******************************************************************************** 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/201/201.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42570 1.0000 500 31725 1.0000 500 32036 1.0000 500 54038 1.0000 500 8777 1.0000 500 17974 1.0000 500 20740 1.0000 500 27905 1.0000 500 51007 1.0000 500 46846 1.0000 500 46994 1.0000 500 47014 1.0000 500 47058 1.0000 500 13820 1.0000 500 14145 1.0000 500 21538 1.0000 500 14068 1.0000 500 37596 1.0000 500 14450 1.0000 500 48320 1.0000 500 48417 1.0000 500 38930 1.0000 500 48486 1.0000 500 22658 1.0000 500 25133 1.0000 500 32758 1.0000 500 9989 1.0000 500 25394 1.0000 500 22868 1.0000 500 40070 1.0000 500 15862 1.0000 500 49433 1.0000 500 49450 1.0000 500 42302 1.0000 500 55141 1.0000 500 16633 1.0000 500 41002 1.0000 500 23865 1.0000 500 50246 1.0000 500 16814 1.0000 500 44047 1.0000 500 44055 1.0000 500 50630 1.0000 500 44555 1.0000 500 10782 1.0000 500 19647 1.0000 500 45441 1.0000 500 12144 1.0000 500 12140 1.0000 500 45727 1.0000 500 12322 1.0000 500 45844 1.0000 500 45888 1.0000 500 46259 1.0000 500 46993 1.0000 500 47259 1.0000 500 36897 1.0000 500 47900 1.0000 500 43528 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/201/201.seqs.fa -oc motifs/201 -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= 59 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= 29500 N= 59 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.279 C 0.237 G 0.224 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.279 C 0.237 G 0.224 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 42 llr = 408 E-value = 1.5e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 351:a7:39a654485 pos.-specific C 5:7a:2651:441123 probability G 152:::42::1:44:1 matrix T :1:::1:::::11111 bits 2.2 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 CGCCAACCAAAAGGAA consensus AA GA CCAA C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21538 309 2.26e-08 AATGGATGCA CGCCAAGCAAACGAAA TGGGTCGACC 49433 422 3.10e-07 CACCATTCAT CGCCAAGGAACCGAAA AAAGTTTGGC 19647 282 4.47e-07 TTGATGAGCT CGGCAACCAACCAAAA AGGTCCCCGC 9989 317 7.25e-07 TCGTCACCAG CACCAAGCAAACAAAT ACATTGCGAC 45441 386 8.41e-07 ATTGCAAGAC AACCAAGCAAAACGAC CAGCTTGAAA 55141 372 9.78e-07 GTCGGTCGCA CAACAACCAACAGGAC TACCAAATCC 14145 258 9.78e-07 TAATCATCGG AGCCAACGAACAAAAC TACCTCTCCC 44055 367 1.32e-06 AGCACTCCAT CACCAAGGAAAACAAA GAACAAATCG 25133 349 1.32e-06 GCGCCTCTGA AACCAACCAAAAAACA CACCCCAACG 43528 306 1.51e-06 TTCGCTTCGC GGCCAAGAAAACGAAA GACAAAAATC 44555 388 2.26e-06 AGATCGCTGT CGCCAAGCCAACGAAA AATTGTCTGA 45727 344 3.32e-06 CTGCCATGAG CACCACGCAAAAAGCA CGGCTACACT 16633 254 3.32e-06 CTAGTGGGAA CAGCAACGAAAATGAA CCCAATACAT 22868 379 3.32e-06 GTGCGTCCTC CACCACCCAAACGAAG CTACAAGCCG 22658 472 3.75e-06 TGCTCGCGTT CAACAAGCAAACAAAC AAACATACAC 51007 124 4.76e-06 GCAGGACAGT AACCAACCAACTACAA ATTTATCTTT 32036 357 5.33e-06 GATACACCCC CGCCAACCAACTGGCT TCCTTACATT 10782 375 5.98e-06 CGACGAAACA GGCCAACAAACCACAC GGTCGTTGAA 50630 382 7.43e-06 AGGCTATCAA AGCCAAGCAAAATTAC