******************************************************************************** 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/247/247.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10078 1.0000 500 20754 1.0000 500 21679 1.0000 500 2194 1.0000 500 21955 1.0000 500 22451 1.0000 500 23094 1.0000 500 23621 1.0000 500 24044 1.0000 500 24158 1.0000 500 25168 1.0000 500 25438 1.0000 500 25547 1.0000 500 25810 1.0000 500 261566 1.0000 500 263010 1.0000 500 263491 1.0000 500 263492 1.0000 500 264293 1.0000 500 268817 1.0000 500 269660 1.0000 500 30193 1.0000 500 31993 1.0000 500 3436 1.0000 500 36425 1.0000 500 37232 1.0000 500 3790 1.0000 500 39741 1.0000 500 41650 1.0000 500 4818 1.0000 500 4960 1.0000 500 5079 1.0000 500 5093 1.0000 500 5410 1.0000 500 5760 1.0000 500 5897 1.0000 500 6539 1.0000 500 6642 1.0000 500 7120 1.0000 500 7419 1.0000 500 7683 1.0000 500 9449 1.0000 500 9519 1.0000 500 bd1815 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/247/247.seqs.fa -oc motifs/247 -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= 44 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= 22000 N= 44 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.235 G 0.244 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.235 G 0.244 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 44 llr = 417 E-value = 8.7e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2333:46:134162:42:531 pos.-specific C 735384265239:39318:27 probability G :1::11::321::1:3:13:: matrix T 2333:124:32:441:71252 bits 2.1 1.9 1.7 * * 1.5 * * Relative 1.3 * * * Entropy 1.0 * * ** * * * (13.7 bits) 0.8 * * ** * ** * 0.6 * * * ** * ** * 0.4 * ******* ** * ** ** 0.2 * ******* ********** 0.0 --------------------- Multilevel CACCCAACCTACATCATCATC consensus CAT CTTGAC TC C GAT sequence TTA CT G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5760 29 1.26e-08 GCGTCGTACA CCCTCCACGTGCACCGTCATC CCGACGTATC 37232 333 1.57e-08 TCACACCATG CTCCCCACGCTCTTCATCAAC CACGGAGGAG 5410 471 2.39e-08 CTCAATCAAG CCAACAATCATCATCATCATC ATCATCACC 25168 214 2.39e-08 TCTATTCAGC TACACCACCTACATCCTCACC TCACTCTCAA 263492 48 7.46e-08 TCGTCTCCTA CATCCCATCTGCTCCCTCGTC TCGTGTGTCC 263491 48 7.46e-08 TCGTCTCCTA CATCCCATCTGCTCCCTCGTC TCGTGTGTCC 30193 466 2.03e-07 CCATCATCGT CACCCATCCACCACCACCAAC ACACAAACTC 7683 121 5.73e-07 ATAACATTAT CAAAGCACGCCCATCGTCATC GTTCAAAGCT 3790 422 5.73e-07 ACACCTTCCA ACCCCAACCCCCAACCTCTTC ACTTTTTTAT bd1815 298 6.58e-07 ACAACATGAT CCTACACTCGACATCCTCAAC AGCATCGTTG 41650 472 7.55e-07 GACAGCACCG CCTCCCATCAACATCAACGTT GCTATCTC 3436 310 1.45e-06 TGTGACACGT CTCTCTCTCTCCTCCATCACC TCACATTTCC 7419 412 1.86e-06 CAACTCTCCT CGAACCTCCAACACCGACAAC CCCGCACGCC 23621 476 2.09e-06 CAACGCCACC AACACCACCAACACCACCAAT AACC 4818 292 3.35e-06 