******************************************************************************** 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/36/36.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10762 1.0000 500 10903 1.0000 500 11436 1.0000 500 11453 1.0000 500 11953 1.0000 500 1681 1.0000 500 1740 1.0000 500 20987 1.0000 500 21108 1.0000 500 21646 1.0000 500 22883 1.0000 500 23243 1.0000 500 23788 1.0000 500 23984 1.0000 500 24113 1.0000 500 24936 1.0000 500 25132 1.0000 500 2562 1.0000 500 261492 1.0000 500 262242 1.0000 500 263475 1.0000 500 264353 1.0000 500 264583 1.0000 500 31011 1.0000 500 33193 1.0000 500 3397 1.0000 500 3867 1.0000 500 413 1.0000 500 5193 1.0000 500 5283 1.0000 500 5729 1.0000 500 7172 1.0000 500 9032 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/36/36.seqs.fa -oc motifs/36 -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= 33 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= 16500 N= 33 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.241 G 0.232 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.241 G 0.232 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 27 llr = 256 E-value = 3.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5:7::71:36:6 pos.-specific C :a:19:1a1:91 probability G ::11:3::6::3 matrix T 4:17::7::41: bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * ** * * Entropy 1.1 * ** * * (13.7 bits) 0.8 ****** ***** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACATCATCGACA consensus T G AT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24936 450 1.31e-07 ACGCAACTGC TCATCATCGACA GCACCCCACA 3397 418 3.25e-07 GCTTCGCAAC ACATCATCGACG CTACCAACAT 264583 133 3.85e-07 GAACTGGAAG TCATCATCGACG TCATCCTAGC 262242 345 6.37e-07 GAGATGAGAA TCATCATCGTCG GTGACACCTC 11953 1 1.27e-06 . TCATCGTCGTCA TCGCTACGGC 23788 477 1.64e-06 GAATACTATC ACATCATCATCG CAACCATATA 9032 441 2.26e-06 ACGCCACGCG ACATCAACGTCA ACACAGCCGT 33193 389 2.26e-06 GCCCTTTATC ACATCACCGACA TGTCACAACT 1740 56 4.30e-06 ACTGGATCAA ACAGCATCAACA AACAGGCATA 24113 363 5.32e-06 ATGCCGGCCA ACATCATCCTCA AAAGGTTCGA 31011 260 7.43e-06 CGCCACTCTT TCACCATCATCA CCCCTTGAGG 5729 484 8.29e-06 CAATCTTCAA TCATCACCAACA AAGCC 10762 266 8.29e-06 AGGTGCAGCC ACATCAACAACG ACGTCTGCCG 22883 227 1.96e-05 TGTTACCAGC TCGTCGTCGTCG GCGTATGGTG 5193 486 2.12e-05 ACACAAAACA ACAGCAACAACA ATA 2562 335 2.31e-05 CTAGCTCCCG ACACCATCCTCA CCGTTGCCCT 21108 428 3.00e-05 CTGATACGAT ACATGGTCGACA CTTCTTCAGT 7172 19 3.81e-05 ATTCTCTCTT TCATTGTCGACA CGTCATCACT 11436 436 