******************************************************************************** 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/232/232.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1255 1.0000 500 168 1.0000 500 17262 1.0000 500 17271 1.0000 500 18557 1.0000 500 19034 1.0000 500 21190 1.0000 500 22031 1.0000 500 22685 1.0000 500 23898 1.0000 500 24763 1.0000 500 25321 1.0000 500 25486 1.0000 500 25795 1.0000 500 261495 1.0000 500 262538 1.0000 500 262785 1.0000 500 262858 1.0000 500 262891 1.0000 500 263786 1.0000 500 268010 1.0000 500 269717 1.0000 500 3009 1.0000 500 31690 1.0000 500 34412 1.0000 500 34710 1.0000 500 35510 1.0000 500 3580 1.0000 500 36411 1.0000 500 38289 1.0000 500 38827 1.0000 500 40402 1.0000 500 4793 1.0000 500 6150 1.0000 500 6379 1.0000 500 9061 1.0000 500 bd763 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/232/232.seqs.fa -oc motifs/232 -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= 37 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= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.249 G 0.238 T 0.250 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.249 G 0.238 T 0.250 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 27 llr = 322 E-value = 9.2e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22:133:222211411:31:1 pos.-specific C ::::::::311:12:11::1: probability G 553931a423:39::791386 matrix T 337:46:43376:39:17713 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.2 * * * * * Entropy 1.0 ** * * * * * (17.2 bits) 0.8 ** * * * ****** 0.6 ** ** *** ******* 0.4 ******** *********** 0.2 ******** ************ 0.0 --------------------- Multilevel GGTGTTGTTGTTGATGGTTGG consensus TTG AA GCTAG T AG T sequence A G AGA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6379 258 5.80e-10 TAACTTGATG TGTGTTGGCTTTGTTGGTTGT GAGGCGGGGA 25795 117 3.90e-09 AGAGAATGAT GATGTGGTCATTGTTGGTTGG TCGAGAGGTG 24763 108 1.03e-08 CTGTCTTTTG GGTGAAGGTTCGGATGGTTGG TTGTGTCCAA 22031 323 2.83e-08 TGCTGGGTGT TGTGTTGTGGTTGCTGGTTTT TCGCGTCCGC 262891 304 4.83e-08 ATCCACCTCC TGTATTGGTATTGCTGGTTGG ACGATGATTT 262538 340 4.83e-08 TTTTGGGTGA GTTGGAGTTCTTGTTGGTGGT GCCGTTGTCA 262858 270 6.24e-08 GTGGCGTGGG GAGGAAGGGCTTGCTGGTTGG AAAAGGTACA 261495 182 1.30e-07 TCTGTTAGGG TTGGTTGTTATTGTTAGTTGT CTGGGGAGAG 3009 9 2.30e-07 TTATCGTT GTTGTTGTTGTTGTTGTTGTG AGATGCATCG 22685 137 2.57e-07 TCCATGTGTG GGTGATGTATTGGATGCTTGA GAGTACGAGC 17271 284 2.57e-07 TTGGGGACGA GAGGAAGTTTTGGATGGTGGA CGAGGAAGGG 21190 190 3.95e-07 GGGTTGGGAG GGGGTTGTGATTGCTCGTTTG GCCACTGTTT 9061 208 