******************************************************************************** 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/109/109.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31492 1.0000 500 31781 1.0000 500 52223 1.0000 500 37671 1.0000 500 1129 1.0000 500 39474 1.0000 500 43529 1.0000 500 32938 1.0000 500 48960 1.0000 500 49083 1.0000 500 49232 1.0000 500 49572 1.0000 500 49839 1.0000 500 17135 1.0000 500 54296 1.0000 500 44765 1.0000 500 50872 1.0000 500 11943 1.0000 500 45511 1.0000 500 41194 1.0000 500 43371 1.0000 500 33932 1.0000 500 44481 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/109/109.seqs.fa -oc motifs/109 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.245 C 0.249 G 0.243 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.245 C 0.249 G 0.243 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 19 llr = 179 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1362915a8117 pos.-specific C 6:1::8::239: probability G :228114::6:3 matrix T 352:::1::::: bits 2.0 * 1.8 * 1.6 * * * 1.4 * ** * Relative 1.2 *** ** ** Entropy 1.0 *** ** ** (13.6 bits) 0.8 * *** ** ** 0.6 * ********* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTAGACAAAGCA consensus TA A G C G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43529 172 5.20e-08 TTTGGTGTAG CTAGACAAAGCA TCTCGTTTGG 45511 169 6.14e-07 TATTTGTTTG CTAGACGAAGCG CGCGCCGAAC 31492 25 1.91e-06 TCTAGATCTA CTCGACAAAGCA AAAGAGGACT 49083 259 4.10e-06 TGTTTGCGCC CAAGACGAACCG AGCCGTACGG 52223 362 4.10e-06 TCAGTGTCAG TGAGACAAACCA AAAAAAGCGT 11943 323 4.67e-06 TTTCAGGCTC TTGGACGAAGCA CCGATTCCGT 43371 289 7.10e-06 AACACAACCC CAAAACGAACCA TCCGTGGCGG 39474 425 8.82e-06 AACGATTGTT CTAGGCAAAGCA TACTTCTATT 54296 44 1.11e-05 AGACTATCTT CTAGACTAACCG TAAGCTCCGT 49839 407 1.58e-05 CTGCGGGTGC CATAACGAAGCA CTCGGCAGAC 50872 470 2.33e-05 AATTGTTGAC ATAAACAAAGCA TCATATAACA 41194 304 2.52e-05 AGCAACGAAA CTTGACGACCCA CAATCTCTGT 37671 60 4.06e-05 GAAGTAGGAG CGAGACGACACA AAAGCCTACT 48960 176 4.71e-05 ACGCTGACGC CGCGAGAAAGCA TCTCCCGCGT 32938 274 6.10e-05 CGGTGCCCAC CATGAAGAAGCA ACATTTGTAG 44481 440 8.12e-05 TTCCGTGAGA TAGGACAAAACG CTTACTCTAA 33932 42 8.12e-05 GAACCGTGGA TTAGAGTAAGCG TTTTGTCCTA 31781 217 8.65e-05 GATGGACCTT TGAAACAACGCG CCATCCTGGT 1129 150 1.04e-04 GAGGTTTTGG TTGGACAAACAA ATATACTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43529 5.2e-08 171_[+1]_317 45511 6.1e-07 168_[+1]_320 31492 1.9e-06 24_[+1]_464 49083 4.1e-06 258_[+1]_230 52223 4.1e-06 361_[+1]_127 11943 4.7e-06 322_[+1]_166 43371 7.1e-06 288_[+1]_200 39474 8.8e-06 424_[+1]_64 54296 1.1e-05 43_[+1]_445 49839 1.6e-05 406_[+1]_82 50872 2.3e-05 469_[+1]_19 41194 2.5e-05 303_[+1]_185 37671 4.1e-05 59_[+1]_429 48960 4.7e-05 175_[+1]_313 32938 6.1e-05 273_[+1]_215 44481 8.1e-05 439_[+1]_49 33932 8.1e-05 41_[+1]_447 31781 8.6e-05 216_[+1]_272 1129 0.0001 149_[+1]_339 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=19 43529 ( 172) CTAGACAAAGCA 1 45511 ( 169) CTAGACGAAGCG 1 31492 ( 25) CTCGACAAAGCA 1 49083 ( 259) CAAGACGAACCG 1 52223 ( 362) TGAGACAAACCA 1 11943 ( 323) TTGGACGAAGCA 1 43371 ( 289) CAAAACGAACCA 1 39474 ( 425) CTAGGCAAAGCA 1 54296 ( 44) CTAGACTAACCG 1 49839 ( 407) CATAACGAAGCA 1 50872 ( 470) ATAAACAAAGCA 1 41194 ( 304) CTTGACGACCCA 1 37671 ( 60) CGAGACGACACA 1 48960 ( 176) CGCGAGAAAGCA 1 32938 ( 274) CATGAAGAAGCA 1 44481 ( 440) TAGGACAAAACG 1 33932 ( 42) TTAGAGTAAGCG 1 31781 ( 217) TGAAACAACGCG 1 1129 ( 150) TTGGACAAACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 10.649 E= 4.0e+000 -221 134 -1089 26 11 -1089 -21 100 124 -124 -62 -74 -22 -1089 170 -1089 195 -1089 -220 -1089 -221 176 -120 -1089 95 -1089 79 -133 203 -1089 -1089 -1089 178 -65 -1089 -1089 -122 34 125 -1089 -221 193 -1089 -1089 148 -1089 38 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 4.0e+000 0.052632 0.631579 0.000000 0.315789 0.263158 0.000000 0.210526 0.526316 0.578947 0.105263 0.157895 0.157895 0.210526 0.000000 0.789474 0.000000 0.947368 0.000000 0.052632 0.000000 0.052632 0.842105 0.105263 0.000000 0.473684 0.000000 0.421053 0.105263 1.000000 0.000000 0.000000 0.000000 0.842105 0.157895 0.000000 0.000000 0.105263 0.315789 0.578947 0.000000 0.052632 0.947368 0.000000 0.000000 0.684211 0.000000 0.315789 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][TAG]A[GA]AC[AG]AA[GC]C[AG] -------------------------------------------------------------------------------- Time 5.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 8 llr = 101 E-value = 6.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1:5:::::493 pos.-specific C ::::8:::::1: probability G ::a:3:a:a1:1 matrix T a9:5:a:a:5:6 bits 2.0 * * * 1.8 * * **** 1.6 * * **** 1.4 *** **** * Relative 1.2 *** ***** * Entropy 1.0 ********* * (18.2 bits) 0.8 ********* * 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGACTGTGTAT consensus TG A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44765 463 1.51e-07 TTATGTGAGT TTGTCTGTGTAT TATGAATTCA 52223 194 2.18e-07 GCTTACATTG TTGACTGTGAAT GTGAGTTGAG 31492 400 4.93e-07 GGTACGGCGA TTGACTGTGAAA AAGATCACTT 49232 184 7.08e-07 AAACTAGTTT TTGTGTGTGTAT AGCTGTGTTT 37671 259 9.11e-07 ATGTTCTTAT TTGACTGTGGAT TCGAACGACG 44481 217 1.80e-06 AATTCTTTTC TAGACTGTGAAT GTAAGAGTTT 39474 188 2.54e-06 TGTGTTAGAA TTGTGTGTGTAG CACACGAGAC 50872 292 3.00e-06 GTGTGTCCTT TTGTCTGTGTCA CAATCGGGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44765 1.5e-07 462_[+2]_26 52223 2.2e-07 193_[+2]_295 31492 4.9e-07 399_[+2]_89 49232 7.1e-07 183_[+2]_305 37671 9.1e-07 258_[+2]_230 44481 1.8e-06 216_[+2]_272 39474 2.5e-06 187_[+2]_301 50872 3e-06 291_[+2]_197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=8 44765 ( 463) TTGTCTGTGTAT 1 52223 ( 194) TTGACTGTGAAT 1 31492 ( 400) TTGACTGTGAAA 1 49232 ( 184) TTGTGTGTGTAT 1 37671 ( 259) TTGACTGTGGAT 1 44481 ( 217) TAGACTGTGAAT 1 39474 ( 188) TTGTGTGTGTAG 1 50872 ( 292) TTGTCTGTGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 11.1936 E= 6.1e+001 -965 -965 -965 192 -97 -965 -965 173 -965 -965 204 -965 103 -965 -965 92 -965 159 4 -965 -965 -965 -965 192 -965 -965 204 -965 -965 -965 -965 192 -965 -965 204 -965 62 -965 -96 92 184 -99 -965 -965 3 -965 -96 124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 6.1e+001 0.000000 0.000000 0.000000 1.