******************************************************************************** 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/326/326.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11367 1.0000 500 11929 1.0000 500 1551 1.0000 500 15822 1.0000 500 18538 1.0000 500 19623 1.0000 500 2024 1.0000 500 20659 1.0000 500 20686 1.0000 500 21088 1.0000 500 21247 1.0000 500 21800 1.0000 500 21951 1.0000 500 21971 1.0000 500 23048 1.0000 500 23084 1.0000 500 23362 1.0000 500 23872 1.0000 500 23897 1.0000 500 24141 1.0000 500 24292 1.0000 500 24347 1.0000 500 24367 1.0000 500 24585 1.0000 500 24977 1.0000 500 25270 1.0000 500 25309 1.0000 500 25490 1.0000 500 26022 1.0000 500 261324 1.0000 500 261601 1.0000 500 262707 1.0000 500 264350 1.0000 500 264799 1.0000 500 26553 1.0000 500 269141 1.0000 500 31145 1.0000 500 34730 1.0000 500 34973 1.0000 500 35748 1.0000 500 36673 1.0000 500 37928 1.0000 500 38051 1.0000 500 39315 1.0000 500 4350 1.0000 500 4408 1.0000 500 4825 1.0000 500 5497 1.0000 500 6151 1.0000 500 6925 1.0000 500 7019 1.0000 500 9818 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/326/326.seqs.fa -oc motifs/326 -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= 52 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= 26000 N= 52 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.232 G 0.242 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.232 G 0.242 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 29 llr = 350 E-value = 4.2e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 233726364273265191382 pos.-specific C 8:53446437257249174:7 probability G :61:31::11::1:1::12:: matrix T :1::::1:1:22:2:::1:2: bits 2.1 1.9 1.7 1.5 ** Relative 1.3 * ** * Entropy 1.1 * * * ** ** (17.4 bits) 0.8 * * *** * * *** ** 0.6 **** *** ** ****** ** 0.4 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel CGCACACAACACCAACACCAC consensus AAACGCACC A CC ATA sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20686 431 1.38e-11 CGTCAACAAC CGCACCCCCCACCACCACCAC CGCCTCCTCT 26022 430 2.17e-09 AACCTGTCTT CGCCGGCACCACCACCACCAC ACGTTCCTCG 6925 133 1.66e-08 AGGAAGCTAA CGCAAAAACAAACACCACAAC CTGAGAGTAG 25309 142 2.20e-08 CTCTCCATAT CGCACCACACAACAGCACGAC GCACCAACAT 34973 80 2.53e-08 GATACTTTCA CGCACACATCACCTACATAAC CAAGCCTATG 24585 393 6.35e-08 CAGGAGGATA CGCCGCCCCCCCCCCCACAAA ATTTCACAGA 5497 106 8.14e-08 CCAGTGACGA CAAAGACCACACCAACCCAAA CCATGAAAAG 19623 477 1.32e-07 TTGAAACTAC CGACGACCTCTCAAACACCAC ACA 261324 358 1.48e-07 TCCTGCCAGC CTCCCCCAGCAACCACACAAC ACCACCTCTC 24141 230 1.86e-07 GACACATATT CAGCCACAAAAACAACACCAA CGCTCCCGTC 21088 477 1.86e-07 AACATCAGAA CAACAATACCAACAACACAAC AGC 1551 462 3.98e-07 CGTTTCAAAA AGAAACCCAACACACCACCAC GCAAGCAATT 25270 473 4.41e-07 AGGAATCAAG CACACCAACCTCCCAAACAAC CATTTGA 34730 385 4.89e-07 GGAAAGCCAC CACACACCTCACACACAACAC TGACCGCCTC 39315 300 1.84e-06 GGAGGAAGAA CGAAGACAAGACGAACAGGAA TCACGTCACA 269141 46 1.84e-06 AGACTTTGTT ATCAGCAACGACGACCACGAC TTGCACTTTA 31145 250 2.60e-06 ACCAACATGA