******************************************************************************** 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/256/256.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 29011 1.0000 500 38312 1.0000 500 22247 1.0000 500 9816 1.0000 500 43671 1.0000 500 16442 1.0000 500 50372 1.0000 500 10848 1.0000 500 34165 1.0000 500 11248 1.0000 500 11649 1.0000 500 6711 1.0000 500 12436 1.0000 500 44663 1.0000 500 46098 1.0000 500 45588 1.0000 500 48993 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/256/256.seqs.fa -oc motifs/256 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.248 G 0.237 T 0.246 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.248 G 0.237 T 0.246 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 17 sites = 11 llr = 137 E-value = 5.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::12512::::::: pos.-specific C :5:25133186131::2 probability G 22a:58:25:451:287 matrix T 83:8::513::469821 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.2 * ** * * *** Entropy 1.0 * **** ** **** (18.0 bits) 0.8 * **** ******** 0.6 ******* ******** 0.4 ******* ********* 0.2 ***************** 0.0 ----------------- Multilevel TCGTGGTAGCCGTTTGG consensus T C CCT GTC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 43671 91 1.42e-08 CTCGAGATTT TCGTGATAGCCGTTTGG CGGCAGGTTT 46098 372 4.27e-08 GCGGCAGCCC TCGTGGCCGCGGTTGGG CCGGAGACTC 29011 98 9.79e-08 ATTCCGAGCT TCGCCGCGGCCTTTTGG AAAGATCGAA 12436 215 3.21e-07 TAAGGTCCAC TGGTCGTCGACTCTTGG GCACGCATTC 50372 416 4.26e-07 AGTTTGGGTC TTGTGGTATCGTCTTTG CCTGCGGACC 16442 431 4.72e-07 CACACACCGT TCGTGCTGGCCGGTTGG CGTTGTCCCC 11248 469 9.56e-07 TCTTTAAACA GTGTCGACGACGTTTGG AAGTATCGTT 38312 81 1.13e-06 GAGGAGGAAC TGGTGGTATCGTTTTTC TGGGTTTCTC 22247 237 2.82e-06 ACATTCTGAT GTGTCGCACCCCTTTGG TGTCATATCT 48993 174 4.80e-06 GAGCGAGCAG TCGCCGTTTCGGTTGGC GCGTCGGGCA 34165 311 9.17e-06 CCAATACGCG TCGTGGAAACCGCCTGT CGGATCAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43671 1.4e-08 90_[+1]_393 46098 4.3e-08 371_[+1]_112 29011 9.8e-08 97_[+1]_386 12436 3.2e-07 214_[+1]_269 50372 4.3e-07 415_[+1]_68 16442 4.7e-07 430_[+1]_53 11248 9.6e-07 468_[+1]_15 38312 1.1e-06 80_[+1]_403 22247 2.8e-06 236_[+1]_247 48993 4.8e-06 173_[+1]_310 34165 9.2e-06 310_[+1]_173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=17 seqs=11 43671 ( 91) TCGTGATAGCCGTTTGG 1 46098 ( 372) TCGTGGCCGCGGTTGGG 1 29011 ( 98) TCGCCGCGGCCTTTTGG 1 12436 ( 215) TGGTCGTCGACTCTTGG 1 50372 ( 416) TTGTGGTATCGTCTTTG 1 16442 ( 431) TCGTGCTGGCCGGTTGG 1 11248 ( 469) GTGTCGACGACGTTTGG 1 38312 ( 81) TGGTGGTATCGTTTTTC 1 22247 ( 237) GTGTCGCACCCCTTTGG 1 48993 ( 174) TCGCCGTTTCGGTTGGC 1 34165 ( 311) TCGTGGAAACCGCCTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 8228 bayes= 10.5724 E= 5.6e+001 -1010 -1010 -38 173 -1010 114 -38 15 -1010 -1010 208 -1010 -1010 -45 -1010 173 -1010 88 120 -1010 -156 -144 179 -1010 -57 14 -1010 115 75 14 -38 -143 -156 -144 120 15 -57 172 -1010 -1010 -1010 136 62 -1010 -1010 -144 120 56 -1010 14 -138 137 -1010 -144 -1010 188 -1010 -1010 -38 173 -1010 -1010 179 -44 -1010 -45 162 -143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 11 E= 5.6e+001 0.000000 0.000000 0.181818 0.818182 0.000000 0.545455 0.181818 0.272727 0.000000 0.000000 1.000000 0.000000 0.000000 0.181818 0.000000 0.818182 0.000000 0.454545 0.545455 0.000000 0.090909 0.090909 0.818182 0.000000 0.181818 0.272727 0.000000 0.545455 0.454545 0.272727 0.181818 0.090909 0.090909 0.090909 0.545455 0.272727 0.181818 0.818182 0.000000 0.000000 0.000000 0.636364 0.363636 0.000000 0.000000 0.090909 0.545455 0.363636 0.000000 0.272727 0.090909 0.636364 0.000000 0.090909 0.000000 0.909091 0.000000 0.000000 0.181818 0.818182 0.000000 0.000000 0.818182 0.181818 0.000000 0.181818 0.727273 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CT]GT[GC]G[TC][AC][GT]C[CG][GT][TC]TTGG -------------------------------------------------------------------------------- Time 2.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 16 llr = 166 E-value = 2.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::1:71311:1::1: pos.-specific C ::116:1::5:43:35 probability G 81:74:23418:1:11 matrix T 3991:36543356a54 bits 2.1 * 1.9 * 1.7 ** * 1.5 ** * Relative 1.2 *** * * Entropy 1.0 *** ** * * (15.0 bits) 0.8 *** ** * ** * 0.6 ****** * **** * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GTTGCATTGCGTTTTC consensus T GT ATTTCC CT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45588 382 6.21e-07 GTTCCTTACT GTTGGTTTGTTCTTTC CGACCGGCTC 12436 2 1.02e-06 C GTTGGATTGTGACTTC GAAAAAAAGG 16442 399 1.15e-06 TCACCAAAAC GTTCCACTGCGCTTTC TTTCATCACA 9816 100 1.46e-06 GAACAAAGAA GTTGGTTTGTGTTTTG TGGAACATGA 10848 107 2.04e-06 TCGCACGATT GTTTGTTGTCGCTTTT ATGGCGAACA 6711 90 2.82e-06 GATTTACAAG GTTGCTCATCTTTTTT CTTTAATGCA 11248 288 3.45e-06 AGTCCTTGGT GTTGCAGAACTTTTTC GTTTCATCGA 11649 67 3.82e-06 TGATTGGTCA GTTCCAAGTCGTTTCT CTTTGCGACT 29011 267 3.82e-06 AGACTCTAGA TTTGGATGGAGCTTCC TTGTATGAAC 44663 426 5.61e-06 TTGTCCTCAC TTTTCATTTTGTCTCT TTTTTTTTTT 48993 373 8.03e-06 ACAGTAAATA TTTGCATTGTGTGTGC TTGGACGGTG 46098 262 1.44e-05 ATAGGAAGGC GTTACTTAACGCTTTT GATTTTTAGT 43671 402 1.44e-05 TTTTTCCGGC TGTGGATTTCGTTTAC CTCCCACTCG 50372 261 1.95e-05 CAAAAAAATG GTTGCAGTTGGTGTAC TAACTGTAAG 38312 143 2.10e-05 GAAATAGGCA GTTGCAGAGATCCTCT CAGAACTAAT 22247 168 6.92e-05 GCTAGTATAT GTCGCAAGTCGACTCT TTTTCATGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45588 6.2e-07 381_[+2]_103 12436 1e-06 1_[+2]_483 16442 1.2e-06 398_[+2]_86 9816 1.5e-06 99_[+2]_385 10848 2e-06 106_[+2]_378 6711 2.8e-06 89_[+2]_395 11248 3.5e-06 287_[+2]_197 11649 3.8e-06 66_[+2]_418 29011 3.8e-06 266_[+2]_218 44663 5.6e-06 425_[+2]_59 48993 8e-06 372_[+2]_112 46098 1.4e-05 261_[+2]_223 43671 1.4e-05 401_[+2]_83 50372 1.9e-05 260_[+2]_224 38312 2.1e-05 142_[+2]_342 22247 6.9e-05 167_[+2]_317 