Mercurial > repos > pjbriggs > weeder2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.markdown	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,20 @@
+weeder2
+=======
+
+Galaxy tool for motif discovery using weeder2.
+
+weeder2_wrapper
+---------------
+
+XML and wrapper script for weeder motif discovery package version 2.0.
+
+`weeder2` can be obtained from <http://159.149.160.51/modtools/downloads/weeder2.html>.
+
+To add to Galaxy add the following to tool_conf.xml:
+
+    <tool file="weeder2/weeder2_wrapper.xml" />
+
+### Changes ###
+
+2.0.0.0: initial version
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/weeder2_matrix.out	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,100 @@
+>MAT1	GTTTCAATTA
+A	0.1739	0.08497	0.1198	0.1538	0.186	0.8184	0.6871	0.09156	0.1002	0.7403
+C	0.06162	0.05256	0.05743	0.07398	0.5592	0.08087	0.0987	0.08757	0.149	0.08036
+G	0.591	0.06033	0.07754	0.07127	0.1033	0.0563	0.08422	0.04673	0.08862	0.06081
+T	0.1735	0.8021	0.7452	0.701	0.1515	0.04446	0.1299	0.7741	0.6622	0.1185
+>MAT2	CATTTTAA
+A	0.216	0.8128	0.1075	0.04678	0.1112	0.1399	0.7346	0.7969
+C	0.5444	0.04193	0.0509	0.03932	0.0429	0.08711	0.1099	0.09147
+G	0.1067	0.03289	0.07156	0.0785	0.0966	0.09202	0.05706	0.0382
+T	0.1328	0.1124	0.77	0.8354	0.7493	0.681	0.09836	0.0734
+>MAT3	GTGAATTA
+A	0.2434	0.0588	0.09038	0.7708	0.7064	0.0692	0.08129	0.7448
+C	0.08343	0.02873	0.1008	0.06039	0.0821	0.07782	0.09324	0.09242
+G	0.5181	0.06202	0.6983	0.08538	0.05523	0.08203	0.1107	0.09517
+T	0.1551	0.8504	0.1106	0.08347	0.1562	0.7709	0.7148	0.0676
+>MAT4	TCAATCAT
+A	0.05132	0.186	0.8183	0.6756	0.1425	0.08545	0.8726	0.1838
+C	0.02852	0.5378	0.07891	0.05957	0.02786	0.6724	0.03639	0.1337
+G	0.0695	0.1008	0.02175	0.09712	0.07326	0.07966	0.0383	0.06208
+T	0.8507	0.1753	0.08099	0.1677	0.7564	0.1625	0.05268	0.6204
+>MAT5	TGTTTAAT
+A	0.1111	0.09112	0.1881	0.1074	0.1057	0.6769	0.7668	0.1993
+C	0.02537	0.03582	0.06521	0.08013	0.08927	0.09377	0.03432	0.08804
+G	0.07262	0.7214	0.06612	0.05896	0.07036	0.1072	0.116	0.09061
+T	0.7909	0.1516	0.6806	0.7536	0.7347	0.1221	0.08288	0.6221
+>MAT6	ATTACT
+A	0.8781	0.0835	0.07038	0.7901	0.03473	0.1075
+C	0.04152	0.05455	0.05837	0.03709	0.7755	0.04605
+G	0.0322	0.01277	0.1088	0.07223	0.04238	0.01572
+T	0.04814	0.8492	0.7624	0.1005	0.1473	0.8308
+>MAT7	TCACAT
+A	0.08233	0.1013	0.9032	0.139	0.8283	0.0876
+C	0.04274	0.7009	0.02867	0.7396	0.0355	0.04803
+G	0.04677	0.1109	0.01307	0.0554	0.0163	0.05845
+T	0.8282	0.08693	0.05509	0.06599	0.1199	0.8059
+>MAT8	TACATT
+A	0.09867	0.7322	0.1194	0.8806	0.101	0.09423
+C	0.1068	0.06715	0.743	0.03825	0.03645	0.02894
+G	0.1046	0.07625	0.0467	0.01049	0.07555	0.07099
+T	0.6899	0.1244	0.09086	0.07061	0.7871	0.8058
+>MAT9	TTGACA
+A	0.1287	0.06713	0.09732	0.8048	0.1278	0.8784
+C	0.07599	0.01615	0.136	0.02754	0.7339	0.02517
+G	0.07764	0.03641	0.6902	0.03821	0.05137	0.01588
+T	0.7176	0.8803	0.0764	0.1295	0.08697	0.0806
+>MAT10	AATAAT
+A	0.821	0.7797	0.1145	0.7009	0.8508	0.1043
+C	0.05975	0.04103	0.05818	0.09164	0.07329	0.07718
+G	0.05042	0.1458	0.06827	0.08449	0.04593	0.05097
+T	0.06887	0.03344	0.759	0.1229	0.02993	0.7675
+>MAT11	ATGACT
+A	0.7923	0.07691	0.08105	0.8363	0.111	0.123
+C	0.07045	0.02479	0.07396	0.02863	0.7081	0.04261
+G	0.06487	0.02256	0.6694	0.03558	0.06369	0.01484
+T	0.07241	0.8757	0.1756	0.0995	0.1172	0.8196
+>MAT12	TTGAAA
+A	0.08972	0.0524	0.2142	0.8734	0.7765	0.8008
+C	0.08565	0.01703	0.08046	0.009563	0.09992	0.05955
+G	0.07526	0.08263	0.6446	0.04169	0.04608	0.03337
+T	0.7494	0.8479	0.06075	0.07533	0.07746	0.1063
+>MAT13	ATTTTA
+A	0.7686	0.09324	0.05315	0.07052	0.1079	0.7442
+C	0.05296	0.05566	0.02564	0.04286	0.09559	0.0825
+G	0.06642	0.0539	0.07598	0.07754	0.08916	0.06427
+T	0.112	0.7972	0.8452	0.8091	0.7073	0.1091
+>MAT14	TAAACA
+A	0.1209	0.7643	0.8407	0.816	0.1373	0.8505
+C	0.06995	0.06399	0.03895	0.04513	0.685	0.05353
+G	0.09693	0.07741	0.05489	0.04938	0.08995	0.02176
+T	0.7122	0.09432	0.06543	0.08946	0.08774	0.07422
+>MAT15	ATGATT
+A	0.7798	0.03895	0.1394	0.8016	0.09996	0.05479
+C	0.04628	0.04674	0.09287	0.04385	0.1069	0.06237
+G	0.07995	0.03341	0.6306	0.0422	0.05873	0.09202
+T	0.09401	0.8809	0.1371	0.1123	0.7344	0.7908
+>MAT16	AGTATT
+A	0.8169	0.03667	0.1017	0.7024	0.1984	0.05968
+C	0.01586	0.0534	0.06469	0.08485	0.01561	0.04079
+G	0.03184	0.739	0.03857	0.072	0.06428	0.04865
+T	0.1354	0.1709	0.7951	0.1407	0.7217	0.8509
+>MAT17	TTGAGT
+A	0.1122	0.08252	0.1535	0.8677	0.167	0.08711
+C	0.05038	0.01835	0.1439	0.01705	0.09193	0.05017
+G	0.1	0.04409	0.647	0.02826	0.5944	0.03802
+T	0.7373	0.855	0.05572	0.08702	0.1467	0.8247
+>MAT18	TAAAAC
+A	0.09976	0.6641	0.8508	0.8037	0.7918	0.1444
+C	0.1021	0.08641	0.05693	0.04963	0.05966	0.5613
+G	0.05432	0.1092	0.04048	0.04923	0.04498	0.06765
+T	0.7438	0.1403	0.05175	0.09743	0.1036	0.2267
+>MAT19	GTGAAT
+A	0.1593	0.04483	0.06949	0.8955	0.7175	0.1105
+C	0.07553	0.01876	0.09003	0.01629	0.08374	0.06563
+G	0.6152	0.0609	0.7443	0.03019	0.08214	0.05749
+T	0.15	0.8755	0.09618	0.05804	0.1166	0.7664
+>MAT20	AATACA
+A	0.8268	0.7796	0.1396	0.6772	0.1349	0.8374
+C	0.05488	0.04317	0.05118	0.06514	0.7076	0.03498
+G	0.04696	0.05148	0.06801	0.08048	0.04932	0.01976
+T	0.0714	0.1257	0.7412	0.1771	0.1081	0.1079
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/weeder2_motifs.out	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,1250 @@
+COMMAND LINE:
+
+weeder2 -f weeder_in.fa -chipseq -sim 0.95 -O MM
+
+MOTIFS SUMMARY:
+
+1)	GTTTCAATTA	(TAATTGAAAC)	2.38
+2)	CATTTTAA	(TTAAAATG)	2.082
+3)	GTGAATTA	(TAATTCAC)	1.969
+4)	TCAATCAT	(ATGATTGA)	1.944
+5)	TGTTTAAT	(ATTAAACA)	1.874
+6)	ATTACT	(AGTAAT)	1.823
+7)	TCACAT	(ATGTGA)	1.8
+8)	TACATT	(AATGTA)	1.773
+9)	TTGACA	(TGTCAA)	1.733
+10)	AATAAT	(ATTATT)	1.714
+11)	ATGACT	(AGTCAT)	1.702
+12)	TTGAAA	(TTTCAA)	1.693
+13)	ATTTTA	(TAAAAT)	1.691
+14)	TAAACA	(TGTTTA)	1.685
+15)	ATGATT	(AATCAT)	1.678
+16)	AGTATT	(AATACT)	1.664
+17)	TTGAGT	(ACTCAA)	1.574
+18)	TAAAAC	(GTTTTA)	1.572
+19)	GTGAAT	(ATTCAC)	1.568
+20)	AATACA	(TGTATT)	1.564
+
+
+DETAILED RESULTS:
+
+1)	GTTTCAATTA	(TAATTGAAAC)	2.38
+
+Matrix: MAT1	GTTTCAATTA
+A	0.1739	0.08497	0.1198	0.1538	0.186	0.8184	0.6871	0.09156	0.1002	0.7403
+C	0.06162	0.05256	0.05743	0.07398	0.5592	0.08087	0.0987	0.08757	0.149	0.08036
+G	0.591	0.06033	0.07754	0.07127	0.1033	0.0563	0.08422	0.04673	0.08862	0.06081
+T	0.1735	0.8021	0.7452	0.701	0.1515	0.04446	0.1299	0.7741	0.6622	0.1185
+
+OCCURRENCES:
+>chr1:8797248-879744	35	GTTTCAATTA	1	174	+
+>chr1:3467418-346761	1	TTTTCAATTA	0.934855	187	-
+>chr1:5072821-507302	8	GTTTGAATTA	0.928879	153	-
+>chr1:9932599-993279	45	GTTTCAATCA	0.919923	124	+
+>chr1:9013525-901372	37	GTTTCACTTA	0.908195	51	+
+>chr1:9956513-995671	48	GTTTCCATTA	0.88494	114	-
+>chr1:9813405-981360	44	TTTTAAATTA	0.876639	141	+
+>chr1:7768736-776893	34	ATTTTAATTA	0.871314	131	-
+>chr1:9956513-995671	48	ATTTCAATCA	0.854845	177	-
+>chr1:7444756-744495	33	GTTTAAATGA	0.852292	99	+
+>chr1:7386917-738711	29	TTTACAATTA	0.849485	45	+
+>chr1:7303541-730374	27	GTTTTAATGA	0.8469	8	-
+>chr1:5805347-580554	10	GTTCAAATTA	0.843965	178	-
+>chr1:7768736-776893	34	GTATTAATTA	0.83883	127	+
+>chr1:6588721-658892	21	GTTGTAATTA	0.83815	138	+
+>chr1:7388025-738822	30	CTTTCAATCA	0.83733	1	+
+>chr1:9962925-996312	49	GTCTAAATTA	0.834485	190	-
+>chr1:4562216-456241	4	ATTTCAACTA	0.827808	147	+
+>chr1:6878570-687877	25	GTTTTGATTA	0.817499	91	-
+>chr1:6396504-639670	18	GTTTCATTTT	0.816051	171	+
+>chr1:7768736-776893	34	GTTTCATCTA	0.805952	147	+
+>chr1:9460371-946057	38	GTATCAATTT	0.805422	84	+
+>chr1:6721868-672206	23	GTTTCAGATA	0.799444	28	-
+>chr1:6090845-609104	11	TTTTTAATCA	0.79117	168	-
+>chr1:9948240-994844	47	GTTTCAACTC	0.789921	109	-
+>chr1:6266967-626716	15	GCTCCAATTA	0.785236	145	-
+>chr1:5072821-507302	8	GTTTAATTCA	0.774774	150	+
+>chr1:6090845-609104	11	ATTGTAATTA	0.773071	87	+
+>chr1:8851545-885174	36	TTTTGACTTA	0.771928	49	-
+>chr1:6878570-687877	25	ATTACAATCA	0.769475	34	-
+>chr1:6090845-609104	11	GTTAAAATGA	0.766922	148	-
+>chr1:4662531-466273	5	GTTTTACTCA	0.764511	34	-
+>chr1:4562216-456241	4	GTTGAAATCA	0.763465	145	-
+>chr1:6090845-609104	11	ATTACAATAA	0.761859	85	-
+>chr1:9013525-901372	37	GTTTAAGTAA	0.760027	162	+
+>chr1:6205539-620573	13	GTTAAAATTT	0.7594	156	+
+>chr1:7413722-741392	32	TTTTCATTGA	0.758428	125	-
+>chr1:9932599-993279	45	GTTTGATTAA	0.754251	45	-
+>chr1:6588721-658892	21	TTATCAATAA	0.749598	145	+
+>chr1:6205539-620573	13	GTATAAATTT	0.747207	160	-
+>chr1:4774948-477514	6	TTTACAATTC	0.74652	118	-
+>chr1:4833767-483396	7	GGTTAAATCA	0.745976	183	+
+>chr1:6588721-658892	21	ATTACAACTA	0.742438	136	-
+>chr1:9948240-994844	47	GTTGAAACTA	0.736427	111	+
+>chr1:4833767-483396	7	ATTACAAGTA	0.736066	103	-
+>chr1:9574131-957433	42	ATTACCATTA	0.734492	157	-
+>chr1:6721868-672206	23	AATTCAGTTA	0.728969	72	+
+>chr1:4774948-477514	6	GATCTAATTA	0.726685	11	-
+>chr1:6266967-626716	15	ATTTCAACTC	0.724842	175	+
+>chr1:4833767-483396	7	GTAACGATTA	0.698174	62	-
+**********
+
+2)	CATTTTAA	(TTAAAATG)	2.082
+
+Matrix: MAT2	CATTTTAA
+A	0.216	0.8128	0.1075	0.04678	0.1112	0.1399	0.7346	0.7969
+C	0.5444	0.04193	0.0509	0.03932	0.0429	0.08711	0.1099	0.09147
+G	0.1067	0.03289	0.07156	0.0785	0.0966	0.09202	0.05706	0.0382
+T	0.1328	0.1124	0.77	0.8354	0.7493	0.681	0.09836	0.0734
+
+OCCURRENCES:
+>chr1:9813405-981360	44	CATTTTAA	1	131	-
+>chr1:7768736-776893	34	CATTTTAA	1	134	-
+>chr1:7388801-738900	31	CATTTTAA	1	62	+
+>chr1:6205539-620573	13	CATTTTAA	1	28	-
+>chr1:6090845-609104	11	CATTTTAA	1	149	+
+>chr1:3467418-346761	1	CATTTTAA	1	182	+
+>chr1:9942670-994287	46	AATTTTAA	0.939956	134	-
+>chr1:9013525-901372	37	AATTTTAA	0.939956	112	-
+>chr1:6205539-620573	13	AATTTTAA	0.939956	157	-
+>chr1:8851545-885174	36	TATTTTAA	0.924741	103	-
+>chr1:6262414-626261	14	TATTTTAA	0.924741	183	+
+>chr1:7386917-738711	29	GATTTTAA	0.919973	30	-
+>chr1:6266967-626716	15	GATTTTAA	0.919973	2	-
+>chr1:5072821-507302	8	GATTTTAA	0.919973	114	-
+>chr1:7444756-744495	33	CATTTAAA	0.901069	100	-
+>chr1:9932599-993279	45	CATTTGAA	0.892317	175	-