CGGACACCACCACTACAGCTC GGCAACAACT 21951 466 3.33e-06 TCGAGAGAGG AGGAGGAACCATCTACACGAC GAATCTACAG 23872 454 3.91e-06 CGGTCGGCAG CGAAGATAACCAACCCATCAC CCTATCAATC 262707 132 4.94e-06 AAGAGGACGA AGACGACAAGATGCACACCTC AAAACGTCAT 11367 470 5.33e-06 GAACTCGCTG CGCATCAATCAGCACCACGAA CACTATTCGT 24292 267 5.75e-06 ATGAGCTTTC CGAAACACCAAACCAAACCTC GACTCTAACA 23362 248 6.68e-06 CACATCTCCT ATCAACCAAGCTCAACACATC ACTGTCCTTA 21247 480 6.68e-06 CACCGTCTAC CACACACCACTTCACCCAATC 264799 475 8.30e-06 CAAAGAACAA ATCAACCAACTCAACCATCAA CCGCC 23084 416 8.30e-06 TCTGCGGCAA CGCCGAAACCATCTCCAAGAG ATTCTCAGAG 37928 2 9.56e-06 A CAAACACAGCACCACTCCAAA TAGGTGACAA 6151 381 1.02e-05 CGAGTGGAGC CGACCAACACACGTGCATCTC GTCTGCATCC 4350 186 2.23e-05 CTTTTTAAAA AAGCCACAAATCAAAAACGAC AAAACGGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20686 1.4e-11 430_[+1]_49 26022 2.2e-09 429_[+1]_50 6925 1.7e-08 132_[+1]_347 25309 2.2e-08 141_[+1]_338 34973 2.5e-08 79_[+1]_400 24585 6.3e-08 392_[+1]_87 5497 8.1e-08 105_[+1]_374 19623 1.3e-07 476_[+1]_3 261324 1.5e-07 357_[+1]_122 24141 1.9e-07 229_[+1]_250 21088 1.9e-07 476_[+1]_3 1551 4e-07 461_[+1]_18 25270 4.4e-07 472_[+1]_7 34730 4.9e-07 384_[+1]_95 39315 1.8e-06 299_[+1]_180 269141 1.8e-06 45_[+1]_434 31145 2.6e-06 249_[+1]_230 21951 3.3e-06 465_[+1]_14 23872 3.9e-06 453_[+1]_26 262707 4.9e-06 131_[+1]_348 11367 5.3e-06 469_[+1]_10 24292 5.8e-06 266_[+1]_213 23362 6.7e-06 247_[+1]_232 21247 6.7e-06 479_[+1] 264799 8.3e-06 474_[+1]_5 23084 8.3e-06 415_[+1]_64 37928 9.6e-06 1_[+1]_478 6151 1e-05 380_[+1]_99 4350 2.2e-05 185_[+1]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=29 20686 ( 431) CGCACCCCCCACCACCACCAC 1 26022 ( 430) CGCCGGCACCACCACCACCAC 1 6925 ( 133) CGCAAAAACAAACACCACAAC 1 25309 ( 142) CGCACCACACAACAGCACGAC 1 34973 ( 80) CGCACACATCACCTACATAAC 1 24585 ( 393) CGCCGCCCCCCCCCCCACAAA 1 5497 ( 106) CAAAGACCACACCAACCCAAA 1 19623 ( 477) CGACGACCTCTCAAACACCAC 1 261324 ( 358) CTCCCCCAGCAACCACACAAC 1 24141 ( 230) CAGCCACAAAAACAACACCAA 1 21088 ( 477) CAACAATACCAACAACACAAC 1 1551 ( 462) AGAAACCCAACACACCACCAC 1 25270 ( 473) CACACCAACCTCCCAAACAAC 1 34730 ( 385) CACACACCTCACACACAACAC 1 39315 ( 300) CGAAGACAAGACGAACAGGAA 1 269141 ( 46) ATCAGCAACGACGACCACGAC 1 31145 ( 250) CGGACACCACCACTACAGCTC 1 21951 ( 466) AGGAGGAACCATCTACACGAC 1 23872 ( 454) CGAAGATAACCAACCCATCAC 1 262707 ( 132) AGACGACAAGATGCACACCTC 1 11367 ( 470) CGCATCAATCAGCACCACGAA 1 24292 ( 267) CGAAACACCAAACCAAACCTC 1 23362 ( 248) ATCAACCAAGCTCAACACATC 1 21247 ( 480) CACACACCACTTCACCCAATC 1 264799 ( 475) ATCAACCAACTCAACCATCAA 1 23084 ( 416) CGCCGAAACCATCTCCAAGAG 1 37928 ( 2) CAAACACAGCACCACTCCAAA 1 6151 ( 381) CGACCAACACACGTGCATCTC 1 4350 ( 186) AAGCCACAAATCAAAAACGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24960 bayes= 11.4369 E= 4.2e-014 -10 171 -1150 -1150 9 -1150 128 -96 42 116 -81 -1150 134 57 -1150 -1150 -32 84 51 -296 109 71 -181 -1150 26 142 -1150 -196 126 71 -1150 -1150 80 57 -181 -96 -58 157 -81 -1150 134 -43 -1150 -64 26 106 -281 -64 -58 157 -81 -1150 118 6 -1150 -64 100 84 -181 -1150 -132 190 -1150 -296 179 -116 -1150 -1150 -132 157 -181 -96 42 84 0 -1150 162 -1150 -1150 -38 -10 164 -281 -1150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 4.2e-014 0.241379 0.758621 0.000000 0.000000 0.275862 0.000000 0.586207 0.137931 0.344828 0.517241 0.137931 0.000000 0.655172 0.344828 0.000000 0.000000 0.206897 0.413793 0.344828 0.034483 0.551724 0.379310 0.068966 0.000000 0.310345 0.620690 0.000000 0.068966 0.620690 0.379310 0.000000 0.000000 0.448276 0.344828 0.068966 0.137931 0.172414 0.689655 0.137931 0.000000 0.655172 0.172414 0.000000 0.172414 0.310345 0.482759 0.034483 0.172414 0.172414 0.689655 0.137931 0.000000 0.586207 0.241379 0.000000 0.172414 0.517241 0.413793 0.068966 0.000000 0.103448 0.862069 0.000000 0.034483 0.896552 0.103448 0.000000 0.000000 0.103448 0.689655 0.068966 0.137931 0.344828 0.413793 0.241379 0.000000 0.793103 0.000000 0.000000 0.206897 0.241379 0.724138 0.034483 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][GA][CA][AC][CGA][AC][CA][AC][AC]CA[CA]C[AC][AC]CAC[CAG][AT][CA] -------------------------------------------------------------------------------- Time 22.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 41 llr = 413 E-value = 1.1e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:1211::1:::1:32125:: pos.-specific C 14::2:::2:1:::::121:4 probability G :43242373184:93282316 matrix T 7165377348:59146:419: bits 2.1 1.9 1.7 1.5 Relative 1.3 ** * Entropy 1.1 * ** ** * (14.5 bits) 0.8 * ** ***** * ** 0.6 * *** ***** ** ** 0.4 **** *** ******** ** 0.2 ******** ******** *** 0.0 --------------------- Multilevel TGTTGTTGTTGTTGTTGTATG consensus CGGT GTG G AA AG C sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31145 423 5.35e-09 TCTGTATTGA TCTGTTTGATGTTGATGTATC TGGTTGCTTT 26022 196 4.37e-08 GAACATCTTG TGTTGGTTTTGTTGGAGTATC GACAGCGCCA 20659 147 8.04e-08 GTTTGACCAT TGTGTTGTTTGTTGTTGTTTG TTGGTAGTAG 34730 238 1.24e-07 TGTTTCCTGC TCTTCTTTCTGTTGTAGTTTG GTCATCTAGT 261601 250 1.43e-07 TGGACACCTC TGGAGTTGGTGGTGATGATTC GGTATCACAC 37928 279 3.21e-07 AGGGAGGAAA CGTTATTGCTGTTGATGCATC TGCCAACACT 15822 228 3.21e-07 CTCCCAGAGA TAGAGTTGCTGTTGTTGAATG ATTGTCGGTG 24977 288 4.70e-07 CTAGTTGTCA ACTTTTGTGTGTTGGGGTATG ATTTTTGCTG 23084 137 6.01e-07 GAGAGAGTGC CTGGGTTGGTGGTGGTGGATG TGGACATGGT 36673 66 8.61e-07 GATGGCTCGT ACGTTTTGCTGTTGTTGGAGG AGCTGGAGGA 262707 314 1.91e-06 ATCCGAATGC ACTTCTTGGTTGTGATGCATC TGAATTAGCT 5497 168 2.36e-06 GTGAGTCTCA TCGTTATGTTGTTGGAGTGCG GCGTTCGCTC 1551 85 2.36e-06 CTTGTGATTG TGTTCTGTTGGTTGGTGCTTC ACCAAACATA 38051 163 2.63e-06 TGTCTGTTCC TGGTGATGATGTTTTGGTGTG TCAGATACTG 21247 325 2.63e-06 GCAAATGAGG AGTGGTGGGTGGTGTACCATG AGGGTCATGT 2024 391 2.63e-06 CAGCAACGAA TGTGTGTGTTGGTTTTGTCTC GTATCATCAT 7019 472 3.24e-06 CACCTCACCC TCCTTGTGTTGGTGTTCTATC ATTCCTCA 4825 329 3.24e-06 GGACAGGATC AGGTCTTGTGCGTGTTGTGTC TGTGTCGGCT 23362 323 3.24e-06 TGTGTTCGTT TGGTCGCGGTGGTGGTGTGTC GTGCTGTGCC 4350 34 3.98e-06 GTGTGTTTGT TTGTTTGTTTGTTTGTGTGTC