******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.6.1 (Release date: Mon Mar 21 15:08:38 EST 2011) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= GATA_Negs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2:27152224-27152414 1.0000 190 chr6:38757479-38757763 1.0000 284 chr6:38856153-38856302 1.0000 149 chr6:88203909-88204133 1.0000 224 chr7:71502866-71503415 1.0000 549 chr7:83063963-83064847 1.0000 884 chr7:92271035-92271634 1.0000 599 chr7:71036918-71037467 1.0000 549 chr7:83097025-83097574 1.0000 549 chr7:103970880-103971429 1.0000 549 chr7:108272128-108272677 1.0000 549 chr7:70144673-70145243 1.0000 570 chr7:63499316-63500135 1.0000 819 chr7:105413005-105413554 1.0000 549 chr7:127921931-127922530 1.0000 599 chr7:81826094-81826693 1.0000 599 chr7:66280165-66280714 1.0000 549 chr7:66763679-66764228 1.0000 549 chr7:67296236-67296942 1.0000 706 chr7:106294602-106295451 1.0000 849 chr7:100578576-100579125 1.0000 549 chr7:66468915-66469464 1.0000 549 chr7:90158171-90158971 1.0000 800 chr7:68211440-68211989 1.0000 549 chr7:69959582-69960631 1.0000 1049 chr8:122108965-122109228 1.0000 263 chrX:150565848-150566190 1.0000 342 chrX:150846672-150846828 1.0000 156 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme GATA_Negs.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATA_Negs.bed.meme.maxw25 model: mod= zoops nmotifs= 10 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 28 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 15121 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.278 C 0.219 G 0.204 T 0.299 Background letter frequencies (from dataset with add-one prior applied): A 0.278 C 0.219 G 0.204 T 0.299 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 20 sites = 28 llr = 267 E-value = 3.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4211433616::15345: pos.-specific C 69232:31217:::4:42:: probability G 2::42532121188532429 matrix T 1:5153:44:1422:31:3: bits 2.3 2.1 1.8 * * 1.6 * ** * Relative 1.4 * ** * Entropy 1.1 * ** * (13.7 bits) 0.9 ** *** * 0.7 ** * ****** * 0.5 *** ** ******* *** 0.2 ******* *********** 0.0 -------------------- Multilevel CCTGTGATTACAGGGACAAG consensus G ACGTCAAG T CGAGT sequence G C TGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- chr7:63499316-63500135 272 4.00e-09 CACTAGGATC CCTGGGCTTACAGGGTAGAG AATTTGTTAT chr7:108272128-108272677 349 1.06e-08 CTCTACCTCT CCTCTGCCAACAGGGACAGG AGACACTTTG chr7:90158171-90158971 334 5.52e-08 CTCATGTAAA CCACCGGGCACAGGGGCCAG CACCTTTTAT chr7:71502866-71503415 15 6.65e-08 CTTCCCAAGT GCTGTGATTACAGGCATGAG CCACCACAGT chr7:66468915-66469464 208 1.59e-07 ATATGCATGA CCTGTGATGGCTGGGGAGGG GGGCAGTTAG chr7:66763679-66764228 320 4.08e-07 AGCCTCAGGA CCTGGGGGCGCTGGGTGCAG TTTCCTTGTT chr7:70144673-70145243 280 7.23e-07 TCATTAGATT CCAGAGATTCCTGGGAGGTG AAGTTAAGAA chr7:92271035-92271634 81 7.23e-07 TATCAGTGGA GCTGTTGTAACATGCACAAG GCCTTTGTTT chr7:81826094-81826693 27 3.28e-06 GGTTCCAGTT CCTCCAGCAACAGGCAGGTG AGGATTGTAA chr8:122108965-122109228 168 5.12e-06 CTCCGTGTCT TCTGAGGACACTGTGACAAG ATCGGTCAAG chr7:100578576-100579125 528 5.70e-06 TGCATAGTTA CCAAAGAAAACAGTCACAGG GA chr7:67296236-67296942 380 6.34e-06 ATGATAAGAA CCAGATAAGACTGGAAAGAG TCAATTTTAA chr7:105413005-105413554 289 7.04e-06 AAGCTCTGAG CCTGTGCTTGTGGGGTCGTG TGCTGTAACT chr7:69959582-69960631 531 1.41e-05 TATTTCAGAA CCAGTGAGTAAATGCAGATG CTCCAGAAAG chr7:83063963-83064847 264 1.41e-05 GTTAAGGGAA CCTCTTACAAGGGGGAAGGG TAGTGAGGAT chr7:66280165-66280714 117 2.04e-05 TGCCAAATCC CTAGCTCCTACTGGGGCGGG GCACAGGCTG chr6:88203909-88204133 85 4.38e-05 TGCTAGGAAT GCTGTTAGTGCAGTAAAAGG CACTGAGTGT chr7:127921931-127922530 229 4.75e-05 GATTCCCAGG GCCAGTGTCAGTGGCGGCAG CCCCCAGGGA chr7:106294602-106295451 533 5.14e-05 TGAGTTCTGT TCTCTTCAAACTTGGAACTG CCATGCTTGC chr7:68211440-68211989 334 5.56e-05 AAGCTTCAGG CCCCCACATCCATGCACATG CATGCATGGG chr2:27152224-27152414 30 5.56e-05 CAAGGGGGAG CCAAGGGTCAGAGGCTCAAA GGAACTAGCC chrX:150565848-150566190 87 6.99e-05 CTCTCAGTAT CCATGGAGGCTTGGCTCCAG CTCTGTCCAT chr7:103970880-103971429 412 8.71e-05 ACATAAAAAC CACATGCAGACATGGGCCAG AGAACAGATA chr6:38757479-38757763 57 1.16e-04 AAATCTGATG TCATGGCATGGAGGGGCTAG CTTTTTCCAT chr7:83097025-83097574 465 1.42e-04 TTATGAAGCA GCCATTCTCAAAGTGTAGAG ACTTAGACCT chr7:71036918-71037467 380 1.52e-04 TGAGTACTCT TCTTTTATAGCTGGAGTAAG GTGTGCTTAG chr6:38856153-38856302 61 2.37e-04 CCAGCATGCA GCCCCAATTCCAGTCTGATG AGATCTGCTT chrX:150846672-150846828 4 4.24e-04 GTG CCATTAGAAATAGGGATAAT ATTAGTGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:63499316-63500135 4e-09 271_[+1]_528 chr7:108272128-108272677 1.1e-08 348_[+1]_181 chr7:90158171-90158971 5.5e-08 333_[+1]_447 chr7:71502866-71503415 6.6e-08 14_[+1]_515 chr7:66468915-66469464 1.6e-07 207_[+1]_322 chr7:66763679-66764228 4.1e-07 319_[+1]_210 chr7:70144673-70145243 7.2e-07 279_[+1]_271 chr7:92271035-92271634 7.2e-07 80_[+1]_499 chr7:81826094-81826693 3.3e-06 26_[+1]_553 chr8:122108965-122109228 5.1e-06 167_[+1]_76 chr7:100578576-100579125 5.7e-06 527_[+1]_2 chr7:67296236-67296942 6.3e-06 379_[+1]_307 chr7:105413005-105413554 7e-06 288_[+1]_241 chr7:69959582-69960631 1.4e-05 530_[+1]_499 chr7:83063963-83064847 1.4e-05 263_[+1]_601 chr7:66280165-66280714 2e-05 116_[+1]_413 chr6:88203909-88204133 4.4e-05 84_[+1]_120 chr7:127921931-127922530 4.7e-05 228_[+1]_351 chr7:106294602-106295451 5.1e-05 532_[+1]_297 chr7:68211440-68211989 5.6e-05 333_[+1]_196 chr2:27152224-27152414 5.6e-05 29_[+1]_141 chrX:150565848-150566190 7e-05 86_[+1]_236 chr7:103970880-103971429 8.7e-05 411_[+1]_118 chr6:38757479-38757763 0.00012 56_[+1]_208 chr7:83097025-83097574 0.00014 464_[+1]_65 