******************************************************************************** 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/367/367.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31772 1.0000 500 32292 1.0000 500 46943 1.0000 500 47114 1.0000 500 37509 1.0000 500 14380 1.0000 500 38720 1.0000 500 32914 1.0000 500 49632 1.0000 500 44028 1.0000 500 44029 1.0000 500 44454 1.0000 500 34685 1.0000 500 45795 1.0000 500 12878 1.0000 500 43543 1.0000 500 42528 1.0000 500 42530 1.0000 500 47748 1.0000 500 41504 1.0000 500 49283 1.0000 500 43310 1.0000 500 44413 1.0000 500 43715 1.0000 500 48036 1.0000 500 40594 1.0000 500 49835 1.0000 500 37837 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/367/367.seqs.fa -oc motifs/367 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.285 C 0.227 G 0.205 T 0.282 Background letter frequencies (from dataset with add-one prior applied): A 0.285 C 0.227 G 0.205 T 0.282 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 18 llr = 197 E-value = 8.2e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::9:5:::a52 pos.-specific C 413:91::3:11 probability G ::7111a:7:3: matrix T 69:::3:a::18 bits 2.3 * 2.1 * 1.8 * ** * 1.6 ** ** * Relative 1.4 **** **** Entropy 1.1 **** **** (15.8 bits) 0.9 ***** **** * 0.7 ***** **** * 0.5 ***** ****** 0.2 ************ 0.0 ------------ Multilevel TTGACAGTGAAT consensus C C T C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42528 431 1.47e-07 GAAGGGAAAC TTGACAGTGAAT TGAAACACAA 42530 431 3.99e-07 GAAGGGAAAC TTGACTGTGAAT TGAAACACAA 47748 163 5.04e-07 CATAATAAAG CTGACTGTGAGT ACCTATCTTG 45795 113 1.48e-06 GCTTTTCTCG TTGACGGTGAGT CGGGCGATGT 32292 30 1.48e-06 TTCACTCTTA CTGACAGTGACT GTGTTGTAAT 32914 266 1.57e-06 GTCTTCTTGG CTGACCGTGAGT TTCCAATGTT 40594 1 2.68e-06 . TCGACAGTGAAT CGGCTAAATT 48036 2 2.68e-06 C TCGACAGTGAAT CGGCTAAATT 41504 480 3.01e-06 TTTCACGCAA CTCACAGTCAGT CCAACAATC 31772 155 3.01e-06 GCTAGCTAGT CTCACAGTCAGT TAGAACGTAG 37837 101 7.43e-06 ACGATCCGAA TTGACTGTGATT TAGGAGCGAG 43715 41 7.43e-06 CTGTTGCAAA CTGACAGTGACA AACCACGAAA 43310 109 9.15e-06 TGCAGTCTTC TTCACCGTCAAT TCTGAAAATT 34685 384 9.15e-06 TCGCAAACCA CTGACTGTGAAC GGAGCGCAAG 37509 85 9.15e-06 TTTGCGACAG CTCACGGTCAGT ATTTGTCCAC 47114 448 9.83e-06 TCACTTTATA TTGGCTGTGAAT CTTCCCTGGA 44413 470 1.13e-05 ACAGGAATCT TTCACAGTCAAA GCTGTTTTAT 46943 329 3.27e-05 TGAAATCTTG TTGAGAGTCAAA TTGACGCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42528 1.5e-07 430_[+1]_58 42530 4e-07 430_[+1]_58 47748 5e-07 162_[+1]_326 45795 1.5e-06 112_[+1]_376 32292 1.5e-06 29_[+1]_459 32914 1.6e-06 265_[+1]_223 40594 2.7e-06 [+1]_488 48036 2.7e-06 1_[+1]_487 41504 3e-06 479_[+1]_9 31772 3e-06 154_[+1]_334 37837 7.4e-06 100_[+1]_388 43715 7.4e-06 40_[+1]_448 43310 9.1e-06 108_[+1]_380 34685 9.1e-06 383_[+1]_105 37509 9.1e-06 84_[+1]_404 47114 9.8e-06 447_[+1]_41 44413 1.1e-05 469_[+1]_19 46943 3.3e-05 328_[+1]_160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=18 42528 ( 431) TTGACAGTGAAT 1 42530 ( 431) TTGACTGTGAAT 1 47748 ( 