******************************************************************************** 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/73/73.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46990 1.0000 500 13855 1.0000 500 14064 1.0000 500 37674 1.0000 500 21794 1.0000 500 47766 1.0000 500 38145 1.0000 500 47859 1.0000 500 47870 1.0000 500 47908 1.0000 500 47942 1.0000 500 47970 1.0000 500 38325 1.0000 500 14544 1.0000 500 48096 1.0000 500 48103 1.0000 500 29340 1.0000 500 48280 1.0000 500 38705 1.0000 500 14990 1.0000 500 48587 1.0000 500 39252 1.0000 500 48777 1.0000 500 49181 1.0000 500 49224 1.0000 500 23203 1.0000 500 6151 1.0000 500 16063 1.0000 500 50185 1.0000 500 41088 1.0000 500 43919 1.0000 500 10532 1.0000 500 50437 1.0000 500 50571 1.0000 500 38787 1.0000 500 38924 1.0000 500 48566 1.0000 500 44186 1.0000 500 15417 1.0000 500 37885 1.0000 500 37978 1.0000 500 40834 1.0000 500 47541 1.0000 500 49547 1.0000 500 47982 1.0000 500 50191 1.0000 500 49958 1.0000 500 40658 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/73/73.seqs.fa -oc motifs/73 -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= 48 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= 24000 N= 48 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.229 G 0.228 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.229 G 0.228 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 13 sites = 37 llr = 341 E-value = 1.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::916:229853 pos.-specific C 4:2:91::4::21 probability G 1:51::9:41116 matrix T 4a3::4181::2: bits 2.1 1.9 1.7 * ** * * 1.5 * ** * * Relative 1.3 * ** * * Entropy 1.1 * ** ** ** (13.3 bits) 0.9 * ** ** ** * 0.6 ******** ** * 0.4 ******** ** * 0.2 ************* 0.0 ------------- Multilevel CTGACAGTGAAAG consensus T T T C TA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 38325 92 2.44e-07 TGGACTCCTA CTGACAGTGAACG CCTCTCCCAA 50191 272 7.73e-07 AAAGGTGAGT CTGACTGTGAAAA TGGGACTTTG 50571 395 1.23e-06 CCCGCTCCCG CTCACAGTCAATG CAGATTCGTA 38145 133 2.98e-06 TCTATATTCG TTCACTGTCAATG AACAACGTTT 38924 460 3.84e-06 TTCTGTTGCA TTGACTGTGAGAG CACAAATCCT 48566 205 4.29e-06 CTTCGAAGTC TTGACTGTAAACG GGCGCTCTTT 47970 140 4.29e-06 CCGGTTCGAC TTGACTGTCAGAG TGTAGATATG 47541 409 4.80e-06 GATGCGGTTT CTCACAGTCAATA AAGGAAACGA 40658 394 5.28e-06 GCTCGTGTTC CTGACTGTGAAGA TTGACATGGC 38787 156 5.90e-06 GAGCAGGTAC TTGACTGAGAACG ATGTTCTATT 49224 61 8.10e-06 CTTCTTAGAT CTCACAGTCAAGA AACCTGATTG 29340 319 8.10e-06 TCAAATGATG CTCACAGTCAAGA GCCGAACAGT 6151 178 9.05e-06 AGCCCGTCGA CTGACCGTGAAAA ATTATCGCCG 49547 286 1.02e-05 GCTTTATATA TTTACTGTAAATG CACTGCCCAT 43919 455 1.12e-05 CTTCTAGTTA GTTACAGACAAAG ACTGTTGTAA 50437 227 1.51e-05 AAGCAAGTAT TTTACTGTTAATG CATATGTCGA 37978 156 1.65e-05 