3.81e-05 CATCCGCAAT ACAGCGTCGACC TTCCACCGCC 23243 1 4.80e-05 . TCAGCAGCGTCA ATCTCCGCTT 1681 473 6.02e-05 GTCCGTCGTC ACGTCATCGAAA TATACGGTGA 263475 453 7.40e-05 GTGTTCTACT ACTTCATCGAGG CTTCCTCATC 10903 417 8.51e-05 GATAGATGGG ACTCCATCGTCC GTCCCCCGTA 261492 101 9.10e-05 TGGCAGCGTA TCTTCATCATTA AACAGTTAGT 20987 26 9.10e-05 ACGTTGGTGC GCATCATCGATG ATGAGAATCG 413 130 1.11e-04 AGGGATGCTC TCGTCGCCATCA CCGCCGCCGT 264353 22 1.41e-04 TCGGCACGCC TCTCCGACGACG ACGTTGGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24936 1.3e-07 449_[+1]_39 3397 3.2e-07 417_[+1]_71 264583 3.8e-07 132_[+1]_356 262242 6.4e-07 344_[+1]_144 11953 1.3e-06 [+1]_488 23788 1.6e-06 476_[+1]_12 9032 2.3e-06 440_[+1]_48 33193 2.3e-06 388_[+1]_100 1740 4.3e-06 55_[+1]_433 24113 5.3e-06 362_[+1]_126 31011 7.4e-06 259_[+1]_229 5729 8.3e-06 483_[+1]_5 10762 8.3e-06 265_[+1]_223 22883 2e-05 226_[+1]_262 5193 2.1e-05 485_[+1]_3 2562 2.3e-05 334_[+1]_154 21108 3e-05 427_[+1]_61 7172 3.8e-05 18_[+1]_470 11436 3.8e-05 435_[+1]_53 23243 4.8e-05 [+1]_488 1681 6e-05 472_[+1]_16 263475 7.4e-05 452_[+1]_36 10903 8.5e-05 416_[+1]_72 261492 9.1e-05 100_[+1]_388 20987 9.1e-05 25_[+1]_463 413 0.00011 129_[+1]_359 264353 0.00014 21_[+1]_467 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=27 24936 ( 450) TCATCATCGACA 1 3397 ( 418) ACATCATCGACG 1 264583 ( 133) TCATCATCGACG 1 262242 ( 345) TCATCATCGTCG 1 11953 ( 1) TCATCGTCGTCA 1 23788 ( 477) ACATCATCATCG 1 9032 ( 441) ACATCAACGTCA 1 33193 ( 389) ACATCACCGACA 1 1740 ( 56) ACAGCATCAACA 1 24113 ( 363) ACATCATCCTCA 1 31011 ( 260) TCACCATCATCA 1 5729 ( 484) TCATCACCAACA 1 10762 ( 266) ACATCAACAACG 1 22883 ( 227) TCGTCGTCGTCG 1 5193 ( 486) ACAGCAACAACA 1 2562 ( 335) ACACCATCCTCA 1 21108 ( 428) ACATGGTCGACA 1 7172 ( 19) TCATTGTCGACA 1 11436 ( 436) ACAGCGTCGACC 1 23243 ( 1) TCAGCAGCGTCA 1 1681 ( 473) ACGTCATCGAAA 1 263475 ( 453) ACTTCATCGAGG 1 10903 ( 417) ACTCCATCGTCC 1 261492 ( 101) TCTTCATCATTA 1 20987 ( 26) GCATCATCGATG 1 413 ( 130) TCGTCGCCATCA 1 264353 ( 22) TCTCCGACGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16137 bayes= 9.79059 E= 3.0e-007 101 -1140 -265 73 -1140 205 -1140 -1140 152 -1140 -106 -86 -1140 -70 -65 139 -1140 194 -265 -285 152 -1140 16 -1140 -80 -112 -265 139 -1140 205 -1140 -1140 20 -170 144 -1140 110 -1140 -1140 73 -280 182 -265 -186 120 -170 52 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 27 E= 3.0e-007 0.518519 0.000000 0.037037 0.444444 0.000000 1.000000 0.000000 0.000000 0.740741 0.000000 0.111111 0.148148 0.000000 0.148148 