ACTTGACTCT 21971 180 5.37e-06 TAGTGTTTTG TGTTGTTGATGTTGAGAAGGG CATGCGACGT 35748 284 6.53e-06 GACCTTACAT TGTTGTGGCTCTTCAGGAATG TGGACGTATC 9818 247 7.91e-06 GTGTTTTGCT TCTCCATTCTGGTGAGGCATG ATCACTTCCA 261324 185 1.05e-05 AGTAACTACG TCTGTTGGTTGGAGGAGGAGG GACGGGGACA 23048 318 1.26e-05 TTCCTTGTTT TTAGGTTTTCGGTGATGTGTC ATCACGGTAA 24585 143 1.64e-05 CGGGTTGCCA TGATGATGATGTTGATTGATG TGTCGTGTTG 23897 269 2.13e-05 TCAAGTTCCG CCGTGATGATCGTGTTATATC TTTTGTACAC 264799 347 2.31e-05 AGTGGAGGGT TCTTCGTTGGGTTGGTAATTG TGTGAATTCT 19623 364 2.31e-05 CAGAACGAGA TCTCGTGGTTGTTGATGAACT CAGCCTATAT 24292 165 2.52e-05 CCGATGGGTA TAGTGTTGATATTGAGGCATG CCATTTAGAC 39315 223 2.74e-05 ATGGGGGTGA TTTAGTGGTGGTAGTTGACTG ATTGGATGGG 269141 377 3.50e-05 ATTATGCGTC TCAAGGTGGTGGAGTTACGTG CTGCTTGTGC 24141 82 3.50e-05 CCTCCCCGTT CCTTGTTGTCGGGGAAGTATC GGGGGGTCAA 4408 69 4.44e-05 GTTGAAGGGG AGTGGTGTGTGGTTGAGATTG TATCATTTGC 26553 123 6.04e-05 CAATGGGTTT AGGATTTGTTGGAGTGGGATT GGTCAATTTA 11929 303 6.04e-05 GTATTCGTGT TTTGTTTGTTCGTCGTCGGTG TTCTTTGTGG 11367 324 6.04e-05 CTGACCAAAC TCTATTTCTTCTTGAAGGCTG TATTAATTTT 24367 81 7.02e-05 TCTTCTGCGG TTGTAGTGCTGCTGTTGCAGC GACTTGCAGT 21088 164 8.75e-05 GATGATACCG CCAAAAGTGTGTTGATGTGTC AATGTGATGA 6925 191 1.08e-04 ACTATATTTG TGTTCTGTGTTCTGTACTGTG GACAAGAGAC 20686 171 1.25e-04 GATGAGTTCG TGTGCGTGCGCTAGTTCAGTG TAAATGTCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31145 5.3e-09 422_[+2]_57 26022 4.4e-08 195_[+2]_284 20659 8e-08 146_[+2]_333 34730 1.2e-07 237_[+2]_242 261601 1.4e-07 249_[+2]_230 37928 3.2e-07 278_[+2]_201 15822 3.2e-07 227_[+2]_252 24977 4.7e-07 287_[+2]_192 23084 6e-07 136_[+2]_343 36673 8.6e-07 65_[+2]_414 262707 1.9e-06 313_[+2]_166 5497 2.4e-06 167_[+2]_312 1551 2.4e-06 84_[+2]_395 38051 2.6e-06 162_[+2]_317 21247 2.6e-06 324_[+2]_155 2024 2.6e-06 390_[+2]_89 7019 3.2e-06 471_[+2]_8 4825 3.2e-06 328_[+2]_151 23362 3.2e-06 322_[+2]_157 4350 4e-06 33_[+2]_446 21971 5.4e-06 179_[+2]_300 35748 6.5e-06 283_[+2]_196 9818 7.9e-06 246_[+2]_233 261324 1e-05 184_[+2]_295 23048 1.3e-05 317_[+2]_162 24585 1.6e-05 142_[+2]_337 23897 2.1e-05 268_[+2]_211 264799 2.3e-05 346_[+2]_133 19623 2.3e-05 363_[+2]_116 24292 2.5e-05 164_[+2]_315 39315 2.7e-05 222_[+2]_257 269141 3.5e-05 376_[+2]_103 24141 3.5e-05 81_[+2]_398 4408 4.4e-05 68_[+2]_411 26553 6e-05 122_[+2]_357 11929 6e-05 302_[+2]_177 11367 6e-05 323_[+2]_156 24367 7e-05 80_[+2]_399 21088 8.7e-05 163_[+2]_316 6925 0.00011 190_[+2]_289 20686 0.00012 170_[+2]_309 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=41 31145 ( 423) TCTGTTTGATGTTGATGTATC 1 26022 ( 196) TGTTGGTTTTGTTGGAGTATC 1 20659 ( 147) TGTGTTGTTTGTTGTTGTTTG 1 34730 ( 238) TCTTCTTTCTGTTGTAGTTTG 1 261601 ( 250) TGGAGTTGGTGGTGATGATTC 1 37928 ( 279) CGTTATTGCTGTTGATGCATC 1 15822 ( 228) TAGAGTTGCTGTTGTTGAATG 1 24977 ( 288) ACTTTTGTGTGTTGGGGTATG 1 23084 ( 137) CTGGGTTGGTGGTGGTGGATG 1 36673 ( 66) ACGTTTTGCTGTTGTTGGAGG 1 262707 ( 314) ACTTCTTGGTTGTGATGCATC 1 5497 ( 168) TCGTTATGTTGTTGGAGTGCG 1 1551 ( 85) TGTTCTGTTGGTTGGTGCTTC 