........)))...)).)	chr3:178952404-178952702(+)$1	1	116	144	17.3027
(((....(((........))).....))	chr14:45396855-45397102(-)$1	1	177	205	14.2005

#PSSM
f : 0.14	e : 0.12	d : 0.10	b : 0.08	c : 0.08	g : 0.08	: : 0.07	= : 0.07	# : 0.05	! : 0.05	h : 0.03	[ : 0.03	$ : 0.01	" : 0.01	a : 0.01	
f : 0.15	c : 0.12	e : 0.10	d : 0.08	! : 0.07	[ : 0.07	g : 0.07	= : 0.07	b : 0.07	# : 0.05	h : 0.03	i : 0.03	$ : 0.01	" : 0.01	a : 0.01	
[ : 0.14	c : 0.14	f : 0.12	e : 0.10	! : 0.07	b : 0.07	g : 0.07	d : 0.07	= : 0.07	" : 0.03	i : 0.03	# : 0.03	$ : 0.01	h : 0.01	
c : 0.17	g : 0.14	e : 0.14	f : 0.08	d : 0.08	b : 0.07	# : 0.07	! : 0.05	= : 0.05	[ : 0.03	i : 0.03	$ : 0.01	a : 0.01	" : 0.01	
f : 0.21	g : 0.12	[ : 0.12	c : 0.12	e : 0.08	" : 0.05	! : 0.05	d : 0.05	= : 0.05	# : 0.05	b : 0.03	i : 0.03	
! : 0.15	e : 0.14	f : 0.14	c : 0.12	g : 0.10	" : 0.05	b : 0.05	d : 0.05	a : 0.05	i : 0.03	= : 0.03	# : 0.03	[ : 0.01	
! : 0.15	e : 0.14	[ : 0.14	f : 0.14	d : 0.10	g : 0.08	" : 0.05	c : 0.05	b : 0.03	i : 0.03	# : 0.03	= : 0.01	
c : 0.42	f : 0.12	e : 0.10	[ : 0.08	g : 0.07	d : 0.07	! : 0.05	i : 0.03	" : 0.01	= : 0.01	
c : 0.38	b : 0.17	f : 0.12	g : 0.07	d : 0.07	e : 0.07	[ : 0.03	i : 0.03	! : 0.01	= : 0.01	
c : 0.38	b : 0.17	f : 0.12	g : 0.07	d : 0.07	e : 0.07	a : 0.05	i : 0.03	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
c : 0.38	b : 0.17	f : 0.12	g : 0.07	d : 0.07	e : 0.07	a : 0.05	i : 0.03	= : 0.01	
c : 0.38	b : 0.17	f : 0.12	e : 0.08	g : 0.07	d : 0.07	i : 0.03	] : 0.01	2 : 0.01	= : 0.01	
c : 0.40	] : 0.12	f : 0.12	e : 0.10	d : 0.08	g : 0.07	i : 0.03	2 : 0.01	4 : 0.01	= : 0.01	
] : 0.15	e : 0.14	f : 0.14	g : 0.12	d : 0.12	2 : 0.08	c : 0.05	i : 0.03	4 : 0.03	= : 0.03	3 : 0.03	a : 0.01	5 : 0.01	
e : 0.17	f : 0.15	g : 0.12	2 : 0.10	c : 0.08	3 : 0.05	b : 0.05	d : 0.05	a : 0.05	i : 0.03	4 : 0.03	= : 0.03	] : 0.01	5 : 0.01	
f : 0.19	g : 0.12	e : 0.10	c : 0.10	3 : 0.08	b : 0.08	] : 0.08	d : 0.05	2 : 0.03	i : 0.03	4 : 0.03	= : 0.03	5 : 0.01	
] : 0.15	g : 0.12	c : 0.12	e : 0.10	b : 0.10	f : 0.10	3 : 0.07	d : 0.05	i : 0.03	4 : 0.03	= : 0.03	2 : 0.03	5 : 0.01	
c : 0.17	e : 0.14	f : 0.14	b : 0.08	2 : 0.07	g : 0.07	] : 0.07	= : 0.05	3 : 0.05	d : 0.03	4 : 0.03	i : 0.03	h : 0.01	5 : 0.01	
c : 0.17	f : 0.15	e : 0.12	d : 0.10	2 : 0.08	g : 0.07	= : 0.07	] : 0.03	4 : 0.03	i : 0.03	b : 0.03	h : 0.01	E : 0.01	3 : 0.01	a : 0.01	
d : 0.15	f : 0.14	c : 0.12	e : 0.08	g : 0.07	2 : 0.07	= : 0.07	b : 0.05	: : 0.05	] : 0.05	4 : 0.03	h : 0.03	E : 0.01	5 : 0.01	a : 0.01	

#score	922.6307348724464
#seq	57
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m1_run1.txt

#BEAR
d[ddddtttttttttttdddd	chr20:39833212-39833452(-)$1	240	95	116	21.6952
""ddddtttttttttttdddd	chr13:39616227-39616467(+)$1	240	115	136	21.6425
ddddwwwwwwwwwwwwwwddd	chr12:39701309-39701549(-)$1	240	133	154	21.1849
iiiiivvvvvvvvvvvvviii	chr8:53568944-53569184(-)$1	240	26	47	22.1715
!eeeeettttttttttteeee	chr21:34958272-34958512(-)$1	240	91	112	21.7291
[eeeeettttttttttteeee	chr2:32626263-32626503(+)$1	240	114	135	21.7243
eeeyyyyyyyyyyyyyyyyee	chr1:197072786-197073026(-)$1	240	103	124	20.6502
$$$bbwwwwwwwwwwwwwwbb	chr11:111753787-111754027(+)$1	240	103	124	19.0199
eeeeeuuuuuuuuuuuueeee	chr1:64095513-64095753(+)$1	240	120	141	22.4905
iiiiivvvvvvvvvvvvviii	chr5:59893537-59893777(-)$1	240	213	234	22.1715
:dddduuuuuuuuuuuudddd	chr1:212241857-212242097(+)$1	240	110	131	21.6672
fffffvvvvvvvvvvvvvfff	chr1:91403203-91403483(-)$1	280	239	260	21.7021
g[bbvvvvvvvvvvvvvbb]g	chr2:48602000-48602240(+)$1	240	111	132	21.8067
eeebbuuuuuuuuuuuubb]e	chr9:79952127-79952367(+)$1	240	215	236	22.0991
ddddvvvvvvvvvvvvvdddd	chr7:44620674-44620914(-)$1	240	54	75	22.3080
!!ddddtttttttttttdddd	chr1:115269503-115269743(-)$1	240	213	234	21.8470
eeeevvvvvvvvvvvvveeee	chr1:32374418-32374658(-)$1	240	83	104	22.3632
!!bbvvvvvvvvvvvvvbb22	chr12:22208302-22208542(+)$1	240	107	128	21.3111
:eeeeettttttttttteeee	chr3:9512111-9512351(+)$1	240	10	31	20.7749
ccc[bbtttttttttttbb]c	chr2:69658954-69659194(-)$1	240	67	88	21.1502
eeeeeuuuuuuuuuuuueeee	chr10:75234621-75234861(-)$1	240	2	23	22.4905
dddbbuuuuuuuuuuuubb22	chr3:9495340-9495580(+)$1	240	150	171	21.3577
cccwwwwwwwwwwwwwwccc>	chr3:69105067-69105307(-)$1	240	92	113	20.6968
iiiiiitttttttttttiiii	chr10:27470354-27470594(+)$1	240	184	205	21.4103
:dddduuuuuuuuuuuudddd	chr16:31102419-31102659(-)$1	240	90	111	21.6672
ddddduuuuuuuuuuuudddd	chr5:95226841-95227081(-)$1	240	125	146	22.4401
:cccvvvvvvvvvvvvvcccc	chr11:66393971-66394211(+)$1	240	85	106	21.6790
c[cccvvvvvvvvvvvvvccc	chr2:178095543-178095783(-)$1	240	83	104	22.5077
cccyyyyyyyyyyyyyyyycc	chrX:106890768-106891008(+)$1	240	38	59	20.5698
fffyyyyyyyyyyyyyyyyff	chr12:133256471-133256711(-)$1	240	18	39	20.2667
fffffftttttttttttffff	chr2:145161442-145161682(-)$1	240	95	116	21.0204
ffcccvvvvvvvvvvvvvccc	chr10:103871146-103871386(-)$1	240	73	94	22.2987
[dddduuuuuuuuuuuudddd	chr2:160599585-160599825(+)$1	240	175	196	22.6166
ddddvvvvvvvvvvvvvdddd	chr9:106862299-106862539(+)$1	240	166	187	22.3080
eeeeeuuuuuuuuuuuueeee	chr5:71494306-71494546(+)$1	240	53	74	22.4905
ggggggtttttttttttgggg	chr12:101017702-101017942(+)$1	240	96	117	21.3472
eeeevvvvvvvvvvvvveeee	chr1:231509630-231509870(-)$1	240	164	185	22.3632
fffffwwwwwwwwwwwwwwff	chr12:57663076-57663316(-)$1	240	86	107	20.3949
ddddvvvvvvvvvvvvvdddd	chr3:42635878-42636118(+)$1	240	70	91	22.3080
!!ddddtttttttttttdddd	chr3:88104889-88105129(-)$1	240	15	36	21.8470
ddddwwwwwwwwwwwwwwddd	chr11:67021640-67021920(+)$1	280	179	200	21.1849
hhhhhuuuuuuuuuuuuhhhh	chr2:74386128-74386368(-)$1	240	102	123	20.5698
fffffuuuuuuuuuuuuffff	chr18:21114378-21114618(-)$1	240	116	137	21.9076
fffffuuuuuuuuuuuuffff	chr10:12279044-12279284(+)$1	240	72	93	21.9076
fffffwwwwwwwwwwwwwwff	chr1:12049188-12049428(+)$1	240	142	163	20.3949
=====vvvvvvvvvvvvv===	chr1:91989879-91990119(+)$1	240	145	166	22.3591
eeeyyyyyyyyyyyyyyyyee	chr7:64168184-64168424(+)$1	240	23	44	20.6502
:cccvvvvvvvvvvvvvccce	chr13:107164962-107165202(-)$1	240	17	38	21.7474
ee[bbuuuuuuuuuuuubbee	chr17:6917618-6917858(+)$1	240	108	129	22.0654
eeeeeuuuuuuuuuuuueeee	chr15:66811244-66811484(+)$1	240	44	65	22.4905
a[bbvvvvvvvvvvvvvbb]a	chr13:77570006-77570246(+)$1	240	176	197	21.6809
::cccuuuuuuuuuuuuccc:	chr12:56385829-56386069(+)$1	240	204	225	19.8250
ddddwwwwwwwwwwwwwwddd	chr10:94393296-94393536(+)$1	240	138	159	21.1849
##ccctttttttttttccc44	chr2:11922293-11922533(+)$1	240	124	145	21.1440
g[ccctttttttttttcccgg	chr5:177637049-177637289(+)$1	240	167	188	21.5416
fffffftttttttttttffff	chr14:50247343-50247583(+)$1	240	111	132	21.0204
:cccvvvvvvvvvvvvvccce	chr7:22999896-23000136(-)$1	240	82	103	21.7474
cccyyyyyyyyyyyyyyyycc	chr1:150902373-150902613(+)$1	240	6	27	20.5698
eeeyyyyyyyyyyyyyyyyee	chr16:3486350-3486590(-)$1	240	120	141	20.6502
[cccwwwwwwwwwwwwwwccc	chr5:79974740-79974980(+)$1	240	199	220	21.4389
gggyyyyyyyyyyyyyyyygg	chr17:60042591-60042831(-)$1	240	117	138	20.5386
fffffftttttttttttffff	chr1:94955392-94955632(+)$1	240	160	181	21.0204
[ddddtttttttttttdddd]	chr6:33288182-33288422(-)$1	240	64	85	21.0170
c[ddddtttttttttttdddd	chr21:44323233-44323473(+)$1	240	121	142	21.7807
iiiiiitttttttttttiiii	chr14:45414558-45414798(-)$1	240	110	131	21.4103
fffffftttttttttttffff	chr7:97939764-97940004(-)$1	240	104	125	21.0204

#otherMatches

#Seq PSSM
GGCAUCGGAGCACUUUAGAUG	chr20:39833212-39833452(-)$1	240	95	116	21.6952
UUUGAUAACCCAGCAGAAUUA	chr13:39616227-39616467(+)$1	240	115	136	21.6425
UUCCUCUAUGCUGCUUCUGGA	chr12:39701309-39701549(-)$1	240	133	154	21.1849
GCUGGAAGAAAGCAGAGCCCA	chr8:53568944-53569184(-)$1	240	26	47	22.1715
UGGAGUAUUAAAACGCGACUC	chr21:34958272-34958512(-)$1	240	91	112	21.7291
GAGCUGCCCUCAUUUUCUAGC	chr2:32626263-32626503(+)$1	240	114	135	21.7243
CUAAUCAAACAACAAUCUAUA	chr1:197072786-197073026(-)$1	240	103	124	20.6502
CAAGCUACAACAACAAAAUGC	chr11:111753787-111754027(+)$1	240	103	124	19.0199
CUGAUAAAAUUUUCCAAAUCA	chr1:64095513-64095753(+)$1	240	120	141	22.4905
AACAGGUGCUAGAGACCACUG	chr5:59893537-59893777(-)$1	240	213	234	22.1715
CUGGCUCUACUUUAUUUGCUA	chr1:212241857-212242097(+)$1	240	110	131	21.6672
UGGGAAAAAGAAUCAGUCUCU	chr1:91403203-91403483(-)$1	280	239	260	21.7021
AAUGCAUUUCAUCAUCCCAGU	chr2:48602000-48602240(+)$1	240	111	132	21.8067
UCUCUAUCAGUGUAUUCAGAA	chr9:79952127-79952367(+)$1	240	215	236	22.0991
UACAUUCCAUGUUUCCUUGUA	chr7:44620674-44620914(-)$1	240	54	75	22.3080
UUCAAAUUUUAUCAAGUUUUG	chr1:115269503-115269743(-)$1	240	213	234	21.8470
UCUUGUAUUUUCAGAAAAAGA	chr1:32374418-32374658(-)$1	240	83	104	22.3632
UUCAAGCUACUUCUCCAUGUU	chr12:22208302-22208542(+)$1	240	107	128	21.3111
CGUUGAUUUUUAUUCUUUCAG	chr3:9512111-9512351(+)$1	240	10	31	20.7749
AUGUUGAAGAAUCCAUACACC	chr2:69658954-69659194(-)$1	240	67	88	21.1502
GGAGCAAAGAUCAAGCAGCUU	chr10:75234621-75234861(-)$1	240	2	23	22.4905
UCAGCACCUAUACCAAAGCAA	chr3:9495340-9495580(+)$1	240	150	171	21.3577
GGCAAAUGAAAUCUCCAGCCA	chr3:69105067-69105307(-)$1	240	92	113	20.6968
ACCAUUGAUUUUUUGCAGAUG	chr10:27470354-27470594(+)$1	240	184	205	21.4103
CGUGCUCUAUGAUUUCUGCAU	chr16:31102419-31102659(-)$1	240	90	111	21.6672
UAUGAGCAACGCCAGAAUUAU	chr5:95226841-95227081(-)$1	240	125	146	22.4401
CCGAUUACGCACGCUAUUCGG	chr11:66393971-66394211(+)$1	240	85	106	21.6790
GAGAAAAUGACAAAAGCCUUC	chr2:178095543-178095783(-)$1	240	83	104	22.5077
GAAUCCAAAUCAACAUUUUUU	chrX:106890768-106891008(+)$1	240	38	59	20.5698
AUAGGCAAGGAAGGAAAUGUA	chr12:133256471-133256711(-)$1	240	18	39	20.2667
GAGAAGAAUGAAGAGAACUUU	chr2:145161442-145161682(-)$1	240	95	116	21.0204
CUCCUUUCUUUCUCGUCUAGG	chr10:103871146-103871386(-)$1	240	73	94	22.2987
UCAGGUAAGAAUGAGUUUCUG	chr2:160599585-160599825(+)$1	240	175	196	22.6166
GCUGAAAGAAAUUAAGACGGU	chr9:106862299-106862539(+)$1	240	166	187	22.3080
AGAGGCCUCCCCGUCCACCUC	chr5:71494306-71494546(+)$1	240	53	74	22.4905
CUUGCUUCAUUAAAUCCAGUA	chr12:101017702-101017942(+)$1	240	96	117	21.3472
AUUUAUUUUUUUCUUACAGGU	chr1:231509630-231509870(-)$1	240	164	185	22.3632
CCAGGUUUCUUACUAUCCCCC	chr12:57663076-57663316(-)$1	240	86	107	20.3949
UGGCUACCAUUGCAGAUGCCA	chr3:42635878-42636118(+)$1	240	70	91	22.3080
GUAGUAACAGCACCACCUGCU	chr3:88104889-88105129(-)$1	240	15	36	21.8470
CAGUCCUCCAAUCUACUCACU	chr11:67021640-67021920(+)$1	280	179	200	21.1849
GGAGGCCCACCUCAACACCUC	chr2:74386128-74386368(-)$1	240	102	123	20.5698
UUCUGCAGCCACAUAACCAGA	chr18:21114378-21114618(-)$1	240	116	137	21.9076
CAGGAUGUAAAAUAUUUUCUU	chr10:12279044-12279284(+)$1	240	72	93	21.9076
AAGAAGAAGAUCAAUGGCAUU	chr1:12049188-12049428(+)$1	240	142	163	20.3949
AGGUAGAAUAAAAAAGAAUAC	chr1:91989879-91990119(+)$1	240	145	166	22.3591
AUCAACUUACUAGACAUAAGA	chr7:64168184-64168424(+)$1	240	23	44	20.6502
UGGCUUUUUUUUCUUAUGCUU	chr13:107164962-107165202(-)$1	240	17	38	21.7474
GACUGAAUCCCUUCUCCCAUC	chr17:6917618-6917858(+)$1	240	108	129	22.0654
UGCCCUUCCUCCCCUUUGGGU	chr15:66811244-66811484(+)$1	240	44	65	22.4905
CGCUGCCUGCUUUUUUGAGGG	chr13:77570006-77570246(+)$1	240	176	197	21.6809
AAGAGCUAAGAAAUAACCUCC	chr12:56385829-56386069(+)$1	240	204	225	19.8250
UGGAUCUCUCACAUCUAUUCC	chr10:94393296-94393536(+)$1	240	138	159	21.1849
CUUCAGACACUUUUAGUGACC	chr2:11922293-11922533(+)$1	240	124	145	21.1440
GCGGCUACGACUACUCGCCCU	chr5:177637049-177637289(+)$1	240	167	188	21.5416
AUGGAUACAAUUUAAUCAUCC	chr14:50247343-50247583(+)$1	240	111	132	21.0204
ACUAUAUUUUUUCUCCUUAGG	chr7:22999896-23000136(-)$1	240	82	103	21.7474
GGAUUCUAUAUCUCUUAAUUC	chr1:150902373-150902613(+)$1	240	6	27	20.5698
UGCAUCUCAUUACUCAUAAGC	chr16:3486350-3486590(-)$1	240	120	141	20.6502
UACCGAUUCUGAAACUUAGGU	chr5:79974740-79974980(+)$1	240	199	220	21.4389
UAAUACUCCAUCUGCCACCUU	chr17:60042591-60042831(-)$1	240	117	138	20.5386
UUAGCACCAUAAAUGUUUGUU	chr1:94955392-94955632(+)$1	240	160	181	21.0204
UGCACUAUCAGAUCCUGUGUU	chr6:33288182-33288422(-)$1	240	64	85	21.0170
AAAACUUAUCUUCACCCAGUU	chr21:44323233-44323473(+)$1	240	121	142	21.7807
UUGCCGUGACCUUUAUUUGGC	chr14:45414558-45414798(-)$1	240	110	131	21.4103
GGAAAGAUUACGACACCCUUU	chr7:97939764-97940004(-)$1	240	104	125	21.0204

#DB
(.((((...........))))	chr20:39833212-39833452(-)$1	1	95	116	21.6952
..((((...........))))	chr13:39616227-39616467(+)$1	1	115	136	21.6425
((((..............)))	chr12:39701309-39701549(-)$1	1	133	154	21.1849
(((((.............)))	chr8:53568944-53569184(-)$1	1	26	47	22.1715
.(((((...........))))	chr21:34958272-34958512(-)$1	1	91	112	21.7291
.(((((...........))))	chr2:32626263-32626503(+)$1	1	114	135	21.7243
(((................))	chr1:197072786-197073026(-)$1	1	103	124	20.6502
...((..............))	chr11:111753787-111754027(+)$1	1	103	124	19.0199
(((((............))))	chr1:64095513-64095753(+)$1	1	120	141	22.4905
(((((.............)))	chr5:59893537-59893777(-)$1	1	213	234	22.1715
.((((............))))	chr1:212241857-212242097(+)$1	1	110	131	21.6672
(((((.............)))	chr1:91403203-91403483(-)$1	1	239	260	21.7021
(.((.............)).)	chr2:48602000-48602240(+)$1	1	111	132	21.8067
(((((............)).)	chr9:79952127-79952367(+)$1	1	215	236	22.0991
((((.............))))	chr7:44620674-44620914(-)$1	1	54	75	22.3080
..((((...........))))	chr1:115269503-115269743(-)$1	1	213	234	21.8470
((((.............))))	chr1:32374418-32374658(-)$1	1	83	104	22.3632
..((.............))..	chr12:22208302-22208542(+)$1	1	107	128	21.3111
.(((((...........))))	chr3:9512111-9512351(+)$1	1	10	31	20.7749
(((.((...........)).)	chr2:69658954-69659194(-)$1	1	67	88	21.1502
(((((............))))	chr10:75234621-75234861(-)$1	1	2	23	22.4905
(((((............))..	chr3:9495340-9495580(+)$1	1	150	171	21.3577
(((..............))).	chr3:69105067-69105307(-)$1	1	92	113	20.6968
((((((...........))))	chr10:27470354-27470594(+)$1	1	184	205	21.4103
.((((............))))	chr16:31102419-31102659(-)$1	1	90	111	21.6672
(((((............))))	chr5:95226841-95227081(-)$1	1	125	146	22.4401
.(((.............)))(	chr11:66393971-66394211(+)$1	1	85	106	21.6790
(.(((.............)))	chr2:178095543-178095783(-)$1	1	83	104	22.5077
(((................))	chrX:106890768-106891008(+)$1	1	38	59	20.5698
(((................))	chr12:133256471-133256711(-)$1	1	18	39	20.2667
((((((...........))))	chr2:145161442-145161682(-)$1	1	95	116	21.0204
(((((.............)))	chr10:103871146-103871386(-)$1	1	73	94	22.2987
.((((............))))	chr2:160599585-160599825(+)$1	1	175	196	22.6166
((((.............))))	chr9:106862299-106862539(+)$1	1	166	187	22.3080
(((((............))))	chr5:71494306-71494546(+)$1	1	53	74	22.4905
((((((...........))))	chr12:101017702-101017942(+)$1	1	96	117	21.3472
((((.............))))	chr1:231509630-231509870(-)$1	1	164	185	22.3632
(((((..............))	chr12:57663076-57663316(-)$1	1	86	107	20.3949
((((.............))))	chr3:42635878-42636118(+)$1	1	70	91	22.3080
..((((...........))))	chr3:88104889-88105129(-)$1	1	15	36	21.8470
((((..............)))	chr11:67021640-67021920(+)$1	1	179	200	21.1849
(((((............))))	chr2:74386128-74386368(-)$1	1	102	123	20.5698
(((((............))))	chr18:21114378-21114618(-)$1	1	116	137	21.9076
(((((............))))	chr10:12279044-12279284(+)$1	1	72	93	21.9076
(((((..............))	chr1:12049188-12049428(+)$1	1	142	163	20.3949
(((((.............)))	chr1:91989879-91990119(+)$1	1	145	166	22.3591
(((................))	chr7:64168184-64168424(+)$1	1	23	44	20.6502
.(((.............)))(	chr13:107164962-107165202(-)$1	1	17	38	21.7474
((.((............))))	chr17:6917618-6917858(+)$1	1	108	129	22.0654
(((((............))))	chr15:66811244-66811484(+)$1	1	44	65	22.4905
(.((.............)).)	chr13:77570006-77570246(+)$1	1	176	197	21.6809
..(((............))).	chr12:56385829-56386069(+)$1	1	204	225	19.8250
((((..............)))	chr10:94393296-94393536(+)$1	1	138	159	21.1849
..(((...........)))..	chr2:11922293-11922533(+)$1	1	124	145	21.1440
(.(((...........)))))	chr5:177637049-177637289(+)$1	1	167	188	21.5416
((((((...........))))	chr14:50247343-50247583(+)$1	1	111	132	21.0204
.(((.............)))(	chr7:22999896-23000136(-)$1	1	82	103	21.7474
(((................))	chr1:150902373-150902613(+)$1	1	6	27	20.5698
(((................))	chr16:3486350-3486590(-)$1	1	120	141	20.6502
.(((..............)))	chr5:79974740-79974980(+)$1	1	199	220	21.4389
(((................))	chr17:60042591-60042831(-)$1	1	117	138	20.5386
((((((...........))))	chr1:94955392-94955632(+)$1	1	160	181	21.0204
.((((...........)))).	chr6:33288182-33288422(-)$1	1	64	85	21.0170
(.((((...........))))	chr21:44323233-44323473(+)$1	1	121	142	21.7807
((((((...........))))	chr14:45414558-45414798(-)$1	1	110	131	21.4103
((((((...........))))	chr7:97939764-97940004(-)$1	1	104	125	21.0204

#PSSM
e : 0.16	f : 0.16	d : 0.13	: : 0.10	c : 0.09	i : 0.06	! : 0.06	[ : 0.06	g : 0.06	" : 0.01	$ : 0.01	h : 0.01	= : 0.01	a : 0.01	# : 0.01	
e : 0.21	d : 0.18	f : 0.16	c : 0.12	[ : 0.09	i : 0.06	! : 0.04	g : 0.03	" : 0.01	$ : 0.01	h : 0.01	= : 0.01	: : 0.01	# : 0.01	
d : 0.25	e : 0.19	c : 0.19	f : 0.15	i : 0.06	b : 0.04	g : 0.03	$ : 0.01	h : 0.01	= : 0.01	[ : 0.01	
d : 0.24	e : 0.13	f : 0.13	c : 0.13	y : 0.10	b : 0.10	i : 0.06	[ : 0.01	w : 0.01	g : 0.01	h : 0.01	= : 0.01	
v : 0.16	d : 0.15	f : 0.13	e : 0.10	y : 0.10	w : 0.07	b : 0.07	c : 0.07	i : 0.06	g : 0.01	h : 0.01	= : 0.01	
v : 0.25	u : 0.22	w : 0.12	y : 0.10	d : 0.07	f : 0.06	e : 0.04	t : 0.04	i : 0.03	b : 0.01	g : 0.01	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
t : 0.28	v : 0.25	u : 0.22	w : 0.12	y : 0.10	
v : 0.25	t : 0.24	u : 0.22	w : 0.12	y : 0.10	c : 0.03	d : 0.01	
d : 0.19	e : 0.13	w : 0.10	y : 0.10	b : 0.10	c : 0.10	v : 0.09	f : 0.09	i : 0.03	g : 0.01	h : 0.01	
d : 0.24	c : 0.15	e : 0.13	y : 0.10	f : 0.10	b : 0.10	i : 0.06	w : 0.04	g : 0.01	h : 0.01	= : 0.01	
d : 0.24	e : 0.19	f : 0.15	c : 0.15	i : 0.06	] : 0.06	g : 0.04	2 : 0.03	b : 0.01	h : 0.01	= : 0.01	4 : 0.01	
e : 0.24	d : 0.22	f : 0.15	c : 0.10	i : 0.06	g : 0.06	2 : 0.03	b : 0.01	> : 0.01	h : 0.01	= : 0.01	a : 0.01	: : 0.01	4 : 0.01	] : 0.01	

#score	1418.4602801514397
#seq	66
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m3_run2.txt

#BEAR
]cccdddd[cccooooooccc]dddd::	chr1:224380274-224380514(+)$1	240	143	171	11.3873
[a[bb!!eeeeeooooooeeeee22bb]	chrX:107327569-107327809(-)$1	240	124	152	12.6670
++eeeee"""bboooooobb333eeeee	chr1:145442009-145442289(+)$1	280	75	103	11.0114
hhhhhhh!!cccooooooccc4444hhh	chr11:19245515-19245755(-)$1	240	28	56	13.0858
ccc"""ccccccooooooccc22ccc33	chr20:48521579-48521819(-)$1	240	23	51	14.9754
fff"""bb[ddddoooooodddd]bb]f	chr5:89813692-89813932(-)$1	240	157	185	11.4366
:cccdddd[cccoooooocccdddd]cc	chr17:26881220-26881460(-)$1	240	174	202	12.3085
=======!!ddddmmmmdddd]======	chr19:2478024-2478264(+)$1	240	163	191	10.1982
cccca[a"""cccnnnnnccc333a]a2	chr7:138982528-138982808(+)$1	280	71	99	10.6783
!eeeeeccccccooooooccc]ccc22e	chr5:137847093-137847333(-)$1	240	79	107	13.5585
[iiiiiiiiirrrrrrrrriiiiiiiii	chr6:16299546-16299826(-)$1	280	223	251	9.5161
"""bb"""bb[bboooooobb]bb4444	chr22:18272467-18272707(-)$1	240	73	101	11.4740
::==========oooooo==========	chr15:29992671-29992911(-)$1	240	88	116	13.1335
f"""eeeee!!aooooooa22eeeeeff	chr16:14042825-14043070(+)$1	245	168	196	11.4888
========[cccooooooccc22=====	chr15:65899510-65899750(-)$1	240	165	193	15.7165
:eeeee!!ddddoooooodddd333eee	chr1:93308404-93308644(-)$1	240	125	153	12.6021
###iiiiiiiiiooooooiiiiiiiii3	chr5:36194716-36194956(-)$1	240	149	177	14.2183
gggggg"""ddddlllddddggggggg]	chr19:57869251-57869491(+)$1	240	38	66	9.2626
a[ccc!!ccc[aooooooaccccccagg	chr19:12841617-12841857(-)$1	240	45	73	13.9984
bb[ccc[a[cccooooooccc]acccbb	chr1:192998452-192998774(-)$1	322	21	49	14.1394
d!!bb"""cccrrrrrrrrrccc333bb	chr5:36687910-36688150(+)$1	240	97	125	9.8655
gg####ffffffooooooffffff4444	chr1:92146022-92146262(-)$1	240	25	53	12.7270
h!!eeeee!!bboooooobb]eeeee22	chr8:144734410-144734650(+)$1	240	69	97	11.5458
eeedddd[ddddoooooodddddddd]e	chr3:23933796-23934036(-)$1	240	2	30	11.9529
####dddd!!bboooooobb22dddd22	chr6:17616078-17616358(-)$1	280	205	233	11.5563
dddd$$$$$cccooooooccc22dddd]	chr12:110928039-110928279(+)$1	240	201	229	13.1865
!!dddd[eeeeeooooooeeeee]dddd	chr3:172115515-172115755(+)$1	240	144	172	12.0698
eee[ccc!!cccooooooccc]ccc22e	chr3:194998938-194999178(-)$1	240	55	83	14.3830
dd[cccbb[cccooooooccc]bb4444	chrX:123043294-123043534(+)$1	240	123	151	13.8537
fffff"""ddddoooooodddd333fff	chr4:20729604-20729844(+)$1	240	184	212	13.5844
==============mmmm==========	chr7:129125832-129126072(+)$1	240	10	38	10.2798
cccbb[ffffffooooooffffffbb]c	chr5:72206031-72206271(+)$1	240	133	161	11.3362
[bb####eeeeeooooooeeeee333bb	chr5:60048198-60048438(-)$1	240	107	135	13.1943
ddd!!ccc[cccooooooccc]ccc22d	chr4:177249907-177250147(+)$1	240	203	231	14.1196
iiiiii[eeeeeooooooeeeee]iiii	chr1:94353796-94354049(-)$1	253	36	64	13.5026
[ccc"""eeeeeooooooeeeee333cc	chr20:61509376-61509616(-)$1	240	83	111	14.0098
====!!ffffffooooooffffff====	chr3:176739003-176739243(-)$1	240	106	134	12.9735
d[ffffffddddoooooodddd22ffff	chr1:212989814-212990054(+)$1	240	171	199	11.5773
bb[bb"""ddddoooooodddd333bbb	chr17:40353521-40353761(-)$1	240	133	161	13.6276
eeebb[ccccccooooooccc]cccbb]	chr6:108364282-108364522(-)$1	240	60	88	13.5997
bb####bb[cccooooooccc]bb333b	chr5:158584438-158584678(-)$1	240	34	62	14.1930
$$bb####dddd[aooooooa]dddd44	chr1:51736990-51737230(+)$1	240	166	194	11.0225
cc[a$$$$$cccooooooccca]ccccc	chr16:87733517-87733757(-)$1	240	87	115	14.0781
iiiiiii!!ddddmmmmdddd4444iii	chr3:140698004-140698244(+)$1	240	153	181	9.7129
ggggg[a!!cccooooooccc]a]gggg	chr14:24607594-24607834(+)$1	240	105	133	15.1938
ddd!!bb!!cccooooooccc22bbddd	chr22:38617224-38617464(-)$1	240	109	137	13.2069
f[dddd[bbcccooooooccc22bb]dd	chr6:57034768-57035008(+)$1	240	138	166	12.5148
gggggg[eeeeeooooooeeeeeggggg	chr5:130727880-130728120(+)$1	240	92	120	12.8308
eeeee"""ddddooooooddddeeeee]	chr14:31088639-31088879(+)$1	240	44	72	13.1231
ddd[ccc[ddddooooooddddcccddd	chr12:110781087-110781328(+)$1	241	19	47	12.6135
gggiiiiiiiiiooooooiiiiiiiii:	chr2:128014816-128015096(-)$1	280	246	274	13.0781
E::iiiiiiiiiooooooiiiiiiiiic	chr12:16189839-16190079(+)$1	240	13	41	11.0630

#otherMatches

#Seq PSSM
ACUCAUGUCUGUCAUUUUAUAAGCAUAU	chr1:224380274-224380514(+)$1	240	143	171	11.3873
UGGACCACAUUUUAAGUUGGAUGGUGUG	chrX:107327569-107327809(-)$1	240	124	152	12.6670
UGUGUCUCUAGGGUUAAGCCAAAAGACA	chr1:145442009-145442289(+)$1	280	75	103	11.0114
GUUGCAGUGUAUCUUUUUGUAAAGUUUG	chr11:19245515-19245755(-)$1	240	28	56	13.0858
CCCCUCCCAUUGCAAAGCCAACUUGGAC	chr20:48521579-48521819(-)$1	240	23	51	14.9754
UAACAUGCCUUAAUUACAUUUAAUGCCU	chr5:89813692-89813932(-)$1	240	157	185	11.4366
CUUCCUGGAGACCCGCAAGUCCUGGAGA	chr17:26881220-26881460(-)$1	240	174	202	12.3085
AUGGGAAGCAUAGAUAUCUAUAUUUUUA	chr19:2478024-2478264(+)$1	240	163	191	10.1982
GAGACGAAAUGUUUAGUUGACUGAUGGA	chr7:138982528-138982808(+)$1	280	71	99	10.6783
UAUGGUGGUGAAAAUGGAUUCAACCAAG	chr5:137847093-137847333(-)$1	240	79	107	13.5585
AAAAAUGGAAGAAUUCAUAUUCUAUUUU	chr6:16299546-16299826(-)$1	280	223	251	9.5161
CCUGGCAAGACGCUCAGCCGCUUCAAAC	chr22:18272467-18272707(-)$1	240	73	101	11.4740
UUGGUUUGUAAAUUAACUUUUAUAAACU	chr15:29992671-29992911(-)$1	240	88	116	13.1335
UAAAGCAAAAUGAAUUACCUGUUUGCAA	chr16:14042825-14043070(+)$1	245	168	196	11.4888
AUUACAAGCUUGAAUUUACAGCACUUGU	chr15:65899510-65899750(-)$1	240	165	193	15.7165
UUUGCACAUUAACAGAAAUUAAGACUGC	chr1:93308404-93308644(-)$1	240	125	153	12.6021
GAAAAAAUUUUCAAGACAGAGAAUUUUG	chr5:36194716-36194956(-)$1	240	149	177	14.2183
CUCACACCAGAGCAAUGCUCUGUGAGUA	chr19:57869251-57869491(+)$1	240	38	66	9.2626
GCGGUGACGAUGAUAAAACUCGGCCCCU	chr19:12841617-12841857(-)$1	240	45	73	13.9984
UGAGUGUGUUACUGAACUGUACCCACCA	chr1:192998452-192998774(-)$1	322	21	49	14.1394
CUGAAAAUGGUGAAGAAUGGACUUAAUU	chr5:36687910-36688150(+)$1	240	97	125	9.8655
AGUCCUAUGUGAUUUUUUUCAUGUUUGU	chr1:92146022-92146262(-)$1	240	25	53	12.7270
gaucauaucugauugauuuccauguguc	chr8:144734410-144734650(+)$1	240	69	97	11.5458
CUUUGCUCAAAUUAGAAUGUUUAGCAUG	chr3:23933796-23934036(-)$1	240	2	30	11.9529
CUUUUUUAAAUAAAUAAAUAGCUAGACU	chr6:17616078-17616358(-)$1	280	205	233	11.5563
CUGUGUUCAUAGUAAGUCCUAAAACAGC	chr12:110928039-110928279(+)$1	240	201	229	13.1865
UCUGUAAACAUGAAUCACCGUGUGUGUA	chr3:172115515-172115755(+)$1	240	144	172	12.0698
CCUAGUGAAAGAAAAAUCUCUGUACAAA	chr3:194998938-194999178(-)$1	240	55	83	14.3830
UCAGGUAGGUAGUUCAAUCUAGUUGUUA	chrX:123043294-123043534(+)$1	240	123	151	13.8537
GUUUAAAAAAUUUUUUCUAAUUCUGUAA	chr4:20729604-20729844(+)$1	240	184	212	13.5844
CUGGGGUCAGUUGGGUGCCCAGUUGGCC	chr7:129125832-129126072(+)$1	240	10	38	10.2798
UUCCAUGUGUAUUUUCUUAUAUACUGUG	chr5:72206031-72206271(+)$1	240	133	161	11.3362
GCUGUUAGAAAUCACACCAUUUCCAAAG	chr5:60048198-60048438(-)$1	240	107	135	13.1943
AAAUUAUUCUAAUUCAUUUUAAAAUCUU	chr4:177249907-177250147(+)$1	240	203	231	14.1196
CAUGAAUGGAAACUUAAAUUUUUUUUUA	chr1:94353796-94354049(-)$1	253	36	64	13.5026
AUAAUUUUUUAUAUUUUCAUAAACUUUU	chr20:61509376-61509616(-)$1	240	83	111	14.0098
UCUUUGGAAUUUCCGGAUAAGUUCAGGA	chr3:176739003-176739243(-)$1	240	106	134	12.9735
CAAUAAAUAUUUUGAAAUGAAUUCAUUU	chr1:212989814-212990054(+)$1	240	171	199	11.5773
UGACCUUAGUGUUUCUGUGCAUGGUGGC	chr17:40353521-40353761(-)$1	240	133	161	13.6276
UAGCACUGUCUUGAUUUGAAGCAUAUGA	chr6:108364282-108364522(-)$1	240	60	88	13.5997
UCAUGGCUACAGGUAGAACUGGGGAGGG	chr5:158584438-158584678(-)$1	240	34	62	14.1930
UUUAGAAACUUAGUGGGAAAAGUAGGAU	chr1:51736990-51737230(+)$1	240	166	194	11.0225
CCAGCAGCUUGGGGACCACCACAGGCCU	chr16:87733517-87733757(-)$1	240	87	115	14.0781
UUAAAUCACUAAAAAUAUUUAUUCGGAU	chr3:140698004-140698244(+)$1	240	153	181	9.7129
GGUGCACGAGCUGGAUGAGGCAGAGUAC	chr14:24607594-24607834(+)$1	240	105	133	15.1938
GGACCAGAAACACUCACAUGUCACUUCC	chr22:38617224-38617464(-)$1	240	109	137	13.2069
AGAAAAGGUAACUGGGUUGUUUAAUGUU	chr6:57034768-57035008(+)$1	240	138	166	12.5148
CAAGCACAAUGAUCAUUUUUAUUUGUUU	chr5:130727880-130728120(+)$1	240	92	120	12.8308
UAAAAUAAGCUAUUAAACUAGUUUUUAU	chr14:31088639-31088879(+)$1	240	44	72	13.1231
GUGACAGAUGGCCUGCCUGCCACUGCAC	chr12:110781087-110781328(+)$1	241	19	47	12.6135
GUUUUUAUGCUUCGUCCUGGGCAUGGGU	chr2:128014816-128015096(-)$1	280	246	274	13.0781
UACUCAUUUCAGGCACAUCUGAAAUGAU	chr12:16189839-16190079(+)$1	240	13	41	11.0630

#DB
.)))((((.(((......))).))))..	chr1:224380274-224380514(+)$1	1	143	171	11.3873
.(.((..(((((......)))))..)).	chrX:107327569-107327809(-)$1	1	124	152	12.6670
..(((((...((......))...)))))	chr1:145442009-145442289(+)$1	1	75	103	11.0114
(((((((..(((......)))....)))	chr11:19245515-19245755(-)$1	1	28	56	13.0858
(((...((((((......)))..)))..	chr20:48521579-48521819(-)$1	1	23	51	14.9754
(((...((.((((......)))).)).)	chr5:89813692-89813932(-)$1	1	157	185	11.4366
.(((((((.(((......))))))).))	chr17:26881220-26881460(-)$1	1	174	202	12.3085
(((((((..((((....)))).))))))	chr19:2478024-2478264(+)$1	1	163	191	10.1982
(((((.(...(((.....)))...).).	chr7:138982528-138982808(+)$1	1	71	99	10.6783
.(((((((((((......))).)))..)	chr5:137847093-137847333(-)$1	1	79	107	13.5585
.(((((((((.........)))))))))	chr6:16299546-16299826(-)$1	1	223	251	9.5161
...((...((.((......)).))....	chr22:18272467-18272707(-)$1	1	73	101	11.4740
..((((((((((......))))))))))	chr15:29992671-29992911(-)$1	1	88	116	13.1335
(...(((((..(......)..)))))))	chr16:14042825-14043070(+)$1	1	168	196	11.4888
((((((((.(((......)))..)))))	chr15:65899510-65899750(-)$1	1	165	193	15.7165
.(((((..((((......))))...)))	chr1:93308404-93308644(-)$1	1	125	153	12.6021
...(((((((((......))))))))).	chr5:36194716-36194956(-)$1	1	149	177	14.2183
((((((...((((...))))))))))).	chr19:57869251-57869491(+)$1	1	38	66	9.2626
(.(((..(((.(......))))))))))	chr19:12841617-12841857(-)$1	1	45	73	13.9984
((.(((.(.(((......))).))))))	chr1:192998452-192998774(-)$1	1	21	49	14.1394
(..((...(((.........)))...))	chr5:36687910-36688150(+)$1	1	97	125	9.8655
((....((((((......))))))....	chr1:92146022-92146262(-)$1	1	25	53	12.7270
(..(((((..((......)).)))))..	chr8:144734410-144734650(+)$1	1	69	97	11.5458
(((((((.((((......)))))))).)	chr3:23933796-23934036(-)$1	1	2	30	11.9529
....((((..((......))..))))..	chr6:17616078-17616358(-)$1	1	205	233	11.5563
((((.....(((......)))..)))).	chr12:110928039-110928279(+)$1	1	201	229	13.1865
..((((.(((((......))))).))))	chr3:172115515-172115755(+)$1	1	144	172	12.0698
(((.(((..(((......))).)))..)	chr3:194998938-194999178(-)$1	1	55	83	14.3830
((.(((((.(((......))).))....	chrX:123043294-123043534(+)$1	1	123	151	13.8537
(((((...((((......))))...)))	chr4:20729604-20729844(+)$1	1	184	212	13.5844
((((((((((((((....))))))))))	chr7:129125832-129126072(+)$1	1	10	38	10.2798
(((((.((((((......)))))))).)	chr5:72206031-72206271(+)$1	1	133	161	11.3362
.((....(((((......)))))...))	chr5:60048198-60048438(-)$1	1	107	135	13.1943
(((..(((.(((......))).)))..)	chr4:177249907-177250147(+)$1	1	203	231	14.1196
((((((.(((((......))))).))))	chr1:94353796-94354049(-)$1	1	36	64	13.5026
.(((...(((((......)))))...))	chr20:61509376-61509616(-)$1	1	83	111	14.0098
((((..((((((......))))))))))	chr3:176739003-176739243(-)$1	1	106	134	12.9735
(.((((((((((......))))..))))	chr1:212989814-212990054(+)$1	1	171	199	11.5773
((.((...((((......))))...)))	chr17:40353521-40353761(-)$1	1	133	161	13.6276
(((((.((((((......))).))))).	chr6:108364282-108364522(-)$1	1	60	88	13.5997
((....((.(((......))).))...)	chr5:158584438-158584678(-)$1	1	34	62	14.1930
..((....((((.(......).))))..	chr1:51736990-51737230(+)$1	1	166	194	11.0225
((.(.....(((......)))).)))))	chr16:87733517-87733757(-)$1	1	87	115	14.0781
(((((((..((((....))))....)))	chr3:140698004-140698244(+)$1	1	153	181	9.7129
(((((.(..(((......))).).))))	chr14:24607594-24607834(+)$1	1	105	133	15.1938
(((..((..(((......)))..)))))	chr22:38617224-38617464(-)$1	1	109	137	13.2069
(.((((.(((((......)))..)).))	chr6:57034768-57035008(+)$1	1	138	166	12.5148
((((((.(((((......))))))))))	chr5:130727880-130728120(+)$1	1	92	120	12.8308
(((((...((((......))))))))).	chr14:31088639-31088879(+)$1	1	44	72	13.1231
(((.(((.((((......))))))))))	chr12:110781087-110781328(+)$1	1	19	47	12.6135
)))(((((((((......))))))))).	chr2:128014816-128015096(-)$1	1	246	274	13.0781
(..(((((((((......)))))))))(	chr12:16189839-16190079(+)$1	1	13	41	11.0630

#PSSM
d : 0.13	g : 0.09	[ : 0.07	c : 0.07	f : 0.07	= : 0.07	e : 0.07	: : 0.05	b : 0.05	h : 0.03	! : 0.03	# : 0.03	i : 0.03	] : 0.01	+ : 0.01	" : 0.01	a : 0.01	$ : 0.01	E : 0.01	
c : 0.13	e : 0.11	g : 0.09	d : 0.09	= : 0.07	b : 0.07	i : 0.05	[ : 0.05	! : 0.05	f : 0.03	" : 0.03	: : 0.03	# : 0.03	a : 0.01	+ : 0.01	h : 0.01	$ : 0.01	
c : 0.13	e : 0.13	d : 0.11	[ : 0.09	= : 0.09	# : 0.07	g : 0.07	f : 0.05	i : 0.05	" : 0.03	! : 0.03	b : 0.03	h : 0.01	: : 0.01	
c : 0.13	b : 0.13	i : 0.11	e : 0.09	= : 0.09	# : 0.07	d : 0.07	" : 0.05	g : 0.05	[ : 0.03	f : 0.03	! : 0.03	h : 0.01	a : 0.01	
d : 0.11	b : 0.11	e : 0.11	i : 0.11	c : 0.09	= : 0.07	# : 0.07	" : 0.05	g : 0.05	! : 0.05	$ : 0.03	f : 0.03	h : 0.01	a : 0.01	
" : 0.15	d : 0.11	i : 0.11	e : 0.09	c : 0.09	= : 0.07	[ : 0.07	# : 0.07	! : 0.05	g : 0.03	$ : 0.03	h : 0.01	f : 0.01	b : 0.01	
" : 0.13	c : 0.11	i : 0.09	[ : 0.09	d : 0.07	b : 0.07	= : 0.07	f : 0.07	! : 0.05	e : 0.05	a : 0.03	$ : 0.03	# : 0.03	h : 0.01	
e : 0.15	" : 0.15	! : 0.13	c : 0.09	b : 0.07	i : 0.07	f : 0.07	d : 0.05	= : 0.05	[ : 0.03	$ : 0.03	a : 0.01	# : 0.01	
[ : 0.15	! : 0.15	d : 0.15	e : 0.13	c : 0.09	i : 0.07	" : 0.05	f : 0.05	b : 0.03	= : 0.03	$ : 0.03	
c : 0.36	d : 0.23	e : 0.11	i : 0.07	! : 0.05	f : 0.05	" : 0.03	= : 0.03	b : 0.01	
c : 0.36	d : 0.23	e : 0.11	b : 0.05	i : 0.05	f : 0.05	[ : 0.03	= : 0.03	r : 0.01	! : 0.01	
c : 0.34	d : 0.23	e : 0.11	b : 0.07	i : 0.05	f : 0.05	r : 0.03	= : 0.03	a : 0.03	
o : 0.80	d : 0.07	r : 0.03	c : 0.01	b : 0.01	= : 0.01	[ : 0.01	
o : 0.84	m : 0.03	r : 0.03	n : 0.01	l : 0.01	= : 0.01	a : 0.01	
o : 0.86	m : 0.05	r : 0.03	n : 0.01	l : 0.01	
o : 0.86	m : 0.05	r : 0.03	n : 0.01	l : 0.01	
o : 0.86	m : 0.05	r : 0.03	n : 0.01	d : 0.01	
o : 0.86	d : 0.05	r : 0.03	n : 0.01	m : 0.01	
c : 0.34	d : 0.19	e : 0.11	b : 0.05	o : 0.05	i : 0.05	f : 0.05	r : 0.03	= : 0.03	a : 0.03	
c : 0.36	d : 0.21	e : 0.11	b : 0.07	i : 0.07	f : 0.05	= : 0.03	2 : 0.01	r : 0.01	o : 0.01	
c : 0.38	d : 0.19	e : 0.11	i : 0.07	f : 0.05	= : 0.03	2 : 0.03	3 : 0.01	b : 0.01	g : 0.01	] : 0.01	a : 0.01	
] : 0.23	d : 0.17	e : 0.15	2 : 0.11	i : 0.07	f : 0.05	3 : 0.03	4 : 0.03	= : 0.03	c : 0.03	g : 0.01	a : 0.01	
e : 0.17	c : 0.13	d : 0.11	2 : 0.11	3 : 0.09	i : 0.07	= : 0.05	b : 0.05	f : 0.05	4 : 0.03	a : 0.03	g : 0.01	] : 0.01	
c : 0.17	3 : 0.13	d : 0.11	b : 0.09	e : 0.07	] : 0.07	= : 0.07	i : 0.07	f : 0.05	2 : 0.03	4 : 0.03	g : 0.03	
c : 0.17	d : 0.13	3 : 0.13	4 : 0.09	= : 0.09	i : 0.09	e : 0.07	b : 0.07	g : 0.05	2 : 0.01	a : 0.01	f : 0.01	
d : 0.15	i : 0.11	b : 0.09	e : 0.09	= : 0.09	3 : 0.07	c : 0.05	] : 0.05	2 : 0.05	4 : 0.05	g : 0.05	f : 0.03	h : 0.01	a : 0.01	
b : 0.11	i : 0.11	= : 0.09	2 : 0.09	d : 0.09	4 : 0.07	g : 0.07	e : 0.05	] : 0.05	c : 0.05	f : 0.05	3 : 0.03	: : 0.01	h : 0.01	a : 0.01	
] : 0.09	e : 0.09	c : 0.09	= : 0.09	b : 0.09	d : 0.09	f : 0.07	4 : 0.07	2 : 0.05	i : 0.05	g : 0.05	: : 0.03	3 : 0.03	h : 0.01	

#score	652.4349691660849
#seq	52
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m2_run1.txt

#BEAR
g[a[bb!!dddd[aooooooadddd22bb]a]gg	chr17:27187642-27187872(+)$1	230	56	90	14.3088
ebb!!ccc!!a[bboooooobb]a22ccc22bb]	chr17:39988556-39988801(-)$1	245	8	42	14.8574
gggggg####ddddoooooodddd55555ggggg	chr16:50067241-50067474(+)$1	233	191	225	13.2382
(dddd[a[ccc[aooooooa]cccadddd]ffff	chr19:3976312-3976612(-)$1	300	141	175	12.2305
ggggggg!!a[cccoooooocccagggggggccc	chr15:83685904-83686150(-)$1	246	120	154	16.5206
ffff[ccc"""cccooooooccc333ccc22fff	chr6:42629845-42630075(+)$1	230	187	221	15.9673
)))ccc!!ccc[bboooooobb]ccc]ccc4444	chr11:119177457-119177699(+)$1	242	26	60	14.5254
ffffff[eeeeebboooooobb]eeeee22ffff	chr7:6144402-6144629(-)$1	227	33	67	13.1553
=======$$$$$cccnnnnnccc===========	chr19:810920-811156(+)$1	236	16	50	13.0871
eeeee"""a[ddddoooooodddd]a333eeeee	chr10:79767398-79767631(-)$1	233	139	173	15.3373
ddddeeeee[ddddoooooodddd]eeeeeeeee	chr17:74001634-74001858(+)$1	224	155	189	13.3689
ggggggg[a"""bboooooobb333a]ggggggg	chr2:39963986-39964210(+)$1	224	44	78	17.7943
gggggg####ddddoooooodddd4444gggggg	chr19:42460898-42461143(-)$1	245	66	100	17.0814
"""ccc!!a[ddddoooooodddd]a22ccc22d	chr11:66203224-66203452(-)$1	228	49	83	14.8469
cc[bbeeeeeddddoooooodddd22eeeee>>>	chr10:72184349-72184574(+)$1	225	148	182	13.2036
a[eeeeeddddcccooooooccc4444dddd]ee	chr20:60963417-60963650(+)$1	233	20	54	14.6842
========="""ddddmmmmdddd==========	chr15:77346481-77346718(-)$1	237	27	61	12.6946
gggggggdddd[bboooooobbdddd4444gggg	chrX:152000085-152000312(-)$1	227	99	133	15.6989
fff[eeeee!!cccooooooccc22eeeeeffff	chr16:30094716-30094965(+)$1	249	83	117	14.7149
ccc!!bb!!eeeeeooooooeeeee22bb]cccb	chr9:35100530-35100768(-)$1	238	60	94	12.7222
gggg[dddd!!cccooooooccc4444dddd444	chr12:12982291-12982526(+)$1	235	183	217	15.9439
ggggg"""bb[cccoooooocccbbggggggg33	chr20:55093108-55093338(+)$1	230	108	142	15.5308
cc"""bb[ccc!!ccclllccc]cccbb22ccc]	chr5:122950508-122950758(+)$1	250	142	176	11.1291
$$eeeee"""a[cccmmmmccc]a333eeeeehh	chr19:42932894-42933118(+)$1	224	14	48	11.7377
ggggggg[ffffffooooooffffff]ggggggg	chr1:228135496-228135723(-)$1	227	21	55	14.1675
c!!iiiiiiiii[ccclllccc]iiiiiiiiicc	chr22:29951700-29951938(-)$1	238	62	96	12.4150
ggggggddddddddoooooodddd]dddd>>>>>	chr9:134357069-134357303(+)$1	234	29	63	13.2299
iiiiiiiii[bbbboooooobb]bb]iiiiiiii	chr6:27778117-27778399(+)$1	282	179	213	15.5461
===========[bboooooobb]===========	chr8:81398497-81398724(+)$1	227	172	206	17.5826
eeccc$$$$$ddddooooooddddccc22eeeee	chr1:33145219-33145446(+)$1	227	132	166	13.4865
cc!!abb[ccc[bboooooobbccc]bb]a22cc	chr3:49135740-49136008(-)$1	268	125	159	14.6399
eee[eeeee[ddddoooooodddd22eeeee]ee	chr3:27490096-27490347(-)$1	251	37	71	14.2208
cc[bb[cccccc[ccclllccc]ccc4444ccc]	chr8:145514859-145515105(-)$1	246	33	67	11.5883
hhhhh"""ccc[bboooooobb]ccchhhhhhhh	chr16:31200393-31200635(+)$1	242	197	231	14.1315
iiiiiiii####cccmmmmccc22iiiiiiiii]	chr3:79067845-79068072(-)$1	227	141	175	12.6093
gggggggccc!!a[aooooooa]a333ccc]ggg	chr16:2827055-2827280(-)$1	225	0	34	16.1886
[a[ccc[ccc!!cccnnnnnccc333cccccc]a	chr16:68298383-68298612(+)$1	229	83	117	12.7406
d[eeeee[ccc[bboooooobb]ccc]eeeee44	chr12:117155317-117155545(-)$1	228	31	65	15.4789
c[ffffff"""cccooooooccc22ffffffccc	chr1:155225933-155226164(-)$1	231	66	100	14.6380
bb"""eeeee!!bboooooobb22eeeee333bb	chr3:184044993-184045232(+)$1	239	130	164	13.7651
ggggggccc[ddddooooooddddccc]gggggg	chr12:109181492-109181722(-)$1	230	81	115	15.8392
[adddd####ddddoooooodddd4444dddd]a	chr17:78120649-78120880(-)$1	231	57	91	14.9754
gggggggccc"""ccclllccc333ccc]ggggg	chr12:56110284-56110515(+)$1	231	173	207	13.2346
ffaeeeee[a[cccooooooccc]a]eeeee666	chr16:48304034-48304300(+)$1	266	34	68	13.6687
iiiii[cccbbcccooooooccc]bb333ccc]i	chr17:42397465-42397696(-)$1	231	91	125	15.3558
iiiiiii[ccc!!aooooooa22ccc]iiiiiii	chrX:153664116-153664352(+)$1	236	145	179	16.3164
ddd!!ffffff[bboooooobbffffff]dddd:	chr17:47131444-47131699(+)$1	255	101	135	11.6082
================mmmm==============	chr12:123253787-123254034(+)$1	247	27	61	12.7976
gg"""dddd"""cccmmmmccc]dddd4444ggg	chr15:77057676-77057908(-)$1	232	100	134	11.3547
ggggggg[ccc[bboooooobb]ccc]ggggggg	chr3:105253429-105253659(+)$1	230	36	70	17.0065

#otherMatches

#Seq PSSM
GCCUGGCCCUGUUGAGUCUGCACAGUCCCUGCCC	chr17:27187642-27187872(+)$1	230	56	90	14.3088
UAGGACGUUGCUGGGAAGAACUUGAUAUGGACUA	chr17:39988556-39988801(-)$1	245	8	42	14.8574
GAUUAAAUUCCAUUCUCUGAAGUGCUUUGUUGAU	chr16:50067241-50067474(+)$1	233	191	225	13.2382
UGGAGACUGUCCCGACACAGCGACGCUCCCCUGA	chr19:3976312-3976612(-)$1	300	141	175	12.2305
GGUGAUGACGACUGGGUGAACAGCCAUCACUUCA	chr15:83685904-83686150(-)$1	246	120	154	16.5206
UAUUUGUCAAGAGAAGUUUAUCUAAGGGCUCAAU	chr6:42629845-42630075(+)$1	230	187	221	15.9673
AGUGUCUUGGCCUUGAAAGAAAAGCCUGACUUCC	chr11:119177457-119177699(+)$1	242	26	60	14.5254
GCCCGGCGGGGGACAAUGACGUGCCUCCAUCCGG	chr7:6144402-6144629(-)$1	227	33	67	13.1553
UUAAAGAGAAAUCAGUUUACCUGUUUUUAAAAAA	chr19:810920-811156(+)$1	236	16	50	13.0871
CACGGCUCGCCAGGCUGGCUCCUGUCUACCUGUG	chr10:79767398-79767631(-)$1	233	139	173	15.3373
AGCUGGGUGUGGGUAUUCAGGCCCUCACCUGCCC	chr17:74001634-74001858(+)$1	224	155	189	13.3689
CUUGAAUGCACCAGUUUUUUCUUCAGGAUUCAAG	chr2:39963986-39964210(+)$1	224	44	78	17.7943
UGGUGGUCAUCGGCUCCCACGCUGCCUUCCACCA	chr19:42460898-42461143(-)$1	245	66	100	17.0814
CACCAAUAUGAUGAUGGUUUUCAUGACUUUGAAU	chr11:66203224-66203452(-)$1	228	49	83	14.8469
CAACAGCAGACAUGCAUUGUCAUGAUUCUGUCUU	chr10:72184349-72184574(+)$1	225	148	182	13.2036
CAUUUGGGCAGAGUGAGUGGACUAGGACUGCUCC	chr20:60963417-60963650(+)$1	233	20	54	14.6842
UAGUAGGAGCCUUGACUAAUGUUACUUUUACUAG	chr15:77346481-77346718(-)$1	237	27	61	12.6946
GAUGAGGGCGUCUCGGCCUGGAAUGCUCCUCCUU	chrX:152000085-152000312(-)$1	227	99	133	15.6989
GCCUGCGCAAGUACGGCUCGGUGACUGUGUGGCG	chr16:30094716-30094965(+)$1	249	83	117	14.7149
GCUUCACUGACUGUGGCCGAGCAGUAUGUCAGCG	chr9:35100530-35100768(-)$1	238	60	94	12.7222
GGAAAGGCCGUUAAUCACUUUUAUGAAGGCUCGA	chr12:12982291-12982526(+)$1	235	183	217	15.9439
GAAGAAUCGGAGGCCUACAAGUCCCUCUUUACCA	chr20:55093108-55093338(+)$1	230	108	142	15.5308
UGAAAUCAUGGUACAGUCACUGCCCAGAGGUACU	chr5:122950508-122950758(+)$1	250	142	176	11.1291
AGCACUGGAAUGAUUUAGGGGUGGGUACAGUGGG	chr19:42932894-42933118(+)$1	224	14	48	11.7377
cggggcggggccgggcccAGCUGGCCGCGCUCCG	chr1:228135496-228135723(-)$1	227	21	55	14.1675
GACAGACAGUGGCACUCCUGGUCCUGCUGUCUUG	chr22:29951700-29951938(-)$1	238	62	96	12.4150
UCCUCCCCUGGCAGCUCUCCCUGUGCAGGCCCCA	chr9:134357069-134357303(+)$1	234	29	63	13.2299
UCUUUUCAGAGCCACCCACAUGCGCGCUGAAAAG	chr6:27778117-27778399(+)$1	282	179	213	15.5461
GGGCAGCGGAGGGUCUCCCCGCACUCCGCUGCUC	chr8:81398497-81398724(+)$1	227	172	206	17.5826
CAACCCUGAGAGUGAUUUAACACUGGUUUUGAGA	chr1:33145219-33145446(+)$1	227	132	166	13.4865
GUGACCUGCAGACGGGCAGAUGCUGGAGAGAAGC	chr3:49135740-49136008(-)$1	268	125	159	14.6399
AUGUUUCUGAACCUUUUAAUAGGUCAUAGAGCUG	chr3:27490096-27490347(-)$1	251	37	71	14.2208
CGGCCGGCGCGCGGUGGGGCAUGGCGGGUUCGCG	chr8:145514859-145515105(-)$1	246	33	67	11.5883
CUUGUGGAUUUCACACAUUAGUAAAAGCAAGUCU	chr16:31200393-31200635(+)$1	242	197	231	14.1315
AGGCAGGAAACGGCACUACUGCGCUUCUGCCUCG	chr3:79067845-79068072(-)$1	227	141	175	12.6093
cggcugcgccggcgcgucgaggggagaggcagca	chr16:2827055-2827280(-)$1	225	0	34	16.1886
GGGCCACUGGGAGGUAACGGGCUGGGCCAUgggc	chr16:68298383-68298612(+)$1	229	83	117	12.7406
GACAAAGGCAGCGUGAGGAAACCUUGGCUUUGAC	chr12:117155317-117155545(-)$1	228	31	65	15.4789
CUGGGGCUGCUGAAAAUGCCUUCCGGGCCCCGUG	chr1:155225933-155226164(-)$1	231	66	100	14.6380
GCGGAGCUUCAGCAAGGAAGUGGAGGAGCGGAGU	chr3:184044993-184045232(+)$1	239	130	164	13.7651
UUUUCCCCUACUCUUGCCAUAGAGAGGAGGAGAA	chr12:109181492-109181722(-)$1	230	81	115	15.8392
aggucggcagcggcagcgaggucggcagcggcgC	chr17:78120649-78120880(-)$1	231	57	91	14.9754
gucaggaguccugggcgcugccgcugacuuccug	chr12:56110284-56110515(+)$1	231	173	207	13.2346
CCCUCCUGGAGUUGGUAAAACAAGUGUGGGAAGA	chr16:48304034-48304300(+)$1	266	34	68	13.6687
GGAGGAUCCGGGCCGAGUCGGGCACCAAGGGACU	chr17:42397465-42397696(-)$1	231	91	125	15.3558
GGUGGGACGGUGUCCGUGUUGUUGCUUUCCCACC	chrX:153664116-153664352(+)$1	236	145	179	16.3164
CGGUCCUGUGCACCGCUUUGGGGCACAGUCUGAU	chr17:47131444-47131699(+)$1	255	101	135	11.6082
auauguauacauauauacacauauauguauacau	chr12:123253787-123254034(+)$1	247	27	61	12.7976
UUUUUCUGAACAGCUCGUGAGUCUUGGCGCCAAA	chr15:77057676-77057908(-)$1	232	100	134	11.3547
AGAUGAAAGACCCUAUCAUCAGUGUUCUUUAUUU	chr3:105253429-105253659(+)$1	230	36	70	17.0065

#DB
(.(.((..((((.(......)))))..)).).))	chr17:27187642-27187872(+)$1	1	56	90	14.3088
(((..(((..(.((......)).)..)))..)).	chr17:39988556-39988801(-)$1	1	8	42	14.8574
((((((....((((......)))).....)))))	chr16:50067241-50067474(+)$1	1	191	225	13.2382
.((((.(.(((.(......).)))))))).))))	chr19:3976312-3976612(-)$1	1	141	175	12.2305
(((((((..(.(((......))))))))))))))	chr15:83685904-83686150(-)$1	1	120	154	16.5206
((((.(((...(((......)))...)))..)))	chr6:42629845-42630075(+)$1	1	187	221	15.9673
...(((..(((.((......)).))).)))....	chr11:119177457-119177699(+)$1	1	26	60	14.5254
((((((.(((((((......)).)))))..))))	chr7:6144402-6144629(-)$1	1	33	67	13.1553
(((((((.....(((.....))))))))))))))	chr19:810920-811156(+)$1	1	16	50	13.0871
(((((...(.((((......)))).)...)))))	chr10:79767398-79767631(-)$1	1	139	173	15.3373
))))(((((.((((......)))).)))))((((	chr17:74001634-74001858(+)$1	1	155	189	13.3689
(((((((.(...((......))...).)))))))	chr2:39963986-39964210(+)$1	1	44	78	17.7943
((((((....((((......))))....))))))	chr19:42460898-42461143(-)$1	1	66	100	17.0814
...(((..(.((((......)))).)..)))..)	chr11:66203224-66203452(-)$1	1	49	83	14.8469
((.(((((((((((......))))..)))))...	chr10:72184349-72184574(+)$1	1	148	182	13.2036
(.((((((((((((......)))....)))).))	chr20:60963417-60963650(+)$1	1	20	54	14.6842
(((((((((...((((....))))))))))))))	chr15:77346481-77346718(-)$1	1	27	61	12.6946
(((((((((((.((......))))))....))))	chrX:152000085-152000312(-)$1	1	99	133	15.6989
(((.(((((..(((......)))..)))))))))	chr16:30094716-30094965(+)$1	1	83	117	14.7149
(((..((..(((((......)))))..)).))))	chr9:35100530-35100768(-)$1	1	60	94	12.7222
((((.((((..(((......)))....))))...	chr12:12982291-12982526(+)$1	1	183	217	15.9439
(((((...((.(((......))))))))))))..	chr20:55093108-55093338(+)$1	1	108	142	15.5308
((...((.(((..(((...))).)))))..))).	chr5:122950508-122950758(+)$1	1	142	176	11.1291
..(((((...(.(((....))).)...)))))))	chr19:42932894-42933118(+)$1	1	14	48	11.7377
(((((((.((((((......)))))).)))))))	chr1:228135496-228135723(-)$1	1	21	55	14.1675
(..(((((((((.(((...))).)))))))))))	chr22:29951700-29951938(-)$1	1	62	96	12.4150
((((((((((((((......)))).)))).....	chr9:134357069-134357303(+)$1	1	29	63	13.2299
(((((((((.((((......)).)).))))))))	chr6:27778117-27778399(+)$1	1	179	213	15.5461
(((((((((((.((......)).)))))))))))	chr8:81398497-81398724(+)$1	1	172	206	17.5826
(((((.....((((......)))))))..)))))	chr1:33145219-33145446(+)$1	1	132	166	13.4865
((..(((.(((.((......))))).)).)..))	chr3:49135740-49136008(-)$1	1	125	159	14.6399
(((.(((((.((((......))))..))))).))	chr3:27490096-27490347(-)$1	1	37	71	14.2208
((.((.((((((.(((...))).)))....))).	chr8:145514859-145515105(-)$1	1	33	67	11.5883
(((((...(((.((......)).)))))))))))	chr16:31200393-31200635(+)$1	1	197	231	14.1315
((((((((....(((....)))..))))))))).	chr3:79067845-79068072(-)$1	1	141	175	12.6093
((((((((((..(.(......).)...))).)))	chr16:2827055-2827280(-)$1	1	0	34	16.1886
.(.(((.(((..(((.....)))...)))))).)	chr16:68298383-68298612(+)$1	1	83	117	12.7406
(.(((((.(((.((......)).))).)))))..	chr12:117155317-117155545(-)$1	1	31	65	15.4789
(.((((((...(((......)))..)))))))))	chr1:155225933-155226164(-)$1	1	66	100	14.6380
((...(((((..((......))..)))))...))	chr3:184044993-184045232(+)$1	1	130	164	13.7651
(((((((((.((((......))))))).))))))	chr12:109181492-109181722(-)$1	1	81	115	15.8392
.(((((....((((......))))....)))).)	chr17:78120649-78120880(-)$1	1	57	91	14.9754
((((((((((...(((...)))...))).)))))	chr12:56110284-56110515(+)$1	1	173	207	13.2346
((((((((.(.(((......))).).)))))...	chr16:48304034-48304300(+)$1	1	34	68	13.6687
(((((.((((((((......))).))...))).)	chr17:42397465-42397696(-)$1	1	91	125	15.3558
(((((((.(((..(......)..))).)))))))	chrX:153664116-153664352(+)$1	1	145	179	16.3164
(((..((((((.((......)))))))).)))).	chr17:47131444-47131699(+)$1	1	101	135	11.6082
((((((((((((((((....))))))))))))))	chr12:123253787-123254034(+)$1	1	27	61	12.7976
((...((((...(((....))).))))....)))	chr15:77057676-77057908(-)$1	1	100	134	11.3547
(((((((.(((.((......)).))).)))))))	chr3:105253429-105253659(+)$1	1	36	70	17.0065

#PSSM
g : 0.30	c : 0.14	e : 0.08	f : 0.08	= : 0.08	i : 0.08	d : 0.06	[ : 0.04	( : 0.02	) : 0.02	" : 0.02	a : 0.02	$ : 0.02	h : 0.02	b : 0.02	
g : 0.27	c : 0.10	[ : 0.08	f : 0.08	= : 0.08	i : 0.08	d : 0.06	e : 0.06	b : 0.04	a : 0.04	) : 0.02	" : 0.02	$ : 0.02	! : 0.02	h : 0.02	
g : 0.25	e : 0.10	d : 0.08	f : 0.08	= : 0.08	" : 0.08	i : 0.08	[ : 0.06	a : 0.04	c : 0.04	! : 0.04	b : 0.02	) : 0.02	h : 0.02	
g : 0.25	e : 0.10	i : 0.10	! : 0.08	c : 0.08	= : 0.08	[ : 0.06	d : 0.06	f : 0.06	" : 0.06	b : 0.04	h : 0.02	
g : 0.23	e : 0.16	i : 0.10	c : 0.08	= : 0.08	b : 0.06	! : 0.06	" : 0.06	d : 0.04	[ : 0.04	f : 0.04	a : 0.02	h : 0.02	
g : 0.21	e : 0.18	c : 0.10	b : 0.08	= : 0.08	i : 0.08	[ : 0.06	f : 0.06	" : 0.06	d : 0.06	$ : 0.02	
e : 0.18	g : 0.14	c : 0.10	= : 0.08	i : 0.08	! : 0.06	# : 0.06	" : 0.06	b : 0.06	d : 0.06	[ : 0.04	f : 0.04	a : 0.02	$ : 0.02	
c : 0.16	[ : 0.16	e : 0.14	! : 0.10	d : 0.10	" : 0.08	# : 0.06	= : 0.06	i : 0.06	$ : 0.04	f : 0.04	
c : 0.27	d : 0.12	e : 0.12	# : 0.08	! : 0.06	" : 0.06	a : 0.06	= : 0.06	$ : 0.04	f : 0.04	i : 0.04	b : 0.02	[ : 0.02	
c : 0.23	" : 0.12	[ : 0.12	d : 0.08	# : 0.08	e : 0.08	! : 0.06	a : 0.04	$ : 0.04	b : 0.04	f : 0.04	= : 0.04	i : 0.02	
d : 0.27	c : 0.18	" : 0.12	! : 0.10	[ : 0.06	a : 0.04	e : 0.04	f : 0.04	b : 0.04	= : 0.04	$ : 0.02	i : 0.02	# : 0.02	
d : 0.23	[ : 0.21	c : 0.19	! : 0.10	" : 0.08	e : 0.04	$ : 0.02	f : 0.02	i : 0.02	b : 0.02	# : 0.02	= : 0.02	
c : 0.27	b : 0.25	d : 0.23	[ : 0.06	a : 0.04	! : 0.04	e : 0.02	f : 0.02	" : 0.02	= : 0.02	
c : 0.36	b : 0.25	d : 0.23	a : 0.04	o : 0.02	e : 0.02	f : 0.02	[ : 0.02	= : 0.02	
o : 0.76	c : 0.18	d : 0.02	a : 0.02	= : 0.02	
o : 0.78	c : 0.08	m : 0.06	n : 0.04	d : 0.02	= : 0.02	
o : 0.78	m : 0.10	l : 0.08	n : 0.04	
o : 0.78	m : 0.10	l : 0.08	n : 0.04	
o : 0.78	m : 0.10	l : 0.08	n : 0.04	
o : 0.76	c : 0.14	n : 0.04	m : 0.04	a : 0.02	
c : 0.36	b : 0.25	d : 0.23	a : 0.04	] : 0.02	e : 0.02	f : 0.02	o : 0.02	= : 0.02	
c : 0.38	d : 0.25	b : 0.25	e : 0.02	f : 0.02	a : 0.02	2 : 0.02	= : 0.02	
d : 0.27	] : 0.27	c : 0.25	2 : 0.06	3 : 0.04	f : 0.04	e : 0.02	= : 0.02	
d : 0.30	c : 0.18	a : 0.08	3 : 0.08	2 : 0.08	= : 0.06	e : 0.04	4 : 0.04	b : 0.04	f : 0.04	] : 0.04	i : 0.02	
c : 0.19	3 : 0.12	2 : 0.10	= : 0.08	] : 0.08	4 : 0.08	d : 0.06	e : 0.06	b : 0.06	a : 0.04	f : 0.04	i : 0.04	5 : 0.02	g : 0.02	
c : 0.19	2 : 0.10	d : 0.08	3 : 0.08	e : 0.08	= : 0.08	4 : 0.08	a : 0.06	f : 0.06	] : 0.06	g : 0.04	i : 0.04	5 : 0.02	b : 0.02	
e : 0.14	c : 0.12	] : 0.12	4 : 0.12	= : 0.08	3 : 0.08	2 : 0.06	d : 0.06	i : 0.06	g : 0.04	b : 0.04	f : 0.04	5 : 0.02	h : 0.02	
e : 0.18	c : 0.12	g : 0.10	4 : 0.10	b : 0.08	d : 0.08	= : 0.08	i : 0.08	3 : 0.04	2 : 0.04	f : 0.04	5 : 0.02	h : 0.02	] : 0.02	
e : 0.16	g : 0.14	c : 0.12	d : 0.10	= : 0.08	i : 0.08	2 : 0.06	4 : 0.06	] : 0.06	b : 0.04	3 : 0.04	5 : 0.02	h : 0.02	f : 0.02	
g : 0.18	e : 0.18	c : 0.10	2 : 0.08	= : 0.08	d : 0.08	i : 0.08	] : 0.06	4 : 0.06	> : 0.02	a : 0.02	h : 0.02	f : 0.02	3 : 0.02	
g : 0.19	e : 0.16	c : 0.12	f : 0.08	= : 0.08	d : 0.08	i : 0.08	2 : 0.06	4 : 0.04	a : 0.02	> : 0.02	h : 0.02	] : 0.02	3 : 0.02	
g : 0.21	c : 0.14	e : 0.10	f : 0.08	= : 0.08	i : 0.08	] : 0.06	4 : 0.04	2 : 0.04	> : 0.04	d : 0.04	b : 0.02	h : 0.02	3 : 0.02	6 : 0.02	
g : 0.21	c : 0.14	e : 0.10	f : 0.08	= : 0.08	4 : 0.06	i : 0.06	] : 0.06	b : 0.04	> : 0.04	h : 0.04	2 : 0.02	3 : 0.02	6 : 0.02	d : 0.02	
g : 0.21	e : 0.10	] : 0.08	f : 0.08	c : 0.08	= : 0.08	4 : 0.06	i : 0.06	> : 0.04	b : 0.04	h : 0.04	a : 0.04	d : 0.02	3 : 0.02	6 : 0.02	: : 0.02	

#score	712.9676931536244
#seq	50
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_UTR_m3_run1.txt

#BEAR
gggggoooooogggg	chr7:90043844-90044080(+)$1	236	75	90	11.0503
###bboooooobb44	chr14:57713467-57713703(-)$1	236	63	78	9.4006
a[cccooooooccc]	chr6:32153576-32154058(-)$1	482	255	270	10.7047
ccc[aooooooa]cc	chr1:205685974-205686348(-)$1	374	41	56	10.2674
fffffooooooffff	chr13:98044547-98044783(+)$1	236	163	178	10.7858
ee[bboooooobb33	chr14:100604326-100604704(+)$1	378	336	351	10.0450
fffbboooooobb]f	chr14:21851512-21851787(-)$1	275	175	190	10.0392
eeeeeooooooeeee	chr11:13751447-13751709(+)$1	262	184	199	11.0184
=====oooooo====	chr9:6469488-6469717(+)$1	229	194	209	10.9937
fffffooooooffff	chr2:242054054-242054302(-)$1	248	141	156	10.7858
eeeeeooooooeeee	chr11:114278083-114278346(+)$1	263	48	63	11.0184
gggggoooooogggg	chr16:89806082-89806338(-)$1	256	73	88	11.0503
eeebboooooobb]e	chr1:202127223-202127486(-)$1	263	187	202	10.2105
c[cccooooooccc]	chr1:243326366-243326602(-)$1	236	213	228	10.7216
eeeeeooooooeeee	chr13:49782289-49782556(+)$1	267	99	114	11.0184
!!cccooooooccc2	chrX:70327369-70327667(-)$1	298	229	244	10.5498
[ddddoooooodddd	chr15:64430140-64430385(+)$1	245	11	26	9.9649
[ddddoooooodddd	chr17:80215046-80215282(-)$1	236	170	185	9.9649
=====oooooo====	chr9:132657468-132657872(-)$1	404	215	230	10.9937
fffffooooooffff	chr20:60883738-60883985(+)$1	247	189	204	10.7858
a[cccooooooccca	chr12:27126469-27126727(-)$1	258	194	209	10.5537
fffffooooooffff	chr12:113426396-113426665(+)$1	269	251	266	10.7858
eeeeeooooooeeee	chr3:152182645-152183076(+)$1	431	131	146	11.0184
""cccooooooccc3	chr3:33430477-33430766(-)$1	289	253	268	10.5655
!ddddoooooodddd	chr5:61684447-61684684(-)$1	237	139	154	9.9442
gggggoooooogggg	chr12:3048970-3049295(+)$1	325	220	235	11.0503
iiiiiooooooiiii	chr17:57777534-57777788(-)$1	254	209	224	10.7496
"ddddoooooodddd	chr2:27532351-27532632(-)$1	281	184	199	9.8511
fffffooooooffff	chr1:198661857-198662295(+)$1	438	274	289	10.7858
[ddddoooooodddd	chrX:118714346-118714591(+)$1	245	38	53	9.9649
fffffooooooffff	chr21:43410023-43410416(-)$1	393	216	231	10.7858
eeeeeooooooeeee	chr17:26521878-26522167(+)$1	289	260	275	11.0184
dd[bboooooobb]d	chr12:46580872-46581193(-)$1	321	291	306	9.6417
eeeeeooooooeeee	chr10:11374712-11374963(+)$1	251	184	199	11.0184
gggggoooooogggg	chr2:197642882-197643118(-)$1	236	204	219	11.0503
ccc[aooooooa]cc	chr9:33046346-33046592(-)$1	246	48	63	10.2674
!ddddoooooodddd	chr17:27585592-27585943(-)$1	351	170	185	9.9442
=====oooooo====	chr2:206860896-206861232(-)$1	336	182	197	10.9937
fffffooooooffff	chr1:160190199-160190435(-)$1	236	119	134	10.7858
eeeeeooooooeeee	chr19:16023429-16023700(-)$1	271	49	64	11.0184
gggggoooooogggg	chr1:150548361-150548619(-)$1	258	70	85	11.0503
eeeeeooooooeeee	chr15:38782049-38782495(-)$1	446	307	322	11.0184
dddbboooooobb]d	chr8:144916105-144916389(-)$1	284	174	189	9.5219
"ddddoooooodddd	chr2:174132221-174132488(+)$1	267	151	166	9.8511
e[cccooooooccc]	chr20:47651456-47651821(+)$1	365	304	319	10.8463
!!cccooooooccc3	chr15:34521965-34522307(+)$1	342	138	153	10.7775
d[cccoooooocccd	chr2:203848776-203849023(+)$1	247	124	139	10.5083
gggggoooooogggg	chr12:390121-390363(-)$1	242	137	152	11.0503
gggggoooooogggg	chr10:104498384-104498637(+)$1	253	106	121	11.0503
fffffooooooffff	chr7:148877668-148877925(+)$1	257	129	144	10.7858
fffffooooooffff	chr1:227843552-227843807(+)$1	255	116	131	10.7858
ff[bboooooobbff	chr5:883302-883573(-)$1	271	107	122	10.0621
eeeeeooooooeeee	chr2:54887125-54887382(+)$1	257	172	187	11.0184
fffffooooooffff	chr19:12299000-12299225(+)$1	225	183	198	10.7858
eeeeeooooooeeee	chr2:178087232-178087665(+)$1	433	225	240	11.0184
eeeeeooooooeeee	chr12:121201844-121202127(-)$1	283	158	173	11.0184
eeeeeooooooeeee	chrX:74523641-74523878(+)$1	237	204	219	11.0184
gggggoooooogggg	chr3:180694062-180694376(+)$1	314	276	291	11.0503
gggggoooooogggg	chr22:40725060-40725349(+)$1	289	244	259	11.0503
fff[aooooooa]ff	chr15:63929137-63929374(-)$1	237	166	181	10.5518
gggggoooooogggg	chr1:113070069-113070337(-)$1	268	35	50	11.0503
eeeeeooooooeeee	chr2:228419150-228419386(+)$1	236	55	70	11.0184
fffffooooooffff	chr4:1947507-1947794(+)$1	287	250	265	10.7858
eeeeeooooooeeee	chr5:139944800-139945056(+)$1	256	86	101	11.0184
eeeeeooooooeeee	chr9:5919894-5920174(-)$1	280	208	223	11.0184
fffffooooooffff	chr5:133483589-133483903(+)$1	314	208	223	10.7858
ee[bboooooobb]e	chrX:41207906-41208157(+)$1	251	214	229	10.1922
gggggoooooogggg	chrX:135954508-135954934(-)$1	426	140	155	11.0503
eeeeeooooooeeee	chr14:67176040-67176278(+)$1	238	115	130	11.0184
""cccooooooccc]	chr3:101368669-101368903(-)$1	234	9	24	10.6092

#otherMatches

#Seq PSSM
AGAGACACAACUUUC	chr7:90043844-90044080(+)$1	236	75	90	11.0503
ACUGGUCAGUUCCUA	chr14:57713467-57713703(-)$1	236	63	78	9.4006
GCAACUAUUCUGUUU	chr6:32153576-32154058(-)$1	482	255	270	10.7047
GAACAUUUUCUUUUU	chr1:205685974-205686348(-)$1	374	41	56	10.2674
UUGUAACUGACUACA	chr13:98044547-98044783(+)$1	236	163	178	10.7858
GUUUCCCCACAGACA	chr14:100604326-100604704(+)$1	378	336	351	10.0450
UCUUCGUAAAGGAGA	chr14:21851512-21851787(-)$1	275	175	190	10.0392
AUUUGAUUUAACAAA	chr11:13751447-13751709(+)$1	262	184	199	11.0184
uauauauacacguau	chr9:6469488-6469717(+)$1	229	194	209	10.9937
UAACCAGUAAGGGUU	chr2:242054054-242054302(-)$1	248	141	156	10.7858
GAAGUAUUAACAUUU	chr11:114278083-114278346(+)$1	263	48	63	11.0184
AAGCACAAACUUGUU	chr16:89806082-89806338(-)$1	256	73	88	11.0503
UGGGCCCUUCAGCGC	chr1:202127223-202127486(-)$1	263	187	202	10.2105
CUGUAUCUCUUUGCU	chr1:243326366-243326602(-)$1	236	213	228	10.7216
guguacacauauaca	chr13:49782289-49782556(+)$1	267	99	114	11.0184
UUUGGCAUUCCCCAC	chrX:70327369-70327667(-)$1	298	229	244	10.5498
UUACUCCUGAUGGUG	chr15:64430140-64430385(+)$1	245	11	26	9.9649
aaguuauaaagaacu	chr17:80215046-80215282(-)$1	236	170	185	9.9649
ACUGAACUGUGUUAG	chr9:132657468-132657872(-)$1	404	215	230	10.9937
UCUUUGCCCAAAGGG	chr20:60883738-60883985(+)$1	247	189	204	10.7858
GUCUCUCACCUGAGC	chr12:27126469-27126727(-)$1	258	194	209	10.5537
caagaacccucucuu	chr12:113426396-113426665(+)$1	269	251	266	10.7858
UUUGCUUUCUUGUGG	chr3:152182645-152183076(+)$1	431	131	146	11.0184
CUGAAUUUUUUUUUU	chr3:33430477-33430766(-)$1	289	253	268	10.5655
AAAGAUGUUACUCUU	chr5:61684447-61684684(-)$1	237	139	154	9.9442
AUUGGCCGGCACCAA	chr12:3048970-3049295(+)$1	325	220	235	11.0503
aaGGAUGACAUUCCU	chr17:57777534-57777788(-)$1	254	209	224	10.7496
AGGCUUCUUGUAGCU	chr2:27532351-27532632(-)$1	281	184	199	9.8511
CAUCACUUAACUGAU	chr1:198661857-198662295(+)$1	438	274	289	10.7858
AAUACACUGAAGUAU	chrX:118714346-118714591(+)$1	245	38	53	9.9649
UCAGACCAGCAUUUG	chr21:43410023-43410416(-)$1	393	216	231	10.7858
UCAUGGAGCCACGUG	chr17:26521878-26522167(+)$1	289	260	275	11.0184
GCUUUUAAUAUAAUG	chr12:46580872-46581193(-)$1	321	291	306	9.6417
AAUAACAACACUUAU	chr10:11374712-11374963(+)$1	251	184	199	11.0184
AUCGAAUAGUCUUGG	chr2:197642882-197643118(-)$1	236	204	219	11.0503
UGUUCUAAAAUGUAC	chr9:33046346-33046592(-)$1	246	48	63	10.2674
CCACUAACAAGAGUG	chr17:27585592-27585943(-)$1	351	170	185	9.9442
UCACACAUCAUUGUG	chr2:206860896-206861232(-)$1	336	182	197	10.9937
CUGGUGAAGUGACCA	chr1:160190199-160190435(-)$1	236	119	134	10.7858
CCUCUUCUCCUAGAG	chr19:16023429-16023700(-)$1	271	49	64	11.0184
GCUUGGAAAAGCAGG	chr1:150548361-150548619(-)$1	258	70	85	11.0503
UAGAAGCCAAUUUCU	chr15:38782049-38782495(-)$1	446	307	322	11.0184
uggcauucugcugac	chr8:144916105-144916389(-)$1	284	174	189	9.5219
AUUUCACCAAAGGAG	chr2:174132221-174132488(+)$1	267	151	166	9.8511
UUUUCUUCAUCGGAU	chr20:47651456-47651821(+)$1	365	304	319	10.8463
AAAGACUCUUUUCUC	chr15:34521965-34522307(+)$1	342	138	153	10.7775
AGCAGCUACAUCUGU	chr2:203848776-203849023(+)$1	247	124	139	10.5083
UCAUUUACAUUGGUG	chr12:390121-390363(-)$1	242	137	152	11.0503
UCUCUAUAAUAAGGG	chr10:104498384-104498637(+)$1	253	106	121	11.0503
AGCCAGUAAGUUGGC	chr7:148877668-148877925(+)$1	257	129	144	10.7858
AAGAUUACAAUAUCU	chr1:227843552-227843807(+)$1	255	116	131	10.7858
ggugacauuaauccu	chr5:883302-883573(-)$1	271	107	122	10.0621
AAAAUGUUAAAAUUU	chr2:54887125-54887382(+)$1	257	172	187	11.0184
UUUAGUUCCACUUGA	chr19:12299000-12299225(+)$1	225	183	198	10.7858
gcagugagcugacug	chr2:178087232-178087665(+)$1	433	225	240	11.0184
AACUGACCCCGCAGU	chr12:121201844-121202127(-)$1	283	158	173	11.0184
ACAUUCCCAUUAAUG	chrX:74523641-74523878(+)$1	237	204	219	11.0184
AAAUGUUAUUUUGUU	chr3:180694062-180694376(+)$1	314	276	291	11.0503
UCUGUAAGAAAACAG	chr22:40725060-40725349(+)$1	289	244	259	11.0503
AGAGCACCGACGGUU	chr15:63929137-63929374(-)$1	237	166	181	10.5518
GGAGUAGGUAAAUUU	chr1:113070069-113070337(-)$1	268	35	50	11.0503
UUAUAGCCUUAUAUA	chr2:228419150-228419386(+)$1	236	55	70	11.0184
UUUUAUGCUUUUAAA	chr4:1947507-1947794(+)$1	287	250	265	10.7858
GACAGUCUUUUUUGU	chr5:139944800-139945056(+)$1	256	86	101	11.0184
AGCUACUCUUUUGGC	chr9:5919894-5920174(-)$1	280	208	223	11.0184
GUCUUGAGAAAAAGA	chr5:133483589-133483903(+)$1	314	208	223	10.7858
CUUUGAGAUCACACA	chrX:41207906-41208157(+)$1	251	214	229	10.1922
UUAUUCCUUCAAAUA	chrX:135954508-135954934(-)$1	426	140	155	11.0503
aucugauaacccaga	chr14:67176040-67176278(+)$1	238	115	130	11.0184
ACUAAGUUAUAUUAA	chr3:101368669-101368903(-)$1	234	9	24	10.6092

#DB
(((((......))))	chr7:90043844-90044080(+)$1	1	75	90	11.0503
...((......))..	chr14:57713467-57713703(-)$1	1	63	78	9.4006
(.(((......))).	chr6:32153576-32154058(-)$1	1	255	270	10.7047
(((.(......).))	chr1:205685974-205686348(-)$1	1	41	56	10.2674
(((((......))))	chr13:98044547-98044783(+)$1	1	163	178	10.7858
((.((......))..	chr14:100604326-100604704(+)$1	1	336	351	10.0450
(((((......)).)	chr14:21851512-21851787(-)$1	1	175	190	10.0392
(((((......))))	chr11:13751447-13751709(+)$1	1	184	199	11.0184
(((((......))))	chr9:6469488-6469717(+)$1	1	194	209	10.9937
(((((......))))	chr2:242054054-242054302(-)$1	1	141	156	10.7858
(((((......))))	chr11:114278083-114278346(+)$1	1	48	63	11.0184
(((((......))))	chr16:89806082-89806338(-)$1	1	73	88	11.0503
(((((......)).)	chr1:202127223-202127486(-)$1	1	187	202	10.2105
(.(((......))).	chr1:243326366-243326602(-)$1	1	213	228	10.7216
(((((......))))	chr13:49782289-49782556(+)$1	1	99	114	11.0184
..(((......))).	chrX:70327369-70327667(-)$1	1	229	244	10.5498
.((((......))))	chr15:64430140-64430385(+)$1	1	11	26	9.9649
.((((......))))	chr17:80215046-80215282(-)$1	1	170	185	9.9649
(((((......))))	chr9:132657468-132657872(-)$1	1	215	230	10.9937
(((((......))))	chr20:60883738-60883985(+)$1	1	189	204	10.7858
(.(((......))))	chr12:27126469-27126727(-)$1	1	194	209	10.5537
(((((......))))	chr12:113426396-113426665(+)$1	1	251	266	10.7858
(((((......))))	chr3:152182645-152183076(+)$1	1	131	146	11.0184
..(((......))).	chr3:33430477-33430766(-)$1	1	253	268	10.5655
.((((......))))	chr5:61684447-61684684(-)$1	1	139	154	9.9442
(((((......))))	chr12:3048970-3049295(+)$1	1	220	235	11.0503
(((((......))))	chr17:57777534-57777788(-)$1	1	209	224	10.7496
.((((......))))	chr2:27532351-27532632(-)$1	1	184	199	9.8511
(((((......))))	chr1:198661857-198662295(+)$1	1	274	289	10.7858
.((((......))))	chrX:118714346-118714591(+)$1	1	38	53	9.9649
(((((......))))	chr21:43410023-43410416(-)$1	1	216	231	10.7858
(((((......))))	chr17:26521878-26522167(+)$1	1	260	275	11.0184
((.((......)).)	chr12:46580872-46581193(-)$1	1	291	306	9.6417
(((((......))))	chr10:11374712-11374963(+)$1	1	184	199	11.0184
(((((......))))	chr2:197642882-197643118(-)$1	1	204	219	11.0503
(((.(......).))	chr9:33046346-33046592(-)$1	1	48	63	10.2674
.((((......))))	chr17:27585592-27585943(-)$1	1	170	185	9.9442
(((((......))))	chr2:206860896-206861232(-)$1	1	182	197	10.9937
(((((......))))	chr1:160190199-160190435(-)$1	1	119	134	10.7858
(((((......))))	chr19:16023429-16023700(-)$1	1	49	64	11.0184
(((((......))))	chr1:150548361-150548619(-)$1	1	70	85	11.0503
(((((......))))	chr15:38782049-38782495(-)$1	1	307	322	11.0184
(((((......)).)	chr8:144916105-144916389(-)$1	1	174	189	9.5219
.((((......))))	chr2:174132221-174132488(+)$1	1	151	166	9.8511
(.(((......))).	chr20:47651456-47651821(+)$1	1	304	319	10.8463
..(((......))).	chr15:34521965-34522307(+)$1	1	138	153	10.7775
(.(((......))))	chr2:203848776-203849023(+)$1	1	124	139	10.5083
(((((......))))	chr12:390121-390363(-)$1	1	137	152	11.0503
(((((......))))	chr10:104498384-104498637(+)$1	1	106	121	11.0503
(((((......))))	chr7:148877668-148877925(+)$1	1	129	144	10.7858
(((((......))))	chr1:227843552-227843807(+)$1	1	116	131	10.7858
((.((......))))	chr5:883302-883573(-)$1	1	107	122	10.0621
(((((......))))	chr2:54887125-54887382(+)$1	1	172	187	11.0184
(((((......))))	chr19:12299000-12299225(+)$1	1	183	198	10.7858
(((((......))))	chr2:178087232-178087665(+)$1	1	225	240	11.0184
(((((......))))	chr12:121201844-121202127(-)$1	1	158	173	11.0184
(((((......))))	chrX:74523641-74523878(+)$1	1	204	219	11.0184
(((((......))))	chr3:180694062-180694376(+)$1	1	276	291	11.0503
(((((......))))	chr22:40725060-40725349(+)$1	1	244	259	11.0503
(((.(......).))	chr15:63929137-63929374(-)$1	1	166	181	10.5518
(((((......))))	chr1:113070069-113070337(-)$1	1	35	50	11.0503
(((((......))))	chr2:228419150-228419386(+)$1	1	55	70	11.0184
(((((......))))	chr4:1947507-1947794(+)$1	1	250	265	10.7858
(((((......))))	chr5:139944800-139945056(+)$1	1	86	101	11.0184
(((((......))))	chr9:5919894-5920174(-)$1	1	208	223	11.0184
(((((......))))	chr5:133483589-133483903(+)$1	1	208	223	10.7858
((.((......)).)	chrX:41207906-41208157(+)$1	1	214	229	10.1922
(((((......))))	chrX:135954508-135954934(-)$1	1	140	155	11.0503
(((((......))))	chr14:67176040-67176278(+)$1	1	115	130	11.0184
..(((......))).	chr3:101368669-101368903(-)$1	1	9	24	10.6092

#PSSM
e : 0.28	f : 0.21	g : 0.15	! : 0.05	" : 0.05	c : 0.04	= : 0.04	[ : 0.04	d : 0.04	a : 0.02	# : 0.01	i : 0.01	
e : 0.27	f : 0.21	g : 0.15	d : 0.12	[ : 0.07	= : 0.04	c : 0.02	! : 0.02	" : 0.02	# : 0.01	i : 0.01	
e : 0.24	f : 0.20	g : 0.15	c : 0.15	d : 0.11	[ : 0.05	= : 0.04	# : 0.01	i : 0.01	
e : 0.22	f : 0.17	g : 0.15	c : 0.12	b : 0.11	d : 0.10	[ : 0.04	= : 0.04	i : 0.01	
e : 0.22	f : 0.17	g : 0.15	c : 0.12	b : 0.11	d : 0.10	a : 0.04	= : 0.04	i : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
e : 0.22	f : 0.17	g : 0.15	c : 0.12	b : 0.11	d : 0.10	a : 0.04	= : 0.04	i : 0.01	
e : 0.22	f : 0.17	g : 0.15	c : 0.12	b : 0.11	d : 0.10	] : 0.04	= : 0.04	i : 0.01	
e : 0.22	f : 0.20	g : 0.15	c : 0.15	d : 0.10	] : 0.07	= : 0.04	4 : 0.01	3 : 0.01	i : 0.01	
e : 0.25	f : 0.21	g : 0.15	d : 0.14	] : 0.05	3 : 0.04	= : 0.04	c : 0.02	4 : 0.01	2 : 0.01	a : 0.01	i : 0.01	

#score	746.5343676671606
#seq	70
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m3_run1.txt

#BEAR
fff!!bbqqqqqqqqbb333ff	chr5:172447168-172447399(+)$1	231	173	195	15.2878
Ca!!cccqqqqqqqqccc22a:	chr3:113225253-113225469(-)$1	216	127	149	13.9812
f"""cccqqqqqqqqccc22ff	chr3:167759125-167759351(-)$1	226	167	189	15.6886
eeee[bbqqqqqqqqbb]eeee	chr6:29598216-29598491(-)$1	275	228	250	14.6842
ggg[cccqqqqqqqqccc]ggg	chr18:54547168-54547393(+)$1	225	62	84	15.9823
ee[acccqqqqqqqqccc]a]e	chr3:129389295-129389528(-)$1	233	98	120	15.8087
[ffffffqqqqqqqqffffff]	chr16:24831477-24831723(+)$1	246	90	112	14.5471
fccc[bbqqqqqqqqbb]ccc:	chr1:52912191-52912414(-)$1	223	184	206	14.0087
!!bb[bbqqqqqqqqbb]bb22	chr5:112238067-112238290(-)$1	223	64	86	14.3856
iiiiiiiqqqqqqqqiiiiiii	chr22:42310291-42310515(-)$1	224	178	200	14.6865
eee[cccqqqqqqqqccc]eee	chr11:57069485-57069716(-)$1	231	188	210	15.7152
cc"""bbqqqqqqqqbb4444c	chr1:6885105-6885335(+)$1	230	127	149	15.3743
ccc[cccqqqqqqqqccccccJ	chr16:29998766-29999006(+)$1	240	65	87	14.2700
"bb[cccqqqqqqqqccc]bb]	chrX:118724944-118725169(-)$1	225	158	180	15.5464
ccc[cccqqqqqqqqccc]ccc	chr2:169622075-169622301(+)$1	226	23	45	15.9541
::a[cccqqqqqqqqcccafff	chr16:24802536-24802763(+)$1	227	57	79	13.9146
""eeeeeqqqqqqqqeeeee22	chr11:64846540-64846759(-)$1	219	83	105	14.3174
d"""cccqqqqqqqqcccdddd	chr1:186113567-186113789(+)$1	222	145	167	15.2792
bb[ddddqqqqqqqqddddbb]	chr9:4662694-4662926(+)$1	232	168	190	13.5250
a[eeeeeqqqqqqqqeeeee]a	chr11:122929263-122929494(-)$1	231	99	121	14.3880
!ffffffqqqqqqqqffffff3	chr10:103550710-103550945(-)$1	235	109	131	14.6705
f!!acccqqqqqqqqccc]a33	chr2:230923861-230924078(-)$1	217	81	103	16.3350
ccc[cccqqqqqqqqcccccc2	chr10:24896674-24896905(-)$1	231	96	118	15.6880
e"""cccqqqqqqqqccc22ee	chr11:94922954-94923185(-)$1	231	141	163	15.7325
d[eeeeeqqqqqqqqeeeeedd	chr16:70714618-70714842(-)$1	224	5	27	13.8398
b[ccc[aqqqqqqqqa]ccc]b	chr19:49403979-49404214(+)$1	235	195	217	14.6574
"bb[cccqqqqqqqqccc]bb4	chr6:21595801-21596074(+)$1	273	66	88	15.5490
b[eeeeeqqqqqqqqeeeee]b	chrX:70472879-70473103(-)$1	224	40	62	13.9564
eeeee[aqqqqqqqqa]eeeee	chr9:117826075-117826306(-)$1	231	74	96	14.2537
!bb[cccqqqqqqqqcccbb]d	chr10:71992934-71993183(-)$1	249	179	201	15.1737
cc!!cccqqqqqqqqccc333c	chr9:135985748-135985973(-)$1	225	79	101	16.3750
iii[cccqqqqqqqqccc]iii	chr5:179247872-179248163(+)$1	291	140	162	16.0011
fffff[aqqqqqqqqa]fffff	chr17:76219941-76220177(+)$1	236	120	142	14.1997
cc[ddddqqqqqqqqdddd444	chr20:37580992-37581215(+)$1	223	138	160	14.4107
ggg[cccqqqqqqqqcccgggg	chr6:24701694-24701920(+)$1	226	78	100	15.7530
ff"""bbqqqqqqqqbb22fff	chr1:91406575-91406798(-)$1	223	160	182	14.7699
##eeeeeqqqqqqqqeeeee66	chr19:52090124-52090348(+)$1	224	9	31	13.6192
!!bb[bbqqqqqqqqbb]bb]g	chr19:2269434-2269681(+)$1	247	92	114	14.5730
:ccc[bbqqqqqqqqbb22ccc	chr1:245019254-245019522(-)$1	268	106	128	13.9286
!!eeeeeqqqqqqqqeeeee]d	chr3:169496465-169496685(+)$1	220	35	57	14.4585
d!!ddddqqqqqqqqdddd333	chr16:47536801-47537034(+)$1	233	76	98	14.7107
ee[ddddqqqqqqqqdddd]ee	chrX:133609234-133609466(+)$1	232	107	129	13.9256
!ccc[aaqqqqqqqqa]a]ccc	chr22:38694722-38694964(-)$1	242	149	171	15.1444
[bb!!bbqqqqqqqqbb22bb3	chr19:13051032-13051287(+)$1	255	76	98	14.6909
eee[cccqqqqqqqqccc]eee	chr17:76967818-76968060(-)$1	242	123	145	15.7152
"ffffffqqqqqqqqffffff3	chr17:73234068-73234296(-)$1	228	106	128	14.6293
ddddd[aqqqqqqqqa]dddd]	chr14:53148957-53149187(-)$1	230	102	124	13.6557
eeeeebbqqqqqqqqbb]eeee	chr19:39923851-39924110(-)$1	259	160	182	14.5347
c"""cccqqqqqqqqccc333c	chr1:113456485-113456752(-)$1	267	220	242	16.4374
!!a[cccqqqqqqqqccca22b	chr19:4409208-4409447(+)$1	239	44	66	15.6965
[ffffffqqqqqqqqffffff]	chr6:43472501-43472725(+)$1	224	123	145	14.5471
bb"""bbqqqqqqqqbb22bbd	chr1:85395161-85395386(-)$1	225	95	117	14.1590
dccc[bbqqqqqqqqbb]ccc]	chrX:84502486-84502709(+)$1	223	104	126	14.8823
eeeeebbqqqqqqqqbb]eeee	chr21:28212224-28212456(-)$1	232	198	220	14.5347
eeeecccqqqqqqqqccc]eee	chr17:49233003-49233235(+)$1	232	115	137	15.4194
###ddddqqqqqqqqdddd22g	chr5:1463680-1463901(-)$1	221	124	146	14.1493
&&a[cccqqqqqqqqccc]a55	chr10:96334245-96334470(+)$1	225	16	38	13.6708
ffbbcccqqqqqqqqccc]bb2	chr7:100279395-100279628(-)$1	233	92	114	14.7664
e[bb[bbqqqqqqqqbbbb]ee	chr18:33706250-33706472(-)$1	222	173	195	13.8999
bbeeeeeqqqqqqqqeeeee]b	chr21:28216749-28216992(-)$1	243	195	217	13.6485
cc[ddddqqqqqqqqdddd]cc	chr12:106633623-106633860(-)$1	237	149	171	14.1406
[ffffffqqqqqqqqffffff2	chr20:31946758-31946982(-)$1	224	169	191	14.4280
[ffffffqqqqqqqqffffffb	chr19:55998477-55998734(+)$1	257	14	36	14.1885
gggggggqqqqqqqqggggggg	chr3:101476972-101477198(+)$1	226	102	124	14.6288
[ddddbbqqqqqqqqbb]dddd	chr1:62916065-62916289(+)$1	224	170	192	14.0002
:ffffffqqqqqqqqffffffe	chr11:93474432-93474659(-)$1	227	165	187	13.4070

#otherMatches

#Seq PSSM
GACAUGCUCUACAGUGCUCAGU	chr5:172447168-172447399(+)$1	231	173	195	15.2878
UGGGAUAGUAAAUAAUGUAACA	chr3:113225253-113225469(-)$1	216	127	149	13.9812
UCAAGGUAAAAGAAAACCAAAC	chr3:167759125-167759351(-)$1	226	167	189	15.6886
GUGGAGCACCCCCAAGCCCCAC	chr6:29598216-29598491(-)$1	275	228	250	14.6842
CGGAAGCAAGCUACCGCUAUUG	chr18:54547168-54547393(+)$1	225	62	84	15.9823
UAGUGAAGAAGAUUGUUCUAGU	chr3:129389295-129389528(-)$1	233	98	120	15.8087
CGUCCCGCCCACCUCCGGGACU	chr16:24831477-24831723(+)$1	246	90	112	14.5471
UGCUCACUGAUAUAUGUUAGCA	chr1:52912191-52912414(-)$1	223	184	206	14.0087
CUGCCUUUCAGAAUUAAAGCUA	chr5:112238067-112238290(-)$1	223	64	86	14.3856
CGGCCUGGGUCCAGACAggccg	chr22:42310291-42310515(-)$1	224	178	200	14.6865
UGGUGAUGUCUCUUGAUCUCUA	chr11:57069485-57069716(-)$1	231	188	210	15.7152
GUUUACCAAAAGAGAGGCACCG	chr1:6885105-6885335(+)$1	230	127	149	15.3743
GCAUAUCUCGACUCUGGUUGCG	chr16:29998766-29999006(+)$1	240	65	87	14.2700
AGCCUGUAACAGCCAACAUGUA	chrX:118724944-118725169(-)$1	225	158	180	15.5464
UAGGGUGUUAAAUACCACAUUA	chr2:169622075-169622301(+)$1	226	23	45	15.9541
UAGUGACAGUGACAGGUCCGUU	chr16:24802536-24802763(+)$1	227	57	79	13.9146
CAUUUCUCUUCCCUCAGAAAAC	chr11:64846540-64846759(-)$1	219	83	105	14.3174
CAUGUGGAGGAGGUGCCAGACA	chr1:186113567-186113789(+)$1	222	145	167	15.2792
GCGAGGUGCUGAUGAACCUGCU	chr9:4662694-4662926(+)$1	232	168	190	13.5250
UGCUGUGGACAAGAGUACGGGA	chr11:122929263-122929494(-)$1	231	99	121	14.3880
AGGGCUGCUUUCCCUCAGCCUG	chr10:103550710-103550945(-)$1	235	109	131	14.6705
CCACCCAAACAUUGAUGGCGGA	chr2:230923861-230924078(-)$1	217	81	103	16.3350
GAUCAUGAUAUUGCACAUAUCC	chr10:24896674-24896905(-)$1	231	96	118	15.6880
UUGAAUGGUUUGGAAUAUGUGC	chr11:94922954-94923185(-)$1	231	141	163	15.7325
GAGGGGCAGGCAGAGGCCCCCC	chr16:70714618-70714842(-)$1	224	5	27	13.8398
CGACUGAGAGUCCCGUGAGUGG	chr19:49403979-49404214(+)$1	235	195	217	14.6574
CGCCCGCCCCGUCCAGCGCGCC	chr6:21595801-21596074(+)$1	273	66	88	15.5490
CUGCCAGAGAAGCCCCUGGCUG	chrX:70472879-70473103(-)$1	224	40	62	13.9564
GGCUGACACAGUAGAGGCAGCC	chr9:117826075-117826306(-)$1	231	74	96	14.2537
CCGUGGCCCCUCCGCGCCCGUC	chr10:71992934-71993183(-)$1	249	179	201	15.1737
UCCUCUGUCCCACCCCAGUAUG	chr9:135985748-135985973(-)$1	225	79	101	16.3750
GCUGCAGCCCCGAGCCUGAGGC	chr5:179247872-179248163(+)$1	291	140	162	16.0011
CCUGUUGAAUCUGAGCUGCAGG	chr17:76219941-76220177(+)$1	236	120	142	14.1997
AGAGAUGUAGCACUUUAUCCUU	chr20:37580992-37581215(+)$1	223	138	160	14.4107
UGGAUCUGACCAACAAGGCCAC	chr6:24701694-24701920(+)$1	226	78	100	15.7530
GUCUAGUCUAUUUAUACAUGCU	chr1:91406575-91406798(-)$1	223	160	182	14.7699
ACGAGGCCCCACCUUGCUUCUU	chr19:52090124-52090348(+)$1	224	9	31	13.6192
AACGGCGAGCAGCGGCGGCGGC	chr19:2269434-2269681(+)$1	247	92	114	14.5730
ACCUAUGUUGAACUUCAGAAGG	chr1:245019254-245019522(-)$1	268	106	128	13.9286
UUUCGAAAGUUUUUCUUUGAUC	chr3:169496465-169496685(+)$1	220	35	57	14.4585
UCAUGAGUUAUCUCUCUCACCC	chr16:47536801-47537034(+)$1	233	76	98	14.7107
GUGAUAGAUCCAUUCCUAUGAC	chrX:133609234-133609466(+)$1	232	107	129	13.9256
CUUUGACUGGAACAUGCUGAAA	chr22:38694722-38694964(-)$1	242	149	171	15.1444
AUGAGGUGAAGAUUGACAACAG	chr19:13051032-13051287(+)$1	255	76	98	14.6909
CUUCUCCUGCUCCUCGGACGAG	chr17:76967818-76968060(-)$1	242	123	145	15.7152
CUCCUUUGGCCCCUAAAAGGAC	chr17:73234068-73234296(-)$1	228	106	128	14.6293
CCAGUGUGGAAGAAGGGACUGU	chr14:53148957-53149187(-)$1	230	102	124	13.6557
CUGGUGCCCGCGCUCGCUACCA	chr19:39923851-39924110(-)$1	259	160	182	14.5347
AGGAGGAAAGUCCAGUCUGAAU	chr1:113456485-113456752(-)$1	267	220	242	16.4374
GACACUGGGGAUCAGCAGGGGU	chr19:4409208-4409447(+)$1	239	44	66	15.6965
UUAGAGAAGCCGGAGUCUCUAC	chr6:43472501-43472725(+)$1	224	123	145	14.5471
GUAUCAGAAAGAGUCCUCAGCC	chr1:85395161-85395386(-)$1	225	95	117	14.1590
GGUGGAAGUCUUGGAUUGCACA	chrX:84502486-84502709(+)$1	223	104	126	14.8823
GUACUGUGAAGGCAAACGAGUG	chr21:28212224-28212456(-)$1	232	198	220	14.5347
UUGUUGGUCUGAAAUUCAUGCA	chr17:49233003-49233235(+)$1	232	115	137	15.4194
AAGCUGGAUUAGGACCCAGGGU	chr5:1463680-1463901(-)$1	221	124	146	14.1493
GUAGUUGUUUAUAUCCAAGUUU	chr10:96334245-96334470(+)$1	225	16	38	13.6708
CAAGGCCAAGAGGCGGGCACUG	chr7:100279395-100279628(-)$1	233	92	114	14.7664
CAGUGUCACAUCAAAGAGCCGG	chr18:33706250-33706472(-)$1	222	173	195	13.8999
GCCGCUGCCCGCCGCCAGCGAG	chr21:28216749-28216992(-)$1	243	195	217	13.6485
CAAGUCCAGAGAGUGGGACAUG	chr12:106633623-106633860(-)$1	237	149	171	14.1406
CCUCCCCAACAGGAAGGGGAGA	chr20:31946758-31946982(-)$1	224	169	191	14.4280
UCAGCAGUGUGAAGUCUGUUGU	chr19:55998477-55998734(+)$1	257	14	36	14.1885
CCCAGAGAUCUGUUGCUUUGGG	chr3:101476972-101477198(+)$1	226	102	124	14.6288
GUUGGUGGAAAUACACAGCCAA	chr1:62916065-62916289(+)$1	224	170	192	14.0002
GUUUUAGGUAGGUUGCUAAGAG	chr11:93474432-93474659(-)$1	227	165	187	13.4070

#DB
(((..((........))...))	chr5:172447168-172447399(+)$1	1	173	195	15.2878
)(..(((........)))..).	chr3:113225253-113225469(-)$1	1	127	149	13.9812
(...(((........)))..))	chr3:167759125-167759351(-)$1	1	167	189	15.6886
((((.((........)).))))	chr6:29598216-29598491(-)$1	1	228	250	14.6842
(((.(((........))).)))	chr18:54547168-54547393(+)$1	1	62	84	15.9823
((.((((........))).).)	chr3:129389295-129389528(-)$1	1	98	120	15.8087
.((((((........)))))).	chr16:24831477-24831723(+)$1	1	90	112	14.5471
)(((.((........)).))).	chr1:52912191-52912414(-)$1	1	184	206	14.0087
..((.((........)).))..	chr5:112238067-112238290(-)$1	1	64	86	14.3856
(((((((........)))))))	chr22:42310291-42310515(-)$1	1	178	200	14.6865
(((.(((........))).)))	chr11:57069485-57069716(-)$1	1	188	210	15.7152
((...((........))....)	chr1:6885105-6885335(+)$1	1	127	149	15.3743
(((.(((........)))))))	chr16:29998766-29999006(+)$1	1	65	87	14.2700
.((.(((........))).)).	chrX:118724944-118725169(-)$1	1	158	180	15.5464
(((.(((........))).)))	chr2:169622075-169622301(+)$1	1	23	45	15.9541
..(.(((........))))(((	chr16:24802536-24802763(+)$1	1	57	79	13.9146
..(((((........)))))..	chr11:64846540-64846759(-)$1	1	83	105	14.3174
(...(((........)))))))	chr1:186113567-186113789(+)$1	1	145	167	15.2792
((.((((........)))))).	chr9:4662694-4662926(+)$1	1	168	190	13.5250
(.(((((........))))).)	chr11:122929263-122929494(-)$1	1	99	121	14.3880
.((((((........)))))).	chr10:103550710-103550945(-)$1	1	109	131	14.6705
(..((((........))).)..	chr2:230923861-230924078(-)$1	1	81	103	16.3350
(((.(((........)))))).	chr10:24896674-24896905(-)$1	1	96	118	15.6880
(...(((........)))..))	chr11:94922954-94923185(-)$1	1	141	163	15.7325
(.(((((........)))))))	chr16:70714618-70714842(-)$1	1	5	27	13.8398
(.(((.(........).))).)	chr19:49403979-49404214(+)$1	1	195	217	14.6574
.((.(((........))).)).	chr6:21595801-21596074(+)$1	1	66	88	15.5490
(.(((((........))))).)	chrX:70472879-70473103(-)$1	1	40	62	13.9564
(((((.(........).)))))	chr9:117826075-117826306(-)$1	1	74	96	14.2537
.((.(((........))))).)	chr10:71992934-71993183(-)$1	1	179	201	15.1737
((..(((........)))...)	chr9:135985748-135985973(-)$1	1	79	101	16.3750
(((.(((........))).)))	chr5:179247872-179248163(+)$1	1	140	162	16.0011
(((((.(........).)))))	chr17:76219941-76220177(+)$1	1	120	142	14.1997
((.((((........))))...	chr20:37580992-37581215(+)$1	1	138	160	14.4107
(((.(((........)))))))	chr6:24701694-24701920(+)$1	1	78	100	15.7530
((...((........))..)))	chr1:91406575-91406798(-)$1	1	160	182	14.7699
..(((((........)))))..	chr19:52090124-52090348(+)$1	1	9	31	13.6192
..((.((........)).)).)	chr19:2269434-2269681(+)$1	1	92	114	14.5730
.(((.((........))..)))	chr1:245019254-245019522(-)$1	1	106	128	13.9286
..(((((........))))).)	chr3:169496465-169496685(+)$1	1	35	57	14.4585
(..((((........))))...	chr16:47536801-47537034(+)$1	1	76	98	14.7107
((.((((........)))).))	chrX:133609234-133609466(+)$1	1	107	129	13.9256
.(((.((........).).)))	chr22:38694722-38694964(-)$1	1	149	171	15.1444
.((..((........))..)).	chr19:13051032-13051287(+)$1	1	76	98	14.6909
(((.(((........))).)))	chr17:76967818-76968060(-)$1	1	123	145	15.7152
.((((((........)))))).	chr17:73234068-73234296(-)$1	1	106	128	14.6293
(((((.(........).)))).	chr14:53148957-53149187(-)$1	1	102	124	13.6557
(((((((........)).))))	chr19:39923851-39924110(-)$1	1	160	182	14.5347
(...(((........)))...)	chr1:113456485-113456752(-)$1	1	220	242	16.4374
..(.(((........))))..)	chr19:4409208-4409447(+)$1	1	44	66	15.6965
.((((((........)))))).	chr6:43472501-43472725(+)$1	1	123	145	14.5471
((...((........))..)))	chr1:85395161-85395386(-)$1	1	95	117	14.1590
((((.((........)).))).	chrX:84502486-84502709(+)$1	1	104	126	14.8823
(((((((........)).))))	chr21:28212224-28212456(-)$1	1	198	220	14.5347
(((((((........))).)))	chr17:49233003-49233235(+)$1	1	115	137	15.4194
...((((........))))..)	chr5:1463680-1463901(-)$1	1	124	146	14.1493
..(.(((........))).)..	chr10:96334245-96334470(+)$1	1	16	38	13.6708
(((((((........))).)).	chr7:100279395-100279628(-)$1	1	92	114	14.7664
(.((.((........)))).))	chr18:33706250-33706472(-)$1	1	173	195	13.8999
(((((((........))))).)	chr21:28216749-28216992(-)$1	1	195	217	13.6485
((.((((........)))).))	chr12:106633623-106633860(-)$1	1	149	171	14.1406
.((((((........)))))).	chr20:31946758-31946982(-)$1	1	169	191	14.4280
.((((((........)))))))	chr19:55998477-55998734(+)$1	1	14	36	14.1885
(((((((........)))))))	chr3:101476972-101477198(+)$1	1	102	124	14.6288
.((((((........)).))))	chr1:62916065-62916289(+)$1	1	170	192	14.0002
.((((((........))))))(	chr11:93474432-93474659(-)$1	1	165	187	13.4070

#PSSM
e : 0.16	c : 0.12	f : 0.10	! : 0.10	[ : 0.09	d : 0.07	b : 0.07	" : 0.06	g : 0.04	: : 0.04	i : 0.03	# : 0.03	C : 0.01	a : 0.01	& : 0.01	
f : 0.16	c : 0.16	e : 0.13	b : 0.10	! : 0.09	" : 0.07	[ : 0.07	g : 0.04	i : 0.03	# : 0.03	d : 0.03	a : 0.01	: : 0.01	& : 0.01	
e : 0.21	f : 0.13	c : 0.12	b : 0.12	" : 0.10	[ : 0.07	! : 0.06	g : 0.04	a : 0.04	i : 0.03	d : 0.03	# : 0.01	
[ : 0.21	e : 0.18	f : 0.12	d : 0.12	" : 0.10	c : 0.07	! : 0.06	b : 0.06	a : 0.03	i : 0.01	g : 0.01	
c : 0.37	e : 0.15	[ : 0.12	f : 0.12	d : 0.12	" : 0.04	! : 0.03	i : 0.01	g : 0.01	
c : 0.36	b : 0.22	f : 0.10	e : 0.10	d : 0.09	[ : 0.06	i : 0.01	a : 0.01	g : 0.01	
c : 0.36	b : 0.22	f : 0.10	e : 0.10	d : 0.09	a : 0.07	i : 0.01	g : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.36	b : 0.22	f : 0.10	e : 0.10	d : 0.09	a : 0.07	i : 0.01	g : 0.01	
c : 0.36	b : 0.22	f : 0.10	e : 0.10	d : 0.09	] : 0.07	i : 0.01	g : 0.01	
c : 0.37	] : 0.12	f : 0.12	e : 0.12	d : 0.10	2 : 0.06	3 : 0.01	i : 0.01	4 : 0.01	a : 0.01	b : 0.01	g : 0.01	
] : 0.19	e : 0.16	d : 0.13	f : 0.12	2 : 0.10	c : 0.07	b : 0.06	3 : 0.04	a : 0.03	g : 0.03	i : 0.01	4 : 0.01	
e : 0.21	f : 0.15	b : 0.13	c : 0.12	2 : 0.07	3 : 0.06	g : 0.04	a : 0.04	d : 0.04	] : 0.04	i : 0.03	4 : 0.03	
f : 0.18	e : 0.15	] : 0.12	c : 0.12	b : 0.09	2 : 0.06	d : 0.06	3 : 0.06	g : 0.04	i : 0.03	4 : 0.03	a : 0.01	6 : 0.01	5 : 0.01	
e : 0.18	c : 0.10	] : 0.09	d : 0.09	f : 0.07	g : 0.07	2 : 0.07	3 : 0.07	b : 0.07	: : 0.03	i : 0.03	4 : 0.03	J : 0.01	a : 0.01	6 : 0.01	5 : 0.01	

#score	972.903723057075
#seq	66
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m3_run1.txt

#BEAR
##cccnnnnncccee	chr1:87811786-87812021(-)$1	235	49	64	10.6615
a[cccnnnnnccc]a	chr14:102695464-102695689(+)$1	225	16	31	10.3960
eeeeennnnneeeee	chr1:36786725-36786947(+)$1	222	195	210	10.3801
:ddddnnnnndddd:	chr6:154722272-154722495(+)$1	223	57	72	10.3099
$$cccnnnnnccc22	chr1:240075830-240076051(+)$1	221	58	73	10.0862
!!cccnnnnnccc]e	chr12:510633-510856(-)$1	223	110	125	10.7734
"ddddnnnnndddd5	chr3:10322234-10322460(-)$1	226	128	143	11.5671
ddcccnnnnnccc33	chr19:35451125-35451348(+)$1	223	94	109	10.6361
b[cccnnnnnccc]b	chr6:33739885-33740107(-)$1	222	16	31	9.7664
:ddddnnnnndddd:	chr17:30817117-30817343(-)$1	226	209	224	10.3099
[ddddnnnnnddddb	chr22:44893447-44893671(+)$1	224	90	105	11.7674
ccc[annnnna]ccc	chr16:87731081-87731304(-)$1	223	175	190	9.6000
%ddddnnnnndddde	chr2:232264212-232264433(+)$1	221	55	70	11.5463
bddddnnnnndddd]	chr20:19702676-19702898(-)$1	222	77	92	11.7378
!ddddnnnnndddd2	chr5:43040735-43040960(+)$1	225	48	63	12.2516
""cccnnnnnccc]c	chr16:1203170-1203407(-)$1	237	4	19	10.5367
eeeeennnnneeeee	chr12:52563039-52563266(+)$1	227	126	141	10.3801
eeeeennnnneeeee	chr14:74167258-74167481(+)$1	223	40	55	10.3801
ccc[annnnna]ccc	chr10:95076419-95076641(-)$1	222	6	21	9.6000
[ddddnnnnndddd]	chr5:31553756-31553977(+)$1	221	107	122	12.2814
!ddddnnnnndddd2	chr21:40817468-40817689(+)$1	221	66	81	12.2516
!!cccnnnnncccdd	chr6:110797725-110797947(+)$1	222	103	118	10.8894
""cccnnnnnccc22	chr1:57460740-57460965(+)$1	225	166	181	10.5143
eeeeennnnneeeee	chr15:101812793-101813015(+)$1	222	188	203	10.3801
eeeeennnnneeeee	chr5:54683750-54683972(+)$1	222	26	41	10.3801
"ddddnnnnnddddd	chrX:106039833-106040058(+)$1	225	29	44	11.9929
!ddddnnnnndddd2	chrX:110187705-110187927(+)$1	222	92	107	12.2516
ffcccnnnnnccc22	chr11:67373993-67374222(-)$1	229	172	187	9.8899
ggg[annnnna]ggg	chr11:58939846-58940070(+)$1	224	44	59	9.3017
eeeeennnnneeeee	chr11:118926886-118927108(-)$1	222	56	71	10.3801
%ddddnnnnndddd4	chr16:9211410-9211641(-)$1	231	28	43	11.6967
eee[annnnna]eee	chr13:52026850-52027071(+)$1	221	71	86	9.9557
:ddddnnnnndddd:	chr10:37890564-37890785(-)$1	221	16	31	10.3099
!ddddnnnnndddd2	chr14:59950503-59950724(+)$1	221	46	61	12.2516
dddbbnnnnnbb]dd	chr17:40761577-40761802(-)$1	225	111	126	8.9370
eeeeennnnneeeee	chr1:149870999-149871220(-)$1	221	184	199	10.3801
eeeeennnnneeeee	chr1:233120954-233121177(-)$1	223	16	31	10.3801
##cccnnnnncccee	chr10:6104116-6104340(+)$1	224	78	93	10.6615
[ddddnnnnnddddf	chr12:102472714-102472940(-)$1	226	197	212	11.9250
!ddddnnnnndddd3	chr3:69024376-69024597(-)$1	221	158	173	12.3983
c[cccnnnnnccc]c	chr19:11032192-11032413(-)$1	221	54	69	10.2246
[ddddnnnnndddd]	chr4:184210575-184210799(+)$1	224	155	170	12.2814
eeeeennnnneeeee	chr22:38453121-38453348(-)$1	227	188	203	10.3801
dddddnnnnndddd4	chr9:112629247-112629469(-)$1	222	146	161	11.8382
fddddnnnnndddd:	chr1:228594170-228594397(+)$1	227	205	220	10.9385
eeeeennnnneeeee	chrX:99664507-99664730(+)$1	223	130	145	10.3801
eddddnnnnndddd]	chr2:100894968-100895191(-)$1	223	110	125	11.9825
fddddnnnnndddd>	chr12:133297384-133297605(-)$1	221	28	43	11.5987
!!cccnnnnncccdd	chr12:109928492-109928721(-)$1	229	161	176	10.8894
ddcccnnnnnccc]d	chrX:24578148-24578372(+)$1	224	134	149	10.3276
eeeeennnnneeeee	chr20:60697604-60697828(-)$1	224	16	31	10.3801
[ddddnnnnndddd]	chr2:131096127-131096351(+)$1	224	202	217	12.2814
[ddddnnnnndddd]	chr3:65346259-65346481(+)$1	222	31	46	12.2814
!ddddnnnnndddd4	chr10:125651072-125651293(-)$1	221	134	149	12.3158
[ddddnnnnndddd]	chr2:20401465-20401688(+)$1	223	118	133	12.2814
[ddddnnnnndddd]	chrX:53221833-53222068(-)$1	235	107	122	12.2814
:ddddnnnnnddddc	chr1:202564542-202564764(+)$1	222	161	176	10.9586

#otherMatches

#Seq PSSM
CUGUGGUGGACACUC	chr1:87811786-87812021(-)$1	235	49	64	10.6615
CAGGGCAGCACCCAG	chr14:102695464-102695689(+)$1	225	16	31	10.3960
GGCCAACAUGUGGCU	chr1:36786725-36786947(+)$1	222	195	210	10.3801
auucaucuguugaaa	chr6:154722272-154722495(+)$1	223	57	72	10.3099
AGCUGGAGCACAGAG	chr1:240075830-240076051(+)$1	221	58	73	10.0862
AAGUUUACAUGGCCC	chr12:510633-510856(-)$1	223	110	125	10.7734
AGAUAGGAAAUAUUA	chr3:10322234-10322460(-)$1	226	128	143	11.5671
UCUCCAACUGGGAAA	chr19:35451125-35451348(+)$1	223	94	109	10.6361
CAAGCGUGGGGCUGG	chr6:33739885-33740107(-)$1	222	16	31	9.7664
CGGCCGGGCAGGCUC	chr17:30817117-30817343(-)$1	226	209	224	10.3099
ACGGCAGGGCGCUGC	chr22:44893447-44893671(+)$1	224	90	105	11.7674
UGCACGCCAAGCGCA	chr16:87731081-87731304(-)$1	223	175	190	9.6000
UCUGACUACCUCAGC	chr2:232264212-232264433(+)$1	221	55	70	11.5463
CUGUAACUCCUGCAU	chr20:19702676-19702898(-)$1	222	77	92	11.7378
UUCAAUGUGUUUGAU	chr5:43040735-43040960(+)$1	225	48	63	12.2516
Ucggcgcccggcccc	chr16:1203170-1203407(-)$1	237	4	19	10.5367
ACCAGCUGCACUGGU	chr12:52563039-52563266(+)$1	227	126	141	10.3801
CUUAAAAGCAUUAGG	chr14:74167258-74167481(+)$1	223	40	55	10.3801
GCUGUCUUAAGGAGC	chr10:95076419-95076641(-)$1	222	6	21	9.6000
UGGUUGAGUAAACUU	chr5:31553756-31553977(+)$1	221	107	122	12.2814
ACCGGCGAUACUGGA	chr21:40817468-40817689(+)$1	221	66	81	12.2516
UAGCGCGCCCCGCCC	chr6:110797725-110797947(+)$1	222	103	118	10.8894
AGGAUGAGGAAUUAA	chr1:57460740-57460965(+)$1	225	166	181	10.5143
UCAUCCGCCAGAUGA	chr15:101812793-101813015(+)$1	222	188	203	10.3801
GAACAUCUUCUGUUU	chr5:54683750-54683972(+)$1	222	26	41	10.3801
AUUAGAUAAACUAAA	chrX:106039833-106040058(+)$1	225	29	44	11.9929
AAGGGCAGAACCCUC	chrX:110187705-110187927(+)$1	222	92	107	12.2516
CCUGCGGUAUGCAUC	chr11:67373993-67374222(-)$1	229	172	187	9.8899
GGUGGAUGCACGGCU	chr11:58939846-58940070(+)$1	224	44	59	9.3017
GAUUAGAGAAUGGUU	chr11:118926886-118927108(-)$1	222	56	71	10.3801
AGGAAGCCCAUUCUC	chr16:9211410-9211641(-)$1	231	28	43	11.6967
CCGUCUGUCUGUCGG	chr13:52026850-52027071(+)$1	221	71	86	9.9557
AUUCAACCUCUGAAC	chr10:37890564-37890785(-)$1	221	16	31	10.3099
ACGCUGUGGAAGCGC	chr14:59950503-59950724(+)$1	221	46	61	12.2516
GCCGCAAGACGCAGG	chr17:40761577-40761802(-)$1	225	111	126	8.9370
CCACUGGUAAGGUGG	chr1:149870999-149871220(-)$1	221	184	199	10.3801
CACUCCUUUUGAGUG	chr1:233120954-233121177(-)$1	223	16	31	10.3801
UUGGCAUCGCGCCGG	chr10:6104116-6104340(+)$1	224	78	93	10.6615
UAUCUCCCACAGAUG	chr12:102472714-102472940(-)$1	226	197	212	11.9250
GGAUGUAUUUCAUUG	chr3:69024376-69024597(-)$1	221	158	173	12.3983
UGAACUGGCUGUUGA	chr19:11032192-11032413(-)$1	221	54	69	10.2246
ACCAGGCGUGCUGGA	chr4:184210575-184210799(+)$1	224	155	170	12.2814
CAGCUUCCUCAGCUG	chr22:38453121-38453348(-)$1	227	188	203	10.3801
AGAUUUAUUUGAUCA	chr9:112629247-112629469(-)$1	222	146	161	11.8382
GGGGCGCGAGGCUCG	chr1:228594170-228594397(+)$1	227	205	220	10.9385
GGCGGGGCCGCCGCC	chrX:99664507-99664730(+)$1	223	130	145	10.3801
cguuugguugaaaca	chr2:100894968-100895191(-)$1	223	110	125	11.9825
GUCAGGCUGUCUGAU	chr12:133297384-133297605(-)$1	221	28	43	11.5987
ACGAGGUUAACUCUA	chr12:109928492-109928721(-)$1	229	161	176	10.8894
GCCUUCCCAAGAGAG	chrX:24578148-24578372(+)$1	224	134	149	10.3276
GGUGUAGAGAAUGCC	chr20:60697604-60697828(-)$1	224	16	31	10.3801
UGAAGCGCUACUUCC	chr2:131096127-131096351(+)$1	224	202	217	12.2814
UAACAGUUUUUGUUU	chr3:65346259-65346481(+)$1	222	31	46	12.2814
CCGCUACCCCAGCGC	chr10:125651072-125651293(-)$1	221	134	149	12.3158
GGCUGAGUCCCAGCA	chr2:20401465-20401688(+)$1	223	118	133	12.2814
UGGGGGCCGGCCCCU	chrX:53221833-53222068(-)$1	235	107	122	12.2814
ACCUGGACCUCAGGA	chr1:202564542-202564764(+)$1	222	161	176	10.9586

#DB
..(((.....)))))	chr1:87811786-87812021(-)$1	1	49	64	10.6615
(.(((.....))).)	chr14:102695464-102695689(+)$1	1	16	31	10.3960
(((((.....)))))	chr1:36786725-36786947(+)$1	1	195	210	10.3801
.((((.....)))).	chr6:154722272-154722495(+)$1	1	57	72	10.3099
..(((.....)))..	chr1:240075830-240076051(+)$1	1	58	73	10.0862
..(((.....))).)	chr12:510633-510856(-)$1	1	110	125	10.7734
.((((.....)))).	chr3:10322234-10322460(-)$1	1	128	143	11.5671
(((((.....)))..	chr19:35451125-35451348(+)$1	1	94	109	10.6361
(.(((.....))).)	chr6:33739885-33740107(-)$1	1	16	31	9.7664
.((((.....)))).	chr17:30817117-30817343(-)$1	1	209	224	10.3099
.((((.....)))))	chr22:44893447-44893671(+)$1	1	90	105	11.7674
(((.(.....).)))	chr16:87731081-87731304(-)$1	1	175	190	9.6000
.((((.....)))))	chr2:232264212-232264433(+)$1	1	55	70	11.5463
(((((.....)))).	chr20:19702676-19702898(-)$1	1	77	92	11.7378
.((((.....)))).	chr5:43040735-43040960(+)$1	1	48	63	12.2516
..(((.....))).)	chr16:1203170-1203407(-)$1	1	4	19	10.5367
(((((.....)))))	chr12:52563039-52563266(+)$1	1	126	141	10.3801
(((((.....)))))	chr14:74167258-74167481(+)$1	1	40	55	10.3801
(((.(.....).)))	chr10:95076419-95076641(-)$1	1	6	21	9.6000
.((((.....)))).	chr5:31553756-31553977(+)$1	1	107	122	12.2814
.((((.....)))).	chr21:40817468-40817689(+)$1	1	66	81	12.2516
..(((.....)))))	chr6:110797725-110797947(+)$1	1	103	118	10.8894
..(((.....)))..	chr1:57460740-57460965(+)$1	1	166	181	10.5143
(((((.....)))))	chr15:101812793-101813015(+)$1	1	188	203	10.3801
(((((.....)))))	chr5:54683750-54683972(+)$1	1	26	41	10.3801
.((((.....)))))	chrX:106039833-106040058(+)$1	1	29	44	11.9929
.((((.....)))).	chrX:110187705-110187927(+)$1	1	92	107	12.2516
(((((.....)))..	chr11:67373993-67374222(-)$1	1	172	187	9.8899
(((.(.....).)))	chr11:58939846-58940070(+)$1	1	44	59	9.3017
(((((.....)))))	chr11:118926886-118927108(-)$1	1	56	71	10.3801
.((((.....)))).	chr16:9211410-9211641(-)$1	1	28	43	11.6967
(((.(.....).)))	chr13:52026850-52027071(+)$1	1	71	86	9.9557
.((((.....)))).	chr10:37890564-37890785(-)$1	1	16	31	10.3099
.((((.....)))).	chr14:59950503-59950724(+)$1	1	46	61	12.2516
(((((.....)).))	chr17:40761577-40761802(-)$1	1	111	126	8.9370
(((((.....)))))	chr1:149870999-149871220(-)$1	1	184	199	10.3801
(((((.....)))))	chr1:233120954-233121177(-)$1	1	16	31	10.3801
..(((.....)))))	chr10:6104116-6104340(+)$1	1	78	93	10.6615
.((((.....)))))	chr12:102472714-102472940(-)$1	1	197	212	11.9250
.((((.....)))).	chr3:69024376-69024597(-)$1	1	158	173	12.3983
(.(((.....))).)	chr19:11032192-11032413(-)$1	1	54	69	10.2246
.((((.....)))).	chr4:184210575-184210799(+)$1	1	155	170	12.2814
(((((.....)))))	chr22:38453121-38453348(-)$1	1	188	203	10.3801
(((((.....)))).	chr9:112629247-112629469(-)$1	1	146	161	11.8382
)((((.....)))).	chr1:228594170-228594397(+)$1	1	205	220	10.9385
(((((.....)))))	chrX:99664507-99664730(+)$1	1	130	145	10.3801
(((((.....)))).	chr2:100894968-100895191(-)$1	1	110	125	11.9825
(((((.....)))).	chr12:133297384-133297605(-)$1	1	28	43	11.5987
..(((.....)))))	chr12:109928492-109928721(-)$1	1	161	176	10.8894
(((((.....))).)	chrX:24578148-24578372(+)$1	1	134	149	10.3276
(((((.....)))))	chr20:60697604-60697828(-)$1	1	16	31	10.3801
.((((.....)))).	chr2:131096127-131096351(+)$1	1	202	217	12.2814
.((((.....)))).	chr3:65346259-65346481(+)$1	1	31	46	12.2814
.((((.....)))).	chr10:125651072-125651293(-)$1	1	134	149	12.3158
.((((.....)))).	chr2:20401465-20401688(+)$1	1	118	133	12.2814
.((((.....)))).	chrX:53221833-53222068(-)$1	1	107	122	12.2814
.((((.....))))(	chr1:202564542-202564764(+)$1	1	161	176	10.9586

#PSSM
e : 0.22	! : 0.15	[ : 0.14	: : 0.07	" : 0.07	d : 0.07	c : 0.05	f : 0.05	# : 0.03	b : 0.03	% : 0.03	a : 0.01	$ : 0.01	g : 0.01	
d : 0.52	e : 0.21	[ : 0.05	! : 0.05	# : 0.03	c : 0.03	" : 0.03	$ : 0.01	f : 0.01	g : 0.01	
d : 0.49	c : 0.28	e : 0.21	g : 0.01	
d : 0.47	c : 0.24	e : 0.19	[ : 0.07	b : 0.01	
d : 0.47	c : 0.24	e : 0.19	a : 0.07	b : 0.01	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
n : 1.00	
d : 0.47	c : 0.24	e : 0.19	a : 0.07	b : 0.01	
d : 0.47	c : 0.24	e : 0.19	] : 0.07	b : 0.01	
d : 0.47	c : 0.28	e : 0.21	g : 0.01	] : 0.01	
d : 0.52	e : 0.24	] : 0.10	2 : 0.05	c : 0.03	3 : 0.01	g : 0.01	
e : 0.28	] : 0.14	2 : 0.12	c : 0.08	d : 0.08	: : 0.07	4 : 0.05	3 : 0.03	b : 0.03	a : 0.01	5 : 0.01	g : 0.01	f : 0.01	> : 0.01	

#score	625.7194651354126
#seq	57
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m2_run1.txt

#BEAR
$$$$$cccdddd[ddddoooooodddd]dddd333ccc4	chr16:31770987-31771203(-)$1	216	78	117	13.3579
ggggggg%%%%%%a[cccooooooccc]a333ggggggg	chr12:54352140-54352355(-)$1	215	12	51	12.8997
!ccc!!ccc[dddd[ddddllldddd]dddd]cccccc3	chr18:9136735-9136952(+)$1	217	112	151	12.3312
ccc!!ccc!!eeeeeddddmmmmdddd333eeeee]ccc	chr3:49572392-49572613(+)$1	221	164	203	13.3239
[ccceeeee"""ccc[ccclllcccccceeeee]ccc]d	chr2:202558655-202558871(-)$1	216	33	72	12.3593
[ccc[dddd!!ccc[cccmmmmccc22ccc333dddd]c	chr9:129645217-129645435(+)$1	218	115	154	11.9938
ccc"""============nnnnn============ccc:	chr19:47112989-47113214(+)$1	225	106	145	13.9377
ccc[dddd[a[dddd"""ccclllccc333dddd]addd	chr5:36102960-36103185(-)$1	225	143	182	11.9910
gggggg[ffffff!!cccooooooccc]ffffff]gggg	chr5:175487666-175487893(+)$1	227	7	46	14.8588
===========[bb[cccooooooccc]bb22=======	chr4:158286801-158287029(+)$1	228	98	137	15.5647
====================mmmm===============	chr2:113096243-113096488(+)$1	245	182	221	14.4294
!!ccc[a[bb[ddddcccmmmmccc]dddd]bb]accc]	chr13:47408549-47408776(-)$1	227	135	174	11.3577
[accc!!ggggggg[cccooooooccc]ggggggg333c	chr5:78618645-78618885(-)$1	240	33	72	16.9527
=ccc"""============nnnnn============ccc	chr19:47112935-47113162(+)$1	227	159	198	14.6697
""ccc####iiiiiiiiillliiiiiiiiiccc333hhh	chr16:69732736-69732960(+)$1	224	180	219	13.5909
!ccc[ccc[a[ccc[cccooooooccc333ccc]acccc	chr4:905695-905921(-)$1	226	101	140	18.7805
eee[dddd[ccc"""ddddmmmmdddd333ccc333ddd	chr19:11562344-11562561(-)$1	217	33	72	13.8303
b####ccc"""cccssssssssssccc333ccc333bb2	chrX:154686776-154687002(-)$1	226	125	164	12.2526
c%%%%%%ccc[cccddddoooooodddd]cccccc333c	chr17:36347526-36347760(-)$1	234	9	48	12.4347
gg####ccc"""eeeeennnnneeeee333ccc333ggg	chr8:133139378-133139593(-)$1	215	163	202	13.4839
d[bb!!ccc[bb"""ddddmmmmdddd333bb333ccc2	chr4:38628215-38628436(-)$1	221	174	213	13.5142
[ccc####ccc[bb[eeeeellleeeee333bb]ccc33	chr5:154196784-154197006(+)$1	222	158	197	12.5663
!ffffffccc[a!!ddddoooooodddd22a]ccc9999	chr11:98891792-98892020(+)$1	228	168	207	11.2099
3cccccc[iiiiiiiiicccmmmmccc]iiiiiiiii22	chr15:68583501-68583721(+)$1	220	134	173	12.8974
eeee[bb[ccc$$$$$cccmmmmccc4444ccc22bbee	chr12:16052748-16052971(+)$1	223	119	158	11.6918
::ffffffffffff"""aooooooa4444ffffff333f	chr2:128928781-128928996(-)$1	215	51	90	11.6094
fffffbb!!iiiiiiiiiooooooiiiiiiiii22bb]f	chr6:170884380-170884600(+)$1	220	98	137	13.7787
ggggggg"""eeeeeccc!!aooooooa22ccc]eeeee	chr1:43917668-43917897(+)$1	229	72	111	11.6298
b"""iiiiiiiii!!cccooooooccc22iiiiiiiii2	chr19:36642338-36642572(+)$1	234	153	192	16.9425
gggg[ccc!!gggggggooooooggggggg]ccc]gggg	chr7:100277408-100277638(-)$1	230	183	222	14.7238
h$$$$$dddd$$$$$cccooooooccc4444dddd333h	chr16:69149865-69150093(-)$1	228	46	85	14.2932
ee"""ccc[eeeee[ddddmmmmdddd]eeeee]ccc33	chr2:199011727-199011958(+)$1	231	157	196	12.4811
iiiiiiiii!!ccc!!annnnna22ccc4444iiiiiii	chr1:38273584-38273808(+)$1	224	147	186	13.1911
ccc"""dddd[ffffffooooooffffff]dddd333cc	chr17:4619007-4619228(+)$1	221	153	192	12.9548
!!ddddiiiiiiiii[aooooooa]iiiiiiiii333dd	chr9:137298956-137299179(+)$1	223	107	146	14.9308
FFFiiiiiiiii[ddddoooooodddd333iiiiiiiii	chr6:33540377-33540594(+)$1	217	147	186	14.5031
ddhhhhhhhh[ccc[cccooooooccc]ccc]hhhhhhh	chr5:175808770-175808998(+)$1	228	105	144	13.1133
ggg!!ffffffccc[ccclllccc]ccc333ffffff]g	chr1:120535985-120536205(-)$1	220	120	159	12.7968
fffff[ccc!!ddddrrrrrrrrrdddd22ccc]fffff	chr3:182733072-182733291(-)$1	219	15	54	10.9611
iiiiiiii"""ccc!!ddddmmmmdddd]ccc4444iii	chr14:25288528-25288743(+)$1	215	130	169	13.6944
[dddd!!ccc[ffffffooooooffffffcccddddccc	chr2:74724816-74725036(+)$1	220	109	148	11.8887
[ccc[a####==========lll==========a]ccce	chr1:72400782-72400999(-)$1	217	46	85	14.9427
ddd[ffffffccc"""bboooooobb4444ccc]fffff	chr17:44051357-44051581(+)$1	224	112	151	13.4571
hhh"""dddd[gggggggoooooogggggggdddd]hhh	chr3:131104418-131104646(+)$1	228	178	217	13.1483
ggggggdddd[ccc[cccnnnnnccc333ccc22ddddB	chr7:6443408-6443628(-)$1	220	144	183	12.4678
!!ddddaggggggg!!cccmmmmcccggggggg]a]ddd	chr4:77969184-77969399(-)$1	215	33	72	12.7323
gcccbbffffff"""cccooooooccc333ffffff22b	chr11:74914209-74914427(+)$1	218	11	50	14.6178
::::dddd"""ccc[cccooooooccc22ccc333dddd	chr13:114111050-114111279(-)$1	229	92	131	12.7244
iiiiiiii[a[bb[a[ddddmmmmdddd]a]bb]a]iii	chr7:44869217-44869438(-)$1	221	93	132	12.0142
[a[a"""ggggggg[ddddmmmmdddd]gggggggaa]=	chr1:162498208-162498443(+)$1	235	15	54	13.7145
!!eeeeeacccddddrrrrrrrrrdddd]ccc333a]ee	chr17:3909999-3910228(-)$1	229	9	48	10.9504
ccc:ffffff[ccc[cccooooooccc]cccffffffEE	chr17:30520150-30520368(+)$1	218	104	143	11.9001
bb!!ccc!!dddd!!ddddmmmmdddd22dddd22ccc2	chr3:169511100-169511319(-)$1	219	59	98	12.1611
==####ccc!!ddddcccooooooccc]dddd]ccc]==	chr7:30407203-30407434(+)$1	231	14	53	15.7074
ggggg"""eeeeeccccccmmmmccc4444ccc]eeeee	chr11:11984554-11984780(-)$1	226	20	59	13.2413
::dddd!!eeeee####aooooooa4444eeeee22ddd	chr16:16313381-16313596(-)$1	215	120	159	11.3575

#otherMatches

#Seq PSSM
CAUAACUGAGGAAUAGAACCAGCUUUACUCCUACCCAGA	chr16:31770987-31771203(-)$1	216	78	117	13.3579
GGGGUACAGUGGGUGACCAGUCAAGGUGGGGAGUGCUUC	chr12:54352140-54352355(-)$1	215	12	51	12.8997
AGCCCGGCUCCGGCGGCUUUACAGGCGGCUGCAGCGGCG	chr18:9136735-9136952(+)$1	217	112	151	12.3312
GGACCACUGGUGACUGGGCUCAUGCCUCCAAGUCAGAGU	chr3:49572392-49572613(+)$1	221	164	203	13.3239
AUCCCAGUGUGUAGCACAGGGCCUGGCUUGCUGAGGAAA	chr2:202558655-202558871(-)$1	216	33	72	12.3593
CUGAAGCACUUGUUCAACUCCUGUUAAAGCCGCGUGCCU	chr9:129645217-129645435(+)$1	218	115	154	11.9938
GAGGUUUGGCUGGGUGGGGACUGCUCAUUUGGCCACUCU	chr19:47112989-47113214(+)$1	225	106	145	13.9377
AAGUGAACAUGUUUGAUUGCAGCAUGCUUGCAGAGAGUU	chr5:36102960-36103185(-)$1	225	143	182	11.9910
GGGGCCAGCCGCCCAGGCAGCAAAGUCAGGCGGUCGGCU	chr5:175487666-175487893(+)$1	227	7	46	14.8588
GGUUUUUUUAUUCAUUUUAUAUAAAAACUGUUAUGGAAA	chr4:158286801-158287029(+)$1	228	98	137	15.5647
auguguguauauauauauauauauauauauauauauaua	chr2:113096243-113096488(+)$1	245	182	221	14.4294
UUGCUGCUAUGCUGUUCAUUGAUGACAUGGGAUUGAGUU	chr13:47408549-47408776(-)$1	227	135	174	11.3577
UCCCUAAUUAUUUUCAAGAAAACACUUUAAAAUAACAAA	chr5:78618645-78618885(-)$1	240	33	72	16.9527
UGAGGUUUGGCUGGGUGGGGACUGCUCAUUUGGCCACUC	chr19:47112935-47113162(+)$1	227	159	198	14.6697
UGUAAAAUUCUAACCCUAAAGUAGGGUUGGUUGAAAUUU	chr16:69732736-69732960(+)$1	224	180	219	13.5909
CAGGUGUGUGUGGCCGGUGUGCCUGCCUUUGUCCCCGCC	chr4:905695-905921(-)$1	226	101	140	18.7805
UGGAGGCCAGCCCCUCCCCGCAGGGGGCCAGGCCGGGGC	chr19:11562344-11562561(-)$1	217	33	72	13.8303
GACAUGAAAAUGACAAUCCCUUUCGUCUCCUUCCUCCGC	chrX:154686776-154687002(-)$1	226	125	164	12.2526
AGGAAAAUGAAGCCUCCUCCUGUUGGGACGGCUCAGAAU	chr17:36347526-36347760(-)$1	234	9	48	12.4347
GACAAAGGGCAUGGGUUAUUUGGGCCUUUUCCCCACUCC	chr8:133139378-133139593(-)$1	215	163	202	13.4839
aagggggguggaucaccugaggucaggaauucgagacca	chr4:38628215-38628436(-)$1	221	174	213	13.5142
CUUUACUAUGUGCUAGGAUAUCAUAUUUAAAAGGACAAA	chr5:154196784-154197006(+)$1	222	158	197	12.5663
GAGUCACAGAGGAAGGACAGUGGAGUCUGGCAUCUUAUU	chr11:98891792-98892020(+)$1	228	168	207	11.2099
UCACAGACAGUAGAAUUAUGUGUUCAUAAAUUCUGCUUU	chr15:68583501-68583721(+)$1	220	134	173	12.8974
ACUGUGUGAGAUUUAGUCCUGAUGGAGAACUCUAUGCCA	chr12:16052748-16052971(+)$1	223	119	158	11.6918
UAAAUCCAUCUGAUCCUCUAACAUGCAAUAUCAGAACUU	chr2:128928781-128928996(-)$1	215	51	90	11.6094
UGCUGCUCUCUACAGCAGAGGGAGCUGCUGUGGCUGGAC	chr6:170884380-170884600(+)$1	220	98	137	13.7787
GUCAGUCACUGGUCAAGGCCCUCACCUGUUCCUCUGACC	chr1:43917668-43917897(+)$1	229	72	111	11.6298
CUUAGAGCGCGCCCCGCCUGCCCCGGCUCGGCGCGCUCC	chr19:36642338-36642572(+)$1	234	153	192	16.9425
GAGGCCUUAACCCUGUGAGGAAGUAUAGGGGGAGCCCUC	chr7:100277408-100277638(-)$1	230	183	222	14.7238
AUUCAAGAGUAUACAGGUUAAAAUACCCAAGACUUCACU	chr16:69149865-69150093(-)$1	228	46	85	14.2932
CUGAGACAUGUGUCAACACCCCUGUGUGGAUGCCUGUGG	chr2:199011727-199011958(+)$1	231	157	196	12.4811
ccggAGCGGGACUCGGCGGGCGGAAGAGGCGACCGCUCC	chr1:38273584-38273808(+)$1	224	147	186	13.1911
CUGAUAGCCCAGCCUGGAGAUCCCCGGGCAGGGCAGCCA	chr17:4619007-4619228(+)$1	221	153	192	12.9548
AACUCUUCCUGUCCCGUGAGAAGGGGGGAUGGGAUUUGG	chr9:137298956-137299179(+)$1	223	107	146	14.9308
GGGUGGGGGAACAGAGUUCAAGUAUUCACAGUUCCCCCA	chr6:33540377-33540594(+)$1	217	147	186	14.5031
GGAGGUGAACUUGAAGAAUAAAGUUUCAUUAUGUUUACU	chr5:175808770-175808998(+)$1	228	105	144	13.1133
CAAAGGAUACUGUAGUCACUGUGAGUAUUUUAGUAUUAU	chr1:120535985-120536205(-)$1	220	120	159	12.7968
CCUUUAGUCGAGUUUGAGGAGGAAGAAUCAGACAAAAGG	chr3:182733072-182733291(-)$1	219	15	54	10.9611
UCCAUUCUGCCAGUAUUCUAUCUGUGGAGGCUCAAAAGG	chr14:25288528-25288743(+)$1	215	130	169	13.6944
CGUCUGGACUGUGGGCCGGAAGAGGCCCAAGUGGACCUC	chr2:74724816-74725036(+)$1	220	109	148	11.8887
ACCGGUCAAGUAUUAUUUUUGCGGGAGGUGAUAAGUGGU	chr1:72400782-72400999(-)$1	217	46	85	14.9427
CCCAGCAGUCUGUUUCACUGCAGCGUUUACACAGGGCUG	chr17:44051357-44051581(+)$1	224	112	151	13.4571
AGGAAAUGGACAUUCCAGUGGCCCCUGGGGUUCCAGCCU	chr3:131104418-131104646(+)$1	228	178	217	13.1483
UUGUAGUGGCUGAAGGGUCCCACGCUGUAUUCUCGCCAG	chr7:6443408-6443628(-)$1	220	144	183	12.4678
ACAAGUGCUACCUUUGAGUGUAAACUAAGGUAGACUACU	chr4:77969184-77969399(-)$1	215	33	72	12.7323
UGGGGCGGGCUUGAGGGCCAGACAGCCAAGAGGCCCCAG	chr11:74914209-74914427(+)$1	218	11	50	14.6178
UAAAACCGAAUGAGCUGGUUCUUUCCAUCCUCUUGUGGU	chr13:114111050-114111279(-)$1	229	92	131	12.7244
UUCGGGUUUUGUUUCAUAGGGAGUCCUGAGUGGGGUAAC	chr7:44869217-44869438(-)$1	221	93	132	12.0142
UGUGAAACCAGAUUAAAUAUCUAUAUUCAGUUUGGCCua	chr1:162498208-162498443(+)$1	235	15	54	13.7145
AACAAGGCCACCCGCCUCUGGAAUGUGGAGUGUUAGCCC	chr17:3909999-3910228(-)$1	229	9	48	10.9504
CCCUGAAAGGUGGGUAAAUGGUAUUUUUCCCCCUUUUGA	chr17:30520150-30520368(+)$1	218	104	143	11.9001
CUGAGUAGGGUAAUUUUUUAAAAGAAAUUUUACAAUAUA	chr3:169511100-169511319(-)$1	219	59	98	12.1611
UUAAAAGGGCAAGUACAGGAGCAACUGCUGCUACCCAGA	chr7:30407203-30407434(+)$1	231	14	53	15.7074
UAAAGUUUAAAGUUGCACAUGAUUGUAUAAGCAUGCUUU	chr11:11984554-11984780(-)$1	226	20	59	13.2413
UUUGGUUACUGGCUUCUCUGCUUUGUCUUGCCAGCUACC	chr16:16313381-16313596(-)$1	215	120	159	11.3575

#DB
.....(((((((.((((......)))).))))...))).	chr16:31770987-31771203(-)$1	1	78	117	13.3579
(((((((......(.(((......))).)...)))))))	chr12:54352140-54352355(-)$1	1	12	51	12.8997
.(((..(((.((((.((((...)))).)))).)))))).	chr18:9136735-9136952(+)$1	1	112	151	12.3312
(((..(((..(((((((((....))))...))))).)))	chr3:49572392-49572613(+)$1	1	164	203	13.3239
.((((((((...(((.(((...))))))))))).))).)	chr2:202558655-202558871(-)$1	1	33	72	12.3593
.(((.((((..(((.(((....)))..)))...)))).)	chr9:129645217-129645435(+)$1	1	115	154	11.9938
(((...((((((((((((.....))))))))))))))).	chr19:47112989-47113214(+)$1	1	106	145	13.9377
(((.((((.(.((((...(((...)))...)))).))))	chr5:36102960-36103185(-)$1	1	143	182	11.9910
((((((.((((((..(((......))).)))))).))))	chr5:175487666-175487893(+)$1	1	7	46	14.8588
(((((((((((.((.(((......))).))..)))))))	chr4:158286801-158287029(+)$1	1	98	137	15.5647
((((((((((((((((((((....)))))))))))))))	chr2:113096243-113096488(+)$1	1	182	221	14.4294
..(((.(.((.(((((((....))).)))).)).)))).	chr13:47408549-47408776(-)$1	1	135	174	11.3577
.((((..(((((((.(((......))).)))))))...)	chr5:78618645-78618885(-)$1	1	33	72	16.9527
)(((...((((((((((((.....)))))))))))))))	chr19:47112935-47113162(+)$1	1	159	198	14.6697
..(((....(((((((((...))))))))))))...)))	chr16:69732736-69732960(+)$1	1	180	219	13.5909
.(((.(((.(.(((.(((......)))...))).)))))	chr4:905695-905921(-)$1	1	101	140	18.7805
(((.((((.(((...((((....))))...)))...)))	chr19:11562344-11562561(-)$1	1	33	72	13.8303
(....(((...(((..........)))...)))...)).	chrX:154686776-154687002(-)$1	1	125	164	12.2526
(......(((.(((((((......)))).))))))...)	chr17:36347526-36347760(-)$1	1	9	48	12.4347
((....(((...(((((.....)))))...)))...)))	chr8:133139378-133139593(-)$1	1	163	202	13.4839
(.((..(((.((...((((....))))...))...))).	chr4:38628215-38628436(-)$1	1	174	213	13.5142
.(((....(((.((.(((((...)))))...)).)))..	chr5:154196784-154197006(+)$1	1	158	197	12.5663
.(((((((((.(..((((......))))..).)))....	chr11:98891792-98892020(+)$1	1	168	207	11.2099
.)))(((.((((((((((((....))).)))))))))..	chr15:68583501-68583721(+)$1	1	134	173	12.8974
((((.((.(((.....(((....)))....)))..))))	chr12:16052748-16052971(+)$1	1	119	158	11.6918
..((((((((((((...(......)....))))))...)	chr2:128928781-128928996(-)$1	1	51	90	11.6094
(((((((..(((((((((......)))))))))..)).)	chr6:170884380-170884600(+)$1	1	98	137	13.7787
(((((((...((((((((..(......)..))).)))))	chr1:43917668-43917897(+)$1	1	72	111	11.6298
(...(((((((((..(((......)))..))))))))).	chr19:36642338-36642572(+)$1	1	153	192	16.9425
((((.(((..(((((((......))))))).))).))))	chr7:100277408-100277638(-)$1	1	183	222	14.7238
(.....((((.....(((......)))....))))...)	chr16:69149865-69150093(-)$1	1	46	85	14.2932
((...(((.(((((.((((....)))).))))).)))..	chr2:199011727-199011958(+)$1	1	157	196	12.4811
(((((((((..(((..(.....)..)))....)))))))	chr1:38273584-38273808(+)$1	1	147	186	13.1911
(((...((((.((((((......)))))).))))...))	chr17:4619007-4619228(+)$1	1	153	192	12.9548
..(((((((((((((.(......).)))))))))...))	chr9:137298956-137299179(+)$1	1	107	146	14.9308
)))(((((((((.((((......))))...)))))))))	chr6:33540377-33540594(+)$1	1	147	186	14.5031
))((((((((.(((.(((......))).))).)))))))	chr5:175808770-175808998(+)$1	1	105	144	13.1133
(((..(((((((((.(((...))).)))...)))))).)	chr1:120535985-120536205(-)$1	1	120	159	12.7968
(((((.(((..((((.........))))..))).)))))	chr3:182733072-182733291(-)$1	1	15	54	10.9611
((((((((...(((..((((....)))).)))....)))	chr14:25288528-25288743(+)$1	1	130	169	13.6944
.((((..(((.((((((......))))))))))))))))	chr2:74724816-74725036(+)$1	1	109	148	11.8887
.(((.(....((((((((((...))))))))))).))))	chr1:72400782-72400999(-)$1	1	46	85	14.9427
(((.(((((((((...((......))....))).)))))	chr17:44051357-44051581(+)$1	1	112	151	13.4571
(((...((((.(((((((......))))))))))).)))	chr3:131104418-131104646(+)$1	1	178	217	13.1483
))))))((((.(((.(((.....)))...)))..)))))	chr7:6443408-6443628(-)$1	1	144	183	12.4678
..((((((((((((..(((....)))))))))).).)))	chr4:77969184-77969399(-)$1	1	33	72	12.7323
((((((((((((...(((......)))...))))))..)	chr11:74914209-74914427(+)$1	1	11	50	14.6178
....((((...(((.(((......)))..)))...))))	chr13:114111050-114111279(-)$1	1	92	131	12.7244
((((((((.(.((.(.((((....)))).).)).).)))	chr7:44869217-44869438(-)$1	1	93	132	12.0142
.(.(...(((((((.((((....)))).))))))))).)	chr1:162498208-162498443(+)$1	1	15	54	13.7145
..(((((((((((((.........)))).)))...).))	chr17:3909999-3910228(-)$1	1	9	48	10.9504
))).((((((.(((.(((......))).)))))))))))	chr17:30520150-30520368(+)$1	1	104	143	11.9001
((..(((..((((..((((....))))..))))..))).	chr3:169511100-169511319(-)$1	1	59	98	12.1611
((....(((..(((((((......))).)))).))).))	chr7:30407203-30407434(+)$1	1	14	53	15.7074
(((((...(((((((((((....)))....))).)))))	chr11:11984554-11984780(-)$1	1	20	59	13.2413
..((((..(((((....(......)....)))))..)))	chr16:16313381-16313596(-)$1	1	120	159	11.3575

#PSSM
g : 0.16	! : 0.12	[ : 0.12	c : 0.10	= : 0.07	e : 0.05	b : 0.05	d : 0.05	: : 0.05	i : 0.05	f : 0.03	h : 0.03	$ : 0.01	" : 0.01	3 : 0.01	F : 0.01	
c : 0.24	g : 0.14	! : 0.07	= : 0.05	e : 0.05	f : 0.05	: : 0.05	i : 0.05	d : 0.05	$ : 0.03	a : 0.03	" : 0.03	# : 0.01	% : 0.01	[ : 0.01	F : 0.01	h : 0.01	b : 0.01	
c : 0.30	g : 0.12	d : 0.08	f : 0.07	e : 0.05	# : 0.05	i : 0.05	$ : 0.03	= : 0.03	" : 0.03	h : 0.03	% : 0.01	b : 0.01	F : 0.01	: : 0.01	[ : 0.01	! : 0.01	
c : 0.21	g : 0.10	" : 0.08	f : 0.07	i : 0.07	d : 0.07	! : 0.05	[ : 0.05	# : 0.05	$ : 0.03	= : 0.03	e : 0.03	: : 0.03	% : 0.01	b : 0.01	h : 0.01	a : 0.01	
d : 0.12	" : 0.10	f : 0.10	g : 0.08	[ : 0.08	c : 0.08	i : 0.08	! : 0.07	# : 0.07	$ : 0.03	e : 0.03	= : 0.03	% : 0.01	h : 0.01	b : 0.01	
c : 0.14	d : 0.12	" : 0.10	f : 0.08	i : 0.08	g : 0.07	! : 0.07	# : 0.07	b : 0.05	e : 0.03	= : 0.03	[ : 0.03	% : 0.01	$ : 0.01	h : 0.01	a : 0.01	
c : 0.23	d : 0.14	f : 0.10	i : 0.10	= : 0.05	! : 0.05	" : 0.05	# : 0.05	g : 0.03	e : 0.03	a : 0.03	b : 0.03	[ : 0.01	% : 0.01	h : 0.01	
c : 0.24	d : 0.14	f : 0.10	i : 0.10	= : 0.07	[ : 0.05	g : 0.05	# : 0.05	! : 0.05	" : 0.03	% : 0.01	e : 0.01	h : 0.01	a : 0.01	
c : 0.19	d : 0.10	f : 0.10	[ : 0.08	i : 0.08	! : 0.07	= : 0.07	" : 0.07	e : 0.05	g : 0.05	# : 0.03	% : 0.01	b : 0.01	h : 0.01	
c : 0.12	d : 0.10	! : 0.10	" : 0.10	f : 0.10	i : 0.10	= : 0.07	a : 0.05	g : 0.05	e : 0.05	[ : 0.03	% : 0.01	b : 0.01	h : 0.01	# : 0.01	
[ : 0.21	i : 0.10	e : 0.08	" : 0.08	= : 0.08	c : 0.08	! : 0.07	f : 0.07	g : 0.07	d : 0.05	% : 0.01	b : 0.01	$ : 0.01	
c : 0.23	d : 0.14	i : 0.10	e : 0.08	f : 0.08	g : 0.08	= : 0.07	" : 0.03	[ : 0.03	b : 0.03	$ : 0.03	% : 0.01	a : 0.01	
c : 0.23	d : 0.12	e : 0.10	g : 0.08	i : 0.08	= : 0.07	f : 0.07	b : 0.05	" : 0.05	[ : 0.03	$ : 0.03	% : 0.01	! : 0.01	
c : 0.23	d : 0.14	g : 0.08	e : 0.07	= : 0.07	! : 0.07	i : 0.07	" : 0.07	f : 0.05	b : 0.03	$ : 0.03	a : 0.01	[ : 0.01	# : 0.01	
[ : 0.24	d : 0.16	! : 0.10	" : 0.08	= : 0.07	i : 0.07	e : 0.05	c : 0.03	$ : 0.03	g : 0.03	f : 0.03	s : 0.01	a : 0.01	# : 0.01	
c : 0.32	d : 0.19	= : 0.07	[ : 0.05	" : 0.05	i : 0.05	! : 0.05	e : 0.03	g : 0.03	f : 0.03	r : 0.03	s : 0.01	$ : 0.01	# : 0.01	
c : 0.37	d : 0.23	= : 0.07	i : 0.05	" : 0.03	e : 0.03	g : 0.03	a : 0.03	f : 0.03	r : 0.03	s : 0.01	b : 0.01	# : 0.01	
c : 0.39	d : 0.19	o : 0.10	= : 0.07	i : 0.03	n : 0.03	a : 0.03	r : 0.03	" : 0.01	s : 0.01	e : 0.01	b : 0.01	g : 0.01	
o : 0.44	d : 0.16	c : 0.10	n : 0.07	= : 0.05	m : 0.03	l : 0.03	r : 0.03	s : 0.01	e : 0.01	! : 0.01	
o : 0.44	m : 0.19	n : 0.08	l : 0.07	c : 0.03	= : 0.03	r : 0.03	d : 0.03	s : 0.01	e : 0.01	! : 0.01	
o : 0.44	m : 0.26	l : 0.10	n : 0.08	r : 0.03	c : 0.01	s : 0.01	a : 0.01	
o : 0.46	m : 0.26	l : 0.08	n : 0.08	r : 0.03	i : 0.01	s : 0.01	c : 0.01	
o : 0.46	m : 0.23	c : 0.07	n : 0.05	l : 0.05	r : 0.03	d : 0.01	i : 0.01	s : 0.01	e : 0.01	a : 0.01	
o : 0.35	d : 0.16	c : 0.14	m : 0.07	= : 0.03	e : 0.03	f : 0.03	r : 0.03	l : 0.01	n : 0.01	i : 0.01	s : 0.01	g : 0.01	2 : 0.01	a : 0.01	
c : 0.39	d : 0.26	= : 0.07	i : 0.03	e : 0.03	a : 0.03	g : 0.03	f : 0.03	] : 0.03	o : 0.01	2 : 0.01	b : 0.01	
c : 0.39	d : 0.26	= : 0.07	i : 0.05	e : 0.03	4 : 0.03	g : 0.03	f : 0.03	2 : 0.01	] : 0.01	o : 0.01	b : 0.01	
c : 0.32	d : 0.26	4 : 0.08	= : 0.07	i : 0.05	g : 0.05	e : 0.03	f : 0.03	] : 0.01	2 : 0.01	o : 0.01	3 : 0.01	
] : 0.19	3 : 0.17	d : 0.14	4 : 0.10	c : 0.07	= : 0.07	i : 0.05	2 : 0.05	g : 0.05	f : 0.03	e : 0.01	a : 0.01	
3 : 0.21	4 : 0.12	2 : 0.10	g : 0.08	d : 0.07	= : 0.07	i : 0.07	] : 0.07	c : 0.05	f : 0.05	e : 0.03	a : 0.01	b : 0.01	
3 : 0.21	c : 0.16	d : 0.08	g : 0.08	i : 0.08	4 : 0.08	= : 0.07	e : 0.05	2 : 0.05	f : 0.03	b : 0.01	] : 0.01	a : 0.01	
c : 0.32	d : 0.10	i : 0.08	3 : 0.07	e : 0.07	= : 0.07	g : 0.07	f : 0.05	] : 0.05	4 : 0.03	2 : 0.01	b : 0.01	a : 0.01	
c : 0.30	d : 0.12	f : 0.08	i : 0.08	e : 0.07	= : 0.07	b : 0.07	] : 0.05	g : 0.05	3 : 0.03	2 : 0.01	4 : 0.01	
c : 0.24	d : 0.10	i : 0.10	3 : 0.08	= : 0.08	f : 0.08	g : 0.07	e : 0.07	b : 0.05	h : 0.01	4 : 0.01	2 : 0.01	] : 0.01	
] : 0.19	3 : 0.14	d : 0.10	c : 0.08	f : 0.08	i : 0.08	= : 0.07	2 : 0.07	g : 0.05	e : 0.03	h : 0.01	4 : 0.01	a : 0.01	
3 : 0.17	c : 0.12	f : 0.10	d : 0.08	= : 0.07	] : 0.07	a : 0.07	i : 0.07	2 : 0.07	g : 0.05	e : 0.05	h : 0.01	4 : 0.01	
c : 0.21	3 : 0.17	f : 0.08	] : 0.07	d : 0.07	i : 0.07	g : 0.05	a : 0.05	= : 0.05	b : 0.03	e : 0.03	9 : 0.01	h : 0.01	4 : 0.01	2 : 0.01	
c : 0.24	d : 0.12	3 : 0.10	i : 0.10	g : 0.07	f : 0.07	h : 0.05	b : 0.05	= : 0.03	e : 0.03	] : 0.03	9 : 0.01	2 : 0.01	a : 0.01	
c : 0.21	d : 0.12	3 : 0.10	] : 0.08	i : 0.08	g : 0.07	e : 0.07	= : 0.05	h : 0.05	2 : 0.03	f : 0.03	b : 0.01	9 : 0.01	E : 0.01	
c : 0.14	d : 0.12	g : 0.08	2 : 0.08	e : 0.08	= : 0.07	h : 0.07	f : 0.07	i : 0.07	3 : 0.05	4 : 0.01	: : 0.01	] : 0.01	9 : 0.01	B : 0.01	b : 0.01	E : 0.01	

#score	744.9124120969642
#seq	56
#width	39
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m1_run1.txt

#BEAR
gggggg^^^^^^^^^^^^^^^^^^^^^^^^	chr18:61655044-61655346(+)$1	302	113	143	37.6482
fffff^^^^^^^^^^^^^^^^^^^^^^fff	chr11:3853134-3853391(-)$1	257	101	131	35.2092
deeeee^^^^^^^^^^^^^^^^^^^^^^^^	chr15:69499645-69499896(+)$1	251	98	128	37.6980
ee[ccc^^^^^^^^^^^^^^^^^^^^^^^^	chr16:78800667-78800926(+)$1	259	105	135	37.5652
cccccc^^^^^^^^^^^^^^^^^^^^^ccc	chr3:148852643-148852905(+)$1	262	127	157	35.9263
eeeee^^^^^^^^^^^^^^^^^^^^^^^ee	chr7:44454113-44454346(-)$1	233	165	195	36.7203
!eeeee^^^^^^^^^^^^^^^^^^^^^^^e	chr4:184058163-184058424(+)$1	261	170	200	37.4235
EEeeeee^^^^^^^^^^^^^^^^^^eeeee	chr13:43462905-43463146(-)$1	241	210	240	30.6727
###dddd^^^^^^^^^^^^^^^^^^^dddd	chr6:74116681-74116902(+)$1	221	149	179	32.7575
b!!ccc^^^^^^^^^^^^^^^^^^^^^^^^	chr2:149007522-149007750(+)$1	228	16	46	37.5471
iiii[a^^^^^^^^^^^^^^^^^^^^^^^^	chr11:110542188-110542417(-)$1	229	136	166	37.6439
cc[a[ccc^^^^^^^^^^^^^^^^^^ccc]	chr22:31943047-31943286(+)$1	239	90	120	32.2080
:eeeee^^^^^^^^^^^^^^^^^^^eeeee	chr2:99769743-99769984(-)$1	241	115	145	33.1510
gggggg^^^^^^^^^^^^^^^^^^^^^^^^	chr9:102928772-102929024(+)$1	252	95	125	37.6482
:eeeee^^^^^^^^^^^^^^^^^^^^eeee	chr5:86674486-86674712(+)$1	226	122	152	34.4451
ggg"""bb^^^^^^^^^^^^^^^^^^bb33	chr8:54975390-54975633(-)$1	243	48	78	31.6684
fffff^^^^^^^^^^^^^^^^^^^^^^^ff	chr7:92333944-92334262(-)$1	318	39	69	35.9864
eeeee^^^^^^^^^^^^^^^^^^^^^^^^e	chr17:53071623-53071866(+)$1	243	208	238	37.3075
c[dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr1:46301303-46301571(+)$1	268	72	102	37.6504
$eeeee^^^^^^^^^^^^^^^^^^^eeeee	chr2:217039721-217040120(+)$1	399	116	146	33.7035
ee!!bb^^^^^^^^^^^^^^^^^^^^^^^^	chr7:110923408-110923671(-)$1	263	95	125	37.1235
iiiiii^^^^^^^^^^^^^^^^^^^^^^^^	chr3:120972170-120972445(+)$1	275	17	47	37.5580
"adddd^^^^^^^^^^^^^^^^^^^^^^^^	chr6:83874750-83875029(-)$1	279	154	184	37.5019
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:46113401-46113641(-)$1	240	5	35	37.8153
!eeeee^^^^^^^^^^^^^^^^^^^^^^^^	chr3:176784137-176784374(-)$1	237	72	102	37.9313
c!!ccc^^^^^^^^^^^^^^^^^^^^^^^^	chr17:46989485-46989715(+)$1	230	143	173	37.7492
""dddd^^^^^^^^^^^^^^^^^^^^dddd	chr15:73578797-73579023(+)$1	226	10	40	34.4553
ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr5:179394581-179394887(-)$1	306	117	147	35.5927
gggggg^^^^^^^^^^^^^^^^^^^^^^^^	chr17:15379556-15379865(-)$1	309	157	187	37.6482
f[dddd^^^^^^^^^^^^^^^^^^^ddddf	chr10:26852111-26852368(+)$1	257	164	194	33.0825
c[dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr12:123291381-123291617(+)$1	236	4	34	37.6504
ffffff^^^^^^^^^^^^^^^^^^^^^^^^	chr2:240119879-240120140(-)$1	261	185	215	37.0967
::eeeee^^^^^^^^^^^^^^^^^^eeeee	chr21:36321695-36321940(-)$1	245	96	126	30.7525
ggdddd^^^^^^^^^^^^^^^^^^^^^^^^	chr14:20862892-20863136(-)$1	244	53	83	37.5688
:eeeee^^^^^^^^^^^^^^^^^^^^eeee	chr7:151967371-151967601(-)$1	230	154	184	34.4451
hhhhhh^^^^^^^^^^^^^^^^^^^^^hhh	chr4:83284045-83284319(-)$1	274	231	261	33.3357
gggggg^^^^^^^^^^^^^^^^^^^^^^^^	chr17:8364570-8364800(+)$1	230	88	118	37.6482
ccc^^^^^^^^^^^^^^^^^^^^^^^^ccc	chr6:161435808-161436066(+)$1	258	197	227	35.5927
ffffff^^^^^^^^^^^^^^^^^^^^^fff	chr5:87551620-87551846(-)$1	226	95	125	35.0371
eeeee^^^^^^^^^^^^^^^^^^^eeeee:	chr12:46646724-46647007(-)$1	283	1	31	31.5805
:::ccc^^^^^^^^^^^^^^^^^^^^ccc:	chr3:196296415-196296653(+)$1	238	61	91	31.5696
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^	chr11:75704255-75704542(+)$1	287	95	125	37.8153
beeeee^^^^^^^^^^^^^^^^^^^^eeee	chr19:58871428-58871652(-)$1	224	96	126	35.0268
::dddd^^^^^^^^^^^^^^^^^^ddddff	chr13:31194887-31195121(+)$1	234	123	153	29.8573
[bb[bb^^^^^^^^^^^^^^^^^^^^^^^^	chr7:98651351-98651584(-)$1	233	93	123	36.6234
gg[ccc^^^^^^^^^^^^^^^^^^^^ccc]	chr8:60006694-60006949(-)$1	255	100	130	35.1305
c[dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr13:79173206-79173473(-)$1	267	69	99	37.6504
ffffff^^^^^^^^^^^^^^^^^^ffffff	chr1:183236639-183236863(-)$1	224	98	128	30.9599
ee"""bb^^^^^^^^^^^^^^^^^^^bb33	chr1:92774011-92774269(+)$1	258	150	180	32.8955
hhhhhh^^^^^^^^^^^^^^^^^^^^hhhh	chr5:100215456-100215772(-)$1	316	146	176	31.8952
D:dddd^^^^^^^^^^^^^^^^^^^^dddd	chr22:24780952-24781192(+)$1	240	207	237	32.6322
:eeeee^^^^^^^^^^^^^^^^^^eeeeec	chr4:109004925-109005320(-)$1	395	252	282	31.6363
ffffff^^^^^^^^^^^^^^^^^^^^^fff	chr1:179036247-179036506(+)$1	259	98	128	35.0371
dddd^^^^^^^^^^^^^^^^^^^^^^^ddd	chr10:28875956-28876193(+)$1	237	142	172	35.0997
======^^^^^^^^^^^^^^^^^^^^^^^^	chr17:27117637-27117887(-)$1	250	165	195	37.6654
[dddd^^^^^^^^^^^^^^^^^^^^^^^^d	chr18:3601332-3601566(-)$1	234	109	139	36.9091
##dddd^^^^^^^^^^^^^^^^^^^^^^^^	chr4:99572482-99572708(-)$1	226	95	125	37.4528
gggggg^^^^^^^^^^^^^^^^^^^^^^^^	chrY:15398788-15399130(-)$1	342	168	198	37.6482
ffffff^^^^^^^^^^^^^^^^^^^^^^^^	chr20:43667839-43668083(+)$1	244	103	133	37.0967
ccc[bb^^^^^^^^^^^^^^^^^^bb]ccc	chr11:67251994-67252269(+)$1	275	99	129	31.6032
::eeeee^^^^^^^^^^^^^^^^^^eeeee	chr1:87395101-87395357(+)$1	256	111	141	30.7525
ccc[a^^^^^^^^^^^^^^^^^^^^^^^a]	chr14:60572458-60572750(+)$1	292	159	189	36.7815
iiiiii^^^^^^^^^^^^^^^^^^^^^^^^	chr9:72355000-72355249(-)$1	249	100	130	37.5580

#otherMatches

#Seq PSSM
UCCUUUUCCCUCUGAAACACACAAAAUACC	chr18:61655044-61655346(+)$1	302	113	143	37.6482
ACACUACCAUACUCAUCAUCCUUUUCCAGU	chr11:3853134-3853391(-)$1	257	101	131	35.2092
agucagccacuacuccauaccccaacuccu	chr15:69499645-69499896(+)$1	251	98	128	37.6980
aucagcauuaccuauaccuaaaauauuuuc	chr16:78800667-78800926(+)$1	259	105	135	37.5652
GGCCCCUUCCUUCCAUUCACAAUAACUGGG	chr3:148852643-148852905(+)$1	262	127	157	35.9263
GCCAGCCCUAACCUAAGUCAUCACAUAACU	chr7:44454113-44454346(-)$1	233	165	195	36.7203
cauuacauuuauuaaaaaauuuuucuucag	chr4:184058163-184058424(+)$1	261	170	200	37.4235
GUGACAACAUUUUCGAACUGUAUAUUUGUC	chr13:43462905-43463146(-)$1	241	210	240	30.6727
AUACUCAUUGCUACAAAuuuuuuuuuugag	chr6:74116681-74116902(+)$1	221	149	179	32.7575
cucAGCUUUUAACUUUUUUUCCGCUACUUU	chr2:149007522-149007750(+)$1	228	16	46	37.5471
aaaugguuuuacuucuuccacucuaauuug	chr11:110542188-110542417(-)$1	229	136	166	37.6439
GGCACGUGCACACAGACACACACACACACC	chr22:31943047-31943286(+)$1	239	90	120	32.2080
agugaccucauuucucuuuccacuugucau	chr2:99769743-99769984(-)$1	241	115	145	33.1510
UAGAGAAUUCAAUUCAACUAACACACACUG	chr9:102928772-102929024(+)$1	252	95	125	37.6482
ACUGUACUAAUAAUCUAUAUACUACUUACA	chr5:86674486-86674712(+)$1	226	122	152	34.4451
CCUCUUCAucuuuccaauuucuugccuguc	chr8:54975390-54975633(-)$1	243	48	78	31.6684
gguauuaacuauacaguuuaacaugcuuau	chr7:92333944-92334262(-)$1	318	39	69	35.9864
aacagcuuccuauuucaacucccauaacac	chr17:53071623-53071866(+)$1	243	208	238	37.3075
cauguucaccaccauccccugcaaaaaaaa	chr1:46301303-46301571(+)$1	268	72	102	37.6504
CACCACUAUCCCCAUACCCGCCAUUGUGGU	chr2:217039721-217040120(+)$1	399	116	146	33.7035
aacugcucaucauuucagauuuuaucauuc	chr7:110923408-110923671(-)$1	263	95	125	37.1235
acucuuuaucucuuccuuccauacauuuuu	chr3:120972170-120972445(+)$1	275	17	47	37.5580
UCCCCUAAAUCAAACUGCAAUUCAACAAUA	chr6:83874750-83875029(-)$1	279	154	184	37.5019
ugucucaaaaaaaaagaaaaaaacauacac	chr1:46113401-46113641(-)$1	240	5	35	37.8153
CCUGCAUUUCAAGCCUUACUCGUCUCUGUC	chr3:176784137-176784374(-)$1	237	72	102	37.9313
GCUGUGGCCUCCAAUCCCUUUCUUCGUCUC	chr17:46989485-46989715(+)$1	230	143	173	37.7492
cuggacuuacucucuucuccuucuguguuc	chr15:73578797-73579023(+)$1	226	10	40	34.4553
GAAACUUCUCUCUAUAAACAUACAAACUUC	chr5:179394581-179394887(-)$1	306	117	147	35.5927
UUAAGAAAACACUAAAAAACAAAAACUAAC	chr17:15379556-15379865(-)$1	309	157	187	37.6482
ugucuuaaaaaaaagaaaaaagaUAAAGAA	chr10:26852111-26852368(+)$1	257	164	194	33.0825
UUGGUUGUaaaaaaaaaaagaaagaaaaaa	chr12:123291381-123291617(+)$1	236	4	34	37.6504
ugccuccacucacacucggcaacacauaac	chr2:240119879-240120140(-)$1	261	185	215	37.0967
UAGGUUACAUCCUCAAACAUCACUUUAACC	chr21:36321695-36321940(-)$1	245	96	126	30.7525
ugguucaucaguaucuuacacuuauuuuua	chr14:20862892-20863136(-)$1	244	53	83	37.5688
UAGCUUUAAUUCCUUUUACUUCACUUAAGC	chr7:151967371-151967601(-)$1	230	154	184	34.4451
GACUUUUCCCCAUUGUACUAUAAAGUUAGA	chr4:83284045-83284319(-)$1	274	231	261	33.3357
UUGUAUUAAAAGCACAUCCUAAAACAUCAC	chr17:8364570-8364800(+)$1	230	88	118	37.6482
uccuauucugaacauuuuauauaaauugga	chr6:161435808-161436066(+)$1	258	197	227	35.5927
GAUAGUUACAUCAAAUUCACACAUUCUACU	chr5:87551620-87551846(-)$1	226	95	125	35.0371
ggaccccuuucuuguaacacuucugguccc	chr12:46646724-46647007(-)$1	283	1	31	31.5805
AAUGCCCUCAUCCUACUUUUCUCCCCGGCC	chr3:196296415-196296653(+)$1	238	61	91	31.5696
AAGGGCCUCAUUACUUCACACUCAUACGUU	chr11:75704255-75704542(+)$1	287	95	125	37.8153
gcuguaucucccauuucucucuucccugca	chr19:58871428-58871652(-)$1	224	96	126	35.0268
CUACCCUCUGUUCACAAAUUUGCUGGGUUU	chr13:31194887-31195121(+)$1	234	123	153	29.8573
GGGGAGGAACUCAACACACUAAAAAAAUAC	chr7:98651351-98651584(-)$1	233	93	123	36.6234
UUCACUCAUACAGAAAUAAAAUAAAAAGUC	chr8:60006694-60006949(-)$1	255	100	130	35.1305
CUCCCUUACUUCUAUCAGAACCAAUUCUAU	chr13:79173206-79173473(-)$1	267	69	99	37.6504
UGCCCUUACACCCCCCCACUCCCCAGGGCA	chr1:183236639-183236863(-)$1	224	98	128	30.9599
CUUUCCUGCCAUCUCUGUUUUCUUCAAGCA	chr1:92774011-92774269(+)$1	258	150	180	32.8955
AUCUAGUCAUCAUCUCCUCUAAAACCUUAG	chr5:100215456-100215772(-)$1	316	146	176	31.8952
uggcuauaauauuuaaaaucacauauUAGc	chr22:24780952-24781192(+)$1	240	207	237	32.6322
UUUCCCAAAUCUAUAUGUCCAUAAGGGAAC	chr4:109004925-109005320(-)$1	395	252	282	31.6363
UGUGGUUUUAACUCCUCUCACUCACCCAUC	chr1:179036247-179036506(+)$1	259	98	128	35.0371
uuauucauuucauuuaaaauaucaauugua	chr10:28875956-28876193(+)$1	237	142	172	35.0997
aacauugacacauuacuuccauauaauuau	chr17:27117637-27117887(-)$1	250	165	195	37.6654
acacacacacacacacacacCCUUGCAUAU	chr18:3601332-3601566(-)$1	234	109	139	36.9091
caaugauacauuaacaccauuuaauccuua	chr4:99572482-99572708(-)$1	226	95	125	37.4528
GGCCUUGCUCUUCAUCUAUACCAAUUAAAA	chrY:15398788-15399130(-)$1	342	168	198	37.6482
auuucauuaaacaauauaaaaaaaccccac	chr20:43667839-43668083(+)$1	244	103	133	37.0967
gcucccuacucaccauauccaccuggaagc	chr11:67251994-67252269(+)$1	275	99	129	31.6032
UCUUCACUCUUUCCUAUUAAUACCUGUGAA	chr1:87395101-87395357(+)$1	256	111	141	30.7525
CAGUCUAUCCCUCCAAGUUCAUUUUCCUGU	chr14:60572458-60572750(+)$1	292	159	189	36.7815
uauauaccuacauacauacauacacacaca	chr9:72355000-72355249(-)$1	249	100	130	37.5580

#DB
((((((........................	chr18:61655044-61655346(+)$1	1	113	143	37.6482
(((((......................)))	chr11:3853134-3853391(-)$1	1	101	131	35.2092
)(((((........................	chr15:69499645-69499896(+)$1	1	98	128	37.6980
((.(((........................	chr16:78800667-78800926(+)$1	1	105	135	37.5652
)))(((.....................)))	chr3:148852643-148852905(+)$1	1	127	157	35.9263
(((((.......................))	chr7:44454113-44454346(-)$1	1	165	195	36.7203
.(((((.......................)	chr4:184058163-184058424(+)$1	1	170	200	37.4235
))(((((..................)))))	chr13:43462905-43463146(-)$1	1	210	240	30.6727
...((((...................))))	chr6:74116681-74116902(+)$1	1	149	179	32.7575
(..(((........................	chr2:149007522-149007750(+)$1	1	16	46	37.5471
((((.(........................	chr11:110542188-110542417(-)$1	1	136	166	37.6439
((.(.(((..................))).	chr22:31943047-31943286(+)$1	1	90	120	32.2080
.(((((...................)))))	chr2:99769743-99769984(-)$1	1	115	145	33.1510
((((((........................	chr9:102928772-102929024(+)$1	1	95	125	37.6482
.(((((....................))))	chr5:86674486-86674712(+)$1	1	122	152	34.4451
(((...((..................))..	chr8:54975390-54975633(-)$1	1	48	78	31.6684
(((((.......................))	chr7:92333944-92334262(-)$1	1	39	69	35.9864
(((((........................)	chr17:53071623-53071866(+)$1	1	208	238	37.3075
(.((((........................	chr1:46301303-46301571(+)$1	1	72	102	37.6504
.(((((...................)))))	chr2:217039721-217040120(+)$1	1	116	146	33.7035
((..((........................	chr7:110923408-110923671(-)$1	1	95	125	37.1235
((((((........................	chr3:120972170-120972445(+)$1	1	17	47	37.5580
.(((((........................	chr6:83874750-83875029(-)$1	1	154	184	37.5019
(((((.........................	chr1:46113401-46113641(-)$1	1	5	35	37.8153
.(((((........................	chr3:176784137-176784374(-)$1	1	72	102	37.9313
(..(((........................	chr17:46989485-46989715(+)$1	1	143	173	37.7492
..((((....................))))	chr15:73578797-73579023(+)$1	1	10	40	34.4553
(((........................)))	chr5:179394581-179394887(-)$1	1	117	147	35.5927
((((((........................	chr17:15379556-15379865(-)$1	1	157	187	37.6482
(.((((...................)))))	chr10:26852111-26852368(+)$1	1	164	194	33.0825
(.((((........................	chr12:123291381-123291617(+)$1	1	4	34	37.6504
((((((........................	chr2:240119879-240120140(-)$1	1	185	215	37.0967
..(((((..................)))))	chr21:36321695-36321940(-)$1	1	96	126	30.7525
((((((........................	chr14:20862892-20863136(-)$1	1	53	83	37.5688
.(((((....................))))	chr7:151967371-151967601(-)$1	1	154	184	34.4451
((((((.....................)))	chr4:83284045-83284319(-)$1	1	231	261	33.3357
((((((........................	chr17:8364570-8364800(+)$1	1	88	118	37.6482
(((........................)))	chr6:161435808-161436066(+)$1	1	197	227	35.5927
((((((.....................)))	chr5:87551620-87551846(-)$1	1	95	125	35.0371
(((((...................))))).	chr12:46646724-46647007(-)$1	1	1	31	31.5805
...(((....................))).	chr3:196296415-196296653(+)$1	1	61	91	31.5696
(((((.........................	chr11:75704255-75704542(+)$1	1	95	125	37.8153
((((((....................))))	chr19:58871428-58871652(-)$1	1	96	126	35.0268
..((((..................))))((	chr13:31194887-31195121(+)$1	1	123	153	29.8573
.((.((........................	chr7:98651351-98651584(-)$1	1	93	123	36.6234
((.(((....................))).	chr8:60006694-60006949(-)$1	1	100	130	35.1305
(.((((........................	chr13:79173206-79173473(-)$1	1	69	99	37.6504
((((((..................))))))	chr1:183236639-183236863(-)$1	1	98	128	30.9599
((...((...................))..	chr1:92774011-92774269(+)$1	1	150	180	32.8955
((((((....................))))	chr5:100215456-100215772(-)$1	1	146	176	31.8952
).((((....................))))	chr22:24780952-24781192(+)$1	1	207	237	32.6322
.(((((..................)))))(	chr4:109004925-109005320(-)$1	1	252	282	31.6363
((((((.....................)))	chr1:179036247-179036506(+)$1	1	98	128	35.0371
((((.......................)))	chr10:28875956-28876193(+)$1	1	142	172	35.0997
((((((........................	chr17:27117637-27117887(-)$1	1	165	195	37.6654
.((((........................)	chr18:3601332-3601566(-)$1	1	109	139	36.9091
..((((........................	chr4:99572482-99572708(-)$1	1	95	125	37.4528
((((((........................	chrY:15398788-15399130(-)$1	1	168	198	37.6482
((((((........................	chr20:43667839-43668083(+)$1	1	103	133	37.0967
(((.((..................)).)))	chr11:67251994-67252269(+)$1	1	99	129	31.6032
..(((((..................)))))	chr1:87395101-87395357(+)$1	1	111	141	30.7525
(((.(.......................).	chr14:60572458-60572750(+)$1	1	159	189	36.7815
((((((........................	chr9:72355000-72355249(-)$1	1	100	130	37.5580

#PSSM
c : 0.15	g : 0.12	f : 0.12	e : 0.12	: : 0.12	i : 0.04	d : 0.03	! : 0.03	# : 0.03	b : 0.03	" : 0.03	h : 0.03	[ : 0.03	E : 0.01	$ : 0.01	D : 0.01	= : 0.01	
e : 0.26	g : 0.12	f : 0.11	c : 0.09	: : 0.07	[ : 0.06	i : 0.04	# : 0.03	! : 0.03	h : 0.03	d : 0.03	E : 0.01	a : 0.01	" : 0.01	b : 0.01	= : 0.01	
e : 0.26	d : 0.19	f : 0.11	g : 0.09	c : 0.07	[ : 0.04	! : 0.04	i : 0.04	h : 0.03	# : 0.01	: : 0.01	b : 0.01	" : 0.01	= : 0.01	
e : 0.26	d : 0.20	f : 0.11	c : 0.09	g : 0.07	i : 0.04	[ : 0.04	" : 0.03	^ : 0.03	h : 0.03	a : 0.01	! : 0.01	= : 0.01	
e : 0.26	d : 0.19	f : 0.11	c : 0.09	g : 0.07	b : 0.04	^ : 0.04	[ : 0.03	" : 0.03	i : 0.03	h : 0.03	= : 0.01	a : 0.01	
^ : 0.19	e : 0.19	d : 0.17	c : 0.11	g : 0.07	f : 0.07	b : 0.06	i : 0.03	h : 0.03	a : 0.01	" : 0.01	= : 0.01	
^ : 0.88	e : 0.04	b : 0.03	d : 0.01	c : 0.01	
^ : 0.96	c : 0.01	b : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.92	e : 0.03	d : 0.01	f : 0.01	b : 0.01	
^ : 0.82	e : 0.11	d : 0.03	f : 0.01	b : 0.01	
^ : 0.63	e : 0.15	d : 0.07	c : 0.04	b : 0.03	f : 0.01	h : 0.01	] : 0.01	
^ : 0.50	e : 0.15	c : 0.11	d : 0.09	f : 0.06	b : 0.03	h : 0.03	
^ : 0.46	e : 0.17	c : 0.11	f : 0.09	d : 0.07	3 : 0.03	h : 0.03	a : 0.01	
^ : 0.41	e : 0.17	f : 0.11	c : 0.07	d : 0.07	] : 0.04	3 : 0.03	h : 0.03	: : 0.03	

#score	2225.0457496604045
#seq	63
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_UTR_m3_run2.txt

#BEAR
eee[bb[ddddnnnnndddd]bb22e	chr3:150918645-150918893(+)$1	248	86	112	12.4061
eeccc!!cccooooooccc22ccc]e	chr19:8586093-8586313(-)$1	220	135	161	11.8757
:eeeee!!cccnnnnnccc22eeeee	chr12:111887220-111887453(+)$1	233	17	43	12.6826
fffffccccccnnnnnccc]ccc000	chr1:39329225-39329458(-)$1	233	157	183	11.0256
bb[ccc!!cccnnnnnccc4444ccc	chr19:9761907-9762145(-)$1	238	121	147	14.2884
dddd####cccnnnnnccc333dddd	chrX:154284358-154284581(+)$1	223	18	44	14.6125
ff[bb!!cccooooooccc22bbfff	chr1:162496010-162496250(+)$1	240	176	202	10.6073
===="""ddddmmmmdddd333====	chr13:52989350-52989585(-)$1	235	118	144	10.8690
cccccca[cccnnnnnccc]a]ccc]	chr1:45285500-45285749(-)$1	249	18	44	13.3922
##ccc!!ddddnnnnndddd22ccc3	chr5:49694674-49694918(-)$1	244	158	184	14.7801
ffff"""ddddnnnnndddd333fff	chr14:100604306-100604667(+)$1	361	11	37	14.8087
eee####ddddnnnnndddd333eee	chr20:20372956-20373204(-)$1	248	142	168	15.1455
eee####ddddnnnnndddd666666	chrX:118749970-118750223(-)$1	253	109	135	11.9380
eeee"""ddddoooooodddd]eeee	chr16:15819652-15819960(+)$1	308	91	117	10.7684
ee[ccc!!cccnnnnnccc22cccee	chr5:180662269-180662503(+)$1	234	92	118	14.5085
::dddd[ddddnnnnndddd22dddd	chr9:5919902-5920259(-)$1	357	220	246	11.4980
fffffff[cccnnnnnccc]ffffff	chr1:115315664-115315918(-)$1	254	30	56	11.4442
:dddd[ccc[annnnnaccc]ddddd	chr4:40198561-40198828(+)$1	267	138	164	10.9882
fff####ddddnnnnndddd333fff	chr17:47924940-47925218(+)$1	278	73	99	14.8110
======="""annnnna333======	chr17:78393868-78394144(+)$1	276	163	189	12.9718
======[a[bbnnnnnbb]a]=====	chr10:126674756-126675037(+)$1	281	137	163	12.3278
e[dddd[ddddnnnnndddd22dddd	chr7:99173180-99173433(+)$1	253	90	116	13.3599
dd[ccc!!ddddllldddd22ccc]d	chr4:106161154-106161424(+)$1	270	7	33	9.8716
$$bbccc[cccnnnnnccc]ccc]bb	chr12:112381042-112381273(-)$1	231	128	154	11.4960
hh[a####cccooooooccc333a]h	chr1:155156588-155156878(+)$1	290	60	86	11.8960
ii####eeeeennnnneeeee>>>>>	chr3:138255642-138255913(-)$1	271	161	187	10.4011
[ccc"""cccooooooccc333ccc]	chr7:138989026-138989253(+)$1	227	160	186	12.8739
ddiiiiiiiiinnnnniiiiiiiii:	chr12:116419829-116420083(-)$1	254	101	127	10.6877
gdddd!!ddddnnnnndddd]dddd]	chr6:7284075-7284386(-)$1	311	133	159	13.3236
:ffffff[cccnnnnnccc]ffffff	chr5:154194157-154194432(+)$1	275	64	90	10.6921
!!eeeee[cccooooooccc]eeeee	chr6:28123847-28124084(+)$1	237	94	120	9.6574
===========nnnnn==========	chr6:90641506-90641731(-)$1	225	41	67	12.8882
===========oooooo=========	chrX:119390422-119390644(+)$1	222	123	149	10.2367
!!bb[a[ddddnnnnndddda]bb33	chr20:3848336-3848570(+)$1	234	136	162	13.0651
eeeee!!ddddnnnnndddd333eee	chr17:46987947-46988183(+)$1	236	133	159	14.7083
ggggggg[cccnnnnnccc]gggggg	chr20:58521612-58521851(+)$1	239	180	206	12.9880
::ccc!!ddddnnnnndddd22ccc:	chr11:47639062-47639295(-)$1	233	20	46	11.9435
####bb[cccooooooccc]bb333g	chr20:60883761-60883986(+)$1	225	41	67	9.9964
cc[a####cccooooooccc4444a]	chrX:6967379-6967604(-)$1	225	151	177	12.0991
gggg"""ddddnnnnnddddgggggg	chr17:37075218-37075498(+)$1	280	179	205	13.9620
::dddd!!cccnnnnnccc22dddd:	chr12:46582397-46582643(-)$1	246	161	187	10.7224
ffffbb[ddddnnnnndddd]bb]ff	chr7:112459469-112459698(-)$1	229	156	182	12.2710
eeeee"""cccnnnnnccc22eeeee	chr12:56554859-56555123(+)$1	264	48	74	14.0983
bb[ccc"""bboooooobb22ccc]b	chr3:44399853-44400141(+)$1	288	240	266	9.2998
iiiiii[ddddnnnnndddd22iiii	chr12:976822-977064(+)$1	242	170	196	14.4440
!!ccc[bbcccnnnnnccc333bb]c	chr4:156265282-156265520(-)$1	238	144	170	13.6653
##dddd[cccooooooccc4444ddd	chr17:42765211-42765453(-)$1	242	154	180	10.8978
eeeee"""cccnnnnnccc4444eee	chr1:213069032-213069268(+)$1	236	67	93	14.6533
f####dddd[annnnna]dddd333f	chr12:52389072-52389320(+)$1	248	54	80	11.5844
[dddd!!cccooooooccc22dddde	chr1:220322079-220322316(-)$1	237	53	79	10.9850
""ccc!!ddddnnnnndddd]ccc22	chr11:108029067-108029334(-)$1	267	83	109	13.9997
ee$$$$$ddddnnnnndddd333eee	chrX:135749313-135749577(-)$1	264	39	65	14.1013
======!!abbnnnnnbb]a22====	chr10:102310595-102310835(+)$1	240	185	211	13.0808
gggggggddddnnnnndddd22gggg	chr19:50185115-50185341(+)$1	226	197	223	13.6689

#otherMatches

#Seq PSSM
uuccagcucagucagucugaucucag	chr3:150918645-150918893(+)$1	248	86	112	12.4061
ugugugugucaaaggggacuaacagc	chr19:8586093-8586313(-)$1	220	135	161	11.8757
UAAUAGCCCACAAUCAGUGUUCUGUU	chr12:111887220-111887453(+)$1	233	17	43	12.6826
uacucugagauuuacugucuucaucu	chr1:39329225-39329458(-)$1	233	157	183	11.0256
ucaagcucuaccuuccguaaaaugcu	chr19:9761907-9762145(-)$1	238	121	147	14.2884
UCUUUGCUGCAUAUUUUGCUAUAAGA	chrX:154284358-154284581(+)$1	223	18	44	14.6125
AGACACUUAUGCAGGGGUACAUGCUA	chr1:162496010-162496250(+)$1	240	176	202	10.6073
AAAUACCUUUAAAAAUGAAAUAAUUU	chr13:52989350-52989585(-)$1	235	118	144	10.8690
AACAACCAUAAGUGUGUUAAGUGUUA	chr1:45285500-45285749(-)$1	249	18	44	13.3922
UCAUGAAAAAGAAAGCCUUUGCCAUU	chr5:49694674-49694918(-)$1	244	158	184	14.7801
CUUUUCCCUCUGAGAGAGAGACCAAG	chr14:100604306-100604667(+)$1	361	11	37	14.8087
GCUGAGACGGGUACCCCCCGAAUGGC	chr20:20372956-20373204(-)$1	248	142	168	15.1455
GGUUUAAGCUUAGUGAGGGCAAAAUU	chrX:118749970-118750223(-)$1	253	109	135	11.9380
uguaauagguucucaaaagcccuaca	chr16:15819652-15819960(+)$1	308	91	117	10.7684
GAAUUUAGCUUCACUUGAGAGAGAUC	chr5:180662269-180662503(+)$1	234	92	118	14.5085
UAAACACAACUGCUAAGGUUCCUGUU	chr9:5919902-5920259(-)$1	357	220	246	11.4980
AAGGUGAGGAAGCAGUUUUGUUACCU	chr1:115315664-115315918(-)$1	254	30	56	11.4442
UUGGGGUGGACUCCCUGCCAGCCCAA	chr4:40198561-40198828(+)$1	267	138	164	10.9882
uguuaaauaaguauuUCUUacacaca	chr17:47924940-47925218(+)$1	278	73	99	14.8110
AUAAUGUCACCUGAAUGAUAACAUUA	chr17:78393868-78394144(+)$1	276	163	189	12.9718
UUUUUUCCUUCCCUGUGAUGAAAAAG	chr10:126674756-126675037(+)$1	281	137	163	12.3278
AAUCUCAGAGACAGUAUUUCAAGAGA	chr7:99173180-99173433(+)$1	253	90	116	13.3599
cacacaacauuuaucagauuauguuu	chr4:106161154-106161424(+)$1	270	7	33	9.8716
CCGUCAAUUACAUCUGGUAUUUGUAC	chr12:112381042-112381273(-)$1	231	128	154	11.4960
UUCGCCAAGCUGGACUGAGCCUUCCA	chr1:155156588-155156878(+)$1	290	60	86	11.8960
aaaauaacugauccuuuuagugaaga	chr3:138255642-138255913(-)$1	271	161	187	10.4011
CGUUAUCGUUUAAAAUAAUAGCAACA	chr7:138989026-138989253(+)$1	227	160	186	12.8739
cuaaacauaaaauuuauuuauguuuc	chr12:116419829-116420083(-)$1	254	101	127	10.6877
GUGUUCAGAUGGAGAACAUCAAGCAU	chr6:7284075-7284386(-)$1	311	133	159	13.3236
CCCUUCUGCCAUCUUCUGGGAGAAGG	chr5:154194157-154194432(+)$1	275	64	90	10.6921
CAUGUGUAUGUACACACACACACACA	chr6:28123847-28124084(+)$1	237	94	120	9.6574
auauauauauaaaauauauauauaua	chr6:90641506-90641731(-)$1	225	41	67	12.8882
AGUGCUAGUACUAAACUGUGCUAGUA	chrX:119390422-119390644(+)$1	222	123	149	10.2367
GGGGAGAUUAUCUACAAUAACACCAG	chr20:3848336-3848570(+)$1	234	136	162	13.0651
UUGAGGUGAUAACAACUGUCCUGCUC	chr17:46987947-46988183(+)$1	236	133	159	14.7083
UUAUGUGAACAAAAGAUGUACAUAUA	chr20:58521612-58521851(+)$1	239	180	206	12.9880
UCAACUCAAGCAUAAAGCUUCUGUUU	chr11:47639062-47639295(-)$1	233	20	46	11.9435
AUGAGCCUGGACUGAGCCACGCGCCG	chr20:60883761-60883986(+)$1	225	41	67	9.9964
UAGAAAUAGAAUUUGAUUUCAGAAUG	chrX:6967379-6967604(-)$1	225	151	177	12.0991
GGGUGAGCCUGACUGCCAGGACCCCA	chr17:37075218-37075498(+)$1	280	179	205	13.9620
ACCCAUCUAACUCUAUGUUUUGUGGC	chr12:46582397-46582643(-)$1	246	161	187	10.7224
UGCAGCUUGAUGCCAGAUCAUGUAUG	chr7:112459469-112459698(-)$1	229	156	182	12.2710
GUAGGUGUAGUGGAGAACUUUUCUGC	chr12:56554859-56555123(+)$1	264	48	74	14.0983
ugggaggauacacauagguuauuugc	chr3:44399853-44400141(+)$1	288	240	266	9.2998
UGAAUGUAUGAAUUACUUGUCUUAUU	chr12:976822-977064(+)$1	242	170	196	14.4440
UCAUAACUGUCCACCAGAUCAAAGCU	chr4:156265282-156265520(-)$1	238	144	170	13.6653
UUCCAGAGCCUCUUCUGGCAAGAUUG	chr17:42765211-42765453(-)$1	242	154	180	10.8978
GCUGACCAGCUGUUCAAGCCACUUCA	chr1:213069032-213069268(+)$1	236	67	93	14.6533
UUUUACUGGACUGUCUGAUCAGGGUG	chr12:52389072-52389320(+)$1	248	54	80	11.5844
UGUAUCUUAUUAAAUUAUAUUGUAUA	chr1:220322079-220322316(-)$1	237	53	79	10.9850
UUAUAAAUUACCUUCAGUAACUAUUC	chr11:108029067-108029334(-)$1	267	83	109	13.9997
GAAAACUGUAGUACCCUUAUUCCUUU	chrX:135749313-135749577(-)$1	264	39	65	14.1013
CCUGUAUAGAGGUCAGCUACGCUGCA	chr10:102310595-102310835(+)$1	240	185	211	13.0808
GGUCAUCGGGGUGAGUCUCCAGGGUG	chr19:50185115-50185341(+)$1	226	197	223	13.6689

#DB
(((.((.((((.....)))).))..)	chr3:150918645-150918893(+)$1	1	86	112	12.4061
(((((..(((......)))..))).)	chr19:8586093-8586313(-)$1	1	135	161	11.8757
.(((((..(((.....)))..)))))	chr12:111887220-111887453(+)$1	1	17	43	12.6826
(((((((((((.....))).)))...	chr1:39329225-39329458(-)$1	1	157	183	11.0256
((.(((..(((.....)))....)))	chr19:9761907-9762145(-)$1	1	121	147	14.2884
((((....(((.....)))...))))	chrX:154284358-154284581(+)$1	1	18	44	14.6125
((.((..(((......)))..)))))	chr1:162496010-162496250(+)$1	1	176	202	10.6073
((((...((((....))))...))))	chr13:52989350-52989585(-)$1	1	118	144	10.8690
(((((((.(((.....))).).))).	chr1:45285500-45285749(-)$1	1	18	44	13.3922
..(((..((((.....))))..))).	chr5:49694674-49694918(-)$1	1	158	184	14.7801
((((...((((.....))))...)))	chr14:100604306-100604667(+)$1	1	11	37	14.8087
(((....((((.....))))...)))	chr20:20372956-20373204(-)$1	1	142	168	15.1455
(((....((((.....))))......	chrX:118749970-118750223(-)$1	1	109	135	11.9380
((((...((((......)))).))))	chr16:15819652-15819960(+)$1	1	91	117	10.7684
((.(((..(((.....)))..)))))	chr5:180662269-180662503(+)$1	1	92	118	14.5085
..((((.((((.....))))..))))	chr9:5919902-5920259(-)$1	1	220	246	11.4980
)((((((.(((.....))).))))))	chr1:115315664-115315918(-)$1	1	30	56	11.4442
.((((.(((.(.....)))).))))(	chr4:40198561-40198828(+)$1	1	138	164	10.9882
(((....((((.....))))...)))	chr17:47924940-47925218(+)$1	1	73	99	14.8110
(((((((...(.....)...))))))	chr17:78393868-78394144(+)$1	1	163	189	12.9718
((((((.(.((.....)).).)))))	chr10:126674756-126675037(+)$1	1	137	163	12.3278
(.((((.((((.....))))..))))	chr7:99173180-99173433(+)$1	1	90	116	13.3599
((.(((..((((...))))..))).)	chr4:106161154-106161424(+)$1	1	7	33	9.8716
..(((((.(((.....))).))).))	chr12:112381042-112381273(-)$1	1	128	154	11.4960
((.(....(((......)))...).)	chr1:155156588-155156878(+)$1	1	60	86	11.8960
((....(((((.....))))).....	chr3:138255642-138255913(-)$1	1	161	187	10.4011
.(((...(((......)))...))).	chr7:138989026-138989253(+)$1	1	160	186	12.8739
))(((((((((.....))))))))).	chr12:116419829-116420083(-)$1	1	101	127	10.6877
(((((..((((.....)))).)))).	chr6:7284075-7284386(-)$1	1	133	159	13.3236
.((((((.(((.....))).))))))	chr5:154194157-154194432(+)$1	1	64	90	10.6921
..(((((.(((......))).)))))	chr6:28123847-28124084(+)$1	1	94	120	9.6574
(((((((((((.....))))))))))	chr6:90641506-90641731(-)$1	1	41	67	12.8882
(((((((((((......)))))))))	chrX:119390422-119390644(+)$1	1	123	149	10.2367
..((.(.((((.....))))).))..	chr20:3848336-3848570(+)$1	1	136	162	13.0651
(((((..((((.....))))...)))	chr17:46987947-46988183(+)$1	1	133	159	14.7083
(((((((.(((.....))).))))))	chr20:58521612-58521851(+)$1	1	180	206	12.9880
..(((..((((.....))))..))).	chr11:47639062-47639295(-)$1	1	20	46	11.9435
....((.(((......))).))...)	chr20:60883761-60883986(+)$1	1	41	67	9.9964
((.(....(((......)))....).	chrX:6967379-6967604(-)$1	1	151	177	12.0991
((((...((((.....))))))))))	chr17:37075218-37075498(+)$1	1	179	205	13.9620
..((((..(((.....)))..)))).	chr12:46582397-46582643(-)$1	1	161	187	10.7224
((((((.((((.....)))).)).))	chr7:112459469-112459698(-)$1	1	156	182	12.2710
(((((...(((.....)))..)))))	chr12:56554859-56555123(+)$1	1	48	74	14.0983
((.(((...((......))..))).)	chr3:44399853-44400141(+)$1	1	240	266	9.2998
((((((.((((.....))))..))))	chr12:976822-977064(+)$1	1	170	196	14.4440
..(((.(((((.....)))...)).)	chr4:156265282-156265520(-)$1	1	144	170	13.6653
..((((.(((......)))....)))	chr17:42765211-42765453(-)$1	1	154	180	10.8978
(((((...(((.....)))....)))	chr1:213069032-213069268(+)$1	1	67	93	14.6533
(....((((.(.....).))))...)	chr12:52389072-52389320(+)$1	1	54	80	11.5844
.((((..(((......)))..)))))	chr1:220322079-220322316(-)$1	1	53	79	10.9850
..(((..((((.....)))).)))..	chr11:108029067-108029334(-)$1	1	83	109	13.9997
((.....((((.....))))...)))	chrX:135749313-135749577(-)$1	1	39	65	14.1013
((((((..(((.....)).)..))))	chr10:102310595-102310835(+)$1	1	185	211	13.0808
(((((((((((.....))))..))))	chr19:50185115-50185341(+)$1	1	197	223	13.6689

#PSSM
e : 0.20	f : 0.12	: : 0.11	= : 0.11	g : 0.07	d : 0.05	# : 0.05	! : 0.05	b : 0.03	c : 0.03	i : 0.03	[ : 0.03	$ : 0.01	h : 0.01	" : 0.01	
e : 0.20	f : 0.12	d : 0.11	= : 0.11	# : 0.07	c : 0.05	: : 0.05	! : 0.05	g : 0.05	b : 0.03	i : 0.03	[ : 0.01	$ : 0.01	h : 0.01	" : 0.01	
e : 0.16	d : 0.14	c : 0.12	[ : 0.12	f : 0.11	= : 0.11	# : 0.05	g : 0.05	b : 0.03	i : 0.03	$ : 0.01	
c : 0.20	d : 0.14	e : 0.11	= : 0.11	# : 0.11	f : 0.09	b : 0.05	g : 0.05	a : 0.03	i : 0.03	[ : 0.01	$ : 0.01	
c : 0.20	# : 0.14	d : 0.12	e : 0.09	" : 0.09	= : 0.09	b : 0.07	f : 0.05	i : 0.03	g : 0.03	[ : 0.01	$ : 0.01	
! : 0.14	c : 0.12	# : 0.12	" : 0.12	d : 0.09	= : 0.09	b : 0.05	e : 0.03	f : 0.03	[ : 0.03	i : 0.03	g : 0.03	a : 0.01	$ : 0.01	
! : 0.25	[ : 0.16	" : 0.14	# : 0.11	c : 0.05	= : 0.05	f : 0.03	e : 0.03	g : 0.03	a : 0.01	i : 0.01	b : 0.01	d : 0.01	$ : 0.01	
d : 0.38	c : 0.14	! : 0.11	[ : 0.11	" : 0.07	# : 0.05	= : 0.03	a : 0.01	e : 0.01	i : 0.01	b : 0.01	
c : 0.44	d : 0.40	" : 0.03	= : 0.03	[ : 0.01	e : 0.01	i : 0.01	a : 0.01	
c : 0.42	d : 0.38	b : 0.05	[ : 0.03	= : 0.03	" : 0.01	e : 0.01	i : 0.01	
d : 0.38	c : 0.31	o : 0.11	a : 0.05	b : 0.05	= : 0.03	e : 0.01	i : 0.01	
n : 0.74	o : 0.22	m : 0.01	d : 0.01	
n : 0.74	o : 0.22	m : 0.01	l : 0.01	
n : 0.74	o : 0.22	m : 0.01	l : 0.01	
n : 0.74	o : 0.22	m : 0.01	l : 0.01	
n : 0.74	o : 0.22	d : 0.03	
d : 0.37	c : 0.37	o : 0.11	a : 0.05	b : 0.03	e : 0.01	i : 0.01	= : 0.01	
c : 0.44	d : 0.38	b : 0.05	= : 0.03	3 : 0.01	e : 0.01	i : 0.01	] : 0.01	
c : 0.44	d : 0.40	] : 0.03	= : 0.03	3 : 0.01	e : 0.01	i : 0.01	b : 0.01	
d : 0.37	2 : 0.16	] : 0.12	3 : 0.09	c : 0.07	4 : 0.05	a : 0.03	= : 0.03	e : 0.01	i : 0.01	
2 : 0.29	3 : 0.18	] : 0.12	4 : 0.07	= : 0.05	c : 0.03	a : 0.03	d : 0.03	f : 0.03	g : 0.03	6 : 0.01	e : 0.01	i : 0.01	b : 0.01	
3 : 0.18	c : 0.12	2 : 0.12	d : 0.09	b : 0.07	4 : 0.07	= : 0.07	e : 0.05	] : 0.05	f : 0.03	g : 0.03	6 : 0.01	> : 0.01	i : 0.01	
c : 0.20	3 : 0.14	d : 0.12	= : 0.11	b : 0.09	e : 0.07	4 : 0.07	g : 0.05	f : 0.03	i : 0.03	6 : 0.01	> : 0.01	
c : 0.18	e : 0.14	d : 0.14	= : 0.11	f : 0.09	g : 0.05	] : 0.03	i : 0.03	b : 0.03	3 : 0.03	2 : 0.01	0 : 0.01	6 : 0.01	a : 0.01	> : 0.01	4 : 0.01	
e : 0.16	d : 0.14	f : 0.11	= : 0.11	] : 0.09	c : 0.09	3 : 0.05	g : 0.05	2 : 0.03	i : 0.03	0 : 0.01	6 : 0.01	b : 0.01	> : 0.01	a : 0.01	
e : 0.22	f : 0.12	d : 0.11	= : 0.11	] : 0.07	g : 0.07	: : 0.05	c : 0.03	3 : 0.03	b : 0.03	0 : 0.01	6 : 0.01	h : 0.01	> : 0.01	i : 0.01	2 : 0.01	

#score	671.371243716972
#seq	54
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m2_run1.txt

#BEAR
!!ggggggg####bbmmmmbb22ggggggg22dd	chr1:17934331-17934562(+)$1	231	45	79	12.3959
cc[==========[ammmma]==========]cc	chr10:135113410-135113632(-)$1	222	23	57	13.9325
c!!eeeee!!eeeeemmmmeeeee333eeeeecc	chr9:101552354-101552579(+)$1	225	130	164	12.3848
eeeebb$$$$$ddddmmmmdddd333bb]eeeee	chr19:18547534-18547763(+)$1	229	52	86	11.9673
ee!!ggggggg[cccmmmmccc]ggggggg]eee	chr22:39479690-39479912(-)$1	222	126	160	13.9216
eeccc####eeeeeammmma]eeeee4444ccc2	chr8:145675760-145675981(-)$1	221	3	37	12.4188
fff!!bb[gggggggmmmmggggggg]bb333ff	chr7:814608-814835(+)$1	227	167	201	11.7444
e####cccgggggggooooooggggggg22ccc2	chr18:47101636-47101857(+)$1	221	93	127	9.9977
dddd$$$$$a[ddddmmmmdddd]a22dddd]bb	chr1:205180533-205180754(-)$1	221	96	130	11.3236
[dddd!!ccc"""bbmmmmbb22ccc22ddddgg	chr14:100165740-100165968(+)$1	228	112	146	11.9456
b[ccc[gggggggbbmmmmbb22ggggggg]ccc	chr9:37746613-37746838(+)$1	225	82	116	12.4919
::ccc[a[gggggggmmmmggggggga]cccbb[	chr1:114201620-114201845(-)$1	225	23	57	10.1368
[dddd[ccca[eeeeemmmmeeeee22a]ccc]d	chr17:80615882-80616105(-)$1	223	103	137	10.5154
ccc"""dddd!!cccmmmmccc4444dddd4444	chr9:14748358-14748580(-)$1	222	124	158	13.1717
iiiiiiii[ccc!!ammmma]ccciiiiiiiii]	chr16:30680489-30680712(-)$1	223	101	135	13.0151
:eeeeecccbb[cccmmmmcccbb]ccc22eeee	chr7:95157231-95157457(+)$1	226	85	119	10.9768
cccccc!!a!!ddddmmmmdddd22a22ccc]cc	chr5:172096754-172096977(-)$1	223	142	176	12.9572
eeeeeffffff!!bbmmmmbb333ffffff]eee	chr22:20229259-20229486(-)$1	227	165	199	11.1605
eeee"""ccc[eeeeemmmmeeeeeccc]eeeee	chr19:51885616-51885837(+)$1	221	134	168	11.1217
[ccca[eeeee!!bbmmmmbb22eeeee333a]c	chr2:217498372-217498595(-)$1	223	18	52	12.6777
ddeeeeedddd!!bbmmmmbb22dddd22eeeee	chr17:40120189-40120416(+)$1	227	176	210	10.4780
ccc[eeeee[cccbbmmmmbb]ccc333eeeeec	chrX:15270317-15270542(+)$1	225	83	117	12.5363
!!ccc!!eeeeecccmmmmccc]eeeee]ccc]c	chr11:3249504-3249725(+)$1	221	36	70	13.6222
dd"""ccc[bb[ccclllccc]bb]ccc4444dd	chr16:11009325-11009548(-)$1	223	31	65	10.2874
deeeee$$$$$a[ccclllccc]a333eeeeedd	chr9:130486533-130486759(+)$1	226	49	83	10.9094
eeee####ccccccooooooccc]ccceeeee]d	chr16:28912064-28912285(-)$1	221	172	206	11.0406
$$$===========ammmma]===========22	chr15:40588396-40588619(+)$1	223	71	105	12.8806
:bb[gggggggddddmmmmdddd22ggggggg]b	chr4:143350245-143350466(+)$1	221	63	97	10.9561
ggggg$$$$$ccc[ammmma]ccc]gggggggEE	chr8:37822786-37823030(-)$1	244	101	135	10.6515
eee####eeeeecccmmmmccc]eeeee4444ee	chr4:154523617-154523842(+)$1	225	5	39	13.5520
!!iiiiiiiii!!bbmmmmbb]iiiiiiiii444	chr17:73498525-73498746(+)$1	221	142	176	13.3595
hhh$$$$$ccc[cccmmmmccc22ccc333hhhh	chr5:176939740-176939962(+)$1	222	164	198	12.0499
!ccc[eeeeea[cccmmmmccc]a]eeeee22cc	chr11:62571230-62571451(-)$1	221	50	84	12.9533
eee!!eeeee!!cccmmmmccceeeeeeeeee88	chr7:154863098-154863325(+)$1	227	29	63	12.3442
d####ccc[a[ddddmmmmdddda]ccc4444dd	chr16:83932792-83933020(-)$1	228	67	101	12.9947
bb####dddd!!cccmmmmcccdddd22bb]ccc	chr5:137501426-137501650(+)$1	224	79	113	11.5775
eeeccceeeeeddddmmmmdddd]eeeee333cc	chr1:201187648-201187871(+)$1	223	25	59	12.2056
eeee!!a[gggggggmmmmggggggg]a]eeeee	chr12:50385798-50386021(-)$1	223	67	101	13.7778
eee!!ccc####cccmmmmcccccc22eeeee::	chr3:33087606-33087828(+)$1	222	161	195	12.2815
[dddd[eeeee[ccclllccc22eeeeedddd]c	chr11:66083892-66084114(-)$1	222	66	100	9.9269
ffffff[ccc[ccc[allla]ccc]ccc]fffff	chr14:90446801-90447030(+)$1	229	0	34	9.8838
eee[ccc[bb"""cccmmmmcccbbccc]eeeee	chr1:154600257-154600479(-)$1	222	135	169	10.7896
eeee!!ccc!!ddddlllddddccc333eeeee:	chr21:33043823-33044045(-)$1	222	185	219	10.9149
gggg[ccc[ccc[bbmmmmbb]ccc22cccgggg	chr17:73150303-73150539(-)$1	236	167	201	12.2464
[eeeeegggggggbblllbb]ggggggg22eeee	chr16:11554336-11554559(+)$1	223	21	55	10.0320
cccbb[ccc"""cccmmmmccc]cccbb]cccff	chr13:113777051-113777274(-)$1	223	155	189	12.6926
##ccc[eeeeeddddmmmmdddd333eeeee]cc	chr1:36565632-36565874(-)$1	242	6	40	12.8634
b[ccc[a!!ffffffmmmmffffff22a]ccc]b	chr17:34883285-34883506(+)$1	221	79	113	11.7694
[ccc[bb[a!!ddddmmmmdddd]a]bbcccccc	chr13:47127434-47127657(-)$1	223	96	130	12.2121
======$$$$$ddddmmmmdddd22=========	chr22:46859945-46860168(+)$1	223	68	102	12.9000
c[bb[dddd"""cccmmmmccc22dddd]bb22c	chr12:120883998-120884221(+)$1	223	57	91	11.0910
E:iiiiiiiiiddddmmmmdddd333iiiiiiii	chr5:140562098-140562319(+)$1	221	60	94	11.5308
dddd"""eeeeecccmmmmccc]eeeee]dddd]	chr7:140396451-140396681(+)$1	230	143	177	12.7680
!dddd[a!!ffffffmmmmffffff22a]dddd4	chr18:74680149-74680372(-)$1	223	172	206	11.5149
eeee!!a!!fffffflllffffff22a22eeeee	chr19:56539092-56539313(+)$1	221	160	194	9.8881
!!ggggggg!!ddddmmmmddddggggggg]ddd	chr10:102250472-102250695(+)$1	223	65	99	13.1037
ffff!!a[a[eeeeemmmmeeeee]a]a22ffff	chr1:1960895-1961116(+)$1	221	170	204	11.6962
[iiiiiiiii[ddddmmmmddddiiiiiiiii]a	chr19:11606668-11606893(-)$1	225	152	186	13.3419

#otherMatches

#Seq PSSM
AGUGAGUUCGAGAGCUACAGCGAGGACUCGGGGG	chr1:17934331-17934562(+)$1	231	45	79	12.3959
UGCAGAGUUUUCUCGUACUCCAGAAGACUUUCUA	chr10:135113410-135113632(-)$1	222	23	57	13.9325
UGAGGUGGUCAGGGUUGGCGCCCUUCUCCACCAG	chr9:101552354-101552579(+)$1	225	130	164	12.3848
CAGGGCCUCCAUGUGCGGCCACAGUUGCUCCUGC	chr19:18547534-18547763(+)$1	229	52	86	11.9673
CAAGGUUCAUUGUUAAAGUUGAAAGUGAAUGUGG	chr22:39479690-39479912(-)$1	222	126	160	13.9216
CAAGGUCACGGCACCGCUGGAGUGCUCCUUCCUG	chr8:145675760-145675981(-)$1	221	3	37	12.4188
AGAAACUCAUCAGGAUUUAUCCUGGUAGGACAUU	chr7:814608-814835(+)$1	227	167	201	11.7444
CUGCUGCAGGUUUGGAUCCUGCCGGGCCCAUGUU	chr18:47101636-47101857(+)$1	221	93	127	9.9977
GGGCGACGGGGUGCCAUGGGGCAGCGAGCCCGUC	chr1:205180533-205180754(-)$1	221	96	130	11.3236
GCUCCAGACUGUGUUUGGUGAGAGGUAAGGAGGU	chr14:100165740-100165968(+)$1	228	112	146	11.9456
GUCAGUGCACGGCCCUCACGGCCGCCGUGUUCUG	chr9:37746613-37746838(+)$1	225	82	116	12.4919
UCAUGAGACAGUUCAACAAUGGACUGCCCAUUCA	chr1:114201620-114201845(-)$1	225	23	57	10.1368
UUGCAAGACCUCUGCUGCCGGGCGGUCGUGUCCU	chr17:80615882-80616105(-)$1	223	103	137	10.5154
CUUUGAUUCUACAGAUCUUUCUCAAAGGAAGCUU	chr9:14748358-14748580(-)$1	222	124	158	13.1717
CGGGGCCUCUCAAACAGCAGGUGAAGGCCCUGGG	chr16:30680489-30680712(-)$1	223	101	135	13.0151
ACAGCACGGAGCACCACCUGGUCUGCCGCAUGCU	chr7:95157231-95157457(+)$1	226	85	119	10.9768
GGCCGCAGCACGGCCGGGUGGCCAGGAGGCGCGC	chr5:172096754-172096977(-)$1	223	142	176	12.9572
AGGCUCAGGUGCCCUACCCAGCCUCACCUGCAGC	chr22:20229259-20229486(-)$1	227	165	199	11.1605
GCCCAUGAUGAUGCCGGAGAUGGCGCAUAGGGCA	chr19:51885616-51885837(+)$1	221	134	168	11.1217
AGCGCAGCCCCUGGCCGCAGCGCGGGGUGUAGAC	chr2:217498372-217498595(-)$1	223	18	52	12.6777
CCUUCUCCGAGGAGUACAAGCGGCUCGAUGAGGA	chr17:40120189-40120416(+)$1	227	176	210	10.4780
GGAUGCCAGAUCACUCUCAGGUUGAACGCUGGCU	chrX:15270317-15270542(+)$1	225	83	117	12.5363
GGUGCAGGCGCCGCUGAGCAGCAGGUGCAGCAGC	chr11:3249504-3249725(+)$1	221	36	70	13.6222
CUAUACUCACUCCAGAUGCUGCAGGGAGGAAAAG	chr16:11009325-11009548(-)$1	223	31	65	10.2874
CUGCUGAACAAGGCCCUCCGGGACGAGCAGCAGG	chr9:130486533-130486759(+)$1	226	49	83	10.9094
UCGAACUCUCGGCCCGUGUAGGCGCGAUCGGCCA	chr16:28912064-28912285(-)$1	221	172	206	11.0406
CCACCCGUAAGUUACUCAUGCUAACUUACGGGCA	chr15:40588396-40588619(+)$1	223	71	105	12.8806
AAGAUGGAAUUUCUUACCAAGGAUGAAUUCCAAC	chr4:143350245-143350466(+)$1	221	63	97	10.9561
CAGCGCCUUCCGCCGUCUUCUGUGCCGCUGCGGC	chr8:37822786-37823030(-)$1	244	101	135	10.6515
UGUCAUUAUUUUGCCUUGUGGCUAAAAUCAAAAC	chr4:154523617-154523842(+)$1	225	5	39	13.5520
AAGGGUAGCAUAACUGCCUAGGGUGCUGCCCACU	chr17:73498525-73498746(+)$1	221	142	176	13.3595
GGGCUAACUGCCUGGGCACCCACCGCACCUCCCC	chr5:176939740-176939962(+)$1	222	164	198	12.0499
GGGUCCCUUCCGGUGGAAAUAUGGUGAAGGAAAC	chr11:62571230-62571451(-)$1	221	50	84	12.9533
UCUGGCCCCGCUGCUUUUUGGCUGGGGAGAGACG	chr7:154863098-154863325(+)$1	227	29	63	12.3442
GCACUGACCCUCGGCGGGCGCCGGUGUCUUCUCG	chr16:83932792-83933020(-)$1	228	67	101	12.9947
UGAAUAGUUACCUUGUCCUCAAUGAUGGCAAUGA	chr5:137501426-137501650(+)$1	224	79	113	11.5775
GGCGGACGUGCGGCAGGGCUGUCAGUAUGAGUUC	chr1:201187648-201187871(+)$1	223	25	59	12.2056
AGCUUUGGAAGUUUGCUAACAGAUUUGCUGGCUU	chr12:50385798-50386021(-)$1	223	67	101	13.7778
CUCUGGGACAAGUUCUUUGGGAUCCAUGAGCUCA	chr3:33087606-33087828(+)$1	222	161	195	12.2815
GUCGACGGCUACCUGUGCCAGUUUGGCUUCGAGG	chr11:66083892-66084114(-)$1	222	66	100	9.9269
UAUGUAUUACAUUUGCAUUGGAAAGGUAUUACAU	chr14:90446801-90447030(+)$1	229	0	34	9.8838
AAGUGCAAGACCCGGUAAGAGCCUCUGUCCUUCU	chr1:154600257-154600479(-)$1	222	135	169	10.7896
AAGUGGGAAAUGUAGACACUGCUUCAGAACUUGA	chr21:33043823-33044045(-)$1	222	185	219	10.9149
GGGCCUCGCGCCGGUCGUUGCGGGUAACGAGCCC	chr17:73150303-73150539(-)$1	236	167	201	12.2464
GUGCAGUGGAGCUCGUGGCGCAGCUCCAGCCUGU	chr16:11554336-11554559(+)$1	223	21	55	10.0320
CAAAGUCCACGCCCCAGCUGGGAUGGCUGUUGUC	chr13:113777051-113777274(-)$1	223	155	189	12.6926
UCUUUGCAGCACGUCCACGGACGCCAUGCUGGGG	chr1:36565632-36565874(-)$1	242	6	40	12.8634
CAGCGGCAGAGCCUUACCUGGGGCUGAGGCGCAG	chr17:34883285-34883506(+)$1	221	79	113	11.7694
AGGUUGGGGUUCGCUUCCCGGCGUCGCCAUCUUC	chr13:47127434-47127657(-)$1	223	96	130	12.2121
AGGAUGUUGGAGCUGACGUCGGUGUCGUUCUGGA	chr22:46859945-46860168(+)$1	223	68	102	12.9000
GAGGUCGGUGCACGGGUCCCCGGAGCUGUCCCCC	chr12:120883998-120884221(+)$1	223	57	91	11.0910
CGGAGACAAAGGCAAGUCCUUGUUUUCUUUGUUU	chr5:140562098-140562319(+)$1	221	60	94	11.5308
UUUCAGAAGCGGCUGCGCACGGACUGCUGGAGAU	chr7:140396451-140396681(+)$1	230	143	177	12.7680
CCGGGUGACCUGCAGACUCCUGCAGAGCUCCUGU	chr18:74680149-74680372(-)$1	223	172	206	11.5149
AUGGUUCAAGGACUCGGGGAGUCUGAGCUCCGUG	chr19:56539092-56539313(+)$1	221	160	194	9.8881
GUGUCCUGGGACCCUGAUAAGGGCUAGGAUGGGA	chr10:102250472-102250695(+)$1	223	65	99	13.1037
GGCACUGGACGUCUACUUCUGGAUCUGCUAUGUC	chr1:1960895-1961116(+)$1	221	170	204	11.6962
AUAGGGGGCCGCCCAUUUCUGGGGGCUUCUUACG	chr19:11606668-11606893(-)$1	225	152	186	13.3419

#DB
..(((((((....((....))..)))))))..))	chr1:17934331-17934562(+)$1	1	45	79	12.3959
((.((((((((((.(....).)))))))))).))	chr10:135113410-135113632(-)$1	1	23	57	13.9325
(..(((((..(((((....)))))...)))))))	chr9:101552354-101552579(+)$1	1	130	164	12.3848
((((((.....((((....))))...)).)))))	chr19:18547534-18547763(+)$1	1	52	86	11.9673
((..(((((((.(((....))).))))))).)))	chr22:39479690-39479912(-)$1	1	126	160	13.9216
(((((....((((((....).)))))....))).	chr8:145675760-145675981(-)$1	1	3	37	12.4188
(((..((.(((((((....))))))).))...))	chr7:814608-814835(+)$1	1	167	201	11.7444
(....((((((((((......)))))))..))).	chr18:47101636-47101857(+)$1	1	93	127	9.9977
((((.....(.((((....)))).)..)))).))	chr1:205180533-205180754(-)$1	1	96	130	11.3236
.((((..(((...((....))..)))..))))))	chr14:100165740-100165968(+)$1	1	112	146	11.9456
(.(((.(((((((((....))..))))))).)))	chr9:37746613-37746838(+)$1	1	82	116	12.4919
..(((.(.(((((((....)))))))).)))((.	chr1:114201620-114201845(-)$1	1	23	57	10.1368
.((((.((((.(((((....)))))..).))).)	chr17:80615882-80616105(-)$1	1	103	137	10.5154
(((...((((..(((....)))....))))....	chr9:14748358-14748580(-)$1	1	124	158	13.1717
((((((((.(((..(....).)))))))))))).	chr16:30680489-30680712(-)$1	1	101	135	13.0151
.((((((((((.(((....))))).)))..))))	chr7:95157231-95157457(+)$1	1	85	119	10.9768
((((((..(..((((....))))..)..))).))	chr5:172096754-172096977(-)$1	1	142	176	12.9572
(((((((((((..((....))...)))))).)))	chr22:20229259-20229486(-)$1	1	165	199	11.1605
((((...(((.(((((....)))))))).)))))	chr19:51885616-51885837(+)$1	1	134	168	11.1217
.((((.(((((..((....))..)))))...).)	chr2:217498372-217498595(-)$1	1	18	52	12.6777
(((((((((((..((....))..))))..)))))	chr17:40120189-40120416(+)$1	1	176	210	10.4780
(((.(((((.(((((....)).)))...))))))	chrX:15270317-15270542(+)$1	1	83	117	12.5363
..(((..((((((((....))).))))).))).)	chr11:3249504-3249725(+)$1	1	36	70	13.6222
((...(((.((.(((...))).)).)))....))	chr16:11009325-11009548(-)$1	1	31	65	10.2874
)(((((.....(.(((...))).)...)))))((	chr9:130486533-130486759(+)$1	1	49	83	10.9094
((((....((((((......))).)))))))).)	chr16:28912064-28912285(-)$1	1	172	206	11.0406
...((((((((((((....).)))))))))))..	chr15:40588396-40588619(+)$1	1	71	105	12.8806
.((.(((((((((((....))))..))))))).)	chr4:143350245-143350466(+)$1	1	63	97	10.9561
(((((.....(((.(....).))).)))))))((	chr8:37822786-37823030(-)$1	1	101	135	10.6515
(((....((((((((....))).)))))....))	chr4:154523617-154523842(+)$1	1	5	39	13.5520
..(((((((((..((....)).)))))))))...	chr17:73498525-73498746(+)$1	1	142	176	13.3595
(((.....(((.(((....)))..)))...))))	chr5:176939740-176939962(+)$1	1	164	198	12.0499
.(((.((((((.(((....))).).)))))..))	chr11:62571230-62571451(-)$1	1	50	84	12.9533
(((..(((((..(((....)))))))))))))..	chr7:154863098-154863325(+)$1	1	29	63	12.3442
(....(((.(.((((....))))).)))....))	chr16:83932792-83933020(-)$1	1	67	101	12.9947
((....((((..(((....)))))))..)).)))	chr5:137501426-137501650(+)$1	1	79	113	11.5775
(((((((((((((((....)))).)))))...))	chr1:201187648-201187871(+)$1	1	25	59	12.2056
((((..(.(((((((....))))))).).)))))	chr12:50385798-50386021(-)$1	1	67	101	13.7778
(((..(((....(((....))))))..)))))..	chr3:33087606-33087828(+)$1	1	161	195	12.2815
.((((.(((((.(((...)))..))))))))).)	chr11:66083892-66084114(-)$1	1	66	100	9.9269
((((((.(((.(((.(...).))).))).)))))	chr14:90446801-90447030(+)$1	1	0	34	9.8838
(((.(((.((...(((....)))))))).)))))	chr1:154600257-154600479(-)$1	1	135	169	10.7896
((((..(((..((((...)))))))...))))).	chr21:33043823-33044045(-)$1	1	185	219	10.9149
((((.(((.(((.((....)).)))..)))))))	chr17:73150303-73150539(-)$1	1	167	201	12.2464
.((((((((((((((...)).)))))))..))))	chr16:11554336-11554559(+)$1	1	21	55	10.0320
(((((.(((...(((....))).))))).)))))	chr13:113777051-113777274(-)$1	1	155	189	12.6926
..(((.(((((((((....))))...))))).))	chr1:36565632-36565874(-)$1	1	6	40	12.8634
(.(((.(..((((((....))))))..).))).)	chr17:34883285-34883506(+)$1	1	79	113	11.7694
.(((.((.(..((((....)))).).))))))))	chr13:47127434-47127657(-)$1	1	96	130	12.2121
((((((.....((((....))))..)))))))))	chr22:46859945-46860168(+)$1	1	68	102	12.9000
(.((.((((...(((....)))..)))).))..)	chr12:120883998-120884221(+)$1	1	57	91	11.0910
(.(((((((((((((....))))...))))))))	chr5:140562098-140562319(+)$1	1	60	94	11.5308
((((...((((((((....))).))))).)))).	chr7:140396451-140396681(+)$1	1	143	177	12.7680
.((((.(..((((((....))))))..).)))).	chr18:74680149-74680372(-)$1	1	172	206	11.5149
((((..(..((((((...))))))..)..)))))	chr19:56539092-56539313(+)$1	1	160	194	9.8881
..(((((((..((((....))))))))))).)))	chr10:102250472-102250695(+)$1	1	65	99	13.1037
((((..(.(.(((((....))))).).)..))))	chr1:1960895-1961116(+)$1	1	170	204	11.6962
.(((((((((.((((....))))))))))))).)	chr19:11606668-11606893(-)$1	1	152	186	13.3419