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.000000 0.125000 0.500000 0.875000 0.125000 0.000000 0.000000 0.250000 0.000000 0.125000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TTG[AT][CG]TGTG[TA]A[TA] -------------------------------------------------------------------------------- Time 11.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 171 E-value = 7.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:3:2:::::2542:213:41 pos.-specific C 655a1:21:14:122::1a52 probability G :5::12::592:4341:4:16 matrix T 3:2:78895:25234792:11 bits 2.0 * * 1.8 * * 1.6 * * * * * 1.4 * * * * * Relative 1.2 * *** * * * Entropy 1.0 * * ***** * * * (19.0 bits) 0.8 ** * ***** * ** * 0.6 ** ******* * ** * * 0.4 ********** * *** *** 0.2 ********** ** ******* 0.0 --------------------- Multilevel CCCCTTTTGGCAAGGTTGCCG consensus TGA T ATGTTA A AC sequence T G CC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 54296 368 8.03e-10 GGGACGATGG TGCCTTTTGGGAAGGTTGCCG CACTCGAAGT 41194 392 5.91e-09 TGTTCGTATT CCACTGTTTGCAATGTTGCCG AGCTTACAGT 49083 28 6.88e-09 CACGTTCGGT CCCCTTTTGGGAGTTTTTCAC CTTTTCCCAT 50872 190 2.10e-08 CCCATCCCCT CGCCTTTTTGATTCGTTTCCG AAGCGTTGGG 31781 357 7.10e-08 GACTAATTTC CCCCTTTTTGCTTGCTTGCTG TTAGTTCGAT 32938 370 1.49e-07 ACTTATCCGT TCACTTCTGGCAAATTTGCCC GATGAAACGA 11943 477 4.51e-07 ACACCGTTCC AGTCATTTGGATGCTTTGCCG GGT 43529 184 1.54e-06 AGACAAAGCA TCTCGTTTGGCTCGGATACAG TCCCTTTTCT 52223 102 1.54e-06 TACATCCCAA CCCCCTTTTGTAATTATACCA TAGAGCCAGC 43371 42 1.77e-06 AGAACATGTG TGTCTGTTGGATGTCGTACAG ACAGGGACAG 17135 266 2.61e-06 CGGACGCCCA CGCCTTTCTCCAACGTTACGG AGCCGAGTAC 49839 246 3.52e-06 TCGTGAGATG CGACATTTTGGAGACTTCCAT AATGGAAACG 39474 356 5.21e-06 AGCTCTTTTC CCACTTCTGGTTGGTAATCAC CGATTGGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54296 8e-10 367_[+3]_112 41194 5.9e-09 391_[+3]_88 49083 6.9e-09 27_[+3]_452 50872 2.1e-08 189_[+3]_290 31781 7.1e-08 356_[+3]_123 32938 1.5e-07 369_[+3]_110 11943 4.5e-07 476_[+3]_3 43529 1.5e-06 183_[+3]_296 52223 1.5e-06 101_[+3]_378 43371 1.8e-06 41_[+3]_438 17135 2.6e-06 265_[+3]_214 49839 3.5e-06 245_[+3]_234 39474 5.2e-06 355_[+3]_124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 54296 ( 368) TGCCTTTTGGGAAGGTTGCCG 1 41194 ( 392) CCACTGTTTGCAATGTTGCCG 1 49083 ( 28) CCCCTTTTGGGAGTTTTTCAC 1 50872 ( 190) CGCCTTTTTGATTCGTTTCCG 1 31781 ( 357) CCCCTTTTTGCTTGCTTGCTG 1 32938 ( 370) TCACTTCTGGCAAATTTGCCC 1 11943 ( 477) AGTCATTTGGATGCTTTGCCG 1 43529 ( 184) TCTCGTTTGGCTCGGATACAG 1 52223 ( 102) CCCCCTTTTGTAATTATACCA 1 43371 ( 