163) CTGACTGTGAGT 1 45795 ( 113) TTGACGGTGAGT 1 32292 ( 30) CTGACAGTGACT 1 32914 ( 266) CTGACCGTGAGT 1 40594 ( 1) TCGACAGTGAAT 1 48036 ( 2) TCGACAGTGAAT 1 41504 ( 480) CTCACAGTCAGT 1 31772 ( 155) CTCACAGTCAGT 1 37837 ( 101) TTGACTGTGATT 1 43715 ( 41) CTGACAGTGACA 1 43310 ( 109) TTCACCGTCAAT 1 34685 ( 384) CTGACTGTGAAC 1 37509 ( 85) CTCACGGTCAGT 1 47114 ( 448) TTGGCTGTGAAT 1 44413 ( 470) TTCACAGTCAAA 1 46943 ( 329) TTGAGAGTCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13692 bayes= 10.4181 E= 8.2e-009 -1081 97 -1081 98 -1081 -103 -1081 166 -1081 29 181 -1081 173 -1081 -188 -1081 -1081 206 -188 -1081 81 -103 -89 -2 -1081 -1081 228 -1081 -1081 -1081 -1081 183 -1081 55 170 -1081 181 -1081 -1081 -1081 81 -103 70 -234 -78 -203 -1081 146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 8.2e-009 0.000000 0.444444 0.000000 0.555556 0.000000 0.111111 0.000000 0.888889 0.000000 0.277778 0.722222 0.000000 0.944444 0.000000 0.055556 0.000000 0.000000 0.944444 0.055556 0.000000 0.500000 0.111111 0.111111 0.277778 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.111111 0.333333 0.055556 0.166667 0.055556 0.000000 0.777778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[GC]AC[AT]GT[GC]A[AG]T -------------------------------------------------------------------------------- Time 6.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 9 llr = 159 E-value = 1.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2:1:::a8281a72447:: pos.-specific C :::3::a::21:3:3:1::6: probability G 112::::a::226::::611: matrix T 99679a::::4::::84:23a bits 2.3 * 2.1 ** 1.8 **** * * 1.6 **** * * Relative 1.4 ** ***** * * Entropy 1.1 ** ****** * * * * * (25.4 bits) 0.9 ** ******* ***** * * 0.7 ** ******* ***** **** 0.5 ********** ********** 0.2 ********************* 0.0 --------------------- Multilevel TTTTTTCGAATAGAATAGACT consensus AC CAGC CATATT sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 40594 73 2.51e-11 ACCTATTTCT TTTTTTCGAATAGACTTAACT TTGAGCGTAA 48036 74 2.51e-11 ACCTATTTCT TTTTTTCGAATAGACTTAACT TTGAGTGTAA 42530 278 2.87e-10 TGCTTCTCAT TTTTTTCGACGACAATAGACT CCTTTTGAAA 42528 266 2.87e-10 TGCCTCTCAT TTTTTTCGACGACAATAGACT CCTTTTGAAA 47748 460 5.98e-09 ATCTTCCCCT TTGCTTCGAACAGAAAAGATT AGCCTTTTGA 49283 225 9.02e-09 ACTTACGTTA TTGCTTCGAAAGGAATTAGCT ATGACCGGGA 41504 331 2.34e-08 TGTGAGCCGG TGATTTCGAATAGAAAAGTTT CTCTATTTTG 46943 425 3.97e-08 CGCGGAGTGG TTTCTTCGAAAGAAATCGAGT GCATGGCTTT 43715 173 7.94e-08 CGTGCCAGTC GTATATCGAATACACTTATTT TCGCTTCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40594 2.5e-11 72_[+2]_407 48036 2.5e-11 73_[+2]_406 42530 2.9e-10 277_[+2]_202 42528 2.9e-10 265_[+2]_214 47748 6e-09 459_[+2]_20 49283 9e-09 224_[+2]_255 41504 2.3e-08 330_[+2]_149 46943 4e-08 424_[+2]_55 43715 7.9e-08 172_[+2]_307 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=9 40594 ( 73) TTTTTTCGAATAGACTTAACT 1 48036 ( 74) TTTTTTCGAATAGACTTAACT 1 42530 ( 278) TTTTTTCGACGACAATAGACT 1 42528 ( 266) TTTTTTCGACGACAATAGACT 1 47748 ( 460) TTGCTTCGAACAGAAAAGATT 1 49283 ( 225) TTGCTTCGAAAGGAATTAGCT 