ACGAAACAGT CTCACTTTCAAAG CGGGTCACGC 41088 270 1.65e-05 TAAAGTGTCA GTCACAGTCAGAG AGTCTCTGGT 38705 296 1.65e-05 ACAAGCAATG CTGAAAGACAAAG CAACAGCGTT 48280 296 1.65e-05 ACAAGCAATG CTGAAAGACAAAG CAACAGCGTT 47942 116 1.65e-05 CGACAAATGC TTTACAGTTAAGG TGGAGCGTAA 47908 219 1.65e-05 TTTTCGTAGA GTTACAGTGAACA GCCCCACACT 47859 410 1.65e-05 TTTTCATACG TTTGCAGTGAAAG CCTTTCCTTT 39252 393 2.85e-05 ACGACCGCAT CTTACATTGAAAA ATGCAACACG 47766 74 2.85e-05 GCACCTACGA TTTACAGTGAATC TTGCGTTACG 37885 323 3.13e-05 CGTCATCGTT TTGACAGGAAAAG ATGAGCACCG 15417 420 3.13e-05 CATAATCCTA TTGACAGTTGAAG TGTTCGACCT 44186 167 4.42e-05 CGACCTACTA CTGACAGAGATAG TTCCGTCTCG 47870 102 5.17e-05 CGCTCAAACT GTGGCAGTAAAAG TGGACTTGTG 21794 2 5.17e-05 A CAGACTGTAAAAG CAGGTTGGCA 37674 439 5.17e-05 CATGACTACC TTCACCGTCAACA ATAGCCAGAG 49181 220 6.54e-05 TGTAAAGATT CTGACAGTCAGAT ACTGTGGAGG 14064 126 8.85e-05 ACAGGAATAC CTGAAAGTGAATC CACAAGGGAA 48096 201 1.25e-04 ATACGTTACA TTTACAGTAACCG ATTGGATTTA 46990 86 1.25e-04 GTAAACTGAA GTGAATGAGAAAA GGACGACAGT 10532 324 1.34e-04 TTTGTTTGGC TTCACTGAGGACG AGCGGAATGC 50185 362 1.34e-04 TTGAATTTTT TTTACTTTTAATG AAGATCCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38325 2.4e-07 91_[+1]_396 50191 7.7e-07 271_[+1]_216 50571 1.2e-06 394_[+1]_93 38145 3e-06 132_[+1]_355 38924 3.8e-06 459_[+1]_28 48566 4.3e-06 204_[+1]_283 47970 4.3e-06 139_[+1]_348 47541 4.8e-06 408_[+1]_79 40658 5.3e-06 393_[+1]_94 38787 5.9e-06 155_[+1]_332 49224 8.1e-06 60_[+1]_427 29340 8.1e-06 318_[+1]_169 6151 9.1e-06 177_[+1]_310 49547 1e-05 285_[+1]_202 43919 1.1e-05 454_[+1]_33 50437 1.5e-05 226_[+1]_261 37978 1.7e-05 155_[+1]_332 41088 1.7e-05 269_[+1]_218 38705 1.7e-05 295_[+1]_192 48280 1.7e-05 295_[+1]_192 47942 1.7e-05 115_[+1]_372 47908 1.7e-05 218_[+1]_269 47859 1.7e-05 409_[+1]_78 39252 2.9e-05 392_[+1]_95 47766 2.9e-05 73_[+1]_414 37885 3.1e-05 322_[+1]_165 15417 3.1e-05 419_[+1]_68 44186 4.4e-05 166_[+1]_321 47870 5.2e-05 101_[+1]_386 21794 5.2e-05 1_[+1]_486 37674 5.2e-05 438_[+1]_49 49181 6.5e-05 219_[+1]_268 14064 8.8e-05 125_[+1]_362 48096 0.00013 200_[+1]_287 46990 0.00013 85_[+1]_402 10532 0.00013 323_[+1]_164 50185 0.00013 361_[+1]_126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=37 38325 ( 92) CTGACAGTGAACG 1 50191 ( 272) CTGACTGTGAAAA 1 50571 ( 395) CTCACAGTCAATG 1 38145 ( 133) TTCACTGTCAATG 1 38924 ( 460) TTGACTGTGAGAG 1 48566 ( 205) TTGACTGTAAACG 1 47970 ( 140) TTGACTGTCAGAG 1 47541 ( 409) CTCACAGTCAATA 1 40658 ( 394) CTGACTGTGAAGA 1 38787 ( 156) TTGACTGAGAACG 1 49224 ( 61) CTCACAGTCAAGA 1 29340 ( 319) CTCACAGTCAAGA 1 6151 ( 178) CTGACCGTGAAAA 1 49547 ( 286) TTTACTGTAAATG 1 43919 ( 455) GTTACAGACAAAG 1 50437 ( 227) TTTACTGTTAATG 1 37978 ( 156) CTCACTTTCAAAG 1 41088 ( 270) GTCACAGTCAGAG 1 38705 ( 296) CTGAAAGACAAAG 1 48280 ( 