******************************************************************************** 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/280/280.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13254 1.0000 500 46808 1.0000 500 54718 1.0000 500 47392 1.0000 500 54738 1.0000 500 47699 1.0000 500 39940 1.0000 500 10458 1.0000 500 34028 1.0000 500 34205 1.0000 500 44756 1.0000 500 46105 1.0000 500 46204 1.0000 500 46205 1.0000 500 27726 1.0000 500 45279 1.0000 500 34157 1.0000 500 49905 1.0000 500 50583 1.0000 500 32860 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/280/280.seqs.fa -oc motifs/280 -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 0.274 C 0.238 G 0.217 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.238 G 0.217 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 20 llr = 203 E-value = 6.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22241115:71::748 pos.-specific C :4:26161a:1:a322 probability G 22712:15::9::13: matrix T 7324383::4:a1:1: bits 2.2 2.0 * * 1.8 * ** 1.5 * ** Relative 1.3 * *** Entropy 1.1 * *** * (14.7 bits) 0.9 * * ******* * 0.7 * * * ******* * 0.4 * * ********** * 0.2 * ************** 0.0 ---------------- Multilevel TCGACTCGCAGTCAAA consensus ATATT TA T CGC sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 46808 112 1.51e-08 ACTTACCCAA TCGTTTCGCAGTCAAA TATATTTTGC 54738 356 5.57e-08 AGAAACGGCC TGGCCTCACAGTCAAA ATAACTGGAT 13254 168 1.39e-07 AGAAACGGAG TGGTCTCACTGTCACA GTCAGTCAAA 49905 179 3.05e-07 CGGCAAAACA TAGTCTCGCAGTCATA GTCACTATCT 34205 293 7.12e-07 TTCCAGCTGT ATGTGTCACAGTCAAA AAGAATTCAT 34157 323 3.00e-06 ATTCTCTGAT TCGCTTCACAGTCCAC AGGCCTTTTT 46105 219 3.34e-06 CTATTTACAA ATAGCTCACAGTCAGA TATATCTGTC 50583 61 4.56e-06 ACTGTACAAC TCGTGTCGCAATCCGA TGAAAACCGT 27726 446 6.13e-06 CTCACGACTT TCGACTTACTGTTAGA AAACCTGTCT 47392 253 9.76e-06 GAATTCAATT TTTATACACAGTCAAA CTACACAATG 54718 412 9.76e-06 CGAAGTCCTA GATACTCGCAGTCAAC AACTAACTTA 44756 248 1.16e-05 TCGATCTTGT TCGAGTGACAGTCGGA CTTTTTATCA 46205 353 1.63e-05 TTCCTTCGTG GGAACTTGCTGTCAGC AACTTTCGTC 46204 347 1.63e-05 TTCCTTCGTG GGAACTTGCTGTCAGC AACTTTCGTC 39940 52 2.62e-05 GTTTTGCTCG ATGGCTCCCAGTCCCA CTCGCTGTCC 45279 438 2.82e-05 GTACATACCA TCGACCTGCACTCCAA GGCCGAACGA 34028 425 3.50e-05 CAGCGCCAGT ATTCCTTGCTGTCATA CGTTGCTATT 32860 285 4.94e-05 CAACCAAATG TCGTACAGCAGTCAAA CATGTTTACA 10458 361 5.28e-05 GGTCGACTAG TTGTTTGGCTATCCCA TTTCATGATT 47699 469 6.80e-05 GGTGTGCATG TAAATATACTGTCACA CGTATCGCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46808 1.5e-08 111_[+1]_373 54738 5.6e-08 355_[+1]_129 13254 1.4e-07 167_[+1]_317 49905 3e-07 178_[+1]_306 34205 7.1e-07 292_[+1]_192 34157 3e-06 322_[+1]_162 46105 3.3e-06 218_[+1]_266 50583 4.6e-06 60_[+1]_424 27726 6.1e-06 445_[+1]_39 47392 9.8e-06 252_[+1]_232 54718 9.8e-06 411_[+1]_73 44756 1.2e-05 