GTATTAATAA CTCACCTTATCCACCGTCGTT CCTGAATCCA 25438 478 3.35e-06 TTTGTTGATA CAAACATCCCACAACATCTCT CA 5079 480 4.69e-06 ACCAACTGAA ACTTCCTCCTTCATCACCACC 4960 425 5.23e-06 TCTACAGTTT CTCTCAATTTACATCATTATC ATAGTACATA 7120 13 5.82e-06 GATCATTTGA CACTCACTCCAATACATCGTC GACGCAAATG 36425 419 5.82e-06 CTTCTTCTTC TTCTCAACATACTTCGACGAC ATGCAGTAGC 23094 441 8.85e-06 CAATTGCAAA TCTCCATCGGACACCCTCTCC AACCCTTCAC 21679 319 1.60e-05 TTTCGTGTTG TTACCCACCGGCTTCGTTGTC TTGTCGACTC 6642 96 1.76e-05 TGCTGCTCGT CGATCTACGCCCATCGCCACC GACAACAGCC 20754 116 1.93e-05 AGCTGCACCT CGTTCAACGATCTGCGACAAC AAGAATTCGC 269660 467 2.32e-05 GTTGGTTTCA AATCCATCGGCCATCAACTCC ATCTCTCAAC 264293 446 2.78e-05 CTGCAAGCAA CAACAAACCAACTACAACAAC GCAACAACTC 24044 432 3.62e-05 AACTAAAGAA GACACCACCTAAATCATCCTC GCCGAGACGA 22451 100 3.94e-05 ATCCTTCTTC TGCCCACTCTTCTTCTTCTTC TTCTTCTTCT 6539 434 4.29e-05 TCGTGCCTCC CTCTCCACTATCACTCTCTCC AACTCTCATC 9449 383 4.67e-05 TGTGTGGTGT ACCTGCACCGCCACCGTCGCA GATTTCTAAT 21955 111 5.07e-05 TCTCTTTTGA ATCACTAGCTGCTTCATCAAC GTGGCAGCTC 263010 282 5.50e-05 TGTGTCTCCC CGCCCGCTCTCCTCCCACAAT CAAACAGCGA 268817 470 6.47e-05 CGTGCCATTT CCAAGCCTCACCACTCTCGTC TCGATTTCAC 25547 234 6.47e-05 GGTGATGATG CAACCAACAACAAACTTCGTC AGGACTTGAG 31993 460 8.85e-05 ATCTCTTCAT CTCCCTTCGGCCTTCGTTGAT ACTCCACAAA 5897 434 1.03e-04 GATTAGACGT CTTTCGGCAAACATCACCGTC GATCACCGAC 24158 77 1.03e-04 TAGGCAACGT CTTTGAACGCTCTCCCTAAAC CAAAGAATAA 261566 14 1.11e-04 AGCGATGTAC TCATCATCGTTCTGCAACAAT GGTAGAAAGC 2194 445 1.59e-04 GAACCTCCCT CCTTCCTTGCACTTCCTGCTT TGCTCGCCGC 9519 423 1.83e-04 TCTCCATAAA TTAACAACCGTCTCCCTGGAA CTTCTCCGGC 10078 238 1.96e-04 TAATTGCCAG CCCATCGCCCGCTGCGTCGTC GCCCATCGCT 39741 381 2.92e-04 AGAATATGTC CACTCAATGTTCAATATGTCT AATATTGACC 25810 345 3.99e-04 GCTGTCAACT CAACGGATGAACTACGTTATT AATGAGAGAT 5093 478 6.36e-04 GTTCCAACAC AATACACTACAAATCATCTTA AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5760 1.3e-08 28_[+1]_451 37232 1.6e-08 332_[+1]_147 5410 2.4e-08 470_[+1]_9 25168 2.4e-08 213_[+1]_266 263492 7.5e-08 47_[+1]_432 263491 7.5e-08 47_[+1]_432 30193 2e-07 465_[+1]_14 7683 5.7e-07 120_[+1]_359 3790 5.7e-07 421_[+1]_58 bd1815 6.6e-07 297_[+1]_182 41650 7.5e-07 471_[+1]_8 3436 1.4e-06 309_[+1]_170 7419 1.9e-06 411_[+1]_68 23621 2.1e-06 475_[+1]_4 4818 3.3e-06 291_[+1]_188 25438 3.3e-06 477_[+1]_2 5079 4.7e-06 479_[+1] 4960 5.2e-06 424_[+1]_55 7120 5.8e-06 12_[+1]_467 36425 5.8e-06 418_[+1]_61 23094 8.9e-06 440_[+1]_39 21679 1.6e-05 318_[+1]_161 6642 1.8e-05 95_[+1]_384 20754 1.9e-05 115_[+1]_364 269660 2.3e-05 466_[+1]_13 264293 2.8e-05 445_[+1]_34 24044 3.6e-05 431_[+1]_48 22451 3.9e-05 99_[+1]_380 6539 4.3e-05 433_[+1]_46 9449 4.7e-05 382_[+1]_97 21955 5.1e-05 110_[+1]_369 263010 5.5e-05 281_[+1]_198 268817 6.5e-05 469_[+1]_10 25547 6.5e-05 