296) CTGAAAGACAAAG 1 47942 ( 116) TTTACAGTTAAGG 1 47908 ( 219) GTTACAGTGAACA 1 47859 ( 410) TTTGCAGTGAAAG 1 39252 ( 393) CTTACATTGAAAA 1 47766 ( 74) TTTACAGTGAATC 1 37885 ( 323) TTGACAGGAAAAG 1 15417 ( 420) TTGACAGTTGAAG 1 44186 ( 167) CTGACAGAGATAG 1 47870 ( 102) GTGGCAGTAAAAG 1 21794 ( 2) CAGACTGTAAAAG 1 37674 ( 439) TTCACCGTCAACA 1 49181 ( 220) CTGACAGTCAGAT 1 14064 ( 126) CTGAAAGTGAATC 1 48096 ( 201) TTTACAGTAACCG 1 46990 ( 86) GTGAATGAGAAAA 1 10532 ( 324) TTCACTGAGGACG 1 50185 ( 362) TTTACTTTTAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 23424 bayes= 10.1782 E= 1.3e-009 -1185 91 -75 65 -330 -1185 -1185 182 -1185 8 109 -3 182 -1185 -208 -1185 -131 196 -1185 -1185 108 -208 -1185 46 -1185 -1185 201 -176 -50 -1185 -307 151 -72 62 73 -135 182 -1185 -208 -1185 165 -308 -108 -334 86 -28 -108 -35 1 -208 151 -334 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 37 E= 1.3e-009 0.000000 0.432432 0.135135 0.432432 0.027027 0.000000 0.000000 0.972973 0.000000 0.243243 0.486486 0.270270 0.945946 0.000000 0.054054 0.000000 0.108108 0.891892 0.000000 0.000000 0.567568 0.054054 0.000000 0.378378 0.000000 0.000000 0.918919 0.081081 0.189189 0.000000 0.027027 0.783784 0.162162 0.351351 0.378378 0.108108 0.945946 0.000000 0.054054 0.000000 0.837838 0.027027 0.108108 0.027027 0.486486 0.189189 0.108108 0.216216 0.270270 0.054054 0.648649 0.027027 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]T[GTC]AC[AT]GT[GC]AA[AT][GA] -------------------------------------------------------------------------------- Time 17.70 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 8 llr = 141 E-value = 5.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3:44118a53959aa15a:18 pos.-specific C :51:691:33:51::94:193 probability G 85:43:::351:::::1:9:: matrix T ::53::1:::::::::::::: bits 2.1 1.9 * ** * 1.7 * ** * 1.5 * * * *** *** Relative 1.3 * * * * **** *** Entropy 1.1 ** * * ****** **** (25.5 bits) 0.9 ** **** ****** **** 0.6 ** **** ************ 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCTACCAAAGAAAAACAAGCA consensus AGAGG CA C C C sequence T GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38705 272 3.50e-12 TGAGGCCAGA GGTACCAAAGAAAAACAAGCA ATGCTGAAAG 48280 272 3.50e-12 TGAGGCCGGC GGTACCAAAGAAAAACAAGCA ATGCTGAAAG 47982 368 8.88e-10 GAAAGCAACC GGAGCCAAAAACAAACAACCA TCCACTTTAC 37978 109 6.55e-09 TTTGCGCTAG GCCGCCTACGAAAAACCAGCC CCCGCATCAA 48096 56 1.44e-08 ACTAATCTCC ACTGCCAACCACAAACCAGAC AGACCGCTGT 41088 462 1.99e-08 CGAAAACACT GGAAGCAAGGGAAAAACAGCA AGCGAGGGTT 48587 379 1.99e-08 TGTATCGTCG ACTTGAAAGCACAAACAAGCA GTAAATGCAC 38325 328 7.04e-08 CTGCAGACTT GCATACCAAAACCAACGAGCA ACGACCGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38705 3.5e-12 271_[+2]_208 48280 3.5e-12 271_[+2]_208 47982 8.9e-10 