******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) 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= motifs/216/216.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11175 1.0000 500 11590 1.0000 500 1649 1.0000 500 18303 1.0000 500 20776 1.0000 500 23675 1.0000 500 24145 1.0000 500 25513 1.0000 500 262201 1.0000 500 263817 1.0000 500 263928 1.0000 500 268078 1.0000 500 269942 1.0000 500 2725 1.0000 500 2808 1.0000 500 35025 1.0000 500 35055 1.0000 500 37427 1.0000 500 39278 1.0000 500 39799 1.0000 500 4042 1.0000 500 4278 1.0000 500 5182 1.0000 500 5701 1.0000 500 6552 1.0000 500 7249 1.0000 500 7588 1.0000 500 780 1.0000 500 8041 1.0000 500 8486 1.0000 500 9351 1.0000 500 9851 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/216/216.seqs.fa -oc motifs/216 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 32 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= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.235 G 0.227 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.235 G 0.227 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 32 llr = 315 E-value = 7.6e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 262671576:3237365189: pos.-specific C 3172235134456352392:8 probability G 411::5::11211::22:::1 matrix T 12:221:21512::2:::::1 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 *** Entropy 1.1 * **** (14.2 bits) 0.9 * * ** **** 0.6 *** ** ** **** 0.4 ********* ********* 0.2 ********************* 0.0 --------------------- Multilevel GACAAGAAATCCCACAACAAC consensus C AT CC CCAAACAGC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25513 410 2.38e-10 CCCTCAACAA CACAACAACTCCCACACCAAC ATCACAAGCC 7249 431 8.16e-09 GGACGGAAGG GACATGAAACACAACGACAAC TTTGAACACT 268078 244 9.74e-09 TTTGTCGTCG CAGAAGCAATCCACCAACAAC GTCGTCGTCG 24145 461 1.07e-07 TTTCCCCAGC CACAAGCCACATCACAACCAC AACCAAACAC 262201 449 2.15e-07 CGCTACATTT GACATCCTACACCCCAGCAAC TGCACTCCAA 263817 302 7.77e-07 ACCCGGTAAG AAGAAGAAAGCCCAAAACAAG AAGGCCACCG 780 471 8.76e-07 TAACTCTAAA CACAAGAGATCTCATCACAAC ATCAAAGCC 11590 458 1.25e-06 GTGTTGCACC GTCAAGCAATTGACCACCAAC CAGTGGAACA 20776 390 1.57e-06 ATTACTTACC GACCAGCAGACCCACGACAAC GACGGTGCGT 8486 466 2.73e-06 CTCCCTCACA AAAAAAAAACCAAACGCCAAC ACATCGAGCA 9351 226 3.03e-06 CTGCTACTTG CAATACAATTCCAAAAGCAAC GGATGAATTG 39799 306 4.16e-06 AACCTTCACA TTCACCCTACACCAAACCAAC TTAATATTAA 4042 369 5.10e-06 ACAATACGAG GACACGATCTGCCAACCCCAC AAGCCCTACT 37427 480 6.87e-06 CAGTAACCCA ACCAACTAACACCACCGCAAC 35055 116 8.35e-06 TGAACTTAAA GTCAATCAATCTCATGCCCAC TGCTGGTTGC 18303 101 8.35e-06 GTGGAATCTC AGCCAGCACCAGAACAACCAC