233_[+1]_246 31993 8.8e-05 459_[+1]_20 5897 0.0001 433_[+1]_46 24158 0.0001 76_[+1]_403 261566 0.00011 13_[+1]_466 2194 0.00016 444_[+1]_35 9519 0.00018 422_[+1]_57 10078 0.0002 237_[+1]_242 39741 0.00029 380_[+1]_99 25810 0.0004 344_[+1]_135 5093 0.00064 477_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=44 5760 ( 29) CCCTCCACGTGCACCGTCATC 1 37232 ( 333) CTCCCCACGCTCTTCATCAAC 1 5410 ( 471) CCAACAATCATCATCATCATC 1 25168 ( 214) TACACCACCTACATCCTCACC 1 263492 ( 48) CATCCCATCTGCTCCCTCGTC 1 263491 ( 48) CATCCCATCTGCTCCCTCGTC 1 30193 ( 466) CACCCATCCACCACCACCAAC 1 7683 ( 121) CAAAGCACGCCCATCGTCATC 1 3790 ( 422) ACCCCAACCCCCAACCTCTTC 1 bd1815 ( 298) CCTACACTCGACATCCTCAAC 1 41650 ( 472) CCTCCCATCAACATCAACGTT 1 3436 ( 310) CTCTCTCTCTCCTCCATCACC 1 7419 ( 412) CGAACCTCCAACACCGACAAC 1 23621 ( 476) AACACCACCAACACCACCAAT 1 4818 ( 292) CTCACCTTATCCACCGTCGTT 1 25438 ( 478) CAAACATCCCACAACATCTCT 1 5079 ( 480) ACTTCCTCCTTCATCACCACC 1 4960 ( 425) CTCTCAATTTACATCATTATC 1 7120 ( 13) CACTCACTCCAATACATCGTC 1 36425 ( 419) TTCTCAACATACTTCGACGAC 1 23094 ( 441) TCTCCATCGGACACCCTCTCC 1 21679 ( 319) TTACCCACCGGCTTCGTTGTC 1 6642 ( 96) CGATCTACGCCCATCGCCACC 1 20754 ( 116) CGTTCAACGATCTGCGACAAC 1 269660 ( 467) AATCCATCGGCCATCAACTCC 1 264293 ( 446) CAACAAACCAACTACAACAAC 1 24044 ( 432) GACACCACCTAAATCATCCTC 1 22451 ( 100) TGCCCACTCTTCTTCTTCTTC 1 6539 ( 434) CTCTCCACTATCACTCTCTCC 1 9449 ( 383) ACCTGCACCGCCACCGTCGCA 1 21955 ( 111) ATCACTAGCTGCTTCATCAAC 1 263010 ( 282) CGCCCGCTCTCCTCCCACAAT 1 268817 ( 470) CCAAGCCTCACCACTCTCGTC 1 25547 ( 234) CAACCAACAACAAACTTCGTC 1 31993 ( 460) CTCCCTTCGGCCTTCGTTGAT 1 5897 ( 434) CTTTCGGCAAACATCACCGTC 1 24158 ( 77) CTTTGAACGCTCTCCCTAAAC 1 261566 ( 14) TCATCATCGTTCTGCAACAAT 1 2194 ( 445) CCTTCCTTGCACTTCCTGCTT 1 9519 ( 423) TTAACAACCGTCTCCCTGGAA 1 10078 ( 238) CCCATCGCCCGCTGCGTCGTC 1 39741 ( 381) CACTCAATGTTCAATATGTCT 1 25810 ( 345) CAACGGATGAACTACGTTATT 1 5093 ( 478) AATACACTACAAATCATCTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 8.90388 E= 8.7e-016 -72 149 -342 -70 38 22 -110 8 5 95 -1210 8 28 54 -1210 40 -353 184 -110 -350 72 80 -184 -151 111 -56 -242 -19 -1210 139 -342 49 -121 122 27 -251 5 -5 -62 40 47 22 -84 -19 -153 195 -1210 -1210 111 -1210 -1210 74 -72 54 -184 74 -1210 199 -1210 -192 64 22 16 -251 -53 -105 -1210 145 -353 180 -184 -151 79 -237 38 -51 28 -5 -1210 81 -194 159 -1210 -19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 44 E= 8.7e-016 0.159091 0.659091 0.022727 0.159091 0.340909 0.272727 0.113636 0.272727 0.272727 0.454545 0.000000 0.272727 0.318182 0.340909 0.000000 0.340909 0.022727 0.840909 0.113636 0.022727 0.431818 0.409091 0.068182 0.090909 0.568182 0.159091 0.045455 0.227273 0.000000 0.613636 0.022727 0.363636 0.113636 0.545455 0.295455 0.045455 0.272727 