#PSSM
e : 0.25	c : 0.12	[ : 0.12	! : 0.10	d : 0.10	f : 0.05	b : 0.05	: : 0.05	g : 0.03	i : 0.01	$ : 0.01	h : 0.01	# : 0.01	= : 0.01	E : 0.01	
e : 0.29	c : 0.13	d : 0.13	! : 0.08	f : 0.05	# : 0.05	[ : 0.05	: : 0.03	i : 0.03	b : 0.03	g : 0.03	$ : 0.01	h : 0.01	= : 0.01	
e : 0.27	c : 0.22	d : 0.10	g : 0.06	i : 0.06	f : 0.05	# : 0.05	! : 0.03	b : 0.03	[ : 0.01	" : 0.01	$ : 0.01	h : 0.01	= : 0.01	
e : 0.20	c : 0.18	d : 0.10	g : 0.06	! : 0.06	# : 0.06	i : 0.06	= : 0.05	[ : 0.05	" : 0.03	f : 0.03	b : 0.03	$ : 0.01	
c : 0.15	e : 0.12	! : 0.12	g : 0.08	# : 0.08	d : 0.06	" : 0.06	i : 0.06	[ : 0.06	= : 0.05	b : 0.03	$ : 0.03	a : 0.01	f : 0.01	
[ : 0.15	e : 0.13	c : 0.13	! : 0.10	g : 0.06	# : 0.06	i : 0.06	= : 0.05	b : 0.05	$ : 0.05	" : 0.05	f : 0.03	d : 0.01	
c : 0.17	e : 0.15	g : 0.10	$ : 0.10	a : 0.10	i : 0.06	# : 0.05	! : 0.05	d : 0.05	= : 0.03	b : 0.03	" : 0.03	f : 0.01	[ : 0.01	
c : 0.20	e : 0.18	g : 0.10	$ : 0.10	[ : 0.10	d : 0.06	i : 0.06	! : 0.06	= : 0.03	# : 0.03	f : 0.01	
g : 0.17	e : 0.17	c : 0.15	$ : 0.08	! : 0.06	d : 0.06	[ : 0.06	a : 0.05	i : 0.05	= : 0.03	# : 0.03	f : 0.01	b : 0.01	
e : 0.17	g : 0.13	c : 0.12	! : 0.08	$ : 0.06	f : 0.06	a : 0.05	d : 0.05	b : 0.05	i : 0.05	# : 0.03	= : 0.03	[ : 0.03	" : 0.03	
e : 0.17	g : 0.13	! : 0.12	[ : 0.10	c : 0.10	" : 0.06	f : 0.06	$ : 0.05	# : 0.03	= : 0.03	b : 0.03	i : 0.03	d : 0.01	a : 0.01	
d : 0.22	e : 0.13	! : 0.12	[ : 0.10	g : 0.10	c : 0.10	" : 0.06	f : 0.05	# : 0.03	= : 0.03	a : 0.01	
c : 0.32	d : 0.22	g : 0.10	e : 0.08	! : 0.08	f : 0.05	= : 0.03	" : 0.03	[ : 0.03	# : 0.01	
c : 0.32	d : 0.22	b : 0.17	e : 0.08	g : 0.06	f : 0.05	[ : 0.03	! : 0.01	= : 0.01	
c : 0.29	d : 0.22	b : 0.17	a : 0.08	e : 0.06	g : 0.06	f : 0.05	o : 0.01	[ : 0.01	
m : 0.79	l : 0.08	o : 0.03	e : 0.03	c : 0.03	a : 0.01	
m : 0.84	l : 0.12	o : 0.03	
m : 0.84	l : 0.12	o : 0.03	
m : 0.84	o : 0.03	c : 0.03	l : 0.03	d : 0.01	b : 0.01	f : 0.01	
c : 0.27	d : 0.22	b : 0.17	a : 0.10	g : 0.05	m : 0.05	f : 0.05	e : 0.03	o : 0.03	
c : 0.31	d : 0.22	b : 0.15	] : 0.12	e : 0.06	g : 0.05	f : 0.05	o : 0.01	
c : 0.32	d : 0.22	2 : 0.10	e : 0.08	g : 0.08	] : 0.06	f : 0.05	= : 0.03	3 : 0.01	
d : 0.22	c : 0.15	2 : 0.13	] : 0.12	e : 0.10	g : 0.08	f : 0.05	= : 0.03	b : 0.03	4 : 0.01	3 : 0.01	i : 0.01	
e : 0.18	g : 0.15	c : 0.15	2 : 0.08	3 : 0.06	] : 0.06	b : 0.05	a : 0.05	f : 0.05	= : 0.03	d : 0.03	i : 0.03	4 : 0.01	
e : 0.17	g : 0.15	c : 0.13	] : 0.12	3 : 0.08	2 : 0.06	i : 0.05	f : 0.05	d : 0.05	= : 0.03	a : 0.03	4 : 0.01	b : 0.01	
g : 0.18	c : 0.17	e : 0.15	3 : 0.12	2 : 0.12	= : 0.05	i : 0.05	d : 0.05	a : 0.03	4 : 0.01	f : 0.01	] : 0.01	
2 : 0.15	e : 0.15	g : 0.13	c : 0.13	3 : 0.06	i : 0.06	= : 0.05	b : 0.05	] : 0.05	d : 0.05	a : 0.03	4 : 0.01	f : 0.01	
e : 0.22	g : 0.13	c : 0.12	2 : 0.08	a : 0.08	b : 0.06	i : 0.06	= : 0.05	d : 0.05	3 : 0.05	4 : 0.01	] : 0.01	f : 0.01	
] : 0.20	e : 0.17	g : 0.10	2 : 0.10	4 : 0.06	d : 0.06	c : 0.06	i : 0.06	= : 0.05	b : 0.03	3 : 0.03	f : 0.01	
e : 0.25	c : 0.13	g : 0.10	d : 0.10	4 : 0.06	3 : 0.06	2 : 0.06	i : 0.06	= : 0.05	f : 0.03	b : 0.03	
e : 0.27	c : 0.15	] : 0.08	d : 0.08	4 : 0.06	i : 0.06	= : 0.05	3 : 0.05	g : 0.05	2 : 0.03	f : 0.03	h : 0.01	b : 0.01	
e : 0.29	c : 0.15	d : 0.08	4 : 0.08	] : 0.06	2 : 0.05	i : 0.05	g : 0.05	3 : 0.03	= : 0.03	f : 0.03	b : 0.01	a : 0.01	h : 0.01	
e : 0.22	c : 0.18	] : 0.13	d : 0.12	f : 0.06	b : 0.03	g : 0.03	4 : 0.03	i : 0.03	2 : 0.03	E : 0.01	h : 0.01	8 : 0.01	: : 0.01	= : 0.01	
c : 0.24	e : 0.18	d : 0.12	f : 0.06	2 : 0.05	b : 0.05	4 : 0.05	g : 0.03	] : 0.03	: : 0.03	[ : 0.01	E : 0.01	h : 0.01	8 : 0.01	= : 0.01	i : 0.01	a : 0.01	

#score	691.8834443738896
#seq	58
#width	34
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m1_run1.txt

#BEAR
gggggggtttttttttttggggg	chr2:136511693-136511965(+)$1	272	193	216	22.5549
$$eeeeevvvvvvvvvvvvveee	chr12:123745636-123746010(+)$1	374	126	149	23.7121
eeeddddtttttttttttddddE	chr2:216981388-216981658(+)$1	270	110	133	20.8597
hhhhhawwwwwwwwwwwwwwa]h	chr7:5566939-5567212(+)$1	273	210	233	20.9409
eeeeevvvvvvvvvvvvveeeee	chr1:226124154-226124537(+)$1	383	31	54	23.3613
=!!ddddtttttttttttdddd5	chr6:99914428-99914693(+)$1	265	10	33	21.4051
))ddddwwwwwwwwwwwwwwddd	chr4:88973069-88973365(+)$1	296	96	119	20.8067
gggggggtttttttttttggggg	chr6:76331194-76331527(+)$1	333	280	303	22.5549
bffffffwwwwwwwwwwwwwwff	chr19:35500712-35501045(+)$1	333	201	224	20.6308
$$$$cccvvvvvvvvvvvvvccc	chr7:148700521-148700785(+)$1	264	151	174	22.2697
ffffffuuuuuuuuuuuufffff	chr19:10265463-10265728(+)$1	265	164	187	21.7826
ffffffvvvvvvvvvvvvvffff	chr14:72054372-72054646(+)$1	274	247	270	22.8625
g"""ccctttttttttttccc33	chr12:123003293-123003597(+)$1	304	65	88	22.4646
eeeeevvvvvvvvvvvvveeeee	chr6:76343206-76343552(+)$1	346	257	280	23.3613
gggggggvvvvvvvvvvvvvggg	chr5:17276166-17276571(+)$1	405	36	59	23.3903
!!cccwwwwwwwwwwwwwwccc4	chrX:147013934-147014223(+)$1	289	29	52	21.9955
eeeee[avvvvvvvvvvvvva]e	chr1:11722230-11722505(+)$1	275	232	255	23.6109
eeeeevvvvvvvvvvvvveeeee	chr9:95012016-95012273(+)$1	257	109	132	23.3613
:fffffftttttttttttfffff	chr15:25207221-25207519(+)$1	298	116	139	20.9728
:eeeeeuuuuuuuuuuuueeeee	chr17:26369702-26370001(+)$1	299	52	75	22.2710
hhhhwwwwwwwwwwwwwwhhhhh	chr11:9430015-9430345(+)$1	330	21	44	19.2185
!!eeeeeuuuuuuuuuuuueeee	chr17:27443316-27443576(+)$1	260	118	141	23.6077
ggeeeeevvvvvvvvvvvvveee	chr12:100733300-100733565(+)$1	265	80	103	23.9807
:eeeeeuuuuuuuuuuuueeeee	chr1:150192426-150192707(+)$1	281	232	255	22.2710
gggggggtttttttttttggggg	chr1:33059069-33059493(+)$1	424	186	209	22.5549
ffddddvvvvvvvvvvvvvdddd	chr17:57279354-57279732(+)$1	378	354	377	22.8339
[cccwwwwwwwwwwwwwwccc]f	chr7:135611548-135611797(+)$1	249	55	78	21.0259
hhhhwwwwwwwwwwwwwwhhhhh	chr5:131915551-131915844(+)$1	293	265	288	19.2185
=======vvvvvvvvvvvvv===	chr12:32875449-32875752(+)$1	303	222	245	23.4125
ggeeeeevvvvvvvvvvvvveee	chr5:139062701-139063183(+)$1	482	163	186	23.9807
=[eeeeewwwwwwwwwwwwwwee	chr1:40758527-40758834(+)$1	307	36	59	22.0730
dd!!ccctttttttttttccc33	chr4:5822947-5823232(+)$1	285	207	230	22.2347
ffffffvvvvvvvvvvvvvffff	chr10:70453442-70453742(+)$1	300	124	147	22.8625
ddeeeeettttttttttteeeee	chr8:101932471-101932734(+)$1	263	17	40	22.7972
eeeewwwwwwwwwwwwwweeeee	chr7:157209013-157209294(+)$1	281	47	70	21.2999
""ddddvvvvvvvvvvvvvdddd	chr17:73237594-73237862(+)$1	268	103	126	23.2248
c[eeeeevvvvvvvvvvvvveee	chr2:219612306-219612609(+)$1	303	9	32	24.0418
f[cccvvvvvvvvvvvvvccc]f	chr6:4060875-4061210(+)$1	335	257	280	23.0410
!!ddddvvvvvvvvvvvvvdddd	chr12:4654321-4654650(+)$1	329	233	256	23.3837
=======vvvvvvvvvvvvv===	chr12:67707163-67707526(+)$1	363	115	138	23.4125
cceeeeettttttttttteeeee	chr15:25219480-25219766(+)$1	286	109	132	23.0640
gggggggvvvvvvvvvvvvvggg	chr19:49110704-49110968(+)$1	264	215	238	23.3903
:ddddvvvvvvvvvvvvvdddde	chrX:12993985-12994254(+)$1	269	0	23	21.6000
%%%ddddtttttttttttdddd7	chr21:34931883-34932179(+)$1	296	72	95	19.5490
!!cccyyyyyyyyyyyyyyyycc	chr10:64948795-64949095(+)$1	300	172	195	19.0851
b[eeeeeuuuuuuuuuuuueeee	chr19:3053375-3053635(+)$1	260	4	27	23.2914
:fffffftttttttttttfffff	chr1:53461207-53461698(+)$1	491	299	322	20.9728
eeeebbuuuuuuuuuuuubb]ee	chrX:153583166-153583423(+)$1	257	16	39	21.6103
"""cccuuuuuuuuuuuuccc33	chr21:44473212-44473540(+)$1	328	57	80	22.6747
##eeeeettttttttttteeeee	chr8:11679247-11679526(+)$1	279	214	237	23.3031
effffffwwwwwwwwwwwwwwff	chr14:56101166-56101546(+)$1	380	7	30	20.7013
gggggggtttttttttttggggg	chrX:70511447-70511782(+)$1	335	267	290	22.5549
bb[cccuuuuuuuuuuuuccc]b	chr11:94604062-94604350(+)$1	288	87	110	21.9719
!!eeeeevvvvvvvvvvvvveee	chr12:123078411-123078712(+)$1	301	13	36	24.2385
=:eeeeeuuuuuuuuuuuueeee	chr2:101621650-101621968(+)$1	318	258	281	22.3004
bb[cccuuuuuuuuuuuucccbb	chr14:32559736-32560059(+)$1	323	141	164	21.5760
ddeeeeettttttttttteeeee	chr4:88059329-88059609(+)$1	280	125	148	22.7972
gggggggtttttttttttggggg	chr10:118644437-118644884(+)$1	447	378	401	22.5549
gggggggvvvvvvvvvvvvvggg	chr12:70726163-70726413(+)$1	250	123	146	23.3903
b[dddduuuuuuuuuuuudddd]	chr14:31588818-31589081(+)$1	263	193	216	22.0686
iiiiiiitttttttttttiiiii	chr3:150177001-150177425(+)$1	424	143	166	22.3416

#otherMatches

#Seq PSSM
UCAGGAAUUGGAuuuuuuuuuuu	chr2:136511693-136511965(+)$1	272	193	216	22.5549
AUUGACUUUGAAGCACUAAUAGU	chr12:123745636-123746010(+)$1	374	126	149	23.7121
CUACCAGAUUUUGAUUUGCUGGA	chr2:216981388-216981658(+)$1	270	110	133	20.8597
AUGUGCAAUCAAAGUCCUCGGCC	chr7:5566939-5567212(+)$1	273	210	233	20.9409
CUAUAUAAAUUUAACUAUUAUAG	chr1:226124154-226124537(+)$1	383	31	54	23.3613
UCUGUCAAAUUUUAAAAAUGACU	chr6:99914428-99914693(+)$1	265	10	33	21.4051
UAACAUAUACAGAACAUCAAAUG	chr4:88973069-88973365(+)$1	296	96	119	20.8067
UAAGGAAAGAAAAAGCAAUUCCU	chr6:76331194-76331527(+)$1	333	280	303	22.5549
CCCUGUGACUCUCCGCCAGCCCG	chr19:35500712-35501045(+)$1	333	201	224	20.6308
uguauccucuguaaaaaucugga	chr7:148700521-148700785(+)$1	264	151	174	22.2697
GCAGGAACUCCACCACAAUCUUG	chr19:10265463-10265728(+)$1	265	164	187	21.7826
AGGCCUCUUGCCACUGACAGGGC	chr14:72054372-72054646(+)$1	274	247	270	22.8625
ACUACAUUAUAAUACAACAUGAC	chr12:123003293-123003597(+)$1	304	65	88	22.4646
UUCCUACAGAAAAGAUAAAGGAA	chr6:76343206-76343552(+)$1	346	257	280	23.3613
UCCCAUCAAGGGAGGGAGGGGGU	chr5:17276166-17276571(+)$1	405	36	59	23.3903
GAGAUUUCAUGAACAGUUUAUCG	chrX:147013934-147014223(+)$1	289	29	52	21.9955
GAACCAGGCCAUCACAGAAACAG	chr1:11722230-11722505(+)$1	275	232	255	23.6109
AUCAUCUACCUUACCUCAAUGAU	chr9:95012016-95012273(+)$1	257	109	132	23.3613
CCUCACUGAGCAACCAAGAGUGA	chr15:25207221-25207519(+)$1	298	116	139	20.9728
AGAUCCUCUAACUUGUUUGGAUU	chr17:26369702-26370001(+)$1	299	52	75	22.2710
UAUCUAUCUGAAAAAUAUGAUAA	chr11:9430015-9430345(+)$1	330	21	44	19.2185
GAAAGCUAACAAGAAACAAGGUU	chr17:27443316-27443576(+)$1	260	118	141	23.6077
AAAAAUCUUGAUGCUGUAUUGAU	chr12:100733300-100733565(+)$1	265	80	103	23.9807
AUGCACCAUACUACACCUGUGUA	chr1:150192426-150192707(+)$1	281	232	255	22.2710
CAGUCUGAAGAACAAGCACAGAU	chr1:33059069-33059493(+)$1	424	186	209	22.5549
cccaggaauucaagacuagccug	chr17:57279354-57279732(+)$1	378	354	377	22.8339
AUGAGAAACCCAACUGCGUCAAA	chr7:135611548-135611797(+)$1	249	55	78	21.0259
auguuuugauauaaguauacauc	chr5:131915551-131915844(+)$1	293	265	288	19.2185
CUAUAAAACAAAAAUAUAACUUU	chr12:32875449-32875752(+)$1	303	222	245	23.4125
CUGUAACCUUUUGAAAUCUAGUU	chr5:139062701-139063183(+)$1	482	163	186	23.9807
UCUUUGACAUCUAAUUUACCAUC	chr1:40758527-40758834(+)$1	307	36	59	22.0730
ACCACUCAGAGAAUCAUGGAGCC	chr4:5822947-5823232(+)$1	285	207	230	22.2347
UUUUAGGCCUUAGCUCCCACUAG	chr10:70453442-70453742(+)$1	300	124	147	22.8625
AAGUGCUCCAAACCUUAAAGUAC	chr8:101932471-101932734(+)$1	263	17	40	22.7972
CGGAUCCUCUUCAUUCUUUUCGG	chr7:157209013-157209294(+)$1	281	47	70	21.2999
AAACUGUUAUCAUUGUCCUCAGU	chr17:73237594-73237862(+)$1	268	103	126	23.2248
GUAGGUAUCUACACAAACCCUAC	chr2:219612306-219612609(+)$1	303	9	32	24.0418
GUUAUGAAAUGAGUAGUAAUAUU	chr6:4060875-4061210(+)$1	335	257	280	23.0410
guugcuaggaggggagaggggua	chr12:4654321-4654650(+)$1	329	233	256	23.3837
AAGUAUUAGUGCAAUUUUCAGAU	chr12:67707163-67707526(+)$1	363	115	138	23.4125
GAACAGCAAUCAUGGUAAGCUGU	chr15:25219480-25219766(+)$1	286	109	132	23.0640
UAUGGuaaaaaauauauauauau	chr19:49110704-49110968(+)$1	264	215	238	23.3903
AGGAAUUCUUGCCGAUUUUUCCC	chrX:12993985-12994254(+)$1	269	0	23	21.6000
UCAUCUGGAUCUCAACAUCGGAA	chr21:34931883-34932179(+)$1	296	72	95	19.5490
CUGCUAUUCUUAUAAUCCUUAAG	chr10:64948795-64949095(+)$1	300	172	195	19.0851
GGUGCCCAGGACGGGAAAGGGGC	chr19:3053375-3053635(+)$1	260	4	27	23.2914
UGGAGCAGUUCACUGCCAUGUUC	chr1:53461207-53461698(+)$1	491	299	322	20.9728
CCCUCCUCACCGUCACUUGGAAG	chrX:153583166-153583423(+)$1	257	16	39	21.6103
aaagugaaauaaguuagacacga	chr21:44473212-44473540(+)$1	328	57	80	22.6747
AAGAAAAGUUGUCCAGUAUUUUC	chr8:11679247-11679526(+)$1	279	214	237	23.3031
AGUAUGUUUUGUUUAUUUCUUAU	chr14:56101166-56101546(+)$1	380	7	30	20.7013
CUUCCUCCCGACAUCACUGAGGA	chrX:70511447-70511782(+)$1	335	267	290	22.5549
GCGAUGGAUUUUAUUACACAUGG	chr11:94604062-94604350(+)$1	288	87	110	21.9719
uuauaggcaugagccaAAACCCU	chr12:123078411-123078712(+)$1	301	13	36	24.2385
uacaggcagccgccaccacgccu	chr2:101621650-101621968(+)$1	318	258	281	22.3004
GAUGGCAAAAAACAAAGAGCCUC	chr14:32559736-32560059(+)$1	323	141	164	21.5760
CAUGCUUACAAUUCCCAAAGGCA	chr4:88059329-88059609(+)$1	280	125	148	22.7972
UUUUAAAUAAACACCAAUUUUGA	chr10:118644437-118644884(+)$1	447	378	401	22.5549
CUCAAGGUUCAUAUAUAAAUUUU	chr12:70726163-70726413(+)$1	250	123	146	23.3903
GCACAUAAUCAUCAUCCCAUGUU	chr14:31588818-31589081(+)$1	263	193	216	22.0686
AGUUAUUGUGAUAUGAUAAAUAA	chr3:150177001-150177425(+)$1	424	143	166	22.3416

#DB
(((((((...........)))))	chr2:136511693-136511965(+)$1	1	193	216	22.5549
..(((((.............)))	chr12:123745636-123746010(+)$1	1	126	149	23.7121
)))((((...........)))))	chr2:216981388-216981658(+)$1	1	110	133	20.8597
((((((..............).)	chr7:5566939-5567212(+)$1	1	210	233	20.9409
(((((.............)))))	chr1:226124154-226124537(+)$1	1	31	54	23.3613
(..((((...........)))).	chr6:99914428-99914693(+)$1	1	10	33	21.4051
..((((..............)))	chr4:88973069-88973365(+)$1	1	96	119	20.8067
(((((((...........)))))	chr6:76331194-76331527(+)$1	1	280	303	22.5549
(((((((..............))	chr19:35500712-35501045(+)$1	1	201	224	20.6308
....(((.............)))	chr7:148700521-148700785(+)$1	1	151	174	22.2697
((((((............)))))	chr19:10265463-10265728(+)$1	1	164	187	21.7826
((((((.............))))	chr14:72054372-72054646(+)$1	1	247	270	22.8625
(...(((...........)))..	chr12:123003293-123003597(+)$1	1	65	88	22.4646
(((((.............)))))	chr6:76343206-76343552(+)$1	1	257	280	23.3613
(((((((.............)))	chr5:17276166-17276571(+)$1	1	36	59	23.3903
..(((..............))).	chrX:147013934-147014223(+)$1	1	29	52	21.9955
(((((.(.............).)	chr1:11722230-11722505(+)$1	1	232	255	23.6109
(((((.............)))))	chr9:95012016-95012273(+)$1	1	109	132	23.3613
.((((((...........)))))	chr15:25207221-25207519(+)$1	1	116	139	20.9728
.(((((............)))))	chr17:26369702-26370001(+)$1	1	52	75	22.2710
((((..............)))))	chr11:9430015-9430345(+)$1	1	21	44	19.2185
..(((((............))))	chr17:27443316-27443576(+)$1	1	118	141	23.6077
(((((((.............)))	chr12:100733300-100733565(+)$1	1	80	103	23.9807
.(((((............)))))	chr1:150192426-150192707(+)$1	1	232	255	22.2710
(((((((...........)))))	chr1:33059069-33059493(+)$1	1	186	209	22.5549
))((((.............))))	chr17:57279354-57279732(+)$1	1	354	377	22.8339
.(((..............))).)	chr7:135611548-135611797(+)$1	1	55	78	21.0259
((((..............)))))	chr5:131915551-131915844(+)$1	1	265	288	19.2185
(((((((.............)))	chr12:32875449-32875752(+)$1	1	222	245	23.4125
))(((((.............)))	chr5:139062701-139063183(+)$1	1	163	186	23.9807
(.(((((..............))	chr1:40758527-40758834(+)$1	1	36	59	22.0730
((..(((...........)))..	chr4:5822947-5823232(+)$1	1	207	230	22.2347
((((((.............))))	chr10:70453442-70453742(+)$1	1	124	147	22.8625
(((((((...........)))))	chr8:101932471-101932734(+)$1	1	17	40	22.7972
((((..............)))))	chr7:157209013-157209294(+)$1	1	47	70	21.2999
..((((.............))))	chr17:73237594-73237862(+)$1	1	103	126	23.2248
(.(((((.............)))	chr2:219612306-219612609(+)$1	1	9	32	24.0418
(.(((.............))).)	chr6:4060875-4061210(+)$1	1	257	280	23.0410
..((((.............))))	chr12:4654321-4654650(+)$1	1	233	256	23.3837
(((((((.............)))	chr12:67707163-67707526(+)$1	1	115	138	23.4125
))(((((...........)))))	chr15:25219480-25219766(+)$1	1	109	132	23.0640
(((((((.............)))	chr19:49110704-49110968(+)$1	1	215	238	23.3903
.((((.............))))(	chrX:12993985-12994254(+)$1	1	0	23	21.6000
...((((...........)))).	chr21:34931883-34932179(+)$1	1	72	95	19.5490
..(((................))	chr10:64948795-64949095(+)$1	1	172	195	19.0851
(.(((((............))))	chr19:3053375-3053635(+)$1	1	4	27	23.2914
.((((((...........)))))	chr1:53461207-53461698(+)$1	1	299	322	20.9728
((((((............)).))	chrX:153583166-153583423(+)$1	1	16	39	21.6103
...(((............)))..	chr21:44473212-44473540(+)$1	1	57	80	22.6747
..(((((...........)))))	chr8:11679247-11679526(+)$1	1	214	237	23.3031
(((((((..............))	chr14:56101166-56101546(+)$1	1	7	30	20.7013
(((((((...........)))))	chrX:70511447-70511782(+)$1	1	267	290	22.5549
((.(((............))).)	chr11:94604062-94604350(+)$1	1	87	110	21.9719
..(((((.............)))	chr12:123078411-123078712(+)$1	1	13	36	24.2385
).(((((............))))	chr2:101621650-101621968(+)$1	1	258	281	22.3004
((.(((............)))))	chr14:32559736-32560059(+)$1	1	141	164	21.5760
(((((((...........)))))	chr4:88059329-88059609(+)$1	1	125	148	22.7972
(((((((...........)))))	chr10:118644437-118644884(+)$1	1	378	401	22.5549
(((((((.............)))	chr12:70726163-70726413(+)$1	1	123	146	23.3903
(.((((............)))).	chr14:31588818-31589081(+)$1	1	193	216	22.0686
(((((((...........)))))	chr3:150177001-150177425(+)$1	1	143	166	22.3416

#PSSM
g : 0.18	e : 0.13	= : 0.08	b : 0.08	f : 0.08	! : 0.08	: : 0.08	h : 0.04	d : 0.04	$ : 0.03	" : 0.03	c : 0.03	) : 0.01	[ : 0.01	% : 0.01	# : 0.01	i : 0.01	
g : 0.16	e : 0.14	f : 0.13	! : 0.09	[ : 0.08	d : 0.06	h : 0.04	" : 0.04	$ : 0.03	c : 0.03	= : 0.03	b : 0.03	) : 0.01	% : 0.01	# : 0.01	: : 0.01	i : 0.01	
e : 0.36	g : 0.13	f : 0.11	d : 0.09	c : 0.06	h : 0.04	! : 0.03	" : 0.03	= : 0.03	[ : 0.03	$ : 0.01	% : 0.01	i : 0.01	
e : 0.34	d : 0.14	g : 0.13	f : 0.11	c : 0.11	h : 0.04	= : 0.03	$ : 0.01	" : 0.01	! : 0.01	i : 0.01	
e : 0.31	d : 0.14	c : 0.14	g : 0.13	f : 0.11	w : 0.06	= : 0.03	h : 0.01	b : 0.01	i : 0.01	
e : 0.24	g : 0.13	d : 0.13	f : 0.11	c : 0.09	v : 0.08	w : 0.08	= : 0.03	a : 0.01	[ : 0.01	y : 0.01	b : 0.01	i : 0.01	
e : 0.21	v : 0.16	g : 0.13	u : 0.13	w : 0.11	f : 0.06	d : 0.04	c : 0.04	= : 0.03	a : 0.01	y : 0.01	i : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.36	t : 0.27	u : 0.18	w : 0.16	y : 0.01	
v : 0.27	e : 0.16	c : 0.11	w : 0.09	g : 0.08	d : 0.08	f : 0.04	u : 0.04	h : 0.03	y : 0.01	b : 0.01	i : 0.01	
e : 0.21	v : 0.19	d : 0.13	c : 0.13	g : 0.08	w : 0.08	f : 0.08	h : 0.03	y : 0.01	b : 0.01	i : 0.01	
e : 0.29	d : 0.14	c : 0.14	g : 0.13	f : 0.08	w : 0.04	a : 0.03	h : 0.03	= : 0.03	y : 0.01	] : 0.01	i : 0.01	
e : 0.32	d : 0.14	g : 0.13	f : 0.11	] : 0.08	c : 0.04	3 : 0.04	h : 0.03	= : 0.03	b : 0.01	i : 0.01	
e : 0.36	f : 0.14	g : 0.13	d : 0.06	h : 0.04	3 : 0.04	c : 0.03	= : 0.03	b : 0.03	E : 0.01	5 : 0.01	4 : 0.01	7 : 0.01	] : 0.01	i : 0.01	

#score	1360.6835939784658
#seq	61
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_UTR_m1_run2.txt

#BEAR
[eeeeevvvvvvvvvvvvveeeee]a]b	chr14:31028333-31028575(+)$1	242	136	164	23.3798
hhhhh[auuuuuuuuuuuua]hhhhhhh	chr1:224573226-224573457(-)$1	231	112	140	22.0840
==[dddduuuuuuuuuuuudddd]====	chr19:39334546-39334795(-)$1	249	159	187	24.5276
fff[cccuuuuuuuuuuuuccc]fffff	chr11:107976442-107976672(+)$1	230	11	39	24.1368
cc[dddduuuuuuuuuuuudddd]cccb	chr6:162683572-162683794(-)$1	222	137	165	24.1269
==fffffftttttttttttffffff:::	chr3:98518102-98518332(-)$1	230	119	147	20.1998
a[eeeeeuuuuuuuuuuuueeeeeaccc	chr8:17077671-17077899(+)$1	228	178	206	23.9448
iifffffftttttttttttffffff333	chr2:235963672-235963915(+)$1	243	27	55	22.9869
!!eeeeewwwwwwwwwwwwwweeeee22	chr4:17625325-17625562(+)$1	237	11	39	22.4021
cccyyyyyyyyyyyyyyyyccc]bb22d	chr16:4411992-4412222(-)$1	230	60	88	21.0712
$$$ddddvvvvvvvvvvvvvdddd4444	chr5:77590328-77590580(-)$1	252	151	179	22.8795
$$$$$bbtttttttttttbb333ccc77	chr6:41861963-41862186(-)$1	223	160	188	20.7292
ddd[ddddtttttttttttdddd]dddd	chr22:40727066-40727293(+)$1	227	117	145	22.2428
$ccc[bbuuuuuuuuuuuubb]ccc444	chr18:19781698-19781926(+)$1	228	33	61	24.0105
ccc!!ccctttttttttttccc]ccc::	chr14:23652312-23652538(+)$1	226	7	35	22.8138
!!fffffftttttttttttffffff22b	chr18:55149271-55149501(+)$1	230	176	204	22.5643
bgggggggtttttttttttggggggg]b	chr3:113415147-113415371(+)$1	224	55	83	23.2171
"eeeeexxxxxxxxxxxxxxxeeeee]b	chr12:56119900-56120145(-)$1	245	175	203	18.2766
d[ddddyyyyyyyyyyyyyyyydddd22	chr3:53318214-53318438(-)$1	224	56	84	21.7306
####ddddtttttttttttdddd4444c	chr8:18390798-18391022(-)$1	224	53	81	23.1891
#ccc[bbuuuuuuuuuuuubb]ccc333	chr13:41764385-41764611(+)$1	226	83	111	24.3750
ffffffwwwwwwwwwwwwwwffffff]c	chr15:55905209-55905438(-)$1	229	180	208	21.8594
ee"""ccctttttttttttccc]eeeee	chr8:41401903-41402154(+)$1	251	11	39	23.3467
!!cccccctttttttttttccc]cccee	chr17:46147682-46147919(-)$1	237	56	84	24.1000
ggggggvvvvvvvvvvvvvggggggg44	chr7:1609080-1609303(+)$1	223	109	137	23.8272
&&eeeeettttttttttteeeeeccc::	chr14:39648266-39648518(+)$1	252	46	74	19.8843
ggeeeeeuuuuuuuuuuuueeeeehhhh	chr11:33377550-33377780(+)$1	230	102	130	23.0900
:ddddwwwwwwwwwwwwwwddddddddn	chr22:32078244-32078495(-)$1	251	156	184	19.9995
b[ddddbbtttttttttttbb]dddd]b	chr11:129992108-129992370(+)$1	262	177	205	22.5128
eeeddddtttttttttttddddffffff	chr19:53397329-53397556(-)$1	227	61	89	21.6688
iiiiiwwwwwwwwwwwwwwiiiiiiiii	chr5:138269941-138270170(+)$1	229	22	50	22.5651
[bb!!ccctttttttttttccc22bb]c	chr15:75663888-75664114(-)$1	226	117	145	23.2220
e:ddddawwwwwwwwwwwwwwa]dddd:	chr22:43035810-43036035(-)$1	225	165	193	20.1758
ffffccctttttttttttccc]ffffff	chr11:14479155-14479385(-)$1	230	38	66	22.1653
ggg[cccyyyyyyyyyyyyyyyyccc]g	chr8:17080763-17080988(+)$1	225	148	176	22.4305
ii"""ccctttttttttttccc>>>>>>	chr13:73282543-73282774(-)$1	231	120	148	22.8014
ffff[bbvvvvvvvvvvvvvbb22ffff	chr15:44057584-44057820(+)$1	236	82	110	21.6947
gggggggyyyyyyyyyyyyyyyyggggg	chr4:17835881-17836121(+)$1	240	150	178	21.7933
cc[dddduuuuuuuuuuuudddd]ccc]	chr3:48309528-48309758(+)$1	230	164	192	24.2015
""cccwwwwwwwwwwwwwwccc]ccc]b	chr10:103544135-103544371(-)$1	236	42	70	23.1826
!eeeeexxxxxxxxxxxxxxxeeeee33	chr22:21976855-21977106(+)$1	251	179	207	18.5583
gg[ddddvvvvvvvvvvvvvdddd]ggg	chr1:151669614-151669840(+)$1	226	14	42	23.1355
iiiiiiiuuuuuuuuuuuuiiiiiiiii	chr1:231353847-231354070(+)$1	223	112	140	24.3831
gggggwwwwwwwwwwwwwwggggggg66	chr1:230825681-230825911(+)$1	230	57	85	22.0842
:gggggggtttttttttttggggggg::	chr8:103219120-103219348(-)$1	228	6	34	20.9685
[ddddwwwwwwwwwwwwwwdddd]bbff	chr16:58584998-58585233(-)$1	235	120	148	21.5542
eeee[ccctttttttttttccc22eeee	chr9:98214105-98214328(+)$1	223	90	118	23.1674
e[eeeeeuuuuuuuuuuuueeeee]eee	chr2:69688555-69688782(-)$1	227	156	184	23.5777
[dddd[bbtttttttttttbb]dddd]a	chr1:150936973-150937199(+)$1	226	3	31	22.8001
========ttttttttttt=========	chr11:64533008-64533254(-)$1	246	158	186	23.8081
[ddddwwwwwwwwwwwwwwddddabb]b	chr17:37827363-37827589(-)$1	226	188	216	21.8985
ggggggguuuuuuuuuuuuggggggg33	chr1:65694452-65694681(+)$1	229	102	130	24.8091
:ccc[ccctttttttttttccc]cccII	chr6:28124227-28124458(+)$1	231	162	190	20.6166
!ffffffuuuuuuuuuuuuffffff444	chr13:100638038-100638268(+)$1	230	45	73	23.8109
eeeeeyyyyyyyyyyyyyyyyeeeee::	chr2:121750002-121750230(+)$1	228	79	107	20.6921
iiiiiiivvvvvvvvvvvvviiiiiiii	chr10:134230722-134230946(+)$1	224	27	55	23.4943
ee!!cccuuuuuuuuuuuuccc22eeee	chr1:110565218-110565447(+)$1	229	118	146	24.0748
dd!!cccvvvvvvvvvvvvvccc]dddd	chr20:5170762-5171016(+)$1	254	184	212	22.9937

#otherMatches

#Seq PSSM
CUCUCCUUGGUGAGUAAAUGGGGAACGG	chr14:31028333-31028575(+)$1	242	136	164	23.3798
AUCAAGAAAAGAACUUAAGUGUUGAUCU	chr1:224573226-224573457(-)$1	231	112	140	22.0840
AGGUGACUGACUGCCCCUUGUCAGCUUC	chr19:39334546-39334795(-)$1	249	159	187	24.5276
GUGGAUUUUUAUUCAUUGUGGUGCACGU	chr11:107976442-107976672(+)$1	230	11	39	24.1368
GGUGGACCUCAGCAGCUCAGUCCUCCCA	chr6:162683572-162683794(-)$1	222	137	165	24.1269
AUGAUGCUGCUUUUUACAAAGCAUCGUU	chr3:98518102-98518332(-)$1	230	119	147	20.1998
GCAGAAUAUGAAUUGAUUAGUUCUCUCC	chr8:17077671-17077899(+)$1	228	178	206	23.9448
GUUGCAUUAAUAACUUUAGGGUGCAGAC	chr2:235963672-235963915(+)$1	243	27	55	22.9869
AAAGCCCGCCGACAUCCCUCAGGGCUCC	chr4:17625325-17625562(+)$1	237	11	39	22.4021
GGCCCCAGUUCCAAGUUCCGCCAUGCUC	chr16:4411992-4412222(-)$1	230	60	88	21.0712
ACCCCGCACCCGCCAGCACCGCGGCAAU	chr5:77590328-77590580(-)$1	252	151	179	22.8795
GAUGGCCAUCUGGGACAAGGAUAACUGG	chr6:41861963-41862186(-)$1	223	160	188	20.7292
GCGGCCAUUACAUUCCCACAUGGGCGUC	chr22:40727066-40727293(+)$1	227	117	145	22.2428
UGUGCUGGAAAAAUUGCAACAACACUUU	chr18:19781698-19781926(+)$1	228	33	61	24.0105
GCGUUUACAAACAAGAAAAGUGUUGCUa	chr14:23652312-23652538(+)$1	226	7	35	22.8138
AAUGAUUUGUUUGUUUCCAAGGUCGGGG	chr18:55149271-55149501(+)$1	230	176	204	22.5643
CCGCAGUCACUUACCCGCCGGCUGCGCG	chr3:113415147-113415371(+)$1	224	55	83	23.2171
UCCUGCUGCAUUAAUGUUACUGUGGGCU	chr12:56119900-56120145(-)$1	245	175	203	18.2766
AGCUUUAUUACUCUCCUCCCCCAAAGAA	chr3:53318214-53318438(-)$1	224	56	84	21.7306
AUAUGAGUCACUAAUAUUAACUCCAGGG	chr8:18390798-18391022(-)$1	224	53	81	23.1891
ACUGGAAAUAACGUUAAACUUGUAGACU	chr13:41764385-41764611(+)$1	226	83	111	24.3750
UUUGAAAACUUAAGAGAAAAUUCAAGUG	chr15:55905209-55905438(-)$1	229	180	208	21.8594
cuuccuagucacguucucccuguagugc	chr8:41401903-41402154(+)$1	251	11	39	23.3467
CAGUAGGGAAAGACAAGGGCCCAUGCUC	chr17:46147682-46147919(-)$1	237	56	84	24.1000
gccaggaauucgagaccagccuggccaa	chr7:1609080-1609303(+)$1	223	109	137	23.8272
AUUGAACAAAAACUUGAAGUUCAGGCAG	chr14:39648266-39648518(+)$1	252	46	74	19.8843
UUUAGGGCCAUGUUUACUACCCUGAAAU	chr11:33377550-33377780(+)$1	230	102	130	23.0900
UGCUGUGAAUCCCAAAACUCAGCGCUCC	chr22:32078244-32078495(-)$1	251	156	184	19.9995
ugguggaggaCCGAGAUUACUACUAUGA	chr11:129992108-129992370(+)$1	262	177	205	22.5128
cagcuaaucuuuguauuuuuaguagaga	chr19:53397329-53397556(-)$1	227	61	89	21.6688
UGCAGGAGCCUACUUCUAGCUGUAUUUU	chr5:138269941-138270170(+)$1	229	22	50	22.5651
UGUGGCCUAACUUUCAAUGAGGGAACCG	chr15:75663888-75664114(-)$1	226	117	145	23.2220
AAAUUCCAAAAAAAAAAAAAAGUGAAUC	chr22:43035810-43036035(-)$1	225	165	193	20.1758
GCUUUACAGUUAAUUUAGGUAUGGGCUU	chr11:14479155-14479385(-)$1	230	38	66	22.1653
ACAAGUGGAUUUUUCACAAAUAACACGU	chr8:17080763-17080988(+)$1	225	148	176	22.4305
CAGAGGACUUCUUUAAAGUGUCACAUUU	chr13:73282543-73282774(-)$1	231	120	148	22.8014
CCUUCACAUCUCACUAACAAGUUUGAGG	chr15:44057584-44057820(+)$1	236	82	110	21.6947
UCAUUGUGAAGGUACAGAAAUAAACAGU	chr4:17835881-17836121(+)$1	240	150	178	21.7933
UCCAGAGACCACCAAUAAGCUCUUGGGG	chr3:48309528-48309758(+)$1	230	164	192	24.2015
UUCCUGGUUAUGAAUAUUAAGGUUGGAA	chr10:103544135-103544371(-)$1	236	42	70	23.1826
CCUGCUGACCCCCUCCUCCAGAGCAGCC	chr22:21976855-21977106(+)$1	251	179	207	18.5583
UGACUUAAAUGAAUUUAAAAUGAGCCAA	chr1:151669614-151669840(+)$1	226	14	42	23.1355
GGAAUUCUCAUCCACCAUCGAAUUCCAU	chr1:231353847-231354070(+)$1	223	112	140	24.3831
CUCCUACCAUCAUCAUUCCAGGAGGUCC	chr1:230825681-230825911(+)$1	230	57	85	22.0842
cagauguuuuuuaccuguuaacaucuca	chr8:103219120-103219348(-)$1	228	6	34	20.9685
GUGGAGCCCCCAGAAAAUAUCCAGGAGA	chr16:58584998-58585233(-)$1	235	120	148	21.5542
GCAAACAGGAAUUUAGGAACUGGCUUGC	chr9:98214105-98214328(+)$1	223	90	118	23.1674
UGCAUGAAAAAACUUUGACUUGUGGAUU	chr2:69688555-69688782(-)$1	227	156	184	23.5777
GACCAGAUGAUCCCUUCCAAUGUGGUGC	chr1:150936973-150937199(+)$1	226	3	31	22.8001
GGCGCCAGCUUGGGCUCUCCUGGCGCCC	chr11:64533008-64533254(-)$1	246	158	186	23.8081
UGCUUAAUAAAUCAAUUCCAAGCCUCAC	chr17:37827363-37827589(-)$1	226	188	216	21.8985
UCUUUCUUACUUAGAACUUGGAAAGGCU	chr1:65694452-65694681(+)$1	229	102	130	24.8091
UAGCAUAGAAUAUUAUUGACUAGGCUGU	chr6:28124227-28124458(+)$1	231	162	190	20.6166
uuuaaaguuuuuuuuuuuuuuuuaauaa	chr13:100638038-100638268(+)$1	230	45	73	23.8109
UUGUCUAUCUGCUUCCCCCUUGACAGUA	chr2:121750002-121750230(+)$1	228	79	107	20.6921
CUGAGUGUAUUUCUUCCCACCACUCAGC	chr10:134230722-134230946(+)$1	224	27	55	23.4943
GCAACCUAAAAUAUUUAAAGGGAGGUAG	chr1:110565218-110565447(+)$1	229	118	146	24.0748
CUGGUGUGACUUAGACAAUGACGAGGCU	chr20:5170762-5171016(+)$1	254	184	212	22.9937

#DB
.(((((.............))))).).)	chr14:31028333-31028575(+)$1	1	136	164	23.3798
(((((.(............).)))))))	chr1:224573226-224573457(-)$1	1	112	140	22.0840
((.((((............)))).))))	chr19:39334546-39334795(-)$1	1	159	187	24.5276
(((.(((............))).)))))	chr11:107976442-107976672(+)$1	1	11	39	24.1368
((.((((............)))).))))	chr6:162683572-162683794(-)$1	1	137	165	24.1269
))((((((...........))))))...	chr3:98518102-98518332(-)$1	1	119	147	20.1998
(.(((((............)))))))))	chr8:17077671-17077899(+)$1	1	178	206	23.9448
((((((((...........))))))...	chr2:235963672-235963915(+)$1	1	27	55	22.9869
..(((((..............)))))..	chr4:17625325-17625562(+)$1	1	11	39	22.4021
(((................))).))..)	chr16:4411992-4412222(-)$1	1	60	88	21.0712
...((((.............))))....	chr5:77590328-77590580(-)$1	1	151	179	22.8795
.....((...........))...)))..	chr6:41861963-41862186(-)$1	1	160	188	20.7292
(((.((((...........)))).))))	chr22:40727066-40727293(+)$1	1	117	145	22.2428
.(((.((............)).)))...	chr18:19781698-19781926(+)$1	1	33	61	24.0105
(((..(((...........))).)))..	chr14:23652312-23652538(+)$1	1	7	35	22.8138
..((((((...........))))))..)	chr18:55149271-55149501(+)$1	1	176	204	22.5643
((((((((...........))))))).)	chr3:113415147-113415371(+)$1	1	55	83	23.2171
.(((((...............))))).)	chr12:56119900-56120145(-)$1	1	175	203	18.2766
(.((((................))))..	chr3:53318214-53318438(-)$1	1	56	84	21.7306
....((((...........))))....)	chr8:18390798-18391022(-)$1	1	53	81	23.1891
.(((.((............)).)))...	chr13:41764385-41764611(+)$1	1	83	111	24.3750
((((((..............)))))).)	chr15:55905209-55905438(-)$1	1	180	208	21.8594
((...(((...........))).)))))	chr8:41401903-41402154(+)$1	1	11	39	23.3467
..((((((...........))).)))))	chr17:46147682-46147919(-)$1	1	56	84	24.1000
((((((.............)))))))..	chr7:1609080-1609303(+)$1	1	109	137	23.8272
..(((((...........))))))))..	chr14:39648266-39648518(+)$1	1	46	74	19.8843
))(((((............)))))((((	chr11:33377550-33377780(+)$1	1	102	130	23.0900
.((((..............))))((((.	chr22:32078244-32078495(-)$1	1	156	184	19.9995
(.((((((...........)).)))).)	chr11:129992108-129992370(+)$1	1	177	205	22.5128
)))((((...........))))((((((	chr19:53397329-53397556(-)$1	1	61	89	21.6688
(((((..............)))))))))	chr5:138269941-138270170(+)$1	1	22	50	22.5651
.((..(((...........)))..)).)	chr15:75663888-75664114(-)$1	1	117	145	23.2220
).(((((..............).)))).	chr22:43035810-43036035(-)$1	1	165	193	20.1758
(((((((...........))).))))))	chr11:14479155-14479385(-)$1	1	38	66	22.1653
(((.(((................))).)	chr8:17080763-17080988(+)$1	1	148	176	22.4305
((...(((...........)))......	chr13:73282543-73282774(-)$1	1	120	148	22.8014
((((.((.............))..))))	chr15:44057584-44057820(+)$1	1	82	110	21.6947
(((((((................)))))	chr4:17835881-17836121(+)$1	1	150	178	21.7933
((.((((............)))).))).	chr3:48309528-48309758(+)$1	1	164	192	24.2015
..(((..............))).))).)	chr10:103544135-103544371(-)$1	1	42	70	23.1826
.(((((...............)))))..	chr22:21976855-21977106(+)$1	1	179	207	18.5583
((.((((.............)))).)))	chr1:151669614-151669840(+)$1	1	14	42	23.1355
(((((((............)))))))))	chr1:231353847-231354070(+)$1	1	112	140	24.3831
(((((..............)))))))..	chr1:230825681-230825911(+)$1	1	57	85	22.0842
.(((((((...........)))))))..	chr8:103219120-103219348(-)$1	1	6	34	20.9685
.((((..............)))).))((	chr16:58584998-58585233(-)$1	1	120	148	21.5542
((((.(((...........)))..))))	chr9:98214105-98214328(+)$1	1	90	118	23.1674
(.(((((............))))).)))	chr2:69688555-69688782(-)$1	1	156	184	23.5777
.((((.((...........)).)))).)	chr1:150936973-150937199(+)$1	1	3	31	22.8001
((((((((...........)))))))))	chr11:64533008-64533254(-)$1	1	158	186	23.8081
.((((..............))))))).)	chr17:37827363-37827589(-)$1	1	188	216	21.8985
(((((((............)))))))..	chr1:65694452-65694681(+)$1	1	102	130	24.8091
.(((.(((...........))).)))))	chr6:28124227-28124458(+)$1	1	162	190	20.6166
.((((((............))))))...	chr13:100638038-100638268(+)$1	1	45	73	23.8109
(((((................)))))..	chr2:121750002-121750230(+)$1	1	79	107	20.6921
(((((((.............))))))))	chr10:134230722-134230946(+)$1	1	27	55	23.4943
((..(((............)))..))))	chr1:110565218-110565447(+)$1	1	118	146	24.0748
((..(((.............))).))))	chr20:5170762-5171016(+)$1	1	184	212	22.9937

#PSSM
e : 0.12	g : 0.12	[ : 0.08	i : 0.08	! : 0.08	f : 0.06	c : 0.06	= : 0.05	$ : 0.05	d : 0.05	: : 0.05	b : 0.03	" : 0.03	# : 0.03	h : 0.01	a : 0.01	& : 0.01	
g : 0.15	e : 0.13	c : 0.12	d : 0.10	f : 0.08	i : 0.08	[ : 0.06	= : 0.05	! : 0.05	$ : 0.03	h : 0.01	# : 0.01	& : 0.01	b : 0.01	: : 0.01	" : 0.01	
e : 0.18	f : 0.13	d : 0.13	c : 0.12	g : 0.12	[ : 0.06	i : 0.05	$ : 0.03	" : 0.03	! : 0.03	h : 0.01	# : 0.01	b : 0.01	= : 0.01	
d : 0.22	e : 0.17	f : 0.12	g : 0.10	c : 0.08	! : 0.06	[ : 0.05	i : 0.05	" : 0.03	h : 0.01	y : 0.01	$ : 0.01	# : 0.01	= : 0.01	
d : 0.25	e : 0.15	c : 0.12	g : 0.10	f : 0.08	[ : 0.08	i : 0.05	! : 0.03	" : 0.03	h : 0.01	y : 0.01	$ : 0.01	= : 0.01	
c : 0.20	d : 0.18	e : 0.13	w : 0.10	f : 0.08	g : 0.08	b : 0.06	[ : 0.03	y : 0.03	i : 0.03	= : 0.01	
c : 0.20	d : 0.13	w : 0.12	b : 0.10	e : 0.08	f : 0.06	g : 0.06	y : 0.05	v : 0.03	a : 0.03	x : 0.03	i : 0.03	= : 0.01	
u : 0.24	w : 0.15	v : 0.12	c : 0.12	y : 0.08	t : 0.06	f : 0.05	d : 0.03	g : 0.03	x : 0.03	b : 0.03	= : 0.01	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.36	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	
t : 0.29	u : 0.24	w : 0.15	v : 0.12	y : 0.08	x : 0.03	b : 0.01	e : 0.01	d : 0.01	c : 0.01	
c : 0.20	d : 0.15	e : 0.08	v : 0.08	b : 0.08	g : 0.08	f : 0.06	y : 0.06	w : 0.05	x : 0.03	i : 0.03	a : 0.01	= : 0.01	
c : 0.22	d : 0.18	e : 0.08	f : 0.08	b : 0.08	g : 0.08	y : 0.06	i : 0.05	w : 0.03	x : 0.03	] : 0.01	3 : 0.01	= : 0.01	
c : 0.20	d : 0.18	e : 0.15	f : 0.08	] : 0.08	g : 0.08	y : 0.05	i : 0.05	h : 0.01	3 : 0.01	a : 0.01	b : 0.01	= : 0.01	
d : 0.22	e : 0.15	] : 0.13	f : 0.12	g : 0.08	2 : 0.06	c : 0.05	i : 0.05	y : 0.03	h : 0.01	3 : 0.01	> : 0.01	= : 0.01	
e : 0.15	c : 0.15	f : 0.13	d : 0.12	] : 0.10	g : 0.10	2 : 0.06	i : 0.05	h : 0.01	b : 0.01	4 : 0.01	> : 0.01	= : 0.01	a : 0.01	
c : 0.18	f : 0.15	e : 0.12	d : 0.12	g : 0.10	b : 0.06	] : 0.05	i : 0.05	h : 0.03	= : 0.03	4 : 0.03	a : 0.01	> : 0.01	
c : 0.17	e : 0.13	d : 0.12	g : 0.12	f : 0.08	4 : 0.06	i : 0.05	b : 0.05	h : 0.03	= : 0.03	3 : 0.03	2 : 0.03	a : 0.01	: : 0.01	> : 0.01	
] : 0.17	f : 0.08	: : 0.08	4 : 0.08	e : 0.08	3 : 0.06	2 : 0.06	d : 0.06	c : 0.05	i : 0.05	h : 0.03	= : 0.03	g : 0.03	7 : 0.01	> : 0.01	6 : 0.01	I : 0.01	
b : 0.13	: : 0.10	f : 0.08	e : 0.08	c : 0.06	3 : 0.06	4 : 0.06	d : 0.05	i : 0.05	g : 0.05	h : 0.03	= : 0.03	2 : 0.03	7 : 0.01	n : 0.01	> : 0.01	] : 0.01	6 : 0.01	a : 0.01	I : 0.01	

#score	1305.8392031555802
#seq	58
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_UTR_m2_run2.txt

#BEAR
ggggggtttttttttttggg	chr1:233807181-233807412(+)$1	231	95	115	21.9159
!dddduuuuuuuuuuuuddd	chr15:41774752-41774957(+)$1	205	115	135	22.3906
::cccuuuuuuuuuuuuccc	chr15:60639626-60639831(-)$1	205	74	94	20.5228
ffffwwwwwwwwwwwwwwff	chr19:56206792-56207035(+)$1	243	77	97	20.0767
ee[ccctttttttttttccc	chr17:79477162-79477404(-)$1	242	39	59	22.0703
[eeeeettttttttttteee	chr1:100757132-100757377(+)$1	245	200	220	22.2105
ddddvvvvvvvvvvvvvddd	chr17:26655464-26655670(-)$1	206	20	40	21.4745
fffffuuuuuuuuuuuufff	chr5:137683205-137683426(+)$1	221	101	121	21.9380
ffffvvvvvvvvvvvvvfff	chr5:172743270-172743506(-)$1	236	12	32	21.3026
ddddvvvvvvvvvvvvvddd	chr12:93793736-93793948(+)$1	212	171	191	21.4745
"eeeeettttttttttteee	chr17:41846299-41846525(-)$1	226	27	47	22.0777
Geeeeettttttttttteee	chr2:190636244-190636476(-)$1	232	58	78	21.7430
"eeeeettttttttttteee	chr2:128948516-128948720(+)$1	204	85	105	22.0777
ffffwwwwwwwwwwwwwwff	chr5:137895550-137895794(-)$1	244	42	62	20.0767
fffffuuuuuuuuuuuufff	chr19:39397819-39398037(+)$1	218	41	61	21.9380
fffffyyyyyyyyyyyyyyy	chr12:66530922-66531131(-)$1	209	144	164	19.3919
ggggggtttttttttttggg	chr19:812021-812238(+)$1	217	1	21	21.9159
eeeeevvvvvvvvvvvvvee	chr5:34905443-34905654(-)$1	211	129	149	21.8262
[eeeeettttttttttteee	chr12:50157930-50158209(+)$1	279	72	92	22.2105
ddddvvvvvvvvvvvvvddd	chr10:103923186-103923437(+)$1	251	56	76	21.4745
b[cccvvvvvvvvvvvvvcc	chr2:54896306-54896524(+)$1	218	39	59	21.4854
gggyyyyyyyyyyyyyyyyg	chr2:160624751-160624966(+)$1	215	165	185	19.8041
gdddduuuuuuuuuuuuddd	chr9:132399132-132399351(-)$1	219	152	172	22.3731
eeeeeuuuuuuuuuuuueee	chr3:160788133-160788411(+)$1	278	209	229	22.6179
eeeeeuuuuuuuuuuuueee	chr1:223968299-223968504(-)$1	205	15	35	22.6179
ee[bbuuuuuuuuuuuubb]	chr2:37074417-37074640(-)$1	223	197	217	21.6072
hhhhhuuuuuuuuuuuuhhh	chr3:129274203-129274421(-)$1	218	28	48	21.1999
ggggggtttttttttttggg	chrX:84502018-84502246(+)$1	228	150	170	21.9159
ffffvvvvvvvvvvvvvfff	chr1:21546092-21546320(-)$1	228	165	185	21.3026
::ddddtttttttttttddd	chr11:66113310-66113521(-)$1	211	159	179	19.7378
c!!bbtttttttttttbb22	chr1:109473825-109474035(-)$1	210	30	50	19.7405
!dddduuuuuuuuuuuuddd	chr1:92327009-92327241(-)$1	232	60	80	22.3906
==cccuuuuuuuuuuuuccc	chr17:48772719-48772987(-)$1	268	27	47	22.5005
F:cccuuuuuuuuuuuuccc	chr19:34719875-34720081(+)$1	206	183	203	21.1401
fffffftttttttttttfff	chr6:7880665-7880879(+)$1	214	5	25	21.3015
g!!bbwwwwwwwwwwwwwwb	chr3:179117713-179117928(-)$1	215	33	53	19.5561
hhhhhuuuuuuuuuuuuhhh	chr5:132440195-132440416(+)$1	221	107	127	21.1999
f[ddddtttttttttttddd	chr3:196313841-196314057(+)$1	216	73	93	21.7159
hh[bbtttttttttttbb]h	chr3:190024193-190024419(-)$1	226	142	162	19.8929
eeeeevvvvvvvvvvvvvee	chr21:28208879-28209093(-)$1	214	73	93	21.8262
&dddduuuuuuuuuuuuddd	chr6:31500537-31500779(-)$1	242	79	99	21.6727
:dddduuuuuuuuuuuuddd	chr16:83846173-83846402(+)$1	229	129	149	21.3852
gggwwwwwwwwwwwwwwggg	chr16:85840287-85840556(+)$1	269	23	43	20.3917
d[ddddtttttttttttddd	chr3:5258903-5259114(+)$1	211	142	162	21.6132
hhhhhyyyyyyyyyyyyyyy	chr20:33969649-33969893(-)$1	244	53	73	18.9247
fffffftttttttttttfff	chr6:56397164-56397379(-)$1	215	9	29	21.3015
ggggggtttttttttttggg	chr17:73016503-73016715(+)$1	212	91	111	21.9159
dyyyyyyyyyyyyyyyyddd	chr2:10271012-10271234(+)$1	222	50	70	18.9416
[eeeeettttttttttteee	chr12:124071234-124071458(+)$1	224	46	66	22.2105
:eeeeettttttttttteee	chr20:21375980-21376187(-)$1	207	171	191	21.1993
eee[awwwwwwwwwwwwwwa	chr5:145665771-145665978(+)$1	207	83	103	20.1203
ggggguuuuuuuuuuuuggg	chr3:14186949-14187185(-)$1	236	27	47	22.6215
gggwwwwwwwwwwwwwwggg	chr18:45366898-45367109(-)$1	211	57	77	20.3917
hhhhhhttttttttttthhh	chr2:241654787-241655017(-)$1	230	197	217	20.2888
iiiiivvvvvvvvvvvvvii	chr7:141450028-141450269(+)$1	241	117	137	21.6797
dd[bbuuuuuuuuuuuubb]	chr15:75931442-75931667(-)$1	225	20	40	21.3951
!eeeeettttttttttteee	chr5:133532780-133532992(-)$1	212	81	101	22.2047
gggwwwwwwwwwwwwwwggg	chr17:40931172-40931403(+)$1	231	108	128	20.3917
:dddduuuuuuuuuuuuddd	chr7:91741537-91741742(-)$1	205	179	199	21.3852

#otherMatches

#Seq PSSM
GCGUAGGAUUUGUUGCAUUA	chr1:233807181-233807412(+)$1	231	95	115	21.9159
GUUAAAAUCAUAUAUACUUG	chr15:41774752-41774957(+)$1	205	115	135	22.3906
UUGCGAAUAACAGUCCCCGU	chr15:60639626-60639831(-)$1	205	74	94	20.5228
UUCCCACCCCACCUCCCCGG	chr19:56206792-56207035(+)$1	243	77	97	20.0767
AUCUGUGCAGGGUAUUAACG	chr17:79477162-79477404(-)$1	242	39	59	22.0703
AUACAUUUUUCUUUUUUAUG	chr1:100757132-100757377(+)$1	245	200	220	22.2105
AGGCAAAACAAAAAAAAGCC	chr17:26655464-26655670(-)$1	206	20	40	21.4745
CAGCAGGGUGUUUUAAGUGC	chr5:137683205-137683426(+)$1	221	101	121	21.9380
GGGUUAUUUAAAACAUCACC	chr5:172743270-172743506(-)$1	236	12	32	21.3026
CAUGGAAUUUGAUUUAGCAU	chr12:93793736-93793948(+)$1	212	171	191	21.4745
CCACAGCCUUCCACACCCUG	chr17:41846299-41846525(-)$1	226	27	47	22.0777
UGUUUCUGUGAUAAUGUGAA	chr2:190636244-190636476(-)$1	232	58	78	21.7430
UGGCCUAAGUGGGCAUGAGG	chr2:128948516-128948720(+)$1	204	85	105	22.0777
GCAGAGCCCCAAGUAAAGCU	chr5:137895550-137895794(-)$1	244	42	62	20.0767
GCCACACCCCACUCCACGUG	chr19:39397819-39398037(+)$1	218	41	61	21.9380
UUUGCUUAAAAGGAAAAAAA	chr12:66530922-66531131(-)$1	209	144	164	19.3919
uauaauuuuuuauaCCUGUU	chr19:812021-812238(+)$1	217	1	21	21.9159
AGUAAAAAUUAAUUAAAAUU	chr5:34905443-34905654(-)$1	211	129	149	21.8262
CCCCAGAAGGGUCAAUGUUG	chr12:50157930-50158209(+)$1	279	72	92	22.2105
GCUGUAACAACACAAACCAG	chr10:103923186-103923437(+)$1	251	56	76	21.4745
CUGAUACUGUUUUAAAUAAU	chr2:54896306-54896524(+)$1	218	39	59	21.4854
AGGAUACACUUUAAAACACC	chr2:160624751-160624966(+)$1	215	165	185	19.8041
UAAGAUUAAACUGACUUUCU	chr9:132399132-132399351(-)$1	219	152	172	22.3731
UAUCAUUUUUCCAACCUUGG	chr3:160788133-160788411(+)$1	278	209	229	22.6179
UUUUGGCAAAAAUUUCACAA	chr1:223968299-223968504(-)$1	205	15	35	22.6179
GUUACUGCUUUAUUAAUGUC	chr2:37074417-37074640(-)$1	223	197	217	21.6072
UUUAAAGCUUUUAUAUAUUA	chr3:129274203-129274421(-)$1	218	28	48	21.1999
ACUAGACAUCUGAGUCCUCU	chrX:84502018-84502246(+)$1	228	150	170	21.9159
UACGCCACAAAUACCACUGU	chr1:21546092-21546320(-)$1	228	165	185	21.3026
uaccacuaacuagcugugug	chr11:66113310-66113521(-)$1	211	159	179	19.7378
UCCCAUACUUGUCUUUUGCU	chr1:109473825-109474035(-)$1	210	30	50	19.7405
AGGGACUUUAAGACUACUUC	chr1:92327009-92327241(-)$1	232	60	80	22.3906
UUGCAUGCUCACAACUCUGC	chr17:48772719-48772987(-)$1	268	27	47	22.5005
CCCAGCCCUCCGAAUCACUG	chr19:34719875-34720081(+)$1	206	183	203	21.1401
AUGAGACUUUGAAACUAUCU	chr6:7880665-7880879(+)$1	214	5	25	21.3015
UAGUAUUUCUUCCCUUCCUU	chr3:179117713-179117928(-)$1	215	33	53	19.5561
UACAGAAAUUAAGUGCAUUG	chr5:132440195-132440416(+)$1	221	107	127	21.1999
GAUCAGGGAAAGUGUAACUG	chr3:196313841-196314057(+)$1	216	73	93	21.7159
guuuuguaauuuaaaaagug	chr3:190024193-190024419(-)$1	226	142	162	19.8929
ACGCCGGAACAAAAAUGAGG	chr21:28208879-28209093(-)$1	214	73	93	21.8262
ccucccccccAGCCAAUGGA	chr6:31500537-31500779(-)$1	242	79	99	21.6727
CUCUGGUUACCCAACUACAG	chr16:83846173-83846402(+)$1	229	129	149	21.3852
UAGUCUUGCCCCAUAACCUG	chr16:85840287-85840556(+)$1	269	23	43	20.3917
UAGGAAAUCCCUAAAACUUC	chr3:5258903-5259114(+)$1	211	142	162	21.6132
UUGGUUAAUCAGCUUUCUAC	chr20:33969649-33969893(-)$1	244	53	73	18.9247
AUUGUACUUUAUAUUCAUAC	chr6:56397164-56397379(-)$1	215	9	29	21.3015
AUCAACAGGUUAGGAGAGUU	chr17:73016503-73016715(+)$1	212	91	111	21.9159
CUACUUUGAAUUAAUCUGCC	chr2:10271012-10271234(+)$1	222	50	70	18.9416
CUCUUGCCUCCAGAUUACAG	chr12:124071234-124071458(+)$1	224	46	66	22.2105
GAAUCAAAAUAAAAUACUGA	chr20:21375980-21376187(-)$1	207	171	191	21.1993
CCACCUUUUUUUUGUUGCUG	chr5:145665771-145665978(+)$1	207	83	103	20.1203
AGGAGAUACUCUUCUGCCUC	chr3:14186949-14187185(-)$1	236	27	47	22.6215
GUAAAUGUAAUUGUUUCUGC	chr18:45366898-45367109(-)$1	211	57	77	20.3917
GUUCUGUGAGGGAGAAUCAG	chr2:241654787-241655017(-)$1	230	197	217	20.2888
AAGGAGUAGAAAGGAUGAUU	chr7:141450028-141450269(+)$1	241	117	137	21.6797
ACUGGAAAUCCCCACGCCCU	chr15:75931442-75931667(-)$1	225	20	40	21.3951
UGUUCUUUGUUAUUGUCAGA	chr5:133532780-133532992(-)$1	212	81	101	22.2047
CACCAGGGAGAAAAUAUGUG	chr17:40931172-40931403(+)$1	231	108	128	20.3917
ACAGUUCUUUUUAAAACACU	chr7:91741537-91741742(-)$1	205	179	199	21.3852

#DB
((((((...........)))	chr1:233807181-233807412(+)$1	1	95	115	21.9159
.((((............)))	chr15:41774752-41774957(+)$1	1	115	135	22.3906
..(((............)))	chr15:60639626-60639831(-)$1	1	74	94	20.5228
((((..............))	chr19:56206792-56207035(+)$1	1	77	97	20.0767
((.(((...........)))	chr17:79477162-79477404(-)$1	1	39	59	22.0703
.(((((...........)))	chr1:100757132-100757377(+)$1	1	200	220	22.2105
((((.............)))	chr17:26655464-26655670(-)$1	1	20	40	21.4745
(((((............)))	chr5:137683205-137683426(+)$1	1	101	121	21.9380
((((.............)))	chr5:172743270-172743506(-)$1	1	12	32	21.3026
((((.............)))	chr12:93793736-93793948(+)$1	1	171	191	21.4745
.(((((...........)))	chr17:41846299-41846525(-)$1	1	27	47	22.0777
((((((...........)))	chr2:190636244-190636476(-)$1	1	58	78	21.7430
.(((((...........)))	chr2:128948516-128948720(+)$1	1	85	105	22.0777
((((..............))	chr5:137895550-137895794(-)$1	1	42	62	20.0767
(((((............)))	chr19:39397819-39398037(+)$1	1	41	61	21.9380
(((((...............	chr12:66530922-66531131(-)$1	1	144	164	19.3919
((((((...........)))	chr19:812021-812238(+)$1	1	1	21	21.9159
(((((.............))	chr5:34905443-34905654(-)$1	1	129	149	21.8262
.(((((...........)))	chr12:50157930-50158209(+)$1	1	72	92	22.2105
((((.............)))	chr10:103923186-103923437(+)$1	1	56	76	21.4745
(.(((.............))	chr2:54896306-54896524(+)$1	1	39	59	21.4854
(((................)	chr2:160624751-160624966(+)$1	1	165	185	19.8041
)((((............)))	chr9:132399132-132399351(-)$1	1	152	172	22.3731
(((((............)))	chr3:160788133-160788411(+)$1	1	209	229	22.6179
(((((............)))	chr1:223968299-223968504(-)$1	1	15	35	22.6179
((.((............)).	chr2:37074417-37074640(-)$1	1	197	217	21.6072
(((((............)))	chr3:129274203-129274421(-)$1	1	28	48	21.1999
((((((...........)))	chrX:84502018-84502246(+)$1	1	150	170	21.9159
((((.............)))	chr1:21546092-21546320(-)$1	1	165	185	21.3026
..((((...........)))	chr11:66113310-66113521(-)$1	1	159	179	19.7378
(..((...........))..	chr1:109473825-109474035(-)$1	1	30	50	19.7405
.((((............)))	chr1:92327009-92327241(-)$1	1	60	80	22.3906
(((((............)))	chr17:48772719-48772987(-)$1	1	27	47	22.5005
).(((............)))	chr19:34719875-34720081(+)$1	1	183	203	21.1401
((((((...........)))	chr6:7880665-7880879(+)$1	1	5	25	21.3015
(..((..............)	chr3:179117713-179117928(-)$1	1	33	53	19.5561
(((((............)))	chr5:132440195-132440416(+)$1	1	107	127	21.1999
(.((((...........)))	chr3:196313841-196314057(+)$1	1	73	93	21.7159
((.((...........)).)	chr3:190024193-190024419(-)$1	1	142	162	19.8929
(((((.............))	chr21:28208879-28209093(-)$1	1	73	93	21.8262
.((((............)))	chr6:31500537-31500779(-)$1	1	79	99	21.6727
.((((............)))	chr16:83846173-83846402(+)$1	1	129	149	21.3852
(((..............)))	chr16:85840287-85840556(+)$1	1	23	43	20.3917
(.((((...........)))	chr3:5258903-5259114(+)$1	1	142	162	21.6132
(((((...............	chr20:33969649-33969893(-)$1	1	53	73	18.9247
((((((...........)))	chr6:56397164-56397379(-)$1	1	9	29	21.3015
((((((...........)))	chr17:73016503-73016715(+)$1	1	91	111	21.9159
(................)))	chr2:10271012-10271234(+)$1	1	50	70	18.9416
.(((((...........)))	chr12:124071234-124071458(+)$1	1	46	66	22.2105
.(((((...........)))	chr20:21375980-21376187(-)$1	1	171	191	21.1993
(((.(..............)	chr5:145665771-145665978(+)$1	1	83	103	20.1203
(((((............)))	chr3:14186949-14187185(-)$1	1	27	47	22.6215
(((..............)))	chr18:45366898-45367109(-)$1	1	57	77	20.3917
((((((...........)))	chr2:241654787-241655017(-)$1	1	197	217	20.2888
(((((.............))	chr7:141450028-141450269(+)$1	1	117	137	21.6797
((.((............)).	chr15:75931442-75931667(-)$1	1	20	40	21.3951
.(((((...........)))	chr5:133532780-133532992(-)$1	1	81	101	22.2047
(((..............)))	chr17:40931172-40931403(+)$1	1	108	128	20.3917
.((((............)))	chr7:91741537-91741742(-)$1	1	179	199	21.3852

#PSSM
g : 0.18	f : 0.16	e : 0.11	d : 0.10	: : 0.08	h : 0.08	! : 0.05	[ : 0.05	" : 0.03	G : 0.01	b : 0.01	c : 0.01	= : 0.01	F : 0.01	& : 0.01	i : 0.01	
e : 0.25	d : 0.16	g : 0.15	f : 0.15	h : 0.08	: : 0.05	[ : 0.05	! : 0.03	= : 0.01	y : 0.01	i : 0.01	
e : 0.22	d : 0.20	g : 0.15	f : 0.15	c : 0.06	[ : 0.06	h : 0.06	! : 0.03	y : 0.01	i : 0.01	
d : 0.20	e : 0.20	f : 0.15	g : 0.08	c : 0.08	b : 0.08	h : 0.06	w : 0.05	y : 0.03	[ : 0.01	i : 0.01	
e : 0.20	d : 0.15	g : 0.08	c : 0.08	w : 0.08	v : 0.08	f : 0.08	b : 0.08	h : 0.06	y : 0.03	a : 0.01	i : 0.01	
u : 0.30	v : 0.15	e : 0.13	w : 0.11	g : 0.06	y : 0.06	d : 0.05	t : 0.03	f : 0.03	c : 0.01	h : 0.01	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.35	u : 0.30	v : 0.15	w : 0.11	y : 0.06	
t : 0.32	u : 0.30	v : 0.15	w : 0.11	y : 0.06	b : 0.03	
d : 0.22	e : 0.16	g : 0.13	f : 0.10	c : 0.06	w : 0.06	v : 0.06	b : 0.06	y : 0.05	h : 0.05	
d : 0.22	e : 0.20	g : 0.13	f : 0.13	c : 0.08	y : 0.05	h : 0.05	b : 0.03	w : 0.03	2 : 0.01	] : 0.01	i : 0.01	
d : 0.22	e : 0.20	g : 0.15	f : 0.13	c : 0.08	h : 0.06	y : 0.03	] : 0.03	2 : 0.01	b : 0.01	a : 0.01	i : 0.01	

#score	1256.0727033855403
#seq	59
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_CDS_m2_run2.txt

#BEAR
ddddvvvvvvvvvvvvvdddd	chr2:74531658-74531907(-)$1	249	103	124	22.3649
!dddduuuuuuuuuuuudddd	chr2:111395376-111395647(-)$1	271	53	74	22.6602
eeeeettttttttttteeeee	chrX:53658422-53658658(-)$1	236	74	95	22.8767
ddddvvvvvvvvvvvvvdddd	chr9:99113323-99113549(-)$1	226	107	128	22.3649
::cccuuuuuuuuuuuuccc:	chr1:204588054-204588274(-)$1	220	137	158	19.6845
ffffftttttttttttfffff	chr8:94935759-94936019(+)$1	260	19	40	22.2987
ffffftttttttttttfffff	chr2:24260830-24261071(-)$1	241	142	163	22.2987
eeeeettttttttttteeeee	chr10:104687015-104687251(+)$1	236	36	57	22.8767
bbccctttttttttttccc]b	chr5:118507495-118507758(+)$1	263	134	155	22.0520
ddddvvvvvvvvvvvvvdddd	chr1:154227657-154227900(+)$1	243	127	148	22.3649
bbcccuuuuuuuuuuuuccc5	chr2:71602274-71602568(+)$1	294	201	222	21.1672
#cccwwwwwwwwwwwwwwccc	chr7:107399112-107399521(+)$1	409	20	41	20.4000
fdddduuuuuuuuuuuudddd	chr9:99581300-99581559(-)$1	259	197	218	22.5630
eeebbtttttttttttbb]ee	chr2:179452784-179453001(-)$1	217	178	199	21.8135
ddddvvvvvvvvvvvvvdddd	chr10:15145740-15145975(+)$1	235	89	110	22.3649
ffffftttttttttttfffff	chr1:204518441-204518676(+)$1	235	32	53	22.2987
"ddddtttttttttttdddd2	chr1:28793052-28793324(+)$1	272	202	223	22.9333
eeeeuuuuuuuuuuuueeeee	chr10:38344416-38344680(+)$1	264	140	161	22.0911
"ddddtttttttttttdddd5	chr11:46780380-46780667(-)$1	287	104	125	22.3875
eeeeettttttttttteeeee	chr13:95673764-95674022(-)$1	258	68	89	22.8767
%%ccctttttttttttccc22	chr3:9798541-9798883(+)$1	342	141	162	21.0633
cccvvvvvvvvvvvvvccc>>	chr9:95227194-95227516(+)$1	322	85	106	20.9949
gggggvvvvvvvvvvvvvggg	chr2:191844401-191844645(-)$1	244	54	75	21.6080
!ddddtttttttttttdddd2	chr3:186272354-186272602(-)$1	248	173	194	23.0035
#ddddtttttttttttdddd4	chr19:37853701-37853952(+)$1	251	107	128	23.0701
ggwwwwwwwwwwwwwwggggg	chr3:121208893-121209119(-)$1	226	45	66	19.1906
fffwwwwwwwwwwwwwwffff	chr1:150436951-150437227(+)$1	276	207	228	19.9257
hhhhhuuuuuuuuuuuuhhhh	chr8:57078753-57079047(-)$1	294	34	55	20.1403
::cccvvvvvvvvvvvvvccc	chr2:136418795-136419051(+)$1	256	66	87	20.0629
"ddddtttttttttttdddd]	chr10:38345300-38345616(+)$1	316	39	60	23.0994
gggguuuuuuuuuuuuggggg	chr22:26114145-26114406(+)$1	261	163	184	21.6487
dd[bbtttttttttttbb]dd	chr5:180662253-180662622(+)$1	369	294	315	21.6216
ffffftttttttttttfffff	chr19:58452567-58452829(-)$1	262	38	59	22.2987
eeeeettttttttttteeeee	chr4:1018930-1019230(+)$1	300	182	203	22.8767
d[cccuuuuuuuuuuuucccd	chr5:41929761-41929986(+)$1	225	98	119	22.1904
:ddddtttttttttttdddd:	chr12:977007-977330(+)$1	323	1	22	21.3940
eeeeuuuuuuuuuuuueeeee	chr11:19256368-19256608(-)$1	240	72	93	22.0911
gggggtttttttttttggggg	chr22:41545845-41546133(+)$1	288	230	251	22.3836
eeeeettttttttttteeeee	chr5:157232755-157233158(-)$1	403	186	207	22.8767
edddduuuuuuuuuuuudddd	chr2:206927595-206927847(-)$1	252	188	209	22.5964
dddduuuuuuuuuuuudddde	chr17:34160770-34161012(+)$1	242	27	48	22.1887
fffffvvvvvvvvvvvvvfff	chr21:47613489-47613770(-)$1	281	185	206	21.4609
d!!bbtttttttttttbbddd	chr16:30771348-30771586(-)$1	238	12	33	21.7011
gg!!attttttttttta22gg	chr8:17613085-17613323(-)$1	238	23	44	21.9958
[dddduuuuuuuuuuuudddd	chr12:49666173-49666607(+)$1	434	324	345	22.6423
::cccvvvvvvvvvvvvvccc	chr17:7417255-7417535(+)$1	280	118	139	20.0629
fffffvvvvvvvvvvvvvfff	chr19:57803333-57803592(+)$1	259	83	104	21.4609
ccccctttttttttttccc:e	chr19:58452868-58453144(-)$1	276	146	167	21.8572
ffffuuuuuuuuuuuufffff	chr5:177636317-177636576(-)$1	259	236	257	21.5284
:ddddtttttttttttdddd:	chr1:236714170-236714407(+)$1	237	197	218	21.3940
eeeeevvvvvvvvvvvvveee	chr9:134381494-134381780(+)$1	286	238	259	21.9477
ffffftttttttttttfffff	chr5:137502085-137502520(-)$1	435	86	107	22.2987
!dddduuuuuuuuuuuudddd	chr12:56214098-56214402(+)$1	304	136	157	22.6602
eeeeuuuuuuuuuuuueeeee	chr17:62496567-62496918(-)$1	351	143	164	22.0911
:ddddtttttttttttdddd:	chr4:102014848-102015088(-)$1	240	1	22	21.3940
e!!bbvvvvvvvvvvvvvbb2	chr6:71235543-71235800(+)$1	257	105	126	20.4755
Gddddtttttttttttdddd:	chr2:209169628-209169881(+)$1	253	33	54	21.8627
ffccctttttttttttccc77	chr19:58290425-58290765(+)$1	340	188	209	21.7332
eeeeuuuuuuuuuuuueeeee	chr2:85779959-85780212(-)$1	253	69	90	22.0911
eeeeettttttttttteeeee	chr11:10822397-10822659(-)$1	262	109	130	22.8767
[dddduuuuuuuuuuuudddd	chr17:2226483-2226766(-)$1	283	39	60	22.6423
ffffftttttttttttfffff	chr1:171553038-171553286(+)$1	248	160	181	22.2987
fffffuuuuuuuuuuuuffff	chr10:70243119-70243379(-)$1	260	120	141	21.8122
ffffuuuuuuuuuuuufffff	chr3:42679195-42679692(+)$1	497	287	308	21.5284
gggggtttttttttttggggg	chr5:134690675-134690988(-)$1	313	30	51	22.3836

#otherMatches

#Seq PSSM
GCCCUCCUAUCCACAUUGGGC	chr2:74531658-74531907(-)$1	249	103	124	22.3649
CUACGUAAUAGGCUAAUUGUA	chr2:111395376-111395647(-)$1	271	53	74	22.6602
UGUCUUUUUUAAUUUUAGACA	chrX:53658422-53658658(-)$1	236	74	95	22.8767
CACUCAACAUCAUCCUCAGUG	chr9:99113323-99113549(-)$1	226	107	128	22.3649
CCGCGCCUUCCACCACCUGCC	chr1:204588054-204588274(-)$1	220	137	158	19.6845
GAGCGCCUCUCUAAAAUGCUU	chr8:94935759-94936019(+)$1	260	19	40	22.2987
UGCUGACAGUUAAUACCAGUA	chr2:24260830-24261071(-)$1	241	142	163	22.2987
AAUACAGUUUUUUAAAGUAUU	chr10:104687015-104687251(+)$1	236	36	57	22.8767
AUUCACCACCCCACCCUGAUA	chr5:118507495-118507758(+)$1	263	134	155	22.0520
CACCACACAACACAGCAGGUG	chr1:154227657-154227900(+)$1	243	127	148	22.3649
gcuccauaauaucuucaggaa	chr2:71602274-71602568(+)$1	294	201	222	21.1672
CGCACCCUCAUCAUAUUAUGC	chr7:107399112-107399521(+)$1	409	20	41	20.4000
UAUGGAAAAAGUUUCAACCGU	chr9:99581300-99581559(-)$1	259	197	218	22.5630
GACCAAAAAUAGCAGAUGCGU	chr2:179452784-179453001(-)$1	217	178	199	21.8135
GGCUUAAAAUGUGUUCUAGCC	chr10:15145740-15145975(+)$1	235	89	110	22.3649
GAAAGAAAACUCCAAACUUUU	chr1:204518441-204518676(+)$1	235	32	53	22.2987
CACAGAAAUAGCAACCCUGUC	chr1:28793052-28793324(+)$1	272	202	223	22.9333
GUGGGAAAACUUUCUACCACA	chr10:38344416-38344680(+)$1	264	140	161	22.0911
CAUGCACAGUAAUACAGCAUC	chr11:46780380-46780667(-)$1	287	104	125	22.3875
UACCUUUUUUUUUUCUAGGUA	chr13:95673764-95674022(-)$1	258	68	89	22.8767
UAGUCUCACCAGCCCUGACCC	chr3:9798541-9798883(+)$1	342	141	162	21.0633
CCCAUUAUUAUCAAGAGGGUU	chr9:95227194-95227516(+)$1	322	85	106	20.9949
AAAAUAUAAAUGAUAAAAAUU	chr2:191844401-191844645(-)$1	244	54	75	21.6080
UUUGUCCAUCUCUUCUACAAC	chr3:186272354-186272602(-)$1	248	173	194	23.0035
ACCUCAUUACCCACCAGAGGG	chr19:37853701-37853952(+)$1	251	107	128	23.0701
GCCCUGUUACAUUCUAGUACA	chr3:121208893-121209119(-)$1	226	45	66	19.1906
CUGCACUUUCCAAAACCCAGA	chr1:150436951-150437227(+)$1	276	207	228	19.9257
CCUAUAAUCCUCUAUCAGUGG	chr8:57078753-57079047(-)$1	294	34	55	20.1403
CAGGCCACUAUCACUCCAGCC	chr2:136418795-136419051(+)$1	256	66	87	20.0629
AUCUCAUUGUACAUCAGAGAA	chr10:38345300-38345616(+)$1	316	39	60	23.0994
UCCAAAUAGACUUGAAUGGAG	chr22:26114145-26114406(+)$1	261	163	184	21.6487
CCUCUCCCCUUUGUUCAGUGG	chr5:180662253-180662622(+)$1	369	294	315	21.6216
CAUAUGAGUGCAGUGAAUGUG	chr19:58452567-58452829(-)$1	262	38	59	22.2987
AGCACAUCCACUAUCAGUGCU	chr4:1018930-1019230(+)$1	300	182	203	22.8767
GCUGUCACUUCUUUUUUACAC	chr5:41929761-41929986(+)$1	225	98	119	22.1904
UUGUCUUAUUCAUGUUGAUAC	chr12:977007-977330(+)$1	323	1	22	21.3940
CCAAAAACAGGUACACUUGGC	chr11:19256368-19256608(-)$1	240	72	93	22.0911
GCAGCCUUCACUUCCUGCUGC	chr22:41545845-41546133(+)$1	288	230	251	22.3836
UCCAAAACCAUUGAUCUUGGA	chr5:157232755-157233158(-)$1	403	186	207	22.8767
AGGCGACUCAACGGCUACGCC	chr2:206927595-206927847(-)$1	252	188	209	22.5964
UGCUACUGUUUUCCUAAGCAC	chr17:34160770-34161012(+)$1	242	27	48	22.1887
gugccacacacagacauaggu	chr21:47613489-47613770(-)$1	281	185	206	21.4609
CCAGGGAGAAGAGGAACCGGG	chr16:30771348-30771586(-)$1	238	12	33	21.7011
CAGAUGAUAAAAUAGAAGAUG	chr8:17613085-17613323(-)$1	238	23	44	21.9958
AAAGCCUACCACGAACAGCUU	chr12:49666173-49666607(+)$1	434	324	345	22.6423
ucgcccaccuccccCAAAGGC	chr17:7417255-7417535(+)$1	280	118	139	20.0629
CCCACGAACCCAUCCAGAGUG	chr19:57803333-57803592(+)$1	259	83	104	21.4609
ACCUCAUUAAACACCGGAGAC	chr19:58452868-58453144(-)$1	276	146	167	21.8572
UGAUCUCACACUAAAAGUCAA	chr5:177636317-177636576(-)$1	259	236	257	21.5284
AUGCCUUGCACUUUCCGGCAA	chr1:236714170-236714407(+)$1	237	197	218	21.3940
caguacucuagaaauauuugc	chr9:134381494-134381780(+)$1	286	238	259	21.9477
UACCUCUUUAUAUGUUAGGUG	chr5:137502085-137502520(-)$1	435	86	107	22.2987
UAUAAAACAUCCUUCUCUUAU	chr12:56214098-56214402(+)$1	304	136	157	22.6602
UUUACACCUAAUAACAUAAAG	chr17:62496567-62496918(-)$1	351	143	164	22.0911
UUCUAUUUUUCUUAGUUAGAC	chr4:102014848-102015088(-)$1	240	1	22	21.3940
UGAUAAAUCUAAUAACUCUAC	chr6:71235543-71235800(+)$1	257	105	126	20.4755
CUGGACAACGUGAACUUCCAU	chr2:209169628-209169881(+)$1	253	33	54	21.8627
GUCUCAUUAAACACAGGAGGA	chr19:58290425-58290765(+)$1	340	188	209	21.7332
GGUGCACUCCCGCUCCCACCA	chr2:85779959-85780212(-)$1	253	69	90	22.0911
AGUGCACAACCACCACGCACU	chr11:10822397-10822659(-)$1	262	109	130	22.8767
GUGGGUCACUUGCUACUCCUA	chr17:2226483-2226766(-)$1	283	39	60	22.6423
AGGCACAAUCCGGUCUUGCCU	chr1:171553038-171553286(+)$1	248	160	181	22.2987
GCUGUAUUCCCUCUCAAGCAG	chr10:70243119-70243379(-)$1	260	120	141	21.8122
GGGAAAAAAAAUAGCGUUUCA	chr3:42679195-42679692(+)$1	497	287	308	21.5284
AAUUCUCCAUGAGCUUGAGUU	chr5:134690675-134690988(-)$1	313	30	51	22.3836

#DB
((((.............))))	chr2:74531658-74531907(-)$1	1	103	124	22.3649
.((((............))))	chr2:111395376-111395647(-)$1	1	53	74	22.6602
(((((...........)))))	chrX:53658422-53658658(-)$1	1	74	95	22.8767
((((.............))))	chr9:99113323-99113549(-)$1	1	107	128	22.3649
..(((............))).	chr1:204588054-204588274(-)$1	1	137	158	19.6845
(((((...........)))))	chr8:94935759-94936019(+)$1	1	19	40	22.2987
(((((...........)))))	chr2:24260830-24261071(-)$1	1	142	163	22.2987
(((((...........)))))	chr10:104687015-104687251(+)$1	1	36	57	22.8767
(((((...........))).)	chr5:118507495-118507758(+)$1	1	134	155	22.0520
((((.............))))	chr1:154227657-154227900(+)$1	1	127	148	22.3649
(((((............))).	chr2:71602274-71602568(+)$1	1	201	222	21.1672
.(((..............)))	chr7:107399112-107399521(+)$1	1	20	41	20.4000
(((((............))))	chr9:99581300-99581559(-)$1	1	197	218	22.5630
(((((...........)).))	chr2:179452784-179453001(-)$1	1	178	199	21.8135
((((.............))))	chr10:15145740-15145975(+)$1	1	89	110	22.3649
(((((...........)))))	chr1:204518441-204518676(+)$1	1	32	53	22.2987
.((((...........)))).	chr1:28793052-28793324(+)$1	1	202	223	22.9333
((((............)))))	chr10:38344416-38344680(+)$1	1	140	161	22.0911
.((((...........)))).	chr11:46780380-46780667(-)$1	1	104	125	22.3875
(((((...........)))))	chr13:95673764-95674022(-)$1	1	68	89	22.8767
..(((...........)))..	chr3:9798541-9798883(+)$1	1	141	162	21.0633
(((.............)))..	chr9:95227194-95227516(+)$1	1	85	106	20.9949
(((((.............)))	chr2:191844401-191844645(-)$1	1	54	75	21.6080
.((((...........)))).	chr3:186272354-186272602(-)$1	1	173	194	23.0035
.((((...........)))).	chr19:37853701-37853952(+)$1	1	107	128	23.0701
((..............)))))	chr3:121208893-121209119(-)$1	1	45	66	19.1906
(((..............))))	chr1:150436951-150437227(+)$1	1	207	228	19.9257
(((((............))))	chr8:57078753-57079047(-)$1	1	34	55	20.1403
..(((.............)))	chr2:136418795-136419051(+)$1	1	66	87	20.0629
.((((...........)))).	chr10:38345300-38345616(+)$1	1	39	60	23.0994
((((............)))))	chr22:26114145-26114406(+)$1	1	163	184	21.6487
((.((...........)).))	chr5:180662253-180662622(+)$1	1	294	315	21.6216
(((((...........)))))	chr19:58452567-58452829(-)$1	1	38	59	22.2987
(((((...........)))))	chr4:1018930-1019230(+)$1	1	182	203	22.8767
(.(((............))))	chr5:41929761-41929986(+)$1	1	98	119	22.1904
.((((...........)))).	chr12:977007-977330(+)$1	1	1	22	21.3940
((((............)))))	chr11:19256368-19256608(-)$1	1	72	93	22.0911
(((((...........)))))	chr22:41545845-41546133(+)$1	1	230	251	22.3836
(((((...........)))))	chr5:157232755-157233158(-)$1	1	186	207	22.8767
(((((............))))	chr2:206927595-206927847(-)$1	1	188	209	22.5964
((((............)))))	chr17:34160770-34161012(+)$1	1	27	48	22.1887
(((((.............)))	chr21:47613489-47613770(-)$1	1	185	206	21.4609
(..((...........)))))	chr16:30771348-30771586(-)$1	1	12	33	21.7011
((..(...........)..))	chr8:17613085-17613323(-)$1	1	23	44	21.9958
.((((............))))	chr12:49666173-49666607(+)$1	1	324	345	22.6423
..(((.............)))	chr17:7417255-7417535(+)$1	1	118	139	20.0629
(((((.............)))	chr19:57803333-57803592(+)$1	1	83	104	21.4609
))(((...........))).(	chr19:58452868-58453144(-)$1	1	146	167	21.8572
((((............)))))	chr5:177636317-177636576(-)$1	1	236	257	21.5284
.((((...........)))).	chr1:236714170-236714407(+)$1	1	197	218	21.3940
(((((.............)))	chr9:134381494-134381780(+)$1	1	238	259	21.9477
(((((...........)))))	chr5:137502085-137502520(-)$1	1	86	107	22.2987
.((((............))))	chr12:56214098-56214402(+)$1	1	136	157	22.6602
((((............)))))	chr17:62496567-62496918(-)$1	1	143	164	22.0911
.((((...........)))).	chr4:102014848-102015088(-)$1	1	1	22	21.3940
(..((.............)).	chr6:71235543-71235800(+)$1	1	105	126	20.4755
(((((...........)))).	chr2:209169628-209169881(+)$1	1	33	54	21.8627
(((((...........)))..	chr19:58290425-58290765(+)$1	1	188	209	21.7332
((((............)))))	chr2:85779959-85780212(-)$1	1	69	90	22.0911
(((((...........)))))	chr11:10822397-10822659(-)$1	1	109	130	22.8767
.((((............))))	chr17:2226483-2226766(-)$1	1	39	60	22.6423
(((((...........)))))	chr1:171553038-171553286(+)$1	1	160	181	22.2987
(((((............))))	chr10:70243119-70243379(-)$1	1	120	141	21.8122
((((............)))))	chr3:42679195-42679692(+)$1	1	287	308	21.5284
(((((...........)))))	chr5:134690675-134690988(-)$1	1	30	51	22.3836

#PSSM
e : 0.21	f : 0.21	d : 0.12	: : 0.09	g : 0.09	! : 0.04	" : 0.04	b : 0.03	# : 0.03	c : 0.03	[ : 0.03	% : 0.01	h : 0.01	G : 0.01	
d : 0.32	f : 0.20	e : 0.18	g : 0.09	: : 0.04	c : 0.04	b : 0.03	! : 0.03	% : 0.01	h : 0.01	[ : 0.01	
d : 0.30	e : 0.18	f : 0.18	c : 0.16	g : 0.06	! : 0.04	w : 0.01	h : 0.01	[ : 0.01	
d : 0.30	e : 0.16	f : 0.16	c : 0.15	b : 0.06	g : 0.06	w : 0.03	v : 0.01	h : 0.01	! : 0.01	
d : 0.23	c : 0.13	f : 0.13	u : 0.12	e : 0.10	v : 0.07	b : 0.06	w : 0.04	g : 0.04	h : 0.01	a : 0.01	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
t : 0.47	u : 0.29	v : 0.18	w : 0.04	
v : 0.16	u : 0.16	e : 0.15	d : 0.15	f : 0.12	c : 0.07	g : 0.06	b : 0.04	w : 0.03	a : 0.01	
d : 0.30	e : 0.15	f : 0.15	c : 0.12	v : 0.10	g : 0.06	b : 0.04	w : 0.01	h : 0.01	2 : 0.01	
d : 0.32	f : 0.18	e : 0.16	c : 0.16	g : 0.07	] : 0.03	h : 0.01	2 : 0.01	b : 0.01	
d : 0.33	e : 0.18	f : 0.18	c : 0.09	g : 0.09	] : 0.01	2 : 0.01	> : 0.01	h : 0.01	: : 0.01	b : 0.01	7 : 0.01	
e : 0.21	d : 0.20	f : 0.18	g : 0.09	: : 0.07	2 : 0.06	c : 0.04	5 : 0.03	b : 0.01	> : 0.01	4 : 0.01	h : 0.01	] : 0.01	7 : 0.01	

#score	1423.2666802730191
#seq	65
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_CDS_m3_run2.txt

#BEAR
b!!cccgggggggnnnnnggggggg22cc	chr12:57458334-57458580(-)$1	246	3	32	10.8320
d:ggggggg[ccclllccc333ggggggg	chr4:2940438-2940678(-)$1	240	210	239	10.0137
ddddbb"""ddddnnnnndddd4444bb]	chr15:83686713-83686953(-)$1	240	92	121	12.1864
"""eeeeeddddoooooodddd333eeee	chr12:105238178-105238458(-)$1	280	208	237	10.2535
gggggggggggggnnnnngggggggffff	chrX:109416567-109416807(+)$1	240	143	172	11.9042
[ggggggg[cccooooooccc]ggggggg	chr12:46758071-46758311(-)$1	240	156	185	12.5633
ggggggg"""cccbblllbb]ccc333gg	chr7:86825896-86826136(-)$1	240	51	80	10.8135
ccc[bb"""cccooooooccc22bb]ccc	chr5:54948256-54948496(-)$1	240	207	236	12.3316
===========[aooooooa=========	chr21:34931511-34931751(+)$1	240	90	119	12.4560
dddd"""a!!cccnnnnnccc22a333dd	chr17:65074249-65074489(-)$1	240	71	100	13.8704
cc[eeeee[acccnnnnnccc]a]eeeee	chr6:70410568-70410848(-)$1	280	21	50	12.5250
fff[a####ddddnnnnnddddaffffff	chr2:37596757-37596997(+)$1	240	96	125	13.0987
eeee[ccc!!cccooooooccc]ccc]ee	chr12:44337974-44338214(+)$1	240	68	97	11.6389
========!!cccmmmmccc=========	chr1:35649878-35650166(-)$1	288	209	238	12.3347
gg!!dddd!!cccnnnnnccc22dddd22	chr13:23915293-23915533(-)$1	240	29	58	12.5455
fff[ccc####ccclllccc333ccc]ff	chr15:42823574-42823814(+)$1	240	21	50	12.4787
ccc"""bb[ddddnnnnndddd22bb22c	chr14:96779596-96779836(-)$1	240	50	79	11.5111
iiiiii!!eeeeennnnneeeee22iiii	chr1:62148993-62149233(-)$1	240	175	204	12.1673
Feeeee####ddddllldddd4444eeee	chr5:37351250-37351490(-)$1	240	39	68	11.5532
cc[ccc####ddddllldddd4444ccc2	chr11:32953710-32953950(+)$1	240	184	213	12.2773
iiiiiiiii[cccnnnnnccc22iiiiii	chr14:31364018-31364258(-)$1	240	179	208	15.2494
ggggg$$$$$ddddmmmmdddd]gggggg	chr6:80626366-80626606(-)$1	240	170	199	10.8875
eee[dddd[ddddnnnnndddd]ddddee	chr11:62342815-62343070(-)$1	255	137	166	11.0617
ggggg"""eeeeennnnneeeee]ggggg	chr15:78337164-78337404(-)$1	240	120	149	12.4528
hhhhhh[bb[cccnnnnnccc333bb]hh	chr10:32097839-32098079(-)$1	240	2	31	12.4972
fff==========nnnnn==========C	chr6:72005958-72006198(+)$1	240	40	69	12.2211
eeee%%%%%%cccnnnnnccc333eeeee	chr11:62344298-62344538(-)$1	240	113	142	11.0928
gg####ccc[aooooooaccc22gggggg	chr14:55510767-55511007(+)$1	240	79	108	11.4897
iiiiiiiii[cccnnnnnccciiiiiiii	chr12:102158925-102159165(-)$1	240	82	111	14.5025
=[eeeee!!ddddnnnnnddddeeeee44	chr2:148709897-148710137(-)$1	240	156	185	11.8275
ffffff####cccooooooccc]ffffff	chrX:107976609-107976849(-)$1	240	28	57	11.9843
gggggccc[cccooooooccc]ccc]ggg	chr21:26957895-26958135(-)$1	240	131	160	12.2530
iiiiiiiii"""annnnna333iiiiiii	chr7:108155185-108155433(-)$1	248	38	67	13.9602
:ffffff!!ddddnnnnndddd333ffff	chrX:41055464-41055704(+)$1	240	165	194	12.3714
============[ammmma==========	chr12:88542115-88542355(+)$1	240	8	37	11.2631
fffccc!!ccc[annnnna]ccc22ccc2	chr11:62348817-62349107(-)$1	290	227	256	11.7166
ggggggg!!ddddmmmmdddd22gggggg	chr15:55474223-55474463(-)$1	240	188	217	11.7711
+ffffff!!cccooooooccc22ffffff	chr21:33747615-33747855(-)$1	240	134	163	11.0976
Fffffff"""ddddllldddd333fffff	chr1:170004503-170004744(-)$1	241	10	39	11.7895
eeeee$$$$$ddddllldddd4444eeee	chr20:47704473-47704713(+)$1	240	140	169	11.0350
iiiiiiiii[ddddllldddd]iiiiiii	chr4:17813907-17814147(+)$1	240	25	54	12.2161
ff[ccc####cccnnnnnccc4444ccc]	chr9:98229448-98229688(-)$1	240	11	40	15.0527
eee[bb"""ddddnnnnndddd]bb]eee	chr12:75893480-75893726(+)$1	246	65	94	12.8688
iiiiiii[eeeeennnnneeeeeiiiiii	chr11:62358799-62359039(-)$1	240	87	116	12.1982
ggggggg"""cccnnnnnccc22gggggg	chr13:103443206-103443446(-)$1	240	136	165	15.8823
ggg!!bb!!ddddmmmmdddd22bb]ggg	chr15:26792865-26793105(-)$1	240	167	196	10.7609
gggggggbb[cccnnnnnccc]bb]gggg	chr7:93623460-93623700(-)$1	240	36	65	13.0757
iiiiiii####ccclllccc333iiiiii	chr8:95392363-95392603(-)$1	240	136	165	13.8524
=========!!cccmmmmccc22======	chr5:145612999-145613239(+)$1	240	187	216	12.5536

#otherMatches

#Seq PSSM
AGUGCUAUGUAUGAAAUAUAUACAUAUGG	chr12:57458334-57458580(-)$1	246	3	32	10.8320
cagcccaggaguucgagaccagccugggc	chr4:2940438-2940678(-)$1	240	210	239	10.0137
AAUAGAAGAUGGACAAAUUCCAGAAAUCA	chr15:83686713-83686953(-)$1	240	92	121	12.1864
GGUAAGAGUUAAAACUUCUUGAAAUCUCU	chr12:105238178-105238458(-)$1	280	208	237	10.2535
AGGAAGCAAGUCGUGACUUGACUUGGAGA	chrX:109416567-109416807(+)$1	240	143	172	11.9042
AUUUUCUCAAAAGAAGAGUUUAGGGAAGA	chr12:46758071-46758311(-)$1	240	156	185	12.5633
UCUUCUUUUAGAUCUACUGGUAUCGACAA	chr7:86825896-86826136(-)$1	240	51	80	10.8135
GGUCUGAUUGGGGAGUUACCUUCCAAGCC	chr5:54948256-54948496(-)$1	240	207	236	12.3316
GAUGAAGAGGAAGAAGAACCUCCUUUUUA	chr21:34931511-34931751(+)$1	240	90	119	12.4560
AGCCUAGGGAGCUCAUCUGGCAGCAAUGG	chr17:65074249-65074489(-)$1	240	71	100	13.8704
AUUUUAUAUGACUGUUAGAGUGCUUAUAG	chr6:70410568-70410848(-)$1	280	21	50	12.5250
UGGAGCUCCAAACCCAACGUUUCCCAAUU	chr2:37596757-37596997(+)$1	240	96	125	13.0987
AAGAUCAUGGGUCGUGGAUGACAAUGUUC	chr12:44337974-44338214(+)$1	240	68	97	11.6389
GAUGUUAGCAGUUUAUUGACCUAAUAUUU	chr1:35649878-35650166(-)$1	288	209	238	12.3347
AGAAUUUUUAGCAGACAUUGUACAAAAAC	chr13:23915293-23915533(-)$1	240	29	58	12.5455
UUUCUUGUUUUUCAGGCUGACACCAACAG	chr15:42823574-42823814(+)$1	240	21	50	12.4787
UUUUGUGAUUAUAGAUUUUAUACUUCUUG	chr14:96779596-96779836(-)$1	240	50	79	11.5111
UAUAGUGGUAUAUUAUUCAUAUAAAAUUA	chr1:62148993-62149233(-)$1	240	175	204	12.1673
AGUUCUUAAUGAUAGUUUGUCUGGUGGAA	chr5:37351250-37351490(-)$1	240	39	68	11.5532
GUAGCCCAAUUGGAGAUUCCACUCAGGUG	chr11:32953710-32953950(+)$1	240	184	213	12.2773
AAAUAUUUUAGCAUUAGUUGCACAAAAUG	chr14:31364018-31364258(-)$1	240	179	208	15.2494
UGGAAAAACAGCCAUGAAUGGUAUUUCAG	chr6:80626366-80626606(-)$1	240	170	199	10.8875
AGGCAGGGAAGGGGGCAUCCCUGCCCUCC	chr11:62342815-62343070(-)$1	255	137	166	11.0617
CCAUUAAUUUUUACUCUUUGAAACAGUGG	chr15:78337164-78337404(-)$1	240	120	149	12.4528
CCAAUUCCUGCUGUUUUUCAGAUGAGAAA	chr10:32097839-32098079(-)$1	240	2	31	12.4972
UUUUAAAUAUUUACUAUUUAGGUGUUUAC	chr6:72005958-72006198(+)$1	240	40	69	12.2211
GGACCCUCCUGUGUUGCCCACUGUGUCCC	chr11:62344298-62344538(-)$1	240	113	142	11.0928
AUUAUAAGGACCCAAGCGCCUGUAUGUUC	chr14:55510767-55511007(+)$1	240	79	108	11.4897
GAUCAUUUUCAUGAAUUGUAUAAAGUGAU	chr12:102158925-102159165(-)$1	240	82	111	14.5025
ACAGACCCCAAUAGCAGUUAUUGGUCUUA	chr2:148709897-148710137(-)$1	240	156	185	11.8275
UAGUGACUACGUCAACAUGGACUUCACUA	chrX:107976609-107976849(-)$1	240	28	57	11.9843
uuaaauauguauaauaaaauaaauguuuu	chr21:26957895-26958135(-)$1	240	131	160	12.2530
GAAGAAGAUAUAGGUAAACGCAGUCUUUU	chr7:108155185-108155433(-)$1	248	38	67	13.9602
AUGCUUAUCAAUGUGAUUCAUUCUUUAAG	chrX:41055464-41055704(+)$1	240	165	194	12.3714
UAAUAGUAGGUGUGGUUACUGCCUGCUAU	chr12:88542115-88542355(+)$1	240	8	37	11.2631
GGUCUUCACAGAGUUCUUCCCUGGUAAGU	chr11:62348817-62349107(-)$1	290	227	256	11.7166
UUUUUUACAUAAGGUCACUUAAAUGAAAA	chr15:55474223-55474463(-)$1	240	188	217	11.7711
ACACUGAAAACAAAGGUAUGUGCUUGGUG	chr21:33747615-33747855(-)$1	240	134	163	11.0976
AAGGAGAAUGAUCGUUUCGGUACCUCUCC	chr1:170004503-170004744(-)$1	241	10	39	11.7895
CUUACACAGAAGCUAUUAGCUGUUAGUAA	chr20:47704473-47704713(+)$1	240	140	169	11.0350
GGUAAUAGAAUUUGCAGCAAAGUUUGUUA	chr4:17813907-17814147(+)$1	240	25	54	12.2161
CUGGGGGUCAGCCUUUAUGGCACCACCCG	chr9:98229448-98229688(-)$1	240	11	40	15.0527
CUUUACAAAAGGAGAUAGUUCUAGUCAAG	chr12:75893480-75893726(+)$1	246	65	94	12.8688
GGCGGUGGAUUCGGAUGUCGAAUCGCUGC	chr11:62358799-62359039(-)$1	240	87	116	12.1982
CACGAUGAAAACCUGUAUGGUCCCAUUGU	chr13:103443206-103443446(-)$1	240	136	165	15.8823
UGACUGUACUUGAUUUUUCAAAGACUUCA	chr15:26792865-26793105(-)$1	240	167	196	10.7609
GGUAAAACUAUGGGCAAACUGAAGAUUUU	chr7:93623460-93623700(-)$1	240	36	65	13.0757
UAAGUUCAAAAGCUGGUGGUGUAGGACUU	chr8:95392363-95392603(-)$1	240	136	165	13.8524
gcccgggcccagguccaggcccaggcccg	chr5:145612999-145613239(+)$1	240	187	216	12.5536

#DB
(..((((((((((.....)))))))..))	chr12:57458334-57458580(-)$1	1	3	32	10.8320
).(((((((.(((...)))...)))))))	chr4:2940438-2940678(-)$1	1	210	239	10.0137
((((((...((((.....))))....)).	chr15:83686713-83686953(-)$1	1	92	121	12.1864
...(((((((((......))))...))))	chr12:105238178-105238458(-)$1	1	208	237	10.2535
))))))(((((((.....)))))))((((	chrX:109416567-109416807(+)$1	1	143	172	11.9042
.(((((((.(((......))).)))))))	chr12:46758071-46758311(-)$1	1	156	185	12.5633
(((((((...(((((...)).)))...))	chr7:86825896-86826136(-)$1	1	51	80	10.8135
(((.((...(((......)))..)).)))	chr5:54948256-54948496(-)$1	1	207	236	12.3316
(((((((((((.(......))))))))))	chr21:34931511-34931751(+)$1	1	90	119	12.4560
((((...(..(((.....)))..)...))	chr17:65074249-65074489(-)$1	1	71	100	13.8704
((.(((((.((((.....))).).)))))	chr6:70410568-70410848(-)$1	1	21	50	12.5250
(((.(....((((.....)))))))))))	chr2:37596757-37596997(+)$1	1	96	125	13.0987
((((.(((..(((......))).))).))	chr12:44337974-44338214(+)$1	1	68	97	11.6389
((((((((..(((....))))))))))))	chr1:35649878-35650166(-)$1	1	209	238	12.3347
((..((((..(((.....)))..))))..	chr13:23915293-23915533(-)$1	1	29	58	12.5455
(((.(((....(((...)))...))).))	chr15:42823574-42823814(+)$1	1	21	50	12.4787
(((...((.((((.....))))..))..)	chr14:96779596-96779836(-)$1	1	50	79	11.5111
((((((..(((((.....)))))..))))	chr1:62148993-62149233(-)$1	1	175	204	12.1673
((((((....((((...))))....))))	chr5:37351250-37351490(-)$1	1	39	68	11.5532
((.(((....((((...))))....))).	chr11:32953710-32953950(+)$1	1	184	213	12.2773
(((((((((.(((.....)))..))))))	chr14:31364018-31364258(-)$1	1	179	208	15.2494
(((((.....((((....)))).))))))	chr6:80626366-80626606(-)$1	1	170	199	10.8875
(((.((((.((((.....)))).))))))	chr11:62342815-62343070(-)$1	1	137	166	11.0617
(((((...(((((.....))))).)))))	chr15:78337164-78337404(-)$1	1	120	149	12.4528
((((((.((.(((.....)))...)).))	chr10:32097839-32098079(-)$1	1	2	31	12.4972
)))((((((((((.....)))))))))))	chr6:72005958-72006198(+)$1	1	40	69	12.2211
((((......(((.....)))...)))))	chr11:62344298-62344538(-)$1	1	113	142	11.0928
((....(((.(......))))..))))))	chr14:55510767-55511007(+)$1	1	79	108	11.4897
(((((((((.(((.....)))))))))))	chr12:102158925-102159165(-)$1	1	82	111	14.5025
(.(((((..((((.....)))))))))..	chr2:148709897-148710137(-)$1	1	156	185	11.8275
((((((....(((......))).))))))	chrX:107976609-107976849(-)$1	1	28	57	11.9843
((((((((.(((......))).))).)))	chr21:26957895-26958135(-)$1	1	131	160	12.2530
(((((((((...(.....)...)))))))	chr7:108155185-108155433(-)$1	1	38	67	13.9602
.((((((..((((.....))))...))))	chrX:41055464-41055704(+)$1	1	165	194	12.3714
((((((((((((.(....)))))))))))	chr12:88542115-88542355(+)$1	1	8	37	11.2631
((((((..(((.(.....).)))..))).	chr11:62348817-62349107(-)$1	1	227	256	11.7166
(((((((..((((....))))..))))))	chr15:55474223-55474463(-)$1	1	188	217	11.7711
.((((((..(((......)))..))))))	chr21:33747615-33747855(-)$1	1	134	163	11.0976
(((((((...((((...))))...)))))	chr1:170004503-170004744(-)$1	1	10	39	11.7895
(((((.....((((...))))....))))	chr20:47704473-47704713(+)$1	1	140	169	11.0350
(((((((((.((((...)))).)))))))	chr4:17813907-17814147(+)$1	1	25	54	12.2161
((.(((....(((.....)))....))).	chr9:98229448-98229688(-)$1	1	11	40	15.0527
(((.((...((((.....)))).)).)))	chr12:75893480-75893726(+)$1	1	65	94	12.8688
(((((((.(((((.....)))))))))))	chr11:62358799-62359039(-)$1	1	87	116	12.1982
(((((((...(((.....)))..))))))	chr13:103443206-103443446(-)$1	1	136	165	15.8823
(((..((..((((....))))..)).)))	chr15:26792865-26793105(-)$1	1	167	196	10.7609
(((((((((.(((.....))).)).))))	chr7:93623460-93623700(-)$1	1	36	65	13.0757
(((((((....(((...)))...))))))	chr8:95392363-95392603(-)$1	1	136	165	13.8524
(((((((((..(((....)))..))))))	chr5:145612999-145613239(+)$1	1	187	216	12.5536

#PSSM
g : 0.22	i : 0.14	f : 0.12	= : 0.10	e : 0.10	c : 0.08	d : 0.06	F : 0.04	b : 0.02	" : 0.02	[ : 0.02	h : 0.02	: : 0.02	+ : 0.02	
g : 0.24	f : 0.18	i : 0.14	e : 0.12	c : 0.08	= : 0.08	d : 0.04	! : 0.02	: : 0.02	" : 0.02	h : 0.02	[ : 0.02	
g : 0.22	f : 0.16	e : 0.14	i : 0.14	= : 0.08	[ : 0.06	! : 0.04	d : 0.04	c : 0.04	" : 0.02	h : 0.02	# : 0.02	
g : 0.20	e : 0.14	i : 0.14	[ : 0.10	= : 0.10	c : 0.08	f : 0.08	d : 0.04	! : 0.04	" : 0.02	h : 0.02	# : 0.02	
g : 0.20	i : 0.14	c : 0.10	e : 0.10	= : 0.10	f : 0.08	b : 0.06	" : 0.04	d : 0.04	a : 0.02	[ : 0.02	h : 0.02	% : 0.02	# : 0.02	! : 0.02	
c : 0.14	g : 0.14	i : 0.14	= : 0.10	b : 0.08	e : 0.08	f : 0.08	" : 0.06	# : 0.04	d : 0.04	$ : 0.04	h : 0.02	% : 0.02	
g : 0.16	i : 0.12	" : 0.10	= : 0.10	# : 0.10	c : 0.08	e : 0.06	f : 0.06	d : 0.04	b : 0.04	! : 0.04	$ : 0.04	[ : 0.02	% : 0.02	
" : 0.14	# : 0.14	! : 0.14	= : 0.10	g : 0.08	i : 0.08	c : 0.06	b : 0.06	e : 0.04	d : 0.04	$ : 0.04	a : 0.02	% : 0.02	[ : 0.02	
! : 0.18	# : 0.14	" : 0.12	[ : 0.10	= : 0.08	i : 0.08	g : 0.06	e : 0.06	$ : 0.04	b : 0.04	c : 0.04	d : 0.02	% : 0.02	
d : 0.20	[ : 0.14	# : 0.12	c : 0.10	! : 0.10	" : 0.08	= : 0.06	e : 0.06	g : 0.04	$ : 0.04	a : 0.02	% : 0.02	
c : 0.40	d : 0.32	= : 0.06	e : 0.06	g : 0.04	# : 0.04	a : 0.02	" : 0.02	! : 0.02	
c : 0.44	d : 0.32	e : 0.06	g : 0.04	[ : 0.04	= : 0.04	o : 0.02	" : 0.02	
c : 0.36	d : 0.30	o : 0.12	a : 0.06	e : 0.06	g : 0.04	= : 0.02	[ : 0.02	
n : 0.51	o : 0.18	d : 0.12	m : 0.06	c : 0.06	l : 0.02	b : 0.02	a : 0.02	
n : 0.51	o : 0.18	l : 0.16	m : 0.12	b : 0.02	
n : 0.51	l : 0.18	o : 0.18	m : 0.12	
n : 0.51	o : 0.18	l : 0.16	m : 0.12	c : 0.02	
n : 0.51	o : 0.16	d : 0.14	c : 0.08	m : 0.06	l : 0.02	a : 0.02	
c : 0.40	d : 0.32	o : 0.06	e : 0.06	a : 0.06	g : 0.04	b : 0.02	= : 0.02	
c : 0.42	d : 0.32	e : 0.06	g : 0.04	3 : 0.04	= : 0.04	b : 0.02	a : 0.02	] : 0.02	
c : 0.38	d : 0.32	3 : 0.08	= : 0.08	e : 0.06	g : 0.04	] : 0.02	
2 : 0.20	d : 0.18	3 : 0.14	] : 0.10	c : 0.08	= : 0.08	4 : 0.08	e : 0.06	g : 0.04	i : 0.02	
2 : 0.22	3 : 0.14	4 : 0.10	] : 0.10	g : 0.08	= : 0.08	e : 0.08	c : 0.06	i : 0.06	a : 0.04	b : 0.02	
g : 0.16	i : 0.12	4 : 0.10	3 : 0.10	= : 0.10	c : 0.08	b : 0.08	f : 0.06	2 : 0.06	] : 0.04	d : 0.04	a : 0.02	e : 0.02	
g : 0.18	i : 0.12	4 : 0.10	b : 0.10	= : 0.10	3 : 0.08	f : 0.08	e : 0.06	c : 0.06	d : 0.04	2 : 0.04	] : 0.02	
g : 0.16	i : 0.14	e : 0.12	f : 0.12	= : 0.10	c : 0.10	] : 0.08	3 : 0.04	d : 0.04	b : 0.04	2 : 0.02	4 : 0.02	
g : 0.20	e : 0.14	i : 0.14	f : 0.12	= : 0.10	c : 0.08	] : 0.06	2 : 0.04	3 : 0.04	d : 0.04	b : 0.02	
g : 0.22	e : 0.16	f : 0.14	i : 0.14	c : 0.10	= : 0.10	2 : 0.04	b : 0.02	d : 0.02	h : 0.02	4 : 0.02	
g : 0.22	e : 0.16	f : 0.14	i : 0.14	= : 0.08	c : 0.06	2 : 0.06	] : 0.04	d : 0.02	h : 0.02	C : 0.02	4 : 0.02	

#score	600.3421452738776
#seq	49
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m2_run1.txt

#BEAR
fffff[cccqqqqqqqqccc333fffff	chr5:134193695-134193935(+)$1	240	11	39	16.7408
b!!ccccccqqqqqqqqccc]cccbb22	chr6:149997608-149997848(-)$1	240	73	101	16.1026
ddddd[ddddqqqqqqqqdddd]dddd2	chr7:10973132-10973372(-)$1	240	46	74	13.7147
cc[bb[cccqqqqqqqqccc]bb]cccf	chr1:118167271-118167511(+)$1	240	48	76	16.6673
c[a[ddddaqqqqqqqqa]dddd]a]cc	chr15:41270980-41271220(-)$1	240	176	204	16.4062
dddd!!cccqqqqqqqqccc]dddd]bb	chr2:85548227-85548467(-)$1	240	107	135	16.5032
iiiiiiiiiqqqqqqqqiiiiiiiiicc	chr9:34087855-34088095(-)$1	240	78	106	17.1597
""gggggggqqqqqqqqgggggggdddd	chr1:40218502-40218742(+)$1	240	48	76	16.6431
=::bb[cccqqqqqqqqcccbb======	chr9:135564324-135564564(+)$1	240	179	207	15.1008
""gggggggqqqqqqqqggggggg]eee	chr14:21853275-21853555(-)$1	280	236	264	16.6300
ggg####bbqqqqqqqqbb4444ggggg	chr11:34904121-34904361(-)$1	240	116	144	16.6952
H:gggggggqqqqqqqqgggggggdddd	chr7:99054237-99054477(+)$1	240	92	120	14.7790
hddddddddqqqqqqqqdddd333dddd	chr5:71515529-71515769(-)$1	240	142	170	16.7119
dddd"""bbqqqqqqqqbb4444dddd3	chr8:61778994-61779234(+)$1	240	91	119	16.0094
ff"""ddddqqqqqqqqdddd333ffff	chr13:77457883-77458123(-)$1	240	15	43	17.1928
=========qqqqqqqq===========	chr20:42344808-42345048(+)$1	240	61	89	17.8743
ddd[eeeeeqqqqqqqqeeeee]dddd4	chr3:11597456-11597696(-)$1	240	106	134	15.7681
eeeee[ddddqqqqqqqqdddd]eeeee	chr14:90873765-90874005(+)$1	240	198	226	13.7931
dddd"""bbqqqqqqqqbb22ddddeee	chr17:27187812-27188052(+)$1	240	125	153	14.8624
eee"""cccqqqqqqqqccc]eeeee]d	chr2:176959486-176959726(+)$1	240	156	184	17.1024
ggggggg[aqqqqqqqqa]gggggggcc	chr17:65979455-65979695(+)$1	240	35	63	16.5882
h"""eeeeeqqqqqqqqeeeee22hhhh	chr17:27589896-27590136(-)$1	240	56	84	15.9622
$$gggggggqqqqqqqqggggggg4444	chr2:176046054-176046294(-)$1	240	81	109	16.0937
eeeeeddddqqqqqqqqdddd333eeee	chr11:44954338-44954578(-)$1	240	141	169	16.6990
ggg!!ddddqqqqqqqqdddd22ggggg	chr10:64927413-64927653(-)$1	240	113	141	17.3145
ddddeeeeeqqqqqqqqeeeee22dddd	chr4:113197071-113197311(-)$1	240	60	88	15.6269
ee"""ddddqqqqqqqqdddd333eeee	chr6:43304565-43304805(-)$1	240	121	149	17.6846
=========qqqqqqqq==========e	chr2:86509196-86509436(-)$1	240	26	54	17.7664
g"""eeeeeqqqqqqqqeeeee]ggggg	chr14:89627008-89627248(-)$1	240	156	184	16.8189
dd"""ddddqqqqqqqqdddd4444ddd	chr12:133497999-133498239(-)$1	240	33	61	17.3542
f[bb!!cccqqqqqqqqccc22bbffff	chr7:123323902-123324142(-)$1	240	125	153	16.0906
d[ddddcccqqqqqqqqccc22dddddd	chr2:211296885-211297125(-)$1	240	126	154	16.5318
d!!bb[cccqqqqqqqqcccbb]dddd=	chr15:81295886-81296126(+)$1	240	199	227	16.9828
g####ddddqqqqqqqqddddggggggg	chr4:71672692-71672932(+)$1	240	111	139	17.2749
gggg!!cccqqqqqqqqccc]ggggggg	chr2:200135690-200135930(-)$1	240	54	82	17.9687
iiiiiiiiiqqqqqqqqiiiiiiiii]d	chr13:42894412-42894652(+)$1	240	161	189	17.0573
=====[cccrrrrrrrrrccc]======	chr6:123130723-123130963(+)$1	240	53	81	12.0503
=####ddddqqqqqqqqdddd]======	chr17:18113126-18113366(+)$1	240	197	225	17.8452
h[ccc[a[aqqqqqqqqaaccc22hhhh	chr13:45008455-45008695(-)$1	240	47	75	16.2701
!!gggggggqqqqqqqqggggggg22cc	chr9:127909775-127910015(-)$1	240	60	88	16.4648
[a!!bb!!aqqqqqqqqa22bb22a]dd	chr1:197876345-197876585(+)$1	240	180	208	15.3877
dddd!!cccqqqqqqqqccc]dddd444	chr1:151314458-151314738(-)$1	280	214	242	16.8946
====!!cccqqqqqqqqccc4444====	chr20:57603685-57603925(-)$1	240	168	196	18.9175
b!!bb[cccqqqqqqqqccc22bb22bb	chr8:104455070-104455310(+)$1	240	91	119	15.6223
bb[ffffffqqqqqqqqffffff]bb44	chr2:131904359-131904599(+)$1	240	83	111	13.8028
hhhhh[cccqqqqqqqqccchhhhhhhh	chr3:32524087-32524327(-)$1	240	211	239	14.9797
$$$$eeeeeqqqqqqqqeeeee]iiiii	chr7:56130931-56131171(+)$1	240	57	85	15.9436
cc!!eeeeeqqqqqqqqeeeee22cccd	chr12:72286919-72287159(+)$1	240	128	156	16.4117
c####cccrrrrrrrrrccc4444ccc=	chr5:132031889-132032129(-)$1	240	102	130	11.9928
d[dddd[bbqqqqqqqqbb]dddd]ddd	chr1:93621882-93622122(-)$1	240	43	71	14.8456
ddcccddddqqqqqqqqdddd333cccH	chr18:211733-211973(+)$1	240	69	97	16.3743
eeee!!cccqqqqqqqqccc333eeeee	chr4:85570093-85570333(+)$1	240	43	71	17.8093
[ccc!!cccqqqqqqqqccc666666cc	chr15:64458140-64458380(-)$1	240	6	34	15.2250

#otherMatches

#Seq PSSM
UGUAUUAUUGUAUAAUGAAUUUUGUAUA	chr5:134193695-134193935(+)$1	240	11	39	16.7408
GCUGCACGCCAGCACCAGCGAUGUCUAG	chr6:149997608-149997848(-)$1	240	73	101	16.1026
UUCCAAGUUCUACUCAGUGAAUGUGGAU	chr7:10973132-10973372(-)$1	240	46	74	13.7147
CUGAGGAAUUGCGAGAUAUUGCUGAGGG	chr1:118167271-118167511(+)$1	240	48	76	16.6673
CUUGGAGGCAAACUAGAGCCCUUGGUGG	chr15:41270980-41271220(-)$1	240	176	204	16.4062
UGCGUUAGUCUUAUAAUACUUUGCACCA	chr2:85548227-85548467(-)$1	240	107	135	16.5032
CCUUACUUCACUCUUGAGAGGUAGGGCU	chr9:34087855-34088095(-)$1	240	78	106	17.1597
UCGGGGAGCUGAUGGUUGUUCUCUCCCU	chr1:40218502-40218742(+)$1	240	48	76	16.6431
UCCAGAGACUAAAGGAUGUCCUUUGAAA	chr9:135564324-135564564(+)$1	240	179	207	15.1008
UGUAUUGAUUUUGAGUUGUUAAUGGUGG	chr14:21853275-21853555(-)$1	280	236	264	16.6300
UAUAUACAGAGAUAAAGCUAAACGUAAU	chr11:34904121-34904361(-)$1	240	116	144	16.6952
UGCAGUCGACAUCAUGUUUGGCUGGGCA	chr7:99054237-99054477(+)$1	240	92	120	14.7790
GCACAUGUGCAUGCACACACAACUUGUG	chr5:71515529-71515769(-)$1	240	142	170	16.7119
UCCCUUUGGAAAAUUAACCUACUGGGAG	chr8:61778994-61779234(+)$1	240	91	119	16.0094
UUACUGUUUUGAGUCCUAAACUUAGAGU	chr13:77457883-77458123(-)$1	240	15	43	17.1928
CAACAGGGCCAUGUGCUGCCCUGUUGCC	chr20:42344808-42345048(+)$1	240	61	89	17.8743
UGUACUUAAAAGUAGCCUUAAGAACAAU	chr3:11597456-11597696(-)$1	240	106	134	15.7681
UAUAAAUGCAUGUCUGAUUGUACUUGUA	chr14:90873765-90874005(+)$1	240	198	226	13.7931
UCUUUCACCUUGAACUUGGAUAAGAACU	chr17:27187812-27188052(+)$1	240	125	153	14.8624
AGUUCUGAUUUUUACUUGUUUAUUAUUG	chr2:176959486-176959726(+)$1	240	156	184	17.1024
GGUAAUGCGACAAGAUACACAUUGCCUU	chr17:65979455-65979695(+)$1	240	35	63	16.5882
GCAUUUAUAUAAAGAGUUGUAGUCUUCU	chr17:27589896-27590136(-)$1	240	56	84	15.9622
AGCCUCUUUUCCUCCGCAGAGAGGAAGC	chr2:176046054-176046294(-)$1	240	81	109	16.0937
GUGUCGGGCGUCUGCUGGCCCUGAGACA	chr11:44954338-44954578(-)$1	240	141	169	16.6990
AGAUUUAAAAUGAUGUAUUUAUUUUUGG	chr10:64927413-64927653(-)$1	240	113	141	17.3145
uguguuggucguaagccacuaaaucaca	chr4:113197071-113197311(-)$1	240	60	88	15.6269
auauauauauauauaucuguaaaaaugu	chr6:43304565-43304805(-)$1	240	121	149	17.6846
AGAUAAAUGAAAAAUCGUAUUUAUUUUU	chr2:86509196-86509436(-)$1	240	26	54	17.7664
ACUCUGUACUGCCUUGUGUGCACUUCAG	chr14:89627008-89627248(-)$1	240	156	184	16.8189
UGUGUAUCACUCUGCUCUGAUCUUUUAG	chr12:133497999-133498239(-)$1	240	33	61	17.3542
CAUAAAAUCACUACAGAGAUACUAGUGG	chr7:123323902-123324142(-)$1	240	125	153	16.0906
ACUGGCACAAUUUUAUAUGUAUGCUAUU	chr2:211296885-211297125(-)$1	240	126	154	16.5318
UUUCACUCCUUAGACAUGGAUGUAGCUA	chr15:81295886-81296126(+)$1	240	199	227	16.9828
UUGUUACUUAUUUUUCCAGGUGCUGUUA	chr4:71672692-71672932(+)$1	240	111	139	17.2749
AAGCCUGCUCGUUUAAAAGUUGUUUGUU	chr2:200135690-200135930(-)$1	240	54	82	17.9687
GACAAAGGUUGUGUCUUGCUUUUGucuc	chr13:42894412-42894652(+)$1	240	161	189	17.0573
UGUAAAUAUUCAGUUUAUAUAAUUAUAU	chr6:123130723-123130963(+)$1	240	53	81	12.0503
UUUACUUUCUUAAACUUGAAACAGGGGU	chr17:18113126-18113366(+)$1	240	197	225	17.8452
ACGUGAGACUGACAUAUGCCAUUAUCUC	chr13:45008455-45008695(-)$1	240	47	75	16.2701
AUGUGACUUUUAUUUUUAAGUCAUUGUG	chr9:127909775-127910015(-)$1	240	60	88	16.4648
CAUUGAUCGUUAUUUUCCUUUCUUUUUG	chr1:197876345-197876585(+)$1	240	180	208	15.3877
CAGUCUACUUAGUACCUGGUUGCUGCCU	chr1:151314458-151314738(-)$1	280	214	242	16.8946
AAAUAUGGUUCACUGUUACUCUUGAUUU	chr20:57603685-57603925(-)$1	240	168	196	18.9175
GAACUCUACAAAUAAAAGUGCUGGGACU	chr8:104455070-104455310(+)$1	240	91	119	15.6223
UAGUUUUAAUCAUUCCUUUGAAAGUAGU	chr2:131904359-131904599(+)$1	240	83	111	13.8028
UCUGUUGGCUAGCAGCUGUCACAGAUAG	chr3:32524087-32524327(-)$1	240	211	239	14.9797
CUUUUAUCCAGUGAACAGGAUGUUUUGC	chr7:56130931-56131171(+)$1	240	57	85	15.9436
AGUCUUUCACAGUCUUUUGAAAAUCUUC	chr12:72286919-72287159(+)$1	240	128	156	16.4117
AAAUCGAUUAGCUAUUUAUCCAACUACU	chr5:132031889-132032129(-)$1	240	102	130	11.9928
AAUACAGGUAACUUAAAACAUGUACUUU	chr1:93621882-93622122(-)$1	240	43	71	14.8456
UGGGCACAAUCAAGUAUUUGUCCAGCCU	chr18:211733-211973(+)$1	240	69	97	16.3743
UCAAACACUAUAAAAUGAGUAAGUUGAC	chr4:85570093-85570333(+)$1	240	43	71	17.8093
AGAUAAUGUAUAAAUCAGCAGUGGAAAU	chr15:64458140-64458380(-)$1	240	6	34	15.2250

#DB
(((((.(((........)))...)))))	chr5:134193695-134193935(+)$1	1	11	39	16.7408
(..((((((........))).)))))..	chr6:149997608-149997848(-)$1	1	73	101	16.1026
(((((.((((........)))).)))).	chr7:10973132-10973372(-)$1	1	46	74	13.7147
((.((.(((........))).)).)))(	chr1:118167271-118167511(+)$1	1	48	76	16.6673
(.(.(((((........).)))).).))	chr15:41270980-41271220(-)$1	1	176	204	16.4062
((((..(((........))).)))).))	chr2:85548227-85548467(-)$1	1	107	135	16.5032
(((((((((........)))))))))((	chr9:34087855-34088095(-)$1	1	78	106	17.1597
..(((((((........)))))))))))	chr1:40218502-40218742(+)$1	1	48	76	16.6431
)..((.(((........)))))((((((	chr9:135564324-135564564(+)$1	1	179	207	15.1008
..(((((((........))))))).)))	chr14:21853275-21853555(-)$1	1	236	264	16.6300
(((....((........))....)))))	chr11:34904121-34904361(-)$1	1	116	144	16.6952
(.(((((((........)))))))((((	chr7:99054237-99054477(+)$1	1	92	120	14.7790
)((((((((........))))...))))	chr5:71515529-71515769(-)$1	1	142	170	16.7119
((((...((........))....)))).	chr8:61778994-61779234(+)$1	1	91	119	16.0094
((...((((........))))...))))	chr13:77457883-77458123(-)$1	1	15	43	17.1928
(((((((((........)))))))))))	chr20:42344808-42345048(+)$1	1	61	89	17.8743
(((.(((((........))))).)))).	chr3:11597456-11597696(-)$1	1	106	134	15.7681
(((((.((((........)))).)))))	chr14:90873765-90874005(+)$1	1	198	226	13.7931
((((...((........))..))))(((	chr17:27187812-27188052(+)$1	1	125	153	14.8624
(((...(((........))).))))).)	chr2:176959486-176959726(+)$1	1	156	184	17.1024
(((((((.(........).)))))))))	chr17:65979455-65979695(+)$1	1	35	63	16.5882
(...(((((........)))))..))))	chr17:27589896-27590136(-)$1	1	56	84	15.9622
..(((((((........)))))))....	chr2:176046054-176046294(-)$1	1	81	109	16.0937
(((((((((........))))...))))	chr11:44954338-44954578(-)$1	1	141	169	16.6990
(((..((((........))))..)))))	chr10:64927413-64927653(-)$1	1	113	141	17.3145
(((((((((........)))))..))))	chr4:113197071-113197311(-)$1	1	60	88	15.6269
((...((((........))))...))))	chr6:43304565-43304805(-)$1	1	121	149	17.6846
(((((((((........)))))))))))	chr2:86509196-86509436(-)$1	1	26	54	17.7664
(...(((((........))))).)))))	chr14:89627008-89627248(-)$1	1	156	184	16.8189
((...((((........))))....)))	chr12:133497999-133498239(-)$1	1	33	61	17.3542
(.((..(((........)))..))))))	chr7:123323902-123324142(-)$1	1	125	153	16.0906
(.(((((((........)))..))))))	chr2:211296885-211297125(-)$1	1	126	154	16.5318
(..((.(((........))))).)))))	chr15:81295886-81296126(+)$1	1	199	227	16.9828
(....((((........)))))))))))	chr4:71672692-71672932(+)$1	1	111	139	17.2749
((((..(((........))).)))))))	chr2:200135690-200135930(-)$1	1	54	82	17.9687
(((((((((........))))))))).)	chr13:42894412-42894652(+)$1	1	161	189	17.0573
(((((.(((.........))).))))))	chr6:123130723-123130963(+)$1	1	53	81	12.0503
(....((((........)))).))))))	chr17:18113126-18113366(+)$1	1	197	225	17.8452
(.(((.(.(........)))))..))))	chr13:45008455-45008695(-)$1	1	47	75	16.2701
..(((((((........)))))))..))	chr9:127909775-127910015(-)$1	1	60	88	16.4648
.(..((..(........)..))..).))	chr1:197876345-197876585(+)$1	1	180	208	15.3877
((((..(((........))).))))...	chr1:151314458-151314738(-)$1	1	214	242	16.8946
((((..(((........)))....))))	chr20:57603685-57603925(-)$1	1	168	196	18.9175
(..((.(((........)))..))..))	chr8:104455070-104455310(+)$1	1	91	119	15.6223
((.((((((........)))))).))..	chr2:131904359-131904599(+)$1	1	83	111	13.8028
(((((.(((........)))))))))))	chr3:32524087-32524327(-)$1	1	211	239	14.9797
....(((((........))))).)))))	chr7:56130931-56131171(+)$1	1	57	85	15.9436
((..(((((........)))))..)))(	chr12:72286919-72287159(+)$1	1	128	156	16.4117
(....(((.........)))....))))	chr5:132031889-132032129(-)$1	1	102	130	11.9928
(.((((.((........)).)))).)))	chr1:93621882-93622122(-)$1	1	43	71	14.8456
))(((((((........))))...)))(	chr18:211733-211973(+)$1	1	69	97	16.3743
((((..(((........)))...)))))	chr4:85570093-85570333(+)$1	1	43	71	17.8093
.(((..(((........)))......))	chr15:64458140-64458380(-)$1	1	6	34	15.2250

#PSSM
d : 0.22	= : 0.11	g : 0.11	e : 0.09	c : 0.07	h : 0.07	f : 0.05	b : 0.05	i : 0.03	" : 0.03	$ : 0.03	[ : 0.03	H : 0.01	! : 0.01	
d : 0.18	[ : 0.09	e : 0.09	! : 0.07	" : 0.07	g : 0.07	= : 0.07	c : 0.05	# : 0.05	f : 0.03	i : 0.03	: : 0.03	$ : 0.03	a : 0.01	b : 0.01	h : 0.01	
d : 0.18	g : 0.16	! : 0.09	" : 0.09	= : 0.07	e : 0.07	# : 0.05	c : 0.05	[ : 0.03	i : 0.03	f : 0.01	a : 0.01	: : 0.01	b : 0.01	h : 0.01	$ : 0.01	
d : 0.16	g : 0.13	" : 0.11	b : 0.09	c : 0.07	# : 0.07	= : 0.07	e : 0.05	! : 0.05	f : 0.03	[ : 0.03	i : 0.03	h : 0.01	$ : 0.01	
! : 0.15	e : 0.15	g : 0.11	" : 0.11	d : 0.09	b : 0.09	# : 0.07	c : 0.05	= : 0.05	f : 0.03	i : 0.03	h : 0.01	
d : 0.22	[ : 0.18	! : 0.13	g : 0.11	e : 0.11	" : 0.05	c : 0.03	i : 0.03	= : 0.03	# : 0.01	b : 0.01	f : 0.01	
c : 0.33	d : 0.22	g : 0.11	e : 0.11	i : 0.03	" : 0.03	= : 0.03	# : 0.01	a : 0.01	! : 0.01	f : 0.01	[ : 0.01	
c : 0.33	d : 0.22	e : 0.11	g : 0.09	b : 0.07	i : 0.03	= : 0.03	[ : 0.03	! : 0.01	f : 0.01	
c : 0.32	d : 0.20	e : 0.11	g : 0.09	a : 0.07	b : 0.07	i : 0.03	= : 0.03	f : 0.01	r : 0.01	
q : 0.92	d : 0.03	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
q : 0.96	r : 0.03	
c : 0.32	d : 0.16	e : 0.11	g : 0.09	a : 0.07	b : 0.07	q : 0.03	i : 0.03	= : 0.03	r : 0.01	f : 0.01	
c : 0.33	d : 0.20	e : 0.11	g : 0.09	b : 0.07	] : 0.03	i : 0.03	= : 0.03	a : 0.01	2 : 0.01	f : 0.01	
c : 0.35	d : 0.22	g : 0.11	e : 0.11	i : 0.03	4 : 0.03	= : 0.03	2 : 0.03	f : 0.01	] : 0.01	
d : 0.24	] : 0.11	g : 0.11	e : 0.11	4 : 0.07	2 : 0.07	b : 0.05	3 : 0.03	i : 0.03	= : 0.03	c : 0.03	f : 0.01	h : 0.01	6 : 0.01	
g : 0.15	3 : 0.13	d : 0.13	e : 0.13	4 : 0.09	b : 0.07	2 : 0.07	c : 0.03	i : 0.03	= : 0.03	] : 0.03	f : 0.01	h : 0.01	6 : 0.01	
g : 0.15	3 : 0.13	] : 0.11	d : 0.11	2 : 0.11	= : 0.09	4 : 0.09	b : 0.05	i : 0.03	c : 0.01	e : 0.01	f : 0.01	h : 0.01	6 : 0.01	
g : 0.20	d : 0.16	= : 0.09	3 : 0.09	2 : 0.09	] : 0.05	i : 0.05	e : 0.05	4 : 0.05	b : 0.03	f : 0.01	c : 0.01	h : 0.01	6 : 0.01	
d : 0.22	= : 0.11	g : 0.11	e : 0.09	c : 0.07	f : 0.05	i : 0.05	h : 0.05	b : 0.03	a : 0.03	] : 0.03	4 : 0.03	2 : 0.03	6 : 0.01	
d : 0.20	e : 0.13	= : 0.11	g : 0.11	c : 0.07	f : 0.05	] : 0.05	i : 0.05	h : 0.05	b : 0.03	4 : 0.03	2 : 0.03	6 : 0.01	
d : 0.22	c : 0.16	= : 0.11	e : 0.11	g : 0.09	f : 0.05	h : 0.05	4 : 0.05	b : 0.03	] : 0.03	2 : 0.01	i : 0.01	
d : 0.20	= : 0.13	e : 0.13	c : 0.09	g : 0.09	f : 0.07	4 : 0.07	h : 0.05	2 : 0.03	b : 0.03	3 : 0.01	i : 0.01	H : 0.01	

#score	859.1115444384113
#seq	53
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m3_run2.txt

#BEAR
:gggggggqqqqqqqqgggggggi	chr6:30692169-30692416(+)$1	247	140	164	14.9889
gggg!!bbqqqqqqqqbb333ggg	chr12:110788701-110788932(+)$1	231	133	157	15.3226
ccc!!cccqqqqqqqqccc22ccc	chr19:12786569-12786800(-)$1	231	31	55	15.8064
ggggg[bbqqqqqqqqbbgggggg	chr2:27664934-27665158(+)$1	224	31	55	15.3209
dd"""cccqqqqqqqqcccdddd]	chr3:122599442-122599663(+)$1	221	177	201	15.3461
fffff[bbqqqqqqqqbb]fffff	chrX:152961391-152961622(+)$1	231	42	66	13.9171
"""eeeeeqqqqqqqqeeeee444	chr1:244219682-244219904(+)$1	222	174	198	15.4027
========qqqqqqqq========	chr4:160279956-160280210(+)$1	254	127	151	16.0518
####ddddqqqqqqqqdddd]ddd	chrX:131351186-131351419(-)$1	233	201	225	15.4369
d"""ddddqqqqqqqqdddd22dd	chr6:80411573-80411822(+)$1	249	25	49	15.3065
f####cccqqqqqqqqccc22fff	chr1:32831041-32831320(-)$1	279	136	160	15.4245
ee[eeeeeqqqqqqqqeeeeeeee	chr19:18679775-18680006(+)$1	231	170	194	14.7068
cgggggggqqqqqqqqggggggg:	chr15:78777128-78777348(+)$1	220	27	51	15.0047
fffffcccqqqqqqqqccc]ffff	chr21:34775760-34776003(+)$1	243	86	110	14.9482
gg[eeeeeqqqqqqqqeeeee]gg	chr21:34948886-34949117(+)$1	231	61	85	15.4307
ddd[ddddqqqqqqqqdddd]ddd	chr10:104417221-104417470(+)$1	249	52	76	14.8513
eeeee[bbqqqqqqqqbb]eeeee	chr5:55235458-55235678(-)$1	220	24	48	14.1052
:eeeee[aqqqqqqqqa]eeeee:	chr1:110776056-110776306(+)$1	250	224	248	12.9340
iiiiiiiiqqqqqqqqiiiiiiii	chr19:11244048-11244279(+)$1	231	194	218	15.9149
cc!!a[bbqqqqqqqqbba22ccc	chr6:36199426-36199685(+)$1	259	15	39	14.9760
!!ffffffqqqqqqqqffffff33	chr3:10168728-10168953(+)$1	225	16	40	15.0897
bgggggggqqqqqqqqggggggg]	chr2:87001157-87001386(+)$1	229	169	193	15.7765
d"""ddddqqqqqqqqdddd4444	chr9:98215747-98215969(-)$1	222	62	86	15.7089
iiiii[bbqqqqqqqqbb22iiii	chr17:7362881-7363105(-)$1	224	5	29	14.8873
[cccbb[aqqqqqqqqa]bb]ccc	chr13:30781419-30781644(-)$1	225	144	168	14.3270
====:cccqqqqqqqqccc:hhhh	chr3:52289460-52289719(-)$1	259	57	81	13.4267
ggbb[cccqqqqqqqqcccbb]gg	chr1:233519676-233519907(+)$1	231	115	139	14.7889
ddddbb[aqqqqqqqqa]bb]ddd	chr2:5837198-5837494(+)$1	296	46	70	13.3427
dddda[bbqqqqqqqqbb]a]ddd	chr17:76102024-76102268(+)$1	244	25	49	13.8619
!!ffffffqqqqqqqqffffff22	chr3:129369474-129369694(-)$1	220	69	93	14.5900
ddffffffqqqqqqqqffffff]d	chr19:47724711-47724940(-)$1	229	151	175	14.2682
[gggggggqqqqqqqqggggggge	chr7:108214606-108214830(+)$1	224	68	92	15.9016
[ddddcccqqqqqqqqccc]dddd	chr9:134372365-134372602(+)$1	237	176	200	14.7866
ii[ccc[aqqqqqqqqa]ccciii	chr2:200790596-200790831(+)$1	235	120	144	15.7104
g"""ddddqqqqqqqqdddd4444	chr8:52731844-52732065(-)$1	221	167	191	15.8522
hhhhhhhhqqqqqqqqhhhhhhhh	chr3:52084082-52084347(-)$1	265	27	51	13.2706
eeffffffqqqqqqqqffffff]e	chr17:27590770-27591004(-)$1	234	157	181	14.3309
bb[eeeeeqqqqqqqqeeeee]bb	chr22:21804703-21804942(+)$1	239	204	228	14.2470
bbccccccqqqqqqqqccc]ccc]	chr8:22879046-22879272(-)$1	226	78	102	15.2203
eeee[cccqqqqqqqqccceeeee	chr14:67852804-67853035(+)$1	231	183	207	15.1085
:gggggggqqqqqqqqggggggg:	chr3:47894138-47894386(-)$1	248	173	197	14.0898
hhh[ddddqqqqqqqqddddhhhh	chr7:27870223-27870448(-)$1	225	75	99	14.4323
""ffffffqqqqqqqqffffff55	chr14:61176232-61176477(-)$1	245	146	170	13.3746
===[ddddqqqqqqqqdddd====	chr11:111889743-111889964(+)$1	221	111	135	15.9547
b"""ddddqqqqqqqqdddd333b	chr3:129034876-129035146(-)$1	270	158	182	15.7140
[gggggggqqqqqqqqggggggg]	chr21:34877828-34878081(-)$1	253	208	232	16.0821
$$ffffffqqqqqqqqffffff33	chr12:69995043-69995269(+)$1	226	163	187	14.5293
$$$$ddddqqqqqqqqdddd333g	chr15:66633388-66633613(-)$1	225	130	154	15.2778
ccc!!cccqqqqqqqqccc22ccc	chr19:36259740-36259960(+)$1	220	67	91	15.8064
gg!!ddddqqqqqqqqddddgggg	chr12:96673632-96673856(-)$1	224	137	161	15.9954
hhhhhhhhqqqqqqqqhhhhhhhh	chr6:111680051-111680268(-)$1	217	31	55	13.2706
$$$eeeeeqqqqqqqqeeeee666	chr17:56081512-56081739(-)$1	227	110	134	13.4875
eeeeddddqqqqqqqqdddd0000	chr16:67181401-67181643(+)$1	242	19	43	13.4690
ffff[cccqqqqqqqqcccfffff	chr3:53003068-53003294(-)$1	226	190	214	14.9886
dd!!ddddqqqqqqqqdddd22dd	chr6:89793993-89794228(+)$1	235	60	84	15.1360
hhhhhhhhqqqqqqqqhhhhhhhh	chr7:150780115-150780387(-)$1	272	121	145	13.2706
gggeeeeeqqqqqqqqeeeeeGGG	chr14:34903385-34903613(-)$1	228	162	186	13.4060
a"""ddddqqqqqqqqdddd333a	chr14:23778232-23778457(+)$1	225	90	114	16.1210

#otherMatches

#Seq PSSM
agugccuggcacauaguaggcgcu	chr6:30692169-30692416(+)$1	247	140	164	14.9889
GUGCUGGUAACAAUGAGCGUCGCA	chr12:110788701-110788932(+)$1	231	133	157	15.3226
ACCCAGGUUCCCCCCUACCCAGGU	chr19:12786569-12786800(-)$1	231	31	55	15.8064
CUGUGUGGAAAGGAGGCCCACGGG	chr2:27664934-27665158(+)$1	224	31	55	15.3209
GGCCCUGCUCCUCUCUGCACCUGU	chr3:122599442-122599663(+)$1	221	177	201	15.3461
GAGGAAGGAGCCCAAACCAUCCUC	chrX:152961391-152961622(+)$1	231	42	66	13.9171
GAAUAACUACUGCACAAGUUGACA	chr1:244219682-244219904(+)$1	222	174	198	15.4027
CAUCUGCUCCUUCCCCAGUGGAUG	chr4:160279956-160280210(+)$1	254	127	151	16.0518
ACUUUCAUUGAGAAAUAUGACCCC	chrX:131351186-131351419(-)$1	233	201	225	15.4369
AAAAUACUAGGAAAGAAGUGGAUG	chr6:80411573-80411822(+)$1	249	25	49	15.3065
ACUCUGGUAAAGCUGCACCUCUGG	chr1:32831041-32831320(-)$1	279	136	160	15.4245
UCUGAGAUAGGUAGAAGUCUUGAG	chr19:18679775-18680006(+)$1	231	170	194	14.7068
CAUUCAUUAUGAAGGAAGUGAAUA	chr15:78777128-78777348(+)$1	220	27	51	15.0047
GCCAUGCGAccgacgcugcugugg	chr21:34775760-34776003(+)$1	243	86	110	14.9482
UUGUAAAUAUUUGGCAAUUUAAGA	chr21:34948886-34949117(+)$1	231	61	85	15.4307
uuuuugauuuuuuuuuauuAUGAA	chr10:104417221-104417470(+)$1	249	52	76	14.8513
CUUAGUUCUACAUUGUGAUUUAGG	chr5:55235458-55235678(-)$1	220	24	48	14.1052
CCUUUGUCUGUUUGUUGUCAAAGA	chr1:110776056-110776306(+)$1	250	224	248	12.9340
GGUUGCUGUAUUUGUUCAGUGACU	chr19:11244048-11244279(+)$1	231	194	218	15.9149
GCCUGCGCUCUGCCCUGCCCUGCC	chr6:36199426-36199685(+)$1	259	15	39	14.9760
CCAAGUCCCCAUGUUUGGACUUUC	chr3:10168728-10168953(+)$1	225	16	40	15.0897
GAAGUGUUCUUAAGUUGAUAUUUA	chr2:87001157-87001386(+)$1	229	169	193	15.7765
CACAGGCCUUUCUGACGGCCAUCG	chr9:98215747-98215969(-)$1	222	62	86	15.7089
UUUUUUUCUUAAAUAUGAUCAAGG	chr17:7362881-7363105(-)$1	224	5	29	14.8873
AGGUUGAGAACUUUUACACACACU	chr13:30781419-30781644(-)$1	225	144	168	14.3270
GAAUAGGCUGUGAAUUGCUAGCAC	chr3:52289460-52289719(-)$1	259	57	81	13.4267
CUCUAGAAUGUGGCUCUUCAGAAG	chr1:233519676-233519907(+)$1	231	115	139	14.7889
AUCCGCCGCCUCUUUUCUGCUGGG	chr2:5837198-5837494(+)$1	296	46	70	13.3427
UUAGCAGCUUUUUAUUGUGGACUA	chr17:76102024-76102268(+)$1	244	25	49	13.8619
UCCCUUGGCCGCACUUUUAAGGUU	chr3:129369474-129369694(-)$1	220	69	93	14.5900
GGGGGUGGGGACUGAGCCGCCCGC	chr19:47724711-47724940(-)$1	229	151	175	14.2682
AUAUUUUUAAAUCCUGAGAAAUGU	chr7:108214606-108214830(+)$1	224	68	92	15.9016
CCUGAGCUAAGCAGUAGGCAUCAG	chr9:134372365-134372602(+)$1	237	176	200	14.7866
GGUAUGGGGGGAAGCACACAUUCC	chr2:200790596-200790831(+)$1	235	120	144	15.7104
GGCUGAGCCUACAUUUGCUUUUGA	chr8:52731844-52732065(-)$1	221	167	191	15.8522
GAGAAAUGUUCAGUUUUGUUUUUC	chr3:52084082-52084347(-)$1	265	27	51	13.2706
UAGUUGAUGGUACAUAGUUAACUU	chr17:27590770-27591004(-)$1	234	157	181	14.3309
CUUAGAGCAGACAAGGGCUCUCAG	chr22:21804703-21804942(+)$1	239	204	228	14.2470
CGGGACCAAAGAGAACUGGAUCCA	chr8:22879046-22879272(-)$1	226	78	102	15.2203
CUUGUGAUUUCUCAUUAUUcaggu	chr14:67852804-67853035(+)$1	231	183	207	15.1085
CGGGGCAGCAGCAGCCCUGCCCCA	chr3:47894138-47894386(-)$1	248	173	197	14.0898
AAACUGUGCUUUAAAUUAUAUUUU	chr7:27870223-27870448(-)$1	225	75	99	14.4323
UUUUAUUUGUUUUCUGAAAUGAUG	chr14:61176232-61176477(-)$1	245	146	170	13.3746
UCUAGUUUGUGUGCCAAAACAGAA	chr11:111889743-111889964(+)$1	221	111	135	15.9547
gucucugacccccaacucgguccc	chr3:129034876-129035146(-)$1	270	158	182	15.7140
GGAAUGGUAAGCAAAAAUUAUUUG	chr21:34877828-34878081(-)$1	253	208	232	16.0821
UUAUAUCCUUAAGUUUGGAUAUUU	chr12:69995043-69995269(+)$1	226	163	187	14.5293
AUUUUAUGCCAAAUUUUAUAUGCU	chr15:66633388-66633613(-)$1	225	130	154	15.2778
gcuauagcccacacaugcuugagc	chr19:36259740-36259960(+)$1	220	67	91	15.8064
UAUUGCGGAAUCAUUGCUGCUAAA	chr12:96673632-96673856(-)$1	224	137	161	15.9954
GUAUUUAUUUGCUUUUAUAGAUAC	chr6:111680051-111680268(-)$1	217	31	55	13.2706
AACCUGUAAUACGCUGUACAGUAA	chr17:56081512-56081739(-)$1	227	110	134	13.4875
CCUUUGGCUCCACAUUGCCACAUG	chr16:67181401-67181643(+)$1	242	19	43	13.4690
uucucagaauuuauucucuaggau	chr3:53003068-53003294(-)$1	226	190	214	14.9886
AGCUUGUAUUAUAUUUUAUAUUUU	chr6:89793993-89794228(+)$1	235	60	84	15.1360
GCUGGGUGGGUGGUGACGCUCGGU	chr7:150780115-150780387(-)$1	272	121	145	13.2706
UUUUAAGGUUUUUAUUCCUUAAAU	chr14:34903385-34903613(-)$1	228	162	186	13.4060
UAGGCCAGGUAGGCGAUUGGAAGA	chr14:23778232-23778457(+)$1	225	90	114	16.1210

#DB
.(((((((........)))))))(	chr6:30692169-30692416(+)$1	1	140	164	14.9889
((((..((........))...)))	chr12:110788701-110788932(+)$1	1	133	157	15.3226
(((..(((........)))..)))	chr19:12786569-12786800(-)$1	1	31	55	15.8064
(((((.((........))))))))	chr2:27664934-27665158(+)$1	1	31	55	15.3209
((...(((........))))))).	chr3:122599442-122599663(+)$1	1	177	201	15.3461
(((((.((........)).)))))	chrX:152961391-152961622(+)$1	1	42	66	13.9171
...(((((........)))))...	chr1:244219682-244219904(+)$1	1	174	198	15.4027
((((((((........))))))))	chr4:160279956-160280210(+)$1	1	127	151	16.0518
....((((........)))).)))	chrX:131351186-131351419(-)$1	1	201	225	15.4369
(...((((........))))..))	chr6:80411573-80411822(+)$1	1	25	49	15.3065
(....(((........)))..)))	chr1:32831041-32831320(-)$1	1	136	160	15.4245
((.(((((........))))))))	chr19:18679775-18680006(+)$1	1	170	194	14.7068
)(((((((........))))))).	chr15:78777128-78777348(+)$1	1	27	51	15.0047
((((((((........))).))))	chr21:34775760-34776003(+)$1	1	86	110	14.9482
((.(((((........))))).))	chr21:34948886-34949117(+)$1	1	61	85	15.4307
(((.((((........)))).)))	chr10:104417221-104417470(+)$1	1	52	76	14.8513
(((((.((........)).)))))	chr5:55235458-55235678(-)$1	1	24	48	14.1052
.(((((.(........).))))).	chr1:110776056-110776306(+)$1	1	224	248	12.9340
((((((((........))))))))	chr19:11244048-11244279(+)$1	1	194	218	15.9149
((..(.((........)))..)))	chr6:36199426-36199685(+)$1	1	15	39	14.9760
..((((((........))))))..	chr3:10168728-10168953(+)$1	1	16	40	15.0897
((((((((........))))))).	chr2:87001157-87001386(+)$1	1	169	193	15.7765
(...((((........))))....	chr9:98215747-98215969(-)$1	1	62	86	15.7089
(((((.((........))..))))	chr17:7362881-7363105(-)$1	1	5	29	14.8873
.(((((.(........).)).)))	chr13:30781419-30781644(-)$1	1	144	168	14.3270
)))).(((........))).((((	chr3:52289460-52289719(-)$1	1	57	81	13.4267
((((.(((........))))).))	chr1:233519676-233519907(+)$1	1	115	139	14.7889
((((((.(........).)).)))	chr2:5837198-5837494(+)$1	1	46	70	13.3427
(((((.((........)).).)))	chr17:76102024-76102268(+)$1	1	25	49	13.8619
..((((((........))))))..	chr3:129369474-129369694(-)$1	1	69	93	14.5900
((((((((........)))))).)	chr19:47724711-47724940(-)$1	1	151	175	14.2682
.(((((((........))))))))	chr7:108214606-108214830(+)$1	1	68	92	15.9016
.(((((((........))).))))	chr9:134372365-134372602(+)$1	1	176	200	14.7866
((.(((.(........).))))))	chr2:200790596-200790831(+)$1	1	120	144	15.7104
(...((((........))))....	chr8:52731844-52732065(-)$1	1	167	191	15.8522
((((((((........))))))))	chr3:52084082-52084347(-)$1	1	27	51	13.2706
((((((((........)))))).)	chr17:27590770-27591004(-)$1	1	157	181	14.3309
((.(((((........))))).))	chr22:21804703-21804942(+)$1	1	204	228	14.2470
((((((((........))).))).	chr8:22879046-22879272(-)$1	1	78	102	15.2203
((((.(((........))))))))	chr14:67852804-67853035(+)$1	1	183	207	15.1085
.(((((((........))))))).	chr3:47894138-47894386(-)$1	1	173	197	14.0898
(((.((((........))))))))	chr7:27870223-27870448(-)$1	1	75	99	14.4323
..((((((........))))))..	chr14:61176232-61176477(-)$1	1	146	170	13.3746
(((.((((........))))))))	chr11:111889743-111889964(+)$1	1	111	135	15.9547
(...((((........))))...)	chr3:129034876-129035146(-)$1	1	158	182	15.7140
.(((((((........))))))).	chr21:34877828-34878081(-)$1	1	208	232	16.0821
..((((((........))))))..	chr12:69995043-69995269(+)$1	1	163	187	14.5293
....((((........))))...)	chr15:66633388-66633613(-)$1	1	130	154	15.2778
(((..(((........)))..)))	chr19:36259740-36259960(+)$1	1	67	91	15.8064
((..((((........))))))))	chr12:96673632-96673856(-)$1	1	137	161	15.9954
((((((((........))))))))	chr6:111680051-111680268(-)$1	1	31	55	13.2706
...(((((........)))))...	chr17:56081512-56081739(-)$1	1	110	134	13.4875
((((((((........))))....	chr16:67181401-67181643(+)$1	1	19	43	13.4690
((((.(((........))))))))	chr3:53003068-53003294(-)$1	1	190	214	14.9886
((..((((........))))..))	chr6:89793993-89794228(+)$1	1	60	84	15.1360
((((((((........))))))))	chr7:150780115-150780387(-)$1	1	121	145	13.2706
)))(((((........))))))))	chr14:34903385-34903613(-)$1	1	162	186	13.4060
(...((((........))))...)	chr14:23778232-23778457(+)$1	1	90	114	16.1210

#PSSM
d : 0.13	g : 0.12	e : 0.08	c : 0.06	f : 0.06	b : 0.06	[ : 0.06	h : 0.06	: : 0.05	= : 0.05	i : 0.05	$ : 0.05	" : 0.03	! : 0.03	# : 0.01	a : 0.01	
g : 0.20	d : 0.12	" : 0.12	e : 0.10	c : 0.06	h : 0.06	f : 0.05	= : 0.05	i : 0.05	$ : 0.05	# : 0.03	! : 0.03	b : 0.03	
g : 0.15	f : 0.15	" : 0.12	c : 0.06	[ : 0.06	d : 0.06	e : 0.06	h : 0.06	= : 0.05	! : 0.05	# : 0.03	i : 0.03	$ : 0.03	b : 0.01	
e : 0.17	f : 0.15	g : 0.13	" : 0.10	! : 0.08	[ : 0.05	c : 0.05	d : 0.05	h : 0.05	= : 0.03	# : 0.03	i : 0.03	b : 0.01	$ : 0.01	
d : 0.24	f : 0.13	e : 0.13	g : 0.12	! : 0.05	[ : 0.05	h : 0.05	i : 0.03	a : 0.03	b : 0.03	c : 0.03	" : 0.01	= : 0.01	# : 0.01	: : 0.01	
d : 0.22	c : 0.20	e : 0.12	g : 0.10	[ : 0.10	f : 0.10	h : 0.05	b : 0.03	! : 0.01	= : 0.01	i : 0.01	
d : 0.22	c : 0.18	b : 0.12	g : 0.10	e : 0.10	f : 0.10	[ : 0.06	h : 0.05	= : 0.01	i : 0.01	
d : 0.22	c : 0.18	b : 0.12	g : 0.10	e : 0.10	f : 0.10	a : 0.06	h : 0.05	= : 0.01	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.22	c : 0.18	b : 0.12	g : 0.10	e : 0.10	f : 0.10	a : 0.06	h : 0.05	= : 0.01	i : 0.01	
d : 0.22	c : 0.18	b : 0.12	g : 0.10	e : 0.10	f : 0.10	] : 0.06	h : 0.05	= : 0.01	i : 0.01	
d : 0.22	c : 0.20	g : 0.12	e : 0.12	f : 0.10	] : 0.05	h : 0.05	b : 0.03	3 : 0.01	= : 0.01	i : 0.01	a : 0.01	2 : 0.01	
d : 0.24	e : 0.15	f : 0.13	g : 0.12	2 : 0.08	] : 0.05	b : 0.05	h : 0.05	3 : 0.01	= : 0.01	i : 0.01	: : 0.01	a : 0.01	c : 0.01	
f : 0.15	e : 0.15	g : 0.13	2 : 0.10	] : 0.08	h : 0.08	3 : 0.06	d : 0.03	= : 0.03	i : 0.03	4 : 0.03	c : 0.03	b : 0.01	0 : 0.01	
f : 0.17	g : 0.15	d : 0.10	c : 0.08	h : 0.08	e : 0.06	4 : 0.05	] : 0.05	i : 0.05	3 : 0.05	= : 0.03	2 : 0.03	6 : 0.01	0 : 0.01	G : 0.01	
g : 0.18	d : 0.13	c : 0.08	3 : 0.08	h : 0.08	f : 0.06	e : 0.06	4 : 0.05	i : 0.05	= : 0.03	] : 0.03	2 : 0.01	b : 0.01	5 : 0.01	6 : 0.01	0 : 0.01	G : 0.01	
d : 0.13	g : 0.10	e : 0.08	h : 0.08	i : 0.06	c : 0.06	] : 0.06	f : 0.06	4 : 0.05	: : 0.05	= : 0.03	3 : 0.03	b : 0.03	2 : 0.01	5 : 0.01	6 : 0.01	0 : 0.01	G : 0.01	a : 0.01	

#score	860.1009526322005
#seq	58
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m3_run1.txt

#BEAR
cdddd[eeeeemmmmeeeeeddd	chr7:149129466-149129688(+)$1	222	100	123	8.5492
eeeee[ddddnnnnndddd333e	chr1:151774152-151774379(-)$1	227	169	192	8.3294
eee[dddd[bbmmmmbbddddee	chr3:15497278-15497502(+)$1	224	94	117	8.3819
ddd[a!!ddddoooooodddd]a	chr8:61735072-61735296(-)$1	224	79	102	8.4530
eee####a[cccmmmmccc]a22	chr12:56651526-56651754(+)$1	228	189	212	7.8755
e!!dddd[ddddllldddd]ddd	chr3:52552437-52552658(-)$1	221	47	70	9.2080
f!!ccc[ddddmmmmdddd0000	chr10:97116664-97116888(-)$1	224	152	175	9.7661
c[ccc[eeeeemmmmeeeee]cc	chr19:17837840-17838061(-)$1	221	114	137	9.0626
eeee"""ddddllldddd22eee	chr2:202526084-202526312(+)$1	228	115	138	9.2988
dddd[a[ddddmmmmdddd]a]d	chr22:23615833-23616054(-)$1	221	105	128	11.4774
ee####eeeeemmmmeeeee]ee	chr15:73075892-73076119(-)$1	227	178	201	9.4171
hh[eeeeeddddllldddd]eee	chr20:46256353-46256576(+)$1	223	152	175	8.9666
c####eeeeeammmma]eeeee4	chr8:145675760-145675981(-)$1	221	7	30	8.9704
""dddd[ddddmmmmdddd]ddd	chr16:24801242-24801463(-)$1	221	23	46	11.2443
ddd[bb[ddddmmmmdddd]bbd	chr6:3259209-3259430(-)$1	221	127	150	10.4851
:bb[a!!ddddmmmmdddd]abb	chr22:29456306-29456528(-)$1	222	16	39	10.0649
gggggg!!cccmmmmccc333gg	chr19:9067728-9067953(-)$1	225	133	156	9.6961
ffffff[ddddmmmmdddd22ff	chr4:154523616-154523842(+)$1	226	43	66	10.5466
f[a[bb[ddddmmmmdddd]bba	chr9:139738905-139739128(-)$1	223	174	197	10.7597
c[iiiiiiiiimmmmiiiiiiii	chr5:135390267-135390488(-)$1	221	6	29	8.8156
eee[cccddddmmmmdddd]ccc	chr16:86565581-86565804(-)$1	223	185	208	11.4949
iiiiiiiddddmmmmdddd333i	chr5:140562098-140562319(+)$1	221	64	87	11.7267
!!a[dddd[cccmmmmccc]ddd	chrX:128599771-128599995(-)$1	224	188	211	7.8367
cccgggggggammmma]gggggg	chr2:202149716-202149940(+)$1	224	64	87	8.3933
eeee"""ddddllldddd22eee	chr11:113845916-113846141(+)$1	225	94	117	9.2988
ggggggg!!bbmmmmbb333ggg	chr1:91980282-91980507(+)$1	225	153	176	8.0202
bb!!ccc[cccmmmmccc]ccc2	chr17:76142821-76143044(-)$1	223	153	176	8.3879
a[dddd[ddddllldddd]dddd	chr1:24432436-24432658(-)$1	222	132	155	8.4504
""iiiiiiiiimmmmiiiiiiii	chr16:24801586-24801813(-)$1	227	148	171	8.7091
##dddd!!cccmmmmcccdddd2	chr5:137501426-137501650(+)$1	224	83	106	8.6146
bb!!gggggggmmmmgggggggb	chr14:24877626-24877851(+)$1	225	172	195	8.1082
ff"""bbddddmmmmdddd4444	chr2:121735910-121736133(-)$1	223	28	51	10.9395
ffff"""ddddllldddd22fff	chr18:71740789-71741017(+)$1	228	152	175	8.5828
ee!!a[eeeeemmmmeeeeea22	chr7:4822855-4823078(-)$1	223	157	180	9.1689
hhddddeeeeemmmmeeeee444	chr11:72300731-72300952(+)$1	221	185	208	8.4582
f[dddd[a!!ammmma22a]ddd	chr17:73819455-73819678(-)$1	223	71	94	8.2663
ee!!ccc[ddddllldddd]ccc	chr7:107706086-107706308(-)$1	222	62	85	9.6965
======eeeeemmmmeeeee]==	chr10:91484714-91484939(-)$1	225	194	217	9.3654
cceeeeeddddmmmmdddd]eee	chr1:201187649-201187877(+)$1	228	28	51	11.1746
ccc####ddddmmmmdddd4444	chr9:37746613-37746836(+)$1	223	156	179	11.7621
eeeeeddddoooooodddd]eee	chr19:15539155-15539377(+)$1	222	98	121	8.6833
ddddddd[ddddllldddd22dd	chr4:85504504-85504726(-)$1	222	17	40	8.5070
ccccca[ddddmmmmdddd]a]c	chr22:42273844-42274069(+)$1	225	107	130	11.6058
ffff[ddddoooooodddd]fff	chr3:69072300-69072530(+)$1	230	174	197	8.1465
eee"""eeeeemmmmeeeeeeee	chr1:165859407-165859628(-)$1	221	43	66	9.4210
eeeeee[ddddmmmmdddd22ee	chr12:80648791-80649015(-)$1	224	5	28	11.3214
da!!ccc[ddddllldddd]ccc	chr22:29168909-29169134(+)$1	225	78	101	9.5477
ffffff[ddddmmmmdddd]fff	chr7:102109191-102109413(-)$1	222	149	172	10.6860
""eeeee[ddddllldddd]eee	chr12:102091540-102091776(+)$1	236	142	165	9.2792
ccc[gggggggmmmmggggggg]	chr19:4891273-4891495(+)$1	222	116	139	8.5382
ffffff[ddddmmmmddddffff	chr1:241798298-241798522(+)$1	224	16	39	10.0780
eee!!ccc[bbmmmmbbccc]ee	chr1:186120371-186120592(-)$1	221	18	41	8.1628
eeeee!!ddddmmmmddddeeee	chr1:150266662-150266890(+)$1	228	85	108	11.2267
bb[a[ddddoooooodddd]a]b	chr8:126114535-126114760(+)$1	225	91	114	8.3317
""iiiiiiiiimmmmiiiiiiii	chrX:38031178-38031400(-)$1	222	8	31	8.7091
:eeeee[ddddmmmmdddd]eee	chr11:67262447-67262668(+)$1	221	1	24	10.5938
cc"""ccc[bbmmmmbbccc333	chr18:3188818-3189061(+)$1	243	47	70	8.3289
!dddd!!ddddmmmmdddd22dd	chr15:66021348-66021571(+)$1	223	8	31	11.1718
bbggggggg[ammmma]gggggg	chr3:49743002-49743223(-)$1	221	161	184	8.0096
bb$$$$$ddddmmmmdddd333b	chr19:18547541-18547765(+)$1	224	49	72	10.4145

#otherMatches

#Seq PSSM
CGCACGCGGUGGAUGCGCUGGUG	chr7:149129466-149129688(+)$1	222	100	123	8.5492
CUGCCUUCCACCUCCUGGAUGUG	chr1:151774152-151774379(-)$1	227	169	192	8.3294
GCCUCAGGUCCUCCUGGUCUGGG	chr3:15497278-15497502(+)$1	224	94	117	8.3819
CAGGUUCGGAAUUCCCUUUCCCA	chr8:61735072-61735296(-)$1	224	79	102	8.4530
CUGAGAGCGGGCUGGAGCCGGAG	chr12:56651526-56651754(+)$1	228	189	212	7.8755
UAGAUCUGCGUGCGGCACGAAGA	chr3:52552437-52552658(-)$1	221	47	70	9.2080
GCAUUUCGGAAAUCCUUCCAUCC	chr10:97116664-97116888(-)$1	224	152	175	9.7661
CUGGGCGGGCUGCGGGGUCCAUU	chr19:17837840-17838061(-)$1	221	114	137	9.0626
GAACGUAUCGAUGCUUGAGAGUU	chr2:202526084-202526312(+)$1	228	115	138	9.2988
CACCGUCAUGGACUGCCGUCGGG	chr22:23615833-23616054(-)$1	221	105	128	11.4774
CGCUGCGCUCUCUCUGGAGCUCG	chr15:73075892-73076119(-)$1	227	178	201	9.4171
AUAUGUUUGUGAUGUUCAUGAAA	chr20:46256353-46256576(+)$1	223	152	175	8.9666
GUCACGGCACCGCUGGAGUGCUC	chr8:145675760-145675981(-)$1	221	7	30	8.9704
UCUGAGGAUGAUUCAUUGUGCUC	chr16:24801242-24801463(-)$1	221	23	46	11.2443
UUGUGCAGGGAGACGUCCCCGCC	chr6:3259209-3259430(-)$1	221	127	150	10.4851
AGGACGAUUCAGUGAUGAAAGCC	chr22:29456306-29456528(-)$1	222	16	39	10.0649
UUCACUCCCCACCUCUGGCCUAG	chr19:9067728-9067953(-)$1	225	133	156	9.6961
UAAAAGUUCAUAAAGAUGACUCU	chr4:154523616-154523842(+)$1	226	43	66	10.5466
AGCACUUGGACGCGGGUCCCGGG	chr9:139738905-139739128(-)$1	223	174	197	10.7597
ACUUAGAGGCCAGCUGGUCUUUA	chr5:135390267-135390488(-)$1	221	6	29	8.8156
UGACCUCGUGGACAGCCACGGAG	chr16:86565581-86565804(-)$1	223	185	208	11.4949
GACAAAGGCAAGUCCUUGUUUUC	chr5:140562098-140562319(+)$1	221	64	87	11.7267
UGUCAAAUUAUUAUUAGAUCGUU	chrX:128599771-128599995(-)$1	224	188	211	7.8367
GCUGGAAAACCCAAAGUGUUUUU	chr2:202149716-202149940(+)$1	224	64	87	8.3933
AGCACUCGGAGGCACUCCUAUGC	chr11:113845916-113846141(+)$1	225	94	117	9.2988
GCUAUUUCUACAAAAGUUAUGAA	chr1:91980282-91980507(+)$1	225	153	176	8.0202
CCCACCUGCUGAAGCCAGGAGGG	chr17:76142821-76143044(-)$1	223	153	176	8.3879
GUGCUACGGCCGCGGGCCCUGGU	chr1:24432436-24432658(-)$1	222	132	155	8.4504
UUGUGUUAACUUGAAAGUUAGUG	chr16:24801586-24801813(-)$1	227	148	171	8.7091
UAGUUACCUUGUCCUCAAUGAUG	chr5:137501426-137501650(+)$1	224	83	106	8.6146
GUAAUAGUUUGGGACCAAACUGG	chr14:24877626-24877851(+)$1	225	172	195	8.1082
GUACUGCGCCUUGAAGGGCUUCU	chr2:121735910-121736133(-)$1	223	28	51	10.9395
AGUUACGUCCAUCAUGGAACAAC	chr18:71740789-71741017(+)$1	228	152	175	8.5828
GGGGUACUGGCCUGUGCCAGAGA	chr7:4822855-4823078(-)$1	223	157	180	9.1689
CCGCCCCCGCUCUACAGUGGACC	chr11:72300731-72300952(+)$1	221	185	208	8.4582
UGACCUUGUCCACUUGUUCCAGG	chr17:73819455-73819678(-)$1	223	71	94	8.2663
AGCUCAGAUGUAAUCUGCAAUUG	chr7:107706086-107706308(-)$1	222	62	85	9.6965
CAGAAAACGAACUACUUUGUGUU	chr10:91484714-91484939(-)$1	225	194	217	9.3654
GACGUGCGGCAGGGCUGUCAGUA	chr1:201187649-201187877(+)$1	228	28	51	11.1746
GGUCAACGGCCCAAGGGCCUCCU	chr9:37746613-37746836(+)$1	223	156	179	11.7621
UGCGGGUCUCAAACCAGGCACCG	chr19:15539155-15539377(+)$1	222	98	121	8.6833
GCCAGGGCGCGGCGUCCGCCUCU	chr4:85504504-85504726(-)$1	222	17	40	8.5070
GGGGCUGGUUUGACUGGAUGAUG	chr22:42273844-42274069(+)$1	225	107	130	11.6058
AAAAAUGUAUUUGUUUACAAUUU	chr3:69072300-69072530(+)$1	230	174	197	8.1465
UGAACUGGCCCUUCAGGGCUUUG	chr1:165859407-165859628(-)$1	221	43	66	9.4210
AAUCAGUGAAUCCAUAUUCCUCU	chr12:80648791-80649015(-)$1	224	5	28	11.3214
CCUAGCAGUCCCGCUGGGAGUGC	chr22:29168909-29169134(+)$1	225	78	101	9.5477
GCUAUUGGUGUGAACACGCGGGU	chr7:102109191-102109413(-)$1	222	149	172	10.6860
GGGCGCUGAGCGAGCCGCUGAGC	chr12:102091540-102091776(+)$1	236	142	165	9.2792
CGUACUGUAUGUGGGCAUACAGG	chr19:4891273-4891495(+)$1	222	116	139	8.5382
CUGAUUUGAUUAAAAGAUCAAUU	chr1:241798298-241798522(+)$1	224	16	39	10.0780
GUUAGUAGUAGCAUUCUCUAGAA	chr1:186120371-186120592(-)$1	221	18	41	8.1628
CCUUUAGGCUCUACAGAGUGAAG	chr1:150266662-150266890(+)$1	228	85	108	11.2267
GGUGUAGAGUCUGCUCUCUCCUC	chr8:126114535-126114760(+)$1	225	91	114	8.3317
CUUUCAGAGUUUCUAGACUCUGA	chrX:38031178-38031400(-)$1	222	8	31	8.7091
GCCUCUGUCUCUUAGGGGAGGGA	chr11:67262447-67262668(+)$1	221	1	24	10.5938
GGAUGCCGUGGACUGCCUGGAUG	chr18:3188818-3189061(+)$1	243	47	70	8.3289
CAUAUGCUACAAAGUUGUAAAAU	chr15:66021348-66021571(+)$1	223	8	31	11.1718
CCAGGACUUCCAGCAGCGAGUUC	chr3:49743002-49743223(-)$1	221	161	184	8.0096
GCCUCCAUGUGCGGCCACAGUUG	chr19:18547541-18547765(+)$1	224	49	72	10.4145

#DB
(((((.(((((....))))))))	chr7:149129466-149129688(+)$1	1	100	123	8.5492
(((((.((((.....))))...)	chr1:151774152-151774379(-)$1	1	169	192	8.3294
(((.((((.((....))))))))	chr3:15497278-15497502(+)$1	1	94	117	8.3819
(((.(..((((......)))).)	chr8:61735072-61735296(-)$1	1	79	102	8.4530
(((....(.(((....))).)..	chr12:56651526-56651754(+)$1	1	189	212	7.8755
(..((((.((((...)))).)))	chr3:52552437-52552658(-)$1	1	47	70	9.2080
(..(((.((((....))))....	chr10:97116664-97116888(-)$1	1	152	175	9.7661
(.(((.(((((....))))).))	chr19:17837840-17838061(-)$1	1	114	137	9.0626
((((...((((...))))..)))	chr2:202526084-202526312(+)$1	1	115	138	9.2988
((((.(.((((....)))).).)	chr22:23615833-23616054(-)$1	1	105	128	11.4774
((....(((((....))))).))	chr15:73075892-73076119(-)$1	1	178	201	9.4171
((.(((((((((...)))).)))	chr20:46256353-46256576(+)$1	1	152	175	8.9666
(....((((((....).))))).	chr8:145675760-145675981(-)$1	1	7	30	8.9704
..((((.((((....)))).)))	chr16:24801242-24801463(-)$1	1	23	46	11.2443
(((.((.((((....)))).)))	chr6:3259209-3259430(-)$1	1	127	150	10.4851
.((.(..((((....)))).)))	chr22:29456306-29456528(-)$1	1	16	39	10.0649
((((((..(((....)))...))	chr19:9067728-9067953(-)$1	1	133	156	9.6961
((((((.((((....))))..))	chr4:154523616-154523842(+)$1	1	43	66	10.5466
(.(.((.((((....)))).)))	chr9:139738905-139739128(-)$1	1	174	197	10.7597
(.(((((((((....))))))))	chr5:135390267-135390488(-)$1	1	6	29	8.8156
(((.(((((((....)))).)))	chr16:86565581-86565804(-)$1	1	185	208	11.4949
(((((((((((....))))...)	chr5:140562098-140562319(+)$1	1	64	87	11.7267
..(.((((.(((....))).)))	chrX:128599771-128599995(-)$1	1	188	211	7.8367
(((((((((((....).))))))	chr2:202149716-202149940(+)$1	1	64	87	8.3933
((((...((((...))))..)))	chr11:113845916-113846141(+)$1	1	94	117	9.2988
(((((((..((....))...)))	chr1:91980282-91980507(+)$1	1	153	176	8.0202
((..(((.(((....))).))).	chr17:76142821-76143044(-)$1	1	153	176	8.3879
(.((((.((((...)))).))))	chr1:24432436-24432658(-)$1	1	132	155	8.4504
..(((((((((....))))))))	chr16:24801586-24801813(-)$1	1	148	171	8.7091
..((((..(((....))))))).	chr5:137501426-137501650(+)$1	1	83	106	8.6146
((..(((((((....))))))))	chr14:24877626-24877851(+)$1	1	172	195	8.1082
((...((((((....))))....	chr2:121735910-121736133(-)$1	1	28	51	10.9395
((((...((((...))))..)))	chr18:71740789-71741017(+)$1	1	152	175	8.5828
((..(.(((((....))))))..	chr7:4822855-4823078(-)$1	1	157	180	9.1689
))(((((((((....)))))...	chr11:72300731-72300952(+)$1	1	185	208	8.4582
(.((((.(..(....)..).)))	chr17:73819455-73819678(-)$1	1	71	94	8.2663
((..(((.((((...)))).)))	chr7:107706086-107706308(-)$1	1	62	85	9.6965
(((((((((((....))))).))	chr10:91484714-91484939(-)$1	1	194	217	9.3654
(((((((((((....)))).)))	chr1:201187649-201187877(+)$1	1	28	51	11.1746
(((....((((....))))....	chr9:37746613-37746836(+)$1	1	156	179	11.7621
(((((((((......)))).)))	chr19:15539155-15539377(+)$1	1	98	121	8.6833
(((((((.((((...))))..))	chr4:85504504-85504726(-)$1	1	17	40	8.5070
))((((.((((....)))).).)	chr22:42273844-42274069(+)$1	1	107	130	11.6058
((((.((((......)))).)))	chr3:69072300-69072530(+)$1	1	174	197	8.1465
(((...(((((....))))))))	chr1:165859407-165859628(-)$1	1	43	66	9.4210
((((((.((((....))))..))	chr12:80648791-80649015(-)$1	1	5	28	11.3214
((..(((.((((...)))).)))	chr22:29168909-29169134(+)$1	1	78	101	9.5477
((((((.((((....)))).)))	chr7:102109191-102109413(-)$1	1	149	172	10.6860
..(((((.((((...)))).)))	chr12:102091540-102091776(+)$1	1	142	165	9.2792
(((.(((((((....))))))).	chr19:4891273-4891495(+)$1	1	116	139	8.5382
((((((.((((....))))))))	chr1:241798298-241798522(+)$1	1	16	39	10.0780
(((..(((.((....))))).))	chr1:186120371-186120592(-)$1	1	18	41	8.1628
(((((..((((....))))))))	chr1:150266662-150266890(+)$1	1	85	108	11.2267
((.(.((((......)))).).)	chr8:126114535-126114760(+)$1	1	91	114	8.3317
..(((((((((....))))))))	chrX:38031178-38031400(-)$1	1	8	31	8.7091
.(((((.((((....)))).)))	chr11:67262447-67262668(+)$1	1	1	24	10.5938
((...(((.((....)))))...	chr18:3188818-3189061(+)$1	1	47	70	8.3289
.((((..((((....))))..))	chr15:66021348-66021571(+)$1	1	8	31	11.1718
(((((((((.(....).))))))	chr3:49743002-49743223(-)$1	1	161	184	8.0096
((.....((((....))))...)	chr19:18547541-18547765(+)$1	1	49	72	10.4145

#PSSM
e : 0.24	c : 0.16	f : 0.15	d : 0.08	b : 0.08	" : 0.06	h : 0.03	: : 0.03	g : 0.03	! : 0.03	i : 0.01	a : 0.01	# : 0.01	= : 0.01	
e : 0.24	d : 0.09	b : 0.09	f : 0.09	c : 0.09	[ : 0.08	" : 0.06	! : 0.05	h : 0.03	# : 0.03	g : 0.03	i : 0.01	= : 0.01	a : 0.01	
e : 0.23	d : 0.18	! : 0.11	c : 0.08	f : 0.08	i : 0.06	g : 0.05	# : 0.03	[ : 0.03	a : 0.03	" : 0.03	b : 0.01	= : 0.01	$ : 0.01	
d : 0.16	e : 0.16	[ : 0.13	! : 0.09	f : 0.08	# : 0.06	g : 0.06	i : 0.06	c : 0.05	" : 0.05	= : 0.01	a : 0.01	$ : 0.01	
d : 0.18	e : 0.13	c : 0.11	" : 0.09	g : 0.09	# : 0.06	i : 0.06	a : 0.05	[ : 0.05	f : 0.05	b : 0.03	= : 0.01	! : 0.01	$ : 0.01	
d : 0.19	c : 0.11	e : 0.09	g : 0.09	[ : 0.06	! : 0.06	" : 0.06	i : 0.06	# : 0.05	b : 0.05	f : 0.05	a : 0.03	= : 0.01	$ : 0.01	
[ : 0.21	e : 0.18	d : 0.13	! : 0.09	c : 0.09	g : 0.08	i : 0.06	" : 0.05	# : 0.03	b : 0.01	$ : 0.01	
d : 0.51	e : 0.15	[ : 0.09	g : 0.06	! : 0.05	i : 0.05	a : 0.03	c : 0.03	
d : 0.58	e : 0.13	[ : 0.08	g : 0.06	c : 0.05	i : 0.05	! : 0.03	
d : 0.53	e : 0.13	c : 0.08	b : 0.06	i : 0.05	g : 0.05	o : 0.05	! : 0.01	[ : 0.01	
d : 0.51	e : 0.11	c : 0.08	b : 0.06	a : 0.06	i : 0.05	o : 0.05	g : 0.03	n : 0.01	
m : 0.71	d : 0.09	o : 0.06	l : 0.06	c : 0.03	n : 0.01	
m : 0.75	l : 0.16	o : 0.06	n : 0.01	
m : 0.75	l : 0.16	o : 0.06	n : 0.01	
m : 0.75	l : 0.09	o : 0.06	d : 0.06	n : 0.01	
d : 0.56	e : 0.11	b : 0.06	a : 0.06	c : 0.05	i : 0.05	m : 0.03	g : 0.03	o : 0.01	
d : 0.56	e : 0.11	c : 0.08	b : 0.06	] : 0.05	i : 0.05	g : 0.03	o : 0.01	2 : 0.01	
d : 0.60	e : 0.13	c : 0.11	g : 0.06	i : 0.05	3 : 0.01	2 : 0.01	
d : 0.55	e : 0.13	c : 0.06	g : 0.06	2 : 0.05	i : 0.05	3 : 0.03	] : 0.03	a : 0.01	
] : 0.35	e : 0.15	2 : 0.11	3 : 0.08	d : 0.06	g : 0.06	i : 0.05	c : 0.05	4 : 0.03	0 : 0.01	f : 0.01	
e : 0.16	d : 0.15	a : 0.09	3 : 0.08	g : 0.08	] : 0.06	2 : 0.06	c : 0.06	f : 0.06	i : 0.05	4 : 0.05	b : 0.03	0 : 0.01	
e : 0.23	d : 0.15	g : 0.09	c : 0.08	f : 0.08	3 : 0.06	] : 0.06	b : 0.05	i : 0.05	4 : 0.05	2 : 0.03	0 : 0.01	= : 0.01	
e : 0.23	d : 0.16	c : 0.08	f : 0.08	2 : 0.06	4 : 0.06	b : 0.06	g : 0.06	i : 0.06	a : 0.03	0 : 0.01	= : 0.01	] : 0.01	3 : 0.01	

#score	566.5895061141533
#seq	60
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m1_run1.txt

#BEAR
=bb[dddduuuuuuuuuuuudddd]bb]===	chr12:49666292-49666552(+)$1	260	202	233	23.2668
ccc[cccvvvvvvvvvvvvvccc333cccgg	chr22:36687931-36688164(-)$1	233	162	193	24.3097
ddbb[bbvvvvvvvvvvvvvbbbb]dddd22	chr1:155720387-155720645(+)$1	258	58	89	21.2227
%%%ccccccuuuuuuuuuuuuccc]cccbb2	chr22:43231278-43231521(-)$1	243	97	128	22.8987
eeee[ddddtttttttttttdddd]eeeee]	chr1:39463863-39464083(+)$1	220	149	180	24.0569
cccccc[bbtttttttttttbb]ccc]ccc=	chr15:75194939-75195181(-)$1	242	32	63	23.8993
iii"""cccssssssssssccc]iiiiiiii	chr17:45773416-45773653(+)$1	237	163	194	18.5478
gggggg[cccssssssssssccc]ggggggg	chr1:145317320-145317557(+)$1	237	200	231	18.3113
bb"""cccvvvvvvvvvvvvvccc333bb::	chrX:51487137-51487379(+)$1	242	33	64	22.7486
hh"""ddddtttttttttttdddd]hhhhhh	chr9:139758180-139758411(-)$1	231	127	158	23.5917
c!!fffffftttttttttttffffff22ccc	chr21:34954388-34954630(-)$1	242	159	190	23.3412
ggg[a[ccctttttttttttccc]a]ggggg	chr15:83101205-83101453(+)$1	248	50	81	25.5470
eeeee[bbwwwwwwwwwwwwwwbb]eeeeeb	chr1:45101599-45101855(+)$1	256	179	210	22.8760
eeee[cccuuuuuuuuuuuuccceeeee333	chr8:56702733-56702955(+)$1	222	119	150	24.7019
cc[ffffffuuuuuuuuuuuuffffff]ccc	chr19:14521700-14521942(-)$1	242	73	104	23.7770
gggggggvvvvvvvvvvvvvgggggggeeee	chr1:214813984-214814262(+)$1	278	166	197	23.2112
cc[eeeeewwwwwwwwwwwwwweeeee]ccc	chr19:41800362-41800584(+)$1	222	77	108	23.6746
dddd[ddddtttttttttttdddd]dddddd	chr10:131964790-131965034(+)$1	244	63	94	22.8141
gggg!!cccssssssssssccc22ggggggg	chr19:40477011-40477243(+)$1	232	190	221	18.1398
ddd!!ddddtttttttttttdddd]dddd]c	chr19:12157405-12157635(-)$1	230	63	94	23.7579
"""ccccccwwwwwwwwwwwwwwccc]ccc3	chr5:176943020-176943294(-)$1	274	181	212	23.7366
d!!ffffffuuuuuuuuuuuuffffff333d	chr5:80604663-80604916(+)$1	253	66	97	23.7593
hhhhhhhbbtttttttttttbb]hhhhhhhh	chr10:135211870-135212113(+)$1	243	110	141	21.7119
gg[eeeeewwwwwwwwwwwwwweeeeegggg	chr7:6840572-6840806(-)$1	234	191	222	23.8247
=========ttttttttttt===========	chr10:51188164-51188369(+)$1	205	94	125	25.2679
c"""eeeeeuuuuuuuuuuuueeeee]ccc]	chr9:33166817-33167060(-)$1	243	153	184	24.7529
eee!!ddddtttttttttttdddd4444eee	chr9:131469074-131469299(+)$1	225	54	85	23.7772
ccc!!cccuuuuuuuuuuuuccc22ccc:::	chr1:19419706-19419911(-)$1	205	62	93	22.4589
[a[a!!abbtttttttttttbb]a22a]a]h	chr12:108954743-108954982(-)$1	239	149	180	24.2690
"eeeeebbwwwwwwwwwwwwwwbb]eeeee5	chr15:68987489-68987695(+)$1	206	141	172	22.3662
####eeeeeyyyyyyyyyyyyyyyyeeeee4	chr2:26357730-26358004(+)$1	274	223	254	21.6606
eee"""ccctttttttttttccc333eeeee	chr1:109813918-109814170(+)$1	252	188	219	25.2460
ggccc[ccctttttttttttccc]ccc]ggg	chr19:49376855-49377097(+)$1	242	135	166	25.1429
fffff!!bbuuuuuuuuuuuubb22ffffff	chr3:51429679-51429927(+)$1	248	217	248	23.0077
bb[ccc[bbtttttttttttbb]cccbb22c	chr10:75005579-75005805(-)$1	226	34	65	22.6275
ee[eeeeeyyyyyyyyyyyyyyyyeeeee]e	chr11:63581115-63581373(+)$1	258	30	61	21.9631
gggggg[cccssssssssssccc]ggggggg	chr1:148270117-148270354(-)$1	237	200	231	18.3113
gggggg[bbvvvvvvvvvvvvvbb]gggggg	chr1:146037338-146037604(-)$1	266	204	235	24.4840
dddd!!bbvvvvvvvvvvvvvbb22dddd::	chr1:186304410-186304646(-)$1	236	0	31	21.3362
gggggggxxxxxxxxxxxxxxxgggggggFF	chr10:126089421-126089653(-)$1	232	37	68	17.9921
::gggggggvvvvvvvvvvvvvggggggg::	chr12:39725915-39726147(-)$1	232	110	141	20.7538
ee!!dddduuuuuuuuuuuuddddeeeee]c	chr16:56643106-56643336(+)$1	230	86	117	24.0176
eeeeeeeeeuuuuuuuuuuuueeeeeeeeee	chr5:6754931-6755178(+)$1	247	107	138	23.5232
ggg[a[ccctttttttttttccc]a]ggggg	chr15:84906987-84907235(+)$1	248	50	81	25.5470
[ccc!!bbwwwwwwwwwwwwwwbb]cccbb]	chr16:56484959-56485214(-)$1	255	155	186	23.3001
iiiiiiiiivvvvvvvvvvvvviiiiiiiii	chr2:28248143-28248379(+)$1	236	96	127	24.6452
ccc"""ccctttttttttttccc22ccc333	chrX:48972031-48972249(-)$1	218	77	108	25.5834
=========vvvvvvvvvvvvv=========	chr20:57561048-57561290(+)$1	242	46	77	25.1545
[gggggggwwwwwwwwwwwwwwggggggg]b	chr2:122122619-122122873(-)$1	254	147	178	23.9199
####eeeeettttttttttteeeee4444bb	chr11:46839840-46840098(-)$1	258	82	113	23.3560
d"""eeeeevvvvvvvvvvvvveeeee4444	chr19:39396009-39396269(+)$1	260	52	83	24.1706
bb!!dddduuuuuuuuuuuudddd]bbccc]	chr15:30431164-30431399(+)$1	235	183	214	23.4846
cc!!eeeeeyyyyyyyyyyyyyyyyeeeee3	chr12:54404928-54405160(+)$1	232	92	123	21.9806
g!!a[cccvvvvvvvvvvvvvccc]a22ggg	chr5:133493307-133493559(-)$1	252	96	127	25.3105
c$$$$$cccvvvvvvvvvvvvvcccccc]gg	chr19:18702825-18703059(+)$1	234	69	100	24.0347
c!!fffffftttttttttttffffff22ccc	chr1:150082534-150082767(+)$1	233	104	135	23.3412
d!!eeeeebbuuuuuuuuuuuubb]eeeee4	chr2:159477789-159478023(+)$1	234	76	107	22.8529

#otherMatches

#Seq PSSM
GAGAAAGCCUACCACGAACAGCUUACUGUAG	chr12:49666292-49666552(+)$1	260	202	233	23.2668
UUUCCUCUCCUUCAAGCACUGAGUCCAAAGC	chr22:36687931-36688164(-)$1	233	162	193	24.3097
UUGCAUCAUCCUCAUCCUCAGAGCUGGCUUC	chr1:155720387-155720645(+)$1	258	58	89	21.2227
UAUAGGGAGAAAAUCAAAUCGCUCGCCUCUC	chr22:43231278-43231521(-)$1	243	97	128	22.8987
AUUAAGAGUUUGUAAAUGGUACUUAUAAUGA	chr1:39463863-39464083(+)$1	220	149	180	24.0569
UUCCCUCCUCUCCUUCUCUUAGCAGGUGAAC	chr15:75194939-75195181(-)$1	242	32	63	23.8993
CGACAUGUGCUCCGCCUCCCACUUUGCCCUC	chr17:45773416-45773653(+)$1	237	163	194	18.5478
AAAACAAGAGUGUGUUCAAUUUCAUGUUUUC	chr1:145317320-145317557(+)$1	237	200	231	18.3113
GGGAGCACAGUAAAGAAGUAAGUGAAGCCGA	chrX:51487137-51487379(+)$1	242	33	64	22.7486
ACUUCCAAGAAAUGUAGGUACUUGUGUUUCC	chr9:139758180-139758411(-)$1	231	127	158	23.5917
AGUAUGUGAUUAAAAUAACUUUAUAUCAUCC	chr21:34954388-34954630(-)$1	242	159	190	23.3412
GGGGGGACAGAACAUCUCCAUGUGCACUCUC	chr15:83101205-83101453(+)$1	248	50	81	25.5470
GUGGUGUGGACAGAAGCGGAUACGGGCCACC	chr1:45101599-45101855(+)$1	256	179	210	22.8760
GAGGAGGUAAGUUACAUGAGACCCCUCUCAC	chr8:56702733-56702955(+)$1	222	119	150	24.7019
GGAGCUUCAGCCUAAAGAAUGUGAAGCACUU	chr19:14521700-14521942(-)$1	242	73	104	23.7770
AAUUCUGCCAUCCUACAAAAUAGAGUUGAUU	chr1:214813984-214814262(+)$1	278	166	197	23.2112
CCCUCACCAAUUCCUGCCCGCAGGUGAUGGG	chr19:41800362-41800584(+)$1	222	77	108	23.6746
CGACAGGGACUCAAAGCCUAUUCCAGUUGGC	chr10:131964790-131965034(+)$1	244	63	94	22.8141
GCCAGACCUGAGUGGGGGGAGGAAUGGCUUC	chr19:40477011-40477243(+)$1	232	190	221	18.1398
UCGGUGGCCUUUGAGGAUGUGGCUGUGAACU	chr19:12157405-12157635(-)$1	230	63	94	23.7579
UUGUAGCCAGGAUAGUGAGAAGGUGGACUGA	chr5:176943020-176943294(-)$1	274	181	212	23.7366
AUUGUCAACUGAAUAGGAACUGUUGAUUUUU	chr5:80604663-80604916(+)$1	253	66	97	23.7593
AUUUUUACCAACUGUGUAAAGGAUGAAAAUG	chr10:135211870-135212113(+)$1	243	110	141	21.7119
UUGAAUCAAAAAAAUGCAAACCUGAUUGAAG	chr7:6840572-6840806(-)$1	234	191	222	23.8247
UCCACGGGCACUGGAUCUCAGUCCGUGGAGA	chr10:51188164-51188369(+)$1	205	94	125	25.2679
UCUAGGCGCCUCCUCCCAGCCGCGCCCGGGU	chr9:33166817-33167060(-)$1	243	153	184	24.7529
CGGAGCAGGGAAGAGCAGGGCCUGAGAGCCG	chr9:131469074-131469299(+)$1	225	54	85	23.7772
AUGCACUUGACUACAUGAAAAAGCACAUCCC	chr1:19419706-19419911(-)$1	205	62	93	22.4589
GGACAAGGAGGAAGGUGUUAUCGCGGGCUGU	chr12:108954743-108954982(-)$1	239	149	180	24.2690
CAGGCCCCUCCCUGCUUCCUUUGGAGGCCUC	chr15:68987489-68987695(+)$1	206	141	172	22.3662
CCACUCUGUCCAUUUUUAACUCUAAACAGAU	chr2:26357730-26358004(+)$1	274	223	254	21.6606
CCUCUUUGCUACCUGCAAUUGCAUCCAGGUA	chr1:109813918-109814170(+)$1	252	188	219	25.2460
AGUUGCUGAAGAGGAGGGAGUUAACAAGUUC	chr19:49376855-49377097(+)$1	242	135	166	25.1429
CCUUCGAGAAAUAUGGCAUCAUCGAGGAGGU	chr3:51429679-51429927(+)$1	248	217	248	23.0077
UCAUUCAGCAAGCUAUUGACGCCGGAGAGGU	chr10:75005579-75005805(-)$1	226	34	65	22.6275
CCACGGCCGCACCAUGGCCCUAAAGGCCGAG	chr11:63581115-63581373(+)$1	258	30	61	21.9631
AAAACAAGAGUGUGUUCAAUUUCAUGUUUUC	chr1:148270117-148270354(-)$1	237	200	231	18.3113
AGGGGUGAUAUUCCUGUUCCAAGUGGCCCUU	chr1:146037338-146037604(-)$1	266	204	235	24.4840
GAGGAGCUUAAACAAAGGAAUGGAGCCUUAG	chr1:186304410-186304646(-)$1	236	0	31	21.3362
UUGUCCUCCAAAAAACAAAAAAAGGACAGUC	chr10:126089421-126089653(-)$1	232	37	68	17.9921
AAUGCAGAUGGAAGAAGCAAAGGUUUGUAAU	chr12:39725915-39726147(-)$1	232	110	141	20.7538
CUGUGGGCUGUGCCAAGUGUGCCCAGGGCUG	chr16:56643106-56643336(+)$1	230	86	117	24.0176
CCGUGAGCCUCAGCAGAUAAUGGCUCCUGGC	chr5:6754931-6755178(+)$1	247	107	138	23.5232
GGGGGGACAGAACAUCUCCAUGUGCACUCUC	chr15:84906987-84907235(+)$1	248	50	81	25.5470
AGUUCGGCAACAAGUACAUCCAGCAGACGAA	chr16:56484959-56485214(-)$1	255	155	186	23.3001
CAGUAUGGAGAGAACAUGGAAAUUUAUGCUG	chr2:28248143-28248379(+)$1	236	96	127	24.6452
AUCCCCCUGACCUGUAUCCCCAGAUGAUAAU	chrX:48972031-48972249(-)$1	218	77	108	25.5834
aGGGUAUUUGUAUUAAUGAAAAAAAUAUCCU	chr20:57561048-57561290(+)$1	242	46	77	25.1545
GAGGAGCACUUCAAGACCAUUCUGCUCCUGC	chr2:122122619-122122873(-)$1	254	147	178	23.9199
GAAGAUCUUCCAGAAAAUAAAGGAUGAAAAG	chr11:46839840-46840098(-)$1	258	82	113	23.3560
CUCCCGACACCAACCAUACCCCUGUCGCCUU	chr19:39396009-39396269(+)$1	260	52	83	24.1706
ACUCAGACAUACAGGCCCCAGUCUCGUCUCA	chr15:30431164-30431399(+)$1	235	183	214	23.4846
CUGGUUCCAGAACCGAAGGAUGAAGUGGAAA	chr12:54404928-54405160(+)$1	232	92	123	21.9806
UUAGGUACGCAAAGAGAACCAGUGGUGUGAA	chr5:133493307-133493559(-)$1	252	96	127	25.3105
AUAGUUCCCAUCCGCUCUUGUAGGGUAAUUA	chr19:18702825-18703059(+)$1	234	69	100	24.0347
GGAGGAGCCACCUAUGAAGAGGCUCUAACAG	chr1:150082534-150082767(+)$1	233	104	135	23.3412
CAUUCAUAGGAUCAACUAACAACCAUGUGGU	chr2:159477789-159478023(+)$1	234	76	107	22.8529

#DB
(((.((((............)))).)).)))	chr12:49666292-49666552(+)$1	1	202	233	23.2668
(((.(((.............)))...)))))	chr22:36687931-36688164(-)$1	1	162	193	24.3097
((((.((.............)))).))))..	chr1:155720387-155720645(+)$1	1	58	89	21.2227
...((((((............))).))))).	chr22:43231278-43231521(-)$1	1	97	128	22.8987
((((.((((...........)))).))))).	chr1:39463863-39464083(+)$1	1	149	180	24.0569
((((((.((...........)).))).))))	chr15:75194939-75195181(-)$1	1	32	63	23.8993
(((...(((..........))).))))))))	chr17:45773416-45773653(+)$1	1	163	194	18.5478
((((((.(((..........))).)))))))	chr1:145317320-145317557(+)$1	1	200	231	18.3113
((...(((.............)))...))..	chrX:51487137-51487379(+)$1	1	33	64	22.7486
((...((((...........)))).))))))	chr9:139758180-139758411(-)$1	1	127	158	23.5917
(..((((((...........))))))..)))	chr21:34954388-34954630(-)$1	1	159	190	23.3412
(((.(.(((...........))).).)))))	chr15:83101205-83101453(+)$1	1	50	81	25.5470
(((((.((..............)).))))))	chr1:45101599-45101855(+)$1	1	179	210	22.8760
((((.(((............))))))))...	chr8:56702733-56702955(+)$1	1	119	150	24.7019
((.((((((............)))))).)))	chr19:14521700-14521942(-)$1	1	73	104	23.7770
(((((((.............)))))))((((	chr1:214813984-214814262(+)$1	1	166	197	23.2112
((.(((((..............))))).)))	chr19:41800362-41800584(+)$1	1	77	108	23.6746
((((.((((...........)))).))))))	chr10:131964790-131965034(+)$1	1	63	94	22.8141
((((..(((..........)))..)))))))	chr19:40477011-40477243(+)$1	1	190	221	18.1398
(((..((((...........)))).)))).)	chr19:12157405-12157635(-)$1	1	63	94	23.7579
...((((((..............))).))).	chr5:176943020-176943294(-)$1	1	181	212	23.7366
(..((((((............))))))...)	chr5:80604663-80604916(+)$1	1	66	97	23.7593
(((((((((...........)).))))))))	chr10:135211870-135212113(+)$1	1	110	141	21.7119
((.(((((..............)))))))))	chr7:6840572-6840806(-)$1	1	191	222	23.8247
(((((((((...........)))))))))))	chr10:51188164-51188369(+)$1	1	94	125	25.2679
(...(((((............))))).))).	chr9:33166817-33167060(-)$1	1	153	184	24.7529
(((..((((...........))))....)))	chr9:131469074-131469299(+)$1	1	54	85	23.7772
(((..(((............)))..)))...	chr1:19419706-19419911(-)$1	1	62	93	22.4589
.(.(..(((...........)).)..).).)	chr12:108954743-108954982(-)$1	1	149	180	24.2690
.(((((((..............)).))))).	chr15:68987489-68987695(+)$1	1	141	172	22.3662
....(((((................))))).	chr2:26357730-26358004(+)$1	1	223	254	21.6606
(((...(((...........)))...)))))	chr1:109813918-109814170(+)$1	1	188	219	25.2460
(((((.(((...........))).))).)))	chr19:49376855-49377097(+)$1	1	135	166	25.1429
(((((..((............))..))))))	chr3:51429679-51429927(+)$1	1	217	248	23.0077
((.(((.((...........)).)))))..)	chr10:75005579-75005805(-)$1	1	34	65	22.6275
((.(((((................))))).)	chr11:63581115-63581373(+)$1	1	30	61	21.9631
((((((.(((..........))).)))))))	chr1:148270117-148270354(-)$1	1	200	231	18.3113
((((((.((.............)).))))))	chr1:146037338-146037604(-)$1	1	204	235	24.4840
((((..((.............))..))))..	chr1:186304410-186304646(-)$1	1	0	31	21.3362
(((((((...............)))))))((	chr10:126089421-126089653(-)$1	1	37	68	17.9921
..(((((((.............)))))))..	chr12:39725915-39726147(-)$1	1	110	141	20.7538
((..((((............))))))))).)	chr16:56643106-56643336(+)$1	1	86	117	24.0176
))))(((((............)))))(((((	chr5:6754931-6755178(+)$1	1	107	138	23.5232
(((.(.(((...........))).).)))))	chr15:84906987-84907235(+)$1	1	50	81	25.5470
.(((..((..............)).))))).	chr16:56484959-56485214(-)$1	1	155	186	23.3001
(((((((((.............)))))))))	chr2:28248143-28248379(+)$1	1	96	127	24.6452
(((...(((...........)))..)))...	chrX:48972031-48972249(-)$1	1	77	108	25.5834
(((((((((.............)))))))))	chr20:57561048-57561290(+)$1	1	46	77	25.1545
.(((((((..............))))))).)	chr2:122122619-122122873(-)$1	1	147	178	23.9199
....(((((...........)))))....))	chr11:46839840-46840098(-)$1	1	82	113	23.3560
(...(((((.............)))))....	chr19:39396009-39396269(+)$1	1	52	83	24.1706
((..((((............)))).))))).	chr15:30431164-30431399(+)$1	1	183	214	23.4846
((..(((((................))))).	chr12:54404928-54405160(+)$1	1	92	123	21.9806
(..(.(((.............))).)..)))	chr5:133493307-133493559(-)$1	1	96	127	25.3105
(.....(((.............)))))).))	chr19:18702825-18703059(+)$1	1	69	100	24.0347
(..((((((...........))))))..)))	chr1:150082534-150082767(+)$1	1	104	135	23.3412
(..(((((((............)).))))).	chr2:159477789-159478023(+)$1	1	76	107	22.8529

#PSSM
c : 0.19	g : 0.19	e : 0.14	d : 0.12	= : 0.05	b : 0.05	[ : 0.05	i : 0.03	h : 0.03	" : 0.03	# : 0.03	% : 0.01	f : 0.01	: : 0.01	
g : 0.19	e : 0.15	c : 0.14	! : 0.08	b : 0.07	d : 0.07	" : 0.05	i : 0.03	h : 0.03	= : 0.03	# : 0.03	% : 0.01	a : 0.01	f : 0.01	: : 0.01	$ : 0.01	
g : 0.17	! : 0.14	e : 0.12	c : 0.10	[ : 0.10	" : 0.08	d : 0.05	b : 0.03	i : 0.03	= : 0.03	# : 0.03	% : 0.01	h : 0.01	f : 0.01	$ : 0.01	
e : 0.15	g : 0.14	" : 0.12	c : 0.10	! : 0.10	f : 0.08	[ : 0.07	d : 0.03	= : 0.03	a : 0.03	# : 0.03	b : 0.01	h : 0.01	i : 0.01	$ : 0.01	
e : 0.21	g : 0.12	! : 0.12	c : 0.10	[ : 0.08	" : 0.08	f : 0.08	d : 0.05	a : 0.03	= : 0.03	h : 0.01	i : 0.01	$ : 0.01	
e : 0.19	c : 0.15	d : 0.14	g : 0.12	! : 0.08	f : 0.07	[ : 0.07	" : 0.05	= : 0.03	b : 0.01	h : 0.01	i : 0.01	$ : 0.01	
c : 0.26	e : 0.17	d : 0.14	b : 0.08	[ : 0.08	f : 0.07	g : 0.07	= : 0.03	h : 0.01	a : 0.01	! : 0.01	i : 0.01	
c : 0.28	b : 0.17	e : 0.17	d : 0.14	f : 0.07	v : 0.05	= : 0.03	g : 0.03	x : 0.01	i : 0.01	
c : 0.21	b : 0.12	v : 0.10	w : 0.10	e : 0.10	u : 0.08	d : 0.08	f : 0.07	= : 0.03	y : 0.01	x : 0.01	g : 0.01	i : 0.01	
t : 0.31	v : 0.21	u : 0.19	w : 0.12	y : 0.05	s : 0.03	c : 0.03	x : 0.01	b : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	s : 0.07	y : 0.05	x : 0.01	
t : 0.31	u : 0.21	v : 0.21	w : 0.12	y : 0.05	c : 0.03	s : 0.03	x : 0.01	
c : 0.21	v : 0.15	d : 0.14	u : 0.12	w : 0.12	b : 0.08	y : 0.05	f : 0.03	g : 0.01	= : 0.01	x : 0.01	e : 0.01	
c : 0.26	d : 0.14	b : 0.12	w : 0.12	v : 0.10	f : 0.07	e : 0.05	y : 0.05	g : 0.01	= : 0.01	x : 0.01	u : 0.01	
c : 0.24	d : 0.14	b : 0.14	e : 0.10	] : 0.08	f : 0.07	g : 0.07	y : 0.05	= : 0.03	2 : 0.01	w : 0.01	i : 0.01	
d : 0.14	c : 0.12	e : 0.12	b : 0.10	] : 0.08	2 : 0.08	f : 0.07	g : 0.07	y : 0.05	3 : 0.03	i : 0.03	= : 0.03	h : 0.01	a : 0.01	
] : 0.24	e : 0.15	g : 0.12	c : 0.08	2 : 0.08	f : 0.07	3 : 0.05	i : 0.03	a : 0.03	= : 0.03	y : 0.03	h : 0.01	4 : 0.01	
e : 0.24	c : 0.15	g : 0.14	f : 0.08	d : 0.07	3 : 0.05	b : 0.03	i : 0.03	h : 0.03	] : 0.03	= : 0.03	4 : 0.03	2 : 0.01	a : 0.01	
e : 0.24	g : 0.17	c : 0.12	d : 0.07	b : 0.05	] : 0.05	2 : 0.05	f : 0.05	i : 0.03	h : 0.03	= : 0.03	4 : 0.03	3 : 0.01	a : 0.01	
e : 0.21	c : 0.17	g : 0.17	] : 0.08	d : 0.07	2 : 0.05	4 : 0.05	i : 0.03	b : 0.03	h : 0.03	= : 0.03	3 : 0.01	f : 0.01	
e : 0.21	g : 0.21	c : 0.15	d : 0.07	= : 0.05	b : 0.05	3 : 0.05	i : 0.03	h : 0.03	4 : 0.03	: : 0.01	a : 0.01	f : 0.01	2 : 0.01	] : 0.01	
g : 0.19	e : 0.17	c : 0.14	] : 0.08	: : 0.07	= : 0.05	b : 0.05	3 : 0.05	2 : 0.03	i : 0.03	h : 0.03	d : 0.01	f : 0.01	F : 0.01	4 : 0.01	
g : 0.19	c : 0.12	e : 0.08	= : 0.07	] : 0.07	: : 0.07	3 : 0.07	h : 0.05	b : 0.05	4 : 0.05	2 : 0.03	i : 0.03	d : 0.03	5 : 0.01	f : 0.01	F : 0.01	

#score	1317.3692835425577
#seq	57
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_UTR_m2_run1.txt

#BEAR
###ddddqqqqqqqqddddee	chr11:65809668-65809893(-)$1	225	80	101	13.4291
eeee!!aqqqqqqqqaeeeee	chr1:204523375-204523603(-)$1	228	44	65	13.8485
dd"""bbqqqqqqqqbb22dd	chr6:149771545-149771773(-)$1	228	61	82	13.5277
ccc!!bbqqqqqqqqbb22cc	chr9:19336691-19336912(-)$1	221	137	158	14.4056
hhhhhhhqqqqqqqqhhhhhh	chr12:123469749-123469970(-)$1	221	89	110	13.3907
bbeeeeeqqqqqqqqeeeee]	chr19:54058812-54059033(+)$1	221	142	163	13.3893
hhhhhhhqqqqqqqqhhhhhh	chr13:110960108-110960330(+)$1	222	44	65	13.3907
cc!!cccqqqqqqqqccc22c	chr16:49522052-49522276(+)$1	224	28	49	15.6423
cceeeeeqqqqqqqqeeeee]	chr3:184052405-184052628(-)$1	223	173	194	13.8504
:ffffffqqqqqqqqffffff	chr17:11900699-11900928(-)$1	229	49	70	13.0353
[a[ddddqqqqqqqqdddd]a	chr3:33414647-33414869(+)$1	222	7	28	13.9870
fff[cccqqqqqqqqcccfff	chr3:143709525-143709746(+)$1	221	25	46	15.1425
gg!!cccqqqqqqqqccc333	chr1:67413725-67413949(+)$1	224	194	215	16.0054
eee:cccqqqqqqqqccchhh	chr1:156288540-156288769(+)$1	229	129	150	13.5397
ddddcccqqqqqqqqccc22d	chr1:110049158-110049383(-)$1	225	187	208	14.4849
gggggggqqqqqqqqgggggg	chrX:24578148-24578372(+)$1	224	79	100	15.0565
gggggggqqqqqqqqgggggg	chr1:179813613-179813839(-)$1	226	185	206	15.0565
b[eeeeeqqqqqqqqeeeee]	chr1:207193850-207194071(+)$1	221	76	97	13.6454
###ddddqqqqqqqqdddd44	chrX:148592983-148593212(+)$1	229	45	66	13.4483
hhhhhhhqqqqqqqqhhhhhh	chr2:43519205-43519428(+)$1	223	88	109	13.3907
!ffffffqqqqqqqqffffff	chr1:201374018-201374242(-)$1	224	27	48	14.1192
"ffffffqqqqqqqqffffff	chr7:22981656-22981881(-)$1	225	90	111	14.0009
fffffbbqqqqqqqqbb22ff	chr1:85391432-85391657(-)$1	225	158	179	13.7800
fff[cccqqqqqqqqccc]ff	chr2:86115325-86115548(+)$1	223	112	133	15.3832
hhhhhhhqqqqqqqqhhhhhh	chr15:50606752-50606974(+)$1	222	150	171	13.3907
hhh[cccqqqqqqqqccc]hh	chr6:108533211-108533435(+)$1	224	43	64	15.1143
:ffffffqqqqqqqqffffff	chr7:98610289-98610515(-)$1	226	4	25	13.0353
eee[cccqqqqqqqqccc22e	chr8:143545388-143545610(-)$1	222	101	122	15.1806
gg[ddddqqqqqqqqdddd]g	chr21:45497496-45497720(+)$1	224	133	154	14.1620
d"""cccqqqqqqqqccc333	chr11:66010775-66011002(-)$1	227	9	30	15.4084
iiiiiiiqqqqqqqqiiiiii	chr11:8939135-8939358(-)$1	223	93	114	14.9420
b"""cccqqqqqqqqccc22b	chr2:232264212-232264433(+)$1	221	135	156	14.7342
!ffffffqqqqqqqqffffff	chr7:155573583-155573806(+)$1	223	104	125	14.1192
gggg[bbqqqqqqqqbb333g	chr19:55863058-55863281(-)$1	223	32	53	14.8910
bb[ddddqqqqqqqqdddd33	chr6:3224504-3224727(-)$1	223	132	153	13.6548
[a"""bbqqqqqqqqbb]ahh	chr19:46142162-46142390(-)$1	228	20	41	14.0982
ccc[a[bbqqqqqqqqbb]ac	chr14:42077569-42077790(+)$1	221	62	83	11.9025
eeeeeeeqqqqqqqqeeeee3	chr3:142838259-142838488(+)$1	229	196	217	13.6168
ddddcccqqqqqqqqccc]dd	chr17:33770708-33770932(+)$1	224	73	94	14.4371
gggggggqqqqqqqqgggggg	chr6:138538707-138538928(+)$1	221	110	131	15.0565
eeeeebbqqqqqqqqbb]eee	chr2:175113214-175113445(-)$1	231	208	229	13.7159
fffffffqqqqqqqqffffff	chrX:152160483-152160706(-)$1	223	145	166	13.9095
gggggggqqqqqqqqgggggg	chr7:138274067-138274292(-)$1	225	17	38	15.0565
gg!!cccrrrrrrrrrccc33	chr16:57417186-57417409(+)$1	223	191	212	9.0926
hhhhcccqqqqqqqqccc:dd	chr10:72013002-72013225(-)$1	223	126	147	13.5136
gggggggqqqqqqqqgggggg	chr10:73958215-73958437(+)$1	222	144	165	15.0565
cc[ddddqqqqqqqqddddcc	chr13:110438683-110438906(-)$1	223	195	216	13.9453
$ffffffqqqqqqqqffffff	chr11:117103002-117103226(-)$1	224	136	157	13.7816
fff[cccqqqqqqqqccc333	chr17:16075045-16075266(-)$1	221	48	69	15.6415
[ccc[bbqqqqqqqqbb]ccc	chr5:137804153-137804374(+)$1	221	156	177	14.3490
ddd[cccqqqqqqqqccc]dd	chr22:44893447-44893671(+)$1	224	6	27	14.7943
[bb[cccqqqqqqqqcccbbe	chr22:51021264-51021486(+)$1	222	19	40	14.2650
ccc!!bbqqqqqqqqbb]ccc	chr2:74593305-74593531(+)$1	226	9	30	14.5082

#otherMatches

#Seq PSSM
CGUGGGCUGAACCUUGCCUUC	chr11:65809668-65809893(-)$1	225	80	101	13.4291
GCAUCAGGAUCAAAACAUGCU	chr1:204523375-204523603(-)$1	228	44	65	13.8485
CUUUUCUUUAAAGAUGGUCAG	chr6:149771545-149771773(-)$1	228	61	82	13.5277
UGUGUGCUCCCCAUUGUUAGC	chr9:19336691-19336912(-)$1	221	137	158	14.4056
CCAGCCUCAGGCCACGGGCUG	chr12:123469749-123469970(-)$1	221	89	110	13.3907
GAGGGGCAGCUCCACGCUUCA	chr19:54058812-54059033(+)$1	221	142	163	13.3893
GGAUGGGCUGCCUCCCUCAUC	chr13:110960108-110960330(+)$1	222	44	65	13.3907
CCCUAGGAACACACACCUUAG	chr16:49522052-49522276(+)$1	224	28	49	15.6423
AGGGAACCCUCCCAAGUUCCA	chr3:184052405-184052628(-)$1	223	173	194	13.8504
AGGAGCUUCGGUAUCAGCUCC	chr17:11900699-11900928(-)$1	229	49	70	13.0353
AAGUAAUGAAGAUUAAUUGGU	chr3:33414647-33414869(+)$1	222	7	28	13.9870
UUAACUAGUCCAAGAUAGUAA	chr3:143709525-143709746(+)$1	221	25	46	15.1425
UGCAUAUGAUUUCCUGUACUC	chr1:67413725-67413949(+)$1	224	194	215	16.0054
CUUUCUUGUAUUCCAGAGAAG	chr1:156288540-156288769(+)$1	229	129	150	13.5397
UCAGGCCAGAGUGGGGGCUGC	chr1:110049158-110049383(-)$1	225	187	208	14.4849
AGAUUCAGGUAAAAGUGAAUC	chrX:24578148-24578372(+)$1	224	79	100	15.0565
GGUCUGUUCCAUUAUAUAGAC	chr1:179813613-179813839(-)$1	226	185	206	15.0565
GCUCAAGCUGCACAACUUGGU	chr1:207193850-207194071(+)$1	221	76	97	13.6454
ACUAAUUAUUAAAAGAAUUUC	chrX:148592983-148593212(+)$1	229	45	66	13.4483
AGAUGGACACAGUGCUCCGUC	chr2:43519205-43519428(+)$1	223	88	109	13.3907
CAGGCUGCCCAUCUCUGGCCU	chr1:201374018-201374242(-)$1	224	27	48	14.1192
UGAUCCCAGUUUUAAGGGAUU	chr7:22981656-22981881(-)$1	225	90	111	14.0009
CAGCAUGAUAUGAAGCAACUG	chr1:85391432-85391657(-)$1	225	158	179	13.7800
CUCCGCAAGGCUGGCUGCAGA	chr2:86115325-86115548(+)$1	223	112	133	15.3832
uuuucaaagauuccauugaaa	chr15:50606752-50606974(+)$1	222	150	171	13.3907
GUUAUACCAGUUUCUGUGCAG	chr6:108533211-108533435(+)$1	224	43	64	15.1143
AAGGCUGGCUGUGUACAGCCU	chr7:98610289-98610515(-)$1	226	4	25	13.0353
ACCAGGUCUUGACAUGCCAGG	chr8:143545388-143545610(-)$1	222	101	122	15.1806
UAAGUUUGUUGGAAAAGAUCU	chr21:45497496-45497720(+)$1	224	133	154	14.1620
UGGGCCUGGAGCaggagggag	chr11:66010775-66011002(-)$1	227	9	30	15.4084
CAGGAGGAUCGUGCCCCUCCU	chr11:8939135-8939358(-)$1	223	93	114	14.9420
UCCUGGCCCCCCGAAGUCCCA	chr2:232264212-232264433(+)$1	221	135	156	14.7342
GGAGCUCUUGUGCUUGAGUUC	chr7:155573583-155573806(+)$1	223	104	125	14.1192
CCCCACUGAUGCCUGAGCCAG	chr19:55863058-55863281(-)$1	223	32	53	14.8910
GUAUGGUAAAAUUGAACCAAU	chr6:3224504-3224727(-)$1	223	132	153	13.6548
ucccugccacuucgugcugug	chr19:46142162-46142390(-)$1	228	20	41	14.0982
GCUAUGGCAAAGGGCAGCGAA	chr14:42077569-42077790(+)$1	221	62	83	11.9025
GCGUCUCCAGCCCCCGAGGCG	chr3:142838259-142838488(+)$1	229	196	217	13.6168
CUGAUGUAAAAACUGGCAGUC	chr17:33770708-33770932(+)$1	224	73	94	14.4371
GUUAGUUUAGUUAUUGACUAA	chr6:138538707-138538928(+)$1	221	110	131	15.0565
GGCAGGACCUUUCUCUCGCUG	chr2:175113214-175113445(-)$1	231	208	229	13.7159
UGUCAGGCCCUGCCUCCUGAC	chrX:152160483-152160706(-)$1	223	145	166	13.9095
AGCUAUUUAUGGACUAGUAGC	chr7:138274067-138274292(-)$1	225	17	38	15.0565
AGUUGCCAGUCACCCCGGCCA	chr16:57417186-57417409(+)$1	223	191	212	9.0926
GAGCUGGUAAUUUCCCCAAAG	chr10:72013002-72013225(-)$1	223	126	147	13.5136
AGACAAGACCAGAUCCUUGUC	chr10:73958215-73958437(+)$1	222	144	165	15.0565
CGAGCGCGUCCCCCGGCGCCG	chr13:110438683-110438906(-)$1	223	195	216	13.9453
GAAGAGCAACGAGUGGCUUUU	chr11:117103002-117103226(-)$1	224	136	157	13.7816
GAACAGGUUUCUGAUUCUCAU	chr17:16075045-16075266(-)$1	221	48	69	15.6415
GAUCCUCUAUUUUGUGAUGAU	chr5:137804153-137804374(+)$1	221	156	177	14.3490
CACACGCUGAGAUCCGCGGGU	chr22:44893447-44893671(+)$1	224	6	27	14.7943
CGCUCGGCUCCUCUUCCGGCC	chr22:51021264-51021486(+)$1	222	19	40	14.2650
CUGCAAGUCUUACUCCUACAG	chr2:74593305-74593531(+)$1	226	9	30	14.5082

#DB
...((((........))))))	chr11:65809668-65809893(-)$1	1	80	101	13.4291
((((..(........))))))	chr1:204523375-204523603(-)$1	1	44	65	13.8485
((...((........))..))	chr6:149771545-149771773(-)$1	1	61	82	13.5277
(((..((........))..))	chr9:19336691-19336912(-)$1	1	137	158	14.4056
(((((((........))))))	chr12:123469749-123469970(-)$1	1	89	110	13.3907
(((((((........))))).	chr19:54058812-54059033(+)$1	1	142	163	13.3893
(((((((........))))))	chr13:110960108-110960330(+)$1	1	44	65	13.3907
((..(((........)))..)	chr16:49522052-49522276(+)$1	1	28	49	15.6423
(((((((........))))).	chr3:184052405-184052628(-)$1	1	173	194	13.8504
.((((((........))))))	chr17:11900699-11900928(-)$1	1	49	70	13.0353
.(.((((........)))).)	chr3:33414647-33414869(+)$1	1	7	28	13.9870
(((.(((........))))))	chr3:143709525-143709746(+)$1	1	25	46	15.1425
((..(((........)))...	chr1:67413725-67413949(+)$1	1	194	215	16.0054
))).(((........)))(((	chr1:156288540-156288769(+)$1	1	129	150	13.5397
(((((((........)))..)	chr1:110049158-110049383(-)$1	1	187	208	14.4849
(((((((........))))))	chrX:24578148-24578372(+)$1	1	79	100	15.0565
(((((((........))))))	chr1:179813613-179813839(-)$1	1	185	206	15.0565
(.(((((........))))).	chr1:207193850-207194071(+)$1	1	76	97	13.6454
...((((........))))..	chrX:148592983-148593212(+)$1	1	45	66	13.4483
(((((((........))))))	chr2:43519205-43519428(+)$1	1	88	109	13.3907
.((((((........))))))	chr1:201374018-201374242(-)$1	1	27	48	14.1192
.((((((........))))))	chr7:22981656-22981881(-)$1	1	90	111	14.0009
(((((((........))..))	chr1:85391432-85391657(-)$1	1	158	179	13.7800
(((.(((........))).))	chr2:86115325-86115548(+)$1	1	112	133	15.3832
(((((((........))))))	chr15:50606752-50606974(+)$1	1	150	171	13.3907
(((.(((........))).))	chr6:108533211-108533435(+)$1	1	43	64	15.1143
.((((((........))))))	chr7:98610289-98610515(-)$1	1	4	25	13.0353
(((.(((........)))..)	chr8:143545388-143545610(-)$1	1	101	122	15.1806
((.((((........)))).)	chr21:45497496-45497720(+)$1	1	133	154	14.1620
(...(((........)))...	chr11:66010775-66011002(-)$1	1	9	30	15.4084
(((((((........))))))	chr11:8939135-8939358(-)$1	1	93	114	14.9420
(...(((........)))..)	chr2:232264212-232264433(+)$1	1	135	156	14.7342
.((((((........))))))	chr7:155573583-155573806(+)$1	1	104	125	14.1192
((((.((........))...)	chr19:55863058-55863281(-)$1	1	32	53	14.8910
((.((((........))))..	chr6:3224504-3224727(-)$1	1	132	153	13.6548
.(...((........)).)))	chr19:46142162-46142390(-)$1	1	20	41	14.0982
(((.(.((........)).))	chr14:42077569-42077790(+)$1	1	62	83	11.9025
(((((((........))))).	chr3:142838259-142838488(+)$1	1	196	217	13.6168
(((((((........))).))	chr17:33770708-33770932(+)$1	1	73	94	14.4371
(((((((........))))))	chr6:138538707-138538928(+)$1	1	110	131	15.0565
(((((((........)).)))	chr2:175113214-175113445(-)$1	1	208	229	13.7159
)((((((........))))))	chrX:152160483-152160706(-)$1	1	145	166	13.9095
(((((((........))))))	chr7:138274067-138274292(-)$1	1	17	38	15.0565
((..(((.........)))..	chr16:57417186-57417409(+)$1	1	191	212	9.0926
))))(((........))).((	chr10:72013002-72013225(-)$1	1	126	147	13.5136
(((((((........))))))	chr10:73958215-73958437(+)$1	1	144	165	15.0565
((.((((........))))))	chr13:110438683-110438906(-)$1	1	195	216	13.9453
.((((((........))))))	chr11:117103002-117103226(-)$1	1	136	157	13.7816
(((.(((........)))...	chr17:16075045-16075266(-)$1	1	48	69	15.6415
.(((.((........)).)))	chr5:137804153-137804374(+)$1	1	156	177	14.3490
(((.(((........))).))	chr22:44893447-44893671(+)$1	1	6	27	14.7943
.((.(((........))))))	chr22:51021264-51021486(+)$1	1	19	40	14.2650
(((..((........)).)))	chr2:74593305-74593531(+)$1	1	9	30	14.5082

#PSSM
g : 0.16	c : 0.11	h : 0.11	e : 0.09	d : 0.09	f : 0.09	b : 0.07	[ : 0.07	# : 0.03	: : 0.03	! : 0.03	" : 0.01	i : 0.01	$ : 0.01	
f : 0.20	g : 0.16	c : 0.13	h : 0.11	e : 0.09	d : 0.07	b : 0.05	# : 0.03	a : 0.03	" : 0.03	[ : 0.01	i : 0.01	
f : 0.20	e : 0.15	h : 0.11	g : 0.11	" : 0.07	c : 0.07	[ : 0.07	! : 0.05	d : 0.05	# : 0.03	i : 0.01	b : 0.01	
d : 0.15	f : 0.15	[ : 0.15	e : 0.11	g : 0.11	! : 0.09	h : 0.09	" : 0.07	: : 0.01	i : 0.01	c : 0.01	
c : 0.30	f : 0.15	d : 0.11	e : 0.09	g : 0.09	h : 0.07	! : 0.05	" : 0.03	[ : 0.03	i : 0.01	a : 0.01	
c : 0.30	b : 0.15	f : 0.13	d : 0.11	g : 0.09	h : 0.07	e : 0.07	! : 0.01	i : 0.01	[ : 0.01	
c : 0.30	b : 0.16	f : 0.13	d : 0.11	g : 0.09	h : 0.07	e : 0.07	a : 0.01	i : 0.01	
q : 0.96	b : 0.01	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
q : 0.98	r : 0.01	
c : 0.28	b : 0.15	f : 0.13	d : 0.11	g : 0.09	h : 0.07	e : 0.07	a : 0.01	i : 0.01	q : 0.01	r : 0.01	
c : 0.30	b : 0.16	f : 0.13	d : 0.11	e : 0.09	g : 0.09	h : 0.07	i : 0.01	
c : 0.30	f : 0.13	d : 0.11	e : 0.09	g : 0.09	h : 0.07	] : 0.07	2 : 0.05	i : 0.01	3 : 0.01	b : 0.01	
f : 0.15	2 : 0.13	d : 0.11	e : 0.11	h : 0.09	g : 0.09	] : 0.09	3 : 0.07	c : 0.05	i : 0.01	a : 0.01	: : 0.01	b : 0.01	
f : 0.18	e : 0.13	h : 0.13	3 : 0.11	g : 0.09	d : 0.07	c : 0.07	2 : 0.07	] : 0.03	4 : 0.01	i : 0.01	a : 0.01	b : 0.01	
f : 0.18	h : 0.13	g : 0.13	c : 0.11	3 : 0.11	e : 0.09	d : 0.09	] : 0.05	a : 0.01	4 : 0.01	i : 0.01	b : 0.01	

#score	748.325901801251
#seq	53
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012b_hg19_CDS_m2_run2.txt

#BEAR
eeeeemmmmeeeee]d	chr15:69560590-69560816(+)$1	226	189	205	11.5731
[eeeeellleeeee]d	chr12:6344542-6344766(+)$1	224	94	110	10.1595
eeeeemmmmeeeee:g	chr9:108536092-108536318(+)$1	226	128	144	10.5907
eeeeennnnneeeee6	chr22:35811738-35811975(+)$1	237	138	154	8.8970
eeeeemmmmeeeee::	chr1:234529308-234529549(-)$1	241	1	17	9.9907
eeeeemmmmeeeee]c	chr3:15282873-15283102(+)$1	229	143	159	11.6604
eeeooooooeeeee]c	chr9:32984575-32984801(-)$1	226	13	29	9.4124
eeeeemmmmeeeee]a	chr1:206858621-206858852(+)$1	231	135	151	11.7398
eeeeemmmmeeeee33	chr8:48777071-48777306(-)$1	235	148	164	12.0668
eeeee4444eeeee33	chr15:91461828-91462058(+)$1	230	135	151	9.9464
eeeeemmmmeeeee33	chr10:93742368-93742614(+)$1	246	149	165	12.0668
eeeeemmmmeeeee44	chr13:23913650-23913874(-)$1	224	65	81	11.8008
eeeeemmmmeeeee]a	chr6:52149357-52149587(-)$1	230	121	137	11.7398
eee[ammmma]eeeee	chr7:150839400-150839629(+)$1	229	126	142	8.8405
eeeeeellleeeee]e	chr9:115923758-115923981(-)$1	223	6	22	10.6539
eeeeemmmmeeeeegg	chr17:48474575-48474796(-)$1	221	84	100	11.0911
eeeeemmmmeeeee22	chr1:16265160-16265392(+)$1	232	22	38	11.7455
eeeeemmmmeeeee]d	chr2:25469455-25469685(-)$1	230	58	74	11.5731
eeeeeooooooeeeee	chr3:45559329-45559559(+)$1	230	207	223	8.8050
eeeeellleeeee333	chr16:1837878-1838108(+)$1	230	98	114	10.4231
eeeeemmmmeeeee55	chr2:201681744-201681984(+)$1	240	80	96	10.5092
eeeeemmmmeeeee::	chr6:27860420-27860681(-)$1	261	47	63	9.9907
eeeeemmmmeeeee44	chr6:25551172-25551395(+)$1	223	103	119	11.8008
eeeeellleeeeeddd	chr2:220476583-220476812(+)$1	229	111	127	9.2981
eeeeemmmmeeeee66	chr11:11950884-11951113(+)$1	229	177	193	10.9792
eeeeemmmmeeeee]d	chr9:123580099-123580322(+)$1	223	169	185	11.5731
!eeeeellleeeee]f	chr2:120702602-120702828(-)$1	226	133	149	10.0802
ceeeeellleeeee:b	chr8:146015112-146015354(-)$1	242	27	43	8.9067
eeeeemmmmeeeeeee	chr20:21311201-21311425(+)$1	224	134	150	11.0203
eeeeellleeeee22c	chr12:88512406-88512635(-)$1	229	204	220	9.8223
eeeeennnnneeeeec	chr17:80048662-80048905(-)$1	243	137	153	9.0243
[eeeeellleeeee]b	chr17:27939654-27939889(-)$1	235	80	96	10.0752
[eeeeellleeeee]c	chr1:207643982-207644207(-)$1	225	34	50	10.2468
eeeooooooeeeee22	chrM:7110-7340(-)$1	230	113	129	9.4974
eeeeemmmmeeeee]c	chr12:92537856-92538085(-)$1	229	210	226	11.6604
eeeeemmmmeeeeeHH	chr3:101405416-101405651(-)$1	235	58	74	9.9018
eeeeemmmmeeeee:e	chr16:51175943-51176173(-)$1	230	197	213	10.5580
eeeeemmmmeeeee22	chr10:101120498-101120723(+)$1	225	79	95	11.7455
eeeeellleeeee22c	chr12:94613788-94614010(-)$1	222	171	187	9.8223
eeeeemmmmeeeee22	chr5:180661256-180661486(+)$1	230	83	99	11.7455
eeeennnnneeeee]b	chr1:160247799-160248025(-)$1	226	120	136	9.3544
eeeeennnnneeeeeb	chr1:186322715-186322943(-)$1	228	65	81	8.8528
eeeeeooooooeeeee	chr17:8167489-8167739(+)$1	250	196	212	8.8050
eeeennnnneeeee]d	chr17:61882393-61882630(+)$1	237	55	71	9.4387
eeeeennnnneeeee7	chr9:86893081-86893304(-)$1	223	123	139	8.8274
eeeeemmmmeeeee99	chr6:47251986-47252210(+)$1	224	29	45	10.5592
eeeeemmmmeeeee33	chr3:41268632-41268883(+)$1	251	22	38	12.0668
eeeeemmmmeeeee22	chrX:135304464-135304701(-)$1	237	191	207	11.7455
eee[ammmma]eeeee	chr17:4451723-4451949(-)$1	226	179	195	8.8405
eeeeellleeeee22e	chr3:182586794-182587021(+)$1	227	95	111	9.7432
eeeeooooooeeeeed	chr11:62396241-62396483(-)$1	242	171	187	8.9662
eeeeemmmmeeeee22	chr12:54427999-54428231(+)$1	232	199	215	11.7455
[eeeeellleeeeebb	chr11:60609649-60609893(+)$1	244	48	64	9.2149
eeeeemmmmeeeee22	chr15:40917445-40917667(+)$1	222	198	214	11.7455
eeeennnnneeeee33	chr11:103907506-103907729(-)$1	223	109	125	9.9323

#otherMatches

#Seq PSSM
ACCAGGGACCUGGUCA	chr15:69560590-69560816(+)$1	226	189	205	11.5731
UGUAGUUGAACUGCUG	chr12:6344542-6344766(+)$1	224	94	110	10.1595
GGCUGGCAGCAGCCGU	chr9:108536092-108536318(+)$1	226	128	144	10.5907
GGGACCCUUCGUCCCG	chr22:35811738-35811975(+)$1	237	138	154	8.8970
UGGACCGACGUUCAGA	chr1:234529308-234529549(-)$1	241	1	17	9.9907
CCAGUACAAACUGGAG	chr3:15282873-15283102(+)$1	229	143	159	11.6604
UCUUACCGUGGACCUC	chr9:32984575-32984801(-)$1	226	13	29	9.4124
UGACUACAAGGUCACC	chr1:206858621-206858852(+)$1	231	135	151	11.7398
GUGGUGGAUGCCAUUG	chr8:48777071-48777306(-)$1	235	148	164	12.0668
CUGCACCACAAGCCAA	chr15:91461828-91462058(+)$1	230	135	151	9.9464
GGUAAGAUUUUGCCCC	chr10:93742368-93742614(+)$1	246	149	165	12.0668
CAUUAAAGUUGAUGAC	chr13:23913650-23913874(-)$1	224	65	81	11.8008
GGUACCGUGGUGCUGG	chr6:52149357-52149587(-)$1	230	121	137	11.7398
UGCCCUGAUGUGCAUU	chr7:150839400-150839629(+)$1	229	126	142	8.8405
UGGUGGGUUCUGCCAA	chr9:115923758-115923981(-)$1	223	6	22	10.6539
CCCCGGAGCCGGGGCC	chr17:48474575-48474796(-)$1	221	84	100	11.0911
CUGCUCACUGGCAGCU	chr1:16265160-16265392(+)$1	232	22	38	11.7455
GGGAAGCUGUUCCCGG	chr2:25469455-25469685(-)$1	230	58	74	11.5731
GGAGUACAAGAACUCC	chr3:45559329-45559559(+)$1	230	207	223	8.8050
CUUCUGUAGGAAGACG	chr16:1837878-1838108(+)$1	230	98	114	10.4231
ACAGCUGCUGCUGUUC	chr2:201681744-201681984(+)$1	240	80	96	10.5092
UGGUAAAGUUACCAUC	chr6:27860420-27860681(-)$1	261	47	63	9.9907
UUGGAGCAGUCUGGAA	chr6:25551172-25551395(+)$1	223	103	119	11.8008
UCCGCUCUGUGGACCA	chr2:220476583-220476812(+)$1	229	111	127	9.2981
UCAUUCAGUGAUGAGC	chr11:11950884-11951113(+)$1	229	177	193	10.9792
UUUGGGUUCCCAAAGA	chr9:123580099-123580322(+)$1	223	169	185	11.5731
AAAGCUGGAGGCUUCC	chr2:120702602-120702828(-)$1	226	133	149	10.0802
AGGUGGCAACCACCAG	chr8:146015112-146015354(-)$1	242	27	43	8.9067
AUUUGACAGUAAGUUU	chr20:21311201-21311425(+)$1	224	134	150	11.0203
CUUUUGAAAGAGGCAA	chr12:88512406-88512635(-)$1	229	204	220	9.8223
CUGCCAUCCAGGUAGG	chr17:80048662-80048905(-)$1	243	137	153	9.0243
AAGCAGGCUCUGCUGG	chr17:27939654-27939889(-)$1	235	80	96	10.0752
GCUAUAUUUUAUAGAU	chr1:207643982-207644207(-)$1	225	34	50	10.2468
CGAGUAACGUCGGGGC	chrM:7110-7340(-)$1	230	113	129	9.4974
UGAUGACUGUAUCAGG	chr12:92537856-92538085(-)$1	229	210	226	11.6604
GACCUUAUAAGGUCUC	chr3:101405416-101405651(-)$1	235	58	74	9.9018
UUUGAAUUAUCAGAUC	chr16:51175943-51176173(-)$1	230	197	213	10.5580
CUGUGACCCCACAGCU	chr10:101120498-101120723(+)$1	225	79	95	11.7455
GCACUUUGAGUGUCUU	chr12:94613788-94614010(-)$1	222	171	187	9.8223
CUACUGGGAGGUAGAG	chr5:180661256-180661486(+)$1	230	83	99	11.7455
AGCUCAGCUGGCUGUC	chr1:160247799-160248025(-)$1	226	120	136	9.3544
UUAUCAAUACGAUGAC	chr1:186322715-186322943(-)$1	228	65	81	8.8528
UGUGGUCCUCUCCACA	chr17:8167489-8167739(+)$1	250	196	212	8.8050
GAAAAAAACUUUUACA	chr17:61882393-61882630(+)$1	237	55	71	9.4387
GUUGAAUCCAUCGACC	chr9:86893081-86893304(-)$1	223	123	139	8.8274
GGUGGUUGACUACCUG	chr6:47251986-47252210(+)$1	224	29	45	10.5592
UCAAGAUUCCUUGACU	chr3:41268632-41268883(+)$1	251	22	38	12.0668
caggggcuccucugcu	chrX:135304464-135304701(-)$1	237	191	207	11.7455
GGGCGCCUGCUCCCUC	chr17:4451723-4451949(-)$1	226	179	195	8.8405
AUUUGAUUCAGAUCGU	chr3:182586794-182587021(+)$1	227	95	111	9.7432
GCGAUAUUCUUUGCUG	chr11:62396241-62396483(-)$1	242	171	187	8.9662
CAGAUCAAGAUCUGGU	chr12:54427999-54428231(+)$1	232	199	215	11.7455
AGUUCGAGUCGAACCC	chr11:60609649-60609893(+)$1	244	48	64	9.2149
UCUAUUAACAUAGAAA	chr15:40917445-40917667(+)$1	222	198	214	11.7455
CGGGGCUGACCUGGAG	chr11:103907506-103907729(-)$1	223	109	125	9.9323

#DB
(((((....))))).)	chr15:69560590-69560816(+)$1	1	189	205	11.5731
.(((((...))))).)	chr12:6344542-6344766(+)$1	1	94	110	10.1595
(((((....))))).(	chr9:108536092-108536318(+)$1	1	128	144	10.5907
(((((.....))))).	chr22:35811738-35811975(+)$1	1	138	154	8.8970
(((((....)))))..	chr1:234529308-234529549(-)$1	1	1	17	9.9907
(((((....))))).)	chr3:15282873-15283102(+)$1	1	143	159	11.6604
(((......))))).)	chr9:32984575-32984801(-)$1	1	13	29	9.4124
(((((....))))).)	chr1:206858621-206858852(+)$1	1	135	151	11.7398
(((((....)))))..	chr8:48777071-48777306(-)$1	1	148	164	12.0668
)))))....)))))..	chr15:91461828-91462058(+)$1	1	135	151	9.9464
(((((....)))))..	chr10:93742368-93742614(+)$1	1	149	165	12.0668
(((((....)))))..	chr13:23913650-23913874(-)$1	1	65	81	11.8008
(((((....))))).)	chr6:52149357-52149587(-)$1	1	121	137	11.7398
(((.(....).)))))	chr7:150839400-150839629(+)$1	1	126	142	8.8405
((((((...))))).)	chr9:115923758-115923981(-)$1	1	6	22	10.6539
(((((....)))))((	chr17:48474575-48474796(-)$1	1	84	100	11.0911
(((((....)))))..	chr1:16265160-16265392(+)$1	1	22	38	11.7455
(((((....))))).)	chr2:25469455-25469685(-)$1	1	58	74	11.5731
(((((......)))))	chr3:45559329-45559559(+)$1	1	207	223	8.8050
(((((...)))))...	chr16:1837878-1838108(+)$1	1	98	114	10.4231
(((((....)))))..	chr2:201681744-201681984(+)$1	1	80	96	10.5092
(((((....)))))..	chr6:27860420-27860681(-)$1	1	47	63	9.9907
(((((....)))))..	chr6:25551172-25551395(+)$1	1	103	119	11.8008
(((((...))))))))	chr2:220476583-220476812(+)$1	1	111	127	9.2981
(((((....)))))..	chr11:11950884-11951113(+)$1	1	177	193	10.9792
(((((....))))).)	chr9:123580099-123580322(+)$1	1	169	185	11.5731
.(((((...))))).)	chr2:120702602-120702828(-)$1	1	133	149	10.0802
)(((((...))))).(	chr8:146015112-146015354(-)$1	1	27	43	8.9067
(((((....)))))))	chr20:21311201-21311425(+)$1	1	134	150	11.0203
(((((...)))))..)	chr12:88512406-88512635(-)$1	1	204	220	9.8223
(((((.....))))))	chr17:80048662-80048905(-)$1	1	137	153	9.0243
.(((((...))))).)	chr17:27939654-27939889(-)$1	1	80	96	10.0752
.(((((...))))).)	chr1:207643982-207644207(-)$1	1	34	50	10.2468
(((......)))))..	chrM:7110-7340(-)$1	1	113	129	9.4974
(((((....))))).)	chr12:92537856-92538085(-)$1	1	210	226	11.6604
(((((....)))))))	chr3:101405416-101405651(-)$1	1	58	74	9.9018
(((((....))))).(	chr16:51175943-51176173(-)$1	1	197	213	10.5580
(((((....)))))..	chr10:101120498-101120723(+)$1	1	79	95	11.7455
(((((...)))))..)	chr12:94613788-94614010(-)$1	1	171	187	9.8223
(((((....)))))..	chr5:180661256-180661486(+)$1	1	83	99	11.7455
((((.....))))).)	chr1:160247799-160248025(-)$1	1	120	136	9.3544
(((((.....))))))	chr1:186322715-186322943(-)$1	1	65	81	8.8528
(((((......)))))	chr17:8167489-8167739(+)$1	1	196	212	8.8050
((((.....))))).)	chr17:61882393-61882630(+)$1	1	55	71	9.4387
(((((.....))))).	chr9:86893081-86893304(-)$1	1	123	139	8.8274
(((((....)))))..	chr6:47251986-47252210(+)$1	1	29	45	10.5592
(((((....)))))..	chr3:41268632-41268883(+)$1	1	22	38	12.0668
(((((....)))))..	chrX:135304464-135304701(-)$1	1	191	207	11.7455
(((.(....).)))))	chr17:4451723-4451949(-)$1	1	179	195	8.8405
(((((...)))))..)	chr3:182586794-182587021(+)$1	1	95	111	9.7432
((((......))))))	chr11:62396241-62396483(-)$1	1	171	187	8.9662
(((((....)))))..	chr12:54427999-54428231(+)$1	1	199	215	11.7455
.(((((...)))))))	chr11:60609649-60609893(+)$1	1	48	64	9.2149
(((((....)))))..	chr15:40917445-40917667(+)$1	1	198	214	11.7455
((((.....)))))..	chr11:103907506-103907729(-)$1	1	109	125	9.9323