CAGCTGCTCA 1649 465 8.35e-06 GAAATGTATT GTATCGCTACAACCCAACAAC ACCGCCTGAA 9851 478 1.22e-05 CGCGCTAACA CTCAAGAAATCACAACCAAAG CA 269942 431 1.22e-05 CATTGCTTTC GAATTCCAACACCAAGACAAT ACAATACACT 23675 473 1.33e-05 AGCACATAGA TACATTAACTCACAAAACCAC TACCACT 8041 91 1.91e-05 TGCACCCTGT CCCAAAAACTGTGCCAACAAC ACAGCGTTCT 4278 439 2.27e-05 GAGGAAGTAT CAAAAGCCTGCCAATGGCAAC ATCACGTACT 35025 42 2.27e-05 TGCTGGCCCT CGCCACCACCTCCACACCATC ACACGCCGAA 7588 8 3.46e-05 TCGCATA GAGTAGAAATGTCAAAACCAT GGATTAACAT 11175 468 3.46e-05 ACTGCACTAC ACCCCACAATACCCTCACAAC ATCGGCATAC 5701 391 3.76e-05 CCGTAGGTGA AAGAAGAAAGGAAACAACAAA GAACAGACAG 2808 446 6.04e-05 AGCATGATGT CACTACCCGTCCAATAGAAAC CTTGACGGGA 5182 476 1.17e-04 GTTCCGGCTC GGCAACAACCAGCCGCAAAAC CGAT 6552 10 1.35e-04 CCCAGCTAT TGATTCAACCCCCATGCCAAG TAAGAAACAT 39278 188 1.55e-04 GTCGGAGTGT GTATTGCATTGACACAAGAAC GGTGGTGATG 263928 313 2.45e-04 GCCTTTCCGT GACAAGATATTAGCTTACAAG CGAAGAGTGA 2725 364 3.14e-04 CTCTCCTCCA CACCCGACCGACGCCAGCACC AGACATTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25513 2.4e-10 409_[+1]_70 7249 8.2e-09 430_[+1]_49 268078 9.7e-09 243_[+1]_236 24145 1.1e-07 460_[+1]_19 262201 2.2e-07 448_[+1]_31 263817 7.8e-07 301_[+1]_178 780 8.8e-07 470_[+1]_9 11590 1.2e-06 457_[+1]_22 20776 1.6e-06 389_[+1]_90 8486 2.7e-06 465_[+1]_14 9351 3e-06 225_[+1]_254 39799 4.2e-06 305_[+1]_174 4042 5.1e-06 368_[+1]_111 37427 6.9e-06 479_[+1] 35055 8.3e-06 115_[+1]_364 18303 8.3e-06 100_[+1]_379 1649 8.3e-06 464_[+1]_15 9851 1.2e-05 477_[+1]_2 269942 1.2e-05 430_[+1]_49 23675 1.3e-05 472_[+1]_7 8041 1.9e-05 90_[+1]_389 4278 2.3e-05 438_[+1]_41 35025 2.3e-05 41_[+1]_438 7588 3.5e-05 7_[+1]_472 11175 3.5e-05 467_[+1]_12 5701 3.8e-05 390_[+1]_89 2808 6e-05 445_[+1]_34 5182 0.00012 475_[+1]_4 6552 0.00013 9_[+1]_470 39278 0.00015 187_[+1]_292 263928 0.00024 312_[+1]_167 2725 0.00031 363_[+1]_116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=32 25513 ( 410) CACAACAACTCCCACACCAAC 1 7249 ( 431) GACATGAAACACAACGACAAC 1 268078 ( 244) CAGAAGCAATCCACCAACAAC 1 24145 ( 461) CACAAGCCACATCACAACCAC 1 262201 ( 449) GACATCCTACACCCCAGCAAC 1 263817 ( 302) AAGAAGAAAGCCCAAAACAAG 1 780 ( 471) CACAAGAGATCTCATCACAAC 1 11590 ( 458) GTCAAGCAATTGACCACCAAC 1 20776 ( 390) GACCAGCAGACCCACGACAAC 1 8486 ( 466) AAAAAAAAACCAAACGCCAAC 1 9351 ( 226) CAATACAATTCCAAAAGCAAC 1 39799 ( 306) TTCACCCTACACCAAACCAAC 1 4042 ( 369) GACACGATCTGCCAACCCCAC 1 37427 ( 480) ACCAACTAACACCACCGCAAC 1 35055 ( 116) GTCAATCAATCTCATGCCCAC 1 18303 ( 101) AGCCAGCACCAGAACAACCAC 1 1649 ( 465) GTATCGCTACAACCCAACAAC 1 9851 ( 478) CTCAAGAAATCACAACCAAAG 1 269942 ( 