chr7:71036918-71037467 0.00015 379_[+1]_150 chr6:38856153-38856302 0.00024 60_[+1]_69 chrX:150846672-150846828 0.00042 3_[+1]_133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=28 chr7:63499316-63500135 ( 272) CCTGGGCTTACAGGGTAGAG 1 chr7:108272128-108272677 ( 349) CCTCTGCCAACAGGGACAGG 1 chr7:90158171-90158971 ( 334) CCACCGGGCACAGGGGCCAG 1 chr7:71502866-71503415 ( 15) GCTGTGATTACAGGCATGAG 1 chr7:66468915-66469464 ( 208) CCTGTGATGGCTGGGGAGGG 1 chr7:66763679-66764228 ( 320) CCTGGGGGCGCTGGGTGCAG 1 chr7:70144673-70145243 ( 280) CCAGAGATTCCTGGGAGGTG 1 chr7:92271035-92271634 ( 81) GCTGTTGTAACATGCACAAG 1 chr7:81826094-81826693 ( 27) CCTCCAGCAACAGGCAGGTG 1 chr8:122108965-122109228 ( 168) TCTGAGGACACTGTGACAAG 1 chr7:100578576-100579125 ( 528) CCAAAGAAAACAGTCACAGG 1 chr7:67296236-67296942 ( 380) CCAGATAAGACTGGAAAGAG 1 chr7:105413005-105413554 ( 289) CCTGTGCTTGTGGGGTCGTG 1 chr7:69959582-69960631 ( 531) CCAGTGAGTAAATGCAGATG 1 chr7:83063963-83064847 ( 264) CCTCTTACAAGGGGGAAGGG 1 chr7:66280165-66280714 ( 117) CTAGCTCCTACTGGGGCGGG 1 chr6:88203909-88204133 ( 85) GCTGTTAGTGCAGTAAAAGG 1 chr7:127921931-127922530 ( 229) GCCAGTGTCAGTGGCGGCAG 1 chr7:106294602-106295451 ( 533) TCTCTTCAAACTTGGAACTG 1 chr7:68211440-68211989 ( 334) CCCCCACATCCATGCACATG 1 chr2:27152224-27152414 ( 30) CCAAGGGTCAGAGGCTCAAA 1 chrX:150565848-150566190 ( 87) CCATGGAGGCTTGGCTCCAG 1 chr7:103970880-103971429 ( 412) CACATGCAGACATGGGCCAG 1 chr6:38757479-38757763 ( 57) TCATGGCATGGAGGGGCTAG 1 chr7:83097025-83097574 ( 465) GCCATTCTCAAAGTGTAGAG 1 chr7:71036918-71037467 ( 380) TCTTTTATAGCTGGAGTAAG 1 chr6:38856153-38856302 ( 61) GCCCCAATTCCAGTCTGATG 1 chrX:150846672-150846828 ( 4) CCATTAGAAATAGGGATAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14589 bayes= 9.02247 E= 3.3e-002 -1145 156 7 -106 -296 209 -1145 -306 36 -29 -1145 64 -64 19 107 -106 -96 -29 7 64 -96 -1145 139 10 50 56 48 -1145 4 -61 -20 39 4 -3 -52 26 121 -61 7 -1145 -196 163 -52 -148 104 -1145 -152 26 -1145 -1145 201 -74 -1145 -1145 201 -74 -137 71 139 -1145 85 -1145 29 -26 -15 97 7 -148 50 -3 80 -306 95 -1145 7 -26 -296 -1145 218 -306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 28 E= 3.3e-002 0.000000 0.642857 0.214286 0.142857 0.035714 0.928571 0.000000 0.035714 0.357143 0.178571 0.000000 0.464286 0.178571 0.250000 0.428571 0.142857 0.142857 0.178571 0.214286 0.464286 0.142857 0.000000 0.535714 0.321429 0.392857 0.321429 0.285714 0.000000 0.285714 0.142857 0.178571 0.392857 0.285714 0.214286 0.142857 0.357143 0.642857 0.142857 0.214286 0.000000 0.071429 0.678571 0.142857 0.107143 0.571429 0.000000 0.071429 0.357143 0.000000 0.000000 0.821429 0.178571 0.000000 0.000000 0.821429 0.178571 0.107143 0.357143 0.535714 0.000000 0.500000 0.000000 0.250000 0.250000 0.250000 0.428571 0.214286 0.107143 0.392857 0.214286 0.357143 0.035714 0.535714 0.000000 0.214286 0.250000 0.035714 0.000000 0.928571 0.035714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]C[TA][GC][TG][GT][ACG][TA][TAC][AG]C[AT]GG[GC][AGT][CAG][AGC][ATG]G -------------------------------------------------------------------------------- Time 11.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 21 sites = 22 llr = 251 E-value = 8.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::41322::9121:31277: pos.-specific C 5:5:1221:11:636:::2:4 probability G ::5:422:55:71:::87:25 matrix T 4a:5434753:21547:::11 bits 2.3 2.1 1.8 1.6 Relative 1.4 * * Entropy 1.1 ** * * ** (16.5 bits) 0.9 *** * ** **** * 0.7 **** ** *** ******* 0.5 **** ************** 0.2 ***** ************** 0.0 --------------------- Multilevel CTGTGATTGGAGCTCTGGAAG consensus T CATTA TT T CTA A C sequence CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr7:83063963-83064847 309 3.05e-09 CTCAGAAAAC CTGATCCTGGATCTCTGGAAC ACAAAATTGT chr7:68211440-68211989 207 7.85e-08 GGCAGCACAC CTGTGATTCCAGCCTTGGAAG GATGAGTTGG chr7:100578576-100579125 479 7.85e-08 ACAAAAATAC TTGTCCCATGAGCTCTGGAAC CAGCAACCAA chr7:66763679-66764228 164 2.60e-07 TTTCAGGAGC TTGATCTTTGATACTTGGAAG CTGTGAGCCC chr2:27152224-27152414 161 2.60e-07 AGTGTATAGA TTCTTCTTGTAGGTCTGGCAC AGAACAGCC chr7:66468915-66469464 352 2.91e-07 TAGTCCTCTG TTCTGACTGGAACACAGGAAC CTGGAAATTT chr7:106294602-106295451 426 2.91e-07 TTAGAGTCAC TTCAGGGTGTAGCTTAGGAAT ATCCTAAATG chr7:105413005-105413554 76 6.18e-07 CTCTTTGGAC TTGTTGATGTAGCCCTGAATG GACTAGACGT chr7:69959582-69960631 625 6.85e-07 GAAAATATAT CTGAGTATTCAGCTTAGGGAG CCATTCCAAC chr7:90158171-90158971 304 1.13e-06 GGATGAGGGC CTGAATTTGGATCCCTAGCAC TCATGTAAAC chr7:127921931-127922530 535 1.24e-06 AAGGGTGGTT CTGTTTGAGTAGTTCTGGAGC CTAGAGACAG chr7:70144673-70145243 100 2.61e-06 TAGTTCTTAT CTCAATCTTGAGCACAAGAGG ACAGCAGTGA chr7:71036918-71037467 320 3.11e-06 ATGCGTCTGT CTCTAGTTTGCGTTCTGAAAG AGCTCTCTAG chr8:122108965-122109228 41 3.70e-06 AACTGAGATT CTCAGATCGGAGCCCTGATGC TCCGTAGTTG chr7:92271035-92271634 396 3.70e-06 CAAGATTGCT CTCCTAACTGAGCCTTGGAAT GTCTTAGCCA chr7:63499316-63500135 189 4.76e-06 CCGTGTGCAC TTCTGAATGGAACACAGCAAG ACAGCTGTTG chr7:81826094-81826693 202 6.59e-06 CGATAGTTTA CTCTTGTAGTTTCTCTGGCAG AAGAGATTAA chr7:83097025-83097574 377 9.01e-06 AATGGCTTTA GTCTTAGTTGAGACCAGGCAT ACTTGGAGCA chr7:103970880-103971429 211 1.22e-05 TAACCAAAAC TTGAGCTTTCAGGTTTAGATG TTCAGGTTTC chr6:88203909-88204133 107 1.31e-05 GTAAAAGGCA CTGAGTGTTTAGATTTTAAAC TGTAGTTAAA chr7:71502866-71503415 133 1.63e-05 GATCCTAGTT CTGTCTCTTGCTATTAGGAGG TCTCAGGGCT chr7:108272128-108272677 101 2.01e-05 GAGCACAACT TAGTGAAAGAAGCTTTGAAAG TGACATGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:83063963-83064847 3e-09 308_[+2]_555 chr7:68211440-68211989 7.9e-08 206_[+2]_322 chr7:100578576-100579125 7.9e-08 478_[+2]_50 