247_[+1]_237 46205 1.6e-05 352_[+1]_132 46204 1.6e-05 346_[+1]_138 39940 2.6e-05 51_[+1]_433 45279 2.8e-05 437_[+1]_47 34028 3.5e-05 424_[+1]_60 32860 4.9e-05 284_[+1]_200 10458 5.3e-05 360_[+1]_124 47699 6.8e-05 468_[+1]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=20 46808 ( 112) TCGTTTCGCAGTCAAA 1 54738 ( 356) TGGCCTCACAGTCAAA 1 13254 ( 168) TGGTCTCACTGTCACA 1 49905 ( 179) TAGTCTCGCAGTCATA 1 34205 ( 293) ATGTGTCACAGTCAAA 1 34157 ( 323) TCGCTTCACAGTCCAC 1 46105 ( 219) ATAGCTCACAGTCAGA 1 50583 ( 61) TCGTGTCGCAATCCGA 1 27726 ( 446) TCGACTTACTGTTAGA 1 47392 ( 253) TTTATACACAGTCAAA 1 54718 ( 412) GATACTCGCAGTCAAC 1 44756 ( 248) TCGAGTGACAGTCGGA 1 46205 ( 353) GGAACTTGCTGTCAGC 1 46204 ( 347) GGAACTTGCTGTCAGC 1 39940 ( 52) ATGGCTCCCAGTCCCA 1 45279 ( 438) TCGACCTGCACTCCAA 1 34028 ( 425) ATTCCTTGCTGTCATA 1 32860 ( 285) TCGTACAGCAGTCAAA 1 10458 ( 361) TTGTTTGGCTATCCCA 1 47699 ( 469) TAAATATACTGTCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 9700 bayes= 9.86371 E= 6.5e-005 -45 -1097 -53 126 -87 56 -12 15 -45 -1097 158 -85 55 -66 -112 37 -245 121 -53 -12 -145 -125 -1097 156 -245 121 -112 15 72 -225 120 -1097 -1097 207 -1097 -1097 125 -1097 -1097 37 -145 -225 197 -1097 -1097 -1097 -1097 188 -1097 200 -1097 -244 135 7 -212 -1097 55 -25 46 -144 155 -25 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 6.5e-005 0.200000 0.000000 0.150000 0.650000 0.150000 0.350000 0.200000 0.300000 0.200000 0.000000 0.650000 0.150000 0.400000 0.150000 0.100000 0.350000 0.050000 0.550000 0.150000 0.250000 0.100000 0.100000 0.000000 0.800000 0.050000 0.550000 0.100000 0.300000 0.450000 0.050000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.650000 0.000000 0.000000 0.350000 0.100000 0.050000 0.850000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.950000 0.000000 0.050000 0.700000 0.250000 0.050000 0.000000 0.400000 0.200000 0.300000 0.100000 0.800000 0.200000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA][CTG][GA][AT][CT]T[CT][GA]C[AT]GTC[AC][AGC][AC] -------------------------------------------------------------------------------- Time 3.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 109 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :8:77::7a::27:23:5:: pos.-specific C 228::::2:2a52822:32: probability G 8:2:3:a::8:2:2::a2:a matrix T :::3:a:2:::22:75::8: bits 2.2 * * * 2.0 ** * * * 1.8 ** * * * * 1.5 * * ** *** * * * Relative 1.3 *** ** *** * * ** Entropy 1.1 *** *** *** * * ** (26.1 bits) 0.9 ******* *** * * ** 0.7 *********** *** * ** 0.4 *********** ******** 0.2 ******************** 0.0 -------------------- Multilevel GACAATGAAGCCACTTGATG consensus TG A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 46205 402 1.80e-12 CGACCGTAAC GACAATGAAGCCACTTGCTG CTAAGCGTCA 46204 396 1.80e-12 CGACCGTAAC GACAATGAAGCCACTTGCTG CTAACTGTAA 