******************************************************************************** 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/481/481.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10595 1.0000 500 11278 1.0000 500 1195 1.0000 500 12171 1.0000 500 12983 1.0000 500 13089 1.0000 500 13343 1.0000 500 21316 1.0000 500 21437 1.0000 500 22042 1.0000 500 22057 1.0000 500 2243 1.0000 500 22505 1.0000 500 22960 1.0000 500 23335 1.0000 500 23566 1.0000 500 23841 1.0000 500 25095 1.0000 500 25476 1.0000 500 25739 1.0000 500 2604 1.0000 500 260917 1.0000 500 262567 1.0000 500 263451 1.0000 500 264297 1.0000 500 264607 1.0000 500 269258 1.0000 500 3614 1.0000 500 36443 1.0000 500 3870 1.0000 500 38845 1.0000 500 4386 1.0000 500 5766 1.0000 500 6743 1.0000 500 9143 1.0000 500 9150 1.0000 500 9463 1.0000 500 bd1822 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/481/481.seqs.fa -oc motifs/481 -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= 38 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= 19000 N= 38 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.237 G 0.241 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.237 G 0.241 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 38 llr = 358 E-value = 6.9e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1211:1::12:423435::14 pos.-specific C :11::1::31211:::1:211 probability G 52:532a2356222241:641 matrix T 458576:8421244433a235 bits 2.1 * 1.9 * * 1.7 * * 1.5 * * Relative 1.2 ** * Entropy 1.0 * ** * (13.6 bits) 0.8 *** ** * * 0.6 * *** ** * ** 0.4 * ****** ** ** ** * 0.2 ********************* 0.0 --------------------- Multilevel GTTGTTGTTGGATTTGATGGT consensus TA TGG GACTGAAAT TA sequence G C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9150 342 3.83e-11 AATTCTCACC TTTTTTGTTGGATTAGATGTT GCACCTGTTA 9143 342 3.83e-11 AATTCTCACC TTTTTTGTTGGATTAGATGTT GCACCTGTTA 23841 176 4.41e-10 TGTATTGGTT GGTTTTGTTGGATATGTTGGT AGAGGGGAAG 3870 226 3.44e-07 GTTTGTGTTT TTTTTTGTTCGCTTTGTTGTT GTACTATTTG 22960 105 4.67e-07 GTTATATTGA TATATGGTTGGATTTGTTGGT AGAGCAGTAT 21316 137 4.67e-07 GTAACGAAGG GGTGTTGTTTGCGATAATGGA ACGAAGTGTT 264297 10 1.45e-06 CATGATGAA GTATTTGGCGGAGAATATGGT GAGTACACCA 25095 343 1.45e-06 CTCGTCTGAT GATGGTGTCGGTCTTGATTGA GGGGCAGTGC 23566 128 1.89e-06 CATCCAATGC GGTGTTGGGAGTTGAGTTGGA GGCGAGGGGG 21437 248 3.51e-06 GAGGAGGAGC AGTTTGGTTGGATGATATGAA GATCGTGCCA bd1822 454 3.95e-06 GTTGAGCAAC ATTTTCGTCAGATTGAATGGA CGTGAGCTCA 1195 72 3.95e-06 ATCTCAGTTG GATGGGGTTGGTGTATTTCGT TGCCACACGA 260917 239 4.45e-06 TGCTGCTGCT GTTGCTGTCGGATGGGATGGC GAAGATGCGC 2604 70 4.45e-06 GGAGGGATGG TTTTGGGTTGGGTTTACTTTT GGTCGGTACA 25476 19 4.45e-06 AGGCAACTCG GTTTGTGTGGCCGAAAATCGA AGATTCTGGC 25739 149 6.26e-06 GGTGTGGGGT GATGTTGTGAGATAATGTCTA CTCTTTCCTC 5766 238 7.80e-06 CAACTGAAGA GTTGATGTCGGTGATGATGCT TCGTGGCTGT 9463 351 8.68e-06 GTGGCCTGTG GTTGTTGTGATACGTGTTTTA CGACGCCATT 22057 35 8.68e-06 TCATTTTTGA TTTTTTGTAGCCAAAGTTGTA TATATTGTTT 38845 326 1.46e-05 ACAAGGGCTA TTTGTGGGCAGGAGTTTTGGT GTTGAGTGGG 262567 264 2.15e-05 GTAGCTTGGA GCTTGTGTCGTGTATTATGGC ACTATCGGCA 