chr7:66763679-66764228 2.6e-07 163_[+2]_365 chr2:27152224-27152414 2.6e-07 160_[+2]_9 chr7:66468915-66469464 2.9e-07 351_[+2]_177 chr7:106294602-106295451 2.9e-07 425_[+2]_403 chr7:105413005-105413554 6.2e-07 75_[+2]_453 chr7:69959582-69960631 6.8e-07 624_[+2]_404 chr7:90158171-90158971 1.1e-06 303_[+2]_476 chr7:127921931-127922530 1.2e-06 534_[+2]_44 chr7:70144673-70145243 2.6e-06 99_[+2]_450 chr7:71036918-71037467 3.1e-06 319_[+2]_209 chr8:122108965-122109228 3.7e-06 40_[+2]_202 chr7:92271035-92271634 3.7e-06 395_[+2]_183 chr7:63499316-63500135 4.8e-06 188_[+2]_610 chr7:81826094-81826693 6.6e-06 201_[+2]_377 chr7:83097025-83097574 9e-06 376_[+2]_152 chr7:103970880-103971429 1.2e-05 210_[+2]_318 chr6:88203909-88204133 1.3e-05 106_[+2]_97 chr7:71502866-71503415 1.6e-05 132_[+2]_396 chr7:108272128-108272677 2e-05 100_[+2]_428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=22 chr7:83063963-83064847 ( 309) CTGATCCTGGATCTCTGGAAC 1 chr7:68211440-68211989 ( 207) CTGTGATTCCAGCCTTGGAAG 1 chr7:100578576-100579125 ( 479) TTGTCCCATGAGCTCTGGAAC 1 chr7:66763679-66764228 ( 164) TTGATCTTTGATACTTGGAAG 1 chr2:27152224-27152414 ( 161) TTCTTCTTGTAGGTCTGGCAC 1 chr7:66468915-66469464 ( 352) TTCTGACTGGAACACAGGAAC 1 chr7:106294602-106295451 ( 426) TTCAGGGTGTAGCTTAGGAAT 1 chr7:105413005-105413554 ( 76) TTGTTGATGTAGCCCTGAATG 1 chr7:69959582-69960631 ( 625) CTGAGTATTCAGCTTAGGGAG 1 chr7:90158171-90158971 ( 304) CTGAATTTGGATCCCTAGCAC 1 chr7:127921931-127922530 ( 535) CTGTTTGAGTAGTTCTGGAGC 1 chr7:70144673-70145243 ( 100) CTCAATCTTGAGCACAAGAGG 1 chr7:71036918-71037467 ( 320) CTCTAGTTTGCGTTCTGAAAG 1 chr8:122108965-122109228 ( 41) CTCAGATCGGAGCCCTGATGC 1 chr7:92271035-92271634 ( 396) CTCCTAACTGAGCCTTGGAAT 1 chr7:63499316-63500135 ( 189) TTCTGAATGGAACACAGCAAG 1 chr7:81826094-81826693 ( 202) CTCTTGTAGTTTCTCTGGCAG 1 chr7:83097025-83097574 ( 377) GTCTTAGTTGAGACCAGGCAT 1 chr7:103970880-103971429 ( 211) TTGAGCTTTCAGGTTTAGATG 1 chr6:88203909-88204133 ( 107) CTGAGTGTTTAGATTTTAAAC 1 chr7:71502866-71503415 ( 133) CTGTCTCTTGCTATTAGGAGG 1 chr7:108272128-108272677 ( 101) TAGTGAAAGAAGCTTTGAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14561 bayes= 9.72378 E= 8.8e-002 -1110 132 -217 45 -261 -1110 -1110 167 -1110 106 141 -1110 56 -226 -1110 87 -103 -127 100 28 20 6 -17 -13 -29 6 -17 28 -61 -127 -1110 128 -1110 -226 129 60 -261 -68 141 -13 164 -127 -1110 -271 -161 -1110 174 -40 -61 154 -117 -172 -103 54 -1110 87 -1110 143 -1110 45 20 -1110 -1110 119 -103 -1110 200 -271 -29 -226 183 -1110 139 -27 -217 -271 139 -1110 -17 -172 -1110 73 129 -113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 8.8e-002 0.000000 0.545455 0.045455 0.409091 0.045455 0.000000 0.000000 0.954545 0.000000 0.454545 0.545455 0.000000 0.409091 0.045455 0.000000 0.545455 0.136364 0.090909 0.409091 0.363636 0.318182 0.227273 0.181818 0.272727 0.227273 0.227273 0.181818 0.363636 0.181818 0.090909 0.000000 0.727273 0.000000 0.045455 0.500000 0.454545 0.045455 0.136364 0.545455 0.272727 0.863636 0.090909 0.000000 0.045455 0.090909 0.000000 0.681818 0.227273 0.181818 0.636364 0.090909 0.090909 0.136364 0.318182 0.000000 0.545455 0.000000 0.590909 0.000000 0.409091 0.318182 0.000000 0.000000 0.681818 0.136364 0.000000 0.818182 0.045455 0.227273 0.045455 0.727273 0.000000 0.727273 0.181818 0.045455 0.045455 0.727273 0.000000 0.181818 0.090909 0.000000 0.363636 0.500000 0.136364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]T[GC][TA][GT][ATC][TAC]T[GT][GT]A[GT]C[TC][CT][TA]G[GA]AA[GC] -------------------------------------------------------------------------------- Time 23.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 28 llr = 207 E-value = 9.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 66:::1:: pos.-specific C 2::59::: probability G :193::aa matrix T 231219:: bits 2.3 * 2.1 ** 1.8 * ** 1.6 * * ** Relative 1.4 * **** Entropy 1.1 * **** (10.6 bits) 0.9 * **** 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAGCCTGG consensus TT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:68211440-68211989 181 1.82e-05 AAGCCAGGTA AAGGCTGG GCTGGTGTGG chr7:105413005-105413554 250 1.82e-05 AATCCTCGGA AAGGCTGG CTTACTTGGG chr7:71036918-71037467 412 1.82e-05 GTGCTTAGTC AAGGCTGG AGCTCGTAAC chr7:100578576-100579125 285 2.83e-05 TTTCCCTGCA ATGCCTGG CATTATTTAT chr7:83063963-83064847 354 2.83e-05 TTATTTGACA ATGCCTGG ATGTTAAGCA chr7:90158171-90158971 697 3.57e-05 GATTCAGAGC CAGCCTGG CGATAGGGAC chr7:81826094-81826693 298 3.57e-05 CAAACCCTGT CAGCCTGG ACAGTGTCCA chr7:92271035-92271634 17 4.58e-05 AGTTTGAGGC TAGCCTGG GCTAGGTAGA chr2:27152224-27152414 55 4.58e-05 TCAAAGGAAC TAGCCTGG GTTCTGTCTG chr7:69959582-69960631 134 5.53e-05 AATCTACATC ATGGCTGG CATCCCAGAT chr7:66468915-66469464 35 5.53e-05 ATCTAAGACT ATGGCTGG TGGGTAGGGC chr7:63499316-63500135 104 5.53e-05 ACCATGGTAG ATGGCTGG GATGATGGCC chr7:66280165-66280714 140 7.50e-05 GGGCGGGGCA CAGGCTGG TTAGGGAGCT chrX:150846672-150846828 90 1.54e-04 ATATTCAACA ATGTCTGG AACGTTGAAA chr7:106294602-106295451 782 1.54e-04 GCTCTCCTGT ATGTCTGG CTCAAATGCT chr7:70144673-70145243 421 1.54e-04 TACATTGAAA AAGCCAGG TTTTGTTTAG chr6:88203909-88204133 201 1.54e-04 AACACACTTT AATCCTGG GCTCCAACTT chr7:71502866-71503415 158 1.81e-04 AGGAGGTCTC AGGGCTGG TGTGGTGACT chr7:83097025-83097574 294 1.94e-04 CAGATGACTT TAGTCTGG GCAGTTCAGT chrX:150565848-150566190 3 2.22e-04 GT GAGCCTGG TAAATCCAGG chr7:66763679-66764228 288 2.79e-04 GGAGCGTGTT AAGCTTGG CTTTCTCATC chr6:38757479-38757763 11 2.79e-04 TCTCTATATT TGGCCTGG TGACATATCA chr7:127921931-127922530 8 3.07e-04 TCCAGGA CAGCCAGG GCTACACAGA chr7:103970880-103971429 346 4.57e-04 ATCCCTGTAA AATTCTGG ATACATCTCC