******************************************************************************** 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/59/59.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10052 1.0000 500 11432 1.0000 500 14106 1.0000 500 1539 1.0000 500 16169 1.0000 500 1666 1.0000 500 20678 1.0000 500 21043 1.0000 500 21428 1.0000 500 23274 1.0000 500 23471 1.0000 500 264121 1.0000 500 264387 1.0000 500 268615 1.0000 500 269004 1.0000 500 270141 1.0000 500 270253 1.0000 500 2892 1.0000 500 30004 1.0000 500 30972 1.0000 500 3202 1.0000 500 32860 1.0000 500 40348 1.0000 500 40725 1.0000 500 41005 1.0000 500 41898 1.0000 500 43076 1.0000 500 4875 1.0000 500 5021 1.0000 500 5078 1.0000 500 5996 1.0000 500 6010 1.0000 500 6028 1.0000 500 6253 1.0000 500 711 1.0000 500 7230 1.0000 500 8119 1.0000 500 bd1652 1.0000 500 bd2028 1.0000 500 bd794 1.0000 500 ThpsCp090 1.0000 500 ThpsCp123 1.0000 500 ThpsCt015 1.0000 500 ThpsCt022 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/59/59.seqs.fa -oc motifs/59 -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 0.273 C 0.223 G 0.226 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.223 G 0.226 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 44 llr = 418 E-value = 2.6e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 275:85283273521563272 pos.-specific C 6:19116127143285:2627 probability G 22112::11:2:23:::311: matrix T :14::32:32:4:41142::1 bits 2.2 1.9 1.7 * 1.5 * Relative 1.3 * Entropy 1.1 * * (13.7 bits) 0.9 ** * ** * * ** 0.6 ** ** ** ** *** *** 0.4 ******** **** *** *** 0.2 ******** **** *** *** 0.0 --------------------- Multilevel CAACAACATCACATCAAGCAC consensus A T TT A GTCG CTAA A sequence G C A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41898 479 1.11e-08 ACCGCAACAC ATACAACAACACAGCAAGCAC C 8119 467 2.76e-08 ATCGGTGGTT CACCATCACCGCAGCCAGCAC AAACACCTCC 40725 261 3.28e-08 GGGAAAACAT CAACCACATCATAACATGCAC CAGAAAGCAG 43076 229 1.21e-07 AACAACAATG CAACAACAACGCAGCAACAAA CGCAGGGACA bd1652 462 4.47e-07 CAGCACCAGC CAACAACAACCCACCATGCCA CCCAAAAAGA 20678 201 4.47e-07 CACTCTGATC CATCACCACCATGACAAACAA AGCAACACAA 270141 460 5.87e-07 CTTGCTACTA GTACATCATCACGCCCTACAC CACTAGCTAT 32860 187 8.73e-07 CGCAAACAAT CAACGCCAACAAAGTAAACAC ATCATGAGGT 30972 113 1.13e-06 TCACCACCAC CACCATCATCATCACCAGAGC TCTAATACAC 21428 337 1.45e-06 CATGCGTGTG GCTCAACAGCACATCCATCAC CCAAGCCAGC 3202 37 2.97e-06 TTTCTTGTTT CAACGAAAGCAAGGCCAACGC TGGAATCAGA 5078 433 3.74e-06 GTCATCAACT CAACAACACAGCTGCCTGAAC AGAACACCGC 1539 332 3.74e-06 ACTATCCTCT CAACATCAGCAACGCAAAGGA CGAGTGAGGA 264121 82 4.68e-06 AACCAAAATG AATGCACATCATCACCAGCAC CCTCGGCGAG 14106 7 4.68e-06 CTTCTG CATCATCTTCAACTCCTAAAC TTTCACTTGT 6028 475 5.22e-06 CGGCAGCGTT CATCATAAATACACAAAACAC ATTCA 40348 78 5.22e-06 ACAAACTTCT