263451 463 2.36e-05 CAACGACTTG GTTGGGGTGAGTGAGTGTGTT AGGGGGGGGC 6743 272 3.70e-05 CCCGCCAAAG TAATTTGTCTCTTTAACTGTT CAAACTTATT 13089 318 4.03e-05 GACGGCCAAC TTTGTCGGGTGGAGGGATGTT GGTGAGACGA 10595 170 4.03e-05 TTTGTTTTGC GTTGTTGGCGTTGATAATGAC GATGACTACA 23335 89 4.39e-05 TCTAACCAAA GCTGGAGTTGCCGTTGTTGGA AAGAGGACTG 13343 145 6.11e-05 ATGGATTGGT TGAGTGGTTGGGATGGATGTG TGCTGTGCAG 36443 55 6.62e-05 GAATTATACC TCCGTTGGTTGATGTGTTCGT GTAGTCATCA 269258 189 9.71e-05 TGAAAGATGA TTTTTTGTGAGGCAGACTCCA GTTCTAATAA 264607 81 1.21e-04 GATGATTGTC TTCTTCGTTGCATCTGTTTTT TGGTTCACTC 11278 170 1.39e-04 ATGTTAAAGA GATTGTGTCTCAATATCTCAA AGACCCCAGT 12983 419 1.49e-04 AGAAAGACAC TATGTCGTGATACTATATTAT GCAGAACCCT 12171 261 1.71e-04 CGTGTGACTC ATTATAGTTACTTGAAATGTT AAGGGACAAT 3614 118 1.82e-04 AGACAGCGCG TGCTTGGTGGCAGAAGATTAC TGATATTGGC 22505 46 1.82e-04 CATCTCATTA ATTTGTGTTCGTCATTGTCGA CCATTCGTTT 22042 56 1.82e-04 CTGGCTGGCT GGATGTGTGTCAATGAATGGG CATGTCAGCG 4386 92 2.08e-04 CCTACCATCG TGAGTTGTGTTGTGTACTTGA TACGCGTGTT 2243 280 2.36e-04 CCATCATGAC GATGTGGTAGGAATTAAAGCT GAAGCTAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9150 3.8e-11 341_[+1]_138 9143 3.8e-11 341_[+1]_138 23841 4.4e-10 175_[+1]_304 3870 3.4e-07 225_[+1]_254 22960 4.7e-07 104_[+1]_375 21316 4.7e-07 136_[+1]_343 264297 1.5e-06 9_[+1]_470 25095 1.5e-06 342_[+1]_137 23566 1.9e-06 127_[+1]_352 21437 3.5e-06 247_[+1]_232 bd1822 4e-06 453_[+1]_26 1195 4e-06 71_[+1]_408 260917 4.4e-06 238_[+1]_241 2604 4.4e-06 69_[+1]_410 25476 4.4e-06 18_[+1]_461 25739 6.3e-06 148_[+1]_331 5766 7.8e-06 237_[+1]_242 9463 8.7e-06 350_[+1]_129 22057 8.7e-06 34_[+1]_445 38845 1.5e-05 325_[+1]_154 262567 2.1e-05 263_[+1]_216 263451 2.4e-05 462_[+1]_17 6743 3.7e-05 271_[+1]_208 13089 4e-05 317_[+1]_162 10595 4e-05 169_[+1]_310 23335 4.4e-05 88_[+1]_391 13343 6.1e-05 144_[+1]_335 36443 6.6e-05 54_[+1]_425 269258 9.7e-05 188_[+1]_291 264607 0.00012 80_[+1]_399 11278 0.00014 169_[+1]_310 12983 0.00015 418_[+1]_61 12171 0.00017 260_[+1]_219 3614 0.00018 117_[+1]_362 22505 0.00018 45_[+1]_434 22042 0.00018 55_[+1]_424 4386 0.00021 91_[+1]_388 2243 0.00024 279_[+1]_200 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=38 9150 ( 342) TTTTTTGTTGGATTAGATGTT 1 9143 ( 342) TTTTTTGTTGGATTAGATGTT 1 23841 ( 176) GGTTTTGTTGGATATGTTGGT 1 3870 ( 226) TTTTTTGTTCGCTTTGTTGTT 1 22960 ( 105) TATATGGTTGGATTTGTTGGT 1 21316 ( 137) GGTGTTGTTTGCGATAATGGA 1 264297 ( 10) GTATTTGGCGGAGAATATGGT 1 25095 ( 343) GATGGTGTCGGTCTTGATTGA 1 23566 ( 128) GGTGTTGGGAGTTGAGTTGGA 1 21437 ( 248) AGTTTGGTTGGATGATATGAA 1 bd1822 ( 454) ATTTTCGTCAGATTGAATGGA 1 1195 ( 72) GATGGGGTTGGTGTATTTCGT 1 260917 ( 239) GTTGCTGTCGGATGGGATGGC 1 2604 ( 70) TTTTGGGTTGGGTTTACTTTT 1 25476 ( 19) GTTTGTGTGGCCGAAAATCGA 1 25739 ( 149) GATGTTGTGAGATAATGTCTA 1 5766 ( 238) GTTGATGTCGGTGATGATGCT 1 9463 ( 351) GTTGTTGTGATACGTGTTTTA 1 22057 ( 35) TTTTTTGTAGCCAAAGTTGTA 1 38845 ( 326) TTTGTGGGCAGGAGTTTTGGT 1 262567 ( 264) GCTTGTGTCGTGTATTATGGC 1 263451 ( 463) GTTGGGGTGAGTGAGTGTGTT 1 6743 ( 272) TAATTTGTCTCTTTAACTGTT 1 13089 ( 318) TTTGTCGGGTGGAGGGATGTT 1 10595 ( 