1 38051 ( 163) TGGTGATGATGTTTTGGTGTG 1 21247 ( 325) AGTGGTGGGTGGTGTACCATG 1 2024 ( 391) TGTGTGTGTTGGTTTTGTCTC 1 7019 ( 472) TCCTTGTGTTGGTGTTCTATC 1 4825 ( 329) AGGTCTTGTGCGTGTTGTGTC 1 23362 ( 323) TGGTCGCGGTGGTGGTGTGTC 1 4350 ( 34) TTGTTTGTTTGTTTGTGTGTC 1 21971 ( 180) TGTTGTTGATGTTGAGAAGGG 1 35748 ( 284) TGTTGTGGCTCTTCAGGAATG 1 9818 ( 247) TCTCCATTCTGGTGAGGCATG 1 261324 ( 185) TCTGTTGGTTGGAGGAGGAGG 1 23048 ( 318) TTAGGTTTTCGGTGATGTGTC 1 24585 ( 143) TGATGATGATGTTGATTGATG 1 23897 ( 269) CCGTGATGATCGTGTTATATC 1 264799 ( 347) TCTTCGTTGGGTTGGTAATTG 1 19623 ( 364) TCTCGTGGTTGTTGATGAACT 1 24292 ( 165) TAGTGTTGATATTGAGGCATG 1 39315 ( 223) TTTAGTGGTGGTAGTTGACTG 1 269141 ( 377) TCAAGGTGGTGGAGTTACGTG 1 24141 ( 82) CCTTGTTGTCGGGGAAGTATC 1 4408 ( 69) AGTGGTGTGTGGTTGAGATTG 1 26553 ( 123) AGGATTTGTTGGAGTGGGATT 1 11929 ( 303) TTTGTTTGTTCGTCGTCGGTG 1 11367 ( 324) TCTATTTCTTCTTGAAGGCTG 1 24367 ( 81) TTGTAGTGCTGCTGTTGCAGC 1 21088 ( 164) CCAAAAGTGTGTTGATGTGTC 1 6925 ( 191) TGTTCTGTGTTCTGTACTGTG 1 20686 ( 171) TGTGCGTGCGCTAGTTCAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24960 bayes= 9.52642 E= 1.1e-010 -60 -92 -1200 140 -240 75 78 -88 -140 -324 39 106 -60 -225 1 100 -182 -8 78 12 -82 -1200 -31 129 -1200 -324 28 135 -1200 -324 150 12 -82 -25 15 54 -1200 -225 -99 163 -340 -66 169 -246 -1200 -225 78 100 -108 -1200 -330 167 -1200 -225 182 -146 40 -1200 15 54 -23 -1200 -50 118 -140 -92 165 -346 -23 -25 -50 63 92 -166 28 -88 -1200 -225 -131 167 -1200 75 122 -246 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 41 E= 1.1e-010 0.170732 0.121951 0.000000 0.707317 0.048780 0.390244 0.414634 0.146341 0.097561 0.024390 0.317073 0.560976 0.170732 0.048780 0.243902 0.536585 0.073171 0.219512 0.414634 0.292683 0.146341 0.000000 0.195122 0.658537 0.000000 0.024390 0.292683 0.682927 0.000000 0.024390 0.682927 0.292683 0.146341 0.195122 0.268293 0.390244 0.000000 0.048780 0.121951 0.829268 0.024390 0.146341 0.780488 0.048780 0.000000 0.048780 0.414634 0.536585 0.121951 0.000000 0.024390 0.853659 0.000000 0.048780 0.853659 0.097561 0.341463 0.000000 0.268293 0.390244 0.219512 0.000000 0.170732 0.609756 0.097561 0.121951 0.756098 0.024390 0.219512 0.195122 0.170732 0.414634 0.487805 0.073171 0.292683 0.146341 0.000000 0.048780 0.097561 0.853659 0.000000 0.390244 0.560976 0.048780 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[GC][TG][TG][GTC]T[TG][GT][TG]TG[TG]TG[TAG][TA]G[TA][AG]T[GC] -------------------------------------------------------------------------------- Time 43.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 33 llr = 355 E-value = 5.1e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 121::1223::21::211:: pos.