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=16 45588 ( 382) GTTGGTTTGTTCTTTC 1 12436 ( 2) GTTGGATTGTGACTTC 1 16442 ( 399) GTTCCACTGCGCTTTC 1 9816 ( 100) GTTGGTTTGTGTTTTG 1 10848 ( 107) GTTTGTTGTCGCTTTT 1 6711 ( 90) GTTGCTCATCTTTTTT 1 11248 ( 288) GTTGCAGAACTTTTTC 1 11649 ( 67) GTTCCAAGTCGTTTCT 1 29011 ( 267) TTTGGATGGAGCTTCC 1 44663 ( 426) TTTTCATTTTGTCTCT 1 48993 ( 373) TTTGCATTGTGTGTGC 1 46098 ( 262) GTTACTTAACGCTTTT 1 43671 ( 402) TGTGGATTTCGTTTAC 1 50372 ( 261) GTTGCAGTTGGTGTAC 1 38312 ( 143) GTTGCAGAGATCCTCT 1 22247 ( 168) GTCGCAAGTCGACTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.0065 E= 2.1e+001 -1064 -1064 166 2 -1064 -1064 -192 193 -1064 -198 -1064 193 -210 -99 154 -98 -1064 134 66 -1064 135 -1064 -1064 34 -111 -99 -34 119 -11 -1064 8 102 -111 -1064 89 83 -111 101 -192 34 -1064 -1064 166 2 -111 60 -1064 102 -1064 1 -92 134 -1064 -1064 -1064 202 -111 34 -192 102 -1064 101 -192 83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 2.1e+001 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.062500 0.937500 0.000000 0.062500 0.000000 0.937500 0.062500 0.125000 0.687500 0.125000 0.000000 0.625000 0.375000 0.000000 0.687500 0.000000 0.000000 0.312500 0.125000 0.125000 0.187500 0.562500 0.250000 0.000000 0.250000 0.500000 0.125000 0.000000 0.437500 0.437500 0.125000 0.500000 0.062500 0.312500 0.000000 0.000000 0.750000 0.250000 0.125000 0.375000 0.000000 0.500000 0.000000 0.250000 0.125000 0.625000 0.000000 0.000000 0.000000 1.000000 0.125000 0.312500 0.062500 0.500000 0.000000 0.500000 0.062500 0.437500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]TTG[CG][AT]T[TAG][GT][CT][GT][TC][TC]T[TC][CT] -------------------------------------------------------------------------------- Time 5.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 8 llr = 123 E-value = 5.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:a14616:4:4a44a1: pos.-specific C 319::9::11:39::63:5: probability G :4:a::54::1414::1:38 matrix T 85::::1:839::3::3:13 bits 2.1 * 1.9 ** * * 1.7 ** * * 1.5 **** * * * * Relative 1.2 * **** * * * * * Entropy 1.0 * **** ** * * ** * * (22.1 bits) 0.8 * **** ** * * ** * * 0.6 *********** * ** * * 0.4 **************** * * 0.2 **************** *** 0.0 -------------------- Multilevel TTCGACGATATACAACAACG consensus CG AG T G G AC GT sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 44663 169 9.12e-10 CTTTGGTGCA TTCGACGGTTTGCGAAAACG AGACTCAGTC 43671 159 4.85e-09 CATGAATTTA TGCGACGATATACAAATATG ACTGAGATTA 45588 212 3.19e-08 GTTGATAGTG TTCGACTATTTCCAACCACT GACTGTCATG 29011 229 4.15e-08 ATAAGGTGTG TGCGAAGGTATGCTACAAAG TGTATCTAAG 46098 211 5.33e-08 TTCTAGTTCA TTCGACGACAGGCGACAACT GCTAGGACGT 38312 121 9.19e-08 GGCAGAGTCC CTCGACAATATAGAAATAGG CAGTTGCAGA 6711 136 1.70e-07 GCACACTTGT TCCGACAAACTACTACCACG TACAGAATAC 34165 212 1.93e-07 CCAATGTGAT CGAGACAGTATCCGACGAGG AATTGCATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44663 9.1e-10 