******************************************************************************** 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/222/222.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 19913 1.0000 500 20887 1.0000 500 21837 1.0000 500 22508 1.0000 500 23315 1.0000 500 23539 1.0000 500 23922 1.0000 500 24288 1.0000 500 24550 1.0000 500 24746 1.0000 500 25639 1.0000 500 261893 1.0000 500 263266 1.0000 500 263801 1.0000 500 26560 1.0000 500 268500 1.0000 500 269120 1.0000 500 270273 1.0000 500 270310 1.0000 500 32577 1.0000 500 38646 1.0000 500 41953 1.0000 500 42624 1.0000 500 6341 1.0000 500 7789 1.0000 500 8502 1.0000 500 8519 1.0000 500 8868 1.0000 500 9458 1.0000 500 bd863 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/222/222.seqs.fa -oc motifs/222 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.237 G 0.237 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.237 G 0.237 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 23 llr = 257 E-value = 1.6e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :61:27613a4:5::a pos.-specific C 922971347:69289: probability G ::4::2:2:::::1:: matrix T :23:::13:::131:: bits 2.1 1.9 * 1.7 * * 1.5 * * * * ** Relative 1.2 * * * * ** Entropy 1.0 * ** **** *** (16.1 bits) 0.8 * ** **** *** 0.6 ** **** **** *** 0.4 ** **** **** *** 0.2 **************** 0.0 ---------------- Multilevel CAGCCAACCACCACCA consensus CT A CTA A T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263266 456 5.96e-10 CTCTACCTAC CAGCCAATCACCACCA ACCCCACTCC 20887 475 1.49e-08 CCAAAGCAAA CCGCCACCCACCACCA TCACACCACC 38646 394 8.54e-08 CCATCAACAG CAGCCCATCAACTCCA TGAGCCATCA 25639 463 1.12e-07 CTACGCTACA CATCCAATAAACTCCA CCTTTCATCT 8519 478 1.45e-07 AAAAGAGATC CTTCCAATCACCCCCA CGCTAGA 8502 478 1.45e-07 AAAAGAGATC CTTCCAATCACCCCCA CGCTAGA 22508 448 3.37e-07 ATATAGACTT CCGCCAACCAACTTCA ACACACTCAC 8868 417 7.17e-07 GGAGGACACA CTTCCAACCAACAGCA GTCCGAAGTA 23315 320 7.17e-07 GTCGACAGCA CTTCCAACCAACAGCA GTCCGAAGTA bd863 325 1.44e-06 CTCCTCCTTT CAGCAACAAACCTCCA CCTCAATCGT 270310 443 3.56e-06 GCGTCACTCC CAACCATCAACCATCA ACAATCAACC 270273 225 3.56e-06 TCTCCTACCA AAGCAAAGCACCTCCA AAAGTCGTTG 19913 442 3.56e-06 GCGTCACTCC CAACCATCAACCATCA ACAATCAACC 32577 198 3.88e-06 CAAACTTCTC CACCATAGCAACACCA CGAGAGAAAA 23922 317 4.23e-06 ACCGTCAACT CCCCACAACAACACCA TCGACAGTTG 24550 483 5.86e-06 CTCTGTGACA CACCCGCTAACTACCA CC 23539 458 6.35e-06 ACCGGCCTCC CACCGCCGCACCACCA TTCAAATAGA 41953 303 8.67e-06 CGAGAAACGT CAACAAAGCAACACGA GAACATTCTA 9458 341 1.56e-05 CTCCCTCCGC CCTCCGCCCCACCCCA CACACCAAGT 268500 392 2.51e-05 ACTGGATTGA CAGCCATCGAAATCCA CACATCGTTC 269120 458 2.87e-05 CGTGCAAACG CAGCCGCAAACCCCAA CACACCTCTC 263801 142 3.70e-05 CTCTTTGATG CCGTCAACCACTGCCA TCGTTGTTGA 7789 445 3.94e-05 