367_[+2]_112 37978 6.5e-09 108_[+2]_371 48096 1.4e-08 55_[+2]_424 41088 2e-08 461_[+2]_18 48587 2e-08 378_[+2]_101 38325 7e-08 327_[+2]_152 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=8 38705 ( 272) GGTACCAAAGAAAAACAAGCA 1 48280 ( 272) GGTACCAAAGAAAAACAAGCA 1 47982 ( 368) GGAGCCAAAAACAAACAACCA 1 37978 ( 109) GCCGCCTACGAAAAACCAGCC 1 48096 ( 56) ACTGCCAACCACAAACCAGAC 1 41088 ( 462) GGAAGCAAGGGAAAAACAGCA 1 48587 ( 379) ACTTGAAAGCACAAACAAGCA 1 38325 ( 328) GCATACCAAAACCAACGAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 23040 bayes= 12.2285 E= 5.1e+000 -10 -965 172 -965 -965 112 113 -965 49 -87 -965 86 49 -965 72 -14 -110 145 13 -965 -110 193 -965 -965 149 -87 -965 -114 190 -965 -965 -965 90 12 13 -965 -10 12 113 -965 171 -965 -87 -965 90 112 -965 -965 171 -87 -965 -965 190 -965 -965 -965 190 -965 -965 -965 -110 193 -965 -965 90 71 -87 -965 190 -965 -965 -965 -965 -87 194 -965 -110 193 -965 -965 149 12 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 5.1e+000 0.250000 0.000000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 0.375000 0.125000 0.000000 0.500000 0.375000 0.000000 0.375000 0.250000 0.125000 0.625000 0.250000 0.000000 0.125000 0.875000 0.000000 0.000000 0.750000 0.125000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.250000 0.250000 0.500000 0.000000 0.875000 0.000000 0.125000 0.000000 0.500000 0.500000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.500000 0.375000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.125000 0.875000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][CG][TA][AGT][CG]CAA[ACG][GAC]A[AC]AAAC[AC]AGC[AC] -------------------------------------------------------------------------------- Time 35.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 24 llr = 234 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2::::::1:::4 pos.-specific C :::2:5a1:466 probability G ::213::1:::: matrix T 8a8775:7a64: bits 2.1 * 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 *** * * Entropy 1.1 *** *** *** (14.0 bits) 0.9 ******* **** 0.6 ******* **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTTCCTTTCC consensus GCGT CTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 38705 418 9.00e-08 AGCTTTCCGC TTTTTCCTTTCC GGATTTCCAC 48566 465 4.53e-07 TTTGTTTCAC TTTTTCCTTTCA CTTTCTAGGA 48280 418 6.51e-07 AGCTTTCCGC TTTTTCCTTTTC GGATTTCCAC 49547 2 1.65e-06 A TTTTTTCTTCCA TCTCTGATCA 47870 455 2.23e-06 CTTCAAAGGA TTTTGTCTTTCA GCCCAAGCAA 43919 205 5.07e-06 CGTTCTCATA TTTGTCCTTTCC CATGTAAATG 23203 88 7.17e-06 GAATTGATGT TTGCTCCTTTCC TTGAGCTGGC 14064 472 8.76e-06 GATGCCACTG TTTTTCCGTCCA TGATCTTTGC 40658 370 1.00e-05 AGACACATAT TTTCGCCTTCCA AGGCTCGTGT 48777 76 1.00e-05 CGTCGCTGCA ATTTTCCTTCCA GCAATTGTTT 15417 454 1.11e-05 GCTAACGTGA TTGTTTCTTCTC GTAGAAGGTC 