170) GTTGTTGGCGTTGATAATGAC 1 23335 ( 89) GCTGGAGTTGCCGTTGTTGGA 1 13343 ( 145) TGAGTGGTTGGGATGGATGTG 1 36443 ( 55) TCCGTTGGTTGATGTGTTCGT 1 269258 ( 189) TTTTTTGTGAGGCAGACTCCA 1 264607 ( 81) TTCTTCGTTGCATCTGTTTTT 1 11278 ( 170) GATTGTGTCTCAATATCTCAA 1 12983 ( 419) TATGTCGTGATACTATATTAT 1 12171 ( 261) ATTATAGTTACTTGAAATGTT 1 3614 ( 118) TGCTTGGTGGCAGAAGATTAC 1 22505 ( 46) ATTTGTGTTCGTCATTGTCGA 1 22042 ( 56) GGATGTGTGTCAATGAATGGG 1 4386 ( 92) TGAGTTGTGTTGTGTACTTGA 1 2243 ( 280) GATGTGGTAGGAATTAAAGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 8.90388 E= 6.9e-008 -134 -1189 97 72 -34 -158 -20 96 -101 -158 -1189 162 -233 -1189 97 89 -333 -317 13 142 -233 -117 -3 124 -1189 -1189 205 -1189 -1189 -1189 -61 172 -233 15 26 62 -17 -217 113 -48 -1189 0 139 -96 75 -85 -39 -11 -53 -85 -3 80 36 -317 -3 62 47 -1189 -39 80 12 -1189 89 4 91 -85 -161 18 -333 -1189 -1189 192 -1189 -36 139 -48 -101 -158 89 42 47 -117 -219 89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 38 E= 6.9e-008 0.105263 0.000000 0.473684 0.421053 0.210526 0.078947 0.210526 0.500000 0.131579 0.078947 0.000000 0.789474 0.052632 0.000000 0.473684 0.473684 0.026316 0.026316 0.263158 0.684211 0.052632 0.105263 0.236842 0.605263 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.157895 0.842105 0.052632 0.263158 0.289474 0.394737 0.236842 0.052632 0.526316 0.184211 0.000000 0.236842 0.631579 0.131579 0.447368 0.131579 0.184211 0.236842 0.184211 0.131579 0.236842 0.447368 0.342105 0.026316 0.236842 0.394737 0.368421 0.000000 0.184211 0.447368 0.289474 0.000000 0.447368 0.263158 0.500000 0.131579 0.078947 0.289474 0.026316 0.000000 0.000000 0.973684 0.000000 0.184211 0.631579 0.184211 0.131579 0.078947 0.447368 0.342105 0.368421 0.105263 0.052632 0.473684 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][TAG]T[GT][TG][TG]GT[TGC][GA][GC][AT][TG][TAG][TA][GAT][AT]TG[GT][TA] -------------------------------------------------------------------------------- Time 10.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 38 llr = 360 E-value = 5.3e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :52361212432775712642 pos.-specific C 7482:6618337135:66228 probability G 1::3211::::12::12112: matrix T 21:12117:33:1::21222: bits 2.1 1.9 1.7 1.5 Relative 1.2 * * * Entropy 1.0 * * * * (13.7 bits) 0.8 * * ** * *** * 0.6 *** ** ****** * 0.4 *** ***** ********* * 0.2 ******************* * 0.0 --------------------- Multilevel CACAACCTCAACAACACCAAC consensus C G A ACTA CAT T sequence C TC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21316 447 1.92e-09 CCATACATAC CACCACCTACCCAAAACCATC ACGAGATACT 13343 298 9.45e-09 GCTGCTCTTG CACGACCTCCACAACACACTC TTTCAACGGA 12983 115 1.90e-08 CCATGGGATG CACCTCCTCCTCACCAGCAAC AGCCGGTAGT 2243 442 2.32e-07 CGCACTTCCT TCCGAACTCCCCACAACTAAC TAGCACACGC 13089 388 3.02e-07 TCCCGCCATT CCCAACCTCTTCCACACCCGA TCACGGATGC 22042 326 3.90e-07 ACAGCCGAAC GCCGACCTCCCAGCCACCAAC AACGCCTCAA 264297 381 7.27e-07 CGACAACGAA CAACACCTCACCAAATCTCAC CGCCGCCGTC 25739 470 8.23e-07 AGAACAATCT CCCATCGTCTTCAAAACATAC CATCACGAGC 269258 378 1.05e-06 ACTCCCTTTG