0.148148 0.703704 0.000000 0.925926 0.037037 0.037037 0.740741 0.000000 0.259259 0.000000 0.148148 0.111111 0.037037 0.703704 0.000000 1.000000 0.000000 0.000000 0.296296 0.074074 0.629630 0.000000 0.555556 0.000000 0.000000 0.444444 0.037037 0.851852 0.037037 0.074074 0.592593 0.074074 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]CATC[AG]TC[GA][AT]C[AG] -------------------------------------------------------------------------------- Time 9.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 31 llr = 304 E-value = 1.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3122:1:11:31431:42:6 pos.-specific C :33:13::41:1:121222:: probability G a4271463:6728326724a1 matrix T :14:544752341241123:3 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * * (14.2 bits) 0.8 * * ** * * * 0.6 * * ***** * ** ** 0.4 * * ****** * ** ** 0.2 *********** ** ** ** 0.0 --------------------- Multilevel GGTGTGGTTGGTGATGGAGGA consensus ACAATTGCTTA GA CT T sequence C C G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20987 155 5.07e-10 GTGGGCGGCT GGCGTTGTTGGGGAGGGCGGA TGCTGCTACG 413 36 6.20e-09 TGCCTACGGA GGCGTCGTCGGTGGAGGGGGT GGCTGTAGTG 23243 33 1.66e-07 GAGGCTATCA GACGACTTTGGAGGTGGCTGT GACGGCAAGA 261492 283 1.94e-07 GATTGGTGGT GATGGCGGTGGAGAAGGTGGA ACAGCTTGAT 3397 303 3.50e-07 GGTGTTTGTG GCTGGTTTCGGAGGTGGGAGA TTTTTCTACA 3867 448 9.07e-07 GAAGACGGAG GGGGTGGTTGGTTGTGGTTGT CCAATAGATA 10903 3 1.03e-06 TC GCCGTTGTCGTCGATTGGTGA GTAGGACGTG 24936 341 1.17e-06 GAGCGAGAGT GGTGTTGTTGTGTTCGGAGGA CCGGTTCTAT 1681 226 1.17e-06 AAGGTTCGGA GGGATCTTTGGGGAGCGAGGA GATAACACAA 5283 281 1.33e-06 AAGAGTGTAG GGGAAGTTTGTGGGAGGATGA GGATGTCAAT 25132 398 1.33e-06 TGTTGTCAAC GCTAATGGCGGAGAAGGCAGA GCCATGGAGA 9032 324 2.42e-06 TTGGTTTGTC GACGTTGTTGTTGATTGGTGG CTGTTTTGTT 23984 154 3.40e-06 GCTGGAAAAA GATGCTGGTGTTGATGCAGGT TCATGGGAGG 22883 134 3.40e-06 TCGGTTGGTT GGAGGTGGATGAGGAGGAGGA GGATTTTAGT 21108 66 3.80e-06 GTATCGTAAA GCAGTGTTTTGTGGAGGACGG AGGGCTGGTG 2562 33 4.72e-06 CAACTACAAC GGTGTGGGAAGTGTCGGCGGA TGAGAAGAGC 5729 98 5.84e-06 CCCTAGATTG GTCGTCATCTGAGATGGTTGA CACCTTGACA 11953 301 9.68e-06 AATGATTCGA GGTGTTTCCTTGGATGGACGA AGAGAGTTGT 10762 239 1.56e-05 AATGATCTAG GGTGTTTTCCGTGATCTAGGT GCAGCCACAT 33193 17 1.86e-05 CGTCCTTGCT GGGGTGTTTTGATGATGGTGA CCATAATGGA 31011 169 3.68e-05 CACGGTTGCT GCCATCGTCGTTGTCACCGGA GGCTCGTGGT 11436 8 4.67e-05 AGCGACA GATGAGTGTAGAGCGGGCTGT GTCTGCGTGG 263475 39 5.45e-05 AAACGAAGGA GGTGCCGTCGTCGAGACGAGA GCGAGAGGTG 5193 408 6.33e-05 GTTCATAGAA GAAGAGGTTTGGATTGGTCGA