1.55e-06 ACGCAAGTTG GGGGGGGGCGTGGATGGATCT AACTTTCATA 268010 286 1.55e-06 CGGGGGGCAT ATGGAGGAGTTGGATGGATGT CGGCCACCTG 3580 320 1.69e-06 TGCATCATGG ATTGGTGATACGGTTGGTTTG CGTTTTGGTG 31690 187 1.85e-06 GATTGGATGC AATGGAGGCATAGATGTTTGG CTAGGAGAGA 18557 67 1.85e-06 GATTCGTCCT GCTGAAGAATATGATGGATGT AGGTGCCTCG 25321 90 4.67e-06 GGACGAGTGA TATCTTGGCTTTATTGGTGGG GCCGTTATTG 38827 362 5.47e-06 GTTGGGAAGA GGTGGAGAGGTTGCAGGAGGA GGAGAGGGGG 263786 305 5.91e-06 GCAGAGTGAT AAGGATGTGGATGATCGTAGG AAGATGATTG 17262 253 6.89e-06 CACTCGTCGT CGCGGTGGTGTTGTTGGGGGG GAGAACAGTG 269717 469 8.00e-06 GAAAGAGGGC GTTGGAGGATAAGATGGGAGG CGCGAAACAC 38289 32 8.62e-06 AACAATGACG TGGGATGAACAGCATGGATGG AATGTCTTGT 168 420 1.07e-05 CGATCATTTG AGTGAGGTCGAAAATAGTTGG ACCAAACATC 23898 18 1.15e-05 GGATTTCAGT GTTGTTGATGAAGATACATGT TTGGAATTGT 35510 39 1.63e-05 GCATACACTG GGTATTGTCGTTGTTTGAGCG GCTGTCTACG 36411 338 2.12e-05 AAATCGCTCT TGTGTTGGATCTCCAAGTTGG TCTAATTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6379 5.8e-10 257_[+1]_222 25795 3.9e-09 116_[+1]_363 24763 1e-08 107_[+1]_372 22031 2.8e-08 322_[+1]_157 262891 4.8e-08 303_[+1]_176 262538 4.8e-08 339_[+1]_140 262858 6.2e-08 269_[+1]_210 261495 1.3e-07 181_[+1]_298 3009 2.3e-07 8_[+1]_471 22685 2.6e-07 136_[+1]_343 17271 2.6e-07 283_[+1]_196 21190 3.9e-07 189_[+1]_290 9061 1.5e-06 207_[+1]_272 268010 1.5e-06 285_[+1]_194 3580 1.7e-06 319_[+1]_160 31690 1.9e-06 186_[+1]_293 18557 1.9e-06 66_[+1]_413 25321 4.7e-06 89_[+1]_390 38827 5.5e-06 361_[+1]_118 263786 5.9e-06 304_[+1]_175 17262 6.9e-06 252_[+1]_227 269717 8e-06 468_[+1]_11 38289 8.6e-06 31_[+1]_448 168 1.1e-05 419_[+1]_60 23898 1.2e-05 17_[+1]_462 35510 1.6e-05 38_[+1]_441 36411 2.1e-05 337_[+1]_142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=27 6379 ( 258) TGTGTTGGCTTTGTTGGTTGT 1 25795 ( 117) GATGTGGTCATTGTTGGTTGG 1 24763 ( 108) GGTGAAGGTTCGGATGGTTGG 1 22031 ( 323) TGTGTTGTGGTTGCTGGTTTT 1 262891 ( 304) TGTATTGGTATTGCTGGTTGG 1 262538 ( 340) GTTGGAGTTCTTGTTGGTGGT 1 262858 ( 270) GAGGAAGGGCTTGCTGGTTGG 1 261495 ( 182) TTGGTTGTTATTGTTAGTTGT 1 3009 ( 9) GTTGTTGTTGTTGTTGTTGTG 1 22685 ( 137) GGTGATGTATTGGATGCTTGA 1 17271 ( 284) GAGGAAGTTTTGGATGGTGGA 1 21190 ( 190) GGGGTTGTGATTGCTCGTTTG 1 9061 ( 208) GGGGGGGGCGTGGATGGATCT 1 268010 ( 286) ATGGAGGAGTTGGATGGATGT 1 3580 ( 320) ATTGGTGATACGGTTGGTTTG 1 31690 ( 187) AATGGAGGCATAGATGTTTGG 1 18557 ( 67) GCTGAAGAATATGATGGATGT 1 25321 ( 90) TATCTTGGCTTTATTGGTGGG 1 38827 ( 362) GGTGGAGAGGTTGCAGGAGGA 1 263786 ( 305) AAGGATGTGGATGATCGTAGG 1 17262 ( 253) CGCGGTGGTGTTGTTGGGGGG 1 269717 ( 