+>chr1:6266967-626716	15	CATTTCAA	0.891418	174	+
+>chr1:6750817-675101	24	CATTTTCA	0.885779	154	-
+>chr1:6090845-609104	11	CATTTTCA	0.885779	5	+
+>chr1:5168670-516887	9	CATTTTCA	0.885779	26	-
+>chr1:6360131-636033	17	CATTTTTA	0.883664	135	+
+>chr1:9948240-994844	47	CATTATAA	0.883344	56	-
+>chr1:5805347-580554	10	CATTGTAA	0.880668	126	-
+>chr1:9948240-994844	47	CAATTTAA	0.878877	16	+
+>chr1:9942670-994287	46	CAATTTAA	0.878877	130	+
+>chr1:6090845-609104	11	CAATTTAA	0.878877	122	+
+>chr1:6396504-639670	18	CATTTTGA	0.876113	175	+
+>chr1:9013525-901372	37	CAGTTTAA	0.872299	108	+
+>chr1:6266967-626716	15	CTTTTTAA	0.871938	44	-
+>chr1:6262414-626261	14	CTTTTTAA	0.871938	187	-
+>chr1:6090845-609104	11	CTTTTTAA	0.871938	171	-
+>chr1:4774948-477514	6	CATTCTAA	0.870849	60	+
+>chr1:6090845-609104	11	CACTTTAA	0.868521	126	-
+>chr1:8797248-879744	35	CATTTTAT	0.867711	146	-
+>chr1:4024990-402519	2	CATTTTAG	0.861275	117	-
+>chr1:8851545-885174	36	AATTTGAA	0.832272	183	-
+>chr1:5805347-580554	10	AATTTGAA	0.832272	179	+
+>chr1:9956513-995671	48	AATTTCAA	0.831373	180	-
+>chr1:6588721-658892	21	AATTTCAA	0.831373	101	-
+>chr1:3467418-346761	1	AATTTTCA	0.825735	191	-
+>chr1:7386917-738711	29	AATTGTAA	0.820624	46	-
+>chr1:4774948-477514	6	AATTGTAA	0.820624	119	+
+>chr1:9956513-995671	48	AATTTTAC	0.810972	184	+
+>chr1:7413722-741392	32	AATTTTAC	0.810972	10	+
+>chr1:6472202-647240	20	AATTTTAC	0.810972	32	+
+>chr1:6090845-609104	11	TATTGTAA	0.805409	86	+
+>chr1:9554705-955490	40	AATGTTAA	0.801568	46	+
+>chr1:8851545-885174	36	AATGTTAA	0.801568	99	+
+>chr1:6878570-687877	25	GATTGTAA	0.800641	35	+
+>chr1:7444756-744495	33	CATTATAC	0.75436	70	-
+**********
+
+3)	GTGAATTA	(TAATTCAC)	1.969
+
+Matrix: MAT3	GTGAATTA
+A	0.2434	0.0588	0.09038	0.7708	0.7064	0.0692	0.08129	0.7448
+C	0.08343	0.02873	0.1008	0.06039	0.0821	0.07782	0.09324	0.09242
+G	0.5181	0.06202	0.6983	0.08538	0.05523	0.08203	0.1107	0.09517
+T	0.1551	0.8504	0.1106	0.08347	0.1562	0.7709	0.7148	0.0676
+
+OCCURRENCES:
+>chr1:6266967-626716	15	GTGAATTA	1	15	+
+>chr1:8851545-885174	36	ATGAATTA	0.94756	84	-
+>chr1:6437830-643803	19	ATGAATTA	0.94756	128	-
+>chr1:5072821-507302	8	TTGAATTA	0.930703	153	-
+>chr1:6878570-687877	25	CTGAATTA	0.917022	85	+
+>chr1:6721868-672206	23	CTGAATTA	0.917022	71	-
+>chr1:9568576-956877	41	GTGATTTA	0.89497	22	+
+>chr1:4833767-483396	7	GTGATTTA	0.89497	186	-
+>chr1:6262414-626261	14	GTGAATGA	0.884673	174	+
+>chr1:4402453-440265	3	GTGAATCA	0.881343	131	-
+>chr1:6437830-643803	19	GTGAATAA	0.879062	123	+
+>chr1:9956513-995671	48	GTGAATTG	0.875981	77	-
+>chr1:6878570-687877	25	GTGAATTG	0.875981	53	+
+>chr1:6277750-627795	16	GTGAATTC	0.875456	27	-
+>chr1:7768736-776893	34	GTGGATTA	0.86916	11	+
+>chr1:6721868-672206	23	GTGGATTA	0.86916	168	+
+>chr1:3467418-346761	1	GTGTATTA	0.868795	4	-
+>chr1:7209035-720923	26	GTGAAGTA	0.868484	12	-
+>chr1:6183701-618390	12	GTGAACTA	0.867682	60	+
+>chr1:4024990-402519	2	GTGAACTA	0.867682	97	-
+>chr1:6396504-639670	18	GGGAATTA	0.849489	51	+
+>chr1:7768736-776893	34	ATTAATTA	0.835366	129	+
+>chr1:9978791-997899	50	ATAAATTA	0.831511	27	+
+>chr1:7768736-776893	34	ATAAATTA	0.831511	104	+
+>chr1:6183701-618390	12	ATGAATCA	0.828904	71	+
+>chr1:5072821-507302	8	ATGAATCA	0.828904	85	-
+>chr1:9932599-993279	45	ATGACTTA	0.828376	12	-
+>chr1:9574131-957433	42	ATGACTTA	0.828376	55	+
+>chr1:5072821-507302	8	ATGAATAA	0.826623	21	+
+>chr1:9574131-957433	42	TTGATTTA	0.825673	145	-
+>chr1:8797248-879744	35	TTGATTTA	0.825673	7	+
+>chr1:8797248-879744	35	TTCAATTA	0.816637	176	+
+>chr1:3467418-346761	1	TTCAATTA	0.816637	187	-
+>chr1:7768736-776893	34	ATGTATTA	0.816356	125	+
+>chr1:5072821-507302	8	ATGTATTA	0.816356	42	+
+>chr1:3467418-346761	1	ATGTATTA	0.816356	26	-
+>chr1:9568576-956877	41	ATGAAGTA	0.816044	150	+
+>chr1:6721868-672206	23	TTGAATGA	0.815376	85	+
+>chr1:7209035-720923	26	ATGAACTA	0.815242	42	+
+>chr1:6878570-687877	25	ATGCATTA	0.81195	43	-
+>chr1:8851545-885174	36	TTGACTTA	0.811518	49	-
+>chr1:9942670-994287	46	TTGAATTG	0.806684	162	+
+>chr1:6090845-609104	11	TTGCATTA	0.795092	39	+
+>chr1:6719561-671976	22	ACGAATTA	0.790695	71	-
+>chr1:9942670-994287	46	GTCATTTA	0.780905	11	-
+>chr1:6472202-647240	20	GTCATTTA	0.780905	144	+
+>chr1:9956513-995671	48	GTGATTGA	0.779643	176	+
+>chr1:9932599-993279	45	GTGATTGA	0.779643	127	-
+>chr1:4774948-477514	6	GTGATCTA	0.762652	15	-
+>chr1:6205539-620573	13	GTCTATTA	0.75473	143	+
+**********
+
+4)	TCAATCAT	(ATGATTGA)	1.944
+
+Matrix: MAT4	TCAATCAT
+A	0.05132	0.186	0.8183	0.6756	0.1425	0.08545	0.8726	0.1838
+C	0.02852	0.5378	0.07891	0.05957	0.02786	0.6724	0.03639	0.1337
+G	0.0695	0.1008	0.02175	0.09712	0.07326	0.07966	0.0383	0.06208
+T	0.8507	0.1753	0.08099	0.1677	0.7564	0.1625	0.05268	0.6204
+
+OCCURRENCES:
+>chr1:8851545-885174	36	TCAATCAT	1	120	+
+>chr1:7444756-744495	33	TCAATCAT	1	11	+
+>chr1:9013525-901372	37	TTAATCAT	0.932721	174	+
+>chr1:6090845-609104	11	TTAATCAT	0.932721	167	-
+>chr1:4774948-477514	6	TTAATCAT	0.932721	139	-
+>chr1:4833767-483396	7	TCAATCAA	0.918952	128	-
+>chr1:5072821-507302	8	TGAATCAT	0.918887	84	-
+>chr1:9956513-995671	48	TCAATCAC	0.909665	176	-
+>chr1:9932599-993279	45	TCAATCAC	0.909665	127	+
+>chr1:9574131-957433	42	TCATTCAT	0.90572	83	-
+>chr1:7303541-730374	27	TCATTCAT	0.90572	107	-
+>chr1:8797248-879744	35	TCAATTAT	0.905366	177	+
+>chr1:7388025-738822	30	TCAATCAG	0.896366	4	+
+>chr1:7444756-744495	33	TCAAACAT	0.886061	130	-
+>chr1:6472202-647240	20	TCACTCAT	0.885652	20	-
+>chr1:8797248-879744	35	TCTATCAT	0.863139	56	+
+>chr1:6277750-627795	16	TCTATCAT	0.863139	95	+
+>chr1:9574131-957433	42	TCCATCAT	0.862751	116	+
+>chr1:6266967-626716	15	TCCATCAT	0.862751	112	-
+>chr1:9574131-957433	42	TAAATCAA	0.853657	145	+
+>chr1:8797248-879744	35	TAAATCAA	0.853657	7	-
+>chr1:9932599-993279	45	TTAATCAA	0.851673	45	+
+>chr1:6878570-687877	25	TTAATCAA	0.851673	90	+
+>chr1:7386917-738711	29	TCAATCCT	0.844783	2	+
+>chr1:9568576-956877	41	TAAATCAC	0.84437	22	-
+>chr1:4833767-483396	7	TAAATCAC	0.84437	186	+
+>chr1:8851545-885174	36	TAATTCAT	0.840425	84	+
+>chr1:6437830-643803	19	TAATTCAT	0.840425	128	+
+>chr1:9962925-996312	49	TAAATTAT	0.84007	189	-
+>chr1:7768736-776893	34	TAAATTAT	0.84007	105	+
+>chr1:7303541-730374	27	TTATTCAT	0.838441	169	+
+>chr1:5072821-507302	8	TTATTCAT	0.838441	21	-
+>chr1:4402453-440265	3	TGAATCAA	0.837839	130	-
+>chr1:9932599-993279	45	TAAGTCAT	0.827328	12	+
+>chr1:9574131-957433	42	TAAGTCAT	0.827328	55	-
+>chr1:6721868-672206	23	TCATTCAA	0.824672	85	-
+>chr1:6183701-618390	12	TGATTCAT	0.824607	71	-
+>chr1:5072821-507302	8	TGATTCAT	0.824607	85	+
+>chr1:3467418-346761	1	TCAATTAA	0.824318	186	-
+>chr1:6437830-643803	19	TGAATTAT	0.824253	127	-
+>chr1:6266967-626716	15	TGAATTAT	0.824253	16	+
+>chr1:4024990-402519	2	TAAAACAT	0.820765	82	+
+>chr1:9942670-994287	46	TTAAACAT	0.818782	80	+
+>chr1:6360131-636033	17	TTAAACAT	0.818782	143	+
+>chr1:5072821-507302	8	TTAAACAT	0.818782	148	-
+>chr1:6588721-658892	21	TCAATAAC	0.800726	148	+
+>chr1:6262414-626261	14	TCAGTTAT	0.797989	137	+
+>chr1:6205539-620573	13	TCTATCAA	0.782091	96	-
+>chr1:4662531-466273	5	TAAATCGT	0.779842	56	+
+>chr1:4833767-483396	7	TTAATCGT	0.777858	61	+
+**********
+
+5)	TGTTTAAT	(ATTAAACA)	1.874
+
+Matrix: MAT5	TGTTTAAT
+A	0.1111	0.09112	0.1881	0.1074	0.1057	0.6769	0.7668	0.1993
+C	0.02537	0.03582	0.06521	0.08013	0.08927	0.09377	0.03432	0.08804
+G	0.07262	0.7214	0.06612	0.05896	0.07036	0.1072	0.116	0.09061
+T	0.7909	0.1516	0.6806	0.7536	0.7347	0.1221	0.08288	0.6221
+
+OCCURRENCES:
+>chr1:6360131-636033	17	TGTTTAAT	1	142	-
+>chr1:5072821-507302	8	TGTTTAAT	1	149	+
+>chr1:9942670-994287	46	TGTTTAAA	0.919846	79	-
+>chr1:6878570-687877	25	TGATTAAT	0.906643	89	-
+>chr1:4774948-477514	6	TGATTAAT	0.906643	140	+
+>chr1:9013525-901372	37	TGTTTAAG	0.899248	161	+
+>chr1:6360131-636033	17	TGTTTAAG	0.899248	6	+
+>chr1:5805347-580554	10	TGTTTAAC	0.898761	16	-
+>chr1:9978791-997899	50	TGTTTGAT	0.892015	68	+
+>chr1:6396504-639670	18	TGTTTGAT	0.892015	10	-
+>chr1:4562216-456241	4	TGTTTGAT	0.892015	141	+
+>chr1:6396504-639670	18	TTTTTAAT	0.891988	59	+
+>chr1:6090845-609104	11	TTTTTAAT	0.891988	170	-
+>chr1:9460371-946057	38	TGTTTCAT	0.889461	121	-
+>chr1:9568576-956877	41	TGTTCAAT	0.877642	144	+
+>chr1:7388801-738900	31	TGTTTAGT	0.876624	88	-
+>chr1:6719561-671976	22	TGTCTAAT	0.872337	67	+
+>chr1:6090845-609104	11	TGATTAAA	0.826489	168	+
+>chr1:7444756-744495	33	TGTTTGAA	0.811861	131	+
+>chr1:5072821-507302	8	TGTTTGAA	0.811861	156	-
+>chr1:9932599-993279	45	TGTTTCAA	0.809307	123	+
+>chr1:8797248-879744	35	TGTTTCAA	0.809307	173	+
+>chr1:6396504-639670	18	TGTTTCAA	0.809307	179	-
+>chr1:9932599-993279	45	TGATTAAC	0.805404	44	-
+>chr1:9013525-901372	37	TGATTAAC	0.805404	173	-
+>chr1:9574131-957433	42	TGATTTAT	0.801481	144	-
+>chr1:9568576-956877	41	TGATTTAT	0.801481	23	+
+>chr1:8797248-879744	35	TGATTTAT	0.801481	8	+
+>chr1:8851545-885174	36	TGATTGAT	0.798658	119	-
+>chr1:4833767-483396	7	TGATTGAT	0.798658	129	+
+>chr1:9948240-994844	47	TGTATAAA	0.797343	126	+
+>chr1:6205539-620573	13	TGTATAAA	0.797343	163	-
+>chr1:9932599-993279	45	TGTTTAGA	0.79647	148	+
+>chr1:4562216-456241	4	TGTTTAGA	0.79647	165	-
+>chr1:6183701-618390	12	TGATTCAT	0.796104	71	-
+>chr1:5072821-507302	8	TGATTCAT	0.796104	85	+
+>chr1:9948240-994844	47	TGTTTATA	0.790191	128	-
+>chr1:9978791-997899	50	TGATAAAT	0.787394	72	+
+>chr1:6437830-643803	19	TGAATAAT	0.78414	124	+
+>chr1:4024990-402519	2	TGATTATT	0.776988	186	+
+>chr1:6183701-618390	12	TGTATAAC	0.776258	8	-
+>chr1:6878570-687877	25	TGTTCTAT	0.77248	74	+
+>chr1:3467418-346761	1	TGTATTAT	0.772335	25	-
+>chr1:3467418-346761	1	TGTATTAT	0.772335	3	-
+>chr1:7413722-741392	32	AGTTTAAC	0.769901	187	+
+>chr1:9574131-957433	42	TGTATGAT	0.769512	119	-
+>chr1:9568576-956877	41	TGTATAGT	0.754121	107	+
+>chr1:7444756-744495	33	AGTATAAT	0.748637	69	+
+>chr1:6090845-609104	11	AGTATAAT	0.748637	93	-
+>chr1:6721868-672206	23	GGTATAAT	0.741335	124	-
+**********
+
+6)	ATTACT	(AGTAAT)	1.823
+
+Matrix: MAT6	ATTACT
+A	0.8781	0.0835	0.07038	0.7901	0.03473	0.1075
+C	0.04152	0.05455	0.05837	0.03709	0.7755	0.04605