CAATTTGCTG GACACGATCACCTCCA CGACCACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263266 6e-10 455_[+1]_29 20887 1.5e-08 474_[+1]_10 38646 8.5e-08 393_[+1]_91 25639 1.1e-07 462_[+1]_22 8519 1.5e-07 477_[+1]_7 8502 1.5e-07 477_[+1]_7 22508 3.4e-07 447_[+1]_37 8868 7.2e-07 416_[+1]_68 23315 7.2e-07 319_[+1]_165 bd863 1.4e-06 324_[+1]_160 270310 3.6e-06 442_[+1]_42 270273 3.6e-06 224_[+1]_260 19913 3.6e-06 441_[+1]_43 32577 3.9e-06 197_[+1]_287 23922 4.2e-06 316_[+1]_168 24550 5.9e-06 482_[+1]_2 23539 6.4e-06 457_[+1]_27 41953 8.7e-06 302_[+1]_182 9458 1.6e-05 340_[+1]_144 268500 2.5e-05 391_[+1]_93 269120 2.9e-05 457_[+1]_27 263801 3.7e-05 141_[+1]_343 7789 3.9e-05 444_[+1]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=23 263266 ( 456) CAGCCAATCACCACCA 1 20887 ( 475) CCGCCACCCACCACCA 1 38646 ( 394) CAGCCCATCAACTCCA 1 25639 ( 463) CATCCAATAAACTCCA 1 8519 ( 478) CTTCCAATCACCCCCA 1 8502 ( 478) CTTCCAATCACCCCCA 1 22508 ( 448) CCGCCAACCAACTTCA 1 8868 ( 417) CTTCCAACCAACAGCA 1 23315 ( 320) CTTCCAACCAACAGCA 1 bd863 ( 325) CAGCAACAAACCTCCA 1 270310 ( 443) CAACCATCAACCATCA 1 270273 ( 225) AAGCAAAGCACCTCCA 1 19913 ( 442) CAACCATCAACCATCA 1 32577 ( 198) CACCATAGCAACACCA 1 23922 ( 317) CCCCACAACAACACCA 1 24550 ( 483) CACCCGCTAACTACCA 1 23539 ( 458) CACCGCCGCACCACCA 1 41953 ( 303) CAACAAAGCAACACGA 1 9458 ( 341) CCTCCGCCCCACCCCA 1 268500 ( 392) CAGCCATCGAAATCCA 1 269120 ( 458) CAGCCGCAAACCCCAA 1 263801 ( 142) CCGTCAACCACTGCCA 1 7789 ( 445) GACACGATCACCTCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 9.70599 E= 1.6e-012 -259 194 -244 -1117 121 -13 -1117 -60 -101 -13 72 -1 -259 194 -1117 -259 -27 164 -244 -1117 131 -86 -45 -259 121 14 -1117 -101 -101 72 -45 21 -1 155 -244 -1117 186 -245 -1117 -1117 73 125 -1117 -1117 -259 187 -1117 -159 86 -45 -244 21 -1117 172 -145 -101 -259 194 -244 -1117 193 -1117 -1117 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 1.6e-012 0.043478 0.913043 0.043478 0.000000 0.608696 0.217391 0.000000 0.173913 0.130435 0.217391 0.391304 0.260870 0.043478 0.913043 0.000000 0.043478 0.217391 0.739130 0.043478 0.000000 0.652174 0.130435 0.173913 0.043478 0.608696 0.260870 0.000000 0.130435 0.130435 0.391304 0.173913 0.304348 0.260870 0.695652 0.043478 0.000000 0.956522 0.043478 0.000000 0.000000 0.434783 0.565217 0.000000 0.000000 0.043478 0.869565 0.000000 0.086957 0.478261 0.173913 0.043478 0.304348 0.000000 0.782609 0.086957 0.130435 0.043478 0.913043 0.043478 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][GTC]C[CA]A[AC][CT][CA]A[CA]C[AT]CCA -------------------------------------------------------------------------------- Time 9.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 23 llr = 275 E-value = 1.1e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::12::::::3::3322::1: pos.