******************************************************************************** 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/87/87.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 54588 1.0000 500 37808 1.0000 500 48315 1.0000 500 49506 1.0000 500 44318 1.0000 500 46220 1.0000 500 48197 1.0000 500 42722 1.0000 500 44929 1.0000 500 50170 1.0000 500 37243 1.0000 500 37689 1.0000 500 40151 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/87/87.seqs.fa -oc motifs/87 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.284 C 0.220 G 0.217 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.284 C 0.220 G 0.217 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 6 llr = 89 E-value = 7.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::2:3::3:2:22 pos.-specific C :27::7:7225:288: probability G a83a:2a:58:522:: matrix T ::::a:::3:255::8 bits 2.2 * * * 2.0 * * * 1.8 * ** * 1.5 ** ** * * ** Relative 1.3 ***** * * ** Entropy 1.1 ***** ** * * *** (21.4 bits) 0.9 ******** * * *** 0.7 ********** * *** 0.4 ************ *** 0.2 **************** 0.0 ---------------- Multilevel GGCGTCGCGGCGTCCT consensus G AT AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 54588 385 8.46e-09 AAAATGCTGA GGCGTCGACGCTTCCT CTCTAGTAGG 48197 27 1.05e-08 TGTTATTTGA GGGGTCGCGGATGCCT TCTGTCGATT 44318 130 1.28e-08 CCTGTGCCTT GCCGTCGCTGCTTCCT TCACGCTGTC 46220 349 1.86e-07 AATATCAAAG GGCGTCGAGCAGTCCA CGAACGAAAC 50170 44 3.12e-07 TGATGGATGT GGCGTGGCGGTGAGCT GCGCACTTTT 37243 117 3.74e-07 AAGAATGAAG GGGGTAGCTGCGCCAT GACGCCATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54588 8.5e-09 384_[+1]_100 48197 1e-08 26_[+1]_458 44318 1.3e-08 129_[+1]_355 46220 1.9e-07 348_[+1]_136 50170 3.1e-07 43_[+1]_441 37243 3.7e-07 116_[+1]_368 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=6 54588 ( 385) GGCGTCGACGCTTCCT 1 48197 ( 27) GGGGTCGCGGATGCCT 1 44318 ( 130) GCCGTCGCTGCTTCCT 1 46220 ( 349) GGCGTCGAGCAGTCCA 1 50170 ( 44) GGCGTGGCGGTGAGCT 1 37243 ( 117) GGGGTAGCTGCGCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.4838 E= 7.6e+001 -923 -923 220 -923 -923 -40 194 -923 -923 160 62 -923 -923 -923 220 -923 -923 -923 -923 184 -77 160 -38 -923 -923 -923 220 -923 23 160 -923 -923 -923 -40 120 26 -923 -40 194 -923 23 119 -923 -74 -923 -923 120 84 -77 -40 -38 84 -923 192 -38 -923 -77 192 -923 -923 -77 -923 -923 158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 7.6e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.833333 0.000000 0.333333 0.500000 0.000000 0.166667 0.000000 0.000000 0.500000 0.500000 0.166667 0.166667 0.166667 0.500000 0.000000 0.833333 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GG[CG]GTCG[CA][GT]G[CA][GT]TCCT -------------------------------------------------------------------------------- Time 1.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 117 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1::96a93a:173:3:119 pos.