0.227273 0.159091 0.340909 0.363636 0.272727 0.136364 0.227273 0.090909 0.909091 0.000000 0.000000 0.568182 0.000000 0.000000 0.431818 0.159091 0.340909 0.068182 0.431818 0.000000 0.931818 0.000000 0.068182 0.409091 0.272727 0.272727 0.045455 0.181818 0.113636 0.000000 0.704545 0.022727 0.818182 0.068182 0.090909 0.454545 0.045455 0.318182 0.181818 0.318182 0.227273 0.000000 0.454545 0.068182 0.704545 0.000000 0.227273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACT][CAT][CTA]C[AC][AT][CT][CG][TAC][ACT]C[AT][TC]C[ACG]TC[AG][TAC][CT] -------------------------------------------------------------------------------- Time 15.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 28 llr = 320 E-value = 4.5e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :26245:83:145451311:4 pos.-specific C :12:31::2::1:31::1::: probability G a71832922a63433957564 matrix T ::1:11::4:321:1:21441 bits 2.1 * 1.9 * * 1.7 * * * * 1.5 * * * * Relative 1.3 * * * * * Entropy 1.0 * * ** * * * (16.5 bits) 0.8 ** * ** ** * * 0.6 ** * ** ** * * **** 0.4 **** ** ** ** ****** 0.2 ******** ************ 0.0 --------------------- Multilevel GGAGAAGATGGAAAAGGGGGA consensus A AGG GA TGGCG A TTG sequence C C T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7419 343 9.66e-10 AGAAAGATTT GGAGCAGAAGGTAAGGGGGGG GGTGGCGGGA 7683 253 4.46e-09 GTCAGCGGAG GGAGCGGAAGGGGAAGGGTGA GGTGACAAAT bd1815 69 4.36e-08 AGAGTCAGCT GGAACGGAGGGAAAAGAGGGA GAGAAAGAGC 6539 165 5.08e-08 GCCCAATGAC GGCAGAGAAGGAGCAGGGGTA GCCAACTTCG 23621 40 9.14e-08 GTGTAGGTGT GGAGGAGATGGTTAGGGGTTG TGTGTTGTGG 22451 360 1.05e-07 CTTTGGAGGT GGAGGAGACGTCGATGGGGGG CGACTTCTTC 261566 166 1.58e-07 ACGCAGGAGT GGCGAAGGCGTGACAGGGTGA TGTCAGGGTT 263492 160 4.31e-07 TTGGTGGAAT GATGAAGATGTAAGAGAGTTG CCTTCGCTAT 263491 160 4.31e-07 TTGGTGGAAT GATGAAGATGTAAGAGAGTTG CCTTCGCTAT 9449 89 4.84e-07 GATGGACGAC GGAGAGGACGGCGAGGAGAGG AGGAGCTCGG 4818 186 6.80e-07 GTAAAGAGAG GGGGCGGGGGGGGGAGGGTGA GTGGTGTTTG 21955 9 1.29e-06 TTTCGTTT GCAAAAGATGGAGCAGTGTGT CCCTTCTCTC 5897 148 1.57e-06 TCGTTTAGTA GAAGAGGAAGAGGAGGTGGGG TGATGATTGC 263010 327 1.74e-06 GGATCCCTTC GGAGAAGAGGTAAGTGTCGGG AGATGATATG 25810 53 2.11e-06 GGGTGTTTGG GGAGTGGATGATACCGGGGTG TTGTTGTTGT 23094 18 2.11e-06 GGAGGGACGA GGAGGAAGTGGGACGGAGGTA AATGTCGGAA 264293 396 4.34e-06 GTTGCGTGTT GGAGCTGATGGAACGAATGGA GAGATTGGTG 25547 262 4.72e-06 GTCAGGACTT GAGACAGAAGGAAAAGGAGTA CGAGGCAACG 7120 369 5.13e-06 GAAGTTAAAT GAAGGTGATGGGAGTGGTAGA AAGAGGGTAT 5410 128 5.13e-06 TCAGGCAGCG GGGAGTGAGGGGGGAGAGAGG GCGATAATGT 31993 111 5.13e-06 ACGAAGGATA GACGAAGACGGTGCCGGTGGT GGTCGGTGTG 269660 82 1.04e-05 ATCGAAGTGG TGTGCAGATGGCAAAGTGAGA GGAGTGCGGA 268817 303 1.12e-05 TTGTTGCGTC GGAGGTCGGGGTGAGGGGTTG GAGGTATGAG 36425 289 1.21e-05 TTGGGATGTG GGTGGCGACGAAACAGTCGGA AGGTGTAAAC 