-specific C ::::2:3:::4::::2:::16 probability G 722541713a:3735641753 matrix T 377348:97:37241:49331 bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.2 * * * * Entropy 1.0 ** * *** * ** (17.3 bits) 0.8 *** ***** ** ** * 0.6 **** ***** ** * ** * 0.4 ********** ******** * 0.2 ********************* 0.0 --------------------- Multilevel GTTGGTGTTGCTGTGGGTGGC consensus TG TT C G TGTAA T TTG sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263266 88 5.58e-09 TGTTGGATGG GTTGGGGTGGATGGGGGTGGC GCAGATGCAG 270273 26 1.18e-08 TGCACGTTTG TTTGGTGTTGTTGGAGTTGAC GGGGATATTA 26560 159 4.52e-08 GGATTTCGCT GTTTCTCTTGATTTGGTTGTC GGAGGGAGAT 22508 97 6.55e-08 AGAATCGTTT GTGGTTCTGGTGGTGGGTGTG GTTGGCACTT 270310 73 1.85e-07 AAGATAGGGT GTTTTTCTTGTTTTAGATTGC ACTGTGAATG 19913 72 1.85e-07 AAGATAGGGT GTTTTTCTTGTTTTAGATTGC ACTGTGAATG 24746 362 2.30e-07 TGTTGCAATC GTTGTTGTTGAGGTAGTTCTG TGCACCAAGT 23922 25 3.16e-07 AAGCGAGGCG GTGTGTGTGGCGGAGGGTTGT GGCTAGCATT 6341 346 4.76e-07 CTTGAAGGTA GTTGTTGTGGAGGACCTTGGG ATCAGAAGAC 25639 113 5.25e-07 ATTATGTTGG GAAATTCTTGCTGAGGGTGGC ATGATGGAGT 24550 383 6.39e-07 GCGGGAAGGC GTTTGTGTGGCTCTGCTTGCC TCCACGTTGC 8519 331 1.35e-06 CATTTAATTT TGAAGTGTTGCTGGGAGTTGC ATCAAGATGT 8502 332 1.47e-06 CTTACAATTT TGAAGTGTTGCTGAGAGTTGC ATCAAGTGTA 7789 268 1.47e-06 GACAGTGCGT TTTGCTGTTGTTGGAGGCTGG TGGGTTGCAG 42624 388 1.47e-06 TGTGTGGCAC GGGTGTGTTGTGTTGCGTGTG CACGTGTCGC 23539 274 1.61e-06 ATATTGAAGA GTTGGGTTTGGTGGAGGTGGC CTCCCGATAC 9458 267 4.35e-06 CGCGTTCTCT GTTGCTCTTGTGGTGTGGGAC TGGTAGCAAA 8868 293 4.35e-06 AAACTCTCTT GTGTTAATGGCTGGAGTTGGC GGCTGCGTCT 268500 81 4.71e-06 CATTTGCAGT TGTGATGTTGATGGGAATGAC GATGCACGTC 21837 216 5.09e-06 TGGATTCGTT GTTGCTGCTGCTGTTCTTGTT TTGTGCGTTT 24288 95 7.41e-06 ATGACGGGTG GTTTGTGGGGAGGAGATGGTG CATGACGATG 261893 212 7.97e-06 ATCCATTTCT GTTATTGTGGCATATGATGTG AGCGTTTGAT 263801 107 2.21e-05 GACGGCGGTA TGTGTCGGTGCTGATGTTGCC CCTGCTCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263266 5.6e-09 87_[+2]_392 270273 1.2e-08 25_[+2]_454 26560 4.5e-08 158_[+2]_321 22508 6.5e-08 96_[+2]_383 270310 1.9e-07 72_[+2]_407 19913 1.9e-07 71_[+2]_408 24746 2.3e-07 361_[+2]_118 23922 3.2e-07 24_[+2]_455 6341 4.8e-07 345_[+2]_134 25639 5.3e-07 112_[+2]_367 24550 6.4e-07 382_[+2]_97 8519 1.3e-06 330_[+2]_149 8502 1.5e-06 331_[+2]_148 7789 1.5e-06 267_[+2]_212 42624 1.5e-06 387_[+2]_92 23539 1.6e-06 273_[+2]_206 9458 4.4e-06 266_[+2]_213 8868 4.4e-06 292_[+2]_187 268500 4.7e-06 80_[+2]_399 21837 5.1e-06 215_[+2]_264 24288 7.4e-06 94_[+2]_385 261893 8e-06 211_[+2]_268 263801 2.2e-05 106_[+2]_373 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=23 263266 ( 88) GTTGGGGTGGATGGGGGTGGC 1 270273 ( 26) TTTGGTGTTGTTGGAGTTGAC 1 26560 ( 159) GTTTCTCTTGATTTGGTTGTC 