47942 240 1.21e-05 CGTGAAGTGT TTTTTCCCTTTC CGGGTCTGTG 37885 302 1.63e-05 ACGGCCTGTT TTTCTCCCTTCC GTCATCGTTT 46990 362 1.63e-05 ATCAACAGCA TTTCGTCTTCTC AATGTATGCA 47908 202 1.97e-05 AACGCTTACT ATTTGTCTTTTC GTAGAGTTAC 38924 368 2.14e-05 GAATTGCGAA TTTTGTCATTTC TCATTATTTT 37674 419 2.50e-05 AAAACTCACA TTTCTCCGTCCA TGACTACCTT 6151 44 3.43e-05 TCGAAGTGTT TTTTTTCTTTTT GTGAGCCAAA 47766 17 3.69e-05 ACAAGTCCAG TTGTTTCATTTC TGGTGATGTG 14544 488 4.22e-05 GTTTGATCGT TCTTTCCTTCTC A 47982 249 4.52e-05 CATATTCAGA ATGTGTCTTTCA GACCTATCAC 50191 21 5.12e-05 TTGGGCACGA TTTTGTCTACCC TCTCGAACCA 29340 26 5.47e-05 TTGCTACTCC ATGTTCCATTCC AGTTGATTTG 13855 409 6.93e-05 GGCTGTGGTT TTTGGTCGTTCA CGACAAATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38705 9e-08 417_[+3]_71 48566 4.5e-07 464_[+3]_24 48280 6.5e-07 417_[+3]_71 49547 1.7e-06 1_[+3]_487 47870 2.2e-06 454_[+3]_34 43919 5.1e-06 204_[+3]_284 23203 7.2e-06 87_[+3]_401 14064 8.8e-06 471_[+3]_17 40658 1e-05 369_[+3]_119 48777 1e-05 75_[+3]_413 15417 1.1e-05 453_[+3]_35 47942 1.2e-05 239_[+3]_249 37885 1.6e-05 301_[+3]_187 46990 1.6e-05 361_[+3]_127 47908 2e-05 201_[+3]_287 38924 2.1e-05 367_[+3]_121 37674 2.5e-05 418_[+3]_70 6151 3.4e-05 43_[+3]_445 47766 3.7e-05 16_[+3]_472 14544 4.2e-05 487_[+3]_1 47982 4.5e-05 248_[+3]_240 50191 5.1e-05 20_[+3]_468 29340 5.5e-05 25_[+3]_463 13855 6.9e-05 408_[+3]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=24 38705 ( 418) TTTTTCCTTTCC 1 48566 ( 465) TTTTTCCTTTCA 1 48280 ( 418) TTTTTCCTTTTC 1 49547 ( 2) TTTTTTCTTCCA 1 47870 ( 455) TTTTGTCTTTCA 1 43919 ( 205) TTTGTCCTTTCC 1 23203 ( 88) TTGCTCCTTTCC 1 14064 ( 472) TTTTTCCGTCCA 1 40658 ( 370) TTTCGCCTTCCA 1 48777 ( 76) ATTTTCCTTCCA 1 15417 ( 454) TTGTTTCTTCTC 1 47942 ( 240) TTTTTCCCTTTC 1 37885 ( 302) TTTCTCCCTTCC 1 46990 ( 362) TTTCGTCTTCTC 1 47908 ( 202) ATTTGTCTTTTC 1 38924 ( 368) TTTTGTCATTTC 1 37674 ( 419) TTTCTCCGTCCA 1 6151 ( 44) TTTTTTCTTTTT 1 47766 ( 17) TTGTTTCATTTC 1 14544 ( 488) TCTTTCCTTCTC 1 47982 ( 249) ATGTGTCTTTCA 1 50191 ( 21) TTTTGTCTACCC 1 29340 ( 26) ATGTTCCATTCC 1 13855 ( 409) TTTGGTCGTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 23472 bayes= 11.0325 E= 1.5e+002 -68 -1123 -1123 160 -1123 -246 -1123 180 -1123 -1123 -13 152 -1123 -14 -145 136 -1123 -1123 55 128 -1123 124 -1123 74 -1123 212 -1123 -1123 -110 -146 -87 128 -268 -1123 -1123 180 -1123 71 -1123 118 -1123 145 -1123 45 49 135 -1123 -272 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 1.5e+002 0.166667 0.000000 0.000000 0.833333 0.000000 0.041667 0.000000 0.958333 0.000000 0.000000 0.208333 0.791667 0.000000 0.208333 0.083333 0.708333 0.000000 0.000000 0.333333 0.666667 0.000000 0.541667 0.000000 0.458333 0.000000 1.000000 0.000000 0.000000 0.125000 0.083333 0.125000 0.666667 0.041667 0.000000 0.000000 0.958333 0.000000 0.375000 0.000000 0.625000 0.000000 0.625000 0.000000 0.375000 0.375000 0.583333 0.000000 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[TG][TC][TG][CT]CTT[TC][CT][CA] -------------------------------------------------------------------------------- Time 51.