#PSSM
e : 0.89	[ : 0.07	! : 0.01	c : 0.01	
e : 1.00	
e : 1.00	
e : 0.92	o : 0.03	[ : 0.03	
e : 0.85	o : 0.05	n : 0.05	a : 0.03	
m : 0.54	e : 0.12	n : 0.12	o : 0.09	l : 0.09	4 : 0.01	
m : 0.54	l : 0.21	n : 0.12	o : 0.09	4 : 0.01	
m : 0.54	l : 0.21	n : 0.12	o : 0.09	4 : 0.01	
m : 0.54	l : 0.12	n : 0.12	o : 0.09	e : 0.09	4 : 0.01	
e : 0.83	n : 0.07	o : 0.05	a : 0.03	
e : 0.92	] : 0.03	o : 0.03	
e : 1.00	
e : 1.00	
e : 0.90	2 : 0.05	3 : 0.01	d : 0.01	
] : 0.27	e : 0.18	2 : 0.18	3 : 0.10	: : 0.09	4 : 0.03	g : 0.01	5 : 0.01	d : 0.01	6 : 0.01	H : 0.01	9 : 0.01	b : 0.01	
e : 0.14	d : 0.12	c : 0.12	2 : 0.12	3 : 0.10	b : 0.09	g : 0.03	6 : 0.03	: : 0.03	a : 0.03	4 : 0.03	5 : 0.01	f : 0.01	H : 0.01	7 : 0.01	9 : 0.01	

#score	572.8750736664056
#seq	55
#width	16
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_UTR_m1_run1.txt

#BEAR
===bb[dddduuuuuuuuuuuudddd]bb]=	chr12:49666174-49666609(+)$1	435	318	349	23.0143
iiiiiiiiiccctttttttttttccc]iiii	chr1:27182053-27182305(+)$1	252	19	50	23.0803
eeee[eeeeeuuuuuuuuuuuueeeee]eee	chr10:23730106-23730396(+)$1	290	129	160	23.9308
####eeeeeuuuuuuuuuuuueeeee333dd	chr6:24705964-24706213(-)$1	249	135	166	23.7487
ccc[fffffftttttttttttffffff]ccc	chr13:46700508-46700747(-)$1	239	39	70	21.6912
::gggggggvvvvvvvvvvvvvggggggga[	chr12:58118880-58119132(-)$1	252	112	143	21.5588
gggg!!cccwwwwwwwwwwwwwwccc22ggg	chr1:150720163-150720456(-)$1	293	21	52	25.0993
==="""dddduuuuuuuuuuuudddd]====	chr2:208476653-208476895(+)$1	242	130	161	24.6113
i[iiiiiiiiitttttttttttiiiiiiiii	chr16:83845087-83845380(+)$1	293	166	197	22.8439
iddddbbbbyyyyyyyyyyyyyyyybb]bb]	chr6:116579623-116579879(-)$1	256	75	106	23.2193
ffff[cccyyyyyyyyyyyyyyyyccc]fff	chr5:172461744-172461989(+)$1	245	199	230	25.1944
ccc"""cccvvvvvvvvvvvvvccc4444cc	chr20:4836030-4836270(-)$1	240	45	76	23.7309
!!gggggggxxxxxxxxxxxxxxxggggggg	chr8:11683467-11683731(+)$1	264	140	171	22.8754
iiiiiiiiiyyyyyyyyyyyyyyyyiiiiii	chr19:34922701-34922940(+)$1	239	198	229	26.7272
c[gggggggvvvvvvvvvvvvvggggggg]c	chr17:7363246-7363507(-)$1	261	152	183	23.7615
eee"""cccuuuuuuuuuuuuccc4444eee	chr12:56693856-56694096(-)$1	240	69	100	23.6038
!ffffff[ayyyyyyyyyyyyyyyya]ffff	chr5:179157788-179158027(+)$1	239	196	227	25.3213
ccc"""ccc^^^^^^^^^^^^^^^^^^cccc	chr12:48437718-48437961(-)$1	243	71	102	18.4042
F:ddddcccwwwwwwwwwwwwwwccc]dddd	chr12:4409177-4409416(+)$1	239	80	111	22.2269
ggggg^^^^^^^^^^^^^^^^^^^ggggggg	chr19:10800318-10800612(+)$1	294	148	179	18.3463
hhffffff[bbuuuuuuuuuuuubb]fffff	chr17:58143539-58143778(-)$1	239	68	99	22.3202
eeee[ddddwwwwwwwwwwwwwwdddd]eee	chr19:8376226-8376471(-)$1	245	184	215	23.3392
Iggggggg[auuuuuuuuuuuua]ggggggg	chr6:163994059-163994329(+)$1	270	52	83	24.3137
GGeeeee[cccuuuuuuuuuuuuccc]eeee	chr12:118853418-118853676(+)$1	258	116	147	22.8524
:::ffffffyyyyyyyyyyyyyyyyffffff	chr10:72183524-72183767(+)$1	243	127	158	21.9070
========[bbuuuuuuuuuuuubb]=====	chr2:172604755-172605008(+)$1	253	20	51	24.6677
fffccceeeeettttttttttteeeee]ccc	chr11:77780796-77781046(-)$1	250	208	239	22.0734
eeeffffffuuuuuuuuuuuuffffff22ee	chr4:152629087-152629325(-)$1	238	41	72	22.2110
!ccc[ffffffuuuuuuuuuuuuffffff]c	chr8:56985641-56985922(-)$1	281	51	82	23.0486
ffffeeeeeyyyyyyyyyyyyyyyyeeeee]	chr8:101930780-101931108(-)$1	328	177	208	25.0805
iiiiiiii^^^^^^^^^^^^^^^^^^^^iii	chr6:111620394-111620633(-)$1	239	2	33	18.9696
===========uuuuuuuuuuuu========	chr5:174936046-174936311(+)$1	265	21	52	25.0769
!gggggggyyyyyyyyyyyyyyyyggggggg	chr1:70700306-70700549(+)$1	243	96	127	26.1351
ffgggggggwwwwwwwwwwwwwwggggggg]	chr4:39783408-39783662(+)$1	254	45	76	24.6819
[a[eeeeexxxxxxxxxxxxxxxeeeee]a]	chr2:216209437-216209684(+)$1	247	190	221	21.5974
:dddd[ddddvvvvvvvvvvvvvdddddddd	chr17:22022553-22022808(+)$1	255	22	53	20.6701
gggffffffuuuuuuuuuuuuffffff333g	chr7:63981289-63981583(-)$1	294	233	264	23.3690
iiiiiiiiixxxxxxxxxxxxxxxiiiiiii	chr19:6413539-6413823(-)$1	284	164	195	23.2343
gggccc!!ayyyyyyyyyyyyyyyya22ccc	chr8:103661642-103661913(-)$1	271	45	76	25.8321
dddccc!!ayyyyyyyyyyyyyyyya22ccc	chr4:26432418-26432696(+)$1	278	112	143	25.1869
iiiiii[bbwwwwwwwwwwwwwwbb]iiiii	chr1:32663220-32663507(+)$1	287	49	80	24.5519
iiiiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr11:118319554-118319793(+)$1	239	93	124	25.4312
hhhheeeeeyyyyyyyyyyyyyyyyeeeee]	chr17:27586587-27586849(-)$1	262	28	59	24.7780
fffff[dddduuuuuuuuuuuudddd]ffff	chr19:6440846-6441116(-)$1	270	202	233	23.1045
ffdddd[bbxxxxxxxxxxxxxxxbb]dddd	chr1:54497256-54497551(-)$1	295	13	44	20.2823
b"""dddd[ccctttttttttttccc]dddd	chr5:135514184-135514420(+)$1	236	52	83	21.0161
dd!!ccc[cccuuuuuuuuuuuuccc]ccc]	chr4:77231322-77231569(+)$1	247	54	85	24.1187
==========ttttttttttt==========	chr17:21731462-21731717(+)$1	255	81	112	23.4749
bb[ffffffuuuuuuuuuuuuffffff]bb8	chr10:104846801-104847042(-)$1	241	163	194	21.5275
!dddd!!bbwwwwwwwwwwwwwwbbdddd22	chr17:1553826-1554094(-)$1	268	176	207	22.1783
f####ffffffuuuuuuuuuuuuffffff55	chr12:42480761-42481001(-)$1	240	93	124	21.0045
####eeeeeuuuuuuuuuuuueeeee22ddd	chr7:98930857-98931096(+)$1	239	181	212	23.2085
cc[eeeeexxxxxxxxxxxxxxxeeeee]cc	chr10:74834534-74834780(-)$1	246	79	110	21.5398
FFffffff[ccctttttttttttccc22fff	chr5:157214862-157215103(-)$1	241	175	206	20.6274
dddd[ddddwwwwwwwwwwwwwwdddd]ddd	chr15:52839489-52839907(-)$1	418	63	94	22.9657
eeeeeeeeevvvvvvvvvvvvveeeee]eee	chr14:78182080-78182324(+)$1	244	9	40	22.9861
!hhhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chr18:48700833-48701109(-)$1	276	232	263	23.5776
iiiiiiiiiwwwwwwwwwwwwwwiiiiiiii	chr20:43248837-43249097(-)$1	260	76	107	25.4312
===[eeeeevvvvvvvvvvvvveeeee333=	chr5:138253328-138253595(+)$1	267	165	196	24.1588
iiiiieeeeeuuuuuuuuuuuueeeee]iii	chr11:122929670-122929958(-)$1	288	208	239	25.0341
dddd"""ccctttttttttttccc4444ddd	chr1:90184033-90184311(+)$1	278	97	128	21.7548
i####eeeeettttttttttteeeee4444i	chr2:196601638-196601877(+)$1	239	171	202	22.4382

#otherMatches

#Seq PSSM
CUGAGAAAGCCUACCACGAACAGCUUACUGU	chr12:49666174-49666609(+)$1	435	318	349	23.0143
CUCAGGGCCCUGGGCCAUCACUGCAGUGGCC	chr1:27182053-27182305(+)$1	252	19	50	23.0803
AGAGAAGUGCUUUAUAUGAAAUGUAUUAUUU	chr10:23730106-23730396(+)$1	290	129	160	23.9308
GAAAUGCUUAAAUGUAUCUGAAAGCACAAGG	chr6:24705964-24706213(-)$1	249	135	166	23.7487
AUAUUAUCAAUGUUUACUUUUUUGGUACUAU	chr13:46700508-46700747(-)$1	239	39	70	21.6912
AUCUUCUUCAACAGCAAUUAAAGAGGAAGUG	chr12:58118880-58119132(-)$1	252	112	143	21.5588
UAAAAAGUAAUACCGUUUUAAAAUGCCCUUU	chr1:150720163-150720456(-)$1	293	21	52	25.0993
aagaaaaCCUAUUCAAGAUUUCAGGUGCuuu	chr2:208476653-208476895(+)$1	242	130	161	24.6113
ACUUUGGCGGUUCUUGCAUAACAUUGUCAGA	chr16:83845087-83845380(+)$1	293	166	197	22.8439
CGUGAGGCUGCCUUCCGGAACAUUAAGACCA	chr6:116579623-116579879(-)$1	256	75	106	23.2193
UACAUAAUGCCUUUUUAAAAAAUGAUUUUGU	chr5:172461744-172461989(+)$1	245	199	230	25.1944
GCCAAAGGUGAUAAGAAAAGCAGCCAACAGG	chr20:4836030-4836270(-)$1	240	45	76	23.7309
UUAGUUGGUGAAGAUACAGAACGUGCCAACU	chr8:11683467-11683731(+)$1	264	140	171	22.8754
AAAGUCAUUCAGCUUUUUUAAAAAAAAUGAU	chr19:34922701-34922940(+)$1	239	198	229	26.7272
auauauauaucuacacacaaauuauauaucu	chr17:7363246-7363507(-)$1	261	152	183	23.7615
UCCCUUUCUUACCUCCCCACCAGAUCCCGGA	chr12:56693856-56694096(-)$1	240	69	100	23.6038
UUAGUGGGUUGAUCUUCGUAUAAUUGGCCAC	chr5:179157788-179158027(+)$1	239	196	227	25.3213
CAACUUGAGAUUUAAAAACUGCUAUUCCUUU	chr12:48437718-48437961(-)$1	243	71	102	18.4042
UAGGGUGAAACUUAAAAAAAAAAUUCUGCCC	chr12:4409177-4409416(+)$1	239	80	111	22.2269
UUCAGGCAGUACAUCUGAAUUAAGCUGAAUG	chr19:10800318-10800612(+)$1	294	148	179	18.3463
UGUUUUCUUUCUACUAUAAAAUCGAUAGAAA	chr17:58143539-58143778(-)$1	239	68	99	22.3202
UCUAGUUUUACuuuaaaaaauaaaaaaauag	chr19:8376226-8376471(-)$1	245	184	215	23.3392
CUUUUAUGGGGAAGAAAGUAAAUGUAUGAAA	chr6:163994059-163994329(+)$1	270	52	83	24.3137
UCUCAAGUGAUUCUCUUCAUGUUGUCUCUUG	chr12:118853418-118853676(+)$1	258	116	147	22.8524
AACUCCAAGUCUCAUUUUACAUAUUCUUGGA	chr10:72183524-72183767(+)$1	243	127	158	21.9070
AAUGUUCUCACUACCCAUAAUAUGUAGGAAC	chr2:172604755-172605008(+)$1	253	20	51	24.6677
UUCACCCAUCUGAAAGAUUUUAAGAUGAGGU	chr11:77780796-77781046(-)$1	250	208	239	22.0734
UCUAAGGAGUUGUUUUCUUCUCUCCUUCCAG	chr4:152629087-152629325(-)$1	238	41	72	22.2110
AAAACGAUAAACACUUGGUUUCCUUUGUCUU	chr8:56985641-56985922(-)$1	281	51	82	23.0486
GUGAGAAACUGAAAUCCCAAACACUGUUUUG	chr8:101930780-101931108(-)$1	328	177	208	25.0805
AGCAUUUUGAAACAUUAUUUUUUUUUAAAAA	chr6:111620394-111620633(-)$1	239	2	33	18.9696
UGAAUUGUGGAGAGCAAAGUACAUCUAUGAU	chr5:174936046-174936311(+)$1	265	21	52	25.0769
UUGGGGGCUCCUACUCUUGAUCCUGCCCUUG	chr1:70700306-70700549(+)$1	243	96	127	26.1351
AUUUAAAAAUUACGUUUCCAUUCUUUUUAGU	chr4:39783408-39783662(+)$1	254	45	76	24.6819
UGUUGUUUUACGAAAUGAUAUUUAAACAUCC	chr2:216209437-216209684(+)$1	247	190	221	21.5974
AGUAGCAAGGACAAACCCCUAUACCUUCUGC	chr17:22022553-22022808(+)$1	255	22	53	20.6701
UUUUACUUGAGAAAGAUUGUACAAGUAUAAA	chr7:63981289-63981583(-)$1	294	233	264	23.3690
AAAAAAAAGUCACUCUUGCUAUUUCUUUUUU	chr19:6413539-6413823(-)$1	284	164	195	23.2343
UAUUCCUAGUCUUUCCAGUCAACAUCGUGGA	chr8:103661642-103661913(-)$1	271	45	76	25.8321
CCCCCUAACGAAUCAAACACAAACAGCGAGG	chr4:26432418-26432696(+)$1	278	112	143	25.1869
UUUCUUAGAUUGCUAGCUUUUCCUCCAGGGG	chr1:32663220-32663507(+)$1	287	49	80	24.5519
AUUUCUUGUCAUACAUUCAGAAAACAAGAGA	chr11:118319554-118319793(+)$1	239	93	124	25.4312
UUGUCUGCAUAAUAAAAACACCCAUUGCAGC	chr17:27586587-27586849(-)$1	262	28	59	24.7780
CCGGUUUCUGAUCUGAAUCUUCCAGGCGCCG	chr19:6440846-6441116(-)$1	270	202	233	23.1045
GAUCAUUGCUCCUUCUCACCUCCUGCCAUGA	chr1:54497256-54497551(-)$1	295	13	44	20.2823
UUUUUAAUUCCCUACAGUUUUAUGGGUGUUA	chr5:135514184-135514420(+)$1	236	52	83	21.0161
CUUCCAGUGAAUGUGAACUUCUUUUCCCUGU	chr4:77231322-77231569(+)$1	247	54	85	24.1187
ACUCUUUCUGACUACAGCAUCCAGAAAGAGU	chr17:21731462-21731717(+)$1	255	81	112	23.4749
CGUGAGAAGACCAUUCUGCCACUUCUUUUGA	chr10:104846801-104847042(-)$1	241	163	194	21.5275
AGGGGCUGGUUUGUUUUUUUUUUCCCCCCCA	chr17:1553826-1554094(-)$1	268	176	207	22.1783
AAAUGUAGUGUUUCAUUUUGUAUGCAUUAAA	chr12:42480761-42481001(-)$1	240	93	124	21.0045
UCGUAAGUAUUUUAUUAACUUUGCUUUUGUA	chr7:98930857-98931096(+)$1	239	181	212	23.2085
UGGCUGCAUUUCUCUCUUUCUUUUGUAGGUG	chr10:74834534-74834780(-)$1	246	79	110	21.5398
UUCCUGUCCGGCCCCAAACUAAUGCUUUGAU	chr5:157214862-157215103(-)$1	241	175	206	20.6274
GUCAUUGUUAAUCUAAGAAUAAAAACACUGA	chr15:52839489-52839907(-)$1	418	63	94	22.9657
CUUUUCCUAUAUUUUGAAUUUUUAGGACAAG	chr14:78182080-78182324(+)$1	244	9	40	22.9861
UAGAAGAUUAGUUAACAGAAUCGAAAAUUUU	chr18:48700833-48701109(-)$1	276	232	263	23.5776
AGUUUCCUCCCAGAAGAUGAAAAGAGGGAGC	chr20:43248837-43249097(-)$1	260	76	107	25.4312
GAUCUUUUUAAAGAACAAUGGGAAAAACAAG	chr5:138253328-138253595(+)$1	267	165	196	24.1588
CUCUUGUUUGGCUUACUGAUAACAGAUAAAG	chr11:122929670-122929958(-)$1	288	208	239	25.0341
UCUAAUUUCAUACCAAAUACCUGAUCAAUAG	chr1:90184033-90184311(+)$1	278	97	128	21.7548
GUUUUAUAUUCUCUCAAAAAUGGUAUUAUCU	chr2:196601638-196601877(+)$1	239	171	202	22.4382

#DB
(((((.((((............)))).)).)	chr12:49666174-49666609(+)$1	1	318	349	23.0143
((((((((((((...........))).))))	chr1:27182053-27182305(+)$1	1	19	50	23.0803
((((.(((((............))))).)))	chr10:23730106-23730396(+)$1	1	129	160	23.9308
....(((((............)))))...))	chr6:24705964-24706213(-)$1	1	135	166	23.7487
(((.((((((...........)))))).)))	chr13:46700508-46700747(-)$1	1	39	70	21.6912
..(((((((.............)))))))(.	chr12:58118880-58119132(-)$1	1	112	143	21.5588
((((..(((..............)))..)))	chr1:150720163-150720456(-)$1	1	21	52	25.0993
(((...((((............)))).))))	chr2:208476653-208476895(+)$1	1	130	161	24.6113
(.(((((((((...........)))))))))	chr16:83845087-83845380(+)$1	1	166	197	22.8439
(((((((((................)).)).	chr6:116579623-116579879(-)$1	1	75	106	23.2193
((((.(((................))).)))	chr5:172461744-172461989(+)$1	1	199	230	25.1944
(((...(((.............)))....))	chr20:4836030-4836270(-)$1	1	45	76	23.7309
..(((((((...............)))))))	chr8:11683467-11683731(+)$1	1	140	171	22.8754
(((((((((................))))))	chr19:34922701-34922940(+)$1	1	198	229	26.7272
(.(((((((.............))))))).)	chr17:7363246-7363507(-)$1	1	152	183	23.7615
(((...(((............)))....)))	chr12:56693856-56694096(-)$1	1	69	100	23.6038
.((((((.(................).))))	chr5:179157788-179158027(+)$1	1	196	227	25.3213
(((...(((..................))))	chr12:48437718-48437961(-)$1	1	71	102	18.4042
(.(((((((..............))).))))	chr12:4409177-4409416(+)$1	1	80	111	22.2269
(((((...................)))))))	chr19:10800318-10800612(+)$1	1	148	179	18.3463
))((((((.((............)).)))))	chr17:58143539-58143778(-)$1	1	68	99	22.3202
((((.((((..............)))).)))	chr19:8376226-8376471(-)$1	1	184	215	23.3392
((((((((.(............).)))))))	chr6:163994059-163994329(+)$1	1	52	83	24.3137
(((((((.(((............))).))))	chr12:118853418-118853676(+)$1	1	116	147	22.8524
...((((((................))))))	chr10:72183524-72183767(+)$1	1	127	158	21.9070
((((((((.((............)).)))))	chr2:172604755-172605008(+)$1	1	20	51	24.6677
)))((((((((...........))))).)))	chr11:77780796-77781046(-)$1	1	208	239	22.0734
(((((((((............))))))..))	chr4:152629087-152629325(-)$1	1	41	72	22.2110
.(((.((((((............)))))).)	chr8:56985641-56985922(-)$1	1	51	82	23.0486
(((((((((................))))).	chr8:101930780-101931108(-)$1	1	177	208	25.0805
((((((((....................)))	chr6:111620394-111620633(-)$1	1	2	33	18.9696
(((((((((((............))))))))	chr5:174936046-174936311(+)$1	1	21	52	25.0769
.(((((((................)))))))	chr1:70700306-70700549(+)$1	1	96	127	26.1351
(((((((((..............))))))).	chr4:39783408-39783662(+)$1	1	45	76	24.6819
.(.(((((...............))))).).	chr2:216209437-216209684(+)$1	1	190	221	21.5974
.((((.((((.............))))))))	chr17:22022553-22022808(+)$1	1	22	53	20.6701
(((((((((............))))))...)	chr7:63981289-63981583(-)$1	1	233	264	23.3690
(((((((((...............)))))))	chr19:6413539-6413823(-)$1	1	164	195	23.2343
((((((..(................)..)))	chr8:103661642-103661913(-)$1	1	45	76	25.8321
)))(((..(................)..)))	chr4:26432418-26432696(+)$1	1	112	143	25.1869
((((((.((..............)).)))))	chr1:32663220-32663507(+)$1	1	49	80	24.5519
(((((((((..............))))))))	chr11:118319554-118319793(+)$1	1	93	124	25.4312
(((((((((................))))).	chr17:27586587-27586849(-)$1	1	28	59	24.7780
(((((.((((............)))).))))	chr19:6440846-6441116(-)$1	1	202	233	23.1045
((((((.((...............)).))))	chr1:54497256-54497551(-)$1	1	13	44	20.2823
(...((((.(((...........))).))))	chr5:135514184-135514420(+)$1	1	52	83	21.0161
((..(((.(((............))).))).	chr4:77231322-77231569(+)$1	1	54	85	24.1187
((((((((((...........))))))))))	chr17:21731462-21731717(+)$1	1	81	112	23.4749
((.((((((............)))))).)).	chr10:104846801-104847042(-)$1	1	163	194	21.5275
.((((..((..............))))))..	chr17:1553826-1554094(-)$1	1	176	207	22.1783
(....((((((............))))))..	chr12:42480761-42481001(-)$1	1	93	124	21.0045
....(((((............)))))..)))	chr7:98930857-98931096(+)$1	1	181	212	23.2085
((.(((((...............))))).))	chr10:74834534-74834780(-)$1	1	79	110	21.5398
))((((((.(((...........)))..)))	chr5:157214862-157215103(-)$1	1	175	206	20.6274
((((.((((..............)))).)))	chr15:52839489-52839907(-)$1	1	63	94	22.9657
(((((((((.............))))).)))	chr14:78182080-78182324(+)$1	1	9	40	22.9861
.((((((((................))))))	chr18:48700833-48701109(-)$1	1	232	263	23.5776
(((((((((..............))))))))	chr20:43248837-43249097(-)$1	1	76	107	25.4312
(((.(((((.............)))))...)	chr5:138253328-138253595(+)$1	1	165	196	24.1588
((((((((((............))))).)))	chr11:122929670-122929958(-)$1	1	208	239	25.0341
((((...(((...........)))....)))	chr1:90184033-90184311(+)$1	1	97	128	21.7548
(....(((((...........)))))....)	chr2:196601638-196601877(+)$1	1	171	202	22.4382

#PSSM
i : 0.17	f : 0.11	= : 0.09	! : 0.09	e : 0.08	c : 0.08	g : 0.06	d : 0.06	: : 0.04	# : 0.03	F : 0.03	h : 0.03	b : 0.03	I : 0.01	G : 0.01	[ : 0.01	
i : 0.12	d : 0.11	f : 0.11	= : 0.09	g : 0.09	e : 0.08	c : 0.08	# : 0.06	: : 0.04	h : 0.04	[ : 0.03	! : 0.01	G : 0.01	a : 0.01	" : 0.01	b : 0.01	F : 0.01	
g : 0.16	i : 0.14	d : 0.12	f : 0.11	= : 0.09	e : 0.09	# : 0.06	c : 0.06	[ : 0.04	h : 0.03	: : 0.01	" : 0.01	! : 0.01	
f : 0.16	i : 0.14	g : 0.12	d : 0.11	e : 0.09	" : 0.08	# : 0.06	c : 0.06	= : 0.04	[ : 0.03	h : 0.03	b : 0.01	! : 0.01	
i : 0.14	e : 0.14	f : 0.14	g : 0.11	d : 0.09	[ : 0.08	" : 0.08	c : 0.06	= : 0.04	# : 0.03	b : 0.01	! : 0.01	h : 0.01	
e : 0.19	f : 0.16	i : 0.12	g : 0.09	" : 0.08	c : 0.08	d : 0.08	[ : 0.04	= : 0.04	! : 0.03	b : 0.01	^ : 0.01	h : 0.01	
e : 0.20	f : 0.16	d : 0.11	i : 0.11	c : 0.11	g : 0.09	= : 0.04	! : 0.04	[ : 0.03	b : 0.01	^ : 0.01	h : 0.01	" : 0.01	
e : 0.19	f : 0.14	d : 0.11	i : 0.11	c : 0.11	g : 0.09	b : 0.06	[ : 0.04	= : 0.04	! : 0.03	^ : 0.01	h : 0.01	
e : 0.16	c : 0.12	f : 0.11	d : 0.09	i : 0.09	[ : 0.08	g : 0.06	b : 0.06	a : 0.04	y : 0.03	^ : 0.03	= : 0.03	x : 0.03	h : 0.01	
y : 0.17	w : 0.14	c : 0.09	u : 0.09	v : 0.08	x : 0.08	d : 0.06	e : 0.06	f : 0.04	^ : 0.04	b : 0.03	= : 0.03	i : 0.01	a : 0.01	
u : 0.19	y : 0.17	w : 0.14	v : 0.09	c : 0.08	x : 0.08	t : 0.06	^ : 0.04	b : 0.03	f : 0.03	i : 0.01	e : 0.01	= : 0.01	
u : 0.30	y : 0.17	w : 0.14	t : 0.09	v : 0.09	x : 0.08	c : 0.04	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.30	y : 0.17	t : 0.14	w : 0.14	v : 0.09	x : 0.08	^ : 0.04	
u : 0.20	y : 0.17	w : 0.14	v : 0.09	t : 0.08	x : 0.08	f : 0.06	e : 0.04	^ : 0.04	c : 0.03	= : 0.01	
y : 0.17	w : 0.14	e : 0.12	u : 0.11	x : 0.08	f : 0.06	d : 0.04	t : 0.04	c : 0.04	^ : 0.04	g : 0.03	i : 0.01	a : 0.01	v : 0.01	= : 0.01	
y : 0.17	c : 0.16	e : 0.16	d : 0.09	f : 0.09	b : 0.06	g : 0.04	i : 0.04	x : 0.04	^ : 0.04	= : 0.03	] : 0.01	
e : 0.16	c : 0.14	y : 0.14	g : 0.11	d : 0.09	f : 0.09	b : 0.08	i : 0.06	4 : 0.03	^ : 0.03	= : 0.03	
e : 0.19	c : 0.12	d : 0.11	f : 0.11	g : 0.11	i : 0.08	4 : 0.04	a : 0.04	] : 0.04	b : 0.03	^ : 0.03	= : 0.03	h : 0.01	
] : 0.16	e : 0.14	f : 0.12	g : 0.11	i : 0.09	2 : 0.08	4 : 0.06	d : 0.06	= : 0.04	^ : 0.03	3 : 0.01	b : 0.01	c : 0.01	h : 0.01	
] : 0.16	i : 0.11	g : 0.11	2 : 0.09	f : 0.09	d : 0.08	e : 0.08	= : 0.06	4 : 0.06	3 : 0.04	c : 0.03	b : 0.01	^ : 0.01	h : 0.01	
i : 0.14	g : 0.12	f : 0.12	d : 0.12	e : 0.11	c : 0.09	= : 0.06	b : 0.04	3 : 0.04	4 : 0.03	] : 0.03	2 : 0.01	h : 0.01	
i : 0.14	e : 0.12	d : 0.12	c : 0.12	g : 0.09	f : 0.09	= : 0.06	] : 0.04	a : 0.03	b : 0.03	3 : 0.03	2 : 0.01	5 : 0.01	h : 0.01	4 : 0.01	
i : 0.16	c : 0.14	d : 0.12	= : 0.09	e : 0.09	g : 0.09	] : 0.09	f : 0.09	[ : 0.01	8 : 0.01	2 : 0.01	5 : 0.01	h : 0.01	

#score	1434.7499593698624
#seq	62
#width	31
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m1_run2.txt

#BEAR
dddd^^^^^^^^^^^^^^^^^^^^^^^^dddd333ddd	chr18:51907450-51907661(+)$1	211	93	131	41.0576
c[ccc^^^^^^^^^^^^^^^^^^^^^^^ccc]cccddd	chr11:118968511-118968734(-)$1	223	99	137	40.4026
eeeee^^^^^^^^^^^^^^^^^^^^^eeeee333bb]g	chr16:29791796-29792013(+)$1	217	13	51	38.5701
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee::eee	chr1:2118280-2118538(-)$1	258	96	134	36.4427
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^eeeee6	chr10:12206660-12206898(+)$1	238	104	142	40.6980
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc22bb44	chr14:81940996-81941217(-)$1	221	65	103	41.7308
ddd^^^^^^^^^^^^^^^^^^^^^^^^^dddd777777	chr10:11374898-11375245(+)$1	347	192	230	39.8955
ggggg^^^^^^^^^^^^^^^^^^^^^^^ggggggg]ff	chr5:127524702-127524923(+)$1	221	69	107	39.3437
ccccc^^^^^^^^^^^^^^^^^^^^^^^ccc]cccddd	chr2:202037117-202037343(+)$1	226	161	199	40.2487
eeeee^^^^^^^^^^^^^^^^^^^^^^^^eeeee:hhh	chr12:60173364-60173577(+)$1	213	78	116	38.5905
b[ccc^^^^^^^^^^^^^^^^^^^^^^^ccc333bb]d	chr12:118470826-118471055(-)$1	229	84	122	41.5029
fffff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chrX:63409240-63409502(-)$1	262	211	249	42.5954
b^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^bb]c	chr5:154199194-154199426(-)$1	232	108	146	42.5760
hhhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr17:26521907-26522157(+)$1	250	98	136	41.5136
fffff^^^^^^^^^^^^^^^^^^^^^^^^ffffff22c	chr11:47639062-47639295(-)$1	233	174	212	39.4017
%eeeee^^^^^^^^^^^^^^^^^^^^eeeee4444ccc	chr22:22116462-22116806(-)$1	344	157	195	37.2743
^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd333gggg	chr3:195242664-195242952(-)$1	288	95	133	40.6730
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc333ffff	chr21:34968256-34968500(-)$1	244	107	145	41.8341
cc!!dddd^^^^^^^^^^^^^^^^^^^dddd22ccc33	chrX:53405521-53405775(-)$1	254	176	214	34.9593
Ddddd^^^^^^^^^^^^^^^^^^^^^^^dddd:::::b	chr1:66838904-66839139(+)$1	235	53	91	35.1861
!eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee]dddd	chr12:56347479-56347875(+)$1	396	330	368	38.6634
ffffff^^^^^^^^^^^^^^^^^^^^^^ffffff::::	chr20:43707465-43707707(+)$1	242	138	176	35.1119
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr10:88494695-88494958(+)$1	263	138	176	43.3388
eee^^^^^^^^^^^^^^^^^^^^^^^^^eeeee77777	chr15:38782100-38782399(-)$1	299	253	291	39.8576
d^^^^^^^^^^^^^^^^^^^^^^^^^^^dddd4444ee	chr13:30779646-30779896(-)$1	250	79	117	41.9762
ffffff^^^^^^^^^^^^^^^^^^^^ffffff22cccb	chr2:202035543-202035843(+)$1	300	104	142	35.5909
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ccc22cccbb	chr3:113370817-113371125(-)$1	308	168	206	40.7904
ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc333eeee	chr5:49693207-49693472(-)$1	265	136	174	41.9430
eee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr1:167887188-167887413(-)$1	225	137	175	43.2744
=====^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^==	chrX:49858124-49858345(+)$1	221	137	175	42.9375
ffffff^^^^^^^^^^^^^^^^^^^ffffff333eeee	chr8:37701205-37701418(+)$1	213	51	89	34.8895
fffff[ccc^^^^^^^^^^^^^^^^^^^ccc]ffffff	chr17:76968840-76969114(-)$1	274	99	137	34.0068
eeeee^^^^^^^^^^^^^^^^^^^^^^^^^^^^^eeee	chr13:40363626-40363871(+)$1	245	133	171	41.9958
b[a[ccc^^^^^^^^^^^^^^^^^^^^^cccabbeeee	chr3:128532219-128532615(+)$1	396	69	107	37.2190
ffffff^^^^^^^^^^^^^^^^^^^^^^ffffffeeee	chr10:97631997-97632276(+)$1	279	36	74	37.7327
fffff^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ff	chr1:67452956-67453250(+)$1	294	118	156	42.3015
eeeee^^^^^^^^^^^^^^^^^^^^^^eeeee4444ff	chr9:100672626-100672870(-)$1	244	95	133	40.0340
iiiii^^^^^^^^^^^^^^^^^^^^^^^^^^^^^iiii	chr4:175852046-175852261(+)$1	215	22	60	41.8589
!!ccc[bb^^^^^^^^^^^^^^^^^^^bb]ccc22ddd	chr9:123578409-123578629(-)$1	220	34	72	34.5693
d[ccc^^^^^^^^^^^^^^^^^^ccc]dddd>>>>>>>	chr22:19881656-19881936(-)$1	280	100	138	33.7350
c[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr5:160716686-160716931(-)$1	245	106	144	43.1973
ggg^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^gg	chr5:176929253-176929480(-)$1	227	31	69	43.2967
=====^^^^^^^^^^^^^^^^^^^^^^^^^========	chr7:17384082-17384320(+)$1	238	148	186	41.1144
"dddd^^^^^^^^^^^^^^^^^^^^^^^dddd4444ee	chr14:53109232-53109481(-)$1	249	47	85	41.1619
e[ccc^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr10:89726101-89726346(+)$1	245	95	133	43.1418
cccccc^^^^^^^^^^^^^^^^^^ccc]ccc22ggggg	chr9:100848859-100849157(-)$1	298	168	206	33.9566
^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff333d	chr2:7182181-7182436(+)$1	255	70	108	40.6027
!!dddd^^^^^^^^^^^^^^^^^^^^^^^^^^dddd]c	chr1:113214050-113214296(+)$1	246	113	151	39.7847
dddd^^^^^^^^^^^^^^^^^^^^^^^^dddd::::::	chr1:193221799-193222060(+)$1	261	69	107	35.8803
d[ccc^^^^^^^^^^^^^^^^^^^^^^^^^ccc]dddd	chr10:112658645-112658901(+)$1	256	119	157	40.9258
gg[ccc^^^^^^^^^^^^^^^^^^^^^^ccc]gggggg	chr11:5731456-5731693(+)$1	237	185	223	39.1519
[eeeeea^^^^^^^^^^^^^^^^^^^^^a]eeeeeddd	chr11:6504584-6505022(+)$1	438	120	158	37.5467
f^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ffffff]c	chr2:206860896-206861218(-)$1	322	100	138	40.9287
=====^^^^^^^^^^^^^^^^^^^^^^^^^========	chr1:87025884-87026099(+)$1	215	123	161	41.1144
hhhhh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr20:37547433-37547783(+)$1	350	214	252	41.5136
d^^^^^^^^^^^^^^^^^^^^^^^^^^dddd333ccc]	chr11:3379316-3379560(-)$1	244	99	137	40.7518
ddd^^^^^^^^^^^^^^^^^^^^^^^^^dddd333ggg	chr15:52357674-52357904(+)$1	230	98	136	41.5368
d!!bb^^^^^^^^^^^^^^^^^^^^^^^^bb22dddd:	chr17:15931012-15931253(+)$1	241	201	239	38.7968
iiiii^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr4:175240780-175241023(+)$1	243	98	136	42.7729
ddd^^^^^^^^^^^^^^^^^^^^^^^^^dddd]a333d	chr6:83874758-83875025(-)$1	267	153	191	41.2355
eee^^^^^^^^^^^^^^^^^^^^^^^eeeee333bb22	chr13:52731500-52731755(-)$1	255	110	148	38.7760
!eeeee^^^^^^^^^^^^^^^^^^^^^eeeee22ffff	chr15:75759580-75759827(-)$1	247	189	227	37.8092
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^d	chr12:102792773-102793026(-)$1	253	104	142	43.4319
ggggg^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^	chr1:59121967-59122248(-)$1	281	110	148	42.8395
##dddd^^^^^^^^^^^^^^^^^^^^^dddd333gggg	chr1:19665760-19666060(-)$1	300	241	279	38.7144
ffffff^^^^^^^^^^^^^^^^^^^^^ffffff]bb::	chr3:189675122-189675370(-)$1	248	48	86	35.2234
#dddd^^^^^^^^^^^^^^^^^^^^^^^^^ddddffff	chr2:190314439-190314674(+)$1	235	103	141	39.7880
dd^^^^^^^^^^^^^^^^^^^^^^^^^^dddd999999	chr12:74934264-74934479(+)$1	215	87	125	39.1421
$$dddd^^^^^^^^^^^^^^^^^^^^^dddd666666b	chr6:158518341-158518565(+)$1	224	49	87	36.9689

#otherMatches

#Seq PSSM
GAAGUUAUUAUUCUCCCAUUUCCUUUUUCUUUUUUUGU	chr18:51907450-51907661(+)$1	211	93	131	41.0576
GUGUUCAACUUCCUCUACUCACUGCCUCAGCUCCUGCA	chr11:118968511-118968734(-)$1	223	99	137	40.4026
UGGCUCAAUAAAAAAAAUAUGGUUAAGGCUAGUCUGUG	chr16:29791796-29792013(+)$1	217	13	51	38.5701
CAGGAUUUUUCAAACCACACUUCAAUACAUCCUUCACU	chr1:2118280-2118538(-)$1	258	96	134	36.4427
CAACAUUCAAAACACUUCAUAUUGCCCCCACUUGUUGA	chr10:12206660-12206898(+)$1	238	104	142	40.6980
AUUGUUAAUGUUCUGAAUUUCCUUUUCUUGGCUUGUUU	chr14:81940996-81941217(-)$1	221	65	103	41.7308
CUCAACCCACCUGCAUGCAUCUCCCCCAGAGGAAACAC	chr10:11374898-11375245(+)$1	347	192	230	39.8955
AUGUAAGAAGCUUUUCACUUAAAAAAAAUGCAUUACUU	chr5:127524702-127524923(+)$1	221	69	107	39.3437
agcugccacucuaauccuccucuucccccagccucuag	chr2:202037117-202037343(+)$1	226	161	199	40.2487
AGAGAAACUAACAUUUAACAAGAAUCACAUCUCUGAUU	chr12:60173364-60173577(+)$1	213	78	116	38.5905
UAGUUAUCUAAUCAAGACACCUCAUUCAAACAAAACCU	chr12:118470826-118471055(-)$1	229	84	122	41.5029
UAGUGCCCCCUGCCCCUUUCCCCCAAUGAAUGAUGAAC	chrX:63409240-63409502(-)$1	262	211	249	42.5954
AACACACACACAAACAUACACACACCAAACACUCUGAG	chr5:154199194-154199426(-)$1	232	108	146	42.5760
UGUUcacacacacacacacacacacacacacacacaaa	chr17:26521907-26522157(+)$1	250	98	136	41.5136
CUGUCAAAACAGCCCCACUGAUAAUAUUAGACAGAACG	chr11:47639062-47639295(-)$1	233	174	212	39.4017
CUUAGGUCUCAAAUAUUCUGUCAAACCCUAACAAAGAA	chr22:22116462-22116806(-)$1	344	157	195	37.2743
AUACGCACACAAUCUUCUACCUUUUAAAGGAUCAUUAA	chr3:195242664-195242952(-)$1	288	95	133	40.6730
CACACCCCUACCACUUCACCACCAGGAUUCUAGAUUGG	chr21:34968256-34968500(-)$1	244	107	145	41.8341
GUCCAUUCUAAUUACCCAAAUAUGCAUGAAUUCAUUCU	chrX:53405521-53405775(-)$1	254	176	214	34.9593
AAGGAUACACUUCUAACCACAUUUUACUUCCUUCCCCU	chr1:66838904-66839139(+)$1	235	53	91	35.1861
AAGUGGUACACUUCCUUCUUUUAUACCUUCACUCCUUA	chr12:56347479-56347875(+)$1	396	330	368	38.6634
cuugaaaaauaaaaaguaccaaaauucauucaagaaga	chr20:43707465-43707707(+)$1	242	138	176	35.1119
acacacacacacacacacacacacGAUCAUUAAAAAGU	chr10:88494695-88494958(+)$1	263	138	176	43.3388
CCUAUUAAACAUGACGUUAUCCAAUUGCAGGUCAACUU	chr15:38782100-38782399(-)$1	299	253	291	39.8576
gcccagccCUAACUUUUAAUGUACAUcacacacacacu	chr13:30779646-30779896(-)$1	250	79	117	41.9762
UUAUUUACUCAAUAUUAAUUACUUACAAAUAACCUCAC	chr2:202035543-202035843(+)$1	300	104	142	35.5909
acucucucucucucucucucucucucCAGUGGCUGUUA	chr3:113370817-113371125(-)$1	308	168	206	40.7904
UUCUUCCAUUUUACCACCACUAACCAUUGAGGCUCAUA	chr5:49693207-49693472(-)$1	265	136	174	41.9430
AACAUAUGUACAUAAAAGAACACACAAAUUCAAGAAGU	chr1:167887188-167887413(-)$1	225	137	175	43.2744
CAGAGCCACCAUCAUCAUUCCAACCACUAUUUCAUUUU	chrX:49858124-49858345(+)$1	221	137	175	42.9375
GAAGAAAAAAAAAAGCUUUGUAUUAUUCUUCCACAUAU	chr8:37701205-37701418(+)$1	213	51	89	34.8895
GGGCUUUGUCCUCCUCCCCUCUUCAAAAGCACAGCCCC	chr17:76968840-76969114(-)$1	274	99	137	34.0068
ugacucauuccauaaccauuuuucccaccaaaccaguc	chr13:40363626-40363871(+)$1	245	133	171	41.9958
GAGUCCUUCACAAACCAAGAACACACGUAGGCCUUCAA	chr3:128532219-128532615(+)$1	396	69	107	37.2190
aaagucaaccuccccaucagacauucaaggcuuucaau	chr10:97631997-97632276(+)$1	279	36	74	37.7327
AUUCCCACCCCCAACAAAGCACUAUCAUUUUCAUUUGG	chr1:67452956-67453250(+)$1	294	118	156	42.3015
UACAGAAUAACCAACAUACACCAAACACUGUGUCCCAG	chr9:100672626-100672870(-)$1	244	95	133	40.0340
CUGAAUUUAAGCUUUAUCUGUCUAAUUAAUAUUCUUCA	chr4:175852046-175852261(+)$1	215	22	60	41.8589
auaaguuguacaaccaucaccaccauccaucuucagaa	chr9:123578409-123578629(-)$1	220	34	72	34.5693
aacuuuuccauuaucuccaaacugagcucuguccccau	chr22:19881656-19881936(-)$1	280	100	138	33.7350
acagucacacacacacacacacacacacucaaacacac	chr5:160716686-160716931(-)$1	245	106	144	43.1973
uguccccacucucuccugcgcccauucauccuaccagc	chr5:176929253-176929480(-)$1	227	31	69	43.2967
AAAAAUGACACCAUCuuuuauucuuuuuuuuuuuuuuu	chr7:17384082-17384320(+)$1	238	148	186	41.1144
agagcucucuuacccagauucacuaauuguucauacgu	chr14:53109232-53109481(-)$1	249	47	85	41.1619
AUCAGUCAACAACUUACACUUAUUUUACUAGUUUUCAA	chr10:89726101-89726346(+)$1	245	95	133	43.1418
GCAUAGUUCCACCUCCACACCUCUCUGCUGCCAGCACA	chr9:100848859-100849157(-)$1	298	168	206	33.9566
UUGUCCAUUUCCUAUAUAAAUACCAGCAAGAUCACUCU	chr2:7182181-7182436(+)$1	255	70	108	40.6027
UCAUACUAUCCAUCCAUACCACACUAUCUUCUGUAUCA	chr1:113214050-113214296(+)$1	246	113	151	39.7847
GCUGUUUAUUCUAAAAAACAAAAAUUUUCAGCCACUCC	chr1:193221799-193222060(+)$1	261	69	107	35.8803
UCAUUCCAUCAUCCUUAAAUUCUGUUACCAAAUAAUGG	chr10:112658645-112658901(+)$1	256	119	157	40.9258
AUCUAGCAAAGUACAUAAGAAUCUAUCACUAAGUAAUG	chr11:5731456-5731693(+)$1	237	185	223	39.1519
CUUUUCCAUUCCUUCAUUCAAACUGCUAGAGAAAAACA	chr11:6504584-6505022(+)$1	438	120	158	37.5467
UUCCACUAUUCUUCAUCUUCACCACCUUCUACUGGUCA	chr2:206860896-206861218(-)$1	322	100	138	40.9287
CUUGGAAAAAAACAAAAUGAAUAUGGACCACCAGGUAG	chr1:87025884-87026099(+)$1	215	123	161	41.1144
cacacacacacacacauauacacacacacacaAGCUCG	chr20:37547433-37547783(+)$1	350	214	252	41.5136
gcaaaaaacaaaccccccuucacugaucccuccaguaa	chr11:3379316-3379560(-)$1	244	99	137	40.7518
AGUAAACUAUUCUUAAUAAAACUCACUCACUGUUUAUA	chr15:52357674-52357904(+)$1	230	98	136	41.5368
CCUGUCUUCUCUUACUUUACUUUAUCAAUACCUGGCAA	chr17:15931012-15931253(+)$1	241	201	239	38.7968
GGACUAAAAAUCAACUCAAUAUAUCAUACAUUUACACU	chr4:175240780-175241023(+)$1	243	98	136	42.7729
CCUAAAUCAAACUGCAAUUCAACAAUAAAGGGCGUACA	chr6:83874758-83875025(-)$1	267	153	191	41.2355
CAAACAAAAAACCACACACACAACCAUUGUgccuuucc	chr13:52731500-52731755(-)$1	255	110	148	38.7760
UUAUACUGUAAUAAGCUCUUUGAAUGUGUAUAUUAUUA	chr15:75759580-75759827(-)$1	247	189	227	37.8092
acacacacacacacacacacacacacacacacacacaU	chr12:102792773-102793026(-)$1	253	104	142	43.4319
AAGGGAAACAUCCUACUACCUUUCUUUCCUCUCCAUUU	chr1:59121967-59122248(-)$1	281	110	148	42.8395
CGCUCUCAGUUCUCUCCACAUUUCCAUAGAGACCGUGU	chr1:19665760-19666060(-)$1	300	241	279	38.7144
GGUUUUUCAUCAUUUCAUGUAUCUAUCAAAGCCCAGUU	chr3:189675122-189675370(-)$1	248	48	86	35.2234
UACUCCAACAUUUUUACAUUCCUCUUCUCUGAGUCCAU	chr2:190314439-190314674(+)$1	235	103	141	39.7880
GCAUUAACUUAAAAAAAAUCAAACCUUGGCAAGAGCUA	chr12:74934264-74934479(+)$1	215	87	125	39.1421
AUAUGUUUGUCUAUAUUUUUUGCCUAUACAUUUUUCCC	chr6:158518341-158518565(+)$1	224	49	87	36.9689

#DB
((((........................))))...)))	chr18:51907450-51907661(+)$1	1	93	131	41.0576
(.(((.......................))).))))))	chr11:118968511-118968734(-)$1	1	99	137	40.4026
(((((.....................)))))...)).)	chr16:29791796-29792013(+)$1	1	13	51	38.5701
.(((((......................)))))..(((	chr1:2118280-2118538(-)$1	1	96	134	36.4427
(((((...........................))))).	chr10:12206660-12206898(+)$1	1	104	142	40.6980
.............................)))..))..	chr14:81940996-81941217(-)$1	1	65	103	41.7308
(((.........................))))......	chr10:11374898-11375245(+)$1	1	192	230	39.8955
(((((.......................))))))).))	chr5:127524702-127524923(+)$1	1	69	107	39.3437
(((((.......................))).)))(((	chr2:202037117-202037343(+)$1	1	161	199	40.2487
(((((........................))))).(((	chr12:60173364-60173577(+)$1	1	78	116	38.5905
(.(((.......................)))...)).)	chr12:118470826-118471055(-)$1	1	84	122	41.5029
(((((.................................	chrX:63409240-63409502(-)$1	1	211	249	42.5954
(.................................)).)	chr5:154199194-154199426(-)$1	1	108	146	42.5760
(((((.................................	chr17:26521907-26522157(+)$1	1	98	136	41.5136
(((((........................))))))..)	chr11:47639062-47639295(-)$1	1	174	212	39.4017
.(((((....................)))))....)))	chr22:22116462-22116806(-)$1	1	157	195	37.2743
...........................))))...))))	chr3:195242664-195242952(-)$1	1	95	133	40.6730
............................)))...))))	chr21:34968256-34968500(-)$1	1	107	145	41.8341
((..((((...................))))..)))..	chrX:53405521-53405775(-)$1	1	176	214	34.9593
(((((.......................)))).....(	chr1:66838904-66839139(+)$1	1	53	91	35.1861
.(((((......................))))).))))	chr12:56347479-56347875(+)$1	1	330	368	38.6634
((((((......................))))))....	chr20:43707465-43707707(+)$1	1	138	176	35.1119
....................................))	chr10:88494695-88494958(+)$1	1	138	176	43.3388
(((.........................))))).....	chr15:38782100-38782399(-)$1	1	253	291	39.8576
(...........................))))....))	chr13:30779646-30779896(-)$1	1	79	117	41.9762
((((((....................))))))..))))	chr2:202035543-202035843(+)$1	1	104	142	35.5909
............................)))..)))))	chr3:113370817-113371125(-)$1	1	168	206	40.7904
(((.........................)))...))))	chr5:49693207-49693472(-)$1	1	136	174	41.9430
(((.................................))	chr1:167887188-167887413(-)$1	1	137	175	43.2744
(((((...............................))	chrX:49858124-49858345(+)$1	1	137	175	42.9375
((((((...................))))))...))))	chr8:37701205-37701418(+)$1	1	51	89	34.8895
(((((.(((...................))).))))))	chr17:76968840-76969114(-)$1	1	99	137	34.0068
(((((.............................))))	chr13:40363626-40363871(+)$1	1	133	171	41.9958
(.(.(((.....................))))))))))	chr3:128532219-128532615(+)$1	1	69	107	37.2190
((((((......................))))))))))	chr10:97631997-97632276(+)$1	1	36	74	37.7327
(((((...............................))	chr1:67452956-67453250(+)$1	1	118	156	42.3015
(((((......................)))))....))	chr9:100672626-100672870(-)$1	1	95	133	40.0340
(((((.............................))))	chr4:175852046-175852261(+)$1	1	22	60	41.8589
..(((.((...................)).)))..)))	chr9:123578409-123578629(-)$1	1	34	72	34.5693
(.(((..................))).)))).......	chr22:19881656-19881936(-)$1	1	100	138	33.7350
(.(((.................................	chr5:160716686-160716931(-)$1	1	106	144	43.1973
(((.................................))	chr5:176929253-176929480(-)$1	1	31	69	43.2967
(((((.........................))))))))	chr7:17384082-17384320(+)$1	1	148	186	41.1144
.((((.......................))))....))	chr14:53109232-53109481(-)$1	1	47	85	41.1619
(.(((.................................	chr10:89726101-89726346(+)$1	1	95	133	43.1418
((((((..................))).)))..)))))	chr9:100848859-100849157(-)$1	1	168	206	33.9566
............................))))))...)	chr2:7182181-7182436(+)$1	1	70	108	40.6027
..((((..........................)))).)	chr1:113214050-113214296(+)$1	1	113	151	39.7847
((((........................))))......	chr1:193221799-193222060(+)$1	1	69	107	35.8803
(.(((.........................))).))))	chr10:112658645-112658901(+)$1	1	119	157	40.9258
((.(((......................))).))))))	chr11:5731456-5731693(+)$1	1	185	223	39.1519
.((((((.....................).))))))))	chr11:6504584-6505022(+)$1	1	120	158	37.5467
(.............................)))))).)	chr2:206860896-206861218(-)$1	1	100	138	40.9287
(((((.........................))))))))	chr1:87025884-87026099(+)$1	1	123	161	41.1144
(((((.................................	chr20:37547433-37547783(+)$1	1	214	252	41.5136
(..........................))))...))).	chr11:3379316-3379560(-)$1	1	99	137	40.7518
(((.........................))))...)))	chr15:52357674-52357904(+)$1	1	98	136	41.5368
(..((........................))..)))).	chr17:15931012-15931253(+)$1	1	201	239	38.7968
(((((.................................	chr4:175240780-175241023(+)$1	1	98	136	42.7729
(((.........................)))).)...)	chr6:83874758-83875025(-)$1	1	153	191	41.2355
(((.......................)))))...))..	chr13:52731500-52731755(-)$1	1	110	148	38.7760
.(((((.....................)))))..))))	chr15:75759580-75759827(-)$1	1	189	227	37.8092
.....................................)	chr12:102792773-102793026(-)$1	1	104	142	43.4319
(((((.................................	chr1:59121967-59122248(-)$1	1	110	148	42.8395
..((((.....................))))...))))	chr1:19665760-19666060(-)$1	1	241	279	38.7144
((((((.....................)))))).))..	chr3:189675122-189675370(-)$1	1	48	86	35.2234
.((((.........................))))))))	chr2:190314439-190314674(+)$1	1	103	141	39.7880
((..........................))))......	chr12:74934264-74934479(+)$1	1	87	125	39.1421
..((((.....................))))......)	chr6:158518341-158518565(+)$1	1	49	87	36.9689

#PSSM
d : 0.15	f : 0.14	e : 0.13	^ : 0.10	c : 0.08	g : 0.05	! : 0.05	b : 0.04	= : 0.04	h : 0.02	i : 0.02	# : 0.02	: : 0.01	% : 0.01	D : 0.01	" : 0.01	[ : 0.01	$ : 0.01	
e : 0.18	^ : 0.15	d : 0.13	f : 0.13	[ : 0.10	g : 0.05	c : 0.05	= : 0.04	! : 0.04	h : 0.02	i : 0.02	# : 0.01	$ : 0.01	
e : 0.18	^ : 0.17	d : 0.15	c : 0.14	f : 0.13	g : 0.04	= : 0.04	h : 0.02	! : 0.02	i : 0.02	a : 0.01	[ : 0.01	
^ : 0.28	c : 0.14	e : 0.14	f : 0.13	d : 0.11	= : 0.04	g : 0.02	h : 0.02	i : 0.02	! : 0.01	[ : 0.01	b : 0.01	
^ : 0.31	c : 0.15	e : 0.14	f : 0.13	d : 0.10	= : 0.04	g : 0.02	h : 0.02	i : 0.02	b : 0.01	
^ : 0.72	e : 0.07	f : 0.07	d : 0.05	c : 0.04	[ : 0.02	
^ : 0.92	c : 0.02	d : 0.01	b : 0.01	a : 0.01	
^ : 0.95	d : 0.01	c : 0.01	b : 0.01	
^ : 0.98	c : 0.01	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.99	
^ : 0.98	c : 0.01	
^ : 0.97	c : 0.02	
^ : 0.95	c : 0.02	f : 0.01	
^ : 0.89	e : 0.04	f : 0.02	] : 0.01	c : 0.01	
^ : 0.76	d : 0.08	e : 0.07	f : 0.04	b : 0.01	] : 0.01	
^ : 0.39	d : 0.21	c : 0.14	e : 0.11	f : 0.08	g : 0.01	b : 0.01	a : 0.01	
^ : 0.33	d : 0.21	c : 0.15	e : 0.13	f : 0.10	] : 0.02	g : 0.01	b : 0.01	
^ : 0.26	d : 0.23	c : 0.18	e : 0.14	f : 0.11	= : 0.02	g : 0.01	b : 0.01	
^ : 0.26	d : 0.14	3 : 0.13	e : 0.10	f : 0.10	] : 0.05	2 : 0.05	c : 0.04	= : 0.02	g : 0.01	4 : 0.01	a : 0.01	> : 0.01	6 : 0.01	
^ : 0.23	3 : 0.15	2 : 0.10	f : 0.10	e : 0.08	c : 0.05	4 : 0.05	g : 0.02	: : 0.02	= : 0.02	d : 0.02	7 : 0.01	b : 0.01	> : 0.01	] : 0.01	9 : 0.01	6 : 0.01	
^ : 0.23	3 : 0.15	f : 0.08	c : 0.05	2 : 0.05	4 : 0.05	: : 0.04	e : 0.04	g : 0.04	] : 0.04	d : 0.04	7 : 0.02	= : 0.02	b : 0.01	> : 0.01	a : 0.01	9 : 0.01	6 : 0.01	
^ : 0.18	e : 0.10	c : 0.08	b : 0.08	f : 0.08	: : 0.07	g : 0.07	3 : 0.05	4 : 0.05	d : 0.05	7 : 0.02	= : 0.02	i : 0.01	2 : 0.01	> : 0.01	9 : 0.01	6 : 0.01	
^ : 0.18	d : 0.13	e : 0.10	b : 0.08	c : 0.07	g : 0.07	f : 0.07	: : 0.04	4 : 0.04	7 : 0.02	= : 0.02	3 : 0.02	] : 0.01	h : 0.01	2 : 0.01	i : 0.01	> : 0.01	9 : 0.01	6 : 0.01	
e : 0.15	d : 0.11	^ : 0.11	f : 0.10	g : 0.08	] : 0.07	: : 0.05	c : 0.04	3 : 0.04	= : 0.04	7 : 0.02	2 : 0.02	4 : 0.01	h : 0.01	b : 0.01	i : 0.01	> : 0.01	9 : 0.01	6 : 0.01	
d : 0.15	e : 0.14	g : 0.10	f : 0.10	^ : 0.10	c : 0.07	b : 0.05	: : 0.05	= : 0.04	7 : 0.02	6 : 0.01	4 : 0.01	h : 0.01	3 : 0.01	i : 0.01	> : 0.01	] : 0.01	2 : 0.01	9 : 0.01	

#score	2737.430867535108
#seq	69
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_CDS_m3_run1.txt

#BEAR
dddd[bboooooobb]ddd	chr11:125891170-125891410(-)$1	240	54	73	10.7062
obbddddooooooddddFF	chr1:237013618-237013858(+)$1	240	86	105	10.1527
####cccooooooccc444	chr15:101109398-101109638(-)$1	240	165	184	12.3084
dd[ddddoooooodddd]d	chr2:85769317-85769563(+)$1	246	27	46	11.8259
dd[ddddoooooodddd22	chr1:97243153-97243393(+)$1	240	178	197	11.6062
fff[cccooooooccc]ff	chrX:44929224-44929464(+)$1	240	25	44	12.0559
!!eeeeeooooooeeeee]	chr18:29867197-29867437(-)$1	240	134	153	10.5068
ee[ddddooooooddddee	chr15:58284874-58285114(-)$1	240	216	235	11.7509
fff[cccoooooocccfff	chr21:28210337-28210577(-)$1	240	192	211	11.8912
ggggcccooooooccc22g	chr7:66274024-66274264(+)$1	240	20	39	11.9147
gggggggoooooogggggg	chr1:220206820-220207060(-)$1	240	17	36	11.2066
dd!!cccoooooocccddd	chr16:71961599-71961839(+)$1	240	129	148	12.4233
cffffffooooooffffff	chr1:155921867-155922107(-)$1	240	124	143	10.0035
eeee[bboooooobb]eee	chr7:128637427-128637667(-)$1	240	83	102	10.6241
cccddddoooooodddd66	chr2:114699719-114699959(+)$1	240	101	120	10.9212
gggggggoooooogggggg	chr10:22002655-22002895(+)$1	240	59	78	11.2066
ccc[cccoooooocccccc	chr16:4779905-4780145(-)$1	240	18	37	12.1968
cc[ddddoooooodddd]c	chr14:45400472-45400712(-)$1	240	212	231	12.0629
eee:cccoooooocccbb!	chr1:36499780-36500020(+)$1	240	154	173	10.0039
eeeeebboooooobb]eee	chr17:11998799-11999039(+)$1	240	152	171	10.4865
!bb[cccooooooccc22b	chr16:69727392-69727632(+)$1	240	120	139	11.4415
f"""ddddoooooodddd]	chr1:182853794-182854034(+)$1	240	124	143	10.6064
%bb[cccoooooocccbb6	chr20:25596965-25597205(-)$1	240	40	59	10.1767
cdddd[aooooooa]dddd	chrX:47099145-47099385(+)$1	240	203	222	10.9252
dffffffooooooffffff	chr8:128753048-128753288(+)$1	240	89	108	9.9462
hh!!ddddoooooodddd4	chrX:24094798-24095038(+)$1	240	9	28	10.4014
ee!!ddddoooooodddd4	chr4:122739141-122739381(-)$1	240	180	199	10.6857
gggggggoooooogggggg	chr6:56426117-56426357(-)$1	240	32	51	11.2066
ff"""bboooooobb22ff	chr5:32126484-32126724(-)$1	240	79	98	10.7726
ccc[cccooooooccc]cc	chr19:45593639-45593879(+)$1	240	53	72	12.2733
gggggggoooooogggggg	chr4:26430295-26430535(+)$1	240	82	101	11.2066
ff[ddddooooooddddff	chrX:53621385-53621625(-)$1	240	185	204	11.7765
++++cccooooooccciii	chr21:47690258-47690498(-)$1	240	164	183	9.5006
d"""cccooooooccc22d	chr2:9657963-9658203(-)$1	240	80	99	12.1599
dddd[bboooooobb]ddd	chr12:72026665-72027151(-)$1	486	107	126	10.7062
hhhhcccooooooccc22h	chr8:71495304-71495544(-)$1	240	126	145	10.8552
dddd[bboooooobb]ddd	chr1:154192780-154193020(-)$1	240	202	221	10.7062
ff"""bboooooobbffff	chr2:128283834-128284074(-)$1	240	70	89	10.9033
e"""cccooooooccc666	chr3:132172050-132172290(+)$1	240	86	105	11.1821
gggddddoooooodddd33	chr15:73414790-73415030(+)$1	240	22	41	11.9636
bb[ddddoooooodddd]b	chr16:10850490-10850730(+)$1	240	185	204	11.3542
ddd[cccoooooocccddd	chr6:56418023-56418263(-)$1	240	61	80	12.0011
cc[ddddoooooodddd]c	chr12:49168405-49168645(-)$1	240	136	155	12.0629
=======oooooo======	chr15:67818720-67818960(+)$1	240	125	144	11.6900
dbb[cccooooooccc]bb	chr1:173921093-173921333(-)$1	240	140	159	11.3036
eee[cccooooooccc]ee	chr4:187629191-187629431(-)$1	240	81	100	12.0525
$$$$ddddoooooodddd2	chr1:220335455-220335695(-)$1	240	108	127	9.4853
g"""cccoooooocccggg	chrX:37586989-37587229(+)$1	240	144	163	12.5106
=======oooooo======	chr8:91029285-91029525(+)$1	240	3	22	11.6900
bb!!ddddoooooodddd]	chr14:58831639-58831879(+)$1	240	10	29	10.3536
fff[cccooooooccc]ff	chr2:27693759-27693999(-)$1	240	194	213	12.0559
cc[ddddoooooodddd]c	chr4:77053623-77053863(-)$1	240	31	50	12.0629
eeee[bboooooobb]eee	chr19:58049020-58049260(+)$1	240	157	176	10.6241
[ccc[bboooooobb]ccc	chr2:232673138-232673378(+)$1	240	128	147	10.8403
e!!ddddoooooodddd22	chr17:65174788-65175028(-)$1	240	92	111	11.7817
ff!!cccoooooocccfff	chr11:6416260-6416500(-)$1	240	14	33	12.2738
dddd!!aooooooa22ddd	chr19:38055971-38056211(-)$1	240	145	164	10.3709
b[eeeeeooooooeeeee]	chr1:179886883-179887123(+)$1	240	58	77	10.2142

#otherMatches

#Seq PSSM
GUAGUACUGCAUUGUUCUG	chr11:125891170-125891410(-)$1	240	54	73	10.7062
AACUGGGCUUUAAUCCAAA	chr1:237013618-237013858(+)$1	240	86	105	10.1527
GAUAAGUAAUAAAACUAUG	chr15:101109398-101109638(-)$1	240	165	184	12.3084
CUGUUCAGCAUGAUGAAGA	chr2:85769317-85769563(+)$1	246	27	46	11.8259
UAAAUUAGAGAAAUAAUAA	chr1:97243153-97243393(+)$1	240	178	197	11.6062
UUGAUGGGAAAAGCCAAUA	chrX:44929224-44929464(+)$1	240	25	44	12.0559
CAUCCUGCCCUAUCAGGAC	chr18:29867197-29867437(-)$1	240	134	153	10.5068
GUAUCUGAAAAACCAGGGC	chr15:58284874-58285114(-)$1	240	216	235	11.7509
CGGCAUUGGAAAGAAUUCG	chr21:28210337-28210577(-)$1	240	192	211	11.8912
UGUCUCAGUUGAAUGAACG	chr7:66274024-66274264(+)$1	240	20	39	11.9147
GAAAUGUUGGAAUGCAUUU	chr1:220206820-220207060(-)$1	240	17	36	11.2066
AGGCAACUUUCACGUUUUG	chr16:71961599-71961839(+)$1	240	129	148	12.4233
GCUCUUGACACCCCGAGAG	chr1:155921867-155922107(-)$1	240	124	143	10.0035
AGAAAUUUCAUUUAACUUU	chr7:128637427-128637667(-)$1	240	83	102	10.6241
AUGGGUCAAAAUGGAUUAA	chr2:114699719-114699959(+)$1	240	101	120	10.9212
AAUGAUGUAGCAGUAUCGU	chr10:22002655-22002895(+)$1	240	59	78	11.2066
CAGCGAGCCGGAACUCCUG	chr16:4779905-4780145(-)$1	240	18	37	12.1968
CAAUGUUUUCUAUAAUGAU	chr14:45400472-45400712(-)$1	240	212	231	12.0629
GUAAGAUAUGCUAAUCGCU	chr1:36499780-36500020(+)$1	240	154	173	10.0039
GUAAUGCGGAGUAGUGAUU	chr17:11998799-11999039(+)$1	240	152	171	10.4865
ACUCUCCAUCCCAGGAAca	chr16:69727392-69727632(+)$1	240	120	139	11.4415
UGGUAUCAACCUUAUGAUU	chr1:182853794-182854034(+)$1	240	124	143	10.6064
UCUGUGAUAAAGUUCAAGU	chr20:25596965-25597205(-)$1	240	40	59	10.1767
UAGUCCCAACUCAGUGACU	chrX:47099145-47099385(+)$1	240	203	222	10.9252
CUUGUUGCGGAAACGACGA	chr8:128753048-128753288(+)$1	240	89	108	9.9462
AUUUAUGAUUUCUUUUAUU	chrX:24094798-24095038(+)$1	240	9	28	10.4014
AAAGUAAGAAUUAACUUGG	chr4:122739141-122739381(-)$1	240	180	199	10.6857
CAUGACUGACAUAAGUCAU	chr6:56426117-56426357(-)$1	240	32	51	11.2066
GAAACAGAACUUCCUACUU	chr5:32126484-32126724(-)$1	240	79	98	10.7726
GCAGACUCCCAUAGGUGUG	chr19:45593639-45593879(+)$1	240	53	72	12.2733
GAUGCAGAUGAUCCUGUGU	chr4:26430295-26430535(+)$1	240	82	101	11.2066
CACAGAGGAGCAUUUCUUG	chrX:53621385-53621625(-)$1	240	185	204	11.7765
UACACUGUUACUUCAGUCA	chr21:47690258-47690498(-)$1	240	164	183	9.5006
UUUAGCUUAUUAUAGCCCA	chr2:9657963-9658203(-)$1	240	80	99	12.1599
AGUAAUUAUUUUAAAAUAC	chr12:72026665-72027151(-)$1	486	107	126	10.7062
AUCUUCUAAAAAAGGAACA	chr8:71495304-71495544(-)$1	240	126	145	10.8552
GGUGAGGAGAUUACCCCAC	chr1:154192780-154193020(-)$1	240	202	221	10.7062
CGCCCGCCAGCCUGCCGGG	chr2:128283834-128284074(-)$1	240	70	89	10.9033
UGCAGCAUUUAUUUGCGUC	chr3:132172050-132172290(+)$1	240	86	105	11.1821
uuuuaaaguaauauuuaaa	chr15:73414790-73415030(+)$1	240	22	41	11.9636
CACGAGCGUUGUGGCUCUU	chr16:10850490-10850730(+)$1	240	185	204	11.3542
GGGUCUGAGAAGGCAGCCU	chr6:56418023-56418263(-)$1	240	61	80	12.0011
ACCGUGCUGAUCUGUGCUG	chr12:49168405-49168645(-)$1	240	136	155	12.0629
AUUUUCUCAAUAAAGAAGA	chr15:67818720-67818960(+)$1	240	125	144	11.6900
CGGCUCCUACAUUGGAACC	chr1:173921093-173921333(-)$1	240	140	159	11.3036
CUUGCCGUACCGCCGGGAA	chr4:187629191-187629431(-)$1	240	81	100	12.0525
ACGUUCUUAGUUAAAAGAU	chr1:220335455-220335695(-)$1	240	108	127	9.4853
CCCUGGAUCCUCUUCUGGU	chrX:37586989-37587229(+)$1	240	144	163	12.5106
AAAAAAUUCAUCUGUUUUU	chr8:91029285-91029525(+)$1	240	3	22	11.6900
CAAUGCCUCUGAUCGGGCC	chr14:58831639-58831879(+)$1	240	10	29	10.3536
UCACUAUUAGGGUAUGUUG	chr2:27693759-27693999(-)$1	240	194	213	12.0559
GGUACUUCAAGAAGAGUUC	chr4:77053623-77053863(-)$1	240	31	50	12.0629
AUAAUGCAGAAAAGCCUUA	chr19:58049020-58049260(+)$1	240	157	176	10.6241
UUCACCCCUCCUUGGCUGA	chr2:232673138-232673378(+)$1	240	128	147	10.8403
UUUGGAGAAGAGCCUUCUU	chr17:65174788-65175028(-)$1	240	92	111	11.7817
GGCCAGGCCUCAUCCUCCU	chr11:6416260-6416500(-)$1	240	14	33	12.2738
AAGGAAUGUGGAAAGGCCU	chr19:38055971-38056211(-)$1	240	145	164	10.3709
UGCCAUCCGGAUUGAUGGG	chr1:179886883-179887123(+)$1	240	58	77	10.2142

#DB
((((.((......)).)))	chr11:125891170-125891410(-)$1	1	54	73	10.7062
.))((((......))))((	chr1:237013618-237013858(+)$1	1	86	105	10.1527
....(((......)))...	chr15:101109398-101109638(-)$1	1	165	184	12.3084
((.((((......)))).)	chr2:85769317-85769563(+)$1	1	27	46	11.8259
((.((((......))))..	chr1:97243153-97243393(+)$1	1	178	197	11.6062
(((.(((......))).))	chrX:44929224-44929464(+)$1	1	25	44	12.0559
..(((((......))))).	chr18:29867197-29867437(-)$1	1	134	153	10.5068
((.((((......))))))	chr15:58284874-58285114(-)$1	1	216	235	11.7509
(((.(((......))))))	chr21:28210337-28210577(-)$1	1	192	211	11.8912
(((((((......)))..)	chr7:66274024-66274264(+)$1	1	20	39	11.9147
(((((((......))))))	chr1:220206820-220207060(-)$1	1	17	36	11.2066
((..(((......))))))	chr16:71961599-71961839(+)$1	1	129	148	12.4233
(((((((......))))))	chr1:155921867-155922107(-)$1	1	124	143	10.0035
((((.((......)).)))	chr7:128637427-128637667(-)$1	1	83	102	10.6241
(((((((......))))..	chr2:114699719-114699959(+)$1	1	101	120	10.9212
(((((((......))))))	chr10:22002655-22002895(+)$1	1	59	78	11.2066
(((.(((......))))))	chr16:4779905-4780145(-)$1	1	18	37	12.1968
((.((((......)))).)	chr14:45400472-45400712(-)$1	1	212	231	12.0629
))).(((......)))((.	chr1:36499780-36500020(+)$1	1	154	173	10.0039
(((((((......)).)))	chr17:11998799-11999039(+)$1	1	152	171	10.4865
.((.(((......)))..)	chr16:69727392-69727632(+)$1	1	120	139	11.4415
(...((((......)))).	chr1:182853794-182854034(+)$1	1	124	143	10.6064
.((.(((......))))).	chr20:25596965-25597205(-)$1	1	40	59	10.1767
(((((.(......).))))	chrX:47099145-47099385(+)$1	1	203	222	10.9252
)((((((......))))))	chr8:128753048-128753288(+)$1	1	89	108	9.9462
((..((((......)))).	chrX:24094798-24095038(+)$1	1	9	28	10.4014
((..((((......)))).	chr4:122739141-122739381(-)$1	1	180	199	10.6857
(((((((......))))))	chr6:56426117-56426357(-)$1	1	32	51	11.2066
((...((......))..))	chr5:32126484-32126724(-)$1	1	79	98	10.7726
(((.(((......))).))	chr19:45593639-45593879(+)$1	1	53	72	12.2733
(((((((......))))))	chr4:26430295-26430535(+)$1	1	82	101	11.2066
((.((((......))))))	chrX:53621385-53621625(-)$1	1	185	204	11.7765
....(((......))))))	chr21:47690258-47690498(-)$1	1	164	183	9.5006
(...(((......)))..)	chr2:9657963-9658203(-)$1	1	80	99	12.1599
((((.((......)).)))	chr12:72026665-72027151(-)$1	1	107	126	10.7062
(((((((......)))..)	chr8:71495304-71495544(-)$1	1	126	145	10.8552
((((.((......)).)))	chr1:154192780-154193020(-)$1	1	202	221	10.7062
((...((......))))))	chr2:128283834-128284074(-)$1	1	70	89	10.9033
(...(((......)))...	chr3:132172050-132172290(+)$1	1	86	105	11.1821
(((((((......))))..	chr15:73414790-73415030(+)$1	1	22	41	11.9636
((.((((......)))).)	chr16:10850490-10850730(+)$1	1	185	204	11.3542
(((.(((......))))))	chr6:56418023-56418263(-)$1	1	61	80	12.0011
((.((((......)))).)	chr12:49168405-49168645(-)$1	1	136	155	12.0629
(((((((......))))))	chr15:67818720-67818960(+)$1	1	125	144	11.6900
(((.(((......))).))	chr1:173921093-173921333(-)$1	1	140	159	11.3036
(((.(((......))).))	chr4:187629191-187629431(-)$1	1	81	100	12.0525
....((((......)))).	chr1:220335455-220335695(-)$1	1	108	127	9.4853
(...(((......))))))	chrX:37586989-37587229(+)$1	1	144	163	12.5106
(((((((......))))))	chr8:91029285-91029525(+)$1	1	3	22	11.6900
((..((((......)))).	chr14:58831639-58831879(+)$1	1	10	29	10.3536
(((.(((......))).))	chr2:27693759-27693999(-)$1	1	194	213	12.0559
((.((((......)))).)	chr4:77053623-77053863(-)$1	1	31	50	12.0629
((((.((......)).)))	chr19:58049020-58049260(+)$1	1	157	176	10.6241
.(((.((......)).)))	chr2:232673138-232673378(+)$1	1	128	147	10.8403
(..((((......))))..	chr17:65174788-65175028(-)$1	1	92	111	11.7817
((..(((......))))))	chr11:6416260-6416500(-)$1	1	14	33	12.2738
((((..(......)..)))	chr19:38055971-38056211(-)$1	1	145	164	10.3709
(.(((((......))))).	chr1:179886883-179887123(+)$1	1	58	77	10.2142

#PSSM
d : 0.18	e : 0.15	f : 0.13	c : 0.13	g : 0.12	b : 0.05	! : 0.03	h : 0.03	= : 0.03	o : 0.01	# : 0.01	% : 0.01	+ : 0.01	$ : 0.01	[ : 0.01	
d : 0.15	f : 0.15	e : 0.12	c : 0.12	b : 0.10	g : 0.10	" : 0.06	! : 0.03	h : 0.03	= : 0.03	# : 0.01	+ : 0.01	$ : 0.01	[ : 0.01	
[ : 0.13	e : 0.12	d : 0.10	g : 0.10	! : 0.10	" : 0.10	f : 0.08	b : 0.06	c : 0.06	= : 0.03	# : 0.01	+ : 0.01	h : 0.01	$ : 0.01	
d : 0.29	[ : 0.17	" : 0.10	e : 0.08	g : 0.08	! : 0.08	f : 0.03	= : 0.03	# : 0.01	: : 0.01	+ : 0.01	h : 0.01	$ : 0.01	c : 0.01	
c : 0.34	d : 0.31	[ : 0.10	g : 0.06	e : 0.05	f : 0.03	" : 0.03	= : 0.03	! : 0.01	
c : 0.34	d : 0.29	b : 0.15	g : 0.06	e : 0.03	f : 0.03	= : 0.03	[ : 0.01	! : 0.01	
c : 0.34	d : 0.29	b : 0.15	g : 0.06	e : 0.03	f : 0.03	a : 0.03	= : 0.03	
o : 0.91	d : 0.08	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.34	d : 0.20	b : 0.15	o : 0.08	g : 0.06	e : 0.03	f : 0.03	a : 0.03	= : 0.03	
c : 0.34	d : 0.29	b : 0.15	g : 0.06	e : 0.03	f : 0.03	= : 0.03	] : 0.01	2 : 0.01	
c : 0.34	d : 0.31	] : 0.12	g : 0.06	f : 0.05	e : 0.03	2 : 0.03	= : 0.03	
d : 0.41	] : 0.08	e : 0.08	f : 0.08	2 : 0.08	g : 0.08	c : 0.03	b : 0.03	= : 0.03	4 : 0.01	i : 0.01	6 : 0.01	
d : 0.20	f : 0.15	e : 0.12	2 : 0.10	] : 0.08	g : 0.08	c : 0.05	b : 0.05	6 : 0.03	= : 0.03	F : 0.01	4 : 0.01	i : 0.01	3 : 0.01	
d : 0.15	f : 0.15	g : 0.10	c : 0.10	e : 0.08	] : 0.06	4 : 0.05	2 : 0.05	6 : 0.05	b : 0.05	= : 0.03	F : 0.01	! : 0.01	i : 0.01	h : 0.01	3 : 0.01	

#score	649.9805476297727
#seq	58
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m2_run2.txt

#BEAR
eeeeooooooeeeee	chr3:53326492-53326767(-)$1	275	132	147	10.4416
#cccoooooocccii	chr1:183496660-183496911(+)$1	251	150	165	10.1843
ddddoooooodddd]	chr5:134705702-134705960(-)$1	258	145	160	13.1253
ddddoooooodddd:	chr1:186281797-186282066(-)$1	269	219	234	12.4769
ddddoooooodddd:	chr12:54920403-54920640(+)$1	237	205	220	12.4769
iiiiooooooiiiii	chr4:159636384-159636605(-)$1	221	34	49	9.5051
ddddooooooddddJ	chr10:70516196-70516473(+)$1	277	180	195	11.6293
ddddoooooodddd]	chr10:38345061-38345306(+)$1	245	54	69	13.1253
ddddoooooodddd]	chr10:38344444-38344784(+)$1	340	251	266	13.1253
ddddoooooodddd:	chr6:28121530-28121810(+)$1	280	150	165	12.4769
ddddoooooodddd5	chr19:58290741-58291004(+)$1	263	106	121	12.4865
ddddoooooodddd:	chr3:169847068-169847440(-)$1	372	343	358	12.4769
ddddoooooodddd:	chr13:39586983-39587219(-)$1	236	197	212	12.4769
eeeeooooooeeeee	chr9:134145767-134145986(-)$1	219	63	78	10.4416
ccccooooooccc]c	chrX:70330003-70330260(-)$1	257	178	193	10.4064
[cccooooooccc]a	chr9:15446999-15447255(+)$1	256	159	174	10.5221
eeeeooooooeeeee	chr2:191844392-191844637(-)$1	245	78	93	10.4416
ddddoooooodddd]	chr5:42800733-42800989(+)$1	256	167	182	13.1253
ddddoooooodddd:	chr10:38241410-38241649(-)$1	239	66	81	12.4769
ddddoooooodddd]	chr10:43088135-43088404(-)$1	269	70	85	13.1253
eeeeooooooeeeee	chr1:63010533-63010799(-)$1	266	144	159	10.4416
eeeeooooooeeeee	chr17:65941779-65942076(+)$1	297	269	284	10.4416
ddddoooooodddd2	chr3:88188953-88189205(-)$1	252	98	113	12.8925
ddddoooooodddd:	chr13:39588419-39588698(-)$1	279	162	177	12.4769
ddddoooooodddd:	chr1:150468857-150469085(+)$1	228	157	172	12.4769
ddddoooooodddd]	chr21:47423292-47423512(+)$1	220	101	116	13.1253
dd[aooooooa]ddd	chr7:110762862-110763105(-)$1	243	150	165	10.9001
ddddoooooodddd]	chr13:99947186-99947460(+)$1	274	200	215	13.1253
ddddooooooddddF	chr8:37993142-37993369(+)$1	227	100	115	12.4635
ddddoooooodddd]	chr5:137502121-137502370(-)$1	249	141	156	13.1253
"cccooooooccc22	chr2:9725280-9725522(-)$1	242	18	33	10.1940
eeeeooooooeeeee	chr19:21366659-21366895(+)$1	236	111	126	10.4416
ddddoooooodddd4	chr7:99077339-99077591(+)$1	252	139	154	13.0155
eeeeooooooeeeee	chr11:72403678-72404061(-)$1	383	69	84	10.4416
ddddoooooodddd8	chr15:58968376-58968624(-)$1	248	166	181	12.7070
ddddoooooodddd]	chr19:57911022-57911271(+)$1	249	12	27	13.1253
[cccooooooccc]a	chr6:43591676-43591895(-)$1	219	133	148	10.5221
!cccooooooccc22	chr11:76255493-76255721(+)$1	228	186	201	10.3178
eeeeooooooeeeee	chr4:108985308-108985597(-)$1	289	14	29	10.4416
ddddoooooodddd]	chr12:7077745-7077998(-)$1	253	115	130	13.1253
ddddoooooodddd:	chr17:42475014-42475290(-)$1	276	126	141	12.4769
ddddoooooodddd:	chr12:110385090-110385321(-)$1	231	170	185	12.4769
acccooooooccc]a	chr17:4848892-4849300(-)$1	408	246	261	10.4844
dd[aooooooadddd	chr1:169446426-169446701(-)$1	275	166	181	11.4228
ddddoooooodddd:	chr13:39588087-39588384(-)$1	297	225	240	12.4769
ddddoooooodddd:	chr17:56051884-56052120(-)$1	236	146	161	12.4769
ddddoooooodddd:	chr1:156553550-156553810(+)$1	260	136	151	12.4769
ccccooooooccc]c	chr10:119805415-119805671(-)$1	256	152	167	10.4064
ddddoooooodddd]	chr1:33149820-33150115(+)$1	295	269	284	13.1253
ddddoooooodddd2	chr14:100604045-100604325(+)$1	280	82	97	12.8925
ddddoooooodddd]	chr6:135358579-135358812(-)$1	233	176	191	13.1253
ddddoooooodddd6	chr19:19105762-19106015(-)$1	253	220	235	12.7027
ddddoooooodddd3	chr3:169846903-169847137(-)$1	234	40	55	13.0750
ddddoooooodddd]	chr11:77332968-77333226(-)$1	258	114	129	13.1253
d[bboooooobbddd	chr12:133634092-133634325(+)$1	233	126	141	9.5792
bcccooooooccc]b	chr12:994107-994394(+)$1	287	72	87	9.9272
ddddoooooodddd0	chr19:36037844-36038121(+)$1	277	164	179	12.6582
eeeeooooooeeeee	chr9:5919902-5920259(-)$1	357	60	75	10.4416
[cccooooooccc]c	chr1:154229514-154229785(+)$1	271	197	212	10.3783
[cccooooooccc]d	chr17:47375772-47376180(-)$1	408	127	142	10.2841

#otherMatches

#Seq PSSM
UCAGUCCAGCCUGAA	chr3:53326492-53326767(-)$1	275	132	147	10.4416
GUCCAUAGUGGGAGC	chr1:183496660-183496911(+)$1	251	150	165	10.1843
GCUGGCAAUGCAGCG	chr5:134705702-134705960(-)$1	258	145	160	13.1253
UUGGAAAGAGCCAGA	chr1:186281797-186282066(-)$1	269	219	234	12.4769
GAGCAUUUUAGCUCC	chr12:54920403-54920640(+)$1	237	205	220	12.4769
GUAUUUUUUUAUACA	chr4:159636384-159636605(-)$1	221	34	49	9.5051
CAGCAGUAUAGUUGU	chr10:70516196-70516473(+)$1	277	180	195	11.6293
GGGGGAGAAACCCUA	chr10:38345061-38345306(+)$1	245	54	69	13.1253
AGGGCAGAAACCCUU	chr10:38344444-38344784(+)$1	340	251	266	13.1253
AGGGGAGAAGCCCUA	chr6:28121530-28121810(+)$1	280	150	165	12.4769
CCUUUAGCUUAAGGU	chr19:58290741-58291004(+)$1	263	106	121	12.4865
AGAGUCAUCCCUCUC	chr3:169847068-169847440(-)$1	372	343	358	12.4769
AGGCUUUUCUGUCUC	chr13:39586983-39587219(-)$1	236	197	212	12.4769
CAGGACCAGCCCUGG	chr9:134145767-134145986(-)$1	219	63	78	10.4416
ACUGGAACAACAGAU	chrX:70330003-70330260(-)$1	257	178	193	10.4064
GAUUCAAUUCGAUGU	chr9:15446999-15447255(+)$1	256	159	174	10.5221
CUUUGGAUUGAAAGC	chr2:191844392-191844637(-)$1	245	78	93	10.4416
UGACUUAUUUGUCAG	chr5:42800733-42800989(+)$1	256	167	182	13.1253
AGGGGAGAAACCCUA	chr10:38241410-38241649(-)$1	239	66	81	12.4769
GGGGGAGAAACCCUA	chr10:43088135-43088404(-)$1	269	70	85	13.1253
GGGGAUCCAACCCCA	chr1:63010533-63010799(-)$1	266	144	159	10.4416
ACUUUAAAUCAAGUU	chr17:65941779-65942076(+)$1	297	269	284	10.4416
AGAAACCCAAUUCUU	chr3:88188953-88189205(-)$1	252	98	113	12.8925
ACUGCAUCCCCAGUC	chr13:39588419-39588698(-)$1	279	162	177	12.4769
GGGAUUUCCUUCCCC	chr1:150468857-150469085(+)$1	228	157	172	12.4769
GCCAAGCGCCUGGCC	chr21:47423292-47423512(+)$1	220	101	116	13.1253
GUGUAAACCAAGGCC	chr7:110762862-110763105(-)$1	243	150	165	10.9001
GCUGACUUCACAGCA	chr13:99947186-99947460(+)$1	274	200	215	13.1253
GGGGUUUACUUCCCA	chr8:37993142-37993369(+)$1	227	100	115	12.4635
CACUACUGAAAGUGU	chr5:137502121-137502370(-)$1	249	141	156	13.1253
AGUAACUUAAUAUGA	chr2:9725280-9725522(-)$1	242	18	33	10.1940
UAUUAAACAAAAUAA	chr19:21366659-21366895(+)$1	236	111	126	10.4416
ucugcaauuccagaa	chr7:99077339-99077591(+)$1	252	139	154	13.0155
CUGUCCACAUGCAGG	chr11:72403678-72404061(-)$1	383	69	84	10.4416
ucacuugAUUGUGGA	chr15:58968376-58968624(-)$1	248	166	181	12.7070
CAAGCAUAUACUUGU	chr19:57911022-57911271(+)$1	249	12	27	13.1253
CUGGACCUCCUCAAA	chr6:43591676-43591895(-)$1	219	133	148	10.5221
CAGGCAGCUUCCUAC	chr11:76255493-76255721(+)$1	228	186	201	10.3178
AUGGUACAAUCUGUG	chr4:108985308-108985597(-)$1	289	14	29	10.4416
UCCUCCCCCCAGGGU	chr12:7077745-7077998(-)$1	253	115	130	13.1253
UGGCCACCCUGCCAC	chr17:42475014-42475290(-)$1	276	126	141	12.4769
GACCGGAUCAGGUCA	chr12:110385090-110385321(-)$1	231	170	185	12.4769
GCUGGAUGGACAGAC	chr17:4848892-4849300(-)$1	408	246	261	10.4844
CUACCUGCCAGAGAG	chr1:169446426-169446701(-)$1	275	166	181	11.4228
CAGCUCUUCUGCUGC	chr13:39588087-39588384(-)$1	297	225	240	12.4769
AUAGCACACCCUGUC	chr17:56051884-56052120(-)$1	236	146	161	12.4769
GGUGAGAUGACACCU	chr1:156553550-156553810(+)$1	260	136	151	12.4769
UGAGAAAACCCUUGA	chr10:119805415-119805671(-)$1	256	152	167	10.4064
CAGUAUUGAGGCUGG	chr1:33149820-33150115(+)$1	295	269	284	13.1253
GCCUCACUCUAGGUA	chr14:100604045-100604325(+)$1	280	82	97	12.8925
CAAAUAAUCCUUUGU	chr6:135358579-135358812(-)$1	233	176	191	13.1253
ACAUGUGCAGGUGUU	chr19:19105762-19106015(-)$1	253	220	235	12.7027
AGAGUCAUCCCUCUC	chr3:169846903-169847137(-)$1	234	40	55	13.0750
uguCAAUUCAGGCAU	chr11:77332968-77333226(-)$1	258	114	129	13.1253
CAUAUCGCAUUGGAG	chr12:133634092-133634325(+)$1	233	126	141	9.5792
UCUGAAUCACCAGUA	chr12:994107-994394(+)$1	287	72	87	9.9272
GCCUCCCUCUAGGUC	chr19:36037844-36038121(+)$1	277	164	179	12.6582
UCUACACCAAUAGAU	chr9:5919902-5920259(-)$1	357	60	75	10.4416
AAGCUCAGUUGCUAC	chr1:154229514-154229785(+)$1	271	197	212	10.3783
CCAGUUCCUUCUGUG	chr17:47375772-47376180(-)$1	408	127	142	10.2841

#DB
((((......)))))	chr3:53326492-53326767(-)$1	1	132	147	10.4416
.(((......)))))	chr1:183496660-183496911(+)$1	1	150	165	10.1843
((((......)))).	chr5:134705702-134705960(-)$1	1	145	160	13.1253
((((......)))).	chr1:186281797-186282066(-)$1	1	219	234	12.4769
((((......)))).	chr12:54920403-54920640(+)$1	1	205	220	12.4769
((((......)))))	chr4:159636384-159636605(-)$1	1	34	49	9.5051
((((......)))))	chr10:70516196-70516473(+)$1	1	180	195	11.6293
((((......)))).	chr10:38345061-38345306(+)$1	1	54	69	13.1253
((((......)))).	chr10:38344444-38344784(+)$1	1	251	266	13.1253
((((......)))).	chr6:28121530-28121810(+)$1	1	150	165	12.4769
((((......)))).	chr19:58290741-58291004(+)$1	1	106	121	12.4865
((((......)))).	chr3:169847068-169847440(-)$1	1	343	358	12.4769
((((......)))).	chr13:39586983-39587219(-)$1	1	197	212	12.4769
((((......)))))	chr9:134145767-134145986(-)$1	1	63	78	10.4416
((((......))).)	chrX:70330003-70330260(-)$1	1	178	193	10.4064
.(((......))).)	chr9:15446999-15447255(+)$1	1	159	174	10.5221
((((......)))))	chr2:191844392-191844637(-)$1	1	78	93	10.4416
((((......)))).	chr5:42800733-42800989(+)$1	1	167	182	13.1253
((((......)))).	chr10:38241410-38241649(-)$1	1	66	81	12.4769
((((......)))).	chr10:43088135-43088404(-)$1	1	70	85	13.1253
((((......)))))	chr1:63010533-63010799(-)$1	1	144	159	10.4416
((((......)))))	chr17:65941779-65942076(+)$1	1	269	284	10.4416
((((......)))).	chr3:88188953-88189205(-)$1	1	98	113	12.8925
((((......)))).	chr13:39588419-39588698(-)$1	1	162	177	12.4769
((((......)))).	chr1:150468857-150469085(+)$1	1	157	172	12.4769
((((......)))).	chr21:47423292-47423512(+)$1	1	101	116	13.1253
((.(......).)))	chr7:110762862-110763105(-)$1	1	150	165	10.9001
((((......)))).	chr13:99947186-99947460(+)$1	1	200	215	13.1253
((((......)))))	chr8:37993142-37993369(+)$1	1	100	115	12.4635
((((......)))).	chr5:137502121-137502370(-)$1	1	141	156	13.1253
.(((......)))..	chr2:9725280-9725522(-)$1	1	18	33	10.1940
((((......)))))	chr19:21366659-21366895(+)$1	1	111	126	10.4416
((((......)))).	chr7:99077339-99077591(+)$1	1	139	154	13.0155
((((......)))))	chr11:72403678-72404061(-)$1	1	69	84	10.4416
((((......)))).	chr15:58968376-58968624(-)$1	1	166	181	12.7070
((((......)))).	chr19:57911022-57911271(+)$1	1	12	27	13.1253
.(((......))).)	chr6:43591676-43591895(-)$1	1	133	148	10.5221
.(((......)))..	chr11:76255493-76255721(+)$1	1	186	201	10.3178
((((......)))))	chr4:108985308-108985597(-)$1	1	14	29	10.4416
((((......)))).	chr12:7077745-7077998(-)$1	1	115	130	13.1253
((((......)))).	chr17:42475014-42475290(-)$1	1	126	141	12.4769
((((......)))).	chr12:110385090-110385321(-)$1	1	170	185	12.4769
((((......))).)	chr17:4848892-4849300(-)$1	1	246	261	10.4844
((.(......)))))	chr1:169446426-169446701(-)$1	1	166	181	11.4228
((((......)))).	chr13:39588087-39588384(-)$1	1	225	240	12.4769
((((......)))).	chr17:56051884-56052120(-)$1	1	146	161	12.4769
((((......)))).	chr1:156553550-156553810(+)$1	1	136	151	12.4769
((((......))).)	chr10:119805415-119805671(-)$1	1	152	167	10.4064
((((......)))).	chr1:33149820-33150115(+)$1	1	269	284	13.1253
((((......)))).	chr14:100604045-100604325(+)$1	1	82	97	12.8925
((((......)))).	chr6:135358579-135358812(-)$1	1	176	191	13.1253
((((......)))).	chr19:19105762-19106015(-)$1	1	220	235	12.7027
((((......)))).	chr3:169846903-169847137(-)$1	1	40	55	13.0750
((((......)))).	chr11:77332968-77333226(-)$1	1	114	129	13.1253
(.((......)))))	chr12:133634092-133634325(+)$1	1	126	141	9.5792
((((......))).)	chr12:994107-994394(+)$1	1	72	87	9.9272
((((......)))).	chr19:36037844-36038121(+)$1	1	164	179	12.6582
((((......)))))	chr9:5919902-5920259(-)$1	1	60	75	10.4416
.(((......))).)	chr1:154229514-154229785(+)$1	1	197	212	10.3783
.(((......))).)	chr17:47375772-47376180(-)$1	1	127	142	10.2841

#PSSM
d : 0.65	e : 0.15	[ : 0.06	c : 0.03	# : 0.01	i : 0.01	" : 0.01	! : 0.01	a : 0.01	b : 0.01	
d : 0.63	c : 0.18	e : 0.15	i : 0.01	[ : 0.01	
d : 0.60	c : 0.18	e : 0.15	[ : 0.03	i : 0.01	b : 0.01	
d : 0.60	c : 0.18	e : 0.15	a : 0.03	i : 0.01	b : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
d : 0.60	c : 0.18	e : 0.15	a : 0.03	i : 0.01	b : 0.01	
d : 0.61	c : 0.18	e : 0.15	i : 0.01	] : 0.01	b : 0.01	
d : 0.65	c : 0.18	e : 0.15	i : 0.01	
d : 0.65	e : 0.15	] : 0.13	i : 0.03	2 : 0.03	
] : 0.21	: : 0.21	e : 0.15	2 : 0.06	d : 0.06	c : 0.05	a : 0.05	i : 0.03	J : 0.01	5 : 0.01	F : 0.01	4 : 0.01	8 : 0.01	6 : 0.01	3 : 0.01	b : 0.01	0 : 0.01	

#score	708.3627198934344
#seq	60
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_UTR_m3_run2.txt

#BEAR
ffffffwwwwwwwwwwwwwwffff	chr12:57106745-57106985(-)$1	240	133	157	21.8671
##eeeeettttttttttteeeee4	chr17:1257404-1257627(-)$1	223	86	110	21.7443
ggggcccuuuuuuuuuuuuccc:C	chr1:154956019-154956258(+)$1	239	181	205	21.8551
####cccuuuuuuuuuuuuccc44	chr2:182780594-182780835(+)$1	241	35	59	23.8542
ggg:ddddtttttttttttdddd:	chr3:44881748-44882007(+)$1	259	126	150	19.9139
:ffffffuuuuuuuuuuuufffff	chr1:1654064-1654305(-)$1	241	93	117	22.2712
ccc[cccuuuuuuuuuuuuccc]c	chr7:99955792-99956025(+)$1	233	112	136	24.0490
ffffffxxxxxxxxxxxxxxxfff	chr3:50099304-50099562(+)$1	258	49	73	17.1802
"""cccxxxxxxxxxxxxxxxccc	chr9:136230270-136230523(-)$1	253	44	68	17.4074
$$$$ccctttttttttttccc444	chr12:25362653-25362897(-)$1	244	85	109	21.6908
:ffffffuuuuuuuuuuuufffff	chr15:44084442-44084674(+)$1	232	75	99	22.2712
ggggggguuuuuuuuuuuuggggg	chr1:117532582-117532829(+)$1	247	119	143	23.5053
!bb[ddddtttttttttttdddd2	chr17:4851523-4851756(-)$1	233	131	155	21.3887
eeeeewwwwwwwwwwwwwweeeee	chr1:32768136-32768377(+)$1	241	209	233	21.4649
ggggddddtttttttttttdddde	chr5:72875907-72876151(+)$1	244	133	157	21.9414
ffeeeeewwwwwwwwwwwwwweee	chr3:184543850-184544068(+)$1	218	166	190	21.5319
gggg[bbuuuuuuuuuuuubb]gg	chr15:75137752-75137986(-)$1	234	31	55	23.2825
:fffffftttttttttttffffff	chr7:73609489-73609736(+)$1	247	125	149	20.7437
bb[dddduuuuuuuuuuuudddd]	chr12:49666292-49666552(+)$1	260	203	227	22.6759
[ddddwwwwwwwwwwwwwwdddd]	chr5:149827116-149827401(-)$1	285	48	72	21.2252
ccc[ccctttttttttttccc]cc	chr17:44407612-44407843(+)$1	231	180	204	22.6458
!ccc[ccctttttttttttccc33	chr19:12834565-12834803(-)$1	238	75	99	22.8879
FFeeeeevvvvvvvvvvvvveeee	chr3:39449106-39449350(+)$1	244	4	28	21.7090
ee!!ddddtttttttttttdddd]	chr3:184043277-184043513(+)$1	236	16	40	21.8653
hhhhhhhvvvvvvvvvvvvvhhhh	chr8:22877286-22877542(+)$1	256	30	54	20.2653
"eeeeevvvvvvvvvvvvveeeee	chr19:39396009-39396269(+)$1	260	55	79	22.5440
ggg"""bbtttttttttttbbggg	chr2:233433698-233433942(+)$1	244	24	48	21.8695
iiiiiiiuuuuuuuuuuuuiiiii	chr19:57831837-57832078(+)$1	241	145	169	23.4091
ccc[cccuuuuuuuuuuuuccccc	chr10:81114074-81114334(+)$1	260	30	54	23.9724
ccc[cccuuuuuuuuuuuuccc]c	chr1:19923460-19923705(+)$1	245	202	226	24.0490
dd!!ccctttttttttttccc22d	chr3:184033077-184033331(+)$1	254	200	224	21.7291
ffff[bbuuuuuuuuuuuubb]ff	chr19:57791838-57792069(+)$1	231	120	144	23.0322
gggggyyyyyyyyyyyyyyyyggg	chr1:3731560-3731798(-)$1	238	177	201	21.3205
f[a!!ccctttttttttttccca]	chr3:142761854-142762089(+)$1	235	166	190	22.8335
fff[ccctttttttttttccc]ff	chr17:80014461-80014692(+)$1	231	84	108	22.7121
iiiiiiiwwwwwwwwwwwwwwiii	chr9:100437719-100437950(-)$1	231	51	75	21.8164
ffffffvvvvvvvvvvvvvfffff	chr14:103988082-103988324(-)$1	242	140	164	22.5216
===dddduuuuuuuuuuuudddd]	chr17:27001511-27001719(+)$1	208	78	102	23.1664
ffffffwwwwwwwwwwwwwwffff	chr17:18639240-18639499(+)$1	259	19	43	21.8671
ggggggguuuuuuuuuuuuggggg	chr19:19420805-19421041(-)$1	236	38	62	23.5053
cceeeeeuuuuuuuuuuuueeeee	chr17:43175729-43175961(+)$1	232	185	209	23.1946
fff[cccuuuuuuuuuuuucccff	chr5:110835540-110835775(-)$1	235	142	166	24.0387
e!!cccvvvvvvvvvvvvvccc]e	chr7:100888159-100888409(-)$1	250	177	201	23.1074
iiiiiyyyyyyyyyyyyyyyyiii	chr1:100731807-100732059(+)$1	252	49	73	21.2110
d!!bbwwwwwwwwwwwwwwbb]dd	chr18:77733657-77733941(-)$1	284	118	142	20.8466
:fffffftttttttttttffffff	chr4:264519-264741(-)$1	222	14	38	20.7437
bb####bbtttttttttttbb333	chr1:149899040-149899274(-)$1	234	172	196	21.2672
====bbvvvvvvvvvvvvvbb]==	chr1:1684915-1685154(-)$1	239	178	202	22.4572
$$$$$ccctttttttttttccc66	chr11:62445296-62445562(-)$1	266	125	149	20.7205
ffeeeeeuuuuuuuuuuuueeeee	chr17:34891035-34891276(-)$1	241	105	129	23.1925
=======uuuuuuuuuuuu=====	chr1:1639530-1639777(-)$1	247	175	199	23.7485
!!eeeeeuuuuuuuuuuuueeeee	chr13:96277003-96277263(-)$1	260	160	184	23.3694
c[bbddddtttttttttttdddd2	chr19:8367625-8367858(-)$1	233	161	185	21.1338
dddd[bbtttttttttttbbdddd	chr19:35499956-35500163(+)$1	207	0	24	20.4935
eeeeddddtttttttttttdddd:	chr19:10248446-10248684(-)$1	238	130	154	20.5367
ffffffvvvvvvvvvvvvvfffff	chr19:58324578-58324818(-)$1	240	1	25	22.5216
::eeeeeuuuuuuuuuuuueeeee	chr2:39008693-39008945(+)$1	252	43	67	21.3203
:ccc!!bbtttttttttttbb22c	chr17:4070195-4070440(-)$1	245	64	88	20.4390
ffffffxxxxxxxxxxxxxxxfff	chr19:56166018-56166260(+)$1	242	102	126	17.1802
[eeeeevvvvvvvvvvvvveeeee	chr14:55429157-55429364(-)$1	207	42	66	22.5808

#otherMatches

#Seq PSSM
GGAAGAGGUAUACUAGGAAAUCUU	chr12:57106745-57106985(-)$1	240	133	157	21.8671
AAUCUGACACUAUGGACUUCAGAC	chr17:1257404-1257627(-)$1	223	86	110	21.7443
CAGAGGCAGGAACAAAGGAGUCGC	chr1:154956019-154956258(+)$1	239	181	205	21.8551
AAUGUUCGAUUAUCUCCAGGAAAA	chr2:182780594-182780835(+)$1	241	35	59	23.8542
AGAAGAAGAAUGAAUAUAACUUCA	chr3:44881748-44882007(+)$1	259	126	150	19.9139
AUUCUUCAGGAAAAGAAACGAAGG	chr1:1654064-1654305(-)$1	241	93	117	22.2712
CCCCUGGAGAAGAACAAGGCCAUG	chr7:99955792-99956025(+)$1	233	112	136	24.0490
GAAACAUUCUGUAGACUUACUUGU	chr3:50099304-50099562(+)$1	258	49	73	17.1802
UUCCUGAAAUACGACUUCUUCCAG	chr9:136230270-136230523(-)$1	253	44	68	17.4074
GAAAUUCGAAAACAUAAAGAAAAG	chr12:25362653-25362897(-)$1	244	85	109	21.6908
AACGUCCGACAGAACGAGGGGACG	chr15:44084442-44084674(+)$1	232	75	99	22.2712
GGGAACUGGGAUUUGGGUAAGUUC	chr1:117532582-117532829(+)$1	247	119	143	23.5053
UCGUGGGCUACAAGGACUCGCCCU	chr17:4851523-4851756(-)$1	233	131	155	21.3887
GAGGUGCUACCGCUCCCUAACCUC	chr1:32768136-32768377(+)$1	241	209	233	21.4649
GAGACUGGAAUAAUUAUGGCCGGA	chr5:72875907-72876151(+)$1	244	133	157	21.9414
GAGGUAAGUGAAUAUUAAUGAUUA	chr3:184543850-184544068(+)$1	218	166	190	21.5319
GGCCUCUUCUUCCCUUUAUAGCGG	chr15:75137752-75137986(-)$1	234	31	55	23.2825
GUCGUUCAAAAGGAGCAAGAAUGA	chr7:73609489-73609736(+)$1	247	125	149	20.7437
AGAAAGCCUACCACGAACAGCUUA	chr12:49666292-49666552(+)$1	260	203	227	22.6759
GGGAUUCUGGAAAUGUUUUGUCUG	chr5:149827116-149827401(-)$1	285	48	72	21.2252
AGCAGUCUCUUCUUUUUUGACAGC	chr17:44407612-44407843(+)$1	231	180	204	22.6458
ACCUCGGAAUCCCAACUGCUCCUU	chr19:12834565-12834803(-)$1	238	75	99	22.8879
GAUUCCCGUCGUAACUUAAAGGGA	chr3:39449106-39449350(+)$1	244	4	28	21.7090
UCAGGGUCCCAAGACCAUUGACCA	chr3:184043277-184043513(+)$1	236	16	40	21.8653
CUGUCGGAACCAGAUGCAACCCGG	chr8:22877286-22877542(+)$1	256	30	54	20.2653
CCGACACCAACCAUACCCCUGUCG	chr19:39396009-39396269(+)$1	260	55	79	22.5440
CAUGACCCUCUCCCUCUCUGGAUG	chr2:233433698-233433942(+)$1	244	24	48	21.8695
CGCCCCGCUUCUUCCCUAACGGGG	chr19:57831837-57832078(+)$1	241	145	169	23.4091
GAGCUUGGCUUUUGAAACACAACU	chr10:81114074-81114334(+)$1	260	30	54	23.9724
GCUGCCCAGGAGGAAGGAAGGGAA	chr1:19923460-19923705(+)$1	245	202	226	24.0490
CCCUCGGAUGCCCAGAACCUGUAG	chr3:184033077-184033331(+)$1	254	200	224	21.7291
CGCCCCGCUUCUCCCCUAACGAGG	chr19:57791838-57792069(+)$1	231	120	144	23.0322
GGCACGGUCCCGCUUUCCUUAGUG	chr1:3731560-3731798(-)$1	238	177	201	21.3205
UGUACUCUAAUCCAAUCAAAGAAG	chr3:142761854-142762089(+)$1	235	166	190	22.8335
GGCAGCCUUCAAUACCACGGUGGC	chr17:80014461-80014692(+)$1	231	84	108	22.7121
GAAAAGAUGACUUUAAAAUUUUUU	chr9:100437719-100437950(-)$1	231	51	75	21.8164
GCCGCGCCAUCGAGAAGCUCGCGG	chr14:103988082-103988324(-)$1	242	140	164	22.5216
GACCUCAUUGAGGAGAAUUUGGGU	chr17:27001511-27001719(+)$1	208	78	102	23.1664
ugccUGUUUGUAGUAAUUUUUAGG	chr17:18639240-18639499(+)$1	259	19	43	21.8671
AAAUGCACACAACUCUUCCUGCAU	chr19:19420805-19421041(-)$1	236	38	62	23.5053
CUGCAGGUAAAACUGUCUUCCUGU	chr17:43175729-43175961(+)$1	232	185	209	23.1946
UGGCAAGCACUUUAACCAACUUCU	chr5:110835540-110835775(-)$1	235	142	166	24.0387
UGGCCCGGACAGAGGGAAAGGGAA	chr7:100888159-100888409(-)$1	250	177	201	23.1074
GGGAGCCAACGUCUCUUCUUUCUC	chr1:100731807-100732059(+)$1	252	49	73	21.2110
CAACAACAACAAGAUUAACUGGGC	chr18:77733657-77733941(-)$1	284	118	142	20.8466
CCCUACAAAUGUAAAGAAUGUGGG	chr4:264519-264741(-)$1	222	14	38	20.7437
UCAACACCCACAUGCCAAAGGAUA	chr1:149899040-149899274(-)$1	234	172	196	21.2672
CCUGCCAACCUCCUCCCCGGGCCA	chr1:1684915-1685154(-)$1	239	178	202	22.4572
GGAGAGGCGGAGGGAAAAGGCCGA	chr11:62445296-62445562(-)$1	266	125	149	20.7205
GAGCGCCUGGAGAGGAAACGGCGC	chr17:34891035-34891276(-)$1	241	105	129	23.1925
AGACAGAGCCCCCUCCUUGUCUGU	chr1:1639530-1639777(-)$1	247	175	199	23.7485
AGUUGAUGAAAUGGAAAAAGUCAA	chr13:96277003-96277263(-)$1	260	160	184	23.3694
GGAAGCCCAACUGCCUAUGGGGUU	chr19:8367625-8367858(-)$1	233	161	185	21.1338
AGGCCUGUCCCCGAAUCCCAGCCU	chr19:35499956-35500163(+)$1	207	0	24	20.4935
UCCGGGGCGCACAGUACCAGCCCA	chr19:10248446-10248684(-)$1	238	130	154	20.5367
UGUGGUUUCAUCUGUCAACAUCAU	chr19:58324578-58324818(-)$1	240	1	25	22.5216
AACUAUGAAUGAAGGGGACCAUAG	chr2:39008693-39008945(+)$1	252	43	67	21.3203
CCGUCUCAUUCUCUCGUCUUGCUG	chr17:4070195-4070440(-)$1	245	64	88	20.4390
UCUCGGAAAAGUUACGGAAACCUG	chr19:56166018-56166260(+)$1	242	102	126	17.1802
AGGAUGACUAUAUUUUCCCCAUUU	chr14:55429157-55429364(-)$1	207	42	66	22.5808

#DB
((((((..............))))	chr12:57106745-57106985(-)$1	1	133	157	21.8671
..(((((...........))))).	chr17:1257404-1257627(-)$1	1	86	110	21.7443
))))(((............))).)	chr1:154956019-154956258(+)$1	1	181	205	21.8551
....(((............)))..	chr2:182780594-182780835(+)$1	1	35	59	23.8542
))).((((...........)))).	chr3:44881748-44882007(+)$1	1	126	150	19.9139
.((((((............)))))	chr1:1654064-1654305(-)$1	1	93	117	22.2712
(((.(((............))).)	chr7:99955792-99956025(+)$1	1	112	136	24.0490
((((((...............)))	chr3:50099304-50099562(+)$1	1	49	73	17.1802
...(((...............)))	chr9:136230270-136230523(-)$1	1	44	68	17.4074
....(((...........)))...	chr12:25362653-25362897(-)$1	1	85	109	21.6908
.((((((............)))))	chr15:44084442-44084674(+)$1	1	75	99	22.2712
(((((((............)))))	chr1:117532582-117532829(+)$1	1	119	143	23.5053
.((.((((...........)))).	chr17:4851523-4851756(-)$1	1	131	155	21.3887
(((((..............)))))	chr1:32768136-32768377(+)$1	1	209	233	21.4649
))))((((...........))))(	chr5:72875907-72876151(+)$1	1	133	157	21.9414
(((((((..............)))	chr3:184543850-184544068(+)$1	1	166	190	21.5319
((((.((............)).))	chr15:75137752-75137986(-)$1	1	31	55	23.2825
.((((((...........))))))	chr7:73609489-73609736(+)$1	1	125	149	20.7437
((.((((............)))).	chr12:49666292-49666552(+)$1	1	203	227	22.6759
.((((..............)))).	chr5:149827116-149827401(-)$1	1	48	72	21.2252
(((.(((...........))).))	chr17:44407612-44407843(+)$1	1	180	204	22.6458
.(((.(((...........)))..	chr19:12834565-12834803(-)$1	1	75	99	22.8879
(((((((.............))))	chr3:39449106-39449350(+)$1	1	4	28	21.7090
((..((((...........)))).	chr3:184043277-184043513(+)$1	1	16	40	21.8653
(((((((.............))))	chr8:22877286-22877542(+)$1	1	30	54	20.2653
.(((((.............)))))	chr19:39396009-39396269(+)$1	1	55	79	22.5440
(((...((...........)))))	chr2:233433698-233433942(+)$1	1	24	48	21.8695
(((((((............)))))	chr19:57831837-57832078(+)$1	1	145	169	23.4091
(((.(((............)))))	chr10:81114074-81114334(+)$1	1	30	54	23.9724
(((.(((............))).)	chr1:19923460-19923705(+)$1	1	202	226	24.0490
((..(((...........)))..)	chr3:184033077-184033331(+)$1	1	200	224	21.7291
((((.((............)).))	chr19:57791838-57792069(+)$1	1	120	144	23.0322
(((((................)))	chr1:3731560-3731798(-)$1	1	177	201	21.3205
(.(..(((...........)))).	chr3:142761854-142762089(+)$1	1	166	190	22.8335
(((.(((...........))).))	chr17:80014461-80014692(+)$1	1	84	108	22.7121
(((((((..............)))	chr9:100437719-100437950(-)$1	1	51	75	21.8164
((((((.............)))))	chr14:103988082-103988324(-)$1	1	140	164	22.5216
(((((((............)))).	chr17:27001511-27001719(+)$1	1	78	102	23.1664
((((((..............))))	chr17:18639240-18639499(+)$1	1	19	43	21.8671
(((((((............)))))	chr19:19420805-19421041(-)$1	1	38	62	23.5053
(((((((............)))))	chr17:43175729-43175961(+)$1	1	185	209	23.1946
(((.(((............)))))	chr5:110835540-110835775(-)$1	1	142	166	24.0387
(..(((.............))).)	chr7:100888159-100888409(-)$1	1	177	201	23.1074
(((((................)))	chr1:100731807-100732059(+)$1	1	49	73	21.2110
(..((..............)).))	chr18:77733657-77733941(-)$1	1	118	142	20.8466
.((((((...........))))))	chr4:264519-264741(-)$1	1	14	38	20.7437
((....((...........))...	chr1:149899040-149899274(-)$1	1	172	196	21.2672
((((((.............)).))	chr1:1684915-1685154(-)$1	1	178	202	22.4572
.....(((...........)))..	chr11:62445296-62445562(-)$1	1	125	149	20.7205
))(((((............)))))	chr17:34891035-34891276(-)$1	1	105	129	23.1925
(((((((............)))))	chr1:1639530-1639777(-)$1	1	175	199	23.7485
..(((((............)))))	chr13:96277003-96277263(-)$1	1	160	184	23.3694
(.((((((...........)))).	chr19:8367625-8367858(-)$1	1	161	185	21.1338
((((.((...........))))))	chr19:35499956-35500163(+)$1	1	0	24	20.4935
))))((((...........)))).	chr19:10248446-10248684(-)$1	1	130	154	20.5367
((((((.............)))))	chr19:58324578-58324818(-)$1	1	1	25	22.5216
..(((((............)))))	chr2:39008693-39008945(+)$1	1	43	67	21.3203
.(((..((...........))..)	chr17:4070195-4070440(-)$1	1	64	88	20.4390
((((((...............)))	chr19:56166018-56166260(+)$1	1	102	126	17.1802
.(((((.............)))))	chr14:55429157-55429364(-)$1	1	42	66	22.5808

#PSSM
f : 0.19	g : 0.13	: : 0.09	c : 0.09	e : 0.06	! : 0.05	i : 0.05	d : 0.05	= : 0.05	# : 0.03	" : 0.03	$ : 0.03	b : 0.03	[ : 0.03	F : 0.01	h : 0.01	
f : 0.24	g : 0.13	c : 0.11	e : 0.08	b : 0.05	d : 0.05	i : 0.05	= : 0.05	! : 0.05	# : 0.03	$ : 0.03	[ : 0.03	" : 0.01	F : 0.01	h : 0.01	: : 0.01	
f : 0.21	e : 0.18	g : 0.13	c : 0.09	! : 0.06	i : 0.05	= : 0.05	# : 0.03	$ : 0.03	b : 0.03	d : 0.03	" : 0.01	[ : 0.01	h : 0.01	a : 0.01	
f : 0.18	e : 0.18	[ : 0.11	g : 0.09	c : 0.06	d : 0.06	! : 0.05	i : 0.05	# : 0.03	$ : 0.03	b : 0.03	= : 0.03	: : 0.01	h : 0.01	" : 0.01	
c : 0.19	f : 0.16	e : 0.16	d : 0.15	[ : 0.06	g : 0.05	i : 0.05	! : 0.03	b : 0.03	h : 0.01	" : 0.01	# : 0.01	$ : 0.01	= : 0.01	
c : 0.24	f : 0.16	e : 0.15	d : 0.13	b : 0.06	w : 0.05	g : 0.03	i : 0.03	y : 0.03	h : 0.01	" : 0.01	# : 0.01	= : 0.01	! : 0.01	
c : 0.21	d : 0.13	e : 0.11	b : 0.09	v : 0.09	w : 0.08	f : 0.06	x : 0.05	g : 0.03	i : 0.03	y : 0.03	h : 0.01	= : 0.01	
u : 0.33	t : 0.13	v : 0.13	w : 0.11	d : 0.09	x : 0.05	c : 0.05	b : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
t : 0.33	u : 0.33	v : 0.13	w : 0.11	x : 0.05	y : 0.03	
u : 0.33	t : 0.19	v : 0.13	w : 0.11	c : 0.06	x : 0.05	f : 0.03	y : 0.03	e : 0.01	b : 0.01	
c : 0.23	d : 0.15	e : 0.13	b : 0.13	f : 0.09	w : 0.06	x : 0.05	g : 0.03	v : 0.03	y : 0.03	i : 0.01	= : 0.01	
c : 0.23	d : 0.16	e : 0.15	f : 0.13	b : 0.11	x : 0.05	g : 0.03	w : 0.03	y : 0.03	h : 0.01	i : 0.01	= : 0.01	
c : 0.18	f : 0.16	e : 0.16	d : 0.16	] : 0.09	g : 0.06	i : 0.05	2 : 0.03	4 : 0.01	h : 0.01	3 : 0.01	= : 0.01	
f : 0.21	d : 0.18	e : 0.16	g : 0.08	] : 0.05	c : 0.05	i : 0.05	4 : 0.03	3 : 0.03	2 : 0.03	= : 0.03	: : 0.01	h : 0.01	a : 0.01	6 : 0.01	
f : 0.21	e : 0.18	c : 0.09	g : 0.08	] : 0.08	4 : 0.05	i : 0.05	d : 0.05	: : 0.03	2 : 0.03	3 : 0.03	= : 0.03	C : 0.01	h : 0.01	6 : 0.01	

#score	1315.6918930518373
#seq	60
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m1_run1.txt

#BEAR
dddd[bbtttttttttttbbdddd]	chr20:62594331-62594584(+)$1	253	148	173	22.1799
gggggggvvvvvvvvvvvvvggggg	chr3:127817617-127817887(-)$1	270	5	30	23.5444
dd[ddddwwwwwwwwwwwwwwdddd	chr6:7401088-7401384(+)$1	296	173	198	20.8980
[dddd[attttttttttta]dddd]	chr22:18209666-18209944(+)$1	278	98	123	23.2311
[ffffffvvvvvvvvvvvvvfffff	chr4:37851832-37852096(+)$1	264	87	112	22.8254
=======ttttttttttt=======	chr1:38353008-38353254(-)$1	246	150	175	23.7417
:eeeeeuuuuuuuuuuuueeeee:F	chr2:228395737-228396028(+)$1	291	47	72	19.8649
hhhhhhhvvvvvvvvvvvvvhhhhh	chr1:155746138-155746371(-)$1	233	176	201	21.4169
[ffffffwwwwwwwwwwwwwwffff	chr11:46907538-46907771(-)$1	233	175	200	21.5065
eeeddddtttttttttttdddd::E	chr6:18149131-18149391(-)$1	260	81	106	19.9913
=======ttttttttttt=======	chr17:74085263-74085503(-)$1	240	148	173	23.7417
b[eeeeettttttttttteeeeebb	chr17:73269491-73269755(-)$1	264	90	115	22.2520
$$$ddddtttttttttttdddd444	chr2:109429175-109429431(+)$1	256	164	189	22.0546
eeeeebbuuuuuuuuuuuubb]eee	chr6:87967017-87967247(+)$1	230	144	169	22.3344
bb[cccuuuuuuuuuuuuccc]bb3	chr19:54485436-54485680(+)$1	244	159	184	22.4600
e!!dddduuuuuuuuuuuudddd22	chr11:110108115-110108494(-)$1	379	185	210	22.8151
[ccc[bbuuuuuuuuuuuubb]ccc	chr9:134064337-134064619(+)$1	282	185	210	23.0856
ee!!ccctttttttttttccc]eee	chr19:19456011-19456255(+)$1	244	139	164	23.6249
gggggggtttttttttttggggggg	chr10:91478488-91478721(+)$1	233	3	28	23.7573
gggg[bbyyyyyyyyyyyyyyyybb	chr9:133760188-133760447(+)$1	259	34	59	20.0880
hhhhhhhuuuuuuuuuuuuhhhhhh	chr4:130003385-130003630(-)$1	245	15	40	21.5839
ee[cccuuuuuuuuuuuuccc333e	chr22:39639814-39640041(-)$1	227	158	183	22.8882
gggggggtttttttttttggggggg	chr10:11791392-11791619(+)$1	227	69	94	23.7573
ccccccuuuuuuuuuuuuccc]ccc	chr22:41735740-41735973(+)$1	233	31	56	23.0317
[ffffffvvvvvvvvvvvvvfffff	chr10:24880053-24880359(-)$1	306	55	80	22.8254
[ffffffvvvvvvvvvvvvvfffff	chr19:41096859-41097254(+)$1	395	164	189	22.8254
[bb[cccuuuuuuuuuuuuccc]bb	chr4:39506877-39507092(-)$1	215	164	189	23.1013
c!!dddduuuuuuuuuuuudddd22	chrX:77298713-77298963(+)$1	250	20	45	22.8780
!ddddvvvvvvvvvvvvvddddggg	chr16:30991245-30991615(+)$1	370	254	279	21.6133
a!!ddddtttttttttttdddd444	chr7:27140784-27141043(+)$1	259	13	38	22.9547
hhhhhhhttttttttttthhhhhhh	chr8:42977532-42977776(+)$1	244	176	201	21.2797
:bb[ccctttttttttttccc]bb:	chr17:76969159-76969393(-)$1	234	76	101	21.2432
dd[ddddtttttttttttddddddd	chr4:109895421-109895649(-)$1	228	24	49	22.5324
!ccc[bbtttttttttttbb22ccc	chr2:234345934-234346227(+)$1	293	163	188	22.4814
gggggggvvvvvvvvvvvvvggggg	chr3:51672120-51672436(+)$1	316	15	40	23.5444
===[ccctttttttttttccc]===	chr16:2161258-2161572(-)$1	314	200	225	24.2502
gggggggtttttttttttggggggg	chr12:121857925-121858177(+)$1	252	214	239	23.7573
gggggggtttttttttttggggggg	chr5:118500102-118500474(+)$1	372	134	159	23.7573
ffffffyyyyyyyyyyyyyyyyfff	chr12:56818730-56818987(-)$1	257	37	62	20.5139
ddd[bbyyyyyyyyyyyyyyyybb]	chr2:20173216-20173569(-)$1	353	273	298	19.7759
gggg!!auuuuuuuuuuuua]gggg	chr20:18529167-18529431(+)$1	264	56	81	23.9357
ee[ddddtttttttttttdddd22e	chr6:152545655-152545906(-)$1	251	68	93	22.5905
:cccwwwwwwwwwwwwwwccc====	chr10:60562862-60563102(+)$1	240	144	169	19.6980
hhhhhhhuuuuuuuuuuuuhhhhhh	chr14:67790341-67790549(+)$1	208	16	41	21.5839
ggg[cccvvvvvvvvvvvvvcccgg	chr6:31918520-31918773(-)$1	253	37	62	23.7137
ff[ddddtttttttttttdddd]ff	chr12:124821481-124821780(-)$1	299	137	162	23.0576
[eeeeeuuuuuuuuuuuueeeeea]	chr3:38357868-38358115(+)$1	247	215	240	22.3632
!fffffftttttttttttffffff3	chr9:115337083-115337324(+)$1	241	137	162	23.0643
::eeeeeuuuuuuuuuuuueeeee:	chr2:32476178-32476416(+)$1	238	105	130	19.8466
c[cccvvvvvvvvvvvvvcccccc]	chrX:106882546-106882751(-)$1	205	134	159	22.2885
fffdddduuuuuuuuuuuudddd22	chr4:88084571-88084843(-)$1	272	158	183	22.6819
ggggggguuuuuuuuuuuugggggg	chr21:34994201-34994464(-)$1	263	100	125	23.8896
[ffffffuuuuuuuuuuuuffffff	chr5:34823500-34823854(+)$1	354	231	256	23.1014
!ffffffwwwwwwwwwwwwwwffff	chr2:32822713-32823066(+)$1	353	311	336	21.4749
gfffffftttttttttttffffff]	chr4:140467973-140468305(-)$1	332	193	218	23.0244
ggg[cccwwwwwwwwwwwwwwcccg	chr2:228159622-228159872(+)$1	250	155	180	22.2021
bffffffuuuuuuuuuuuuffffff	chr17:38451492-38451816(+)$1	324	92	117	22.6994
ddd[cccvvvvvvvvvvvvvcccdd	chr10:5798473-5798743(+)$1	270	236	261	22.6263
ff[ddddwwwwwwwwwwwwwwdddd	chr2:219618238-219618492(+)$1	254	197	222	21.0964
beeeeeuuuuuuuuuuuueeeee]b	chr12:2997284-2997543(+)$1	259	94	119	21.6537
ffbb[bbuuuuuuuuuuuubbbb::	chr11:122930080-122930512(-)$1	432	221	246	19.7984

#otherMatches

#Seq PSSM
CGUGGCCAGCCUUGGAUCGGUACGU	chr20:62594331-62594584(+)$1	253	148	173	22.1799
AUCCCAUGUUGAGUUGAUGAGUGGG	chr3:127817617-127817887(-)$1	270	5	30	23.5444
CUGCAUUAGCACAGGAAAAGAAGUG	chr6:7401088-7401384(+)$1	296	173	198	20.8980
UGCACGUGGAGAAAGAAGAGGUGCC	chr22:18209666-18209944(+)$1	278	98	123	23.2311
UGUGGCAAAUUUGAAAUUUCUGCCA	chr4:37851832-37852096(+)$1	264	87	112	22.8254
UUUCUUUCACGAUACCCCAAAGGAG	chr1:38353008-38353254(-)$1	246	150	175	23.7417
UGUUGUUCCUUACCAUUUACAGCUC	chr2:228395737-228396028(+)$1	291	47	72	19.8649
GAUAUUUCUUGUAAGUUUCCAAAUA	chr1:155746138-155746371(-)$1	233	176	201	21.4169
CUUGUUUAAAACCCUGGCCUCAGAU	chr11:46907538-46907771(-)$1	233	175	200	21.5065
GAGGUACAGAAAAACCAAGUACUAA	chr6:18149131-18149391(-)$1	260	81	106	19.9913
CGUCAGUGCCUUCGUCAAGCUGGCG	chr17:74085263-74085503(-)$1	240	148	173	23.7417
GCGCCCUGGGCUUCUUCAAGGGCCU	chr17:73269491-73269755(-)$1	264	90	115	22.2520
AAAGUUUAAAACAAGAAAAAGCACC	chr2:109429175-109429431(+)$1	256	164	189	22.0546
UGUCUCUCUUCCCUUCACCAGCAGA	chr6:87967017-87967247(+)$1	230	144	169	22.3344
CUCGGCCAUCCUCCGUCUGCCCAGU	chr19:54485436-54485680(+)$1	244	159	184	22.4600
GAACGACUUGAAAAGGAGCGUCGAG	chr11:110108115-110108494(-)$1	379	185	210	22.8151
GUUUGCAUUUUUGUUUUCUUGAAAA	chr9:134064337-134064619(+)$1	282	185	210	23.0856
GGAAGCCCAGUUCACCACGGCCCUG	chr19:19456011-19456255(+)$1	244	139	164	23.6249
GAAAGUAAACUGACUCACUAUUUUC	chr10:91478488-91478721(+)$1	233	3	28	23.7573
AGCCAGUGACCCCCACCAGCAAAGC	chr9:133760188-133760447(+)$1	259	34	59	20.0880
GGAUACAUCAAAUAAUUACUGUAUU	chr4:130003385-130003630(-)$1	245	15	40	21.5839
GCUGGUUCUUCAUUCAUUACCUUCG	chr22:39639814-39640041(-)$1	227	158	183	22.8882
UGUUUUCUUUUCUCAAUUGGAAACA	chr10:11791392-11791619(+)$1	227	69	94	23.7573
GGGCAGUCCUGUUUUCCUCUGACCC	chr22:41735740-41735973(+)$1	233	31	56	23.0317
UAUCUUUGAAGAGAUGAUGAAGAGA	chr10:24880053-24880359(-)$1	306	55	80	22.8254
CGGCCACCCACACCAGCCCCGUGGC	chr19:41096859-41097254(+)$1	395	164	189	22.8254
AUGAUCCAAAAGUACCUAGGGAACA	chr4:39506877-39507092(-)$1	215	164	189	23.1013
UCAACAUACACAGUAUCAAAUGUAA	chrX:77298713-77298963(+)$1	250	20	45	22.8780
UGGGUCCAUCACACAAAUAUCCUGA	chr16:30991245-30991615(+)$1	370	254	279	21.6133
GUCCUCCUCUACUUUCUCGGAGUCC	chr7:27140784-27141043(+)$1	259	13	38	22.9547
GAGCUGCAUGGGGAUUUCGUGGCUC	chr8:42977532-42977776(+)$1	244	176	201	21.2797
CGCCCCUUCUUAGAAACCAGGAGCA	chr17:76969159-76969393(-)$1	234	76	101	21.2432
UUACAUUUUGAUCUUUUUAAUGAAC	chr4:109895421-109895649(-)$1	228	24	49	22.5324
ACGGCUCUCAACAGCAUCGACUCCG	chr2:234345934-234346227(+)$1	293	163	188	22.4814
UUUCUGUUCUGUUUGCCUCCAUAGG	chr3:51672120-51672436(+)$1	316	15	40	23.5444
CGGGCACAGAACUGCACAGUGACCG	chr16:2161258-2161572(-)$1	314	200	225	24.2502
GAGGCCACCUAUAAAAUUUGGUUUC	chr12:121857925-121858177(+)$1	252	214	239	23.7573
UCAGUAGCAGAAGAAGAACUGCUGA	chr5:118500102-118500474(+)$1	372	134	159	23.7573
UUCUUUCCCCACAGAACAAACAAaa	chr12:56818730-56818987(-)$1	257	37	62	20.5139
CUUUCUAUUUAAAUGUGCAGUGAGU	chr2:20173216-20173569(-)$1	353	273	298	19.7759
AUUUCUCUUUCCGUUCUUUGUGAAU	chr20:18529167-18529431(+)$1	264	56	81	23.9357
UAUUAUGAAAUUAUAAGCCAUAUUU	chr6:152545655-152545906(-)$1	251	68	93	22.5905
UGGUAAUAAAAUAGGAAAGCCACUC	chr10:60562862-60563102(+)$1	240	144	169	19.6980
UAUUAUUAGGAAGUAAUUAAAUGAU	chr14:67790341-67790549(+)$1	208	16	41	21.5839
CCAAGUAUGUCUUACUUUGUUGCUG	chr6:31918520-31918773(-)$1	253	37	62	23.7137
GGGUCUACCCUACCCUCAUGGAGCC	chr12:124821481-124821780(-)$1	299	137	162	23.0576
UGCGGGACAUUGUCCAUCCCCGCCC	chr3:38357868-38358115(+)$1	247	215	240	22.3632
AUCUCUGGCUUCACCAAACAGAGGA	chr9:115337083-115337324(+)$1	241	137	162	23.0643
AGAGGGUUUCAAAAAGUCCACCCUG	chr2:32476178-32476416(+)$1	238	105	130	19.8466
AUCAAAAGCUCCAUUAAAUUGUCAU	chrX:106882546-106882751(-)$1	205	134	159	22.2885
GUUGACUGUAUGUGAUUUGAGUUCU	chr4:88084571-88084843(-)$1	272	158	183	22.6819
AAAUGAAGAUGAAAAAGGAUUUAUU	chr21:34994201-34994464(-)$1	263	100	125	23.8896
AUUUUUGUUUGAGAAAUACCAAGAA	chr5:34823500-34823854(+)$1	354	231	256	23.1014
AUAUCAUGAAGGUAAAAAAUAAUGA	chr2:32822713-32823066(+)$1	353	311	336	21.4749
AAAGAACGGACGGGGGAAGUUCUUC	chr4:140467973-140468305(-)$1	332	193	218	23.0244
GGUACAACUUGCUCAUUAUCUUUGA	chr2:228159622-228159872(+)$1	250	155	180	22.2021
CAUCUUCUAUGUCUUGUCUGAAGGU	chr17:38451492-38451816(+)$1	324	92	117	22.6994
GAAAUACCUUACAAAGAAACGUAUU	chr10:5798473-5798743(+)$1	270	236	261	22.6263
UGUAGAGUUUUCUUCCUUCCCCUCU	chr2:219618238-219618492(+)$1	254	197	222	21.0964
CCAGACCCCAGAGUCAUCGUCUGUG	chr12:2997284-2997543(+)$1	259	94	119	21.6537
UUGGUGGUUCUACUCGUAUCCCCAA	chr11:122930080-122930512(-)$1	432	221	246	19.7984

#DB
((((.((...........)))))).	chr20:62594331-62594584(+)$1	1	148	173	22.1799
(((((((.............)))))	chr3:127817617-127817887(-)$1	1	5	30	23.5444
((.((((..............))))	chr6:7401088-7401384(+)$1	1	173	198	20.8980
.((((.(...........).)))).	chr22:18209666-18209944(+)$1	1	98	123	23.2311
.((((((.............)))))	chr4:37851832-37852096(+)$1	1	87	112	22.8254
(((((((...........)))))))	chr1:38353008-38353254(-)$1	1	150	175	23.7417
.(((((............))))).(	chr2:228395737-228396028(+)$1	1	47	72	19.8649
(((((((.............)))))	chr1:155746138-155746371(-)$1	1	176	201	21.4169
.((((((..............))))	chr11:46907538-46907771(-)$1	1	175	200	21.5065
)))((((...........))))..)	chr6:18149131-18149391(-)$1	1	81	106	19.9913
(((((((...........)))))))	chr17:74085263-74085503(-)$1	1	148	173	23.7417
(.(((((...........)))))))	chr17:73269491-73269755(-)$1	1	90	115	22.2520
...((((...........))))...	chr2:109429175-109429431(+)$1	1	164	189	22.0546
(((((((............)).)))	chr6:87967017-87967247(+)$1	1	144	169	22.3344
((.(((............))).)).	chr19:54485436-54485680(+)$1	1	159	184	22.4600
(..((((............))))..	chr11:110108115-110108494(-)$1	1	185	210	22.8151
.(((.((............)).)))	chr9:134064337-134064619(+)$1	1	185	210	23.0856
((..(((...........))).)))	chr19:19456011-19456255(+)$1	1	139	164	23.6249
(((((((...........)))))))	chr10:91478488-91478721(+)$1	1	3	28	23.7573
((((.((................))	chr9:133760188-133760447(+)$1	1	34	59	20.0880
(((((((............))))))	chr4:130003385-130003630(-)$1	1	15	40	21.5839
((.(((............)))...)	chr22:39639814-39640041(-)$1	1	158	183	22.8882
(((((((...........)))))))	chr10:11791392-11791619(+)$1	1	69	94	23.7573
((((((............))).)))	chr22:41735740-41735973(+)$1	1	31	56	23.0317
.((((((.............)))))	chr10:24880053-24880359(-)$1	1	55	80	22.8254
.((((((.............)))))	chr19:41096859-41097254(+)$1	1	164	189	22.8254
.((.(((............))).))	chr4:39506877-39507092(-)$1	1	164	189	23.1013
(..((((............))))..	chrX:77298713-77298963(+)$1	1	20	45	22.8780
.((((.............)))))))	chr16:30991245-30991615(+)$1	1	254	279	21.6133
(..((((...........))))...	chr7:27140784-27141043(+)$1	1	13	38	22.9547
(((((((...........)))))))	chr8:42977532-42977776(+)$1	1	176	201	21.2797
.((.(((...........))).)).	chr17:76969159-76969393(-)$1	1	76	101	21.2432
((.((((...........)))))))	chr4:109895421-109895649(-)$1	1	24	49	22.5324
.(((.((...........))..)))	chr2:234345934-234346227(+)$1	1	163	188	22.4814
(((((((.............)))))	chr3:51672120-51672436(+)$1	1	15	40	23.5444
(((.(((...........))).)))	chr16:2161258-2161572(-)$1	1	200	225	24.2502
(((((((...........)))))))	chr12:121857925-121858177(+)$1	1	214	239	23.7573
(((((((...........)))))))	chr5:118500102-118500474(+)$1	1	134	159	23.7573
((((((................)))	chr12:56818730-56818987(-)$1	1	37	62	20.5139
(((.((................)).	chr2:20173216-20173569(-)$1	1	273	298	19.7759
((((..(............).))))	chr20:18529167-18529431(+)$1	1	56	81	23.9357
((.((((...........))))..)	chr6:152545655-152545906(-)$1	1	68	93	22.5905
.(((..............)))((((	chr10:60562862-60563102(+)$1	1	144	169	19.6980
(((((((............))))))	chr14:67790341-67790549(+)$1	1	16	41	21.5839
(((.(((.............)))))	chr6:31918520-31918773(-)$1	1	37	62	23.7137
((.((((...........)))).))	chr12:124821481-124821780(-)$1	1	137	162	23.0576
.(((((............)))))).	chr3:38357868-38358115(+)$1	1	215	240	22.3632
.((((((...........)))))).	chr9:115337083-115337324(+)$1	1	137	162	23.0643
..(((((............))))).	chr2:32476178-32476416(+)$1	1	105	130	19.8466
(.(((.............)))))).	chrX:106882546-106882751(-)$1	1	134	159	22.2885
(((((((............))))..	chr4:88084571-88084843(-)$1	1	158	183	22.6819
(((((((............))))))	chr21:34994201-34994464(-)$1	1	100	125	23.8896
.((((((............))))))	chr5:34823500-34823854(+)$1	1	231	256	23.1014
.((((((..............))))	chr2:32822713-32823066(+)$1	1	311	336	21.4749
(((((((...........)))))).	chr4:140467973-140468305(-)$1	1	193	218	23.0244
(((.(((..............))))	chr2:228159622-228159872(+)$1	1	155	180	22.2021
)((((((............))))))	chr17:38451492-38451816(+)$1	1	92	117	22.6994
(((.(((.............)))))	chr10:5798473-5798743(+)$1	1	236	261	22.6263
((.((((..............))))	chr2:219618238-219618492(+)$1	1	197	222	21.0964
((((((............))))).)	chr12:2997284-2997543(+)$1	1	94	119	21.6537
))((.((............))))..	chr11:122930080-122930512(-)$1	1	221	246	19.7984

#PSSM
g : 0.19	[ : 0.14	e : 0.09	d : 0.08	f : 0.08	: : 0.06	h : 0.06	b : 0.06	! : 0.06	= : 0.04	c : 0.04	$ : 0.01	a : 0.01	
f : 0.22	g : 0.18	e : 0.13	d : 0.11	h : 0.06	c : 0.06	= : 0.04	b : 0.04	! : 0.04	[ : 0.03	$ : 0.01	: : 0.01	
g : 0.18	f : 0.18	[ : 0.11	e : 0.11	d : 0.08	c : 0.08	h : 0.06	! : 0.06	= : 0.04	b : 0.04	$ : 0.01	
d : 0.22	f : 0.16	g : 0.14	c : 0.11	[ : 0.11	e : 0.09	h : 0.06	= : 0.03	! : 0.01	b : 0.01	
d : 0.21	c : 0.18	f : 0.16	g : 0.11	e : 0.09	[ : 0.08	h : 0.06	= : 0.03	b : 0.01	! : 0.01	w : 0.01	
d : 0.18	f : 0.16	c : 0.16	b : 0.11	g : 0.11	e : 0.08	h : 0.06	= : 0.03	v : 0.03	[ : 0.01	! : 0.01	w : 0.01	
d : 0.18	f : 0.14	g : 0.11	c : 0.11	b : 0.09	u : 0.09	h : 0.06	a : 0.03	= : 0.03	e : 0.03	v : 0.03	y : 0.03	w : 0.01	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
t : 0.36	u : 0.32	v : 0.16	w : 0.09	y : 0.04	
u : 0.22	v : 0.13	c : 0.13	d : 0.11	w : 0.08	e : 0.06	g : 0.06	y : 0.04	b : 0.03	= : 0.03	f : 0.03	a : 0.01	h : 0.01	
d : 0.16	c : 0.14	v : 0.13	b : 0.08	w : 0.08	e : 0.08	g : 0.08	f : 0.06	y : 0.04	h : 0.04	= : 0.03	] : 0.01	a : 0.01	
d : 0.19	c : 0.18	g : 0.11	f : 0.11	w : 0.08	e : 0.08	h : 0.06	b : 0.04	y : 0.04	= : 0.03	2 : 0.01	] : 0.01	
d : 0.22	f : 0.14	g : 0.13	] : 0.11	e : 0.08	c : 0.08	h : 0.06	= : 0.04	y : 0.04	3 : 0.01	2 : 0.01	b : 0.01	
f : 0.16	g : 0.14	d : 0.13	e : 0.11	c : 0.11	= : 0.06	h : 0.06	b : 0.06	4 : 0.03	] : 0.03	: : 0.01	y : 0.01	3 : 0.01	2 : 0.01	
f : 0.18	g : 0.16	d : 0.09	b : 0.09	c : 0.08	= : 0.06	h : 0.06	2 : 0.06	: : 0.04	e : 0.04	4 : 0.03	3 : 0.01	a : 0.01	] : 0.01	
g : 0.18	f : 0.14	] : 0.09	d : 0.06	= : 0.06	h : 0.06	b : 0.06	e : 0.06	2 : 0.04	c : 0.04	: : 0.04	4 : 0.03	3 : 0.03	F : 0.01	E : 0.01	

#score	1362.4021662448595
#seq	61
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m3_run2.txt

#BEAR
h[cccqqqqqqqqccc]hhh	chr2:20232498-20232769(-)$1	271	86	106	14.8850
g!!bbqqqqqqqqbb]gggg	chr7:2400318-2400584(+)$1	266	17	37	14.5801
eeeeeqqqqqqqqeeeeedd	chr9:127280759-127281003(-)$1	244	170	190	14.3140
e!!bbqqqqqqqqbb22eee	chr22:41922245-41922513(+)$1	268	23	43	13.9765
ddcccqqqqqqqqccc]ddd	chr8:144872996-144873310(-)$1	314	259	279	14.6299
[ddddqqqqqqqqddddccc	chr2:48034380-48034759(-)$1	379	145	165	14.3044
===[aqqqqqqqqa======	chr19:1038826-1039166(+)$1	340	271	291	15.4669
eeeeeqqqqqqqqeeeee22	chr19:2039053-2039406(-)$1	353	135	155	14.2823
gggggqqqqqqqqggggggg	chr12:102512147-102512410(-)$1	263	188	208	15.3230
dd[bbqqqqqqqqbb]dddd	chr11:9801169-9801416(-)$1	247	208	228	13.3584
e[cccqqqqqqqqccceeee	chr8:30037925-30038208(+)$1	283	230	250	15.3163
"""bbqqqqqqqqbb333gg	chr5:173384993-173385323(+)$1	330	273	293	14.5039
ggg[aqqqqqqqqa]ggggg	chr22:21803727-21803990(+)$1	263	125	145	15.2406
ffcccqqqqqqqqccc4444	chr1:154441743-154442030(+)$1	287	158	178	14.8182
i!!bbqqqqqqqqbb22iii	chr9:14313385-14313721(-)$1	336	98	118	14.2440
""cccqqqqqqqqccc333e	chr19:23541464-23541756(-)$1	292	157	177	15.5924
eeeeeqqqqqqqqeeeee:g	chr7:64865791-64866078(+)$1	287	125	145	13.6458
gggbbqqqqqqqqbb]gggg	chr3:113507455-113507794(+)$1	339	114	134	14.4686
fffffqqqqqqqqffffffe	chr19:12778887-12779238(-)$1	351	79	99	13.6814
eeeeeqqqqqqqqeeeeeee	chr11:57510307-57510593(+)$1	286	77	97	14.5048
e[cccqqqqqqqqccceeee	chr14:67852807-67853075(+)$1	268	183	203	15.3163
"""bbqqqqqqqqbb333hh	chr7:10972985-10973425(-)$1	440	399	419	14.1108
eecccqqqqqqqqccc22ee	chr3:194123330-194123686(-)$1	356	202	222	15.0089
c[cccqqqqqqqqcccccc:	chr16:16379165-16379453(+)$1	288	211	231	14.1318
eeeeeqqqqqqqqeeeeebb	chr19:4361247-4361519(-)$1	272	132	152	13.9378
c[cccqqqqqqqqccc]ccc	chr7:92030418-92030694(+)$1	276	174	194	15.3342
eeeeeqqqqqqqqeeeee33	chr12:69235041-69235381(+)$1	340	203	223	14.7176
eecccqqqqqqqqccc4444	chr17:57771491-57771868(+)$1	377	222	242	15.0608
eeeeeqqqqqqqqeeeee22	chr4:10075896-10076162(-)$1	266	213	233	14.2823
eeeeeqqqqqqqqeeeee]a	chr10:120795187-120795432(-)$1	245	17	37	14.5633
gg!!aqqqqqqqqa22gggg	chr6:43753553-43753822(+)$1	269	30	50	14.6814
iiiiiqqqqqqqqiiiiiii	chr12:76453496-76453755(-)$1	259	85	105	15.2674
eee[aqqqqqqqqa]eeeee	chr19:4360270-4360554(-)$1	284	18	38	14.7384
[ddddqqqqqqqqdddd]cc	chr7:102191555-102191797(-)$1	242	187	207	14.4233
iiiiiqqqqqqqqiiiiiii	chr2:85549670-85549943(-)$1	273	196	216	15.2674
!!cccqqqqqqqqcccccc3	chr2:176042834-176043117(-)$1	283	100	120	15.3836
eddddqqqqqqqqdddd22e	chr3:48711229-48711511(-)$1	282	148	168	14.0846
iiiiiqqqqqqqqiiiiiii	chr6:36458731-36459000(+)$1	269	65	85	15.2674
""cccqqqqqqqqccc22ee	chr4:15640023-15640325(-)$1	302	183	203	15.0600
gggggqqqqqqqqggggggg	chr13:48832156-48832465(+)$1	309	119	139	15.3230
ddd[aqqqqqqqqa]dddd3	chr12:69973329-69973628(+)$1	299	24	44	14.1328
f[cccqqqqqqqqccc]fff	chr15:80430436-80430828(+)$1	392	248	268	15.0730
c[cccqqqqqqqqccc]ccc	chr5:115166963-115167222(-)$1	259	229	249	15.3342
eeeeeqqqqqqqqeeeee]g	chr3:127788505-127788756(+)$1	251	92	112	14.6992
!ddddqqqqqqqqdddd22a	chr17:45656696-45656983(+)$1	287	117	137	14.1186
[ddddqqqqqqqqdddd]cc	chr5:6756127-6756371(+)$1	244	72	92	14.4233
Gddddqqqqqqqqddddfff	chr20:3127069-3127323(-)$1	254	54	74	13.4085
gggggqqqqqqqqggggggg	chr4:185550081-185550413(-)$1	332	78	98	15.3230
gggggqqqqqqqqggggggg	chr1:22005363-22005608(-)$1	245	183	203	15.3230
""cccqqqqqqqqccc333e	chr9:14321963-14322202(+)$1	239	103	123	15.5924
fffffqqqqqqqqffffff]	chr5:114951729-114952009(-)$1	280	164	184	13.7020
cddddqqqqqqqqdddd333	chr15:74890164-74890512(+)$1	348	91	111	14.4571
eeeeeqqqqqqqqeeeee:d	chr11:75283336-75283697(+)$1	361	105	125	13.4526
iiiiiqqqqqqqqiiiiiii	chr3:121355916-121356202(-)$1	286	38	58	15.2674
ccc[aqqqqqqqqaccc]gg	chr2:148778940-148779211(+)$1	271	71	91	15.0468
gggggqqqqqqqqggggggg	chr10:98336371-98336684(-)$1	313	104	124	15.3230
gggggqqqqqqqqggggggg	chr12:74933109-74933375(+)$1	266	108	128	15.3230
gggggqqqqqqqqggggggg	chr12:69233481-69233870(+)$1	389	170	190	15.3230
e[cccqqqqqqqqccc22ee	chr17:56082370-56082654(-)$1	284	62	82	15.1774
eee[aqqqqqqqqa]eeeee	chr7:157178449-157178822(+)$1	373	81	101	14.7384
"ddddqqqqqqqqddddccc	chr7:129471420-129471692(-)$1	272	126	146	14.2254
gggggqqqqqqqqggggggg	chr1:224563402-224563786(+)$1	384	259	279	15.3230
gggggqqqqqqqqggggggg	chr19:13054952-13055216(+)$1	264	74	94	15.3230
!!cccqqqqqqqqccc]ddd	chr1:56961812-56962144(-)$1	332	296	316	15.1538
=====qqqqqqqq=======	chr19:39875080-39875347(+)$1	267	6	26	15.5090
gggggqqqqqqqqggggggg	chr20:48698581-48698903(-)$1	322	92	112	15.3230
"ddddqqqqqqqqddddddd	chr21:30302128-30302414(-)$1	286	156	176	13.8750
fffffqqqqqqqqffffffc	chr12:7965005-7965248(-)$1	243	192	212	13.6851

#otherMatches

#Seq PSSM
GUACUUGCCACAUAGUUUCC	chr2:20232498-20232769(-)$1	271	86	106	14.8850
CUUGUUCAGAAUUACUGGGA	chr7:2400318-2400584(+)$1	266	17	37	14.5801
UUCCACCAAGUGUUGGAAAC	chr9:127280759-127281003(-)$1	244	170	190	14.3140
AAAGGGAAGUGUACCACUGA	chr22:41922245-41922513(+)$1	268	23	43	13.9765
UUCCUGCCCUCCGAGGCGAG	chr8:144872996-144873310(-)$1	314	259	279	14.6299
UCCAGCAAUGUUUCUGGUAU	chr2:48034380-48034759(-)$1	379	145	165	14.3044
CGUGCUUUGCUUUGAUGCUU	chr19:1038826-1039166(+)$1	340	271	291	15.4669
GCCAUCUGCCCACGUGGCUU	chr19:2039053-2039406(-)$1	353	135	155	14.2823
UCCCUUUGAGAAUGGGGAUU	chr12:102512147-102512410(-)$1	263	188	208	15.3230
UUUCAAAAUAACAUGCAAAA	chr11:9801169-9801416(-)$1	247	208	228	13.3584
CCUCUCUUUAAAAAGAGUUC	chr8:30037925-30038208(+)$1	283	230	250	15.3163
UUUGUUAUGCACUACUUUUG	chr5:173384993-173385323(+)$1	330	273	293	14.5039
GUUUCAGACCUCAGCAGCUG	chr22:21803727-21803990(+)$1	263	125	145	15.2406
UUGGAAUAAAUACUCUUAAA	chr1:154441743-154442030(+)$1	287	158	178	14.8182
UCCUGAUUGAUCGCAUCGCG	chr9:14313385-14313721(-)$1	336	98	118	14.2440
UGCUGAGAAAUCCUAGAAAU	chr19:23541464-23541756(-)$1	292	157	177	15.5924
UGAGAAAAAAACAUUUUAAA	chr7:64865791-64866078(+)$1	287	125	145	13.6458
GGAGGAACUACUGCUAUCCC	chr3:113507455-113507794(+)$1	339	114	134	14.4686
GGGUCACAUUUUGGACCCUG	chr19:12778887-12779238(-)$1	351	79	99	13.6814
UUCAGUCAUGAUCCUGAAGC	chr11:57510307-57510593(+)$1	286	77	97	14.5048
GUGAUUUCUCAUUAUUcagg	chr14:67852807-67853075(+)$1	268	183	203	15.3163
AACUAUUAGAAUUUAAAGAA	chr7:10972985-10973425(-)$1	440	399	419	14.1108
GUACAUUCAGCAUUGUAAAU	chr3:194123330-194123686(-)$1	356	202	222	15.0089
CCGGAUUCUACCUUCUGCCU	chr16:16379165-16379453(+)$1	288	211	231	14.1318
CGCUGACUCCCAACGGUGAC	chr19:4361247-4361519(-)$1	272	132	152	13.9378
CCACUUUAUAUACAGUAGGA	chr7:92030418-92030694(+)$1	276	174	194	15.3342
GUUAUCUGUGAAAAUAGCCA	chr12:69235041-69235381(+)$1	340	203	223	14.7176
ACAUCGUACACUGGAUUGCA	chr17:57771491-57771868(+)$1	377	222	242	15.0608
ACUUUGUGUGAUGGGGGUGU	chr4:10075896-10076162(-)$1	266	213	233	14.2823
UAUUAAUCCUAUAUAAUAGA	chr10:120795187-120795432(-)$1	245	17	37	14.5633
UAGGGUUUUUUUUCAGUAUU	chr6:43753553-43753822(+)$1	269	30	50	14.6814
AAAUCAUUUUAGCGAUUUGA	chr12:76453496-76453755(-)$1	259	85	105	15.2674
UCCAGUGAAGCCUCCGGACC	chr19:4360270-4360554(-)$1	284	18	38	14.7384
GGAACUGGGGCUUGUUUGAU	chr7:102191555-102191797(-)$1	242	187	207	14.4233
UUUCUAAAUCAAAAGAAAUG	chr2:85549670-85549943(-)$1	273	196	216	15.2674
AACAAAUUACUGCUUGACAU	chr2:176042834-176043117(-)$1	283	100	120	15.3836
CUCUGUAAAAAUGUAGACUG	chr3:48711229-48711511(-)$1	282	148	168	14.0846
AAAAUGCUUGUAGGUUUUGC	chr6:36458731-36459000(+)$1	269	65	85	15.2674
AGUCAGAUAAAGGUGAGAUU	chr4:15640023-15640325(-)$1	302	183	203	15.0600
UUUAGAUCUUAACCUGGAUA	chr13:48832156-48832465(+)$1	309	119	139	15.3230
AUGCCUUACUGUUGUCAUUC	chr12:69973329-69973628(+)$1	299	24	44	14.1328
AUUCACCAGUCUUUGAUUAA	chr15:80430436-80430828(+)$1	392	248	268	15.0730
UGCUGGGGAAUAAUAGGGGA	chr5:115166963-115167222(-)$1	259	229	249	15.3342
UUUAAUAAUGUUUUUGAAUU	chr3:127788505-127788756(+)$1	251	92	112	14.6992
CUAUAGAAGUAAAUAUACUA	chr17:45656696-45656983(+)$1	287	117	137	14.1186
GCCCAGUGCGCCGUGGGGAG	chr5:6756127-6756371(+)$1	244	72	92	14.4233
GUUACUGUGAAUUGUAAUGU	chr20:3127069-3127323(-)$1	254	54	74	13.4085
CUCUCAUGCUGCAGAGGGUA	chr4:185550081-185550413(-)$1	332	78	98	15.3230
UUUCAAUAAAGCAUGAAAGU	chr1:22005363-22005608(-)$1	245	183	203	15.3230
UGUUUAGUUaaaaaaaaaaa	chr9:14321963-14322202(+)$1	239	103	123	15.5924
UAGGUACUGAAGAACUUAAU	chr5:114951729-114952009(-)$1	280	164	184	13.7020
CCUGAAGGUGCCAUCAGCCA	chr15:74890164-74890512(+)$1	348	91	111	14.4571
CAGGUACCUUCUCACCUGUG	chr11:75283336-75283697(+)$1	361	105	125	13.4526
AGCGCUUCCCUGUGUGCUGG	chr3:121355916-121356202(-)$1	286	38	58	15.2674
CAGACCCUUugcugcugcug	chr2:148778940-148779211(+)$1	271	71	91	15.0468
GAUAAAGAGGAAGUUGUCUU	chr10:98336371-98336684(-)$1	313	104	124	15.3230
GGGCACUUUCAGCUGCCCUC	chr12:74933109-74933375(+)$1	266	108	128	15.3230
AUAUAUUUCUAACUAUAUAA	chr12:69233481-69233870(+)$1	389	170	190	15.3230
AAAUUGUAUUUUAAGUGAUG	chr17:56082370-56082654(-)$1	284	62	82	15.1774
GACCAUUUUUUUUUUGUCUU	chr7:157178449-157178822(+)$1	373	81	101	14.7384
UGACAUUUGGCUUUGUCGUC	chr7:129471420-129471692(-)$1	272	126	146	14.2254
AUUUUUACCAUAUAAAGUAU	chr1:224563402-224563786(+)$1	384	259	279	15.3230
UCCCCUCCAACCUGGGGGGC	chr19:13054952-13055216(+)$1	264	74	94	15.3230
GCCAGAAAUAGCACUGAAUC	chr1:56961812-56962144(-)$1	332	296	316	15.1538
GGUCUGGUUGGUGAGACUUG	chr19:39875080-39875347(+)$1	267	6	26	15.5090
GUGGGGUGUUUCGCCUGCAC	chr20:48698581-48698903(-)$1	322	92	112	15.3230
AAGCUAUUAAUACGGCUUGU	chr21:30302128-30302414(-)$1	286	156	176	13.8750
agcuuuaaauccugaguugg	chr12:7965005-7965248(-)$1	243	192	212	13.6851

#DB
(.(((........))).)))	chr2:20232498-20232769(-)$1	1	86	106	14.8850
(..((........)).))))	chr7:2400318-2400584(+)$1	1	17	37	14.5801
(((((........)))))))	chr9:127280759-127281003(-)$1	1	170	190	14.3140
(..((........))..)))	chr22:41922245-41922513(+)$1	1	23	43	13.9765
(((((........))).)))	chr8:144872996-144873310(-)$1	1	259	279	14.6299
.((((........)))))))	chr2:48034380-48034759(-)$1	1	145	165	14.3044
(((.(........)))))))	chr19:1038826-1039166(+)$1	1	271	291	15.4669
(((((........)))))..	chr19:2039053-2039406(-)$1	1	135	155	14.2823
(((((........)))))))	chr12:102512147-102512410(-)$1	1	188	208	15.3230
((.((........)).))))	chr11:9801169-9801416(-)$1	1	208	228	13.3584
(.(((........)))))))	chr8:30037925-30038208(+)$1	1	230	250	15.3163
...((........))...))	chr5:173384993-173385323(+)$1	1	273	293	14.5039
(((.(........).)))))	chr22:21803727-21803990(+)$1	1	125	145	15.2406
(((((........)))....	chr1:154441743-154442030(+)$1	1	158	178	14.8182
(..((........))..)))	chr9:14313385-14313721(-)$1	1	98	118	14.2440
..(((........)))...)	chr19:23541464-23541756(-)$1	1	157	177	15.5924
(((((........))))).(	chr7:64865791-64866078(+)$1	1	125	145	13.6458
(((((........)).))))	chr3:113507455-113507794(+)$1	1	114	134	14.4686
(((((........))))))(	chr19:12778887-12779238(-)$1	1	79	99	13.6814
(((((........)))))))	chr11:57510307-57510593(+)$1	1	77	97	14.5048
(.(((........)))))))	chr14:67852807-67853075(+)$1	1	183	203	15.3163
...((........))...))	chr7:10972985-10973425(-)$1	1	399	419	14.1108
(((((........)))..))	chr3:194123330-194123686(-)$1	1	202	222	15.0089
(.(((........)))))).	chr16:16379165-16379453(+)$1	1	211	231	14.1318
(((((........)))))))	chr19:4361247-4361519(-)$1	1	132	152	13.9378
(.(((........))).)))	chr7:92030418-92030694(+)$1	1	174	194	15.3342
(((((........)))))..	chr12:69235041-69235381(+)$1	1	203	223	14.7176
(((((........)))....	chr17:57771491-57771868(+)$1	1	222	242	15.0608
(((((........)))))..	chr4:10075896-10076162(-)$1	1	213	233	14.2823
(((((........))))).)	chr10:120795187-120795432(-)$1	1	17	37	14.5633
((..(........)..))))	chr6:43753553-43753822(+)$1	1	30	50	14.6814
(((((........)))))))	chr12:76453496-76453755(-)$1	1	85	105	15.2674
(((.(........).)))))	chr19:4360270-4360554(-)$1	1	18	38	14.7384
.((((........)))).))	chr7:102191555-102191797(-)$1	1	187	207	14.4233
(((((........)))))))	chr2:85549670-85549943(-)$1	1	196	216	15.2674
..(((........)))))).	chr2:176042834-176043117(-)$1	1	100	120	15.3836
(((((........))))..)	chr3:48711229-48711511(-)$1	1	148	168	14.0846
(((((........)))))))	chr6:36458731-36459000(+)$1	1	65	85	15.2674
..(((........)))..))	chr4:15640023-15640325(-)$1	1	183	203	15.0600
(((((........)))))))	chr13:48832156-48832465(+)$1	1	119	139	15.3230
(((.(........).)))).	chr12:69973329-69973628(+)$1	1	24	44	14.1328
(.(((........))).)))	chr15:80430436-80430828(+)$1	1	248	268	15.0730
(.(((........))).)))	chr5:115166963-115167222(-)$1	1	229	249	15.3342
(((((........))))).)	chr3:127788505-127788756(+)$1	1	92	112	14.6992
.((((........))))..)	chr17:45656696-45656983(+)$1	1	117	137	14.1186
.((((........)))).))	chr5:6756127-6756371(+)$1	1	72	92	14.4233
(((((........))))(((	chr20:3127069-3127323(-)$1	1	54	74	13.4085
(((((........)))))))	chr4:185550081-185550413(-)$1	1	78	98	15.3230
(((((........)))))))	chr1:22005363-22005608(-)$1	1	183	203	15.3230
..(((........)))...)	chr9:14321963-14322202(+)$1	1	103	123	15.5924
(((((........)))))).	chr5:114951729-114952009(-)$1	1	164	184	13.7020
(((((........))))...	chr15:74890164-74890512(+)$1	1	91	111	14.4571
(((((........))))).(	chr11:75283336-75283697(+)$1	1	105	125	13.4526
(((((........)))))))	chr3:121355916-121356202(-)$1	1	38	58	15.2674
(((.(........)))).))	chr2:148778940-148779211(+)$1	1	71	91	15.0468
(((((........)))))))	chr10:98336371-98336684(-)$1	1	104	124	15.3230
(((((........)))))))	chr12:74933109-74933375(+)$1	1	108	128	15.3230
(((((........)))))))	chr12:69233481-69233870(+)$1	1	170	190	15.3230
(.(((........)))..))	chr17:56082370-56082654(-)$1	1	62	82	15.1774
(((.(........).)))))	chr7:157178449-157178822(+)$1	1	81	101	14.7384
.((((........)))))))	chr7:129471420-129471692(-)$1	1	126	146	14.2254
(((((........)))))))	chr1:224563402-224563786(+)$1	1	259	279	15.3230
(((((........)))))))	chr19:13054952-13055216(+)$1	1	74	94	15.3230
..(((........))).)))	chr1:56961812-56962144(-)$1	1	296	316	15.1538
(((((........)))))))	chr19:39875080-39875347(+)$1	1	6	26	15.5090
(((((........)))))))	chr20:48698581-48698903(-)$1	1	92	112	15.3230
.((((........)))))))	chr21:30302128-30302414(-)$1	1	156	176	13.8750
(((((........))))))(	chr12:7965005-7965248(-)$1	1	192	212	13.6851

#PSSM
e : 0.27	g : 0.20	" : 0.10	f : 0.07	i : 0.07	c : 0.07	d : 0.04	[ : 0.04	! : 0.04	= : 0.02	h : 0.01	G : 0.01	
e : 0.20	g : 0.19	d : 0.17	[ : 0.11	! : 0.07	" : 0.07	f : 0.05	i : 0.05	= : 0.02	c : 0.01	
c : 0.26	e : 0.17	g : 0.17	d : 0.14	! : 0.05	i : 0.05	f : 0.04	= : 0.02	" : 0.02	[ : 0.01	
c : 0.25	e : 0.14	g : 0.14	d : 0.13	b : 0.10	[ : 0.08	i : 0.05	f : 0.04	! : 0.01	= : 0.01	
c : 0.25	e : 0.14	g : 0.14	d : 0.13	b : 0.10	a : 0.10	i : 0.05	f : 0.04	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.25	e : 0.14	g : 0.14	d : 0.13	b : 0.10	a : 0.10	i : 0.05	f : 0.04	= : 0.01	
c : 0.26	e : 0.14	g : 0.14	d : 0.13	b : 0.10	] : 0.05	i : 0.05	f : 0.04	= : 0.02	2 : 0.01	
c : 0.26	e : 0.17	g : 0.16	d : 0.14	i : 0.05	] : 0.04	2 : 0.04	f : 0.04	= : 0.02	3 : 0.02	
g : 0.20	e : 0.20	d : 0.16	] : 0.08	2 : 0.07	3 : 0.05	i : 0.05	f : 0.04	c : 0.04	= : 0.02	4 : 0.02	
e : 0.22	g : 0.20	c : 0.08	d : 0.07	3 : 0.07	i : 0.07	f : 0.07	2 : 0.07	] : 0.04	= : 0.02	4 : 0.02	h : 0.01	
g : 0.23	e : 0.13	c : 0.11	d : 0.08	i : 0.07	f : 0.07	2 : 0.05	3 : 0.05	h : 0.02	= : 0.02	4 : 0.02	: : 0.02	] : 0.02	b : 0.01	
g : 0.26	e : 0.19	c : 0.10	d : 0.08	i : 0.07	3 : 0.05	h : 0.02	= : 0.02	2 : 0.02	4 : 0.02	a : 0.02	f : 0.02	: : 0.01	b : 0.01	] : 0.01	

#score	1000.7561037359632
#seq	68
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m1_run1.txt

#BEAR
ffffffuuuuuuuuuuuuffff	chr5:149493511-149493750(-)$1	239	203	225	21.5406
ddddvvvvvvvvvvvvvddddd	chr1:10439190-10439416(+)$1	226	66	88	21.1977
ffffwwwwwwwwwwwwwwffff	chr1:114307224-114307441(-)$1	217	96	118	23.3320
ee[avvvvvvvvvvvvva]eee	chr1:11722440-11722683(+)$1	243	25	47	22.2840
eeeeevvvvvvvvvvvvveeee	chr3:156869879-156870096(-)$1	217	172	194	22.4812
eeeexxxxxxxxxxxxxxxeee	chr11:1774983-1775213(-)$1	230	77	99	19.8887
eeeexxxxxxxxxxxxxxxeee	chr5:76371821-76372040(-)$1	219	78	100	19.8887
iddddvvvvvvvvvvvvvdddd	chr10:105358060-105358276(+)$1	216	110	132	21.8561
ffffffuuuuuuuuuuuuffff	chr8:87520430-87520667(-)$1	237	201	223	21.5406
ddddwwwwwwwwwwwwwwdddd	chr17:76851618-76851841(-)$1	223	96	118	22.6786
"cccwwwwwwwwwwwwwwccc3	chr19:46844144-46844363(+)$1	219	166	188	23.6925
[cccwwwwwwwwwwwwwwcccc	chr1:160183796-160184033(+)$1	237	20	42	23.7855
iiiiivvvvvvvvvvvvviiii	chr7:94298744-94298976(+)$1	232	75	97	22.0822
!cccxxxxxxxxxxxxxxxccc	chr16:12758409-12758624(+)$1	215	62	84	20.1625
ggggwwwwwwwwwwwwwwgggg	chr3:141645199-141645422(+)$1	223	178	200	23.4996
[ccc^^^^^^^^^^^^^^^^^^	chr22:37767755-37767986(-)$1	231	137	159	16.5030
[eeeeettttttttttteeeee	chr4:167983560-167983784(-)$1	224	187	209	19.5757
ffffffuuuuuuuuuuuuffff	chr2:26953442-26953664(+)$1	222	163	185	21.5406
ffffffuuuuuuuuuuuuffff	chr9:125609636-125609859(-)$1	223	145	167	21.5406
#dddduuuuuuuuuuuudddd3	chr16:4854684-4854921(-)$1	237	147	169	21.3309
ddddyyyyyyyyyyyyyyyydd	chr18:9958603-9958845(+)$1	242	151	173	19.8518
ddddxxxxxxxxxxxxxxxddd	chr11:9160513-9160732(-)$1	219	127	149	19.2432
!cccwwwwwwwwwwwwwwccc]	chr16:79631763-79631987(-)$1	224	159	181	23.8513
ffffxxxxxxxxxxxxxxxfff	chrX:79931408-79931625(+)$1	217	150	172	19.8765
!!bbuuuuuuuuuuuubb22ee	chr11:787721-787949(-)$1	228	81	103	19.8821
[cccuuuuuuuuuuuuccc]ee	chr3:197399849-197400064(+)$1	215	117	139	21.5758
cccxxxxxxxxxxxxxxxccc]	chr9:32973330-32973554(-)$1	224	145	167	19.7239
eeeeevvvvvvvvvvvvveeee	chr19:15532468-15532692(-)$1	224	164	186	22.4812
eeeexxxxxxxxxxxxxxxeee	chr20:56938942-56939164(+)$1	222	63	85	19.8887
"cccvvvvvvvvvvvvvccc33	chr11:110125889-110126126(-)$1	237	160	182	22.2606
##cccvvvvvvvvvvvvvccc5	chr7:151874188-151874413(-)$1	225	30	52	21.7009
eeeeuuuuuuuuuuuueeeee:	chr5:131154425-131154643(+)$1	218	187	209	19.8788
ggggwwwwwwwwwwwwwwgggg	chr12:66345887-66346106(+)$1	219	172	194	23.4996
gggggguuuuuuuuuuuugggg	chr5:139062894-139063109(+)$1	215	22	44	21.5112
ffffyyyyyyyyyyyyyyyyff	chr1:23885834-23886058(-)$1	224	114	136	20.4187
ffffwwwwwwwwwwwwwwffff	chr14:20917171-20917396(-)$1	225	32	54	23.3320
d!!avvvvvvvvvvvvva22dd	chr6:30584190-30584430(-)$1	240	96	118	21.4265
gggggvvvvvvvvvvvvvgggg	chr1:62702947-62703163(-)$1	216	6	28	22.4003
[cccwwwwwwwwwwwwwwccc]	chr7:102952724-102952939(+)$1	215	112	134	23.9147
[eeeeettttttttttteeeee	chr4:159046657-159046897(-)$1	240	152	174	19.5757
[dddduuuuuuuuuuuudddd]	chr20:31294263-31294489(-)$1	226	158	180	21.5908
iiiiwwwwwwwwwwwwwwiiii	chr5:41731357-41731596(-)$1	239	94	116	23.2470
[dddduuuuuuuuuuuudddd]	chr22:18583952-18584178(+)$1	226	103	125	21.5908
hhhhwwwwwwwwwwwwwwhhhh	chr6:116839661-116839877(+)$1	216	21	43	21.8893
hhhhwwwwwwwwwwwwwwhhhh	chr17:34591068-34591293(-)$1	225	72	94	21.8893
ggggwwwwwwwwwwwwwwgggg	chr4:83345304-83345525(+)$1	221	122	144	23.4996
eeeewwwwwwwwwwwwwweeee	chr13:27261308-27261524(+)$1	216	29	51	23.4242
fffffvvvvvvvvvvvvvffff	chr20:3148209-3148434(-)$1	225	75	97	22.3009
gggg[atttttttttttagggg	chr20:1106045-1106270(+)$1	225	180	202	20.3081
ffffxxxxxxxxxxxxxxxfff	chr12:13714308-13714525(-)$1	217	43	65	19.8765
[ddddvvvvvvvvvvvvvdddd	chr5:41934980-41935206(+)$1	226	178	200	22.0623
ffffwwwwwwwwwwwwwwffff	chr12:74932182-74932405(+)$1	223	29	51	23.3320
eeeeevvvvvvvvvvvvveeee	chr3:39136881-39137100(+)$1	219	187	209	22.4812
#ccc^^^^^^^^^^^^^^^^^^	chr10:129763137-129763357(+)$1	220	100	122	16.3076
ffffffuuuuuuuuuuuuffff	chr17:80616432-80616658(-)$1	226	197	219	21.5406
"cccxxxxxxxxxxxxxxxccc	chr14:91698898-91699118(+)$1	220	48	70	20.0681
!!cccvvvvvvvvvvvvvccc]	chr2:11680077-11680298(+)$1	221	75	97	22.9315
ffffffuuuuuuuuuuuuffff	chr4:56898120-56898335(-)$1	215	175	197	21.5406

#otherMatches

#Seq PSSM
CCUAGGUUUACAAAUAUUUUUA	chr5:149493511-149493750(-)$1	239	203	225	21.5406
AGUGAAAUUAUGUGAUACACUG	chr1:10439190-10439416(+)$1	226	66	88	21.1977
CCAGAUUCUUAUAUCUCCCUGG	chr1:114307224-114307441(-)$1	217	96	118	23.3320
CCAGGCCAUCACAGAAACAGGU	chr1:11722440-11722683(+)$1	243	25	47	22.2840
GAAGCAGAAAUAAAGUAAGUUU	chr3:156869879-156870096(-)$1	217	172	194	22.4812
CUUAGUACAUGAUCCCCUGUGA	chr11:1774983-1775213(-)$1	230	77	99	19.8887
GCUGCCUAUCCUUCCUCCCCAG	chr5:76371821-76372040(-)$1	219	78	100	19.8887
CCCUUGCAAUAAAAGAAAAAGG	chr10:105358060-105358276(+)$1	216	110	132	21.8561
UCUUGUGCGAAAUGUAAAACAG	chr8:87520430-87520667(-)$1	237	201	223	21.5406
GGCCUCCAACGCCCCUGUGGCC	chr17:76851618-76851841(-)$1	223	96	118	22.6786
CACCCUCCAACGCCCUCCGGUU	chr19:46844144-46844363(+)$1	219	166	188	23.6925
UCCCUUUUUGUCUCUCAUGGGC	chr1:160183796-160184033(+)$1	237	20	42	23.7855
AGUGAUAAAUAAAAACCCUUGC	chr7:94298744-94298976(+)$1	232	75	97	22.0822
AGGAGAAUUUAUUCAAACAUCC	chr16:12758409-12758624(+)$1	215	62	84	20.1625
AGCUUCAAAGCAAACAACAGUU	chr3:141645199-141645422(+)$1	223	178	200	23.4996
CCACCCAACAUCAAACAAAGCA	chr22:37767755-37767986(-)$1	231	137	159	16.5030
AUCAUUGUACUUUUAGAAAUGA	chr4:167983560-167983784(-)$1	224	187	209	19.5757
GCCCUCUGUGUUUAUGUUGGGG	chr2:26953442-26953664(+)$1	222	163	185	21.5406
UAAGAUUUUAAAAUUGCUAUUU	chr9:125609636-125609859(-)$1	223	145	167	21.5406
UGUCCCCAUCCCCCACUGGAUU	chr16:4854684-4854921(-)$1	237	147	169	21.3309
GCUUAAAAAAAAUUGCAUAAAA	chr18:9958603-9958845(+)$1	242	151	173	19.8518
GUUUCACAGAAGUAAACAUAAG	chr11:9160513-9160732(-)$1	219	127	149	19.2432
UAGUCUGCCAUUAAAAAAACUC	chr16:79631763-79631987(-)$1	224	159	181	23.8513
GAGUAAAAUAAUCCAGAUCGCU	chrX:79931408-79931625(+)$1	217	150	172	19.8765
AACGGCAAGAAAGGAAUGGACC	chr11:787721-787949(-)$1	228	81	103	19.8821
AUUCUUAAAGCUCCCUGAAGGA	chr3:197399849-197400064(+)$1	215	117	139	21.5758
CAUUUCCUAAAUUAAAACAUGC	chr9:32973330-32973554(-)$1	224	145	167	19.7239
CCAGUGGGGUUGUAGAGAGCUG	chr19:15532468-15532692(-)$1	224	164	186	22.4812
CUGCGAAUUUCUCUUGACAGCG	chr20:56938942-56939164(+)$1	222	63	85	19.8887
UAGUUUCCCAUGAUAUCACUUG	chr11:110125889-110126126(-)$1	237	160	182	22.2606
AACUUAAAUUUAGAUACAGAGG	chr7:151874188-151874413(-)$1	225	30	52	21.7009
UUGCUUUAUUUCAAAUGCAACU	chr5:131154425-131154643(+)$1	218	187	209	19.8788
CAUGUAAUUUUAAGUAUCCAUG	chr12:66345887-66346106(+)$1	219	172	194	23.4996
GUUUAACUCCACCCUCAUUUAA	chr5:139062894-139063109(+)$1	215	22	44	21.5112
GGGGCACCUCUGGACUCACUCC	chr1:23885834-23886058(-)$1	224	114	136	20.4187
GUAAUUGUCUGGAUCGUUUUGC	chr14:20917171-20917396(-)$1	225	32	54	23.3320
GUUGUUUUAUUUUUUUUCCUCC	chr6:30584190-30584430(-)$1	240	96	118	21.4265
GAUUCUCUCAGCUAUUUUGAGU	chr1:62702947-62703163(-)$1	216	6	28	22.4003
AAGGAUAAAAAGACUACCCCUC	chr7:102952724-102952939(+)$1	215	112	134	23.9147
UUAAGAUCCUUUUCUUCUCUUA	chr4:159046657-159046897(-)$1	240	152	174	19.5757
uucuuuuuuuuuuuuuugagau	chr20:31294263-31294489(-)$1	226	158	180	21.5908
AUGUGGCUUUCCUCUUAAAUAU	chr5:41731357-41731596(-)$1	239	94	116	23.2470
CUGGGAGAUUCAGAAACCUCAA	chr22:18583952-18584178(+)$1	226	103	125	21.5908
UUUCAGAAUAAAGGGAGAGAAA	chr6:116839661-116839877(+)$1	216	21	43	21.8893
AGGCCUCGCCCUCCUUUUGCCU	chr17:34591068-34591293(-)$1	225	72	94	21.8893
AAAAGGAGCUACUAACAAUUUU	chr4:83345304-83345525(+)$1	221	122	144	23.4996
UUGAUUAUAGAUACGACUUCAA	chr13:27261308-27261524(+)$1	216	29	51	23.4242
ACCCUCAAUUUUUGGAUAGGGG	chr20:3148209-3148434(-)$1	225	75	97	22.3009
AGGAUGGGUCCAGAAAGCUCCU	chr20:1106045-1106270(+)$1	225	180	202	20.3081
GGAUGUUUCCAAUGCUUUGAUC	chr12:13714308-13714525(-)$1	217	43	65	19.8765
AUCUAUAAAAAGAAAACUUAGA	chr5:41934980-41935206(+)$1	226	178	200	22.0623
CCAGGACAAUAACAUAGACUGG	chr12:74932182-74932405(+)$1	223	29	51	23.3320
CAUCAAAAUUUAAGACCAUGAU	chr3:39136881-39137100(+)$1	219	187	209	22.4812
AACCUUUUAUUCUCCCACUGAC	chr10:129763137-129763357(+)$1	220	100	122	16.3076
UCUGUGCAAUUUCAACAUCACA	chr17:80616432-80616658(-)$1	226	197	219	21.5406
CUUGGCAAAAAGGACAAUACAA	chr14:91698898-91699118(+)$1	220	48	70	20.0681
CUGCACACUUUCCACCUCUGCU	chr2:11680077-11680298(+)$1	221	75	97	22.9315
ACAUUUUACAUAAUAUAUAAAU	chr4:56898120-56898335(-)$1	215	175	197	21.5406

#DB
((((((............))))	chr5:149493511-149493750(-)$1	1	203	225	21.5406
((((.............))))(	chr1:10439190-10439416(+)$1	1	66	88	21.1977
((((..............))))	chr1:114307224-114307441(-)$1	1	96	118	23.3320
((.(.............).)))	chr1:11722440-11722683(+)$1	1	25	47	22.2840
(((((.............))))	chr3:156869879-156870096(-)$1	1	172	194	22.4812
((((...............)))	chr11:1774983-1775213(-)$1	1	77	99	19.8887
((((...............)))	chr5:76371821-76372040(-)$1	1	78	100	19.8887
(((((.............))))	chr10:105358060-105358276(+)$1	1	110	132	21.8561
((((((............))))	chr8:87520430-87520667(-)$1	1	201	223	21.5406
((((..............))))	chr17:76851618-76851841(-)$1	1	96	118	22.6786
.(((..............))).	chr19:46844144-46844363(+)$1	1	166	188	23.6925
.(((..............))))	chr1:160183796-160184033(+)$1	1	20	42	23.7855
(((((.............))))	chr7:94298744-94298976(+)$1	1	75	97	22.0822
.(((...............)))	chr16:12758409-12758624(+)$1	1	62	84	20.1625
((((..............))))	chr3:141645199-141645422(+)$1	1	178	200	23.4996
.(((..................	chr22:37767755-37767986(-)$1	1	137	159	16.5030
.(((((...........)))))	chr4:167983560-167983784(-)$1	1	187	209	19.5757
((((((............))))	chr2:26953442-26953664(+)$1	1	163	185	21.5406
((((((............))))	chr9:125609636-125609859(-)$1	1	145	167	21.5406
.((((............)))).	chr16:4854684-4854921(-)$1	1	147	169	21.3309
((((................))	chr18:9958603-9958845(+)$1	1	151	173	19.8518
((((...............)))	chr11:9160513-9160732(-)$1	1	127	149	19.2432
.(((..............))).	chr16:79631763-79631987(-)$1	1	159	181	23.8513
((((...............)))	chrX:79931408-79931625(+)$1	1	150	172	19.8765
..((............))..))	chr11:787721-787949(-)$1	1	81	103	19.8821
.(((............))).))	chr3:197399849-197400064(+)$1	1	117	139	21.5758
(((...............))).	chr9:32973330-32973554(-)$1	1	145	167	19.7239
(((((.............))))	chr19:15532468-15532692(-)$1	1	164	186	22.4812
((((...............)))	chr20:56938942-56939164(+)$1	1	63	85	19.8887
.(((.............)))..	chr11:110125889-110126126(-)$1	1	160	182	22.2606
..(((.............))).	chr7:151874188-151874413(-)$1	1	30	52	21.7009
((((............))))).	chr5:131154425-131154643(+)$1	1	187	209	19.8788
((((..............))))	chr12:66345887-66346106(+)$1	1	172	194	23.4996
((((((............))))	chr5:139062894-139063109(+)$1	1	22	44	21.5112
((((................))	chr1:23885834-23886058(-)$1	1	114	136	20.4187
((((..............))))	chr14:20917171-20917396(-)$1	1	32	54	23.3320
(..(.............)..))	chr6:30584190-30584430(-)$1	1	96	118	21.4265
(((((.............))))	chr1:62702947-62703163(-)$1	1	6	28	22.4003
.(((..............))).	chr7:102952724-102952939(+)$1	1	112	134	23.9147
.(((((...........)))))	chr4:159046657-159046897(-)$1	1	152	174	19.5757
.((((............)))).	chr20:31294263-31294489(-)$1	1	158	180	21.5908
((((..............))))	chr5:41731357-41731596(-)$1	1	94	116	23.2470
.((((............)))).	chr22:18583952-18584178(+)$1	1	103	125	21.5908
((((..............))))	chr6:116839661-116839877(+)$1	1	21	43	21.8893
((((..............))))	chr17:34591068-34591293(-)$1	1	72	94	21.8893
((((..............))))	chr4:83345304-83345525(+)$1	1	122	144	23.4996
((((..............))))	chr13:27261308-27261524(+)$1	1	29	51	23.4242
(((((.............))))	chr20:3148209-3148434(-)$1	1	75	97	22.3009
((((.(...........)))))	chr20:1106045-1106270(+)$1	1	180	202	20.3081
((((...............)))	chr12:13714308-13714525(-)$1	1	43	65	19.8765
.((((.............))))	chr5:41934980-41935206(+)$1	1	178	200	22.0623
((((..............))))	chr12:74932182-74932405(+)$1	1	29	51	23.3320
(((((.............))))	chr3:39136881-39137100(+)$1	1	187	209	22.4812
.(((..................	chr10:129763137-129763357(+)$1	1	100	122	16.3076
((((((............))))	chr17:80616432-80616658(-)$1	1	197	219	21.5406
.(((...............)))	chr14:91698898-91699118(+)$1	1	48	70	20.0681
..(((.............))).	chr2:11680077-11680298(+)$1	1	75	97	22.9315
((((((............))))	chr4:56898120-56898335(-)$1	1	175	197	21.5406

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

#score	1246.578175122388
#seq	58
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012d_hg19_UTR_m1_run1.txt

#BEAR
ggggg[cccwwwwwwwwwwwwwwccc22g	chr11:129979348-129979596(+)$1	248	30	59	23.7081
dhhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr14:74416627-74416857(+)$1	230	174	203	20.7037
cc"""ddddwwwwwwwwwwwwwwdddd33	chr7:104742429-104742661(+)$1	232	71	100	23.4432
ffffff[bbwwwwwwwwwwwwwwbb]fff	chr1:225682987-225683216(-)$1	229	92	121	21.0102
d[ffffffwwwwwwwwwwwwwwffffff]	chr17:61699896-61700120(-)$1	224	17	46	21.1206
[ccc####bbuuuuuuuuuuuubb333cc	chr20:36146676-36146907(-)$1	231	136	165	24.1286
ccc!!eeeeettttttttttteeeee]cc	chr1:115300450-115300683(-)$1	233	156	185	23.2592
cccddddwwwwwwwwwwwwwwdddd333c	chr17:76851572-76851803(-)$1	231	55	84	21.9012
f"""a[cccwwwwwwwwwwwwwwccc]a3	chr16:89351592-89351828(-)$1	236	165	194	23.8589
EEEccc[bbwwwwwwwwwwwwwwbb]ccc	chr7:148511027-148511265(-)$1	238	2	31	19.6849
bb$$$$$ccctttttttttttccc4444b	chr13:75923301-75923529(-)$1	228	77	106	22.6064
ddd!!ddddwwwwwwwwwwwwwwdddddd	chr5:71615889-71616135(-)$1	246	158	187	22.5928
:hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr6:3118956-3119181(-)$1	225	85	114	20.2958
:dddd[ddddtttttttttttdddddddd	chr16:4802193-4802423(-)$1	230	113	142	21.8804
==ccc[ddddassssssssssa]ddddcc	chr4:890152-890379(-)$1	227	167	196	17.7121
dd[gggggggtttttttttttggggggg]	chrX:134482300-134482530(+)$1	230	122	151	23.1304
bb[gggggggtttttttttttggggggg]	chr7:137561193-137561445(-)$1	252	189	218	22.9027
c####eeeeettttttttttteeeee444	chr16:3333193-3333416(-)$1	223	25	54	22.8307
dddd####bbtttttttttttbbddddee	chr18:12329536-12329813(-)$1	277	202	231	22.0509
eeebb[ddddtttttttttttdddd]bb]	chr22:40806525-40806749(-)$1	224	149	178	22.3748
"gggggggxxxxxxxxxxxxxxxgggggg	chr16:2818921-2819198(+)$1	277	48	77	19.4378
!!gggggggvvvvvvvvvvvvvggggggg	chr12:120703333-120703555(-)$1	222	129	158	23.4855
[ccc!!ddddtttttttttttdddd22cc	chr10:121356412-121356637(+)$1	225	27	56	24.0325
!ffffffcccuuuuuuuuuuuuccc]fff	chr2:131808731-131808976(-)$1	245	28	57	23.4991
:bb[a!!ccctttttttttttccc22a]b	chr18:29672565-29672789(-)$1	224	149	178	22.6044
[ccc!!bbyyyyyyyyyyyyyyyybb]cc	chr15:45410540-45410770(-)$1	230	108	137	22.4267
ee!!a[ddddvvvvvvvvvvvvvdddd]a	chr15:72491523-72491805(-)$1	282	214	243	23.3333
d!!cccyyyyyyyyyyyyyyyycccdddd	chr17:73034892-73035121(-)$1	229	39	68	22.2405
dd!!fffffftttttttttttffffff22	chr19:1434846-1435074(+)$1	228	108	137	21.4875
dddd!!cccxxxxxxxxxxxxxxxccc22	chr2:85770809-85771041(+)$1	232	110	139	19.0945
gggg[cccxxxxxxxxxxxxxxxccc]gg	chr5:132094292-132094521(-)$1	229	74	103	19.7345
ccc"""cccwwwwwwwwwwwwwwccc]cc	chr1:150190881-150191111(-)$1	230	173	202	24.1295
eeegggggggtttttttttttggggggg:	chr14:81610702-81610923(+)$1	221	20	49	21.9483
d[ccc[cccwwwwwwwwwwwwwwcccccc	chr5:176884037-176884267(-)$1	230	115	144	23.7689
iiiiii[cccuuuuuuuuuuuuccc]iii	chr9:73002201-73002438(-)$1	237	4	33	25.0240
ggggggggxxxxxxxxxxxxxxxgggggg	chr12:93167943-93168169(-)$1	226	184	213	19.4171
hhh####cccuuuuuuuuuuuuccc333h	chr14:58718789-58719016(-)$1	227	63	92	24.7217
::::eeeeeuuuuuuuuuuuueeeeeccc	chr2:271941-272186(+)$1	245	17	46	19.5109
ffdddddddduuuuuuuuuuuudddd555	chr2:217365980-217366228(+)$1	248	58	87	20.9628
EEEgggggggtttttttttttggggggg:	chr17:46023229-46023461(+)$1	232	58	87	19.6703
"dddd[cccwwwwwwwwwwwwwwcccddd	chr19:18418082-18418324(-)$1	242	44	73	22.7370
ii"""ddddwwwwwwwwwwwwwwdddd]i	chr17:8166978-8167224(+)$1	246	36	65	23.2004
ff[gggggggtttttttttttggggggg]	chr16:30435576-30435805(-)$1	229	43	72	23.0042
d[ccc[ddddtttttttttttddddcccd	chr14:103995438-103995666(-)$1	228	119	148	23.5917
cccbb!!ccctttttttttttccc22bb2	chr5:149602072-149602298(-)$1	226	155	184	22.8279
========[attttttttttta]======	chr7:148892538-148892766(+)$1	228	74	103	24.2078
eee[ayyyyyyyyyyyyyyyya]eeeee:	chr15:83685179-83685408(-)$1	229	35	64	20.1161
::ccceeeeettttttttttteeeee22c	chr18:33289660-33289890(+)$1	230	29	58	20.9182
ggggg[ddddtttttttttttddddgggg	chr2:159477429-159477659(+)$1	230	179	208	23.8283
========xxxxxxxxxxxxxxx======	chr2:196599579-196599816(+)$1	237	85	114	19.7130
eeee!!dddduuuuuuuuuuuudddd22e	chr1:110292820-110293043(+)$1	223	100	129	23.9367
ggggggyyyyyyyyyyyyyyyyggggggg	chr7:32625261-32625493(+)$1	232	89	118	22.5848
!dddd[ddddtttttttttttdddddddd	chr3:47627629-47627879(-)$1	250	27	56	22.7470
:ccc"""ccctttttttttttccc333cc	chr1:28298134-28298360(-)$1	226	42	71	23.8819
==bb!!ddddtttttttttttdddd22bb	chr17:72744701-72744931(+)$1	230	169	198	22.8239
####ccc[bbuuuuuuuuuuuubb]ccc2	chr19:40827155-40827384(-)$1	229	145	174	23.1873

#otherMatches

#Seq PSSM
UGUUUUGUGGGAAGUUAAAUAUGCAUGUG	chr11:129979348-129979596(+)$1	248	30	59	23.7081
GGCCAGGGUCCACCCCUUUCUAGCUUUGG	chr14:74416627-74416857(+)$1	230	174	203	20.7037
GUUACUUCACAACAAAAUGAUAUUGAAAA	chr7:104742429-104742661(+)$1	232	71	100	23.4432
CAGAUUGCUAAAUGUUCUUUCCAAGAAGU	chr1:225682987-225683216(-)$1	229	92	121	21.0102
GCGGUGGCUAAGGUCCGUGAGUGUCACCU	chr17:61699896-61700120(-)$1	224	17	46	21.1206
CGCUUUUUCAUCCUUCUUUCCUUGUUCAG	chr20:36146676-36146907(-)$1	231	136	165	24.1286
UCCAACUGGGGGUAGCAGAAACCCAGGGG	chr1:115300450-115300683(-)$1	233	156	185	23.2592
GCAGGCCUCCAACGCCCCUGUGGCCAACU	chr17:76851572-76851803(-)$1	231	55	84	21.9012
GGCACAUACGAUAUUGCCUGGUAGUAAGA	chr16:89351592-89351828(-)$1	236	165	194	23.8589
GAUGAGUGAAGAACCUCCAAACCUCUCUC	chr7:148511027-148511265(-)$1	238	2	31	19.6849
GUUUCUUCCUGUAGGUUGAUGAGGUAAUG	chr13:75923301-75923529(-)$1	228	77	106	22.6064
AGGUUGGCCGGACAGCUUCAUUAGGCCCC	chr5:71615889-71616135(-)$1	246	158	187	22.5928
GGUGGCCGCCAUUACCCGAACGCGGCCGC	chr6:3118956-3119181(-)$1	225	85	114	20.2958
ACAGCCUGGUCCGAAAGCAUUGCCAGCUG	chr16:4802193-4802423(-)$1	230	113	142	21.8804
UCCGUGCGCCCUACUUAACCUGAGGCGGC	chr4:890152-890379(-)$1	227	167	196	17.7121
CUCUUUUCAGAAGUGCCGUGACUGAGAGA	chrX:134482300-134482530(+)$1	230	122	151	23.1304
AAGACUUUUCAGUUUCAUAAGGAAGAGUG	chr7:137561193-137561445(-)$1	252	189	218	22.9027
GCCUACCAAUGAGAAGGGAAGAUUGGCCU	chr16:3333193-3333416(-)$1	223	25	54	22.8307
CGGGAAAAGGAGAAAGAGGAGCCCCCGGG	chr18:12329536-12329813(-)$1	277	202	231	22.0509
GCUUCCUGGCUCCUUAUCAGUGCCAUGAG	chr22:40806525-40806749(-)$1	224	149	178	22.3748
UCCUUGUGACACUCCUCUCCUCCCACAGG	chr16:2818921-2819198(+)$1	277	48	77	19.4378
GACCUCGGUGAGUGAGCGGGAGGCCGAGG	chr12:120703333-120703555(-)$1	222	129	158	23.4855
UUGUGGUCCUGGAAAUGAGAGAGGGAAGC	chr10:121356412-121356637(+)$1	225	27	56	24.0325
AGAAUGAGUUAAAAGGGAACAAAACUUUA	chr2:131808731-131808976(-)$1	245	28	57	23.4991
GGGGGAUCGCAUCAGGAUACAGCGCGCGC	chr18:29672565-29672789(-)$1	224	149	178	22.6044
UGGCCCUCAAACACCACCUCACAAGAAGC	chr15:45410540-45410770(-)$1	230	108	137	22.4267
GCACUGGGCUGUUGUUCCAUUGAAGCCGA	chr15:72491523-72491805(-)$1	282	214	243	23.3333
AAUUAGACAAGAAAAAGUAUCCCUAUUGG	chr17:73034892-73035121(-)$1	229	39	68	22.2405
AAACUUGUGAACUCGUGACAAUCACAAAC	chr19:1434846-1435074(+)$1	228	108	137	21.4875
CUUGUUGGCGUAGGCUACAGAGAAGCCUU	chr2:85770809-85771041(+)$1	232	110	139	19.0945
CACCUUGUGACCCUUCUCCCAUAACAUGG	chr5:132094292-132094521(-)$1	229	74	103	19.7345
UUCCUCAAGAAUCUCCUUAAAAACUUUGA	chr1:150190881-150191111(-)$1	230	173	202	24.1295
UAGGGGAACUUACAAAAUAAUAGUUUCUU	chr14:81610702-81610923(+)$1	221	20	49	21.9483
GAUUGUAGCUCUUAGUCCUCCCUGCUCAG	chr5:176884037-176884267(-)$1	230	115	144	23.7689
GGCAAAUGCUUUUGGGUUuuuugguuuuu	chr9:73002201-73002438(-)$1	237	4	33	25.0240
UAAUAGUUGGAUAAUAUAAACUGAACUAU	chr12:93167943-93168169(-)$1	226	184	213	19.4171
ACAUGCCGAUCAACAUUAAAAAGUCUUUU	chr14:58718789-58719016(-)$1	227	63	92	24.7217
UUAAAGAGGCCAACCUGAACUCCUCUGGG	chr2:271941-272186(+)$1	245	17	46	19.5109
UUGGAAACUGAAUCUUUCUUUCCAGUACC	chr2:217365980-217366228(+)$1	248	58	87	20.9628
CCCGCCCCAAGAGCAGCCAGAUUGGGGCU	chr17:46023229-46023461(+)$1	232	58	87	19.6703
ACAGUGAGCGCCCACCCAGACCGGCUGCU	chr19:18418082-18418324(-)$1	242	44	73	22.7370
ACCCAUCUCUCUUGCAACAACAUGAGACG	chr17:8166978-8167224(+)$1	246	36	65	23.2004
ACCUGGUGGCAUUAGCAGCCCGCUGCCGU	chr16:30435576-30435805(-)$1	229	43	72	23.0042
GGCGGCGGCCACAACACUUCCGGCUCCGC	chr14:103995438-103995666(-)$1	228	119	148	23.5917
UGUACCUGCAUCAAGAAAACCUGCUUGUU	chr5:149602072-149602298(-)$1	226	155	184	22.8279
AGGGGGAAGGCGCCUGGAAAACGUUCUUC	chr7:148892538-148892766(+)$1	228	74	103	24.2078
CUGCCUUAAAAAAUAUGAUAUGCCAGAGA	chr15:83685179-83685408(-)$1	229	35	64	20.1161
CAGCAGUGGCUUCUUCGAAACGUCACCCU	chr18:33289660-33289890(+)$1	230	29	58	20.9182
CAGACAUCUCUCCAUGAAAGUGAGGGUCU	chr2:159477429-159477659(+)$1	230	179	208	23.8283
GGCAAUUCAUCCUUCAGAAUUUAGGAUUG	chr2:196599579-196599816(+)$1	237	85	114	19.7130
UCCAGAAGAGGAAUUCUCGGGGCUCUAAU	chr1:110292820-110293043(+)$1	223	100	129	23.9367
UUCAGCGAUGAUAAAUUGAAGGGCUGAAU	chr7:32625261-32625493(+)$1	232	89	118	22.5848
AUGGCCAGGGUUUUACCUACUUCCUGCCA	chr3:47627629-47627879(-)$1	250	27	56	22.7470
CUCCACCCCAACACAAAAAUCUGGAAAGG	chr1:28298134-28298360(-)$1	226	42	71	23.8819
GGCUCAGGGCUUCUCUGCUGCGCUCCCGG	chr17:72744701-72744931(+)$1	230	169	198	22.8239
UCCUGCCCGACCCUCCUGUACCUCCGGCC	chr19:40827155-40827384(-)$1	229	145	174	23.1873

#DB
(((((.(((..............)))..)	chr11:129979348-129979596(+)$1	1	30	59	23.7081
(((((((((.............)))))))	chr14:74416627-74416857(+)$1	1	174	203	20.7037
((...((((..............))))..	chr7:104742429-104742661(+)$1	1	71	100	23.4432
((((((.((..............)).)))	chr1:225682987-225683216(-)$1	1	92	121	21.0102
(.((((((..............)))))).	chr17:61699896-61700120(-)$1	1	17	46	21.1206
.(((....((............))...))	chr20:36146676-36146907(-)$1	1	136	165	24.1286
(((..(((((...........))))).))	chr1:115300450-115300683(-)$1	1	156	185	23.2592
(((((((..............))))...)	chr17:76851572-76851803(-)$1	1	55	84	21.9012
(...(.(((..............))).).	chr16:89351592-89351828(-)$1	1	165	194	23.8589
((((((.((..............)).)))	chr7:148511027-148511265(-)$1	1	2	31	19.6849
((.....(((...........)))....)	chr13:75923301-75923529(-)$1	1	77	106	22.6064
(((..((((..............))))))	chr5:71615889-71616135(-)$1	1	158	187	22.5928
.((((((((............))))))))	chr6:3118956-3119181(-)$1	1	85	114	20.2958
.((((.((((...........))))))))	chr16:4802193-4802423(-)$1	1	113	142	21.8804
(((((.(((((..........).))))))	chr4:890152-890379(-)$1	1	167	196	17.7121
((.(((((((...........))))))).	chrX:134482300-134482530(+)$1	1	122	151	23.1304
((.(((((((...........))))))).	chr7:137561193-137561445(-)$1	1	189	218	22.9027
(....(((((...........)))))...	chr16:3333193-3333416(-)$1	1	25	54	22.8307
((((....((...........))))))((	chr18:12329536-12329813(-)$1	1	202	231	22.0509
(((((.((((...........)))).)).	chr22:40806525-40806749(-)$1	1	149	178	22.3748
.(((((((...............))))))	chr16:2818921-2819198(+)$1	1	48	77	19.4378
..(((((((.............)))))))	chr12:120703333-120703555(-)$1	1	129	158	23.4855
.(((..((((...........))))..))	chr10:121356412-121356637(+)$1	1	27	56	24.0325
.(((((((((............))).)))	chr2:131808731-131808976(-)$1	1	28	57	23.4991
.((.(..(((...........)))..).)	chr18:29672565-29672789(-)$1	1	149	178	22.6044
.(((..((................)).))	chr15:45410540-45410770(-)$1	1	108	137	22.4267
((..(.((((.............)))).)	chr15:72491523-72491805(-)$1	1	214	243	23.3333
(..(((................)))))))	chr17:73034892-73035121(-)$1	1	39	68	22.2405
((..((((((...........))))))..	chr19:1434846-1435074(+)$1	1	108	137	21.4875
((((..(((...............)))..	chr2:85770809-85771041(+)$1	1	110	139	19.0945
((((.(((...............))).))	chr5:132094292-132094521(-)$1	1	74	103	19.7345
(((...(((..............))).))	chr1:150190881-150191111(-)$1	1	173	202	24.1295
)))(((((((...........))))))).	chr14:81610702-81610923(+)$1	1	20	49	21.9483
(.(((.(((..............))))))	chr5:176884037-176884267(-)$1	1	115	144	23.7689
((((((.(((............))).)))	chr9:73002201-73002438(-)$1	1	4	33	25.0240
((((((((...............))))))	chr12:93167943-93168169(-)$1	1	184	213	19.4171
(((....(((............)))...)	chr14:58718789-58719016(-)$1	1	63	92	24.7217
....(((((............)))))(((	chr2:271941-272186(+)$1	1	17	46	19.5109
))((((((((............))))...	chr2:217365980-217366228(+)$1	1	58	87	20.9628
((((((((((...........))))))).	chr17:46023229-46023461(+)$1	1	58	87	19.6703
.((((.(((..............))))))	chr19:18418082-18418324(-)$1	1	44	73	22.7370
((...((((..............)))).)	chr17:8166978-8167224(+)$1	1	36	65	23.2004
((.(((((((...........))))))).	chr16:30435576-30435805(-)$1	1	43	72	23.0042
(.(((.((((...........))))))))	chr14:103995438-103995666(-)$1	1	119	148	23.5917
(((((..(((...........)))..)).	chr5:149602072-149602298(-)$1	1	155	184	22.8279
((((((((.(...........).))))))	chr7:148892538-148892766(+)$1	1	74	103	24.2078
(((.(................).))))).	chr15:83685179-83685408(-)$1	1	35	64	20.1161
..((((((((...........)))))..)	chr18:33289660-33289890(+)$1	1	29	58	20.9182
(((((.((((...........))))))))	chr2:159477429-159477659(+)$1	1	179	208	23.8283
((((((((...............))))))	chr2:196599579-196599816(+)$1	1	85	114	19.7130
((((..((((............))))..)	chr1:110292820-110293043(+)$1	1	100	129	23.9367
((((((................)))))))	chr7:32625261-32625493(+)$1	1	89	118	22.5848
.((((.((((...........))))))))	chr3:47627629-47627879(-)$1	1	27	56	22.7470
.(((...(((...........)))...))	chr1:28298134-28298360(-)$1	1	42	71	23.8819
((((..((((...........))))..))	chr17:72744701-72744931(+)$1	1	169	198	22.8239
....(((.((............)).))).	chr19:40827155-40827384(-)$1	1	145	174	23.1873

#PSSM
d : 0.17	c : 0.10	: : 0.10	g : 0.08	e : 0.08	f : 0.07	= : 0.07	[ : 0.05	! : 0.05	E : 0.03	b : 0.03	" : 0.03	i : 0.03	h : 0.01	# : 0.01	
c : 0.16	d : 0.14	g : 0.10	e : 0.08	f : 0.07	= : 0.07	h : 0.05	[ : 0.05	b : 0.05	E : 0.03	# : 0.03	! : 0.03	i : 0.03	: : 0.03	" : 0.01	
c : 0.21	g : 0.12	d : 0.12	e : 0.07	h : 0.05	" : 0.05	f : 0.05	[ : 0.05	! : 0.05	E : 0.03	# : 0.03	b : 0.03	= : 0.03	$ : 0.01	i : 0.01	: : 0.01	
g : 0.21	c : 0.17	d : 0.12	" : 0.07	! : 0.07	f : 0.05	# : 0.05	b : 0.05	h : 0.03	[ : 0.03	= : 0.03	$ : 0.01	i : 0.01	: : 0.01	e : 0.01	
g : 0.19	! : 0.12	c : 0.12	d : 0.08	" : 0.07	f : 0.07	# : 0.07	a : 0.07	h : 0.03	b : 0.03	= : 0.03	$ : 0.01	[ : 0.01	i : 0.01	e : 0.01	
[ : 0.19	g : 0.16	! : 0.12	d : 0.08	f : 0.07	e : 0.07	c : 0.07	# : 0.05	h : 0.03	" : 0.03	= : 0.03	$ : 0.01	i : 0.01	y : 0.01	
d : 0.26	c : 0.14	g : 0.14	e : 0.07	[ : 0.05	f : 0.05	# : 0.05	y : 0.05	h : 0.03	! : 0.03	= : 0.03	$ : 0.01	b : 0.01	" : 0.01	
c : 0.24	d : 0.24	g : 0.14	e : 0.07	b : 0.05	y : 0.05	h : 0.03	f : 0.03	# : 0.03	= : 0.03	w : 0.01	[ : 0.01	
d : 0.24	c : 0.23	g : 0.10	b : 0.08	e : 0.07	x : 0.07	y : 0.07	h : 0.03	w : 0.03	f : 0.01	[ : 0.01	
w : 0.21	d : 0.19	c : 0.12	g : 0.08	x : 0.08	y : 0.07	b : 0.05	e : 0.05	v : 0.03	u : 0.03	f : 0.01	a : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	a : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
t : 0.39	w : 0.21	u : 0.16	x : 0.08	y : 0.07	v : 0.05	s : 0.01	
w : 0.19	d : 0.14	u : 0.12	g : 0.08	x : 0.08	e : 0.07	c : 0.07	v : 0.05	a : 0.05	y : 0.05	h : 0.01	b : 0.01	f : 0.01	
w : 0.17	d : 0.17	c : 0.14	g : 0.12	x : 0.08	e : 0.07	b : 0.05	] : 0.05	h : 0.03	f : 0.03	y : 0.01	v : 0.01	
d : 0.28	c : 0.24	g : 0.16	e : 0.08	b : 0.07	h : 0.03	f : 0.03	= : 0.03	y : 0.01	x : 0.01	
d : 0.28	c : 0.19	g : 0.16	e : 0.08	b : 0.05	h : 0.03	f : 0.03	3 : 0.03	2 : 0.03	= : 0.03	4 : 0.01	] : 0.01	
d : 0.19	g : 0.17	c : 0.16	] : 0.08	e : 0.08	3 : 0.07	2 : 0.07	h : 0.03	f : 0.03	= : 0.03	4 : 0.01	b : 0.01	
d : 0.17	g : 0.17	c : 0.10	2 : 0.08	] : 0.08	f : 0.07	3 : 0.07	h : 0.03	4 : 0.03	b : 0.03	= : 0.03	a : 0.01	i : 0.01	5 : 0.01	e : 0.01	
c : 0.21	g : 0.19	2 : 0.08	d : 0.08	3 : 0.05	f : 0.05	b : 0.05	] : 0.05	h : 0.03	4 : 0.03	e : 0.03	= : 0.03	a : 0.01	i : 0.01	5 : 0.01	
c : 0.21	g : 0.12	d : 0.10	] : 0.08	2 : 0.07	h : 0.05	b : 0.05	: : 0.05	3 : 0.03	f : 0.03	e : 0.03	i : 0.03	= : 0.03	4 : 0.01	a : 0.01	5 : 0.01	

#score	1245.033860571163
#seq	56
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_CDS_m1_run1.txt

#BEAR
cccccc[ddddoooooodddd]cccFF	chr10:96162772-96162995(+)$1	223	47	74	13.5804
d$$$$$bb[cccooooooccc]bbddd	chr6:46976720-46976941(-)$1	221	121	148	10.2436
''a[gggggggooooooggggggg]ac	chrX:132160270-132160496(+)$1	226	32	59	10.9441
ddd####eeeeennnnneeeee333dd	chr10:102822539-102822760(-)$1	221	192	219	10.4741
dddd[ffffffooooooffffff22dd	chr10:23326136-23326358(+)$1	222	187	214	10.6910
ff[bb[eeeeeooooooeeeee22bbf	chr3:150289704-150289925(+)$1	221	93	120	11.3805
##ccc!!ddddoooooodddd22ccc2	chr12:116428760-116428984(-)$1	224	157	184	15.4407
ccc####eeeeellleeeee4444ccc	chr3:38180349-38180571(+)$1	222	16	43	10.0656
##dddd[ddddoooooodddd22dddd	chr11:66637770-66637995(+)$1	225	170	197	14.6885
gggg"""ddddoooooodddd4444gg	chrX:128895046-128895267(+)$1	221	163	190	15.6307
dddd####cccooooooccc4444ddd	chr7:27239496-27239734(-)$1	238	42	69	15.2435
ba!!a[bbcccooooooccc]bb]a22	chr12:53709076-53709301(+)$1	225	63	90	11.7496
###eeeeecccooooooccc]eeeeee	chr19:46094219-46094440(+)$1	221	140	167	12.0046
:ccc[aeeeeeooooooeeeee22a]c	chr16:11933741-11933971(-)$1	230	13	40	12.1581
::dddd[ddddoooooodddd]ddddf	chr13:75923239-75923465(-)$1	226	154	181	12.2248
[bb[bb[ddddoooooodddd]bb444	chr8:20054848-20055072(+)$1	224	23	50	12.9335
[dddd[ccc[aooooooa]cccdddd]	chr1:202287688-202287912(+)$1	224	49	76	12.7428
!ccc"""aooooooa4444ccc22bbE	chr8:143435969-143436192(+)$1	223	153	180	9.7971
==========oooooo==========d	chr20:18005220-18005442(+)$1	222	139	166	12.1071
ddd!!ffffffooooooffffff22dd	chr5:160033810-160034033(-)$1	223	89	116	10.8301
:==========oooooo==========	chr13:40229896-40230119(-)$1	223	136	163	12.4122
fff####ddddoooooodddd22ffff	chr3:36986171-36986392(-)$1	221	103	130	14.4536
ccdddd[ddddoooooodddd]dddd:	chr5:74324443-74324666(-)$1	223	156	183	13.2488
!dddd!!aooooooa22dddd22ccc4	chrX:49104032-49104253(+)$1	221	102	129	10.7191
eeeee[eeeeeooooooeeeee22eee	chr11:64600035-64600258(-)$1	223	80	107	12.2696
ee[ccc!!cccooooooccc22cccee	chr16:11009325-11009548(-)$1	223	193	220	13.7714
""iiiiiiiiiooooooiiiiiiiii3	chr1:33480077-33480299(-)$1	222	23	50	12.6504
bdddd!!ddddoooooodddddddd]b	chr1:26310898-26311122(-)$1	224	143	170	13.6345
[dddd!!ddddoooooodddd]ddddc	chr21:33043823-33044045(-)$1	222	149	176	14.9361
cccccc!!cccooooooccc22ccc]c	chr11:20940728-20940950(+)$1	222	89	116	14.0977
ggggg####cccnnnnnccc333gggg	chr11:124615309-124615531(-)$1	222	101	128	10.6147
ddd####eeeeeooooooeeeeedddd	chr1:33955053-33955276(+)$1	223	172	199	12.0285
$$ccc!!ddddoooooodddd22ccc5	chr8:107725953-107726176(+)$1	223	78	105	14.5190
[ccc"""ddddnnnnndddd22ccca2	chr16:21261451-21261677(-)$1	226	147	174	11.4562
ffff!!ccc[aooooooa]ccc4444f	chr9:136598855-136599077(+)$1	222	10	37	12.7576
ccccc[eeeeennnnneeeee333ccc	chr9:140002852-140003076(-)$1	224	24	51	10.1651
[ccc"""ccc[ccclllccc]cccccc	chr3:50137866-50138143(+)$1	277	147	174	9.8438
'eeeeea[cccooooooccc22a]eee	chr14:61747100-61747325(-)$1	225	52	79	12.5581
$$ccc"""cccooooooccc333ccc3	chr19:497744-497971(+)$1	227	99	126	15.3532
dddd"""ddddoooooodddd333ddd	chr19:10625449-10625670(+)$1	221	1	28	16.3148
!dddd"""cccooooooccc333dddd	chr1:109704523-109704746(+)$1	223	37	64	15.4641
eeee[a[ddddnnnnndddd]a]eeee	chr9:139324649-139324871(-)$1	222	20	47	9.8206
dddd[ccc[bboooooobbccc]dddd	chr8:121243740-121243962(-)$1	222	53	80	11.6151
dddddddddddoooooodddd]dddd:	chr8:39782190-39782415(+)$1	225	146	173	12.5517
:dddd[addddoooooodddd4444a]	chr5:17275242-17275469(-)$1	227	130	157	14.1968
cccccccddddoooooodddd]cccbb	chr14:76427211-76427436(-)$1	225	180	207	13.5567
eccc####cccoooooocccccc]eee	chr11:2441348-2441575(+)$1	227	163	190	14.1752
gggggg!!cccooooooccc22ggggg	chr1:38423781-38424004(+)$1	223	179	206	13.5672
======!!ddddnnnnndddd22====	chr20:62577698-62577926(+)$1	228	27	54	11.2222
eee####ddddoooooodddd4444ee	chr3:45046751-45046974(-)$1	223	128	155	15.4052

#otherMatches

#Seq PSSM
AGAGGCUcgcgggcuggcgcgcgccgg	chr10:96162772-96162995(+)$1	223	47	74	13.5804
CCACCAUCAUCCGCGUGGGGAAGAGCC	chr6:46976720-46976941(-)$1	221	121	148	10.2436
AUGAAUGCUCGAUCUCCUGAGUAUACA	chrX:132160270-132160496(+)$1	226	32	59	10.9441
GCGCACCCUGCCCGCCAGGCAGCCCCG	chr10:102822539-102822760(-)$1	221	192	219	10.4741
GAUGUACGUGAUUGACCUCAUGUUCCA	chr10:23326136-23326358(+)$1	222	187	214	10.6910
UGUGCUGUAUAUGGUUUUAUGCCUGCC	chr3:150289704-150289925(+)$1	221	93	120	11.3805
AUGGUAGGUGUCCCAGAACACAAAUUU	chr12:116428760-116428984(-)$1	224	157	184	15.4407
UUGGAGAUCCGGCAACUGGAGACACAA	chr3:38180349-38180571(+)$1	222	16	43	10.0656
ACUGGGCUUAGCUUUUACUGGAAUCUA	chr11:66637770-66637995(+)$1	225	170	197	14.6885
GGGACAGGCCACGGCAUUGGCAACUUC	chrX:128895046-128895267(+)$1	221	163	190	15.6307
CAGCCUCCGUGCUCCUCCACCCCCGCU	chr7:27239496-27239734(-)$1	238	42	69	15.2435
CCCAUGGAGGGAAGAGGCCCAUCGACA	chr12:53709076-53709301(+)$1	225	63	90	11.7496
GGGGCGGCCCAGGUAGAUGGCGCUGCG	chr19:46094219-46094440(+)$1	221	140	167	12.0046
GAUCGAGGUCCAUUUAGGGGCUUAUGG	chr16:11933741-11933971(-)$1	230	13	40	12.1581
UUGAAGGUACAGUUUAAUGUGGCUUUG	chr13:75923239-75923465(-)$1	226	154	181	12.2248
GCGUGCGCGGCGUCGCUGCUGGGCCAG	chr8:20054848-20055072(+)$1	224	23	50	12.9335
CGCCAUGGUGAGGCACGUGGCCUGGCU	chr1:202287688-202287912(+)$1	224	49	76	12.7428
AGCUGGAGGAAACACGAAAAGCAGGGG	chr8:143435969-143436192(+)$1	223	153	180	9.7971
GUUUUUUAGAUGUCUUUUUGAGAAACG	chr20:18005220-18005442(+)$1	222	139	166	12.1071
GGUCAUCGAUGGGAAGACAUUGAAUGC	chr5:160033810-160034033(-)$1	223	89	116	10.8301
AUGCAGCUUGCGCGACAGCGGGUUGCA	chr13:40229896-40230119(-)$1	223	136	163	12.4122
GCGGGCAGCUAGGUGCGUAGCGGCGCG	chr3:36986171-36986392(-)$1	221	103	130	14.4536
CACAUCAUGAUAGUAAAAUCAGGAUGG	chr5:74324443-74324666(-)$1	223	156	183	13.2488
AGCUCGAGUCCCUUCGGGAGCAGCUGG	chrX:49104032-49104253(+)$1	221	102	129	10.7191
GCGUGUUUGCUGCCCUGAGUGACUCAC	chr11:64600035-64600258(-)$1	223	80	107	12.2696
AGAGACAAGGCACAGAAGUCAGGUCCU	chr16:11009325-11009548(-)$1	223	193	220	13.7714
UGUCAUUCUGGAGCCCCCUAGAGUGGA	chr1:33480077-33480299(-)$1	222	23	50	12.6504
GGCUUUGUGGUUGCUGUGCCAGAGCAC	chr1:26310898-26311122(-)$1	224	143	170	13.6345
CAGGUGGUAACAAAACCGUUGAACCUC	chr21:33043823-33044045(-)$1	222	149	176	14.9361
UUCUUAAGCCUGGUGCAAGGAAUAAUG	chr11:20940728-20940950(+)$1	222	89	116	14.0977
AUGUCGUCGUCCGGCUUGGAGCAGGCG	chr11:124615309-124615531(-)$1	222	101	128	10.6147
GUGAUGUUGUCAUGCUUCUGAUACACC	chr1:33955053-33955276(+)$1	223	172	199	12.0285
UAGUCACUUCUCCUAACAGGACAGAUC	chr8:107725953-107726176(+)$1	223	78	105	14.5190
UAUCUUUGUUCUUCUUGAACUUGAUCU	chr16:21261451-21261677(-)$1	226	147	174	11.4562
CUGGUUGUUGUGAACCAAGAACUGUCC	chr9:136598855-136599077(+)$1	222	10	37	12.7576
CCAUCCACCCUAGGCAGGGGUCCAGAU	chr9:140002852-140003076(-)$1	224	24	51	10.1651
UACCAGCUGGAUGGAAGCCAAUCAGGU	chr3:50137866-50138143(+)$1	277	147	174	9.8438
GGUGGACCGACUACCACGUCAAGUUCC	chr14:61747100-61747325(-)$1	225	52	79	12.5581
CAGGUGAAGCCCCUGCAGGUGGAGCCC	chr19:497744-497971(+)$1	227	99	126	15.3532
CGUGAGGCUGCCCAGGAGCAGGAACAU	chr19:10625449-10625670(+)$1	221	1	28	16.3148
AGGUGGAGGGUCGCCGUGCCGCAUACC	chr1:109704523-109704746(+)$1	223	37	64	15.4641
CAGAAGCCGCCACAAGGGUGACAUCUG	chr9:139324649-139324871(-)$1	222	20	47	9.8206
AGCUGUGUUAGUAACAUCUGCAGAGUU	chr8:121243740-121243962(-)$1	222	53	80	11.6151
AACACCACCAAAUUCUCUUGGUUGGUC	chr8:39782190-39782415(+)$1	225	146	173	12.5517
AGCUUGCCUCCCAUCUUGGAGUUCUGG	chr5:17275242-17275469(-)$1	227	130	157	14.1968
AGGCUCAUGCCAUCUGAGGCACUGGGG	chr14:76427211-76427436(-)$1	225	180	207	13.5567
GCCCAUCGCCCUUCCCCGGGGGGCCUG	chr11:2441348-2441575(+)$1	227	163	190	14.1752
UAGACAGCUCUCCUAAAAGAAAUGUUU	chr1:38423781-38424004(+)$1	223	179	206	13.5672
CCUUCUCCUGCUCCACAGGCACUGGAG	chr20:62577698-62577926(+)$1	228	27	54	11.2222
GUCAUCUGACAAUUCAAUGUCCUUCGA	chr3:45046751-45046974(-)$1	223	128	155	15.4052

#DB
)))(((.((((......)))).)))((	chr10:96162772-96162995(+)$1	1	47	74	13.5804
(.....((.(((......))).)))))	chr6:46976720-46976941(-)$1	1	121	148	10.2436
..(.(((((((......))))))).))	chrX:132160270-132160496(+)$1	1	32	59	10.9441
(((....(((((.....)))))...))	chr10:102822539-102822760(-)$1	1	192	219	10.4741
((((.((((((......))))))..))	chr10:23326136-23326358(+)$1	1	187	214	10.6910
((.((.(((((......)))))..)))	chr3:150289704-150289925(+)$1	1	93	120	11.3805
..(((..((((......))))..))).	chr12:116428760-116428984(-)$1	1	157	184	15.4407
(((....(((((...)))))....)))	chr3:38180349-38180571(+)$1	1	16	43	10.0656
..((((.((((......))))..))))	chr11:66637770-66637995(+)$1	1	170	197	14.6885
((((...((((......))))....))	chrX:128895046-128895267(+)$1	1	163	190	15.6307
((((....(((......)))....)))	chr7:27239496-27239734(-)$1	1	42	69	15.2435
((..(.(((((......))).)).)..	chr12:53709076-53709301(+)$1	1	63	90	11.7496
...((((((((......))).))))))	chr19:46094219-46094440(+)$1	1	140	167	12.0046
.(((.((((((......)))))..).)	chr16:11933741-11933971(-)$1	1	13	40	12.1581
..((((.((((......)))).))))(	chr13:75923239-75923465(-)$1	1	154	181	12.2248
.((.((.((((......)))).))...	chr8:20054848-20055072(+)$1	1	23	50	12.9335
.((((.(((.(......).))))))).	chr1:202287688-202287912(+)$1	1	49	76	12.7428
.(((...(......)....)))..)))	chr8:143435969-143436192(+)$1	1	153	180	9.7971
((((((((((......))))))))))(	chr20:18005220-18005442(+)$1	1	139	166	12.1071
(((..((((((......))))))..))	chr5:160033810-160034033(-)$1	1	89	116	10.8301
.((((((((((......))))))))))	chr13:40229896-40230119(-)$1	1	136	163	12.4122
(((....((((......))))..))))	chr3:36986171-36986392(-)$1	1	103	130	14.4536
))((((.((((......)))).)))).	chr5:74324443-74324666(-)$1	1	156	183	13.2488
.((((..(......)..))))..))).	chrX:49104032-49104253(+)$1	1	102	129	10.7191
(((((.(((((......)))))..)))	chr11:64600035-64600258(-)$1	1	80	107	12.2696
((.(((..(((......)))..)))))	chr16:11009325-11009548(-)$1	1	193	220	13.7714
..(((((((((......))))))))).	chr1:33480077-33480299(-)$1	1	23	50	12.6504
(((((..((((......)))))))).)	chr1:26310898-26311122(-)$1	1	143	170	13.6345
.((((..((((......)))).)))))	chr21:33043823-33044045(-)$1	1	149	176	14.9361
((((((..(((......)))..))).)	chr11:20940728-20940950(+)$1	1	89	116	14.0977
(((((....(((.....)))...))))	chr11:124615309-124615531(-)$1	1	101	128	10.6147
(((....(((((......)))))))))	chr1:33955053-33955276(+)$1	1	172	199	12.0285
..(((..((((......))))..))).	chr8:107725953-107726176(+)$1	1	78	105	14.5190
.(((...((((.....))))..)))).	chr16:21261451-21261677(-)$1	1	147	174	11.4562
((((..(((.(......).)))....)	chr9:136598855-136599077(+)$1	1	10	37	12.7576
(((((.(((((.....)))))...)))	chr9:140002852-140003076(-)$1	1	24	51	10.1651
.(((...(((.(((...))).))))))	chr3:50137866-50138143(+)$1	1	147	174	9.8438
.((((((.(((......)))..).)))	chr14:61747100-61747325(-)$1	1	52	79	12.5581
..(((...(((......)))...))).	chr19:497744-497971(+)$1	1	99	126	15.3532
((((...((((......))))...)))	chr19:10625449-10625670(+)$1	1	1	28	16.3148
.((((...(((......)))...))))	chr1:109704523-109704746(+)$1	1	37	64	15.4641
((((.(.((((.....)))).).))))	chr9:139324649-139324871(-)$1	1	20	47	9.8206
((((.(((.((......))))).))))	chr8:121243740-121243962(-)$1	1	53	80	11.6151
)))((((((((......)))).)))).	chr8:39782190-39782415(+)$1	1	146	173	12.5517
.((((.(((((......))))....).	chr5:17275242-17275469(-)$1	1	130	157	14.1968
))))(((((((......)))).)))((	chr14:76427211-76427436(-)$1	1	180	207	13.5567
((((....(((......)))))).)))	chr11:2441348-2441575(+)$1	1	163	190	14.1752
((((((..(((......)))..)))))	chr1:38423781-38424004(+)$1	1	179	206	13.5672
((((((..((((.....))))..))))	chr20:62577698-62577926(+)$1	1	27	54	11.2222
(((....((((......))))....))	chr3:45046751-45046974(-)$1	1	128	155	15.4052

#PSSM
d : 0.18	c : 0.12	[ : 0.10	e : 0.10	: : 0.08	f : 0.06	# : 0.06	g : 0.06	! : 0.06	' : 0.04	b : 0.04	= : 0.04	$ : 0.04	" : 0.02	
d : 0.27	c : 0.21	e : 0.10	$ : 0.06	f : 0.06	# : 0.06	g : 0.06	= : 0.06	' : 0.02	a : 0.02	: : 0.02	b : 0.02	" : 0.02	
d : 0.34	c : 0.25	e : 0.08	g : 0.06	= : 0.06	[ : 0.04	f : 0.04	$ : 0.02	a : 0.02	! : 0.02	# : 0.02	b : 0.02	i : 0.02	
d : 0.27	c : 0.25	# : 0.10	e : 0.08	g : 0.06	= : 0.06	[ : 0.04	! : 0.04	$ : 0.02	b : 0.02	i : 0.02	f : 0.02	
d : 0.19	c : 0.16	# : 0.14	" : 0.10	[ : 0.08	g : 0.06	e : 0.06	= : 0.06	b : 0.04	! : 0.04	$ : 0.02	a : 0.02	i : 0.02	
# : 0.16	" : 0.14	[ : 0.12	! : 0.12	c : 0.10	d : 0.08	= : 0.06	g : 0.04	f : 0.04	e : 0.04	a : 0.04	$ : 0.02	b : 0.02	i : 0.02	
! : 0.18	# : 0.16	" : 0.14	[ : 0.12	e : 0.10	c : 0.08	b : 0.04	f : 0.04	= : 0.04	a : 0.04	g : 0.02	i : 0.02	d : 0.02	
d : 0.36	e : 0.16	c : 0.08	! : 0.08	# : 0.06	b : 0.04	f : 0.04	a : 0.04	= : 0.04	" : 0.04	g : 0.02	i : 0.02	[ : 0.02	
d : 0.38	c : 0.25	e : 0.14	[ : 0.04	f : 0.04	o : 0.04	= : 0.04	g : 0.02	i : 0.02	# : 0.02	
d : 0.38	c : 0.25	e : 0.14	f : 0.04	[ : 0.04	o : 0.04	= : 0.04	g : 0.02	i : 0.02	b : 0.02	
d : 0.38	c : 0.23	e : 0.14	o : 0.06	f : 0.04	a : 0.04	g : 0.02	= : 0.02	i : 0.02	[ : 0.02	b : 0.02	
o : 0.80	c : 0.06	e : 0.06	n : 0.06	d : 0.02	
o : 0.84	n : 0.12	l : 0.02	c : 0.02	
o : 0.84	n : 0.12	l : 0.02	c : 0.02	
o : 0.80	n : 0.12	l : 0.04	a : 0.04	
o : 0.80	n : 0.12	e : 0.02	4 : 0.02	2 : 0.02	l : 0.02	
o : 0.78	n : 0.06	e : 0.04	d : 0.04	4 : 0.02	= : 0.02	2 : 0.02	l : 0.02	
d : 0.40	c : 0.23	e : 0.12	o : 0.04	f : 0.04	a : 0.04	= : 0.04	g : 0.02	4 : 0.02	i : 0.02	b : 0.02	
d : 0.40	c : 0.25	e : 0.14	f : 0.04	] : 0.04	= : 0.04	g : 0.02	4 : 0.02	i : 0.02	b : 0.02	
d : 0.40	c : 0.34	e : 0.14	f : 0.04	= : 0.04	g : 0.02	i : 0.02	
d : 0.36	c : 0.12	e : 0.12	2 : 0.10	] : 0.08	3 : 0.06	f : 0.04	4 : 0.04	= : 0.04	g : 0.02	i : 0.02	
2 : 0.21	] : 0.16	e : 0.12	c : 0.12	4 : 0.10	3 : 0.10	f : 0.04	= : 0.04	g : 0.02	b : 0.02	i : 0.02	d : 0.02	a : 0.02	
2 : 0.19	c : 0.14	3 : 0.12	4 : 0.12	d : 0.12	b : 0.06	g : 0.04	f : 0.04	e : 0.04	= : 0.04	] : 0.04	i : 0.02	a : 0.02	
c : 0.19	d : 0.19	2 : 0.12	4 : 0.12	g : 0.06	3 : 0.06	] : 0.06	= : 0.06	b : 0.04	e : 0.04	f : 0.02	i : 0.02	
d : 0.25	c : 0.23	4 : 0.10	e : 0.10	= : 0.06	2 : 0.04	b : 0.04	a : 0.04	g : 0.04	] : 0.02	3 : 0.02	f : 0.02	i : 0.02	
d : 0.30	c : 0.14	e : 0.14	a : 0.06	b : 0.06	g : 0.06	] : 0.06	= : 0.06	4 : 0.04	F : 0.02	2 : 0.02	f : 0.02	i : 0.02	
d : 0.21	c : 0.14	e : 0.14	f : 0.08	2 : 0.06	g : 0.06	4 : 0.04	] : 0.04	= : 0.04	: : 0.04	3 : 0.04	b : 0.04	F : 0.02	E : 0.02	5 : 0.02	

#score	634.3124013010962
#seq	50
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_CDS_m1_run1.txt

#BEAR
=========ttttttttttt======	chr2:219525710-219525979(+)$1	269	24	50	23.5176
:gggggggtttttttttttggggggg	chr11:47269962-47270182(-)$1	220	63	89	21.8445
dd!!ddddvvvvvvvvvvvvvddddd	chr2:179318178-179318411(+)$1	233	109	135	23.1791
ooccccccwwwwwwwwwwwwwwccc:	chr9:125512539-125512754(+)$1	215	153	179	21.0110
ff[fffffftttttttttttffffff	chrX:47775724-47776006(+)$1	282	59	85	22.4465
$$$$eeeeettttttttttteeeee5	chr19:24116486-24116699(+)$1	213	35	61	21.8433
hhhhhh[auuuuuuuuuuuua]hhhh	chr2:103431317-103431535(+)$1	218	34	60	21.6661
::ffffffuuuuuuuuuuuuffffff	chr8:67507769-67507998(-)$1	229	187	213	22.1289
cc"""ddddtttttttttttdddd44	chr22:22890923-22891139(-)$1	216	50	76	22.7560
=======vvvvvvvvvvvvv======	chr12:1137235-1137459(+)$1	224	161	187	24.2584
$$$$eeeeettttttttttteeeeef	chr1:193149501-193149779(+)$1	278	192	218	22.4113
cccfffffftttttttttttffffff	chr1:11083129-11083377(+)$1	248	146	172	22.6385
=========ttttttttttt======	chr1:220357306-220357567(-)$1	261	186	212	23.5176
[dddd[bbuuuuuuuuuuuubb]ddd	chr21:34944802-34945053(+)$1	251	93	119	21.7951
ee"""bbvvvvvvvvvvvvvbb333e	chr17:65105525-65105801(-)$1	276	58	84	22.3827
iii!!cccuuuuuuuuuuuuccc]ii	chr12:978075-978459(+)$1	384	149	175	24.4927
ffffcccvvvvvvvvvvvvvccc]ff	chr15:98513016-98513231(+)$1	215	143	169	23.3957
e"""ddddvvvvvvvvvvvvvdddd]	chr2:170911897-170912110(+)$1	213	91	117	23.7706
$$$$ddddvvvvvvvvvvvvvdddd5	chr18:34376852-34377099(-)$1	247	95	121	22.7852
fff!!cccwwwwwwwwwwwwwwccc2	chr16:68155988-68156248(+)$1	260	141	167	22.0720
$$$$$cccwwwwwwwwwwwwwwccc3	chr3:101383999-101384231(-)$1	232	125	151	22.2377
iiiiiiiiitttttttttttiiiiii	chr21:15745837-15746064(-)$1	227	159	185	22.9472
GGGGdddduuuuuuuuuuuudddd::	chr11:35211398-35211671(+)$1	273	115	141	19.7312
cccfffffftttttttttttffffff	chr5:71490122-71490339(+)$1	217	183	209	22.6385
:::eeeeeuuuuuuuuuuuueeeee:	chr1:248525400-248525614(+)$1	214	62	88	20.2053
:::eeeeeuuuuuuuuuuuueeeee:	chr11:125765167-125765424(+)$1	257	4	30	20.2053
ggffffffwwwwwwwwwwwwwwffff	chrY:20710215-20710430(+)$1	215	166	192	22.0313
:::fffffftttttttttttffffff	chr13:86370257-86370472(-)$1	215	31	57	20.4280
iiiiiiivvvvvvvvvvvvviiiiii	chr8:17579221-17579470(-)$1	249	51	77	23.9029
=="""cccwwwwwwwwwwwwwwccc3	chr9:15469162-15469383(-)$1	221	126	152	22.8693
=======vvvvvvvvvvvvv======	chr15:86124998-86125239(+)$1	241	180	206	24.2584
c[ccccccuuuuuuuuuuuuccc]cc	chr7:107398659-107398892(+)$1	233	61	87	24.0624
!eeeeebbvvvvvvvvvvvvvbb]ee	chr1:185276978-185277284(-)$1	306	129	155	22.6612
b[ffffffvvvvvvvvvvvvvfffff	chr20:44998869-44999130(-)$1	261	156	182	23.6354
fggggggguuuuuuuuuuuugggggg	chr3:141299126-141299378(+)$1	252	113	139	23.9046
h####ddddtttttttttttdddd55	chr5:178310123-178310338(+)$1	215	176	202	21.0481
bb[eeeeeuuuuuuuuuuuueeeeeb	chr11:1097723-1097938(+)$1	215	188	214	22.8877
d:ffffffuuuuuuuuuuuuffffff	chr15:44921333-44921576(-)$1	243	101	127	22.5499
iiiiiiiwwwwwwwwwwwwwwiiiii	chr2:128938435-128938651(+)$1	216	131	157	22.6782
!gggggggtttttttttttggggggg	chr3:38038836-38039080(+)$1	244	135	161	22.6289
ddd[ddddtttttttttttdddd]dd	chr19:4305858-4306072(+)$1	214	114	140	21.1839
dddd[cccuuuuuuuuuuuuccc444	chr12:29493975-29494226(-)$1	251	84	110	23.2262
##ffffffwwwwwwwwwwwwwwffff	chr7:104753243-104753644(+)$1	401	331	357	22.2658
$$$$dddduuuuuuuuuuuudddd33	chr17:44632409-44632687(-)$1	278	145	171	23.3582
ccc[ddddvvvvvvvvvvvvvdddd]	chr14:64520072-64520295(+)$1	223	18	44	23.7014
:ggggggguuuuuuuuuuuugggggg	chr3:12942483-12942886(-)$1	403	33	59	23.4755
&&&&ddddvvvvvvvvvvvvvdddd8	chr12:7045390-7045614(+)$1	224	148	174	21.3921
[eeeee[awwwwwwwwwwwwwwa]ee	chr9:27048138-27048349(+)$1	211	35	61	21.8388
!gggggggtttttttttttggggggg	chr15:45007652-45007995(+)$1	343	288	314	22.6289
!eeeee[auuuuuuuuuuuua]eeee	chr1:27057806-27058079(+)$1	273	76	102	23.4458
ggg[a[ccctttttttttttccc]a]	chr2:202001042-202001372(+)$1	330	172	198	23.4936
:::fffffftttttttttttffffff	chr8:18080139-18080354(+)$1	215	0	26	20.4280
hhhhhhhhvvvvvvvvvvvvvhhhhh	chr19:53014932-53015145(+)$1	213	0	26	21.0806
fcccyyyyyyyyyyyyyyyyccc]ff	chr12:119624774-119624987(+)$1	213	147	173	19.5386
:gggggggvvvvvvvvvvvvvggggg	chr17:3324308-3324524(+)$1	216	95	121	23.6606
ccceeeeewwwwwwwwwwwwwweeee	chr19:21606875-21607098(+)$1	223	95	121	21.8266
ggggyyyyyyyyyyyyyyyygggggg	chr4:79373293-79373508(+)$1	215	51	77	19.7752
$$$$$ddddtttttttttttdddd55	chr2:178095783-178096049(-)$1	266	175	201	20.7534
:ffffffvvvvvvvvvvvvvffffff	chr3:52283576-52283868(+)$1	292	200	226	22.5483
::bb[ddddtttttttttttddddbb	chr7:121650786-121651001(+)$1	215	153	179	20.1489
::ffffffuuuuuuuuuuuuffffff	chr11:96124420-96124634(+)$1	214	72	98	22.1289