CACGATACAAACAAAACCAGC CGAGCAACCC 22505 433 1.89e-06 TTCAACACAT CACGTGCTCATCAAAACAATA CCAATATTAG 25476 465 2.37e-06 TCTTGCCAAA CACATCCTACAATACACCATC AACATCATCA 1195 404 3.29e-06 CGAACACAAA CACGAGCACAAAACCACAAAC CAACCGTTGA 11278 448 4.07e-06 CTTTCAAGCA CACCATTTCACAACAAGCAGC TTCACGAAAC 38845 198 5.03e-06 CGCTATCCTC CACGACTTCCTCTCCTCCCTC TGGTTCATCC 23566 424 1.13e-05 AACACTCGCC CACAACCCACTCACAGCCTCC AACGATGATT 23335 193 1.13e-05 ACAACGTTGA CACAAACTCAAGAACAGAACA AAATGCCACT 3614 297 1.25e-05 TGATCTCCAG CCCTGGCTCTCCAACACCAGG TAGAAGTTGG 22960 475 1.25e-05 CAACAAGAGA CCCAAAATCACAAAATCTTTC GACCA 260917 44 1.37e-05 TCCGACGACG ATCATCCTCTTCAAAACTAGC AGAGGCACTC 6743 169 1.51e-05 TGTGCCGGAA CCCGTCTTCTTCAAAATGTGC AAATAAATAA 3870 479 1.51e-05 CCGCGGGCAA CCAAACGTACCAAAATCCCAC G 9150 469 2.18e-05 CAATCGTTGC TCCCGCCTATAGCACAGCAAC CGTTTCTTAC 9143 469 2.18e-05 CAATCGTTGC TCCCGCCTATAGCACAGCAAC CGTTTCTTAC 36443 475 2.18e-05 AACGTGCTTC TCCATTCTCCTGAACACAAAA CAACA 9463 8 2.62e-05 CTTTTGA CAAGACCCCGCCAAAACCGCC CGCCTCTTTC 22057 227 2.86e-05 TCTATACTTT CACTACCAACACAACAACACA GATTGATTAT bd1822 285 3.13e-05 ACGCCTTAAA CCCAAGTCCCTCGAAACTCTC GTCTTGTACT 263451 187 3.13e-05 TGGATTTCGT CCCGGCAGCAACACAATCTAC GTAAGCAGTC 10595 457 4.06e-05 GTGTCATTGT TTCAAAACCACAACCACCAAC CCCTACCGCC 5766 189 4.42e-05 TACCTGAGAT GACGACAAAATCGACATCAAC CATCGTCAAG 23841 433 6.69e-05 AGACACCGCC CCCCCCCTCTCCCCCGCCTGC TTGCATCCAC 262567 3 7.26e-05 CC CCAAGCAACAACAACTCCGCC GCTCGTTCGA 25095 279 8.51e-05 ATGTACACTT CACTGCGTCTACAAACACAGC CCCTGCCTGA 12171 455 1.16e-04 GTCTTTTATC TCCCACCTCATCGCATATACA GTCAGCCAGT 21437 35 1.81e-04 GTTTTGAACT CACCACTTCAAGGAGAGGATC TGTCCTCTCC 264607 224 2.24e-04 AGATTCAGGG CTTGATATCTTCACATCCAAA GGGGGTTCAC 4386 37 3.16e-04 CGACAAGATC GAAGGTATCAACGACAGTATC GAATCTGCTT 2604 115 5.62e-04 ATGAGTCGTT TCAAAAGTCTCAAACTTGAAC ATACAGTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21316 1.9e-09 446_[+2]_33 13343 9.4e-09 297_[+2]_182 12983 1.9e-08 114_[+2]_365 2243 2.3e-07 441_[+2]_38 13089 3e-07 387_[+2]_92 22042 3.9e-07 325_[+2]_154 264297 7.3e-07 380_[+2]_99 25739 8.2e-07 469_[+2]_10 269258 1.1e-06 377_[+2]_102 22505 1.9e-06 432_[+2]_47 25476 2.4e-06 464_[+2]_15 1195 3.3e-06 403_[+2]_76 11278 4.1e-06 447_[+2]_32 38845 5e-06 197_[+2]_282 23566 1.1e-05 423_[+2]_56 23335 1.1e-05 192_[+2]_287 3614 1.2e-05 296_[+2]_183 22960 1.2e-05 474_[+2]_5 260917 1.4e-05 43_[+2]_436 6743 1.5e-05 168_[+2]_311 3870 1.5e-05 478_[+2]_1 9150 2.2e-05 468_[+2]_11 9143 2.2e-05 468_[+2]_11 36443 2.2e-05 474_[+2]_5 9463 2.6e-05 7_[+2]_472 22057 2.9e-05 226_[+2]_253 bd1822 3.1e-05 284_[+2]_195 263451 3.1e-05 186_[+2]_293 10595 4.1e-05 456_[+2]_23 5766 4.4e-05 188_[+2]_291 23841 6.7e-05 432_[+2]_47 262567 7.3e-05 2_[+2]_477 25095 8.5e-05 278_[+2]_201 12171 0.00012 454_[+2]_25 21437 0.00018 34_[+2]_445 264607 0.00022 223_[+2]_256 4386 0.00032 36_[+2]_443 2604 0.00056 114_[+2]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=38 21316 ( 447) CACCACCTACCCAAAACCATC 1 13343 ( 298) CACGACCTCCACAACACACTC 1 12983 ( 115) CACCTCCTCCTCACCAGCAAC 1 2243 ( 442) TCCGAACTCCCCACAACTAAC 1 13089 ( 