chr8:122108965-122109228 11 6.35e-04 AGCTCCAAGT AAGGCTTG CACCGTGAAC chr7:108272128-108272677 8 9.68e-04 AGAATCC TTGCTTGG TGTACTTACA chr6:38856153-38856302 3 1.20e-03 CA CATCCAGG ACCAAACAGA chr7:67296236-67296942 285 1.28e-03 TGATGGCTTC TTTTCTGG CTCCTTTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:68211440-68211989 1.8e-05 180_[+3]_361 chr7:105413005-105413554 1.8e-05 249_[+3]_292 chr7:71036918-71037467 1.8e-05 411_[+3]_130 chr7:100578576-100579125 2.8e-05 284_[+3]_257 chr7:83063963-83064847 2.8e-05 353_[+3]_523 chr7:90158171-90158971 3.6e-05 696_[+3]_96 chr7:81826094-81826693 3.6e-05 297_[+3]_294 chr7:92271035-92271634 4.6e-05 16_[+3]_575 chr2:27152224-27152414 4.6e-05 54_[+3]_128 chr7:69959582-69960631 5.5e-05 133_[+3]_908 chr7:66468915-66469464 5.5e-05 34_[+3]_507 chr7:63499316-63500135 5.5e-05 103_[+3]_708 chr7:66280165-66280714 7.5e-05 139_[+3]_402 chrX:150846672-150846828 0.00015 89_[+3]_59 chr7:106294602-106295451 0.00015 781_[+3]_60 chr7:70144673-70145243 0.00015 420_[+3]_142 chr6:88203909-88204133 0.00015 200_[+3]_16 chr7:71502866-71503415 0.00018 157_[+3]_384 chr7:83097025-83097574 0.00019 293_[+3]_248 chrX:150565848-150566190 0.00022 2_[+3]_332 chr7:66763679-66764228 0.00028 287_[+3]_254 chr6:38757479-38757763 0.00028 10_[+3]_266 chr7:127921931-127922530 0.00031 7_[+3]_584 chr7:103970880-103971429 0.00046 345_[+3]_196 chr8:122108965-122109228 0.00064 10_[+3]_245 chr7:108272128-108272677 0.00097 7_[+3]_534 chr6:38856153-38856302 0.0012 2_[+3]_139 chr7:67296236-67296942 0.0013 284_[+3]_414 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=28 chr7:68211440-68211989 ( 181) AAGGCTGG 1 chr7:105413005-105413554 ( 250) AAGGCTGG 1 chr7:71036918-71037467 ( 412) AAGGCTGG 1 chr7:100578576-100579125 ( 285) ATGCCTGG 1 chr7:83063963-83064847 ( 354) ATGCCTGG 1 chr7:90158171-90158971 ( 697) CAGCCTGG 1 chr7:81826094-81826693 ( 298) CAGCCTGG 1 chr7:92271035-92271634 ( 17) TAGCCTGG 1 chr2:27152224-27152414 ( 55) TAGCCTGG 1 chr7:69959582-69960631 ( 134) ATGGCTGG 1 chr7:66468915-66469464 ( 35) ATGGCTGG 1 chr7:63499316-63500135 ( 104) ATGGCTGG 1 chr7:66280165-66280714 ( 140) CAGGCTGG 1 chrX:150846672-150846828 ( 90) ATGTCTGG 1 chr7:106294602-106295451 ( 782) ATGTCTGG 1 chr7:70144673-70145243 ( 421) AAGCCAGG 1 chr6:88203909-88204133 ( 201) AATCCTGG 1 chr7:71502866-71503415 ( 158) AGGGCTGG 1 chr7:83097025-83097574 ( 294) TAGTCTGG 1 chrX:150565848-150566190 ( 3) GAGCCTGG 1 chr7:66763679-66764228 ( 288) AAGCTTGG 1 chr6:38757479-38757763 ( 11) TGGCCTGG 1 chr7:127921931-127922530 ( 8) CAGCCAGG 1 chr7:103970880-103971429 ( 346) AATTCTGG 1 chr8:122108965-122109228 ( 11) AAGGCTTG 1 chr7:108272128-108272677 ( 8) TTGCTTGG 1 chr6:38856153-38856302 ( 3) CATCCAGG 1 chr7:67296236-67296942 ( 285) TTTTCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 14925 bayes= 9.66203 E= 9.7e+000 104 -29 -252 -48 113 -1145 -152 10 -1145 -1145 207 -106 -1145 119 65 -74 -1145 209 -1145 -206 -137 -1145 -1145 158 -1145 -1145 224 -306 -1145 -1145 229 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.7e+000 0.571429 0.178571 0.035714 0.214286 0.607143 0.000000 0.071429 0.321429 0.000000 0.000000 0.857143 0.142857 0.000000 0.500000 0.321429 0.178571 0.000000 0.928571 0.000000 0.071429 0.107143 0.000000 0.000000 0.892857 0.000000 0.000000 0.964286 0.035714 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AT][AT]G[CG]CTGG -------------------------------------------------------------------------------- Time 34.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 21 sites = 4 llr = 86 E-value = 4.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 5::::::a:53::3a:3:::: pos.-specific C :53:::8:::::35::8588a probability G 55:aaa::853a8::a:3::: matrix T ::8:::3:3:5::3:::333: bits 2.3 *** * * * 2.1 *** * * * 1.8 *** * * ** * 1.6 *** * * ** * Relative 1.4 ****** ** *** *** Entropy 1.1 ********** ** *** *** (31.2 bits) 0.9 ********** ** *** *** 0.7 ********** ** ******* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ACTGGGCAGATGGCAGCCCCC consensus GGC T TGA CA AGTT sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr7:127921931-127922530 376 1.99e-11 TATTGCCTCT GCCGGGCAGAGGCCAGCCCCC AGTGAGTATC chr7:63499316-63500135 151 4.54e-11 AACCCATGGA ACTGGGCAGGTGGCAGCCTTC TGTGTGCCCG chr7:106294602-106295451 235 1.69e-10 TTCACAAAAT GGTGGGCATGTGGAAGAGCCC TATATGGTAG chr7:68211440-68211989 298 2.26e-10 TGCCTCAACC AGTGGGTAGAAGGTAGCTCCC AACATAAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127921931-127922530 2e-11 375_[+4]_203 chr7:63499316-63500135 4.5e-11 150_[+4]_648 chr7:106294602-106295451 1.7e-10 234_[+4]_594 chr7:68211440-68211989 2.3e-10 297_[+4]_231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=21 seqs=4 chr7:127921931-127922530 ( 376) GCCGGGCAGAGGCCAGCCCCC 1 chr7:63499316-63500135 ( 151) ACTGGGCAGGTGGCAGCCTTC 1 chr7:106294602-106295451 ( 235) GGTGGGCATGTGGAAGAGCCC 1 chr7:68211440-68211989 ( 298) AGTGGGTAGAAGGTAGCTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14561 bayes= 11.8294 E= 4.1e+003 85 -865 129 -865 -865 119 129 -865 -865 19 -865 133 -865 -865 229 -865 -865 -865 229 -865 -865 -865 229 -865 -865 178 -865 -26 184 -865 -865 -865 -865 -865 187 -26 85 -865 129 -865 -15 -865 29 74 -865 -865 229 -865 -865 19 187 -865 -15 119 -865 -26 184 -865 -865 -865 -865 -865 229 -865 -15 178 -865 -865 -865 119 29 -26 -865 178 -865 -26 -865 178 -865 -26 -865 219 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 4.1e+003 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.500000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.500000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [AG][CG][TC]GGG[CT]A[GT][AG][TAG]G[GC][CAT]AG[CA][CGT][CT][CT]C -------------------------------------------------------------------------------- Time 44.