+G	0.0322	0.01277	0.1088	0.07223	0.04238	0.01572
+T	0.04814	0.8492	0.7624	0.1005	0.1473	0.8308
+
+OCCURRENCES:
+>chr1:9978791-997899	50	ATTACT	1	31	+
+>chr1:9568576-956877	41	ATTACT	1	154	-
+>chr1:9013525-901372	37	ATTACT	1	183	-
+>chr1:7209035-720923	26	ATTACT	1	183	+
+>chr1:6878570-687877	25	ATTACT	1	64	-
+>chr1:6719561-671976	22	ATTACT	1	137	+
+>chr1:6588721-658892	21	ATTACT	1	9	-
+>chr1:6472202-647240	20	ATTACT	1	176	-
+>chr1:6472202-647240	20	ATTACT	1	29	-
+>chr1:6360131-636033	17	ATTACT	1	86	+
+>chr1:6262414-626261	14	ATTACT	1	160	+
+>chr1:6090845-609104	11	ATTACT	1	20	-
+>chr1:5805347-580554	10	ATTACT	1	176	-
+>chr1:5072821-507302	8	ATTACT	1	46	+
+>chr1:4774948-477514	6	ATTACT	1	194	-
+>chr1:3467418-346761	1	ATTACT	1	32	+
+>chr1:9962925-996312	49	ATTATT	0.866209	188	-
+>chr1:9962925-996312	49	ATTATT	0.866209	133	+
+>chr1:9942670-994287	46	ATTATT	0.866209	73	+
+>chr1:8797248-879744	35	ATTATT	0.866209	192	+
+>chr1:6878570-687877	25	ATTATT	0.866209	41	-
+>chr1:6719561-671976	22	ATTATT	0.866209	181	-
+>chr1:6719561-671976	22	ATTATT	0.866209	145	-
+>chr1:6472202-647240	20	ATTATT	0.866209	5	+
+>chr1:6437830-643803	19	ATTATT	0.866209	126	-
+>chr1:6396504-639670	18	ATTATT	0.866209	55	+
+>chr1:6090845-609104	11	ATTATT	0.866209	84	+
+>chr1:6090845-609104	11	ATTATT	0.866209	43	+
+>chr1:5805347-580554	10	ATTATT	0.866209	65	-
+>chr1:4024990-402519	2	ATTATT	0.866209	188	+
+>chr1:3467418-346761	1	ATTATT	0.866209	24	-
+>chr1:9942670-994287	46	ATGACT	0.860789	34	+
+>chr1:9932599-993279	45	ATGACT	0.860789	14	-
+>chr1:9574131-957433	42	ATGACT	0.860789	55	+
+>chr1:9013525-901372	37	ATGACT	0.860789	193	+
+>chr1:7768736-776893	34	ATGACT	0.860789	121	-
+>chr1:7444756-744495	33	ATGACT	0.860789	194	-
+>chr1:7444756-744495	33	ATGACT	0.860789	40	-
+>chr1:7303541-730374	27	ATGACT	0.860789	111	+
+>chr1:6472202-647240	20	ATGACT	0.860789	143	-
+>chr1:6183701-618390	12	ATGACT	0.860789	175	-
+>chr1:4662531-466273	5	ATGACT	0.860789	126	+
+>chr1:6878570-687877	25	ATTACA	0.845949	38	-
+>chr1:6719561-671976	22	ATTACA	0.845949	127	+
+>chr1:6588721-658892	21	ATTACA	0.845949	140	-
+>chr1:6090845-609104	11	ATTACA	0.845949	89	-
+>chr1:5805347-580554	10	ATTACA	0.845949	147	+
+>chr1:5805347-580554	10	ATTACA	0.845949	125	+
+>chr1:4833767-483396	7	ATTACA	0.845949	107	-
+>chr1:4774948-477514	6	ATTACA	0.845949	9	-
+**********
+
+7)	TCACAT	(ATGTGA)	1.8
+
+Matrix: MAT7	TCACAT
+A	0.08233	0.1013	0.9032	0.139	0.8283	0.0876
+C	0.04274	0.7009	0.02867	0.7396	0.0355	0.04803
+G	0.04677	0.1109	0.01307	0.0554	0.0163	0.05845
+T	0.8282	0.08693	0.05509	0.06599	0.1199	0.8059
+
+OCCURRENCES:
+>chr1:9956513-995671	48	TCACAT	1	18	+
+>chr1:9813405-981360	44	TCACAT	1	66	-
+>chr1:9568576-956877	41	TCACAT	1	33	+
+>chr1:8797248-879744	35	TCACAT	1	32	+
+>chr1:7303541-730374	27	TCACAT	1	80	+
+>chr1:7209035-720923	26	TCACAT	1	127	-
+>chr1:6878570-687877	25	TCACAT	1	101	+
+>chr1:6878570-687877	25	TCACAT	1	51	-
+>chr1:6588721-658892	21	TCACAT	1	22	-
+>chr1:6472202-647240	20	TCACAT	1	74	-
+>chr1:6277750-627795	16	TCACAT	1	31	+
+>chr1:6266967-626716	15	TCACAT	1	171	+
+>chr1:6205539-620573	13	TCACAT	1	33	-
+>chr1:5805347-580554	10	TCACAT	1	131	-
+>chr1:4774948-477514	6	TCACAT	1	132	-
+>chr1:4774948-477514	6	TCACAT	1	19	+
+>chr1:4662531-466273	5	TCACAT	1	31	-
+>chr1:4402453-440265	3	TCACAT	1	135	+
+>chr1:4024990-402519	2	TCACAT	1	66	-
+>chr1:3467418-346761	1	TCACAT	1	79	+
+>chr1:3467418-346761	1	TCACAT	1	53	+
+>chr1:9978791-997899	50	TGACAT	0.870153	84	-
+>chr1:9942670-994287	46	TGACAT	0.870153	93	+
+>chr1:9574131-957433	42	TGACAT	0.870153	111	+
+>chr1:9554705-955490	40	TGACAT	0.870153	53	-
+>chr1:7303541-730374	27	TGACAT	0.870153	99	+
+>chr1:7209035-720923	26	TGACAT	0.870153	121	-
+>chr1:6878570-687877	25	TGACAT	0.870153	69	+
+>chr1:6437830-643803	19	TGACAT	0.870153	6	-
+>chr1:6183701-618390	12	TGACAT	0.870153	140	+
+>chr1:4833767-483396	7	TGACAT	0.870153	29	-
+>chr1:9956513-995671	48	TAACAT	0.868041	137	+
+>chr1:9574131-957433	42	TAACAT	0.868041	104	-
+>chr1:9554705-955490	40	TAACAT	0.868041	47	-
+>chr1:8851545-885174	36	TAACAT	0.868041	100	-
+>chr1:8797248-879744	35	TAACAT	0.868041	103	+
+>chr1:7768736-776893	34	TAACAT	0.868041	80	-
+>chr1:6090845-609104	11	TAACAT	0.868041	154	+
+>chr1:9962925-996312	49	TCAAAT	0.867804	40	-
+>chr1:9932599-993279	45	TCAAAT	0.867804	176	+
+>chr1:9813405-981360	44	TCAAAT	0.867804	55	+
+>chr1:8851545-885174	36	TCAAAT	0.867804	188	-
+>chr1:8851545-885174	36	TCAAAT	0.867804	184	+
+>chr1:8851545-885174	36	TCAAAT	0.867804	96	+
+>chr1:6719561-671976	22	TCAAAT	0.867804	142	+
+>chr1:5805347-580554	10	TCAAAT	0.867804	180	-
+>chr1:5805347-580554	10	TCAAAT	0.867804	121	+
+>chr1:4833767-483396	7	TCAAAT	0.867804	126	-
+>chr1:4833767-483396	7	TCAAAT	0.867804	25	+
+>chr1:4774948-477514	6	TTACAT	0.864876	8	-
+**********
+
+8)	TACATT	(AATGTA)	1.773
+
+Matrix: MAT8	TACATT
+A	0.09867	0.7322	0.1194	0.8806	0.101	0.09423
+C	0.1068	0.06715	0.743	0.03825	0.03645	0.02894
+G	0.1046	0.07625	0.0467	0.01049	0.07555	0.07099
+T	0.6899	0.1244	0.09086	0.07061	0.7871	0.8058
+
+OCCURRENCES:
+>chr1:9962925-996312	49	TACATT	1	130	+
+>chr1:9942670-994287	46	TACATT	1	158	+
+>chr1:9932599-993279	45	TACATT	1	105	-
+>chr1:9460371-946057	38	TACATT	1	173	+
+>chr1:9013525-901372	37	TACATT	1	59	+
+>chr1:6721868-672206	23	TACATT	1	46	+
+>chr1:6588721-658892	21	TACATT	1	160	-
+>chr1:6472202-647240	20	TACATT	1	92	-
+>chr1:6396504-639670	18	TACATT	1	64	-
+>chr1:6205539-620573	13	TACATT	1	167	+
+>chr1:4024990-402519	2	TACATT	1	121	-
+>chr1:3467418-346761	1	TACATT	1	29	+
+>chr1:4662531-466273	5	CACATT	0.865945	30	-
+>chr1:4024990-402519	2	CACATT	0.865945	65	-
+>chr1:3467418-346761	1	CACATT	0.865945	54	+
+>chr1:9942670-994287	46	GACATT	0.865452	94	+
+>chr1:9554705-955490	40	GACATT	0.865452	52	-
+>chr1:7388801-738900	31	GACATT	0.865452	176	-
+>chr1:7303541-730374	27	GACATT	0.865452	100	+
+>chr1:6437830-643803	19	GACATT	0.865452	84	-
+>chr1:6437830-643803	19	GACATT	0.865452	5	-
+>chr1:6205539-620573	13	GACATT	0.865452	114	+
+>chr1:6183701-618390	12	GACATT	0.865452	83	+
+>chr1:4833767-483396	7	GACATT	0.865452	28	-
+>chr1:4562216-456241	4	GACATT	0.865452	157	+
+>chr1:9978791-997899	50	TAAATT	0.856652	28	+
+>chr1:9962925-996312	49	TAAATT	0.856652	191	-
+>chr1:9948240-994844	47	TAAATT	0.856652	17	-
+>chr1:9942670-994287	46	TAAATT	0.856652	131	-
+>chr1:9813405-981360	44	TAAATT	0.856652	144	+
+>chr1:7768736-776893	34	TAAATT	0.856652	105	+
+>chr1:6205539-620573	13	TAAATT	0.856652	161	-
+>chr1:6090845-609104	11	TAAATT	0.856652	123	-
+>chr1:4774948-477514	6	TAAATT	0.856652	73	+
+>chr1:9956513-995671	48	TATATT	0.85009	155	+
+>chr1:9942670-994287	46	TATATT	0.85009	119	+
+>chr1:9813405-981360	44	TATATT	0.85009	31	-
+>chr1:9013525-901372	37	TATATT	0.85009	78	-
+>chr1:7768736-776893	34	TATATT	0.85009	2	-
+>chr1:7413722-741392	32	TATATT	0.85009	87	+
+>chr1:7413722-741392	32	TATATT	0.85009	85	-
+>chr1:6472202-647240	20	TATATT	0.85009	2	+
+>chr1:6360131-636033	17	TATATT	0.85009	26	-
+>chr1:9813405-981360	44	TACAAT	0.842287	28	+
+>chr1:9535189-953538	39	TACAAT	0.842287	43	+
+>chr1:7386917-738711	29	TACAAT	0.842287	47	+
+>chr1:6878570-687877	25	TACAAT	0.842287	36	-
+>chr1:6090845-609104	11	TACAAT	0.842287	87	-
+>chr1:5805347-580554	10	TACAAT	0.842287	127	+
+>chr1:4774948-477514	6	TACAAT	0.842287	120	-
+**********
+
+9)	TTGACA	(TGTCAA)	1.733
+
+Matrix: MAT9	TTGACA
+A	0.1287	0.06713	0.09732	0.8048	0.1278	0.8784
+C	0.07599	0.01615	0.136	0.02754	0.7339	0.02517
+G	0.07764	0.03641	0.6902	0.03821	0.05137	0.01588
+T	0.7176	0.8803	0.0764	0.1295	0.08697	0.0806
+
+OCCURRENCES:
+>chr1:9942670-994287	46	TTGACA	1	92	+
+>chr1:8851545-885174	36	TTGACA	1	190	+
+>chr1:8797248-879744	35	TTGACA	1	125	-
+>chr1:7768736-776893	34	TTGACA	1	75	-
+>chr1:7444756-744495	33	TTGACA	1	9	-
+>chr1:7209035-720923	26	TTGACA	1	122	-
+>chr1:6437830-643803	19	TTGACA	1	7	-
+>chr1:6205539-620573	13	TTGACA	1	136	+
+>chr1:6090845-609104	11	TTGACA	1	181	+
+>chr1:5805347-580554	10	TTGACA	1	119	-
+>chr1:4833767-483396	7	TTGACA	1	30	-
+>chr1:4024990-402519	2	TTGACA	1	21	+
+>chr1:6719561-671976	22	TTCACA	0.875237	86	-
+>chr1:6437830-643803	19	TTCACA	0.875237	122	-
+>chr1:6277750-627795	16	TTCACA	0.875237	30	+
+>chr1:6266967-626716	15	TTCACA	0.875237	170	+
+>chr1:6262414-626261	14	TTCACA	0.875237	59	+
+>chr1:6090845-609104	11	TTCACA	0.875237	30	+
+>chr1:5805347-580554	10	TTCACA	0.875237	132	-
+>chr1:5805347-580554	10	TTCACA	0.875237	43	+
+>chr1:5168670-516887	9	TTCACA	0.875237	155	+
+>chr1:5168670-516887	9	TTCACA	0.875237	24	-
+>chr1:4774948-477514	6	TTCACA	0.875237	133	-
+>chr1:4402453-440265	3	TTCACA	0.875237	134	+
+>chr1:9978791-997899	50	ATGACA	0.867422	85	-
+>chr1:9956513-995671	48	ATGACA	0.867422	106	+
+>chr1:9932599-993279	45	ATGACA	0.867422	140	+
+>chr1:9574131-957433	42	ATGACA	0.867422	179	-
+>chr1:9574131-957433	42	ATGACA	0.867422	110	+
+>chr1:7768736-776893	34	ATGACA	0.867422	139	+
+>chr1:6878570-687877	25	ATGACA	0.867422	68	+
+>chr1:6360131-636033	17	ATGACA	0.867422	149	+
+>chr1:6262414-626261	14	ATGACA	0.867422	102	-
+>chr1:6183701-618390	12	ATGACA	0.867422	108	-
+>chr1:6183701-618390	12	ATGACA	0.867422	42	+
+>chr1:6090845-609104	11	ATGACA	0.867422	146	-
+>chr1:9962925-996312	49	TTAACA	0.866518	121	+
+>chr1:9932599-993279	45	TTAACA	0.866518	43	-
+>chr1:9574131-957433	42	TTAACA	0.866518	105	-
+>chr1:9554705-955490	40	TTAACA	0.866518	48	-
+>chr1:8851545-885174	36	TTAACA	0.866518	101	-
+>chr1:6266967-626716	15	TTAACA	0.866518	42	-
+>chr1:6090845-609104	11	TTAACA	0.866518	153	+
+>chr1:4024990-402519	2	TTAACA	0.866518	79	-
+>chr1:9978791-997899	50	TTGATA	0.854356	71	+
+>chr1:9568576-956877	41	TTGATA	0.854356	190	-
+>chr1:9460371-946057	38	TTGATA	0.854356	85	-
+>chr1:6588721-658892	21	TTGATA	0.854356	146	-
+>chr1:6205539-620573	13	TTGATA	0.854356	96	+
+>chr1:4833767-483396	7	TTGATA	0.854356	23	-
+**********
+
+10)	AATAAT	(ATTATT)	1.714
+
+Matrix: MAT10	AATAAT
+A	0.821	0.7797	0.1145	0.7009	0.8508	0.1043
+C	0.05975	0.04103	0.05818	0.09164	0.07329	0.07718
+G	0.05042	0.1458	0.06827	0.08449	0.04593	0.05097