388) CCCAACCTCTTCCACACCCGA 1 22042 ( 326) GCCGACCTCCCAGCCACCAAC 1 264297 ( 381) CAACACCTCACCAAATCTCAC 1 25739 ( 470) CCCATCGTCTTCAAAACATAC 1 269258 ( 378) CACGATACAAACAAAACCAGC 1 22505 ( 433) CACGTGCTCATCAAAACAATA 1 25476 ( 465) CACATCCTACAATACACCATC 1 1195 ( 404) CACGAGCACAAAACCACAAAC 1 11278 ( 448) CACCATTTCACAACAAGCAGC 1 38845 ( 198) CACGACTTCCTCTCCTCCCTC 1 23566 ( 424) CACAACCCACTCACAGCCTCC 1 23335 ( 193) CACAAACTCAAGAACAGAACA 1 3614 ( 297) CCCTGGCTCTCCAACACCAGG 1 22960 ( 475) CCCAAAATCACAAAATCTTTC 1 260917 ( 44) ATCATCCTCTTCAAAACTAGC 1 6743 ( 169) CCCGTCTTCTTCAAAATGTGC 1 3870 ( 479) CCAAACGTACCAAAATCCCAC 1 9150 ( 469) TCCCGCCTATAGCACAGCAAC 1 9143 ( 469) TCCCGCCTATAGCACAGCAAC 1 36443 ( 475) TCCATTCTCCTGAACACAAAA 1 9463 ( 8) CAAGACCCCGCCAAAACCGCC 1 22057 ( 227) CACTACCAACACAACAACACA 1 bd1822 ( 285) CCCAAGTCCCTCGAAACTCTC 1 263451 ( 187) CCCGGCAGCAACACAATCTAC 1 10595 ( 457) TTCAAAACCACAACCACCAAC 1 5766 ( 189) GACGACAAAATCGACATCAAC 1 23841 ( 433) CCCCCCCTCTCCCCCGCCTGC 1 262567 ( 3) CCAAGCAACAACAACTCCGCC 1 25095 ( 279) CACTGCGTCTACAAACACAGC 1 12171 ( 455) TCCCACCTCATCGCATATACA 1 21437 ( 35) CACCACTTCAAGGAGAGGATC 1 264607 ( 224) CTTGATATCTTCACATCCAAA 1 4386 ( 37) GAAGGTATCAACGACAGTATC 1 2604 ( 115) TCAAAAGTCTCAAACTTGAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 9.09908 E= 5.3e-007 -333 158 -161 -48 83 92 -1189 -170 -75 178 -1189 -328 36 0 50 -170 119 -317 -39 -48 -101 141 -119 -96 -34 122 -119 -96 -134 -85 -319 152 -17 169 -1189 -1189 47 41 -319 18 36 41 -1189 42 -34 147 -87 -1189 136 -117 -61 -228 136 41 -1189 -1189 83 108 -319 -1189 142 -317 -219 -28 -175 141 -39 -128 -75 129 -161 -48 125 -58 -219 -70 57 -58 -20 -11 -53 174 -319 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 38 E= 5.3e-007 0.026316 0.710526 0.078947 0.184211 0.473684 0.447368 0.000000 0.078947 0.157895 0.815789 0.000000 0.026316 0.342105 0.236842 0.342105 0.078947 0.605263 0.026316 0.184211 0.184211 0.131579 0.631579 0.105263 0.131579 0.210526 0.552632 0.105263 0.131579 0.105263 0.131579 0.026316 0.736842 0.236842 0.763158 0.000000 0.000000 0.368421 0.315789 0.026316 0.289474 0.342105 0.315789 0.000000 0.342105 0.210526 0.657895 0.131579 0.000000 0.684211 0.105263 0.157895 0.052632 0.684211 0.315789 0.000000 0.000000 0.473684 0.500000 0.026316 0.000000 0.710526 0.026316 0.052632 0.210526 0.078947 0.631579 0.184211 0.105263 0.157895 0.578947 0.078947 0.184211 0.631579 0.157895 0.052632 0.157895 0.394737 0.157895 0.210526 0.236842 0.184211 0.789474 0.026316 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AC]C[AGC]AC[CA]T[CA][ACT][ATC][CA]A[AC][CA][AT]CCA[ATG]C -------------------------------------------------------------------------------- Time 21.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 38 llr = 355 E-value = 1.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3221474125:65133:32: pos.