-specific C :a::6:4:::::6:6::1::1 probability G 6:36::::11::11::1::1: matrix T 4:6441:::6:a111a6997: bits 2.2 * 2.0 * 1.8 * * ** * 1.5 * * ** * Relative 1.3 * * ** ** * ** * Entropy 1.1 ** *** ** ** * ** * (24.1 bits) 0.9 ** ****** ** * ** * 0.7 ********* ** *** **** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCTGCAAAATATCACTTTTTA consensus T GTT C A A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44929 20 1.51e-11 CCGAGGCTTA TCTGTAAAATATCACTTTTTA CTGCCTGCCA 44318 468 3.18e-09 TCTCTCGAAC GCATCAAAAAATCACTTTTGA GAGAAAACGA 48315 470 1.10e-08 GCTAGAGCTA TCTTTACAAGATCGATTTTTA CCAAGTCAAG 42722 195 1.68e-08 TTTCTAGGCA GCTGCAAAGTATCACTACTAA ATACCTAAGC 37689 402 1.97e-08 TCTCGACAAA GCTTCACAAAATTACTGTTTC GCAATATGGT 37808 201 4.37e-08 GTCCTGCGAT GCGGCACAATATATATTTATA TTGAAAAAAA 50170 413 5.99e-08 TGTTATCCGT TCGGTTAAATATGATTATTTA TTGTTAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44929 1.5e-11 19_[+2]_460 44318 3.2e-09 467_[+2]_12 48315 1.1e-08 469_[+2]_10 42722 1.7e-08 194_[+2]_285 37689 2e-08 401_[+2]_78 37808 4.4e-08 200_[+2]_279 50170 6e-08 412_[+2]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 44929 ( 20) TCTGTAAAATATCACTTTTTA 1 44318 ( 468) GCATCAAAAAATCACTTTTGA 1 48315 ( 470) TCTTTACAAGATCGATTTTTA 1 42722 ( 195) GCTGCAAAGTATCACTACTAA 1 37689 ( 402) GCTTCACAAAATTACTGTTTC 1 37808 ( 201) GCGGCACAATATATATTTATA 1 50170 ( 413) TCGGTTAAATATGATTATTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 9.64205 E= 1.1e+002 -945 -945 139 62 -945 219 -945 -945 -99 -945 39 104 -945 -945 139 62 -945 138 -945 62 159 -945 -945 -96 101 96 -945 -945 181 -945 -945 -945 159 -945 -60 -945 1 -945 -60 104 181 -945 -945 -945 -945 -945 -945 184 -99 138 -60 -96 133 -945 -60 -96 1 138 -945 -96 -945 -945 -945 184 1 -945 -60 104 -945 -62 -945 162 -99 -945 -945 162 -99 -945 -60 136 159 -62 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.1e+002 0.000000 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.285714 0.571429 0.000000 0.000000 0.571429 0.428571 0.000000 0.571429 0.000000 0.428571 0.857143 0.000000 0.000000 0.142857 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.000000 0.142857 0.571429 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.571429 0.142857 0.142857 0.714286 0.000000 0.142857 0.142857 0.285714 0.571429 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.285714 0.000000 0.142857 0.571429 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.714286 0.857143 0.142857 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]C[TG][GT][CT]A[AC]AA[TA]ATCA[CA]T[TA]TTTA -------------------------------------------------------------------------------- Time 2.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 119 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3a:61:48433 pos.-specific C 22:a:::1:2:: probability G :6:::9:4:417 matrix T 8:::4:a12:7: bits 2.2 * 2.0 * 1.8 ** ** 1.5 ** ** Relative 1.3 * ** ** Entropy 1.1 * ** ** * * (14.3 bits) 0.9 * ***** * * 0.7 ******* **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TGACAGTAAATG consensus A T G GAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 40151 469 3.32e-07 GTACAAGGGC TGACAGTAAATG CGCTCTCTAA 44318 83 4.68e-07 GGCTACTAAT TGACTGTAAGTG TTATGGATAA 37808 45 8.01e-07 