+T	0.06887	0.03344	0.759	0.1229	0.02993	0.7675
+
+OCCURRENCES:
+>chr1:9962925-996312	49	AATAAT	1	188	+
+>chr1:9962925-996312	49	AATAAT	1	133	-
+>chr1:9942670-994287	46	AATAAT	1	73	-
+>chr1:8797248-879744	35	AATAAT	1	192	-
+>chr1:6878570-687877	25	AATAAT	1	41	+
+>chr1:6719561-671976	22	AATAAT	1	181	+
+>chr1:6719561-671976	22	AATAAT	1	145	+
+>chr1:6472202-647240	20	AATAAT	1	5	-
+>chr1:6437830-643803	19	AATAAT	1	126	+
+>chr1:6396504-639670	18	AATAAT	1	55	-
+>chr1:6090845-609104	11	AATAAT	1	84	-
+>chr1:6090845-609104	11	AATAAT	1	43	-
+>chr1:5805347-580554	10	AATAAT	1	65	+
+>chr1:4024990-402519	2	AATAAT	1	188	-
+>chr1:3467418-346761	1	AATAAT	1	24	+
+>chr1:9962925-996312	49	AATTAT	0.867789	189	-
+>chr1:8797248-879744	35	AATTAT	0.867789	179	+
+>chr1:7768736-776893	34	AATTAT	0.867789	107	+
+>chr1:6719561-671976	22	AATTAT	0.867789	182	-
+>chr1:6719561-671976	22	AATTAT	0.867789	146	-
+>chr1:6588721-658892	21	AATTAT	0.867789	143	+
+>chr1:6437830-643803	19	AATTAT	0.867789	127	-
+>chr1:6396504-639670	18	AATTAT	0.867789	54	+
+>chr1:6266967-626716	15	AATTAT	0.867789	18	+
+>chr1:6090845-609104	11	AATTAT	0.867789	92	+
+>chr1:6090845-609104	11	AATTAT	0.867789	83	+
+>chr1:5805347-580554	10	AATTAT	0.867789	66	-
+>chr1:8851545-885174	36	AATCAT	0.860628	122	+
+>chr1:8797248-879744	35	AATCAT	0.860628	138	-
+>chr1:7444756-744495	33	AATCAT	0.860628	13	+
+>chr1:6090845-609104	11	AATCAT	0.860628	167	-
+>chr1:5168670-516887	9	AATCAT	0.860628	31	-
+>chr1:5072821-507302	8	AATCAT	0.860628	84	-
+>chr1:4774948-477514	6	AATCAT	0.860628	139	-
+>chr1:9978791-997899	50	AGTAAT	0.854996	31	-
+>chr1:9568576-956877	41	AGTAAT	0.854996	154	+
+>chr1:9013525-901372	37	AGTAAT	0.854996	183	+
+>chr1:7209035-720923	26	AGTAAT	0.854996	183	-
+>chr1:6878570-687877	25	AGTAAT	0.854996	64	+
+>chr1:6719561-671976	22	AGTAAT	0.854996	137	-
+>chr1:6588721-658892	21	AGTAAT	0.854996	9	+
+>chr1:6472202-647240	20	AGTAAT	0.854996	176	+
+>chr1:6472202-647240	20	AGTAAT	0.854996	29	+
+>chr1:6360131-636033	17	AGTAAT	0.854996	86	-
+>chr1:6262414-626261	14	AGTAAT	0.854996	160	-
+>chr1:6090845-609104	11	AGTAAT	0.854996	20	+
+>chr1:5805347-580554	10	AGTAAT	0.854996	176	+
+>chr1:5072821-507302	8	AGTAAT	0.854996	46	-
+>chr1:4774948-477514	6	AGTAAT	0.854996	194	+
+>chr1:3467418-346761	1	AGTAAT	0.854996	32	-
+**********
+
+11)	ATGACT	(AGTCAT)	1.702
+
+Matrix: MAT11	ATGACT
+A	0.7923	0.07691	0.08105	0.8363	0.111	0.123
+C	0.07045	0.02479	0.07396	0.02863	0.7081	0.04261
+G	0.06487	0.02256	0.6694	0.03558	0.06369	0.01484
+T	0.07241	0.8757	0.1756	0.0995	0.1172	0.8196
+
+OCCURRENCES:
+>chr1:9942670-994287	46	ATGACT	1	34	+
+>chr1:9932599-993279	45	ATGACT	1	14	-
+>chr1:9574131-957433	42	ATGACT	1	55	+
+>chr1:9013525-901372	37	ATGACT	1	193	+
+>chr1:7768736-776893	34	ATGACT	1	121	-
+>chr1:7444756-744495	33	ATGACT	1	194	-
+>chr1:7444756-744495	33	ATGACT	1	40	-
+>chr1:7303541-730374	27	ATGACT	1	111	+
+>chr1:6472202-647240	20	ATGACT	1	143	-
+>chr1:6183701-618390	12	ATGACT	1	175	-
+>chr1:4662531-466273	5	ATGACT	1	126	+
+>chr1:9978791-997899	50	ATTACT	0.888601	31	+
+>chr1:9568576-956877	41	ATTACT	0.888601	154	-
+>chr1:9013525-901372	37	ATTACT	0.888601	183	-
+>chr1:7209035-720923	26	ATTACT	0.888601	183	+
+>chr1:6878570-687877	25	ATTACT	0.888601	64	-
+>chr1:6719561-671976	22	ATTACT	0.888601	137	+
+>chr1:6588721-658892	21	ATTACT	0.888601	9	-
+>chr1:6472202-647240	20	ATTACT	0.888601	176	-
+>chr1:6472202-647240	20	ATTACT	0.888601	29	-
+>chr1:6360131-636033	17	ATTACT	0.888601	86	+
+>chr1:6262414-626261	14	ATTACT	0.888601	160	+
+>chr1:6090845-609104	11	ATTACT	0.888601	20	-
+>chr1:5805347-580554	10	ATTACT	0.888601	176	-
+>chr1:5072821-507302	8	ATTACT	0.888601	46	+
+>chr1:4774948-477514	6	ATTACT	0.888601	194	-
+>chr1:3467418-346761	1	ATTACT	0.888601	32	+
+>chr1:8797248-879744	35	ATAACT	0.867272	132	+
+>chr1:7209035-720923	26	ATAACT	0.867272	79	+
+>chr1:6360131-636033	17	ATAACT	0.867272	111	-
+>chr1:6262414-626261	14	ATAACT	0.867272	139	-
+>chr1:6183701-618390	12	ATAACT	0.867272	7	-
+>chr1:5072821-507302	8	ATAACT	0.867272	25	+
+>chr1:9956513-995671	48	ATGATT	0.866692	35	-
+>chr1:9013525-901372	37	ATGATT	0.866692	176	-
+>chr1:8851545-885174	36	ATGATT	0.866692	122	-
+>chr1:8797248-879744	35	ATGATT	0.866692	138	+
+>chr1:7444756-744495	33	ATGATT	0.866692	13	-
+>chr1:6090845-609104	11	ATGATT	0.866692	167	+
+>chr1:5168670-516887	9	ATGATT	0.866692	31	+
+>chr1:5072821-507302	8	ATGATT	0.866692	84	+
+>chr1:4774948-477514	6	ATGATT	0.866692	139	+
+>chr1:8851545-885174	36	ATGAAT	0.865302	86	-
+>chr1:7303541-730374	27	ATGAAT	0.865302	171	-
+>chr1:7303541-730374	27	ATGAAT	0.865302	107	+
+>chr1:6437830-643803	19	ATGAAT	0.865302	130	-
+>chr1:6183701-618390	12	ATGAAT	0.865302	71	+
+>chr1:5072821-507302	8	ATGAAT	0.865302	127	+
+>chr1:5072821-507302	8	ATGAAT	0.865302	87	-
+>chr1:5072821-507302	8	ATGAAT	0.865302	21	+
+**********
+
+12)	TTGAAA	(TTTCAA)	1.693
+
+Matrix: MAT12	TTGAAA
+A	0.08972	0.0524	0.2142	0.8734	0.7765	0.8008
+C	0.08565	0.01703	0.08046	0.009563	0.09992	0.05955
+G	0.07526	0.08263	0.6446	0.04169	0.04608	0.03337
+T	0.7494	0.8479	0.06075	0.07533	0.07746	0.1063
+
+OCCURRENCES:
+>chr1:9956513-995671	48	TTGAAA	1	180	+
+>chr1:9948240-994844	47	TTGAAA	1	112	+
+>chr1:9932599-993279	45	TTGAAA	1	125	-
+>chr1:8797248-879744	35	TTGAAA	1	175	-
+>chr1:7444756-744495	33	TTGAAA	1	161	-
+>chr1:7388025-738822	30	TTGAAA	1	2	-
+>chr1:7309743-730994	28	TTGAAA	1	146	-
+>chr1:7209035-720923	26	TTGAAA	1	54	-
+>chr1:6750817-675101	24	TTGAAA	1	153	+
+>chr1:6588721-658892	21	TTGAAA	1	101	+
+>chr1:6396504-639670	18	TTGAAA	1	179	+
+>chr1:6266967-626716	15	TTGAAA	1	176	-
+>chr1:6090845-609104	11	TTGAAA	1	102	+
+>chr1:4562216-456241	4	TTGAAA	1	148	-
+>chr1:3467418-346761	1	TTGAAA	1	190	+
+>chr1:6205539-620573	13	TTAAAA	0.903286	157	+
+>chr1:6205539-620573	13	TTAAAA	0.903286	28	+
+>chr1:6090845-609104	11	TTAAAA	0.903286	171	+
+>chr1:6090845-609104	11	TTAAAA	0.903286	151	-
+>chr1:5072821-507302	8	TTAAAA	0.903286	114	+
+>chr1:4024990-402519	2	TTAAAA	0.903286	81	+
+>chr1:3467418-346761	1	TTAAAA	0.903286	184	-
+>chr1:9942670-994287	46	TTGACA	0.847972	92	+
+>chr1:8851545-885174	36	TTGACA	0.847972	190	+
+>chr1:8797248-879744	35	TTGACA	0.847972	125	-
+>chr1:7768736-776893	34	TTGACA	0.847972	75	-
+>chr1:7444756-744495	33	TTGACA	0.847972	9	-
+>chr1:7209035-720923	26	TTGACA	0.847972	122	-
+>chr1:6437830-643803	19	TTGACA	0.847972	7	-
+>chr1:6205539-620573	13	TTGACA	0.847972	136	+
+>chr1:6090845-609104	11	TTGACA	0.847972	181	+
+>chr1:5805347-580554	10	TTGACA	0.847972	119	-
+>chr1:4833767-483396	7	TTGACA	0.847972	30	-
+>chr1:4024990-402519	2	TTGACA	0.847972	21	+
+>chr1:9942670-994287	46	TTGAAT	0.843956	162	+
+>chr1:7444756-744495	33	TTGAAT	0.843956	134	+
+>chr1:7413722-741392	32	TTGAAT	0.843956	123	-
+>chr1:6721868-672206	23	TTGAAT	0.843956	85	+
+>chr1:6277750-627795	16	TTGAAT	0.843956	35	-
+>chr1:6277750-627795	16	TTGAAT	0.843956	25	+
+>chr1:6183701-618390	12	TTGAAT	0.843956	87	+
+>chr1:6090845-609104	11	TTGAAT	0.843956	119	-
+>chr1:6090845-609104	11	TTGAAT	0.843956	115	+
+>chr1:5072821-507302	8	TTGAAT	0.843956	155	-
+>chr1:9978791-997899	50	TTGATA	0.842925	71	+
+>chr1:9568576-956877	41	TTGATA	0.842925	190	-
+>chr1:9460371-946057	38	TTGATA	0.842925	85	-
+>chr1:6588721-658892	21	TTGATA	0.842925	146	-
+>chr1:6205539-620573	13	TTGATA	0.842925	96	+
+>chr1:4833767-483396	7	TTGATA	0.842925	23	-
+**********
+
+13)	ATTTTA	(TAAAAT)	1.691
+
+Matrix: MAT13	ATTTTA
+A	0.7686	0.09324	0.05315	0.07052	0.1079	0.7442
+C	0.05296	0.05566	0.02564	0.04286	0.09559	0.0825
+G	0.06642	0.0539	0.07598	0.07754	0.08916	0.06427
+T	0.112	0.7972	0.8452	0.8091	0.7073	0.1091
+
+OCCURRENCES:
+>chr1:9956513-995671	48	ATTTTA	1	185	+
+>chr1:9942670-994287	46	ATTTTA	1	135	-
+>chr1:9813405-981360	44	ATTTTA	1	132	-
+>chr1:9013525-901372	37	ATTTTA	1	135	-
+>chr1:9013525-901372	37	ATTTTA	1	113	-
+>chr1:8851545-885174	36	ATTTTA	1	104	-
+>chr1:8797248-879744	35	ATTTTA	1	147	-
+>chr1:7768736-776893	34	ATTTTA	1	135	-
+>chr1:7413722-741392	32	ATTTTA	1	11	+
+>chr1:7388801-738900	31	ATTTTA	1	63	+
+>chr1:7386917-738711	29	ATTTTA	1	31	-
+>chr1:6472202-647240	20	ATTTTA	1	33	+
+>chr1:6266967-626716	15	ATTTTA	1	3	-
+>chr1:6262414-626261	14	ATTTTA	1	184	+
+>chr1:6205539-620573	13	ATTTTA	1	158	-
+>chr1:6205539-620573	13	ATTTTA	1	29	-
+>chr1:6090845-609104	11	ATTTTA	1	150	+
+>chr1:5805347-580554	10	ATTTTA	1	155	+
+>chr1:5072821-507302	8	ATTTTA	1	115	-
+>chr1:4833767-483396	7	ATTTTA	1	122	-
+>chr1:4024990-402519	2	ATTTTA	1	118	-
+>chr1:3467418-346761	1	ATTTTA	1	183	+
+>chr1:3467418-346761	1	ATTTTA	1	134	+
+>chr1:8851545-885174	36	ATTTGA	0.857659	188	+
+>chr1:8851545-885174	36	ATTTGA	0.857659	184	-
+>chr1:8851545-885174	36	ATTTGA	0.857659	96	-
+>chr1:6719561-671976	22	ATTTGA	0.857659	142	-
+>chr1:5805347-580554	10	ATTTGA	0.857659	180	+
+>chr1:5805347-580554	10	ATTTGA	0.857659	121	-
+>chr1:4833767-483396	7	ATTTGA	0.857659	126	+
+>chr1:4833767-483396	7	ATTTGA	0.857659	25	-
+>chr1:9813405-981360	44	ATTGTA	0.83155	28	-
+>chr1:9535189-953538	39	ATTGTA	0.83155	43	-
+>chr1:7386917-738711	29	ATTGTA	0.83155	47	-
+>chr1:6878570-687877	25	ATTGTA	0.83155	36	+
+>chr1:6090845-609104	11	ATTGTA	0.83155	87	+
+>chr1:5805347-580554	10	ATTGTA	0.83155	127	-
+>chr1:4774948-477514	6	ATTGTA	0.83155	120	+
+>chr1:9948240-994844	47	ATTATA	0.829934	57	-
+>chr1:7444756-744495	33	ATTATA	0.829934	71	-
+>chr1:6721868-672206	23	ATTATA	0.829934	124	+
+>chr1:6266967-626716	15	ATTATA	0.829934	19	+
+>chr1:6090845-609104	11	ATTATA	0.829934	93	+
+>chr1:9956513-995671	48	ATGTTA	0.822869	137	-
+>chr1:9574131-957433	42	ATGTTA	0.822869	104	+
+>chr1:9554705-955490	40	ATGTTA	0.822869	47	+
+>chr1:8851545-885174	36	ATGTTA	0.822869	100	+
+>chr1:8797248-879744	35	ATGTTA	0.822869	103	-
+>chr1:7768736-776893	34	ATGTTA	0.822869	80	+
+>chr1:6090845-609104	11	ATGTTA	0.822869	154	-
+**********
+
+14)	TAAACA	(TGTTTA)	1.685
+
+Matrix: MAT14	TAAACA
+A	0.1209	0.7643	0.8407	0.816	0.1373	0.8505
+C	0.06995	0.06399	0.03895	0.04513	0.685	0.05353
+G	0.09693	0.07741	0.05489	0.04938	0.08995	0.02176
+T	0.7122	0.09432	0.06543	0.08946	0.08774	0.07422