10078 332 1.30e-05 CGCGTTTGAT GCCGTCGGCGGAAAAGTGGTG CGAGACGCCG 24158 270 1.97e-05 AGACTGCGGT GGAGGAGTTGTTGGCGGTGTT CATGAGGAGT 9519 187 3.68e-05 TTTGAGTGAC GCAAACGAAGTGTACGGGTTA GTAGTTCAAG 25168 303 4.13e-05 AAGCGACACT GGCGAAGGAGGAAGAAAATTT GAGCTCGCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7419 9.7e-10 342_[+2]_137 7683 4.5e-09 252_[+2]_227 bd1815 4.4e-08 68_[+2]_411 6539 5.1e-08 164_[+2]_315 23621 9.1e-08 39_[+2]_440 22451 1.1e-07 359_[+2]_120 261566 1.6e-07 165_[+2]_314 263492 4.3e-07 159_[+2]_320 263491 4.3e-07 159_[+2]_320 9449 4.8e-07 88_[+2]_391 4818 6.8e-07 185_[+2]_294 21955 1.3e-06 8_[+2]_471 5897 1.6e-06 147_[+2]_332 263010 1.7e-06 326_[+2]_153 25810 2.1e-06 52_[+2]_427 23094 2.1e-06 17_[+2]_462 264293 4.3e-06 395_[+2]_84 25547 4.7e-06 261_[+2]_218 7120 5.1e-06 368_[+2]_111 5410 5.1e-06 127_[+2]_352 31993 5.1e-06 110_[+2]_369 269660 1e-05 81_[+2]_398 268817 1.1e-05 302_[+2]_177 36425 1.2e-05 288_[+2]_191 10078 1.3e-05 331_[+2]_148 24158 2e-05 269_[+2]_210 9519 3.7e-05 186_[+2]_293 25168 4.1e-05 302_[+2]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=28 7419 ( 343) GGAGCAGAAGGTAAGGGGGGG 1 7683 ( 253) GGAGCGGAAGGGGAAGGGTGA 1 bd1815 ( 69) GGAACGGAGGGAAAAGAGGGA 1 6539 ( 165) GGCAGAGAAGGAGCAGGGGTA 1 23621 ( 40) GGAGGAGATGGTTAGGGGTTG 1 22451 ( 360) GGAGGAGACGTCGATGGGGGG 1 261566 ( 166) GGCGAAGGCGTGACAGGGTGA 1 263492 ( 160) GATGAAGATGTAAGAGAGTTG 1 263491 ( 160) GATGAAGATGTAAGAGAGTTG 1 9449 ( 89) GGAGAGGACGGCGAGGAGAGG 1 4818 ( 186) GGGGCGGGGGGGGGAGGGTGA 1 21955 ( 9) GCAAAAGATGGAGCAGTGTGT 1 5897 ( 148) GAAGAGGAAGAGGAGGTGGGG 1 263010 ( 327) GGAGAAGAGGTAAGTGTCGGG 1 25810 ( 53) GGAGTGGATGATACCGGGGTG 1 23094 ( 18) GGAGGAAGTGGGACGGAGGTA 1 264293 ( 396) GGAGCTGATGGAACGAATGGA 1 25547 ( 262) GAGACAGAAGGAAAAGGAGTA 1 7120 ( 369) GAAGGTGATGGGAGTGGTAGA 1 5410 ( 128) GGGAGTGAGGGGGGAGAGAGG 1 31993 ( 111) GACGAAGACGGTGCCGGTGGT 1 269660 ( 82) TGTGCAGATGGCAAAGTGAGA 1 268817 ( 303) GGAGGTCGGGGTGAGGGGTTG 1 36425 ( 289) GGTGGCGACGAAACAGTCGGA 1 10078 ( 332) GCCGTCGGCGGAAAAGTGGTG 1 24158 ( 270) GGAGGAGTTGTTGGCGGTGTT 1 9519 ( 187) GCAAACGAAGTGTACGGGTTA 1 25168 ( 303) GGCGAAGGAGGAAGAAAATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 10.1634 E= 4.5e-010 -1145 -1145 198 -285 -29 -113 147 -1145 112 -39 -119 -85 -29 -1145 169 -1145 44 9 40 -185 103 -113 -19 -85 -288 -271 193 -1145 151 -1145 -19 -285 -7 -13 -45 47 -1145 -1145 203 -1145 -129 -1145 140 -5 58 -113 23 -27 103 -1145 69 -185 71 28 23 -1145 93 -72 3 -127 -188 -1145 193 -1145 12 -1145 103 -27 -188 -171 155 -85 -88 -1145 103 47 -1145 -1145 123 73 71 -1145 81 -85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 28 E= 4.5e-010 0.000000 0.000000 0.964286 0.035714 0.214286 0.107143 0.678571 0.000000 0.571429 0.178571 0.107143 0.142857 0.214286 