GTAACACCGC 21646 187 8.44e-05 TGTCAGATAT GACACCTTTGGGAGAGTATGA CATCACACCC 264353 77 9.70e-05 TCTTCGGCTG GCTATTGGCTTTGTGCTAGGA AGGACTGCCA 11453 369 1.35e-04 GCACCAGCGT GCCGTGTTTCGTGACTTTCGT GATCACGTGT 262242 18 1.53e-04 TGGTCACTTT GCTTGGGTTGGCGTGGCAAGT TTGTACTTGG 23788 201 1.53e-04 CTCTCTCGAT GTCGTGAGCGGTGCCGAATGA ATCAACCATA 24113 135 1.95e-04 TTCGGGTCGA GTGAACGGAGGAGGTAGCAGT GAAAGTGCTT 1740 242 1.95e-04 AGTAGATATT GAAGAGGTAGGCGAGACACGG TGTTGAAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20987 5.1e-10 154_[+2]_325 413 6.2e-09 35_[+2]_444 23243 1.7e-07 32_[+2]_447 261492 1.9e-07 282_[+2]_197 3397 3.5e-07 302_[+2]_177 3867 9.1e-07 447_[+2]_32 10903 1e-06 2_[+2]_477 24936 1.2e-06 340_[+2]_139 1681 1.2e-06 225_[+2]_254 5283 1.3e-06 280_[+2]_199 25132 1.3e-06 397_[+2]_82 9032 2.4e-06 323_[+2]_156 23984 3.4e-06 153_[+2]_326 22883 3.4e-06 133_[+2]_346 21108 3.8e-06 65_[+2]_414 2562 4.7e-06 32_[+2]_447 5729 5.8e-06 97_[+2]_382 11953 9.7e-06 300_[+2]_179 10762 1.6e-05 238_[+2]_241 33193 1.9e-05 16_[+2]_463 31011 3.7e-05 168_[+2]_311 11436 4.7e-05 7_[+2]_472 263475 5.4e-05 38_[+2]_441 5193 6.3e-05 407_[+2]_72 21646 8.4e-05 186_[+2]_293 264353 9.7e-05 76_[+2]_403 11453 0.00013 368_[+2]_111 262242 0.00015 17_[+2]_462 23788 0.00015 200_[+2]_279 24113 0.0002 134_[+2]_345 1740 0.0002 241_[+2]_238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=31 20987 ( 155) GGCGTTGTTGGGGAGGGCGGA 1 413 ( 36) GGCGTCGTCGGTGGAGGGGGT 1 23243 ( 33) GACGACTTTGGAGGTGGCTGT 1 261492 ( 283) GATGGCGGTGGAGAAGGTGGA 1 3397 ( 303) GCTGGTTTCGGAGGTGGGAGA 1 3867 ( 448) GGGGTGGTTGGTTGTGGTTGT 1 10903 ( 3) GCCGTTGTCGTCGATTGGTGA 1 24936 ( 341) GGTGTTGTTGTGTTCGGAGGA 1 1681 ( 226) GGGATCTTTGGGGAGCGAGGA 1 5283 ( 281) GGGAAGTTTGTGGGAGGATGA 1 25132 ( 398) GCTAATGGCGGAGAAGGCAGA 1 9032 ( 324) GACGTTGTTGTTGATTGGTGG 1 23984 ( 154) GATGCTGGTGTTGATGCAGGT 1 22883 ( 134) GGAGGTGGATGAGGAGGAGGA 1 21108 ( 66) GCAGTGTTTTGTGGAGGACGG 1 2562 ( 33) GGTGTGGGAAGTGTCGGCGGA 1 5729 ( 98) GTCGTCATCTGAGATGGTTGA 1 11953 ( 301) GGTGTTTCCTTGGATGGACGA 1 10762 ( 239) GGTGTTTTCCGTGATCTAGGT 1 33193 ( 17) GGGGTGTTTTGATGATGGTGA 1 31011 ( 169) GCCATCGTCGTTGTCACCGGA 1 11436 ( 8) GATGAGTGTAGAGCGGGCTGT 1 263475 ( 39) GGTGCCGTCGTCGAGACGAGA 1 5193 ( 408) GAAGAGGTTTGGATTGGTCGA 1 21646 ( 187) GACACCTTTGGGAGAGTATGA 1 264353 ( 77) GCTATTGGCTTTGTGCTAGGA 1 11453 ( 369) GCCGTGTTTCGTGACTTTCGT 1 262242 ( 18) GCTTGGGTTGGCGTGGCAAGT 1 23788 ( 201) GTCGTGAGCGGTGCCGAATGA 1 24113 ( 135) GTGAACGGAGGAGGTAGCAGT 1 1740 ( 242) GAAGAGGTAGGCGAGACACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 8.95743 E= 1.6e-004 -1160 -1160 211 -1160 0 10 74 -147 -100 42 -53 53 -19 -1160 168 -305 -19 -132 -85 103 -1160 27 61 40 -200 -1160 132 40 -1160 -290 32 134 -100 56 -1160 94 -200 -190 147 -25 -1160 -1160 161 11 17 -90 -4 40 -200 -1160 185 -147 70 -190 47 -47 0 -58 -4 40 -100 -132 147 -106 -300 -58 154 -106 70 -10 -26 -73 -68 -58 61 27 -1160 -1160 211 -1160 125 -1160 -126 11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 1.6e-004 0.000000 0.000000 1.000000 0.000000 0.258065 0.258065 0.387097 0.096774 0.129032 0.322581 0.161290 0.387097 0.225806 0.000000 0.741935 0.032258 0.225806 0.096774 0.129032 0.548387 0.000000 0.290323 0.354839 0.354839 0.064516 0.000000 0.580645 0.354839 0.000000 0.032258 0.290323 0.677419 0.129032 0.354839 0.000000 0.516129 0.064516 0.064516 0.645161 0.225806 0.000000 0.000000 0.709677 0.290323 0.290323 0.129032 0.225806 0.354839 0.064516 0.000000 0.838710 0.096774 0.419355 0.064516 0.322581 0.193548 0.258065 0.161290 0.225806 0.354839 0.129032 0.096774 0.645161 0.129032 0.032258 0.161290 0.677419 0.129032 0.419355 0.225806 0.193548 0.161290 0.161290 0.161290 0.354839 0.322581 0.000000 0.000000 1.000000 0.000000 0.612903 0.000000 0.096774 0.290323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GAC][TC][GA][TA][GTC][GT][TG][TC][GT][GT][TAG]G[AG][TAG]GG[AC][GT]G[AT] -------------------------------------------------------------------------------- Time 19.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 22 llr = 206 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2443:738::aa pos.-specific C 7:619172:a:: probability G 1::2::::5::: matrix T :5:512::5::: bits 2.1 * 1.9 * * 1.7 *** 1.5 * *** Relative 1.3 * *** Entropy 1.1 * * ** *** (13.5 bits) 0.8 * * * ****** 0.6 *** ******** 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel CTCTCACATCAA consensus AAA A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23788 449 6.25e-07 ACAGCGACAA CTATCACATCAA AACAGCGAAT 24936 473 9.49e-07 CACCCCACAA CAATCACAGCAA CGAAGGACGA 5729 441 1.83e-06 TTCAATTCAT CTCACAAATCAA AAGTACAAAC 21646 464 1.83e-06 TTCGGCCGAT CTCACAAATCAA AATCATAAGT 10903 466 1.83e-06 ACTCCCAGTT CTAGCACAGCAA CGAGTTCACA 21108 360 2.29e-06 TGTCAACTGT CTCTCTCATCAA TCGAGGGTGA 22883 485 5.51e-06 CATCAGAAGC ATCGCACAGCAA CTAC 5283 476 6.45e-06 ACGAAAGCAC CTCTCAACGCAA TACGTGGTCT 264353 422 2.05e-05 CTACGGATAG AAATCAAATCAA TACAAACCAA 1740 153 2.25e-05 GCAGCCAGCA GACCCACAGCAA CCAACTCACT 263475 488 2.66e-05 ATTAATCATA AACACTCAGCAA