GAAAAAGCAA 46846 200 8.28e-06 CGCACGCACG CACGAACCAACACGAA TACCACGATT 12322 20 1.02e-05 ATGATGGGGA CGCCACCCAAACGGTT GCTTGGTCTA 27905 165 1.02e-05 GTGATGGCTT GACCAACAAACAGTAC GTTGTTCTCC 12144 242 1.51e-05 ATCCAATGAG AGCCACCGAACAAGAG CTCGCTTTGC 14450 403 1.51e-05 ATGCAGAAAC GGGCATCCAACAAGAA AGAAACAGCC 47259 355 1.66e-05 CGAGCTGCAA CACCAACCAACATGTT CGGAACACGG 48417 446 1.99e-05 TTTCGGTCTC GTCCAACGAAACGCAA TACCTATTTC 32758 262 2.18e-05 CGGCAGGACA CGCCAAGCACAAACAA AGATCAAAGC 17974 172 2.18e-05 CGCACCGTAC CGGCACCCAAAACTAC AACTTCCACA 14068 135 2.38e-05 AAGTTTGCCT CAGCAACAAACCACCA GTATAACAGC 12140 39 2.82e-05 TTATCCGGTT CACCATCAAAATTGAA TCAGATTCCG 45888 370 3.07e-05 AACACCACTC CGGCATCCAAGCAAAA AGTGAAAACT 44047 429 3.34e-05 TTCGAAAAAC ATGCAAGGAAAAAGAC AAACCCAACA 8777 290 3.34e-05 AGGAAGAGGA CGCCAGCGAAGCGGAA GAAAGTGGAG 48320 319 4.24e-05 GGACAGTGAA CACCAACCAAATTTCC GAAGTGGCCT 47014 137 5.73e-05 GTAGTGCAAG AAGCAACAAAGAGGCC CTCATTCGGG 25394 27 6.16e-05 TTCATTTGCG ATCCAAGAAACTCGAA GATCATCTCC 16814 287 7.09e-05 ATAGCCTTCT AAAGAACCAAAAGGAT GAAGAAGAAT 41002 139 7.60e-05 CAGCTAACGA CGACATGAAAACGGAG GTCTTTCACA 54038 295 8.14e-05 AAGACACAGT AGACAAGACACAGAAA AGGCAATTTG 46994 346 8.70e-05 AACGCATCAA AGCCAAAGAAAAGCAT CGTCGTTCCA 46993 371 1.13e-04 CCTCGTCCAG GACCACCAAAAACATC CGTGAGTGGG 42570 443 1.20e-04 CGGGCAAGAT AGCCACCACAACAACC GTTAAGGGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21538 2.3e-08 308_[+1]_176 49433 3.1e-07 421_[+1]_63 19647 4.5e-07 281_[+1]_203 9989 7.3e-07 316_[+1]_168 45441 8.4e-07 385_[+1]_99 55141 9.8e-07 371_[+1]_113 14145 9.8e-07 257_[+1]_227 44055 1.3e-06 366_[+1]_118 25133 1.3e-06 348_[+1]_136 43528 1.5e-06 305_[+1]_179 44555 2.3e-06 387_[+1]_97 45727 3.3e-06 343_[+1]_141 16633 3.3e-06 253_[+1]_231 22868 3.3e-06 378_[+1]_106 22658 3.7e-06 471_[+1]_13 51007 4.8e-06 123_[+1]_361 32036 5.3e-06 356_[+1]_128 10782 6e-06 374_[+1]_110 50630 7.4e-06 381_[+1]_103 46846 8.3e-06 199_[+1]_285 12322 1e-05 19_[+1]_465 27905 1e-05 164_[+1]_320 12144 1.5e-05 241_[+1]_243 14450 1.5e-05 402_[+1]_82 47259 1.7e-05 354_[+1]_130 48417 2e-05 445_[+1]_39 32758 2.2e-05 261_[+1]_223 17974 2.2e-05 171_[+1]_313 14068 2.4e-05 134_[+1]_350 12140 2.8e-05 38_[+1]_446 45888 3.1e-05 369_[+1]_115 44047 3.3e-05 428_[+1]_56 8777 3.3e-05 289_[+1]_195 48320 4.2e-05 318_[+1]_166 47014 5.7e-05 136_[+1]_348 25394 6.2e-05 26_[+1]_458 16814 7.1e-05 286_[+1]_198 41002 7.6e-05 138_[+1]_346 54038 8.1e-05 294_[+1]_190 46994 8.7e-05 345_[+1]_139 46993 0.00011 370_[+1]_114 42570 0.00012 442_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=42 21538 ( 309) CGCCAAGCAAACGAAA 1 49433 ( 422) CGCCAAGGAACCGAAA 1 19647 ( 282) CGGCAACCAACCAAAA 1 9989 ( 317) CACCAAGCAAACAAAT 1 45441 ( 386) AACCAAGCAAAACGAC 1 55141 ( 372) CAACAACCAACAGGAC 1 14145 ( 258) AGCCAACGAACAAAAC 1 44055 ( 367) CACCAAGGAAAACAAA 1 25133 ( 349) AACCAACCAAAAAACA 1 43528 ( 306) GGCCAAGAAAACGAAA 1 44555 ( 388) CGCCAAGCCAACGAAA 1 45727 ( 344) CACCACGCAAAAAGCA 1 16633 ( 254) CAGCAACGAAAATGAA 1 22868 ( 379) CACCACCCAAACGAAG 1 22658 ( 472) CAACAAGCAAACAAAC 