#otherMatches

#Seq PSSM
GCUCUGAAGGACAAUCCCUACUUUGG	chr2:219525710-219525979(+)$1	269	24	50	23.5176
ACUGGCCUGGGUAGUUGGGAGGCUGG	chr11:47269962-47270182(-)$1	220	63	89	21.8445
UUACUUCAACACCUUUUACACUGAAA	chr2:179318178-179318411(+)$1	233	109	135	23.1791
CUGCUCUGACACAUCCUCCAGCCAGA	chr9:125512539-125512754(+)$1	215	153	179	21.0110
AGCCUUAUAAAUGUCCUGACUGUGAG	chrX:47775724-47776006(+)$1	282	59	85	22.4465
AACCCUACAAAUGUGAAGAAUGUGGC	chr19:24116486-24116699(+)$1	213	35	61	21.8433
AGCUGGGAUAUUUUUUUCUUUGCUAG	chr2:103431317-103431535(+)$1	218	34	60	21.6661
ACUUUUAAUACCUUUAUUAUUUAAAA	chr8:67507769-67507998(-)$1	229	187	213	22.1289
ACUAACUGCUUUGUCUAUUUGCAGGC	chr22:22890923-22891139(-)$1	216	50	76	22.7560
AGCCCCAAUAUAGCUAGCAGUGGGGU	chr12:1137235-1137459(+)$1	224	161	187	24.2584
ACCUAAAGAAACUUUAAAAAUCUUUU	chr1:193149501-193149779(+)$1	278	192	218	22.4113
AGAAGCACUUCAUUGAAAGUAGUGCU	chr1:11083129-11083377(+)$1	248	146	172	22.6385
UAAUGUGAGUAAUCCCACauuuuaua	chr1:220357306-220357567(-)$1	261	186	212	23.5176
CCAGCCGUACUAUUCACAACACUGCU	chr21:34944802-34945053(+)$1	251	93	119	21.7951
UCCCAGUACCAAAUUUCCUCGCAAAG	chr17:65105525-65105801(-)$1	276	58	84	22.3827
CUUAACUGCCUCAUUUUCUUCAGGAG	chr12:978075-978459(+)$1	384	149	175	24.4927
AUUAGUGAUCGGUACAAUUCCAUAUA	chr15:98513016-98513231(+)$1	215	143	169	23.3957
GAAGGUACUUUUUACCCUACUGUACA	chr2:170911897-170912110(+)$1	213	91	117	23.7706
AGCAUGUAUAAACCUAUCACCUACAA	chr18:34376852-34377099(-)$1	247	95	121	22.7852
CUAUCUCUCCUAACUGUCAUCAAGAA	chr16:68155988-68156248(+)$1	260	141	167	22.0720
CAAAAGAGAAUGUAAUUAGUAGCUCG	chr3:101383999-101384231(-)$1	232	125	151	22.2377
GUCUGAUGAUCUCUUCCCAUUUAUCA	chr21:15745837-15746064(-)$1	227	159	185	22.9472
CAGGAGGUUACAUCUUUUACACCUUU	chr11:35211398-35211671(+)$1	273	115	141	19.7312
AGAGAAGCAUAGAAGAAGCCUGCUUC	chr5:71490122-71490339(+)$1	217	183	209	22.6385
UCACCAUGACCUUCCCCUUCCGUGGA	chr1:248525400-248525614(+)$1	214	62	88	20.2053
CUCUGGCUUCUCCAUUCCUUGGCCAA	chr11:125765167-125765424(+)$1	257	4	30	20.2053
UAUGAAUGACAACAGAGACUAACAUU	chrY:20710215-20710430(+)$1	215	166	192	22.0313
AACUAAGCUUAUUAAAUAACGGCUUG	chr13:86370257-86370472(-)$1	215	31	57	20.4280
UCCUUUUAAAUGACUGUACCAGGAGG	chr8:17579221-17579470(-)$1	249	51	77	23.9029
GUUUAACUUCAUUUAAUACUUCAGUA	chr9:15469162-15469383(-)$1	221	126	152	22.8693
AGUGCUUUUACAGAAAAAGUGAGUAC	chr15:86124998-86125239(+)$1	241	180	206	24.2584
AGAGCUGGAAAACCUGUUACCCGUGC	chr7:107398659-107398892(+)$1	233	61	87	24.0624
UUGCAGCAUCUUCUCUACUUCUGUCU	chr1:185276978-185277284(-)$1	306	129	155	22.6612
GAAUGUUUUAUUaagaauuuugaaca	chr20:44998869-44999130(-)$1	261	156	182	23.6354
AUCUCAAAAACUAUACAAACUUUGGG	chr3:141299126-141299378(+)$1	252	113	139	23.9046
GCAUCCCUUUGUAAGCAUUUAAGGAC	chr5:178310123-178310338(+)$1	215	176	202	21.0481
GGACAGGUGACCCCGCCCAGGCCUGC	chr11:1097723-1097938(+)$1	215	188	214	22.8877
CUUUCCUUAACAACCAAAUAAAGGAG	chr15:44921333-44921576(-)$1	243	101	127	22.5499
UCUGGGGUUACAAGAUCCUCUUCCUG	chr2:128938435-128938651(+)$1	216	131	157	22.6782
AGGGGCUGGCUUUGACCUACAGCCUC	chr3:38038836-38039080(+)$1	244	135	161	22.6289
GCUGUGAAGAAUGAAGAAAUUCAGAG	chr19:4305858-4306072(+)$1	214	114	140	21.1839
GAGGAUGGCCACACAGACAACCACUU	chr12:29493975-29494226(-)$1	251	84	110	23.2262
CAGGUCCUCAUCUCCAGCCCCAAGGA	chr7:104753243-104753644(+)$1	401	331	357	22.2658
CCAUGGCAGAAAUCUGAAAAUGCCCC	chr17:44632409-44632687(-)$1	278	145	171	23.3582
UGUCAGGACAAACUAGAAACUUCCUU	chr14:64520072-64520295(+)$1	223	18	44	23.7014
UGGCCACCCCCCCACCCACCGGUGGU	chr3:12942483-12942886(-)$1	403	33	59	23.4755
CCAUGAGGUUUCCUUAUUCAUCCUCU	chr12:7045390-7045614(+)$1	224	148	174	21.3921
CUAUCACCAAUCAAGAGCUAAAGAUG	chr9:27048138-27048349(+)$1	211	35	61	21.8388
UGAGUAGUCAUAUCAUAAAGCUGCUU	chr15:45007652-45007995(+)$1	343	288	314	22.6289
CCGGCUCCAUACCCCUCCCAGCAGUC	chr1:27057806-27058079(+)$1	273	76	102	23.4458
GGGUCUCAUACCUUCCUUGCAUGUGU	chr2:202001042-202001372(+)$1	330	172	198	23.4936
AGCCUCGAACAAUUGAAGAUUUUGAG	chr8:18080139-18080354(+)$1	215	0	26	20.4280
UAAGGCUUUUAUUCAUCAGUCAAGCC	chr19:53014932-53015145(+)$1	213	0	26	21.0806
GGUGGGAGUGGAGGAGGGGGCACACC	chr12:119624774-119624987(+)$1	213	147	173	19.5386
UGAGGUCAAUCACUUCUACUGUGACC	chr17:3324308-3324524(+)$1	216	95	121	23.6606
CUUAGUAUACAUAAAAUAAUUCAUAC	chr19:21606875-21607098(+)$1	223	95	121	21.8266
AGUCAUCACCACCAAUAAAGGACUGG	chr4:79373293-79373508(+)$1	215	51	77	19.7752
CCAAAGAGCAGUUCAAUGAAGCUCAA	chr2:178095783-178096049(-)$1	266	175	201	20.7534
UCUGUGUUCGUGAUUCCCUUGCACAG	chr3:52283576-52283868(+)$1	292	200	226	22.5483
CCAGAGACAAUAACAUAUGAUGUCCU	chr7:121650786-121651001(+)$1	215	153	179	20.1489
uuguggggaaagcaaagaaaccucgc	chr11:96124420-96124634(+)$1	214	72	98	22.1289

#DB
(((((((((...........))))))	chr2:219525710-219525979(+)$1	1	24	50	23.5176
.(((((((...........)))))))	chr11:47269962-47270182(-)$1	1	63	89	21.8445
((..((((.............)))))	chr2:179318178-179318411(+)$1	1	109	135	23.1791
..)))(((..............))).	chr9:125512539-125512754(+)$1	1	153	179	21.0110
((.((((((...........))))))	chrX:47775724-47776006(+)$1	1	59	85	22.4465
....(((((...........))))).	chr19:24116486-24116699(+)$1	1	35	61	21.8433
((((((.(............).))))	chr2:103431317-103431535(+)$1	1	34	60	21.6661
..((((((............))))))	chr8:67507769-67507998(-)$1	1	187	213	22.1289
((...((((...........))))..	chr22:22890923-22891139(-)$1	1	50	76	22.7560
(((((((.............))))))	chr12:1137235-1137459(+)$1	1	161	187	24.2584
....(((((...........))))))	chr1:193149501-193149779(+)$1	1	192	218	22.4113
(((((((((...........))))))	chr1:11083129-11083377(+)$1	1	146	172	22.6385
(((((((((...........))))))	chr1:220357306-220357567(-)$1	1	186	212	23.5176
.((((.((............)).)))	chr21:34944802-34945053(+)$1	1	93	119	21.7951
((...((.............))...)	chr17:65105525-65105801(-)$1	1	58	84	22.3827
(((..(((............))).))	chr12:978075-978459(+)$1	1	149	175	24.4927
(((((((.............))).))	chr15:98513016-98513231(+)$1	1	143	169	23.3957
(...((((.............)))).	chr2:170911897-170912110(+)$1	1	91	117	23.7706
....((((.............)))).	chr18:34376852-34377099(-)$1	1	95	121	22.7852
(((..(((..............))).	chr16:68155988-68156248(+)$1	1	141	167	22.0720
.....(((..............))).	chr3:101383999-101384231(-)$1	1	125	151	22.2377
(((((((((...........))))))	chr21:15745837-15746064(-)$1	1	159	185	22.9472
))))((((............))))..	chr11:35211398-35211671(+)$1	1	115	141	19.7312
(((((((((...........))))))	chr5:71490122-71490339(+)$1	1	183	209	22.6385
...(((((............))))).	chr1:248525400-248525614(+)$1	1	62	88	20.2053
...(((((............))))).	chr11:125765167-125765424(+)$1	1	4	30	20.2053
))((((((..............))))	chrY:20710215-20710430(+)$1	1	166	192	22.0313
...((((((...........))))))	chr13:86370257-86370472(-)$1	1	31	57	20.4280
(((((((.............))))))	chr8:17579221-17579470(-)$1	1	51	77	23.9029
((...(((..............))).	chr9:15469162-15469383(-)$1	1	126	152	22.8693
(((((((.............))))))	chr15:86124998-86125239(+)$1	1	180	206	24.2584
(.((((((............))).))	chr7:107398659-107398892(+)$1	1	61	87	24.0624
.(((((((.............)).))	chr1:185276978-185277284(-)$1	1	129	155	22.6612
(.((((((.............)))))	chr20:44998869-44999130(-)$1	1	156	182	23.6354
((((((((............))))))	chr3:141299126-141299378(+)$1	1	113	139	23.9046
(....((((...........))))..	chr5:178310123-178310338(+)$1	1	176	202	21.0481
((.(((((............))))))	chr11:1097723-1097938(+)$1	1	188	214	22.8877
).((((((............))))))	chr15:44921333-44921576(-)$1	1	101	127	22.5499
(((((((..............)))))	chr2:128938435-128938651(+)$1	1	131	157	22.6782
.(((((((...........)))))))	chr3:38038836-38039080(+)$1	1	135	161	22.6289
(((.((((...........)))).))	chr19:4305858-4306072(+)$1	1	114	140	21.1839
((((.(((............)))...	chr12:29493975-29494226(-)$1	1	84	110	23.2262
..((((((..............))))	chr7:104753243-104753644(+)$1	1	331	357	22.2658
....((((............))))..	chr17:44632409-44632687(-)$1	1	145	171	23.3582
(((.((((.............)))).	chr14:64520072-64520295(+)$1	1	18	44	23.7014
.(((((((............))))))	chr3:12942483-12942886(-)$1	1	33	59	23.4755
....((((.............)))).	chr12:7045390-7045614(+)$1	1	148	174	21.3921
.(((((.(..............).))	chr9:27048138-27048349(+)$1	1	35	61	21.8388
.(((((((...........)))))))	chr15:45007652-45007995(+)$1	1	288	314	22.6289
.(((((.(............).))))	chr1:27057806-27058079(+)$1	1	76	102	23.4458
(((.(.(((...........))).).	chr2:202001042-202001372(+)$1	1	172	198	23.4936
...((((((...........))))))	chr8:18080139-18080354(+)$1	1	0	26	20.4280
((((((((.............)))))	chr19:53014932-53015145(+)$1	1	0	26	21.0806
((((................))).))	chr12:119624774-119624987(+)$1	1	147	173	19.5386
.(((((((.............)))))	chr17:3324308-3324524(+)$1	1	95	121	23.6606
((((((((..............))))	chr19:21606875-21607098(+)$1	1	95	121	21.8266
((((................))))))	chr4:79373293-79373508(+)$1	1	51	77	19.7752
.....((((...........))))..	chr2:178095783-178096049(-)$1	1	175	201	20.7534
.((((((.............))))))	chr3:52283576-52283868(+)$1	1	200	226	22.5483
..((.((((...........))))))	chr7:121650786-121651001(+)$1	1	153	179	20.1489
..((((((............))))))	chr11:96124420-96124634(+)$1	1	72	98	22.1289

#PSSM
: : 0.18	$ : 0.09	c : 0.09	= : 0.08	f : 0.08	d : 0.06	i : 0.06	! : 0.06	h : 0.04	g : 0.04	[ : 0.03	e : 0.03	b : 0.03	o : 0.01	G : 0.01	# : 0.01	& : 0.01	
g : 0.14	: : 0.13	$ : 0.09	c : 0.09	= : 0.08	d : 0.06	f : 0.06	e : 0.06	i : 0.06	h : 0.03	[ : 0.03	# : 0.03	o : 0.01	" : 0.01	G : 0.01	b : 0.01	& : 0.01	
f : 0.14	g : 0.13	c : 0.11	$ : 0.09	= : 0.06	" : 0.06	i : 0.06	: : 0.06	d : 0.04	e : 0.04	[ : 0.03	h : 0.03	! : 0.01	G : 0.01	# : 0.01	& : 0.01	b : 0.01	
f : 0.21	g : 0.11	e : 0.11	$ : 0.09	= : 0.06	" : 0.06	! : 0.04	c : 0.04	i : 0.04	[ : 0.04	h : 0.03	d : 0.03	G : 0.01	# : 0.01	& : 0.01	b : 0.01	
f : 0.19	d : 0.14	e : 0.14	g : 0.09	= : 0.06	c : 0.04	" : 0.04	i : 0.04	h : 0.03	! : 0.03	$ : 0.03	[ : 0.03	y : 0.03	# : 0.01	a : 0.01	
d : 0.19	f : 0.19	e : 0.14	c : 0.13	g : 0.09	= : 0.06	i : 0.04	h : 0.03	[ : 0.03	y : 0.03	b : 0.01	
d : 0.19	f : 0.19	c : 0.14	g : 0.09	e : 0.09	= : 0.06	[ : 0.04	b : 0.04	i : 0.04	y : 0.03	h : 0.01	
d : 0.19	f : 0.18	c : 0.13	g : 0.09	e : 0.09	v : 0.09	a : 0.04	= : 0.03	b : 0.03	y : 0.03	i : 0.01	w : 0.01	h : 0.01	
u : 0.26	v : 0.24	w : 0.14	f : 0.08	t : 0.06	d : 0.06	= : 0.03	e : 0.03	y : 0.03	i : 0.01	c : 0.01	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
t : 0.31	u : 0.26	v : 0.24	w : 0.14	y : 0.03	
u : 0.26	t : 0.24	v : 0.24	w : 0.14	g : 0.04	y : 0.03	d : 0.01	
v : 0.14	w : 0.14	f : 0.14	d : 0.11	g : 0.09	c : 0.09	e : 0.08	= : 0.06	a : 0.03	b : 0.03	i : 0.03	
d : 0.19	f : 0.16	w : 0.13	g : 0.11	c : 0.09	e : 0.08	= : 0.06	b : 0.04	i : 0.04	] : 0.03	h : 0.01	
d : 0.19	f : 0.19	c : 0.16	g : 0.11	e : 0.11	= : 0.06	i : 0.04	h : 0.03	] : 0.01	3 : 0.01	b : 0.01	a : 0.01	
d : 0.19	f : 0.19	] : 0.13	g : 0.11	e : 0.11	= : 0.06	c : 0.06	i : 0.04	h : 0.03	3 : 0.01	4 : 0.01	
f : 0.22	e : 0.14	g : 0.11	d : 0.11	c : 0.08	= : 0.06	i : 0.06	h : 0.03	4 : 0.03	3 : 0.03	5 : 0.03	: : 0.01	a : 0.01	b : 0.01	
f : 0.24	g : 0.11	e : 0.08	= : 0.06	: : 0.06	5 : 0.06	i : 0.06	d : 0.04	] : 0.04	3 : 0.04	h : 0.03	4 : 0.03	b : 0.03	2 : 0.01	c : 0.01	8 : 0.01	

#score	1363.326471178037
#seq	61
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_CDS_m1_run2.txt

#BEAR
c:==========oooooo==========c	chr1:55075022-55075237(+)$1	215	109	138	12.4894
e!!bb!!dddd[allla]dddd22bbeee	chr7:147914349-147914575(+)$1	226	49	78	10.9794
[ggggggg[cccoooooocccgggggggc	chr17:43333628-43333848(+)$1	220	43	72	12.7672
g[dddd####ddddllldddd333ddddg	chr2:97267332-97267551(+)$1	219	65	94	10.6599
HH==========oooooo==========f	chr12:9224945-9225171(-)$1	226	49	78	11.9159
eeeee####ddddnnnnndddd]eeeee]	chr17:67257701-67257920(-)$1	219	20	49	10.2547
cc!!bb!!ddddoooooodddd22bb]cc	chr1:184677230-184677456(-)$1	226	19	48	13.7704
f!!bb"""ddddnnnnndddd333bb22f	chr5:50130699-50130921(+)$1	222	95	124	11.9498
[bb[dddd[cccooooooccc22dddd]b	chr14:90870692-90870946(+)$1	254	135	164	12.2593
d!!ffffffcccooooooccc]ffffff3	chr1:39797734-39797959(+)$1	225	131	160	11.3916
cccbb!!bb!!cccnnnnnccc22bb22b	chr1:43880770-43881000(+)$1	230	133	162	9.1827
!!cccddddcccammmma]ccc4444ddd	chr1:109883249-109883471(-)$1	222	109	138	9.6557
dccc####ddddoooooodddd22ccc]d	chr5:43446296-43446527(-)$1	231	130	159	14.3253
eeeccc!!ddddoooooodddd22ccc77	chr3:31674497-31674721(+)$1	224	21	50	12.8683
cc[bb"""ddddnnnnndddd333bbccc	chr11:209185-209401(+)$1	216	85	114	11.9580
c!!iiiiiiiiiooooooiiiiiiiiicc	chr18:60646273-60646489(+)$1	216	45	74	12.7533
ggccc[a!!cccooooooccc22a]ccc]	chr3:197273152-197273382(-)$1	230	100	129	14.2967
+++iiiiiiiiiooooooiiiiiiiii66	chr12:30887807-30888023(+)$1	216	107	136	10.0623
fffbb[dddd[annnnnadddd22bb22f	chr17:74448873-74449100(-)$1	227	192	221	9.9839
ddd####eeeeeooooooeeeeeddddff	chr16:56692525-56692744(+)$1	219	163	192	10.3744
g!!bb$$$$$ddddllldddd4444bb33	chr6:31998095-31998336(+)$1	241	38	67	10.6419
+++dddd!!cccooooooccc]dddd22g	chr4:123271056-123271295(+)$1	239	73	102	10.6615
""ffffffddddoooooodddd4444fff	chr13:40175182-40175408(-)$1	226	62	91	12.2873
dd[bb!!a[cccnnnnnccca22bb]ddd	chr17:26970102-26970320(-)$1	218	158	187	10.2822
e!!ccc!!cccnnnnncccccc22eeeee	chr4:9365193-9365441(-)$1	248	190	219	9.7989
bb!!iiiiiiiiinnnnniiiiiiiii]b	chr5:120022004-120022219(-)$1	215	15	44	9.5370
:ggggggga[bboooooobb]a]gggggg	chr20:57484315-57484535(+)$1	220	84	113	10.1107
eee[dddd[cccooooooccc]dddd22e	chr17:74057533-74057751(-)$1	218	46	75	11.5252
ddd####cccrrrrrrrrrccc4444ddd	chr2:203420511-203420729(+)$1	218	108	137	9.4408
cc[dddd!!cccooooooccc22ddddcc	chr19:40540525-40540745(-)$1	220	34	63	13.1799
ccccc[a[ddddoooooodddd]a]ccc]	chr19:31769842-31770074(-)$1	232	187	216	13.5484
==========ddddmmmmdddd]======	chr19:1474867-1475087(-)$1	220	138	167	9.9691
"ccc!!ffffffooooooffffffccc33	chr4:141888759-141888977(-)$1	218	56	85	10.7644
##eeeee[ddddoooooodddd]eeeee3	chrX:54949113-54949333(-)$1	220	121	150	12.2591
bb[ccc!!ccc[bblllbbccc22ccc]b	chr1:33359319-33359544(+)$1	225	25	54	9.5261
"ggggggg[a[ccclllccc]a]gggggg	chr17:73499352-73499604(-)$1	252	60	89	9.6120
eee"""dddd[aooooooa]dddd>>>>>	chr10:93608262-93608486(+)$1	224	118	147	10.8531
c!!a####ddddoooooodddd4444a22	chr2:113159015-113159231(-)$1	216	160	189	14.6293
g[bb!!bb!!cccooooooccc22bb444	chr12:56526476-56526702(+)$1	226	16	45	12.7028
d[abb[a!!ddddnnnnndddd]a]bb]a	chr16:58534828-58535044(+)$1	216	82	111	11.0200
dd[dddd[acccooooooccc]a]ddddd	chr16:89627595-89627834(+)$1	239	124	153	12.3536
fffff####cccooooooccc22ffffff	chr17:76075459-76075685(+)$1	226	41	70	12.8518
:dddd[ccccccooooooccc]cccdddd	chr16:226607-226850(+)$1	243	71	100	11.1263
g####gggggggooooooggggggg333g	chr1:11333546-11333766(+)$1	220	161	190	12.2070
####dddd!!ddddllldddd333dddd5	chr8:144461932-144462147(+)$1	215	90	119	9.8745
iiiiiiiii!!cccmmmmccc22iiiiii	chr7:89861744-89861978(+)$1	234	29	58	9.5862
hhhhhhhhcccaooooooa]ccc]hhhhh	chr8:19816759-19816978(+)$1	219	143	172	9.6358
!!==========oooooo==========3	chr19:18252694-18252911(+)$1	217	39	68	13.8348
bb[bb"""bb[aooooooa]bb333bb]b	chr4:111543327-111543543(-)$1	216	144	173	12.2014
"bb$$$$$ddddoooooodddd4444bb3	chr7:150774688-150774910(-)$1	222	23	52	12.5677
d!!ccc"""cccooooooccc4444cccd	chr5:37722921-37723137(+)$1	216	184	213	14.7743
eeee!!bb[ddddoooooodddd]bbeee	chr15:32744591-32744811(-)$1	220	176	205	10.8120
"ccc$$$$$cccooooooccc666666cc	chr3:141162978-141163205(+)$1	227	131	160	10.9658
[dddd[bb[ddddnnnnndddd22bb]dd	chr19:14038857-14039076(+)$1	219	87	116	10.1314
e[ccc!!cccrrrrrrrrrccc]ccc]ee	chrX:53239924-53240141(-)$1	217	30	59	9.5074
e:eeeee"""cccnnnnnccc333eeeee	chr15:43990860-43991086(-)$1	226	184	213	9.8538
##bb[dddd!!ddddllldddd22dddd]	chr6:78400341-78400561(+)$1	220	48	77	9.1081

#otherMatches

#Seq PSSM
CAGCUGUGCUGUGGCCCAGCAGCAUGGCC	chr1:55075022-55075237(+)$1	215	109	138	12.4894
AGAAGGGAUGUGGCUACGAUAUAACUUUC	chr7:147914349-147914575(+)$1	226	49	78	10.9794
UGGUGGGGACUUAGGGAAGAGCCCUGCCG	chr17:43333628-43333848(+)$1	220	43	72	12.7672
CACCUGGGAAGAGGACUCCUCGGAUGGGG	chr2:97267332-97267551(+)$1	219	65	94	10.6599
GAAAGGGCAAAAAACUGAUUUUGUCUUUG	chr12:9224945-9225171(-)$1	226	49	78	11.9159
CUGAUUUACAGGUUUUUUGCCUUAUUGGU	chr17:67257701-67257920(-)$1	219	20	49	10.2547
GCAGGAGAUGAUUGAAUUGUCAAGUCAGC	chr1:184677230-184677456(-)$1	226	19	48	13.7704
GAGAGAUAUGGGUUGUCCCCAAUACUGAC	chr5:50130699-50130921(+)$1	222	95	124	11.9498
AUUGAUGGAGACGGACAAGUCAACUAUGA	chr14:90870692-90870946(+)$1	254	135	164	12.2593
GUAUUGUGUCUACUGAACUAGCACAUAAA	chr1:39797734-39797959(+)$1	225	131	160	11.3916
GGCAGAGGCAACUUAGAAAGAGGAGCAGC	chr1:43880770-43881000(+)$1	230	133	162	9.1827
AAGCGUGCUCUCCGAAGGUGAGUCUCGGC	chr1:109883249-109883471(-)$1	222	109	138	9.6557
GUUCAUUCGUUAUGUAUUUAACAGGAACC	chr5:43446296-43446527(-)$1	231	130	159	14.3253
UACAUCAGAACACUGGCUUGUUAGGAUAU	chr3:31674497-31674721(+)$1	224	21	50	12.8683
CACUCCCAGAGCUUCACGUUUGAUGAUGC	chr11:209185-209401(+)$1	216	85	114	11.9580
GCCAGGUCUGCCCAGGAAGGCAGACUUCU	chr18:60646273-60646489(+)$1	216	45	74	12.7533
ACGGCUCCCAGGAAAAACCCUAAGUGCCU	chr3:197273152-197273382(-)$1	230	100	129	14.2967
UUCUUUCAGGGCAGGUCAGUUUUGAAAAC	chr12:30887807-30888023(+)$1	216	107	136	10.0623
GGCGCGGGCCACGAGGAGGGCCGGGCCAG	chr17:74448873-74449100(-)$1	227	192	221	9.9839
GCUAAGGUUGGGAUGGAACCCAAGGCUGG	chr16:56692525-56692744(+)$1	219	163	192	10.3744
UGAGGAAGGAGAUAAGUUAUUGGAGCCGC	chr6:31998095-31998336(+)$1	241	38	67	10.6419
UUUGAUACCAGCAAACGAGCUCUGUCUAC	chr4:123271056-123271295(+)$1	239	73	102	10.6615
CCAGCCUGACUUGUACUGGAGUAAUCUGG	chr13:40175182-40175408(-)$1	226	62	91	12.2873
UAUCCUGGACUGUACUUUGGCAUGGUUGG	chr17:26970102-26970320(-)$1	218	158	187	10.2822
UGAUGUGAGCUUGCAUAGUACAGAGCAUG	chr4:9365193-9365441(-)$1	248	190	219	9.7989
GGACAGGUUCACUGUGUAAGUGGACCUCC	chr5:120022004-120022219(-)$1	215	15	44	9.5370
UUCAGGACCUGCUUCGCUGCCGUGUCCUG	chr20:57484315-57484535(+)$1	220	84	113	10.1107
GAGCACUGGUUUGCUGUUGAAGCAGUUCC	chr17:74057533-74057751(-)$1	218	46	75	11.5252
UCUCCCCAAGCAGCAGAACCUUCCCAAGA	chr2:203420511-203420729(+)$1	218	108	137	9.4408
UCAGCAUCAGAAAACUCAUUCCAGUGCGA	chr19:40540525-40540745(-)$1	220	34	63	13.1799
CCCAGAAGGUGCUGAAGUGCAUGUACUGU	chr19:31769842-31770074(-)$1	232	187	216	13.5484
GGCAUUCACGGGGUCCCAGCCCACGUGGG	chr19:1474867-1475087(-)$1	220	138	167	9.9691
CCGGAACUUGCAGAAAUAUGUGAGCCGCA	chr4:141888759-141888977(-)$1	218	56	85	10.7644
CAGCCUUAGUAAUAGUCUUUAUAGGGGCC	chrX:54949113-54949333(-)$1	220	121	150	12.2591
ACCGCUCCCCUCGCCCUGCAGGCAAGCUG	chr1:33359319-33359544(+)$1	225	25	54	9.5261
GCGGCUACGACUCCAUGGGGCUGGUGGCC	chr17:73499352-73499604(-)$1	252	60	89	9.6120
AGAAAAAGGAGGGUGAGACGUUCUACAAA	chr10:93608262-93608486(+)$1	224	118	147	10.8531
GCCCUUUCCUGUGUGUAAACAGCUUUGUA	chr2:113159015-113159231(-)$1	216	160	189	14.6293
UGUUCCCCAGGUGAUGGUACACGAGGUCC	chr12:56526476-56526702(+)$1	226	16	45	12.7028
GAGCCGUGAAGCUGGCAGGGCUAGGGGAC	chr16:58534828-58535044(+)$1	216	82	111	11.0200
GUUCGGUACCACACGAAGGUGCGCGCCGG	chr16:89627595-89627834(+)$1	239	124	153	12.3536
UUGGCAAUAGUGGAGCAGCACAAGCCAGG	chr17:76075459-76075685(+)$1	226	41	70	12.8518
ACUCUUCUGGUCCCCACAGACUCAGAGAG	chr16:226607-226850(+)$1	243	71	100	11.1263
CUCCUGGAGGCAGAAGUGUGCCUCCUACG	chr1:11333546-11333766(+)$1	220	161	190	12.2070
CACCGGACCAUGGCCCAGCCACCCGUCCA	chr8:144461932-144462147(+)$1	215	90	119	9.8745
GUUUUGCCCUCAAUUGUAAUUCUGGGUAA	chr7:89861744-89861978(+)$1	234	29	58	9.5862
AGGGGGGCGGUCAUCAUGGCACCAGUCCC	chr8:19816759-19816978(+)$1	219	143	172	9.6358
ACCUUCGCUGAAAGGAGCUUCAGUGAAGA	chr19:18252694-18252911(+)$1	217	39	68	13.8348
GCCGCCCUGCAGACAUUCCCGCUCAGCUG	chr4:111543327-111543543(-)$1	216	144	173	12.2014
CAGUCCCCGCCUCCCCACAGGCACCCCUC	chr7:150774688-150774910(-)$1	222	23	52	12.5677
UUAGAGACAGAGAAAGCCCUCAGAAUUCA	chr5:37722921-37723137(+)$1	216	184	213	14.7743
CCCUUGGGGCCCUGAAGAAAGGGGCUGGG	chr15:32744591-32744811(-)$1	220	176	205	10.8120
ACAGUCCAGCCAUCCCAUUGGAAACAUCU	chr3:141162978-141163205(+)$1	227	131	160	10.9658
UGGGCCCAAAGGGAAGGCCCCUCCUGUGC	chr19:14038857-14039076(+)$1	219	87	116	10.1314
AAGAAAAUGACUUAAGAUCUCAGUUCCUU	chrX:53239924-53240141(-)$1	217	30	59	9.5074
CCACUCCUCCAGUACCACGCUUUUGGAGU	chr15:43990860-43991086(-)$1	226	184	213	9.8538
UGGAUGUUCAAAAAUGGUAUUUGAGAACU	chr6:78400341-78400561(+)$1	220	48	77	9.1081

#DB
).((((((((((......))))))))))(	chr1:55075022-55075237(+)$1	1	109	138	12.4894
(..((..((((.(...).))))..)))))	chr7:147914349-147914575(+)$1	1	49	78	10.9794
.(((((((.(((......)))))))))))	chr17:43333628-43333848(+)$1	1	43	72	12.7672
(.((((....((((...))))...)))))	chr2:97267332-97267551(+)$1	1	65	94	10.6599
((((((((((((......))))))))))(	chr12:9224945-9225171(-)$1	1	49	78	11.9159
(((((....((((.....)))).))))).	chr17:67257701-67257920(-)$1	1	20	49	10.2547
((..((..((((......))))..)).))	chr1:184677230-184677456(-)$1	1	19	48	13.7704
(..((...((((.....))))...))..)	chr5:50130699-50130921(+)$1	1	95	124	11.9498
.((.((((.(((......)))..)))).)	chr14:90870692-90870946(+)$1	1	135	164	12.2593
(..(((((((((......))).)))))).	chr1:39797734-39797959(+)$1	1	131	160	11.3916
)))((..((..(((.....)))..))..)	chr1:43880770-43881000(+)$1	1	133	162	9.1827
..(((((((((((....).)))....)))	chr1:109883249-109883471(-)$1	1	109	138	9.6557
((((....((((......))))..))).)	chr5:43446296-43446527(-)$1	1	130	159	14.3253
((((((..((((......))))..)))..	chr3:31674497-31674721(+)$1	1	21	50	12.8683
((.((...((((.....))))...)))))	chr11:209185-209401(+)$1	1	85	114	11.9580
(..(((((((((......)))))))))))	chr18:60646273-60646489(+)$1	1	45	74	12.7533
(((((.(..(((......)))..).))).	chr3:197273152-197273382(-)$1	1	100	129	14.2967
...(((((((((......)))))))))..	chr12:30887807-30888023(+)$1	1	107	136	10.0623
(((((.((((.(.....)))))..))..)	chr17:74448873-74449100(-)$1	1	192	221	9.9839
(((....(((((......)))))))))))	chr16:56692525-56692744(+)$1	1	163	192	10.3744
(..((.....((((...))))....))..	chr6:31998095-31998336(+)$1	1	38	67	10.6419
...((((..(((......))).))))..)	chr4:123271056-123271295(+)$1	1	73	102	10.6615
..((((((((((......))))....)))	chr13:40175182-40175408(-)$1	1	62	91	12.2873
((.((..(.(((.....))))..)).)))	chr17:26970102-26970320(-)$1	1	158	187	10.2822
(..(((..(((.....))))))..)))))	chr4:9365193-9365441(-)$1	1	190	219	9.7989
((..(((((((((.....))))))))).)	chr5:120022004-120022219(-)$1	1	15	44	9.5370
.((((((((.((......)).).))))))	chr20:57484315-57484535(+)$1	1	84	113	10.1107
(((.((((.(((......))).))))..)	chr17:74057533-74057751(-)$1	1	46	75	11.5252
(((....(((.........)))....)))	chr2:203420511-203420729(+)$1	1	108	137	9.4408
((.((((..(((......)))..))))))	chr19:40540525-40540745(-)$1	1	34	63	13.1799
(((((.(.((((......)))).).))).	chr19:31769842-31770074(-)$1	1	187	216	13.5484
((((((((((((((....)))).))))))	chr19:1474867-1475087(-)$1	1	138	167	9.9691
.(((..((((((......)))))))))..	chr4:141888759-141888977(-)$1	1	56	85	10.7644
..(((((.((((......)))).))))).	chrX:54949113-54949333(-)$1	1	121	150	12.2591
((.(((..(((.((...)))))..))).)	chr1:33359319-33359544(+)$1	1	25	54	9.5261
.(((((((.(.(((...))).).))))))	chr17:73499352-73499604(-)$1	1	60	89	9.6120
(((...((((.(......).)))).....	chr10:93608262-93608486(+)$1	1	118	147	10.8531
(..(....((((......))))....)..	chr2:113159015-113159231(-)$1	1	160	189	14.6293
(.((..((..(((......)))..))...	chr12:56526476-56526702(+)$1	1	16	45	12.7028
(.(((.(..((((.....)))).).)).)	chr16:58534828-58535044(+)$1	1	82	111	11.0200
((.((((.((((......))).).)))))	chr16:89627595-89627834(+)$1	1	124	153	12.3536
(((((....(((......)))..))))))	chr17:76075459-76075685(+)$1	1	41	70	12.8518
.((((.((((((......))).)))))))	chr16:226607-226850(+)$1	1	71	100	11.1263
(....(((((((......)))))))...)	chr1:11333546-11333766(+)$1	1	161	190	12.2070
....((((..((((...))))...)))).	chr8:144461932-144462147(+)$1	1	90	119	9.8745
(((((((((..(((....)))..))))))	chr7:89861744-89861978(+)$1	1	29	58	9.5862
((((((((((((......).))).)))))	chr8:19816759-19816978(+)$1	1	143	172	9.6358
..((((((((((......)))))))))).	chr19:18252694-18252911(+)$1	1	39	68	13.8348
((.((...((.(......).))...)).)	chr4:111543327-111543543(-)$1	1	144	173	12.2014
.((.....((((......))))....)).	chr7:150774688-150774910(-)$1	1	23	52	12.5677
(..(((...(((......)))....))))	chr5:37722921-37723137(+)$1	1	184	213	14.7743
((((..((.((((......)))).)))))	chr15:32744591-32744811(-)$1	1	176	205	10.8120
.(((.....(((......)))......))	chr3:141162978-141163205(+)$1	1	131	160	10.9658
.((((.((.((((.....))))..)).))	chr19:14038857-14039076(+)$1	1	87	116	10.1314
(.(((..(((.........))).))).))	chrX:53239924-53240141(-)$1	1	30	59	9.5074
).(((((...(((.....)))...)))))	chr15:43990860-43991086(-)$1	1	184	213	9.8538
..((.((((..((((...))))..)))).	chr6:78400341-78400561(+)$1	1	48	77	9.1081

#PSSM
e : 0.15	c : 0.14	d : 0.14	g : 0.08	" : 0.08	[ : 0.05	f : 0.05	b : 0.05	# : 0.05	! : 0.03	+ : 0.03	: : 0.03	H : 0.01	= : 0.01	i : 0.01	h : 0.01	
! : 0.17	c : 0.14	d : 0.10	e : 0.08	b : 0.08	g : 0.07	[ : 0.07	# : 0.07	: : 0.03	+ : 0.03	f : 0.03	H : 0.01	" : 0.01	= : 0.01	i : 0.01	h : 0.01	
! : 0.17	c : 0.14	e : 0.12	[ : 0.10	d : 0.08	= : 0.07	b : 0.07	g : 0.05	f : 0.05	+ : 0.03	# : 0.03	a : 0.01	i : 0.01	h : 0.01	
b : 0.19	c : 0.19	d : 0.10	= : 0.07	e : 0.07	# : 0.07	g : 0.05	f : 0.05	i : 0.05	! : 0.03	[ : 0.03	" : 0.01	a : 0.01	h : 0.01	$ : 0.01	
b : 0.17	d : 0.15	c : 0.14	# : 0.08	= : 0.07	i : 0.07	g : 0.05	e : 0.05	f : 0.05	! : 0.05	$ : 0.03	" : 0.01	h : 0.01	[ : 0.01	
d : 0.15	! : 0.12	# : 0.10	[ : 0.10	= : 0.07	g : 0.07	" : 0.07	c : 0.07	i : 0.07	$ : 0.05	f : 0.03	e : 0.03	b : 0.01	h : 0.01	
d : 0.17	! : 0.14	# : 0.12	= : 0.07	g : 0.07	" : 0.07	i : 0.07	f : 0.05	a : 0.05	$ : 0.05	b : 0.05	e : 0.03	c : 0.01	h : 0.01	
d : 0.14	! : 0.14	# : 0.08	" : 0.08	= : 0.07	g : 0.07	b : 0.07	i : 0.07	f : 0.05	$ : 0.05	c : 0.05	[ : 0.05	e : 0.01	a : 0.01	h : 0.01	
d : 0.26	[ : 0.12	! : 0.10	c : 0.10	= : 0.07	i : 0.07	# : 0.05	f : 0.03	b : 0.03	$ : 0.03	a : 0.03	" : 0.03	e : 0.01	g : 0.01	
c : 0.33	d : 0.29	! : 0.08	= : 0.07	i : 0.05	# : 0.01	e : 0.01	$ : 0.01	[ : 0.01	f : 0.01	a : 0.01	g : 0.01	b : 0.01	" : 0.01	
d : 0.33	c : 0.33	[ : 0.07	= : 0.05	! : 0.05	i : 0.05	r : 0.03	e : 0.01	b : 0.01	f : 0.01	g : 0.01	
c : 0.33	d : 0.33	a : 0.07	= : 0.05	i : 0.05	[ : 0.03	r : 0.03	e : 0.01	n : 0.01	b : 0.01	f : 0.01	g : 0.01	
o : 0.56	d : 0.15	n : 0.08	c : 0.08	a : 0.03	r : 0.03	i : 0.01	b : 0.01	
o : 0.59	n : 0.17	d : 0.08	c : 0.05	r : 0.03	l : 0.01	m : 0.01	b : 0.01	
o : 0.59	n : 0.19	l : 0.10	m : 0.05	r : 0.03	d : 0.01	
o : 0.59	n : 0.19	l : 0.12	m : 0.05	r : 0.03	
o : 0.59	n : 0.17	l : 0.10	m : 0.05	r : 0.03	a : 0.01	c : 0.01	
o : 0.59	n : 0.10	d : 0.08	c : 0.05	a : 0.03	r : 0.03	m : 0.03	] : 0.01	b : 0.01	l : 0.01	
d : 0.35	c : 0.29	= : 0.05	i : 0.05	a : 0.05	b : 0.03	r : 0.03	o : 0.03	n : 0.01	] : 0.01	e : 0.01	f : 0.01	g : 0.01	
c : 0.40	d : 0.36	= : 0.05	i : 0.05	] : 0.05	e : 0.01	b : 0.01	f : 0.01	g : 0.01	
d : 0.38	c : 0.38	= : 0.05	i : 0.05	] : 0.03	e : 0.01	a : 0.01	f : 0.01	g : 0.01	b : 0.01	
d : 0.29	c : 0.14	2 : 0.10	3 : 0.08	] : 0.08	= : 0.05	i : 0.05	g : 0.03	4 : 0.03	a : 0.03	e : 0.01	f : 0.01	b : 0.01	6 : 0.01	
2 : 0.29	] : 0.14	4 : 0.12	3 : 0.10	d : 0.07	= : 0.05	i : 0.05	g : 0.03	f : 0.03	c : 0.03	e : 0.01	a : 0.01	6 : 0.01	
2 : 0.19	4 : 0.12	3 : 0.10	d : 0.10	= : 0.07	g : 0.07	i : 0.07	f : 0.05	a : 0.05	] : 0.05	e : 0.03	c : 0.03	b : 0.01	6 : 0.01	
b : 0.17	d : 0.15	4 : 0.12	c : 0.10	= : 0.07	g : 0.07	e : 0.07	i : 0.07	] : 0.05	f : 0.03	> : 0.01	h : 0.01	3 : 0.01	6 : 0.01	
b : 0.21	d : 0.17	c : 0.14	4 : 0.08	= : 0.07	e : 0.07	i : 0.07	g : 0.05	f : 0.03	] : 0.01	> : 0.01	3 : 0.01	h : 0.01	6 : 0.01	
d : 0.19	c : 0.14	e : 0.10	2 : 0.08	= : 0.07	i : 0.07	b : 0.07	g : 0.05	] : 0.05	f : 0.05	> : 0.01	a : 0.01	4 : 0.01	3 : 0.01	h : 0.01	6 : 0.01	
d : 0.15	c : 0.14	e : 0.12	2 : 0.10	] : 0.10	= : 0.07	f : 0.07	g : 0.05	3 : 0.05	7 : 0.01	6 : 0.01	> : 0.01	4 : 0.01	i : 0.01	h : 0.01	b : 0.01	
d : 0.14	c : 0.12	e : 0.10	f : 0.10	3 : 0.10	g : 0.08	b : 0.08	] : 0.07	7 : 0.01	6 : 0.01	= : 0.01	> : 0.01	2 : 0.01	4 : 0.01	a : 0.01	5 : 0.01	i : 0.01	h : 0.01	

#score	647.6427172133012
#seq	57
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_CDS_m1_run1.txt

#BEAR
gggggggvvvvvvvvvvvvvgggggg	chrX:41088409-41088643(+)$1	234	89	115	24.9507
ggggggguuuuuuuuuuuuggggggg	chr16:46715273-46715500(-)$1	227	141	167	24.9813
[dddd[bbtttttttttttbb]dddd	chr16:20807584-20807806(-)$1	222	65	91	22.1289
ccc[cccvvvvvvvvvvvvvccc]cc	chr9:125673689-125673932(-)$1	243	159	185	24.8056
ccbb[bbwwwwwwwwwwwwwwbb22b	chr17:76993574-76993812(-)$1	238	55	81	21.0228
dcccbbvvvvvvvvvvvvvbb]ccc]	chr5:471878-472128(-)$1	250	196	222	22.5954
$$$dddduuuuuuuuuuuudddd22f	chr12:56641859-56642108(-)$1	249	20	46	22.6995
[ffffffuuuuuuuuuuuuffffff=	chr1:147096427-147096647(+)$1	220	149	175	23.1615
c"""ddddtttttttttttddddccc	chr10:32310976-32311241(-)$1	265	142	168	23.2959
c[eeeeevvvvvvvvvvvvveeeee]	chr20:43560904-43561129(+)$1	225	169	195	23.5245
!!eeeeevvvvvvvvvvvvveeeee2	chr16:29822295-29822559(+)$1	264	181	207	23.3239
d[bbddddtttttttttttdddd]bb	chr9:131484720-131484943(-)$1	223	177	203	22.1861
dd"""ccctttttttttttccc4444	chr1:155290229-155290476(+)$1	247	139	165	24.0786
iiiiiiiitttttttttttiiiiiii	chr3:48731490-48731730(-)$1	240	158	184	24.6732
eee[cccuuuuuuuuuuuuccc22ee	chr3:28304719-28304953(+)$1	234	20	46	24.2584
gggggggvvvvvvvvvvvvvgggggg	chr3:160119688-160119911(+)$1	223	83	109	24.9507
:gggggggtttttttttttggggggg	chr12:109536235-109536486(+)$1	251	5	31	23.4174
gggggggvvvvvvvvvvvvvgggggg	chrX:84525564-84525792(+)$1	228	170	196	24.9507
iiiiiiiuuuuuuuuuuuuiiiiiii	chr5:94851986-94852213(-)$1	227	73	99	25.1966
ccc[cccvvvvvvvvvvvvvccc22c	chr3:50608410-50608637(+)$1	227	0	26	24.6315
dd!!ddddtttttttttttdddd22d	chr10:33468947-33469178(-)$1	231	121	147	23.1098
hhhhhhhyyyyyyyyyyyyyyyyhhh	chrX:47072081-47072335(+)$1	254	194	220	20.7427
Ggggggggtttttttttttggggggg	chr6:87965702-87965934(+)$1	232	136	162	23.8079
cc!!cccvvvvvvvvvvvvvccc22c	chr9:98209310-98209541(-)$1	231	31	57	24.7851
cgggggggtttttttttttggggggg	chr2:31488967-31489190(+)$1	223	94	120	24.4361
cceeeeevvvvvvvvvvvvveeeee]	chr12:121766134-121766370(-)$1	236	49	75	23.4207
[gggggggtttttttttttggggggg	chrX:47085146-47085365(+)$1	219	99	125	24.5445
====[bbuuuuuuuuuuuubb22===	chr11:9602998-9603251(+)$1	253	36	62	24.2242
dddd[ccctttttttttttccc333d	chr7:6189398-6189632(+)$1	234	15	41	24.0570
a[a[ddddtttttttttttdddd]a]	chr6:25600722-25600952(+)$1	230	158	184	23.6482
[cccyyyyyyyyyyyyyyyyccc333	chr5:78746769-78746994(-)$1	225	80	106	22.2292
iiii!!avvvvvvvvvvvvva22iii	chr20:7967888-7968113(-)$1	225	24	50	24.5573
g[ayyyyyyyyyyyyyyyya]ggggg	chr7:112555361-112555588(-)$1	227	14	40	21.4109
ee[cccwwwwwwwwwwwwwwccceee	chr6:24706303-24706545(-)$1	242	109	135	22.3108
hhh[cccwwwwwwwwwwwwwwccc]h	chr12:118463464-118463688(+)$1	224	179	205	22.5987
'gggggggtttttttttttggggggg	chr17:40476949-40477168(-)$1	219	168	194	23.7756
[ccccccvvvvvvvvvvvvvccc]cc	chrX:106882447-106882678(+)$1	231	145	171	24.6895
ggggggguuuuuuuuuuuuggggggg	chr9:131671158-131671389(+)$1	231	12	38	24.9813
dd!!cccyyyyyyyyyyyyyyyyccc	chr1:43829935-43830161(-)$1	226	173	199	21.9750
+ccccccuuuuuuuuuuuuccc]ccc	chr16:2815070-2815306(+)$1	236	156	182	23.8618
ddd!!ccctttttttttttccc22dd	chr22:31822998-31823229(+)$1	231	189	215	23.7698
eeeeyyyyyyyyyyyyyyyyeeeee]	chr3:128356624-128356858(-)$1	234	55	81	20.9857
d!!ddddyyyyyyyyyyyyyyyyddd	chr10:112057257-112057483(-)$1	226	99	125	20.9661
hh[a[bbuuuuuuuuuuuubba]hhh	chr1:155228518-155228744(-)$1	226	123	149	23.4788
ggggggguuuuuuuuuuuuggggggg	chr1:115282350-115282573(-)$1	223	143	169	24.9813
[ddddwwwwwwwwwwwwwwddddbb]	chr1:113460252-113460492(-)$1	240	40	66	20.3913
cc"""bbvvvvvvvvvvvvvbb22cc	chr14:90429400-90429625(+)$1	225	118	144	23.6794
ccc[ddddtttttttttttddddccc	chr5:174919038-174919283(+)$1	245	8	34	23.3640
fff!!ccctttttttttttcccffff	chr3:194162047-194162278(-)$1	231	44	70	23.8223
hhhhhhhyyyyyyyyyyyyyyyyhhh	chr6:144128113-144128337(+)$1	224	103	129	20.7427
========ttttttttttt=======	chr5:64957797-64958024(+)$1	227	156	182	25.1152
b####bbuuuuuuuuuuuubb4444b	chr17:77757671-77757896(+)$1	225	87	113	22.9730
fffffbbwwwwwwwwwwwwwwbb]ff	chr7:30395257-30395497(+)$1	240	142	168	21.1569
d!!eeeeettttttttttteeeee22	chr3:128889271-128889497(-)$1	226	57	83	22.8701
========ttttttttttt=======	chr6:36493282-36493509(-)$1	227	69	95	25.1152
a[fffffftttttttttttffffff]	chr4:15646173-15646404(-)$1	231	122	148	22.7494
gggggggvvvvvvvvvvvvvgggggg	chr2:74392353-74392574(-)$1	221	62	88	24.9507
[a[eeeeettttttttttteeeee]a	chr19:42462355-42462580(-)$1	225	23	49	23.1200
gggggggtttttttttttggggggg]	chr11:75282842-75283075(+)$1	233	18	44	23.5443
eeeecccvvvvvvvvvvvvvccc444	chr2:153515369-153515594(-)$1	225	40	66	23.9861
$fffffftttttttttttffffff33	chr12:110565159-110565390(+)$1	231	25	51	21.6591
gggg[ccctttttttttttccc]ggg	chr17:73234632-73234872(-)$1	240	120	146	24.9792
=======uuuuuuuuuuuu=======	chr21:34925501-34925724(+)$1	223	80	106	25.5074
gggddddtttttttttttdddd22gg	chr19:59067976-59068199(-)$1	223	16	42	22.5988
iiiiiiivvvvvvvvvvvvviiiiii	chr21:43338888-43339112(-)$1	224	162	188	25.0925
eee[ddddtttttttttttddddeee	chr1:93299070-93299299(+)$1	229	160	186	22.8561
gggggbbwwwwwwwwwwwwwwbb]gg	chrX:105905155-105905381(+)$1	226	155	181	22.4781
=======vvvvvvvvvvvvv======	chr9:117825976-117826203(-)$1	227	92	118	25.3312
ee"""bbtttttttttttbb]eeeee	chr1:16263790-16264041(+)$1	251	119	145	22.0134

#otherMatches

#Seq PSSM
CUUUCAGAAUUCAUAAUGCACUGAAA	chrX:41088409-41088643(+)$1	234	89	115	24.9507
UUUGCUAAAGGAAGGAAAGUGGCAGA	chr16:46715273-46715500(-)$1	227	141	167	24.9813
UGAUCAUGUGACUUGUAAUCAGGAUU	chr16:20807584-20807806(-)$1	222	65	91	22.1289
GACAUCAGAGAGAAAGGAAAUGAAGU	chr9:125673689-125673932(-)$1	243	159	185	24.8056
UGACUCCUCUCCUCCCUCCCUGGCUG	chr17:76993574-76993812(-)$1	238	55	81	21.0228
GUCAGCCACACAAAAGCCUGCAUGAC	chr5:471878-472128(-)$1	250	196	222	22.5954
GGACCCCAAGAGCAGAGAAGGGGAAG	chr12:56641859-56642108(-)$1	249	20	46	22.6995
CGGGCUCUACACCCACCCUGGGCCUG	chr1:147096427-147096647(+)$1	220	149	175	23.1615
CAGUGAAGAACUAGUCCAGCUUCGAG	chr10:32310976-32311241(-)$1	265	142	168	23.2959
GUGAGUGACCCAGCCCCUUCCACUCU	chr20:43560904-43561129(+)$1	225	169	195	23.5245
AAAAUCCUGUUUCUGGCUCUGGAUUG	chr16:29822295-29822559(+)$1	264	181	207	23.3239
CUGUGUCACUCAUGGACCCUGGCUAC	chr9:131484720-131484943(-)$1	223	177	203	22.1861
UUGCGCGCAAAAUCUACAAGCGGAGA	chr1:155290229-155290476(+)$1	247	139	165	24.0786
CCCGGCUCCUCUGCACCCAGAGCUGG	chr3:48731490-48731730(-)$1	240	158	184	24.6732
UUUGCUUGAGACUUUAUUAAAGAAAG	chr3:28304719-28304953(+)$1	234	20	46	24.2584
CUCCAGCAAUGACCAAUGAAGCUGGA	chr3:160119688-160119911(+)$1	223	83	109	24.9507
UCCCAGCCAAGAAGGCCCCGGCUGGG	chr12:109536235-109536486(+)$1	251	5	31	23.4174
GAUUCUUAAAAAGACACAUGAAGAAU	chrX:84525564-84525792(+)$1	228	170	196	24.9507
UAAGAAAAAAAAUGUUAUGUUUUUUA	chr5:94851986-94852213(-)$1	227	73	99	25.1966
GCUUGUGACCUCUCCAUCUCCACCCA	chr3:50608410-50608637(+)$1	227	0	26	24.6315
GUGAAGUUGAAAAAAGACAAACUGAA	chr10:33468947-33469178(-)$1	231	121	147	23.1098
AAAUCUGAUGUUCCACCCUCCUCCAG	chrX:47072081-47072335(+)$1	254	194	220	20.7427
ACAGUACUCCUCCUGAAAAAGUGCUG	chr6:87965702-87965934(+)$1	232	136	162	23.8079
GGGCCCGUUCUCACAACCCUCGGAAC	chr9:98209310-98209541(-)$1	231	31	57	24.7851
ACUUUAGCAAGUUCCAGCCGCUGAAG	chr2:31488967-31489190(+)$1	223	94	120	24.4361
UGGGUAUAUCUGUCCCCUUAGUACCU	chr12:121766134-121766370(-)$1	236	49	75	23.4207
CCCUUGUCUUUGAGUACCUGGUAAGG	chrX:47085146-47085365(+)$1	219	99	125	24.5445
UAUUUCAGAAAGAAGAAAAUGCUAAU	chr11:9602998-9603251(+)$1	253	36	62	24.2242
GUUGCCUGUUCGCCAGUGUCAGUCUC	chr7:6189398-6189632(+)$1	234	15	41	24.0570
GGCAGGGCGGAGGUAUGGGGUCCAGG	chr6:25600722-25600952(+)$1	230	158	184	23.6482
AUGACAUUUACUAAAACAUCUCAGAA	chr5:78746769-78746994(-)$1	225	80	106	22.2292
UAUUUUUGGUUCUCUUAAAAAUUAAU	chr20:7967888-7968113(-)$1	225	24	50	24.5573
UGUGCUAAAACUUAUUUCAAGAGUCU	chr7:112555361-112555588(-)$1	227	14	40	21.4109
CCACAGGAACAGCUCACCCACUGGGC	chr6:24706303-24706545(-)$1	242	109	135	22.3108
AAGCAAAUCCuuuuuuuuuuuuuuuu	chr12:118463464-118463688(+)$1	224	179	205	22.5987
UGCUGACCAACAAUCCCAAGGUUAGU	chr17:40476949-40477168(-)$1	219	168	194	23.7756
AUGACAAUUUAAUGGAGCUUUUGAUC	chrX:106882447-106882678(+)$1	231	145	171	24.6895
UGAGGGCACCAAGCUCAUCGUCCUCA	chr9:131671158-131671389(+)$1	231	12	38	24.9813
GGCUUGGCCUGACUUACCUAUAACCA	chr1:43829935-43830161(-)$1	226	173	199	21.9750
AGCCAAGACAAGAACCCCACUUCGGC	chr16:2815070-2815306(+)$1	236	156	182	23.8618
GGUCCCUCCUUUUUCCUAUGAGUUAC	chr22:31822998-31823229(+)$1	231	189	215	23.7698
GGGAACCAUUAUUUCUACUCUCCCUA	chr3:128356624-128356858(-)$1	234	55	81	20.9857
CAAGCCUGUAGAAGAAGGAAGGAAGG	chr10:112057257-112057483(-)$1	226	99	125	20.9661
GAUGUGUGAGUAGUGAGAAGCCUUUU	chr1:155228518-155228744(-)$1	226	123	149	23.4788
GGGGUUAUUGAAAAACUGUUAACCUC	chr1:115282350-115282573(-)$1	223	143	169	24.9813
AGCCCUCAUGCGACCAAUCGGGCCCA	chr1:113460252-113460492(-)$1	240	40	66	20.3913
GAAAAGCCAAAACCAGACAAGCCAUC	chr14:90429400-90429625(+)$1	225	118	144	23.6794
CGUAGUGACAUUGUAAGCCUUACACG	chr5:174919038-174919283(+)$1	245	8	34	23.3640
AAUCUUAGAAUUUAUGAAACUAAUUC	chr3:194162047-194162278(-)$1	231	44	70	23.8223
UGAAUUUAAAAGCACAGAAAUGGAAG	chr6:144128113-144128337(+)$1	224	103	129	20.7427
UACCUGUAAAAUAACAAACUGCAGGU	chr5:64957797-64958024(+)$1	227	156	182	25.1152
CAAAAGGCAACCCGAAGACCCGUGAG	chr17:77757671-77757896(+)$1	225	87	113	22.9730
CAGGGAGAUACUAUAGCACGACUGCC	chr7:30395257-30395497(+)$1	240	142	168	21.1569
UGUGAAAACUUUUAAUUUCUUUUUUA	chr3:128889271-128889497(-)$1	226	57	83	22.8701
UUUUGUUUUUGUUUGUUUUAGACAAA	chr6:36493282-36493509(-)$1	227	69	95	25.1152
AGUCUUUGUAUGCUACUUUCAAGGAG	chr4:15646173-15646404(-)$1	231	122	148	22.7494
GAAAAAUUUAUCAGUAAAACAUUUUU	chr2:74392353-74392574(-)$1	221	62	88	24.9507
CCUCCCUGCACUCCUCCUCCAGGGUG	chr19:42462355-42462580(-)$1	225	23	49	23.1200
UGACAAGAACAAGGCCGACUUGUCAC	chr11:75282842-75283075(+)$1	233	18	44	23.5443
CUGACACUUUUUAUCCUUUUGUGCUA	chr2:153515369-153515594(-)$1	225	40	66	23.9861
UAUGAGUGAUCAAAUUAAAUUCAUUA	chr12:110565159-110565390(+)$1	231	25	51	21.6591
UGCUGGCCAAUCCACUGAAGGUGAGC	chr17:73234632-73234872(-)$1	240	120	146	24.9792
AUGGCUGCCCCAGAGUCUUCAGCUAU	chr21:34925501-34925724(+)$1	223	80	106	25.5074
UCUCUCUUUUCUUUUCCUGGAGCCAG	chr19:59067976-59068199(-)$1	223	16	42	22.5988
UUUUAUGAUUCUUCCAUUGGCGUGAG	chr21:43338888-43339112(-)$1	224	162	188	25.0925
UAGACAGUCCCCUUUUUUUAUUGCUA	chr1:93299070-93299299(+)$1	229	160	186	22.8561
GUCAGCUGUGGAGAGAGAAAAAGUUU	chrX:105905155-105905381(+)$1	226	155	181	22.4781
UUCAGCACAACCCCUCUCUCUGUUGA	chr9:117825976-117826203(-)$1	227	92	118	25.3312
GGCCCGACUUCCUUCCCCUCCCCUGU	chr1:16263790-16264041(+)$1	251	119	145	22.0134

#DB
(((((((.............))))))	chrX:41088409-41088643(+)$1	1	89	115	24.9507
(((((((............)))))))	chr16:46715273-46715500(-)$1	1	141	167	24.9813
.((((.((...........)).))))	chr16:20807584-20807806(-)$1	1	65	91	22.1289
(((.(((.............))).))	chr9:125673689-125673932(-)$1	1	159	185	24.8056
((((.((..............))..)	chr17:76993574-76993812(-)$1	1	55	81	21.0228
((((((.............)).))).	chr5:471878-472128(-)$1	1	196	222	22.5954
...((((............))))..)	chr12:56641859-56642108(-)$1	1	20	46	22.6995
.((((((............)))))))	chr1:147096427-147096647(+)$1	1	149	175	23.1615
(...((((...........)))))))	chr10:32310976-32311241(-)$1	1	142	168	23.2959
(.(((((.............))))).	chr20:43560904-43561129(+)$1	1	169	195	23.5245
..(((((.............))))).	chr16:29822295-29822559(+)$1	1	181	207	23.3239
(.((((((...........)))).))	chr9:131484720-131484943(-)$1	1	177	203	22.1861
((...(((...........)))....	chr1:155290229-155290476(+)$1	1	139	165	24.0786
((((((((...........)))))))	chr3:48731490-48731730(-)$1	1	158	184	24.6732
(((.(((............)))..))	chr3:28304719-28304953(+)$1	1	20	46	24.2584
(((((((.............))))))	chr3:160119688-160119911(+)$1	1	83	109	24.9507
.(((((((...........)))))))	chr12:109536235-109536486(+)$1	1	5	31	23.4174
(((((((.............))))))	chrX:84525564-84525792(+)$1	1	170	196	24.9507
(((((((............)))))))	chr5:94851986-94852213(-)$1	1	73	99	25.1966
(((.(((.............)))..)	chr3:50608410-50608637(+)$1	1	0	26	24.6315
((..((((...........))))..)	chr10:33468947-33469178(-)$1	1	121	147	23.1098
(((((((................)))	chrX:47072081-47072335(+)$1	1	194	220	20.7427
)(((((((...........)))))))	chr6:87965702-87965934(+)$1	1	136	162	23.8079
((..(((.............)))..)	chr9:98209310-98209541(-)$1	1	31	57	24.7851
)(((((((...........)))))))	chr2:31488967-31489190(+)$1	1	94	120	24.4361
(((((((.............))))).	chr12:121766134-121766370(-)$1	1	49	75	23.4207
.(((((((...........)))))))	chrX:47085146-47085365(+)$1	1	99	125	24.5445
((((.((............))..)))	chr11:9602998-9603251(+)$1	1	36	62	24.2242
((((.(((...........)))...)	chr7:6189398-6189632(+)$1	1	15	41	24.0570
(.(.((((...........)))).).	chr6:25600722-25600952(+)$1	1	158	184	23.6482
.(((................)))...	chr5:78746769-78746994(-)$1	1	80	106	22.2292
((((..(.............)..)))	chr20:7967888-7968113(-)$1	1	24	50	24.5573
(.(................).)))))	chr7:112555361-112555588(-)$1	1	14	40	21.4109
((.(((..............))))))	chr6:24706303-24706545(-)$1	1	109	135	22.3108
(((.(((..............))).)	chr12:118463464-118463688(+)$1	1	179	205	22.5987
.(((((((...........)))))))	chr17:40476949-40477168(-)$1	1	168	194	23.7756
.((((((.............))).))	chrX:106882447-106882678(+)$1	1	145	171	24.6895
(((((((............)))))))	chr9:131671158-131671389(+)$1	1	12	38	24.9813
((..(((................)))	chr1:43829935-43830161(-)$1	1	173	199	21.9750
.((((((............))).)))	chr16:2815070-2815306(+)$1	1	156	182	23.8618
(((..(((...........)))..))	chr22:31822998-31823229(+)$1	1	189	215	23.7698
((((................))))).	chr3:128356624-128356858(-)$1	1	55	81	20.9857
(..((((................)))	chr10:112057257-112057483(-)$1	1	99	125	20.9661
((.(.((............))).)))	chr1:155228518-155228744(-)$1	1	123	149	23.4788
(((((((............)))))))	chr1:115282350-115282573(-)$1	1	143	169	24.9813
.((((..............)))))).	chr1:113460252-113460492(-)$1	1	40	66	20.3913
((...((.............))..))	chr14:90429400-90429625(+)$1	1	118	144	23.6794
(((.((((...........)))))))	chr5:174919038-174919283(+)$1	1	8	34	23.3640
(((..(((...........)))))))	chr3:194162047-194162278(-)$1	1	44	70	23.8223
(((((((................)))	chr6:144128113-144128337(+)$1	1	103	129	20.7427
((((((((...........)))))))	chr5:64957797-64958024(+)$1	1	156	182	25.1152
(....((............))....)	chr17:77757671-77757896(+)$1	1	87	113	22.9730
(((((((..............)).))	chr7:30395257-30395497(+)$1	1	142	168	21.1569
(..(((((...........)))))..	chr3:128889271-128889497(-)$1	1	57	83	22.8701
((((((((...........)))))))	chr6:36493282-36493509(-)$1	1	69	95	25.1152
(.((((((...........)))))).	chr4:15646173-15646404(-)$1	1	122	148	22.7494
(((((((.............))))))	chr2:74392353-74392574(-)$1	1	62	88	24.9507
.(.(((((...........))))).)	chr19:42462355-42462580(-)$1	1	23	49	23.1200
(((((((...........))))))).	chr11:75282842-75283075(+)$1	1	18	44	23.5443
(((((((.............)))...	chr2:153515369-153515594(-)$1	1	40	66	23.9861
.((((((...........))))))..	chr12:110565159-110565390(+)$1	1	25	51	21.6591
((((.(((...........))).)))	chr17:73234632-73234872(-)$1	1	120	146	24.9792
(((((((............)))))))	chr21:34925501-34925724(+)$1	1	80	106	25.5074
(((((((...........))))..))	chr19:59067976-59068199(-)$1	1	16	42	22.5988
(((((((.............))))))	chr21:43338888-43339112(-)$1	1	162	188	25.0925
(((.((((...........)))))))	chr1:93299070-93299299(+)$1	1	160	186	22.8561
(((((((..............)).))	chrX:105905155-105905381(+)$1	1	155	181	22.4781
(((((((.............))))))	chr9:117825976-117826203(-)$1	1	92	118	25.3312
((...((...........)).)))))	chr1:16263790-16264041(+)$1	1	119	145	22.0134

#PSSM
g : 0.17	c : 0.14	d : 0.13	[ : 0.10	e : 0.08	= : 0.07	i : 0.05	h : 0.05	$ : 0.02	a : 0.02	f : 0.02	! : 0.01	: : 0.01	G : 0.01	' : 0.01	+ : 0.01	b : 0.01	
g : 0.23	c : 0.15	d : 0.10	e : 0.08	[ : 0.07	= : 0.07	f : 0.05	i : 0.05	h : 0.05	! : 0.04	$ : 0.01	" : 0.01	# : 0.01	a : 0.01	
g : 0.23	c : 0.10	e : 0.10	f : 0.07	! : 0.07	= : 0.07	d : 0.05	" : 0.05	i : 0.05	h : 0.04	[ : 0.04	b : 0.02	a : 0.02	$ : 0.01	# : 0.01	
g : 0.21	[ : 0.10	e : 0.10	d : 0.08	c : 0.07	! : 0.07	= : 0.07	f : 0.05	" : 0.05	i : 0.05	b : 0.02	h : 0.02	y : 0.01	a : 0.01	# : 0.01	
g : 0.20	d : 0.15	c : 0.14	[ : 0.07	e : 0.07	f : 0.05	= : 0.05	" : 0.04	i : 0.04	y : 0.04	! : 0.04	h : 0.02	b : 0.01	# : 0.01	
c : 0.21	g : 0.18	b : 0.13	d : 0.13	e : 0.07	= : 0.05	f : 0.04	i : 0.04	y : 0.04	h : 0.02	[ : 0.01	! : 0.01	w : 0.01	
c : 0.20	g : 0.18	b : 0.13	d : 0.13	e : 0.07	= : 0.05	f : 0.04	i : 0.04	y : 0.04	h : 0.02	w : 0.02	v : 0.01	a : 0.01	
v : 0.24	u : 0.17	y : 0.10	w : 0.08	d : 0.08	c : 0.07	g : 0.07	t : 0.05	= : 0.02	e : 0.02	b : 0.01	i : 0.01	f : 0.01	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.39	v : 0.24	u : 0.17	y : 0.10	w : 0.08	
t : 0.33	v : 0.24	u : 0.17	y : 0.10	w : 0.08	g : 0.01	f : 0.01	d : 0.01	b : 0.01	
v : 0.23	g : 0.13	d : 0.13	c : 0.10	b : 0.08	y : 0.08	w : 0.07	f : 0.04	= : 0.04	i : 0.02	e : 0.02	a : 0.01	
c : 0.20	g : 0.18	d : 0.13	b : 0.08	e : 0.08	w : 0.05	y : 0.05	= : 0.05	f : 0.04	i : 0.04	] : 0.02	a : 0.01	
c : 0.21	g : 0.20	d : 0.13	e : 0.10	b : 0.05	y : 0.05	= : 0.05	f : 0.04	i : 0.04	] : 0.02	2 : 0.02	a : 0.01	4 : 0.01	
g : 0.20	d : 0.13	c : 0.13	e : 0.10	2 : 0.08	f : 0.05	y : 0.05	= : 0.05	b : 0.04	i : 0.04	] : 0.04	4 : 0.02	3 : 0.01	
g : 0.21	2 : 0.13	e : 0.13	] : 0.08	c : 0.08	= : 0.07	f : 0.05	i : 0.05	4 : 0.04	h : 0.04	d : 0.02	3 : 0.02	b : 0.01	
g : 0.24	c : 0.11	e : 0.11	2 : 0.08	= : 0.07	f : 0.05	i : 0.05	d : 0.04	4 : 0.04	h : 0.04	3 : 0.04	b : 0.02	] : 0.02	a : 0.01	
g : 0.23	c : 0.13	] : 0.11	= : 0.08	d : 0.07	i : 0.05	e : 0.05	h : 0.05	b : 0.04	f : 0.04	2 : 0.02	4 : 0.02	3 : 0.02	a : 0.01	

#score	1618.2812430653348
#seq	69
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m2_run1.txt

#BEAR
ggggggg!!eeeeerrrrrrrrreeeee22ggggggg]cc	chr1:8073523-8073747(-)$1	224	140	180	11.1405
##dddd[eeeee[a[cccnnnnnccc]a]eeeee22dddd	chr3:52696063-52696306(-)$1	243	134	174	13.2085
ggggg[a!!bb[ffffffnnnnnffffff]bb22a]gggg	chr10:49628116-49628350(+)$1	234	128	168	13.2013
cc:============cccnnnnnccc]============F	chr4:78080482-78080708(+)$1	226	77	117	15.2249
eeeee####bb"""ddddnnnnndddd22bb22eeeee::	chr19:2271784-2272004(+)$1	220	76	116	12.6340
e!!bb"""dddd[cccoooooocccddddbb22eeeee]d	chr5:98115383-98115613(+)$1	230	9	49	13.1265
iiiiiiiiibb[a[cccooooooccc]a]bb]iiiiiiii	chr3:113508550-113508773(+)$1	223	14	54	16.7067
eeccc"""ccc[cccooooooccc]cccccc]eeeee]bb	chr4:1695263-1695494(-)$1	231	180	220	12.4646
eeee####ccc[gggggggoooooogggggggccc22eee	chr1:150550714-150550978(-)$1	264	31	71	13.9276
#dddd"""a[eeeee[cccooooooccc]eeeeea]dddd	chr18:657974-658194(-)$1	220	154	194	13.2928
[a[bb"""ccc[a!!cccnnnnnccc]a]ccc]bb]a]cc	chr6:26158672-26158924(+)$1	252	27	67	16.9345
cc[eeeee[bb"""cccooooooccc]bb]eeeee22ccc	chr6:107955530-107955768(+)$1	238	65	105	14.0756
[bb[ccc[eeeee[ddddoooooodddd]eeeee333ccc	chr19:58906002-58906242(+)$1	240	17	57	13.7124
gggggg$$$$$bb!!cccooooooccc22bb22ggggggg	chr21:28304247-28304498(-)$1	251	95	135	15.7208
ffff$$$$$eeeee[bboooooobbeeeee333ffffff]	chr6:32943095-32943323(+)$1	228	36	76	13.1228
====$$$$$eeeee[cccnnnnnccc]eeeee========	chr5:145561950-145562192(-)$1	242	104	144	14.9106
!ccc[ddddagggggggooooooggggggg]a]dddd]cc	chr2:220435376-220435611(-)$1	235	18	58	13.2420
=============[ddddoooooodddd]===========	chrX:47087869-47088100(+)$1	231	20	60	16.8158
hhhhh[ccca[ccc!!cccmmmmccc333ccc22a]ccc2	chrX:153627769-153628003(+)$1	234	141	181	12.6071
eedddd####ccc!!ddddmmmmdddd22ccc4444dddd	chr9:4662779-4663018(+)$1	239	172	212	12.1370
iiiiiiiiccc[ffffffmmmmffffff333ccc22iiii	chr1:245019949-245020211(-)$1	262	207	247	11.7308
!a!!ffffff"""ddddnnnnndddd333ffffff]a22a	chr1:36074871-36075102(-)$1	231	113	153	12.3686
dddd[ccc!!bb"""cccnnnnnccc]bb22ccc]dddd]	chr5:472916-473139(-)$1	223	8	48	13.2162
iiiiii!!ccc####bboooooobb22ccc22iiiiiiii	chr1:245027044-245027310(-)$1	266	43	83	16.1616
ggggggggffffff[bboooooobb]ffffff]ggggggg	chr12:12873977-12874226(+)$1	249	7	47	13.3653
ffffff"""cccddddoooooodddd]ccc333ffffff3	chr9:113018594-113018855(-)$1	261	49	89	13.9505
=======ccc[accca[bbnnnnnbb]a]ccc]a]ccc]=	chr9:136234142-136234381(-)$1	239	146	186	13.3684
[a[eeeee!!ccc!!ddddllldddd]ccc]eeeeea]cc	chr11:77348598-77348823(-)$1	225	183	223	12.4484
ddd[ccc[ccc!!eeeeennnnneeeee22ccc333ccc]	chr11:15197277-15197500(+)$1	223	30	70	13.7407
c!!============cccnnnnnccc]============2	chr4:78080503-78080724(+)$1	221	56	96	16.8158
fff!!cccccc"""cccooooooccc333ccc]ccc>>>>	chr8:125498079-125498330(+)$1	251	90	130	15.6514
===####dddd[ccccccooooooccc4444ccc]dddd=	chr2:74386150-74386407(-)$1	257	192	232	15.1651
a!!gggggggbb[eeeeennnnneeeee]bb22ggggggg	chr4:141589997-141590220(-)$1	223	129	169	13.3020
""ccc"""ccc!!fffffflllffffffccc333cccfff	chr7:128657923-128658159(-)$1	236	189	229	13.0754
$$$$ccc####gggggggnnnnnggggggg333ccceeee	chr15:78305498-78305725(-)$1	227	120	160	13.7310
eee[ddddbb[ccc!!aaooooooa]a22ccc]bb]dddd	chr1:179077597-179077817(-)$1	220	8	48	13.4462
ffff[ccc!!bb"""cccnnnnnccc333bb22ccc22ff	chr14:21820799-21821057(-)$1	258	70	110	14.7411
[eeeee[ffffff!!cccooooooccc22ffffff]eeee	chr7:26236330-26236595(-)$1	265	158	198	14.2301
ggggg"""gggggggddddllldddd]ggggggggggggg	chr4:77969606-77969840(-)$1	234	16	56	13.9009
eee[bb!!ccc!!eeeeennnnneeeee4444ccc]bb]e	chr21:27283997-27284224(-)$1	227	75	115	13.5275
iiiiiiiii!!ccc!!bbnnnnnbb22ccciiiiiiiii]	chr21:34924431-34924658(+)$1	227	102	142	14.2814
::::===========cccooooooccc333==========	chr12:95650871-95651097(+)$1	226	185	225	13.5488
ggggggg!!eeeee[bboooooobb]eeeee]ggggggg:	chr1:78193991-78194217(-)$1	226	26	66	13.2052
fa!!bb!!ccc[bb[aooooooa]bb22ccc22bb22a]f	chr5:52397923-52398147(-)$1	224	29	69	13.6499
d[eeeee####ccc[cccnnnnnccc]ccc333eeeee]d	chr16:2817675-2817934(+)$1	259	119	159	15.3717
:dddd[eeeee"""ccc[aooooooa]ccc4444eeeeed	chr14:103986153-103986395(-)$1	242	146	186	12.9430
d!!a[ffffff"""ddddoooooodddd]ffffff]a22d	chr15:73925398-73925688(-)$1	290	146	186	13.5174
ggggg[bbccc[a!!bboooooobb22a22ccc]bb22gg	chr22:38881915-38882167(-)$1	252	19	59	13.9480
iiiii"""iiiiiiiii[aooooooa]iiiiiiiiiiiii	chr20:34240850-34241076(-)$1	226	115	155	16.1993
eeeee"""bb!!ddddoooooodddd4444bb4444eeee	chr11:9606729-9606976(+)$1	247	103	143	13.6431
"cccccc####bb[ddddooooooddddbb22ccc]ccc3	chr7:30639486-30639716(+)$1	230	64	104	14.1996
[dddd[a[ccc!!bb[ddddoooooodddd333bb22ccc	chr5:140085168-140085425(+)$1	257	108	148	11.7410

#otherMatches

#Seq PSSM
GCUUUGCCCCUGAUCCCAAGUAUGUCAGCAGCAAAGCACU	chr1:8073523-8073747(-)$1	224	140	180	11.1405
AAUCAGGGCACAGUGACUGAAGGAGUAAGUGUGUAGCUGG	chr3:52696063-52696306(-)$1	243	134	174	13.2085
GAUUCUUGACUUCGGUCUGGCCAGGACUGCAGGAACGAGU	chr10:49628116-49628350(+)$1	234	128	168	13.2013
UUGAAGAUUUAAGGAGUUUAGCCAACUUUUUUGGAUCUUG	chr4:78080482-78080708(+)$1	226	77	117	15.2249
CGCCAAACGCAUUAACUGGCGAACAGUGCUGAGUGGCGGC	chr19:2271784-2272004(+)$1	220	76	116	12.6340
CAAGGCCUUGCGUGCCUAUGCUGGCUGCACCCAGCGAACU	chr5:98115383-98115613(+)$1	230	9	49	13.1265
UAUUUUACCUCUAGCUCACAAUGGAGGUUGAUGGUAAGGU	chr3:113508550-113508773(+)$1	223	14	54	16.7067
GGCGGCCAGGAAGAGAAACAGCUCCUCCCCGACUAGGUGG	chr4:1695263-1695494(-)$1	231	180	220	12.4646
AUCAAAAACGAAGACGAUGUGAAAUCGUUGUCUCGAGUGA	chr1:150550714-150550978(-)$1	264	31	71	13.9276
CGGGGUCCGCAGCGCCCGGCAGCUCCCGAGCGCUCUCCCC	chr18:657974-658194(-)$1	220	154	194	13.2928
GCUGCUUCCGGGGGAGCUGGCCAAGCACGCCGUGUCGGAG	chr6:26158672-26158924(+)$1	252	27	67	16.9345
GCUGGUGCCGCCCCCGACCCUGCUCGUGCCGUACCCCGUG	chr6:107955530-107955768(+)$1	238	65	105	14.0756
AGAAUUCAGAGCUGUGUGUCUCCUUGCAGGGCUCCUCGAA	chr19:58906002-58906242(+)$1	240	17	57	13.7124
GCAGGUGUCCUGCCAGCGGAUGUGUGCAAGCUGACCUGCA	chr21:28304247-28304498(-)$1	251	95	135	15.7208
UGGUUCUGACCUAACAUUUUUUUAUUUAGGAUUAUCACAA	chr6:32943095-32943323(+)$1	228	36	76	13.1228
UCGUGGAUUUGCACAGUCGGCUGGGCGGUGCAAUGGCGGU	chr5:145561950-145562192(-)$1	242	104	144	14.9106
CGGGGUCCGGGGAGGGCGCCCCGGUCUUCCUCACGGGGCC	chr2:220435376-220435611(-)$1	235	18	58	13.2420
cccauggggucauaugggGCUGGUCCUAGAUGACCUCAUG	chrX:47087869-47088100(+)$1	231	20	60	16.8158
GAAUAUGAGCAGCUGUCCUCUGAAGGUAAGGCAGGAUUCU	chrX:153627769-153628003(+)$1	234	141	181	12.6071
GCCCACAACCAGAUGGACAUGUUUGUCACUCUCUCGGUGG	chr9:4662779-4663018(+)$1	239	172	212	12.1370
AAUAUUAACUGAUAAUUUAGAUAGAUUGGUGUAGAAUUAA	chr1:245019949-245020211(-)$1	262	207	247	11.7308
CCUCCUGGCUGGCUAUGAUGAGCAUGAAGGGCCAGCGCUG	chr1:36074871-36075102(-)$1	231	113	153	12.3686
CCUCGUGCCACGCACCGCCGCACGCGCUGGAGCAGGAGGA	chr5:472916-473139(-)$1	223	8	48	13.2162
GCGGCCGACUCGGGCCCGAUGGAGGAGGAGGAGGCCGCCU	chr1:245027044-245027310(-)$1	266	43	83	16.1616
UCCUUGUUUAUCAGAUACAUCACUGCUUGAUGAAGCAAGG	chr12:12873977-12874226(+)$1	249	7	47	13.3653
AGAGCAAGCAGCGAGUCUUGAAGCUCUGUUUGGUGCUUUG	chr9:113018594-113018855(-)$1	261	49	89	13.9505
GUUCCAGUGGAGCGAGCAGCGCGACUACAUCGACACCACC	chr9:136234142-136234381(-)$1	239	146	186	13.3684
UGAGAGGUAGGGUUCCUGGUCCCCAGCGCUGGCCUCCUGC	chr11:77348598-77348823(-)$1	225	183	223	12.4484
CUCAGUCCAGCGCUGGAUGGAAGAUCUGAAGCUCAUGACC	chr11:15197277-15197500(+)$1	223	30	70	13.7407
UUGAAGAUUUAAGGAGUUUAGCCAACUUUUUUGGAUCUUG	chr4:78080503-78080724(+)$1	221	56	96	16.8158
UUGGUGAAUUAUUAUGCUUCUUUGCACAUUGACUUCUAUG	chr8:125498079-125498330(+)$1	251	90	130	15.6514
AAGUUGAUCCAUGUUGAUUUCUGUGUCCUGUGACUUGGAC	chr2:74386150-74386407(-)$1	257	192	232	15.1651
AGCUCUGGCUGCUGCUGUCAGGUACGGCCGCUGGGCUGGG	chr4:141589997-141590220(-)$1	223	129	169	13.3020
UUUGGAUUUAUCAGGAUUGUUUUAAUUCGUAUUGCUAGGC	chr7:128657923-128658159(-)$1	236	189	229	13.0754
AUUGGUUGCCAAGGUCCGCGCGUUGGAUCUGAAGACUCUC	chr15:78305498-78305725(-)$1	227	120	160	13.7310
CCCUCUGGGGAUCUAGCCAUUACAGAGAAGGACCCUCCAG	chr1:179077597-179077817(-)$1	220	8	48	13.4462
UUCUAUUUAGCGGACCGAGAAAGUCGUUACGAGGAAGAAG	chr14:21820799-21821057(-)$1	258	70	110	14.7411
UAAAAUCGUAUGUAAGUGUCUAACCACAAAUGUACUGUUU	chr7:26236330-26236595(-)$1	265	158	198	14.2301
CUGGCCCAGAUGGAUAGCUCCCAGUUGAUCCAUUGUCGGG	chr4:77969606-77969840(-)$1	234	16	56	13.9009
GAGCUCCUUCCCGUGAAUGGAGAGUUCAGCCUGGACGAUC	chr21:27283997-27284224(-)$1	227	75	115	13.5275
GAUGAUGUCCUAUGCUGCAGAACGUUCCAUGAUGUCAUCU	chr21:34924431-34924658(+)$1	227	102	142	14.2814
UUAUUAGUGAAAUAAUUGGUGAAUCAGAAUUUGUUUUGCU	chr12:95650871-95651097(+)$1	226	185	225	13.5488
UUCUGAAGAUAAUAAUGAAACAACAAUGUUAAUUCAGGAU	chr1:78193991-78194217(-)$1	226	26	66	13.2052
UAUAAGUUGUUGAGUGUUUUACCCCUAGGACUUCUGUUAA	chr5:52397923-52398147(-)$1	224	29	69	13.6499
ACGGGCUCCCUCCCCUUCCUCUAGAAUGGGCCAGGCUCCU	chr16:2817675-2817934(+)$1	259	119	159	15.3717
GCUGGAGCAGGGCCAGGCCAUCGACGACCUCAUGCCUGCC	chr14:103986153-103986395(-)$1	242	146	186	12.9430
GCUGCCCAGCGCCCUGGCCCUCUCGCUGUUGCUGGUCUCU	chr15:73925398-73925688(-)$1	290	146	186	13.5174
GAGCUAGUAGCACCACCUCAACUGGGAGAAGUUCACAGAG	chr22:38881915-38882167(-)$1	252	19	59	13.9480
UUGCCUGGUCUAGGACUGGAUGUUCCGGGUUUUGGAGGUG	chr20:34240850-34241076(-)$1	226	115	155	16.1993
CCCAAAUGCUGCCUCUGAAGAAGGAGACGAAGAUGAUUGG	chr11:9606729-9606976(+)$1	247	103	143	13.6431
AAUCUCUAACAGGAGCUGGCGUUACAGCCCAAAGAUGAUA	chr7:30639486-30639716(+)$1	230	64	104	14.1996
AGGACGAUGAGAUGGCAGCUGUGAUGGGCUUCUCUGGCUU	chr5:140085168-140085425(+)$1	257	108	148	11.7410

#DB
(((((((..(((((.........)))))..))))))).))	chr1:8073523-8073747(-)$1	1	140	180	11.1405
..((((.(((((.(.(((.....))).).)))))..))))	chr3:52696063-52696306(-)$1	1	134	174	13.2085
(((((.(..((.((((((.....)))))).))..).))))	chr10:49628116-49628350(+)$1	1	128	168	13.2013
)).(((((((((((((((.....))).))))))))))))(	chr4:78080482-78080708(+)$1	1	77	117	15.2249
(((((....((...((((.....))))..))..)))))..	chr19:2271784-2272004(+)$1	1	76	116	12.6340
(..((...((((.(((......)))))))))..))))).)	chr5:98115383-98115613(+)$1	1	9	49	13.1265
(((((((((((.(.(((......))).).)).))))))))	chr3:113508550-113508773(+)$1	1	14	54	16.7067
(((((...(((.(((......))).)))))).))))).))	chr4:1695263-1695494(-)$1	1	180	220	12.4646
((((....(((.(((((((......))))))))))..)))	chr1:150550714-150550978(-)$1	1	31	71	13.9276
.((((...(.(((((.(((......))).)))))).))))	chr18:657974-658194(-)$1	1	154	194	13.2928
.(.((...(((.(..(((.....))).).))).)).).))	chr6:26158672-26158924(+)$1	1	27	67	16.9345
((.(((((.((...(((......))).)).)))))..)))	chr6:107955530-107955768(+)$1	1	65	105	14.0756
.((.(((.(((((.((((......)))).)))))...)))	chr19:58906002-58906242(+)$1	1	17	57	13.7124
((((((.....((..(((......)))..))..)))))))	chr21:28304247-28304498(-)$1	1	95	135	15.7208
((((.....(((((.((......)))))))...)))))).	chr6:32943095-32943323(+)$1	1	36	76	13.1228
((((.....(((((.(((.....))).)))))))))))))	chr5:145561950-145562192(-)$1	1	104	144	14.9106
.(((.((((((((((((......))))))).).)))).))	chr2:220435376-220435611(-)$1	1	18	58	13.2420
(((((((((((((.((((......)))).)))))))))))	chrX:47087869-47088100(+)$1	1	20	60	16.8158
(((((.((((.(((..(((....)))...)))..).))).	chrX:153627769-153628003(+)$1	1	141	181	12.6071
))((((....(((..((((....))))..)))....))))	chr9:4662779-4663018(+)$1	1	172	212	12.1370
(((((((((((.((((((....))))))...)))..))))	chr1:245019949-245020211(-)$1	1	207	247	11.7308
.(..((((((...((((.....))))...)))))).)..)	chr1:36074871-36075102(-)$1	1	113	153	12.3686
((((.(((..((...(((.....))).))..))).)))).	chr5:472916-473139(-)$1	1	8	48	13.2162
((((((..(((....((......))..)))..))))))))	chr1:245027044-245027310(-)$1	1	43	83	16.1616
((((((((((((((.((......)).)))))).)))))))	chr12:12873977-12874226(+)$1	1	7	47	13.3653
((((((...(((((((......)))).)))...)))))).	chr9:113018594-113018855(-)$1	1	49	89	13.9505
((((((((((.(((((.((.....)).).))).).))).)	chr9:136234142-136234381(-)$1	1	146	186	13.3684
.(.(((((..(((..((((...)))).))).)))))).))	chr11:77348598-77348823(-)$1	1	183	223	12.4484
(((.(((.(((..(((((.....)))))..)))...))).	chr11:15197277-15197500(+)$1	1	30	70	13.7407
(..(((((((((((((((.....))).)))))))))))).	chr4:78080503-78080724(+)$1	1	56	96	16.8158
(((..((((((...(((......)))...))).)))....	chr8:125498079-125498330(+)$1	1	90	130	15.6514
(((....((((.((((((......)))....))).)))))	chr2:74386150-74386407(-)$1	1	192	232	15.1651
(..(((((((((.(((((.....))))).))..)))))))	chr4:141589997-141590220(-)$1	1	129	169	13.3020
..(((...(((..((((((...)))))))))...))))))	chr7:128657923-128658159(-)$1	1	189	229	13.0754
....(((....(((((((.....)))))))...)))))))	chr15:78305498-78305725(-)$1	1	120	160	13.7310
(((.((((((.(((..((......).)..))).)).))))	chr1:179077597-179077817(-)$1	1	8	48	13.4462
((((.(((..((...(((.....)))...))..)))..))	chr14:21820799-21821057(-)$1	1	70	110	14.7411
.(((((.((((((..(((......)))..)))))).))))	chr7:26236330-26236595(-)$1	1	158	198	14.2301
(((((...(((((((((((...)))).)))))))))))))	chr4:77969606-77969840(-)$1	1	16	56	13.9009
(((.((..(((..(((((.....)))))....))).)).)	chr21:27283997-27284224(-)$1	1	75	115	13.5275
(((((((((..(((..((.....))..)))))))))))).	chr21:34924431-34924658(+)$1	1	102	142	14.2814
....((((((((((((((......)))...))))))))))	chr12:95650871-95651097(+)$1	1	185	225	13.5488
(((((((..(((((.((......)).))))).))))))).	chr1:78193991-78194217(-)$1	1	26	66	13.2052
((..((..(((.((.(......).))..)))..))..).)	chr5:52397923-52398147(-)$1	1	29	69	13.6499
(.(((((....(((.(((.....))).)))...))))).)	chr16:2817675-2817934(+)$1	1	119	159	15.3717
.((((.(((((...(((.(......).)))....))))))	chr14:103986153-103986395(-)$1	1	146	186	12.9430
(..(.((((((...((((......)))).)))))).)..)	chr15:73925398-73925688(-)$1	1	146	186	13.5174
(((((.(((((.(..((......))..)..))).))..))	chr22:38881915-38882167(-)$1	1	19	59	13.9480
(((((...(((((((((.(......).)))))))))))))	chr20:34240850-34241076(-)$1	1	115	155	16.1993
(((((...((..((((......))))....))....))))	chr11:9606729-9606976(+)$1	1	103	143	13.6431
.((((((....((.((((......))))))..))).))).	chr7:30639486-30639716(+)$1	1	64	104	14.1996
.((((.(.(((..((.((((......))))...))..)))	chr5:140085168-140085425(+)$1	1	108	148	11.7410

#PSSM
e : 0.15	g : 0.13	i : 0.09	[ : 0.09	f : 0.09	= : 0.07	d : 0.07	c : 0.05	# : 0.03	! : 0.03	" : 0.03	: : 0.03	h : 0.01	a : 0.01	$ : 0.01	
e : 0.15	g : 0.13	i : 0.09	d : 0.09	c : 0.07	! : 0.07	a : 0.07	f : 0.07	= : 0.07	# : 0.01	b : 0.01	h : 0.01	" : 0.01	$ : 0.01	: : 0.01	[ : 0.01	
g : 0.13	d : 0.13	e : 0.13	! : 0.11	i : 0.09	c : 0.07	f : 0.07	= : 0.07	[ : 0.05	: : 0.03	b : 0.01	h : 0.01	$ : 0.01	
g : 0.15	e : 0.13	d : 0.11	= : 0.09	i : 0.09	c : 0.07	[ : 0.07	f : 0.05	! : 0.05	b : 0.03	h : 0.01	# : 0.01	$ : 0.01	: : 0.01	a : 0.01	
g : 0.15	d : 0.11	e : 0.11	c : 0.11	= : 0.09	i : 0.09	b : 0.07	[ : 0.07	# : 0.03	$ : 0.03	f : 0.03	h : 0.01	! : 0.01	
" : 0.15	c : 0.13	g : 0.09	[ : 0.09	= : 0.09	d : 0.07	i : 0.07	e : 0.07	# : 0.05	f : 0.05	$ : 0.03	b : 0.03	
" : 0.17	c : 0.15	= : 0.09	g : 0.07	# : 0.07	e : 0.07	i : 0.05	$ : 0.05	! : 0.05	[ : 0.03	a : 0.03	d : 0.03	f : 0.03	b : 0.01	
" : 0.17	! : 0.11	# : 0.11	c : 0.09	e : 0.07	= : 0.07	i : 0.05	[ : 0.05	$ : 0.05	d : 0.05	f : 0.05	g : 0.03	b : 0.01	
c : 0.26	! : 0.11	# : 0.09	= : 0.07	f : 0.07	e : 0.05	d : 0.05	i : 0.05	$ : 0.05	g : 0.03	b : 0.03	a : 0.01	[ : 0.01	" : 0.01	
c : 0.26	e : 0.13	b : 0.11	= : 0.07	# : 0.07	f : 0.07	! : 0.07	d : 0.03	a : 0.03	g : 0.03	[ : 0.01	$ : 0.01	i : 0.01	
c : 0.28	e : 0.15	b : 0.13	= : 0.07	[ : 0.05	f : 0.05	# : 0.05	d : 0.03	g : 0.03	! : 0.03	$ : 0.01	" : 0.01	i : 0.01	
[ : 0.17	e : 0.13	c : 0.13	" : 0.11	b : 0.09	! : 0.09	= : 0.07	g : 0.05	f : 0.03	d : 0.01	# : 0.01	a : 0.01	i : 0.01	
c : 0.17	" : 0.15	e : 0.11	f : 0.07	= : 0.07	g : 0.07	! : 0.07	[ : 0.05	a : 0.05	b : 0.05	d : 0.03	# : 0.01	i : 0.01	
e : 0.15	c : 0.15	" : 0.13	! : 0.11	f : 0.07	[ : 0.07	g : 0.07	= : 0.05	d : 0.05	b : 0.03	a : 0.01	# : 0.01	i : 0.01	
! : 0.17	d : 0.15	c : 0.15	[ : 0.13	g : 0.07	e : 0.07	f : 0.05	= : 0.05	" : 0.03	r : 0.01	# : 0.01	i : 0.01	b : 0.01	
c : 0.32	d : 0.21	b : 0.09	f : 0.05	g : 0.05	! : 0.05	e : 0.05	[ : 0.03	a : 0.03	r : 0.01	o : 0.01	i : 0.01	
c : 0.34	d : 0.19	b : 0.11	o : 0.09	f : 0.05	g : 0.05	e : 0.05	r : 0.01	[ : 0.01	a : 0.01	i : 0.01	
c : 0.26	o : 0.26	d : 0.17	f : 0.05	e : 0.05	g : 0.03	b : 0.03	[ : 0.03	r : 0.01	n : 0.01	a : 0.01	
o : 0.44	n : 0.30	d : 0.07	c : 0.03	a : 0.03	r : 0.01	g : 0.01	m : 0.01	b : 0.01	f : 0.01	
o : 0.51	n : 0.32	m : 0.05	l : 0.05	r : 0.01	d : 0.01	
o : 0.53	n : 0.32	m : 0.05	l : 0.05	r : 0.01	
o : 0.51	n : 0.32	m : 0.05	l : 0.05	r : 0.01	c : 0.01	
o : 0.44	n : 0.30	d : 0.09	c : 0.03	m : 0.03	f : 0.03	r : 0.01	a : 0.01	
c : 0.26	o : 0.26	d : 0.13	b : 0.11	e : 0.07	f : 0.05	g : 0.03	n : 0.01	] : 0.01	
c : 0.32	d : 0.21	b : 0.15	o : 0.09	e : 0.07	f : 0.05	g : 0.03	] : 0.01	a : 0.01	
c : 0.34	d : 0.23	e : 0.09	f : 0.05	g : 0.05	2 : 0.05	] : 0.05	b : 0.03	a : 0.03	o : 0.01	
] : 0.28	d : 0.15	e : 0.11	c : 0.11	f : 0.07	3 : 0.07	2 : 0.07	g : 0.05	a : 0.01	4 : 0.01	
c : 0.15	e : 0.13	2 : 0.11	d : 0.11	a : 0.09	3 : 0.09	f : 0.07	g : 0.07	= : 0.03	b : 0.03	4 : 0.03	i : 0.01	
] : 0.17	c : 0.17	2 : 0.15	3 : 0.11	g : 0.07	b : 0.05	e : 0.05	4 : 0.05	f : 0.03	= : 0.03	d : 0.03	i : 0.01	
c : 0.28	b : 0.13	e : 0.11	2 : 0.07	g : 0.07	f : 0.07	= : 0.05	4 : 0.05	] : 0.03	3 : 0.03	i : 0.01	d : 0.01	
c : 0.21	b : 0.15	e : 0.11	3 : 0.11	= : 0.07	f : 0.07	g : 0.05	2 : 0.05	4 : 0.05	] : 0.03	i : 0.03	
c : 0.21	2 : 0.15	e : 0.11	3 : 0.11	= : 0.07	f : 0.07	g : 0.05	] : 0.05	b : 0.03	4 : 0.03	i : 0.03	a : 0.01	
2 : 0.15	c : 0.15	e : 0.11	] : 0.11	3 : 0.11	= : 0.09	i : 0.07	g : 0.05	4 : 0.05	f : 0.05	
e : 0.17	c : 0.17	g : 0.11	= : 0.09	f : 0.09	i : 0.07	b : 0.07	4 : 0.05	2 : 0.03	3 : 0.03	d : 0.01	a : 0.01	] : 0.01	
e : 0.13	c : 0.13	g : 0.11	= : 0.09	b : 0.09	f : 0.09	i : 0.07	a : 0.05	] : 0.05	2 : 0.03	3 : 0.03	4 : 0.03	d : 0.01	
] : 0.19	g : 0.11	2 : 0.11	e : 0.11	= : 0.09	c : 0.09	i : 0.07	d : 0.05	3 : 0.03	f : 0.03	4 : 0.03	b : 0.01	
e : 0.15	g : 0.13	d : 0.13	2 : 0.11	= : 0.09	i : 0.09	c : 0.09	a : 0.07	f : 0.03	3 : 0.01	> : 0.01	b : 0.01	
e : 0.15	c : 0.13	d : 0.11	g : 0.11	] : 0.09	= : 0.09	i : 0.09	2 : 0.07	f : 0.05	> : 0.01	b : 0.01	a : 0.01	
c : 0.19	g : 0.13	d : 0.11	= : 0.09	] : 0.09	i : 0.09	e : 0.09	f : 0.07	2 : 0.03	: : 0.01	b : 0.01	> : 0.01	
d : 0.15	c : 0.13	g : 0.11	e : 0.09	= : 0.09	i : 0.07	] : 0.07	f : 0.05	: : 0.03	2 : 0.03	3 : 0.03	F : 0.01	b : 0.01	a : 0.01	> : 0.01	

#score	722.3940108256054
#seq	52
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_CDS_m2_run1.txt

#BEAR
d[ccc[cccoooooocccccc22d	chr10:28824485-28824767(+)$1	282	102	126	13.3728
ceeeeecccooooooccc]eeeee	chr5:154187959-154188344(+)$1	385	137	161	13.9647
d[ccc[cccooooooccc]ccc]d	chr8:27462402-27462667(+)$1	265	114	138	14.0986
feeeeecccooooooccc333eee	chr12:86268096-86268382(+)$1	286	146	170	14.6700
dddbb[cccoooooocccbb]ddd	chr15:58001234-58001569(+)$1	335	38	62	12.3912
d$$$$$cccooooooccc4444dd	chr2:109389316-109389633(+)$1	317	62	86	13.8698
#eeeee[bboooooobb]eeeee4	chr12:69653149-69653484(+)$1	335	134	158	13.0203
ddbb!!cccooooooccc22bb::	chr11:62649353-62649700(+)$1	347	87	111	11.3513
%%%%%%cccooooooccc333fff	chr12:32875449-32875752(+)$1	303	87	111	11.3843
ddd"""cccooooooccc4444dd	chrX:16850670-16851001(+)$1	331	119	143	14.6855
[cccbbcccooooooccc]bb444	chrX:96684577-96684903(+)$1	326	105	129	13.0805
eeeee!!bboooooobb22eeeee	chr16:18888318-18888604(+)$1	286	201	225	12.9798
ffffff[bboooooobb]ffffff	chr22:42024095-42024369(+)$1	274	150	174	11.5769
!!ccc[cccooooooccc]ccc99	chr4:2886242-2886510(+)$1	268	73	97	13.0627
ffffffcccoooooocccccc[ee	chr12:69202920-69203232(+)$1	312	121	145	12.8077
"eeeeecccooooooccc22eeee	chr1:40535793-40536063(+)$1	270	14	38	14.2587
[dddd[cccoooooocccddddcc	chr1:200819197-200819504(+)$1	307	245	269	13.1984
eeeee[cccooooooccc]eeeee	chrX:135581780-135582040(+)$1	260	178	202	14.1966
ffccc[cccooooooccc22ccc]	chr9:131755412-131755721(+)$1	309	228	252	13.9008
fffff[cccooooooccc]fffff	chr6:144128137-144128460(+)$1	323	168	192	13.2395
ddd!!ddddoooooodddd22ddd	chr10:64948795-64949095(+)$1	300	105	129	12.5953
eeeccc[bboooooobb]ccc]ee	chr21:45739894-45740180(+)$1	286	21	45	12.5375
=========oooooo=========	chr1:97243348-97243667(+)$1	319	196	220	13.3313
##gggggggooooooggggggg44	chr1:214794017-214794368(+)$1	351	276	300	12.5853
[eeeee[bboooooobb333eeee	chr12:25362009-25362321(+)$1	312	58	82	13.7793
iiiiiiiiiooooooiiiiiiiii	chrX:153689419-153689783(+)$1	364	235	259	12.4508
==####cccooooooccc333===	chr9:131456098-131456471(+)$1	373	72	96	15.1689
%bb!!ddddoooooodddd]bb44	chr10:105331331-105331629(+)$1	298	147	171	11.6210
[eeeee[bboooooobb]eeeeeb	chr19:39217567-39217902(+)$1	335	84	108	12.7280
dd"""ddddoooooodddd]dddd	chr19:39212146-39212473(+)$1	327	289	313	12.5264
dddaddddoooooodddd333a]d	chr20:31434398-31434672(+)$1	274	167	191	11.7726
bbaffffffooooooffffff444	chr2:74592561-74592825(+)$1	264	133	157	11.0743
fff"""cccooooooccc4444ff	chr10:70532707-70533048(+)$1	341	139	163	14.3978
:ccc[ddddoooooodddd]cccc	chr2:231740267-231740587(+)$1	320	181	205	11.7132
dddd[ddddoooooodddd22ddd	chr2:47707846-47708167(+)$1	321	131	155	12.3344
ffff!!cccooooooccc]fffff	chr7:134613501-134613836(+)$1	335	142	166	13.5236
eeeee!!bboooooobbeeeee]b	chr16:89703616-89704109(+)$1	493	321	345	12.6573
eeeee!!bboooooobb22eeeee	chr22:46733686-46733957(+)$1	271	24	48	12.9798
!ccc[ddddoooooodddd]ccc2	chrX:47775320-47775655(+)$1	335	30	54	12.5952
d:eeeeebboooooobb]eeeeeb	chr8:64099771-64100088(+)$1	317	130	154	11.3153
fffffddddoooooodddd4444f	chr5:56526894-56527231(+)$1	337	252	276	12.5992
d!!ffffffooooooffffff444	chr7:35923458-35923731(+)$1	273	9	33	11.7507
c"""ddddoooooodddd333ccc	chr13:113873210-113873460(+)$1	250	143	167	11.9277
==="""cccooooooccc333===	chr7:158448851-158449113(+)$1	262	148	172	15.3051
##dddd[aooooooa]dddd4444	chr15:72499406-72499668(+)$1	262	14	38	11.5842
g$$$$$cccooooooccc22gggg	chr1:227946944-227947318(+)$1	374	134	158	13.3042
=========oooooo=========	chr6:76331194-76331527(+)$1	333	84	108	13.3313
#eeeee[bboooooobb]eeeeeb	chr5:132426848-132427207(+)$1	359	237	261	12.7154
))))))cccooooooccc4444dd	chr10:112343898-112344316(+)$1	418	225	249	12.0532
##a[ddddoooooodddd]a333d	chr16:31004330-31004603(+)$1	273	86	110	11.8086
"eeeee[bboooooobbeeeee33	chr1:71532374-71532624(+)$1	250	133	157	12.9416
dddd[ddddoooooodddd]dddd	chr6:4044034-4044363(+)$1	329	143	167	12.2935
2dddd:cccooooooccceeeee"	chr21:47817200-47817529(+)$1	329	142	166	11.5166

#otherMatches

#Seq PSSM
UGCGGAGAUCUGAUAGUCCUGAAA	chr10:28824485-28824767(+)$1	282	102	126	13.3728
ACUUCAACAAAAAGAUGUAUGAGG	chr5:154187959-154188344(+)$1	385	137	161	13.9647
UAUCAUCUCAAGGAAGGGCUGGAA	chr8:27462402-27462667(+)$1	265	114	138	14.0986
GUCUGUGCUCAGGUAAGCAAAACA	chr12:86268096-86268382(+)$1	286	146	170	14.6700
AGAGACAGGGUACCACCUUCAUCU	chr15:58001234-58001569(+)$1	335	38	62	12.3912
GGCAAAAGCAGAUACGUUAAAACU	chr2:109389316-109389633(+)$1	317	62	86	13.8698
AGCAGUGCUAUUUCGAGAGCUGUG	chr12:69653149-69653484(+)$1	335	134	158	13.0203
GAAGGAUGAUGUCGCUCAGACUGA	chr11:62649353-62649700(+)$1	347	87	111	11.3513
GAACUGCAAAAUAUAUUGAAACUU	chr12:32875449-32875752(+)$1	303	87	111	11.3843
CGUGGAUGCCAAACUGCAGCAAAC	chrX:16850670-16851001(+)$1	331	119	143	14.6855
AGAAGCCCUACAAUCAGGUGCAGC	chrX:96684577-96684903(+)$1	326	105	129	13.0805
GAUGAUGGCAGUUUCGUAUUUAUC	chr16:18888318-18888604(+)$1	286	201	225	12.9798
UUUUAAUUUAAGACAAAUUUAAAA	chr22:42024095-42024369(+)$1	274	150	174	11.5769
UUACGGUGUAAAUUGGCAGCGUUU	chr4:2886242-2886510(+)$1	268	73	97	13.0627
ACAGAUUCCAGCUUCGGAACAAGA	chr12:69202920-69203232(+)$1	312	121	145	12.8077
AUCCUGGGAUCUCUCUCUAACAGG	chr1:40535793-40536063(+)$1	270	14	38	14.2587
AUGCUUGCUUCUUUCAGUAGCAGU	chr1:200819197-200819504(+)$1	307	245	269	13.1984
AUUUUAAGUGUAAAAAUUAAAAAU	chrX:135581780-135582040(+)$1	260	178	202	14.1966
UUUCUGAACCUGGAAGUUAAGGAU	chr9:131755412-131755721(+)$1	309	228	252	13.9008
CUUAAGAUGUGAUCCCAUGUUGAG	chr6:144128137-144128460(+)$1	323	168	192	13.2395
UGUUCUUUAUCAGCCUAAAAUACA	chr10:64948795-64949095(+)$1	300	105	129	12.5953
UACGCCGUGGCGCUGCAGGGCUGU	chr21:45739894-45740180(+)$1	286	21	45	12.5375
guauauguagaaaaauauauauau	chr1:97243348-97243667(+)$1	319	196	220	13.3313
CAUUGAGCUAAGUUAAGUUUAAAU	chr1:214794017-214794368(+)$1	351	276	300	12.5853
AAAUGGCCUUAUAAUAGUUUCCAU	chr12:25362009-25362321(+)$1	312	58	82	13.7793
GAGUUCUACUCAUACGUGGAAUUC	chrX:153689419-153689783(+)$1	364	235	259	12.4508
UAAGGUUCCCGAUAUGGAUGAUga	chr9:131456098-131456471(+)$1	373	72	96	15.1689
CGACUCGGCUGUUAUGCUGUUCUU	chr10:105331331-105331629(+)$1	298	147	171	11.6210
AGGUGGAGAACCAGAUCCUCACCC	chr19:39217567-39217902(+)$1	335	84	108	12.7280
GUCCCCAGUGCCCCAACUGCACCU	chr19:39212146-39212473(+)$1	327	289	313	12.5264
AUGCCACAGAUGUAUGUGUUUGAC	chr20:31434398-31434672(+)$1	274	167	191	11.7726
CUCGAUGCGCUCAUCUGCAUCCUU	chr2:74592561-74592825(+)$1	264	133	157	11.0743
GAAGAAGAUGGUAUGAUUGAAAUU	chr10:70532707-70533048(+)$1	341	139	163	14.3978
UACGAGCGCAUCAACGUGCCUGUG	chr2:231740267-231740587(+)$1	320	181	205	11.7132
CCAGCAGCAAAGAAGUGCUAUCUG	chr2:47707846-47708167(+)$1	321	131	155	12.3344
CAGAACAGGUACUGUCCUCUUUGG	chr7:134613501-134613836(+)$1	335	142	166	13.5236
GGCCAACCUGUCCCAAGUGGCCGG	chr16:89703616-89704109(+)$1	493	321	345	12.6573
GACUCACUGGAUGAACAUGGGGUC	chr22:46733686-46733957(+)$1	271	24	48	12.9798
CAUACAGGAGAGAGGUCCUAUAUC	chrX:47775320-47775655(+)$1	335	30	54	12.5952
AAUAAGCGUUUGGAUGCAGCUUAC	chr8:64099771-64100088(+)$1	317	130	154	11.3153
UUGUAAGUUUUUUAUGACUUUUAU	chr5:56526894-56527231(+)$1	337	252	276	12.5992
GAUGUAUUUGAACAAGAAUACUUU	chr7:35923458-35923731(+)$1	273	9	33	11.7507
GUUUAGAGAAUAUCCUUUUUUUGG	chr13:113873210-113873460(+)$1	250	143	167	11.9277
AGCAGAGAGCAAGCACUCGCGGUU	chr7:158448851-158449113(+)$1	262	148	172	15.3051
AACAUGCGAGUGUGCACAUGAGAA	chr15:72499406-72499668(+)$1	262	14	38	11.5842
UAGAAGUGCAGUUCAGCAAGAAGA	chr1:227946944-227947318(+)$1	374	134	158	13.3042
AGGUUUUAAAAAUAAUUGGAGCUU	chr6:76331194-76331527(+)$1	333	84	108	13.3313
CCACUUGUGAUGGCCCAGAGGUGA	chr5:132426848-132427207(+)$1	359	237	261	12.7154
AAAUAAAGAGAAAAAUCUGGAGCA	chr10:112343898-112344316(+)$1	418	225	249	12.0532
CCCCGCCUACCCCCAGGCCGCCUG	chr16:31004330-31004603(+)$1	273	86	110	11.8086
AAGAAGAUCUAGAACGACUUCUCU	chr1:71532374-71532624(+)$1	250	133	157	12.9416
GUAUGAACGGGAAAAUGUUGAUAC	chr6:4044034-4044363(+)$1	329	143	167	12.2935
ACUGCCCUGGAACAGCAGGUGGCA	chr21:47817200-47817529(+)$1	329	142	166	11.5166

#DB
(.(((.(((......))))))..)	chr10:28824485-28824767(+)$1	1	102	126	13.3728
(((((((((......))).)))))	chr5:154187959-154188344(+)$1	1	137	161	13.9647
(.(((.(((......))).))).)	chr8:27462402-27462667(+)$1	1	114	138	14.0986
)((((((((......)))...)))	chr12:86268096-86268382(+)$1	1	146	170	14.6700
(((((.(((......))))).)))	chr15:58001234-58001569(+)$1	1	38	62	12.3912
(.....(((......)))....))	chr2:109389316-109389633(+)$1	1	62	86	13.8698
.(((((.((......)).))))).	chr12:69653149-69653484(+)$1	1	134	158	13.0203
))((..(((......)))..))..	chr11:62649353-62649700(+)$1	1	87	111	11.3513
......(((......)))...)))	chr12:32875449-32875752(+)$1	1	87	111	11.3843
(((...(((......)))....))	chrX:16850670-16851001(+)$1	1	119	143	14.6855
.((((((((......))).))...	chrX:96684577-96684903(+)$1	1	105	129	13.0805
(((((..((......))..)))))	chr16:18888318-18888604(+)$1	1	201	225	12.9798
((((((.((......)).))))))	chr22:42024095-42024369(+)$1	1	150	174	11.5769
..(((.(((......))).)))..	chr4:2886242-2886510(+)$1	1	73	97	13.0627
))))))(((......)))(((.((	chr12:69202920-69203232(+)$1	1	121	145	12.8077
.((((((((......)))..))))	chr1:40535793-40536063(+)$1	1	14	38	14.2587
.((((.(((......)))))))))	chr1:200819197-200819504(+)$1	1	245	269	13.1984
(((((.(((......))).)))))	chrX:135581780-135582040(+)$1	1	178	202	14.1966
(((((.(((......)))..))).	chr9:131755412-131755721(+)$1	1	228	252	13.9008
(((((.(((......))).)))))	chr6:144128137-144128460(+)$1	1	168	192	13.2395
(((..((((......))))..)))	chr10:64948795-64949095(+)$1	1	105	129	12.5953
((((((.((......)).))).))	chr21:45739894-45740180(+)$1	1	21	45	12.5375
(((((((((......)))))))))	chr1:97243348-97243667(+)$1	1	196	220	13.3313
..(((((((......)))))))..	chr1:214794017-214794368(+)$1	1	276	300	12.5853
.(((((.((......))...))))	chr12:25362009-25362321(+)$1	1	58	82	13.7793
(((((((((......)))))))))	chrX:153689419-153689783(+)$1	1	235	259	12.4508
((....(((......)))...)))	chr9:131456098-131456471(+)$1	1	72	96	15.1689
.((..((((......)))).))..	chr10:105331331-105331629(+)$1	1	147	171	11.6210
.(((((.((......)).))))))	chr19:39217567-39217902(+)$1	1	84	108	12.7280
((...((((......)))).))))	chr19:39212146-39212473(+)$1	1	289	313	12.5264
((((((((......))))...).)	chr20:31434398-31434672(+)$1	1	167	191	11.7726
(((((((((......))))))...	chr2:74592561-74592825(+)$1	1	133	157	11.0743
(((...(((......)))....))	chr10:70532707-70533048(+)$1	1	139	163	14.3978
.(((.((((......)))).)))(	chr2:231740267-231740587(+)$1	1	181	205	11.7132
((((.((((......))))..)))	chr2:47707846-47708167(+)$1	1	131	155	12.3344
((((..(((......))).)))))	chr7:134613501-134613836(+)$1	1	142	166	13.5236
(((((..((......))))))).)	chr16:89703616-89704109(+)$1	1	321	345	12.6573
(((((..((......))..)))))	chr22:46733686-46733957(+)$1	1	24	48	12.9798
.(((.((((......)))).))).	chrX:47775320-47775655(+)$1	1	30	54	12.5952
).(((((((......)).)))))(	chr8:64099771-64100088(+)$1	1	130	154	11.3153
(((((((((......))))....)	chr5:56526894-56527231(+)$1	1	252	276	12.5992
(..((((((......))))))...	chr7:35923458-35923731(+)$1	1	9	33	11.7507
(...((((......))))...)))	chr13:113873210-113873460(+)$1	1	143	167	11.9277
(((...(((......)))...)))	chr7:158448851-158449113(+)$1	1	148	172	15.3051
..((((.(......).))))....	chr15:72499406-72499668(+)$1	1	14	38	11.5842
(.....(((......)))..))))	chr1:227946944-227947318(+)$1	1	134	158	13.3042
(((((((((......)))))))))	chr6:76331194-76331527(+)$1	1	84	108	13.3313
.(((((.((......)).))))))	chr5:132426848-132427207(+)$1	1	237	261	12.7154
......(((......)))....))	chr10:112343898-112344316(+)$1	1	225	249	12.0532
..(.((((......)))).)...)	chr16:31004330-31004603(+)$1	1	86	110	11.8086
.(((((.((......)))))))..	chr1:71532374-71532624(+)$1	1	133	157	12.9416
((((.((((......)))).))))	chr6:4044034-4044363(+)$1	1	143	167	12.2935
.)))).(((......)))(((((.	chr21:47817200-47817529(+)$1	1	142	166	11.5166

#PSSM
d : 0.24	f : 0.15	# : 0.09	e : 0.09	[ : 0.07	= : 0.07	c : 0.03	% : 0.03	! : 0.03	" : 0.03	i : 0.01	b : 0.01	: : 0.01	g : 0.01	) : 0.01	2 : 0.01	
e : 0.24	d : 0.18	f : 0.13	= : 0.07	c : 0.05	# : 0.05	[ : 0.03	$ : 0.03	! : 0.03	b : 0.03	% : 0.01	i : 0.01	: : 0.01	" : 0.01	) : 0.01	
e : 0.26	d : 0.16	c : 0.13	f : 0.11	= : 0.05	$ : 0.03	b : 0.03	" : 0.03	a : 0.03	% : 0.01	g : 0.01	i : 0.01	# : 0.01	! : 0.01	) : 0.01	
e : 0.24	c : 0.15	f : 0.13	" : 0.09	d : 0.09	b : 0.03	$ : 0.03	! : 0.03	= : 0.03	% : 0.01	g : 0.01	i : 0.01	# : 0.01	a : 0.01	) : 0.01	[ : 0.01	
e : 0.24	f : 0.11	d : 0.11	c : 0.09	! : 0.07	" : 0.07	[ : 0.07	b : 0.03	$ : 0.03	= : 0.03	% : 0.01	g : 0.01	i : 0.01	# : 0.01	) : 0.01	
d : 0.22	e : 0.16	[ : 0.15	! : 0.09	f : 0.07	" : 0.05	$ : 0.03	= : 0.03	% : 0.01	b : 0.01	c : 0.01	g : 0.01	i : 0.01	# : 0.01	) : 0.01	: : 0.01	
c : 0.45	d : 0.20	[ : 0.15	! : 0.05	= : 0.03	f : 0.03	g : 0.01	i : 0.01	e : 0.01	
c : 0.45	b : 0.20	d : 0.20	= : 0.03	f : 0.03	g : 0.01	i : 0.01	a : 0.01	
c : 0.45	b : 0.20	d : 0.15	o : 0.07	= : 0.03	f : 0.03	g : 0.01	i : 0.01	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.99	
o : 0.92	d : 0.05	a : 0.01	
c : 0.45	b : 0.20	d : 0.20	= : 0.03	f : 0.03	g : 0.01	i : 0.01	] : 0.01	
c : 0.45	d : 0.22	b : 0.20	= : 0.03	f : 0.03	g : 0.01	i : 0.01	
c : 0.45	d : 0.22	] : 0.11	2 : 0.03	= : 0.03	f : 0.03	e : 0.03	g : 0.01	3 : 0.01	i : 0.01	
d : 0.18	] : 0.15	3 : 0.13	e : 0.13	2 : 0.11	4 : 0.07	c : 0.05	f : 0.05	= : 0.03	b : 0.01	g : 0.01	i : 0.01	
e : 0.20	3 : 0.13	2 : 0.11	c : 0.09	4 : 0.09	f : 0.09	] : 0.09	b : 0.03	d : 0.03	= : 0.03	g : 0.01	i : 0.01	a : 0.01	
e : 0.24	c : 0.15	3 : 0.13	4 : 0.11	f : 0.09	b : 0.05	d : 0.05	2 : 0.03	= : 0.03	g : 0.03	] : 0.01	i : 0.01	
e : 0.26	4 : 0.16	c : 0.11	d : 0.11	f : 0.07	= : 0.07	b : 0.03	g : 0.03	2 : 0.01	[ : 0.01	] : 0.01	i : 0.01	a : 0.01	3 : 0.01	
e : 0.26	d : 0.15	4 : 0.13	f : 0.09	c : 0.09	= : 0.07	] : 0.05	3 : 0.03	2 : 0.01	: : 0.01	9 : 0.01	i : 0.01	g : 0.01	
d : 0.22	e : 0.16	4 : 0.13	f : 0.11	= : 0.07	b : 0.07	c : 0.05	: : 0.01	9 : 0.01	] : 0.01	i : 0.01	2 : 0.01	g : 0.01	3 : 0.01	" : 0.01	

#score	681.9314065796094
#seq	53
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m3_run1.txt

#BEAR
[ffffffrrrrrrrrrffff	chr16:30435649-30435875(-)$1	226	8	28	10.4463
gggggggpppppppgggggg	chr13:26793629-26793870(-)$1	241	45	65	14.4857
ddddcccpppppppccc22d	chr7:5568055-5568317(-)$1	262	123	143	13.2372
iicccrrrrrrrrrccc]ii	chr19:2248272-2248573(+)$1	301	93	113	10.3508
iiiiiiipppppppiiiiii	chr2:190531649-190531870(+)$1	221	8	28	14.1611
###ddddpppppppddddcc	chr12:56575716-56575935(-)$1	219	166	186	13.5941
:ffffffpppppppffffff	chr11:62334794-62335029(-)$1	235	94	114	13.1990
[ffffffpppppppffffff	chr5:72875061-72875292(+)$1	231	13	33	14.1180
eee[cccpppppppccc]ee	chr8:42977264-42977499(+)$1	235	126	146	14.1780
ff"""bbpppppppbb333f	chr1:156756424-156756652(+)$1	228	27	47	13.2053
a!!ddddpppppppdddd22	chr14:95577591-95577874(-)$1	283	173	193	13.4299
"""ddddpppppppdddd]d	chr6:56966191-56966436(+)$1	245	6	26	13.6129
f[eeeeerrrrrrrrreeee	chr2:224640588-224640813(-)$1	225	182	202	10.5917
##eeeeepppppppeeeee5	chr3:14703046-14703269(+)$1	223	12	32	13.6441
iiiiiiipppppppiiiiii	chrX:41200710-41200960(+)$1	250	89	109	14.1611
dffffffpppppppffffff	chr16:23646976-23647195(-)$1	219	173	193	13.8373
##eeeeepppppppeeeee2	chr19:6413378-6413653(-)$1	275	179	199	14.3173
gggggggrrrrrrrrrgggg	chrX:71492359-71492629(-)$1	270	225	245	10.8472
"bb[cccpppppppccc]bb	chr18:8633174-8633425(+)$1	251	128	148	13.4478
gggggggrrrrrrrrrgggg	chr5:179047809-179048051(-)$1	242	133	153	10.8472
d[eeeeepppppppeeeee]	chr5:132150218-132150436(+)$1	218	22	42	14.2518
"dddd[apppppppa]dddd	chr17:73036086-73036321(-)$1	235	68	88	12.9969
b!!ddddpppppppdddd22	chr22:50167735-50167989(-)$1	254	3	23	13.2530
bb[ddddpppppppdddd]b	chr14:95569748-95569986(-)$1	238	89	109	13.1374
cc!!cccpppppppcccccc	chr2:198352496-198352735(-)$1	239	17	37	14.2491
::eeeeepppppppeeeeeF	chr16:30740257-30740508(+)$1	251	211	231	12.2449
ddddcccpppppppccc22d	chr17:79478465-79478706(-)$1	241	210	230	13.2372
ffeeeeerrrrrrrrreeee	chr16:29989073-29989318(+)$1	245	124	144	10.4879
:ffffffpppppppffffff	chr2:62103202-62103444(-)$1	242	151	171	13.1990
gggggggpppppppgggggg	chr17:62496242-62496521(-)$1	279	139	159	14.4857
ggga[bbpppppppbb]a]g	chr17:72868955-72869178(-)$1	223	78	98	13.5335
eeeecccpppppppccc]ee	chr3:49053120-49053349(+)$1	229	139	159	14.1569
bbeeeeepppppppeeeee2	chr17:65955799-65956047(+)$1	248	153	173	13.7897
ddeeeeepppppppeeeeeF	chr6:43589778-43589999(-)$1	221	144	164	13.6429
gggggggpppppppgggggg	chr19:1257135-1257370(+)$1	235	46	66	14.4857
fffffbbpppppppbb]fff	chr12:49444089-49444379(-)$1	290	42	62	13.2894
F:eeeeepppppppeeeeeg	chr12:99059269-99059505(+)$1	236	73	93	13.0596
(ccc[bbpppppppbbccch	chr2:239234437-239234668(+)$1	231	171	191	12.6110
bb[ddddpppppppddddbb	chr2:38536456-38536689(-)$1	233	207	227	12.7319
eee[cccpppppppccc]ee	chr10:119805258-119805481(-)$1	223	173	193	14.1780
ff[cccrrrrrrrrrccc]f	chr6:26056503-26056766(-)$1	263	97	117	10.4587
##eeeeepppppppeeeeeb	chr3:43344698-43344923(+)$1	225	190	210	14.2584
:ffffffpppppppffffff	chr1:76260185-76260428(+)$1	243	193	213	13.1990
gggggggpppppppgggggg	chr10:116620922-116621151(+)$1	229	169	189	14.4857
gg[ddddpppppppdddd44	chr12:126135149-126135375(+)$1	226	30	50	13.6411
ccc[cccpppppppccc]cc	chr10:114925527-114925761(+)$1	234	152	172	14.2695
[ffffffpppppppffffff	chr7:156931848-156932107(+)$1	259	235	255	14.1180
ggg!!bbpppppppbb333g	chr4:52765420-52765644(+)$1	224	5	25	13.7833
gggggggpppppppgggggg	chr17:62496149-62496394(-)$1	245	12	32	14.4857
[ffffffpppppppffffff	chr19:42754407-42754639(-)$1	232	65	85	14.1180
gggggggpppppppgggggg	chr3:37323359-37323594(+)$1	235	4	24	14.4857
##eeeeepppppppeeeee8	chr9:134346093-134346357(+)$1	264	110	130	14.0723
dccc[bbpppppppbbccce	chr13:28196989-28197220(+)$1	231	112	132	13.1500
$$eeeeepppppppeeeee4	chr1:8601225-8601446(-)$1	221	149	169	14.0611
ccc!!bbpppppppbb]ccc	chr2:101898245-101898500(-)$1	255	77	97	13.3138

#otherMatches

#Seq PSSM
GUUCUGCCCCUAGUCAGUGG	chr16:30435649-30435875(-)$1	226	8	28	10.4463
UUGUUUAUAUUGUUUGAACA	chr13:26793629-26793870(-)$1	241	45	65	14.4857
GCCAUCCUGCGUCUGGACCU	chr7:5568055-5568317(-)$1	262	123	143	13.2372
GGGGUCCACCCCCAACCUCC	chr19:2248272-2248573(+)$1	301	93	113	10.3508
GAGAGAUACUUCAAGUCUUU	chr2:190531649-190531870(+)$1	221	8	28	14.1611
CCCUCUUCCCCAAAAAGAAU	chr12:56575716-56575935(-)$1	219	166	186	13.5941
CCAGCCCCAGUUCCGGGCUG	chr11:62334794-62335029(-)$1	235	94	114	13.1990
CAAAUCUGUUUUAAGGAUUU	chr5:72875061-72875292(+)$1	231	13	33	14.1180
GAGGAUGACAACACUAUGCU	chr8:42977264-42977499(+)$1	235	126	146	14.1780
UGACUGUGAAAGAGACUAAC	chr1:156756424-156756652(+)$1	228	27	47	13.2053
CCAGGAAGACCAGGUUCCAC	chr14:95577591-95577874(-)$1	283	173	193	13.4299
AUAUCCUGUGGCCAAGGACA	chr6:56966191-56966436(+)$1	245	6	26	13.6129
AAUAUUUUGGAAAUGUAAGU	chr2:224640588-224640813(-)$1	225	182	202	10.5917
CCUUGUGGAUUUCACACAGA	chr3:14703046-14703269(+)$1	223	12	32	13.6441
UUGGAUCUCGUAGUGAUUCA	chrX:41200710-41200960(+)$1	250	89	109	14.1611
GAUUUACUUCACCUGUAAGU	chr16:23646976-23647195(-)$1	219	173	193	13.8373
UGUUCAAGAGGAGAUUGAAA	chr19:6413378-6413653(-)$1	275	179	199	14.3173
UUACUGUAUAACAUGAACAG	chrX:71492359-71492629(-)$1	270	225	245	10.8472
AAUGGAUGAAGAUGAUUGAU	chr18:8633174-8633425(+)$1	251	128	148	13.4478
GGAAGAAAUUGUUCAGUUCU	chr5:179047809-179048051(-)$1	242	133	153	10.8472
UCCGAGCACGAGUGGCUCGU	chr5:132150218-132150436(+)$1	218	22	42	14.2518
UGCGCUGAAGGUUCCCGUGC	chr17:73036086-73036321(-)$1	235	68	88	12.9969
GAAUUCCAGCAUCCGGAAGG	chr22:50167735-50167989(-)$1	254	3	23	13.2530
AGAGCCCUUCUAUUGGGUAC	chr14:95569748-95569986(-)$1	238	89	109	13.1374
CCAUUGCUAAGAAUGCAGGU	chr2:198352496-198352735(-)$1	239	17	37	14.2491
CUUUUGGACUUAUACCGAGG	chr16:30740257-30740508(+)$1	251	211	231	12.2449
GCCAUCCUGCGUCUGGACCU	chr17:79478465-79478706(-)$1	241	210	230	13.2372
CCAUGGCAGCUUUGGAGCCG	chr16:29989073-29989318(+)$1	245	124	144	10.4879
AUUUAGUGAAGCAAAUUAAA	chr2:62103202-62103444(-)$1	242	151	171	13.1990
AGGGGUGGAUUUAAUACCUU	chr17:62496242-62496521(-)$1	279	139	159	14.4857
CAGAUCCACUUGCAGGUUGC	chr17:72868955-72869178(-)$1	223	78	98	13.5335
AGUAGGAGCUGAAAUCCAUG	chr3:49053120-49053349(+)$1	229	139	159	14.1569
GCUUUACUGUAUCUGUAAAA	chr17:65955799-65956047(+)$1	248	153	173	13.7897
UUGAGGCAGAGAUAGUCUUA	chr6:43589778-43589999(-)$1	221	144	164	13.6429
GAGGCCUCCGGCUUGGGCCU	chr19:1257135-1257370(+)$1	235	46	66	14.4857
GCUUCUCCCAUCCUGAUGGA	chr12:49444089-49444379(-)$1	290	42	62	13.2894
UAGUAUCUUUAAUUGGUGCA	chr12:99059269-99059505(+)$1	236	73	93	13.0596
AAGGUACUACUGCUGUCCUG	chr2:239234437-239234668(+)$1	231	171	191	12.6110
UGUAGUUGACUUAAAACUCA	chr2:38536456-38536689(-)$1	233	207	227	12.7319
UUUAUUUUGAAUUUGGGGGA	chr10:119805258-119805481(-)$1	223	173	193	14.1780
UUUGAUUCUCAACAUGUCCG	chr6:26056503-26056766(-)$1	263	97	117	10.4587
GAUGCAUGAAACUAGUGCAG	chr3:43344698-43344923(+)$1	225	190	210	14.2584
ACAUUUCUGUAUUUGAAGUG	chr1:76260185-76260428(+)$1	243	193	213	13.1990
AUGUAAGUUAGUGUUUUACA	chr10:116620922-116621151(+)$1	229	169	189	14.4857
ACUUCUUAACAAUGAAGACU	chr12:126135149-126135375(+)$1	226	30	50	13.6411
GGCCGGGACCCAGCCCCAGC	chr10:114925527-114925761(+)$1	234	152	172	14.2695
gcucggggcugggacucggg	chr7:156931848-156932107(+)$1	259	235	255	14.1180
GUUUUUCUAGAUGUGAUACA	chr4:52765420-52765644(+)$1	224	5	25	13.7833
AGGGGUGGAUUUAAUACCUU	chr17:62496149-62496394(-)$1	245	12	32	14.4857
GUCAUCAAAGACCCUGAUGA	chr19:42754407-42754639(-)$1	232	65	85	14.1180
UUAUUAGAUUAUUGCUGGUG	chr3:37323359-37323594(+)$1	235	4	24	14.4857
GCCGGUGUACCCCCCGCCGU	chr9:134346093-134346357(+)$1	264	110	130	14.0723
UGUGACAUUUGUAUUGCACG	chr13:28196989-28197220(+)$1	231	112	132	13.1500
UAUUAGGAUAUAACCCUGAG	chr1:8601225-8601446(-)$1	221	149	169	14.0611
GGAAGUGAUGACAGCAGUCC	chr2:101898245-101898500(-)$1	255	77	97	13.3138

#DB
.((((((.........))))	chr16:30435649-30435875(-)$1	1	8	28	10.4463
(((((((.......))))))	chr13:26793629-26793870(-)$1	1	45	65	14.4857
(((((((.......)))..)	chr7:5568055-5568317(-)$1	1	123	143	13.2372
(((((.........))).))	chr19:2248272-2248573(+)$1	1	93	113	10.3508
(((((((.......))))))	chr2:190531649-190531870(+)$1	1	8	28	14.1611
...((((.......))))))	chr12:56575716-56575935(-)$1	1	166	186	13.5941
.((((((.......))))))	chr11:62334794-62335029(-)$1	1	94	114	13.1990
.((((((.......))))))	chr5:72875061-72875292(+)$1	1	13	33	14.1180
(((.(((.......))).))	chr8:42977264-42977499(+)$1	1	126	146	14.1780
((...((.......))...)	chr1:156756424-156756652(+)$1	1	27	47	13.2053
(..((((.......))))..	chr14:95577591-95577874(-)$1	1	173	193	13.4299
...((((.......)))).)	chr6:56966191-56966436(+)$1	1	6	26	13.6129
(.(((((.........))))	chr2:224640588-224640813(-)$1	1	182	202	10.5917
..(((((.......))))).	chr3:14703046-14703269(+)$1	1	12	32	13.6441
(((((((.......))))))	chrX:41200710-41200960(+)$1	1	89	109	14.1611
)((((((.......))))))	chr16:23646976-23647195(-)$1	1	173	193	13.8373
..(((((.......))))).	chr19:6413378-6413653(-)$1	1	179	199	14.3173
(((((((.........))))	chrX:71492359-71492629(-)$1	1	225	245	10.8472
.((.(((.......))).))	chr18:8633174-8633425(+)$1	1	128	148	13.4478
(((((((.........))))	chr5:179047809-179048051(-)$1	1	133	153	10.8472
(.(((((.......))))).	chr5:132150218-132150436(+)$1	1	22	42	14.2518
.((((.(.......).))))	chr17:73036086-73036321(-)$1	1	68	88	12.9969
(..((((.......))))..	chr22:50167735-50167989(-)$1	1	3	23	13.2530
((.((((.......)))).)	chr14:95569748-95569986(-)$1	1	89	109	13.1374
((..(((.......))))))	chr2:198352496-198352735(-)$1	1	17	37	14.2491
..(((((.......))))))	chr16:30740257-30740508(+)$1	1	211	231	12.2449
(((((((.......)))..)	chr17:79478465-79478706(-)$1	1	210	230	13.2372
))(((((.........))))	chr16:29989073-29989318(+)$1	1	124	144	10.4879
.((((((.......))))))	chr2:62103202-62103444(-)$1	1	151	171	13.1990
(((((((.......))))))	chr17:62496242-62496521(-)$1	1	139	159	14.4857
((((.((.......)).).)	chr17:72868955-72869178(-)$1	1	78	98	13.5335
(((((((.......))).))	chr3:49053120-49053349(+)$1	1	139	159	14.1569
(((((((.......))))).	chr17:65955799-65956047(+)$1	1	153	173	13.7897
))(((((.......))))))	chr6:43589778-43589999(-)$1	1	144	164	13.6429
(((((((.......))))))	chr19:1257135-1257370(+)$1	1	46	66	14.4857
(((((((.......)).)))	chr12:49444089-49444379(-)$1	1	42	62	13.2894
(.(((((.......)))))(	chr12:99059269-99059505(+)$1	1	73	93	13.0596
.(((.((.......))))))	chr2:239234437-239234668(+)$1	1	171	191	12.6110
((.((((.......))))))	chr2:38536456-38536689(-)$1	1	207	227	12.7319
(((.(((.......))).))	chr10:119805258-119805481(-)$1	1	173	193	14.1780
((.(((.........))).)	chr6:26056503-26056766(-)$1	1	97	117	10.4587
..(((((.......))))))	chr3:43344698-43344923(+)$1	1	190	210	14.2584
.((((((.......))))))	chr1:76260185-76260428(+)$1	1	193	213	13.1990
(((((((.......))))))	chr10:116620922-116621151(+)$1	1	169	189	14.4857
((.((((.......))))..	chr12:126135149-126135375(+)$1	1	30	50	13.6411
(((.(((.......))).))	chr10:114925527-114925761(+)$1	1	152	172	14.2695
.((((((.......))))))	chr7:156931848-156932107(+)$1	1	235	255	14.1180
(((..((.......))...)	chr4:52765420-52765644(+)$1	1	5	25	13.7833
(((((((.......))))))	chr17:62496149-62496394(-)$1	1	12	32	14.4857
.((((((.......))))))	chr19:42754407-42754639(-)$1	1	65	85	14.1180
(((((((.......))))))	chr3:37323359-37323594(+)$1	1	4	24	14.4857
..(((((.......))))).	chr9:134346093-134346357(+)$1	1	110	130	14.0723
)(((.((.......)))))(	chr13:28196989-28197220(+)$1	1	112	132	13.1500
..(((((.......))))).	chr1:8601225-8601446(-)$1	1	149	169	14.0611
(((..((.......)).)))	chr2:101898245-101898500(-)$1	1	77	97	13.3138

#PSSM
g : 0.20	d : 0.10	# : 0.09	f : 0.09	[ : 0.07	: : 0.07	b : 0.07	i : 0.05	e : 0.05	" : 0.05	c : 0.05	a : 0.01	F : 0.01	( : 0.01	$ : 0.01	
f : 0.21	g : 0.20	# : 0.09	c : 0.09	d : 0.07	b : 0.07	i : 0.05	e : 0.05	! : 0.03	[ : 0.03	: : 0.03	" : 0.01	$ : 0.01	
e : 0.27	g : 0.18	f : 0.16	c : 0.09	[ : 0.07	d : 0.05	! : 0.05	i : 0.03	" : 0.03	# : 0.01	b : 0.01	
e : 0.23	d : 0.18	f : 0.16	g : 0.14	c : 0.07	[ : 0.07	! : 0.05	i : 0.03	" : 0.01	a : 0.01	
e : 0.21	c : 0.18	f : 0.16	g : 0.14	d : 0.14	[ : 0.05	i : 0.03	! : 0.03	" : 0.01	
e : 0.21	c : 0.16	f : 0.14	g : 0.14	d : 0.12	b : 0.12	i : 0.03	r : 0.01	[ : 0.01	
e : 0.21	f : 0.14	g : 0.14	c : 0.14	d : 0.12	b : 0.12	r : 0.03	i : 0.03	a : 0.01	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
p : 0.87	r : 0.12	
e : 0.18	c : 0.16	d : 0.12	f : 0.12	b : 0.12	r : 0.10	g : 0.10	i : 0.03	a : 0.01	
c : 0.18	e : 0.18	d : 0.12	f : 0.12	b : 0.12	g : 0.10	r : 0.09	i : 0.03	] : 0.01	
c : 0.21	e : 0.21	f : 0.14	g : 0.14	d : 0.14	] : 0.05	i : 0.03	3 : 0.03	
e : 0.21	f : 0.16	g : 0.14	d : 0.14	] : 0.10	c : 0.09	2 : 0.03	i : 0.03	3 : 0.03	a : 0.01	
e : 0.27	f : 0.16	g : 0.14	c : 0.10	2 : 0.07	] : 0.07	i : 0.05	3 : 0.03	b : 0.03	d : 0.01	4 : 0.01	
f : 0.20	g : 0.20	e : 0.10	d : 0.07	c : 0.07	2 : 0.07	b : 0.07	i : 0.05	F : 0.03	4 : 0.03	5 : 0.01	] : 0.01	h : 0.01	8 : 0.01	

#score	732.6357799855763
#seq	55
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012c_hg19_UTR_m3_run1.txt

#BEAR
ffffftttttttttttfffff	chr6:139308723-139308948(+)$1	225	123	144	20.6690
ddddtttttttttttdddddd	chr14:50319628-50319849(-)$1	221	77	98	21.8291
dddduuuuuuuuuuuudddd:	chrX:14938612-14938837(+)$1	225	124	145	22.3619
dddvvvvvvvvvvvvvdddd]	chr6:112079973-112080195(+)$1	222	87	108	22.7799
eeeeuuuuuuuuuuuueeeee	chr22:37880268-37880494(+)$1	226	19	40	22.9879
eeeeuuuuuuuuuuuueeeee	chr13:98827971-98828192(-)$1	221	164	185	22.9879
dddvvvvvvvvvvvvvdddd4	chr1:33475239-33475461(-)$1	222	70	91	22.6898
ggggvvvvvvvvvvvvvgggg	chr6:97590829-97591051(-)$1	222	111	132	22.5366
eeeeyyyyyyyyyyyyyyyye	chr5:115803908-115804129(-)$1	221	69	90	19.5016
ddddtttttttttttddddii	chr2:109510995-109511219(+)$1	224	28	49	21.9058
eeeettttttttttteeeee3	chr3:107526058-107526282(-)$1	224	153	174	21.9820
====wwwwwwwwwwwwww===	chr13:28874762-28874983(-)$1	221	6	27	21.0218
!!bbwwwwwwwwwwwwwwbb2	chr2:122125159-122125384(-)$1	225	150	171	20.0945
eeeevvvvvvvvvvvvveeee	chr8:37716143-37716364(-)$1	221	168	189	23.0250
[cccuuuuuuuuuuuuccc]e	chr9:90283416-90283639(-)$1	223	23	44	22.9114
dddvvvvvvvvvvvvvdddd]	chr19:46142165-46142390(-)$1	225	83	104	22.7799
eeeeettttttttttteeeee	chr2:186697909-186698132(+)$1	223	171	192	22.2394
gggggtttttttttttggggg	chr16:67840428-67840657(+)$1	229	52	73	21.5490
:cccvvvvvvvvvvvvvccc:	chr15:49169940-49170164(-)$1	224	144	165	20.8306
"""bbtttttttttttbb333	chr12:53893252-53893474(+)$1	222	131	152	21.0151
ddddwwwwwwwwwwwwwwddd	chr20:3758321-3758549(+)$1	228	158	179	21.2995
hhhhhttttttttttthhhhh	chr16:24801586-24801813(-)$1	227	8	29	20.0614
[ddddtttttttttttdddd]	chr3:47458707-47458931(-)$1	224	17	38	22.7423
[ddddtttttttttttdddd2	chr14:39646731-39646953(+)$1	222	13	34	22.5970
hhhhuuuuuuuuuuuuhhhhh	chr11:13331446-13331667(+)$1	221	60	81	21.1131
""ccctttttttttttccc]b	chr12:49495825-49496047(-)$1	222	57	78	21.7676
ffffvvvvvvvvvvvvvffff	chr16:72818837-72819063(-)$1	226	157	178	21.6296
dddduuuuuuuuuuuuddddD	chrX:119660030-119660253(+)$1	223	52	73	22.0116
eeeeettttttttttteeeee	chr16:29827047-29827270(+)$1	223	34	55	22.2394
[cccuuuuuuuuuuuuccc]e	chr1:212873106-212873330(+)$1	224	194	215	22.9114
dddduuuuuuuuuuuudddd4	chr11:62341309-62341530(-)$1	221	45	66	23.3158
d[ccctttttttttttccc]d	chr16:84599757-84599979(+)$1	222	188	209	22.1007
bbbbvvvvvvvvvvvvvbb]b	chr16:47733157-47733388(+)$1	231	198	219	20.8420
dddduuuuuuuuuuuudddd2	chr4:158286950-158287173(-)$1	223	112	133	23.2605
f!!bbtttttttttttbb22f	chr7:138274065-138274291(-)$1	226	45	66	20.5053
dddduuuuuuuuuuuuddddd	chr22:46635284-46635507(+)$1	223	128	149	23.1034
dddduuuuuuuuuuuudddd]	chr21:40817468-40817689(+)$1	221	10	31	23.4058
gg[bbtttttttttttbb]gg	chr17:5972341-5972567(-)$1	226	87	108	21.0775
eeeettttttttttteeeee6	chr4:185011881-185012104(+)$1	223	71	92	21.3945
eeeevvvvvvvvvvvvveeee	chr6:26205277-26205505(-)$1	228	52	73	23.0250
eeeeyyyyyyyyyyyyyyyye	chr16:29001486-29001707(+)$1	221	150	171	19.5016
eeeeuuuuuuuuuuuueeeee	chr4:141782228-141782457(+)$1	229	179	200	22.9879
ffffvvvvvvvvvvvvvffff	chr15:25583454-25583677(-)$1	223	65	86	21.6296
dddduuuuuuuuuuuudddd2	chr19:10671589-10671811(+)$1	222	53	74	23.2605
[ddddtttttttttttdddd3	chr16:9211410-9211631(-)$1	221	171	192	22.7736
!cccvvvvvvvvvvvvvccc3	chr1:11751739-11751961(+)$1	222	10	31	23.0529
hhhhuuuuuuuuuuuuhhhhh	chr12:50474239-50474461(-)$1	222	179	200	21.1131
eeeevvvvvvvvvvvvveeee	chr12:120881771-120881994(-)$1	223	135	156	23.0250
[cccwwwwwwwwwwwwwwccc	chr12:91348622-91348845(-)$1	223	148	169	21.0791
bddddtttttttttttdddd]	chr12:120882271-120882493(-)$1	222	32	53	22.3223
ggggwwwwwwwwwwwwwwggg	chrX:9900256-9900480(+)$1	224	43	64	20.9176
eeeettttttttttteeeee]	chr11:67406893-67407118(+)$1	225	199	220	21.9507
""bbvvvvvvvvvvvvvbb33	chr2:102929274-102929502(+)$1	228	45	66	21.8176

#otherMatches

#Seq PSSM
CCCCGCAUGCACUACUCGGGG	chr6:139308723-139308948(+)$1	225	123	144	20.6690
GCCCAAGACACAAUGGGGCAC	chr14:50319628-50319849(-)$1	221	77	98	21.8291
GCCUAAUUUAUUAUAAAGGCC	chrX:14938612-14938837(+)$1	225	124	145	22.3619
AUUAGCAACUUUCUCCGAUCU	chr6:112079973-112080195(+)$1	222	87	108	22.7799
CGCCCUUAACCAGCCAGGCGG	chr22:37880268-37880494(+)$1	226	19	40	22.9879
guaugauuuuucacuaauaua	chr13:98827971-98828192(-)$1	221	164	185	22.9879
GCAUAUGAGAUAAGCCUGCAA	chr1:33475239-33475461(-)$1	222	70	91	22.6898
CAUGGCAAGGAAGGAAGCAUG	chr6:97590829-97591051(-)$1	222	111	132	22.5366
UUGGAAACCACUAACUAAUCC	chr5:115803908-115804129(-)$1	221	69	90	19.5016
AGGGCCACAGACCUACCCUGG	chr2:109510995-109511219(+)$1	224	28	49	21.9058
UCCUCCAUCCCCACCAGGAAU	chr3:107526058-107526282(-)$1	224	153	174	21.9820
AUUUGCCAUUUAUGACAAAAA	chr13:28874762-28874983(-)$1	221	6	27	21.0218
CAUCAACACCUACGACAAGAC	chr2:122125159-122125384(-)$1	225	150	171	20.0945
CUGCCCCCUUUUCCUUUGCAG	chr8:37716143-37716364(-)$1	221	168	189	23.0250
CUUCAGACCUAUAACAGAACU	chr9:90283416-90283639(-)$1	223	23	44	22.9114
cucugcaagauCAACCGAGCA	chr19:46142165-46142390(-)$1	225	83	104	22.7799
GGACCAGGCAAAGAAGGGUUU	chr2:186697909-186698132(+)$1	223	171	192	22.2394
GCGGGACCAGAUCCGCCCCGC	chr16:67840428-67840657(+)$1	229	52	73	21.5490
CCCCUUCCUCUUCCCCUGGGC	chr15:49169940-49170164(-)$1	224	144	165	20.8306
UCAGCUUCAGCUUUCUGCCCC	chr12:53893252-53893474(+)$1	222	131	152	21.0151
GUGGACAGAGCCAAGGGACCG	chr20:3758321-3758549(+)$1	228	158	179	21.2995
GCUGGGUAAAUUAGUGCCAGU	chr16:24801586-24801813(-)$1	227	8	29	20.0614
UGGCUCCCCCGAGAAAGGCUC	chr3:47458707-47458931(-)$1	224	17	38	22.7423
AAGCACACCACUCAUAUGCUA	chr14:39646731-39646953(+)$1	222	13	34	22.5970
CUAAACUUUUAUUUCAUUGGC	chr11:13331446-13331667(+)$1	221	60	81	21.1131
UCCCUGCACAGAGAAGAGGCG	chr12:49495825-49496047(-)$1	222	57	78	21.7676
CUUCUUUCCCCAGUGCUGAAG	chr16:72818837-72819063(-)$1	226	157	178	21.6296
UAGUAAAAUAUCAAUAGCUAU	chrX:119660030-119660253(+)$1	223	52	73	22.0116
AAGAAAAAAACUAAAAUUCUU	chr16:29827047-29827270(+)$1	223	34	55	22.2394
CCGUCCUUCCCGUCCCACGUC	chr1:212873106-212873330(+)$1	224	194	215	22.9114
UCCAAUUCAGCGCCACUGGAU	chr11:62341309-62341530(-)$1	221	45	66	23.3158
ugugcuuaugaaggcugcagg	chr16:84599757-84599979(+)$1	222	188	209	22.1007
GCCAUUAAUAUACGAACUGAG	chr16:47733157-47733388(+)$1	231	198	219	20.8420
UGUCUUCUUGGAGUUUGACAC	chr4:158286950-158287173(-)$1	223	112	133	23.2605
AUAUGGAUCAAUGUUACAGCU	chr7:138274065-138274291(-)$1	226	45	66	20.5053
CUUCGGUUGUGUAAAGGGAGC	chr22:46635284-46635507(+)$1	223	128	149	23.1034
CCGCGAGGAGGAAACGGCGGG	chr21:40817468-40817689(+)$1	221	10	31	23.4058
CAGCAGGAGCAGGUGGUGGUG	chr17:5972341-5972567(-)$1	226	87	108	21.0775
UCCUUUGUGCAAGGUGGGACA	chr4:185011881-185012104(+)$1	223	71	92	21.3945
CCUUUUCAGUGCAAUCUAAGG	chr6:26205277-26205505(-)$1	228	52	73	23.0250
CCCGUAACUUAUUAUCACUUU	chr16:29001486-29001707(+)$1	221	150	171	19.5016
CAGUCCCUUGCUUAUAACUGC	chr4:141782228-141782457(+)$1	229	179	200	22.9879
UAGUAACAGCACAACAAAUUA	chr15:25583454-25583677(-)$1	223	65	86	21.6296
GGUCUACUCCAUCAGCGACCA	chr19:10671589-10671811(+)$1	222	53	74	23.2605
ACAGUUUAAUAAUAAUACUGC	chr16:9211410-9211631(-)$1	221	171	192	22.7736
cacucccccuuccuuccaguc	chr1:11751739-11751961(+)$1	222	10	31	23.0529
CCCUgcacagggauuggggga	chr12:50474239-50474461(-)$1	222	179	200	21.1131
AGGUGCUCGCUUCAUUUGCCU	chr12:120881771-120881994(-)$1	223	135	156	23.0250
GUGCAAACCAGGAAGAGAGCA	chr12:91348622-91348845(-)$1	223	148	169	21.0791
UAAAAUUGAACAAUUUUUUUG	chr12:120882271-120882493(-)$1	222	32	53	22.3223
UCUGAACUAUCUCACUGCCGG	chrX:9900256-9900480(+)$1	224	43	64	20.9176
GGUCCUUGCCUCCUCGAUCGC	chr11:67406893-67407118(+)$1	225	199	220	21.9507
CCCAAAGCUUUAUCCACUGAA	chr2:102929274-102929502(+)$1	228	45	66	21.8176

#DB
(((((...........)))))	chr6:139308723-139308948(+)$1	1	123	144	20.6690
((((...........))))((	chr14:50319628-50319849(-)$1	1	77	98	21.8291
((((............)))).	chrX:14938612-14938837(+)$1	1	124	145	22.3619
(((.............)))).	chr6:112079973-112080195(+)$1	1	87	108	22.7799
((((............)))))	chr22:37880268-37880494(+)$1	1	19	40	22.9879
((((............)))))	chr13:98827971-98828192(-)$1	1	164	185	22.9879
(((.............)))).	chr1:33475239-33475461(-)$1	1	70	91	22.6898
((((.............))))	chr6:97590829-97591051(-)$1	1	111	132	22.5366
((((................)	chr5:115803908-115804129(-)$1	1	69	90	19.5016
((((...........))))((	chr2:109510995-109511219(+)$1	1	28	49	21.9058
((((...........))))).	chr3:107526058-107526282(-)$1	1	153	174	21.9820
((((..............)))	chr13:28874762-28874983(-)$1	1	6	27	21.0218
..((..............)).	chr2:122125159-122125384(-)$1	1	150	171	20.0945
((((.............))))	chr8:37716143-37716364(-)$1	1	168	189	23.0250
.(((............))).)	chr9:90283416-90283639(-)$1	1	23	44	22.9114
(((.............)))).	chr19:46142165-46142390(-)$1	1	83	104	22.7799
(((((...........)))))	chr2:186697909-186698132(+)$1	1	171	192	22.2394
(((((...........)))))	chr16:67840428-67840657(+)$1	1	52	73	21.5490
.(((.............))).	chr15:49169940-49170164(-)$1	1	144	165	20.8306
...((...........))...	chr12:53893252-53893474(+)$1	1	131	152	21.0151
((((..............)))	chr20:3758321-3758549(+)$1	1	158	179	21.2995
(((((...........)))))	chr16:24801586-24801813(-)$1	1	8	29	20.0614
.((((...........)))).	chr3:47458707-47458931(-)$1	1	17	38	22.7423
.((((...........)))).	chr14:39646731-39646953(+)$1	1	13	34	22.5970
((((............)))))	chr11:13331446-13331667(+)$1	1	60	81	21.1131
..(((...........))).)	chr12:49495825-49496047(-)$1	1	57	78	21.7676
((((.............))))	chr16:72818837-72819063(-)$1	1	157	178	21.6296
((((............))))(	chrX:119660030-119660253(+)$1	1	52	73	22.0116
(((((...........)))))	chr16:29827047-29827270(+)$1	1	34	55	22.2394
.(((............))).)	chr1:212873106-212873330(+)$1	1	194	215	22.9114
((((............)))).	chr11:62341309-62341530(-)$1	1	45	66	23.3158
(.(((...........))).)	chr16:84599757-84599979(+)$1	1	188	209	22.1007
((((.............)).)	chr16:47733157-47733388(+)$1	1	198	219	20.8420
((((............)))).	chr4:158286950-158287173(-)$1	1	112	133	23.2605
(..((...........))..)	chr7:138274065-138274291(-)$1	1	45	66	20.5053
((((............)))))	chr22:46635284-46635507(+)$1	1	128	149	23.1034
((((............)))).	chr21:40817468-40817689(+)$1	1	10	31	23.4058
((.((...........)).))	chr17:5972341-5972567(-)$1	1	87	108	21.0775
((((...........))))).	chr4:185011881-185012104(+)$1	1	71	92	21.3945
((((.............))))	chr6:26205277-26205505(-)$1	1	52	73	23.0250
((((................)	chr16:29001486-29001707(+)$1	1	150	171	19.5016
((((............)))))	chr4:141782228-141782457(+)$1	1	179	200	22.9879
((((.............))))	chr15:25583454-25583677(-)$1	1	65	86	21.6296
((((............)))).	chr19:10671589-10671811(+)$1	1	53	74	23.2605
.((((...........)))).	chr16:9211410-9211631(-)$1	1	171	192	22.7736
.(((.............))).	chr1:11751739-11751961(+)$1	1	10	31	23.0529
((((............)))))	chr12:50474239-50474461(-)$1	1	179	200	21.1131
((((.............))))	chr12:120881771-120881994(-)$1	1	135	156	23.0250
.(((..............)))	chr12:91348622-91348845(-)$1	1	148	169	21.0791
(((((...........)))).	chr12:120882271-120882493(-)$1	1	32	53	22.3223
((((..............)))	chrX:9900256-9900480(+)$1	1	43	64	20.9176
((((...........))))).	chr11:67406893-67407118(+)$1	1	199	220	21.9507
..((.............))..	chr2:102929274-102929502(+)$1	1	45	66	21.8176

#PSSM
d : 0.26	e : 0.24	[ : 0.11	f : 0.07	g : 0.07	" : 0.05	h : 0.05	! : 0.03	b : 0.03	= : 0.01	: : 0.01	
d : 0.32	e : 0.24	c : 0.09	g : 0.07	f : 0.05	" : 0.05	h : 0.05	! : 0.03	= : 0.01	[ : 0.01	b : 0.01	
d : 0.32	e : 0.24	c : 0.13	f : 0.05	g : 0.05	b : 0.05	h : 0.05	= : 0.01	" : 0.01	! : 0.01	[ : 0.01	
d : 0.26	e : 0.24	c : 0.13	b : 0.11	f : 0.05	v : 0.05	g : 0.05	h : 0.05	= : 0.01	
u : 0.26	v : 0.24	t : 0.09	w : 0.09	d : 0.07	b : 0.05	y : 0.03	e : 0.03	c : 0.03	f : 0.01	g : 0.01	h : 0.01	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.35	u : 0.26	v : 0.24	w : 0.09	y : 0.03	
t : 0.26	u : 0.26	v : 0.24	w : 0.09	e : 0.05	d : 0.03	y : 0.03	
d : 0.30	v : 0.18	e : 0.15	w : 0.09	c : 0.07	b : 0.05	h : 0.05	y : 0.03	f : 0.01	g : 0.01	
d : 0.30	e : 0.20	c : 0.11	w : 0.09	b : 0.09	f : 0.05	h : 0.05	g : 0.03	y : 0.03	
d : 0.32	e : 0.20	c : 0.13	f : 0.05	g : 0.05	b : 0.05	h : 0.05	y : 0.03	= : 0.01	3 : 0.01	2 : 0.01	] : 0.01	
d : 0.30	e : 0.20	] : 0.09	g : 0.07	f : 0.05	c : 0.05	h : 0.05	y : 0.03	3 : 0.03	i : 0.01	= : 0.01	b : 0.01	2 : 0.01	
e : 0.22	] : 0.11	3 : 0.09	f : 0.07	d : 0.07	g : 0.07	2 : 0.07	h : 0.05	: : 0.03	4 : 0.03	b : 0.03	i : 0.01	= : 0.01	D : 0.01	6 : 0.01	c : 0.01	

#score	1163.5357198418906
#seq	53
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_Ago2_Kishore2011a_hg19_UTR_m1_run1.txt

#BEAR
iiiiiiiiitttttttttttiiiiiiiii	chr2:55199840-55200080(-)$1	240	50	79	23.9417
iiiiiiiiwwwwwwwwwwwwwwiiiiiii	chr2:20449536-20449776(-)$1	240	55	84	25.4543
ggggggggwwwwwwwwwwwwwwggggggg	chr17:62499270-62499510(-)$1	240	20	49	25.2186
DDggggggguuuuuuuuuuuuggggggg:	chr11:10818733-10818973(-)$1	240	24	53	22.0738
===========ttttttttttt=======	chr5:60840862-60841102(+)$1	240	196	225	23.5206
[ccc"""ddddtttttttttttddddccc	chr15:81271128-81271368(-)$1	240	195	224	22.0729
[ccc[eeeeettttttttttteeeeeccc	chr22:43266515-43266755(-)$1	240	32	61	23.1357
iiiiiiiiyyyyyyyyyyyyyyyyiiiii	chr13:50273998-50274278(-)$1	280	147	176	24.1868
cc[ffffffvvvvvvvvvvvvvffffff]	chr2:159490579-159490826(+)$1	247	168	197	23.9100
hhhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr11:93471272-93471512(-)$1	240	210	239	23.4379
bb"""dddduuuuuuuuuuuudddd4444	chr1:207533029-207533269(+)$1	240	75	104	22.9263
##dddd[cccuuuuuuuuuuuuccc]ddd	chr21:34669344-34669584(+)$1	240	104	133	23.6036
ggggg[ddddtttttttttttdddd22gg	chr5:180004589-180004869(+)$1	280	160	189	23.0366
dd!!eeeeevvvvvvvvvvvvveeeee22	chr9:123526130-123526370(-)$1	240	6	35	23.7878
hhhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr21:46269476-46269716(-)$1	240	89	118	23.4379
:dddd[cccvvvvvvvvvvvvvcccdddd	chr7:12692679-12692919(+)$1	240	2	31	22.8015
ccc!!dddduuuuuuuuuuuudddd22cc	chr17:4624549-4624789(+)$1	240	92	121	24.0010
::ggggggguuuuuuuuuuuuggggggg:	chr5:37064106-37064346(+)$1	240	132	161	22.5130
a!!ffffffwwwwwwwwwwwwwwffffff	chr10:116736831-116737071(+)$1	240	33	62	22.6508
hhhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr1:26450176-26450416(+)$1	240	61	90	23.4379
ggg!!bb[ccctttttttttttccc]bb2	chr8:81432332-81432572(+)$1	240	120	149	22.5894
!agggggggtttttttttttggggggg]a	chr19:38697300-38697540(+)$1	240	43	72	23.7274
ggggggyyyyyyyyyyyyyyyyggggggg	chr13:100615906-100616146(-)$1	240	156	185	24.0968
:hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr6:36456533-36456773(+)$1	240	166	195	23.3569
::gggggggvvvvvvvvvvvvvggggggg	chr9:80944587-80944827(+)$1	240	138	167	24.1997
ee!!eeeeettttttttttteeeee]eee	chr9:131482797-131483037(+)$1	240	101	130	22.1067
[hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr5:78980996-78981236(+)$1	240	107	136	24.4268
hhhhhhcccvvvvvvvvvvvvvccc]hhh	chr2:29170811-29171051(+)$1	240	111	140	25.1379
ccc[cccxxxxxxxxxxxxxxxccc]ccc	chr4:39783922-39784162(+)$1	240	202	231	20.1897
###ggggggguuuuuuuuuuuuggggggg	chr11:63594993-63595233(+)$1	240	44	73	25.1602
"""eeeeewwwwwwwwwwwwwweeeee]c	chr13:36048370-36048610(-)$1	240	200	229	23.5697
==========uuuuuuuuuuuu=======	chr3:18389478-18389718(-)$1	240	161	190	25.3033
[a[bbbbyyyyyyyyyyyyyyyybb]bb]	chr17:48829499-48829739(+)$1	240	147	176	21.5972
::gggggggvvvvvvvvvvvvvggggggg	chr10:95288685-95288925(+)$1	240	126	155	24.1997
dccc[dddduuuuuuuuuuuudddd]ccc	chr6:53132105-53132385(-)$1	280	188	217	24.3392
eee[eeeeevvvvvvvvvvvvveeeee22	chr10:101151729-101151969(+)$1	240	43	72	23.5130
ffff[ayyyyyyyyyyyyyyyya]fffff	chr6:89321459-89321699(-)$1	240	39	68	22.1592
[ffffff[bbuuuuuuuuuuuubb]ffff	chr1:224344964-224345204(+)$1	240	167	196	22.6078
%%%ggggggguuuuuuuuuuuuggggggg	chr5:77782738-77782978(-)$1	240	69	98	23.2346
$$$ffffffvvvvvvvvvvvvvffffffi	chr6:117883672-117883912(-)$1	240	150	179	23.2201
""ggggggguuuuuuuuuuuuggggggg]	chr3:55502496-55502736(-)$1	240	119	148	25.5439
cc[a[dddduuuuuuuuuuuudddd]acc	chr15:65410352-65410592(-)$1	240	142	171	24.6030
gggggg!!bbtttttttttttbb]ggggg	chr10:103922167-103922407(+)$1	240	174	203	23.7180
ee:eeeeeyyyyyyyyyyyyyyyyeeeee	chr15:89745408-89745688(+)$1	280	51	80	20.6311
ffff[ddddvvvvvvvvvvvvvddddfff	chr1:229653378-229653658(-)$1	280	7	36	23.6859
ccc"""ccctttttttttttccc333ccc	chr18:57570463-57570743(+)$1	280	151	180	23.2901
cc[cccyyyyyyyyyyyyyyyyccc]ccc	chr9:35075506-35075746(-)$1	240	162	191	23.6524
=========yyyyyyyyyyyyyyyy====	chr5:102613209-102613449(+)$1	240	162	191	23.2154
gggggg[bbtttttttttttbbggggggg	chr10:70743763-70744003(+)$1	240	174	203	23.4289
hhhhhhhhwwwwwwwwwwwwwwhhhhhhh	chr5:60048090-60048332(-)$1	242	177	206	23.4379
g####cccwwwwwwwwwwwwwwcccgggg	chr1:226172783-226173103(-)$1	320	270	299	24.6167
!!bb[eeeeeuuuuuuuuuuuueeeee]b	chr14:31087959-31088239(+)$1	280	56	85	23.3678
[hhhhhhhhvvvvvvvvvvvvvhhhhhhh	chr11:57510257-57510497(+)$1	240	194	223	24.4268
fffff[ccctttttttttttccc]fffff	chr1:244219717-244220009(+)$1	292	53	82	22.2790
[ccc[ddddvvvvvvvvvvvvvdddd]cc	chr6:97594497-97594737(-)$1	240	40	69	24.7802
iiiii[cccvvvvvvvvvvvvvccc]iii	chr1:38279530-38279770(-)$1	240	178	207	26.3405
ggggggyyyyyyyyyyyyyyyyggggggg	chr1:226107771-226108012(-)$1	241	40	69	24.0968
gggg"""awwwwwwwwwwwwwwa333ggg	chr5:60454301-60454541(-)$1	240	51	80	24.3558
ee[bbddddwwwwwwwwwwwwwwdddd]b	chr7:95034335-95034575(-)$1	240	88	117	22.0223
!a[a[dddduuuuuuuuuuuudddd]a]a	chr14:64152557-64152797(-)$1	240	166	195	24.7207
iiiiiiiiiuuuuuuuuuuuuiiiiiiii	chr7:99667512-99667752(-)$1	240	163	192	25.7728
ccc!!bb[ccctttttttttttccc]bb2	chr12:4409589-4409829(+)$1	240	66	95	22.4771

#otherMatches

#Seq PSSM
GGUGGAAUAAAAAACCUGUAUAUUUUACU	chr2:55199840-55200080(-)$1	240	50	79	23.9417
AUGUACAUUUACAAGCGGCCUUAUGUACA	chr2:20449536-20449776(-)$1	240	55	84	25.4543
UUACACUUACGUAUUUAAUUAAAGGUGUG	chr17:62499270-62499510(-)$1	240	20	49	25.2186
UUGUUACAGAAAAAUUCUUAACUGUAAUU	chr11:10818733-10818973(-)$1	240	24	53	22.0738
auguauauauauuuauacaacuuauguau	chr5:60840862-60841102(+)$1	240	196	225	23.5206
CUUUAAAACUCUUGACUUAAUUGAGUAAA	chr15:81271128-81271368(-)$1	240	195	224	22.0729
GGGAAUGCUCUUUGUGCUUUUGGGCAUCU	chr22:43266515-43266755(-)$1	240	32	61	23.1357
UUCAACUCUUGUGCACAUAAAAUUGAGUU	chr13:50273998-50274278(-)$1	280	147	176	24.1868
UGAUGAUGGCACCACAAGAUCCCCAUCAA	chr2:159490579-159490826(+)$1	247	168	197	23.9100
ACCUUGGAGAAAAAUUUUAACGUUUGAGG	chr11:93471272-93471512(-)$1	240	210	239	23.4379
GAGCAAGGAGAAAAAAGGCAGUCCUGGAA	chr1:207533029-207533269(+)$1	240	75	104	22.9263
UUGAAUUUAUUUUUCUACCUAUAUAUGUU	chr21:34669344-34669584(+)$1	240	104	133	23.6036
AAAGAAUGUCACAUCCGCCCAGACAGCUC	chr5:180004589-180004869(+)$1	280	160	189	23.0366
GCCAGUGUUAAAACUUCCACCAAAUACCA	chr9:123526130-123526370(-)$1	240	6	35	23.7878
CUGCUUUUUUCUGAAAUACACUAAGAGCA	chr21:46269476-46269716(-)$1	240	89	118	23.4379
auugcgccaccacacuccagccugggcaa	chr7:12692679-12692919(+)$1	240	2	31	22.8015
AGGGGGAGACAAAACUCCUACUCUCAACC	chr17:4624549-4624789(+)$1	240	92	121	24.0010
UCCUUUUGUAGAAAGUUUAACAUAAAAGA	chr5:37064106-37064346(+)$1	240	132	161	22.5130
GAGAUUGUUGACCAUUUUUAAAAAACGAU	chr10:116736831-116737071(+)$1	240	33	62	22.6508
CACAGUAUGGCAAAUGGAUAAAAUAUUGU	chr1:26450176-26450416(+)$1	240	61	90	23.4379
UUACUACUUCACAAAUGAAGAAUGAUGUU	chr8:81432332-81432572(+)$1	240	120	149	22.5894
ACCCUUUCUUCCCCACACCCAGAGAGGUG	chr19:38697300-38697540(+)$1	240	43	72	23.7274
ACCAAAGAAUUAUAUUAUACAUUUUGGUG	chr13:100615906-100616146(-)$1	240	156	185	24.0968
ACUAUUGGCAUCCAUUUGCAAGGCCAAUG	chr6:36456533-36456773(+)$1	240	166	195	23.3569
CCUCUUUUUAAGCUGUUUUAUGAAAAAGA	chr9:80944587-80944827(+)$1	240	138	167	24.1997
CACCUCUGUCCCCUUCCCCCACAGACUGU	chr9:131482797-131483037(+)$1	240	101	130	22.1067
CUAUUUCUUAAUAAAUUCUUCCAAGAAAU	chr5:78980996-78981236(+)$1	240	107	136	24.4268
UGUGUGCUCAUCUUAAGAGCCAGAGCCAU	chr2:29170811-29171051(+)$1	240	111	140	25.1379
AUCUCUAUUCUAAACAAUCUGUUAGUGAU	chr4:39783922-39784162(+)$1	240	202	231	20.1897
AACCAGGAGGCCUCCAUUACCUCUUCCUG	chr11:63594993-63595233(+)$1	240	44	73	25.1602
UUUGUGAUUUAGAUUUUAAUUUGUUGCUG	chr13:36048370-36048610(-)$1	240	200	229	23.5697
AAAACAGCUAUUUUGUUACAGCUGGCUGU	chr3:18389478-18389718(-)$1	240	161	190	25.3033
UAGUGGCAUAGAAAAAGUAUAAAGCUCAG	chr17:48829499-48829739(+)$1	240	147	176	21.5972
UGUAAAUGAGAAAAGAAUAAAAUUAUUUA	chr10:95288685-95288925(+)$1	240	126	155	24.1997
UGCCUGCAUUUUACAUUUUUUGUGCUGGC	chr6:53132105-53132385(-)$1	280	188	217	24.3392
UUCAGGGGAUGGACCAAGAAUUUCCCCCA	chr10:101151729-101151969(+)$1	240	43	72	23.5130
CUGGGAGACUUCUUUUUUUAAAUGCCAGG	chr6:89321459-89321699(-)$1	240	39	68	22.1592
UCCAGCAGCAGGUUAAAACAAAUGGUGCU	chr1:224344964-224345204(+)$1	240	167	196	22.6078
UUGGUGAAGAAAAAAACGGGUAUCUUCAU	chr5:77782738-77782978(-)$1	240	69	98	23.2346
CUCAAAAGUUACUAAACAUUUUACUUUUU	chr6:117883672-117883912(-)$1	240	150	179	23.2201
UACUCUGGGGUUAUUUCUCUGUCUAGAGC	chr3:55502496-55502736(-)$1	240	119	148	25.5439
GGAGAACUUAGAAAACCUGAAGAGUACCC	chr15:65410352-65410592(-)$1	240	142	171	24.6030
AAUCACUUACUAUUGAUUUUUGUUGUGAU	chr10:103922167-103922407(+)$1	240	174	203	23.7180
UUCUCAUAUUACUUUUGAUUCUACUAUGA	chr15:89745408-89745688(+)$1	280	51	80	20.6311
AGCAUGGCACCUCAUUUUCUUUUGCCUGC	chr1:229653378-229653658(-)$1	280	7	36	23.6859
GUUGGGCGUUACUAGAAACUAUGGAAAAC	chr18:57570463-57570743(+)$1	280	151	180	23.2901
UGCCAGAAAAGGAACCAAGGAACUGCCAU	chr9:35075506-35075746(-)$1	240	162	191	23.6524
GUUGCUAAAGAAAUAAUGCCCUGGGUUUA	chr5:102613209-102613449(+)$1	240	162	191	23.2154
CUAUGCUAGGAAAUUUAAAGCUGCAUGGU	chr10:70743763-70744003(+)$1	240	174	203	23.4289
CAUGUAAUAAAACACAUACUCAAUUAUAU	chr5:60048090-60048332(-)$1	242	177	206	23.4379
aucugggccuuaaauuuucuuugucuggu	chr1:226172783-226173103(-)$1	320	270	299	24.6167
AUUAUAAUUGUUCUUUUCUUAUUAAUUUU	chr14:31087959-31088239(+)$1	280	56	85	23.3678
CUCUAGUAAGGCAUUGUAAAAGUUACUGG	chr11:57510257-57510497(+)$1	240	194	223	24.4268
GUGCAUUUAUAACAAACUUCUAAUUGCAC	chr1:244219717-244220009(+)$1	292	53	82	22.2790
AAAUGAUAAUACUUAAUAUAUUUUGUGAU	chr6:97594497-97594737(-)$1	240	40	69	24.7802
AUGUUGCAAUAAGUUAUCUCAUUUGGAAU	chr1:38279530-38279770(-)$1	240	178	207	26.3405
GCUUCCUCUCCUGUCCCAUGUUGGAAGUU	chr1:226107771-226108012(-)$1	241	40	69	24.0968
CUAGCAGCUACAGUUUAAAAAUGAAACUA	chr5:60454301-60454541(-)$1	240	51	80	24.3558
GCACUUUUAACAAAAAAGGAAAAUGAACA	chr7:95034335-95034575(-)$1	240	88	117	22.0223
UUCGUUACUGAGAAAAUGAUAAGUAUCCA	chr14:64152557-64152797(-)$1	240	166	195	24.7207
GUGUGGUUUUGUGCAAUGUUUGGACCAUA	chr7:99667512-99667752(-)$1	240	163	192	25.7728
AUGGGGAAGGAGUACAAAACAAUCUCUCA	chr12:4409589-4409829(+)$1	240	66	95	22.4771

#DB
(((((((((...........)))))))))	chr2:55199840-55200080(-)$1	1	50	79	23.9417
((((((((..............)))))))	chr2:20449536-20449776(-)$1	1	55	84	25.4543
((((((((..............)))))))	chr17:62499270-62499510(-)$1	1	20	49	25.2186
(((((((((............))))))).	chr11:10818733-10818973(-)$1	1	24	53	22.0738
(((((((((((...........)))))))	chr5:60840862-60841102(+)$1	1	196	225	23.5206
.(((...((((...........)))))))	chr15:81271128-81271368(-)$1	1	195	224	22.0729
.(((.(((((...........))))))))	chr22:43266515-43266755(-)$1	1	32	61	23.1357
((((((((................)))))	chr13:50273998-50274278(-)$1	1	147	176	24.1868
((.((((((.............)))))).	chr2:159490579-159490826(+)$1	1	168	197	23.9100
((((((((..............)))))))	chr11:93471272-93471512(-)$1	1	210	239	23.4379
((...((((............))))....	chr1:207533029-207533269(+)$1	1	75	104	22.9263
..((((.(((............))).)))	chr21:34669344-34669584(+)$1	1	104	133	23.6036
(((((.((((...........))))..))	chr5:180004589-180004869(+)$1	1	160	189	23.0366
((..(((((.............)))))..	chr9:123526130-123526370(-)$1	1	6	35	23.7878
((((((((..............)))))))	chr21:46269476-46269716(-)$1	1	89	118	23.4379
.((((.(((.............)))))))	chr7:12692679-12692919(+)$1	1	2	31	22.8015
(((..((((............))))..))	chr17:4624549-4624789(+)$1	1	92	121	24.0010
..(((((((............))))))).	chr5:37064106-37064346(+)$1	1	132	161	22.5130
(..((((((..............))))))	chr10:116736831-116737071(+)$1	1	33	62	22.6508
((((((((..............)))))))	chr1:26450176-26450416(+)$1	1	61	90	23.4379
(((..((.(((...........))).)).	chr8:81432332-81432572(+)$1	1	120	149	22.5894
.((((((((...........))))))).)	chr19:38697300-38697540(+)$1	1	43	72	23.7274
((((((................)))))))	chr13:100615906-100616146(-)$1	1	156	185	24.0968
.((((((((.............)))))))	chr6:36456533-36456773(+)$1	1	166	195	23.3569
..(((((((.............)))))))	chr9:80944587-80944827(+)$1	1	138	167	24.1997
((..(((((...........))))).)))	chr9:131482797-131483037(+)$1	1	101	130	22.1067
.((((((((.............)))))))	chr5:78980996-78981236(+)$1	1	107	136	24.4268
(((((((((.............))).)))	chr2:29170811-29171051(+)$1	1	111	140	25.1379
(((.(((...............))).)))	chr4:39783922-39784162(+)$1	1	202	231	20.1897
...(((((((............)))))))	chr11:63594993-63595233(+)$1	1	44	73	25.1602
...(((((..............))))).)	chr13:36048370-36048610(-)$1	1	200	229	23.5697
((((((((((............)))))))	chr3:18389478-18389718(-)$1	1	161	190	25.3033
.(.((((................)).)).	chr17:48829499-48829739(+)$1	1	147	176	21.5972
..(((((((.............)))))))	chr10:95288685-95288925(+)$1	1	126	155	24.1997
)(((.((((............)))).)))	chr6:53132105-53132385(-)$1	1	188	217	24.3392
(((.(((((.............)))))..	chr10:101151729-101151969(+)$1	1	43	72	23.5130
((((.(................).)))))	chr6:89321459-89321699(-)$1	1	39	68	22.1592
.((((((.((............)).))))	chr1:224344964-224345204(+)$1	1	167	196	22.6078
...(((((((............)))))))	chr5:77782738-77782978(-)$1	1	69	98	23.2346
...((((((.............)))))))	chr6:117883672-117883912(-)$1	1	150	179	23.2201
..(((((((............))))))).	chr3:55502496-55502736(-)$1	1	119	148	25.5439
((.(.((((............)))).)))	chr15:65410352-65410592(-)$1	1	142	171	24.6030
((((((..((...........)).)))))	chr10:103922167-103922407(+)$1	1	174	203	23.7180
)).(((((................)))))	chr15:89745408-89745688(+)$1	1	51	80	20.6311
((((.((((.............)))))))	chr1:229653378-229653658(-)$1	1	7	36	23.6859
(((...(((...........)))...)))	chr18:57570463-57570743(+)$1	1	151	180	23.2901
((.(((................))).)))	chr9:35075506-35075746(-)$1	1	162	191	23.6524
(((((((((................))))	chr5:102613209-102613449(+)$1	1	162	191	23.2154
((((((.((...........)))))))))	chr10:70743763-70744003(+)$1	1	174	203	23.4289
((((((((..............)))))))	chr5:60048090-60048332(-)$1	1	177	206	23.4379
(....(((..............)))))))	chr1:226172783-226173103(-)$1	1	270	299	24.6167
..((.(((((............))))).)	chr14:31087959-31088239(+)$1	1	56	85	23.3678
.((((((((.............)))))))	chr11:57510257-57510497(+)$1	1	194	223	24.4268
(((((.(((...........))).)))))	chr1:244219717-244220009(+)$1	1	53	82	22.2790
.(((.((((.............)))).))	chr6:97594497-97594737(-)$1	1	40	69	24.7802
(((((.(((.............))).)))	chr1:38279530-38279770(-)$1	1	178	207	26.3405
((((((................)))))))	chr1:226107771-226108012(-)$1	1	40	69	24.0968
((((...(..............)...)))	chr5:60454301-60454541(-)$1	1	51	80	24.3558
((.((((((..............)))).)	chr7:95034335-95034575(-)$1	1	88	117	22.0223
.(.(.((((............)))).).)	chr14:64152557-64152797(-)$1	1	166	195	24.7207
(((((((((............))))))))	chr7:99667512-99667752(-)$1	1	163	192	25.7728
(((..((.(((...........))).)).	chr12:4409589-4409829(+)$1	1	66	95	22.4771

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

#score	1462.3501278337396
#seq	62
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_UTR_m2_run2.txt

#BEAR
ddddwwwwwwwwwwwwwwddd	chr6:28323706-28323995(+)$1	289	112	133	21.6736
::cccuuuuuuuuuuuucccc	chr1:201790535-201790799(+)$1	264	68	89	20.8459
hhhhhwwwwwwwwwwwwwwhh	chr1:152056932-152057170(-)$1	238	186	207	20.4551
[ddddvvvvvvvvvvvvvddd	chr10:97635534-97635754(+)$1	220	47	68	23.6437
ddddwwwwwwwwwwwwwwddd	chr12:57450116-57450355(-)$1	239	8	29	21.6736
edddduuuuuuuuuuuudddd	chr7:75510641-75510895(+)$1	254	185	206	22.8608
:dddduuuuuuuuuuuudddd	chrX:64742548-64742813(-)$1	265	95	116	21.9375
ddddwwwwwwwwwwwwwwddd	chr22:41363698-41363935(+)$1	237	105	126	21.6736
fffffftttttttttttffff	chr12:122618960-122619177(+)$1	217	67	88	20.7937
[ddddwwwwwwwwwwwwwwdd	chr2:231334993-231335216(+)$1	223	165	186	22.0400
eeeeevvvvvvvvvvvvveee	chr2:102960599-102960844(+)$1	245	92	113	23.2266
!!ccctttttttttttccc22	chr19:58375886-58376136(+)$1	250	182	203	21.1837
[cccwwwwwwwwwwwwwwccc	chr1:89737073-89737321(-)$1	248	202	223	21.8690
eeeeewwwwwwwwwwwwwwee	chr17:4931340-4931561(+)$1	221	96	117	21.6716
=====vvvvvvvvvvvvv===	chr8:146075694-146075917(-)$1	223	12	33	23.2336
!dddduuuuuuuuuuuudddd	chr17:4624548-4624805(+)$1	257	97	118	23.0731
fffffuuuuuuuuuuuuffff	chr9:15460050-15460300(+)$1	250	78	99	22.0440
"cccvvvvvvvvvvvvvccc3	chr17:27871066-27871414(+)$1	348	143	164	22.8232
ffffvvvvvvvvvvvvvffff	chr1:159997758-159998003(-)$1	245	109	130	22.0441
gggggvvvvvvvvvvvvvggg	chr10:81914923-81915171(-)$1	248	93	114	23.2655
ggggguuuuuuuuuuuugggg	chr2:128494456-128494700(-)$1	244	94	115	22.7306
%cccvvvvvvvvvvvvvccc4	chr16:69342709-69342950(+)$1	241	24	45	22.1317
[ddddvvvvvvvvvvvvvddd	chr6:118880505-118880745(-)$1	240	64	85	23.6437
[eeeeettttttttttteeee	chr16:28332389-28332658(+)$1	269	15	36	21.6403
ggggggtttttttttttgggg	chr17:19808752-19809012(-)$1	260	107	128	21.3774
ggggggtttttttttttgggg	chr11:47269962-47270182(-)$1	220	65	86	21.3774
ddd[bbtttttttttttbbdd	chr11:31832430-31832648(-)$1	218	162	183	20.6302
#ddddwwwwwwwwwwwwwwdd	chr19:54942714-54942933(+)$1	219	99	120	21.8565
===[avvvvvvvvvvvvva==	chr4:763102-763352(+)$1	250	7	28	23.2252
ggggggtttttttttttgggg	chr17:19808866-19809129(-)$1	263	224	245	21.3774
iiiiiyyyyyyyyyyyyyyyy	chr10:98721056-98721312(+)$1	256	46	67	18.9759
ddddvvvvvvvvvvvvvdddd	chr2:219269251-219269506(+)$1	255	21	42	22.6493
eeeeevvvvvvvvvvvvveee	chr3:141465283-141465525(+)$1	242	218	239	23.2266
heeeeettttttttttteeee	chr3:142841423-142841636(+)$1	213	38	59	21.2798
ffffvvvvvvvvvvvvvffff	chr22:29703451-29703664(+)$1	213	41	62	22.0441
[ddddtttttttttttdddd]	chr16:57286269-57286555(+)$1	286	12	33	21.5442
[cccvvvvvvvvvvvvvcccg	chr21:34968267-34968500(-)$1	233	62	83	23.0332
fffffftttttttttttffff	chr11:102194727-102194988(+)$1	261	179	200	20.7937
eeeeewwwwwwwwwwwwwwee	chr4:10076713-10077019(-)$1	306	249	270	21.6716
hhhhhyyyyyyyyyyyyyyyy	chr1:182367475-182367695(-)$1	220	18	39	18.1779
hhhhhhttttttttttthhhh	chr1:24973512-24973745(+)$1	233	126	147	19.3672
ffffvvvvvvvvvvvvvffff	chr10:25890913-25891128(+)$1	215	22	43	22.0441
h[ccctttttttttttccc33	chr19:32875662-32875894(+)$1	232	182	203	21.2458
:dddduuuuuuuuuuuudddd	chr5:148731925-148732147(+)$1	222	97	118	21.9375
gggggwwwwwwwwwwwwwwgg	chr12:108105993-108106288(+)$1	295	18	39	21.7067
cddddvvvvvvvvvvvvvddd	chr11:43467437-43467737(+)$1	300	180	201	23.3951
eeeeevvvvvvvvvvvvveee	chr6:168364194-168364407(+)$1	213	83	104	23.2266
c[cccuuuuuuuuuuuucccc	chrX:23412429-23412673(+)$1	244	203	224	22.8786
ggggggtttttttttttgggg	chr10:12206545-12206768(+)$1	223	168	189	21.3774
iiiiiyyyyyyyyyyyyyyyy	chr11:85345558-85345770(+)$1	212	34	55	18.9759
[dddduuuuuuuuuuuudddd	chr17:2226516-2226767(-)$1	251	40	61	23.1098
"ddddvvvvvvvvvvvvvddd	chr17:7215912-7216177(-)$1	265	170	191	23.4928
fffffuuuuuuuuuuuuffff	chr12:93802272-93802530(-)$1	258	227	248	22.0440
fffffftttttttttttffff	chr7:17382824-17383053(+)$1	229	41	62	20.7937
fffffuuuuuuuuuuuuffff	chr9:135866517-135866734(+)$1	217	186	207	22.0440
eeeeettttttttttteeeee	chr9:116148785-116149011(-)$1	226	137	158	21.1330
:ddddtttttttttttdddd:	chr19:3468224-3468491(+)$1	267	174	195	19.3840
"""bbwwwwwwwwwwwwwwbb	chr5:140591437-140591651(+)$1	214	16	37	20.0933
eeeeevvvvvvvvvvvvveee	chr3:167401806-167402072(-)$1	266	72	93	23.2266
[ddddtttttttttttdddd]	chr19:17462366-17462585(-)$1	219	101	122	21.5442
eeeeewwwwwwwwwwwwwwee	chr2:99811395-99811619(+)$1	224	38	59	21.6716
eeeeeuuuuuuuuuuuueeee	chr1:10436787-10437032(+)$1	245	37	58	22.6654
:dddduuuuuuuuuuuudddd	chr15:48415441-48415652(+)$1	211	107	128	21.9375
!!cccuuuuuuuuuuuuccc]	chr15:34678951-34679245(-)$1	294	118	139	23.0926
gggggvvvvvvvvvvvvvggg	chr2:143704740-143704974(+)$1	234	200	221	23.2655

#otherMatches

#Seq PSSM
ugaccagcuuucauaaccguc	chr6:28323706-28323995(+)$1	289	112	133	21.6736
CACUAUAUACAAAUCAUUAGG	chr1:201790535-201790799(+)$1	264	68	89	20.8459
AAAUUUUAUCCUUCAAAAUAA	chr1:152056932-152057170(-)$1	238	186	207	20.4551
cgugagacuuauucacuauca	chr10:97635534-97635754(+)$1	220	47	68	23.6437
GUCCUUCUAGUAUUCUCUGGA	chr12:57450116-57450355(-)$1	239	8	29	21.6736
AAAAGGAUUAUAAAGCACUUU	chr7:75510641-75510895(+)$1	254	185	206	22.8608
cagugacuuucauucuccacu	chrX:64742548-64742813(-)$1	265	95	116	21.9375
AUGCUUUUCACUUCCACUGCA	chr22:41363698-41363935(+)$1	237	105	126	21.6736
cucagccucccgaguuagcug	chr12:122618960-122619177(+)$1	217	67	88	20.7937
AUUUGUAAUUGUAAAgccuca	chr2:231334993-231335216(+)$1	223	165	186	22.0400
ucaugaugaacucacccccau	chr2:102960599-102960844(+)$1	245	92	113	23.2266
UAUCUAGAAGUUUAAAAGGGC	chr19:58375886-58376136(+)$1	250	182	203	21.1837
CGCUCACUCUCUUUCAUAAGC	chr1:89737073-89737321(-)$1	248	202	223	21.8690
UGAGAAGUCACCCAAACAAUC	chr17:4931340-4931561(+)$1	221	96	117	21.6716
UUUCUGUUUAAUUGAAAAAGA	chr8:146075694-146075917(-)$1	223	12	33	23.2336
GGAGACAAAACUCCUACUCUC	chr17:4624548-4624805(+)$1	257	97	118	23.0731
cugacuuuaaauccuuuguca	chr9:15460050-15460300(+)$1	250	78	99	22.0440
UAGCCAAUUAUUUAAAUGUUU	chr17:27871066-27871414(+)$1	348	143	164	22.8232
GUAUAUUCACAUUAUAAAUAC	chr1:159997758-159998003(-)$1	245	109	130	22.0441
UUUUUAGAAAAAACAAAAAAA	chr10:81914923-81915171(-)$1	248	93	114	23.2655
UAGAAGAUUGACACACAUUUU	chr2:128494456-128494700(-)$1	244	94	115	22.7306
ACCCAACGCGUAAAACAGGGC	chr16:69342709-69342950(+)$1	241	24	45	22.1317
UGGUGAAGACCUGAAAAAUAC	chr6:118880505-118880745(-)$1	240	64	85	23.6437
GAGGGGGCCACCAAAGACCCC	chr16:28332389-28332658(+)$1	269	15	36	21.6403
AUUUUAAUUCCUCCUCCUGAG	chr17:19808752-19809012(-)$1	260	107	128	21.3774
UGGCCUGGGUAGUUGGGAGGC	chr11:47269962-47270182(-)$1	220	65	86	21.3774
CCGUCAUUUCAAACCAUUGUG	chr11:31832430-31832648(-)$1	218	162	183	20.6302
uucccucacuuauaaaccugg	chr19:54942714-54942933(+)$1	219	99	120	21.8565
UGGACGUUCUGGGUACAAGCC	chr4:763102-763352(+)$1	250	7	28	23.2252
AUUUUAAUUCCUCCUCCUGAG	chr17:19808866-19809129(-)$1	263	224	245	21.3774
GAUAUAGCaaauauuauuaua	chr10:98721056-98721312(+)$1	256	46	67	18.9759
GGGCGUCUCCCCCACCAGCCC	chr2:219269251-219269506(+)$1	255	21	42	22.6493
UAAGAAAAAACCUUAGAAUCU	chr3:141465283-141465525(+)$1	242	218	239	23.2266
GACUUGAACGUUCUGACCAGG	chr3:142841423-142841636(+)$1	213	38	59	21.2798
uuccucaucuauaaaauggag	chr22:29703451-29703664(+)$1	213	41	62	22.0441
GUAACUCUUCAUUUAUGUUAA	chr16:57286269-57286555(+)$1	286	12	33	21.5442
CUGAUUUUCCAACACCCUCAU	chr21:34968267-34968500(-)$1	233	62	83	23.0332
GAUGCCUGCCAUUAAAUGGCA	chr11:102194727-102194988(+)$1	261	179	200	20.7937
UGUGGAGCAUAACUAAAACCC	chr4:10076713-10077019(-)$1	306	249	270	21.6716
AGAACUCUUACUGAUUCCCUU	chr1:182367475-182367695(-)$1	220	18	39	18.1779
GAGUGAGUGUCCCAAUGUCGC	chr1:24973512-24973745(+)$1	233	126	147	19.3672
GUAGGACUGAAAAAACACUGC	chr10:25890913-25891128(+)$1	215	22	43	22.0441
AUUUCAAAUUCAAAUAGAACA	chr19:32875662-32875894(+)$1	232	182	203	21.2458
UGGUACUCACAAAUCACUACC	chr5:148731925-148732147(+)$1	222	97	118	21.9375
UUUCCUGCUUACCUUAACUGG	chr12:108105993-108106288(+)$1	295	18	39	21.7067
caggauaaaauucaaacuucc	chr11:43467437-43467737(+)$1	300	180	201	23.3951
GAGUGAAUAAUGUAAGGACAC	chr6:168364194-168364407(+)$1	213	83	104	23.2266
CCUGCCUUAUCCAAACUGCAG	chrX:23412429-23412673(+)$1	244	203	224	22.8786
UGCUGUGUUAAAUCAUGACAG	chr10:12206545-12206768(+)$1	223	168	189	21.3774
cauacaacgcacaucauuuca	chr11:85345558-85345770(+)$1	212	34	55	18.9759
GUGGGUCACUUGCUACUCCUA	chr17:2226516-2226767(-)$1	251	40	61	23.1098
CCAGGCCAAUAAAAUCUACCU	chr17:7215912-7216177(-)$1	265	170	191	23.4928
CCUUGUCUCUUGCAGUUUAAG	chr12:93802272-93802530(-)$1	258	227	248	22.0440
UGGUAUCAAAAUUACAUAUAC	chr7:17382824-17383053(+)$1	229	41	62	20.7937
CUAGCAGAGCACAGAAAGCUA	chr9:135866517-135866734(+)$1	217	186	207	22.0440
GUCUAACAAUGUUUUAUagac	chr9:116148785-116149011(-)$1	226	137	158	21.1330
CCCCAUCCUCUCAUCUUGGGU	chr19:3468224-3468491(+)$1	267	174	195	19.3840
uuugcucccauuccauacugu	chr5:140591437-140591651(+)$1	214	16	37	20.0933
UCCUGAAGGGAUCUAAUCCAG	chr3:167401806-167402072(-)$1	266	72	93	23.2266
CCACUUCCUCACCCCCAGUGC	chr19:17462366-17462585(-)$1	219	101	122	21.5442
AUACAUUUAUUAUUUAUUUUG	chr2:99811395-99811619(+)$1	224	38	59	21.6716
UUCUUUUUUCUUGUGCUGAGA	chr1:10436787-10437032(+)$1	245	37	58	22.6654
CCUGUAUUUCCAUCUACACAG	chr15:48415441-48415652(+)$1	211	107	128	21.9375
AGGGCCCUACAUCAUCUGCUA	chr15:34678951-34679245(-)$1	294	118	139	23.0926
UCUUUUUAAAAAAUAGUUGAA	chr2:143704740-143704974(+)$1	234	200	221	23.2655

#DB
((((..............)))	chr6:28323706-28323995(+)$1	1	112	133	21.6736
..(((............)))(	chr1:201790535-201790799(+)$1	1	68	89	20.8459
(((((..............))	chr1:152056932-152057170(-)$1	1	186	207	20.4551
.((((.............)))	chr10:97635534-97635754(+)$1	1	47	68	23.6437
((((..............)))	chr12:57450116-57450355(-)$1	1	8	29	21.6736
(((((............))))	chr7:75510641-75510895(+)$1	1	185	206	22.8608
.((((............))))	chrX:64742548-64742813(-)$1	1	95	116	21.9375
((((..............)))	chr22:41363698-41363935(+)$1	1	105	126	21.6736
((((((...........))))	chr12:122618960-122619177(+)$1	1	67	88	20.7937
.((((..............))	chr2:231334993-231335216(+)$1	1	165	186	22.0400
(((((.............)))	chr2:102960599-102960844(+)$1	1	92	113	23.2266
..(((...........)))..	chr19:58375886-58376136(+)$1	1	182	203	21.1837
.(((..............)))	chr1:89737073-89737321(-)$1	1	202	223	21.8690
(((((..............))	chr17:4931340-4931561(+)$1	1	96	117	21.6716
(((((.............)))	chr8:146075694-146075917(-)$1	1	12	33	23.2336
.((((............))))	chr17:4624548-4624805(+)$1	1	97	118	23.0731
(((((............))))	chr9:15460050-15460300(+)$1	1	78	99	22.0440
.(((.............))).	chr17:27871066-27871414(+)$1	1	143	164	22.8232
((((.............))))	chr1:159997758-159998003(-)$1	1	109	130	22.0441
(((((.............)))	chr10:81914923-81915171(-)$1	1	93	114	23.2655
(((((............))))	chr2:128494456-128494700(-)$1	1	94	115	22.7306
.(((.............))).	chr16:69342709-69342950(+)$1	1	24	45	22.1317
.((((.............)))	chr6:118880505-118880745(-)$1	1	64	85	23.6437
.(((((...........))))	chr16:28332389-28332658(+)$1	1	15	36	21.6403
((((((...........))))	chr17:19808752-19809012(-)$1	1	107	128	21.3774
((((((...........))))	chr11:47269962-47270182(-)$1	1	65	86	21.3774
(((.((...........))))	chr11:31832430-31832648(-)$1	1	162	183	20.6302
.((((..............))	chr19:54942714-54942933(+)$1	1	99	120	21.8565
(((.(.............)))	chr4:763102-763352(+)$1	1	7	28	23.2252
((((((...........))))	chr17:19808866-19809129(-)$1	1	224	245	21.3774
(((((................	chr10:98721056-98721312(+)$1	1	46	67	18.9759
((((.............))))	chr2:219269251-219269506(+)$1	1	21	42	22.6493
(((((.............)))	chr3:141465283-141465525(+)$1	1	218	239	23.2266
((((((...........))))	chr3:142841423-142841636(+)$1	1	38	59	21.2798
((((.............))))	chr22:29703451-29703664(+)$1	1	41	62	22.0441
.((((...........)))).	chr16:57286269-57286555(+)$1	1	12	33	21.5442
.(((.............))))	chr21:34968267-34968500(-)$1	1	62	83	23.0332
((((((...........))))	chr11:102194727-102194988(+)$1	1	179	200	20.7937
(((((..............))	chr4:10076713-10077019(-)$1	1	249	270	21.6716
(((((................	chr1:182367475-182367695(-)$1	1	18	39	18.1779
((((((...........))))	chr1:24973512-24973745(+)$1	1	126	147	19.3672
((((.............))))	chr10:25890913-25891128(+)$1	1	22	43	22.0441
(.(((...........)))..	chr19:32875662-32875894(+)$1	1	182	203	21.2458
.((((............))))	chr5:148731925-148732147(+)$1	1	97	118	21.9375
(((((..............))	chr12:108105993-108106288(+)$1	1	18	39	21.7067
(((((.............)))	chr11:43467437-43467737(+)$1	1	180	201	23.3951
(((((.............)))	chr6:168364194-168364407(+)$1	1	83	104	23.2266
(.(((............))))	chrX:23412429-23412673(+)$1	1	203	224	22.8786
((((((...........))))	chr10:12206545-12206768(+)$1	1	168	189	21.3774
(((((................	chr11:85345558-85345770(+)$1	1	34	55	18.9759
.((((............))))	chr17:2226516-2226767(-)$1	1	40	61	23.1098
.((((.............)))	chr17:7215912-7216177(-)$1	1	170	191	23.4928
(((((............))))	chr12:93802272-93802530(-)$1	1	227	248	22.0440
((((((...........))))	chr7:17382824-17383053(+)$1	1	41	62	20.7937
(((((............))))	chr9:135866517-135866734(+)$1	1	186	207	22.0440
(((((...........)))))	chr9:116148785-116149011(-)$1	1	137	158	21.1330
.((((...........)))).	chr19:3468224-3468491(+)$1	1	174	195	19.3840
...((..............))	chr5:140591437-140591651(+)$1	1	16	37	20.0933
(((((.............)))	chr3:167401806-167402072(-)$1	1	72	93	23.2266
.((((...........)))).	chr19:17462366-17462585(-)$1	1	101	122	21.5442
(((((..............))	chr2:99811395-99811619(+)$1	1	38	59	21.6716
(((((............))))	chr1:10436787-10437032(+)$1	1	37	58	22.6654
.((((............))))	chr15:48415441-48415652(+)$1	1	107	128	21.9375
..(((............))).	chr15:34678951-34679245(-)$1	1	118	139	23.0926
(((((.............)))	chr2:143704740-143704974(+)$1	1	200	221	23.2655

#PSSM
e : 0.15	[ : 0.13	f : 0.13	g : 0.12	d : 0.07	: : 0.07	h : 0.07	! : 0.04	" : 0.04	= : 0.03	i : 0.03	c : 0.03	% : 0.01	# : 0.01	
d : 0.30	e : 0.16	f : 0.13	g : 0.12	c : 0.06	h : 0.04	! : 0.03	= : 0.03	i : 0.03	[ : 0.03	: : 0.01	" : 0.01	
d : 0.30	e : 0.16	c : 0.13	f : 0.13	g : 0.12	h : 0.04	= : 0.03	i : 0.03	" : 0.01	
d : 0.29	e : 0.16	c : 0.13	f : 0.13	g : 0.12	h : 0.04	[ : 0.03	i : 0.03	= : 0.01	b : 0.01	
d : 0.23	e : 0.16	g : 0.12	v : 0.10	f : 0.09	c : 0.07	w : 0.06	h : 0.04	b : 0.03	i : 0.03	= : 0.01	a : 0.01	
v : 0.29	u : 0.21	w : 0.18	t : 0.09	g : 0.06	f : 0.04	y : 0.04	e : 0.03	b : 0.01	h : 0.01	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	t : 0.26	u : 0.21	w : 0.18	y : 0.04	
v : 0.29	u : 0.21	w : 0.18	t : 0.16	y : 0.04	d : 0.04	c : 0.03	e : 0.01	
w : 0.18	v : 0.18	d : 0.15	f : 0.13	c : 0.12	g : 0.07	e : 0.06	y : 0.04	b : 0.01	h : 0.01	
d : 0.26	c : 0.13	f : 0.13	w : 0.12	e : 0.12	g : 0.10	y : 0.04	= : 0.01	b : 0.01	a : 0.01	h : 0.01	
d : 0.30	e : 0.16	f : 0.13	g : 0.12	c : 0.10	y : 0.04	h : 0.03	= : 0.03	2 : 0.01	3 : 0.01	b : 0.01	
d : 0.26	e : 0.16	f : 0.13	g : 0.13	c : 0.04	y : 0.04	] : 0.04	h : 0.03	= : 0.03	3 : 0.03	2 : 0.01	4 : 0.01	: : 0.01	b : 0.01	

#score	1421.074349719235
#seq	65
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013c_hg19_UTR_m3_run2.txt

#BEAR
eeeeqqqqqqqqeee	chr4:53476612-53476832(-)$1	220	189	204	13.6578
ddddqqqqqqqqddd	chr2:100055226-100055461(-)$1	235	65	80	13.0719
eeeeqqqqqqqqeee	chr1:145763512-145763729(-)$1	217	87	102	13.6578
"cccqqqqqqqqccc	chr12:111894970-111895209(-)$1	239	74	89	13.1269
b!!aqqqqqqqqa22	chr1:155172949-155173179(-)$1	230	147	162	11.8087
e[bbqqqqqqqqbb]	chr4:140429488-140429705(-)$1	217	133	148	12.2331
ccccqqqqqqqqccc	chr17:1399022-1399248(-)$1	226	107	122	13.2171
ddddqqqqqqqqddd	chr22:40730555-40730774(+)$1	219	105	120	13.0719
hhhhqqqqqqqqhhh	chr2:25344434-25344653(-)$1	219	146	161	12.1272
ggggqqqqqqqqggg	chr6:90077456-90077684(-)$1	228	118	133	13.2028
eeeeqqqqqqqqeee	chr12:14939362-14939582(-)$1	220	201	216	13.6578
dcccqqqqqqqqccc	chr1:201123175-201123432(-)$1	257	10	25	13.2504
ffffqqqqqqqqfff	chr12:82152140-82152373(-)$1	233	145	160	12.9467
eeeeqqqqqqqqeee	chr5:132151554-132151780(+)$1	226	83	98	13.6578
ggggqqqqqqqqggg	chr9:20995481-20995697(-)$1	216	103	118	13.2028
eeeeqqqqqqqqeee	chr8:134488660-134488882(+)$1	222	161	176	13.6578
ffffqqqqqqqqfff	chr5:149781353-149781569(+)$1	216	11	26	12.9467
ddddqqqqqqqqddd	chr1:21929640-21929858(-)$1	218	27	42	13.0719
ffffqqqqqqqqfff	chr2:68488230-68488446(+)$1	216	190	205	12.9467
ffffqqqqqqqqfff	chr14:77607724-77607962(+)$1	238	204	219	12.9467
iiiiqqqqqqqqiii	chr2:179390851-179391066(+)$1	215	15	30	12.9975
eeeeqqqqqqqqeee	chr19:39077946-39078211(+)$1	265	21	36	13.6578
ffffqqqqqqqqfff	chr7:155571636-155571862(+)$1	226	178	193	12.9467
ffffqqqqqqqqfff	chr13:45606072-45606296(+)$1	224	49	64	12.9467
eeeeqqqqqqqqeee	chr16:29870513-29870732(-)$1	219	33	48	13.6578
eeeeqqqqqqqqeee	chr5:149782595-149782812(+)$1	217	80	95	13.6578
eeeeqqqqqqqqeee	chr14:21485488-21485714(-)$1	226	168	183	13.6578
ffbbqqqqqqqqbb]	chr17:74136510-74136727(-)$1	217	48	63	12.1184
hhhhqqqqqqqqhhh	chr2:80529061-80529276(-)$1	215	8	23	12.1272
!cccqqqqqqqqccc	chr18:32290270-32290499(+)$1	229	50	65	13.2789
eeeeqqqqqqqqeee	chr1:40026384-40026606(-)$1	222	140	155	13.6578
ddddqqqqqqqqddd	chr17:37688633-37688853(+)$1	220	18	33	13.0719
ddddqqqqqqqqddd	chr2:65248201-65248427(+)$1	226	196	211	13.0719
fcccqqqqqqqqccc	chr17:37077620-37077849(+)$1	229	162	177	13.2418
eeeeqqqqqqqqeee	chr7:87835677-87835892(-)$1	215	57	72	13.6578
hhhhqqqqqqqqhhh	chr15:52103156-52103398(+)$1	242	30	45	12.1272
[cccqqqqqqqqccc	chr12:46355507-46355725(-)$1	218	163	178	13.3042
ggggqqqqqqqqggg	chr22:19838590-19838811(-)$1	221	114	129	13.2028
:cccqqqqqqqqccc	chr7:102193528-102193763(-)$1	235	41	56	12.1602
ddddqqqqqqqqddd	chr21:45717549-45717768(-)$1	219	106	121	13.0719
ggggqqqqqqqqggg	chr2:169984001-169984216(+)$1	215	102	117	13.2028
eeeeqqqqqqqqeee	chr11:110448096-110448317(-)$1	221	8	23	13.6578
[cccqqqqqqqqccc	chr12:89742391-89742608(+)$1	217	165	180	13.3042
[cccqqqqqqqqccc	chr15:74338750-74338968(+)$1	218	192	207	13.3042
eeeeqqqqqqqqeee	chr5:14697974-14698198(+)$1	224	39	54	13.6578
eeeeqqqqqqqqeee	chr7:50658396-50658620(-)$1	224	78	93	13.6578
ffffqqqqqqqqfff	chr17:56050631-56050857(-)$1	226	147	162	12.9467
ddddqqqqqqqqddd	chr14:99863998-99864217(-)$1	219	5	20	13.0719
eeeeqqqqqqqqeee	chr2:191109574-191109791(-)$1	217	57	72	13.6578
eeeeqqqqqqqqeee	chr14:68116789-68117010(-)$1	221	193	208	13.6578
ddddqqqqqqqqddd	chr20:18004966-18005200(-)$1	234	190	205	13.0719
eeeeqqqqqqqqeee	chr15:80888633-80888879(+)$1	246	176	191	13.6578
eeeeqqqqqqqqeee	chr7:102193579-102193812(-)$1	233	157	172	13.6578
ffffqqqqqqqqfff	chr17:28793251-28793467(+)$1	216	95	110	12.9467
ddddqqqqqqqqddd	chr11:1774066-1774299(-)$1	233	171	186	13.0719
ddddqqqqqqqqddd	chr15:40831223-40831442(-)$1	219	85	100	13.0719
!cccqqqqqqqqccc	chr7:138916224-138916442(+)$1	218	25	40	13.2789
ddddqqqqqqqqddd	chr14:21492650-21492867(-)$1	217	132	147	13.0719
ffffqqqqqqqqfff	chr6:90342454-90342680(-)$1	226	9	24	12.9467
ddddqqqqqqqqddd	chr9:33464785-33465016(-)$1	231	113	128	13.0719
ffffqqqqqqqqfff	chr9:20413620-20413839(-)$1	219	182	197	12.9467
[cccqqqqqqqqccc	chr7:36493103-36493339(+)$1	236	74	89	13.3042
ffffqqqqqqqqfff	chr1:27662751-27662976(+)$1	225	116	131	12.9467
!!bbqqqqqqqqbb2	chr12:122691933-122692155(+)$1	222	43	58	11.8609
ccbbqqqqqqqqbb]	chr11:46342190-46342406(+)$1	216	110	125	12.1387
ggggqqqqqqqqggg	chr2:30382846-30383063(+)$1	217	5	20	13.2028
eebbqqqqqqqqbb]	chr15:31669815-31670041(+)$1	226	109	124	12.3527
ddddqqqqqqqqddd	chr7:44259742-44259973(-)$1	231	81	96	13.0719

#otherMatches

#Seq PSSM
CCUGUAUUUCUUCAG	chr4:53476612-53476832(-)$1	220	189	204	13.6578
AGAACUAAUUCUUUC	chr2:100055226-100055461(-)$1	235	65	80	13.0719
AAGCUAUUACUUGUU	chr1:145763512-145763729(-)$1	217	87	102	13.6578
UGCGCACCCUAACGC	chr12:111894970-111895209(-)$1	239	74	89	13.1269
GGAUGAUAUACGAGA	chr1:155172949-155173179(-)$1	230	147	162	11.8087
GACACAAAGGAAUGA	chr4:140429488-140429705(-)$1	217	133	148	12.2331
GGGUGAAGCACAGCC	chr17:1399022-1399248(-)$1	226	107	122	13.2171
UCCUACCAAAUCAGG	chr22:40730555-40730774(+)$1	219	105	120	13.0719
GGUGACCCACCAUGC	chr2:25344434-25344653(-)$1	219	146	161	12.1272
AAAUCCAUUGUCAUU	chr6:90077456-90077684(-)$1	228	118	133	13.2028
AUAAUACCUAUUUUA	chr12:14939362-14939582(-)$1	220	201	216	13.6578
GAGCGGGGAGGAGCU	chr1:201123175-201123432(-)$1	257	10	25	13.2504
GUUGUCAUUGAUCAA	chr12:82152140-82152373(-)$1	233	145	160	12.9467
ACAGAAUAACGAUUG	chr5:132151554-132151780(+)$1	226	83	98	13.6578
UUCUUAAACUCUGGG	chr9:20995481-20995697(-)$1	216	103	118	13.2028
GGCACAGAAGGUUGU	chr8:134488660-134488882(+)$1	222	161	176	13.6578
CCUGCAGGUAAAUAG	chr5:149781353-149781569(+)$1	216	11	26	12.9467
AGCCAAUUUGGAGGU	chr1:21929640-21929858(-)$1	218	27	42	13.0719
AGUUUGACUUUUGAU	chr2:68488230-68488446(+)$1	216	190	205	12.9467
UGAGGAAAUCAACUC	chr14:77607724-77607962(+)$1	238	204	219	12.9467
CAGCUUUAUUUUGUU	chr2:179390851-179391066(+)$1	215	15	30	12.9975
UCUUAUGUCUGGAAG	chr19:39077946-39078211(+)$1	265	21	36	13.6578
GGCCUCAGCUAUGGC	chr7:155571636-155571862(+)$1	226	178	193	12.9467
GUUCUUACCAUUGAA	chr13:45606072-45606296(+)$1	224	49	64	12.9467
GCCCCCUCCUUCGGG	chr16:29870513-29870732(-)$1	219	33	48	13.6578
CUGCUUACCACUGCA	chr5:149782595-149782812(+)$1	217	80	95	13.6578
AGGGACCCAGACCCC	chr14:21485488-21485714(-)$1	226	168	183	13.6578
GGGUAGUGCUCAGCU	chr17:74136510-74136727(-)$1	217	48	63	12.1184
UUGACUGAAACUUUA	chr2:80529061-80529276(-)$1	215	8	23	12.1272
UGUAAGGUCAAAUAC	chr18:32290270-32290499(+)$1	229	50	65	13.2789
GUUUUACUCUAUGAA	chr1:40026384-40026606(-)$1	222	140	155	13.6578
CCUCCAUUCCUAGAG	chr17:37688633-37688853(+)$1	220	18	33	13.0719
GGCCCAGUCGCUGGC	chr2:65248201-65248427(+)$1	226	196	211	13.0719
UUUGCCUCUGUCCAA	chr17:37077620-37077849(+)$1	229	162	177	13.2418
CUGAUUUUUCUUUCA	chr7:87835677-87835892(-)$1	215	57	72	13.6578
UUUUUACCUUAUGAA	chr15:52103156-52103398(+)$1	242	30	45	12.1272
GUCUAUUAGAAAAGG	chr12:46355507-46355725(-)$1	218	163	178	13.3042
GGUUCUGAACACAGC	chr22:19838590-19838811(-)$1	221	114	129	13.2028
CUAGUCUCCGUUCUG	chr7:102193528-102193763(-)$1	235	41	56	12.1602
GUGUCCUUCUCAGCA	chr21:45717549-45717768(-)$1	219	106	121	13.0719
CAUUCUAAUAUAAAU	chr2:169984001-169984216(+)$1	215	102	117	13.2028
GGGACUCCCCUUUCC	chr11:110448096-110448317(-)$1	221	8	23	13.6578
AUUUUUUUUUCCAAA	chr12:89742391-89742608(+)$1	217	165	180	13.3042
CGCUGGUUCUGAAGC	chr15:74338750-74338968(+)$1	218	192	207	13.3042
AGUAAUAUUUUAUAC	chr5:14697974-14698198(+)$1	224	39	54	13.6578
AGUUUUGUAUGUAGC	chr7:50658396-50658620(-)$1	224	78	93	13.6578
UUGUUCAACUUUGUA	chr17:56050631-56050857(-)$1	226	147	162	12.9467
CCACAGCUUCACGUG	chr14:99863998-99864217(-)$1	219	5	20	13.0719
CACUUACACAUUGGU	chr2:191109574-191109791(-)$1	217	57	72	13.6578
CUUGUACUUGAUCAA	chr14:68116789-68117010(-)$1	221	193	208	13.6578
GGGAUUUUUUUUUCC	chr20:18004966-18005200(-)$1	234	190	205	13.0719
UUCAAGACAAACUGG	chr15:80888633-80888879(+)$1	246	176	191	13.6578
UCUCAAGCCUAGGAG	chr7:102193579-102193812(-)$1	233	157	172	13.6578
AGGGGUUUACCACCU	chr17:28793251-28793467(+)$1	216	95	110	12.9467
GGGCAUGUAUUGGCC	chr11:1774066-1774299(-)$1	233	171	186	13.0719
GCUGGGGAGAAACAG	chr15:40831223-40831442(-)$1	219	85	100	13.0719
UAGCGUUCAUUAGCU	chr7:138916224-138916442(+)$1	218	25	40	13.2789
GCACCAAUCUUUGUG	chr14:21492650-21492867(-)$1	217	132	147	13.0719
UUUUGGUAAGUGAAA	chr6:90342454-90342680(-)$1	226	9	24	12.9467
UUGUCAACCUCAAUA	chr9:33464785-33465016(-)$1	231	113	128	13.0719
UUGUAAUAAAGAAUG	chr9:20413620-20413839(-)$1	219	182	197	12.9467
aaauuauaaaauauu	chr7:36493103-36493339(+)$1	236	74	89	13.3042
GGACAAUAAAGAGUU	chr1:27662751-27662976(+)$1	225	116	131	12.9467
AUUCUCUAUCGUGAU	chr12:122691933-122692155(+)$1	222	43	58	11.8609
UGCCAAGACCCAGGA	chr11:46342190-46342406(+)$1	216	110	125	12.1387
UGUACCCUCACAUAC	chr2:30382846-30383063(+)$1	217	5	20	13.2028
UGGCCUUGGCUUGCU	chr15:31669815-31670041(+)$1	226	109	124	12.3527
GCUGGCCAAGAACAG	chr7:44259742-44259973(-)$1	231	81	96	13.0719

#DB
((((........)))	chr4:53476612-53476832(-)$1	1	189	204	13.6578
((((........)))	chr2:100055226-100055461(-)$1	1	65	80	13.0719
((((........)))	chr1:145763512-145763729(-)$1	1	87	102	13.6578
.(((........)))	chr12:111894970-111895209(-)$1	1	74	89	13.1269
(..(........)..	chr1:155172949-155173179(-)$1	1	147	162	11.8087
(.((........)).	chr4:140429488-140429705(-)$1	1	133	148	12.2331
((((........)))	chr17:1399022-1399248(-)$1	1	107	122	13.2171
((((........)))	chr22:40730555-40730774(+)$1	1	105	120	13.0719
((((........)))	chr2:25344434-25344653(-)$1	1	146	161	12.1272
((((........)))	chr6:90077456-90077684(-)$1	1	118	133	13.2028
((((........)))	chr12:14939362-14939582(-)$1	1	201	216	13.6578
((((........)))	chr1:201123175-201123432(-)$1	1	10	25	13.2504
((((........)))	chr12:82152140-82152373(-)$1	1	145	160	12.9467
((((........)))	chr5:132151554-132151780(+)$1	1	83	98	13.6578
((((........)))	chr9:20995481-20995697(-)$1	1	103	118	13.2028
((((........)))	chr8:134488660-134488882(+)$1	1	161	176	13.6578
((((........)))	chr5:149781353-149781569(+)$1	1	11	26	12.9467
((((........)))	chr1:21929640-21929858(-)$1	1	27	42	13.0719
((((........)))	chr2:68488230-68488446(+)$1	1	190	205	12.9467
((((........)))	chr14:77607724-77607962(+)$1	1	204	219	12.9467
((((........)))	chr2:179390851-179391066(+)$1	1	15	30	12.9975
((((........)))	chr19:39077946-39078211(+)$1	1	21	36	13.6578
((((........)))	chr7:155571636-155571862(+)$1	1	178	193	12.9467
((((........)))	chr13:45606072-45606296(+)$1	1	49	64	12.9467
((((........)))	chr16:29870513-29870732(-)$1	1	33	48	13.6578
((((........)))	chr5:149782595-149782812(+)$1	1	80	95	13.6578
((((........)))	chr14:21485488-21485714(-)$1	1	168	183	13.6578
((((........)).	chr17:74136510-74136727(-)$1	1	48	63	12.1184
((((........)))	chr2:80529061-80529276(-)$1	1	8	23	12.1272
.(((........)))	chr18:32290270-32290499(+)$1	1	50	65	13.2789
((((........)))	chr1:40026384-40026606(-)$1	1	140	155	13.6578
((((........)))	chr17:37688633-37688853(+)$1	1	18	33	13.0719
((((........)))	chr2:65248201-65248427(+)$1	1	196	211	13.0719
((((........)))	chr17:37077620-37077849(+)$1	1	162	177	13.2418
((((........)))	chr7:87835677-87835892(-)$1	1	57	72	13.6578
((((........)))	chr15:52103156-52103398(+)$1	1	30	45	12.1272
.(((........)))	chr12:46355507-46355725(-)$1	1	163	178	13.3042
((((........)))	chr22:19838590-19838811(-)$1	1	114	129	13.2028
.(((........)))	chr7:102193528-102193763(-)$1	1	41	56	12.1602
((((........)))	chr21:45717549-45717768(-)$1	1	106	121	13.0719
((((........)))	chr2:169984001-169984216(+)$1	1	102	117	13.2028
((((........)))	chr11:110448096-110448317(-)$1	1	8	23	13.6578
.(((........)))	chr12:89742391-89742608(+)$1	1	165	180	13.3042
.(((........)))	chr15:74338750-74338968(+)$1	1	192	207	13.3042
((((........)))	chr5:14697974-14698198(+)$1	1	39	54	13.6578
((((........)))	chr7:50658396-50658620(-)$1	1	78	93	13.6578
((((........)))	chr17:56050631-56050857(-)$1	1	147	162	12.9467
((((........)))	chr14:99863998-99864217(-)$1	1	5	20	13.0719
((((........)))	chr2:191109574-191109791(-)$1	1	57	72	13.6578
((((........)))	chr14:68116789-68117010(-)$1	1	193	208	13.6578
((((........)))	chr20:18004966-18005200(-)$1	1	190	205	13.0719
((((........)))	chr15:80888633-80888879(+)$1	1	176	191	13.6578
((((........)))	chr7:102193579-102193812(-)$1	1	157	172	13.6578
((((........)))	chr17:28793251-28793467(+)$1	1	95	110	12.9467
((((........)))	chr11:1774066-1774299(-)$1	1	171	186	13.0719
((((........)))	chr15:40831223-40831442(-)$1	1	85	100	13.0719
.(((........)))	chr7:138916224-138916442(+)$1	1	25	40	13.2789
((((........)))	chr14:21492650-21492867(-)$1	1	132	147	13.0719
((((........)))	chr6:90342454-90342680(-)$1	1	9	24	12.9467
((((........)))	chr9:33464785-33465016(-)$1	1	113	128	13.0719
((((........)))	chr9:20413620-20413839(-)$1	1	182	197	12.9467
.(((........)))	chr7:36493103-36493339(+)$1	1	74	89	13.3042
((((........)))	chr1:27662751-27662976(+)$1	1	116	131	12.9467
..((........)).	chr12:122691933-122692155(+)$1	1	43	58	11.8609
((((........)).	chr11:46342190-46342406(+)$1	1	110	125	12.1387
((((........)))	chr2:30382846-30383063(+)$1	1	5	20	13.2028
((((........)).	chr15:31669815-31670041(+)$1	1	109	124	12.3527
((((........)))	chr7:44259742-44259973(-)$1	1	81	96	13.0719

#PSSM
e : 0.29	d : 0.20	f : 0.19	g : 0.07	[ : 0.05	h : 0.04	! : 0.04	c : 0.02	" : 0.01	b : 0.01	i : 0.01	: : 0.01	
e : 0.27	d : 0.19	c : 0.17	f : 0.17	g : 0.07	h : 0.04	! : 0.02	[ : 0.01	i : 0.01	
e : 0.26	d : 0.19	c : 0.16	f : 0.16	b : 0.07	g : 0.07	h : 0.04	! : 0.01	i : 0.01	
e : 0.26	d : 0.19	c : 0.16	f : 0.16	b : 0.07	g : 0.07	h : 0.04	a : 0.01	i : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
e : 0.26	d : 0.19	c : 0.16	f : 0.16	b : 0.07	g : 0.07	h : 0.04	a : 0.01	i : 0.01	
e : 0.26	d : 0.19	c : 0.16	f : 0.16	b : 0.07	g : 0.07	h : 0.04	2 : 0.01	i : 0.01	
e : 0.26	d : 0.19	c : 0.16	f : 0.16	g : 0.07	] : 0.05	h : 0.04	2 : 0.02	i : 0.01	

#score	890.8702229178173
#seq	68
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m1_run1.txt

#BEAR
=========[ccc[ccclllccc22ccc========	chr3:71019831-71020056(-)$1	225	45	81	14.4390
iiiiiiiii[ffffffnnnnnffffff]iiiiiiii	chr15:68500167-68500382(-)$1	215	149	185	11.4205
!bb[ccc[ccc"""ccclllccc333cccccc22bb	chr18:33572933-33573156(+)$1	223	129	165	11.3383
ggggg!!hhhhhhhhoooooohhhhhhhh22ggggg	chr10:1063366-1063584(+)$1	218	87	123	13.3843
e####bb[gggggggooooooggggggg]bbeeeee	chr15:101419509-101419725(-)$1	216	11	47	14.0905
:dddd!!dddd[cccooooooccc22dddd]dddd:	chr1:162338335-162338552(+)$1	217	78	114	11.8515
gggg!!a[ccc!!cccmmmmccc22ccc22a22ggg	chr21:46934759-46934981(-)$1	222	101	137	12.6026
[dddd[ggggggg[aooooooa]gggggggddddgg	chr6:32939453-32939676(+)$1	223	145	181	14.4257
""ffffff####ccc[aooooooa]ccc333fffff	chr14:23794762-23794992(+)$1	230	102	138	13.1424
fff"""dddd[ddddoooooodddd333dddd]fff	chr3:5221958-5222177(+)$1	219	82	118	12.7064
$$ggggggg"""cccmmmmccc333ggggggg]fff	chr9:132996563-132996790(+)$1	227	140	176	12.7572
dd"""eeeee!!cccooooooccc22eeeee]dddd	chr21:42648472-42648690(+)$1	218	37	73	15.1109
iiiiiiiii"""cccqqqqqqqqccc]iiiiiiiii	chr14:90872706-90872926(+)$1	220	126	162	11.7790
cc####bb[bb!!bboooooobb22bb]bb22cccG	chr22:39778237-39778457(+)$1	220	4	40	13.0216
!!ggggggg####ddddmmmmddddggggggg4444	chr22:39619844-39620070(-)$1	226	165	201	11.3311
===========ddddoooooodddd22=========	chr18:2918549-2918769(-)$1	220	121	157	16.0702
iii"""bb!!ccc[cccmmmmccc333ccc22bb]i	chr1:155882814-155883036(-)$1	222	169	205	12.6484
eeee!!cccffffffooooooffffff]ccceeeee	chr3:183638392-183638614(-)$1	222	104	140	12.1398
=========[a[cccooooooccc]a==========	chr5:140053557-140053792(-)$1	235	158	194	18.6085
e[ccc!!dddd[cccooooooccc]ddddccc]eee	chr20:44048760-44048977(-)$1	217	40	76	14.4828
+++eeeee[a!!cccooooooccc]a]eeeeehhhh	chr14:23341034-23341258(+)$1	224	106	142	12.7120
gg####bb"""ddddoooooodddd]bbggggggg]	chr14:70517633-70517852(-)$1	219	21	57	14.1184
""bb!!ccc"""ccclllccc]ccc22bb4444ccc	chr20:34204996-34205224(+)$1	228	159	195	11.9011
[iiiiiiiii!!ddddmmmmdddd22iiiiiiiii]	chr22:39827067-39827297(+)$1	230	22	58	12.8819
b!!bb[iiiiiiiiiooooooiiiiiiiii]bb22b	chr18:8782072-8782295(+)$1	223	185	221	14.7667
"""eeeeegggggggooooooggggggg]eeeee33	chr1:224346032-224346249(+)$1	217	30	66	14.4854
hddddeeeee!!cccooooooccc22eeeee]dddd	chr16:5066230-5066451(+)$1	221	74	110	13.8826
""iiiiiiiii!!bbmmmmbb]iiiiiiiiieeeee	chr3:33481222-33481450(-)$1	228	147	183	11.6336
^^^^^gggggggcccooooooccc:===========	chr14:100143945-100144161(-)$1	216	77	113	15.3088
dd!!bb!!gggggggoooooogggggggbb22dddd	chr9:132997381-132997610(+)$1	229	155	191	14.0944
[ccc!!bb!!eeeeeooooooeeeee]bb22ccc]d	chr17:75282325-75282545(-)$1	220	18	54	13.4791
$$ggggggg"""cccmmmmcccggggggg22=====	chr5:149933276-149933501(+)$1	225	43	79	13.3141
[bb[ccc[a[eeeeeooooooeeeee]accc]bbcc	chr4:3243402-3243620(+)$1	218	153	189	12.7413
[a[ggggggga[cccmmmmccc]a]ggggggg]a]b	chr6:42985225-42985458(+)$1	233	187	223	12.7278
dd####eeeee[cccooooooccc]eeeeedddd]d	chr9:101495517-101495734(-)$1	217	39	75	14.8900
ffccc[iiiiiiiiiooooooiiiiiiiii4444cc	chr7:100217952-100218175(-)$1	223	22	58	15.7792
[a####eeeee[cccooooooccc]eeeee333add	chr18:32915989-32916211(-)$1	222	174	210	16.6569
:a[a!!eeeee!!bboooooobb22eeeee22a]ag	chr6:163992906-163993127(+)$1	221	135	171	13.9504
fff$$$$$gggggggoooooogggggggffffffcc	chrX:103296575-103296792(-)$1	217	94	130	13.2584
ff"""bb[ccc!!bboooooobb]ccc]bb333fff	chr16:1827016-1827242(+)$1	226	187	223	14.3390
ggggg"""ccc!!bboooooobb22ccc333ggggg	chr12:31146988-31147215(-)$1	227	172	208	15.9953
iiiiiiii####cccrrrrrrrrrccc333iiiiii	chr4:83848895-83849123(-)$1	228	74	110	12.8952
!!gggggggeeeee[ccclllccc]eeeee]ggggg	chr6:13287946-13288167(+)$1	221	37	73	11.5845
iiiiiii####bbacccmmmmccc]a]bb22iiiii	chr10:118608911-118609129(-)$1	218	72	108	12.1137
ddddeeeee[eeeeeooooooeeeeeeeeee22ddd	chr17:74385598-74385820(-)$1	222	120	156	11.4681
iiiiiiiii[ccc!!bbmmmmbb22ccciiiiiiii	chr17:3414272-3414488(+)$1	216	104	140	12.0635
[ffffff"""ddddbboooooobb]dddd333ffff	chrX:134429632-134429847(+)$1	215	6	42	11.7760
gggg####gggggggooooooggggggg4444gggg	chr2:86442318-86442544(-)$1	226	142	178	16.0943
ddd[a[eeeee!!bboooooobb22eeeeeadddd]	chr3:13547434-13547651(-)$1	217	33	69	13.3656
=============ssssssssss=============	chr1:33240376-33240597(+)$1	221	131	167	12.0212
!a[bb[dddd"""bboooooobb22dddd22bb22a	chr10:78318401-78318616(+)$1	215	127	163	13.1878
mmbb===========oooooo===========:::g	chr1:32371999-32372220(-)$1	221	89	125	12.3256
iiiiiiiii[ccc[annnnnaccciiiiiiiii:==	chr19:19362703-19362927(+)$1	224	158	194	12.8793
=========!!ddddoooooodddd22=========	chr2:55776284-55776518(-)$1	234	54	90	16.3334
[dddd!!bb[bbcccooooooccc4444bb]bb22d	chr2:97504040-97504260(-)$1	220	165	201	13.1232
ii####dddd!!cccmmmmccc4444dddd22iiii	chr17:80797812-80798027(-)$1	215	7	43	12.2251
eeeee[aggggggg[annnnna]ggggggg]a333e	chr15:69564287-69564508(+)$1	221	150	186	11.8343
###ggggggg"""cccmmmmcccggggggg333ddd	chr1:26604232-26604450(-)$1	218	181	217	13.5855
==[bb"""gggggggnnnnnggggggg333bb]===	chr3:49706127-49706350(+)$1	223	37	73	12.0379

#otherMatches

#Seq PSSM
GGAACUCAGCAGUCGACUGUGUUUAACUUUGAGUUU	chr3:71019831-71020056(-)$1	225	45	81	14.4390
CGGAUUCUGUUUUAGAGUGUUUCUGGGCCAGGAUCC	chr15:68500167-68500382(-)$1	215	149	185	11.4205
ACCUGUCUCCAUCUCUUGCAAAGUCCUGGGACCUGG	chr18:33572933-33573156(+)$1	223	129	165	11.3383
UUUUGAUGGAGAAAAACCUUAUUUUCUUUUGUAAGA	chr10:1063366-1063584(+)$1	218	87	123	13.3843
GCUGAGCCGCGGGGCCACGGCGCCCCGCUGCCUCCC	chr15:101419509-101419725(-)$1	216	11	47	14.0905
UGCAAUUGUCUUAUCUUUUAUGAUCUAGGCUUUGCC	chr1:162338335-162338552(+)$1	217	78	114	11.8515
CCUCAGCUGCUCCCACACUUGUGCCAGCCCGGAGGG	chr21:46934759-46934981(-)$1	222	101	137	12.6026
AGUGCUGGAGGCUCUGGGGCGAUGGCUUCCGCACCU	chr6:32939453-32939676(+)$1	223	145	181	14.4257
CUGGAAGGACACCAAACUGUUCUGCUUGUUACCUUC	chr14:23794762-23794992(+)$1	230	102	138	13.1424
GGUUCUGUAAAUGAAGGGAUAUUUAAACUUGCUACU	chr3:5221958-5222177(+)$1	219	82	118	12.7064
CCCUGGACCAGAGGUAGGAGCCCAAGGUCCGGCCcu	chr9:132996563-132996790(+)$1	227	140	176	12.7572
GAAAAAACUAUUCUAUUUCACUAGCUUAGUUGUCUC	chr21:42648472-42648690(+)$1	218	37	73	15.1109
GGCUGCUAGCAAGGCAGUGAGAAGCUCUUGGCAGCC	chr14:90872706-90872926(+)$1	220	126	162	11.7790
GCAGAAAUGGCCACUGGAAAGGGGAGCGAUGAGCUG	chr22:39778237-39778457(+)$1	220	4	40	13.0216
AAAGAUCCCCAAGACCCCCUGGGGUGGGAUCUGAGC	chr22:39619844-39620070(-)$1	226	165	201	11.3311
AAGGCUCAUGUUCCCAGAGAAGGGACCACAUGAGCC	chr18:2918549-2918769(-)$1	220	121	157	16.0702
UAAUUUCAUUAUAAAUAAAUCUAUAAAUAUUCUGCU	chr1:155882814-155883036(-)$1	222	169	205	12.6484
CCACGGCCGCUCCAGGGGUGGCUGGAGACGGGUGGG	chr3:183638392-183638614(-)$1	222	104	140	12.1398
GCCCAGGAGGCUUAGUCCAGUCUGUGCUCCUGGGCU	chr5:140053557-140053792(-)$1	235	158	194	18.6085
GGCCUAGGCCUAGUCCACAUAGAUAAGGCAGGGCUG	chr20:44048760-44048977(-)$1	217	40	76	14.4828
AAGUGGUCUCAAACCCCGGCAGGUGGCGACCAGGCC	chr14:23341034-23341258(+)$1	224	106	142	12.7120
UUAACAGACUACGGUGGACAAACUGAUCAAGAAGAC	chr14:70517633-70517852(-)$1	219	21	57	14.1184
UUUCUGAGUACGGGCCAGGCCAGCUGCGAUCCCCUC	chr20:34204996-34205224(+)$1	228	159	195	11.9011
GGGCCUCUGCCGGCUGAGGGUAGCAAGCAGGGGUUG	chr22:39827067-39827297(+)$1	230	22	58	12.8819
ACGAGGGCUGUGGGAUUUGACUCCCGCAGUGCUGUU	chr18:8782072-8782295(+)$1	223	185	221	14.7667
UAUACAUGUUUUCAGUUCUCUUUGGGGGCCAUGUCC	chr1:224346032-224346249(+)$1	217	30	66	14.4854
GCCAGUCAGGGGUCACCAACUUGAAGCCUGAUCUGG	chr16:5066230-5066451(+)$1	221	74	110	13.8826
CCGGGCUGGUGCACGACUUCGACGCCAGCCUCUCGG	chr3:33481222-33481450(-)$1	228	147	183	11.6336
AAUCCAGCUCUGAGCAAAACAGCUUCUGGGGCCAGG	chr14:100143945-100144161(-)$1	216	77	113	15.3088
AGCACCAACGGCUGAAGUUUCUCAGCUGGGCUCUGA	chr9:132997381-132997610(+)$1	229	155	191	14.0944
GUACCUGUCCUGGCUUGAGCUGGUCACACUUGUGGG	chr17:75282325-75282545(-)$1	220	18	54	13.4791
GGGAGACAGACUGGACAUUUCCCUGUUUCGAGCCAG	chr5:149933276-149933501(+)$1	225	43	79	13.3141
UCCCCCAGCCAGGACCACCUCGUCCUCGUGGCGGGG	chr4:3243402-3243620(+)$1	218	153	189	12.7413
UGCUCUAUGCCUUUGACGUCAGUGAGUAUGGAUCUC	chr6:42985225-42985458(+)$1	233	187	223	12.7278
GGCAUUGAGCUGAGGCUCCACCCUGAGCUCUCCUGC	chr9:101495517-101495734(-)$1	217	39	75	14.8900
CAGCUCUGUUAGUGGGAGAGAUCGCUGGCACCAUAG	chr7:100217952-100218175(-)$1	223	22	58	15.7792
AGCAUUCCUCAGGGGAGGUCACCUGUGAGGUUCCCA	chr18:32915989-32916211(-)$1	222	174	210	16.6569
AGGAUUUUUGCCACGUUACCUUGAUGCAAAUUUGCC	chr6:163992906-163993127(+)$1	221	135	171	13.9504
UGUAAUAUUUUUCUAAUAAUCUGGAAAAACAGAAAG	chrX:103296575-103296792(-)$1	217	94	130	13.2584
CAACUCAUGCUCAGGACCCAGCCCAGCUUGUUGUGU	chr16:1827016-1827242(+)$1	226	187	223	14.3390
CAAGCCCUGGGUUGUUCUACCACUGUCUGCCGCUUG	chr12:31146988-31147215(-)$1	227	172	208	15.9953
AAAUUGAAUUUUUCUUUAUUAUAUAGAUUUUUUAAU	chr4:83848895-83849123(-)$1	228	74	110	12.8952
GCCUGAGCUGAGCUGCCUUUCAGGAAGCUCUGGUUU	chr6:13287946-13288167(+)$1	221	37	73	11.5845
AGCGGGGUUUAGCCUGGGGUCCCACGAGCGUCCCUG	chr10:118608911-118609129(-)$1	218	72	108	12.1137
CAGUGCAUUGUACAUGUGGAGAUGUGAAUGCCUACU	chr17:74385598-74385820(-)$1	222	120	156	11.4681
CCUGAAAUUACUGAAAUGUCAAUCACGGAGUUUUAG	chr17:3414272-3414488(+)$1	216	104	140	12.0635
AUUUCUCAGGGGAUCGCUAAAACGAAUCUAAAGAGA	chrX:134429632-134429847(+)$1	215	6	42	11.7760
UUGCAAAAGGGUAUAGGAAAAUAUACCUAAAAGCGA	chr2:86442318-86442544(-)$1	226	142	178	16.0943
GUUAGAGCCUCGGGGUCUGGUCCAGGAGGCCAGCAU	chr3:13547434-13547651(-)$1	217	33	69	13.3656
UGAGUGAGACACAUGAAGAAAACUGUGUUUCAUUUA	chr1:33240376-33240597(+)$1	221	131	167	12.0212
GCCUCUGGCCCACUGAGUCAACACAGGCCUUGAAUG	chr10:78318401-78318616(+)$1	215	127	163	13.1878
AAGCCAGUUUGACAUAGAGAGAUGUCAGAUUGAUUU	chr1:32371999-32372220(-)$1	221	89	125	12.3256
Augugcgugugugucugcgugugccaugugcguggc	chr19:19362703-19362927(+)$1	224	158	194	12.8793
CAUGUUGAGUUUUCUACACCAGGAAUUUUCAAUAUG	chr2:55776284-55776518(-)$1	234	54	90	16.3334
UGGGCCCCUAAACGCCAGAAAGUGAAUCUUAAGAAG	chr2:97504040-97504260(-)$1	220	165	201	13.1232
GCAGCUCGGUGGGUGCAAACACAUGAAUCGUAGCUG	chr17:80797812-80798027(-)$1	215	7	43	12.2251
UUUGCAGAUGGAAAGGUAUUUUGUUUCUAUACAAAG	chr15:69564287-69564508(+)$1	221	150	186	11.8343
AAAGCCAGCUCAGUUCCCAAGAAGGCUGGCACAUGG	chr1:26604232-26604450(-)$1	218	181	217	13.5855
GUGGCACUGUCUAUCCAUCCGGUGGACUGGGCAGCA	chr3:49706127-49706350(+)$1	223	37	73	12.0379

#DB
(((((((((.(((.(((...)))..)))))))))))	chr3:71019831-71020056(-)$1	1	45	81	14.4390
(((((((((.((((((.....)))))).))))))))	chr15:68500167-68500382(-)$1	1	149	185	11.4205
.((.(((.(((...(((...)))...))))))..))	chr18:33572933-33573156(+)$1	1	129	165	11.3383
(((((..((((((((......))))))))..)))))	chr10:1063366-1063584(+)$1	1	87	123	13.3843
(....((.(((((((......))))))).)))))))	chr15:101419509-101419725(-)$1	1	11	47	14.0905
.((((..((((.(((......)))..)))).)))).	chr1:162338335-162338552(+)$1	1	78	114	11.8515
((((..(.(((..(((....)))..)))..)..)))	chr21:46934759-46934981(-)$1	1	101	137	12.6026
.((((.(((((((.(......).)))))))))))))	chr6:32939453-32939676(+)$1	1	145	181	14.4257
..((((((....(((.(......).)))...)))))	chr14:23794762-23794992(+)$1	1	102	138	13.1424
(((...((((.((((......))))...)))).)))	chr3:5221958-5222177(+)$1	1	82	118	12.7064
..(((((((...(((....)))...))))))).)))	chr9:132996563-132996790(+)$1	1	140	176	12.7572
((...(((((..(((......)))..))))).))))	chr21:42648472-42648690(+)$1	1	37	73	15.1109
(((((((((...(((........))).)))))))))	chr14:90872706-90872926(+)$1	1	126	162	11.7790
((....((.((..((......))..)).))..)))(	chr22:39778237-39778457(+)$1	1	4	40	13.0216
..(((((((....((((....)))))))))))....	chr22:39619844-39620070(-)$1	1	165	201	11.3311
(((((((((((((((......))))..)))))))))	chr18:2918549-2918769(-)$1	1	121	157	16.0702
(((...((..(((.(((....)))...)))..)).)	chr1:155882814-155883036(-)$1	1	169	205	12.6484
((((..(((((((((......)))))).))))))))	chr3:183638392-183638614(-)$1	1	104	140	12.1398
(((((((((.(.(((......))).)))))))))))	chr5:140053557-140053792(-)$1	1	158	194	18.6085
(.(((..((((.(((......))).))))))).)))	chr20:44048760-44048977(-)$1	1	40	76	14.4828
...(((((.(..(((......))).).)))))))))	chr14:23341034-23341258(+)$1	1	106	142	12.7120
((....((...((((......)))).))))))))).	chr14:70517633-70517852(-)$1	1	21	57	14.1184
..((..(((...(((...))).)))..))....)))	chr20:34204996-34205224(+)$1	1	159	195	11.9011
.(((((((((..((((....))))..))))))))).	chr22:39827067-39827297(+)$1	1	22	58	12.8819
(..((.(((((((((......))))))))).))..)	chr18:8782072-8782295(+)$1	1	185	221	14.7667
...((((((((((((......))))))).)))))..	chr1:224346032-224346249(+)$1	1	30	66	14.4854
((((((((((..(((......)))..))))).))))	chr16:5066230-5066451(+)$1	1	74	110	13.8826
..(((((((((..((....)).))))))))))))))	chr3:33481222-33481450(-)$1	1	147	183	11.6336
.....)))))))(((......))).(((((((((((	chr14:100143945-100144161(-)$1	1	77	113	15.3088
((..((..(((((((......)))))))))..))))	chr9:132997381-132997610(+)$1	1	155	191	14.0944
.(((..((..(((((......))))).))..))).)	chr17:75282325-75282545(-)$1	1	18	54	13.4791
..(((((((...(((....))))))))))..)))))	chr5:149933276-149933501(+)$1	1	43	79	13.3141
.((.(((.(.(((((......))))).)))).))))	chr4:3243402-3243620(+)$1	1	153	189	12.7413
.(.((((((((.(((....))).).))))))).).)	chr6:42985225-42985458(+)$1	1	187	223	12.7278
((....(((((.(((......))).))))))))).)	chr9:101495517-101495734(-)$1	1	39	75	14.8900
(((((.(((((((((......)))))))))....))	chr7:100217952-100218175(-)$1	1	22	58	15.7792
.(....(((((.(((......))).)))))...)))	chr18:32915989-32916211(-)$1	1	174	210	16.6569
.(.(..(((((..((......))..)))))..).)(	chr6:163992906-163993127(+)$1	1	135	171	13.9504
(((.....(((((((......)))))))))))))))	chrX:103296575-103296792(-)$1	1	94	130	13.2584
((...((.(((..((......)).))).))...)))	chr16:1827016-1827242(+)$1	1	187	223	14.3390
(((((...(((..((......))..)))...)))))	chr12:31146988-31147215(-)$1	1	172	208	15.9953
((((((((....(((.........)))...))))))	chr4:83848895-83849123(-)$1	1	74	110	12.8952
..((((((((((((.(((...))).))))).)))))	chr6:13287946-13288167(+)$1	1	37	73	11.5845
(((((((....((((((....))).).))..)))))	chr10:118608911-118609129(-)$1	1	72	108	12.1137
(((((((((.(((((......))))))))))..)))	chr17:74385598-74385820(-)$1	1	120	156	11.4681
(((((((((.(((..((....))..)))))))))))	chr17:3414272-3414488(+)$1	1	104	140	12.0635
.((((((...((((((......)).))))...))))	chrX:134429632-134429847(+)$1	1	6	42	11.7760
((((....(((((((......)))))))....))))	chr2:86442318-86442544(-)$1	1	142	178	16.0943
(((.(.(((((..((......))..)))))))))).	chr3:13547434-13547651(-)$1	1	33	69	13.3656
(((((((((((((..........)))))))))))))	chr1:33240376-33240597(+)$1	1	131	167	12.0212
.(.((.((((...((......))..))))..))..)	chr10:78318401-78318616(+)$1	1	127	163	13.1878
..))(((((((((((......)))))))))))...(	chr1:32371999-32372220(-)$1	1	89	125	12.3256
(((((((((.(((.(.....))))))))))))).((	chr19:19362703-19362927(+)$1	1	158	194	12.8793
(((((((((..((((......))))..)))))))))	chr2:55776284-55776518(-)$1	1	54	90	16.3334
.((((..((.(((((......)))....)).))..)	chr2:97504040-97504260(-)$1	1	165	201	13.1232
((....((((..(((....)))....))))..))))	chr17:80797812-80798027(-)$1	1	7	43	12.2251
(((((.((((((((.(.....).))))))).)...)	chr15:69564287-69564508(+)$1	1	150	186	11.8343
...(((((((...(((....))))))))))...)))	chr1:26604232-26604450(-)$1	1	181	217	13.5855
((.((...(((((((.....)))))))...)).)))	chr3:49706127-49706350(+)$1	1	37	73	12.0379