1 22508 ( 97) GTGGTTCTGGTGGTGGGTGTG 1 270310 ( 73) GTTTTTCTTGTTTTAGATTGC 1 19913 ( 72) GTTTTTCTTGTTTTAGATTGC 1 24746 ( 362) GTTGTTGTTGAGGTAGTTCTG 1 23922 ( 25) GTGTGTGTGGCGGAGGGTTGT 1 6341 ( 346) GTTGTTGTGGAGGACCTTGGG 1 25639 ( 113) GAAATTCTTGCTGAGGGTGGC 1 24550 ( 383) GTTTGTGTGGCTCTGCTTGCC 1 8519 ( 331) TGAAGTGTTGCTGGGAGTTGC 1 8502 ( 332) TGAAGTGTTGCTGAGAGTTGC 1 7789 ( 268) TTTGCTGTTGTTGGAGGCTGG 1 42624 ( 388) GGGTGTGTTGTGTTGCGTGTG 1 23539 ( 274) GTTGGGTTTGGTGGAGGTGGC 1 9458 ( 267) GTTGCTCTTGTGGTGTGGGAC 1 8868 ( 293) GTGTTAATGGCTGGAGTTGGC 1 268500 ( 81) TGTGATGTTGATGGGAATGAC 1 21837 ( 216) GTTGCTGCTGCTGTTCTTGTT 1 24288 ( 95) GTTTGTGGGGAGGAGATGGTG 1 261893 ( 212) GTTATTGTGGCATATGATGTG 1 263801 ( 107) TGTGTCGGTGCTGATGTTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.69102 E= 1.1e-008 -1117 -1117 164 -1 -259 -1117 -13 149 -101 -1117 -45 140 -59 -1117 101 40 -259 -45 72 57 -259 -245 -145 165 -259 14 146 -259 -1117 -245 -145 173 -1117 -1117 55 131 -1117 -1117 208 -1117 -1 72 -244 21 -259 -1117 36 131 -1117 -245 164 -27 21 -1117 36 57 21 -245 114 -101 -59 -45 136 -259 -59 -1117 87 57 -1117 -245 -145 173 -1117 -245 155 -1 -101 -145 101 21 -1117 136 36 -159 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 1.1e-008 0.000000 0.000000 0.739130 0.260870 0.043478 0.000000 0.217391 0.739130 0.130435 0.000000 0.173913 0.695652 0.173913 0.000000 0.478261 0.347826 0.043478 0.173913 0.391304 0.391304 0.043478 0.043478 0.086957 0.826087 0.043478 0.260870 0.652174 0.043478 0.000000 0.043478 0.086957 0.869565 0.000000 0.000000 0.347826 0.652174 0.000000 0.000000 1.000000 0.000000 0.260870 0.391304 0.043478 0.304348 0.043478 0.000000 0.304348 0.652174 0.000000 0.043478 0.739130 0.217391 0.304348 0.000000 0.304348 0.391304 0.304348 0.043478 0.521739 0.130435 0.173913 0.173913 0.608696 0.043478 0.173913 0.000000 0.434783 0.391304 0.000000 0.043478 0.086957 0.869565 0.000000 0.043478 0.695652 0.260870 0.130435 0.086957 0.478261 0.304348 0.000000 0.608696 0.304348 0.086957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][TG]T[GT][GT]T[GC]T[TG]G[CTA][TG][GT][TAG][GA]G[GT]T[GT][GT][CG] -------------------------------------------------------------------------------- Time 17.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 14 llr = 196 E-value = 8.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :32:3:1::::1:321532:3 pos.