1 51007 ( 124) AACCAACCAACTACAA 1 32036 ( 357) CGCCAACCAACTGGCT 1 10782 ( 375) GGCCAACAAACCACAC 1 50630 ( 382) AGCCAAGCAAAATTAC 1 46846 ( 200) CACGAACCAACACGAA 1 12322 ( 20) CGCCACCCAAACGGTT 1 27905 ( 165) GACCAACAAACAGTAC 1 12144 ( 242) AGCCACCGAACAAGAG 1 14450 ( 403) GGGCATCCAACAAGAA 1 47259 ( 355) CACCAACCAACATGTT 1 48417 ( 446) GTCCAACGAAACGCAA 1 32758 ( 262) CGCCAAGCACAAACAA 1 17974 ( 172) CGGCACCCAAAACTAC 1 14068 ( 135) CAGCAACAAACCACCA 1 12140 ( 39) CACCATCAAAATTGAA 1 45888 ( 370) CGGCATCCAAGCAAAA 1 44047 ( 429) ATGCAAGGAAAAAGAC 1 8777 ( 290) CGCCAGCGAAGCGGAA 1 48320 ( 319) CACCAACCAAATTTCC 1 47014 ( 137) AAGCAACAAAGAGGCC 1 25394 ( 27) ATCCAAGAAACTCGAA 1 16814 ( 287) AAAGAACCAAAAGGAT 1 41002 ( 139) CGACATGAAAACGGAG 1 54038 ( 295) AGACAAGACACAGAAA 1 46994 ( 346) AGCCAAAGAAAAGCAT 1 46993 ( 371) GACCACCAAAAACATC 1 42570 ( 443) AGCCACCACAACAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 28615 bayes= 10.3974 E= 1.5e-013 15 121 -65 -1204 70 -1204 109 -186 -123 154 -23 -1204 -1204 200 -223 -1204 184 -1204 -1204 -1204 136 -51 -323 -145 -355 138 67 -1204 -9 114 -6 -1204 174 -173 -1204 -1204 181 -331 -1204 -1204 104 59 -165 -1204 84 68 -1204 -113 36 -73 77 -113 36 -73 85 -145 145 -51 -1204 -186 77 38 -165 -86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 42 E= 1.5e-013 0.309524 0.547619 0.142857 0.000000 0.452381 0.000000 0.476190 0.071429 0.119048 0.690476 0.190476 0.000000 0.000000 0.952381 0.047619 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.166667 0.023810 0.095238 0.023810 0.619048 0.357143 0.000000 0.261905 0.523810 0.214286 0.000000 0.928571 0.071429 0.000000 0.000000 0.976190 0.023810 0.000000 0.000000 0.571429 0.357143 0.071429 0.000000 0.500000 0.380952 0.000000 0.119048 0.357143 0.142857 0.380952 0.119048 0.357143 0.142857 0.404762 0.095238 0.761905 0.166667 0.000000 0.071429 0.476190 0.309524 0.071429 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][GA]CCAA[CG][CAG]AA[AC][AC][GA][GA]A[AC] -------------------------------------------------------------------------------- Time 26.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 34 llr = 343 E-value = 4.8e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::a:5:1:a6231 pos.-specific C 6:2:a1::3:1113 probability G 1:4:::9:4:3:22 matrix T 3a4::4193::644 bits 2.2 * 1.9 * * * 1.7 * ** * * 1.5 * ** ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (14.6 bits) 0.9 ** ** ** * 0.6 ** ***** *** 0.4 ************ 0.2 ************** 0.0 -------------- Multilevel CTGACAGTGAATTT consensus T T T T GAAC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 25394 158 2.70e-08 ACAGAGGAAG CTGACAGTGAATTC CAAGCTTCTG 42570 87 1.47e-07 GTTCTGGTTT CTTACAGTTAATTT CTGGCTACCG 47900 302 3.79e-07 CATCATTCCA CTGACAGTGAATGC TAAAGCAACA 55141 421 7.75e-07 ACATGTCAGT CTTACTGTTAGTAT CTGCACTCGT 50630 418 1.34e-06 GGAACGCCAA CTTACAGTTAAATT GAACTCGGCG 14068 11 1.48e-06 TTTCTGTTGC CTGACAGTGAGCTT ATCTTAAATT 42302 429 1.81e-06 GTTCATCTGT TTGACTGTGAATGC TGACAATCGC 17974 73 1.98e-06 TACCACATGC CTGACAGTGACTTC CATTCCTCGA 