469) GTTGGAGGATAAGATGGGAGG 1 38289 ( 32) TGGGATGAACAGCATGGATGG 1 168 ( 420) AGTGAGGTCGAAAATAGTTGG 1 23898 ( 18) GTTGTTGATGAAGATACATGT 1 35510 ( 39) GGTATTGTCGTTGTTTGAGCG 1 36411 ( 338) TGTGTTGGATCTCCAAGTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 9.929 E= 9.2e-016 -51 -274 112 5 -24 -274 102 5 -1140 -274 32 141 -183 -274 190 -1140 34 -1140 12 70 17 -1140 -68 115 -1140 -1140 207 -1140 -24 -1140 64 70 -51 6 -10 41 -24 -116 49 41 -24 -116 -1140 141 -83 -1140 12 124 -183 -175 184 -1140 76 -16 -1140 41 -183 -1140 -1140 189 -83 -175 164 -275 -1140 -175 184 -176 -2 -1140 -168 141 -183 -1140 12 141 -1140 -175 171 -76 -124 -1140 132 24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 9.2e-016 0.185185 0.037037 0.518519 0.259259 0.222222 0.037037 0.481481 0.259259 0.000000 0.037037 0.296296 0.666667 0.074074 0.037037 0.888889 0.000000 0.333333 0.000000 0.259259 0.407407 0.296296 0.000000 0.148148 0.555556 0.000000 0.000000 1.000000 0.000000 0.222222 0.000000 0.370370 0.407407 0.185185 0.259259 0.222222 0.333333 0.222222 0.111111 0.333333 0.333333 0.222222 0.111111 0.000000 0.666667 0.148148 0.000000 0.259259 0.592593 0.074074 0.074074 0.851852 0.000000 0.444444 0.222222 0.000000 0.333333 0.074074 0.000000 0.000000 0.925926 0.148148 0.074074 0.740741 0.037037 0.000000 0.074074 0.851852 0.074074 0.259259 0.000000 0.074074 0.666667 0.074074 0.000000 0.259259 0.666667 0.000000 0.074074 0.777778 0.148148 0.111111 0.000000 0.592593 0.296296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][GTA][TG]G[TAG][TA]G[TGA][TCG][GTA][TA][TG]G[ATC]TGG[TA][TG]G[GT] -------------------------------------------------------------------------------- Time 12.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 35 llr = 361 E-value = 1.9e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1142:61:6416253836357 pos.-specific C 74269:4a:682753:73553 probability G 1231:22:3:111:2:::1:: matrix T 1321:24:1::1::22::11: bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.2 * * Entropy 1.0 * * ** * * * (14.9 bits) 0.8 * * ** ** ** * 0.6 * ** **** ** *** ** 0.4 * *** ******* *** ** 0.2 ** *********** ****** 0.0 --------------------- Multilevel CCACCACCACCACACACACAA consensus TGA TT GA C CATACACC sequence T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35510 449 1.63e-09 TTCCACGGCT CCGCCACCGCCACACACACAC ATCCTTCGGA 1255 459 2.06e-08 GATGTGAACG CAACCACCACAACCAACACCA CGCATCCAAG 9061 262 3.98e-08 GGTAGAGGGA CCGCCACCACCAGCCTCACCA TCCATCCCTC 38289 303 6.37e-08 GTAAAAGCAC CTACCAGCACCCAAAACACAA CGCTCTCTCT bd763 480 1.15e-07 