431) GAATTCCAACACCAAGACAAT 1 23675 ( 473) TACATTAACTCACAAAACCAC 1 8041 ( 91) CCCAAAAACTGTGCCAACAAC 1 4278 ( 439) CAAAAGCCTGCCAATGGCAAC 1 35025 ( 42) CGCCACCACCTCCACACCATC 1 7588 ( 8) GAGTAGAAATGTCAAAACCAT 1 11175 ( 468) ACCCCACAATACCCTCACAAC 1 5701 ( 391) AAGAAGAAAGGAAACAACAAA 1 2808 ( 446) CACTACCCGTCCAATAGAAAC 1 5182 ( 476) GGCAACAACCAGCCGCAAAAC 1 6552 ( 10) TGATTCAACCCCCATGCCAAG 1 39278 ( 188) GTATTGCATTGACACAAGAAC 1 263928 ( 313) GACAAGATATTAGCTTACAAG 1 2725 ( 364) CACCCGACCGACGCCAGCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 8.90388 E= 7.6e-006 -54 55 73 -150 113 -133 -86 -50 -31 148 -86 -1164 120 -59 -1164 -28 127 -59 -1164 -50 -154 41 123 -209 88 99 -1164 -308 134 -91 -286 -77 105 26 -186 -150 -312 67 -86 82 34 79 -54 -150 -31 117 -127 -77 5 141 -127 -1164 140 26 -1164 -1164 -12 109 -286 -28 105 -33 -5 -308 97 26 -27 -1164 -154 189 -286 -1164 158 -33 -1164 -1164 178 -291 -1164 -308 -312 173 -86 -209 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 7.6e-006 0.187500 0.343750 0.375000 0.093750 0.593750 0.093750 0.125000 0.187500 0.218750 0.656250 0.125000 0.000000 0.625000 0.156250 0.000000 0.218750 0.656250 0.156250 0.000000 0.187500 0.093750 0.312500 0.531250 0.062500 0.500000 0.468750 0.000000 0.031250 0.687500 0.125000 0.031250 0.156250 0.562500 0.281250 0.062500 0.093750 0.031250 0.375000 0.125000 0.468750 0.343750 0.406250 0.156250 0.093750 0.218750 0.531250 0.093750 0.156250 0.281250 0.625000 0.093750 0.000000 0.718750 0.281250 0.000000 0.000000 0.250000 0.500000 0.031250 0.218750 0.562500 0.187500 0.218750 0.031250 0.531250 0.281250 0.187500 0.000000 0.093750 0.875000 0.031250 0.000000 0.812500 0.187500 0.000000 0.000000 0.937500 0.031250 0.000000 0.031250 0.031250 0.781250 0.125000 0.062500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC]A[CA][AT]A[GC][AC]A[AC][TC][CA][CA][CA][AC][CAT][AG][AC]CAAC -------------------------------------------------------------------------------- Time 9.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 32 llr = 278 E-value = 1.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :51231:3417:2522 pos.-specific C :13:2:131:31:211 probability G 82183494:8::8138 matrix T 225:35::4::9:23: bits 2.1 1.9 1.7 1.5 * * * Relative 1.3 * * * * ** Entropy 1.1 * * * * ** * (12.5 bits) 0.9 * * * **** * 0.6 * * * **** * 0.4 * * ******** * 0.2 **** *********** 0.0 ---------------- Multilevel GATGTTGGAGATGAGG consensus TGC AG AT C CT sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11175 199 2.05e-08 CTCAACCAAT GATGATGATGATGATG CTGCAATGCG 6552 157 2.91e-07 CCGATTTCCG GACGTTGCAGCTGATG