25133 23 2.41e-06 AAGAATGGTG CTCACTGTCAATTG ACATACGGCC 47014 474 2.41e-06 GCAAAAAACA CTTACTGTTAGATT CACAGCAACA 47259 427 3.08e-06 CAAAAGTAGT TTTACAGTGAGTGT TCCTTTCATG 51007 282 3.08e-06 CTCATTGTCA CTCACTGTCAGTAC CTGCCTATGC 16814 37 3.45e-06 TTTTTGGCTC TTCACAGTCAATTC TTTCCACTAC 43528 394 5.95e-06 CCGAGTGCAG TTGACTGTGAGTGG CACACAACTT 45727 459 6.70e-06 ATAGTTAGCC TTGACCGTGAATAC AATACAAACA 19647 195 8.71e-06 TTCCTCTTCA CTGACCGTGAACAT TGTACTCGAC 46846 233 9.57e-06 ATTTCGATGC CTTACTGTCAAACC TACCCATGTA 22658 132 1.04e-05 ATACGTTTGA TTGACTGTGACTTG GGAGATTGCC 14450 77 1.04e-05 GTCCTCCTTG CTTACTGATAATTT GTTCTTTAAA 50246 461 1.23e-05 AAATAGCTCA CTCACAGTCACTAC TATTCTAACA 10782 132 1.45e-05 AGATGAAAAT GTGACTGTCAAAAT GATCAAAGCA 48417 292 1.55e-05 CGTTCGGGTT TTCACTGTGAGCAT TCAGGGACAG 49450 342 1.81e-05 CAAACAATAT TTTACCGTCAATAG GTAGTTCTCC 37596 152 2.10e-05 CTTTCGGTTC CTTACTGTTAGACG ATTCTAGCCC 15862 98 2.26e-05 ACATGGTCAT GTTACTGTTAGTCT ACTGCATTAT 44555 241 2.43e-05 ATTGCTACTG CTTACAGTTAGAAA CCACCAGCGC 9989 175 2.60e-05 GGTTGTAGAT CTAACAGTCAAATC ACTTTTTGTG 21538 161 3.00e-05 TTCGATCGAC CTCACAGGTAATTC TTGACTCGTG 32036 421 3.00e-05 CCCATTGATT CTGACATTCAACTT CTAATAAAGC 23865 196 3.22e-05 ACATAATCAA TTTACATTTAATAT AAGTCCAACC 27905 196 3.44e-05 TCTCCCCTTG GTGACTGTGAGAGG TGCATGGTCT 45888 261 4.49e-05 AGCCAATAGT CTGACAGACAACGT ACCTAACCCT 46993 340 5.11e-05 CCATTCCCAG CTGTCTGTGAATTA CCAATTCCCT 46259 212 5.43e-05 CATATCTGAC TTTACAATTAATAT AAGTAGTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25394 2.7e-08 157_[+2]_329 42570 1.5e-07 86_[+2]_400 47900 3.8e-07 301_[+2]_185 55141 7.8e-07 420_[+2]_66 50630 1.3e-06 417_[+2]_69 14068 1.5e-06 10_[+2]_476 42302 1.8e-06 428_[+2]_58 17974 2e-06 72_[+2]_414 25133 2.4e-06 22_[+2]_464 47014 2.4e-06 473_[+2]_13 47259 3.1e-06 426_[+2]_60 51007 3.1e-06 281_[+2]_205 16814 3.5e-06 36_[+2]_450 43528 5.9e-06 393_[+2]_93 45727 6.7e-06 458_[+2]_28 19647 8.7e-06 194_[+2]_292 46846 9.6e-06 232_[+2]_254 22658 1e-05 131_[+2]_355 14450 1e-05 76_[+2]_410 50246 1.2e-05 460_[+2]_26 10782 1.4e-05 131_[+2]_355 48417 1.6e-05 291_[+2]_195 49450 1.8e-05 341_[+2]_145 37596 2.1e-05 151_[+2]_335 15862 2.3e-05 97_[+2]_389 44555 2.4e-05 240_[+2]_246 9989 2.6e-05 174_[+2]_312 21538 3e-05 160_[+2]_326 32036 3e-05 420_[+2]_66 23865 3.2e-05 195_[+2]_291 27905 3.4e-05 195_[+2]_291 45888 4.5e-05 260_[+2]_226 46993 5.1e-05 339_[+2]_147 46259 5.4e-05 211_[+2]_275 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=34 25394 ( 158) CTGACAGTGAATTC 1 42570 ( 87) CTTACAGTTAATTT 1 47900 ( 302) CTGACAGTGAATGC 1 55141 ( 421) CTTACTGTTAGTAT 1 50630 ( 418) CTTACAGTTAAATT 1 14068 ( 11) CTGACAGTGAGCTT 1 42302 ( 429) TTGACTGTGAATGC 1 17974 ( 73) CTGACAGTGACTTC 1 25133 ( 23) CTCACTGTCAATTG 1 47014 ( 474) CTTACTGTTAGATT 1 47259 ( 427) TTTACAGTGAGTGT 1 51007 ( 282) CTCACTGTCAGTAC 1 16814 ( 37) TTCACAGTCAATTC 1 43528 ( 394) TTGACTGTGAGTGG 1 45727 ( 459) TTGACCGTGAATAC 1 19647 ( 195) CTGACCGTGAACAT 1 46846 ( 233) CTTACTGTCAAACC 1 22658 ( 132) TTGACTGTGACTTG 1 14450 ( 77) CTTACTGATAATTT 1 50246 ( 