AAACATTATCATCTCATTCAT GCTCTCTCAT 270253 474 5.22e-06 CGGCAGCGTT CATCATAAATACACAAAACAC ATTCAA bd794 413 6.49e-06 TCACACACTC CATCATCAATCCATCAATACC AAAACAGAGA 7230 170 7.22e-06 TGCTTCCCTT GAACGAAACCAAGGCTAACAC TAATTTGTGC 268615 318 7.22e-06 CAAATCGTCC CGACATCCCCAACCAAAACAC TTCATCCGCC 16169 67 8.02e-06 CAAAGCTTGG AAACAATGTCAAGACATTCAC GCCATCCTAC 6010 424 8.91e-06 TGTGCTTAGG AGACAAAATAACACCCTGCCC TCCCGCGCTG 21043 459 8.91e-06 ATTATCTAGG CGTCCACATCATATCAACAGC GTTTAGAAAC ThpsCt022 362 9.88e-06 TTAACTTGTT GATCACTAACATATTCTTCAC CGTTTAAAAA ThpsCp090 220 9.88e-06 TTAACTTGTT GATCACTAACATATTCTTCAC CGTTTAAAAA 4875 445 9.88e-06 ACGTTGTCAT CAACATCATCCTATCCTATCC TGTCACATCA 30004 479 1.09e-05 ACAACATACG CAACAATAATGTTACAACCAC T 2892 315 1.48e-05 GATTGATCGT CAACGTTCGTACAGCCAGCCC GATTGGTGCT 6253 469 1.98e-05 GTATGTAACA AAACGTCCTCAACTCAACCAT TCCTACAGAC 5021 401 2.39e-05 AACACACGGA GAGCAACGTCGAGGCAAACAA CGAACCTCCC ThpsCt015 233 2.88e-05 ATCTTTCTAC GTACACCACAAAACCAAGGAC TTGCAAGTTT 711 180 2.88e-05 ATGATACAGC GTTCAGTATCACATCCAACAA ACAATCATCT 264387 339 3.45e-05 CACCGACGTC AGTCAAACGCACAACATGAAC ACAACTGTTG 1666 433 5.82e-05 GTGGTGCTGC AGACAACACAATCACCCACCC GTCGTCGATA ThpsCp123 270 6.33e-05 ACGTTGGATT ATTCAATATTCACGCCAGCGC GTGGGCCGTA 5996 278 8.11e-05 CACAATTGCA AAACAACACAATCTCTACGCA AGCAGAGGAA 23471 299 9.52e-05 CACATCAACA CAGTGTCACCGTCTCCATCAC TGTCAACGAC 41005 423 1.75e-04 GCTGTGAACG CGCGAACAATCTCTCCTGAAC AGATGGAGAC 10052 143 1.75e-04 ACGACGACGA CGACGACGACGTCGTCTGCCA GCCGCACCCG 23274 126 3.29e-04 AGAAAGATGG CATCAACAGAGTGTTTACAAA CATCCTCGTT bd2028 199 4.85e-04 TCATTTAGAT CATCAATATAAAAAATTTGAA GGAATATTTA 269004 235 4.85e-04 ATCGGCGATT GAGCAACCATGCATACAGAAT TTGTACGGAG 11432 462 5.84e-04 CGGTCCTTCT CATGAAAGACACGTCATCGAT ACACGTCAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41898 1.1e-08 478_[+1]_1 8119 2.8e-08 466_[+1]_13 40725 3.3e-08 260_[+1]_219 43076 1.2e-07 228_[+1]_251 bd1652 4.5e-07 461_[+1]_18 20678 4.5e-07 200_[+1]_279 270141 5.9e-07 459_[+1]_20 32860 8.7e-07 186_[+1]_293 30972 1.1e-06 112_[+1]_367 21428 1.4e-06 336_[+1]_143 3202 3e-06 36_[+1]_443 5078 3.7e-06 432_[+1]_47 1539 3.7e-06 331_[+1]_148 264121 4.7e-06 81_[+1]_398 14106 4.7e-06 6_[+1]_473 6028 5.2e-06 474_[+1]_5 40348 5.2e-06 77_[+1]_402 270253 5.2e-06 473_[+1]_6 bd794 6.5e-06 412_[+1]_67 7230 7.2e-06 169_[+1]_310 268615 7.2e-06 317_[+1]_162 16169 8e-06 66_[+1]_413 6010 8.9e-06 423_[+1]_56 21043 8.9e-06 458_[+1]_21 ThpsCt022 9.9e-06 361_[+1]_118 ThpsCp090 9.9e-06 219_[+1]_260 4875 9.9e-06 444_[+1]_35 30004 1.1e-05 478_[+1]_1 2892 1.5e-05 314_[+1]_165 6253 2e-05 468_[+1]_11 5021 2.4e-05 400_[+1]_79 ThpsCt015 2.9e-05 232_[+1]_247 711 2.9e-05 179_[+1]_300 264387 3.5e-05 338_[+1]_141 1666 5.8e-05 432_[+1]_47 ThpsCp123 6.3e-05 269_[+1]_210 5996 8.1e-05 277_[+1]_202 23471 