TGCTAGAAAT 35025 232 2.91e-07 TTGGACGGAC GATGGTGGAGATGGTG CTGAGGTAGA 269942 191 2.91e-07 CCAATTTGCT GACGTGGATGATGACG TGAAATGAGC 8041 342 1.38e-06 GCATGGTTAG GAGGGTGGCGATGAGG ACGGTTAGGA 39278 209 2.37e-06 ACACAAGAAC GGTGGTGATGCTGAGA TACCTTGAAA 263817 377 5.61e-06 ATCGTCATCG GAGGAGGAAGATAAGG GTCTCAGTAG 1649 176 5.61e-06 AGGTGGAGGA GAAGCGGCTGATGTGG GTGTGGAGGT 263928 111 6.30e-06 AGAGGCCTTG TGTAGTGGTGATGAGG TGTAGGAAGG 35055 376 9.85e-06 CTGGCGTATT GTTGTGGCGGATGCGG CGGTGTGCTA 5182 420 1.67e-05 CTTCGACAAG GTTGTTGGAGACAAGG GTACAGTAAT 9851 178 1.84e-05 GGACTAACGG GATGGTCGTGATAATG AAAAACGTTC 2725 73 2.04e-05 CGGACAGTAT GATAATGATAATGATG TGCTTAGGAT 24145 3 2.04e-05 CT TCCGTTGCTGCTGAAG CAAGGTGTTT 7249 371 2.48e-05 GGGGGGGGGG GTTGAAGGTGATACTG AAATTCAAAG 39799 455 2.48e-05 GCAGCGGTGT GATGCAGCAGCTGTCG CTCGTGTTGG 2808 17 3.00e-05 GGTCCTGCTT GAAGAGGAAGCCGATG GAGACGGCAT 11590 36 3.96e-05 GAGGAACATC GGTGATGGTACTGATA CATAGCAAAA 268078 268 4.74e-05 CAACAACGTC GTCGTCGACGATGATG TACCAGTTGT 9351 140 5.64e-05 GAAACAGTTG GCTGTGGCAGTTGCAG CCATCTTCAC 780 205 6.15e-05 CTCACCACAC GACGTGGCCGACGCCG ACTGCCGACG 37427 70 9.32e-05 ATTGTTGATT GTTGGAGAAGATGGAA ATTATGAGCT 25513 32 9.32e-05 CAGCGCAGTT GGAACGGGTGCTGTGG ATAGGCGGCG 18303 148 9.32e-05 AACATCCGCG GCTGAGGAAGCTACGA CATAAGCGTT 262201 7 1.01e-04 AGTCTT GACGTGGGACATGATC TAGAGGGGAT 8486 146 1.09e-04 TAACGCTGGT GACAGGGGAGCTGCTC AAGTGCCGTT 4042 115 1.09e-04 TCGGTTGCCC TTGGCTGGAGATGGCG CACGGTGTCT 20776 191 1.49e-04 TAAATTATCG TGTGCTGCAACTGTGG AAAACTCCTA 7588 263 2.66e-04 TATCCTCAAA TATATAGATGATGCAA GTATCAGTTC 5701 19 2.85e-04 CACTGCATCT TGCGATTGTGATGAGA TAACCCGAGA 4278 420 3.26e-04 CATCGATTAA TCGGTGGCTGAGGAAG TATCAAAAGC 23675 297 6.15e-04 TTTTTGAGAA GGTGGTCAATATGTAG ACATTAAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11175 2.1e-08 198_[+2]_286 6552 2.9e-07 156_[+2]_328 35025 2.9e-07 231_[+2]_253 269942 2.9e-07 190_[+2]_294 8041 1.4e-06 341_[+2]_143 39278 2.4e-06 208_[+2]_276 263817 5.6e-06 376_[+2]_108 1649 5.6e-06 175_[+2]_309 263928 6.3e-06 110_[+2]_374 35055 9.8e-06 375_[+2]_109 5182 1.7e-05 419_[+2]_65 9851 1.8e-05 177_[+2]_307 2725 2e-05 72_[+2]_412 24145 2e-05 2_[+2]_482 7249 2.5e-05 370_[+2]_114 39799 2.5e-05 454_[+2]_30 2808 3e-05 16_[+2]_468 11590 4e-05 35_[+2]_449 268078 4.7e-05 267_[+2]_217 9351 5.6e-05 139_[+2]_345 780 6.1e-05 204_[+2]_280 37427 9.3e-05 69_[+2]_415 25513 9.3e-05 31_[+2]_453 18303 9.3e-05 147_[+2]_337 262201 0.0001 6_[+2]_478 8486 0.00011 145_[+2]_339 4042 0.00011 114_[+2]_370 20776 0.00015 190_[+2]_294 7588 0.00027 262_[+2]_222 5701 0.00028 18_[+2]_466 4278 0.00033 419_[+2]_65 23675 0.00061 