461) CTCACAGTCACTAC 1 10782 ( 132) GTGACTGTCAAAAT 1 48417 ( 292) TTCACTGTGAGCAT 1 49450 ( 342) TTTACCGTCAATAG 1 37596 ( 152) CTTACTGTTAGACG 1 15862 ( 98) GTTACTGTTAGTCT 1 44555 ( 241) CTTACAGTTAGAAA 1 9989 ( 175) CTAACAGTCAAATC 1 21538 ( 161) CTCACAGGTAATTC 1 32036 ( 421) CTGACATTCAACTT 1 23865 ( 196) TTTACATTTAATAT 1 27905 ( 196) GTGACTGTGAGAGG 1 45888 ( 261) CTGACAGACAACGT 1 46993 ( 340) CTGTCTGTGAATTA 1 46259 ( 212) TTTACAATTAATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 28733 bayes= 11.0873 E= 4.8e-011 -1173 138 -134 18 -1173 -1173 -1173 194 -324 -43 88 56 180 -1173 -1173 -314 -1173 208 -1173 -1173 76 -143 -1173 76 -324 -1173 203 -214 -224 -1173 -293 181 -1173 31 77 31 184 -1173 -1173 -1173 108 -143 53 -1173 -24 -69 -1173 125 21 -143 -34 66 -224 45 -34 76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 34 E= 4.8e-011 0.000000 0.617647 0.088235 0.294118 0.000000 0.000000 0.000000 1.000000 0.029412 0.176471 0.411765 0.382353 0.970588 0.000000 0.000000 0.029412 0.000000 1.000000 0.000000 0.000000 0.470588 0.088235 0.000000 0.441176 0.029412 0.000000 0.911765 0.058824 0.058824 0.000000 0.029412 0.911765 0.000000 0.294118 0.382353 0.323529 1.000000 0.000000 0.000000 0.000000 0.588235 0.088235 0.323529 0.000000 0.235294 0.147059 0.000000 0.617647 0.323529 0.088235 0.176471 0.411765 0.058824 0.323529 0.176471 0.441176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]T[GT]AC[AT]GT[GTC]A[AG][TA][TA][TC] -------------------------------------------------------------------------------- Time 50.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 52 llr = 419 E-value = 4.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::1:::::3:: pos.-specific C :1:1:6:36211 probability G :1332::11:34 matrix T a88584a52565 bits 2.2 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * Entropy 1.1 *** *** (11.6 bits) 0.9 *** *** 0.6 *** ***** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTTCTTCTTT consensus GG T CTAGG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42302 378 4.71e-07 GTTCGTTTCC TTTTTCTCCTTG AAAGAGAAAA 47900 219 6.98e-07 GAGGACAGCG TTTTTCTCCTTT TTCACCCTTG 9989 232 1.25e-06 CGACCTCGGC TTTGTCTTCTGT GTTCCTCCCC 46846 403 1.25e-06 ATCCATTTTT TTTGTTTTCTTT TTGTTCTTCG 51007 13 1.66e-06 GCCACCGCAG TTTTTTTTCTGT GTTCTCGCTT 38930 263 2.62e-06 GAAAACCCAT TTTGTCTCCTGT AAATCCGCTC 42570 162 2.62e-06 TTCTGGCGTT TTGGTCTTCTTG CACGTGACCT 31725 404 3.56e-06 GTGAGGGACC TTTTTCTCCATG GGAAAGCCGC 45844 147 5.02e-06 GCACCTTCGG TTTTTTTTTTTG CGAAAGTCGA 43528 462 6.11e-06 CCCCATCTGG TTTTTCTTGTTG ACACGTGCAT 12322 371 7.77e-06 TCCCGCAACC TCTTTCTTCTTT GAAGGGAAAT 23865 98 9.41e-06 CGTTATGCAG TTTTTCTCCTCT CGATTTCGAG 15862 428 1.25e-05 CTGGAAGAAG TGTTTCTTCTTT GAACTTACAT 40070 420 1.46e-05 GTTACTCATG TTTGTCTCCTCT CTGCCAGAAC 17974 211 1.46e-05 CTGTGCCAAA TTTGTTTTCAGT GGATATATAG 44055 179 1.65e-05 CGGGGTTGGT TTTGTCTCTTGG TCAGACACAA 49450 232 2.54e-05 ACGACGGTCC TTTTTTTCGTTT TTACAGGCTG 13820 36 2.54e-05 ATAATTGGTA TTGTTTTTTTTT GCAATCGACG 22868 274 2.83e-05 ATCAACCTTA TTTTGCTTTTTG TCGCAGCTTA 