AGCAGCAAGG CCAGCACCGCCTCCAACAACA 21190 351 1.32e-07 CTTCCGAATC CACCCATCGACAACCACACAA CCAGAGTGGT 6379 442 4.37e-07 TTCAAGCCTC CGTCCGTCGCCTCCTACACAA CATCCCGTCT 17262 440 4.95e-07 GTCTCAGCTT CGACCTTCCACACACACACCA ACCCCACCAG 4793 441 6.32e-07 CTCGCCCAGC CAAGCATCAACACCGAACACA CAACGCACAC 269717 31 1.27e-06 CCGCGGAACG ATACCATCAACAACAACAGCA AAGCAATAGT 3009 477 2.69e-06 TCGGCTACAC CCAACAACAACAACGACAGCA ACG 6150 480 2.98e-06 GCTTCTGGAC TCTCCTCCGCCTCCGAAACAA 23898 320 2.98e-06 ACGCGGCTGC CTGCCGCCGCCACCAATCAAA GCCGCCTCTT 262538 439 3.30e-06 AAACAGCTTC TCTCCGTCGCCGCACACAACA AATCAATCAA 24763 422 3.65e-06 CACCGACCGA CCGACAGCGACACCGTCAGAC TGACCTCTAT 31690 353 4.03e-06 GCCGATTCTA GAAACATCAACAGCTACCCAA CGAACGAACC 168 457 4.44e-06 CATCTATTCG GGGACATCAAAACAAAAACAA CCACCAACAC 34710 479 4.90e-06 GGCAACATCT CTGCCGGCTACCCACACCCAC G 18557 464 5.39e-06 TATCTCACGT ATCACATCAACACATAACACA TCACATCATC 22031 471 7.15e-06 ACACAAGCGT GGTCCACCACCCAATACCCAC AATATCCAA 19034 67 7.15e-06 GCCAACCTCG CCTCCTCCACCACAGTACTAC TTCTGAACCA 40402 39 7.84e-06 AAACAGTCTC GCGCCATCAAGTCAAAACCAA GGCCGGACGC 262858 412 8.59e-06 CCTCCAGCTC CCTGCTCCTCCCCAAACAAAC CCACAACCGT 25486 364 1.46e-05 TTGTCAAGGA CGCCCATCAACACCATACATC AAATCAAATC 25795 447 2.03e-05 TAGTACAGCA CCATCACCGCAACAGAGCCAA ACAACCAACA 36411 403 2.80e-05 TCTGCCGTAT CTCGCATCTCCACCATCTCCA TTTGCAAATC 261495 477 2.80e-05 CCATCAACCT CAGCCCTCGCCAGCCTCCACA AGT 262891 77 3.03e-05 AACCCTCCTG CGTCCTGCACGCCACAAAACC TCCTCTCAAC 25321 478 3.03e-05 TTCATATTTA CTACATGCACCTCCGACATAA AG 38827 105 3.54e-05 TGGAAGTAGC ACCTCAGCAACCACGACAACA TCAACGACAG 34412 457 4.43e-05 CCGCTCTCTG CCACGGCCAAAACACAAATAA CCCGACAGAG 263786 211 4.43e-05 TGGCTCAACC GCAACAGCAACAGATGCAACA GGCGAGGGCT 268010 125 7.33e-05 ACATCGCCCA TCAACTCTACCGCATACACCA CCACTGACGA 17271 58 7.85e-05 GGACTACAAC TTCCCACCACCACACTCGCCT CTCCGACAGG 22685 388 1.82e-04 CCAGATCATG CTGCCGACACACCACACCGTC GGGAAAGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35510 1.6e-09 448_[+2]_31 1255 2.1e-08 458_[+2]_21 9061 4e-08 261_[+2]_218 38289 6.4e-08 302_[+2]_177 bd763 1.1e-07 479_[+2] 21190 1.3e-07 350_[+2]_129 6379 4.4e-07 441_[+2]_38 17262 4.9e-07 439_[+2]_40 4793 6.3e-07 440_[+2]_39 269717 1.3e-06 30_[+2]_449 3009 2.7e-06 476_[+2]_3 6150 3e-06 479_[+2] 23898 3e-06 319_[+2]_160 262538 3.3e-06 438_[+2]_41 24763 3.6e-06 421_[+2]_58 31690 4e-06 352_[+2]_127 168 4.4e-06 456_[+2]_23 34710 4.9e-06 478_[+2]_1 18557 5.4e-06 463_[+2]_16 22031 7.2e-06 470_[+2]_9 19034 7.2e-06 66_[+2]_413 40402 7.8e-06 38_[+2]_441 262858 8.6e-06 411_[+2]_68 25486 1.5e-05 363_[+2]_116 25795 2e-05 