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 20 sites = 3 llr = 68 E-value = 8.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :::::::3a:7:3:33a3:: pos.-specific C :::7a::7:::::33::::a probability G aaa3::a::a:737:7:7a: matrix T :::::a::::333:3::::: bits 2.3 *** * * * ** 2.1 *** * * * ** 1.8 *** *** ** * ** 1.6 *** *** ** * ** Relative 1.4 ******* ** * * ** Entropy 1.1 ********** * * ***** (32.6 bits) 0.9 ************ * ***** 0.7 ************ * ***** 0.5 ************** ***** 0.2 ******************** 0.0 -------------------- Multilevel GGGCCTGCAGAGAGAGAGGC consensus G A TTGCCA A sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- chr7:66468915-66469464 49 6.75e-13 CTGGTGGGTA GGGCCTGCAGAGAGAGAGGC ATCAAGATTA chr7:127921931-127922530 121 8.02e-11 GTTATACATA GGGCCTGCAGATGGCAAAGC TAAGAGTTAC chr7:105413005-105413554 319 1.40e-10 TGCTGTAACT GGGGCTGAAGTGTCTGAGGC AAAGCAATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:66468915-66469464 6.8e-13 48_[+5]_481 chr7:127921931-127922530 8e-11 120_[+5]_459 chr7:105413005-105413554 1.4e-10 318_[+5]_211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=20 seqs=3 chr7:66468915-66469464 ( 49) GGGCCTGCAGAGAGAGAGGC 1 chr7:127921931-127922530 ( 121) GGGCCTGCAGATGGCAAAGC 1 chr7:105413005-105413554 ( 319) GGGGCTGAAGTGTCTGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14589 bayes= 12.6949 E= 8.5e+003 -823 -823 229 -823 -823 -823 229 -823 -823 -823 229 -823 -823 160 70 -823 -823 219 -823 -823 -823 -823 -823 174 -823 -823 229 -823 26 160 -823 -823 184 -823 -823 -823 -823 -823 229 -823 126 -823 -823 16 -823 -823 170 16 26 -823 70 16 -823 61 170 -823 26 61 -823 16 26 -823 170 -823 184 -823 -823 -823 26 -823 170 -823 -823 -823 229 -823 -823 219 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 3 E= 8.5e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- GGG[CG]CTG[CA]AG[AT][GT][AGT][GC][ACT][GA]A[GA]GC -------------------------------------------------------------------------------- Time 54.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 15 sites = 7 llr = 103 E-value = 6.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A 1:1a::::67414:: pos.-specific C 7a9::::a31::::3 probability G ::::931:::69:a7 matrix T 1:::179:11::6:: bits 2.3 * * * 2.1 * * * 1.8 * * * * 1.6 **** * * * Relative 1.4 **** * * ** Entropy 1.1 ******* ** ** (21.1 bits) 0.9 ******** ***** 0.7 ******** ****** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCCAGTTCAAGGTGG consensus G C A A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr7:90158171-90158971 89 4.67e-10 TACTGCTGTG CCCAGTTCAAGGTGG GTGTTTTGGA chr7:66763679-66764228 439 1.82e-08 TCCACAATAT CCCAGTTCCAAGTGC TGAGGATACG chr7:70144673-70145243 511 4.71e-08 TTGGGACACA CCCAGGTCAAGATGG AATGCAGGAT chr7:83063963-83064847 84 5.61e-08 AGTGCATTGG CCCATTTCCAGGAGG GATTTATGAA chr7:66280165-66280714 410 2.53e-07 AGGTGAGTAG ACCAGTTCATAGAGG CCTGTCTGAC chr7:103970880-103971429 241 4.21e-07 GTTCAGGTTT CCAAGTTCACAGTGC AGTACAAAAA chr8:122108965-122109228 244 5.86e-07 GGACTTCAGC TCCAGGGCTAGGAGG AACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:90158171-90158971 4.7e-10 88_[+6]_697 chr7:66763679-66764228 1.8e-08 438_[+6]_96 chr7:70144673-70145243 4.7e-08 510_[+6]_45 chr7:83063963-83064847 5.6e-08 83_[+6]_786 chr7:66280165-66280714 2.5e-07 409_[+6]_125 chr7:103970880-103971429 4.2e-07 240_[+6]_294 chr8:122108965-122109228 5.9e-07 243_[+6]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=15 seqs=7 chr7:90158171-90158971 ( 89) CCCAGTTCAAGGTGG 1 chr7:66763679-66764228 ( 439) CCCAGTTCCAAGTGC 1 chr7:70144673-70145243 ( 511) CCCAGGTCAAGATGG 1 chr7:83063963-83064847 ( 84) CCCATTTCCAGGAGG 1 chr7:66280165-66280714 ( 410) ACCAGTTCATAGAGG 1 chr7:103970880-103971429 ( 241) CCAAGTTCACAGTGC 1 chr8:122108965-122109228 ( 244) TCCAGGGCTAGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 14729 bayes= 11.6443 E= 6.4e+003 -96 171 -945 -106 -945 219 -945 -945 -96 197 -945 -945 185 -945 -945 -945 -945 -945 207 -106 -945 -945 48 126 -945 -945 -52 152 -945 219 -945 -945 104 39 -945 -106 136 -61 -945 -106 62 -945 148 -945 -96 -945 207 -945 62 -945 -945 93 -945 -945 229 -945 -945 39 180 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 6.4e+003 0.142857 0.714286 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.571429 0.285714 0.000000 0.142857 0.714286 0.142857 0.000000 0.142857 0.428571 0.000000 0.571429 0.000000 0.142857 0.000000 0.857143 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- CCCAG[TG]TC[AC]A[GA]G[TA]G[GC] -------------------------------------------------------------------------------- Time 65.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 15 sites = 7 llr = 100 E-value = 9.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :9:a:13a1a:4:4: pos.