-specific C 92:6731861978169335a1 probability G 11:1:11:4:111:::131:6 matrix T :484:672:9:1162:111:: bits 2.1 * 1.9 * 1.7 * * * * 1.5 * ** * * Relative 1.2 * * * * ** * * Entropy 1.0 * * * **** * * * (20.2 bits) 0.8 * **** ****** * ** 0.6 * ************** ** 0.4 * ************** ** 0.2 ***************** *** 0.0 --------------------- Multilevel CTTCCTTCCTCCCTCCAACCG consensus AATAC TG AA CCA A sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 270310 415 5.28e-11 CCCTTACGAT CTTTCTTCCTCCCTCCACGCG TCACTCCCAA 19913 414 5.28e-11 CCCTTACGAT CTTTCTTCCTCCCTCCACGCG TCACTCCCAA 8519 392 7.70e-09 TGTAAAACAG CTTCATTTCTCCCTACGGCCG ATGAACAAAC 8502 392 7.70e-09 TGTAAAACGA CTTCATTTCTCCCTACGGCCG ATGAACAAAC 38646 32 6.66e-08 AGATGTTTAC CAACCTTCGTCCTTTCAAACG ATCAGAAGGG 270273 304 6.66e-08 AGATGTTTAC CAACCTTCGTCCTTTCAAACG ATCAGAAGGG 261893 138 2.55e-07 GCGTAGGTAC CATTCCTCGTGCCACCTCCCA CCCGTCCAAT 9458 319 3.53e-07 TTTAACGACC CATCCCGCCCGCCTCCCTCCG CCCTCCGCCC 41953 23 3.83e-07 ATCTCCACCA CCTCATTCGTCACCTCCGTCG AATACAAATA 263266 415 6.06e-07 CCATCAACCA CTTCATTCGTCGCACACCCCA CCCAACACAG 23315 427 6.06e-07 AGTGCCGCGT CTACCTGCCTCTCCACAACCA CACAACCTAA 268500 413 1.23e-06 ATCCACACAT CGTTCCACCTCACACCATCCA TTCCATCGAG 32577 447 1.94e-06 GCACCACACA CCTGCCTCCTCCGACCAATCC GTCGGACGCA 42624 88 2.96e-06 TCGCTGACGA GCTTCGCTCTCCCTCCCGACG GACAGCCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270310 5.3e-11 414_[+3]_65 19913 5.3e-11 413_[+3]_66 8519 7.7e-09 391_[+3]_88 8502 7.7e-09 391_[+3]_88 38646 6.7e-08 31_[+3]_448 270273 6.7e-08 303_[+3]_176 261893 2.6e-07 137_[+3]_342 9458 3.5e-07 318_[+3]_161 41953 3.8e-07 22_[+3]_457 263266 6.1e-07 414_[+3]_65 23315 6.1e-07 426_[+3]_53 268500 1.2e-06 412_[+3]_67 32577 1.9e-06 446_[+3]_33 42624 3e-06 87_[+3]_392 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=14 270310 ( 415) CTTTCTTCCTCCCTCCACGCG 1 19913 ( 414) CTTTCTTCCTCCCTCCACGCG 1 8519 ( 392) CTTCATTTCTCCCTACGGCCG 1 8502 ( 392) CTTCATTTCTCCCTACGGCCG 1 38646 ( 32) CAACCTTCGTCCTTTCAAACG 1 270273 ( 304) CAACCTTCGTCCTTTCAAACG 1 261893 ( 138) CATTCCTCGTGCCACCTCCCA 1 9458 ( 319) CATCCCGCCCGCCTCCCTCCG 1 41953 ( 23) CCTCATTCGTCACCTCCGTCG 1 263266 ( 415) CTTCATTCGTCGCACACCCCA 1 23315 ( 427) CTACCTGCCTCTCCACAACCA 1 268500 ( 413) CGTTCCACCTCACACCATCCA 1 32577 ( 447) CCTGCCTCCTCCGACCAATCC 1 42624 ( 88) GCTTCGCTCTCCCTCCCGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 11.2282 E= 8.0e-004 -1045 197 -173 -1045 12 -15 -173 71 -29 -1045 -1045 158 -1045 127 -173 44 12 159 -1045 -1045 -1045 27 -173 129 -188 -173 -73 144 -1045 173 -1045 -29 -1045 144 59 -1045 -1045 -173 -1045 182 -1045 185 -73 -1045 -88 159 -173 -188 -1045 173 -173 -88 12 -73 -1045 112 -29 127 -1045 -29 -188 197 -1045 -1045 93 27 -73 -188 12 27 27 -88 -29 107 -73 -88 -1045 207 -1045 -1045 12 -173 144 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 8.0e-004 0.000000 0.928571 0.071429 0.000000 0.285714 0.214286 0.071429 0.428571 0.214286 0.000000 0.000000 0.785714 0.000000 0.571429 0.071429 0.357143 0.285714 0.714286 0.000000 0.000000 0.000000 0.285714 0.071429 0.642857 0.071429 0.071429 0.142857 0.714286 0.000000 0.785714 0.000000 