446_[+2]_33 36411 2.8e-05 402_[+2]_77 261495 2.8e-05 476_[+2]_3 262891 3e-05 76_[+2]_403 25321 3e-05 477_[+2]_2 38827 3.5e-05 104_[+2]_375 34412 4.4e-05 456_[+2]_23 263786 4.4e-05 210_[+2]_269 268010 7.3e-05 124_[+2]_355 17271 7.9e-05 57_[+2]_422 22685 0.00018 387_[+2]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=35 35510 ( 449) CCGCCACCGCCACACACACAC 1 1255 ( 459) CAACCACCACAACCAACACCA 1 9061 ( 262) CCGCCACCACCAGCCTCACCA 1 38289 ( 303) CTACCAGCACCCAAAACACAA 1 bd763 ( 480) CCAGCACCGCCTCCAACAACA 1 21190 ( 351) CACCCATCGACAACCACACAA 1 6379 ( 442) CGTCCGTCGCCTCCTACACAA 1 17262 ( 440) CGACCTTCCACACACACACCA 1 4793 ( 441) CAAGCATCAACACCGAACACA 1 269717 ( 31) ATACCATCAACAACAACAGCA 1 3009 ( 477) CCAACAACAACAACGACAGCA 1 6150 ( 480) TCTCCTCCGCCTCCGAAACAA 1 23898 ( 320) CTGCCGCCGCCACCAATCAAA 1 262538 ( 439) TCTCCGTCGCCGCACACAACA 1 24763 ( 422) CCGACAGCGACACCGTCAGAC 1 31690 ( 353) GAAACATCAACAGCTACCCAA 1 168 ( 457) GGGACATCAAAACAAAAACAA 1 34710 ( 479) CTGCCGGCTACCCACACCCAC 1 18557 ( 464) ATCACATCAACACATAACACA 1 22031 ( 471) GGTCCACCACCCAATACCCAC 1 19034 ( 67) CCTCCTCCACCACAGTACTAC 1 40402 ( 39) GCGCCATCAAGTCAAAACCAA 1 262858 ( 412) CCTGCTCCTCCCCAAACAAAC 1 25486 ( 364) CGCCCATCAACACCATACATC 1 25795 ( 447) CCATCACCGCAACAGAGCCAA 1 36411 ( 403) CTCGCATCTCCACCATCTCCA 1 261495 ( 477) CAGCCCTCGCCAGCCTCCACA 1 262891 ( 77) CGTCCTGCACGCCACAAAACC 1 25321 ( 478) CTACATGCACCTCCGACATAA 1 38827 ( 105) ACCTCAGCAACCACGACAACA 1 34412 ( 457) CCACGGCCAAAACACAAATAA 1 263786 ( 211) GCAACAGCAACAGATGCAACA 1 268010 ( 125) TCAACTCTACCGCATACACCA 1 17271 ( 58) TTCCCACCACCACACTCGCCT 1 22685 ( 388) CTGCCGACACACCACACCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 9.08689 E= 1.9e-014 -162 140 -74 -113 -88 78 -47 4 50 -54 11 -32 -40 134 -106 -213 -320 192 -305 -1177 119 -312 -47 -32 -220 58 -25 57 -1177 197 -1177 -313 119 -312 26 -155 70 120 -1177 -1177 -88 168 -206 -1177 119 -31 -206 -81 -62 152 -106 -1177 97 97 -1177 -1177 12 34 -6 -55 155 -1177 -305 -32 -3 146 -305 -313 119 46 -305 -313 26 97 -106 -155 88 88 -1177 -213 144 5 -1177 -313 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 35 E= 1.9e-014 0.085714 0.657143 0.142857 0.114286 0.142857 0.428571 0.171429 0.257143 0.371429 0.171429 0.257143 0.200000 0.200000 0.628571 0.114286 0.057143 0.028571 0.942857 0.028571 0.000000 0.600000 0.028571 0.171429 0.200000 0.057143 0.371429 0.200000 0.371429 0.000000 0.971429 0.000000 0.028571 0.600000 0.028571 0.285714 0.085714 0.428571 0.571429 0.000000 0.000000 0.142857 0.800000 0.057143 0.000000 0.600000 0.200000 0.057143 0.142857 