54738 235 1.02e-08 CACGTGTCGT CACTGTGCAGCCACCAGATG GTTCCCCTCA 32860 372 1.48e-08 CACTGACTGT GACAATGAAGCACGACGATG GCGTAATTGT 47392 461 1.85e-08 GAAACGGTCA GAGAGTGTAGCGTCTTGGTG AATAAGCATT 44756 40 2.39e-08 GTGGCGGCGT GCCTATGAACCTACTAGACG GATGGATCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46205 1.8e-12 401_[+2]_79 46204 1.8e-12 395_[+2]_85 54738 1e-08 234_[+2]_246 32860 1.5e-08 371_[+2]_109 47392 1.9e-08 460_[+2]_20 44756 2.4e-08 39_[+2]_441 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 46205 ( 402) GACAATGAAGCCACTTGCTG 1 46204 ( 396) GACAATGAAGCCACTTGCTG 1 54738 ( 235) CACTGTGCAGCCACCAGATG 1 32860 ( 372) GACAATGAAGCACGACGATG 1 47392 ( 461) GAGAGTGTAGCGTCTTGGTG 1 44756 ( 40) GCCTATGAACCTACTAGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 9620 bayes= 10.3047 E= 1.9e+000 -923 -51 194 -923 160 -51 -923 -923 -923 181 -38 -923 128 -923 -923 30 128 -923 62 -923 -923 -923 -923 188 -923 -923 220 -923 128 -51 -923 -70 187 -923 -923 -923 -923 -51 194 -923 -923 207 -923 -923 -71 107 -38 -70 128 -51 -923 -70 -923 181 -38 -923 -71 -51 -923 130 28 -51 -923 88 -923 -923 220 -923 87 49 -38 -923 -923 -51 -923 162 -923 -923 220 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 1.9e+000 0.000000 0.166667 0.833333 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.166667 0.000000 0.166667 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.500000 0.166667 0.166667 0.666667 0.166667 0.000000 0.166667 0.000000 0.833333 0.166667 0.000000 0.166667 0.166667 0.000000 0.666667 0.333333 0.166667 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.500000 0.333333 0.166667 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GAC[AT][AG]TGAAGCCACT[TA]G[AC]TG -------------------------------------------------------------------------------- Time 6.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 11 llr = 124 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :222:7:2:::a pos.-specific C 152::38::::: probability G 13:1a::1a1a: matrix T 8:67::27:9:: bits 2.2 * * * 2.0 * * * 1.8 * * ** 1.5 * **** Relative 1.3 * * **** Entropy 1.1 * *** **** (16.3 bits) 0.9 * ********* 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCTTGACTGTGA consensus G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39940 292 6.35e-08 GCACCCGGAT TCTTGACTGTGA GTTCCGAAAT 54738 323 1.77e-07 TCGTGAAATA TCTTGCCTGTGA ATGCGAACGC 32860 466 6.72e-07 ACGATCAATT TGCTGACTGTGA AGCCTTTCTT 10458 241 1.95e-06 TCTGCACGAT TCTTGCTTGTGA ACGATGCTAG 27726 59 2.46e-06 CCGGATGCAA TATTGACAGTGA AATTGACCGT 47699 111 4.44e-06 CTGGCGCTCC TGAAGACTGTGA AAAATGCCGG 47392 405 4.44e-06 TCTCTTTTTC TCTGGACAGTGA GATCCCATCG 46105 91 6.35e-06 TGACAGAAAT CGCTGACTGTGA CGGTAGCGAC 54718 166 7.22e-06 ATAGTTAGAT TCTTGACGGGGA CGGTATTTGC 49905 123 8.46e-06 GAGGTTCTTG GATTGCCTGTGA GCACATCCGA 13254 392 1.10e-05 