******************************************************************************** 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/56/56.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 12088 1.0000 500 1294 1.0000 500 19069 1.0000 500 20469 1.0000 500 24777 1.0000 500 261607 1.0000 500 262700 1.0000 500 263565 1.0000 500 263665 1.0000 500 264768 1.0000 500 270037 1.0000 500 270256 1.0000 500 39536 1.0000 500 40200 1.0000 500 42169 1.0000 500 5013 1.0000 500 5668 1.0000 500 6952 1.0000 500 7271 1.0000 500 8831 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/56/56.seqs.fa -oc motifs/56 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.230 G 0.246 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.230 G 0.246 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 17 llr = 198 E-value = 7.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 851:812a422:182 pos.-specific C 2298177:661a918 probability G 12:1:11:::5::1: matrix T :::1111::22::1: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * ** * Relative 1.3 ** * ** * Entropy 1.1 * ** ** ** * (16.8 bits) 0.8 * ******* **** 0.6 * ******** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AACCACCACCGCCAC consensus C AAT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 8831 54 1.30e-08 AACACATCAT AACCACCACCGCCGC CAACGTCAAA 19069 206 2.60e-08 ACACCACAAC AACCACCACAACCAC ACCTCTCTCA 263565 416 7.75e-08 GCAACACAGC AGACACCACCGCCAC TGACAAGTCG 20469 477 9.63e-08 GCTCCTCGTT CACCACCAACACCAC CCCGACAAC 42169 484 2.02e-07 ACTTCTATCA AACCACCACATCCAA AG 270037 424 9.57e-07 GCTCCTTTTG AACCACAACCGCCGA CCACGCTTTT 6952 306 1.27e-06 TGCCTCCTCG ACCCCGCACAGCCAC AAAAATTGCG 39536 453 1.27e-06 CACAAAACCG ACCGACGACCGCCAC AGCAACTAAC 24777 46 1.68e-06 TCATCGGTAG AACCACTAATTCCAC CAACTTGGCA 262700 456 1.83e-06 TCACACTTCA CCCCTACACCGCCAC CACCTTCTCA 5013 272 2.01e-06 AGTCCCAAGT AGCCCCAAAAGCCAC TGCTAGCTGG 5668 353 3.94e-06 CTCAACCATC AACCATCAACTCAAC CCTCAATGTT 270256 475 3.94e-06 AACCACAGAC AGCCACCACTCCAAC GACAACGCAG 264768 478 4.61e-06 ACAGCATCCA AAACAACAACGCCAA ACAACACA 263665 419 4.61e-06 CAACTCTTGC ACCGACAACCGCCCC CCGACACCCG 1294 443 2.44e-05 TAAATGCGCT CGCTTCCACTTCCAC TTCCAGTTCA 12088 291 2.44e-05 CCTTCGATTC GACCAGCAACACCTC CGTAGACTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8831 1.3e-08 53_[+1]_432 19069 2.6e-08 205_[+1]_280 263565 7.8e-08 415_[+1]_70 20469 9.6e-08 476_[+1]_9 42169 2e-07 483_[+1]_2 270037 9.6e-07 423_[+1]_62 6952 1.3e-06 305_[+1]_180 39536 1.3e-06 452_[+1]_33 24777 1.7e-06 45_[+1]_440 262700 1.8e-06 455_[+1]_30 5013 2e-06 271_[+1]_214 5668 3.9e-06 352_[+1]_133 270256 3.9e-06 474_[+1]_11 264768 4.6e-06 477_[+1]_8 263665 4.6e-06 418_[+1]_67 1294 2.4e-05 442_[+1]_43 12088 2.4e-05 290_[+1]_195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=17 8831 ( 54) AACCACCACCGCCGC 1 19069 ( 206) AACCACCACAACCAC 1 263565 ( 416) AGACACCACCGCCAC 1 20469 ( 477) CACCACCAACACCAC 1 42169 ( 484) AACCACCACATCCAA 1 270037 ( 424) AACCACAACCGCCGA 1 6952 ( 306) ACCCCGCACAGCCAC 1 39536 ( 453) ACCGACGACCGCCAC 1 24777 ( 46) AACCACTAATTCCAC 1 262700 ( 456) CCCCTACACCGCCAC 1 5013 ( 272) AGCCCCAAAAGCCAC 1 5668 ( 353) AACCATCAACTCAAC 1 270256 ( 475) AGCCACCACTCCAAC 1 264768 ( 478) AAACAACAACGCCAA 1 263665 ( 419) ACCGACAACCGCCCC 1 1294 ( 443) CGCTTCCACTTCCAC 1 12088 ( 291) GACCAGCAACACCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 9720 bayes= 9.9525 E= 7.8e-009 154 -38 -206 -1073 101 3 -7 -1073 -116 194 -1073 -1073 -1073 184 -107 -215 154 -97 -1073 -115 -116 162 -107 -215 -57 162 -206 -215 193 -1073 -1073 -1073 43 149 -1073 -1073 -16 135 -1073 -57 -57 -197 110 -15 -1073 212 -1073 -1073 -116 194 -1073 -1073 154 -197 -107 -215 -57 184 -1073 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 17 E= 7.8e-009 0.764706 0.176471 0.058824 0.000000 0.529412 0.235294 0.235294 0.000000 0.117647 0.882353 0.000000 0.000000 0.000000 0.823529 0.117647 0.058824 0.764706 0.117647 0.000000 0.117647 0.117647 0.705882 0.117647 0.058824 0.176471 0.705882 0.058824 0.058824 1.000000 0.000000 0.000000 0.000000 0.352941 0.647059 0.000000 0.000000 0.235294 0.588235 0.000000 0.176471 0.176471 0.058824 0.529412 0.235294 0.000000 1.000000 0.000000 0.000000 0.117647 0.882353 0.000000 0.000000 0.764706 0.058824 0.117647 0.058824 0.176471 0.823529 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[ACG]CCACCA[CA][CA][GT]CCAC -------------------------------------------------------------------------------- Time 3.45 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 16 llr = 179 E-value = 7.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3115:11236:341: pos.-specific C ::411:1143:313:1 probability G a819468944486399 matrix T ::4::4::::::::11 bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 ** * * * ** Entropy 1.1 ** * *** ** ** (16.1 bits) 0.8 ** * *** ** ** 0.6 ** ****** *** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GGTGAGGGGGAGGAGG consensus AC GT CCGCAC sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 42169 213 3.23e-09 TGGAGGCGGT GGTGAGGGCGAGGCGG GGATGTTGAC 7271 315 8.50e-08 CGATAGTGAC GGTGGTGGCGACGAGG ATAGCTGCAG 270256 279 9.91e-08 GGGCTTGAGT GGCGGTGGGCGGGGGG GACATTCCAC 8831 298 1.16e-07 GTTGTTGAGC GGAGAGGGGGAGGGGG TGTAGCACTT 263665 363 1.53e-07 GGGAGAGGTG GGCGATGGGAGGGGGG GTTCGAATAA 12088 82 1.66e-06 TTCTTCCGAT GGCGGGCGACGGGCGG CAGGAAACAG 270037 64 3.14e-06 GTGGCATACG GATGATGGCCAGGATG TTGGACAGAA 1294 287 4.05e-06 CGTTGTCTGA GATGATGGAAAGAGGG AGGCGTTGTG 20469 452 4.39e-06 TTGACGGACA GACGCTGGGGACAAGG CTCCTCGTTC 6952 65 5.13e-06 GTCCAACTTC GATGAGGACGACGAGG AGTAATGGGT 19069 17 5.13e-06 AAAGGCGGGG GGCCGTGGCCGGACGG CGTTCGCGAA 40200 99 6.96e-06 CGAGTTTAGC GGTGCGGGGGAGCAGC AGCTTCGGCA 39536 364 1.08e-05 GCGAGCAAGA GGGGAGAGCGACGCGG GTTTGTTCTC 5668 421 1.52e-05 GATGAAACTA