0.000000 0.785714 0.000000 0.357143 0.250000 0.321429 0.071429 0.535714 0.107143 0.214286 0.142857 0.035714 0.035714 0.928571 0.000000 0.750000 0.000000 0.214286 0.035714 0.250000 0.214286 0.178571 0.357143 0.000000 0.000000 1.000000 0.000000 0.107143 0.000000 0.642857 0.250000 0.392857 0.107143 0.285714 0.214286 0.535714 0.000000 0.392857 0.071429 0.428571 0.285714 0.285714 0.000000 0.500000 0.142857 0.250000 0.107143 0.071429 0.000000 0.928571 0.000000 0.285714 0.000000 0.500000 0.214286 0.071429 0.071429 0.714286 0.142857 0.142857 0.000000 0.500000 0.357143 0.000000 0.000000 0.571429 0.428571 0.428571 0.000000 0.428571 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GA]A[GA][AGC][AG]G[AG][TAC]G[GT][AGT][AG][ACG][AG]G[GAT]G[GT][GT][AG] -------------------------------------------------------------------------------- Time 30.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 23 llr = 257 E-value = 1.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 11::::::::334::2 pos.-specific C :2::22:31:11:1:: probability G 9::a338:67:54:a4 matrix T :7a:4526337:28:4 bits 2.1 * 1.9 * * 1.7 * ** * 1.5 * ** * Relative 1.3 * ** * * ** Entropy 1.0 * ** * * ** (16.2 bits) 0.8 **** ** ** ** 0.6 **** ******* ** 0.4 **** ******* *** 0.2 **************** 0.0 ---------------- Multilevel GTTGTTGTGGTGATGG consensus GG CTTAAG T sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5897 212 1.17e-08 CTTGATGGCG GTTGTGGTGGTAGTGT CATGGTTTTG 5760 172 2.46e-08 CGGCTGTGCT GTTGCTGTGGTAGTGT TGTTGGCCGT 261566 200 5.41e-08 CAGGGTTGAT GTTGTCGCGGTGATGG CCACTGCGAG 21955 249 1.89e-07 TTTAGGCATT GTTGGTGTTGTCGTGG GCAGCCGTTG 10078 421 1.89e-07 GTGCGTGTGA GTTGTCGTTGTGATGA TGCGAGTTAA 268817 281 2.19e-07 TGTAGCGGTG GTTGGTGCTGTGTTGT TGCGTCGGAG 36425 166 2.87e-07 GGGGTTGAAC GATGTGGTGGTGGTGT TGGAGGTATC 25438 210 4.22e-07 CACTTCTTCA GTTGTTTTGGTAGTGA TACTGTCTGG 25810 141 6.89e-07 ATTGTGGATG GATGGGGCGGTGGTGG AGGTGGAAGC 31993 38 8.62e-07 TCCTGGAGAG GTTGTTGTCGTCATGG TTATTCGAGT 5093 297 1.19e-06 GCTCTGCCTC GCTGTTGTGTAGATGT CTGATGGTGT 9449 131 2.40e-06 CATCAATGAT GTTGTCGTTTAGATGA CATTTTGATG 4818 347 7.24e-06 ATGGTTGCGA GTTGCGGTTGTGCCGT GAGGTATCGA 23094 374 7.82e-06 ACAATCCAAT GCTGCTGCGGAAGCGG AAGGTGCACG 21679 53 8.43e-06 ACGGTCACGC GTTGGTGCTTTGGTCT GATGCCTATA 6539 345 9.08e-06 ATTACCTAAT GTTGAGGGGGTAATGG AAGGACAATA bd1815 40 9.77e-06 TAGGGTTAGG GTTGGCTCGTTATTGG CGAAGAGTCA 30193 301 1.05e-05 CGGTGTGATC GTTGCGTCGGCGTTGT TGGTGACGGT 9519 7 1.13e-05 TCTAGT GTTGCGGTGTCCATGA TGCGGTATTG 2194 63 1.30e-05 GTTCATTGAC GCTGGGTTTGAAGTGA TGTCACTGCG 23621 331 1.58e-05 CACAATCAAG ATTGTTGTGGAATCGG CGGGAGAGTG 25547 65 3.27e-05 TGACAAGAAA ATTGTTGCTTTGAAGG AAGAACACAA 4960 201 3.46e-05 TCTGTTCCGA GCCGGTGTCGAGATGT TGCGATTGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5897 