9.5e-05 298_[+1]_181 41005 0.00018 422_[+1]_57 10052 0.00018 142_[+1]_337 23274 0.00033 125_[+1]_354 bd2028 0.00048 198_[+1]_281 269004 0.00048 234_[+1]_245 11432 0.00058 461_[+1]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=44 41898 ( 479) ATACAACAACACAGCAAGCAC 1 8119 ( 467) CACCATCACCGCAGCCAGCAC 1 40725 ( 261) CAACCACATCATAACATGCAC 1 43076 ( 229) CAACAACAACGCAGCAACAAA 1 bd1652 ( 462) CAACAACAACCCACCATGCCA 1 20678 ( 201) CATCACCACCATGACAAACAA 1 270141 ( 460) GTACATCATCACGCCCTACAC 1 32860 ( 187) CAACGCCAACAAAGTAAACAC 1 30972 ( 113) CACCATCATCATCACCAGAGC 1 21428 ( 337) GCTCAACAGCACATCCATCAC 1 3202 ( 37) CAACGAAAGCAAGGCCAACGC 1 5078 ( 433) CAACAACACAGCTGCCTGAAC 1 1539 ( 332) CAACATCAGCAACGCAAAGGA 1 264121 ( 82) AATGCACATCATCACCAGCAC 1 14106 ( 7) CATCATCTTCAACTCCTAAAC 1 6028 ( 475) CATCATAAATACACAAAACAC 1 40348 ( 78) AAACATTATCATCTCATTCAT 1 270253 ( 474) CATCATAAATACACAAAACAC 1 bd794 ( 413) CATCATCAATCCATCAATACC 1 7230 ( 170) GAACGAAACCAAGGCTAACAC 1 268615 ( 318) CGACATCCCCAACCAAAACAC 1 16169 ( 67) AAACAATGTCAAGACATTCAC 1 6010 ( 424) AGACAAAATAACACCCTGCCC 1 21043 ( 459) CGTCCACATCATATCAACAGC 1 ThpsCt022 ( 362) GATCACTAACATATTCTTCAC 1 ThpsCp090 ( 220) GATCACTAACATATTCTTCAC 1 4875 ( 445) CAACATCATCCTATCCTATCC 1 30004 ( 479) CAACAATAATGTTACAACCAC 1 2892 ( 315) CAACGTTCGTACAGCCAGCCC 1 6253 ( 469) AAACGTCCTCAACTCAACCAT 1 5021 ( 401) GAGCAACGTCGAGGCAAACAA 1 ThpsCt015 ( 233) GTACACCACAAAACCAAGGAC 1 711 ( 180) GTTCAGTATCACATCCAACAA 1 264387 ( 339) AGTCAAACGCACAACATGAAC 1 1666 ( 433) AGACAACACAATCACCCACCC 1 ThpsCp123 ( 270) ATTCAATATTCACGCCAGCGC 1 5996 ( 278) AAACAACACAATCTCTACGCA 1 23471 ( 299) CAGTGTCACCGTCTCCATCAC 1 41005 ( 423) CGCGAACAATCTCTCCTGAAC 1 10052 ( 143) CGACGACGACGTCGTCTGCCA 1 23274 ( 126) CATCAACAGAGTGTTTACAAA 1 bd2028 ( 199) CATCAATATAAAAAATTTGAA 1 269004 ( 235) GAGCAACCATGCATACAGAAT 1 11432 ( 462) CATGAAAGACACGTCATCGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 8.90388 E= 2.6e-015 -27 135 -14 -1210 137 -329 -51 -129 87 -171 -173 39 -1210 203 -173 -361 150 -171 -51 -1210 100 -97 -331 20 -78 151 -1210 -44 150 -97 -131 -361 22 -13 -73 29 -78 156 -1210 -61 132 -97 -14 -1210 0 70 -1210 39 81 41 -31 -261 -42 -49 27 39 -126 179 -1210 -129 73 103 -1210 -161 117 -329 -1210 39 22 -49 59 -61 -27 151 -99 -361 137 -30 -99 -1210 -27 161 -1210 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 44 E= 2.6e-015 0.227273 0.568182 0.204545 0.000000 0.704545 0.022727 0.159091 0.113636 0.500000 0.068182 0.068182 0.363636 0.000000 0.909091 0.068182 0.022727 0.772727 0.068182 0.159091 0.000000 0.545455 0.113636 0.022727 0.318182 0.159091 0.636364 0.000000 0.204545 0.772727 0.113636 0.090909 0.022727 0.318182 0.204545 0.136364 0.340909 0.159091 0.659091 0.000000 0.181818 0.681818 0.113636 0.204545 0.000000 0.272727 