GGTGAGGCGAGGGAAG GTGGAATTTG 24777 391 2.08e-05 TCCGCTGTCC GGAGGGGGAAAGAAGT GGATTGTATC 5013 315 2.66e-05 GAGAAACCGA GGCAGGCGGCGGCCGG ACAAGCAACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42169 3.2e-09 212_[+2]_272 7271 8.5e-08 314_[+2]_170 270256 9.9e-08 278_[+2]_206 8831 1.2e-07 297_[+2]_187 263665 1.5e-07 362_[+2]_122 12088 1.7e-06 81_[+2]_403 270037 3.1e-06 63_[+2]_421 1294 4.1e-06 286_[+2]_198 20469 4.4e-06 451_[+2]_33 6952 5.1e-06 64_[+2]_420 19069 5.1e-06 16_[+2]_468 40200 7e-06 98_[+2]_386 39536 1.1e-05 363_[+2]_121 5668 1.5e-05 420_[+2]_64 24777 2.1e-05 390_[+2]_94 5013 2.7e-05 314_[+2]_170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=16 42169 ( 213) GGTGAGGGCGAGGCGG 1 7271 ( 315) GGTGGTGGCGACGAGG 1 270256 ( 279) GGCGGTGGGCGGGGGG 1 8831 ( 298) GGAGAGGGGGAGGGGG 1 263665 ( 363) GGCGATGGGAGGGGGG 1 12088 ( 82) GGCGGGCGACGGGCGG 1 270037 ( 64) GATGATGGCCAGGATG 1 1294 ( 287) GATGATGGAAAGAGGG 1 20469 ( 452) GACGCTGGGGACAAGG 1 6952 ( 65) GATGAGGACGACGAGG 1 19069 ( 17) GGCCGTGGCCGGACGG 1 40200 ( 99) GGTGCGGGGGAGCAGC 1 39536 ( 364) GGGGAGAGCGACGCGG 1 5668 ( 421) GGTGAGGCGAGGGAAG 1 24777 ( 391) GGAGGGGGAAAGAAGT 1 5013 ( 315) GGCAGGCGGCGGCCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 9700 bayes= 9.97931 E= 7.7e-002 -1064 -1064 202 -1064 -7 -1064 161 -1064 -107 70 -198 74 -207 -188 183 -1064 93 -88 61 -1064 -1064 -1064 119 74 -207 -88 172 -1064 -207 -188 183 -1064 -48 70 83 -1064 -7 44 83 -1064 125 -1064 61 -1064 -1064 12 161 -1064 -7 -88 134 -1064 74 44 2 -1064 -207 -1064 183 -206 -1064 -188 183 -206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 7.7e-002 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.125000 0.375000 0.062500 0.437500 0.062500 0.062500 0.875000 0.000000 0.500000 0.125000 0.375000 0.000000 0.000000 0.000000 0.562500 0.437500 0.062500 0.125000 0.812500 0.000000 0.062500 0.062500 0.875000 0.000000 0.187500 0.375000 0.437500 0.000000 0.250000 0.312500 0.437500 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.125000 0.625000 0.000000 0.437500 0.312500 0.250000 0.000000 0.062500 0.000000 0.875000 0.062500 0.000000 0.062500 0.875000 0.062500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GA][TC]G[AG][GT]GG[GC][GCA][AG][GC][GA][ACG]GG -------------------------------------------------------------------------------- Time 6.78 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 6 llr = 99 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :82:a3::::27::5: pos.