-specific C 1111::2111:::1121:31: probability G 8:4366146645248439329 matrix T :543311:21252:1141:6: bits 2.1 1.9 1.7 * 1.5 * * Relative 1.2 * * * Entropy 1.0 * * * * (13.5 bits) 0.8 * * * * * * 0.6 * ****** **** * * 0.4 ** *********** * ** 0.2 **************** **** 0.0 --------------------- Multilevel GTGGGGAAGGAGAAGGTGGTG consensus ATTTA GTAGTGG AA AA sequence A CG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6743 129 5.85e-08 TCGTATCAAA GTGAGAAAGGGGAAGAGGAGG AGTGTTCCCT 9143 241 8.14e-08 ACGGTTGGCT GCTTGGAGGGAGACGAAGATG GCTTAAATCA 23566 61 1.12e-07 GCGGCGGCGT GAGCGGAGGAGTAGGGTGGTG ATCCTTCAAG 9150 241 3.15e-07 ACGGTTGGCT GCTTGGAGGGAGACGACGATG GCTTAAATCA 11278 33 3.62e-07 AATGTGAAAT GTATGAAAGGATGAGATGAGG TGCGTATCTG 264297 252 4.16e-07 TATCAGGAAC GAGAGGAAGCAGAGGGGGGAG GGCGAAGCTT 21316 174 4.77e-07 TGTTGAATCA GATTGGAAGAGTAATGTGCTG ACGTAGCAAG 36443 402 6.22e-07 GTTGTGGATT GTTGTAAGGAGTAGGAGGAGG TCCGTCTCAA 22042 118 7.09e-07 GTAGCGTAGG GTGAGAAGTGATAGTGTGATG ATGTCAAGAG 10595 261 1.17e-06 GGTGCTCAAT GCAAGGAGAGAGAAGATGATG AGATAATGCC bd1822 55 1.50e-06 GTTGGTACTT GTTTGGAGGGTGTAGAGTGTG AAATCATAAG 12171 118 2.69e-06 GCCAATGGCT GTGAGGAGGATGACGGCGGAG GGTCTTGTCA 3614 398 5.19e-06 CCAGCGCAGA GTTTGGAACGATTGGATGGCG GCGAGGTCGG 263451 79 5.19e-06 ACTGTACAAA GAAATGAATGGTGCGATGCTG CGAGTAGCTC 262567 375 7.87e-06 GTCAATCGAA GCCGGCAGGGGGAAGGGGGTG GAAGTCGGGG 38845 75 8.71e-06 CGCCAAGAGA GTGATGAAGGAGTGGCAGCTC AATCAGCAGC 22960 38 1.06e-05 AGAGAAGCCA GTTGTAGATGATAGAATGATG GATGCAAAAA 22505 378 1.06e-05 CCACAAACTT GAGGTACAGGAGAAGGAGGTA TTTACACATC 21437 226 1.29e-05 TTCGTTAGAG CTGGGAACGAGGGAGGAGGAG CAGTTTGGTT 25476 55 1.57e-05 CTGGCGGGGA GTTCTGAGCGGGAAGAGTCTG AGCGGGAAGA 4386 221 1.72e-05 TAGAAACTAC GTGTAGCAGAAGAGCGTGATG CATATGAATA 264607 477 1.72e-05 ACTGTTTACT GTGGGAACGTGGTAGCAGAAG GCC 1195 36 1.89e-05 CCGAACTTGC GTAGGTACGAAGAAGGCGGAG GGCTGATCTC 9463 285 2.07e-05 CCACTGTGTT GGTGTAGGGGAGTGGCTGCTG TGCTGGACTG 3870 254 2.49e-05 GTTGTACTAT TTGTGGCAGGTGGAGCGGGTG TTCTCGTGTG 13089 126 2.72e-05 AGATATCTTG GTGTTTGGTGATAAGCAGCAG CAGAGGAGGT 25095 461 4.21e-05 GCCTCCGGTC GTTTGAACTGGTGGGAGACTG CTCCACAAAG 12983 341 4.98e-05 GAAGCATGCC GAAAAGAATGGTGAGTTGATG TGAATGTTTC 22057 390 5.41e-05 TCAGTCTTAC GAAAGGAGCGAGAGGCAGTGG CTCGTATCGT 5766 132 6.38e-05 GTTTTGCGGT GAGGTGTGGTGTACGGGGCAG CATAGGTCGA 269258 145 8.11e-05 GATGTCTACC GTGTGAAGTGATGAATCGAAG ATCAAAAATG 23841 343 1.11e-04 CATGACACTA AACTGGTAGGATAAGAAGGTG ATCAACCCTG 25739 356 1.29e-04 TCTCAAACCC GTGGTAGCAGGGGGTGTGCTG ACAGATGGTG 2243 134 1.49e-04 ATTAGTTTTA CAACTGAAGATTAAAGTGCTG ATTCAATCCC 23335 27 1.99e-04 CTATCGGGAG GATTGGCAGCGTTGGCATCGG AGTTGGCTTT 260917 389 2.82e-04 CAACATATTA CATGTACATGATAAACAGGGG ACAAAAGAGG 2604 27 4.46e-04 GCGGGTTGGT CTTGAAAGAATGAGGGTGCCG AGCGCAAGCG 13343 167 5.39e-04 ATGGATGTGT GCTGTGCAGCTTTGCGGGGAG CATCCCTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6743 5.9e-08 128_[+3]_351 9143 8.1e-08 240_[+3]_239 23566 1.1e-07 60_[+3]_419 9150 3.2e-07 240_[+3]_239 11278 3.6e-07 32_[+3]_447 264297 4.2e-07 251_[+3]_228 21316 4.8e-07 173_[+3]_306 36443 6.2e-07 401_[+3]_78 22042 7.1e-07 117_[+3]_362 10595 1.2e-06 260_[+3]_219 bd1822 1.5e-06 54_[+3]_425 12171 2.7e-06 117_[+3]_362 3614 5.2e-06 397_[+3]_82 263451 5.2e-06 78_[+3]_401 262567 7.9e-06 374_[+3]_105 38845 8.7e-06 74_[+3]_405 22960 1.1e-05 37_[+3]_442 22505 