GAAAGGTATC TAACAGTGAGTG GATATGACCG 37689 227 1.05e-06 AGAGTTATTG TGACAGTAACTG TAAATTTGTA 37243 254 8.94e-06 CAACGGAAGC TAACAGTAAATA TTTTTACCCA 42722 118 1.33e-05 AGATTATATA TGACAGTGTAAG ACCAATAGGA 54588 273 1.33e-05 TGCTTTTTGT TCACAGTCAGTG TCTGTCACTG 46220 139 1.70e-05 GCGGTCATGC TGACTGTGAGGA ACCAGTTTTA 48315 134 3.25e-05 TACGCTGATC TGACAATGAAAG AACATTTCAC 49506 87 3.98e-05 CTTTGAAGTC TGACTGTTAGAA ACTTGTATTT 50170 390 4.72e-05 TTGCTTCACA CCACTGTAAATA CTGTTATCCG 48197 383 8.08e-05 AGCCGATTGA CAACTGTGTCTG TCAAGCCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40151 3.3e-07 468_[+3]_20 44318 4.7e-07 82_[+3]_406 37808 8e-07 44_[+3]_444 37689 1.1e-06 226_[+3]_262 37243 8.9e-06 253_[+3]_235 42722 1.3e-05 117_[+3]_371 54588 1.3e-05 272_[+3]_216 46220 1.7e-05 138_[+3]_350 48315 3.2e-05 133_[+3]_355 49506 4e-05 86_[+3]_402 50170 4.7e-05 389_[+3]_99 48197 8.1e-05 382_[+3]_106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 40151 ( 469) TGACAGTAAATG 1 44318 ( 83) TGACTGTAAGTG 1 37808 ( 45) TAACAGTGAGTG 1 37689 ( 227) TGACAGTAACTG 1 37243 ( 254) TAACAGTAAATA 1 42722 ( 118) TGACAGTGTAAG 1 54588 ( 273) TCACAGTCAGTG 1 46220 ( 139) TGACTGTGAGGA 1 48315 ( 134) TGACAATGAAAG 1 49506 ( 87) TGACTGTTAGAA 1 50170 ( 390) CCACTGTAAATA 1 48197 ( 383) CAACTGTGTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.49463 E= 1.1e+002 -1023 -40 -1023 158 -19 -40 142 -1023 181 -1023 -1023 -1023 -1023 219 -1023 -1023 104 -1023 -1023 58 -177 -1023 208 -1023 -1023 -1023 -1023 184 55 -140 94 -174 155 -1023 -1023 -74 55 -40 94 -1023 -19 -1023 -138 126 23 -1023 162 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 1.1e+002 0.000000 0.166667 0.000000 0.833333 0.250000 0.166667 0.583333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.583333 0.000000 0.000000 0.416667 0.083333 0.000000 0.916667 0.000000 0.000000 0.000000 0.000000 1.000000 0.416667 0.083333 0.416667 0.083333 0.833333 0.000000 0.000000 0.166667 0.416667 0.166667 0.416667 0.000000 0.250000 0.000000 0.083333 0.666667 0.333333 0.000000 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GA]AC[AT]GT[AG]A[AG][TA][GA] -------------------------------------------------------------------------------- Time 4.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54588 4.10e-06 272_[+3(1.33e-05)]_100_\ [+1(8.46e-09)]_100 37808 1.44e-06 44_[+3(8.01e-07)]_144_\ [+2(4.37e-08)]_279 48315 2.11e-06 133_[+3(3.25e-05)]_324_\ [+2(1.10e-08)]_10 49506 1.53e-01 86_[+3(3.98e-05)]_402 44318 1.31e-12 82_[+3(4.68e-07)]_35_[+1(1.28e-08)]_\ 129_[+3(9.58e-05)]_181_[+2(3.18e-09)]_12 46220 6.97e-05 138_[+3(1.70e-05)]_198_\ [+1(1.86e-07)]_136 48197 2.50e-05 26_[+1(1.05e-08)]_340_\ [+3(8.08e-05)]_106 42722 3.45e-06 117_[+3(1.33e-05)]_65_\ [+2(1.68e-08)]_285 44929 8.53e-07 19_[+2(1.51e-11)]_460 50170 2.87e-08 43_[+1(3.12e-07)]_79_[+1(4.07e-05)]_\ 235_[+3(4.72e-05)]_11_[+2(5.99e-08)]_67 37243 7.20e-05 116_[+1(3.74e-07)]_121_\ [+3(8.94e-06)]_235 37689 8.66e-07 226_[+3(1.05e-06)]_163_\ [+2(1.97e-08)]_78 40151 7.54e-04 468_[+3(3.32e-07)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************