+
+OCCURRENCES:
+>chr1:9948240-994844	47	TAAACA	1	130	+
+>chr1:9942670-994287	46	TAAACA	1	81	+
+>chr1:9932599-993279	45	TAAACA	1	148	-
+>chr1:9574131-957433	42	TAAACA	1	5	+
+>chr1:9013525-901372	37	TAAACA	1	161	-
+>chr1:7768736-776893	34	TAAACA	1	169	+
+>chr1:7388801-738900	31	TAAACA	1	90	+
+>chr1:6472202-647240	20	TAAACA	1	12	-
+>chr1:6360131-636033	17	TAAACA	1	144	+
+>chr1:6360131-636033	17	TAAACA	1	6	-
+>chr1:5805347-580554	10	TAAACA	1	18	+
+>chr1:5072821-507302	8	TAAACA	1	149	-
+>chr1:5072821-507302	8	TAAACA	1	15	+
+>chr1:4562216-456241	4	TAAACA	1	167	+
+>chr1:7209035-720923	26	TAAAGA	0.862934	168	+
+>chr1:6721868-672206	23	TAAAGA	0.862934	96	-
+>chr1:6588721-658892	21	TAAAGA	0.862934	84	-
+>chr1:6437830-643803	19	TAAAGA	0.862934	173	-
+>chr1:6396504-639670	18	TAAAGA	0.862934	5	+
+>chr1:6205539-620573	13	TAAAGA	0.862934	190	+
+>chr1:6205539-620573	13	TAAAGA	0.862934	25	-
+>chr1:4024990-402519	2	TAAAGA	0.862934	36	+
+>chr1:9962925-996312	49	TTAACA	0.845673	121	+
+>chr1:9932599-993279	45	TTAACA	0.845673	43	-
+>chr1:9574131-957433	42	TTAACA	0.845673	105	-
+>chr1:9554705-955490	40	TTAACA	0.845673	48	-
+>chr1:8851545-885174	36	TTAACA	0.845673	101	-
+>chr1:6266967-626716	15	TTAACA	0.845673	42	-
+>chr1:6090845-609104	11	TTAACA	0.845673	153	+
+>chr1:4024990-402519	2	TTAACA	0.845673	79	-
+>chr1:9956513-995671	48	TCAACA	0.838688	85	+
+>chr1:9568576-956877	41	TCAACA	0.838688	88	-
+>chr1:8797248-879744	35	TCAACA	0.838688	127	+
+>chr1:6878570-687877	25	TCAACA	0.838688	2	-
+>chr1:6262414-626261	14	TCAACA	0.838688	130	-
+>chr1:6205539-620573	13	TCAACA	0.838688	134	-
+>chr1:6183701-618390	12	TCAACA	0.838688	54	-
+>chr1:9932599-993279	45	TAATCA	0.832635	46	+
+>chr1:9013525-901372	37	TAATCA	0.832635	175	+
+>chr1:6878570-687877	25	TAATCA	0.832635	91	+
+>chr1:6090845-609104	11	TAATCA	0.832635	168	-
+>chr1:4774948-477514	6	TAATCA	0.832635	140	-
+>chr1:4024990-402519	2	TAATCA	0.832635	186	-
+>chr1:3467418-346761	1	TAATCA	0.832635	50	+
+>chr1:9956513-995671	48	TATACA	0.821406	153	-
+>chr1:9948240-994844	47	TATACA	0.821406	126	-
+>chr1:9568576-956877	41	TATACA	0.821406	107	-
+>chr1:6437830-643803	19	TATACA	0.821406	105	+
+>chr1:6205539-620573	13	TATACA	0.821406	165	+
+>chr1:6183701-618390	12	TATACA	0.821406	10	+
+**********
+
+15)	ATGATT	(AATCAT)	1.678
+
+Matrix: MAT15	ATGATT
+A	0.7798	0.03895	0.1394	0.8016	0.09996	0.05479
+C	0.04628	0.04674	0.09287	0.04385	0.1069	0.06237
+G	0.07995	0.03341	0.6306	0.0422	0.05873	0.09202
+T	0.09401	0.8809	0.1371	0.1123	0.7344	0.7908
+
+OCCURRENCES:
+>chr1:9956513-995671	48	ATGATT	1	35	-
+>chr1:9013525-901372	37	ATGATT	1	176	-
+>chr1:8851545-885174	36	ATGATT	1	122	-
+>chr1:8797248-879744	35	ATGATT	1	138	+
+>chr1:7444756-744495	33	ATGATT	1	13	-
+>chr1:6090845-609104	11	ATGATT	1	167	+
+>chr1:5168670-516887	9	ATGATT	1	31	+
+>chr1:5072821-507302	8	ATGATT	1	84	+
+>chr1:4774948-477514	6	ATGATT	1	139	+
+>chr1:9962925-996312	49	ATAATT	0.885497	189	+
+>chr1:8797248-879744	35	ATAATT	0.885497	179	-
+>chr1:7768736-776893	34	ATAATT	0.885497	107	-
+>chr1:6719561-671976	22	ATAATT	0.885497	182	+
+>chr1:6719561-671976	22	ATAATT	0.885497	146	+
+>chr1:6588721-658892	21	ATAATT	0.885497	143	-
+>chr1:6437830-643803	19	ATAATT	0.885497	127	+
+>chr1:6396504-639670	18	ATAATT	0.885497	54	-
+>chr1:6266967-626716	15	ATAATT	0.885497	18	-
+>chr1:6090845-609104	11	ATAATT	0.885497	92	-
+>chr1:6090845-609104	11	ATAATT	0.885497	83	-
+>chr1:5805347-580554	10	ATAATT	0.885497	66	+
+>chr1:9962925-996312	49	ATTATT	0.884969	188	-
+>chr1:9962925-996312	49	ATTATT	0.884969	133	+
+>chr1:9942670-994287	46	ATTATT	0.884969	73	+
+>chr1:8797248-879744	35	ATTATT	0.884969	192	+
+>chr1:6878570-687877	25	ATTATT	0.884969	41	-
+>chr1:6719561-671976	22	ATTATT	0.884969	181	-
+>chr1:6719561-671976	22	ATTATT	0.884969	145	-
+>chr1:6472202-647240	20	ATTATT	0.884969	5	+
+>chr1:6437830-643803	19	ATTATT	0.884969	126	-
+>chr1:6396504-639670	18	ATTATT	0.884969	55	+
+>chr1:6090845-609104	11	ATTATT	0.884969	84	+
+>chr1:6090845-609104	11	ATTATT	0.884969	43	+
+>chr1:5805347-580554	10	ATTATT	0.884969	65	-
+>chr1:4024990-402519	2	ATTATT	0.884969	188	+
+>chr1:3467418-346761	1	ATTATT	0.884969	24	-
+>chr1:9978791-997899	50	ATCATT	0.874651	77	-
+>chr1:9932599-993279	45	ATCATT	0.874651	18	+
+>chr1:9013525-901372	37	ATCATT	0.874651	40	-
+>chr1:7444756-744495	33	ATCATT	0.874651	104	-
+>chr1:6277750-627795	16	ATCATT	0.874651	98	+
+>chr1:6205539-620573	13	ATCATT	0.874651	38	+
+>chr1:5168670-516887	9	ATCATT	0.874651	30	-
+>chr1:4774948-477514	6	ATCATT	0.874651	138	-
+>chr1:6472202-647240	20	ATGACT	0.853739	143	-
+>chr1:6183701-618390	12	ATGACT	0.853739	175	-
+>chr1:4662531-466273	5	ATGACT	0.853739	126	+
+>chr1:9942670-994287	46	ACGATT	0.805545	105	-
+>chr1:4833767-483396	7	ACGATT	0.805545	63	-
+>chr1:4662531-466273	5	ACGATT	0.805545	58	-
+**********
+
+16)	AGTATT	(AATACT)	1.664
+
+Matrix: MAT16	AGTATT
+A	0.8169	0.03667	0.1017	0.7024	0.1984	0.05968
+C	0.01586	0.0534	0.06469	0.08485	0.01561	0.04079
+G	0.03184	0.739	0.03857	0.072	0.06428	0.04865
+T	0.1354	0.1709	0.7951	0.1407	0.7217	0.8509
+
+OCCURRENCES:
+>chr1:9574131-957433	42	AGTATT	1	164	-
+>chr1:8851545-885174	36	AGTATT	1	143	-
+>chr1:7444756-744495	33	AGTATT	1	137	-
+>chr1:7388801-738900	31	AGTATT	1	75	-
+>chr1:7209035-720923	26	AGTATT	1	10	-
+>chr1:6262414-626261	14	AGTATT	1	181	+
+>chr1:5805347-580554	10	AGTATT	1	152	+
+>chr1:4833767-483396	7	AGTATT	1	18	+
+>chr1:4402453-440265	3	AGTATT	1	177	+
+>chr1:9978791-997899	50	AGTAAT	0.881262	31	-
+>chr1:9568576-956877	41	AGTAAT	0.881262	154	+
+>chr1:9013525-901372	37	AGTAAT	0.881262	183	+
+>chr1:7209035-720923	26	AGTAAT	0.881262	183	-
+>chr1:6878570-687877	25	AGTAAT	0.881262	64	+
+>chr1:6719561-671976	22	AGTAAT	0.881262	137	-
+>chr1:6588721-658892	21	AGTAAT	0.881262	9	+
+>chr1:6472202-647240	20	AGTAAT	0.881262	176	+
+>chr1:6472202-647240	20	AGTAAT	0.881262	29	+
+>chr1:6360131-636033	17	AGTAAT	0.881262	86	-
+>chr1:6262414-626261	14	AGTAAT	0.881262	160	-
+>chr1:6090845-609104	11	AGTAAT	0.881262	20	+
+>chr1:5805347-580554	10	AGTAAT	0.881262	176	+
+>chr1:5072821-507302	8	AGTAAT	0.881262	46	-
+>chr1:4774948-477514	6	AGTAAT	0.881262	194	+
+>chr1:3467418-346761	1	AGTAAT	0.881262	32	-
+>chr1:9962925-996312	49	ATTATT	0.871068	188	-
+>chr1:9962925-996312	49	ATTATT	0.871068	133	+
+>chr1:9942670-994287	46	ATTATT	0.871068	73	+
+>chr1:8797248-879744	35	ATTATT	0.871068	192	+
+>chr1:6878570-687877	25	ATTATT	0.871068	41	-
+>chr1:6719561-671976	22	ATTATT	0.871068	181	-
+>chr1:6719561-671976	22	ATTATT	0.871068	145	-
+>chr1:6472202-647240	20	ATTATT	0.871068	5	+
+>chr1:6437830-643803	19	ATTATT	0.871068	126	-
+>chr1:6396504-639670	18	ATTATT	0.871068	55	+
+>chr1:6090845-609104	11	ATTATT	0.871068	84	+
+>chr1:6090845-609104	11	ATTATT	0.871068	43	+
+>chr1:5805347-580554	10	ATTATT	0.871068	65	-
+>chr1:4024990-402519	2	ATTATT	0.871068	188	+
+>chr1:3467418-346761	1	ATTATT	0.871068	24	-
+>chr1:9956513-995671	48	TGTATT	0.845348	68	-
+>chr1:9948240-994844	47	TGTATT	0.845348	84	+
+>chr1:9942670-994287	46	TGTATT	0.845348	156	-
+>chr1:9574131-957433	42	TGTATT	0.845348	48	+
+>chr1:7768736-776893	34	TGTATT	0.845348	126	+
+>chr1:5072821-507302	8	TGTATT	0.845348	43	+
+>chr1:4024990-402519	2	TGTATT	0.845348	173	+
+>chr1:3467418-346761	1	TGTATT	0.845348	114	+
+>chr1:3467418-346761	1	TGTATT	0.845348	27	-
+>chr1:3467418-346761	1	TGTATT	0.845348	5	-
+**********
+
+17)	TTGAGT	(ACTCAA)	1.574
+
+Matrix: MAT17	TTGAGT
+A	0.1122	0.08252	0.1535	0.8677	0.167	0.08711
+C	0.05038	0.01835	0.1439	0.01705	0.09193	0.05017
+G	0.1	0.04409	0.647	0.02826	0.5944	0.03802
+T	0.7373	0.855	0.05572	0.08702	0.1467	0.8247
+
+OCCURRENCES:
+>chr1:9978791-997899	50	TTGAGT	1	34	-
+>chr1:9956513-995671	48	TTGAGT	1	83	-
+>chr1:9574131-957433	42	TTGAGT	1	43	+
+>chr1:9568576-956877	41	TTGAGT	1	90	+
+>chr1:8851545-885174	36	TTGAGT	1	94	-
+>chr1:7413722-741392	32	TTGAGT	1	165	+
+>chr1:7388801-738900	31	TTGAGT	1	78	-
+>chr1:7309743-730994	28	TTGAGT	1	133	+
+>chr1:7209035-720923	26	TTGAGT	1	90	+
+>chr1:6719561-671976	22	TTGAGT	1	140	-
+>chr1:6262414-626261	14	TTGAGT	1	132	+
+>chr1:6183701-618390	12	TTGAGT	1	56	+
+>chr1:5072821-507302	8	TTGAGT	1	174	-
+>chr1:4833767-483396	7	TTGAGT	1	3	+
+>chr1:9942670-994287	46	TTGAAT	0.89953	162	+
+>chr1:7444756-744495	33	TTGAAT	0.89953	134	+
+>chr1:7413722-741392	32	TTGAAT	0.89953	123	-
+>chr1:6721868-672206	23	TTGAAT	0.89953	85	+
+>chr1:6277750-627795	16	TTGAAT	0.89953	35	-
+>chr1:6277750-627795	16	TTGAAT	0.89953	25	+
+>chr1:6183701-618390	12	TTGAAT	0.89953	87	+
+>chr1:6090845-609104	11	TTGAAT	0.89953	119	-
+>chr1:6090845-609104	11	TTGAAT	0.89953	115	+
+>chr1:5072821-507302	8	TTGAAT	0.89953	155	-
+>chr1:9932599-993279	45	TTGATT	0.89477	47	-
+>chr1:9574131-957433	42	TTGATT	0.89477	147	-
+>chr1:8851545-885174	36	TTGATT	0.89477	118	-
+>chr1:8797248-879744	35	TTGATT	0.89477	7	+
+>chr1:6878570-687877	25	TTGATT	0.89477	92	-
+>chr1:4833767-483396	7	TTGATT	0.89477	128	+
+>chr1:4562216-456241	4	TTGATT	0.89477	144	+
+>chr1:4402453-440265	3	TTGATT	0.89477	130	+
+>chr1:4024990-402519	2	TTGATT	0.89477	185	+
+>chr1:9962925-996312	49	TTAAGT	0.884013	119	-
+>chr1:9932599-993279	45	TTAAGT	0.884013	11	+
+>chr1:9932599-993279	45	TTAAGT	0.884013	9	-
+>chr1:9574131-957433	42	TTAAGT	0.884013	58	-
+>chr1:9013525-901372	37	TTAAGT	0.884013	164	+
+>chr1:8797248-879744	35	TTAAGT	0.884013	120	+
+>chr1:8797248-879744	35	TTAAGT	0.884013	84	-
+>chr1:6396504-639670	18	TTAAGT	0.884013	109	-
+>chr1:6360131-636033	17	TTAAGT	0.884013	43	-
+>chr1:6396504-639670	18	TTGACT	0.881899	34	-
+>chr1:4833767-483396	7	TTGACT	0.881899	6	-
+>chr1:9813405-981360	44	ATGAGT	0.853079	136	+
+>chr1:6588721-658892	21	ATGAGT	0.853079	75	-
+>chr1:6472202-647240	20	ATGAGT	0.853079	20	+
+>chr1:6277750-627795	16	ATGAGT	0.853079	42	-
+>chr1:6262414-626261	14	ATGAGT	0.853079	178	+
+>chr1:6205539-620573	13	ATGAGT	0.853079	20	+
+**********
+
+18)	TAAAAC	(GTTTTA)	1.572
+
+Matrix: MAT18	TAAAAC
+A	0.09976	0.6641	0.8508	0.8037	0.7918	0.1444
+C	0.1021	0.08641	0.05693	0.04963	0.05966	0.5613
+G	0.05432	0.1092	0.04048	0.04923	0.04498	0.06765