-specific C 6:4:::::4:967:1 probability G 313:a97:4:1:3:9 matrix T 1:3::::::::::6: bits 2.3 * 2.1 * 1.8 ** * * 1.6 *** * ** * Relative 1.4 * ***** ** * * Entropy 1.1 * ***** **** * (20.7 bits) 0.9 * ***** ****** 0.7 ** ************ 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CACAGGGACACCCTG consensus G G A G AGA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr7:68211440-68211989 275 1.86e-08 GGTTGGGTTT GATAGGGACACCCTG CCTCAACCAG chr7:90158171-90158971 706 2.41e-08 CCAGCCTGGC GATAGGGACACCCAG TTTTTAAACA chr7:81826094-81826693 346 5.37e-08 AAATAAGCTA CGCAGGGAGACACAG TGTACGTCAA chr7:66763679-66764228 355 7.48e-08 TTGTTACATG CAGAGGAAGACCGTG AGAGCTCGTC chr7:127921931-127922530 20 2.69e-07 GCCAGGGCTA CACAGAGAAACCCTG TCTCAAAAAC chr7:66280165-66280714 6 4.08e-07 ACATC CACAGGGAGAGACTC TTGGTCGCTG chr7:83063963-83064847 826 6.92e-07 TTCTTTTTTG TAGAGGAACACAGAG CTAAGAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:68211440-68211989 1.9e-08 274_[+7]_260 chr7:90158171-90158971 2.4e-08 705_[+7]_80 chr7:81826094-81826693 5.4e-08 345_[+7]_239 chr7:66763679-66764228 7.5e-08 354_[+7]_180 chr7:127921931-127922530 2.7e-07 19_[+7]_565 chr7:66280165-66280714 4.1e-07 5_[+7]_529 chr7:83063963-83064847 6.9e-07 825_[+7]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=15 seqs=7 chr7:68211440-68211989 ( 275) GATAGGGACACCCTG 1 chr7:90158171-90158971 ( 706) GATAGGGACACCCAG 1 chr7:81826094-81826693 ( 346) CGCAGGGAGACACAG 1 chr7:66763679-66764228 ( 355) CAGAGGAAGACCGTG 1 chr7:127921931-127922530 ( 20) CACAGAGAAACCCTG 1 chr7:66280165-66280714 ( 6) CACAGGGAGAGACTC 1 chr7:83063963-83064847 ( 826) TAGAGGAACACAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 14729 bayes= 12.2611 E= 9.5e+003 -945 138 48 -106 162 -945 -52 -945 -945 97 48 -7 185 -945 -945 -945 -945 -945 229 -945 -96 -945 207 -945 4 -945 180 -945 185 -945 -945 -945 -96 97 107 -945 185 -945 -945 -945 -945 197 -52 -945 62 138 -945 -945 -945 171 48 -945 62 -945 -945 93 -945 -61 207 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 9.5e+003 0.000000 0.571429 0.285714 0.142857 0.857143 0.000000 0.142857 0.000000 0.000000 0.428571 0.285714 0.285714 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.428571 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.142857 0.857143 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- [CG]A[CGT]AGG[GA]A[CG]AC[CA][CG][TA]G -------------------------------------------------------------------------------- Time 75.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 19 sites = 6 llr = 105 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A :52::::2::22:::3::2 pos.-specific C 7:::a2::a:287:a38:7 probability G 3:85::3:::2:::::2:2 matrix T :5:5:878:a5:3a:3:a: bits 2.3 * * * 2.1 * * * 1.8 * ** ** * 1.6 * * ** ** ** Relative 1.4 * * * ** * ** ** Entropy 1.1 * * ** *** **** ** (25.3 bits) 0.9 * ******** **** *** 0.7 ********** **** *** 0.5 ********** **** *** 0.2 ******************* 0.0 ------------------- Multilevel CAGGCTTTCTTCCTCACTC consensus GT T G T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- chr7:63499316-63500135 313 1.70e-10 CTTGTGGCTT CTGTCTGTCTTCCTCTCTC TACCACACTT chr7:69959582-69960631 904 3.21e-09 CTACAGAGGA CAGTCTTACTACCTCCCTC GTGTATAAGA chr2:27152224-27152414 66 3.83e-09 AGCCTGGGTT CTGTCTGTCTCCCTCACTG TGTGATCTTG chr7:106294602-106295451 295 5.12e-09 ACTTCTGAAA GTGGCTTTCTTCTTCCCTA TGTGTTATTC chr7:103970880-103971429 282 1.50e-08 CTGAACAAGA GAGGCTTTCTGATTCTCTC CCTTGAGGAC chr7:81826094-81826693 102 2.29e-08 TGTTTTCTCT CAAGCCTTCTTCCTCAGTC CCCCAAATCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:63499316-63500135 1.7e-10 312_[+8]_488 chr7:69959582-69960631 3.2e-09 903_[+8]_127 chr2:27152224-27152414 3.8e-09 65_[+8]_106 chr7:106294602-106295451 5.1e-09 294_[+8]_536 chr7:103970880-103971429 1.5e-08 281_[+8]_249 chr7:81826094-81826693 2.3e-08 101_[+8]_479 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=19 seqs=6 chr7:63499316-63500135 ( 313) CTGTCTGTCTTCCTCTCTC 1 chr7:69959582-69960631 ( 904) CAGTCTTACTACCTCCCTC 1 chr2:27152224-27152414 ( 66) CTGTCTGTCTCCCTCACTG 1 chr7:106294602-106295451 ( 295) GTGGCTTTCTTCTTCCCTA 1 chr7:103970880-103971429 ( 282) GAGGCTTTCTGATTCTCTC 1 chr7:81826094-81826693 ( 102) CAAGCCTTCTTCCTCAGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 14617 bayes= 10.9086 E= 1.0e+004 -923 161 70 -923 85 -923 -923 74 -74 -923 203 -923 -923 -923 129 74 -923 219 -923 -923 -923 -39 -923 148 -923 -923 70 116 -74 -923 -923 148 -923 219 -923 -923 -923 -923 -923 174 -74 -39 -29 74 -74 193 -923 -923 -923 161 -923 16 -923 -923 -923 174 -923 219 -923 -923 26 61 -923 16 -923 193 -29 -923 -923 -923 -923 174 -74 161 -29 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 6 E= 1.0e+004 0.000000 0.666667 0.333333 0.000000 0.500000 0.000000 0.000000 0.500000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.333333 0.666667 0.166667 0.000000 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.166667 0.500000 0.166667 0.833333 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.666667 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- [CG][AT]G[GT]CT[TG]TCTTC[CT]TC[ACT]CTC -------------------------------------------------------------------------------- Time 85.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 19 sites = 16 llr = 191 E-value = 9.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A 8126261::818:42171: pos.-specific C 124:2:18a:4::2291:1 probability G :21:6482:14:a21::27 matrix T 163411:::213:35:273 bits 2.3 * * 2.1 * * 1.8 * * 1.6 ** * * Relative 1.4 ** * * Entropy 1.1 *** * * (17.2 bits) 0.9 * * **** ** * * 0.7 * * ***** ** **** 0.5 * ********** **** 0.2 ************* ***** 0.0 ------------------- Multilevel ATCAGAGCCACAGATCATG consensus TT G GT T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- chr7:106294602-106295451 326 6.57e-09 TGTTATTCTG ATCAGAACCACAGACCATG TGATGACTCT chr8:122108965-122109228 85 1.42e-08 CTTGGAGGTG ATCATGGCCAGAGGTCATG AGAGCAGAGC chr7:68211440-68211989 145 1.69e-07 GGTCACAGGC ATAAGGACCAGAGTTCAGG TCGTCAGAAG chr7:70144673-70145243 191 3.29e-07 TAACTCTAGT ATGAGAGGCAAAGCACATG AAGAAAGAAT chr7:66468915-66469464 434 7.43e-07 GGATGAGACA ATGTGGGCCAGAGTACCAG AGAGAAACAT chr7:63499316-63500135 81 9.00e-07 GATTGCCATG AGTAAGGGCACTGACCATG GTAGATGGCT chr7:103970880-103971429 379 9.00e-07 GGTCTCCTAT ATTTCAGCCTGAGATCATC AGTGACATAA chr7:92271035-92271634 219 1.19e-06 CCCAAAATAT