0.214286 0.000000 0.642857 0.357143 0.000000 0.000000 0.071429 0.000000 0.928571 0.000000 0.857143 0.142857 0.000000 0.142857 0.714286 0.071429 0.071429 0.000000 0.785714 0.071429 0.142857 0.285714 0.142857 0.000000 0.571429 0.214286 0.571429 0.000000 0.214286 0.071429 0.928571 0.000000 0.000000 0.500000 0.285714 0.142857 0.071429 0.285714 0.285714 0.285714 0.142857 0.214286 0.500000 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 0.285714 0.071429 0.642857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TAC][TA][CT][CA][TC]T[CT][CG]TCCC[TA][CAT]C[AC][ACG][CA]C[GA] -------------------------------------------------------------------------------- Time 24.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19913 2.28e-12 71_[+2(1.85e-07)]_321_\ [+3(5.28e-11)]_7_[+1(3.56e-06)]_43 20887 2.92e-04 451_[+1(1.92e-05)]_7_[+1(1.49e-08)]_\ 10 21837 3.32e-02 215_[+2(5.09e-06)]_264 22508 7.87e-07 96_[+2(6.55e-08)]_30_[+2(2.83e-05)]_\ 279_[+1(3.37e-07)]_37 23315 1.10e-05 319_[+1(7.17e-07)]_91_\ [+3(6.06e-07)]_35_[+1(8.41e-05)]_2 23539 1.68e-05 273_[+2(1.61e-06)]_33_\ [+2(8.64e-05)]_109_[+1(6.35e-06)]_27 23922 1.89e-05 24_[+2(3.16e-07)]_10_[+2(2.68e-06)]_\ 240_[+1(4.23e-06)]_168 24288 2.02e-02 94_[+2(7.41e-06)]_385 24550 3.40e-05 382_[+2(6.39e-07)]_79_\ [+1(5.86e-06)]_2 24746 2.63e-03 361_[+2(2.30e-07)]_118 25639 1.40e-06 112_[+2(5.25e-07)]_246_\ [+1(1.45e-05)]_67_[+1(1.12e-07)]_22 261893 2.63e-05 137_[+3(2.55e-07)]_53_\ [+2(7.97e-06)]_268 263266 1.54e-13 87_[+2(5.58e-09)]_306_\ [+3(6.06e-07)]_20_[+1(5.96e-10)]_4_[+1(5.02e-05)]_9 263801 2.58e-03 106_[+2(2.21e-05)]_14_\ [+1(3.70e-05)]_343 26560 9.28e-04 158_[+2(4.52e-08)]_321 268500 2.90e-06 49_[+2(7.41e-05)]_10_[+2(4.71e-06)]_\ 43_[+2(3.82e-05)]_226_[+1(2.51e-05)]_5_[+3(1.23e-06)]_67 269120 1.27e-02 457_[+1(2.87e-05)]_27 270273 1.38e-10 25_[+2(1.18e-08)]_105_\ [+2(5.37e-05)]_52_[+1(3.56e-06)]_63_[+3(6.66e-08)]_176 270310 2.28e-12 72_[+2(1.85e-07)]_321_\ [+3(5.28e-11)]_7_[+1(3.56e-06)]_42 32577 1.65e-04 197_[+1(3.88e-06)]_233_\ [+3(1.94e-06)]_33 38646 2.43e-07 31_[+3(6.66e-08)]_165_\ [+1(2.35e-05)]_160_[+1(8.54e-08)]_12_[+1(4.98e-06)]_63 41953 7.01e-05 22_[+3(3.83e-07)]_259_\ [+1(8.67e-06)]_182 42624 7.53e-05 87_[+3(2.96e-06)]_256_\ [+2(9.89e-06)]_2_[+2(1.47e-06)]_92 6341 2.84e-03 345_[+2(4.76e-07)]_134 7789 7.18e-04 267_[+2(1.47e-06)]_3_[+2(8.57e-06)]_\ 132_[+1(3.94e-05)]_40 8502 8.48e-11 331_[+2(1.47e-06)]_39_\ [+3(7.70e-09)]_65_[+1(1.45e-07)]_7 8519 7.81e-11 330_[+2(1.35e-06)]_40_\ [+3(7.70e-09)]_65_[+1(1.45e-07)]_7 8868 7.45e-05 292_[+2(4.35e-06)]_103_\ [+1(7.17e-07)]_68 9458 5.75e-07 266_[+2(4.35e-06)]_31_\ [+3(3.53e-07)]_1_[+1(1.56e-05)]_144 bd863 4.28e-03 324_[+1(1.44e-06)]_160 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************