0.171429 0.714286 0.114286 0.000000 0.514286 0.485714 0.000000 0.000000 0.285714 0.314286 0.228571 0.171429 0.771429 0.000000 0.028571 0.200000 0.257143 0.685714 0.028571 0.028571 0.600000 0.342857 0.028571 0.028571 0.314286 0.485714 0.114286 0.085714 0.485714 0.457143 0.000000 0.057143 0.714286 0.257143 0.000000 0.028571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CT][AGT][CA]C[AT][CTG]C[AG][CA]C[AC]C[AC][CAG][AT][CA][AC][CA][AC][AC] -------------------------------------------------------------------------------- Time 23.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 23 llr = 240 E-value = 3.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :71:3::5:423:721 pos.-specific C 21:::5::1:21::1: probability G 8:5a51934651a::9 matrix T :23:24134:16:27: bits 2.1 * * 1.9 * * 1.7 * * * * 1.5 * * * * Relative 1.2 * * * * * Entropy 1.0 * * * ** * (15.0 bits) 0.8 ** * * * **** 0.6 ** * ** * **** 0.4 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel GAGGGCGAGGGTGATG consensus CTT AT GTAAA T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 31690 88 3.83e-08 ATTGTATTCA GAGGGCGGGAGAGATG ATTTATGTAC 262858 103 8.89e-08 GTTGATGGGT GAGGACGTTGATGATG ATATCCCATC 17271 441 8.11e-07 TGCCATATTG GATGGTGTCGATGATG AATGATGGAA 261495 155 9.23e-07 TGGTGGAGGA GAGGGTGGGGTTGTTG TTCTGTTAGG 25321 39 9.23e-07 CCAAGCCCGA CAAGGCGATGGAGATG GCGATGAGTG 21190 21 1.87e-06 AGAGCAGATA GTGGCCGGTGGTGATG GTGTACCCCA 38827 386 3.18e-06 AGGAGGAGGA GAGGGGGAAGGTGTTG AAAGGTCAGT 38289 172 3.18e-06 ACCAATACTC GTGGGCGAGAGGGAAG CAAGCAAAAG 3009 407 3.54e-06 ACCGCAAAGG GCTGGTGATGGCGATG GAGCCACACT 22685 288 4.78e-06 GGGCGGCACT CATGACGAGTGTGATG AAAATAAGAC 35510 115 5.77e-06 ACCTCAGAAG GATGATGTTAGTGGTG GCAGAAACTG 269717 344 6.98e-06 TATTCTCGAA GTGGGTGGGGGTGTTA CCGAGGTCAT 6379 128 7.66e-06 GTTGATGTGT GTGGTCTTGAGTGATG TAAACTAATG 3580 399 7.66e-06 CTCTCTTCAA CCGGGCGAGAAAGATG AGTCCACTAC 22031 22 9.95e-06 TATCATATCT GATGGCTGGATTGATG TCCTTGGAAG 19034 378 9.95e-06 CCAGATCAAC CAAGATGATGGAGAAG AACACTTGCA 262785 102 1.40e-05 CAACGTCTGG GAAGTTGGCAGTGTTG GACAAGTTGT 40402 371 1.64e-05 GAGAAAACAC GATGATGTGGACGACG AGGCGATTGA 268010 427 1.64e-05 CCTAGACCAC GATGACGATGCTGAAA CGCGAAATGC 25795 142 1.77e-05 GGTTGGTCGA GAGGTGGTGACAGTTG GAGGCGAATG 262538 473 1.91e-05 CAATCAACGT GACGGTGACGCTGAAG GCCAGTGTAA 6150 241 2.40e-05 ACAGATGTAC CAGGAGGATGCAGACG AGATGCACGT 1255 33 3.42e-05 TCAGAAGCAA GTGGTCGATAAGGACG ACCTTTACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31690 3.8e-08 87_[+3]_397 262858 8.9e-08 102_[+3]_382 17271 8.1e-07 440_[+3]_44 261495 