0.363636 0.000000 0.363636 0.477273 0.295455 0.181818 0.045455 0.204545 0.159091 0.272727 0.363636 0.113636 0.772727 0.000000 0.113636 0.454545 0.454545 0.000000 0.090909 0.613636 0.022727 0.000000 0.363636 0.318182 0.159091 0.340909 0.181818 0.227273 0.636364 0.113636 0.022727 0.704545 0.181818 0.113636 0.000000 0.227273 0.681818 0.000000 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CAG]A[AT]CA[AT][CT]A[TAC]C[AG][CTA][AC][TGA]C[AC][AT][GA][CA]A[CA] -------------------------------------------------------------------------------- Time 13.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 30 llr = 317 E-value = 2.4e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 293:21121:1:22:: pos.-specific C ::::52:51:12:432 probability G 81:a2:9::8228:27 matrix T :17:17:38267:561 bits 2.2 * 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 GATGCTGCTGTTGTTG consensus A A A T G CCC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6028 18 7.51e-09 ACCAGTCACT GATGCTGCTGGTGCCG TCTTTCGTTT 270253 17 7.51e-09 ACCAGTCACT GATGCTGCTGGTGCCG TCTTTCGTTT 5021 49 1.38e-08 ATGGGGTACG GATGATGTTGTTGTTG TTGTTGGATG 264387 122 2.86e-08 TCGCCGGTTT AATGATGCTGTTGCTG AAAGCGTCGT 41005 23 7.51e-08 GGATGGATAC GATGCTGCTGATGTGG CCAAGGGAGG 268615 95 2.79e-07 TGTTTGATTT GATGATGTTGTTGTTT CAATCTCATT 7230 88 5.25e-07 TAGGATCTTT GATGGTGCTGCTACTG CCGATGCCAG 10052 58 1.07e-06 AAGAAATGCC AAAGCTGCTGTCGATG ATGACACTGC 270141 193 1.18e-06 TGGTGGGGGA GAAGGTGCTGGTATTG TTTCACGGGG 1666 117 1.84e-06 GAAGGCAGAA GAAGCTGCTGCCGACG CTGCAAATAA 5996 59 2.27e-06 TTCTGTTCAA AAAGTTGTTGTTGCCG AGATTTGATG 41898 96 2.27e-06 CTTGGGATGA GATGCTGCAGTTGAGC GGCGACGGAG 264121 279 2.27e-06 GATGAATGCC GATGCTGATGTGATGG CACAGAAGGA 32860 33 2.53e-06 AGCCTCTTCG GGTGCTGCTTTTGCTC CTAGCACTTG 21428 113 4.57e-06 TGTGCATGTA AAAGATGTTGTCGTCG TAAGAAGCGG 3202 81 5.03e-06 TGTAACATGT GATGATGCCGTGGCTT CGACCGCCTA 20678 43 5.52e-06 TGGTGTGTTT GATGATGATGTGGTGT AGTGATGGGG 40725 87 7.31e-06 GATCCTTTCG GATGCTTCTGCTGCCC ATTAAGGGGG 711 481 1.58e-05 TGCTGAGTTC AATGCTGTATTGGTTG TCTG 30972 347 2.01e-05 AGGTGGGAGT GATGTCAATGGTGCTG TGAGTTCGTG 16169 306 2.01e-05 TTACATCTGG GATGACGTAGCTGTTC AAGTGAGTAT 8119 220 2.18e-05 GCTGGGGTGT GATGCTGAGTATGCTG GCTAGAGTGA bd2028 361 2.35e-05 CCAACTTTGG GTTGGTCTTGTTGTTG CAATCGCTAC 11432 400 2.35e-05 CCAACGAGGC GATGTCGCTTGTACCG CTCTCATCAT 2892 145 2.74e-05 TGCTTTCAAA GAAGTAGCTGTCGTTT AAAAGCCATT 6253 27 3.42e-05 CTGATAATTG ATTGCCGATTTTGTTG TTTGTGGTAA 6010 138 3.68e-05 TGGTGGAGGC GGTGGGGTTGTTGTGG GCGTGGAGGT 23274 301 3.95e-05 CGGATCCGAT GAAGCCAATGGTGTTC GTCATGTTGT 21043 367 5.23e-05 CTTCCACTGT GAAGGTGCCGACGACG GACGACGCTT 269004 145 6.39e-05 TCGCCTTGAA AATGCAGCTGTGAATC CTAAAGCAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6028 7.5e-09 17_[+2]_467 270253 7.5e-09 16_[+2]_468 