12140 18 3.28e-05 AAATTTCTTG TTTTTCTCCACT TATCCGGTTC 46259 335 3.74e-05 CACAATCAGT TCTTTTTCCTGG TTGTGACGTC 44047 374 3.74e-05 ACGCAGCGCG TCTGTCTTCCTG CCCCACGATG 36897 451 4.32e-05 CCGACAGCGA TTGTGCTTCTGT TTCCATCAAA 12144 306 4.32e-05 CCAATATCAT TTGTTCTTTATG TCGACAGCGC 46994 42 6.02e-05 TCTGGGAAAG TTTGTCTTTTGC AACATTGCTT 25394 11 6.83e-05 AAATGAGGCC TGTTTTTTCATT TGCGATCCAA 20740 43 6.83e-05 CCGGTGGACG TTGATTTTCTTG TCACTCGACA 45441 3 7.64e-05 AG TTTGTTTGCCGT ATCTGGTGGT 27905 409 7.64e-05 CGGCTGTGGC TTTTTCTTTCTC GAAAACGAAA 45888 122 9.13e-05 ACAACGCAGC TTTCTTTGCTGT CAATCTACGA 41002 392 9.13e-05 CAATAGAAAG TTTGTTTCGCTG GGCGCAGTCT 45727 243 1.34e-04 TTGGTCGCGG TTTGGTTCCCGT GAAATGTCTC 48417 36 1.60e-04 ATTCGTCTCG TTGATTTTCATG TCCGGTATTT 10782 219 1.76e-04 GCGCAAGAGA TCTGTCTCTCTG AAAATACCAA 46993 4 2.06e-04 ACA TTGTGTTGCTGG CAGTTAGTCA 49433 157 2.06e-04 GTTTTCGCTG TTGCTCTTCACG TTCCATGACG 14450 119 2.06e-04 AATACAATCG TTTATCTTTAGT AGATCCCCAT 47014 83 2.22e-04 TCATCTTATT TTGTGCTGCATG TCGAAAGGAT 54038 198 2.22e-04 TTCAAAAATA TGTTGCTTTTTT TAAGTCATAG 50246 359 2.60e-04 TTATTTTGAC TTTATCTCTAGG TTATGAGTAC 22658 306 2.79e-04 ACCAACGAAA TTTCTTTTATTT GCCAAAGGTC 21538 428 2.79e-04 GTACCAGGGT TTTGGTTGCTCT CTAGAATCAT 32036 382 2.79e-04 TTCCTTACAT TTGCTTTGCATG ATTCCTCCCC 44555 132 2.98e-04 GGTTATGGTT TCTGTTTCCCTC TGAGGTGAAG 32758 126 3.41e-04 GCTCCATTAT TTTCGCTTCATC TGTAAGTTCT 48320 50 3.41e-04 AAAGTGTGGG TGTGTCTTGCGT TTCAAAATAT 14145 312 3.41e-04 CACATTTCCT TCGCTCTTCTCG CAAATAATTT 19647 127 4.38e-04 TCCCTCCTAG TCGTTCTCCCGC CGTCCGCAAA 16814 25 4.38e-04 TCTAAACACA TTTTTTTGGCTC TTCACAGTCA 25133 186 4.38e-04 GAAAATGGAA TTGTTTTCACTG TCAATTAGGA 47058 228 4.38e-04 GATCCTCACA TTTTTCCTGTTT GTAATCCTAC 37596 99 5.21e-04 TCTATAATCT TGTGTTTTTACG CCTTTGGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42302 4.7e-07 377_[+3]_111 47900 7e-07 218_[+3]_270 9989 1.2e-06 231_[+3]_257 46846 1.2e-06 402_[+3]_86 51007 1.7e-06 12_[+3]_476 38930 2.6e-06 262_[+3]_226 42570 2.6e-06 161_[+3]_327 31725 3.6e-06 403_[+3]_85 45844 5e-06 146_[+3]_342 43528 6.1e-06 461_[+3]_27 12322 7.8e-06 370_[+3]_118 23865 9.4e-06 97_[+3]_391 15862 1.3e-05 427_[+3]_61 40070 1.5e-05 419_[+3]_69 17974 1.5e-05 210_[+3]_278 44055 1.6e-05 178_[+3]_310 49450 2.5e-05 231_[+3]_257 13820 2.5e-05 35_[+3]_453 22868 2.8e-05 273_[+3]_215 12140 3.3e-05 17_[+3]_471 46259 3.7e-05 334_[+3]_154 44047 3.7e-05 373_[+3]_115 36897 4.3e-05 450_[+3]_38 12144 4.3e-05 305_[+3]_183 46994 6e-05 41_[+3]_447 25394 6.8e-05 10_[+3]_478 20740 6.8e-05 42_[+3]_446 45441 7.6e-05 2_[+3]_486 27905 7.6e-05 408_[+3]_80 45888 9.1e-05 121_[+3]_367 41002 9.1e-05 391_[+3]_97 45727 0.00013 242_[+3]_246 48417 0.00016 35_[+3]_453 10782 0.00018 218_[+3]_270 46993 0.00021 3_[+3]_485 49433 0.00021 156_[+3]_332 14450 0.00021 118_[+3]_370 47014 0.00022 82_[+3]_406 54038 0.00022 197_[+3]_291 50246 0.00026 358_[+3]_130 22658 0.00028 305_[+3]_183 21538 0.00028 427_[+3]_61 32036 0.00028 381_[+3]_107 44555 0.0003 131_[+3]_357 32758 0.00034 125_[+3]_363 48320 0.00034 49_[+3]_439 14145 0.00034 