1.2e-08 211_[+3]_273 5760 2.5e-08 171_[+3]_313 261566 5.4e-08 199_[+3]_285 21955 1.9e-07 248_[+3]_236 10078 1.9e-07 420_[+3]_64 268817 2.2e-07 280_[+3]_204 36425 2.9e-07 165_[+3]_319 25438 4.2e-07 209_[+3]_275 25810 6.9e-07 140_[+3]_344 31993 8.6e-07 37_[+3]_447 5093 1.2e-06 296_[+3]_188 9449 2.4e-06 130_[+3]_354 4818 7.2e-06 346_[+3]_138 23094 7.8e-06 373_[+3]_111 21679 8.4e-06 52_[+3]_432 6539 9.1e-06 344_[+3]_140 bd1815 9.8e-06 39_[+3]_445 30193 1e-05 300_[+3]_184 9519 1.1e-05 6_[+3]_478 2194 1.3e-05 62_[+3]_422 23621 1.6e-05 330_[+3]_154 25547 3.3e-05 64_[+3]_420 4960 3.5e-05 200_[+3]_284 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=23 5897 ( 212) GTTGTGGTGGTAGTGT 1 5760 ( 172) GTTGCTGTGGTAGTGT 1 261566 ( 200) GTTGTCGCGGTGATGG 1 21955 ( 249) GTTGGTGTTGTCGTGG 1 10078 ( 421) GTTGTCGTTGTGATGA 1 268817 ( 281) GTTGGTGCTGTGTTGT 1 36425 ( 166) GATGTGGTGGTGGTGT 1 25438 ( 210) GTTGTTTTGGTAGTGA 1 25810 ( 141) GATGGGGCGGTGGTGG 1 31993 ( 38) GTTGTTGTCGTCATGG 1 5093 ( 297) GCTGTTGTGTAGATGT 1 9449 ( 131) GTTGTCGTTTAGATGA 1 4818 ( 347) GTTGCGGTTGTGCCGT 1 23094 ( 374) GCTGCTGCGGAAGCGG 1 21679 ( 53) GTTGGTGCTTTGGTCT 1 6539 ( 345) GTTGAGGGGGTAATGG 1 bd1815 ( 40) GTTGGCTCGTTATTGG 1 30193 ( 301) GTTGCGTCGGCGTTGT 1 9519 ( 7) GTTGCGGTGTCCATGA 1 2194 ( 63) GCTGGGTTTGAAGTGA 1 23621 ( 331) ATTGTTGTGGAATCGG 1 25547 ( 65) ATTGTTGCTTTGAAGG 1 4960 ( 201) GCCGGTGTCGAGATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 21340 bayes= 10.2591 E= 1.9e-006 -159 -1117 190 -1117 -159 -43 -1117 152 -1117 -243 -1117 189 -1117 -1117 203 -1117 -259 -11 32 75 -1117 -43 51 89 -1117 -1117 176 -57 -1117 57 -249 124 -1117 -143 121 43 -1117 -1117 160 1 -1 -143 -1117 133 40 -85 109 -1117 57 -243 68 -57 -259 -85 -1117 168 -1117 -243 197 -1117 -27 -1117 68 60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 1.9e-006 0.086957 0.000000 0.913043 0.000000 0.086957 0.173913 0.000000 0.739130 0.000000 0.043478 0.000000 0.956522 0.000000 0.000000 1.000000 0.000000 0.043478 0.217391 0.304348 0.434783 0.000000 0.173913 0.347826 0.478261 0.000000 0.000000 0.826087 0.173913 0.000000 0.347826 0.043478 0.608696 0.000000 0.086957 0.565217 0.347826 0.000000 0.000000 0.739130 0.260870 0.260870 0.086957 0.000000 0.652174 0.347826 0.130435 0.521739 0.000000 0.391304 0.043478 0.391304 0.173913 0.043478 0.130435 0.000000 0.826087 0.000000 0.043478 0.956522 0.000000 0.217391 0.000000 0.391304 0.391304 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GTTG[TGC][TG]G[TC][GT][GT][TA][GA][AG]TG[GTA] -------------------------------------------------------------------------------- Time 46.