5021 1.4e-08 48_[+2]_436 264387 2.9e-08 121_[+2]_363 41005 7.5e-08 22_[+2]_462 268615 2.8e-07 94_[+2]_390 7230 5.3e-07 87_[+2]_397 10052 1.1e-06 57_[+2]_427 270141 1.2e-06 192_[+2]_292 1666 1.8e-06 116_[+2]_368 5996 2.3e-06 58_[+2]_426 41898 2.3e-06 95_[+2]_389 264121 2.3e-06 278_[+2]_206 32860 2.5e-06 32_[+2]_452 21428 4.6e-06 112_[+2]_372 3202 5e-06 80_[+2]_404 20678 5.5e-06 42_[+2]_442 40725 7.3e-06 86_[+2]_398 711 1.6e-05 480_[+2]_4 30972 2e-05 346_[+2]_138 16169 2e-05 305_[+2]_179 8119 2.2e-05 219_[+2]_265 bd2028 2.4e-05 360_[+2]_124 11432 2.4e-05 399_[+2]_85 2892 2.7e-05 144_[+2]_340 6253 3.4e-05 26_[+2]_458 6010 3.7e-05 137_[+2]_347 23274 4e-05 300_[+2]_184 21043 5.2e-05 366_[+2]_118 269004 6.4e-05 144_[+2]_340 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=30 6028 ( 18) GATGCTGCTGGTGCCG 1 270253 ( 17) GATGCTGCTGGTGCCG 1 5021 ( 49) GATGATGTTGTTGTTG 1 264387 ( 122) AATGATGCTGTTGCTG 1 41005 ( 23) GATGCTGCTGATGTGG 1 268615 ( 95) GATGATGTTGTTGTTT 1 7230 ( 88) GATGGTGCTGCTACTG 1 10052 ( 58) AAAGCTGCTGTCGATG 1 270141 ( 193) GAAGGTGCTGGTATTG 1 1666 ( 117) GAAGCTGCTGCCGACG 1 5996 ( 59) AAAGTTGTTGTTGCCG 1 41898 ( 96) GATGCTGCAGTTGAGC 1 264121 ( 279) GATGCTGATGTGATGG 1 32860 ( 33) GGTGCTGCTTTTGCTC 1 21428 ( 113) AAAGATGTTGTCGTCG 1 3202 ( 81) GATGATGCCGTGGCTT 1 20678 ( 43) GATGATGATGTGGTGT 1 40725 ( 87) GATGCTTCTGCTGCCC 1 711 ( 481) AATGCTGTATTGGTTG 1 30972 ( 347) GATGTCAATGGTGCTG 1 16169 ( 306) GATGACGTAGCTGTTC 1 8119 ( 220) GATGCTGAGTATGCTG 1 bd2028 ( 361) GTTGGTCTTGTTGTTG 1 11432 ( 400) GATGTCGCTTGTACCG 1 2892 ( 145) GAAGTAGCTGTCGTTT 1 6253 ( 27) ATTGCCGATTTTGTTG 1 6010 ( 138) GGTGGGGTTGTTGTGG 1 23274 ( 301) GAAGCCAATGGTGTTC 1 21043 ( 367) GAAGGTGCCGACGACG 1 269004 ( 145) AATGCAGCTGTGAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 21340 bayes= 10.1473 E= 2.4e-011 -23 -1155 176 -1155 167 -1155 -176 -206 -3 -1155 -1155 140 -1155 -1155 215 -1155 -23 106 -44 -106 -203 -42 -276 140 -203 -274 194 -306 -45 126 -1155 -6 -145 -174 -276 153 -1155 -1155 188 -74 -145 -74 -18 103 -1155 -42 -44 126 -71 -1155 188 -1155 -71 72 -1155 75 -1155 26 -44 103 -1155 -16 156 -106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 30 E= 2.4e-011 0.233333 0.000000 0.766667 0.000000 0.866667 0.000000 0.066667 0.066667 0.266667 0.000000 0.000000 0.733333 0.000000 0.000000 1.000000 0.000000 0.233333 0.466667 0.166667 0.133333 0.066667 0.166667 0.033333 0.733333 0.066667 0.033333 0.866667 0.033333 0.200000 0.533333 0.000000 0.266667 0.100000 0.066667 0.033333 0.800000 0.000000 0.000000 0.833333 0.166667 0.100000 0.133333 0.200000 0.566667 0.000000 0.166667 0.166667 0.666667 0.166667 0.000000 0.833333 0.000000 0.166667 0.366667 0.000000 0.466667 0.000000 0.266667 0.166667 0.566667 0.000000 0.200000 0.666667 0.133333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]A[TA]G[CA]TG[CTA]TG[TG]TG[TC][TC][GC] -------------------------------------------------------------------------------- Time 27.