-specific C 94375517149246627:63 probability G :1:::2:::::11:1::21: matrix T :4635271661454252736 bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * * Entropy 1.1 * ** ** * (15.5 bits) 0.8 * ** * ** * * ** 0.6 * *** ***** ** **** 0.4 * ********* ******** 0.2 ******************** 0.0 -------------------- Multilevel CTTCTCTCTTCTTCCTCTCT consensus CCTCG AC ACTTCTGTC sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 23084 384 4.03e-11 CACAGACTGC CTTCCCTCTTCATCCTCTCT CATCTGCGGC 261324 381 8.96e-08 CACACAACAC CACCTCTCATCCCTCCCTCC CCACGTTTCA 24292 296 1.37e-07 TCGACTCTAA CAACTCTCTTCTTCGTCTCT CACCAAACGA 261601 278 2.06e-07 TTCGGTATCA CACCTCACTTCCTTCACTCT GACATATGAA 4350 280 5.64e-07 CGACGCTGCT CTTTTTTCTTCCTTCCCTTT CCACGGCATC 262707 34 8.02e-07 GTGCCCGTAA CCTTCGTCACCGTCTCCTCT TTACTCGTAA 19623 271 8.02e-07 GTGATAGTGA CATCTCTCTCCTCTTACACC GATATCTGTG 38051 410 1.01e-06 ACAATTGTCC ATTCCCTCATCATCCAATCT CTTCTTATTC 23872 94 1.01e-06 ATCTCGTCAA CATCCCCCACCCCCCTCGTC TCCAAAGTGC 11929 16 1.01e-06 AGTAGCTATC CCTCTCGCTTCTTCCTCATT CTCTCCTTCT 4825 420 1.13e-06 TAAAAATGGC CCTCCCTTTCCTCCTCTTTT CCTTCTTCCA 31145 218 1.40e-06 CTCTCACCAG CTCTCCACACCTTCCTCTGC AGACCAACAT 24367 386 1.74e-06 ATGACCACGT CTTCCGTCCTCCTTCCTTCC GACTACCGAG 25309 118 1.93e-06 CGGTACACCT CACCCCCCATCAACCTCTCC ATATCGCACC 6925 408 2.15e-06 CAACAAACAG CTTCTCTCCTTCCCCTCGCT TCTTGAGCAT 5497 408 2.38e-06 CAACGCGTTG CCACTGACACCGCTCTCTCT ACCAACCACT 23048 456 2.63e-06 CGAATCAACA CTTTCCCCTCCTCCGCCGCC CGATTCTCCC 24585 479 2.91e-06 ACGCCGGCAC CCTCTCTCACCACTCATTCA CA 1551 283 2.91e-06 GACGGCTTCT CGTCTATATTCTCCCTCTTT CCAACTTGCT 24141 30 3.21e-06 GAAGCATCTT CTACTGTTTCCCCTCTCTTT GTTGCAGAAG 21971 452 5.70e-06 ACCCAAGCGA CCTCCTCCTTCCTCATCGCT ACCTACCATC 36673 246 7.48e-06 ATCTGTCTGT CGTCCGTCGTCTTCCTTTTT CTCTCTCCGC 18538 373 1.06e-05 CACTGTTCTA ACCTTCAATCCTTCCTTTCT TCTAAGCGAC 264799 34 1.15e-05 AGATAACAAC CCTTCCTTTTCAGCCTTTGT ATCGGCATAC 21951 387 1.15e-05 CTTTCCTGCT CTTCTTTGTTCTCCTCTTCC CAGTCAGCGG 15822 186 1.60e-05 CACTAGTGAT CTTGTCTAATCTTCCACACC TGCCATGTCG 26022 35 1.74e-05 CCAGAGCATG CTCCCGTCTCCGGTTCATCT AACCCATCCA 21088 251 1.74e-05 CCCATCTCGT CTTCCCTAACCATTGAAGCT GAACTTACAG 34973 396 2.56e-05 GAACCAAACA CTCCTATTTCCACTTACTTT GGCAAACAGA 6151 330 2.75e-05 GAACTCATGA ACCTCGAATCCTCTCTCGCT TGAACTCCAA 34730 24 4.55e-05 TTGTCTGGCT ACTTTTTCTTCTGTTTCGTT ACGTTGGCTT 25270 22 4.87e-05 AGTTCTTTGT CCTCCTTCTTTAACTTATCC GCCTGTCCGT 23897 342 5.57e-05 TTTAACAAAA CCCTTGACATCTTCGTCAGC GAAACGGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23084 4e-11 383_[+3]_97 261324 9e-08 380_[+3]_100 24292 1.4e-07 295_[+3]_185 261601 2.1e-07 277_[+3]_203 4350 5.6e-07 279_[+3]_201 262707 8e-07 33_[+3]_447 19623 8e-07 270_[+3]_210 38051 1e-06 409_[+3]_71 23872 1e-06 93_[+3]_387 11929 1e-06 15_[+3]_465 4825 1.1e-06 419_[+3]_61 31145 1.4e-06 217_[+3]_263 24367 1.7e-06 385_[+3]_95 25309 1.9e-06 117_[+3]_363 6925 2.1e-06 407_[+3]_73 5497 2.4e-06 407_[+3]_73 23048 2.6e-06 455_[+3]_25 24585 2.9e-06 478_[+3]_2 1551 2.9e-06 282_[+3]_198 24141 3.2e-06 29_[+3]_451 21971 5.7e-06 451_[+3]_29 36673 7.5e-06 245_[+3]_235 18538 1.1e-05 372_[+3]_108 264799 1.2e-05 33_[+3]_447 21951 1.2e-05 386_[+3]_94 15822 1.6e-05 185_[+3]_295 26022 1.7e-05 34_[+3]_446 21088 1.7e-05 250_[+3]_230 34973 2.6e-05 395_[+3]_85 6151 2.8e-05 329_[+3]_151 34730 4.5e-05 