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46990 1.10e-02 361_[+3(1.63e-05)]_127 13855 8.34e-02 408_[+3(6.93e-05)]_80 14064 1.51e-03 125_[+1(8.85e-05)]_333_\ [+3(8.76e-06)]_17 37674 1.03e-02 418_[+3(2.50e-05)]_8_[+1(5.17e-05)]_\ 49 21794 8.61e-02 1_[+1(5.17e-05)]_486 47766 9.23e-03 16_[+3(3.69e-05)]_45_[+1(2.85e-05)]_\ 414 38145 8.94e-03 132_[+1(2.98e-06)]_355 47859 2.12e-02 409_[+1(1.65e-05)]_78 47870 1.71e-03 101_[+1(5.17e-05)]_254_\ [+3(5.12e-05)]_74_[+3(2.23e-06)]_34 47908 2.83e-03 201_[+3(1.97e-05)]_5_[+1(1.65e-05)]_\ 179_[+3(5.80e-05)]_78 47942 7.99e-04 115_[+1(1.65e-05)]_90_\ [+3(5.47e-05)]_9_[+3(1.21e-05)]_249 47970 1.03e-02 139_[+1(4.29e-06)]_348 38325 5.65e-07 91_[+1(2.44e-07)]_56_[+1(1.65e-05)]_\ 154_[+2(7.04e-08)]_152 14544 8.88e-02 487_[+3(4.22e-05)]_1 48096 1.71e-05 55_[+2(1.44e-08)]_424 48103 3.30e-01 500 29340 4.21e-03 25_[+3(5.47e-05)]_281_\ [+1(8.10e-06)]_169 48280 2.49e-12 271_[+2(3.50e-12)]_3_[+1(1.65e-05)]_\ 109_[+3(6.51e-07)]_71 38705 3.86e-13 271_[+2(3.50e-12)]_3_[+1(1.65e-05)]_\ 109_[+3(9.00e-08)]_71 14990 1.23e-01 500 48587 4.10e-04 378_[+2(1.99e-08)]_101 39252 2.70e-02 392_[+1(2.85e-05)]_95 48777 8.78e-02 75_[+3(1.00e-05)]_413 49181 3.14e-02 219_[+1(6.54e-05)]_268 49224 1.20e-02 60_[+1(8.10e-06)]_427 23203 6.48e-02 87_[+3(7.17e-06)]_194_\ [+3(4.22e-05)]_195 6151 1.93e-03 43_[+3(3.43e-05)]_122_\ [+1(9.05e-06)]_310 16063 5.72e-01 500 50185 8.10e-02 500 41088 1.13e-05 269_[+1(1.65e-05)]_179_\ [+2(1.99e-08)]_18 43919 1.82e-04 204_[+3(5.07e-06)]_238_\ [+1(1.12e-05)]_33 10532 2.15e-01 500 50437 1.15e-02 226_[+1(1.51e-05)]_261 50571 7.85e-03 394_[+1(1.23e-06)]_29_\ [+1(7.04e-05)]_51 38787 4.10e-02 155_[+1(5.90e-06)]_332 38924 5.41e-06 22_[+2(3.46e-06)]_324_\ [+3(2.14e-05)]_80_[+1(3.84e-06)]_28 48566 2.27e-05 204_[+1(4.29e-06)]_247_\ [+3(4.53e-07)]_24 44186 3.38e-02 166_[+1(4.42e-05)]_321 15417 3.20e-03 419_[+1(3.13e-05)]_21_\ [+3(1.11e-05)]_35 37885 4.27e-03 301_[+3(1.63e-05)]_9_[+1(3.13e-05)]_\ 165 37978 3.34e-06 108_[+2(6.55e-09)]_26_\ [+1(1.65e-05)]_332 40834 4.91e-01 500 47541 1.10e-02 278_[+1(8.23e-05)]_117_\ [+1(4.80e-06)]_79 49547 2.31e-04 1_[+3(1.65e-06)]_272_[+1(1.02e-05)]_\ 60_[+1(8.10e-06)]_129 47982 1.68e-06 248_[+3(4.52e-05)]_107_\ [+2(8.88e-10)]_112 50191 6.24e-04 20_[+3(5.12e-05)]_239_\ [+1(7.73e-07)]_216 49958 2.70e-01 439_[+2(9.04e-05)]_40 40658 9.53e-04 47_[+1(6.06e-05)]_309_\ [+3(1.00e-05)]_12_[+1(5.28e-06)]_94 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************