311_[+3]_177 19647 0.00044 126_[+3]_362 16814 0.00044 24_[+3]_464 25133 0.00044 185_[+3]_303 47058 0.00044 227_[+3]_261 37596 0.00052 98_[+3]_390 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=52 42302 ( 378) TTTTTCTCCTTG 1 47900 ( 219) TTTTTCTCCTTT 1 9989 ( 232) TTTGTCTTCTGT 1 46846 ( 403) TTTGTTTTCTTT 1 51007 ( 13) TTTTTTTTCTGT 1 38930 ( 263) TTTGTCTCCTGT 1 42570 ( 162) TTGGTCTTCTTG 1 31725 ( 404) TTTTTCTCCATG 1 45844 ( 147) TTTTTTTTTTTG 1 43528 ( 462) TTTTTCTTGTTG 1 12322 ( 371) TCTTTCTTCTTT 1 23865 ( 98) TTTTTCTCCTCT 1 15862 ( 428) TGTTTCTTCTTT 1 40070 ( 420) TTTGTCTCCTCT 1 17974 ( 211) TTTGTTTTCAGT 1 44055 ( 179) TTTGTCTCTTGG 1 49450 ( 232) TTTTTTTCGTTT 1 13820 ( 36) TTGTTTTTTTTT 1 22868 ( 274) TTTTGCTTTTTG 1 12140 ( 18) TTTTTCTCCACT 1 46259 ( 335) TCTTTTTCCTGG 1 44047 ( 374) TCTGTCTTCCTG 1 36897 ( 451) TTGTGCTTCTGT 1 12144 ( 306) TTGTTCTTTATG 1 46994 ( 42) TTTGTCTTTTGC 1 25394 ( 11) TGTTTTTTCATT 1 20740 ( 43) TTGATTTTCTTG 1 45441 ( 3) TTTGTTTGCCGT 1 27905 ( 409) TTTTTCTTTCTC 1 45888 ( 122) TTTCTTTGCTGT 1 41002 ( 392) TTTGTTTCGCTG 1 45727 ( 243) TTTGGTTCCCGT 1 48417 ( 36) TTGATTTTCATG 1 10782 ( 219) TCTGTCTCTCTG 1 46993 ( 4) TTGTGTTGCTGG 1 49433 ( 157) TTGCTCTTCACG 1 14450 ( 119) TTTATCTTTAGT 1 47014 ( 83) TTGTGCTGCATG 1 54038 ( 198) TGTTGCTTTTTT 1 50246 ( 359) TTTATCTCTAGG 1 22658 ( 306) TTTCTTTTATTT 1 21538 ( 428) TTTGGTTGCTCT 1 32036 ( 382) TTGCTTTGCATG 1 44555 ( 132) TCTGTTTCCCTC 1 32758 ( 126) TTTCGCTTCATC 1 48320 ( 50) TGTGTCTTGCGT 1 14145 ( 312) TCGCTCTTCTCG 1 19647 ( 127) TCGTTCTCCCGC 1 16814 ( 25) TTTTTTTGGCTC 1 25133 ( 186) TTGTTTTCACTG 1 47058 ( 228) TTTTTCCTGTTT 1 37596 ( 99) TGTGTTTTTACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 28851 bayes= 9.64461 E= 4.4e-004 -1234 -1234 -1234 194 -1234 -82 -122 156 -1234 -1234 16 153 -186 -104 55 89 -1234 -1234 -54 170 -1234 128 -1234 70 -1234 -362 -1234 191 -1234 46 -73 105 -286 137 -96 -17 -16 -17 -1234 105 -1234 -82 46 110 -1234 -104 92 83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 52 E= 4.4e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.134615 0.096154 0.769231 0.000000 0.000000 0.250000 0.750000 0.076923 0.115385 0.326923 0.480769 0.000000 0.000000 0.153846 0.846154 0.000000 0.576923 0.000000 0.423077 0.000000 0.019231 0.000000 0.980769 0.000000 0.326923 0.134615 0.538462 0.038462 0.615385 0.115385 0.230769 0.250000 0.211538 0.000000 0.538462 0.000000 0.134615 0.307692 0.557692 0.000000 0.115385 0.423077 0.461538 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[TG][TG]T[CT]T[TC][CT][TAC][TG][TG] -------------------------------------------------------------------------------- Time 74.