23_[+3]_457 25270 4.9e-05 21_[+3]_459 23897 5.6e-05 341_[+3]_139 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=33 23084 ( 384) CTTCCCTCTTCATCCTCTCT 1 261324 ( 381) CACCTCTCATCCCTCCCTCC 1 24292 ( 296) CAACTCTCTTCTTCGTCTCT 1 261601 ( 278) CACCTCACTTCCTTCACTCT 1 4350 ( 280) CTTTTTTCTTCCTTCCCTTT 1 262707 ( 34) CCTTCGTCACCGTCTCCTCT 1 19623 ( 271) CATCTCTCTCCTCTTACACC 1 38051 ( 410) ATTCCCTCATCATCCAATCT 1 23872 ( 94) CATCCCCCACCCCCCTCGTC 1 11929 ( 16) CCTCTCGCTTCTTCCTCATT 1 4825 ( 420) CCTCCCTTTCCTCCTCTTTT 1 31145 ( 218) CTCTCCACACCTTCCTCTGC 1 24367 ( 386) CTTCCGTCCTCCTTCCTTCC 1 25309 ( 118) CACCCCCCATCAACCTCTCC 1 6925 ( 408) CTTCTCTCCTTCCCCTCGCT 1 5497 ( 408) CCACTGACACCGCTCTCTCT 1 23048 ( 456) CTTTCCCCTCCTCCGCCGCC 1 24585 ( 479) CCTCTCTCACCACTCATTCA 1 1551 ( 283) CGTCTATATTCTCCCTCTTT 1 24141 ( 30) CTACTGTTTCCCCTCTCTTT 1 21971 ( 452) CCTCCTCCTTCCTCATCGCT 1 36673 ( 246) CGTCCGTCGTCTTCCTTTTT 1 18538 ( 373) ACCTTCAATCCTTCCTTTCT 1 264799 ( 34) CCTTCCTTTTCAGCCTTTGT 1 21951 ( 387) CTTCTTTGTTCTCCTCTTCC 1 15822 ( 186) CTTGTCTAATCTTCCACACC 1 26022 ( 35) CTCCCGTCTCCGGTTCATCT 1 21088 ( 251) CTTCCCTAACCATTGAAGCT 1 34973 ( 396) CTCCTATTTCCACTTACTTT 1 6151 ( 330) ACCTCGAATCCTCTCTCGCT 1 34730 ( 24) ACTTTTTCTTCTGTTTCGTT 1 25270 ( 22) CCTCCTTCTTTAACTTATCC 1 23897 ( 342) CCCTTGACATCTTCGTCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 25012 bayes= 10.3312 E= 5.1e-007 -109 192 -1169 -1169 -51 65 -199 55 -151 24 -1169 124 -1169 159 -299 2 -1169 107 -1169 94 -209 124 1 -83 -51 -93 -299 131 -77 159 -299 -115 37 -193 -299 110 -1169 87 -1169 110 -1169 202 -1169 -215 -9 7 -141 66 -209 77 -141 76 -1169 139 -1169 55 -309 139 -99 -15 -28 7 -1169 102 -109 153 -1169 -34 -109 -1169 -19 131 -1169 146 -141 2 -309 53 -1169 124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 33 E= 5.1e-007 0.121212 0.878788 0.000000 0.000000 0.181818 0.363636 0.060606 0.393939 0.090909 0.272727 0.000000 0.636364 0.000000 0.696970 0.030303 0.272727 0.000000 0.484848 0.000000 0.515152 0.060606 0.545455 0.242424 0.151515 0.181818 0.121212 0.030303 0.666667 0.151515 0.696970 0.030303 0.121212 0.333333 0.060606 0.030303 0.575758 0.000000 0.424242 0.000000 0.575758 0.000000 0.939394 0.000000 0.060606 0.242424 0.242424 0.090909 0.424242 0.060606 0.393939 0.090909 0.454545 0.000000 0.606061 0.000000 0.393939 0.030303 0.606061 0.121212 0.242424 0.212121 0.242424 0.000000 0.545455 0.121212 0.666667 0.000000 0.212121 0.121212 0.000000 0.212121 0.666667 0.000000 0.636364 0.090909 0.272727 0.030303 0.333333 0.000000 0.636364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TC][TC][CT][TC][CG]TC[TA][TC]C[TAC][TC][CT][CT][TCA][CT][TG][CT][TC] -------------------------------------------------------------------------------- Time 65.