#PSSM
i : 0.13	[ : 0.13	= : 0.10	g : 0.08	d : 0.08	! : 0.06	e : 0.06	" : 0.06	f : 0.06	: : 0.03	$ : 0.03	c : 0.01	+ : 0.01	b : 0.01	h : 0.01	^ : 0.01	m : 0.01	# : 0.01	
i : 0.15	d : 0.15	= : 0.10	g : 0.08	f : 0.08	" : 0.06	a : 0.06	! : 0.05	b : 0.03	# : 0.03	$ : 0.03	c : 0.03	e : 0.03	[ : 0.01	+ : 0.01	^ : 0.01	m : 0.01	
i : 0.15	g : 0.13	# : 0.11	d : 0.10	= : 0.08	b : 0.06	f : 0.06	[ : 0.06	" : 0.05	c : 0.05	e : 0.03	! : 0.03	+ : 0.01	^ : 0.01	
g : 0.16	i : 0.13	# : 0.10	= : 0.08	d : 0.08	b : 0.08	" : 0.06	e : 0.06	[ : 0.05	c : 0.05	f : 0.03	^ : 0.01	! : 0.01	a : 0.01	$ : 0.01	
i : 0.13	g : 0.13	# : 0.11	= : 0.10	! : 0.08	c : 0.06	d : 0.06	" : 0.06	e : 0.06	b : 0.06	f : 0.03	^ : 0.01	$ : 0.01	a : 0.01	
! : 0.15	i : 0.13	g : 0.11	= : 0.10	[ : 0.10	# : 0.10	e : 0.08	" : 0.06	b : 0.05	c : 0.03	f : 0.03	$ : 0.01	
i : 0.16	e : 0.15	g : 0.13	= : 0.10	b : 0.10	! : 0.08	c : 0.06	d : 0.05	a : 0.03	f : 0.03	" : 0.03	$ : 0.01	# : 0.01	
i : 0.15	g : 0.15	e : 0.15	= : 0.10	[ : 0.08	d : 0.08	b : 0.08	" : 0.05	c : 0.03	# : 0.03	h : 0.01	f : 0.01	! : 0.01	$ : 0.01	
g : 0.25	i : 0.13	e : 0.11	= : 0.10	c : 0.10	d : 0.08	# : 0.05	[ : 0.03	! : 0.03	" : 0.03	h : 0.01	a : 0.01	b : 0.01	
g : 0.18	[ : 0.13	e : 0.11	" : 0.10	d : 0.08	c : 0.06	# : 0.06	i : 0.06	= : 0.05	! : 0.05	h : 0.01	b : 0.01	f : 0.01	a : 0.01	
g : 0.15	c : 0.13	e : 0.13	" : 0.11	! : 0.10	# : 0.06	d : 0.05	= : 0.05	i : 0.05	f : 0.03	b : 0.03	a : 0.03	h : 0.01	[ : 0.01	
! : 0.20	g : 0.15	" : 0.11	[ : 0.10	d : 0.08	c : 0.06	e : 0.06	# : 0.05	f : 0.03	i : 0.03	b : 0.03	= : 0.03	h : 0.01	
c : 0.37	g : 0.13	! : 0.11	d : 0.10	e : 0.06	" : 0.05	f : 0.03	i : 0.03	= : 0.03	h : 0.01	# : 0.01	b : 0.01	
c : 0.33	g : 0.11	d : 0.11	b : 0.11	[ : 0.06	e : 0.06	f : 0.03	i : 0.03	" : 0.01	h : 0.01	a : 0.01	! : 0.01	s : 0.01	= : 0.01	
c : 0.40	b : 0.13	g : 0.10	d : 0.10	e : 0.05	f : 0.03	a : 0.03	i : 0.03	[ : 0.03	h : 0.01	! : 0.01	s : 0.01	= : 0.01	
o : 0.57	c : 0.11	m : 0.08	d : 0.03	b : 0.03	n : 0.03	f : 0.01	[ : 0.01	q : 0.01	l : 0.01	r : 0.01	s : 0.01	a : 0.01	
o : 0.59	m : 0.13	c : 0.08	n : 0.06	a : 0.01	q : 0.01	d : 0.01	l : 0.01	r : 0.01	b : 0.01	s : 0.01	
o : 0.61	m : 0.20	n : 0.06	l : 0.05	q : 0.01	r : 0.01	c : 0.01	s : 0.01	
o : 0.61	m : 0.20	n : 0.06	l : 0.05	q : 0.01	c : 0.01	r : 0.01	s : 0.01	
o : 0.61	m : 0.11	c : 0.08	n : 0.06	l : 0.05	q : 0.01	b : 0.01	r : 0.01	s : 0.01	
o : 0.61	c : 0.15	m : 0.06	n : 0.03	q : 0.01	d : 0.01	b : 0.01	r : 0.01	l : 0.01	s : 0.01	a : 0.01	g : 0.01	
c : 0.37	b : 0.11	g : 0.10	d : 0.10	e : 0.05	f : 0.03	a : 0.03	o : 0.03	] : 0.03	i : 0.03	h : 0.01	q : 0.01	r : 0.01	s : 0.01	= : 0.01	
c : 0.32	b : 0.13	g : 0.11	d : 0.10	] : 0.05	i : 0.05	e : 0.05	f : 0.03	h : 0.01	o : 0.01	3 : 0.01	q : 0.01	r : 0.01	s : 0.01	= : 0.01	4 : 0.01	
c : 0.27	g : 0.16	2 : 0.13	d : 0.10	i : 0.05	e : 0.05	f : 0.03	3 : 0.03	a : 0.03	= : 0.03	h : 0.01	] : 0.01	r : 0.01	b : 0.01	4 : 0.01	
2 : 0.20	g : 0.16	] : 0.16	d : 0.08	c : 0.06	i : 0.06	3 : 0.05	e : 0.05	f : 0.03	= : 0.03	4 : 0.03	h : 0.01	: : 0.01	
g : 0.22	c : 0.13	e : 0.13	2 : 0.11	i : 0.06	3 : 0.05	a : 0.05	d : 0.05	= : 0.05	f : 0.03	4 : 0.03	h : 0.01	b : 0.01	] : 0.01	
g : 0.22	c : 0.13	e : 0.13	d : 0.08	] : 0.08	i : 0.08	= : 0.06	2 : 0.05	f : 0.03	3 : 0.03	b : 0.03	h : 0.01	4 : 0.01	
g : 0.20	e : 0.15	c : 0.11	i : 0.10	= : 0.10	d : 0.08	] : 0.06	b : 0.06	3 : 0.05	h : 0.01	a : 0.01	4 : 0.01	
e : 0.15	i : 0.13	g : 0.13	= : 0.11	b : 0.11	d : 0.10	c : 0.06	3 : 0.06	] : 0.03	h : 0.01	2 : 0.01	f : 0.01	4 : 0.01	
e : 0.16	i : 0.13	= : 0.11	g : 0.11	2 : 0.10	c : 0.08	b : 0.08	3 : 0.08	d : 0.05	4 : 0.03	f : 0.01	
2 : 0.16	= : 0.11	i : 0.11	3 : 0.10	] : 0.08	e : 0.08	c : 0.06	g : 0.06	d : 0.05	4 : 0.05	b : 0.03	a : 0.03	f : 0.01	
= : 0.13	i : 0.11	g : 0.11	2 : 0.11	e : 0.08	d : 0.08	b : 0.06	3 : 0.06	c : 0.05	] : 0.05	4 : 0.05	f : 0.03	a : 0.01	
i : 0.13	= : 0.11	d : 0.11	g : 0.08	] : 0.08	b : 0.08	e : 0.06	3 : 0.06	2 : 0.05	f : 0.05	4 : 0.05	c : 0.03	h : 0.01	a : 0.01	: : 0.01	
d : 0.15	= : 0.13	i : 0.11	g : 0.10	f : 0.10	e : 0.08	2 : 0.06	c : 0.05	4 : 0.03	b : 0.03	a : 0.03	: : 0.03	h : 0.01	] : 0.01	3 : 0.01	
= : 0.15	d : 0.13	i : 0.11	g : 0.11	f : 0.08	c : 0.08	e : 0.06	] : 0.06	2 : 0.05	3 : 0.03	b : 0.01	4 : 0.01	h : 0.01	a : 0.01	: : 0.01	
= : 0.15	d : 0.15	g : 0.13	i : 0.11	e : 0.08	f : 0.08	c : 0.06	b : 0.05	] : 0.05	: : 0.01	G : 0.01	4 : 0.01	h : 0.01	3 : 0.01	a : 0.01	

#score	791.1841635045132
#seq	59
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m3_run1.txt

#BEAR
cc[cccqqqqqqqqcccccc	chr19:7707075-7707389(+)$1	314	235	255	14.8845
##ddddqqqqqqqqdddd44	chr16:67217037-67217298(+)$1	261	33	53	14.2621
a[ddddqqqqqqqqdddd]a	chr16:721001-721315(+)$1	314	97	117	14.5438
eee[bbqqqqqqqqbb]eee	chr16:2163055-2163353(+)$1	298	110	130	14.1148
ffddddqqqqqqqqdddd]f	chr17:57279354-57279732(+)$1	378	132	152	14.5223
c[ddddqqqqqqqqdddd22	chr11:94604062-94604350(+)$1	288	4	24	14.2429
bbddddqqqqqqqqdddd22	chr10:64958226-64958495(+)$1	269	215	235	13.5563
ffffffqqqqqqqqffffff	chr1:116947031-116947383(+)$1	352	254	274	14.4039
ffffffqqqqqqqqffffff	chr3:109045181-109045513(+)$1	332	35	55	14.4039
e[ddddqqqqqqqqdddd]e	chr8:11687766-11688015(+)$1	249	148	168	14.5615
ffffffqqqqqqqqffffff	chr7:134625726-134626140(+)$1	414	356	376	14.4039
ggggggqqqqqqqqgggggg	chr8:109468027-109468336(+)$1	309	169	189	15.0360
ggggggqqqqqqqqgggggg	chr8:11683583-11683898(+)$1	315	160	180	15.0360
eeecccqqqqqqqqccc444	chrX:122754258-122754562(+)$1	304	261	281	14.6041
eeeebbqqqqqqqqbb]eee	chr12:121867978-121868273(+)$1	295	127	147	14.0149
ggggggqqqqqqqqgggggg	chr19:36729101-36729430(+)$1	329	230	250	15.0360
ffffffqqqqqqqqffffff	chr11:62649353-62649700(+)$1	347	237	257	14.4039
eee[bbqqqqqqqqbbeeee	chr7:888015-888365(+)$1	350	71	91	14.0341
[eeeeeqqqqqqqqeeeee]	chr2:48713745-48714030(+)$1	285	101	121	14.1001
ffffffqqqqqqqqffffff	chr5:137891321-137891623(+)$1	302	240	260	14.4039
cc!!bbqqqqqqqqbb22cc	chr4:129003280-129003597(+)$1	317	118	138	13.9891
eeecccqqqqqqqqccc]ee	chr1:33065626-33065929(+)$1	303	171	191	14.7407
ffffffqqqqqqqqffffff	chr19:1418167-1418428(+)$1	261	216	236	14.4039
ggggggqqqqqqqqgggggg	chr17:62510324-62510652(+)$1	328	154	174	15.0360
"""cccqqqqqqqqccc]hh	chr2:190323432-190323739(+)$1	307	84	104	14.6978
ggg[bbqqqqqqqqbbgggg	chr3:141632411-141632806(+)$1	395	248	268	14.7177
ggggggqqqqqqqqgggggg	chr2:204303549-204303841(+)$1	292	234	254	15.0360
ggggggqqqqqqqqgggggg	chrX:70800148-70800420(+)$1	272	16	36	15.0360
ffffffqqqqqqqqffffff	chr5:71479508-71479814(+)$1	306	185	205	14.4039
d!!cccqqqqqqqqcccddd	chr5:139062701-139063183(+)$1	482	86	106	14.5306
!eeeeeqqqqqqqqeeeee4	chr3:50099024-50099276(+)$1	252	71	91	13.9874
##ddddqqqqqqqqddddii	chr16:24551800-24552133(+)$1	333	80	100	14.4164
b!!cccqqqqqqqqccc22b	chr20:57480347-57480688(+)$1	341	238	258	14.3414
ba!!bbqqqqqqqqbb22a]	chr1:53461207-53461698(+)$1	491	248	268	13.7405
eeeebbqqqqqqqqbb]eee	chr4:174253017-174253358(+)$1	341	31	51	14.0149
g[ddddqqqqqqqqddddgg	chr12:105519748-105520004(+)$1	256	74	94	14.7257
#cccbbqqqqqqqqbb]ccc	chr1:29314039-29314325(+)$1	286	174	194	14.2359
ggggggqqqqqqqqgggggg	chr15:69714622-69714902(+)$1	280	149	169	15.0360
ffffffqqqqqqqqffffff	chr7:94296590-94296912(+)$1	322	207	227	14.4039
h[ddddqqqqqqqqdddd22	chr5:179147357-179147663(+)$1	306	159	179	14.0757
ggggbbqqqqqqqqbb]ggg	chr8:48206435-48206690(+)$1	255	191	211	14.6892
bbddddqqqqqqqqdddd]b	chr7:100781415-100781737(+)$1	322	211	231	13.6803
"""cccqqqqqqqqccc]dd	chr9:114983077-114983410(+)$1	333	38	58	14.6503
#eeeeeqqqqqqqqeeeeec	chr6:111306180-111306483(+)$1	303	265	285	13.9659
ffffffqqqqqqqqffffff	chr17:40134168-40134433(+)$1	265	64	84	14.4039
ggggggqqqqqqqqgggggg	chr14:56122685-56122978(+)$1	293	123	143	15.0360
f[ddddqqqqqqqqdddd]f	chr19:35500712-35501045(+)$1	333	299	319	14.7003
g!!cccqqqqqqqqccc22g	chr5:134146868-134147201(+)$1	333	127	147	15.0067
ggddddqqqqqqqqdddd]g	chr2:236402715-236403050(+)$1	335	54	74	14.7015
"a[cccqqqqqqqqccc]ae	chr17:61895819-61896188(+)$1	369	334	354	14.8872
ffffffqqqqqqqqffffff	chr4:83277815-83278089(+)$1	274	220	240	14.4039
ddddddqqqqqqqqdddd]d	chr19:5641677-5642063(+)$1	386	275	295	13.9116
ccc!!aqqqqqqqqa22ccc	chrX:153583166-153583423(+)$1	257	123	143	13.8059
e[a!!aqqqqqqqqa22a]e	chr5:151170457-151170751(+)$1	294	133	153	13.9387
ggggggqqqqqqqqgggggg	chr2:61405801-61406103(+)$1	302	150	170	15.0360
c[ddddqqqqqqqqddddcc	chr8:38281884-38282193(+)$1	309	134	154	14.4986
icccbbqqqqqqqqbb]ccc	chr17:40986738-40987038(+)$1	300	215	235	14.2836
======qqqqqqqq======	chr15:40328107-40328360(+)$1	253	79	99	14.9278
c[ddddqqqqqqqqdddd]c	chr5:112211977-112212286(+)$1	309	35	55	14.6789
"""cccqqqqqqqqccc]dd	chr5:112174577-112174912(+)$1	335	18	38	14.6503
"""cccqqqqqqqqccc333	chr19:41784956-41785221(+)$1	265	97	117	15.1127
ffffffqqqqqqqqffffff	chr1:150192426-150192707(+)$1	281	6	26	14.4039
ccccccqqqqqqqqccc]cc	chr19:55497526-55497849(+)$1	323	129	149	14.8802
ffffffqqqqqqqqffffff	chr22:38881598-38881872(+)$1	274	56	76	14.4039
bb[cccqqqqqqqqcccbb]	chr12:7283556-7283835(+)$1	279	169	189	13.7929
[eeeeeqqqqqqqqeeeee]	chr12:25362009-25362321(+)$1	312	165	185	14.1001
ggggggqqqqqqqqgggggg	chr16:18803227-18803486(+)$1	259	175	195	15.0360
ggg[bbqqqqqqqqbbgggg	chr15:59205604-59205904(+)$1	300	158	178	14.7177
ccddddqqqqqqqqdddd]c	chr1:70610397-70610750(+)$1	353	126	146	14.4717
hhhcccqqqqqqqqccc]hh	chr2:74435676-74435927(+)$1	251	12	32	14.1436
ggggggqqqqqqqqgggggg	chr14:73586377-73586875(+)$1	498	236	256	15.0360
eeee[aqqqqqqqqaeeeee	chr6:34213555-34213862(+)$1	307	233	253	14.0214
ffffffqqqqqqqqffffff	chr1:24975279-24975682(+)$1	403	266	286	14.4039
ccc[bbqqqqqqqqbbccc3	chr12:123745636-123746010(+)$1	374	279	299	14.2970
!!ddddqqqqqqqqdddd44	chrX:70520023-70520364(+)$1	341	129	149	14.4717
ee!!bbqqqqqqqqbb22ee	chr10:96336363-96336724(+)$1	361	14	34	13.8328

#otherMatches

#Seq PSSM
CCAGGUAUGAGACCACCGGG	chr19:7707075-7707389(+)$1	314	235	255	14.8845
UUAACUAACUGUACAGUUUU	chr16:67217037-67217298(+)$1	261	33	53	14.2621
CACGCUCUUCAUCCAGCGCG	chr16:721001-721315(+)$1	314	97	117	14.5438
AGCUUGAAGACCGCCGCGCU	chr16:2163055-2163353(+)$1	298	110	130	14.1148
CUAGUUUGCAUGAUGAUUAA	chr17:57279354-57279732(+)$1	378	132	152	14.5223
AACUGAUAAAGAUUUCAGAC	chr11:94604062-94604350(+)$1	288	4	24	14.2429
AGAGAAACCAUCUAUUCUAA	chr10:64958226-64958495(+)$1	269	215	235	13.5563
GAAGGUUUUUAUGUGCCUUU	chr1:116947031-116947383(+)$1	352	254	274	14.4039
AUUAUUUAUUACACAAUAAU	chr3:109045181-109045513(+)$1	332	35	55	14.4039
UGUGCUAUUCCACAGGUAGG	chr8:11687766-11688015(+)$1	249	148	168	14.5615
CGUGCUAAGCAGGCAGCAUG	chr7:134625726-134626140(+)$1	414	356	376	14.4039
UAAUUUAAAAGAUAAAAUUA	chr8:109468027-109468336(+)$1	309	169	189	15.0360
UUGGGGGAAAAUAACUUUAG	chr8:11683583-11683898(+)$1	315	160	180	15.0360
ACUUUGAAACACUACAAAAU	chrX:122754258-122754562(+)$1	304	261	281	14.6041
CAGGAGUUUUUCUUCUACUU	chr12:121867978-121868273(+)$1	295	127	147	14.0149
aaaggggacuucagcuuuuu	chr19:36729101-36729430(+)$1	329	230	250	15.0360
AAAAGUAGGCUAGAACUUUU	chr11:62649353-62649700(+)$1	347	237	257	14.4039
UGGCUGGCCAGAUACACUGC	chr7:888015-888365(+)$1	350	71	91	14.0341
AAUGACUGUAUCCUGUCAUC	chr2:48713745-48714030(+)$1	285	101	121	14.1001
UGAUCACUAGCUAAUGGUCA	chr5:137891321-137891623(+)$1	302	240	260	14.4039
CUCAAGAUGUCAACCUGAAG	chr4:129003280-129003597(+)$1	317	118	138	13.9891
UCUUGCAGAAUUUGGCAUAG	chr1:33065626-33065929(+)$1	303	171	191	14.7407
GGGAGCUCACACCCGCUCUC	chr19:1418167-1418428(+)$1	261	216	236	14.4039
AAGUUUAAGAAUGGAAAUUU	chr17:62510324-62510652(+)$1	328	154	174	15.0360
AAAACAAUUUUACAUGUGUA	chr2:190323432-190323739(+)$1	307	84	104	14.6978
UCUUGUGAAAAUGAACAGAG	chr3:141632411-141632806(+)$1	395	248	268	14.7177
UUCUAAAUAAGUGAUUAGAA	chr2:204303549-204303841(+)$1	292	234	254	15.0360
AGUUUGCAACAAAACAAAUU	chrX:70800148-70800420(+)$1	272	16	36	15.0360
CACUGGAUAGGGACCCAGUG	chr5:71479508-71479814(+)$1	306	185	205	14.4039
AAUCAGUUUCCUUCCUGUGU	chr5:139062701-139063183(+)$1	482	86	106	14.5306
CUCAUUGCAUGAAAAGUGGA	chr3:50099024-50099276(+)$1	252	71	91	13.9874
UUUAUAAAUAUACGUAUAUU	chr16:24551800-24552133(+)$1	333	80	100	14.4164
AAAACAUGAAAACCUGUGAU	chr20:57480347-57480688(+)$1	341	238	258	14.3414
UCACCUUAAUCGGCAGCAGC	chr1:53461207-53461698(+)$1	491	248	268	13.7405
AAAAGCUACAACCUGCAUUU	chr4:174253017-174253358(+)$1	341	31	51	14.0149
AUCUGUGUCAAAAAAUAGUA	chr12:105519748-105520004(+)$1	256	74	94	14.7257
AGGCCCAAAUCUCAGGUGUC	chr1:29314039-29314325(+)$1	286	174	194	14.2359
CAAGUAAGUAAUUAUAUUUG	chr15:69714622-69714902(+)$1	280	149	169	15.0360
AAAAUUUUUAGUAUAAUUUU	chr7:94296590-94296912(+)$1	322	207	227	14.4039
AAAGGCAAAUGGAAGCCUCC	chr5:179147357-179147663(+)$1	306	159	179	14.0757
UGAAGUAUUUCAAAACUUUU	chr8:48206435-48206690(+)$1	255	191	211	14.6892
GUCCAGCCACUUGACUGGCA	chr7:100781415-100781737(+)$1	322	211	231	13.6803
AGACACCUUGAAAAGUGAUG	chr9:114983077-114983410(+)$1	333	38	58	14.6503
AUAAGAACUACUAGUCUUAG	chr6:111306180-111306483(+)$1	303	265	285	13.9659
GGGUUCUUCCCACUGAGCCC	chr17:40134168-40134433(+)$1	265	64	84	14.4039
GAGAGGGAGAGUGAUCUUUC	chr14:56122685-56122978(+)$1	293	123	143	15.0360
GCAGCGUGAGAUCCUGCUCC	chr19:35500712-35501045(+)$1	333	299	319	14.7003
UACCUCCUGAUUUAGAGAAA	chr5:134146868-134147201(+)$1	333	127	147	15.0067
GCGACUCGGUCCCAGGUcgg	chr2:236402715-236403050(+)$1	335	54	74	14.7015
CAGUCCCCAUUUUAGGAGUU	chr17:61895819-61896188(+)$1	369	334	354	14.8872
CUUUUAUUUCACACUAAAAG	chr4:83277815-83278089(+)$1	274	220	240	14.4039
AUGCUGUAGGUAACCGGCAA	chr19:5641677-5642063(+)$1	386	275	295	13.9116
GUGCCGUCCUCAUUCUCCAC	chrX:153583166-153583423(+)$1	257	123	143	13.8059
AGAUUCAUGCAAACGUUUGU	chr5:151170457-151170751(+)$1	294	133	153	13.9387
AAUUUGAUAGAAAGCAGGUU	chr2:61405801-61406103(+)$1	302	150	170	15.0360
AUGAUUACCUUCAAGAUCUG	chr8:38281884-38282193(+)$1	309	134	154	14.4986
UUGUCAGUUUAAGAUGUACA	chr17:40986738-40987038(+)$1	300	215	235	14.2836
GUAGUUAUUGCCAGAACUAU	chr15:40328107-40328360(+)$1	253	79	99	14.9278
ACUUAAAACUUUCCUUAAAU	chr5:112211977-112212286(+)$1	309	35	55	14.6789
ACAGGUCACGGGGAGCCAAU	chr5:112174577-112174912(+)$1	335	18	38	14.6503
UCCCUGGACUCCUGCAGCAC	chr19:41784956-41785221(+)$1	265	97	117	15.1127
GAAUAGAACCUUUACUAUUC	chr1:150192426-150192707(+)$1	281	6	26	14.4039
AUCCAGAAUGUAACCUGCGA	chr19:55497526-55497849(+)$1	323	129	149	14.8802
GGAAGAAAUUAAUCUCUUCC	chr22:38881598-38881872(+)$1	274	56	76	14.4039
CCUCCAUCCCAUCCUGGGGA	chr12:7283556-7283835(+)$1	279	169	189	13.7929
GAAAGGAGACAAAACCUUUG	chr12:25362009-25362321(+)$1	312	165	185	14.1001
AUUUCUAGCUACCAAGAAGU	chr16:18803227-18803486(+)$1	259	175	195	15.0360
UCUUGUUUUCUUCUGCAGAG	chr15:59205604-59205904(+)$1	300	158	178	14.7177
GUAGUAUUUAUCUUUAUUAG	chr1:70610397-70610750(+)$1	353	126	146	14.4717
UUUUCAGAGCAUAUUGAUGA	chr2:74435676-74435927(+)$1	251	12	32	14.1436
UUUUUUUUUUUUGUAGAAAA	chr14:73586377-73586875(+)$1	498	236	256	15.0360
UGGGUGACCGACUACCCCAG	chr6:34213555-34213862(+)$1	307	233	253	14.0214
GUCGAUUUGAGAGUAUUGGC	chr1:24975279-24975682(+)$1	403	266	286	14.4039
CUUAUGAAAAGGAACAAAGA	chr12:123745636-123746010(+)$1	374	279	299	14.2970
GAAGUCUCUAAUGUGACUGU	chrX:70520023-70520364(+)$1	341	129	149	14.4717
UUGUUCUUAAGUCUGAUAAA	chr10:96336363-96336724(+)$1	361	14	34	13.8328

#DB
((.(((........))))))	chr19:7707075-7707389(+)$1	1	235	255	14.8845
..((((........))))..	chr16:67217037-67217298(+)$1	1	33	53	14.2621
(.((((........)))).)	chr16:721001-721315(+)$1	1	97	117	14.5438
(((.((........)).)))	chr16:2163055-2163353(+)$1	1	110	130	14.1148
((((((........)))).)	chr17:57279354-57279732(+)$1	1	132	152	14.5223
(.((((........))))..	chr11:94604062-94604350(+)$1	1	4	24	14.2429
((((((........))))..	chr10:64958226-64958495(+)$1	1	215	235	13.5563
((((((........))))))	chr1:116947031-116947383(+)$1	1	254	274	14.4039
((((((........))))))	chr3:109045181-109045513(+)$1	1	35	55	14.4039
(.((((........)))).)	chr8:11687766-11688015(+)$1	1	148	168	14.5615
((((((........))))))	chr7:134625726-134626140(+)$1	1	356	376	14.4039
((((((........))))))	chr8:109468027-109468336(+)$1	1	169	189	15.0360
((((((........))))))	chr8:11683583-11683898(+)$1	1	160	180	15.0360
((((((........)))...	chrX:122754258-122754562(+)$1	1	261	281	14.6041
((((((........)).)))	chr12:121867978-121868273(+)$1	1	127	147	14.0149
((((((........))))))	chr19:36729101-36729430(+)$1	1	230	250	15.0360
((((((........))))))	chr11:62649353-62649700(+)$1	1	237	257	14.4039
(((.((........))))))	chr7:888015-888365(+)$1	1	71	91	14.0341
.(((((........))))).	chr2:48713745-48714030(+)$1	1	101	121	14.1001
((((((........))))))	chr5:137891321-137891623(+)$1	1	240	260	14.4039
((..((........))..))	chr4:129003280-129003597(+)$1	1	118	138	13.9891
((((((........))).))	chr1:33065626-33065929(+)$1	1	171	191	14.7407
((((((........))))))	chr19:1418167-1418428(+)$1	1	216	236	14.4039
((((((........))))))	chr17:62510324-62510652(+)$1	1	154	174	15.0360
...(((........))).))	chr2:190323432-190323739(+)$1	1	84	104	14.6978
(((.((........))))))	chr3:141632411-141632806(+)$1	1	248	268	14.7177
((((((........))))))	chr2:204303549-204303841(+)$1	1	234	254	15.0360
((((((........))))))	chrX:70800148-70800420(+)$1	1	16	36	15.0360
((((((........))))))	chr5:71479508-71479814(+)$1	1	185	205	14.4039
(..(((........))))))	chr5:139062701-139063183(+)$1	1	86	106	14.5306
.(((((........))))).	chr3:50099024-50099276(+)$1	1	71	91	13.9874
..((((........))))))	chr16:24551800-24552133(+)$1	1	80	100	14.4164
(..(((........)))..)	chr20:57480347-57480688(+)$1	1	238	258	14.3414
((..((........))..).	chr1:53461207-53461698(+)$1	1	248	268	13.7405
((((((........)).)))	chr4:174253017-174253358(+)$1	1	31	51	14.0149
(.((((........))))))	chr12:105519748-105520004(+)$1	1	74	94	14.7257
.(((((........)).)))	chr1:29314039-29314325(+)$1	1	174	194	14.2359
((((((........))))))	chr15:69714622-69714902(+)$1	1	149	169	15.0360
((((((........))))))	chr7:94296590-94296912(+)$1	1	207	227	14.4039
(.((((........))))..	chr5:179147357-179147663(+)$1	1	159	179	14.0757
((((((........)).)))	chr8:48206435-48206690(+)$1	1	191	211	14.6892
((((((........)))).)	chr7:100781415-100781737(+)$1	1	211	231	13.6803
...(((........))).))	chr9:114983077-114983410(+)$1	1	38	58	14.6503
.(((((........))))))	chr6:111306180-111306483(+)$1	1	265	285	13.9659
((((((........))))))	chr17:40134168-40134433(+)$1	1	64	84	14.4039
((((((........))))))	chr14:56122685-56122978(+)$1	1	123	143	15.0360
(.((((........)))).)	chr19:35500712-35501045(+)$1	1	299	319	14.7003
(..(((........)))..)	chr5:134146868-134147201(+)$1	1	127	147	15.0067
((((((........)))).)	chr2:236402715-236403050(+)$1	1	54	74	14.7015
.(.(((........))).))	chr17:61895819-61896188(+)$1	1	334	354	14.8872
((((((........))))))	chr4:83277815-83278089(+)$1	1	220	240	14.4039
((((((........)))).)	chr19:5641677-5642063(+)$1	1	275	295	13.9116
(((..(........)..)))	chrX:153583166-153583423(+)$1	1	123	143	13.8059
(.(..(........)..).)	chr5:151170457-151170751(+)$1	1	133	153	13.9387
((((((........))))))	chr2:61405801-61406103(+)$1	1	150	170	15.0360
(.((((........))))))	chr8:38281884-38282193(+)$1	1	134	154	14.4986
((((((........)).)))	chr17:40986738-40987038(+)$1	1	215	235	14.2836
((((((........))))))	chr15:40328107-40328360(+)$1	1	79	99	14.9278
(.((((........)))).)	chr5:112211977-112212286(+)$1	1	35	55	14.6789
...(((........))).))	chr5:112174577-112174912(+)$1	1	18	38	14.6503
...(((........)))...	chr19:41784956-41785221(+)$1	1	97	117	15.1127
((((((........))))))	chr1:150192426-150192707(+)$1	1	6	26	14.4039
((((((........))).))	chr19:55497526-55497849(+)$1	1	129	149	14.8802
((((((........))))))	chr22:38881598-38881872(+)$1	1	56	76	14.4039
((.(((........))))).	chr12:7283556-7283835(+)$1	1	169	189	13.7929
.(((((........))))).	chr12:25362009-25362321(+)$1	1	165	185	14.1001
((((((........))))))	chr16:18803227-18803486(+)$1	1	175	195	15.0360
(((.((........))))))	chr15:59205604-59205904(+)$1	1	158	178	14.7177
((((((........)))).)	chr1:70610397-70610750(+)$1	1	126	146	14.4717
((((((........))).))	chr2:74435676-74435927(+)$1	1	12	32	14.1436
((((((........))))))	chr14:73586377-73586875(+)$1	1	236	256	15.0360
((((.(........))))))	chr6:34213555-34213862(+)$1	1	233	253	14.0214
((((((........))))))	chr1:24975279-24975682(+)$1	1	266	286	14.4039
(((.((........))))).	chr12:123745636-123746010(+)$1	1	279	299	14.2970
..((((........))))..	chrX:70520023-70520364(+)$1	1	129	149	14.4717
((..((........))..))	chr10:96336363-96336724(+)$1	1	14	34	13.8328

#PSSM
g : 0.22	f : 0.19	e : 0.13	c : 0.11	b : 0.06	" : 0.06	# : 0.05	[ : 0.02	d : 0.02	! : 0.02	h : 0.02	a : 0.01	i : 0.01	= : 0.01	
g : 0.19	f : 0.18	e : 0.15	[ : 0.11	c : 0.10	" : 0.05	! : 0.05	b : 0.03	# : 0.02	a : 0.02	d : 0.01	= : 0.01	h : 0.01	
d : 0.22	g : 0.18	f : 0.17	e : 0.14	! : 0.07	c : 0.06	" : 0.05	[ : 0.03	a : 0.01	= : 0.01	h : 0.01	
d : 0.22	c : 0.21	f : 0.17	g : 0.15	e : 0.09	[ : 0.06	! : 0.06	= : 0.01	
d : 0.22	c : 0.18	b : 0.17	f : 0.17	g : 0.14	e : 0.05	! : 0.02	= : 0.01	[ : 0.01	
d : 0.22	c : 0.18	b : 0.17	f : 0.17	g : 0.14	e : 0.05	a : 0.03	= : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
d : 0.22	c : 0.18	b : 0.17	f : 0.17	g : 0.14	e : 0.05	a : 0.03	= : 0.01	
d : 0.22	c : 0.18	b : 0.17	f : 0.17	g : 0.14	e : 0.06	2 : 0.02	= : 0.01	
d : 0.22	c : 0.19	f : 0.17	g : 0.17	] : 0.07	e : 0.07	2 : 0.06	= : 0.01	
d : 0.23	g : 0.18	f : 0.17	e : 0.11	] : 0.09	c : 0.06	2 : 0.06	4 : 0.01	a : 0.01	= : 0.01	3 : 0.01	b : 0.01	
g : 0.19	f : 0.17	e : 0.14	] : 0.13	c : 0.10	2 : 0.06	4 : 0.03	d : 0.03	h : 0.02	a : 0.02	i : 0.01	= : 0.01	3 : 0.01	b : 0.01	
g : 0.22	f : 0.19	c : 0.13	e : 0.13	4 : 0.05	] : 0.05	d : 0.05	2 : 0.03	h : 0.02	b : 0.02	3 : 0.02	a : 0.01	i : 0.01	= : 0.01	

#score	1099.1255007132131
#seq	76
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m3_run2.txt

#BEAR
eeeee"""cccmmmmccc333eeeeef	chr19:1440326-1440558(+)$1	232	152	179	14.0235
dddeeeee[ccclllccc333eeeee]	chr17:72205271-72205521(+)$1	250	39	66	10.3905
[eeeee!!cccmmmmccc22eeeee]d	chr9:33941682-33941897(-)$1	215	168	195	12.8371
bb!!a"""cccmmmmccc]a22bb]a]	chr17:18152615-18152842(-)$1	227	78	105	13.1066
e"""ccc!!bbmmmmbb22ccc4444e	chr11:5878772-5878992(-)$1	220	150	177	12.3719
!!ffffff[ccclllccc333ffffff	chr17:33884090-33884309(-)$1	219	79	106	10.5451
c[ccc####bbmmmmbb4444ccc22c	chr5:71495220-71495431(+)$1	211	95	122	13.2831
e[==========lll==========ee	chr8:53853032-53853245(+)$1	213	116	143	10.8934
[ccc####cccmmmmcccccc]eeeee	chr5:64103471-64103717(+)$1	246	27	54	13.0387
ggggggga[ccclllccc]a]gggggg	chr19:5844566-5844789(-)$1	223	60	87	11.2210
ggggggg!!ccclllccc]ggggggg:	chr17:33433109-33433382(-)$1	273	31	58	10.5805
e[dddd"""bbmmmmbb22dddd]eee	chr3:49201238-49201457(-)$1	219	127	154	11.4419
ee!!a"""cccmmmmccc333a22eee	chr5:135277192-135277404(+)$1	212	180	207	14.5683
e:dddd!!cccmmmmccc4444ddddD	chr7:8043466-8043763(+)$1	297	122	149	10.4408
ff[ccc"""bbmmmmbb333ccc]fff	chr14:69256248-69256572(-)$1	324	225	252	13.3452
ee[bb"""cccmmmmccc22bbeeeee	chr19:7695368-7695583(+)$1	215	118	145	13.4289
iiiiii!!cccooooooccc22iiiii	chr3:101572437-101572743(+)$1	306	252	279	10.5726
ggggggg!!bbmmmmbb22ggggggg2	chr21:47613456-47613816(-)$1	360	38	65	12.3773
ee[bb"""ddddllldddd333bb]ee	chr14:20249174-20249389(+)$1	215	8	35	9.8205
gggbb####bbmmmmbb4444bb4444	chr11:125786883-125787094(+)$1	211	63	90	12.9836
bb!!bb!!cccmmmmccc22bbbbggg	chr19:18649100-18649322(-)$1	222	109	136	12.3840
%%ccc"""cccmmmmccc333ccc666	chrX:110931116-110931377(+)$1	261	24	51	12.6515
$$$ccc!!cccmmmmccc22cccdddd	chr13:39587629-39587862(-)$1	233	169	196	13.1221
[ccc####cccmmmmccc4444ccc]b	chr1:53684336-53684653(-)$1	317	70	97	14.0324
!!bb[ccc[bbmmmmbbcccbb]eeee	chr1:36933601-36933818(-)$1	217	54	81	10.3361
[dddd!!a[bbmmmmbba22dddda22	chr11:34482741-34482964(+)$1	223	147	174	11.7441
iiiiii!!cccmmmmccc22iiiiiii	chr10:70502082-70502346(+)$1	264	203	230	14.7108
f"""gggggggmmmmgggggggfffff	chr4:1018949-1019253(+)$1	304	43	70	9.9354
====="""cccmmmmccc]========	chr10:103988491-103988704(+)$1	213	31	58	15.0877
ggg[a[eeeeemmmmeeeeeagggggg	chr6:31935416-31935630(+)$1	214	117	144	9.1480
$$$ccc!!cccmmmmccc22cccdddd	chr13:39587475-39587717(-)$1	242	24	51	13.1221
cccbb"""cccmmmmccc]bb]ccc33	chr18:74607089-74607400(+)$1	311	102	129	12.9519
iiiiiiii[bbmmmmbb]iiiiiiiii	chr7:150721202-150721421(-)$1	219	41	68	12.0090
iiii$$$$$bbmmmmbb333iiiiiii	chr9:130648946-130649186(-)$1	240	64	91	13.6433
ggggggg[ccclllcccggggggg]bb	chr3:14518632-14518845(+)$1	213	29	56	9.6571
$$$eeeeecccmmmmccc]eeeee333	chr22:18609088-18609301(+)$1	213	25	52	10.8001
iiiidddd[bbmmmmbb333dddd22i	chr4:24810192-24810413(-)$1	221	26	53	11.3497
ddd"""ccc[ammmma22ccc333ddd	chr20:44640724-44640940(+)$1	216	114	141	9.7738
ggg[bb!!cccmmmmccc]bb22gggg	chr19:53855346-53855559(+)$1	213	47	74	12.3257
====####cccmmmmccc22=======	chr2:62450010-62450223(+)$1	213	18	45	15.4481
iiiiii!!cccmmmmccc22iiiiiii	chr1:228584340-228584607(-)$1	267	108	135	14.7108
!dddd!!ddddmmmmdddd333dddd6	chr15:35274882-35275157(-)$1	275	15	42	9.9458
ee!!ccc!!bbmmmmbb22ccc333ee	chr16:53190523-53190830(+)$1	307	134	161	12.4366
===========nnnnn===========	chr3:128532095-128532323(+)$1	228	56	83	9.5360
##bb"""ddddmmmmdddd333bb666	chr16:15045657-15045964(+)$1	307	195	222	9.4681
ddd[ccc!!bbmmmmbbcccddddeee	chrX:70330000-70330281(-)$1	281	249	276	10.7557
ggggg####ccclllccc333gggggg	chr3:19384049-19384262(+)$1	213	19	46	13.5895
!!a[ccc[cccmmmmccc333ccc]a2	chr6:35438307-35438540(+)$1	233	70	97	14.1688
iiiiiiiicccnnnnnccc]iiiiiii	chr13:25378333-25378553(+)$1	220	172	199	9.6651
[ffffff!!ccclllccc22ffffff]	chr15:71211385-71211599(+)$1	214	139	166	10.5030

#otherMatches

#Seq PSSM
GCGCACAUGACUCCAGUCCUUUGCGCA	chr19:1440326-1440558(+)$1	232	152	179	14.0235
UCUGGUCUCCGGUAGCUGUCAAGAUCA	chr17:72205271-72205521(+)$1	250	39	66	10.3905
CUUAUGACCAGAGUUCUGUGCAUAACA	chr9:33941682-33941897(-)$1	215	168	195	12.8371
GGGGCAGCUCAGUGAUGAAGAACCACA	chr17:18152615-18152842(-)$1	227	78	105	13.1066
AUUUGGAUUGGAGUCCCUUUUUUCUUU	chr11:5878772-5878992(-)$1	220	150	177	12.3719
CUGUGAGAAGCCAAAGGUAAAUUUCAC	chr17:33884090-33884309(-)$1	219	79	106	10.5451
CAGAGAAAAUCACUAGAACCCCUCAGG	chr5:71495220-71495431(+)$1	211	95	122	13.2831
UGCCGGCUGCAUGCCAUGCGGCUGGAC	chr8:53853032-53853245(+)$1	213	116	143	10.8934
UAUUAUUAUGGAUUUCUAGAUUCCAGC	chr5:64103471-64103717(+)$1	246	27	54	13.0387
CCACUGGAUCCCCUAGGGCUCCCAGUG	chr19:5844566-5844789(-)$1	223	60	87	11.2210
UCUGUGGGCAGGUGUCCUACUACAGAC	chr17:33433109-33433382(-)$1	273	31	58	10.5805
AACUGCCAUGCGGUUGCCUGCAGGUCG	chr3:49201238-49201457(-)$1	219	127	154	11.4419
GAUUCUGAAAUUGUUGUUGUUGUUUUU	chr5:135277192-135277404(+)$1	212	180	207	14.5683
CCUCCUCUUUGGAUACAAUAACAGGAC	chr7:8043466-8043763(+)$1	297	122	149	10.4408
GCAGCUCCAGCAGCAGCCACAGUGGCU	chr14:69256248-69256572(-)$1	324	225	252	13.3452
CUAUGUUCUGGGUUUCCAAUCAGGCCG	chr19:7695368-7695583(+)$1	215	118	145	13.4289
GGAUGCAGAUGGUGACACGUGAGUAUU	chr3:101572437-101572743(+)$1	306	252	279	10.5726
cugugcacacacguaugcaugcacagg	chr21:47613456-47613816(-)$1	360	38	65	12.3773
UACCAACAGGGCCAUGUCCACCUGCUA	chr14:20249174-20249389(+)$1	215	8	35	9.8205
CAACCUUUGAGGACUCUGUGUGGCACU	chr11:125786883-125787094(+)$1	211	63	90	12.9836
GUGCCUGGAGGUGACCCUGAAGACGGC	chr19:18649100-18649322(-)$1	222	109	136	12.3840
UGGACUUAUCAACACUGAAAUGUUAUC	chrX:110931116-110931377(+)$1	261	24	51	12.6515
UCAGCUUCCACGUCAGUGCCAGUUAGC	chr13:39587629-39587862(-)$1	233	169	196	13.1221
AACUGUGGUGAGAUUUCGGACAAGUGG	chr1:53684336-53684653(-)$1	317	70	97	14.0324
GGAGUGGGUGCCUGAGCCCCCUGAGCU	chr1:36933601-36933818(-)$1	217	54	81	10.3361
UGGCCAACUACCAGCGUGACGGCCCGA	chr11:34482741-34482964(+)$1	223	147	174	11.7441
ACGUUUGGAUUUGUGGAUGAAGAUGUA	chr10:70502082-70502346(+)$1	264	203	230	14.7108
ACUUACUGGGCCCAGGCCCAGUUGCUG	chr4:1018949-1019253(+)$1	304	43	70	9.9354
AGUGCAGAGGGUGGUCCCAGCACUGGG	chr10:103988491-103988704(+)$1	213	31	58	15.0877
UUGUGUGAUAAGCCCUUGUCCCAGGAC	chr6:31935416-31935630(+)$1	214	117	144	9.1480
UCAGCUUCCACGUCAGUGCCAGUUAGC	chr13:39587475-39587717(-)$1	242	24	51	13.1221
GAGCUUCUCCACCUCUGGCAGCCUCAA	chr18:74607089-74607400(+)$1	311	102	129	12.9519
GGGGAGGGAGGAUCUCCAUCUUCUCUC	chr7:150721202-150721421(-)$1	219	41	68	12.0090
aaggacccugccagcgcucaccuugcc	chr9:130648946-130649186(-)$1	240	64	91	13.6433
GGGUGGCCUGAGCGUCAGCCGCUCACC	chr3:14518632-14518845(+)$1	213	29	56	9.6571
UCCCUAGACAGAUGCUUGCUCUGGCCU	chr22:18609088-18609301(+)$1	213	25	52	10.8001
CAGCGCCUGAGGAUGCUGGGAGGCCCG	chr4:24810192-24810413(-)$1	221	26	53	11.3497
UGGGUAAGGAGUACUCGACCUGUACCA	chr20:44640724-44640940(+)$1	216	114	141	9.7738
AUACUGGAGAGAAACCUUACAAAUGUG	chr19:53855346-53855559(+)$1	213	47	74	12.3257
UGCUGUUUCUCAGGUGGGUAAGUACUU	chr2:62450010-62450223(+)$1	213	18	45	15.4481
ucauacuucugacaucaguuguguggg	chr1:228584340-228584607(-)$1	267	108	135	14.7108
GUGGCAAGAUGUUUCCAUCACAGUCAA	chr15:35274882-35275157(-)$1	275	15	42	9.9458
AUCUAAUUCACAACAGUCUAUUUCAAU	chr16:53190523-53190830(+)$1	307	134	161	12.4366
CUCUGUUUCCUUGUCCAGGAAACGGAG	chr3:128532095-128532323(+)$1	228	56	83	9.5360
CCUCAGCGGAUGAUAAUCUCAAGAAAC	chr16:15045657-15045964(+)$1	307	195	222	9.4681
CGGACUGACUGGGACCACAGCUGGACU	chrX:70330000-70330281(-)$1	281	249	276	10.7557
UUUCCCCCAGACAAAGUCAAAGGAAGA	chr3:19384049-19384262(+)$1	213	19	46	13.5895
GUUGGUCACGUGAAGAUGACAGACGAU	chr6:35438307-35438540(+)$1	233	70	97	14.1688
UGACAGAUGUUUCAGUAACGGUUUGUC	chr13:25378333-25378553(+)$1	220	172	199	9.6651
CUUUCGUGGUGAGUAUUAAAAUGGAGU	chr15:71211385-71211599(+)$1	214	139	166	10.5030

#DB
(((((...(((....)))...)))))(	chr19:1440326-1440558(+)$1	1	152	179	14.0235
((((((((.(((...)))...))))).	chr17:72205271-72205521(+)$1	1	39	66	10.3905
.(((((..(((....)))..))))).)	chr9:33941682-33941897(-)$1	1	168	195	12.8371
((..(...(((....))).)..)).).	chr17:18152615-18152842(-)$1	1	78	105	13.1066
(...(((..((....))..)))....)	chr11:5878772-5878992(-)$1	1	150	177	12.3719
..((((((.(((...)))...))))))	chr17:33884090-33884309(-)$1	1	79	106	10.5451
(.(((....((....))....)))..)	chr5:71495220-71495431(+)$1	1	95	122	13.2831
(.((((((((((...))))))))))))	chr8:53853032-53853245(+)$1	1	116	143	10.8934
.(((....(((....)))))).)))))	chr5:64103471-64103717(+)$1	1	27	54	13.0387
((((((((.(((...))).).))))))	chr19:5844566-5844789(-)$1	1	60	87	11.2210
(((((((..(((...))).))))))).	chr17:33433109-33433382(-)$1	1	31	58	10.5805
(.((((...((....))..)))).)))	chr3:49201238-49201457(-)$1	1	127	154	11.4419
((..(...(((....)))...)..)))	chr5:135277192-135277404(+)$1	1	180	207	14.5683
).((((..(((....)))....)))))	chr7:8043466-8043763(+)$1	1	122	149	10.4408
((.(((...((....))...))).)))	chr14:69256248-69256572(-)$1	1	225	252	13.3452
((.((...(((....)))..)))))))	chr19:7695368-7695583(+)$1	1	118	145	13.4289
((((((..(((......)))..)))))	chr3:101572437-101572743(+)$1	1	252	279	10.5726
(((((((..((....))..))))))).	chr21:47613456-47613816(-)$1	1	38	65	12.3773
((.((...((((...))))...)).))	chr14:20249174-20249389(+)$1	1	8	35	9.8205
(((((....((....))....))....	chr11:125786883-125787094(+)$1	1	63	90	12.9836
((..((..(((....)))..)))))))	chr19:18649100-18649322(-)$1	1	109	136	12.3840
..(((...(((....)))...)))...	chrX:110931116-110931377(+)$1	1	24	51	12.6515
...(((..(((....)))..)))))))	chr13:39587629-39587862(-)$1	1	169	196	13.1221
.(((....(((....)))....))).)	chr1:53684336-53684653(-)$1	1	70	97	14.0324
..((.(((.((....))))))).))))	chr1:36933601-36933818(-)$1	1	54	81	10.3361
.((((..(.((....)))..)))))..	chr11:34482741-34482964(+)$1	1	147	174	11.7441
((((((..(((....)))..)))))))	chr10:70502082-70502346(+)$1	1	203	230	14.7108
(...(((((((....))))))))))))	chr4:1018949-1019253(+)$1	1	43	70	9.9354
(((((...(((....))).))))))))	chr10:103988491-103988704(+)$1	1	31	58	15.0877
(((.(.(((((....))))))))))))	chr6:31935416-31935630(+)$1	1	117	144	9.1480
...(((..(((....)))..)))))))	chr13:39587475-39587717(-)$1	1	24	51	13.1221
(((((...(((....))).)).)))..	chr18:74607089-74607400(+)$1	1	102	129	12.9519
((((((((.((....)).)))))))))	chr7:150721202-150721421(-)$1	1	41	68	12.0090
((((.....((....))...)))))))	chr9:130648946-130649186(-)$1	1	64	91	13.6433
(((((((.(((...)))))))))).))	chr3:14518632-14518845(+)$1	1	29	56	9.6571
...((((((((....))).)))))...	chr22:18609088-18609301(+)$1	1	25	52	10.8001
((((((((.((....))...))))..)	chr4:24810192-24810413(-)$1	1	26	53	11.3497
(((...(((.(....)..)))...)))	chr20:44640724-44640940(+)$1	1	114	141	9.7738
(((.((..(((....))).))..))))	chr19:53855346-53855559(+)$1	1	47	74	12.3257
((((....(((....)))..)))))))	chr2:62450010-62450223(+)$1	1	18	45	15.4481
((((((..(((....)))..)))))))	chr1:228584340-228584607(-)$1	1	108	135	14.7108
.((((..((((....))))...)))).	chr15:35274882-35275157(-)$1	1	15	42	9.9458
((..(((..((....))..)))...))	chr16:53190523-53190830(+)$1	1	134	161	12.4366
(((((((((((.....)))))))))))	chr3:128532095-128532323(+)$1	1	56	83	9.5360
..((...((((....))))...))...	chr16:15045657-15045964(+)$1	1	195	222	9.4681
(((.(((..((....))))))))))))	chrX:70330000-70330281(-)$1	1	249	276	10.7557
(((((....(((...)))...))))))	chr3:19384049-19384262(+)$1	1	19	46	13.5895
..(.(((.(((....)))...))).).	chr6:35438307-35438540(+)$1	1	70	97	14.1688
(((((((((((.....))).)))))))	chr13:25378333-25378553(+)$1	1	172	199	9.6651
.((((((..(((...)))..)))))).	chr15:71211385-71211599(+)$1	1	139	166	10.5030

#PSSM
e : 0.18	g : 0.16	i : 0.14	[ : 0.10	! : 0.08	d : 0.06	$ : 0.06	= : 0.06	b : 0.04	c : 0.04	f : 0.04	% : 0.02	# : 0.02	
g : 0.16	i : 0.14	e : 0.12	d : 0.10	! : 0.06	[ : 0.06	c : 0.06	$ : 0.06	= : 0.06	b : 0.04	" : 0.04	f : 0.04	: : 0.02	% : 0.02	# : 0.02	
g : 0.16	d : 0.14	i : 0.14	c : 0.10	! : 0.08	= : 0.08	[ : 0.06	$ : 0.06	e : 0.04	" : 0.04	f : 0.04	b : 0.04	a : 0.02	
c : 0.14	i : 0.14	b : 0.12	g : 0.10	e : 0.08	! : 0.08	= : 0.08	d : 0.08	[ : 0.08	" : 0.06	f : 0.04	
c : 0.18	g : 0.12	b : 0.12	d : 0.10	i : 0.10	e : 0.08	a : 0.06	= : 0.06	# : 0.06	f : 0.04	" : 0.04	[ : 0.02	$ : 0.02	
" : 0.19	c : 0.16	# : 0.12	g : 0.10	i : 0.10	e : 0.06	d : 0.06	f : 0.04	= : 0.04	b : 0.04	! : 0.04	[ : 0.02	$ : 0.02	
" : 0.21	! : 0.21	c : 0.12	# : 0.12	g : 0.10	e : 0.06	f : 0.04	= : 0.04	i : 0.04	$ : 0.02	d : 0.02	
! : 0.30	" : 0.19	# : 0.12	e : 0.06	d : 0.06	= : 0.04	a : 0.04	c : 0.04	i : 0.04	[ : 0.04	f : 0.02	g : 0.02	$ : 0.02	
c : 0.48	[ : 0.14	! : 0.12	# : 0.06	d : 0.06	= : 0.04	" : 0.04	g : 0.02	e : 0.02	$ : 0.02	
c : 0.58	b : 0.25	d : 0.06	= : 0.04	g : 0.02	e : 0.02	[ : 0.02	
c : 0.58	b : 0.25	d : 0.06	= : 0.04	g : 0.02	e : 0.02	a : 0.02	
m : 0.76	c : 0.12	n : 0.04	= : 0.02	o : 0.02	d : 0.02	l : 0.02	
m : 0.76	l : 0.18	n : 0.04	o : 0.02	
m : 0.76	l : 0.18	n : 0.04	o : 0.02	
m : 0.76	l : 0.16	n : 0.04	o : 0.02	c : 0.02	
c : 0.54	b : 0.25	d : 0.06	n : 0.04	= : 0.02	o : 0.02	g : 0.02	e : 0.02	a : 0.02	
c : 0.56	b : 0.25	d : 0.06	= : 0.04	o : 0.02	g : 0.02	e : 0.02	2 : 0.02	
c : 0.60	2 : 0.10	3 : 0.06	d : 0.06	4 : 0.04	= : 0.04	g : 0.04	a : 0.02	e : 0.02	] : 0.02	
2 : 0.27	3 : 0.19	] : 0.14	c : 0.12	4 : 0.08	d : 0.06	= : 0.04	g : 0.04	e : 0.02	i : 0.02	
3 : 0.25	2 : 0.19	c : 0.14	4 : 0.08	g : 0.08	= : 0.06	a : 0.04	e : 0.04	b : 0.04	d : 0.02	i : 0.02	] : 0.02	
3 : 0.19	c : 0.14	b : 0.10	i : 0.10	4 : 0.08	= : 0.08	g : 0.08	d : 0.08	e : 0.04	2 : 0.04	] : 0.02	a : 0.02	f : 0.02	
c : 0.16	g : 0.14	i : 0.10	e : 0.08	= : 0.08	d : 0.08	b : 0.08	3 : 0.08	2 : 0.06	f : 0.04	] : 0.04	4 : 0.04	a : 0.02	
c : 0.16	e : 0.12	g : 0.12	d : 0.12	i : 0.12	b : 0.10	= : 0.08	f : 0.06	2 : 0.04	3 : 0.04	4 : 0.02	] : 0.02	
e : 0.14	g : 0.14	d : 0.14	i : 0.12	c : 0.10	b : 0.08	= : 0.08	f : 0.06	4 : 0.04	] : 0.04	3 : 0.04	2 : 0.02	
e : 0.18	g : 0.14	i : 0.12	d : 0.10	] : 0.08	f : 0.08	= : 0.08	4 : 0.04	2 : 0.04	6 : 0.04	c : 0.04	3 : 0.04	a : 0.02	
e : 0.21	g : 0.14	i : 0.12	d : 0.10	f : 0.08	2 : 0.06	= : 0.06	] : 0.04	a : 0.04	4 : 0.04	6 : 0.04	3 : 0.04	b : 0.02	
e : 0.19	i : 0.14	g : 0.10	f : 0.08	d : 0.08	] : 0.06	2 : 0.06	6 : 0.06	= : 0.06	b : 0.04	3 : 0.04	c : 0.02	: : 0.02	D : 0.02	4 : 0.02	

#score	600.2857028264741
#seq	50
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_CDS_m2_run1.txt

#BEAR
bb"""bb[cccooooooccc]bb]bb]c	chr4:77941582-77941813(+)$1	231	136	164	14.6610
[ggggggg[bboooooobb22ggggggg	chr17:55693241-55693463(+)$1	222	63	91	14.8699
:ggggggg[bboooooobb]ggggggg:	chr3:32932660-32932891(+)$1	231	162	190	12.6926
ffffff"""bboooooobb333ffffff	chr17:38458092-38458318(+)$1	226	114	142	14.0737
e[dddd!!cccooooooccc333dddde	chrX:129189765-129189989(+)$1	224	159	187	15.1291
hhhhhhh[cccooooooccc]hhhhhhh	chr12:46123528-46123752(+)$1	224	44	72	13.5763
"bbccc[a[cccnnnnnccc22a]ccc]	chr21:45379462-45379693(+)$1	231	168	196	10.8680
[ccc[bb[cccooooooccc]bb]ccc]	chr11:59434262-59434493(-)$1	231	65	93	15.4336
=====####bboooooobb4444=====	chr1:51210265-51210487(-)$1	222	183	211	15.6947
eeee[ccc[bboooooobb]ccc]eeee	chr12:57037114-57037336(-)$1	222	55	83	13.2141
[eeeee!!cccooooooccc333eeeee	chr1:203276436-203276711(+)$1	275	222	250	15.0650
dd!!ccc!!bboooooobb22ccc22dd	chr6:151670607-151670838(+)$1	231	58	86	14.3094
b[ffffffcccooooooccc]ffffff]	chr15:69747483-69747722(+)$1	239	39	67	13.8048
:eeeee"""bboooooobb333eeeeeB	chr19:1257135-1257389(+)$1	254	156	184	12.5405
f[bb!!bbcccooooooccc]bbbbfff	chr16:29998611-29998844(+)$1	233	65	93	13.6441
b[ccceeeeeooooooeeeee333cccb	chr7:138916385-138916609(+)$1	224	42	70	11.6100
!!dddd[a[bboooooobba]dddd22b	chr19:50880768-50880992(+)$1	224	134	162	13.6630
[ccc!!ddddoooooodddd22cccccc	chr2:97529913-97530136(-)$1	223	171	199	12.6767
d####ccccccooooooccc]ccc]ddd	chr9:33916945-33917186(+)$1	241	115	143	14.8442
===$$$$$cccnnnnnccc4444=====	chr19:6413418-6413688(-)$1	270	27	55	10.3810
cc[ccc!!cccooooooccc22ccc22c	chr1:145585456-145585689(+)$1	233	151	179	16.3712
ddddccc[cccooooooccc]ccc9999	chr22:50666326-50666550(-)$1	224	43	71	12.5353
:cccccc[a!!aooooooa22accc]cc	chr11:66114026-66114249(-)$1	223	34	62	13.0824
ggggggg[cccooooooccc22gggggg	chr2:27448515-27448747(+)$1	232	9	37	16.1008
bb!!gggggggooooooggggggg22bb	chr10:74127869-74128111(-)$1	242	62	90	13.0229
cccbb[a[cccooooooccc]a]bb]cc	chr17:73227920-73228145(+)$1	225	136	164	15.0290
b[iiiiiiiiiooooooiiiiiiiiibb	chr18:32917256-32917482(-)$1	226	21	49	14.2599
[bb[ccc[cccooooooccc22ccc]bb	chr9:136910431-136910643(-)$1	212	128	156	15.7535
##bb!!eeeeeooooooeeeee]bb444	chr1:205117269-205117494(-)$1	225	165	193	12.0026
========[bboooooobb]========	chrX:68381773-68382004(-)$1	231	181	209	15.3753
hh"""dddd[aooooooa]dddd4444h	chr4:83350398-83350656(-)$1	258	13	41	12.5115
!ffffff[cccoooooocccffffff33	chr14:93263775-93263999(+)$1	224	21	49	13.8911
!ccc[ccc[bboooooobb333ccc22c	chr19:1254177-1254432(+)$1	255	83	111	15.8569
b[bb!!a!!bboooooobb22a22bb]b	chr11:94180319-94180554(-)$1	235	74	102	14.5217
iiiigggggggoooooogggggggccc!	chr6:31506825-31507046(-)$1	221	62	90	13.8605
ee[dddd"""aooooooa4444dddd]e	chr2:27659822-27660042(+)$1	220	115	143	13.7041
"""a[dddd[bboooooobb22dddd]a	chr19:45368612-45368853(+)$1	241	31	59	12.2377
d[bb[dddd[aooooooa]dddd]bb]d	chr11:14498364-14498598(-)$1	234	41	69	12.2779
========cccooooooccc4444====	chr2:222307510-222307735(-)$1	225	59	87	16.3272
b!!a####cccooooooccc22a22bb]	chr9:117838257-117838498(-)$1	241	145	173	15.3356
!!bbccc[cccooooooccc22ccc22b	chr5:126154597-126154820(+)$1	223	158	186	16.1153
c[iiiiiiiiiooooooiiiiiiiii]c	chr17:34169293-34169510(+)$1	217	160	188	14.8474
$ccc[bb[cccooooooccc]bb]ccc]	chr3:129034461-129034680(-)$1	219	169	197	15.1812
cc[dddd[cccooooooccc22ddddcc	chr7:2303832-2304047(-)$1	215	146	174	15.0759
======bbcccooooooccc]bb66666	chr17:76810452-76810683(-)$1	231	85	113	12.6605
cc[ccceeeeeooooooeeeee]ccc]c	chr11:111728224-111728436(-)$1	212	11	39	12.6546
hhhhhhh[cccooooooccc]hhhhhhh	chrX:84519289-84519525(+)$1	236	138	166	13.5763
ggiiiiiiiiiooooooiiiiiiiii::	chr16:30750587-30750810(+)$1	223	146	174	12.9112
d!!ccccccaooooooa]ccc333ccc]	chr12:57618809-57619038(+)$1	229	189	217	13.9075

#otherMatches

#Seq PSSM
GGACUUGCGAGAGCAGACUCACACCCGC	chr4:77941582-77941813(+)$1	231	136	164	14.6610
CAUUUGUUCGCCUUUCUGUUUAACAGGU	chr17:55693241-55693463(+)$1	222	63	91	14.8699
UUCUGAGGGCAAGAUCCUGGUCUCAGAC	chr3:32932660-32932891(+)$1	231	162	190	12.6926
AAGAUAAAGCUUUAAUUGGAAAUAUCUU	chr17:38458092-38458318(+)$1	226	114	142	14.0737
CAUGCCCAAGGCCGAGUUCUACAGGCAG	chrX:129189765-129189989(+)$1	224	159	187	15.1291
UUUAAAACACCGAUCUGGGUUUUUUAAA	chr12:46123528-46123752(+)$1	224	44	72	13.5763
GAGUGGUCUGGUCAUCAACUUCGUCCAG	chr21:45379462-45379693(+)$1	231	168	196	10.8680
GAUUGUCCUCUGGAUGAAGAUGAAGAUG	chr11:59434262-59434493(-)$1	231	65	93	15.4336
UUAAAUGAUAUGUAAAAAUUGGUUUUAA	chr1:51210265-51210487(-)$1	222	183	211	15.6947
UUGCUGGUGUUGGUGAGAGGACCCGUGA	chr12:57037114-57037336(-)$1	222	55	83	13.2141
UGAAGAGCuauuuauauauauuauuuuu	chr1:203276436-203276711(+)$1	275	222	250	15.0650
CUCAGAGGAGCAAGUCAGUGGCUCGCAG	chr6:151670607-151670838(+)$1	231	58	86	14.3094
CAACAUUGGGAGCCUCAUCUGCAAUGUA	chr15:69747483-69747722(+)$1	239	39	67	13.8048
UCGCCCCUCGCACCCCAGCCCAGGGCGG	chr19:1257135-1257389(+)$1	254	156	184	12.5405
CGUCCUGGGCCUGAGCUGGCGCCGAGGC	chr16:29998611-29998844(+)$1	233	65	93	13.6441
GUCGCGGGAGAAGCCGCUCCCCCAGCGC	chr7:138916385-138916609(+)$1	224	42	70	11.6100
CUGGUGAGUGACUCUCUUCCCCACCCAG	chr19:50880768-50880992(+)$1	224	134	162	13.6630
AGGGCAGGGAUGCAUCUCCCCACCCAGC	chr2:97529913-97530136(-)$1	223	171	199	12.6767
GAAGGUCCCCACAACCCUGGCGGAAUAC	chr9:33916945-33917186(+)$1	241	115	143	14.8442
AAAAAAAAAAGUCACUCUUGCUAUUUCU	chr19:6413418-6413688(-)$1	270	27	55	10.3810
AUUUCCCUGGACUGAGUUCCCUGGAUUA	chr1:145585456-145585689(+)$1	233	151	179	16.3712
GGCUGCGUCCAUGUGCCUGGCCGCCCUC	chr22:50666326-50666550(-)$1	224	43	71	12.5353
AUGCCCAUGAACAAAAACGAGCUGGUGC	chr11:66114026-66114249(-)$1	223	34	62	13.0824
UGGACAGUAGGAAAUAACCUGUUUGUUC	chr2:27448515-27448747(+)$1	232	9	37	16.1008
GGAAAAGCCCAAAGACAUGGGUUUCACU	chr10:74127869-74128111(-)$1	242	62	90	13.0229
GGCAGAUGACUGAACAAGGUGAGCUGGC	chr17:73227920-73228145(+)$1	225	136	164	15.0290
GUGUUGAGUGUGGGAAAGCAUUCAGCCG	chr18:32917256-32917482(-)$1	226	21	49	14.2599
ACGCACAGGGCUUUGCUGCUGAUGUCCG	chr9:136910431-136910643(-)$1	212	128	156	15.7535
AGAGCCACAAGUACUACCUUGUCCUAAC	chr1:205117269-205117494(-)$1	225	165	193	12.0026
GUGCUAGUGCCAGUGCCGGGGCUGGCGC	chrX:68381773-68382004(-)$1	231	181	209	15.3753
CCGAUUGGCGGGCGGGGCGGCUAUAAAG	chr4:83350398-83350656(-)$1	258	13	41	12.5115
UGAUCUUGCUGGAAAGGCAGAAGAUCUU	chr14:93263775-93263999(+)$1	224	21	49	13.8911
CGCUCCACUGCAACACCGCCAUGUGCUG	chr19:1254177-1254432(+)$1	255	83	111	15.8569
CAGCAGCAACCAACAAAGGAAGAGGCCG	chr11:94180319-94180554(-)$1	235	74	102	14.5217
GGGAAAGACAGCAGUGUUUGUCUUGGCC	chr6:31506825-31507046(-)$1	221	62	90	13.8605
UGGACAUCUACUCCUUUGGCAUGUGUGC	chr2:27659822-27660042(+)$1	220	115	143	13.7041
ACCUGGCAGCGCCCAGAUGCACCUGCGA	chr19:45368612-45368853(+)$1	241	31	59	12.2377
UACCGAGGAGCAUUAUGGAUCCUGGGAG	chr11:14498364-14498598(-)$1	234	41	69	12.2779
UGUGGCUAUCAAGACUCUGAAAGCUGGU	chr2:222307510-222307735(-)$1	225	59	87	16.3272
GAAGACAAGGAGAGCAAUCCAGCGACCA	chr9:117838257-117838498(-)$1	241	145	173	15.3356
AACAGCUUCUUGAUGUAAAGUUAGCCCU	chr5:126154597-126154820(+)$1	223	158	186	16.1153
GGGCGGCGAGGUAAGAUCCUUGCUGCGU	chr17:34169293-34169510(+)$1	217	160	188	14.8474
UGGUUCGACCAGCAGAAUGGGCGCACCU	chr3:129034461-129034680(-)$1	219	169	197	15.1812
GCGCGGUGGGACGGGAAUCCAUGCUGGU	chr7:2303832-2304047(-)$1	215	146	174	15.0759
UAUAUGUCCCAGAAUAAUGGUGAUCCUG	chr17:76810452-76810683(-)$1	231	85	113	12.6605
UUGAUAGCCAUGACUGGAUGGUAUAUGG	chr11:111728224-111728436(-)$1	212	11	39	12.6546
UUGAAAUAGGUACAAACACUAAUUUUAA	chrX:84519289-84519525(+)$1	236	138	166	13.5763
GGGUCUCUAGUCCCCCCACUAGAGACUG	chr16:30750587-30750810(+)$1	223	146	174	12.9112
GAACGGUACCUUCAGUGUGUAUUUCCGC	chr12:57618809-57619038(+)$1	229	189	217	13.9075

#DB
((...((.(((......))).)).)).)	chr4:77941582-77941813(+)$1	1	136	164	14.6610
.(((((((.((......))..)))))))	chr17:55693241-55693463(+)$1	1	63	91	14.8699
.(((((((.((......)).))))))).	chr3:32932660-32932891(+)$1	1	162	190	12.6926
((((((...((......))...))))))	chr17:38458092-38458318(+)$1	1	114	142	14.0737
(.((((..(((......)))...)))))	chrX:129189765-129189989(+)$1	1	159	187	15.1291
(((((((.(((......))).)))))))	chr12:46123528-46123752(+)$1	1	44	72	13.5763
.(((((.(.(((.....)))..).))).	chr21:45379462-45379693(+)$1	1	168	196	10.8680
.(((.((.(((......))).)).))).	chr11:59434262-59434493(-)$1	1	65	93	15.4336
(((((....((......))....)))))	chr1:51210265-51210487(-)$1	1	183	211	15.6947
((((.(((.((......)).))).))))	chr12:57037114-57037336(-)$1	1	55	83	13.2141
.(((((..(((......)))...)))))	chr1:203276436-203276711(+)$1	1	222	250	15.0650
((..(((..((......))..)))..))	chr6:151670607-151670838(+)$1	1	58	86	14.3094
(.(((((((((......))).)))))).	chr15:69747483-69747722(+)$1	1	39	67	13.8048
.(((((...((......))...))))))	chr19:1257135-1257389(+)$1	1	156	184	12.5405
(.((..(((((......))).)))))))	chr16:29998611-29998844(+)$1	1	65	93	13.6441
(.((((((((......)))))...))))	chr7:138916385-138916609(+)$1	1	42	70	11.6100
..((((.(.((......))).))))..)	chr19:50880768-50880992(+)$1	1	134	162	13.6630
.(((..((((......))))..))))))	chr2:97529913-97530136(-)$1	1	171	199	12.6767
(....((((((......))).))).)))	chr9:33916945-33917186(+)$1	1	115	143	14.8442
(((.....(((.....)))....)))))	chr19:6413418-6413688(-)$1	1	27	55	10.3810
((.(((..(((......)))..)))..)	chr1:145585456-145585689(+)$1	1	151	179	16.3712
(((((((.(((......))).)))....	chr22:50666326-50666550(-)$1	1	43	71	12.5353
.((((((.(..(......)..)))).))	chr11:66114026-66114249(-)$1	1	34	62	13.0824
(((((((.(((......)))..))))))	chr2:27448515-27448747(+)$1	1	9	37	16.1008
((..(((((((......)))))))..))	chr10:74127869-74128111(-)$1	1	62	90	13.0229
(((((.(.(((......))).).)).))	chr17:73227920-73228145(+)$1	1	136	164	15.0290
(.(((((((((......)))))))))))	chr18:32917256-32917482(-)$1	1	21	49	14.2599
.((.(((.(((......)))..))).))	chr9:136910431-136910643(-)$1	1	128	156	15.7535
..((..(((((......))))).))...	chr1:205117269-205117494(-)$1	1	165	193	12.0026
((((((((.((......)).))))))))	chrX:68381773-68382004(-)$1	1	181	209	15.3753
((...((((.(......).))))....)	chr4:83350398-83350656(-)$1	1	13	41	12.5115
.((((((.(((......)))))))))..	chr14:93263775-93263999(+)$1	1	21	49	13.8911
.(((.(((.((......))...)))..)	chr19:1254177-1254432(+)$1	1	83	111	15.8569
(.((..(..((......))..)..)).)	chr11:94180319-94180554(-)$1	1	74	102	14.5217
))))(((((((......)))))))(((.	chr6:31506825-31507046(-)$1	1	62	90	13.8605
((.((((...(......)....)))).)	chr2:27659822-27660042(+)$1	1	115	143	13.7041
...(.((((.((......))..)))).)	chr19:45368612-45368853(+)$1	1	31	59	12.2377
(.((.((((.(......).)))).)).)	chr11:14498364-14498598(-)$1	1	41	69	12.2779
(((((((((((......)))....))))	chr2:222307510-222307735(-)$1	1	59	87	16.3272
(..(....(((......)))..)..)).	chr9:117838257-117838498(-)$1	1	145	173	15.3356
..(((((.(((......)))..)))..)	chr5:126154597-126154820(+)$1	1	158	186	16.1153
(.(((((((((......))))))))).)	chr17:34169293-34169510(+)$1	1	160	188	14.8474
.(((.((.(((......))).)).))).	chr3:129034461-129034680(-)$1	1	169	197	15.1812
((.((((.(((......)))..))))))	chr7:2303832-2304047(-)$1	1	146	174	15.0759
(((((((((((......))).)).....	chr17:76810452-76810683(-)$1	1	85	113	12.6605
((.((((((((......))))).))).)	chr11:111728224-111728436(-)$1	1	11	39	12.6546
(((((((.(((......))).)))))))	chrX:84519289-84519525(+)$1	1	138	166	13.5763
))(((((((((......)))))))))..	chr16:30750587-30750810(+)$1	1	146	174	12.9112
(..(((((((......).)))...))).	chr12:57618809-57619038(+)$1	1	189	217	13.9075

#PSSM
b : 0.14	[ : 0.10	= : 0.10	d : 0.10	c : 0.10	! : 0.08	: : 0.06	e : 0.06	h : 0.06	f : 0.04	" : 0.04	g : 0.04	# : 0.02	i : 0.02	$ : 0.02	
c : 0.18	[ : 0.16	= : 0.10	b : 0.08	g : 0.08	e : 0.08	! : 0.08	h : 0.06	f : 0.04	d : 0.04	# : 0.04	i : 0.02	" : 0.02	
b : 0.14	c : 0.14	= : 0.10	! : 0.08	[ : 0.08	i : 0.08	" : 0.06	g : 0.06	f : 0.06	d : 0.06	e : 0.06	h : 0.04	# : 0.02	
c : 0.20	b : 0.12	d : 0.10	= : 0.08	i : 0.08	g : 0.06	f : 0.06	e : 0.06	" : 0.04	h : 0.04	! : 0.04	a : 0.04	# : 0.02	$ : 0.02	[ : 0.02	
c : 0.20	[ : 0.12	g : 0.10	d : 0.08	= : 0.08	! : 0.08	f : 0.06	i : 0.06	" : 0.04	h : 0.04	e : 0.04	# : 0.04	$ : 0.02	b : 0.02	
c : 0.24	d : 0.14	g : 0.10	! : 0.08	b : 0.06	f : 0.06	e : 0.06	i : 0.06	= : 0.06	h : 0.04	# : 0.04	$ : 0.02	[ : 0.02	
c : 0.18	d : 0.12	b : 0.10	g : 0.10	! : 0.06	e : 0.06	i : 0.06	" : 0.04	h : 0.04	[ : 0.04	# : 0.04	f : 0.04	a : 0.04	= : 0.04	$ : 0.02	
[ : 0.26	! : 0.10	g : 0.08	c : 0.08	d : 0.08	" : 0.06	e : 0.06	i : 0.06	a : 0.04	# : 0.04	b : 0.04	= : 0.04	f : 0.02	$ : 0.02	
c : 0.46	[ : 0.14	d : 0.08	" : 0.06	e : 0.06	i : 0.06	! : 0.04	g : 0.04	# : 0.02	a : 0.02	
c : 0.46	b : 0.22	e : 0.06	i : 0.06	[ : 0.06	g : 0.04	d : 0.02	! : 0.02	" : 0.02	a : 0.02	
c : 0.46	b : 0.24	o : 0.06	i : 0.06	a : 0.06	g : 0.04	e : 0.04	! : 0.02	
o : 0.91	c : 0.02	n : 0.02	a : 0.02	b : 0.02	
o : 0.95	n : 0.04	
o : 0.95	n : 0.04	
o : 0.95	n : 0.04	
o : 0.95	n : 0.04	
o : 0.89	n : 0.02	e : 0.02	d : 0.02	c : 0.02	a : 0.02	
c : 0.46	b : 0.22	e : 0.06	i : 0.06	a : 0.06	o : 0.04	g : 0.04	d : 0.02	] : 0.02	
c : 0.48	b : 0.24	e : 0.06	i : 0.06	g : 0.04	] : 0.04	d : 0.02	a : 0.02	4 : 0.02	
c : 0.46	2 : 0.08	] : 0.06	3 : 0.06	4 : 0.06	e : 0.06	d : 0.06	i : 0.06	g : 0.04	a : 0.02	b : 0.02	
2 : 0.26	] : 0.24	3 : 0.10	4 : 0.08	g : 0.06	e : 0.06	i : 0.06	c : 0.04	d : 0.04	= : 0.02	f : 0.02	
2 : 0.18	3 : 0.14	b : 0.10	g : 0.08	4 : 0.08	c : 0.08	d : 0.06	a : 0.06	i : 0.06	h : 0.04	f : 0.04	e : 0.04	= : 0.02	
c : 0.20	d : 0.12	b : 0.10	g : 0.10	3 : 0.08	f : 0.06	4 : 0.06	] : 0.06	i : 0.06	h : 0.04	a : 0.04	e : 0.02	= : 0.02	2 : 0.02	
c : 0.20	] : 0.12	g : 0.10	d : 0.10	f : 0.06	= : 0.06	b : 0.06	i : 0.06	h : 0.04	e : 0.04	3 : 0.04	4 : 0.04	2 : 0.04	6 : 0.02	
c : 0.26	b : 0.12	d : 0.10	= : 0.08	g : 0.06	f : 0.06	e : 0.06	2 : 0.06	i : 0.06	h : 0.04	] : 0.02	9 : 0.02	4 : 0.02	6 : 0.02	
c : 0.16	2 : 0.12	d : 0.10	b : 0.08	f : 0.08	= : 0.08	g : 0.06	e : 0.06	] : 0.06	i : 0.06	h : 0.04	4 : 0.04	9 : 0.02	6 : 0.02	
c : 0.20	] : 0.14	= : 0.08	2 : 0.08	b : 0.08	g : 0.06	f : 0.06	d : 0.06	e : 0.06	h : 0.04	4 : 0.04	9 : 0.02	3 : 0.02	6 : 0.02	: : 0.02	
c : 0.18	b : 0.14	] : 0.12	e : 0.08	= : 0.08	h : 0.06	d : 0.06	g : 0.04	: : 0.04	f : 0.04	B : 0.02	9 : 0.02	4 : 0.02	3 : 0.02	! : 0.02	a : 0.02	6 : 0.02	

#score	683.7411447967884
#seq	49
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m2_run1.txt

#BEAR
:eeeeeooooooeeeee	chr19:12902576-12902790(+)$1	214	21	38	10.0916
b[ddddoooooodddd]	chr10:38344231-38344448(+)$1	217	126	143	12.7908
"""cccooooooccccc	chr7:129916435-129916652(+)$1	217	148	165	11.3941
cc!!bboooooobb333	chr19:53086332-53086545(+)$1	213	81	98	9.4235
cc[cccooooooccc]c	chr12:46245035-46245247(+)$1	212	42	59	10.6845
""ddddoooooodddd5	chr7:143882336-143882548(+)$1	212	21	38	12.5559
$$ddddoooooodddd3	chr15:71211385-71211599(+)$1	214	67	84	12.7929
"""cccooooooccc33	chr1:198668642-198668931(+)$1	289	18	35	11.9402
d!!cccooooooccc22	chr14:50759850-50760084(-)$1	234	56	73	11.1238
bbddddoooooodddd:	chrX:154610579-154610793(+)$1	214	66	83	11.3711
h[ddddoooooodddd]	chr21:47423225-47423439(+)$1	214	166	183	12.4814
::ddddoooooodddd:	chr13:39586911-39587219(-)$1	308	195	212	10.2353
ffddddoooooodddd2	chr19:53855346-53855559(+)$1	213	93	110	11.9549
""ddddoooooodddd4	chr5:35014083-35014303(-)$1	220	25	42	13.1294
::ddddoooooodddd:	chr6:139694908-139695166(-)$1	258	135	152	10.2353
:eeeeeooooooeeeee	chr19:12885285-12885518(-)$1	233	162	179	10.0916
b[ddddoooooodddd]	chrX:140995798-140996014(+)$1	216	18	35	12.7908
[eeeeeooooooeeeee	chr3:57107985-57108200(+)$1	215	120	137	10.8055
bb[cccooooooccc]b	chr11:60167812-60168027(+)$1	215	76	93	10.2730
:eeeeeooooooeeeee	chr9:33941682-33941897(-)$1	215	141	158	10.0916
::ddddoooooodddd:	chr3:169847048-169847440(-)$1	392	341	358	10.2353
Beeeeeooooooeeeee	chrX:118920491-118920765(-)$1	274	15	32	10.1362
ceeeeeooooooeeeee	chr11:60233424-60233705(+)$1	281	84	101	10.6625
e:ddddoooooodddd:	chr15:52902247-52902494(-)$1	247	84	101	10.6049
$$ddddoooooodddd5	chr10:38344640-38345036(+)$1	396	137	154	12.1339
"""ddddnnnnndddd]	chr15:35275256-35275474(-)$1	218	57	74	8.3661
b[ddddoooooodddd]	chr1:155292214-155292427(+)$1	213	111	128	12.7908
!!ddddooooooddddc	chr1:233248540-233248809(-)$1	269	141	158	12.6847
h"""bboooooobb333	chr17:74077869-74078082(+)$1	213	53	70	9.3474
[eeeeeooooooeeeee	chr9:114994334-114994584(-)$1	250	219	236	10.8055
###cccooooooccc55	chr11:66050683-66050899(+)$1	216	31	48	10.3216
%eeeeeooooooeeeee	chr19:52778691-52778973(+)$1	282	72	89	10.4344
!!ddddooooooddddc	chr6:36168171-36168389(+)$1	218	45	62	12.6847
hh[cccooooooccchh	chr12:108011853-108012131(+)$1	278	246	263	9.7066
d[ddddoooooodddd]	chr1:185277000-185277380(-)$1	380	284	301	12.6152
"""ddddnnnnndddd]	chr10:76735213-76735459(+)$1	246	51	68	8.3661
fffcccooooooccc]f	chr17:72245091-72245320(+)$1	229	60	77	9.9494
aeeeeeooooooeeeee	chr14:74400837-74401062(-)$1	225	10	27	10.8138
"""ddddnnnnndddd]	chr17:2226520-2226751(-)$1	231	131	148	8.3661
ccddddoooooodddd]	chr19:21300776-21300996(+)$1	220	200	217	12.4407
bb[cccooooooccc]b	chr5:37351250-37351484(-)$1	234	133	150	10.2730
ddddcccooooooccc]	chr20:49509437-49509680(-)$1	243	60	77	9.4547
!!ddddoooooodddd>	chr7:38299695-38299931(-)$1	236	65	82	12.7814
"""cccooooooccc33	chr7:100641505-100641718(+)$1	213	173	190	11.9402
ddddcccooooooccc]	chr2:242009503-242009717(+)$1	214	70	87	9.4547
b!!cccooooooccc44	chr3:123046469-123046686(-)$1	217	25	42	11.5890
b!!cccooooooccc22	chr3:40558052-40558263(+)$1	211	23	40	11.2993
"""cccooooooccc22	chr3:183960538-183960770(-)$1	232	2	19	11.5672
d[ddddooooooddddd	chr1:10477047-10477259(+)$1	212	147	164	12.0665
ccddddoooooodddd5	chr16:30681305-30681606(+)$1	301	205	222	11.8203
a[ddddoooooodddd]	chr6:35438307-35438540(+)$1	233	207	224	12.9375
[eeeeeooooooeeeee	chr3:195968640-195968875(-)$1	235	128	145	10.8055
f[ddddoooooodddd]	chr1:19446710-19447010(-)$1	300	34	51	12.5824
eeddddoooooodddd:	chr17:75471761-75472008(+)$1	247	119	136	11.3557
"eeeeeooooooeeeee	chrX:110931116-110931377(+)$1	261	165	182	10.9825
(eeeeeooooooeeeee	chr19:21366674-21366894(+)$1	220	94	111	10.1969

#otherMatches

#Seq PSSM
AUGGAACAGCCCUUCUA	chr19:12902576-12902790(+)$1	214	21	38	10.0916
ACAGGGCUGAAACCCUA	chr10:38344231-38344448(+)$1	217	126	143	12.7908
CCUGGAUUUUGUUCCCU	chr7:129916435-129916652(+)$1	217	148	165	11.3941
CACCUGGCACAACAUAC	chr19:53086332-53086545(+)$1	213	81	98	9.4235
AGUCUGAUUAAACAGCU	chr12:46245035-46245247(+)$1	212	42	59	10.6845
CACAGGGCUCCUUCUGA	chr7:143882336-143882548(+)$1	212	21	38	12.5559
UUUUAAGUCAUGUUGAU	chr15:71211385-71211599(+)$1	214	67	84	12.7929
ACUGAUGUAAUGAUCUC	chr1:198668642-198668931(+)$1	289	18	35	11.9402
gucaagguguauuuuuu	chr14:50759850-50760084(-)$1	234	56	73	11.1238
GCGGGCAACGAGGCCCA	chrX:154610579-154610793(+)$1	214	66	83	11.3711
UCGCCAAGCGCCUGGCC	chr21:47423225-47423439(+)$1	214	166	183	12.4814
CCAGGCUUUUCUGUCUC	chr13:39586911-39587219(-)$1	308	195	212	10.2353
CAGUUUCAAAUCAAACC	chr19:53855346-53855559(+)$1	213	93	110	11.9549
UCGAAAACAGCAUUUCU	chr5:35014083-35014303(-)$1	220	25	42	13.1294
CAAUGGGCUGCACCAUC	chr6:139694908-139695166(-)$1	258	135	152	10.2353
auccauucaucuaugga	chr19:12885285-12885518(-)$1	233	162	179	10.0916
AUGAAUAUACAAGUUCC	chrX:140995798-140996014(+)$1	216	18	35	12.7908
auuucuugguauggaag	chr3:57107985-57108200(+)$1	215	120	137	10.8055
GGAUACCUCACAGUAAC	chr11:60167812-60168027(+)$1	215	76	93	10.2730
CUGCUAGUCCAGUAGCA	chr9:33941682-33941897(-)$1	215	141	158	10.0916
UCAGAGUCAUCCCUCUC	chr3:169847048-169847440(-)$1	392	341	358	10.2353
AACAGCUACAUUGCUGU	chrX:118920491-118920765(-)$1	274	15	32	10.1362
GUCUGAAUUUUAUUAGA	chr11:60233424-60233705(+)$1	281	84	101	10.6625
GCCUUUAUGAGAAAAGA	chr15:52902247-52902494(-)$1	247	84	101	10.6049
ACAGGGGAGAAACCCUA	chr10:38344640-38345036(+)$1	396	137	154	12.1339
UCAACUAACUCAUAGUC	chr15:35275256-35275474(-)$1	218	57	74	8.3661
UGGUUGGAAAAACAACG	chr1:155292214-155292427(+)$1	213	111	128	12.7908
CAUGCAAGUUACUGCAG	chr1:233248540-233248809(-)$1	269	141	158	12.6847
ACUGGCCCCUGAGCAUC	chr17:74077869-74078082(+)$1	213	53	70	9.3474
UAUUAUAUGUAAAUAGU	chr9:114994334-114994584(-)$1	250	219	236	10.8055
CCAGGUACUUCCACCGU	chr11:66050683-66050899(+)$1	216	31	48	10.3216
ccuguaguaguguacag	chr19:52778691-52778973(+)$1	282	72	89	10.4344
AUUGUCGAGGUAGACAU	chr6:36168171-36168389(+)$1	218	45	62	12.6847
GUAUCACAGCGCUGAGC	chr12:108011853-108012131(+)$1	278	246	263	9.7066
CCCAGUUCAGAUACUGC	chr1:185277000-185277380(-)$1	380	284	301	12.6152
AUCUGGGAAGGACUCAA	chr10:76735213-76735459(+)$1	246	51	68	8.3661
CACCAGUGACUUCUGUG	chr17:72245091-72245320(+)$1	229	60	77	9.9494
UUUAGAAGGAUCUCUAG	chr14:74400837-74401062(-)$1	225	10	27	10.8138
ACAGUGAAGAUAUCAUC	chr17:2226520-2226751(-)$1	231	131	148	8.3661
cagggcaugguggcuca	chr19:21300776-21300996(+)$1	220	200	217	12.4407
GAUAAUGGCAGAAUUUU	chr5:37351250-37351484(-)$1	234	133	150	10.2730
CAGAUUCUACUUUGAGU	chr20:49509437-49509680(-)$1	243	60	77	9.4547
UAUUCUGUAAAAAGAAC	chr7:38299695-38299931(-)$1	236	65	82	12.7814
CAAGUGGAACAACACCC	chr7:100641505-100641718(+)$1	213	173	190	11.9402
GGGCCGCAGCACAGCGA	chr2:242009503-242009717(+)$1	214	70	87	9.4547
ACAUUAUGACUUUGAGU	chr3:123046469-123046686(-)$1	217	25	42	11.5890
ACUGGGGAGAAACCUUA	chr3:40558052-40558263(+)$1	211	23	40	11.2993
CCUUGGCCUUGACCACC	chr3:183960538-183960770(-)$1	232	2	19	11.5672
GUGGUCUUUGUUGGUCC	chr1:10477047-10477259(+)$1	212	147	164	12.0665
GUGCUGUGUUCCUAGCC	chr16:30681305-30681606(+)$1	301	205	222	11.8203
GCGCCUAUAUUAAGGCA	chr6:35438307-35438540(+)$1	233	207	224	12.9375
GAACUGGCUUUGCAGUU	chr3:195968640-195968875(-)$1	235	128	145	10.8055
CAGAAUAUCAGCAUUCA	chr1:19446710-19447010(-)$1	300	34	51	12.5824
ACCGGCUCCCCUGCCGU	chr17:75471761-75472008(+)$1	247	119	136	11.3557
GUGauuaaaucaaauua	chrX:110931116-110931377(+)$1	261	165	182	10.9825
CUUAUUAAACAAAAUAA	chr19:21366674-21366894(+)$1	220	94	111	10.1969

#DB
.(((((......)))))	chr19:12902576-12902790(+)$1	1	21	38	10.0916
(.((((......)))).	chr10:38344231-38344448(+)$1	1	126	143	12.7908
...(((......)))))	chr7:129916435-129916652(+)$1	1	148	165	11.3941
((..((......))...	chr19:53086332-53086545(+)$1	1	81	98	9.4235
((.(((......))).)	chr12:46245035-46245247(+)$1	1	42	59	10.6845
..((((......)))).	chr7:143882336-143882548(+)$1	1	21	38	12.5559
..((((......)))).	chr15:71211385-71211599(+)$1	1	67	84	12.7929
...(((......)))..	chr1:198668642-198668931(+)$1	1	18	35	11.9402
(..(((......)))..	chr14:50759850-50760084(-)$1	1	56	73	11.1238
))((((......)))).	chrX:154610579-154610793(+)$1	1	66	83	11.3711
(.((((......)))).	chr21:47423225-47423439(+)$1	1	166	183	12.4814
..((((......)))).	chr13:39586911-39587219(-)$1	1	195	212	10.2353
((((((......)))).	chr19:53855346-53855559(+)$1	1	93	110	11.9549
..((((......)))).	chr5:35014083-35014303(-)$1	1	25	42	13.1294
..((((......)))).	chr6:139694908-139695166(-)$1	1	135	152	10.2353
.(((((......)))))	chr19:12885285-12885518(-)$1	1	162	179	10.0916
(.((((......)))).	chrX:140995798-140996014(+)$1	1	18	35	12.7908
.(((((......)))))	chr3:57107985-57108200(+)$1	1	120	137	10.8055
((.(((......))).)	chr11:60167812-60168027(+)$1	1	76	93	10.2730
.(((((......)))))	chr9:33941682-33941897(-)$1	1	141	158	10.0916
..((((......)))).	chr3:169847048-169847440(-)$1	1	341	358	10.2353
((((((......)))))	chrX:118920491-118920765(-)$1	1	15	32	10.1362
((((((......)))))	chr11:60233424-60233705(+)$1	1	84	101	10.6625
).((((......)))).	chr15:52902247-52902494(-)$1	1	84	101	10.6049
..((((......)))).	chr10:38344640-38345036(+)$1	1	137	154	12.1339
...((((.....)))).	chr15:35275256-35275474(-)$1	1	57	74	8.3661
(.((((......)))).	chr1:155292214-155292427(+)$1	1	111	128	12.7908
..((((......)))))	chr1:233248540-233248809(-)$1	1	141	158	12.6847
(...((......))...	chr17:74077869-74078082(+)$1	1	53	70	9.3474
.(((((......)))))	chr9:114994334-114994584(-)$1	1	219	236	10.8055
...(((......)))..	chr11:66050683-66050899(+)$1	1	31	48	10.3216
.(((((......)))))	chr19:52778691-52778973(+)$1	1	72	89	10.4344
..((((......)))))	chr6:36168171-36168389(+)$1	1	45	62	12.6847
((.(((......)))))	chr12:108011853-108012131(+)$1	1	246	263	9.7066
(.((((......)))).	chr1:185277000-185277380(-)$1	1	284	301	12.6152
...((((.....)))).	chr10:76735213-76735459(+)$1	1	51	68	8.3661
((((((......))).)	chr17:72245091-72245320(+)$1	1	60	77	9.9494
((((((......)))))	chr14:74400837-74401062(-)$1	1	10	27	10.8138
...((((.....)))).	chr17:2226520-2226751(-)$1	1	131	148	8.3661
((((((......)))).	chr19:21300776-21300996(+)$1	1	200	217	12.4407
((.(((......))).)	chr5:37351250-37351484(-)$1	1	133	150	10.2730
(((((((......))).	chr20:49509437-49509680(-)$1	1	60	77	9.4547
..((((......)))).	chr7:38299695-38299931(-)$1	1	65	82	12.7814
...(((......)))..	chr7:100641505-100641718(+)$1	1	173	190	11.9402
(((((((......))).	chr2:242009503-242009717(+)$1	1	70	87	9.4547
(..(((......)))..	chr3:123046469-123046686(-)$1	1	25	42	11.5890
(..(((......)))..	chr3:40558052-40558263(+)$1	1	23	40	11.2993
...(((......)))..	chr3:183960538-183960770(-)$1	1	2	19	11.5672
(.((((......)))))	chr1:10477047-10477259(+)$1	1	147	164	12.0665
((((((......)))).	chr16:30681305-30681606(+)$1	1	205	222	11.8203
(.((((......)))).	chr6:35438307-35438540(+)$1	1	207	224	12.9375
.(((((......)))))	chr3:195968640-195968875(-)$1	1	128	145	10.8055
(.((((......)))).	chr1:19446710-19447010(-)$1	1	34	51	12.5824
))((((......)))).	chr17:75471761-75472008(+)$1	1	119	136	11.3557
.(((((......)))))	chrX:110931116-110931377(+)$1	1	165	182	10.9825
.(((((......)))))	chr19:21366674-21366894(+)$1	1	94	111	10.1969

#PSSM
" : 0.17	b : 0.14	: : 0.10	c : 0.08	d : 0.08	h : 0.05	f : 0.05	[ : 0.05	! : 0.05	$ : 0.03	e : 0.03	a : 0.03	B : 0.01	# : 0.01	% : 0.01	( : 0.01	
e : 0.23	" : 0.17	[ : 0.14	! : 0.10	c : 0.07	: : 0.07	b : 0.05	$ : 0.03	f : 0.03	d : 0.03	# : 0.01	h : 0.01	
d : 0.46	e : 0.21	" : 0.14	! : 0.07	[ : 0.07	# : 0.01	f : 0.01	
d : 0.51	c : 0.23	e : 0.21	! : 0.01	" : 0.01	
d : 0.48	c : 0.26	e : 0.21	b : 0.03	
d : 0.48	c : 0.26	e : 0.21	b : 0.03	
o : 0.91	d : 0.05	c : 0.03	
o : 0.94	n : 0.05	
o : 0.94	n : 0.05	
o : 0.94	n : 0.05	
o : 0.94	n : 0.05	
o : 0.94	n : 0.05	
d : 0.48	c : 0.23	e : 0.21	b : 0.03	o : 0.03	
d : 0.48	c : 0.26	e : 0.21	b : 0.03	
d : 0.48	c : 0.26	e : 0.21	3 : 0.03	
d : 0.48	e : 0.21	3 : 0.07	] : 0.07	c : 0.05	2 : 0.05	5 : 0.01	h : 0.01	4 : 0.01	
] : 0.23	e : 0.21	: : 0.10	3 : 0.08	c : 0.07	5 : 0.07	2 : 0.07	4 : 0.03	b : 0.03	h : 0.01	f : 0.01	> : 0.01	d : 0.01	

#score	620.8328565014558
#seq	56
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_LIN28A_Wilbert2012b_hg19_CDS_m3_run2.txt

#BEAR
==========oooooo===========	chr9:100426535-100426771(+)$1	236	28	55	15.9198
hh"""ccc[aooooooa]ccc333hhh	chr11:63743609-63743901(+)$1	292	6	33	14.7371
bb[dddd[bboooooobb]dddd]bb]	chr1:182354812-182355045(-)$1	233	163	190	11.7664
dddd"""cccooooooccc]dddd]ee	chr8:124357138-124357351(-)$1	213	169	196	13.7778
$eeeee!!bboooooobb22eeeee44	chr15:78577546-78577750(-)$1	204	160	187	12.4083
dddd[ccc[aooooooa]ccc]dddd]	chr7:22852613-22852896(-)$1	283	142	169	13.8218
ccc!!ccc[aooooooa]ccccccbb3	chr1:233807023-233807237(+)$1	214	108	135	14.7276
e[cccccc[aooooooa]ccc]ccc]e	chr16:46990857-46991096(-)$1	239	95	122	14.6130
:::ccc[cccooooooccc]ccceeee	chr20:47710647-47710859(+)$1	212	87	114	11.7791
)iiiiiiiiiooooooiiiiiiiii00	chr20:4680354-4680593(+)$1	239	191	218	14.1582
[iiiiiiiiiooooooiiiiiiiii]e	chrY:251535-251742(-)$1	207	95	122	15.0781
cc[a[eeeeeooooooeeeee]a]ccc	chr12:58145338-58145553(-)$1	215	28	55	14.0354
==========oooooo==========:	chr2:152325117-152325322(+)$1	205	19	46	15.3109
cc[gggggggooooooggggggg]ccc	chr4:154557605-154557809(+)$1	204	117	144	14.1672
bbb!!eeeeeooooooeeeee22bb::	chr14:100705520-100705753(+)$1	233	114	141	11.5079
hhhh"""cccooooooccc]hhhhhhh	chr22:37425383-37425613(+)$1	230	21	48	12.8982
gg"""eeeeeooooooeeeee4444gg	chr6:101095036-101095237(-)$1	201	157	184	14.3372
eeeee!!cccooooooccc22eeeee:	chr19:39370196-39370415(-)$1	219	71	98	13.0251
dddd[eeeeeooooooeeeee22dddd	chr17:57725509-57725715(+)$1	206	157	184	12.4610
[a[ccc[cccoooooocccccc]a]ee	chr8:146016569-146016814(-)$1	245	16	43	14.6583
dd####ddddoooooodddd4444ddd	chr5:89988347-89988553(+)$1	206	16	43	13.9719
==========oooooo===========	chr17:18088171-18088400(+)$1	229	115	142	15.9198
::bb[eeeeeooooooeeeee]bbeee	chr1:45316513-45316732(-)$1	219	45	72	10.8623
:iiiiiiiiiooooooiiiiiiiii:H	chr19:29698469-29698707(-)$1	238	165	192	12.8795
%%%ccc!!bboooooobb22ccc333e	chr15:78836440-78836645(+)$1	205	63	90	12.1659
ffbb!!a!!aooooooa22a22bb333	chrX:24006367-24006586(-)$1	219	93	120	13.4837
ggggg[ddddoooooodddd22ggggg	chr3:33729743-33729945(-)$1	202	32	59	13.6431
b[a[a[ddddoooooodddda]a]bb4	chr6:34838730-34838944(+)$1	214	90	117	13.8076
#bb!!ccc[aooooooa]ccc22bbbb	chr6:28403671-28403881(-)$1	210	74	101	13.9474
:ccc[eeeeeooooooeeeee]cccGG	chr15:66793209-66793514(-)$1	305	263	290	11.9143
========[aooooooa==========	chr12:46318602-46318807(-)$1	205	91	118	15.9711
###ccc"""aooooooa333ccc4444	chr12:57605883-57606095(+)$1	212	148	175	15.1785
==========oooooo==========:	chr4:151765230-151765449(-)$1	219	42	69	15.3109
cc####ddddoooooodddd22ccc22	chr1:36360654-36360858(+)$1	204	24	51	14.1254
cccccc[cccooooooccc]ccc333c	chr10:72645554-72645760(-)$1	206	151	178	15.1691
eeee!!ddddoooooodddd]eeeeee	chr19:531856-532092(+)$1	236	95	122	13.0378
==========oooooo==========:	chr10:38343860-38344094(+)$1	234	6	33	15.3109
ccc[bb[cccooooooccc]bb]ccc]	chr20:18296540-18296750(+)$1	210	164	191	13.8315
ggg"""ddddoooooodddd333gggg	chr1:21327616-21327822(-)$1	206	133	160	14.7665
eeee[eeeeeooooooeeeee]eeeee	chr7:73101236-73101476(+)$1	240	205	232	12.9709
ccc####cccooooooccc4444ccc:	chr17:71232908-71233135(+)$1	227	176	203	14.8580
ee!!bb[cccooooooccc]bb22eee	chr12:57038902-57039190(-)$1	288	102	129	13.5080
###ccc!!bboooooobb333ccc444	chr12:62926213-62926447(+)$1	234	135	162	14.4942
eee[ccccccooooooccc]ccc333e	chr7:135327917-135328146(+)$1	229	74	101	14.8675
cc[a!!ddddoooooodddd22a]ccc	chr11:18418345-18418583(+)$1	238	175	202	14.3928
eeeee!!cccooooooccc>>>>>>>>	chr16:2813893-2814114(+)$1	221	63	90	13.0314
eeeee!!cccooooooccc333eeeee	chr10:102746760-102746964(-)$1	204	148	175	14.5779
#iiiiiiiiiooooooiiiiiiiii55	chr1:12032928-12033133(+)$1	205	93	120	13.9930
b"""ccc[bboooooobbccc333bbC	chr9:35717597-35717815(-)$1	218	11	38	13.2567

#otherMatches

#Seq PSSM
CAUAUAUAUGUGUGUGUAUGUGUGUGU	chr9:100426535-100426771(+)$1	236	28	55	15.9198
UGCUGCCUGGGAACUGCAAGGACUUAG	chr11:63743609-63743901(+)$1	292	6	33	14.7371
CCAAUCCAUCAAUGAAGAAGGGUAGGU	chr1:182354812-182355045(-)$1	233	163	190	11.7664
UUGCUCCAGUUUUACUACUUGCAACUU	chr8:124357138-124357351(-)$1	213	169	196	13.7778
UAUUUCAUCUUUAGAUAGUCGGGGUUG	chr15:78577546-78577750(-)$1	204	160	187	12.4083
AGCGGACAGCAUGGAAGAUGUGUGCUC	chr7:22852613-22852896(-)$1	283	142	169	13.8218
UCAGGUGCACAUCAUAGAGCAUGACCA	chr1:233807023-233807237(+)$1	214	108	135	14.7276
UAGCUCUGAUGAAGAAAGCAGCAGCCA	chr16:46990857-46991096(-)$1	239	95	122	14.6130
AAUGUAGAGAAAAAGAUCUGUGCGGUU	chr20:47710647-47710859(+)$1	212	87	114	11.7791
AGAGAGGAUCGAGCAUGGUCCUCUUCU	chr20:4680354-4680593(+)$1	239	191	218	14.1582
CUGGACGGGGACGGCGCCCUGUCCAUG	chrY:251535-251742(-)$1	207	95	122	15.0781
UUGUAGGGUCUCCCUUGAUCUGAGAAU	chr12:58145338-58145553(-)$1	215	28	55	14.0354
UCUGAAAUUUAUUCUAAGAUUUCAGAA	chr2:152325117-152325322(+)$1	205	19	46	15.3109
GUGUGAAAAUAAUUGGAUUUUUAAACA	chr4:154557605-154557809(+)$1	204	117	144	14.1672
CGAGAUCGUGGAGCUGCACGAGAUCGA	chr14:100705520-100705753(+)$1	233	114	141	11.5079
UGGCUCUGGCGUCACAGCCUGCCACGU	chr22:37425383-37425613(+)$1	230	21	48	12.8982
UUGAAUGUAUUGUUUUGUGCAAAUAAA	chr6:101095036-101095237(-)$1	201	157	184	14.3372
AGUCGGACCCUUUCCUGGGGAUGAUUA	chr19:39370196-39370415(-)$1	219	71	98	13.0251
GGACAUGCAGCUAGCUUUGCACAGUUU	chr17:57725509-57725715(+)$1	206	157	184	12.4610
AGACCGUGGCAAGCUGGCCCGGGCAUC	chr8:146016569-146016814(-)$1	245	16	43	14.6583
UUUUUAUUCUAAUUUCAGAACUGUGAU	chr5:89988347-89988553(+)$1	206	16	43	13.9719
CUUUCCCUGCCGGUGCGCAGGGGAAGC	chr17:18088171-18088400(+)$1	229	115	142	15.9198
UUUCUUUUGUAGCUAAACGAGUGAAUG	chr1:45316513-45316732(-)$1	219	45	72	10.8623
UGGCAGGAUCAGAUUGGGUCCUGCUCC	chr19:29698469-29698707(-)$1	238	165	192	12.8795
UACAGAUCAAUGUCUUUUUUUCUUCAA	chr15:78836440-78836645(+)$1	205	63	90	12.1659
AUAGAACAACGGACCAGGAGAACUCAA	chrX:24006367-24006586(-)$1	219	93	120	13.4837
UAACAUGAAUAAUUUAGUUUUUUGUUA	chr3:33729743-33729945(-)$1	202	32	59	13.6431
CUUGGAGGAUGAGGAGAUCCCGGUGGU	chr6:34838730-34838944(+)$1	214	90	117	13.8076
AGAGAUGCACACCAAGGAGCAGAUCCU	chr6:28403671-28403881(-)$1	210	74	101	13.9474
UAUUGUGGAUAUUAACAUUCAGAAUUG	chr15:66793209-66793514(-)$1	305	263	290	11.9143
GUGUUCAUGCUCCUUUGAUGAACAUCC	chr12:46318602-46318807(-)$1	205	91	118	15.9711
GGACCCUGACAAGGUGGGCUGGGAGGC	chr12:57605883-57606095(+)$1	212	148	175	15.1785
UGuauauaugaauauauauauauacaa	chr4:151765230-151765449(-)$1	219	42	69	15.3109
AAUGCUGGGUUAUGACACCCCCUUCCU	chr1:36360654-36360858(+)$1	204	24	51	14.1254
GCUGGAAGGCCGUGAUGCCAUCUUCAA	chr10:72645554-72645760(-)$1	206	151	178	15.1691
CAGCUCGCAGAAGGCGCUGCUGCUGGA	chr19:531856-532092(+)$1	236	95	122	13.0378
ACAAUCACUAUGAAUUUAGUGAUUGUG	chr10:38343860-38344094(+)$1	234	6	33	15.3109
CACUCAAAGGAGAAGCCCUAUGUGUGC	chr20:18296540-18296750(+)$1	210	164	191	13.8315
AAGCAAUAUAACAAACUGUACUUCUUG	chr1:21327616-21327822(-)$1	206	133	160	14.7665
CCUGCuuuuauuuauuuagagacaggg	chr7:73101236-73101476(+)$1	240	205	232	12.9709
GACCCAGAAGCCACAACUUAUCAGUCC	chr17:71232908-71233135(+)$1	227	176	203	14.8580
CACCGGGCGCAUCGUGGCGGUCAUUGG	chr12:57038902-57039190(-)$1	288	102	129	13.5080
AAACAGAAUGUCAAACCACCACUGAAG	chr12:62926213-62926447(+)$1	234	135	162	14.4942
CAUCUACCUGCUGAAACAGAGUGCUAA	chr7:135327917-135328146(+)$1	229	74	101	14.8675
UGAGAGUCUACCACACUGGAAGCCCAU	chr11:18418345-18418583(+)$1	238	175	202	14.3928
CUUCAUAUCCUACAGUGGACUCGAAUU	chr16:2813893-2814114(+)$1	221	63	90	13.0314
GGGAUCAGGGGCUCGACCCGCUAUCCU	chr10:102746760-102746964(-)$1	204	148	175	14.5779
AUCGCCCUGAACCGAGUCGGGGUGGAU	chr1:12032928-12033133(+)$1	205	93	120	13.9930
CUAACUGCUGUUUUCUCACAGGAUGCG	chr9:35717597-35717815(-)$1	218	11	38	13.2567

#DB
((((((((((......)))))))))))	chr9:100426535-100426771(+)$1	1	28	55	15.9198
((...(((.(......).)))...)))	chr11:63743609-63743901(+)$1	1	6	33	14.7371
((.((((.((......)).)))).)).	chr1:182354812-182355045(-)$1	1	163	190	11.7664
((((...(((......))).)))).))	chr8:124357138-124357351(-)$1	1	169	196	13.7778
.(((((..((......))..)))))..	chr15:78577546-78577750(-)$1	1	160	187	12.4083
((((.(((.(......).))).)))).	chr7:22852613-22852896(-)$1	1	142	169	13.8218
(((..(((.(......).)))))))).	chr1:233807023-233807237(+)$1	1	108	135	14.7276
(.((((((.(......).))).))).)	chr16:46990857-46991096(-)$1	1	95	122	14.6130
...(((.(((......))).)))((((	chr20:47710647-47710859(+)$1	1	87	114	11.7791
.(((((((((......)))))))))..	chr20:4680354-4680593(+)$1	1	191	218	14.1582
.(((((((((......))))))))).)	chrY:251535-251742(-)$1	1	95	122	15.0781
((.(.(((((......))))).).)))	chr12:58145338-58145553(-)$1	1	28	55	14.0354
((((((((((......)))))))))).	chr2:152325117-152325322(+)$1	1	19	46	15.3109
((.(((((((......))))))).)))	chr4:154557605-154557809(+)$1	1	117	144	14.1672
)((..(((((......)))))..))..	chr14:100705520-100705753(+)$1	1	114	141	11.5079
((((...(((......))).)))))))	chr22:37425383-37425613(+)$1	1	21	48	12.8982
((...(((((......)))))....))	chr6:101095036-101095237(-)$1	1	157	184	14.3372
(((((..(((......)))..))))).	chr19:39370196-39370415(-)$1	1	71	98	13.0251
((((.(((((......)))))..))))	chr17:57725509-57725715(+)$1	1	157	184	12.4610
.(.(((.(((......)))))).).))	chr8:146016569-146016814(-)$1	1	16	43	14.6583
((....((((......))))....)))	chr5:89988347-89988553(+)$1	1	16	43	13.9719
((((((((((......)))))))))))	chr17:18088171-18088400(+)$1	1	115	142	15.9198
..((.(((((......))))).))(((	chr1:45316513-45316732(-)$1	1	45	72	10.8623
.(((((((((......))))))))).)	chr19:29698469-29698707(-)$1	1	165	192	12.8795
...(((..((......))..)))...)	chr15:78836440-78836645(+)$1	1	63	90	12.1659
((((..(..(......)..)..))...	chrX:24006367-24006586(-)$1	1	93	120	13.4837
(((((.((((......))))..)))))	chr3:33729743-33729945(-)$1	1	32	59	13.6431
(.(.(.((((......))))).).)).	chr6:34838730-34838944(+)$1	1	90	117	13.8076
.((..(((.(......).)))..))))	chr6:28403671-28403881(-)$1	1	74	101	13.9474
.(((.(((((......))))).)))))	chr15:66793209-66793514(-)$1	1	263	290	11.9143
((((((((.(......)))))))))))	chr12:46318602-46318807(-)$1	1	91	118	15.9711
...(((...(......)...)))....	chr12:57605883-57606095(+)$1	1	148	175	15.1785
((((((((((......)))))))))).	chr4:151765230-151765449(-)$1	1	42	69	15.3109
((....((((......))))..)))..	chr1:36360654-36360858(+)$1	1	24	51	14.1254
((((((.(((......))).)))...)	chr10:72645554-72645760(-)$1	1	151	178	15.1691
((((..((((......)))).)))))(	chr19:531856-532092(+)$1	1	95	122	13.0378
((((((((((......)))))))))).	chr10:38343860-38344094(+)$1	1	6	33	15.3109
(((.((.(((......))).)).))).	chr20:18296540-18296750(+)$1	1	164	191	13.8315
(((...((((......))))...))))	chr1:21327616-21327822(-)$1	1	133	160	14.7665
((((.(((((......))))).)))))	chr7:73101236-73101476(+)$1	1	205	232	12.9709
(((....(((......)))....))).	chr17:71232908-71233135(+)$1	1	176	203	14.8580
((..((.(((......))).))..)))	chr12:57038902-57039190(-)$1	1	102	129	13.5080
...(((..((......))...)))...	chr12:62926213-62926447(+)$1	1	135	162	14.4942
(((.((((((......))).)))...)	chr7:135327917-135328146(+)$1	1	74	101	14.8675
((.(..((((......))))..).)))	chr11:18418345-18418583(+)$1	1	175	202	14.3928
(((((..(((......)))........	chr16:2813893-2814114(+)$1	1	63	90	13.0314
(((((..(((......)))...)))))	chr10:102746760-102746964(-)$1	1	148	175	14.5779
.(((((((((......)))))))))..	chr1:12032928-12033133(+)$1	1	93	120	13.9930
(...(((.((......)))))...))(	chr9:35717597-35717815(-)$1	1	11	38	13.2567

#PSSM
c : 0.16	e : 0.16	= : 0.12	b : 0.08	d : 0.08	: : 0.08	# : 0.08	g : 0.06	h : 0.04	[ : 0.04	$ : 0.02	) : 0.02	% : 0.02	f : 0.02	
c : 0.18	e : 0.16	= : 0.12	d : 0.08	i : 0.08	b : 0.06	g : 0.06	h : 0.04	[ : 0.04	: : 0.04	# : 0.04	a : 0.02	% : 0.02	f : 0.02	" : 0.02	
e : 0.14	= : 0.12	c : 0.12	[ : 0.10	i : 0.08	b : 0.08	# : 0.08	" : 0.06	d : 0.06	g : 0.04	: : 0.02	h : 0.02	% : 0.02	a : 0.02	! : 0.02	
c : 0.16	= : 0.12	e : 0.12	" : 0.08	d : 0.08	! : 0.08	i : 0.08	# : 0.06	[ : 0.06	a : 0.04	g : 0.04	b : 0.04	h : 0.02	
c : 0.18	= : 0.12	[ : 0.12	! : 0.12	" : 0.10	e : 0.08	i : 0.08	# : 0.06	g : 0.04	b : 0.04	d : 0.02	a : 0.02	
c : 0.26	e : 0.16	= : 0.12	! : 0.12	i : 0.08	" : 0.06	# : 0.06	[ : 0.04	b : 0.04	d : 0.02	g : 0.02	
d : 0.16	c : 0.14	e : 0.14	= : 0.12	! : 0.12	[ : 0.10	i : 0.08	" : 0.06	g : 0.02	a : 0.02	# : 0.02	
c : 0.34	e : 0.14	d : 0.14	= : 0.12	! : 0.08	i : 0.08	[ : 0.04	g : 0.02	" : 0.02	
c : 0.24	e : 0.14	d : 0.14	[ : 0.12	= : 0.10	b : 0.10	i : 0.08	g : 0.02	! : 0.02	" : 0.02	
c : 0.24	a : 0.16	e : 0.14	d : 0.14	= : 0.10	b : 0.10	i : 0.08	g : 0.02	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
c : 0.24	a : 0.16	e : 0.14	d : 0.14	= : 0.10	b : 0.10	i : 0.08	g : 0.02	
c : 0.24	e : 0.14	d : 0.14	= : 0.12	] : 0.10	b : 0.10	i : 0.08	g : 0.02	2 : 0.02	3 : 0.02	
c : 0.36	e : 0.14	d : 0.14	= : 0.12	i : 0.08	2 : 0.06	3 : 0.04	] : 0.02	g : 0.02	
d : 0.16	c : 0.14	] : 0.14	e : 0.14	= : 0.12	i : 0.08	2 : 0.06	3 : 0.06	g : 0.02	a : 0.02	4 : 0.02	> : 0.02	
c : 0.24	e : 0.16	= : 0.12	2 : 0.10	i : 0.08	3 : 0.06	d : 0.04	4 : 0.04	b : 0.04	g : 0.02	h : 0.02	a : 0.02	] : 0.02	> : 0.02	
c : 0.16	] : 0.14	2 : 0.14	= : 0.12	3 : 0.08	i : 0.08	e : 0.06	4 : 0.06	d : 0.04	b : 0.04	g : 0.02	h : 0.02	> : 0.02	
c : 0.20	= : 0.12	e : 0.10	i : 0.08	2 : 0.08	3 : 0.06	d : 0.06	a : 0.06	4 : 0.06	g : 0.04	] : 0.04	b : 0.04	h : 0.02	> : 0.02	
c : 0.14	= : 0.12	e : 0.12	3 : 0.10	] : 0.10	i : 0.08	b : 0.08	d : 0.06	4 : 0.06	g : 0.04	h : 0.02	a : 0.02	2 : 0.02	> : 0.02	
e : 0.16	c : 0.16	= : 0.12	b : 0.12	i : 0.08	3 : 0.08	d : 0.06	4 : 0.06	h : 0.04	] : 0.04	g : 0.04	> : 0.02	
e : 0.18	= : 0.12	b : 0.10	c : 0.10	3 : 0.08	4 : 0.06	d : 0.06	g : 0.06	h : 0.04	] : 0.04	: : 0.04	0 : 0.02	G : 0.02	2 : 0.02	> : 0.02	5 : 0.02	
e : 0.24	: : 0.12	4 : 0.08	c : 0.08	= : 0.06	] : 0.06	g : 0.06	h : 0.04	3 : 0.04	d : 0.04	0 : 0.02	H : 0.02	b : 0.02	G : 0.02	2 : 0.02	> : 0.02	5 : 0.02	C : 0.02	

#score	680.4388298666537
#seq	49
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m3_run1.txt

#BEAR
d[ddddqqqqqqqqdddd]d	chr13:95280387-95280638(+)$1	251	207	227	13.9759
beeeeeqqqqqqqqeeeee]	chr2:173369352-173369584(+)$1	232	167	187	14.2170
ffffffqqqqqqqqffffff	chr3:120048143-120048366(-)$1	223	167	187	15.0886
ffffffqqqqqqqqffffff	chr5:141380166-141380389(-)$1	223	7	27	15.0886
ggggggqqqqqqqqgggggg	chr17:27585625-27585850(-)$1	225	2	22	15.2030
eee[bbqqqqqqqqbbeeee	chr4:123844191-123844415(+)$1	224	171	191	13.5526
###cccqqqqqqqqcccccc	chr6:82950391-82950622(-)$1	231	26	46	14.7124
ggggggqqqqqqqqgggggg	chr14:34903301-34903531(-)$1	230	11	31	15.2030
ggggggqqqqqqqqgggggg	chr18:47008332-47008553(-)$1	221	70	90	15.2030
deeeeeqqqqqqqqeeeee]	chr9:131570766-131571008(+)$1	242	165	185	14.3362
ffffffqqqqqqqqffffff	chr1:156262778-156263025(-)$1	247	20	40	15.0886
ffffffqqqqqqqqffffff	chr2:55199950-55200197(-)$1	247	22	42	15.0886
ffffffqqqqqqqqffffff	chr18:19781622-19781870(+)$1	248	209	229	15.0886
ffffffqqqqqqqqffffff	chr3:176740939-176741214(-)$1	275	137	157	15.0886
!bbcccqqqqqqqqccc]bb	chr6:32943095-32943323(+)$1	228	139	159	13.6328
ffffffqqqqqqqqffffff	chr5:162871574-162871811(+)$1	237	63	83	15.0886
eeee[aqqqqqqqqa]eeee	chr12:56991351-56991584(-)$1	233	46	66	14.0281
ffffffqqqqqqqqffffff	chr16:50264518-50264753(+)$1	235	214	234	15.0886
geeeeeqqqqqqqqeeeee:	chr17:40966487-40966728(-)$1	241	91	111	13.4604
###cccqqqqqqqqccc444	chr17:4801035-4801289(+)$1	254	195	215	14.8601
ffffffqqqqqqqqffffff	chr1:201434610-201434881(-)$1	271	216	236	15.0886
fffffaqqqqqqqqa]ffff	chr17:48211913-48212163(-)$1	250	163	183	14.7289
ggggggqqqqqqqqgggggg	chr10:70776128-70776406(+)$1	278	126	146	15.2030
ffffffqqqqqqqqffffff	chr1:145442331-145442597(+)$1	266	0	20	15.0886
[eeeeeqqqqqqqqeeeee]	chr12:56635560-56635821(-)$1	261	210	230	14.6353
iiicccqqqqqqqqccc444	chr3:178739810-178740053(-)$1	243	30	50	14.9382
ceeeeeqqqqqqqqeeeee0	chr20:17922647-17922888(-)$1	241	185	205	14.0725
e!!cccqqqqqqqqccc333	chr4:85570086-85570329(+)$1	243	53	73	15.3042
ggggggqqqqqqqqgggggg	chrX:150575909-150576165(+)$1	256	25	45	15.2030
ggggggqqqqqqqqgggggg	chr1:225589301-225589532(-)$1	231	157	177	15.2030
ggggggqqqqqqqqgggggg	chr21:34003095-34003336(-)$1	241	64	84	15.2030
"""cccqqqqqqqqccc333	chr6:80625014-80625254(-)$1	240	205	225	15.2780
""ddddqqqqqqqqdddd44	chr6:15522033-15522278(+)$1	245	81	101	14.2966
ffffffqqqqqqqqffffff	chr10:114925527-114925761(+)$1	234	18	38	15.0886
======qqqqqqqq======	chr7:27202596-27202846(-)$1	250	4	24	14.9677
d!!cccqqqqqqqqcccddd	chr19:3630493-3630719(-)$1	226	166	186	14.4125
!!ddddqqqqqqqqdddd22	chr9:36338107-36338334(-)$1	227	182	202	14.1814
ffffffqqqqqqqqffffff	chr3:53226257-53226481(+)$1	224	169	189	15.0886
ffffffqqqqqqqqffffff	chr22:38687127-38687383(-)$1	256	116	136	15.0886
$$ddddqqqqqqqqdddd22	chr17:20903035-20903271(-)$1	236	95	115	13.5730
[eeeeeqqqqqqqqeeeee]	chr12:56991294-56991569(-)$1	275	234	254	14.6353
ffffffqqqqqqqqffffff	chrX:153173036-153173264(-)$1	228	187	207	15.0886
dd!!bbqqqqqqqqbb22dd	chr3:42707350-42707587(+)$1	237	45	65	12.6117
ggggggqqqqqqqqgggggg	chr1:94354107-94354331(-)$1	224	133	153	15.2030
!!ddddqqqqqqqqdddd33	chr1:162495081-162495333(+)$1	252	84	104	14.6707
d[ddddqqqqqqqqdddd]d	chr12:4411775-4412014(+)$1	239	185	205	13.9759
dd!!bbqqqqqqqqbb333d	chr12:56632569-56632812(-)$1	243	6	26	13.4655
!!ddddqqqqqqqqdddd22	chr1:145442285-145442565(+)$1	280	66	86	14.1814
c[ddddqqqqqqqqddddcc	chr9:130209883-130210105(-)$1	222	143	163	14.1534
ggggggqqqqqqqqgggggg	chr19:13054834-13055086(+)$1	252	191	211	15.2030
##ddddqqqqqqqqdddd44	chr6:143073725-143073946(-)$1	221	87	107	14.2231
ggggggqqqqqqqqgggggg	chrX:41208508-41208769(+)$1	261	187	207	15.2030
c!!cccqqqqqqqqccc22c	chr13:100638189-100638473(+)$1	284	180	200	14.7442
f"""bbqqqqqqqqbb4444	chr19:56153449-56153687(+)$1	238	51	71	13.7214
hhddddqqqqqqqqdddd]h	chr9:130871274-130871515(+)$1	241	204	224	13.4771
ggggggqqqqqqqqgggggg	chr1:145441449-145441718(+)$1	269	131	151	15.2030
ccc[bbqqqqqqqqbb]ccc	chr13:107143781-107144039(-)$1	258	114	134	13.6002
"eeeeeqqqqqqqqeeeee4	chr16:84087538-84087769(-)$1	231	61	81	14.5043
cc[cccqqqqqqqqcccccc	chr3:113680277-113680496(+)$1	219	167	187	14.7219

#otherMatches

#Seq PSSM
CCAUUAAUAGUCACUGAUUG	chr13:95280387-95280638(+)$1	251	207	227	13.9759
GUGUGAAUACCUGCUCACGU	chr2:173369352-173369584(+)$1	232	167	187	14.2170
GCUUACUUCUCCAUGUGGGC	chr3:120048143-120048366(-)$1	223	167	187	15.0886
UAGCCCAGGCCUAAGGGCUA	chr5:141380166-141380389(-)$1	223	7	27	15.0886
AUGUGAUGCACUUUUUACAU	chr17:27585625-27585850(-)$1	225	2	22	15.2030
UGCUGCUUCCUCUUGUGCGG	chr4:123844191-123844415(+)$1	224	171	191	13.5526
UUUGAAUUUUUAUUUUCUCU	chr6:82950391-82950622(-)$1	231	26	46	14.7124
UGUUGUUAAAAAUUAUAGCA	chr14:34903301-34903531(-)$1	230	11	31	15.2030
GUUAUUGCUGUUUGAAUAAU	chr18:47008332-47008553(-)$1	221	70	90	15.2030
GCUCCCCUGAACCUGGGAGA	chr9:131570766-131571008(+)$1	242	165	185	14.3362
UCUAGGUCGAUGCUCCUGGG	chr1:156262778-156263025(-)$1	247	20	40	15.0886
GUUAGAUCUUUAUUUUUAGC	chr2:55199950-55200197(-)$1	247	22	42	15.0886
CUAACCCACAGGCAGGUUGG	chr18:19781622-19781870(+)$1	248	209	229	15.0886
GGAAUAGACACAAAUGUUUU	chr3:176740939-176741214(-)$1	275	137	157	15.0886
GGCUGCUUCAGAGUGUAUGC	chr6:32943095-32943323(+)$1	228	139	159	13.6328
CUUCAUAACUAUGAAUGAAG	chr5:162871574-162871811(+)$1	237	63	83	15.0886
UCAGGGACAACUACUGCUGA	chr12:56991351-56991584(-)$1	233	46	66	14.0281
CUGAAAAUGCUUUCUUUCAG	chr16:50264518-50264753(+)$1	235	214	234	15.0886
UGUUCCCGUGGAAUGGAAUG	chr17:40966487-40966728(-)$1	241	91	111	13.4604
CCUUGCUUGCAUCUGUAUAU	chr17:4801035-4801289(+)$1	254	195	215	14.8601
GUCUUUCCCCAAAUGAAGAU	chr1:201434610-201434881(-)$1	271	216	236	15.0886
CCCAGCUCCCCAUUGCCUGG	chr17:48211913-48212163(-)$1	250	163	183	14.7289
UUACCUUUAUAGCCAGGUGA	chr10:70776128-70776406(+)$1	278	126	146	15.2030
UUCCUGCCCUGUGUUAGGAG	chr1:145442331-145442597(+)$1	266	0	20	15.0886
UGAAGAGGGGGCAGUUUUCU	chr12:56635560-56635821(-)$1	261	210	230	14.6353
GCAGCCGACUUAAGGGCUUG	chr3:178739810-178740053(-)$1	243	30	50	14.9382
CUUCUGGAAACAAGUAGAAG	chr20:17922647-17922888(-)$1	241	185	205	14.0725
AACACUAUAAAAUGAGUAAG	chr4:85570086-85570329(+)$1	243	53	73	15.3042
GUAUAUACUUCAAGAUGUAU	chrX:150575909-150576165(+)$1	256	25	45	15.2030
GAAGGACAUUAAAUUCUUUC	chr1:225589301-225589532(-)$1	231	157	177	15.2030
UUUGGCAGGAUAGAGCUAAG	chr21:34003095-34003336(-)$1	241	64	84	15.2030
UCAGAACUAUAACAUUCAAU	chr6:80625014-80625254(-)$1	240	205	225	15.2780
ACAGUUUGACAUUUAAUUUA	chr6:15522033-15522278(+)$1	245	81	101	14.2966
GAGGCCACCCACAAGGCCUC	chr10:114925527-114925761(+)$1	234	18	38	15.0886
GUAUAGUUUUUAGUCUGUGU	chr7:27202596-27202846(-)$1	250	4	24	14.9677
CAGUCCCCACCCCAGGAGAG	chr19:3630493-3630719(-)$1	226	166	186	14.4125
GUCUGCCUCUUCCUGCAGUU	chr9:36338107-36338334(-)$1	227	182	202	14.1814
UCAUGGUACUUCCUCUGUGA	chr3:53226257-53226481(+)$1	224	169	189	15.0886
GUGUCUACUAACAAGGACAU	chr22:38687127-38687383(-)$1	256	116	136	15.0886
GUGCUAUUGUAUUUUGGCUU	chr17:20903035-20903271(-)$1	236	95	115	13.5730
CCCUGUAUUGUUUGAUAGGA	chr12:56991294-56991569(-)$1	275	234	254	14.6353
CUGCACUUCACCCUGUGCAG	chrX:153173036-153173264(-)$1	228	187	207	15.0886
CUACAUGUUUCCUAGUUAAG	chr3:42707350-42707587(+)$1	237	45	65	12.6117
UUUUUUAUUUCCAAAAAAAA	chr1:94354107-94354331(-)$1	224	133	153	15.2030
GUGUUUCAUUCCCUAAAUUA	chr1:162495081-162495333(+)$1	252	84	104	14.6707
AGAAGGGUUCAGGACUUUGU	chr12:4411775-4412014(+)$1	239	185	205	13.9759
CCCUCACCCACUCCUGCUAG	chr12:56632569-56632812(-)$1	243	6	26	13.4655
AUAGGGAUAUUGGCCCCUCA	chr1:145442285-145442565(+)$1	280	66	86	14.1814
AACUGGUGGAUUUUCUGGUG	chr9:130209883-130210105(-)$1	222	143	163	14.1534
CUCCCCUCCAACCUGGGGGG	chr19:13054834-13055086(+)$1	252	191	211	15.2030
CAGCAUCAAUAUAUAUGUGA	chr6:143073725-143073946(-)$1	221	87	107	14.2231
AUAGUUGGGAAGAAAACUAU	chrX:41208508-41208769(+)$1	261	187	207	15.2030
AUUGCGUUCCUCCCCGCCUU	chr13:100638189-100638473(+)$1	284	180	200	14.7442
UAAGAUGUAAAGAGGUAAAC	chr19:56153449-56153687(+)$1	238	51	71	13.7214
AGUUGUCAUUUAAAGCAGCC	chr9:130871274-130871515(+)$1	241	204	224	13.4771
UUUUGUAAAUUGUGAUAGGA	chr1:145441449-145441718(+)$1	269	131	151	15.2030
GGAAGUAAAUUAUGAUGUCC	chr13:107143781-107144039(-)$1	258	114	134	13.6002
CCAAGCUAAAAGACGCUUGU	chr16:84087538-84087769(-)$1	231	61	81	14.5043
GCCACAUAUGUGUUUGUGUU	chr3:113680277-113680496(+)$1	219	167	187	14.7219

#DB
(.((((........)))).)	chr13:95280387-95280638(+)$1	1	207	227	13.9759
((((((........))))).	chr2:173369352-173369584(+)$1	1	167	187	14.2170
((((((........))))))	chr3:120048143-120048366(-)$1	1	167	187	15.0886
((((((........))))))	chr5:141380166-141380389(-)$1	1	7	27	15.0886
((((((........))))))	chr17:27585625-27585850(-)$1	1	2	22	15.2030
(((.((........))))))	chr4:123844191-123844415(+)$1	1	171	191	13.5526
...(((........))))))	chr6:82950391-82950622(-)$1	1	26	46	14.7124
((((((........))))))	chr14:34903301-34903531(-)$1	1	11	31	15.2030
((((((........))))))	chr18:47008332-47008553(-)$1	1	70	90	15.2030
((((((........))))).	chr9:131570766-131571008(+)$1	1	165	185	14.3362
((((((........))))))	chr1:156262778-156263025(-)$1	1	20	40	15.0886
((((((........))))))	chr2:55199950-55200197(-)$1	1	22	42	15.0886
((((((........))))))	chr18:19781622-19781870(+)$1	1	209	229	15.0886
((((((........))))))	chr3:176740939-176741214(-)$1	1	137	157	15.0886
.(((((........))).))	chr6:32943095-32943323(+)$1	1	139	159	13.6328
((((((........))))))	chr5:162871574-162871811(+)$1	1	63	83	15.0886
((((.(........).))))	chr12:56991351-56991584(-)$1	1	46	66	14.0281
((((((........))))))	chr16:50264518-50264753(+)$1	1	214	234	15.0886
)(((((........))))).	chr17:40966487-40966728(-)$1	1	91	111	13.4604
...(((........)))...	chr17:4801035-4801289(+)$1	1	195	215	14.8601
((((((........))))))	chr1:201434610-201434881(-)$1	1	216	236	15.0886
((((((........).))))	chr17:48211913-48212163(-)$1	1	163	183	14.7289
((((((........))))))	chr10:70776128-70776406(+)$1	1	126	146	15.2030
((((((........))))))	chr1:145442331-145442597(+)$1	1	0	20	15.0886
.(((((........))))).	chr12:56635560-56635821(-)$1	1	210	230	14.6353
((((((........)))...	chr3:178739810-178740053(-)$1	1	30	50	14.9382
((((((........))))).	chr20:17922647-17922888(-)$1	1	185	205	14.0725
(..(((........)))...	chr4:85570086-85570329(+)$1	1	53	73	15.3042
((((((........))))))	chrX:150575909-150576165(+)$1	1	25	45	15.2030
((((((........))))))	chr1:225589301-225589532(-)$1	1	157	177	15.2030
((((((........))))))	chr21:34003095-34003336(-)$1	1	64	84	15.2030
...(((........)))...	chr6:80625014-80625254(-)$1	1	205	225	15.2780
..((((........))))..	chr6:15522033-15522278(+)$1	1	81	101	14.2966
((((((........))))))	chr10:114925527-114925761(+)$1	1	18	38	15.0886
((((((........))))))	chr7:27202596-27202846(-)$1	1	4	24	14.9677
(..(((........))))))	chr19:3630493-3630719(-)$1	1	166	186	14.4125
..((((........))))..	chr9:36338107-36338334(-)$1	1	182	202	14.1814
((((((........))))))	chr3:53226257-53226481(+)$1	1	169	189	15.0886
((((((........))))))	chr22:38687127-38687383(-)$1	1	116	136	15.0886
..((((........))))..	chr17:20903035-20903271(-)$1	1	95	115	13.5730
.(((((........))))).	chr12:56991294-56991569(-)$1	1	234	254	14.6353
((((((........))))))	chrX:153173036-153173264(-)$1	1	187	207	15.0886
((..((........))..))	chr3:42707350-42707587(+)$1	1	45	65	12.6117
((((((........))))))	chr1:94354107-94354331(-)$1	1	133	153	15.2030
..((((........))))..	chr1:162495081-162495333(+)$1	1	84	104	14.6707
(.((((........)))).)	chr12:4411775-4412014(+)$1	1	185	205	13.9759
((..((........))...)	chr12:56632569-56632812(-)$1	1	6	26	13.4655
..((((........))))..	chr1:145442285-145442565(+)$1	1	66	86	14.1814
(.((((........))))))	chr9:130209883-130210105(-)$1	1	143	163	14.1534
((((((........))))))	chr19:13054834-13055086(+)$1	1	191	211	15.2030
..((((........))))..	chr6:143073725-143073946(-)$1	1	87	107	14.2231
((((((........))))))	chrX:41208508-41208769(+)$1	1	187	207	15.2030
(..(((........)))..)	chr13:100638189-100638473(+)$1	1	180	200	14.7442
(...((........))....	chr19:56153449-56153687(+)$1	1	51	71	13.7214
((((((........)))).)	chr9:130871274-130871515(+)$1	1	204	224	13.4771
((((((........))))))	chr1:145441449-145441718(+)$1	1	131	151	15.2030
(((.((........)).)))	chr13:107143781-107144039(-)$1	1	114	134	13.6002
.(((((........))))).	chr16:84087538-84087769(-)$1	1	61	81	14.5043
((.(((........))))))	chr3:113680277-113680496(+)$1	1	167	187	14.7219

#PSSM
f : 0.27	g : 0.20	d : 0.10	c : 0.08	! : 0.06	e : 0.05	# : 0.05	" : 0.05	[ : 0.03	b : 0.01	i : 0.01	= : 0.01	$ : 0.01	h : 0.01	
f : 0.25	g : 0.18	e : 0.15	! : 0.10	[ : 0.05	# : 0.05	" : 0.05	d : 0.03	c : 0.03	b : 0.01	i : 0.01	= : 0.01	$ : 0.01	h : 0.01	
f : 0.25	g : 0.18	d : 0.16	e : 0.15	! : 0.08	# : 0.03	" : 0.03	b : 0.01	i : 0.01	= : 0.01	c : 0.01	[ : 0.01	
f : 0.25	g : 0.18	d : 0.16	c : 0.15	e : 0.13	[ : 0.03	! : 0.03	= : 0.01	" : 0.01	
f : 0.25	g : 0.18	d : 0.16	c : 0.15	e : 0.11	b : 0.08	[ : 0.01	= : 0.01	
f : 0.23	g : 0.18	d : 0.16	c : 0.15	e : 0.11	b : 0.08	a : 0.03	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
f : 0.23	g : 0.18	d : 0.16	c : 0.15	e : 0.11	b : 0.08	a : 0.03	= : 0.01	
f : 0.23	g : 0.18	d : 0.16	c : 0.15	e : 0.11	b : 0.08	] : 0.03	= : 0.01	
f : 0.25	g : 0.18	d : 0.16	e : 0.15	c : 0.15	= : 0.01	2 : 0.01	3 : 0.01	4 : 0.01	] : 0.01	
f : 0.25	d : 0.18	g : 0.18	e : 0.15	c : 0.05	4 : 0.05	3 : 0.05	2 : 0.03	] : 0.01	= : 0.01	
f : 0.25	g : 0.18	e : 0.15	4 : 0.08	c : 0.06	3 : 0.06	2 : 0.06	] : 0.05	d : 0.03	b : 0.01	= : 0.01	
f : 0.25	g : 0.18	4 : 0.10	d : 0.08	c : 0.08	] : 0.06	3 : 0.05	2 : 0.05	e : 0.03	b : 0.01	: : 0.01	0 : 0.01	= : 0.01	h : 0.01	

#score	862.3270231284122
#seq	59
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_CDS_m3_run2.txt

#BEAR
==========nnnnn==========	chr14:97326903-97327158(+)$1	255	159	184	11.8782
hhhhhh[cccnnnnnccchhhhhhh	chr19:9271346-9271579(+)$1	233	168	193	10.6743
eeee"""cccnnnnnccc22eeeee	chr19:44981837-44982063(-)$1	226	196	221	14.9150
eeeee"""bbnnnnnbb333eeeee	chr17:62496705-62496961(-)$1	256	24	49	13.4247
fff"""ddddnnnnndddd333fff	chr1:36074871-36075102(-)$1	231	120	145	12.3360
fff####cccnnnnnccc333ffff	chr16:30094002-30094230(+)$1	228	69	94	14.3108
hhhhhh"""annnnna333hhhhhh	chr17:34171676-34171931(+)$1	255	58	83	10.6115
gccc[a!!bbnnnnnbb22a]ccc2	chr1:32841958-32842236(-)$1	278	128	153	11.9311
ggggg!!cccmmmmccc333ggggg	chr3:49053120-49053349(+)$1	229	99	124	10.4311
c[ccc!!bboooooobb]ccc]ccc	chrX:47088180-47088413(+)$1	233	144	169	8.6193
ddd[bb[cccnnnnnccc22bb]dd	chr19:13049388-13049634(+)$1	246	82	107	12.0933
dddd"""cccnnnnnccc]dddd::	chr2:10584133-10584384(-)$1	251	131	156	10.5105
==========nnnnn==========	chr5:81573517-81573769(-)$1	252	44	69	11.8782
eeee[ddddoooooodddd]eeeee	chr6:18258175-18258393(-)$1	218	89	114	9.1277
ggccc!!cccmmmmccc333ccc]g	chr2:3481420-3481649(+)$1	229	106	131	10.3972
cccc!!ddddnnnnndddd333ccc	chr17:80543805-80544045(+)$1	240	95	120	12.4728
fff!!a[cccmmmmccca22fffff	chr2:64112668-64112891(+)$1	223	184	209	9.4548
ff$$$$$cccooooooccc]fffff	chrX:107975775-107976064(-)$1	289	204	229	9.0140
ccc[a!!cccnnnnnccc]a]ccc]	chr6:26158672-26158924(+)$1	252	35	60	13.7907
[eeeee!!cccmmmmccc22eeeee	chr11:43400737-43400968(+)$1	231	41	66	9.8877
eeeee!!cccnnnnnccc4444eee	chr9:139357910-139358135(-)$1	225	19	44	14.1924
fff####cccnnnnnccc333ffff	chr2:10584174-10584414(-)$1	240	21	46	14.3108
hhh"""ddddnnnnndddd]hhhhh	chr15:35275259-35275485(-)$1	226	65	90	11.1499
dddd!!ddddnnnnndddd22dddd	chr3:49049352-49049585(+)$1	233	92	117	11.2189
:eeeee!!bbnnnnnbb333eeeee	chr20:6011864-6012087(+)$1	223	76	101	11.9454
:eeeee!!cccmmmmccc22eeeee	chrX:84519298-84519536(+)$1	238	101	126	8.8344
bb[ddddcccnnnnnccc]dddd]b	chr16:29818830-29819087(+)$1	257	109	134	10.6769
ffffff[cccnnnnncccffffffe	chr7:98957223-98957448(+)$1	225	89	114	11.6648
eeee[ddddoooooodddd]eeeee	chr14:31574505-31574730(-)$1	225	97	122	9.1277
hhhh"""a[ccclllccca333hhh	chr3:39140805-39141028(-)$1	223	163	188	9.2548
cc[cccddddnnnnndddd]ccc]c	chr4:6863673-6863912(+)$1	239	159	184	11.4548
d[ccc[ddddnnnnnddddccc]dd	chr16:30435649-30435875(-)$1	226	40	65	11.0737
:eeeee!!cccmmmmccc22eeeee	chr5:175815767-175816014(+)$1	247	1	26	8.8344
eeee"""cccmmmmccc333eeeee	chr10:70775940-70776185(+)$1	245	153	178	10.8191
""a[bb!!bbnnnnnbb22bba333	chr10:114925527-114925761(+)$1	234	189	214	10.0202
gggggg[bbannnnna]bb]ggggg	chr5:140953536-140953799(-)$1	263	66	91	11.1663
b[ccc[cccooooooccc22ccc]b	chr22:28503523-28503745(-)$1	222	106	131	10.2394
ffffff[cccnnnnnccc]ffffff	chr5:90678783-90679015(-)$1	232	36	61	12.0731
eeee!!ddddnnnnnddddeeeee]	chr8:42977220-42977461(+)$1	241	85	110	11.9861
eeeee[ddddnnnnndddd]eeeee	chr10:93719712-93719940(+)$1	228	27	52	12.1352
ggccc!!cccnnnnnccc22ccc]g	chr6:122779605-122779851(-)$1	246	194	219	14.4931
hh!!a!!cccnnnnnccc22a22hh	chr7:156974225-156974462(+)$1	237	108	133	13.4417
====="""cccmmmmccc22=====	chr13:28197007-28197229(+)$1	222	156	181	10.2915
[eeeee[cccnnnnnccc]eeeee]	chr17:56083140-56083371(-)$1	231	72	97	13.0617
!!ccc[ddddnnnnnddddccc]cc	chr17:79478499-79478747(-)$1	248	202	227	11.3742
ffffff!!bbnnnnnbb4444ffff	chr2:150427561-150427784(-)$1	223	143	168	11.5632
eeee[ccc[annnnna]ccc]eeee	chrX:47088667-47088903(+)$1	236	193	218	11.7791

#otherMatches

#Seq PSSM
AAUAACAAAGGUGAAUUUUGUUAUU	chr14:97326903-97327158(+)$1	255	159	184	11.8782
CUUUGGCGAUCUCGUGUCCCGGAGG	chr19:9271346-9271579(+)$1	233	168	193	10.6743
CCGUAUUCAAUCUUUUUGCCAUGGU	chr19:44981837-44982063(-)$1	226	196	221	14.9150
CAAAACUCCGUACAUUGCUAUUUUG	chr17:62496705-62496961(-)$1	256	24	49	13.4247
GCUGGCUAUGAUGAGCAUGAAGGGC	chr1:36074871-36075102(-)$1	231	120	145	12.3360
UGGCGACGUCCCUGAGACCAACUAC	chr16:30094002-30094230(+)$1	228	69	94	14.3108
ggcuauggaggagaucgagguggcu	chr17:34171676-34171931(+)$1	255	58	83	10.6115
ACCUGUCCCAAAAGCUGCUAGAGGC	chr1:32841958-32842236(-)$1	278	128	153	11.9311
UUUUGCUGUGUGCUCACCCCCAGGA	chr3:49053120-49053349(+)$1	229	99	124	10.4311
AUUGGCCUGUCAACCCACCCAUUGG	chrX:47088180-47088413(+)$1	233	144	169	8.6193
CGUUGCCGCCCCCUCGGCCCGCCAU	chr19:13049388-13049634(+)$1	246	82	107	12.0933
GAUGAAAGUUGCCAGAGCACAUCCC	chr2:10584133-10584384(-)$1	251	131	156	10.5105
GGAAACACGUAGAUGGCGUGUUUUU	chr5:81573517-81573769(-)$1	252	44	69	11.8782
UUUUUCCCCAGGAAAGGGGCAGAAA	chr6:18258175-18258393(-)$1	218	89	114	9.1277
UAGAUGGACUACAGGGUAAAAUCAU	chr2:3481420-3481649(+)$1	229	106	131	10.3972
CGUGCAGACGGUUCACGUCGUCCAC	chr17:80543805-80544045(+)$1	240	95	120	12.4728
CUUGAUACCUUUAUAGGAGAAGGCA	chr2:64112668-64112891(+)$1	223	184	209	9.4548
GUGAGAAUGGAUUUUGCCAGACGUG	chrX:107975775-107976064(-)$1	289	204	229	9.0140
CGGGGGAGCUGGCCAAGCACGCCGU	chr6:26158672-26158924(+)$1	252	35	60	13.7907
GCAGGUGGAUUCACCAAUGAACUUG	chr11:43400737-43400968(+)$1	231	41	66	9.8877
GAGGCAUUUCUUUGUGAGCCCGGCC	chr9:139357910-139358135(-)$1	225	19	44	14.1924
ACUGAAAUACAGUUGGUGCAGAGUC	chr2:10584174-10584414(-)$1	240	21	46	14.3108
GCAUCAACUAACUCAUAGUCUGCCU	chr15:35275259-35275485(-)$1	226	65	90	11.1499
CUCUCUUCAGCCUGCCUGAUUGGAG	chr3:49049352-49049585(+)$1	233	92	117	11.2189
UUACAUGAUCAUUUCGAGAGAUGUA	chr20:6011864-6012087(+)$1	223	76	101	11.9454
AUAUUUAAAGCGGAGGCUGAAGAUG	chrX:84519298-84519536(+)$1	238	101	126	8.8344
CCAUGCCUGCGAGAUGUGUGGCAAG	chr16:29818830-29819087(+)$1	257	109	134	10.6769
CUGAGGACCGCAACACGGCCUUGGA	chr7:98957223-98957448(+)$1	225	89	114	11.6648
UUUGUAUGCAUACGGGUAUUCAGAA	chr14:31574505-31574730(-)$1	225	97	122	9.1277
GUGCAGCGAGUUAUGGACCCAGGUA	chr3:39140805-39141028(-)$1	223	163	188	9.2548
GUGCUGAGGGCUUAUUCCUGCAGGA	chr4:6863673-6863912(+)$1	239	159	184	11.4548
GAACCUGGCCCCCAAGGCUGGUCCC	chr16:30435649-30435875(-)$1	226	40	65	11.0737
CCGGGAGGCUGAGGUCGGAGUCCCG	chr5:175815767-175816014(+)$1	247	1	26	8.8344
GCUAGAACUUAGUAAAGAGAUGGUU	chr10:70775940-70776185(+)$1	245	153	178	10.8191
AAGUCUUUAGAAUAGCUUUAGCGUC	chr10:114925527-114925761(+)$1	234	189	214	10.0202
AUGGCUUCCCUCUCUGCGGCAGCUA	chr5:140953536-140953799(-)$1	263	66	91	11.1663
GGUGCAAUAAAAUUCUAUGAGCAGC	chr22:28503523-28503745(-)$1	222	106	131	10.2394
AAGAUCACAUUUUAUAUGCGAUCUU	chr5:90678783-90679015(-)$1	232	36	61	12.0731
GGAGAUGAAAGAUGAUUUCCUCCAU	chr8:42977220-42977461(+)$1	241	85	110	11.9861
GGCACCAGUUCGUGAAACUUGUGCU	chr10:93719712-93719940(+)$1	228	27	52	12.1352
UCGUUUCUUAUUUAUUGAUUAACUG	chr6:122779605-122779851(-)$1	246	194	219	14.4931
UUUACUUACAACUCCUGUCCGGAAG	chr7:156974225-156974462(+)$1	237	108	133	13.4417
UGAAGAACCCGGAAGUGGAAUUUUG	chr13:28197007-28197229(+)$1	222	156	181	10.2915
GAUCACAUGCGUGAAGCAGGUGAUG	chr17:56083140-56083371(-)$1	231	72	97	13.0617
CGGGGUCACCCACACGGUGCCCAUC	chr17:79478499-79478747(-)$1	248	202	227	11.3742
GGGUUAUUGGGCUGACUUUAUUGAC	chr2:150427561-150427784(-)$1	223	143	168	11.5632
GGCUAUGGGAAAGCAUGCCACAGCC	chrX:47088667-47088903(+)$1	236	193	218	11.7791

#DB
((((((((((.....))))))))))	chr14:97326903-97327158(+)$1	1	159	184	11.8782
((((((.(((.....))))))))))	chr19:9271346-9271579(+)$1	1	168	193	10.6743
((((...(((.....)))..)))))	chr19:44981837-44982063(-)$1	1	196	221	14.9150
(((((...((.....))...)))))	chr17:62496705-62496961(-)$1	1	24	49	13.4247
(((...((((.....))))...)))	chr1:36074871-36075102(-)$1	1	120	145	12.3360
(((....(((.....)))...))))	chr16:30094002-30094230(+)$1	1	69	94	14.3108
((((((...(.....)...))))))	chr17:34171676-34171931(+)$1	1	58	83	10.6115
((((.(..((.....))..).))).	chr1:32841958-32842236(-)$1	1	128	153	11.9311
(((((..(((....)))...)))))	chr3:49053120-49053349(+)$1	1	99	124	10.4311
(.(((..((......)).))).)))	chrX:47088180-47088413(+)$1	1	144	169	8.6193
(((.((.(((.....)))..)).))	chr19:13049388-13049634(+)$1	1	82	107	12.0933
((((...(((.....))).))))..	chr2:10584133-10584384(-)$1	1	131	156	10.5105
((((((((((.....))))))))))	chr5:81573517-81573769(-)$1	1	44	69	11.8782
((((.((((......)))).)))))	chr6:18258175-18258393(-)$1	1	89	114	9.1277
(((((..(((....)))...))).)	chr2:3481420-3481649(+)$1	1	106	131	10.3972
((((..((((.....))))...)))	chr17:80543805-80544045(+)$1	1	95	120	12.4728
(((..(.(((....))))..)))))	chr2:64112668-64112891(+)$1	1	184	209	9.4548
((.....(((......))).)))))	chrX:107975775-107976064(-)$1	1	204	229	9.0140
(((.(..(((.....))).).))).	chr6:26158672-26158924(+)$1	1	35	60	13.7907
.(((((..(((....)))..)))))	chr11:43400737-43400968(+)$1	1	41	66	9.8877
(((((..(((.....)))....)))	chr9:139357910-139358135(-)$1	1	19	44	14.1924
(((....(((.....)))...))))	chr2:10584174-10584414(-)$1	1	21	46	14.3108
(((...((((.....)))).)))))	chr15:35275259-35275485(-)$1	1	65	90	11.1499
((((..((((.....))))..))))	chr3:49049352-49049585(+)$1	1	92	117	11.2189
.(((((..((.....))...)))))	chr20:6011864-6012087(+)$1	1	76	101	11.9454
.(((((..(((....)))..)))))	chrX:84519298-84519536(+)$1	1	101	126	8.8344
((.(((((((.....))).)))).)	chr16:29818830-29819087(+)$1	1	109	134	10.6769
((((((.(((.....)))))))))(	chr7:98957223-98957448(+)$1	1	89	114	11.6648
((((.((((......)))).)))))	chr14:31574505-31574730(-)$1	1	97	122	9.1277
((((...(.(((...))))...)))	chr3:39140805-39141028(-)$1	1	163	188	9.2548
((.(((((((.....)))).))).)	chr4:6863673-6863912(+)$1	1	159	184	11.4548
(.(((.((((.....))))))).))	chr16:30435649-30435875(-)$1	1	40	65	11.0737
.(((((..(((....)))..)))))	chr5:175815767-175816014(+)$1	1	1	26	8.8344
((((...(((....)))...)))))	chr10:70775940-70776185(+)$1	1	153	178	10.8191
..(.((..((.....))..)))...	chr10:114925527-114925761(+)$1	1	189	214	10.0202
((((((.(((.....).)).)))))	chr5:140953536-140953799(-)$1	1	66	91	11.1663
(.(((.(((......)))..))).)	chr22:28503523-28503745(-)$1	1	106	131	10.2394
((((((.(((.....))).))))))	chr5:90678783-90679015(-)$1	1	36	61	12.0731
((((..((((.....))))))))).	chr8:42977220-42977461(+)$1	1	85	110	11.9861
(((((.((((.....)))).)))))	chr10:93719712-93719940(+)$1	1	27	52	12.1352
(((((..(((.....)))..))).)	chr6:122779605-122779851(-)$1	1	194	219	14.4931
((..(..(((.....)))..)..))	chr7:156974225-156974462(+)$1	1	108	133	13.4417
(((((...(((....)))..)))))	chr13:28197007-28197229(+)$1	1	156	181	10.2915
.(((((.(((.....))).))))).	chr17:56083140-56083371(-)$1	1	72	97	13.0617
..(((.((((.....))))))).))	chr17:79478499-79478747(-)$1	1	202	227	11.3742
((((((..((.....))....))))	chr2:150427561-150427784(-)$1	1	143	168	11.5632
((((.(((.(.....).))).))))	chrX:47088667-47088903(+)$1	1	193	218	11.7791

#PSSM
e : 0.19	f : 0.17	h : 0.10	g : 0.10	c : 0.08	d : 0.08	= : 0.06	: : 0.06	[ : 0.04	b : 0.04	" : 0.02	! : 0.02	
e : 0.29	f : 0.17	h : 0.10	c : 0.08	g : 0.08	= : 0.06	[ : 0.06	d : 0.06	b : 0.02	" : 0.02	! : 0.02	
e : 0.29	c : 0.19	f : 0.14	h : 0.08	= : 0.06	d : 0.06	g : 0.04	[ : 0.04	$ : 0.02	a : 0.02	! : 0.02	
e : 0.29	c : 0.19	= : 0.06	h : 0.06	[ : 0.06	d : 0.06	f : 0.06	" : 0.04	# : 0.04	g : 0.04	! : 0.04	$ : 0.02	
e : 0.17	c : 0.14	" : 0.12	[ : 0.08	! : 0.08	= : 0.06	f : 0.06	h : 0.04	# : 0.04	g : 0.04	b : 0.04	a : 0.04	$ : 0.02	d : 0.02	
! : 0.21	" : 0.17	e : 0.10	[ : 0.08	d : 0.06	f : 0.06	= : 0.04	h : 0.04	# : 0.04	a : 0.04	b : 0.04	c : 0.04	$ : 0.02	g : 0.02	
! : 0.29	d : 0.25	[ : 0.14	" : 0.14	= : 0.04	# : 0.04	c : 0.04	$ : 0.02	
c : 0.44	d : 0.23	! : 0.14	" : 0.06	= : 0.04	b : 0.04	a : 0.02	
c : 0.51	d : 0.23	b : 0.14	= : 0.04	[ : 0.04	" : 0.02	
c : 0.51	d : 0.19	b : 0.10	o : 0.08	a : 0.06	= : 0.04	
n : 0.70	o : 0.10	c : 0.10	m : 0.08	
n : 0.70	m : 0.17	o : 0.10	c : 0.02	
n : 0.70	m : 0.17	o : 0.10	l : 0.02	
n : 0.70	m : 0.17	o : 0.10	l : 0.02	
n : 0.70	o : 0.10	c : 0.08	m : 0.08	l : 0.02	
c : 0.51	d : 0.23	b : 0.12	a : 0.06	= : 0.04	o : 0.02	
c : 0.53	d : 0.23	b : 0.12	= : 0.04	] : 0.04	3 : 0.02	
c : 0.46	d : 0.23	3 : 0.12	= : 0.04	2 : 0.04	] : 0.02	a : 0.02	b : 0.02	4 : 0.02	
2 : 0.25	d : 0.23	3 : 0.17	] : 0.10	c : 0.06	= : 0.04	4 : 0.04	h : 0.02	f : 0.02	a : 0.02	b : 0.02	
2 : 0.23	3 : 0.21	] : 0.14	c : 0.08	= : 0.04	h : 0.04	a : 0.04	d : 0.04	4 : 0.04	f : 0.04	e : 0.04	b : 0.02	
e : 0.25	c : 0.14	3 : 0.10	f : 0.08	= : 0.06	h : 0.06	] : 0.06	g : 0.04	b : 0.04	d : 0.04	4 : 0.04	2 : 0.02	a : 0.02	
e : 0.27	c : 0.17	f : 0.14	= : 0.06	h : 0.06	3 : 0.06	d : 0.06	g : 0.04	] : 0.02	b : 0.02	4 : 0.02	a : 0.02	2 : 0.02	
e : 0.29	f : 0.17	c : 0.17	h : 0.08	= : 0.06	] : 0.06	d : 0.06	g : 0.04	3 : 0.02	2 : 0.02	
e : 0.29	f : 0.17	h : 0.10	c : 0.10	] : 0.10	= : 0.06	d : 0.06	g : 0.04	: : 0.02	3 : 0.02	
e : 0.27	f : 0.14	h : 0.10	g : 0.08	c : 0.08	= : 0.06	d : 0.06	] : 0.06	b : 0.04	2 : 0.02	: : 0.02	3 : 0.02	

#score	535.9443988495168
#seq	47
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_CDS_m1_run1.txt

#BEAR
eeevvvvvvvvvvvvveeeeed	chr22:17600201-17600417(-)$1	216	31	53	23.4637
cccvvvvvvvvvvvvvccc]ee	chr2:102781291-102781507(+)$1	216	173	195	24.2839
dbbuuuuuuuuuuuubb]dddd	chr6:30880789-30881003(+)$1	214	94	116	21.1504
cccvvvvvvvvvvvvvccc]bb	chr2:171912879-171913130(-)$1	251	152	174	23.8025
f[bbuuuuuuuuuuuubb]fff	chr11:118764329-118764545(+)$1	216	155	177	22.1654
ddwwwwwwwwwwwwwwddddFF	chr6:34212522-34212818(+)$1	296	233	255	21.7012
cccuuuuuuuuuuuuccc]iii	chr12:978178-978452(+)$1	274	51	73	22.6121
eeeeuuuuuuuuuuuueeeee2	chr7:65444513-65444883(-)$1	370	39	61	22.5685
eeeeuuuuuuuuuuuueeeee4	chr16:16381589-16381804(+)$1	215	25	47	22.8247
[ddddtttttttttttdddd]a	chr9:33941682-33941897(-)$1	215	43	65	20.7487
fffwwwwwwwwwwwwwwfffff	chr2:175436596-175436849(-)$1	253	17	39	22.7214
cccwwwwwwwwwwwwwwccc]e	chr9:100672626-100672870(-)$1	244	182	204	22.9218
bcccuuuuuuuuuuuuccc555	chr2:71602273-71602593(+)$1	320	203	225	21.0570
ccwwwwwwwwwwwwwwccc]ff	chr17:65941778-65942047(+)$1	269	73	95	23.2187
ddduuuuuuuuuuuudddd]bb	chr12:49666218-49666567(+)$1	349	281	303	21.5535
eewwwwwwwwwwwwwweeeee]	chr19:21606876-21607098(+)$1	222	100	122	22.6442
cccvvvvvvvvvvvvvccc]==	chr3:46944151-46944364(+)$1	213	117	139	24.3723
dddvvvvvvvvvvvvvddddii	chr1:154227547-154227855(+)$1	308	238	260	23.3618
eeeeuuuuuuuuuuuueeeee>	chr21:15516847-15517067(-)$1	220	108	130	22.6507
ffffuuuuuuuuuuuuffffff	chr4:156825110-156825325(+)$1	215	66	88	22.8839
cccvvvvvvvvvvvvvcccfff	chr5:56777818-56778040(-)$1	222	173	195	24.2599
bbwwwwwwwwwwwwwwbb333f	chr13:97639467-97639689(-)$1	222	102	124	21.9263
eeeeuuuuuuuuuuuueeeee]	chr1:3750432-3750667(-)$1	235	133	155	22.8119
ffffftttttttttttffffff	chr19:58046558-58046772(+)$1	214	124	146	21.1273
yyyyyyyyyyyyyyyygggggg	chr2:201768159-201768377(+)$1	218	16	38	19.7138
[bbuuuuuuuuuuuubb]dddd	chr16:22546588-22546857(+)$1	269	29	51	21.2303
eeewwwwwwwwwwwwwweeeee	chr16:75673954-75674275(-)$1	321	125	147	22.5244
cccvvvvvvvvvvvvvccc]ee	chr7:122635238-122635470(-)$1	232	114	136	24.2839
dddvvvvvvvvvvvvvdddd66	chr19:19414637-19414876(-)$1	239	128	150	22.8071
dbbuuuuuuuuuuuubb]dddd	chr6:45514600-45514844(+)$1	244	109	131	21.1504
ffffuuuuuuuuuuuuffffff	chr5:177636293-177636582(-)$1	289	242	264	22.8839
[cccuuuuuuuuuuuuccc]cc	chr18:32825874-32826103(+)$1	229	122	144	23.5079
cccvvvvvvvvvvvvvccc22e	chr14:90650696-90650912(+)$1	216	99	121	23.7407
fffwwwwwwwwwwwwwwfffff	chr15:98513017-98513231(+)$1	214	93	115	22.7214
fffwwwwwwwwwwwwwwfffff	chr7:106508184-106508400(+)$1	216	140	162	22.7214
eeeeuuuuuuuuuuuueeeee2	chr8:40011087-40011296(+)$1	209	126	148	22.5685
ecccuuuuuuuuuuuuccc555	chr1:151867350-151867579(-)$1	229	128	150	21.3322
[cccuuuuuuuuuuuuccc444	chr12:29493975-29494226(-)$1	251	88	110	23.6098
yyyyyyyyyyyyyyyybbffff	chr11:373376-373587(+)$1	211	101	123	19.5275
yyyyyyyyyyyyyyyyeeeee]	chr8:145736357-145736574(+)$1	217	107	129	19.8339
i[ccctttttttttttccc]ii	chr1:84679845-84680058(+)$1	213	179	201	21.7648
eeeeuuuuuuuuuuuueeeee]	chr5:140501866-140502080(+)$1	214	76	98	22.8119
ffffuuuuuuuuuuuuffffff	chr19:57956710-57956939(+)$1	229	196	218	22.8839
fffvvvvvvvvvvvvvffffff	chr12:123087559-123087775(+)$1	216	165	187	23.7496
dddduuuuuuuuuuuudddddd	chr4:39850301-39850594(-)$1	293	219	241	22.1793
dddduuuuuuuuuuuudddd::	chr21:48071766-48072031(+)$1	265	116	138	20.6742
[bbvvvvvvvvvvvvvbb]ggg	chr2:220028864-220029087(-)$1	223	112	134	22.9757
dddvvvvvvvvvvvvvdddd44	chr19:54783729-54783949(-)$1	220	134	156	23.5449
fffvvvvvvvvvvvvvffffff	chr12:132522423-132522634(+)$1	211	19	41	23.7496
eeeeuuuuuuuuuuuueeeeeb	chr11:1097717-1097938(+)$1	221	198	220	22.5019
ggguuuuuuuuuuuuggggggg	chr1:19446710-19447010(-)$1	300	120	142	21.8890
fffwwwwwwwwwwwwwwfffff	chr1:150436991-150437212(+)$1	221	167	189	22.7214
ffffftttttttttttffffff	chr1:11083097-11083367(+)$1	270	182	204	21.1273
ffffuuuuuuuuuuuuffffff	chr17:729162-729381(-)$1	219	73	95	22.8839
ddduuuuuuuuuuuudddd]cc	chr3:173998908-173999125(+)$1	217	65	87	21.9841
===vvvvvvvvvvvvv======	chr16:78056458-78056674(+)$1	216	7	29	23.6957
cccuuuuuuuuuuuuccc333e	chr10:48389055-48389271(-)$1	216	176	198	22.7598
cccvvvvvvvvvvvvvccc:::	chr17:7417060-7417421(+)$1	361	315	337	21.3860
cccwwwwwwwwwwwwwwccc]e	chr12:52450261-52450475(+)$1	214	53	75	22.9218
[cccuuuuuuuuuuuuccc]dd	chr14:20585864-20586079(+)$1	215	138	160	23.3028
dddvvvvvvvvvvvvvdddd55	chr18:34376861-34377098(-)$1	237	99	121	22.1059

#otherMatches

#Seq PSSM
UCCGCCACCACCUCAGGGAGGC	chr22:17600201-17600417(-)$1	216	31	53	23.4637
UAAGGUAAGAGAGGAAUUAGUA	chr2:102781291-102781507(+)$1	216	173	195	24.2839
UAGAUAAUCCAUUUCCUAAGGA	chr6:30880789-30881003(+)$1	214	94	116	21.1504
AAGUCAUCUUUCAAGUUUUUCA	chr2:171912879-171913130(-)$1	251	152	174	23.8025
CGGCACCGGCAGACACGCAGUU	chr11:118764329-118764545(+)$1	216	155	177	22.1654
gcccaccaucaccaccgccucu	chr6:34212522-34212818(+)$1	296	233	255	21.7012
CUGCCUCAUUUUCUUCAGGAGG	chr12:978178-978452(+)$1	274	51	73	22.6121
GCCGACAUCAGCAACCUGGUCC	chr7:65444513-65444883(-)$1	370	39	61	22.5685
CUGGACUCCACACUCCCCAGAU	chr16:16381589-16381804(+)$1	215	25	47	22.8247
UUUGAAUACAUCUUUAUCAAUG	chr9:33941682-33941897(-)$1	215	43	65	20.7487
CAAUACGUCAGUCCCCCUUGAG	chr2:175436596-175436849(-)$1	253	17	39	22.7214
AUGAGCCACAACCCCACCAUAG	chr9:100672626-100672870(-)$1	244	182	204	22.9218
cuccauaauaucuucaggaacc	chr2:71602273-71602593(+)$1	320	203	225	21.0570
UCCAAAGUCCAUCACAGACUCG	chr17:65941778-65942047(+)$1	269	73	95	23.2187
AGCCUACCACGAACAGCUUACU	chr12:49666218-49666567(+)$1	349	281	303	21.5535
AUACAUAAAAUAAUUCAUACUG	chr19:21606876-21607098(+)$1	222	100	122	22.6442
UGCAAUGGCGAGGUAAGCAGGA	chr3:46944151-46944364(+)$1	213	117	139	24.3723
ACCACACAACACAGCAGGUGAU	chr1:154227547-154227855(+)$1	308	238	260	23.3618
UUACAUACCCAGAAAGGUAAGA	chr21:15516847-15517067(-)$1	220	108	130	22.6507
UUUAAAAAACUCCCCGUAGAAG	chr4:156825110-156825325(+)$1	215	66	88	22.8839
ACUUUGAGCAGGAGAUGGUCAG	chr5:56777818-56778040(-)$1	222	173	195	24.2599
UCCAUUCACAAAACUCGAUGUG	chr13:97639467-97639689(-)$1	222	102	124	21.9263
GAGUAAACUUGAAACAGCUCAC	chr1:3750432-3750667(-)$1	235	133	155	22.8119
CUCUUCCCCUUUUUCCAGGAGU	chr19:58046558-58046772(+)$1	214	124	146	21.1273
CAUAUUUAGCAUUUAAGAAUUU	chr2:201768159-201768377(+)$1	218	16	38	19.7138
AUGAUAAUAUCAAGACACCUGC	chr16:22546588-22546857(+)$1	269	29	51	21.2303
ACUUCAUCCAAAAAUAUAGUCA	chr16:75673954-75674275(-)$1	321	125	147	22.5244
CCAUCACAUCUUUCUCUGGCUG	chr7:122635238-122635470(-)$1	232	114	136	24.2839
CACCCCCUCUGUCGUUGUGGUC	chr19:19414637-19414876(-)$1	239	128	150	22.8071
AUGUCCGCCACCACUCACUACC	chr6:45514600-45514844(+)$1	244	109	131	21.1504
UGAUCUCACACUAAAAGUCAAG	chr5:177636293-177636582(-)$1	289	242	264	22.8839
AUCAGAGAAUACAUAGUGGAGA	chr18:32825874-32826103(+)$1	229	122	144	23.5079
GACUCACUCUACUUCUGUUUUG	chr14:90650696-90650912(+)$1	216	99	121	23.7407
AGGUAUACAUUCACAUUCCUGG	chr15:98513017-98513231(+)$1	214	93	115	22.7214
UACGAGAUCUACGACAAGUACC	chr7:106508184-106508400(+)$1	216	140	162	22.7214
UCUGGAGACAAGAAAGCAGAGG	chr8:40011087-40011296(+)$1	209	126	148	22.5685
GAGCAUCAAAUAUAAAGCUAAG	chr1:151867350-151867579(-)$1	229	128	150	21.3322
AUGGCCACACAGACAACCACUU	chr12:29493975-29494226(-)$1	251	88	110	23.6098
AUUCACCAAGUUCAGCUCCCAG	chr11:373376-373587(+)$1	211	101	123	19.5275
CACAUCCCUGCUUCUUGCUCCU	chr8:145736357-145736574(+)$1	217	107	129	19.8339
AAGCUUUUUUAAAGUUGGUGUU	chr1:84679845-84680058(+)$1	213	179	201	21.7648
GAUCCAGGACAUAAAUGAUCAC	chr5:140501866-140502080(+)$1	214	76	98	22.8119
GUUCACAUCGGACCAAGAACCU	chr19:57956710-57956939(+)$1	229	196	218	22.8839
UCUCUAUAGUCAACCCAGAGUG	chr12:123087559-123087775(+)$1	216	165	187	23.7496
CAGAGUAAAGAAAAAAUCUGGG	chr4:39850301-39850594(-)$1	293	219	241	22.1793
GGCCUUCAUCUCUCCUGGCCCA	chr21:48071766-48072031(+)$1	265	116	138	20.6742
CCAUCCCACUGCCUGUUGUUGG	chr2:220028864-220029087(-)$1	223	112	134	22.9757
GGAGAAAAAAUCAGCAUCUUGG	chr19:54783729-54783949(-)$1	220	134	156	23.5449
GUCAGAUGCACACUUGGACCUU	chr12:132522423-132522634(+)$1	211	19	41	23.7496
AGGUGACCCCGCCCAGGCCUGC	chr11:1097717-1097938(+)$1	221	198	220	22.5019
AGGACUUCUUCCUACUCUUCAG	chr1:19446710-19447010(-)$1	300	120	142	21.8890
CUGCACUUUCCAAAACCCAGAC	chr1:150436991-150437212(+)$1	221	167	189	22.7214
GCACUUCAUUGAAAGUAGUGCU	chr1:11083097-11083367(+)$1	270	182	204	21.1273
GGAACAAAUACCGAAUUUCCAA	chr17:729162-729381(-)$1	219	73	95	22.8839
CCCAACACUAUACCAGGGAUUC	chr3:173998908-173999125(+)$1	217	65	87	21.9841
CUUCCAUAGCUGCUCUAAGGGG	chr16:78056458-78056674(+)$1	216	7	29	23.6957
GUCCUCACCUUCAUCGACAAUC	chr10:48389055-48389271(-)$1	216	176	198	22.7598
gcccaccuccccCAAAGGCUCA	chr17:7417060-7417421(+)$1	361	315	337	21.3860
GCUACCUUCAAAACCCAAGCAG	chr12:52450261-52450475(+)$1	214	53	75	22.9218
GGUCUCCAUGGCUUUUGACAGA	chr14:20585864-20586079(+)$1	215	138	160	23.3028
GUAUAAACCUAUCACCUACAAC	chr18:34376861-34377098(-)$1	237	99	121	22.1059

#DB
(((.............)))))(	chr22:17600201-17600417(-)$1	1	31	53	23.4637
(((.............))).))	chr2:102781291-102781507(+)$1	1	173	195	24.2839
(((............)).))))	chr6:30880789-30881003(+)$1	1	94	116	21.1504
(((.............))).))	chr2:171912879-171913130(-)$1	1	152	174	23.8025
(.((............)).)))	chr11:118764329-118764545(+)$1	1	155	177	22.1654
((..............))))))	chr6:34212522-34212818(+)$1	1	233	255	21.7012
(((............))).)))	chr12:978178-978452(+)$1	1	51	73	22.6121
((((............))))).	chr7:65444513-65444883(-)$1	1	39	61	22.5685
((((............))))).	chr16:16381589-16381804(+)$1	1	25	47	22.8247
.((((...........)))).)	chr9:33941682-33941897(-)$1	1	43	65	20.7487
(((..............)))))	chr2:175436596-175436849(-)$1	1	17	39	22.7214
(((..............))).)	chr9:100672626-100672870(-)$1	1	182	204	22.9218
((((............)))...	chr2:71602273-71602593(+)$1	1	203	225	21.0570
((..............))).))	chr17:65941778-65942047(+)$1	1	73	95	23.2187
(((............)))).))	chr12:49666218-49666567(+)$1	1	281	303	21.5535
((..............))))).	chr19:21606876-21607098(+)$1	1	100	122	22.6442
(((.............))).))	chr3:46944151-46944364(+)$1	1	117	139	24.3723
(((.............))))))	chr1:154227547-154227855(+)$1	1	238	260	23.3618
((((............))))).	chr21:15516847-15517067(-)$1	1	108	130	22.6507
((((............))))))	chr4:156825110-156825325(+)$1	1	66	88	22.8839
(((.............))))))	chr5:56777818-56778040(-)$1	1	173	195	24.2599
((..............))...)	chr13:97639467-97639689(-)$1	1	102	124	21.9263
((((............))))).	chr1:3750432-3750667(-)$1	1	133	155	22.8119
(((((...........))))))	chr19:58046558-58046772(+)$1	1	124	146	21.1273
................))))))	chr2:201768159-201768377(+)$1	1	16	38	19.7138
.((............)).))))	chr16:22546588-22546857(+)$1	1	29	51	21.2303
(((..............)))))	chr16:75673954-75674275(-)$1	1	125	147	22.5244
(((.............))).))	chr7:122635238-122635470(-)$1	1	114	136	24.2839
(((.............))))..	chr19:19414637-19414876(-)$1	1	128	150	22.8071
(((............)).))))	chr6:45514600-45514844(+)$1	1	109	131	21.1504
((((............))))))	chr5:177636293-177636582(-)$1	1	242	264	22.8839
.(((............))).))	chr18:32825874-32826103(+)$1	1	122	144	23.5079
(((.............)))..)	chr14:90650696-90650912(+)$1	1	99	121	23.7407
(((..............)))))	chr15:98513017-98513231(+)$1	1	93	115	22.7214
(((..............)))))	chr7:106508184-106508400(+)$1	1	140	162	22.7214
((((............))))).	chr8:40011087-40011296(+)$1	1	126	148	22.5685
((((............)))...	chr1:151867350-151867579(-)$1	1	128	150	21.3322
.(((............)))...	chr12:29493975-29494226(-)$1	1	88	110	23.6098
................))))))	chr11:373376-373587(+)$1	1	101	123	19.5275
................))))).	chr8:145736357-145736574(+)$1	1	107	129	19.8339
(.(((...........))).))	chr1:84679845-84680058(+)$1	1	179	201	21.7648
((((............))))).	chr5:140501866-140502080(+)$1	1	76	98	22.8119
((((............))))))	chr19:57956710-57956939(+)$1	1	196	218	22.8839
(((.............))))))	chr12:123087559-123087775(+)$1	1	165	187	23.7496
((((............))))))	chr4:39850301-39850594(-)$1	1	219	241	22.1793
((((............))))..	chr21:48071766-48072031(+)$1	1	116	138	20.6742
.((.............)).)))	chr2:220028864-220029087(-)$1	1	112	134	22.9757
(((.............))))..	chr19:54783729-54783949(-)$1	1	134	156	23.5449
(((.............))))))	chr12:132522423-132522634(+)$1	1	19	41	23.7496
((((............))))))	chr11:1097717-1097938(+)$1	1	198	220	22.5019
(((............)))))))	chr1:19446710-19447010(-)$1	1	120	142	21.8890
(((..............)))))	chr1:150436991-150437212(+)$1	1	167	189	22.7214
(((((...........))))))	chr1:11083097-11083367(+)$1	1	182	204	21.1273
((((............))))))	chr17:729162-729381(-)$1	1	73	95	22.8839
(((............)))).))	chr3:173998908-173999125(+)$1	1	65	87	21.9841
(((.............))))))	chr16:78056458-78056674(+)$1	1	7	29	23.6957
(((............)))...)	chr10:48389055-48389271(-)$1	1	176	198	22.7598
(((.............)))...	chr17:7417060-7417421(+)$1	1	315	337	21.3860
(((..............))).)	chr12:52450261-52450475(+)$1	1	53	75	22.9218
.(((............))).))	chr14:20585864-20586079(+)$1	1	138	160	23.3028
(((.............))))..	chr18:34376861-34377098(-)$1	1	99	121	22.1059

#PSSM
f : 0.21	c : 0.19	e : 0.18	d : 0.18	[ : 0.09	y : 0.04	b : 0.03	i : 0.01	g : 0.01	= : 0.01	
c : 0.27	f : 0.19	e : 0.16	d : 0.16	b : 0.08	y : 0.04	[ : 0.03	g : 0.01	= : 0.01	
c : 0.27	f : 0.19	e : 0.14	d : 0.14	b : 0.08	w : 0.06	y : 0.04	g : 0.01	= : 0.01	
v : 0.26	w : 0.18	u : 0.13	e : 0.11	c : 0.09	f : 0.09	d : 0.04	y : 0.04	b : 0.01	
u : 0.44	v : 0.26	w : 0.18	y : 0.04	f : 0.03	d : 0.01	c : 0.01	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.44	v : 0.26	w : 0.18	t : 0.06	y : 0.04	
u : 0.31	v : 0.26	w : 0.18	t : 0.06	b : 0.04	y : 0.04	c : 0.03	d : 0.03	g : 0.01	
c : 0.26	e : 0.16	d : 0.16	f : 0.13	b : 0.11	w : 0.11	g : 0.03	= : 0.01	
c : 0.29	f : 0.19	e : 0.18	d : 0.16	b : 0.06	] : 0.04	g : 0.03	= : 0.01	
c : 0.26	d : 0.21	f : 0.21	e : 0.18	] : 0.04	3 : 0.03	g : 0.03	= : 0.01	
f : 0.24	e : 0.18	d : 0.18	] : 0.16	g : 0.04	c : 0.03	5 : 0.03	3 : 0.03	i : 0.01	2 : 0.01	4 : 0.01	= : 0.01	: : 0.01	
f : 0.26	e : 0.21	d : 0.08	i : 0.04	] : 0.04	5 : 0.04	g : 0.04	b : 0.03	= : 0.03	3 : 0.03	c : 0.03	4 : 0.03	: : 0.03	F : 0.01	6 : 0.01	2 : 0.01	
f : 0.27	e : 0.11	d : 0.09	] : 0.06	b : 0.04	i : 0.04	4 : 0.04	5 : 0.04	g : 0.04	2 : 0.03	= : 0.03	c : 0.03	: : 0.03	F : 0.01	a : 0.01	> : 0.01	6 : 0.01	

#score	1370.605426179632
#seq	61
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m2_run1.txt

#BEAR
ff[ffffff####eeeeeooooooeeeee22fffffffff	chr12:12870641-12870877(+)$1	236	67	107	11.9465
dd[ccca[==========oooooo==========]a6666	chr17:55184383-55184629(+)$1	246	57	97	14.3324
eee[bb!!bb[ccc[cccrrrrrrrrrccc]ccc]bbbb]	chr6:34741122-34741352(+)$1	230	148	188	11.5757
d[bb####ggggggg[bboooooobbgggggggbbdddde	chr19:6380830-6381070(-)$1	240	94	134	13.0100
hhhh####eeeee!!cccooooooccc22eeeee22hhhh	chr18:199113-199353(+)$1	240	163	203	13.4518
[ccc!!ffffffbbeeeeeooooooeeeee333bb]ffff	chr20:62698227-62698500(+)$1	273	82	122	11.9325
ddd####eeeee"""cccooooooccc22eeeee333ddd	chr16:28890762-28891006(-)$1	244	116	156	15.1812
$$$$bbeeeeeccc"""cccaooooooa]ccc333ccc>>	chr10:293263-293506(+)$1	243	62	102	11.7335
ggg[bba[bb[cccddddoooooodddd]ccc]bb]a]bb	chr1:45480319-45480587(+)$1	268	12	52	15.6859
occc:ggggggg"""cccooooooccc4444ggggggg::	chr10:70532722-70532959(+)$1	237	115	155	12.9393
a!!bbdddd[ccc[ddddoooooodddd]ccc22dddd22	chr7:148700847-148701082(-)$1	235	131	171	14.1493
!!ggggggg$$$$$ddddoooooodddd4444ggggggg2	chr10:96114724-96114950(-)$1	226	58	98	14.8643
ggggggdddddddd[ccclllcccdddd333dddd]gggg	chr17:8404054-8404293(-)$1	239	139	179	10.4354
eee[bb####eeeee!!ccclllccc4444eeeeebb]ee	chr4:76580915-76581150(-)$1	235	164	204	11.2173
ddd[bb!!bb!!ddddoooooodddd22bb4444bb]ddd	chr20:62624659-62624883(+)$1	224	171	211	11.9392
bb[dddd!!a!!ccc!!aooooooa22ccc22a22dddd2	chr3:56114867-56115110(-)$1	243	157	197	13.9523
cc"""a[bb!!ccc[cccbboooooobb]ccc]ccc22bb	chr12:54812691-54812927(-)$1	236	32	72	12.6137
ddd[gggggggdddd[ddddllldddddddd333gggggg	chr5:139625463-139625720(-)$1	257	144	184	10.9172
e[dddda[a[a!!a[cccooooooccca22a]a]a]dddd	chr10:104486431-104486654(+)$1	223	72	112	15.7275
"bb[bb"""ggggggg!!bboooooobb]ggggggg333b	chr19:18652463-18652707(-)$1	244	184	224	12.2404
iiiiiiiibb[ccc!!cccnnnnncccccc]bb]iiiiii	chr9:124914421-124914696(-)$1	275	178	218	12.2549
========="""ffffffooooooffffff]=========	chr12:8245436-8245660(+)$1	224	12	52	14.2372
b[bbbb!!a[ffffff[aooooooaffffff]a22bb]bb	chr22:47058899-47059153(+)$1	254	84	124	12.1239
!=============ssssssssss=============333	chr17:79214689-79214941(+)$1	252	32	72	10.9356
dddd####bb!!ccc!!cccmmmmccc22ccc]bbdddd]	chr10:135176289-135176537(-)$1	248	32	72	12.8205
gggggga####ccc!!bbmmmmbb22ccc4444a]ggggg	chr17:4085510-4085746(-)$1	236	146	186	10.7328
ddd[a[ccc!!bb[ddddoooooodddd333bb22ccca]	chr5:140085168-140085398(+)$1	230	110	150	15.0195
G:ccc"""dddd[dddd[allla]dddd333dddd333cc	chr11:62327177-62327417(-)$1	240	148	188	11.7820
##ccc####bb[bb[cccooooooccc]bbbbccc]ccc]	chr11:105880213-105880483(-)$1	270	15	55	14.8785
b!!ffffffdddd[ddddoooooodddd]dddd>>>>>>>	chr16:31766325-31766558(+)$1	233	81	121	12.2956
:ffffff[eeeee!!cccooooooccc22eeeee]fffff	chr10:82180156-82180404(+)$1	248	88	128	12.0718
f$$$$$a[ffffff!!cccooooooccc]ffffff]a22f	chr13:52603919-52604177(+)$1	258	112	152	12.7557
hhh[bb!!bb!!accccccnnnnnccc333ccc]a22bb3	chr11:10789520-10789727(+)$1	207	91	131	13.5604
iiiii####ccc[eeeeeooooooeeeee]ccc4444iii	chr17:61877759-61877993(+)$1	234	10	50	15.4623
[dddd[bb[bb!!eeeeeooooooeeeee]bb]bb]dddd	chr13:99127011-99127249(-)$1	238	41	81	12.6550
##dddd!!bb"""eeeeennnnneeeee22bb22dddd44	chr7:50513198-50513432(-)$1	234	111	151	11.2623
!ccc####bb####cccmmmmcccbb333ccc]ffffff]	chr2:74598005-74598231(-)$1	226	62	102	11.2730
ff[a[bb!!a[dddd"""ccclllccc22dddd]a22bb2	chrX:153665502-153665742(+)$1	240	91	131	11.0225
gggga[dddd####ddddmmmmdddddddd]a]ggggggg	chr15:65114477-65114690(-)$1	213	53	93	10.4000
$$$$$eeeee[eeeee[aooooooa]eeeee]eeeeebb2	chrX:118774557-118774792(-)$1	235	146	186	11.5942
eee[bb"""a[ccc"""aqqqqqqqqa]ccc]a4444bbe	chr20:35444489-35444724(-)$1	235	83	123	10.7099
dd!!ccc####dddd[cccmmmmccc]dddd333cccddd	chr2:27592194-27592455(-)$1	261	165	205	11.9185
!dddd[a[a[ccc[bb[cccmmmmccc]bbccc]a]a]dd	chr19:39877235-39877490(-)$1	255	55	95	10.8373
eeeccc!!bb"""ddddxxxxxxxxxxxxxxxdddd4444	chr10:60148416-60148669(+)$1	253	38	78	10.6906
ggggccc[ffffff[cccoooooocccffffff22ccc]g	chr19:36109452-36109693(+)$1	241	144	184	13.6415
bb[cccbb[ccc!!eeeeemmmmeeeee]ccc]bb]cccb	chr4:88988983-88989255(+)$1	272	104	144	10.2122
ffffff!!dddd[bb[bboooooobb]bb]dddd4444ff	chr2:239353184-239353447(+)$1	263	65	105	11.3666
dddd[bb!!bb####cccmmmmccc333bb333bb]dddd	chr19:20229266-20229504(+)$1	238	126	166	10.9978
e[ccc"""bb[ccc!!cccoooooocccccc]bb333ccc	chr19:12812521-12812761(-)$1	240	118	158	15.9389
CCCccc[dddd"""ddddoooooodddd333ddddccc:a	chr1:1452612-1452884(+)$1	272	87	127	11.0794
$$$$$dddd[ccc[ddddoooooodddd]ccc22dddd66	chr7:148700735-148701000(-)$1	265	49	89	13.2208
ebb[dddd!!bb!!ddddoooooodddd22bb22dddd22	chr3:128339237-128339477(-)$1	240	18	58	12.9987
ccc[iiiiiiiiiccccccmmmmccc]ccc]iiiiiiiii	chr11:122931377-122931607(-)$1	230	110	150	11.7519
###ccc!!bb!!bbccc[abblllbb]a]ccc]bb22bbc	chr16:2263754-2263991(-)$1	237	37	77	11.5424
:::dddd!!iiiiiiiiiooooooiiiiiiiii4444ddd	chr19:47673033-47673265(+)$1	232	15	55	11.7709
dccc####bb"""eeeeeooooooeeeee4444bb4444c	chr1:156714771-156715006(-)$1	235	96	136	16.0986
[dddd[eeeee[ccc[ddddllldddd22ccc]eeeee33	chr17:49244087-49244324(+)$1	237	30	70	11.0344
dd$$$$$ccc[ccc[ddddnnnnndddd]ccccccdddd2	chr9:38396678-38396941(+)$1	263	210	250	11.6191

#otherMatches

#Seq PSSM
UUGUUUUGUUCGGUUUUGUUUUUUUGAGAGUGCGAGAGAG	chr12:12870641-12870877(+)$1	236	67	107	11.9465
GUACUGUGCCCUUCAGCAAUGGGGUGCUGAAGGGGGAGUU	chr17:55184383-55184629(+)$1	246	57	97	14.3324
GGCCCCCAAUGAUGAGACCUCCUGCCCGUCCCAUGAUGGU	chr6:34741122-34741352(+)$1	230	148	188	11.5757
CAGCGCAGAGGGUGGCAGCACCUCCUCCACCCUGCGGGCG	chr19:6380830-6381070(-)$1	240	94	134	13.0100
CAAUCAGGAAGUCAAGUAUCUUUUUACAGGACUUAAAUUG	chr18:199113-199353(+)$1	240	163	203	13.4518
AGCUCGGAUGAGGAGGUCAUUGCACUGGCCAAGUCUCUCA	chr20:62698227-62698500(+)$1	273	82	122	11.9325
CGGCCAGGAGGAGAAUCCGCACCAGGAGGUCUUCAAACUG	chr16:28890762-28891006(-)$1	244	116	156	15.1812
UAAUGCCCACAGCUAAAGGUCACUCAAGAACCAAGAGCAA	chr10:293263-293506(+)$1	243	62	102	11.7335
GGCAGCAGAAGUACAGUCAAGAAAGAUUAGUGGUUGUAGC	chr1:45480319-45480587(+)$1	268	12	52	15.6859
GCUGAGGAUGAAGAAGAUGGUAUGAUUGAAAUUUAUUUAU	chr10:70532722-70532959(+)$1	237	115	155	12.9393
GAGCAUUUGAGCAAGUUUAUAGAAGAACAUGCCACAAAAC	chr7:148700847-148701082(-)$1	235	131	171	14.1493
GUAAGCAGAGGAAUAUGUAAGGGAACAUCUAAUCUGUUUU	chr10:96114724-96114950(-)$1	226	58	98	14.8643
AGGCCAAGCGGGUAAGGGAGGCCCUGCCGUGUGCUGUGGC	chr17:8404054-8404293(-)$1	239	139	179	10.4354
GCUAACAGUGGUUACUAUGAAGCUCACCCUGUGACGUAAG	chr4:76580915-76581150(-)$1	235	164	204	11.2173
ACCUCAAGGUGAGCCGAUGAAGCGGUGAAUGGUGUGCGGU	chr20:62624659-62624883(+)$1	224	171	211	11.9392
ACAGCUACAGGACCUCACAGAAGAGAAGGGGACACUGGCC	chr3:56114867-56115110(-)$1	243	157	197	13.9523
uugcugcugcugccgccgcCACCCAGGGUCGGGGGCUUCA	chr12:54812691-54812927(-)$1	236	32	72	12.6137
GCACGAAGGGCCCAGUAGGGAGCCUCUCUGGGAAGCUCUU	chr5:139625463-139625720(-)$1	257	144	184	10.9172
UGUAUCUGAGCGGGAGCUGGACUGGGCCAAGGUGAUGGUG	chr10:104486431-104486654(+)$1	223	72	112	15.7275
AGCCCCGGCCCCAGAAGAGUGGCUGGACAUUCUGGGUAAG	chr19:18652463-18652707(-)$1	244	184	224	12.2404
AAUCUUUGGUAUCAGUGCCUACUUGGUUGAAGCAUAAAGG	chr9:124914421-124914696(-)$1	275	178	218	12.2549
UUCUUUUUUUCUUUUGUAGAACAUUACAAACAAGAAAGGA	chr12:8245436-8245660(+)$1	224	12	52	14.2372
GAGCGGUUUGGGGAGUACGUGGAGGACUUCCGGUUCCAGC	chr22:47058899-47059153(+)$1	254	84	124	12.1239
AGCUUGCUUUUGAGGCGUAUCUAACUUGGAAGCAAGCCAU	chr17:79214689-79214941(+)$1	252	32	72	10.9356
GGACAUUGGCAUCAGGCUCUGUGAGGAUACUGCGCGUCCA	chr10:135176289-135176537(-)$1	248	32	72	12.8205
AGCUUCCACUCGUAGUUGAUGCCAUAUGCACCCGAGGAGC	chr17:4085510-4085746(-)$1	236	146	186	10.7328
GACGAUGAGAUGGCAGCUGUGAUGGGCUUCUCUGGCUUUG	chr5:140085168-140085398(+)$1	230	110	150	15.0195
GGCGGAAACUGGAUCCUGGCAGCGAGGAGACCCAGACGCU	chr11:62327177-62327417(-)$1	240	148	188	11.7820
AAUGAACUUGGUCAAGGAGAAAAAUCCAUGCUUCAACCAC	chr11:105880213-105880483(-)$1	270	15	55	14.8785
AGCCCUUACUCAGCAUGAGAGAAUUCAUACUGGAGAGAAA	chr16:31766325-31766558(+)$1	233	81	121	12.2956
AGUUUCUUCACCAUGGGGAUGUGGUCCAUUGGUGCAGGAG	chr10:82180156-82180404(+)$1	248	88	128	12.0718
GAUGAAUGUGGACGGACCGAAUCCCUGGAUGUUCAGGAGC	chr13:52603919-52604177(+)$1	258	112	152	12.7557
UUUCUAUAGGAAAAGCGUCAUCAAGAUCGUGCUCUGGCCA	chr11:10789520-10789727(+)$1	207	91	131	13.5604
GAGCAGAAACAUUCUCAAUUGUACUUGGGUGUGAUUAUGU	chr17:61877759-61877993(+)$1	234	10	50	15.4623
AUGGCGAGGUGAAGCUGGCGGACUUUGGCGUGGCUGGCCA	chr13:99127011-99127249(-)$1	238	41	81	12.6550
CCGGAGAAGAUUGGUGAAAAGGCUUUAUAUUCCCCUCCCA	chr7:50513198-50513432(-)$1	234	111	151	11.2623
AUGGAAGAGCAAAAUGCAGGAGCAGCAGGCCGACCUGCAG	chr2:74598005-74598231(-)$1	226	62	102	11.2730
CCUGACCAUGGACGAGGAAUACGAUGUGAUCGUGCUGGGG	chrX:153665502-153665742(+)$1	240	91	131	11.0225
GUGGGAUAGAGGAACAGGGAGACCUGUCUAACUUUGCCCC	chr15:65114477-65114690(-)$1	213	53	93	10.4000
GUCUCCGGGAAGGGCUACACACAGGAAGCCCCUUUUGUCU	chrX:118774557-118774792(-)$1	235	146	186	11.5942
CUCACUAAGCUUGCCAAGGAGAAUGACAGCAUGAAGGAGG	chr20:35444489-35444724(-)$1	235	83	123	10.7099
CAAUGUCAAGGUGAGUGAGGGGUCUCUUUUAAAGGGCUGG	chr2:27592194-27592455(-)$1	261	165	205	11.9185
CGCCUUAGUAAGCGCCGGGCCAAGGCUGGGGUUCAGUCAG	chr19:39877235-39877490(-)$1	255	55	95	10.8373
AGUGGCAGGUAUAUAAAGAAGAGAUAAGCAGAUUUAAAGA	chr10:60148416-60148669(+)$1	253	38	78	10.6906
GAGAGGUGGGGGGCUCUCCGAGAAGAGGUCUCUAGGCCAU	chr19:36109452-36109693(+)$1	241	144	184	13.6415
CAUGAGCAGCCGAAGUUUCCCUCGAAGCCUGGAUGACUCU	chr4:88988983-88989255(+)$1	272	104	144	10.2122
CCUGCUGGUAGAAUUUGGAGCCAACCUGAAUCUAGUGAAG	chr2:239353184-239353447(+)$1	263	65	105	11.3666
GAAGAAUGUGGCAAAGCCUUCAGGCGCUCCUUAGUCCUUC	chr19:20229266-20229504(+)$1	238	126	166	10.9978
AGGGACAACGAGGAGAAGGACUCAGCCUUCCGCGGCAUCU	chr19:12812521-12812761(-)$1	240	118	158	15.9389
GCCGCCGUGGAGCAGCUCAAGAGCGAGCAGAUCCGGGCGC	chr1:1452612-1452884(+)$1	272	87	127	11.0794
GAGCAUUUGAGCAAGUUUAUAGAAGAACAUGCCACAAAAC	chr7:148700735-148701000(-)$1	265	49	89	13.2208
UGCCCUGCUCUUGCCUCGGCCAGGUGAGCGAAAUGCAGAA	chr3:128339237-128339477(-)$1	240	18	58	12.9987
GUCUGAUUGGACGCAGAUUUGAUGAUGCUGUUGUCCAGUC	chr11:122931377-122931607(-)$1	230	110	150	11.7519
AUACGGCAUCAACCCCGAGCGCACCGUCAUGGUGGGAGAC	chr16:2263754-2263991(-)$1	237	37	77	11.5424
UAAGCAGUUCUGCCUUUUUUCCACAGAAGGUGGUCUUCUG	chr19:47673033-47673265(+)$1	232	15	55	11.7709
CCUUACGAGGAAUCCAAGGAGAAGUUUGGCAAGCCCAACA	chr1:156714771-156715006(-)$1	235	96	136	16.0986
CGCCCACGUGGCCUCCGCGGGCCCCGCCAGAGCCUGCGCC	chr17:49244087-49244324(+)$1	237	30	70	11.0344
GCAAAACUCCUCUGUGGCGGAGAGCGUUUCGGGGAGCGUG	chr9:38396678-38396941(+)$1	263	210	250	11.6191

#DB
((.((((((....(((((......)))))..)))))))))	chr12:12870641-12870877(+)$1	1	67	107	11.9465
((.((((.((((((((((......)))))))))).)....	chr17:55184383-55184629(+)$1	1	57	97	14.3324
(((.((..((.(((.(((.........))).))).)))).	chr6:34741122-34741352(+)$1	1	148	188	11.5757
(.((....(((((((.((......)))))))))))))))(	chr19:6380830-6381070(-)$1	1	94	134	13.0100
((((....(((((..(((......)))..)))))..))))	chr18:199113-199353(+)$1	1	163	203	13.4518
.(((..(((((((((((((......)))))...)).))))	chr20:62698227-62698500(+)$1	1	82	122	11.9325
(((....(((((...(((......)))..)))))...)))	chr16:28890762-28891006(-)$1	1	116	156	15.1812
....((((((((((...((((......).)))...)))..	chr10:293263-293506(+)$1	1	62	102	11.7335
(((.(((.((.(((((((......)))).))).)).).))	chr1:45480319-45480587(+)$1	1	12	52	15.6859
.))).(((((((...(((......)))....)))))))..	chr10:70532722-70532959(+)$1	1	115	155	12.9393
(..((((((.(((.((((......)))).)))..))))..	chr7:148700847-148701082(-)$1	1	131	171	14.1493
..(((((((.....((((......))))....))))))).	chr10:96114724-96114950(-)$1	1	58	98	14.8643
((((((((((((((.(((...)))))))...)))).))))	chr17:8404054-8404293(-)$1	1	139	179	10.4354
(((.((....(((((..(((...)))....))))))).))	chr4:76580915-76581150(-)$1	1	164	204	11.2173
(((.((..((..((((......))))..))....)).)))	chr20:62624659-62624883(+)$1	1	171	211	11.9392
((.((((..(..(((..(......)..)))..)..)))).	chr3:56114867-56115110(-)$1	1	157	197	13.9523
((...(.((..(((.(((((......)).))).)))..))	chr12:54812691-54812927(-)$1	1	32	72	12.6137
(((.(((((((((((.((((...))))))))...))))))	chr5:139625463-139625720(-)$1	1	144	184	10.9172
(.(((((.(.(..(.(((......))))..).).).))))	chr10:104486431-104486654(+)$1	1	72	112	15.7275
.((.((...(((((((..((......)).)))))))...)	chr19:18652463-18652707(-)$1	1	184	224	12.2404
((((((((((.(((..(((.....)))))).)).))))))	chr9:124914421-124914696(-)$1	1	178	218	12.2549
(((((((((...((((((......)))))).)))))))))	chr12:8245436-8245660(+)$1	1	12	52	14.2372
(.((((..(.((((((.(......))))))).)..)).))	chr22:47058899-47059153(+)$1	1	84	124	12.1239
.(((((((((((((..........)))))))))))))...	chr17:79214689-79214941(+)$1	1	32	72	10.9356
((((....((..(((..(((....)))..))).)))))).	chr10:135176289-135176537(-)$1	1	32	72	12.8205
(((((((....(((..((....))..)))....).)))))	chr17:4085510-4085746(-)$1	1	146	186	10.7328
(((.(.(((..((.((((......))))...))..)))).	chr5:140085168-140085398(+)$1	1	110	150	15.0195
).(((...((((.((((.(...).))))...))))...))	chr11:62327177-62327417(-)$1	1	148	188	11.7820
..(((....((.((.(((......))).))))))).))).	chr11:105880213-105880483(-)$1	1	15	55	14.8785
(..((((((((((.((((......)))).)))).......	chr16:31766325-31766558(+)$1	1	81	121	12.2956
.((((((.(((((..(((......)))..))))).)))))	chr10:82180156-82180404(+)$1	1	88	128	12.0718
(.....(.((((((..(((......))).)))))).)..)	chr13:52603919-52604177(+)$1	1	112	152	12.7557
(((.((..((..(((((((.....)))...))).)..)).	chr11:10789520-10789727(+)$1	1	91	131	13.5604
(((((....(((.(((((......))))).)))....)))	chr17:61877759-61877993(+)$1	1	10	50	15.4623
.((((.((.((..(((((......))))).)).)).))))	chr13:99127011-99127249(-)$1	1	41	81	12.6550
..((((..((...(((((.....)))))..))..))))..	chr7:50513198-50513432(-)$1	1	111	151	11.2623
.(((....((....(((....)))))...))).)))))).	chr2:74598005-74598231(-)$1	1	62	102	11.2730
((.(.((..(.((((...(((...)))..)))).)..)).	chrX:153665502-153665742(+)$1	1	91	131	11.0225
(((((.((((....((((....)))))))).).)))))))	chr15:65114477-65114690(-)$1	1	53	93	10.4000
.....(((((.(((((.(......).))))).))))))).	chrX:118774557-118774792(-)$1	1	146	186	11.5942
(((.((...(.(((...(........).))).)....)))	chr20:35444489-35444724(-)$1	1	83	123	10.7099
((..(((....((((.(((....))).))))...))))))	chr2:27592194-27592455(-)$1	1	165	205	11.9185
.((((.(.(.(((.((.(((....))).))))).).).))	chr19:39877235-39877490(-)$1	1	55	95	10.8373
((((((..((...((((...............))))....	chr10:60148416-60148669(+)$1	1	38	78	10.6906
(((((((.((((((.(((......)))))))))..))).)	chr19:36109452-36109693(+)$1	1	144	184	13.6415
((.(((((.(((..(((((....))))).))).)).))))	chr4:88988983-88989255(+)$1	1	104	144	10.2122
((((((..((((.((.((......)).)).))))....))	chr2:239353184-239353447(+)$1	1	65	105	11.3666
((((.((..((....(((....)))...))...)).))))	chr19:20229266-20229504(+)$1	1	126	166	10.9978
(.(((...((.(((..(((......)))))).))...)))	chr19:12812521-12812761(-)$1	1	118	158	15.9389
((((((.((((...((((......))))...))))))).(	chr1:1452612-1452884(+)$1	1	87	127	11.0794
.....((((.(((.((((......)))).)))..))))..	chr7:148700735-148701000(-)$1	1	49	89	13.2208
)((.((((..((..((((......))))..))..))))..	chr3:128339237-128339477(-)$1	1	18	58	12.9987
(((.(((((((((((((((....))).))).)))))))))	chr11:122931377-122931607(-)$1	1	110	150	11.7519
...(((..((..(((((.(((...)).).))).))..)))	chr16:2263754-2263991(-)$1	1	37	77	11.5424
...((((..(((((((((......)))))))))....)))	chr19:47673033-47673265(+)$1	1	15	55	11.7709
((((....((...(((((......)))))....))....)	chr1:156714771-156715006(-)$1	1	96	136	16.0986
.((((.(((((.(((.((((...))))..))).)))))..	chr17:49244087-49244324(+)$1	1	30	70	11.0344
((.....(((.(((.((((.....)))).)))))))))).	chr9:38396678-38396941(+)$1	1	210	250	11.6191

#PSSM
d : 0.18	e : 0.12	g : 0.08	f : 0.06	! : 0.06	b : 0.06	[ : 0.05	$ : 0.05	# : 0.05	h : 0.03	c : 0.03	i : 0.03	: : 0.03	o : 0.01	a : 0.01	" : 0.01	= : 0.01	G : 0.01	C : 0.01	
d : 0.20	c : 0.10	g : 0.08	f : 0.06	e : 0.06	[ : 0.06	$ : 0.06	b : 0.06	! : 0.05	# : 0.05	h : 0.03	i : 0.03	= : 0.03	: : 0.03	C : 0.01	
d : 0.18	c : 0.13	g : 0.10	[ : 0.08	$ : 0.08	e : 0.06	b : 0.06	! : 0.05	h : 0.03	i : 0.03	= : 0.03	f : 0.03	" : 0.01	C : 0.01	# : 0.01	: : 0.01	
c : 0.20	[ : 0.18	d : 0.15	$ : 0.08	g : 0.08	f : 0.06	b : 0.05	i : 0.03	= : 0.03	h : 0.01	# : 0.01	" : 0.01	a : 0.01	! : 0.01	
c : 0.17	b : 0.17	d : 0.13	# : 0.10	f : 0.06	g : 0.06	$ : 0.06	i : 0.05	= : 0.03	a : 0.03	[ : 0.03	! : 0.01	: : 0.01	" : 0.01	
b : 0.18	# : 0.13	c : 0.12	d : 0.12	g : 0.08	[ : 0.08	f : 0.06	i : 0.03	= : 0.03	" : 0.03	$ : 0.03	! : 0.01	a : 0.01	e : 0.01	
# : 0.15	! : 0.13	d : 0.12	a : 0.10	f : 0.06	" : 0.06	b : 0.06	e : 0.05	g : 0.05	c : 0.05	[ : 0.03	i : 0.03	= : 0.03	$ : 0.01	
! : 0.20	# : 0.17	[ : 0.12	d : 0.10	e : 0.06	" : 0.06	f : 0.05	g : 0.05	b : 0.05	i : 0.03	= : 0.03	c : 0.03	
b : 0.22	d : 0.12	e : 0.10	f : 0.08	# : 0.08	! : 0.08	g : 0.06	= : 0.05	a : 0.05	" : 0.03	c : 0.03	[ : 0.03	i : 0.01	
b : 0.25	e : 0.10	d : 0.10	[ : 0.08	# : 0.06	g : 0.06	f : 0.05	a : 0.05	! : 0.05	c : 0.05	= : 0.03	i : 0.03	$ : 0.01	" : 0.01	
[ : 0.13	! : 0.12	e : 0.10	# : 0.08	c : 0.08	d : 0.08	g : 0.06	f : 0.06	" : 0.06	b : 0.06	= : 0.03	i : 0.03	$ : 0.01	a : 0.01	
c : 0.24	d : 0.12	! : 0.12	e : 0.08	" : 0.08	# : 0.06	f : 0.06	g : 0.05	= : 0.03	b : 0.03	[ : 0.03	i : 0.03	$ : 0.01	
c : 0.25	" : 0.10	d : 0.10	# : 0.06	e : 0.06	b : 0.06	! : 0.06	f : 0.06	[ : 0.05	= : 0.03	g : 0.03	i : 0.03	$ : 0.01	a : 0.01	
c : 0.24	e : 0.12	d : 0.12	[ : 0.08	! : 0.06	b : 0.06	f : 0.06	" : 0.05	# : 0.05	= : 0.03	g : 0.03	$ : 0.01	a : 0.01	i : 0.01	
d : 0.25	e : 0.15	[ : 0.12	c : 0.12	! : 0.10	" : 0.06	g : 0.03	f : 0.03	b : 0.03	= : 0.01	s : 0.01	# : 0.01	i : 0.01	
c : 0.25	d : 0.22	e : 0.13	! : 0.12	[ : 0.08	" : 0.05	f : 0.03	= : 0.01	g : 0.01	s : 0.01	b : 0.01	i : 0.01	
c : 0.32	d : 0.24	e : 0.12	! : 0.06	b : 0.05	" : 0.05	[ : 0.05	= : 0.01	o : 0.01	f : 0.01	s : 0.01	i : 0.01	
c : 0.36	d : 0.20	e : 0.12	a : 0.06	b : 0.05	[ : 0.03	= : 0.01	o : 0.01	! : 0.01	f : 0.01	s : 0.01	m : 0.01	" : 0.01	x : 0.01	i : 0.01	
o : 0.48	c : 0.18	m : 0.06	d : 0.05	e : 0.03	b : 0.03	a : 0.03	r : 0.01	l : 0.01	s : 0.01	n : 0.01	q : 0.01	x : 0.01	
o : 0.53	m : 0.12	c : 0.08	n : 0.06	b : 0.05	l : 0.03	d : 0.03	r : 0.01	s : 0.01	q : 0.01	x : 0.01	
o : 0.56	m : 0.15	l : 0.08	n : 0.06	r : 0.01	a : 0.01	s : 0.01	c : 0.01	q : 0.01	x : 0.01	b : 0.01	
o : 0.58	m : 0.13	l : 0.10	n : 0.06	c : 0.03	r : 0.01	s : 0.01	q : 0.01	x : 0.01	
o : 0.56	l : 0.08	m : 0.08	n : 0.06	c : 0.05	d : 0.03	r : 0.01	s : 0.01	b : 0.01	a : 0.01	q : 0.01	x : 0.01	
o : 0.56	c : 0.10	d : 0.06	n : 0.05	m : 0.03	e : 0.03	l : 0.03	r : 0.01	s : 0.01	b : 0.01	] : 0.01	q : 0.01	x : 0.01	
c : 0.27	d : 0.25	e : 0.10	o : 0.10	b : 0.06	a : 0.05	= : 0.03	r : 0.01	f : 0.01	2 : 0.01	q : 0.01	x : 0.01	i : 0.01	
c : 0.29	d : 0.25	e : 0.12	b : 0.06	o : 0.05	= : 0.03	2 : 0.03	f : 0.03	r : 0.01	] : 0.01	q : 0.01	x : 0.01	3 : 0.01	i : 0.01	
c : 0.25	d : 0.24	e : 0.13	] : 0.06	= : 0.03	2 : 0.03	b : 0.03	f : 0.03	3 : 0.03	r : 0.01	g : 0.01	o : 0.01	4 : 0.01	a : 0.01	x : 0.01	i : 0.01	
d : 0.24	e : 0.13	c : 0.12	2 : 0.12	a : 0.05	b : 0.05	f : 0.05	] : 0.05	3 : 0.05	= : 0.03	4 : 0.03	g : 0.01	x : 0.01	i : 0.01	
] : 0.18	2 : 0.15	c : 0.12	e : 0.10	3 : 0.10	b : 0.08	4 : 0.05	d : 0.05	f : 0.05	= : 0.03	g : 0.01	x : 0.01	i : 0.01	
c : 0.29	e : 0.08	4 : 0.08	3 : 0.08	d : 0.08	2 : 0.06	b : 0.06	f : 0.06	] : 0.05	= : 0.03	g : 0.03	x : 0.01	i : 0.01	
c : 0.27	3 : 0.10	] : 0.08	e : 0.08	4 : 0.08	d : 0.08	b : 0.06	f : 0.05	2 : 0.03	= : 0.03	g : 0.03	a : 0.01	x : 0.01	i : 0.01	
c : 0.25	d : 0.10	b : 0.10	] : 0.08	e : 0.06	3 : 0.06	4 : 0.06	f : 0.05	= : 0.05	g : 0.05	i : 0.03	2 : 0.01	a : 0.01	x : 0.01	
] : 0.15	d : 0.12	c : 0.10	e : 0.08	3 : 0.08	g : 0.06	2 : 0.06	a : 0.06	f : 0.05	= : 0.05	4 : 0.05	b : 0.05	i : 0.03	
b : 0.17	2 : 0.13	e : 0.10	d : 0.08	] : 0.08	c : 0.06	g : 0.06	4 : 0.06	f : 0.05	= : 0.05	3 : 0.05	a : 0.01	> : 0.01	i : 0.01	
b : 0.17	d : 0.13	2 : 0.08	g : 0.08	] : 0.06	c : 0.06	a : 0.06	4 : 0.06	f : 0.05	3 : 0.05	e : 0.05	i : 0.03	= : 0.03	> : 0.01	
] : 0.17	d : 0.15	c : 0.10	g : 0.10	4 : 0.08	b : 0.06	2 : 0.06	f : 0.05	3 : 0.05	i : 0.03	= : 0.03	e : 0.03	a : 0.01	> : 0.01	
d : 0.18	c : 0.12	g : 0.10	4 : 0.10	f : 0.06	3 : 0.06	2 : 0.06	b : 0.05	a : 0.05	i : 0.03	= : 0.03	e : 0.03	6 : 0.01	h : 0.01	] : 0.01	> : 0.01	
d : 0.25	c : 0.12	b : 0.10	g : 0.10	f : 0.06	] : 0.06	3 : 0.05	i : 0.05	4 : 0.05	2 : 0.03	6 : 0.01	h : 0.01	= : 0.01	> : 0.01	e : 0.01	
d : 0.20	b : 0.15	f : 0.08	g : 0.08	c : 0.06	2 : 0.05	3 : 0.05	i : 0.05	4 : 0.05	6 : 0.03	> : 0.03	: : 0.03	h : 0.01	e : 0.01	= : 0.01	a : 0.01	] : 0.01	
d : 0.13	2 : 0.12	f : 0.08	] : 0.08	b : 0.08	g : 0.08	c : 0.06	e : 0.05	i : 0.05	3 : 0.05	6 : 0.03	> : 0.03	4 : 0.03	h : 0.01	: : 0.01	= : 0.01	a : 0.01	

#score	726.4154980551109
#seq	58
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m3_run2.txt

#BEAR
ee!!bbpppppppbbeeee	chr1:32636928-32637170(+)$1	242	204	223	13.2513
c[ddddpppppppddddcc	chr13:21721414-21721654(+)$1	240	105	124	13.5656
:eeeeepppppppeeeee:	chr6:24705040-24705280(+)$1	240	81	100	12.4061
dd!!bbpppppppbb22dd	chr6:89872170-89872410(+)$1	240	201	220	12.2127
ffffffpppppppffffff	chr5:106715496-106715736(-)$1	240	169	188	12.8949
b!!cccpppppppccc22b	chr12:118469355-118469595(+)$1	240	133	152	13.4899
"""cccpppppppccc333	chr12:29654771-29655011(-)$1	240	159	178	14.0851
ffffffpppppppffffff	chr9:125670569-125670809(-)$1	240	37	56	12.8949
ggggggrrrrrrrrrgggg	chr21:45114933-45115213(+)$1	280	168	187	10.3173
e[ddddrrrrrrrrrdddd	chr3:47628631-47628871(-)$1	240	28	47	9.7062
deeeeepppppppeeeee>	chr17:30190096-30190336(-)$1	240	66	85	13.9081
c"""bbpppppppbb333c	chr3:56656781-56657021(-)$1	240	147	166	12.7763
ceeeeepppppppeeeee>	chr12:39687431-39687671(-)$1	240	107	126	14.0517
eeeeeepppppppeeeeeG	chr21:45115347-45115587(+)$1	240	155	174	13.6218
!eeeeepppppppeeeee2	chr19:24103487-24103727(+)$1	240	27	46	14.2366
ff[cccpppppppccc333	chr2:234385641-234385881(-)$1	240	50	69	14.0655
$$$cccpppppppccc333	chr1:173903996-173904242(-)$1	246	145	164	13.4353
"eeeeepppppppeeeee5	chr6:149731467-149731707(+)$1	240	26	45	13.5191
ffffffpppppppffffff	chr2:39477098-39477338(-)$1	240	179	198	12.8949
!!ddddpppppppdddddd	chr3:15483841-15484081(+)$1	240	69	88	13.5790
#a[cccpppppppccc]a4	chr3:193413705-193413945(+)$1	240	129	148	13.8731
eee[bbpppppppbb]eee	chr2:37075371-37075611(-)$1	240	15	34	13.1259
b[ddddpppppppdddd]b	chr13:52988051-52988291(-)$1	240	63	82	13.2815
bb[cccpppppppccc]bb	chr20:464296-464576(-)$1	280	132	151	12.8341
c[ddddpppppppdddd22	chr1:21133473-21133713(-)$1	240	68	87	13.5257
hhhhhhppppppphhhhhh	chr1:244572527-244572767(-)$1	240	182	201	11.9808
eeddddpppppppdddd]e	chr18:48473980-48474220(+)$1	240	106	125	13.4813
ggggggpppppppgggggg	chr12:96259747-96259987(+)$1	240	138	157	14.0106
hhh[bbpppppppbbhhhh	chr17:49041854-49042094(-)$1	240	185	204	12.0062
dddddapppppppa]dddd	chr6:24719044-24719284(-)$1	240	215	234	12.9184
ddddbbpppppppbb]ddd	chr1:178886920-178887160(+)$1	240	176	195	12.4315
ggggggpppppppgggggg	chr3:176740927-176741167(-)$1	240	28	47	14.0106
ggggggpppppppgggggg	chr18:9400729-9400969(+)$1	240	67	86	14.0106
eee[bbpppppppbb]eee	chr16:75327553-75327793(-)$1	240	65	84	13.1259
[eeeeerrrrrrrrreeee	chr17:74731360-74731600(-)$1	240	62	81	10.4182
ffffffpppppppffffff	chr15:42823574-42823814(+)$1	240	55	74	12.8949
ggggggpppppppgggggg	chr7:97837588-97837828(+)$1	240	212	231	14.0106
!!ddddpppppppdddd33	chr5:42800191-42800431(-)$1	240	156	175	14.0253
:eeeeepppppppeeeee:	chr9:134374248-134374488(+)$1	240	125	144	12.4061
feeeeepppppppeeeee]	chr20:40032438-40032678(-)$1	240	201	220	14.1582
:eeeeepppppppeeeee:	chr12:110476333-110476575(+)$1	242	178	197	12.4061
=!!cccpppppppccc22=	chr7:56147837-56148077(+)$1	240	174	193	13.9618
g!!cccpppppppcccggg	chr3:196657908-196658148(+)$1	240	187	206	14.2790
hhhhhhppppppphhhhhh	chr15:44165626-44165866(-)$1	240	134	153	11.9808
[eeeeepppppppeeeee]	chr8:124260719-124260959(-)$1	240	82	101	14.3303
!!ddddpppppppdddd33	chr10:70101894-70102141(+)$1	247	175	194	14.0253
$ddddrrrrrrrrrdddd3	chr4:156728475-156728715(+)$1	240	106	125	9.4859
%%ddddpppppppddddee	chr1:35886038-35886278(+)$1	240	34	53	12.2770
ggggggrrrrrrrrrgggg	chr2:44460236-44460476(+)$1	240	11	30	10.3173
ffffffpppppppffffff	chr5:146771139-146771379(-)$1	240	170	189	12.8949
ggggggpppppppgggggg	chr2:100899580-100899822(-)$1	242	32	51	14.0106
!eeeeepppppppeeeeed	chr10:35859226-35859466(+)$1	240	154	173	14.1606
hhhhhhppppppphhhhhh	chr1:67452343-67452583(+)$1	240	151	170	11.9808
ggggggpppppppgggggg	chr6:93951236-93951482(-)$1	246	204	223	14.0106
ggggggrrrrrrrrrgggg	chr1:224380925-224381165(+)$1	240	200	219	10.3173
ff[cccpppppppccc22f	chr9:34086678-34086918(-)$1	240	208	227	13.5656
ddddddrrrrrrrrrdddd	chr1:57179281-57179521(+)$1	240	55	74	9.3627
Feeeeepppppppeeeee:	chr20:2128843-2129088(+)$1	245	87	106	12.9535
ffffffpppppppffffff	chr11:95564372-95564612(+)$1	240	16	35	12.8949

#otherMatches

#Seq PSSM
AGCUGCCUGCAUUGCCUGG	chr1:32636928-32637170(+)$1	242	204	223	13.2513
UUAUGUAAAAUAAACAUAC	chr13:21721414-21721654(+)$1	240	105	124	13.5656
CACCUAUUUUAUUUAGGuu	chr6:24705040-24705280(+)$1	240	81	100	12.4061
AAACCUUAUAUUCAGAAUU	chr6:89872170-89872410(+)$1	240	201	220	12.2127
UAUGCUGAGAGUGAGUAUA	chr5:106715496-106715736(-)$1	240	169	188	12.8949
AUUUAUGAUUCUAAUAUUU	chr12:118469355-118469595(+)$1	240	133	152	13.4899
GAACAGAAAAUAACUGCAA	chr12:29654771-29655011(-)$1	240	159	178	14.0851
AAGAUUGUUGUAAAAUUUU	chr9:125670569-125670809(-)$1	240	37	56	12.8949
UUUUUAUUUCAGCUUUAAA	chr21:45114933-45115213(+)$1	280	168	187	10.3173
UCAACUAGCCUGGAAAGUU	chr3:47628631-47628871(-)$1	240	28	47	9.7062
CUGUCUGGUUUUGAGACAC	chr17:30190096-30190336(-)$1	240	66	85	13.9081
AUUAUCUCAUGUUGGCACU	chr3:56656781-56657021(-)$1	240	147	166	12.7763
UAAAAUGCUGUUAAUUUUU	chr12:39687431-39687671(-)$1	240	107	126	14.0517
UCACAUAAAGAAAAUGUGU	chr21:45115347-45115587(+)$1	240	155	174	13.6218
UCUCUUUUUGCACAAGAGU	chr19:24103487-24103727(+)$1	240	27	46	14.2366
CUCUGGAUGUCGCCCACCC	chr2:234385641-234385881(-)$1	240	50	69	14.0655
CAUGUAUUUCUUUUGCCUA	chr1:173903996-173904242(-)$1	246	145	164	13.4353
ACAGAUCUCUCGAGUCUGC	chr6:149731467-149731707(+)$1	240	26	45	13.5191
UGUGAUGUAUUAAGUCACA	chr2:39477098-39477338(-)$1	240	179	198	12.8949
AUGUGAGUUUUUGUUACUU	chr3:15483841-15484081(+)$1	240	69	88	13.5790
AGGUCUAGGGACAGGAGUG	chr3:193413705-193413945(+)$1	240	129	148	13.8731
UCACGUUCAAGUUAUCUGA	chr2:37075371-37075611(-)$1	240	15	34	13.1259
GAGCUACUCAAUCUAGCGC	chr13:52988051-52988291(-)$1	240	63	82	13.2815
AAUAGGCUGAUUUUCUUUU	chr20:464296-464576(-)$1	280	132	151	12.8341
GGUACUGGAUAAAAGUAAA	chr1:21133473-21133713(-)$1	240	68	87	13.5257
AAUUACUUUUAAUGUAGUU	chr1:244572527-244572767(-)$1	240	182	201	11.9808
GGAAAUAUUAAAAAUUUAC	chr18:48473980-48474220(+)$1	240	106	125	13.4813
AGACAAUAAAGAUUUGUUU	chr12:96259747-96259987(+)$1	240	138	157	14.0106
uggugcgaucucagcucac	chr17:49041854-49042094(-)$1	240	185	204	12.0062
GUCUGCUAAUAUUGACAGA	chr6:24719044-24719284(-)$1	240	215	234	12.9184
UUGAGUCCAUGAAACUUCA	chr1:178886920-178887160(+)$1	240	176	195	12.4315
UGuuuaaaaaaaauaaaua	chr3:176740927-176741167(-)$1	240	28	47	14.0106
ACUAUGUGCCCUUCAUAGU	chr18:9400729-9400969(+)$1	240	67	86	14.0106
CAUUGAAGUUCUGUCUAUG	chr16:75327553-75327793(-)$1	240	65	84	13.1259
CAAUUCUCUGAUCUCGAGU	chr17:74731360-74731600(-)$1	240	62	81	10.4182
GUAUUGAUAUUGCCAAUGC	chr15:42823574-42823814(+)$1	240	55	74	12.8949
UCUCUAGAUAAUGUGGGGG	chr7:97837588-97837828(+)$1	240	212	231	14.0106
CCUGAUUUUUACUAUCACA	chr5:42800191-42800431(-)$1	240	156	175	14.0253
UAAACAUUCAUAUUGUUUU	chr9:134374248-134374488(+)$1	240	125	144	12.4061
GGUGGGGCAAGGACCCGCG	chr20:40032438-40032678(-)$1	240	201	220	14.1582
AGGUUAUACAUUUUAACCA	chr12:110476333-110476575(+)$1	242	178	197	12.4061
gcacuggugaucacggcuc	chr7:56147837-56148077(+)$1	240	174	193	13.9618
UUAGUAGAUUUGGUGCAGC	chr3:196657908-196658148(+)$1	240	187	206	14.2790
UUACUGAUUAUUGCAGUAG	chr15:44165626-44165866(-)$1	240	134	153	11.9808
AAUAUGUUAACUCUGUGUA	chr8:124260719-124260959(-)$1	240	82	101	14.3303
GAUGUGCUGCCUUCAUAAG	chr10:70101894-70102141(+)$1	247	175	194	14.0253
UGAUAACUUAUUAAUAUCU	chr4:156728475-156728715(+)$1	240	106	125	9.4859
AUGCCCCUUCUCUGGGUGU	chr1:35886038-35886278(+)$1	240	34	53	12.2770
AUUUGCCUUUAUAAUGUAA	chr2:44460236-44460476(+)$1	240	11	30	10.3173
AGGCCUAUACAAAAGGUUU	chr5:146771139-146771379(-)$1	240	170	189	12.8949
UCUAUUCCAGGAAAAUAGA	chr2:100899580-100899822(-)$1	242	32	51	14.0106
CCUUAUGGACUCAAUAAGA	chr10:35859226-35859466(+)$1	240	154	173	14.1606
GCAGAUGGUCACAAUCUGU	chr1:67452343-67452583(+)$1	240	151	170	11.9808
AUUUUAAUUUCACUAAAAU	chr6:93951236-93951482(-)$1	246	204	223	14.0106
GAAUUUCCACCAUUCAAAU	chr1:224380925-224381165(+)$1	240	200	219	10.3173
UCUGGAAUUCUCAUCUUCG	chr9:34086678-34086918(-)$1	240	208	227	13.5656
UGUUGAUUUAAAAUUUCAA	chr1:57179281-57179521(+)$1	240	55	74	9.3627
GUUAGUUUCCAAUACUAGU	chr20:2128843-2129088(+)$1	245	87	106	12.9535
UACAAAGCAGUAGUUUGUG	chr11:95564372-95564612(+)$1	240	16	35	12.8949

#DB
((..((.......))))))	chr1:32636928-32637170(+)$1	1	204	223	13.2513
(.((((.......))))))	chr13:21721414-21721654(+)$1	1	105	124	13.5656
.(((((.......))))).	chr6:24705040-24705280(+)$1	1	81	100	12.4061
((..((.......))..))	chr6:89872170-89872410(+)$1	1	201	220	12.2127
((((((.......))))))	chr5:106715496-106715736(-)$1	1	169	188	12.8949
(..(((.......)))..)	chr12:118469355-118469595(+)$1	1	133	152	13.4899
...(((.......)))...	chr12:29654771-29655011(-)$1	1	159	178	14.0851
((((((.......))))))	chr9:125670569-125670809(-)$1	1	37	56	12.8949
((((((.........))))	chr21:45114933-45115213(+)$1	1	168	187	10.3173
(.((((.........))))	chr3:47628631-47628871(-)$1	1	28	47	9.7062
((((((.......))))).	chr17:30190096-30190336(-)$1	1	66	85	13.9081
(...((.......))...)	chr3:56656781-56657021(-)$1	1	147	166	12.7763
((((((.......))))).	chr12:39687431-39687671(-)$1	1	107	126	14.0517
)(((((.......))))))	chr21:45115347-45115587(+)$1	1	155	174	13.6218
.(((((.......))))).	chr19:24103487-24103727(+)$1	1	27	46	14.2366
((.(((.......)))...	chr2:234385641-234385881(-)$1	1	50	69	14.0655
...(((.......)))...	chr1:173903996-173904242(-)$1	1	145	164	13.4353
.(((((.......))))).	chr6:149731467-149731707(+)$1	1	26	45	13.5191
((((((.......))))))	chr2:39477098-39477338(-)$1	1	179	198	12.8949
..((((.......))))))	chr3:15483841-15484081(+)$1	1	69	88	13.5790
.(.(((.......))).).	chr3:193413705-193413945(+)$1	1	129	148	13.8731
(((.((.......)).)))	chr2:37075371-37075611(-)$1	1	15	34	13.1259
(.((((.......)))).)	chr13:52988051-52988291(-)$1	1	63	82	13.2815
((.(((.......))).))	chr20:464296-464576(-)$1	1	132	151	12.8341
(.((((.......))))..	chr1:21133473-21133713(-)$1	1	68	87	13.5257
((((((.......))))))	chr1:244572527-244572767(-)$1	1	182	201	11.9808
((((((.......)))).)	chr18:48473980-48474220(+)$1	1	106	125	13.4813
((((((.......))))))	chr12:96259747-96259987(+)$1	1	138	157	14.0106
(((.((.......))))))	chr17:49041854-49042094(-)$1	1	185	204	12.0062
)(((((.......).))))	chr6:24719044-24719284(-)$1	1	215	234	12.9184
((((((.......)).)))	chr1:178886920-178887160(+)$1	1	176	195	12.4315
((((((.......))))))	chr3:176740927-176741167(-)$1	1	28	47	14.0106
((((((.......))))))	chr18:9400729-9400969(+)$1	1	67	86	14.0106
(((.((.......)).)))	chr16:75327553-75327793(-)$1	1	65	84	13.1259
.(((((.........))))	chr17:74731360-74731600(-)$1	1	62	81	10.4182
((((((.......))))))	chr15:42823574-42823814(+)$1	1	55	74	12.8949
((((((.......))))))	chr7:97837588-97837828(+)$1	1	212	231	14.0106
..((((.......))))..	chr5:42800191-42800431(-)$1	1	156	175	14.0253
.(((((.......))))).	chr9:134374248-134374488(+)$1	1	125	144	12.4061
((((((.......))))).	chr20:40032438-40032678(-)$1	1	201	220	14.1582
.(((((.......))))).	chr12:110476333-110476575(+)$1	1	178	197	12.4061
(..(((.......)))..)	chr7:56147837-56148077(+)$1	1	174	193	13.9618
(..(((.......))))))	chr3:196657908-196658148(+)$1	1	187	206	14.2790
((((((.......))))))	chr15:44165626-44165866(-)$1	1	134	153	11.9808
.(((((.......))))).	chr8:124260719-124260959(-)$1	1	82	101	14.3303
..((((.......))))..	chr10:70101894-70102141(+)$1	1	175	194	14.0253
.((((.........)))).	chr4:156728475-156728715(+)$1	1	106	125	9.4859
..((((.......))))))	chr1:35886038-35886278(+)$1	1	34	53	12.2770
((((((.........))))	chr2:44460236-44460476(+)$1	1	11	30	10.3173
((((((.......))))))	chr5:146771139-146771379(-)$1	1	170	189	12.8949
((((((.......))))))	chr2:100899580-100899822(-)$1	1	32	51	14.0106
.(((((.......))))))	chr10:35859226-35859466(+)$1	1	154	173	14.1606
((((((.......))))))	chr1:67452343-67452583(+)$1	1	151	170	11.9808
((((((.......))))))	chr6:93951236-93951482(-)$1	1	204	223	14.0106
((((((.........))))	chr1:224380925-224381165(+)$1	1	200	219	10.3173
((.(((.......)))..)	chr9:34086678-34086918(-)$1	1	208	227	13.5656
))((((.........))))	chr1:57179281-57179521(+)$1	1	55	74	9.3627
((((((.......))))).	chr20:2128843-2129088(+)$1	1	87	106	12.9535
((((((.......))))))	chr11:95564372-95564612(+)$1	1	16	35	12.8949

#PSSM
g : 0.16	f : 0.15	e : 0.10	d : 0.08	! : 0.08	c : 0.06	h : 0.06	: : 0.05	b : 0.05	" : 0.03	$ : 0.03	[ : 0.03	# : 0.01	= : 0.01	% : 0.01	F : 0.01	
e : 0.28	g : 0.15	f : 0.13	! : 0.10	d : 0.08	[ : 0.06	h : 0.06	" : 0.03	$ : 0.01	a : 0.01	b : 0.01	% : 0.01	
e : 0.25	d : 0.22	g : 0.15	f : 0.10	! : 0.08	[ : 0.06	h : 0.06	" : 0.03	$ : 0.01	
d : 0.22	e : 0.22	c : 0.15	g : 0.15	f : 0.10	[ : 0.05	h : 0.05	! : 0.03	" : 0.01	
e : 0.22	d : 0.20	c : 0.15	g : 0.15	b : 0.11	f : 0.10	h : 0.05	
e : 0.22	d : 0.16	c : 0.15	g : 0.15	b : 0.11	f : 0.10	h : 0.05	a : 0.01	r : 0.01	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
p : 0.88	r : 0.11	
e : 0.20	c : 0.15	d : 0.13	b : 0.11	r : 0.11	f : 0.10	g : 0.10	h : 0.05	a : 0.01	
e : 0.20	d : 0.15	c : 0.15	b : 0.11	f : 0.10	r : 0.10	g : 0.10	h : 0.05	] : 0.01	
e : 0.23	d : 0.20	c : 0.15	g : 0.15	f : 0.10	h : 0.06	] : 0.05	2 : 0.01	3 : 0.01	
e : 0.27	d : 0.22	g : 0.16	f : 0.10	2 : 0.06	3 : 0.06	h : 0.06	] : 0.03	
e : 0.28	g : 0.16	d : 0.11	f : 0.10	3 : 0.10	2 : 0.06	h : 0.06	] : 0.03	c : 0.01	a : 0.01	b : 0.01	
g : 0.16	d : 0.11	f : 0.11	e : 0.10	3 : 0.10	: : 0.06	h : 0.06	b : 0.05	c : 0.03	> : 0.03	2 : 0.03	] : 0.03	G : 0.01	5 : 0.01	4 : 0.01	= : 0.01	

#score	762.6598698508619
#seq	59
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m2_run2.txt

#BEAR
eee"""iiiiiiiiinnnnniiiiiiiii22eeeee	chr19:51301087-51301361(-)$1	274	224	260	14.9700
""===========[annnnna]===========333	chr12:6675218-6675440(-)$1	222	158	194	19.3011
$$$ccc[ccceeeeeooooooeeeee]ccc]ccc66	chr1:36068590-36068816(-)$1	226	9	45	11.8716
gggggg!!gggggggnnnnnggggggg]ggggggg:	chr15:73852292-73852539(-)$1	247	105	141	14.4909
ccc[==========ppppppp==========]ccc:	chr19:3630621-3630844(-)$1	223	68	104	12.2031
giiiiiiiii[eeeeemmmmeeeee22iiiiiiiii	chr19:10795886-10796159(+)$1	273	31	67	13.9018
ff============ssssssssss============	chr15:68583500-68583722(+)$1	222	72	108	12.7968
ff$$$$$gggggggooooooggggggg333ffffff	chr17:73774350-73774631(-)$1	281	18	54	12.8837
hhhhcccccc[ddddoooooodddd]ccc333ccc]	chr1:205684301-205684572(-)$1	271	132	168	12.5008
dd==========[bbnnnnnbb==========]ddd	chr1:206907308-206907533(+)$1	225	113	149	16.1919
gggg[bb"""eeeeennnnneeeee22bb]gggggg	chr7:92244162-92244396(-)$1	234	31	67	13.3651
gg"""ccc!!eeeeennnnneeeee22cccgggggg	chr12:110779973-110780225(+)$1	252	58	94	14.1232
$$ggggggg[ddddoooooodddd333ggggggg55	chr3:23961137-23961413(+)$1	276	199	235	13.1060
!!ccc!!bb!!ddddnnnnndddd22bb22ccc22b	chr3:196728786-196729008(-)$1	222	148	184	12.3505
================mmmm================	chr10:116623690-116623921(+)$1	231	166	202	17.3953
cdddd!!==========lll==========4444dd	chr13:100617477-100617701(-)$1	224	65	101	14.9886
"ccc[ccc[ffffffooooooffffff]ccc]ccc8	chr6:24785961-24786198(+)$1	237	156	192	12.0535
==========eeeeeooooooeeeee22========	chr2:20401659-20401886(-)$1	227	145	181	16.1759
ggccc[ccc!!ddddnnnnndddd]ccc]ccc22gg	chr20:5171592-5171827(+)$1	235	144	180	13.2585
cc$$$$$iiiiiiiiimmmmiiiiiiiii22ccc]e	chr11:9610579-9610820(+)$1	241	65	101	13.2508
=============[annnnna]==============	chr1:42643284-42643539(-)$1	255	61	97	18.9999
fff!!ccc!!ddddoooooodddd]ccc22ffffff	chr19:33791053-33791301(-)$1	248	16	52	11.9415
=====!!a[ffffffooooooffffff]a22=====	chr8:104344344-104344581(+)$1	237	126	162	13.8215
a[==========[bbmmmmbb]==========a]a]	chr6:138203111-138203334(+)$1	223	126	162	15.1818
fff[a[a[iiiiiiiiillliiiiiiiiia]a]fff	chr2:20648239-20648510(+)$1	271	129	165	13.8222
$ggggggg####cccnnnnnccc333ggggggg22f	chr1:93308559-93308781(-)$1	222	51	87	14.9643
cc[============nnnnn============]ccc	chr12:27573937-27574190(+)$1	253	125	161	18.4305
b[==========ssssssssss==========4444	chr1:7839825-7840054(+)$1	229	162	198	12.8748
ggggggg[eeeee[annnnna]eeeeeggggggg::	chrX:131351288-131351573(-)$1	285	201	237	12.1202
dggggggg!!eeeeennnnneeeee]ggggggg:ee	chr1:38275337-38275562(-)$1	225	70	106	13.2093
====[eeeee[a[aooooooa]a]eeeee]======	chr7:127231602-127231849(+)$1	247	42	78	13.7932
d[============qqqqqqqq============]d	chr7:134653315-134653547(+)$1	232	133	169	13.7328
gggggg$$$$$ddddnnnnndddd333ggggggg:G	chr12:124499014-124499269(+)$1	255	78	114	12.6580
"""ggggggg[ddddnnnnndddd]gggggggeeee	chr2:175938654-175938876(-)$1	222	9	45	14.5128
cc$$$$$iiiiiiiiimmmmiiiiiiiii22ccc]e	chr11:9610610-9610840(+)$1	230	34	70	13.2508
!!ccc!!bb####bbnnnnnbb333bb]ccc22a]d	chr1:109822145-109822390(-)$1	245	86	122	12.1141
ccc[===========lll===========]cccddd	chr19:4794399-4794632(+)$1	233	82	118	15.7700
:============oooooo============::eee	chr2:5834717-5834954(+)$1	237	94	130	13.5415
[ccc[ccc!!ggggggglllggggggg]ccc]ccc2	chr17:72199722-72199959(+)$1	237	182	218	13.1886
"""ffffff[eeeeeooooooeeeee22ffffff33	chr13:76100506-76100736(-)$1	230	18	54	12.0381
""a[dddd"""ddddnnnnndddd]dddd]a4444g	chr17:2587855-2588096(+)$1	241	116	152	12.5845
[a[a!!ggggggg[bblllbb]ggggggg]aa]eee	chr10:43881463-43881696(-)$1	233	78	114	12.6789
=========="""cccmmmmccc333==========	chr1:162492841-162493085(+)$1	244	51	87	16.0684
============cccooooooccc]===========	chr5:98129447-98129690(+)$1	243	159	195	17.9124
cc[============nnnnn============ccc5	chr22:38879801-38880025(-)$1	224	30	66	17.8556
c[ffffff####cccnnnnnccc333ffffffccc2	chr16:30094002-30094230(+)$1	228	64	100	12.6680
[iiiiiiiiifffffflllffffff22iiiiiiiii	chr13:113538154-113538378(+)$1	224	175	211	13.3391
[ccc!!bb[gggggggmmmmggggggg]bb333ccc	chr3:150345810-150346044(+)$1	234	138	174	12.1462
ggggggg!!ggggggglllggggggg333ggggggg	chr12:118470670-118470893(-)$1	223	126	162	13.8808
iiii"""ccc[cccmmmmccc]ccc333iiiiiiii	chr17:47131724-47131950(+)$1	226	79	115	12.6429
[iiiiiiiii[ddddmmmmdddd]iiiiiiiii333	chr11:69467024-69467254(+)$1	230	70	106	14.7465
!==========!!ddddllldddd==========22	chr19:13055031-13055270(+)$1	239	49	85	16.2718
!==========!!ddddllldddd==========22	chr19:13054978-13055230(+)$1	252	102	138	16.2718

#otherMatches

#Seq PSSM
UGAGUCCCUGGGGGGAGUGAUCCCCCAGGCAUCGUG	chr19:51301087-51301361(-)$1	274	224	260	14.9700
GGAGGAAGGUGAAGCGGUGAGAUUCAUCUUUUUGGG	chr12:6675218-6675440(-)$1	222	158	194	19.3011
UCUACUCUUUUCAGGCGCACUCUUGAUAAAUGGUUA	chr1:36068590-36068816(-)$1	226	9	45	11.8716
UUUGUGUAAUUAUUGAAGUGCAAUGAUGUAUAAAAA	chr15:73852292-73852539(-)$1	247	105	141	14.4909
UGGCUGCUGUCCACUGAGAACGUGGGCAGUGUCCAA	chr19:3630621-3630844(-)$1	223	68	104	12.2031
UGUUGCUUUUUAGUUUAAUGGGACUUUAAAAGUAAU	chr19:10795886-10796159(+)$1	273	31	67	13.9018
UUCAUUAAGUGACUGGAUAUGUAAAGUCGUUUAAUG	chr15:68583500-68583722(+)$1	222	72	108	12.7968
ACUUUUUUUGUAAGAAAUUGUUUAUAAUAUGUUGCA	chr17:73774350-73774631(-)$1	281	18	54	12.8837
CAGUAGUUGAUUUCCCUUGAAGGAGCUUACAUAUUG	chr1:205684301-205684572(-)$1	271	132	168	12.5008
AGGGAGAGGUGGCAGGAAUACUUCACCUUUCCUCUC	chr1:206907308-206907533(+)$1	225	113	149	16.1919
GGAUUGCUAUCUGGAGGCCUUCCAGCUGCUGUCUUC	chr7:92244162-92244396(-)$1	234	31	67	13.3651
GACUGGCGAUGGCGUGAACGAUGCUCCUGCUCUGAA	chr12:110779973-110780225(+)$1	252	58	94	14.1232
UCGGAGUGAUGGCAAUGCUCUGCUGGUUUAUUUUCA	chr3:23961137-23961413(+)$1	276	199	235	13.1060
CUGACGAUUGCUUGGUUUUUUCAAAAGGGAGUUUUG	chr3:196728786-196729008(-)$1	222	148	184	12.3505
UUGUGUGuguauauauguauauauguauauauauaA	chr10:116623690-116623921(+)$1	231	166	202	17.3953
CAUUAGaauuuauuauuaauaauaauaaGUGAAAUA	chr13:100617477-100617701(-)$1	224	65	101	14.9886
ACUCUGGAAUCAAAUUUCCUUGUUUGAAUCCUGGGA	chr6:24785961-24786198(+)$1	237	156	192	12.0535
UGGUGGUCUGUUGGCAGGCUGGCCAGUCCAGGCUGC	chr2:20401659-20401886(-)$1	227	145	181	16.1759
CAGGGAGCAGAGGGCUUCUCGUUCAUGCACCCUUUG	chr20:5171592-5171827(+)$1	235	144	180	13.2585
GCAUGAACCAUGGGAUGAUGAUUCUGUGGAGGUAUU	chr11:9610579-9610820(+)$1	241	65	101	13.2508
gugugugugugcugugugugagagugugcgcgcgcg	chr1:42643284-42643539(-)$1	255	61	97	18.9999
UAUCUGGCCUCUGUGCCCCAGCAGUGCCUUGUGCAA	chr19:33791053-33791301(-)$1	248	16	52	11.9415
UCCUUCUGCAUAUUUAAAAUAAAAUGUCCUAAAGGG	chr8:104344344-104344581(+)$1	237	126	162	13.8215
UACAUAUAUAAUAUACCCUUACAUUAUGUAUGAGGG	chr6:138203111-138203334(+)$1	223	126	162	15.1818
GUGAGCGCUCUGGCCCAGGCUGGGCCAGACUCCCGC	chr2:20648239-20648510(+)$1	271	129	165	13.8222
UGUUACAUCUCCGAAGUACAUUCAUUGUGUAACUAU	chr1:93308559-93308781(-)$1	222	51	87	14.9643
GAAUUUUAAGUGAGAUGAUUUCUUGCUUAAAACUCA	chr12:27573937-27574190(+)$1	253	125	161	18.4305
ACUAAUUAAUUGCCAUUACUCCCAGUUAGUUACCCU	chr1:7839825-7840054(+)$1	229	162	198	12.8748
CGCCUCGUCUAGCCGCGCCACAGCUAGCGGGGUGAU	chrX:131351288-131351573(-)$1	285	201	237	12.1202
CACUGAGCGAUGUGAAAACGUUACAGGUUCAGUACU	chr1:38275337-38275562(-)$1	225	70	106	13.2093
UCUGUUUUGGGUGUACUCUAGGGGCCAGGUUGGGAG	chr7:127231602-127231849(+)$1	247	42	78	13.7932
UCUAGAAAAAUGAACCGUAGUUUUUGUUUUUUUAAA	chr7:134653315-134653547(+)$1	232	133	169	13.7328
AUUUCCCACAUGUAGUCCUUUUGCUCAGGAAGUCUU	chr12:124499014-124499269(+)$1	255	78	114	12.6580
AGAGAAAGAUAGAAAUUUGCUUUUAAUCUUUUUGCC	chr2:175938654-175938876(-)$1	222	9	45	14.5128
GCAUGAACCAUGGGAUGAUGAUUCUGUGGAGGUAUU	chr11:9610610-9610840(+)$1	230	34	70	13.2508
GGCACCUGGUCUUCAGAAAUUGUUUCCUGUGAAUUC	chr1:109822145-109822390(-)$1	245	86	122	12.1141
GUGUUCUGUUUAUUUAAUAAGUGGGCAGGUUGCAAG	chr19:4794399-4794632(+)$1	233	82	118	15.7700
uuuuuuuuuuuuuuuuuuuGGAGGGAGAAAACUGAU	chr2:5834717-5834954(+)$1	237	94	130	13.5415
GCCAGGUGAAAUCUGGGGACCCCAGGUCCGCGUGGA	chr17:72199722-72199959(+)$1	237	182	218	13.1886
AUUCUUUGGUUGAUAAAUUGCUAUCAUUCUAAAGUC	chr13:76100506-76100736(-)$1	230	18	54	12.0381
UAGGAGACUAAGACCGUCCUGGUUCGUCUGUGUGUG	chr17:2587855-2588096(+)$1	241	116	152	12.5845
ACACAAUACUAAUACUGUAGGAAUUGGUGAGGCCUU	chr10:43881463-43881696(-)$1	233	78	114	12.6789
UAAAGGAACUGCAGUGAGCCUAUCUAAGUUUUUUUA	chr1:162492841-162493085(+)$1	244	51	87	16.0684
ACUGUGUUUGGCUGUUUUCACAUAUGUUGGAUGUAG	chr5:98129447-98129690(+)$1	243	159	195	17.9124
GGCAAGCAAGUGGUUAUUUGGAUUGCUUGCUUCCCU	chr22:38879801-38880025(-)$1	224	30	66	17.8556
GUAGGUGGCGACGUCCCUGAGACCAACUACCUCUUC	chr16:30094002-30094230(+)$1	228	64	100	12.6680
UUUUAAAAAUAGGUUUUUAAAGCUUUCAUUUUUAAG	chr13:113538154-113538378(+)$1	224	175	211	13.3391
AUGCAAGAUUAUGGGGGAAAUCCUAUAUUCAGAGUA	chr3:150345810-150346044(+)$1	234	138	174	12.1462
UCUUUUCAAAAUGAGAGGCUUUCAUUGAAGAAAAGA	chr12:118470670-118470893(-)$1	223	126	162	13.8808
AAGUGAGUUGAGGCUUGUGCCACAAAAGGUUUGUCC	chr17:47131724-47131950(+)$1	226	79	115	12.6429
CGCUGUUUUUGUUGUGUGUGCAGGGAGGGCAGUUUU	chr11:69467024-69467254(+)$1	230	70	106	14.7465
UCUGCUCUCCUUCCUGGAGCCCAGAGGAGGGCAGCA	chr19:13055031-13055270(+)$1	239	49	85	16.2718
UCUGCUCUCCUUCCUGGAGCCCAGAGGAGGGCAGCA	chr19:13054978-13055230(+)$1	252	102	138	16.2718