CCATGGGCCAAAGATCTTG CCAACTAATT chr7:127921931-127922530 472 1.31e-06 ATATATAGTG AACACAGCCTCAGGCCAGG TCTCCCAACT chr7:83063963-83064847 448 1.31e-06 CATTGACCAC ACATGAGCCAGTGAGCAGT TATGACTATT chr7:66280165-66280714 266 2.20e-06 GAATCCCCTT CCTAAAGCCACTGTACATG TTGGTCACTC chr6:38856153-38856302 117 3.07e-06 CCTTGGTTCA AGTAGACCCACAGCTAATT GTTCTTATCT chr7:67296236-67296942 347 3.90e-06 TCAAGCCCTT ATCAAGCCCTCAGATCTAG CCAAATGATA chr7:83097025-83097574 436 4.54e-06 CTTTGATCTG ATCTCAGCCAGAGTGATTT TTATGAAGCA chr7:69959582-69960631 227 6.12e-06 TGCTTGTGTT AGCTGAGGCGTTGGTCATG CTTCGGTGGC chr2:27152224-27152414 112 6.12e-06 TAATTAACTT TTCTGTGCCACAGCTCCTT TGTCTATTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:106294602-106295451 6.6e-09 325_[+9]_505 chr8:122108965-122109228 1.4e-08 84_[+9]_160 chr7:68211440-68211989 1.7e-07 144_[+9]_386 chr7:70144673-70145243 3.3e-07 190_[+9]_361 chr7:66468915-66469464 7.4e-07 433_[+9]_97 chr7:63499316-63500135 9e-07 80_[+9]_720 chr7:103970880-103971429 9e-07 378_[+9]_152 chr7:92271035-92271634 1.2e-06 218_[+9]_362 chr7:127921931-127922530 1.3e-06 471_[+9]_109 chr7:83063963-83064847 1.3e-06 447_[+9]_418 chr7:66280165-66280714 2.2e-06 265_[+9]_265 chr6:38856153-38856302 3.1e-06 116_[+9]_14 chr7:67296236-67296942 3.9e-06 346_[+9]_341 chr7:83097025-83097574 4.5e-06 435_[+9]_95 chr7:69959582-69960631 6.1e-06 226_[+9]_804 chr2:27152224-27152414 6.1e-06 111_[+9]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=19 seqs=16 chr7:106294602-106295451 ( 326) ATCAGAACCACAGACCATG 1 chr8:122108965-122109228 ( 85) ATCATGGCCAGAGGTCATG 1 chr7:68211440-68211989 ( 145) ATAAGGACCAGAGTTCAGG 1 chr7:70144673-70145243 ( 191) ATGAGAGGCAAAGCACATG 1 chr7:66468915-66469464 ( 434) ATGTGGGCCAGAGTACCAG 1 chr7:63499316-63500135 ( 81) AGTAAGGGCACTGACCATG 1 chr7:103970880-103971429 ( 379) ATTTCAGCCTGAGATCATC 1 chr7:92271035-92271634 ( 219) CCATGGGCCAAAGATCTTG 1 chr7:127921931-127922530 ( 472) AACACAGCCTCAGGCCAGG 1 chr7:83063963-83064847 ( 448) ACATGAGCCAGTGAGCAGT 1 chr7:66280165-66280714 ( 266) CCTAAAGCCACTGTACATG 1 chr6:38856153-38856302 ( 117) AGTAGACCCACAGCTAATT 1 chr7:67296236-67296942 ( 347) ATCAAGCCCTCAGATCTAG 1 chr7:83097025-83097574 ( 436) ATCTCAGCCAGAGTGATTT 1 chr7:69959582-69960631 ( 227) AGCTGAGGCGTTGGTCATG 1 chr2:27152224-27152414 ( 112) TTCTGTGCCACAGCTCCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 14617 bayes= 10.5714 E= 9.5e+002 155 -81 -1064 -225 -215 -22 -13 91 -57 100 -71 -26 102 -1064 -1064 55 -57 -22 146 -225 102 -1064 87 -225 -115 -81 187 -1064 -1064 189 -13 -1064 -1064 219 -1064 -1064 143 -1064 -171 -67 -115 100 87 -225 143 -1064 -1064 -26 -1064 -1064 229 -1064 43 -22 -13 -26 -57 -22 -71 74 -115 200 -1064 -1064 131 -81 -1064 -67 -115 -1064 -13 120 -1064 -180 175 -26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 16 E= 9.5e+002 0.812500 0.125000 0.000000 0.062500 0.062500 0.187500 0.187500 0.562500 0.187500 0.437500 0.125000 0.250000 0.562500 0.000000 0.000000 0.437500 0.187500 0.187500 0.562500 0.062500 0.562500 0.000000 0.375000 0.062500 0.125000 0.125000 0.750000 0.000000 0.000000 0.812500 0.187500 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.062500 0.187500 0.125000 0.437500 0.375000 0.062500 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.375000 0.187500 0.187500 0.250000 0.187500 0.187500 0.125000 0.500000 0.125000 0.875000 0.000000 0.000000 0.687500 0.125000 0.000000 0.187500 0.125000 0.000000 0.187500 0.687500 0.000000 0.062500 0.687500 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- AT[CT][AT]G[AG]GCCA[CG][AT]G[AT]TCAT[GT] -------------------------------------------------------------------------------- Time 95.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 14 sites = 15 llr = 165 E-value = 4.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A 17a:5515::::79 pos.-specific C 11::2113::58:: probability G 81:a:37:1a31:1 matrix T ::::31229:2131 bits 2.3 * * 2.1 * * 1.8 ** * 1.6 ** * Relative 1.4 * ** * * Entropy 1.1 * ** ** * * (15.8 bits) 0.9 **** ** *** 0.7 **** * ****** 0.5 ***** ******** 0.2 ************** 0.0 -------------- Multilevel GAAGAAGATGCCAA consensus TGTC G T sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:127921931-127922530 294 5.49e-08 CTCTGTGTAT GAAGTGGATGGCAA AGACCACAAG chr7:100578576-100579125 408 3.56e-07 TCTGCAAACA GAAGAGGAGGGCAA TAGCATCACT chr2:27152224-27152414 9 6.90e-07 ATTAGGTG GAAGAAACTGCCAA GGGGGAGCCA chr7:90158171-90158971 235 7.91e-07 TTCAGCTTTG GAAGTACATGCCAA AGAGGTTGGG chr7:106294602-106295451 270 1.38e-06 TGGTAGGCAT GAAGCAGAGGCCTA AACTTCTGAA chr7:83063963-83064847 5 1.69e-06 CCTG GCAGATGATGGCAA CGATTCTGTA chr7:63499316-63500135 5 2.72e-06 ATGA GAAGTGGCTGCCTG ACCAAGAGAC chr7:105413005-105413554 523 3.61e-06 GCTCTTGCCT GAAGAAGATGTGTA TCAATAAGCT chr7:71502866-71503415 192 4.33e-06 TTGGGTAGCT GGAGAGGATGCTAA GTTTGAGGTA chr7:69959582-69960631 323 5.16e-06 GCAACAGTGT GAAGTGGCTGTCAT ACTGTACTTT chr7:67296236-67296942 569 5.62e-06 CCTGAACACC CCAGTAGCTGCCAA GTAACAGCCA chr7:83097025-83097574 112 5.62e-06 AAAGATAGCC AAAGAATTTGCCAA GTGAACATAC chr6:88203909-88204133 47 1.41e-05 TAGTCTTTTT GAAGCCTCTGGCTA GTATGACTAT chr7:70144673-70145243 341 1.51e-05 GGAAAATGAA AGAGAAGTTGTCAA GGATGACTTC chr7:92271035-92271634 471 2.12e-05 GGAGAATCGA GAAGCTTTTGCGAA ATGTTATCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127921931-127922530 5.5e-08 293_[+10]_292 chr7:100578576-100579125 3.6e-07 407_[+10]_128 chr2:27152224-27152414 6.9e-07 8_[+10]_168 chr7:90158171-90158971 7.9e-07 234_[+10]_552 chr7:106294602-106295451 1.4e-06 269_[+10]_566 chr7:83063963-83064847 1.7e-06 4_[+10]_866 chr7:63499316-63500135 2.7e-06 4_[+10]_801 