9.2e-07 154_[+3]_330 25321 9.2e-07 38_[+3]_446 21190 1.9e-06 20_[+3]_464 38827 3.2e-06 385_[+3]_99 38289 3.2e-06 171_[+3]_313 3009 3.5e-06 406_[+3]_78 22685 4.8e-06 287_[+3]_197 35510 5.8e-06 114_[+3]_370 269717 7e-06 343_[+3]_141 6379 7.7e-06 127_[+3]_357 3580 7.7e-06 398_[+3]_86 22031 9.9e-06 21_[+3]_463 19034 9.9e-06 377_[+3]_107 262785 1.4e-05 101_[+3]_383 40402 1.6e-05 370_[+3]_114 268010 1.6e-05 426_[+3]_58 25795 1.8e-05 141_[+3]_343 262538 1.9e-05 472_[+3]_12 6150 2.4e-05 240_[+3]_244 1255 3.4e-05 32_[+3]_452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=23 31690 ( 88) GAGGGCGGGAGAGATG 1 262858 ( 103) GAGGACGTTGATGATG 1 17271 ( 441) GATGGTGTCGATGATG 1 261495 ( 155) GAGGGTGGGGTTGTTG 1 25321 ( 39) CAAGGCGATGGAGATG 1 21190 ( 21) GTGGCCGGTGGTGATG 1 38827 ( 386) GAGGGGGAAGGTGTTG 1 38289 ( 172) GTGGGCGAGAGGGAAG 1 3009 ( 407) GCTGGTGATGGCGATG 1 22685 ( 288) CATGACGAGTGTGATG 1 35510 ( 115) GATGATGTTAGTGGTG 1 269717 ( 344) GTGGGTGGGGGTGTTA 1 6379 ( 128) GTGGTCTTGAGTGATG 1 3580 ( 399) CCGGGCGAGAAAGATG 1 22031 ( 22) GATGGCTGGATTGATG 1 19034 ( 378) CAAGATGATGGAGAAG 1 262785 ( 102) GAAGTTGGCAGTGTTG 1 40402 ( 371) GATGATGTGGACGACG 1 268010 ( 427) GATGACGATGCTGAAA 1 25795 ( 142) GAGGTGGTGACAGTTG 1 262538 ( 473) GACGGTGACGCTGAAG 1 6150 ( 241) CAGGAGGATGCAGACG 1 1255 ( 33) GTGGTCGATAAGGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17945 bayes= 10.0089 E= 3.5e-001 -1117 -19 172 -1117 140 -152 -1117 -20 -101 -251 113 28 -1117 -1117 207 -1117 21 -251 101 -52 -1117 94 -87 64 -1117 -1117 194 -152 86 -1117 13 6 -259 -93 87 64 57 -1117 125 -252 -28 -52 113 -152 -1 -152 -145 117 -1117 -1117 207 -1117 149 -1117 -245 -20 -60 -93 -1117 147 -160 -1117 194 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 3.5e-001 0.000000 0.217391 0.782609 0.000000 0.695652 0.086957 0.000000 0.217391 0.130435 0.043478 0.521739 0.304348 0.000000 0.000000 1.000000 0.000000 0.304348 0.043478 0.478261 0.173913 0.000000 0.478261 0.130435 0.391304 0.000000 0.000000 0.913043 0.086957 0.478261 0.000000 0.260870 0.260870 0.043478 0.130435 0.434783 0.391304 0.391304 0.000000 0.565217 0.043478 0.217391 0.173913 0.521739 0.086957 0.260870 0.086957 0.086957 0.565217 0.000000 0.000000 1.000000 0.000000 0.739130 0.000000 0.043478 0.217391 0.173913 0.130435 0.000000 0.695652 0.086957 0.000000 0.913043 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][AT][GT]G[GA][CT]G[AGT][GT][GA][GA][TA]G[AT]TG -------------------------------------------------------------------------------- Time 34.