-specific C ::8::7::::8:572: probability G a::a::aa:a::322a matrix T :2::::::a::3222: bits 2.1 * * ** * * 1.9 * ** **** * 1.7 * ** **** * 1.5 * *** ***** * Relative 1.3 ***** ***** * Entropy 1.1 ************ * (23.9 bits) 0.8 ************ * * 0.6 ************** * 0.4 ************** * 0.2 **************** 0.0 ---------------- Multilevel GACGACGGTGCACCAG consensus A TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 264768 431 1.75e-10 CACCATCGAC GACGACGGTGCACCAG CTGTTCAGCT 6952 449 7.70e-09 TGTGGTGCCA GACGACGGTGCATCGG TCCCTCTCAC 20469 227 1.35e-08 TCGTTCGTTC GTCGACGGTGCACCTG CGTTTTGTGT 42169 173 3.15e-08 GACGGCGAAT GACGAAGGTGCTGTAG GATGTGGTGT 263665 251 3.98e-08 CGGCTAAGAA GACGACGGTGATGCCG TGCCGCTGAA 40200 77 4.84e-08 TTTTGGGTGG GAAGAAGGTGCACGAG TTTAGCGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264768 1.8e-10 430_[+3]_54 6952 7.7e-09 448_[+3]_36 20469 1.3e-08 226_[+3]_258 42169 3.1e-08 172_[+3]_312 263665 4e-08 250_[+3]_234 40200 4.8e-08 76_[+3]_408 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=6 264768 ( 431) GACGACGGTGCACCAG 1 6952 ( 449) GACGACGGTGCATCGG 1 20469 ( 227) GTCGACGGTGCACCTG 1 42169 ( 173) GACGAAGGTGCTGTAG 1 263665 ( 251) GACGACGGTGATGCCG 1 40200 ( 77) GAAGAAGGTGCACGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 9700 bayes= 10.3166 E= 1.0e+000 -923 -923 202 -923 167 -923 -923 -65 -65 185 -923 -923 -923 -923 202 -923 193 -923 -923 -923 35 153 -923 -923 -923 -923 202 -923 -923 -923 202 -923 -923 -923 -923 194 -923 -923 202 -923 -65 185 -923 -923 134 -923 -923 35 -923 112 44 -65 -923 153 -56 -65 93 -47 -56 -65 -923 -923 202 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 1.0e+000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.500000 0.333333 0.166667 0.000000 0.666667 0.166667 0.166667 0.500000 0.166667 0.166667 0.166667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GACGA[CA]GGTGC[AT][CG]CAG -------------------------------------------------------------------------------- Time 9.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12088 3.86e-04 81_[+2(1.66e-06)]_193_\ [+1(2.44e-05)]_195 1294 1.47e-03 286_[+2(4.05e-06)]_140_\ [+1(2.44e-05)]_43 19069 1.57e-06 16_[+2(5.13e-06)]_173_\ [+1(2.60e-08)]_280 20469 2.75e-10 226_[+3(1.35e-08)]_209_\ [+2(4.39e-06)]_9_[+1(9.63e-08)]_9 24777 3.91e-04 45_[+1(1.68e-06)]_330_\ [+2(2.08e-05)]_94 261607 2.03e-01 500 262700 1.34e-02 455_[+1(1.83e-06)]_30 263565 8.13e-04 234_[+1(3.85e-07)]_25_\ [+1(6.24e-05)]_126_[+1(7.75e-08)]_70 263665 1.21e-09 250_[+3(3.98e-08)]_96_\ [+2(1.53e-07)]_40_[+1(4.61e-06)]_67 264768 3.85e-08 430_[+3(1.75e-10)]_31_\ [+1(4.61e-06)]_8 270037 1.56e-05 63_[+2(3.14e-06)]_344_\ [+1(9.57e-07)]_62 270256 7.23e-06 278_[+2(9.91e-08)]_180_\ [+1(3.94e-06)]_11 39536 2.14e-04 363_[+2(1.08e-05)]_73_\ [+1(1.27e-06)]_33 40200 4.29e-06 76_[+3(4.84e-08)]_6_[+2(6.96e-06)]_\ 386 42169 1.41e-12 43_[+3(1.35e-05)]_39_[+3(2.71e-05)]_\ 58_[+3(3.15e-08)]_24_[+2(3.23e-09)]_255_[+1(2.02e-07)]_2 5013 1.41e-04 271_[+1(2.01e-06)]_28_\ [+2(2.66e-05)]_170 5668 1.04e-03 352_[+1(3.94e-06)]_53_\ [+2(1.52e-05)]_64 6952 2.08e-09 64_[+2(5.13e-06)]_225_\ [+1(1.27e-06)]_128_[+3(7.70e-09)]_36 7271 2.72e-04 314_[+2(8.50e-08)]_170 8831 6.81e-08 53_[+1(1.30e-08)]_229_\ [+2(1.16e-07)]_187 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************