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 24 llr = 279 E-value = 1.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 291:1:1:3:2:2::4:133: pos.-specific C 81394339236:3a419533a probability G ::2:36113::7::32:221: matrix T ::41225:37235:33:324: bits 2.2 * 1.9 * * 1.7 * * * 1.5 * * * * * Relative 1.3 ** * * * * * Entropy 1.1 ** * * * * * * (16.8 bits) 0.9 ** * * * * * * * 0.6 ** * * * *** * * * 0.4 ** * * * *** * * * 0.2 ******** ********* * 0.0 --------------------- Multilevel CATCCGTCGTCGTCCACCCTC consensus C GCC ACATC GT TAA sequence T T TG TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5996 429 1.19e-11 ATACGTCATC CATCGGTCGTCGTCGACCCTC TCCTTCGAGC 6028 124 2.05e-08 TTGGTAGACG CAGCCGTCTTAGTCTGCCCAC TAGGAGCCTT 270253 123 2.05e-08 TTGGTAGACG CAGCCGTCTTAGTCTGCCCAC TAGGAGCCTT 40348 216 3.27e-08 TCGTCGGCAT CATCGGCCGTCGTCGTCGTGC CGCCTACGCC 2892 417 1.69e-07 GCTTGTGAGT CACTCGCCTCCGCCGTCCATC CGAATCTCGT 41898 402 3.86e-07 CGCAAATCAC AATCCTTCGTCGACCACGCAC AGCCGCCGAC 264387 315 5.37e-07 AACTCAATGA CACCCCACCCCGACCACCGAC GTCAGTCAAA 4875 280 8.16e-07 TCCCGCCTAA AATCGTGCGTCGTCGGCCATC AACAAGATTG bd794 156 1.21e-06 TCTTCCCGCT CACCTCTCCTTTCCCACTCAC TGTCATCATA 6253 433 1.21e-06 CCGCTTCGCT CAACCGTCATAGCCTCCTTCC TCACTGTATG 14106 459 1.34e-06 ACAAAAACAA CAACCGTCACCGTCCACTCTT TGTTGACACC 32860 442 1.61e-06 TCCAGATCTG CACCAGCCGTCTTCCAGCAAC AATCTCAATC 3202 384 2.53e-06 CGTGGCTGCC CATTTGGCATCTTCTTCCACC ACAACGAACG 270141 346 3.01e-06 CGTTTTTTGC CAGCCGACGACGACGACGACC GCTCGTAATC 7230 203 3.28e-06 ATTTGTGCTT CATCGCTCATCTTCTTTCGCC TTCGCAGGTT 264121 55 3.56e-06 ATCTCCTCTC CATTCGCCACAGCCCTCAACC AAAATGAATG 23274 471 3.56e-06 CCCTGACGAG CCTCTGACCTCTACCTCTCTC TTGAGATTG 6010 241 6.24e-06 AGAGAGATGG TAGCGCTGGTCGTCGGCCGTC GGTTGATGAG 23471 399 7.26e-06 TAATTCGAAC CACCGTTGGTATTCTACTCGC ACAAAAGATT 30004 429 7.83e-06 ACACTCTTGA CACCTCTCTCTGCCGCCATTC ACCCGCACAG 10052 77 9.74e-06 GTCGATGATG ACACTGCCTTCGCCTGCGATC ATGTTGGTGG 30972 4 1.05e-05 CCA CCTCAGTCATCGTCATCATGC CAATCTCCAT 268615 351 1.38e-05 CATCCGCCGA AACCACTGCTTGCCCACCTCC TTCAGTGTAT bd1652 172 1.80e-05 TTGCTTCTAG CATCCTCCTCTTGCCTCTGTC ATTGGTTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5996 1.2e-11 428_[+3]_51 6028 2e-08 123_[+3]_356 270253 2e-08 122_[+3]_357 40348 3.3e-08 215_[+3]_264 2892 1.7e-07 416_[+3]_63 41898 3.9e-07 401_[+3]_78 264387 5.4e-07 314_[+3]_165 4875 8.2e-07 279_[+3]_200 bd794 1.2e-06 155_[+3]_324 6253 1.2e-06 432_[+3]_47 14106 1.3e-06 458_[+3]_21 32860 1.6e-06 441_[+3]_38 3202 2.5e-06 383_[+3]_96 270141 3e-06 345_[+3]_134 7230 3.3e-06 202_[+3]_277 264121 3.6e-06 54_[+3]_425 23274 3.6e-06 