168_[+3]_312 43671 4.8e-09 158_[+3]_322 45588 3.2e-08 211_[+3]_269 29011 4.1e-08 228_[+3]_252 46098 5.3e-08 210_[+3]_270 38312 9.2e-08 120_[+3]_360 6711 1.7e-07 135_[+3]_345 34165 1.9e-07 211_[+3]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=8 44663 ( 169) TTCGACGGTTTGCGAAAACG 1 43671 ( 159) TGCGACGATATACAAATATG 1 45588 ( 212) TTCGACTATTTCCAACCACT 1 29011 ( 229) TGCGAAGGTATGCTACAAAG 1 46098 ( 211) TTCGACGACAGGCGACAACT 1 38312 ( 121) CTCGACAATATAGAAATAGG 1 6711 ( 136) TCCGACAAACTACTACCACG 1 34165 ( 212) CGAGACAGTATCCGACGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.99594 E= 5.3e+002 -965 1 -965 161 -965 -98 66 102 -111 182 -965 -965 -965 -965 208 -965 189 -965 -965 -965 -111 182 -965 -965 48 -965 108 -98 121 -965 66 -965 -111 -98 -965 161 121 -98 -965 2 -965 -965 -92 183 48 1 66 -965 -965 182 -92 -965 48 -965 66 2 189 -965 -965 -965 48 133 -965 -965 48 1 -92 2 189 -965 -965 -965 -111 101 8 -98 -965 -965 166 2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.3e+002 0.000000 0.250000 0.000000 0.750000 0.000000 0.125000 0.375000 0.500000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.375000 0.000000 0.500000 0.125000 0.625000 0.000000 0.375000 0.000000 0.125000 0.125000 0.000000 0.750000 0.625000 0.125000 0.000000 0.250000 0.000000 0.000000 0.125000 0.875000 0.375000 0.250000 0.375000 0.000000 0.000000 0.875000 0.125000 0.000000 0.375000 0.000000 0.375000 0.250000 1.000000 0.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.375000 0.250000 0.125000 0.250000 1.000000 0.000000 0.000000 0.000000 0.125000 0.500000 0.250000 0.125000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][TG]CGAC[GA][AG]T[AT]T[AGC]C[AGT]A[CA][ACT]A[CG][GT] -------------------------------------------------------------------------------- Time 7.89 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29011 6.89e-10 97_[+1(9.79e-08)]_13_[+1(2.48e-05)]_\ 84_[+3(4.15e-08)]_18_[+2(3.82e-06)]_218 38312 6.56e-08 80_[+1(1.13e-06)]_23_[+3(9.19e-08)]_\ 2_[+2(2.10e-05)]_342 22247 1.19e-03 167_[+2(6.92e-05)]_53_\ [+1(2.82e-06)]_247 9816 5.43e-03 99_[+2(1.46e-06)]_385 43671 5.29e-11 90_[+1(1.42e-08)]_51_[+3(4.85e-09)]_\ 223_[+2(1.44e-05)]_83 16442 1.55e-05 398_[+2(1.15e-06)]_16_\ [+1(4.72e-07)]_53 50372 1.52e-04 260_[+2(1.95e-05)]_139_\ [+1(4.26e-07)]_68 10848 4.88e-03 106_[+2(2.04e-06)]_378 34165 3.78e-05 211_[+3(1.93e-07)]_79_\ [+1(9.17e-06)]_173 11248 6.13e-05 287_[+2(3.45e-06)]_165_\ [+1(9.56e-07)]_15 11649 1.57e-02 66_[+2(3.82e-06)]_418 6711 1.32e-05 89_[+2(2.82e-06)]_30_[+3(1.70e-07)]_\ 345 12436 6.95e-06 1_[+2(1.02e-06)]_197_[+1(3.21e-07)]_\ 269 44663 4.98e-08 168_[+3(9.12e-10)]_237_\ [+2(5.61e-06)]_59 46098 1.38e-09 210_[+3(5.33e-08)]_31_\ [+2(1.44e-05)]_94_[+1(4.27e-08)]_19_[+1(5.60e-05)]_76 45588 2.62e-07 211_[+3(3.19e-08)]_150_\ [+2(6.21e-07)]_103 48993 2.16e-04 173_[+1(4.80e-06)]_182_\ [+2(8.03e-06)]_112 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************