CAGCTTTCGG TCAAGATTGTGA TCGGCCTGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39940 6.4e-08 291_[+3]_197 54738 1.8e-07 322_[+3]_166 32860 6.7e-07 465_[+3]_23 10458 1.9e-06 240_[+3]_248 27726 2.5e-06 58_[+3]_430 47699 4.4e-06 110_[+3]_378 47392 4.4e-06 404_[+3]_84 46105 6.4e-06 90_[+3]_398 54718 7.2e-06 165_[+3]_323 49905 8.5e-06 122_[+3]_366 13254 1.1e-05 391_[+3]_97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=11 39940 ( 292) TCTTGACTGTGA 1 54738 ( 323) TCTTGCCTGTGA 1 32860 ( 466) TGCTGACTGTGA 1 10458 ( 241) TCTTGCTTGTGA 1 27726 ( 59) TATTGACAGTGA 1 47699 ( 111) TGAAGACTGTGA 1 47392 ( 405) TCTGGACAGTGA 1 46105 ( 91) CGCTGACTGTGA 1 54718 ( 166) TCTTGACGGGGA 1 49905 ( 123) GATTGCCTGTGA 1 13254 ( 392) TCAAGATTGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9780 bayes= 10.15 E= 2.4e+000 -1010 -139 -126 159 -59 120 33 -1010 -59 -39 -1010 123 -59 -1010 -126 142 -1010 -1010 220 -1010 141 20 -1010 -1010 -1010 178 -1010 -58 -59 -1010 -126 142 -1010 -1010 220 -1010 -1010 -1010 -126 174 -1010 -1010 220 -1010 187 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 2.4e+000 0.000000 0.090909 0.090909 0.818182 0.181818 0.545455 0.272727 0.000000 0.181818 0.181818 0.000000 0.636364 0.181818 0.000000 0.090909 0.727273 0.000000 0.000000 1.000000 0.000000 0.727273 0.272727 0.000000 0.000000 0.000000 0.818182 0.000000 0.181818 0.181818 0.000000 0.090909 0.727273 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CG]TTG[AC]CTGTGA -------------------------------------------------------------------------------- Time 9.93 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13254 1.58e-05 167_[+1(1.39e-07)]_208_\ [+3(1.10e-05)]_97 46808 2.03e-04 111_[+1(1.51e-08)]_373 54718 6.86e-04 165_[+3(7.22e-06)]_234_\ [+1(9.76e-06)]_73 47392 2.65e-08 252_[+1(9.76e-06)]_136_\ [+3(4.44e-06)]_44_[+2(1.85e-08)]_20 54738 6.29e-12 234_[+2(1.02e-08)]_68_\ [+3(1.77e-07)]_21_[+1(5.57e-08)]_129 47699 7.13e-04 110_[+3(4.44e-06)]_346_\ [+1(6.80e-05)]_16 39940 3.31e-05 51_[+1(2.62e-05)]_224_\ [+3(6.35e-08)]_197 10458 4.73e-04 240_[+3(1.95e-06)]_108_\ [+1(5.28e-05)]_124 34028 1.77e-01 424_[+1(3.50e-05)]_60 34205 5.17e-03 292_[+1(7.12e-07)]_192 44756 5.43e-07 39_[+2(2.39e-08)]_137_\ [+3(8.06e-05)]_39_[+1(1.16e-05)]_237 46105 1.53e-04 90_[+3(6.35e-06)]_116_\ [+1(3.34e-06)]_266 46204 1.50e-09 346_[+1(1.63e-05)]_33_\ [+2(1.80e-12)]_85 46205 1.93e-09 352_[+1(1.63e-05)]_33_\ [+2(1.80e-12)]_79 27726 7.00e-05 58_[+3(2.46e-06)]_375_\ [+1(6.13e-06)]_39 45279 3.97e-03 118_[+2(6.51e-05)]_299_\ [+1(2.82e-05)]_47 34157 1.88e-02 322_[+1(3.00e-06)]_162 49905 2.30e-05 122_[+3(8.46e-06)]_44_\ [+1(3.05e-07)]_306 50583 8.62e-03 60_[+1(4.56e-06)]_424 32860 1.68e-08 284_[+1(4.94e-05)]_71_\ [+2(1.48e-08)]_74_[+3(6.72e-07)]_23 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************