1.1e-05 377_[+3]_102 21437 1.3e-05 225_[+3]_254 25476 1.6e-05 54_[+3]_425 4386 1.7e-05 220_[+3]_259 264607 1.7e-05 476_[+3]_3 1195 1.9e-05 35_[+3]_444 9463 2.1e-05 284_[+3]_195 3870 2.5e-05 253_[+3]_226 13089 2.7e-05 125_[+3]_354 25095 4.2e-05 460_[+3]_19 12983 5e-05 340_[+3]_139 22057 5.4e-05 389_[+3]_90 5766 6.4e-05 131_[+3]_348 269258 8.1e-05 144_[+3]_335 23841 0.00011 342_[+3]_137 25739 0.00013 355_[+3]_124 2243 0.00015 133_[+3]_346 23335 0.0002 26_[+3]_453 260917 0.00028 388_[+3]_91 2604 0.00045 26_[+3]_453 13343 0.00054 166_[+3]_313 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=38 6743 ( 129) GTGAGAAAGGGGAAGAGGAGG 1 9143 ( 241) GCTTGGAGGGAGACGAAGATG 1 23566 ( 61) GAGCGGAGGAGTAGGGTGGTG 1 9150 ( 241) GCTTGGAGGGAGACGACGATG 1 11278 ( 33) GTATGAAAGGATGAGATGAGG 1 264297 ( 252) GAGAGGAAGCAGAGGGGGGAG 1 21316 ( 174) GATTGGAAGAGTAATGTGCTG 1 36443 ( 402) GTTGTAAGGAGTAGGAGGAGG 1 22042 ( 118) GTGAGAAGTGATAGTGTGATG 1 10595 ( 261) GCAAGGAGAGAGAAGATGATG 1 bd1822 ( 55) GTTTGGAGGGTGTAGAGTGTG 1 12171 ( 118) GTGAGGAGGATGACGGCGGAG 1 3614 ( 398) GTTTGGAACGATTGGATGGCG 1 263451 ( 79) GAAATGAATGGTGCGATGCTG 1 262567 ( 375) GCCGGCAGGGGGAAGGGGGTG 1 38845 ( 75) GTGATGAAGGAGTGGCAGCTC 1 22960 ( 38) GTTGTAGATGATAGAATGATG 1 22505 ( 378) GAGGTACAGGAGAAGGAGGTA 1 21437 ( 226) CTGGGAACGAGGGAGGAGGAG 1 25476 ( 55) GTTCTGAGCGGGAAGAGTCTG 1 4386 ( 221) GTGTAGCAGAAGAGCGTGATG 1 264607 ( 477) GTGGGAACGTGGTAGCAGAAG 1 1195 ( 36) GTAGGTACGAAGAAGGCGGAG 1 9463 ( 285) GGTGTAGGGGAGTGGCTGCTG 1 3870 ( 254) TTGTGGCAGGTGGAGCGGGTG 1 13089 ( 126) GTGTTTGGTGATAAGCAGCAG 1 25095 ( 461) GTTTGAACTGGTGGGAGACTG 1 12983 ( 341) GAAAAGAATGGTGAGTTGATG 1 22057 ( 390) GAAAGGAGCGAGAGGCAGTGG 1 5766 ( 132) GAGGTGTGGTGTACGGGGCAG 1 269258 ( 145) GTGTGAAGTGATGAATCGAAG 1 23841 ( 343) AACTGGTAGGATAAGAAGGTG 1 25739 ( 356) GTGGTAGCAGGGGGTGTGCTG 1 2243 ( 134) CAACTGAAGATTAAAGTGCTG 1 23335 ( 27) GATTGGCAGCGTTGGCATCGG 1 260917 ( 389) CATGTACATGATAAACAGGGG 1 2604 ( 27) CTTGAAAGAATGAGGGTGCCG 1 13343 ( 167) GCTGTGCAGCTTTGCGGGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 8.90388 E= 1.2e-005 -333 -117 180 -328 25 -85 -319 104 -53 -217 71 52 -17 -158 50 42 -175 -1189 126 42 47 -317 120 -228 136 -58 -119 -228 75 -85 80 -1189 -175 -158 139 -28 -17 -158 139 -228 83 -1189 61 -70 -1189 -1189 113 89 119 -1189 -20 -48 83 -85 71 -1189 -134 -217 166 -170 36 -17 71 -228 -1 -117 13 52 -333 -1189 189 -170 25 41 50 -328 -17 -217 -61 111 -333 -317 197 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 38 E= 1.2e-005 0.026316 0.105263 0.842105 0.026316 0.315789 0.131579 0.026316 0.526316 0.184211 0.052632 0.394737 0.368421 0.236842 0.078947 0.342105 0.342105 0.078947 0.000000 0.578947 0.342105 0.368421 0.026316 0.552632 0.052632 0.684211 0.157895 0.105263 0.052632 0.447368 0.131579 0.421053 0.000000 0.078947 0.078947 0.631579 0.210526 0.236842 0.078947 0.631579 0.052632 0.473684 0.000000 0.368421 0.157895 0.000000 0.000000 0.526316 0.473684 0.605263 0.000000 0.210526 0.184211 0.473684 0.131579 0.394737 0.000000 0.105263 0.052632 0.763158 0.078947 0.342105 0.210526 0.394737 0.052632 0.263158 0.105263 0.263158 0.368421 0.026316 0.000000 0.894737 0.078947 0.315789 0.315789 0.342105 0.026316 0.236842 0.052632 0.157895 0.552632 0.026316 0.026316 0.947368 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TA][GT][GTA][GT][GA]A[AG][GT][GA][AG][GT][AG][AG]G[GAC][TAG]G[GAC][TA]G -------------------------------------------------------------------------------- Time 31.