T 262242 413 2.93e-05 CACATCAAAC CACTTTCAGCAA CAACTACCGC 31011 457 3.51e-05 TACAACCTTC CGCTCTCATCAA CCCTTGTCAT 10762 36 3.51e-05 CCTTTTCTCC CTCTCAATTCAA AACGACGTGA 9032 488 3.82e-05 GACACAGCTA CACACACATCCA A 7172 172 3.82e-05 CTGCTGTCAC AAACCACATCAA CGGGTGTCAG 5193 429 4.37e-05 GATTGGTCGA GTAACACCGCAA GATAGTCGAC 1681 190 4.37e-05 TGATGTGGTA GAAGCAAAGCAA CCCTCTCTGC 23243 425 5.11e-05 CTGACTTCAT CTCTTAACTCAA CTTCAACTTT 24113 252 6.43e-05 CTTCGTTCAC CTCTTGCAGCAA AGGCACATCT 2562 102 8.33e-05 TTTACAAACA CTCACCCAACAA GAATCAGTCA 264583 46 9.50e-05 GCCCCACTAT CAAGCCCCTCAA GATCCATCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23788 6.2e-07 448_[+3]_40 24936 9.5e-07 472_[+3]_16 5729 1.8e-06 440_[+3]_48 21646 1.8e-06 463_[+3]_25 10903 1.8e-06 465_[+3]_23 21108 2.3e-06 359_[+3]_129 22883 5.5e-06 484_[+3]_4 5283 6.4e-06 475_[+3]_13 264353 2.1e-05 421_[+3]_67 1740 2.3e-05 152_[+3]_336 263475 2.7e-05 487_[+3]_1 262242 2.9e-05 412_[+3]_76 31011 3.5e-05 456_[+3]_32 10762 3.5e-05 35_[+3]_453 9032 3.8e-05 487_[+3]_1 7172 3.8e-05 171_[+3]_317 5193 4.4e-05 428_[+3]_60 1681 4.4e-05 189_[+3]_299 23243 5.1e-05 424_[+3]_64 24113 6.4e-05 251_[+3]_237 2562 8.3e-05 101_[+3]_387 264583 9.5e-05 45_[+3]_443 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=22 23788 ( 449) CTATCACATCAA 1 24936 ( 473) CAATCACAGCAA 1 5729 ( 441) CTCACAAATCAA 1 21646 ( 464) CTCACAAATCAA 1 10903 ( 466) CTAGCACAGCAA 1 21108 ( 360) CTCTCTCATCAA 1 22883 ( 485) ATCGCACAGCAA 1 5283 ( 476) CTCTCAACGCAA 1 264353 ( 422) AAATCAAATCAA 1 1740 ( 153) GACCCACAGCAA 1 263475 ( 488) AACACTCAGCAA 1 262242 ( 413) CACTTTCAGCAA 1 31011 ( 457) CGCTCTCATCAA 1 10762 ( 36) CTCTCAATTCAA 1 9032 ( 488) CACACACATCCA 1 7172 ( 172) AAACCACATCAA 1 5193 ( 429) GTAACACCGCAA 1 1681 ( 190) GAAGCAAAGCAA 1 23243 ( 425) CTCTTAACTCAA 1 24113 ( 252) CTCTTGCAGCAA 1 2562 ( 102) CTCACCCAACAA 1 264583 ( 46) CAAGCCCCTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16137 bayes= 9.87221 E= 1.1e+002 -51 150 -77 -1110 66 -1110 -235 102 49 140 -1110 -1110 8 -141 -35 76 -1110 184 -1110 -98 140 -141 -235 -56 30 150 -1110 -1110 158 -41 -1110 -256 -250 -1110 97 90 -1110 205 -1110 -1110 189 -240 -1110 -1110 195 -1110 -1110 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 22 E= 1.1e+002 0.181818 0.681818 0.136364 0.000000 0.409091 0.000000 0.045455 0.545455 0.363636 0.636364 0.000000 0.000000 0.272727 0.090909 0.181818 0.454545 0.000000 0.863636 0.000000 0.136364 0.681818 0.090909 0.045455 0.181818 0.318182 0.681818 0.000000 0.000000 0.772727 0.181818 0.000000 0.045455 0.045455 0.000000 0.454545 0.500000 0.000000 1.000000 0.000000 0.000000 0.954545 0.045455 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TA][CA][TA]CA[CA]A[TG]CAA -------------------------------------------------------------------------------- Time 28.