+T	0.7438	0.1403	0.05175	0.09743	0.1036	0.2267
+
+OCCURRENCES:
+>chr1:9813405-981360	44	TAAAAC	1	140	-
+>chr1:7388801-738900	31	TAAAAC	1	51	+
+>chr1:7303541-730374	27	TAAAAC	1	12	+
+>chr1:6472202-647240	20	TAAAAC	1	133	-
+>chr1:4774948-477514	6	TAAAAC	1	124	+
+>chr1:4662531-466273	5	TAAAAC	1	38	+
+>chr1:4024990-402519	2	TAAAAC	1	82	+
+>chr1:9956513-995671	48	TAAAAT	0.917837	185	-
+>chr1:9942670-994287	46	TAAAAT	0.917837	135	+
+>chr1:9813405-981360	44	TAAAAT	0.917837	132	+
+>chr1:9013525-901372	37	TAAAAT	0.917837	135	+
+>chr1:9013525-901372	37	TAAAAT	0.917837	113	+
+>chr1:8851545-885174	36	TAAAAT	0.917837	104	+
+>chr1:8797248-879744	35	TAAAAT	0.917837	147	+
+>chr1:7768736-776893	34	TAAAAT	0.917837	135	+
+>chr1:7413722-741392	32	TAAAAT	0.917837	11	-
+>chr1:7388801-738900	31	TAAAAT	0.917837	63	-
+>chr1:7386917-738711	29	TAAAAT	0.917837	31	+
+>chr1:6472202-647240	20	TAAAAT	0.917837	33	-
+>chr1:6266967-626716	15	TAAAAT	0.917837	3	+
+>chr1:6262414-626261	14	TAAAAT	0.917837	184	-
+>chr1:6205539-620573	13	TAAAAT	0.917837	158	+
+>chr1:6205539-620573	13	TAAAAT	0.917837	29	+
+>chr1:6090845-609104	11	TAAAAT	0.917837	150	-
+>chr1:5805347-580554	10	TAAAAT	0.917837	155	-
+>chr1:5072821-507302	8	TAAAAT	0.917837	115	+
+>chr1:4833767-483396	7	TAAAAT	0.917837	122	+
+>chr1:4024990-402519	2	TAAAAT	0.917837	118	+
+>chr1:3467418-346761	1	TAAAAT	0.917837	183	-
+>chr1:3467418-346761	1	TAAAAT	0.917837	134	-
+>chr1:9962925-996312	49	TTAAAC	0.871367	7	+
+>chr1:9942670-994287	46	TTAAAC	0.871367	80	+
+>chr1:9013525-901372	37	TTAAAC	0.871367	162	-
+>chr1:9013525-901372	37	TTAAAC	0.871367	110	-
+>chr1:8797248-879744	35	TTAAAC	0.871367	118	-
+>chr1:7444756-744495	33	TTAAAC	0.871367	99	-
+>chr1:7413722-741392	32	TTAAAC	0.871367	188	-
+>chr1:7388801-738900	31	TTAAAC	0.871367	37	+
+>chr1:6360131-636033	17	TTAAAC	0.871367	143	+
+>chr1:6360131-636033	17	TTAAAC	0.871367	7	-
+>chr1:5805347-580554	10	TTAAAC	0.871367	17	+
+>chr1:5072821-507302	8	TTAAAC	0.871367	150	-
+>chr1:4833767-483396	7	TAAATC	0.831007	94	-
+>chr1:4662531-466273	5	TAAATC	0.831007	56	+
+>chr1:9574131-957433	42	TAATAC	0.826572	163	+
+>chr1:7768736-776893	34	TAATAC	0.826572	127	-
+>chr1:5072821-507302	8	TAATAC	0.826572	44	-
+>chr1:4833767-483396	7	TAATAC	0.826572	19	-
+>chr1:3467418-346761	1	TAATAC	0.826572	26	+
+>chr1:3467418-346761	1	TAATAC	0.826572	4	+
+**********
+
+19)	GTGAAT	(ATTCAC)	1.568
+
+Matrix: MAT19	GTGAAT
+A	0.1593	0.04483	0.06949	0.8955	0.7175	0.1105
+C	0.07553	0.01876	0.09003	0.01629	0.08374	0.06563
+G	0.6152	0.0609	0.7443	0.03019	0.08214	0.05749
+T	0.15	0.8755	0.09618	0.05804	0.1166	0.7664
+
+OCCURRENCES:
+>chr1:9956513-995671	48	GTGAAT	1	79	-
+>chr1:7209035-720923	26	GTGAAT	1	156	-
+>chr1:6878570-687877	25	GTGAAT	1	53	+
+>chr1:6588721-658892	21	GTGAAT	1	30	-
+>chr1:6437830-643803	19	GTGAAT	1	123	+
+>chr1:6277750-627795	16	GTGAAT	1	29	-
+>chr1:6266967-626716	15	GTGAAT	1	15	+
+>chr1:6262414-626261	14	GTGAAT	1	174	+
+>chr1:5168670-516887	9	GTGAAT	1	154	-
+>chr1:4402453-440265	3	GTGAAT	1	133	-
+>chr1:4024990-402519	2	GTGAAT	1	62	+
+>chr1:9574131-957433	42	ATGAAT	0.89386	83	+
+>chr1:9574131-957433	42	ATGAAT	0.89386	51	-
+>chr1:9013525-901372	37	ATGAAT	0.89386	117	-
+>chr1:8851545-885174	36	ATGAAT	0.89386	86	-
+>chr1:7303541-730374	27	ATGAAT	0.89386	171	-
+>chr1:7303541-730374	27	ATGAAT	0.89386	107	+
+>chr1:6437830-643803	19	ATGAAT	0.89386	130	-
+>chr1:6183701-618390	12	ATGAAT	0.89386	71	+
+>chr1:5072821-507302	8	ATGAAT	0.89386	127	+
+>chr1:5072821-507302	8	ATGAAT	0.89386	87	-
+>chr1:5072821-507302	8	ATGAAT	0.89386	21	+
+>chr1:9942670-994287	46	TTGAAT	0.891676	162	+
+>chr1:7444756-744495	33	TTGAAT	0.891676	134	+
+>chr1:7413722-741392	32	TTGAAT	0.891676	123	-
+>chr1:6721868-672206	23	TTGAAT	0.891676	85	+
+>chr1:6277750-627795	16	TTGAAT	0.891676	35	-
+>chr1:6277750-627795	16	TTGAAT	0.891676	25	+
+>chr1:6183701-618390	12	TTGAAT	0.891676	87	+
+>chr1:6090845-609104	11	TTGAAT	0.891676	119	-
+>chr1:6090845-609104	11	TTGAAT	0.891676	115	+
+>chr1:5072821-507302	8	TTGAAT	0.891676	155	-
+>chr1:9956513-995671	48	GTGATT	0.860082	176	+
+>chr1:9932599-993279	45	GTGATT	0.860082	129	-
+>chr1:9568576-956877	41	GTGATT	0.860082	22	+
+>chr1:9554705-955490	40	GTGATT	0.860082	126	+
+>chr1:6472202-647240	20	GTGATT	0.860082	76	+
+>chr1:4833767-483396	7	GTGATT	0.860082	188	-
+>chr1:3467418-346761	1	GTGATT	0.860082	51	-
+>chr1:9956513-995671	48	GTTAAT	0.849088	112	+
+>chr1:9932599-993279	45	GTTAAT	0.849088	44	+
+>chr1:9574131-957433	42	GTTAAT	0.849088	106	+
+>chr1:9554705-955490	40	GTTAAT	0.849088	49	+
+>chr1:9013525-901372	37	GTTAAT	0.849088	173	+
+>chr1:6721868-672206	23	GTTAAT	0.849088	172	-
+>chr1:4662531-466273	5	GTTAAT	0.849088	159	-
+>chr1:9942670-994287	46	GTCAAT	0.847655	91	-
+>chr1:7768736-776893	34	GTCAAT	0.847655	76	+
+>chr1:7444756-744495	33	GTCAAT	0.847655	10	+
+>chr1:7209035-720923	26	GTCAAT	0.847655	123	+
+**********
+
+20)	AATACA	(TGTATT)	1.564
+
+Matrix: MAT20	AATACA
+A	0.8268	0.7796	0.1396	0.6772	0.1349	0.8374
+C	0.05488	0.04317	0.05118	0.06514	0.7076	0.03498
+G	0.04696	0.05148	0.06801	0.08048	0.04932	0.01976
+T	0.0714	0.1257	0.7412	0.1771	0.1081	0.1079
+
+OCCURRENCES:
+>chr1:9962925-996312	49	AATACA	1	83	+
+>chr1:9956513-995671	48	AATACA	1	68	+
+>chr1:9948240-994844	47	AATACA	1	84	-
+>chr1:9942670-994287	46	AATACA	1	156	+
+>chr1:9574131-957433	42	AATACA	1	48	-
+>chr1:7768736-776893	34	AATACA	1	126	-
+>chr1:5072821-507302	8	AATACA	1	43	-
+>chr1:4024990-402519	2	AATACA	1	173	-
+>chr1:3467418-346761	1	AATACA	1	114	-
+>chr1:3467418-346761	1	AATACA	1	27	+
+>chr1:3467418-346761	1	AATACA	1	5	+
+>chr1:9956513-995671	48	AATTCA	0.883548	78	+
+>chr1:9942670-994287	46	AATTCA	0.883548	163	-
+>chr1:9013525-901372	37	AATTCA	0.883548	116	+
+>chr1:8851545-885174	36	AATTCA	0.883548	85	+
+>chr1:7303541-730374	27	AATTCA	0.883548	56	+
+>chr1:6878570-687877	25	AATTCA	0.883548	86	-
+>chr1:6878570-687877	25	AATTCA	0.883548	54	-
+>chr1:6721868-672206	23	AATTCA	0.883548	72	+
+>chr1:6437830-643803	19	AATTCA	0.883548	129	+
+>chr1:6277750-627795	16	AATTCA	0.883548	28	+
+>chr1:6277750-627795	16	AATTCA	0.883548	26	-
+>chr1:6266967-626716	15	AATTCA	0.883548	16	-
+>chr1:6090845-609104	11	AATTCA	0.883548	118	+
+>chr1:6090845-609104	11	AATTCA	0.883548	116	-
+>chr1:5072821-507302	8	AATTCA	0.883548	154	+
+>chr1:9956513-995671	48	AATATA	0.860396	155	-
+>chr1:9942670-994287	46	AATATA	0.860396	119	-
+>chr1:9813405-981360	44	AATATA	0.860396	31	+
+>chr1:9013525-901372	37	AATATA	0.860396	78	+
+>chr1:7768736-776893	34	AATATA	0.860396	2	+
+>chr1:7413722-741392	32	AATATA	0.860396	87	-
+>chr1:7413722-741392	32	AATATA	0.860396	85	+
+>chr1:6472202-647240	20	AATATA	0.860396	2	-
+>chr1:6360131-636033	17	AATATA	0.860396	26	+
+>chr1:9813405-981360	44	ATTACA	0.84772	147	+
+>chr1:6878570-687877	25	ATTACA	0.84772	38	-
+>chr1:6719561-671976	22	ATTACA	0.84772	127	+
+>chr1:6588721-658892	21	ATTACA	0.84772	140	-
+>chr1:6090845-609104	11	ATTACA	0.84772	89	-
+>chr1:5805347-580554	10	ATTACA	0.84772	147	+
+>chr1:5805347-580554	10	ATTACA	0.84772	125	+
+>chr1:4833767-483396	7	ATTACA	0.84772	107	-
+>chr1:4774948-477514	6	ATTACA	0.84772	9	-
+>chr1:7388801-738900	31	AATACT	0.830134	75	+
+>chr1:7209035-720923	26	AATACT	0.830134	10	+
+>chr1:6262414-626261	14	AATACT	0.830134	181	-
+>chr1:5805347-580554	10	AATACT	0.830134	152	-
+>chr1:4833767-483396	7	AATACT	0.830134	18	-
+>chr1:4402453-440265	3	AATACT	0.830134	177	-
+**********
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/weeder_in.fa	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,100 @@
+>chr1:3467418-3467618
+CCATAATACACCCTTGTATAGCTAATAATACATTACTTTGATCCTGTGCTAATCACATTGATCCTGGGAAAAGGAAACTCACATACCTCTGTGTATGAGGAAGCTCACTGTACTGTATTCTTCAAGGAGTGGAATTTTATCACCACTTCACACCATTTGGAACAGGCAGAGGAATTCTAGGCATTTTAATTGAAAATTCA
+>chr1:4024990-4025190
+CTTACTTTGCAGTGATCCCGTTGACACAAACTGTGTAAAGAAATCAGAGTGAGAACAGGTGGTGAATGTGACTCAGAGTGTTAAAACATGTGCACGTAGTTCACTTGCTGTCTTACCTAAAATGTAGCACAGCAGTGTGCCCAAAGGAATTTGGGGGTCTAGTAGATCTACATGTATTTATTGCTTGATTATTTCTCTTG
+>chr1:4402453-4402653
+TAAAACATGTCTCTAGTAGTCACAGTGCCCACACTGCTGATGGAGTCACCTTTTCCAGGGAACGGCTGCTGCTCTCGATATCTGGTGGATCTCTGGAAAGACTTGTGCTGATCTCTCTCTGCCCCTTCCTTGATTCACATCTCAAGGGACCGAGAAGGGAGGGAAAACACCAGTCCAGTATTTCCTATCAGTTCAGCGGG
+>chr1:4562216-4562416
+TTGCTGAGCCCTGCTGCCCGCACTGCAACGCTGGGCTCTCTCATCACCTTTGCCAACACCTGCCTCTTCTGTGCAGCCTTCCATCAAGTATGACGGGAGCCCTCACCAAGGACGATTCTAGACATATTTAGCAGCAATATTGTTTGATTTCAACTAGACATTGTTCTAAACACAAAGGAGTTCAAGGCTGGGGCTTTGAT
+>chr1:4662531-4662731
+GTCAACTTCAGCCTCCTGGGACAACGCACAATGTGAGTAAAACTGCCTTTCATCATAAATCGTTCTTACCCACCCCGAATCCCAGGGAGAACTGACAAACAGCCTGCCTGTGAGAGGAAAGGCAGATGACTCCTTCAACTTCGAGGTAGGAGCAAAACATTAACCCAGTGCAACCACAACAATCTAGGCAGGATGAAGGG
+>chr1:4774948-4775148
+CGTAAATATGTAATTAGATCACATATGGCTAAGGAAAACTCCAATTTTTGCTAGGGACACATTCTAATTTCCTAAATTCCTAAAAGATAAGCTCCTGGCAACTTGTCCCCCTCCACAGAATTGTAAAACTGATGTGAAATGATTAATTGCTTCGGTAAAGTTCCTCATGTAGCTGTAAGTTCCCCAGAAATAAAGTAATT
+>chr1:4833767-4833967
+TTTTGAGTCAAGATAGAAGTATTATCAAATGTCAAGAGCGGGAGCAGAGTTCTTGGGAGCTTAATCGTTACTTAGATGAGAAACACCTGGATGGATTTAGGGTACTTGTAATGGCCTAGAATAAAATTTGATTGATGGCTAATCTCTGGGGTATAGTCCACTGTTGTACAACCACTAAGTGAGGTTAAATCACTTGCTTC
+>chr1:5072821-5073021
+AAAATGAAGTTAGGTAAACAATGAATAACTTTTTCTGAGACATGTATTACTGGTGGGTCTACATATACTTATACCATGGGTCTATGATTCATTTCTCAGTCTGAGTCTTATGCTTAAAATCGGAGTATGAATGCCTGGCCCGCTGAGATGTTTAATTCAAACAAACCCAAACCACTCAAAGGTCATAAACCAAGCTTCTT
+>chr1:5168670-5168870
+AAAGTCAGCACTCCTCAGGAACTTGTGAAAATGATTTCCATCTGCTAAAAGAAAACATTTCCCTTGCCTCTGGCAGAATGGACATATGGGATATGCATGGACCCCTCTCAGCAGATCAGAGCCCATGCAGGCCTCCAGGCTCCCACAGTCCCTATTCACAAGTACTTAGTCCTTGCTGCCCTCCCCACCTACTTATCCTC
+>chr1:5805347-5805547
+TCTATTTCAGAGAAGGTTAAACAAAAAACAGGTCTGGATATTTTCACAACCACTTGAAGTCAGCAATAATTTCTTAGTCTGACAAGGACCATGAGAAATTCTTTCTATACCTTGTCTGTGTCAAATTACAATGTGAAGTTTCCAGAATTACAGTATTTTATTTCTGAACTTGCAAAGTAATTTGAACAGGTTTTTCCTGG
+>chr1:6090845-6091045
+GAGCCATTTTCATATGTACAGTAATGCTTTTCACAAAGTTGCATTATTCTAGATGCGTATGTGTGTGTCTGCAGACTGAACCAATTATTGTAATTATACTCTTGAAAAAACTGCTTGAATTCAATTTAAAGTGGCTTCTGCTAGCTGTCATTTTAACATCCTGCTTATGATTAAAAAGACTTGACACTTGGAATAAACTA
+>chr1:6183701-6183901