#DB
(((...(((((((((.....)))))))))..)))))	chr19:51301087-51301361(-)$1	1	224	260	14.9700
..(((((((((((.(.....).)))))))))))...	chr12:6675218-6675440(-)$1	1	158	194	19.3011
...(((.((((((((......))))).))).)))..	chr1:36068590-36068816(-)$1	1	9	45	11.8716
((((((..(((((((.....))))))).))))))).	chr15:73852292-73852539(-)$1	1	105	141	14.4909
(((.((((((((((.......)))))))))).))).	chr19:3630621-3630844(-)$1	1	68	104	12.2031
((((((((((.(((((....)))))..)))))))))	chr19:10795886-10796159(+)$1	1	31	67	13.9018
))((((((((((((..........))))))))))))	chr15:68583500-68583722(+)$1	1	72	108	12.7968
((.....(((((((......)))))))...))))))	chr17:73774350-73774631(-)$1	1	18	54	12.8837
((((((((((.((((......)))).)))...))).	chr1:205684301-205684572(-)$1	1	132	168	12.5008
((((((((((((.((.....)))))))))))).)))	chr1:206907308-206907533(+)$1	1	113	149	16.1919
((((.((...(((((.....)))))..)).))))))	chr7:92244162-92244396(-)$1	1	31	67	13.3651
((...(((..(((((.....)))))..)))))))))	chr12:110779973-110780225(+)$1	1	58	94	14.1232
..(((((((.((((......))))...)))))))..	chr3:23961137-23961413(+)$1	1	199	235	13.1060
..(((..((..((((.....))))..))..)))..)	chr3:196728786-196729008(-)$1	1	148	184	12.3505
((((((((((((((((....))))))))))))))))	chr10:116623690-116623921(+)$1	1	166	202	17.3953
(((((..((((((((((...))))))))))....))	chr13:100617477-100617701(-)$1	1	65	101	14.9886
.(((.(((.((((((......)))))).))).))).	chr6:24785961-24786198(+)$1	1	156	192	12.0535
(((((((((((((((......)))))..))))))))	chr2:20401659-20401886(-)$1	1	145	181	16.1759
(((((.(((..((((.....)))).))).)))..))	chr20:5171592-5171827(+)$1	1	144	180	13.2585
((.....(((((((((....)))))))))..))).)	chr11:9610579-9610820(+)$1	1	65	101	13.2508
(((((((((((((.(.....).))))))))))))))	chr1:42643284-42643539(-)$1	1	61	97	18.9999
(((..(((..((((......)))).)))..))))))	chr19:33791053-33791301(-)$1	1	16	52	11.9415
(((((..(.((((((......)))))).)..)))))	chr8:104344344-104344581(+)$1	1	126	162	13.8215
(.((((((((((.((....)).))))))))))).).	chr6:138203111-138203334(+)$1	1	126	162	15.1818
(((.(.(.(((((((((...)))))))))).).)))	chr2:20648239-20648510(+)$1	1	129	165	13.8222
.(((((((....(((.....)))...)))))))..)	chr1:93308559-93308781(-)$1	1	51	87	14.9643
((.((((((((((((.....)))))))))))).)))	chr12:27573937-27574190(+)$1	1	125	161	18.4305
(.((((((((((..........))))))))))....	chr1:7839825-7840054(+)$1	1	162	198	12.8748
(((((((.(((((.(.....).))))))))))))..	chrX:131351288-131351573(-)$1	1	201	237	12.1202
)(((((((..(((((.....))))).))))))).((	chr1:38275337-38275562(-)$1	1	70	106	13.2093
((((.(((((.(.(......).).))))).))))))	chr7:127231602-127231849(+)$1	1	42	78	13.7932
(.((((((((((((........)))))))))))).)	chr7:134653315-134653547(+)$1	1	133	169	13.7328
((((((.....((((.....))))...))))))).)	chr12:124499014-124499269(+)$1	1	78	114	12.6580
...(((((((.((((.....)))).)))))))))))	chr2:175938654-175938876(-)$1	1	9	45	14.5128
((.....(((((((((....)))))))))..))).)	chr11:9610610-9610840(+)$1	1	34	70	13.2508
..(((..((....((.....))...)).)))..).)	chr1:109822145-109822390(-)$1	1	86	122	12.1141
(((.(((((((((((...))))))))))).))))))	chr19:4794399-4794632(+)$1	1	82	118	15.7700
.((((((((((((......))))))))))))..(((	chr2:5834717-5834954(+)$1	1	94	130	13.5415
.(((.(((..(((((((...))))))).))).))).	chr17:72199722-72199959(+)$1	1	182	218	13.1886
...((((((.(((((......)))))..))))))..	chr13:76100506-76100736(-)$1	1	18	54	12.0381
..(.((((...((((.....)))).)))).)....)	chr17:2587855-2588096(+)$1	1	116	152	12.5845
.(.(..(((((((.((...)).))))))).)).)))	chr10:43881463-43881696(-)$1	1	78	114	12.6789
((((((((((...(((....)))...))))))))))	chr1:162492841-162493085(+)$1	1	51	87	16.0684
(((((((((((((((......))).)))))))))))	chr5:98129447-98129690(+)$1	1	159	195	17.9124
((.((((((((((((.....))))))))))))))).	chr22:38879801-38880025(-)$1	1	30	66	17.8556
(.((((((....(((.....)))...))))))))).	chr16:30094002-30094230(+)$1	1	64	100	12.6680
.(((((((((((((((...))))))..)))))))))	chr13:113538154-113538378(+)$1	1	175	211	13.3391
.(((..((.(((((((....))))))).))...)))	chr3:150345810-150346044(+)$1	1	138	174	12.1462
(((((((..(((((((...)))))))...)))))))	chr12:118470670-118470893(-)$1	1	126	162	13.8808
((((...(((.(((....))).)))...))))))))	chr17:47131724-47131950(+)$1	1	79	115	12.6429
.(((((((((.((((....)))).)))))))))...	chr11:69467024-69467254(+)$1	1	70	106	14.7465
.((((((((((..((((...))))))))))))))..	chr19:13055031-13055270(+)$1	1	49	85	16.2718
.((((((((((..((((...))))))))))))))..	chr19:13054978-13055230(+)$1	1	102	138	16.2718

#PSSM
g : 0.15	c : 0.15	= : 0.13	" : 0.09	[ : 0.09	f : 0.07	! : 0.07	$ : 0.05	d : 0.05	e : 0.01	h : 0.01	a : 0.01	b : 0.01	: : 0.01	i : 0.01	
= : 0.18	g : 0.16	c : 0.16	" : 0.07	i : 0.07	f : 0.07	[ : 0.07	$ : 0.03	d : 0.03	! : 0.03	e : 0.01	h : 0.01	a : 0.01	
= : 0.30	g : 0.15	c : 0.15	$ : 0.07	i : 0.07	" : 0.05	f : 0.05	[ : 0.05	e : 0.01	h : 0.01	d : 0.01	a : 0.01	
= : 0.33	g : 0.16	c : 0.13	[ : 0.07	i : 0.07	$ : 0.05	" : 0.03	f : 0.03	h : 0.01	d : 0.01	! : 0.01	a : 0.01	
= : 0.35	g : 0.15	c : 0.09	[ : 0.07	" : 0.05	i : 0.05	$ : 0.05	! : 0.05	d : 0.03	f : 0.03	a : 0.01	
= : 0.33	g : 0.15	c : 0.11	! : 0.11	i : 0.05	$ : 0.05	" : 0.03	[ : 0.03	f : 0.03	b : 0.01	e : 0.01	d : 0.01	
= : 0.33	g : 0.13	c : 0.11	! : 0.09	i : 0.07	$ : 0.07	b : 0.03	f : 0.03	[ : 0.01	a : 0.01	e : 0.01	d : 0.01	" : 0.01	
= : 0.35	c : 0.15	i : 0.11	g : 0.11	b : 0.05	! : 0.03	[ : 0.03	f : 0.03	" : 0.01	a : 0.01	e : 0.01	$ : 0.01	d : 0.01	
= : 0.35	i : 0.13	g : 0.09	! : 0.09	c : 0.07	[ : 0.05	" : 0.03	b : 0.03	# : 0.03	e : 0.03	$ : 0.01	f : 0.01	
= : 0.35	i : 0.13	g : 0.11	! : 0.11	c : 0.05	# : 0.05	" : 0.03	[ : 0.03	f : 0.03	e : 0.03	$ : 0.01	
= : 0.32	e : 0.13	g : 0.11	[ : 0.11	i : 0.07	f : 0.05	# : 0.05	d : 0.03	! : 0.03	" : 0.03	$ : 0.01	
= : 0.28	d : 0.16	e : 0.15	g : 0.11	i : 0.07	f : 0.05	# : 0.05	! : 0.03	a : 0.01	" : 0.01	c : 0.01	
= : 0.20	d : 0.16	e : 0.15	g : 0.11	i : 0.07	c : 0.07	[ : 0.05	f : 0.05	! : 0.03	s : 0.01	# : 0.01	" : 0.01	
d : 0.20	= : 0.15	e : 0.13	g : 0.09	c : 0.09	i : 0.07	[ : 0.07	b : 0.05	f : 0.05	s : 0.01	a : 0.01	o : 0.01	
d : 0.16	e : 0.13	o : 0.09	= : 0.09	i : 0.07	g : 0.07	b : 0.07	c : 0.07	a : 0.05	f : 0.05	s : 0.03	p : 0.01	q : 0.01	m : 0.01	
n : 0.35	o : 0.22	i : 0.05	m : 0.05	g : 0.05	s : 0.03	= : 0.03	d : 0.03	p : 0.01	e : 0.01	q : 0.01	l : 0.01	b : 0.01	c : 0.01	f : 0.01	
n : 0.35	o : 0.22	m : 0.16	l : 0.07	s : 0.03	d : 0.03	p : 0.01	= : 0.01	i : 0.01	q : 0.01	g : 0.01	
n : 0.35	o : 0.22	m : 0.16	l : 0.16	s : 0.03	p : 0.01	q : 0.01	
n : 0.35	o : 0.22	m : 0.15	l : 0.15	s : 0.03	p : 0.01	q : 0.01	= : 0.01	c : 0.01	
n : 0.35	o : 0.20	m : 0.11	l : 0.09	s : 0.03	b : 0.03	= : 0.03	p : 0.01	q : 0.01	f : 0.01	g : 0.01	c : 0.01	d : 0.01	
d : 0.18	o : 0.13	= : 0.11	g : 0.09	i : 0.07	a : 0.07	e : 0.07	b : 0.07	c : 0.07	s : 0.03	p : 0.01	q : 0.01	f : 0.01	
d : 0.20	] : 0.13	e : 0.13	= : 0.13	g : 0.09	i : 0.07	c : 0.07	f : 0.05	s : 0.03	b : 0.03	q : 0.01	
= : 0.24	d : 0.20	e : 0.15	g : 0.11	c : 0.09	i : 0.07	f : 0.05	s : 0.01	a : 0.01	3 : 0.01	
= : 0.24	d : 0.18	e : 0.15	g : 0.11	i : 0.07	3 : 0.07	f : 0.05	] : 0.03	c : 0.03	s : 0.01	
= : 0.30	e : 0.16	g : 0.11	3 : 0.11	i : 0.09	] : 0.09	f : 0.05	d : 0.01	2 : 0.01	c : 0.01	
= : 0.32	g : 0.13	3 : 0.11	i : 0.09	e : 0.09	2 : 0.09	] : 0.03	f : 0.03	c : 0.03	b : 0.01	d : 0.01	
= : 0.33	g : 0.15	2 : 0.11	i : 0.09	3 : 0.07	c : 0.05	f : 0.05	b : 0.03	e : 0.03	] : 0.01	d : 0.01	
= : 0.33	i : 0.13	g : 0.13	] : 0.11	c : 0.09	3 : 0.05	b : 0.03	2 : 0.03	e : 0.01	d : 0.01	f : 0.01	
= : 0.35	i : 0.15	g : 0.15	c : 0.11	3 : 0.03	b : 0.03	2 : 0.03	f : 0.03	] : 0.01	a : 0.01	e : 0.01	d : 0.01	
= : 0.33	g : 0.15	2 : 0.11	c : 0.11	] : 0.09	i : 0.07	3 : 0.03	f : 0.03	a : 0.01	b : 0.01	
= : 0.33	g : 0.18	c : 0.11	2 : 0.07	i : 0.07	f : 0.07	] : 0.03	3 : 0.03	a : 0.03	4 : 0.01	
= : 0.32	g : 0.18	c : 0.11	i : 0.07	f : 0.07	] : 0.05	3 : 0.03	4 : 0.03	a : 0.03	e : 0.01	2 : 0.01	: : 0.01	
= : 0.22	c : 0.20	g : 0.16	i : 0.07	] : 0.07	f : 0.05	4 : 0.05	e : 0.03	2 : 0.03	a : 0.01	: : 0.01	3 : 0.01	
c : 0.20	= : 0.20	g : 0.13	e : 0.07	f : 0.07	i : 0.05	2 : 0.05	4 : 0.05	3 : 0.03	d : 0.03	] : 0.01	: : 0.01	a : 0.01	
c : 0.15	= : 0.15	e : 0.09	g : 0.09	2 : 0.07	] : 0.07	3 : 0.05	i : 0.05	f : 0.05	d : 0.05	4 : 0.03	: : 0.03	6 : 0.01	5 : 0.01	a : 0.01	
= : 0.15	e : 0.13	d : 0.09	g : 0.09	f : 0.07	2 : 0.07	3 : 0.05	: : 0.05	i : 0.05	] : 0.03	5 : 0.03	c : 0.03	6 : 0.01	b : 0.01	8 : 0.01	4 : 0.01	G : 0.01	

#score	750.2145301290581
#seq	53
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_UTR_m2_run1.txt

#BEAR
ffffvvvvvvvvvvvvvfffff	chr22:41641790-41642014(-)$1	224	187	209	22.0922
ddddwwwwwwwwwwwwwwdddd	chr1:231155299-231155530(-)$1	231	197	219	20.4775
#ddddtttttttttttdddd44	chr19:42752382-42752634(-)$1	252	155	177	21.8137
ggggwwwwwwwwwwwwwwgggg	chr6:33282361-33282586(-)$1	225	176	198	21.5340
eeeeettttttttttteeeeeF	chr7:129126157-129126380(+)$1	223	190	212	21.8910
ffffftttttttttttffffff	chr17:47005508-47005748(+)$1	240	36	58	21.5287
hhhhhttttttttttthhhhhh	chr1:179074303-179074534(-)$1	231	95	117	20.9659
dddbbtttttttttttbb]ddd	chr6:7611542-7611773(+)$1	231	66	88	20.7905
[ddddtttttttttttddddee	chr1:155305139-155305364(-)$1	225	130	152	22.0979
eeeeuuuuuuuuuuuueeeee:	chrX:39956419-39956685(-)$1	266	226	248	21.3555
ggggguuuuuuuuuuuuggggg	chr6:52850171-52850393(-)$1	222	178	200	22.8817
eeeeettttttttttteeeee3	chr20:46282794-46283029(+)$1	235	45	67	22.4280
gggyyyyyyyyyyyyyyyyggg	chr12:4412738-4412968(+)$1	230	88	110	20.2072
##ccctttttttttttccc444	chr3:110853617-110853841(+)$1	224	175	197	22.0093
hhhhvvvvvvvvvvvvvhhhhh	chr19:4045321-4045552(-)$1	231	99	121	21.8220
cccvvvvvvvvvvvvvccceee	chr11:74045265-74045488(-)$1	223	160	182	21.9643
hhhhwwwwwwwwwwwwwwhhhh	chr13:53049787-53050014(+)$1	227	120	142	20.4181
hhhhvvvvvvvvvvvvvhhhhh	chr14:54942697-54942921(-)$1	224	144	166	21.8220
dddvvvvvvvvvvvvvdddd:d	chr10:32298581-32298807(-)$1	226	55	77	20.2675
!cccvvvvvvvvvvvvvccc]c	chr16:67472288-67472519(-)$1	231	69	91	23.0158
gggggtttttttttttgggggg	chr7:27180975-27181226(-)$1	251	7	29	22.6016
iiiiyyyyyyyyyyyyyyyyii	chr4:15627248-15627475(-)$1	227	40	62	19.7573
gggggtttttttttttgggggg	chr9:140098955-140099205(-)$1	250	219	241	22.6016
[ddddtttttttttttdddd22	chr17:4851525-4851774(-)$1	249	152	174	22.1071
::ccctttttttttttcccfff	chr2:136542356-136542581(+)$1	225	121	143	20.2811
eeevvvvvvvvvvvvveeeee]	chr16:29822250-29822492(+)$1	242	149	171	21.9553
eeeeewwwwwwwwwwwwwweee	chr17:48445432-48445652(-)$1	220	67	89	20.1828
ggggguuuuuuuuuuuuggggg	chr2:183790140-183790378(-)$1	238	128	150	22.8817
hhhhhuuuuuuuuuuuuhhhhh	chr13:33351551-33351780(+)$1	229	68	90	21.4155
!!cccuuuuuuuuuuuuccc22	chr4:76569104-76569330(-)$1	226	103	125	22.7864
hhhhhttttttttttthhhhhh	chr17:7364256-7364491(-)$1	235	29	51	20.9659
ggggwwwwwwwwwwwwwwgggg	chr1:207222204-207222466(-)$1	262	193	215	21.5340
%%ccctttttttttttccc444	chr4:56277752-56277975(+)$1	223	51	73	20.7166
ccc[atttttttttttaccc22	chr1:75669184-75669410(-)$1	226	25	47	22.8937
!cccvvvvvvvvvvvvvccc]b	chr12:56635205-56635478(-)$1	273	212	234	22.7527
hhhhhttttttttttthhhhhh	chr11:68382246-68382491(+)$1	245	5	27	20.9659
fffffuuuuuuuuuuuufffff	chr16:71763972-71764197(-)$1	225	110	132	21.8266
[ddddtttttttttttddddcc	chr9:131911035-131911260(+)$1	225	62	84	22.0882
dddwwwwwwwwwwwwwwdddd:	chr5:179289011-179289236(-)$1	225	46	68	19.6408
ffffvvvvvvvvvvvvvfffff	chr10:102122501-102122727(+)$1	226	134	156	22.0922
eeeeevvvvvvvvvvvvveeee	chr3:67060641-67060878(+)$1	237	138	160	21.9351
iiiiiuuuuuuuuuuuuiiiii	chr15:66841648-66841869(+)$1	221	126	148	22.7449
eeeeuuuuuuuuuuuueeeee:	chr6:93950741-93950976(-)$1	235	4	26	21.3555
dddduuuuuuuuuuuudddd22	chr7:30198525-30198777(+)$1	252	143	165	21.9240
eddddtttttttttttdddd22	chr1:203274564-203274820(+)$1	256	115	137	22.0071
ffffwwwwwwwwwwwwwwffff	chr8:30536187-30536415(-)$1	228	27	49	20.6362
hddddtttttttttttdddd22	chr18:25531854-25532085(-)$1	231	191	213	21.9404
fffyyyyyyyyyyyyyyyyfff	chr15:99874188-99874412(+)$1	224	95	117	19.5429
eeeevvvvvvvvvvvvveeeee	chr2:27477510-27477739(-)$1	229	197	219	22.6268
ggggguuuuuuuuuuuuggggg	chrX:123041170-123041401(+)$1	231	181	203	22.8817
fffffuuuuuuuuuuuufffff	chr13:100638036-100638267(+)$1	231	49	71	21.8266
eeevvvvvvvvvvvvveeeee3	chr17:40854305-40854548(-)$1	243	35	57	21.9828
eeeeettttttttttteeeeei	chr19:3976057-3976300(-)$1	243	25	47	22.3341
ggggguuuuuuuuuuuuggggg	chr14:61177521-61177752(-)$1	231	90	112	22.8817
fffyyyyyyyyyyyyyyyyfff	chr12:53806779-53807005(+)$1	226	183	205	19.5429
ffffvvvvvvvvvvvvvfffff	chr3:57611317-57611557(-)$1	240	70	92	22.0922
ddwwwwwwwwwwwwwwdddd33	chr1:154129654-154129882(-)$1	228	121	143	19.8441

#otherMatches

#Seq PSSM
GGGAGGGAGAGGCAGGGUCCCC	chr22:41641790-41642014(-)$1	224	187	209	22.0922
GAGAAUAUAACAAGAGGAUCUC	chr1:231155299-231155530(-)$1	231	197	219	20.4775
UAAAACUUUAAUUUCUUUUUUU	chr19:42752382-42752634(-)$1	252	155	177	21.8137
AAGGCCUUUGAGCCCCACCCUU	chr6:33282361-33282586(-)$1	225	176	198	21.5340
GCUCUGCCAUUUUUAAAGAGCC	chr7:129126157-129126380(+)$1	223	190	212	21.8910
GGGCUGGGACUCUGGAGGCUCC	chr17:47005508-47005748(+)$1	240	36	58	21.5287
GCUCUAUUUUCCCUUGAGAGUU	chr1:179074303-179074534(-)$1	231	95	117	20.9659
agacaggaucucacuauguucu	chr6:7611542-7611773(+)$1	231	66	88	20.7905
AUAUAAAUGCUGCUAAUAUAUU	chr1:155305139-155305364(-)$1	225	130	152	22.0979
CCGGAACACCUUUCCCCCGGGA	chrX:39956419-39956685(-)$1	266	226	248	21.3555
CAGCUUACUGAUGCCUUAGCUG	chr6:52850171-52850393(-)$1	222	178	200	22.8817
UAGCAAACUUUUCACAUGCUAA	chr20:46282794-46283029(+)$1	235	45	67	22.4280
GGUCCAUAACAGCCAAGAAGCC	chr12:4412738-4412968(+)$1	230	88	110	20.2072
UACAUACCUUUCAAACAUGAUA	chr3:110853617-110853841(+)$1	224	175	197	22.0093
CAGGAUCCCCCCUCUCCCCUGG	chr19:4045321-4045552(-)$1	231	99	121	21.8220
GCUAAAAUGAAUCAACGGCUCA	chr11:74045265-74045488(-)$1	223	160	182	21.9643
CCUCUUUUGAUUAUAACUGGGG	chr13:53049787-53050014(+)$1	227	120	142	20.4181
GACAUUUUUAUUCCAUCUGUCC	chr14:54942697-54942921(-)$1	224	144	166	21.8220
UUAUAAGUAAUAUAGUUAACAA	chr10:32298581-32298807(-)$1	226	55	77	20.2675
ACUACAUCCCUAUCUUCUAGCG	chr16:67472288-67472519(-)$1	231	69	91	23.0158
UUUUAACUUAUUUAUAUGAAGC	chr7:27180975-27181226(-)$1	251	7	29	22.6016
GUGGAAAAAUAAAGACAUUACC	chr4:15627248-15627475(-)$1	227	40	62	19.7573
UAGAUGCCUUUGUUAGAUCUAU	chr9:140098955-140099205(-)$1	250	219	241	22.6016
UGGGCUACAAGGACUCGCCCUC	chr17:4851525-4851774(-)$1	249	152	174	22.1071
AUGAGAAUUCUGCCCCCucacc	chr2:136542356-136542581(+)$1	225	121	143	20.2811
UGUUCCUGUGUCCCCUGCAUGU	chr16:29822250-29822492(+)$1	242	149	171	21.9553
GCCUCAUCCCAGAAACACGGAG	chr17:48445432-48445652(-)$1	220	67	89	20.1828
UUUAGGUUGCACAUUCACUGAA	chr2:183790140-183790378(-)$1	238	128	150	22.8817
UACUUUACAGUAAAAUUAAGUG	chr13:33351551-33351780(+)$1	229	68	90	21.4155
CAUUUUGCACAAUUCUUGAACU	chr4:76569104-76569330(-)$1	226	103	125	22.7864
GAGGUAAGCAGAUCACACCUCU	chr17:7364256-7364491(-)$1	235	29	51	20.9659
GGAUACAAUGCUUGAACCAUCC	chr1:207222204-207222466(-)$1	262	193	215	21.5340
AGUUCAUACCAAUAAAGAAGAU	chr4:56277752-56277975(+)$1	223	51	73	20.7166
GUGUGUUACCUUUUCUCCAUCU	chr1:75669184-75669410(-)$1	226	25	47	22.8937
UUACCCAUCUUUUAGUUGUAUA	chr12:56635205-56635478(-)$1	273	212	234	22.7527
UCUGGAAGCAGCACCCCCAGAG	chr11:68382246-68382491(+)$1	245	5	27	20.9659
CAGUCACGGAAGUUUUAGGCUG	chr16:71763972-71764197(-)$1	225	110	132	21.8266
AGAGGCCCAGCGUCCACCUCUC	chr9:131911035-131911260(+)$1	225	62	84	22.0882
acaaaccuuauacauacuguuu	chr5:179289011-179289236(-)$1	225	46	68	19.6408
AGGGUUUAUUUUCAGUCCCCUC	chr10:102122501-102122727(+)$1	226	134	156	22.0922
UUUAGAAAAAUGUAUUACUUGA	chr3:67060641-67060878(+)$1	237	138	160	21.9351
UCUCUGAUUGCCCUUAUGGAGA	chr15:66841648-66841869(+)$1	221	126	148	22.7449
UGAAGUUCUUUUCUUGUUCAUA	chr6:93950741-93950976(-)$1	235	4	26	21.3555
GCUGCUCGUGGUAAAACAGCGU	chr7:30198525-30198777(+)$1	252	143	165	21.9240
UGUGGACCCGCACUUCCCACCC	chr1:203274564-203274820(+)$1	256	115	137	22.0071
GCUUGCUAAUUUUCACAGAAGU	chr8:30536187-30536415(-)$1	228	27	49	20.6362
AGCACUGGGAUUUUAUGUGCCU	chr18:25531854-25532085(-)$1	231	191	213	21.9404
GCCUCAAUGAGCUCUCCAUGGC	chr15:99874188-99874412(+)$1	224	95	117	19.5429
GGGGUCUAUCUCUCCAUCCCUC	chr2:27477510-27477739(-)$1	229	197	219	22.6268
CUGGAUUUUUUAUUCUUUUCAG	chrX:123041170-123041401(+)$1	231	181	203	22.8817
uaaaguuuuuuuuuuuuuuuua	chr13:100638036-100638267(+)$1	231	49	71	21.8266
CACUGUCUUGGCUUUCGUGCUC	chr17:40854305-40854548(-)$1	243	35	57	21.9828
UUUCCAUUUCUUCAGAGGGAAA	chr19:3976057-3976300(-)$1	243	25	47	22.3341
UUUCUCCCUUAUGAAAAAGAAA	chr14:61177521-61177752(-)$1	231	90	112	22.8817
UAGAAAUCUAUCUUAAAACCUG	chr12:53806779-53807005(+)$1	226	183	205	19.5429
GUUUAUCUCUUAAUUUCAAACU	chr3:57611317-57611557(-)$1	240	70	92	22.0922
AGCAGCAAUCGAAUCCCUUUCU	chr1:154129654-154129882(-)$1	228	121	143	19.8441

#DB
((((.............)))))	chr22:41641790-41642014(-)$1	1	187	209	22.0922
((((..............))))	chr1:231155299-231155530(-)$1	1	197	219	20.4775
.((((...........))))..	chr19:42752382-42752634(-)$1	1	155	177	21.8137
((((..............))))	chr6:33282361-33282586(-)$1	1	176	198	21.5340
(((((...........))))))	chr7:129126157-129126380(+)$1	1	190	212	21.8910
(((((...........))))))	chr17:47005508-47005748(+)$1	1	36	58	21.5287
(((((...........))))))	chr1:179074303-179074534(-)$1	1	95	117	20.9659
(((((...........)).)))	chr6:7611542-7611773(+)$1	1	66	88	20.7905
.((((...........))))))	chr1:155305139-155305364(-)$1	1	130	152	22.0979
((((............))))).	chrX:39956419-39956685(-)$1	1	226	248	21.3555
(((((............)))))	chr6:52850171-52850393(-)$1	1	178	200	22.8817
(((((...........))))).	chr20:46282794-46283029(+)$1	1	45	67	22.4280
(((................)))	chr12:4412738-4412968(+)$1	1	88	110	20.2072
..(((...........)))...	chr3:110853617-110853841(+)$1	1	175	197	22.0093
((((.............)))))	chr19:4045321-4045552(-)$1	1	99	121	21.8220
(((.............))))))	chr11:74045265-74045488(-)$1	1	160	182	21.9643
((((..............))))	chr13:53049787-53050014(+)$1	1	120	142	20.4181
((((.............)))))	chr14:54942697-54942921(-)$1	1	144	166	21.8220
(((.............)))).(	chr10:32298581-32298807(-)$1	1	55	77	20.2675
.(((.............))).)	chr16:67472288-67472519(-)$1	1	69	91	23.0158
(((((...........))))))	chr7:27180975-27181226(-)$1	1	7	29	22.6016
((((................))	chr4:15627248-15627475(-)$1	1	40	62	19.7573
(((((...........))))))	chr9:140098955-140099205(-)$1	1	219	241	22.6016
.((((...........))))..	chr17:4851525-4851774(-)$1	1	152	174	22.1071
..(((...........)))(((	chr2:136542356-136542581(+)$1	1	121	143	20.2811
(((.............))))).	chr16:29822250-29822492(+)$1	1	149	171	21.9553
(((((..............)))	chr17:48445432-48445652(-)$1	1	67	89	20.1828
(((((............)))))	chr2:183790140-183790378(-)$1	1	128	150	22.8817
(((((............)))))	chr13:33351551-33351780(+)$1	1	68	90	21.4155
..(((............)))..	chr4:76569104-76569330(-)$1	1	103	125	22.7864
(((((...........))))))	chr17:7364256-7364491(-)$1	1	29	51	20.9659
((((..............))))	chr1:207222204-207222466(-)$1	1	193	215	21.5340
..(((...........)))...	chr4:56277752-56277975(+)$1	1	51	73	20.7166
(((.(...........))))..	chr1:75669184-75669410(-)$1	1	25	47	22.8937
.(((.............))).)	chr12:56635205-56635478(-)$1	1	212	234	22.7527
(((((...........))))))	chr11:68382246-68382491(+)$1	1	5	27	20.9659
(((((............)))))	chr16:71763972-71764197(-)$1	1	110	132	21.8266
.((((...........))))))	chr9:131911035-131911260(+)$1	1	62	84	22.0882
(((..............)))).	chr5:179289011-179289236(-)$1	1	46	68	19.6408
((((.............)))))	chr10:102122501-102122727(+)$1	1	134	156	22.0922
(((((.............))))	chr3:67060641-67060878(+)$1	1	138	160	21.9351
(((((............)))))	chr15:66841648-66841869(+)$1	1	126	148	22.7449
((((............))))).	chr6:93950741-93950976(-)$1	1	4	26	21.3555
((((............))))..	chr7:30198525-30198777(+)$1	1	143	165	21.9240
(((((...........))))..	chr1:203274564-203274820(+)$1	1	115	137	22.0071
((((..............))))	chr8:30536187-30536415(-)$1	1	27	49	20.6362
(((((...........))))..	chr18:25531854-25532085(-)$1	1	191	213	21.9404
(((................)))	chr15:99874188-99874412(+)$1	1	95	117	19.5429
((((.............)))))	chr2:27477510-27477739(-)$1	1	197	219	22.6268
(((((............)))))	chrX:123041170-123041401(+)$1	1	181	203	22.8817
(((((............)))))	chr13:100638036-100638267(+)$1	1	49	71	21.8266
(((.............))))).	chr17:40854305-40854548(-)$1	1	35	57	21.9828
(((((...........)))))(	chr19:3976057-3976300(-)$1	1	25	47	22.3341
(((((............)))))	chr14:61177521-61177752(-)$1	1	90	112	22.8817
(((................)))	chr12:53806779-53807005(+)$1	1	183	205	19.5429
((((.............)))))	chr3:57611317-57611557(-)$1	1	70	92	22.0922
((..............))))..	chr1:154129654-154129882(-)$1	1	121	143	19.8441

#PSSM
e : 0.19	f : 0.15	g : 0.15	h : 0.14	d : 0.10	[ : 0.05	! : 0.05	# : 0.03	c : 0.03	i : 0.03	: : 0.01	% : 0.01	
d : 0.21	e : 0.17	f : 0.15	g : 0.15	h : 0.12	c : 0.07	i : 0.03	# : 0.01	: : 0.01	! : 0.01	% : 0.01	
d : 0.19	e : 0.17	f : 0.15	g : 0.15	c : 0.14	h : 0.12	i : 0.03	w : 0.01	
d : 0.14	g : 0.14	e : 0.14	f : 0.12	h : 0.12	c : 0.10	v : 0.07	y : 0.05	i : 0.03	w : 0.03	b : 0.01	[ : 0.01	
v : 0.21	w : 0.12	d : 0.10	g : 0.10	e : 0.08	h : 0.07	y : 0.07	c : 0.07	f : 0.05	u : 0.05	b : 0.01	a : 0.01	i : 0.01	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
t : 0.35	v : 0.22	u : 0.21	w : 0.14	y : 0.07	
v : 0.15	d : 0.15	u : 0.15	w : 0.12	e : 0.12	y : 0.07	c : 0.07	h : 0.05	g : 0.03	f : 0.01	b : 0.01	a : 0.01	
d : 0.17	e : 0.14	c : 0.14	f : 0.10	w : 0.10	h : 0.10	g : 0.10	y : 0.07	b : 0.01	v : 0.01	i : 0.01	
d : 0.19	e : 0.15	g : 0.14	c : 0.14	f : 0.12	h : 0.12	y : 0.07	] : 0.01	w : 0.01	i : 0.01	
d : 0.21	e : 0.19	f : 0.17	g : 0.15	h : 0.12	c : 0.07	4 : 0.03	y : 0.01	i : 0.01	
e : 0.21	f : 0.17	g : 0.15	h : 0.12	2 : 0.10	d : 0.05	4 : 0.05	] : 0.03	i : 0.03	: : 0.01	c : 0.01	3 : 0.01	
f : 0.17	g : 0.15	h : 0.12	2 : 0.10	e : 0.08	d : 0.05	4 : 0.05	: : 0.05	3 : 0.05	i : 0.05	c : 0.03	F : 0.01	] : 0.01	b : 0.01	

#score	1231.5315292446144
#seq	57
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_UTR_m3_run1.txt

#BEAR
d!!ddddqqqqqqqqdddd333	chr7:156765538-156765779(+)$1	241	202	224	14.8186
ggggg[aqqqqqqqqagggggg	chr5:6755432-6755666(+)$1	234	9	31	15.8281
ddeeeeeqqqqqqqqeeeee33	chr1:82457642-82457867(+)$1	225	41	63	14.1130
dddd[bbqqqqqqqqbb]dddd	chr5:137088601-137088832(-)$1	231	176	198	13.5973
ffffcccqqqqqqqqccc333f	chr2:136664614-136664847(-)$1	233	162	184	15.5571
[ccc[bbqqqqqqqqbbccc]b	chr14:71196860-71197092(-)$1	232	153	175	14.9045
bb!!cccqqqqqqqqccc22bb	chr9:113018594-113018855(-)$1	261	148	170	14.4708
####cccqqqqqqqqccc7777	chr1:109351696-109351921(+)$1	225	84	106	13.5410
ffffcccqqqqqqqqccc]fff	chr9:37439707-37439940(-)$1	233	10	32	15.2322
[ffffffqqqqqqqqffffff]	chr14:81643805-81644051(-)$1	246	83	105	15.3952
f####bbqqqqqqqqbb4444f	chr17:41246537-41246780(-)$1	243	139	161	14.5967
[ffffffqqqqqqqqffffffd	chr17:46626591-46626826(-)$1	235	126	148	15.1597
""eeeeeqqqqqqqqeeeee22	chr17:37006285-37006519(-)$1	234	207	229	14.2553
gggggggqqqqqqqqggggggg	chr2:74441178-74441442(+)$1	264	40	62	16.1497
gggggggqqqqqqqqggggggg	chr5:176868733-176868984(+)$1	251	203	225	16.1497
=======qqqqqqqq=======	chr11:8705701-8705941(+)$1	240	91	113	16.0611
fffa[bbqqqqqqqqbb]a]ff	chr10:74035084-74035320(+)$1	236	152	174	14.8541
ddddcccqqqqqqqqccc]ddd	chr12:50158507-50158782(+)$1	275	236	258	14.0636
$$$$$bbqqqqqqqqbb333dd	chr10:116623162-116623395(+)$1	233	153	175	13.9639
##eeeeeqqqqqqqqeeeeeff	chr17:4801146-4801390(+)$1	244	171	193	14.2951
#ffffffqqqqqqqqffffff7	chr1:145441644-145441913(+)$1	269	37	59	14.8674
gggggggqqqqqqqqggggggg	chr5:179156432-179156673(+)$1	241	4	26	16.1497
cc!!cccqqqqqqqqccc22cc	chr13:100638154-100638423(+)$1	269	214	236	15.3900
cc"""bbqqqqqqqqbb4444c	chr22:39081563-39081802(-)$1	239	87	109	14.8760
gggggggqqqqqqqqggggggg	chr18:12449314-12449542(-)$1	228	8	30	16.1497
cc[ddddqqqqqqqqdddd]cc	chr12:56366278-56366532(+)$1	254	117	139	14.5143
"ffffffqqqqqqqqffffff3	chr5:172461588-172461920(+)$1	332	60	82	15.4844
""eeeeeqqqqqqqqeeeee00	chr1:36385843-36386115(+)$1	272	223	245	13.8310
gggggggqqqqqqqqggggggg	chr14:35181122-35181358(-)$1	236	168	190	16.1497
cc[ddddqqqqqqqqddddccc	chr21:27253519-27253752(-)$1	233	179	201	14.3411
:ffffffqqqqqqqqffffffB	chr1:200827650-200827904(+)$1	254	176	198	13.3259
ee"""bbqqqqqqqqbb4444e	chr19:58906002-58906242(+)$1	240	169	191	14.4622
c!!ddddqqqqqqqqdddd22c	chr15:77242065-77242305(+)$1	240	111	133	14.3363
gggggggqqqqqqqqggggggg	chrX:24001764-24002018(-)$1	254	163	185	16.1497
""bb[bbqqqqqqqqbb]bb22	chrX:118377086-118377317(+)$1	231	48	70	13.8673
iiiiiiiqqqqqqqqiiiiiii	chr7:155100851-155101112(+)$1	261	120	142	15.6882
gggggggqqqqqqqqggggggg	chr10:72188031-72188303(+)$1	272	249	271	16.1497
h!!ddddqqqqqqqqdddd]hh	chr1:228645388-228645647(-)$1	259	195	217	14.0708
gggg[bbqqqqqqqqbbggggg	chr2:27664955-27665210(+)$1	255	11	33	15.7364
gggggggqqqqqqqqggggggg	chrX:41208508-41208769(+)$1	261	186	208	16.1497
#ffffffqqqqqqqqffffff7	chr1:145441553-145441805(+)$1	252	128	150	14.8674
gg[ddddqqqqqqqqdddd333	chr17:7833584-7833819(-)$1	235	193	215	15.1051
"""ddddqqqqqqqqdddd444	chr4:169848079-169848301(+)$1	222	167	189	14.6396
gggggggqqqqqqqqggggggg	chr3:169805628-169805854(-)$1	226	170	192	16.1497
[ffffffqqqqqqqqffffffd	chrX:123041365-123041656(+)$1	291	9	31	15.1597
gggg[bbqqqqqqqqbb]gggg	chr11:47491325-47491576(-)$1	251	73	95	15.7114
gggggggqqqqqqqqggggggg	chr8:81431820-81432046(+)$1	226	192	214	16.1497
gggggggqqqqqqqqggggggg	chr7:63980727-63980962(-)$1	235	70	92	16.1497
:ffffffqqqqqqqqffffff:	chr4:15070995-15071231(+)$1	236	41	63	13.3389
bb[ddddqqqqqqqqdddd]bb	chr1:172580455-172580680(+)$1	225	7	29	13.5950
:ffffffqqqqqqqqffffff:	chrX:153173036-153173264(-)$1	228	186	208	13.3389
ee!!cccqqqqqqqqccc22ee	chr2:198256849-198257097(-)$1	248	23	45	14.8484
gggggggqqqqqqqqggggggg	chr7:108214558-108214815(+)$1	257	117	139	16.1497
gggggggqqqqqqqqggggggg	chr1:205684044-205684296(-)$1	252	84	106	16.1497
!bb[cccqqqqqqqqccc]bb2	chr11:9610643-9610876(+)$1	233	194	216	14.5395
hhh[cccqqqqqqqqccc]hhh	chr5:114951325-114951572(-)$1	247	135	157	14.3843
[ffffffqqqqqqqqffffff]	chr17:36923639-36923867(-)$1	228	127	149	15.3952
"ccc[bbqqqqqqqqbb]ccc3	chr17:27875904-27876172(+)$1	268	214	236	15.2384
=======qqqqqqqq=======	chr3:186504249-186504504(+)$1	255	23	45	16.0611
gggggggqqqqqqqqggggggg	chr3:169805426-169805694(-)$1	268	10	32	16.1497

#otherMatches

#Seq PSSM
AAUGCAGGUUGAGAACUGCUAA	chr7:156765538-156765779(+)$1	241	202	224	14.8186
UCGUGUGUCUUUCCUCCACGGA	chr5:6755432-6755666(+)$1	234	9	31	15.8281
AUUUCUUAUUGCCAAAAGAACG	chr1:82457642-82457867(+)$1	225	41	63	14.1130
GUCUCUCCCUCUGAAGAUGGAC	chr5:137088601-137088832(-)$1	231	176	198	13.5973
UAGGUUCGUUUAAAAGAGAUUU	chr2:136664614-136664847(-)$1	233	162	184	15.5571
UCAGAGGGUCUCCUGCCCUGCA	chr14:71196860-71197092(-)$1	232	153	175	14.9045
GCAGAUCGAGAGCAAGGUACGC	chr9:113018594-113018855(-)$1	261	148	170	14.4708
UUUCACAGCCACCUAUGUACAU	chr1:109351696-109351921(+)$1	225	84	106	13.5410
UCCAGAGUGAGCAUUCUCUUGG	chr9:37439707-37439940(-)$1	233	10	32	15.2322
GUAUUAUGAAAAUAAGUAAUGG	chr14:81643805-81644051(-)$1	246	83	105	15.3952
GAAUUCUGUAAUAAAAGCAAAC	chr17:41246537-41246780(-)$1	243	139	161	14.5967
UCUGGGCCUGCAGAAGUCCAGC	chr17:46626591-46626826(-)$1	235	126	148	15.1597
CUCCCUGuucacuuccaggguu	chr17:37006285-37006519(-)$1	234	207	229	14.2553
AGCUGGGUAUAUCACUCCAGUU	chr2:74441178-74441442(+)$1	264	40	62	16.1497
CUCAGCCCCUGGCCUGGCUGAG	chr5:176868733-176868984(+)$1	251	203	225	16.1497
UUGGGUAUCGGCUAUUGCCUGA	chr11:8705701-8705941(+)$1	240	91	113	16.0611
UACUGACAGUUAACAGUGGUGU	chr10:74035084-74035320(+)$1	236	152	174	14.8541
UACAGCUGGUCAUGGAGCUUGU	chr12:50158507-50158782(+)$1	275	236	258	14.0636
UAAUGACUUUAAUUUGUAAUCA	chr10:116623162-116623395(+)$1	233	153	175	13.9639
CCUGUUUGUUAAUAAAGACAAU	chr17:4801146-4801390(+)$1	244	171	193	14.2951
AAACUUUGGGAAAAGGAGGUUC	chr1:145441644-145441913(+)$1	269	37	59	14.8674
CUUGUUAAGGAAUGCUAGCAGG	chr5:179156432-179156673(+)$1	241	4	26	16.1497
GAUUGCGUUCCUCCCCGCCUUC	chr13:100638154-100638423(+)$1	269	214	236	15.3900
CUUUUAUUCCUUUUUGUUGUUG	chr22:39081563-39081802(-)$1	239	87	109	14.8760
GAAUUUGCAUUAGAUCAGAUUU	chr18:12449314-12449542(-)$1	228	8	30	16.1497
UGGGUGGAUUUGUUGCCAUGUG	chr12:56366278-56366532(+)$1	254	117	139	14.5143
UGAGAGAUACGUUACUCUCUCC	chr5:172461588-172461920(+)$1	332	60	82	15.4844
GAUGGGGAAGAAAUACCCCAGA	chr1:36385843-36386115(+)$1	272	223	245	13.8310
UUUUGCAAAAUGUUAUGUGAAA	chr14:35181122-35181358(-)$1	236	168	190	16.1497
AACGUGGGAGUUCAGCUGCUUC	chr21:27253519-27253752(-)$1	233	179	201	14.3411
AUUCUCUAUUAAAUAAGAGGAG	chr1:200827650-200827904(+)$1	254	176	198	13.3259
CCUGUGCUGUUGUCUGUCUUCG	chr19:58906002-58906242(+)$1	240	169	191	14.4622
GUGAGUGGAAUUUGACAUUGUC	chr15:77242065-77242305(+)$1	240	111	133	14.3363
auauuuuuaaucuuuaaaauau	chrX:24001764-24002018(-)$1	254	163	185	16.1497
AACUGCUGAAGGAGGGGGAGGA	chrX:118377086-118377317(+)$1	231	48	70	13.8673
ACCUAAUUUGCAAGUAUUGGGU	chr7:155100851-155101112(+)$1	261	120	142	15.6882
UCCAAACCAGCAGAUGUUUGGA	chr10:72188031-72188303(+)$1	272	249	271	16.1497
GGGCUGCAGUUCCCCGUGGGCC	chr1:228645388-228645647(-)$1	259	195	217	14.0708
UGUGUGGAAAGGAGGCCCACGG	chr2:27664955-27665210(+)$1	255	11	33	15.7364
GAUAGUUGGGAAGAAAACUAUU	chrX:41208508-41208769(+)$1	261	186	208	16.1497
AAACUUUGGGAAAAGGAGGUUC	chr1:145441553-145441805(+)$1	252	128	150	14.8674
GCCCCACGCAUGAAGGUGGAAA	chr17:7833584-7833819(-)$1	235	193	215	15.1051
aaGUGCUCUGAAUAAAGCAGAA	chr4:169848079-169848301(+)$1	222	167	189	14.6396
GUAUGAAUUUAGAUUUUCAUAU	chr3:169805628-169805854(-)$1	226	170	192	16.1497
UAGGCUUAACAAAUGGAGCUUU	chrX:123041365-123041656(+)$1	291	9	31	15.1597
UCUGUCUUCCUCCUUAGCCAGA	chr11:47491325-47491576(-)$1	251	73	95	15.7114
AUAUUUUUUAUUUAUAGGAUAU	chr8:81431820-81432046(+)$1	226	192	214	16.1497
UGUAAAUAUUAAAUAAUUUACA	chr7:63980727-63980962(-)$1	235	70	92	16.1497
CACAGUGUCAUUUUUUACUGUC	chr4:15070995-15071231(+)$1	236	41	63	13.3389
UUUUUUUGUCUUUAAAAAAUAA	chr1:172580455-172580680(+)$1	225	7	29	13.5950
CCUGCACUUCACCCUGUGCAGA	chrX:153173036-153173264(-)$1	228	186	208	13.3389
GAUGAUAAGAACACCUAUAUUC	chr2:198256849-198257097(-)$1	248	23	45	14.8484
UAUUUUUAAAUCCUGAGAAAUG	chr7:108214558-108214815(+)$1	257	117	139	16.1497
UUAUCUGUGAACAUUCAGAUAA	chr1:205684044-205684296(-)$1	252	84	106	16.1497
UUGAACUUUGAAGCUAGUGCAU	chr11:9610643-9610876(+)$1	233	194	216	14.5395
UGGAGGAAAAAUAAAUCUACCA	chr5:114951325-114951572(-)$1	247	135	157	14.3843
UAGCAUUCUGUUUCAAAUGCUU	chr17:36923639-36923867(-)$1	228	127	149	15.3952
UAUUGGGCUCUUUAACUGAAUU	chr17:27875904-27876172(+)$1	268	214	236	15.2384
UAAUUUUCUCUUUUUAAGGUUG	chr3:186504249-186504504(+)$1	255	23	45	16.0611
GUAUGAAUUUAGAUUUUCAUAU	chr3:169805426-169805694(-)$1	268	10	32	16.1497

#DB
(..((((........))))...	chr7:156765538-156765779(+)$1	1	202	224	14.8186
(((((.(........)))))))	chr5:6755432-6755666(+)$1	1	9	31	15.8281
(((((((........)))))..	chr1:82457642-82457867(+)$1	1	41	63	14.1130
((((.((........)).))))	chr5:137088601-137088832(-)$1	1	176	198	13.5973
(((((((........)))...)	chr2:136664614-136664847(-)$1	1	162	184	15.5571
.(((.((........))))).)	chr14:71196860-71197092(-)$1	1	153	175	14.9045
((..(((........)))..))	chr9:113018594-113018855(-)$1	1	148	170	14.4708
....(((........)))....	chr1:109351696-109351921(+)$1	1	84	106	13.5410
(((((((........))).)))	chr9:37439707-37439940(-)$1	1	10	32	15.2322
.((((((........)))))).	chr14:81643805-81644051(-)$1	1	83	105	15.3952
(....((........))....)	chr17:41246537-41246780(-)$1	1	139	161	14.5967
.((((((........)))))))	chr17:46626591-46626826(-)$1	1	126	148	15.1597
..(((((........)))))..	chr17:37006285-37006519(-)$1	1	207	229	14.2553
(((((((........)))))))	chr2:74441178-74441442(+)$1	1	40	62	16.1497
(((((((........)))))))	chr5:176868733-176868984(+)$1	1	203	225	16.1497
(((((((........)))))))	chr11:8705701-8705941(+)$1	1	91	113	16.0611
((((.((........)).).))	chr10:74035084-74035320(+)$1	1	152	174	14.8541
(((((((........))).)))	chr12:50158507-50158782(+)$1	1	236	258	14.0636
.....((........))...))	chr10:116623162-116623395(+)$1	1	153	175	13.9639
..(((((........)))))))	chr17:4801146-4801390(+)$1	1	171	193	14.2951
.((((((........)))))).	chr1:145441644-145441913(+)$1	1	37	59	14.8674
(((((((........)))))))	chr5:179156432-179156673(+)$1	1	4	26	16.1497
((..(((........)))..))	chr13:100638154-100638423(+)$1	1	214	236	15.3900
((...((........))....)	chr22:39081563-39081802(-)$1	1	87	109	14.8760
(((((((........)))))))	chr18:12449314-12449542(-)$1	1	8	30	16.1497
((.((((........)))).))	chr12:56366278-56366532(+)$1	1	117	139	14.5143
.((((((........)))))).	chr5:172461588-172461920(+)$1	1	60	82	15.4844
..(((((........)))))..	chr1:36385843-36386115(+)$1	1	223	245	13.8310
(((((((........)))))))	chr14:35181122-35181358(-)$1	1	168	190	16.1497
((.((((........)))))))	chr21:27253519-27253752(-)$1	1	179	201	14.3411
.((((((........)))))))	chr1:200827650-200827904(+)$1	1	176	198	13.3259
((...((........))....)	chr19:58906002-58906242(+)$1	1	169	191	14.4622
(..((((........))))..)	chr15:77242065-77242305(+)$1	1	111	133	14.3363
(((((((........)))))))	chrX:24001764-24002018(-)$1	1	163	185	16.1497
..((.((........)).))..	chrX:118377086-118377317(+)$1	1	48	70	13.8673
(((((((........)))))))	chr7:155100851-155101112(+)$1	1	120	142	15.6882
(((((((........)))))))	chr10:72188031-72188303(+)$1	1	249	271	16.1497
(..((((........)))).))	chr1:228645388-228645647(-)$1	1	195	217	14.0708
((((.((........)))))))	chr2:27664955-27665210(+)$1	1	11	33	15.7364
(((((((........)))))))	chrX:41208508-41208769(+)$1	1	186	208	16.1497
.((((((........)))))).	chr1:145441553-145441805(+)$1	1	128	150	14.8674
((.((((........))))...	chr17:7833584-7833819(-)$1	1	193	215	15.1051
...((((........))))...	chr4:169848079-169848301(+)$1	1	167	189	14.6396
(((((((........)))))))	chr3:169805628-169805854(-)$1	1	170	192	16.1497
.((((((........)))))))	chrX:123041365-123041656(+)$1	1	9	31	15.1597
((((.((........)).))))	chr11:47491325-47491576(-)$1	1	73	95	15.7114
(((((((........)))))))	chr8:81431820-81432046(+)$1	1	192	214	16.1497
(((((((........)))))))	chr7:63980727-63980962(-)$1	1	70	92	16.1497
.((((((........)))))).	chr4:15070995-15071231(+)$1	1	41	63	13.3389
((.((((........)))).))	chr1:172580455-172580680(+)$1	1	7	29	13.5950
.((((((........)))))).	chrX:153173036-153173264(-)$1	1	186	208	13.3389
((..(((........)))..))	chr2:198256849-198257097(-)$1	1	23	45	14.8484
(((((((........)))))))	chr7:108214558-108214815(+)$1	1	117	139	16.1497
(((((((........)))))))	chr1:205684044-205684296(-)$1	1	84	106	16.1497
.((.(((........))).)).	chr11:9610643-9610876(+)$1	1	194	216	14.5395
(((.(((........))).)))	chr5:114951325-114951572(-)$1	1	135	157	14.3843
.((((((........)))))).	chr17:36923639-36923867(-)$1	1	127	149	15.3952
.(((.((........)).))).	chr17:27875904-27876172(+)$1	1	214	236	15.2384
(((((((........)))))))	chr3:186504249-186504504(+)$1	1	23	45	16.0611
(((((((........)))))))	chr3:169805426-169805694(-)$1	1	10	32	16.1497

#PSSM
g : 0.30	" : 0.09	[ : 0.08	c : 0.08	d : 0.06	f : 0.06	# : 0.06	: : 0.05	b : 0.03	= : 0.03	e : 0.03	h : 0.03	$ : 0.01	i : 0.01	! : 0.01	
g : 0.30	f : 0.21	c : 0.09	" : 0.06	! : 0.05	d : 0.05	b : 0.05	# : 0.05	= : 0.03	e : 0.03	$ : 0.01	i : 0.01	h : 0.01	
g : 0.28	f : 0.21	! : 0.09	e : 0.06	[ : 0.06	" : 0.05	d : 0.03	c : 0.03	# : 0.03	= : 0.03	b : 0.03	$ : 0.01	i : 0.01	h : 0.01	
g : 0.28	f : 0.19	d : 0.16	e : 0.06	! : 0.05	c : 0.03	# : 0.03	= : 0.03	" : 0.03	[ : 0.03	a : 0.01	$ : 0.01	b : 0.01	i : 0.01	
g : 0.24	f : 0.16	c : 0.15	d : 0.13	[ : 0.11	e : 0.06	= : 0.03	" : 0.03	# : 0.01	$ : 0.01	i : 0.01	
g : 0.23	b : 0.18	f : 0.16	c : 0.15	d : 0.13	e : 0.06	= : 0.03	[ : 0.01	i : 0.01	
g : 0.23	b : 0.18	f : 0.16	c : 0.15	d : 0.13	e : 0.06	= : 0.03	a : 0.01	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
g : 0.23	b : 0.18	f : 0.16	c : 0.15	d : 0.13	e : 0.06	= : 0.03	a : 0.01	i : 0.01	
g : 0.24	b : 0.18	f : 0.16	c : 0.15	d : 0.13	e : 0.06	= : 0.03	i : 0.01	
g : 0.26	c : 0.16	f : 0.16	d : 0.13	] : 0.08	e : 0.06	4 : 0.05	= : 0.03	3 : 0.01	i : 0.01	
g : 0.28	f : 0.16	d : 0.15	e : 0.06	] : 0.06	2 : 0.05	4 : 0.05	3 : 0.03	c : 0.03	= : 0.03	7 : 0.01	a : 0.01	b : 0.01	i : 0.01	
g : 0.28	f : 0.18	3 : 0.06	e : 0.06	2 : 0.06	4 : 0.06	] : 0.06	c : 0.05	d : 0.03	= : 0.03	b : 0.03	7 : 0.01	i : 0.01	h : 0.01	
g : 0.28	f : 0.21	3 : 0.06	4 : 0.06	c : 0.06	d : 0.05	b : 0.05	2 : 0.05	= : 0.03	h : 0.03	] : 0.01	7 : 0.01	0 : 0.01	i : 0.01	e : 0.01	
g : 0.28	3 : 0.08	d : 0.08	f : 0.08	c : 0.08	b : 0.05	7 : 0.05	2 : 0.05	] : 0.03	= : 0.03	e : 0.03	h : 0.03	: : 0.03	0 : 0.01	B : 0.01	i : 0.01	4 : 0.01	

#score	901.8194465486392
#seq	60
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_transcript_m2_run2.txt

#BEAR
ddduuuuuuuuuuuuddddb	chr17:35800569-35800792(+)$1	223	43	63	22.3363
cyyyyyyyyyyyyyyyyccc	chr5:53270623-53270871(-)$1	248	117	137	19.8910
dddyyyyyyyyyyyyyyyyd	chr7:111153664-111153898(-)$1	234	35	55	19.5310
eeeettttttttttteeeee	chr1:117981044-117981343(+)$1	299	107	127	22.2017
ddduuuuuuuuuuuudddd3	chr18:46915560-46915829(-)$1	269	82	102	22.7305
gggvvvvvvvvvvvvvgggg	chr14:89703595-89703844(-)$1	249	59	79	22.1357
dddyyyyyyyyyyyyyyyyd	chrX:76910520-76910760(-)$1	240	159	179	19.5310
cccvvvvvvvvvvvvvccc2	chrX:123225299-123225526(+)$1	227	29	49	22.1310
iiiitttttttttttiiiii	chr13:48535675-48536002(-)$1	327	165	185	21.3006
eeeuuuuuuuuuuuueeeee	chr8:126217663-126217942(+)$1	279	23	43	23.0354
eeevvvvvvvvvvvvveeee	chr2:55819732-55819979(-)$1	247	61	81	22.9273
dddvvvvvvvvvvvvvdddd	chr4:1170716-1170974(-)$1	258	52	72	22.5941
yyyyyyyyyyyyyyybbeee	chr8:126245903-126246198(+)$1	295	67	87	19.7388
cccvvvvvvvvvvvvvccc2	chr2:75901363-75901592(-)$1	229	143	163	22.1310
eeeettttttttttteeeee	chr2:210880023-210880268(+)$1	245	222	242	22.2017
dddvvvvvvvvvvvvvdddd	chr10:11355430-11355802(+)$1	372	182	202	22.5941
fffvvvvvvvvvvvvvffff	chr2:122151154-122151409(-)$1	255	82	102	21.4698
[bbvvvvvvvvvvvvvbbii	chr11:68354511-68354773(+)$1	262	27	47	21.2900
yyyyyyyyyyyyyyyeeeee	chr14:103961730-103961986(+)$1	256	158	178	20.2933
yyyyyyyyyyyyyyyeeeee	chr20:45286893-45287145(-)$1	252	204	224	20.2933
fffwwwwwwwwwwwwwwfff	chr2:144052747-144052983(+)$1	236	12	32	19.9444
eeeettttttttttteeeee	chr1:193208985-193209285(+)$1	300	180	200	22.2017
eeeettttttttttteeeee	chr16:78904143-78904377(+)$1	234	163	183	22.2017
g[auuuuuuuuuuuua]ggg	chr6:12064879-12065109(+)$1	230	84	104	22.3827
dddtttttttttttdddddd	chr14:73344377-73344730(-)$1	353	210	230	21.2634
dddvvvvvvvvvvvvvdddd	chr14:24736435-24736692(-)$1	257	8	28	22.5941
yyyyyyyyyyyyyyyfffff	chr7:39731787-39732017(+)$1	230	61	81	19.3493
ddduuuuuuuuuuuudddd]	chr10:114399488-114399728(+)$1	240	143	163	22.7569
e[bbtttttttttttbbeee	chr1:217717235-217717465(-)$1	230	156	176	21.1801
eeevvvvvvvvvvvvveeee	chr3:11726196-11726427(-)$1	231	74	94	22.9273
hhhuuuuuuuuuuuuhhhhh	chr4:103487811-103488123(+)$1	312	57	77	20.6909
eeevvvvvvvvvvvvveeee	chr9:95237530-95237795(+)$1	265	83	103	22.9273
yyyyyyyyyyyyyyyiiiii	chr3:196800029-196800299(-)$1	270	185	205	19.8037
eeeuuuuuuuuuuuueeeee	chrX:110946310-110946563(+)$1	253	6	26	23.0354
cccuuuuuuuuuuuuccc33	chr2:143930868-143931116(+)$1	248	132	152	22.3987
ccvvvvvvvvvvvvvccc==	chr8:11169029-11169282(+)$1	253	180	200	21.7661
yyyyyyyyyyyyyyyfffff	chr5:42793131-42793358(+)$1	227	80	100	19.3493
dddtttttttttttdddd44	chr1:6389993-6390245(-)$1	252	118	138	21.1549
ccwwwwwwwwwwwwwwccc]	chr13:96333900-96334134(+)$1	234	200	220	20.8279
!bbwwwwwwwwwwwwwwbb2	chr9:5710003-5710249(+)$1	246	72	92	19.4023
dddwwwwwwwwwwwwwwddd	chr1:113989121-113989367(+)$1	246	146	166	20.9285
[ccctttttttttttccc]e	chr11:63520253-63520487(+)$1	234	89	109	21.7769
dddtttttttttttdddd]e	chr11:108604317-108604559(+)$1	242	22	42	21.3701
iiiuuuuuuuuuuuuiiiii	chr4:141918181-141918416(-)$1	235	91	111	22.2876
====ttttttttttt=====	chr2:208444856-208445149(+)$1	293	237	257	21.6565
dddvvvvvvvvvvvvvdddd	chr8:17875792-17876082(+)$1	290	103	123	22.5941
dddtttttttttttdddd]g	chr4:83975045-83975272(+)$1	227	14	34	21.2475
fffvvvvvvvvvvvvvffff	chr1:108192458-108192776(-)$1	318	262	282	21.4698
d[bbtttttttttttbb333	chr19:3445057-3445392(+)$1	335	232	252	20.6343
ggggtttttttttttggggg	chr1:211922839-211923074(-)$1	235	8	28	21.1907
eeeettttttttttteeeee	chr6:112134635-112134880(-)$1	245	77	97	22.2017
eeeettttttttttteeeee	chr14:56761257-56761651(+)$1	394	253	273	22.2017
eeeettttttttttteeeee	chr2:15442567-15442799(-)$1	232	24	44	22.2017
ddduuuuuuuuuuuudddd]	chr9:95271326-95271550(+)$1	224	116	136	22.7569
dddvvvvvvvvvvvvvdddd	chr8:101289009-101289241(-)$1	232	11	31	22.5941
eeeuuuuuuuuuuuueeeee	chr4:68348547-68348801(-)$1	254	159	179	23.0354
fffftttttttttttfffff	chr4:20446289-20446521(+)$1	232	13	33	20.5619
cccvvvvvvvvvvvvvccc2	chr1:198640663-198640935(+)$1	272	183	203	22.1310
eewwwwwwwwwwwwwweeee	chr7:131065740-131066010(+)$1	270	9	29	21.3726
ddduuuuuuuuuuuudddd:	chr2:238999522-238999772(+)$1	250	98	118	21.6955
eeeettttttttttteeeee	chr14:100826677-100826925(-)$1	248	205	225	22.2017
ddddtttttttttttdddd]	chr14:88688662-88688886(-)$1	224	99	119	21.8638
dddvvvvvvvvvvvvvdddd	chr5:158708275-158708536(+)$1	261	186	206	22.5941
eeevvvvvvvvvvvvveeee	chr15:34483526-34483789(-)$1	263	225	245	22.9273
[bbvvvvvvvvvvvvvbbdd	chr3:89306749-89306985(+)$1	236	140	160	21.2677
ggguuuuuuuuuuuuggggg	chr2:71649652-71649916(+)$1	264	202	222	22.1563
cwwwwwwwwwwwwwwccc]e	chr8:61435450-61435675(+)$1	225	107	127	20.2888
ggguuuuuuuuuuuuggggg	chr1:29500747-29500982(-)$1	235	158	178	22.1563
dddwwwwwwwwwwwwwwddd	chr6:128034275-128034533(-)$1	258	99	119	20.9285
eeevvvvvvvvvvvvveeee	chr14:73152277-73152516(-)$1	239	182	202	22.9273
eeevvvvvvvvvvvvveeee	chr6:74177293-74177530(+)$1	237	99	119	22.9273
yyyyyyyyyyyyyyyeeeee	chr12:32503431-32503688(+)$1	257	30	50	20.2933
cccvvvvvvvvvvvvvccc:	chr17:18206945-18207218(-)$1	273	55	75	21.2746
eeeuuuuuuuuuuuueeeee	chr5:112135445-112135695(+)$1	250	223	243	23.0354
ddddtttttttttttdddd]	chr2:182380453-182380704(+)$1	251	96	116	21.8638

#otherMatches

#Seq PSSM
GUAGCCAAUCAAAUGUGCAC	chr17:35800569-35800792(+)$1	223	43	63	22.3363
GAUUACCACCUCACAGACAG	chr5:53270623-53270871(-)$1	248	117	137	19.8910
uauauacaccugcagaagaa	chr7:111153664-111153898(-)$1	234	35	55	19.5310
auguccuaggccuucacauu	chr1:117981044-117981343(+)$1	299	107	127	22.2017
CUACUACUUAUUCAAUAGAU	chr18:46915560-46915829(-)$1	269	82	102	22.7305
aguuuuuuaacaaaccgcua	chr14:89703595-89703844(-)$1	249	59	79	22.1357
uucuauuuucugucucuaug	chrX:76910520-76910760(-)$1	240	159	179	19.5310
ggauaaacucccaacuuccu	chrX:123225299-123225526(+)$1	227	29	49	22.1310
aggaaugucguagaauccug	chr13:48535675-48536002(-)$1	327	165	185	21.3006
CUGUCCCUUAUCCAUCAGUA	chr8:126217663-126217942(+)$1	279	23	43	23.0354
CUUACUAGAAAUGAUGGAGG	chr2:55819732-55819979(-)$1	247	61	81	22.9273
UCCUGAAAACCACCUUGGGG	chr4:1170716-1170974(-)$1	258	52	72	22.5941
AACUCCCAAAUAUAUUGUAA	chr8:126245903-126246198(+)$1	295	67	87	19.7388
CAUUUCCAAUUUUUUUAUGU	chr2:75901363-75901592(-)$1	229	143	163	22.1310
gaguuucauguuuuugcucu	chr2:210880023-210880268(+)$1	245	222	242	22.2017
cugacacagucuauuccaga	chr10:11355430-11355802(+)$1	372	182	202	22.5941
CCUCAAACUCUACAUUAGGG	chr2:122151154-122151409(-)$1	255	82	102	21.4698
UACUCCUGAUUAAUACGUAA	chr11:68354511-68354773(+)$1	262	27	47	21.2900
cucccuuuAGAAAAAACAGU	chr14:103961730-103961986(+)$1	256	158	178	20.2933
uugccucuuuuaacucuuca	chr20:45286893-45287145(-)$1	252	204	224	20.2933
UUUGAAAACAAAGGGGAAAA	chr2:144052747-144052983(+)$1	236	12	32	19.9444
aguaucuuaucauuuuacug	chr1:193208985-193209285(+)$1	300	180	200	22.2017
gguccaagcuugaaugaccu	chr16:78904143-78904377(+)$1	234	163	183	22.2017
UCCCCUCCCCACGCCGUACA	chr6:12064879-12065109(+)$1	230	84	104	22.3827
ACCAUUCAAUUUUAGGUCAC	chr14:73344377-73344730(-)$1	353	210	230	21.2634
CUCACUUUCAAAUCCCGAGU	chr14:24736435-24736692(-)$1	257	8	28	22.5941
UCCUCGUCUAUAUAUGCAAU	chr7:39731787-39732017(+)$1	230	61	81	19.3493
UUGAAGACUAAAAAAUAGAC	chr10:114399488-114399728(+)$1	240	143	163	22.7569
UAGUCCAUUCACAUUACAGA	chr1:217717235-217717465(-)$1	230	156	176	21.1801
aaaacaaaacugcacauuua	chr3:11726196-11726427(-)$1	231	74	94	22.9273
UUGCUCCAACUUUCACAAUA	chr4:103487811-103488123(+)$1	312	57	77	20.6909
ugugaaauaaaaaaaagcaa	chr9:95237530-95237795(+)$1	265	83	103	22.9273
CUUUCUUCUCACUUUAAAGA	chr3:196800029-196800299(-)$1	270	185	205	19.8037
ugaucuuuuuugcuuucauu	chrX:110946310-110946563(+)$1	253	6	26	23.0354
AACAUAUCAAUCCUGGUUCA	chr2:143930868-143931116(+)$1	248	132	152	22.3987
uagacaagacagcaaugaag	chr8:11169029-11169282(+)$1	253	180	200	21.7661
uaaaaagcaacaaacugcug	chr5:42793131-42793358(+)$1	227	80	100	19.3493
ccacacacacacacUGGUUU	chr1:6389993-6390245(-)$1	252	118	138	21.1549
gagaaaaugaaagccaucac	chr13:96333900-96334134(+)$1	234	200	220	20.8279
AAGAGAAAGAUAAAUAACUA	chr9:5710003-5710249(+)$1	246	72	92	19.4023
auccagagacacaaauagau	chr1:113989121-113989367(+)$1	246	146	166	20.9285
UUGGACCUCAGAAAACUACA	chr11:63520253-63520487(+)$1	234	89	109	21.7769
ggccccucugacuUGCCUCG	chr11:108604317-108604559(+)$1	242	22	42	21.3701
cauuauuucacauaugugua	chr4:141918181-141918416(-)$1	235	91	111	22.2876
UGUUCAUUUUGCUAAAAUAU	chr2:208444856-208445149(+)$1	293	237	257	21.6565
UAAAAAUACAAAUACAUUAU	chr8:17875792-17876082(+)$1	290	103	123	22.5941
AAAAUUUAUAGUUCUUUAUG	chr4:83975045-83975272(+)$1	227	14	34	21.2475
uuugucuccuccacuaaaau	chr1:108192458-108192776(-)$1	318	262	282	21.4698
CUGCCACAUCCUCCUGCCCU	chr19:3445057-3445392(+)$1	335	232	252	20.6343
AGUAAUAUAAUGACCUGCUA	chr1:211922839-211923074(-)$1	235	8	28	21.1907
GAGUCCUGCAUGCUAGCUCU	chr6:112134635-112134880(-)$1	245	77	97	22.2017
UCAGCACACCCAAAACUGAA	chr14:56761257-56761651(+)$1	394	253	273	22.2017
CAAAUUGUCUCUUCCUUUGA	chr2:15442567-15442799(-)$1	232	24	44	22.2017
GCUGUCAGAAAGCUAGGCCA	chr9:95271326-95271550(+)$1	224	116	136	22.7569
agaucguauguaccuuucuc	chr8:101289009-101289241(-)$1	232	11	31	22.5941
uggggauuauggcagcuaca	chr4:68348547-68348801(-)$1	254	159	179	23.0354
UUUAUAACUUUCUUUUAAAA	chr4:20446289-20446521(+)$1	232	13	33	20.5619
ugcugucauauuuccuguau	chr1:198640663-198640935(+)$1	272	183	203	22.1310
uuuucaucagcuaaucaaug	chr7:131065740-131066010(+)$1	270	9	29	21.3726
UGAACACCCAACACAUCACC	chr2:238999522-238999772(+)$1	250	98	118	21.6955
cuuguccaucacccucaggc	chr14:100826677-100826925(-)$1	248	205	225	22.2017
auuucacucuccuaaaaauc	chr14:88688662-88688886(-)$1	224	99	119	21.8638
AGCCCCCACAUUCACUGCUG	chr5:158708275-158708536(+)$1	261	186	206	22.5941
ggaaacaacccaaaugucca	chr15:34483526-34483789(-)$1	263	225	245	22.9273
acugauccuaaauaaaaggu	chr3:89306749-89306985(+)$1	236	140	160	21.2677
UUCUUUAUAAUGGUUGAAUU	chr2:71649652-71649916(+)$1	264	202	222	22.1563
UUCAAAAAACAACCUGGGAA	chr8:61435450-61435675(+)$1	225	107	127	20.2888
cauauacacauuuuaaugcu	chr1:29500747-29500982(-)$1	235	158	178	22.1563
GAUACAAUACUCACUUAAUC	chr6:128034275-128034533(-)$1	258	99	119	20.9285
ccaagucauguauccauggu	chr14:73152277-73152516(-)$1	239	182	202	22.9273
GAAAACAACCAUcuccuucc	chr6:74177293-74177530(+)$1	237	99	119	22.9273
UACCUAGACUACUUAAAGUG	chr12:32503431-32503688(+)$1	257	30	50	20.2933
ggggaagaaaagugggccca	chr17:18206945-18207218(-)$1	273	55	75	21.2746
gaguauaucauaucucucug	chr5:112135445-112135695(+)$1	250	223	243	23.0354
UGUGACCAUAUGUUCCAUAC	chr2:182380453-182380704(+)$1	251	96	116	21.8638

#DB
(((............)))))	chr17:35800569-35800792(+)$1	1	43	63	22.3363
(................)))	chr5:53270623-53270871(-)$1	1	117	137	19.8910
(((................)	chr7:111153664-111153898(-)$1	1	35	55	19.5310
((((...........)))))	chr1:117981044-117981343(+)$1	1	107	127	22.2017
(((............)))).	chr18:46915560-46915829(-)$1	1	82	102	22.7305
(((.............))))	chr14:89703595-89703844(-)$1	1	59	79	22.1357
(((................)	chrX:76910520-76910760(-)$1	1	159	179	19.5310
(((.............))).	chrX:123225299-123225526(+)$1	1	29	49	22.1310
((((...........)))))	chr13:48535675-48536002(-)$1	1	165	185	21.3006
(((............)))))	chr8:126217663-126217942(+)$1	1	23	43	23.0354
(((.............))))	chr2:55819732-55819979(-)$1	1	61	81	22.9273
(((.............))))	chr4:1170716-1170974(-)$1	1	52	72	22.5941
...............)))))	chr8:126245903-126246198(+)$1	1	67	87	19.7388
(((.............))).	chr2:75901363-75901592(-)$1	1	143	163	22.1310
((((...........)))))	chr2:210880023-210880268(+)$1	1	222	242	22.2017
(((.............))))	chr10:11355430-11355802(+)$1	1	182	202	22.5941
(((.............))))	chr2:122151154-122151409(-)$1	1	82	102	21.4698
.((.............))))	chr11:68354511-68354773(+)$1	1	27	47	21.2900
...............)))))	chr14:103961730-103961986(+)$1	1	158	178	20.2933
...............)))))	chr20:45286893-45287145(-)$1	1	204	224	20.2933
(((..............)))	chr2:144052747-144052983(+)$1	1	12	32	19.9444
((((...........)))))	chr1:193208985-193209285(+)$1	1	180	200	22.2017
((((...........)))))	chr16:78904143-78904377(+)$1	1	163	183	22.2017
(.(............).)))	chr6:12064879-12065109(+)$1	1	84	104	22.3827
(((...........))))))	chr14:73344377-73344730(-)$1	1	210	230	21.2634
(((.............))))	chr14:24736435-24736692(-)$1	1	8	28	22.5941
...............)))))	chr7:39731787-39732017(+)$1	1	61	81	19.3493
(((............)))).	chr10:114399488-114399728(+)$1	1	143	163	22.7569
(.((...........)))))	chr1:217717235-217717465(-)$1	1	156	176	21.1801
(((.............))))	chr3:11726196-11726427(-)$1	1	74	94	22.9273
(((............)))))	chr4:103487811-103488123(+)$1	1	57	77	20.6909
(((.............))))	chr9:95237530-95237795(+)$1	1	83	103	22.9273
...............)))))	chr3:196800029-196800299(-)$1	1	185	205	19.8037
(((............)))))	chrX:110946310-110946563(+)$1	1	6	26	23.0354
(((............)))..	chr2:143930868-143931116(+)$1	1	132	152	22.3987
((.............)))))	chr8:11169029-11169282(+)$1	1	180	200	21.7661
...............)))))	chr5:42793131-42793358(+)$1	1	80	100	19.3493
(((...........))))..	chr1:6389993-6390245(-)$1	1	118	138	21.1549
((..............))).	chr13:96333900-96334134(+)$1	1	200	220	20.8279
.((..............)).	chr9:5710003-5710249(+)$1	1	72	92	19.4023
(((..............)))	chr1:113989121-113989367(+)$1	1	146	166	20.9285
.(((...........))).)	chr11:63520253-63520487(+)$1	1	89	109	21.7769
(((...........)))).)	chr11:108604317-108604559(+)$1	1	22	42	21.3701
(((............)))))	chr4:141918181-141918416(-)$1	1	91	111	22.2876
((((...........)))))	chr2:208444856-208445149(+)$1	1	237	257	21.6565
(((.............))))	chr8:17875792-17876082(+)$1	1	103	123	22.5941
(((...........)))).)	chr4:83975045-83975272(+)$1	1	14	34	21.2475
(((.............))))	chr1:108192458-108192776(-)$1	1	262	282	21.4698
(.((...........))...	chr19:3445057-3445392(+)$1	1	232	252	20.6343
((((...........)))))	chr1:211922839-211923074(-)$1	1	8	28	21.1907
((((...........)))))	chr6:112134635-112134880(-)$1	1	77	97	22.2017
((((...........)))))	chr14:56761257-56761651(+)$1	1	253	273	22.2017
((((...........)))))	chr2:15442567-15442799(-)$1	1	24	44	22.2017
(((............)))).	chr9:95271326-95271550(+)$1	1	116	136	22.7569
(((.............))))	chr8:101289009-101289241(-)$1	1	11	31	22.5941
(((............)))))	chr4:68348547-68348801(-)$1	1	159	179	23.0354
((((...........)))))	chr4:20446289-20446521(+)$1	1	13	33	20.5619
(((.............))).	chr1:198640663-198640935(+)$1	1	183	203	22.1310
((..............))))	chr7:131065740-131066010(+)$1	1	9	29	21.3726
(((............)))).	chr2:238999522-238999772(+)$1	1	98	118	21.6955
((((...........)))))	chr14:100826677-100826925(-)$1	1	205	225	22.2017
((((...........)))).	chr14:88688662-88688886(-)$1	1	99	119	21.8638
(((.............))))	chr5:158708275-158708536(+)$1	1	186	206	22.5941
(((.............))))	chr15:34483526-34483789(-)$1	1	225	245	22.9273
.((.............))))	chr3:89306749-89306985(+)$1	1	140	160	21.2677
(((............)))))	chr2:71649652-71649916(+)$1	1	202	222	22.1563
(..............))).)	chr8:61435450-61435675(+)$1	1	107	127	20.2888
(((............)))))	chr1:29500747-29500982(-)$1	1	158	178	22.1563
(((..............)))	chr6:128034275-128034533(-)$1	1	99	119	20.9285
(((.............))))	chr14:73152277-73152516(-)$1	1	182	202	22.9273
(((.............))))	chr6:74177293-74177530(+)$1	1	99	119	22.9273
...............)))))	chr12:32503431-32503688(+)$1	1	30	50	20.2933
(((.............))).	chr17:18206945-18207218(-)$1	1	55	75	21.2746
(((............)))))	chr5:112135445-112135695(+)$1	1	223	243	23.0354
((((...........)))).	chr2:182380453-182380704(+)$1	1	96	116	21.8638

#PSSM
d : 0.29	e : 0.26	c : 0.12	y : 0.09	g : 0.06	f : 0.05	[ : 0.04	i : 0.02	h : 0.01	! : 0.01	= : 0.01	
d : 0.27	e : 0.25	y : 0.10	c : 0.10	g : 0.05	f : 0.05	b : 0.04	[ : 0.04	i : 0.02	h : 0.01	= : 0.01	w : 0.01	
d : 0.27	e : 0.24	y : 0.10	c : 0.08	b : 0.06	g : 0.05	f : 0.05	w : 0.04	i : 0.02	a : 0.01	h : 0.01	v : 0.01	= : 0.01	
v : 0.29	u : 0.20	y : 0.13	e : 0.10	w : 0.09	t : 0.05	b : 0.02	d : 0.02	i : 0.01	c : 0.01	= : 0.01	g : 0.01	f : 0.01	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.27	u : 0.20	y : 0.13	w : 0.09	
v : 0.29	t : 0.22	u : 0.20	y : 0.13	w : 0.09	d : 0.05	
v : 0.27	e : 0.20	d : 0.14	w : 0.08	c : 0.05	y : 0.04	i : 0.04	b : 0.04	f : 0.04	g : 0.04	a : 0.01	h : 0.01	= : 0.01	
e : 0.29	d : 0.22	c : 0.12	b : 0.06	f : 0.06	g : 0.05	w : 0.05	y : 0.04	i : 0.04	] : 0.01	h : 0.01	= : 0.01	
e : 0.31	d : 0.25	c : 0.13	f : 0.08	g : 0.06	i : 0.04	b : 0.04	y : 0.02	h : 0.01	= : 0.01	3 : 0.01	
e : 0.31	d : 0.22	c : 0.08	f : 0.08	g : 0.06	i : 0.05	] : 0.05	y : 0.02	3 : 0.02	= : 0.02	h : 0.01	4 : 0.01	b : 0.01	
e : 0.35	d : 0.16	g : 0.08	f : 0.08	] : 0.06	2 : 0.05	i : 0.05	3 : 0.04	= : 0.02	: : 0.02	b : 0.01	c : 0.01	h : 0.01	4 : 0.01	

#score	1623.1338416462938
#seq	75
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_CDS_m3_run1.txt

#BEAR
[bb$$$$$ddddmmmmdddd333bb]e	chr12:57038453-57038832(-)$1	379	275	302	12.9945
c"""bb!!ddddmmmmdddd]bbccc]	chr22:47103657-47103916(-)$1	259	225	252	12.8696
eeeee"""ddddmmmmddddeeeee::	chr22:39711274-39711661(-)$1	387	215	242	11.0792
:===========mmmm===========	chr22:39477450-39477689(+)$1	239	126	153	9.2966
b[dddd"""cccmmmmccc]ddddbbc	chr16:2816022-2816315(+)$1	293	2	29	9.9303
[dddd"""ddddmmmmdddd22dddd]	chr11:62295927-62296321(-)$1	394	121	148	14.6284
fffff!!eeeeemmmmeeeee22ffff	chr12:56120381-56120661(-)$1	280	147	174	9.4174
ggggggg!!cccmmmmccc]ggggggg	chr7:75052268-75052577(-)$1	309	32	59	10.7152
gggggg"""cccmmmmccc4444gggg	chr11:61102017-61102306(+)$1	289	83	110	12.3057
iiiiii"""cccmmmmccc]iiiiiii	chr15:48633388-48633647(+)$1	259	5	32	11.4226
gggggg!!ddddmmmmdddd22ggggg	chr6:27107141-27107472(+)$1	331	205	232	14.5588
ccc[ccc!!ddddllldddd22ccc]c	chr16:30080046-30080407(+)$1	361	74	101	12.2397
ceeeee!!ddddmmmmdddd4444eee	chr3:15093914-15094231(-)$1	317	8	35	13.7751
ffff####ddddoooooodddd]ffff	chr16:28735623-28735887(+)$1	264	170	197	9.9637
d[bb"""ddddnnnnndddd333bb]d	chr17:7403987-7404270(+)$1	283	116	143	10.5984
$$eeeee[ddddmmmmdddd22eeeee	chr1:23667266-23667568(-)$1	302	199	226	12.8190
####ddddddddmmmmdddd]dddd22	chr7:2414932-2415267(+)$1	335	117	144	11.4433
ddd####ddddnnnnndddd22dddd2	chr2:86831910-86832167(-)$1	257	101	128	10.8008
iiiiiiiddddnnnnndddd22iiiii	chr8:120620056-120620319(-)$1	263	6	33	10.6351
ddccc"""ddddnnnnndddd]ccc]d	chr8:97243906-97244270(-)$1	364	285	312	10.6644
ddd!!cccddddllldddd4444ccc2	chr7:44839210-44839527(+)$1	317	98	125	11.0837
gggggg"""cccmmmmccc333ggggg	chr20:2442191-2442599(-)$1	408	286	313	12.6673
!!bbccc[ddddmmmmdddd]ccc]bb	chr1:31230420-31230695(-)$1	275	173	200	12.0429
ffff[ccc[ddddllldddd]ccc]ff	chr7:23353074-23353348(-)$1	274	168	195	10.1168
::dddd!!ddddmmmmdddd4444ddd	chr2:54849451-54849723(+)$1	272	188	215	11.9176
ccc!!bb[ddddmmmmdddd]bb22cc	chr7:99669013-99669293(-)$1	280	54	81	12.1307
ccc[ccc[ddddnnnnndddd]ccc]c	chr7:30655430-30655755(+)$1	325	44	71	9.9548
ccdddd[addddmmmmdddd]a]dddd	chr8:61504358-61504604(+)$1	246	131	158	12.8842
ddd[a[a[ddddmmmmddddaa]dddd	chr19:13054475-13054793(+)$1	318	245	272	12.9906
$$$dddd[ddddmmmmdddddddd333	chr3:128889111-128889456(-)$1	345	139	166	11.2096
fff####ccc[ammmmaccc22fffff	chr6:116579896-116580188(-)$1	292	214	241	10.9197
===[bb!!ddddllldddd]bb]====	chr12:57036137-57036465(-)$1	328	21	48	10.6683
fffff!!a[cccmmmmccc]a]fffff	chr22:43567737-43568001(-)$1	264	91	118	10.3841
ddccc"""ddddmmmmdddd22cccJJ	chr4:77102015-77102324(-)$1	309	29	56	11.9710
eeeee"""ddddllldddd333eeeee	chr6:101110212-101110467(-)$1	255	139	166	12.5208
ffffff!!ddddmmmmdddd22fffff	chr3:179519452-179519725(-)$1	273	48	75	13.5007
ee[ccca[ddddllldddd333a]ccc	chr7:99489873-99490130(-)$1	257	106	133	12.0829
cc"""bb!!cccmmmmccc22bb22cc	chr17:26964923-26965200(-)$1	277	93	120	10.1750
ffddddddddoooooodddd333dddd	chr17:73774814-73775168(-)$1	354	10	37	10.3538
b[gggggggcccmmmmccc]ggggggg	chr19:10368827-10369077(+)$1	250	50	77	9.7865
:dddd"""ddddmmmmdddd]dddd::	chr17:41151852-41152228(+)$1	376	228	255	10.8656
ggg!!a!!ddddmmmmdddd22a22gg	chr17:47007755-47008037(-)$1	282	52	79	14.5295
eeeee"""ddddmmmmdddd333eeee	chr16:30078446-30078790(+)$1	344	61	88	14.7568
d[dddd!!ddddmmmmdddd22ddddd	chr18:47017064-47017402(-)$1	338	24	51	14.1092
eeeeeaddddoooooodddd22a]eee	chr12:62775223-62775483(+)$1	260	67	94	10.2895
ggggg!!eeeeemmmmeeeee333ggg	chr13:27830545-27830805(+)$1	260	91	118	10.6491
!!dddd"""cccmmmmccc22dddd22	chr7:11062405-11062700(+)$1	295	236	263	11.1448
=============lll===========	chr11:47498747-47499000(-)$1	253	52	79	8.9115
"""eeeeeddddmmmmdddd]eeeee5	chr2:54876966-54877230(+)$1	264	17	44	10.8447
dddd[bb!!cccmmmmccc22bb]ddd	chr11:119229640-119229936(-)$1	296	97	124	10.3191
f[ccc"""ddddmmmmdddd22cccff	chr17:57746037-57746400(+)$1	363	118	145	14.8879
(ccc[a!!ddddmmmmdddd22a]ccc	chr1:24022244-24022497(+)$1	253	129	156	14.1495
fffff[a!!a[ammmma]a22afffff	chr16:56481603-56481890(-)$1	287	59	86	9.8890
ffeeeee!!ddddllldddd22eeeee	chr7:139060712-139061007(+)$1	295	104	131	11.2679
dddd[bb[ddddmmmmddddbb]dddd	chr17:79477852-79478132(-)$1	280	220	247	11.5571
dddd$$$$$cccmmmmccc333ddddf	chr5:179147343-179147637(+)$1	294	45	72	11.2994
dd::ddddddddmmmmdddd4444ddd	chr1:19504032-19504302(-)$1	270	175	202	10.4381

#otherMatches

#Seq PSSM
GCUCUUAUUGCAUCUAUGCACAAAGGA	chr12:57038453-57038832(-)$1	379	275	302	12.9945
GAAUUGUUCUGCACAAGUAGCCACCUC	chr22:47103657-47103916(-)$1	259	225	252	12.8696
CCUGUGAACCAAGUGUUUGGGCAGGAU	chr22:39711274-39711661(-)$1	387	215	242	11.0792
GGGGAGAUUCUCAGGUGAGGGUCUCCC	chr22:39477450-39477689(+)$1	239	126	153	9.2966
GACCUCCUCUCGACGCCGAAGAGGCCG	chr16:2816022-2816315(+)$1	293	2	29	9.9303
GAGCUGGAGUGUCCUGAUGCAAAGUUG	chr11:62295927-62296321(-)$1	394	121	148	14.6284
UGCUUCGAUCCUGGACAGGAUGCAGGC	chr12:56120381-56120661(-)$1	280	147	174	9.4174
UGAAUACCAUCAUCUUUGAAGUGUUUA	chr7:75052268-75052577(-)$1	309	32	59	10.7152
CUGCCUCCACUGUACUCAGACCCAGGU	chr11:61102017-61102306(+)$1	289	83	110	12.3057
UCAGAGCUACAUGAUAAUGAUUUUGAG	chr15:48633388-48633647(+)$1	259	5	32	11.4226
UGGUCUACGCGCUCAAGCGCCAGGGCC	chr6:27107141-27107472(+)$1	331	205	232	14.5588
CCCUUCCUCUUCUCUUAGGGUUGGAUG	chr16:30080046-30080407(+)$1	361	74	101	12.2397
UGGGGUUGUCUCGGCUGAGAAACUGCC	chr3:15093914-15094231(-)$1	317	8	35	13.7751
GUGAAGAGGCUCAUCUCAGGGCAUCGC	chr16:28735623-28735887(+)$1	264	170	197	9.9637
CAGUACCCAUCCCGAUGAUGAAGACAG	chr17:7403987-7404270(+)$1	283	116	143	10.5984
AGACUUGAUGAAAUAUUUCAGACAGGU	chr1:23667266-23667568(-)$1	302	199	226	12.8190
ACACUUCGGACUGCACGGUCAUGAACA	chr7:2414932-2415267(+)$1	335	117	144	11.4433
CAACCCGAGGUAAAUGAUCUGUUUGUU	chr2:86831910-86832167(-)$1	257	101	128	10.8008
GAGUAUAAGAUAUCUGAUCUAAUGUAU	chr8:120620056-120620319(-)$1	263	6	33	10.6351
UACCUGACAGUGUUGCUCAUUAAGGAU	chr8:97243906-97244270(-)$1	364	285	312	10.6644
CUUCACACGCCAUAAUGGCACUGGUGG	chr7:44839210-44839527(+)$1	317	98	125	11.0837
UAUAAUAAACUCUUAAGAGAACAUUAU	chr20:2442191-2442599(-)$1	408	286	313	12.6673
UGGCCAUCUACCAUGUGGUGAGUGUGC	chr1:31230420-31230695(-)$1	275	173	200	12.0429
CUUUGCUGCUGGCAGAGUUAUUGGAAA	chr7:23353074-23353348(-)$1	274	168	195	10.1168
UAGUGUGAUCAUUAAUAUGGAAAGACA	chr2:54849451-54849723(+)$1	272	188	215	11.9176
GGGAAGACCUUCAGCUGGAGCUCCACC	chr7:99669013-99669293(-)$1	280	54	81	12.1307
AAAUAUGCAGGUUUAUCGCUUACGUUU	chr7:30655430-30655755(+)$1	325	44	71	9.9548
AUGGAAACGUCUGCUAAGACUGCUUCC	chr8:61504358-61504604(+)$1	246	131	158	12.8842
GCUGUAGAGAGGCCUGCCUCCAGGGCU	chr19:13054475-13054793(+)$1	318	245	272	12.9906
CACAAUUGAGGCUACAGCCUAAUUAUU	chr3:128889111-128889456(-)$1	345	139	166	11.2096
UGCUCACAGGCGAGAACCCUCUGCAGG	chr6:116579896-116580188(-)$1	292	214	241	10.9197
GCUUGAGAGGACCUGGUUCAUCUGGCC	chr12:57036137-57036465(-)$1	328	21	48	10.6683
CCAGGGCCUUUGCACUCAACGACCUGG	chr22:43567737-43568001(-)$1	264	91	118	10.3841
GUGGUGUCUAUUUUCAAAUAAAACCCU	chr4:77102015-77102324(-)$1	309	29	56	11.9710
AGAAAUUUAGUUGAAAACUUGUUUUCU	chr6:101110212-101110467(-)$1	255	139	166	12.5208
UCCAGGCGGCUAAUCUUGGUGACCUGG	chr3:179519452-179519725(-)$1	273	48	75	13.5007
GUGCUGCUGGCUAUUGGCCCUUGAUAG	chr7:99489873-99490130(-)$1	257	106	133	12.0829
CUAUAACCAGCCUCUGGGCCUGUCCAG	chr17:26964923-26965200(-)$1	277	93	120	10.1750
CCGGCGGGGUGAAGAAGCCUCAUCGCU	chr17:73774814-73775168(-)$1	354	10	37	10.3538
ACAUGCCUCUGUCCCCGCAGGAGGUGU	chr19:10368827-10369077(+)$1	250	50	77	9.7865
UGUGAAAGUGUAUAACUACAAUCACCU	chr17:41151852-41152228(+)$1	376	228	255	10.8656
UUUCCCUCCAGGAACACCUGCUGAAGG	chr17:47007755-47008037(-)$1	282	52	79	14.5295
GGGAAACCCUAGCUAACUAGUCCUUCC	chr16:30078446-30078790(+)$1	344	61	88	14.7568
GCUGAAAAUUGAAAAUUUAACGUUUAC	chr18:47017064-47017402(-)$1	338	24	51	14.1092
ACUUACUGAGUAUUUCCUCAAUGAUAA	chr12:62775223-62775483(+)$1	260	67	94	10.2895
CUAUUCCCUAUGAAUUCAUGGCAUAAU	chr13:27830545-27830805(+)$1	260	91	118	10.6491
AAAGGUUUUACUUGUUAGUUUACCUGG	chr7:11062405-11062700(+)$1	295	236	263	11.1448
GCUGCACUAGCUGCUGCAGCUAGUGCA	chr11:47498747-47499000(-)$1	253	52	79	8.9115
ACGAUGCCAAGGAGAUCUUUGGGCGUA	chr2:54876966-54877230(+)$1	264	17	44	10.8447
AGGAUGCUCAGGAGUUCCUUCGCUUUC	chr11:119229640-119229936(-)$1	296	97	124	10.3191
GAUCCAUUGUUAACUUUAGCCAGGACC	chr17:57746037-57746400(+)$1	363	118	145	14.8879
GGCCAUGCGCUGGUUCCAGCAGAAGGU	chr1:24022244-24022497(+)$1	253	129	156	14.1495
AGAUUUCAGCGCAUGAGGGAAGAAUUU	chr16:56481603-56481890(-)$1	287	59	86	9.8890
CUCGUCAACGAAUCAAAUUCAGUGAUG	chr7:139060712-139061007(+)$1	295	104	131	11.2679
AGCUGACUGGGGGGCGCUCUGUGAGCU	chr17:79477852-79478132(-)$1	280	220	247	11.5571
GUUUGUACCUCCGUAGGGAUGAAGACA	chr5:179147343-179147637(+)$1	294	45	72	11.2994
CCGAGACAGGCCGGCGGGCCAUAUUGU	chr1:19504032-19504302(-)$1	270	175	202	10.4381

#DB
.((.....((((....))))...)).)	chr12:57038453-57038832(-)$1	1	275	302	12.9945
(...((..((((....)))).))))).	chr22:47103657-47103916(-)$1	1	225	252	12.8696
(((((...((((....)))))))))..	chr22:39711274-39711661(-)$1	1	215	242	11.0792
.(((((((((((....)))))))))))	chr22:39477450-39477689(+)$1	1	126	153	9.2966
(.((((...(((....))).))))))(	chr16:2816022-2816315(+)$1	1	2	29	9.9303
.((((...((((....))))..)))).	chr11:62295927-62296321(-)$1	1	121	148	14.6284
(((((..(((((....)))))..))))	chr12:56120381-56120661(-)$1	1	147	174	9.4174
(((((((..(((....))).)))))))	chr7:75052268-75052577(-)$1	1	32	59	10.7152
((((((...(((....)))....))))	chr11:61102017-61102306(+)$1	1	83	110	12.3057
((((((...(((....))).)))))))	chr15:48633388-48633647(+)$1	1	5	32	11.4226
((((((..((((....))))..)))))	chr6:27107141-27107472(+)$1	1	205	232	14.5588
(((.(((..((((...))))..))).)	chr16:30080046-30080407(+)$1	1	74	101	12.2397
((((((..((((....))))....)))	chr3:15093914-15094231(-)$1	1	8	35	13.7751
((((....((((......)))).))))	chr16:28735623-28735887(+)$1	1	170	197	9.9637
(.((...((((.....))))...)).)	chr17:7403987-7404270(+)$1	1	116	143	10.5984
..(((((.((((....))))..)))))	chr1:23667266-23667568(-)$1	1	199	226	12.8190
....((((((((....)))).))))..	chr7:2414932-2415267(+)$1	1	117	144	11.4433
(((....((((.....))))..)))).	chr2:86831910-86832167(-)$1	1	101	128	10.8008
(((((((((((.....))))..)))))	chr8:120620056-120620319(-)$1	1	6	33	10.6351
(((((...((((.....)))).))).)	chr8:97243906-97244270(-)$1	1	285	312	10.6644
(((..(((((((...))))....))).	chr7:44839210-44839527(+)$1	1	98	125	11.0837
((((((...(((....)))...)))))	chr20:2442191-2442599(-)$1	1	286	313	12.6673
..(((((.((((....)))).))).))	chr1:31230420-31230695(-)$1	1	173	200	12.0429
((((.(((.((((...)))).))).))	chr7:23353074-23353348(-)$1	1	168	195	10.1168
..((((..((((....))))....)))	chr2:54849451-54849723(+)$1	1	188	215	11.9176
(((..((.((((....)))).))..))	chr7:99669013-99669293(-)$1	1	54	81	12.1307
(((.(((.((((.....)))).))).)	chr7:30655430-30655755(+)$1	1	44	71	9.9548
((((((.(((((....)))).).))))	chr8:61504358-61504604(+)$1	1	131	158	12.8842
(((.(.(.((((....)))))).))))	chr19:13054475-13054793(+)$1	1	245	272	12.9906
...((((.((((....))))))))...	chr3:128889111-128889456(-)$1	1	139	166	11.2096
(((....(((.(....))))..)))))	chr6:116579896-116580188(-)$1	1	214	241	10.9197
(((.((..((((...)))).)).))))	chr12:57036137-57036465(-)$1	1	21	48	10.6683
(((((..(.(((....))).).)))))	chr22:43567737-43568001(-)$1	1	91	118	10.3841
))(((...((((....))))..)))))	chr4:77102015-77102324(-)$1	1	29	56	11.9710
(((((...((((...))))...)))))	chr6:101110212-101110467(-)$1	1	139	166	12.5208
((((((..((((....))))..)))))	chr3:179519452-179519725(-)$1	1	48	75	13.5007
((.((((.((((...))))...).)))	chr7:99489873-99490130(-)$1	1	106	133	12.0829
((...((..(((....)))..))..))	chr17:26964923-26965200(-)$1	1	93	120	10.1750
((((((((((......))))...))))	chr17:73774814-73775168(-)$1	1	10	37	10.3538
(.((((((((((....))).)))))))	chr19:10368827-10369077(+)$1	1	50	77	9.7865
.((((...((((....)))).))))..	chr17:41151852-41152228(+)$1	1	228	255	10.8656
(((..(..((((....))))..)..))	chr17:47007755-47008037(-)$1	1	52	79	14.5295
(((((...((((....))))...))))	chr16:30078446-30078790(+)$1	1	61	88	14.7568
(.((((..((((....))))..)))))	chr18:47017064-47017402(-)$1	1	24	51	14.1092
((((((((((......))))..).)))	chr12:62775223-62775483(+)$1	1	67	94	10.2895
(((((..(((((....)))))...)))	chr13:27830545-27830805(+)$1	1	91	118	10.6491
..((((...(((....)))..))))..	chr7:11062405-11062700(+)$1	1	236	263	11.1448
(((((((((((((...)))))))))))	chr11:47498747-47499000(-)$1	1	52	79	8.9115
...(((((((((....)))).))))).	chr2:54876966-54877230(+)$1	1	17	44	10.8447
((((.((..(((....)))..)).)))	chr11:119229640-119229936(-)$1	1	97	124	10.3191
(.(((...((((....))))..)))))	chr17:57746037-57746400(+)$1	1	118	145	14.8879
.(((.(..((((....))))..).)))	chr1:24022244-24022497(+)$1	1	129	156	14.1495
(((((.(..(.(....).)..))))))	chr16:56481603-56481890(-)$1	1	59	86	9.8890
))(((((..((((...))))..)))))	chr7:139060712-139061007(+)$1	1	104	131	11.2679
((((.((.((((....)))))).))))	chr17:79477852-79478132(-)$1	1	220	247	11.5571
((((.....(((....)))...)))))	chr5:179147343-179147637(+)$1	1	45	72	11.2994
))..((((((((....))))....)))	chr1:19504032-19504302(-)$1	1	175	202	10.4381

#PSSM
d : 0.19	f : 0.17	c : 0.12	g : 0.10	e : 0.08	: : 0.05	[ : 0.03	b : 0.03	i : 0.03	$ : 0.03	! : 0.03	= : 0.03	# : 0.01	" : 0.01	( : 0.01	
d : 0.19	f : 0.15	e : 0.10	g : 0.10	c : 0.10	[ : 0.08	= : 0.05	" : 0.03	i : 0.03	$ : 0.03	! : 0.03	b : 0.01	# : 0.01	: : 0.01	
d : 0.24	e : 0.12	f : 0.12	g : 0.12	c : 0.12	b : 0.05	" : 0.05	= : 0.05	i : 0.03	# : 0.01	$ : 0.01	[ : 0.01	: : 0.01	
d : 0.21	e : 0.14	f : 0.10	g : 0.10	c : 0.08	[ : 0.07	# : 0.05	! : 0.05	" : 0.03	= : 0.03	i : 0.03	b : 0.03	$ : 0.01	: : 0.01	
d : 0.19	e : 0.14	c : 0.12	g : 0.10	f : 0.07	[ : 0.07	# : 0.05	! : 0.05	$ : 0.03	b : 0.03	= : 0.03	i : 0.03	" : 0.03	a : 0.01	
" : 0.15	d : 0.15	b : 0.10	c : 0.10	g : 0.08	e : 0.07	! : 0.05	# : 0.05	a : 0.05	$ : 0.03	= : 0.03	i : 0.03	[ : 0.03	f : 0.01	
" : 0.24	! : 0.21	c : 0.08	d : 0.08	b : 0.07	# : 0.05	e : 0.05	a : 0.05	$ : 0.03	= : 0.03	g : 0.03	i : 0.01	[ : 0.01	
! : 0.26	" : 0.22	[ : 0.14	d : 0.12	e : 0.05	c : 0.05	$ : 0.03	= : 0.03	a : 0.03	# : 0.01	g : 0.01	
d : 0.64	! : 0.10	" : 0.08	= : 0.03	e : 0.03	[ : 0.03	c : 0.01	g : 0.01	$ : 0.01	
d : 0.70	c : 0.21	= : 0.03	e : 0.03	a : 0.01	
d : 0.66	c : 0.19	= : 0.03	e : 0.03	[ : 0.03	o : 0.03	
d : 0.61	c : 0.19	n : 0.05	= : 0.03	e : 0.03	a : 0.03	o : 0.03	
m : 0.71	n : 0.08	l : 0.07	d : 0.05	o : 0.05	= : 0.01	
m : 0.71	l : 0.14	n : 0.08	o : 0.05	
m : 0.71	l : 0.14	n : 0.08	o : 0.05	
m : 0.71	n : 0.08	l : 0.07	d : 0.07	o : 0.05	
d : 0.64	c : 0.19	= : 0.03	e : 0.03	n : 0.03	a : 0.03	o : 0.01	
d : 0.68	c : 0.21	= : 0.03	e : 0.03	o : 0.01	] : 0.01	
d : 0.70	c : 0.21	= : 0.03	e : 0.03	a : 0.01	
d : 0.63	] : 0.10	3 : 0.07	2 : 0.07	= : 0.03	e : 0.03	4 : 0.03	c : 0.01	
2 : 0.33	3 : 0.14	] : 0.14	d : 0.08	4 : 0.08	e : 0.05	= : 0.03	g : 0.03	a : 0.03	b : 0.03	i : 0.01	
2 : 0.28	3 : 0.15	b : 0.10	d : 0.10	4 : 0.08	] : 0.05	a : 0.05	e : 0.03	= : 0.03	g : 0.03	c : 0.03	i : 0.01	
d : 0.15	c : 0.12	3 : 0.08	e : 0.08	4 : 0.08	] : 0.08	b : 0.07	g : 0.07	f : 0.07	a : 0.07	= : 0.03	i : 0.03	2 : 0.01	
d : 0.22	c : 0.15	e : 0.10	f : 0.10	g : 0.08	] : 0.07	= : 0.05	4 : 0.05	2 : 0.05	b : 0.03	i : 0.03	3 : 0.01	
d : 0.24	c : 0.15	e : 0.14	f : 0.10	g : 0.10	b : 0.05	= : 0.05	2 : 0.05	i : 0.03	] : 0.03	3 : 0.01	
d : 0.19	f : 0.14	g : 0.12	e : 0.12	c : 0.10	] : 0.08	= : 0.05	: : 0.03	b : 0.03	i : 0.03	2 : 0.03	3 : 0.01	J : 0.01	
d : 0.17	f : 0.15	e : 0.12	c : 0.12	g : 0.12	2 : 0.07	= : 0.05	] : 0.03	: : 0.03	i : 0.03	b : 0.01	3 : 0.01	J : 0.01	5 : 0.01	

#score	661.4303416966176
#seq	57
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013e_hg19_UTR_m2_run1.txt

#BEAR
==========nnnnn==========4	chrX:106957187-106957420(-)$1	233	126	152	11.5064
fffff!!cccooooooccc22fffff	chr3:183145787-183146015(-)$1	228	199	225	12.7447
========[cccmmmmccc]======	chr4:68338026-68338248(-)$1	222	152	178	9.2957
:iiiiiiiiiooooooiiiiiiiii:	chr9:131572313-131572535(+)$1	222	49	75	11.8036
"""gggggggoooooogggggggggg	chr16:75271110-75271331(+)$1	221	112	138	12.9913
eeeeccccccooooooccc22ccc]e	chr15:26788944-26789167(-)$1	223	181	207	12.6685
b!!gggggggooooooggggggg22b	chr7:90043849-90044074(+)$1	225	65	91	12.1524
dd!!ffffffooooooffffff333d	chr1:167391787-167392003(-)$1	216	10	36	11.1942
ddddccc[bboooooobbccc]dddd	chr12:49331690-49331949(-)$1	259	17	43	11.2301
"eeeee!!bboooooobb22eeeeee	chr19:54058012-54058231(-)$1	219	138	164	12.1528
ccc[bb!!bboooooobb22bbccce	chr7:8126449-8126664(-)$1	215	74	100	11.8384
[eeeeeddddoooooodddd4444ee	chr13:36910344-36910569(-)$1	225	119	145	11.5117
##iiiiiiiiinnnnniiiiiiiii6	chr13:114748143-114748359(-)$1	216	172	198	10.1061
eee"""ddddoooooodddd4444ee	chr14:94192213-94192434(-)$1	221	11	37	11.9595
"""gggggggooooooggggggg]dd	chr6:33663775-33664003(-)$1	228	175	201	12.6564
fccc[eeeeeooooooeeeee]ccc]	chr2:158388239-158388458(-)$1	219	91	117	11.0753
gggggg[cccooooooccc]gggggg	chr17:7529616-7529834(-)$1	218	81	107	13.8359
ff####ddddoooooodddd]fffff	chr7:99047801-99048020(+)$1	219	105	131	11.6431
ffff"""cccnnnnnccc333fffff	chrX:103435696-103435925(+)$1	229	52	78	10.2555
H:dddd[cccooooooccc]ddddee	chr19:2476193-2476412(+)$1	219	110	136	9.9623
gggg!!ddddnnnnndddd22ggggg	chr21:41033967-41034184(-)$1	217	70	96	9.5882
b[dddd!!bboooooobbdddd]bb3	chr2:206482494-206482710(+)$1	216	98	124	10.9772
####ffffffooooooffffff4444	chr15:43268925-43269148(-)$1	223	101	127	11.1048
gg[bb"""bboooooobb22bb]ggg	chr22:32586416-32586653(-)$1	237	171	197	12.3279
eee[ffffffooooooffffff22ee	chr11:22759159-22759375(-)$1	216	87	113	10.7730
==========oooooo==========	chr1:11346185-11346407(+)$1	222	132	158	14.3874
cffffff[bboooooobb]ffffff:	chr8:1953776-1953994(+)$1	218	181	207	10.8378
fffff"""bboooooobb]ffffff:	chr8:26269215-26269436(+)$1	221	62	88	11.4087
!!ccc"""bboooooobb]ccc22ii	chr1:182352842-182353077(-)$1	235	49	75	12.9664
ffffff[cccnnnnnccc333fffff	chr1:160914744-160914964(-)$1	220	86	112	9.8046
fffff[ddddoooooodddd]fffff	chr2:86364609-86364826(+)$1	217	89	115	11.3620
d[iiiiiiiiinnnnniiiiiiiiid	chr17:44101803-44102020(+)$1	217	109	135	10.3619
hhhhh!!cccooooooccc]hhhhhh	chr9:73149683-73149910(-)$1	227	127	153	11.6767
ccc!!bb[bboooooobbbb333ccc	chr1:155204522-155204748(-)$1	226	144	170	11.8992
ggggggg[cccnnnnnccc]gggggg	chr1:8413939-8414174(-)$1	235	135	161	10.4934
eeeee!!cccooooooccc4444eee	chr11:88240870-88241100(-)$1	230	1	27	13.0026
ddd"""ddddoooooodddd]dddd:	chr5:64813932-64814147(-)$1	215	63	89	10.2331
eeeee!!cccooooooccc22eeeee	chr19:57333911-57334127(+)$1	216	20	46	12.7248
eeeccc[cccnnnnnccc333ccc]e	chr10:98758571-98758792(-)$1	221	100	126	10.4136
=iiiiiiiiiooooooiiiiiiiii0	chr9:34660409-34660630(+)$1	221	163	189	13.4056
h[a####cccooooooccc333a]hh	chr1:155156530-155156752(+)$1	222	119	145	13.3782
hhhhhhddddoooooodddd4444hh	chr5:110823704-110823924(+)$1	220	95	121	10.5364
[gggggggbboooooobb]ggggggg	chr1:154556467-154556688(-)$1	221	39	65	13.3221
ccc!!ccc[bboooooobb]ccc]cc	chr3:149458681-149458902(-)$1	221	93	119	10.7724
ff[ccc!!bboooooobb22ccc]ff	chr7:112756733-112756955(-)$1	222	158	184	12.7831
]eeeeeddddooooooddddgggggg	chr6:136664259-136664487(-)$1	228	51	77	11.3936
!!iiiiiiiiinnnnniiiiiiiii]	chr16:14359948-14360165(+)$1	217	131	157	10.8169
iiiii"""bbnnnnnbb333iiiiii	chr2:69472888-69473104(+)$1	216	50	76	10.8762
dddd!!ddddoooooodddd]dddd:	chr13:48650168-48650385(+)$1	217	11	37	10.0546
======[cccnnnnnccc========	chr2:11680077-11680298(+)$1	221	153	179	11.4251
c####eeeeeooooooeeeeeccc22	chr12:49160242-49160458(-)$1	216	83	109	10.7601
!!eeeee[bboooooobb]eeeee22	chr14:104164064-104164288(+)$1	224	82	108	11.6715
[iiiiiiiiinnnnniiiiiiiii]a	chr22:31678657-31678877(-)$1	220	188	214	10.7637
=========rrrrrrrrr========	chr1:92145831-92146049(-)$1	218	131	157	9.5906

#otherMatches

#Seq PSSM
UCCUCUGUUUCGUGAAGGCAGGGGAC	chrX:106957187-106957420(-)$1	233	126	152	11.5064
GUAGAAACAGUUUUGUUUGGCUUUAU	chr3:183145787-183146015(-)$1	228	199	225	12.7447
UUUUUAUAAUUUGACAAGAAUAUGAA	chr4:68338026-68338248(-)$1	222	152	178	9.2957
CCUUGACCUUGAGAUGAAGGUCAAGA	chr9:131572313-131572535(+)$1	222	49	75	11.8036
ACGCGGGUGGGCACCACCACCUGGGG	chr16:75271110-75271331(+)$1	221	112	138	12.9913
AUGAACAUGUUUUGUCACGUUUGUCU	chr15:26788944-26789167(-)$1	223	181	207	12.6685
CAACCAGAGACACAACUUUCUGGCAG	chr7:90043849-90044074(+)$1	225	65	91	12.1524
UGUCUUUGGUAUCUAAACCAAAUCCC	chr1:167391787-167392003(-)$1	216	10	36	11.1942
AAGGAGAUGCCACUCUGCUCUGCCUU	chr12:49331690-49331949(-)$1	259	17	43	11.2301
GUUCCGUCGCCCCAAAGCCUCGGGAG	chr19:54058012-54058231(-)$1	219	138	164	12.1528
GUUAGAAACAAACACCUGGAUCAAUU	chr7:8126449-8126664(-)$1	215	74	100	11.8384
AACCUGCCACCUUUAAGUGGAAAUCA	chr13:36910344-36910569(-)$1	225	119	145	11.5117
GUUUGAUUCCUGGCUGAGGGGUCAGU	chr13:114748143-114748359(-)$1	216	172	198	10.1061
CCACCCUCCUACAAGCAGGAAUCCUG	chr14:94192213-94192434(-)$1	221	11	37	11.9595
CUAGGUAGGAUUUAUCUUCUGCUAAG	chr6:33663775-33664003(-)$1	228	175	201	12.6564
UGAGUUCUGCAUGACAGUGGGUUUCU	chr2:158388239-158388458(-)$1	219	91	117	11.0753
GGAGGAUCUCUGUCUUGAGUUUCUCC	chr17:7529616-7529834(-)$1	218	81	107	13.8359
AGCAACAAGGAAUGUCCCUUCCUGCA	chr7:99047801-99048020(+)$1	219	105	131	11.6431
UUUAUAUUGUGGAUAGCAUUUUGAAG	chrX:103435696-103435925(+)$1	229	52	78	10.2555
UUCUCCCUGGGGACUGCCGUGGAGCC	chr19:2476193-2476412(+)$1	219	110	136	9.9623
GUGUUCCUCAGCAUGUGAGCUGCAUC	chr21:41033967-41034184(-)$1	217	70	96	9.5882
AUUUUAACCAAACUACUGUAGACUAC	chr2:206482494-206482710(+)$1	216	98	124	10.9772
UUCCCAUCCUUGUAUUGGGAUGACCC	chr15:43268925-43269148(-)$1	223	101	127	11.1048
UGCAAGUUCAAAUUAAUGUAUUAUAG	chr22:32586416-32586653(-)$1	237	171	197	12.3279
CAGACAGAGACACACUUCUCUGGGUU	chr11:22759159-22759375(-)$1	216	87	113	10.7730
AUUGUUUUUGUGUUCUUAAAGAUAAU	chr1:11346185-11346407(+)$1	222	132	158	14.3874
GGCCUUUCCAAAUGUCUGAAAAGGCA	chr8:1953776-1953994(+)$1	218	181	207	10.8378
UCAGAACAUCUAGCAUGACUCUGAAG	chr8:26269215-26269436(+)$1	221	62	88	11.4087
UUGCUUGUGGGACUAGCCUGGCUUGG	chr1:182352842-182353077(-)$1	235	49	75	12.9664
UUGGAGACGGAAAAACUGGAAUUCUA	chr1:160914744-160914964(-)$1	220	86	112	9.8046
GCAGCAAUGGGUCUCACCAUAGCUGC	chr2:86364609-86364826(+)$1	217	89	115	11.3620
GACUGGGGGUGCCAACCACCUCUGGC	chr17:44101803-44102020(+)$1	217	109	135	10.3619
ACCAUUUUGUAUAUGAAUAUAUGGUU	chr9:73149683-73149910(-)$1	227	127	153	11.6767
GGCCCCUAGAAAAAGAUCAGUAAGCC	chr1:155204522-155204748(-)$1	226	144	170	11.8992
GACAUAUGCCUGCCAAAGGGAUGUGU	chr1:8413939-8414174(-)$1	235	135	161	10.4934
GGGUUGUGAAAUACUCUUCCAAAAGC	chr11:88240870-88241100(-)$1	230	1	27	13.0026
UGCAGGUAGAUAAUAUUCUAGGCAUA	chr5:64813932-64814147(-)$1	215	63	89	10.2331
UGGUGAAACCUGUGCUGGUGGUACCG	chr19:57333911-57334127(+)$1	216	20	46	12.7248
AAGGGCACUGGCUGGCAGGAGGCCUC	chr10:98758571-98758792(-)$1	221	100	126	10.4136
CUGGGGCCCUGGCACUGGGGCUCUGG	chr9:34660409-34660630(+)$1	221	163	189	13.4056
UCGCCAAGCUGGACUGAGCCUUCCAG	chr1:155156530-155156752(+)$1	222	119	145	13.3782
AUGUGUCUUCAUUCAGGAAGAACUGC	chr5:110823704-110823924(+)$1	220	95	121	10.5364
AUCCUGCACUUUAGCCAGCUGCAGGG	chr1:154556467-154556688(-)$1	221	39	65	13.3221
AGUAAAGUUCCUUUCCUGGUGCUAAC	chr3:149458681-149458902(-)$1	221	93	119	10.7724
AUAAACCCAUUAUGUUAUAAGUUAAU	chr7:112756733-112756955(-)$1	222	158	184	12.7831
GGUUUUGCUCGUUUAAGAGCAAUGAG	chr6:136664259-136664487(-)$1	228	51	77	11.3936
CUUAUUGUUUUCAUGUAAAAUAGUAU	chr16:14359948-14360165(+)$1	217	131	157	10.8169
UCUGAAGGUGAAAUGCAGAGUUGGAU	chr2:69472888-69473104(+)$1	216	50	76	10.8762
UCAUUUUACAAAAAAGUGUAUGUGAA	chr13:48650168-48650385(+)$1	217	11	37	10.0546
UAAGGUACGGUUUAUUUGACUUUGCA	chr2:11680077-11680298(+)$1	221	153	179	11.4251
ACUUGUUUUCCAGACAGAAAAUCUAC	chr12:49160242-49160458(-)$1	216	83	109	10.7601
CUGCUUUCCAGCCAGAUGUAAGGCCU	chr14:104164064-104164288(+)$1	224	82	108	11.6715
UUGAGUGGCAUACACUGUUAUUCAUG	chr22:31678657-31678877(-)$1	220	188	214	10.7637
GAUAUAUAUCAGUUAUUAAUAUGUGU	chr1:92145831-92146049(-)$1	218	131	157	9.5906

#DB
((((((((((.....)))))))))).	chrX:106957187-106957420(-)$1	1	126	152	11.5064
(((((..(((......)))..)))))	chr3:183145787-183146015(-)$1	1	199	225	12.7447
((((((((.(((....))).))))))	chr4:68338026-68338248(-)$1	1	152	178	9.2957
.(((((((((......))))))))).	chr9:131572313-131572535(+)$1	1	49	75	11.8036
...(((((((......))))))))))	chr16:75271110-75271331(+)$1	1	112	138	12.9913
((((((((((......)))..))).)	chr15:26788944-26789167(-)$1	1	181	207	12.6685
(..(((((((......)))))))..)	chr7:90043849-90044074(+)$1	1	65	91	12.1524
((..((((((......))))))...)	chr1:167391787-167392003(-)$1	1	10	36	11.1942
(((((((.((......))))).))))	chr12:49331690-49331949(-)$1	1	17	43	11.2301
.(((((..((......))..))))))	chr19:54058012-54058231(-)$1	1	138	164	12.1528
(((.((..((......))..))))))	chr7:8126449-8126664(-)$1	1	74	100	11.8384
.(((((((((......))))....))	chr13:36910344-36910569(-)$1	1	119	145	11.5117
..(((((((((.....))))))))).	chr13:114748143-114748359(-)$1	1	172	198	10.1061
(((...((((......))))....))	chr14:94192213-94192434(-)$1	1	11	37	11.9595
...(((((((......))))))).))	chr6:33663775-33664003(-)$1	1	175	201	12.6564
((((.(((((......))))).))).	chr2:158388239-158388458(-)$1	1	91	117	11.0753
((((((.(((......))).))))))	chr17:7529616-7529834(-)$1	1	81	107	13.8359
((....((((......)))).)))))	chr7:99047801-99048020(+)$1	1	105	131	11.6431
((((...(((.....)))...)))))	chrX:103435696-103435925(+)$1	1	52	78	10.2555
(.((((.(((......))).))))((	chr19:2476193-2476412(+)$1	1	110	136	9.9623
((((..((((.....))))..)))))	chr21:41033967-41034184(-)$1	1	70	96	9.5882
(.((((..((......)))))).)).	chr2:206482494-206482710(+)$1	1	98	124	10.9772
....((((((......))))))....	chr15:43268925-43269148(-)$1	1	101	127	11.1048
((.((...((......))..)).)))	chr22:32586416-32586653(-)$1	1	171	197	12.3279
(((.((((((......))))))..))	chr11:22759159-22759375(-)$1	1	87	113	10.7730
((((((((((......))))))))))	chr1:11346185-11346407(+)$1	1	132	158	14.3874
)((((((.((......)).)))))).	chr8:1953776-1953994(+)$1	1	181	207	10.8378
(((((...((......)).)))))).	chr8:26269215-26269436(+)$1	1	62	88	11.4087
..(((...((......)).)))..))	chr1:182352842-182353077(-)$1	1	49	75	12.9664
((((((.(((.....)))...)))))	chr1:160914744-160914964(-)$1	1	86	112	9.8046
(((((.((((......)))).)))))	chr2:86364609-86364826(+)$1	1	89	115	11.3620
(.(((((((((.....))))))))))	chr17:44101803-44102020(+)$1	1	109	135	10.3619
(((((..(((......))).))))))	chr9:73149683-73149910(-)$1	1	127	153	11.6767
(((..((.((......))))...)))	chr1:155204522-155204748(-)$1	1	144	170	11.8992
(((((((.(((.....))).))))))	chr1:8413939-8414174(-)$1	1	135	161	10.4934
(((((..(((......)))....)))	chr11:88240870-88241100(-)$1	1	1	27	13.0026
(((...((((......)))).)))).	chr5:64813932-64814147(-)$1	1	63	89	10.2331
(((((..(((......)))..)))))	chr19:57333911-57334127(+)$1	1	20	46	12.7248
((((((.(((.....)))...))).)	chr10:98758571-98758792(-)$1	1	100	126	10.4136
((((((((((......))))))))).	chr9:34660409-34660630(+)$1	1	163	189	13.4056
(.(....(((......)))...).))	chr1:155156530-155156752(+)$1	1	119	145	13.3782
((((((((((......))))....))	chr5:110823704-110823924(+)$1	1	95	121	10.5364
.(((((((((......)).)))))))	chr1:154556467-154556688(-)$1	1	39	65	13.3221
(((..(((.((......)).))).))	chr3:149458681-149458902(-)$1	1	93	119	10.7724
((.(((..((......))..))).))	chr7:112756733-112756955(-)$1	1	158	184	12.7831
.)))))((((......))))((((((	chr6:136664259-136664487(-)$1	1	51	77	11.3936
..(((((((((.....))))))))).	chr16:14359948-14360165(+)$1	1	131	157	10.8169
(((((...((.....))...))))))	chr2:69472888-69473104(+)$1	1	50	76	10.8762
((((..((((......)))).)))).	chr13:48650168-48650385(+)$1	1	11	37	10.0546
((((((.(((.....)))))))))))	chr2:11680077-11680298(+)$1	1	153	179	11.4251
(....(((((......))))))))..	chr12:49160242-49160458(-)$1	1	83	109	10.7601
..(((((.((......)).)))))..	chr14:104164064-104164288(+)$1	1	82	108	11.6715
.(((((((((.....))))))))).)	chr22:31678657-31678877(-)$1	1	188	214	10.7637
(((((((((.........))))))))	chr1:92145831-92146049(-)$1	1	131	157	9.5906

#PSSM
f : 0.14	= : 0.11	e : 0.11	d : 0.09	c : 0.09	g : 0.07	" : 0.05	[ : 0.05	! : 0.05	h : 0.05	b : 0.03	# : 0.03	: : 0.01	H : 0.01	] : 0.01	i : 0.01	
e : 0.16	f : 0.14	= : 0.09	g : 0.09	i : 0.07	! : 0.07	d : 0.07	c : 0.07	# : 0.05	[ : 0.05	" : 0.03	h : 0.03	: : 0.01	
e : 0.18	i : 0.12	f : 0.11	= : 0.09	d : 0.09	c : 0.09	g : 0.07	# : 0.05	" : 0.03	! : 0.03	[ : 0.03	h : 0.03	a : 0.01	
i : 0.12	g : 0.12	e : 0.12	f : 0.11	= : 0.09	d : 0.07	c : 0.07	# : 0.07	! : 0.05	[ : 0.03	" : 0.03	h : 0.03	b : 0.01	
f : 0.14	i : 0.12	g : 0.11	e : 0.11	= : 0.09	c : 0.09	! : 0.07	" : 0.05	# : 0.05	b : 0.03	d : 0.03	h : 0.03	[ : 0.01	
" : 0.12	! : 0.11	i : 0.11	g : 0.11	e : 0.11	= : 0.09	c : 0.09	f : 0.09	b : 0.03	# : 0.03	d : 0.03	[ : 0.01	h : 0.01	
d : 0.16	! : 0.14	i : 0.11	g : 0.09	[ : 0.09	" : 0.09	= : 0.07	f : 0.07	c : 0.05	e : 0.05	b : 0.01	# : 0.01	
c : 0.24	d : 0.16	i : 0.11	[ : 0.09	= : 0.07	g : 0.07	! : 0.07	" : 0.07	f : 0.05	e : 0.03	
c : 0.24	b : 0.24	d : 0.16	i : 0.11	= : 0.05	g : 0.05	f : 0.05	[ : 0.03	e : 0.03	
c : 0.25	b : 0.25	d : 0.16	i : 0.11	g : 0.05	f : 0.05	= : 0.03	e : 0.03	r : 0.01	
o : 0.72	n : 0.14	i : 0.05	c : 0.03	b : 0.01	r : 0.01	
o : 0.74	n : 0.22	c : 0.01	r : 0.01	
o : 0.74	n : 0.22	m : 0.01	r : 0.01	
o : 0.74	n : 0.22	m : 0.01	r : 0.01	
o : 0.74	n : 0.22	m : 0.01	r : 0.01	
o : 0.74	n : 0.07	c : 0.07	= : 0.01	m : 0.01	d : 0.01	b : 0.01	i : 0.01	r : 0.01	
c : 0.25	b : 0.24	d : 0.16	i : 0.11	g : 0.05	f : 0.05	= : 0.03	e : 0.03	o : 0.01	r : 0.01	
c : 0.25	b : 0.24	d : 0.16	i : 0.11	g : 0.05	f : 0.05	= : 0.03	e : 0.03	3 : 0.01	r : 0.01	
c : 0.20	d : 0.18	i : 0.11	] : 0.09	= : 0.07	2 : 0.07	3 : 0.07	g : 0.05	f : 0.05	e : 0.03	b : 0.03	
d : 0.16	2 : 0.14	] : 0.11	i : 0.11	f : 0.09	3 : 0.09	= : 0.07	g : 0.07	e : 0.05	c : 0.03	b : 0.01	4 : 0.01	
i : 0.12	g : 0.12	= : 0.09	f : 0.09	3 : 0.09	2 : 0.07	c : 0.07	e : 0.07	4 : 0.07	] : 0.07	b : 0.03	d : 0.03	h : 0.01	
f : 0.18	g : 0.14	i : 0.12	c : 0.11	= : 0.09	4 : 0.07	d : 0.07	e : 0.05	] : 0.03	b : 0.03	3 : 0.03	h : 0.01	
g : 0.14	f : 0.12	i : 0.12	c : 0.12	= : 0.09	4 : 0.09	d : 0.07	e : 0.05	3 : 0.03	] : 0.03	2 : 0.03	h : 0.01	a : 0.01	
f : 0.12	i : 0.12	g : 0.12	c : 0.11	= : 0.09	d : 0.07	e : 0.07	4 : 0.07	] : 0.07	2 : 0.05	3 : 0.01	b : 0.01	h : 0.01	
f : 0.14	i : 0.12	g : 0.12	e : 0.12	= : 0.09	d : 0.07	c : 0.07	] : 0.05	2 : 0.05	h : 0.05	3 : 0.01	b : 0.01	4 : 0.01	
e : 0.18	g : 0.12	f : 0.11	: : 0.09	= : 0.07	d : 0.07	h : 0.05	4 : 0.03	] : 0.03	i : 0.03	c : 0.03	2 : 0.03	b : 0.01	6 : 0.01	3 : 0.01	0 : 0.01	a : 0.01	

#score	620.4800698338406
#seq	54
#width	26
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_UTR_m3_run2.txt

#BEAR
eeeeeqqqqqqqqeeeee:	chr20:30960064-30960302(+)$1	238	29	48	13.0485
"ddddqqqqqqqqdddd]f	chr3:141165305-141165568(+)$1	263	169	188	13.5822
((cccqqqqqqqqcccfff	chr22:38339440-38339657(-)$1	217	108	127	13.0811
ee[bbqqqqqqqqbbeeee	chr20:57604813-57605072(-)$1	259	84	103	13.3778
!!cccqqqqqqqqccc22e	chr2:121749480-121749733(+)$1	253	14	33	14.4581
[ddddqqqqqqqqdddd]c	chr2:70315980-70316202(+)$1	222	158	177	13.7556
fffffqqqqqqqqffffff	chr12:1020122-1020391(+)$1	269	220	239	12.9156
a[cccqqqqqqqqccc]a]	chr1:63836389-63836618(+)$1	229	115	134	14.6931
hhhhhqqqqqqqqhhhhhh	chr5:96109511-96109781(+)$1	270	239	258	12.4879
hhhhhqqqqqqqqhhhhhh	chr6:108041323-108041551(-)$1	228	128	147	12.4879
""cccqqqqqqqqccc333	chr11:10530013-10530304(-)$1	291	260	279	14.9000
[ddddqqqqqqqqdddd]b	chr10:75530212-75530451(+)$1	239	101	120	13.5349
ee[bbqqqqqqqqbbeeee	chr8:12883755-12883975(+)$1	220	113	132	13.3778
+ddddqqqqqqqqdddd>>	chr20:5527615-5527866(-)$1	251	183	202	12.7133
=====qqqqqqqq======	chr19:44601763-44601994(+)$1	231	11	30	14.0574
""cccqqqqqqqqccc333	chr8:66634951-66635233(-)$1	282	83	102	14.9000
eeeeeqqqqqqqqeeeee]	chr3:11598203-11598465(-)$1	262	205	224	13.9256
ccc[aqqqqqqqqa]ccc:	chr1:145282068-145282335(+)$1	267	242	261	12.9008
eeeeeqqqqqqqqeeeee]	chr2:120735038-120735280(+)$1	242	63	82	13.9256
hhhbbqqqqqqqqbb22hh	chr9:100848612-100848841(-)$1	229	8	27	12.2967
[ddddqqqqqqqqdddd]d	chr5:39106430-39106663(-)$1	233	40	59	13.6221
fffffqqqqqqqqffffff	chr9:7797631-7797862(-)$1	231	38	57	12.9156
$$cccqqqqqqqqccc333	chr3:57302386-57302606(+)$1	220	125	144	14.5939
eeeeeqqqqqqqqeeeee5	chr19:42731488-42731705(+)$1	217	90	109	13.2880
fffffqqqqqqqqffffff	chr3:197682551-197682767(+)$1	216	1	20	12.9156
cddddqqqqqqqqdddd]c	chr5:49692276-49692544(-)$1	268	85	104	13.5705
cddddqqqqqqqqdddd::	chr5:115166645-115166886(-)$1	241	75	94	11.7687
fffffqqqqqqqqffffff	chr7:30122911-30123139(+)$1	228	97	116	12.9156
e!!bbqqqqqqqqbb22ee	chr8:67545441-67545672(-)$1	231	66	85	13.1717
hhhhhqqqqqqqqhhhhhh	chr6:42658794-42659041(+)$1	247	167	186	12.4879
eeeeeqqqqqqqqeeeee4	chr2:197001742-197001972(-)$1	230	95	114	13.9263
"""bbqqqqqqqqbb22dd	chr8:23118038-23118264(+)$1	226	176	195	12.8146
((cccqqqqqqqqccc777	chr20:57475212-57475517(+)$1	305	236	255	12.0406
dd[bbqqqqqqqqbb]ddd	chr5:127522862-127523099(+)$1	237	184	203	12.8500
gggggqqqqqqqqgggggg	chr7:12273636-12273858(+)$1	222	174	193	13.9454
eeeeeqqqqqqqqeeeee:	chr19:1611490-1611727(-)$1	237	35	54	13.0485
[bb[aqqqqqqqqa]bb]b	chr9:125884081-125884300(-)$1	219	79	98	12.5467
d[cccqqqqqqqqccc]dd	chr2:201687831-201688066(+)$1	235	214	233	14.2176
gggggqqqqqqqqgggggg	chr1:161647511-161647724(+)$1	213	146	165	13.9454
ddcccqqqqqqqqccc]dd	chr7:86824392-86824741(+)$1	349	300	319	14.0444
iiiiiqqqqqqqqiiiiii	chr1:206635099-206635379(+)$1	280	236	255	13.9327
eeeeeqqqqqqqqeeeee3	chr1:159997758-159998003(-)$1	245	62	81	13.9764
eeeeeqqqqqqqqeeeee2	chr2:169626563-169626799(+)$1	236	43	62	13.7314
c[cccqqqqqqqqcccccc	chr1:162494340-162494612(+)$1	272	198	217	14.3731
gggggqqqqqqqqgggggg	chr7:6369382-6369616(-)$1	234	79	98	13.9454
cccccqqqqqqqqccc]cc	chr1:152056932-152057170(-)$1	238	52	71	14.3647
eeeeeqqqqqqqqeeeeec	chr1:41975756-41976028(-)$1	272	189	208	13.8033
!bbbbqqqqqqqqbb]bb]	chr20:4834890-4835170(-)$1	280	222	241	12.4470
%%cccqqqqqqqqccc666	chr17:15620024-15620256(+)$1	232	207	226	12.3187
&&cccqqqqqqqqccc777	chrX:77911698-77911917(-)$1	219	162	181	12.1114
e[cccqqqqqqqqccceee	chr16:70607080-70607296(+)$1	216	102	121	14.4634

#otherMatches

#Seq PSSM
AUUGAAUAUUUGCUCAGUA	chr20:30960064-30960302(+)$1	238	29	48	13.0485
AUUAUGAGGAGCAAUAGAU	chr3:141165305-141165568(+)$1	263	169	188	13.5822
AAACCUCUGCAACGGUUCA	chr22:38339440-38339657(-)$1	217	108	127	13.0811
GCAUGAAAAACUACAGUUC	chr20:57604813-57605072(-)$1	259	84	103	13.3778
ACCCACCUGGAAAUGGAAU	chr2:121749480-121749733(+)$1	253	14	33	14.4581
UAAGCUUUUCCCUGUUUUU	chr2:70315980-70316202(+)$1	222	158	177	13.7556
UUAUUUUUGUGUUAAUAGU	chr12:1020122-1020391(+)$1	269	220	239	12.9156
CUCAAACUCCUAAUUGCGA	chr1:63836389-63836618(+)$1	229	115	134	14.6931
AAUAGUCAUUAUUCUAUUU	chr5:96109511-96109781(+)$1	270	239	258	12.4879
caaaagcuggucauuuugc	chr6:108041323-108041551(-)$1	228	128	147	12.4879
AACUGACAAUUAACAGCCC	chr11:10530013-10530304(-)$1	291	260	279	14.9000
ACCCUCAAAUAUCAGGGAA	chr10:75530212-75530451(+)$1	239	101	120	13.5349
cacacugggaccuguugug	chr8:12883755-12883975(+)$1	220	113	132	13.3778
AGUUGUUUUACAUCAAUGU	chr20:5527615-5527866(-)$1	251	183	202	12.7133
uagaccaugauuugucuau	chr19:44601763-44601994(+)$1	231	11	30	14.0574
UAGAGUUAUUUUUCUUGAA	chr8:66634951-66635233(-)$1	282	83	102	14.9000
CACUUUUCUAUAUGGGUGA	chr3:11598203-11598465(-)$1	262	205	224	13.9256
AGCACUUUUUGAUGAGCUG	chr1:145282068-145282335(+)$1	267	242	261	12.9008
AAUAUCGUUCUUAAUAUUA	chr2:120735038-120735280(+)$1	242	63	82	13.9256
CAACUAAAUUGGAGGCUUU	chr9:100848612-100848841(-)$1	229	8	27	12.2967
ACUGGAAAGUUGGCCAGCA	chr5:39106430-39106663(-)$1	233	40	59	13.6221
UCUUCCCUUUCAUGGAGGC	chr9:7797631-7797862(-)$1	231	38	57	12.9156
aaAGGUAUACAGUCCUAAU	chr3:57302386-57302606(+)$1	220	125	144	14.5939
ugugacauagauuucauau	chr19:42731488-42731705(+)$1	217	90	109	13.2880
UACGGUUCUUGAUUUGUAG	chr3:197682551-197682767(+)$1	216	1	20	12.9156
agucucuugaacuagacuu	chr5:49692276-49692544(-)$1	268	85	104	13.5705
GUCCUAACAUUUAAGGAUU	chr5:115166645-115166886(-)$1	241	75	94	11.7687
GAGUUCUUUCAACAAUUCC	chr7:30122911-30123139(+)$1	228	97	116	12.9156
ACUAUUUUAUUUUAUUCUG	chr8:67545441-67545672(-)$1	231	66	85	13.1717
UUUUUAAGAAAGAAAGAAG	chr6:42658794-42659041(+)$1	247	167	186	12.4879
UUUUGCAUAUCAACAAAAA	chr2:197001742-197001972(-)$1	230	95	114	13.9263
GAAAGGAGAACCACUGAUU	chr8:23118038-23118264(+)$1	226	176	195	12.8146
UCUGCAUGUUUCAGCAAUC	chr20:57475212-57475517(+)$1	305	236	255	12.0406
GAAGAUUGAAGAUUCAUCC	chr5:127522862-127523099(+)$1	237	184	203	12.8500
AGAUUUUUCUGAUGAUCUG	chr7:12273636-12273858(+)$1	222	174	193	13.9454
GUGGGACGAGCCACCCGCU	chr19:1611490-1611727(-)$1	237	35	54	13.0485
UUAGGAUAUAACACGUAUG	chr9:125884081-125884300(-)$1	219	79	98	12.5467
AUGAGCCAAAUACUUCUUG	chr2:201687831-201688066(+)$1	235	214	233	14.2176
UAUGUUACAGGUUACGUGA	chr1:161647511-161647724(+)$1	213	146	165	13.9454
CCUGUUUAGUGUUACAUGG	chr7:86824392-86824741(+)$1	349	300	319	14.0444
UUGUGGCAGUUCACACAGU	chr1:206635099-206635379(+)$1	280	236	255	13.9327
UGUGGCUUACUCUUCAUAC	chr1:159997758-159998003(-)$1	245	62	81	13.9764
AGAGUCUCGUUCAGCUCUA	chr2:169626563-169626799(+)$1	236	43	62	13.7314
UCAUCUUAUUGCUGAUACA	chr1:162494340-162494612(+)$1	272	198	217	14.3731
UUUUGGUCUGCAGCAAAAU	chr7:6369382-6369616(-)$1	234	79	98	13.9454
UCAUUGAAUUUAAAAUAGA	chr1:152056932-152057170(-)$1	238	52	71	14.3647
AGGCUGAUGGUGAAGCCUC	chr1:41975756-41976028(-)$1	272	189	208	13.8033
UGGGUUUAAGCACACACCU	chr20:4834890-4835170(-)$1	280	222	241	12.4470
UAAGCAUCAGAGAGUUCAU	chr17:15620024-15620256(+)$1	232	207	226	12.3187
CAAUUAUACUAACAAUACA	chrX:77911698-77911917(-)$1	219	162	181	12.1114
CUCAUUUUUUCCUGUGGCC	chr16:70607080-70607296(+)$1	216	102	121	14.4634

#DB
(((((........))))).	chr20:30960064-30960302(+)$1	1	29	48	13.0485
.((((........)))).)	chr3:141165305-141165568(+)$1	1	169	188	13.5822
..(((........))))))	chr22:38339440-38339657(-)$1	1	108	127	13.0811
((.((........))))))	chr20:57604813-57605072(-)$1	1	84	103	13.3778
..(((........)))..)	chr2:121749480-121749733(+)$1	1	14	33	14.4581
.((((........)))).)	chr2:70315980-70316202(+)$1	1	158	177	13.7556
(((((........))))))	chr12:1020122-1020391(+)$1	1	220	239	12.9156
(.(((........))).).	chr1:63836389-63836618(+)$1	1	115	134	14.6931
(((((........))))))	chr5:96109511-96109781(+)$1	1	239	258	12.4879
(((((........))))))	chr6:108041323-108041551(-)$1	1	128	147	12.4879
..(((........)))...	chr11:10530013-10530304(-)$1	1	260	279	14.9000
.((((........)))).)	chr10:75530212-75530451(+)$1	1	101	120	13.5349
((.((........))))))	chr8:12883755-12883975(+)$1	1	113	132	13.3778
.((((........))))..	chr20:5527615-5527866(-)$1	1	183	202	12.7133
(((((........))))))	chr19:44601763-44601994(+)$1	1	11	30	14.0574
..(((........)))...	chr8:66634951-66635233(-)$1	1	83	102	14.9000
(((((........))))).	chr3:11598203-11598465(-)$1	1	205	224	13.9256
(((.(........).))).	chr1:145282068-145282335(+)$1	1	242	261	12.9008
(((((........))))).	chr2:120735038-120735280(+)$1	1	63	82	13.9256
(((((........))..))	chr9:100848612-100848841(-)$1	1	8	27	12.2967
.((((........)))).)	chr5:39106430-39106663(-)$1	1	40	59	13.6221
(((((........))))))	chr9:7797631-7797862(-)$1	1	38	57	12.9156
..(((........)))...	chr3:57302386-57302606(+)$1	1	125	144	14.5939
(((((........))))).	chr19:42731488-42731705(+)$1	1	90	109	13.2880
(((((........))))))	chr3:197682551-197682767(+)$1	1	1	20	12.9156
(((((........)))).)	chr5:49692276-49692544(-)$1	1	85	104	13.5705
)((((........))))..	chr5:115166645-115166886(-)$1	1	75	94	11.7687
(((((........))))))	chr7:30122911-30123139(+)$1	1	97	116	12.9156
(..((........))..))	chr8:67545441-67545672(-)$1	1	66	85	13.1717
(((((........))))))	chr6:42658794-42659041(+)$1	1	167	186	12.4879
(((((........))))).	chr2:197001742-197001972(-)$1	1	95	114	13.9263
...((........))..))	chr8:23118038-23118264(+)$1	1	176	195	12.8146
..(((........)))...	chr20:57475212-57475517(+)$1	1	236	255	12.0406
((.((........)).)))	chr5:127522862-127523099(+)$1	1	184	203	12.8500
(((((........))))))	chr7:12273636-12273858(+)$1	1	174	193	13.9454
(((((........))))).	chr19:1611490-1611727(-)$1	1	35	54	13.0485
.((.(........).)).)	chr9:125884081-125884300(-)$1	1	79	98	12.5467
(.(((........))).))	chr2:201687831-201688066(+)$1	1	214	233	14.2176
(((((........))))))	chr1:161647511-161647724(+)$1	1	146	165	13.9454
(((((........))).))	chr7:86824392-86824741(+)$1	1	300	319	14.0444
(((((........))))))	chr1:206635099-206635379(+)$1	1	236	255	13.9327
(((((........))))).	chr1:159997758-159998003(-)$1	1	62	81	13.9764
(((((........))))).	chr2:169626563-169626799(+)$1	1	43	62	13.7314
(.(((........))))))	chr1:162494340-162494612(+)$1	1	198	217	14.3731
(((((........))))))	chr7:6369382-6369616(-)$1	1	79	98	13.9454
(((((........))).))	chr1:152056932-152057170(-)$1	1	52	71	14.3647
(((((........)))))(	chr1:41975756-41976028(-)$1	1	189	208	13.8033
.((((........)).)).	chr20:4834890-4835170(-)$1	1	222	241	12.4470
..(((........)))...	chr17:15620024-15620256(+)$1	1	207	226	12.3187
..(((........)))...	chrX:77911698-77911917(-)$1	1	162	181	12.1114
(.(((........))))))	chr16:70607080-70607296(+)$1	1	102	121	14.4634

#PSSM
e : 0.25	c : 0.09	" : 0.07	[ : 0.07	f : 0.07	h : 0.07	d : 0.05	g : 0.05	( : 0.03	! : 0.03	a : 0.01	+ : 0.01	= : 0.01	$ : 0.01	i : 0.01	% : 0.01	& : 0.01	
e : 0.21	d : 0.17	f : 0.07	[ : 0.07	h : 0.07	" : 0.05	g : 0.05	( : 0.03	! : 0.03	c : 0.03	b : 0.03	= : 0.01	$ : 0.01	i : 0.01	% : 0.01	& : 0.01	
c : 0.29	e : 0.17	d : 0.13	f : 0.07	h : 0.07	[ : 0.05	g : 0.05	b : 0.03	= : 0.01	! : 0.01	" : 0.01	i : 0.01	
c : 0.27	e : 0.17	d : 0.13	b : 0.13	f : 0.07	h : 0.05	g : 0.05	[ : 0.03	= : 0.01	i : 0.01	
c : 0.27	e : 0.17	d : 0.13	b : 0.13	f : 0.07	h : 0.05	g : 0.05	a : 0.03	= : 0.01	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.27	e : 0.17	d : 0.13	b : 0.13	f : 0.07	h : 0.05	g : 0.05	a : 0.03	= : 0.01	i : 0.01	
c : 0.27	e : 0.17	d : 0.13	b : 0.13	f : 0.07	h : 0.05	g : 0.05	] : 0.03	= : 0.01	i : 0.01	
c : 0.29	e : 0.21	d : 0.13	f : 0.07	h : 0.05	2 : 0.05	g : 0.05	] : 0.03	= : 0.01	b : 0.01	i : 0.01	
e : 0.23	d : 0.15	f : 0.09	2 : 0.07	] : 0.07	h : 0.05	3 : 0.05	g : 0.05	c : 0.03	7 : 0.03	b : 0.03	= : 0.01	i : 0.01	6 : 0.01	
e : 0.25	] : 0.11	f : 0.09	h : 0.07	d : 0.07	3 : 0.05	c : 0.05	g : 0.05	7 : 0.03	2 : 0.01	a : 0.01	> : 0.01	= : 0.01	: : 0.01	i : 0.01	b : 0.01	6 : 0.01	
f : 0.11	e : 0.09	c : 0.09	d : 0.09	: : 0.07	] : 0.07	h : 0.07	3 : 0.07	g : 0.05	b : 0.03	7 : 0.03	> : 0.01	= : 0.01	5 : 0.01	4 : 0.01	i : 0.01	2 : 0.01	6 : 0.01	

#score	684.5188840093807
#seq	51
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014b_hg19_CDS_m1_run2.txt

#BEAR
b[ccc^^^^^^^^^^^^^^^^^^^^cc	chr13:31338104-31338350(+)$1	246	123	150	23.5272
^^^^^^^^^^^^^^^^^^^^^^^^eee	chr18:9254753-9254986(+)$1	233	183	210	25.1412
gggggxxxxxxxxxxxxxxxggggggg	chr10:38343949-38344282(+)$1	333	147	174	19.6120
!dddd^^^^^^^^^^^^^^^^^^dddd	chr7:104746928-104747159(+)$1	231	159	186	22.6921
eeeee^^^^^^^^^^^^^^^^^^^^ee	chr12:108147615-108147868(-)$1	253	84	111	23.0994
dd[bb^^^^^^^^^^^^^^^^^^^bb]	chr2:243402-243662(-)$1	260	165	192	22.7411
""dddd^^^^^^^^^^^^^^^^^^^^^	chr17:18832712-18832984(+)$1	272	94	121	21.7765
eeebb^^^^^^^^^^^^^^^^^^bb]e	chr13:39587213-39587577(-)$1	364	106	133	22.2839
dddd^^^^^^^^^^^^^^^^^^dddd:	chr16:22545729-22545989(+)$1	260	1	28	21.1839
eeeeeuuuuuuuuuuuueeeee22eee	chr11:19256385-19256608(-)$1	223	71	98	19.3449
dyyyyyyyyyyyyyyyydddd>>>>>>	chr1:225705409-225705643(-)$1	234	185	212	19.0122
hhh^^^^^^^^^^^^^^^^^^^^^hhh	chr11:62438631-62438917(-)$1	286	120	147	22.9094
^^^^^^^^^^^^^^^^^^^^^^^^ggg	chr10:64973398-64973658(-)$1	260	52	79	25.2930
ggggguuuuuuuuuuuuggggggg333	chr15:58968376-58968624(-)$1	248	111	138	18.9883
f[cccwwwwwwwwwwwwwwcccfffff	chr3:57303557-57303778(-)$1	221	178	205	20.8177
""ccc^^^^^^^^^^^^^^^^^^^^^^	chr20:49509422-49509694(-)$1	272	179	206	23.6491
eeeeeuuuuuuuuuuuueeeee:dddd	chr10:38344201-38344476(+)$1	275	126	153	18.2183
g^^^^^^^^^^^^^^^^^^^^^^^ggg	chr16:31196124-31196363(+)$1	239	53	80	25.0696
f[cccwwwwwwwwwwwwwwccc]ffff	chr17:65941779-65942076(+)$1	297	69	96	21.0341
:dddd^^^^^^^^^^^^^^^^^^dddd	chr1:42657168-42657456(-)$1	288	13	40	21.5818
fffffuuuuuuuuuuuuffffffeeee	chr9:134473588-134473822(-)$1	234	88	115	18.3541
!ddddvvvvvvvvvvvvvdddd22fff	chr11:134180417-134180653(+)$1	236	74	101	19.7474
d[cccuuuuuuuuuuuuccc4444ddd	chr12:29493977-29494226(-)$1	249	87	114	21.5856
"ddddvvvvvvvvvvvvvdddd22ggg	chr2:149240749-149241010(+)$1	261	91	118	20.0811
^^^^^^^^^^^^^^^^^^^^^^^^eee	chr12:80199933-80200169(-)$1	236	8	35	25.1412
i[cccxxxxxxxxxxxxxxxccciiii	chr10:70516196-70516473(+)$1	277	40	67	20.3559
gggggyyyyyyyyyyyyyyyygggggg	chr20:33329118-33329358(-)$1	240	9	36	21.1062
##cccwwwwwwwwwwwwwwccc22ddd	chr7:107399061-107399331(+)$1	270	70	97	21.6315
^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr9:5920448-5920704(-)$1	256	106	133	24.9962
^^^^^^^^^^^^^^^^^^^^^^^^ggg	chr5:56532818-56533099(+)$1	281	156	183	25.2930
cccwwwwwwwwwwwwwwccc55555dd	chr12:49444826-49445077(-)$1	251	182	209	18.5360
e!!bbvvvvvvvvvvvvvbb22eeeee	chr6:53156482-53156758(-)$1	276	157	184	19.6949
!ddddvvvvvvvvvvvvvdddd]gggg	chr7:155503997-155504243(+)$1	246	176	203	19.9872
gggggxxxxxxxxxxxxxxxggggggg	chr1:169446426-169446701(-)$1	275	226	253	19.6120
fffffuuuuuuuuuuuuffffffcccn	chr11:18536220-18536487(-)$1	267	76	103	17.8303
##cccxxxxxxxxxxxxxxxccc333f	chr2:29072689-29072917(-)$1	228	28	55	21.0038
^^^^^^^^^^^^^^^^^^^^^^^^eee	chrX:64721887-64722114(+)$1	227	110	137	25.1412
!!ccc^^^^^^^^^^^^^^^^^^^ccc	chrX:134421149-134421409(-)$1	260	42	69	24.2321
d!!bbuuuuuuuuuuuubb22dddd]e	chr3:182987471-182987706(-)$1	235	112	139	18.9088
###bbuuuuuuuuuuuubb4444ccc:	chr19:3660877-3661092(-)$1	215	52	79	20.4088
gg^^^^^^^^^^^^^^^^^^^^^^ggg	chr14:50558072-50558334(-)$1	262	35	62	24.7622
^^^^^^^^^^^^^^^^^^^^^^^^ggg	chr11:16769571-16769801(+)$1	230	135	162	25.2930
^^^^^^^^^^^^^^^^^^^^^^^^fff	chr13:39586983-39587219(-)$1	236	38	65	24.9508
eeeevvvvvvvvvvvvveeeee]bb]e	chr19:57803361-57803591(+)$1	230	56	83	18.9607
#ddddtttttttttttdddd4444ccc	chr8:57079199-57079440(-)$1	241	163	190	17.4176
cccwwwwwwwwwwwwwwcccccc]hhh	chr11:88029209-88029474(-)$1	265	184	211	19.9962
e^^^^^^^^^^^^^^^^^^^^^^^eee	chr15:50884078-50884320(-)$1	242	14	41	24.8822
gggggxxxxxxxxxxxxxxxggggggg	chr11:68216381-68216657(+)$1	276	227	254	19.6120
^^^^^^^^^^^^^^^^^^^^^^^^bb]	chr13:39587825-39588050(-)$1	225	110	137	24.7775
^^^^^^^^^^^^^^^^^^^^^^^^bb]	chr2:9725280-9725522(-)$1	242	154	181	24.7775
^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr4:1215476-1215716(-)$1	240	46	73	24.9962
""cccuuuuuuuuuuuuccc4444ggg	chr3:194371480-194371717(-)$1	237	127	154	22.2882
eeeeeuuuuuuuuuuuueeeee]ccc2	chr12:49089772-49090001(-)$1	229	174	201	19.1872
ggggguuuuuuuuuuuuggggggg]==	chr12:49522189-49522436(-)$1	247	177	204	18.9716
^^^^^^^^^^^^^^^^^^^^^^^^eee	chr15:68378786-68379050(+)$1	264	199	226	25.1412
fffffyyyyyyyyyyyyyyyyffffff	chr12:6646736-6646996(+)$1	260	87	114	20.2283
#ddddvvvvvvvvvvvvvddddddddf	chr6:26452468-26452739(+)$1	271	173	200	19.2990
^^^^^^^^^^^^^^^^^^^bb333ccc	chr17:42475014-42475290(-)$1	276	156	183	22.8757
eeebbvvvvvvvvvvvvvbb]eeeee2	chr1:185276991-185277256(-)$1	265	104	131	19.1409
[dddduuuuuuuuuuuuddddbb22a]	chr17:35800569-35800792(+)$1	223	41	68	18.7611
^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr17:47375772-47376180(-)$1	408	95	122	24.9962
===wwwwwwwwwwwwww==========	chr2:20478254-20478517(-)$1	263	178	205	20.4013
fffwwwwwwwwwwwwwwffffff333d	chr6:139264612-139264847(-)$1	235	101	128	19.4750
dyyyyyyyyyyyyyyyydddd333bb2	chr1:31405914-31406168(-)$1	254	162	189	19.7655
fffwwwwwwwwwwwwwwffffff333c	chr1:151400556-151400807(-)$1	251	10	37	19.5215

#otherMatches

#Seq PSSM
ACUUCUCAUUCCCUAACUCUCUGCUGA	chr13:31338104-31338350(+)$1	246	123	150	23.5272
CUAAAACAAGAACAUACUAAAACAUGU	chr18:9254753-9254986(+)$1	233	183	210	25.1412
AGGGUGCACACAGGACAGAAACCCUUU	chr10:38343949-38344282(+)$1	333	147	174	19.6120
AUGGACCCAUCUUUUGCCACGCCUCCA	chr7:104746928-104747159(+)$1	231	159	186	22.6921
GUGGGUUACCUGAAAGAAACUACACCC	chr12:108147615-108147868(-)$1	253	84	111	23.0994
uugugucuucauuuuccuuaaucucaa	chr2:243402-243662(-)$1	260	165	192	22.7411
uagcugucacuucacauuuucucucac	chr17:18832712-18832984(+)$1	272	94	121	21.7765
GGCCGUGCAUAUACUUCAACAUCCGUG	chr13:39587213-39587577(-)$1	364	106	133	22.2839
AGCUCACUCCCCUUCCACCCUCAGCUC	chr16:22545729-22545989(+)$1	260	1	28	21.1839
GCCAAAAACAGGUACACUUGGCACGGG	chr11:19256385-19256608(-)$1	223	71	98	19.3449
UUCUUCCCCAUUACGCUACAGUUCCUC	chr1:225705409-225705643(-)$1	234	185	212	19.0122
GGGCAUCUACACACAUACACAUCCCUC	chr11:62438631-62438917(-)$1	286	120	147	22.9094
UACCUACCAUUAACACUCAUCCUCUGA	chr10:64973398-64973658(-)$1	260	52	79	25.2930
ccuauuauucccacuuuauaggugaag	chr15:58968376-58968624(-)$1	248	111	138	18.9883
GCAGCUAUCAACCGACUUUGUUCUUCC	chr3:57303557-57303778(-)$1	221	178	205	20.8177
UUGCUUACCAUGCCCAAAAUAAUCCUC	chr20:49509422-49509694(-)$1	272	179	206	23.6491
UCUGACCUCACUAAACAUCAGAGAACA	chr10:38344201-38344476(+)$1	275	126	153	18.2183
UUGUCAAACCUUUUCAAACCUUUUAGU	chr16:31196124-31196363(+)$1	239	53	80	25.0696
GUGUCCAAAGUCCAUCACAGACUCGAA	chr17:65941779-65942076(+)$1	297	69	96	21.0341
UGUCAUAAAAUACAACUGAAAUCUGAC	chr1:42657168-42657456(-)$1	288	13	40	21.5818
GUUUGACACUUGCAACACAAACCACUU	chr9:134473588-134473822(-)$1	234	88	115	18.3541
GAGAUUACACAGAAAAAUAUCUGAAGC	chr11:134180417-134180653(+)$1	236	74	101	19.7474
GAUGGCCACACAGACAACCACUUACCU	chr12:29493977-29494226(-)$1	249	87	114	21.5856
AGGAGCACGCACUUCAUUUUCCAUCCA	chr2:149240749-149241010(+)$1	261	91	118	20.0811
GAAUACACAUACAAACACAUCCUAUAU	chr12:80199933-80200169(-)$1	236	8	35	25.1412
ACAGGCACUGAACGCUAAUCCCUUUUU	chr10:70516196-70516473(+)$1	277	40	67	20.3559
GUUGCACCAAGCAUCCCUCCAGUAAUG	chr20:33329118-33329358(-)$1	240	9	36	21.1062
UCGCACCCUCAUCAUAUUAUGCCUCCA	chr7:107399061-107399331(+)$1	270	70	97	21.6315
AAUGUAAACACAAAUAAACCUCAAACU	chr9:5920448-5920704(-)$1	256	106	133	24.9962
AAAAUCUCCCAAGCUCCUCUCUUAGGU	chr5:56532818-56533099(+)$1	281	156	183	25.2930
GCCACCCCUGUCCCCUCGGCCUGAAAA	chr12:49444826-49445077(-)$1	251	182	209	18.5360
ACUGCUGUCUCUGUAUAUGUUCUGUGA	chr6:53156482-53156758(-)$1	276	157	184	19.6949
AAAGCAUagauggccccagcuuccaau	chr7:155503997-155504243(+)$1	246	176	203	19.9872
CAGCUUCUAACCACCUUCCUGGCUGGG	chr1:169446426-169446701(-)$1	275	226	253	19.6120
UGAAGUUUCUAUUUCUUUUUCAGGUAA	chr11:18536220-18536487(-)$1	267	76	103	17.8303
AAACAUCCCAUUUUGACACUUGUCUUG	chr2:29072689-29072917(-)$1	228	28	55	21.0038
AUCCCACCCCCCAAAAGCCAUGCAGUG	chrX:64721887-64722114(+)$1	227	110	137	25.1412
UCAUGACCCAUCAAGGAAUAAAACCAU	chrX:134421149-134421409(-)$1	260	42	69	24.2321
AUUCUCAUAUCCACUCAAGUCUGUUUU	chr3:182987471-182987706(-)$1	235	112	139	18.9088
UCCGCUUCAAGACCUAUGCACCUGUCG	chr19:3660877-3661092(-)$1	215	52	79	20.4088
AGAGCAUCACCCCUCAUUUUAUAGCUG	chr14:50558072-50558334(-)$1	262	35	62	24.7622
AAGAAAGUAAAGUGUAAUUAAAAUGGA	chr11:16769571-16769801(+)$1	230	135	162	25.2930
AUCUCUCCCUCAUCCUAGCUCAACGGC	chr13:39586983-39587219(-)$1	236	38	65	24.9508
CCACGAACCCAUCCAGAGUGGGAACGU	chr19:57803361-57803591(+)$1	230	56	83	18.9607
UUUCUAUUCCUGAAAAAGAACAGCCAU	chr8:57079199-57079440(-)$1	241	163	190	17.4176
CAUUUCAGACACCAUUUAUGAGCUAUU	chr11:88029209-88029474(-)$1	265	184	211	19.9962
aaaauauuuaauaaaaaucaaaaauua	chr15:50884078-50884320(-)$1	242	14	41	24.8822
uauuuuaugauuuaaaaaauaaauaua	chr11:68216381-68216657(+)$1	276	227	254	19.6120
AAUCAACUCCUCUGCUUUAUCCUCUGC	chr13:39587825-39588050(-)$1	225	110	137	24.7775
ACAUCUCCAUUCCUUAUUCCACUUGGA	chr2:9725280-9725522(-)$1	242	154	181	24.7775
uccuucccuuccuuccuuccuucUGAA	chr4:1215476-1215716(-)$1	240	46	73	24.9962
AACACUCUAGUUAUUACGUGCAUAUUA	chr3:194371480-194371717(-)$1	237	127	154	22.2882
UGGUGGGAGUAUGUUGACGCCACUGUG	chr12:49089772-49090001(-)$1	229	174	201	19.1872
AAAGCCUACCAUGAACAGCUUUCUGUA	chr12:49522189-49522436(-)$1	247	177	204	18.9716
CCACAUCUUACAUCAGCUCUUCACCCA	chr15:68378786-68379050(+)$1	264	199	226	25.1412
CGGGGCUCUCCAGAACAUCAUCCCUGC	chr12:6646736-6646996(+)$1	260	87	114	20.2283
uucauuccauuauuccauaugacaguu	chr6:26452468-26452739(+)$1	271	173	200	19.2990
UCCCAUCCACAUCAUUCCCGCCUCAGC	chr17:42475014-42475290(-)$1	276	156	183	22.8757
CAGCAUCUUCUCUACUUCUGUCUGCAU	chr1:185276991-185277256(-)$1	265	104	131	19.1409
AUGUAGCCAAUCAAAUGUGCACCAAGA	chr17:35800569-35800792(+)$1	223	41	68	18.7611
UCCAGAUCCCACUUACAACUUCCCCAG	chr17:47375772-47376180(-)$1	408	95	122	24.9962
AAAAAAAACCAAAACCCUUUUUAUUug	chr2:20478254-20478517(-)$1	263	178	205	20.4013
AUAACAUUAAACAACACUGUUUUAAUA	chr6:139264612-139264847(-)$1	235	101	128	19.4750
GCAAAUCCAACCAGCAACCAGAAAUGU	chr1:31405914-31406168(-)$1	254	162	189	19.7655
AGGCCCACCACCAACACCUUCACCACC	chr1:151400556-151400807(-)$1	251	10	37	19.5215

#DB
(.(((....................))	chr13:31338104-31338350(+)$1	1	123	150	23.5272
........................)))	chr18:9254753-9254986(+)$1	1	183	210	25.1412
(((((...............)))))))	chr10:38343949-38344282(+)$1	1	147	174	19.6120
.((((..................))))	chr7:104746928-104747159(+)$1	1	159	186	22.6921
(((((....................))	chr12:108147615-108147868(-)$1	1	84	111	23.0994
((.((...................)).	chr2:243402-243662(-)$1	1	165	192	22.7411
..((((.....................	chr17:18832712-18832984(+)$1	1	94	121	21.7765
(((((..................)).)	chr13:39587213-39587577(-)$1	1	106	133	22.2839
((((..................)))).	chr16:22545729-22545989(+)$1	1	1	28	21.1839
(((((............)))))..)))	chr11:19256385-19256608(-)$1	1	71	98	19.3449
(................))))......	chr1:225705409-225705643(-)$1	1	185	212	19.0122
(((.....................)))	chr11:62438631-62438917(-)$1	1	120	147	22.9094
........................)))	chr10:64973398-64973658(-)$1	1	52	79	25.2930
(((((............)))))))...	chr15:58968376-58968624(-)$1	1	111	138	18.9883
(.(((..............))))))))	chr3:57303557-57303778(-)$1	1	178	205	20.8177
..(((......................	chr20:49509422-49509694(-)$1	1	179	206	23.6491
(((((............))))).((((	chr10:38344201-38344476(+)$1	1	126	153	18.2183
(.......................)))	chr16:31196124-31196363(+)$1	1	53	80	25.0696
(.(((..............))).))))	chr17:65941779-65942076(+)$1	1	69	96	21.0341
.((((..................))))	chr1:42657168-42657456(-)$1	1	13	40	21.5818
(((((............))))))((((	chr9:134473588-134473822(-)$1	1	88	115	18.3541
.((((.............))))..)))	chr11:134180417-134180653(+)$1	1	74	101	19.7474
(.(((............)))....)))	chr12:29493977-29494226(-)$1	1	87	114	21.5856
.((((.............))))..)))	chr2:149240749-149241010(+)$1	1	91	118	20.0811
........................)))	chr12:80199933-80200169(-)$1	1	8	35	25.1412
(.(((...............)))))))	chr10:70516196-70516473(+)$1	1	40	67	20.3559
(((((................))))))	chr20:33329118-33329358(-)$1	1	9	36	21.1062
..(((..............)))..)))	chr7:107399061-107399331(+)$1	1	70	97	21.6315
........................)))	chr9:5920448-5920704(-)$1	1	106	133	24.9962
........................)))	chr5:56532818-56533099(+)$1	1	156	183	25.2930
(((..............))).....))	chr12:49444826-49445077(-)$1	1	182	209	18.5360
(..((.............))..)))))	chr6:53156482-53156758(-)$1	1	157	184	19.6949
.((((.............)))).))))	chr7:155503997-155504243(+)$1	1	176	203	19.9872
(((((...............)))))))	chr1:169446426-169446701(-)$1	1	226	253	19.6120
(((((............))))))(((.	chr11:18536220-18536487(-)$1	1	76	103	17.8303
..(((...............)))...)	chr2:29072689-29072917(-)$1	1	28	55	21.0038
........................)))	chrX:64721887-64722114(+)$1	1	110	137	25.1412
..(((...................)))	chrX:134421149-134421409(-)$1	1	42	69	24.2321
(..((............))..)))).)	chr3:182987471-182987706(-)$1	1	112	139	18.9088
...((............))....))).	chr19:3660877-3661092(-)$1	1	52	79	20.4088
((......................)))	chr14:50558072-50558334(-)$1	1	35	62	24.7622
........................)))	chr11:16769571-16769801(+)$1	1	135	162	25.2930
........................)))	chr13:39586983-39587219(-)$1	1	38	65	24.9508
((((.............))))).)).)	chr19:57803361-57803591(+)$1	1	56	83	18.9607
.((((...........))))....)))	chr8:57079199-57079440(-)$1	1	163	190	17.4176
(((..............)))))).)))	chr11:88029209-88029474(-)$1	1	184	211	19.9962
(.......................)))	chr15:50884078-50884320(-)$1	1	14	41	24.8822
(((((...............)))))))	chr11:68216381-68216657(+)$1	1	227	254	19.6120
........................)).	chr13:39587825-39588050(-)$1	1	110	137	24.7775
........................)).	chr2:9725280-9725522(-)$1	1	154	181	24.7775
........................)))	chr4:1215476-1215716(-)$1	1	46	73	24.9962
..(((............)))....)))	chr3:194371480-194371717(-)$1	1	127	154	22.2882
(((((............))))).))).	chr12:49089772-49090001(-)$1	1	174	201	19.1872
(((((............))))))).))	chr12:49522189-49522436(-)$1	1	177	204	18.9716
........................)))	chr15:68378786-68379050(+)$1	1	199	226	25.1412
(((((................))))))	chr12:6646736-6646996(+)$1	1	87	114	20.2283
.((((.............)))))))))	chr6:26452468-26452739(+)$1	1	173	200	19.2990
...................))...)))	chr17:42475014-42475290(-)$1	1	156	183	22.8757
(((((.............)).))))).	chr1:185276991-185277256(-)$1	1	104	131	19.1409
.((((............))))))..).	chr17:35800569-35800792(+)$1	1	41	68	18.7611
........................)))	chr17:47375772-47376180(-)$1	1	95	122	24.9962
(((..............))))))))))	chr2:20478254-20478517(-)$1	1	178	205	20.4013
(((..............))))))...)	chr6:139264612-139264847(-)$1	1	101	128	19.4750
(................))))...)).	chr1:31405914-31406168(-)$1	1	162	189	19.7655
(((..............))))))...)	chr1:151400556-151400807(-)$1	1	10	37	19.5215

#PSSM
^ : 0.21	e : 0.13	g : 0.12	f : 0.10	d : 0.09	# : 0.07	! : 0.06	" : 0.06	c : 0.03	b : 0.01	h : 0.01	: : 0.01	i : 0.01	[ : 0.01	= : 0.01	
^ : 0.24	d : 0.15	g : 0.10	e : 0.10	[ : 0.07	f : 0.07	" : 0.04	# : 0.04	! : 0.04	y : 0.03	c : 0.03	h : 0.01	= : 0.01	
^ : 0.26	c : 0.18	d : 0.15	e : 0.10	g : 0.09	f : 0.07	y : 0.03	! : 0.03	[ : 0.01	h : 0.01	# : 0.01	= : 0.01	
^ : 0.27	c : 0.15	d : 0.15	g : 0.09	b : 0.09	e : 0.07	w : 0.07	f : 0.04	y : 0.03	
^ : 0.29	c : 0.15	d : 0.13	g : 0.09	b : 0.09	w : 0.07	e : 0.06	f : 0.04	y : 0.03	v : 0.01	
^ : 0.41	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	d : 0.01	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	t : 0.01	
^ : 0.43	u : 0.18	w : 0.12	v : 0.10	x : 0.07	y : 0.06	d : 0.01	
^ : 0.43	v : 0.09	x : 0.07	e : 0.06	d : 0.06	f : 0.06	c : 0.06	w : 0.04	g : 0.03	y : 0.03	b : 0.03	= : 0.01	
^ : 0.43	d : 0.12	x : 0.07	e : 0.06	f : 0.06	c : 0.06	b : 0.06	w : 0.04	g : 0.03	y : 0.03	= : 0.01	
^ : 0.41	d : 0.12	c : 0.10	x : 0.07	e : 0.06	f : 0.06	b : 0.04	g : 0.03	y : 0.03	2 : 0.01	4 : 0.01	= : 0.01	
^ : 0.41	d : 0.10	c : 0.09	g : 0.07	e : 0.06	f : 0.06	4 : 0.06	y : 0.03	2 : 0.03	5 : 0.01	b : 0.01	] : 0.01	= : 0.01	
^ : 0.41	g : 0.09	c : 0.09	e : 0.07	f : 0.07	d : 0.07	4 : 0.06	3 : 0.03	> : 0.01	5 : 0.01	2 : 0.01	b : 0.01	= : 0.01	
^ : 0.40	g : 0.09	f : 0.09	2 : 0.06	] : 0.06	4 : 0.06	d : 0.04	c : 0.04	e : 0.03	3 : 0.03	> : 0.01	: : 0.01	5 : 0.01	b : 0.01	= : 0.01	
^ : 0.35	g : 0.10	d : 0.09	2 : 0.07	3 : 0.07	f : 0.04	e : 0.04	4 : 0.04	c : 0.04	b : 0.03	> : 0.01	i : 0.01	5 : 0.01	] : 0.01	= : 0.01	
g : 0.18	d : 0.16	e : 0.13	b : 0.09	c : 0.09	f : 0.07	^ : 0.06	3 : 0.06	h : 0.03	> : 0.01	i : 0.01	5 : 0.01	] : 0.01	2 : 0.01	= : 0.01	
g : 0.18	d : 0.16	e : 0.15	c : 0.10	f : 0.07	b : 0.06	3 : 0.06	] : 0.04	^ : 0.03	h : 0.03	= : 0.03	> : 0.01	i : 0.01	a : 0.01	
e : 0.18	g : 0.18	d : 0.15	f : 0.10	c : 0.07	] : 0.06	2 : 0.04	^ : 0.03	: : 0.03	h : 0.03	= : 0.03	> : 0.01	3 : 0.01	i : 0.01	n : 0.01	

#score	1402.1045764453797
#seq	65
#width	27
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_UTR_m2_run2.txt

#BEAR
i[ddddqqqqqqqqdddd>>>	chr19:2251801-2252060(+)$1	259	192	213	15.3700
eee[bbqqqqqqqqbbeeeee	chr12:120125869-120126098(+)$1	229	126	147	14.0639
ceeeeeqqqqqqqqeeeee]c	chr16:50350886-50351145(+)$1	259	199	220	15.2642
bb[cccqqqqqqqqccc]bb:	chr15:41795556-41795785(+)$1	229	191	212	13.5219
[a!!bbqqqqqqqqbb22a]c	chr5:149012875-149013134(-)$1	259	211	232	14.0702
d!!cccqqqqqqqqccc22dd	chr4:6114554-6114813(+)$1	259	149	170	15.6349
e[ddddqqqqqqqqddddeee	chr12:112591289-112591518(+)$1	229	206	227	15.6613
ceeeeeqqqqqqqqeeeee22	chr7:70256614-70256843(-)$1	229	109	130	15.0352
b!!cccqqqqqqqqccc22bb	chr12:109971553-109971813(+)$1	260	165	186	15.4234
e!!cccqqqqqqqqccc]eee	chr6:20491553-20491812(+)$1	259	44	65	15.7280
c[ddddqqqqqqqqdddd333	chr10:122664743-122664972(-)$1	229	106	127	16.3677
[eeeeeqqqqqqqqeeeeeff	chr5:72877274-72877533(+)$1	259	108	129	15.0554
[eeeeeqqqqqqqqeeeee]e	chr1:24021277-24021536(+)$1	259	27	48	15.3470
ceeeeeqqqqqqqqeeeee]c	chr1:110602472-110602731(-)$1	259	101	122	15.2642
:eeeeeqqqqqqqqeeeeedd	chr4:2930757-2930986(+)$1	229	82	103	14.1402
""ddddqqqqqqqqdddd444	chr19:15770177-15770406(+)$1	229	48	69	16.1291
e!!cccqqqqqqqqccc22ee	chr16:30905244-30905473(+)$1	229	139	160	15.8261
dddd[aqqqqqqqqa]dddd2	chr9:5919607-5919867(+)$1	260	127	148	14.1307
ffffffqqqqqqqqffffff3	chr7:99170024-99170283(+)$1	259	206	227	13.1206
"""cccqqqqqqqqccc22gg	chr2:65539690-65539949(+)$1	259	118	139	15.8116
"eeeeeqqqqqqqqeeeee33	chr6:27371386-27371645(-)$1	259	156	177	15.6524
a[ddddqqqqqqqqdddd]a2	chr12:122326659-122326918(+)$1	259	225	246	15.8653
:eeeeeqqqqqqqqeeeeegg	chr17:46326108-46326367(-)$1	259	101	122	14.2982
eeddddqqqqqqqqdddd]ee	chr16:66600094-66600353(-)$1	259	5	26	15.5176
c!!cccqqqqqqqqccc22cc	chr2:69702284-69702513(+)$1	229	124	145	15.9692
!a[cccqqqqqqqqccc]a]a	chr19:54740748-54740977(+)$1	229	9	30	15.7160
c[ddddqqqqqqqqddddccc	chr22:41347275-41347504(+)$1	229	187	208	15.6781
ccccccqqqqqqqqccc]ccc	chr2:23930291-23930550(+)$1	259	72	93	15.1259
gggcccqqqqqqqqccc22gg	chr13:111957550-111957809(-)$1	259	226	247	15.3928
:eeeeeqqqqqqqqeeeeebb	chr3:45724643-45724902(+)$1	259	178	199	13.9642
eee[bbqqqqqqqqbb]eeee	chr2:69473229-69473488(+)$1	259	233	254	13.9240
b[ddddqqqqqqqqddddbbi	chr22:50618037-50618296(+)$1	259	119	140	15.0028
d[ddddqqqqqqqqddddddd	chr17:46196236-46196465(+)$1	229	172	193	15.2938
eee[bbqqqqqqqqbb]eeee	chr2:240274438-240274697(-)$1	259	94	115	13.9240
eeecccqqqqqqqqcccdddd	chr16:19073302-19073531(+)$1	229	72	93	15.1179
#cccbbqqqqqqqqbb]ccc2	chr14:74873485-74873744(+)$1	259	26	47	13.6376
ggggggqqqqqqqqggggggg	chr3:46751984-46752213(+)$1	229	94	115	14.2137
"eeeeeqqqqqqqqeeeee]d	chr1:161493174-161493403(+)$1	229	34	55	15.3120
dd[cccqqqqqqqqcccdddd	chr22:18613727-18613986(-)$1	259	217	238	14.8529
[addddqqqqqqqqdddd]a]	chr17:47590898-47591127(+)$1	229	66	87	15.7041
g!!cccqqqqqqqqcccgggg	chr2:68870787-68871016(+)$1	229	172	193	15.5690
ccc!!aqqqqqqqqa22cccc	chr4:151178364-151178623(-)$1	259	98	119	13.5583
cc!!bbqqqqqqqqbb22ccc	chr3:127454857-127455116(+)$1	259	169	190	13.7122
c!!cccqqqqqqqqccc22cc	chr2:171807734-171807993(+)$1	259	73	94	15.9692
ff[cccqqqqqqqqccc]fff	chr4:467843-468102(+)$1	259	9	30	14.8219
[eeeeeqqqqqqqqeeeeeee	chr16:57220363-57220622(+)$1	259	23	44	15.2020
""ddddqqqqqqqqdddd333	chr5:112353070-112353329(-)$1	259	66	87	16.4167
eeecccqqqqqqqqccc]eee	chr17:27870028-27870287(+)$1	259	150	171	15.4213
d[ddddqqqqqqqqdddd]dd	chr7:138518008-138518267(-)$1	259	77	98	15.5479
!!ddddqqqqqqqqdddd22b	chr5:122758864-122759123(+)$1	259	73	94	15.8234
[eeeeeqqqqqqqqeeeee]a	chr7:150646584-150646843(+)$1	259	56	77	15.3830
e[ddddqqqqqqqqdddd]ee	chr5:138264916-138265145(-)$1	229	88	109	15.7390
""ddddqqqqqqqqdddd333	chr22:46725918-46726177(+)$1	259	151	172	16.4167
b!!cccqqqqqqqqccc22bb	chr4:107156372-107156631(+)$1	259	197	218	15.4234
#eeeeeqqqqqqqqeeeee33	chr18:77663647-77663906(+)$1	259	130	151	15.6159
b!!cccqqqqqqqqccc22bb	chr2:242606126-242606385(+)$1	259	3	24	15.4234
b!!cccqqqqqqqqccc22bb	chr4:57301609-57301868(+)$1	259	80	101	15.4234
e[ddddqqqqqqqqdddd333	chr18:12657795-12658054(+)$1	259	114	135	16.3000
cc[cccqqqqqqqqcccccce	chr5:112359881-112360110(+)$1	229	24	45	15.1039
"eeeeeqqqqqqqqeeeee]e	chr15:82576800-82577029(+)$1	229	13	34	15.3799
a[ddddqqqqqqqqddddabb	chr2:7179766-7180025(+)$1	259	132	153	15.4067
eeddddqqqqqqqqdddd444	chr4:38699186-38699445(-)$1	259	94	115	15.7909

#otherMatches

#Seq PSSM
ACGCGCCCCAGCUCGCGCCCC	chr19:2251801-2252060(+)$1	259	192	213	15.3700
CCUGCAGAUCAAGAUGAGGAG	chr12:120125869-120126098(+)$1	229	126	147	14.0639
ggcagcucuCAUGUGCUGCAC	chr16:50350886-50351145(+)$1	259	199	220	15.2642
GAUGCAGCUUCCUGUGCCUCA	chr15:41795556-41795785(+)$1	229	191	212	13.5219
UAUACUGAUGAACAAGGUUUG	chr5:149012875-149013134(-)$1	259	211	232	14.0702
AAACCACCAUCACUUGGGAUC	chr4:6114554-6114813(+)$1	259	149	170	15.6349
GUGAGCAGGGCUGGGCUUUCU	chr12:112591289-112591518(+)$1	229	206	227	15.6613
CGUUUGAAAAAAAACAAGCAA	chr7:70256614-70256843(-)$1	229	109	130	15.0352
ggcgcagacucgaaugcuacu	chr12:109971553-109971813(+)$1	260	165	186	15.4234
AGAGCAUCUAAACCUGUGUGA	chr6:20491553-20491812(+)$1	259	44	65	15.7280
CAGCCUUAUCUAUCAGGCAGA	chr10:122664743-122664972(-)$1	229	106	127	16.3677
AGAUUUUGUAAUGCGAAUCUC	chr5:72877274-72877533(+)$1	259	108	129	15.0554
GCUCCUGGUCUGUGAGGAGAG	chr1:24021277-24021536(+)$1	259	27	48	15.3470
GAUUUCUACAGACUGAGAUCC	chr1:110602472-110602731(-)$1	259	101	122	15.2642
AACGUGAUGCUAUGCAUGUCU	chr4:2930757-2930986(+)$1	229	82	103	14.1402
AAAUGACCCCUgauucaucaa	chr19:15770177-15770406(+)$1	229	48	69	16.1291
GCCGCGCCCUCUCUCGUCCCC	chr16:30905244-30905473(+)$1	229	139	160	15.8261
GAAGACAGACGCAGGACUUCG	chr9:5919607-5919867(+)$1	260	127	148	14.1307
ACCAGAAUUCAGCCUCUGGUA	chr7:99170024-99170283(+)$1	259	206	227	13.1206
GGCUCAUAGAAACCUGAAAUC	chr2:65539690-65539949(+)$1	259	118	139	15.8116
AAUGGGCCAAAAUACCUAUGA	chr6:27371386-27371645(-)$1	259	156	177	15.6524
UGACGUGCUGGAAAGCGUGAG	chr12:122326659-122326918(+)$1	259	225	246	15.8653
UUCUUAUCUAAACUUGGGGUA	chr17:46326108-46326367(-)$1	259	101	122	14.2982
GCGUCGCGUCCCAACGGCUGU	chr16:66600094-66600353(-)$1	259	5	26	15.5176
GCUGGGCUCAAUUUCUCUUCU	chr2:69702284-69702513(+)$1	229	124	145	15.9692
gaggcuggcaagggagugugg	chr19:54740748-54740977(+)$1	229	9	30	15.7160
CGCUUUGAAGUGAAAAAGGUU	chr22:41347275-41347504(+)$1	229	187	208	15.6781
UCUCAUUUUUCUAUGUGCAGA	chr2:23930291-23930550(+)$1	259	72	93	15.1259
CCUGCUCCCUAAAAAGCCGAG	chr13:111957550-111957809(-)$1	259	226	247	15.3928
aggaaaaccccaacuuuccac	chr3:45724643-45724902(+)$1	259	178	199	13.9642
AUCAUGUUAAAAAUCAAGGUU	chr2:69473229-69473488(+)$1	259	233	254	13.9240
CAUGGGGUCACAUGCUCAGGG	chr22:50618037-50618296(+)$1	259	119	140	15.0028
GAGAUAGAAGCCUGUGUCCAG	chr17:46196236-46196465(+)$1	229	172	193	15.2938
AGAAGCCAGCGGACGCCUCUG	chr2:240274438-240274697(-)$1	259	94	115	13.9240
UUUGCCUGCAGACCGGCCACU	chr16:19073302-19073531(+)$1	229	72	93	15.1179
UCAGGACCCUCUAUUCUCUGU	chr14:74873485-74873744(+)$1	259	26	47	13.6376
AGCAGGGCCUUCUGCCUGCUG	chr3:46751984-46752213(+)$1	229	94	115	14.2137
UCCUCCAGCCUUUAGGAGGUA	chr1:161493174-161493403(+)$1	229	34	55	15.3120
GCACAAAGGCCCGCUUGGCGU	chr22:18613727-18613986(-)$1	259	217	238	14.8529
gaggcccagggagaggccaug	chr17:47590898-47591127(+)$1	229	66	87	15.7041
CCGGGCUCCGCGAUGCCGCAG	chr2:68870787-68871016(+)$1	229	172	193	15.5690
GAGAACGAACUAUAGGGCUCG	chr4:151178364-151178623(-)$1	259	98	119	13.5583
UAUUGUUAAGUAUCACUUUAA	chr3:127454857-127455116(+)$1	259	169	190	13.7122
GAAACAUUUUCUCCUGUGACA	chr2:171807734-171807993(+)$1	259	73	94	15.9692
CUCUGGCAAAAUCACCGAGGC	chr4:467843-468102(+)$1	259	9	30	14.8219
CUGCUCUGAGCCCUGGGCACG	chr16:57220363-57220622(+)$1	259	23	44	15.2020
CAUCUUUCUGACACAGGAGUA	chr5:112353070-112353329(-)$1	259	66	87	16.4167
AAAGCGUUCUGUUUUGUGUUU	chr17:27870028-27870287(+)$1	259	150	171	15.4213
UAGGAGUCUCCCGUUUCCCGU	chr7:138518008-138518267(-)$1	259	77	98	15.5479
CAGUCUGCAAGCAGAGACAAG	chr5:122758864-122759123(+)$1	259	73	94	15.8234
guguauuuguguuuguacaga	chr7:150646584-150646843(+)$1	259	56	77	15.3830
GCGCUUCCUUACCCGGGCACU	chr5:138264916-138265145(-)$1	229	88	109	15.7390
GUUUUCAACCCUCAGAAACAA	chr22:46725918-46726177(+)$1	259	151	172	16.4167
CCAUCUUUUAGUCUAGACAGU	chr4:107156372-107156631(+)$1	259	197	218	15.4234
CCGCUGAGCACAAACAGCGUC	chr18:77663647-77663906(+)$1	259	130	151	15.6159
CAACGGAUUCCCUGCCGGAGC	chr2:242606126-242606385(+)$1	259	3	24	15.4234
GUAAGCACCAACCAGCUGCCA	chr4:57301609-57301868(+)$1	259	80	101	15.4234
GUCUCCUCAGCUCCGGAGCAU	chr18:12657795-12658054(+)$1	259	114	135	16.3000
CAAUUUUAAAAGUUAAGUGCU	chr5:112359881-112360110(+)$1	229	24	45	15.1039
GUAGGUAAUUUUGCACCUAAU	chr15:82576800-82577029(+)$1	229	13	34	15.3799
GCGAUGCUGGAACACAUCCCU	chr2:7179766-7180025(+)$1	259	132	153	15.4067
UGCAAGGGGCCACACUUGUUU	chr4:38699186-38699445(-)$1	259	94	115	15.7909

#DB
(.((((........))))...	chr19:2251801-2252060(+)$1	1	192	213	15.3700
(((.((........)))))))	chr12:120125869-120126098(+)$1	1	126	147	14.0639
((((((........))))).)	chr16:50350886-50351145(+)$1	1	199	220	15.2642
((.(((........))).)).	chr15:41795556-41795785(+)$1	1	191	212	13.5219
.(..((........))..).)	chr5:149012875-149013134(-)$1	1	211	232	14.0702
(..(((........)))..))	chr4:6114554-6114813(+)$1	1	149	170	15.6349
(.((((........)))))))	chr12:112591289-112591518(+)$1	1	206	227	15.6613
((((((........)))))..	chr7:70256614-70256843(-)$1	1	109	130	15.0352
(..(((........)))..))	chr12:109971553-109971813(+)$1	1	165	186	15.4234
(..(((........))).)))	chr6:20491553-20491812(+)$1	1	44	65	15.7280
(.((((........))))...	chr10:122664743-122664972(-)$1	1	106	127	16.3677
.(((((........)))))))	chr5:72877274-72877533(+)$1	1	108	129	15.0554
.(((((........))))).)	chr1:24021277-24021536(+)$1	1	27	48	15.3470
((((((........))))).)	chr1:110602472-110602731(-)$1	1	101	122	15.2642
.(((((........)))))((	chr4:2930757-2930986(+)$1	1	82	103	14.1402
..((((........))))...	chr19:15770177-15770406(+)$1	1	48	69	16.1291
(..(((........)))..))	chr16:30905244-30905473(+)$1	1	139	160	15.8261
((((.(........).)))).	chr9:5919607-5919867(+)$1	1	127	148	14.1307
((((((........)))))).	chr7:99170024-99170283(+)$1	1	206	227	13.1206
...(((........)))..))	chr2:65539690-65539949(+)$1	1	118	139	15.8116
.(((((........)))))..	chr6:27371386-27371645(-)$1	1	156	177	15.6524
(.((((........)))).).	chr12:122326659-122326918(+)$1	1	225	246	15.8653
.(((((........)))))((	chr17:46326108-46326367(-)$1	1	101	122	14.2982
((((((........)))).))	chr16:66600094-66600353(-)$1	1	5	26	15.5176
(..(((........)))..))	chr2:69702284-69702513(+)$1	1	124	145	15.9692
.(.(((........))).).)	chr19:54740748-54740977(+)$1	1	9	30	15.7160
(.((((........)))))))	chr22:41347275-41347504(+)$1	1	187	208	15.6781
((((((........))).)))	chr2:23930291-23930550(+)$1	1	72	93	15.1259
((((((........)))..))	chr13:111957550-111957809(-)$1	1	226	247	15.3928
.(((((........)))))((	chr3:45724643-45724902(+)$1	1	178	199	13.9642
(((.((........)).))))	chr2:69473229-69473488(+)$1	1	233	254	13.9240
(.((((........)))))))	chr22:50618037-50618296(+)$1	1	119	140	15.0028
(.((((........)))))))	chr17:46196236-46196465(+)$1	1	172	193	15.2938
(((.((........)).))))	chr2:240274438-240274697(-)$1	1	94	115	13.9240
)))(((........)))((((	chr16:19073302-19073531(+)$1	1	72	93	15.1179
.(((((........)).))).	chr14:74873485-74873744(+)$1	1	26	47	13.6376
((((((........)))))))	chr3:46751984-46752213(+)$1	1	94	115	14.2137
.(((((........))))).)	chr1:161493174-161493403(+)$1	1	34	55	15.3120
((.(((........)))))))	chr22:18613727-18613986(-)$1	1	217	238	14.8529
.(((((........)))).).	chr17:47590898-47591127(+)$1	1	66	87	15.7041
(..(((........)))))))	chr2:68870787-68871016(+)$1	1	172	193	15.5690
(((..(........)..)))(	chr4:151178364-151178623(-)$1	1	98	119	13.5583
((..((........))..)))	chr3:127454857-127455116(+)$1	1	169	190	13.7122
(..(((........)))..))	chr2:171807734-171807993(+)$1	1	73	94	15.9692
((.(((........))).)))	chr4:467843-468102(+)$1	1	9	30	14.8219
.(((((........)))))))	chr16:57220363-57220622(+)$1	1	23	44	15.2020
..((((........))))...	chr5:112353070-112353329(-)$1	1	66	87	16.4167
((((((........))).)))	chr17:27870028-27870287(+)$1	1	150	171	15.4213
(.((((........)))).))	chr7:138518008-138518267(-)$1	1	77	98	15.5479
..((((........))))..)	chr5:122758864-122759123(+)$1	1	73	94	15.8234
.(((((........))))).)	chr7:150646584-150646843(+)$1	1	56	77	15.3830
(.((((........)))).))	chr5:138264916-138265145(-)$1	1	88	109	15.7390
..((((........))))...	chr22:46725918-46726177(+)$1	1	151	172	16.4167
(..(((........)))..))	chr4:107156372-107156631(+)$1	1	197	218	15.4234
.(((((........)))))..	chr18:77663647-77663906(+)$1	1	130	151	15.6159
(..(((........)))..))	chr2:242606126-242606385(+)$1	1	3	24	15.4234
(..(((........)))..))	chr4:57301609-57301868(+)$1	1	80	101	15.4234
(.((((........))))...	chr18:12657795-12658054(+)$1	1	114	135	16.3000
((.(((........)))))))	chr5:112359881-112360110(+)$1	1	24	45	15.1039
.(((((........))))).)	chr15:82576800-82577029(+)$1	1	13	34	15.3799
(.((((........)))))))	chr2:7179766-7180025(+)$1	1	132	153	15.4067
((((((........))))...	chr4:38699186-38699445(-)$1	1	94	115	15.7909

#PSSM
e : 0.19	c : 0.17	" : 0.11	b : 0.09	[ : 0.09	d : 0.08	: : 0.04	g : 0.04	f : 0.03	a : 0.03	! : 0.03	# : 0.03	i : 0.01	
e : 0.33	[ : 0.17	! : 0.17	c : 0.08	" : 0.06	a : 0.04	d : 0.03	f : 0.03	g : 0.03	b : 0.01	
d : 0.30	e : 0.30	! : 0.19	[ : 0.08	c : 0.04	g : 0.03	f : 0.01	" : 0.01	
c : 0.33	d : 0.30	e : 0.22	[ : 0.04	! : 0.04	f : 0.01	g : 0.01	
c : 0.32	d : 0.29	e : 0.22	b : 0.09	[ : 0.01	f : 0.01	g : 0.01	! : 0.01	
c : 0.32	d : 0.29	e : 0.22	b : 0.09	a : 0.03	f : 0.01	g : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.32	d : 0.29	e : 0.22	b : 0.09	a : 0.03	f : 0.01	g : 0.01	
c : 0.32	d : 0.29	e : 0.22	b : 0.09	] : 0.01	f : 0.01	g : 0.01	2 : 0.01	
c : 0.32	d : 0.30	e : 0.24	2 : 0.04	] : 0.04	f : 0.01	g : 0.01	
d : 0.33	e : 0.27	2 : 0.19	] : 0.09	c : 0.04	g : 0.03	f : 0.01	
e : 0.32	2 : 0.17	c : 0.09	] : 0.08	3 : 0.06	d : 0.06	a : 0.04	b : 0.03	4 : 0.03	f : 0.03	g : 0.03	> : 0.01	
e : 0.16	] : 0.12	b : 0.12	c : 0.12	d : 0.11	3 : 0.09	g : 0.08	f : 0.04	2 : 0.03	4 : 0.03	a : 0.03	> : 0.01	
e : 0.20	c : 0.14	d : 0.11	b : 0.11	3 : 0.11	g : 0.08	2 : 0.06	f : 0.03	4 : 0.03	a : 0.03	> : 0.01	: : 0.01	i : 0.01	] : 0.01	

#score	940.5794363689719
#seq	62
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013b_hg19_UTR_m1_run1.txt

#BEAR
g[ccceeeeettttttttttteeeee66	chr3:167401647-167401876(-)$1	229	31	59	23.0899
ccc!!cccxxxxxxxxxxxxxxxccc]c	chr17:79478128-79478371(-)$1	243	171	199	19.3968
bbggggggguuuuuuuuuuuuggggggg	chrX:24004911-24005157(-)$1	246	144	172	24.4140
!!ggggggguuuuuuuuuuuuggggggg	chr13:20660653-20660893(+)$1	240	10	38	25.1353
dddd:dddduuuuuuuuuuuuddddggg	chr17:61898841-61899063(-)$1	222	114	142	22.7268
==========ttttttttttt=======	chr1:150547237-150547481(-)$1	244	154	182	25.0243
fff[cccbbwwwwwwwwwwwwwwbb]cc	chr17:61823531-61823798(-)$1	267	147	175	21.8992
eeee!!cccvvvvvvvvvvvvvccceee	chr1:145441644-145441913(+)$1	269	141	169	24.1413
ccc"""cccuuuuuuuuuuuuccc333c	chr11:9610329-9610580(+)$1	251	209	237	25.0620
eeee[ddddvvvvvvvvvvvvvdddd]e	chr8:91636783-91637005(-)$1	222	179	207	23.7679
==dddd[ccctttttttttttccc]ddd	chr6:15520704-15520930(+)$1	226	71	99	23.4927
=========vvvvvvvvvvvvv======	chr11:4127304-4127536(+)$1	232	177	205	25.3501
ii"""ddddattttttttttta]dddd]	chr1:205683181-205683443(-)$1	262	108	136	24.5847
eeeeecccwwwwwwwwwwwwwwccc]ee	chr16:30958513-30958763(+)$1	250	81	109	23.0118
ddd[fffffftttttttttttffffff]	chr2:20232822-20233085(-)$1	263	153	181	22.7749
[a!!eeeeeuuuuuuuuuuuueeeee]a	chr6:36654244-36654504(+)$1	260	47	75	25.3447
!!eeeeeyyyyyyyyyyyyyyyyeeeee	chr7:98957223-98957448(+)$1	225	118	146	23.6341
$$$$$eeeeettttttttttteeeee55	chr5:142660940-142661171(-)$1	231	10	38	21.7267
dddffffffvvvvvvvvvvvvvffffff	chr8:104344435-104344666(+)$1	231	127	155	22.8324
dddd!!cccvvvvvvvvvvvvvccc22d	chr19:47113877-47114105(+)$1	228	105	133	23.6010
dddd[bbyyyyyyyyyyyyyyyybb]dd	chr16:3631090-3631324(-)$1	234	108	136	21.6793
e[bbddddwwwwwwwwwwwwwwdddd]b	chr7:95034283-95034508(-)$1	225	22	50	22.3042
:dddd[cccvvvvvvvvvvvvvccc]dd	chr3:184052434-184052677(+)$1	243	143	171	22.6643
::eeeeebbuuuuuuuuuuuubb]eeee	chr1:200827650-200827904(+)$1	254	82	110	21.7425
"""eeeeevvvvvvvvvvvvveeeee]b	chr16:29822248-29822489(+)$1	241	146	174	24.1566
gg[ccc[bbtttttttttttbb]cccgg	chr6:31802939-31803189(+)$1	250	18	46	22.5856
eeegggggggtttttttttttggggggg	chr17:8076700-8076952(-)$1	252	140	168	23.6415
ddd[eeeeeuuuuuuuuuuuueeeee]d	chr13:23903512-23903741(-)$1	229	1	29	24.5901
::ggggggguuuuuuuuuuuuggggggg	chr11:10818831-10819083(-)$1	252	134	162	22.9439
ffffffa[awwwwwwwwwwwwwwa]a]f	chr17:46684696-46684939(-)$1	243	206	234	22.4792
ii"""ddddattttttttttta]dddd]	chr1:205683147-205683375(-)$1	228	40	68	24.5847
======yyyyyyyyyyyyyyyy======	chr5:10433993-10434243(+)$1	250	60	88	24.3311
!ffffffyyyyyyyyyyyyyyyyfffff	chr19:59061839-59062125(+)$1	286	127	155	22.8544
!gggggggwwwwwwwwwwwwwwgggggg	chr10:70104032-70104264(-)$1	232	131	159	23.7666
[ccc!!ddddtttttttttttdddd444	chr1:92146220-92146462(-)$1	242	43	71	23.7010
g"""eeeeeuuuuuuuuuuuueeeee22	chr6:109688686-109688943(-)$1	257	37	65	24.8908
[ccccccyyyyyyyyyyyyyyyyccc]c	chr8:38962000-38962235(+)$1	235	135	163	23.7341
:bb[eeeeevvvvvvvvvvvvveeeeeb	chr7:27202717-27202969(-)$1	252	58	86	22.7782
======yyyyyyyyyyyyyyyy======	chr22:22117846-22118111(-)$1	265	131	159	24.3311
iiiiiiawwwwwwwwwwwwwwa]iiiii	chr1:156435200-156435446(-)$1	246	213	241	23.4595
=====ddddvvvvvvvvvvvvvdddd]=	chr22:20228946-20229186(-)$1	240	197	225	24.6302
h"""eeeeeuuuuuuuuuuuueeeee44	chrX:123234721-123234952(+)$1	231	59	87	25.0196
fccc[dddduuuuuuuuuuuudddd]cc	chr13:80910064-80910288(-)$1	224	59	87	24.1633
eeee[cccwwwwwwwwwwwwwwccceee	chr2:61764614-61764913(-)$1	299	161	189	23.1803
eee[fffffftttttttttttffffff]	chr3:156260426-156260647(-)$1	221	124	152	22.9399
!iiiiiiiiitttttttttttiiiiiii	chr2:55199824-55200076(-)$1	252	45	73	24.3819
bbb[eeeeeuuuuuuuuuuuueeeee22	chr1:33764766-33764996(+)$1	230	101	129	24.0498
ffffff[ccctttttttttttccc]fff	chr1:244219676-244219904(+)$1	228	93	121	23.3751
iiiiiiiiivvvvvvvvvvvvviiiiii	chr5:109202646-109202872(+)$1	226	187	215	24.8312
[a[eeeeevvvvvvvvvvvvveeeee]a	chr12:111180513-111180745(-)$1	232	156	184	24.2627
fffffyyyyyyyyyyyyyyyyffffffg	chr9:117406627-117406861(+)$1	234	2	30	21.5100
c[bb!!cccvvvvvvvvvvvvvccc22b	chr20:17922647-17922888(-)$1	241	68	96	23.6042
"""dddd[bbtttttttttttbbdddd4	chr5:112213915-112214152(-)$1	237	182	210	22.9562
###gggggggtttttttttttggggggg	chr19:46190653-46190905(-)$1	252	155	183	24.0861
fff[cccccctttttttttttccc]ccc	chr1:6281476-6281700(-)$1	224	139	167	23.8165
ii"""eeeeettttttttttteeeee]i	chr22:32353086-32353328(+)$1	242	153	181	24.6149
gg"""dddduuuuuuuuuuuudddd444	chr1:153920233-153920481(-)$1	248	57	85	24.7370
eeeeeeeyyyyyyyyyyyyyyyyeeeee	chr2:135712629-135712860(+)$1	231	169	197	23.1846
iiiiiiiiivvvvvvvvvvvvviiiiii	chr7:94298772-94299006(+)$1	234	43	71	24.8312
"""ddddyyyyyyyyyyyyyyyydddd7	chr19:47112446-47112739(+)$1	293	124	152	22.6804
"ffffff[auuuuuuuuuuuua]fffff	chr10:74035579-74035801(+)$1	222	112	140	24.3555
iiiiiiiiiuuuuuuuuuuuuiiiiiii	chr11:118405697-118405920(+)$1	223	87	115	25.3160
cbb[fffffftttttttttttffffff]	chr19:50001075-50001323(+)$1	248	204	232	22.7417

#otherMatches

#Seq PSSM
GCCUUAAUGUGUCAUUAUAUAACAUUCC	chr3:167401647-167401876(-)$1	229	31	59	23.0899
GCUAAAGGUUUCUACUCUUACAUCCUCG	chr17:79478128-79478371(-)$1	243	171	199	19.3968
GCAUUUAGGUAAUACCAGACUCCUAAAU	chrX:24004911-24005157(-)$1	246	144	172	24.4140
uugguuuuACAUUUUAGUUACUGAAGCC	chr13:20660653-20660893(+)$1	240	10	38	25.1353
GCCCAGCUGUUAUUUGAGAACCGGCGGA	chr17:61898841-61899063(-)$1	222	114	142	22.7268
CAAAUCCUCCAAAAGGGAAAGGGAGGAU	chr1:150547237-150547481(-)$1	244	154	182	25.0243
GCUGAUAACAAAAUUAAUAGGAAGUCUG	chr17:61823531-61823798(-)$1	267	147	175	21.8992
GCUUUCCCUGUGAUUAUAAAAAAGGAAG	chr1:145441644-145441913(+)$1	269	141	169	24.1413
CAUUACUACUCAGCCUUCAAUGUACCUG	chr11:9610329-9610580(+)$1	251	209	237	25.0620
UUUUUUCAGUACUUGUUUUUCUCUGAUA	chr8:91636783-91637005(-)$1	222	179	207	23.7679
UUGGUUUUGAUUUUUUUUUUUUUGUAAC	chr6:15520704-15520930(+)$1	226	71	99	23.4927
UAGUACUCUCAGAAAAGUAAUAAGGGUA	chr11:4127304-4127536(+)$1	232	177	205	25.3501
UAAAAACCCCUGAAGUAUUGUGUGGGUG	chr1:205683181-205683443(-)$1	262	108	136	24.5847
CCUCCGGCUUCAUUUCACCCCUGCUGGG	chr16:30958513-30958763(+)$1	250	81	109	23.0118
AGCUUUUUGUUUGUUUAUGUUACAGAAU	chr2:20232822-20233085(-)$1	263	153	181	22.7749
UGUUGAGCCUUUUCCCUCUUUGGCUCCC	chr6:36654244-36654504(+)$1	260	47	75	25.3447
CUGCACCAGAAUAGCAUCACGUAGGUGC	chr7:98957223-98957448(+)$1	225	118	146	23.6341
AGGAUGGCACCUAAACCACCAGUGCCCA	chr5:142660940-142661171(-)$1	231	10	38	21.7267
UUUUUAAUGUUUCAUGACCACCCAUUGA	chr8:104344435-104344666(+)$1	231	127	155	22.8324
AAGCUGUGAAGAAAAAUAUAUAUCAAUG	chr19:47113877-47114105(+)$1	228	105	133	23.6010
AUGAUGUGCAAUAAACCAAAAAGGCUUU	chr16:3631090-3631324(-)$1	234	108	136	21.6793
CACUUUUAACAAAAAAGGAAAAUGAACA	chr7:95034283-95034508(-)$1	225	22	50	22.3042
ACAGUUGGGAGAGUAGCAAGGACCCCGC	chr3:184052434-184052677(+)$1	243	143	171	22.6643
CAGUAACCCUCAUAUUUUAAUGGUGUUA	chr1:200827650-200827904(+)$1	254	82	110	21.7425
CAUCGUGUUCCUGUGUCCCCUGCAUGUA	chr16:29822248-29822489(+)$1	241	146	174	24.1566
CCUGCUGACUCAAAACAACUGUGAGUGG	chr6:31802939-31803189(+)$1	250	18	46	22.5856
cguaaucaggacuugcaacacccugauu	chr17:8076700-8076952(-)$1	252	140	168	23.6415
GGUAGAGUAUUUUAAUCCUAUUACUUGA	chr13:23903512-23903741(-)$1	229	1	29	24.5901
UUGUUACAGAAAAAUUCUUAACUGUAAU	chr11:10818831-10819083(-)$1	252	134	162	22.9439
GGGAGCCCCAAAACCUACCACUCGCGUG	chr17:46684696-46684939(-)$1	243	206	234	22.4792
UAAAAACCCCUGAAGUAUUGUGUGGGUG	chr1:205683147-205683375(-)$1	228	40	68	24.5847
UGCAUUGUACAUCUUUAAACAAAAUGUA	chr5:10433993-10434243(+)$1	250	60	88	24.3311
UGUCACCCCAUCCCCACUCCCCUGGUGG	chr19:59061839-59062125(+)$1	286	127	155	22.8544
CCUAUAAAAAAUACAUAGAAAAUUUAUG	chr10:70104032-70104264(-)$1	232	131	159	23.7666
UUUUUUUCUUUGCCUUGUAAUAAGAUUG	chr1:92146220-92146462(-)$1	242	43	71	23.7010
AUGUAAUUUCACAACACCUAAGGAUUUU	chr6:109688686-109688943(-)$1	257	37	65	24.8908
UUUCAAAGCUUGCUAUUAAAUCAUUUAG	chr8:38962000-38962235(+)$1	235	135	163	23.7341
CCUGUUCCUGACUUAAAACAAAAGGAAA	chr7:27202717-27202969(-)$1	252	58	86	22.7782
GCUUCCGUCUCCGGAAUCCUUGGGGAGC	chr22:22117846-22118111(-)$1	265	131	159	24.3311
UCAGCUCUGACACAUUGAACUGCAGUUG	chr1:156435200-156435446(-)$1	246	213	241	23.4595
UUUACUUGUGUAAAAAUAUCGGACGACG	chr22:20228946-20229186(-)$1	240	197	225	24.6302
GAUAUGAAUUCUCUUACAUUUAUUUACU	chrX:123234721-123234952(+)$1	231	59	87	25.0196
uaaGAGGCAUCUUACAAAUUUUGCCCCU	chr13:80910064-80910288(-)$1	224	59	87	24.1633
UUCCCUCGCCCUAAUCCCCCAACGAGGA	chr2:61764614-61764913(-)$1	299	161	189	23.1803
UGAAUUUGUGAUCUGAAAUAACACAAAA	chr3:156260426-156260647(-)$1	221	124	152	22.9399
UGGUGGAAUAAAAAACCUGUAUAUUUUA	chr2:55199824-55200076(-)$1	252	45	73	24.3819
AUCUCAGAGCACUUUGAACCUCUCUGUU	chr1:33764766-33764996(+)$1	230	101	129	24.0498
UGUGCAUUUAUAACAAACUUCUAAUUGC	chr1:244219676-244219904(+)$1	228	93	121	23.3751
UUUUUUCUUUUACCAGUACAGUaagaaa	chr5:109202646-109202872(+)$1	226	187	215	24.8312
GCGUGGGAAAGGAGGUGUGAGUcccggg	chr12:111180513-111180745(-)$1	232	156	184	24.2627
ggacuccuauucaugcuucaaaguccag	chr9:117406627-117406861(+)$1	234	2	30	21.5100
CUACUUGGACAUAACUAAUUUUUCCUUG	chr20:17922647-17922888(-)$1	241	68	96	23.6042
GUAUGUGUCAUUUAUAACUUCUGUACAG	chr5:112213915-112214152(-)$1	237	182	210	22.9562
GUUGAGAAUAAUAAAGCUCUGUGUUUUU	chr19:46190653-46190905(-)$1	252	155	183	24.0861
GCCCACCCUAGUUUGCUUUUGUAGUGGU	chr1:6281476-6281700(-)$1	224	139	167	23.8165
AUACAGAGAGACAACUUGCUCCUUUCCA	chr22:32353086-32353328(+)$1	242	153	181	24.6149
GUGGCCCCUGAAUUCUGCGCAAGGGAUG	chr1:153920233-153920481(-)$1	248	57	85	24.7370
GUCCAUCACUAAUCUAAAACAAAGGUGG	chr2:135712629-135712860(+)$1	231	169	197	23.1846
UAAAAGUGAUAAAUAAAAACCCUUGCUU	chr7:94298772-94299006(+)$1	234	43	71	24.8312
AUUGCUCUUUCUCCUUCUUCCCUGAGUC	chr19:47112446-47112739(+)$1	293	124	152	22.6804
ACAUGAAGAUAAGAUACUCACUGUUCAU	chr10:74035579-74035801(+)$1	222	112	140	24.3555
CUGUGCAGAACCCAAUUGCCCUUUGCAC	chr11:118405697-118405920(+)$1	223	87	115	25.3160
UGUACACCUGUCCCCCUGCUUCAGGUGA	chr19:50001075-50001323(+)$1	248	204	232	22.7417

#DB
(.((((((((...........)))))..	chr3:167401647-167401876(-)$1	1	31	59	23.0899
(((..(((...............))).)	chr17:79478128-79478371(-)$1	1	171	199	19.3968
(((((((((............)))))))	chrX:24004911-24005157(-)$1	1	144	172	24.4140
..(((((((............)))))))	chr13:20660653-20660893(+)$1	1	10	38	25.1353
)))).((((............))))(((	chr17:61898841-61899063(-)$1	1	114	142	22.7268
((((((((((...........)))))))	chr1:150547237-150547481(-)$1	1	154	182	25.0243
(((.(((((..............)).))	chr17:61823531-61823798(-)$1	1	147	175	21.8992
((((..(((.............))))))	chr1:145441644-145441913(+)$1	1	141	169	24.1413
(((...(((............)))...)	chr11:9610329-9610580(+)$1	1	209	237	25.0620
((((.((((.............)))).)	chr8:91636783-91637005(-)$1	1	179	207	23.7679
((((((.(((...........))).)))	chr6:15520704-15520930(+)$1	1	71	99	23.4927
(((((((((.............))))))	chr11:4127304-4127536(+)$1	1	177	205	25.3501
((...(((((...........).)))).	chr1:205683181-205683443(-)$1	1	108	136	24.5847
((((((((..............))).))	chr16:30958513-30958763(+)$1	1	81	109	23.0118
(((.((((((...........)))))).	chr2:20232822-20233085(-)$1	1	153	181	22.7749
.(..(((((............))))).)	chr6:36654244-36654504(+)$1	1	47	75	25.3447
..(((((................)))))	chr7:98957223-98957448(+)$1	1	118	146	23.6341
.....(((((...........)))))..	chr5:142660940-142661171(-)$1	1	10	38	21.7267
)))((((((.............))))))	chr8:104344435-104344666(+)$1	1	127	155	22.8324
((((..(((.............)))..)	chr19:47113877-47114105(+)$1	1	105	133	23.6010
((((.((................)).))	chr16:3631090-3631324(-)$1	1	108	136	21.6793
(.((((((..............)))).)	chr7:95034283-95034508(-)$1	1	22	50	22.3042
.((((.(((.............))).))	chr3:184052434-184052677(+)$1	1	143	171	22.6643
..(((((((............)).))))	chr1:200827650-200827904(+)$1	1	82	110	21.7425
...(((((.............))))).)	chr16:29822248-29822489(+)$1	1	146	174	24.1566
((.(((.((...........)).)))))	chr6:31802939-31803189(+)$1	1	18	46	22.5856
)))(((((((...........)))))))	chr17:8076700-8076952(-)$1	1	140	168	23.6415
(((.(((((............))))).)	chr13:23903512-23903741(-)$1	1	1	29	24.5901
..(((((((............)))))))	chr11:10818831-10819083(-)$1	1	134	162	22.9439
(((((((.(..............).).)	chr17:46684696-46684939(-)$1	1	206	234	22.4792
((...(((((...........).)))).	chr1:205683147-205683375(-)$1	1	40	68	24.5847
((((((................))))))	chr5:10433993-10434243(+)$1	1	60	88	24.3311
.((((((................)))))	chr19:59061839-59062125(+)$1	1	127	155	22.8544
.(((((((..............))))))	chr10:70104032-70104264(-)$1	1	131	159	23.7666
.(((..((((...........))))...	chr1:92146220-92146462(-)$1	1	43	71	23.7010
(...(((((............)))))..	chr6:109688686-109688943(-)$1	1	37	65	24.8908
.((((((................))).)	chr8:38962000-38962235(+)$1	1	135	163	23.7341
.((.(((((.............))))))	chr7:27202717-27202969(-)$1	1	58	86	22.7782
((((((................))))))	chr22:22117846-22118111(-)$1	1	131	159	24.3311
(((((((..............).)))))	chr1:156435200-156435446(-)$1	1	213	241	23.4595
(((((((((.............)))).)	chr22:20228946-20229186(-)$1	1	197	225	24.6302
(...(((((............)))))..	chrX:123234721-123234952(+)$1	1	59	87	25.0196
)(((.((((............)))).))	chr13:80910064-80910288(-)$1	1	59	87	24.1633
((((.(((..............))))))	chr2:61764614-61764913(-)$1	1	161	189	23.1803
(((.((((((...........)))))).	chr3:156260426-156260647(-)$1	1	124	152	22.9399
.(((((((((...........)))))))	chr2:55199824-55200076(-)$1	1	45	73	24.3819
(((.(((((............)))))..	chr1:33764766-33764996(+)$1	1	101	129	24.0498
((((((.(((...........))).)))	chr1:244219676-244219904(+)$1	1	93	121	23.3751
(((((((((.............))))))	chr5:109202646-109202872(+)$1	1	187	215	24.8312
.(.(((((.............))))).)	chr12:111180513-111180745(-)$1	1	156	184	24.2627
(((((................))))))(	chr9:117406627-117406861(+)$1	1	2	30	21.5100
(.((..(((.............)))..)	chr20:17922647-17922888(-)$1	1	68	96	23.6042
...((((.((...........)))))).	chr5:112213915-112214152(-)$1	1	182	210	22.9562
...(((((((...........)))))))	chr19:46190653-46190905(-)$1	1	155	183	24.0861
(((.((((((...........))).)))	chr1:6281476-6281700(-)$1	1	139	167	23.8165
((...(((((...........))))).)	chr22:32353086-32353328(+)$1	1	153	181	24.6149
((...((((............))))...	chr1:153920233-153920481(-)$1	1	57	85	24.7370
(((((((................)))))	chr2:135712629-135712860(+)$1	1	169	197	23.1846
(((((((((.............))))))	chr7:94298772-94299006(+)$1	1	43	71	24.8312
...((((................)))).	chr19:47112446-47112739(+)$1	1	124	152	22.6804
.((((((.(............).)))))	chr10:74035579-74035801(+)$1	1	112	140	24.3555
(((((((((............)))))))	chr11:118405697-118405920(+)$1	1	87	115	25.3160
)((.((((((...........)))))).	chr19:50001075-50001323(+)$1	1	204	232	22.7417

#PSSM
e : 0.12	i : 0.11	d : 0.09	= : 0.09	f : 0.09	! : 0.07	g : 0.06	c : 0.06	[ : 0.06	: : 0.06	" : 0.06	b : 0.03	$ : 0.01	h : 0.01	# : 0.01	
i : 0.12	d : 0.11	f : 0.11	e : 0.11	= : 0.09	c : 0.07	" : 0.07	b : 0.06	[ : 0.04	g : 0.04	! : 0.03	a : 0.03	: : 0.03	$ : 0.01	# : 0.01	
e : 0.14	" : 0.14	d : 0.12	f : 0.11	c : 0.09	= : 0.07	b : 0.07	i : 0.07	g : 0.06	[ : 0.03	! : 0.01	$ : 0.01	# : 0.01	
e : 0.14	[ : 0.12	d : 0.11	" : 0.11	g : 0.09	f : 0.09	c : 0.07	= : 0.07	i : 0.07	! : 0.03	b : 0.03	$ : 0.01	
e : 0.19	f : 0.14	g : 0.09	c : 0.07	! : 0.07	= : 0.07	" : 0.07	d : 0.07	i : 0.07	[ : 0.06	: : 0.01	$ : 0.01	
e : 0.22	d : 0.17	f : 0.12	c : 0.11	g : 0.09	i : 0.07	= : 0.06	! : 0.06	" : 0.01	b : 0.01	[ : 0.01	y : 0.01	
e : 0.22	c : 0.17	d : 0.17	g : 0.09	f : 0.09	i : 0.06	[ : 0.04	y : 0.04	= : 0.03	a : 0.03	b : 0.01	
e : 0.17	c : 0.17	d : 0.14	y : 0.14	g : 0.09	f : 0.06	i : 0.06	b : 0.04	[ : 0.04	= : 0.03	w : 0.01	
e : 0.14	y : 0.14	d : 0.12	c : 0.12	g : 0.07	w : 0.07	b : 0.06	f : 0.06	i : 0.06	= : 0.03	v : 0.03	a : 0.03	x : 0.01	
u : 0.23	v : 0.20	y : 0.14	w : 0.11	e : 0.04	c : 0.04	f : 0.04	a : 0.03	g : 0.03	x : 0.01	= : 0.01	t : 0.01	d : 0.01	i : 0.01	b : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.28	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	
t : 0.26	u : 0.23	v : 0.20	y : 0.14	w : 0.11	x : 0.01	b : 0.01	
v : 0.17	e : 0.15	y : 0.12	w : 0.09	g : 0.07	d : 0.06	c : 0.06	a : 0.06	f : 0.06	b : 0.04	i : 0.03	x : 0.01	= : 0.01	
e : 0.17	c : 0.15	d : 0.11	g : 0.09	y : 0.09	] : 0.07	f : 0.07	= : 0.06	i : 0.06	w : 0.03	b : 0.03	x : 0.01	
e : 0.20	c : 0.20	d : 0.17	f : 0.11	g : 0.09	i : 0.07	= : 0.06	b : 0.03	] : 0.01	a : 0.01	
e : 0.22	d : 0.17	c : 0.14	f : 0.11	g : 0.09	i : 0.07	= : 0.06	] : 0.06	b : 0.03	3 : 0.01	
e : 0.25	d : 0.12	f : 0.12	g : 0.11	] : 0.07	i : 0.07	c : 0.06	= : 0.06	2 : 0.03	4 : 0.03	3 : 0.01	a : 0.01	
] : 0.17	g : 0.12	f : 0.12	e : 0.11	d : 0.11	i : 0.07	= : 0.06	2 : 0.06	c : 0.04	4 : 0.04	6 : 0.01	3 : 0.01	5 : 0.01	
g : 0.14	e : 0.11	c : 0.09	i : 0.09	= : 0.07	d : 0.07	] : 0.07	f : 0.07	b : 0.06	4 : 0.06	a : 0.03	2 : 0.03	6 : 0.01	5 : 0.01	7 : 0.01	

#score	1487.500860211065
#seq	63
#width	28
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_UTR_m3_run1.txt

#BEAR
======="""eeeeerrrrrrrrreeeee333======	chr11:102194727-102195058(+)$1	331	118	156	16.8496
!bb[ccc[ccc!!eeeeeooooooeeeee22ccc]ccc	chr1:236712968-236713188(+)$1	220	42	80	13.8039
ddccc"""bb[ccc[cccnnnnncccccc]bb4444cc	chr17:37921329-37921587(-)$1	258	169	207	12.8515
iiiiiii####ccc[bboooooobb]ccc22iiiiiii	chr13:97874483-97874746(+)$1	263	125	163	17.2559
e[ggggggg"""eeeeeooooooeeeee333ggggggg	chr6:97001594-97001848(+)$1	254	24	62	16.5286
ffffff####gggggggrrrrrrrrrggggggg4444f	chrX:118750898-118751214(-)$1	316	44	82	13.7755
"ffffff####dddd[bbnnnnnbbdddd22ffffff3	chr1:166820736-166820997(+)$1	261	213	251	12.3280
ff!!ccc[eeeee"""cccooooooccc333eeeee]c	chr8:10645052-10645280(-)$1	228	26	64	13.6733
gggggg!!a[ffffff[aooooooa]ffffffaggggg	chrX:47489578-47489796(-)$1	218	33	71	13.4508
eeccc[ccc[dddd[cccmmmmcccdddd333ccc]cc	chr17:42255888-42256102(+)$1	214	159	197	12.1535
[eeeeeccc[eeeeeooooooeeeeeccc333eeeee]	chr20:49521218-49521461(-)$1	243	151	189	12.2866
cc"""ccc!!a!!cccpppppppccc22a22ccc4444	chr1:22418929-22419153(+)$1	224	162	200	12.2687
eeeeccc"""bb"""cccmmmmccc]bb333ccc22ee	chr15:52101229-52101469(+)$1	240	66	104	13.1342
ggggggg!!===========lll===========gggg	chr11:83166603-83166825(-)$1	222	29	67	14.3911
g[ggggggg!!ccc!!cccooooooccc333ccc6666	chr2:113345900-113346138(+)$1	238	105	143	14.0666
"ffffff"""ccc!!eeeeellleeeee4444ccc444	chr17:30326095-30326339(+)$1	244	8	46	13.9170
:eeeee"""eeeee[cccooooooccceeeee4444ee	chr8:71485542-71485810(-)$1	268	4	42	12.3085
cc[eeeeeiiiiiiiiillliiiiiiiii4444eeeee	chr4:76452363-76452641(+)$1	278	151	189	11.3527
ccc[eeeee"""eeeeennnnneeeee4444eeeee33	chr7:80372198-80372420(-)$1	222	86	124	12.7833
ff!!ccc####ggggggglllggggggg333ccc22ff	chr1:78482280-78482493(+)$1	213	32	70	14.8055
f"""ccc"""ccc[cccnnnnnccc]ccc333ccc333	chr16:22346190-22346463(+)$1	273	83	121	16.5510
ffffff!!bb[ccc[bboooooobb]ccc]bb]fffff	chr14:24682812-24683041(-)$1	229	115	153	12.1661
=======####eeeeepppppppeeeee333=======	chr12:51374440-51374681(-)$1	241	162	200	15.0103
ee!!ccc####cccrrrrrrrrrccc4444ccceeeee	chr9:125637069-125637323(-)$1	254	64	102	14.6898
ccggggggg!!ffffffooooooffffff333gggggg	chr14:21820439-21820670(-)$1	231	140	178	15.5425
dd####ggggggg!!cccnnnnncccggggggg333dd	chr1:213070553-213070841(+)$1	288	70	108	12.5257
dd[bb[ccc!!ffffffooooooffffff]ccc]bb]d	chr15:41028374-41028591(-)$1	217	155	193	12.5471
dd!!ccc####cccxxxxxxxxxxxxxxxccc333ccc	chr10:93810557-93810786(-)$1	229	133	171	13.2177
$a[eeeee"""ffffffnnnnnffffff333eeeee]a	chr11:35250817-35251054(+)$1	237	45	83	13.0197
==========[ccc[arrrrrrrrraccc=========	chr17:7215123-7215411(+)$1	288	240	278	15.2514
ggg"""bb####ddddqqqqqqqqdddd333bb333gg	chr15:40623674-40623916(-)$1	242	17	55	12.9763
ggggggg"""dddd[a[cccooooooccc]a]dddd33	chr18:51679552-51679824(-)$1	272	202	240	13.2393
ggggggg$$$$$eeeeeooooooeeeee666666gggg	chrX:101768783-101769004(-)$1	221	139	177	13.0410
cccggggggg!!a[cccqqqqqqqqccca22ggggggg	chr15:41164918-41165138(-)$1	220	91	129	12.3150
!ggggggg!!dddd[cccmmmmccc]dddd22gggggg	chr19:16686103-16686331(-)$1	228	29	67	11.8558
eeeeee$$$$$bb[cccooooooccc]bb]eeeee]ee	chr9:34634930-34635294(-)$1	364	240	278	12.9735
cccbb[iiiiiiiiibboooooobb]iiiiiiiii]bb	chr1:162334505-162334723(+)$1	218	131	169	12.6741
iiiiiiiii####eeeeennnnneeeee22iiiiiiii	chr10:75531463-75531755(+)$1	292	172	210	14.1484
dd"""dddd"""ddddrrrrrrrrrdddd22dddd333	chr1:35482839-35483072(-)$1	233	134	172	13.1034
ee[===========!!bbnnnnnbb]===========e	chr11:17798054-17798268(+)$1	214	136	174	13.6969
$$dddd####ccc[ddddllldddd]ccc333dddd33	chr6:136581651-136581937(-)$1	286	133	171	12.6955
cc####ggggggg[eeeeemmmmeeeee333ggggggg	chr10:104497556-104497788(+)$1	232	151	189	12.3718
dddd####ccc[ddddrrrrrrrrrdddd22ccc22dd	chr10:5567998-5568211(+)$1	213	135	173	12.3720
ddd[ccc####bb[cccoooooocccbbccc22dddd5	chr10:97633606-97633827(+)$1	221	65	103	12.9832
======="""gggggggqqqqqqqqggggggg======	chr5:148732547-148732821(+)$1	274	23	61	13.6264
:eeeee####gggggggnnnnnggggggg333eeeee:	chr4:152042230-152042448(-)$1	218	72	110	12.0513
ee[ccc[bb[gggggggooooooggggggg]bbccc]e	chr19:17935505-17935774(-)$1	269	148	186	13.2905
============[ddddqqqqqqqqdddd]========	chr3:63985686-63985928(+)$1	242	99	137	12.2950
======="""==========rrrrrrrrr=========	chr5:87498293-87498517(-)$1	224	152	190	14.1651
"a[ccc####ccc####cccmmmmccc4444ccc333c	chr8:144989691-144989916(-)$1	225	123	161	13.5800
c!!accc"""eeeeerrrrrrrrreeeee4444ccc]a	chr2:121749479-121749730(+)$1	251	74	112	15.1861
ccc!!bb[iiiiiiiiiooooooiiiiiiiiibb22cc	chr21:19161786-19162019(-)$1	233	51	89	13.4668
ggg!!bb####ffffffooooooffffff22bbggggg	chr3:98240672-98240944(-)$1	272	42	80	15.3975

#otherMatches

#Seq PSSM
UGGGUUGAUUGAAUGCCACUGAAACAUUCUAGUAGCCU	chr11:102194727-102195058(+)$1	331	118	156	16.8496
ACCAUCAGAGUGCUUAACUGAGCUGUUGGAGACUGUGA	chr1:236712968-236713188(+)$1	220	42	80	13.8039
UACCUUCCCAUCUCCAGUGAAAAGCUGAGCUGCUUUGG	chr17:37921329-37921587(-)$1	258	169	207	12.8515
UGAAGGUAAAAUUUUCCAGAUACGGCAGACGGCUUUCA	chr13:97874483-97874746(+)$1	263	125	163	17.2559
GAAAUUUUUCACAUUAUUUUCACAUAAUUUUAAAAAUU	chr6:97001594-97001848(+)$1	254	24	62	16.5286
CCAGUCAUUAGAAAUGGUCUGUGCUUUUAUUUUCCCAG	chrX:118750898-118751214(-)$1	316	44	82	13.7755
UUAUAAAUUAAAUUGAUCCUCCAGACAGUGUUUUAUAU	chr1:166820736-166820997(+)$1	261	213	251	12.3280
ggcuuuaauguauucACUUCGUAAAGAGACCGUACACU	chr8:10645052-10645280(-)$1	228	26	64	13.6733
GGUGGAAGGUGGAGCAACUGACUCGAUGCUCCCUCCAC	chrX:47489578-47489796(-)$1	218	33	71	13.4508
caggcuggucucacacugaccucaggugauccacccgc	chr17:42255888-42256102(+)$1	214	159	197	12.1535
AUGAACUGGUAAGCAUUUUUCUGUUUUCAGAUGUUCAA	chr20:49521218-49521461(-)$1	243	151	189	12.2866
GUAGGGUGGGGGUGGGGAGAACACUUAACAACAUGGGG	chr1:22418929-22419153(+)$1	224	162	200	12.2687
GUAGCAUCAAGCCAGACUCACAGGUAGCAAAAUGAAUU	chr15:52101229-52101469(+)$1	240	66	104	13.1342
UGUGUAUGUAUGGUAUAUAUGGUAUGUAUACCAUGUAC	chr11:83166603-83166825(-)$1	222	29	67	14.3911
aaacauucucaucuccugcagcauggcauacagacuuu	chr2:113345900-113346138(+)$1	238	105	143	14.0666
UAAUCAUAUGUUCCAAACAGGCACUGUUAGAUGAAGUA	chr17:30326095-30326339(+)$1	244	8	46	13.9170
CUGGAAAAAGUAGUAGCUCUCUGUAGCAUUAUGGAGUU	chr8:71485542-71485810(-)$1	268	4	42	12.3085
UAAAGUGCUGCUUUGGAUUCUCUGGAGCAUUAUGCAUU	chr4:76452363-76452641(+)$1	278	151	189	11.3527
GUCACAGUUCCCUUUAUUUCACAUAAGCCCAAACUGAU	chr7:80372198-80372420(-)$1	222	86	124	12.7833
UUAACUAAACUAUACAUGUAAUAUGUAUUUCUAGAAGA	chr1:78482280-78482493(+)$1	213	32	70	14.8055
UAAUAUUUUAGCUAUAGAAUCACUAAGGCAUUGAUCAA	chr16:22346190-22346463(+)$1	273	83	121	16.5510
AUUUCCUUCCGGAGAACAAGCACGUACUCAGGUGGAGA	chr14:24682812-24683041(-)$1	229	115	153	12.1661
CUAGGAGUGGCCAAUAUUUGUAUUGUUGAAUCUCCUAG	chr12:51374440-51374681(-)$1	241	162	200	15.0103
CAUUGCCAUUCCACCCUCAAUUAGUGCCCAGGCUGAAA	chr9:125637069-125637323(-)$1	254	64	102	14.6898
UGAUGGCUUCUGACAUCUUAUUUGGUGUCUCAAAGCUG	chr14:21820439-21820670(-)$1	231	140	178	15.5425
auuugaggccaggaguugaagaccagucuggccaacau	chr1:213070553-213070841(+)$1	288	70	108	12.5257
CCAAUUGCUGGUGAGGUGGAUGAACUUCAAAGCUAUAG	chr15:41028374-41028591(-)$1	217	155	193	12.5471
AAUCUCUUAGUGCUUGCACCAUUUUACAUAGCUUCAGA	chr10:93810557-93810786(-)$1	229	133	171	13.2177
AUGAAGAUUGGGGUGUAACACCUACACCAUUAUCUUGG	chr11:35250817-35251054(+)$1	237	45	83	13.0197
UCUUCUCCCCUCACACUACAGCCCUGGUGGGGGAGAAG	chr17:7215123-7215411(+)$1	288	240	278	15.2514
ccuguuuugaaggguugcugagaaaauuaaagauaaGG	chr15:40623674-40623916(-)$1	242	17	55	12.9763
cagaagcccaggagugagcacaaugcugcccuuucccu	chr18:51679552-51679824(-)$1	272	202	240	13.2393
GCCAAUGUUUCCUUAAAUUCAUUUUUAAACUUACCAUU	chrX:101768783-101769004(-)$1	221	139	177	13.0410
CCAGUCAAAGCUCACAGAAAAAAACCUGGCACUUUGAU	chr15:41164918-41165138(-)$1	220	91	129	12.3150
UGUGCCAGAAGCUUCUCAGCUGUGGUGAGCCACUGGCA	chr19:16686103-16686331(-)$1	228	29	67	11.8558
UCCCCAACCCCCUCAGCAACAAAGCUCAGCUGGGGAAC	chr9:34634930-34635294(-)$1	364	240	278	12.9735
UUCCUAUUUCUCACUAUGUUUGGGUGAGUGGGAGAGGG	chr1:162334505-162334723(+)$1	218	131	169	12.6741
CUGCUUCUCCAGGCCCGGGGUUGUUGGGGAGAGAGGCA	chr10:75531463-75531755(+)$1	292	172	210	14.1484
GUAUAAGCAUAUUCUUUUGGUUUCUAAGAUUUGCUGUC	chr1:35482839-35483072(-)$1	233	134	172	13.1034
GCCUGGGGGCCCUGGGCUGGGGGAGGCAGGGCCCCCAG	chr11:17798054-17798268(+)$1	214	136	174	13.6969
UUAAUUUGAACACACUACAUCGUAGGGUGACUGAUUUU	chr6:136581651-136581937(-)$1	286	133	171	12.6955
GAAAAAGGGUAGCAAAGGCCAAUGUCUUCUAGCUGCUU	chr10:104497556-104497788(+)$1	232	151	189	12.3718
AGCUGUAACCUGUUCCUAUUCAUCUGGAAGGAGGGAGG	chr10:5567998-5568211(+)$1	213	135	173	12.3720
ucacgagaauagcacagaaaagacuggccuccaugauu	chr10:97633606-97633827(+)$1	221	65	103	12.9832
UUCCACUGGAACUCUAUGACAUUCAGUGGAGUGGUGGA	chr5:148732547-148732821(+)$1	274	23	61	13.6264
CUGUGUCUUGUUAUAGUAGUACAUUAUGAAUCACAUAU	chr4:152042230-152042448(-)$1	218	72	110	12.0513
auguuuguugacugaauaaaGGAAUUCAGUGGAAAAGA	chr19:17935505-17935774(-)$1	269	148	186	13.2905
GUCAGAAGUUUCUAACUUACAAACUGGUUUGAAAUUUU	chr3:63985686-63985928(+)$1	242	99	137	12.2950
ugcuucauccauucuuuguuuuguuuuuugaugaagga	chr5:87498293-87498517(-)$1	224	152	190	14.1651
UGAGACCCCUGGCCUCCGGCGUCAGCCUCCAGCCUCUG	chr8:144989691-144989916(-)$1	225	123	161	13.5800
UAGGGUGAAUUGGUGCAUCUUCCCCACcauacacacac	chr2:121749479-121749730(+)$1	251	74	112	15.1861
UGGUAACAUUGAUAUGAACCAUAUUAUAUCAAGUCUCC	chr21:19161786-19162019(-)$1	233	51	89	13.4668
AGAUUGCUAUCUAGCAUUAUUACAUGUUAUUGUUCUCU	chr3:98240672-98240944(-)$1	272	42	80	15.3975

#DB
(((((((...(((((.........)))))...))))))	chr11:102194727-102195058(+)$1	1	118	156	16.8496
.((.(((.(((..(((((......)))))..))).)))	chr1:236712968-236713188(+)$1	1	42	80	13.8039
(((((...((.(((.(((.....)))))).))....))	chr17:37921329-37921587(-)$1	1	169	207	12.8515
(((((((....(((.((......)).)))..)))))))	chr13:97874483-97874746(+)$1	1	125	163	17.2559
(.(((((((...(((((......)))))...)))))))	chr6:97001594-97001848(+)$1	1	24	62	16.5286
((((((....(((((((.........)))))))....)	chrX:118750898-118751214(-)$1	1	44	82	13.7755
.((((((....((((.((.....))))))..)))))).	chr1:166820736-166820997(+)$1	1	213	251	12.3280
((..(((.(((((...(((......)))...))))).)	chr8:10645052-10645280(-)$1	1	26	64	13.6733
((((((..(.((((((.(......).))))))))))))	chrX:47489578-47489796(-)$1	1	33	71	13.4508
(((((.(((.((((.(((....)))))))...))).))	chr17:42255888-42256102(+)$1	1	159	197	12.1535
.((((((((.(((((......))))))))...))))).	chr20:49521218-49521461(-)$1	1	151	189	12.2866
((...(((..(..(((.......)))..)..)))....	chr1:22418929-22419153(+)$1	1	162	200	12.2687
(((((((...((...(((....))).))...)))..))	chr15:52101229-52101469(+)$1	1	66	104	13.1342
(((((((..(((((((((((...)))))))))))))))	chr11:83166603-83166825(-)$1	1	29	67	14.3911
(.(((((((..(((..(((......)))...)))....	chr2:113345900-113346138(+)$1	1	105	143	14.0666
.((((((...(((..(((((...)))))....)))...	chr17:30326095-30326339(+)$1	1	8	46	13.9170
.(((((...(((((.(((......))))))))....))	chr8:71485542-71485810(-)$1	1	4	42	12.3085
((.((((((((((((((...)))))))))....)))))	chr4:76452363-76452641(+)$1	1	151	189	11.3527
(((.(((((...(((((.....)))))....)))))..	chr7:80372198-80372420(-)$1	1	86	124	12.7833
((..(((....(((((((...)))))))...)))..))	chr1:78482280-78482493(+)$1	1	32	70	14.8055
(...(((...(((.(((.....))).)))...)))...	chr16:22346190-22346463(+)$1	1	83	121	16.5510
((((((..((.(((.((......)).))).)).)))))	chr14:24682812-24683041(-)$1	1	115	153	12.1661
(((((((....(((((.......)))))...)))))))	chr12:51374440-51374681(-)$1	1	162	200	15.0103
((..(((....(((.........)))....))))))))	chr9:125637069-125637323(-)$1	1	64	102	14.6898
(((((((((..((((((......))))))...))))))	chr14:21820439-21820670(-)$1	1	140	178	15.5425
((....(((((((..(((.....))))))))))...))	chr1:213070553-213070841(+)$1	1	70	108	12.5257
((.((.(((..((((((......)))))).))).)).)	chr15:41028374-41028591(-)$1	1	155	193	12.5471
((..(((....(((...............)))...)))	chr10:93810557-93810786(-)$1	1	133	171	13.2177
.(.(((((...((((((.....))))))...))))).)	chr11:35250817-35251054(+)$1	1	45	83	13.0197
((((((((((.(((.(.........)))))))))))))	chr17:7215123-7215411(+)$1	1	240	278	15.2514
(((...((....((((........))))...))...))	chr15:40623674-40623916(-)$1	1	17	55	12.9763
(((((((...((((.(.(((......))).).))))..	chr18:51679552-51679824(-)$1	1	202	240	13.2393
(((((((.....(((((......)))))......))))	chrX:101768783-101769004(-)$1	1	139	177	13.0410
((((((((((..(.(((........))))..)))))))	chr15:41164918-41165138(-)$1	1	91	129	12.3150
.(((((((..((((.(((....))).))))..))))))	chr19:16686103-16686331(-)$1	1	29	67	11.8558
((((((.....((.(((......))).)).))))).))	chr9:34634930-34635294(-)$1	1	240	278	12.9735
(((((.(((((((((((......)).))))))))).))	chr1:162334505-162334723(+)$1	1	131	169	12.6741
(((((((((....(((((.....)))))..))))))))	chr10:75531463-75531755(+)$1	1	172	210	14.1484
((...((((...((((.........))))..))))...	chr1:35482839-35483072(-)$1	1	134	172	13.1034
((.(((((((((((..((.....)).))))))))))))	chr11:17798054-17798268(+)$1	1	136	174	13.6969
..((((....(((.((((...)))).)))...))))..	chr6:136581651-136581937(-)$1	1	133	171	12.6955
((....(((((((.(((((....)))))...)))))))	chr10:104497556-104497788(+)$1	1	151	189	12.3718
((((....(((.((((.........))))..)))..))	chr10:5567998-5568211(+)$1	1	135	173	12.3720
(((.(((....((.(((......))))))))..)))).	chr10:97633606-97633827(+)$1	1	65	103	12.9832
(((((((...(((((((........)))))))))))))	chr5:148732547-148732821(+)$1	1	23	61	13.6264
.(((((....(((((((.....)))))))...))))).	chr4:152042230-152042448(-)$1	1	72	110	12.0513
((.(((.((.(((((((......))))))).))))).)	chr19:17935505-17935774(-)$1	1	148	186	13.2905
((((((((((((.((((........)))).))))))))	chr3:63985686-63985928(+)$1	1	99	137	12.2950
(((((((...((((((((((.........)))))))))	chr5:87498293-87498517(-)$1	1	152	190	14.1651
.(.(((....(((....(((....)))....)))...)	chr8:144989691-144989916(-)$1	1	123	161	13.5800
(..((((...(((((.........)))))....))).)	chr2:121749479-121749730(+)$1	1	74	112	15.1861
(((..((.(((((((((......)))))))))))..))	chr21:19161786-19162019(-)$1	1	51	89	13.4668
(((..((....((((((......))))))..)))))))	chr3:98240672-98240944(-)$1	1	42	80	15.3975