chr7:105413005-105413554 3.6e-06 522_[+10]_13 chr7:71502866-71503415 4.3e-06 191_[+10]_344 chr7:69959582-69960631 5.2e-06 322_[+10]_713 chr7:67296236-67296942 5.6e-06 568_[+10]_124 chr7:83097025-83097574 5.6e-06 111_[+10]_424 chr6:88203909-88204133 1.4e-05 46_[+10]_164 chr7:70144673-70145243 1.5e-05 340_[+10]_216 chr7:92271035-92271634 2.1e-05 470_[+10]_115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=14 seqs=15 chr7:127921931-127922530 ( 294) GAAGTGGATGGCAA 1 chr7:100578576-100579125 ( 408) GAAGAGGAGGGCAA 1 chr2:27152224-27152414 ( 9) GAAGAAACTGCCAA 1 chr7:90158171-90158971 ( 235) GAAGTACATGCCAA 1 chr7:106294602-106295451 ( 270) GAAGCAGAGGCCTA 1 chr7:83063963-83064847 ( 5) GCAGATGATGGCAA 1 chr7:63499316-63500135 ( 5) GAAGTGGCTGCCTG 1 chr7:105413005-105413554 ( 523) GAAGAAGATGTGTA 1 chr7:71502866-71503415 ( 192) GGAGAGGATGCTAA 1 chr7:69959582-69960631 ( 323) GAAGTGGCTGTCAT 1 chr7:67296236-67296942 ( 569) CCAGTAGCTGCCAA 1 chr7:83097025-83097574 ( 112) AAAGAATTTGCCAA 1 chr6:88203909-88204133 ( 47) GAAGCCTCTGGCTA 1 chr7:70144673-70145243 ( 341) AGAGAAGTTGTCAA 1 chr7:92271035-92271634 ( 471) GAAGCTTTTGCGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 14757 bayes= 10.6155 E= 4.0e+003 -106 -171 197 -1055 140 -71 -62 -1055 185 -1055 -1055 -1055 -1055 -1055 229 -1055 75 -13 -1055 16 75 -171 70 -116 -206 -171 170 -58 75 61 -1055 -58 -1055 -1055 -62 154 -1055 -1055 229 -1055 -1055 129 38 -58 -1055 187 -62 -216 140 -1055 -1055 -16 164 -1055 -162 -216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 15 E= 4.0e+003 0.133333 0.066667 0.800000 0.000000 0.733333 0.133333 0.133333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.466667 0.200000 0.000000 0.333333 0.466667 0.066667 0.333333 0.133333 0.066667 0.066667 0.666667 0.200000 0.466667 0.333333 0.000000 0.200000 0.000000 0.000000 0.133333 0.866667 0.000000 0.000000 1.000000 0.000000 0.000000 0.533333 0.266667 0.200000 0.000000 0.800000 0.133333 0.066667 0.733333 0.000000 0.000000 0.266667 0.866667 0.000000 0.066667 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- GAAG[ATC][AG][GT][ACT]TG[CGT]C[AT]A -------------------------------------------------------------------------------- Time 105.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:27152224-27152414 9.09e-16 8_[+10(6.90e-07)]_7_[+1(5.56e-05)]_5_[+3(4.58e-05)]_3_[+8(3.83e-09)]_27_[+9(6.12e-06)]_30_[+2(2.60e-07)]_9 chr6:38757479-38757763 6.22e-03 284 chr6:38856153-38856302 1.34e-03 116_[+9(3.07e-06)]_14 chr6:88203909-88204133 1.25e-04 46_[+10(1.41e-05)]_24_[+1(4.38e-05)]_2_[+2(1.31e-05)]_97 chr7:71502866-71503415 4.78e-06 14_[+1(6.65e-08)]_98_[+2(1.63e-05)]_38_[+10(4.33e-06)]_219_[+5(3.59e-05)]_105 chr7:83063963-83064847 8.97e-16 4_[+10(1.69e-06)]_14_[+8(7.36e-05)]_32_[+6(5.61e-08)]_165_[+1(1.41e-05)]_25_[+2(3.05e-09)]_24_[+3(2.83e-05)]_86_[+9(1.31e-06)]_189_[+8(4.58e-06)]_151_[+7(6.92e-07)]_44 chr7:92271035-92271634 1.96e-06 16_[+3(4.58e-05)]_56_[+1(7.23e-07)]_118_[+9(1.19e-06)]_158_[+2(3.70e-06)]_54_[+10(2.12e-05)]_115 chr7:71036918-71037467 4.20e-02 319_[+2(3.11e-06)]_71_[+3(1.82e-05)]_130 chr7:83097025-83097574 1.78e-05 111_[+10(5.62e-06)]_251_[+2(9.01e-06)]_38_[+9(4.54e-06)]_95 chr7:103970880-103971429 7.19e-10 210_[+2(1.22e-05)]_9_[+6(4.21e-07)]_26_[+8(1.50e-08)]_78_[+9(9.00e-07)]_23_[+9(8.68e-05)]_110 chr7:108272128-108272677 1.30e-04 100_[+2(2.01e-05)]_227_[+1(1.06e-08)]_181 chr7:70144673-70145243 8.59e-12 99_[+2(2.61e-06)]_70_[+9(3.29e-07)]_70_[+1(7.23e-07)]_41_[+10(1.51e-05)]_58_[+7(5.84e-05)]_83_[+6(4.71e-08)]_45 chr7:63499316-63500135 1.37e-20 4_[+10(2.72e-06)]_62_[+9(9.00e-07)]_4_[+3(5.53e-05)]_39_[+4(4.54e-11)]_17_[+2(4.76e-06)]_40_[+2(9.34e-05)]_1_[+1(4.00e-09)]_21_[+8(1.70e-10)]_488 chr7:105413005-105413554 1.75e-10 75_[+2(6.18e-07)]_153_[+3(1.82e-05)]_31_[+1(7.04e-06)]_10_[+5(1.40e-10)]_184_[+10(3.61e-06)]_13 chr7:127921931-127922530 1.72e-22 19_[+7(2.69e-07)]_86_[+5(8.02e-11)]_88_[+1(4.75e-05)]_45_[+10(5.49e-08)]_68_[+4(1.99e-11)]_75_[+9(1.31e-06)]_44_[+2(1.24e-06)]_44 chr7:81826094-81826693 5.52e-11 26_[+1(3.28e-06)]_55_[+8(2.29e-08)]_81_[+2(6.59e-06)]_75_[+3(3.57e-05)]_40_[+7(5.37e-08)]_239 chr7:66280165-66280714 4.14e-09 5_[+7(4.08e-07)]_96_[+1(2.04e-05)]_3_[+3(7.50e-05)]_118_[+9(2.20e-06)]_125_[+6(2.53e-07)]_125 chr7:66763679-66764228 4.08e-14 163_[+2(2.60e-07)]_135_[+1(4.08e-07)]_15_[+7(7.48e-08)]_69_[+6(1.82e-08)]_96 chr7:67296236-67296942 7.22e-05 162_[+8(8.82e-06)]_165_[+9(3.90e-06)]_14_[+1(6.34e-06)]_169_[+10(5.62e-06)]_124 chr7:106294602-106295451 5.69e-19 234_[+4(1.69e-10)]_14_[+10(1.38e-06)]_11_[+8(5.12e-09)]_12_[+9(6.57e-09)]_81_[+2(2.91e-07)]_86_[+1(5.14e-05)]_16_[+5(8.55e-06)]_261 chr7:100578576-100579125 4.79e-07 284_[+3(2.83e-05)]_115_[+10(3.56e-07)]_57_[+2(7.85e-08)]_28_[+1(5.70e-06)]_2 chr7:66468915-66469464 1.13e-16 34_[+3(5.53e-05)]_6_[+5(6.75e-13)]_139_[+1(1.59e-07)]_124_[+2(2.91e-07)]_61_[+9(7.43e-07)]_97 chr7:90158171-90158971 2.86e-15 28_[+6(2.96e-05)]_45_[+6(4.67e-10)]_131_[+10(7.91e-07)]_55_[+2(1.13e-06)]_9_[+1(5.52e-08)]_343_[+3(3.57e-05)]_1_[+7(2.41e-08)]_80 chr7:68211440-68211989 1.23e-15 144_[+9(1.69e-07)]_17_[+3(1.82e-05)]_18_[+2(7.85e-08)]_47_[+7(1.86e-08)]_8_[+4(2.26e-10)]_15_[+1(5.56e-05)]_122_[+2(6.68e-05)]_53 chr7:69959582-69960631 1.84e-09 133_[+3(5.53e-05)]_85_[+9(6.12e-06)]_77_[+10(5.16e-06)]_194_[+1(1.41e-05)]_74_[+2(6.85e-07)]_145_[+2(8.37e-05)]_92_[+8(3.21e-09)]_127 chr8:122108965-122109228 2.76e-10 40_[+2(3.70e-06)]_23_[+9(1.42e-08)]_64_[+1(5.12e-06)]_56_[+6(5.86e-07)]_5 chrX:150565848-150566190 2.35e-01 86_[+1(6.99e-05)]_236 chrX:150846672-150846828 3.86e-01 156 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************