+GTAATTAGTTATACAAGAACACCTGTCACAGTGGCTGATCCATGACAGGTCTTTGTTGAGTGAACTAACCATGAATCAGTAAGACATTGAATGCAGGGCATGCTGAGTGTCATGGTGTGGACACGTGTCAGACGGTGGCTGACATCCTTAGGAACTGCAATGCCTAAGGGAAGTAGTCATAGGTATAGCTGGTGTTCTCC
+>chr1:6205539-6205739
+TAATCCTGTCCCTTCCGTCATGAGTCTTTAAAATGTGATCATTCCATGAACTGGTACATAGGACTGATGCCACGGAACACTCGTGGACTCACTTATTGATAGAGTCCCTGCAAGACATTCAGTTGGGTGCGGATGTTGACAAGTCTATTATGAGCGTTAAAATTTATACATTTTGCTAACCATTTTCTGTAAAGAATTGG
+>chr1:6262414-6262614
+CTGAGTCCAAGTTGTGTGTGTGTTGCTGCTGCTGTGCTAGGCACTGGTTACAGCTTCCTTCACACACTGACCGACTGCCAGCCACTCAGAAGTCTGGAGGTTGTCATTCGTTCCTTCAGTAGGTGGCAGTGTTGAGTCAGTTATTGGTTCATCACTTAGATTACTAGTGTTCCGTGAATGAGTATTTTAAAAAGCACACA
+>chr1:6266967-6267167
+ATTAAAATCTGATAGTGAATTAtagttacctttctgttggctgttaaaaagccaaggtaacctgtagaagaaagggtggtgtttggcatatggtttcagatgtccatgatgatgatggagcagaggtgacaggtggcagacagctaattggagcagcagcagctgagagttcacatttcaacTCTCTTCCAGGTTCAACC
+>chr1:6277750-6277950
+CCCGTCTCCTTTCAGCTTGTCTTATTGAATTCACATTCAAAACTCATTGCCACCATCAAGGAGGAAAAATCTGGAAAACAAAAGTGCTCTGCTATCTATCATTCCAAGACCAGCTTACAGCTGCCAGAAACACCCAGAAAAGCAAGCATCTCAGGAAGCTGAAATCAGTCCTCAGAGCTAATGCCAGGAAAGGGCTCTCT
+>chr1:6360131-6360331
+gtttttgtttaaggcagagttttgcaatatagtccagggtaaacttaagctccagtcctcctgcttcagcctccggagtgccaagattactggcatgtgccaccctgactagttatgtgggttctTTCTTAAAGCATTTTTATTAAACATGACAGAGGTTCCTAGCCTGATGCTTTGCTGTACACTTACATAGAAAATGA
+>chr1:6396504-6396704
+TAAATAAAGATCAAACAACAAACAAAACTGGGAAGTCAACTGATCACTGCGGGAATTATTTTTAATGTAGGGTCATCTTTCTTCCACACGGTGGCGCCTCGCTGTCAGACTTAAAAACACTGAAACATTGTGGCCACCAACAACTCCAGATGGGCTTCTCTGTGCTAGTAGTTTCATTTTGAAACAGAAAGTCAGTACTT
+>chr1:6437830-6438030
+GTTAAATGTCAAGTTCTTGCACCCCCTGAACCTCGGTGCAAGGAAGGCAGGGCTGAAAGGAGGGGATTGTGTCTTCTCCAGGAAATGTCTGAAGTTTTGTTGGATATACAACCGCTGCAGGTGTGAATAATTCATCTTTTGTTTCAGTCCTGAATGCAGTCCAGGAGTCAGCTCTTTACAAAGCCTCATCTCACTTACTG
+>chr1:6472202-6472402
+ATATATTATTCTGTTTAGGATGAGTGACAGTAATTTTACTAGTTCTTAGTGTCCACCTTATTTGGTGGCTAGGATGTGATTGTGGGACAGAAATGTACAGTGACAGAGTGCTAAGTAGTTCTATGCAGGTTTGTTTTAGGCTAGTCATTTATGTTGCATTCCCATAGGTCCCAACAGTAATCTCCCTTATAGTTACCATA
+>chr1:6588721-6588921
+GGTCAGTTAGTAATGCCTTCCATGTGAGCATTCACCCAAGTGTGGAATCTCCAGGTGGGATCTCTCCTGACAGGACTCATTTTTCTTTATAAAAGTAGTCTTGAAATTTCCCTTTTTGCTCTGATGAGCACTGTCTAGTTGTAATTATCAATAACAATAAATGTAGACACAAAATGTTTGGCATATTGTGATGCAGTGTC
+>chr1:6719561-6719761
+AAGTGACAGCGCTCCTGCAAGCTCTCCTGCTGTATCTTGAGGCACTTTTCTTTTCAGTATCGGTGCTGTCTAATTCGTGAGCTTCTGTGAAGCAAGCGCAGGAGGGTACAAGGCCTACAGGGAGGAATTACACCTAATTACTCAAATAATTGCTAGGCTGTTGCCTTCTTAGTCACTGAAAATAATTTCCAGGTCCCTGG
+>chr1:6721868-6722068
+ACTGTGTCCTGGAGCACATGGGGTTTGTATCTGAAACCTGTAAAGTACATTGGAACCTTTCTCAAGAGTCTAATTCAGTTAGCCTTGAATGAGAGTCTTTATAGTGACTGCCATTCTTCTGCTATTATACCAACCACAAAGATTTAAAGTTTTGTGTTTCCTTGTCTGTGGATTAACTACAGGTGACAAGGAAAGGCAAG
+>chr1:6750817-6751017
+GTTCTAGTCTCCAGGGAGGGAAGCCACAGCAGATGGGGTTAGGGCAGAGGGCTGACGCATCTGACAGCAAACGGCGGTGAGGCTGCAGAGTAGAAACTATGAGCGTCAGGAAGCTCCTTCTCCCAGGAGACCCAACTAACCACTGAAGAAAGTTGAAAATGAGCCCTTTGAGAAACGCTATTAAAAGTAGTAAAAAAATG
+>chr1:6878570-6878770
+ATGTTGATCTTGCCTCATGGGCTTTTGTCAGGCTGATTGTAATAATGCATATGTGAATTGTGGAGTAATGACATGTTCTATGTCCTGAATTAATCAAAACTCACATCCTTCCTGTCTTTGTACATGTGGAAACAGATGTTCTGCATTATCAGCAATCTGAACCCTGCCAGCCAGCCAGCCTCCTCCATCAGTCTCTTTTC
+>chr1:7209035-7209235
+aatcaggaaaatacttcacagtcttgctttcaggcaatctgatgaactaattttttcaactgatgatgcttgtcccaaataactctagcttgagtgatggtgacaaaaaTCCTCAAACACATGTCAATGTGAACATTTTGCCAAAAGAGGGCAGCATTCACCTACTATAAAGAGCCTGAAAAATTACTGCAGAGGAGGAT
+>chr1:7303541-7303741
+AATTGCTTCATTAAAACCAAGTTTTTCTTTGTTCATTAGGCGTTAGCCAGATGGGAATTCAGTGTTTTTAAGCAGACACTCACATGGGGTTTTGTTTCTGACATTGATGAATGACTGCCTGCATCCCAAGATGGAAGTTTCCACCCTGGGCTCTGACTGCAACTTTTGTTATTCATAGCAGAAGTCACACCAGTCCACAG
+>chr1:7309743-7309943
+ttcatccttctctcctccccccacccccacctctcctcgtcctttttcacttccagtccccctttcaggttatccagttcatccaatgctgctggagagctacatgtagtgaggtttgggtggagaggagctttgagttttgagctttcaaaagccatcggttgtttccagtgtgttttctctgcttcctatgtgtggtt
+>chr1:7386917-7387117
+ttcaatcctttaaaaatatccaatatcttttaaaatccaaagtctttacaattaaaagtctcttaactgtgggatctgagttcgaggccagcctagagtacagagtgagttccagggctacacagagaaacccagcctcaaaaaaaaaacaaaaAACAAAACAAAACAAAAAGCAAACAAAAAGCGAGCGGGAGCATTGC
+>chr1:7388025-7388225
+CTTTCAATCAGGAAGCTTCCCCACTTGCTATTTCCAGGAGCAGGGAATAGCGCCAGAAGTCCCGCCCGCCCGGCTGTGACTGACAGCCGCGCCTTCCAATGGAAGGCTGGATTTCTTCCCCCCCCCCTCCCCCACACACACCCACCGTCCATGTCTGACAAGAGGCAGTGTCTGAGGCTTTTTTTCCCTCTATAAAGGAA
+>chr1:7388801-7389001
+ggcgtgtgccacccctgcctggcGACCCTAACACTCTTAAACCCCCCAAATAAAACCCTAGCATTTTAAATAAAAATACTCAAGAGCACTAAACACTACTCttaaaaaaaaaaaaaaaaaaaGCAGCAAAACCCTGACCCTCCCCCCCaaaaaaaaaaaaaaaaaaaaaaCTCTAAATGTCTGGGGCGGGGCCGGAGCAC
+>chr1:7413722-7413922
+tacaggggcaattttacagagacaaattgcagagagaacaggtaaagacagaataagttagagactgagaacgagccagatcagaatatattgccagagttagtttgagactaagcagaactattcaatgaaaaggagagagaagtcagaccaagtcagtcaacttgagtcaacccagaattgctgagtttaaccagcca
+>chr1:7444756-7444956
+gagatatttgtcaatcatccttattttctaagtgacaggagtcatattcagaagtctttacctatgccagtataatgaagTGTTTTCCATTtgtggtggtttaaatgatgatggcctctataggcttctatgtttgaatactcggATTCTTCCAAAACAGTTTCAAAACTGTACCTGGAAACACTATTTAACTAGTCATA
+>chr1:7768736-7768936
+aaatatagtggtggattaccttagggtaaggagctacgtctgttttctagctctcaagctacagttaccttacctgtcaatgttatcagaagtctggggaagaataaattatgatctaagagtcatgtattaattaaaatgacagagtttcatctatggtccattacctaaacagttcccaagtccctgcggtaaccatg
+>chr1:8797248-8797448
+catttattgatttatgtaggctgaaccaccttcacatctgtgggatgaagtctactctatcatggtggtgctattttttatgtacttaattccatttcttcataacatctttatgtggtttaagtgtcaacataactatgatttcataaaatgagctgggaaaggtttcttctgtttcaattatgtggaacattattgga
+>chr1:8851545-8851745
+gaggtgtagtggcttagaacagctctgctttatcagcacccaattttgtaagtcaaaagtcagacatgggatagatggactcttaattcatagactcaaatgttaaaatagaggGGGAATCAATCATCCATGAAGACAAAAGAATACTGGTGGTCTGTTTGGATTTCAGCCAGAGCAATCTGTTCAAATTTGACAGCAGA
+>chr1:9013525-9013725
+AGAAACACCACACACACATTTCATTTTTCTGAAGAAAGAAATGATCTGCTGTTTCACTTACATTCCACACACCAGGGAATATAAAGTCTAAATAGCACTCTAGTCTGCAGTTTAAAATTCATGTGTCACAAGAATAAAATAACAAGTCAGAGTCTCCAGTTGTTTAAGTAAGGTTAATCATAAGTAATCTTTATGACTCT
+>chr1:9460371-9460571
+ccaaccaccaagtcaccgggttcaaggcctgtgcttgactgggaaccaggctgtctatgcactgcctcacTGCACCGCAGCTGGTATCAATTtgtcttagtcagagttactattgttatgatgaaacaccatgagcaaagagcaaattggggaggaaatggcttatttagcttacatttccactgttcatcatcaaaaga
+>chr1:9535189-9535389
+TTTACCCATAGACACTGTGGTGTAGACGCTCCATTCGGAAGCTACAATGCAGGCACTTCCAAGAGTTTGAGCAGCCCGCGTCCTACTGCACTACCTCTGCCCCACAGCATGCTGGGAAACGTAGTCCCAACCAGGTCCTGAGCTGGTTAGCCAACCCTCAGCGCCAGTCGGGCCAACATCCGGTGACGAATCCAAGTCCC
+>chr1:9554705-9554905
+ACACCAGCCCTTTGTGTGCCCCAGGGCTCCAGGTGCTGTGTGGGGAATGTTAATGTCAGAAGCCCGGGACTTGGACCCAAGCCCAGGCTTCAGTTCACAGTATGTACTGTGTGCACACATTGGCAGTGATTCCAGGGGCCTGTATCCCTTCTCCCTTTAGGGAAGGGAATTTCGGCCATGCTGAGACATAGCTCTGGCCT
+>chr1:9568576-9568776
+TCTAAGTTGAGCCACGTCACTGTGATTTATTGTCACATGCCACAATAAGCATGTTTTGCTCTCTTGTCCCTTCTGCAGGAAGGGCTGTGTTGAGTTGGGCATTGTTTGTATAGTGCTGGACACAGCTGCAGGGTGTTTTTACGTGTTCAATGAAGTAATTCTGTTCTCAGAAAGCTCAGACAAGTACAGTATCAAAACAG
+>chr1:9574131-9574331
+AGGGTAAACAGTTCCATTTGTGACCATGAAATCCCCCATCTGTTGAGTGTATTCATGACTTAAGAGTTCTCGGCAGAGACAGATGAATGAACCTGCCTCCCCGATGTTAATGACATCCATCATACAACTGAACATGTGGCTTCATAAATCAAGGGCTAATGGTAATACTGTCTGCTCGTGTCATGAACAAGCTATCCGAT
+>chr1:9738400-9738600
+CTTCTCACTTCTCCACTGCCTTAGCCGTTGCCCCGAACGTAACGGCCACCACCCCACCCCGCACTCACACTCACTCACTCTCGCTCTCTCCCTCAGACACAGACATACACGCCCTCACTGAGACTGCGCAGGCGTAGCTTCTGCTCTGCCCTCTGGGAACCAGAGTCTTCCGGCTCCTCTCTCGCGAAGGAGTGCTAGGC
+>chr1:9813405-9813605
+TTTAGTTTGCTAGCAGCTGTCAGGAAGTACAATATAGGTCGAAGGACCCCATGTTCAAATCTCTAATGTGAGGACAGCCTGGGCCCCTCAGGAAAGTGAAAGCGGTGTGTCTTTCCCGTTCTCTGGTTTTTTAAAATGAGTTTTAAATTACAAgcatgtgccgctggagtccaggtgttggcttctctggggttggggtt
+>chr1:9932599-9932799
+CGGCAAAAACTTAAGTCATCATTGTGCCAGCTATTAAGGCCCTGTTAATCAAACCTCAAAGAAAAAAAAAAACCACACACACAATTTGTACCTTGTTATTGGCAAATGTAGTCCTGGCAGCTTGTTTCAATCACTCTCCATGACAAGTGTTTAGAAAATATTTGTTCAAGCACCTTCAAATGAGCAGGTTTTGTTGCACC
+>chr1:9942670-9942870
+AAGAGAAACATAAATGACCCTAGTCAGAAATGCATGACTTTCCTATATAAAAGCCTTTCACCCTCCGGCAAGATTATTTTTAAACATAATATTGACATTGAGATAATCGTAGCACTTATATATTTTGTCCAATTTAAAATTCCAAATCTGTGGAAAATACATTGAATTGTCAGAAAATAGGGCATTGATCTAGATGAAAC
+>chr1:9948240-9948440
+CAATTCTCCAGCTCACAATTTAAAAGCTTCTGAGAGTTAAATGCTATGGCATAGTTTATAATGGAGCACTCGAGTGACTGATGTGTATTTCAGTGAACTGGTCTCTCGGAGTTGAAACTACGACTTGTATAAACAGGAATGGAAATCCTTCTGGGTTTATGTAGTTAGGCAAGAATATTCCCAACTGTGTGCCGCTCCCA
+>chr1:9956513-9956713
+TCCCACTCATGACCACTTCACATATACGTAAAGAAATCATGCAAAATGGTTTCTCTTGGCTAATCTGAATACAGACCAATTCACTCAACATACAGGCAATCTAATATGACAGTTAATGGAAACATGGGTTTTCTTCTAACATTCTTGGTGGCTGTATATTCCACTAGATTTAACTGTGATTGAAATTTTACTCTATGGGG
+>chr1:9962925-9963125
+TATTTTTTAAACCACCAAGGTTCAAGCACCCCCTAGCATATTTGAAGAAAGGAAACGTCTGTCAGAAGTGCTCGCTGTGACAAATACAGAGGGAAGTGACAATGTGCTGCCTTTGCTTACTTAACACCATACATTATTTTTAACTGAACAGTGAAGGCATTTGTTCAGAACCAGCCTTTACATAAAAAATAATTTAGACC
+>chr1:9978791-9978991
+AAATCCTTTCACTCTCCTGCCCCTCGATAAATTACTCAAGGCACCAGACACTTTTCTGGACAGTCTCTGTTTGATAAATGATCATGTCATGCTATCGCTTAGAGGCGCACTGCAAAATTCTGAGTGGCCAATTGTCTTTCCCTGCAGGCTGGTGCCCTGCTCCTGCCTGGGTGTTTGTGGCAGGCGGTCTCAGCTTTAAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="weeder" version="2.0">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">http://159.149.160.51/modtools/downloads/weeder2.0.tar.gz</action>
+	<action type="shell_command">
+	  g++ weeder2.cpp -o weeder2 -O3
+	</action>
+	<!-- Move weeder2 executable -->
+	<action type="move_file">
+	  <source>weeder2</source>
+	  <destination>$INSTALL_DIR/bin</destination>
+	</action>
+	<!-- Move data files -->
+        <action type="move_directory_files">
+          <source_directory>FreqFiles</source_directory>
+          <destination_directory>$INSTALL_DIR/FreqFiles</destination_directory>
+        </action>
+	<!-- Set environment variables -->
+	<action type="set_environment">
+	  <environment_variable name="WEEDER_DIR" action="set_to">$INSTALL_DIR</environment_variable>
+	</action>
+	<action type="set_environment">
+	  <environment_variable name="WEEDER_FREQFILES_DIR" action="set_to">$INSTALL_DIR/FreqFiles</environment_variable>
+        </action>
+        <action type="set_environment">
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>Installs Weeder 2.0
+
+      See http://159.149.160.51/modtools/downloads/weeder2.html
+      and http://159.149.160.51/modtools/