470_[+3]_9 6010 6.2e-06 240_[+3]_239 23471 7.3e-06 398_[+3]_81 30004 7.8e-06 428_[+3]_51 10052 9.7e-06 76_[+3]_403 30972 1e-05 3_[+3]_476 268615 1.4e-05 350_[+3]_129 bd1652 1.8e-05 171_[+3]_308 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=24 5996 ( 429) CATCGGTCGTCGTCGACCCTC 1 6028 ( 124) CAGCCGTCTTAGTCTGCCCAC 1 270253 ( 123) CAGCCGTCTTAGTCTGCCCAC 1 40348 ( 216) CATCGGCCGTCGTCGTCGTGC 1 2892 ( 417) CACTCGCCTCCGCCGTCCATC 1 41898 ( 402) AATCCTTCGTCGACCACGCAC 1 264387 ( 315) CACCCCACCCCGACCACCGAC 1 4875 ( 280) AATCGTGCGTCGTCGGCCATC 1 bd794 ( 156) CACCTCTCCTTTCCCACTCAC 1 6253 ( 433) CAACCGTCATAGCCTCCTTCC 1 14106 ( 459) CAACCGTCACCGTCCACTCTT 1 32860 ( 442) CACCAGCCGTCTTCCAGCAAC 1 3202 ( 384) CATTTGGCATCTTCTTCCACC 1 270141 ( 346) CAGCCGACGACGACGACGACC 1 7230 ( 203) CATCGCTCATCTTCTTTCGCC 1 264121 ( 55) CATTCGCCACAGCCCTCAACC 1 23274 ( 471) CCTCTGACCTCTACCTCTCTC 1 6010 ( 241) TAGCGCTGGTCGTCGGCCGTC 1 23471 ( 399) CACCGTTGGTATTCTACTCGC 1 30004 ( 429) CACCTCTCTCTGCCGCCATTC 1 10052 ( 77) ACACTGCCTTCGCCTGCGATC 1 30972 ( 4) CCTCAGTCATCGTCATCATGC 1 268615 ( 351) AACCACTGCTTGCCCACCTCC 1 bd1652 ( 172) CATCCTCCTCTTGCCTCTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 10.2276 E= 1.4e-006 -71 183 -1123 -273 168 -84 -1123 -1123 -113 39 -44 58 -1123 197 -1123 -115 -113 90 15 -42 -1123 16 137 -74 -113 16 -144 96 -1123 197 -85 -1123 -13 -42 56 -15 -271 16 -1123 135 -39 149 -1123 -74 -1123 -1123 165 7 -71 39 -244 85 -1123 216 -1123 -1123 -271 75 37 7 46 -142 -12 26 -1123 204 -244 -273 -113 104 -44 -15 9 58 -44 -42 -13 16 -85 43 -1123 210 -1123 -273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 1.4e-006 0.166667 0.791667 0.000000 0.041667 0.875000 0.125000 0.000000 0.000000 0.125000 0.291667 0.166667 0.416667 0.000000 0.875000 0.000000 0.125000 0.125000 0.416667 0.250000 0.208333 0.000000 0.250000 0.583333 0.166667 0.125000 0.250000 0.083333 0.541667 0.000000 0.875000 0.125000 0.000000 0.250000 0.166667 0.333333 0.250000 0.041667 0.250000 0.000000 0.708333 0.208333 0.625000 0.000000 0.166667 0.000000 0.000000 0.708333 0.291667 0.166667 0.291667 0.041667 0.500000 0.000000 1.000000 0.000000 0.000000 0.041667 0.375000 0.291667 0.291667 0.375000 0.083333 0.208333 0.333333 0.000000 0.916667 0.041667 0.041667 0.125000 0.458333 0.166667 0.250000 0.291667 0.333333 0.166667 0.208333 0.250000 0.250000 0.125000 0.375000 0.000000 0.958333 0.000000 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[TC]C[CGT][GC][TC]C[GAT][TC][CA][GT][TC]C[CGT][ATG]C[CT][CAT][TAC]C -------------------------------------------------------------------------------- Time 40.43 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10052 2.65e-05 57_[+2(1.07e-06)]_3_[+3(9.74e-06)]_\ 403 11432 5.79e-02 399_[+2(2.35e-05)]_85 14106 1.12e-04 