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1255 1.30e-05 32_[+3(3.42e-05)]_410_\ [+2(2.06e-08)]_21 168 8.27e-04 419_[+1(1.07e-05)]_16_\ [+2(4.44e-06)]_23 17262 4.39e-05 252_[+1(6.89e-06)]_166_\ [+2(4.95e-07)]_40 17271 4.02e-07 57_[+2(7.85e-05)]_205_\ [+1(2.57e-07)]_7_[+1(9.97e-06)]_73_[+1(9.90e-05)]_14_[+3(8.11e-07)]_44 18557 1.59e-04 66_[+1(1.85e-06)]_376_\ [+2(5.39e-06)]_16 19034 1.15e-03 66_[+2(7.15e-06)]_290_\ [+3(9.95e-06)]_107 21190 3.75e-09 20_[+3(1.87e-06)]_153_\ [+1(3.95e-07)]_140_[+2(1.32e-07)]_129 22031 6.05e-08 21_[+3(9.95e-06)]_285_\ [+1(2.83e-08)]_127_[+2(7.15e-06)]_9 22685 4.12e-06 136_[+1(2.57e-07)]_130_\ [+3(4.78e-06)]_197 23898 2.08e-05 17_[+1(1.15e-05)]_281_\ [+2(2.98e-06)]_160 24763 1.62e-06 107_[+1(1.03e-08)]_293_\ [+2(3.65e-06)]_58 25321 2.63e-06 38_[+3(9.23e-07)]_35_[+1(4.67e-06)]_\ 367_[+2(3.03e-05)]_2 25486 6.78e-02 363_[+2(1.46e-05)]_116 25795 4.33e-08 116_[+1(3.90e-09)]_4_[+3(1.77e-05)]_\ 242_[+2(6.37e-05)]_26_[+2(2.03e-05)]_33 261495 9.64e-08 154_[+3(9.23e-07)]_11_\ [+1(1.30e-07)]_274_[+2(2.80e-05)]_3 262538 8.82e-08 339_[+1(4.83e-08)]_78_\ [+2(3.30e-06)]_13_[+3(1.91e-05)]_12 262785 5.24e-02 101_[+3(1.40e-05)]_383 262858 1.94e-09 102_[+3(8.89e-08)]_151_\ [+1(6.24e-08)]_121_[+2(8.59e-06)]_68 262891 2.04e-05 76_[+2(3.03e-05)]_206_\ [+1(4.83e-08)]_176 263786 1.32e-03 210_[+2(4.43e-05)]_73_\ [+1(5.91e-06)]_175 268010 2.74e-05 124_[+2(7.33e-05)]_140_\ [+1(1.55e-06)]_120_[+3(1.64e-05)]_58 269717 1.53e-06 30_[+2(1.27e-06)]_292_\ [+3(6.98e-06)]_109_[+1(8.00e-06)]_11 3009 6.56e-08 8_[+1(2.30e-07)]_166_[+3(5.75e-05)]_\ 195_[+3(3.54e-06)]_54_[+2(2.69e-06)]_3 31690 1.01e-08 87_[+3(3.83e-08)]_83_[+1(1.85e-06)]_\ 145_[+2(4.03e-06)]_127 34412 4.74e-02 456_[+2(4.43e-05)]_23 34710 3.26e-03 478_[+2(4.90e-06)]_1 35510 5.68e-09 38_[+1(1.63e-05)]_55_[+3(5.77e-06)]_\ 242_[+2(2.03e-05)]_55_[+2(1.63e-09)]_31 3580 2.84e-04 319_[+1(1.69e-06)]_58_\ [+3(7.66e-06)]_86 36411 4.50e-03 337_[+1(2.12e-05)]_44_\ [+2(2.80e-05)]_77 38289 5.32e-08 31_[+1(8.62e-06)]_119_\ [+3(3.18e-06)]_115_[+2(6.37e-08)]_177 38827 1.05e-05 104_[+2(3.54e-05)]_236_\ [+1(5.47e-06)]_3_[+3(3.18e-06)]_99 40402 8.61e-04 38_[+2(7.84e-06)]_311_\ [+3(1.64e-05)]_59_[+2(7.33e-05)]_34 4793 9.88e-03 440_[+2(6.32e-07)]_39 6150 6.34e-04 240_[+3(2.40e-05)]_223_\ [+2(2.98e-06)] 6379 9.86e-11 127_[+3(7.66e-06)]_114_\ [+1(5.80e-10)]_163_[+2(4.37e-07)]_38 9061 1.18e-06 207_[+1(1.55e-06)]_33_\ [+2(3.98e-08)]_138_[+2(1.46e-05)]_21_[+2(8.59e-06)]_17 bd763 3.80e-04 224_[+2(7.15e-06)]_207_\ [+2(6.83e-05)]_6_[+2(1.15e-07)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************