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10595 2.81e-05 169_[+1(4.03e-05)]_70_\ [+3(1.17e-06)]_42_[+3(5.41e-05)]_112_[+2(4.06e-05)]_23 11278 3.82e-06 32_[+3(3.62e-07)]_394_\ [+2(4.07e-06)]_32 1195 4.59e-06 35_[+3(1.89e-05)]_15_[+1(3.95e-06)]_\ 311_[+2(3.29e-06)]_76 12171 4.75e-04 117_[+3(2.69e-06)]_362 12983 2.70e-06 114_[+2(1.90e-08)]_205_\ [+3(4.98e-05)]_139 13089 5.94e-06 125_[+3(2.72e-05)]_171_\ [+1(4.03e-05)]_49_[+2(3.02e-07)]_92 13343 5.03e-06 144_[+1(6.11e-05)]_132_\ [+2(9.45e-09)]_182 21316 2.37e-11 136_[+1(4.67e-07)]_16_\ [+3(4.77e-07)]_252_[+2(1.92e-09)]_33 21437 9.74e-05 88_[+1(8.36e-05)]_116_\ [+3(1.29e-05)]_1_[+1(3.51e-06)]_232 22042 1.07e-06 117_[+3(7.09e-07)]_187_\ [+2(3.90e-07)]_154 22057 1.52e-04 34_[+1(8.68e-06)]_171_\ [+2(2.86e-05)]_142_[+3(5.41e-05)]_90 2243 9.31e-05 441_[+2(2.32e-07)]_38 22505 4.83e-05 377_[+3(1.06e-05)]_34_\ [+2(1.89e-06)]_47 22960 1.34e-06 37_[+3(1.06e-05)]_46_[+1(4.67e-07)]_\ 349_[+2(1.25e-05)]_5 23335 8.08e-04 88_[+1(4.39e-05)]_83_[+2(1.13e-05)]_\ 287 23566 7.01e-08 60_[+3(1.12e-07)]_46_[+1(1.89e-06)]_\ 275_[+2(1.13e-05)]_56 23841 9.00e-08 175_[+1(4.41e-10)]_236_\ [+2(6.69e-05)]_47 25095 6.63e-05 278_[+2(8.51e-05)]_43_\ [+1(1.45e-06)]_97_[+3(4.21e-05)]_19 25476 3.22e-06 18_[+1(4.45e-06)]_15_[+3(1.57e-05)]_\ 389_[+2(2.37e-06)]_15 25739 1.09e-05 148_[+1(6.26e-06)]_300_\ [+2(8.23e-07)]_10 2604 5.14e-03 69_[+1(4.45e-06)]_410 260917 1.80e-04 43_[+2(1.37e-05)]_174_\ [+1(4.45e-06)]_241 262567 1.40e-04 2_[+2(7.26e-05)]_79_[+1(7.74e-05)]_\ 140_[+1(2.15e-05)]_90_[+3(7.87e-06)]_105 263451 5.15e-05 78_[+3(5.19e-06)]_87_[+2(3.13e-05)]_\ 255_[+1(2.36e-05)]_17 264297 1.49e-08 9_[+1(1.45e-06)]_176_[+3(5.77e-06)]_\ 24_[+3(4.16e-07)]_108_[+2(7.27e-07)]_99 264607 2.86e-03 476_[+3(1.72e-05)]_3 269258 9.84e-05 144_[+3(8.11e-05)]_23_\ [+1(9.71e-05)]_168_[+2(1.05e-06)]_102 3614 1.33e-04 296_[+2(1.25e-05)]_80_\ [+3(5.19e-06)]_82 36443 1.44e-05 54_[+1(6.62e-05)]_294_\ [+3(1.17e-05)]_11_[+3(6.22e-07)]_52_[+2(2.18e-05)]_5 3870 2.58e-06 225_[+1(3.44e-07)]_7_[+3(2.49e-05)]_\ 204_[+2(1.51e-05)]_1 38845 1.07e-05 74_[+3(8.71e-06)]_102_\ [+2(5.03e-06)]_107_[+1(1.46e-05)]_154 4386 5.67e-03 220_[+3(1.72e-05)]_259 5766 2.31e-04 131_[+3(6.38e-05)]_36_\ [+2(4.42e-05)]_28_[+1(7.80e-06)]_242 6743 7.47e-07 128_[+3(5.85e-08)]_19_\ [+2(1.51e-05)]_82_[+1(3.70e-05)]_208 9143 4.22e-12 240_[+3(8.14e-08)]_80_\ [+1(3.83e-11)]_106_[+2(2.18e-05)]_11 9150 1.50e-11 240_[+3(3.15e-07)]_80_\ [+1(3.83e-11)]_106_[+2(2.18e-05)]_11 9463 6.18e-05 7_[+2(2.62e-05)]_256_[+3(2.07e-05)]_\ 45_[+1(8.68e-06)]_129 bd1822 3.57e-06 54_[+3(1.50e-06)]_209_\ [+2(3.13e-05)]_148_[+1(3.95e-06)]_26 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************