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42570 1.05e-06 86_[+2(1.47e-07)]_61_[+3(2.62e-06)]_\ 327 31725 3.14e-03 403_[+3(3.56e-06)]_85 32036 4.22e-04 65_[+1(9.93e-05)]_275_\ [+1(5.33e-06)]_48_[+2(3.00e-05)]_66 54038 6.68e-02 294_[+1(8.14e-05)]_190 8777 1.79e-01 289_[+1(3.34e-05)]_195 17974 1.10e-05 72_[+2(1.98e-06)]_85_[+1(2.18e-05)]_\ 23_[+3(1.46e-05)]_278 20740 9.71e-02 42_[+3(6.83e-05)]_446 27905 2.83e-04 164_[+1(1.02e-05)]_1_[+3(9.13e-05)]_\ 2_[+2(3.44e-05)]_199_[+3(7.64e-05)]_80 51007 6.03e-07 12_[+3(1.66e-06)]_99_[+1(4.76e-06)]_\ 142_[+2(3.08e-06)]_205 46846 2.12e-06 199_[+1(8.28e-06)]_17_\ [+2(9.57e-06)]_156_[+3(1.25e-06)]_86 46994 1.83e-02 41_[+3(6.02e-05)]_292_\ [+1(8.70e-05)]_139 47014 3.08e-04 136_[+1(5.73e-05)]_321_\ [+2(2.41e-06)]_13 47058 5.74e-01 500 13820 6.06e-02 35_[+3(2.54e-05)]_453 14145 1.23e-03 257_[+1(9.78e-07)]_227 21538 3.56e-06 160_[+2(3.00e-05)]_134_\ [+1(2.26e-08)]_176 14068 4.67e-04 10_[+2(1.48e-06)]_110_\ [+1(2.38e-05)]_350 37596 2.52e-02 151_[+2(2.10e-05)]_335 14450 3.26e-04 76_[+2(1.04e-05)]_312_\ [+1(1.51e-05)]_82 48320 3.28e-02 318_[+1(4.24e-05)]_166 48417 4.71e-04 291_[+2(1.55e-05)]_140_\ [+1(1.99e-05)]_39 38930 1.99e-02 45_[+3(1.92e-05)]_205_\ [+3(2.62e-06)]_226 48486 8.31e-01 500 22658 1.27e-04 131_[+2(1.04e-05)]_267_\ [+2(6.93e-05)]_45_[+1(3.75e-06)]_13 25133 2.03e-05 22_[+2(2.41e-06)]_154_\ [+2(1.96e-05)]_144_[+1(1.32e-06)]_136 32758 3.90e-02 261_[+1(2.18e-05)]_223 9989 5.83e-07 174_[+2(2.60e-05)]_43_\ [+3(1.25e-06)]_73_[+1(7.25e-07)]_168 25394 2.34e-06 10_[+3(6.83e-05)]_4_[+1(6.16e-05)]_\ 115_[+2(2.70e-08)]_94_[+2(1.55e-05)]_221 22868 5.53e-04 273_[+3(2.83e-05)]_93_\ [+1(3.32e-06)]_106 40070 9.01e-02 419_[+3(1.46e-05)]_69 15862 3.14e-03 97_[+2(2.26e-05)]_316_\ [+3(1.25e-05)]_61 49433 5.15e-04 421_[+1(3.10e-07)]_63 49450 3.55e-03 231_[+3(2.54e-05)]_98_\ [+2(1.81e-05)]_145 42302 2.24e-05 377_[+3(4.71e-07)]_39_\ [+2(1.81e-06)]_58 55141 1.67e-05 371_[+1(9.78e-07)]_33_\ [+2(7.75e-07)]_66 16633 2.14e-02 253_[+1(3.32e-06)]_231 41002 2.19e-02 138_[+1(7.60e-05)]_237_\ [+3(9.13e-05)]_97 23865 3.15e-03 97_[+3(9.41e-06)]_86_[+2(3.22e-05)]_\ 291 50246 7.54e-03 198_[+2(3.44e-05)]_248_\ [+2(1.23e-05)]_26 16814 8.50e-04 36_[+2(3.45e-06)]_236_\ [+1(7.09e-05)]_198 44047 6.51e-03 373_[+3(3.74e-05)]_43_\ [+1(3.34e-05)]_56 44055 3.65e-04 17_[+1(6.62e-05)]_145_\ [+3(1.65e-05)]_176_[+1(1.32e-06)]_118 50630 2.06e-04 381_[+1(7.43e-06)]_20_\ [+2(1.34e-06)]_69 44555 1.79e-04 240_[+2(2.43e-05)]_133_\ [+1(2.26e-06)]_97 10782 1.72e-04 131_[+2(1.45e-05)]_179_\ [+1(4.94e-05)]_34_[+1(5.98e-06)]_110 19647 2.43e-05 194_[+2(8.71e-06)]_73_\ [+1(4.47e-07)]_203 45441 1.10e-03 2_[+3(7.64e-05)]_371_[+1(8.41e-07)]_\ 22_[+1(4.24e-05)]_61 12144 2.26e-03 241_[+1(1.51e-05)]_48_\ [+3(4.32e-05)]_183 12140 1.77e-03 17_[+3(3.28e-05)]_9_[+1(2.82e-05)]_\ 446 45727 4.21e-05 343_[+1(3.32e-06)]_99_\ [+2(6.70e-06)]_28 12322 7.63e-04 19_[+1(1.02e-05)]_335_\ [+3(7.77e-06)]_118 45844 3.53e-02 146_[+3(5.02e-06)]_342 45888 1.04e-03 121_[+3(9.13e-05)]_127_\ [+2(4.49e-05)]_95_[+1(3.07e-05)]_115 46259 6.05e-03 211_[+2(5.43e-05)]_109_\ [+3(3.74e-05)]_154 46993 6.29e-03 339_[+2(5.11e-05)]_147 47259 4.85e-04 354_[+1(1.66e-05)]_56_\ [+2(3.08e-06)]_60 36897 6.08e-02 450_[+3(4.32e-05)]_38 47900 2.86e-06 218_[+3(6.98e-07)]_71_\ [+2(3.79e-07)]_185 43528 1.25e-06 305_[+1(1.51e-06)]_72_\ [+2(5.95e-06)]_54_[+3(6.11e-06)]_27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************