296_[+2]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=32 11175 ( 199) GATGATGATGATGATG 1 6552 ( 157) GACGTTGCAGCTGATG 1 35025 ( 232) GATGGTGGAGATGGTG 1 269942 ( 191) GACGTGGATGATGACG 1 8041 ( 342) GAGGGTGGCGATGAGG 1 39278 ( 209) GGTGGTGATGCTGAGA 1 263817 ( 377) GAGGAGGAAGATAAGG 1 1649 ( 176) GAAGCGGCTGATGTGG 1 263928 ( 111) TGTAGTGGTGATGAGG 1 35055 ( 376) GTTGTGGCGGATGCGG 1 5182 ( 420) GTTGTTGGAGACAAGG 1 9851 ( 178) GATGGTCGTGATAATG 1 2725 ( 73) GATAATGATAATGATG 1 24145 ( 3) TCCGTTGCTGCTGAAG 1 7249 ( 371) GTTGAAGGTGATACTG 1 39799 ( 455) GATGCAGCAGCTGTCG 1 2808 ( 17) GAAGAGGAAGCCGATG 1 11590 ( 36) GGTGATGGTACTGATA 1 268078 ( 268) GTCGTCGACGATGATG 1 9351 ( 140) GCTGTGGCAGTTGCAG 1 780 ( 205) GACGTGGCCGACGCCG 1 37427 ( 70) GTTGGAGAAGATGGAA 1 25513 ( 32) GGAACGGGTGCTGTGG 1 18303 ( 148) GCTGAGGAAGCTACGA 1 262201 ( 7) GACGTGGGACATGATC 1 8486 ( 146) GACAGGGGAGCTGCTC 1 4042 ( 115) TTGGCTGGAGATGGCG 1 20776 ( 191) TGTGCTGCAACTGTGG 1 7588 ( 263) TATATAGATGATGCAA 1 5701 ( 19) TGCGATTGTGATGAGA 1 4278 ( 420) TCGGTGGCTGAGGAAG 1 23675 ( 297) GGTGGTCAATATGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 8.91886 E= 1.9e-002 -1164 -1164 178 -28 78 -91 -5 -50 -154 9 -86 100 -80 -1164 189 -1164 -12 -59 14 37 -112 -291 73 82 -1164 -191 200 -308 34 26 73 -1164 69 -133 -286 72 -154 -291 189 -308 127 41 -1164 -308 -1164 -133 -286 172 -80 -1164 189 -1164 97 -11 -127 -77 -54 -91 60 37 -54 -191 173 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 32 E= 1.9e-002 0.000000 0.000000 0.781250 0.218750 0.468750 0.125000 0.218750 0.187500 0.093750 0.250000 0.125000 0.531250 0.156250 0.000000 0.843750 0.000000 0.250000 0.156250 0.250000 0.343750 0.125000 0.031250 0.375000 0.468750 0.000000 0.062500 0.906250 0.031250 0.343750 0.281250 0.375000 0.000000 0.437500 0.093750 0.031250 0.437500 0.093750 0.031250 0.843750 0.031250 0.656250 0.312500 0.000000 0.031250 0.000000 0.093750 0.031250 0.875000 0.156250 0.000000 0.843750 0.000000 0.531250 0.218750 0.093750 0.156250 0.187500 0.125000 0.343750 0.343750 0.187500 0.062500 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][AG][TC]G[TAG][TG]G[GAC][AT]G[AC]TG[AC][GT]G -------------------------------------------------------------------------------- Time 19.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 18 llr = 190 E-value = 3.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:::::::::3: pos.