6_[+1(4.68e-06)]_431_[+3(1.34e-06)]_\ 21 1539 5.60e-03 331_[+1(3.74e-06)]_148 16169 1.92e-04 66_[+1(8.02e-06)]_218_\ [+2(2.01e-05)]_179 1666 3.42e-04 116_[+2(1.84e-06)]_300_\ [+1(5.82e-05)]_47 20678 3.50e-05 42_[+2(5.52e-06)]_142_\ [+1(4.47e-07)]_279 21043 5.49e-03 366_[+2(5.23e-05)]_76_\ [+1(8.91e-06)]_21 21428 9.04e-05 112_[+2(4.57e-06)]_208_\ [+1(1.45e-06)]_143 23274 4.19e-04 300_[+2(3.95e-05)]_154_\ [+3(3.56e-06)]_9 23471 6.10e-03 298_[+1(9.52e-05)]_79_\ [+3(7.26e-06)]_81 264121 8.70e-07 54_[+3(3.56e-06)]_6_[+1(4.68e-06)]_\ 176_[+2(2.27e-06)]_206 264387 1.77e-08 121_[+2(2.86e-08)]_177_\ [+3(5.37e-07)]_3_[+1(3.45e-05)]_54_[+3(5.49e-05)]_66 268615 6.57e-07 94_[+2(2.79e-07)]_207_\ [+1(7.22e-06)]_12_[+3(1.38e-05)]_129 269004 7.03e-02 144_[+2(6.39e-05)]_340 270141 6.26e-08 192_[+2(1.18e-06)]_137_\ [+3(3.01e-06)]_93_[+1(5.87e-07)]_20 270253 4.32e-11 16_[+2(7.51e-09)]_59_[+3(3.53e-05)]_\ 10_[+3(2.05e-08)]_330_[+1(5.22e-06)]_6 2892 1.47e-06 144_[+2(2.74e-05)]_154_\ [+1(1.48e-05)]_81_[+3(1.69e-07)]_63 30004 5.86e-04 428_[+3(7.83e-06)]_29_\ [+1(1.09e-05)]_1 30972 4.50e-06 3_[+3(1.05e-05)]_88_[+1(1.13e-06)]_\ 213_[+2(2.01e-05)]_138 3202 8.71e-07 36_[+1(2.97e-06)]_23_[+2(5.03e-06)]_\ 287_[+3(2.53e-06)]_96 32860 1.02e-07 32_[+2(2.53e-06)]_138_\ [+1(8.73e-07)]_187_[+1(2.88e-05)]_26_[+3(1.61e-06)]_38 40348 3.80e-06 77_[+1(5.22e-06)]_117_\ [+3(3.27e-08)]_264 40725 3.21e-06 86_[+2(7.31e-06)]_158_\ [+1(3.28e-08)]_219 41005 2.45e-04 22_[+2(7.51e-08)]_323_\ [+2(4.56e-05)]_123 41898 4.45e-10 95_[+2(2.27e-06)]_290_\ [+3(3.86e-07)]_13_[+1(5.82e-06)]_22_[+1(1.11e-08)]_1 43076 2.03e-03 186_[+1(5.22e-06)]_21_\ [+1(1.21e-07)]_2_[+1(6.33e-05)]_9_[+1(5.35e-05)]_198 4875 1.74e-04 279_[+3(8.16e-07)]_144_\ [+1(9.88e-06)]_35 5021 1.05e-05 48_[+2(1.38e-08)]_6_[+2(4.88e-05)]_\ 21_[+2(5.23e-05)]_277_[+1(2.39e-05)]_79 5078 2.41e-02 432_[+1(3.74e-06)]_47 5996 1.08e-10 58_[+2(2.27e-06)]_203_\ [+1(8.11e-05)]_130_[+3(1.19e-11)]_51 6010 3.01e-05 137_[+2(3.68e-05)]_87_\ [+3(6.24e-06)]_162_[+1(8.91e-06)]_2_[+3(7.45e-05)]_33 6028 4.32e-11 17_[+2(7.51e-09)]_59_[+3(3.53e-05)]_\ 10_[+3(2.05e-08)]_330_[+1(5.22e-06)]_5 6253 1.35e-05 26_[+2(3.42e-05)]_390_\ [+3(1.21e-06)]_15_[+1(1.98e-05)]_11 711 8.25e-04 179_[+1(2.88e-05)]_280_\ [+2(1.58e-05)]_4 7230 3.18e-07 87_[+2(5.25e-07)]_66_[+1(7.22e-06)]_\ 12_[+3(3.28e-06)]_277 8119 8.57e-06 219_[+2(2.18e-05)]_231_\ [+1(2.76e-08)]_13 bd1652 3.38e-05 171_[+3(1.80e-05)]_269_\ [+1(4.47e-07)]_18 bd2028 5.97e-02 360_[+2(2.35e-05)]_124 bd794 3.58e-05 155_[+3(1.21e-06)]_172_\ [+1(8.11e-05)]_43_[+1(6.49e-06)]_67 ThpsCp090 7.31e-02 219_[+1(9.88e-06)]_260 ThpsCp123 2.67e-01 269_[+1(6.33e-05)]_210 ThpsCt015 1.58e-01 232_[+1(2.88e-05)]_247 ThpsCt022 8.71e-02 361_[+1(9.88e-06)]_118 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************