+    </readme>
+  </package>
+</tool_dependency>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weeder2_wrapper.sh	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,62 @@
+#!/bin/sh -e
+#
+# Wrapper script to run weeder2 as a Galaxy tool
+#
+# Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE MOTIFS_OUT MATRIX_OUT [ ARGS... ]
+#
+# ARGS: one or more arguments to supply directly to weeder2
+#
+# Process command line
+FASTA_IN=$1
+SPECIES_CODE=$2
+MOTIFS_OUT=$3
+MATRIX_OUT=$4
+#
+# Other arguments
+ARGS=""
+while [ ! -z "$5" ] ; do
+    ARGS="$ARGS $5"
+    shift
+done
+#
+# Link to input file
+ln -s $FASTA_IN
+#
+# Link to the FreqFiles directory as weeder2 executable
+# expects it to be the same directory
+freqfiles_dir=$WEEDER_FREQFILES_DIR
+if [ -d $freqfiles_dir ] ; then
+    echo "Linking to FreqFiles directory"
+    ln -s $freqfiles_dir FreqFiles
+else
+    echo "ERROR FreqFiles directory not found" >&2
+    exit 1
+fi
+#
+# Construct names of input and output files
+fasta=`basename $FASTA_IN`
+motifs_out=$fasta.w2
+matrix_out=$fasta.matrix.w2
+#
+# Construct and run weeder command
+# NB weeder logs output to stderr so redirect to stdout
+# to prevent the Galaxy tool reporting failure
+weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
+echo "Running $weeder_cmd"
+$weeder_cmd 2>&1
+status=$?
+if [ $status -ne 0 ] ; then
+    echo weeder2 command finished with nonzero exit code $status >&2
+    echo Command was: $weeder_cmd
+    exit $status
+fi
+#
+# Move outputs to final destinations
+if [ -e $motifs_out ] ; then
+    /bin/mv $motifs_out $MOTIFS_OUT
+fi
+if [ -e $matrix_out ] ; then
+    /bin/mv $matrix_out $MATRIX_OUT
+fi
+#
+# Done
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weeder2_wrapper.xml	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,181 @@
+<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.0">
+  <description>Motif discovery in sequences from coregulated genes of a single species</description>
+  <command interpreter="bash">weeder2_wrapper.sh
+  $sequence_file $species_code
+  $output_motifs_file $output_matrix_file
+  $strands
+  #if $chipseq.use_chipseq
+     -chipseq -top $chipseq.top
+  #end if
+  #if str( $advanced_options.advanced_options_selector ) == "on"
+     -maxm $advanced_options.n_motifs_report
+     -b $advanced_options.n_motifs_build
+     -sim $advanced_options.sim_threshold
+     -em $advanced_options.em_cycles
+  #end if
+</command>
+  <requirements>
+    <requirement type="package" version="2.0">weeder</requirement>
+  </requirements>
+  <inputs>
+    <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
+    <param name="species_code" type="select" label="Species to use for background comparison">
+      <!-- Hard code options for now
+	   See weeder's "organisms.txt" for full list
+      -->
+      <option value="HS">Homo sapiens (HS)</option>
+      <option value="MM">Mus musculus (MM)</option>
+      <option value="DM">Drosophila melanogaster (DM)</option>
+      <option value="SC">Saccharomyces cerevisiae (SC)</option>
+      <option value="AT">Arabidopsis thaliana (AT)</option>
+    </param>
+    <param name="strands" label="Use both strands of sequence" type="boolean"
+	   truevalue="" falsevalue="-ss" checked="True"
+	   help="If not checked then use -ss option" />
+    <conditional name="chipseq">
+      <param name="use_chipseq" type="boolean"
+	     label="Use the ChIP-seq heuristic"
+	     help="Speeds up the computation (-chipseq)"
+	     truevalue="yes" falsevalue="no" checked="on" />
+      <when value="yes">
+	<param name="top" type="integer" value="100"
+	       label="Number of top input sequences with oligos to scan for"
+	       help="Increase this value to improve the chance of finding motifs enriched only in a subset of your input sequences (-top)" />
+      </when>
+      <when value="no"></when>
+    </conditional>
+    <conditional name="advanced_options">
+      <param name="advanced_options_selector" type="select"
+	     label="Display advanced options">
+	<option value="off">Hide</option>
+	<option value="on">Display</option>
+      </param>
+      <when value="on">
+	<param name="n_motifs_report" type="integer" value="25"
+	       label="Number of discovered motifs to report" help="(-maxm)" />
+	<param name="n_motifs_build" type="integer" value="50"
+	       label="Number of top scoring motifs to build occurrences matrix profiles and outputs for"
+	       help="(-b)" />
+	<param name="sim_threshold" type="float" min="0.0" max="1.0" value="0.95"
+	       label="Similarity threshold for the redundancy filter"
+	       help="Remove motifs that are too similar, with lower values imposing a stricter filter. Must be between 0.0 and 1.0 (-sim)" />
+	<param name="em_cycles" type="integer" min="0" max="100" value="1"
+	       label="Number of expectation maximization (EM) cycles to perform"
+	       help="Number of cycles must be between 0 and 100 (-em)" />
+      </when>
+      <when value="off">
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="output_motifs_file" format="txt" label="Weeder2 on ${on_string} (motifs)" />
+    <data name="output_matrix_file" format="txt" label="Weeder2 on ${on_string} (matrix)" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="sequence_file" value="weeder_in.fa" ftype="fasta" />
+      <param name="species_code" value="MM" />
+      <output name="output_motifs_file" file="weeder2_motifs.out" lines_diff="2" />
+      <output name="output_matrix_file" file="weeder2_matrix.out" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+Weeder2 is a program for finding novel motifs (transcription factor binding sites)
+conserved in a set of regulatory regions of related genes.
+
+-------------
+
+.. class:: infomark
+
+**Usage advice**
+
+Guidelines on how to use this tool can be seen in Zambelli et al. 2014 (see link
+below), but the following is a brief guide. Please note that **motifs** are a model
+or matrix that describes a set of sequences that may differ in the base composition.
+**Oligos** are specific sequences found within the input sequences or genomic
+background.
+
+**Input sequence** (in FASTA format) should be short (100-200bp) and be reasonably
+expected to contain an enriched motif(s).  This is not generally an issue with
+transcription factor ChIP-seq derived sequences centred on the summit of binding
+regions that are expected to contain a dominant motif and possibly secondary motifs.
+
+There is **no need to mask sequence for repetitive sequence** as factors may
+legitimately bind repetitive sequence.
+
+**Use both strands of sequence** by default, unless there is a specific reason not
+to do so.
+
+**Species to use for background comparison** should match the genome used to
+generate the **input sequence**. The background genome motif frequencies are
+generated from within the promoter regions of annotated genes and are shown to be a
+good background for both promoter and other regulatory regions.
+
+**Use the ChIP-seq heuristic** (-chipseq) when there are a large number of
+input sequences (hundreds or thousands). When -chipseq is used Weeder will use
+only oligos from the first 100 sequences to build motifs with which it scans
+all of the input sequences. This speeds up the computational time without too much
+risk of losing important motifs. Even if not strictly necessary it's advisable to
+order input sequences by their significance, e.g. fold enrichment or Pvalue. For
+large data sets (-top) should be set to a number equating at least 10 to 20% of
+input sequences (as recommended by the authors).
+
+**Number of discovered motifs to report** (-maxm) limits the number of reported
+motifs even if there are more than -maxm. **Number of top scoring motifs to build
+occurrences matrix profiles and outputs for** (-b) changes the number of top
+scoring motifs of length 6, 8 and 10 for which the occurrence matrix is built.
+Increasing -b may result in a larger number of reported motifs, but with potentially
+more of low significance and increases the computational time. If increasing -b does
+not result in more motifs in your results it means that the additional motifs are
+filtered out by the redundancy filter or that the maximum number of reported motifs
+set by -maxm has been reached.
+
+**Similarity threshold for the redundancy filter** (-sim) default setting is
+recommended.
+
+**Number of expectation maximization (EM) cycles to perform** (-em) default is
+recommended.  The option is included to help "clean up" the resulting motif matrices.
+In this version the number of EM steps can be increased, which can be useful for
+motifs with highly redundant stretches of sequence.
+
+-------------
+
+.. class:: infomark
+
+**A note on the results**
+
+The resulting matrices are the result of scanning (by default both strands) for
+oligos of length 6, 8 and 8, allowing 1, 2 and 3 substitutions respectively. The
+matrices within the matrix.w2 file can be input into other tools. The recommended
+next step is to use **STAMP** (http://www.benoslab.pitt.edu/stamp/), which displays
+the motifs as logos and identifies matches with libraries of known DNA binding
+motifs, such as TRANSFAC or JASPAR.
+
+-------------
+
+.. class:: infomark
+
+**Credits**
+
+This Galaxy tool has been developed by Peter Briggs and Ian Donaldson within the
+Bioinformatics Core Facility at the University of Manchester, and runs the Weeder2
+motif discovery package:
+
+ * Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
+   for the Discovery of Enriched Transcription Factor Binding Site Motifs in
+   Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
+ * http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full
+
+This tool is compatible with Weeder 2.0:
+
+ * http://159.149.160.51/modtools/downloads/weeder2.html
+
+Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility
+scripts if you use it in your work.
+  </help>
+</tool>