#PSSM
c : 0.16	d : 0.13	e : 0.13	g : 0.13	= : 0.11	f : 0.09	" : 0.05	! : 0.03	i : 0.03	: : 0.03	$ : 0.03	[ : 0.01	
e : 0.16	c : 0.15	d : 0.13	g : 0.13	= : 0.11	f : 0.11	i : 0.03	[ : 0.03	a : 0.03	b : 0.01	" : 0.01	$ : 0.01	! : 0.01	
g : 0.18	= : 0.11	c : 0.11	[ : 0.11	! : 0.09	e : 0.09	f : 0.07	" : 0.05	d : 0.05	i : 0.03	# : 0.03	b : 0.01	
g : 0.16	= : 0.13	e : 0.13	! : 0.11	c : 0.07	f : 0.07	" : 0.07	[ : 0.05	i : 0.03	# : 0.03	b : 0.03	d : 0.03	a : 0.01	
c : 0.24	g : 0.16	= : 0.13	e : 0.13	f : 0.07	" : 0.05	# : 0.05	i : 0.03	b : 0.03	! : 0.03	d : 0.01	
c : 0.22	g : 0.16	= : 0.13	e : 0.13	f : 0.07	[ : 0.05	# : 0.05	" : 0.03	i : 0.03	d : 0.03	b : 0.03	
c : 0.24	g : 0.18	= : 0.13	# : 0.09	i : 0.05	e : 0.05	b : 0.05	" : 0.03	f : 0.03	! : 0.03	$ : 0.01	d : 0.01	[ : 0.01	
# : 0.24	" : 0.18	g : 0.13	c : 0.07	[ : 0.05	! : 0.05	e : 0.05	= : 0.05	b : 0.03	$ : 0.03	i : 0.03	d : 0.01	
# : 0.24	" : 0.18	g : 0.11	c : 0.09	i : 0.07	b : 0.05	! : 0.05	= : 0.05	e : 0.03	$ : 0.03	a : 0.01	d : 0.01	
# : 0.26	" : 0.22	! : 0.09	[ : 0.07	= : 0.07	i : 0.05	g : 0.05	c : 0.03	b : 0.03	e : 0.03	$ : 0.03	
# : 0.18	c : 0.11	g : 0.11	e : 0.09	" : 0.07	= : 0.07	! : 0.07	[ : 0.05	d : 0.05	i : 0.05	$ : 0.03	f : 0.01	a : 0.01	b : 0.01	
c : 0.20	g : 0.13	e : 0.11	f : 0.09	d : 0.07	= : 0.07	! : 0.05	" : 0.05	b : 0.05	i : 0.05	# : 0.03	$ : 0.01	[ : 0.01	
c : 0.20	e : 0.16	g : 0.13	d : 0.13	f : 0.09	= : 0.05	i : 0.05	! : 0.03	b : 0.03	" : 0.01	a : 0.01	# : 0.01	[ : 0.01	
e : 0.18	c : 0.15	d : 0.15	[ : 0.11	g : 0.09	f : 0.09	= : 0.05	i : 0.05	" : 0.03	! : 0.03	# : 0.01	
e : 0.18	[ : 0.15	d : 0.11	g : 0.09	f : 0.09	c : 0.09	! : 0.07	i : 0.05	" : 0.03	= : 0.03	r : 0.01	x : 0.01	# : 0.01	
c : 0.20	e : 0.15	g : 0.09	f : 0.09	d : 0.09	r : 0.05	b : 0.05	= : 0.03	! : 0.03	i : 0.03	a : 0.03	[ : 0.01	" : 0.01	o : 0.01	x : 0.01	# : 0.01	
c : 0.22	e : 0.13	r : 0.11	b : 0.09	g : 0.09	f : 0.07	[ : 0.03	p : 0.03	= : 0.03	i : 0.03	d : 0.03	o : 0.01	x : 0.01	q : 0.01	# : 0.01	
o : 0.24	c : 0.18	r : 0.13	e : 0.07	n : 0.07	q : 0.07	b : 0.03	p : 0.03	= : 0.03	a : 0.01	l : 0.01	g : 0.01	x : 0.01	d : 0.01	
o : 0.30	n : 0.16	r : 0.13	c : 0.07	q : 0.07	m : 0.05	l : 0.05	p : 0.03	= : 0.03	e : 0.03	x : 0.01	
o : 0.33	n : 0.16	r : 0.13	m : 0.07	q : 0.07	l : 0.05	p : 0.03	= : 0.03	c : 0.03	e : 0.01	x : 0.01	
o : 0.35	n : 0.16	r : 0.15	m : 0.09	l : 0.07	q : 0.07	p : 0.03	i : 0.01	x : 0.01	
o : 0.33	n : 0.16	r : 0.15	m : 0.09	q : 0.07	p : 0.03	l : 0.03	e : 0.01	i : 0.01	g : 0.01	x : 0.01	d : 0.01	
o : 0.33	r : 0.15	n : 0.09	c : 0.07	q : 0.07	e : 0.03	p : 0.03	l : 0.03	g : 0.03	m : 0.03	i : 0.01	x : 0.01	f : 0.01	d : 0.01	
c : 0.18	e : 0.15	r : 0.13	o : 0.11	b : 0.09	f : 0.07	q : 0.07	g : 0.05	i : 0.03	= : 0.01	x : 0.01	d : 0.01	m : 0.01	
c : 0.22	e : 0.20	b : 0.09	r : 0.09	f : 0.07	o : 0.05	g : 0.05	q : 0.05	i : 0.03	d : 0.03	a : 0.01	= : 0.01	x : 0.01	
e : 0.20	c : 0.20	] : 0.16	d : 0.11	g : 0.07	f : 0.07	r : 0.03	i : 0.03	= : 0.01	x : 0.01	a : 0.01	o : 0.01	
c : 0.24	e : 0.18	d : 0.13	g : 0.11	f : 0.09	i : 0.05	b : 0.03	= : 0.03	2 : 0.01	4 : 0.01	x : 0.01	] : 0.01	r : 0.01	
c : 0.20	e : 0.18	d : 0.13	g : 0.11	f : 0.09	b : 0.05	i : 0.05	4 : 0.05	= : 0.03	2 : 0.01	x : 0.01	r : 0.01	
c : 0.16	3 : 0.16	d : 0.11	g : 0.09	e : 0.07	f : 0.07	4 : 0.07	i : 0.05	a : 0.03	= : 0.03	x : 0.01	6 : 0.01	b : 0.01	2 : 0.01	r : 0.01	
3 : 0.30	2 : 0.16	] : 0.11	4 : 0.11	g : 0.07	= : 0.07	c : 0.03	i : 0.03	f : 0.01	e : 0.01	6 : 0.01	d : 0.01	
3 : 0.30	2 : 0.16	= : 0.09	4 : 0.09	c : 0.07	g : 0.05	i : 0.05	b : 0.03	e : 0.03	f : 0.01	a : 0.01	6 : 0.01	] : 0.01	
c : 0.18	3 : 0.13	g : 0.11	= : 0.11	b : 0.09	e : 0.09	i : 0.07	4 : 0.05	f : 0.03	2 : 0.03	] : 0.01	6 : 0.01	d : 0.01	
c : 0.22	= : 0.15	g : 0.13	e : 0.11	4 : 0.07	b : 0.07	i : 0.05	d : 0.05	f : 0.01	a : 0.01	] : 0.01	3 : 0.01	6 : 0.01	2 : 0.01	
c : 0.22	= : 0.15	e : 0.15	g : 0.13	d : 0.07	4 : 0.05	i : 0.05	3 : 0.05	f : 0.03	] : 0.01	6 : 0.01	b : 0.01	
g : 0.16	e : 0.15	= : 0.13	c : 0.09	4 : 0.07	2 : 0.07	3 : 0.07	d : 0.07	i : 0.05	f : 0.03	] : 0.01	6 : 0.01	b : 0.01	
g : 0.16	= : 0.13	e : 0.13	4 : 0.09	3 : 0.09	c : 0.07	2 : 0.07	] : 0.05	d : 0.05	i : 0.03	f : 0.03	6 : 0.01	b : 0.01	
g : 0.18	= : 0.13	e : 0.13	3 : 0.11	c : 0.09	] : 0.09	4 : 0.05	f : 0.05	d : 0.05	i : 0.03	6 : 0.01	b : 0.01	
g : 0.18	c : 0.13	e : 0.13	= : 0.11	3 : 0.11	f : 0.05	d : 0.05	i : 0.03	4 : 0.03	a : 0.03	] : 0.01	6 : 0.01	b : 0.01	5 : 0.01	: : 0.01	

#score	718.013632554049
#seq	53
#width	38
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m2_run1.txt

#BEAR
!cccbbyyyyyyyyyyyyyyyybb]	chr16:27472319-27472551(-)$1	232	19	44	20.1249
#eeeeevvvvvvvvvvvvveeeee4	chr12:99128483-99128713(-)$1	230	64	89	23.2635
eeyyyyyyyyyyyyyyyyeeeee22	chr14:104152432-104152657(+)$1	225	93	118	20.8381
[cccwwwwwwwwwwwwwwccc]bb3	chr22:17592878-17593095(+)$1	217	67	92	21.6663
ggggggvvvvvvvvvvvvvgggggg	chr17:5335828-5336045(+)$1	217	2	27	22.9990
d[bbvvvvvvvvvvvvvbb]dddd]	chr2:42588636-42588857(-)$1	221	15	40	20.3379
!!eeeeettttttttttteeeee22	chr6:111982653-111982883(-)$1	230	46	71	23.0771
!!ddddwwwwwwwwwwwwwwddddd	chr11:59939941-59940172(-)$1	231	54	79	21.7269
eeeeewwwwwwwwwwwwwweeeee]	chr2:85771889-85772115(+)$1	226	122	147	21.9826
g[cccwwwwwwwwwwwwwwccc22g	chr5:52393192-52393411(+)$1	219	94	119	22.8210
gggggavvvvvvvvvvvvva]gggg	chr3:7782951-7783167(+)$1	216	124	149	23.2042
####ccctttttttttttccc333d	chr12:22697050-22697269(-)$1	219	97	122	23.2266
hhhhhhuuuuuuuuuuuuhhhhhhh	chr1:86195536-86195772(-)$1	236	21	46	21.3761
"""cccuuuuuuuuuuuuccc22ee	chr2:44547712-44547927(-)$1	215	12	37	23.9307
b[cccvvvvvvvvvvvvvccc]bb2	chr7:65439885-65440137(-)$1	252	187	212	22.5969
!!cccwwwwwwwwwwwwwwccc22c	chr6:31626326-31626547(+)$1	221	21	46	23.0468
ddddyyyyyyyyyyyyyyyydddd:	chr17:61504779-61505005(+)$1	226	0	25	20.0316
ddyyyyyyyyyyyyyyyydddd22a	chr19:10753718-10753936(+)$1	218	123	148	20.6872
"eeeeettttttttttteeeee333	chr1:144900575-144900799(-)$1	224	124	149	23.1569
"""cccvvvvvvvvvvvvvccc22f	chr14:74526611-74526836(+)$1	225	6	31	23.8749
b[cccwwwwwwwwwwwwwwccc22b	chrX:153581897-153582113(-)$1	216	130	155	22.2714
ff[cccuuuuuuuuuuuuccc]fff	chr11:18343534-18343752(-)$1	218	31	56	23.2212
:eeeeeuuuuuuuuuuuueeeee::	chr9:102730802-102731020(+)$1	218	154	179	20.8705
!!eeeeettttttttttteeeee22	chr20:42092115-42092338(+)$1	223	17	42	23.0771
b!!ddddtttttttttttdddd22b	chr11:33880669-33880886(+)$1	217	82	107	22.2243
###cccuuuuuuuuuuuuccc22ee	chr17:62502829-62503057(+)$1	228	147	172	23.8319
""eeeeettttttttttteeeee]f	chr3:145910927-145911142(-)$1	215	141	166	22.7175
gggggggtttttttttttggggggg	chr22:50810356-50810574(+)$1	218	154	179	22.0559
eeeeevvvvvvvvvvvvveeeee33	chr11:60703075-60703301(+)$1	226	106	131	23.3254
dccc[avvvvvvvvvvvvva]ccce	chr8:38095024-38095245(+)$1	221	38	63	22.8801
:ddddyyyyyyyyyyyyyyyydddd	chr11:71714267-71714493(-)$1	226	153	178	19.5996
cc"""bbtttttttttttbb333cc	chr11:33127021-33127242(-)$1	221	122	147	21.4553
iiiiiiuuuuuuuuuuuuiiiiiii	chr16:24228534-24228770(+)$1	236	48	73	23.6840
"""ddddtttttttttttdddd777	chr2:198284205-198284422(-)$1	217	13	38	21.2693
d[ddddwwwwwwwwwwwwwwdddd]	chr1:163045836-163046067(+)$1	231	101	126	21.6682
[eeeeeuuuuuuuuuuuueeeee22	chr12:132198912-132199140(+)$1	228	58	83	23.9928
eeee[auuuuuuuuuuuuaeeeee:	chr1:36388984-36389219(+)$1	235	209	234	22.7907
d[cccwwwwwwwwwwwwwwccc]dd	chr12:96661718-96661945(+)$1	227	8	33	22.1395
ddddwwwwwwwwwwwwwwdddd444	chr4:169848235-169848453(-)$1	218	116	141	21.6274
[fffffftttttttttttffffffe	chr11:868763-868981(-)$1	218	162	187	20.9983
""ddddvvvvvvvvvvvvvdddd]f	chr1:38462861-38463083(-)$1	222	52	77	23.2237
##dddduuuuuuuuuuuudddd333	chr1:220835578-220835796(+)$1	218	75	100	24.5308
!!dddduuuuuuuuuuuudddd22e	chr11:58295456-58295699(-)$1	243	14	39	24.1026
hhhhhhvvvvvvvvvvvvvhhhhhh	chr9:134184367-134184585(+)$1	218	2	27	21.1502
:eeeeeuuuuuuuuuuuueeeeegg	chr2:96919225-96919442(-)$1	217	9	34	22.5766
$$ddddtttttttttttdddd4444	chrX:47446035-47446257(+)$1	222	112	137	22.1665
ccc[bbtttttttttttbbccc444	chr16:4013350-4013567(-)$1	217	71	96	22.1474
[fffffftttttttttttffffff]	chr6:349478-349695(-)$1	217	179	204	21.3005
[a[ccctttttttttttccc]addd	chr16:67517386-67517611(+)$1	225	119	144	22.2802
hhhhhhuuuuuuuuuuuuhhhhhhh	chr3:113530693-113530925(+)$1	232	192	217	21.3761
ffffffuuuuuuuuuuuufffffff	chr14:60759561-60759787(+)$1	226	36	61	21.8475
i[bbyyyyyyyyyyyyyyyybb22i	chr5:37226616-37226841(-)$1	225	45	70	20.8754
cc!!bbtttttttttttbb22ccc6	chr18:72911847-72912094(-)$1	247	172	197	20.8011
ccc[bbuuuuuuuuuuuubb]ccc]	chr5:179339193-179339414(-)$1	221	16	41	22.8709
g[ddddtttttttttttdddd]ggg	chr17:42153546-42153765(+)$1	219	60	85	22.1504
!eeeeeuuuuuuuuuuuueeeee]e	chr7:72419622-72419847(-)$1	225	30	55	23.8314
ddyyyyyyyyyyyyyyyydddd444	chr1:38280295-38280512(+)$1	217	66	91	20.8048
iiiiiiwwwwwwwwwwwwwwiiiii	chr16:4561520-4561742(-)$1	222	155	180	21.9433
hhhhhhwwwwwwwwwwwwwwhhhhh	chr5:137782284-137782501(+)$1	217	102	127	20.0180
gggggggtttttttttttggggggg	chr11:61291785-61292001(-)$1	216	88	113	22.0559
[eeeeettttttttttteeeee555	chr2:99236187-99236417(-)$1	230	152	177	20.5541
iiiiiivvvvvvvvvvvvviiiiii	chr2:191828026-191828245(+)$1	219	105	130	23.2219
ffffwwwwwwwwwwwwwwffffff4	chr6:151343342-151343563(+)$1	221	23	48	20.4646

#otherMatches

#Seq PSSM
ACAGACUGACACGUUUCCCACUGUA	chr16:27472319-27472551(-)$1	232	19	44	20.1249
AAGGUAAUACUUUAUACUCUGCCUA	chr12:99128483-99128713(-)$1	230	64	89	23.2635
GUGUCUUUCUAACUUCUAAUAAACU	chr14:104152432-104152657(+)$1	225	93	118	20.8381
ACACCUACCAUGCAUUCUGUGACCU	chr22:17592878-17593095(+)$1	217	67	92	21.6663
UUAAGCUAAUUAUUUUCCUGUUUAA	chr17:5335828-5336045(+)$1	217	2	27	22.9990
CUUCAACCCGACGACCAGACGGUGG	chr2:42588636-42588857(-)$1	221	15	40	20.3379
GAUCAGAUUGCAUGUGACUCUGAAG	chr6:111982653-111982883(-)$1	230	46	71	23.0771
CUAGUCUCUUUAAUAGUAUUGACUU	chr11:59939941-59940172(-)$1	231	54	79	21.7269
AUGGCGUAAGUACAGAGAAGCCAUC	chr2:85771889-85772115(+)$1	226	122	147	21.9826
UAAGAAAAAAAUCCUUCAAUCUAAG	chr5:52393192-52393411(+)$1	219	94	119	22.8210
AAGUACUUUCGUUAAUCUUGCUGCU	chr3:7782951-7783167(+)$1	216	124	149	23.2042
CUCCGCCCCUCUCCCGCCGGCCCCG	chr12:22697050-22697269(-)$1	219	97	122	23.2266
UGAUACACUACCUCUUACGUGUUGC	chr1:86195536-86195772(-)$1	236	21	46	21.3761
UAAAGCAGUUACAUUCAAGCUACAG	chr2:44547712-44547927(-)$1	215	12	37	23.9307
AAACCUUUCUAUUUCCACGGUGUCA	chr7:65439885-65440137(-)$1	252	187	212	22.5969
UCCAGACCCCCUAAUCCACUUGCCU	chr6:31626326-31626547(+)$1	221	21	46	23.0468
GUUCUCUCUCCUGAUAUAUUGAACA	chr17:61504779-61505005(+)$1	226	0	25	20.0316
CUGCUUUCUAACCCUCUGAGGCUUC	chr19:10753718-10753936(+)$1	218	123	148	20.6872
UCUUCAAAUAAAAAUAAUGAAGUAA	chr1:144900575-144900799(-)$1	224	124	149	23.1569
UUGAGCAGAAAAGAAAGAAGCUGUU	chr14:74526611-74526836(+)$1	225	6	31	23.8749
CAUUCUAGUCAAGUACAAUGAACAG	chrX:153581897-153582113(-)$1	216	130	155	22.2714
CGCGAGGGGAGACUGAAGUUCACGU	chr11:18343534-18343752(-)$1	218	31	56	23.2212
AACCAAAUUUCAGUAUUAUUGGUGC	chr9:102730802-102731020(+)$1	218	154	179	20.8705
UUGAGUCCUGCCUACUUUGACUUUU	chr20:42092115-42092338(+)$1	223	17	42	23.0771
AUGUCUUGAUACCCAAUAAAGGUCU	chr11:33880669-33880886(+)$1	217	82	107	22.2243
GAAUGGUCUCUAAACUUCCCAAACC	chr17:62502829-62503057(+)$1	228	147	172	23.8319
CAGCAUGCCAGUAAAUAAUAUGUAG	chr3:145910927-145911142(-)$1	215	141	166	22.7175
AGAAAAAAACCACAAAUGUUUUUCU	chr22:50810356-50810574(+)$1	218	154	179	22.0559
ACGCGUCCCCUCUCUCCCUGUGUUU	chr11:60703075-60703301(+)$1	226	106	131	23.3254
ACAUGCUUGCUGUAACUUUGGAUGA	chr8:38095024-38095245(+)$1	221	38	63	22.8801
CUUGCCUCCUUUUUUCUUAAAGCAA	chr11:71714267-71714493(-)$1	226	153	178	19.5996
AUGAAGAGGUAAAUUAGGUCAGAGU	chr11:33127021-33127242(-)$1	221	122	147	21.4553
AUAGAUACUCAAGCCAAAGUCUGUU	chr16:24228534-24228770(+)$1	236	48	73	23.6840
UUCACAGGCCCAUACUAACUGUCCU	chr2:198284205-198284422(-)$1	217	13	38	21.2693
AAUUUUCUUCUCAUUCUUCUAAAAC	chr1:163045836-163046067(+)$1	231	101	126	21.6682
ACAAAGAAUUUUCCCAGCUUUUGAG	chr12:132198912-132199140(+)$1	228	58	83	23.9928
GGGCACUUUUUACUAUUUGGCCUUC	chr1:36388984-36389219(+)$1	235	209	234	22.7907
AAAGCUACAUCAAGUUCAUGCUAUU	chr12:96661718-96661945(+)$1	227	8	33	22.1395
CCAAAUACUAUAUAUGCCUUGGUCA	chr4:169848235-169848453(-)$1	218	116	141	21.6274
CUCACUCAGAAUGCCGUGGGGUGAG	chr11:868763-868981(-)$1	218	162	187	20.9983
CUGUGGCUCCUUUUCUAAACCACCU	chr1:38462861-38463083(-)$1	222	52	77	23.2237
GAACUGUAAAAUUAAAGUCAGUAUG	chr1:220835578-220835796(+)$1	218	75	100	24.5308
UUCCUGAUUUUAUCUCUCCAGGCUU	chr11:58295456-58295699(-)$1	243	14	39	24.1026
uuggggaacagcuauuaacccccaa	chr9:134184367-134184585(+)$1	218	2	27	21.1502
UUCUCCAAACCUUCCCCAGGAGAGA	chr2:96919225-96919442(-)$1	217	9	34	22.5766
UCUUUCUUCCGGACAAUGAAAUAAA	chrX:47446035-47446257(+)$1	222	112	137	22.1665
CUGAGCCUUCCUAAACAGCCAGUGC	chr16:4013350-4013567(-)$1	217	71	96	22.1474
CCUGAGUUCUCACGGUCUGCUCAGA	chr6:349478-349695(-)$1	217	179	204	21.3005
UGACUGAUCCCUGCAGCCAGGCCGU	chr16:67517386-67517611(+)$1	225	119	144	22.2802
AAAGUGGAUUUAAAUUAACAUUUUU	chr3:113530693-113530925(+)$1	232	192	217	21.3761
CAAGUCAUGUUGUGUUUGGACUUGG	chr14:60759561-60759787(+)$1	226	36	61	21.8475
UUUGUAUCUUUCAACUUUUUCAUCA	chr5:37226616-37226841(-)$1	225	45	70	20.8754
ACAAGAUUUACUCAUUUUCAGGUAC	chr18:72911847-72912094(-)$1	247	172	197	20.8011
UCCCGUGUGAUUACAAAAACAGGAA	chr5:179339193-179339414(-)$1	221	16	41	22.8709
UCCUCUCAAGCCCCCAAAGAGCAAA	chr17:42153546-42153765(+)$1	219	60	85	22.1504
GAGGUCCACAGCAGCUUAGACCUGG	chr7:72419622-72419847(-)$1	225	30	55	23.8314
UCAGCCUCAGAUUCAAAAGACACAU	chr1:38280295-38280512(+)$1	217	66	91	20.8048
GCCUGCUCACACCUGCUCCUGCAGG	chr16:4561520-4561742(-)$1	222	155	180	21.9433
GGCCCCUCUCCUCUGCCCCUGGGGU	chr5:137782284-137782501(+)$1	217	102	127	20.0180
GUCCAUCCCCCUUAACAAGGUGGAC	chr11:61291785-61292001(-)$1	216	88	113	22.0559
CCUAGUUGUUUCAUUGUAUUAGUAA	chr2:99236187-99236417(-)$1	230	152	177	20.5541
AAAUACAAAUUUAGUUUAAGUGUUU	chr2:191828026-191828245(+)$1	219	105	130	23.2219
AAGAAAUUAUUUUCUACAUCUUGAA	chr6:151343342-151343563(+)$1	221	23	48	20.4646

#DB
.(((((................)).	chr16:27472319-27472551(-)$1	1	19	44	20.1249
.(((((.............))))).	chr12:99128483-99128713(-)$1	1	64	89	23.2635
((................)))))..	chr14:104152432-104152657(+)$1	1	93	118	20.8381
.(((..............))).)).	chr22:17592878-17593095(+)$1	1	67	92	21.6663
((((((.............))))))	chr17:5335828-5336045(+)$1	1	2	27	22.9990
(.((.............)).)))).	chr2:42588636-42588857(-)$1	1	15	40	20.3379
..(((((...........)))))..	chr6:111982653-111982883(-)$1	1	46	71	23.0771
..((((..............)))))	chr11:59939941-59940172(-)$1	1	54	79	21.7269
(((((..............))))).	chr2:85771889-85772115(+)$1	1	122	147	21.9826
(.(((..............)))..)	chr5:52393192-52393411(+)$1	1	94	119	22.8210
((((((.............).))))	chr3:7782951-7783167(+)$1	1	124	149	23.2042
....(((...........)))...)	chr12:22697050-22697269(-)$1	1	97	122	23.2266
((((((............)))))))	chr1:86195536-86195772(-)$1	1	21	46	21.3761
...(((............)))..))	chr2:44547712-44547927(-)$1	1	12	37	23.9307
(.(((.............))).)).	chr7:65439885-65440137(-)$1	1	187	212	22.5969
..(((..............)))..)	chr6:31626326-31626547(+)$1	1	21	46	23.0468
((((................)))).	chr17:61504779-61505005(+)$1	1	0	25	20.0316
((................))))..)	chr19:10753718-10753936(+)$1	1	123	148	20.6872
.(((((...........)))))...	chr1:144900575-144900799(-)$1	1	124	149	23.1569
...(((.............)))..)	chr14:74526611-74526836(+)$1	1	6	31	23.8749
(.(((..............)))..)	chrX:153581897-153582113(-)$1	1	130	155	22.2714
((.(((............))).)))	chr11:18343534-18343752(-)$1	1	31	56	23.2212
.(((((............)))))..	chr9:102730802-102731020(+)$1	1	154	179	20.8705
..(((((...........)))))..	chr20:42092115-42092338(+)$1	1	17	42	23.0771
(..((((...........))))..)	chr11:33880669-33880886(+)$1	1	82	107	22.2243
...(((............)))..))	chr17:62502829-62503057(+)$1	1	147	172	23.8319
..(((((...........))))).)	chr3:145910927-145911142(-)$1	1	141	166	22.7175
(((((((...........)))))))	chr22:50810356-50810574(+)$1	1	154	179	22.0559
(((((.............)))))..	chr11:60703075-60703301(+)$1	1	106	131	23.3254
)(((.(.............).)))(	chr8:38095024-38095245(+)$1	1	38	63	22.8801
.((((................))))	chr11:71714267-71714493(-)$1	1	153	178	19.5996
((...((...........))...))	chr11:33127021-33127242(-)$1	1	122	147	21.4553
((((((............)))))))	chr16:24228534-24228770(+)$1	1	48	73	23.6840
...((((...........))))...	chr2:198284205-198284422(-)$1	1	13	38	21.2693
(.((((..............)))).	chr1:163045836-163046067(+)$1	1	101	126	21.6682
.(((((............)))))..	chr12:132198912-132199140(+)$1	1	58	83	23.9928
((((.(............)))))).	chr1:36388984-36389219(+)$1	1	209	234	22.7907
(.(((..............))).))	chr12:96661718-96661945(+)$1	1	8	33	22.1395
((((..............))))...	chr4:169848235-169848453(-)$1	1	116	141	21.6274
.((((((...........)))))))	chr11:868763-868981(-)$1	1	162	187	20.9983
..((((.............)))).)	chr1:38462861-38463083(-)$1	1	52	77	23.2237
..((((............))))...	chr1:220835578-220835796(+)$1	1	75	100	24.5308
..((((............))))..)	chr11:58295456-58295699(-)$1	1	14	39	24.1026
((((((.............))))))	chr9:134184367-134184585(+)$1	1	2	27	21.1502
.(((((............)))))((	chr2:96919225-96919442(-)$1	1	9	34	22.5766
..((((...........))))....	chrX:47446035-47446257(+)$1	1	112	137	22.1665
(((.((...........)))))...	chr16:4013350-4013567(-)$1	1	71	96	22.1474
.((((((...........)))))).	chr6:349478-349695(-)$1	1	179	204	21.3005
.(.(((...........))).))))	chr16:67517386-67517611(+)$1	1	119	144	22.2802
((((((............)))))))	chr3:113530693-113530925(+)$1	1	192	217	21.3761
((((((............)))))))	chr14:60759561-60759787(+)$1	1	36	61	21.8475
(.((................))..)	chr5:37226616-37226841(-)$1	1	45	70	20.8754
((..((...........))..))).	chr18:72911847-72912094(-)$1	1	172	197	20.8011
(((.((............)).))).	chr5:179339193-179339414(-)$1	1	16	41	22.8709
(.((((...........)))).)))	chr17:42153546-42153765(+)$1	1	60	85	22.1504
.(((((............))))).)	chr7:72419622-72419847(-)$1	1	30	55	23.8314
((................))))...	chr1:38280295-38280512(+)$1	1	66	91	20.8048
((((((..............)))))	chr16:4561520-4561742(-)$1	1	155	180	21.9433
((((((..............)))))	chr5:137782284-137782501(+)$1	1	102	127	20.0180
(((((((...........)))))))	chr11:61291785-61292001(-)$1	1	88	113	22.0559
.(((((...........)))))...	chr2:99236187-99236417(-)$1	1	152	177	20.5541
((((((.............))))))	chr2:191828026-191828245(+)$1	1	105	130	23.2219
((((..............)))))).	chr6:151343342-151343563(+)$1	1	23	48	20.4646

#PSSM
d : 0.12	! : 0.11	[ : 0.09	g : 0.09	" : 0.09	# : 0.06	e : 0.06	h : 0.06	c : 0.06	i : 0.06	b : 0.04	f : 0.04	: : 0.04	$ : 0.01	
e : 0.17	[ : 0.12	c : 0.11	! : 0.09	" : 0.07	d : 0.07	f : 0.07	g : 0.06	h : 0.06	# : 0.04	i : 0.04	$ : 0.01	a : 0.01	
e : 0.20	c : 0.15	d : 0.15	g : 0.06	h : 0.06	" : 0.06	f : 0.06	y : 0.04	i : 0.04	b : 0.03	# : 0.03	[ : 0.03	! : 0.03	
c : 0.20	e : 0.20	d : 0.19	g : 0.06	h : 0.06	f : 0.06	y : 0.04	i : 0.04	b : 0.03	[ : 0.03	# : 0.01	" : 0.01	! : 0.01	
e : 0.19	c : 0.17	d : 0.15	y : 0.07	b : 0.06	g : 0.06	h : 0.06	w : 0.04	i : 0.04	f : 0.04	[ : 0.03	v : 0.01	" : 0.01	
e : 0.15	d : 0.14	w : 0.12	y : 0.09	c : 0.09	b : 0.07	h : 0.06	g : 0.04	v : 0.04	a : 0.04	i : 0.04	f : 0.04	
u : 0.23	w : 0.19	v : 0.17	y : 0.11	t : 0.11	e : 0.04	d : 0.03	g : 0.03	f : 0.03	c : 0.01	b : 0.01	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
t : 0.28	u : 0.23	w : 0.19	v : 0.17	y : 0.11	
u : 0.23	w : 0.19	t : 0.17	v : 0.15	y : 0.11	b : 0.04	e : 0.03	d : 0.03	c : 0.01	
e : 0.17	w : 0.14	d : 0.14	v : 0.12	c : 0.11	b : 0.07	y : 0.06	f : 0.06	h : 0.03	g : 0.03	i : 0.01	a : 0.01	
e : 0.22	c : 0.20	d : 0.15	y : 0.06	w : 0.06	f : 0.06	g : 0.04	h : 0.04	a : 0.03	b : 0.03	i : 0.03	] : 0.01	2 : 0.01	
e : 0.22	d : 0.22	c : 0.19	] : 0.06	h : 0.06	f : 0.06	g : 0.04	i : 0.04	y : 0.03	3 : 0.01	b : 0.01	2 : 0.01	
e : 0.22	d : 0.20	c : 0.14	] : 0.06	g : 0.06	h : 0.06	f : 0.06	i : 0.04	3 : 0.03	2 : 0.03	y : 0.01	4 : 0.01	a : 0.01	b : 0.01	
e : 0.19	2 : 0.15	d : 0.11	g : 0.07	f : 0.07	3 : 0.06	h : 0.06	4 : 0.06	b : 0.04	c : 0.04	i : 0.04	7 : 0.01	] : 0.01	5 : 0.01	
2 : 0.19	d : 0.11	g : 0.09	e : 0.07	f : 0.07	3 : 0.06	h : 0.06	c : 0.06	4 : 0.06	b : 0.04	] : 0.04	i : 0.04	: : 0.01	7 : 0.01	5 : 0.01	
g : 0.11	] : 0.09	4 : 0.09	e : 0.09	2 : 0.07	d : 0.07	f : 0.07	3 : 0.06	h : 0.06	i : 0.06	: : 0.04	c : 0.03	b : 0.03	a : 0.01	7 : 0.01	6 : 0.01	5 : 0.01	

#score	1395.9663433079272
#seq	63
#width	25
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FOX2_Yeo2009_hg19_UTR_m2_run1.txt

#BEAR
i==========rrrrrrrrr==========	chr10:28824485-28824767(+)$1	282	214	244	12.7336
ffffccc"""cccnnnnnccc4444ccc]f	chr4:40103644-40103937(+)$1	293	130	160	11.1067
###ccc"""ddddoooooodddd4444ccc	chr13:98634688-98634982(+)$1	294	226	256	14.1014
=======####bboooooobb22=======	chr14:69340961-69341216(+)$1	255	25	55	15.6466
!dddd"""eeeeeooooooeeeeeddddcc	chr6:30851172-30851454(+)$1	282	196	226	12.1013
ggggg!!ccccccrrrrrrrrrccc]ccc2	chr12:105519748-105520004(+)$1	256	213	243	9.8999
d[dddd!!eeeeeooooooeeeee22dddd	chr13:48830325-48830682(+)$1	357	94	124	11.7457
!ccc[ccc####aooooooa4444ccc]cc	chr6:109688667-109688944(+)$1	277	136	166	14.5006
iiiiiiii[ddddoooooodddd333iiii	chr5:133492548-133492886(+)$1	338	105	135	15.2551
bb[ggggggg[bboooooobbgggggggbb	chr12:70726163-70726413(+)$1	250	31	61	12.6425
dddd[a####cccooooooccc4444a]dd	chr16:89949743-89950001(+)$1	258	199	229	14.6614
::ccc[gggggggooooooggggggg22cc	chr19:34890854-34891144(+)$1	290	221	251	11.5327
:ggggggg[ccc[annnnna]ccc]ggggg	chr10:3171090-3171461(+)$1	371	217	247	10.2748
!===========cccmmmmccc]=======	chr1:90482842-90483205(+)$1	363	26	56	12.4467
ee[ccc[ffffffooooooffffffccc33	chr7:134644666-134644970(+)$1	304	244	274	12.2342
:::==========oooooo==========:	chr2:9725103-9725361(+)$1	258	213	243	12.8024
b[ccc[bb[ddddoooooodddd]bb]ccc	chr16:30938613-30938897(+)$1	284	114	144	12.5057
iiiiiiii!!cccmmmmccc22iiiiiiii	chr10:70502102-70502428(+)$1	326	181	211	10.6852
=============oooooo===========	chr4:95210833-95211104(+)$1	271	195	225	17.1625
eee==========oooooo==========:	chr11:719988-720337(+)$1	349	310	340	15.5419
ccc"""gggggggooooooggggggg5555	chrX:123156340-123156671(+)$1	331	181	211	10.6574
eeeffffffbb[aooooooabb]ffffff2	chrX:70800148-70800420(+)$1	272	226	256	11.3159
ff[a!!bb"""bboooooobbbb22a]fff	chr12:4766861-4767118(+)$1	257	20	50	12.6857
===$$$$$eeeeeooooooeeeee22====	chr2:196573369-196573635(+)$1	266	87	117	13.1963
gggggg[ccc!!aooooooa22ccc]gggg	chr22:46746209-46746546(+)$1	337	250	280	13.7381
biiiiiiiii[ddddlllddddiiiiiiii	chr15:44705776-44706094(+)$1	318	27	57	10.5501
eeee[===========lll===========	chr21:34931883-34932179(+)$1	296	199	229	12.9337
[==========cccnnnnnccc333=====	chr5:115780960-115781224(+)$1	264	167	197	13.7457
ffffff!!bbcccooooooccc]bb22fff	chr11:71707194-71707526(+)$1	332	21	51	12.6316
ffff[dddd[cccoooooocccdddd]fff	chr18:33243569-33243908(+)$1	339	127	157	12.4063
gggg!!iiiiiiiiimmmmiiiiiiiii22	chr17:57279354-57279732(+)$1	378	312	342	10.7723
[ffffff[eeeeeooooooeeeeeffffff	chr21:45744972-45745282(+)$1	310	183	213	11.9665
ddd[ccc[eeeeeooooooeeeeeccc22d	chr12:56094490-56094754(+)$1	264	127	157	11.9658
gggbb"""bbcccooooooccc]bb]bb]g	chr1:1717281-1717547(+)$1	266	38	68	13.1903
iiiiiiiii[cccooooooccc]iiiiiii	chr7:5566939-5567212(+)$1	273	110	140	16.1561
f[bb[bb"""cccooooooccc333bb]bb	chr12:67707163-67707526(+)$1	363	207	237	14.2704
)ffffff"""cccooooooccc333fffff	chr11:10328504-10328830(+)$1	326	212	242	14.3622
ee!!==========nnnnn==========2	chr7:94298355-94298777(+)$1	422	11	41	12.9667
======="""cccooooooccc333=====	chr7:158448851-158449113(+)$1	262	144	174	17.7834
ggggggg"""cccooooooccc4444gggg	chr10:111987332-111987803(+)$1	471	239	269	16.1417
dddd[eeeee[bboooooobb333eeeee]	chr12:25362009-25362321(+)$1	312	54	84	12.0765
]bb:===========mmmm===========	chr9:36337590-36337877(+)$1	287	49	79	10.7807
d"""eeeeeddddoooooodddd22eeeee	chr7:888015-888365(+)$1	350	290	320	11.6534
eeeeccc!!bb[aooooooa]bb22ccc]e	chr17:19559689-19559946(+)$1	257	59	89	12.8544
cc[dddd[eeeeeooooooeeeeedddd]c	chr19:1206659-1206968(+)$1	309	80	110	11.7114
"""==========ppppppp==========	chr11:9303194-9303472(+)$1	278	80	110	10.6024
!!eeeee!!ddddoooooodddd]eeeee5	chr9:114983077-114983410(+)$1	333	154	184	11.8116
c[bb!!bb!!cccooooooccc22bb]bb]	chr5:17276166-17276571(+)$1	405	206	236	13.3736

#otherMatches

#Seq PSSM
UUGUUGAAACUUUGACAUACAGUUUUAACA	chr10:28824485-28824767(+)$1	282	214	244	12.7336
GCUUCUGAGAACCAAGUAGGUGCAGCAGAA	chr4:40103644-40103937(+)$1	293	130	160	11.1067
AAUGAGAAUUGUGAUUAACCACAUAGACUU	chr13:98634688-98634982(+)$1	294	226	256	14.1014
GGAUUUAAAAAUGAGAAGCCACAUAAAUUC	chr14:69340961-69341216(+)$1	255	25	55	15.6466
CUCAUUUUUGGCCUCUUCUGGCCAGUGAUC	chr6:30851172-30851454(+)$1	282	196	226	12.1013
CAUAAUUGAAGUAUAUUUGUUCUGCUUUCU	chr12:105519748-105520004(+)$1	256	213	243	9.8999
UAUUAAAAUCUUUGAAGAAGAAGAAGUUGA	chr13:48830325-48830682(+)$1	357	94	124	11.7457
GGGAGAGAAAAAGAAAAAGCACAGUCUAUU	chr6:109688667-109688944(+)$1	277	136	166	14.5006
AAUUAUUCUUUACAUGCAAGUAGUGUGAAU	chr5:133492548-133492886(+)$1	338	105	135	15.2551
ACACUAACCUGCAUAUUUUUGAGGUUAGGU	chr12:70726163-70726413(+)$1	250	31	61	12.6425
GGUGGCAUCAGACGGGAGAGUUCCAAGGCA	chr16:89949743-89950001(+)$1	258	199	229	14.6614
CAGGGAAGGCUGGUCUCCCCCAGCCUAACC	chr19:34890854-34891144(+)$1	290	221	251	11.5327
UGAUGUAUGGGUGGGAAGGCGGCCGAUGCA	chr10:3171090-3171461(+)$1	371	217	247	10.2748
CUUACAGAAUGGCAUUUACAUGUUCAUUUU	chr1:90482842-90483205(+)$1	363	26	56	12.4467
GCAUGUCGAUUUUGAUUUAGGAAUCACACU	chr7:134644666-134644970(+)$1	304	244	274	12.2342
GAAUGGGUUUCUUUGCUAUAGGAAAUCCAA	chr2:9725103-9725361(+)$1	258	213	243	12.8024
GAGUGUACAAUCUGCAACGAGAUCGUCCAC	chr16:30938613-30938897(+)$1	284	114	144	12.5057
AUACGUUUGGAUUUGUGGAUGAAGAUGUAU	chr10:70502102-70502428(+)$1	326	181	211	10.6852
AUAUAUAUUGUCUUUCACUGGAUAAUGUGU	chr4:95210833-95211104(+)$1	271	195	225	17.1625
UGCGGCCGGUCCUCUCUGCAGGGCCGGCCA	chr11:719988-720337(+)$1	349	310	340	15.5419
GUAAGUAAAUUAUAUUCUGAUAAUUUUUAA	chrX:123156340-123156671(+)$1	331	181	211	10.6574
agugcaguggcacaaucucggcucacugca	chrX:70800148-70800420(+)$1	272	226	256	11.3159
UGUUUUCAUCCGAUUGCUUUCUGCUAUUAU	chr12:4766861-4767118(+)$1	257	20	50	12.6857
UUUGGAAGAAUAUGAUGCUGUAUUGAAAGG	chr2:196573369-196573635(+)$1	266	87	117	13.1963
UCCAGGACCUAACAUCAAAGGCGGGCCUUG	chr22:46746209-46746546(+)$1	337	250	280	13.7381
UUUUUUGGUUAUGAUACAGUUAAGCCAAAA	chr15:44705776-44706094(+)$1	318	27	57	10.5501
UAAGUAGGAGGAAUAUUAUGUAUUUUUCCU	chr21:34931883-34932179(+)$1	296	199	229	12.9337
UUGCUGUCUCACAUGCAAGGUGAAAUGGGA	chr5:115780960-115781224(+)$1	264	167	197	13.7457
UCUCUUUUCUUUAACACACUGACAGCUGGG	chr11:71707194-71707526(+)$1	332	21	51	12.6316
AUCAGUUCAAUUUAAUGGCAAGUGAGAUGA	chr18:33243569-33243908(+)$1	339	127	157	12.4063
aucccaccacuuugggaggccaagguggga	chr17:57279354-57279732(+)$1	378	312	342	10.7723
CAGGGGUGAGGCUCUGAGAGGCCUGCCCCU	chr21:45744972-45745282(+)$1	310	183	213	11.9665
CAACCCUGUCUCUGAGGUAAGAGGAGGUUU	chr12:56094490-56094754(+)$1	264	127	157	11.9658
UUCCGAUAUGUGCCACAGAGCAGCAACGAG	chr1:1717281-1717547(+)$1	266	38	68	13.1903
GGCCAUUCUCCUUAGAGAGAAGUGGGGUGG	chr7:5566939-5567212(+)$1	273	110	140	16.1561
UUAAUGCCAGUGUGAAUUUGCAGAUGUUUU	chr12:67707163-67707526(+)$1	363	207	237	14.2704
AAGGGCAUUUUAAAAGCAAUUAUAUUGUCC	chr11:10328504-10328830(+)$1	326	212	242	14.3622
UCUUUGUUGUUUUAGAUUGUAGAAUGGUAU	chr7:94298355-94298777(+)$1	422	11	41	12.9667
GAGGAGCAGAGAGCAAGCACUCGCGGUUCU	chr7:158448851-158449113(+)$1	262	144	174	17.7834
CUCUUUAGAACAGAGAGAGUUGAAAGUAAA	chr10:111987332-111987803(+)$1	471	239	269	16.1417
AAGGAAAUGGCCUUAUAAUAGUUUCCAUUG	chr12:25362009-25362321(+)$1	312	54	84	12.0765
AACAUGAUUUUUUUUCAUUAAAAAAGAUUA	chr9:36337590-36337877(+)$1	287	49	79	10.7807
GAAAGUGCUGUGACUUUCCUCGCCAGGCGC	chr7:888015-888365(+)$1	350	290	320	11.6534
UUUUCUAUACGGGAAACACUGCGGUUGGCA	chr17:19559689-19559946(+)$1	257	59	89	12.8544
AACAAUCGUUUCUGUUGGAAGAAGGGUUUU	chr19:1206659-1206968(+)$1	309	80	110	11.7114
AAUUUUACUUUGUGAGUUAGAUAAAGUAAA	chr11:9303194-9303472(+)$1	278	80	110	10.6024
CCAAAACAGAGAUACACAGAUCUAGUUUUU	chr9:114983077-114983410(+)$1	333	154	184	11.8116
GCUGAGAGUUGAAUAGCUUUUCUUCUGCAA	chr5:17276166-17276571(+)$1	405	206	236	13.3736

#DB
)((((((((((.........))))))))))	chr10:28824485-28824767(+)$1	1	214	244	12.7336
(((((((...(((.....)))....))).)	chr4:40103644-40103937(+)$1	1	130	160	11.1067
...(((...((((......))))....)))	chr13:98634688-98634982(+)$1	1	226	256	14.1014
(((((((....((......))..)))))))	chr14:69340961-69341216(+)$1	1	25	55	15.6466
.((((...(((((......)))))))))))	chr6:30851172-30851454(+)$1	1	196	226	12.1013
(((((..((((((.........))).))).	chr12:105519748-105520004(+)$1	1	213	243	9.8999
(.((((..(((((......)))))..))))	chr13:48830325-48830682(+)$1	1	94	124	11.7457
.(((.(((....(......)....))).))	chr6:109688667-109688944(+)$1	1	136	166	14.5006
((((((((.((((......))))...))))	chr5:133492548-133492886(+)$1	1	105	135	15.2551
((.(((((((.((......)))))))))))	chr12:70726163-70726413(+)$1	1	31	61	12.6425
((((.(....(((......)))....).))	chr16:89949743-89950001(+)$1	1	199	229	14.6614
..(((.(((((((......)))))))..))	chr19:34890854-34891144(+)$1	1	221	251	11.5327
.(((((((.(((.(.....).))).)))))	chr10:3171090-3171461(+)$1	1	217	247	10.2748
.((((((((((((((....))).)))))))	chr1:90482842-90483205(+)$1	1	26	56	12.4467
((.(((.((((((......)))))))))..	chr7:134644666-134644970(+)$1	1	244	274	12.2342
...((((((((((......)))))))))).	chr2:9725103-9725361(+)$1	1	213	243	12.8024
(.(((.((.((((......)))).)).)))	chr16:30938613-30938897(+)$1	1	114	144	12.5057
((((((((..(((....)))..))))))))	chr10:70502102-70502428(+)$1	1	181	211	10.6852
(((((((((((((......)))))))))))	chr4:95210833-95211104(+)$1	1	195	225	17.1625
)))((((((((((......)))))))))).	chr11:719988-720337(+)$1	1	310	340	15.5419
(((...(((((((......)))))))....	chrX:123156340-123156671(+)$1	1	181	211	10.6574
(((((((((((.(......))).)))))).	chrX:70800148-70800420(+)$1	1	226	256	11.3159
((.(..((...((......))))..).)))	chr12:4766861-4767118(+)$1	1	20	50	12.6857
(((.....(((((......)))))..))))	chr2:196573369-196573635(+)$1	1	87	117	13.1963
((((((.(((..(......)..))).))))	chr22:46746209-46746546(+)$1	1	250	280	13.7381
((((((((((.((((...))))))))))))	chr15:44705776-44706094(+)$1	1	27	57	10.5501
((((.(((((((((((...)))))))))))	chr21:34931883-34932179(+)$1	1	199	229	12.9337
.(((((((((((((.....)))...)))))	chr5:115780960-115781224(+)$1	1	167	197	13.7457
((((((..(((((......))).))..)))	chr11:71707194-71707526(+)$1	1	21	51	12.6316
((((.((((.(((......))))))).)))	chr18:33243569-33243908(+)$1	1	127	157	12.4063
((((..(((((((((....)))))))))..	chr17:57279354-57279732(+)$1	1	312	342	10.7723
.((((((.(((((......)))))))))))	chr21:45744972-45745282(+)$1	1	183	213	11.9665
(((.(((.(((((......))))))))..)	chr12:56094490-56094754(+)$1	1	127	157	11.9658
(((((...(((((......))).)).)).)	chr1:1717281-1717547(+)$1	1	38	68	13.1903
(((((((((.(((......))).)))))))	chr7:5566939-5567212(+)$1	1	110	140	16.1561
(.((.((...(((......)))...)).))	chr12:67707163-67707526(+)$1	1	207	237	14.2704
.((((((...(((......)))...)))))	chr11:10328504-10328830(+)$1	1	212	242	14.3622
((..((((((((((.....)))))))))).	chr7:94298355-94298777(+)$1	1	11	41	12.9667
(((((((...(((......)))...)))))	chr7:158448851-158449113(+)$1	1	144	174	17.7834
(((((((...(((......)))....))))	chr10:111987332-111987803(+)$1	1	239	269	16.1417
((((.(((((.((......))...))))).	chr12:25362009-25362321(+)$1	1	54	84	12.0765
.)).(((((((((((....)))))))))))	chr9:36337590-36337877(+)$1	1	49	79	10.7807
(...(((((((((......))))..)))))	chr7:888015-888365(+)$1	1	290	320	11.6534
(((((((..((.(......).))..))).)	chr17:19559689-19559946(+)$1	1	59	89	12.8544
((.((((.(((((......))))))))).)	chr19:1206659-1206968(+)$1	1	80	110	11.7114
...((((((((((.......))))))))))	chr11:9303194-9303472(+)$1	1	80	110	10.6024
..(((((..((((......)))).))))).	chr9:114983077-114983410(+)$1	1	154	184	11.8116
(.((..((..(((......)))..)).)).	chr5:17276166-17276571(+)$1	1	206	236	13.3736

#PSSM
e : 0.12	f : 0.10	g : 0.10	d : 0.10	i : 0.08	= : 0.08	! : 0.08	b : 0.06	: : 0.06	c : 0.06	[ : 0.04	# : 0.02	) : 0.02	] : 0.02	" : 0.02	
= : 0.14	f : 0.12	g : 0.12	e : 0.12	d : 0.08	[ : 0.08	i : 0.08	c : 0.06	b : 0.04	: : 0.04	" : 0.04	# : 0.02	! : 0.02	
= : 0.14	g : 0.12	f : 0.10	d : 0.10	e : 0.10	c : 0.08	i : 0.08	[ : 0.08	b : 0.06	" : 0.04	# : 0.02	: : 0.02	! : 0.02	
= : 0.18	f : 0.12	g : 0.12	c : 0.10	d : 0.10	i : 0.08	e : 0.06	b : 0.06	" : 0.04	a : 0.02	$ : 0.02	[ : 0.02	! : 0.02	: : 0.02	
= : 0.22	c : 0.14	[ : 0.12	g : 0.10	i : 0.08	f : 0.08	d : 0.06	! : 0.06	e : 0.04	" : 0.02	$ : 0.02	b : 0.02	
= : 0.25	c : 0.12	! : 0.08	i : 0.08	g : 0.08	f : 0.08	" : 0.06	d : 0.06	e : 0.06	[ : 0.04	a : 0.02	$ : 0.02	b : 0.02	
= : 0.25	i : 0.10	g : 0.10	c : 0.08	b : 0.08	" : 0.06	! : 0.06	f : 0.06	e : 0.06	[ : 0.04	d : 0.04	# : 0.02	$ : 0.02	
= : 0.20	" : 0.16	i : 0.10	! : 0.08	g : 0.08	c : 0.06	b : 0.06	[ : 0.06	# : 0.04	f : 0.04	e : 0.04	$ : 0.02	d : 0.02	
= : 0.20	e : 0.16	" : 0.14	! : 0.08	# : 0.06	[ : 0.06	g : 0.06	i : 0.06	c : 0.04	f : 0.04	b : 0.04	d : 0.02	
= : 0.20	e : 0.14	" : 0.12	d : 0.10	b : 0.08	# : 0.06	c : 0.06	g : 0.06	! : 0.04	i : 0.04	[ : 0.04	f : 0.02	
c : 0.29	= : 0.20	e : 0.12	d : 0.10	[ : 0.06	# : 0.04	g : 0.04	b : 0.04	f : 0.02	" : 0.02	! : 0.02	i : 0.02	
c : 0.31	= : 0.16	d : 0.12	e : 0.12	b : 0.08	g : 0.04	[ : 0.04	r : 0.02	# : 0.02	f : 0.02	! : 0.02	i : 0.02	
c : 0.31	= : 0.14	d : 0.12	e : 0.12	b : 0.08	a : 0.08	g : 0.04	r : 0.02	[ : 0.02	f : 0.02	i : 0.02	
o : 0.72	= : 0.06	r : 0.04	c : 0.04	n : 0.02	a : 0.02	m : 0.02	d : 0.02	i : 0.02	p : 0.02	
o : 0.72	n : 0.08	r : 0.04	= : 0.04	c : 0.02	m : 0.02	d : 0.02	i : 0.02	p : 0.02	
o : 0.72	n : 0.08	m : 0.08	r : 0.04	l : 0.02	= : 0.02	p : 0.02	
o : 0.72	n : 0.08	m : 0.08	r : 0.04	l : 0.04	p : 0.02	
o : 0.72	n : 0.08	m : 0.06	r : 0.04	l : 0.04	c : 0.02	p : 0.02	
o : 0.72	n : 0.06	m : 0.06	r : 0.04	c : 0.04	d : 0.02	l : 0.02	p : 0.02	
c : 0.29	d : 0.12	e : 0.12	= : 0.12	a : 0.10	b : 0.08	r : 0.04	g : 0.04	f : 0.02	i : 0.02	p : 0.02	
c : 0.27	= : 0.16	d : 0.12	e : 0.12	b : 0.10	g : 0.04	] : 0.04	2 : 0.04	r : 0.02	4 : 0.02	f : 0.02	i : 0.02	
c : 0.27	= : 0.16	d : 0.12	e : 0.12	2 : 0.06	g : 0.06	b : 0.06	4 : 0.04	r : 0.02	f : 0.02	i : 0.02	3 : 0.02	
= : 0.16	d : 0.12	e : 0.12	] : 0.10	3 : 0.10	4 : 0.08	c : 0.06	g : 0.06	i : 0.06	2 : 0.04	b : 0.04	f : 0.02	
= : 0.20	e : 0.12	3 : 0.12	4 : 0.10	i : 0.08	2 : 0.08	c : 0.06	g : 0.06	f : 0.04	] : 0.04	b : 0.04	d : 0.02	
= : 0.20	2 : 0.10	3 : 0.10	4 : 0.08	c : 0.08	b : 0.08	i : 0.08	d : 0.06	g : 0.06	f : 0.06	e : 0.04	] : 0.02	
= : 0.25	c : 0.10	g : 0.08	i : 0.08	4 : 0.06	d : 0.06	] : 0.06	2 : 0.06	b : 0.06	f : 0.06	e : 0.06	3 : 0.02	a : 0.02	
= : 0.27	c : 0.12	i : 0.10	g : 0.08	] : 0.08	d : 0.06	f : 0.06	e : 0.06	2 : 0.04	b : 0.04	4 : 0.02	a : 0.02	5 : 0.02	
= : 0.27	c : 0.12	f : 0.12	i : 0.10	g : 0.08	d : 0.06	] : 0.06	e : 0.06	2 : 0.04	b : 0.04	5 : 0.02	
= : 0.27	c : 0.12	f : 0.12	] : 0.08	i : 0.08	b : 0.06	g : 0.06	e : 0.06	d : 0.04	2 : 0.04	3 : 0.02	5 : 0.02	
= : 0.20	f : 0.12	c : 0.12	2 : 0.08	i : 0.08	g : 0.08	d : 0.06	b : 0.04	: : 0.04	5 : 0.04	] : 0.04	e : 0.04	3 : 0.02	

#score	617.8834103116538
#seq	48
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m1_run2.txt

#BEAR
^^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhh	chr15:62157590-62157970(-)$1	380	334	366	34.9174
ggggggg^^^^^^^^^^^^^^^^^^^gggggg	chr14:81440732-81441014(+)$1	282	57	89	33.0959
ggggggg^^^^^^^^^^^^^^^^^^^gggggg	chr6:45299676-45299902(+)$1	226	145	177	33.0959
^^^^^^^^^^^^^^^^^^^^^^^^^ccc]ccc	chr2:9640380-9640625(-)$1	245	77	109	36.7962
ee!!dddd^^^^^^^^^^^^^^^^^^^^dddd	chr1:8437288-8437534(-)$1	246	11	43	31.7279
^^^^^^^^^^^^^^^^^^^^^^^^^^bbdddd	chr1:29381814-29382050(+)$1	236	69	101	36.6687
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr1:46411532-46411759(+)$1	227	162	194	37.7165
cc!!ccc^^^^^^^^^^^^^^^^^^^^ccccc	chr11:120899210-120899490(+)$1	280	91	123	34.1477
::ccc^^^^^^^^^^^^^^^^^^^^ccc:fff	chrX:38138795-38139067(-)$1	272	30	62	32.1110
^^^^^^^^^^^^^^^^^^^^^^^^^ccc]ddd	chr19:41942640-41942917(-)$1	277	65	97	36.7243
hhhhhhh^^^^^^^^^^^^^^^^^^hhhhhhh	chr4:76685991-76686293(+)$1	302	213	245	28.1693
:eeeee^^^^^^^^^^^^^^^^^^^eeeee::	chr14:64352793-64353049(+)$1	256	125	157	30.8731
iiiiiii^^^^^^^^^^^^^^^^^^iiiiiii	chr12:71537652-71537872(-)$1	220	82	114	32.2325
[eeeee^^^^^^^^^^^^^^^^^^^eeeeeee	chr7:27185767-27186042(-)$1	275	65	97	33.3975
iiiccc^^^^^^^^^^^^^^^^^^^^ccc]ii	chr6:75986141-75986407(-)$1	266	159	191	34.3397
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr3:44507907-44508145(-)$1	238	175	207	37.6916
^^^^^^^^^^^^^^^^^^^^^^^^^iiiiiii	chr3:142047241-142047477(-)$1	236	200	232	36.5629
bdddd^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr20:30994350-30994797(+)$1	447	269	301	35.1291
iiiiiii^^^^^^^^^^^^^^^^^^^iiiiii	chr1:50994999-50995251(-)$1	252	109	141	32.9137
:dddd^^^^^^^^^^^^^^^^^^^^^^dddde	chr13:50317071-50317323(-)$1	252	48	80	34.0873
^^^^^^^^^^^^^^^^^^^^^^^^^ccc]ddd	chr2:37272328-37272564(-)$1	236	107	139	36.7243
=======^^^^^^^^^^^^^^^^^^=======	chr8:90956199-90956490(-)$1	291	242	274	33.1134
feeeee^^^^^^^^^^^^^^^^^^^^^^^eee	chr3:33467740-33468017(-)$1	277	96	128	34.7062
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr6:35852119-35852398(-)$1	279	217	249	37.6916
JJeeeee^^^^^^^^^^^^^^^^^^eeeee::	chr11:14596005-14596283(-)$1	278	211	243	27.8685
gg^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr5:172331444-172331718(+)$1	274	200	232	35.8482
ggggggg^^^^^^^^^^^^^^^^^^^^^gggg	chrX:147625778-147626113(+)$1	335	120	152	33.6984
::eeeee^^^^^^^^^^^^^^^^^^eeeee:E	chr20:2696108-2696338(+)$1	230	89	121	29.0876
b^^^^^^^^^^^^^^^^^^^^^^^^bb333cc	chr6:131985615-131985856(+)$1	241	100	132	36.1434
!ffffff^^^^^^^^^^^^^^^^^^ffffff3	chrX:38512428-38512670(+)$1	242	106	138	31.6173
:dddd^^^^^^^^^^^^^^^^^^^^^^^dddd	chr15:64666159-64666418(-)$1	259	157	189	34.4655
^^^^^^^^^^^^^^^^^^^^^^^^^=======	chr1:51917144-51917400(-)$1	256	209	241	36.7957
^^^^^^^^^^^^^^^^^^^^^^^^^ggggggg	chr2:178405085-178405347(+)$1	262	118	150	36.5828
dd!!ccc^^^^^^^^^^^^^^^^^^ccc22dd	chr7:92199382-92199677(-)$1	295	117	149	32.8123
Deeeee^^^^^^^^^^^^^^^^^^^^^^^^ee	chr6:41045014-41045297(+)$1	283	114	146	34.0341
:ffffff^^^^^^^^^^^^^^^^^^^^^ffff	chr7:72146440-72146676(-)$1	236	93	125	32.4421
h^^^^^^^^^^^^^^^^^^^^^^^^hhhhhhh	chr18:13418058-13418331(+)$1	273	119	151	34.2135
f^^^^^^^^^^^^^^^^^^^^^^^^ffffffd	chr11:63458215-63458462(+)$1	247	67	99	35.4686
ee^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr16:67490152-67490393(-)$1	241	109	141	36.8691
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^dd	chr6:135712066-135712320(-)$1	254	120	152	37.6916
b^^^^^^^^^^^^^^^^^^^^^^^^^bb]eee	chr3:35805361-35805618(+)$1	257	130	162	36.6929
cc^^^^^^^^^^^^^^^^^^^^^^^ccc]iii	chr3:122496946-122497194(-)$1	248	35	67	36.2916
((eeeee^^^^^^^^^^^^^^^^^^eeeee00	chr3:89168300-89168549(+)$1	249	134	166	31.0530
gg[bb^^^^^^^^^^^^^^^^^^^^^^bb]gg	chr13:94304166-94304397(+)$1	231	86	118	34.6235
====[bb^^^^^^^^^^^^^^^^^^bb=====	chr14:48099438-48099674(-)$1	236	64	96	32.4499
!dddd^^^^^^^^^^^^^^^^^^^dddd333e	chr5:77017029-77017309(-)$1	280	140	172	32.0830
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ee	chr9:123176750-123177007(-)$1	257	173	205	37.7165
fffff^^^^^^^^^^^^^^^^^^^^ffffff3	chr14:66192654-66192895(+)$1	241	177	209	33.1820
::eeeee^^^^^^^^^^^^^^^^^^eeeee::	chr14:67010373-67010680(+)$1	307	188	220	29.1115
ggg[bb^^^^^^^^^^^^^^^^^^^^bbgggg	chr13:49837844-49838109(+)$1	265	9	41	33.8045
:eeeee^^^^^^^^^^^^^^^^^^^^^^eeee	chr5:79930764-79931026(-)$1	262	13	45	34.2936
:dddd^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr5:129043980-129044230(+)$1	250	6	38	34.6750
dd^^^^^^^^^^^^^^^^^^^^^^^^^^^ddd	chr17:63041835-63042156(-)$1	321	81	113	36.7528
^^^^^^^^^^^^^^^^^^^^^^^^^^bb]ggg	chr10:30018348-30018584(-)$1	236	186	218	37.1669
Gffffff^^^^^^^^^^^^^^^^^^^^^ffff	chr7:32538279-32538515(+)$1	236	93	125	32.6734
'ffffff^^^^^^^^^^^^^^^^^^^ffffff	chr20:36713145-36713426(+)$1	281	54	86	32.0050
^^^^^^^^^^^^^^^^^^^^^^^^^ccc22ee	chr4:123244889-123245162(+)$1	273	97	129	36.4489
hh^^^^^^^^^^^^^^^^^^^^^^^hhhhhhh	chr4:144116149-144116393(+)$1	244	88	120	33.5048

#otherMatches

#Seq PSSM
uuuaguuauauuuuuccauguucuuagaaaug	chr15:62157590-62157970(-)$1	380	334	366	34.9174
GUUUGGCUGAAAAUCCUGUUAGUACUGCCAAA	chr14:81440732-81441014(+)$1	282	57	89	33.0959
AGCGCUAAUCAAUUACAAACCUUUUCUAGUGC	chr6:45299676-45299902(+)$1	226	145	177	33.0959
cuccaauccccccauuccccacaacucagagc	chr2:9640380-9640625(-)$1	245	77	109	36.7962
CAGCUUGUGGGAAAGAAAAGUGAUGUCAACAA	chr1:8437288-8437534(-)$1	246	11	43	31.7279
UCACUUUUUCUCCUUUUUGCCUAUAACACAGA	chr1:29381814-29382050(+)$1	236	69	101	36.6687
AAUACAUUACAAAACCAUUAUCUCCCUUUCCU	chr1:46411532-46411759(+)$1	227	162	194	37.7165
cuaagugagauaauacauauaaaacaacacag	chr11:120899210-120899490(+)$1	280	91	123	34.1477
AUAGCACAAAAUUUUAUACUUUAUAGCUCUGG	chrX:38138795-38139067(-)$1	272	30	62	32.1110
UAUUUAUUCAACCAUCCUAAUUCAAGUCUCUG	chr19:41942640-41942917(-)$1	277	65	97	36.7243
AUUAUGCUAUAAAUUACUUUCAAACGCAUGAU	chr4:76685991-76686293(+)$1	302	213	245	28.1693
ACAGGGAAACACACAAACUUAUCACCUCUGAU	chr14:64352793-64353049(+)$1	256	125	157	30.8731
GAUUUUAUAAUUCAGUUCAAUCAAUUAAAAUU	chr12:71537652-71537872(-)$1	220	82	114	32.2325
CUGGUCACAGUAGCAUCCUCAGAGAGACCACU	chr7:27185767-27186042(-)$1	275	65	97	33.3975
guucugacaccagauucuccagcacacagcaa	chr6:75986141-75986407(-)$1	266	159	191	34.3397
auaacauauacuaauaacacauuuacacaaau	chr3:44507907-44508145(-)$1	238	175	207	37.6916
caaauaaauggaaauuaaacauuauguuucug	chr3:142047241-142047477(-)$1	236	200	232	36.5629
GAUCUCCAACUCUCACGUCAUACCACACUCAG	chr20:30994350-30994797(+)$1	447	269	301	35.1291
uaaauuauauucuuccaaaucccauuuaauuu	chr1:50994999-50995251(-)$1	252	109	141	32.9137
UGGGAUUUUGCUUUGAAUAUUUCAUUUUCCCU	chr13:50317071-50317323(-)$1	252	48	80	34.0873
caacaucauaaaauucacaauauccuguaucc	chr2:37272328-37272564(-)$1	236	107	139	36.7243
AAAUUCUCUUUCUACUUCAUAUAUUGGAAUUU	chr8:90956199-90956490(-)$1	291	242	274	33.1134
gcuguuaAAACCAAACAACAUCCAAUAAAAAC	chr3:33467740-33468017(-)$1	277	96	128	34.7062
GGACCACUAUCGUUUCUCAUAUUAAAAUAUAA	chr6:35852119-35852398(-)$1	279	217	249	37.6916
ugggugagaacacagccaaaccauaucaccau	chr11:14596005-14596283(-)$1	278	211	243	27.8685
GCCUUUUAAAAUCAGUUCAGCCCUAGCCAAUG	chr5:172331444-172331718(+)$1	274	200	232	35.8482
AAGCAGGUUUACAUAUCCCCAUCCCCACCCUG	chrX:147625778-147626113(+)$1	335	120	152	33.6984
aaggugguuugacuaaguaacacucccaccca	chr20:2696108-2696338(+)$1	230	89	121	29.0876
auuuucacauucacucaccacucacucacuga	chr6:131985615-131985856(+)$1	241	100	132	36.1434
AACAGCCAAUCAAAUCCCCCUCCCAGGCUGUG	chrX:38512428-38512670(+)$1	242	106	138	31.6173
UGUGCUAACAACUUUUAACAAAAAAUUUGCAU	chr15:64666159-64666418(-)$1	259	157	189	34.4655
uucuuucuuucuuuuuuuuuuuuuuuuuugag	chr1:51917144-51917400(-)$1	256	209	241	36.7957
CAGCCCCCACUUUCACAUACCUUCUGGGAGGU	chr2:178405085-178405347(+)$1	262	118	150	36.5828
CUGGGUAGAAACAAAAGAAUUAGAAUACAAAG	chr7:92199382-92199677(-)$1	295	117	149	32.8123
uuuccugucucccuguauucuccacucccaag	chr6:41045014-41045297(+)$1	283	114	146	34.0341
aaagaaGUAAAUAUAACACUCCAACACUCUUC	chr7:72146440-72146676(-)$1	236	93	125	32.4421
GCUCUCUUCCAACUCCCAACUCAACCCUGGUU	chr18:13418058-13418331(+)$1	273	119	151	34.2135
auuauucucuccuugaaaugcuuuuuuaauuu	chr11:63458215-63458462(+)$1	247	67	99	35.4686
UUACCAUUUCACAUCCACAAAAACCACAUCAG	chr16:67490152-67490393(-)$1	241	109	141	36.8691
CCUAUAAAAAUUAAAACUAUAACAUCUUCCCU	chr6:135712066-135712320(-)$1	254	120	152	37.6916
ccaaacaaacaaaCAACCAUACAAAAGAAAUA	chr3:35805361-35805618(+)$1	257	130	162	36.6929
auuggaaCUAUAUAUACUUUUUAUUGUUAAUA	chr3:122496946-122497194(-)$1	248	35	67	36.2916
UCUGUAGGUGCUAUUCCUAUUAUGACUACACU	chr3:89168300-89168549(+)$1	249	134	166	31.0530
GGAGGAAAAACAAGAUAACCACCAUAACCACC	chr13:94304166-94304397(+)$1	231	86	118	34.6235
UAUGAUGCAAacacacacacuuauacacauac	chr14:48099438-48099674(-)$1	236	64	96	32.4499
UGCAUAAACACAUUACAUAUCAAAGUGCCUCU	chr5:77017029-77017309(-)$1	280	140	172	32.0830
CUCCACUUUUUUCUuuucuucuguauccuuaa	chr9:123176750-123177007(-)$1	257	173	205	37.7165
CAUUUGGGCACAAAACACAAUAAAAAAAUGUA	chr14:66192654-66192895(+)$1	241	177	209	33.1820
uaguaaccuccuaucuugucucucaguuaccc	chr14:67010373-67010680(+)$1	307	188	220	29.1115
uugagcauccaguugucuucuauuaagccaaa	chr13:49837844-49838109(+)$1	265	9	41	33.8045
acugcagccgacUUAUAAUCAACUUUAAUGCA	chr5:79930764-79931026(-)$1	262	13	45	34.2936
CUGGCUUGCAUUAACUUACACAAUUAUAUGCC	chr5:129043980-129044230(+)$1	250	6	38	34.6750
caccaaaccaUUUUACUAGCACUCAAACAUGG	chr17:63041835-63042156(-)$1	321	81	113	36.7528
cacacacacacacacacacCUCCAUAAACACA	chr10:30018348-30018584(-)$1	236	186	218	37.1669
AAAGUUGUUUCAAAAUAUUUACUCAUUUCAAC	chr7:32538279-32538515(+)$1	236	93	125	32.6734
UAGGCUUUAUCUCAGAACUACACAUUGGGCCU	chr20:36713145-36713426(+)$1	281	54	86	32.0050
CUGCAUUCUUAACACAUCUCAUUCCACAUAUU	chr4:123244889-123245162(+)$1	273	97	129	36.4489
CUUUUUAAACAGUACAUUUCAUAUUAGACUGU	chr4:144116149-144116393(+)$1	244	88	120	33.5048

#DB
.........................)))))))	chr15:62157590-62157970(-)$1	1	334	366	34.9174
(((((((...................))))))	chr14:81440732-81441014(+)$1	1	57	89	33.0959
(((((((...................))))))	chr6:45299676-45299902(+)$1	1	145	177	33.0959
.........................))).)))	chr2:9640380-9640625(-)$1	1	77	109	36.7962
((..((((....................))))	chr1:8437288-8437534(-)$1	1	11	43	31.7279
..........................))))))	chr1:29381814-29382050(+)$1	1	69	101	36.6687
..............................))	chr1:46411532-46411759(+)$1	1	162	194	37.7165
((..(((....................)))))	chr11:120899210-120899490(+)$1	1	91	123	34.1477
..(((....................))).(((	chrX:38138795-38139067(-)$1	1	30	62	32.1110
.........................))).)))	chr19:41942640-41942917(-)$1	1	65	97	36.7243
(((((((..................)))))))	chr4:76685991-76686293(+)$1	1	213	245	28.1693
.(((((...................)))))..	chr14:64352793-64353049(+)$1	1	125	157	30.8731
(((((((..................)))))))	chr12:71537652-71537872(-)$1	1	82	114	32.2325
.(((((...................)))))))	chr7:27185767-27186042(-)$1	1	65	97	33.3975
((((((....................))).))	chr6:75986141-75986407(-)$1	1	159	191	34.3397
..............................))	chr3:44507907-44508145(-)$1	1	175	207	37.6916
.........................)))))))	chr3:142047241-142047477(-)$1	1	200	232	36.5629
(((((.........................))	chr20:30994350-30994797(+)$1	1	269	301	35.1291
(((((((...................))))))	chr1:50994999-50995251(-)$1	1	109	141	32.9137
.((((......................))))(	chr13:50317071-50317323(-)$1	1	48	80	34.0873
.........................))).)))	chr2:37272328-37272564(-)$1	1	107	139	36.7243
(((((((..................)))))))	chr8:90956199-90956490(-)$1	1	242	274	33.1134
)(((((.......................)))	chr3:33467740-33468017(-)$1	1	96	128	34.7062
..............................))	chr6:35852119-35852398(-)$1	1	217	249	37.6916
))(((((..................)))))..	chr11:14596005-14596283(-)$1	1	211	243	27.8685
((.......................)))))))	chr5:172331444-172331718(+)$1	1	200	232	35.8482
(((((((.....................))))	chrX:147625778-147626113(+)$1	1	120	152	33.6984
..(((((..................))))).)	chr20:2696108-2696338(+)$1	1	89	121	29.0876
(........................))...))	chr6:131985615-131985856(+)$1	1	100	132	36.1434
.((((((..................)))))).	chrX:38512428-38512670(+)$1	1	106	138	31.6173
.((((.......................))))	chr15:64666159-64666418(-)$1	1	157	189	34.4655
.........................)))))))	chr1:51917144-51917400(-)$1	1	209	241	36.7957
.........................)))))))	chr2:178405085-178405347(+)$1	1	118	150	36.5828
((..(((..................)))..))	chr7:92199382-92199677(-)$1	1	117	149	32.8123
((((((........................))	chr6:41045014-41045297(+)$1	1	114	146	34.0341
.((((((.....................))))	chr7:72146440-72146676(-)$1	1	93	125	32.4421
(........................)))))))	chr18:13418058-13418331(+)$1	1	119	151	34.2135
(........................)))))))	chr11:63458215-63458462(+)$1	1	67	99	35.4686
((............................))	chr16:67490152-67490393(-)$1	1	109	141	36.8691
..............................))	chr6:135712066-135712320(-)$1	1	120	152	37.6916
(.........................)).)))	chr3:35805361-35805618(+)$1	1	130	162	36.6929
((.......................))).)))	chr3:122496946-122497194(-)$1	1	35	67	36.2916
..(((((..................)))))..	chr3:89168300-89168549(+)$1	1	134	166	31.0530
((.((......................)).))	chr13:94304166-94304397(+)$1	1	86	118	34.6235
((((.((..................)))))))	chr14:48099438-48099674(-)$1	1	64	96	32.4499
.((((...................))))...)	chr5:77017029-77017309(-)$1	1	140	172	32.0830
..............................))	chr9:123176750-123177007(-)$1	1	173	205	37.7165
(((((....................)))))).	chr14:66192654-66192895(+)$1	1	177	209	33.1820
..(((((..................)))))..	chr14:67010373-67010680(+)$1	1	188	220	29.1115
(((.((....................))))))	chr13:49837844-49838109(+)$1	1	9	41	33.8045
.(((((......................))))	chr5:79930764-79931026(-)$1	1	13	45	34.2936
.((((........................)))	chr5:129043980-129044230(+)$1	1	6	38	34.6750
((...........................)))	chr17:63041835-63042156(-)$1	1	81	113	36.7528
..........................)).)))	chr10:30018348-30018584(-)$1	1	186	218	37.1669
(((((((.....................))))	chr7:32538279-32538515(+)$1	1	93	125	32.6734
.((((((...................))))))	chr20:36713145-36713426(+)$1	1	54	86	32.0050
.........................)))..))	chr4:123244889-123245162(+)$1	1	97	129	36.4489
((.......................)))))))	chr4:144116149-144116393(+)$1	1	88	120	33.5048

#PSSM
^ : 0.25	: : 0.15	g : 0.10	h : 0.05	i : 0.05	b : 0.05	f : 0.05	e : 0.03	c : 0.03	= : 0.03	! : 0.03	d : 0.03	[ : 0.01	J : 0.01	D : 0.01	( : 0.01	G : 0.01	' : 0.01	
^ : 0.32	e : 0.12	d : 0.12	g : 0.10	f : 0.08	: : 0.05	i : 0.05	c : 0.03	h : 0.03	= : 0.03	J : 0.01	( : 0.01	
^ : 0.41	e : 0.15	d : 0.08	f : 0.08	g : 0.06	! : 0.05	i : 0.05	= : 0.03	c : 0.01	h : 0.01	[ : 0.01	
^ : 0.41	e : 0.15	d : 0.08	f : 0.08	g : 0.05	! : 0.05	c : 0.03	i : 0.03	= : 0.03	h : 0.01	b : 0.01	[ : 0.01	
^ : 0.41	e : 0.15	d : 0.10	f : 0.08	c : 0.06	g : 0.05	i : 0.03	b : 0.03	h : 0.01	= : 0.01	[ : 0.01	
^ : 0.55	e : 0.15	f : 0.06	g : 0.05	c : 0.05	i : 0.03	b : 0.03	d : 0.01	h : 0.01	= : 0.01	
^ : 0.67	e : 0.06	f : 0.06	g : 0.05	c : 0.03	i : 0.03	d : 0.01	h : 0.01	= : 0.01	b : 0.01	
^ : 0.98	d : 0.01	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 1.00	
^ : 0.98	d : 0.01	
^ : 0.49	c : 0.12	e : 0.10	h : 0.06	f : 0.05	i : 0.03	= : 0.03	g : 0.03	b : 0.03	d : 0.01	
^ : 0.34	c : 0.13	b : 0.10	e : 0.10	h : 0.06	g : 0.06	f : 0.06	i : 0.05	= : 0.03	d : 0.01	
^ : 0.29	c : 0.15	e : 0.10	b : 0.08	h : 0.06	g : 0.06	f : 0.06	i : 0.05	= : 0.05	d : 0.03	3 : 0.01	
^ : 0.18	e : 0.12	g : 0.10	] : 0.10	f : 0.10	h : 0.06	d : 0.06	i : 0.05	= : 0.05	c : 0.03	3 : 0.03	2 : 0.03	: : 0.01	b : 0.01	
e : 0.15	d : 0.13	^ : 0.13	g : 0.12	f : 0.12	h : 0.06	i : 0.06	= : 0.05	c : 0.03	] : 0.03	3 : 0.03	2 : 0.03	
d : 0.22	e : 0.15	g : 0.13	f : 0.12	i : 0.08	h : 0.06	: : 0.06	c : 0.05	= : 0.05	0 : 0.01	3 : 0.01	
d : 0.22	e : 0.18	g : 0.13	i : 0.08	h : 0.06	f : 0.06	c : 0.05	: : 0.05	= : 0.05	3 : 0.03	E : 0.01	0 : 0.01	

#score	1984.804015739874
#seq	58
#width	32
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EIF4A3_Sauliere2012a_hg19_CDS_m3_run1.txt

#BEAR
cccqqqqqqqqccc22d	chr8:38205545-38205835(-)$1	290	49	66	13.4179
cccqqqqqqqqccc22d	chr8:57228478-57228707(-)$1	229	79	96	13.4179
hhhqqqqqqqqhhhhhh	chr2:74655293-74655608(-)$1	315	202	219	12.6841
c[aqqqqqqqqa]cccf	chr9:132400417-132400662(-)$1	245	27	44	13.8048
d[aqqqqqqqqa]dddd	chr6:31964536-31964762(+)$1	226	113	130	13.0861
[bbqqqqqqqqbb]fff	chr2:62998371-62998628(+)$1	257	54	71	13.0204
eeeqqqqqqqqeeeee:	chr19:36852912-36853141(-)$1	229	212	229	12.4655
fffqqqqqqqqffffff	chr12:132380201-132380473(+)$1	272	207	224	13.5589
eeeqqqqqqqqeeeee>	chr1:235498463-235498701(+)$1	238	173	190	13.2144
c[aqqqqqqqqa]ccc2	chr12:50195499-50195747(+)$1	248	51	68	13.6388
dddqqqqqqqqdddd]d	chr3:158384041-158384271(+)$1	230	75	92	12.7751
cccqqqqqqqqccc444	chr2:68361733-68362002(-)$1	269	190	207	13.7302
cccqqqqqqqqccc]ff	chr1:150315714-150316028(+)$1	314	262	279	14.1185
cccqqqqqqqqccc]a]	chr22:44333017-44333252(+)$1	235	133	150	14.0851
fffqqqqqqqqffffff	chr1:235826187-235826451(-)$1	264	3	20	13.5589
cccqqqqqqqqccceee	chr5:132160243-132160482(-)$1	239	31	48	13.8941
eeeqqqqqqqqeeeee:	chr2:158634683-158634918(-)$1	235	17	34	12.4655
!!aqqqqqqqqa22eee	chr7:5792374-5792712(-)$1	338	189	206	13.0410
gggqqqqqqqqgggggg	chr4:4440061-4440336(-)$1	275	168	185	14.1147
dddqqqqqqqqdddd]b	chr6:74171477-74171770(+)$1	293	172	189	12.7251
dddqqqqqqqqddddbb	chr2:200188530-200188778(-)$1	248	123	140	12.4313
dddqqqqqqqqdddd33	chr12:120596163-120596520(-)$1	357	140	157	12.9700
fffqqqqqqqqffffff	chr6:34827153-34827449(+)$1	296	112	129	13.5589
hhhqqqqqqqqhhhhhh	chr17:1703272-1703494(-)$1	222	122	139	12.6841
fffqqqqqqqqffffff	chr12:100478253-100478504(-)$1	251	142	159	13.5589
dddqqqqqqqqddddFF	chr8:119940963-119941223(-)$1	260	143	160	12.2186
[bbqqqqqqqqbb]eee	chr2:48017977-48018202(+)$1	225	7	24	12.8876
dddqqqqqqqqdddddd	chr17:43190762-43191074(-)$1	312	31	48	12.5861
[bbqqqqqqqqbb]ccc	chr8:67971359-67971661(-)$1	302	230	247	12.9055
f[aqqqqqqqqafffff	chr21:17205571-17205792(+)$1	221	169	186	13.7702
gggqqqqqqqqgggggg	chr15:40477588-40477944(+)$1	356	178	195	14.1147
f[aqqqqqqqqa]ffff	chr16:1390846-1391078(+)$1	232	42	59	13.7647
g[aqqqqqqqqa]gggg	chr11:60669978-60670191(-)$1	213	141	158	14.0399
gggqqqqqqqqgggggg	chr19:3028753-3028988(-)$1	235	214	231	14.1147
cccqqqqqqqqccc]ee	chr2:220336869-220337110(+)$1	241	63	80	13.9907
f[aqqqqqqqqa]ffff	chr6:26369006-26369234(+)$1	228	102	119	13.7647
fffqqqqqqqqffffff	chr17:56283391-56283622(-)$1	231	125	142	13.5589
gggqqqqqqqqgggggg	chr15:91172625-91172864(+)$1	239	72	89	14.1147
[bbqqqqqqqqbb]ccc	chr1:29313845-29314123(+)$1	278	132	149	12.9055
fffqqqqqqqqffffff	chr1:200377001-200377233(-)$1	232	10	27	13.5589
fffqqqqqqqqffffff	chr4:39236279-39236539(+)$1	260	243	260	13.5589
eeeqqqqqqqqeeeee:	chr2:29354989-29355211(+)$1	222	205	222	12.4655
hhhqqqqqqqqhhhhhh	chr16:28835748-28836034(+)$1	286	89	106	12.6841
gggqqqqqqqqgggggg	chr14:78365406-78365635(+)$1	229	22	39	14.1147
dddqqqqqqqqdddd22	chr12:6619715-6619966(+)$1	251	144	161	12.5662
eeeqqqqqqqqeeeee]	chr14:93022151-93022400(+)$1	249	106	123	13.4275
gggqqqqqqqqgggggg	chr3:47912616-47912880(-)$1	264	71	88	14.1147
gggqqqqqqqqgggggg	chr4:2747071-2747362(-)$1	291	68	85	14.1147
fffqqqqqqqqffffff	chr11:102991564-102991792(+)$1	228	120	137	13.5589
cccqqqqqqqqccc888	chr19:42738370-42738619(-)$1	249	178	195	12.5249
eeeqqqqqqqqeeeee2	chr15:40277954-40278194(+)$1	240	205	222	13.2186
!bbqqqqqqqqbbgggg	chr14:78288706-78288961(+)$1	255	142	159	13.1919
===qqqqqqqq======	chr3:27493805-27494115(-)$1	310	213	230	13.8373
cccqqqqqqqqccc]bb	chr9:97203240-97203483(+)$1	243	106	123	13.5843
cccqqqqqqqqcccbb!	chr2:190531729-190531987(+)$1	258	100	117	13.1357
eeeqqqqqqqqeeeeec	chr2:197002131-197002403(-)$1	272	18	35	13.3554
eeeqqqqqqqqeeeee]	chr14:24036216-24036517(+)$1	301	242	259	13.4275
!bbqqqqqqqqbb22a2	chr7:27196055-27196302(-)$1	247	108	125	12.2821
fffqqqqqqqqffffff	chr8:17808029-17808333(+)$1	304	23	40	13.5589
gggqqqqqqqqgggggg	chr20:34810132-34810404(+)$1	272	79	96	14.1147
eeeqqqqqqqqeeeee3	chr15:59185370-59185666(-)$1	296	229	246	13.4145
cccqqqqqqqqcccccc	chr14:75489341-75489617(-)$1	276	207	224	13.9120
gggqqqqqqqqgggggg	chr11:126145089-126145408(+)$1	319	161	178	14.1147
cccqqqqqqqqccc]a]	chr3:184059441-184059672(+)$1	231	117	134	14.0851
dddqqqqqqqqdddd]b	chr16:53725916-53726200(-)$1	284	224	241	12.7251
cccqqqqqqqqccc]dd	chr2:20135922-20136172(-)$1	250	102	119	13.7392
eeeqqqqqqqqeeeee:	chr11:28090686-28090979(-)$1	293	115	132	12.4655
gggqqqqqqqqgggggg	chr20:34208541-34208795(+)$1	254	115	132	14.1147
cccqqqqqqqqccc]a5	chr1:183471367-183471627(+)$1	260	32	49	13.1996
hhhqqqqqqqqhhhhhh	chr3:142238410-142238728(-)$1	318	113	130	12.6841
fffqqqqqqqqffffff	chr6:43578298-43578556(+)$1	258	216	233	13.5589
hhhqqqqqqqqhhhhhh	chr20:34215230-34215473(-)$1	243	142	159	12.6841
fffqqqqqqqqffffff	chr10:31138309-31138540(-)$1	231	155	172	13.5589
#bbqqqqqqqqbb333f	chr14:55218074-55218329(+)$1	255	153	170	12.7138
iiiqqqqqqqqiiiiii	chr14:88851986-88852281(+)$1	295	91	108	13.8347
cccqqqqqqqqccc]ee	chr14:76107214-76107468(+)$1	254	207	224	13.9907

#otherMatches

#Seq PSSM
CUCUAGCCUAUGAGAAU	chr8:38205545-38205835(-)$1	290	49	66	13.4179
CGCCUAUACCUGCGAUU	chr8:57228478-57228707(-)$1	229	79	96	13.4179
GCUGUCAACAAGGUGAU	chr2:74655293-74655608(-)$1	315	202	219	12.6841
AUGAUCAACCGCUUCUG	chr9:132400417-132400662(-)$1	245	27	44	13.8048
GUGUCGCCCACCCCGGC	chr6:31964536-31964762(+)$1	226	113	130	13.0861
CUAAAGACAUGUAUUUC	chr2:62998371-62998628(+)$1	257	54	71	13.0204
UCUAUUCUCAAAGGAAU	chr19:36852912-36853141(-)$1	229	212	229	12.4655
GGGGACUGUGGCCCCAG	chr12:132380201-132380473(+)$1	272	207	224	13.5589
CUUCAGUUACCAGGUAA	chr1:235498463-235498701(+)$1	238	173	190	13.2144
UGAGAAGACAGUGAUGG	chr12:50195499-50195747(+)$1	248	51	68	13.6388
CCUUGUAUCACAGGAAA	chr3:158384041-158384271(+)$1	230	75	92	12.7751
GCUCCUUUUAAAGUUAC	chr2:68361733-68362002(-)$1	269	190	207	13.7302
UCUUUAAUCCUGGAGGA	chr1:150315714-150316028(+)$1	314	262	279	14.1185
AGGUACCCACUCCUCGG	chr22:44333017-44333252(+)$1	235	133	150	14.0851
AUGAUGACCAAUAUGCU	chr1:235826187-235826451(-)$1	264	3	20	13.5589
CUGACAGUGAACAGAGG	chr5:132160243-132160482(-)$1	239	31	48	13.8941
AAGCAGUGAUCCUUACA	chr2:158634683-158634918(-)$1	235	17	34	12.4655
AGCAGCAUGAAGAAGAG	chr7:5792374-5792712(-)$1	338	189	206	13.0410
GUCCUUCAAAAGACUCU	chr4:4440061-4440336(-)$1	275	168	185	14.1147
UUGAGCAGUGACAGCGC	chr6:74171477-74171770(+)$1	293	172	189	12.7251
CCUCCCUAUUAAGGUGG	chr2:200188530-200188778(-)$1	248	123	140	12.4313
CAGAGUGUGUCCUGGAU	chr12:120596163-120596520(-)$1	357	140	157	12.9700
UCCCUGACUAAGGAUGC	chr6:34827153-34827449(+)$1	296	112	129	13.5589
ACAAAUUCCUCUGUGCU	chr17:1703272-1703494(-)$1	222	122	139	12.6841
CAUGAAUUUGAGUGCAA	chr12:100478253-100478504(-)$1	251	142	159	13.5589
CACAAAUUGCAGUGUCU	chr8:119940963-119941223(-)$1	260	143	160	12.2186
GAAUUGUUUAUUUGUAG	chr2:48017977-48018202(+)$1	225	7	24	12.8876
AGUCCCCUGAAACUGAG	chr17:43190762-43191074(-)$1	312	31	48	12.5861
UCUUAUAGUUUAGUAAU	chr8:67971359-67971661(-)$1	302	230	247	12.9055
GAGGAAGACAACCAACG	chr21:17205571-17205792(+)$1	221	169	186	13.7702
GCUUCACUGAUAGCUGU	chr15:40477588-40477944(+)$1	356	178	195	14.1147
GCCUAGGCCCUGCCAAC	chr16:1390846-1391078(+)$1	232	42	59	13.7647
GUGUCCCCCUUCCCUUA	chr11:60669978-60670191(-)$1	213	141	158	14.0399
AAGUUCUCGAUCUUGGA	chr19:3028753-3028988(-)$1	235	214	231	14.1147
GAACUGCGGCUUUCAGA	chr2:220336869-220337110(+)$1	241	63	80	13.9907
UGAAAAAGCCCUGGUGG	chr6:26369006-26369234(+)$1	228	102	119	13.7647
GGCCCGGGAAAGCCUCC	chr17:56283391-56283622(-)$1	231	125	142	13.5589
AGCACAUCAAGGUUUCA	chr15:91172625-91172864(+)$1	239	72	89	14.1147
AGGCCGAAAAUUCACAG	chr1:29313845-29314123(+)$1	278	132	149	12.9055
UUCAAAGAAAAGAAGAU	chr1:200377001-200377233(-)$1	232	10	27	13.5589
UCAGUAGCUAAUGACUG	chr4:39236279-39236539(+)$1	260	243	260	13.5589
GGGGgaaggcacccagc	chr2:29354989-29355211(+)$1	222	205	222	12.4655
ACCUGGCGAUUGGUGAU	chr16:28835748-28836034(+)$1	286	89	106	12.6841
UUGUUGGAUUUCAGGUG	chr14:78365406-78365635(+)$1	229	22	39	14.1147
AGAAACGCCCAUCUAAA	chr12:6619715-6619966(+)$1	251	144	161	12.5662
CCAGGCAGAGGUGGCCA	chr14:93022151-93022400(+)$1	249	106	123	13.4275
UAAAUGUUAUAUUAAUA	chr3:47912616-47912880(-)$1	264	71	88	14.1147
GAGUGUCUUCUCUCUGU	chr4:2747071-2747362(-)$1	291	68	85	14.1147
UGGUAAAGCGUCCAACU	chr11:102991564-102991792(+)$1	228	120	137	13.5589
gcuguaugccaagcuug	chr19:42738370-42738619(-)$1	249	178	195	12.5249
UUAGAACAAGAUAAUGG	chr15:40277954-40278194(+)$1	240	205	222	13.2186
GCUGAGAUCUAAGGUAA	chr14:78288706-78288961(+)$1	255	142	159	13.1919
UUGGUUUAAAAUAACUU	chr3:27493805-27494115(-)$1	310	213	230	13.8373
CUCAGGAGCACGAGCGA	chr9:97203240-97203483(+)$1	243	106	123	13.5843
CCUGUUUUCUGGGGGCA	chr2:190531729-190531987(+)$1	258	100	117	13.1357
UUCACCCUGAAGAAACU	chr2:197002131-197002403(-)$1	272	18	35	13.3554
GCCUGAGUCUUGGCCCC	chr14:24036216-24036517(+)$1	301	242	259	13.4275
CUGCCGGACAACAAAUC	chr7:27196055-27196302(-)$1	247	108	125	12.2821
uuuaGCUUCUCAGAGAU	chr8:17808029-17808333(+)$1	304	23	40	13.5589
GCCAUCAAGGAGGCCAA	chr20:34810132-34810404(+)$1	272	79	96	14.1147
UUUACAAAAGAAGAUAA	chr15:59185370-59185666(-)$1	296	229	246	13.4145
GGAGAAUACAAUUUAGA	chr14:75489341-75489617(-)$1	276	207	224	13.9120
UGGUGUCUGCUCCAGGG	chr11:126145089-126145408(+)$1	319	161	178	14.1147
CCUAACUAUCCAGGAGA	chr3:184059441-184059672(+)$1	231	117	134	14.0851
UAAAACAAAGCUUACGU	chr16:53725916-53726200(-)$1	284	224	241	12.7251
UCCUGAAAACUGGAUCU	chr2:20135922-20136172(-)$1	250	102	119	13.7392
GGCUCCAUCGUGUCGAA	chr11:28090686-28090979(-)$1	293	115	132	12.4655
GAUGUUGAGAAAUCGGA	chr20:34208541-34208795(+)$1	254	115	132	14.1147
CAUUCUACCUUAUGAGA	chr1:183471367-183471627(+)$1	260	32	49	13.1996
UAUUUAUGACUGUAGAG	chr3:142238410-142238728(-)$1	318	113	130	12.6841
CUUAGCUCUACAAGACA	chr6:43578298-43578556(+)$1	258	216	233	13.5589
CCAGGGCAUUGUGGAUG	chr20:34215230-34215473(-)$1	243	142	159	12.6841
UUUUCUUUACCAGGACC	chr10:31138309-31138540(-)$1	231	155	172	13.5589
ACAAAAUCUCCUGAAGU	chr14:55218074-55218329(+)$1	255	153	170	12.7138
CCUCCACUGCCGGGGCU	chr14:88851986-88852281(+)$1	295	91	108	13.8347
GUUUGUUUCCUGGCUGG	chr14:76107214-76107468(+)$1	254	207	224	13.9907

#DB
(((........)))..)	chr8:38205545-38205835(-)$1	1	49	66	13.4179
(((........)))..)	chr8:57228478-57228707(-)$1	1	79	96	13.4179
(((........))))))	chr2:74655293-74655608(-)$1	1	202	219	12.6841
(.(........).))))	chr9:132400417-132400662(-)$1	1	27	44	13.8048
(.(........).))))	chr6:31964536-31964762(+)$1	1	113	130	13.0861
.((........)).)))	chr2:62998371-62998628(+)$1	1	54	71	13.0204
(((........))))).	chr19:36852912-36853141(-)$1	1	212	229	12.4655
(((........))))))	chr12:132380201-132380473(+)$1	1	207	224	13.5589
(((........))))).	chr1:235498463-235498701(+)$1	1	173	190	13.2144
(.(........).))).	chr12:50195499-50195747(+)$1	1	51	68	13.6388
(((........)))).)	chr3:158384041-158384271(+)$1	1	75	92	12.7751
(((........)))...	chr2:68361733-68362002(-)$1	1	190	207	13.7302
(((........))).))	chr1:150315714-150316028(+)$1	1	262	279	14.1185
(((........))).).	chr22:44333017-44333252(+)$1	1	133	150	14.0851
(((........))))))	chr1:235826187-235826451(-)$1	1	3	20	13.5589
(((........))))))	chr5:132160243-132160482(-)$1	1	31	48	13.8941
(((........))))).	chr2:158634683-158634918(-)$1	1	17	34	12.4655
..(........)..)))	chr7:5792374-5792712(-)$1	1	189	206	13.0410
(((........))))))	chr4:4440061-4440336(-)$1	1	168	185	14.1147
(((........)))).)	chr6:74171477-74171770(+)$1	1	172	189	12.7251
(((........))))((	chr2:200188530-200188778(-)$1	1	123	140	12.4313
(((........))))..	chr12:120596163-120596520(-)$1	1	140	157	12.9700
(((........))))))	chr6:34827153-34827449(+)$1	1	112	129	13.5589
(((........))))))	chr17:1703272-1703494(-)$1	1	122	139	12.6841
(((........))))))	chr12:100478253-100478504(-)$1	1	142	159	13.5589
(((........))))))	chr8:119940963-119941223(-)$1	1	143	160	12.2186
.((........)).)))	chr2:48017977-48018202(+)$1	1	7	24	12.8876
(((........))))((	chr17:43190762-43191074(-)$1	1	31	48	12.5861
.((........)).)))	chr8:67971359-67971661(-)$1	1	230	247	12.9055
(.(........))))))	chr21:17205571-17205792(+)$1	1	169	186	13.7702
(((........))))))	chr15:40477588-40477944(+)$1	1	178	195	14.1147
(.(........).))))	chr16:1390846-1391078(+)$1	1	42	59	13.7647
(.(........).))))	chr11:60669978-60670191(-)$1	1	141	158	14.0399
(((........))))))	chr19:3028753-3028988(-)$1	1	214	231	14.1147
(((........))).))	chr2:220336869-220337110(+)$1	1	63	80	13.9907
(.(........).))))	chr6:26369006-26369234(+)$1	1	102	119	13.7647
(((........))))))	chr17:56283391-56283622(-)$1	1	125	142	13.5589
(((........))))))	chr15:91172625-91172864(+)$1	1	72	89	14.1147
.((........)).)))	chr1:29313845-29314123(+)$1	1	132	149	12.9055
(((........))))))	chr1:200377001-200377233(-)$1	1	10	27	13.5589
(((........))))))	chr4:39236279-39236539(+)$1	1	243	260	13.5589
(((........))))).	chr2:29354989-29355211(+)$1	1	205	222	12.4655
(((........))))))	chr16:28835748-28836034(+)$1	1	89	106	12.6841
(((........))))))	chr14:78365406-78365635(+)$1	1	22	39	14.1147
(((........))))..	chr12:6619715-6619966(+)$1	1	144	161	12.5662
(((........))))).	chr14:93022151-93022400(+)$1	1	106	123	13.4275
(((........))))))	chr3:47912616-47912880(-)$1	1	71	88	14.1147
(((........))))))	chr4:2747071-2747362(-)$1	1	68	85	14.1147
(((........))))))	chr11:102991564-102991792(+)$1	1	120	137	13.5589
(((........)))...	chr19:42738370-42738619(-)$1	1	178	195	12.5249
(((........))))).	chr15:40277954-40278194(+)$1	1	205	222	13.2186
.((........))))))	chr14:78288706-78288961(+)$1	1	142	159	13.1919
(((........))))))	chr3:27493805-27494115(-)$1	1	213	230	13.8373
(((........))).))	chr9:97203240-97203483(+)$1	1	106	123	13.5843
(((........)))((.	chr2:190531729-190531987(+)$1	1	100	117	13.1357
(((........))))))	chr2:197002131-197002403(-)$1	1	18	35	13.3554
(((........))))).	chr14:24036216-24036517(+)$1	1	242	259	13.4275
.((........))..).	chr7:27196055-27196302(-)$1	1	108	125	12.2821
(((........))))))	chr8:17808029-17808333(+)$1	1	23	40	13.5589
(((........))))))	chr20:34810132-34810404(+)$1	1	79	96	14.1147
(((........))))).	chr15:59185370-59185666(-)$1	1	229	246	13.4145
(((........))))))	chr14:75489341-75489617(-)$1	1	207	224	13.9120
(((........))))))	chr11:126145089-126145408(+)$1	1	161	178	14.1147
(((........))).).	chr3:184059441-184059672(+)$1	1	117	134	14.0851
(((........)))).)	chr16:53725916-53726200(-)$1	1	224	241	12.7251
(((........))).))	chr2:20135922-20136172(-)$1	1	102	119	13.7392
(((........))))).	chr11:28090686-28090979(-)$1	1	115	132	12.4655
(((........))))))	chr20:34208541-34208795(+)$1	1	115	132	14.1147
(((........))).).	chr1:183471367-183471627(+)$1	1	32	49	13.1996
(((........))))))	chr3:142238410-142238728(-)$1	1	113	130	12.6841
(((........))))))	chr6:43578298-43578556(+)$1	1	216	233	13.5589
(((........))))))	chr20:34215230-34215473(-)$1	1	142	159	12.6841
(((........))))))	chr10:31138309-31138540(-)$1	1	155	172	13.5589
.((........))...)	chr14:55218074-55218329(+)$1	1	153	170	12.7138
(((........))))))	chr14:88851986-88852281(+)$1	1	91	108	13.8347
(((........))).))	chr14:76107214-76107468(+)$1	1	207	224	13.9907

#PSSM
c : 0.22	f : 0.18	g : 0.14	e : 0.13	d : 0.11	h : 0.06	[ : 0.05	! : 0.03	= : 0.01	# : 0.01	i : 0.01	
c : 0.19	f : 0.14	e : 0.13	g : 0.13	d : 0.10	[ : 0.09	b : 0.09	h : 0.06	! : 0.01	= : 0.01	i : 0.01	
c : 0.19	f : 0.14	e : 0.13	g : 0.13	a : 0.10	d : 0.10	b : 0.09	h : 0.06	= : 0.01	i : 0.01	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
q : 1.00	
c : 0.19	f : 0.14	e : 0.13	g : 0.13	a : 0.10	d : 0.10	b : 0.09	h : 0.06	= : 0.01	i : 0.01	
c : 0.19	f : 0.15	e : 0.13	g : 0.13	d : 0.10	b : 0.09	] : 0.07	h : 0.06	2 : 0.01	= : 0.01	i : 0.01	
c : 0.22	f : 0.18	g : 0.15	e : 0.13	d : 0.11	h : 0.06	] : 0.05	2 : 0.02	= : 0.01	3 : 0.01	i : 0.01	
f : 0.19	e : 0.17	g : 0.15	d : 0.11	] : 0.10	h : 0.06	c : 0.06	2 : 0.03	4 : 0.01	8 : 0.01	= : 0.01	b : 0.01	3 : 0.01	i : 0.01	
f : 0.21	e : 0.19	g : 0.15	h : 0.06	c : 0.06	a : 0.05	2 : 0.03	d : 0.03	] : 0.03	b : 0.03	3 : 0.02	4 : 0.01	F : 0.01	8 : 0.01	= : 0.01	i : 0.01	
f : 0.23	g : 0.15	d : 0.07	h : 0.06	e : 0.06	: : 0.05	2 : 0.05	] : 0.05	b : 0.05	c : 0.05	3 : 0.02	> : 0.01	4 : 0.01	F : 0.01	8 : 0.01	= : 0.01	! : 0.01	5 : 0.01	i : 0.01	

#score	1015.9516514433919
#seq	76
#width	17
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_EWSR1_Paronetto2014_hg19_CDS_m3_run1.txt

#BEAR
!eeeeeqqqqqqqqeeeee	chr4:74365618-74365877(+)$1	259	30	49	13.5958
""ddddqqqqqqqqdddd]	chr11:76751099-76751358(+)$1	259	187	206	14.4931
!eeeeeqqqqqqqqeeeee	chr7:23340516-23340745(+)$1	229	140	159	13.5958
"a[cccqqqqqqqqccc]a	chr5:68799949-68800178(+)$1	229	139	158	15.7489
ii[cccqqqqqqqqcccii	chr1:156784819-156785078(+)$1	259	74	93	15.4627
ccccccqqqqqqqqccc22	chr11:70185235-70185494(+)$1	259	127	146	15.2598
ee[cccqqqqqqqqccc22	chr7:23238987-23239216(+)$1	229	23	42	15.5101
ddddddqqqqqqqqdddd:	chr5:170883519-170883748(+)$1	229	80	99	13.2141
[eeeeeqqqqqqqqeeeee	chr1:153633573-153633832(+)$1	259	86	105	13.5742
ff[cccqqqqqqqqccc]f	chr7:141750460-141750689(-)$1	229	129	148	15.2343
d!!cccqqqqqqqqccc22	chr16:29996872-29997131(+)$1	259	65	84	15.7676
iiiiiiqqqqqqqqiiiii	chr2:7179766-7180025(+)$1	259	75	94	14.3791
ddddddqqqqqqqqdddd3	chrX:2715202-2715461(-)$1	259	40	59	14.2463
!!ddddqqqqqqqqdddd2	chr18:224804-225063(-)$1	259	147	166	14.5381
e!!cccqqqqqqqqccc22	chr20:60890908-60891167(+)$1	259	12	31	15.7455
cc!!bbqqqqqqqqbbccc	chr2:216809564-216809823(+)$1	259	136	155	14.4383
[a!!bbqqqqqqqqbb22a	chr6:30994067-30994326(+)$1	259	92	111	14.6163
d"""bbqqqqqqqqbb22d	chr2:54128484-54128743(-)$1	259	132	151	14.2399
ggggbbqqqqqqqqbb]gg	chr11:6644610-6644869(+)$1	259	225	244	14.1048
[cccbbqqqqqqqqbb]cc	chr16:88929985-88930244(+)$1	259	171	190	14.1835
d[ddddqqqqqqqqdddd]	chr1:210111521-210111750(-)$1	229	13	32	14.3834
###cccqqqqqqqqccc44	chrX:101911437-101911696(+)$1	259	139	158	15.5727
c!!cccqqqqqqqqccc]c	chr17:37761702-37761967(+)$1	265	67	86	15.7998
[eeeeeqqqqqqqqeeeee	chr18:12325208-12325467(+)$1	259	210	229	13.5742
dddcccqqqqqqqqccc]d	chrX:15599270-15599499(+)$1	229	87	106	15.1304
fffcccqqqqqqqqccc::	chr3:50382797-50383026(+)$1	229	23	42	13.0032
dd[cccqqqqqqqqccc]d	chr9:77407452-77407681(-)$1	229	59	78	15.4368
======qqqqqqqq=====	chr1:879974-880233(+)$1	259	202	221	14.7111
iiiiiiqqqqqqqqiiiii	chr19:8137794-8138053(+)$1	259	43	62	14.3791
f!!cccqqqqqqqqccc]f	chr7:107638702-107638931(+)$1	229	167	186	15.5714
eeecccqqqqqqqqcccFF	chr8:144999517-144999776(+)$1	259	215	234	13.8633
cc!!bbqqqqqqqqbb22c	chr12:14613909-14614168(-)$1	259	96	115	14.4117
ccddddqqqqqqqqdddd:	chr3:167006555-167006784(+)$1	229	188	207	13.3224
eeeebbqqqqqqqqbb]ee	chr6:100062170-100062399(+)$1	229	96	115	13.7538
d[ddddqqqqqqqqddddd	chr17:46196236-46196465(+)$1	229	172	191	14.1533
c!!cccqqqqqqqqccc44	chr1:68512581-68512810(+)$1	229	142	161	15.8133
bbddddqqqqqqqqdddd3	chr3:52561708-52561967(-)$1	259	110	129	13.8703
!eeeeeqqqqqqqqeeeee	chr7:148851284-148851543(+)$1	259	229	248	13.5958
ggggggqqqqqqqqggggg	chr4:39246847-39247106(+)$1	259	122	141	14.1185
a[ddddqqqqqqqqdddd]	chr1:38272469-38272728(+)$1	259	19	38	14.3947
dd[cccqqqqqqqqccc]d	chr9:117821938-117822167(+)$1	229	98	117	15.4368
!!ddddqqqqqqqqddddd	chr19:35769557-35769816(+)$1	259	63	82	14.4036
####bbqqqqqqqqbb333	chr19:38774145-38774374(+)$1	229	106	125	14.8253
ggggggqqqqqqqqggggg	chr3:48608155-48608414(-)$1	259	11	30	14.1185
dd[cccqqqqqqqqccc]d	chr10:105200396-105200625(-)$1	229	86	105	15.4368
e!!cccqqqqqqqqccc22	chr15:75498756-75499015(+)$1	259	33	52	15.7455
[a[cccqqqqqqqqccca]	chr12:56415227-56415486(-)$1	259	152	171	15.6353
fffffaqqqqqqqqa]fff	chr19:12776205-12776464(+)$1	259	154	173	12.9394
bb[cccqqqqqqqqcccbb	chr22:43539193-43539452(+)$1	259	49	68	14.1991
iiii[aqqqqqqqqa]iii	chr17:48193107-48193366(+)$1	259	74	93	14.1249
iiiiiiqqqqqqqqiiiii	chr5:134245930-134246189(+)$1	259	37	56	14.3791
dddcccqqqqqqqqccc]d	chr8:105503310-105503539(+)$1	229	8	27	15.1304
bb[cccqqqqqqqqccc]b	chr2:220404447-220404706(+)$1	259	148	167	14.8510
bbddddqqqqqqqqdddd]	chr1:226834902-226835161(+)$1	259	50	69	13.7914
cc[cccqqqqqqqqccc22	chr10:114200322-114200551(-)$1	229	116	135	15.6058
e!!cccqqqqqqqqccc]e	chr19:47184829-47185088(+)$1	259	125	144	15.7077
ddd[bbqqqqqqqqbb22d	chrX:135431487-135431716(-)$1	229	80	99	13.9222
ccc[bbqqqqqqqqbb]cc	chr1:200008700-200008929(+)$1	229	129	148	13.9503
feeeeeqqqqqqqqeeeee	chr3:47456531-47456790(-)$1	259	104	123	13.3238
ee[cccqqqqqqqqccc33	chr13:20207981-20208210(-)$1	229	131	150	15.7863
!!ddddqqqqqqqqdddd]	chr17:4692396-4692655(+)$1	259	196	215	14.6337
ddd[bbqqqqqqqqbb]dd	chr6:159653789-159654018(+)$1	229	196	215	13.8480
!a!!bbqqqqqqqqbb22a	chr1:9657010-9657239(-)$1	229	116	135	14.6379

#otherMatches

#Seq PSSM
AUCUAACCAUAUUUUUAGA	chr4:74365618-74365877(+)$1	259	30	49	13.5958
ACGUAGUCCGCUUCCUGCA	chr11:76751099-76751358(+)$1	259	187	206	14.4931
UUUUGGACCAUUAACUGAG	chr7:23340516-23340745(+)$1	229	140	159	13.5958
UGAAAGUCCACCUCCUUAC	chr5:68799949-68800178(+)$1	229	139	158	15.7489
GGUCUUCUGGAACCAAGCC	chr1:156784819-156785078(+)$1	259	74	93	15.4627
GGCGCCCACAGAAAGGCCG	chr11:70185235-70185494(+)$1	259	127	146	15.2598
GUAUAGAAAAGAUACUGGA	chr7:23238987-23239216(+)$1	229	23	42	15.5101
ACGGCCCUGAUGUCGGCUA	chr5:170883519-170883748(+)$1	229	80	99	13.2141
CUUCCUUGUCUUGUAGGAA	chr1:153633573-153633832(+)$1	259	86	105	13.5742
CAUUAAAUGCUAAAUUAUU	chr7:141750460-141750689(-)$1	229	129	148	15.2343
CCAGGUGGGUCCUGACCCU	chr16:29996872-29997131(+)$1	259	65	84	15.7676
GCUGCAAGUGCAAGUGCAG	chr2:7179766-7180025(+)$1	259	75	94	14.3791
AUGCCCAGAUGUAGGGGUA	chrX:2715202-2715461(-)$1	259	40	59	14.2463
CAUACUGAAAGAAAGGUAA	chr18:224804-225063(-)$1	259	147	166	14.5381
UCACCAACCACAUGUGGCC	chr20:60890908-60891167(+)$1	259	12	31	15.7455
UCAAGUGCAAUGAGACGGU	chr2:216809564-216809823(+)$1	259	136	155	14.4383
ACCACCACCUCUACGGCAG	chr6:30994067-30994326(+)$1	259	92	111	14.6163
CAGCGAUUGUUUCUUCAGG	chr2:54128484-54128743(-)$1	259	132	151	14.2399
GUGCCAAAGCAAAGUGUGC	chr11:6644610-6644869(+)$1	259	225	244	14.1048
CUUCCCUUUAAUACGGUGA	chr16:88929985-88930244(+)$1	259	171	190	14.1835
GGCUCCAGACCACAGGAGG	chr1:210111521-210111750(-)$1	229	13	32	14.3834
GGAUGGAAAAGAAGUCAGU	chrX:101911437-101911696(+)$1	259	139	158	15.5727
GUAAGACAAGAGAUUCUCC	chr17:37761702-37761967(+)$1	265	67	86	15.7998
UGCUUCCGCACUCUGAAGC	chr18:12325208-12325467(+)$1	259	210	229	13.5742
CCCCAGGUCCCAAGCUGUG	chrX:15599270-15599499(+)$1	229	87	106	15.1304
AGCCCCUCCACACUGGGCA	chr3:50382797-50383026(+)$1	229	23	42	13.0032
AAAGUGGGCACCAACACCU	chr9:77407452-77407681(-)$1	229	59	78	15.4368
CCAUCUGCGGGGAGAGAUG	chr1:879974-880233(+)$1	259	202	221	14.7111
UGCACAAAGCCCCgugugu	chr19:8137794-8138053(+)$1	259	43	62	14.3791
UGGCUGUCAGGAUUCAGGG	chr7:107638702-107638931(+)$1	229	167	186	15.5714
CGGAUCUCCUCCUCGAUGC	chr8:144999517-144999776(+)$1	259	215	234	13.8633
CUUACCAAUUCUUGGGGUG	chr12:14613909-14614168(-)$1	259	96	115	14.4117
CUAUGGUCUGGAAUCCAUU	chr3:167006555-167006784(+)$1	229	188	207	13.3224
UAUGGGCUCAAGAUCCACA	chr6:100062170-100062399(+)$1	229	96	115	13.7538
GAGAUAGAAGCCUGUGUCC	chr17:46196236-46196465(+)$1	229	172	191	14.1533
GAAAGCACACCGUGGCUGC	chr1:68512581-68512810(+)$1	229	142	161	15.8133
CUUUCAGCUUCGUGUGAGU	chr3:52561708-52561967(-)$1	259	110	129	13.8703
UUUUUAUUUCCUUUUAAAG	chr7:148851284-148851543(+)$1	259	229	248	13.5958
CCUGGACCUACCUUUCCAG	chr4:39246847-39247106(+)$1	259	122	141	14.1185
CGCUGGUGACAUUUCCAGG	chr1:38272469-38272728(+)$1	259	19	38	14.3947
UGUUCUAUAGCCCCGGAUC	chr9:117821938-117822167(+)$1	229	98	117	15.4368
AAGAUCAACAACUGGAUCG	chr19:35769557-35769816(+)$1	259	63	82	14.4036
UGCUUCGCGUUUCAGACUU	chr19:38774145-38774374(+)$1	229	106	125	14.8253
AGGGAGAUCUGGGCCUCCC	chr3:48608155-48608414(-)$1	259	11	30	14.1185
CGUCCUCCUCUGACAGGCC	chr10:105200396-105200625(-)$1	229	86	105	15.4368
ACCGCAACCCUCUGUGCUA	chr15:75498756-75499015(+)$1	259	33	52	15.7455
GGUGCGAACGCGGCCGCCG	chr12:56415227-56415486(-)$1	259	152	171	15.6353
GCUCUCAGGGAACAGCAGA	chr19:12776205-12776464(+)$1	259	154	173	12.9394
GCUCCGCUACACCCUGGGC	chr22:43539193-43539452(+)$1	259	49	68	14.1991
GGCACCUCUCACCUGCUGC	chr17:48193107-48193366(+)$1	259	74	93	14.1249
AGUUUGAGUUUGAGUAAAC	chr5:134245930-134246189(+)$1	259	37	56	14.3791
GGACUCACACUUGGGGGUU	chr8:105503310-105503539(+)$1	229	8	27	15.1304
GCAGGAACAGUGUGUCCAG	chr2:220404447-220404706(+)$1	259	148	167	14.8510
UCACCACAUCCCCAUGGUA	chr1:226834902-226835161(+)$1	259	50	69	13.7914
ACAGUGAAGAUCGACAUGA	chr10:114200322-114200551(-)$1	229	116	135	15.6058
GUCACAGUGGACAAUGUUC	chr19:47184829-47185088(+)$1	259	125	144	15.7077
GCUGUGAAUGUUGACAAAG	chrX:135431487-135431716(-)$1	229	80	99	13.9222
GGUCGCCUUGUCAUGCUGC	chr1:200008700-200008929(+)$1	229	129	148	13.9503
UGUUCUUCUCUUCCAGGAU	chr3:47456531-47456790(-)$1	259	104	123	13.3238
AUCUUCUCCACCUCGAACA	chr13:20207981-20208210(-)$1	229	131	150	15.7863
AGGCGCAGGAUUGGGCGCG	chr17:4692396-4692655(+)$1	259	196	215	14.6337
UGGACACUUCCAUUUGCUC	chr6:159653789-159654018(+)$1	229	196	215	13.8480
ACCCGGCCUCACCUCCUCG	chr1:9657010-9657239(-)$1	229	116	135	14.6379

#DB
.(((((........)))))	chr4:74365618-74365877(+)$1	1	30	49	13.5958
..((((........)))).	chr11:76751099-76751358(+)$1	1	187	206	14.4931
.(((((........)))))	chr7:23340516-23340745(+)$1	1	140	159	13.5958
.(.(((........))).)	chr5:68799949-68800178(+)$1	1	139	158	15.7489
((.(((........)))))	chr1:156784819-156785078(+)$1	1	74	93	15.4627
((((((........)))..	chr11:70185235-70185494(+)$1	1	127	146	15.2598
((.(((........)))..	chr7:23238987-23239216(+)$1	1	23	42	15.5101
))((((........)))).	chr5:170883519-170883748(+)$1	1	80	99	13.2141
.(((((........)))))	chr1:153633573-153633832(+)$1	1	86	105	13.5742
((.(((........))).)	chr7:141750460-141750689(-)$1	1	129	148	15.2343
(..(((........)))..	chr16:29996872-29997131(+)$1	1	65	84	15.7676
((((((........)))))	chr2:7179766-7180025(+)$1	1	75	94	14.3791
((((((........)))).	chrX:2715202-2715461(-)$1	1	40	59	14.2463
..((((........)))).	chr18:224804-225063(-)$1	1	147	166	14.5381
(..(((........)))..	chr20:60890908-60891167(+)$1	1	12	31	15.7455
((..((........)))))	chr2:216809564-216809823(+)$1	1	136	155	14.4383
.(..((........))..)	chr6:30994067-30994326(+)$1	1	92	111	14.6163
(...((........))..)	chr2:54128484-54128743(-)$1	1	132	151	14.2399
((((((........)).))	chr11:6644610-6644869(+)$1	1	225	244	14.1048
.(((((........)).))	chr16:88929985-88930244(+)$1	1	171	190	14.1835
(.((((........)))).	chr1:210111521-210111750(-)$1	1	13	32	14.3834
...(((........)))..	chrX:101911437-101911696(+)$1	1	139	158	15.5727
(..(((........))).)	chr17:37761702-37761967(+)$1	1	67	86	15.7998
.(((((........)))))	chr18:12325208-12325467(+)$1	1	210	229	13.5742
((((((........))).)	chrX:15599270-15599499(+)$1	1	87	106	15.1304
)))(((........)))..	chr3:50382797-50383026(+)$1	1	23	42	13.0032
((.(((........))).)	chr9:77407452-77407681(-)$1	1	59	78	15.4368
((((((........)))))	chr1:879974-880233(+)$1	1	202	221	14.7111
((((((........)))))	chr19:8137794-8138053(+)$1	1	43	62	14.3791
(..(((........))).)	chr7:107638702-107638931(+)$1	1	167	186	15.5714
)))(((........)))))	chr8:144999517-144999776(+)$1	1	215	234	13.8633
((..((........))..)	chr12:14613909-14614168(-)$1	1	96	115	14.4117
))((((........)))).	chr3:167006555-167006784(+)$1	1	188	207	13.3224
((((((........)).))	chr6:100062170-100062399(+)$1	1	96	115	13.7538
(.((((........)))))	chr17:46196236-46196465(+)$1	1	172	191	14.1533
(..(((........)))..	chr1:68512581-68512810(+)$1	1	142	161	15.8133
((((((........)))).	chr3:52561708-52561967(-)$1	1	110	129	13.8703
.(((((........)))))	chr7:148851284-148851543(+)$1	1	229	248	13.5958
((((((........)))))	chr4:39246847-39247106(+)$1	1	122	141	14.1185
(.((((........)))).	chr1:38272469-38272728(+)$1	1	19	38	14.3947
((.(((........))).)	chr9:117821938-117822167(+)$1	1	98	117	15.4368
..((((........)))))	chr19:35769557-35769816(+)$1	1	63	82	14.4036
....((........))...	chr19:38774145-38774374(+)$1	1	106	125	14.8253
((((((........)))))	chr3:48608155-48608414(-)$1	1	11	30	14.1185
((.(((........))).)	chr10:105200396-105200625(-)$1	1	86	105	15.4368
(..(((........)))..	chr15:75498756-75499015(+)$1	1	33	52	15.7455
.(.(((........)))).	chr12:56415227-56415486(-)$1	1	152	171	15.6353
((((((........).)))	chr19:12776205-12776464(+)$1	1	154	173	12.9394
((.(((........)))))	chr22:43539193-43539452(+)$1	1	49	68	14.1991
((((.(........).)))	chr17:48193107-48193366(+)$1	1	74	93	14.1249
((((((........)))))	chr5:134245930-134246189(+)$1	1	37	56	14.3791
((((((........))).)	chr8:105503310-105503539(+)$1	1	8	27	15.1304
((.(((........))).)	chr2:220404447-220404706(+)$1	1	148	167	14.8510
((((((........)))).	chr1:226834902-226835161(+)$1	1	50	69	13.7914
((.(((........)))..	chr10:114200322-114200551(-)$1	1	116	135	15.6058
(..(((........))).)	chr19:47184829-47185088(+)$1	1	125	144	15.7077
(((.((........))..)	chrX:135431487-135431716(-)$1	1	80	99	13.9222
(((.((........)).))	chr1:200008700-200008929(+)$1	1	129	148	13.9503
((((((........)))))	chr3:47456531-47456790(-)$1	1	104	123	13.3238
((.(((........)))..	chr13:20207981-20208210(-)$1	1	131	150	15.7863
..((((........)))).	chr17:4692396-4692655(+)$1	1	196	215	14.6337
(((.((........)).))	chr6:159653789-159654018(+)$1	1	196	215	13.8480
.(..((........))..)	chr1:9657010-9657239(-)$1	1	116	135	14.6379

#PSSM
d : 0.20	c : 0.12	! : 0.11	e : 0.11	i : 0.07	[ : 0.07	f : 0.07	b : 0.06	g : 0.04	" : 0.03	# : 0.03	= : 0.01	a : 0.01	
e : 0.15	! : 0.15	d : 0.14	c : 0.11	i : 0.07	a : 0.06	b : 0.06	f : 0.04	g : 0.04	[ : 0.04	" : 0.03	# : 0.03	= : 0.01	
d : 0.25	[ : 0.19	! : 0.17	e : 0.12	i : 0.06	c : 0.04	g : 0.04	# : 0.03	f : 0.03	" : 0.01	= : 0.01	
c : 0.41	d : 0.19	e : 0.11	i : 0.06	! : 0.06	g : 0.04	[ : 0.04	" : 0.01	= : 0.01	# : 0.01	f : 0.01	
c : 0.39	d : 0.19	b : 0.19	e : 0.09	i : 0.04	g : 0.03	= : 0.01	f : 0.01	[ : 0.01	
c : 0.39	d : 0.19	b : 0.19	e : 0.09	i : 0.04	g : 0.03	a : 0.03	= : 0.01	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
c : 0.39	d : 0.19	b : 0.19	e : 0.09	i : 0.04	g : 0.03	a : 0.03	= : 0.01	
c : 0.39	d : 0.19	b : 0.19	e : 0.09	i : 0.04	g : 0.03	] : 0.03	= : 0.01	
c : 0.41	d : 0.19	e : 0.09	2 : 0.07	] : 0.07	i : 0.06	g : 0.03	= : 0.01	3 : 0.01	f : 0.01	
d : 0.20	] : 0.17	2 : 0.17	e : 0.11	i : 0.07	c : 0.04	g : 0.04	4 : 0.03	3 : 0.03	: : 0.01	= : 0.01	F : 0.01	a : 0.01	f : 0.01	b : 0.01	
d : 0.15	e : 0.12	2 : 0.11	] : 0.09	i : 0.07	c : 0.07	3 : 0.06	a : 0.04	: : 0.04	f : 0.04	g : 0.04	4 : 0.03	b : 0.03	= : 0.01	F : 0.01	

#score	917.2428747253324
#seq	63
#width	19
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_CDS_m3_run1.txt

#BEAR
:eeeee!!bb!!bbmmmmbb4444bb22ee	chr2:27565791-27566015(-)$1	224	168	198	10.0634
:cccdddd!!acccmmmmccc]a22dddd]	chr17:7399261-7399484(+)$1	223	188	218	12.8500
eccc[eeeee!!ccclllccc]eeeee]cc	chr15:75499128-75499365(+)$1	237	7	37	11.4908
""eeeee!!a[cccmmmmccc]a333eeee	chr15:77344638-77344864(-)$1	226	149	179	15.0593
ggggg####ccc[ammmma]ccc22ggggg	chr11:59564726-59564950(+)$1	224	49	79	12.3905
:eeeee"""a[ddddllldddda333eeee	chrX:107978908-107979161(-)$1	253	97	127	10.5991
cc[ddddeeeeeccclllccc]eeeee]dd	chr2:44161805-44162032(-)$1	227	70	100	10.4984
)eeeee"""ccc[ammmma]ccc333eeee	chr11:6238538-6238780(-)$1	242	131	161	12.3119
gggg"""ccc[cccmmmmccc]ccc66666	chr10:27470308-27470539(+)$1	231	99	129	12.0701
bbdddd!!bb[cccmmmmcccbb22dddd:	chr17:46675410-46675641(-)$1	231	93	123	11.0911
eee[ccc!!eeeeemmmmeeeee22cccee	chr9:139333523-139333768(-)$1	245	184	214	10.5392
gggggg!!ccc[ccclllccc]ccc]gggg	chr19:9949111-9949343(+)$1	232	83	113	12.3301
dddd!!eeeeecccmmmmccc22eeeee22	chr7:5567919-5568163(-)$1	244	140	170	11.7718
ggggggg####ddddllldddd4444gggg	chr17:17174109-17174327(-)$1	218	10	40	11.0625
!a[ffffffa[cccmmmmccc]a]ffffff	chr11:125496568-125496795(+)$1	227	76	106	12.6412
a[eeeee!!a[cccmmmmccc]aeeeee]a	chr2:98421512-98421739(-)$1	227	172	202	14.1226
ffffff"""eeeeemmmmeeeee333ffff	chr19:36224417-36224643(+)$1	226	194	224	10.4701
dddd[dddd!!cccmmmmccc]dddd]ddd	chr3:38522751-38522993(+)$1	242	109	139	12.6001
ccc[ccc!!a[ddddllldddd]accc]cc	chr21:34925501-34925724(+)$1	223	130	160	10.6716
bb[ccc!!ddddccclllccc]dddd333c	chr3:124739672-124739898(-)$1	226	28	58	10.9739
[ccc!!ccc"""bbmmmmbb]ccc]ccccc	chr3:78676409-78676641(-)$1	232	149	179	11.7570
gg[ddddbb!!cccmmmmccc333bb]ddd	chr12:49521724-49521948(-)$1	224	62	92	13.0888
d!!aggggggg[bbmmmmbb]ggggggg]a	chr16:28847618-28847874(+)$1	256	170	200	10.5136
cccccc####ddddmmmmdddd333ccc]c	chr14:69847168-69847395(-)$1	227	126	156	12.6417
dd[ccc[ccc[cccmmmmccc]ccc]ccc]	chr8:37555010-37555257(+)$1	247	212	242	14.3036
[a[ccc[a[ddddammmma]dddd]a22cc	chr17:40028284-40028515(-)$1	231	114	144	10.9066
:ggggggg!!a[ccclllccc]a22ggggg	chr9:117835952-117836211(-)$1	259	195	225	11.7786
cccbb[eeeeecccmmmmccc]eeeee]bb	chr1:160209398-160209626(-)$1	228	76	106	11.6540
"""dddd####cccmmmmccc4444dddd3	chr6:158923385-158923609(+)$1	224	111	141	13.8403
:eeeee"""eeeeemmmmeeeee22eeeee	chr5:89970966-89971192(+)$1	226	188	218	10.0190
b[bb"""gggggggmmmmggggggg4444b	chr2:113410213-113410440(+)$1	227	27	57	10.5423
ccc[a!!bb[ddddmmmmddddbb4444a]	chr18:59941144-59941373(+)$1	229	136	166	10.9348
eeggggggg!!ccclllcccggggggg]ee	chr4:84205629-84205849(-)$1	220	84	114	11.2448
cc[a[eeeee[ccclllccceeeee]a]cc	chr9:139935165-139935468(-)$1	303	185	215	10.7622
a[ggggggg"""ccclllccc]ggggggg]	chr8:103851784-103852011(-)$1	227	60	90	12.2287
GGGGcccccc[cccmmmmccc]ccc]ccc:	chr11:14512040-14512267(-)$1	227	155	185	11.0318
ccc####ccc[cccmmmmcccccc22ccc]	chr9:102744773-102745002(-)$1	229	28	58	13.7096
gggggg[bb!!cccmmmmccc22bbggggg	chr13:77581308-77581535(-)$1	227	180	210	13.1249
cc[ddddgggggggmmmmggggggg]dddd	chr10:135184051-135184275(-)$1	224	163	193	10.7612
gggcccccc!!cccmmmmccc22ccccccn	chr14:69584755-69584989(-)$1	234	105	135	13.3962
hhhhh!!ccc[cccmmmmccc]ccc333hh	chr14:70235257-70235486(+)$1	229	193	223	13.8676
!eeeee####ddddmmmmdddd333eeeee	chr2:112858155-112858372(+)$1	217	4	34	12.2725
ggg:eeeee!!cccmmmmccc22eeeeedd	chr6:26285419-26285675(-)$1	256	115	145	12.2009
dddbb!!ccc[cccmmmmccc]ccc22bb:	chr16:28187245-28187476(-)$1	231	118	148	11.8236
ddd[eeeee!!cccmmmmccc22eeeeedd	chr11:43400729-43400968(+)$1	239	46	76	12.7325
[accc[dddd[cccmmmmcccdddd]ccc4	chr6:133136028-133136282(+)$1	254	70	100	12.6663
#ccc[eeeee[cccmmmmccc]eeeee]cc	chr21:17250106-17250377(+)$1	271	30	60	13.4920
ggggggccc!!cccmmmmccc4444ccc]g	chr17:7803776-7804001(+)$1	225	96	126	14.5376
:dddd!!ccc[cccmmmmccc333ccc22d	chr10:28897054-28897299(+)$1	245	212	242	13.4330
gggggggccc!!bbmmmmbb333ccc]ggg	chr17:7365402-7365655(-)$1	253	74	104	12.1909
"""dddd[bb[cccmmmmcccbb333dddd	chr1:54666029-54666262(+)$1	233	159	189	12.6452
!!dddd"""eeeeemmmmeeeeedddd22a	chr9:91077423-91077658(+)$1	235	2	32	10.0434
eeee!!dddd[cccmmmmccc]dddd]eee	chr1:224377486-224377721(+)$1	235	28	58	12.7221
eeeee[ccc"""bbmmmmbb22ccceeeee	chr19:54971892-54972139(+)$1	247	68	98	10.9926
ccc!!ccc[a[cccmmmmccc]accc22cc	chr5:149825072-149825319(-)$1	247	133	163	14.3009
bccc[ccc[a[ccclllccca]cccccc]b	chr17:57744148-57744368(+)$1	220	79	109	11.8066
:ggggggg"""ddddllldddd333ggggg	chr6:135317870-135318096(-)$1	226	5	35	10.5592
c[ccc!!bb!!cccmmmmccc]bb22ccc]	chr1:115256372-115256602(-)$1	230	46	76	13.8876
ggg[cccccc[cccmmmmccc]ccc]ccc]	chr17:8110488-8110721(-)$1	233	79	109	14.3491

#otherMatches

#Seq PSSM
AUGCCUAAGAAACGAGGUCGAAAGUCCAAG	chr2:27565791-27566015(-)$1	224	168	198	10.0634
CUAGGGCUGACGGUUGACACCUGGAGGCCU	chr17:7399261-7399484(+)$1	223	188	218	12.8500
UUGGACCCAGCUGGCCCAGCCCCUGGGGCC	chr15:75499128-75499365(+)$1	237	7	37	11.4908
UUGCCAAGGAGUUCUAUCGGAGUGAGUUGG	chr15:77344638-77344864(-)$1	226	149	179	15.0593
GCUAGUAGUUGUGUUGCUGGGCAUUUUAGC	chr11:59564726-59564950(+)$1	224	49	79	12.3905
UUCACCCAAGACGAAUACUUCGCGAUGGUG	chrX:107978908-107979161(-)$1	253	97	127	10.5991
GUAUUACCAAGGAUUCAUGAUGUCUUGUGU	chr2:44161805-44162032(-)$1	227	70	100	10.4984
AGCAGCCCUUUGCGGACUCUCAACCAGCUG	chr11:6238538-6238780(-)$1	242	131	161	12.3119
GAUAUCCCUUGGCCAGAAGGUGAAGAAAAG	chr10:27470308-27470539(+)$1	231	99	129	12.0701
GCGGAGCAGCAGCGGCCGCGCGCGCCUCCC	chr17:46675410-46675641(-)$1	231	93	123	11.0911
UCGAGGCAGCCAGGAGGACCUGGAAGCCCG	chr9:139333523-139333768(-)$1	245	184	214	10.5392
GGGCAGGGGGAGCCUGCCAGGGUCCGCUGC	chr19:9949111-9949343(+)$1	232	83	113	12.3301
GCUUCCAGCUCCUCCCUGGAGAAGAGCUAC	chr7:5567919-5568163(-)$1	244	140	170	11.7718
UGAAGUUUUCUAUGCCCAGUGUUCCUGACU	chr17:17174109-17174327(-)$1	218	10	40	11.0625
CGAGGUGCUCGGUGGAGUCAUGGCAGUGCC	chr11:125496568-125496795(+)$1	227	76	106	12.6412
GAAAAUUCAGGUCAUAGGUGAGUGGUUUAU	chr2:98421512-98421739(-)$1	227	172	202	14.1226
GGAGGGUCUGGGACCUCUGUCCUUCCCCUU	chr19:36224417-36224643(+)$1	226	194	224	10.4701
GUAUUGCUGAAGAGCGACCUCACAGCCGUG	chr3:38522751-38522993(+)$1	242	109	139	12.6001
GACCGUCCUGGAGUCUUCGACUGUGACUGU	chr21:34925501-34925724(+)$1	223	130	160	10.6716
CCGAGAACGCUGCGAUCUUUGACGGUCAGU	chr3:124739672-124739898(-)$1	226	28	58	10.9739
UGCAGCACCAGCCCGACAGGAGGUAUGUUG	chr3:78676409-78676641(-)$1	232	149	179	11.7570
UUGUUCACUGGUACGUGGGUGAGGGGAUGG	chr12:49521724-49521948(-)$1	224	62	92	13.0888
UCUCCUGACUUAGCCGAGGUAAGGUCAGUG	chr16:28847618-28847874(+)$1	256	170	200	10.5136
CAGGCUGGGAAAUAAUUGUGUUGGAAGCAC	chr14:69847168-69847395(-)$1	227	126	156	12.6417
GCACGGUGGCGCCGAGUCCGGGGCCUCCGG	chr8:37555010-37555257(+)$1	247	212	242	14.3036
UGUCUGAUGGUGACAGCUGAUCACGGGCCA	chr17:40028284-40028515(-)$1	231	114	144	10.9066
UGGGAGUGCAGCUUCCAAGAAACACCACUU	chr9:117835952-117836211(-)$1	259	195	225	11.7786
GGAUUGGGUACGGCGGCAGCCAGUACUGGA	chr1:160209398-160209626(-)$1	228	76	106	11.6540
CCCUCAGCCCUGCAGCAGUGCCACCCUGAA	chr6:158923385-158923609(+)$1	224	111	141	13.8403
GAUGGAGAAAUCAGGUUAUUGGUCAUCCGU	chr5:89970966-89971192(+)$1	226	188	218	10.0190
AUACCUUUUAAGAUAUUGAUCUUAAUGAUG	chr2:113410213-113410440(+)$1	227	27	57	10.5423
UCCUCUUGAUAGCCUGAAGGCUUCUUUUGU	chr18:59941144-59941373(+)$1	229	136	166	10.9348
GCGCGGGCGCCAGCUCAGUUUGUCCGCGGC	chr4:84205629-84205849(-)$1	220	84	114	11.2448
GCGACGGCCUCGCCCUUGGUAGGUCUUGGU	chr9:139935165-139935468(-)$1	303	185	215	10.7622
UGAAGUGCAACUCUGCUCCAGCUGUACUUG	chr8:103851784-103852011(-)$1	227	60	90	12.2287
AGGUGAGGUACUUUUUAAAAAAUACUCUUA	chr11:14512040-14512267(-)$1	227	155	185	11.0318
AGUCCACCUGAGAGCUCCUUCCAGAAACUA	chr9:102744773-102745002(-)$1	229	28	58	13.7096
UUUGGAGCAGAUUCACUGGGAAGUGUCCAA	chr13:77581308-77581535(-)$1	227	180	210	13.1249
CCGGCCGUGGGGGCCAUUGUCCUCACCGGC	chr10:135184051-135184275(-)$1	224	163	193	10.7612
UUGGGACAUUCGGGAAUCCCCCCAUGGAGG	chr14:69584755-69584989(-)$1	234	105	135	13.3962
UAUUUUUCUAAGUAGAUUUAUGUAGCUUAA	chr14:70235257-70235486(+)$1	229	193	223	13.8676
UAAACAUACUAGUAAAACUACUCCUUGUUU	chr2:112858155-112858372(+)$1	217	4	34	12.2725
UGGUGUUCUGAAGGUGUUCCUGGAGAACGU	chr6:26285419-26285675(-)$1	256	115	145	12.2009
GCUGUCUGCCCAAACUCCUUUUGGCUCACC	chr16:28187245-28187476(-)$1	231	118	148	11.8236
CUUGCAGGUGGAUUCACCAAUGAACUUGAA	chr11:43400729-43400968(+)$1	239	46	76	12.7325
GUCGCGUUUAAGCAUUGCUGCUGGAGGUGU	chr6:133136028-133136282(+)$1	254	70	100	12.6663
AACUCUUCGAAUCUGGAGAGGAUCGAGAAG	chr21:17250106-17250377(+)$1	271	30	60	13.4920
UAGCAACUUGGAGGGCUUCCUGGAGGAGUU	chr17:7803776-7804001(+)$1	225	96	126	14.5376
CAGGACCCAAAUCUUCUUAGACAAUUGCUU	chr10:28897054-28897299(+)$1	245	212	242	13.4330
UGGAGGGGAUAGGGGCUGCCAAAGUCACUU	chr17:7365402-7365655(-)$1	253	74	104	12.1909
CCCUCUUCACGAGCAUCCGCUGUACAAAGA	chr1:54666029-54666262(+)$1	233	159	189	12.6452
UGUGGGUCCGAGCAAACCUGUUUCCCAGCC	chr9:91077423-91077658(+)$1	235	2	32	10.0434
UGGUUUGGAAUGUUUGCUAAUCUUCCUAUU	chr1:224377486-224377721(+)$1	235	28	58	12.7221
GCCAGUCUCCUACCUGCAGGCCGAGCUGGC	chr19:54971892-54972139(+)$1	247	68	98	10.9926
AGAUCGGGCGGAUUGGUAAGUGCCCCCCUC	chr5:149825072-149825319(-)$1	247	133	163	14.3009
CCAACAUCCGUCAGAAUCUGCAGAUUUGUG	chr17:57744148-57744368(+)$1	220	79	109	11.8066
AUUUUCUUUAGGUCAUGUUGAUGCUGGGAA	chr6:135317870-135318096(-)$1	226	5	35	10.5592
UGUUGGACAUACUGGAUACAGCUGGACAAG	chr1:115256372-115256602(-)$1	230	46	76	13.8876
GGCAAAGGCAAGUUUGGAAACGUGUACUUG	chr17:8110488-8110721(-)$1	233	79	109	14.3491

#DB
.(((((..((..((....))....))..))	chr2:27565791-27566015(-)$1	1	168	198	10.0634
.(((((((..((((....))).)..)))).	chr17:7399261-7399484(+)$1	1	188	218	12.8500
((((.(((((..(((...))).))))).))	chr15:75499128-75499365(+)$1	1	7	37	11.4908
..(((((..(.(((....))).)...))))	chr15:77344638-77344864(-)$1	1	149	179	15.0593
(((((....(((.(....).)))..)))))	chr11:59564726-59564950(+)$1	1	49	79	12.3905
.(((((...(.((((...)))))...))))	chrX:107978908-107979161(-)$1	1	97	127	10.5991
((.((((((((((((...))).))))).))	chr2:44161805-44162032(-)$1	1	70	100	10.4984
.(((((...(((.(....).)))...))))	chr11:6238538-6238780(-)$1	1	131	161	12.3119
((((...(((.(((....))).))).....	chr10:27470308-27470539(+)$1	1	99	129	12.0701
))((((..((.(((....)))))..)))).	chr17:46675410-46675641(-)$1	1	93	123	11.0911
(((.(((..(((((....)))))..)))))	chr9:139333523-139333768(-)$1	1	184	214	10.5392
((((((..(((.(((...))).))).))))	chr19:9949111-9949343(+)$1	1	83	113	12.3301
((((..((((((((....)))..)))))..	chr7:5567919-5568163(-)$1	1	140	170	11.7718
(((((((....((((...))))....))))	chr17:17174109-17174327(-)$1	1	10	40	11.0625
.(.(((((((.(((....))).).))))))	chr11:125496568-125496795(+)$1	1	76	106	12.6412
(.(((((..(.(((....))).)))))).)	chr2:98421512-98421739(-)$1	1	172	202	14.1226
((((((...(((((....)))))...))))	chr19:36224417-36224643(+)$1	1	194	224	10.4701
((((.((((..(((....))).)))).)))	chr3:38522751-38522993(+)$1	1	109	139	12.6001
(((.(((..(.((((...)))).)))).))	chr21:34925501-34925724(+)$1	1	130	160	10.6716
((.(((..(((((((...))).))))...)	chr3:124739672-124739898(-)$1	1	28	58	10.9739
.(((..(((...((....)).))).)))))	chr3:78676409-78676641(-)$1	1	149	179	11.7570
((.((((((..(((....)))...)).)))	chr12:49521724-49521948(-)$1	1	62	92	13.0888
(..((((((((.((....)).))))))).)	chr16:28847618-28847874(+)$1	1	170	200	10.5136
((((((....((((....))))...))).)	chr14:69847168-69847395(-)$1	1	126	156	12.6417
((.(((.(((.(((....))).))).))).	chr8:37555010-37555257(+)$1	1	212	242	14.3036
.(.(((.(.(((((....).)))).)..))	chr17:40028284-40028515(-)$1	1	114	144	10.9066
.(((((((..(.(((...))).)..)))))	chr9:117835952-117836211(-)$1	1	195	225	11.7786
(((((.((((((((....))).))))).))	chr1:160209398-160209626(-)$1	1	76	106	11.6540
...((((....(((....)))....)))).	chr6:158923385-158923609(+)$1	1	111	141	13.8403
.(((((...(((((....)))))..)))))	chr5:89970966-89971192(+)$1	1	188	218	10.0190
(.((...(((((((....)))))))....)	chr2:113410213-113410440(+)$1	1	27	57	10.5423
(((.(..((.((((....))))))....).	chr18:59941144-59941373(+)$1	1	136	166	10.9348
(((((((((..(((...)))))))))).))	chr4:84205629-84205849(-)$1	1	84	114	11.2448
((.(.(((((.(((...)))))))).).))	chr9:139935165-139935468(-)$1	1	185	215	10.7622
(.(((((((...(((...))).))))))).	chr8:103851784-103852011(-)$1	1	60	90	12.2287
))))((((((.(((....))).))).))).	chr11:14512040-14512267(-)$1	1	155	185	11.0318
(((....(((.(((....))))))..))).	chr9:102744773-102745002(-)$1	1	28	58	13.7096
((((((.((..(((....)))..)))))))	chr13:77581308-77581535(-)$1	1	180	210	13.1249
((.(((((((((((....))))))).))))	chr10:135184051-135184275(-)$1	1	163	193	10.7612
))))))(((..(((....)))..)))(((.	chr14:69584755-69584989(-)$1	1	105	135	13.3962
(((((..(((.(((....))).)))...))	chr14:70235257-70235486(+)$1	1	193	223	13.8676
.(((((....((((....))))...)))))	chr2:112858155-112858372(+)$1	1	4	34	12.2725
))).(((((..(((....)))..)))))((	chr6:26285419-26285675(-)$1	1	115	145	12.2009
)))((..(((.(((....))).)))..)).	chr16:28187245-28187476(-)$1	1	118	148	11.8236
(((.(((((..(((....)))..)))))))	chr11:43400729-43400968(+)$1	1	46	76	12.7325
.((((.((((.(((....))))))).))).	chr6:133136028-133136282(+)$1	1	70	100	12.6663
.(((.(((((.(((....))).))))).))	chr21:17250106-17250377(+)$1	1	30	60	13.4920
(((((((((..(((....)))....))).)	chr17:7803776-7804001(+)$1	1	96	126	14.5376
.((((..(((.(((....)))...)))..)	chr10:28897054-28897299(+)$1	1	212	242	13.4330
((((((((((..((....))...))).)))	chr17:7365402-7365655(-)$1	1	74	104	12.1909
...((((.((.(((....)))))...))))	chr1:54666029-54666262(+)$1	1	159	189	12.6452
..((((...(((((....)))))))))..)	chr9:91077423-91077658(+)$1	1	2	32	10.0434
((((..((((.(((....))).)))).)))	chr1:224377486-224377721(+)$1	1	28	58	12.7221
(((((.(((...((....))..))))))))	chr19:54971892-54972139(+)$1	1	68	98	10.9926
(((..(((.(.(((....))).))))..))	chr5:149825072-149825319(-)$1	1	133	163	14.3009
((((.(((.(.(((...)))).)))))).)	chr17:57744148-57744368(+)$1	1	79	109	11.8066
.(((((((...((((...))))...)))))	chr6:135317870-135318096(-)$1	1	5	35	10.5592
(.(((..((..(((....))).))..))).	chr1:115256372-115256602(-)$1	1	46	76	13.8876
(((.((((((.(((....))).))).))).	chr17:8110488-8110721(-)$1	1	79	109	14.3491

#PSSM
g : 0.18	c : 0.16	: : 0.11	d : 0.10	e : 0.08	b : 0.06	" : 0.05	! : 0.05	[ : 0.05	a : 0.03	) : 0.01	f : 0.01	G : 0.01	h : 0.01	# : 0.01	
c : 0.23	g : 0.22	e : 0.15	d : 0.10	[ : 0.06	" : 0.05	a : 0.05	b : 0.03	! : 0.03	f : 0.01	G : 0.01	h : 0.01	
g : 0.23	c : 0.22	e : 0.16	[ : 0.13	d : 0.11	" : 0.03	f : 0.01	! : 0.01	b : 0.01	G : 0.01	h : 0.01	
c : 0.20	g : 0.18	d : 0.16	e : 0.15	[ : 0.08	b : 0.05	f : 0.03	a : 0.03	G : 0.01	# : 0.01	h : 0.01	: : 0.01	! : 0.01	
g : 0.18	c : 0.18	e : 0.16	d : 0.15	[ : 0.08	! : 0.06	" : 0.03	f : 0.03	b : 0.03	a : 0.01	# : 0.01	h : 0.01	
e : 0.20	c : 0.18	g : 0.16	d : 0.15	! : 0.13	[ : 0.05	# : 0.03	" : 0.03	f : 0.03	
c : 0.16	! : 0.15	d : 0.15	e : 0.15	" : 0.11	g : 0.11	# : 0.06	[ : 0.05	f : 0.01	
c : 0.25	! : 0.13	e : 0.13	g : 0.11	# : 0.08	" : 0.08	d : 0.06	b : 0.06	f : 0.01	a : 0.01	[ : 0.01	
c : 0.23	e : 0.13	b : 0.11	! : 0.10	" : 0.10	# : 0.08	g : 0.08	d : 0.06	[ : 0.05	f : 0.01	
c : 0.20	! : 0.18	e : 0.16	a : 0.11	# : 0.06	d : 0.06	" : 0.06	b : 0.05	g : 0.05	[ : 0.01	
[ : 0.35	! : 0.20	e : 0.11	d : 0.08	" : 0.06	c : 0.05	g : 0.05	a : 0.03	# : 0.03	
c : 0.57	d : 0.15	e : 0.08	! : 0.05	[ : 0.05	" : 0.05	g : 0.03	
c : 0.64	d : 0.13	b : 0.08	e : 0.06	[ : 0.03	g : 0.03	
c : 0.64	d : 0.11	b : 0.08	e : 0.06	a : 0.05	g : 0.03	
m : 0.77	c : 0.10	d : 0.06	l : 0.05	
m : 0.77	l : 0.22	
m : 0.77	l : 0.22	
m : 0.77	l : 0.16	c : 0.05	
c : 0.64	d : 0.11	b : 0.08	e : 0.06	a : 0.05	g : 0.03	
c : 0.64	d : 0.11	b : 0.08	e : 0.06	] : 0.05	g : 0.03	
c : 0.62	d : 0.13	e : 0.08	g : 0.05	] : 0.03	4 : 0.01	3 : 0.01	2 : 0.01	a : 0.01	
] : 0.38	d : 0.15	2 : 0.10	e : 0.08	c : 0.06	g : 0.06	4 : 0.05	3 : 0.05	b : 0.03	
c : 0.22	e : 0.15	a : 0.11	3 : 0.10	2 : 0.08	d : 0.08	g : 0.08	4 : 0.06	b : 0.06	] : 0.01	
c : 0.23	3 : 0.16	e : 0.15	2 : 0.10	d : 0.10	g : 0.08	4 : 0.06	b : 0.05	] : 0.01	a : 0.01	
c : 0.23	e : 0.15	2 : 0.13	3 : 0.13	d : 0.08	g : 0.08	4 : 0.06	b : 0.05	] : 0.03	f : 0.01	
e : 0.18	c : 0.16	d : 0.11	g : 0.11	] : 0.11	3 : 0.10	4 : 0.05	2 : 0.05	b : 0.03	6 : 0.01	f : 0.01	a : 0.01	
e : 0.23	c : 0.23	g : 0.15	d : 0.10	2 : 0.06	] : 0.06	f : 0.03	3 : 0.03	4 : 0.03	6 : 0.01	a : 0.01	
c : 0.20	e : 0.18	g : 0.15	d : 0.11	] : 0.11	2 : 0.08	f : 0.03	3 : 0.03	4 : 0.03	6 : 0.01	b : 0.01	
c : 0.23	e : 0.16	d : 0.16	g : 0.13	] : 0.08	2 : 0.05	f : 0.03	b : 0.03	6 : 0.01	3 : 0.01	4 : 0.01	a : 0.01	h : 0.01	
e : 0.16	c : 0.15	g : 0.13	d : 0.13	] : 0.11	: : 0.05	a : 0.05	b : 0.05	f : 0.03	6 : 0.01	2 : 0.01	3 : 0.01	n : 0.01	h : 0.01	4 : 0.01	

#score	714.3739361320658
#seq	59
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014c_hg19_transcript_m2_run1.txt

#BEAR
ddddvvvvvvvvvvvvvdddd2	chr11:47516892-47517140(-)$1	248	130	152	21.3180
yyyyyyyyyyyyyyyyeeeee]	chrX:147602800-147603038(+)$1	238	176	198	20.5926
!!bbuuuuuuuuuuuubb22cc	chr6:108363001-108363251(-)$1	250	57	79	21.7284
yyyyyyyyyyyyyyyyeeeee]	chrX:14889292-14889542(-)$1	250	17	39	20.5926
eeeeettttttttttteeeee2	chr8:3213038-3213259(-)$1	221	129	151	22.2644
eeeeuuuuuuuuuuuueeeee]	chr3:127318934-127319152(+)$1	218	24	46	23.4165
eeeeuuuuuuuuuuuueeeee:	chr7:696764-697054(-)$1	290	28	50	22.6789
ddddwwwwwwwwwwwwwwdddd	chr3:179582202-179582425(-)$1	223	129	151	20.2157
ffffvvvvvvvvvvvvvfffff	chr15:49430819-49431044(-)$1	225	37	59	21.9803
ddddwwwwwwwwwwwwwwdddd	chr2:69864786-69865027(-)$1	241	95	117	20.2157
ffffftttttttttttffffff	chrX:38426610-38426830(+)$1	220	78	100	21.9143
ffffuuuuuuuuuuuuffffff	chr2:208451009-208451289(+)$1	280	217	239	22.8019
eeeeettttttttttteeeee:	chr3:149579030-149579276(+)$1	246	217	239	21.8036
ffffwwwwwwwwwwwwwwffff	chr11:47740762-47740995(-)$1	233	76	98	20.7888
iiiiitttttttttttiiiiii	chr8:66711713-66711957(-)$1	244	157	179	21.7312
hhhhuuuuuuuuuuuuhhhhhh	chr19:52588680-52588946(-)$1	266	80	102	20.8040
eeeeettttttttttteeeee]	chr14:66160725-66160939(+)$1	214	7	29	22.5411
#ddddtttttttttttdddd77	chr9:131844499-131844756(+)$1	257	208	230	20.2504
gggggtttttttttttgggggg	chr15:49776058-49776301(-)$1	243	91	113	22.0941
eeeevvvvvvvvvvvvveeeee	chr9:95011279-95011562(-)$1	283	121	143	22.2921
dddduuuuuuuuuuuudddd::	chr4:108986812-108987040(-)$1	228	97	119	20.6258
gggggtttttttttttgggggg	chr5:140934674-140934933(-)$1	259	120	142	22.0941
g[ccctttttttttttcccggg	chr18:47902926-47903144(+)$1	218	6	28	22.4234
ddddyyyyyyyyyyyyyyyydd	chr4:172848740-172848955(+)$1	215	163	185	19.5116
ddddtttttttttttddddfff	chr1:92633052-92633279(+)$1	227	31	53	20.7256
eeeeuuuuuuuuuuuueeeeeD	chr3:42892743-42892956(+)$1	213	50	72	22.4100
ffffvvvvvvvvvvvvvfffff	chr10:18687494-18687752(+)$1	258	229	251	21.9803
ffffwwwwwwwwwwwwwwffff	chr17:60674275-60674492(+)$1	217	70	92	20.7888
eeeeuuuuuuuuuuuueeeee:	chr5:80776010-80776252(-)$1	242	51	73	22.6789
eeeeuuuuuuuuuuuueeeee:	chr6:84275957-84276180(-)$1	223	13	35	22.6789
hhhhuuuuuuuuuuuuhhhhhh	chr11:27070957-27071179(+)$1	222	4	26	20.8040
!!ccctttttttttttccc22c	chr10:14183921-14184142(-)$1	221	100	122	21.8750
ffffftttttttttttffffff	chr1:118527538-118527770(-)$1	232	61	83	21.9143
ddddyyyyyyyyyyyyyyyydd	chr12:7124517-7124762(-)$1	245	0	22	19.5116
dddduuuuuuuuuuuudddd::	chrX:123131311-123131556(+)$1	245	124	146	20.6258
ffccctttttttttttccc333	chr8:27392803-27393027(+)$1	224	186	208	22.2174
ddddvvvvvvvvvvvvvdddd:	chr8:146108952-146109180(-)$1	228	136	158	20.8571
ffffuuuuuuuuuuuuffffff	chr11:18536219-18536488(-)$1	269	78	100	22.8019
eeeeettttttttttteeeee:	chr12:12885079-12885332(+)$1	253	103	125	21.8036
yyyyyyyyyyyyyyyyffffff	chr19:48165836-48166077(+)$1	241	136	158	20.1525
iiiivvvvvvvvvvvvviiiii	chr10:14363062-14363283(-)$1	221	117	139	22.0443
d!!bbtttttttttttbb]ddd	chr10:129876704-129876984(+)$1	280	253	275	21.0396
gggguuuuuuuuuuuugggggg	chr8:42784501-42784737(+)$1	236	125	147	23.0865
ffffwwwwwwwwwwwwwwffff	chr8:99038296-99038528(+)$1	232	51	73	20.7888
bbwwwwwwwwwwwwwwbb4444	chr4:79746524-79746738(+)$1	214	43	65	19.2697
eeeeuuuuuuuuuuuueeeee:	chr19:20841009-20841235(-)$1	226	200	222	22.6789
yyyyyyyyyyyyyyyyeeeee:	chr18:67148453-67148695(+)$1	242	220	242	19.8550
d[ccctttttttttttcccddd	chr2:28490172-28490450(+)$1	278	190	212	21.9472
yyyyyyyyyyyyyyyyeeeee:	chr3:32453872-32454152(+)$1	280	163	185	19.8550
ggwwwwwwwwwwwwwwgggggg	chr14:68488039-68488289(+)$1	250	148	170	20.7559
!cccuuuuuuuuuuuuccc22b	chr6:133689388-133689599(+)$1	211	37	59	22.4258
iiiivvvvvvvvvvvvviiiii	chr5:93102985-93103276(-)$1	291	203	225	22.0443
cccavvvvvvvvvvvvva]ccc	chr6:154539198-154539475(-)$1	277	194	216	21.9416
ggggvvvvvvvvvvvvvggggg	chr3:141272416-141272692(+)$1	276	239	261	22.2516
ffffuuuuuuuuuuuuffffff	chr11:115310335-115310559(-)$1	224	134	156	22.8019
====uuuuuuuuuuuu======	chr10:52572926-52573145(-)$1	219	124	146	23.0588
#cccuuuuuuuuuuuucccfff	chr19:56900413-56900644(-)$1	231	128	150	22.9013
c[bbuuuuuuuuuuuubbccc:	chr3:156654120-156654362(+)$1	242	47	69	21.5091
eeeeettttttttttteeeee:	chr17:21213056-21213306(+)$1	250	31	53	21.8036
gggguuuuuuuuuuuugggggg	chr8:109249967-109250186(-)$1	219	124	146	23.0865
ffffftttttttttttffffff	chr7:37063831-37064100(-)$1	269	11	33	21.9143
ffbbuuuuuuuuuuuubb]fff	chr12:50033088-50033386(-)$1	298	60	82	22.1974
ggwwwwwwwwwwwwwwgggggg	chr4:154245782-154246007(+)$1	225	72	94	20.7559
ffbbuuuuuuuuuuuubb]fff	chr14:92819270-92819489(+)$1	219	127	149	22.1974
eeewwwwwwwwwwwwwweeeee	chr3:56773732-56773999(-)$1	267	55	77	21.1233
ffffftttttttttttffffff	chr9:78523600-78523865(+)$1	265	110	132	21.9143
!cccuuuuuuuuuuuuccc22d	chr13:36889515-36889759(-)$1	244	63	85	22.4325
eeeeuuuuuuuuuuuueeeee:	chr2:217032371-217032642(+)$1	271	150	172	22.6789

#otherMatches

#Seq PSSM
uuucaucacccuuaaaagaaac	chr11:47516892-47517140(-)$1	248	130	152	21.3180
AAAUAAUAUGUCUACCUUUGGU	chrX:147602800-147603038(+)$1	238	176	198	20.5926
CAUCAAAUAAGUAAUAGACAUC	chr6:108363001-108363251(-)$1	250	57	79	21.7284
gccaaauuaccuucagagucau	chrX:14889292-14889542(-)$1	250	17	39	20.5926
ccacaucgugcaguucugugga	chr8:3213038-3213259(-)$1	221	129	151	22.2644
cuaaaaauacaaaaaauuagcu	chr3:127318934-127319152(+)$1	218	24	46	23.4165
ugcacacauucauucaugcauc	chr7:696764-697054(-)$1	290	28	50	22.6789
ccauucuacucugcuucuaugg	chr3:179582202-179582425(-)$1	223	129	151	20.2157
UAUUUCUUAGAAUAUUUGAUAC	chr15:49430819-49431044(-)$1	225	37	59	21.9803
GUUUGAUAAAUAUUAACAAAAC	chr2:69864786-69865027(-)$1	241	95	117	20.2157
augggaaaaaccuaccuucaug	chrX:38426610-38426830(+)$1	220	78	100	21.9143
uggcaaaaacuucauggcuaag	chr2:208451009-208451289(+)$1	280	217	239	22.8019
caugucauuugucacaacauga	chr3:149579030-149579276(+)$1	246	217	239	21.8036
AGGAACUAAAUGAACCUCUUCU	chr11:47740762-47740995(-)$1	233	76	98	20.7888
cuagaccaucuucucuucugga	chr8:66711713-66711957(-)$1	244	157	179	21.7312
ugauaucaccuucuccauuggg	chr19:52588680-52588946(-)$1	266	80	102	20.8040
ccacgugauuaguuguuguggc	chr14:66160725-66160939(+)$1	214	7	29	22.5411
ACAGGCCUGAAAUAUCCCUGCA	chr9:131844499-131844756(+)$1	257	208	230	20.2504
AGUAACAGGCCUCAUAUUACUU	chr15:49776058-49776301(-)$1	243	91	113	22.0941
UCCACCCCAUUUCUCCCUGGAG	chr9:95011279-95011562(-)$1	283	121	143	22.2921
UGGAACACAUAUCAUAUCCAAU	chr4:108986812-108987040(-)$1	228	97	119	20.6258
AUAGUUACAUUAUCACACUAUG	chr5:140934674-140934933(-)$1	259	120	142	22.0941
acugugagggccuaggacauca	chr18:47902926-47903144(+)$1	218	6	28	22.4234
agcaucuccaacugauccuuug	chr4:172848740-172848955(+)$1	215	163	185	19.5116
CCUAUUGUUUAUUUCUAGGUUC	chr1:92633052-92633279(+)$1	227	31	53	20.7256
GCAGGAUAUACAUAGGCUGCUG	chr3:42892743-42892956(+)$1	213	50	72	22.4100
UACUCUAAAGAUCAAUUGGUAG	chr10:18687494-18687752(+)$1	258	229	251	21.9803
UUUAUUUUUGUUUUuuuuuaaa	chr17:60674275-60674492(+)$1	217	70	92	20.7888
uaugguguaaacaaaacauaua	chr5:80776010-80776252(-)$1	242	51	73	22.6789
ACCCUGUUGAAAUGAUGGGUAA	chr6:84275957-84276180(-)$1	223	13	35	22.6789
uuaauuuuuuauuguuuuagag	chr11:27070957-27071179(+)$1	222	4	26	20.8040
ACCAGUCACUCAAACCCUGCCU	chr10:14183921-14184142(-)$1	221	100	122	21.8750
ACCAUUACAGGGCUAUGUGGUU	chr1:118527538-118527770(-)$1	232	61	83	21.9143
aggcaaacaaaucagauccagc	chr12:7124517-7124762(-)$1	245	0	22	19.5116
ggcuuuuauuucacuuagccca	chrX:123131311-123131556(+)$1	245	124	146	20.6258
cAAGAUUUUUAUUAUUUCUGAG	chr8:27392803-27393027(+)$1	224	186	208	22.2174
CAUGAAAUUAUCUUCCACAUgg	chr8:146108952-146109180(-)$1	228	136	158	20.8571
GAAGUUUCUAUUUCUUUUUCAG	chr11:18536219-18536488(-)$1	269	78	100	22.8019
GGAGAAAAAUAUUAAAUCUCCC	chr12:12885079-12885332(+)$1	253	103	125	21.8036
caaagcaagucaagaagccagc	chr19:48165836-48166077(+)$1	241	136	158	20.1525
ucuggacacuguuuuaauagga	chr10:14363062-14363283(-)$1	221	117	139	22.0443
CUCGGUUUUUGGUUUUCCUGGU	chr10:129876704-129876984(+)$1	280	253	275	21.0396
UAACAAAACUGUAUGAGUUGGG	chr8:42784501-42784737(+)$1	236	125	147	23.0865
agugagccaagaucacaccauu	chr8:99038296-99038528(+)$1	232	51	73	20.7888
Gcaacaaaaucaaaaagcaaaa	chr4:79746524-79746738(+)$1	214	43	65	19.2697
GUCUGCAUGCAAACAAAGAUAA	chr19:20841009-20841235(-)$1	226	200	222	22.6789
uguucaauucccaccuaugagu	chr18:67148453-67148695(+)$1	242	220	242	19.8550
ucaggaaagucuaacaccuaua	chr2:28490172-28490450(+)$1	278	190	212	21.9472
AUCAUUAAUUCCUCCAGCAGUU	chr3:32453872-32454152(+)$1	280	163	185	19.8550
agucuucccugccacuuuuaga	chr14:68488039-68488289(+)$1	250	148	170	20.7559
CCCCGCUUUAAGAUUAGGGAAG	chr6:133689388-133689599(+)$1	211	37	59	22.4258
uguaucauggccguucuugcag	chr5:93102985-93103276(-)$1	291	203	225	22.0443
GUGCAUCCAUCUACUUAGCCAC	chr6:154539198-154539475(-)$1	277	194	216	21.9416
UAACUGGAAUCUAAUAUGUUAA	chr3:141272416-141272692(+)$1	276	239	261	22.2516
GUCACUAAAGUCGACCUGACAA	chr11:115310335-115310559(-)$1	224	134	156	22.8019
UUUAUUAUUGGAAAAUUAAAAG	chr10:52572926-52573145(-)$1	219	124	146	23.0588
augugaaagaaaaagaacaggu	chr19:56900413-56900644(-)$1	231	128	150	22.9013
cacuuaacaaaaaacuggggcu	chr3:156654120-156654362(+)$1	242	47	69	21.5091
gcuaauuuuuguauuuuuagua	chr17:21213056-21213306(+)$1	250	31	53	21.8036
AUCAGCCAGAGGACAGUGAUUA	chr8:109249967-109250186(-)$1	219	124	146	23.0865
GAUUCCAGAAUAACAAGAAUCC	chr7:37063831-37064100(-)$1	269	11	33	21.9143
accuacauagaaacccagagug	chr12:50033088-50033386(-)$1	298	60	82	22.1974
AUGAGAAAAUCAGGAAAUAAUA	chr4:154245782-154246007(+)$1	225	72	94	20.7559
AUGAUAAAAUAAAACCUCUGUC	chr14:92819270-92819489(+)$1	219	127	149	22.1974
aaaaaaaaaaaaaaaUCUUUGA	chr3:56773732-56773999(-)$1	267	55	77	21.1233
GGCAUUUUCAUCUUACAUGCCa	chr9:78523600-78523865(+)$1	265	110	132	21.9143
aaauuucuaauuauuuauuaca	chr13:36889515-36889759(-)$1	244	63	85	22.4325
UAAAAUUUUAAACAUCUUUAGC	chr2:217032371-217032642(+)$1	271	150	172	22.6789

#DB
((((.............)))).	chr11:47516892-47517140(-)$1	1	130	152	21.3180
................))))).	chrX:147602800-147603038(+)$1	1	176	198	20.5926
..((............))..))	chr6:108363001-108363251(-)$1	1	57	79	21.7284
................))))).	chrX:14889292-14889542(-)$1	1	17	39	20.5926
(((((...........))))).	chr8:3213038-3213259(-)$1	1	129	151	22.2644
((((............))))).	chr3:127318934-127319152(+)$1	1	24	46	23.4165
((((............))))).	chr7:696764-697054(-)$1	1	28	50	22.6789
((((..............))))	chr3:179582202-179582425(-)$1	1	129	151	20.2157
((((.............)))))	chr15:49430819-49431044(-)$1	1	37	59	21.9803
((((..............))))	chr2:69864786-69865027(-)$1	1	95	117	20.2157
(((((...........))))))	chrX:38426610-38426830(+)$1	1	78	100	21.9143
((((............))))))	chr2:208451009-208451289(+)$1	1	217	239	22.8019
(((((...........))))).	chr3:149579030-149579276(+)$1	1	217	239	21.8036
((((..............))))	chr11:47740762-47740995(-)$1	1	76	98	20.7888
(((((...........))))))	chr8:66711713-66711957(-)$1	1	157	179	21.7312
((((............))))))	chr19:52588680-52588946(-)$1	1	80	102	20.8040
(((((...........))))).	chr14:66160725-66160939(+)$1	1	7	29	22.5411
.((((...........))))..	chr9:131844499-131844756(+)$1	1	208	230	20.2504
(((((...........))))))	chr15:49776058-49776301(-)$1	1	91	113	22.0941
((((.............)))))	chr9:95011279-95011562(-)$1	1	121	143	22.2921
((((............))))..	chr4:108986812-108987040(-)$1	1	97	119	20.6258
(((((...........))))))	chr5:140934674-140934933(-)$1	1	120	142	22.0941
(.(((...........))))))	chr18:47902926-47903144(+)$1	1	6	28	22.4234
((((................))	chr4:172848740-172848955(+)$1	1	163	185	19.5116
((((...........)))))))	chr1:92633052-92633279(+)$1	1	31	53	20.7256
((((............))))))	chr3:42892743-42892956(+)$1	1	50	72	22.4100
((((.............)))))	chr10:18687494-18687752(+)$1	1	229	251	21.9803
((((..............))))	chr17:60674275-60674492(+)$1	1	70	92	20.7888
((((............))))).	chr5:80776010-80776252(-)$1	1	51	73	22.6789
((((............))))).	chr6:84275957-84276180(-)$1	1	13	35	22.6789
((((............))))))	chr11:27070957-27071179(+)$1	1	4	26	20.8040
..(((...........)))..)	chr10:14183921-14184142(-)$1	1	100	122	21.8750
(((((...........))))))	chr1:118527538-118527770(-)$1	1	61	83	21.9143
((((................))	chr12:7124517-7124762(-)$1	1	0	22	19.5116
((((............))))..	chrX:123131311-123131556(+)$1	1	124	146	20.6258
(((((...........)))...	chr8:27392803-27393027(+)$1	1	186	208	22.2174
((((.............)))).	chr8:146108952-146109180(-)$1	1	136	158	20.8571
((((............))))))	chr11:18536219-18536488(-)$1	1	78	100	22.8019
(((((...........))))).	chr12:12885079-12885332(+)$1	1	103	125	21.8036
................))))))	chr19:48165836-48166077(+)$1	1	136	158	20.1525
((((.............)))))	chr10:14363062-14363283(-)$1	1	117	139	22.0443
(..((...........)).)))	chr10:129876704-129876984(+)$1	1	253	275	21.0396
((((............))))))	chr8:42784501-42784737(+)$1	1	125	147	23.0865
((((..............))))	chr8:99038296-99038528(+)$1	1	51	73	20.7888
((..............))....	chr4:79746524-79746738(+)$1	1	43	65	19.2697
((((............))))).	chr19:20841009-20841235(-)$1	1	200	222	22.6789
................))))).	chr18:67148453-67148695(+)$1	1	220	242	19.8550
(.(((...........))))))	chr2:28490172-28490450(+)$1	1	190	212	21.9472
................))))).	chr3:32453872-32454152(+)$1	1	163	185	19.8550
((..............))))))	chr14:68488039-68488289(+)$1	1	148	170	20.7559
.(((............)))..)	chr6:133689388-133689599(+)$1	1	37	59	22.4258
((((.............)))))	chr5:93102985-93103276(-)$1	1	203	225	22.0443
((((.............).)))	chr6:154539198-154539475(-)$1	1	194	216	21.9416
((((.............)))))	chr3:141272416-141272692(+)$1	1	239	261	22.2516
((((............))))))	chr11:115310335-115310559(-)$1	1	134	156	22.8019
((((............))))))	chr10:52572926-52573145(-)$1	1	124	146	23.0588
.(((............))))))	chr19:56900413-56900644(-)$1	1	128	150	22.9013
(.((............))))).	chr3:156654120-156654362(+)$1	1	47	69	21.5091
(((((...........))))).	chr17:21213056-21213306(+)$1	1	31	53	21.8036
((((............))))))	chr8:109249967-109250186(-)$1	1	124	146	23.0865
(((((...........))))))	chr7:37063831-37064100(-)$1	1	11	33	21.9143
((((............)).)))	chr12:50033088-50033386(-)$1	1	60	82	22.1974
((..............))))))	chr4:154245782-154246007(+)$1	1	72	94	20.7559
((((............)).)))	chr14:92819270-92819489(+)$1	1	127	149	22.1974
(((..............)))))	chr3:56773732-56773999(-)$1	1	55	77	21.1233
(((((...........))))))	chr9:78523600-78523865(+)$1	1	110	132	21.9143
.(((............)))..)	chr13:36889515-36889759(-)$1	1	63	85	22.4325
((((............))))).	chr2:217032371-217032642(+)$1	1	150	172	22.6789

#PSSM
f : 0.22	e : 0.20	d : 0.16	g : 0.11	y : 0.07	! : 0.05	i : 0.04	h : 0.02	# : 0.02	c : 0.02	b : 0.01	= : 0.01	
f : 0.22	e : 0.20	d : 0.14	g : 0.10	y : 0.07	c : 0.05	! : 0.04	i : 0.04	[ : 0.04	h : 0.02	b : 0.01	= : 0.01	
e : 0.20	f : 0.17	d : 0.14	c : 0.11	y : 0.07	g : 0.07	b : 0.05	i : 0.04	w : 0.04	h : 0.02	! : 0.01	= : 0.01	
e : 0.19	f : 0.17	d : 0.14	c : 0.10	y : 0.07	b : 0.07	g : 0.07	w : 0.05	i : 0.04	h : 0.02	a : 0.01	= : 0.01	
u : 0.35	v : 0.13	w : 0.13	y : 0.10	e : 0.07	f : 0.05	c : 0.05	g : 0.02	i : 0.01	d : 0.01	t : 0.01	b : 0.01	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.27	v : 0.13	w : 0.13	y : 0.10	
u : 0.35	t : 0.26	v : 0.13	w : 0.13	y : 0.10	d : 0.01	
e : 0.23	v : 0.13	f : 0.11	c : 0.10	b : 0.08	w : 0.08	g : 0.08	d : 0.05	h : 0.02	y : 0.02	i : 0.01	= : 0.01	
e : 0.26	f : 0.14	g : 0.10	c : 0.10	d : 0.08	b : 0.08	w : 0.07	i : 0.04	h : 0.02	y : 0.02	a : 0.01	= : 0.01	
e : 0.26	f : 0.19	d : 0.11	c : 0.11	g : 0.10	] : 0.05	i : 0.04	h : 0.02	y : 0.02	2 : 0.01	4 : 0.01	= : 0.01	
e : 0.26	f : 0.25	d : 0.13	g : 0.11	2 : 0.05	i : 0.04	h : 0.02	y : 0.02	c : 0.02	3 : 0.01	4 : 0.01	= : 0.01	
e : 0.26	f : 0.25	d : 0.11	g : 0.11	c : 0.04	i : 0.04	2 : 0.04	h : 0.02	: : 0.02	7 : 0.01	3 : 0.01	4 : 0.01	= : 0.01	
f : 0.25	: : 0.20	g : 0.11	d : 0.10	] : 0.05	c : 0.04	i : 0.04	2 : 0.02	h : 0.02	e : 0.02	7 : 0.01	D : 0.01	3 : 0.01	4 : 0.01	b : 0.01	= : 0.01	

#score	1470.8685029168098
#seq	68
#width	22
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013f_hg19_CDS_m1_run2.txt

#BEAR
[ffffffyyyyyyyyyyyyyyyyffffff	chr1:45244222-45244455(+)$1	233	164	193	22.2241
==========ttttttttttt========	chr14:34985550-34985777(-)$1	227	8	37	24.4991
hhh[cccwwwwwwwwwwwwwwccc]hhhh	chr12:118463481-118463712(+)$1	231	162	191	22.2875
$$$$cccwwwwwwwwwwwwwwcccfffff	chr7:27204470-27204724(-)$1	254	34	63	22.1915
d:gggggggvvvvvvvvvvvvvggggggg	chr20:18464042-18464266(+)$1	224	142	171	23.5619
eeedddd[auuuuuuuuuuuua]dddd]e	chr1:20234011-20234232(+)$1	221	42	71	24.2665
mmdddd:ccctttttttttttcccddddn	chr6:30691541-30691795(+)$1	254	6	35	20.3140
[gggggggwwwwwwwwwwwwwwggggggg	chr12:132400862-132401096(+)$1	234	46	75	24.1426
[cccbb[bbwwwwwwwwwwwwwwbb22bb	chr17:76993574-76993812(-)$1	238	53	82	21.1196
ffffffyyyyyyyyyyyyyyyyffffff]	chr10:117001356-117001579(+)$1	223	190	219	21.8651
hhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chr17:57759910-57760140(+)$1	230	32	61	20.9341
cc[eeeeexxxxxxxxxxxxxxxeeeeec	chr19:45648276-45648525(+)$1	249	216	245	18.7834
ffff[dddduuuuuuuuuuuudddd]fff	chr3:107508580-107508813(+)$1	233	51	80	24.5828
ggggggddddtttttttttttdddd]ggg	chr12:96259024-96259259(+)$1	235	62	91	24.1227
[eeeeecccwwwwwwwwwwwwwwccc>>>	chr5:145883407-145883635(+)$1	228	103	132	22.5022
+++++dddduuuuuuuuuuuudddddddd	chr15:101718481-101718740(-)$1	259	111	140	21.0091
[ccc[dddduuuuuuuuuuuuddddccc]	chr6:139495542-139495774(+)$1	232	177	206	25.2269
ccbb!!ddddtttttttttttdddd22bb	chr4:6642726-6642955(+)$1	229	35	64	22.6137
ddddeeeeettttttttttteeeee4444	chr17:56435054-56435277(-)$1	223	77	106	21.7949
=======yyyyyyyyyyyyyyyy======	chr1:109617521-109617780(-)$1	259	89	118	23.6525
ccceeeeevvvvvvvvvvvvveeeee]cc	chr12:121766134-121766370(-)$1	236	48	77	23.9052
[dddd!!bbuuuuuuuuuuuubb]dddd]	chr8:141570429-141570685(-)$1	256	175	204	24.1121
[bb!!cccvvvvvvvvvvvvvccc22bbb	chr5:68647884-68648110(-)$1	226	128	157	23.0883
c!!bbddddwwwwwwwwwwwwwwdddd22	chr11:17141298-17141524(-)$1	226	145	174	22.4362
gggg[ddddtttttttttttdddd]gggg	chr6:167040405-167040699(-)$1	294	24	53	23.5011
d$$$$$ddddtttttttttttdddd4444	chr1:77626909-77627136(-)$1	227	106	135	22.2334
:eeeeebbvvvvvvvvvvvvvbb]eeeee	chr1:156713462-156713683(-)$1	221	150	179	22.4783
eeeee[ddddtttttttttttddddeeee	chr10:74034352-74034576(+)$1	224	23	52	23.3500
!hhhhhhhhuuuuuuuuuuuuhhhhhhhh	chr13:31725732-31725953(-)$1	221	42	71	22.1348
:eeeee[bbuuuuuuuuuuuubb]eeeee	chr5:44815187-44815412(+)$1	225	65	94	23.2023
bbggggggguuuuuuuuuuuuggggggg4	chr1:115282303-115282546(-)$1	243	114	143	24.5521
cc"""ddddwwwwwwwwwwwwwwdddd44	chr2:44032274-44032485(+)$1	211	105	134	23.1088
!!ffffff[attttttttttta]ffffff	chr2:131883291-131883514(+)$1	223	81	110	23.5620
=========vvvvvvvvvvvvv=======	chr10:96109848-96110069(-)$1	221	35	64	25.2318
b[ggggggguuuuuuuuuuuuggggggg]	chr20:37580851-37581089(+)$1	238	24	53	25.0374
fffff[cccuuuuuuuuuuuucccfffff	chr14:21992953-21993203(-)$1	250	212	241	24.5219
c!!ffffffuuuuuuuuuuuuffffffcc	chr16:21982807-21983027(+)$1	220	125	154	23.8363
ddd!!ddddvvvvvvvvvvvvvdddd]dd	chr11:61487551-61487774(+)$1	223	102	131	23.9007
f[gggggggvvvvvvvvvvvvvggggggg	chr17:6014031-6014255(+)$1	224	108	137	24.6676
dd[ddddyyyyyyyyyyyyyyyydddd]d	chr5:82837335-82837569(+)$1	234	164	193	22.2024
=========uuuuuuuuuuuu========	chr10:93768780-93769000(+)$1	220	72	101	25.7013
cc[a[eeeeettttttttttteeeee]a]	chr6:158923385-158923609(+)$1	224	27	56	23.5369
ffffff[bbuuuuuuuuuuuubb]fffff	chr16:87867975-87868224(-)$1	249	67	96	23.8455
eeeee[bbvvvvvvvvvvvvvbb]eeeee	chr17:34171426-34171666(+)$1	240	153	182	23.4410
==========ttttttttttt========	chr6:36493282-36493509(-)$1	227	67	96	24.4991
ccc"""ddddtttttttttttddddccc2	chr10:32310976-32311241(-)$1	265	140	169	23.5381
ffffff!!bbtttttttttttbb22ffff	chr3:132229910-132230131(+)$1	221	91	120	22.2931
dd[ffffffvvvvvvvvvvvvvffffff]	chr14:64689855-64690080(+)$1	225	114	143	23.3934
edddd[ddddtttttttttttdddd22dd	chr1:40030043-40030289(-)$1	246	159	188	22.5830
b[ggggggguuuuuuuuuuuuggggggg]	chr9:131386580-131386821(+)$1	241	135	164	25.0374
[gggggggwwwwwwwwwwwwwwggggggg	chr6:31508148-31508457(-)$1	309	28	57	24.1426
$$$eeeeebbtttttttttttbb]eeeee	chr5:34686901-34687126(+)$1	225	81	110	22.5062
$$ccc[cccuuuuuuuuuuuuccc]ccc]	chr6:114292088-114292384(-)$1	296	214	243	24.8583
eeee[cccvvvvvvvvvvvvvccc]eeee	chr12:49495975-49496196(-)$1	221	7	36	24.2091
ccc[ddddwwwwwwwwwwwwwwdddd]cc	chr7:120446507-120446732(-)$1	225	80	109	23.5812
ddbbddddvvvvvvvvvvvvvdddd]bb]	chr10:21827679-21827936(+)$1	257	220	249	23.1884
hhhh[a[bbuuuuuuuuuuuubba]hhhh	chr1:155228533-155228752(-)$1	219	129	158	23.3127

#otherMatches

#Seq PSSM
AAGGUGUUUAUUGUUUUGUUCCCACAUUU	chr1:45244222-45244455(+)$1	233	164	193	22.2241
AUAGAGCAAUGUUUGUAAUGAAUUGUUCU	chr14:34985550-34985777(-)$1	227	8	37	24.4991
AAGCAAAUCCuuuuuuuuuuuuuuuuuug	chr12:118463481-118463712(+)$1	231	162	191	22.2875
UUAUGGCAUUAAACCUGAACCGCUGUCGG	chr7:27204470-27204724(-)$1	254	34	63	22.1915
GAGUGGCUCGAAUUUUAAUAGAGAGCUAU	chr20:18464042-18464266(+)$1	224	142	171	23.5619
CUCUCUCAGGUCACAAACAAACAGAGGCG	chr1:20234011-20234232(+)$1	221	42	71	24.2665
ACCACCUGCCUCCGUUUCCCUGGCCAGCU	chr6:30691541-30691795(+)$1	254	6	35	20.3140
CGGGGCAGUCUUCACCCCAUCUCUGUCCU	chr12:132400862-132401096(+)$1	234	46	75	24.1426
GCUGACUCCUCUCCUCCCUCCCUGGCUGU	chr17:76993574-76993812(-)$1	238	53	82	21.1196
AAUAUCAGAAAUUUUCCAUAUAGAUAUUC	chr10:117001356-117001579(+)$1	223	190	219	21.8651
GCUCACACUAAUAUCUUGCUGAAUGUGGG	chr17:57759910-57760140(+)$1	230	32	61	20.9341
UCGACCGUGAACCCAAGAAAGAGGCGGUG	chr19:45648276-45648525(+)$1	249	216	245	18.7834
AGGUCCUUUCCAGUCUCAGAAAAAGAACU	chr3:107508580-107508813(+)$1	233	51	80	24.5828
UCUUUUUAUUGAAAGCUUGCAAAUACAGA	chr12:96259024-96259259(+)$1	235	62	91	24.1227
GAGAGCAGCACAAACGAGAAGAAGCUAUC	chr5:145883407-145883635(+)$1	228	103	132	22.5022
ACAAAGGGAAGAAAAUGACGGUCCCUGUG	chr15:101718481-101718740(-)$1	259	111	140	21.0091
UUCUGUCCCCAAGUGAAUGUAGGGAAGAU	chr6:139495542-139495774(+)$1	232	177	206	25.2269
GGGAGAUGGACAAUAUGCUCAUCCAGAUC	chr4:6642726-6642955(+)$1	229	35	64	22.6137
GCCUCUCUGCCCGACACCCACAGAGGAAA	chr17:56435054-56435277(-)$1	223	77	106	21.7949
CUAGUUUGAGGAAGAAAAUGAAGAAAUUG	chr1:109617521-109617780(-)$1	259	89	118	23.6525
GUGGGUAUAUCUGUCCCCUUAGUACCUCG	chr12:121766134-121766370(-)$1	236	48	77	23.9052
CCGGCCUUCUCUCUGGAAAAUGAUGCUGA	chr8:141570429-141570685(-)$1	256	175	204	24.1121
AUCAGCUGCCCAGUAAUAAACCAGAAGAG	chr5:68647884-68648110(-)$1	226	128	157	23.0883
UGGCCUGCAUUGUACCCACUAAUUGCAUU	chr11:17141298-17141524(-)$1	226	145	174	22.4362
gcggccUGCCCUUUGUGACCGCAGCUCGC	chr6:167040405-167040699(-)$1	294	24	53	23.5011
GAAUUUUUGGAAGAAAUUAACCCAGCUAG	chr1:77626909-77627136(-)$1	227	106	135	22.2334
GCCUCCCCAAgaggaagaagaggaggagg	chr1:156713462-156713683(-)$1	221	150	179	22.4783
GAAACAGCACCUCCCCCGCCUGUGCGUUU	chr10:74034352-74034576(+)$1	224	23	52	23.3500
CCAAAGAAUUGAAACAUACUUAUUUUUUG	chr13:31725732-31725953(-)$1	221	42	71	22.1348
CUUUCUACUGAAUAGACCAAAAGAAGAAA	chr5:44815187-44815412(+)$1	225	65	94	23.2023
CUGGGGUUAUUGAAAAACUGUUAACCUCU	chr1:115282303-115282546(-)$1	243	114	143	24.5521
GAUCUGGUAUUAUCCUAAACAUUUACUUA	chr2:44032274-44032485(+)$1	211	105	134	23.1088
GAUGGUCACCUGAUCUAUUAUGAUGACCA	chr2:131883291-131883514(+)$1	223	81	110	23.5620
AGGAAGCUGAAGAAAAGUAAUGUAGUUUC	chr10:96109848-96110069(-)$1	221	35	64	25.2318
ACUGGUUCUCCCGCUUCCAUCAGAACCAC	chr20:37580851-37581089(+)$1	238	24	53	25.0374
GGGGUUGGGCGAAGCCACAAACCCACCCC	chr14:21992953-21993203(-)$1	250	212	241	24.5219
ACCGUGGAGGUAAGCAUUUCAUUCUAUUA	chr16:21982807-21983027(+)$1	220	125	154	23.8363
GCGCUGGUCUGUGGGCAGUGAUGACCUCG	chr11:61487551-61487774(+)$1	223	102	131	23.9007
UGUGGCUUUGUCAAGCUUCCCAGGAGCCG	chr17:6014031-6014255(+)$1	224	108	137	24.6676
CUCCUGACACAAAAUUAGAACCUUCAGAA	chr5:82837335-82837569(+)$1	234	164	193	22.2024
GUGGUUUGUCCGCCAACAUUAACAGGCCA	chr10:93768780-93769000(+)$1	220	72	101	25.7013
GAUGCUGUGCUCCCAGAACACGUACACCC	chr6:158923385-158923609(+)$1	224	27	56	23.5369
UCUUCCUGAUCGCCGUCUCCUUCUGGAAG	chr16:87867975-87868224(-)$1	249	67	96	23.8455
gcuaugguggagacagaagcagcgguggu	chr17:34171426-34171666(+)$1	240	153	182	23.4410
UCUUUUGUUUUUGUUUGUUUUAGACAAAA	chr6:36493282-36493509(-)$1	227	67	96	24.4991
CUCAGUGAAGAACUAGUCCAGCUUCGAGC	chr10:32310976-32311241(-)$1	265	140	169	23.5381
AAGUGGAGUCAGAGCAACAUGGAGAUCGC	chr3:132229910-132230131(+)$1	221	91	120	22.2931
AGCCUUCUCAUUAAGGGACAUGGAGAAGA	chr14:64689855-64690080(+)$1	225	114	143	23.3934
CCUCUCGUGGCCUCCCUACUACCACUCAG	chr1:40030043-40030289(-)$1	246	159	188	22.5830
CGGCCUUCCUUCAGUUCAACUGGAAGGCG	chr9:131386580-131386821(+)$1	241	135	164	25.0374
AAAUAGUAUCUUUGUUUUCCUUUGCUGUU	chr6:31508148-31508457(-)$1	309	28	57	24.1426
AAAAGUCUCCUCUAGAGCUUUGGAAGGCU	chr5:34686901-34687126(+)$1	225	81	110	22.5062
CCCUCAGCCCUUUUCUCUCCCGGCCGagc	chr6:114292088-114292384(-)$1	296	214	243	24.8583
UGAGAGCAACACCAUCUUCUCUGCCCUCA	chr12:49495975-49496196(-)$1	221	7	36	24.2091
GAUGUUCCAAACAGGCCCACCAGGAAGAU	chr7:120446507-120446732(-)$1	225	80	109	23.5812
UGCACUCCUGUUGUGGUUUGUGGGGUUGU	chr10:21827679-21827936(+)$1	257	220	249	23.1884
UGGAUGUGUGAGUAGUGAGAAGCCUUUUG	chr1:155228533-155228752(-)$1	219	129	158	23.3127

#DB
.((((((................))))))	chr1:45244222-45244455(+)$1	1	164	193	22.2241
((((((((((...........))))))))	chr14:34985550-34985777(-)$1	1	8	37	24.4991
(((.(((..............))).))))	chr12:118463481-118463712(+)$1	1	162	191	22.2875
....(((..............))))))))	chr7:27204470-27204724(-)$1	1	34	63	22.1915
).(((((((.............)))))))	chr20:18464042-18464266(+)$1	1	142	171	23.5619
(((((((.(............).)))).)	chr1:20234011-20234232(+)$1	1	42	71	24.2665
..)))).(((...........)))((((.	chr6:30691541-30691795(+)$1	1	6	35	20.3140
.(((((((..............)))))))	chr12:132400862-132401096(+)$1	1	46	75	24.1426
.(((((.((..............))..))	chr17:76993574-76993812(-)$1	1	53	82	21.1196
((((((................)))))).	chr10:117001356-117001579(+)$1	1	190	219	21.8651
(((((((................))))))	chr17:57759910-57760140(+)$1	1	32	61	20.9341
((.(((((...............))))))	chr19:45648276-45648525(+)$1	1	216	245	18.7834
((((.((((............)))).)))	chr3:107508580-107508813(+)$1	1	51	80	24.5828
((((((((((...........)))).)))	chr12:96259024-96259259(+)$1	1	62	91	24.1227
.((((((((..............)))...	chr5:145883407-145883635(+)$1	1	103	132	22.5022
.....((((............))))))))	chr15:101718481-101718740(-)$1	1	111	140	21.0091
.(((.((((............))))))).	chr6:139495542-139495774(+)$1	1	177	206	25.2269
))((..((((...........))))..))	chr4:6642726-6642955(+)$1	1	35	64	22.6137
(((((((((...........)))))....	chr17:56435054-56435277(-)$1	1	77	106	21.7949
(((((((................))))))	chr1:109617521-109617780(-)$1	1	89	118	23.6525
((((((((.............))))).))	chr12:121766134-121766370(-)$1	1	48	77	23.9052
.((((..((............)).)))).	chr8:141570429-141570685(-)$1	1	175	204	24.1121
.((..(((.............)))..)))	chr5:68647884-68648110(-)$1	1	128	157	23.0883
(..((((((..............))))..	chr11:17141298-17141524(-)$1	1	145	174	22.4362
((((.((((...........)))).))))	chr6:167040405-167040699(-)$1	1	24	53	23.5011
(.....((((...........))))....	chr1:77626909-77627136(-)$1	1	106	135	22.2334
.(((((((.............)).)))))	chr1:156713462-156713683(-)$1	1	150	179	22.4783
(((((.((((...........))))))))	chr10:74034352-74034576(+)$1	1	23	52	23.3500
.((((((((............))))))))	chr13:31725732-31725953(-)$1	1	42	71	22.1348
.(((((.((............)).)))))	chr5:44815187-44815412(+)$1	1	65	94	23.2023
(((((((((............))))))).	chr1:115282303-115282546(-)$1	1	114	143	24.5521
((...((((..............))))..	chr2:44032274-44032485(+)$1	1	105	134	23.1088
..((((((.(...........).))))))	chr2:131883291-131883514(+)$1	1	81	110	23.5620
(((((((((.............)))))))	chr10:96109848-96110069(-)$1	1	35	64	25.2318
(.(((((((............))))))).	chr20:37580851-37581089(+)$1	1	24	53	25.0374
(((((.(((............))))))))	chr14:21992953-21993203(-)$1	1	212	241	24.5219
(..((((((............))))))))	chr16:21982807-21983027(+)$1	1	125	154	23.8363
(((..((((.............)))).))	chr11:61487551-61487774(+)$1	1	102	131	23.9007
(.(((((((.............)))))))	chr17:6014031-6014255(+)$1	1	108	137	24.6676
((.((((................)))).)	chr5:82837335-82837569(+)$1	1	164	193	22.2024
(((((((((............))))))))	chr10:93768780-93769000(+)$1	1	72	101	25.7013
((.(.(((((...........))))).).	chr6:158923385-158923609(+)$1	1	27	56	23.5369
((((((.((............)).)))))	chr16:87867975-87868224(-)$1	1	67	96	23.8455
(((((.((.............)).)))))	chr17:34171426-34171666(+)$1	1	153	182	23.4410
((((((((((...........))))))))	chr6:36493282-36493509(-)$1	1	67	96	24.4991
(((...((((...........))))))).	chr10:32310976-32311241(-)$1	1	140	169	23.5381
((((((..((...........))..))))	chr3:132229910-132230131(+)$1	1	91	120	22.2931
((.((((((.............)))))).	chr14:64689855-64690080(+)$1	1	114	143	23.3934
(((((.((((...........))))..))	chr1:40030043-40030289(-)$1	1	159	188	22.5830
(.(((((((............))))))).	chr9:131386580-131386821(+)$1	1	135	164	25.0374
.(((((((..............)))))))	chr6:31508148-31508457(-)$1	1	28	57	24.1426
...(((((((...........)).)))))	chr5:34686901-34687126(+)$1	1	81	110	22.5062
..(((.(((............))).))).	chr6:114292088-114292384(-)$1	1	214	243	24.8583
((((.(((.............))).))))	chr12:49495975-49496196(-)$1	1	7	36	24.2091
(((.((((..............)))).))	chr7:120446507-120446732(-)$1	1	80	109	23.5812
((((((((.............)))).)).	chr10:21827679-21827936(+)$1	1	220	249	23.1884
((((.(.((............))).))))	chr1:155228533-155228752(-)$1	1	129	158	23.3127

#PSSM
c : 0.15	[ : 0.14	d : 0.12	f : 0.10	= : 0.08	e : 0.08	h : 0.05	$ : 0.05	b : 0.05	g : 0.03	: : 0.03	! : 0.03	m : 0.01	+ : 0.01	
c : 0.15	e : 0.12	d : 0.12	f : 0.10	= : 0.08	h : 0.07	$ : 0.07	g : 0.07	! : 0.05	[ : 0.05	b : 0.03	: : 0.01	m : 0.01	+ : 0.01	
g : 0.15	f : 0.12	e : 0.12	c : 0.10	= : 0.08	d : 0.08	h : 0.07	[ : 0.07	$ : 0.05	b : 0.05	! : 0.03	+ : 0.01	" : 0.01	
f : 0.15	g : 0.15	e : 0.15	d : 0.10	= : 0.08	c : 0.05	h : 0.05	b : 0.05	[ : 0.03	$ : 0.03	! : 0.03	" : 0.03	+ : 0.01	a : 0.01	
e : 0.15	f : 0.14	g : 0.14	d : 0.12	[ : 0.10	= : 0.08	c : 0.05	! : 0.05	b : 0.03	h : 0.03	" : 0.03	+ : 0.01	$ : 0.01	
d : 0.21	g : 0.14	e : 0.14	f : 0.12	= : 0.08	[ : 0.08	c : 0.07	h : 0.03	! : 0.03	b : 0.01	$ : 0.01	" : 0.01	a : 0.01	
d : 0.29	c : 0.12	g : 0.12	= : 0.08	e : 0.08	f : 0.07	[ : 0.07	h : 0.03	! : 0.03	b : 0.03	: : 0.01	y : 0.01	
d : 0.26	g : 0.12	b : 0.12	c : 0.10	y : 0.08	e : 0.08	= : 0.07	f : 0.05	w : 0.03	[ : 0.01	h : 0.01	! : 0.01	
d : 0.22	b : 0.12	v : 0.10	y : 0.08	w : 0.08	g : 0.08	= : 0.07	c : 0.07	e : 0.03	f : 0.03	a : 0.01	x : 0.01	h : 0.01	[ : 0.01	
u : 0.28	v : 0.19	w : 0.15	d : 0.10	y : 0.08	= : 0.03	t : 0.03	b : 0.03	c : 0.01	x : 0.01	a : 0.01	e : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.26	v : 0.19	w : 0.15	y : 0.08	x : 0.01	
u : 0.28	t : 0.22	v : 0.19	w : 0.15	y : 0.08	x : 0.01	e : 0.01	d : 0.01	
d : 0.19	b : 0.14	c : 0.12	w : 0.12	y : 0.08	v : 0.08	= : 0.05	e : 0.05	g : 0.05	a : 0.03	x : 0.01	h : 0.01	f : 0.01	
d : 0.22	b : 0.14	c : 0.12	g : 0.12	y : 0.07	= : 0.07	w : 0.07	f : 0.05	e : 0.05	] : 0.03	x : 0.01	h : 0.01	
d : 0.29	c : 0.14	g : 0.12	] : 0.10	f : 0.08	= : 0.08	e : 0.07	h : 0.03	b : 0.01	2 : 0.01	a : 0.01	
d : 0.31	f : 0.14	e : 0.14	g : 0.12	= : 0.08	] : 0.08	h : 0.03	2 : 0.03	b : 0.01	c : 0.01	
f : 0.15	d : 0.15	e : 0.15	g : 0.14	= : 0.08	h : 0.07	2 : 0.07	c : 0.07	] : 0.05	4 : 0.03	
f : 0.17	g : 0.15	d : 0.12	e : 0.12	= : 0.08	h : 0.07	] : 0.07	2 : 0.05	c : 0.05	4 : 0.03	b : 0.03	> : 0.01	
f : 0.15	g : 0.15	e : 0.12	c : 0.10	= : 0.08	d : 0.08	h : 0.07	b : 0.07	4 : 0.05	] : 0.03	> : 0.01	2 : 0.01	a : 0.01	
] : 0.15	f : 0.12	e : 0.12	g : 0.10	= : 0.08	h : 0.07	c : 0.07	d : 0.07	4 : 0.07	b : 0.05	2 : 0.03	n : 0.01	> : 0.01	

#score	1326.42674803371
#seq	57
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_HuR_Kishore2011d_hg19_UTR_m1_run2.txt

#BEAR
b!!gggggggvvvvvvvvvvvvvggggggg	chr10:89512796-89513036(-)$1	240	81	111	21.3337
cc[ccc"""cccuuuuuuuuuuuuccc333	chr11:9610460-9610703(+)$1	243	75	105	21.1175
gggg[bb^^^^^^^^^^^^^^^^^^bb]gg	chr13:52987709-52987949(-)$1	240	198	228	22.8070
::gggggggxxxxxxxxxxxxxxxgggggg	chr8:67773833-67774075(+)$1	242	23	53	21.6197
iihhhhhhhhwwwwwwwwwwwwwwhhhhhh	chr5:102365176-102365416(+)$1	240	96	126	20.6575
a[gggggggvvvvvvvvvvvvvggggggg]	chr15:44854030-44854278(+)$1	248	143	173	21.1278
===========vvvvvvvvvvvvv======	chr1:68942004-68942250(-)$1	246	147	177	22.0451
dd[ffffffxxxxxxxxxxxxxxxffffff	chr22:24313488-24313728(-)$1	240	122	152	21.3410
iiiiiiiii^^^^^^^^^^^^^^^^^^^^i	chr3:98234314-98234559(-)$1	245	196	226	24.9066
ggggggg^^^^^^^^^^^^^^^^^^^^^^^	chr7:23741751-23741991(+)$1	240	95	125	24.3150
:eeeee[ayyyyyyyyyyyyyyyya]eeee	chr1:31342234-31342514(-)$1	280	151	181	22.7870
gggggdddd^^^^^^^^^^^^^^^^^^^^^	chr15:64447953-64448193(-)$1	240	108	138	23.8576
ggggggg^^^^^^^^^^^^^^^^^^^gggg	chr18:5289161-5289401(-)$1	240	207	237	24.2212
hhhhhhhh^^^^^^^^^^^^^^^^^^^^^h	chr12:117581621-117581862(-)$1	241	105	135	23.1747
:gggggggyyyyyyyyyyyyyyyygggggg	chr19:13250031-13250271(+)$1	240	186	216	23.9608
ggggggg^^^^^^^^^^^^^^^^^^ggggg	chr9:33046437-33046717(-)$1	280	111	141	24.0178
iiiiiiiii^^^^^^^^^^^^^^^^^^iii	chr2:118866263-118866503(+)$1	240	103	133	24.9119
!bb"""ddddwwwwwwwwwwwwwwdddd22	chr15:69740306-69740546(+)$1	240	183	213	21.6262
cc"""dddd^^^^^^^^^^^^^^^^^^ddd	chrX:16779345-16779585(+)$1	240	132	162	22.9754
dd"""eeeeeuuuuuuuuuuuueeeee333	chr6:139225929-139226169(-)$1	240	108	138	20.6383
dddd[ddddxxxxxxxxxxxxxxxdddddd	chr7:26230896-26231136(-)$1	240	145	175	21.1837
iiiiiiiiixxxxxxxxxxxxxxxiiiiii	chr19:6413578-6413818(-)$1	240	159	189	24.0633
ddd[a!!bbxxxxxxxxxxxxxxxbb22a]	chr11:107977060-107977300(+)$1	240	79	109	21.9147
cccffffffwwwwwwwwwwwwwwffffff]	chr16:2227914-2228154(+)$1	240	30	60	21.5968
$$$ffffffwwwwwwwwwwwwwwffffffg	chr17:61671249-61671489(+)$1	240	22	52	20.9276
::gggggggxxxxxxxxxxxxxxxgggggg	chr13:21721414-21721654(+)$1	240	62	92	21.6197
=====!!bbyyyyyyyyyyyyyyyybb22=	chr2:46852006-46852248(+)$1	242	169	199	24.3333
!!cccdddd^^^^^^^^^^^^^^^^^^^^^	chr12:63037684-63037924(-)$1	240	106	136	23.6470
======[bbwwwwwwwwwwwwwwbb]====	chr16:24226246-24226486(+)$1	240	74	104	23.6376
cc[ccc[ddddvvvvvvvvvvvvvdddd]c	chr6:97594493-97594733(-)$1	240	34	64	20.1962
b[gggggggwwwwwwwwwwwwwwggggggg	chr7:64865567-64865807(+)$1	240	9	39	23.3685
dddgggggggvvvvvvvvvvvvvggggggg	chr22:36134800-36135040(-)$1	240	41	71	20.8375
iiiiiiiiiwwwwwwwwwwwwwwiiiiiii	chr14:68143511-68143751(-)$1	240	153	183	23.9644
iiiiiiiii^^^^^^^^^^^^^^^^^^^^^	chr20:39752248-39752488(+)$1	240	104	134	24.7855
=========xxxxxxxxxxxxxxx======	chr22:40727547-40727788(+)$1	241	104	134	24.3675
$eeeee[bbxxxxxxxxxxxxxxxbb]eee	chr1:183113512-183113752(+)$1	240	176	206	21.4779
ggggggg^^^^^^^^^^^^^^^^^^^^^^^	chr20:61576593-61576880(+)$1	287	100	130	24.3150
!!ccc[ddddwwwwwwwwwwwwwwdddd]c	chr1:90180511-90180752(+)$1	241	108	138	22.5252
ccc!!ccc^^^^^^^^^^^^^^^^^^^^^^	chr2:145146484-145146724(-)$1	240	187	217	24.1191
!ccc[dddd^^^^^^^^^^^^^^^^^^^^^	chr15:31668973-31669213(+)$1	240	104	134	23.7121
======[bb^^^^^^^^^^^^^^^^^^bb2	chr1:115314408-115314648(-)$1	240	40	70	23.6882
bb[ffffff^^^^^^^^^^^^^^^^^^^^^	chr16:70695222-70695462(-)$1	240	91	121	22.8611
:bb!!ddddxxxxxxxxxxxxxxxdddd22	chr12:56386127-56386372(+)$1	245	24	54	20.7136
fffff!!cccwwwwwwwwwwwwwwccc]ff	chr2:128238294-128238534(-)$1	240	85	115	22.4120
dddd!!ccc^^^^^^^^^^^^^^^^^^ccc	chr10:93038329-93038578(+)$1	249	111	141	23.3244
ff!!eeeee^^^^^^^^^^^^^^^^^^^^^	chr19:37035053-37035293(-)$1	240	107	137	23.4042
hhhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chr12:46299119-46299359(+)$1	240	96	126	22.1580
==========uuuuuuuuuuuu========	chr17:7215440-7215680(+)$1	240	158	188	22.2049
hhhhhhhh^^^^^^^^^^^^^^^^^^^^hh	chr20:48697776-48698020(-)$1	244	111	141	22.9426
eeeeeeeeexxxxxxxxxxxxxxxeeeee:	chr10:104417300-104417541(+)$1	241	171	201	20.7671
hhhhhhhhyyyyyyyyyyyyyyyyhhhhhh	chrX:15844787-15845028(-)$1	241	163	193	22.1580
####eeeeeyyyyyyyyyyyyyyyyeeeee	chr1:245017351-245017591(-)$1	240	103	133	23.6396
iiiiiiiii^^^^^^^^^^^^^^^^^^iii	chrX:8500550-8500790(-)$1	240	149	179	24.9119
##ccc!!cccuuuuuuuuuuuuccc22ccc	chr6:43582233-43582473(+)$1	240	193	223	21.0128
ddddd!!eeeeeuuuuuuuuuuuueeeee2	chr9:91092784-91093031(+)$1	247	167	197	19.2467
eeeee^^^^^^^^^^^^^^^^^^^^eeeee	chr5:64961742-64961982(-)$1	240	40	70	21.8460
ee[ddddbb^^^^^^^^^^^^^^^^^^^^^	chrX:132436224-132436464(-)$1	240	64	94	22.8415
iiiiiiiiiyyyyyyyyyyyyyyyyiiiii	chr12:56144117-56144372(+)$1	255	20	50	25.5493
ccc!!ddddvvvvvvvvvvvvvdddd]ccc	chr2:152657854-152658094(-)$1	240	74	104	20.0942
dhhhhhhhhxxxxxxxxxxxxxxxhhhhhh	chr2:47387312-47387552(-)$1	240	180	210	20.6720
==========vvvvvvvvvvvvv=======	chr8:103839970-103840210(-)$1	240	31	61	22.3806
====####cccvvvvvvvvvvvvvccc444	chr2:151326029-151326269(-)$1	240	51	81	21.3823
d"""eeeee^^^^^^^^^^^^^^^^^^^^^	chr5:133492257-133492497(-)$1	240	47	77	23.4843
====^^^^^^^^^^^^^^^^^^^^======	chr17:38991838-38992079(+)$1	241	81	111	23.0767
eeeeeeeeyyyyyyyyyyyyyyyyeeeee]	chr2:38790764-38791004(-)$1	240	87	117	23.2131
iiiiiiiiivvvvvvvvvvvvviiiiiiii	chr6:143746838-143747078(-)$1	240	117	147	21.4935
::gggggggxxxxxxxxxxxxxxxgggggg	chr16:15960298-15960538(-)$1	240	93	123	21.6197
####ffffffwwwwwwwwwwwwwwffffff	chr6:130461187-130461427(+)$1	240	76	106	21.4768
hhhhhddddxxxxxxxxxxxxxxxdddd]h	chr11:130097720-130097960(-)$1	240	115	145	21.5992

#otherMatches

#Seq PSSM
ACCAAAAAUGAAAAAAAGUGUCCCAUUUUU	chr10:89512796-89513036(-)$1	240	81	111	21.3337
ACUCAUUACUACUCAGCCUUCAAUGUACCU	chr11:9610460-9610703(+)$1	243	75	105	21.1175
ACUGUCAAAAAAUUUUUUUACAUUGUGUUA	chr13:52987709-52987949(-)$1	240	198	228	22.8070
CUUGAGAAAGAAAUCACAGAAGCAUUUCUC	chr8:67773833-67774075(+)$1	242	23	53	21.6197
AAUAAAAAAGUCUCUAUUUAAAUUCUUUUU	chr5:102365176-102365416(+)$1	240	96	126	20.6575
AGCAAACUGCACCAGUUAACUACAGUUUGG	chr15:44854030-44854278(+)$1	248	143	173	21.1278
UAUAUAUAUGUAUGUGUUUUUAAAAUAUGU	chr1:68942004-68942250(-)$1	246	147	177	22.0451
CUUCUUCAUCCUCAUAUGAAAUAAAUGAAG	chr22:24313488-24313728(-)$1	240	122	152	21.3410
GUCuuuuuuaaaaaauaaaauuaaaaauGA	chr3:98234314-98234559(-)$1	245	196	226	24.9066
AUACAGUUUAUUUUUCCUGAAAUUAUUUAC	chr7:23741751-23741991(+)$1	240	95	125	24.3150
CUUCCUGUGCUGUGCCCAUUUAUAAGAGGA	chr1:31342234-31342514(-)$1	280	151	181	22.7870
CUCACUUUUGUAACAAACUCCUACCAACAC	chr15:64447953-64448193(-)$1	240	108	138	23.8576
AAGUAGUCCUGUCACUGUGUUUUUAUGCUA	chr18:5289161-5289401(-)$1	240	207	237	24.2212
UUUUAAAAAUUUUCCAAAACUUUUCUCCAU	chr12:117581621-117581862(-)$1	241	105	135	23.1747
UGGGGCUGUGUCUAUUGUCCCCCUCGGUCC	chr19:13250031-13250271(+)$1	240	186	216	23.9608
CAUCuuuuuuuuuuuuuuuuuuuuuAAAGA	chr9:33046437-33046717(-)$1	280	111	141	24.0178
ACUGUUGUGCCUUUUUAUUUUUCUAAUCAC	chr2:118866263-118866503(+)$1	240	103	133	24.9119
UAAGGAAGACUAUAUCUAGAUCAUGUCUGA	chr15:69740306-69740546(+)$1	240	183	213	21.6262
ACCUUCAGAAGCCCAUUCCCCUUAAAGUCU	chrX:16779345-16779585(+)$1	240	132	162	22.9754
UGUAUUUAAGUAUCUUUUAUUUUUUAAUUU	chr6:139225929-139226169(-)$1	240	108	138	20.6383
ACUAAUACUCUUAAAUGGUCUUUCAGUAUA	chr7:26230896-26231136(-)$1	240	145	175	21.1837
AAAAAAAAGUCACUCUUGCUAUUUCUUUUU	chr19:6413578-6413818(-)$1	240	159	189	24.0633
AAAGUGGGUAACACUACAUUCAUAGCAAAG	chr11:107977060-107977300(+)$1	240	79	109	21.9147
AGCCUGGGCCUCUAACAGCUUUUGUCCGGA	chr16:2227914-2228154(+)$1	240	30	60	21.5968
UUUAAACUUUCCCUCUAUAUUAUAGGUUUU	chr17:61671249-61671489(+)$1	240	22	52	20.9276
AUUAAAUUCUAUUUACUAUUUGUUGAAUUU	chr13:21721414-21721654(+)$1	240	62	92	21.6197
AAACAUCUUGACUCUCCCUUUUUAAAAuuu	chr2:46852006-46852248(+)$1	242	169	199	24.3333
CAAUGACauuuuaaaauaaaauauuauaua	chr12:63037684-63037924(-)$1	240	106	136	23.6470
AUGCAGAUGGCCUAUGGAAAAUGCAGCUGC	chr16:24226246-24226486(+)$1	240	74	104	23.6376
GAAAAUGAUAAUACUUAAUAUAUUUUGUGA	chr6:97594493-97594733(-)$1	240	34	64	20.1962
UUUUUUGGAGAUUUAUAAUUACAUUCAAAG	chr7:64865567-64865807(+)$1	240	9	39	23.3685
UUGGGUUACUCCUAUUAUUAUCAAGUAGCU	chr22:36134800-36135040(-)$1	240	41	71	20.8375
AAAUAAAAAUUCUUUUUGAUUAUUUUUUGU	chr14:68143511-68143751(-)$1	240	153	183	23.9644
UAAAUUCCUAAACUCCCUUCCCUCUCUCCC	chr20:39752248-39752488(+)$1	240	104	134	24.7855
uuuuuuuuuuuuuuuuuuuuuuuCAAAAAA	chr22:40727547-40727788(+)$1	241	104	134	24.3675
UGGGUCCUCUUCCAUUGCAGUCCUGAUGAU	chr1:183113512-183113752(+)$1	240	176	206	21.4779
CCUGUGGUUUUUGUGUUUUUUUUUUUUUCU	chr20:61576593-61576880(+)$1	287	100	130	24.3150
CCUAUUUUUUUUUCCUUUUCACACAAAAUG	chr1:90180511-90180752(+)$1	241	108	138	22.5252
CUUUCGCUAUUCAUCAAUUUCCCAUUUUUU	chr2:145146484-145146724(-)$1	240	187	217	24.1191
ACAGCUUUAAAACUUUACUACUUUUAUUUA	chr15:31668973-31669213(+)$1	240	104	134	23.7121
UUAGUGUUCUUCAAAAUGUGCUUcccugac	chr1:115314408-115314648(-)$1	240	40	70	23.6882
GGUGCUGUUGUUAACUCGUUCCUUUUUUUA	chr16:70695222-70695462(-)$1	240	91	121	22.8611
CGCUUCAGCAACAAACACCAGGCAGCUGUU	chr12:56386127-56386372(+)$1	245	24	54	20.7136
UUGUACAAAGGAAUACUAGUCAUACUUCUA	chr2:128238294-128238534(-)$1	240	85	115	22.4120
GUUUUCACAUACUUACUCUUUUAUUCUUGU	chr10:93038329-93038578(+)$1	249	111	141	23.3244
UAUUUUUAUCAUAUUAACAUUUUUCACUUA	chr19:37035053-37035293(-)$1	240	107	137	23.4042
AGAUGAAAUAGAAGCAUUAAAUAUUUUUAU	chr12:46299119-46299359(+)$1	240	96	126	22.1580
UCUCUCCCCAAACCCCUUUAGAUggggagg	chr17:7215440-7215680(+)$1	240	158	188	22.2049
GUACUAAAGGuuuuuuuuuuuuuuuuaauu	chr20:48697776-48698020(-)$1	244	111	141	22.9426
AGCUUGGGGGUCCCACCCUUCUUACCCCAC	chr10:104417300-104417541(+)$1	241	171	201	20.7671
GGAGUGAUACUUCUUACACUAAAAAUUAUU	chrX:15844787-15845028(-)$1	241	163	193	22.1580
AAAAUGUGACUUUUUUUUUUUUUUAUCACA	chr1:245017351-245017591(-)$1	240	103	133	23.6396
AAUCAAUAAAAUAUAUUUUUGACUAAAUUA	chrX:8500550-8500790(-)$1	240	149	179	24.9119
AGGUGCUGAGUUACGGUCCCAUCUCUUCAC	chr6:43582233-43582473(+)$1	240	193	223	21.0128
UGUGCCGUUUUAGUGGUUUUAGGAUAAAAA	chr9:91092784-91093031(+)$1	247	167	197	19.2467
UUUCAUCAUUUAAUCUUAAUCAUUUUGAAA	chr5:64961742-64961982(-)$1	240	40	70	21.8460
AUUUCUCCCUGUUAUUUUAGUUGCCUUAUC	chrX:132436224-132436464(-)$1	240	64	94	22.8415
AGGAGAAGAAAUCAAAAAUCCAUUCUUUUC	chr12:56144117-56144372(+)$1	255	20	50	25.5493
GUACUUUCUCAAAUCCCUAUAAAGAAUUAC	chr2:152657854-152658094(-)$1	240	74	104	20.0942
CACAAUUUGCCUCAAAAUCCAUUCCAAGUU	chr2:47387312-47387552(-)$1	240	180	210	20.6720
UUUGAAAUAGAUGUGUAUAUGGACUGUUUU	chr8:103839970-103840210(-)$1	240	31	61	22.3806
UACCUCCAAGAAGAAAAAUCACACUCUGAA	chr2:151326029-151326269(-)$1	240	51	81	21.3823
CUGCUGACAUAACCAUAACUUCUGUCCCUU	chr5:133492257-133492497(-)$1	240	47	77	23.4843
UAUUUAGGAUCAAUAUAAAGGaauaauauu	chr17:38991838-38992079(+)$1	241	81	111	23.0767
AGUAUGUUGCAGUUACUCAUAUUAAACAUA	chr2:38790764-38791004(-)$1	240	87	117	23.2131
AUUUUUCUUUAAACUUUUUACUGGGAAAAG	chr6:143746838-143747078(-)$1	240	117	147	21.4935
CUUGUUUGGGCUCCGAAACUCUUACCAAAC	chr16:15960298-15960538(-)$1	240	93	123	21.6197
CACUGUUUCUUUUUCAAUACUUUCAGAAAC	chr6:130461187-130461427(+)$1	240	76	106	21.4768
ACUUUAAAAUUCCUGUAUUUCCAUUUUUAA	chr11:130097720-130097960(-)$1	240	115	145	21.5992

#DB
(..(((((((.............)))))))	chr10:89512796-89513036(-)$1	1	81	111	21.3337
((.(((...(((............)))...	chr11:9610460-9610703(+)$1	1	75	105	21.1175
((((.((..................)).))	chr13:52987709-52987949(-)$1	1	198	228	22.8070
..(((((((...............))))))	chr8:67773833-67774075(+)$1	1	23	53	21.6197
((((((((((..............))))))	chr5:102365176-102365416(+)$1	1	96	126	20.6575
(.(((((((.............))))))).	chr15:44854030-44854278(+)$1	1	143	173	21.1278
(((((((((((.............))))))	chr1:68942004-68942250(-)$1	1	147	177	22.0451
((.((((((...............))))))	chr22:24313488-24313728(-)$1	1	122	152	21.3410
(((((((((....................)	chr3:98234314-98234559(-)$1	1	196	226	24.9066
(((((((.......................	chr7:23741751-23741991(+)$1	1	95	125	24.3150
.(((((.(................).))))	chr1:31342234-31342514(-)$1	1	151	181	22.7870
(((((((((.....................	chr15:64447953-64448193(-)$1	1	108	138	23.8576
(((((((...................))))	chr18:5289161-5289401(-)$1	1	207	237	24.2212
((((((((.....................)	chr12:117581621-117581862(-)$1	1	105	135	23.1747
.(((((((................))))))	chr19:13250031-13250271(+)$1	1	186	216	23.9608
(((((((..................)))))	chr9:33046437-33046717(-)$1	1	111	141	24.0178
(((((((((..................)))	chr2:118866263-118866503(+)$1	1	103	133	24.9119
.((...((((..............))))..	chr15:69740306-69740546(+)$1	1	183	213	21.6262
((...((((..................)))	chrX:16779345-16779585(+)$1	1	132	162	22.9754
((...(((((............)))))...	chr6:139225929-139226169(-)$1	1	108	138	20.6383
((((.((((...............))))))	chr7:26230896-26231136(-)$1	1	145	175	21.1837
(((((((((...............))))))	chr19:6413578-6413818(-)$1	1	159	189	24.0633
(((.(..((...............))..).	chr11:107977060-107977300(+)$1	1	79	109	21.9147
(((((((((..............)))))).	chr16:2227914-2228154(+)$1	1	30	60	21.5968
...((((((..............)))))))	chr17:61671249-61671489(+)$1	1	22	52	20.9276
..(((((((...............))))))	chr13:21721414-21721654(+)$1	1	62	92	21.6197
(((((..((................))..)	chr2:46852006-46852248(+)$1	1	169	199	24.3333
..(((((((.....................	chr12:63037684-63037924(-)$1	1	106	136	23.6470
((((((.((..............)).))))	chr16:24226246-24226486(+)$1	1	74	104	23.6376
((.(((.((((.............)))).)	chr6:97594493-97594733(-)$1	1	34	64	20.1962
(.(((((((..............)))))))	chr7:64865567-64865807(+)$1	1	9	39	23.3685
)))(((((((.............)))))))	chr22:36134800-36135040(-)$1	1	41	71	20.8375
(((((((((..............)))))))	chr14:68143511-68143751(-)$1	1	153	183	23.9644
(((((((((.....................	chr20:39752248-39752488(+)$1	1	104	134	24.7855
(((((((((...............))))))	chr22:40727547-40727788(+)$1	1	104	134	24.3675
.(((((.((...............)).)))	chr1:183113512-183113752(+)$1	1	176	206	21.4779
(((((((.......................	chr20:61576593-61576880(+)$1	1	100	130	24.3150
..(((.((((..............)))).)	chr1:90180511-90180752(+)$1	1	108	138	22.5252
(((..(((......................	chr2:145146484-145146724(-)$1	1	187	217	24.1191
.(((.((((.....................	chr15:31668973-31669213(+)$1	1	104	134	23.7121
((((((.((..................)).	chr1:115314408-115314648(-)$1	1	40	70	23.6882
((.((((((.....................	chr16:70695222-70695462(-)$1	1	91	121	22.8611
.((..((((...............))))..	chr12:56386127-56386372(+)$1	1	24	54	20.7136
(((((..(((..............))).))	chr2:128238294-128238534(-)$1	1	85	115	22.4120
((((..(((..................)))	chr10:93038329-93038578(+)$1	1	111	141	23.3244
((..(((((.....................	chr19:37035053-37035293(-)$1	1	107	137	23.4042
((((((((................))))))	chr12:46299119-46299359(+)$1	1	96	126	22.1580
((((((((((............))))))))	chr17:7215440-7215680(+)$1	1	158	188	22.2049
((((((((....................))	chr20:48697776-48698020(-)$1	1	111	141	22.9426
))))(((((...............))))).	chr10:104417300-104417541(+)$1	1	171	201	20.7671
((((((((................))))))	chrX:15844787-15845028(-)$1	1	163	193	22.1580
....(((((................)))))	chr1:245017351-245017591(-)$1	1	103	133	23.6396
(((((((((..................)))	chrX:8500550-8500790(-)$1	1	149	179	24.9119
..(((..(((............)))..)))	chr6:43582233-43582473(+)$1	1	193	223	21.0128
(((((..(((((............))))).	chr9:91092784-91093031(+)$1	1	167	197	19.2467
(((((....................)))))	chr5:64961742-64961982(-)$1	1	40	70	21.8460
((.((((((.....................	chrX:132436224-132436464(-)$1	1	64	94	22.8415
(((((((((................)))))	chr12:56144117-56144372(+)$1	1	20	50	25.5493
(((..((((.............)))).)))	chr2:152657854-152658094(-)$1	1	74	104	20.0942
)((((((((...............))))))	chr2:47387312-47387552(-)$1	1	180	210	20.6720
((((((((((.............)))))))	chr8:103839970-103840210(-)$1	1	31	61	22.3806
((((....(((.............)))...	chr2:151326029-151326269(-)$1	1	51	81	21.3823
(...(((((.....................	chr5:133492257-133492497(-)$1	1	47	77	23.4843
((((....................))))))	chr17:38991838-38992079(+)$1	1	81	111	23.0767
((((((((................))))).	chr2:38790764-38791004(-)$1	1	87	117	23.2131
(((((((((.............))))))))	chr6:143746838-143747078(-)$1	1	117	147	21.4935
..(((((((...............))))))	chr16:15960298-15960538(-)$1	1	93	123	21.6197
....((((((..............))))))	chr6:130461187-130461427(+)$1	1	76	106	21.4768
(((((((((...............)))).)	chr11:130097720-130097960(-)$1	1	115	145	21.5992

#PSSM
i : 0.13	= : 0.13	d : 0.13	c : 0.08	g : 0.08	: : 0.08	h : 0.07	! : 0.05	e : 0.05	b : 0.04	# : 0.04	$ : 0.02	f : 0.02	a : 0.01	
i : 0.13	= : 0.13	c : 0.10	g : 0.10	d : 0.10	e : 0.08	h : 0.08	! : 0.04	: : 0.04	b : 0.04	# : 0.04	[ : 0.02	f : 0.02	$ : 0.01	" : 0.01	
g : 0.17	= : 0.13	i : 0.11	h : 0.10	c : 0.10	[ : 0.07	e : 0.07	d : 0.07	" : 0.04	! : 0.02	b : 0.02	# : 0.02	$ : 0.01	f : 0.01	
g : 0.20	= : 0.13	i : 0.11	h : 0.10	c : 0.08	f : 0.07	e : 0.07	" : 0.05	d : 0.05	! : 0.05	# : 0.02	[ : 0.01	
g : 0.18	i : 0.11	e : 0.11	h : 0.10	= : 0.10	f : 0.08	c : 0.07	! : 0.05	[ : 0.04	" : 0.04	d : 0.02	a : 0.01	# : 0.01	^ : 0.01	
g : 0.17	d : 0.13	i : 0.11	e : 0.11	h : 0.08	= : 0.08	! : 0.08	f : 0.07	c : 0.04	^ : 0.02	b : 0.01	" : 0.01	[ : 0.01	# : 0.01	
g : 0.17	d : 0.15	i : 0.11	h : 0.08	e : 0.08	f : 0.07	[ : 0.07	! : 0.07	= : 0.05	c : 0.02	^ : 0.02	" : 0.01	b : 0.01	# : 0.01	
d : 0.15	g : 0.11	i : 0.11	^ : 0.10	e : 0.10	h : 0.08	b : 0.08	f : 0.07	= : 0.05	c : 0.05	" : 0.01	a : 0.01	# : 0.01	
d : 0.15	^ : 0.14	i : 0.11	g : 0.10	e : 0.08	b : 0.08	f : 0.07	y : 0.07	= : 0.05	c : 0.05	h : 0.02	" : 0.01	
^ : 0.34	x : 0.18	y : 0.11	w : 0.07	c : 0.05	v : 0.04	= : 0.04	d : 0.04	g : 0.02	e : 0.02	h : 0.01	f : 0.01	
^ : 0.34	x : 0.18	w : 0.14	y : 0.11	v : 0.08	u : 0.04	c : 0.02	= : 0.01	d : 0.01	e : 0.01	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.04	c : 0.01	e : 0.01	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	v : 0.13	y : 0.11	u : 0.07	
^ : 0.34	x : 0.18	w : 0.14	y : 0.11	v : 0.08	u : 0.02	g : 0.01	e : 0.01	= : 0.01	c : 0.01	d : 0.01	i : 0.01	
^ : 0.34	x : 0.18	y : 0.11	w : 0.07	g : 0.05	v : 0.04	u : 0.02	f : 0.02	i : 0.02	= : 0.02	e : 0.01	b : 0.01	c : 0.01	d : 0.01	
^ : 0.33	g : 0.11	d : 0.10	= : 0.07	c : 0.05	h : 0.05	f : 0.05	e : 0.05	i : 0.04	b : 0.04	y : 0.04	a : 0.01	
^ : 0.28	g : 0.13	d : 0.10	e : 0.08	= : 0.07	b : 0.05	h : 0.05	f : 0.05	i : 0.05	c : 0.04	] : 0.02	2 : 0.01	
^ : 0.27	g : 0.14	e : 0.10	= : 0.08	d : 0.08	h : 0.05	f : 0.05	i : 0.05	c : 0.04	b : 0.02	2 : 0.02	] : 0.02	
^ : 0.20	g : 0.14	e : 0.10	d : 0.10	= : 0.08	i : 0.08	h : 0.05	f : 0.05	c : 0.04	3 : 0.02	] : 0.02	2 : 0.02	b : 0.01	4 : 0.01	
^ : 0.18	g : 0.15	e : 0.10	= : 0.08	i : 0.08	h : 0.07	f : 0.07	2 : 0.04	] : 0.04	c : 0.04	3 : 0.02	d : 0.02	a : 0.01	b : 0.01	4 : 0.01	
g : 0.15	^ : 0.15	h : 0.10	= : 0.10	i : 0.10	c : 0.07	] : 0.05	e : 0.05	2 : 0.05	f : 0.04	3 : 0.02	d : 0.02	: : 0.01	4 : 0.01	

#score	1556.212672631945
#seq	69
#width	30
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013c_hg19_UTR_m1_run1.txt

#BEAR
eedddd[ddddtttttttttttdddd22d	chr1:156262786-156263063(-)$1	277	178	207	21.1436
gggg####cccxxxxxxxxxxxxxxxccc	chr19:13054693-13054917(+)$1	224	157	186	19.7477
eeeeeffffffuuuuuuuuuuuuffffff	chr10:91343995-91344220(-)$1	225	170	199	22.8268
iiiiiiiiiwwwwwwwwwwwwwwiiiiii	chr6:31797511-31797767(+)$1	256	166	195	23.7979
b!!ccc[ddddvvvvvvvvvvvvvdddd]	chr12:76748791-76749035(-)$1	244	150	179	23.8640
============ttttttttttt======	chr6:75965319-75965552(-)$1	233	102	131	23.1478
cc!!bb[ddddxxxxxxxxxxxxxxxddd	chr3:5259750-5259971(+)$1	221	108	137	19.4281
eeee::eeeeevvvvvvvvvvvvveeeee	chr1:112255069-112255312(+)$1	243	28	57	21.2367
eeeeeeee[bbuuuuuuuuuuuubb]eee	chr1:222839616-222839841(+)$1	225	183	212	22.7816
bb[ccc[ddddtttttttttttddddccc	chr17:65069336-65069560(-)$1	224	185	214	21.8304
ffffff[ddddwwwwwwwwwwwwwwdddd	chr5:71516281-71516505(-)$1	224	119	148	22.8041
hhffffff[ccctttttttttttccc]ff	chr1:179068456-179068689(-)$1	233	178	207	21.7103
qddddffffffuuuuuuuuuuuuffffff	chr3:38207250-38207498(+)$1	248	157	186	21.9291
d"""ddddxxxxxxxxxxxxxxxdddddd	chr8:12579867-12580091(-)$1	224	55	84	18.5640
======eeeeevvvvvvvvvvvvveeeee	chr13:77457653-77457890(-)$1	237	43	72	24.0143
f!!ccc[ddddwwwwwwwwwwwwwwdddd	chr15:83686394-83686615(-)$1	221	5	34	23.8075
==========vvvvvvvvvvvvv======	chr1:16266622-16266868(+)$1	246	27	56	24.3662
d####ddddwwwwwwwwwwwwwwdddd44	chr17:47004688-47004919(+)$1	231	77	106	22.7907
:::ffffffwwwwwwwwwwwwwwffffff	chr13:77458782-77459006(-)$1	224	191	220	19.2757
===========wwwwwwwwwwwwww====	chr11:71708192-71708451(+)$1	259	47	76	24.4493
e[iiiiiiiiiyyyyyyyyyyyyyyyyii	chr3:43743719-43743950(+)$1	231	13	42	22.9322
egggggggxxxxxxxxxxxxxxxgggggg	chr11:9160604-9160827(-)$1	223	191	220	19.5178
ddd[ggggggguuuuuuuuuuuugggggg	chr12:4413533-4413769(+)$1	236	167	196	24.1184
$$gggggggccctttttttttttccc22g	chr5:176860473-176860702(+)$1	229	168	197	22.4311
]bbbb!!ddddtttttttttttdddd22b	chr1:233463501-233463724(+)$1	223	143	172	20.6111
c[hhhhhhhhvvvvvvvvvvvvvhhhhhh	chr6:24705091-24705337(-)$1	246	136	165	21.1235
g[dddd[cccxxxxxxxxxxxxxxxccc]	chr12:8928991-8929217(+)$1	226	135	164	19.9499
dd!!eeeeewwwwwwwwwwwwwweeeee]	chr1:6284673-6284906(-)$1	233	184	213	23.1914
gg[ffffffyyyyyyyyyyyyyyyyffff	chr4:56296665-56296901(-)$1	236	7	36	22.3957
e[iiiiiiiiivvvvvvvvvvvvviiiii	chrX:108885444-108885667(-)$1	223	87	116	24.2512
]ccc:ffffffwwwwwwwwwwwwwwffff	chr4:10076686-10076911(-)$1	225	98	127	21.5335
eeeebb[cccyyyyyyyyyyyyyyyyccc	chr11:494551-494782(-)$1	231	91	120	22.5248
gggg####cccvvvvvvvvvvvvvccc44	chr20:46284635-46284874(+)$1	239	140	169	23.8182
d"""cccyyyyyyyyyyyyyyyyccc22d	chr12:56151180-56151400(-)$1	220	138	167	21.8975
d!!ccc[dddduuuuuuuuuuuuddddcc	chrX:119390128-119390355(+)$1	227	122	151	24.7324
eeeee[eeeeeuuuuuuuuuuuueeeee]	chr1:36770065-36770296(+)$1	231	160	189	24.0891
!bb[bb[cccyyyyyyyyyyyyyyyyccc	chr12:54763532-54763759(-)$1	227	144	173	22.4373
b[bb[gggggggtttttttttttgggggg	chrX:135044482-135044718(-)$1	236	81	110	21.6850
cc[gggggggvvvvvvvvvvvvvgggggg	chr6:139229733-139229956(-)$1	223	162	191	23.7741
g!!ggggggg[attttttttttta]gggg	chr4:99993235-99993494(-)$1	259	141	170	23.7269
ffffcccddddtttttttttttdddd22c	chr2:5839397-5839618(+)$1	221	150	179	21.1502
ee"""cccxxxxxxxxxxxxxxxccc333	chr12:56598270-56598501(-)$1	231	57	86	19.6781
c!!ccc[eeeeewwwwwwwwwwwwwweee	chr13:52706803-52707028(-)$1	225	117	146	22.5555
:bb!!eeeeevvvvvvvvvvvvveeeee2	chr2:158592932-158593156(-)$1	224	27	56	22.0169
h####eeeeevvvvvvvvvvvvveeeeeh	chr4:39825652-39825873(-)$1	221	115	144	23.3116
hhhh!!dddd[attttttttttta]dddd	chr10:6157520-6157748(+)$1	228	131	160	22.0469
ffdddd[ddddxxxxxxxxxxxxxxxddd	chr8:92097367-92097591(+)$1	224	81	110	18.6762
ggggg[eeeeeuuuuuuuuuuuueeeee]	chr22:39131266-39131484(-)$1	218	154	183	24.7318
c!!eeeeeyyyyyyyyyyyyyyyyeeeee	chr12:69667707-69667938(+)$1	231	185	214	22.7133
f[iiiiiiiiivvvvvvvvvvvvviiiii	chr5:109202646-109202881(+)$1	235	185	214	24.1617
::ccc!!cccvvvvvvvvvvvvvccc22c	chr22:21305465-21305687(+)$1	222	103	132	21.8395
e[iiiiiiiiivvvvvvvvvvvvviiiii	chr2:159313552-159313779(+)$1	227	77	106	24.2512
gggggg"""ccctttttttttttccc444	chr17:76220078-76220297(+)$1	219	143	172	22.8244
ddd[ggggggguuuuuuuuuuuugggggg	chr11:108343366-108343592(-)$1	226	115	144	24.1184
%ccc[ffffffuuuuuuuuuuuuffffff	chr19:17389736-17389962(+)$1	226	124	153	22.4975
ggggbb!!a[axxxxxxxxxxxxxxxa]a	chr1:205683965-205684191(-)$1	226	110	139	19.5080
gggg"""eeeeettttttttttteeeee2	chr7:143002576-143002805(+)$1	229	112	141	22.5337

#otherMatches

#Seq PSSM
GUUCUGCUGCUGCACCACAAGAAGUACUC	chr1:156262786-156263063(-)$1	277	178	207	21.1436
GUGGAUUUUGGUUUUGUUCCCCUCCUCCA	chr19:13054693-13054917(+)$1	224	157	186	19.7477
CUGCUGGAUUUGUAAAUAAUUUAAAAUCC	chr10:91343995-91344220(-)$1	225	170	199	22.8268
GUCUUUGAGGUGGACUGUUGGGACUCAAG	chr6:31797511-31797767(+)$1	256	166	195	23.7979
CUUUUGUCUUAUUUUUGUUUUUCUUAAGU	chr12:76748791-76749035(-)$1	244	150	179	23.8640
AUGUAUUUUGUGGAGAAAGGGAUUACAAG	chr6:75965319-75965552(-)$1	233	102	131	23.1478
UUGACUUCUGGGUACUGGAAUUAAUACCA	chr3:5259750-5259971(+)$1	221	108	137	19.4281
UCCAGACUUCAAAAAUAAAAAAUCUGAAG	chr1:112255069-112255312(+)$1	243	28	57	21.2367
GGUGCACAACAGAAAAAUGAAAAUGAUGU	chr1:222839616-222839841(+)$1	225	183	212	22.7816
UUGCCUGCCUUAGAACUAUGUAGAGGAGG	chr17:65069336-65069560(-)$1	224	185	214	21.8304
GAAGCACAGGCuuuuguuuuuuguuguuu	chr5:71516281-71516505(-)$1	224	119	148	22.8041
AAGUUGUGUUCUGUUUUAAAUAAAGGUUG	chr1:179068456-179068689(-)$1	233	178	207	21.7103
GGGACGAUUACGAGCUGCAGGAGGUGAUC	chr3:38207250-38207498(+)$1	248	157	186	21.9291
GAACUGUCUUGACCAUUGACUAUGACACA	chr8:12579867-12580091(-)$1	224	55	84	18.5640
UUUGUUUGAAGUUAAGUGGAAUCCUUUCA	chr13:77457653-77457890(-)$1	237	43	72	24.0143
GAACUGGGUUUAAUGGUUUAAAAAAAAGC	chr15:83686394-83686615(-)$1	221	5	34	23.8075
AUACGUUUUUUUUAAUCUGUGCCAAAAAU	chr1:16266622-16266868(+)$1	246	27	56	24.3662
GGCCUUUGGCAAAAACAAAACAACCAACA	chr17:47004688-47004919(+)$1	231	77	106	22.7907
ACAAGGUCAUUACACAGUCUUUUUGACCU	chr13:77458782-77459006(-)$1	224	191	220	19.2757
gugcguaugcgugugugugugugugugug	chr11:71708192-71708451(+)$1	259	47	76	24.4493
CCUGUUCGUAUAUCUAAUGGAAAUAAAAU	chr3:43743719-43743950(+)$1	231	13	42	22.9322
CGUGCCAAAUACCACAUUUCCUGUUGGCA	chr11:9160604-9160827(-)$1	223	191	220	19.5178
GAUGAUUCUGGAUUCUAAACAACCCAGAA	chr12:4413533-4413769(+)$1	236	167	196	24.1184
AAGCAGAUCCUGGAGAAAGUGAACAGUAG	chr5:176860473-176860702(+)$1	229	168	197	22.4311
ACCGAUCGCGAUUCCUACCCCCUCGCCUU	chr1:233463501-233463724(+)$1	223	143	172	20.6111
GUUUCCAAUUGUAUUUAGCUUCUGGUUGG	chr6:24705091-24705337(-)$1	246	136	165	21.1235
GUAUAUUGUUAAAAUUGUAAUUCUAAAUU	chr12:8928991-8929217(+)$1	226	135	164	19.9499
GUAAAAAUGCAUUUACAACCUUUCAUUUA	chr1:6284673-6284906(-)$1	233	184	213	23.1914
UUUAGAAUAUAAUAAUUUCAAGAAUUAUU	chr4:56296665-56296901(-)$1	236	7	36	22.3957
UCUCAUUCUUCCCAACUUGCCUUUGAAGA	chrX:108885444-108885667(-)$1	223	87	116	24.2512
UAACAGUUUGCACAUGAAAAAUAAAGCGA	chr4:10076686-10076911(-)$1	225	98	127	21.5335
AGGCUCUUCCUGCUGCUGCUCUCCCUGGA	chr11:494551-494782(-)$1	231	91	120	22.5248
AGCACCCCCCAUUUUUUCAAACCUUGGUA	chr20:46284635-46284874(+)$1	239	140	169	23.8182
UUUUCCAUUUCUCUCCUUCUUCUUGGUCA	chr12:56151180-56151400(-)$1	220	138	167	21.8975
CUGGCAUAUAUUUUUAAAUGUUCAUAUUG	chrX:119390128-119390355(+)$1	227	122	151	24.7324
GGAGUUUAAGGCCUUUCCGACCACCUUGU	chr1:36770065-36770296(+)$1	231	160	189	24.0891
AACUGAAGCGCUUCCGUGAACACCCCCGU	chr12:54763532-54763759(-)$1	227	144	173	22.4373
UAGGGUAGUUCAAAAAUAUGAUGUGAGCU	chrX:135044482-135044718(-)$1	236	81	110	21.6850
CUAUUCCUAGACACAUUUAAUUACUAGGA	chr6:139229733-139229956(-)$1	223	162	191	23.7741
UAGUUUAUUAAGGAAUAUUUUAACAUAAU	chr4:99993235-99993494(-)$1	259	141	170	23.7269
CAGGGAUUUACAAGUUCCCAAAGUAACCG	chr2:5839397-5839618(+)$1	221	150	179	21.1502
UCAUACUGUCCUGUCCUUACCCUCAGAUG	chr12:56598270-56598501(-)$1	231	57	86	19.6781
agagggaugcugACCACAGACCUUUAUAG	chr13:52706803-52707028(-)$1	225	117	146	22.5555
AAGAUUUCAGUAGAAUUUUAGUCCUGAAC	chr2:158592932-158593156(-)$1	224	27	56	22.0169
AGGAACAUGAAAUUUGUCUUUUCUCAUGU	chr4:39825652-39825873(-)$1	221	115	144	23.3116
UUGAUUGAUCCCUUUUUUAUUUUGUGGUU	chr10:6157520-6157748(+)$1	228	131	160	22.0469
UUUCAAAAUAACCAUUUCAAUGUAAUUUG	chr8:92097367-92097591(+)$1	224	81	110	18.6762
GCCCCCACAUCUAACCAGGCCCUGAUGUA	chr22:39131266-39131484(-)$1	218	154	183	24.7318
UUUUUUUUUUUUUUUGCUGUCCAUGAGAA	chr12:69667707-69667938(+)$1	231	185	214	22.7133
UCUUUUUUCUUUUACCAGUACAGUaagaa	chr5:109202646-109202881(+)$1	235	185	214	24.1617
GCUCCCAAGCAAAGGAAAUGCAAGCUCUG	chr22:21305465-21305687(+)$1	222	103	132	21.8395
ccgcggcACUUUUUUAAUUUUUUCGGGUG	chr2:159313552-159313779(+)$1	227	77	106	24.2512
UAACAACAUGGCUUUCUUAUUUUGUUUGA	chr17:76220078-76220297(+)$1	219	143	172	22.8244
GCAAGAAAGGUUGCCUAACUCAUACCUUU	chr11:108343366-108343592(-)$1	226	115	144	24.1184
AUCCCUGUACAUCUGCACCUUCUUGUGCA	chr19:17389736-17389962(+)$1	226	124	153	22.4975
ACGGGGAAAGCUUUAUAAAAGAUCAUGGU	chr1:205683965-205684191(-)$1	226	110	139	19.5080
GCACCUUGCUGCAGUGUCCAGAAGCGGCC	chr7:143002576-143002805(+)$1	229	112	141	22.5337