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10078 8.11e-06 331_[+2(1.30e-05)]_68_\ [+3(1.89e-07)]_64 20754 1.05e-01 115_[+1(1.93e-05)]_364 21679 1.18e-03 52_[+3(8.43e-06)]_250_\ [+1(1.60e-05)]_161 2194 4.97e-03 62_[+3(1.30e-05)]_422 21955 3.12e-07 8_[+2(1.29e-06)]_81_[+1(5.07e-05)]_\ 117_[+3(1.89e-07)]_236 22451 5.16e-05 99_[+1(3.94e-05)]_239_\ [+2(1.05e-07)]_120 23094 2.92e-06 17_[+2(2.11e-06)]_151_\ [+2(5.46e-05)]_163_[+3(7.82e-06)]_51_[+1(8.85e-06)]_39 23621 8.79e-08 39_[+2(9.14e-08)]_123_\ [+1(2.32e-05)]_126_[+3(1.58e-05)]_129_[+1(2.09e-06)]_4 24044 3.16e-02 431_[+1(3.62e-05)]_48 24158 9.51e-04 269_[+2(1.97e-05)]_210 25168 2.01e-05 213_[+1(2.39e-08)]_68_\ [+2(4.13e-05)]_177 25438 3.29e-05 209_[+3(4.22e-07)]_252_\ [+1(3.35e-06)]_2 25547 1.19e-04 64_[+3(3.27e-05)]_153_\ [+1(6.47e-05)]_7_[+2(4.72e-06)]_218 25810 9.19e-06 52_[+2(2.11e-06)]_67_[+3(6.89e-07)]_\ 344 261566 2.98e-08 91_[+3(4.86e-06)]_58_[+2(1.58e-07)]_\ 13_[+3(5.41e-08)]_285 263010 9.19e-04 281_[+1(5.50e-05)]_24_\ [+2(1.74e-06)]_153 263491 3.62e-07 47_[+1(7.46e-08)]_7_[+1(1.45e-05)]_\ 63_[+2(4.31e-07)]_176_[+1(4.67e-05)]_123 263492 3.62e-07 47_[+1(7.46e-08)]_7_[+1(1.45e-05)]_\ 63_[+2(4.31e-07)]_176_[+1(4.67e-05)]_123 264293 1.24e-03 395_[+2(4.34e-06)]_29_\ [+1(2.78e-05)]_34 268817 3.11e-06 280_[+3(2.19e-07)]_6_[+2(1.12e-05)]_\ 146_[+1(6.47e-05)]_10 269660 1.79e-03 81_[+2(1.04e-05)]_364_\ [+1(2.32e-05)]_13 30193 3.24e-05 300_[+3(1.05e-05)]_149_\ [+1(2.03e-07)]_14 31993 6.93e-06 37_[+3(8.62e-07)]_57_[+2(5.13e-06)]_\ 328_[+1(8.85e-05)]_20 3436 5.48e-03 309_[+1(1.45e-06)]_82_\ [+1(9.80e-06)]_67 36425 4.93e-07 165_[+3(2.87e-07)]_36_\ [+2(9.09e-05)]_50_[+2(1.21e-05)]_109_[+1(5.82e-06)]_39_[+1(9.55e-05)]_1 37232 5.68e-05 241_[+1(7.20e-06)]_70_\ [+1(1.57e-08)]_147 3790 4.45e-03 421_[+1(5.73e-07)]_58 39741 3.49e-01 500 41650 1.14e-02 471_[+1(7.55e-07)]_8 4818 4.11e-07 140_[+2(2.71e-05)]_24_\ [+2(6.80e-07)]_85_[+1(3.35e-06)]_34_[+3(7.24e-06)]_138 4960 1.50e-03 200_[+3(3.46e-05)]_208_\ [+1(5.23e-06)]_55 5079 2.43e-02 479_[+1(4.69e-06)] 5093 5.55e-03 296_[+3(1.19e-06)]_188 5410 2.00e-06 1_[+1(5.50e-05)]_105_[+2(5.13e-06)]_\ 180_[+1(7.20e-06)]_121_[+1(2.39e-08)]_9 5760 3.64e-09 28_[+1(1.26e-08)]_122_\ [+3(2.46e-08)]_252_[+1(2.32e-05)]_40 5897 5.60e-08 147_[+2(1.57e-06)]_43_\ [+3(1.17e-08)]_17_[+2(1.72e-05)]_235 6539 4.80e-07 164_[+2(5.08e-08)]_159_\ [+3(9.08e-06)]_73_[+1(4.29e-05)]_12_[+3(3.27e-05)]_18 6642 6.08e-02 95_[+1(1.76e-05)]_384 7120 5.25e-04 12_[+1(5.82e-06)]_335_\ [+2(5.13e-06)]_111 7419 7.74e-08 342_[+2(9.66e-10)]_48_\ [+1(1.86e-06)]_68 7683 1.39e-07 120_[+1(5.73e-07)]_111_\ [+2(4.46e-09)]_186_[+1(3.94e-05)]_20 9449 1.19e-06 88_[+2(4.84e-07)]_21_[+3(2.40e-06)]_\ 236_[+1(4.67e-05)]_97 9519 6.54e-04 6_[+3(1.13e-05)]_164_[+2(3.68e-05)]_\ 293 bd1815 9.93e-09 39_[+3(9.77e-06)]_13_[+2(4.36e-08)]_\ 208_[+1(6.58e-07)]_182 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************