-specific C 869a29471872 probability G :2:::11::1:: matrix T 131:8:639118 bits 2.1 * 1.9 * 1.7 * * 1.5 ** * * Relative 1.3 * **** *** * Entropy 1.1 * **** *** * (15.2 bits) 0.9 * ********** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCCCTCTCTCCT consensus T C CT AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 262201 306 2.94e-07 TACTTCGTAC CTCCTCCCTCCT ACTTTCGAAT 780 435 6.27e-07 ATCCCCTGCT CCCCCCCCTCCT GCATTGAGGC 7588 287 1.33e-06 AAGTATCAGT TCCCTCTCTCCT TATTGCTTTT 35025 21 1.69e-06 CGATGAAGGT CCTCTCTCTCCT GCTGGCCCTC 25513 446 2.04e-06 AAGCCACACC CGCCTCCCTCAT ATCACCAGTA 2808 191 2.73e-06 GCTATCGCCA CCCCTCCCTCTT CCACGGCCCC 1649 431 3.97e-06 TGATGACTCA CCCCTCTCCCCC GGCATTCGGC 8486 453 4.54e-06 TGGTCGACAT CTCCTCCCTCAC AAAAAAAAAA 2725 316 4.54e-06 ATCCTCTTCC CCCCTCGTTCCT CTTACCGTAC 268078 133 5.22e-06 ACAGCATCAC TGCCTCTCTCCT TCGCCATTTA 269942 270 5.85e-06 AGAAATAATA CCCCCCCCCCCT TAGTTAATCA 18303 432 7.63e-06 CTTGCATTTT CCCCTGTTTCCT CCGCCGTCCA 5182 317 8.37e-06 GAGGACTTGT CCCCTCTTTTCT TGTACCCCCT 4278 37 8.37e-06 ACAACGAAAG CTCCTCTCTGCC CTCTGATTGG 20776 438 9.36e-06 TTGGGCAAGC CTCCCCTTTCAT TGTAGCGACC 11175 357 1.39e-05 CTTGAATCTT CCTCTCTCTCAC AGCCCACGTT 4042 402 2.30e-05 GCCCTACTAC ATCCCCCCTCCT TGCATGCAGG 263928 420 2.51e-05 TTAAATTGAC CGCCTCTTTGAT TTCACATCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262201 2.9e-07 305_[+3]_183 780 6.3e-07 434_[+3]_54 7588 1.3e-06 286_[+3]_202 35025 1.7e-06 20_[+3]_468 25513 2e-06 445_[+3]_43 2808 2.7e-06 190_[+3]_298 1649 4e-06 430_[+3]_58 8486 4.5e-06 452_[+3]_36 2725 4.5e-06 315_[+3]_173 268078 5.2e-06 132_[+3]_356 269942 5.8e-06 269_[+3]_219 18303 7.6e-06 431_[+3]_57 5182 8.4e-06 316_[+3]_172 4278 8.4e-06 36_[+3]_452 20776 9.4e-06 437_[+3]_51 11175 1.4e-05 356_[+3]_132 4042 2.3e-05 401_[+3]_87 263928 2.5e-05 419_[+3]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=18 262201 ( 306) CTCCTCCCTCCT 1 780 ( 435) CCCCCCCCTCCT 1 7588 ( 287) TCCCTCTCTCCT 1 35025 ( 21) CCTCTCTCTCCT 1 25513 ( 446) CGCCTCCCTCAT 1 2808 ( 191) CCCCTCCCTCTT 1 1649 ( 431) CCCCTCTCCCCC 1 8486 ( 453) CTCCTCCCTCAC 1 2725 ( 316) CCCCTCGTTCCT 1 268078 ( 133) TGCCTCTCTCCT 1 269942 ( 270) CCCCCCCCCCCT 1 18303 ( 432) CCCCTGTTTCCT 1 5182 ( 317) CCCCTCTTTTCT 1 4278 ( 37) CTCCTCTCTGCC 1 20776 ( 438) CTCCCCTTTCAT 1 11175 ( 357) CCTCTCTCTCAC 1 4042 ( 402) ATCCCCCCTCCT 1 263928 ( 420) CGCCTCTTTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15648 bayes= 10.6108 E= 3.6e-003 -229 182 -1081 -126 -1081 124 -44 6 -1081 192 -1081 -126 -1081 209 -1081 -1081 -1081 -8 -1081 155 -1081 200 -203 -1081 -1081 72 -203 106 -1081 162 -1081 6 -1081 -108 -1081 174 -1081 182 -103 -226 3 150 -1081 -226 -1081 -8 -1081 155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 3.6e-003 0.055556 0.833333 0.000000 0.111111 0.000000 0.555556 0.166667 0.277778 