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10762 6.16e-05 35_[+3(3.51e-05)]_191_\ [+2(1.56e-05)]_6_[+1(8.29e-06)]_223 10903 3.20e-06 2_[+2(1.03e-06)]_393_[+1(8.51e-05)]_\ 37_[+3(1.83e-06)]_23 11436 9.44e-03 7_[+2(4.67e-05)]_407_[+1(3.81e-05)]_\ 53 11453 1.78e-01 500 11953 2.71e-04 [+1(1.27e-06)]_216_[+1(4.46e-05)]_\ 60_[+2(9.68e-06)]_116_[+1(8.51e-05)]_51 1681 4.37e-05 189_[+3(4.37e-05)]_24_\ [+2(1.17e-06)]_226_[+1(6.02e-05)]_16 1740 2.06e-04 55_[+1(4.30e-06)]_85_[+3(2.25e-05)]_\ 336 20987 3.78e-07 25_[+1(9.10e-05)]_117_\ [+2(5.07e-10)]_325 21108 5.01e-06 65_[+2(3.80e-06)]_201_\ [+2(4.67e-05)]_51_[+3(2.29e-06)]_56_[+1(3.00e-05)]_61 21646 9.96e-04 186_[+2(8.44e-05)]_256_\ [+3(1.83e-06)]_25 22883 6.80e-06 133_[+2(3.40e-06)]_74_\ [+2(1.17e-05)]_235_[+3(5.51e-06)]_4 23243 7.34e-06 [+1(4.80e-05)]_20_[+2(1.66e-07)]_\ 371_[+3(5.11e-05)]_64 23788 3.10e-06 448_[+3(6.25e-07)]_16_\ [+1(1.64e-06)]_12 23984 2.73e-02 153_[+2(3.40e-06)]_326 24113 5.97e-04 251_[+3(6.43e-05)]_99_\ [+1(5.32e-06)]_126 24936 5.58e-09 340_[+2(1.17e-06)]_88_\ [+1(1.31e-07)]_11_[+3(9.49e-07)]_16 25132 1.81e-02 397_[+2(1.33e-06)]_82 2562 1.12e-04 32_[+2(4.72e-06)]_48_[+3(8.33e-05)]_\ 93_[+1(4.46e-05)]_116_[+1(2.31e-05)]_154 261492 2.83e-04 100_[+1(9.10e-05)]_170_\ [+2(1.94e-07)]_197 262242 4.02e-05 344_[+1(6.37e-07)]_56_\ [+3(2.93e-05)]_76 263475 9.08e-04 38_[+2(5.45e-05)]_393_\ [+1(7.40e-05)]_23_[+3(2.66e-05)]_1 264353 1.99e-03 76_[+2(9.70e-05)]_324_\ [+3(2.05e-05)]_67 264583 2.32e-04 45_[+3(9.50e-05)]_75_[+1(3.85e-07)]_\ 356 31011 1.18e-04 168_[+2(3.68e-05)]_70_\ [+1(7.43e-06)]_185_[+3(3.51e-05)]_32 33193 2.42e-04 16_[+2(1.86e-05)]_351_\ [+1(2.26e-06)]_100 3397 3.16e-06 302_[+2(3.50e-07)]_94_\ [+1(3.25e-07)]_71 3867 1.11e-02 447_[+2(9.07e-07)]_32 413 2.00e-05 35_[+2(6.20e-09)]_146_\ [+2(7.32e-05)]_277 5193 5.50e-04 407_[+2(6.33e-05)]_[+3(4.37e-05)]_\ 45_[+1(2.12e-05)]_3 5283 1.04e-04 280_[+2(1.33e-06)]_174_\ [+3(6.45e-06)]_13 5729 1.91e-06 97_[+2(5.84e-06)]_322_\ [+3(1.83e-06)]_31_[+1(8.29e-06)]_5 7172 1.40e-02 18_[+1(3.81e-05)]_141_\ [+3(3.82e-05)]_95_[+1(9.10e-05)]_210 9032 4.09e-06 323_[+2(2.42e-06)]_96_\ [+1(2.26e-06)]_35_[+3(3.82e-05)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************