1 41504 ( 331) TGATTTCGAATAGAAAAGTTT 1 46943 ( 425) TTTCTTCGAAAGAAATCGAGT 1 43715 ( 173) GTATATCGAATACACTTATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 10.6777 E= 1.5e-005 -982 -982 -89 165 -982 -982 -89 165 -36 -982 11 98 -982 55 -982 124 -136 -982 -982 165 -982 -982 -982 182 -982 214 -982 -982 -982 -982 228 -982 181 -982 -982 -982 145 -3 -982 -982 -36 -103 11 66 145 -982 11 -982 -136 55 143 -982 181 -982 -982 -982 122 55 -982 -982 -36 -982 -982 146 64 -103 -982 66 64 -982 143 -982 122 -982 -89 -34 -982 129 -89 24 -982 -982 -982 182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.5e-005 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.111111 0.888889 0.222222 0.000000 0.222222 0.555556 0.000000 0.333333 0.000000 0.666667 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 0.222222 0.111111 0.222222 0.444444 0.777778 0.000000 0.222222 0.000000 0.111111 0.333333 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.222222 0.000000 0.000000 0.777778 0.444444 0.111111 0.000000 0.444444 0.444444 0.000000 0.555556 0.000000 0.666667 0.000000 0.111111 0.222222 0.000000 0.555556 0.111111 0.333333 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TT[TAG][TC]TTCGA[AC][TAG][AG][GC]A[AC][TA][AT][GA][AT][CT]T -------------------------------------------------------------------------------- Time 12.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 152 E-value = 9.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2::1:::::2:41:12431:1 pos.-specific C :3::8:4:a2::9:92:274: probability G 8414:14a:18::a:264:4: matrix T :294291::426:::3::219 bits 2.3 * * 2.1 ** * 1.8 ** * 1.6 ** *** Relative 1.4 * * ** ** * *** * Entropy 1.1 * * ** ** * *** * * (24.3 bits) 0.9 * * ** ** ***** * * * 0.7 ********* ***** * *** 0.5 ********* ***** ***** 0.2 ********* ***** ***** 0.0 --------------------- Multilevel GGTGCTCGCTGTCGCTGGCCT consensus AC TT G ATA AAATG sequence T C C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 42530 78 6.94e-12 TTTCAGCACA GGTGCTGGCAGTCGCTGGCCT CTACTAGTAA 42528 66 6.94e-12 TTTCAGTACA GGTGCTGGCAGTCGCTGGCCT CTACTAGTAA 40594 381 2.03e-10 ATTCCAAATA GCTTCTCGCTGACGCCAACCT TCAAACATAT 48036 381 2.03e-10 ATTCCAAATA GCTTCTCGCTGACGCCAACCT TCAAACATAT 43543 466 3.63e-08 AAAAACGTGC AGTGCTGGCGTACGCGGCTGT ATCATAAGTA 44028 228 6.91e-08 CCATTTTCGT GCTACGGGCCGAAGCTGCCGT ATTCCACAAA 49835 98 7.34e-08 AGACAACGCT GTTTTTTGCCGTCGAAGGCGT GACACCCTTT 45795 212 1.15e-07 TTGCGCTTTT GGTGTTCGCTTTCGCAAGAGA CGGAGTAGGT 14380 236 1.72e-07 AATCTAACGG ATGTCTCGCTGTCGCGAATTT TGGACTATCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42530 6.9e-12 77_[+3]_402 42528 6.9e-12 65_[+3]_414 40594 2e-10 380_[+3]_99 48036 2e-10 380_[+3]_99 43543 3.6e-08 465_[+3]_14 44028 6.9e-08 227_[+3]_252 49835 7.3e-08 97_[+3]_382 45795 1.1e-07 211_[+3]_268 14380 1.7e-07 235_[+3]_244 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 42530 ( 78) GGTGCTGGCAGTCGCTGGCCT 1 42528 ( 66) GGTGCTGGCAGTCGCTGGCCT 1 40594 ( 381) GCTTCTCGCTGACGCCAACCT 1 48036 ( 381) GCTTCTCGCTGACGCCAACCT 1 43543 ( 466) AGTGCTGGCGTACGCGGCTGT 1 44028 ( 228) GCTACGGGCCGAAGCTGCCGT 1 49835 ( 98) GTTTTTTGCCGTCGAAGGCGT 1 45795 ( 212) GGTGTTCGCTTTCGCAAGAGA 1 14380 ( 236) ATGTCTCGCTGTCGCGAATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 11.9483 E= 9.3e-004 -36 -982 192 -982 -982 55 111 -34 -982 -982 -89 165 -136 -982 111 66 -982 177 -982 -34 -982 -982 -89 165 -982 97 111 -134 -982 -982 228 -982 -982 214 -982 -982 -36 -3 -89 66 -982 -982 192 -34 64 -982 -982 98 -136 197 -982 -982 -982 -982 228 -982 -136 197 -982 -982 -36 -3 11 24 64 -982 143 -982 22 -3 111 -982 -136 155 -982 -34 -982 97 111 -134 -136 -982 -982 165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 9.3e-004 0.222222 0.000000 0.777778 0.000000 0.000000 0.333333 0.444444 0.222222 0.000000 0.000000 0.111111 0.888889 0.111111 0.000000 0.444444 0.444444 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.111111 0.888889 0.000000 0.444444 0.444444 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.222222 0.222222 0.111111 0.444444 0.000000 0.000000 0.777778 0.222222 0.444444 0.000000 0.000000 0.555556 0.111111 0.888889 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.222222 0.222222 0.222222 0.333333 0.444444 0.000000 0.555556 0.000000 0.333333 0.222222 0.444444 0.000000 0.111111 0.666667 0.000000 0.222222 0.000000 0.444444 0.444444 0.111111 0.111111 0.000000 0.000000 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][GCT]T[GT][CT]T[CG]GC[TAC][GT][TA]CGC[TACG][GA][GAC][CT][CG]T -------------------------------------------------------------------------------- Time 18.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31772 7.02e-04 154_[+1(3.01e-06)]_14_\ [+1(1.23e-05)]_125_[+2(6.51e-05)]_162 32292 4.28e-03 29_[+1(1.48e-06)]_459 46943 6.13e-06 328_[+1(3.27e-05)]_84_\ [+2(3.97e-08)]_55 47114 2.01e-02 67_[+1(1.51e-05)]_368_\ [+1(9.83e-06)]_41 37509 3.71e-03 84_[+1(9.15e-06)]_404 14380 3.42e-03 235_[+3(1.72e-07)]_244 38720 7.38e-01 500 32914 1.43e-03 265_[+1(1.57e-06)]_160_\ [+2(7.29e-05)]_42 49632 9.70e-01 500 44028 4.59e-04 227_[+3(6.91e-08)]_252 44029 4.96e-01 500 44454 4.20e-01 500 34685 2.23e-02 383_[+1(9.15e-06)]_31_\ [+1(5.22e-05)]_62 45795 5.53e-06 112_[+1(1.48e-06)]_87_\ [+3(1.15e-07)]_218_[+1(1.81e-05)]_38 12878 8.60e-01 500 43543 7.81e-05 465_[+3(3.63e-08)]_14 42528 3.47e-17 65_[+3(6.94e-12)]_179_\ [+2(2.87e-10)]_144_[+1(1.47e-07)]_58 42530 9.01e-17 77_[+3(6.94e-12)]_179_\ [+2(2.87e-10)]_132_[+1(3.99e-07)]_58 47748 1.33e-07 162_[+1(5.04e-07)]_285_\ [+2(5.98e-09)]_20 41504 1.87e-06 330_[+2(2.34e-08)]_128_\ [+1(3.01e-06)]_9 49283 1.02e-04 224_[+2(9.02e-09)]_255 43310 9.60e-03 108_[+1(9.15e-06)]_380 44413 1.60e-02 469_[+1(1.13e-05)]_19 43715 8.71e-06 40_[+1(7.43e-06)]_120_\ [+2(7.94e-08)]_307 48036 1.35e-15 1_[+1(2.68e-06)]_60_[+2(2.51e-11)]_\ 286_[+3(2.03e-10)]_99 40594 1.35e-15 [+1(2.68e-06)]_60_[+2(2.51e-11)]_\ 287_[+3(2.03e-10)]_99 49835 1.11e-04 97_[+3(7.34e-08)]_166_\ [+3(4.09e-06)]_195 37837 2.97e-02 100_[+1(7.43e-06)]_388 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************