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.777778 0.000000 0.944444 0.055556 0.000000 0.000000 0.388889 0.055556 0.555556 0.000000 0.722222 0.000000 0.277778 0.000000 0.111111 0.000000 0.888889 0.000000 0.833333 0.111111 0.055556 0.277778 0.666667 0.000000 0.055556 0.000000 0.222222 0.000000 0.777778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[CT]CC[TC]C[TC][CT]TC[CA][TC] -------------------------------------------------------------------------------- Time 27.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11175 2.60e-07 198_[+2(2.05e-08)]_142_\ [+3(1.39e-05)]_99_[+1(3.46e-05)]_12 11590 2.06e-04 35_[+2(3.96e-05)]_406_\ [+1(1.25e-06)]_22 1649 3.68e-06 175_[+2(5.61e-06)]_239_\ [+3(3.97e-06)]_22_[+1(8.35e-06)]_15 18303 7.67e-05 100_[+1(8.35e-06)]_26_\ [+2(9.32e-05)]_268_[+3(7.63e-06)]_57 20776 3.17e-05 389_[+1(1.57e-06)]_27_\ [+3(9.36e-06)]_51 23675 2.90e-02 472_[+1(1.33e-05)]_7 24145 5.28e-05 2_[+2(2.04e-05)]_442_[+1(1.07e-07)]_\ 19 25513 1.84e-09 31_[+2(9.32e-05)]_362_\ [+1(2.38e-10)]_15_[+3(2.04e-06)]_43 262201 1.73e-07 305_[+3(2.94e-07)]_131_\ [+1(2.15e-07)]_31 263817 1.47e-05 154_[+2(5.64e-05)]_131_\ [+1(7.77e-07)]_54_[+2(5.61e-06)]_108 263928 3.73e-04 44_[+2(2.73e-05)]_50_[+2(6.30e-06)]_\ 293_[+3(2.51e-05)]_69 268078 7.18e-08 132_[+3(5.22e-06)]_99_\ [+1(9.74e-09)]_3_[+2(4.74e-05)]_217 269942 5.12e-07 190_[+2(2.91e-07)]_63_\ [+3(5.85e-06)]_15_[+2(2.48e-05)]_118_[+1(1.22e-05)]_49 2725 2.88e-04 72_[+2(2.04e-05)]_227_\ [+3(4.54e-06)]_173 2808 6.57e-05 16_[+2(3.00e-05)]_158_\ [+3(2.73e-06)]_243_[+1(6.04e-05)]_34 35025 2.92e-07 20_[+3(1.69e-06)]_9_[+1(2.27e-05)]_\ 169_[+2(2.91e-07)]_23_[+2(2.08e-06)]_214 35055 1.31e-03 115_[+1(8.35e-06)]_239_\ [+2(9.85e-06)]_109 37427 3.49e-03 69_[+2(9.32e-05)]_394_\ [+1(6.87e-06)] 39278 3.87e-03 208_[+2(2.37e-06)]_276 39799 7.94e-04 305_[+1(4.16e-06)]_128_\ [+2(2.48e-05)]_30 4042 1.49e-04 368_[+1(5.10e-06)]_12_\ [+3(2.30e-05)]_87 4278 5.47e-04 36_[+3(8.37e-06)]_390_\ [+1(2.27e-05)]_41 5182 1.83e-04 316_[+3(8.37e-06)]_91_\ [+2(1.67e-05)]_65 5701 3.49e-02 390_[+1(3.76e-05)]_89 6552 5.85e-04 156_[+2(2.91e-07)]_83_\ [+2(3.96e-05)]_229 7249 5.46e-06 370_[+2(2.48e-05)]_44_\ [+1(8.16e-09)]_49 7588 1.38e-04 7_[+1(3.46e-05)]_258_[+3(1.33e-06)]_\ 202 780 7.90e-07 204_[+2(6.15e-05)]_214_\ [+3(6.27e-07)]_24_[+1(8.76e-07)]_9 8041 9.29e-05 90_[+1(1.91e-05)]_230_\ [+2(1.38e-06)]_143 8486 2.10e-05 452_[+3(4.54e-06)]_1_[+1(2.73e-06)]_\ 14 9351 2.14e-03 139_[+2(5.64e-05)]_70_\ [+1(3.03e-06)]_254 9851 3.09e-03 177_[+2(1.84e-05)]_284_\ [+1(1.22e-05)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************