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11367 4.07e-03 323_[+2(6.04e-05)]_125_\ [+1(5.33e-06)]_10 11929 3.11e-04 15_[+3(1.01e-06)]_267_\ [+2(6.04e-05)]_99_[+3(6.35e-05)]_58 1551 7.97e-08 84_[+2(2.36e-06)]_177_\ [+3(2.91e-06)]_159_[+1(3.98e-07)]_18 15822 1.82e-05 185_[+3(1.60e-05)]_22_\ [+2(3.21e-07)]_252 18538 3.91e-02 372_[+3(1.06e-05)]_108 19623 7.16e-08 270_[+3(8.02e-07)]_73_\ [+2(2.31e-05)]_92_[+1(1.32e-07)]_3 2024 1.15e-02 390_[+2(2.63e-06)]_89 20659 6.76e-05 51_[+2(3.79e-05)]_38_[+2(7.02e-05)]_\ 15_[+2(8.04e-08)]_333 20686 2.11e-09 430_[+1(1.38e-11)]_49 21088 5.12e-06 163_[+2(8.75e-05)]_66_\ [+3(1.74e-05)]_206_[+1(1.86e-07)]_3 21247 1.91e-04 324_[+2(2.63e-06)]_134_\ [+1(6.68e-06)] 21800 9.93e-01 500 21951 4.39e-04 386_[+3(1.15e-05)]_59_\ [+1(3.33e-06)]_14 21971 8.01e-05 179_[+2(5.37e-06)]_251_\ [+3(5.70e-06)]_29 23048 4.33e-04 317_[+2(1.26e-05)]_28_\ [+3(2.37e-05)]_69_[+3(2.63e-06)]_25 23084 1.17e-11 136_[+2(6.01e-07)]_88_\ [+2(1.15e-05)]_76_[+3(6.24e-06)]_21_[+3(4.03e-11)]_12_[+1(8.30e-06)]_64 23362 3.06e-05 42_[+2(2.31e-05)]_184_\ [+1(6.68e-06)]_54_[+2(3.24e-06)]_157 23872 7.52e-05 93_[+3(1.01e-06)]_308_\ [+3(8.20e-05)]_12_[+1(3.91e-06)]_26 23897 3.56e-03 268_[+2(2.13e-05)]_52_\ [+3(5.57e-05)]_139 24141 5.02e-07 29_[+3(3.21e-06)]_32_[+2(3.50e-05)]_\ 127_[+1(1.86e-07)]_250 24292 4.80e-07 164_[+2(2.52e-05)]_81_\ [+1(5.75e-06)]_8_[+3(1.37e-07)]_185 24347 7.86e-01 500 24367 2.91e-04 80_[+2(7.02e-05)]_284_\ [+3(1.74e-06)]_95 24585 8.72e-08 142_[+2(1.64e-05)]_229_\ [+1(6.35e-08)]_65_[+3(2.91e-06)]_2 24977 3.57e-03 287_[+2(4.70e-07)]_192 25270 2.98e-04 21_[+3(4.87e-05)]_431_\ [+1(4.41e-07)]_7 25309 1.26e-06 63_[+1(4.57e-06)]_33_[+3(1.93e-06)]_\ 4_[+1(2.20e-08)]_338 25490 7.68e-01 500 26022 8.36e-11 34_[+3(1.74e-05)]_141_\ [+2(4.37e-08)]_213_[+1(2.17e-09)]_50 261324 5.15e-09 184_[+2(1.05e-05)]_152_\ [+1(1.48e-07)]_2_[+3(8.96e-08)]_100 261601 1.04e-06 249_[+2(1.43e-07)]_7_[+3(2.06e-07)]_\ 203 262707 2.01e-07 33_[+3(8.02e-07)]_12_[+3(4.30e-06)]_\ 46_[+1(4.94e-06)]_22_[+1(7.57e-05)]_118_[+2(1.91e-06)]_166 264350 8.81e-01 500 264799 3.21e-05 33_[+3(1.15e-05)]_293_\ [+2(2.31e-05)]_107_[+1(8.30e-06)]_5 26553 1.37e-01 122_[+2(6.04e-05)]_357 269141 1.07e-03 45_[+1(1.84e-06)]_310_\ [+2(3.50e-05)]_103 31145 8.39e-10 217_[+3(1.40e-06)]_12_\ [+1(2.60e-06)]_152_[+2(5.35e-09)]_57 34730 7.97e-08 23_[+3(4.55e-05)]_194_\ [+2(1.24e-07)]_126_[+1(4.89e-07)]_95 34973 7.91e-06 79_[+1(2.53e-08)]_295_\ [+3(2.56e-05)]_85 35748 6.45e-02 283_[+2(6.53e-06)]_196 36673 1.17e-04 65_[+2(8.61e-07)]_159_\ [+3(7.48e-06)]_235 37928 8.10e-05 1_[+1(9.56e-06)]_256_[+2(3.21e-07)]_\ 201 38051 2.21e-05 162_[+2(2.63e-06)]_226_\ [+3(1.01e-06)]_71 39315 4.13e-04 222_[+2(2.74e-05)]_56_\ [+1(1.84e-06)]_180 4350 1.11e-06 33_[+2(3.98e-06)]_131_\ [+1(2.23e-05)]_73_[+3(5.64e-07)]_201 4408 4.37e-02 68_[+2(4.44e-05)]_411 4825 2.93e-05 328_[+2(3.24e-06)]_70_\ [+3(1.13e-06)]_61 5497 1.55e-08 105_[+1(8.14e-08)]_41_\ [+2(2.36e-06)]_219_[+3(2.38e-06)]_73 6151 1.35e-03 329_[+3(2.75e-05)]_31_\ [+1(1.02e-05)]_99 6925 1.07e-07 132_[+1(1.66e-08)]_91_\ [+1(4.16e-05)]_142_[+3(2.15e-06)]_73 7019 4.79e-03 471_[+2(3.24e-06)]_8 9818 5.45e-02 246_[+2(7.91e-06)]_233 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************