#DB
((((((.((((...........))))..)	chr1:156262786-156263063(-)$1	1	178	207	21.1436
((((....(((...............)))	chr19:13054693-13054917(+)$1	1	157	186	19.7477
)))))((((((............))))))	chr10:91343995-91344220(-)$1	1	170	199	22.8268
(((((((((..............))))))	chr6:31797511-31797767(+)$1	1	166	195	23.7979
(..(((.((((.............)))).	chr12:76748791-76749035(-)$1	1	150	179	23.8640
((((((((((((...........))))))	chr6:75965319-75965552(-)$1	1	102	131	23.1478
((..((.((((...............)))	chr3:5259750-5259971(+)$1	1	108	137	19.4281
))))..(((((.............)))))	chr1:112255069-112255312(+)$1	1	28	57	21.2367
)))(((((.((............)).)))	chr1:222839616-222839841(+)$1	1	183	212	22.7816
((.(((.((((...........)))))))	chr17:65069336-65069560(-)$1	1	185	214	21.8304
((((((.((((..............))))	chr5:71516281-71516505(-)$1	1	119	148	22.8041
((((((((.(((...........))).))	chr1:179068456-179068689(-)$1	1	178	207	21.7103
.))))((((((............))))))	chr3:38207250-38207498(+)$1	1	157	186	21.9291
(...((((...............))))))	chr8:12579867-12580091(-)$1	1	55	84	18.5640
(((((((((((.............)))))	chr13:77457653-77457890(-)$1	1	43	72	24.0143
(..(((.((((..............))))	chr15:83686394-83686615(-)$1	1	5	34	23.8075
((((((((((.............))))))	chr1:16266622-16266868(+)$1	1	27	56	24.3662
(....((((..............))))..	chr17:47004688-47004919(+)$1	1	77	106	22.7907
...((((((..............))))))	chr13:77458782-77459006(-)$1	1	191	220	19.2757
(((((((((((..............))))	chr11:71708192-71708451(+)$1	1	47	76	24.4493
(.(((((((((................))	chr3:43743719-43743950(+)$1	1	13	42	22.9322
)(((((((...............))))))	chr11:9160604-9160827(-)$1	1	191	220	19.5178
(((.(((((((............))))))	chr12:4413533-4413769(+)$1	1	167	196	24.1184
..((((((((((...........)))..)	chr5:176860473-176860702(+)$1	1	168	197	22.4311
.))((..((((...........))))..)	chr1:233463501-233463724(+)$1	1	143	172	20.6111
(.((((((((.............))))))	chr6:24705091-24705337(-)$1	1	136	165	21.1235
(.((((.(((...............))).	chr12:8928991-8929217(+)$1	1	135	164	19.9499
((..(((((..............))))).	chr1:6284673-6284906(-)$1	1	184	213	23.1914
((.((((((................))))	chr4:56296665-56296901(-)$1	1	7	36	22.3957
(.(((((((((.............)))))	chrX:108885444-108885667(-)$1	1	87	116	24.2512
.))).((((((..............))))	chr4:10076686-10076911(-)$1	1	98	127	21.5335
((((((.(((................)))	chr11:494551-494782(-)$1	1	91	120	22.5248
((((....(((.............)))..	chr20:46284635-46284874(+)$1	1	140	169	23.8182
(...(((................)))..)	chr12:56151180-56151400(-)$1	1	138	167	21.8975
(..(((.((((............))))))	chrX:119390128-119390355(+)$1	1	122	151	24.7324
(((((.(((((............))))).	chr1:36770065-36770296(+)$1	1	160	189	24.0891
.((.((.(((................)))	chr12:54763532-54763759(-)$1	1	144	173	22.4373
(.((.(((((((...........))))))	chrX:135044482-135044718(-)$1	1	81	110	21.6850
((.(((((((.............))))))	chr6:139229733-139229956(-)$1	1	162	191	23.7741
(..(((((((.(...........).))))	chr4:99993235-99993494(-)$1	1	141	170	23.7269
))))(((((((...........))))..)	chr2:5839397-5839618(+)$1	1	150	179	21.1502
((...(((...............)))...	chr12:56598270-56598501(-)$1	1	57	86	19.6781
(..(((.(((((..............)))	chr13:52706803-52707028(-)$1	1	117	146	22.5555
.((..(((((.............))))).	chr2:158592932-158593156(-)$1	1	27	56	22.0169
(....(((((.............))))))	chr4:39825652-39825873(-)$1	1	115	144	23.3116
((((..((((.(...........).))))	chr10:6157520-6157748(+)$1	1	131	160	22.0469
((((((.((((...............)))	chr8:92097367-92097591(+)$1	1	81	110	18.6762
(((((.(((((............))))).	chr22:39131266-39131484(-)$1	1	154	183	24.7318
(..(((((................)))))	chr12:69667707-69667938(+)$1	1	185	214	22.7133
(.(((((((((.............)))))	chr5:109202646-109202881(+)$1	1	185	214	24.1617
..(((..(((.............)))..)	chr22:21305465-21305687(+)$1	1	103	132	21.8395
(.(((((((((.............)))))	chr2:159313552-159313779(+)$1	1	77	106	24.2512
((((((...(((...........)))...	chr17:76220078-76220297(+)$1	1	143	172	22.8244
(((.(((((((............))))))	chr11:108343366-108343592(-)$1	1	115	144	24.1184
.(((.((((((............))))))	chr19:17389736-17389962(+)$1	1	124	153	22.4975
((((((..(.(...............).)	chr1:205683965-205684191(-)$1	1	110	139	19.5080
((((...(((((...........))))).	chr7:143002576-143002805(+)$1	1	112	141	22.5337

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

#score	1272.8745840586146
#seq	57
#width	29
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_DGCR8_Macias2012a_hg19_CDS_m1_run1.txt

#BEAR
c[accc####ffffffooooooffffff4444ccc]a]cc	chr1:1474980-1475204(-)$1	224	25	65	13.5604
"ccca[ffffff!!a[annnnna]a22ffffff]a]ccc3	chr7:100334483-100334707(+)$1	224	21	61	15.9734
cc[hhhhhhhh"""cccnnnnnccc333hhhhhhhh>>>>	chr19:4697538-4697761(-)$1	223	51	91	14.6132
ddccc[dddd!!bb[cccmmmmccc333bb22dddd333c	chr3:47037132-47037356(-)$1	224	21	61	11.5448
###ggggggg####cccnnnnncccggggggg333a]ddd	chr3:12632357-12632579(+)$1	222	86	126	17.8770
ffff!!bb[cccbbcccnnnnnccc]bb]ccc]bbfffff	chr16:726159-726382(-)$1	223	107	147	14.8473
eeee[bb!!ccc!!cccammmma]ccc22ccc333bb]ee	chr12:78513279-78513503(-)$1	224	70	110	12.6477
b####ffffff[a[cccnnnnnccc]affffffbb]bb]b	chr16:774397-774621(+)$1	224	69	109	15.0898
####bb[dddd!!ddddnnnnndddd]dddd]bbadddd]	chr6:3118958-3119179(-)$1	221	155	195	12.6984
a[eeeeeccc####cccnnnnnccc333ccc]eeeee]a]	chr9:990423-990648(+)$1	225	14	54	18.0068
b[bb"""a[ffffffccclllccc]ffffff]a333bb]b	chr19:36003912-36004135(+)$1	223	68	108	12.1987
!!dddd$$$$$bb[cccooooooccc]bbdddd22=====	chr6:46976720-46976941(-)$1	221	116	156	13.5132
c[ffffff####cccbbnnnnnbb]ccc333ffffff]cc	chr15:44581237-44581459(-)$1	222	22	62	15.1272
bb[ggggggg[bb[cccnnnnnccc]bb]ggggggg]bb2	chr7:27204778-27205001(-)$1	223	27	67	15.6793
###bb$$$$$bb!!cccooooooccc]bb]bb4444ccc]	chr12:14840805-14841026(+)$1	221	144	184	14.6557
gggg[ccc####eeeeennnnneeeee22cccggggggg:	chr9:35076604-35076826(-)$1	222	153	193	13.0984
d!!eeeee!!ccc[cccooooooccc]ccc333eeeee44	chr10:15138543-15138764(-)$1	221	152	192	16.2612
[bb"""ccc[bb[ddddnnnnndddd]bb]ccc333bbdd	chr14:65009121-65009344(-)$1	223	99	139	14.5019
EE:ggggggg####cccnnnnnccc4444ggggggg:ccc	chr16:71109762-71109997(-)$1	235	114	154	14.3783
eeeee"""iiiiiiiiiooooooiiiiiiiii333eeeee	chr1:33480077-33480299(-)$1	222	17	57	14.4729
#ffffff"""eeeee[aooooooa]eeeee333ffffff]	chr10:17243513-17243737(-)$1	224	72	112	13.1580
eeee[a"""ccc!!cccoooooocccccc333aeeeee:f	chr10:105362440-105362667(+)$1	227	60	100	15.4364
bb[a"""ccc[bb[cccnnnnncccbbccc333a]bb]ff	chr19:14073694-14073918(-)$1	224	105	145	16.4694
""bb####gggggggooooooggggggg4444bb22gggg	chr16:58616940-58617163(+)$1	223	14	54	12.7399
cffffff!!dddd"""annnnna4444dddd22ffffff]	chr17:3526582-3526808(+)$1	226	60	100	14.6192
cc"""ggggggg"""bbnnnnnbb333ggggggg333ccc	chr16:31504898-31505122(-)$1	224	161	201	17.7845
"dddd[cccccc!!cccooooooccc22ccc]ccc]dddd	chr11:20940727-20940950(+)$1	223	84	124	15.3708
fffff[a[bbbb!!ddddllldddd22bb333bba]ffff	chr12:440992-441216(+)$1	224	166	206	11.9558
[ccc[a[eeeee[ddddnnnnnddddeeeee]a]ccc22c	chr1:160302156-160302379(+)$1	223	148	188	13.3679
[bbffffff[bb!!cccooooooccc]bb]ffffff333b	chr1:52981491-52981715(+)$1	224	139	179	14.5078
ffffdddd[ccc[a[bbnnnnnbbaccc]dddd]ffffff	chr4:129783061-129783286(+)$1	225	78	118	13.4268
ccc[a[gggggggcccooooooccc]ggggggga]ccc:g	chr17:71390268-71390492(+)$1	224	119	159	14.6537
"ccc[ggggggg"""bbnnnnnbb333ggggggg333ccc	chr14:59113165-59113386(-)$1	221	38	78	17.7540
cc===========ddddnnnnndddd4444==========	chr16:88876160-88876383(+)$1	223	112	152	16.1030
dddd!!ggggggg[aooooooa]gggggggdddd]ccc44	chr8:11412795-11413016(+)$1	221	20	60	12.5913
eeeee!!ccc####cccnnnnnccc333ccc22eeeee]b	chr19:42132209-42132430(+)$1	221	56	96	17.8409
####gggggggccc[bboooooobb22ccc]ggggggg33	chr6:131931174-131931395(+)$1	221	95	135	14.9660
===========a"""aooooooa333a]===========e	chr4:144468479-144468709(+)$1	230	58	98	16.6502
!!eeeee[a[gggggggnnnnnggggggg]a]eeeee22c	chr2:33809976-33810198(-)$1	222	145	185	14.6795
fff[eeeee[ccc[cccnnnnnccc]ccc]eeeee]ffff	chr12:6496925-6497147(-)$1	222	23	63	15.7439
ccc"""ccc[ccc!!bboooooobb22ccc]ccc333ccc	chr17:27277109-27277330(-)$1	221	75	115	15.8454
c!!ccc[dddd"""cccnnnnnccc333ddddccc333cc	chr4:158224718-158224940(-)$1	222	165	205	17.7286
ffffffggggggg[cccoooooocccggggggg333ffff	chr11:3659863-3660085(+)$1	222	30	70	15.9292
d[bb!!cccffffff[annnnna]ffffff22ccc22bb2	chr1:245530530-245530752(+)$1	222	89	129	13.5922
==========[ffffffnnnnnffffff]==========f	chr22:25423944-25424169(-)$1	225	64	104	15.2073
bb[eeeee!!ccc"""ccclllccc22ccc22eeeee]bb	chr1:40318335-40318558(-)$1	223	97	137	13.0852
e"""ccc!!a####cccnnnnnccc4444a22ccc]eeee	chr8:39782190-39782415(+)$1	225	62	102	18.2060
ffffff[ccc"""cccooooooccc333ccc333ffffff	chr5:146257553-146257784(-)$1	231	53	93	16.8127
ffff!!bb!!bb!!cccnnnnnccc333bb22bb22ffff	chr3:48463445-48463673(+)$1	228	105	145	17.2521
cc[bbccc[a"""ddddnnnnndddd]a]ccc]bbccc::	chr10:93811891-93812112(+)$1	221	124	164	13.1316
iiiiccc"""gggggggnnnnnggggggg22ccc4444ii	chr3:50137863-50138143(+)$1	280	216	256	15.6757
gggg!!eeeee!!ccc!!annnnna22ccc333eeeee]g	chr19:46996750-46996975(-)$1	225	46	86	13.8188
b[cccggggggg!!cccoooooocccggggggg]ccc]bb	chr7:23213664-23213889(+)$1	225	96	136	15.8565

#otherMatches

#Seq PSSM
CUCUUCCAGGCCAUCGCGUGCUUGAUGGACAUGAACGCGC	chr1:1474980-1475204(-)$1	224	25	65	13.5604
AUGGGAGCAAGGCCCCCUCUGUGUGCACUUUGCCCACCAC	chr7:100334483-100334707(+)$1	224	21	61	15.9734
CGCCGGGCAGGCCAGGGCAUGACCCACACCUGUUUGUUUC	chr19:4697538-4697761(-)$1	223	51	91	14.6132
CAGGCAGAGUCGGCAAAGGACACUUCGGGCAAACUCAUGG	chr3:47037132-47037356(-)$1	224	21	61	11.5448
AAAAGCAGAAUGUUCACAUGCCGUGUUUUGCUggggaggg	chr3:12632357-12632579(+)$1	222	86	126	17.8770
UGGGCCAGGCUGGCUGGGAGCAUCAGGCUCAGGCUCCCAG	chr16:726159-726382(-)$1	223	107	147	14.8473
CUCGGCCAGGAAUGCCACUGGUGCUGGAUUUUGAAGGGCG	chr12:78513279-78513503(-)$1	224	70	110	12.6477
GGGCCGUGGUGGCUGGCGCUUGGCCUGCACCAUCUGCGUG	chr16:774397-774621(+)$1	224	69	109	15.0898
AGAAGCAGCCGCAGGCGCAACACGCCCCGGCCGCCCAGCA	chr6:3118958-3119179(-)$1	221	155	195	12.6984
CCUUCUGUCCAGCCGAUCCUCAGUCACGGGAGCAGAGCGA	chr9:990423-990648(+)$1	225	14	54	18.0068
GCCAGGAGCCGCGGACAGCAUCUGCUCCGUGUCGAAUGAC	chr19:36003912-36004135(+)$1	223	68	108	12.1987
CAAGGCCACCAUCAUCCGCGUGGGGAAGAGCCUCCUCAUU	chr6:46976720-46976941(-)$1	221	116	156	13.5132
GAGGUCCGAAUUGCGCUUUUCCAGCCGCCCGCGGGCCACU	chr15:44581237-44581459(-)$1	222	22	62	15.1272
CUGGGCCAGCCUCCCCGGCAGGCGGCGACGCUGGCCGAGC	chr7:27204778-27205001(-)$1	223	27	67	15.6793
UCAGACCAUCCGAAUACAUGAAAGUAGCGUUCACAGUCAC	chr12:14840805-14841026(+)$1	221	144	184	14.6557
CUUGUGAUGGGGUGACUUGACUAGUCAAGAUCCAAGUAUA	chr9:35076604-35076826(-)$1	222	153	193	13.0984
UACCAUCGGAGUCGCUGCAAAGUCGGGGACAAGUGAUGAA	chr10:15138543-15138764(-)$1	221	152	192	16.2612
UCUCGUCUUCCACCGUCUGCUUGAUGUUGUAGGUAUAGGA	chr14:65009121-65009344(-)$1	223	99	139	14.5019
GAACUGAGAGAUCCUCAAGUACUGAUUCCCUUUCAGCGUA	chr16:71109762-71109997(-)$1	235	114	154	14.3783
UCUGCUUGUCAUUCUGGAGCCCCCUAGAGUGGAGUGCAGG	chr1:33480077-33480299(-)$1	222	17	57	14.4729
AGCUCCGGGGCUGCGGCGGCUGAGGCGCGGGGAUGGAGCC	chr10:17243513-17243737(-)$1	224	72	112	13.1580
AGGGUGAUGAGGUCGGAUGAGCUUCUCCUAGACCCCUCAC	chr10:105362440-105362667(+)$1	227	60	100	15.4364
CGACAAAGGUAGGCGAGGCGUGUUCCCACCCAGGGCGCGG	chr19:14073694-14073918(-)$1	224	105	145	16.4694
CACACCUGUAAUGGAAUGCCAUCUGUUAAUCCUGAAUGAG	chr16:58616940-58617163(+)$1	223	14	54	12.7399
UCCAGCUUUGGCUCUGCGUGUUGAAAUAGCCCCAGCUGGC	chr17:3526582-3526808(+)$1	226	60	100	14.6192
CCCAACUGCAGCCAAUCGCAUGGAGCCGCUGUGGACAGGU	chr16:31504898-31505122(-)$1	224	161	201	17.7845
AGUGAUUUCUUAAGCCUGGUGCAAGGAAUAAUGGAUUUAC	chr11:20940727-20940950(+)$1	223	84	124	15.3708
GAGGAAGACAGAUUUUAUUAGAUAAUUUCAGAUGCAUUUU	chr12:440992-441216(+)$1	224	166	206	11.9558
GAACUGAGCACACAUCACAUAAUGGUUGUGCCCUGUUAAC	chr1:160302156-160302379(+)$1	223	148	188	13.3679
CAGGUGUCAAUGCAGAUUCAUCUAUCACAGUGGCAUUUUC	chr1:52981491-52981715(+)$1	224	139	179	14.5078
GCAGUUGGAGGAUGAGUUCUACACCUUCGUCAACCUGCUG	chr4:129783061-129783286(+)$1	225	78	118	13.4268
ACCUCGCUCCAGCGCACCAGCAUGCUGCUGGAGGUGGUGG	chr17:71390268-71390492(+)$1	224	119	159	14.6537
AGGUUUGGCCACCACCGCCUCCCGUCCGUGGCCAUGCGCC	chr14:59113165-59113386(-)$1	221	38	78	17.7540
CAGUUGGCCUGGGCUGCAGAGAGCAGGUGCUCCAGGCCAG	chr16:88876160-88876383(+)$1	223	112	152	16.1030
CCCUGUCUUUUCUUCCCUAAUGCAGAGAAGGGGGAUGGUC	chr8:11412795-11413016(+)$1	221	20	60	12.5913
CACUGGACGGCAGGGCUUCAAUAGUGAACUGGACAGUGGU	chr19:42132209-42132430(+)$1	221	56	96	17.8409
CCACAGGAGUUGGCUUGUUCCCCCAUCGUCAAACUUCUCC	chr6:131931174-131931395(+)$1	221	95	135	14.9660
CUGUGUUUUGGGAAAGGUGCAACGAGCUCCAGGACAUAGA	chr4:144468479-144468709(+)$1	230	58	98	16.6502
AGAUGGCGGGCACCAuggugaucguggugguggucguggu	chr2:33809976-33810198(-)$1	222	145	185	14.6795
CAGAGGGGCUGCUGUAGAGGAGCUAGGGUUGCCCUGCUGU	chr12:6496925-6497147(-)$1	222	23	63	15.7439
GCUCUGCUGGCUCCCCCCAAGACGGACGAGGCAGAAAAGC	chr17:27277109-27277330(-)$1	221	75	115	15.8454
UGAUGGUAUUUACAGACUUCUUGUCAUAAAAUCCAAAAAU	chr4:158224718-158224940(-)$1	222	165	205	17.7286
GUGGCCUCCCCAGGCCAACAUCCUGGUUGGGGAGAAGGCU	chr11:3659863-3660085(+)$1	222	30	70	15.9292
GCACCUGGUCCCUGUCGAGAACCAACGGGGUCACCCUGUA	chr1:245530530-245530752(+)$1	222	89	129	13.5922
UCCGGGCUGGGGGAGCCCCAGAGGCUUCGCCGGCCUGGAG	chr22:25423944-25424169(-)$1	225	64	104	15.2073
CAGGUGGACCCAGAAAUGGCUGCCAAGCUGCAUCCACAUG	chr1:40318335-40318558(-)$1	223	97	137	13.0852
AAAAGCAUUUUUCAGUGUUCUUCGCAUAUAUUUGUCUGGG	chr8:39782190-39782415(+)$1	225	62	102	18.2060
CUCCCCUGCCCCCCUCUCCUGUGAGACUGGCUGCGGGGAG	chr5:146257553-146257784(-)$1	231	53	93	16.8127
UGUGAGCAAGGCAAGAUGCACAGUCCAGGUGCUGAGCACA	chr3:48463445-48463673(+)$1	228	105	145	17.2521
UCACCAGCGGUUUGUGGAACUCCCGCCCGGCUCGGGAAUG	chr10:93811891-93812112(+)$1	221	124	164	13.1316
CAAGUCUGUACAAUUUUAAAAAAAGGUUGAAGGAGUGGUU	chr3:50137863-50138143(+)$1	280	216	256	15.6757
CGCCGGGGCCCAUGCCAGGGCAGGCGAGGCCAAGGGCCAG	chr19:46996750-46996975(-)$1	225	46	86	13.8188
UUUUCAGGGUGUUGGUCGAUUAGGACACAUUCUCGAAUAU	chr7:23213664-23213889(+)$1	225	96	136	15.8565

#DB
(.((((....((((((......))))))....))).).))	chr1:1474980-1475204(-)$1	1	25	65	13.5604
.((((.((((((..(.(.....).)..)))))).).))).	chr7:100334483-100334707(+)$1	1	21	61	15.9734
((.((((((((...(((.....)))...))))))))....	chr19:4697538-4697761(-)$1	1	51	91	14.6132
))(((.((((..((.(((....)))...))..))))...)	chr3:47037132-47037356(-)$1	1	21	61	11.5448
...(((((((....(((.....))))))))))...).)))	chr3:12632357-12632579(+)$1	1	86	126	17.8770
((((..((.((((((((.....))).)).))).)))))))	chr16:726159-726382(-)$1	1	107	147	14.8473
((((.((..(((..((((....).)))..)))...)).))	chr12:78513279-78513503(-)$1	1	70	110	12.6477
(....((((((.(.(((.....))).))))))))).)).)	chr16:774397-774621(+)$1	1	69	109	15.0898
....((.((((..((((.....)))).)))).))))))).	chr6:3118958-3119179(-)$1	1	155	195	12.6984
(.((((((((....(((.....)))...))).))))).).	chr9:990423-990648(+)$1	1	14	54	18.0068
(.((...(.(((((((((...))).)))))).)...)).)	chr19:36003912-36004135(+)$1	1	68	108	12.1987
..((((.....((.(((......))).))))))..)))))	chr6:46976720-46976941(-)$1	1	116	156	13.5132
(.((((((....(((((.....)).)))...)))))).))	chr15:44581237-44581459(-)$1	1	22	62	15.1272
((.(((((((.((.(((.....))).)).))))))).)).	chr7:27204778-27205001(-)$1	1	27	67	15.6793
...((.....((..(((......))).)).))....))).	chr12:14840805-14841026(+)$1	1	144	184	14.6557
((((.(((....(((((.....)))))..)))))))))).	chr9:35076604-35076826(-)$1	1	153	193	13.0984
(..(((((..(((.(((......))).)))...)))))..	chr10:15138543-15138764(-)$1	1	152	192	16.2612
.((...(((.((.((((.....)))).)).)))...))))	chr14:65009121-65009344(-)$1	1	99	139	14.5019
((.(((((((....(((.....)))....))))))).(((	chr16:71109762-71109997(-)$1	1	114	154	14.3783
(((((...(((((((((......)))))))))...)))))	chr1:33480077-33480299(-)$1	1	17	57	14.4729
.((((((...(((((.(......).)))))...)))))).	chr10:17243513-17243737(-)$1	1	72	112	13.1580
((((.(...(((..(((......))))))...)))))).(	chr10:105362440-105362667(+)$1	1	60	100	15.4364
((.(...(((.((.(((.....))))))))...).)).))	chr19:14073694-14073918(-)$1	1	105	145	16.4694
..((....(((((((......)))))))....))..))))	chr16:58616940-58617163(+)$1	1	14	54	12.7399
(((((((..((((...(.....)....))))..)))))).	chr17:3526582-3526808(+)$1	1	60	100	14.6192
((...(((((((...((.....))...)))))))...)))	chr16:31504898-31505122(-)$1	1	161	201	17.7845
.((((.((((((..(((......)))..))).))).))))	chr11:20940727-20940950(+)$1	1	84	124	15.3708
(((((.(.((((..((((...))))..))...))).))))	chr12:440992-441216(+)$1	1	166	206	11.9558
.(((.(.(((((.((((.....))))))))).).)))..)	chr1:160302156-160302379(+)$1	1	148	188	13.3679
.((((((((.((..(((......))).)).))))))...)	chr1:52981491-52981715(+)$1	1	139	179	14.5078
((((((((.(((.(.((.....)))))).)))).))))))	chr4:129783061-129783286(+)$1	1	78	118	13.4268
(((.(.((((((((((......))).)))))))).))).(	chr17:71390268-71390492(+)$1	1	119	159	14.6537
.(((.(((((((...((.....))...)))))))...)))	chr14:59113165-59113386(-)$1	1	38	78	17.7540
(((((((((((((((((.....))))....))))))))))	chr16:88876160-88876383(+)$1	1	112	152	16.1030
((((..(((((((.(......).))))))))))).)))..	chr8:11412795-11413016(+)$1	1	20	60	12.5913
(((((..(((....(((.....)))...)))..))))).)	chr19:42132209-42132430(+)$1	1	56	96	17.8409
....((((((((((.((......))..))).)))))))..	chr6:131931174-131931395(+)$1	1	95	135	14.9660
((((((((((((...(......)...).))))))))))))	chr4:144468479-144468709(+)$1	1	58	98	16.6502
..(((((.(.(((((((.....))))))).).)))))..)	chr2:33809976-33810198(-)$1	1	145	185	14.6795
(((.(((((.(((.(((.....))).))).))))).))))	chr12:6496925-6497147(-)$1	1	23	63	15.7439
(((...(((.(((..((......))..))).)))...)))	chr17:27277109-27277330(-)$1	1	75	115	15.8454
(..(((.((((...(((.....)))...)))))))...))	chr4:158224718-158224940(-)$1	1	165	205	17.7286
(((((((((((((.(((......))))))))))...))))	chr11:3659863-3660085(+)$1	1	30	70	15.9292
(.((..(((((((((.(.....).))))))..)))..)).	chr1:245530530-245530752(+)$1	1	89	129	13.5922
((((((((((.((((((.....)))))).)))))))))))	chr22:25423944-25424169(-)$1	1	64	104	15.2073
((.(((((..(((...(((...)))..)))..))))).))	chr1:40318335-40318558(-)$1	1	97	137	13.0852
(...(((..(....(((.....)))....)..))).))))	chr8:39782190-39782415(+)$1	1	62	102	18.2060
((((((.(((...(((......)))...)))...))))))	chr5:146257553-146257784(-)$1	1	53	93	16.8127
((((..((..((..(((.....)))...))..))..))))	chr3:48463445-48463673(+)$1	1	105	145	17.2521
((.(((((.(...((((.....)))).).))).)))))..	chr10:93811891-93812112(+)$1	1	124	164	13.1316
(((((((...(((((((.....)))))))..)))....))	chr3:50137863-50138143(+)$1	1	216	256	15.6757
((((..(((((..(((..(.....)..)))...))))).)	chr19:46996750-46996975(-)$1	1	46	86	13.8188
(.((((((((((..(((......)))))))))).))).))	chr7:23213664-23213889(+)$1	1	96	136	15.8565

#PSSM
c : 0.18	f : 0.13	b : 0.11	# : 0.09	e : 0.09	" : 0.07	d : 0.07	[ : 0.05	! : 0.03	g : 0.03	= : 0.03	a : 0.01	E : 0.01	i : 0.01	
c : 0.16	f : 0.16	[ : 0.11	# : 0.09	b : 0.09	e : 0.07	! : 0.07	d : 0.05	g : 0.03	" : 0.03	= : 0.03	E : 0.01	i : 0.01	
f : 0.18	c : 0.13	e : 0.11	[ : 0.09	# : 0.09	b : 0.09	d : 0.05	= : 0.05	g : 0.03	! : 0.03	" : 0.03	a : 0.01	: : 0.01	i : 0.01	
f : 0.18	e : 0.15	c : 0.13	g : 0.09	b : 0.09	" : 0.07	# : 0.05	d : 0.05	= : 0.05	[ : 0.03	h : 0.01	a : 0.01	i : 0.01	
e : 0.13	f : 0.13	c : 0.11	! : 0.09	[ : 0.09	" : 0.09	g : 0.07	b : 0.05	d : 0.05	= : 0.05	a : 0.03	# : 0.03	h : 0.01	
g : 0.13	f : 0.13	c : 0.11	! : 0.11	[ : 0.09	e : 0.09	" : 0.09	= : 0.05	b : 0.03	d : 0.03	a : 0.03	h : 0.01	$ : 0.01	# : 0.01	
g : 0.18	c : 0.15	f : 0.11	e : 0.11	[ : 0.07	" : 0.07	b : 0.05	= : 0.05	# : 0.03	d : 0.03	$ : 0.03	h : 0.01	a : 0.01	! : 0.01	
g : 0.18	c : 0.18	e : 0.09	f : 0.07	d : 0.07	" : 0.07	! : 0.05	= : 0.05	# : 0.03	b : 0.03	$ : 0.03	[ : 0.03	h : 0.01	a : 0.01	
g : 0.20	c : 0.15	! : 0.11	[ : 0.07	# : 0.05	f : 0.05	d : 0.05	" : 0.05	e : 0.05	= : 0.05	$ : 0.03	h : 0.01	i : 0.01	b : 0.01	a : 0.01	
g : 0.20	c : 0.16	[ : 0.09	f : 0.07	d : 0.07	# : 0.05	! : 0.05	= : 0.05	$ : 0.03	" : 0.03	e : 0.03	a : 0.03	h : 0.01	i : 0.01	b : 0.01	
g : 0.18	c : 0.16	# : 0.13	f : 0.09	b : 0.09	d : 0.05	[ : 0.05	e : 0.05	= : 0.03	" : 0.03	h : 0.01	! : 0.01	$ : 0.01	i : 0.01	
c : 0.18	g : 0.16	b : 0.15	# : 0.13	f : 0.09	" : 0.07	! : 0.05	e : 0.03	[ : 0.01	i : 0.01	d : 0.01	= : 0.01	a : 0.01	
! : 0.20	" : 0.13	c : 0.11	g : 0.11	b : 0.09	# : 0.09	f : 0.07	[ : 0.05	e : 0.03	a : 0.01	i : 0.01	d : 0.01	= : 0.01	
! : 0.18	[ : 0.15	" : 0.13	# : 0.09	d : 0.09	c : 0.09	f : 0.07	g : 0.05	b : 0.03	e : 0.03	i : 0.01	a : 0.01	
c : 0.49	d : 0.11	" : 0.09	f : 0.07	[ : 0.05	g : 0.05	a : 0.03	e : 0.03	i : 0.01	! : 0.01	
c : 0.50	d : 0.11	b : 0.11	[ : 0.05	f : 0.03	o : 0.03	" : 0.03	g : 0.03	e : 0.01	i : 0.01	a : 0.01	
c : 0.47	o : 0.11	d : 0.11	b : 0.11	a : 0.07	g : 0.03	e : 0.01	i : 0.01	f : 0.01	! : 0.01	
n : 0.54	o : 0.33	c : 0.05	a : 0.01	d : 0.01	! : 0.01	
n : 0.54	o : 0.33	m : 0.03	l : 0.03	c : 0.01	a : 0.01	
n : 0.56	o : 0.33	l : 0.05	m : 0.03	
n : 0.56	o : 0.33	l : 0.05	m : 0.03	
n : 0.56	o : 0.30	m : 0.03	c : 0.01	g : 0.01	d : 0.01	a : 0.01	l : 0.01	
c : 0.33	o : 0.22	d : 0.11	a : 0.09	b : 0.07	g : 0.05	f : 0.03	e : 0.01	] : 0.01	n : 0.01	
c : 0.49	d : 0.11	b : 0.11	g : 0.07	] : 0.05	f : 0.03	e : 0.01	i : 0.01	a : 0.01	4 : 0.01	3 : 0.01	n : 0.01	
c : 0.49	d : 0.11	g : 0.07	f : 0.05	a : 0.05	] : 0.05	3 : 0.05	b : 0.03	e : 0.01	i : 0.01	4 : 0.01	
c : 0.20	3 : 0.18	2 : 0.11	g : 0.09	] : 0.09	d : 0.09	f : 0.07	4 : 0.05	e : 0.03	i : 0.01	b : 0.01	
3 : 0.16	g : 0.15	2 : 0.13	] : 0.13	c : 0.09	f : 0.07	4 : 0.07	b : 0.05	e : 0.05	a : 0.03	i : 0.01	
g : 0.18	c : 0.18	3 : 0.13	b : 0.13	f : 0.11	2 : 0.05	4 : 0.05	d : 0.03	e : 0.03	i : 0.01	] : 0.01	a : 0.01	
c : 0.22	g : 0.16	b : 0.13	4 : 0.09	] : 0.09	f : 0.07	d : 0.05	2 : 0.03	e : 0.03	h : 0.01	3 : 0.01	i : 0.01	= : 0.01	
c : 0.26	g : 0.16	d : 0.09	] : 0.09	f : 0.07	4 : 0.05	3 : 0.05	b : 0.03	e : 0.03	= : 0.03	h : 0.01	i : 0.01	a : 0.01	2 : 0.01	
c : 0.16	g : 0.15	3 : 0.13	2 : 0.11	d : 0.11	f : 0.07	= : 0.05	4 : 0.03	e : 0.03	] : 0.03	h : 0.01	b : 0.01	i : 0.01	a : 0.01	
g : 0.16	2 : 0.13	c : 0.13	3 : 0.13	] : 0.11	f : 0.07	d : 0.07	= : 0.05	4 : 0.03	h : 0.01	b : 0.01	i : 0.01	e : 0.01	
g : 0.16	c : 0.15	3 : 0.15	f : 0.07	d : 0.07	b : 0.07	e : 0.07	a : 0.05	= : 0.05	] : 0.03	2 : 0.03	h : 0.01	4 : 0.01	
e : 0.15	c : 0.13	3 : 0.13	b : 0.13	g : 0.11	] : 0.07	f : 0.07	= : 0.05	d : 0.03	a : 0.03	h : 0.01	2 : 0.01	4 : 0.01	
3 : 0.16	e : 0.15	c : 0.13	f : 0.11	g : 0.07	a : 0.05	b : 0.05	2 : 0.05	] : 0.05	= : 0.05	4 : 0.03	h : 0.01	d : 0.01	
e : 0.15	] : 0.13	f : 0.13	3 : 0.13	c : 0.09	= : 0.07	g : 0.07	2 : 0.05	d : 0.03	b : 0.03	4 : 0.03	h : 0.01	a : 0.01	
f : 0.18	e : 0.16	c : 0.13	3 : 0.11	b : 0.09	= : 0.07	g : 0.05	] : 0.03	d : 0.03	a : 0.01	> : 0.01	: : 0.01	2 : 0.01	4 : 0.01	
c : 0.16	f : 0.16	] : 0.13	e : 0.11	b : 0.09	= : 0.07	3 : 0.05	d : 0.05	g : 0.05	2 : 0.03	> : 0.01	4 : 0.01	
f : 0.18	c : 0.16	d : 0.07	] : 0.07	= : 0.07	b : 0.07	3 : 0.05	e : 0.05	: : 0.05	g : 0.03	4 : 0.03	2 : 0.03	> : 0.01	a : 0.01	i : 0.01	
c : 0.18	f : 0.18	b : 0.11	] : 0.09	e : 0.07	d : 0.05	g : 0.05	3 : 0.03	= : 0.03	2 : 0.03	: : 0.03	4 : 0.03	> : 0.01	i : 0.01	

#score	792.708209870426
#seq	53
#width	40
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m3_run2.txt

#BEAR
ff[ddddoooooodddd333	chr22:50277276-50277542(+)$1	266	84	104	13.9078
ddd!!cccooooooccc22d	chr19:804047-804306(+)$1	259	155	175	10.0135
)a[ddddoooooodddd]a5	chr20:49508135-49508392(-)$1	257	189	209	12.7516
bbeeeeeooooooeeeee]b	chr2:96962274-96962529(-)$1	255	217	237	10.9885
"""ddddoooooodddd333	chr17:79803677-79803916(-)$1	239	132	152	14.5005
cc[ddddooooooddddccc	chr1:160309615-160309848(-)$1	233	82	102	13.1524
d[a!!cccooooooccc22a	chr6:26234522-26234776(-)$1	254	23	43	10.5722
cc[ddddoooooodddd]cc	chr9:139838340-139838620(-)$1	280	178	198	13.5513
ccc[cccooooooccc]ccc	chr20:18448061-18448306(+)$1	245	209	229	10.7989
####ddddnnnnndddd444	chr12:7044766-7045062(+)$1	296	263	283	9.4953
ee[ddddoooooodddd]ee	chr1:224379963-224380229(+)$1	266	137	157	13.2989
%%%ddddoooooodddd666	chr19:884830-885073(-)$1	243	143	163	11.1431
dd[ddddoooooodddd]dd	chr12:99059269-99059507(+)$1	238	134	154	13.0430
:ddddcccooooooccc22d	chr12:56214044-56214319(+)$1	275	51	71	9.7098
:::ddddooooooddddfff	chr7:73011720-73011994(-)$1	274	141	161	10.1334
!eeeeeooooooeeeee22b	chr18:12657727-12657968(-)$1	241	187	207	10.1468
cccddddoooooodddd]cc	chr2:24475211-24475444(-)$1	233	100	120	13.2448
eee!!cccooooooccc22e	chr2:61723974-61724238(-)$1	264	125	145	10.3577
cc[ddddooooooddddccc	chr12:56994866-56995105(-)$1	239	147	167	13.1524
eeeee[aooooooa]eeeee	chr13:24460482-24460728(-)$1	246	167	187	10.6503
eee!!cccooooooccc22e	chr19:39370177-39370422(-)$1	245	80	100	10.3577
dddddddoooooodddd]dd	chr1:203768450-203768688(+)$1	238	193	213	12.6653
c!!ddddoooooodddd22c	chr1:41483489-41483777(+)$1	288	8	28	14.0530
eeee[bboooooobbeeeee	chr1:54518659-54518956(-)$1	297	30	50	9.5665
!!a[ddddnnnnnddddacc	chr1:877839-878128(+)$1	289	223	243	8.8426
"""ddddooooooddddddd	chr19:46295568-46295828(-)$1	260	190	210	13.1025
%%%ddddoooooodddd666	chr7:135358782-135359040(+)$1	258	148	168	11.1431
gggggggooooooggggggg	chr20:62694490-62694805(+)$1	315	110	130	10.1064
eeeee[aooooooaeeeee5	chr19:55738610-55738842(-)$1	232	173	193	10.4254
gggggggooooooggggggg	chr1:2160702-2160982(+)$1	280	76	96	10.1064
"""ddddoooooodddd444	chr1:35654716-35654979(-)$1	263	17	37	14.2428
f!!ddddooooooddddfff	chr10:102763571-102763840(+)$1	269	188	208	13.0048
!!cccddddmmmmdddd22c	chr15:50763853-50764089(+)$1	236	124	144	7.8227
cc!!ddddnnnnndddd444	chr8:30401910-30402161(+)$1	251	226	246	9.4732
b[eeeeeooooooeeeee33	chr11:836150-836366(+)$1	216	8	28	11.9762
ee[ddddoooooodddd]ee	chr12:49523200-49523482(-)$1	282	215	235	13.2989
e[eeeeeooooooeeeee]e	chr8:145734793-145735104(+)$1	311	16	36	11.7123
cceeeeeooooooeeeee]c	chr1:27023716-27023940(+)$1	224	132	152	11.7025
$$$ddddooooooddddfff	chr5:126161605-126161847(+)$1	242	86	106	12.6829
ccc[cccooooooccc]ccc	chr3:49051959-49052248(+)$1	289	142	162	10.7989
a[eeeeeooooooeeeee]a	chr1:116946466-116946697(+)$1	231	111	131	11.8727
""eeeeeooooooeeeeeee	chr15:70347448-70347737(-)$1	289	211	231	11.6807
[bbddddoooooodddd]bb	chr1:151664906-151665155(+)$1	249	203	223	12.1986
bbeeeeeooooooeeeee44	chr19:50985559-50985905(+)$1	346	239	259	11.4760
eee[cccooooooccc]eee	chr16:30785209-30785481(+)$1	272	114	134	10.7153
fffddddoooooodddd22f	chr11:64853896-64854140(+)$1	244	58	78	12.9974

#otherMatches

#Seq PSSM
UGAUAAAAUAAAGUUUAAAA	chr22:50277276-50277542(+)$1	266	84	104	13.9078
AACCAGGUACCUGAGCCGCG	chr19:804047-804306(+)$1	259	155	175	10.0135
GGCUACCAUGCAAGGUGACA	chr20:49508135-49508392(-)$1	257	189	209	12.7516
CGCUCCUUGGUGCAGGAGAU	chr2:96962274-96962529(-)$1	255	217	237	10.9885
GGCUUUUGAUGAGAAAAAAA	chr17:79803677-79803916(-)$1	239	132	152	14.5005
UGCGAGGCAUUGACUUCCAU	chr1:160309615-160309848(-)$1	233	82	102	13.1524
AAGAAGCCCAAGAAGGUGGC	chr6:26234522-26234776(-)$1	254	23	43	10.5722
GUGUGCCGCCAAUGGCAGGC	chr9:139838340-139838620(-)$1	280	178	198	13.5513
GGACCCCUUCUCCGGGAUCC	chr20:18448061-18448306(+)$1	245	209	229	10.7989
CCCCACAUCUCGAAUGUUCC	chr12:7044766-7045062(+)$1	296	263	283	9.4953
AUGAUUUUGUGAUGGAUGAU	chr1:224379963-224380229(+)$1	266	137	157	13.2989
AACAUCUUCCAGCAGAUCUC	chr19:884830-885073(-)$1	243	143	163	11.1431
ACAGCUUCAGAAUAAGCAGU	chr12:99059269-99059507(+)$1	238	134	154	13.0430
AACACAGCCUCAUUGCUAAG	chr12:56214044-56214319(+)$1	275	51	71	9.7098
CCACUGCUUUGCUGCAGGAA	chr7:73011720-73011994(-)$1	274	141	161	10.1334
gccggcggcgcggccggggg	chr18:12657727-12657968(-)$1	241	187	207	10.1468
CUGGAGAUUUGACUUUCACA	chr2:24475211-24475444(-)$1	233	100	120	13.2448
CUCUCUGAAGUGCCUCACUG	chr2:61723974-61724238(-)$1	264	125	145	10.3577
UGACCUUGGAGUGAGGGCAU	chr12:56994866-56995105(-)$1	239	147	167	13.1524
GUGGACCGUGCAUGUUCCAC	chr13:24460482-24460728(-)$1	246	167	187	10.6503
UCGGACCCUUUCCUGGGGAU	chr19:39370177-39370422(-)$1	245	80	100	10.3577
UUCACCAUAGUCUUGGUAGA	chr1:203768450-203768688(+)$1	238	193	213	12.6653
CGCCCUCGCUGUUGAGGAAG	chr1:41483489-41483777(+)$1	288	8	28	14.0530
GAGGAGGAGGAAACCCUUCC	chr1:54518659-54518956(-)$1	297	30	50	9.5665
CUGCUGGUGCUGAACCACGG	chr1:877839-878128(+)$1	289	223	243	8.8426
UCUGCUUCAACUUGGGCCGU	chr19:46295568-46295828(-)$1	260	190	210	13.1025
CCUUCAGGAUAUACUGAUUC	chr7:135358782-135359040(+)$1	258	148	168	11.1431
GGCCGGGGUCCUGCCCGGCU	chr20:62694490-62694805(+)$1	315	110	130	10.1064
CUGGGACACCUUCGCCCAGC	chr19:55738610-55738842(-)$1	232	173	193	10.4254
GGCGGCGCCUACCCGCCGCC	chr1:2160702-2160982(+)$1	280	76	96	10.1064
UUUUGCCCAGCAUGGCACGU	chr1:35654716-35654979(-)$1	263	17	37	14.2428
CUGACAGCAGCUCCUGUGGG	chr10:102763571-102763840(+)$1	269	188	208	13.0048
GAUGCACUUUUCAAGGUUUG	chr15:50763853-50764089(+)$1	236	124	144	7.8227
CCCAGGUAAUUGAUACCCAU	chr8:30401910-30402161(+)$1	251	226	246	9.4732
GAGGGGUCGCCUUGccccca	chr11:836150-836366(+)$1	216	8	28	11.9762
UAACCUGAGAUCCCAGGAUG	chr12:49523200-49523482(-)$1	282	215	235	13.2989
GCCGGCGGCCUCUCGCUGAC	chr8:145734793-145735104(+)$1	311	16	36	11.7123
GGGCCCCAGGACGGGGGCGC	chr1:27023716-27023940(+)$1	224	132	152	11.7025
AACGCUGGUGUCACAGCCAG	chr5:126161605-126161847(+)$1	242	86	106	12.6829
CCAUGACUCCACUGUCCUGG	chr3:49051959-49052248(+)$1	289	142	162	10.7989
CAUCAGGCGACGCCCUGGCG	chr1:116946466-116946697(+)$1	231	111	131	11.8727
CAGCCACGGGGAGGUGGUGU	chr15:70347448-70347737(-)$1	289	211	231	11.6807
UGCUCACUUGCUUGUGACGU	chr1:151664906-151665155(+)$1	249	203	223	12.1986
UCCUGGCCACUAUGCCAGUU	chr19:50985559-50985905(+)$1	346	239	259	11.4760
CGUUUUCUGCUUCGAGUGCG	chr16:30785209-30785481(+)$1	272	114	134	10.7153
UAUCAGUGCCCCAGCUGCAA	chr11:64853896-64854140(+)$1	244	58	78	12.9974

#DB
((.((((......))))...	chr22:50277276-50277542(+)$1	1	84	104	13.9078
(((..(((......)))..)	chr19:804047-804306(+)$1	1	155	175	10.0135
.(.((((......)))).).	chr20:49508135-49508392(-)$1	1	189	209	12.7516
(((((((......))))).)	chr2:96962274-96962529(-)$1	1	217	237	10.9885
...((((......))))...	chr17:79803677-79803916(-)$1	1	132	152	14.5005
((.((((......)))))))	chr1:160309615-160309848(-)$1	1	82	102	13.1524
(.(..(((......)))..)	chr6:26234522-26234776(-)$1	1	23	43	10.5722
((.((((......)))).))	chr9:139838340-139838620(-)$1	1	178	198	13.5513
(((.(((......))).)))	chr20:18448061-18448306(+)$1	1	209	229	10.7989
....((((.....))))...	chr12:7044766-7045062(+)$1	1	263	283	9.4953
((.((((......)))).))	chr1:224379963-224380229(+)$1	1	137	157	13.2989
...((((......))))...	chr19:884830-885073(-)$1	1	143	163	11.1431
((.((((......)))).))	chr12:99059269-99059507(+)$1	1	134	154	13.0430
.(((((((......)))..)	chr12:56214044-56214319(+)$1	1	51	71	9.7098
...((((......))))(((	chr7:73011720-73011994(-)$1	1	141	161	10.1334
.(((((......)))))..)	chr18:12657727-12657968(-)$1	1	187	207	10.1468
(((((((......)))).))	chr2:24475211-24475444(-)$1	1	100	120	13.2448
(((..(((......)))..)	chr2:61723974-61724238(-)$1	1	125	145	10.3577
((.((((......)))))))	chr12:56994866-56995105(-)$1	1	147	167	13.1524
(((((.(......).)))))	chr13:24460482-24460728(-)$1	1	167	187	10.6503
(((..(((......)))..)	chr19:39370177-39370422(-)$1	1	80	100	10.3577
(((((((......)))).))	chr1:203768450-203768688(+)$1	1	193	213	12.6653
(..((((......))))..)	chr1:41483489-41483777(+)$1	1	8	28	14.0530
((((.((......)))))))	chr1:54518659-54518956(-)$1	1	30	50	9.5665
..(.((((.....)))))))	chr1:877839-878128(+)$1	1	223	243	8.8426
...((((......)))))))	chr19:46295568-46295828(-)$1	1	190	210	13.1025
...((((......))))...	chr7:135358782-135359040(+)$1	1	148	168	11.1431
(((((((......)))))))	chr20:62694490-62694805(+)$1	1	110	130	10.1064
(((((.(......)))))).	chr19:55738610-55738842(-)$1	1	173	193	10.4254
(((((((......)))))))	chr1:2160702-2160982(+)$1	1	76	96	10.1064
...((((......))))...	chr1:35654716-35654979(-)$1	1	17	37	14.2428
(..((((......)))))))	chr10:102763571-102763840(+)$1	1	188	208	13.0048
..(((((((....))))..)	chr15:50763853-50764089(+)$1	1	124	144	7.8227
((..((((.....))))...	chr8:30401910-30402161(+)$1	1	226	246	9.4732
(.(((((......)))))..	chr11:836150-836366(+)$1	1	8	28	11.9762
((.((((......)))).))	chr12:49523200-49523482(-)$1	1	215	235	13.2989
(.(((((......))))).)	chr8:145734793-145735104(+)$1	1	16	36	11.7123
(((((((......))))).)	chr1:27023716-27023940(+)$1	1	132	152	11.7025
...((((......)))))))	chr5:126161605-126161847(+)$1	1	86	106	12.6829
(((.(((......))).)))	chr3:49051959-49052248(+)$1	1	142	162	10.7989
(.(((((......))))).)	chr1:116946466-116946697(+)$1	1	111	131	11.8727
..(((((......)))))))	chr15:70347448-70347737(-)$1	1	211	231	11.6807
.((((((......)))).))	chr1:151664906-151665155(+)$1	1	203	223	12.1986
(((((((......)))))..	chr19:50985559-50985905(+)$1	1	239	259	11.4760
(((.(((......))).)))	chr16:30785209-30785481(+)$1	1	114	134	10.7153
(((((((......))))..)	chr11:64853896-64854140(+)$1	1	58	78	12.9974

#PSSM
c : 0.19	e : 0.19	d : 0.08	" : 0.08	f : 0.06	b : 0.06	! : 0.06	% : 0.04	: : 0.04	g : 0.04	) : 0.02	# : 0.02	$ : 0.02	a : 0.02	[ : 0.02	
e : 0.19	c : 0.17	d : 0.08	" : 0.08	[ : 0.08	! : 0.08	b : 0.06	f : 0.04	% : 0.04	g : 0.04	a : 0.02	# : 0.02	: : 0.02	$ : 0.02	
e : 0.30	[ : 0.17	c : 0.08	d : 0.06	" : 0.06	! : 0.06	a : 0.04	% : 0.04	g : 0.04	# : 0.02	: : 0.02	$ : 0.02	b : 0.02	f : 0.02	
d : 0.47	e : 0.23	! : 0.10	[ : 0.08	g : 0.04	# : 0.02	c : 0.02	
d : 0.54	e : 0.21	! : 0.08	c : 0.08	g : 0.04	[ : 0.02	
d : 0.54	c : 0.17	e : 0.17	[ : 0.04	g : 0.04	b : 0.02	
d : 0.54	c : 0.17	e : 0.15	a : 0.04	g : 0.04	o : 0.02	b : 0.02	
o : 0.80	c : 0.10	d : 0.08	
o : 0.91	n : 0.06	d : 0.02	
o : 0.91	n : 0.06	m : 0.02	
o : 0.91	n : 0.06	m : 0.02	
o : 0.91	n : 0.06	m : 0.02	
o : 0.89	n : 0.06	e : 0.02	m : 0.02	
d : 0.54	e : 0.17	o : 0.10	c : 0.06	a : 0.04	g : 0.04	b : 0.02	
d : 0.54	e : 0.19	c : 0.17	g : 0.04	] : 0.02	b : 0.02	
d : 0.54	e : 0.23	c : 0.17	g : 0.04	
d : 0.54	e : 0.23	c : 0.10	] : 0.06	g : 0.04	
e : 0.23	2 : 0.19	] : 0.17	c : 0.08	4 : 0.06	f : 0.06	3 : 0.04	6 : 0.04	g : 0.04	a : 0.02	d : 0.02	
2 : 0.19	c : 0.15	e : 0.15	] : 0.08	4 : 0.08	3 : 0.06	d : 0.06	f : 0.06	6 : 0.04	g : 0.04	a : 0.02	b : 0.02	
c : 0.21	e : 0.19	d : 0.10	4 : 0.08	f : 0.08	3 : 0.06	b : 0.06	5 : 0.04	a : 0.04	6 : 0.04	g : 0.04	

#score	532.6393079423734
#seq	46
#width	20
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012a_hg19_CDS_m2_run2.txt

#BEAR
###bb####ccc[cccnnnnncccccc333bb444	chr12:46320551-46320791(-)$1	240	80	115	11.4768
::dddd"""gggggggooooooggggggg4444dd	chr2:230663897-230664145(-)$1	248	132	167	10.6882
b[hhhhhhhh[eeeeeooooooeeeee]hhhhhhh	chr1:8926359-8926659(-)$1	300	27	62	9.9111
ccc[bb[a[ccc!!ddddllldddd333ccc]a]b	chr1:113197118-113197368(+)$1	250	113	148	12.0654
========!!bb[cccnnnnnccc]bb22======	chr17:80049348-80049611(-)$1	263	133	168	11.6540
iiiiiii[ccc[ddddoooooodddd]ccc333ii	chr3:142166622-142166866(-)$1	244	40	75	13.5205
[ccc[ccc!!ccc[bboooooobb]ccc]ccc]cc	chr21:27462175-27462464(-)$1	289	63	98	12.8705
eeeeffffff!!eeeeellleeeee333ffffff]	chr10:103557642-103557914(-)$1	272	109	144	10.6508
ffff[eeeee[ccc[aooooooaccc]eeeeefff	chr2:173431509-173431765(+)$1	256	67	102	12.7689
d[eeeee[dddd[a[aooooooa]a]dddd]eeee	chr1:161332033-161332312(+)$1	279	172	207	11.9571
$$$dddd####eeeeeooooooeeeee4444dddd	chr12:56530916-56531188(+)$1	272	222	257	11.4841
##eeeee[a[ffffffooooooffffff]a]eeee	chrM:3573-3815(-)$1	242	102	137	11.3761
ggggg!!dddd!!cccoooooocccdddd]ggggg	chr14:103807234-103807485(+)$1	251	41	76	14.0790
fffffggggggg[cccccclllccc]ccc]ggggg	chr13:32709177-32709429(+)$1	252	205	240	12.0975
iiiii"""bb[arrrrrrrrra]bb333iiiiiii	chr19:1106626-1106880(+)$1	254	36	71	10.7363
gccc[ggggggg!!cccnnnnnccc22ggggggg3	chr11:64074836-64075090(+)$1	254	169	204	13.3501
ccc[ffffff"""cccooooooccc333ffffff]	chr5:179250824-179251089(+)$1	265	10	45	16.2011
d[cccccc!!a"""ddddllldddd333a22ccc]	chr19:13245941-13246214(+)$1	273	93	128	12.7759
:ccc!!bb[gggggggoooooogggggggbb22cc	chr12:56677469-56677736(-)$1	267	189	224	11.4653
ee[cccdddd"""cccooooooccc333dddd]cc	chr6:26055875-26056141(-)$1	266	59	94	15.7822
[ddddbb!!dddd!!cccmmmmccc333dddd22b	chr11:67953218-67953467(-)$1	249	168	203	10.3625
eeee####ccc!!cccooooooccc22ccc55555	chr1:120572432-120572697(-)$1	265	205	240	11.3030
fff!!dddd!!cccddddllldddd4444ccc22d	chr7:44839228-44839479(+)$1	251	74	109	11.0835
fffffggggggg!!cccmmmmccc4444ggggggg	chr6:32726763-32727004(-)$1	241	77	112	12.3188
dd####==========oooooo==========444	chr16:24834689-24835002(+)$1	313	169	204	14.3621
ccc[a[eeeee!!cccooooooccc22eeeeeacc	chr6:31324523-31324796(-)$1	273	173	208	14.6775
edddd[a!!eeeee[aooooooaeeeee22a]ddd	chr1:89430408-89430650(-)$1	242	137	172	11.0613
ddd[cccbb[cccrrrrrrrrrccc333bb]cccd	chr19:46341707-46341946(-)$1	239	196	231	11.1210
$$$$$ggggggg!!cccnnnnnccc]ggggggg66	chr19:37241081-37241353(-)$1	272	226	261	10.9680
###ffffff[eeeeeooooooeeeee22ffffff3	chr18:48452098-48452340(+)$1	242	172	207	11.5435
c::ffffff[bb[cccooooooccc]bb22fffff	chr19:23158146-23158485(-)$1	339	181	216	11.1403
dddd!!==========oooooo==========22d	chr17:40844411-40844677(+)$1	266	35	70	14.0366
ccc!!a[ccc[eeeeeooooooeeeee4444ccca	chr6:41755409-41755675(+)$1	266	155	190	12.9891
ggggggeeeee####ccclllccc4444eeeee]g	chr16:30078666-30078981(+)$1	315	221	256	12.2149
eeee[dddd"""eeeeellleeeee333ddddeee	chr17:42429752-42429995(+)$1	243	187	222	10.3774
FFFF:::ccc"""cccooooooccc333cccdddd	chr6:27834528-27834784(-)$1	256	45	80	11.4640
eeeeggggggg[cccrrrrrrrrrccc]ggggggg	chr7:26236110-26236374(-)$1	264	188	223	10.9701
iiiiiiidddd!!ccclllccc]dddd]iiiiiii	chr16:58587616-58587858(-)$1	242	87	122	10.5641
iiiiiiiii####eeeeemmmmeeeee]iiiiiii	chr16:46711121-46711372(-)$1	251	128	163	10.6838
gggg!!ffffff[cccoooooocccffffff22gg	chr19:17515098-17515339(-)$1	241	7	42	13.4347
eeeggggggg####cccnnnnnccc]ggggggg::	chr5:31322847-31323063(+)$1	216	122	157	10.8834
dddaccc"""cccrrrrrrrrrccc333ccc]a44	chr5:76785226-76785491(-)$1	265	140	175	12.1607
&&&ffffff####cccooooooccc]ffffff22d	chr14:31597726-31597965(-)$1	239	39	74	12.9228
[bb"""ccc[a[bbddddllldddd333bb]a]cc	chr19:34856116-34856401(+)$1	285	95	130	11.1096
:eeeee[bb[ccca[cccmmmmccc333a]cccbb	chr20:35827351-35827611(+)$1	260	51	86	10.5211
]ccciiiiiiiiicccooooooccc333iiiiiii	chr1:87558138-87558377(+)$1	239	108	143	16.4148
FFFeeeee[gggggggooooooggggggg]eeeee	chr19:1010347-1010568(-)$1	221	41	76	11.2911
e!!eeeee!!bb[ccclllccc]bb4444eeeee4	chr6:31237978-31238360(-)$1	382	175	210	10.4849
=========####cccqqqqqqqqccc========	chr22:32789804-32790045(-)$1	241	101	136	10.7375
[ffffff%%%%%%cccooooooccc333ffffffb	chr12:32875390-32875655(+)$1	265	139	174	12.2602
ff!!dddddddd"""cccmmmmccc333dddd]dd	chr2:130951714-130951967(-)$1	253	154	189	11.0087
cc!!hhhhhhhh"""cccmmmmccc333hhhhhhh	chr5:68687589-68687845(+)$1	256	199	234	10.4807
cc[ffffff!!dddd!!aooooooa22dddd333f	chr10:75888781-75889061(-)$1	280	4	39	11.5025
!!ffffff"""bb!!cccmmmmccc22bb333fff	chr15:89811531-89811770(+)$1	239	65	100	11.0147
""cccccc[a!!ddddoooooodddd22a]ccc]c	chr3:101399837-101400120(-)$1	283	216	251	14.0374
c[ccc!!ggggggg!!ccclllccc22gggggggc	chr2:216209437-216209684(+)$1	247	106	141	12.2765
cffffffccc"""cccnnnnnccccccffffff""	chr19:10203226-10203471(+)$1	245	148	183	10.9548
[ccc[cccdddd[cccooooooccc]dddd]cccc	chr11:27406863-27407119(-)$1	256	50	85	13.9617
&&&ffffff####cccooooooccc4444ffffff	chrX:134930542-134930838(-)$1	296	153	188	14.1038

#otherMatches

#Seq PSSM
AGAGAAAGGAGAACCAGAAAGUGGUCUAGGUCCAG	chr12:46320551-46320791(-)$1	240	80	115	11.4768
AAGUAGACAAUCAAGGUAACCCCUUUGAUGAAACU	chr2:230663897-230664145(-)$1	248	132	167	10.6882
GACCAGAGGGGCUUACUGCCCUGUGGGGCUCUCUG	chr1:8926359-8926659(-)$1	300	27	62	9.9111
AAUCCUGUGACAGUGCUUUAAGAGCCUAUGUGAAA	chr1:113197118-113197368(+)$1	250	113	148	12.0654
AUGGGCGGCUGCAGGUGGUGGACCAGCCCCUGCCC	chr17:80049348-80049611(-)$1	263	133	168	11.6540
UUCGGUUUGGCCCUGACUGGGAUUAGUGUUGACGA	chr3:142166622-142166866(-)$1	244	40	75	13.5205
UGUGCUCUCCCAGGUCUACCCUGAACUGCAGAUCA	chr21:27462175-27462464(-)$1	289	63	98	12.8705
ACAUGUACUCCUAUGUUUGGGAUAUCAAGAGUAUA	chr10:103557642-103557914(-)$1	272	109	144	10.6508
ACACUAGAUGGCUAUGAAAAUGCUAGGCGUCUGUG	chr2:173431509-173431765(+)$1	256	67	102	12.7689
GGGCUGGCAGCCAUGUGAAGAAAGGAGGCUCCCAG	chr1:161332033-161332312(+)$1	279	172	207	11.9571
UAGCCAGUUUGGGACUGAGGUGAGUCUAUAUCUGG	chr12:56530916-56531188(+)$1	272	222	257	11.4841
CUGCUCGCAGUGCGCCGAUCAGGGCGUAGUUUGAG	chrM:3573-3815(-)$1	242	102	137	11.3761
GAAUAAAAUCAUUCCUCUUAACAGGUGGUGUAUUC	chr14:103807234-103807485(+)$1	251	41	76	14.0790
GGAAUCUGUUUGAGGAUCCUAAGGACUCCACAGAU	chr13:32709177-32709429(+)$1	252	205	240	12.0975
UGGGGCAGACCCGAAAAUCCAGCGUGCACCCCGCC	chr19:1106626-1106880(+)$1	254	36	71	10.7363
UGCCCUGCACCCUCUGGGUACACUGCUGGGUGCAA	chr11:64074836-64075090(+)$1	254	169	204	13.3501
GGCUCUCUUUACCCUUCCUGUAGAGAAAAAAGAGU	chr5:179250824-179251089(+)$1	265	10	45	16.2011
UGCAGAUGGAGAUCCCGAACUUCGGCAACAGCAUC	chr19:13245941-13246214(+)$1	273	93	128	12.7759
AAUCAUUGAGUUUGUGCAAAUACGCAAACCGUGGA	chr12:56677469-56677736(-)$1	267	189	224	11.4653
CUGUGAAGCCCAAGGCCGCUAAGCCCAAGGUUGUC	chr6:26055875-26056141(-)$1	266	59	94	15.7822
GUUUGGUUCUUGAUCCCUAUUUAGGUUUUCAAACA	chr11:67953218-67953467(-)$1	249	168	203	10.3625
AGAACACUGGACAAGAUUUGAUUCUACUCCUCUAU	chr1:120572432-120572697(-)$1	265	205	240	11.3030
UGGUGACUUCACACGCCAUAAUGGCACUGGUGGCA	chr7:44839228-44839479(+)$1	251	74	109	11.0835
UGUCUGUUACUGCCCUCAGUGGAGCCCACAGUGAC	chr6:32726763-32727004(-)$1	241	77	112	12.3188
UCUCUCGGGUCCAGCCAGAGCCGGCUGGGCUCCCU	chr16:24834689-24835002(+)$1	313	169	204	14.3621
GCGACGCCGCGAGUCCGAGAGAGGAGCCGCGGGCG	chr6:31324523-31324796(-)$1	273	173	208	14.6775
AAGUAAGUAUAUUAACAUUAUCGUAAUACCCAUAU	chr1:89430408-89430650(-)$1	242	137	172	11.0613
CUCUGCUGACGCCUGAUAAUGUGGCUAAUCUGGUG	chr19:46341707-46341946(-)$1	239	196	231	11.1210
GGAGAAUUCAUACUGGUGACAAACCUUAUGAAUGU	chr19:37241081-37241353(-)$1	272	226	261	10.9680
AUUAAUAAUCACaugaauugauauguauauuauuu	chr18:48452098-48452340(+)$1	242	172	207	11.5435
GAAUUCAUACUGGAGGAAAAACCCUACAAAUGUGA	chr19:23158146-23158485(-)$1	339	181	216	11.1403
GGGCAAGGAUCUAUGAAGGGUCUUGUAGGUCUGAG	chr17:40844411-40844677(+)$1	266	35	70	14.0366
UAACCGAGCCCGAGGAACUUGGUCCUUUUCUGGCC	chr6:41755409-41755675(+)$1	266	155	190	12.9891
UCAUCCUCUUCCAUGAGACACUCUACCAGAAGGCG	chr16:30078666-30078981(+)$1	315	221	256	12.2149
GUCAGUGCCAACCCCCAUCCUGGGGCUGGGUAUGG	chr17:42429752-42429995(+)$1	243	187	222	10.3774
CUGCCAAGCCCAAGGCAGUUAAGCCGAAGGCGGCA	chr6:27834528-27834784(-)$1	256	45	80	11.4640
GGAAGAGGAGGUAAUUUUAAUUCUGUUUCUUCUUU	chr7:26236110-26236374(-)$1	264	188	223	10.9701
UUGGCAGAUUGAAGGACUAUCCCCAGUAUUGUCAG	chr16:58587616-58587858(-)$1	242	87	122	10.5641
AUGGAGUGUAUUAUUCAGGUAGCUGGGAACAUUUC	chr16:46711121-46711372(-)$1	251	128	163	10.6838
UCCCCAGGACCUAGGGAGGAGGCCCAGGUCCCAGG	chr19:17515098-17515339(-)$1	241	7	42	13.4347
AGCCUUUGAUCAUUUCCAAAGAGGACAUCAGAGAU	chr5:31322847-31323063(+)$1	216	122	157	10.8834
ACACUGAACUGCUAGUACUGAAGGCUCAUCAUGAU	chr5:76785226-76785491(-)$1	265	140	175	12.1607
AGAGUGGCAAACAUAGCACGGACUAAUGCCACGAA	chr14:31597726-31597965(-)$1	239	39	74	12.9228
AGCAAUGGUACCGCGAGCACCGCUCCGAGCUGAAC	chr19:34856116-34856401(+)$1	285	95	130	11.1096
AAAUUGCCAAGACCUGUUCUAAAACUCUGUGUCUG	chr20:35827351-35827611(+)$1	260	51	86	10.5211
UGUCAUAAGGGAUCCUAUUGAGAGGCUAGUUUCUU	chr1:87558138-87558377(+)$1	239	108	143	16.4148
UGGAGCGGCGUCCAGCCAGCCCGCUGGGCCCUGCU	chr19:1010347-1010568(-)$1	221	41	76	11.2911
UACCCUGCGGAGAUCACACUGACCUGGCAGCGGGA	chr6:31237978-31238360(-)$1	382	175	210	10.4849
AGUUAUGUUCUUACUGGCACUGAACAGGGCAUGAC	chr22:32789804-32790045(-)$1	241	101	136	10.7375
AUUGAAGGAACUGCAAAAUAUAUUGAAACUUCGGA	chr12:32875390-32875655(+)$1	265	139	174	12.2602
CCUUCAUGGUCGACAAUGAAGCCAUCUAUGACAUA	chr2:130951714-130951967(-)$1	253	154	189	11.0087
GAUGUUUCUCUGUUUCUCUUCAGAGCUUUGGGGAA	chr5:68687589-68687845(+)$1	256	199	234	10.4807
AGUACAGUUCCCAUAUUCAUUAUAGUCUAUGAACG	chr10:75888781-75889061(-)$1	280	4	39	11.5025
UUAUAGCUCAUAACUUUCUGUUGAAUCUUUUAGGC	chr15:89811531-89811770(+)$1	239	65	100	11.0147
ACAGGCAUGUUGGACUUUACACGGUCAUAGGUGAC	chr3:101399837-101400120(-)$1	283	216	251	14.0374
GCUGUCAAGUACACUCAGUCUAACUCUGUGUGCUA	chr2:216209437-216209684(+)$1	247	106	141	12.2765
CGUGGUGCCACACACCGUUGAGGUUGGAGUGGGCA	chr19:10203226-10203471(+)$1	245	148	183	10.9548
UGACUCAUUUCACUAGAAUUUGUUACUGAACAUGG	chr11:27406863-27407119(-)$1	256	50	85	13.9617
UAAAACGUAAAUUAGUGAAGGAACUCCGAUGCGUU	chrX:134930542-134930838(-)$1	296	153	188	14.1038

#DB
...((....(((.(((.....))))))...))...	chr12:46320551-46320791(-)$1	1	80	115	11.4768
..((((...(((((((......)))))))....))	chr2:230663897-230664145(-)$1	1	132	167	10.6882
(.((((((((.(((((......))))).)))))))	chr1:8926359-8926659(-)$1	1	27	62	9.9111
(((.((.(.(((..((((...))))...))).).)	chr1:113197118-113197368(+)$1	1	113	148	12.0654
((((((((..((.(((.....))).))..))))))	chr17:80049348-80049611(-)$1	1	133	168	11.6540
(((((((.(((.((((......)))).)))...))	chr3:142166622-142166866(-)$1	1	40	75	13.5205
.(((.(((..(((.((......)).))).))).))	chr21:27462175-27462464(-)$1	1	63	98	12.8705
((((((((((..(((((...)))))...)))))).	chr10:103557642-103557914(-)$1	1	109	144	10.6508
((((.(((((.(((.(......)))).))))))))	chr2:173431509-173431765(+)$1	1	67	102	12.7689
(.(((((.((((.(.(......).).)))).))))	chr1:161332033-161332312(+)$1	1	172	207	11.9571
...((((....(((((......)))))....))))	chr12:56530916-56531188(+)$1	1	222	257	11.4841
..(((((.(.((((((......)))))).).))))	chrM:3573-3815(-)$1	1	102	137	11.3761
(((((..((((..(((......))))))).)))))	chr14:103807234-103807485(+)$1	1	41	76	14.0790
)))))(((((((.((((((...))).))).)))))	chr13:32709177-32709429(+)$1	1	205	240	12.0975
(((((...((.(.........).))...)))))))	chr19:1106626-1106880(+)$1	1	36	71	10.7363
)(((.(((((((..(((.....)))..))))))).	chr11:64074836-64075090(+)$1	1	169	204	13.3501
(((.((((((...(((......)))...)))))).	chr5:179250824-179251089(+)$1	1	10	45	16.2011
(.((((((..(...((((...))))...)..))).	chr19:13245941-13246214(+)$1	1	93	128	12.7759
.(((..((.(((((((......)))))))))..))	chr12:56677469-56677736(-)$1	1	189	224	11.4653
((.(((((((...(((......)))...)))).))	chr6:26055875-26056141(-)$1	1	59	94	15.7822
.((((((..((((..(((....)))...))))..)	chr11:67953218-67953467(-)$1	1	168	203	10.3625
((((....(((..(((......)))..))).....	chr1:120572432-120572697(-)$1	1	205	240	11.3030
(((..((((..(((((((...))))....)))..)	chr7:44839228-44839479(+)$1	1	74	109	11.0835
((((((((((((..(((....)))....)))))))	chr6:32726763-32727004(-)$1	1	77	112	12.3188
((....((((((((((......))))))))))...	chr16:24834689-24835002(+)$1	1	169	204	14.3621
(((.(.(((((..(((......)))..))))))))	chr6:31324523-31324796(-)$1	1	173	208	14.6775
(((((.(..(((((.(......))))))..).)))	chr1:89430408-89430650(-)$1	1	137	172	11.0613
(((.(((((.(((.........)))...)).))))	chr19:46341707-46341946(-)$1	1	196	231	11.1210
.....(((((((..(((.....))).)))))))..	chr19:37241081-37241353(-)$1	1	226	261	10.9680
...((((((.(((((......)))))..)))))).	chr18:48452098-48452340(+)$1	1	172	207	11.5435
)..((((((.((.(((......))).))..)))))	chr19:23158146-23158485(-)$1	1	181	216	11.1403
((((..((((((((((......))))))))))..)	chr17:40844411-40844677(+)$1	1	35	70	14.0366
(((..(.(((.(((((......)))))....))))	chr6:41755409-41755675(+)$1	1	155	190	12.9891
(((((((((((....(((...)))....))))).)	chr16:30078666-30078981(+)$1	1	221	256	12.2149
((((.((((...(((((...)))))...)))))))	chr17:42429752-42429995(+)$1	1	187	222	10.3774
((((...(((...(((......)))...)))((((	chr6:27834528-27834784(-)$1	1	45	80	11.4640
))))(((((((.(((.........))).)))))))	chr7:26236110-26236374(-)$1	1	188	223	10.9701
(((((((((((..(((...))).)))).)))))))	chr16:58587616-58587858(-)$1	1	87	122	10.5641
(((((((((....(((((....))))).)))))))	chr16:46711121-46711372(-)$1	1	128	163	10.6838
((((..((((((.(((......)))))))))..))	chr19:17515098-17515339(-)$1	1	7	42	13.4347
)))(((((((....(((.....))).)))))))..	chr5:31322847-31323063(+)$1	1	122	157	10.8834
(((((((...(((.........)))...))).)..	chr5:76785226-76785491(-)$1	1	140	175	12.1607
...((((((....(((......))).))))))..)	chr14:31597726-31597965(-)$1	1	39	74	12.9228
.((...(((.(.((((((...))))...)).).))	chr19:34856116-34856401(+)$1	1	95	130	11.1096
.(((((.((.((((.(((....)))...).)))))	chr20:35827351-35827611(+)$1	1	51	86	10.5211
.)))((((((((((((......)))...)))))))	chr1:87558138-87558377(+)$1	1	108	143	16.4148
((((((((.(((((((......))))))).)))))	chr19:1010347-1010568(-)$1	1	41	76	11.2911
(..(((((..((.(((...))).))....))))).	chr6:31237978-31238360(-)$1	1	175	210	10.4849
(((((((((....(((........)))))))))))	chr22:32789804-32790045(-)$1	1	101	136	10.7375
.((((((......(((......)))...)))))))	chr12:32875390-32875655(+)$1	1	139	174	12.2602
((..((((((((...(((....)))...)))).))	chr2:130951714-130951967(-)$1	1	154	189	11.0087
((..((((((((...(((....)))...)))))))	chr5:68687589-68687845(+)$1	1	199	234	10.4807
((.((((((..((((..(......)..))))...)	chr10:75888781-75889061(-)$1	1	4	39	11.5025
..((((((...((..(((....)))..))...)))	chr15:89811531-89811770(+)$1	1	65	100	11.0147
..((((((.(..((((......))))..).))).)	chr3:101399837-101400120(-)$1	1	216	251	14.0374
(.(((..(((((((..(((...)))..))))))))	chr2:216209437-216209684(+)$1	1	106	141	12.2765
)))))))(((...(((.....))))))((((((..	chr19:10203226-10203471(+)$1	1	148	183	10.9548
.(((.(((((((.(((......))).)))).))))	chr11:27406863-27407119(-)$1	1	50	85	13.9617
...((((((....(((......)))....))))))	chrX:134930542-134930838(-)$1	1	153	188	14.1038

#PSSM
c : 0.15	e : 0.13	d : 0.10	[ : 0.08	f : 0.08	i : 0.06	g : 0.06	# : 0.05	: : 0.05	= : 0.03	$ : 0.03	F : 0.03	& : 0.03	b : 0.01	] : 0.01	! : 0.01	" : 0.01	
c : 0.18	e : 0.11	f : 0.11	d : 0.10	[ : 0.06	i : 0.06	# : 0.05	g : 0.05	: : 0.03	= : 0.03	$ : 0.03	F : 0.03	& : 0.03	! : 0.03	b : 0.01	" : 0.01	
c : 0.20	e : 0.13	f : 0.11	d : 0.10	i : 0.06	# : 0.05	g : 0.05	! : 0.05	= : 0.03	$ : 0.03	[ : 0.03	F : 0.03	& : 0.03	h : 0.01	: : 0.01	b : 0.01	
f : 0.18	c : 0.15	e : 0.15	d : 0.08	[ : 0.06	i : 0.06	g : 0.06	! : 0.06	= : 0.03	b : 0.01	h : 0.01	# : 0.01	$ : 0.01	F : 0.01	a : 0.01	" : 0.01	
f : 0.20	c : 0.10	d : 0.08	i : 0.08	[ : 0.08	e : 0.08	! : 0.08	g : 0.06	b : 0.03	h : 0.03	= : 0.03	# : 0.03	a : 0.01	$ : 0.01	: : 0.01	" : 0.01	
f : 0.16	c : 0.11	g : 0.11	e : 0.10	d : 0.08	! : 0.08	i : 0.06	# : 0.05	h : 0.03	b : 0.03	= : 0.03	" : 0.03	[ : 0.03	a : 0.01	: : 0.01	
f : 0.18	c : 0.11	e : 0.11	g : 0.10	d : 0.08	= : 0.06	i : 0.06	[ : 0.05	# : 0.03	" : 0.03	h : 0.03	! : 0.03	b : 0.03	a : 0.01	: : 0.01	
f : 0.15	c : 0.13	g : 0.11	d : 0.10	e : 0.08	= : 0.06	# : 0.05	" : 0.05	[ : 0.05	b : 0.05	h : 0.03	! : 0.03	i : 0.03	a : 0.01	% : 0.01	
f : 0.13	d : 0.13	g : 0.11	! : 0.10	c : 0.10	[ : 0.06	" : 0.05	e : 0.05	b : 0.05	= : 0.05	# : 0.03	h : 0.03	i : 0.03	a : 0.01	% : 0.01	
g : 0.16	c : 0.11	d : 0.11	! : 0.10	[ : 0.10	# : 0.08	e : 0.06	f : 0.05	" : 0.05	h : 0.03	= : 0.03	b : 0.01	i : 0.01	% : 0.01	a : 0.01	
g : 0.15	c : 0.13	d : 0.10	# : 0.10	" : 0.10	[ : 0.06	! : 0.06	e : 0.06	b : 0.05	f : 0.03	a : 0.03	= : 0.03	i : 0.01	% : 0.01	h : 0.01	
c : 0.13	g : 0.13	! : 0.10	" : 0.10	# : 0.10	e : 0.08	d : 0.08	b : 0.06	[ : 0.05	f : 0.03	= : 0.03	a : 0.01	i : 0.01	% : 0.01	h : 0.01	
[ : 0.13	! : 0.13	e : 0.11	c : 0.11	" : 0.11	# : 0.10	g : 0.06	d : 0.06	= : 0.03	b : 0.03	f : 0.01	r : 0.01	i : 0.01	% : 0.01	
c : 0.38	e : 0.13	! : 0.10	g : 0.06	d : 0.05	r : 0.05	" : 0.05	a : 0.03	= : 0.03	# : 0.03	[ : 0.01	f : 0.01	b : 0.01	
c : 0.42	e : 0.11	d : 0.11	[ : 0.06	g : 0.05	r : 0.05	! : 0.05	= : 0.03	" : 0.03	b : 0.01	f : 0.01	# : 0.01	
c : 0.50	e : 0.10	d : 0.10	r : 0.06	g : 0.05	a : 0.05	= : 0.03	! : 0.03	b : 0.01	f : 0.01	o : 0.01	
o : 0.49	c : 0.20	d : 0.06	r : 0.06	n : 0.05	e : 0.05	l : 0.03	q : 0.01	! : 0.01	
o : 0.49	c : 0.13	n : 0.10	d : 0.06	l : 0.06	r : 0.06	m : 0.01	e : 0.01	q : 0.01	a : 0.01	
o : 0.50	l : 0.15	m : 0.11	n : 0.10	r : 0.06	c : 0.03	q : 0.01	
o : 0.50	l : 0.15	m : 0.11	n : 0.10	r : 0.06	c : 0.03	q : 0.01	
o : 0.50	l : 0.11	m : 0.11	n : 0.10	r : 0.06	e : 0.03	c : 0.03	q : 0.01	
o : 0.49	c : 0.11	m : 0.10	d : 0.06	e : 0.05	n : 0.05	r : 0.05	l : 0.03	a : 0.01	q : 0.01	
c : 0.50	e : 0.11	d : 0.10	g : 0.05	a : 0.05	] : 0.05	= : 0.03	b : 0.01	f : 0.01	r : 0.01	q : 0.01	o : 0.01	
c : 0.52	e : 0.13	d : 0.11	g : 0.05	b : 0.05	= : 0.03	] : 0.01	f : 0.01	r : 0.01	q : 0.01	o : 0.01	
c : 0.50	e : 0.13	d : 0.11	g : 0.05	] : 0.03	a : 0.03	b : 0.03	4 : 0.03	= : 0.03	f : 0.01	
3 : 0.28	] : 0.11	c : 0.10	e : 0.10	2 : 0.10	4 : 0.08	d : 0.06	g : 0.05	f : 0.03	= : 0.03	b : 0.01	
3 : 0.28	2 : 0.13	c : 0.10	g : 0.08	e : 0.08	4 : 0.08	d : 0.06	f : 0.05	b : 0.03	] : 0.03	= : 0.03	
3 : 0.30	g : 0.11	4 : 0.11	] : 0.06	c : 0.06	d : 0.06	f : 0.06	2 : 0.05	e : 0.05	= : 0.05	b : 0.03	
g : 0.15	d : 0.13	f : 0.11	c : 0.10	4 : 0.08	i : 0.06	2 : 0.05	e : 0.05	a : 0.05	= : 0.05	b : 0.05	h : 0.03	] : 0.03	3 : 0.01	
f : 0.13	c : 0.11	d : 0.11	g : 0.10	] : 0.08	= : 0.06	e : 0.06	i : 0.06	4 : 0.05	2 : 0.05	b : 0.05	3 : 0.03	h : 0.03	a : 0.01	
f : 0.15	g : 0.13	c : 0.11	e : 0.08	] : 0.08	d : 0.08	= : 0.06	i : 0.06	4 : 0.05	b : 0.03	h : 0.03	3 : 0.03	2 : 0.01	5 : 0.01	a : 0.01	
c : 0.13	f : 0.13	g : 0.13	e : 0.11	d : 0.10	= : 0.06	i : 0.06	] : 0.05	3 : 0.05	h : 0.03	2 : 0.03	b : 0.01	4 : 0.01	5 : 0.01	a : 0.01	
f : 0.15	g : 0.13	e : 0.10	c : 0.10	2 : 0.10	] : 0.06	i : 0.06	4 : 0.05	a : 0.05	d : 0.05	h : 0.03	= : 0.03	3 : 0.03	5 : 0.01	
c : 0.15	f : 0.13	g : 0.11	d : 0.08	i : 0.08	e : 0.08	2 : 0.06	4 : 0.05	] : 0.05	h : 0.03	= : 0.03	5 : 0.01	6 : 0.01	: : 0.01	b : 0.01	3 : 0.01	" : 0.01	
d : 0.15	c : 0.13	g : 0.10	i : 0.08	f : 0.08	4 : 0.06	b : 0.06	e : 0.06	] : 0.05	h : 0.03	= : 0.03	3 : 0.03	5 : 0.01	6 : 0.01	a : 0.01	: : 0.01	" : 0.01	

#score	711.7168662391896
#seq	59
#width	35
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_FUS_Nakaya2013d_hg19_UTR_m3_run2.txt

#BEAR
ddddoooooodddd	chr6:30865916-30866138(+)$1	222	86	100	11.4452
ffffooooooffff	chr5:40835333-40835553(+)$1	220	22	36	9.3129
[cccooooooccc]	chr3:100428133-100428355(-)$1	222	70	84	10.1799
ggggoooooogggg	chr6:99317899-99318115(+)$1	216	94	108	9.9323
eeeeooooooeeee	chrX:16729860-16730077(-)$1	217	162	176	11.0418
%cccooooooccc7	chr20:5177092-5177308(+)$1	216	23	37	8.9231
ddddoooooodddd	chr15:31668142-31668360(+)$1	218	19	33	11.4452
ddddoooooodddd	chr18:43309497-43309718(+)$1	221	205	219	11.4452
ddddoooooodddd	chr11:62393190-62393409(-)$1	219	185	199	11.4452
ffffooooooffff	chr21:46591413-46591635(-)$1	222	186	200	9.3129
eeeeooooooeeee	chr3:38167873-38168091(-)$1	218	161	175	11.0418
gcccooooooccc2	chr10:94414318-94414533(+)$1	215	164	178	9.9581
ddddoooooodddd	chr2:74719723-74719940(-)$1	217	39	53	11.4452
ffffooooooffff	chr1:3649914-3650138(-)$1	224	147	161	9.3129
eeeeooooooeeee	chr2:204267217-204267439(-)$1	222	120	134	11.0418
eeeeooooooeeee	chr14:100745196-100745413(-)$1	217	64	78	11.0418
eeeeooooooeeee	chr15:49620280-49620508(+)$1	228	166	180	11.0418
ddddoooooodddd	chr11:35275507-35275730(-)$1	223	185	199	11.4452
eeeeooooooeeee	chr16:1828818-1829034(-)$1	216	169	183	11.0418
ggggoooooogggg	chr4:954007-954231(-)$1	224	3	17	9.9323
eeeeooooooeeee	chr5:114859571-114859789(-)$1	218	86	100	11.0418
d[bboooooobb]d	chr2:165811902-165812118(-)$1	216	62	76	8.9231
ddddoooooodddd	chr8:82607720-82607939(+)$1	219	157	171	11.4452
eeeeooooooeeee	chr10:127542852-127543067(-)$1	215	138	152	11.0418
#cccooooooccc4	chr20:48249596-48249814(-)$1	218	127	141	10.0690
eeeeooooooeeee	chr11:93463900-93464116(-)$1	216	141	155	11.0418
eeeeooooooeeee	chr4:146056274-146056496(+)$1	222	144	158	11.0418
ddddoooooodddd	chr9:109775049-109775270(+)$1	221	11	25	11.4452
ggggoooooogggg	chr5:138613933-138614150(+)$1	217	105	119	9.9323
ffffooooooffff	chr16:30394066-30394283(-)$1	217	50	64	9.3129
ddddoooooodddd	chr2:242035204-242035420(+)$1	216	84	98	11.4452
ddddoooooodddd	chr1:52882577-52882803(+)$1	226	0	14	11.4452
iiiiooooooiiii	chr12:69969710-69969935(+)$1	225	13	27	9.7501
[cccooooooccc2	chr16:46722693-46722911(-)$1	218	50	64	9.9809
ddddoooooodddd	chr14:69926881-69927110(+)$1	229	44	58	11.4452
ddddoooooodddd	chr9:98206586-98206807(-)$1	221	188	202	11.4452
ddddoooooodddd	chr1:70033992-70034214(+)$1	222	136	150	11.4452
ffffooooooffff	chr4:2968075-2968299(+)$1	224	154	168	9.3129
!cccooooooccc9	chr5:54922299-54922554(-)$1	255	149	163	9.5815
eeeeooooooeeee	chr12:56420682-56420903(+)$1	221	205	219	11.0418
eeeeooooooeeee	chr7:91509915-91510130(+)$1	215	5	19	11.0418
eeeeooooooeeee	chr19:54941010-54941242(-)$1	232	68	82	11.0418
ggggoooooogggg	chr20:62588756-62588979(-)$1	223	22	36	9.9323
ddddoooooodddd	chr2:98264404-98264670(+)$1	266	199	213	11.4452
eeeeooooooeeee	chr17:30817942-30818167(+)$1	225	156	170	11.0418
ddddoooooodddd	chr10:61469320-61469545(-)$1	225	121	135	11.4452
ddddoooooodddd	chr2:202001814-202002047(+)$1	233	210	224	11.4452
eeeeooooooeeee	chr1:25167476-25167702(+)$1	226	46	60	11.0418
ddddoooooodddd	chr1:26146231-26146461(+)$1	230	91	105	11.4452
ddddoooooodddd	chrX:153072150-153072372(-)$1	222	103	117	11.4452
ddddoooooodddd	chr19:41381488-41381709(+)$1	221	173	187	11.4452
[cccooooooccce	chr4:1642598-1642817(-)$1	219	113	127	10.3760
%cccooooooccc4	chr5:141531977-141532196(+)$1	219	173	187	9.4833
ddddoooooodddd	chr9:130453850-130454069(+)$1	219	75	89	11.4452
ddddoooooodddd	chr3:129226448-129226663(+)$1	215	91	105	11.4452
ddddoooooodddd	chr2:73485541-73485764(-)$1	223	101	115	11.4452

#otherMatches

#Seq PSSM
CCUCUAUGCUGGGG	chr6:30865916-30866138(+)$1	222	86	100	11.4452
UUCCGCCCAGGGAA	chr5:40835333-40835553(+)$1	220	22	36	9.3129
GUGGACAUACCCAG	chr3:100428133-100428355(-)$1	222	70	84	10.1799
UGUUUUUUCUAACA	chr6:99317899-99318115(+)$1	216	94	108	9.9323
AGAAUAGCUUUUUU	chrX:16729860-16730077(-)$1	217	162	176	11.0418
GAGGACCUUGCCUG	chr20:5177092-5177308(+)$1	216	23	37	8.9231
GGGUACAAACAUCU	chr15:31668142-31668360(+)$1	218	19	33	11.4452
GUGUCAACACACAC	chr18:43309497-43309718(+)$1	221	205	219	11.4452
CUUCUGCCUUGGAG	chr11:62393190-62393409(-)$1	219	185	199	11.4452
UAAUUACAACAUUA	chr21:46591413-46591635(-)$1	222	186	200	9.3129
CUGGAAUAGACCAG	chr3:38167873-38168091(-)$1	218	161	175	11.0418
CUUGUUGCCCCAAA	chr10:94414318-94414533(+)$1	215	164	178	9.9581
GCAUGACAGUGUGC	chr2:74719723-74719940(-)$1	217	39	53	11.4452
UAGGAUGAAGCCUG	chr1:3649914-3650138(-)$1	224	147	161	9.3129
UGUAGAACUGUACA	chr2:204267217-204267439(-)$1	222	120	134	11.0418
GGCACUCAAUUGCC	chr14:100745196-100745413(-)$1	217	64	78	11.0418
UUGUAUUAUGAUGA	chr15:49620280-49620508(+)$1	228	166	180	11.0418
UAGCUUGUUUGCUA	chr11:35275507-35275730(-)$1	223	185	199	11.4452
AGGCCAGGCAGCCU	chr16:1828818-1829034(-)$1	216	169	183	11.0418
ACACAUGUUGGUGU	chr4:954007-954231(-)$1	224	3	17	9.9323
CCAUUUCUCCAUGG	chr5:114859571-114859789(-)$1	218	86	100	11.0418
GGAGACAGGGCUGC	chr2:165811902-165812118(-)$1	216	62	76	8.9231
GGAUGAUUUAAUCU	chr8:82607720-82607939(+)$1	219	157	171	11.4452
UUUACUUAUUUAAA	chr10:127542852-127543067(-)$1	215	138	152	11.0418
CCAUCACUACGUGU	chr20:48249596-48249814(-)$1	218	127	141	10.0690
AGUUAACUCAGGCU	chr11:93463900-93464116(-)$1	216	141	155	11.0418
AGGAGCUAUAUUCU	chr4:146056274-146056496(+)$1	222	144	158	11.0418
GCUGAGAUGACAGU	chr9:109775049-109775270(+)$1	221	11	25	11.4452
UUCACCCAUCUGAA	chr5:138613933-138614150(+)$1	217	105	119	9.9323
cgagagccaccuug	chr16:30394066-30394283(-)$1	217	50	64	9.3129
AAGAGACCAGUUUU	chr2:242035204-242035420(+)$1	216	84	98	11.4452
UUCAAACUUAUGAG	chr1:52882577-52882803(+)$1	226	0	14	11.4452
UGAAGGUUCAUUUG	chr12:69969710-69969935(+)$1	225	13	27	9.7501
GGCCGGGGUGGGCG	chr16:46722693-46722911(-)$1	218	50	64	9.9809
CGUUUUCUAUGACG	chr14:69926881-69927110(+)$1	229	44	58	11.4452
GGCGUGCCCUCGCU	chr9:98206586-98206807(-)$1	221	188	202	11.4452
CAUGGUCUAACGUG	chr1:70033992-70034214(+)$1	222	136	150	11.4452
GUGAGAGUAUUUGC	chr4:2968075-2968299(+)$1	224	154	168	9.3129
CGUCUGACAUGGCC	chr5:54922299-54922554(-)$1	255	149	163	9.5815
GCUGGGACAACAGC	chr12:56420682-56420903(+)$1	221	205	219	11.0418
UCUUAACAAAAAGA	chr7:91509915-91510130(+)$1	215	5	19	11.0418
UGCCCAACCCGGCG	chr19:54941010-54941242(-)$1	232	68	82	11.0418
GAUACCUUGAUGUU	chr20:62588756-62588979(-)$1	223	22	36	9.9323
AAAGUUUCUUCUUU	chr2:98264404-98264670(+)$1	266	199	213	11.4452
AUAUUAAUUUAUAU	chr17:30817942-30818167(+)$1	225	156	170	11.0418
GCGGGACCGAUUGC	chr10:61469320-61469545(-)$1	225	121	135	11.4452
GGGCAGCCUGGCCC	chr2:202001814-202002047(+)$1	233	210	224	11.4452
UGCACGAACAUGCA	chr1:25167476-25167702(+)$1	226	46	60	11.0418
GCCCACUCGGGGGC	chr1:26146231-26146461(+)$1	230	91	105	11.4452
CCGGGACAAGCUGG	chrX:153072150-153072372(-)$1	222	103	117	11.4452
GACACGUCAAUGUC	chr19:41381488-41381709(+)$1	221	173	187	11.4452
AGCUGGUCGGGGCC	chr4:1642598-1642817(-)$1	219	113	127	10.3760
AAAGAAGUAGCUUG	chr5:141531977-141532196(+)$1	219	173	187	9.4833
UCCAUCUCUUUGGA	chr9:130453850-130454069(+)$1	219	75	89	11.4452
AAGUUCUACCACUU	chr3:129226448-129226663(+)$1	215	91	105	11.4452
AGGGCUCUUCUCCU	chr2:73485541-73485764(-)$1	223	101	115	11.4452

#DB
((((......))))	chr6:30865916-30866138(+)$1	1	86	100	11.4452
((((......))))	chr5:40835333-40835553(+)$1	1	22	36	9.3129
.(((......))).	chr3:100428133-100428355(-)$1	1	70	84	10.1799
((((......))))	chr6:99317899-99318115(+)$1	1	94	108	9.9323
((((......))))	chrX:16729860-16730077(-)$1	1	162	176	11.0418
.(((......))).	chr20:5177092-5177308(+)$1	1	23	37	8.9231
((((......))))	chr15:31668142-31668360(+)$1	1	19	33	11.4452
((((......))))	chr18:43309497-43309718(+)$1	1	205	219	11.4452
((((......))))	chr11:62393190-62393409(-)$1	1	185	199	11.4452
((((......))))	chr21:46591413-46591635(-)$1	1	186	200	9.3129
((((......))))	chr3:38167873-38168091(-)$1	1	161	175	11.0418
((((......))).	chr10:94414318-94414533(+)$1	1	164	178	9.9581
((((......))))	chr2:74719723-74719940(-)$1	1	39	53	11.4452
((((......))))	chr1:3649914-3650138(-)$1	1	147	161	9.3129
((((......))))	chr2:204267217-204267439(-)$1	1	120	134	11.0418
((((......))))	chr14:100745196-100745413(-)$1	1	64	78	11.0418
((((......))))	chr15:49620280-49620508(+)$1	1	166	180	11.0418
((((......))))	chr11:35275507-35275730(-)$1	1	185	199	11.4452
((((......))))	chr16:1828818-1829034(-)$1	1	169	183	11.0418
((((......))))	chr4:954007-954231(-)$1	1	3	17	9.9323
((((......))))	chr5:114859571-114859789(-)$1	1	86	100	11.0418
(.((......)).)	chr2:165811902-165812118(-)$1	1	62	76	8.9231
((((......))))	chr8:82607720-82607939(+)$1	1	157	171	11.4452
((((......))))	chr10:127542852-127543067(-)$1	1	138	152	11.0418
.(((......))).	chr20:48249596-48249814(-)$1	1	127	141	10.0690
((((......))))	chr11:93463900-93464116(-)$1	1	141	155	11.0418
((((......))))	chr4:146056274-146056496(+)$1	1	144	158	11.0418
((((......))))	chr9:109775049-109775270(+)$1	1	11	25	11.4452
((((......))))	chr5:138613933-138614150(+)$1	1	105	119	9.9323
((((......))))	chr16:30394066-30394283(-)$1	1	50	64	9.3129
((((......))))	chr2:242035204-242035420(+)$1	1	84	98	11.4452
((((......))))	chr1:52882577-52882803(+)$1	1	0	14	11.4452
((((......))))	chr12:69969710-69969935(+)$1	1	13	27	9.7501
.(((......))).	chr16:46722693-46722911(-)$1	1	50	64	9.9809
((((......))))	chr14:69926881-69927110(+)$1	1	44	58	11.4452
((((......))))	chr9:98206586-98206807(-)$1	1	188	202	11.4452
((((......))))	chr1:70033992-70034214(+)$1	1	136	150	11.4452
((((......))))	chr4:2968075-2968299(+)$1	1	154	168	9.3129
.(((......))).	chr5:54922299-54922554(-)$1	1	149	163	9.5815
((((......))))	chr12:56420682-56420903(+)$1	1	205	219	11.0418
((((......))))	chr7:91509915-91510130(+)$1	1	5	19	11.0418
((((......))))	chr19:54941010-54941242(-)$1	1	68	82	11.0418
((((......))))	chr20:62588756-62588979(-)$1	1	22	36	9.9323
((((......))))	chr2:98264404-98264670(+)$1	1	199	213	11.4452
((((......))))	chr17:30817942-30818167(+)$1	1	156	170	11.0418
((((......))))	chr10:61469320-61469545(-)$1	1	121	135	11.4452
((((......))))	chr2:202001814-202002047(+)$1	1	210	224	11.4452
((((......))))	chr1:25167476-25167702(+)$1	1	46	60	11.0418
((((......))))	chr1:26146231-26146461(+)$1	1	91	105	11.4452
((((......))))	chrX:153072150-153072372(-)$1	1	103	117	11.4452
((((......))))	chr19:41381488-41381709(+)$1	1	173	187	11.4452
.(((......))))	chr4:1642598-1642817(-)$1	1	113	127	10.3760
.(((......))).	chr5:141531977-141532196(+)$1	1	173	187	9.4833
((((......))))	chr9:130453850-130454069(+)$1	1	75	89	11.4452
((((......))))	chr3:129226448-129226663(+)$1	1	91	105	11.4452
((((......))))	chr2:73485541-73485764(-)$1	1	101	115	11.4452

#PSSM
d : 0.41	e : 0.26	f : 0.08	g : 0.08	[ : 0.05	% : 0.03	# : 0.01	i : 0.01	! : 0.01	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	[ : 0.01	i : 0.01	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	b : 0.01	i : 0.01	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	b : 0.01	i : 0.01	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
o : 1.00	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	b : 0.01	i : 0.01	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	b : 0.01	i : 0.01	
d : 0.39	e : 0.26	c : 0.14	f : 0.08	g : 0.07	] : 0.01	i : 0.01	
d : 0.41	e : 0.28	f : 0.08	g : 0.07	2 : 0.03	4 : 0.03	] : 0.01	7 : 0.01	i : 0.01	9 : 0.01	

#score	600.9423017786678
#seq	56
#width	14
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Haecker2012b_hg19_UTR_m2_run2.txt

#BEAR
dddd[============oooooo============d	chr9:112932099-112932347(+)$1	248	182	218	18.2924
eeee"""ddddbb!!bboooooobb22bb]dddd]e	chr12:9848113-9848386(+)$1	273	123	159	13.3435
::===========[ccclllccc22===========	chr12:7965601-7965892(-)$1	291	198	234	13.7180
bb]============bboooooobbbb[ccc[bbmm	chr12:80772710-80772951(+)$1	241	71	107	13.7637
:bbffffff[ccc[cccoooooocccccc]ffffff	chr3:112642410-112642707(-)$1	297	33	69	13.4794
=========$$$$$cccooooooccc666666====	chr4:109543003-109543276(+)$1	273	17	53	16.1089
eeeee[ccc$$$$$cccooooooccc4444ccc]ee	chr5:86686777-86687038(+)$1	261	12	48	16.7256
fffiiiiiiiii!!ccclllccc]iiiiiiiii:gg	chr15:31669875-31670192(+)$1	317	197	233	13.0410
:===========[bb[aooooooabb==========	chr3:9519589-9519932(+)$1	343	233	269	17.3821
ff[==========[bbmmmmbb]==========333	chrX:62569761-62569999(-)$1	238	96	132	13.4682
[a[bb[ccc####ddddccclllccc4444dddd33	chr19:7537071-7537413(+)$1	342	18	54	11.8570
=============cccqqqqqqqqccc22=======	chr5:167927549-167927821(+)$1	272	145	181	13.5385
%%%%ggggggg"""cccooooooccc4444gggggg	chr13:58298665-58299027(+)$1	362	29	65	15.7649
:ggggggg!!bb[ddddooooooddddbb22ggggg	chr15:58000850-58001118(+)$1	268	1	37	13.4540
eeeee!!bb[bb!!cccooooooccc22bb]bb22e	chr17:77806855-77807178(-)$1	323	170	206	15.2629
ee[ccc!!cccgggggggooooooggggggg4444c	chr6:10627265-10627581(+)$1	316	247	283	13.8708
f============[cccmmmmccc]===========	chr4:139979526-139979841(-)$1	315	260	296	15.6942
%%%ggggggg####cccooooooccc666666gggg	chr4:109588711-109589020(+)$1	309	203	239	13.3792
ccc]cccffffff[a[aooooooa]a]ffffffddd	chr19:8381286-8381596(-)$1	310	209	245	13.0924
====!!bb$$$$$ddddoooooodddd333bb22==	chr13:31035273-31035590(-)$1	317	78	114	15.1804
GGG==========rrrrrrrrr==========ccc[	chr2:132241448-132241690(-)$1	242	57	93	12.0324
!ccc"""bb!!bb!!bboooooobb]bb22bb22cc	chr17:1553828-1554151(-)$1	323	43	79	13.6629
==========ffffffrrrrrrrrrffffff333==	chr8:28748040-28748285(+)$1	245	73	109	11.7956
eee[dddd!!bb[ddddoooooodddd]bb4444dd	chr17:33951393-33951667(+)$1	274	77	113	13.3626
eee$$$$$dddd!!cccooooooccc22dddd22ee	chr4:185676778-185677067(-)$1	289	95	131	14.3277
dd:============ssssssssss===========	chr5:162945901-162946260(+)$1	359	262	298	12.5252
gg####ccc"""a!!cccnnnnnccc22a333ccc2	chr12:98995181-98995507(+)$1	326	57	93	13.4910
ggggg[dddd"""ddddoooooodddd22dddd]gg	chr7:103112618-103112863(-)$1	245	64	100	14.6910
ddd[ffffff"""ddddoooooodddd4444fffff	chr16:81051283-81051549(+)$1	266	206	242	14.3950
ccc[==========rrrrrrrrr==========]cc	chr17:56051334-56051595(-)$1	261	209	245	14.8133
ddd==========[cccooooooccc==========	chr19:18284503-18284886(+)$1	383	183	219	19.6649
a[ccc[===========oooooo===========]c	chr19:50002667-50003044(+)$1	377	294	330	18.7471
ggggggffffff!!ddddoooooodddd333fffff	chr2:100016077-100016340(+)$1	263	139	175	13.3834
cc[ccc[bb[ccc!!bboooooobbccc]bb]cccc	chr14:19584950-19585210(+)$1	260	66	102	14.6205
iiiiiii!!ccc!!cccooooooccc22ccc22iii	chr1:155306310-155306730(-)$1	420	229	265	17.6152
b!!iiiiiiiii"""bboooooobb333iiiiiiii	chr8:107764303-107764583(+)$1	280	167	203	18.3354
=========="""ddddllldddd333=========	chr11:62397762-62398011(-)$1	249	211	247	15.2978
eee[ccc!!ccc!!cccooooooccc22cccccc33	chr19:18285755-18286137(+)$1	382	137	173	17.0265
ee[==========[cccooooooccc==========	chr11:58386095-58386439(+)$1	344	222	258	20.1525
dddd[a[dddd!!ddddoooooodddd]dddd]a]d	chr1:193054593-193054848(+)$1	255	37	73	13.4301
d[ccc[bb[ccc!!cccooooooccc22ccc]bb]c	chr9:14082737-14083020(-)$1	283	141	177	16.1930
bb$$$$$dddd[a[cccooooooccc]a]dddd444	chr8:124027427-124027749(-)$1	322	120	156	14.6842
eeee[iiiiiiiiicccmmmmccc]iiiiiiiiiee	chr3:67060503-67060786(+)$1	283	112	148	13.0722
eeeee[dddd[ccc[bboooooobb22cccddddee	chr17:38145909-38146222(+)$1	313	124	160	12.9230
gggggg[ccc!!a[ccclllccca]ccc]ggggggg	chr1:202896218-202896463(-)$1	245	16	52	13.3344
ggggggg"""ccc[ddddmmmmdddd4444ccc444	chr19:11944590-11944837(+)$1	247	71	107	12.2263
hhhhh!!ffffff!!bboooooobb4444ffffff]	chr12:69973329-69973628(+)$1	299	123	159	14.0494
========="""a[bbmmmmbb]a4444========	chr1:120457599-120457914(-)$1	315	17	53	13.8688
bb:::ccciiiiiiiiiooooooiiiiiiiii]ccc	chr7:112726350-112726600(-)$1	250	19	55	12.7145
Geeeee[ffffff[cccooooooccc]ffffff]ee	chr6:158365291-158365670(+)$1	379	146	182	14.0963
iiii!!===========oooooo===========33	chr12:8073450-8073728(-)$1	278	113	149	19.3913
hhhhhh[eeeee!!cccooooooccc333eeeee]h	chr1:203276444-203276771(+)$1	327	208	244	15.0139
ee####============mmmm============ee	chr7:129770520-129770772(+)$1	252	197	233	14.6421

#otherMatches

#Seq PSSM
GUCACAAUUACAAAGUUUUGAGCGGUUUUGUAAUUU	chr9:112932099-112932347(+)$1	248	182	218	18.2924
GUUUCUCUUGGGGGCUUUGAAAUAACACCACCAGUG	chr12:9848113-9848386(+)$1	273	123	159	13.3435
UAAAGUGUGUUGUUGCUUUAGGCUCACGGCACGCUU	chr12:7965601-7965892(-)$1	291	198	234	13.7180
CUGUUGAAGUUGAGUGCUGUUUUGCUGUUAAUGCUG	chr12:80772710-80772951(+)$1	241	71	107	13.7637
UUGAUUUUAACUUUGAGUUCUUUCUUAGGAUGAAAU	chr3:112642410-112642707(-)$1	297	33	69	13.4794
GAAUGAAAUAGACCACAUGAUACUGUUUUGAGAUUU	chr4:109543003-109543276(+)$1	273	17	53	16.1089
AUAGCACACUUUUCCACAUUCCAGUGAUGUGUGAGC	chr5:86686777-86687038(+)$1	261	12	48	16.7256
UUGAAAUAAAAUUUAUGAUUCAUUAUUUUAUUUGCU	chr15:31669875-31670192(+)$1	317	197	233	13.0410
AUCAUAAAGUUGAGAACUUCUUUGUCCAAUUUUGUG	chr3:9519589-9519932(+)$1	343	233	269	17.3821
UUAUUUUGUGUUCUCGUAGUUGUGAACGCAGAGAAG	chrX:62569761-62569999(-)$1	238	96	132	13.4682
CGUGCUAGGCAUCGGGCGGCAGCGCCGACAGCCCUU	chr19:7537071-7537413(+)$1	342	18	54	11.8570
UGGAAGCUUAUCUGUGAUGUCUCCCGCCAAGGUGAG	chr5:167927549-167927821(+)$1	272	145	181	13.5385
UUAAAGAAAACUCUAAUGAUUGGAUUUGCUGUUUUC	chr13:58298665-58299027(+)$1	362	29	65	15.7649
UGUUAUAUCUCAAGUUAAAAAAAUGGCUGUAAUGUA	chr15:58000850-58001118(+)$1	268	1	37	13.4540
UUCCAACUAUUACCUGCUUGAAUGUAAAUAUUAAAU	chr17:77806855-77807178(-)$1	323	170	206	15.2629
UAUAUGCCAGAAUGUAGGCUGGUCCCUAUGUCAUGU	chr6:10627265-10627581(+)$1	316	247	283	13.8708
uauauauauauauauauauacauacauauauauaua	chr4:139979526-139979841(-)$1	315	260	296	15.6942
AAACUGUUUCCUGAACAAUAAGAUGUAUGAACGGAG	chr4:109588711-109589020(+)$1	309	203	239	13.3792
GCAGAGAGGUGAGGAUCUCCAGCGCUGCUCACCACA	chr19:8381286-8381596(-)$1	310	209	245	13.0924
agaugaUGAUGAUGAAUAAGUUGGUUCUAGCGCAGU	chr13:31035273-31035590(-)$1	317	78	114	15.1804
GAUGGGGCAGAGACUUGUCACAUCUUUGUCCCCAGC	chr2:132241448-132241690(-)$1	242	57	93	12.0324
CCUGUAUGCCUGACCGUUUCCCUGCCUCCUGCUUCA	chr17:1553828-1554151(-)$1	323	43	79	13.6629
CUCCUCCCUAUCUCAGCCCUUCGUACUGGGACGUUG	chr8:28748040-28748285(+)$1	245	73	109	11.7956
GCAACUUACUUGAUCUGAACCCACAGAACAUUAAUA	chr17:33951393-33951667(+)$1	274	77	113	13.3626
CAAGCACAACAGGGCUUGCACUAAAGAAUUGUCAUU	chr4:185676778-185677067(-)$1	289	95	131	14.3277
GUUUUCUUGUAUUUACUUCUUUUUUUAAAUGUAAGG	chr5:162945901-162946260(+)$1	359	262	298	12.5252
GACUUCCUCGCCCUCCUCCACCCGAGAUGCCAGAGU	chr12:98995181-98995507(+)$1	326	57	93	13.4910
CAAUACAACACAUUGAAACUGUAUUUACUUGUUAUG	chr7:103112618-103112863(-)$1	245	64	100	14.6910
GCACUUAAAAUUUGCUACUAUCAUAGUUUUUUUUUA	chr16:81051283-81051549(+)$1	266	206	242	14.3950
UGUCUGUGUUUAUUGUUUUUAUGAGUAAAUACAUGC	chr17:56051334-56051595(-)$1	261	209	245	14.8133
gcugcugcugcugcugGACGUCCCCACGGCGGCGGU	chr19:18284503-18284886(+)$1	383	183	219	19.6649
CUUCCGCGCCUUUACCAGAGCAUUGGUGGGGGUGGG	chr19:50002667-50003044(+)$1	377	294	330	18.7471
UCAGUACUGCAGUAUUUGAUUAACCAAGCUUCUGCA	chr2:100016077-100016340(+)$1	263	139	175	13.3834
GGCAUCAUCACCAACUGGGACGACAUGGAGAAGAUC	chr14:19584950-19585210(+)$1	260	66	102	14.6205
UGAAAACACUACUCUUGUUUUCUUAAUUGUACAGUU	chr1:155306310-155306730(-)$1	420	229	265	17.6152
CAGAAAGUGUUGAUUGCCAGGUUGCUUAUAGCACUU	chr8:107764303-107764583(+)$1	280	167	203	18.3354
GGUGGCUCUUUUGCCCCUUAGGGGAUUGAGAGCCAC	chr11:62397762-62398011(-)$1	249	211	247	15.2978
CACCGCUUGUCAAUGUGACCCUCUACUAUGAAGCAC	chr19:18285755-18286137(+)$1	382	137	173	17.0265
UUUGAGAUUUUUACAGUGUUGAAACUUAAGAAUUUU	chr11:58386095-58386439(+)$1	344	222	258	20.1525
GAUUUCCUCUGAAUUAUAAUAACAUAGCCAGAUGUA	chr1:193054593-193054848(+)$1	255	37	73	13.4301
AUUACUGUAUUUUUGACAGAAUGGUUUUGAAAACUG	chr9:14082737-14083020(-)$1	283	141	177	16.1930
CACUUAACAACUGCGUUCUGGCUAACACUGUUGGAC	chr8:124027427-124027749(-)$1	322	120	156	14.6842
UGAUGUUUUGGAGUUAUUACUGUGUAUUUUAGAAAU	chr3:67060503-67060786(+)$1	283	112	148	13.0722
CGCAGACGGGCAGGCCACCCUGUUGAACCUCCUGCU	chr17:38145909-38146222(+)$1	313	124	160	12.9230
CUCCUCACGUGACGCAGACUCUGGAGCGGGGGGAGG	chr1:202896218-202896463(-)$1	245	16	52	13.3344
GCGUUCAGACCUGACAAGAUUCUUUGAAUACAGAUA	chr19:11944590-11944837(+)$1	247	71	107	12.2263
AAAAGCUGCUUUAUUGAAUAAAGUCUGAUUGGAGUU	chr12:69973329-69973628(+)$1	299	123	159	14.0494
GACUUUUGUAAAUGCUGCUGAGGAACAAAUGAAGGU	chr1:120457599-120457914(-)$1	315	17	53	13.8688
AGGACGCGGCUGGAGCUCAAGGAGGCUCCAGCGCGC	chr7:112726350-112726600(-)$1	250	19	55	12.7145
UAAUAUAUGUACAAAUUGUAAAGAAUAUGUAUAAAU	chr6:158365291-158365670(+)$1	379	146	182	14.0963
GAAGCCGGAGGGUGUUUAUGUAAGAGCACCUUCCUC	chr12:8073450-8073728(-)$1	278	113	149	19.3913
UUUAAAUGAAGAGCuauuuauauauauuauuuuuuu	chr1:203276444-203276771(+)$1	327	208	244	15.0139
UGCCUUUCUGUAAAUUGGUUUUUCAGUUUAUGGACA	chr7:129770520-129770772(+)$1	252	197	233	14.6421

#DB
((((.((((((((((((......)))))))))))))	chr9:112932099-112932347(+)$1	1	182	218	18.2924
((((...((((((..((......))..)).)))).)	chr12:9848113-9848386(+)$1	1	123	159	13.3435
..(((((((((((.(((...)))..)))))))))))	chr12:7965601-7965892(-)$1	1	198	234	13.7180
)).))))))))))))((......))((.(((.((..	chr12:80772710-80772951(+)$1	1	71	107	13.7637
.((((((((.(((.(((......)))))).))))))	chr3:112642410-112642707(-)$1	1	33	69	13.4794
(((((((((.....(((......)))......))))	chr4:109543003-109543276(+)$1	1	17	53	16.1089
(((((.(((.....(((......)))....))).))	chr5:86686777-86687038(+)$1	1	12	48	16.7256
)))(((((((((..(((...))).))))))))).((	chr15:31669875-31670192(+)$1	1	197	233	13.0410
.(((((((((((.((.(......)))))))))))))	chr3:9519589-9519932(+)$1	1	233	269	17.3821
((.((((((((((.((....)).))))))))))...	chrX:62569761-62569999(-)$1	1	96	132	13.4682
.(.((.(((....(((((((...)))....))))..	chr19:7537071-7537413(+)$1	1	18	54	11.8570
((((((((((((((((........)))..)))))))	chr5:167927549-167927821(+)$1	1	145	181	13.5385
....(((((((...(((......)))....))))))	chr13:58298665-58299027(+)$1	1	29	65	15.7649
.(((((((..((.((((......))))))..)))))	chr15:58000850-58001118(+)$1	1	1	37	13.4540
(((((..((.((..(((......)))..)).))..)	chr17:77806855-77807178(-)$1	1	170	206	15.2629
((.(((..((((((((((......)))))))....)	chr6:10627265-10627581(+)$1	1	247	283	13.8708
(((((((((((((.(((....))).)))))))))))	chr4:139979526-139979841(-)$1	1	260	296	15.6942
...(((((((....(((......)))......))))	chr4:109588711-109589020(+)$1	1	203	239	13.3792
))).)))((((((.(.(......).).))))))(((	chr19:8381286-8381596(-)$1	1	209	245	13.0924
((((..((.....((((......))))...))..))	chr13:31035273-31035590(-)$1	1	78	114	15.1804
(((((((((((((.........))))))))))(((.	chr2:132241448-132241690(-)$1	1	57	93	12.0324
.(((...((..((..((......)).))..))..))	chr17:1553828-1554151(-)$1	1	43	79	13.6629
((((((((((((((((.........))))))...))	chr8:28748040-28748285(+)$1	1	73	109	11.7956
(((.((((..((.((((......)))).))....))	chr17:33951393-33951667(+)$1	1	77	113	13.3626
(((.....((((..(((......)))..))))..))	chr4:185676778-185677067(-)$1	1	95	131	14.3277
)).((((((((((((..........)))))))))))	chr5:162945901-162946260(+)$1	1	262	298	12.5252
((....(((...(..(((.....)))..)...))).	chr12:98995181-98995507(+)$1	1	57	93	13.4910
(((((.((((...((((......))))..)))).))	chr7:103112618-103112863(-)$1	1	64	100	14.6910
(((.((((((...((((......))))....)))))	chr16:81051283-81051549(+)$1	1	206	242	14.3950
(((.((((((((((.........)))))))))).))	chr17:56051334-56051595(-)$1	1	209	245	14.8133
(((((((((((((.(((......)))))))))))))	chr19:18284503-18284886(+)$1	1	183	219	19.6649
(.(((.(((((((((((......))))))))))).)	chr19:50002667-50003044(+)$1	1	294	330	18.7471
))))))((((((..((((......))))...)))))	chr2:100016077-100016340(+)$1	1	139	175	13.3834
((.(((.((.(((..((......))))).)).))))	chr14:19584950-19585210(+)$1	1	66	102	14.6205
(((((((..(((..(((......)))..)))..)))	chr1:155306310-155306730(-)$1	1	229	265	17.6152
(..(((((((((...((......))...))))))))	chr8:107764303-107764583(+)$1	1	167	203	18.3354
((((((((((...((((...))))...)))))))))	chr11:62397762-62398011(-)$1	1	211	247	15.2978
(((.(((..(((..(((......)))..))))))..	chr19:18285755-18286137(+)$1	1	137	173	17.0265
((.((((((((((.(((......)))))))))))))	chr11:58386095-58386439(+)$1	1	222	258	20.1525
((((.(.((((..((((......)))).)))).).)	chr1:193054593-193054848(+)$1	1	37	73	13.4301
(.(((.((.(((..(((......)))..))).)).)	chr9:14082737-14083020(-)$1	1	141	177	16.1930
((.....((((.(.(((......))).).))))...	chr8:124027427-124027749(-)$1	1	120	156	14.6842
((((.((((((((((((....))).)))))))))))	chr3:67060503-67060786(+)$1	1	112	148	13.0722
(((((.((((.(((.((......))..)))))))))	chr17:38145909-38146222(+)$1	1	124	160	12.9230
((((((.(((..(.(((...)))).))).)))))))	chr1:202896218-202896463(-)$1	1	16	52	13.3344
(((((((...(((.((((....))))....)))...	chr19:11944590-11944837(+)$1	1	71	107	12.2263
(((((..((((((..((......))....)))))).	chr12:69973329-69973628(+)$1	1	123	159	14.0494
(((((((((...(.((....)).)....))))))))	chr1:120457599-120457914(-)$1	1	17	53	13.8688
))...((((((((((((......))))))))).)))	chr7:112726350-112726600(-)$1	1	19	55	12.7145
((((((.((((((.(((......))).)))))).))	chr6:158365291-158365670(+)$1	1	146	182	14.0963
((((..(((((((((((......)))))))))))..	chr12:8073450-8073728(-)$1	1	113	149	19.3913
((((((.(((((..(((......)))...))))).)	chr1:203276444-203276771(+)$1	1	208	244	15.0139
((....((((((((((((....))))))))))))))	chr7:129770520-129770772(+)$1	1	197	233	14.6421

#PSSM
e : 0.20	d : 0.11	= : 0.11	g : 0.09	: : 0.07	b : 0.07	f : 0.05	c : 0.05	% : 0.03	G : 0.03	i : 0.03	h : 0.03	[ : 0.01	! : 0.01	a : 0.01	
e : 0.22	= : 0.15	g : 0.11	d : 0.09	b : 0.07	c : 0.07	f : 0.03	% : 0.03	[ : 0.03	i : 0.03	h : 0.03	: : 0.01	a : 0.01	G : 0.01	! : 0.01	
e : 0.16	= : 0.16	[ : 0.09	g : 0.09	c : 0.09	d : 0.07	% : 0.03	: : 0.03	# : 0.03	i : 0.03	h : 0.03	] : 0.01	b : 0.01	f : 0.01	G : 0.01	! : 0.01	$ : 0.01	
= : 0.28	e : 0.11	g : 0.11	c : 0.09	i : 0.07	[ : 0.07	d : 0.03	$ : 0.03	# : 0.03	h : 0.03	f : 0.01	b : 0.01	% : 0.01	] : 0.01	: : 0.01	
= : 0.28	g : 0.13	c : 0.11	e : 0.07	[ : 0.05	i : 0.05	" : 0.03	f : 0.03	! : 0.03	$ : 0.03	# : 0.03	h : 0.03	b : 0.01	d : 0.01	: : 0.01	
= : 0.30	[ : 0.11	g : 0.11	c : 0.09	i : 0.07	! : 0.07	" : 0.03	f : 0.03	$ : 0.03	# : 0.03	d : 0.01	a : 0.01	e : 0.01	h : 0.01	
= : 0.35	c : 0.11	[ : 0.09	i : 0.07	g : 0.07	f : 0.05	! : 0.05	d : 0.05	" : 0.03	b : 0.03	$ : 0.03	
= : 0.35	d : 0.11	f : 0.11	c : 0.09	b : 0.09	i : 0.05	g : 0.05	! : 0.05	$ : 0.01	" : 0.01	e : 0.01	
= : 0.35	d : 0.11	f : 0.11	c : 0.09	i : 0.07	! : 0.07	b : 0.05	g : 0.03	$ : 0.01	[ : 0.01	" : 0.01	e : 0.01	
= : 0.32	d : 0.11	c : 0.09	f : 0.09	i : 0.07	[ : 0.05	$ : 0.05	! : 0.05	" : 0.05	g : 0.03	# : 0.01	e : 0.01	
= : 0.28	c : 0.13	f : 0.09	" : 0.09	d : 0.07	i : 0.07	$ : 0.05	b : 0.05	# : 0.03	! : 0.03	g : 0.01	[ : 0.01	e : 0.01	
= : 0.28	c : 0.13	" : 0.11	b : 0.09	f : 0.09	i : 0.07	$ : 0.05	# : 0.03	! : 0.03	g : 0.01	d : 0.01	[ : 0.01	e : 0.01	
= : 0.26	! : 0.16	" : 0.09	c : 0.07	f : 0.07	a : 0.07	$ : 0.05	[ : 0.05	b : 0.03	# : 0.03	i : 0.03	g : 0.01	
! : 0.24	[ : 0.22	d : 0.15	= : 0.13	$ : 0.03	c : 0.03	" : 0.03	i : 0.03	b : 0.01	g : 0.01	# : 0.01	r : 0.01	f : 0.01	
c : 0.39	d : 0.18	= : 0.11	! : 0.09	b : 0.05	r : 0.03	g : 0.01	a : 0.01	f : 0.01	" : 0.01	[ : 0.01	i : 0.01	
c : 0.41	d : 0.18	b : 0.16	= : 0.07	[ : 0.03	r : 0.03	g : 0.01	f : 0.01	s : 0.01	i : 0.01	
c : 0.39	d : 0.18	b : 0.13	= : 0.07	r : 0.05	a : 0.03	m : 0.03	q : 0.01	g : 0.01	s : 0.01	i : 0.01	
o : 0.64	l : 0.07	m : 0.07	r : 0.05	c : 0.03	d : 0.03	q : 0.01	g : 0.01	s : 0.01	= : 0.01	
o : 0.67	m : 0.11	l : 0.07	r : 0.05	c : 0.01	q : 0.01	s : 0.01	n : 0.01	
o : 0.67	m : 0.11	l : 0.07	r : 0.05	c : 0.01	q : 0.01	s : 0.01	n : 0.01	
o : 0.67	m : 0.07	c : 0.05	r : 0.05	b : 0.03	l : 0.01	q : 0.01	s : 0.01	n : 0.01	d : 0.01	
o : 0.67	c : 0.09	r : 0.05	b : 0.03	m : 0.03	l : 0.01	q : 0.01	s : 0.01	n : 0.01	d : 0.01	
o : 0.67	c : 0.09	] : 0.03	= : 0.03	r : 0.03	d : 0.03	l : 0.01	q : 0.01	s : 0.01	n : 0.01	
c : 0.35	d : 0.15	= : 0.13	b : 0.13	a : 0.07	o : 0.03	2 : 0.01	] : 0.01	q : 0.01	r : 0.01	s : 0.01	i : 0.01	
c : 0.33	b : 0.15	d : 0.15	= : 0.13	] : 0.07	i : 0.03	2 : 0.01	g : 0.01	r : 0.01	s : 0.01	3 : 0.01	4 : 0.01	
c : 0.37	= : 0.18	d : 0.15	i : 0.05	2 : 0.03	b : 0.03	3 : 0.03	4 : 0.03	g : 0.01	a : 0.01	] : 0.01	f : 0.01	
= : 0.24	2 : 0.15	d : 0.13	4 : 0.11	c : 0.07	i : 0.05	] : 0.05	3 : 0.05	b : 0.03	6 : 0.03	g : 0.01	f : 0.01	
= : 0.26	2 : 0.15	4 : 0.13	c : 0.07	b : 0.05	i : 0.05	f : 0.05	3 : 0.05	6 : 0.03	] : 0.03	[ : 0.01	g : 0.01	d : 0.01	a : 0.01	
= : 0.28	c : 0.11	4 : 0.11	b : 0.07	i : 0.07	2 : 0.05	f : 0.05	3 : 0.05	] : 0.05	6 : 0.03	d : 0.03	g : 0.01	a : 0.01	
= : 0.30	c : 0.09	4 : 0.09	i : 0.07	f : 0.07	d : 0.07	b : 0.05	3 : 0.05	] : 0.03	6 : 0.03	2 : 0.03	g : 0.03	e : 0.01	
= : 0.30	d : 0.13	c : 0.11	f : 0.09	i : 0.07	g : 0.05	b : 0.05	6 : 0.03	4 : 0.03	3 : 0.03	2 : 0.01	] : 0.01	e : 0.01	
= : 0.30	d : 0.13	f : 0.11	i : 0.07	c : 0.05	g : 0.05	b : 0.05	6 : 0.03	4 : 0.03	3 : 0.03	] : 0.03	[ : 0.01	2 : 0.01	e : 0.01	
= : 0.30	f : 0.11	c : 0.11	d : 0.09	g : 0.07	2 : 0.07	b : 0.05	i : 0.05	4 : 0.03	] : 0.03	3 : 0.01	e : 0.01	
= : 0.26	c : 0.09	d : 0.07	f : 0.07	] : 0.07	g : 0.07	2 : 0.07	4 : 0.07	i : 0.05	b : 0.03	3 : 0.03	: : 0.01	a : 0.01	e : 0.01	
= : 0.24	e : 0.11	g : 0.11	c : 0.11	] : 0.09	f : 0.07	3 : 0.07	4 : 0.05	d : 0.03	i : 0.03	m : 0.01	2 : 0.01	
= : 0.22	e : 0.15	c : 0.13	g : 0.11	d : 0.07	3 : 0.07	f : 0.05	i : 0.03	4 : 0.03	m : 0.01	[ : 0.01	2 : 0.01	] : 0.01	h : 0.01	

#score	779.9990970642166
#seq	53
#width	36
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014d_hg19_transcript_m3_run1.txt

#BEAR
Dcccqqqqqqqqccc	chr3:49013374-49013605(+)$1	231	186	201	12.9586
iiiiqqqqqqqqiii	chr4:110557128-110557410(+)$1	282	250	265	12.9825
ddddqqqqqqqqddd	chrX:18838901-18839117(+)$1	216	54	69	14.0881
"cccqqqqqqqqccc	chr3:14795522-14795733(+)$1	211	172	187	13.5187
ddddqqqqqqqqddd	chr2:204600012-204600259(+)$1	247	170	185	14.0881
ddddqqqqqqqqddd	chr5:56116016-56116269(+)$1	253	237	252	14.0881
f!!aqqqqqqqqa]f	chr17:2914941-2915163(+)$1	222	177	192	12.5171
ddddqqqqqqqqddd	chr16:78915491-78915712(+)$1	221	150	165	14.0881
eeeeqqqqqqqqeee	chr9:102882411-102882641(+)$1	230	143	158	13.1215
"cccqqqqqqqqccc	chr16:81504711-81505001(+)$1	290	197	212	13.5187
[cccqqqqqqqqccc	chr5:134193529-134193782(+)$1	253	182	197	13.5914
eeeeqqqqqqqqeee	chr7:22262778-22262998(-)$1	220	17	32	13.1215
ffffqqqqqqqqfff	chr7:87523978-87524235(+)$1	257	30	45	12.2054
:cccqqqqqqqqccc	chr10:35732310-35732547(+)$1	237	133	148	12.7002
ggggqqqqqqqqggg	chr6:20592677-20592918(+)$1	241	139	154	13.0091
ddddqqqqqqqqddd	chr3:14498160-14498373(+)$1	213	93	108	14.0881
ddddqqqqqqqqddd	chr5:133472317-133472535(+)$1	218	90	105	14.0881
:cccqqqqqqqqccc	chr17:62092355-62092614(-)$1	259	116	131	12.7002
eeeeqqqqqqqqeee	chr1:234411248-234411491(+)$1	243	168	183	13.1215
ffffqqqqqqqqfff	chr1:118677887-118678161(-)$1	274	175	190	12.2054
ddddqqqqqqqqddd	chr1:198641841-198642152(+)$1	311	199	214	14.0881
dd[aqqqqqqqqa]d	chr7:18451043-18451259(+)$1	216	178	193	13.2841
gcccqqqqqqqqccc	chr13:43625703-43625923(+)$1	220	175	190	13.5584
ddddqqqqqqqqddd	chr11:14889765-14890044(+)$1	279	182	197	14.0881
====qqqqqqqq===	chr2:197924279-197924534(-)$1	255	158	173	13.1051
'cccqqqqqqqqccc	chr19:14045360-14045589(-)$1	229	177	192	12.9891
eeeeqqqqqqqqeee	chr11:96057548-96057831(-)$1	283	5	20	13.1215
ddddqqqqqqqqddd	chr15:63915142-63915466(-)$1	324	210	225	14.0881
ddbbqqqqqqqqbb]	chr20:3947277-3947521(-)$1	244	8	23	12.1687
:cccqqqqqqqqccc	chr22:47105359-47105652(-)$1	293	97	112	12.7002
:cccqqqqqqqqccc	chr22:42909245-42909490(-)$1	245	107	122	12.7002
ddddqqqqqqqqddd	chr18:57001437-57001675(-)$1	238	0	15	14.0881
ddddqqqqqqqqddd	chr6:81002888-81003108(+)$1	220	34	49	14.0881
eeeeqqqqqqqqeee	chr3:140670177-140670414(+)$1	237	106	121	13.1215
ddddqqqqqqqqddd	chr12:3328245-3328457(+)$1	212	170	185	14.0881
ddddqqqqqqqqddd	chr5:175920086-175920393(+)$1	307	182	197	14.0881
!cccqqqqqqqqccc	chr11:65922993-65923213(+)$1	220	55	70	13.6289
ddddqqqqqqqqddd	chrX:37281988-37282205(+)$1	217	100	115	14.0881
ddddqqqqqqqqddd	chr18:72409616-72409850(+)$1	234	55	70	14.0881
[cccqqqqqqqqccc	chr3:139889443-139889657(+)$1	214	19	34	13.5914
ddddqqqqqqqqddd	chr3:56654392-56654610(-)$1	218	95	110	14.0881
ggggqqqqqqqqggg	chr3:114376965-114377248(-)$1	283	27	42	13.0091
[cccqqqqqqqqccc	chr1:89286944-89287178(+)$1	234	17	32	13.5914
ggggqqqqqqqqggg	chr18:55246391-55246653(-)$1	262	164	179	13.0091
ddddqqqqqqqqddd	chr1:3145407-3145622(+)$1	215	178	193	14.0881
ddddqqqqqqqqddd	chr3:132341654-132341899(-)$1	245	20	35	14.0881
:cccqqqqqqqqccc	chr1:232092224-232092467(+)$1	243	140	155	12.7002
ddddqqqqqqqqddd	chr8:81908391-81908665(-)$1	274	167	182	14.0881
ggggqqqqqqqqggg	chr6:21042374-21042629(+)$1	255	73	88	13.0091
iiiiqqqqqqqqiii	chr5:119908011-119908224(+)$1	213	154	169	12.9825
dd[aqqqqqqqqa]d	chr12:51101789-51102023(+)$1	234	169	184	13.2841
ddddqqqqqqqqddd	chr6:146467264-146467497(+)$1	233	81	96	14.0881
!cccqqqqqqqqccc	chr7:70085172-70085393(+)$1	221	97	112	13.6289
ffffqqqqqqqqfff	chr7:141774924-141775148(+)$1	224	111	126	12.2054
gcccqqqqqqqqccc	chr1:23391984-23392264(+)$1	280	153	168	13.5584
ffffqqqqqqqqfff	chr1:181542903-181543117(+)$1	214	145	160	12.2054
eeeeqqqqqqqqeee	chr10:28891228-28891503(+)$1	275	190	205	13.1215
eeeeqqqqqqqqeee	chr3:71397520-71397964(-)$1	444	425	440	13.1215
c[bbqqqqqqqqbb]	chr15:26101587-26101828(-)$1	241	20	35	11.7657
ddddqqqqqqqqddd	chr17:37942193-37942469(-)$1	276	128	143	14.0881
eeeeqqqqqqqqeee	chr18:55333183-55333445(+)$1	262	79	94	13.1215
====qqqqqqqq===	chr7:42976160-42976449(+)$1	289	138	153	13.1051
ggggqqqqqqqqggg	chr20:7877725-7877948(-)$1	223	115	130	13.0091
ggggqqqqqqqqggg	chr20:60588832-60589219(-)$1	387	23	38	13.0091
:cccqqqqqqqqccc	chr19:36712595-36712847(+)$1	252	9	24	12.7002
ddddqqqqqqqqddd	chr5:94418432-94418652(-)$1	220	103	118	14.0881
ddddqqqqqqqqddd	chr3:61727228-61727452(+)$1	224	45	60	14.0881
eeeeqqqqqqqqeee	chr21:43362026-43362246(-)$1	220	157	172	13.1215
ddddqqqqqqqqddd	chr17:11312081-11312295(+)$1	214	58	73	14.0881
ddddqqqqqqqqddd	chr2:12863010-12863252(+)$1	242	81	96	14.0881
eeeeqqqqqqqqeee	chr16:23861396-23861644(+)$1	248	182	197	13.1215
ddddqqqqqqqqddd	chr3:59862710-59862974(-)$1	264	108	123	14.0881
ddddqqqqqqqqddd	chr11:111718795-111719033(-)$1	238	124	139	14.0881
[cccqqqqqqqqccc	chr16:22331347-22331583(+)$1	236	33	48	13.5914

#otherMatches

#Seq PSSM
uguccaacucuugac	chr3:49013374-49013605(+)$1	231	186	201	12.9586
UUCUAAAACAUCGGA	chr4:110557128-110557410(+)$1	282	250	265	12.9825
cagaauaaagucucu	chrX:18838901-18839117(+)$1	216	54	69	14.0881
cuguuuccccuugca	chr3:14795522-14795733(+)$1	211	172	187	13.5187
GCUGUUUUCCUUUAG	chr2:204600012-204600259(+)$1	247	170	185	14.0881
GACCAUGAGCUAGGU	chr5:56116016-56116269(+)$1	253	237	252	14.0881
gcugaucuugaacuc	chr17:2914941-2915163(+)$1	222	177	192	12.5171
UGGCUUGUCUACGCC	chr16:78915491-78915712(+)$1	221	150	165	14.0881
UACUGCUAUCAAGGU	chr9:102882411-102882641(+)$1	230	143	158	13.1215
auguacccacacgca	chr16:81504711-81505001(+)$1	290	197	212	13.5187
UAUUGUAUAAUGAAU	chr5:134193529-134193782(+)$1	253	182	197	13.5914
aaguuaccaauuacu	chr7:22262778-22262998(-)$1	220	17	32	13.1215
gagaguucuuugucu	chr7:87523978-87524235(+)$1	257	30	45	12.2054
acugucuuccaccag	chr10:35732310-35732547(+)$1	237	133	148	12.7002
agccucccacguggc	chr6:20592677-20592918(+)$1	241	139	154	13.0091
gagUCACACUUCACU	chr3:14498160-14498373(+)$1	213	93	108	14.0881
AGGGGCCAUGAACCC	chr5:133472317-133472535(+)$1	218	90	105	14.0881
aggacucucauuucc	chr17:62092355-62092614(-)$1	259	116	131	12.7002
UGACCUCAGAUAGUC	chr1:234411248-234411491(+)$1	243	168	183	13.1215
GCUGAUAAACCACAG	chr1:118677887-118678161(-)$1	274	175	190	12.2054
UCCUGUCACCUGAGG	chr1:198641841-198642152(+)$1	311	199	214	14.0881
ucuccugaccucgug	chr7:18451043-18451259(+)$1	216	178	193	13.2841
ccauaaacaugcaug	chr13:43625703-43625923(+)$1	220	175	190	13.5584
UUCACAUAGACUUGA	chr11:14889765-14890044(+)$1	279	182	197	14.0881
AUAUCUGAAUACAUG	chr2:197924279-197924534(-)$1	255	158	173	13.1051
cugcacaccuacgca	chr19:14045360-14045589(-)$1	229	177	192	12.9891
UCUCAUUACCUGGAG	chr11:96057548-96057831(-)$1	283	5	20	13.1215
UUCAUUUUAAAUUGA	chr15:63915142-63915466(-)$1	324	210	225	14.0881
UCUCUUCCCUCUGAU	chr20:3947277-3947521(-)$1	244	8	23	12.1687
GUGUUAUAAAUUGCA	chr22:47105359-47105652(-)$1	293	97	112	12.7002
CUGCAUUCACCAGCA	chr22:42909245-42909490(-)$1	245	107	122	12.7002
UGCAUCUUUCUUUGU	chr18:57001437-57001675(-)$1	238	0	15	14.0881
acugaccuagcacag	chr6:81002888-81003108(+)$1	220	34	49	14.0881
CAUAUACCCACUUAU	chr3:140670177-140670414(+)$1	237	106	121	13.1215
uugugaacaaugaca	chr12:3328245-3328457(+)$1	212	170	185	14.0881
cucaacaaaaacuga	chr5:175920086-175920393(+)$1	307	182	197	14.0881
agagacugauagcuc	chr11:65922993-65923213(+)$1	220	55	70	13.6289
aguaaacaaaccuac	chrX:37281988-37282205(+)$1	217	100	115	14.0881
AAUUAAAACUUAGAU	chr18:72409616-72409850(+)$1	234	55	70	14.0881
AAGGAAGGCAGACCU	chr3:139889443-139889657(+)$1	214	19	34	13.5914
UAGUGAAUCAAAACU	chr3:56654392-56654610(-)$1	218	95	110	14.0881
uauaaguucauauau	chr3:114376965-114377248(-)$1	283	27	42	13.0091
caucuauaauaugau	chr1:89286944-89287178(+)$1	234	17	32	13.5914
uuuuuuuuuuuugag	chr18:55246391-55246653(-)$1	262	164	179	13.0091
GCUCUUCAAGAUGAG	chr1:3145407-3145622(+)$1	215	178	193	14.0881
UGGGUAAGAAAUCCU	chr3:132341654-132341899(-)$1	245	20	35	14.0881
cugugcaacaaaaca	chr1:232092224-232092467(+)$1	243	140	155	12.7002
CCUAAAGAAGAGUAG	chr8:81908391-81908665(-)$1	274	167	182	14.0881
UUGGUCUUCUAUCUA	chr6:21042374-21042629(+)$1	255	73	88	13.0091
gaaaaucagacauuu	chr5:119908011-119908224(+)$1	213	154	169	12.9825
uuuguucugucucua	chr12:51101789-51102023(+)$1	234	169	184	13.2841
ucccuaguagcuggg	chr6:146467264-146467497(+)$1	233	81	96	14.0881
CUGAAAACACAAUCA	chr7:70085172-70085393(+)$1	221	97	112	13.6289
uauucauccacugau	chr7:141774924-141775148(+)$1	224	111	126	12.2054
AGAUGCAGUCCUGUC	chr1:23391984-23392264(+)$1	280	153	168	13.5584
ugguacauauacacc	chr1:181542903-181543117(+)$1	214	145	160	12.2054
GUAACACCACUAUUA	chr10:28891228-28891503(+)$1	275	190	205	13.1215
GUCCAACAUCUGGGA	chr3:71397520-71397964(-)$1	444	425	440	13.1215
auugccuauauccau	chr15:26101587-26101828(-)$1	241	20	35	11.7657
cugugcucauuagca	chr17:37942193-37942469(-)$1	276	128	143	14.0881
UUAGAAAUAAGACUA	chr18:55333183-55333445(+)$1	262	79	94	13.1215
auauacacacacaua	chr7:42976160-42976449(+)$1	289	138	153	13.1051
gugucaguccuugca	chr20:7877725-7877948(-)$1	223	115	130	13.0091
UUUUAAGGCACCAAG	chr20:60588832-60589219(-)$1	387	23	38	13.0091
cacauucuucuuugu	chr19:36712595-36712847(+)$1	252	9	24	12.7002
gccuugAACCCUAGG	chr5:94418432-94418652(-)$1	220	103	118	14.0881
GAACUUUGGGAUGUU	chr3:61727228-61727452(+)$1	224	45	60	14.0881
guccacauaauggga	chr21:43362026-43362246(-)$1	220	157	172	13.1215
UAUUGACGUGAUGAU	chr17:11312081-11312295(+)$1	214	58	73	14.0881
ugcauuacguuuugc	chr2:12863010-12863252(+)$1	242	81	96	14.0881
uguaaguaguacugc	chr16:23861396-23861644(+)$1	248	182	197	13.1215
aagaauauaacaucu	chr3:59862710-59862974(-)$1	264	108	123	14.0881
cucaaaacacucuga	chr11:111718795-111719033(-)$1	238	124	139	14.0881
caugacuuaacacau	chr16:22331347-22331583(+)$1	236	33	48	13.5914

#DB
)(((........)))	chr3:49013374-49013605(+)$1	1	186	201	12.9586
((((........)))	chr4:110557128-110557410(+)$1	1	250	265	12.9825
((((........)))	chrX:18838901-18839117(+)$1	1	54	69	14.0881
.(((........)))	chr3:14795522-14795733(+)$1	1	172	187	13.5187
((((........)))	chr2:204600012-204600259(+)$1	1	170	185	14.0881
((((........)))	chr5:56116016-56116269(+)$1	1	237	252	14.0881
(..(........).)	chr17:2914941-2915163(+)$1	1	177	192	12.5171
((((........)))	chr16:78915491-78915712(+)$1	1	150	165	14.0881
((((........)))	chr9:102882411-102882641(+)$1	1	143	158	13.1215
.(((........)))	chr16:81504711-81505001(+)$1	1	197	212	13.5187
.(((........)))	chr5:134193529-134193782(+)$1	1	182	197	13.5914
((((........)))	chr7:22262778-22262998(-)$1	1	17	32	13.1215
((((........)))	chr7:87523978-87524235(+)$1	1	30	45	12.2054
.(((........)))	chr10:35732310-35732547(+)$1	1	133	148	12.7002
((((........)))	chr6:20592677-20592918(+)$1	1	139	154	13.0091
((((........)))	chr3:14498160-14498373(+)$1	1	93	108	14.0881
((((........)))	chr5:133472317-133472535(+)$1	1	90	105	14.0881
.(((........)))	chr17:62092355-62092614(-)$1	1	116	131	12.7002
((((........)))	chr1:234411248-234411491(+)$1	1	168	183	13.1215
((((........)))	chr1:118677887-118678161(-)$1	1	175	190	12.2054
((((........)))	chr1:198641841-198642152(+)$1	1	199	214	14.0881
((.(........).)	chr7:18451043-18451259(+)$1	1	178	193	13.2841
((((........)))	chr13:43625703-43625923(+)$1	1	175	190	13.5584
((((........)))	chr11:14889765-14890044(+)$1	1	182	197	14.0881
((((........)))	chr2:197924279-197924534(-)$1	1	158	173	13.1051
.(((........)))	chr19:14045360-14045589(-)$1	1	177	192	12.9891
((((........)))	chr11:96057548-96057831(-)$1	1	5	20	13.1215
((((........)))	chr15:63915142-63915466(-)$1	1	210	225	14.0881
((((........)).	chr20:3947277-3947521(-)$1	1	8	23	12.1687
.(((........)))	chr22:47105359-47105652(-)$1	1	97	112	12.7002
.(((........)))	chr22:42909245-42909490(-)$1	1	107	122	12.7002
((((........)))	chr18:57001437-57001675(-)$1	1	0	15	14.0881
((((........)))	chr6:81002888-81003108(+)$1	1	34	49	14.0881
((((........)))	chr3:140670177-140670414(+)$1	1	106	121	13.1215
((((........)))	chr12:3328245-3328457(+)$1	1	170	185	14.0881
((((........)))	chr5:175920086-175920393(+)$1	1	182	197	14.0881
.(((........)))	chr11:65922993-65923213(+)$1	1	55	70	13.6289
((((........)))	chrX:37281988-37282205(+)$1	1	100	115	14.0881
((((........)))	chr18:72409616-72409850(+)$1	1	55	70	14.0881
.(((........)))	chr3:139889443-139889657(+)$1	1	19	34	13.5914
((((........)))	chr3:56654392-56654610(-)$1	1	95	110	14.0881
((((........)))	chr3:114376965-114377248(-)$1	1	27	42	13.0091
.(((........)))	chr1:89286944-89287178(+)$1	1	17	32	13.5914
((((........)))	chr18:55246391-55246653(-)$1	1	164	179	13.0091
((((........)))	chr1:3145407-3145622(+)$1	1	178	193	14.0881
((((........)))	chr3:132341654-132341899(-)$1	1	20	35	14.0881
.(((........)))	chr1:232092224-232092467(+)$1	1	140	155	12.7002
((((........)))	chr8:81908391-81908665(-)$1	1	167	182	14.0881
((((........)))	chr6:21042374-21042629(+)$1	1	73	88	13.0091
((((........)))	chr5:119908011-119908224(+)$1	1	154	169	12.9825
((.(........).)	chr12:51101789-51102023(+)$1	1	169	184	13.2841
((((........)))	chr6:146467264-146467497(+)$1	1	81	96	14.0881
.(((........)))	chr7:70085172-70085393(+)$1	1	97	112	13.6289
((((........)))	chr7:141774924-141775148(+)$1	1	111	126	12.2054
((((........)))	chr1:23391984-23392264(+)$1	1	153	168	13.5584
((((........)))	chr1:181542903-181543117(+)$1	1	145	160	12.2054
((((........)))	chr10:28891228-28891503(+)$1	1	190	205	13.1215
((((........)))	chr3:71397520-71397964(-)$1	1	425	440	13.1215
(.((........)).	chr15:26101587-26101828(-)$1	1	20	35	11.7657
((((........)))	chr17:37942193-37942469(-)$1	1	128	143	14.0881
((((........)))	chr18:55333183-55333445(+)$1	1	79	94	13.1215
((((........)))	chr7:42976160-42976449(+)$1	1	138	153	13.1051
((((........)))	chr20:7877725-7877948(-)$1	1	115	130	13.0091
((((........)))	chr20:60588832-60589219(-)$1	1	23	38	13.0091
.(((........)))	chr19:36712595-36712847(+)$1	1	9	24	12.7002
((((........)))	chr5:94418432-94418652(-)$1	1	103	118	14.0881
((((........)))	chr3:61727228-61727452(+)$1	1	45	60	14.0881
((((........)))	chr21:43362026-43362246(-)$1	1	157	172	13.1215
((((........)))	chr17:11312081-11312295(+)$1	1	58	73	14.0881
((((........)))	chr2:12863010-12863252(+)$1	1	81	96	14.0881
((((........)))	chr16:23861396-23861644(+)$1	1	182	197	13.1215
((((........)))	chr3:59862710-59862974(-)$1	1	108	123	14.0881
((((........)))	chr11:111718795-111719033(-)$1	1	124	139	14.0881
.(((........)))	chr16:22331347-22331583(+)$1	1	33	48	13.5914

#PSSM
d : 0.40	e : 0.13	g : 0.10	: : 0.08	f : 0.06	[ : 0.05	i : 0.02	" : 0.02	= : 0.02	! : 0.02	D : 0.01	' : 0.01	c : 0.01	
d : 0.40	c : 0.24	e : 0.13	g : 0.08	f : 0.05	i : 0.02	= : 0.02	! : 0.01	[ : 0.01	
d : 0.36	c : 0.24	e : 0.13	g : 0.08	f : 0.05	i : 0.02	[ : 0.02	= : 0.02	b : 0.02	! : 0.01	
d : 0.36	c : 0.24	e : 0.13	g : 0.08	f : 0.05	a : 0.04	i : 0.02	= : 0.02	b : 0.02	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
d : 0.36	c : 0.24	e : 0.13	g : 0.08	f : 0.05	a : 0.04	i : 0.02	= : 0.02	b : 0.02	
d : 0.36	c : 0.24	e : 0.13	g : 0.08	f : 0.05	] : 0.04	i : 0.02	= : 0.02	b : 0.02	
d : 0.39	c : 0.24	e : 0.13	g : 0.08	f : 0.06	i : 0.02	= : 0.02	] : 0.02	

#score	991.5937424011903
#seq	74
#width	15
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_HNRNPL_Shankarling2014a_hg19_transcript_m2_run2.txt

#BEAR
(((dddduuuuuuuuuuuudddd9	chr13:25879652-25879901(+)$1	249	95	119	18.6035
ceeeeevvvvvvvvvvvvveeeee	chr11:94232208-94232451(+)$1	243	115	139	22.8407
eeeeeyyyyyyyyyyyyyyyyeee	chr2:162022597-162022834(+)$1	237	98	122	23.2698
ggggggguuuuuuuuuuuuggggg	chr5:10739409-10739746(-)$1	337	141	165	22.5968
:fffffftttttttttttffffff	chr14:36774151-36774445(-)$1	294	216	240	19.2394
eeeeeuuuuuuuuuuuueeeee33	chr16:24053705-24053937(+)$1	232	16	40	21.5746
eeeeeeeettttttttttteeeee	chr12:94777510-94777773(-)$1	263	179	203	21.0048
eeeeeeeettttttttttteeeee	chr4:74089893-74090203(-)$1	310	75	99	21.0048
eeeeeyyyyyyyyyyyyyyyyeee	chr1:41580939-41581198(-)$1	259	184	208	23.2698
eeee[ccctttttttttttcccee	chr1:87358726-87358971(-)$1	245	189	213	21.2956
fffffuuuuuuuuuuuuffffff]	chr17:28448860-28449104(+)$1	244	25	49	20.7469
=====xxxxxxxxxxxxxxx====	chr3:45528805-45529051(+)$1	246	88	112	19.7493
:eeeeevvvvvvvvvvvvveeeee	chr4:25394243-25394481(+)$1	238	88	112	21.9020
[ddddxxxxxxxxxxxxxxxdddd	chr22:39117975-39118221(+)$1	246	115	139	18.7203
eeeeebbtttttttttttbb]eee	chr13:111288484-111288966(+)$1	482	338	362	21.0185
hhhhhwwwwwwwwwwwwwwhhhhh	chr8:48529221-48529491(+)$1	270	241	265	21.0575
hhhhhhvvvvvvvvvvvvvhhhhh	chr2:149450794-149451065(+)$1	271	80	104	20.3311
eeeeewwwwwwwwwwwwwweeeee	chr5:40686273-40686551(+)$1	278	152	176	23.2906
eeeecccuuuuuuuuuuuuccc]e	chr10:70256072-70256315(-)$1	243	105	129	23.1458
eeeeeyyyyyyyyyyyyyyyyeee	chr5:82823795-82824032(+)$1	237	87	111	23.2698
ffeeeeeuuuuuuuuuuuueeeee	chr4:88965546-88965805(+)$1	259	70	94	22.8618
eeeebbvvvvvvvvvvvvvbb]ee	chr15:57432421-57432732(+)$1	311	282	306	22.2348
iiiiivvvvvvvvvvvvviiiiii	chr5:179464148-179464411(-)$1	263	69	93	21.6009
ff[bbwwwwwwwwwwwwwwbb]ff	chr5:74643446-74643667(+)$1	221	41	65	21.7534
ddd!!bbtttttttttttbb22dd	chr12:21614108-21614356(+)$1	248	129	153	19.3648
g[cccwwwwwwwwwwwwwwcccgg	chr14:96989503-96989729(+)$1	226	106	130	22.8762
b[ddddvvvvvvvvvvvvvdddd]	chr1:183472920-183473186(+)$1	266	190	214	21.3166
[eeeeevvvvvvvvvvvvveeeee	chr6:158768567-158768842(+)$1	275	72	96	22.9409
ggggggguuuuuuuuuuuuggggg	chr13:31207221-31207461(+)$1	240	132	156	22.5968
eee[cccuuuuuuuuuuuucccee	chr18:54340969-54341231(+)$1	262	218	242	23.1421
========ttttttttttt=====	chr1:224436713-224436949(-)$1	236	176	200	20.5202
c!!bbwwwwwwwwwwwwwwbb22c	chr14:81986017-81986287(-)$1	270	150	174	21.2503
ffffffuuuuuuuuuuuuffffff	chr10:63968499-63968752(-)$1	253	124	148	21.7572
fffffyyyyyyyyyyyyyyyyfff	chr20:20443710-20443944(-)$1	234	132	156	22.4653
d[cccyyyyyyyyyyyyyyyyccc	chr2:63790022-63790275(-)$1	253	14	38	22.3850
eeeeewwwwwwwwwwwwwweeeee	chr1:46300582-46300820(+)$1	238	79	103	23.2906
ffffffvvvvvvvvvvvvvfffff	chr18:60622049-60622294(+)$1	245	151	175	21.8781
gggyyyyyyyyyyyyyyyyggggg	chr8:99504687-99504971(-)$1	284	17	41	22.1584
:eeeeevvvvvvvvvvvvveeeee	chr2:63701755-63702024(-)$1	269	234	258	21.9020
iddddyyyyyyyyyyyyyyyyddd	chr15:56210293-56210544(-)$1	251	57	81	21.9587
dddbbyyyyyyyyyyyyyyyybb]	chr2:225822808-225823065(-)$1	257	67	91	21.1842
ffffffuuuuuuuuuuuuffffff	chr4:39866662-39866912(-)$1	250	131	155	21.7572
=====xxxxxxxxxxxxxxx====	chr10:114299640-114299944(+)$1	304	8	32	19.7493
fffffwwwwwwwwwwwwwwfffff	chr18:59972310-59972569(+)$1	259	200	224	22.3080
e[fffffftttttttttttfffff	chr5:36979825-36980077(+)$1	252	50	74	19.9525
gggggggtttttttttttgggggg	chr2:70448673-70448951(-)$1	278	192	216	20.7958
ggggxxxxxxxxxxxxxxxggggg	chr3:44961042-44961365(-)$1	323	121	145	19.5188
iiiiiyyyyyyyyyyyyyyyyiii	chr9:95251074-95251343(+)$1	269	116	140	22.8004
fffffyyyyyyyyyyyyyyyyfff	chr2:63124055-63124321(+)$1	266	197	221	22.4653
GGcccwwwwwwwwwwwwwwcccGG	chr12:118805736-118805992(-)$1	256	191	215	20.4871
dddcccvvvvvvvvvvvvvccc]d	chr17:64345640-64346004(+)$1	364	46	70	21.9887
eeeeevvvvvvvvvvvvveeeee2	chr3:101032282-101032526(-)$1	244	181	205	21.9259
:cccyyyyyyyyyyyyyyyyccc:	chr1:98159879-98160116(-)$1	237	19	43	20.1706
ggggggguuuuuuuuuuuuggggg	chr5:10384124-10384353(+)$1	229	64	88	22.5968
!!cccxxxxxxxxxxxxxxxccce	chr17:33462999-33463251(-)$1	252	203	227	19.5536
""cccwwwwwwwwwwwwwwccc22	chr6:106727996-106728248(-)$1	252	164	188	21.9897
gggggwwwwwwwwwwwwwwggggg	chr5:132417446-132417771(+)$1	325	195	219	23.0071
[dddduuuuuuuuuuuudddd]gg	chr21:38226175-38226412(-)$1	237	167	191	20.7051
eeeeewwwwwwwwwwwwwweeeee	chr11:128381591-128381915(-)$1	324	202	226	23.2906
hhhhhwwwwwwwwwwwwwwhhhhh	chrX:46438653-46438921(+)$1	268	169	193	21.0575
cceeeeeuuuuuuuuuuuueeeee	chr11:3395853-3396137(-)$1	284	158	182	22.7893
[dddduuuuuuuuuuuudddd]dd	chr5:179426843-179427102(-)$1	259	217	241	20.3470
bb!!cccuuuuuuuuuuuuccc22	chr2:101637329-101637571(-)$1	242	178	202	21.6621
eeeeettttttttttteeeeeeee	chr13:60976672-60976909(+)$1	237	55	79	19.5143
ffffffvvvvvvvvvvvvvfffff	chr4:22478593-22478853(-)$1	260	79	103	21.8781
ggggbbtttttttttttbb]gggg	chr2:144089829-144090081(+)$1	252	222	246	20.1576
ee!!bbvvvvvvvvvvvvvbb22e	chr6:71235543-71235800(+)$1	257	104	128	21.4698

#otherMatches

#Seq PSSM
UCAAGUUCUACCCUUAAUAAGCUC	chr13:25879652-25879901(+)$1	249	95	119	18.6035
ACCACAAUUUACACAAUCCUGUGG	chr11:94232208-94232451(+)$1	243	115	139	22.8407
UGGAAAAAUACAAAAUUCAAAUUC	chr2:162022597-162022834(+)$1	237	98	122	23.2698
AAUCAUAAUAUUUGCCUCAUGUGA	chr5:10739409-10739746(-)$1	337	141	165	22.5968
GUCCUAUAGCUUCUAAAGAUAGGA	chr14:36774151-36774445(-)$1	294	216	240	19.2394
GUAGAUCUCCCUUCCCUUUUACAU	chr16:24053705-24053937(+)$1	232	16	40	21.5746
auaaguuacauaaauauaauaacu	chr12:94777510-94777773(-)$1	263	179	203	21.0048
UGAAUGAAUAUUAUCCCAUUUCAU	chr4:74089893-74090203(-)$1	310	75	99	21.0048
ucaaaguauaauagagcaaaauuu	chr1:41580939-41581198(-)$1	259	184	208	23.2698
aaucugccuaccguuaacuggcga	chr1:87358726-87358971(-)$1	245	189	213	21.2956
aauucacugguuuuuaagaguugu	chr17:28448860-28449104(+)$1	244	25	49	20.7469
UGGGACCUUUAGAACAUGUCUCCC	chr3:45528805-45529051(+)$1	246	88	112	19.7493
AGUUUACAUUUGUUCAUAAUAAAC	chr4:25394243-25394481(+)$1	238	88	112	21.9020
AUAACUAUCCUUUAUAAUCCGUUA	chr22:39117975-39118221(+)$1	246	115	139	18.7203
gcacacucauccacacacaGCUGU	chr13:111288484-111288966(+)$1	482	338	362	21.0185
gauagcacauuacaucucauuguc	chr8:48529221-48529491(+)$1	270	241	265	21.0575
UCAGGUUCAUCACAUACUUGCCUG	chr2:149450794-149451065(+)$1	271	80	104	20.3311
CCUGCAAACAAAUUAUUAAGUAGG	chr5:40686273-40686551(+)$1	278	152	176	23.2906
UGUUACCACCACUAUUCAAGGUAA	chr10:70256072-70256315(-)$1	243	105	129	23.1458
GUGGUCAUAAAAGAAACAUAAACC	chr5:82823795-82824032(+)$1	237	87	111	23.2698
CCUUGUAUUUAACAACAUUUGCAG	chr4:88965546-88965805(+)$1	259	70	94	22.8618
gacuguggaaacaaaggaaacaag	chr15:57432421-57432732(+)$1	311	282	306	22.2348
CACAUUUCACCUCCAACCGUGUGA	chr5:179464148-179464411(-)$1	263	69	93	21.6009
UUGUGUUUUAAUUAUCAUGUAGGG	chr5:74643446-74643667(+)$1	221	41	65	21.7534
AACUCACUUCAUUUCACUGUCUGU	chr12:21614108-21614356(+)$1	248	129	153	19.3648
CAUACUAAUAUCUAAAAAUGUAGU	chr14:96989503-96989729(+)$1	226	106	130	22.8762
AUAAUUCAACAAauucaacaauuu	chr1:183472920-183473186(+)$1	266	190	214	21.3166
caucuccugccaucucuuugaggu	chr6:158768567-158768842(+)$1	275	72	96	22.9409
uacagcauauuguuauaauuguug	chr13:31207221-31207461(+)$1	240	132	156	22.5968
augacuggcuuuuaucauguagca	chr18:54340969-54341231(+)$1	262	218	242	23.1421
uagaagugcuuuguuucuacauuu	chr1:224436713-224436949(-)$1	236	176	200	20.5202
uccacugucacaaauuucuguuca	chr14:81986017-81986287(-)$1	270	150	174	21.2503
cucaucuuaacaaccacugaugag	chr10:63968499-63968752(-)$1	253	124	148	21.7572
GUUGACUACAAACUGAAUUCUUUA	chr20:20443710-20443944(-)$1	234	132	156	22.4653
UAGAAUUAGAAAUGCAAUCCUUUC	chr2:63790022-63790275(-)$1	253	14	38	22.3850
GUACACAGACAUUUCCAUUUGUAC	chr1:46300582-46300820(+)$1	238	79	103	23.2906
cggggagaaacagcagcaaucccu	chr18:60622049-60622294(+)$1	245	151	175	21.8781
UAAUUACUCCCCUCUCUUUUUAUC	chr8:99504687-99504971(-)$1	284	17	41	22.1584
cccaucccucucAGAUACAGAUGG	chr2:63701755-63702024(-)$1	269	234	258	21.9020
UGCCUAGUAAACUGAAAAUAAAGG	chr15:56210293-56210544(-)$1	251	57	81	21.9587
UGCACUCAUAAACCAUACACUGUA	chr2:225822808-225823065(-)$1	257	67	91	21.1842
UCUUUUCAUUACAAAUCAGAAAGA	chr4:39866662-39866912(-)$1	250	131	155	21.7572
AUUAUGAUUGAAAUUUAUAAAUAG	chr10:114299640-114299944(+)$1	304	8	32	19.7493
AACUACCCUCCAUAAAUAUUAGUU	chr18:59972310-59972569(+)$1	259	200	224	22.3080
AAAAAAGUAAUAUUACUCAGCUUU	chr5:36979825-36980077(+)$1	252	50	74	19.9525
aaucuacuuucugucucuguagau	chr2:70448673-70448951(-)$1	278	192	216	20.7958
uauacaaccauaauacaaauauaa	chr3:44961042-44961365(-)$1	323	121	145	19.5188
GUGGAUUCACAUUCUUCACAUUUU	chr9:95251074-95251343(+)$1	269	116	140	22.8004
guguauucuccucguaguuuuuac	chr2:63124055-63124321(+)$1	266	197	221	22.4653
CUACCUUGAUAUCUAAUUUGGUGU	chr12:118805736-118805992(-)$1	256	191	215	20.4871
CAUCCCUUUUGAACAGUUUGGGUA	chr17:64345640-64346004(+)$1	364	46	70	21.9887
UUUGUACAUCUUCUCAAAAUAGAA	chr3:101032282-101032526(-)$1	244	181	205	21.9259
cccaagugaacauaaaagucugga	chr1:98159879-98160116(-)$1	237	19	43	20.1706
guauggcagcaaucagauggccgu	chr5:10384124-10384353(+)$1	229	64	88	22.5968
UUGCAAUCCUAAAAUACUAAUGUG	chr17:33462999-33463251(-)$1	252	203	227	19.5536
ugucuguuuacucuucuuaagaaa	chr6:106727996-106728248(-)$1	252	164	188	21.9897
cauguccacagaaaaacucauaug	chr5:132417446-132417771(+)$1	325	195	219	23.0071
cuuuuauuaaucacuccaggaugc	chr21:38226175-38226412(-)$1	237	167	191	20.7051
gucaguuucuccaaauccCCUGAC	chr11:128381591-128381915(-)$1	324	202	226	23.2906
GUGCUAUCCUGUCCUUUUCAGCAU	chrX:46438653-46438921(+)$1	268	169	193	21.0575
GCUUUUAUCACUACACUUUUAAAA	chr11:3395853-3396137(-)$1	284	158	182	22.7893
auaggaauaaguccucaccuacca	chr5:179426843-179427102(-)$1	259	217	241	20.3470
gauaguaccaaacccuauauacac	chr2:101637329-101637571(-)$1	242	178	202	21.6621
CAGGCAGAUAUAAAUAGCUUGGUA	chr13:60976672-60976909(+)$1	237	55	79	19.5143
AAAGCAUAAAUUAUUUACUUGUUU	chr4:22478593-22478853(-)$1	260	79	103	21.8781
GAGGGAAAAGAUGAAUAUCACUUC	chr2:144089829-144090081(+)$1	252	222	246	20.1576
CUGAUAAAUCUAAUAACUCUACAG	chr6:71235543-71235800(+)$1	257	104	128	21.4698

#DB
...((((............)))).	chr13:25879652-25879901(+)$1	1	95	119	18.6035
((((((.............)))))	chr11:94232208-94232451(+)$1	1	115	139	22.8407
(((((................)))	chr2:162022597-162022834(+)$1	1	98	122	23.2698
(((((((............)))))	chr5:10739409-10739746(-)$1	1	141	165	22.5968
.((((((...........))))))	chr14:36774151-36774445(-)$1	1	216	240	19.2394
(((((............)))))..	chr16:24053705-24053937(+)$1	1	16	40	21.5746
)))(((((...........)))))	chr12:94777510-94777773(-)$1	1	179	203	21.0048
((((((((...........)))))	chr4:74089893-74090203(-)$1	1	75	99	21.0048
(((((................)))	chr1:41580939-41581198(-)$1	1	184	208	23.2698
((((.(((...........)))))	chr1:87358726-87358971(-)$1	1	189	213	21.2956
(((((............)))))).	chr17:28448860-28449104(+)$1	1	25	49	20.7469
(((((...............))))	chr3:45528805-45529051(+)$1	1	88	112	19.7493
.(((((.............)))))	chr4:25394243-25394481(+)$1	1	88	112	21.9020
.((((...............))))	chr22:39117975-39118221(+)$1	1	115	139	18.7203
(((((((...........)).)))	chr13:111288484-111288966(+)$1	1	338	362	21.0185
(((((..............)))))	chr8:48529221-48529491(+)$1	1	241	265	21.0575
((((((.............)))))	chr2:149450794-149451065(+)$1	1	80	104	20.3311
(((((..............)))))	chr5:40686273-40686551(+)$1	1	152	176	23.2906
(((((((............))).)	chr10:70256072-70256315(-)$1	1	105	129	23.1458
(((((................)))	chr5:82823795-82824032(+)$1	1	87	111	23.2698
))(((((............)))))	chr4:88965546-88965805(+)$1	1	70	94	22.8618
((((((.............)).))	chr15:57432421-57432732(+)$1	1	282	306	22.2348
(((((.............))))))	chr5:179464148-179464411(-)$1	1	69	93	21.6009
((.((..............)).))	chr5:74643446-74643667(+)$1	1	41	65	21.7534
(((..((...........))..))	chr12:21614108-21614356(+)$1	1	129	153	19.3648
(.(((..............)))))	chr14:96989503-96989729(+)$1	1	106	130	22.8762
(.((((.............)))).	chr1:183472920-183473186(+)$1	1	190	214	21.3166
.(((((.............)))))	chr6:158768567-158768842(+)$1	1	72	96	22.9409
(((((((............)))))	chr13:31207221-31207461(+)$1	1	132	156	22.5968
(((.(((............)))))	chr18:54340969-54341231(+)$1	1	218	242	23.1421
((((((((...........)))))	chr1:224436713-224436949(-)$1	1	176	200	20.5202
(..((..............))..)	chr14:81986017-81986287(-)$1	1	150	174	21.2503
((((((............))))))	chr10:63968499-63968752(-)$1	1	124	148	21.7572
(((((................)))	chr20:20443710-20443944(-)$1	1	132	156	22.4653
(.(((................)))	chr2:63790022-63790275(-)$1	1	14	38	22.3850
(((((..............)))))	chr1:46300582-46300820(+)$1	1	79	103	23.2906
((((((.............)))))	chr18:60622049-60622294(+)$1	1	151	175	21.8781
(((................)))))	chr8:99504687-99504971(-)$1	1	17	41	22.1584
.(((((.............)))))	chr2:63701755-63702024(-)$1	1	234	258	21.9020
)((((................)))	chr15:56210293-56210544(-)$1	1	57	81	21.9587
(((((................)).	chr2:225822808-225823065(-)$1	1	67	91	21.1842
((((((............))))))	chr4:39866662-39866912(-)$1	1	131	155	21.7572
(((((...............))))	chr10:114299640-114299944(+)$1	1	8	32	19.7493
(((((..............)))))	chr18:59972310-59972569(+)$1	1	200	224	22.3080
(.((((((...........)))))	chr5:36979825-36980077(+)$1	1	50	74	19.9525
(((((((...........))))))	chr2:70448673-70448951(-)$1	1	192	216	20.7958
((((...............)))))	chr3:44961042-44961365(-)$1	1	121	145	19.5188
(((((................)))	chr9:95251074-95251343(+)$1	1	116	140	22.8004
(((((................)))	chr2:63124055-63124321(+)$1	1	197	221	22.4653
))(((..............)))))	chr12:118805736-118805992(-)$1	1	191	215	20.4871
((((((.............))).)	chr17:64345640-64346004(+)$1	1	46	70	21.9887
(((((.............))))).	chr3:101032282-101032526(-)$1	1	181	205	21.9259
.(((................))).	chr1:98159879-98160116(-)$1	1	19	43	20.1706
(((((((............)))))	chr5:10384124-10384353(+)$1	1	64	88	22.5968
..(((...............))))	chr17:33462999-33463251(-)$1	1	203	227	19.5536
..(((..............)))..	chr6:106727996-106728248(-)$1	1	164	188	21.9897
(((((..............)))))	chr5:132417446-132417771(+)$1	1	195	219	23.0071
.((((............)))).))	chr21:38226175-38226412(-)$1	1	167	191	20.7051
(((((..............)))))	chr11:128381591-128381915(-)$1	1	202	226	23.2906
(((((..............)))))	chrX:46438653-46438921(+)$1	1	169	193	21.0575
(((((((............)))))	chr11:3395853-3396137(-)$1	1	158	182	22.7893
.((((............)))).))	chr5:179426843-179427102(-)$1	1	217	241	20.3470
((..(((............)))..	chr2:101637329-101637571(-)$1	1	178	202	21.6621
(((((...........))))))))	chr13:60976672-60976909(+)$1	1	55	79	19.5143
((((((.............)))))	chr4:22478593-22478853(-)$1	1	79	103	21.8781
((((((...........)).))))	chr2:144089829-144090081(+)$1	1	222	246	20.1576
((..((.............))..)	chr6:71235543-71235800(+)$1	1	104	128	21.4698

#PSSM
e : 0.26	f : 0.14	g : 0.13	: : 0.05	[ : 0.05	d : 0.05	c : 0.04	= : 0.04	h : 0.04	i : 0.04	b : 0.02	( : 0.01	G : 0.01	! : 0.01	" : 0.01	
e : 0.31	f : 0.16	g : 0.11	d : 0.10	[ : 0.05	= : 0.04	h : 0.04	i : 0.02	! : 0.02	c : 0.02	( : 0.01	G : 0.01	" : 0.01	b : 0.01	
e : 0.32	f : 0.14	g : 0.11	d : 0.11	c : 0.08	= : 0.04	h : 0.04	! : 0.04	i : 0.02	( : 0.01	[ : 0.01	
e : 0.31	f : 0.14	g : 0.10	c : 0.10	d : 0.08	= : 0.04	h : 0.04	b : 0.04	! : 0.04	i : 0.02	[ : 0.01	y : 0.01	
e : 0.26	f : 0.14	c : 0.13	d : 0.08	b : 0.08	g : 0.07	= : 0.04	h : 0.04	i : 0.02	y : 0.02	[ : 0.01	! : 0.01	x : 0.01	
w : 0.17	y : 0.16	e : 0.11	f : 0.08	c : 0.07	x : 0.07	b : 0.07	g : 0.05	u : 0.05	d : 0.02	v : 0.02	h : 0.01	= : 0.01	t : 0.01	
v : 0.19	w : 0.17	y : 0.16	u : 0.08	x : 0.07	g : 0.05	e : 0.05	c : 0.05	f : 0.02	b : 0.02	t : 0.02	d : 0.01	= : 0.01	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.08	x : 0.07	e : 0.02	c : 0.01	= : 0.01	f : 0.01	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.16	x : 0.07	
u : 0.22	v : 0.19	w : 0.17	y : 0.16	t : 0.14	x : 0.07	e : 0.01	
v : 0.19	w : 0.17	u : 0.16	y : 0.16	t : 0.13	x : 0.07	e : 0.02	d : 0.02	f : 0.01	b : 0.01	
w : 0.17	v : 0.16	y : 0.16	u : 0.13	t : 0.07	x : 0.07	f : 0.05	e : 0.04	b : 0.04	d : 0.02	i : 0.01	g : 0.01	
e : 0.20	y : 0.14	f : 0.11	c : 0.11	g : 0.10	b : 0.08	d : 0.05	x : 0.05	h : 0.04	i : 0.01	= : 0.01	] : 0.01	
e : 0.20	c : 0.14	y : 0.13	g : 0.11	f : 0.11	d : 0.07	b : 0.05	= : 0.04	h : 0.04	] : 0.01	i : 0.01	2 : 0.01	
e : 0.26	c : 0.16	f : 0.14	g : 0.11	d : 0.05	] : 0.05	= : 0.04	h : 0.04	2 : 0.04	i : 0.02	b : 0.01	
e : 0.29	f : 0.16	g : 0.14	d : 0.08	2 : 0.05	= : 0.04	h : 0.04	c : 0.04	] : 0.02	i : 0.02	3 : 0.01	b : 0.01	G : 0.01	
e : 0.32	g : 0.14	f : 0.14	d : 0.07	] : 0.04	= : 0.04	h : 0.04	2 : 0.04	i : 0.02	c : 0.02	9 : 0.01	3 : 0.01	G : 0.01	: : 0.01	

#score	1443.3114733539742
#seq	67
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013a_hg19_CDS_m2_run1.txt

#BEAR
hhhhh[ccctttttttttttccch	chr9:131467583-131467879(+)$1	296	101	125	22.6505
!!ffffffuuuuuuuuuuuuffff	chr5:132412304-132412567(+)$1	263	64	88	22.5055
ebb[dddduuuuuuuuuuuudddd	chr8:145736436-145736672(+)$1	236	91	115	22.9717
Gcccyyyyyyyyyyyyyyyycccf	chr9:135553932-135554204(+)$1	272	39	63	19.1012
dddd[ddddtttttttttttdddd	chr6:133138010-133138261(+)$1	251	222	246	23.0443
$$$$ddddvvvvvvvvvvvvvddd	chr7:103008371-103008626(+)$1	255	166	190	22.6270
$$$$eeeeettttttttttteeee	chr17:43180357-43180589(+)$1	232	153	177	22.6888
:bb[eeeeettttttttttteeee	chr19:10277195-10277450(-)$1	255	181	205	22.2609
:eeeee[bbtttttttttttbbee	chr10:43882244-43882481(-)$1	237	51	75	21.2431
ccc!!dddduuuuuuuuuuuuddd	chr12:76780298-76780537(-)$1	239	18	42	23.1727
FFeeeeevvvvvvvvvvvvveeee	chr21:33039470-33039703(+)$1	233	20	44	21.5406
a[gggggggvvvvvvvvvvvvvgg	chr2:27430259-27430492(-)$1	233	198	222	22.3253
eeeea[ccctttttttttttccc]	chr4:39077555-39077780(+)$1	225	39	63	23.1827
gggggcccuuuuuuuuuuuuccc]	chr19:1987543-1987776(-)$1	233	141	165	23.5350
gcccdddduuuuuuuuuuuudddd	chr21:47832718-47832951(+)$1	233	141	165	23.2933
=!!cccccctttttttttttccc3	chr5:98129212-98129459(+)$1	247	115	139	23.7588
Fccc!!ccctttttttttttcccc	chr6:21595088-21595328(+)$1	240	62	86	23.4044
::ffffffuuuuuuuuuuuuffff	chr6:160204907-160205191(-)$1	284	57	81	20.6185
GGGGeeeeettttttttttteeee	chr19:2229683-2229918(+)$1	235	94	118	21.2017
dcccdddduuuuuuuuuuuudddd	chr15:66995539-66995776(+)$1	237	191	215	23.1728
eeee!!cccwwwwwwwwwwwwwwc	chr17:1554330-1554554(-)$1	224	9	33	20.5477
ddd[cccvvvvvvvvvvvvvccc]	chr2:183866801-183867040(-)$1	239	111	135	22.5734
!!a!!ddddvvvvvvvvvvvvvdd	chr17:48940297-48940566(-)$1	269	55	79	23.1045
ddddeeeeettttttttttteeee	chr1:201858534-201858808(+)$1	274	9	33	22.6541
e:::ddddvvvvvvvvvvvvvddd	chr1:186321079-186321334(-)$1	255	221	245	20.2655
hhhhddddvvvvvvvvvvvvvddd	chr7:156974788-156975037(+)$1	249	42	66	22.4000
eeee[cccuuuuuuuuuuuuccc]	chr1:1021195-1021430(-)$1	235	48	72	23.0890
!!bb[ddddtttttttttttdddd	chr17:4851537-4851777(-)$1	240	151	175	23.4112
ccc[ddddyyyyyyyyyyyyyyyy	chr4:83977978-83978226(+)$1	248	106	130	20.3479
dda[dddduuuuuuuuuuuudddd	chr21:18966407-18966647(-)$1	240	69	93	23.2487
b!!fffffftttttttttttffff	chr6:82914518-82914749(-)$1	231	117	141	22.4514
dddd!!ccctttttttttttccc]	chr8:12586686-12586923(-)$1	237	135	159	23.2508
hhhhhddddtttttttttttdddd	chr1:45244214-45244467(+)$1	253	154	178	22.6161
b[ccc[cccuuuuuuuuuuuuccc	chr6:26199050-26199286(-)$1	236	157	181	22.8714
[ggggggguuuuuuuuuuuugggg	chr1:46745983-46746216(-)$1	233	129	153	23.1653
dddd!!ccctttttttttttccc2	chr4:186272526-186272779(+)$1	253	105	129	23.0363
ggggggwwwwwwwwwwwwwwgggg	chr8:95897602-95897857(-)$1	255	39	63	20.9167
EEeeeeevvvvvvvvvvvvveeee	chr15:35273485-35273721(-)$1	236	28	52	20.6044
=========vvvvvvvvvvvvv==	chr18:57022511-57022749(-)$1	238	189	213	22.2277
%%%%dddduuuuuuuuuuuudddd	chr22:50944622-50944948(-)$1	326	165	189	21.1311
gggggddddtttttttttttdddd	chr19:59067973-59068199(-)$1	226	14	38	23.6155
::ccc[ccctttttttttttcccc	chr7:100028489-100028752(+)$1	263	17	41	22.0308
ffffeeeeevvvvvvvvvvvvvee	chr17:72860017-72860274(-)$1	257	57	81	21.8195
=[a[bbbbyyyyyyyyyyyyyyyy	chr17:48829445-48829710(+)$1	265	200	224	19.1572
iiiieeeeeuuuuuuuuuuuueee	chr16:30793280-30793534(-)$1	254	106	130	22.6333
dddd!!a[attttttttttta]a2	chr6:42978798-42979039(+)$1	241	144	168	22.6270
$$bb[ddddtttttttttttdddd	chr16:23701131-23701403(+)$1	272	58	82	22.9070
dd!!cccwwwwwwwwwwwwwwccc	chr22:39884197-39884443(+)$1	246	126	150	21.5178
ccc[dddduuuuuuuuuuuudddd	chr2:160599579-160599843(+)$1	264	178	202	23.4849
####eeeeettttttttttteeee	chr1:117504159-117504390(+)$1	231	98	122	23.3081
ccc[dddduuuuuuuuuuuudddd	chr9:139323990-139324258(-)$1	268	95	119	23.4849
h####cccuuuuuuuuuuuuccch	chr19:13051565-13051799(+)$1	234	89	113	22.9958
bggggggguuuuuuuuuuuugggg	chr1:168034811-168035042(+)$1	231	133	157	22.9163
dhhhhhhhhvvvvvvvvvvvvvhh	chr6:168281008-168281245(+)$1	237	190	214	20.4124
ggggggwwwwwwwwwwwwwwgggg	chr19:55912801-55913083(-)$1	282	208	232	20.9167
ffff[ddddtttttttttttdddd	chr19:19790944-19791175(+)$1	231	169	193	23.1055
:bb[bb[bbtttttttttttbb]b	chrX:70472685-70472944(-)$1	259	8	32	20.1624
!!a!!ddddvvvvvvvvvvvvvdd	chr17:48940429-48940664(-)$1	235	153	177	23.1045
[ggggggguuuuuuuuuuuugggg	chr1:46746000-46746271(-)$1	271	184	208	23.1653
eeefffffftttttttttttffff	chr19:49119902-49120170(-)$1	268	106	130	22.0535
!!ffffffuuuuuuuuuuuuffff	chr9:131493530-131493769(-)$1	239	38	62	22.5055
bb:fffffftttttttttttffff	chr21:28209964-28210204(-)$1	240	64	88	21.0940
ff!!eeeeevvvvvvvvvvvvvee	chr13:108863087-108863328(-)$1	241	132	156	22.2555
[eeeeecccwwwwwwwwwwwwwwc	chr16:30958447-30958764(+)$1	317	146	170	20.6176
:ffffffvvvvvvvvvvvvvffff	chr16:24583052-24583287(+)$1	235	105	129	20.8750
g[gggggggtttttttttttgggg	chr7:45614090-45614360(+)$1	270	40	64	23.2234
"ggggggguuuuuuuuuuuugggg	chr2:220435132-220435385(-)$1	253	50	74	23.1587
$$$$eeeeettttttttttteeee	chr7:44618979-44619249(-)$1	270	225	249	22.6888
ccdddd!!avvvvvvvvvvvvva2	chr1:70716267-70716539(+)$1	272	188	212	21.8251

#otherMatches

#Seq PSSM
UGGCCACAGACCGCCGCCACUUGG	chr9:131467583-131467879(+)$1	296	101	125	22.6505
GACAUUGGGAGGUAGAAAAUUUGA	chr5:132412304-132412567(+)$1	263	64	88	22.5055
CACCCAGCACCUUUCUCUGAGCUG	chr8:145736436-145736672(+)$1	236	91	115	22.9717
GCACAAUAAUCGAAAAAUGAGUGG	chr9:135553932-135554204(+)$1	272	39	63	19.1012
AUGCUGGGUAAUCAUAUAAAACCU	chr6:133138010-133138261(+)$1	251	222	246	23.0443
AUCCUAACCUUAUAUAGACUUGUU	chr7:103008371-103008626(+)$1	255	166	190	22.6270
CAGGUCUCUAACACGUUCCCAGAG	chr17:43180357-43180589(+)$1	232	153	177	22.6888
AGGCGGGUUAUUUGUUUCUGAACU	chr19:10277195-10277450(-)$1	255	181	205	22.2609
CGAGAACGACAUUUACAACUUCUU	chr10:43882244-43882481(-)$1	237	51	75	21.2431
CUCGGUUAUUGGUUAAUAAAUGUG	chr12:76780298-76780537(-)$1	239	18	42	23.1727
CAAGUUUUAAUUUAGCUCAUGAAC	chr21:33039470-33039703(+)$1	233	20	44	21.5406
GCUGGCCACCUUCCAGUCAGCCGU	chr2:27430259-27430492(-)$1	233	198	222	22.3253
AGUAGUCAGACAUUAUCAUCCUGU	chr4:39077555-39077780(+)$1	225	39	63	23.1827
UUCACCGUCAACCCCAAGCCACGA	chr19:1987543-1987776(-)$1	233	141	165	23.5350
UCUUGGUGAAAAAUGAAAUGCGCC	chr21:47832718-47832951(+)$1	233	141	165	23.2933
GGAGGCCCUGCACCCAAGGAAGGA	chr5:98129212-98129459(+)$1	247	115	139	23.7588
GGCCCAGGAAGAAGGUGAAGUCCG	chr6:21595088-21595328(+)$1	240	62	86	23.4044
UAGACGUAUUAACUUAAUCUUAUG	chr6:160204907-160205191(-)$1	284	57	81	20.6185
CUGCAGGUAACUAGGAUUUCUACC	chr19:2229683-2229918(+)$1	235	94	118	21.2017
GGCCCCGCGGGCAAGAGAGGGCGG	chr15:66995539-66995776(+)$1	237	191	215	23.1728
GGGGCCGCCAGAACACAGACAAGG	chr17:1554330-1554554(-)$1	224	9	33	20.5477
GCUGUCUCGAAUUGAAGAAAGGAA	chr2:183866801-183867040(-)$1	239	111	135	22.5734
UUCCCAGGUGACAGCCCCCUUAAC	chr17:48940297-48940566(-)$1	269	55	79	23.1045
CACUGGGCACCCCCAAUCCCUGCC	chr1:201858534-201858808(+)$1	274	9	33	22.6541
AUUCAGGUAACCAAAUAAAAAGCC	chr1:186321079-186321334(-)$1	255	221	245	20.2655
AGUUUCUGGCAGCACCUUUUACAG	chr7:156974788-156975037(+)$1	249	42	66	22.4000
CGUGGCCGCCUCCCUCUUCCUGGG	chr1:1021195-1021430(-)$1	235	48	72	23.0890
AUCGUGGGCUACAAGGACUCGCCC	chr17:4851537-4851777(-)$1	240	151	175	23.4112
CAAUGUAGAUUAUAAACUGGAGAC	chr4:83977978-83978226(+)$1	248	106	130	20.3479
GGGAAUGGCCAUCAGAAUCACUAU	chr21:18966407-18966647(-)$1	240	69	93	23.2487
UGAUCAACUUCUCAUAACCCGGUU	chr6:82914518-82914749(-)$1	231	117	141	22.4514
CUUGCCCUCUCCAUGUAUUUGAGC	chr8:12586686-12586923(-)$1	237	135	159	23.2508
GUCUUCACCCAUGUAAUAAAGGUG	chr1:45244214-45244467(+)$1	253	154	178	22.6161
GUACUGCUCCCCAAGAAGACUGAG	chr6:26199050-26199286(-)$1	236	157	181	22.8714
UGUUUUGCAAACACUCAAAGGUAG	chr1:46745983-46746216(-)$1	233	129	153	23.1653
GAAGCACUUUAUGCCUUCUUGAGC	chr4:186272526-186272779(+)$1	253	105	129	23.0363
AUUGUACUCAAUAAAAAUAUUACA	chr8:95897602-95897857(-)$1	255	39	63	20.9167
CAGGGCAGAAACCAUUUGAAUGCU	chr15:35273485-35273721(-)$1	236	28	52	20.6044
UGACAAUGAUGGAAAGGUAUAUUU	chr18:57022511-57022749(-)$1	238	189	213	22.2277
UUCCGCCUCAUGUUCGCCUCAGGC	chr22:50944622-50944948(-)$1	326	165	189	21.1311
CAUCUCUCUUUUCUUUUCCUGGAG	chr19:59067973-59068199(-)$1	226	14	38	23.6155
CUCUCACCCCCUUACUCCACGGGG	chr7:100028489-100028752(+)$1	263	17	41	22.0308
CUGGUGUUGCCCACACUCUCCCCA	chr17:72860017-72860274(-)$1	257	57	81	21.8195
AUAGUGGCAUAGAAAAAGUAUAAA	chr17:48829445-48829710(+)$1	265	200	224	19.1572
AGCUCCCAGAAGAGUCCAGAGCUG	chr16:30793280-30793534(-)$1	254	106	130	22.6333
CCAGGACGUGUACACCAUCAAGGC	chr6:42978798-42979039(+)$1	241	144	168	22.6270
AAGCUCAUCUUGUGCCCACUGAUG	chr16:23701131-23701403(+)$1	272	58	82	22.9070
UGACGGCGUCCUUUUCCUCAAGCU	chr22:39884197-39884443(+)$1	246	126	150	21.5178
UUAUCAGGUAAGAAUGAGUUUCUG	chr2:160599579-160599843(+)$1	264	178	202	23.4849
CCAAGCCUGUUAACAUAUUUUGGG	chr1:117504159-117504390(+)$1	231	98	122	23.3081
GAGUCAGAACUCCAGCACCAUCUG	chr9:139323990-139324258(-)$1	268	95	119	23.4849
UCUAUGCCUAUGAUAACUUUGGCG	chr19:13051565-13051799(+)$1	234	89	113	22.9958
CAUGUGGUAAACUGCCUGCAGCCA	chr1:168034811-168035042(+)$1	231	133	157	22.9163
UAAGGAACUUUAUCAAAUCAGUAG	chr6:168281008-168281245(+)$1	237	190	214	20.4124
GCUGGCGAGCGCGAUAAGAAGCUG	chr19:55912801-55913083(-)$1	282	208	232	20.9167
agccugggcaacauaagaaggccc	chr19:19790944-19791175(+)$1	231	169	193	23.1055
UGGACCUGCUUGAUACCCCUGCUG	chrX:70472685-70472944(-)$1	259	8	32	20.1624
UUCCCAGGUGACAGCCCCCUUAAC	chr17:48940429-48940664(-)$1	235	153	177	23.1045
UGUUUUGCAAACACUCAAAGGUAG	chr1:46746000-46746271(-)$1	271	184	208	23.1653
UCCUGGCCGGGAAAACAAGACGGC	chr19:49119902-49120170(-)$1	268	106	130	22.0535
GCUGGGCUCACCCCCACCCAAGCC	chr9:131493530-131493769(-)$1	239	38	62	22.5055
CCUGCUUCCGAGUGUGCAAAGGAA	chr21:28209964-28210204(-)$1	240	64	88	21.0940
GGAAGUUUAACCAUACAGCAAGUA	chr13:108863087-108863328(-)$1	241	132	156	22.2555
ACCUCCGGCUUCAUUUCACCCCUG	chr16:30958447-30958764(+)$1	317	146	170	20.6176
CUUAACCCACCAGAGACACAGGUU	chr16:24583052-24583287(+)$1	235	105	129	20.8750
CAUGGCGCUGAGAUggcgggggcg	chr7:45614090-45614360(+)$1	270	40	64	23.2234
ACGUGUGCCACGCCCGCAACGCGC	chr2:220435132-220435385(-)$1	253	50	74	23.1587
ACACAGUCCUUUAUCCACCUGGAU	chr7:44618979-44619249(-)$1	270	225	249	22.6888
CAUCAUGAAGAAGACAUGGAUAUG	chr1:70716267-70716539(+)$1	272	188	212	21.8251

#DB
(((((.(((...........))))	chr9:131467583-131467879(+)$1	1	101	125	22.6505
..((((((............))))	chr5:132412304-132412567(+)$1	1	64	88	22.5055
(((.((((............))))	chr8:145736436-145736672(+)$1	1	91	115	22.9717
((((................)))(	chr9:135553932-135554204(+)$1	1	39	63	19.1012
((((.((((...........))))	chr6:133138010-133138261(+)$1	1	222	246	23.0443
....((((.............)))	chr7:103008371-103008626(+)$1	1	166	190	22.6270
....(((((...........))))	chr17:43180357-43180589(+)$1	1	153	177	22.6888
.((.(((((...........))))	chr19:10277195-10277450(-)$1	1	181	205	22.2609
.(((((.((...........))))	chr10:43882244-43882481(-)$1	1	51	75	21.2431
(((..((((............)))	chr12:76780298-76780537(-)$1	1	18	42	23.1727
(((((((.............))))	chr21:33039470-33039703(+)$1	1	20	44	21.5406
(.(((((((.............))	chr2:27430259-27430492(-)$1	1	198	222	22.3253
(((((.(((...........))).	chr4:39077555-39077780(+)$1	1	39	63	23.1827
((((((((............))).	chr19:1987543-1987776(-)$1	1	141	165	23.5350
)(((((((............))))	chr21:47832718-47832951(+)$1	1	141	165	23.2933
(..((((((...........))).	chr5:98129212-98129459(+)$1	1	115	139	23.7588
((((..(((...........))))	chr6:21595088-21595328(+)$1	1	62	86	23.4044
..((((((............))))	chr6:160204907-160205191(-)$1	1	57	81	20.6185
(((((((((...........))))	chr19:2229683-2229918(+)$1	1	94	118	21.2017
((((((((............))))	chr15:66995539-66995776(+)$1	1	191	215	23.1728
((((..(((..............)	chr17:1554330-1554554(-)$1	1	9	33	20.5477
(((.(((.............))).	chr2:183866801-183867040(-)$1	1	111	135	22.5734
..(..((((.............))	chr17:48940297-48940566(-)$1	1	55	79	23.1045
(((((((((...........))))	chr1:201858534-201858808(+)$1	1	9	33	22.6541
)...((((.............)))	chr1:186321079-186321334(-)$1	1	221	245	20.2655
((((((((.............)))	chr7:156974788-156975037(+)$1	1	42	66	22.4000
((((.(((............))).	chr1:1021195-1021430(-)$1	1	48	72	23.0890
..((.((((...........))))	chr17:4851537-4851777(-)$1	1	151	175	23.4112
(((.((((................	chr4:83977978-83978226(+)$1	1	106	130	20.3479
(((.((((............))))	chr21:18966407-18966647(-)$1	1	69	93	23.2487
(..((((((...........))))	chr6:82914518-82914749(-)$1	1	117	141	22.4514
((((..(((...........))).	chr8:12586686-12586923(-)$1	1	135	159	23.2508
)))))((((...........))))	chr1:45244214-45244467(+)$1	1	154	178	22.6161
(.(((.(((............)))	chr6:26199050-26199286(-)$1	1	157	181	22.8714
.(((((((............))))	chr1:46745983-46746216(-)$1	1	129	153	23.1653
((((..(((...........))).	chr4:186272526-186272779(+)$1	1	105	129	23.0363
((((((..............))))	chr8:95897602-95897857(-)$1	1	39	63	20.9167
(((((((.............))))	chr15:35273485-35273721(-)$1	1	28	52	20.6044
(((((((((.............))	chr18:57022511-57022749(-)$1	1	189	213	22.2277
....((((............))))	chr22:50944622-50944948(-)$1	1	165	189	21.1311
(((((((((...........))))	chr19:59067973-59068199(-)$1	1	14	38	23.6155
..(((.(((...........))))	chr7:100028489-100028752(+)$1	1	17	41	22.0308
))))(((((.............))	chr17:72860017-72860274(-)$1	1	57	81	21.8195
(.(.((((................	chr17:48829445-48829710(+)$1	1	200	224	19.1572
(((((((((............)))	chr16:30793280-30793534(-)$1	1	106	130	22.6333
((((..(.(...........).).	chr6:42978798-42979039(+)$1	1	144	168	22.6270
..((.((((...........))))	chr16:23701131-23701403(+)$1	1	58	82	22.9070
((..(((..............)))	chr22:39884197-39884443(+)$1	1	126	150	21.5178
(((.((((............))))	chr2:160599579-160599843(+)$1	1	178	202	23.4849
....(((((...........))))	chr1:117504159-117504390(+)$1	1	98	122	23.3081
(((.((((............))))	chr9:139323990-139324258(-)$1	1	95	119	23.4849
(....(((............))))	chr19:13051565-13051799(+)$1	1	89	113	22.9958
((((((((............))))	chr1:168034811-168035042(+)$1	1	133	157	22.9163
)((((((((.............))	chr6:168281008-168281245(+)$1	1	190	214	20.4124
((((((..............))))	chr19:55912801-55913083(-)$1	1	208	232	20.9167
((((.((((...........))))	chr19:19790944-19791175(+)$1	1	169	193	23.1055
.((.((.((...........)).)	chrX:70472685-70472944(-)$1	1	8	32	20.1624
..(..((((.............))	chr17:48940429-48940664(-)$1	1	153	177	23.1045
.(((((((............))))	chr1:46746000-46746271(-)$1	1	184	208	23.1653
)))((((((...........))))	chr19:49119902-49120170(-)$1	1	106	130	22.0535
..((((((............))))	chr9:131493530-131493769(-)$1	1	38	62	22.5055
)).((((((...........))))	chr21:28209964-28210204(-)$1	1	64	88	21.0940
((..(((((.............))	chr13:108863087-108863328(-)$1	1	132	156	22.2555
.((((((((..............)	chr16:30958447-30958764(+)$1	1	146	170	20.6176
.((((((.............))))	chr16:24583052-24583287(+)$1	1	105	129	20.8750
(.(((((((...........))))	chr7:45614090-45614360(+)$1	1	40	64	23.2234
.(((((((............))))	chr2:220435132-220435385(-)$1	1	50	74	23.1587
....(((((...........))))	chr7:44618979-44619249(-)$1	1	225	249	22.6888
((((((..(.............).	chr1:70716267-70716539(+)$1	1	188	212	21.8251

#PSSM
d : 0.14	e : 0.08	: : 0.08	g : 0.08	! : 0.07	c : 0.07	h : 0.05	$ : 0.05	b : 0.05	= : 0.04	[ : 0.04	f : 0.04	G : 0.02	F : 0.02	a : 0.01	E : 0.01	% : 0.01	i : 0.01	# : 0.01	" : 0.01	
c : 0.13	d : 0.11	g : 0.11	! : 0.10	e : 0.08	h : 0.05	b : 0.05	$ : 0.05	[ : 0.05	f : 0.05	: : 0.04	# : 0.02	F : 0.01	G : 0.01	E : 0.01	= : 0.01	% : 0.01	i : 0.01	
c : 0.14	g : 0.14	e : 0.11	d : 0.10	f : 0.08	b : 0.07	h : 0.05	! : 0.05	a : 0.05	$ : 0.04	: : 0.02	# : 0.02	G : 0.01	= : 0.01	% : 0.01	i : 0.01	
g : 0.14	f : 0.13	[ : 0.13	c : 0.10	e : 0.10	d : 0.08	! : 0.07	h : 0.05	$ : 0.04	b : 0.02	# : 0.02	G : 0.01	: : 0.01	= : 0.01	% : 0.01	i : 0.01	
e : 0.18	d : 0.17	g : 0.14	! : 0.11	f : 0.10	[ : 0.07	c : 0.07	h : 0.04	b : 0.02	y : 0.01	a : 0.01	= : 0.01	# : 0.01	
d : 0.30	e : 0.18	g : 0.11	f : 0.10	c : 0.08	! : 0.07	[ : 0.05	b : 0.02	y : 0.01	= : 0.01	h : 0.01	
d : 0.28	c : 0.21	e : 0.15	f : 0.10	g : 0.08	[ : 0.02	w : 0.02	y : 0.01	= : 0.01	b : 0.01	a : 0.01	h : 0.01	! : 0.01	
d : 0.28	c : 0.18	e : 0.13	f : 0.08	g : 0.08	v : 0.05	b : 0.04	w : 0.04	y : 0.01	= : 0.01	[ : 0.01	h : 0.01	! : 0.01	
u : 0.24	c : 0.14	d : 0.13	e : 0.13	v : 0.10	y : 0.04	f : 0.04	w : 0.04	b : 0.02	g : 0.02	a : 0.02	= : 0.01	h : 0.01	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
t : 0.37	u : 0.28	v : 0.21	w : 0.07	y : 0.04	
d : 0.18	c : 0.17	v : 0.15	e : 0.11	f : 0.10	g : 0.10	u : 0.04	w : 0.04	b : 0.02	y : 0.02	a : 0.01	
d : 0.24	c : 0.20	e : 0.13	v : 0.11	f : 0.10	g : 0.10	b : 0.02	w : 0.02	y : 0.02	] : 0.01	
d : 0.27	c : 0.20	e : 0.17	g : 0.11	f : 0.10	w : 0.02	y : 0.02	a : 0.02	= : 0.01	h : 0.01	] : 0.01	
d : 0.27	e : 0.17	f : 0.11	g : 0.11	c : 0.08	] : 0.07	h : 0.04	2 : 0.04	y : 0.02	3 : 0.01	= : 0.01	b : 0.01	

#score	1535.8771775844828
#seq	69
#width	24
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
CLIPSeq_SFRS1_Sanford2009_hg19_CDS_m3_run1.txt

#BEAR
g"""bbqqqqqqqqbb333gg	chr4:2959237-2959480(-)$1	243	66	87	14.5871
ccddddqqqqqqqqdddd]cc	chr22:39772010-39772254(+)$1	244	175	196	14.0128
bb!!bbqqqqqqqqbb333bb	chr17:42882761-42882994(-)$1	233	113	134	13.9830
ffffffqqqqqqqqffffff:	chr17:27993865-27994111(-)$1	246	57	78	13.0350
!eeeeeqqqqqqqqeeeee44	chr1:160251860-160252094(-)$1	234	114	135	14.7209
ddd[bbqqqqqqqqbb]dddd	chr12:66696381-66696625(+)$1	244	222	243	13.7428
:ddddaqqqqqqqqa]dddd:	chr7:1275457-1275699(+)$1	242	175	196	12.1606
ccc[cccqqqqqqqqcccccc	chr7:141341510-141341763(+)$1	253	15	36	12.2570
[bb[bbqqqqqqqqbb]bb]d	chr9:103212993-103213229(+)$1	236	59	80	13.9829
""ddddqqqqqqqqdddd333	chr7:26235918-26236152(-)$1	234	182	203	14.7925
!!bbbbqqqqqqqqbb]bb]f	chr1:85131764-85132011(-)$1	247	130	151	13.7792
iiiiiiqqqqqqqqiiiiiii	chr1:54518533-54518775(-)$1	242	124	145	14.5930
b!!cccqqqqqqqqccc]bb6	chr6:26285579-26285827(-)$1	248	104	125	13.6144
beeeeeqqqqqqqqeeeee::	chr6:79911319-79911543(-)$1	224	101	122	12.6017
[eeeeeqqqqqqqqeeeee]f	chr19:22271370-22271606(+)$1	236	197	218	14.6106
ggggggqqqqqqqqggggggg	chr12:56500345-56500600(+)$1	255	23	44	14.6218
[eeeeeqqqqqqqqeeeee]b	chr10:51246062-51246320(-)$1	258	218	239	14.6748
ggggggqqqqqqqqggggggg	chr17:79980601-79980826(-)$1	225	175	196	14.6218
ffffffqqqqqqqqffffff3	chr5:131066565-131066807(-)$1	242	92	113	13.8505
ffffffqqqqqqqqffffff]	chr21:44524347-44524590(-)$1	243	135	156	13.7467
ffffffqqqqqqqqffffff:	chrX:53244876-53245121(-)$1	245	51	72	13.0350
dddd[aqqqqqqqqa]dddd2	chr10:79743860-79744109(-)$1	249	146	167	13.5320
[bb[bbqqqqqqqqbb]bbbb	chr2:238972961-238973194(+)$1	233	174	195	13.6966
eee!!aqqqqqqqqa22eeee	chr5:176638425-176638679(+)$1	254	88	109	13.8392
[eeeeeqqqqqqqqeeeee]a	chr1:145916633-145916872(+)$1	239	96	117	14.8195
ggggggqqqqqqqqggggggg	chr17:29850812-29851049(+)$1	237	23	44	14.6218
ccc[bbqqqqqqqqbb]cccd	chr19:5641509-5641769(+)$1	260	115	136	14.2969
ffffffqqqqqqqqffffff:	chr2:214215217-214215454(+)$1	237	73	94	13.0350
[ccc[aqqqqqqqqaccc]bb	chr4:1730090-1730338(+)$1	248	73	94	14.5549
ffffffqqqqqqqqffffff5	chr17:80041323-80041569(-)$1	246	213	234	13.0979
d!!cccqqqqqqqqccc22dd	chr6:52137055-52137291(-)$1	236	64	85	13.7529
ggggggqqqqqqqqggggggg	chr4:89941608-89941873(-)$1	265	52	73	14.6218
e[a[cccqqqqqqqqccc22a	chr2:70315216-70315452(+)$1	236	58	79	12.4101
b[ddddqqqqqqqqdddd]bb	chr3:33576805-33577053(-)$1	248	112	133	13.7517
ddd[bbqqqqqqqqbb]dddd	chr20:46293852-46294119(-)$1	267	145	166	13.7428
eeddddqqqqqqqqdddd]ee	chr19:19216261-19216491(-)$1	230	119	140	13.6734
b[ddddqqqqqqqqdddd]bb	chr11:67376012-67376252(+)$1	240	77	98	13.7517
======qqqqqqqq=======	chr4:20618434-20618665(+)$1	231	34	55	15.0966
gg!!bbqqqqqqqqbb]gggg	chr19:49376855-49377097(+)$1	242	196	217	14.7205
ggggggqqqqqqqqggggggg	chr1:19582404-19582638(+)$1	234	151	172	14.6218
!eeeeeqqqqqqqqeeeee22	chr10:116204981-116205221(-)$1	240	195	216	14.4951
ccc[bbqqqqqqqqbb]ccc]	chr1:27333207-27333445(-)$1	238	46	67	14.5109
[eeeeeqqqqqqqqeeeee]b	chr10:47213167-47213425(-)$1	258	218	239	14.6748
ggggggqqqqqqqqggggggg	chr1:148274881-148275118(-)$1	237	144	165	14.6218
####bbqqqqqqqqbb22bb]	chr1:155722946-155723191(-)$1	245	163	184	13.6987
iiiiiiqqqqqqqqiiiiiii	chr6:155577515-155577755(-)$1	240	143	164	14.5930
###cccqqqqqqqqccc4444	chr19:21366344-21366580(+)$1	236	104	125	14.6389
!!a!!aqqqqqqqqa22a22b	chr7:100481929-100482229(+)$1	300	208	229	14.4549
"eeeeeqqqqqqqqeeeee]f	chr3:53265379-53265619(-)$1	240	109	130	14.5571
!eeeeeqqqqqqqqeeeee33	chr18:7050753-7050989(-)$1	236	27	48	14.9378
[eeeeeqqqqqqqqeeeee]c	chr19:10822795-10823040(+)$1	245	156	177	14.7304
$eeeeeqqqqqqqqeeeeebb	chr22:41246726-41246970(-)$1	244	210	231	14.0300
$bb!!aqqqqqqqqa22bb33	chr19:34959912-34960174(+)$1	262	170	191	13.7580
ccc[bbqqqqqqqqbbccc]d	chr12:53432919-53433173(+)$1	254	197	218	14.3835
ggggggqqqqqqqqggggggg	chr1:44446927-44447161(+)$1	234	202	223	14.6218
$$ddddqqqqqqqqdddd888	chr4:84367104-84367343(-)$1	239	138	159	12.7851
ddddddqqqqqqqqdddd]dd	chr17:7811108-7811318(+)$1	210	52	73	13.4646
a[ddddqqqqqqqqdddd]a]	chr21:27269823-27270072(-)$1	249	133	154	14.2747
!!ddddqqqqqqqqdddd22a	chr5:179249850-179250085(+)$1	235	130	151	14.4275
e[ddddqqqqqqqqdddd22e	chr2:86693664-86693895(+)$1	231	70	91	13.8138
"bb[bbqqqqqqqqbb]bbgg	chr16:88643980-88644230(+)$1	250	212	233	13.9095
[bb[bbqqqqqqqqbb22bbb	chr1:7792418-7792671(+)$1	253	164	185	13.4958
ffffffqqqqqqqqffffff:	chr2:55776950-55777225(-)$1	275	204	225	13.0350
[ccc[aqqqqqqqqa]ccc]c	chr10:102045817-102046068(-)$1	251	198	219	14.7401
=eeeeeqqqqqqqqeeeee22	chr5:36124249-36124467(-)$1	218	67	88	14.3458
======qqqqqqqq=======	chr6:105607494-105607737(-)$1	243	203	224	15.0966
fffcccqqqqqqqqccc]fff	chr11:118888003-118888241(-)$1	238	10	31	13.9218
!a!!cccqqqqqqqqccc22a	chr5:68470670-68470920(+)$1	250	137	158	12.6750

#otherMatches

#Seq PSSM
CAGAGAUAAACGCUUCGGAGA	chr4:2959237-2959480(-)$1	243	66	87	14.5871
UCUCCAUCUUCACCUGGGUGA	chr22:39772010-39772254(+)$1	244	175	196	14.0128
UGGAGCACGGUGAAGCAGACA	chr17:42882761-42882994(-)$1	233	113	134	13.9830
GGACUUUAAGAGAUGGGUCCA	chr17:27993865-27994111(-)$1	246	57	78	13.0350
UGUCGGAAGAAGAGCUGACCA	chr1:160251860-160252094(-)$1	234	114	135	14.7209
GAGGGUCCAAAGUAGCGCUUC	chr12:66696381-66696625(+)$1	244	222	243	13.7428
AAGCACGAGAAGAAGCUGCUG	chr7:1275457-1275699(+)$1	242	175	196	12.1606
GCUGAGCAGCUAGCAGCUAGC	chr7:141341510-141341763(+)$1	253	15	36	12.2570
ACUGAUACAAAUGAAUGAGGU	chr9:103212993-103213229(+)$1	236	59	80	13.9829
AUAUGAUUAGGUUUUCAUUAG	chr7:26235918-26236152(-)$1	234	182	203	14.7925
GGCUUCAGGAAAGAGACAGAC	chr1:85131764-85132011(-)$1	247	130	151	13.7792
CUGCGACCCUUCCCUUGCAGC	chr1:54518533-54518775(-)$1	242	124	145	14.5930
CUGGCCGUGGUAAAGGUGGAA	chr6:26285579-26285827(-)$1	248	104	125	13.6144
CACAGAAAACUGAAUCUGUAG	chr6:79911319-79911543(-)$1	224	101	122	12.6017
CUGGAGAGAAACCCUUCCAAU	chr19:22271370-22271606(+)$1	236	197	218	14.6106
cagggguacuucgguccuugg	chr12:56500345-56500600(+)$1	255	23	44	14.6218
UCGAGCUCCUUUCUGCUUGUA	chr10:51246062-51246320(-)$1	258	218	239	14.6748
CUCACGCGUGACACUGUGAGG	chr17:79980601-79980826(-)$1	225	175	196	14.6218
CUCAAGUUAAAGUCUUUGGGA	chr5:131066565-131066807(-)$1	242	92	113	13.8505
UCGGUUGCACAAUAAACCGAC	chr21:44524347-44524590(-)$1	243	135	156	13.7467
CUUCCUGGAGAGCAAGGAGGA	chrX:53244876-53245121(-)$1	245	51	72	13.0350
GGUAAGAAGAAAUCCCUAUUG	chr10:79743860-79744109(-)$1	249	146	167	13.5320
ACUGAUGGGAGAUAAUGGGGA	chr2:238972961-238973194(+)$1	233	174	195	13.6966
GGUAAAGAACACAGUGAACCG	chr5:176638425-176638679(+)$1	254	88	109	13.8392
CAUCAAUAUUGUUUUUGAUCG	chr1:145916633-145916872(+)$1	239	96	117	14.8195
AACCUCAUGGCGUCGAGGUUC	chr17:29850812-29851049(+)$1	237	23	44	14.6218
GGUGUGGAAGAUAACGGGCUG	chr19:5641509-5641769(+)$1	260	115	136	14.2969
GGUGUUACAUGAGAAACACCA	chr2:214215217-214215454(+)$1	237	73	94	13.0350
CGCCACCAGCAAAAGGGCACC	chr4:1730090-1730338(+)$1	248	73	94	14.5549
AUGGGUGUGGGUGGACCUGUG	chr17:80041323-80041569(-)$1	246	213	234	13.0979
UUCAUGAAGAAGUACAUCCAU	chr6:52137055-52137291(-)$1	236	64	85	13.7529
GGACUUACCCAAGAAGGUCUU	chr4:89941608-89941873(-)$1	265	52	73	14.6218
GCGGGGGAUAUGCUGCCCAAC	chr2:70315216-70315452(+)$1	236	58	79	12.4101
CCUGGGAUGUCUGACCCAAGA	chr3:33576805-33577053(-)$1	248	112	133	13.7517
CGGCCAGAAGAAUGUGACUGU	chr20:46293852-46294119(-)$1	267	145	166	13.7428
CUCCUGGAGAUAAGCGGGAAG	chr19:19216261-19216491(-)$1	230	119	140	13.6734
UGGAUCCUGGGCGAGAUCAAG	chr11:67376012-67376252(+)$1	240	77	98	13.7517
CUGAGUAGCAAAUGGCUCAGA	chr4:20618434-20618665(+)$1	231	34	55	15.0966
CCAGCCGUGGAGGAGGAGGAC	chr19:49376855-49377097(+)$1	242	196	217	14.7205
AGGGGGAGGAAGGCCCUUCUG	chr1:19582404-19582638(+)$1	234	151	172	14.6218
AUAAGAUCUauauuuuuugaa	chr10:116204981-116205221(-)$1	240	195	216	14.4951
GGCUGCAUGGUUCAGCUGCCA	chr1:27333207-27333445(-)$1	238	46	67	14.5109
UCGAGCUCCUUUCUGCUUGUA	chr10:47213167-47213425(-)$1	258	218	239	14.6748
UGAGCAAUUAUGGAUGCUUAA	chr1:148274881-148275118(-)$1	237	144	165	14.6218
AGGACCACCAGAAAGGGAGAG	chr1:155722946-155723191(-)$1	245	163	184	13.6987
GUGAGAAAAACACAUUUCGCU	chr6:155577515-155577755(-)$1	240	143	164	14.5930
UAAUUCAUACUGGAGAGAAAC	chr19:21366344-21366580(+)$1	236	104	125	14.6389
AACGACAAGGAUGAGAAGAAG	chr7:100481929-100482229(+)$1	300	208	229	14.4549
CAGAUCAUCCAGGAGAUCUAC	chr3:53265379-53265619(-)$1	240	109	130	14.5571
UGAGACUUUUCAGUGUCUUUG	chr18:7050753-7050989(-)$1	236	27	48	14.9378
GCCCCGAUAUCUGAUGGGGGU	chr19:10822795-10823040(+)$1	245	156	177	14.7304
AAACUGCUGCUCUCCAGUUAU	chr22:41246726-41246970(-)$1	244	210	231	14.0300
UAGAACAGAAGGAAGAGCUUG	chr19:34959912-34960174(+)$1	262	170	191	13.7580
GAGUCAGAUAGGUAUGCUUGU	chr12:53432919-53433173(+)$1	254	197	218	14.3835
UCGCCACCUGGUCUUGGUGAG	chr1:44446927-44447161(+)$1	234	202	223	14.6218
CACUGGAAAUGACCCUAGCAA	chr4:84367104-84367343(-)$1	239	138	159	12.7851
CUGGGAGGAGGGUGUCCUGAG	chr17:7811108-7811318(+)$1	210	52	73	13.4646
GAUGGAUGCAGAAUUCCGACA	chr21:27269823-27270072(-)$1	249	133	154	14.2747
UUUUCCAGUGACGAGGAAUUG	chr5:179249850-179250085(+)$1	235	130	151	14.4275
GUGCUUACCUACAAAGGCUUC	chr2:86693664-86693895(+)$1	231	70	91	13.8138
GGUGCUGGAAAGGAGGGACUC	chr16:88643980-88644230(+)$1	250	212	233	13.9095
AGCAGCACAAACAGGCGAGCG	chr1:7792418-7792671(+)$1	253	164	185	13.4958
UGUGGUCUUACAAUGCUGCAA	chr2:55776950-55777225(-)$1	275	204	225	13.0350
GACUGGGGAACUGACGGGUGA	chr10:102045817-102046068(-)$1	251	198	219	14.7401
GAAAUAUUUUUAUUUAUUUUA	chr5:36124249-36124467(-)$1	218	67	88	14.3458
UGUUUAAAAAUAAGUAAACAA	chr6:105607494-105607737(-)$1	243	203	224	15.0966
GACAAGCUCAAUAACUUAGUC	chr11:118888003-118888241(-)$1	238	10	31	13.9218
UUUUGUGACUGACAACACUUA	chr5:68470670-68470920(+)$1	250	137	158	12.6750

#DB
(...((........))...))	chr4:2959237-2959480(-)$1	1	66	87	14.5871
((((((........)))).))	chr22:39772010-39772254(+)$1	1	175	196	14.0128
((..((........))...))	chr17:42882761-42882994(-)$1	1	113	134	13.9830
((((((........)))))).	chr17:27993865-27994111(-)$1	1	57	78	13.0350
.(((((........)))))..	chr1:160251860-160252094(-)$1	1	114	135	14.7209
(((.((........)).))))	chr12:66696381-66696625(+)$1	1	222	243	13.7428
.(((((........).)))).	chr7:1275457-1275699(+)$1	1	175	196	12.1606
(((.(((........))))))	chr7:141341510-141341763(+)$1	1	15	36	12.2570
.((.((........)).)).)	chr9:103212993-103213229(+)$1	1	59	80	13.9829
..((((........))))...	chr7:26235918-26236152(-)$1	1	182	203	14.7925
..((((........)).)).)	chr1:85131764-85132011(-)$1	1	130	151	13.7792
((((((........)))))))	chr1:54518533-54518775(-)$1	1	124	145	14.5930
(..(((........))).)).	chr6:26285579-26285827(-)$1	1	104	125	13.6144
)(((((........)))))..	chr6:79911319-79911543(-)$1	1	101	122	12.6017
.(((((........))))).)	chr19:22271370-22271606(+)$1	1	197	218	14.6106
((((((........)))))))	chr12:56500345-56500600(+)$1	1	23	44	14.6218
.(((((........))))).)	chr10:51246062-51246320(-)$1	1	218	239	14.6748
((((((........)))))))	chr17:79980601-79980826(-)$1	1	175	196	14.6218
((((((........)))))).	chr5:131066565-131066807(-)$1	1	92	113	13.8505
((((((........)))))).	chr21:44524347-44524590(-)$1	1	135	156	13.7467
((((((........)))))).	chrX:53244876-53245121(-)$1	1	51	72	13.0350
((((.(........).)))).	chr10:79743860-79744109(-)$1	1	146	167	13.5320
.((.((........)).))))	chr2:238972961-238973194(+)$1	1	174	195	13.6966
(((..(........)..))))	chr5:176638425-176638679(+)$1	1	88	109	13.8392
.(((((........))))).)	chr1:145916633-145916872(+)$1	1	96	117	14.8195
((((((........)))))))	chr17:29850812-29851049(+)$1	1	23	44	14.6218
(((.((........)).)))(	chr19:5641509-5641769(+)$1	1	115	136	14.2969
((((((........)))))).	chr2:214215217-214215454(+)$1	1	73	94	13.0350
.(((.(........)))).))	chr4:1730090-1730338(+)$1	1	73	94	14.5549
((((((........)))))).	chr17:80041323-80041569(-)$1	1	213	234	13.0979
(..(((........)))..))	chr6:52137055-52137291(-)$1	1	64	85	13.7529
((((((........)))))))	chr4:89941608-89941873(-)$1	1	52	73	14.6218
(.(.(((........)))..)	chr2:70315216-70315452(+)$1	1	58	79	12.4101
(.((((........)))).))	chr3:33576805-33577053(-)$1	1	112	133	13.7517
(((.((........)).))))	chr20:46293852-46294119(-)$1	1	145	166	13.7428
((((((........)))).))	chr19:19216261-19216491(-)$1	1	119	140	13.6734
(.((((........)))).))	chr11:67376012-67376252(+)$1	1	77	98	13.7517
((((((........)))))))	chr4:20618434-20618665(+)$1	1	34	55	15.0966
((..((........)).))))	chr19:49376855-49377097(+)$1	1	196	217	14.7205
((((((........)))))))	chr1:19582404-19582638(+)$1	1	151	172	14.6218
.(((((........)))))..	chr10:116204981-116205221(-)$1	1	195	216	14.4951
(((.((........)).))).	chr1:27333207-27333445(-)$1	1	46	67	14.5109
.(((((........))))).)	chr10:47213167-47213425(-)$1	1	218	239	14.6748
((((((........)))))))	chr1:148274881-148275118(-)$1	1	144	165	14.6218
....((........))..)).	chr1:155722946-155723191(-)$1	1	163	184	13.6987
((((((........)))))))	chr6:155577515-155577755(-)$1	1	143	164	14.5930
...(((........)))....	chr19:21366344-21366580(+)$1	1	104	125	14.6389
..(..(........)..)..)	chr7:100481929-100482229(+)$1	1	208	229	14.4549
.(((((........))))).)	chr3:53265379-53265619(-)$1	1	109	130	14.5571
.(((((........)))))..	chr18:7050753-7050989(-)$1	1	27	48	14.9378
.(((((........))))).)	chr19:10822795-10823040(+)$1	1	156	177	14.7304
.(((((........)))))))	chr22:41246726-41246970(-)$1	1	210	231	14.0300
.((..(........)..))..	chr19:34959912-34960174(+)$1	1	170	191	13.7580
(((.((........))))).)	chr12:53432919-53433173(+)$1	1	197	218	14.3835
((((((........)))))))	chr1:44446927-44447161(+)$1	1	202	223	14.6218
..((((........))))...	chr4:84367104-84367343(-)$1	1	138	159	12.7851
((((((........)))).))	chr17:7811108-7811318(+)$1	1	52	73	13.4646
(.((((........)))).).	chr21:27269823-27270072(-)$1	1	133	154	14.2747
..((((........))))..)	chr5:179249850-179250085(+)$1	1	130	151	14.4275
(.((((........))))..)	chr2:86693664-86693895(+)$1	1	70	91	13.8138
.((.((........)).))))	chr16:88643980-88644230(+)$1	1	212	233	13.9095
.((.((........))..)))	chr1:7792418-7792671(+)$1	1	164	185	13.4958
((((((........)))))).	chr2:55776950-55777225(-)$1	1	204	225	13.0350
.(((.(........).))).)	chr10:102045817-102046068(-)$1	1	198	219	14.7401
((((((........)))))..	chr5:36124249-36124467(-)$1	1	67	88	14.3458
((((((........)))))))	chr6:105607494-105607737(-)$1	1	203	224	15.0966
((((((........))).)))	chr11:118888003-118888241(-)$1	1	10	31	13.9218
.(..(((........)))..)	chr5:68470670-68470920(+)$1	1	137	158	12.6750

#PSSM
[ : 0.14	g : 0.13	f : 0.11	! : 0.10	c : 0.07	b : 0.07	d : 0.07	e : 0.05	" : 0.04	= : 0.04	$ : 0.04	i : 0.02	# : 0.02	: : 0.01	a : 0.01	
e : 0.20	f : 0.11	g : 0.11	c : 0.10	b : 0.08	d : 0.07	! : 0.07	[ : 0.07	" : 0.02	i : 0.02	= : 0.02	# : 0.02	$ : 0.01	a : 0.01	
d : 0.20	e : 0.19	f : 0.11	g : 0.10	c : 0.08	b : 0.08	! : 0.07	i : 0.02	a : 0.02	= : 0.02	# : 0.02	" : 0.01	
d : 0.17	e : 0.17	[ : 0.16	f : 0.10	g : 0.10	! : 0.08	c : 0.08	i : 0.02	= : 0.02	" : 0.01	b : 0.01	# : 0.01	
b : 0.20	e : 0.17	d : 0.16	f : 0.10	c : 0.10	g : 0.10	[ : 0.04	! : 0.04	i : 0.02	= : 0.02	
b : 0.20	e : 0.17	d : 0.14	f : 0.10	a : 0.10	c : 0.10	g : 0.10	i : 0.02	= : 0.02	
q : 0.95	c : 0.04	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
q : 0.99	
b : 0.20	e : 0.17	d : 0.14	f : 0.10	a : 0.10	g : 0.10	c : 0.05	q : 0.04	i : 0.02	= : 0.02	
b : 0.20	e : 0.17	d : 0.14	c : 0.11	f : 0.10	g : 0.10	] : 0.04	2 : 0.04	i : 0.02	= : 0.02	
d : 0.17	e : 0.17	c : 0.14	] : 0.13	f : 0.10	g : 0.10	2 : 0.07	3 : 0.02	i : 0.02	= : 0.02	
d : 0.20	e : 0.19	c : 0.11	g : 0.11	f : 0.10	b : 0.07	2 : 0.04	3 : 0.02	i : 0.02	] : 0.02	= : 0.02	4 : 0.01	a : 0.01	
e : 0.19	f : 0.11	b : 0.11	g : 0.11	] : 0.10	2 : 0.08	c : 0.07	d : 0.05	3 : 0.04	i : 0.02	= : 0.02	4 : 0.01	8 : 0.01	
g : 0.14	] : 0.14	b : 0.13	f : 0.11	2 : 0.10	d : 0.08	c : 0.05	3 : 0.04	4 : 0.02	i : 0.02	e : 0.02	= : 0.02	: : 0.01	8 : 0.01	a : 0.01	
g : 0.14	b : 0.14	d : 0.10	: : 0.08	c : 0.05	3 : 0.05	f : 0.05	] : 0.05	a : 0.05	2 : 0.04	e : 0.04	4 : 0.02	i : 0.02	= : 0.02	6 : 0.01	5 : 0.01	8 : 0.01	

#score	953.3564545245094
#seq	68
#width	21
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000
#NAME
HITSCLIP_AGO2_Karginov2013e_hg19_CDS_m1_run1.txt

#BEAR
ffffwwwwwwwwwwwwwwfffff	chr19:18390744-18390969(-)$1	225	194	217	20.5524
====yyyyyyyyyyyyyyyy===	chrX:41206561-41206782(+)$1	221	177	200	22.0230
fffffftttttttttttffffff	chr5:126156603-126156825(+)$1	222	166	189	20.0346
eeeeeyyyyyyyyyyyyyyyyee	chr16:23646976-23647195(-)$1	219	110	133	21.3684
[cccuuuuuuuuuuuucccbb22	chr1:203276460-203276712(+)$1	252	162	185	20.6442
!!cccxxxxxxxxxxxxxxxccc	chr20:57605330-57605569(-)$1	239	9	32	17.6733
c[ccctttttttttttccc]ccc	chr12:98993687-98993957(+)$1	270	129	152	21.6391
[a[ccctttttttttttcccadd	chr17:79478465-79478706(-)$1	241	109	132	21.6615
h[ddddtttttttttttdddd]h	chr13:48522975-48523211(-)$1	236	8	31	21.1315
======ttttttttttt======	chr16:29818751-29819003(+)$1	252	24	47	21.4054
iiiiivvvvvvvvvvvvviiiii	chr19:8528383-8528627(+)$1	244	10	33	21.8412
:dddduuuuuuuuuuuudddddd	chr1:212241877-212242104(+)$1	227	90	113	21.4685
f[cccuuuuuuuuuuuuccc]ff	chr2:74755906-74756138(-)$1	232	156	179	22.8502
gggggxxxxxxxxxxxxxxxggg	chr6:109690011-109690249(-)$1	238	148	171	17.2435
[a!!auuuuuuuuuuuua22a]f	chr19:8381331-8381580(-)$1	249	142	165	22.8620
eeeeeyyyyyyyyyyyyyyyyee	chr14:95569853-95570102(-)$1	249	156	179	21.3684
[ddddvvvvvvvvvvvvvdddd]	chr1:228680695-228680926(+)$1	231	149	172	21.7561
fffffftttttttttttffffff	chr15:66170120-66170341(+)$1	221	181	204	20.0346
ddd[bbtttttttttttbbdddd	chr17:79803682-79803916(-)$1	234	11	34	20.3180
eeeeevvvvvvvvvvvvveeeee	chr9:124103454-124103680(-)$1	226	134	157	21.6775
eeeeeuuuuuuuuuuuueeeee]	chr17:62496705-62496961(-)$1	256	185	208	22.8008
!bbvvvvvvvvvvvvvbb22ccc	chr6:112041124-112041355(-)$1	231	190	213	18.7402
eeeeeuuuuuuuuuuuueeeee:	chr21:30435691-30435928(-)$1	237	0	23	21.8147
:dddduuuuuuuuuuuuddddcc	chr19:2328291-2328522(-)$1	231	9	32	21.7125
ggggggtttttttttttgggggg	chr16:30435649-30435875(-)$1	226	117	140	20.9421
[dddduuuuuuuuuuuudddd]c	chr19:46341741-46341963(-)$1	222	169	192	22.9726
ccc[auuuuuuuuuuuua]ccc]	chr3:172486760-172486986(+)$1	226	74	97	22.9967
"""bbvvvvvvvvvvvvvbb]ee	chr5:134121127-134121360(+)$1	233	146	169	20.9116
##cccxxxxxxxxxxxxxxxccc	chr1:78193991-78194217(-)$1	226	112	135	17.4069
[eeeeettttttttttteeeeef	chr1:115275248-115275516(-)$1	268	190	213	21.4305
==[bbuuuuuuuuuuuubb22==	chr11:9603019-9603283(+)$1	264	17	40	22.0675
eeeeevvvvvvvvvvvvveeeee	chr9:94172554-94172807(-)$1	253	29	52	21.6775
=====uuuuuuuuuuuu======	chr5:37333484-37333711(-)$1	227	178	201	23.0607
b[cccuuuuuuuuuuuucccbb:	chr2:62103202-62103444(-)$1	242	120	143	21.4317
!!cccxxxxxxxxxxxxxxxccc	chr11:9610040-9610296(+)$1	256	120	143	17.6733
eeeeettttttttttteeeee]h	chr1:44010656-44010882(+)$1	226	140	163	21.2105
[ccctttttttttttccc]bb33	chr1:224377361-224377603(+)$1	242	76	99	19.0168
ggggguuuuuuuuuuuugggggg	chr15:77239718-77239954(+)$1	236	77	100	22.5987
h[ccctttttttttttccc333h	chr3:51455485-51455715(-)$1	230	194	217	21.4578
eeeeevvvvvvvvvvvvveeeee	chr5:10264771-10265035(+)$1	264	12	35	21.6775
ccddddtttttttttttdddd]c	chrX:84520076-84520339(+)$1	263	199	222	21.3294
fdddduuuuuuuuuuuudddd22	chr1:149858761-149858986(+)$1	225	55	78	22.1722
hhhhhuuuuuuuuuuuuhhhhhh	chr4:123844191-123844415(+)$1	224	6	29	20.7136
ggggggtttttttttttgggggg	chr2:20234670-20234910(-)$1	240	162	185	20.9421
eeeeettttttttttteeeee::	chr19:1272237-1272498(+)$1	261	199	222	19.3154
cccxxxxxxxxxxxxxxxccc]c	chr20:42087766-42088001(+)$1	235	5	28	17.1633
:dddduuuuuuuuuuuuddddii	chr6:121768382-121768608(+)$1	226	32	55	21.7723
!!cccuuuuuuuuuuuuccc333	chr12:50152377-50152632(+)$1	255	34	57	23.3967
ddddwwwwwwwwwwwwwwdddd:	chr9:136216724-136216989(+)$1	265	59	82	20.2192
cc[ccctttttttttttcccccc	chr1:231509656-231509876(-)$1	220	32	55	21.7810
:dddduuuuuuuuuuuuddddgg	chr17:61898841-61899063(-)$1	222	118	141	21.7336
eeeeettttttttttteeeeeii	chr19:3976060-3976328(-)$1	268	53	76	21.3172
eeeevvvvvvvvvvvvveeeee]	chr1:150549760-150549995(-)$1	235	30	53	21.4165
!ddddyyyyyyyyyyyyyyyydd	chrX:47088137-47088410(+)$1	273	189	212	21.3389
cc[bbtttttttttttbbccc]d	chr16:18809936-18810197(-)$1	261	221	244	20.8737
d!!bbtttttttttttbb22ddd	chr3:51423624-51423857(+)$1	233	172	195	20.1757
cc[bbuuuuuuuuuuuubbcccd	chr11:20409534-20409753(+)$1	219	104	127	22.1663
[bbyyyyyyyyyyyyyyyybb]c	chr22:20073864-20074096(+)$1	232	159	182	20.7349
bb[bbvvvvvvvvvvvvvbb]bb	chr2:232326331-232326600(-)$1	269	170	193	19.9436
=====vvvvvvvvvvvvv=====	chr11:4127304-4127536(+)$1	232	181	204	22.0630
fffffuuuuuuuuuuuuffffff	chr5:143541810-143542039(-)$1	229	154	177	21.5608
eeeeexxxxxxxxxxxxxxxeee	chr17:33689933-33690166(-)$1	233	164	187	17.0767
d[ddddtttttttttttdddd]d	chr19:6413378-6413653(-)$1	275	9	32	21.1810
##cccxxxxxxxxxxxxxxxccc	chr19:13054690-13054918(+)$1	228	166	189	17.4069

#otherMatches

#Seq PSSM
UCUUGUGUUGGUUUUUUAAAGAA	chr19:18390744-18390969(-)$1	225	194	217	20.5524
GGGUUUUUUUCCUUUUAGUCAUC	chrX:41206561-41206782(+)$1	221	177	200	22.0230
CAUCGAAGAAAUUGAUGUUGAUG	chr5:126156603-126156825(+)$1	222	166	189	20.0346
ACCUUGAACACAUUCCUCCUAAA	chr16:23646976-23647195(-)$1	219	110	133	21.3684
ACCACAUACCUCAACCUGGGGAA	chr1:203276460-203276712(+)$1	252	162	185	20.6442
AAAGCGAAAACACAGUAACAGCU	chr20:57605330-57605569(-)$1	239	9	32	17.6733
AGCACUGUACAAGUUUGUGGUUC	chr12:98993687-98993957(+)$1	270	129	152	21.6391
UGUCCCUCUACGCCUCUGGGCGC	chr17:79478465-79478706(-)$1	241	109	132	21.6615
GUGUAUUUAAAACAUUUAUAUUU	chr13:48522975-48523211(-)$1	236	8	31	21.1315
GCUAUGAAGAUGCCGACCAUGGU	chr16:29818751-29819003(+)$1	252	24	47	21.4054
UAUCGUCUAGUUACUUAUUGGUA	chr19:8528383-8528627(+)$1	244	10	33	21.8412
CUGGCUCUACUUUAUUUGCUAAU	chr1:212241877-212242104(+)$1	227	90	113	21.4685
GUCACUCAAGAGAUUCUGUGCUU	chr2:74755906-74756138(-)$1	232	156	179	22.8502
CUUUAUAAAUUCUGCAAAUCUAA	chr6:109690011-109690249(-)$1	238	148	171	17.2435
CCCCCUUCCAUCAUCAUGUCGUC	chr19:8381331-8381580(-)$1	249	142	165	22.8620
GGUACGACAGACACUAUUCAAGU	chr14:95569853-95570102(-)$1	249	156	179	21.3684
AGGCUGAGAAGGAGGAGGGGCUC	chr1:228680695-228680926(+)$1	231	149	172	21.7561
UAGGAAUUCCAUGAUAUUUCUUA	chr15:66170120-66170341(+)$1	221	181	204	20.0346
GCAUCGCCGCCCCUCACCGUGCC	chr17:79803682-79803916(-)$1	234	11	34	20.3180
UGUCUUCCCUCUGCCCAUAGAUA	chr9:124103454-124103680(-)$1	226	134	157	21.6775
CUUUACACCUAAUAACAUAAAGC	chr17:62496705-62496961(-)$1	256	185	208	22.8008
UGGCACAGACCCCACCCCUCAGC	chr6:112041124-112041355(-)$1	231	190	213	18.7402
AGUCAACUAUUAUCUAAUGACUU	chr21:30435691-30435928(-)$1	237	0	23	21.8147
CGCGCUCCAGGUCUCAUGCGCUC	chr19:2328291-2328522(-)$1	231	9	32	21.7125
GGUGGCAUUAGCAGCCCGCUGCC	chr16:30435649-30435875(-)$1	226	117	140	20.9421
CUCCGGCCAGUCAGACACGGACA	chr19:46341741-46341963(-)$1	222	169	192	22.9726
ACUCCAGUUCCUUCAAAGCAGUC	chr3:172486760-172486986(+)$1	226	74	97	22.9967
CAGGUAGUUAUAUAAGAAACAUU	chr5:134121127-134121360(+)$1	233	146	169	20.9116
UGUGCAAUAAGAUUAAUAAAGUA	chr1:78193991-78194217(-)$1	226	112	135	17.4069
AGGUUUAAUAUUUCAACAGACCG	chr1:115275248-115275516(-)$1	268	190	213	21.4305
UUUCAGAAAGAAGAAAAUGCUAA	chr11:9603019-9603283(+)$1	264	17	40	22.0675
GGCGGAAAAAUAAUGAAGCUGCC	chr9:94172554-94172807(-)$1	253	29	52	21.6775
AAAUAAGCGAUGUAUAAUAUUUU	chr5:37333484-37333711(-)$1	227	178	201	23.0607
GUGCUGCGAGAAGAGAGAGCCUA	chr2:62103202-62103444(-)$1	242	120	143	21.4317
CCCACCUCCCCCUGAACACUGUG	chr11:9610040-9610296(+)$1	256	120	143	17.6733
ACUGGUGAUGCUUGGUUUGGUGG	chr1:44010656-44010882(+)$1	226	140	163	21.2105
ACCACUCAAUGACUCUGGCUAUU	chr1:224377361-224377603(+)$1	242	76	99	19.0168
ACAAAAAUGGUGAUGGAUUUGUU	chr15:77239718-77239954(+)$1	236	77	100	22.5987
AUACCCCCCUUCAUUUGGUUCUU	chr3:51455485-51455715(-)$1	230	194	217	21.4578
UGUCAUAGAAACCUUGAUUGGCA	chr5:10264771-10265035(+)$1	264	12	35	21.6775
GCACUGUAGUGACUUAUCAGUAG	chrX:84520076-84520339(+)$1	263	199	222	21.3294
UGGGCAAAGUCACCAUCGCCCAG	chr1:149858761-149858986(+)$1	225	55	78	22.1722
GCGGACCCUCGCUGACUUCUGCC	chr4:123844191-123844415(+)$1	224	6	29	20.7136
GCCUUAUUCAUCAUUUUUAAGGU	chr2:20234670-20234910(-)$1	240	162	185	20.9421
gaguaaaaacccuuccugcucaa	chr19:1272237-1272498(+)$1	261	199	222	19.3154
CUUGAUGUUUCAAUUUGAAAGUG	chr20:42087766-42088001(+)$1	235	5	28	17.1633
AGCAUGGUAAGGUGAAAAUGCGA	chr6:121768382-121768608(+)$1	226	32	55	21.7723
UUGCUUUACUUUGCCUUGGCUUC	chr12:50152377-50152632(+)$1	255	34	57	23.3967
CUGGCCCACAAGUACAGACCAGA	chr9:136216724-136216989(+)$1	265	59	82	20.2192
CCAUGGUUGCUUGUUAUCCGGGC	chr1:231509656-231509876(-)$1	220	32	55	21.7810
AGCUGUUAUUUGAGAACCGGCGG	chr17:61898841-61899063(-)$1	222	118	141	21.7336
UUUCCAUUUCUUCAGAGGGAAAC	chr19:3976060-3976328(-)$1	268	53	76	21.3172
UGGGUUUGUGGAGUUCUUCCAUG	chr1:150549760-150549995(-)$1	235	30	53	21.4165
UGGCCUGUCAACCCACCCAUUGG	chrX:47088137-47088410(+)$1	273	189	212	21.3389
AGACUUUUUAAUAUAUAGCUUCU	chr16:18809936-18810197(-)$1	261	221	244	20.8737
CCUGGCUCAUGUUAACCCUCGGC	chr3:51423624-51423857(+)$1	233	172	195	20.1757
GAUGAGGACGAUGCAGAUCUCCC	chr11:20409534-20409753(+)$1	219	104	127	22.1663
GAUAAGAAGGAUGAGGAGAAUGA	chr22:20073864-20074096(+)$1	232	159	182	20.7349
Gugaugaagaggaggaugaugac	chr2:232326331-232326600(-)$1	269	170	193	19.9436
ACUCUCAGAAAAGUAAUAAGGGU	chr11:4127304-4127536(+)$1	232	181	204	22.0630
AUGAGUAUGACAGGUGUUUCAUU	chr5:143541810-143542039(-)$1	229	154	177	21.5608
ACAAGCCAUAUACAAACUACCUU	chr17:33689933-33690166(-)$1	233	164	187	17.0767
UUGCUAUUUCUUUUUUUUAGUUA	chr19:6413378-6413653(-)$1	275	9	32	21.1810
UUUGGUUUUGUUCCCCUCCUCCA	chr19:13054690-13054918(+)$1	228	166	189	17.4069

#DB
((((..............)))))	chr19:18390744-18390969(-)$1	1	194	217	20.5524
((((................)))	chrX:41206561-41206782(+)$1	1	177	200	22.0230
((((((...........))))))	chr5:126156603-126156825(+)$1	1	166	189	20.0346
(((((................))	chr16:23646976-23647195(-)$1	1	110	133	21.3684
.(((............)))))..	chr1:203276460-203276712(+)$1	1	162	185	20.6442
..(((...............)))	chr20:57605330-57605569(-)$1	1	9	32	17.6733
(.(((...........))).)))	chr12:98993687-98993957(+)$1	1	129	152	21.6391
.(.(((...........))))))	chr17:79478465-79478706(-)$1	1	109	132	21.6615
(.((((...........)))).)	chr13:48522975-48523211(-)$1	1	8	31	21.1315
((((((...........))))))	chr16:29818751-29819003(+)$1	1	24	47	21.4054
(((((.............)))))	chr19:8528383-8528627(+)$1	1	10	33	21.8412
.((((............))))((	chr1:212241877-212242104(+)$1	1	90	113	21.4685
(.(((............))).))	chr2:74755906-74756138(-)$1	1	156	179	22.8502
(((((...............)))	chr6:109690011-109690249(-)$1	1	148	171	17.2435
.(..(............)..).)	chr19:8381331-8381580(-)$1	1	142	165	22.8620
(((((................))	chr14:95569853-95570102(-)$1	1	156	179	21.3684
.((((.............)))).	chr1:228680695-228680926(+)$1	1	149	172	21.7561
((((((...........))))))	chr15:66170120-66170341(+)$1	1	181	204	20.0346
(((.((...........))))))	chr17:79803682-79803916(-)$1	1	11	34	20.3180
(((((.............)))))	chr9:124103454-124103680(-)$1	1	134	157	21.6775
(((((............))))).	chr17:62496705-62496961(-)$1	1	185	208	22.8008
.((.............))..)))	chr6:112041124-112041355(-)$1	1	190	213	18.7402
(((((............))))).	chr21:30435691-30435928(-)$1	1	0	23	21.8147
.((((............))))((	chr19:2328291-2328522(-)$1	1	9	32	21.7125
((((((...........))))))	chr16:30435649-30435875(-)$1	1	117	140	20.9421
.((((............)))).)	chr19:46341741-46341963(-)$1	1	169	192	22.9726
(((.(............).))).	chr3:172486760-172486986(+)$1	1	74	97	22.9967
...((.............)).))	chr5:134121127-134121360(+)$1	1	146	169	20.9116
..(((...............)))	chr1:78193991-78194217(-)$1	1	112	135	17.4069
.(((((...........))))))	chr1:115275248-115275516(-)$1	1	190	213	21.4305
((.((............))..))	chr11:9603019-9603283(+)$1	1	17	40	22.0675
(((((.............)))))	chr9:94172554-94172807(-)$1	1	29	52	21.6775
(((((............))))))	chr5:37333484-37333711(-)$1	1	178	201	23.0607
(.(((............))))).	chr2:62103202-62103444(-)$1	1	120	143	21.4317
..(((...............)))	chr11:9610040-9610296(+)$1	1	120	143	17.6733
(((((...........))))).)	chr1:44010656-44010882(+)$1	1	140	163	21.2105
.(((...........))).))..	chr1:224377361-224377603(+)$1	1	76	99	19.0168
(((((............))))))	chr15:77239718-77239954(+)$1	1	77	100	22.5987
(.(((...........)))...)	chr3:51455485-51455715(-)$1	1	194	217	21.4578
(((((.............)))))	chr5:10264771-10265035(+)$1	1	12	35	21.6775
((((((...........)))).)	chrX:84520076-84520339(+)$1	1	199	222	21.3294
(((((............))))..	chr1:149858761-149858986(+)$1	1	55	78	22.1722
(((((............))))))	chr4:123844191-123844415(+)$1	1	6	29	20.7136
((((((...........))))))	chr2:20234670-20234910(-)$1	1	162	185	20.9421
(((((...........)))))..	chr19:1272237-1272498(+)$1	1	199	222	19.3154
(((...............))).)	chr20:42087766-42088001(+)$1	1	5	28	17.1633
.((((............))))((	chr6:121768382-121768608(+)$1	1	32	55	21.7723
..(((............)))...	chr12:50152377-50152632(+)$1	1	34	57	23.3967
((((..............)))).	chr9:136216724-136216989(+)$1	1	59	82	20.2192
((.(((...........))))))	chr1:231509656-231509876(-)$1	1	32	55	21.7810
.((((............))))((	chr17:61898841-61899063(-)$1	1	118	141	21.7336
(((((...........)))))((	chr19:3976060-3976328(-)$1	1	53	76	21.3172
((((.............))))).	chr1:150549760-150549995(-)$1	1	30	53	21.4165
.((((................))	chrX:47088137-47088410(+)$1	1	189	212	21.3389
((.((...........))))).)	chr16:18809936-18810197(-)$1	1	221	244	20.8737
(..((...........))..)))	chr3:51423624-51423857(+)$1	1	172	195	20.1757
((.((............))))))	chr11:20409534-20409753(+)$1	1	104	127	22.1663
.((................)).)	chr22:20073864-20074096(+)$1	1	159	182	20.7349
((.((.............)).))	chr2:232326331-232326600(-)$1	1	170	193	19.9436
(((((.............)))))	chr11:4127304-4127536(+)$1	1	181	204	22.0630
(((((............))))))	chr5:143541810-143542039(-)$1	1	154	177	21.5608
(((((...............)))	chr17:33689933-33690166(-)$1	1	164	187	17.0767
(.((((...........)))).)	chr19:6413378-6413653(-)$1	1	9	32	21.1810
..(((...............)))	chr19:13054690-13054918(+)$1	1	166	189	17.4069

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

#score	1340.951354511875
#seq	64
#width	23
#escape	false
#onStep	15000
#minSteps	10000
#maxSteps	15000