# HG changeset patch
# User pjbriggs
# Date 1537971176 14400
# Node ID 89315bdc1a8c6b69c36bf7e94daa595f40a2b2e0
# Parent f19e18ab01b146a3338b12fa9dc9a97766ffd3ae
Uploaded tool version 2.0.3.
diff -r f19e18ab01b1 -r 89315bdc1a8c README.rst
--- a/README.rst Mon Mar 05 10:19:50 2018 -0500
+++ b/README.rst Wed Sep 26 10:12:56 2018 -0400
@@ -79,6 +79,8 @@
========== ======================================================================
Version Changes
---------- ----------------------------------------------------------------------
+2.0.3 - Update handling of frequency files to accommodate changes in
+ latest bioconda version of weeder2.
2.0.2 - Drop ``tool_dependencies.xml`` & use conda to resolve dependencies
2.0.1 - Explicitly specify frequency files in ``weeder2.loc``.
2.0.0 - Initial version
diff -r f19e18ab01b1 -r 89315bdc1a8c test-data/weeder_in.fa.matrix.w2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/weeder_in.fa.matrix.w2 Wed Sep 26 10:12:56 2018 -0400
@@ -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
diff -r f19e18ab01b1 -r 89315bdc1a8c test-data/weeder_in.fa.w2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/weeder_in.fa.w2 Wed Sep 26 10:12:56 2018 -0400
@@ -0,0 +1,1250 @@
+COMMAND LINE:
+
+./weeder2 -f /home/pjb/projects/galaxy-tools/tools/weeder2/test-data/weeder_in.fa -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 -
+**********
+
diff -r f19e18ab01b1 -r 89315bdc1a8c weeder2_macros.xml
--- a/weeder2_macros.xml Mon Mar 05 10:19:50 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
- if [ -z "\$WEEDER_FREQFILES_DIR" ]; then export WEEDER_FREQFILES_DIR=\$(dirname \$(readlink -e \$(which weeder2)))/FreqFiles; fi
-
diff -r f19e18ab01b1 -r 89315bdc1a8c weeder2_wrapper.sh
--- a/weeder2_wrapper.sh Mon Mar 05 10:19:50 2018 -0500
+++ b/weeder2_wrapper.sh Wed Sep 26 10:12:56 2018 -0400
@@ -25,8 +25,9 @@
#
# Locate the FreqFiles directory
if [ $FREQFILES_DIR == "." ] ; then
- # Use the files in the Weeder2 distribution
- freqfiles_dir=$WEEDER_FREQFILES_DIR
+ # Don't explicitly set the location - Weeder2 from
+ # bioconda handles this automatically
+ freqfiles_dir=
else
# Alternative location
freqfiles_dir=$FREQFILES_DIR
@@ -34,18 +35,22 @@
#
# Link to the FreqFiles directory as weeder2 executable
# expects it to be the same directory
-if [ -d $freqfiles_dir ] ; then
- echo "Linking to FreqFiles directory: $freqfiles_dir"
- ln -s $freqfiles_dir FreqFiles
+if [ ! -z "$freqfiles_dir" ] ; then
+ if [ -d $freqfiles_dir ] ; then
+ echo "Linking to FreqFiles directory: $freqfiles_dir"
+ ln -s $freqfiles_dir FreqFiles
+ else
+ echo "ERROR FreqFiles directory not found" >&2
+ exit 1
+ fi
else
- echo "ERROR FreqFiles directory not found" >&2
- exit 1
+ echo "WARNING FreqFiles directory not set" >&2
fi
#
# Construct names of input and output files
-fasta=`basename $FASTA_IN`
-motifs_out=$fasta.w2
-matrix_out=$fasta.matrix.w2
+fasta=$(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
@@ -63,9 +68,16 @@
# Move outputs to final destinations
if [ -e $motifs_out ] ; then
/bin/mv $motifs_out $MOTIFS_OUT
+else
+ echo ERROR missing output file: $motifs_out >&2
+ status=1
fi
if [ -e $matrix_out ] ; then
/bin/mv $matrix_out $MATRIX_OUT
+else
+ echo ERROR missing output file: $matrix_out >&2
+ status=1
fi
#
# Done
+exit $status
diff -r f19e18ab01b1 -r 89315bdc1a8c weeder2_wrapper.xml
--- a/weeder2_wrapper.xml Mon Mar 05 10:19:50 2018 -0500
+++ b/weeder2_wrapper.xml Wed Sep 26 10:12:56 2018 -0400
@@ -1,13 +1,9 @@
-
+
Motif discovery in sequences from coregulated genes of a single species
-
- weeder2_macros.xml
-
weeder
-