42) TGTCTGTTGGATGTCGTACAG 1 17135 ( 266) CGCCTTTCTCCAACGTTACGG 1 49839 ( 246) CGACATTTTGGAGACTTCCAT 1 39474 ( 356) CCACTTCTGGTTGGTAATCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 9.48358 E= 7.9e+001 -167 131 -1035 22 -1035 111 93 -1035 33 89 -1035 -19 -1035 201 -1035 -1035 -67 -169 -166 139 -1035 -1035 -66 168 -1035 -69 -1035 168 -1035 -169 -1035 181 -1035 -1035 115 81 -1035 -169 193 -1035 -8 63 -7 -78 114 -1035 -1035 81 65 -169 66 -78 -67 -11 34 22 -1035 -11 66 54 -8 -1035 -166 139 -167 -1035 -1035 181 33 -169 66 -19 -1035 201 -1035 -1035 65 89 -166 -178 -167 -11 134 -178 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 7.9e+001 0.076923 0.615385 0.000000 0.307692 0.000000 0.538462 0.461538 0.000000 0.307692 0.461538 0.000000 0.230769 0.000000 1.000000 0.000000 0.000000 0.153846 0.076923 0.076923 0.692308 0.000000 0.000000 0.153846 0.846154 0.000000 0.153846 0.000000 0.846154 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.538462 0.461538 0.000000 0.076923 0.923077 0.000000 0.230769 0.384615 0.230769 0.153846 0.538462 0.000000 0.000000 0.461538 0.384615 0.076923 0.384615 0.153846 0.153846 0.230769 0.307692 0.307692 0.000000 0.230769 0.384615 0.384615 0.230769 0.000000 0.076923 0.692308 0.076923 0.000000 0.000000 0.923077 0.307692 0.076923 0.384615 0.230769 0.000000 1.000000 0.000000 0.000000 0.384615 0.461538 0.076923 0.076923 0.076923 0.230769 0.615385 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CG][CAT]CTTTT[GT]G[CAG][AT][AG][GTC][GTC][TA]T[GAT]C[CA][GC] -------------------------------------------------------------------------------- Time 16.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31492 2.76e-05 24_[+1(1.91e-06)]_363_\ [+2(4.93e-07)]_89 31781 1.01e-04 216_[+1(8.65e-05)]_128_\ [+3(7.10e-08)]_123 52223 4.40e-08 46_[+2(2.36e-05)]_43_[+3(1.54e-06)]_\ 71_[+2(2.18e-07)]_156_[+1(4.10e-06)]_127 37671 5.69e-04 41_[+2(3.97e-05)]_6_[+1(4.06e-05)]_\ 187_[+2(9.11e-07)]_230 1129 2.06e-01 500 39474 2.45e-06 187_[+2(2.54e-06)]_156_\ [+3(5.21e-06)]_48_[+1(8.82e-06)]_64 43529 7.42e-07 171_[+1(5.20e-08)]_[+3(1.54e-06)]_\ 296 32938 3.89e-05 273_[+1(6.10e-05)]_84_\ [+3(1.49e-07)]_110 48960 8.40e-02 175_[+1(4.71e-05)]_313 49083 4.97e-07 27_[+3(6.88e-09)]_210_\ [+1(4.10e-06)]_230 49232 9.99e-03 183_[+2(7.08e-07)]_305 49572 9.36e-01 500 49839 4.83e-04 245_[+3(3.52e-06)]_140_\ [+1(1.58e-05)]_82 17135 2.43e-02 265_[+3(2.61e-06)]_214 54296 4.02e-07 43_[+1(1.11e-05)]_312_\ [+3(8.03e-10)]_112 44765 7.31e-04 462_[+2(1.51e-07)]_26 50872 4.64e-08 189_[+3(2.10e-08)]_81_\ [+2(3.00e-06)]_166_[+1(2.33e-05)]_19 11943 5.69e-05 322_[+1(4.67e-06)]_142_\ [+3(4.51e-07)]_3 45511 1.64e-03 168_[+1(6.14e-07)]_320 41194 1.29e-06 303_[+1(2.52e-05)]_76_\ [+3(5.91e-09)]_88 43371 1.94e-04 41_[+3(1.77e-06)]_226_\ [+1(7.10e-06)]_200 33932 1.68e-01 41_[+1(8.12e-05)]_447 44481 2.06e-03 216_[+2(1.80e-06)]_211_\ [+1(8.12e-05)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************